@article {pmid40301143,
year = {2025},
author = {Weitzman, CL and Day, K and Brown, GP and Gibb, K and Christian, K},
title = {Differential Temporal Shifts in Skin Bacteria on Wild and Captive Toads.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {35},
pmid = {40301143},
issn = {1432-184X},
support = {DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; },
abstract = {Skin bacteria on amphibian hosts play an important role in host health, but those communities are also constantly shifting based on environmental and host-related feedback. On some hosts, stability of skin communities depends on relatively abundant taxa, with less abundant taxa more readily entering and exiting the system. Cane toads (Rhinella marina) have invaded widespread, diverse tropical ecosystems, with varying ecology, physiology, and behaviour in different environments. In this study, we described temporal patterns of skin bacterial communities on cane toads at a site in northern Australia through the wet and dry seasons over two years. Toads in the wild population were paired with a captive-held population, housed in a semi-natural environment, to detect effects of time and season on wild toads, explore bacterial transience and volatility in skin taxa, and determine the extent to which skin communities on captive toads represent those on the wild population. We found community differences by captivity status, sampling timepoint, and season, with increased richness in the wet season on wild toads. Bacterial communities also became more similar among individuals (lower dispersion) in the wet season. Captive toads harboured more stable communities over time, likely owing to the reduced bacterial reservoirs experienced while in captivity. We propose that cane toads, with varied movement patterns among their diverse invaded habitats, provide an interesting direction for future work understanding the influences of habitat and movement on skin microbes, and the flexibility of microbial symbiotic interactions in invasive hosts.},
}
@article {pmid40300605,
year = {2025},
author = {Lopez, JA and McKeithen-Mead, S and Shi, H and Nguyen, TH and Huang, KC and Good, BH},
title = {Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.03.073},
pmid = {40300605},
issn = {1879-0445},
abstract = {The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.},
}
@article {pmid40299544,
year = {2025},
author = {Veenhof, RJ and McGrath, AH and Champion, C and Dworjanyn, SA and Marzinelli, EM and Coleman, MA},
title = {The role of microbiota in kelp gametophyte development and resilience to thermal stress.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70018},
pmid = {40299544},
issn = {1529-8817},
support = {//The University of Sydney/ ; DP200100201//Australian Research Council/ ; //NSW Climate Change Fund/ ; //Holsworth Wildlife Research Endowment/ ; },
abstract = {Ocean warming is driving profound changes in the ecology of marine habitat formers such as kelps, with negative implications for the biodiversity and ecosystem services they support. Thermal stress can disturb associated microbiota that are essential to the healthy functioning of kelp, but little is known about how this process influences early-life stages. Because kelps have a biphasic life cycle, thermal stress dynamics of adult sporophyte microbiota may not reflect those of the free-living haploid gametophyte. We investigated the role of microbial disruption under thermal stress on gametophytes of the kelp Ecklonia radiata and compared sporophyte and gametophyte microbiota. The microbiota of gametophytes changed significantly when the microbiome was disrupted and under increased temperature (26°C), in which putative generalist bacterial taxa proliferated and bacterial families associated with nitrogen fixation decreased. Concurrently, the survival of gametophytes decreased to <10%, and surviving gametophytes did not become fertile when the microbiome was disrupted. The length of gametophytes decreased under both microbial disruption and thermal stress. Taken together, this suggests that the associated microbiota of Ecklonia gametophytes is important for their survival, fertility, and response to warming. Gametophyte and parental sporophyte microbiota were also distinct from the water column but not each other, suggesting vertical transmission of microbiota from one life stage to the next. This study furthers our understanding of the role of microbiota in gametophyte stress tolerance as well as the acquisition of microbiota, which may prove vital in protecting and increasing the stress resilience of these foundation species.},
}
@article {pmid40298441,
year = {2025},
author = {Peng, S-X and Gao, S-M and Lin, Z-L and Luo, Z-H and Zhang, S-Y and Shu, W-S and Meng, F and Huang, L-N},
title = {Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments.},
journal = {mBio},
volume = {},
number = {},
pages = {e0070525},
doi = {10.1128/mbio.00705-25},
pmid = {40298441},
issn = {2150-7511},
abstract = {Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.},
}
@article {pmid40297467,
year = {2025},
author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D},
title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19120},
pmid = {40297467},
issn = {2167-8359},
mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.},
}
@article {pmid40294427,
year = {2025},
author = {Ran, X and Wang, T and Zhou, M and Li, Z and Wang, H and Tsybekmitova, GT and Guo, J and Wang, Y},
title = {A Novel Perspective on the Instability of Mainstream Partial Nitrification: The Niche Differentiation of Nitrifying Guilds.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01214},
pmid = {40294427},
issn = {1520-5851},
abstract = {Short-cut biological nitrogen removal (sBNR) favors the paradigm shift toward energy-positive and carbon-neutral wastewater treatment processes. Partial nitrification (PN) is a key approach to provide nitrite for anammox or denitritation during sBNR, and its stability is the precondition for achieving robust nitrogen removal performance. However, maintaining a stable mainstream PN process has been a long-standing challenge. This review analyzes the mainstream PN process from a microbial ecology perspective, focusing on the niche differentiation among nitrifiers. First, we propose that mainstream PN systems are ecologically unstable, and the failure of the mainstream PN process due to the reactivation of nitrite-oxidizing bacteria (NOB) can be regarded as a behavior to restore system stabilization. Thus, maintaining mainstream PN systems primarily relies on enhancing the niche differentiation between ammonia-oxidizing bacteria (AOB) and NOB. We then summarize the realized niches of indigenous nitrifiers within nitrification systems and discuss their ecophysiological characteristics (e.g., cell structure and substrate affinity) that define their specific ecological niches. By comparing the niche breadths of AOB and NOB on various niche axes, we further discuss their niche differentiation and identify the different responses of AOB (resistance) and NOB (resilience) to exogenous perturbations. Finally, we propose outlook for achieving a stable mainstream PN process through an ecological lens. This review provides ecological insights into the instability of the mainstream PN process, which is intended to guide the derivation of optimized strategies from a single-factor approach to integrated solutions.},
}
@article {pmid40294268,
year = {2025},
author = {Sun, W and Wang, J and Wang, G and Jiang, L and Feng, W and Dang, S and Li, M and Jiao, S and Wei, G and Gu, J and Tiedje, JM and Qian, X},
title = {Exposure and health risks of livestock air resistomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {18},
pages = {e2403866122},
doi = {10.1073/pnas.2403866122},
pmid = {40294268},
issn = {1091-6490},
support = {42277412 and 42207463//NSF of China/ ; 2024RS-CXTD-68//Shaanxi Innovation Support Program/ ; },
mesh = {Animals ; *Livestock/microbiology ; Humans ; *Air Microbiology ; Anti-Bacterial Agents/pharmacology ; Farms ; Swine ; China ; Chickens ; *Drug Resistance, Microbial/genetics ; *Occupational Exposure ; *Drug Resistance, Bacterial/genetics ; Europe ; },
abstract = {Most of the global antibiotic consumption is by the livestock industry, making livestock farms a hotspot of antibiotic resistance genes (ARGs). Farm air poses direct ARG exposure to workers, but the health risks of air resistomes remain unclear. We evaluated the human exposure and health risks of air resistomes in pig and chicken farms and compared air resistomes in Chinese farms to those in European farms given their long-term restrictions on use of antibiotics in livestock. We found that livestock air was highly enriched in ARGs, with each cell harboring seven times more ARGs than urban air. The daily ARG inhalation of farm workers was equivalent to several years of ARG inhalation by urban residents. ARGs encoding resistance to last-resort antibiotics such as mcr-1 and tetX were detected in farm air, and tetX variants were prevalent in both Chinese and European farms. ARGs in livestock air were highly associated with mobile genetic elements, and conjugation experiments confirmed their cross-phyla transferability. The projected resistome risk of farm air was significantly higher than well-recognized ARG hotspots like air from hospitals, sewage treatment plants, and from animal manures. The diversity, abundance, and risk score of air resistomes in Chinese farms were significantly higher than those in European farms, suggesting that long-term restriction of antibiotic use mitigates antibiotic resistance in the livestock environment. Our results underscore the high exposure of farm workers to ARGs via farm air and highlight its role in ARG dissemination, supporting the importance of antibiotic stewardship practices in combating antibiotic resistance.},
}
@article {pmid40293502,
year = {2025},
author = {Cao, X and Liu, H and Zhang, R and Wen, Y and Ma, L and Xu, Z and Wen, L and Zhuo, Y and Liu, D and Wang, L},
title = {Composition, Predicted Functions, and Co-occurrence Networks of Bacteria and Fungi in Hummock Wetlands of Northeastern Inner Mongolia, China.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {34},
pmid = {40293502},
issn = {1432-184X},
support = {YSS2021007//the Funds of Yinshanbeilu Grassland Eco-hydrology National Observation and Research Station/ ; 32160279, 32161143025, 31960249//the National Natural Science Funds, P.R. China/ ; 2022YFHH0017//Science and Technology Major Project of Inner Mongolia/ ; 2022EEDSKJZDZX010, 2022EEDSKJXM005//Ordos Science and Technology Plan/ ; },
mesh = {*Wetlands ; China ; *Fungi/classification/genetics/isolation &amp; purification ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Ecosystem ; Microbiota ; Biodiversity ; Hydrogen-Ion Concentration ; },
abstract = {Wetland microhabitats, varying in water table position, pH, and biochemical properties, have been understudied in terms of their influence on soil microbial community structure. This study employed amplicon-based gene sequencing to investigate the responses of both fungal and bacterial communities to habitat changes in northeastern Inner Mongolia, China. The results showed that while α-diversity indices (Shannon and Chao1) did not significantly differ between hummocks and hollows, β-diversity analyses revealed distinct microbial community structures in these habitats. Bacterial communities were primarily influenced by soil pH, EC, and AP, whereas fungal communities were affected by pH, AKP, MBC, MBN, and AP. Bacterial interactions were predominant in hollows, whereas fungal interactions were predominant in hummocks. Hummocks significantly enhanced amino acid metabolism function, whereas hollows significantly increased the abundance of endophyte-litter saprotroph-soil saprotroph-undefined saprotroph. This study underscores the importance of habitats in regulating microbial networks and functions, thereby enhancing our understanding of the influence of microhabitats, such as hummocks, on wetland ecosystem structure and function.},
}
@article {pmid40287826,
year = {2025},
author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT},
title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.},
journal = {Nucleic acids research},
volume = {53},
number = {8},
pages = {},
pmid = {40287826},
issn = {1362-4962},
support = {DBI1356288NSF//NSF/ ; },
mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; },
abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.},
}
@article {pmid40287775,
year = {2025},
author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W},
title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {105},
pmid = {40287775},
issn = {2049-2618},
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Glycine max/microbiology/growth &amp; development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation &amp; purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.<br><br>RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r&#x2009;= 0.5, p&#x2009;= 0.039) between microbial diversity and seed yield.<br><br>CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.},
}
@article {pmid40287657,
year = {2025},
author = {De Maayer, P and Green, T and Jordan, S and Smits, THM and Coutinho, TA},
title = {Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {408},
pmid = {40287657},
issn = {1471-2164},
support = {310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Enterobacter/genetics/classification/drug effects/pathogenicity ; *Genome, Bacterial ; Phylogeny ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genomics/methods ; Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Plasmids/genetics ; },
abstract = {BACKGROUND: Enterobacter hormaechei is of increasing concern as both an opportunistic and nosocomial pathogen, exacerbated by its evolving multidrug resistance. However, its taxonomy remains contentious, and little is known about its pathogenesis and the broader context of its resistome. In this study, a comprehensive comparative genomic analysis was undertaken to address these issues.<br><br>RESULTS: Phylogenomic analysis revealed that E. hormaechei represents a complex, comprising three predicted species, E. hormaechei, E. hoffmannii and E. xiangfangensis, with the latter putatively comprising three distinct subspecies, namely oharae, steigerwaltii and xiangfangensis. The species and subspecies all display open and distinct pan-genomes, with diversification driven by an array of mobile genetic elements including numerous plasmid replicons and prophages, integrative conjugative elements (ICE) and transposable elements. These elements have given rise to a broad, relatively conserved set of pathogenicity determinants, but also a variable set of secretion systems. The E. hormaechei complex displays a highly mutable resistome, with most taxa being multidrug resistant.<br><br>CONCLUSIONS: This study addressed key issues pertaining to the taxonomy of the E. hormaechei complex, which may contribute towards more accurate identification of strains belonging to this species complex in the clinical setting. The pathogenicity determinants identified in this study could serve as a basis for a deeper understanding of E. hormaechei complex pathogenesis and virulence. The extensive nature of multidrug resistance among E. hormaechei complex strains highlights the need for responsible antibiotic stewardship to ensure effective treatment of these emerging pathogens.},
}
@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
mesh = {Workflow ; *Software ; *Gene Expression Profiling/methods ; *Computational Biology/methods ; *Transcriptome ; Microbiota/genetics ; Humans ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.<br><br>RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.<br><br>CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}
@article {pmid40287414,
year = {2025},
author = {Bull, F and Tavaddod, S and Bommer, N and Perry, M and Brackley, CA and Allen, RJ},
title = {Different factors control long-term versus short-term outcomes for bacterial colonisation of a urinary catheter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3940},
pmid = {40287414},
issn = {2041-1723},
support = {682237 EVOSTRUC//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council(H2020 Excellent Science - European Research Council)/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft(German Research Foundation)/ ; EP/L015110/1//RCUK | Engineering and Physical Sciences Research Council(EPSRC)/ ; },
mesh = {*Urinary Catheters/microbiology/adverse effects ; Humans ; *Urinary Tract Infections/microbiology/prevention &amp; control/etiology ; *Catheter-Related Infections/microbiology/prevention &amp; control ; *Urinary Catheterization/adverse effects ; Computer Simulation ; *Bacteria/growth &amp; development ; Urinary Bladder/microbiology ; Models, Theoretical ; Models, Biological ; Time Factors ; },
abstract = {Urinary catheters are used extensively in hospitals and long-term care and they are highly prone to infection. Understanding the pathways by which bacteria colonise a urinary catheter could guide strategies to mitigate infection, but quantitative models for this colonisation process are lacking. Here we present a mathematical model for bacterial colonisation of a urinary catheter that integrates population dynamics and fluid dynamics. The model describes bacteria migrating up the outside surface of the catheter, spreading into the bladder and being swept through the catheter lumen. Computer simulations of the model reveal that clinical outcomes for long-term versus short-term catheterisation are controlled by different factors: the rate of urine production by the kidneys as opposed to urethral length, catheter surface properties and bacterial motility. Our work may help explain variable susceptibility to catheter-associated urinary tract infection (CAUTI) among individuals and the mixed success of antimicrobial surface coatings. Our model suggests that for long-term catheterised patients, increasing fluid intake or reducing residual urine volume in the bladder may help prevent infection, while antimicrobial surface coatings are predicted to be effective only for short-term catheterised patients. Therefore, different catheter management strategies could be rationally targeted to long-term vs short-term catheterised patients.},
}
@article {pmid40286617,
year = {2025},
author = {Kang, S and Lee, JY and Natsagdorj, A and Matsuki, A and Cho, KS},
title = {Functional adaptation of PM2.5 microbiomes to varying environmental conditions in Northeast Asia: Ulaanbaatar, Seoul, and Noto.},
journal = {The Science of the total environment},
volume = {979},
number = {},
pages = {179495},
doi = {10.1016/j.scitotenv.2025.179495},
pmid = {40286617},
issn = {1879-1026},
abstract = {This study examined the bacterial and fungal communities associated with PM2.5 collected from three geographically distinct locations in Northeast Asia-Ulaanbaatar (high pollution), Seoul (moderate pollution), and Noto (low pollution)-which collectively represent a gradient of urbanization and environmental conditions during the spring sampling period from March 15 to April 7, 2022. Ulaanbaatar exhibited the highest abundance of both bacteria and fungi, yet exhibited the lowest fungal diversity. In contrast, Noto exhibited the lowest microbial abundance but the highest fungal diversity, while Seoul displayed intermediate values. Dominant bacterial genera, including Caldalkalibacillus, Halomonas, and Nesterenkonia, demonstrated notable resilience across all three locations, highlighting their adaptability to diverse environmental conditions. The dominant fungal genera were Cladosporium and Candida. Analyses revealed significant correlations between microbial community structures and environmental factors. In Ulaanbaatar, microbial communities were strongly associated with meteorological parameters such as temperature, humidity, and wind speed. In Seoul, stronger correlations were observed with polycyclic aromatic hydrocarbons (PAHs). Noto exhibited weaker correlations with both meteorological factors and organic compounds. Across all sites, bacteria consistently showed broader niche breadths compared to fungi, reflecting their greater metabolic versatility and resource utilization capacity. Both bacterial and fungal niche breadths generally increased at intermediate concentrations of alkanes and DCAs but declined at extreme concentrations, suggesting optimal survival ranges. These findings highlight the complex interplay of environmental factors and pollutants in shaping microbial community structures and functional diversity across diverse geographical settings during the spring season.},
}
@article {pmid40285533,
year = {2025},
author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A},
title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.},
journal = {Global change biology},
volume = {31},
number = {4},
pages = {e70211},
doi = {10.1111/gcb.70211},
pmid = {40285533},
issn = {1365-2486},
support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; },
mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; },
abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.},
}
@article {pmid40284744,
year = {2025},
author = {Yahya, R and Albaqami, A and Alzahrani, A and Althubaiti, SM and Alhariri, M and Alrashidi, ET and Alhazmi, N and Al-Matary, MA and Alharbi, N},
title = {Comprehensive Genomic Analysis of Klebsiella pneumoniae and Its Temperate N-15-like Phage: From Isolation to Functional Annotation.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
pmid = {40284744},
issn = {2076-2607},
support = {NRC21R/053/02//King Abdullah International Medical Research Center/ ; },
abstract = {Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin-antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research.},
}
@article {pmid40284675,
year = {2025},
author = {Li, M and Liu, X and Chen, W and Xu, H and Huang, F and Yao, Q and Jia, X and Huang, Y},
title = {Alleviating Effect of Lactiplantibacillus plantarum HYY-S10 on Colitis in Mice Based on an Analysis of the Immune Axis in the Intestine.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040840},
pmid = {40284675},
issn = {2076-2607},
support = {32302242//the National Natural Science Foundation of China/ ; 2022A1515110426//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023B0202040002//Guangdong Provincial Key Research and Development Program/ ; 2022B1212010015//Key Laboratory Project of Guangdong Province/ ; },
abstract = {The pathogenesis of ulcerative colitis (UC) has been fundamentally associated with intestinal microbiota dysbiosis and disruption of immune homeostasis. This study systematically investigates the therapeutic potential of Lactiplantibacillus plantarum HYY-S10 (HYY-S10), a novel strain isolated from De'ang sour tea in Yun an, China, with a focus on its mechanisms for alleviating colitis through the modulation of gut microbiota. Using a dextran sulfate sodium (DSS)-induced colitis model in C57BL/6J mice, our findings demonstrated that seven days of oral supplementation with HYY-S10 (1 × 10[8] CFU/mL, 0.2 mL/10 g body weight) significantly improved Disease Activity Index (DAI) scores and attenuated characteristic colitis symptoms, including progressive weight loss, rectal bleeding, and abnormal stool consistency. Administration of HYY-S10 exhibited significant immunomodulatory effects characterized by the downregulation of pro-inflammatory mediators (such as IL-1β, IL-6, IFN-γ, and LPS) while concomitantly upregulating anti-inflammatory IL-10 expression. Additionally, the strain enhanced intestinal antioxidant capacity by increasing GSH-Px activity, which collectively contributed to the reduction in intestinal inflammation. Furthermore, HYY-S10 demonstrated multifaceted protective effects by ameliorating oxidative stress through the restoration of redox homeostasis and modulation of gut microbial ecology. Probiotic intervention significantly increased short-chain fatty acids (SCFAs) production and notably enhanced the relative abundance of beneficial taxa, including Akkermansia and Ruminococcus_B, while restoring microbial diversity and ecological stability. Collectively, our results demonstrate that HYY-S10 alleviates experimental colitis by modulating the intestinal immune axis and microbiota composition, providing mechanistic insights to support its potential as a probiotic-based therapeutic strategy for UC.},
}
@article {pmid40284595,
year = {2025},
author = {Frazier, AN and Willis, W and Robbe, H and Ortiz, A and Koziel, JA},
title = {Characterization and Assembly Dynamics of the Microbiome Associated with Swine Anaerobic Lagoon Manure Treated with Biochar.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040758},
pmid = {40284595},
issn = {2076-2607},
support = {3090-31630-006//USDA-ARS CRIS/ ; },
abstract = {Biochar has significant potential for livestock microbiomes and crop agriculture regarding greenhouse gas emissions reduction. Therefore, a pilot study was designed to investigate the effect of biochar application on the surface of swine manure from an open lagoon and the associated microbial communities. Samples were collected from four different treatment groups: control (n = 4), coarse biochar (n = 4), fine biochar (n = 4), and ultra-fine biochar (n = 4). Additionally, aged manure in bulk was collected (n = 4) to assess alterations from the control group. The method of 16S rRNA amplicon sequencing along with microbial analyses was performed. Diversity was significantly different between aged manure in bulk samples and all treatment groups (Kruskal-Wallis; p < 0.05). Additionally, distinct community compositions were seen using both weighted and unweighted UniFrac distance matrices (PERMANOVA; p < 0.01). Differential abundance analysis revealed four distinct features within all treatment groups that were enriched (q < 0.001): Idiomarina spp., Geovibrio thiophilus, Parapusillimonas granuli, and an uncultured Gammaproteobacteria species. Similarly, Comamonas spp. and Brumimicrobium aurantiacum (q-value < 0.001) were significantly depleted by all the treatments. Stochastic and functional analyses revealed that biochar treatments were not deterministically altering assembly patterns, and functional redundancy was evident regardless of compositional shifts.},
}
@article {pmid40280843,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Plant-microbe interactions: plants modulating their defenses.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.001},
pmid = {40280843},
issn = {1878-4372},
abstract = {Plant immunity is mediated by multiple factors, including microbial interactions and gene expression. Keppler et al. identified a set of microbe-responsive genes (general non-self response genes) whose expression or products affect bacterial strain abundance and enhance immunity. We explore how these genes shape alternative plant defense strategies for sustainable agriculture.},
}
@article {pmid40280003,
year = {2025},
author = {Cholet, F and Vignola, M and Quinn, D and Ijaz, UZ and Sloan, WT and Smith, CJ},
title = {Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: A meta-analysis.},
journal = {Water research},
volume = {281},
number = {},
pages = {123684},
doi = {10.1016/j.watres.2025.123684},
pmid = {40280003},
issn = {1879-2448},
abstract = {Biofiltration, a sustainable water treatment technology relying on microbial processes to remove contaminants, offers a promising approach to achieving the United Nations Sustainable Goal 6 of universal access to clean water and sanitation by 2030. However, a key barrier to optimising biofiltration is the incomplete understanding of the biological mechanisms governing its performance. Despite numerous studies examining how engineering decisions impact biofilter performance and the associated microbiome, the significant influence of geographical location on microbial communities raises the question of whether these findings are universally applicable or location-specific. To address this, we conducted a meta-analysis of 15 biofilter microbiomes using 16S rRNA high-throughput sequencing (HTS) data, mainly originating from rapid gravity and/or granular activated carbon (GAC) filters. Despite different types and scales, results highlight geographical location as the major contributor to microbiome dissimilarity in biofilter samples (Top and Bottom) (R[2]∼ 0.5; p-value<0.001). The same was observed for influent waters (PERMANOVA R[2]= 0.76; p-value<0.001), indicating location-specific microbiomes as opposed to differences driven by different biofilter operating parameters. Irrespective of location, the higher percentage of the microbiome was assembled through deterministic processes (∼55 %) compared to stochastic processes (∼45 %). Finally, our findings suggest that the depth stratification of biofilter microbiomes may be associated with the enrichment of taxa capable of metabolising more complex organic carbon in deeper filter layers (10 enriched pathways in biofilter Bottom layers compared to 3 at the Top). These insights provide a broader understanding of biofiltration microbiomes and offer possible research avenues for targeted and effective biofilter design strategies.},
}
@article {pmid40279085,
year = {2025},
author = {Zheng, F and Zhao, J and Yuan, Z and Gao, Y and Li, Y and Li, Y and Geng, Y and Qiang, Y},
title = {Interpretable drug-target affinity prediction based on pre-trained models' output as embeddings and based on structure-aware cross-attention for feature fusion.},
journal = {Molecular diversity},
volume = {},
number = {},
pages = {},
pmid = {40279085},
issn = {1573-501X},
support = {U21A20469//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 62376183//National Natural Science Foundation of China/ ; 202304051001009//the special fund for Science and Technology Innovation Teams of Shanxi Province/ ; 2020-PT320-005//National Health Commission Key Laboratory of Pneumoconiosis/ ; },
abstract = {The characteristics of protein pockets can better capture the interaction information between proteins and small molecules, thereby improving the performance of drug-target interaction (DTI) prediction tasks. However, pocket data typically need to be predicted using software such as AlphaFold, which would entail a massive workload for datasets ranging from tens of thousands to hundreds of thousands of samples. Moreover, feature representation networks for 3D pocket data are computationally intensive. To address this, we propose simulating 3D pocket data using sequence data through feature fusion of two different objects based on structure cross-attention (CASD). Additionally, precise feature representation is a prerequisite for accurately identifying pocket information. We introduce a method that leverages the output of the last layer of a pre-trained model as an embedding layer for training a new model from scratch. This approach not only incorporates prior knowledge from the pre-trained model but also expands model capacity, enabling more accurate feature representation. Furthermore, we enhance the multimodal representation of small molecule compounds using feature fusion based on structure cross-attention for the same object (CASS), further improving feature representation capabilities. Our cross-attention mechanisms operate at the token-level or node-level, allowing fine-grained capture of interactions between amino acids and atoms. This enables the identification of the contribution score of each atom or amino acid to the task, making our model interpretable for drug-target prediction. Experimental validation demonstrates that our model achieves state-of-the-art predictive performance.},
}
@article {pmid40277367,
year = {2025},
author = {Thapa, BS and Flynn, TM and Jensvold, ZD and Kemner, KM and Sladek, MF and O'Loughlin, EJ and Marshall, CW},
title = {Effects of soluble electron shuttles on microbial iron reduction and methanogenesis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0222224},
doi = {10.1128/aem.02222-24},
pmid = {40277367},
issn = {1098-5336},
abstract = {In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and -0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.IMPORTANCEIron is the fourth most abundant element in the Earth's crust, and the reduction of iron by microbes is an important component of global biogeochemical cycles. A phylogenetically diverse group of microbes is capable of conserving energy with oxidized iron as a terminal electron acceptor, but the environmental conditions favoring certain taxonomic clades in iron-reducing environments are unclear. One complicating factor often overlooked in small-scale enrichments is the influence of soluble, redox-active electron shuttles on the rate and microbial ecology of iron reduction. We tested the effects of eight different electron shuttles on microbial physiology and ecology in iron-reducing enrichments derived from a local wetland. Each electron shuttle varied the microbial activity and enriched for a microbial community distinct from the no shuttle control condition. Therefore, in complex subsurface environments with many redox-active compounds present, we propose electron shuttles as a reason for the coexistence of multiple clades of iron-reducing bacteria.},
}
@article {pmid40277363,
year = {2025},
author = {Wang, Y and Yang, L and Wu, W and Feng, Z and He, J and Guo, C and He, J},
title = {Bacillus haimaensis sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0245624},
doi = {10.1128/aem.02456-24},
pmid = {40277363},
issn = {1098-5336},
abstract = {Deep-sea cold seeps harbor unique microbial communities that play crucial roles in biogeochemical cycles and possess potential biotechnological applications. Herein, we report the isolation, characterization, and genomic analysis of a novel Bacillus species, Bacillus haimaensis sp. nov. (type strain CSS-39[T], CCTCC M20241382), obtained from sediments collected at a depth of 1,350 m in the Haima cold seep, South China Sea. Phylogenomic analysis, revealing an average nucleotide identity of 87.78% and a digital DNA-DNA hybridization value of 34.0% with its closest relative B. tianshenii DSM 25879[T], confirms the taxonomic novelty of the genus Bacillus. The complete 4.54 Mb genome of B. haimaensis reveals adaptations to the cold seep environment, including enhanced nutrient acquisition capabilities and stress response mechanisms. Comparative genomic analysis identifies 27 unique gene clusters related to spore germination and sulfate assimilation, suggesting specialized metabolic strategies for this extreme habitat. Furthermore, six biosynthetic gene clusters, including a novel lassopeptide cluster, indicate a potential for secondary metabolite production. Phenotypic characterization demonstrates the strain's ability to utilize diverse carbon sources and tolerate a wide range of environmental conditions. Our findings provide insights into microbial adaptations to deep-sea cold seeps and highlight the potential of B. haimaensis for biotechnological applications in bioremediation and natural product discovery. This study expands our understanding of microbial diversity in extreme marine environments and offers a new model bacterium for investigating bacterial adaptations to deep-sea ecosystems.IMPORTANCEThe discovery of Bacillus haimaensis sp. nov. in the Haima cold seep of the South China Sea represents a significant advancement in our understanding of microbial adaptations to extreme marine environments. This novel species exhibits remarkable metabolic versatility and unique genomic features, providing insights into bacterial survival strategies in nutrient-variable, high-pressure deep-sea ecosystems. Comprehensive genomic analysis reveals distinctive biosynthetic gene clusters, suggesting untapped potential for discovering novel natural product. Furthermore, B. haimaensis exhibits promising capabilities for aromatic compound degradation, indicating potential applications in marine bioremediation. This work not only expands our knowledge of microbial diversity in understudied deep-sea habitats but also highlights the biotechnological promise of extremophiles. The adaptive mechanisms elucidated in B. haimaensis, particularly those related to sporulation and sulfate assimilation, contribute to our broader understanding of microbial ecology in cold seeps and may inform future research on climate change impacts on deep-sea ecosystems.},
}
@article {pmid40276016,
year = {2025},
author = {Papazlatani, C and Wagner, A and Chen, Z and Zweers, H and de Boer, W and Garbeva, P},
title = {Enhancement of production of pathogen-suppressing volatiles using amino acids.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100385},
pmid = {40276016},
issn = {2666-5174},
abstract = {Bacterial volatile organic compounds can play a significant role in antagonistic interactions. Enhancing the production of bacterial volatiles that suppress the growth of soil-borne phytopathogenic fungi, has perspective as a sustainable disease control strategy. In the present study, we explored the potential of stimulating Burkholderia AD24 and Paenibacillus AD87 to produce volatiles that suppress the growth of the plant pathogenic fungi Fusarium culmorum PV and Rhizoctonia solani AG2.2IIIb. We provided the bacterial strains with a mixture of amino acids that can serve as precursor molecules in metabolic routes leading to emission of suppressive bacterial volatiles. Only Burkholderia AD24 was stimulated to produce a volatile blend that led to higher suppression of both pathogens. Subsequent analysis of the volatile composition emitted by Burkholderia AD24 in the presence of amino acids, showed higher abundance of antifungal compounds, including sulfur compounds (DMDS), pyrazines (2,5-dimethyl pyrazine) and carbohydrates (3-methyl-1-butanol). Follow-up trials with single amino acids revealed a pathogen specific response effect. When Burkholderia AD24 was cultivated in the presence of glutamine and asparagine, the emitted volatile blend suppressed the growth of F. culmorum, whereas when cultivated in the presence of glycine, glutamine, arginine and lysine the volatile blend suppressed the growth of R. solani. Analysis of the volatile blend composition showed differences between the amino acid treatments. Our findings show that amino acid precursor molecules can stimulate the production of fungistatic volatiles but the sensitivity of the fungal pathogens to these bacterial volatiles varies. This should be considered in future application strategies.},
}
@article {pmid40275504,
year = {2025},
author = {Ekemezie, SC and Davis, CC and Russo, MV and Carpenter, LP and Russell, AL},
title = {Pollen-microbe interactions in nectar weakly influence bee foraging behavior.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf017},
pmid = {40275504},
issn = {1557-7023},
abstract = {Plant-pollinator interactions are frequently affected by microbes that grow on flowers. Bacteria and yeast commonly grow within floral nectar, which is a sugar-rich floral reward often sought out by pollinators. Nectar is also commonly contaminated with protein-rich pollen. Microbes can induce this pollen to germinate or burst within the nectar, which potentially results in pollen nutrients being made available to nectar foraging pollinators. Yet whether pollen-microbe interactions in nectar impact pollinator behavior remains unknown. We therefore investigated how a common nectar yeast (Metschnikowia reukaufii) and bacteria (Acinetobacter nectaris) affected pollen germination and bursting within artificial nectar and effects on bumble bee (Bombus impatiens) foraging behavior. We found that both bacteria and yeast reduced the proportion of intact pollen in nectar, with bacteria inducing the most germination and bursting. Although microbes may thus potentially increase the quality of the nectar reward via increased access to pollen nutrients, we did not observe effects on bee flower preference. Similarly, bees did not show increased constancy (i.e., fidelity to one flower type across flower visits) to nectar contaminated with pollen and microbes. In contrast, bees were much more likely to reject flowers with nectar contaminated with pollen and yeast alone or together, relative to flowers that offered uncontaminated nectar. Altogether, our work suggests pollen-microbe interactions within nectar may have relatively minor influences on pollinator foraging behavior. We discuss possible explanations and implications of these results for plant and pollinator ecology.},
}
@article {pmid40273553,
year = {2025},
author = {Ballan, D and Picot, A and Rolland, N and Bovo, C and Prévost, C and Coton, E and Mounier, J},
title = {Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households.},
journal = {International journal of food microbiology},
volume = {437},
number = {},
pages = {111204},
doi = {10.1016/j.ijfoodmicro.2025.111204},
pmid = {40273553},
issn = {1879-3460},
abstract = {Food loss and waste generated throughout the food chain are major concerns in today's society. A high level of food waste occurs at the household's level and fresh fruit and vegetable (FFV) spoilage caused by microbial growth accounts for a large part of these losses. While numerous studies focused on spoilage microorganism diversity from primary production to distribution, little is known about those involved at the household level. In this context, this study aimed at investigating which FFV are usually wasted depending on the season and storage conditions at households, and identifying the microorganisms associated with spoiled FFV. During two periods (summer and autumn), 346 spoiled FFV samples were collected using a citizen science approach in 49 households in the Brest area (Finistère, Brittany, France). About three quarters of spoiled FFV collected originated from room temperature storage and 75 % were collected during summer. Among the studied samples, 75 % showed microbial growth after plating onto agar-based medium, and therefore, were likely spoiled because of microbial spoilage. Overall, 183 molds, 31 yeasts and 96 bacteria were isolated and identified using MALDI-TOF MS and sequencing. Among the 42 different mold species identified, Penicillium spp. were the most common representing more than 50 % of mold isolates followed by Botrytis (12.4 %), Mucor (8.6 %) and Cladosporium (7.6 %) spp. Hanseniaspora uvarum and Aureobasidium pullulans were the most prevalent yeast species while bacterial isolates showed the highest diversity of all identified organisms (49 species) with Pseudomonas spp., enterobacteria and lactic acid bacteria representing the most frequently isolated taxa. This study shows for the first time the microbial diversity associated with spoiled FFV of which a large proportion were stored at room temperature, suggesting that a better usage of FFV refrigeration could help reduce FFV waste in households.},
}
@article {pmid40270585,
year = {2025},
author = {Zheng, Z and Gong, Z and Zhang, R and Lin, X and Hong, W and Song, L},
title = {Potential pathogens drive ARGs enrichment during biofilms formation on environmental surfaces.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf057},
pmid = {40270585},
issn = {2730-6151},
abstract = {The enrichment of antibiotic resistance genes (ARGs) on environmental surfaces is a fundamental question in microbial ecology. Understanding the processes driving ARG variations can provide clues into their transfer mechanisms between phases and offer insights for public health management. In this study, we examined microbiota, potential pathogen, and ARG dynamics on two common environment surfaces-polyvinyl chloride (PVC) and carbon steel (CS)-under environmental stress (induced by landfill leachate flow) in a Center for Disease Control and Prevention Biofilm Reactor using metagenomics and quantitative polymerase chain reaction-Chip techniques. Contrary to the expected changes in biofilms morphology and physiochemical properties, microbiota, potential pathogens, and ARGs exhibited a divergence-convergence pattern, primarily shaped by attachment surface properties and, subsequently, biofilm maturity during biofilms formation. During this process, ARG levels in biofilms gradually increased to and exceeded the levels in the surrounding environment, but with a distinct structure (P < .05). Furthermore, 1.93- and 3.05-fold increases in the concentrations of mobile genetic elements intI-1 in PVC and CS biofilms, respectively, suggested their important role in the transfer and spread of ARGs within the biofilm matrix. Although potential pathogens were less abundant (3.48%-5.63%) in the biofilms microbiota, they accounted for 18.28%-45.16% of the ARG hosts and harbored multiple ARGs. Pathogens significantly impacted ARG enrichment (Procrustes analysis: P = .0136, M[2] = 0.34) although microbiota development also influenced this process (P = .0385, M[2] = 0.67). These results suggest that pathogens are key in shaping ARG enrichment in biofilms. Our findings provide dynamic insights into resistome enrichment on environmental surfaces.},
}
@article {pmid40270532,
year = {2025},
author = {Ma, J and Wang, M and Sun, Y and Zheng, Y and Lai, S and Zhang, Y and Wu, Y and Jiang, C and Shen, F},
title = {Cockroach Microbiome Disrupts Indoor Environmental Microbial Ecology with Potential Public Health Implications.},
journal = {Environment &amp; health (Washington, D.C.)},
volume = {3},
number = {4},
pages = {380-391},
doi = {10.1021/envhealth.4c00216},
pmid = {40270532},
issn = {2833-8278},
abstract = {Cockroaches pose a significant global public health concern. However, besides the well-recognized cockroach-induced allergy, the potential impact of the cockroach microbiome on human health through various means is not yet fully elucidated. This study aimed to clarify the health impacts of cockroaches by investigating the microbial interactions among cockroaches, the indoor environment, and humans. We simultaneously collected cockroach, indoor environment (indoor air and floor dust), and human (exhaled breath condensate and skin) samples from residential areas in five cities representing distinct climate zones in China. The 16S rDNA sequencing results revealed that cockroaches harbor diverse bacterial populations that vary across different cities. The prevalence of potential pathogenic bacteria (PPB) in cockroaches ranged from 1.1% to 58.9%, with dominant resistance genes conferring resistance to tetracycline, macrolide, and beta-lactam. The relationships between the cockroach microbiome and the associated environmental and human microbiomes were explored by using fast expectation-maximization microbial source tracking (FEAST). The potential contribution of cockroach bacteria to the floor dust-borne microbiome and indoor airborne microbiome was estimated to be 5.6% and 1.3%, respectively. Similarly, the potential contribution of cockroach PPB to the floor dust-borne microbiome and indoor airborne microbiome was calculated to be 4.0% and 1.2%, respectively. In residences with cockroach infestations, the contribution of other sources to the indoor environment was slightly increased. Collectively, the role of cockroaches in the transmission of microorganisms, particularly pathogenic bacteria and antibiotic resistance genes, cannot be overlooked.},
}
@article {pmid40268300,
year = {2025},
author = {Goyal, A and Chure, G},
title = {Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70094},
doi = {10.1111/1462-2920.70094},
pmid = {40268300},
issn = {1462-2920},
mesh = {*Biodiversity ; *Microbiota ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Ecosystem ; Biological Evolution ; },
abstract = {Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially-restricted environments. Within these species, genetic and ecological variation often exists at a much finer scale, with closely related strains coexisting and competing. While the coexistence of strains in communities has been heavily explored over the past two decades, we have no self-consistent theory of how this diversity is maintained. This question challenges our conventional understanding of ecological coexistence, typically framed around species with clear phenotypic and ecological differences. In this review, we synthesise plausible mechanisms underlying strain-level diversity (termed microdiversity), focusing on niche-based mechanisms such as nutrient competition, neutral mechanisms such as migration, and evolutionary mechanisms such as horizontal gene transfer. We critically assess the strengths and caveats of these mechanisms, acknowledging key gaps that persist in linking genetic similarity to ecological divergence. Finally, we highlight how the origin and maintenance of microdiversity could pose a major challenge to conventional ecological thinking. We articulate a call-to-arms for a dialogue between well-designed experiments and new theoretical frameworks to address this grand conceptual challenge in understanding microbial biodiversity.},
}
@article {pmid40267173,
year = {2025},
author = {Bull, CT and Salgado-Salazar, C and Romberg, MK and Allen, C and Kantor, M and Handoo, Z and Aboughanem-Sabanadzovic, N and Sabanadzovic, S and Coutinho, T},
title = {Plant Pathogen Name Game: Cross Kingdom Review for the Naming of Biotic Agents Associated with Plants.},
journal = {Annual review of phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-phyto-111424-090412},
pmid = {40267173},
issn = {1545-2107},
abstract = {To communicate across scientific disciplines, regulatory bodies, and the agricultural community, the naming of plant pathogens assigned to specific taxa is critical. Here, we provide an overview of the nomenclatural systems governing the naming of plant-pathogenic nematodes, fungi, oomycetes, prokaryotes, and viruses. Although we focus on the nature of the nomenclatural codes, we briefly discuss fundamental principles of taxonomy, including classification and identification. Key elements of the codes of nomenclature that ensure stability and clarity when naming species of pathogens are defined. When comparing the practice of nomenclature across different kingdoms, the classification and nomenclatural systems differ, and thus unique challenges are faced. We provide guidance from the codes and current practice for naming novel species. When there are nomenclatural conflicts, international committees play a critical role in their resolution. They also play a role in updating the codes to reflect new advancements in science. With this review, we aim to assist plant pathologists, journal editors, and those in related fields by providing an entrée to the legalistic requirements of the codes. Authors must consult and follow the rules of the appropriate code for any proposal of new or new combinations of names. To those interested in naming new species (or renaming the current ones), we recommend collaborations with experts in the field of taxonomy to ensure that rules for accurate and consistent naming practices and procedures are followed and to increase the likelihood that the proposed nomenclature is correct and acceptable.},
}
@article {pmid40196585,
year = {2025},
author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P},
title = {Comparative performance of novel viral landscape phylogeography approaches.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40196585},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; },
abstract = {The fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information about the processes that govern their transmission and dispersal. In particular, landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the scientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.},
}
@article {pmid40266732,
year = {2025},
author = {Duque-Granda, D and Vivero-Gómez, RJ and González Ceballos, LA and Junca, H and Duque, SR and Aroca Aguilera, MC and Castañeda-Espinosa, A and Cadavid-Restrepo, G and Gómez, GF and Moreno-Herrera, CX},
title = {Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon.},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030269},
pmid = {40266732},
issn = {2075-4450},
support = {Hermes 57545//Universidad Nacional de Colombia/ ; },
abstract = {Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.},
}
@article {pmid40266381,
year = {2025},
author = {Cuny, MAC and Gloder, G and Bourne, ME and Kalisvaart, SN and Verreth, C and Crauwels, S and Cusumano, A and Lievens, B and Poelman, EH},
title = {Parasitoid Calyx Fluid and Venom Affect Bacterial Communities in Their Lepidopteran Host Labial Salivary Glands.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {33},
pmid = {40266381},
issn = {1432-184X},
support = {ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; },
mesh = {Animals ; *Salivary Glands/microbiology ; *Wasps/physiology ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Microbiota ; Larva/parasitology/microbiology ; Host-Parasite Interactions ; *Butterflies/microbiology/parasitology ; Hemolymph/microbiology ; Polydnaviridae/physiology ; *Wasp Venoms/pharmacology ; *Moths/microbiology/parasitology ; },
abstract = {The influence of gut and gonad bacterial communities on insect physiology, behaviour, and ecology is increasingly recognised. Parasitism by parasitoid wasps alters many physiological processes in their hosts, including gut bacterial communities. However, it remains unclear whether these changes are restricted to the gut or also occur in other tissues and fluids, and the mechanisms underlying such changes are unknown. We hypothesise that host microbiome changes result from the injection of calyx fluid (that contain symbiotic viruses known as polydnaviruses) and venom during parasitoid oviposition and that these effects vary by host tissue. To test this, we microinjected Pieris brassicae caterpillars with calyx fluid and venom from Cotesia glomerata, using saline solution and natural parasitism by C. glomerata as controls. We analysed changes in the bacterial community composition in the gut, regurgitate, haemolymph, and labial salivary glands of the host insects. Multivariate analysis revealed distinct bacterial communities across tissues and fluids, with high diversity in the salivary glands and haemolymph. Parasitism and injection of calyx fluid and venom significantly altered bacterial communities in the salivary glands. Differential abundance analysis showed that parasitism affected bacterial relative abundance in the haemolymph, and that Wolbachia was only found in the haemolymph of parasitized caterpillars. Altogether, our findings reveal that parasitism influences the host haemolymph microbiome, and both parasitism and injection of calyx fluid and venom drive changes in the bacterial community composition within the host salivary glands. Given that the composition of salivary glands can influence plant response to herbivory, we discuss these results in the broader context of plant-parasitoid interactions.},
}
@article {pmid40262702,
year = {2025},
author = {Zhang, S and Sun, C},
title = {Ecological divergence of marine bacteria Alteromonas mediterranea.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108359},
doi = {10.1016/j.ympev.2025.108359},
pmid = {40262702},
issn = {1095-9513},
abstract = {Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.},
}
@article {pmid40262432,
year = {2025},
author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z},
title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.},
journal = {Water research},
volume = {282},
number = {},
pages = {123626},
doi = {10.1016/j.watres.2025.123626},
pmid = {40262432},
issn = {1879-2448},
abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.},
}
@article {pmid40261360,
year = {2025},
author = {Cho, KH and Kwon, Y and Kasani, PH and Lee, SG and Jeong, SJ},
title = {Influence of Maternal Weight Dynamics Prior to and Throughout Gestation on Early Infant Gut Microbiome Colonization.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {32},
pmid = {40261360},
issn = {1432-184X},
support = {HR22C1605//Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; *Bacteria/classification/genetics/isolation &amp; purification ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Adult ; Body Mass Index ; Feces/microbiology ; *Gestational Weight Gain ; Male ; Meconium/microbiology ; Infant ; *Body Weight ; },
abstract = {This study is aimed at exploring the relationship between maternal weight categories, including pre-pregnancy body mass index (P-BMI) and gestational weight gain (GWG), and the composition of the infant gut microbiome in the early days of life. We recruited 71 mother-infant pairs from Kangwon National University Hospital and Bundang CHA Hospital, collecting meconium samples from the infants within the first 5 days postpartum. Using 16S ribosomal RNA gene sequencing (V3-V4 region), this study assessed microbial diversity and the relative abundance of specific bacterial taxa in these initial stool samples. Participants were categorized into groups based on maternal P-BMI and GWG, enabling a comprehensive comparison of the microbiota composition in the infants' meconium across different maternal weight metrics. Our analysis identified significant variations in the infant gut microbiome correlated with maternal weight categories. Key findings include a differential abundance of genera such as Sphingobacteriaceae, Bacillaceae, Cytophagaceae, and Alteromonadaceae across maternal P-BMI groups, whereas Moraxellaceae and Rhodospirillaceae varied across GWG groups. In the P-BMI category, infants born to overweight mothers demonstrated a higher abundance of Pseudopedobacter, and a lower abundance of Citrobacter and Lachnospira, while infants in the underweight group showed a higher abundance of Lachnospira and Weissella. In the normal weight group, Citrobacter and Pseudopedobacter were more abundant. Within the GWG category, infants in the inadequate group showed a higher abundance of Klebsiella, whereas the normal group showed a higher abundance of Holdemania. The composition of the infant gut microbiome in the early postnatal period is significantly influenced by maternal weight categories. Understanding the role of maternal weight in shaping early microbial colonization may provide insights into developing strategies to optimize infant health outcomes through targeted interventions before and during pregnancy.},
}
@article {pmid40261136,
year = {2025},
author = {Elias Masiques, N and De Vrieze, J and Hemeryck, LY and Vanhaecke, L and De Smet, S and Van Hecke, T},
title = {Dietary fiber mitigates the differential impact of beef and chicken meat consumption on rat intestinal health.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo00900f},
pmid = {40261136},
issn = {2042-650X},
abstract = {In this rat feeding study, it was hypothesized that the impact of red (vs. white) meat consumption on gut health is more pronounced in fiber-deprived diets, whereas fiber-rich diets may attenuate meat-related differences. For this purpose, rats were fed a red (beef) or white (chicken) meat diet with and without fructo-oligosaccharides (FOS) for three weeks. Gut health was assessed through colonic microbiota, fermentation metabolites, oxidative stress, inflammation, DNA adducts and histology. In rats on the fiber-deprived diets, beef consumption resulted in higher abundance of mucin-degrading bacteria Akkermansia and lower blood glutathione levels compared to chicken-fed rats. Adding FOS to the meat diets modulated the gut microbiota and fermentation metabolites, affected oxidative stress and inflammation markers in tissues and blood, increased colon length, and reduced fat deposition and liver weight. Thus, results showed that the dietary context should be considered when evaluating the impact of red meat consumption on gut health.},
}
@article {pmid40260087,
year = {2025},
author = {Matsumura, E and Kato, H and Hara, S and Ohbayashi, T and Ito, K and Shingubara, R and Kawakami, T and Mitsunobu, S and Saeki, T and Tsuda, S and Minamisawa, K and Wagai, R},
title = {Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1557188},
pmid = {40260087},
issn = {1664-302X},
abstract = {Soil particles in plant rooting zones are largely clustered to form porous structural units called aggregates where highly diverse microorganisms inhabit and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microorganisms exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. However, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus, adequate cell extraction methods from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) from the topsoil of cultivated Acrisol. We postulated that the extraction of microorganisms with distinct taxonomy and functions could be achieved depending on the degree of soil aggregate dispersion. To test this idea, we used six individual aggregates and performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion techniques improved the extractability of bacterial cells compared to previous ones, the sonication technique led to more efficient dispersion and yielded a higher number and more diverse microorganisms than the bead technique. Furthermore, the analyses of nitrogen cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to the greater recovery of microorganisms strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microorganisms holding the genes (potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. Overall, all six aggregates studied showed similarities in pore characteristics, phylum-level composition, and microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggests that conventional methods employed for the extraction of cells and DNA may not be optimal. The findings of this study emphasize the necessity of advancing extraction methodologies to facilitate a more comprehensive understanding of microbial diversity and function in soil environments.},
}
@article {pmid40259028,
year = {2025},
author = {Hsieh, YE and Yang, SY and Liu, SL and Wang, SW and Wang, WL and Tang, SL and Yang, SH},
title = {Microbial Community Shifts and Nitrogen Utilization in Peritidal Microbialites: The Role of Salinity and pH in Microbially Induced Carbonate Precipitation.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {31},
pmid = {40259028},
issn = {1432-184X},
support = {MOST 111-2621-B-029 -002 -MY3//National Science and Technology Council, Taiwan/ ; MOST 110-2611-M-002-024//National Science and Technology Council/ ; },
mesh = {*Carbonates/metabolism/chemistry ; Hydrogen-Ion Concentration ; Salinity ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Microbiota ; *Seawater/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Chemical Precipitation ; },
abstract = {Microbialites have the potential to record environmental changes and act as biosignatures of past geochemical conditions. As such, they could be used as indicators to decipher ancient rock records. Modern microbialites are primarily found in environments where competitors and destructors are absent or where biogeochemical conditions favor their continuous formation. Many previous studies have essentially focused on the role of photosynthetic microbes in controlling pH and carbonate speciation and potentially overlooked alternative non-photosynthetic pathways of carbonate precipitation. Given that microbial activity induces subtle geochemical changes, microbially induced carbonate precipitation (MICP) can involve several mechanisms, from extracellular polymeric substances (EPS), sulfate reduction, anaerobic oxidation of methane, to nitrogen cycling processes, such as ammonification, ureolysis, and denitrification. Moreover, the peritidal zone where temperate microbialites are mostly found today, is under the influence of both freshwater and seawater, arguing for successive biogeochemical processes leading to mineral saturation, and questioning interpretations of fossil records. This study investigates microbialites in three tide pools from the peritidal zone of Fongchueisha, Hengchun, Taiwan, to address the influence of salinity on microbial community composition and carbonate precipitation mechanisms. Microbial samples were collected across varying salinity gradients at multiple time points and analyzed using next-generation sequencing (NGS) of bacterial 16S and eukaryotic 18S rRNA genes. Our results indicate that dominant bacterial groups, including Cyanobacteria and Alphaproteobacteria, were largely influenced by salinity variations, albeit pH exhibited stronger correlation with community composition. Combining our results on geochemistry and taxonomic diversity over time, we inferred a shift in the trophic mode under high salinity conditions, during which the use of urea and amino acids as a nitrogen source outcompetes diazotrophy, ureolysis and ammonification of amino acids reinforcing carbonate precipitation dynamics by triggering an increase in both pH and dissolved inorganic carbon.},
}
@article {pmid40258091,
year = {2025},
author = {Hashem, I and Wang, J and Van Impe, JFM},
title = {A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012974},
doi = {10.1371/journal.pcbi.1012974},
pmid = {40258091},
issn = {1553-7358},
abstract = {Individual-based modeling (IbM) is an instrumental tool for simulating spatial microbial growth, with applications in both microbial ecology and biochemical engineering. Unlike Cellular Automata (CA), which use a fixed grid of cells with predefined rules for interactions, IbMs model the individual behaviors of cells, allowing complex population dynamics to emerge. IbMs require more detailed modeling of individual interactions, which introduces significant computational challenges, particularly in resolving spatial overlaps between cells. Traditionally, this is managed using arrays or kd-trees, which require numerous pairwise comparisons and become inefficient as population size increases. To address this bottleneck, we introduce the Discretized Overlap Resolution Algorithm (DORA), which employs a grid-based framework to efficiently manage overlaps. By discretizing the simulation space further and assigning circular cells to specific grid units, DORA transforms the computationally intensive pairwise comparison process into a more efficient grid-based operation. This approach significantly reduces the computational load, particularly in simulations with large cell populations. Our evaluation of DORA, through simulations of microbial colonies and biofilms under varied nutrient conditions, demonstrates its superior computational efficiency and ability to accurately capture microbial growth dynamics compared to conventional methods. DORA's grid-based strategy enables the modeling of densely populated microbial communities within practical computational timeframes, thereby expanding the scope and applicability of individual-based modeling.},
}
@article {pmid40257249,
year = {2025},
author = {Maggiori, C and John, Z and Bower, DM and Millan, M and Hahn, AS and McAdam, A and Johnson, SS},
title = {Draft genome sequence of a member of a putatively novel Rubrobacteraceae genus from lava tubes in Lava Beds National Monument.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0133524},
doi = {10.1128/mra.01335-24},
pmid = {40257249},
issn = {2576-098X},
abstract = {We report the draft genome sequence of a member of a potentially novel genus of Rubrobacteraceae isolated from Golden Dome Cave in Lava Beds National Monument. Members of this family are known to inhabit thermophilic environments. The metagenome-assembled genome presented here helps illuminate the genetic capacity of basaltic lava tube environments.},
}
@article {pmid40253969,
year = {2025},
author = {Achouri, H and Derguini, A and Idres, T and Selamoglu, Z and Hamadi, NB and Jalouli, M and Elfalleh, W and Bendif, H and Badraoui, R and Boufahja, F and Dellali, M},
title = {Impact of climate change on the toxicity of bisphenol A in Mytilus galloprovincialis and assessment of phycoremediation using Nannochloropsis salina via a multi-biomarker strategy and modeling.},
journal = {Marine pollution bulletin},
volume = {216},
number = {},
pages = {118010},
doi = {10.1016/j.marpolbul.2025.118010},
pmid = {40253969},
issn = {1879-3363},
abstract = {In the current study, the mussels Mytilus galloprovincialis, exposed to four varying temperatures (17, 20, 23, and 26 °C), were contaminated with 50 μg/L of bisphenol A both with and without Nannochloropsis salina. The toxicity evaluation is determined by quantifying various biomarkers related to oxidative stress, neurotoxicity, and cellular damage. The key findings indicate that the toxicity of bisphenol A is heightened by rising temperature. The impact of bisphenol A is most evident at 26 °C, leading to excessive production of reactive oxygen species, depletion of non-enzymatic antioxidants, and activation of antioxidant enzymes (catalase and glutathione-S-transferase). The rise in malondialdehyde levels confirms lipid peroxidation caused by bisphenol A and intensified by thermal stress. These findings have been supported by strong molecular interactions between bisphenol A and lectin mytilec apo-form and proximal thread matrix protein 1 from M. galloprovincialis following the computational modeling assay. The incorporation of N. salina as a food additive helped, firstly, to mitigate the stress effects and, secondly, resulted in a noticeable enhancement of oxidative balance and filtration ability, along with decreased lipid peroxidation.},
}
@article {pmid40252751,
year = {2025},
author = {Tuts, L and Heyndrickx, M and Becue, I and Boon, N and De Maesschalck, P and Rasschaert, G},
title = {Tracking antibiotics and antibiotic resistant E. coli in the aquatic environment linked to agriculture.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126265},
doi = {10.1016/j.envpol.2025.126265},
pmid = {40252751},
issn = {1873-6424},
abstract = {The application of manure to fertilize agricultural land is associated with the introduction of antibiotic residues and bacteria, including antibiotic resistant bacteria, which can reach surface water through runoff and drainage and groundwater through leaching from the soil. This was investigated by sampling 50 surface water locations (before and after fertilization) and 50 groundwater wells for the presence of antibiotic residues and the presence of antibiotic-resistant bacteria. For the latter, Escherichia coli and extended-spectrum β-lactamase (ESBL) producing E. coli were used as indicators and profiled for antibiotic resistance. The presence of a wide range of antibiotic residues, though at low concentrations (0.01 - 10 μg/L), in freshwater ecosystems highlights the extensive spread of these substances. Only 16% of the samples were consistently free of antibiotic residues throughout both sampling periods. Notably, the frequent occurrence of sulfonamides and lincomycin in surface waters raises concerns as their concentrations occasionally exceed the predicted no-effect levels for antimicrobial resistance selection. Maximum concentrations were reported at 8.83 μg/L and 1.60 μg/L for sulfamethoxazole and lincomycin, respectively. Additionally, resistance patterns in E. coli indicate increased resistance to sulfamethoxazole following the fertilization period, suggesting that the application of manure on fields contributes to a rise in antibiotic resistance from 20% to 48%. Although antibiotic contamination in groundwater is less prevalent, antibiotic resistance remains widespread. In particular, ESBL-producing E. coli exhibit heightened resistance levels, not limited to β-lactam antibiotics. The detection of resistance to critical last-resort antibiotics such as carbapenems and colistin further emphasizes the urgency of addressing antibiotic resistance in environmental contexts. This study highlights the need for continued monitoring and the implementation of legislation to reduce antibiotic pollution and tackle resistance in aquatic ecosystems.},
}
@article {pmid40251008,
year = {2025},
author = {Rizaludin, MS and Diaz, ASL and Zweers, H and Raaijmakers, JM and Garbeva, P},
title = {Foliar infections by Botrytis cinerea modulate the tomato root volatilome and microbiome.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf042},
pmid = {40251008},
issn = {1574-6941},
abstract = {The fungal pathogen Botrytis cinerea causes significant damage to aboveground plant parts, but its impact on root chemistry and microbiome composition is less understood. This study investigated how B. cinerea foliar infection influences the root volatilome and microbiome of two tomato genotypes: wild Solanum pimpinellifolium and domesticated Solanum lycopersicum var. Moneymaker. In the absence of infection, wild tomato roots emitted higher levels of monoterpenes such as α-pinene and terpinene compared to domesticated tomato roots. The fungal infection induced elevated levels of benzyl alcohol and benzofuran in the root headspace and/or rhizosphere of both genotypes, alongside genotype-specific changes. Multivariate analyses revealed that B. cinerea significantly altered bacterial and fungal community compositions in the rhizosphere and rhizoplane, with stronger bacterial community shifts in the rhizoplane. Taxa depletion and enrichment were observed, particularly among Proteobacteria and Ascomycota. Mantel tests showed significant correlations between rhizoplane bacterial community compositions and root volatilome compounds. Notably, enriched bacterial taxa such as Pelomonas and Comamonadaceae positively correlated with benzyl alcohol and benzofuran levels in the root volatilome. These findings demonstrate that B. cinerea foliar infection might induce profound changes in root volatilome and microbiome composition, highlighting its systemic effects on plant-root chemistry and microbiome composition.},
}
@article {pmid40250533,
year = {2025},
author = {Rosario Rodero, MD and Steyer, JP and Pérez-Bernal, MF and Verstraete, W and Escudié, R and Capson-Tojo, G},
title = {Dinitrogen fixation by open purple non-sulfur bacteria cultures for protein production: Diazotrophy boosts photoheterotrophic uptake rates.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132554},
doi = {10.1016/j.biortech.2025.132554},
pmid = {40250533},
issn = {1873-2976},
abstract = {Purple non-sulfur bacteria (PNSB) offer a sustainable alternative to current inefficient protein production systems thanks to their high yields. This study explored the potential of specialized diazotrophic PNSB open cultures for protein production, benchmarking their performance against ammonium-grown PNSB and other diazotrophs. While diazotrophic yields (0.85-0.93 gCODbiomass·gCODsubstrate[-1]; COD being chemical oxygen demand) were slightly lower than non-diazotrophic (∼1.0), they were over double those of heterotrophic-diazotrophic rhizobacteria, with full N recovery as biomass (∼1.0 gNbiomass·gNfixed[-1]). Photoheterotrophic-diazotrophic uptake rates were the fastest ever reported for PNSB and any other diazotroph (e.g., 5.20 ± 0.83 vs. 2.64 ± 0.34 gCODsubstrate·gCODbiomass[-1]·d[-1] for PNSB on NH4[+]). Optimal rates required high light intensities, aligning with diazotrophic energy demands. Photoheterotrophic-diazotrophic conditions were highly selective, enriching a specialized Rhodopseudomonas palustris strain. Biomass protein contents and essential amino acid metrics confirmed nutritional suitability for humans. This work lays the background to exploit PNSB's potential to address global protein demands through sustainable nitrogen fixation.},
}
@article {pmid40248914,
year = {2025},
author = {Zhang, RG and Shang, HY and Milne, RI and Almeida-Silva, F and Chen, H and Zhou, MJ and Shu, H and Jia, KH and Van de Peer, Y and Ma, YP},
title = {SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.},
journal = {Nucleic acids research},
volume = {53},
number = {7},
pages = {},
doi = {10.1093/nar/gkaf320},
pmid = {40248914},
issn = {1362-4962},
support = {2022YFF1301700//National Key Research and Development Program/ ; KIBXD202401//Kunming Institute of Botany, Chinese Academy of Sciences/ ; //Light of West China/ ; 202101BC070003//Key Basic Research Programs of Yunnan Province/ ; 2022SJ07X-03//PSESP/ ; },
mesh = {*Synteny/genetics ; *Genomics/methods ; *Evolution, Molecular ; *Genome, Plant ; Phylogeny ; Polyploidy ; Algorithms ; Plants/genetics ; },
abstract = {With the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods for identifying orthologous synteny face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable and robust approach, based on the Orthology Index (OI), to effectively identify orthologous synteny. Our evaluation across a large-scale empirical dataset with diverse polyploidization events demonstrated the high reliability and robustness of the OI method. Simulation-based benchmarks further validated the accuracy of our method, showing its superior performance against existing methods across a wide range of scenarios. Additionally, we explored its broad applications in reconstructing the evolutionary histories of plant genomes, including the inference of polyploidy, identification of reticulation, and phylogenomics. In conclusion, OI offers a robust, interpretable, and scalable approach for identifying orthologous synteny, facilitating more accurate and efficient analyses in plant evolutionary genomics.},
}
@article {pmid40248762,
year = {2025},
author = {Flores, C and Millard, S and Seekatz, AM},
title = {Bridging Ecology and Microbiomes: Applying Ecological Theories in Host-associated Microbial Ecosystems.},
journal = {Current clinical microbiology reports},
volume = {12},
number = {1},
pages = {9},
pmid = {40248762},
issn = {2196-5471},
abstract = {PURPOSE OF REVIEW: This review explores the application of classical ecological theory to host-associated microbiomes during initial colonization, maintenance, and recovery. We discuss unique challenges of applying these theories to host-associated microbiomes and host factors to consider going forward.<br><br>RECENT FINDINGS: Recent studies applying community ecology principles to host microbiomes continue to demonstrate a role for both selective and stochastic processes in shaping host-associated microbiomes. However, ecological frameworks developed to describe dynamics during homeostasis do not necessarily apply during diseased or highly perturbed states, where large variations can potentially lead to alternate stable states.<br><br>SUMMARY: Despite providing valuable insights, the application of ecological theories to host-associated microbiomes has some unique challenges. The integration of host-specific factors, such as genotype or immune dynamics in ecological models or frameworks is crucial for understanding host microbiome assembly and stability, which could improve our ability to predict microbiome outcomes and improve host health.},
}
@article {pmid40247944,
year = {2025},
author = {Sun, Y and Sun, S and Zahid, MS and Qiu, Q and Wang, L and Wang, S},
title = {Root-applied brassinosteroid and salicylic acid enhance thermotolerance and fruit quality in heat-stressed 'Kyoho' grapevines.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1563270},
pmid = {40247944},
issn = {1664-462X},
abstract = {INTRODUCTION: The increasingly severe global greenhouse effect has become an irreversible trend, significantly impacting viticulture regions through heat stress during various grape growth stages, especially under protected cultivation conditions where high temperatures frequently occur. Therefore, studying the impact of heat stress on grapevine growth and fruit quality across the entire growth and development period, along with effective mitigation measures, is crucial.<br><br>METHODS: In this study, three-year-old 'Kyoho' grapevines were used as experimental materials, with four treatment groups: a control group, a hightemperature group (heat stress, HT), a high-temperature + brassinolide group (BR), and a high-temperature + salicylic acid group (SA). During the flowering, young berry swelling, and veraison stages, BR and SA were applied via nutrient solutions every seven days.<br><br>RESULTS: The results demonstrated that BR restored the maximum photosynthetic rate (Amax) to 96.14% of CK by the 18th day of flowering, significantly outperforming SA's recovery rate of 86.64%. Both treatments maintained light saturation points (1200 &#x3bc;mol&#x2022;m[&#x207b;&#xb2;]&#x2022;s[&#x207b;&#xb9;]) and CO2 saturation thresholds equivalent to CK. The decline in PSII photochemical efficiency (Fv/Fm) was reduced from 18% in HT to 5-8% in BR/SA-treated groups, with BR showing minimal deviation (2.3%) from CK during veraison, effectively mitigating PSII photoinhibition caused by heat stress. Furthermore, both treatments reduced leaf malondialdehyde (MDA) content, minimizing membrane lipid peroxidation, while increasing soluble protein (SP) content to protect leaves. Under heat stress, BR notably improved the fruit set rate by 22.67% compared to HT (SA: 13%), promoted berry expansion, and enhanced the accumulation of sugars and anthocyanins in the fruit skin, with SA showing similar, though slightly less pronounced, effects.<br><br>DISCUSSION: These findings provide valuable theoretical insights into the use of exogenous hormones in root nutrient solutions as a strategy to mitigate the adverse effects of heat stress in grape production.},
}
@article {pmid40247820,
year = {2025},
author = {Liu, M and Yao, X and Wang, H and Xu, X and Kong, J and Wang, Y and Chen, W and Bai, H and Wang, Z and Setati, ME and Crauwels, S and Blancquaert, E and Fan, P and Liang, Z and Dai, Z},
title = {Carposphere microbiota alters grape volatiles and shapes the wine grape typicality.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70152},
pmid = {40247820},
issn = {1469-8137},
support = {NXNYYZ202101//Agricultural Breeding Project of Ningxia Hui Autonomous Region/ ; U20A2041//National Natural Science Foundation of China/ ; JCTD-2022-06//CAS Youth Interdisciplinary Team/ ; 2021YFE0109500//National Key Research and Development Program of China/ ; YSBR-093//CAS Project for Young Scientists in Basic Research/ ; },
abstract = {While specific environments are known to shape plant metabolomes and the makeup of their associated microbiome, it is as yet unclear whether carposphere microbiota contribute to the characteristics of grape fruit flavor of a particular wine region. Here, carposphere microbiomes and berry transcriptomes and metabolomes of three grape cultivars growing at six geographic sites were analyzed. The composition of the carposphere microbiome was determined mainly by environmental conditions, rather than grape genotype. Bacterial microbiota likely contributed to grape volatile profiles. Particularly, candidate operational taxonomic units (OTUs) in genus Sphingomonas were highly correlated with grape C6 aldehyde volatiles (also called green leaf volatiles, GLVs), which contribute to a fresh taste. Furthermore, a core set of expressed genes was enriched in lipid metabolism, which is responsible for bacterial colonization and C6 aldehyde volatile synthesis activation. Finally, a similar grape volatile profile was observed after inoculating the berry skin of two grape cultivars with Sphingomonas sp., thus providing evidence for the hypothetical microbe-metabolite relationship. These results provide novel insight into how the environment-microbiome-plant quality (E × Mi × Q) interaction may shape berry flavor and thereby typicality, serving as a foundation for decision-making in vineyard microbial management.},
}
@article {pmid40247656,
year = {2025},
author = {Bonazzi, E and De Barba, C and Lorenzon, G and Maniero, D and Bertin, L and Barberio, B and Facciotti, F and Caprioli, F and Scaldaferri, F and Zingone, F and Savarino, EV},
title = {Recent developments in managing luminal microbial ecology in patients with inflammatory bowel disease: from evidence to microbiome-based diagnostic and personalized therapy.},
journal = {Expert review of gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2495087},
pmid = {40247656},
issn = {1747-4132},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic condition characterized by abnormal immune responses and intestinal inflammation. Emerging evidence highlights the vital role of gut microbiota in IBD's onset and progression. Recent advances have shaped diagnostic and therapeutic strategies, increasingly focusing on microbiome-based personalized care. Methodology: this review covers studies from 2004 to 2024, reflecting the surge in research on luminal microbial ecology in IBD. Human studies were prioritized, with select animal studies included for mechanistic insights. Only English-language, peer-reviewed articles - clinical trials, systematic reviews, and meta-analyses - were considered. Studies without clinical validation were excluded unless offering essential insights. Searches were conducted using PubMed, Scopus, and Web of Science.<br><br>AREAS COVERED: we explore mechanisms for managing IBD-related microbiota, including microbial markers for diagnosis and novel therapies such as fecal microbiota transplantation, metabolite-based treatments, and precision microbiome modulation. Additionally, we review technologies and diagnostic tools used to analyze gut microbiota composition and function in clinical settings. Emerging data supporting personalized therapeutic strategies based on individual microbial profiles are discussed.<br><br>EXPERT OPINION: Standardized microbiome research integration into clinical practice will enhance precision in IBD care, signaling a shift toward microbiota-based personalized medicine.},
}
@article {pmid40246153,
year = {2025},
author = {Bharathan, A and Arafath, Y and Fathima, A and Hassan, S and Singh, P and Kiran, GS and Selvin, J},
title = {Affection of Environmental Factors on the Pathogenicity of Vibrio vulnificus: Insights into Gene Activation and Disease.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107591},
doi = {10.1016/j.micpath.2025.107591},
pmid = {40246153},
issn = {1096-1208},
abstract = {Climate change, particularly rising sea surface temperatures and altered salinity levels has contributed to the increased prevalence of Vibrio vulnificus infections in humans and marine life. This opportunistic pathogen thrives in warm, estuarine environments, and its virulence is influenced by temperature-dependent gene expression, such as the activation of pVvBt2. Elevated temperatures and iron availability enhance pathogenicity by upregulating key virulence factors, including hemolysin, exotoxins, and biofilm-associated genes. Climate-driven shifts in microbial ecology have also facilitated the global expansion of V. vulnificus, leading to more frequent outbreaks and an increasing threat to public health. The unregulated use of antibiotics has also contributed to the emergence of resistant strains, complicating treatment strategies. This review explores the complex interplay between climate change and the molecular mechanisms driving V. vulnificus pathogenicity, global gene expression responses, and the implications for disease outbreaks. We also discuss current and emerging therapeutic approaches, including antibiotic stewardship and vaccine development, to mitigate the rising health risks posed by this climate-sensitive pathogen.},
}
@article {pmid40244660,
year = {2025},
author = {Narla, AV and Hwa, T and Murugan, A},
title = {Dynamic coexistence driven by physiological transitions in microbial communities.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {16},
pages = {e2405527122},
doi = {10.1073/pnas.2405527122},
pmid = {40244660},
issn = {1091-6490},
support = {542387//Simons Foundation (SF)/ ; 2029480//NSF | BIO | Division of Molecular and Cellular Biosciences (MCB)/ ; R35GM151211//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 2317138//NSF | MPS | Division of Physics (PHY)/ ; },
mesh = {*Ecosystem ; *Models, Biological ; Biomass ; *Microbiota/physiology ; *Microbial Interactions/physiology ; Bacteria/growth &amp; development ; },
abstract = {Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes in exponential growth often modify their environments so strongly that they are forced out of the growth state into stressed, nongrowing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State Model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states during cyclic succession. Our model specifies the growth preference of each species along a global ecological coordinate, taken to be the biomass density of the community, but is otherwise agnostic to specific interactions (e.g., nutrient starvation, stress, aggregation), in order to focus on self-consistency conditions on combinations of physiological states, "community states," in a stable ecosystem. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: enhanced community stability through staggered dominance of different species in different community states, increased tolerance of community diversity to fast growing species dominating distinct community states, and increased requirement of growth dominance by late-growing species. These features, derived explicitly for simplified models, are proposed here as principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on fixed, idealized interspecies interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.},
}
@article {pmid40243315,
year = {2025},
author = {Weng, L and Cui, Y and Jian, W and Zhang, Y and Pang, L and Cao, Y and Zhou, Y and Liu, W and Lin, H and Tao, Y},
title = {Inter-kingdom interactions and environmental influences on the oral microbiome in severe early childhood caries.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0251824},
doi = {10.1128/spectrum.02518-24},
pmid = {40243315},
issn = {2165-0497},
abstract = {UNLABELLED: Dental caries arise from intricate interactions among oral microorganisms, impacting ecological stability and disease progression. In this study, we aimed to investigate the microbial diversity and inter-kingdom interactions in severe early childhood caries (S-ECC) and assess the influence of environmental factors such as salivary pH and trace elements. We analyzed 61 children aged 3-4 years with complete deciduous dentition, evaluating salivary pH, buffering capacity, and trace elements (iron, fluoride). We examined the performance of 16S rRNA V1-V9 regions gene and internal transcribed spacer (ITS) primers for bacteria and fungi from plaque and saliva to characterize community compositions and diversity. Findings revealed significant shifts in bacterial diversity in S-ECC saliva samples, marked by decreased diversity and elevated abundance of cariogenic species, particularly Streptococcus mutans. Candida albicans was notably more prevalent in the S-ECC group, implicating its potential role in pathogenesis. Iron and fluoride concentrations showed no significant correlation with microbial community structure. Network analyses uncovered complex intra- and inter-kingdom interactions, underscoring cooperative and competitive dynamics. S-ECC children exhibited higher abundances of bacteria (Streptococcus mutans, Granulicatella, Actinomyces) and fungi (Candida albicans), with specific microbial taxa associated with reduced salivary pH.<br><br>IMPORTANCE: This study illuminates the intricate relationship between bacteria and fungi within the oral microbial community of children, specifically highlighting differences between those with S-ECC and those without caries. Through an extensive analysis of the microbial composition in both saliva and dental plaque, we identified a significant increase in the abundance of specific bacterial taxa (e.g., S. mutans, Granulicatella, Actinomyces) and fungal species (e.g., C. albicans) in the oral cavities of children with S-ECC. This finding underscores the potential role of these microorganisms in the development of caries. Contrary to previous studies that emphasize the importance of iron and fluoride in oral health, our research found no significant correlation between the concentrations of these elements and the composition of oral microbial communities. This result challenges conventional understanding and opens new avenues for future research. Additionally, our findings revealed an association between Veillonella sp., Propionibacterium sp., and Candida sp. and reduced salivary pH. This provides novel insights into the relationship between the oral microenvironment and caries development. The implications of our findings are substantial for the development of prevention and intervention strategies targeting childhood caries. They also underscore the critical need for a deeper exploration of oral microbial interactions and their environmental influences.},
}
@article {pmid40241747,
year = {2025},
author = {Takahashi, M and Hiraoka, S and Matsumoto, Y and Shibagaki, R and Ujihara, T and Maeda, H and Seo, S and Nagasaki, K and Takeuchi, H and Matsuzaki, S},
title = {Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112264},
pmid = {40241747},
issn = {2589-0042},
abstract = {Restriction modification (RM) systems are ubiquitous bacterial defense systems; however, some phages evade RM system and adapt to their bacterial hosts. In such cases, phages are thought to stochastically acquire DNA methylation from host-encoded DNA methyltransferases (MTases), facilitating host adaptation. However, no studies have directly compared the methylomes of host bacteria and their infecting phages. Here, we demonstrate the epigenetic landscape of adapted phages with diverse infection histories, focusing on the broad host-range phage KHP30T as its adapts to three Helicobacter pylori strains. Using a multistage infection system, we observed that the adapted phages displayed significantly high titers against the last infected H. pylori strain, suggesting an attendant change in host tropism. Single-molecule real-time sequencing revealed that methylated motifs were predominantly shared between the adapted phages and their most recent host. Our findings enhance our understanding of epigenetic phage-host interactions, which have significant implications for microbial ecology.},
}
@article {pmid40240613,
year = {2025},
author = {Dhungana, I and Nguyen, NH},
title = {Legacy of Repeated Cultivation Drives Cyclical Microbial Community Development in a Tropical Oxisol Soil.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {30},
pmid = {40240613},
issn = {1432-184X},
support = {HAW08042-H//U.S. Department of Agriculture/ ; },
mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; *Fungi/classification/growth &amp; development/genetics/isolation &amp; purification ; Soil/chemistry ; Agriculture/methods ; Zea mays/growth &amp; development/microbiology ; *Archaea/classification/growth &amp; development/genetics/isolation &amp; purification ; *Microbiota ; Tropical Climate ; Crops, Agricultural/growth &amp; development/microbiology ; Lactuca/growth &amp; development/microbiology ; Mustard Plant/growth &amp; development/microbiology ; },
abstract = {Agricultural practices and the crop being actively cultivated are some of the most important contributors to soil microbial community assembly processes in agroecosystems. However, it is not well-understood how the cultivation of diverse crop species can directionally shift complex soil microbial communities, especially under continuous monoculture systems. Here, we conducted a field experiment to assess how three crop species (Lactuca sativa, Brassica juncea, and Zea mays) may shift soil microbial (bacteria/archaea and fungi) communities when planted in a monoculture and repeatedly grown for three cycles in a tropical Oxisol soil. We found that while plant species made limited contributions to microbial community differentiation, repeated cultivation was a strong driver of community development over time. The bacterial/archaeal communities exhibited a cyclical community development pattern, initially with strong differentiation that attenuated to a steady state at the end of the three cycles. In contrast, fungal communities generally developed more linearly and may have only started to stabilize after three cropping cycles. These developments may speak to the stronger legacy effects on fungal communities. Together, these results highlight the differences between how bacteria/archaea and fungal communities develop, especially in tropical, underdeveloped, intensively degraded, or marginal soils.},
}
@article {pmid40239902,
year = {2025},
author = {Ma, H and Chen, S and Lv, L and Ye, Z and Yang, J and Wang, B and Zou, J and Li, J and Ganigué, R},
title = {Large-sized aerobic granular biofilm: stable biotechnology to improve nitrogen removal and reduce sludge yield.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132543},
doi = {10.1016/j.biortech.2025.132543},
pmid = {40239902},
issn = {1873-2976},
abstract = {Three parallel sequencing batch reactors (control, small-sized polyurethane sponge (PUS) (3.0 mm), and large-sized PUS (10.0 mm)) were used to investigate aerobic granular biofilm (AGB) characteristics. Results show that 10.0 mm PUS facilitated rapid formation of large-sized AGB (AGBL), which exhibited higher biomass concentration (8.5 g/L) and faster settling velocity (69.2-159.3 m/h) than aerobic granular sludge (AGS) (3.2 g/L and 38.6-80.0 m/h). The AGBL system also maintained long-term structural stability with a lower instability coefficient (0.004-0.018 min[-1]) than AGS (0.053-0.090 min[-1]). Additionally, during long-term operation, the AGBL system achieved excellent removal efficiencies for NH4[+]-N (99.6 ± 0.4 %) and total nitrogen (92.3 ± 2.6 %), and exhibited a lower sludge yield (0.05 gVSS/gCOD) than AGS (0.14 gVSS/gCOD). The larger size and compact structure of AGBL increased anoxic/anaerobic zones, enriching denitrifying and hydrolytic/fermentative bacteria. These findings highlight AGBL with large PUS as a more promising biotechnology for practical applications than conventional AGS.},
}
@article {pmid40238873,
year = {2025},
author = {Bukhdruker, S and Gushchin, I and Shevchenko, V and Kovalev, K and Polovinkin, V and Tsybrov, F and Astashkin, R and Alekseev, A and Mikhaylov, A and Bukhalovich, S and Bratanov, D and Ryzhykau, Y and Kuklina, D and Caramello, N and Rokitskaya, T and Antonenko, Y and Rulev, M and Stoev, C and Zabelskii, D and Round, E and Rogachev, A and Borshchevskiy, V and Ghai, R and Bourenkov, G and Zeghouf, M and Cherfils, J and Engelhard, M and Chizhov, I and Rodriguez-Valera, F and Bamberg, E and Gordeliy, V},
title = {Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.},
journal = {Science advances},
volume = {11},
number = {16},
pages = {eadu5303},
doi = {10.1126/sciadv.adu5303},
pmid = {40238873},
issn = {2375-2548},
mesh = {*Protons ; *Rhodopsins, Microbial/chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Proton Pumps/chemistry/metabolism ; Protein Conformation ; },
abstract = {Bacterial proton pumps, proteorhodopsins (PRs), are a major group of light-driven membrane proteins found in marine bacteria. They are functionally and structurally distinct from archaeal and eukaryotic proton pumps. To elucidate the proton transfer mechanism by PRs and understand the differences to nonbacterial pumps on a molecular level, high-resolution structures of PRs' functional states are needed. In this work, we have determined atomic-resolution structures of MAR, a PR from marine actinobacteria, in various functional states, notably the challenging late O intermediate state. These data and information from recent atomic-resolution structures on an archaeal outward proton pump bacteriorhodopsin and bacterial inward proton pump xenorhodopsin allow for deducing key universal elements for light-driven proton pumping. First, long hydrogen-bonded chains characterize proton pathways. Second, short hydrogen bonds allow proton storage and inhibit their backflow. Last, the retinal Schiff base is the active proton donor and acceptor to and from hydrogen-bonded chains.},
}
@article {pmid40238292,
year = {2025},
author = {Zhang, Y and Lin, H and Xiong, Y and Zhang, Z and Zeng, L and Liu, Z},
title = {Fu Brick Tea Protects the Intestinal Barrier and Ameliorates Colitis in Mice by Regulating Gut Microbiota.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071122},
pmid = {40238292},
issn = {2304-8158},
support = {2024HX118//Horizontal project of Shaoyang University/ ; 2024JJ7497//Foundation regional joint fund of Hunan Province natural Science/ ; 202401001313//The teaching reform research project of Hunan Province in 2024/ ; 2022YFE0111200//Innovation and transformation of key technologies for efficient preparation of catechin oxidation polymerization products/ ; },
abstract = {Ulcerative colitis (UC) pathogenesis is strongly linked to gut microbiota dysbiosis and compromised intestinal barrier integrity. Emerging evidence suggests that targeted dietary interventions may restore microbial homeostasis and ameliorate colitis progression. In this study, we evaluated the therapeutic potential of Fu Brick tea (FBT) using a dextran sulfate sodium (DSS)-induced murine colitis model. The results indicated that oral administration of FBT extract significantly improved the disease index, reduced inflammatory response, protected intestinal barrier protein (e.g., ZO-1), and maintained intestinal structure integrity. Furthermore, FBT intake increased the diversity of gut microbiota, promoted the growth of beneficial bacteria (e.g., Akkermansia), inhibited the proliferation of harmful bacteria (e.g., Desulfovibrioceae, Escherichia, and Helicobacter), restored intestinal homeostasis, and alleviated colitis symptoms including diarrhea. These findings position FBT as a promising nutraceutical candidate for UC management via multi-target modulation of mucosal immunity and microbial ecology.},
}
@article {pmid40238218,
year = {2025},
author = {Zhadyra, S and Tao, F and Xu, P},
title = {Exploring the Microbiome and Functional Metabolism of Fermented Camel Milk (Shubat) Using Metagenomics.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071102},
pmid = {40238218},
issn = {2304-8158},
abstract = {Shubat is a traditional fermented camel milk drink that originated in Central Asia, with especially deep cultural roots in Kazakhstan. However, systematic studies on the microbial ecology and functional genes of Shubat remain scarce. As a distinctive fer-mented food, its microbial diversity and functional properties have not been fully ex-plored. This study investigates the microbial diversity and functional potential of Shubat by using advanced metagenomic techniques. Its microbial community is mainly composed of bacteria (96.6%), with Lactobacillus, Lactococcus, and Streptococcus being the dominant genera. Functional annotations through EggNOG, KEGG, and CAZy databases highlighted the metabolic versatility of Shubat's microbiota. Key pathways included amino acid and carbohydrate metabolism, vitamin biosynthesis, and central carbon metabolism, emphasizing their roles in fermentation and nutritional enhancement. The identification of various enzymes related to chemical synthesis further emphasizes the contribution of the microbiota to Shubat's unique flavor and texture. This study not only provides an important basis for the scientific understanding of Shubat but also expands the application possibilities of fermented food in the field of health and nutrition and confers modern value and significance to traditional food. This integration of science and tradition has not only facilitated the development of food microbiology but also paved new pathways for the global dissemination of traditional foods and the development of functional foods.},
}
@article {pmid40237447,
year = {2025},
author = {Choudoir, MJ and Ishaq, SL and Beiko, RG and Silva, DS and Allen-Vercoe, E and O'Doherty, KC},
title = {The case for microbiome stewardship: what it is and how to get there.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0006225},
doi = {10.1128/msystems.00062-25},
pmid = {40237447},
issn = {2379-5077},
abstract = {Microbiomes are essential for human, animal, plant, and ecosystem health. Despite widespread recognition of the importance of microbiomes, there is little attention paid to monitoring and safeguarding microbial ecologies on policy levels. We observe that microbiomes are deteriorating owing to practices at societal levels such as pesticide use in agriculture, air and water pollution, and overuse of antibiotics. Potential policy on these issues would cross multiple domains such as public health, environmental protection, and agriculture. We propose microbiome stewardship as a foundational concept that can act across policy domains to facilitate healthy microbiomes for human and ecosystem health. We examine challenges to be addressed and steps to take toward developing meaningful microbiome stewardship.},
}
@article {pmid40235320,
year = {2025},
author = {Bahram Wlia, A and Majedi, S},
title = {Optimizing hygiene and microbial aspect of paper recycling: a sustainable approach for environmental conservation.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {71},
number = {3},
pages = {151-157},
doi = {10.14715/cmb/2025.71.3.18},
pmid = {40235320},
issn = {1165-158X},
mesh = {*Recycling/methods ; *Paper ; *Hygiene ; *Bacteria/isolation &amp; purification/classification/genetics ; *Conservation of Natural Resources/methods ; Iraq ; Waste Management/methods ; },
abstract = {This study explores microbial dynamics in paper recycling, emphasizing the significance of sustainable practices for environmental preservation. Samples were collected from various urban waste sources in Erbil city, Kurdistan Region, Iraq, including materials such as pizza boxes, cigarette packets, and coffee cups. Pure bacterial colonies were isolated using standard methods, and their morphological and physiological traits were characterized through biochemical tests. Identification of bacterial species followed established protocols. The study identified diverse bacterial species associated with paper waste, highlighting potential hygiene concerns in the recycling process. The findings of this study contribute to understanding the microbial ecology associated with paper waste and recycling processes. By optimizing hygiene measures and gaining insights into the microbial communities present, this research underscores the importance of sustainable practices in paper recycling to mitigate environmental impacts and promote a healthier ecosystem. Policies for future waste management and reduction of environmental risks have been proposed.},
}
@article {pmid40234253,
year = {2025},
author = {Yao, B and Mou, X and Li, Y and Lian, J and Niu, Y and Liu, J and Lu, J and Li, Y and Li, Y and Wang, X},
title = {Distinct Assembly Patterns of Soil Bacterial and Fungal Communities along Altitudinal Gradients in the Loess Plateau's Highest Mountain.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {29},
pmid = {40234253},
issn = {1432-184X},
support = {23JRRA672//Youth Science and Technology Fund Program of Gansu Province/ ; 2023449//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 22JR5RA076//Gansu Province Natural Science Foundation Program/ ; },
mesh = {*Soil Microbiology ; *Altitude ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Ecosystem ; *Microbiota ; Biodiversity ; *Mycobiome ; China ; High-Throughput Nucleotide Sequencing ; },
abstract = {A critical issue in microbial ecology is quantifying the relative contributions of deterministic and stochastic processes to microbial community assembly, and predicting ecosystem function by understanding the ecological processes of community composition is an integral part. However, the mechanisms driving microbial community assembly along altitudinal gradients in mountain ecosystems remain largely unexplored. Here, we used high-throughput sequencing to examine the structural characteristics and diversity maintenance mechanisms of soil bacterial and fungal communities along an altitudinal gradient (2632-3661 m) in Mahan Mountain, the highest peak of the Loess Plateau. Proteobacteria, Acidobacteriota and Actinobacteriota dominated the bacterial communities, while Ascomycota, Basidiomycota and Mortierellomycota were the predominant fungal groups. Although elevation did not significantly affect bacterial and fungal alpha diversity, notable shifts in community structure were observed along the altitudinal gradients. Bacterial communities were predominantly shaped by deterministic processes, leading to pronounced structural and compositional differentiation across altitudes. In contrast, fungal community assembly was primarily determined by a combination of deterministic and stochastic processes, leading to small pronounced structural divergence. The interplay of topography, climate, and soil conditions influenced the altitudinal distribution and community structure of soil bacteria in this mountain ecosystem.},
}
@article {pmid40230839,
year = {2025},
author = {Zhao, T and Wang, C and Liu, Y and Li, B and Shao, M and Zhao, W and Zhou, C},
title = {The role of polysaccharides in immune regulation through gut microbiota: mechanisms and implications.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1555414},
pmid = {40230839},
issn = {1664-3224},
mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; *Polysaccharides/immunology/metabolism ; Animals ; Fatty Acids, Volatile/metabolism ; *Immunomodulation ; Cytokines/metabolism ; },
abstract = {Polysaccharides, as complex carbohydrates, play a pivotal role in immune modulation and interactions with the gut microbiota. The diverse array of dietary polysaccharides influences gut microbial ecology, impacting immune responses, metabolism, and overall well-being. Despite their recognized benefits, there is limited understanding of the precise mechanisms by which polysaccharides modulate the immune system through the gut microbiota. A comprehensive search of Web of Science, PubMed, Google Scholar, and Embase up to May 2024 was conducted to identify relevant studies. This study employs a systematic approach to explore the interplay between polysaccharides and the gut microbiota, focusing on cytokine-mediated and short-chain fatty acid (SCFA)-mediated pathways. The findings underscore the significant role of polysaccharides in shaping the composition and function of the gut microbiota, thereby influencing immune regulation and metabolic processes. However, further research is necessary to elucidate the detailed molecular mechanisms and translate these findings into clinical applications.},
}
@article {pmid40229524,
year = {2025},
author = {Sakae, K and Kitagami, Y and Matsuda, Y},
title = {Rhizosphere Bacterial Communities Alter in Process to Mycorrhizal Developments of a Mixotrophic Pyrola japonica.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {28},
pmid = {40229524},
issn = {1432-184X},
support = {2023-4099//Japan Science Society/ ; JRMJSP2137//Japan Science and Technology Agency/ ; 24K01796//Japan Society for the Promotion of Science/ ; },
mesh = {*Mycorrhizae/growth &amp; development/physiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Ericaceae/microbiology/growth &amp; development ; *Microbiota ; Biodiversity ; DNA, Bacterial/genetics ; },
abstract = {Rhizosphere bacteria work in synergy with mycorrhizal fungi to promote plant growth. The community structure of rhizosphere bacteria may be influenced by continuous changes in fungal associations with host plants. Asiatic herbaceous plant Pyrola japonica (Ericaceae) forms arbutoid mycorrhizas without fungal mantles, with its mycorrhizal development being visually distinguishable at the cellular level. This study aimed to investigate roles of rhizosphere bacteria and their community shifts along with mycorrhizal developments. We examined bacterial communities at three different developmental stages of mycorrhizal roots-limited, full, and digested-via a partial 16S rRNA amplicon sequencing. Both α- and β-diversities in the full condition were significantly lower than those in the limited and digested conditions. Significant clusters of bacterial compositions were found among all treatments. In terms of ecological processes of community assembly, communities in limited conditions and bulk soil were influenced by both deterministic and stochastic processes, whereas those in full and digested conditions were regulated only by stochastic ways. Furthermore, the order Rhizobiales and Actinomycetales known as mycorrhizal helper bacteria were characterized in the full and digested conditions through phylogenetic analysis and detection of indicator taxa. These results suggest that mycorrhizal fungi may play ecologically important roles not only as temporal drivers initiating the formation rhizosphere bacterial communities but also as key founders exerting continuous influences to establish priority effects. Moreover, the rhizosphere bacterial community remains after mycorrhizal degeneration and their historical continuity may contribute to maintaining plant-mycorrhizal fungi-bacterial associations.},
}
@article {pmid40228732,
year = {2025},
author = {Zhang, R and Gong, C and Gao, Y and Chen, Y and Zhou, L and Lou, Q and Zhao, Y and Zhuang, H and Zhang, J and Shan, S and Wang, X and Qian, X and Lei, L and Wong, MH},
title = {Reducing antibiotic resistance genes in soil: The role of organic materials in reductive soil disinfestation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126245},
doi = {10.1016/j.envpol.2025.126245},
pmid = {40228732},
issn = {1873-6424},
abstract = {Increasing attention has been given to the role of reductive soil disinfestation (RSD) on antibiotic resistance genes (ARGs) in soil. The selection of organic materials in RSD is crucial to the effectiveness of the RSD method. However, the effects of distinct organic materials on ARGs remains unclear. In this study, we selected straw and rapeseed meal as the organic materials in RSD and explored their effects on ARGs. The results showed that using straw significantly reduced the abundance of ARGs, high-risk ARGs, and mobile genetic elements (MGEs) by 31.5%-65.8%, while using rapeseed meal led to ARGs enrichment. Structural equation modeling (SEM) analysis identified MGEs and microbial communities as the primary drivers of ARGS changes under different organic materials. The abundance of MGEs was effectively controlled in straw treatments, reducing the potential for horizontal gene transfer of ARGs. Bacterial diversity was significantly lower in the straw treatments compared to the rapeseed meal treatments, potentially leading to a reduced abundance of ARGs host bacteria. Network co-occurrence analysis further revealed that Symbiobacteraceae and Bacillus were potential bacterial hosts of ARGs. In straw treatments, these genera' abundance decreased by 12%-100% compared to the control (CK) and rapeseed meal groups, further inhibiting the spread of ARGs. These findings demonstrate that RSD with straw as the organic material is more effective in mitigating ARGs compared to rapeseed meal, providing insights into controlling soil antibiotic resistance risks and utilizing agricultural waste resources.},
}
@article {pmid40227232,
year = {2025},
author = {Prochera, A and Muppirala, AN and Kuziel, GA and Soualhi, S and Shepherd, A and Sun, L and Issac, B and Rosenberg, HJ and Karim, F and Perez, K and Smith, KH and Archibald, TH and Rakoff-Nahoum, S and Hagen, SJ and Rao, M},
title = {Enteric glia regulate Paneth cell secretion and intestinal microbial ecology.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.97144},
pmid = {40227232},
issn = {2050-084X},
support = {R01DK130836/NH/NIH HHS/United States ; K08DK110532/NH/NIH HHS/United States ; R01DK135707/NH/NIH HHS/United States ; Fellowship//Schmidt Family Foundation/ ; Graduate Research Fellowship Program//National Science Foundation/ ; Fellowship//National Defense Science and Engineering Graduate/ ; Odyssey Award//Smith Family Foundation/ ; },
mesh = {Animals ; *Paneth Cells/metabolism/physiology ; Mice ; *Neuroglia/physiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Myelin Proteolipid Protein/metabolism/genetics ; *Intestinal Mucosa/metabolism/microbiology ; *Enteric Nervous System/physiology ; Mice, Inbred C57BL ; Male ; Female ; },
abstract = {Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions (Prochera and Rao, 2023). To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express the gene Proteolipid protein 1 (PLP1) in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1[+] cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1[+] glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.},
}
@article {pmid40223273,
year = {2025},
author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW},
title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412001},
doi = {10.4014/jmb.2412.12001},
pmid = {40223273},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; },
abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.},
}
@article {pmid40222749,
year = {2025},
author = {Belda, I and Izquierdo-Gea, S and Benitez-Dominguez, B and Ruiz, J and Vila, JCC},
title = {Wine Fermentation as a Model System for Microbial Ecology and Evolution.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70092},
doi = {10.1111/1462-2920.70092},
pmid = {40222749},
issn = {1462-2920},
support = {//Center for Computational, Evolutionary and Human Genomics, Stanford University. Postdoc Fellowship to Jean CC VIla/ ; FPU21/06830//Spanish Ministry of Science, Innovation and Universities/ ; PID2019-105834GA-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PID2022-138343NB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PRE2022-103063//Agencia Estatal de Investigaci&#xf3;n/ ; },
mesh = {*Wine/microbiology ; *Fermentation ; *Biological Evolution ; Microbiota ; *Bacteria/metabolism/genetics ; Ecosystem ; Models, Biological ; Ecology ; },
abstract = {In vitro microbial communities have proven to be invaluable model systems for studying ecological and evolutionary processes experimentally. However, it remains unclear whether quantitative insights obtained from these laboratory systems can be applied to complex communities assembling and evolving in their natural ecological context. To bridge the gap between the lab and the 'real-world', there is a need for laboratory model systems that better approximate natural and semi-natural ecosystems. Wine fermentation presents an ideal system for this purpose, balancing experimental tractability with rich ecological and evolutionary dynamics. In this perspective piece we outline the key features that make wine fermentation a fruitful model system for ecologists and evolutionary biologists. We highlight the diversity of environmentally mediated interactions that shape community dynamics during fermentation, the complex evolutionary history of wine microbial populations, and the opportunity to study the impact of complex ecologies on evolutionary dynamics. By integrating knowledge from both wine research and microbial ecology and evolution we aim to enhance understanding and foster collaboration between these fields.},
}
@article {pmid40220383,
year = {2025},
author = {Li, C and Zhu, L and Axe, L and Li, M},
title = {Acclimation of sludge-derived biofilms for effective removal of emerging contaminants: Impacts of inoculum source and carbon supplementation.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138235},
doi = {10.1016/j.jhazmat.2025.138235},
pmid = {40220383},
issn = {1873-3336},
abstract = {Contaminants of emerging concern (CECs) have gathered significant public attention due to their widespread occurrence, high persistence, and increasing exposure potential. In this study, we used polyethylene biocarriers for acclimating biofilms from singular or combined activated sludges collected from three wastewater treatment plants (R, P, and L) over 5 month-long cycles. The acclimated biofilms achieved an average removal rate at 0.333, 0.313, and 0.185 week[-1] for N, N-diethyl-meta-toluamide (DEET), sulfamethoxazole (SMX), and carbamazepine (CBZ), respectively, when external carbon was supplemented, which were significantly higher (p < 0.05) than biofilms that did not receive external carbons. Metabolite screening revealed SMX transformation through ipso-hydroxylation and acetyl conjugation, while CBZ degradation could be initiated by epoxidation. Significant but slower degradation rates (0.024∼0.031 week[-1]) were observed for aminotriazole (AMT), lidocaine (LDC), and trimethoprim (TMP), whereas atrazine (ATZ) exhibited minimal removal, highlighting its high recalcitrance. Biofilms acclimated from individual R and P sludges, with external carbon supplementation, attained the greatest removal efficiencies for 7 CECs. Multivariate statistical correlations (p < 0.05) identified potential degraders, including Sphingomonas and Zoogolea for AMT, Labrys and Koazkia for CBZ, and Asprobacter, unclassified Cyclobacteriaceae (ELB16-189) and Bryobacteraceae (Fen-178) for LDC. Abundance distribution of potential degraders among biofilms revealed that Sludge R favored the enrichment of key degraders for AMT, CBZ and LDC, while Sludge P was more conducive to acclimating CBZ degraders. This study advances our understanding of strategies in biofilm acclimation to improve CEC removal and provides insights into degradation pathways and associated microbial communities for future research.},
}
@article {pmid40220189,
year = {2025},
author = {Knoppersen, RS and Bose, T and Coutinho, TA and Hammerbacher, A},
title = {Inside the Belly of the Beast: Exploring the Gut Bacterial Diversity of Gonipterus sp. n. 2.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {27},
pmid = {40220189},
issn = {1432-184X},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Eucalyptus/parasitology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Diet ; South Africa ; *Coleoptera/microbiology/physiology ; Gas Chromatography-Mass Spectrometry ; Introduced Species ; Biodiversity ; },
abstract = {The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.},
}
@article {pmid40216640,
year = {2025},
author = {Huttunen, KL and Malazarte, J and Jyväsjärvi, J and Lehosmaa, K and Muotka, T},
title = {Temporal Beta Diversity of Bacteria in Streams: Network Position Matters But Differently for Bacterioplankton and Biofilm Communities.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {26},
pmid = {40216640},
issn = {1432-184X},
support = {356403//Research Council of Finland/ ; 318230//Research Council of Finland/ ; 318230//Research Council of Finland/ ; },
mesh = {*Biofilms/growth &amp; development ; *Rivers/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; *Plankton/classification/genetics ; Soil Microbiology ; Ecosystem ; Seasons ; },
abstract = {Concern about biodiversity loss has yielded a surge of studies on temporal change in α-diversity, whereas temporal β-diversity has gained less interest. We sampled bacterioplankton, biofilm, and riparian soil bacteria repeatedly across the open-water season in a pristine stream network to determine the level of temporal β-diversity in relation to stream network position and environmental variability. We tested the hypothesis that aquatic bacterial communities in isolated and environmentally heterogenous headwaters exhibit high temporal β-diversity while the better-connected and environmentally more stable mainstem sections support more stable communities, and soil communities bear no relationship to network position. As expected, temporal β-diversity decreased from headwaters toward mainstems for bacterioplankton. Against expectations, an opposite pattern was observed for biofilm. For bacterioplankton, temporal β-diversity was positively related to temporal variability in water chemistry. For biofilm bacteria, temporal variability was negatively related to variability in temperature. Temporal β-diversity of soil communities did not show any response to stream network position, but was strongly related to variability in the soil environment. The two aquatic habitats and riparian soils supported distinctly different bacterial communities. The number of ASVs shared between the soil and the aquatic communities decreased along the network, and more so for bacterioplankton. The higher temporal variability of bacterial communities in the headwaters likely results from temporally variable input of propagules from riparian soil, emphasizing the role of land-water connection and network position to bacterioplankton community composition. Overall, bacterial communities exhibited high temporal variability, highlighting the importance of temporal replication to fully capture their network-scale biodiversity.},
}
@article {pmid40214404,
year = {2025},
author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, M&#xd8; and Rudi, K},
title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12464},
pmid = {40214404},
issn = {1520-5851},
abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.},
}
@article {pmid40209676,
year = {2025},
author = {Schell, LD and Carmody, RN},
title = {An energetic framework for gut microbiome-mediated obesity induced by early-life exposure to antibiotics.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {4},
pages = {470-483},
doi = {10.1016/j.chom.2025.03.009},
pmid = {40209676},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; *Obesity/chemically induced/microbiology/etiology/metabolism ; Animals ; Humans ; *Energy Metabolism/drug effects ; Female ; Mice ; Male ; },
abstract = {Early-life antibiotic (ELA) exposure has garnered attention for its potential role in modulating obesity risk, although outcomes from mouse experiments and human epidemiological studies often vary based on dosage and sex. Low-dose (subtherapeutic) antibiotics can enhance energy availability through moderate alterations in gut microbiome profile, while high-dose (therapeutic) antibiotics substantially deplete the gut microbiota, thereby contributing to short-term negative energy balance. In this perspective, we propose a framework to understand how these distinct impacts of antibiotics on the gut microbiome during critical developmental windows shape long-term obesity risk through their influence on host energy balance. Using this framework, we then propose several hypotheses to explain variation in ELA-induced obesity outcomes across males and females. We conclude by discussing the evolutionary implications of ELAs, positing that the response of the gut microbiome to ELAs may signal energy availability and environmental volatility, influencing metabolic programming and adaptive traits across generations.},
}
@article {pmid40208324,
year = {2025},
author = {Mazzella, V and Zahn, G and Dell'Anno, A and Pons, LN},
title = {Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {25},
pmid = {40208324},
issn = {1432-184X},
support = {C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; },
mesh = {Animals ; *Porifera/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; Mediterranean Sea ; *Mycobiome ; *Seawater/microbiology ; Phylogeny ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Ecosystem ; },
abstract = {Marine sponges are widespread, sessile, filter-feeding animals, known for living in association with complex prokaryotic communities structured by host species. Though marine fungi are ubiquitous across marine environments, little is known about sponge-associated fungal communities (mycobiome). Indeed, aside from a few studies based on the isolation of fungal strains for biotechnological purposes, little information is available to understand the diversity and structure of sponge mycobiome. Here, a metabarcoding approach based on the ITS1 marker was applied to examine the structure and composition of fungal communities associated with four Mediterranean sponges. The species: Petrosia ficiformis, Chondrosia reniformis, Crambe crambe, and Chondrilla nucula were analyzed along with the surrounding seawater, revealing Aspergillus (1-56%), Cladosporium (1-75%), Malassezia (1-38.5%), and Pennicillium (1.5-36%) as the most represented fungal genera. Our data showed high intra-specific variability and no clear core mycobiome within each of the sponge species host, suggesting stochastic and perhaps transient community membership. This study sheds light on one of the most abundant yet least understood components of the marine ecosystem. Unraveling the dynamics of fungal interactions within sponge holobionts is essential to advance our understanding of their ecological roles and functions. By addressing the enigmatic nature of sponge-associated fungi, this research opens new avenues for exploring their contributions to marine ecosystems and resolving the many unanswered questions in this field.},
}
@article {pmid40208265,
year = {2025},
author = {DiPietri, VT and Grady, ZS and Frost, AN and Stitzel, SE and Sivey, JD},
title = {Toilet Bowl Cleaning Tablets as Sources of Chlorine, Bromine, and Disinfection Byproducts in Wastewater.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12026},
pmid = {40208265},
issn = {1520-5851},
abstract = {Commercial toilet bowl cleaning tablets were examined in laboratory systems to characterize their release of active halogens and their potential to form trihalomethanes (THMs) when combined with synthetic sewage. Active halogens (e.g., HOCl, HOBr, and reactive halamines) were quantified via derivatization with 1,3,5-trimethoxybenzene prior to analysis by liquid chromatography. The effects of several variables on halogen release profiles were examined, including pH, ionic strength, temperature, tank solution volume, flushing frequency, and tablet brand. Changes in pH resulted in modest or no appreciable changes in halogen release profiles. Release of active halogens increased as ionic strength decreased and as temperature increased. Tank volume, flushing frequency, and tablet brand had pronounced impacts on halogen release profiles. Maximum measured active chlorine and bromine concentrations in toilet tank water were 189 mg/L as Cl2 and 164 mg/L as Cl2, respectively. Active halogens persisted in toilet bowl water for >24 h. When toilet-tablet-treated water was combined with synthetic sewage, THMs formed at up to 219 ppb with bromine incorporation factors up to 2.86. Active halogens and highly brominated THMs released into wastewater from toilet tablets could have implications for downstream microbial ecology, septic system performance, and overall water quality.},
}
@article {pmid40206699,
year = {2025},
author = {Connors, E and Gallagher, KL and Dutta, A and Oliver, M and Bowman, JS},
title = {Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot.},
journal = {Polar biology},
volume = {48},
number = {2},
pages = {62},
pmid = {40206699},
issn = {0722-4060},
abstract = {UNLABELLED: The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-025-03380-y.},
}
@article {pmid40205489,
year = {2025},
author = {Soares, A and Rassner, SME and Edwards, A and Farr, G and Blackwell, N and Sass, H and Guglielmo, P and Schofield, D and Mitchell, AC},
title = {Hydrogeological and geological partitioning of iron and sulfur cycling bacterial consortia in subsurface coal-based mine waters.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf039},
pmid = {40205489},
issn = {1574-6941},
abstract = {Pyrite oxidation drives iron and sulfur availability across Earth's subsurface and is partly microbially mediated. Subsurface microbial communities accelerate this process at circumneutral pH directly by weathering pyritic surfaces and indirectly by causing changes to the surrounding microenvironment thereby further accelerating pyrite weathering. However, our understanding of community structure dynamics and associated biogeochemistry in Fe- and S-rich lithologies, e.g. pyritic coal, is limited. Here we present the first comprehensive regional and seasonal genus-level survey of bacterial groundwater communities in a pyritic coal-based aquifer in the South Wales Coalfield (SWC), using 16S rRNA gene amplicon sequencing. Seasonal changes in community structure were limited, suggesting limited influence of surface processes on subsurface communities. Instead, hydrogeologically distinct mine water blocks (MWB) and coal rank largely explained bacterial community structure variation across sites. Fe(II)-oxidising Betaproteobacteriales genera Gallionella and Sideroxydans dominated the bacterial communities across nine sites and seven MWBs, while three sites within a single MWB, were dominated by S-oxidising Epsilonbacteraeota genera Sulfuricurvum and Sulfurovum. The co-occurrence of pairs of Fe(II)- and S-oxidising bacterial genera suggests functional redundancy, which coupled with genus-specific morphologies and life strategies, indicates the importance of distinct environmental and ecological niches within the SWC groundwater at seasonal and regional scales.},
}
@article {pmid40205473,
year = {2025},
author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V},
title = {Running against the clock: Exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf033},
pmid = {40205473},
issn = {1574-6941},
abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas and Archean Domes. Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from Pozas Rojas and Archean Domes: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and Archean Domes: Halanaerobium sp. (63%) and Desulfovermiculus halophilus (60%). Furthermore, metagenome assembled genomes from Ectothiorhodospira genus were found in both Archean Domes and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the Archean Domes system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.},
}
@article {pmid40205253,
year = {2025},
author = {Dasgupta, M and Paul, R and Chowdhury, P and Mondal, S and Ahmed, J and Mukherjee, C and Das, S and Tribedi, P},
title = {Management of Enterococcus faecalis biofilms: a combinatorial approach with phytochemical.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40205253},
issn = {1678-4405},
support = {TNU/R&amp;D/MP/2021/010//The Neotia University/ ; },
abstract = {The rapid emergence of antimicrobial resistance in Enterococcus faecalis infections was primarily due to their robust biofilm formation, highlighting the urgent need for meaningful strategies. Since combinatorial application of natural phytochemical often offer promising outcomes in dealing with microbial infections, present study indicated the pharmacological, antimicrobial and antibiofilm potential of combinatorial strategies of natural phytochemical involving cuminaldehyde and thymoquinone against E. faecalis. Towards this direction, in silico analysis suggested that both compounds could show favourable oral bioavailability and high GI absorption, with a considerable solubility and drug-likeness profiles. Furthermore, in vitro antimicrobial assay indicated that the minimum inhibitory concentrations (MIC) of cuminaldehyde and thymoquinone were found to be 500 µg/mL and 30 µg/mL, respectively against E. faecalis. Thereafter, the fractional inhibitory concentration (FIC) index score of 0.73 indicated an additive effect prevailed between cuminaldehyde and thymoquinone, enhancing their antimicrobial potential. Thereafter, sub-MIC doses of cuminaldehyde (40 µg/mL) and thymoquinone (8 µg/mL) were selected to assess their antibiofilm potential. Though the compounds were able to show antibiofilm activity separately, their combination was significantly more effective, reduced biofilm formation by approximately 80%, and decreased production of extracellular polymeric substance (EPS) and protein content by ~ 76% and ~ 70%, respectively. Further studies revealed that the antibiofilm activity of the test compounds could likely to be attributed to the accumulation of reactive oxygen species (ROS) and enhancement of membrane permeability. Taken together, all this experimental observation revealed that combination of these natural compounds could potentially improve the treatment outcomes of biofilm-borne infections of E. faecalis.},
}
@article {pmid40203032,
year = {2025},
author = {Timilsina, S and Iruegas-Bocardo, F and Jibrin, MO and Sharma, A and Subedi, A and Kaur, A and Minsavage, GV and Huguet-Tapia, JC and Klein-Gordon, J and Adhikari, P and Adhikari, TB and Cirvilleri, G and de la Barrera, LBT and Bernal, E and Creswell, TC and Doan, TTK and Coutinho, TA and Egel, DS and Félix-Gastélum, R and Francis, DM and Kebede, M and Ivey, ML and Louws, FJ and Luo, L and Maynard, ET and Miller, SA and Nguyen, NTT and Osdaghi, E and Quezado-Duval, AM and Roach, R and Rotondo, F and Ruhl, GE and Shutt, VM and Thummabenjapone, P and Trueman, C and Roberts, PD and Jones, JB and Vallad, GE and Goss, EM},
title = {Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans.},
journal = {PLoS pathogens},
volume = {21},
number = {4},
pages = {e1013036},
doi = {10.1371/journal.ppat.1013036},
pmid = {40203032},
issn = {1553-7374},
abstract = {Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.},
}
@article {pmid40202691,
year = {2025},
author = {Pimentel, AC and Cesar, CS and Martins, AHB and Martins, M and Cogni, R},
title = {Wolbachia Offers Protection Against Two Common Natural Viruses of Drosophila.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {24},
pmid = {40202691},
issn = {1432-184X},
mesh = {Animals ; *Wolbachia/physiology ; *Drosophila melanogaster/virology/microbiology ; *Drosophila/virology/microbiology ; Symbiosis ; Female ; },
abstract = {Wolbachia pipientis is a maternally transmitted endosymbiont infecting more than half of terrestrial arthropod species. Wolbachia can express parasitic phenotypes such as manipulation of host reproduction and mutualist phenotypes such as protection against RNA virus infections. Because Wolbachia can invade populations by reproductive manipulation and block virus infection, it is used to modify natural insect populations. However, the ecological importance of virus protection is not yet clear, especially due to scarce information on Wolbachia protection against viruses that are common in nature. We used systemic infection to investigate whether Wolbachia protects its host by suppressing the titer of DMELDAV and DMelNora virus, two viruses that commonly infect Drosophila melanogaster flies in natural populations. Antiviral protection was tested in three systems to assess the impact of Wolbachia strains across species: (1) a panel of Wolbachia strains transfected into Drosophila simulans, (2) two Wolbachia strains introgressed into the natural host D. melanogaster, and (3) two native Wolbachia strains in their natural hosts Drosophila baimaii and Drosophila tropicalis. We showed that certain Wolbachia strains provide protection against DMelNora virus and DMELDAV, and this protection is correlated with Wolbachia density, which is consistent with what has been observed in protection against other RNA viruses. Additionally, we found that Wolbachia does not protect its original host, D. melanogaster, from DMELDAV infection. While native Wolbachia can reduce DMELDAV titers in D. baimaii, this effect was not detected in D. tropicalis. Although the Wolbachia protection-induced phenotype seems to depend on the virus, the specific Wolbachia strain, and the host species, our findings suggest that antiviral protection may be one of the mutualistic effects that helps explain why Wolbachia is so widespread in arthropod populations.},
}
@article {pmid40201423,
year = {2025},
author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Boenigk, J},
title = {The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf049},
pmid = {40201423},
issn = {2730-6151},
abstract = {Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.},
}
@article {pmid40200306,
year = {2025},
author = {Bindels, LB and Watts, JEM and Theis, KR and Carrion, VJ and Ossowicki, A and Seifert, J and Oh, J and Shao, Y and Hilty, M and Kumar, P and Hildebrand, F and Lovejoy, C and Wigley, P and Yu, K and Zhang, M and Zhang, T and Walter, J and Desai, MS and Huws, SA and Schriml, LM and Ravel, J and Fricke, WF and Eloe-Fadrosh, EA and Lee, CK and Clavel, T},
title = {A blueprint for contemporary studies of microbiomes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {95},
pmid = {40200306},
issn = {2049-2618},
mesh = {*Microbiota ; Humans ; },
abstract = {This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submitted to the journal. At Microbiome, we are seeking studies that provide either new mechanistic insights into the role of microbiomes in health and environmental systems or substantial conceptual or technical advances. Manuscripts need to meet high standards of language accuracy, quality of microbiome analyses, and data and protocol availability, including detailed reporting of wet-lab and in silico protocols, all of which can critically enhance transparency and reproducibility. We think that such efforts are essential to push the boundaries of our knowledge on microbiomes in a concerted, international effort.},
}
@article {pmid40197060,
year = {2025},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of the Neisseriaceae family in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0327524},
doi = {10.1128/spectrum.03275-24},
pmid = {40197060},
issn = {2165-0497},
abstract = {The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the oral cavity. The Neisseriaceae family, which includes human oral species in the genera Neisseria, Eikenella, Kingella, and Simonsiella, plays a significant role in both commensal and pathogenic relationships. In this study, we investigate the distribution and functional adaptations of Neisseriaceae species across oral habitats, focusing on their site tropisms and ecological roles. We employed a metapangenomic approach in which a curated set of reference genomes representing Neisseriaceae diversity was used for competitive mapping of metagenomic reads. Our analysis revealed distinct habitat preferences among Neisseriaceae species, with Kingella oralis, Neisseria elongata, and Neisseria mucosa primarily found in dental plaque; Neisseria subflava on the tongue dorsum; and Neisseria cinerea in the keratinized gingiva. Functional enrichment analyses identified genes and pathways underpinning habitat-specific adaptations. Plaque specialists showed metabolic versatility, with adaptations in nitrogen metabolism, including nitrate reduction and denitrification, lysine degradation, and galactose metabolism. Tongue dorsum specialists exhibited adaptations including enhanced capabilities for amino acid biosynthesis, short-chain fatty acid and glycerol transport, as well as lipopolysaccharide glycosylation, which may aid in resisting antimicrobial peptides and maintaining membrane integrity. These findings provide insights into the ecological roles and adaptive strategies of Neisseriaceae species within the human oral microbiome and establish a foundation for exploring functional specialization and microbial interactions in these niches.IMPORTANCEUnraveling the distribution and functional adaptations of Neisseriaceae within the human oral microbiome is essential for understanding the roles of these abundant and prevalent commensals in both health and disease. Through a metapangenomic approach, we uncovered distinct habitat preferences of various Neisseriaceae taxa across the oral cavity and identified key genetic traits that may drive their habitat specialization and role in host-microbe interactions. These insights enhance our understanding of the microbial dynamics that shape oral microbial ecology, offering potential pathways for advancing oral health research.},
}
@article {pmid40197052,
year = {2025},
author = {Liu, S and Ru, J and Guo, X and Gao, Q and Deng, S and Lei, J and Song, J and Zhai, C and Wan, S and Yang, Y},
title = {Altered precipitation and nighttime warming reshape the vertical distribution of soil microbial communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0124824},
doi = {10.1128/msystems.01248-24},
pmid = {40197052},
issn = {2379-5077},
abstract = {Soil depth determines microbial community composition. Yet, it remains largely unexplored how climate changes affect the vertical distribution of soil microbial communities. Here, we investigated the effects of altered precipitation and nighttime warming on microbial communities in the topsoils (0-20 cm) and subsoils (20-50 cm) of a temperate grassland in Inner Mongolia, China. As commonly observed under nutrient scarcity conditions, bacterial and fungal α-diversity and network complexity decreased with soil depth. However, protistan α-diversity and network complexity increased, which was attributed to less niche overlap and smaller body size. Strikingly, the slopes of linear regressions of microbial α-diversity/network complexity and soil depth were all reduced by altered precipitation. Microbial community composition was significantly influenced by both depth and reduced precipitation, and to a lesser extent by nighttime warming and elevated precipitation. The ribosomal RNA gene operon (rrn) copy number, a genomic proxy of bacterial nutrient demand, decreased with soil depth, and the percentages of positive network links were higher in the subsoil, supporting the "hunger game" hypothesis. Both reduced precipitation and nighttime warming decreased the rrn copy number in the subsoils while increasing the percentages of positive links, enhancing potential niche sharing among bacterial species. The stochasticity level of bacterial and fungal community assemblies decreased with soil depth, showing that depth acted as a selection force. Altered precipitation increased stochasticity, attenuating the depth's filtering effect and diminishing its linear relationship with microbial diversity. Collectively, we unveiled the predominant influence of altered precipitation in affecting the vertical distribution of soil microbial communities.IMPORTANCEUnderstanding how climate change impacts the vertical distribution of soil microbial communities is critical for predicting ecosystem responses to global environmental shifts. Soil microbial communities exhibit strong depth-related stratification, yet the effects of climate change variables, such as altered precipitation and nighttime warming, on these vertical patterns have been inadequately studied. Our research uncovers that altered precipitation disrupts the previously observed relationships between soil depth and microbial diversity, a finding that challenges traditional models of soil microbial ecology. Furthermore, our study provides experimental support for the hunger game hypothesis, highlighting that oligotrophic microbes, characterized by lower ribosomal RNA gene operon (rrn) copy numbers, are selectively favored in nutrient-poor subsoils, fostering increased microbial cooperation for resource exchange. By unraveling these complexities in soil microbial communities, our findings offer crucial insights for predicting ecosystem responses to climate change and for developing strategies to mitigate its adverse impacts.},
}
@article {pmid40195174,
year = {2025},
author = {Burazerović, J and Jovanović, M and Savković, &#x17d; and Breka, K and Stupar, M},
title = {Finding the Right Host in the Darkness of the Cave-New Insights into the Ecology and Spatio-temporal Dynamics of Hyperparasitic Fungi (Arthrorhynchus nycteribiae, Laboulbeniales).},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {23},
pmid = {40195174},
issn = {1432-184X},
support = {451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; },
mesh = {Animals ; *Chiroptera/parasitology/microbiology ; *Caves/microbiology ; *Ascomycota/genetics/isolation &amp; purification/physiology/classification ; *Diptera/microbiology ; Serbia ; Male ; Female ; Phylogeny ; },
abstract = {The aim of this study was to determine the presence of the hyperparasitic fungus Arthrorhynchus nycteribiae and to analyze its spatio-temporal pattern in the two bat flies (Penicillidia conspicua and P. dufourii) parasitizing on bats. We collected 612 samples of bat flies from 400 bats in 20 caves in the Central Balkans. Hyperparasite was identified based on morphological and molecular analyses of rDNA genes (LSU and SSU). A. nycteribiae was reported for the first time in Bosnia and Herzegovina and Montenegro, and confirmed in Serbia. Of the 20 sites examined, we found A. nycteribiae at 11 sites. The prevalence of A. nycteribiae infection in the bats examined was approximately 17%. Miniopterus schreibersii harbored the highest number of bat flies and was the only bat species hosting the infected bat flies of the species P. conspicua. Our results showed significant differences in infection patterns during the different seasons: the highest prevalence of bat flies with hyperparasitic fungi was found in the summer season (23%) and the lowest in spring (2%). Female bat fly hosts showed a significantly higher prevalence of infection than male bat flies. This study makes an important contribution to the knowledge of the distribution of A. nycteribiae and to the understanding of complex parasite-host relationships in the poorly studied areas of the Central Balkans.},
}
@article {pmid40186763,
year = {2025},
author = {Huang, YD and Zhao, XL and Lin, Y and Ouyang, XM and Cheng, XS and Liang, LY and Huo, YN and Xie, GJ and Lin, JH and Jazag, A and Guleng, B},
title = {Mindin orchestrates the macrophage-mediated resolution of liver fibrosis in mice.},
journal = {Hepatology international},
volume = {},
number = {},
pages = {},
pmid = {40186763},
issn = {1936-0541},
support = {No. 81970460//National Natural Science Foundation of China/ ; No. 2023J011598//Natural Science Foundation of Fujian Province/ ; },
abstract = {BACKGROUND &amp; AIMS: Liver disease that progresses to cirrhosis is an enormous health problem worldwide. The extracellular matrix protein Mindin is known to have immune functions, but its role in liver homeostasis remains largely unexplored. We aimed to characterize the role of Mindin in the regulation of liver fibrosis.<br><br>APPROACH &amp; RESULTS: Mindin was upregulated in mice with carbon tetrachloride (CCl4) or thioacetamide (TAA)-induced liver fibrosis, and was primarily expressed in hepatocytes. Global Mindin knockout mice were generated, which were susceptible to liver fibrosis. Notably, Mindin failed to activate hepatic stellate cells directly; however, it played a role in promoting the recruitment and phagocytosis of macrophages, and caused a phenotypic switch toward restorative macrophages during liver fibrosis. Furthermore, Mindin was found to bind to the &#x3b1;M-I domain of CD11b/CD18 heterodimeric receptors. To further explore this mechanism, we created Mindin and CD11b double-knockout (DKO) mice. In DKO mice, phagocytosis was further reduced, and liver fibrosis was markedly exacerbated.<br><br>CONCLUSIONS: Mindin promotes the resolution of liver fibrosis and the Mindin/CD11b axis might represent a novel target for the macrophage-mediated regression of liver fibrosis.},
}
@article {pmid40186595,
year = {2025},
author = {Pérez, J and Boyero, L and Pearson, RG and Gessner, MO and Tonin, A and López-Rojo, N and Rubio-Ríos, J and Correa-Araneda, F and Alonso, A and Cornejo, A and Albariño, RJ and Anbalagan, S and Barmuta, LA and Boulton, AJ and Burdon, FJ and Caliman, A and Callisto, M and Campbell, IC and Cardinale, BJ and Carneiro, LS and Casas, JJ and Chará-Serna, AM and Chauvet, E and Colón-Gaud, C and Davis, AM and de Eyto, E and Degebrodt, M and Díaz, ME and Douglas, MM and Encalada, AC and Figueroa, R and Flecker, AS and Fleituch, T and Frainer, A and García, EA and García, G and García, PE and Giller, PS and Gómez, JE and Gonçalves, JF and Graça, MAS and Hall, RO and Hamada, N and Hepp, LU and Hui, C and Imazawa, D and Iwata, T and Junior, ESA and Landeira-Dabarca, A and Leal, M and Lehosmaa, K and M'Erimba, CM and Marchant, R and Martins, RT and Masese, FO and Maul, M and McKie, BG and Medeiros, AO and Middleton, JA and Muotka, T and Negishi, JN and Ramírez, A and Rezende, RS and Richardson, JS and Rincón, J and Serrano, C and Shaffer, AR and Sheldon, F and Swan, CM and Tenkiano, NSD and Tiegs, SD and Tolod, JR and Vernasky, M and Wanderi, EW and Watson, A and Yule, CM},
title = {Positive Feedback on Climate Warming by Stream Microbial Decomposers Indicated by a Global Space-For-Time Substitution Study.},
journal = {Global change biology},
volume = {31},
number = {4},
pages = {e70171},
doi = {10.1111/gcb.70171},
pmid = {40186595},
issn = {1365-2486},
support = {UAL18-RNM-B006-B//2014-2020 Operational Programme FEDER Andalusia/ ; IT951-16//Eusko Jaurlaritza/ ; IT1471-22//Eusko Jaurlaritza/ ; UIDB/04292/2020//Funda &#xe7; &#xe3;o para a Ci &#xea;ncia e a Tecnologia, Portugal/ ; //UAL-HIPATIA/ ; },
mesh = {*Rivers/microbiology ; *Climate Change ; Temperature ; *Global Warming ; Plants/metabolism ; Carbon Cycle ; },
abstract = {Decomposition of plant litter is a key ecological process in streams, whose contribution to the global carbon cycle is large relative to their extent on Earth. We examined the mechanisms underlying the temperature sensitivity (TS) of instream decomposition and forecast effects of climate warming on this process. Comparing data from 41 globally distributed sites, we assessed the TS of microbial and total decomposition using litter of nine plant species combined in six mixtures. Microbial decomposition conformed to the metabolic theory of ecology and its TS was consistently higher than that of total decomposition, which was higher than found previously. Litter quality influenced the difference between microbial and total decomposition, with total decomposition of more recalcitrant litter being more sensitive to temperature. Our projections suggest that (i) warming will enhance the microbial contribution to decomposition, increasing CO2 outgassing and intensifying the warming trend, especially in colder regions; and (ii) riparian species composition will have a major influence on this process.},
}
@article {pmid40185870,
year = {2025},
author = {Ripoll, J and Stenger, PL and Nuñez, NF and Demenois, J and Stokes, A and Gourmelon, V and Dinh, K and Robert, N and Drouin, J and Mournet, P and Léopold, A and Read, J and Gardes, M and Maggia, L and Carriconde, F},
title = {Unexpected microbial diversity in new Caledonia's ultramafic ecosystems with conservation implications in a biodiversity hotspot.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11564},
pmid = {40185870},
issn = {2045-2322},
support = {IAC-SLN Research Collaboration N&#xb0;DE2013-041//Soci&#xe9;t&#xe9; Le Nickel (SLN-Eramet Group)/ ; agreement CSF N&#xb0;1PS2013-CNRT.IAC/BIOINDIC//CNRT "Nickel &amp; son Environnement"/ ; },
mesh = {New Caledonia ; *Biodiversity ; *Soil Microbiology ; *Ecosystem ; Mycorrhizae/genetics/classification ; Conservation of Natural Resources ; Fungi/genetics/classification ; *Bacteria/genetics/classification ; },
abstract = {Soils harbour an incredible diversity of microorganisms that play crucial roles in ecosystem functioning. However, this biodiversity remains largely overlooked, with a poor understanding of how patterns form across landscapes. An eDNA metabarcoding approach was used to identify potential overarching patterns in fungal and bacterial communities from ultramafic ecosystems in New Caledonia, a renowned biodiversity hotspot. Our comprehensive analysis revealed several key findings, notably an important microbial diversity in the extreme environments of iron crust soils. Clear tendencies in phyla composition were also observed, with the fungal groups Ascomycota and Mucoromycota acting as potential indicators of land degradation (only in lateritic soils for Mucoromycota). For bacteria, Chloroflexi was characteristic of open vegetation, while Proteobacteria and Cyanobacteria were observed in higher relative abundances in the closed vegetation. The ectomycorrhizal fungal functional group was also found to be rich and unique, with a hypothetical endemism rate of 87%, and over-represented by the Cortinarius genus in rainforests and maquis (shrublands) dominated by ectomycorrhizal plants. Finally, each ultramafic Massif demonstrated a unique microbial community. Thus, our findings provide valuable insights into microbial ecology and emphasize the need for tailored conservation strategies for this biodiversity hotspot.},
}
@article {pmid40184706,
year = {2025},
author = {He, L and Li, J and Tang, L and Wang, Y and Zhao, X and Ding, K and Xu, L and Gu, L and Cheng, S and Wei, YY},
title = {Applying side-stream gas recirculation to promote anaerobic digestion of food waste under ammonia stress: Overlooked impact of gaseous atmospheres on microorganisms.},
journal = {Water research},
volume = {281},
number = {},
pages = {123571},
doi = {10.1016/j.watres.2025.123571},
pmid = {40184706},
issn = {1879-2448},
abstract = {High ammonia concentrations can be toxic to microorganisms, leading to the accumulation of hydrogen (H2) and acids in anaerobic digestion (AD) system. In this study, a side gas recycling strategy (SGR), coupled with a primary reactor and a small side-stream reactor, which recirculates biogas between primary reactor and side reactor was employed to mitigate ammonia inhibition. This approach enabled the mesophilic side-stream gas recirculation system (SMGR) and the thermophilic side-stream gas recirculation system (STGR) to ultimately withstand ammonia stress levels of 2.5 g/L and 3.5 g/L, respectively, while maintaining lower hydrogen partial pressures. In contrast, the control group experienced system failure at an ammonia concentration of 2 g/L. Enzyme activity, microbial community, and metaproteomic analysis indicated that the side reactor enriched microorganisms with strong hydrogen-utilizing capacity, while the primary reactor was enriched with Methanosaeta. Furthermore, key pathways related to propionate metabolism, ABC transporters, and methane production were enhanced in the primary reactor, along with increased ATPase activity. The activity of key enzymes involved in AD was also significantly enhanced. This study enhances the understanding of the impact of gas atmosphere control on the microbial ecology and metabolic characteristics of AD system, providing valuable insights and practical guidance for the development of Engineering applications in this field.},
}
@article {pmid40184705,
year = {2025},
author = {Barrantes-Jiménez, K and Lejzerowicz, F and Tran, T and Calderón-Osorno, M and Rivera-Montero, L and Rodríguez-Sánchez, C and Wikmark, OG and Eiler, A and Grossart, HP and Arias-Andrés, M and Rojas-Jiménez, K},
title = {Anthropogenic imprint on riverine plasmidome diversity and proliferation of antibiotic resistance genes following pollution and urbanization.},
journal = {Water research},
volume = {281},
number = {},
pages = {123553},
doi = {10.1016/j.watres.2025.123553},
pmid = {40184705},
issn = {1879-2448},
abstract = {Plasmids are key determinants in microbial ecology and evolution, facilitating the dissemination of adaptive traits and antibiotic resistance genes (ARGs). Although the molecular mechanisms governing plasmid replication, maintenance, and transfer have been extensively studied, the specific impacts of urbanization-induced pollution on plasmid ecology, diversity, and associated ARGs in tropical regions remain underexplored. This study investigates these dynamics in a tropical aquatic ecosystem, providing novel insights into how pollution shapes plasmid composition and function. In contrast to the observed decrease in chromosomal diversity, we demonstrate that pollution associated with urbanization increases the diversity and taxonomic composition of plasmids within a bacterial community (plasmidome). We analyzed eighteen water and sediment metagenomes, capturing a gradient of pollution and ARG contamination along a tropical urban river. Plasmid and chromosomal diversity profiles were found to be anti-correlated. Plasmid species enrichment along the pollution gradient led to significant compositional differences in water samples, where differentially abundant species suggest plasmid maintenance within specific taxonomic classes. Additionally, the diversity and abundance of ARGs related to the plasmidome increased concomitantly with the intensity of fecal and chemical pollution. These findings highlight the critical need for targeted plasmidome studies to better understand plasmids' environmental spread, as their dynamics are independent of chromosomal patterns. This research is crucial for understanding the consequences of bacterial evolution, particularly in the context of environmental and public health.},
}
@article {pmid40184632,
year = {2025},
author = {Huang, Y and Mao, X and Zheng, X and Zhao, Y and Wang, D and Wang, M and Chen, Y and Liu, L and Wang, Y and Polz, MF and Zhang, T},
title = {Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf058},
pmid = {40184632},
issn = {1751-7370},
abstract = {Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analyzed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.},
}
@article {pmid40183581,
year = {2025},
author = {Aminian-Dehkordi, J and Dickson, A and Valiei, A and Mofrad, MRK},
title = {MetaBiome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0165224},
doi = {10.1128/msystems.01652-24},
pmid = {40183581},
issn = {2379-5077},
abstract = {Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we present MetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach-encompassing microenvironmental conditions, agent information, and metabolic pathways-we simulated different communities to showcase the potential of the model. Using our in-silico platform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases. MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities.IMPORTANCEOur study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes in E. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.},
}
@article {pmid40179787,
year = {2025},
author = {Wang, Z and Tu, S and Shehzad, K and Hou, J and Xiong, S and Cao, M},
title = {Comparative study of organosilicon and inorganic silicon in reducing cadmium accumulation in wheat: Insights into rhizosphere microbial communities and molecular regulation mechanisms.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138061},
doi = {10.1016/j.jhazmat.2025.138061},
pmid = {40179787},
issn = {1873-3336},
abstract = {Silicon is widely used as a "quality element" and "stress resistance element" in crop production and the remediation of heavy metal-contamination soils. Compared to inorganic silicon, organosilicon has unique properties such as amphiphilicity, low surface energy and high biocompatibility. Our previous research has confirmed the effectiveness of organosilicon-modified fertilizers in inhibiting Cadmium (Cd) absorption in wheat. Therefore, it is of great importance to further explore the potential mechanisms and comprehensive benefits of organosilicon. In this study, the microbiological and molecular mechanisms by which organosilicon reduces Cd concentration in wheat compared to inorganic silicon were investigated in depth. The findings indicated that, in comparison with inorganic silicon, organosilicon exhibited a more remarkable efficacy. Specifically, it was more effective in reducing the Cd concentration in wheat grains, achieving a reduction range of 35-39 % as opposed to the 23-28 % reduction achieved by inorganic silicon. Moreover, it manifested a greater ability to mitigate health risks, with a reduction range of 33-42 % compared to the 25-30 % reduction of inorganic silicon. Furthermore, organosilicon contributed to a significant increase in wheat yield, with a growth range of 11-14 % in contrast to the 8-11 % increase from inorganic silicon. Additionally, it enhanced the quality of the grains, substantially improving the protein content and amino acid content. The comparative advantages of organosilicon over inorganic silicon would be firstly due to the reduction of the bioavailability of soil Cd by increasing the available silicon content in the soil and improving the soil microbial ecology (increasing the abundance of Bacillus, Pseudomonas, Massilia and Talaromyces and reducing the enrichment of Fusarium). Secondly, organosilicon achieved vacuolar compartmentalization of Cd by upregulating the expression of the ABC transporter gene (TaABCB7), thereby alleviating Cd toxicity and restricting Cd transport from leaves to grains. Meanwhile, organosilicon increased the wheat yield by optimizing the availability of soil nutrients and enhancing photosynthesis. These results demonstrate the immense potential of organosilicon in mitigating heavy metal contamination in crops.},
}
@article {pmid40179176,
year = {2025},
author = {Lentsch, V and Woller, A and Rocker, A and Aslani, S and Moresi, C and Ruoho, N and Larsson, L and Fattinger, SA and Wenner, N and Barazzone, EC and Hardt, WD and Loverdo, C and Diard, M and Slack, E},
title = {Vaccine-enhanced competition permits rational bacterial strain replacement in the gut.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {74-81},
doi = {10.1126/science.adp5011},
pmid = {40179176},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Escherichia coli/immunology/growth &amp; development/physiology ; *Salmonella Vaccines/immunology/administration &amp; dosage ; *Salmonella typhimurium/immunology/growth &amp; development/physiology ; Immunity, Mucosal ; Mice, Inbred C57BL ; Administration, Oral ; Escherichia coli Infections/prevention &amp; control/immunology/microbiology ; Gastrointestinal Microbiome ; Female ; Adaptive Immunity ; *Antibiosis ; Antibodies, Bacterial/immunology ; },
abstract = {Colonization of the intestinal lumen precedes invasive infection for a wide range of enteropathogenic and opportunistic pathogenic bacteria. We show that combining oral vaccination with engineered or selected niche-competitor strains permits pathogen exclusion and strain replacement in the mouse gut lumen. This approach can be applied either prophylactically to prevent invasion of nontyphoidal Salmonella strains, or therapeutically to displace an established Escherichia coli. Both intact adaptive immunity and metabolic niche competition are necessary for efficient vaccine-enhanced competition. Our findings imply that mucosal antibodies have evolved to work in the context of gut microbial ecology by influencing the outcome of competition. This has broad implications for the elimination of pathogenic and antibiotic-resistant bacterial reservoirs and for rational microbiota engineering.},
}
@article {pmid40177466,
year = {2025},
author = {Hwang, J and Hayward, A and Sofen, LE and Pitz, KJ and Chavez, FP and Edwards, BR},
title = {Daily microbial rhythms of the surface ocean interrupted by the new moon-a lipidomic study.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf044},
doi = {10.1093/ismeco/ycaf044},
pmid = {40177466},
issn = {2730-6151},
abstract = {Lipids are essential biomolecules for cell physiology and are commonly used as biomarkers to elucidate biogeochemical processes over a large range of environments and timescales. Here, we use high-temporal-resolution lipidomic analysis to characterize the surface ocean community in the productive upwelling region overlying the Monterey Bay Canyon. We observed a strong diel signal with a drawdown of lipids at night and an increase during the day that seemed to correspond to wholesale removal of lipids from the surface ocean as opposed to internal metabolism. Individual lipid species were organized into coregulated groups that were interpreted as representing different phytoplankton guilds. Concentrations of long-chained triacylglycerols (TAGs) showed unique patterns over the course of five days. TAGs were used to estimate the amount of energy cycled through the surface ocean. These calculations revealed diurnal carbon cycling that was on scales comparable to net primary production. The diel pattern dissipated from most lipid modules on Day 3 as tidal forcing increased at our site with the advent of the new moon. Pigment analysis indicated that the community shifted from a diatom-dominated community to a more diverse assemblage, including more haptophytes, chlorophytes, and Synechococcus during the new moon. The shift in community appears to promote higher nutritional quality of biomass, with more essential fatty acids in the surface ocean during the spring tide. This analysis showcases the utility of lipidomics in characterizing community dynamics and underscores the importance of considering both diel and tidal timescales when sampling in productive coastal regions.},
}
@article {pmid40177465,
year = {2025},
author = {Krause, SMB and van den Berg, NI and Brenzinger, K and Zweers, H and Bodelier, PLE},
title = {Beyond methane consumption: exploring the potential of methanotrophic bacteria to produce secondary metabolites.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf030},
doi = {10.1093/ismeco/ycaf030},
pmid = {40177465},
issn = {2730-6151},
abstract = {Microbial methane-consuming communities significantly impact biogeochemical processes and greenhouse gas emissions. In this study, we explored secondary metabolites produced by methane-oxidizing bacteria (MOB) and their ecological roles. We analyzed the volatile profiles of four MOB strains under controlled conditions and conducted a meta-analysis using high-quality genomes from 62 cultured MOB strains and 289 metagenome-assembled genomes to investigate their potential for producing secondary metabolites. Results show species-specific volatile production, such as germacrene by Methylobacter luteus, which may play a role in the regulation of environmental methane consumption. The meta-analysis revealed that biosynthetic gene clusters (BGCs) for terpenes and β-lactones were more prevalent in the Methylocystaceae and/or Beijerinckiaceae families, while aryl polyene BGCs were dominant in the Methylococcaceae family, reflecting habitat-specific adaptations. These findings advance our understanding of the metabolic capabilities of MOB and underscore the importance of integrating experimental data with genomic and metabolomic analyses to elucidate their ecology, environmental interactions, and contributions to methane cycling.},
}
@article {pmid40177402,
year = {2025},
author = {Pellengahr, F and Corella-Puertas, E and Mattelin, V and Saadi, N and Bertella, F and Boulay, AM and van der Meer, Y},
title = {Modeling marine microplastic emissions in Life Cycle Assessment: characterization factors for biodegradable polymers and their application in a textile case study.},
journal = {Frontiers in toxicology},
volume = {7},
number = {},
pages = {1494220},
doi = {10.3389/ftox.2025.1494220},
pmid = {40177402},
issn = {2673-3080},
abstract = {INTRODUCTION: With the continuous increase of plastics production, it is imperative to carefully examine their environmental profile through Life Cycle Assessment (LCA). However, current LCA modeling is not considering the potential impacts of plastic emissions on the biosphere. To integrate plastic emissions into LCA, characterization factors are needed that commonly consist of three elements: a fate factor, an exposure factor, and an effect factor. In this context, fate factors quantify the distribution and longevity of plastics in the environment. Research on these fate factors is still limited, especially for biodegradable polymers. Hence, the main objective of this research was to determine the fate factors of biodegradable polymers [poly (lactic acid), poly (butylene succinate), and poly (ε-caprolactam)] based on primary experimental data for the marine environment.<br><br>METHODS: The validity of former research is tested by comparing the degradation evolution of i. macro- and microplastic particles, ii. two different grades of the polymer, and iii. different temperature levels. The degradation data are obtained by monitoring the oxygen consumption over a period of six months in natural seawater. The determined degradation rates are combined with sedimentation, resuspension, and deep burial rates to obtain fate factors. These fate factors are used to develop polymer-specific characterization factors. The resulting characterization factors are tested in an LCA case study of a synthetic sports shirt made from biodegradable polymer fibers. It allows to assess the relative importance of microplastic impacts compared to other life cycle impacts.<br><br>RESULTS AND DISCUSSION: Comparing the resulting specific surface degradation rates indicates that microplastic degradation rates could be overestimated when using macroplastic degradation data. Pertaining to the case study, the results show that the impact on ecosystem quality by microplastic emissions could account for up to 30% of the total endpoint category. Overall, this work aims to foster interdisciplinary collaboration to leverage the accuracy of LCA studies and thus provide guidance for novel material development.},
}
@article {pmid40175811,
year = {2025},
author = {Alexander, NR and Brown, RS and Duwadi, S and Womble, SG and Ludwig, DW and Moe, KC and Murdock, JN and Phillips, JL and Veach, AM and Walker, DM},
title = {Leveraging Fine-Scale Variation and Heterogeneity of the Wetland Soil Microbiome to Predict Nutrient Flux on the Landscape.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {22},
pmid = {40175811},
issn = {1432-184X},
support = {DEB 1933925//National Science Foundation/ ; EF-2125065//National Science Foundation/ ; sub-award 220858//Natural Resource Conservation Services/ ; Molecular Biosciences Program//Middle Tennessee State University/ ; },
mesh = {*Wetlands ; *Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Soil/chemistry ; Nitrogen/metabolism ; *Nutrients/metabolism ; Nitrogen Cycle ; Phosphorus/metabolism ; Ecosystem ; Agriculture ; },
abstract = {Shifts in agricultural land use over the past 200 years have led to a loss of nearly 50% of existing wetlands in the USA, and agricultural activities contribute up to 65% of the nutrients that reach the Mississippi River Basin, directly contributing to biological disasters such as the hypoxic Gulf of Mexico "Dead" Zone. Federal efforts to construct and restore wetland habitats have been employed to mitigate the detrimental effects of eutrophication, with an emphasis on the restoration of ecosystem services such as nutrient cycling and retention. Soil microbial assemblages drive biogeochemical cycles and offer a unique and sensitive framework for the accurate evaluation, restoration, and management of ecosystem services. The purpose of this study was to elucidate patterns of soil bacteria within and among wetlands by developing diversity profiles from high-throughput sequencing data, link functional gene copy number of nitrogen cycling genes to measured nutrient flux rates collected from flow-through incubation cores, and predict nutrient flux using microbial assemblage composition. Soil microbial assemblages showed fine-scale turnover in soil cores collected across the topsoil horizon (0-5 cm; top vs bottom partitions) and were structured by restoration practices on the easements (tree planting, shallow water, remnant forest). Connections between soil assemblage composition, functional gene copy number, and nutrient flux rates show the potential for soil bacterial assemblages to be used as bioindicators for nutrient cycling on the landscape. In addition, the predictive accuracy of flux rates was improved when implementing deep learning models that paired connected samples across time.},
}
@article {pmid40175529,
year = {2025},
author = {Pascoal, F and Branco, P and Torgo, L and Costa, R and Magalhães, C},
title = {Definition of the microbial rare biosphere through unsupervised machine learning.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {544},
pmid = {40175529},
issn = {2399-3642},
abstract = {The microbial rare biosphere, composed of low-abundance microorganisms in a community, lacks a standardized delineation method for its definition. Currently, most studies rely on arbitrary thresholds to define the microbial rare biosphere (e.g., 0.1% relative abundance per sample), hampering comparisons across studies. To address this challenge, we present ulrb (Unsupervised Learning based Definition of the Rare Biosphere), available as an R package. ulrb uses unsupervised machine learning to optimally classify taxa into abundance categories (e.g., rare, intermediate, or abundant) within microbial communities. We show that ulrb is more consistent than threshold-based approaches and can be applied to data derived from common microbial ecology protocols and non-microbial studies. ulrb can be used to identify different types of rarity and is statistically valid for the analysis of various dataset sizes. In conclusion, ulrb discerns rare from abundant organisms in a user-independent manner, finding applicability in selected ecological datasets.},
}
@article {pmid40174026,
year = {2024},
author = {Shimano, S and Hiruta, SF and Sánchez-Chávez, DI and Pfingstl, T},
title = {Coastal mites (Oribatida, Ameronothridae) found far from the coast in moss growing on the Cathédrale Notre-Dame de Paris, France, fifty years after their first discovery in this historic site.},
journal = {Zootaxa},
volume = {5556},
number = {1},
pages = {62-71},
doi = {10.11646/zootaxa.5556.1.6},
pmid = {40174026},
issn = {1175-5334},
abstract = {A species of oribatid mite, Ameronothrus maculatus (Michael, 1882), was collected from moss growing on the building of the Cathédrale Notre-Dame de Paris. This species of Ameronothridae is usually found in coastal Holarctic environments. The specimens were studied by Scanning Electron Microscope and could be clearly assigned to this taxon. This population was first discovered by F. Grandjean approximately 50 years ago, and the present record demonstrates that it has persisted despite its habitat being a tourist destination visited by over 14 million people annually. The record of this species far upstream and on anthropogenic structures is rare but not out of the ordinary in Northern Europe where its distribution can reach far beyond the edges of the estuaries. For further confirmation, we obtained DNA sequences for the COI gene (1554 bp, LC848687), and they were almost identical to those of an earlier found and sequenced specimen of A. maculatus from Germany, differing by only a single base. As supplemental information on A. maculatus from Paris, the region includes whole nucleic ribosomal RNA genes (18S, 5.8S, and 28S, LC848688), partial elongation factor 1 alpha (LC848689), and the complete nucleotide sequence of mitochondrion were also determined.},
}
@article {pmid40172536,
year = {2025},
author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR},
title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0056924},
doi = {10.1128/iai.00569-24},
pmid = {40172536},
issn = {1098-5522},
abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.},
}
@article {pmid40170918,
year = {2025},
author = {Hager, K and Luo, ZH and Montserrat-Diez, M and Ponce-Toledo, RI and Baur, P and Dahlke, S and Andrei, AS and Bulzu, PA and Ghai, R and Urich, T and Glatzel, S and Schleper, C and Rodrigues-Oliveira, T},
title = {Diversity and environmental distribution of Asgard archaea in shallow saline sediments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549128},
pmid = {40170918},
issn = {1664-302X},
abstract = {In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.},
}
@article {pmid40168336,
year = {2025},
author = {Brangsch, H and Marcordes, S and Busch, A and Weber, M and Wolf, SA and Semmler, T and Höper, D and Calvelage, S and Linde, J and Barth, SA},
title = {Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0320499},
pmid = {40168336},
issn = {1932-6203},
mesh = {Animals ; *Perissodactyla/microbiology ; *Polymorphism, Single Nucleotide ; *Mycobacterium avium/genetics/isolation &amp; purification/classification ; *Genomics/methods ; Genome, Bacterial ; Phylogeny ; Multilocus Sequence Typing ; Whole Genome Sequencing ; },
abstract = {Within a group of three captive lowland tapirs (Tapirus terrestris) suffering from clinically apparent mycobacteriosis, non-tuberculous Mycobacterium avium subsp. hominissuis (MAH) strains were isolated from the animals and the tapir's enclosure. Based on MIRU-VNTR findings, which identified two closely related INMV profiles (124 and 246), a micro-evolutionary event was assumed, and four available MAH strains were submitted to whole genome sequencing (short- and long-read technologies). Surprisingly, the differences based on single nucleotide polymorphisms (SNPs) were exceptionally high between the four strains, i.e., between 841 and 11,166 bases, due to a strong impact of homologous recombination. Thus, an ad hoc core genome multilocus sequence typing (cgMLST) scheme was created and pangenome analysis was conducted for determining the genomic similarity between the strains. The INMV246 isolate obtained from sputum on the enclosure floor and one INMV124 isolate of tapir #2 showed the highest congruence, suggesting that both originated from a shared source. The other two INMV124 isolates were genomically distinct from these strains. Nevertheless, in all four strains two plasmids were detected, which were highly conserved between the strains. The study showed that the genomic variability between MAH strains isolated from the same site within a short period of time can be exceptionally high and the influence of homologous recombination needs to be considered when determining MAH strain relationships, particularly via SNP analyses.},
}
@article {pmid40167801,
year = {2025},
author = {Banu, S and Valero, KCW and Rivero, F},
title = {Simulated Heat Waves Affect Cell Fate and Fitness in the Social Amoeba Dictyostelium discoideum.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {21},
pmid = {40167801},
issn = {1432-184X},
support = {#101044202/ERC_/European Research Council/International ; },
mesh = {*Dictyostelium/genetics/physiology/growth &amp; development ; *Hot Temperature ; Cyclic AMP/metabolism ; Spores, Protozoan/genetics/physiology/growth &amp; development ; Protozoan Proteins/genetics/metabolism ; },
abstract = {The effects of heatwaves at organism and population levels have been widely investigated; however, little is known about how they affect the development of cell populations and the fitness of the resulting organism. Disruptions caused by heatwaves are especially critical during early developmental stages in organisms lacking parental developmental protection or care. Here we use the social amoeba Dictyostelium discoideum, a soil microbe with a life cycle that transitions between single-cell and multicellular stages. D. discoideum thrives optimally at 22 °C and elevated temperatures impair (27 °C) or completely arrest (30 °C) growth, development, and spore yield. We established a simulated heatwave model in which vegetative cells were exposed to 27 °C for 3 days and studied the effects on the expression of early and cell type specific developmental genes using real-time quantitative PCR. A single heatwave severely impaired the expression of cyclic AMP-dependent early developmental gene markers (carA, acaA, pkaR, gtaC, tgrC1, and csaA) as well as that of prespore markers (cotB and spiA), while the expression of the prestalk marker ecmA was less affected. When mixed with heat-stressed cells, reporter cells expressing β-galactosidase grown at 22 °C preferentially occupy the spore mass of the fruiting body. Chimera assays of wild-type and reporter cells grown at optimal temperature or subjected to a heatwave confirmed a decreased fitness (contribution to chimeric fruiting bodies). We conclude that exposure of unprotected organisms at the single cell stage to a single heatwave has the potential to negatively impact their ability to cope with environmental extremes.},
}
@article {pmid40167318,
year = {2025},
author = {Détain, A and Suzuki, H and Wijffels, RH and Leborgne-Castel, N and Hulatt, CJ},
title = {Snow algae exhibit diverse motile behaviors and thermal responses.},
journal = {mBio},
volume = {},
number = {},
pages = {e0295424},
doi = {10.1128/mbio.02954-24},
pmid = {40167318},
issn = {2150-7511},
abstract = {Snow algal blooms influence snow and glacier melt dynamics, yet the mechanisms involved in community assemblage, development, and dispersal are not well understood. While microbial swimming behavior contributes significantly to the productivity and organization of aquatic and terrestrial microbiomes, the potential impact of algal cell motility in melting snow on the formation of visible, large-scale surface bloom patterns is largely unknown. Here, using video tracking and phototaxis experiments of unique isolates, we evaluated the motility of diverse snow algal taxa from green, red, and golden colored snow blooms in response to light and thermal gradients. We show that many species are efficient cryophilic microswimmers with speed thermal optima below 10°C although taxa with cryotolerant swimming traits were also identified. The significant motility of snow algae at low temperatures, a result of specialized adaptations, supports the importance of active movement in the life histories of algae inhabiting snow meltwater. However, diversity in swimming performance and behavior reveal a range of evolutionary outcomes and sensitivity of motile life stages to dynamic environments.IMPORTANCESwimming motility is a fundamental mechanism that controls the assembly, structure, and productivity of microbiomes across diverse environments and is highly sensitive to temperature. Especially, the role of cell swimming activity in algal bloom formation at the very low temperatures of snowmelt has been hypothesized, but not studied. By examining the movement patterns of snow algae and modeling the thermal response curves of swimming speed, the data reveal the key role of active cell movement that may have further important impacts on the microbial ecology and melt rates of snow and ice in polar and alpine regions.},
}
@article {pmid40162837,
year = {2025},
author = {Major, SR and Polinski, JM and Penn, K and Rodrigue, M and Harke, MJ},
title = {Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0259324},
doi = {10.1128/aem.02593-24},
pmid = {40162837},
issn = {1098-5336},
abstract = {Hydrothermal vent plumes (HVPs), formed by high-temperature vent emissions, are rich in compounds that support chemosynthesis and serve as reservoirs of microbial diversity and genetic innovation. Through turbulence, mixing, and interaction with subsea currents, vent communities are thought to disperse across ocean basins. In this study, we focused on the plume of the Moytirra hydrothermal vent field, a relatively unexplored site, to investigate its microbial inhabitants. We cultured bacteria from the Moytirra HVP using 11 different media types and performed complete genome sequencing on 12 isolates. Our analyses revealed four putatively novel species from the Thalassobaculum, Sulfitobacter, Idiomarina, and Christiangramia genera. Comparative genomics identified unique genomic islands containing biosynthetic gene clusters, including a novel Non-Ribosomal Peptide Synthetase/Polyketide Synthase cluster, toxin-antitoxin systems, and evidence of horizontal gene transfer facilitated by prophages. These findings underscore the potential of HVPs as a source of novel microbial species and biotechnologically relevant genes, contributing to our understanding of the biodiversity and genetic complexity of these extreme environments.IMPORTANCEHydrothermal vents are dynamic environments that offer unique nutrients for chemosynthetic organisms to drive biology in the deep-sea. The dynamics of these ecosystems are thought to drive genomic innovation in resident populations. Hydrothermal vent plumes (HVPs) mix with surrounding water, carrying local microbiota with them and dispersing for hundreds of kilometers. This study isolated bacteria from a HVP to capture a genomic snapshot of the microbial community, revealing four putatively novel species of bacteria within three taxonomic classes. The addition of these genomes to public databases provides valuable insights into the genomic function, architecture, and novel biosynthetic gene clusters of bacteria found in these extreme environments.},
}
@article {pmid40162703,
year = {2025},
author = {Souza Beraldo, C},
title = {An interactive art activity to promote student reflection and learning about host-microbe interactions.},
journal = {Journal of microbiology &amp; biology education},
volume = {},
number = {},
pages = {e0006325},
doi = {10.1128/jmbe.00063-25},
pmid = {40162703},
issn = {1935-7877},
abstract = {The use of art in science teaching can effectively help students understand complex and abstract concepts, particularly in the fields of Microbiology and Microbial Ecology, where the study objects-the microbes-are invisible to human eyes. To explore how different factors shape host-microbe interactions, I developed the activity MicrobiART, which uses mixed art materials to create analogies that illustrate the dynamic relationships between hosts, microbes, and their environments. MicrobiART was presented as an alternative session at a PhD students' conference in Espoo, Finland. Participants were invited to combine papers, balls, and paint-representing hosts, microbes, and environmental factors, respectively-to create paintings that depict the outcomes of these interactions. The completed artworks were then displayed in a mini exhibition. Following this session, participants were invited to engage in discussion to identify patterns in the paintings and reflect on the analogies' meanings and limitations. The activity is adaptable to various age groups and to both non-specialist and specialist audiences. Anecdotal evidence suggests that participants understood how interaction outcomes depend on the specific combination of players (host, microbes, and environment), while also recognizing emergent patterns. For instance, interactions within the same environment often share similar colors, contrasting with those from a different environment. Moreover, participants found the experience enjoyable, particularly due to its interactive and aesthetic appeal. These findings highlight the value of integrating science and art in science communication, especially in conference spaces: such integration fosters connections, inspires new ideas and teaching approaches, and provides a relaxed setting for discussion.},
}
@article {pmid40161817,
year = {2025},
author = {Band, VI and Gribonika, I and Stacy, A and Bouladoux, N and Mistry, S and Burns, A and Perez-Chaparro, PJ and Chau, J and Enamorado, M and Nagai, M and Bhushan, V and Golec, DP and Schwartzberg, PL and Hourigan, SK and Nita-Lazar, A and Belkaid, Y},
title = {Sulfide is a keystone metabolite for gut homeostasis and immunity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.06.641928},
pmid = {40161817},
issn = {2692-8205},
abstract = {Hydrogen sulfide is a gaseous, reactive molecule specifically enriched in the gastrointestinal tract. Here, we uncover a non-redundant role for sulfide in the control of both microbial and immune homeostasis of the gut. Notably, depletion of sulfide via both pharmaceutical and dietary interventions led to a profound collapse of CD4 T cells in the ileum of the small intestine lamina propria and significant impact on microbial ecology. As a result, mice with reduced sulfide within the gut were deficient in their ability to mount T cell dependent antibody responses to oral vaccine. Mechanistically, our results support the idea that sulfide could act directly on CD4 T cells via enhanced AP-1 activation, leading to heightened proliferation and cytokine production. This study uncovers sulfides as keystone components in gut ecology and provides mechanistic insight between diet, gut sulfide production and mucosal immunity.},
}
@article {pmid40160925,
year = {2025},
author = {Amirmijani, A and Pordel, A and Dehghani, K and Pourmoghaddam, MJ and Masigol, H and Grossart, HP},
title = {Two new pestalotioid fungi from tropical fruits in Iran.},
journal = {MycoKeys},
volume = {115},
number = {},
pages = {221-240},
doi = {10.3897/mycokeys.115.136469},
pmid = {40160925},
issn = {1314-4049},
abstract = {In a survey of tropical plant diseases in southern and southeastern Iran, samples of diseased Mangiferaindica and Psidiumguava leaves with necrotic symptoms were collected between 2021 and 2022. Six representative isolates of Neopestalotiopsis and Robillarda (three isolates for each) were studied using morphological characteristics as well as multi-locus phylogenetic analysis based on (i) the internal transcribed spacer (ITS) region of the nuclear rDNA, (ii) part of the translation elongation factor 1-alpha (tef1), and (iii) the β-tubulin (tub2). After morphological investigation, our phylogenetic analysis revealed that the Neopestalotiopsis and Robillarda isolates under study differed from all previously described species within these genera. Based on our polyphasic approach, two new species, including Neopestalotiopsisguava sp. nov. from necrotic Mangiferaindica and Robillardakhodaparastii sp. nov. from Psidiumguava are described and illustrated from Iran.},
}
@article {pmid40157674,
year = {2025},
author = {Wu, X and Yu, D and Ma, Y and Fang, X and Sun, P},
title = {Function and therapeutic potential of Amuc_1100, an outer membrane protein of Akkermansia muciniphila: A review.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {142442},
doi = {10.1016/j.ijbiomac.2025.142442},
pmid = {40157674},
issn = {1879-0003},
abstract = {The gut microbiota-derived protein Amuc_1100, a key outer membrane component of Akkermansia muciniphila, has emerged as a groundbreaking therapeutic agent with unique structural and functional properties. Amuc_1100 exerts multifaceted immune-metabolic effects through novel mechanisms, including modulation of TLR2/4 and JAK/STAT pathways. This review highlights its unique multi-component structure that enables synergistic biological activity, and its pharmacological properties, which underlies its ability to enhance intestinal barrier integrity, restore microbiota balance, and suppress systemic inflammation. Crucially, Amuc_1100 demonstrates unprecedented therapeutic versatility across both intestinal disorders (e.g., inflammatory bowel disease, antibiotic-associated diarrhea) and extraintestinal conditions-notably improving neuropsychiatric symptoms via gut-serotonin axis regulation, combating cancer through CD8+ T cell activation, and mitigating cardiotoxicity via gut-heart immune crosstalk. Emerging innovations in targeted delivery systems, including gut-retentive nano-formulations and engineered probiotic vectors, further amplify its clinical potential. We critically evaluate recent advances distinguishing Amuc_1100's mechanisms from live bacterial interventions. By synthesizing evidence from preclinical models, this work positions Amuc_1100 as a prototype for next-generation microbiome-derived therapeutics, bridging microbial ecology with precision medicine.},
}
@article {pmid40152585,
year = {2025},
author = {Wang, F and Luo, J and Zhang, Z and Liu, Y and Sheng, Dh and Zhuo, L and Li, Y-z},
title = {Differential crosstalk between toxin-immunity protein homologs divides Myxococcus nonself siblings into close and distant social relatives.},
journal = {mBio},
volume = {},
number = {},
pages = {e0390224},
doi = {10.1128/mbio.03902-24},
pmid = {40152585},
issn = {2150-7511},
abstract = {Many bacteria discriminate self and nonself using toxins and their corresponding immunity proteins. The toxin-immunity systems often include homologs, potentially creating crosstalk with unknown influences on kin discrimination. In this study, we investigated the kinship controlled by four homologous toxin-immunity systems in the social bacterium Myxococcus xanthus. We determined that the four homologous systems each play an independent role in the discrimination of self and nonself. However, the immunity proteins inactivate not only the corresponding nuclease toxin proteins but also some non-corresponding toxin proteins, depending on their sequence and structural similarities. The nonself relatives controlled by toxin-immunity proteins with or without crosstalk exhibit differential co-growth and collaborative behaviors. We concluded that differential crosstalk between toxin-immunity protein homologs can divide bacterial nonself lineages into close and distant relatives displaying differential collaboration and antagonistic behaviors.IMPORTANCEThis study significantly contributes to our knowledge of kin selection and social behavior in bacteria. The interactions between four homologous toxin-immunity protein systems of Myxococcus xanthus were investigated, and evidence was obtained that these systems can distinguish between self and nonself cells within a species. Importantly, this study revealed that nonself lineages, which display varying degrees of genetic relatedness, can co-grow and collaborate in distinct patterns. This discovery implies that the differential crosstalk between homologous toxin-immunity proteins can mimic the degree of kinship; through this activity, bacteria can differentiate close and distant relatives. This novel insight into bacterial social dynamics and kin discrimination supports kin selection theory and enriches our knowledge on microbial interactions and evolutionary strategies. These findings have broad implications for microbial ecology, evolution, and the development of cooperation strategies.},
}
@article {pmid40151948,
year = {2025},
author = {Šulčius, S and Alzbutas, G and Lukashevich, V},
title = {Cyanophage Lysis of the Cyanobacterium Nodularia spumigena Affects the Variability and Fitness of the Host-Associated Microbiome.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70042},
doi = {10.1111/1462-2920.70042},
pmid = {40151948},
issn = {1462-2920},
support = {S-LL-21-10//Lietuvos Mokslo Taryba/ ; },
mesh = {*Microbiota ; *Bacteriophages/genetics/physiology ; *Nodularia/metabolism/virology ; Bacteriolysis ; Viral Load ; Cyanobacteria/virology/metabolism/genetics ; },
abstract = {Cyanobacteria are intricately linked with its microbiome through multiple metabolic interactions. We assessed how these interactions might be affected by cyanophage infection and lysis in cyanobacterium Nodularia spumigena. The genome-scale metabolic models and analysis of putative metabolic interactions revealed a bidirectional cross-feeding potential within the N. spumigena microbiome, with heterotrophic bacteria exhibiting a greater level of trophic dependency on the cyanobacterium. Our results indicate that microbes associated with N. spumigena rely on the supply of various amino acids, reduced carbon compounds and protein synthesis cofactors released by the cyanobacterial host. We observed that compositional changes in the N. spumigena microbiome were associated with the multiplicity of infection and increased with increasing initial viral load. Higher mortality of N. spumigena led to decreased variability in the relative abundances of bacteria, suggesting an indirect restriction of their niche space. Lysis of N. spumigena resulted in a substantial decline in the estimated absolute abundances of heterotrophic bacteria, indicating reduced fitness of co-occurring bacteria in the absence of N. spumigena. Altogether, we demonstrate how a gradual increase in viral pressure on the photosynthetic host propagates through the co-occurring microbial community, disrupting cooperative nature and microbial connectivity within the N. spumigena microbiome.},
}
@article {pmid40149089,
year = {2025},
author = {Nussbaumer-Pröll, A and Hausmann, B and Weber, M and Pjevac, P and Berry, D and Zeitlinger, M},
title = {A Pilot Study on the Impact of Cranberry and Ascorbic Acid Supplementation on the Urinary Microbiome of Healthy Women: A Randomized Controlled Trial.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/antibiotics14030278},
pmid = {40149089},
issn = {2079-6382},
abstract = {Background: The collection of microorganisms that colonize the human genital and urinary tract is referred to as the genitourinary microbiome. Urinary tract infections (UTIs), which predominantly affect women, are linked to alterations in the genitourinary microbiome. Cranberries (Vaccinium oxycoccos), rich in proanthocyanidins, and ascorbic acid (vitamin C), known for their urinary acidification properties, are commonly used for UTI prevention. However, their effects on the genitourinary microbiome remain inadequately characterized. This pilot study assesses the genitourinary microbiome composition in healthy women and evaluates the influence of cranberry and ascorbic acid supplementation. Methods: In a randomized, controlled, and open-label trial, 27 healthy women in their reproductive age (18-40 years) were assigned to three groups: cranberry (n = 8), ascorbic acid (n = 10), and control (n = 9). Urine samples were collected at three time points and processed for 16S rRNA gene amplicon-based microbial community composition analysis. Microbiome composition was compared within and between groups, and between study visits. Results: Sufficient microbial DNA was extracted from all midstream urine samples. The genitourinary microbiome was predominantly composed of Lactobacillus spp., as reported previously. No significant shifts in microbial composition were observed in response to cranberry or ascorbic acid supplementation, and no statistically significant differences were detected between the intervention and control groups or between study visits. Conclusion: The genitourinary microbiome of healthy women remained stable during cranberry or ascorbic acid supplementation. Further studies in patients with recurrent UTIs are needed to explore the potential impacts of these supplements on the genitourinary microbiome in disease states.},
}
@article {pmid40149015,
year = {2025},
author = {Fournier, P and Pellan, L and Jaswa, A and Cambon, MC and Chataigner, A and Bonnard, O and Raynal, M and Debord, C and Poeydebat, C and Labarthe, S and Delmotte, F and This, P and Vacher, C},
title = {Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {37},
pmid = {40149015},
issn = {2524-6372},
support = {20-PCPA-0010//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant and soil microbiomes and long-term epidemiological records of grapevine downy mildew, a major disease caused by the oomycete Plasmopara viticola.<br><br>RESULTS: We found that certain microbial taxa were consistently more abundant in plots with lower disease incidence and severity and that the microbial community composition could predict disease incidence and severity. Microbial diversity was not strongly linked to epidemiological records, suggesting that disease incidence and severity is more related to the abundance of specific microbial taxa. These key taxa were identified in the topsoil, where the pathogen's oospores overwinter, and in the phyllosphere, where zoospores infect leaves. By contrast, the leaf endosphere, where the pathogen's mycelium develops, contained few taxa of interest. Surprisingly, the soil microbiota was a better predictor of disease incidence and severity than the leaf microbiota, suggesting that the soil microbiome could be a key indicator of the dynamics&#xa0;of this primarily aerial disease.<br><br>CONCLUSION: Our study integrates long-term epidemiological data with microbiome profiles of healthy plants to reveal fungi and bacteria relevant for the biocontrol of grapevine downy mildew. The resulting database provides a valuable resource for designing microbial consortia with potential biocontrol activity. The framework can be applied to other crop systems to guide the development of biocontrol strategies and reduce pesticide use in agriculture.},
}
@article {pmid40148178,
year = {2025},
author = {Hodžić, A and Duscher, GG and Alić, A and Beck, R and Berry, D},
title = {Peritrophic matrix: an important determinant of vector competence in hematophagous arthropods.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2025.03.005},
pmid = {40148178},
issn = {1471-5007},
abstract = {The peritrophic matrix (PM) is a non-cellular, glycan-rich structure that lines the gut epithelium of most invertebrates, including arthropod vectors that transmit diseases of public health and veterinary concern. This semipermeable barrier, functionally analogous to the vertebrate mucosal layer, separates the gut lumen from epithelial cells and provides protection against invading pathogens and their toxins. Beyond its mechanical protective role in the gut, the PM plays a crucial part in arthropod innate immunity. Here, we summarize the most recent advances in understanding the molecular mechanisms of vector-pathogen interactions in blood-feeding arthropods and discuss the significance of the PM in modulating vector competence. This knowledge could contribute to the development of novel strategies to control vector-borne infections.},
}
@article {pmid40147302,
year = {2025},
author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD},
title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.},
journal = {Water research},
volume = {280},
number = {},
pages = {123511},
doi = {10.1016/j.watres.2025.123511},
pmid = {40147302},
issn = {1879-2448},
abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.},
}
@article {pmid40146382,
year = {2025},
author = {Nain, D and Rana, A and Raychoudhury, R and Sen, R},
title = {Parasite-Induced Replacement of Host Microbiota: Impact of Xenos gadagkari Parasitization on the Microbiota of Polistes wattii.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {20},
pmid = {40146382},
issn = {1432-184X},
support = {DST/INSPIRE/03/2021/000175, IF200146//Department of Science and Technology, Ministry of Science and Technology, India/ ; 1061830779//Council of Scientific and Industrial Research, India/ ; CRG-2021/007010//Science and Engineering Research Board/ ; CRG-2021/007010//Science and Engineering Research Board/ ; },
mesh = {Animals ; *Wasps/microbiology/physiology ; *Microbiota ; Female ; Male ; *RNA, Ribosomal, 16S/genetics ; Host-Parasite Interactions ; Seasons ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {The study of microbiota of social insects under different ecological conditions can provide important insights into the role of microbes in their biology and behavior. Polistes is one of the most widely distributed and extensively studied genera of social wasps, yet a comprehensive study on the microbiota of any species of Polistes or any primitively eusocial wasp is missing. Polistes wattii is an Asian wasp, which hibernates in winter and exhibits a biannual nest founding strategy. It is often parasitized by the strepsipteran endoparasite/parasitoid Xenos gadagkari, which changes the morpho-physiology and behavior of their hosts. In this study, we employ 16S rRNA amplicon sequencing, using the Oxford Nanopore platform, to study the microbial community of P. wattii and investigate the effects of seasonality, sex, and Xenos parasitism. We show that the microbiota differs in females from solitary foundress spring nests and multiple foundress summer nests. The microbiota also differs in males and females. Finally, we show that X. gadagkari parasitism replaces and homogenizes the microbiota of P. wattii. Unlike the unparasitized wasps, the microbiota of X. gadagkari parasitoids and parasitized wasps are dominated by Wolbachia and Providencia. Although the normal microbiota of P. wattii resembles that of highly eusocial vespid wasps, we show that the microbiota of parasitized P. wattii becomes more like the microbiota of strepsipterans. Therefore, it appears that X. gadagkari and other such strepsipteran parasitoids may have a bigger impact on the biology of their hosts than previously thought.},
}
@article {pmid40146077,
year = {2025},
author = {Savchenko, V and Yu, XA and Polz, MF and Böttcher, T},
title = {Chitinivorax: The New Kid on the Block of Bacterial 2-Alkyl-4(1H)-quinolone Producers.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.5c00046},
pmid = {40146077},
issn = {1554-8937},
abstract = {2-Alkyl-4(1H)-quinolones play a key role in bacterial communication, regulating biofilm formation, and virulence. Their antimicrobial properties also support bacterial survival and interspecies competition in microbial communities. In addition to the human pathogen Pseudomonas aeruginosa various species of Burkholderia and Pseudoalteromonas are known to produce 2-alkyl-4(1H)-quinolones. However, the evolutionary relationships of their biosynthetic gene clusters remain largely unexplored. To address this, we investigated the phylogeny of 2-alkyl-4(1H)-quinolone biosynthetic gene clusters, leading to the discovery of Chitinivorax as a fourth genus capable of producing 2-alkyl-4(1H)-quinolones, expanding our knowledge of the diversity of bacteria involved in quinolone-biosynthesis.},
}
@article {pmid40143451,
year = {2025},
author = {Jenkins, G and Boyd, ES and Danchin, A and Hervé, V},
title = {Microbiome Notes-Building a Library of Descriptive Microbial Ecology.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70085},
doi = {10.1111/1758-2229.70085},
pmid = {40143451},
issn = {1758-2229},
}
@article {pmid40142506,
year = {2025},
author = {Govaert, M and Duysburgh, C and Kesler, B and Marzorati, M},
title = {Effects of NatureKnit™, a Blend of Fruit and Vegetable Fibers Rich in Naturally Occurring Bound Polyphenols, on the Metabolic Activity and Community Composition of the Human Gut Microbiome Using the M-SHIME[®] Gastrointestinal Model.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030613},
pmid = {40142506},
issn = {2076-2607},
support = {Not applicable//VDF FutureCeuticals, Inc./ ; },
abstract = {This study evaluated the impact of a proprietary blend of fruit and vegetable fibers rich in naturally occurring bound polyphenols (commercially marketed as NatureKnit[TM]), compared to purified fibers (inulin and psyllium), on the human gut microbiome using the validated M-SHIME[®] gastrointestinal model. A short-term single-stage colonic M-SHIME[®] experiment (with fecal inoculum from three healthy human donors) was used to evaluate the test products compared to a negative control. Samples were assessed for pH, gas pressure, short-chain fatty acid (SCFA) production, lactate, and ammonium from 0 h to 48 h. Microbial community composition was assessed at 0 h (negative control only), 24 h, and 48 h (lumen) or 48 h (mucosal). All test products were fermented well in the colon as demonstrated by decreases in pH and increases in gas pressure over time; these changes occurred faster with the purified fibers, whereas NatureKnit™ demonstrated slow, steady changes, potentially indicating a gentler fermentation process. SCFA production significantly increased over the course of the 48 h experiment with all test products versus negative control. SCFA production was significantly greater with NatureKnit™ versus the purified fibers. Shifts in the microbial community composition were observed with all test products versus negative control. At the conclusion of the 48 h experiment, the absolute bacterial abundance and the richness of observed bacterial taxa in the lumen compartment was significantly greater with NatureKnit™ compared with inulin, psyllium, and negative control. Overall, NatureKnit™ demonstrated greater or similar prebiotic effects on study measures compared with established prebiotic fibers.},
}
@article {pmid40142410,
year = {2025},
author = {Hassen, AI and Muema, EK and Diale, MO and Mpai, T and Bopape, FL},
title = {Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant-Microbe Interactions.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030518},
pmid = {40142410},
issn = {2076-2607},
support = {A-089//Department of Agriculture Land Reform and Rural Development/ ; },
abstract = {Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant-microbe interactions that occur in the soil rhizosphere and one of the oldest plant-microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs).},
}
@article {pmid40141768,
year = {2025},
author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM},
title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/life15030423},
pmid = {40141768},
issn = {2075-1729},
support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; },
abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.},
}
@article {pmid40138093,
year = {2025},
author = {Demeulenaere, &#xc9;},
title = {In search of the microbial path to Terroir: a place-based history of the ecologization of French cheese microbiology, 1990-2000s.},
journal = {History and philosophy of the life sciences},
volume = {47},
number = {2},
pages = {22},
pmid = {40138093},
issn = {1742-6316},
support = {EXORIGINS//Emergence(s) Ville de Paris/ ; },
mesh = {*Cheese/microbiology/history ; France ; History, 20th Century ; *Food Microbiology/history ; Milk/history/microbiology ; Animals ; },
abstract = {At the crossroads between food studies and science and technology studies, this paper analyzes the role of laboratories located within traditional cheese territories in the ecologization of cheese microbiology in France at the turn of the twentieth century. The paper argues that their connectedness with Protected Designation of Origin raw-milk cheese organizations advocating for a strong understanding of terroir played a key role in challenging the modern strain-by-strain approach and fostering a shift towards a new research object: microbial communities in their ecologies. Modernization and standardization in cheese production from the 1950s onwards laid indeed on the improvement of hygiene to get "cleaner" milks, and on lab research on microbial strains to develop selected starter cultures. This led to a dramatic loss of microbial abundance within raw milks, which progressively provoked milk processing issues, as well as a loss of cheese typicality, an issue for place-based cheeses. To face it, the modernist approach promoted more laboratorial research on microbial strains to develop new starter cultures and the diversification of microbial collections, within an ex-situ conservation framework. In contrast, microbiologists conducting applied research for raw-milk terroir cheeses investigated environmental microbial reservoirs, microbial fluxes, as well as farming practices that favor "natural seeding" and enrich milk native microflora. A new approach emerged, namely "practice-driven microbial ecology" (écologie microbienne dirigée), which enacts the dynamic and ubiquitous properties of microbial life. The paper offers a situated account on the "microbial (ecology) turn" described by other authors, highlighting the ecological approach developed in the 1990s-2000s by French microbiologists in search of "the microbial path to terroir".},
}
@article {pmid40137691,
year = {2025},
author = {Maitre, A and Mateos-Hernandez, L and Kratou, M and Egri, N and Maye, J and Juan, M and Hodžić, A and Obregón, D and Abuin-Denis, L and Piloto-Sardinas, E and Fogaça, AC and Cabezas-Cruz, A},
title = {Effects of Live and Peptide-Based Antimicrobiota Vaccines on Ixodes ricinus Fitness, Microbiota, and Acquisition of Tick-Borne Pathogens.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/pathogens14030206},
pmid = {40137691},
issn = {2076-0817},
mesh = {Animals ; *Ixodes/microbiology/immunology ; Mice ; *Microbiota/immunology/drug effects ; *Bacterial Vaccines/immunology/pharmacology ; Staphylococcus epidermidis/immunology/drug effects ; Rickettsia/immunology ; Tick-Borne Diseases/prevention &amp; control/immunology/microbiology ; Female ; Vaccines, Subunit/immunology/administration &amp; dosage ; Borrelia burgdorferi Group/immunology ; Vaccination ; Vaccines, Attenuated/immunology/administration &amp; dosage ; },
abstract = {This study explored the effects of antimicrobiota vaccines on the acquisition of Borrelia and Rickettsia, and on the microbiota composition of Ixodes ricinus ticks. Using a murine model, we investigated the immunological responses to live Staphylococcus epidermidis and multi-antigenic peptide (MAP) vaccines. Immunized mice were infected with either Borrelia afzelii or Rickettsia helvetica, and subsequently infested with pathogen-free I. ricinus nymphs. We monitored the tick feeding behavior, survival rates, and infection levels. Additionally, we employed comprehensive microbiota analyses, including the alpha and beta diversity assessments and microbial co-occurrence network construction. Our results indicate that both live S. epidermidis and MAP vaccines elicited significant antibody responses in mice, with notable bactericidal effects against S. epidermidis. The vaccination altered the feeding patterns and fitness of the ticks, with the Live vaccine group showing a higher weight and faster feeding time. Microbiota analysis revealed significant shifts in the beta diversity between vaccine groups, with distinct microbial networks and taxa abundances observed. Notably, the MAP vaccine group exhibited a more robust and complex network structure, while the Live vaccine group demonstrated resilience to microbial perturbations. However, the effects of antimicrobiota vaccination on Borrelia acquisition appeared taxon-dependent, as inferred from our results and previous findings on microbiota-driven pathogen refractoriness. Staphylococcus-based vaccines altered the microbiota composition but had no effect on B. afzelii infection, and yielded inconclusive results for R. helvetica. In contrast, previous studies suggest that E. coli-based microbiota modulation can induce a pathogen-refractory state, highlighting the importance of both bacterial species and peptide selection in shaping microbiota-driven pathogen susceptibility. However, a direct comparison under identical experimental conditions across multiple taxa is required to confirm this taxon-specific effect. These findings suggest that antimicrobiota vaccination influences tick fitness and microbiota assembly, but its effects on pathogen transmission depend on the bacterial taxon targeted and the selected peptide epitopes. This research provides insights into the need for strategic bacterial taxon selection to enhance vaccine efficacy in controlling tick-borne diseases.},
}
@article {pmid40134242,
year = {2025},
author = {Trombley, J and Celenza, JL and Frey, SD and Anthony, MA},
title = {Arbuscular Mycorrhizal Fungi Boost Development of an Invasive Brassicaceae.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15508},
pmid = {40134242},
issn = {1365-3040},
support = {//This study was supported by the Dick George Invasives Fund awarded to S.D.F. and M.A.A. M.A.A. was supported by a Vienna Science and Technology Fund (WWTF) Vienna Research Groups for Young Investigators grant awarded to MAA (VRG22-007)./ ; },
abstract = {Invasive plant growth is affected by interactions with arbuscular mycorrhizal fungi (AMF). AMF are mutualists of most land plants but suppress the growth of many plants within the Brassicaceae, a large plant family including many invasive species. Alliaria petiolata (garlic mustard) is a nonnative, nonmycorrhizal Brassicaceae distributed throughout North America in forest understories where native species rely on AMF. If AMF suppress growth of garlic mustard, it may be possible to inoculate AMF to manage invasions. Here, we show that in contrast to expectation, garlic mustard growth nearly doubled in response to AMF inoculation under both laboratory and field conditions. This effect was negatively linked to investments in glucosinolates, a class of defensive compounds. In contrast to typical symbiosis, AMF did not produce arbuscules where nutrient exchange occurs in roots, but AMF inoculation increased plant and soil nitrogen availability. Our findings reveal an adjacent pathway by which AMF promote invasive plant growth without classic symbiotic exchanges. Prior assumptions that garlic mustard suppresses AMF are inadequate to explain invasion success since it benefits from interactions with AMF. This study is the first to demonstrate extensive growth promotion following AMF inoculation in mustard plants, with important implications for invasion biology and agriculture.},
}
@article {pmid40131450,
year = {2025},
author = {Sun, L and Guan, W and Tai, X and Qi, W and Zhang, Y and Ma, Y and Sun, X and Lu, Y and Lin, D},
title = {Research Progress on Microbial Nitrogen Conservation Technology and Mechanism of Microorganisms in Aerobic Composting.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {19},
pmid = {40131450},
issn = {1432-184X},
support = {32160756//National Natural Science Foundation of China/ ; GAUfx-04J03//Fuxi Foundation of Gansu Agricultural University/ ; 23CXNN0007//Gansu Province Science and Technology Plan Project Technology Innovation Guidance Program - LuGan Science and Technology Collaboration topic/ ; 2023-3-66//Science and Technology Plan Project of Lanzhou city/ ; GNKJ-2024-46//Research and Application of Supporting Technologies for Gansu Pig Industry/ ; GAU-XKTD-2022-24//The Discipline Team Project of Gansu Agricultural University/ ; },
mesh = {*Nitrogen/metabolism ; *Composting ; *Manure/microbiology ; *Soil Microbiology ; Livestock/microbiology ; Bacteria/metabolism/genetics/classification ; Aerobiosis ; Animals ; Soil/chemistry ; Microbiota/physiology ; },
abstract = {With economic development and improvements in living standards, the demand for livestock products has steadily increased, resulting in the generation of large amounts of livestock manure, which seriously pollutes the ecological environment and poses a threat to human health. High-temperature aerobic composting is an effective method for treating livestock manure; however, traditional composting processes often lead to considerable nitrogen loss, reduced efficiency of soil conditioners, and increased emissions of harmful gases. The incorporation of physical, chemical, and biological additives can effectively retain nitrogen within the compost. Among these, microbial agents are particularly noteworthy as they precisely regulate the microbial community structure associated with nitrogen transformation during aerobic composting, altering the abundance of functional genes and enzyme activities involved in nitrogen transformation. This approach significantly reduces nitrogen loss and harmful gas emissions. This paper reviews the application effects of microbial agents on nitrogen retention during aerobic composting and explores the underlying regulatory mechanisms, aiming to provide theoretical guidance and new research directions for the application of microbial agents in enhancing nitrogen retention during aerobic composting.},
}
@article {pmid40129674,
year = {2025},
author = {Hussain, N and Ibrahim Al Haddad, AH and Abbass, S and Alfahl, Z},
title = {The potential impact of habitual sleep quality on glycaemic control and inflammation: A study on geriatric patients recently diagnosed with type 2 diabetes mellitus (T2DM).},
journal = {Sleep medicine: X},
volume = {9},
number = {},
pages = {100139},
doi = {10.1016/j.sleepx.2025.100139},
pmid = {40129674},
issn = {2590-1427},
abstract = {Sleep quality and its relationship with glycaemic control is of particular interest in the context of geriatric diabetes. We aimed to investigate the potential impact of habitual sleep quality on glycaemic control status among geriatric patients recently diagnosed with type 2 diabetes mellitus (T2DM). A total of 193 geriatric patients recently diagnosed with T2DM in a tertiary-care hospital were selected. A developed questionnaire was used to assess various aspects of sleep quality. Glycaemic control was evaluated through fasting blood glucose levels, HbA1c measurements and number of admissions to the hospital for hypoglycaemic or hyperglycaemic episodes. Patients were divided into Poor Sleep Quality (PSQ, n = 132) and Adequate Sleep Quality (ASQ, n = 61) groups. The PSQ group exhibited significantly worse sleep outcomes, including longer sleep latency (35 ± 9.2 min vs. 15 ± 6.4 min), shorter sleep duration (5 h 42 min vs. 7 h 18 min) and greater use of sleep medications (72 % vs. 22 %). Glycaemic control, measured by HbA1c, was worse in the PSQ group (8.7 ± 1.9 vs. 7.2 ± 1.2; p < 0.01), which also had more frequent severe hypoglycaemic (35 ± 1.4 vs. 8 ± 2.1; p = 0.02) and ketoacidotic episodes (72 ± 1.0 vs. 5 ± 1.1; p = 0.01). These findings suggest an association between poor sleep quality and poorer glycaemic control, with more frequent diabetes-related complications, highlighting the need for further research to explore potential causal relationships and targeted interventions in this population.},
}
@article {pmid40127879,
year = {2025},
author = {Mirsalami, SM and Mirsalami, M},
title = {Assessing microbial ecology and antibiotic resistance genes in river sediments.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105738},
doi = {10.1016/j.meegid.2025.105738},
pmid = {40127879},
issn = {1567-7257},
abstract = {Anthropogenic activities greatly affect the Karon River leading to deterioration of water quality. This investigation utilizes environmental genomic techniques to delineate microbial populations, examine functional genomics, and evaluate the occurrence of virulence determinants and antibiotic resistance genes (ARGs) in fluvial sediment. Taxonomic assessment identified that Firmicutes were the predominant phyla, with Bacillus being the most abundant genus across samples. Functional analysis revealed the metabolic capabilities of sediment-associated bacteria, linking them to biogeochemical processes and potential health impacts. The S2 samples exhibited the highest virulence factor genes, while the S3 samples had the most ARGs (30), highlighting concerns about pathogenicity. Analyzing ARGs provides critical insights into environmental data collected, such as water quality parameters (e.g., nutrient concentrations, pH) or pollution levels, prevalence, and distribution of these resistance factors within the sediment samples, helping to identify potential hotspots of antibiotic resistance in the Karon River ecosystem. The study identified similar operational taxonomic units (OTUs) across sampling sites at the phylogenetic level, indicating a consistent presence of certain microbial taxa. However, the lack of variation in functional classification suggests that while these taxa may be present, they are not exhibiting significant differences in metabolic capabilities or functional roles. These findings emphasize the significance of metagenomic methods in understanding microbial ecology and antibiotic resistance in aquatic environments, suggesting a need for further research into the restoration of microbial functions related to ARGs and virulence factors.},
}
@article {pmid40121181,
year = {2025},
author = {Eaton, WD and McGee, KM and Glahn, A and Lemenze, A and Soteropoulos, P},
title = {Use of a logging road in a Costa Rican forest changes the composition and stability of soil microbial decomposer communities, and the conversion of organic carbon into biomass.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf075},
pmid = {40121181},
issn = {1365-2672},
abstract = {AIMS: The effects of a tropical forest logging road on soil C and N, and the compositions of Actinobacteria, Acidobacteria, and wood rot/lignin-degrading fungal (WRT/LD) decomposer communities were evaluated.<br><br>METHODS AND RESULTS: Soils from a healthy Costa Rican old growth forest before Hurricane Otto and from an adjacent, recently formed logging road built after Hurricane Otto were collected over 4 years and assessed for C and N metrics, and characteristics of the 3 decomposer communities determined by Illumina amplicon sequencing methods. The Logging Road negatively impacted the soil total organic C, respiration, biomass C, qCO2, and total N, while the Actinobacterial and Acidobacterial communities changed from stable compositions of copiotrophic taxa in the rich forest soil to stable compositions of oligotrophic taxa in the poor logging road soil, and the wood rot/lignin degrading (WRT/LD) community changed from stable compositions of copiotrophic taxa in the forest soils to an unstable community of oligotrophic taxa with almost no overlap in genera between Logging Road soils.<br><br>CONCLUSIONS: The logging road negatively influenced 3 decomposer communities and associated C and N metrics, with the two bacterial communities taxonomically stabilizing, but the fungal community taxonomically diverging into an unstable composition over time. Monitoring efforts are on-going to provide local forest land managers with potential indicators of soil ecosystem damage and recovery.},
}
@article {pmid40120670,
year = {2025},
author = {San-Blas, E and Cornejo, MJ and Guerra, M and Olivares, M and Faundez, S and Bastidas, B and Morales-Montero, P and Pizarro, L and Aponte, H and Castañeda-Álvarez, C and Lankin, G},
title = {Where are my nematodes? labelling and visualising entomopathogenic nematodes in vivo using carbon quantum dots.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108317},
doi = {10.1016/j.jip.2025.108317},
pmid = {40120670},
issn = {1096-0805},
abstract = {Identifying single or groups of animals has significantly advanced our understanding of animal biology and ecology. However, labelling is extremely difficult in small animals, like soil invertebrates. Due to the complexity of current methods, the dynamics and interactions of these populations are often studied indirectly. Labelling nematodes or microarthropods such as collembolans or soil acari has been challenging due to the high cost, potential toxicity, genetic modification requirements, cellular processes interference, and photobleaching. In this scenario, no methods can be applied to large numbers of microorganisms at once due to their mentioned practical and biological limitations and cost. In this work we show that quantum carbon dots (Cdots) are effective for labelling infective juveniles (IJs) of entomopathogenic nematodes (EPNs). In in vitro assays the IJs gradually acquired fluorescence, as Cdots accumulated in the lysosome-related organelles from their intestine cells, peaking at day 14, and with no lethal or sub-lethal effects on IJs. Fluorescence was clearly distinguishable from the natural auto-fluorescence of non-labelled IJs and persisted for months in IJs transferred to water. We and non-experts easily differentiated between similar species of EPNs and between two strains of S. feltiae placed in the same matrix (soil or water). We demonstrated for the first time the feasibility of labelling large numbers of IJs (hundreds of thousands/millions) with Cdots at minimal cost without any adverse effects for over a year. Our findings could be the starting point for detailed and large-scale field investigations on nematodes and other small organisms, allowing deeper understanding of their roles in soil ecosystems. This method provides a cost-effective and reliable tool for advancing research in the ecology of soil invertebrates, such as the interactions occurring in communities or between specific organisms, movement and dispersal, population dynamics or ecosystem services in a cryptic environment difficult to study.},
}
@article {pmid40119062,
year = {2025},
author = {Acharya, P and Yegon, MJ and Haferkemper, L and Misteli, B and Griebler, C and Vitecek, S and Attermeyer, K},
title = {Leaf Conditioning and Shredder Activity Shape Microbial Dynamics on Fine Particulate Organic Matter Produced During Decomposition of Different Leaf Litter in Streams.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {18},
pmid = {40119062},
issn = {1432-184X},
mesh = {*Plant Leaves/chemistry ; Animals ; *Particulate Matter/analysis ; *Bacteria/metabolism/classification ; *Microbiota ; Acer/microbiology/chemistry ; Rivers/microbiology/chemistry ; Larva/growth &amp; development ; Fatty Acids/metabolism/analysis ; Fagus/microbiology ; Ecosystem ; Feces/microbiology/chemistry ; Alnus/microbiology/chemistry ; },
abstract = {Leaf litter decomposition (LLD) is a key ecosystem function where invertebrate shredders produce large amounts of fine particulate organic matter (FPOM) that serves as a substrate for microbial assemblages. Here, we explore the shredder-produced FPOM composition and activity of FPOM-associated microbial communities in response to different leaf species and their conditioning. In a laboratory experiment, we fed leaves of different elemental compositions (alder, beech and maple), conditioned under oxic or anoxic conditions, to caddisfly larvae (Sericostoma sp.). We hypothesized differences in FPOM elemental and fatty acid composition and FPOM-associated microbial activity among the leaf species, conditioning, and two types of shredder-produced FPOM, i.e. shredded leaves and faecal pellets. Our results suggest that leaf conditioning and shredder activity play pivotal roles in shaping FPOM composition and FPOM-associated microbial activity. We observed lower C/N ratios with high-C/N litter (beech and maple leaves) after conditioning and no change in the elemental composition of the faecal pellets compared to the leaves. However, we observed differences in microbial fatty acid proportions and composition on leaves and faecal pellets with significantly higher fractions of bacterial fatty acids on faecal pellets than on leaves. We also noted a significant impact of leaf conditioning on the microbial activity of shredded leaves and faecal pellets, with a higher microbial growth efficiency observed on faecal pellets compared to ingested leaves. These findings highlight the crucial influence of leaf species and conditioning on the activity of shredder-produced FPOM, emphasizing the complex interplay between leaf properties and fate and microbial processes in streams.},
}
@article {pmid40118512,
year = {2025},
author = {Gomes, IB},
title = {The Overlooked Interaction of Emerging Contaminants and Microbial Communities: A Threat to Ecosystems and Public Health.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf064},
pmid = {40118512},
issn = {1365-2672},
abstract = {Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment. The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of "One Health." The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance. So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.},
}
@article {pmid40118002,
year = {2025},
author = {Wan, W and Grossart, HP and Wu, QL and Xiong, X and Yuan, W and Zhang, W and Zhang, Q and Liu, W and Yang, Y},
title = {Global meta-analysis deciphering ecological restoration performance of dredging: Divergent variabilities of pollutants and hydrobiontes.},
journal = {Water research},
volume = {280},
number = {},
pages = {123506},
doi = {10.1016/j.watres.2025.123506},
pmid = {40118002},
issn = {1879-2448},
abstract = {Global "Sustainable Development Goals" propose ambitious targets to protect water resource and provide clean water, whereas comprehensive understanding of restoration performance and ecological mechanisms are lacking for dredging adopted for purifying polluted waterbodies and maintaining navigation channels. Here, we conducted a global meta-analysis to estimate ecological restoration consequence of dredging as pollution mitigation and navigation channel maintenance measures using a dataset compiled from 191 articles covering 696 studies and 84 environmental and ecological parameters (e.g., pollutants and hydrobiontes). We confirm that dredging shows negative influences on 77.50% pollutants in the BA model (before dredging vs. after dredging) and 84.21% pollutants in the CI model (control vs. impact) as well as on sediment nutrient fluxes. Additionally, 57.14% attributes (i.e., richness, diversity, biomass, and density) of hydrobiontes in the BA model and 89.47% attributes of hydrobiontes in the CI model responded negatively to dredging. As a result, 76.32% of the pollutants and 61.11% of the hydrobiont attributes responded uniformly to dredging in the BA and CI models. Our findings emphasize that dredging generally decreases pollutants and mitigates algal blooms, controlling phosphorus is easier than controlling nitrogen by dredging, and attributes (i.e., richness, diversity, and biomass) of hydrobiontes (i.e., zooplankton, phytoplankton, and zoobenthos) are density-dependent in dredging-disturbed environments. Our findings broaden our knowledge on ecological restoration performance of dredging as a mitigation measure in global aquatic ecosystems, and these findings might be helpful to use and optimize dredging to efficiently and sustainably purify polluted aquatic ecosystems.},
}
@article {pmid40116066,
year = {2025},
author = {Cusenza, BS and Scelfo, G and Licata, G and Capri, FC and Vicari, F and Alduina, R and Villanova, V},
title = {First Insights Into the Biological and Physical-Chemical Diversity of Various Salt Ponds of Trapani, Sicily.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70075},
doi = {10.1111/1758-2229.70075},
pmid = {40116066},
issn = {1758-2229},
support = {MSCA_0000011//Next Generation EU/ ; },
mesh = {Sicily ; *Ponds/microbiology/chemistry ; *Archaea/classification/genetics/isolation &amp; purification ; *Salinity ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Microbiota ; Phylogeny ; Ecosystem ; Temperature ; Hydrogen-Ion Concentration ; },
abstract = {The salt ponds of Trapani, Sicily, represent an extreme and under-explored ecosystem characterised by varying salinity gradients and environmental conditions. These ponds, integral to traditional salt extraction, include cold, driving, hot and crystallizer ponds, each hosting diverse microbial communities. This study aimed to explore the biological and physical-chemical diversity of 11 ponds during the salt production season in Trapani. We conducted comprehensive physical-chemical characterizations, including measurements of pH, conductivity, viscosity, density, organic carbon and ion concentration. Microbial DNA was extracted from salt pond waters and subjected to metabarcoding of 16S rRNA genes to determine the diversity of archaea and bacteria. High-throughput sequencing revealed significant variations in microbial communities across different pond types and seasons. Cold ponds showed a higher diversity of moderately halophilic organisms, while crystallizer and feeding ponds were dominated by extreme halophiles, particularly archaeal genus Halorubrum and Haloquadratum and bacterial genus Salinibacter. Statistical analyses indicated that environmental parameters, especially salinity and temperature, significantly influenced microbial community composition. Our findings enhance the understanding of microbial ecology in saline environments and highlight the potential of halophilic microorganisms. This study provides a foundation for future research into the functional roles of these microorganisms and their industrial applications.},
}
@article {pmid40113629,
year = {2025},
author = {Moldovan, OT and Levei, E and Ferreira, RL and Silva, MS and Mirea, IC},
title = {Exploring the Bacteriome Diversity and Use as a Proxy for Climate Change and Human Impacts on Groundwater in Temperate and Tropical Countries.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {17},
pmid = {40113629},
issn = {1432-184X},
support = {PN-III-P4-ID-PCCF-2016-0016 (DARKFOOD)//Ministry of Research and Innovation, CNCS - UEFISCDI/ ; PN-III-P4-ID-PCCF-2016-0016 (DARKFOOD)//Ministry of Research and Innovation, CNCS - UEFISCDI/ ; PN-III-P4-ID-PCCF-2016-0016 (DARKFOOD)//Ministry of Research and Innovation, CNCS - UEFISCDI/ ; GA N&#xb0;101052342//Biodiversa+, the European Biodiversity Partnership/ ; CNPq n. 302925/2022-8//National Council for Scientific and Technological Development/ ; CNPq n. 302925/2022-8//National Council for Scientific and Technological Development/ ; },
mesh = {*Groundwater/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Brazil ; *Climate Change ; *Caves/microbiology ; Romania ; Humans ; Microbiota ; Seasons ; Biodiversity ; Tropical Climate ; Ecosystem ; Water Microbiology ; },
abstract = {This research investigates bacterial communities in various cave pool water and substrates from Brazil and Romania for their use as indicators of environmental impacts on groundwater. Regional and seasonal differences were observed even if, at the phylum level, common bacteria for both countries were found. Distinct patterns emerged at the genus level due to the different climates (tropical vs. temperate) and ecosystems. Chemoautotrophic conditions define an utterly different groundwater bacteriome than oligotrophic conditions independent of the temperature. Bacteria as a proxy for climate change were explored using seasonal changes in Romanian caves; specific genera become dominant in summer months, such as Acinetobacter, Paeniglutamicibacter, Polaromonas, and Saccharimonadales, indicating processes that occur during the low-water season. Climate change, particularly dryness, is expected to exacerbate these variations, threatening the stability of groundwater ecosystems. The research also identified anthropic pollution indicators (Vogesella, Cutibacterium) and potential decontaminants (Bacillus) in Brazilian cave waters. Anthropic pollution indicators, like Pseudoarthrobacter. were also found in Romanian caves. Other key bacteria genera, such as Flavobacterium, Pseudomonas, and Acinetobacter, are chemolithotrophs or involved in the nitrogen cycle, which is critical in supplying nutrients for the cave food web. Marked differences between water and substrate microbiomes within the same pools suggested that substrates may play a crucial, underexplored role in groundwater ecosystem processes. Our study found unassigned taxa, 3 phyla, 2 families, and 832 genera (> 40%) in the studied pools. The results underscore the need to further explore groundwater microbiomes as potentially crucial yet fragile ecosystems in the face of climate change and human impacts.},
}
@article {pmid40112476,
year = {2025},
author = {Xu, RZ and Cao, JS and Cheng, S and Luo, JY and Ni, BJ and Fang, F and Liu, W and Wang, P},
title = {Heterotrophic nitrification-aerobic denitrification strains: An overlooked microbial interaction nexus in the anaerobic-swing-anoxic-oxic (ASAO) plug-flow system.},
journal = {Journal of environmental management},
volume = {380},
number = {},
pages = {125030},
doi = {10.1016/j.jenvman.2025.125030},
pmid = {40112476},
issn = {1095-8630},
abstract = {This study aims to clarify the overlooked functions of heterotrophic nitrification-aerobic denitrification (HNAD) bacteria in a novel anaerobic-swing-anoxic-oxic (ASAO) continuous plug-flow system. The dissolved oxygen (DO) levels and aerated hydraulic retention time (HRT) varied in the swing zones, providing a more diverse redox environment. High nitrogen (85.0 %) and phosphorus (80.0 %) removal were achieved by enriched HNAD bacteria (e.g., Thauera and Malikia) and phosphate accumulating organisms (PAO, e.g., Rhodocyclus and Azonexus) under middle DO level (1.0-2.0 mg/L) and longer aerated HRT (5.0 h). More importantly, microbial network revealed that HNAD bacteria became a connection point for other functional microorganisms associated with pollutant metabolism, and promoted the cooperation and functional evolution of microbial communities. The microbial ecology analysis captured the high importance of homogeneous selection, diffusion restriction, and drift for microbial community assembly in the ASAO system. Among them, HNAD bacteria contributed to both deterministic and stochastic processes, whereas the community assembly of PAO was mainly affected by the deterministic processes. The upregulation of denitrification genes (i.e., napA, napB, nirS, norB and norC) further confirmed the nitrogen removal contribution of aerobic denitrification by HNAD bacteria. Through this study, a comprehensive analysis of microbial interactions in the ASAO system was achieved, providing valuable insights into the targeted regulation of functional microorganisms in wastewater biological treatment processes.},
}
@article {pmid40112457,
year = {2025},
author = {Liu, J and Xu, G and Zhao, S and He, J},
title = {Microbiomes of coastal sediments and plastispheres shaped by microplastics and decabrominated diphenyl ether.},
journal = {Water research},
volume = {280},
number = {},
pages = {123417},
doi = {10.1016/j.watres.2025.123417},
pmid = {40112457},
issn = {1879-2448},
abstract = {Deciphering the impact of microplastic and persistent organic pollutants (POPs) co-contamination on coastal sediment is critical for developing effective remediation strategies for polluted sites yet remains underexplored. This study investigated the interactions between microplastics, decabrominated diphenyl ether (deca-BDE), and their co-contamination effects on the evolvement of coastal sediment and plastisphere microbiomes for over 2 years. Results showed that deca-BDE was naturally debrominated in sediments via diverse pathways, with microplastic polystyrene stimulating the debromination rate by up to 78.7 ± 10.0 %. The putative OHRB Dehalobacter and uncultured Dehalococcoidia populations were identified responsible for the complete debromination. Co-exposure to microplastics and deca-BDE induced significant shifts in community composition, diversity, and function in the sediment microbiomes, while plastisphere microbiomes exhibited distinct compositions and functional profiles, specializing in pathogenicity, pollutant degradation, and biogeochemical cycling. The type of plastics and the presence of deca-BDE influenced the plastisphere composition. Changes in sediment properties and debromination activity profoundly shaped microbial communities, with deterministic assembly dominating the plastisphere. Co-contamination increased the complexity, modularity, and stability of the plastisphere networks, creating unique niches for OHRB. These findings highlight the intricate interplay between microplastics, deca-BDE, and microbiomes, with significant implications for ecosystem health and remediation efforts.},
}
@article {pmid40109964,
year = {2025},
author = {Figueiredo, JEF and Diniz, GFD and Marins, MS and Silva, FC and Ribeiro, VP and Lanza, FE and de Oliveira-Paiva, CA and Cruz-Magalhães, V},
title = {Bacillus velezensis CNPMS-22 as biocontrol agent of pathogenic fungi and plant growth promoter.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1522136},
pmid = {40109964},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacillus velezensis is a ubiquitous bacterium with potent antifungal activity and a plant growth promoter. This study investigated the potential of B. velezensis CNPMS-22 as a biocontrol agent against phytopathogenic fungi under diverse experimental conditions and its potential as a plant growth promoter. Genome sequencing and analysis revealed putative genes involved in these traits.<br><br>METHODS: This research performed in vitro experiments to evaluate the CNPMS-22 antagonistic activity against 10 phytopathogenic fungi using dual culture in plate (DCP) and inverted sealed plate assay (ISP). Greenhouse and field tests evaluated the ability of CNPMS-22 to control Fusarium verticillioides in maize plants in vivo. The CNPMS-22 genome was sequenced using the Illumina HiSeq 4,000 platform, and genomic analysis also included manual procedures to identify genes of interest accurately.<br><br>RESULTS: CNPMS-22 showed antifungal activity in vitro against all fungi tested, with notable reductions in mycelial growth in both DCP and ISP experiments. In the ISP, volatile organic compounds (VOCs) produced by CNPMS-22 also altered the mycelium coloration of some fungi. Scanning electron microscopy revealed morphological alterations in the hyphae of F. verticillioides in contact with CNPMS-22, including twisted, wrinkled, and ruptured hyphae. Eight cluster candidates for synthesizing non-ribosomal lipopeptides and ribosomal genes for extracellular lytic enzymes, biofilm, VOCs, and other secondary metabolites with antifungal activity and plant growth promoters were identified by genomic analysis. The greenhouse and field experiments showed that seed treatment with CNPMS-22 reduced Fusarium symptoms in plants and increased maize productivity.<br><br>CONCLUSION: Our findings highlight the CNPMS-22's potential as bioinoculant for fungal disease control and plant growth with valuable implications for a sustainable crop productivity.},
}
@article {pmid40109356,
year = {2025},
author = {Kantor, RS and Kennedy, LC and Miller, SE and Favere, J and Nelson, KL},
title = {Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community.},
journal = {ACS ES&amp;T engineering},
volume = {5},
number = {3},
pages = {772-781},
pmid = {40109356},
issn = {2690-0645},
abstract = {Potable water reuse has become a key component of water sustainability planning in arid regions. Many advanced water purification facilities use reverse osmosis (RO) as part of treatment, including as a barrier for microorganisms; however, regrowth after RO treatment has been observed. Questions remain about the identity, source, and survival mechanisms of microorganisms in RO permeate, but the extremely low biomass of this water is a limitation for common microbiological methods. Here, we performed high-throughput sequencing on samples collected throughout a potable reuse train, including samples collected by filtering large volumes of RO permeate and biomass collected from RO membranes during an autopsy. We observed a stable, consistent microbial community across three months and in two parallel RO trains. RO permeate samples contained Burkholderiaceae at high relative abundance, including one Aquabacterium sp. that accounted for 29% of the community, on average. Like most other RO permeate microorganisms, this sequence was not seen in upstream samples and we suggest that biofilm growing on unit process infrastructure, rather than active treatment breakthrough, was the primary source. A metagenome-assembled genome corresponding to Aquabacterium sp. from RO permeate was found to lack most sugar-utilization pathways and to be able to consume low molecular weight organic molecules, potentially those that pass through RO.},
}
@article {pmid40107140,
year = {2025},
author = {Quattrocelli, P and Piccirillo, C and Kuramae, EE and Pullar, RC and Ercoli, L and Pellegrino, E},
title = {Synergistic interaction of phosphate nanoparticles from fish by-products and phosphate-solubilizing bacterial consortium on maize growth and phosphorus cycling.},
journal = {The Science of the total environment},
volume = {973},
number = {},
pages = {179082},
doi = {10.1016/j.scitotenv.2025.179082},
pmid = {40107140},
issn = {1879-1026},
abstract = {Phosphate nanomaterials, such as hydroxyapatite/β-tricalcium nanoparticles (nHAs) derived from food industry by-products, offer a sustainable alternative to enhance P-use efficiency in agriculture. However, their limited solubility remains a challenge. This study first investigated the mechanisms of P solubilization of salmon and tuna bones (SnHAs and TnHAs) in fifteen strains of phosphate-solubilizing bacteria (PSB) by an in vitro system. Then, best-performing strains were assembled in a consortium and tested in vivo on maize. We hypothesized that combining nHAs and the PSB consortium inoculated as seed coating (SC) outperforms single treatments alone in promoting plant growth and P cycling, and ensures the establishment in plant-soil system without a bacterial reinforcement (BR) by an additional inoculum suspension. The synergistic effect of nHAs and PSB was proved, improving maize root (+22 %) and total plant biomass (+29 %), as well as P (+32 %) and K (66 %) uptake compared to single treatments. With nHAs and SC, P-use efficiency and recovery increased by 25 % and three-fold, respectively, compared to nHAs alone or with bacterial reinforcement. Consistently, root and substrate bacterial biomass were associated with nHAs plus SC, while nHAs alone or with PSB upregulated PHT1;1 and PHT1;2 transporter genes in maize. Finally, linking the in vitro and in vivo system, we demonstrated that propionic acid production and P-solubilization efficiency of PSB co-applied with nHAs are key drivers of maize growth and P uptake. Our findings indicated that co-applying nHAs and PSB through SC offers a sustainable strategy to improve maize P-use efficiency.},
}
@article {pmid40106821,
year = {2025},
author = {Yang, CC and Washio, J and Lin, YC and Hsu, ML and Wang, DH and Tsai, FT and Lin, YM and Tu, HF and Chang, HC and Takahashi, N},
title = {Microbiome Signatures and Dysbiotic Patterns in Oral Cancer and Precancerous Lesions.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15317},
pmid = {40106821},
issn = {1601-0825},
support = {112-2314-B-A49-027//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-028-MY2//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-026-MY3//the National Science and Technology Council, Taiwan/ ; 112-2314-B-A49-058//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-087-MY3//the National Science and Technology Council, Taiwan/ ; 21H03151//the Japan Society for the Promotion of Science/ ; 20K10241//the Japan Society for the Promotion of Science/ ; 23K18349//the Japan Society for the Promotion of Science/ ; 23K21499//the Japan Society for the Promotion of Science/ ; //the National Yang Ming Chiao Tung University and Ministry of Education (MOE), Taiwan/ ; },
abstract = {BACKGROUND: The oral microbiome has been shown to be associated with the development of oral squamous cell carcinoma (OSCC). Research has primarily focused on elucidating the oncogenic mechanisms of specific pathogens by comparing the microbiomes of OSCC and normal tissues. However, the characteristics of the microbiome in the precancerous state remain less understood, as does the influence of metabolic and environmental factors on OSCC-associated microbiomes.<br><br>METHODS: In this study, we analyzed mucosa-associated microbiomes in normal, precancerous, and OSCC lesions from a cohort of 51 patients using 16S rRNA amplicon sequencing. We investigated compositional changes in the microbiome, including the specific abundances and co-occurrences of OSCC-associated bacteria.<br><br>RESULTS: Our findings indicate that the microbiome associated with precancerous lesions is indistinguishable from that of the normal mucosa, whereas the OSCC microbiome significantly differs from both normal and precancerous conditions. Specifically, the OSCC microbiome harbors less Streptococcus, coupled with an increase in amino-acid-degrading anaerobes such as Fusobacterium and Prevotella. The metabolic properties of individual microbes reported suggest that the overrepresentation of OSCC-specific bacteria is a result of metabolic adaptation to tumor microenvironments, although this possibility needs to be experimentally confirmed.<br><br>CONCLUSIONS: Our results demonstrate oral microbiome patterns across OSCC progression, offering insights into microbial ecological perspectives.},
}
@article {pmid40106330,
year = {2025},
author = {Maguire, M and DeLappe, N and Clarke, C and Touhy, A and Carlino-MacDonald, U and Hutson, A and Cormican, M and Brennan, W and Devane, G and Morris, D and Coughlan, SC and Miliotis, G and Russo, TA and Burke, LP},
title = {Genomic and phylogenetic analysis of hypervirulent Klebsiella pneumoniae ST23 in Ireland.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001373},
pmid = {40106330},
issn = {2057-5858},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/isolation &amp; purification/classification ; Ireland/epidemiology ; *Klebsiella Infections/microbiology/epidemiology ; Animals ; Virulence/genetics ; *Phylogeny ; Humans ; *beta-Lactamases/genetics ; Retrospective Studies ; Mice ; Bacterial Proteins/genetics ; Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; Microbial Sensitivity Tests ; Genomics ; Genotype ; Female ; },
abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a pathogen of global concern associated with invasive community-acquired infections. The combination of hypervirulence and carbapenem resistance can result in severe and difficult-to-treat infections. This retrospective study aimed to investigate the spread of hvKp sequence type 23 (ST23) in Ireland and the convergence of hypervirulent (hv) and antimicrobial resistance genotypes. Short-read sequences (PE300) for 90 K. pneumoniae ST23 isolates were generated by the Galway Reference Laboratory Services (GRLS). Isolates were from screening swabs (n=59), invasive infections (n=18), non-invasive sites (n=12) and the hospital environment (n=1). The virulence and resistance content were assessed genomically using Kleborate (v2.2.0), ABRicate (v1.0.1) and Platon (v1.6). The in vivo virulence of the isolates was assessed using a murine model. All isolates were genotypically hv with 88/90 isolates having a maximal Kleborate virulence score of 5 including carriage of key genes. Eighty-two per cent of isolates (74/90) carried a carbapenemase gene (bla OXA-48/bla OXA-181/bla NDM-1), and 42% carried resistance genes to 3 or more antimicrobial classes. Core genomic delineation revealed the isolates to be clonal with similar resistance and virulence profiles. Two distinct clusters of Irish isolates were detected consisting of 82/90 of the isolates. Isolates associated with carriage and infection demonstrated similar in vivo virulence. An established clone of hvKp ST23 is circulating within Ireland and causing both colonization and infection of patients. The lack of reliable screening methods for hvKp makes its detection and control in the healthcare setting challenging.},
}
@article {pmid40100630,
year = {2025},
author = {Feng, W and Wan, X and Zhang, Y and Quensen, J and Williams, TA and Thompson, M and Streeter, M and Zhang, Y and Jiao, S and Wei, G and Zhu, Y and Gu, J and Tiedje, JM and Qian, X},
title = {Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {12},
pages = {e2424463122},
doi = {10.1073/pnas.2424463122},
pmid = {40100630},
issn = {1091-6490},
mesh = {*Bacteria/genetics/metabolism/classification ; *Phylogeny ; *Soil Microbiology ; Microbiota/genetics ; Adaptation, Physiological/genetics ; Genome, Bacterial ; Evolution, Molecular ; Biological Evolution ; },
abstract = {The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.},
}
@article {pmid40099901,
year = {2025},
author = {Lysenko, V and Machushynets, NV and van Dam, JL and Sterk, FAC and Speer, A and Ram, AFJ and Slingerland, CJ and Van Wezel, GP and Martin, NI},
title = {Total Synthesis, Structure Elucidation, and Bioactivity Evaluation of the Cyclic Lipopeptide Natural Product Paenilipoheptin A.},
journal = {Organic letters},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.orglett.5c00232},
pmid = {40099901},
issn = {1523-7052},
abstract = {In this study, we further investigated the structure of the recently reported cyclic lipopeptide natural product paenilipoheptin A. Here, we disclose the first total synthesis of the compound, allowing for its complete structural assignment. The route developed employs automated SPPS, providing access to the compound in quantities suitable for antibacterial and antifungal testing. These studies unequivocally establish the stereochemical framework of paenilipoheptin A and further reveal that the compound possesses moderate activity against Gram-positive bacteria.},
}
@article {pmid40099871,
year = {2025},
author = {Bittleston, L and Gilbert, J and Klassen, J and Mackelprang, R and Mandel, MJ and Newton, RJ and Paudel, A and Rodriguez-Verdugo, A and Shade, A and Wilhelm, RC and Zhang, Y},
title = {Embracing the systems complexity of microbial ecology and evolution: call for papers.},
journal = {mSystems},
volume = {10},
number = {3},
pages = {e0009125},
doi = {10.1128/msystems.00091-25},
pmid = {40099871},
issn = {2379-5077},
}
@article {pmid40099188,
year = {2025},
author = {Silverio, MP and Schultz, J and Parise, MTD and Parise, D and Viana, MVC and Nogueira, W and Ramos, RTJ and Góes-Neto, A and Azevedo, VAC and Brenig, B and Bonelli, RR and Rosado, AS},
title = {Genomic and phenotypic insight into antimicrobial resistance of Pseudomonas fluorescens from King George Island, Antarctica.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1535420},
pmid = {40099188},
issn = {1664-302X},
abstract = {The genus Pseudomonas includes metabolically versatile microorganisms occupying diverse niches, from environmental habitats to plant pathogens, and has clinically significant strains. For this reason, Pseudomonas spp. might act as a reservoir of antimicrobial resistance genes, which have been detected even in isolated environments. The aim of this study was to report the antimicrobial susceptibility profile of 25 Pseudomonas fluorescens isolates from soil samples collected on King George Island (Antarctic Peninsula), and to select non-clonal isolates with unusual phenotypes for whole genome sequencing (WGS). Six classes of antimicrobials were assessed with disk diffusion and colistin with minimum inhibitory concentration (MIC) by broth microdilution. In order to confirm the discrepant phenotypes, MIC by agar dilution was performed for the beta-lactams aztreonam, ceftazidime, cefepime and the aminoglycoside neomycin. The genus Pseudomonas was confirmed by matrix-assisted laser desorption/ionization - time of flight (MALDI-TOF) and the clonal relationships were examined using repetitive extragenic palindromic polymerase chain reaction (BOX-PCR), from which 14 strains were selected for WGS. Antimicrobial susceptibility testing revealed that all strains were susceptible to neomycin and exhibited varying degrees of intermediate or full resistance to aztreonam and colistin. Additionally, 11 strains demonstrated intermediate resistance to ceftazidime, and six were resistant to cefepime. The genomic analysis identified various efflux pumps, predominantly from the ABC transporter and resistance-nodulation-division families. Resistance genes were detected against eight classes of antimicrobials, listed by prevalence: beta-lactams, tetracyclines, polymyxins, aminoglycosides, fosmidomycin, fosfomycin, quinolones, and chloramphenicol. Genes associated with heavy-metal resistance, prophages, and adaptations to extreme environments were also investigated. One notable isolate exhibited not only the highest number of pathogenicity and resistance islands, but also presented a carbapenemase-encoding gene (bla PFM-2) in its genome. Overall, one plasmid was identified in a distinct isolate, which did not exhibit antimicrobial resistance determinants. The genotypic and phenotypic findings are consistent, suggesting that efflux pumps play a critical role in antimicrobial extrusion. This study offers valuable insight into the evolution of antimicrobial resistance in P. fluorescens, particularly in extreme environments, such as Antarctica. By exploring the antimicrobial resistance mechanisms in P. fluorescens, the study sheds light on how isolated ecosystems drive the natural evolution of resistance genes.},
}
@article {pmid40098226,
year = {2025},
author = {Frühe, L and Klein, SG and Angulo-Preckler, C and Martynova, A and Alamoudi, T and García, JVA and Arossa, S and Breavington, J and Frappi, S and Laiolo, E and Lim, KK and Parry, AJ and Re, E and Rosas, DER and Rodrigue, M and Steckbauer, A and Pieribone, VA and Qurban, MA and Duarte, CM},
title = {Particle-Associated Bacterioplankton Communities Across the Red Sea.},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70075},
doi = {10.1111/1462-2920.70075},
pmid = {40098226},
issn = {1462-2920},
support = {//National Center of Wildlife/ ; //King Abdullah University of Science and Technology/ ; },
mesh = {Indian Ocean ; *Seawater/microbiology ; *Plankton/genetics/classification ; *Bacteria/genetics/classification/isolation &amp; purification ; Ecosystem ; Microbiota/genetics ; Saudi Arabia ; Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Pelagic particle-associated bacterioplankton play crucial roles in marine ecosystems, influencing biogeochemical cycling and ecosystem functioning. However, their diversity, composition, and dynamics remain poorly understood, particularly in unique environments such as the Red Sea. In this study, we employed eDNA metabarcoding to comprehensively characterise bacterioplankton communities associated with pelagic particles in a three-dimensional assessment spanning depths from the surface to a depth of 2300 m along the full length of the eastern Red Sea within the exclusive economic zone of the Kingdom of Saudi Arabia. Our results reveal a diverse assemblage of taxa, with Pseudomonadota, Cyanobacteriota, and Planctomycetota being the dominant phyla. We identified pronounced spatial variability in community composition among five major Red Sea geographical regions, with a third of all amplicon sequence variants being unique to the Southern Red Sea in contrast to a relatively homogenous distribution along the water column depth gradient. Our findings contribute to a deeper understanding of microbial ecology in the Red Sea and provide valuable insights into the factors governing pelagic particle-associated bacterioplankton communities in this basin.},
}
@article {pmid40097839,
year = {2025},
author = {Blanco, S and Viso, R and Borrego-Ramos, M and López-Flores, R and Mota-Echeandía, D and Tierra, M and Herrero, J and C Castañeda, },
title = {The Ecology of Benthic Diatom Assemblages in Saline Wetlands of the Ebro Basin, NE Spain.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {16},
pmid = {40097839},
issn = {1432-184X},
support = {TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; TED2021-130303B-I00//MCIN/AEI/ ; },
mesh = {*Diatoms/classification/physiology/growth &amp; development ; *Wetlands ; Spain ; *Biodiversity ; Salinity ; Ecosystem ; Electric Conductivity ; },
abstract = {Benthic diatoms play a crucial role in aquatic ecosystems as indicators of environmental conditions and contributors to primary productivity. This study explores the ecology of benthic diatom assemblages in saline wetlands in NE Spain, focusing on the relationships between community parameters, species distributions, and environmental factors, particularly conductivity. Samples were collected from several wetlands representing a range of conductivity and trophic state. A total of 25 diatom taxa were identified, with assemblages dominated by halophilous species. Non-metric multidimensional scaling analysis revealed electrical conductivity (EC) as a primary factor shaping diatom communities, with nutrient levels as a secondary influence. Species exhibited varying responses to the EC gradient, with some showing overlapping niches and others clearly separated. The study found strong correlations between species abundance, occupancy, and their contribution to dissimilarity between sampling sites. More abundant and widespread species were key drivers of community structure and differentiation. Additionally, a significant relationship was observed between taxa occurrence and niche breadth, measured as EC tolerance. Species with broader tolerances tended to have higher occupancy rates, supporting ecological theories about generalist strategies in variable environments. Contrary to some previous research, rare taxa (3-5% in relative abundance) had a negligible effect on assemblage segregation among habitats. The findings suggest that both environmental filtering based on EC tolerance and species' inherent characteristics play important roles in shaping diatom community composition across these saline wetlands. This study contributes to our understanding of diatom ecology in saline habitats and highlights the importance of considering both local abundance and environmental tolerance in ecological studies of these communities. The insights gained can inform more accurate ecological models and improve our understanding of species distribution and community dynamics in saline aquatic ecosystems.},
}
@article {pmid40097820,
year = {2025},
author = {Blanchette, RA and Rajtar, NN and Lochridge, AG and Held, BW},
title = {Intercontinental movement of exotic fungi on decorative wood used in aquatic and terrestrial aquariums.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9142},
pmid = {40097820},
issn = {2045-2322},
support = {no number//Minnesota Invasive Terrestrial Plants and Pests Center, University of Minnesota/ ; },
mesh = {*Wood/microbiology ; *Fungi/classification/isolation &amp; purification ; Introduced Species ; United States ; Asia ; Phylogeny ; },
abstract = {The intercontinental movement of fungi or fungus-like organisms brings nonnative species into areas where they may become invasive pathogens of trees and other plants. In the past century, many examples such as Dutch elm disease, sudden oak death, laurel wilt, and others have resulted in large economic losses and ecological disasters. Although various safeguards to prevent the transport of potential pathogens have been in effect, new avenues of introduction have occurred causing new disease outbreaks. This study examined fungi in wood shipped from Asia that is used for decorative purposes in aquatic and terrestrial aquariums. From 44 imported wood samples, 202 cultures representing 123 different fungal taxa were obtained and identified using molecular methods. These included 31 species not previously reported in the United States, 21 potential plant pathogens, 37 species of wood decay fungi and 24 taxa with a 97% sequence match or less to known isolates suggesting these are unknown species. The results demonstrate that wood used for decorative purposes in aquariums harbor large numbers of diverse fungi that remain viable during shipping and storage. These fungi are currently being imported into areas where they are not native, and they may pose serious biosecurity threats to the United States and other countries around the world.},
}
@article {pmid40097298,
year = {2025},
author = {Morin, C and Alfahl, Z},
title = {A Systematic Review on the Utility of Wastewater Surveillance for Monitoring Yellow Fever Virus and Other Arboviruses.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf066},
pmid = {40097298},
issn = {1365-2672},
abstract = {AIMS: This review aims to examine wastewater surveillance for the detection of Yellow Fever Virus (YFV) and related arboviruses, focusing on concentration and extraction methodology, viral decay kinetics, and quantification techniques.<br><br>METHODS: A literature search was conducted across 5 databases: PubMed, Science Direct, Web of Science, Embase, and Google Scholar following the PRISMA guidelines. Studies included were original scientific articles published between April 2014 and April 2024. Human research studies investigating wastewater surveillance and YFV or other arboviruses/flaviviruses were assessed.<br><br>RESULTS: 17 studies were included in this review. YFV was not detected in population-based wastewater samples; however, successful detection of similar viruses suggest potential for YFV monitoring with wastewater surveillance. YFV-spiked wastewater studies reveal similar concentration efficiency and decay rates between arboviruses. Effective concentration methods for YFV likely include centrifugation ultrafiltration and solid pellet extraction. YFV and arboviruses decay faster at higher temperatures, though YFV remains detectable for several days at these temperatures.<br><br>CONCLUSIONS: Wastewater surveillance presents a promising approach for monitoring YFV and other arboviruses. However, further research is needed to overcome existing limitations and enhance its effectiveness.},
}
@article {pmid40092580,
year = {2025},
author = {Li, G and Wang, Z and Wu, C and Wang, D and Han, I and Lee, J and Kaeli, DR and Dy, JG and Weinberger, KQ and Gu, AZ},
title = {Towards high-accuracy bacterial taxonomy identification using phenotypic single-cell Raman spectroscopy data.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf015},
pmid = {40092580},
issn = {2730-6151},
abstract = {Single-cell Raman Spectroscopy (SCRS) emerges as a promising tool for single-cell phenotyping in environmental ecological studies, offering non-intrusive, high-resolution, and high-throughput capabilities. In this study, we obtained a large and the first comprehensive SCRS dataset that captured phenotypic variations with cell growth status for 36 microbial strains, and we compared and optimized analysis techniques and classifiers for SCRS-based taxonomy identification. First, we benchmarked five dimensionality reduction (DR) methods, 10 classifiers, and the impact of cell growth variances using a SCRS dataset with both taxonomy and cellular growth stage labels. Unsupervised DR methods and non-neural network classifiers are recommended for at a balance between accuracy and time efficiency, achieved up to 96.1% taxonomy classification accuracy. Second, accuracy variances caused by cellular growth variance (<2.9% difference) was found less than the influence from model selection (up to 41.4% difference). Remarkably, simultaneous high accuracy in growth stage classification (93.3%) and taxonomy classification (94%) were achievable using an innovative two-step classifier model. Third, this study is the first to successfully apply models trained on pure culture SCRS data to achieve taxonomic identification of microbes in environmental samples at an accuracy of 79%, and with validation via Raman-FISH (fluorescence in situ hybridization). This study paves the groundwork for standardizing SCRS-based biotechnologies in single-cell phenotyping and taxonomic classification beyond laboratory pure culture to real environmental microorganisms and promises advances in SCRS applications for elucidating organismal functions, ecological adaptability, and environmental interactions.},
}
@article {pmid40090302,
year = {2025},
author = {Wang, J and Hu, Y and An, L and Wang, J and Wu, F and Gu, J and Wang, X and Tiedje, JM},
title = {An efficient strategy for bdd electrode drive electro-catalysis triggering active species on lincomycin and antibiotic resistance genes removal: Electron transfer based on calculation modeling.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {137915},
doi = {10.1016/j.jhazmat.2025.137915},
pmid = {40090302},
issn = {1873-3336},
abstract = {Identifying the degradation pathway and the final by-products is essential, as their ecological risks are pertinent to the advancement of this technology and its potential application in practical environmental pollution treatment. Elucidating the reaction mechanisms of the degradation system represents the most effective strategy for controlling this process. This study thoroughly revealed that indirect oxidation predominates throughout the electrochemical system, while direct oxidation serves a significant auxiliary role under the synergistic influence. It elucidates the critical importance of electron transfer behavior at the electrode surface for pollutant degradation and unveil potential mechanisms underlying primary degradation reactions via integrating charge density differences and Bader atomic charge analysis. In situ electrochemical infrared spectroscopy (In situ EC-FTIR) and density functional calculation (DFT) were used to analyze the final by-product generation path. It further elucidated the correlation between antibiotic resistance gene (ARGs) and binding strength among base pairs. The oxidative stress process of antibiotic resistance bacteria (ARB) was explained in detail. To comprehensively assess the impact of electrochemical treatment on environmental microbial communities, combined horizontal gene transfer (HGT) experiments were conducted to confirm that electrolytically treated wastewater does not induce ecological stress effects on microorganisms. Finally, a small cyclic electrochemical system was employed to evaluate both ecological impacts and economic benefits associated with wastewater treatment, thereby providing a novel theoretical framework for this domain.},
}
@article {pmid40087979,
year = {2025},
author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A},
title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14099},
doi = {10.1111/1755-0998.14099},
pmid = {40087979},
issn = {1755-0998},
support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; },
abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.},
}
@article {pmid40086056,
year = {2025},
author = {Liang, L and Dang, B and Ouyang, X and Zhao, X and Huang, Y and Lin, Y and Cheng, X and Xie, G and Lin, J and Mi, P and Ye, Z and Guleng, B and Cheng, SC},
title = {Dietary succinate supplementation alleviates DSS-induced colitis via the IL-4Rα/Hif-1α Axis.},
journal = {International immunopharmacology},
volume = {152},
number = {},
pages = {114408},
doi = {10.1016/j.intimp.2025.114408},
pmid = {40086056},
issn = {1878-1705},
abstract = {Inflammatory bowel disease (IBD) remains a pressing global health challenge, necessitating novel therapeutic strategies. Succinate, a metabolite known for its role in type 2 immunity and tuft cell activation in the small intestine, presents its potential in IBD management. However, its impact on colonic inflammation has not been explored. Here, we demonstrate that succinate administration induces a type 2 immune response, significantly alleviating dextran sulfate sodium (DSS)-induced colonic inflammation. Succinate enhances antibacterial capacity, reduces intestinal permeability, and reshapes the colonic cytokine milieu. Mechanistically, succinate promotes myeloid cell expansion in peripheral blood, mesenteric lymph nodes, and the colonic lamina propria. The protective effects of succinate were abolished in Ccr2[-/-] mice, confirming the role of monocyte recruitment, but persisted in Rag1[-/-] mice, indicating independence from adaptive immunity. Adoptive transfer of monocytes from succinate-treated donors mitigated intestinal inflammation in recipient mice. Transcriptomic analysis revealed heightened expression of Il1b and Il6, and higher lactate production in monocytes upon lipopolysaccharide (LPS) stimulation, highlighting a reprogrammed pro-inflammatory trained immunity phenotype. Finally, we identify the IL-4Rα/Hif-1α axis is critical for succinate-mediated protection. These findings reveal the ability of succinate to reprogram monocytes into protective intestinal macrophages via induction of type 2 response, restoring homeostasis through enhanced barrier function and immune modulation. Our study positions thus uncover succinate as a promising therapeutic candidate for IBD.},
}
@article {pmid40085655,
year = {2025},
author = {Muratore, D and Gilbert, NE and LeCleir, GR and Wilhelm, SW and Weitz, JS},
title = {Diel partitioning in microbial phosphorus acquisition in the Sargasso Sea.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {11},
pages = {e2410268122},
doi = {10.1073/pnas.2410268122},
pmid = {40085655},
issn = {1091-6490},
support = {OCE-1829641//National Science Foundation (NSF)/ ; OCE-1829636//National Science Foundation (NSF)/ ; 721231//Simons Foundation (SF)/ ; },
mesh = {*Phosphorus/metabolism ; *Phytoplankton/metabolism ; Ecosystem ; Cyanobacteria/metabolism/genetics ; Seawater/microbiology ; Bacteria/metabolism/genetics ; Oceans and Seas ; Nitrogen/metabolism ; },
abstract = {The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. Microbial competition for these scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism that can structure uptake of limiting nutrients and facilitate coexistence of diverse microbes in open ocean ecosystems.},
}
@article {pmid40085287,
year = {2025},
author = {Micciulla, JL and Baubin, C and Fierer, N},
title = {Effects of Geosmin on the Behavior of Soil Protists.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {14},
pmid = {40085287},
issn = {1432-184X},
support = {2126106//National Science Foundation/ ; 2126106//National Science Foundation/ ; 2126106//National Science Foundation/ ; },
mesh = {*Acanthamoeba castellanii/physiology ; *Soil Microbiology ; *Naphthols/metabolism ; Ciliophora/physiology ; Soil/chemistry/parasitology ; Cercozoa/physiology ; },
abstract = {Geosmin is a volatile organic compound (VOC) produced by a range of different soil microorganisms, and is most commonly recognized for its characteristic "earthy" scent evident after rainfall. Though it remains unclear why microorganisms produce geosmin, we know that exposure to geosmin can influence behaviors across a wide range of organisms, serving as both an attractant and a repellant, but geosmin effects on soil protists remain largely unstudied. We investigated how soil protists respond to geosmin exposures, focusing on representatives of three morphological groups of protists, Colpoda sp. (ciliate), Cercomonas sp. (flagellate), and Acanthamoeba castellanii (naked amoeba), testing the hypothesis that geosmin production by bacteria influences soil protist behavior. We conducted experiments to evaluate protist excystment (waking up) and predation responses to geosmin-producing (Streptomyces coelicolor M145) and non-producing (S. coelicolor J3003) bacteria, as well as synthetic geosmin. All three protists excysted at higher rates when exposed to geosmin-producing bacteria or synthetic geosmin, while no significant excystment occurred with the non-producing strains or in the absence of synthetic geosmin. Protist feeding preferences were also affected, with two of the three protists (Cercomonas sp. and A. castellanii) less likely to predate geosmin-producing versus non-producing bacterial strains. Our findings suggest that soil protists can detect geosmin as a signal indicating favorable soil conditions and geosmin production by bacteria may serve as a deterrent to predation by protists. More generally, our results highlight the ecological significance of geosmin in the soil food web and its role in mediating bacteria-protist interactions.},
}
@article {pmid40085262,
year = {2025},
author = {Castelli, M and Petroni, G},
title = {An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {15},
pmid = {40085262},
issn = {1432-184X},
mesh = {*Phylogeny ; Animals ; *Alphaproteobacteria/genetics/classification/isolation &amp; purification ; Biological Evolution ; Biodiversity ; },
abstract = {The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this is similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales and Chlamydiae). Here, we provide a detailed and comprehensive account on the current knowledge on the Holosporales. First, acknowledging the up-to-date phylogenetic reconstructions and recent nomenclatural proposals, we reevaluate their taxonomy, thus re-ranking them as a suborder, i.e. Holosporineae, within the order Rhodospirillales. Then, we examine the phylogenetic diversity of the Holosporineae, presenting the 20 described genera and many yet undescribed sub-lineages, as well as the variety of the respective environments of provenance and hosts, which belong to several different eukaryotic supergroups. Noteworthy representatives of the Holosporineae are the infectious intranuclear Holospora, the host manipulator 'Caedimonas', and the farmed shrimp pathogen 'Candidatus Hepatobacter'. Next, we put these bacteria in the broad context of the whole Holosporineae, by comparing with the available data on the least studied representatives, including genome sequences. Accordingly, we reason on the most probable evolutionary trajectories for host interactions, host specificity, and emergence of potential pathogens in aquaculture and possibly humans, as well as on future research directions to investigate those many open points on the Holosporineae.},
}
@article {pmid40084873,
year = {2025},
author = {Soh, M and Er, S and Low, A and Jaafar, Z and de Boucher, R and Seedorf, H},
title = {Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0198924},
doi = {10.1128/spectrum.01989-24},
pmid = {40084873},
issn = {2165-0497},
abstract = {UNLABELLED: The microbiota composition of healthy farmed fishes remains poorly characterized for many species. This study explores the influence of the external environment and innate factors that may shape the gut microbiota of farmed Asian seabass, Lates calcarifer. The α-diversity based on Shannon, Simpson, and Chao1 indices was lower for fishes reared in sea cages and tanks than for fishes that experienced a transfer from sea cages to tanks. Longitudinal analyses of gut segments revealed no significant differences in alpha diversity between segments within the same containment type, except for the Chao1 index between the stomach and pyloric cecum of sea-caged fishes. β-diversity analysis using weighted UniFrac distance and Bray-Curtis dissimilarity demonstrated that fish reared in the same containment type shared similar microbial communities. PERMANOVA tests confirmed that containment type, farm, and batch significantly influenced these distances. Containment type accounted for 10.4% of the observed diversity, farm for 29.8%, and batch for 10.7%. Genera comprising potential pathogens such as Aeromonas, Flavobacterium, and Vibrio were differentially abundant along the guts of fish from different containment types and particularly increased in tanks. Microbiota changes were observed with host age and gut segment, with differentially abundant microbial genera identified along the gut and as the seabass grew. Comparing the hindgut microbiota of Asian seabass to other species of farmed fishes revealed host-specific clustering as indicated by PERMANOVA. Overall, these findings underscore the significance of containment conditions on the gut microbiota of Asian seabass, with broad implications for aquaculture practices.<br><br>IMPORTANCE: Understanding the microbiota composition of healthy farmed fishes is crucial for optimizing aquaculture practices. This study highlights the significant influence of containment conditions on the gut microbiota of farmed Asian seabass (Lates calcarifer). By demonstrating that gut microbiota diversity and community composition are shaped by containment type, farm location, and batch, the research provides valuable insights into how external environmental factors and innate host factors interact to influence fish health. The findings, particularly the differential abundance of potential pathogens in various containment types, underscore the need for tailored management strategies in aquaculture. This research not only advances our knowledge of fish microbiota but also has broad implications for improving the sustainability and productivity of aquaculture practices.},
}
@article {pmid40084850,
year = {2025},
author = {Machushynets, NV and Lysenko, V and Du, C and Slingerland, CJ and Elsayed, SS and Liles, MR and Martin, NI and van Wezel, GP},
title = {Exploring the Chemical Space of Paenibacillus NRPs and Discovery of Paenilipoheptin B.},
journal = {Organic letters},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.orglett.5c00231},
pmid = {40084850},
issn = {1523-7052},
abstract = {A combination of genomic and metabolomic analyses paired with molecular networking was applied to a collection of Paenibacillus spp. to identify the producers of a little-studied class of lipopeptides known as paenilipoheptins. Mass spectrometry and NMR spectroscopy allowed revision of the structure of previously reported paenilipoheptin A and elucidation of the structure of novel paenilipoheptin B.},
}
@article {pmid40083115,
year = {2025},
author = {Dodds, IL and Watts, EC and Schuster, M and Buscaill, P and Tumas, Y and Holton, NJ and Song, S and Stuttmann, J and Joosten, MHAJ and Bozkurt, T and van der Hoorn, RAL},
title = {Immunity gene silencing increases transient protein expression in Nicotiana benthamiana.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70005},
pmid = {40083115},
issn = {1467-7652},
support = {BB/R017913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S003193/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DDT00060/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DDT00230/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101019324/ERC_/European Research Council/International ; },
}
@article {pmid40082592,
year = {2025},
author = {Thomas, PW and Kothamasi, D},
title = {Hunting dog behaviour is a key driver impacting harvest quantity and quality of truffles.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8662},
pmid = {40082592},
issn = {2045-2322},
mesh = {Animals ; *Behavior, Animal/physiology ; *Ascomycota/physiology ; Dogs ; Humans ; Seasons ; },
abstract = {Truffles are an iconic food that have long held high regard. Here we explore the seasonality and eco-physiological interactions affecting truffle quality and quantity across time and space. Collaborating with professional truffle hunters working eight different locations, detailed metrics of 3180 recovered truffles from 236 hunt events and spanning a full fruiting period, were recorded. Contrary to expectations, truffle weight showed no correlation with climate variables, suggesting a limited influence of environmental factors such as temperature and precipitation on truffle size. We also found that truffle maturity and damage from mycophagy were strongly linked, with deeper truffles being more mature but also more susceptible to damage. Finally, we observe that scent-dog behaviour significantly impacts the quantity and quality of recovered truffles, and we address the necessity of considering this in truffle ecophysiology studies. Alongside advances in our biological understanding, we make recommendations of how training methods can be improved to lead to greater detection and quality targeting with immediate socioeconomic impact. These findings highlight the complex interplay between truffle physiology, environmental factors, and human and animal behaviours, emphasizing the need for further considered research to enhance our understanding of truffle biology and to improve truffle cultivation practices.},
}
@article {pmid40080573,
year = {2025},
author = {Shumilova, O and Sukhodolov, A and Osadcha, N and Oreshchenko, A and Constantinescu, G and Afanasyev, S and Koken, M and Osadchyi, V and Rhoads, B and Tockner, K and Monaghan, MT and Schröder, B and Nabyvanets, J and Wolter, C and Lietytska, O and van de Koppel, J and Magas, N and Jähnig, SC and Lakisova, V and Trokhymenko, G and Venohr, M and Komorin, V and Stepanenko, S and Khilchevskyi, V and Domisch, S and Blettler, M and Gleick, P and De Meester, L and Grossart, HP},
title = {Environmental effects of the Kakhovka Dam destruction by warfare in Ukraine.},
journal = {Science (New York, N.Y.)},
volume = {387},
number = {6739},
pages = {1181-1186},
doi = {10.1126/science.adn8655},
pmid = {40080573},
issn = {1095-9203},
mesh = {Ukraine ; *Ecosystem ; Geologic Sediments ; Warfare ; Water Supply ; },
abstract = {The use of water as a weapon in highly industrialized areas in the Russo-Ukrainian war has resulted in catastrophic economic and environmental damages. We analyze environmental effects caused by the military destruction of the Kakhovka Dam. We link field, remote sensing, and modeling data to demarcate the disaster's spatial-temporal scales and outline trends in reestablishment of damaged ecosystems. Although media attention has focused on the immediate impacts of flooding on society, politics, and the economy, our results show that toxic contamination within newly exposed sediments of the former reservoir bed poses a largely overlooked long-term threat to freshwater, estuarine, and marine ecosystems. The continued use of water as a weapon may lead to even greater risks for people and the environment.},
}
@article {pmid40080167,
year = {2025},
author = {Kouakou, AK and Collart, P and Perron, T and Kolo, Y and Gay, F and Brauman, A and Brunel, C},
title = {Soil Microbial Recovery to the Rubber Tree Replanting Process in Ivory Coast.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {13},
pmid = {40080167},
issn = {1432-184X},
support = {(PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; (PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; (PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; (PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; ARTS, 2019//IRD PhD Grant Program/ ; },
mesh = {*Soil Microbiology ; *Hevea/microbiology/growth &amp; development ; Cote d'Ivoire ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Agriculture/methods ; RNA, Ribosomal, 18S/genetics ; },
abstract = {The resistance and resilience of soil microbial communities to an environmental disturbance are poorly documented, due to the lack on onfield diachronic experiments, limiting our ability to design adapted agroecological practices. This is especially true in rubber plantations, one of the most planted tree in tropical areas. We aimed to understand (1) how soil disturbances occurring during the rubber replanting phase affect the soil microbiome, (2) how agricultural practices combining legumes cover crops and tree logging residues shape community resilience and (3) how microbial responses vary across different edaphic contexts. In two plantations with distinct soil properties in Ivory Coast, soil microbial communities were surveyed every 6 months for 24 months after soil perturbation. Community structure, functioning and networks were described based on a 16S/18S rRNA gene investigation. Prokaryotes were generally more resistant to soil perturbation than microeukaryote communities. Prokaryotic resilience dynamics were faster than those of microeukaryotes, the latter being deeply modulated by cover treatments. These specific dynamics were exacerbated in the sandy site. Co-occurrence network modelling provided useful insights into microbial resilience trajectories. We argue that this tool should be more widely used to describe microbial community dynamics. Practices involving a combination of logging residues and legume cover crops have shown beneficial effects on the community resilience in the sandy site and appears as promising agroecological practices. However, the major influence of soil texture warns of the need to consider pedological context when designing pertinent agroecological practices.},
}
@article {pmid40078544,
year = {2025},
author = {Acciardo, AS and Arnet, M and Gholizadeh Doonechaly, N and Ceccato, A and Rodriguez, P and Tran, HNH and Wenning, Q and Zimmerman, E and Hertrich, M and Brixel, B and Magnabosco, C},
title = {Spatial and temporal groundwater biogeochemical variability help inform subsurface connectivity within a high-altitude Alpine catchment (Riale di Ronco, Switzerland).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1522714},
pmid = {40078544},
issn = {1664-302X},
abstract = {Accessing the deep terrestrial subsurface (greater than 1 km below the surface) presents significant practical challenges, leaving these ecosystems largely uncharacterized despite their extensive presence beneath Earth's landmasses. In this study, we introduce the BedrettoLab Deep Life Observatory (DELOS), a new underground laboratory to study the biogeochemical diversity of groundwater in a high-altitude Alpine catchment tens of meters to 1.6 km underground. Biogeochemical monitoring of DELOS over spatial and temporal scales highlight three dominant ecotypes throughout DELOS: (1) Shallow groundwater with low electrical conductivity enriched in Leptospirillia; (2) High-inflow fault zones enriched in ultra-small bacteria and archaea; (3) Bicarbonate-enriched waters that are enriched in Candidatus Kryptonia and Spirochaetota. Despite a consistent lithology throughout DELOS, groundwater from fractures that are spatially near each other are not always represented by the same ecotype and can be more similar to groundwater emitted from fractures thousands of meters away. Despite this heterogeneity, the biological and hydrochemical compositions of the groundwater of individual fractures remained relatively stable throughout the course of a 1-year monitoring period. An exception to this trend occurred after a series of seismic events near one groundwater-bearing fracture. Here, the microbial community and hydrochemical composition of the groundwater changed after the seismic events but returned to the site's "baseline" composition within 3 weeks. Taken together, these findings provide new insights into the spatial and temporal heterogeneity of deep subsurface ecosystems and the subsurface connectivity of an Alpine subsurface environment.},
}
@article {pmid40077554,
year = {2025},
author = {Smirani, N and Bouazizi, S and Bettaieb, E and Torkhani, R and Hamdi, M},
title = {Effect of Environmentally Friendly Betalain Extraction Methods on Antioxidant Compounds of Tunisian Opuntia stricta Fruit.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/foods14050851},
pmid = {40077554},
issn = {2304-8158},
abstract = {This study focuses on the extraction of betalain compounds from Opuntia stricta as a natural alternative to synthetic colorants and sustainable environmentally friendly technology solutions. Non-conventional extraction technologies including microwave (MW) and ultrasound (US) were used alone or in combination. The extraction process was conducted for both undried Opuntia stricta (OS) and dried Opuntia stricta (DOS) plant material at two distinct drying temperatures, 40 °C and 60 °C, to assess the stability of betalain molecules. The colorant's potential was evaluated by determining the betalain content, total phenolic content, and antioxidant activity. The MW (2 min) and MW (2 min) + US (10 min) extraction processes yielded the greatest betalain content in OS fresh weight (FW), with 48.54 ± 0.29 mg/100 g FW and 51.01 ± 0.16 mg/100 g FW, respectively. Furthermore, the results showed a considerable drop in betalain content when the plant material was dried at 40 °C and 60 °C, with reduction rates of 53.75% and 24.82%, respectively, compared to the betalain content before the drying process. The LC-DAD-ESI-MS analysis supported this result, revealing the presence of 17-decarboxy betanin, 17-decarboxy neobetanin, and Cyclo-dopa5-O-βglucoside in DOS at 40 °C. This study highlights the potential future in the sustainable green extraction of betalain compounds with less heat degradation to offer a stable natural colorant.},
}
@article {pmid40072629,
year = {2025},
author = {Dyczko, D and Szymański, DM and Szymański, D and Kupczak, M and Kolenda, K},
title = {First European record of Rickettsia bellii in Amblyomma rotundatum from Rhinella marina imported to Poland.},
journal = {Experimental &amp; applied acarology},
volume = {94},
number = {3},
pages = {43},
pmid = {40072629},
issn = {1572-9702},
mesh = {Animals ; Poland ; *Rickettsia/isolation &amp; purification ; Female ; *Amblyomma/microbiology/growth &amp; development/physiology ; Tick Infestations/veterinary/parasitology ; },
abstract = {This study reports on the first documented case of Amblyomma rotundatum ticks, a species typically found in the Americas, parasitising an imported toad in Poland. A total of 12 ticks were collected from a single Rhinella marina toad. These ticks were identified as female specimens of A. rotundatum using an examination of morphological characteristics and a molecular analysis. Polymerase chain reaction testing revealed that 75.0% (9/12) of these females were positive for Rickettsia spp. Sequencing of positive samples confirmed the presence of R. bellii. However, no DNA evidence of Borrelia spp. and Anaplasma spp. was detected in the tested ticks. Nevertheless, given the limited number of tick specimens collected from a single host, further research is required to elucidate the pathogen profile of a tick species. This finding represents the second European report of A. rotundatum associated with exported animals, underscoring the importance of vigilance in monitoring the potential spread of ticks and tick-borne pathogens through the global wildlife trade.},
}
@article {pmid40072582,
year = {2025},
author = {Barjau-Aguilar, M and Reyes-Hernández, AMJ and Merino-Ibarra, M and Vilaclara, G and Ramírez-Zierold, JA and Alcántara-Hernández, RJ},
title = {Diversity and Structure of the Prokaryotic Community in Tropical Monomictic Reservoir.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {12},
pmid = {40072582},
issn = {1432-184X},
support = {CVU: 747276//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CVU: 1249011//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CF-2023-G-155//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CVU: 41120//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; UNAM, PAPIIT-IN207702//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; UNAM-PAPIIT IN217622//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; },
mesh = {*Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Archaea/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; *Tropical Climate ; Fresh Water/microbiology/chemistry ; Microbiota ; Nitrogen/metabolism ; Phosphorus/metabolism/analysis ; Phylogeny ; Water Microbiology ; Eutrophication ; },
abstract = {Bacteria and Archaea are microorganisms that play key roles in the biogeochemical transformations that control water quality in freshwater ecosystems, such as in reservoirs. In this study, we characterize the prokaryotic community of a high-relevance tropical eutrophic reservoir using a 16S rRNA gene survey during a low-water level fluctuation period mainly used for storage, associating the distribution of these microorganisms with the hydrogeochemical conditions of the water column. Our findings revealed that diversity and structure of the prokaryotic community exhibited spatio-temporal variations driven by the annual circulation-stratification hydrodynamic cycle and are significantly correlated with the concentrations of dissolved oxygen (DO), soluble reactive phosphorus (SRP), and dissolved inorganic nitrogen (DIN). During the heterotrophic circulation, the breakdown of thermal gradient leads to a homogeneous distribution of the nutrients, where the presence of DO promotes the dominance of aerobic and facultative heterotrophic bacteria such as Bacteroidota, Actinobacteriota, and Verrucomicrobiota. Also, the autotrophic circulation was characterized by an increase of DO and NO3[-] concentrations, with abundant Cyanobacteria. Finally, during the stratification, the presence of prokaryotes associated with the metabolism of CH4 was detected, mainly in the hypolimnion, as well as others related to sulfate reduction and nitrification. This study shows the diversity of the prokaryotic community in tropical eutrophic reservoirs, and how the continuous monitoring with metabarcoding techniques can provide critical insights for a deeper understanding of the biogeochemical dynamics and improve the water resource management in the future.},
}
@article {pmid40070274,
year = {2025},
author = {Cidan, Y and Wang, J and Wang, H and Xu, C and Zhu, Y and Khan, MK and Basang, W and Li, K},
title = {Composition and diversity of rumen mycobiota in Jiani yaks (Bos grunniens jiani): insights into microbial ecology and functions.},
journal = {Animal biotechnology},
volume = {36},
number = {1},
pages = {2476539},
doi = {10.1080/10495398.2025.2476539},
pmid = {40070274},
issn = {1532-2378},
mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; *Fungi/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Mycobiome ; },
abstract = {This study aimed to explore the diversity and functions of rumen mycobiota in 14‑ (PLf) and 15‑rib (DLf) Jiani yaks using ITS sequencing. A total of 1,079,105 and 1,086,799 filtered sequences were obtained for the PLf and DLf groups, respectively, with 491 ASVs common to both. No significant difference regarding the α‑diversity of mycobiota within the two groups was observed. While β‑diversity analysis indicated that the abundance of fifteen (15) genera in the PLf group and two (2) genera in the DLf group was found to be significantly different (p < 0.05). 16S rRNA sequencing results indicated that at the phylum level, in 14 ribs yaks Ascomycota, Basidiomycota, and Olpidiomycota, while in 15 rib yaks, Neocallimastigomycota, Mortierellomycota, and Rozellomycota were found to be significantly different (p < 0.05). At the genus level, Rhodotorula, Kluyveromyces, Comoclathris, Arthrinium, Cladophialophora, Seimatosporium, Lambertella, and Sphacelotheca in 14 rib yaks, and Orpinomyces, Ustilago, Fusarium, Aspergillus, Caecomyces, Alternaria, Trichoderma and Acremonium in 15 rib yaks were found to be significantly (p < 0.05) different. Predictive functional analysis based on ruminal fungal DNA sequences from 15‑rib yaks (DLf) demonstrated that genes involved in energy metabolism were upregulated. This study sheds novel insights into how genetic variations influence gut mycobiota in Jiani yak.},
}
@article {pmid40068413,
year = {2025},
author = {Yang, H and Cappitelli, F and Li, X},
title = {Pollution gradients shape structure and functions of stone heritage bacterial communities at global scale.},
journal = {The Science of the total environment},
volume = {971},
number = {},
pages = {179087},
doi = {10.1016/j.scitotenv.2025.179087},
pmid = {40068413},
issn = {1879-1026},
abstract = {Previous studies mainly focused on the impact of climatic conditions on stone heritage microbial communities, while ignoring a global ecological perspective of pollution on heritage microorganisms. In particular, there is a lack of detailed analysis of the impact of pollution levels on microbial metabolic function. In this study, >6000 bacterial OTUs from 17 world cultural heritage sites were considered. The microbial diversity indexes and potential functions under different pollution levels were analyzed. The results show that particulate matter pollution, such as PM2.5, has an effect on the microbial community in heritage sites comparable to that of temperature and precipitation. High concentrations of particulate matter increased bacterial richness and facilitated the introduction of unique species. Among them, phototrophic bacteria (e.g., Cyanobacteria) and some heterotrophic bacteria (e.g., Actinobacteria and Proteobacteria) formed the core of the microbial community. However, high concentrations of particulate matter reduced the complexity and stability of microbial ecological networks, favoring pollution-tolerant species. Furthermore, elevated particulate concentrations partially suppressed the expression of certain metabolic pathways, particularly genes related to denitrification (e.g., nosZ and nirS). This study reveals the long-term impact of polluted environments on the diversity and potential functions of microbial communities, providing a theoretical basis for developing sustainable strategies for cultural heritage conservation.},
}
@article {pmid40066860,
year = {2025},
author = {Defoirdt, T},
title = {Resistance to quorum sensing inhibition spreads more slowly during host infection than antibiotic resistance.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2476582},
doi = {10.1080/19490976.2025.2476582},
pmid = {40066860},
issn = {1949-0984},
mesh = {*Quorum Sensing/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Bacteria/drug effects/genetics/metabolism ; Drug Resistance, Bacterial ; Bacterial Infections/microbiology/drug therapy ; Animals ; },
abstract = {Antibiotic resistance is a rising problem and new and sustainable strategies to combat bacterial (intestinal) infections are therefore urgently needed. One promising strategy under intense investigation is the inhibition of quorum sensing, bacterial cell-to-cell communication with small molecules. A key question with respect to the application of quorum sensing inhibition is whether it will impose selective pressure for the spread of resistance. It was recently shown that resistance to quorum sensing inhibition will spread more slowly during infection of a host than resistance to traditional antibiotics.},
}
@article {pmid40065660,
year = {2025},
author = {Guislain, ALN and Nejstgaard, JC and Köhler, J and Sperfeld, E and Mischke, U and Skjelbred, B and Grossart, HP and Lyche Solheim, A and Gessner, MO and Berger, SA},
title = {Cell size explains shift in phytoplankton community structure following storm-induced changes in light and nutrients.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70043},
doi = {10.1002/ecy.70043},
pmid = {40065660},
issn = {1939-9170},
support = {731065//European Commission/ ; 871081//European Commission/ ; 01LC1501//German Federal Ministry of Education and Research (BMBF)/ ; GE 1775/2-1//German Research Foundation (DFG)/ ; 603378//the European Commission under its 7th Framework Programme/ ; SAW-2015-IGB-1//Leibniz Association/ ; K45/2017//Leibniz Association/ ; 033L041B//BMBF Infrastructure/ ; },
mesh = {*Phytoplankton/physiology ; Light ; Nutrients ; Animals ; Ecosystem ; Rain ; Lakes ; },
abstract = {Understanding the mechanisms driving community structure and dynamics is crucial in the face of escalating climate change, including increasing incidences of extreme weather. Cell size is a master trait of small organisms that is subject to a trade-off between resistance to grazing and competition for resources, and thus holds potential to explain and predict community dynamics in response to disturbances. Here, we aimed at determining whether cell size can explain shifts in phytoplankton communities following changes in nutrient and light conditions resulting from storm-induced inputs of nutrients and colored dissolved organic matter (cDOM) to deep clearwater lakes. To ensure realistic environmental conditions, we used a crossed gradient design to conduct a large-scale enclosure experiment over 6 weeks. Cell size explained phytoplankton community structure when light availability declined as a result of cDOM supply. Initially unimodal, with small-celled species accounting for up to 60% of the total community biovolume, the cell-size distribution gradually shifted toward large-celled species as light levels declined following cDOM addition. Neither nutrients nor mesozooplankton affected the shift in cell-size distribution. These results suggest a distinct competitive advantage of larger over smaller species at reduced light levels following cDOM inputs during storm events. Importantly, the clustering of species in two distinct size classes implies that interspecific size differences matter as much as cell size per se to understand community dynamics. Given that shifts in cell-size distribution have strong implications for food-web structure and biogeochemical cycles, our results point to the importance of analyzing cell-size distributions of small organisms as an essential element to forecast community and ecosystem dynamics in response to environmental change.},
}
@article {pmid40064943,
year = {2025},
author = {Roegiers, I and Gheysens, T and Minsart, M and De Clercq, P and Vanbeversluys, K and Rać, N and Stroka, G and de Croock, J and Van de Wiele, T and Dubruel, P and Arroyo, MC},
title = {GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8214},
pmid = {40064943},
issn = {2045-2322},
support = {3G062519//Fonds Wetenschappelijk Onderzoek/ ; 3G062519//Fonds Wetenschappelijk Onderzoek/ ; 1S51925N//Fonds Wetenschappelijk Onderzoek/ ; 40007505//Excellence Of Science (F.W.O.-F.R.S.-FNRS.)/ ; },
mesh = {Humans ; *Tissue Scaffolds/chemistry ; *Gelatin/chemistry ; *Intestine, Small/cytology/metabolism ; *Epithelial Cells/metabolism ; Caco-2 Cells ; *Hydrogels/chemistry ; Acrylamides/chemistry/pharmacology ; Permeability ; Biocompatible Materials/chemistry ; Cell Survival ; Coculture Techniques ; Cellular Microenvironment ; Cell Adhesion ; Intestinal Mucosa/metabolism/microbiology/cytology ; },
abstract = {Host-microbe interactions in the intestine play a significant role in health and disease. Novel scaffolds for host cells, capable of potentially supporting these intricate interactions, are necessary to improve our current systems for mimicking host-microbiota interplay in vitro/ex vivo. In this research paper, we study the application of gelatin methacrylamide (GelMA) as scaffold material for intestinal epithelial cells in terms of permeability, mechanical strength, and biocompatibility. We investigated whether the degree of substitution (DS) of GelMA influences the permeability and found that both high and low DS GelMA show sufficient permeability of biorelevant transport markers. Additionally, we researched epithelial cell adherence and viability, as well as mechanical characteristics of different concentrations of GelMA. All concentrations of hydrogel show long-term biocompatibility for the mono- and co-cultures, despite the goblet-like cells (LS174T) showing lower performance than enterocyte-like cells (Caco-2). The mechanical strength of all hydrogel concentrations was in a physiologically relevant range to be used as scaffold material for intestinal cells. Lastly, we examined the effect of the two sterilization methods, ethylene oxide (EO) and 70% ethanol followed by UVC (EtOH/UVC). We found that the impact of the two methods on the mechanical characteristics was minimal, and we did not find a significant effect between the two methods on cell viability and confluency of Caco-2 cells seeded on the GelMA hydrogels. Based on these results, we conclude that GelMA is a suitable material as a scaffold for intestinal cell types in terms of permeability, mechanical strength and biocompatibility. These findings contribute to the growing field of in vitro modeling of the gut and moves the field further to ensuring more translatable research on host-microbe interactions.},
}
@article {pmid40062895,
year = {2025},
author = {McDonald, MD and Lewis, KL and Gentry, TJ},
title = {No-tillage systems promote bacterial photosynthetic gene expression in low carbon, semi-arid surface soils.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0018425},
doi = {10.1128/aem.00184-25},
pmid = {40062895},
issn = {1098-5336},
abstract = {Managing soils in semi-arid agricultural croplands generally focuses on reducing wind erosion, increasing fertility, and storing carbon. Thus, converting conventionally tilled systems to no-tillage and cover-cropped systems are often the first steps towards a conservation management approach across the growing area of semi-arid croplands. From a soil biological perspective, introducing cover crops to semi-arid soils has been shown to alter microbial community structure, which may lead to changes in the biogeochemical pathways expressed in these soils. In this study, we examined the impact of single-species wheat cover cropping and no-tillage on microbial gene expression after 4 and 5 years of implementation. We sequenced the metatranscriptomes of three production systems with varying levels of conservation management: conventional tillage winter fallow, no-tillage winter fallow, and no-tillage with a winter wheat cover crop. Removing tillage was the biggest factor altering microbial gene expression in this study, specifically resulting in upregulation of several photosystem-associated functions. These functions were taxonomically linked to organisms that make up the early stages of biological soil crusts, which may introduce additional benefits to these semi-arid agricultural systems beyond a reduction in wind erosion. Implementing a cover crop did not clearly alter gene expression beyond the effect of tillage removal; however, it did indicate a potential to reduce fungal disease incidence in 1 year of the study. These alterations of microbial activities and selection for potentially beneficial functions should be considered and further studied to aid in maintaining sustainable croplands for our changing climate.IMPORTANCEEliminating tillage from semi-arid agricultural soils has the potential to significantly alter the activities of the soil bacterial community compared with conventionally tilled soils. A major driver of this change was the activities of biological soil crust forming organisms that can provide several environmental benefits to the soil ecosystem beyond the typically associated benefits of conservation management. Furthermore, this study revealed that the implementation of a cover crop regime on no-tillage soils does not confer a major change in the function of the organisms present. Overall, the study reported here reveals that soil management practices aimed at reducing wind erosion and improving sustainability will positively impact the function of the microbial community and suggests that future investigations into the consequences of these functional changes may provide valuable services to these agricultural ecosystems.},
}
@article {pmid40062772,
year = {2025},
author = {Connolly, JP and Kelly, L},
title = {The physical biogeography of Fusobacterium nucleatum in health and disease.},
journal = {mBio},
volume = {},
number = {},
pages = {e0298924},
doi = {10.1128/mbio.02989-24},
pmid = {40062772},
issn = {2150-7511},
abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.<br><br>IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.},
}
@article {pmid40062764,
year = {2025},
author = {Watkins, E and Lin, J and Lingohr-Smith, M and Yong, C and Tangirala, K and Collins, K},
title = {Biological, Clinical, and Sociobehavioral Factors Associated with Disproportionate Burden of Bacterial Vaginosis in the United States: A Comprehensive Literature Review.},
journal = {Journal of women's health (2002)},
volume = {},
number = {},
pages = {},
doi = {10.1089/jwh.2024.0583},
pmid = {40062764},
issn = {1931-843X},
abstract = {Background: Bacterial vaginosis (BV), a common gynecological infection characterized by reduced lactic acid-producing bacteria and increased anerobic bacteria in the vaginal microbiome, is associated with adverse health outcomes. Methods: A PubMed search for English-language articles about BV in the USA and factors contributing to disparities in BV risk, with an emphasis on the role of the vaginal microbiome, published from August 2012 to August 2022, identified 760 articles. Results: Among the 52 articles meeting the prespecified criteria, BV prevalence varied among different populations and disproportionately impacted Black women (49-51%), Hispanic ethnicity (32-43%), and women of reproductive age (30%). Differences in microbial ecology and host genetics were important factors underlying these disparities. Colonization of BV-associated bacteria was more common in women of color than in non-Hispanic White women. Other factors linked with disproportionate burden included multiple/same-sex partners, obesity, immunosuppression, and C-section birth. Conclusions: BV prevalence was multifactorial, with some populations having higher prevalence rates and distinctive microbiome profiles that may predispose them to the condition. BV treatment and recurrence prevention were challenging due to the complex interplay of biological, clinical, and sociobehavioral factors. Understanding these disparate risk factors is critical to reducing BV burden.},
}
@article {pmid40062709,
year = {2025},
author = {Jeong, IJ and Hong, JK and Bae, YJ and Lee, TK},
title = {Enhancing Bacterial Phenotype Classification Through the Integration of Autogating and Automated Machine Learning in Flow Cytometric Analysis.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {},
number = {},
pages = {},
doi = {10.1002/cyto.a.24923},
pmid = {40062709},
issn = {1552-4930},
support = {2020R1C1C100624912//National Research Foundation of Korea/ ; },
abstract = {Although flow cytometry produces reliable results, the data processing from gating to fingerprinting is prone to subjective bias. Here, we integrated autogating with Automated Machine Learning in flow cytometry to enhance the classification of bacterial phenotypes. We analyzed six bacterial strains prevalent in the soil and groundwater-Bacillus subtilis, Burkholderia thailandensis, Corynebacterium glutamicum, Escherichia coli, Pseudomonas putida, and Pseudomonas stutzeri. Using the H2O-AutoML framework, we applied gradient-boosting machine (GBM) models to classify bacteria across different metabolic phases. Our results demonstrated an overall classification accuracy of 82.34% for GBM. Notably, accuracy varied across metabolic phases, with the highest observed during the late log (88.06%), lag (88.43%), and early log phases (89.37%), whereas the stationary phase showed a slightly lower accuracy of 80.73%. P. stutzeri exhibited consistently high sensitivity and specificity across all the phases, which indicated that it was the most distinctly identifiable strain. In contrast, E. coli showed low sensitivity, particularly in the stationary phase, which indicated challenges in its classification. Overall, this study with incorporating autogating and the AutoML framework, substantially reduces subjective biases and enhances the reproducibility and accuracy of microbial classification. Our methodology offers a robust framework for microbial classification in flow cytometric analysis, paving the way for more precise and comprehensive analyses of microbial ecology.},
}
@article {pmid40060716,
year = {2025},
author = {Zhao, Y and Yuan, X and Ran, W and Zhao, Z and Su, D and Song, Y},
title = {The Ecological Restoration Strategies in Terrestrial Ecosystems Were Reviewed: A New Trend Based on Soil Microbiomics.},
journal = {Ecology and evolution},
volume = {15},
number = {3},
pages = {e70994},
pmid = {40060716},
issn = {2045-7758},
abstract = {Soil microorganisms play a pivotal role in the biogeochemical cycle and serve as crucial indicators of ecological restoration in terrestrial ecosystems. The soil microbial community is regarded as a pivotal participant in environmental processes, offering both positive and negative feedback to diverse media within the ecosystem. This community can serve as a potential indicator in ecological monitoring and restoration processes. Consequently, an increasing number of scholars are directing their research towards the field of soil microbial ecology in diverse ecosystems and fragile areas, with the aim of elucidating the intricate interactions between microbes and vegetation. However, the implementation of soil microbiome in ecological restoration remains in the experimental stage due to the interference of extreme events and the complexity of governance measures. Consequently, a comprehensive evaluation of existing research is imperative. This review aims to address the ecological crises currently experienced by diverse terrestrial ecosystems and to provide a comprehensive overview of the specific practices of soil microorganisms in the context of ecological restoration. We also incorporate them into fragile habitats and identify urgent issues that need to be addressed in the ecological restoration process of fragile areas.},
}
@article {pmid40060289,
year = {2025},
author = {Sarkar, A and Bhattacharjee, S},
title = {Biofilm-mediated bioremediation of xenobiotics and heavy metals: a comprehensive review of microbial ecology, molecular mechanisms, and emerging biotechnological applications.},
journal = {3 Biotech},
volume = {15},
number = {4},
pages = {78},
pmid = {40060289},
issn = {2190-572X},
abstract = {Environmental pollution, driven by rapid industrialization and urbanization, has emerged as a critical global challenge in the twenty-first century. This comprehensive review explores the potential of bacterial biofilms in bioremediation, focusing on their ability to degrade and transform a wide array of pollutants, including heavy metals, persistent organic pollutants (POPs), oil spills, pesticides, and emerging contaminants, such as pharmaceuticals and microplastics. The unique structural and functional characteristics of biofilms, including their extracellular polymeric substance (EPS) matrix, enhanced genetic exchange, and metabolic cooperation, contribute to their superior pollutant degradation capabilities compared to planktonic bacteria. Recent advancements in biofilm-mediated bioremediation include the application of genetically engineered microorganisms, nanoparticle-biofilm interactions, and innovative biofilm reactor designs. The CRISPR-Cas9 system has shown promise in enhancing the degradative capabilities of biofilm-forming bacteria while integrating nanoparticles with bacterial biofilms demonstrates significant improvements in pollutant degradation efficiency. As global pollution rises, biofilm-based bioremediation emerges as a cost-effective and environmentally friendly approach to address diverse contaminants. This review signifies the need for further research to optimize these techniques and harness their full potential in addressing pressing environmental challenges.},
}
@article {pmid40060287,
year = {2025},
author = {Maity, A and Das, A and Roy, R and Malik, M and Das, S and Paul, P and Sarker, RK and Sarkar, S and Dasgupta, A and Chakraborty, P and Tribedi, P},
title = {Development of novel strategies against the threats of drug-resistant Escherichia coli: an in silico and in vitro investigation.},
journal = {3 Biotech},
volume = {15},
number = {4},
pages = {77},
pmid = {40060287},
issn = {2190-572X},
abstract = {UNLABELLED: Escherichia coli (E. coli) biofilms pose alarming threats in healthcare due to their invulnerability to drug therapy. Stand-alone therapies of antimicrobial compounds/antibiotics are not particularly effective against those resistant strains. However, combination therapy of compounds could be used to deal with such threats. Towards this direction, the natural compound cuminaldehyde was employed in combination with the aminoglycoside antibiotic tobramycin to target the biofilm-forming multidrug-resistant (MDR) clinical strains of E. coli, which were isolated from urine samples of patient's at Suraksha Diagnostic Private Limited (Kolkata, India). At first, an integrated in silico approach (PASS online, Swiss ADME, PROTOX 3.0, and OSIRIS) was explored to predict the potential biological activities, and other relevant pharmacokinetic parameters of cuminaldehyde and tobramycin. The in silico analysis suggested that tobramycin might not be bioavailable orally due to its molecular size, polarity, and poor GI absorption. However, cuminaldehyde was well absorbed in the GI but could cause irritation if swallowed in LD50 amounts. Further, in vitro assessments were performed to analyse the antimicrobial and antibiofilm activity of both compounds, alone and in combination, against clinical strains of E. coli. The results suggested that cuminaldehyde and tobramycin together could show an additive effect against the clinical strains of E. coli. The combination of the compounds showed a substantial decrease in minimum inhibitory concentration (MIC) and biofilm formation compared to individual application. The present study indicates that combinatorial application involving cuminaldehyde and tobramycin could inhibit the formation of biofilms in E. coli, potentially aiding in the management of microbial infections.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04246-0.},
}
@article {pmid40058043,
year = {2025},
author = {Zhong, Q and Santás-Miguel, V and Cruz-Paredes, C and Rousk, J},
title = {Does the land-use impact the risk of inducing antibiotic tolerance by heavy metal pollution?.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124883},
doi = {10.1016/j.jenvman.2025.124883},
pmid = {40058043},
issn = {1095-8630},
abstract = {The rise of antibiotic-resistant soil microbial communities is a critical global issue. Evidence suggests that heavy metals can select or co-select for tolerance to metals and antibiotics in soil bacteria, but it is unclear if this tolerance varies with land use. We tested the potential of bacterial communities to develop resistance to copper (Cu) or tetracycline (Tet) after amending soils from pristine forests, contaminated forests, and agricultural lands with 3000 mg kg[-1] Cu and 6000 mg kg[-1] tetracycline, separately. Results showed that bacterial communities of unamended contaminated forest soils had the highest initial tolerance to Cu, while unamended agricultural soils exhibited the highest initial tolerance to tetracycline. The inducibility of bacterial resistance to antibiotics after Cu amendment varied by land use. In pristine forests, Cu amendment significantly increased microbial tetracycline resistance, as indicated by bacterial community tolerance, likely due to higher biodiversity. In contaminated forests, Cu amendment did not induce tetracycline-resistance, as indicated by unchanged bacterial community tolerance, possibly because of existing metal pollution and compromised bacterial communities by metal pollution. In agricultural soils, microbial tetracycline resistance as indicated by bacterial community tolerance developed slowly, becoming evident only after 42 days. These findings reveal significant differences in environmental risks related to soil metal pollution across different land uses, highlighting the need for systematic studies on the mechanisms of bacterial resistance to antibiotics in metal-contaminated soils due to their human health implications.},
}
@article {pmid40052378,
year = {2025},
author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H},
title = {Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf055},
pmid = {40052378},
issn = {1365-2672},
abstract = {AIMS: Microbial communities in paddy soils act as potential sinks of nitrous oxide (N2O), a notorious greenhouse gas, but their potential to reduce external N2O is unclear. The direct observation of N2O reduction in submerged field soils is technically difficult. Here, we aimed to identify soil microbial clades that underpin the strong N2O mitigation capacity.<br><br>METHODS AND RESULTS: We constructed paddy soil microcosms with external N2O amendment that enabled the simultaneous evaluation of N2O reductase gene (nosZ) transcripts and N2O consumption. Although the amount of N2O amended was large, it was mostly consumed after 6-8 days of microcosm incubation. Metatranscriptomic sequencing revealed that betaproteobacterial nosZ, especially those classified as clade II nosZ belonging to the orders Rhodocyclales or Nitrosomonadales, occupied&#xa0;>&#xa0;50% of the nosZ transcripts in three of the five paddy soils used. On the other hand, publicly available shotgun metagenomic sequences of 46 paddy soils were not dominated by betaproteobacterial clade II nosZ sequences, although they were ubiquitous. The same applied to the 16S rRNA sequences of Rhodocyclales or Nitrosomonadales.<br><br>CONCLUSIONS: The results indicated that betaproteobacterial N2O reducers potentially serve as powerful N2O sinks. Betaproteobacteria holding clade II nosZ can be targets of biostimulation, although further studies are required to understand their ecophysiology.},
}
@article {pmid39883081,
year = {2025},
author = {Shin, GY and Asselin, JA and Smith, A and Aegerter, B and Coutinho, T and Zhao, M and Dutta, B and Mazzone, J and Neupane, R and Gugino, B and Hoepting, C and Khanal, M and Malla, S and Nischwitz, C and Sidhu, J and Burke, AM and Davey, J and Uchanski, M and Derie, ML and du Toit, LJ and Stresow-Cortez, S and Bonasera, JM and Stodghill, P and Kvitko, B},
title = {Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf019},
pmid = {39883081},
issn = {1751-7370},
support = {2019-51181-30013//Specialty Crops Research Initiative Award/ ; //National Institute of Food and Agriculture/ ; //U.S. Department of Agriculture/ ; },
mesh = {*Pantoea/genetics/pathogenicity/isolation &amp; purification ; *Onions/microbiology ; *Plant Diseases/microbiology ; *Plasmids/genetics ; Genome, Bacterial ; Phylogeny ; Multigene Family ; Virulence/genetics ; },
abstract = {Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion were only identified in Phylogroup II and encoded the HiVir pantaphos biosynthetic cluster, supporting the role of HiVir as a pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two distinct plasmid contexts: (i) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or (ii) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes revealed that the pOnion plasmids harbored alt genes conferring tolerance to Allium thiosulfinate defensive chemistry and many harbored cop genes conferring resistance to copper. We demonstrated that the pOnion plasmid pCB1C can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.},
}
@article {pmid40049093,
year = {2025},
author = {Fonvielle, J and Thuile Bistarelli, L and Tao, Y and Woodhouse, JN and Shatwell, T and Villalba, LA and Berger, SA and Kyba, CCM and Nejstgaard, JC and Jechow, A and Kupprat, F and Stephan, S and Walles, TJW and Wollrab, S and Hölker, F and Dittmar, T and Gessner, MO and Singer, GA and Grossart, HP},
title = {Skyglow increases cyanobacteria abundance and organic matter cycling in lakes.},
journal = {Water research},
volume = {278},
number = {},
pages = {123315},
doi = {10.1016/j.watres.2025.123315},
pmid = {40049093},
issn = {1879-2448},
abstract = {Artificial light propagating towards the night sky can be scattered back to Earth and reach ecosystems tens of kilometres away from the original light source. This phenomenon is known as artificial skyglow. Its consequences on freshwaters are largely unknown. In a large-scale lake enclosure experiment, we found that skyglow at levels of 0.06 and 6 lux increased the abundance of anoxygenic aerobic phototrophs and cyanobacteria by 32 (±22) times. An ecosystem metabolome analysis revealed that skyglow increased the production of algal-derived metabolites, which appeared to stimulate heterotrophic activities as well. Furthermore, we found evidence that skyglow decreased the number of bacteria-bacteria interactions. Effects of skyglow were more pronounced at night, suggesting that responses to skyglow can occur on short time scales. Overall, our results call for considering skyglow as a reality of increasing importance for microbial communities and carbon cycling in lake ecosystems.},
}
@article {pmid40048904,
year = {2025},
author = {Chen, L and Zhao, B and Zhang, M and Yan, Y and Nie, C and Yu, K and Tu, Z and Xia, Y},
title = {Micron-scale heterogeneity reduction leads to increased interspecies competition in thermophilic digestion microbiome.},
journal = {Water research},
volume = {279},
number = {},
pages = {123419},
doi = {10.1016/j.watres.2025.123419},
pmid = {40048904},
issn = {1879-2448},
abstract = {Microbial spatial heterogeneity is an important determinant of larger-scale community properties, whereas most studies neglect it and therefore only provide average information, potentially obscuring the signal of microbial interactions. Our study takes a step toward addressing this problem by characterizing the spatial heterogeneity of a microbiome with micron-scale resolution. Micron-scale single clusters (40-70 μm) were randomly collected from lab-scale anaerobic digestion (AD) biosystems, and a comparative analysis was performed to evaluate differences between mesophilic and thermophilic systems. Here we reveal a cascading effect from high-temperature selection to global microbial interactions. We observed that thermophilic communities exhibited less spatial heterogeneity than mesophilic communities, which we attribute to the considerable extinction of low-abundant species by high-temperature selection. Then, the low spatial heterogeneity and the high-temperature selection acting in conjunction resulted in a high proportion of competitive interactions in thermophilic communities. Unexpectedly, however, the thermophilic AD, characterized by lower micron-scale spatial heterogeneity, showed more efficient synergistic and syntrophic cooperations involving around Clostridiales, which significantly enhanced hydrolysis performance under thermophilic conditions. In addition, the fact that high temperatures favor slower growers, along with functional redundancy-related competitive advantage, led to the selection of more proficient methanogens in more competitive environments, which are also potentially associated with enhanced methanogenic performance. In summary, our findings underscore the significance of micron-scale resolution for revealing the microbial ecology in spatially structured environments.},
}
@article {pmid40047954,
year = {2025},
author = {Sobhy, IS and Goelen, T and Wäckers, F and Verstrepen, KJ and Wenseleers, T and Jacquemyn, H and Lievens, B},
title = {Impact of Nectar Composition and Nectar Yeasts on Volatile Emissions and Parasitoid Behavior.},
journal = {Journal of chemical ecology},
volume = {51},
number = {2},
pages = {29},
pmid = {40047954},
issn = {1573-1561},
support = {C3 grant (IOF-C32/15/020)//KU Leuven/ ; C3 grant (IOF-C32/15/020)//KU Leuven/ ; C3 grant (IOF-C32/15/020)//KU Leuven/ ; },
mesh = {*Plant Nectar/chemistry/metabolism ; *Volatile Organic Compounds/analysis/metabolism/chemistry ; Animals ; *Metschnikowia/metabolism/physiology/chemistry ; *Aphids/physiology/chemistry ; Female ; *Amino Acids/analysis/metabolism/chemistry ; Fermentation ; Wasps/physiology/chemistry ; Behavior, Animal ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Nectar yeasts can significantly influence the scent of floral nectar and therefore the foraging behavior of flower-visiting insects. While these effects likely depend on nectar chemistry and yeast species, their joint impact on nectar volatile profiles and associated insect responses remain poorly understood. Here, we used four synthetic nectar types varying in sugar and amino acid concentration and two specialist nectar yeasts (Metschnikowia gruessii and Metschnikowia reukaufii) to investigate how nectar composition and yeast species affect volatile profiles and the olfactory responses of the generalist aphid parasitoid Aphidius ervi. Olfactometer assays showed that A. ervi females significantly preferred fermented nectars with high amino acid-low sugar content (HL) and low amino acid-high sugar (LH) content, regardless being fermented by M. gruessii or M. reukaufii, over non-inoculated nectars. This effect was not observed for nectars with low amino acid-low sugar (LL) and high amino acid-high sugar (HH) content. Moreover, LL nectar fermented with M. gruessii became even repellent to the parasitoids. GC-MS analysis of volatile organic compounds (VOCs) revealed that VOC profiles of fermented nectars depended significantly on nectar type (i.e., chemical composition), yeast species, and their interaction. Whereas propyl acetate, isobutyl acetate, styrene, α-guaiene and pentyl-octanoate were associated with the LH fermented nectars, ethyl acetate and E-methyl isoeugenol were mainly associated with the HL fermented nectars, suggesting possible involvement in A. ervi attraction to these nectars. In contrast, isopropyl-hexadecanoate was associated with the non-attractive or repellent LL fermented nectars. Altogether, our results indicate that nectar composition has a strong impact on nectar scent when fermented by specialist nectar yeasts and subsequently on insect foraging behavior.},
}
@article {pmid40046987,
year = {2025},
author = {Scott, WT and Rockx, S and Mariën, Q and Regueira, A and Candry, P and Ganigué, R and Koehorst, JJ and Schaap, PJ},
title = {Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {649-660},
pmid = {40046987},
issn = {2001-0370},
abstract = {Syngas fermentation is a powerful platform for converting waste streams into sustainable carboxylic acid precursors for value-added biochemicals. Steel mills produce significant syngas, yet industrial microbial syngas valorization remains unrealized. The most promising syngas-converting biocatalysts consist of Clostridia species, such as Clostridium kluyveri, Clostridium autoethanogenum, and Clostridium ljungdahlii. Clostridium luticellarii, a recently discovered species, shares close phylogenetic ties with these organisms. Preliminary metabolic studies suggest its potential for syngas acetogenesis as well as chain elongation. In this study, we create iSJ444, a constraint-based metabolic model of C. luticellarii using iHN637 of a close relative C. ljungdahlii as a starting point. Model predictions support hypothesized methanol and syngas pathways from the metabolic characterization studies; however, the use of propionate could not be accurately predicted. Thermodynamic Flux Analysis (TFA) reveals that C. luticellarii maintains stable energy dissipation across most reactions when exposed to varying pH, with significant increases observed in reactions associated with the Wood-Ljungdahl pathway (WLP), such as the HACD1 reaction, at higher pH (6.5), suggesting an adaptive role in energy management under neutral conditions. Flux sampling simulations exploring metabolic flux distributions show that C. luticellarii might fit into syngas fermenting platforms. In both cases, high hydrogen-to-carbon source ratios result in better production of (iso)butyrate and caproate. We present a minimal genome-scale metabolic model of C. luticellarii as a foundation for further exploration and optimization. Although our predictions of its metabolic behavior await experimental validation, they underscore the potential of C. luticellarii to enhance syngas fermentation platforms.},
}
@article {pmid40045231,
year = {2025},
author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD},
title = {Cross-validation for training and testing co-occurrence network inference algorithms.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {74},
pmid = {40045231},
issn = {1471-2105},
support = {2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; },
mesh = {*Algorithms ; *Microbiota ; Computational Biology/methods ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.<br><br>RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.<br><br>CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.},
}
@article {pmid40044467,
year = {2025},
author = {Sharma, P and Reitz, T and Singh, SP and Worrich, A and Muehe, EM},
title = {Going beyond improving soil health: cover plants as contaminant removers in agriculture.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.01.009},
pmid = {40044467},
issn = {1878-4372},
abstract = {Agriculture faces the increasing demands of a growing global population amid simultaneous challenges to soils from climate change and human-induced contamination. Cover plants are vital in sustainable agriculture, contributing to soil health improvement, erosion prevention, and enhanced climate resilience, but their role in contaminant management is underexplored. Herein we review the utilization of cover plants for remediating contaminants such as metals, organic pollutants, nitrate, antibiotics, antimicrobial resistance genes, plastics, and salts. We explore phytoremediation strategies - including phytoextraction, phytodegradation, and phytostabilization - in cover plant management. We highlight the challenges of selecting effective cover plants and the need for biomass removal of non-biodegradable contaminants, and we advocate incorporating phytoremediation concepts into sustainable agricultural management practices beyond nutrient cycling and climate resilience.},
}
@article {pmid40042720,
year = {2025},
author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y},
title = {Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.},
journal = {Bioresources and bioprocessing},
volume = {12},
number = {1},
pages = {14},
pmid = {40042720},
issn = {2197-4365},
abstract = {The fermentation process of strong-flavor Baijiu represents a complex and unique ecosystem, characterized by the involvement of various microorganisms that drive intricate biochemical reactions, ultimately contributing to the distinct flavor profile of the Baijiu. Viruses may affect the succession of microorganisms and thus affect the style and quality of the product. However, the interaction between viruses and microorganisms during the fermentation of Baijiu is still unclear. Here we combined viral metagenomics and amplicon sequencing, physicochemical analysis, and GC-MS detection with temporal sampling to study the dynamics of viral and microbial communities, physicochemical properties, and flavor compounds during strong-flavor Baijiu fermentation. Viral metagenomic analysis revealed 513 viral operational taxonomic units (vOTUs), encompassing 34 viral families. Principal coordinates analysis (PCoA) demonstrated significant differences in vOTUs at different fermentation stages. Notably, the microbial community exhibited distinct succession patterns at various fermentation stages; it changed rapidly during the initial five days, with similarities observed between days 10 and 20. Volatile profile analysis identified 38 flavor components in fermented grains, comprising 16 ester compounds, 11 alcohols, and 8 acids, with the majority formed between days 10 and 30. The Spearman's rank correlation analysis revealed that Peduoviridae exhibited a negative correlation with Gluconobacter. Genomoviridae showed a negative correlation with Issatchenkia, Penicillium, and Monascus. These findings highlight the potential for complex interactions between viruses and microbial communities during Baijiu fermentation, underscoring the importance of considering viral communities in studies of the microbial ecology of fermented foods.},
}
@article {pmid40042690,
year = {2025},
author = {Zhang, T and Wang, XL and Zhou, J and Zhou, W and Zhou, SQ},
title = {Construction of Phosphate-Solubilizing Microbial Consortium and Its Effect on the Remediation of Saline-Alkali Soil.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {11},
pmid = {40042690},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Phosphates/metabolism ; *Soil/chemistry ; *Phosphorus/metabolism ; *Bacteria/metabolism/classification/growth &amp; development ; *Microbial Consortia ; Arachis/microbiology/growth &amp; development/metabolism ; Alkalies/chemistry ; Hydrogen-Ion Concentration ; Calcium Sulfate ; Biomass ; Salinity ; },
abstract = {In this study, phosphate solubilizing bacteria (PSB) with good phosphate-solubilizing capability were isolated from phosphogypsum (PG) storage yard, and phosphate-solubilizing bacteria without antagonistic effect were selected to construct phosphate solubilizing microbial consortium (PSMC), and the synergistic effect of PSMC and PG on the physical and chemical properties of saline-alkali soil, soil enzyme activity, soil bacterial diversity, and the growth index and biomass of peanut plants were explored. The results showed that the effect of phosphorus containing soil amendment on saline-alkali soil was better than that of single PSMC or PG. In the T6 group (untreated saline-alkali soil (1.5 kg) + PSMC stock solution (15 mL) + PG (6.0 g)), the pH of saline-alkali soil decreased from 8.54 to 7.03, the content of organic matter increased by 6.64%, the content of alkali hydrolyzable nitrogen, available phosphorus and available potassium increased by 81.68%, 60.31%, and 42.03%, respectively, and the activity of alkaline phosphatase increased by 94.95%. In addition, the electrical conductivity value in T4 group (untreated saline-alkali soil (1.5 kg) + PSMC stock solution (15 mL) + PG (3.0g)) decreased significantly by 20.21%. The diversity and richness of bacterial community in T4 group were the highest, and the growth of peanut plants was the best. The fresh weight of roots and stems increased by 73.34% and 116.6%, respectively. In conclusion, the phosphorus containing soil conditioner prepared by PSMC and PG can effectively improve the soil environment of saline-alkali soil and promote the resource utilization of saline alkali soil.},
}
@article {pmid40042528,
year = {2025},
author = {Zaki, H and Hussein, MA and El-Dawy, EGAM},
title = {Diversity and Symbiotic Associations of Endophytic Fungi in Calotropis procera (Aiton) W.T. Aiton (Asclepiadaceae) Across Three Egyptian Regions: Phenotypic Characterization and Mitotic Activity.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {10},
pmid = {40042528},
issn = {1432-184X},
mesh = {*Endophytes/physiology/isolation &amp; purification/classification ; Egypt ; *Fungi/classification/physiology/isolation &amp; purification ; *Calotropis/microbiology ; *Biodiversity ; *Symbiosis ; Soil Microbiology ; Mitosis ; Phenotype ; },
abstract = {Endophytic fungi are essential contributors to fungal biodiversity, playing key roles in plant defense against pathogens, alleviation of abiotic stress, and promotion of growth. This study conducted a comprehensive survey of the phenotypic characterization of Calotropis procera and its associated endophytic fungi across three regions in Egypt: Qena-Safaga, Qena, and Qena-Kosseir. Positive and significant Pearson correlations among plant morphological traits suggest intrinsic connections. Fungal species diversity exhibited significant variation across the three regions examined. Particularly, the Qena-Kosseir region demonstrated the highest fungal species richness both in soil samples and endophytic fungi. Unique to this region, Allocanariomyces tritici, Aspergillus terreus, Chaetomium globosum, C. murorum, Cladosporium cladosporioides, C. sphaerospermum, Fusarium proliferatum, Penicillium crustosum, P. granulatum, P. spinuloseum, and Roussoella intermedia were identified as endophytes. Additionally, compared to other regions, the Qena-Kosseir area exhibited the presence of Aspergillus fumigatus, A. ochraceus, A. ornatus, A. sclerotiocabonarus, Drechslera halodes, Emericella echinulata, Fusarium oxysporum, and Macrophomina phaseolina in soil samples, underscoring its distinct fungal community composition. Furthermore, antimitotic assays using the Allium cepa test revealed distinct effects of endophytic extracts on various mitotic stages. Of the 33 treatments, 11 showed an increase in the mitotic index (MI), indicating a potential positive effect on plant growth and cell division. This study offers valuable insights into the diversity and functional roles of endophytic fungi associated with C. procera, highlighting their promising applications in sustainable agriculture and plant health management.},
}
@article {pmid40042412,
year = {2025},
author = {Hicks, LC and Leizeaga, A and Cruz Paredes, C and Brangarí, AC and Tájmel, D and Wondie, M and Sandén, H and Rousk, J},
title = {Simulated Climate Change Enhances Microbial Drought Resilience in Ethiopian Croplands but Not Forests.},
journal = {Global change biology},
volume = {31},
number = {3},
pages = {e70065},
doi = {10.1111/gcb.70065},
pmid = {40042412},
issn = {1365-2486},
support = {2016-06327//Vetenskapsr&#xe5;det/ ; 2020-03858//Vetenskapsr&#xe5;det/ ; CTS 22:2131//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; 2022-00672//Svenska Forskningsr&#xe5;det Formas/ ; 2023-02438//Svenska Forskningsr&#xe5;det Formas/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2023.0384//Knut och Alice Wallenbergs Stiftelse/ ; },
mesh = {*Droughts ; Ethiopia ; *Climate Change ; *Soil Microbiology ; *Forests ; Soil/chemistry ; Fungi/physiology ; Bacteria ; Microbiota ; Crops, Agricultural/growth &amp; development ; Rain ; },
abstract = {Climate change and land-use change represent a dual threat to terrestrial ecosystem functioning. In the tropics, forest conversion to agriculture is occurring alongside warming and more pronounced periods of drought. Rainfall after drought induces enormous dynamics in microbial growth (potential soil carbon storage) and respiration (determining carbon loss), affecting the ecosystem carbon budget. We investigated how legacies of drought and warming affected microbial functional (growth and respiration) and structural (16S and ITS amplicon) responses after drought. Rain shelters and open-top chambers (OTCs) were used to simulate drought and warming in tropical cropland and forest sites in Ethiopia. Rain shelters reduced soil moisture by up to 25 vol%, with a bigger effect in the forest, while OTCs increased soil temperature by up to 6°C in the cropland and also reduced soil moisture but had no clear effect in the forest. Soils from these field treatments were then exposed to a standardized drought cycle to test how microbial community traits had been shaped by the different climate legacies. Microbial growth started increasing immediately after rewetting in all soils, reflecting a resilient response and indicating that microbial communities perceived the perturbation as relatively mild. Fungi recovered faster than bacteria, and the recovery of fungal growth was generally accelerated in soils with a legacy of drought. Microbial community functions and structures were both more responsive in the cropland than in forest soils, and a legacy of drought particularly enhanced microbial growth and respiration responses in the cropland but not the forest. Microbial communities in cropland soils also used carbon with a higher efficiency after rewetting. Together, these results suggest contrasting feedbacks to climate change determined by land use, where croplands will be associated with mitigated losses of soil carbon by microorganisms in response to future cycles of drought, compared to forests where soil carbon reservoirs remain more sensitive.},
}
@article {pmid40042334,
year = {2025},
author = {Venturini, AM and Gontijo, JB and Berrios, L and Rodrigues, JLM and Peay, KG and Tsai, SM},
title = {Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156124},
doi = {10.1128/spectrum.01561-24},
pmid = {40042334},
issn = {2165-0497},
abstract = {Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.},
}
@article {pmid40041707,
year = {2025},
author = {Liu, X and Gong, X and Ma, K and Song, W and Zhou, J and Wang, M and Li, Y and Ji, M and Li, Y and Han, H and Wang, Y and Tu, Q},
title = {Resolving ecological drivers of temporal variations of β-diversity across intertidal microbiomes.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf025},
pmid = {40041707},
issn = {2730-6151},
abstract = {Resolving the ecological drivers mediating the diversity patterns of microbial communities across space and through time is a central issue in microbial ecology. Both regional species pools and local community assembly contribute to the spatial turnover of biodiversity. In this study, we extended the concept of regional species pool to temporal, and investigated the seasonal dynamics of intertidal microbiomes across four microbial domains/kingdoms (bacteria, archaea, fungi, and protists). The results showed that the seasonal variations of microbial β-diversity were primarily governed by community assembly processes rather than temporal species pools. Different microbial domains/kingdoms were structured by different ecological processes, with homogeneous selection as the major process for all of them. Additionally, bacteria and fungi were critically shaped by drift, and protists by drift and homogeneous dispersal. Among various factors, temperature was important in shaping the temporal patterns of microbial β-diversity. The fluctuation in temperature was strongly associated with fungi and protists, resulting in high drift of community composition. This study demonstrated that community assembly processes governed the dynamic seasonal β-variations of intertidal microbiomes, expanding our understanding from spatial ecology.},
}
@article {pmid40041702,
year = {2025},
author = {Xu, Z and Chen, J and Liang, W and Chen, ZL and Wu, W and Xia, X and Chen, B and He, D and Liu, H},
title = {Contrasting diversity patterns between microeukaryotic and prokaryotic communities in cold-seep sediments.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf002},
pmid = {40041702},
issn = {2730-6151},
abstract = {Cold seeps are hotspots of biodiversity. However, the quantification of the microbial diversity, particularly that of microeukaryotes, remains scarce and little is known about the active groups. In this study we investigated the diversity and activity of prokaryotes and microeukaryotes in the Haima cold seep sediments in the northern South China Sea using both DNA (whole community) and RNA (active community) signatures. We found that, in general, prokaryotes had lower diversity in the seep sediment than in non-seep regions while microeukaryotes showed the opposite pattern. This finding could be explained by the dominance of homogeneous selection in the prokaryotic community while microeukaryotic communities were less affected by environmental selection, harboring high richness of abundant groups in the seep regions. The compositional difference between DNA and RNA communities was much larger in microeukaryotes than prokaryotes, which could be reflected by the large number of inactive microeukaryotic taxa. Compared to the whole community, the seep-active groups, e.g. among microeukaryotes, Breviatea, Labyrinthulomycetes, and Apicomplexa were more sensitive to and directly influenced by environmental factors, suggesting their pivotal roles in ecosystem biodiversity and functions. This study provides insight into the distinct diversity patterns and regulating mechanisms that occur between prokaryotic and microeukaryotic communities in cold-seep sediments, deepening our understanding of microbial ecology in deep-sea extreme habitats.},
}
@article {pmid40041671,
year = {2025},
author = {Zernadji, W and Rahmani, F and Jebri, S and Hamdi, M and Khammassi, M and Dhib, S and Hmaied, F},
title = {Distribution of Microbial Contaminants of Minimally Processed Salads Produced in Tunisia: Need to Strengthen Good Hygiene Practices.},
journal = {International journal of food science},
volume = {2025},
number = {},
pages = {9570620},
pmid = {40041671},
issn = {2314-5765},
abstract = {The microbiological safety of ready-to-eat (RTE) salads is considered as a major concern due to the absence of lethal treatments during processing. In this study, we aimed to investigate the microbiological quality of RTE salads commercialized in Tunisia and to determine the antibiotic resistance of isolated pathogens, in particular Staphylococcus aureus (S. aureus). A total of 100 samples were analyzed for total aerobic bacteria, total coliforms, Escherichia coli (E. coli), yeasts and molds, Salmonella spp., Listeria monocytogenes (L. monocytogenes), and S. aureus as well as norovirus (NoV) GI and GII using specific standard methods described by the International Organization for Standardization (ISO). All samples presented unacceptable microbiological quality due to high concentrations of total aerobic bacteria and yeasts (> 10[6] CFU/g) and total coliforms (> 10[4] CFU/g). E. coli and molds were detected at unsatisfactory levels in 4% and 12% of samples, respectively. The pathogens Salmonella spp. and L. monocytogenes were not detected. S. aureus were detected at unsatisfactory levels in 6% of samples. S. aureus isolates were resistant to more than five antibiotic classes. Thus, RTE salads could be a vehicle of multiresistant S. aureus. The total prevalence of NoV GII was 2% (mean 3.81 ± 0.30 Log GC/25 g), and no NoV GI-positive samples were identified. This study showed that the microbiological quality of RTE salads commercialized in Tunisia was unacceptable, highlighting the need to ensure good agricultural and hygiene practices from farm to fork to improve the quality and safety of these products.},
}
@article {pmid40037241,
year = {2025},
author = {Lu, Z and Zeng, J and Wang, L and Zhu, D and Cheng, X and Huang, D and Zhang, J and Yuan, L},
title = {The influence of turbulence caused by hydraulic structures on the community assembly of epilithic biofilms in rivers.},
journal = {Journal of environmental management},
volume = {378},
number = {},
pages = {124645},
doi = {10.1016/j.jenvman.2025.124645},
pmid = {40037241},
issn = {1095-8630},
abstract = {The assembly mechanisms of riverine biofilm communities in river systems represent a central question in aquatic microbial ecology. However, the influence of turbulence on the assembly of generalists and specialists within biofilms remains poorly understood. This study aimed to address this gap by examining a river with multiple spur dikes, using high-throughput sequencing, ecological network analysis, and partial least squares path modeling to explore the assembly process and community structure of biofilms. The results revealed that turbulence intensity (0.029 m/s) and kinetic energy (0.0018 m[2]/s[2]) were significantly higher at the heads of spur dikes compared to the tails. Notably, hydrodynamic parameters explained 6.50% of biofilm community variance, highlighting their underappreciated role as deterministic drivers of microbial assembly. Habitat specialists exhibited heightened sensitivity to hydrodynamic fluctuations, occupying central positions in co-occurrence networks. Additionally, turbulence intensity and kinetic energy emerged as the primary drivers of community assembly, influencing critical ecological processes such as homogeneous selection, drift and dispersal limitation. At the head of spur dikes, a high turbulence region, the weakened impact of homogeneous selection, combined with an increase in dispersal limitation, created conditions that particularly favored habitat generalists. Conversely, low turbulence dike tails supported specialist proliferation via strengthened deterministic selection and nutrient-driven niche partitioning. Furthermore, the partial least squares path modeling confirmed that turbulence dominates the assembly process of microbial specialists and generalists. This study revealed the pivotal role of turbulence in shaping biofilm assembly and driving the spatial differentiation of generalists and specialists, offering fresh insights into the complex interplay between hydrodynamics and microbial ecology in rivers impacted by hydraulic structures. These findings significantly enhance the understanding of biofilm assembly mechanisms and their broader implications for effective river ecosystem management.},
}
@article {pmid40036370,
year = {2025},
author = {Duysburgh, C and Nicolas, C and Van den Broeck, M and Lloret, F and Monginoux, P and Rème, C and Marzorati, M},
title = {A specific blend of prebiotics and postbiotics improved gut microbiome of dogs with soft stools in the in vitro Simulator of the Canine Intestinal Microbial Ecosystem (SCIME).},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf056},
pmid = {40036370},
issn = {1525-3163},
abstract = {The Simulator of the Canine Intestinal Microbial Ecosystem (SCIME) allows for the study of long-term effects of food, supplements, or ingredients on the canine gut microbiome in a simulated proximal and distal colon. This model has been used to evaluate the impact of repeated administration of a test product blend composed of a mixture of baobab fruit pulp, acacia gum, heat-killed Lactobacillus helveticus HA-122, and specific fractions of selected inactivated yeast strains (including Saccharomyces cerevisiae AQP 12260 and AQP 12988 and Cyberlindnera jadinii AQP 12549), on the activity and composition of the gut microbiome of canine donors with soft stools. The SCIME colonic reactors were inoculated with fecal material from 3 different canine donors. After two days of stabilization, the 8-day parallel control/treatment period was initiated; reactors were fed with SCIME nutritional medium with or without test product. Changes in microbial metabolic activity were assessed by measuring levels of acetate, propionate, butyrate, lactate, branched short-chain fatty acids, and ammonium. Changes in microbial community composition were assessed using 16S-targeted Illumina sequencing. Overall, test product supplementation resulted in increased saccharolytic fermentation, as evidenced by increases in the health-promoting bacterial metabolites as propionate (donor-dependent), acetate and butyrate (donor-dependent) as well as increased abundances of several saccharolytic fermenting microbes, including Bifidobacterium. Conversely, proteolytic bacteria like Proteobacteria were reduced with test product compared to control. Repeated supplementation with the test product was therefore able to induce - in vitro - a positive modulation of the microbiome originated from dogs with soft stools.},
}
@article {pmid40035794,
year = {2025},
author = {Vieira, AR and Camacho, F and Sousa, ML and Luelmo, S and Santarém, N and Cordeiro-da-Silva, A and Leão, PN},
title = {The Cyanobacterial Oxadiazine Nocuolin A Shows Broad-Spectrum Toxicity Against Protozoans and the Nematode C. elegans.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {9},
pmid = {40035794},
issn = {1432-184X},
support = {2022.04572.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.04572.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2021.04285.CEECIND/CP1663/CT0004//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 952374//Horizon 2020/ ; 952374//Horizon 2020/ ; 952374//Horizon 2020/ ; },
mesh = {Animals ; *Cyanobacteria/metabolism/drug effects ; *Caenorhabditis elegans/drug effects/microbiology ; Dictyostelium/microbiology/drug effects ; Acanthamoeba/drug effects/microbiology ; Antiprotozoal Agents/pharmacology/metabolism ; },
abstract = {Cyanobacteria, known to be rich sources of valuable natural products (NPs) with relevant biological properties, are a unique subject to study the interplay between chemistry and ecology. Cultivation of cyanobacteria as isolated strains may only reveal a small fraction of their NPs. In contrast, investigating microbial interactions from an ecological perspective is a particularly fruitful approach to unveil both new chemistry and bioactivity. Cyanobacteria and amoebae are known to co-exist in diverse environments, but the interaction between these organisms has been poorly investigated. Defense strategies against grazer organisms may rely on morphological changes including biofilm formation or increased motility; however, secretion of toxic metabolites seems to be more effective on this regard. Among the most structurally unique cyanobacterial secondary metabolites is nocuolin A, an 1,2,3-oxadiazine metabolite isolated from the cyanobacterial strain Nodularia sp. LEGE 06071 that exhibits potent anti-proliferative activity against several human cancer lines, associated with impairment of mitochondrial oxidative phosphorylation. In this work, we show that nocuolin A is toxic against two well-known model amoebae, Acanthamoeba and Dictyostelium, leading to amoebae encystation and decrease in viability. In addition, in lawn grazing assays, we observed that Nodularia sp. LEGE 06071, the producer strain of nocuolin A, was not grazed by amoeba, while a related strain, which does not produce detectable levels of nocuolin A, was. These results support the possible involvement of nocuolin A as a chemical mediator during the interaction between these organisms. Furthermore, we show that this cyanobacterial metabolite also exhibits potent toxicity against other protozoan organisms and a free-living nematode, making it an interesting broad-spectrum scaffold for the development of antiprotozoal or anti-helminthic drugs.},
}
@article {pmid40034844,
year = {2024},
author = {Thompson, MA and Valentine, DL and Peng, X},
title = {Size fractionation informs microbial community composition and interactions in the eastern tropical North Pacific Ocean.},
journal = {FEMS microbes},
volume = {5},
number = {},
pages = {xtae028},
pmid = {40034844},
issn = {2633-6685},
abstract = {Marine microorganisms are drivers of biogeochemical cycles in the world's oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.},
}
@article {pmid40033656,
year = {2025},
author = {Orr, JA and Armitage, DW and Letten, AD},
title = {Coexistence Theory for Microbial Ecology, and Vice Versa.},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70072},
doi = {10.1111/1462-2920.70072},
pmid = {40033656},
issn = {1462-2920},
support = {DE230100373//Australian Research Council/ ; DP220103350//Australian Research Council/ ; DE250100656//Australian Research Council/ ; },
mesh = {*Ecology ; Ecosystem ; Microbiota/physiology ; Models, Biological ; Bacteria/classification/genetics ; Microbial Interactions/physiology ; },
abstract = {Classical models from theoretical ecology are seeing increasing uptake in microbial ecology, but there remains rich potential for closer cross-pollination. Here we explore opportunities for stronger integration of ecological theory into microbial research (and vice versa) through the lens of so-called "modern" coexistence theory. Coexistence theory can be used to disentangle the contributions different mechanisms (e.g., resource partitioning, environmental variability) make to species coexistence. We begin with a short primer on the fundamental concepts of coexistence theory, with an emphasis on the relevance to microbial communities. We next present a systematic review, which highlights the paucity of empirical applications of coexistence theory in microbial systems. In light of this gap, we then identify and discuss ways in which: (i) coexistence theory can help to answer fundamental and applied questions in microbial ecology, particularly in spatio-temporally heterogeneous environments, and (ii) experimental microbial systems can be leveraged to validate and advance coexistence theory. Finally, we address several unique but often surmountable empirical challenges posed by microbial systems, as well as some conceptual limitations. Nevertheless, thoughtful integration of coexistence theory into microbial ecology presents a wealth of opportunities for the advancement of both theoretical and microbial ecology.},
}
@article {pmid40028056,
year = {2025},
author = {Vignolle, A and Zehl, M and Kirkegaard, RH and Vignolle, GA and Zotchev, SB},
title = {Secondary Metabolite Biosynthesis Potential of Streptomyces Spp. from the Rhizosphere of Leontopodium nivale Subsp. alpinum.},
journal = {ACS omega},
volume = {10},
number = {7},
pages = {7163-7171},
pmid = {40028056},
issn = {2470-1343},
abstract = {Bacteria of the phylum Actinomycetota, particularly those of the genus Streptomyces, are prolific producers of secondary metabolites (SMs), many of which have been developed into antibiotics, immunosuppressants, and cancer therapeutics. With high rediscovery rates, the attention has shifted to Streptomyces from unique ecological niches for the discovery of new SMs. The plant rhizosphere is one such niche, characterized by complex chemical interactions between the plant and its rhizobiome, which can elicit the production of SMs in Streptomyces. In the present study, 18 Streptomyces strains were previously isolated from the rhizosphere of the rare alpine medicinal plant Leontopodium nivale subsp. alpinum were investigated for their capacity to produce secondary metabolites. Genomes of these strains were analyzed for the presence of SM biosynthetic gene clusters (BGCs). In total, 551 BGCs were detected, of which 217 could not be linked to known SMs. These isolates were cultivated in different media known to support the production of SMs, and 15 out of the 54 methanolic extracts from these cultures exhibited antimicrobial activities. Subsequent liquid chromatography-mass spectrometry analyses of the bioactive extracts led to a putative identification of 69 known SMs as well as 16 potentially new molecules. The results of this study may provide a basis for the discovery of unique molecules with the potential to be developed as drugs against a variety of human diseases.},
}
@article {pmid40025674,
year = {2025},
author = {Abdolahpur Monikh, F and Quik, JTK and Wiesner, MR and Tapparo, A and Pastore, P and Grossart, HP and Akkanen, J and Kortet, R and Kukkonen, JVK},
title = {Importance of Attachment Efficiency in Determining the Fate of PS and PVC Nanoplastic Heteroaggregation with Natural Colloids Using a Multimedia Model.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10918},
pmid = {40025674},
issn = {1520-5851},
abstract = {Here, we assessed the heteroaggregation of polystyrene (PS) and poly(vinyl chloride) (PVC) nanoplastics with SiO2 as a model of natural colloids. Homoaggregation and heteroaggregation were evaluated as a function of CaCl2 (0-100 mM) and natural organic matter (NOM) (50 mg L[-1]) at a designated concentration of nanoplastics (200 μg L[-1]). Critical coagulation concentrations (CCC) of nanoplastics were determined in homoaggregation and heteroaggregation experiments with SiO2 and CaCl2. The attachment efficiency (α) was calculated by quantifying the number of nanoplastics in the presence of CaCl2, NOM, and SiO2 using single-particle inductively coupled plasma mass spectrometry (spICP-MS) and pseudo-first-order kinetics. The calculated α was fed into the SimpleBox4Plastics model to predict the fate of nanoplastics across air, water, soil, and sediment compartments. Nanoplastics exhibited high stability against homoaggregation, while significant heteroaggregation with SiO2 occurred at CaCl2 concentrations above 100 mM. The influence of NOM was also evaluated, showing a reduction in heteroaggregation with SiO2 for both nanoplastic types. Sensitivity analysis indicated that the degradation half-life of the tested nanoplastics had a more significant impact on persistence than did α. The results emphasize the environmental stability of nanoplastics, particularly in freshwater and soil compartments, and the critical role of NOM and emission pathways in determining their fate.},
}
@article {pmid40024538,
year = {2025},
author = {Sliti, A and Kim, RH and Lee, D and Shin, JH},
title = {Whole Genome Sequencing and In Silico Analysis of the Safety and Probiotic Features of Lacticaseibacillus paracasei FMT2 Isolated from Fecal Microbiota Transplantation (FMT) Capsules.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107405},
doi = {10.1016/j.micpath.2025.107405},
pmid = {40024538},
issn = {1096-1208},
abstract = {Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2,838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3,358 orthologous clusters, including 1,775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.},
}
@article {pmid40022977,
year = {2025},
author = {Noiset, P and Héger, M and Salmon, C and Kwapong, P and Combey, R and Thevan, K and Warrit, N and Rojas-Oropeza, M and Cabirol, N and Zaragoza-Trello, C and Rasmussen, C and Nkoba, K and Vereecken, NJ},
title = {Ecological and evolutionary drivers of stingless bee honey variation at the global scale.},
journal = {The Science of the total environment},
volume = {969},
number = {},
pages = {178945},
doi = {10.1016/j.scitotenv.2025.178945},
pmid = {40022977},
issn = {1879-1026},
abstract = {Stingless bee honey (SBH) is a prime natural product consumed and used for diverse medicinal and traditional purposes by local communities across the (sub-)tropics. Despite its ecological and cultural significance, the drivers of its compositional variation within and among species remain poorly understood, particularly throughout Asia and sub-Saharan Africa. Addressing this issue at the global scale has the potential to inform broader and less explored eco-evolutionary and how variation in SBH across the (sub-)tropics has led human communities to develop diverse and sometimes specific patterns of practices that are now integral to their cultural and economic life. In this study, we aimed to disentangle the roles of evolutionary and environmental drivers of SBH compositional variation using a sampling design that combines honey profiling by H1-NMR spectroscopy with the collection of honeys from honey bees and stingless bees at the global scale. The results show a clear differentiation between the chemical composition and functional diversity of honey bee and stingless bee honeys, mainly due to the production of a range of bioproducts during sugar fermentation. The study of compositional variation of stingless bee honey showed that the role of ecological and evolutionary drivers and their joint effects varied within each tropical region, preventing the identification of a clear continental, phylogenetic or ecological pattern. We provide the first global and comprehensive characterization of SBH composition, a prerequisite for defining and accepting SBH in the different Codex Alimentarius. We also highlight the need for more interdisciplinary and trans-sectoral research adopting a holistic approach to investigate stingless bee honey characteristics.},
}
@article {pmid40022770,
year = {2025},
author = {Attiani, V and Smidt, H and van der Wielen, PWJJ},
title = {Impact of environmental and process conditions on the microbial ecology and performance of full-scale slow sand filters in drinking water treatment.},
journal = {Water research},
volume = {277},
number = {},
pages = {123328},
doi = {10.1016/j.watres.2025.123328},
pmid = {40022770},
issn = {1879-2448},
abstract = {Slow sand filters (SSFs) are commonly used for treating drinking water, effectively removing contaminants such as particles, organic matter, and microorganisms. However, the ecological dynamics of prokaryotic communities within SSFs remain poorly understood. This study investigated the top sand layer, the Schmutzdecke (SCM), along with the influent and effluent water of full-scale SSFs at four drinking water treatment plants (DWTPs) in the Netherlands. These plants use SSFs as the final step in their treatment to produce unchlorinated drinking water. Two DWTPs treat surface water after dune infiltration and do not apply advanced oxidation processes prior the SSF. In contrast, the other two DWTPs treat reservoir-stored surface water and incorporate ozonation or UV and activated carbon filtration as part of their treatment train. All SSFs consistently reduced biomass in the effluent compared to the influent, confirming their role in biomass load reduction. Key biological and chemical parameters showed that pretreatment with dune infiltration produced more biologically stable drinking water compared to reservoir storage. Moreover, while SSFs act as polishing filters when treating dune-infiltrated surface water, they significantly alter the prokaryotic community and biological stability of the water when treating reservoir-stored surface water. Prokaryotic communities in the SCM and water samples showed distinct compositions rather than merely the accumulation of microorganisms in the SCM from the influent water, demonstrating that SSF are active ecosystems different from water. The SCM exhibited a higher relative abundance of the genera SWB02, Gemmata, Pedomicrobium, Nitrospira, and mle1-7, while in the water samples the genus Candidatus Omnitrophus was relatively more abundant. Moreover, each DWTP hosts a unique prokaryotic profiles in both the SCM and water samples. Source water, upstream treatment and/or the biological stability of the influent water are identified as potential causes affecting the prokaryotic communities in SSFs that affect the microbial water quality of the effluent water.},
}
@article {pmid40016229,
year = {2025},
author = {Chang, J and Costa, OYA and Sun, Y and Wang, J and Tian, L and Shi, S and Wang, E and Ji, L and Wang, C and Pang, Y and Yao, Z and Ye, L and Zhang, J and Chen, H and Cai, Y and Chen, D and Song, Z and Rong, J and Raaijmakers, JM and Tian, C and Kuramae, EE},
title = {Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2038},
pmid = {40016229},
issn = {2041-1723},
mesh = {*Oryza/microbiology/metabolism ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Soil Microbiology ; *Nitrogen Fixation ; *Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Nitrogen/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Agriculture/methods ; },
abstract = {Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.},
}
@article {pmid40012773,
year = {2025},
author = {Sun, P and Wu, Y and Zhu, P and Wang, J and Yu, X and Guo, W},
title = {Spartina alterniflora invasion significantly alters the assembly and structure of soil bacterial communities in the Yellow River Delta.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1525632},
pmid = {40012773},
issn = {1664-302X},
abstract = {Soil microbial communities are integral to almost all terrestrial biogeochemical cycles, which are essential to coastal wetland functioning. However, how soil bacterial community assembly, composition, and structure respond to native and non-native plant invasions in coastal wetlands remains unclear. In this study of the coastal wetlands of the Yellow River Delta in China, the assembly, community composition, and diversity of soil bacterial communities associated with four wetland plant species (Phragmites australis, Spartina alterniflora, Suaeda salsa, and Tamarix chinensis) and four soil depths (0-10 cm, 10-20 cm, 20-30 cm, and 30-40 cm) were characterized using high-throughput sequencing. Plant species identity, as well as environmental factors, rather than soil depth, was found to play predominant roles in shaping the diversity and structure of wetland soil bacterial communities. S. alterniflora invasion altered bacterial community structure and increased bacterial diversity. Phragmites australis-associated bacterial communities were enriched with sulfate-reducing bacteria such as Desulfurivibrio and Desulfuromonas. In comparison, S. alterniflora-associated bacterial communities were enriched with both sulfate-reducing bacteria (SEEP-SRB1) and sulfate-oxidizing bacteria (Sulfurimonas), which maintained a dynamic balance in the local sulfur-cycle, and thereby enhanced S. alterniflora growth. In addition, stochastic processes dominated the assembly of soil bacterial communities associated with all four plant species, but were most important for the S. alterniflora community. The S. alterniflora-associated bacterial community also showed stronger interactions and more extensive connections among bacterial taxa; a co-occurrence network for this community had the greatest average clustering coefficient, average degree, modularity, and number of links and nodes, but the lowest average path length. Altogether, individual plant species had distinct effects on soil bacterial community assembly and structure, with the invasive species having the strongest impact. These results provide insights into microbial ecology and inform management strategies for coastal wetland restoration.},
}
@article {pmid40008244,
year = {2025},
author = {Xu, LL and McIlroy, SE and Ni, Y and Guibert, I and Chen, J and Rocha, U and Baker, DM and Panagiotou, G},
title = {Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycae141},
pmid = {40008244},
issn = {2730-6151},
abstract = {Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.},
}
@article {pmid40005728,
year = {2025},
author = {Yi, S and Wu, H and Lin, Y and Cha, X and Shang, Y},
title = {Antibiotic Resistance Profiles and Genomic Analysis of Endophytic Bacteria Isolates from Wild Edible Fungi in Yunnan.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020361},
pmid = {40005728},
issn = {2076-2607},
support = {32260624//the National Natural Science Foundation of China/ ; 202202AG050009//Yunnan Major Scientific and Technological Projects/ ; },
abstract = {The use of antibiotics has led to the emergence of antibiotic resistance, posing significant challenges in the prevention, control, and treatment of microbial diseases, while threatening public health, the environment, and food safety. In this study, the antibiotic resistance phenotypes and genotypes of 56 endophytic bacteria isolates from three species of wild edible fungi in Yunnan were analyzed using the Kirby-Bauer disk diffusion method and PCR amplification. The results revealed that all isolates were sensitive to ofloxacin, but resistance was observed against 17 other antibiotics. Specifically, 55, 53, and 51 isolates exhibited resistance to amoxicillin, penicillin, and vancomycin, respectively. Antibiotic resistance gene (ARG) detection indicated that the sulfonamide sul1 gene had the highest detection rate (53.57%). Excluding the ARG that was not detected, the lowest detection rates were the sulfonamide sul2 and sul3 genes, both at 1.79%. Among six tetracycline resistance genes, only tetK and tetM were detected. For β-lactam antibiotics, blaTEM, blaVIM, and blaSHV genes were present, while blaOXA was absent. In aminoglycoside resistance genes, aadB was not detected, while detection rates for aac(3')-IIa, acrB, and aadA1 were 3.57%, 1.79%, and 37.5%, respectively. The chloramphenicol Cat gene was detected at a rate of 14.29%, whereas floR was absent. For polypeptide resistance, VanC was detected at 3.57%, with EmgrB not detected. All three quinolone genes were detected, with detection rates of 8.92% for GyrA, 39.29% for GyrB, and 37.5% for ParC. Through phylogenetic analysis, 12 isolates that are closely related to ten common foodborne pathogenic bacteria were further selected for whole-genome sequencing and assembly. Gene annotations revealed that each isolate contained more than 15 ARGs and over 30 virulence factors. Notably, the detection rate of antibiotic resistance phenotypes was higher than that of genotypes, highlighting the importance of studying phenotypic antibiotic resistance that lacks identifiable ARGs. This study enriches the research on endophytes in wild edible fungi and provides new data for microbial ecology and antibiotic resistance research. It also offers critical insights for monitoring microbial antibiotic resistance in wild edible fungi and potentially other food sources, contributing to more effective strategies for ecological protection, sustainable agricultural development, and public health security.},
}
@article {pmid40005607,
year = {2025},
author = {Li, S and Zhuang, W and Feng, X and Warren, A and Gong, J},
title = {Morphology and Molecular Phylogeny of Four Anaerobic Ciliates (Protista, Ciliophora, Armophorea), with Report of a New Species and a Unique Arrangement Pattern of Dikinetids in Family Metopidae.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020240},
pmid = {40005607},
issn = {2076-2607},
support = {41976086, 42276094//National Natural Science Foundation of China/ ; },
abstract = {The diversity of anaerobic ciliates is greatly underestimated owing to the limitation in sampling and cultivation when compared with their aerobic counterparts. In this study, four anaerobic ciliates, viz. Brachonella abnormalis sp. nov., Brachonella contorta (Levander, 1894) Jankowski, 1964, Metopus contortus (Quennerstedt, 1867) Kahl, 1932, and Metopus major Kahl, 1932, were investigated by live observation, protargol staining and 18S rRNA gene sequencing. B. abnormalis sp. nov. can be separated from its congeners by a combination of the following features: bullet-shaped cell with a life size of about 130-190 × 90-120 μm, dikinetids distributed along dorsal dome kineties, highly developed adoral zone comprised of 87-107 polykinetids, making about 450° spiralization around the long axis. The present work demonstrates that two known species, M. contortus and M. major, have a special trait never previously reported, viz. short, regularly arranged preoral dome dikinetids. Species with short, regularly arranged dome dikinetids appear in divergent clades in SSU rRNA gene trees, which may infer that this trait evolved several times. Phylogenetic analyses based on SSU rRNA gene sequence data also support the monophyly of the genus Brachonella and the paraphyly of the order Metopida, respectively.},
}
@article {pmid40005589,
year = {2025},
author = {Warkhade, Y and Schaerer, LG and Bigcraft, I and Hazen, TC and Techtmann, SM},
title = {Diversity and Distribution of Hydrocarbon-Degrading Genes in the Cold Seeps from the Mediterranean and Caspian Seas.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020222},
pmid = {40005589},
issn = {2076-2607},
support = {Merck Future Insight Prize//Merck KGaA/ ; },
abstract = {Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA and metagenomic sequencing to elucidate microbial community structure and functional potential. Our findings reveal distinct differences in hydrocarbon degrading gene profiles between the two seas, with pathways for aerobic and anaerobic hydrocarbon degradation co-existing in sediments from both basins. Aerobic pathways predominate in the surface sediments of the Mediterranean Sea, while anaerobic pathways are favored in the surface sediments of the anoxic Caspian Sea. Additionally, sediment depths significantly influence microbial diversity, with variations in gene abundance and community composition observed at different depths. Aerobic hydrocarbon-degrading genes decrease in diversity with depth in the Mediterranean Sea, whereas the diversity of aerobic hydrocarbon-degrading genes increases with depth in the Caspian Sea. These results enhance our understanding of microbial ecology in cold seep environments and have implications for bioremediation practices targeting hydrocarbon pollutants in marine ecosystems.},
}
@article {pmid40003826,
year = {2025},
author = {Castañeda-Espinosa, A and Duque-Granda, D and Cadavid-Restrepo, G and Murcia, LM and Junca, H and Moreno-Herrera, CX and Vivero-Gómez, RJ},
title = {Study of Bacterial Communities in Water and Different Developmental Stages of Aedes aegypti from Aquatic Breeding Sites in Leticia City, Colombian Amazon Biome.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/insects16020195},
pmid = {40003826},
issn = {2075-4450},
support = {57545//Universidad Nacional de Colombia/ ; },
abstract = {Aedes aegypti is a key vector in the transmission of arboviral diseases in the Colombian Amazon. This study aimed to characterize microbiota composition using DNA extracted from water in artificial breeding sites, immature stages, and adults of Ae. aegypti in Leticia, Amazonas. Additionally, the physicochemical water variables were correlated with the bacterial communities present. Eight artificial breeding sites were identified, with bucket, plant pot, and tire being the most frequent. The breeding sites exhibited similar physicochemical profiles, with significant temperature and salinity differences (p-value < 0.03). The most representative bacterial genera included Ottowia (82%), Xanthobacter (70.59%), and Rhodocyclaceae (92.78%) in breeding site water; Aquabacterium (61.07%), Dechloromonas (82.85%), and Flectobacillus (58.94%) in immature stages; and Elizabethkingia (70.89%) and Cedecea (39.19%) in males and females of Ae. aegypti. Beta diversity analysis revealed distinct clustering between adults and the water and immature communities (p-value < 0.001). Multivariate analysis showed strong correlations among bacterial communities, breeding sites, and physicochemical variables such as tire and drum cover which exhibited high levels of total dissolved solids, conductivity, and salinity associated with Flectobacillus, Leifsonia, Novosphingobium, Ottowia, and Rhodobacter. Bacterial genera such as Mycobacterium, Escherichia, Salmonella, and Clostridium, present in artificial breeding sites, are associated with public health relevance. This study provides insights into bacterial community dynamics across Ae. aegypti's life cycle and underscores the importance of water physicochemical and biological characteristics for developing new vector control strategies.},
}
@article {pmid40003751,
year = {2025},
author = {Rampanti, G and Cardinali, F and Ferrocino, I and Milanović, V and Garofalo, C and Osimani, A and Aquilanti, L},
title = {Deciphering the Microbiota of Edible Insects Sold by Street Vendors in Thailand Using Metataxonomic Analysis.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/insects16020122},
pmid = {40003751},
issn = {2075-4450},
abstract = {The aim of the present study was to investigate the microbiota of processed ready-to-eat (fried or boiled) edible insects sold by street vendors at local green markets in Thailand (Bangkok and Koh Samui). To this end, samples of 4 insect species (rhino beetle adults, silkworm pupae, giant waterbugs adults, and black scorpions) were collected and analyzed through viable counting and metataxonomic analysis. Enterobacteriaceae showed counts below 1 log cfu g[-1] in all samples, except for black scorpions, which showed elevated counts reaching up to 4 log cfu g[-1]. Total mesophilic aerobes counts were up to 8 log cfu g[-1] in all the analyzed samples. Counts below 1 log cfu g[-1] were observed for Escherichia coli, Staphylococcus aureus, sulfite-reducing clostridia viable cells and spores, and Bacillus cereus. All the samples showed the absence of Listeria monocytogenes and Salmonella spp. According to metataxonomic analysis, 14 taxa were consistently present across all insect samples, including Dellaglioa algida, Latilactobacillus curvatus, Latilactobacillus sakei, Acetobacteraceae, Apilactobacillus kunkeei, Bombilactobacillus spp., Enterobacteriaceae, Gilliamella spp., Lactobacillus spp., Lactobacillus apis, Streptococcus thermophilus, Lacticaseibacillus rhamnosus, Lactiplantibacillus plantarum, and Weissella spp. Minority taxa included Alcaligenes spp., Brochothrix thermosphacta, Psychrobacter spp., Staphylococcus saprophyticus, Lactobacillus melliventris, Pediococcus spp., Levilactobacillus brevis, and Snodgrassella alvi.},
}
@article {pmid39998093,
year = {2025},
author = {Varini, C and Manganelli, M and Scardala, S and Antonelli, P and Losasso, C and Testai, E},
title = {An Update of Tetrodotoxins Toxicity and Risk Assessment Associated to Contaminated Seafood Consumption in Europe: A Systematic Review.},
journal = {Toxins},
volume = {17},
number = {2},
pages = {},
doi = {10.3390/toxins17020076},
pmid = {39998093},
issn = {2072-6651},
support = {project n. RF-2021-12373885//Ministry of Health of Italy/ ; },
mesh = {Risk Assessment ; *Seafood/analysis ; Europe ; Animals ; Humans ; *Food Contamination/analysis ; *Tetrodotoxin/analysis/toxicity ; Dietary Exposure/analysis ; },
abstract = {Following the occurrence of Tetrodotoxins (TTXs) in Europe-a group of neurotoxins identified in Asia, where fatalities occurred after the ingestion of contaminated pufferfish-the EFSA proposed a limit of 44 µg of TTX/kg of shellfish meat in mollusks in 2017, to protect heavy consumers. The limit was based on an acute reference dose (ARfD) derived from the few available data on TTX toxicity. TTX is expected to increase with sea-surface warming; indeed, it has been found in spring/summer in mollusks in Europe, with concentrations often exceeding this limit. Due to the numerous uncertainties of the EFSA's ARfD, we conducted a systematic review to provide an update on TTX toxicity. Out of 12,741 articles retrieved from PubMed, Science Direct, and Scopus since 2017, only 17 were eligible for data extraction. Our results show that they are not sufficient to modify the EFSA's conclusions. Furthermore, our analysis of occurrence data in European seafood, to assess the current risk of exposure to TTX, reveals several gaps, such as different LODs/LOQs and seasonal monitoring not allowing comparisons between areas and too few analyzed sites. However, the presence of positive samples exceeding the EFSA limit indicates a potential risk even for general consumers, highlighting the urgency to address these knowledge gaps.},
}
@article {pmid39996333,
year = {2025},
author = {Medeiros, W and Kralova, S and Oliveira, V and Ziemert, N and Sehnal, L},
title = {Antarctic bacterial natural products: from genomic insights to drug discovery.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4np00045e},
pmid = {39996333},
issn = {1460-4752},
abstract = {Covering: up to the end of 2024Microbial life dominates the extreme continent Antarctica, playing a pivotal role in ecosystem functioning and serving as a reservoir of specialized metabolites known as natural products (NPs). NPs not only contribute to microbial adaptation to harsh conditions but also modulate microbial community structure. Long-term isolation and environmental pressures have shaped the genomes of Antarctic bacteria, suggesting that they also encode unique NPs. Since NPs are also an important source of drugs, we argue that investigating Antarctic bacterial NPs is essential not only for understanding their ecological role and evolution, but also for discovering new chemical structures, biosynthetic mechanisms, and potential new drugs. Yet, despite advances in omics technologies and increased scientific activities in Antarctica, relatively few new bacterial NPs have been discovered. The lack of systematic research activities focused on the exploration of Antarctic bacteria and their NPs constitutes a big problem considering the climate change issue, to which ecosystems in polar regions are the most sensitive areas on the Earth. Here, we highlight the currently available data on Antarctic bacteria, their biosynthetic potential, and the successful NP discoveries, while addressing the challenges in NP research and advocating for systematic, collaborative efforts aligned with the Antarctic Treaty System and the Antarctic Conservation Biogeographic Regions.},
}
@article {pmid39992142,
year = {2025},
author = {Sun, L and Wang, Q and Huang, J and Wang, H and Yu, Z},
title = {Disrupting the balance: how acne duration impacts skin microbiota assembly processes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0260324},
doi = {10.1128/spectrum.02603-24},
pmid = {39992142},
issn = {2165-0497},
abstract = {Growing interest in the impact of microbial balance on health has driven studies on the ecological processes shaping the skin microbiota. Skin diseases, which alter the skin's local environment, can disrupt the microbial structure and interact with the disease itself. However, research on microbial assembly in diseased skin remains limited. In this study, we applied ecological models to characterize the processes shaping the skin microbiota in acne patients, considering the impact of disease duration on both skin pores and surfaces using bacterial amplicon sequencing. Our results revealed a significant shift in microbial diversity on the skin surface of patients with long-term acne. Further microbial community analyses showed a transition in ecological processes from healthy to diseased skin. Microbial communities on the skin surfaces of healthy controls and individuals with short-duration acne were primarily driven by heterogeneous selection, whereas microbial drift dominated the assembly process in the long-duration groups. Using the Sloan neutral model, we classified amplicon sequence variants (ASVs) into high-effect and low-effect groups based on relative abundance and sample occurrence. High-effect ASVs, likely exerting a greater ecological influence, were predominantly represented by Cutibacterium across all acne-affected skin groups, while Staphylococcus became enriched among high-effect ASVs in patients with long-term acne. Functional profiling further demonstrated that high-effect ASVs were significantly enriched in motility-related pathways. Additionally, we observed a reduction in microbial network complexity on skin surfaces as disease duration increased. Overall, the ecological dynamics of skin microbial communities may offer valuable insights into the mechanisms underlying disease onset and persistence.IMPORTANCEThe skin microbiota plays a critical role in acne development, yet the processes governing microbial assembly during acne progression remain poorly understood. Previous studies predominantly focused on factors such as acne severity, location, and duration in relation to skin microbial structure, with little attention given to the ecological mechanisms shaping the communities. In this study, we applied ecological models to investigate the processes influencing microbial assembly of skin microbiota in acne patients with varying disease durations and examined functions of ecologically important non-neutral amplicon sequence variants (ASVs). Our findings reveal a transition in ecological processes from deterministic to neutral processes as acne duration increased, with non-neutral ASVs potentially contributing to acne pathogenicity and persistence. These insights contribute to a deeper understanding of the ecological dynamics underlying acne and indicate that targeting these non-neutral ASVs or their associated functions may serve as the basis for future therapeutic strategies.},
}
@article {pmid39992122,
year = {2025},
author = {Li, X and Wang, H and Zang, Y and Xue, S and Xin, J and Liu, L and Tang, X and Chen, J},
title = {Exploring the structure and assembly of seagrass microbial communities in rhizosphere and phyllosphere.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0243724},
doi = {10.1128/aem.02437-24},
pmid = {39992122},
issn = {1098-5336},
abstract = {Microbial community assembly and interactions are pivotal research areas within microbial ecology, yet relevant studies in seagrass rhizospheres and phyllosphere remain relatively scarce. In this study, we utilized high-throughput sequencing technology to investigate the microbial communities in different periods and microhabitats (rhizosphere and phyllosphere) of two seagrass species (Zostera marina and Phyllospadix iwatensis). Our findings suggest that microhabitats have a more pronounced impact on the composition of seagrass-associated microbial communities compared to periods and species. Further investigations reveal that the phyllosphere microbial community exhibits a more intricate co-occurrence network and interactions than the rhizosphere microbial community. Keystone taxa show distinct functional roles in different microhabitats of seagrasses. Additionally, we observed that differences in seagrass microhabitats influence community assembly, with the rhizosphere microbial community being more influenced by deterministic processes (heterogeneous selection) compared to the phyllosphere. These findings contribute to our understanding of the intricate interactions between seagrasses and their associated microbial communities, providing valuable insights into their distribution patterns and microhabitat preferences.IMPORTANCEStudying the community structure and assembly of different microhabitats in seagrass beds contributes to revealing the complexity and dynamic processes of seagrass ecosystems. In the rhizosphere microhabitat of seagrasses, microbial communities may assist in disease resistance or enhance nutrient uptake efficiency in seagrasses. On the other hand, in the microhabitat on the surface of seagrass blades, microorganisms may be closely associated with the physiological functions and nutrient cycling of seagrass blades. Therefore, understanding the structure and assembly mechanisms of rhizosphere and phyllosphere microbial communities is crucial for exploring the interactions between seagrass and microbial communities, as well as for enhancing our comprehension of the stability and resilience of seagrass bed ecosystems.},
}
@article {pmid39991271,
year = {2025},
author = {Morales, SE and Tobias-Hünefeldt, SP and Armstrong, E and Pearman, WS and Bogdanov, K},
title = {Marine phytoplankton impose strong selective pressures on in vitro microbiome assembly, but drift is the dominant process.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf001},
pmid = {39991271},
issn = {2730-6151},
abstract = {Phytoplankton are known ecosystem engineers that modulate ocean community assembly processes, but the universality and extent of their microbiome control remains unclear. We used in vitro incubations and 16S ribosomal RNA gene amplicon sequencing to test the influence of Southern and South Pacific oceans dominant phytoplankton on assembly processes and community successions in response to phytoplankton blooms. Phytoplankton grown with reduced-diversity cultures or supplemented with exogenously added microbiomes showed reduced diversity, suggesting environmental filtering. Community profiles were distinct under all culture conditions, further confirming strong selection for specific microbiomes based on phytoplankton. Analysis of core, abundant, and rare organisms in each culture condition showed a conserved response in which core organisms were enriched under conditions of exogenously added phytoplankton. Progression through phytoplankton growth phases selected first for rare and abundant organisms, with increased selection for core members during the exponential phase and relaxing of selection during the death phase, as seen throughout incubations for microbiome-only controls. Surprisingly, selection process quantification identified drift as the dominant process across all conditions and growth phases, with homogenous selection and dispersal limitation accounting for the remainder. Altogether, using Southern Ocean-derived model organisms we confirmed the role phytoplankton play in community assembly but also demonstrated that stochastic processes still predominately drive community selection.},
}
@article {pmid39988434,
year = {2025},
author = {Howells, G and Sezmis, AL and Blake, C and McDonald, MJ},
title = {Co-Existence Slows Diversification in Experimental Populations of E. coli and P. fluorescens.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70061},
doi = {10.1111/1462-2920.70061},
pmid = {39988434},
issn = {1462-2920},
support = {APP1186140//National Health and Medical Research Council/ ; DP220103548//Australian Research Council/ ; },
mesh = {*Pseudomonas fluorescens/genetics/growth &amp; development ; *Escherichia coli/genetics/growth &amp; development/radiation effects ; *Coculture Techniques ; Adaptation, Physiological ; Genome, Bacterial ; Whole Genome Sequencing ; },
abstract = {Microbes grown in heterogeneous laboratory environments can rapidly diversify into multiple, coexisting variants. While the genetic and evolutionary mechanisms of laboratory adaptive radiations are well studied, how the presence of other species alters the outcomes of diversification is less well understood. To test the effect of co-culture growth on the Pseudomonas fluorescens SBW25 adaptive radiation, Escherichia coli and P. fluorescens were cultured in monoculture and co-culture for 8 weeks. In P. fluorescens monoculture, Wrinkly and Smooth Spreader types rapidly evolved and were maintained over 8 weeks, while E. coli monocultures evolved two colony types, a big and a small colony variant. In contrast, we found that in co-culture, E. coli did not evolve small colony variants. Whole genome sequencing revealed the genetic basis of possible co-culture specific adaptations in both E. coli and P. fluorescens. Altogether, our data support that the presence of multiple species changed the outcome of adaptive radiation.},
}
@article {pmid39987915,
year = {2025},
author = {De Luca, G and Barakat, M and Verméglio, A and Achouak, W and Heulin, T},
title = {The Bacterial Genus Ramlibacter: Betaproteobacteria Capable of Surviving in Oligotrophic Environments Thanks to Several Shared Genetic Adaptation Traits.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70059},
doi = {10.1111/1462-2920.70059},
pmid = {39987915},
issn = {1462-2920},
mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Adaptation, Physiological ; Soil Microbiology ; Genome, Bacterial ; Betaproteobacteria/genetics ; DNA, Bacterial/genetics ; Carbon/metabolism ; Ecosystem ; Sequence Analysis, DNA ; },
abstract = {Ramlibacter tataouinensis, the type species of the genus Ramlibacter, is renowned for its ability to thrive in hot, arid and nutrient-poor desert soils. To investigate whether its adaptive properties are shared across all 20 currently described Ramlibacter species found in diverse terrestrial and aquatic habitats worldwide, we conducted a comprehensive analysis of 16S rRNA sequences and genomic information available from the literature. Our study encompassed approximately 40 deposited genomes, allowing us to propose a genomic phylogeny that aligns with the 16S rRNA phylogeny. Our findings reveal several conserved features across the genus Ramlibacter. This includes the presence of light sensors, environmental sensing networks, organic carbon and phosphate acquisition systems and the ability to store carbon and energy in the form of polyhydroxyalkanoate or polyphosphate granules. These shared traits rationalise the widespread distribution of Ramlibacter in oligotrophic terrestrial and aquatic environments. They also explain the genus' ability to withstand desiccation, endure extended periods of starvation, and survive in nutrient-depleted conditions. Notably, certain adaptive features are further enhanced in several species by their pleiomorphism and ability to form cysts. Overall, our study not only highlights the ecological adaptations of Ramlibacter species but also extends our understanding of microbial ecology in oligotrophic environments.},
}
@article {pmid39987257,
year = {2025},
author = {Zhang, X and Ta, N and Yi, S and Xiong, H},
title = {Intolerance of uncertainty and mental health in patients with IBD: the mediating role of maladaptive coping.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6464},
pmid = {39987257},
issn = {2045-2322},
mesh = {Humans ; Uncertainty ; Male ; Female ; *Adaptation, Psychological ; *Inflammatory Bowel Diseases/psychology ; Adult ; Middle Aged ; *Mental Health ; Surveys and Questionnaires ; *Anxiety/psychology ; *Depression/psychology ; Young Adult ; Aged ; },
abstract = {The aim of this study was to investigate the relationship between intolerance of uncertainty (IU) and mental health in patients with Inflammatory Bowel Disease (IBD), and to explore the mediating role of coping styles. A questionnaire was administered to adult patients with IBD, which included general demographic information, the Intolerance of Uncertainty Scale, the Generalized Anxiety Disorder-7, and the Patient Health Questionnaire-9. The study ultimately included validated questionnaires from 163 IBD patients. Intolerance of uncertainty was significantly and positively correlated with anxiety (r = 0.738, p < 0.01) and depression (r = 0.683, p < 0.01). The mediating effect of adaptive coping style was not significant. The maladaptive coping style partially mediated the relationship between IU and anxiety, as well as between IU and depression, with the mediating effect size of 25.5% and 34.2%, respectively. Our findings emphasize the impact of the inability to tolerate uncertainty on the mental health of patients with IBD. It suggests that interventions can be implemented to enhance IBD patients' tolerance of uncertainty and to modify their maladaptive coping styles to promote mental health. This offers a valuable framework for psychological interventions for IBD patients.},
}
@article {pmid39985718,
year = {2025},
author = {Gufwan, LA and Peng, L and Gufwan, NM and Lan, S and Wu, L},
title = {Enhancing Soil Health Through Biocrusts: A Microbial Ecosystem Approach for Degradation Control and Restoration.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {8},
pmid = {39985718},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Ecosystem ; *Environmental Restoration and Remediation/methods ; Fungi/metabolism/genetics/physiology ; Biodiversity ; Cyanobacteria/metabolism ; Lichens/microbiology ; Microbiota ; Bryophyta/microbiology ; Biodegradation, Environmental ; },
abstract = {Escalating global concerns about soil degradation, driven by erosion, salinization, compaction, pollution, and organic matter loss, highlights the critical need for sustainable remediation. Biocrusts-complex communities of cyanobacteria, algae, lichens, bryophytes, and fungi-play a pivotal role in soil stabilization, erosion prevention, and nutrient cycling. This study presents recent advancements in biocrust application for soil management and restoration, focusing on artificial biocrusts as a nature-based solution biotechnology. It emphasizes their effectiveness in enhancing soil quality, biodiversity, and ecosystem functionality. Researchers are leveraging these microbial communities to develop strategies that improve soil health and rehabilitate degraded landscapes. The review concludes that biocrusts are a viable strategy for boosting soil resilience and enhancing soil health against environmental stressors. It recommends future research on their long-term ecological impacts and methods to enhance their functionality.},
}
@article {pmid39978646,
year = {2025},
author = {Kij, A and Kieronska-Rudek, A and Bar, A and Czyzynska-Cichon, I and Strus, M and Kozien, L and Wiecek, G and Zeber-Lubecka, N and Kulecka, M and Kwiatkowski, G and Przyborowski, K and Mohaissen, T and Sternak, M and Buczek, E and Zakrzewska, A and Proniewski, B and Kus, K and Franczyk-Zarow, M and Kostogrys, RB and Pieterman, EJ and Princen, HMG and Chlopicki, S},
title = {Low phylloquinone intake deteriorates endothelial function in normolipidemic and dyslipidaemic mice.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109867},
doi = {10.1016/j.jnutbio.2025.109867},
pmid = {39978646},
issn = {1873-4847},
abstract = {While the plasma phylloquinone (PK) concentration is inversely correlated with cardiovascular risk, the involvement of PK in regulating endothelial function has not been directly investigated. Therefore, in this study we assessed the effects of short-term treatment with PK-deficient diets (5-10 weeks) on endothelial function in normolipidemic 14-week-old male C57BL/6JCmd mice and age-matched dyslipidaemic male E3L.CETP mice. Our results show that in normolipidemic mice dietary PK deficiency was associated with a marked reduction of PK levels in the plasma and liver (liquid chromatography-mass spectrometry measurements) and with impaired endothelium-dependent vasodilation assessed in vivo by magnetic resonance imaging (MRI). Dietary PK deficiency-induced endothelial dysfunction was fully reversed by PK supplementation. In dyslipidaemic E3L.CETP mice, dietary PK deficiency exacerbated preexisting endothelial dysfunction. Furthermore, dietary PK deficiency decreased menaquinone-4 (MK-4) levels in the aorta but did not affect blood coagulation (calibrated automated thrombography), microbiota composition (culturing and next-generation sequencing), and gut menaquinone production. In conclusion, our study demonstrated for the first time that sufficient dietary PK intake supports endothelial function in normolipidemic and dyslipidaemic mice indicating nutritional significance of dietary PK in the maintenance of endothelial function in humans.},
}
@article {pmid39976768,
year = {2025},
author = {Kauserud, H and Martin-Sanchez, PM and Estensmo, EL and Botnen, S and Morgado, L and Maurice, S and Høiland, K and Skrede, I},
title = {Yeasts Prefer Daycares and Molds Prefer Private Homes.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {7},
pmid = {39976768},
issn = {1432-184X},
support = {741332//Horizon 2020/ ; 741332//Horizon 2020/ ; PID2021-123184OA-I00//MICIN/AEI, Spain/ ; },
mesh = {*Fungi/classification/genetics/isolation &amp; purification ; Norway ; *Housing ; *Air Pollution, Indoor/analysis ; *Yeasts/classification/isolation &amp; purification/genetics ; *Mycobiome ; Humans ; *Child Day Care Centers ; Air Microbiology ; Dust/analysis ; Child ; Child, Preschool ; },
abstract = {Worldwide, people spend most of their time indoors; in their homes, workplaces, schools, and daycares. Indoor fungi can cause negative health effects due to the production of toxins or volatiles that trigger the immune system of the occupants. To what degree indoor fungi (mycobiomes) differ between buildings with different usage is poorly known. Here, we compare the indoor mycobiomes in 123 children's daycare centers and 214 private homes throughout Norway, as revealed by metabarcoding of DNA extracted from dust samples collected by community scientists. Although the fungal richness per se was similar in dust samples from daycares and homes, the fungal community composition differed. Yeast fungi, distributed mainly across the orders Saccharomycetales, Filobasidiales, and Tremellales, were proportionally more abundant in the daycares, while filamentous fungi, including spore-producing molds such as Aspergillus, Penicillum, and Cladosporium, were relatively more abundant in homes. Number of occupants, which is considerably higher in daycares, correlated significantly with the fungal community shift. We hypothesize that the density of occupants and their age distribution drive the systematic difference of yeasts and filamentous fungi in the two building types.},
}
@article {pmid39976447,
year = {2025},
author = {Bittleston, L and Gilbert, J and Klassen, J and Mackelprang, R and Mandel, MJ and Newton, RJ and Paudel, A and Rodriguez-Verdugo, A and Shade, A and Wilhelm, RC and Zhang, Y},
title = {Embracing the systems complexity of microbial ecology and evolution: call for papers.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0009125},
doi = {10.1128/msystems.00091-25},
pmid = {39976447},
issn = {2379-5077},
}
@article {pmid39972634,
year = {2025},
author = {de Sousa, T and Silva, C and Igrejas, G and Hébraud, M and Poeta, P},
title = {The Interactive Dynamics of Pseudomonas aeruginosa in Global Ecology.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70004},
doi = {10.1002/jobm.70004},
pmid = {39972634},
issn = {1521-4028},
support = {//This work was supported by grant 2020.05332.BD, and the projects UI/00772 and LA/P/0059/2020 funded by the Portuguese Foundation for Science and Technology (FCT)./ ; },
abstract = {Pseudomonas aeruginosa is an opportunistic bacterium widely distributed in both natural and urban environments, playing a crucial role in global microbial ecology. This article reviews the interactive dynamics of P. aeruginosa across different ecosystems, highlighting its capacity for adaptation and resistance in response to environmental and therapeutic pressures. We analyze the mechanisms of antibiotic resistance, including the presence of resistance genes and efflux systems, which contribute to its persistence in both clinical and nonclinical settings. The interconnection between human, animal, and environmental health, within the context of the One Health concept, is discussed, emphasizing the importance of monitoring and sustainable management practices to mitigate the spread of resistance. Through a holistic approach, this work offers insights into the influence of P. aeruginosa on public health and biodiversity.},
}
@article {pmid39971349,
year = {2025},
author = {Russo, CJ and Husain, K and Murugan, A},
title = {Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales.},
journal = {Annual review of biophysics},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biophys-081624-030543},
pmid = {39971349},
issn = {1936-1238},
abstract = {All biological systems are subject to perturbations arising from thermal fluctuations, external environments, or mutations. Yet, while biological systems consist of thousands of interacting components, recent high-throughput experiments have shown that their response to perturbations is surprisingly low dimensional: confined to only a few stereotyped changes out of the many possible. In this review, we explore a unifying dynamical systems framework-soft modes-to explain and analyze low dimensionality in biology, from molecules to ecosystems. We argue that this soft mode framework makes nontrivial predictions that generalize classic ideas from developmental biology to disparate systems, namely phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.},
}
@article {pmid39970705,
year = {2025},
author = {Yuan, K and Xu, H and Li, S and Coker, OO and Liu, W and Wang, L and Zhang, X and Yu, J},
title = {Intraneoplastic fungal dysbiosis is associated with colorectal cancer progression and host gene mutation.},
journal = {EBioMedicine},
volume = {113},
number = {},
pages = {105608},
doi = {10.1016/j.ebiom.2025.105608},
pmid = {39970705},
issn = {2352-3964},
abstract = {BACKGROUND: The relationship between intraneoplastic fungi and colorectal cancer (CRC) progression remains largely unclear. Here, we investigated fungal community changes in adenoma and CRC and their correlation with host genetic mutations.<br><br>METHODS: We obtained 261 tissue biopsies from two geographically distinct cohorts of CRC and adenoma patients, with each individual contributing 2-5 biopsies from lesions and 2 from adjacent normal tissues. 18S ribosomal RNA gene sequencing was used for microbial profiling. Host genetic alterations including KRAS mutations and microsatellite instability (MSI) were detected concurrently.<br><br>FINDINGS: Intra-neoplastic fungal composition significantly differed between CRC and adenoma in two independent cohorts, with enrichment of highly variable fungi (HVF) in CRC. Six HVFs exhibited higher abundances in adenoma and CRC compared to adjacent normal tissues with Malassezia showing a progressive increase from adenoma to CRC. Fungi intratumoral heterogeneity index also increased from adenoma through stages I to IV of CRC. Intra-tumoral fungi-fungi co-abundance analysis indicated stronger positive interactions in CRC than in adenoma, with increasingly robust links among intra-tumoral fungi along adenoma-CRC progression, primarily driven by Malassezia and Aspergillus. Furthermore, fungal heterogeneity was significantly correlated with host genetic mutations, with higher risk indices in CRC tissues harboring KRAS and MSI mutations. Thirteen fungi stratified CRC samples with KRAS mutations, achieving an area under the curve (AUC) of 0.86, while those associated with MSI status showed an AUC of 0.89.<br><br>INTERPRETATION: This study demonstrates that intraneoplastic fungal community alterations occur between adenoma and CRC, with increasing heterogeneity associated with host genetic mutations, emphasizing the role of fungal dysbiosis in CRC.<br><br>FUNDING: This work was supported by RGC Research Impact Fund Hong Kong (R4032-21F); RGC-CRF (C4008-23W); Strategic Seed Funding Collaboration Research Scheme CUHK (3133344); Strategic Impact Enhancement Fund CUHK (3135509); Impact case for RAE CUHK (3134277).},
}
@article {pmid39970561,
year = {2025},
author = {Gullì, M and Cangioli, L and Frusciante, S and Graziano, S and Caldara, M and Fiore, A and Klonowski, AM and Maestri, E and Brunori, A and Mengoni, A and Pihlanto, A and Diretto, G and Marmiroli, N and Bevivino, A},
title = {The relevance of biochar and co-applied SynComs on maize quality and sustainability: Evidence from field experiments.},
journal = {The Science of the total environment},
volume = {968},
number = {},
pages = {178872},
doi = {10.1016/j.scitotenv.2025.178872},
pmid = {39970561},
issn = {1879-1026},
abstract = {Adoption of sustainable maize cropping practices is urgently needed. Synthetic microbial communities (SynComs) made of plant growth-promoting microorganisms (PGPMs), coupled with biochar from residual biomass, offer an environmentally compatible alternative to inorganic fertilizers and may improve soil fertility. This article extends in a two-year field trial with preliminary results obtained in previous pot experiments, monitoring plant physiology, soil biology and chemistry, and kernel metabolomics. Here, we report the synergistic effect of the co-application of biochar, SynComs, and arbuscular mycorrhizal fungi on the soil microbiome, maize growth, and kernel metabolomic profile. SynComs application did not affect the diversity and richness of soil microbial communities; therefore, it posed a low risk of long-term effects on soil microbial ecology. With SynComs and biochar co-application to the soil, the physiology of maize plants was characterized by higher chlorophyll content, ear weight, and kernel weight. The combination of SynComs and biochar also affected the kernel metabolome, resulting in enriched health-beneficial and anti-stress metabolites. Since the preliminary evidence on the environmental and economic impact of these new associations was more favorable than that of conventional fertilizers, it seems reasonable that their large-scale implementation can eventually favor the transition to more sustainable agriculture.},
}
@article {pmid39970001,
year = {2025},
author = {Vo, L and Avgidis, F and Mattingly, HH and Edmonds, K and Burger, I and Balasubramanian, R and Shimizu, TS and Kazmierczak, BI and Emonet, T},
title = {Nongenetic adaptation by collective migration.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {8},
pages = {e2423774122},
doi = {10.1073/pnas.2423774122},
pmid = {39970001},
issn = {1091-6490},
support = {R01GM138533//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01GM106189//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F31GM149174-01//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Escherichia coli/genetics/physiology ; *Chemotaxis/physiology ; *Adaptation, Physiological ; Phenotype ; Escherichia coli Proteins/metabolism/genetics ; Gene Expression Regulation, Bacterial ; },
abstract = {Cell populations must adjust their phenotypic composition to adapt to changing environments. One adaptation strategy is to maintain distinct phenotypic subsets within the population and to modulate their relative abundances via gene regulation. Another strategy involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. We found that the migrating populations became enriched with high-performing swimming phenotypes in each environment, allowing the populations to adapt without requiring mutations or gene regulation. This adaptation is dynamic and rapid, reversing in a few doubling times when migration ceases. By measuring the chemoreceptor abundance distributions during migration toward different attractants, we demonstrated that adaptation acts on multiple chemotaxis-related traits simultaneously. These measurements are consistent with a general mechanism in which adaptation results from a balance between cell growth generating diversity and collective migration eliminating underperforming phenotypes. Thus, collective migration enables cell populations with continuous, multidimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions.},
}
@article {pmid39963424,
year = {2024},
author = {Höner Zu Siederdissen, C and Spangenberg, J and Bisdorf, K and Krautwurst, S and Srivastava, A and Marz, M and Taubert, M},
title = {Nanopore sequencing enables novel detection of deuterium incorporation in DNA.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {3584-3594},
pmid = {39963424},
issn = {2001-0370},
abstract = {Identifying active microbes is crucial to understand their role in ecosystem functions. Metabolic labeling with heavy, non-radioactive isotopes, i.e., stable isotope probing (SIP), can track active microbes by detecting heavy isotope incorporation in biomolecules such as DNA. However, the detection of heavy isotope-labeled nucleotides directly during sequencing has, to date, not been achieved. In this study, Oxford nanopore sequencing was utilized to detect heavy isotopes incorporation in DNA molecules. Two isotopes widely used in SIP experiments were employed to label a bacterial isolate: deuterium (D, as D2O) and carbon-13 ([13]C, as glucose). We hypothesize that labeled DNA is distinguishable from unlabeled DNA by changes in the nanopore signal. To verify this distinction, we employed a Bayesian classifier trained on signal distributions of short oligonucleotides (k-mers) from labeled and unlabeled sequencing reads. Our results show a clear distinction between D-labeled and unlabeled reads, based on changes in median and median absolute deviation (MAD) of the nanopore signals for different k-mers. In contrast, [13]C-labeled DNA cannot be distinguished from unlabeled DNA. For D, the model employed correctly predicted more than 85% of the reads. Even when metabolic labeling was conducted with only 30% D2O, 80% of the obtained reads were correctly classified with a 5% false discovery rate. Our work demonstrates the feasibility of direct detection of deuterium incorporation in DNA molecules during Oxford nanopore sequencing. This finding represents a first step in establishing the combined use of nanopore sequencing and SIP for tracking active organisms in microbial ecology.},
}
@article {pmid39962695,
year = {2025},
author = {Peng, SW and Zhang, GY and Jiao, YY},
title = {[Microbial Ecology in the Mask-derived Plastisphere in a Water Environment].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {2},
pages = {1193-1202},
doi = {10.13227/j.hjkx.202402057},
pmid = {39962695},
issn = {0250-3301},
mesh = {*Masks ; Microbiota ; Water Microbiology ; Microplastics ; Ecosystem ; COVID-19 ; },
abstract = {As a result of the impact of COVID-19 and other respiratory diseases, the regular use of medical masks and the associated risk that the mask waste enters the water environment have increased, and the mask-derived microplastics are finally posing a potential impact on the aquatic ecological environment. This study explored the microbial diversity, function, assembly mechanism, and ecological network in the plastisphere derived from different layers of masks. The results indicated that the plastisphere in each layer had a unique microbial community, and the community richness gradually increased over time. The functions of microbial communities in the plastisphere, including pathogenicity, phototrophy, compound degradation, and the functions related to the cycling of carbon, nitrogen, and sulfur, changed significantly over time. As to the microbial assembly mechanism in the plastisphere, stochastic processes were more dominant （NST>0.5）, but the influence of deterministic processes gradually grew. The ecological network results indicated that all the plastispheres exhibited a high number of modules and high modularity, and the complexity of the microbial community gradually decreased with colonization time. This study indicates that the mask-derived plastisphere has a unique ecological process, which strengthens our understanding of the ecological effects and microbial colonization processes of the mask-derived plastisphere.},
}
@article {pmid39961999,
year = {2025},
author = {Popov, IV and Popov, IV and Chebotareva, IP and Tikhmeneva, IA and Peshkova, DA and Krikunova, AA and Tkacheva, EV and Algburi, AR and Abdulhameed, AM and Jargalsaikhan, A and Ganbold, O and Chikindas, ML and Venema, K and Ermakov, AM},
title = {Differences in gut microbiota composition, diversity, and predicted functional activity between wild and captive zoo Carollia perspicillata in a One Health perspective.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39961999},
issn = {1678-4405},
support = {075-10-2021-093//Ministry of Science and Higher Education of the Russian Federation/ ; 23-14-00316//Russian Science Foundation/ ; },
abstract = {Bats play an important role in global microbial ecology, as they are the host of various microbes. Carollia perspicillata is one of the most popular bat species in zoos. The influence of the captive environment on the gut microbiota of this species is underinvestigated. In this study, we compared gut microbiota composition, diversity, and the potential functional activity of wild and captive C. perspicillata from Panama and Russia (Moscow Zoo), respectively, based on high-throughput 16S rRNA sequencing data. The abundance of 13 bacterial phyla and 35 bacterial genera significantly differed. Environment- and farm animal health-related bacteria (Mannheimia, unclassified Pasteurellaceae, Staphylococcus, and Mycoplasma) dominated wild bats, while bacteria important for public health (Bacteroides, Clostridium sensu stricto 1, and Acinetobacter) were higher in zoo bats. We also observed significantly greater alpha diversity in zoo bats, while there were no significant differences in beta diversity. These findings were accompanied by significant differences in the abundance of 32 functional pathways of gut bacteria, which are probably associated with the different diets of wild and zoo bats. This study shows that the rearing environment significantly affects the gut microbiota of C. perspicillata and highlights that the outcomes of microbiome research of captive bats need to be interpreted with care. Such differences in gut bacterial communities should be the basis for the development of new handling and veterinary care protocols, and also be the justification for further studies of the impact of microbiota of wild and zoo bats on One Health.},
}
@article {pmid39961275,
year = {2025},
author = {Wang, A and Bong, CW and Tao, S and Ye, X and Liu, B and Liang, H and Zheng, X and Wong, YY and Loh, KH and Li, H and Chen, K and Lim, SH and Lee, CW},
title = {Evaluation of heavy metal pollution and ecological risk of surface sediments in a tropical mountainous River-Estuary-Shelf Continuum system: A case study of the Selangor River, Malaysia.},
journal = {Marine environmental research},
volume = {205},
number = {},
pages = {107017},
doi = {10.1016/j.marenvres.2025.107017},
pmid = {39961275},
issn = {1879-0291},
abstract = {As human activities continue to increase, the global production of pollutants has increased significantly, with the majority of pollutants being transported to the ocean via rivers, resulting in intensified pollution in estuaries and coastal areas. To maintain a healthy marine ecological environment, it is necessary to consider rivers, estuaries, and coastal seas as integrated systems and implement pollution management based on the concept of land-ocean integration. In this study, heavy metal elements in the surface sediments of Selangor River-Estuary-Coastal Shelf Continuum were collected and analysed to assess their pollution levels and potential ecological risks. The results show that the heavy metal content is high in the downstream and estuarine regions, with a general decreasing trend observed from nearshore to offshore in the coastal shelf area. The heavy metal pollution assessment indicates that the surface sediments of the Selangor River-Estuary-Coastal Shelf continuum were contaminated, with the most severe pollution occurring downstream and within the estuary. The pollution levels gradually decrease after exiting the estuary. The ecological risk associated with heavy metal pollution in rivers, estuaries, and southeastern coastal areas was classified as moderate to serious, whereas other areas exhibited only slight ecological risks. Specifically, As causes serious pollution in the river and estuary, with moderate-to-serious pollution in the coastal shelf area and moderate-to-serious ecological risks, mainly originating from mining within the river basin. Pb causes moderate pollution in the river, estuary, and coastal areas, with slight ecological risks due to mining within the river basin and inputs from nearby rivers, ports, and industrial activities. Other heavy metals cause minor pollution and pose minimal ecological risks.},
}
@article {pmid39961017,
year = {2025},
author = {Colman, DR and Templeton, AS and Spear, JR and Boyd, ES},
title = {Microbial ecology of Serpentinite-hosted ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf029},
pmid = {39961017},
issn = {1751-7370},
abstract = {Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.},
}
@article {pmid39960660,
year = {2025},
author = {Gomi, R and Adachi, F},
title = {Quinolone Resistance Genes qnr, aac(6')-Ib-cr, oqxAB, and qepA in Environmental Escherichia coli: Insights into Their Genetic Contexts from Comparative Genomics.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {6},
pmid = {39960660},
issn = {1432-184X},
support = {JP22K18038//JSPS KAKENHI/ ; 22B006//Kurita Water and Environment Foundation, Japan/ ; 2230113//Sumitomo Foundation, Japan/ ; JPMEERF20235R01//Environment Research and Technology Development Fund/ ; },
mesh = {*Escherichia coli/genetics/drug effects ; *Quinolones/pharmacology ; *Escherichia coli Proteins/genetics ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics ; Genomics ; Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; },
abstract = {Previous studies have reported the occurrence of transferable quinolone resistance determinants in environmental Escherichia coli. However, little is known about their vectors and genetic contexts. To gain insights into these genetic characteristics, we analyzed the complete genomes of 53 environmental E. coli isolates containing one or more transferable quinolone resistance determinants, including 20 sequenced in this study and 33 sourced from RefSeq. The studied genomes carried the following transferable quinolone resistance determinants alone or in combination: aac(6')-Ib-cr, oqxAB, qepA1, qnrA1, qnrB4, qnrB7, qnrB19, qnrD1, qnrS1, and qnrS2, with qnrS1 being predominant. These resistance genes were detected on plasmids of diverse replicon types; however, aac(6')-Ib-cr, qnrS1, and qnrS2 were also detected on the chromosome. The genetic contexts surrounding these genes included not only those found in clinical isolates but also novel contexts, such as qnrD1 embedded within a composite transposon-like structure bounded by Tn3-derived inverted-repeat miniature elements (TIMEs). This study provides deep insights into mobile genetic elements associated with transferable quinolone resistance determinants, highlighting the importance of genomic surveillance of antimicrobial-resistant bacteria in the environment.},
}
@article {pmid39954521,
year = {2025},
author = {Hernández-Villamor, D and Li, P and Aydogan, M and Verhelst, M and Van de Wiele, T and Rabaey, K and Prévoteau, A},
title = {Low electrode potentials enhance current generation by Geobacter sulfurreducens biofilms: A high-throughput study.},
journal = {Biosensors &amp; bioelectronics},
volume = {276},
number = {},
pages = {117232},
doi = {10.1016/j.bios.2025.117232},
pmid = {39954521},
issn = {1873-4235},
abstract = {The microbial species Geobacter sulfurreducens uses different extracellular electron transfer (EET) pathways depending on the potential of the final electron acceptor, yet a complete understanding of EET mechanisms and the impact of thermodynamically limiting potentials remains elusive. Here, we employ a custom-designed high-throughput system that enables the simultaneous and continuous execution of 128 parallel experiments to investigate the complete spectrum of potentials ([-0.25 to 0] V vs. SHE) impacting the metabolic energy generation in axenic G. sulfurreducens electroactive biofilms (EABs). These were grown for 500 h in three consecutive stages and characterized electrochemically. The EABs grown on electrodes poised below the apparent midpoint potential ([-0.18 to -0.16] V) grew slower than those grown at conventional, non-limiting potential (0 V), developing 50% smaller biofilms and 2.4-fold higher anodic plateau currents on average ([0.1 vs. 0.04] mA cm[-2]). These also exhibited enhanced charge transport coupled to higher average concentrations of charge carriers ([1.6 vs. 0.4] mMe[-]), the latter impacting linearly the anodic plateau current. Low- and high-potential redox pools were discriminated with the former comprising 50%-70% of storable charge. Overall, these findings strongly suggest an overexpression of charge carriers in G. sulfurreducens EABs cultivated at lower potentials and highlight the useful contribution of high-throughput tools for boosting research in electromicrobiology.},
}
@article {pmid39954444,
year = {2025},
author = {He, M and Tang, R and Guan, F and Peng, W and Lu, J and Li, K and Zhou, L and Wang, Y and Yuan, Y},
title = {Methanogenic response of paddy soils exposed to zinc oxide nanoparticles and sulfurized products.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137608},
doi = {10.1016/j.jhazmat.2025.137608},
pmid = {39954444},
issn = {1873-3336},
abstract = {The use of zinc oxide nanoparticles (ZnO NPs) in agriculture is expanding, yet their effects on microbial ecology in flooded paddy soils remain unclear. This study examined the influence of ZnO NPs and their sulfide derivatives (S-ZnO NPs) on methane production in paddy soils. Results showed that ZnO NPs at a concentration of 1000 mg/kg significantly inhibited methane production by 28.97 % in an acid soil and by 26.83 % in an alkaline soil. S-ZnO NPs at the same concentration did not significantly affect methane production in the alkaline soil and increased it by 15.33 % in the acid soil. High-throughput sequencing revealed that ZnO NPs significantly altered the microbial community structure, affecting the prevalence of methanogenic organisms like Methanosarcina in the acid soil and Methanobacterium in the alkaline soil. Quantitative PCR analysis showed a reduction in the expression of methanogenic gene (mcrA) and total bacterial 16S rRNA genes with ZnO NPs exposure, but S-ZnO NPs had a lesser impact on these genes. This research highlights the more toxic impact of ZnO NPs compared to S-ZnO NPs on methane production and microbial communities in paddy soils, emphasizing the necessity for careful evaluation of nanoparticles in agricultural use to avoid ecological disturbances.},
}
@article {pmid39954056,
year = {2025},
author = {Ren, Z and Gao, H and Martyniuk, N and Ren, H and Xiong, X and Luo, W},
title = {Dual-Domain Primary Succession of Bacteria in Glacier Forefield Streams and Soils of a Maritime and Continental Glacier.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {5},
pmid = {39954056},
issn = {1432-184X},
support = {2023YFF1303700//National Key Research and Development Program of China/ ; },
mesh = {*Soil Microbiology ; *Ice Cover/microbiology ; *Bacteria/classification/isolation &amp; purification/genetics ; China ; *Rivers/microbiology ; Biodiversity ; Ecosystem ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; },
abstract = {Glaciers retreat rapidly and create newly exposed terrestrial and aquatic habitats in glacier forefields, where primary succession proceeds synchronously in glacier forefields. Here, we introduced the "Dual-Domain Primary Succession" concept to examine the parallel yet distinct primary succession processes in soil and stream ecosystems within glacier forefields, by focusing on Hailuogou Glacier and Urumqi Glacier No.1 in China. Findings showed that soil bacterial communities exhibited higher α-diversity with a decreasing pattern in Hailuogou Glacier, in contrast to Urumqi Glacier No.1, which displayed lower and unimodally distributed α-diversity along the glacier forefield chronosequence (GFC). A similar pattern emerged in streams, except for an increasing α-diversity trend in Urumqi Glacier No.1 stream along the GFC. Additionally, α-diversity in streams changed more rapidly than in soils for Hailuogou Glacier, but more slowly for Urumqi Glacier No.1. Along GFC, both soil and stream bacterial communities experienced spatial variations, primarily due to species turnover. The succession of community composition was evident at the OTU level, with each module in the co-occurrence network consisting of OTUs enriched at specific successional stages. A substantial number of OTUs shared between paired soil and stream samples showed a decreasing trend along the GFC, while β-diversity increased. The results suggested that bacterial communities have a similar succession pattern but in different pace between soil and stream while having distinct successional trajectories between the studied glaciers. This study highlighted the "Dual-Domain Primary Succession" in glacier forefields, but further studies with more glaciers are necessary to make broader generalizations.},
}
@article {pmid39953673,
year = {2025},
author = {Kotsakis, GA and Ganesan, SM},
title = {Microbial Dysbiosis, Titanium Release, and Peri-implantitis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345241307939},
doi = {10.1177/00220345241307939},
pmid = {39953673},
issn = {1544-0591},
abstract = {The peri-implant mucosal barrier is a unique microenvironment where host-microbiome interactions take place on the surface of an implanted biomaterial. Therefore, peri-implant immunity not only is quintessential to oral health but also contributes to the maintenance of the biomaterial-tissue equilibrium in health. This review delves into the intricate interplay between host factors, biomaterial properties, and the microbiome with a focus on the mechanisms underlying peri-implant dysbiosis. Investigations into this complex milieu have led to the emerging understanding of titanium particles released from the implant as significant exposomes. When biomaterial breakdown occurs, implant degradation products form particles that are released in the peri-implant crevice, exerting profound effects on the local immune surveillance. Comparative analyses with natural dentition highlight the distinct immune responses elicited by titanium particles, thereby implicating them as a key modulator of peri-implant dysbiosis that differentiates peri-implant from periodontal inflammation. Nonetheless, disruptions in the homeostatic balance of host-biomaterial interactions are linked to pathogenic shifts of the peri-implant microbiome that are correlated with titanium particles in humans. Collectively, it is now well established that to elucidate the mechanisms governing peri-implant dysbiosis, this triangle of host-microbiome-biomaterial has to be conjointly investigated. This review highlights findings from studies that have underscored the multifaceted nature of peri-implant dysbiosis, emphasizing the intricate crosstalk between host immunity, biomaterial characteristics, and microbial ecology. These findings suggest that the titanium particle exposome may alter key inflammatory cascades in the peri-implant tissues including toll-like receptor activation and inflammasome and complement signaling, which lead to nonresolving destructive inflammation. The presence of abiotic danger signals in the form of implant degradation products in peri-implant tissues may make antimicrobial monotherapies largely ineffective for managing peri-implantitis. In turn, the future of peri-implantitis therapy seems to lie in the development of targeted host modulatory interventions against titanium-mediated inflammatory pathways.},
}
@article {pmid39952886,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Restoring unbalanced rhizosphere: microbiome transplants combatting leaf diseases.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.01.011},
pmid = {39952886},
issn = {1878-4372},
abstract = {Similar to humans, plants experience microbiome imbalance, which increases their vulnerability to pathogens. In a recent study, Ketehouli et al. applied a soil microbiome transplant (SMT) to restore the microbiome balance, which potentially reduced the severity of leaf diseases. Here, we examine this approach, highlighting its limitation and offering perspectives on its use for controlling leaf diseases in plants.},
}
@article {pmid39952771,
year = {2025},
author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E},
title = {Exploring viral diversity in fermented vegetables through viral metagenomics.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104733},
doi = {10.1016/j.fm.2025.104733},
pmid = {39952771},
issn = {1095-9998},
mesh = {*Metagenomics ; *Vegetables/virology/microbiology ; *Fermentation ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Microbiota ; Brassica/microbiology/virology ; Fermented Foods/microbiology/virology ; Bacteria/genetics/classification/isolation &amp; purification/virology ; Biodiversity ; Daucus carota/microbiology/virology ; Food Microbiology ; Viruses/isolation &amp; purification/classification/genetics ; Enterobacteriaceae/isolation &amp; purification/genetics/virology/classification ; Metagenome ; Lactobacillaceae/isolation &amp; purification/genetics/classification ; },
abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.},
}
@article {pmid39952743,
year = {2025},
author = {Wu, Y and Ma, F and Tan, S and Niu, A and Chen, Y and Liu, Y and Qiu, W and Wang, G},
title = {The aprD-mutated strain modulates the development of Pseudomonas fragi population but has limited effects on the spoilage profiles of native residents.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104708},
doi = {10.1016/j.fm.2024.104708},
pmid = {39952743},
issn = {1095-9998},
mesh = {Animals ; *Pseudomonas fragi/genetics/metabolism/growth &amp; development ; *Chickens/microbiology ; *Bacterial Proteins/genetics/metabolism ; *Food Microbiology ; *Meat/microbiology ; Mutation ; Biofilms/growth &amp; development ; Microbiota ; Food Storage ; Food Contamination/analysis ; },
abstract = {Extracellular enzymes produced by predominant bacteria exert important roles in inducing and accelerating spoilage, with their secretion regulated by specific genes. In Pseudomonas fragi, the aprD gene is a recognized regulator for secreting an alkaline extracellular protease. However, limited studies have focused on this gene in P. fragi population and its impact on meat microbial community structure and function. This study addressed this gap by monitoring the changes in biological properties of P. fragi populations and analyzing the discrepancies in spoilage phenotypes and microbial community structures of chilled chicken among groups differentiated by the initial prevalence of aprD-positive strains. The results showed that aprD-positive strains were disseminated in P. fragi populations, and its prevalence was associated with significant increases in swimming motility and biofilm formation capacities in specific groups. In situ contamination experiments revealed varying spoilage characteristics and community compositions among groups by day 3 of storage. Correlation analysis demonstrated a strong association between spoilage phenotypes and certain bacterial genera, such as Pseudomonadaceae_Pseudomonas and Carnobacterium. However, the microbial community structure and spoilage characteristics of samples from each group were not significantly different on the 5th day of storage. These findings suggest that even a small number of aprD mutants can significantly affect the assembly of the chilled meat microbial community. Nonetheless, the regulatory effect of aprD on spoilage at the strain and population levels of P. fragi is negligible in the context of complex natural microbiota. This work underscores the complex interactions between specific bacterial genes and the broader microbial ecology in refrigerated meat environments, providing deeper insights into the meat spoilage mechanisms.},
}
@article {pmid39951503,
year = {2025},
author = {Bauermann, J and Benzi, R and Nelson, DR and Shankar, S and Toschi, F},
title = {Turbulent mixing controls fixation of growing antagonistic populations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {7},
pages = {e2417075122},
doi = {10.1073/pnas.2417075122},
pmid = {39951503},
issn = {1091-6490},
mesh = {*Models, Biological ; Population Dynamics ; Computer Simulation ; },
abstract = {Unlike coffee and cream that homogenize when stirred, growing micro-organisms (e.g., bacteria, baker's yeast) can actively kill each other and avoid mixing. How do such antagonistic interactions impact the growth and survival of competing strains, while being spatially advected by turbulent flows? By using numerical simulations of a continuum model, we study the dynamics of two antagonistic strains that are dispersed by incompressible turbulent flows in two spatial dimensions. A key parameter is the ratio of the fluid transport time to that of biological reproduction, which determines the winning organism that ultimately takes over the whole population from an initial heterogeneous state, a process known as fixation. By quantifying the probability and mean time for fixation along with the spatial structure of concentration fluctuations, we demonstrate how turbulence raises the threshold for biological nucleation and antagonism suppresses flow-induced mixing by depleting the population at interfaces. Our work highlights the unusual biological consequences of the interplay of turbulent fluid flows with antagonistic population dynamics, with potential implications for marine microbial ecology and origins of biological chirality.},
}
@article {pmid39950593,
year = {2025},
author = {Kiesewetter, KN and Rawstern, AH and Cline, E and Ortiz, GR and Santamaria, F and Coronado-Molina, C and Sklar, FH and Afkhami, ME},
title = {Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {35},
number = {1},
pages = {e70007},
doi = {10.1002/eap.70007},
pmid = {39950593},
issn = {1051-0761},
support = {//South Florida Water Management District/ ; 1922521//Division of Environmental Biology/ ; 2030060//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; //University of Miami Dissertation Year Fellowship/ ; //USDA NIFA Predoctoral Fellowship/ ; },
mesh = {*Soil Microbiology ; *Trees ; *Fungi/physiology ; Environmental Restoration and Remediation/methods ; Microbiota ; Conservation of Natural Resources/methods ; },
abstract = {As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they are integral to ecosystem health and functioning. Despite microbiomes' importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration-fungal microbiomes' importance in "reconstructive" restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature-tree islands-in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared with their natural counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.},
}
@article {pmid39945937,
year = {2025},
author = {Gharbi, D and Neumann, FH and Staats, J and McDonald, M and Linde, JH and Mmatladi, T and Podile, K and Piketh, S and Burger, R and Garland, RM and Bester, P and Lebre, PH and Ricci, C},
title = {Prevalence of aeroallergen sensitization in a polluted and industrialized area: a pilot study in South Africa's Vaal Triangle.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {3},
pages = {287},
pmid = {39945937},
issn = {1573-2959},
support = {ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; ST-POC-2312-61906//South African Medical Research Council/ ; },
mesh = {Humans ; South Africa/epidemiology ; Male ; Adult ; *Allergens ; Pilot Projects ; Female ; Young Adult ; Adolescent ; Prevalence ; Middle Aged ; *Air Pollutants/analysis ; Pollen ; Hypersensitivity/epidemiology ; Skin Tests ; },
abstract = {This pioneering study evaluates the prevalence of aeroallergens reactivity among atopic populations living in the Vaal Triangle Airshed Priority Area (VTAPA), South Africa. A total of 138 volunteers (51 males and 87 females), of African, colored, white, and Asian ethnicity, and with a mean (range) age of 22 (18-56) years were participating in the study. The study was conducted on the North-West University (NWU) campus in Vanderbijlpark/VTAPA. The International Study of Asthma and Allergies in Childhood questionnaire was utilized for pre-screening to identify individuals with probable allergic dispositions. Subsequently, skin prick testing was conducted using commercial aeroallergen extracts for all confirmed participants with allergy symptoms. One hundred six participants were clinically diagnosed with pollen and fungal spore allergies. The highest allergy prevalence was attributed to Cynodon dactylon ((L.) Pers) (Bermuda grass) (41.5%), followed by Lolium perenne (L.) (ryegrass), grass mix, and Zea mays (L.) (maize) (31.1%), respectively. Moreover, among the tree allergens, Olea (L.) (olive tree) was the most prevalent allergen (20; 18.8%), followed by Platanus (L.) (plane tree) (18; 16.9%). Among the weeds, 16 (15.1%) participants were allergic to the weed mix (Artemisia (L.) (wormwood), Chenopodium (Link) (goosefoot), Salsola (L.) (saltwort), Plantago (L.) (plantain), and 11 (10.3%) to Ambrosia (L.) (ragweed)). Regarding the fungal spores, Alternaria (Fr.) (9; 8.5%) followed by Cladosporium (Link) (5; 4.7%) had the highest skin sensitivity. In this pilot study, our findings provide insights into the prevalence of allergic responses in the study population-underlining the strong impact of allergens of exotic plants-and contribute to the existing aerobiological data in South Africa.},
}
@article {pmid39945839,
year = {2025},
author = {Márquez-Sanz, R and Garrido-Benavent, I and Durán, J and de Los Ríos, A},
title = {The Establishment of a Terrestrial Macroalga Canopy Impacts Microbial Soil Communities in Antarctica.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {4},
pmid = {39945839},
issn = {1432-184X},
support = {PID2019-105469RB-C22//AEI, MICINN/ ; PID2019-105469RB-C22//AEI, MICINN/ ; TED2021-130908A-C43//Agencia Estatal de Investigaci&#xf3;n/ ; CNS2023-145367//EU Next Generation PRTR program/ ; PCI2023-143393//EIG EU-CELAC 2022/ ; 20224AT022//Consejo Superior de Investigaciones Cient&#xed;ficas/ ; RYC2020-029331-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {*Soil Microbiology ; Antarctic Regions ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Microbiota ; *Soil/chemistry ; Phylogeny ; Chlorophyta ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; },
abstract = {Prasiola is a genus of foliose green algae that forms extensive cryptogamic canopies that contribute to the greening of ice-free areas in the Antarctic tundra. To better understand the impact of Prasiola canopy establishment on colonization in these areas, this study compared the taxonomic and functional structures of bacterial and fungal communities in adjacent soils with and without extensive Prasiola colonization. DNA metabarcoding was employed to analyze the microbial community structure in these soils and in the canopy. Additionally, a phylogenetic study of Prasiola samples was conducted to characterize the taxonomic composition of the analyzed canopies, revealing the presence of Prasiola crispa (Lightfoot) Kützing and P. antarctica Kützing. Key soil attributes were assessed to examine the canopy's influence. Higher pH and carbon, nitrogen, and organic matter contents were found in Prasiola-covered soils than in bare soils. Furthermore, Prasiola canopy establishment not only influenced abiotic soil properties but also shaped soil microbial community structure and its functions. For instance, while Actinobacteriota predominated in bacterial communities both within the Prasiola canopy and beneath it, Bacteroidota dominated in the bare soil. Despite significant variability across soil types, fungal communities showed a trend of higher abundances in certain Ascomycetes, such as Helotiales, Hypocreales, or Xylariales, in soils beneath Prasiola compared to bare soils. Regarding functional diversity, covered soils exhibited a statistically significant lower potential for bacterial methanogenesis and autotrophic CO2 fixation compared to bare soils. Finally, lichenized fungi, plant pathogens, and fungal wood saprotrophs tended to be more abundant in covered soils.},
}
@article {pmid39943131,
year = {2025},
author = {Frazier, AN and Ferree, L and Belk, AD and Al-Lakhen, K and Cramer, MC and Metcalf, JL},
title = {Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/ani15030361},
pmid = {39943131},
issn = {2076-2615},
abstract = {The microbiome of dairy calves undergoes extensive change due to various forces during the first weeks of life. Importantly, diseases such as bovine respiratory disease (BRD) and calf diarrhea can have profound impacts on the early-life microbiome. Therefore, a longitudinal, repeated-measures pilot study was designed to characterize the establishment of nasal and fecal microbiomes of dairy calves, assess the governing forces of microbial assembly, and evaluate how disease states impact these microbial ecologies. Dairy calves (n = 19) were clinically evaluated for gastrointestinal and respiratory disease across three weeks beginning at age ≤ seven days old. Fecal (n = 57) and nasal (n = 57) microbial samples were taken for paired-end 16S rRNA gene amplicon sequencing. Taxonomy and diversity analyses were used to characterize early-life nasal and fecal microbiomes. Stochasticity and determinism were measured using normalized stochasticity testing (NST) and Dirichlet multinomial model (DMM). All analyses were tested for statistical significance. Clinical diarrhea was observed in 11 of the 19 calves. Clinical BRD was not independently observed among the cohort; however, two calves presented clinical signs of both BRD and diarrhea. Taxonomic analysis revealed that fecal samples were highlighted by Bacteroidaceae (40%; relative abundance), Ruminococcaceae (13%), and Lachnospiraceae (10%), with changes in diversity (Kruskal-Wallis; p < 0.05) and composition (PERMANOVA; p < 0.05). Clinical diarrhea reduced diversity in the fecal microbiome but did not impact composition. Nasal samples featured Moraxellaceae (49%), Mycoplasmataceae (16%), and Pasteurellaceae (3%). While no diversity changes were seen in nasal samples, compositional changes were observed (p < 0.05). NST metrics (Kruskal-Wallis; p > 0.01) and DMM (PERMANOVA; p < 0.01) revealed that stochastic, neutral theory-based assembly dynamics govern early-life microbial composition and that distinct microbial populations drive community composition in healthy and diarrheic calves.},
}
@article {pmid39942291,
year = {2025},
author = {Santás-Miguel, V and Lalín-Pousa, V and Conde-Cid, M and Rodríguez-Seijo, A and Pérez-Rodríguez, P},
title = {Use of Biopowders as Adsorbents of Potentially Toxic Elements Present in Aqueous Solutions.},
journal = {Materials (Basel, Switzerland)},
volume = {18},
number = {3},
pages = {},
doi = {10.3390/ma18030625},
pmid = {39942291},
issn = {1996-1944},
support = {ED481D-2021/016//Conseller&#xed;a de Cultura, Educaci&#xf3;n e Universidade (Xunta de Galicia)/ ; IJC2020-044197-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; IJC2020-044426-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 101112754//MRV4SOC project/ ; ED481B-2022-081//Xunta de Galicia/ ; },
abstract = {This study examines the adsorption and desorption behaviors of phosphorus (P), arsenic (As), fluoride (F), and chromium (Cr) in aqueous solutions on green materials such as cork bark (CB) and pine bark (PB). These materials are characterized by active functional groups and net negative charges on their surfaces and porous structures. The evaluation considers variations in contaminant concentrations (0.01-10 mM) and pH (3.5-12). Cork bark exhibited higher adsorption capacity for As and F, while PB was more effective for P and Cr. Adsorption isotherms followed the Freundlich and Langmuir models, indicating surface heterogeneity and multilayer adsorption for most potentially toxic elements (PTEs). Desorption tests demonstrated low rates, with CB retaining up to 99% of F and 85% of As, and PB achieving up to 86% retention for Cr and 70% for P. The influence of pH was minimal for As, P, and F, but acidic conditions significantly enhanced Cr adsorption, showing similar behavior for both biopowders. These findings suggest that CB and PB biopowders are promising, environmentally friendly biosorbents for the removal of PTEs from aqueous solutions. Their effectiveness varies depending on the specific contaminant. This study highlights the potential of these natural materials for sustainable applications in water treatment and soil remediation.},
}
@article {pmid39942061,
year = {2025},
author = {Di Biase, M and Scicchitano, D and Valerio, F and Lonigro, SL and Cifarelli, V and Ostante, G and D'Antuono, I and Candela, M and Ferrara, M},
title = {Microbial Ecology and Nutritional Features in Liquid Sourdough Containing Hemp Flour Fermented by Lactic Acid Bacterial Strains.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/foods14030469},
pmid = {39942061},
issn = {2304-8158},
support = {MicroBHE Project//IBISBA - IT/ ; DAB.AD005.225//FOE - 2021/ ; },
abstract = {Hemp seed flour (Cannabis sativa) is a non-traditional matrix alternative to wheat for baked goods production. The aim of this study was to investigate the microbiota of two liquid sourdoughs (SLs) based on hemp or a wheat-hemp mixture, before and after spontaneous or piloted fermentation (Lactiplantibacillus plantarum ITM21B or Weissella cibaria C43-11 used as starters). Culture-dependent and -independent (high-throughput sequencing of bacterial phylogenetic V3-V4 regions of the 16S rRNA gene) methods, were used to evaluate the microbial community. The effect of fermentation on the content of bioactive molecules (polyphenols, organic acids, proteins, and amino acids) was also investigated. Results indicated that the microbial community of all SLs was mainly (99.7 ÷ 100%) composed of Firmicutes and Proteobacteria, and the latter was the unique phylum before fermentation in formulations produced exclusively with hemp flour. Two PCoA plots (Test adonis with pseudo-F ratio, p > 0.05) showed no significance difference between the microbial communities of the formulations. However, the relative abundance variation at the family level in the wheat-hemp-based mixture SLs showed a significant enrichment of the Lactobacillaceae family (Kruskal-Wallis test, p = 0.04). Moreover, results confirmed hemp seed flour as a suitable fermentation substrate to obtain microbial consortia allowing for an increase in organic acids, especially lactic acid (9.12 ± 1.22 and 7.45 ± 0.75 mmol/kg with Lpb. plantarum and W. cibaria, respectively), in both piloted fermentations, and in polyphenols by 21% and amino acids by 158% in SL fermented by the C43-11 strain.},
}
@article {pmid39937305,
year = {2025},
author = {Argentino, ICV and Godoy, MG and Seldin, L and Jurelevicius, D},
title = {Distribution of Bacillota in Water and Sediments from Aquatic Environments.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {3},
pmid = {39937305},
issn = {1432-184X},
mesh = {*Geologic Sediments/microbiology ; Brazil ; *RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Water Microbiology ; Microbiota ; Phylogeny ; Fresh Water/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; },
abstract = {The phylum Bacillota comprises metabolically diverse bacteria with potential relevance in several fields. Although some genera, such as Bacillus and others, have been extensively studied, the distribution of Bacillota in the environment is still poorly understood. This study aimed to analyze the distribution of Bacillota present in water and sediment samples from different environments. For this purpose, water (W) and sediment (S) samples were collected from different marine environments (Dois Rios Beach - DR, Abraão Beach - AB, Massambaba Beach - MB, and Guanabara Bay - GB), freshwater lagoons (Jacarepiá Lagoon- JL) and hypersaline lagoons (Vermelha Lagoon - VL), all of which are located in Rio de Janeiro, Brazil. The microbial communities present in each sample were determined by sequencing 16S rRNA-encoding genes. The distribution and diversity of Bacillota were analyzed via QIIME2. The results revealed that Bacillota represented an average of 1% of the microbial community of aquatic microbiomes and were unevenly distributed in aquatic water and sediment. The highest abundances of Bacillota were detected in JL_S and VL_S, and the lowest abundances were observed in MB_W and AB_W. Only sequences related to the Bacilli and Clostridia classes were identified. The main Bacillota genera identified were Bacillus and an unidentified Clostridiales order genus. The VL_S and JL_S samples had the highest numbers of exclusive Bacillota genera. On the other hand, 15 Bacillota genera, which are generally observed in the human and animal guts, were found only in anthropogenically impacted GB_W and AB_W. The obtained results revealed how Bacillota are distributed in different aquatic environments.},
}
@article {pmid39936183,
year = {2025},
author = {Brait, N and Hackl, T and Lequime, S},
title = {detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14083},
doi = {10.1111/1755-0998.14083},
pmid = {39936183},
issn = {1755-0998},
abstract = {Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.},
}
@article {pmid39935057,
year = {2025},
author = {Ruiz-Ruiz, P and Mohedano-Caballero, P and De Vrieze, J},
title = {Ectoine production through a marine methanotroph-microalgae culture allows complete biogas valorization.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124223},
doi = {10.1016/j.jenvman.2025.124223},
pmid = {39935057},
issn = {1095-8630},
mesh = {*Biofuels ; *Microalgae/metabolism/growth &amp; development ; *Amino Acids, Diamino/metabolism ; *Methane/metabolism ; Carbon Dioxide/metabolism ; },
abstract = {Methanotrophs have recently emerged as a promising platform for producing bio-based chemicals, like ectoine, from biogas, offering an economical alternative to glucose. However, most studies have focused solely on CH4 consumption, often overlooking the CO2, which is both produced by methanotrophs and present in biogas, despite its potential as a carbon source for microorganisms, such as microalgae. In this study, marine methanotrophic-microalgal cultures were enriched from environmental samples collected at the North Sea coast to explore ectoine production from both CH4 and CO2 in biogas. The sediment-derived culture exhibited the highest CH4 removal efficiency and CO2 uptake, and was selected for further experiments. The culture was primarily composed of Methylobacter marinus, Methylophaga marina, and the microalga Picochlorum oklahomensis. Gas consumption, growth, and ectoine production were evaluated under varying salinity levels and osmotic stress. The NaCl concentrations above 6% negatively impacted CH4 oxidation and inhibited ectoine synthesis, while osmotic shocks enhanced ectoine accumulation, with a maximum ectoine content of 51.3 mgectoine gVSS[-1] at 4.5% NaCl. This study is the first to report ectoine production from methanotroph-microalgal cultures, showing its potential for biogas valorization into high-value bio-based chemicals, like ectoine, marking a significant step toward sustainable biogas utilization.},
}
@article {pmid39934529,
year = {2025},
author = {Roy, R and Das, A and Ganguly, D and Chakraborty, P and Paul, P and Das, S and Maity, A and Malik, M and Tribedi, P},
title = {Cuminaldehyde synergistically enhances the antimicrobial and antibiofilm potential of gentamicin: A direction towards an effective combination for the control of biofilm-linked threats of Staphylococcus aureus.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39934529},
issn = {1678-4405},
support = {TNU/R&amp;D/M/11//The Neotia University/ ; },
abstract = {Staphylococcus aureus, a Gram-positive, coccus-shaped bacterium often causes several infections on human hosts by exploiting biofilm. This current work investigates a potential strategy to manage the threats of biofilm-linked infections by embracing a combinatorial approach involving cuminaldehyde (phytochemical) and gentamicin (antibiotic). Despite showing antimicrobial properties individually, cuminaldehyde and gentamicin could exhibit enhanced antimicrobial potential when used together against S. aureus. The fractional inhibitory concentration index (FICI = 0.36) suggested that the selected compounds (cuminaldehyde and gentamicin) offered synergistic interaction while showing antimicrobial potential against the same organism. A series of experiments indicated that the selected compounds (cuminaldehyde and gentamicin) showed substantial antibiofilm potential against S. aureus when combined. The increased antibiofilm potential was linked to the accumulation of reactive oxygen species (ROS) and increased cell membrane permeability. Additionally, the combination of the selected compounds (cuminaldehyde and gentamicin) also impeded the cell surface hydrophobicity of S. aureus, aiding in the prevention of biofilm formation. The present study also showed that combining the mentioned compounds (cuminaldehyde and gentamicin) notably reduced the secretion of several virulence factors from S. aureus. Furthermore, the current research showed that these compounds (cuminaldehyde and gentamicin) could also exhibit antibiofilm potential against the clinical strains of Methicillin-Resistant S. aureus (MRSA). Taken together, this innovative approach not only enhances the potential of existing standard antibiotics but also opens up new therapeutic possibilities for combating biofilm-related infections.},
}
@article {pmid39933594,
year = {2025},
author = {Verdon, N and Popescu, O and Titmuss, S and Allen, RJ},
title = {Habitat fragmentation enhances microbial collective defence.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {223},
pages = {20240611},
doi = {10.1098/rsif.2024.0611},
pmid = {39933594},
issn = {1742-5662},
support = {//Deutsche Forschungsgemeinschaft/ ; //H2020 European Research Council/ ; //Engineering and Physical Sciences Research Council/ ; },
mesh = {*Ecosystem ; *Models, Biological ; Bacteria/metabolism ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Microbes often inhabit complex, spatially partitioned environments such as host tissue or soil, but the effects of habitat fragmentation on microbial ecology and infection dynamics are poorly understood. Here, we investigate how habitat fragmentation impacts a prevalent microbial collective defence mechanism: enzymatic degradation of an environmental toxin. Using a theoretical model, we predict that habitat fragmentation can strongly enhance the collective benefits of enzymatic toxin degradation. For the example of [Formula: see text]-lactamase-producing bacteria that mount a collective defence by degrading a [Formula: see text]-lactam antibiotic, we find that realistic levels of habitat fragmentation can allow a population to survive antibiotic doses that greatly exceed those required to kill a non-fragmented population. This 'habitat-fragmentation rescue' is a stochastic effect that originates from variation in bacterial density among different subpopulations and demographic noise. We also study the contrasting case of collective enzymatic foraging, where enzyme activity releases nutrients from the environment; here we find that increasing habitat fragmentation decreases the lag time for population growth but does not change the ecological outcome. Taken together, this work predicts that stochastic effects arising from habitat fragmentation can greatly enhance the effectiveness of microbial collective defence via enzymatic toxin degradation.},
}
@article {pmid39928396,
year = {2025},
author = {Nakajima, M and Nakai, R and Hirakata, Y and Kubota, K and Satoh, H and Nobu, MK and Narihiro, T and Kuroda, K},
title = {Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. formerly referred to as Candidatus Patescibacteria or candidate phyla radiation.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.006668},
pmid = {39928396},
issn = {1466-5034},
mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; *Sequence Analysis, DNA ; *Base Composition ; Bacterial Typing Techniques ; Fatty Acids ; Symbiosis ; DNA, Archaeal/genetics ; },
abstract = {In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108[T], in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864[T] (JF-1[T]), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108[T] was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108[T]; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108[T] (=JCM 39522[T]). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.},
}
@article {pmid39924526,
year = {2025},
author = {Díez López, C and Van Herreweghen, F and De Pessemier, B and Minnebo, Y and Taelman, S and Judge, K and Ransley, K and Hammond, C and Batson, M and Stock, M and Van Criekinge, W and Van de Wiele, T and Macmaster, A and Callewaert, C},
title = {Unravelling the hidden side of laundry: malodour, microbiome and pathogenome.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {40},
pmid = {39924526},
issn = {1741-7007},
support = {HBC.2020.2292//Agentschap Innoveren en Ondernemen/ ; FWO19/PSD/084//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {*Microbiota ; Humans ; *Odorants/analysis ; Laundering/methods ; Volatile Organic Compounds/analysis ; Clothing ; Skin/microbiology ; },
abstract = {BACKGROUND: Recent trends towards lower washing temperatures and a reduction in the use of bleaching agents in laundry undoubtedly benefit our environment. However, these conditions impair microbial removal on clothes, leading to malodour generation and negative impacts on consumer well-being. Clothing undergoes cycles of wearing, washing and drying, with variable exposure to microorganisms and volatilomes originating from the skin, washing machine, water and laundry products. Laundry malodour is therefore a complex problem that reflects its dynamic ecosystem. To date, comprehensive investigations that encompass the evaluation of both microbial community and malodorous volatile organic compounds throughout all stages of the wash-wear-dry cycle are scarce. Furthermore, the microbial and malodour profiles associated with extended humid-drying conditions are poorly defined.<br><br>RESULTS: Here we present olfaction-directed chemical and microbiological studies of synthetic T-shirts after wearing, washing and drying. Results show that although washing reduces the occurrence of known malodour volatile organic compounds, membrane-intact bacterial load on clothing is increased. Skin commensals are displaced by washing machine microbiomes, and for the first time, we show that this shift is accompanied by an altered pathogenomic profile, with many genes involved in biofilm build-up. We additionally highlight that humid-drying conditions are associated with characteristic malodours and favour the growth of specific Gram-negative bacteria.<br><br>CONCLUSIONS: These findings have important implications for the development of next-generation laundry products that enhance consumer well-being, while supporting environmentally friendly laundry practices.},
}
@article {pmid39915510,
year = {2025},
author = {Rabbani, G and Afiq-Rosli, L and Lee, JN and Waheed, Z and Wainwright, BJ},
title = {Effects of life history strategy on the diversity and composition of the coral holobiont communities of Sabah, Malaysia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {4459},
pmid = {39915510},
issn = {2045-2322},
mesh = {*Anthozoa/microbiology ; Animals ; Malaysia ; *Microbiota ; *Symbiosis ; Biodiversity ; Bacteria/genetics/classification ; Climate Change ; Coral Reefs ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Coral-associated microbes have essential roles in promoting and regulating host function and health. As climate change advances and other environmental perturbations increasingly impact corals, it is becoming ever more important that we understand the composition of the microbial communities hosted. Without this baseline it is impossible to assess the magnitude and direction of any future changes in microbial community structure. Here, we characterised both the bacterial and Symbiodiniaceae communities in four coral species (Diploastrea heliopora, Porites lutea, Pachyseris speciosa, and Pocillopora acuta) collected from Sabah, Malaysia. Our findings reveal distinct microbial communities associated with different coral species tending to reflect the varied life history strategies of their hosts. Microbial communities could be differentiated by collection site, with shifts in Symbiodiniaceae communities towards more stress tolerant types seen in samples collected on the shallow Sunda Shelf. Additionally, we identified a core microbiome within species and a more discrete core between all species. We show bacterial and Symbiodiniaceae communities are structured by host species and appear to be influenced by host life history characteristics. Furthermore, we identified a core microbiome for each species finding that several amplicon sequence variants were shared between hosts, this suggests a key role in coral health regardless of species identity. Given the paucity of work performed in megadiverse regions such as the Coral Triangle, this research takes on increased importance in our efforts to understand how the coral holobiont functions and how it could be altered as climate change advances.},
}
@article {pmid39914458,
year = {2025},
author = {Wenger, A and Bakkeren, E and Granato, E and Tecon, R and Mitri, S and Möbius, W},
title = {MEEhubs2024: A hub-based conference on microbial ecology and evolution fostering sustainability.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf022},
pmid = {39914458},
issn = {1574-6968},
abstract = {Scientific conferences are essential to academic exchange. However, related air travel contributes to greenhouse gas emissions, while expensive registration and travel costs limit the participation of early-career researchers and those from low-income countries. Virtual conferences offer promising solutions for reducing emissions and enhancing accessibility and inclusivity but often limit networking and personal interaction. Hybrid multi-hub conferences, which combine virtually connected in-person venues with individual virtual participation, combine the benefits of both conference formats. Thus, we present and discuss MEEhubs2024, a multi-hub conference on microbial ecology and evolution held in January 2024. During this three-day conference, attendees participated virtually or at one of six hubs in Europe and North America. We analyzed the participants' and organizers' feedback to create a template and provide insights into the scientific community's adoption of this new conference format, which was positively evaluated by most participants. Because technical, logistical and structural challenges remain, including limited opportunities to interact and network across hubs and participation modes, we provide recommendations for improvement like hiring technical hosts and offering virtual-only social activities. Finally, we used the participants' feedback to reflect on conference expectations, highlighting research gaps and the need for organizers to define and communicate goals when organizing conferences.},
}
@article {pmid39914213,
year = {2025},
author = {Ma, R and Huang, Z and Jiang, Y and Zhao, A and Yu, G and Lin, C and Zhu, L and Zhang, X and Li, X and Wang, C},
title = {Regulation of ethanol production from anaerobic fermentation of food waste using aromatic alcohol-based quorum-sensing molecules.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124382},
doi = {10.1016/j.jenvman.2025.124382},
pmid = {39914213},
issn = {1095-8630},
abstract = {Quorum-sensing molecules (QSMs) are used to regulate microbial metabolites to effectively improve food waste anaerobic fermentation to produce high-value products of ethanol and lactic acid. In this study, low concentrations (25 and 50 μmol/L) of aromatic alcohol favored the synthesis of ethanol and lactic products. Among the aromatic alcohol QSMs, 50 μmol/L of tyrosol enhanced the yield of products. The correlations between substrate composition indicators confirmed that tyrosol was conducive to the anaerobic fermentation of food waste. The regulation mechanism of tyrosol, such as microbial diversity in anaerobic fermentation, was analyzed from the perspective of microbial ecology. The result revealed that tyrosol increased the microbial diversity in the system. Limosilactobacillus, Weissella, and Pediococcus were the dominant bacterial species in the early stages of fermentation, whereas Clostridiaceae and Bacillus were dominant in the later stages. Meanwhile, the main dominant fungal species were Saccharomyces, Aspergillus, and Pichia. The results of this study show that using QSMs, including tyrosol, to regulate the physiological characteristics of anaerobic fermentation microorganisms, promote the synthesis of cell metabolites, and regulate the diversity and succession of microbial communities is a feasible measure. This approach improves the resource utilization efficiency of anaerobic fermentation technology for food waste, which is significant for promoting sustainable development.},
}
@article {pmid39913585,
year = {2025},
author = {Pertierra, LR and Convey, P and Barbosa, A and Biersma, EM and Cowan, D and Diniz-Filho, JAF and de Los Ríos, A and Escribano-Álvarez, P and Fraser, CI and Fontaneto, D and Greve, M and Griffiths, HJ and Harris, M and Hughes, KA and Lynch, HJ and Ladle, RJ and Liu, XP and le Roux, PC and Majewska, R and Molina-Montenegro, MA and Peck, LS and Quesada, A and Ronquillo, C and Ropert-Coudert, Y and Sancho, LG and Terauds, A and Varliero, G and Vianna, JA and Wilmotte, A and Chown, SL and Olalla-Tárraga, M&#xc1; and Hortal, J},
title = {Advances and shortfalls in knowledge of Antarctic terrestrial and freshwater biodiversity.},
journal = {Science (New York, N.Y.)},
volume = {387},
number = {6734},
pages = {609-615},
doi = {10.1126/science.adk2118},
pmid = {39913585},
issn = {1095-9203},
mesh = {Antarctic Regions ; *Biodiversity ; Animals ; *Fresh Water ; *Invertebrates/physiology ; Vertebrates/physiology ; Biological Evolution ; Plants ; Conservation of Natural Resources ; },
abstract = {Antarctica harbors many distinctive features of life, yet much about the diversity and functioning of Antarctica's life remains unknown. Evolutionary histories and functional ecology are well understood only for vertebrates, whereas research on invertebrates is largely limited to species descriptions and some studies on environmental tolerances. Knowledge on Antarctic vegetation cover showcases the challenges of characterizing population trends for most groups. Recent community-level microbial studies have provided insights into the functioning of life at its limits. Overall, biotic interactions remain largely unknown across all groups, restricted to basic information on trophic level placement. Insufficient knowledge of many groups limits the understanding of ecological processes on the continent. Remedies for the current situation rely on identifying the caveats of each ecological discipline and finding targeted solutions. Such precise delimitation of knowledge gaps will enable a more aware, representative, and strategic systematic conservation planning of Antarctica.},
}
@article {pmid39912641,
year = {2025},
author = {Hamovit, N and RoyChowdhury, T and Akob, DM and Zhang, X and McCarty, G and Yarwood, S},
title = {Comparative assessment of a restored and natural wetland using [13]C-DNA SIP reveals a higher potential for methane production in the restored wetland.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0216124},
doi = {10.1128/aem.02161-24},
pmid = {39912641},
issn = {1098-5336},
abstract = {Wetlands are the largest natural source of methane (CH4), a potent greenhouse gas produced by methanogens. Methanogenesis rates are controlled by environmental factors such as redox potential, temperature, and carbon and electron acceptor availability and are presumably dependent on the composition of the active methanogen community. We collected intact soil cores from a restored and natural freshwater depressional wetland on Maryland's Delmarva Peninsula (USA) to assess the effects of wetland restoration and redox shifts on microbial processes. Intact soil cores were incubated under either saturated (anoxic) or unsaturated (oxic) conditions and amended with [13]C-acetate for quantitative stable isotope probing (qSIP) of the 16S rRNA gene. Restored wetland cores supported a distinct community of methanogens compared to natural cores, and acetoclastic methanogens putatively identified in the genus Methanosarcina were among the most abundant taxa in restored anoxic and oxic cores. The active microbial communities in the restored wetland cores were also distinguished by the unique presence of facultatively anaerobic bacteria belonging to the orders Firmicutes and Bacteroidetes. In natural wetland incubations, methanogen populations were not among the most abundant taxa, and these communities were instead distinguished by the unique presence of aerobic bacteria in the phyla Acidobacteria, Actinobacteria, and class Alphaproteobacteria. Iron-reducing bacteria, in the genus Geobacter, were active across all redox conditions in both the restored and the natural cores, except the natural oxic-anoxic condition. These findings suggest an overall higher potential for methanogenesis in the restored wetland site compared to the natural wetland site, even when there is evidence of Fe reduction.IMPORTANCEMethane (CH4) is a potent greenhouse gas with an atmospheric half-life of ~10 years. Wetlands are the largest natural emitters of CH4, but CH4 dynamics are difficult to constrain due to high spatial and temporal variability. In the past, wetlands were drained for agriculture. Now, restoration is an important strategy to increase these ecosystems' potential for sequestering carbon. However, the consequences of wetland restoration on carbon biogeochemistry are under-evaluated, and a thorough assessment of the active microbial community as a driver of biogeochemical changes is needed. Particularly, the effects of seasonal flooding/drying cycles in geographically isolated wetlands might have implications for CH4 emissions in both natural and restored wetlands. Here, we found that active microbial communities in natural and restored wetlands responded differently to flooding and drying regimes, resulting in differences in CH4 production potentials. Restored wetlands had a higher potential for CH4 production compared to natural wetlands. Our results show that controls on CH4 production in a restored wetland are complex, and dynamics of active microbial communities are linked to seasonal dry-wet cycles.},
}
@article {pmid39912591,
year = {2025},
author = {Porras-Socias, P and Mattiussi, R and Silveira, KA and O'Flaherty, V},
title = {Methan-o-poly: a giant collaborative game to "digest" the microbiology of green biogas production.},
journal = {Journal of microbiology &amp; biology education},
volume = {},
number = {},
pages = {e0011624},
doi = {10.1128/jmbe.00116-24},
pmid = {39912591},
issn = {1935-7877},
abstract = {In an era of rapid change and global challenges, impactful educational experiences about sustainability become imperative. Especially in organic waste conversion bioprocess such as anaerobic digestion (AD). Here proposed, is a gamified approach to learn AD and hidden microbial interactions, bringing to real-life size an invisible phenomenon. In Methan-o-poly, participants roleplay cooperating microbes within a bioreactor engaged in four sequential mini-games to mimic organic waste degradation and methane production. Perturbations in the activity simulate real challenges, enhancing adaptability and problem-solving skills. Overall, this cooperative game promotes motivation, collaboration, and experiential learning. Its initial implementation received positive feedback across various age groups, enhancing green education initiatives.},
}
@article {pmid39911734,
year = {2025},
author = {Jia, C and Li, J and Li, Z and Zhang, L},
title = {Influence of high-load shocks on achieving mainstream partial nitrification: Microbial community succession.},
journal = {Water research X},
volume = {27},
number = {},
pages = {100304},
pmid = {39911734},
issn = {2589-9147},
abstract = {Driving microbial community succession through the regulation of operational strategies is crucial for achieving partial nitrification (PN) in municipal wastewater. However, at present, there is a decoupling between the strategic regulation of PN systems and the succession characteristics of the microbial community. This study examined the correlation between microbial community succession and PN performance under two high-load shocks (HLS1 and HLS2) treating actual sewage. During HLS1, the influent organic loading rate (OLR) and nitrogen loading rate (NLR) increased from 116.7 ± 37.7 to 219.7 ± 24.7 mg COD/(g VSS·d) and 0.21±0.02 to 0.33±0.02 kg N/m[3]/d respectively, with the nitrite concentration and nitrite accumulation ratio only reaching 11.7 ± 2.7 mg/L and 49.3 ± 13.9 %, respectively. During HLS2, the influent OLR and NLR increased from 123.5 ± 17.2 to 300.3 ± 49.2 mg COD/(g VSS·d) and 0.19±0.03 to 0.32±0.03 kg N/m[3]/d respectively, resulting in a nitrite accumulation ratio of 89.4 ± 10.7 %. The system achieved efficient PN performance and sustained for 124 days. High-throughput sequencing results showed that community diversity remained consistently high, and the community composition returned to its initial state following a minor succession during HLS1. During HLS2, the high-load shock reduced the richness and evenness of the microbial community. The community underwent succession in a new direction, leading to community composition and function changes. The results indicate that the realization, stabilization, and disruption of PN are influenced not only by operational parameters but also by microbial community structure.},
}
@article {pmid39911603,
year = {2025},
author = {Sikombe, TW and Linnemann, AR and Moonga, HB and Quilitz, S and Schoustra, SE and Smid, EJ and Alekseeva, A},
title = {Odor-active aroma compounds in traditional fermented dairy products: The case of mabisi in supporting food and nutrition security in Zambia.},
journal = {Current research in food science},
volume = {10},
number = {},
pages = {100976},
pmid = {39911603},
issn = {2665-9271},
abstract = {Aroma is a key sensory attribute that determines consumer preference and acceptability of foods. The aroma of fermented dairy products comprises the volatile organic compounds (VOCs) produced by the activity of fermenting microbes and the compounds originally present in unfermented raw milk. A unique combination of specific compounds detectable by human olfactory senses creates the distinct odor profile of fermented products. This study investigated the influence of different production methods on the VOCs responsible for the odor-active compounds, and the microbial communities present in mabisi, a traditional Zambian fermented dairy product. The VOCs and microbial community composition of four mabisi variants were investigated using GC-O-MS and PTR-QiTOF-MS techniques, and 16S rRNA amplicon sequencing, respectively. A panel of three assessors identified the odor-active compounds from the GC-O-MS, and the compound's quantitative aspects were obtained by the PTR-QiTOF-MS. Twelve volatile compounds were identified as odor-active compounds during the GC-O-MS analysis. The most prominent were ketones and esters, which imparted a buttery and fruity aroma, respectively. The PTR-QiTOF-MS run identified and quantified a total of 390 m/z peaks, 55 of which were tentatively identified. 16S rRNA amplicon sequencing revealed a diverse microbial community, with Lactococcus species dominating. While the VOC profiles showed significant variation in functionality among the variants, minor differences were observed in microbial composition. The study confirms that high compound concentration does not necessarily correlate with compound odor activity. Our findings offer insights into the significance of aromas and microbial ecology to support optimization strategies for upscaling traditional fermented products.},
}
@article {pmid39911488,
year = {2024},
author = {Vaselek, S and Alten, B},
title = {Microbial ecology of sandflies-the correlation between nutrition, Phlebotomus papatasi sandfly development and microbiome.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1522917},
pmid = {39911488},
issn = {2297-1769},
abstract = {The role and the impact of the microbial component on the biology, ecology, and development of sandflies is largely unknown. We evaluated the impact of larval nutrition on laboratory-reared sandflies in correlation to the abundance of food, light starvation, and food with/without live microbiome, by monitoring the survival and development of immature stages, and the longevity of adult sandflies. Within this study we examined 360 larvae, 116 pupae, and 120 adult flies of Phlebotomus papatasi for the microbial gut content. The data showed that the presence of a live and diverse microbiome plays a role in the development and survival of larvae. The mortality rate of the larvae was higher, and larval development was longer for sandflies maintained on microbiome-depleted medium, in comparison to the larvae fed with medium containing alive and complex microbiome. Actively feeding larvae reduce microbial abundance and diversity of the medium. The microbial content of the larval gut depends on the composition of the rearing medium, indicating a potential attraction to certain bacteria. The microbial content of the pupa gut was severely diminished, with overall survival of two bacterial species in adult insects - Ochrobactrum intermedium (found in 95% of dissected adults) and Bacillus subtilis (16%). Further microbial studies may aid in developing biological control methods for sandfly larval or adult stages.},
}
@article {pmid39909903,
year = {2025},
author = {Panico, SC and Alberti, G and Foscari, A and Sciabbarrasi, GL and Tomao, A and Incerti, G},
title = {Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {2},
pmid = {39909903},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/genetics/classification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Grassland ; Italy ; *Biodiversity ; *Carbon/analysis ; Microbiota ; Nitrogen/analysis ; Phosphorus/analysis ; Forests ; Hydrogen-Ion Concentration ; Climate Change ; Mycobiome ; },
abstract = {Spontaneous afforestation following land abandonment has been increasingly recognized as a nature-based solution to mitigate climate change and provide measurable benefits to biodiversity. However, afforestation effects on biodiversity, particularly on soil microbial communities, are still poorly characterized, with most previous studies focusing on artificial plantations rather than forest rewilding dynamics. Here, we assessed changes in topsoil physical-chemical properties and related dynamics of bacterial and fungal community composition and structure following spontaneous afforestation of abandoned grasslands in Northeast Italy over the last 70 years. With a space-for-time approach, we selected four chronosequences representing different successional stages: grassland, early (2000-2020), intermediate (1978-2000), and late (1954-1978). Results showed that spontaneous afforestation progressively reduced topsoil pH and total phosphorus (P), while soil organic carbon (SOC), nitrogen (N), and C:N ratio increased. Correspondingly, the overall α-diversity of the fungal community, assessed by ITS DNA metabarcoding, progressively decreased after an initial increase from grassland conditions, following substrate acidification and trophic specialization. Bacterial diversity, assessed by 16S DNA metabarcoding, was highest at the initial stages, then progressively decreased at later stages, likely limited by lower organic matter quality. Shifts of fungal community composition included an increase of ectomycorrhizal Basidiomycota linked to topsoil's higher SOC, N, and C:N ratio. Differently, bacterial community composition responded substantially to pH, with topsoil acidity favoring Proteobacteria (Pseudomonadota) and Acidobacteria (Acidobacteriota) at the late afforestation stages. Our findings provide a first contribution to clarify how fungi and bacteria respond to spontaneous afforestation. This is particularly relevant in the context of climate change mitigation, considering the fundamental role of microorganisms in shaping soil carbon storage dynamics.},
}
@article {pmid39907926,
year = {2025},
author = {Breedt, G and Korsten, L and Gokul, JK},
title = {Enhancing multi-season wheat yield through plant growth-promoting rhizobacteria using consortium and individual isolate applications.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39907926},
issn = {1874-9356},
abstract = {In recent decades, there has been a growing interest in harnessing plant growth-promoting rhizobacteria (PGPR) as a possible mechanism to mitigate the environmental impact of conventional agricultural practices and promote sustainable agricultural production. This study investigated the transferability of promising PGPR research from maize to another Poaceae cereal crop, wheat. This multi-seasonal study evaluated the wheat grain yield effect of Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29) when applied i. individually, ii. as a consortium with Bacillus safensis (S7), and iii. at a 75% reduced fertilizer rate. Whole genome sequencing allowed annotation of genes linked to plant growth promotion, providing potential genomic explanations for the observed in-field findings. Application of the consortium compared to a commercial PGPR showed significantly increased wheat yield by 30.71%, and 25.03%, respectively, in season one, and 63.92% and 58.45%, respectively, under reduced fertilizer rates in season two. Individual application of T19 and T29 showed varying results, with T19 increasing wheat yield by 9.33% and 16.22% during seasons three and four but a substantial reduction (33.39%) during season five. T29 exhibited yield increases during season three (9.31%) and five (5.61%) but led to a significant reduction (21.15%) in season four. Genomic analysis unveiled a spectrum of plant growth-promoting genes including those associated with ammonification, phosphate solubilization, ethylene, siderophore, catalase, and superoxide dismutase production. These findings offer valuable insights into the mechanisms behind observed field results, with potential implications for advancing sustainable agriculture and crop productivity in evolving agricultural landscapes.},
}
@article {pmid39905550,
year = {2025},
author = {Martínez Rendón, C and Braun, C and Kappelsberger, M and Boy, J and Casanova-Katny, A and Glaser, K and Dumack, K},
title = {Enhancing microbial predator-prey detection with network and trait-based analyses.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {37},
pmid = {39905550},
issn = {2049-2618},
mesh = {Animals ; *Microbiota ; Antarctic Regions ; Food Chain ; Predatory Behavior ; },
abstract = {BACKGROUND: Network analyses are often applied to microbial communities using sequencing survey datasets. However, associations in such networks do not necessarily indicate actual biotic interactions, and even if they do, the nature of the interactions commonly remains unclear. While network analyses are valuable for generating hypotheses, the inferred hypotheses are rarely experimentally confirmed.<br><br>RESULTS: We employed cross-kingdom network analyses, applied trait-based functions to the microorganisms, and subsequently experimentally investigated the found putative predator-prey interactions to evaluate whether, and to what extent, correlations indicate actual predator-prey relationships. For this, we investigated algae and their protistan predators in biocrusts of three distinct polar regions, i.e., Svalbard, the Antarctic Peninsula, and Continental Antarctica. Network analyses using FlashWeave indicated that 89, 138, and 51 correlations occurred between predatory protists and algae, respectively. However, trait assignment revealed that only 4.7-9.3% of said correlations link predators to actually suitable prey. We further confirmed these results with HMSC modeling, which resulted in similar numbers of 7.5% and 4.8% linking predators to suitable prey for full co-occurrence and abundance models, respectively. The combination of network analyses and trait assignment increased confidence in the prediction of predator-prey interactions, as we show that 82% of all experimentally investigated correlations could be verified. Furthermore, we found that more vicious predators, i.e., predators with the highest growth rate in co-culture with their prey, exhibit higher stress and betweenness centrality - giving rise to the future possibility of determining important predators from their network statistics.<br><br>CONCLUSIONS: Our results support the idea of using network analyses for inferring predator-prey interactions, but at the same time call for cautionary consideration of the results, by combining them with trait-based approaches to increase confidence in the prediction of biological interactions. Video Abstract.},
}
@article {pmid39903999,
year = {2025},
author = {Mondal, A and Parvez, SS and Majumder, A and Sharma, K and Das, B and Bakshi, U and Alam, M and Banik, A},
title = {Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128084},
doi = {10.1016/j.micres.2025.128084},
pmid = {39903999},
issn = {1618-0623},
abstract = {Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.},
}
@article {pmid39902955,
year = {2025},
author = {Li, Q and Marietou, A and Andersen, FF and Hosek, J and Scavenius, C and Zhang, J and Schwab, C},
title = {In vitro investigations on the impact of fermented dairy constituents on fecal microbiota composition and fermentation activity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0219324},
doi = {10.1128/spectrum.02193-24},
pmid = {39902955},
issn = {2165-0497},
abstract = {UNLABELLED: Fermented dairy constitutes a major dietary source and contains lactose as the main carbohydrate and living starter cultures, which can encounter the intestinal microbiota after ingestion. To investigate whether dairy-related nutritional and microbial modulation impacted intestinal microbiota composition and activity, we employed static fecal microbiota fermentations and a dairy model system consisting of lactose and Streptococcus thermophilus wild type and β-galactosidase deletion mutant. In addition, we conducted single-culture validation studies. 16S rRNA gene-based microbial community analysis showed that lactose increased the abundance of Bifidobacteriaceae and Anaerobutyricum and Faecalibacterium spp. The supplied lactose was hydrolyzed within 24 h of fermentation and led to higher expression of community-indigenous β-galactosidases. Targeted protein analysis confirmed that bifidobacteria contributed most β-galactosidases together with other taxa, including Escherichia coli and Anaerobutyricum hallii. Lactose addition led to higher (P < 0.05) levels of butyrate compared to controls, likely due to lactate-based cross-feeding and direct lactose metabolism by butyrate-producing Anaerobutyricum and Faecalibacterium spp. Representatives of both genera used lactose to produce butyrate in single cultures. When supplemented at around 5.5 log cells mL[-1], S. thermophilus or its β-galactosidase-negative mutant outnumbered the indigenous Streptococcaceae population at the beginning of fermentation but had no impact on lactose utilization and final short-chain fatty acid profiles.<br><br>IMPORTANCE: The consumption of fermented food has been linked to positive health outcomes, possibly due to interactions of food components with the intestinal microbiota. This study brings forward new insights into how major constituents of fermented dairy affect intestinal microbial ecology and activity when supplied together or alone. We provide evidence that lactose availability increased the production of butyrate by fecal microbiota through cross-feeding and did not observe a contribution of starter cultures to lactose metabolism, possibly due to a lack of competitiveness. The methodological setup used in this study can be implemented in future investigations to determine the impact of other fermented foods and their major components on intestinal microbiota composition and activity.},
}
@article {pmid39897492,
year = {2025},
author = {Keleher, JG and Strope, TA and Estrada, NE and Griggs Mathis, AM and Easson, CG and Fiore, C},
title = {Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18807},
pmid = {39897492},
issn = {2167-8359},
mesh = {*Porifera/microbiology ; *Microbiota ; Animals ; *Fresh Water/microbiology ; North Carolina ; *Symbiosis ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities.},
}
@article {pmid39890664,
year = {2025},
author = {Zhou, Y and Jiang, P and Ding, Y and Zhang, Y and Yang, S and Liu, X and Cao, C and Luo, G and Ou, L},
title = {Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {1},
pmid = {39890664},
issn = {1432-184X},
support = {2023YFD1201502//National Key Research and Development Program of China/ ; 42107262//National Natural Science Foundation of China/ ; CARS-24-A05//China Agriculture Research System of MOF and MARA/ ; },
mesh = {*Capsicum/microbiology/growth &amp; development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Endophytes/isolation &amp; purification/classification/physiology/genetics ; Plant Diseases/microbiology ; Plant Roots/microbiology ; Fungi/classification/genetics/isolation &amp; purification/physiology ; },
abstract = {Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.},
}
@article {pmid39890294,
year = {2025},
author = {Baker, JM and Dickson, RP},
title = {The Microbiome and Pulmonary Immune Function.},
journal = {Clinics in chest medicine},
volume = {46},
number = {1},
pages = {77-91},
doi = {10.1016/j.ccm.2024.10.006},
pmid = {39890294},
issn = {1557-8216},
mesh = {Humans ; *Microbiota/immunology/physiology ; *Lung/microbiology/immunology ; Lung Diseases/immunology/microbiology ; },
abstract = {In the last decade, the lung microbiome field has matured into a promising area of translational and clinical research due to emerging evidence indicating a role for respiratory microbiota in lung immunity and pathogenesis. Here, we review recent insights pertaining to the lung microbiome's relationship with pulmonary immune function. We discuss areas of future investigation that will be essential to the development of immunomodulatory therapies targeting the respiratory microbiome.},
}
@article {pmid39889603,
year = {2025},
author = {Fu, P and Zhai, J and Yang, X and Gao, J and Ren, Z and Guo, B and Qi, P},
title = {Distribution and influencing factors of antibiotic resistance genes in two mussel species along the coasts of the East China Sea and the Yellow Sea.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137399},
doi = {10.1016/j.jhazmat.2025.137399},
pmid = {39889603},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) raise a global public health concern. The ARGs profile in marine aquaculture environments was well reported, yet it is poorly revealed in marine bivalves. This study investigated the microbiota, resistome, and environmental factors within the digestive glands of two mussel species (Mytilus coruscus and Mytilus galloprovincialis) cultivated in the East China Sea and Yellow Sea. The microbial communities in the digestive glands of mussels exhibit significant variations across different sampling sites and between the two seas. The three bacterial phyla that predominated in all samples were Firmicutes, Bacteroidota, and Proteobacteria. A total of 88 ARGs were detected, with aminoglycoside resistance genes and multidrug resistance genes being the dominant categories. Analysis revealed that the quinolone resistance gene qnrB, associated with clinically relevant human pathogens, was ubiquitous in all samples. Members of the Enterobacteriaceae family may serve as a reservoir for qnrB within the investigated environment. The distribution of ARGs shows potential associations with the composition of microbial communities in the digestive glands, environmental factors, and mobile genetic elements (MGEs). These findings enhance the elucidation of microbial ecology and antibiotic resistance in marine aquaculture.},
}
@article {pmid39587684,
year = {2025},
author = {DuBose, JG and Crook, TB and Matzkin, LM and Haselkorn, TS},
title = {The relative importance of host phylogeny and dietary convergence in shaping the bacterial communities hosted by several Sonoran Desert Drosophila species.},
journal = {Journal of evolutionary biology},
volume = {38},
number = {2},
pages = {180-189},
doi = {10.1093/jeb/voae143},
pmid = {39587684},
issn = {1420-9101},
support = {//University of Central Arkansas Southwest Energy Research Fellowship program/ ; },
mesh = {Animals ; *Drosophila/microbiology/genetics ; *Phylogeny ; *Diet ; *Desert Climate ; *Microbiota ; Bacteria/genetics/classification ; Symbiosis ; Arizona ; },
abstract = {Complex eukaryotes vary greatly in the mode and extent that their evolutionary histories have been shaped by the microbial communities that they host. A general understanding of the evolutionary consequences of host-microbe symbioses requires that we understand the relative importance of host phylogenetic divergence and other ecological processes in shaping variation in host-associated microbial communities. To contribute to this understanding, we described the bacterial communities hosted by several Drosophila species native to the Sonoran Desert of North America. Our sampling consisted of four species that span multiple dietary shifts to cactophily, as well as the dietary generalist D. melanogaster, allowing us to partition the influences of host phylogeny and extant ecology. We found that bacterial communities were compositionally indistinguishable when considering incidence only but varied when considering the relative abundances of bacterial taxa. Variation in community composition was not explained by host phylogenetic divergence but could be partially explained by dietary variation. In support of the important role of diet as a source of ecological selection, we found that specialist cactophilic Drosophila deviated more from neutral predictions than dietary generalists. Overall, our findings provide insight into the evolutionary and ecological factors that shape host-associated microbial communities in a natural context.},
}
@article {pmid39885242,
year = {2025},
author = {Grafmüller, J and Möllmer, J and Muehe, EM and Kammann, CI and Kray, D and Schmidt, HP and Hagemann, N},
title = {Publisher Correction: Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3796},
doi = {10.1038/s41598-025-87051-2},
pmid = {39885242},
issn = {2045-2322},
}
@article {pmid39884152,
year = {2025},
author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA},
title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128076},
doi = {10.1016/j.micres.2025.128076},
pmid = {39884152},
issn = {1618-0623},
abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.},
}
@article {pmid39883228,
year = {2024},
author = {Han, JR and Li, S and Li, WJ and Dong, L},
title = {Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.},
journal = {Advanced biotechnology},
volume = {2},
number = {3},
pages = {26},
pmid = {39883228},
issn = {2948-2801},
support = {32270076//National Natural Science Foundation of China/ ; 2022xjkk1200//The Third Xinjiang Scientific Expedition Program/ ; 2022B0202110001//The Key-Area Research and Development Program of Guangdong Province/ ; },
abstract = {Extreme environments such as hyperarid, hypersaline, hyperthermal environments, and the deep sea harbor diverse microbial communities, which are specially adapted to extreme conditions and are known as extremophiles. These extremophilic organisms have developed unique survival strategies, making them ideal models for studying microbial diversity, evolution, and adaptation to adversity. They also play critical roles in biogeochemical cycles. Additionally, extremophiles often produce novel bioactive compounds in response to corresponding challenging environments. Recent advances in technologies, including genomic sequencing and untargeted metabolomic analysis, have significantly enhanced our understanding of microbial diversity, ecology, evolution, and the genetic and physiological characteristics in extremophiles. The integration of advanced multi-omics technologies into culture-dependent research has notably improved the efficiency, providing valuable insights into the physiological functions and biosynthetic capacities of extremophiles. The vast untapped microbial resources in extreme environments present substantial opportunities for discovering novel natural products and advancing our knowledge of microbial ecology and evolution. This review highlights the current research status on extremophilic microbiomes, focusing on microbial diversity, ecological roles, isolation and cultivation strategies, and the exploration of their biosynthetic potential. Moreover, we emphasize the importance and potential of discovering more strain resources and metabolites, which would be boosted greatly by harnessing the power of multi-omics data.},
}
@article {pmid39882875,
year = {2025},
author = {Cross, K and Beckman, N and Jahnes, B and Sabree, ZL},
title = {Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0236824},
doi = {10.1128/aem.02368-24},
pmid = {39882875},
issn = {1098-5336},
abstract = {UNLABELLED: Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.<br><br>IMPORTANCE: Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.},
}
@article {pmid39882867,
year = {2025},
author = {Asmus, AE and Gaire, TN and Schweisthal, KJ and Staben, SM and Noyes, NR},
title = {Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0220924},
doi = {10.1128/spectrum.02209-24},
pmid = {39882867},
issn = {2165-0497},
abstract = {The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.},
}
@article {pmid39880965,
year = {2025},
author = {Contreras-Negrete, G and Valiente-Banuet, A and Molina-Freaner, F and Partida-Martínez, LP and Hernández-López, A},
title = {Agricultural Practices and Environmental Factors Drive Microbial Communities in the Mezcal-Producing Agave angustifolia Haw.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {181},
pmid = {39880965},
issn = {1432-184X},
support = {CV549242//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; },
mesh = {*Agave/microbiology ; *Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; *Fungi/genetics/classification/isolation &amp; purification ; *Agriculture ; *RNA, Ribosomal, 16S/genetics ; Mexico ; Alcoholic Beverages/microbiology ; Biodiversity ; Rhizosphere ; },
abstract = {Mezcal, a traditional Mexican alcoholic beverage, has been a vital source of livelihood for indigenous and rural communities for centuries. However, increasing international demand is exerting pressure on natural resources and encouraging intensive agricultural practices. This study investigates the impact of management practices (wild, traditional, and conventional) and environmental factors on the microbial communities associated with Agave angustifolia, a key species in mezcal production. High-throughput sequencing of the 16S rRNA and ITS2 gene regions revealed distinct prokaryotic and fungal community structures across different plant compartments (endosphere, episphere, and soil), identifying 8214 prokaryotic and 7459 fungal ASVs. Core microbial communities were dominated by Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota. Alpha diversity analyses showed significant increases in prokaryotic diversity from the endosphere to soil, while fungal diversity remained stable. Notably, conventional management practices were associated with reductions in beneficial microbial taxa. Environmental factors such as precipitation and temperature significantly influenced microbial diversity and composition, especially in the rhizosphere. Beta diversity patterns underscored the strong impact of plant compartment, with management practices and aridity further shaping microbial communities. These results reveal the intricate interactions between management practices, environmental conditions, and microbial diversity, providing valuable insights for the sustainable cultivation of A. angustifolia.},
}
@article {pmid39880083,
year = {2025},
author = {Moortele, TV and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T},
title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.},
journal = {Molecular &amp; cellular proteomics : MCP},
volume = {},
number = {},
pages = {100918},
doi = {10.1016/j.mcpro.2025.100918},
pmid = {39880083},
issn = {1535-9484},
abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a case study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.},
}
@article {pmid39878512,
year = {2025},
author = {Flanagan, K and Gassner, K and Lang, M and Ozelyte, J and Hausmann, B and Crepaz, D and Pjevac, P and Gasche, C and Berry, D and Vesely, C and Pereira, FC},
title = {Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron.},
journal = {mBio},
volume = {},
number = {},
pages = {e0392824},
doi = {10.1128/mbio.03928-24},
pmid = {39878512},
issn = {2150-7511},
abstract = {UNLABELLED: In the gut, microRNAs (miRNAs) produced by intestinal epithelial cells are secreted into the lumen and can shape the composition and function of the gut microbiome. Crosstalk between gut microbes and the host plays a key role in irritable bowel syndrome (IBS) and inflammatory bowel diseases, yet little is known about how the miRNA-gut microbiome axis contributes to the pathogenesis of these conditions. Here, we investigate the ability of miR-21, a miRNA that we found decreased in fecal samples from IBS patients, to associate with and regulate gut microbiome function. When incubated with the human fecal microbiota, miR-21 revealed a rapid internalization or binding to microbial cells, which varied in extent across different donor samples. Fluorescence-activated cell sorting and sequencing of microbial cells incubated with fluorescently labeled miR-21 identified organisms belonging to the genera Bacteroides, Limosilactobacillus, Ruminococcus, or Coprococcus, which predominantly interacted with miR-21. Surprisingly, these and other genera also interacted with a miRNA scramble control, suggesting that physical interaction and/or uptake of these miRNAs by gut microbiota is not sequence-dependent. Nevertheless, transcriptomic analysis of the gut commensal Bacteroides thetaiotaomicron revealed a miRNA sequence-specific effect on bacterial transcript levels. Supplementation of miR-21, but not of small RNA controls, resulted in significantly altered levels of many cellular transcripts and increased transcription of a biosynthetic operon for indole and L-tryptophan, metabolites known to regulate host inflammation and colonic motility. Our study identifies a novel putative miR-21-dependent pathway of regulation of intestinal function through the gut microbiome with implications for gastrointestinal conditions.<br><br>IMPORTANCE: The mammalian gut represents one of the largest and most dynamic host-microbe interfaces. Host-derived microRNAs (miRNAs), released from the gut epithelium into the lumen, have emerged as important contributors to host-microbe crosstalk. Levels of several miRNAs are altered in the stool of patients with irritable bowel syndrome or inflammatory bowel disease. Understanding how miRNAs interact with and shape gut microbiota function is crucial as it may enable the development of new targeted treatments for intestinal diseases. This study provides evidence that the miRNA miR-21 can rapidly associate with diverse microbial cells form the gut and increase levels of transcripts involved in tryptophan synthesis in a ubiquitous gut microbe. Tryptophan catabolites regulate key functions, such as gut immune response or permeability. Therefore, this mechanism represents an unexpected host-microbe interaction and suggests that host-derived miR-21 may help regulate gut function via the gut microbiota.},
}
@article {pmid39878482,
year = {2025},
author = {Rodriguez-Garcia, C and Wall, H and Ottesen, E and Grainy, J},
title = {Characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae from recreational water in Athens, GA, using an undergraduate laboratory module.},
journal = {Journal of microbiology &amp; biology education},
volume = {},
number = {},
pages = {e0005624},
doi = {10.1128/jmbe.00056-24},
pmid = {39878482},
issn = {1935-7877},
abstract = {We present a laboratory module that uses isolation of antibiotic-resistant bacteria from locally collected stream water samples to introduce undergraduate students to basic microbiological culture-based and molecular techniques. This module also educates them on the global public health threat of antibiotic-resistant organisms. Through eight laboratory sessions, students are involved in quality testing of water sources from their neighborhoods, followed by isolation of extended-spectrum beta-lactamase-producing Enterobacteriaceae. By the end of the module, students should be able to isolate Enterobacteriaceae from the environment using selective and differential media, identify isolates using biochemical tests, characterize antibiotic resistance phenotypes using Kirby Bauer and MIC tests, and evaluate the presence of select beta-lactamase genes of interest using PCR. To complement laboratory sessions, students participated in a weekly flipped classroom session with collaborative peer discussions and activities to reinforce concepts applied in the laboratory. Learning outcomes were measured over four semesters with concept checks, in-lecture activities, exams, and laboratory reports. We hypothesized that more than 50% of the student population would achieve each learning objective through the implementation of this authentic research laboratory module. Here, we highlight specific questions used to assess learning objective comprehension and demonstrate that each learning objective was achieved by 65%-100% of the student population. We present a ready-to-adapt module with flexible resources that can be implemented in courses across disciplines in biology, microbiology, environmental sciences, and public health.},
}
@article {pmid39876091,
year = {2025},
author = {Tocarruncho, OI and Neuta, Y and Lesmes, Y and Castillo, DM and Leal, S and Chambrone, L and Lafaurie, GI},
title = {Submucosal Microbiome Profiles in Paired and Unpaired Samples From Healthy and Peri-Implantitis Dental Implants.},
journal = {Clinical implant dentistry and related research},
volume = {27},
number = {1},
pages = {e13423},
doi = {10.1111/cid.13423},
pmid = {39876091},
issn = {1708-8208},
support = {490-21//Research Vice Rectory of Universidad El Bosque/ ; },
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Microbiota ; Cross-Sectional Studies ; Female ; Male ; *Dental Implants/microbiology/adverse effects ; Middle Aged ; RNA, Ribosomal, 16S/analysis ; Adult ; Aged ; },
abstract = {BACKGROUND: This cross-sectional study aimed to compare the composition of the submucosal microbiome of peri-implantitis with paired and unpaired healthy implant samples.<br><br>METHODS: We evaluated submucosal plaque samples obtained in 39 cases, including 13 cases of peri-implantitis, 13 cases involving healthy implants from the same patient (paired samples), and 13 cases involving healthy implants from different individuals (unpaired samples). The patients were evaluated using next-generation genomic sequencing (Illumina) based on 16S rRNA gene amplification. The sequences were grouped according to the amplicon sequence variant (ASV) to define the taxonomic categories. Alpha diversity was analyzed using Shannon's and Simpson's indices, while beta diversity was evaluated using principal coordinate analysis, analysis of similarities, and permutational multivariate variance analysis. Additionally, UniFrac distances were evaluated using Quantitative Insights into Microbial Ecology 2. Finally, we evaluated between-group differences in the taxonomic components.<br><br>RESULTS: There were no significant between-group differences in alpha diversity. The average bacterial ratios of Filifactor alocis, Porphyromona endodontalis, Tannerella forsythia, Treponema denticola, Peptostreptococcaceae [Eubacterium nodatum], Desulfobulbus sp. HTM 041, and Mogibacterium timidum significantly differed between peri-implantitis samples and unpaired samples from the healthy implants (p&#x2009;<&#x2009;0.05). However, there were few differences in the microbiota between peri-implantitis samples and those paired with healthy implants in the same patient.<br><br>CONCLUSIONS: Future studies comparing the microbiome compositions using sequencing techniques between healthy implants and implants with peri-implantitis should focus on retrieving samples from the same patient, especially in individuals with a history of periodontitis.},
}
@article {pmid39874167,
year = {2025},
author = {Zhang, F and Zhang, S and Wu, Y and Liu, J and Zhao, S and Qiu, Z and Zhu 朱, M&#x58a8;},
title = {Powdery Mildew of Echinacea purpurea Caused by Podosphaera xanthii in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-12-24-2632-PDN},
pmid = {39874167},
issn = {0191-2917},
abstract = {Echinacea purpurea (Eastern Purple Coneflower) is a perennial herbaceous plant belonging to the Asteraceae. It originated from North America and is cultivated all over the world. Extracts of E. purpurea are widely used for the treatments of colds and sore throats (Jiao et al. 2020). In October 2024, powdery mildew-like signs and symptoms were observed on leaves of E. purpurea plants (n=100) cultivated in a garden (20 m2) in Xinxiang city, Henan Province, China (35.32° N, 113.92° E). A specimen (PX-ZM20241024) was stored in Xinxiang Key Laboratory of Plant Stress Biology. The infected leaves were covered with white and thin masses and showed senescence symptoms. More than 80% of plants (n=100) exhibited these signs and symptoms. White colonies were on both sides surfaces of the leaves, covering about 80% of the leaf area. The slightly curved or straight Conidia chain (n = 50) were 70 to 156 × 8 to 12 μm in size and consisted of foot cells, shorter cells, and conidia. Foot cells were straight, 30 to 60 μm long. Conidia were ellipsoid to oval, 20 to 35 × 12 to 17 μm (n = 50), with a length/width ratio of 1.8 to 2.2, containing fibrosin bodies. These morphological characteristics were similar to Podosphaera xanthii (Braun and Cook 2012). Following a previously reported method (Zhu et al. 2022), the internal transcribed spacer (ITS) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regions of a selected specimen of the fungus were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022). The resulting sequences were deposited in GenBank (Accession No. PQ508348 and PQ734986). BLASTn analysis indicated that the ITS and GAPDH sequences had 99.82 % (564/565 bp) and 100% (238/238 bp) identity with reported P. xanthii (MW300956 and ON075660) on Xanthium strumarium and Cucurbita moschata, respectively (Zhu et al. 2024; Bradshaw et al. 2022). By phylogenetic analysis, the isolated fungus clustered with previously reported P. xanthii (Zhu et al. 2024; Bradshaw et al. 2022). Therefore, the morphology and phylogenetic analysis indicated that the pathogen was P. xanthii. To complete Koch's postulates, mature leaves of three healthy E. purpurea (30 cm high) were inoculated with fungal conidia by gently pressing surfaces of infested leaves onto leaves of healthy plants. Three untreated plants served as controls. Both the control and inoculated plants were separately placed in greenhouses (humidity, 60%; light/dark, 16 h/8 h; temperature, 18°C). 10 to 12 days post inoculation, the leaves of the inoculated plants exhibited signs of powdery mildew, whereas the control group remained unaffected. The experiments were repeated three times and the same results were obtained. Therefore, the pathogenicity of this fungal pathogen was confirmed. Previously, P. xanthii was reported on E. purpurea in Korea (Choi et al. 2020). To the best of our knowledge, this is the first report of P. xanthii on E. purpurea in China. The sudden presence of powdery mildew caused by P. xanthii may adversely affect plant health and thus reduce the medicinal value of E. purpurea. Therefore, the identification and confirmation of P. xanthii infecting E. purpurea enhances our comprehension of hosts of this pathogen and provides fundamental information for forthcoming disease control studies.},
}
@article {pmid39873755,
year = {2025},
author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE},
title = {Correction to: Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {180},
doi = {10.1007/s00248-025-02498-0},
pmid = {39873755},
issn = {1432-184X},
}
@article {pmid39871445,
year = {2025},
author = {Zahir, Z and Khan, F and Hall, BD},
title = {Sulfate and Dissolved Organic Carbon Concentrations Drive Distinct Microbial Community Patterns in Prairie Wetland Ponds.},
journal = {Environmental microbiology reports},
volume = {17},
number = {1},
pages = {e70069},
doi = {10.1111/1758-2229.70069},
pmid = {39871445},
issn = {1758-2229},
support = {//Agricultural Development Fund/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Faculty of Graduate Studies and Research, University of Regina/ ; //Government of Canada/ ; },
mesh = {*Wetlands ; *Carbon/metabolism/analysis ; *Sulfates/metabolism ; *Ponds/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; Phylogeny ; Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; },
abstract = {Prairie wetland ponds on the Great Plains of North America offer a diverse array of geochemical scenarios that can be informative about their impact on microbial communities. These ecosystems offer invaluable ecological services while experiencing significant stressors, primarily through drainage and climate change. In this first study systematically combining environmental conditions with microbial community composition to identify various niches in prairie wetland ponds, sediments had higher microbial abundance but lower phylogenetic diversity in ponds with lower concentrations of dissolved organic carbon ([DOC]; 10-18 mg/L) and sulfate ([SO4 [2-]]; 37-58 mg/L) in water. As [DOC] and [SO4 [2-]] increased, there was an initial decline in abundance but not phylogenetic diversity. Maximum values of both abundance and phylogenetic diversity occurred between 56 and 115 mg/L [DOC] and 5,000-6,000 mg/L [SO4 [2-]] and decreased thereafter in ponds with 150-180 mg/L and 8,000-14,000 mg/L [DOC] and [SO4 [2-]], respectively. These findings confirm that environmental variables shape the microbial communities and that key microbial taxa involved in sulfur and carbon cycling dominated these ponds potentially impacting vital biogeochemical processes such as bioavailability of heavy metals, carbon sequestration, and methane emissions.},
}
@article {pmid39871406,
year = {2025},
author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR},
title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70032},
doi = {10.1111/1462-2920.70032},
pmid = {39871406},
issn = {1462-2920},
support = {18-UOW-028//Marsden Fund/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Archaea/classification/genetics ; *Bacteria/classification/isolation &amp; purification/genetics ; *Ecosystem ; Microbiota ; Phylogeny ; Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.},
}
@article {pmid39871020,
year = {2025},
author = {Zhang, Z and Zhang, Q and Guo, X and Zeng, Z and Wang, Y and Zhang, P and Gao, D and Deng, G and Sun, G and Yang, Y and Wang, J},
title = {Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {177},
pmid = {39871020},
issn = {1432-184X},
support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B1212060002//Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Forests ; *Carbon/metabolism ; Hydrogen-Ion Concentration ; China ; *Microbiota ; Carbon Cycle ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Ecosystem ; Organic Chemicals/metabolism ; Microbial Interactions ; },
abstract = {The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.},
}
@article {pmid39870904,
year = {2025},
author = {Stenger, PL and Tribollet, A and Guilhaumon, F and Cuet, P and Pennober, G and Jourand, P},
title = {A Multimarker Approach to Identify Microbial Bioindicators for Coral Reef Health Monitoring-Case Study in La Réunion Island.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {179},
pmid = {39870904},
issn = {1432-184X},
mesh = {*Coral Reefs ; *Microbiota ; *Anthozoa/microbiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Reunion ; *Fungi/classification/genetics/isolation &amp; purification/metabolism ; Seawater/microbiology ; Indian Ocean ; Seasons ; Biodiversity ; Environmental Monitoring/methods ; Islands ; Microalgae/classification/metabolism ; Geologic Sediments/microbiology ; },
abstract = {The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.},
}
@article {pmid39870843,
year = {2025},
author = {Li, Q and Shao, H},
title = {The Role of Pathogens in Plant Invasion: Accumulation of Local Pathogens Hypothesis.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {178},
pmid = {39870843},
issn = {1432-184X},
support = {No.2023E01012//Ministry of Science and Technology of the People's Republic of China/ ; 2022D01D02//Science and Technology Department of Xinjiang Uygur Autonomous Region/ ; },
mesh = {*Introduced Species ; *Plants/microbiology ; *Plant Diseases/microbiology ; *Soil Microbiology ; Host-Pathogen Interactions ; Bacteria/genetics/metabolism ; },
abstract = {In the past decades, dozens of invasion hypotheses have been proposed to elucidate the invasion mechanisms of exotic species. Among them, the accumulation of local pathogens hypothesis (ALPH) posits that invasive plants can accumulate local generalist pathogens that have more negative effect on native species than on themselves; as a result, invasive plants might gain competitive advantages that eventually lead to their invasion success. However, research on this topic is still quite insufficient. In this context, we performed a comprehensive literature survey in order to provide a detailed description of the origin and theoretical framework of ALPH; in addition, challenges in contemporary research such as limitations in technical methods and the complexity of interactions between plants and soil microorganisms, as well as future directions of ALPH research, are also discussed in this review. So far, there are less than ten case studies supporting ALPH; therefore, more work is needed to demonstrate whether ALPH is a suitable hypothesis to elucidate the invasion success of certain plant species.},
}
@article {pmid39868213,
year = {2025},
author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM},
title = {Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.15.633187},
pmid = {39868213},
issn = {2692-8205},
abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.},
}
@article {pmid39868180,
year = {2025},
author = {Peters, DI and Shin, IJ and Deever, AN and Kaspar, JR},
title = {Design, Development and Validation of New Fluorescent Strains for Studying Oral Streptococci.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.14.632972},
pmid = {39868180},
issn = {2692-8205},
abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans , and Streptococcus sanguinis . Gene fragments, developed to contain the constitutive promoter P veg , the fluorescent gene of interest as well as aad9 , providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis , were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans , and S. sanguinis grown with and without addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.},
}
@article {pmid39862387,
year = {2025},
author = {Almeida-Silva, F and Van de Peer, Y},
title = {doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf043},
pmid = {39862387},
issn = {1367-4811},
abstract = {SUMMARY: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface.<br><br>doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online and at https://github.com/almeidasilvaf/doubletrouble_paper.},
}
@article {pmid39861970,
year = {2025},
author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I},
title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf014},
pmid = {39861970},
issn = {1751-7370},
abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the reorganisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.},
}
@article {pmid39857259,
year = {2025},
author = {Chung, CC and Gong, GC and Tseng, HC and Chou, WC and Ho, CH},
title = {Dominance of Sulfur-Oxidizing Bacteria, Thiomicrorhabdus, in the Waters Affected by a Shallow-Sea Hydrothermal Plume.},
journal = {Biology},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/biology14010028},
pmid = {39857259},
issn = {2079-7737},
support = {NSTC 113-2611-M-019-006//National Science and Technology Council of Taiwan/ ; },
abstract = {The shallow-sea hydrothermal vent at Guishan Islet, located off the coast of Taiwan, serves as a remarkable natural site for studying microbial ecology in extreme environments. In April 2019, we investigated the composition of prokaryotic picoplankton communities, their gene expression profiles, and the dissolved inorganic carbon uptake efficiency. Our results revealed that the chemolithotrophs Thiomicrorhabdus spp. contributed to the majority of primary production in the waters affected by the hydrothermal vent plume. The metatranscriptomic analysis aligned with the primary productivity measurements, indicating the significant gene upregulations associated with carboxysome-mediated carbon fixation in Thiomicrorhabdus. Synechococcus and Prochlorococcus served as the prokaryotic photoautotrophs for primary productivity in the waters with lower influence from hydrothermal vent emissions. Thiomicrorhabdus and picocyanobacteria jointly provided organic carbon for sustaining the shallow-sea hydrothermal vent ecosystem. In addition to the carbon fixation, the upregulation of genes involved in the SOX (sulfur-oxidizing) pathway, and the dissimilatory sulfate reduction indicated that energy generation and detoxification co-occurred in Thiomicrorhabdus. This study improved our understanding of the impacts of shallow-sea hydrothermal vents on the operation of marine ecosystems and biogeochemical cycles.},
}
@article {pmid39856188,
year = {2025},
author = {Tokodi, N and Łobodzińska, A and Klimczak, B and Antosiak, A and Młynarska, S and Šulčius, S and Avrani, S and Yoshida, T and Dziga, D},
title = {Proliferative and viability effects of two cyanophages on freshwater bloom-forming species Microcystis aeruginosa and Raphidiopsis raciborskii vary between strains.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3152},
pmid = {39856188},
issn = {2045-2322},
support = {PPN/ULM/2019/1/00219//Narodowa Agencja Wymiany Akademickiej/ ; 2021/41/N/NZ9/02957//Narodowym Centrum Nauki/ ; 2021/41/N/NZ9/02957//Narodowym Centrum Nauki/ ; 2020/38/L/NZ9/00135//Narodowym Centrum Nauki/ ; S-LL-21-10//Research Council of Lithuania/ ; 1386/20//Israel Science Foundation/ ; },
mesh = {*Microcystis/virology/physiology ; *Bacteriophages/physiology ; *Fresh Water/virology ; Eutrophication ; Ecosystem ; Cyanobacteria/virology/physiology ; Photosynthesis ; Host Specificity ; },
abstract = {Viruses that infect cyanobacteria are an integral part of aquatic food webs, influencing nutrient cycling and ecosystem health. However, the significance of virus host range, replication efficiency, and host compatibility on cyanobacterial dynamics, growth, and toxicity remains poorly understood. In this study, we examined the effects of cyanophage additions on the dynamics and activity of optimal, sub-optimal, and non-permissive cyanobacterial hosts in cultures of Microcystis aeruginosa and Raphidiopsis raciborskii. Our findings reveal that cross-infectivity can substantially reduce the proliferative success of the cyanophage under conditions of high-density of sub-optimal hosts which suggests phage dispersal limitation as a result of shared infections, in turn impairing their top-down control over the host community. Furthermore, we found that cyanophage addition triggers host strain-specific responses in photosynthetic performance, population size and toxin production, even among non-permissive hosts. These non-lytic effects suggest indirect impacts on co-existing cyanobacteria, increasing the overall complexity and variance in many ecologically relevant cyanobacterial traits. The high variability in responses observed with a limited subset of cyanophage-cyanobacteria combinations not only highlights the intricate role of viral infections in microbial ecosystems but also underscores the significant challenges in predicting the composition, toxicity, and dynamics of cyanobacterial blooms.},
}
@article {pmid39855017,
year = {2025},
author = {Savadova-Ratkus, K and Grendaitė, D and Karosienė, J and Stonevičius, E and Kasperovičienė, J and Koreivienė, J},
title = {Modelling harmful algal blooms in a mono- and a polydominant eutrophic lake under temperature and nutrient changes.},
journal = {Water research},
volume = {275},
number = {},
pages = {123138},
doi = {10.1016/j.watres.2025.123138},
pmid = {39855017},
issn = {1879-2448},
abstract = {Cyanobacterial blooms, driven by nutrient loading and temperature, pose significant ecological and economic challenges. This study employs a combined data-driven and trait-based modelling approach to predict changes in cyanobacterial communities in a mono- and a polydominant shallow temperate lakes under varying temperature and nutrient scenarios. Results of the AQUATOX simulation model for two aquatic systems suggest that a 2 °C temperature increase, consistent with Intergovernmental Panel on Climate Change's predictions, may influence cyanobacteria species composition and dominance, with trends indicating a possible shift favouring Nostocales over Oscillatoriales and Chroococcales. Temperature increases by 4 °C clearly promoted the dominance of Nostocales. Nutrient dynamics appear to influence community structure. In a nutrient-rich monodominant lake, temperature was the primary driver, while in a nutrient-limited polydominant lake, phosphorus availability influenced cyanobacteria species dominance. Combined warming and phosphorus alterations significantly affected cyanobacteria bloom intensity and duration, particularly enhancing Nostocales growth. The study highlights the complexity of cyanobacterial responses to climate change, emphasizing the need for more analysis and comprehensive models to predict harmful algal blooms (HABs) in freshwater ecosystems. While the findings suggest that temperature and nutrient availability may be critical drivers of cyanobacterial dominance, additional research across a broader range of systems is necessary.},
}
@article {pmid39854900,
year = {2025},
author = {Reid, CJ and Farrell, M and Kirby, JK},
title = {Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124203},
doi = {10.1016/j.jenvman.2025.124203},
pmid = {39854900},
issn = {1095-8630},
abstract = {Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.},
}
@article {pmid39853499,
year = {2025},
author = {Lucia, Z and Giulio, G and Matteo, G and Stefano, C and Irene, LP and Paolo, P and Giorgio, B and Hauffe, HC},
title = {More Than Meets the Eye: Unraveling the Interactions Between Skin Microbiota and Habitat in an Opportunistic Amphibian.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {176},
pmid = {39853499},
issn = {1432-184X},
mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Ecosystem ; *Anura/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Italy ; Fungi/classification/isolation &amp; purification/genetics ; Hydrogen-Ion Concentration ; Batrachochytrium ; Wetlands ; Temperature ; },
abstract = {With amphibians still holding the record as the most threatened class of terrestrial vertebrates, their skin microbiota has been shown to play a relevant role in their survival in a fast-changing world. Yet little is known about how abiotic factors associated with different aquatic habitats impact these skin microorganisms. Here we chose the yellow-bellied toad (Bombina variegata), a small anuran that colonizes a wide range of wetland habitats, to investigate how the diversity and composition of both its bacterial and fungal skin communities vary across different habitats and with water characteristics (temperature, pH, and dissolved oxygen) of these habitats. Skin microbiota was sampled from 14 sites in the Province of Trento (Italy), including natural pools, ephemeral ponds, irrigation tanks, and farm ponds. Interestingly, the diversity of the two microbial components was also highly correlated. Close associations between both the diversity and composition of water and skin communities were noted for each habitat and sampling site, suggesting that water bodies actively contribute to the skin microbiota assemblage. In addition, water pH, temperature, and dissolved oxygen affected both bacterial and fungal diversity of skin. We confirmed the presence of Batrachochytrium dendrobatidis in skin samples of animals collected from eight waterbodies, as well as more than 60 microbial taxa previously associated with resistance to this pathogen. We concluded that both skin bacterial and fungal communities appear to be influenced by each other as well as by environmental communities and conditions, and these relationships connecting the whole ecosystem should be considered in future research concerning amphibian conservation.},
}
@article {pmid39849986,
year = {2025},
author = {Liu, Y and Geng, Y and Jiang, Y and Li, P and Li, YZ and Zhang, Z},
title = {Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf012},
pmid = {39849986},
issn = {1751-7370},
abstract = {One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.},
}
@article {pmid39849009,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K},
title = {The influence of depth on the global deep-sea plasmidome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2959},
pmid = {39849009},
issn = {2045-2322},
support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; },
mesh = {*Plasmids/genetics ; Metagenome ; Seawater/microbiology ; Ecosystem ; Oceans and Seas ; Gammaproteobacteria/genetics/classification ; Alphaproteobacteria/genetics ; },
abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.},
}
@article {pmid39848193,
year = {2025},
author = {Odales-Bernal, L and González, LML and Ghysels, S and Lobanov, V and De Vrieze, J and Barrera, EL and Ronsse, F},
title = {Optimized hydrothermal carbonization of chicken manure and anaerobic digestion of its process water for better energy management.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124191},
doi = {10.1016/j.jenvman.2025.124191},
pmid = {39848193},
issn = {1095-8630},
abstract = {Modern poultry production is faced with the challenge of properly managing its associated wastes, in particular chicken manure (CM). There is a need to improve the management of CM through conversion processes that allow the production of value-added products, particularly for energy purposes, such as hydrothermal carbonization (HTC) and anaerobic digestion (AD). The objectives of this study were: i) to optimize the CM-HTC, using response surface methodology with simultaneous optimization of mass yield and higher heating value (HHV), and ii) to evaluate the biomethane potential of the process water generated from hydrochar production under the optimized condition. An analysis of the overall energy potential was also performed. The optimal condition for HTC was 234 °C for 30 min, resulting in hydrochar with an HHV of 14.88 ± 0.22 MJ/kg and a mass yield of 50.00 ± 3.13 wt%. The cumulative methane yield was 179.2 ± 13.1 NmL CH4/g VSadded and 255.5 ± 14.5 NmL CH4/g VSadded for process water at 180 °C and 234 °C, respectively. The addition of hydrochar improved the methane yield by 49.6 ± 10.8%, indicating that this is a valuable option for energy recovery from CM. Overall, the HTC-AD integration approach achieved an energy recovery potential of more than 79%, offering an efficient strategy for CM valorization.},
}
@article {pmid39847340,
year = {2025},
author = {Ganley, JG and Seyedsayamdost, MR},
title = {Iron limitation triggers roseoceramide biosynthesis and membrane remodeling in marine roseobacter.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {4},
pages = {e2414434122},
doi = {10.1073/pnas.2414434122},
pmid = {39847340},
issn = {1091-6490},
support = {Postdoctoral Fellowship in Marine Microbial Ecology//Simons Foundation (SF)/ ; R35 GM152049/GM/NIGMS NIH HHS/United States ; },
mesh = {*Roseobacter/metabolism ; *Iron/metabolism ; Cell Membrane/metabolism ; Seaweed/metabolism ; Symbiosis/physiology ; },
abstract = {Chemical communication between marine bacteria and their algal hosts drives population dynamics and ultimately determines the fate of major biogeochemical cycles in the ocean. To gain deeper insights into this small molecule exchange, we screened niche-specific metabolites as potential modulators of the secondary metabolome of the roseobacter, Roseovarius tolerans. Metabolomic analysis led to the identification of a group of cryptic lipids that we have termed roseoceramides. The roseoceramides are elicited by iron-binding algal flavonoids, which are produced by macroalgae that Roseovarius species associate with. Investigations into the mechanism of elicitation show that iron limitation in R. tolerans initiates a stress response that results in lowered oxidative phosphorylation, increased import and catabolism of algal exudates, and reconfiguration of lipid ynthesis to prioritize production of roseoceramides over phospholipids, likely to fortify membrane integrity as well as promote a sessile and symbiotic lifestyle. Our findings add new small molecule words and their "meanings" to the algal-bacterial lexicon and have implications for the initiation of these interactions.},
}
@article {pmid39845484,
year = {2024},
author = {Tóth, VR},
title = {Photosynthetic traits of Phragmites australis along an ecological gradient and developmental stages.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1476142},
pmid = {39845484},
issn = {1664-462X},
abstract = {Common reed (Phragmites australis) is a cosmopolitan species, though its dieback is a worldwide phenomenon. In order to assess the evolutionary role of phenotypic plasticity in a successful plant, the values and plasticity of photophysiological traits of Phragmites australis were investigated in the Lake Fertő wetlands at 5 sites with different degrees of reed degradation and along a seasonal sequence. On the one hand, along the established ecological degradation gradient, photophysiological traits of Phragmites changed significantly, affecting plant productivity, although no consistent gradient-type trends were observed. Gradual changes within a season in the values of photosynthetic traits were observed that were recorded in both degraded and stable stands, suggesting a universal response to seasonally changing environmental conditions that could not be overridden by the ecological gradient. On the other hand, reed plants exposed to different levels of degradation showed comparable physiological plasticity; there was no difference in trait variability between stable and degraded stands. This relatively uniform plasticity is likely to contribute to the resilience of reed plants by providing a wider range of adaptive traits under different conditions. In contrast, the 150-200% gradual change in photophysiological trait plasticity with senescence in Phragmites was also demonstrated, reflecting a more dynamic response of the photosynthetic apparatus to seasonal changes. Senescence affected the plasticity of plant traits independently of their degradation status, suggesting a more universal nature of seasonal changes. This research shows that under conditions of conservative resource use determined by stressful habitats, trait values respond to conditions, while trait plasticity shows minimal changes. Furthermore, phenological sequence significantly influenced both the values and the plasticity of the photosynthetic traits studied. Our results underline the impact of ecological degradation on reed physiology and highlight the importance of understanding both trait values and plasticity in plant responses to environmental and seasonal change.},
}
@article {pmid39844349,
year = {2025},
author = {de Souza, LF and Oliveira, HG and Pellegrinetti, TA and Mendes, LW and Bonatelli, ML and Romão Dumaresq, AS and Sinatti, VVC and Pinheiro, JB and Azevedo, JL and Quecine, MC},
title = {Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf013},
pmid = {39844349},
issn = {1574-6941},
abstract = {Despite the beneficial effects of Plant Growth-Promoting Rhizobacteria (PGPR) on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 Days After Sowing (DAS). However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.},
}
@article {pmid39844346,
year = {2025},
author = {Melville, DW and Meyer, M and Kümmerle, C and Alvarado-Barrantes, KA and Wilhelm, K and Sommer, S and Tschapka, M and Risely, A},
title = {Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf012},
pmid = {39844346},
issn = {1574-6941},
abstract = {Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the fecal microbiota and gut pH every two hours. We detected strong diurnal rhythms in both microbial alpha- and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.},
}
@article {pmid39843903,
year = {2025},
author = {Tóth, AB and Terauds, A and Chown, SL and Hughes, KA and Convey, P and Hodgson, DA and Cowan, DA and Gibson, J and Leihy, RI and Murray, NJ and Robinson, SA and Shaw, JD and Stark, JS and Stevens, MI and van den Hoff, J and Wasley, J and Keith, DA},
title = {A dataset of Antarctic ecosystems in ice-free lands: classification, descriptions, and maps.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {133},
pmid = {39843903},
issn = {2052-4463},
support = {LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; },
abstract = {Antarctica, Earth's least understood and most remote continent, is threatened by human disturbances and climate-related changes, underscoring the imperative for biodiversity inventories to inform conservation. Antarctic ecosystems support unique species and genetic diversity, deliver essential ecosystem services and contribute to planetary stability. We present Antarctica's first comprehensive ecosystem classification and map of ice-free lands, which host most of the continent's biodiversity. We used latent variables in factor analyses to partition continental-scale abiotic variation, then biotic variation represented in spatial models, and finally recognised regional-scale variation among biogeographic units. This produced a spatially explicit hierarchical classification with nine Major Environment Units (Tier 1), 33 Habitat Complexes (Tier 2) and 269 Bioregional Ecosystem Types (Tier 3) mapped at 100 m resolution and aligned with 'level 4' of the IUCN Global Ecosystem Typology. This comprehensive ecosystem inventory provides foundational data to inform protected area designation under the Antarctic Treaty's Environmental Protocol and track risks to Antarctic ecosystems. Its tiered structure and workflow accommodate data scarcity and facilitate updates, promoting robustness as knowledge builds.},
}
@article {pmid39840338,
year = {2024},
author = {Salerno, B and Cornaggia, M and Sabatino, R and Di Cesare, A and Mantovani, C and Barco, L and Cordioli, B and Bano, L and Losasso, C},
title = {The "best practices for farming" successfully contributed to decrease the antibiotic resistance gene abundances within dairy farms.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1420282},
pmid = {39840338},
issn = {2297-1769},
abstract = {INTRODUCTION: Farms are significant hotspots for the dissemination of antibiotic-resistant bacteria and genes (ARGs) into the environment and directly to humans. The prevalence of ARGs on farms underscores the need for effective strategies to reduce their spread. This study aimed to evaluate the impact of a guideline on "best practices for farming" aimed at reducing the dissemination of antibiotic resistance.<br><br>METHODS: A guideline focused on prudent antibiotic use, selective therapy, and hygienic and immune-prophylactic practices was developed and provided to the owners of 10 selected dairy farms and their veterinarians. Fecal samples were collected from lactating cows, dry cows, and calves both before and after the implementation of the guideline. ARGs (bla TEM, ermB, sul2, and tetA) were initially screened by end-point PCR, followed by quantification using digital droplet PCR. ARG abundance was expressed in relative terms by dividing the copy number of ARGs by the copy number of the 16S rRNA gene.<br><br>RESULTS: The ARG abundances were higher in lactating cows compared to other categories. Despite similar levels of antibiotic administration (based on veterinary prescription data from the sampled farms) in both sampling campaigns, the total abundance of selected ARGs, particularly bla TEM and tetA, significantly decreased after the adoption of the farming guidelines.<br><br>DISCUSSION: This study highlights the positive impact of prudent antibiotic use and the implementation of farming best practices in reducing the abundance of ARGs. The lactating cow category emerged as a crucial point of intervention for reducing the spread of antibiotic resistance. These findings contribute to ongoing efforts to address antibiotic resistance in farm environments and strengthen the evidence supporting the adoption of good farming practices.},
}
@article {pmid39838963,
year = {2024},
author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y},
title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf014},
pmid = {39838963},
issn = {1477-4054},
support = {11209823//City University of Hong Kong/ ; },
mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Molecular Sequence Annotation ; *Viral Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; Software ; },
abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.},
}
@article {pmid39838210,
year = {2025},
author = {Ouyang, XM and Lin, JH and Lin, Y and Zhao, XL and Huo, YN and Liang, LY and Huang, YD and Xie, GJ and Mi, P and Ye, ZY and Guleng, B},
title = {The SERPINB4 gene mutation identified in twin patients with Crohn's disease impaires the intestinal epithelial cell functions.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2638},
pmid = {39838210},
issn = {2045-2322},
support = {81970460//National Natural Science Foundation of China/ ; 2023J011598//Natural Science Foundation Program, Fujian Province, China/ ; },
mesh = {Humans ; *Crohn Disease/genetics/pathology ; *Mutation ; Female ; Male ; Serpins/genetics/metabolism ; Apoptosis/genetics ; Exome Sequencing ; Epithelial Cells/metabolism/pathology ; Intestinal Mucosa/metabolism/pathology ; Genetic Predisposition to Disease ; Cell Proliferation ; Adult ; Cell Movement/genetics ; Twins/genetics ; },
abstract = {Crohn's disease (CD) is a chronic inflammatory autoimmune disease of unknown etiology. To identify new targets related to the initiation of CD, we screened a pair of twins with CD, which is a rare phenomenon in the Chinese population, for genetic susceptibility factors. Whole-exome sequencing (WES) of these patients revealed a mutation in their SERPINB4 gene. Therefore, we studied a wider clinical cohort of patients with CD or ulcerous colitis (UC), healthy individuals, and those with a family history of CD for this mutation by Sanger sequencing. The single-nucleotide difference in the SERPINB4 gene, which was unique to the twin patients with CD, led to the substitution of lysine by a glutamic acid residue. Functional analysis indicated that this mutation of SERPINB4 inhibited the proliferation, colony formation, wound healing, and migration of intestinal epithelial cells (IECs). Furthermore, mutation of SERPINB4 induced apoptosis and activated apoptosis-related proteins in IECs, and a caspase inhibitor significantly reduced these effects. Transcriptome sequencing revealed that the expression of genes encoding proinflammatory proteins (IL1B, IL6, IL17, IL24, CCL2, and CXCR2) and key proteins in the immune response (S100A9, MMP3, and MYC) was significantly upregulated during SERPINB4 mutant-induced apoptosis. Thus, the heterozygous SERPINB4 gene mutation causes the dysfunction of IECs, which would disrupt the intestinal epithelial barrier and contribute to the development of intestinal inflammation. The activation of SERPINB4 might represent a novel therapeutic target for inflammatory bowel disease.},
}
@article {pmid39838107,
year = {2025},
author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM},
title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {175},
pmid = {39838107},
issn = {1432-184X},
support = {PEJ2018-003019-A//Plan Estatal de Garant&#xed;a Juvenil (Fondo Social Europeo, Gobierno de Espa&#xf1;a/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andaluc&#xed;a 2014-2020/ ; },
mesh = {*Cheese/microbiology ; *Bacteriocins/metabolism/biosynthesis ; *Enterococcus/metabolism/genetics ; *Microbiota ; Biodiversity ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Milk/microbiology ; Animals ; },
abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.},
}
@article {pmid39716385,
year = {2025},
author = {Lu, Z and Entwistle, E and Kuhl, MD and Durrant, AR and Barreto Filho, MM and Goswami, A and Morris, JJ},
title = {Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {39716385},
issn = {1751-7370},
mesh = {*Phytoplankton/genetics/metabolism/growth &amp; development ; *Carbon Dioxide/metabolism ; *Alteromonas/genetics/metabolism ; *Prochlorococcus/genetics/metabolism/growth &amp; development ; Seawater/microbiology ; Coculture Techniques ; Biological Coevolution ; Diatoms/genetics/growth &amp; development/metabolism ; Microbial Interactions ; },
abstract = {As a result of human activity, Earth's atmosphere and climate are changing at an unprecedented pace. Models based on short-term experiments predict major changes will occur in marine phytoplankton communities in the future ocean, but rarely consider how evolution or interactions with other microbes may influence these changes. Here, we experimentally evolved several phytoplankton in coculture with a heterotrophic bacterium, Alteromonas sp. EZ55, under either present-day or predicted future pCO2 conditions. Growth rates of phytoplankton generally increased over time under both conditions, but only Thalassiosira oceanica had evidence of a growth rate tradeoff in the ancestral environment after evolution at elevated pCO2. The growth defects observed in ancestral Prochlorococcus cultures at elevated pCO2 and in axenic culture were diminished after evolution, possibly due to regulatory mutations in antioxidant genes. Except for Prochlorococcus, mutational profiles suggested phytoplankton experienced primarily purifying selection, but most Alteromonas lineages showed evidence of directional selection, where evolution appeared to favor a metabolic switch between growth on small organic acids with cyanobacteria versus catabolism of more complex carbon substrates with eukaryotic phytoplankton. Evolved Alteromonas were also poorer "helpers" for Prochlorococcus, consistent with that interaction being a competitive Black Queen process rather than a true mutualism. This work provides new insights on how phytoplankton will respond to increased pCO2 and on the evolutionary mechanisms governing phytoplankton:bacteria interactions. It also clearly demonstrates that both evolution and interspecies interactions must be considered to predict future marine biogeochemistry.},
}
@article {pmid39836327,
year = {2025},
author = {Flores Clavo, R and Suclupe-Campos, DO and Castillo Rivadeneira, L and Velez Chicoma, RLJ and Sánchez-Purihuamán, M and Quispe Choque, KG and Casado Peña, FL and Binatti Ferreira, M and Fantinatti Garboggini, F and Carreño-Farfan, C},
title = {Harnessing PGPRs from Asparagus officinalis to Increase the Growth and Yield of Zea mays L.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {174},
pmid = {39836327},
issn = {1432-184X},
mesh = {*Asparagus Plant/microbiology/growth &amp; development ; *Zea mays/microbiology/growth &amp; development ; *Soil Microbiology ; *Rhizosphere ; *Plant Roots/microbiology/growth &amp; development ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism/growth &amp; development ; *RNA, Ribosomal, 16S/genetics ; Indoleacetic Acids/metabolism ; Peru ; Phosphates/metabolism ; Salt Tolerance ; Soil/chemistry ; },
abstract = {Microbial biotechnology employs techniques that rely on the natural interactions that occur in ecosystems. Bacteria, including rhizobacteria, play an important role in plant growth, providing crops with an alternative that can mitigate the negative effects of abiotic stress, such as those caused by saline environments, and increase the excessive use of chemical fertilizers. The present study examined the promoting potential of bacterial isolates obtained from the rhizospheric soil and roots of the Asparagus officinalis cultivar UF-157 F2 in Viru, la Libertad, Peru. This region has high soil salinity levels. Seventeen strains were isolated, four of which are major potential plant growth-promoting traits, and were characterized based on their morphological and molecular characteristics. These salt-tolerant bacteria were screened for phosphate solubilization, indole acetic acid, deaminase activity, and molecular characterization by 16S rDNA sequencing. Fifteen samples were from saline soils of A. officinalis plants in the northern coastal desert of San Jose, Lambayeque, Peru. The bacterial isolates were screened in a range of salt tolerances from 3 to 6%. Isolates 05, 08, 09, and 11 presented maximum salt tolerance, ammonium quantification, phosphate solubilization, and IAA production. The four isolates were identified by sequencing the amplified 16S rRNA gene and were found to be Enterobacter sp. 05 (OQ885483), Enterobacter sp. 08 (OQ885484), Pseudomonas sp. 09 (OR398704) and Klebsiella sp. 11 (OR398705). These microorganisms promoted the germination of Zea mays L. plants, increased the germination rates in the treatments with chemical fertilizers at 100% and 50%, and the PGPRs increased the height and length of the roots 40 days after planting. The beneficial effects of salt-tolerant PGPR isolates isolated from saline environments may lead to new species that can be used to overcome the detrimental effects of salt stress on plants. The biochemical response and inoculation of the three isolates prove the potential of these strains as sources of products to develop new compounds, confirming their potential as biofertilizers for saline environments.},
}
@article {pmid39833680,
year = {2025},
author = {Sbissi, I and Chouikhi, F and Ghodhbane-Gtari, F and Gtari, M},
title = {Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {51},
pmid = {39833680},
issn = {1471-2164},
mesh = {*Extreme Environments ; Genome, Bacterial ; Phylogeny ; Genomics/methods ; Ecosystem ; Adaptation, Physiological/genetics ; Metals, Heavy/toxicity ; Biodegradation, Environmental ; Soil Microbiology ; },
abstract = {BACKGROUND: The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.<br><br>RESULTS: Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.<br><br>CONCLUSIONS: This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.},
}
@article {pmid39830292,
year = {2024},
author = {Crous, PW and Wingfield, MJ and Jurjević, &#x17d; and Balashov, S and Osieck, ER and Marin-Felix, Y and Luangsa-Ard, JJ and Mejía, LC and Cappelli, A and Parra, LA and Lucchini, G and Chen, J and Moreno, G and Faraoni, M and Zhao, RL and Weholt, &#xd8; and Borovička, J and Jansen, GM and Shivas, RG and Tan, YP and Akulov, A and Alfenas, AC and Alfenas, RF and Altés, A and Avchar, R and Barreto, RW and Catcheside, DEA and Chi, TY and Esteve-Raventós, F and Fryar, SC and Hanh, LTM and Larsbrink, J and Oberlies, NH and Olsson, L and Pancorbo, F and Raja, HA and Thanh, VN and Thuy, NT and Ajithkumar, K and Akram, W and Alvarado, P and Angeletti, B and Arumugam, E and Khalilabad, AA and Bandini, D and Baroni, TJ and Barreto, GG and Boertmann, D and Bose, T and Castañeda Ruiz, RF and Couceiro, A and Cykowska-Marzencka, B and Dai, YC and Darmostuk, V and da Silva, SBG and Dearnaley, JDW and de Azevedo Santiago, ALCM and Declercq, B and de Freitas, LWS and De la Peña-Lastra, S and Delgado, G and de Lima, CLF and Dhotre, D and Dirks, AC and Eisvand, P and Erhard, A and Ferro, LO and García, D and García-Martín, A and Garrido-Benavent, I and Gené, J and Ghobad-Nejhad, M and Gore, G and Gunaseelan, S and Gusmão, LFP and Hammerbacher, A and Hernández-Perez, AT and Hernández-Restrepo, M and Hofmann, TA and Hubka, V and Jiya, N and Kaliyaperumal, M and Keerthana, KS and Ketabchi, M and Kezo, K and Knoppersen, R and Kolarczyková, D and Kumar, TKA and Læssøe, T and Langer, E and Larsson, E and Lodge, DJ and Lynch, MJ and Maciá-Vicente, JG and Mahadevakumar, S and Mateos, A and Mehrabi-Koushki, M and Miglio, BV and Noor, A and Oliveira, JA and Pereira, OL and Piątek, M and Pinto, A and Ramírez, GH and Raphael, B and Rawat, G and Renuka, M and Reschke, K and Mateo, AR and Saar, I and Saba, M and Safi, A and Sánchez, RM and Sandoval-Denis, M and Savitha, AS and Sharma, A and Shelke, D and Sonawane, H and Souza, MGAP and Stryjak-Bogacka, M and Thines, M and Thomas, A and Torres-Garcia, D and Traba, JM and Vauras, J and Vermaas, M and Villarreal, M and Vu, D and Whiteside, EJ and Zafari, D and Starink-Willemse, M and Groenewald, JZ},
title = {Fungal Planet description sheets: 1697-1780.},
journal = {Fungal systematics and evolution},
volume = {14},
number = {},
pages = {325-577},
doi = {10.3114/fuse.2024.14.19},
pmid = {39830292},
issn = {2589-3831},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Wingfield MJ, Jurjević Ž, et al. (2024). Fungal Planet description sheets: 1697-1780. Fungal Systematics and Evolution 14: 325-577. doi: 10.3114/fuse.2024.14.19.},
}
@article {pmid39828718,
year = {2025},
author = {Wang, Z and Fuad, MTI and Liu, J and Lin, K and Liu, L and Gao, C and Wang, W and Liu, X},
title = {Spatial Patterns of Microbial Communities in Intertidal Sediments of the Yellow River Estuary, China.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {173},
pmid = {39828718},
issn = {1432-184X},
support = {41976131//National Natural Science Foundation of China/ ; },
mesh = {*Geologic Sediments/microbiology ; *Archaea/classification/genetics/isolation &amp; purification ; China ; *Bacteria/classification/genetics/isolation &amp; purification ; *Estuaries ; *Rivers/microbiology ; *Microbiota ; Biodiversity ; Ecosystem ; Metals, Heavy/analysis ; },
abstract = {Estuarine ecosystems are among the most important natural ecosystems on Earth and contribute substantially to human survival and development. The Yellow River Estuary (YRE) is the second largest estuary in China. Microbial communities play an essential role in the material cycle and energy flow in estuarine ecosystems. To date, our knowledge of the spatial patterns of bacterial and archaeal communities is limited. In this study, we investigated the spatial profile of bacterial and archaeal communities and their co-occurrence patterns, functional roles, and environmental driving factors in the intertidal sediments of the YRE from June to July, 2019. The results showed that Proteobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were the dominant bacterial phyla, whereas Nanoarchaeaeota, Euryarchaeota and Thaumarchaeota were the dominant archaeal phyla in the intertidal sediments of the YRE. Diversity indices and differential abundance analyses revealed significant (p < 0.05) differences in the bacterial and archaeal communities in the intertidal sediments of the YRE. Bacterial communities demonstrated distinct correlations with heavy metals and pollutants. Six archaeal genera exhibited co-occurrence patterns with bacterial genera. Functions associated with sulfur cycles, disease, and pollution were specific to bacterial communities. This study presents a detailed outline of the spatial patterns of microbial communities in the YRE, enriching our understanding of microbial ecology, especially of bacteria and archaea.},
}
@article {pmid39826456,
year = {2025},
author = {Wang, Y and Zhang, F and Yang, L and Zhang, G and Wang, H and Zhu, S and Zhang, H and Guo, T},
title = {Synergy of plastics and heavy metals weakened soil bacterial diversity by regulating microbial functions in the Qinghai-Tibet Plateau.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137241},
doi = {10.1016/j.jhazmat.2025.137241},
pmid = {39826456},
issn = {1873-3336},
abstract = {How plastics coupled with metals regulate microbial functions-diversity relationships remain unknown in plateau soil environment. Three representative catchments in the Qinghai-Tibet Plateau, focusing on microplastics, their plasticisers, and metals in soils, were investigated. This research explores responses of bacterial diversity and functions to the co-existence of target pollutants, and pathways by which target pollutants regulate the diversity. Soil bacterial beta diversity and functional genes exhibited negative correlations with phthalate esters across three catchments (p < 0.05). Dibutyl phthalate emerged as a primary factor affecting beta diversity, rather than the quantity of microplastics. Additionally, the synergy of cadmium and fiber-shaped microplastics exacerbated the impact on diversity. Structural equation modeling further elucidated that plastics, copper, and iron influenced nirK/nirS genes and phoD gene, subsequently affected cbbL/cbbM genes, and ultimately the diversity. In this context, microplastics, phthalate esters and copper, iron exerted antagonistic effects on one another. Consequently, the co-existence of plastics and cadmium weakened soil bacterial diversity in the Qinghai-Tibet Plateau by disrupting microbial functions, but micronutrients alleviated these negative impacts. This research reveals that the co-existence of plastics and metals regulates soil bacterial diversity in the Qinghai-Tibet Plateau, providing a valuable reference for the protection of microbial ecology in plateau regions.},
}
@article {pmid39826104,
year = {2025},
author = {Lin, A and Jiang, A and Huang, L and Li, Y and Zhang, C and Zhu, L and Mou, W and Liu, Z and Zhang, J and Cheng, Q and Wei, T and Luo, P},
title = {From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2452277},
doi = {10.1080/19490976.2025.2452277},
pmid = {39826104},
issn = {1949-0984},
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome ; *Neoplasms/therapy/microbiology ; Animals ; Immunotherapy/methods ; Tumor Microenvironment/drug effects ; Treatment Outcome ; Combined Modality Therapy ; },
abstract = {The integration of fecal microbiota transplantation (FMT) with immune checkpoint inhibitors (ICIs) presents a promising approach for enhancing cancer treatment efficacy and overcoming therapeutic resistance. This review critically examines the controversial effects of FMT on ICIs outcomes and elucidates the underlying mechanisms. We investigate how FMT modulates gut microbiota composition, microbial metabolite profiles, and the tumor microenvironment, thereby influencing ICIs effectiveness. Key factors influencing FMT efficacy, including donor selection criteria, recipient characteristics, and administration protocols, are comprehensively discussed. The review delineates strategies for optimizing FMT formulations and systematically monitoring post-transplant microbiome dynamics. Through a comprehensive synthesis of evidence from clinical trials and preclinical studies, we elucidate the potential benefits and challenges of combining FMT with ICIs across diverse cancer types. While some studies report improved outcomes, others indicate no benefit or potential adverse effects, emphasizing the complexity of host-microbiome interactions in cancer immunotherapy. We outline critical research directions, encompassing the need for large-scale, multi-center randomized controlled trials, in-depth microbial ecology studies, and the integration of multi-omics approaches with artificial intelligence. Regulatory and ethical challenges are critically addressed, underscoring the imperative for standardized protocols and rigorous long-term safety assessments. This comprehensive review seeks to guide future research endeavors and clinical applications of FMT-ICIs combination therapy, with the potential to improve cancer patient outcomes while ensuring both safety and efficacy. As this rapidly evolving field advances, maintaining a judicious balance between openness to innovation and cautious scrutiny is crucial for realizing the full potential of microbiome modulation in cancer immunotherapy.},
}
@article {pmid39825576,
year = {2025},
author = {Fouché, J and Lebre, PH and Melville, HA and Cowan, DA},
title = {The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70022},
doi = {10.1111/1462-2920.70022},
pmid = {39825576},
issn = {1462-2920},
mesh = {*Soil Microbiology ; Animals ; *Microbiota ; *Herbivory ; *Grassland ; *Bacteria/classification/genetics/metabolism ; *RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Carbon/metabolism ; },
abstract = {Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.},
}
@article {pmid39825218,
year = {2025},
author = {de Freitas, AS and Zagatto, LFG and Rocha, GS and Muchalak, F and Martins, GL and Silva-Zagatto, SDS and Hanada, RE and Muniz, AW and Tsai, SM},
title = {Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {27},
pmid = {39825218},
issn = {1471-2180},
support = {2021/10626-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/05561-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 01.02.016301.00293/2021//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas/ ; },
mesh = {*Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Plant Roots/microbiology ; Brazil ; *Poaceae/microbiology ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Rainforest ; Biodiversity ; },
abstract = {Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil's most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.},
}
@article {pmid39821365,
year = {2025},
author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y},
title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.},
journal = {Drug development research},
volume = {86},
number = {1},
pages = {e70045},
doi = {10.1002/ddr.70045},
pmid = {39821365},
issn = {1098-2299},
support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; },
mesh = {Humans ; *Famotidine/adverse effects ; *Adverse Drug Reaction Reporting Systems/statistics &amp; numerical data ; United States/epidemiology ; *Histamine H2 Antagonists/adverse effects ; *Pharmacovigilance ; *United States Food and Drug Administration ; Female ; Male ; Adult ; Middle Aged ; Aged ; Adolescent ; Young Adult ; Child ; Child, Preschool ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Databases, Factual ; Infant ; },
abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.},
}
@article {pmid39820572,
year = {2025},
author = {Azpiazu-Muniozguren, M and García-Martínez, M and Zabaleta, A and Antiguedad, I and Garaizar, J and Laorden, L and Martinez-Malaxetxebarria, I and Martinez-Ballesteros, I},
title = {Prokaryotic Diversity and Community Distribution in the Complex Hydrogeological System of the Añana Continental Saltern.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {171},
pmid = {39820572},
issn = {1432-184X},
support = {US19/01//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; GIU21/021//Euskal Herriko Unibertsitatea/ ; US19/01//Euskal Herriko Unibertsitatea/ ; IT1678-22//Eusko Jaurlaritza/ ; IT1678-22//Eusko Jaurlaritza/ ; },
mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; *Archaea/genetics/classification/isolation &amp; purification ; Spain ; *RNA, Ribosomal, 16S/genetics ; *Salinity ; *Microbiota ; *Biodiversity ; Phylogeny ; Natural Springs/microbiology ; Water Microbiology ; },
abstract = {The Añana Salt Valley (northern Spain) is a continental saltern consisting of a series of natural springs that have been used for salt production for at least 7000 years. This habitat has been relatively understudied; therefore, prokaryotic diversity was investigated through Illumina-based 16S rRNA gene sequencing to determine if the waters within the valley exhibit distinctive microbiological characteristics. Two main types of water were found in the valley: salty (approximately 200 g/L salinity) from the diapiric structure and brackish (≤ 20 g/L salinity) from shallow streams. The beta diversity indices showed that salinity was the primary factor influencing the prokaryotic distribution. However, a niche-specific influence was observed between waters of the same origin, with significant differences in the relative abundance of the ASVs. The microbiome of the saltern revealed that the archaeal domain was mainly restricted to salty waters, while the bacterial domain was ubiquitous throughout the saltern, with a notable prevalence in brackish waters. The main bacterial and archaeal phyla identified were Pseudomonadota and Halobacterota, respectively. The genus Halorubrum was abundant and widespread in salty waters, while Pseudomonas was a significant part of the prokaryote community, mainly in brackish waters. The relative abundance of the genera Haloplanus and Salinibacter increased in the salt ponds used for salt production. The taxa involved in chemoheterotrophy and fermentation were widespread, sharing the same niche. Overall, the location of this saltern on a diapiric structure favors the occurrence of waters with different origins that affect the prokaryotic distribution beyond the niche location in the valley.},
}
@article {pmid39820498,
year = {2025},
author = {Luo, H and Xie, K and Dong, P and Zhang, Y and Ren, T and Sui, C and Ma, C and Zhao, C and Dewangan, NK and Gong, Z},
title = {Assessing the Risks of Potential Pathogens and Antibiotic Resistance Genes Among Heterogeneous Habitats in a Temperate Estuary Wetland: a Meta-analysis.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {172},
pmid = {39820498},
issn = {1432-184X},
support = {H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 32303039//National Natural Science Foundation of China/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; },
mesh = {*Wetlands ; *Estuaries ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Soil Microbiology ; Ecosystem ; Drug Resistance, Microbial/genetics ; Geologic Sediments/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Temperate estuary wetlands act as natural filters for microbiological contamination and have a profound impact on "One Health." However, knowledge of microbiological ecology security across the different habitats in temperate estuarine wetlands remains limited. This study employed meta-analysis to explore the characteristics of bacterial communities, potential pathogens, and antibiotic resistance genes (ARGs) across three heterogeneous habitats (water, soil, and sediment) within the Liaohe Estuary landscape. The diversity and composition of the three bacterial communities differed with biogeography, temperature, and pH, with the highest α-diversity showing a significantly negative correlation along latitude in soil. Furthermore, aminoglycosides were significantly enriched in water and soil, while dihydrofolate was more likely to be enriched in soil. The potential pathogens, Pseudoalteromonas and Planococcus, were dominant in water and sediment, while Stenotrophomonas was the dominant bacterium in soil. The network topology parameter revealed interspecific interactions within the community. PLS-PM highlights the main direct factors affecting the abundance of potential pathogens and the spread of ARGs, while temperature and pH indirectly influence these potential pathogens. This study advances our understanding of bacterial communities in estuarine wetlands, while highlighting the need for effective monitoring to mitigate the risks associated with potential pathogens and ARGs in these ecosystems.},
}
@article {pmid39820407,
year = {2025},
author = {Hahn, MW and Kisand, V},
title = {Editorial FEMS EC Thematic Issue Aquatic Microbial Ecology.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf005},
pmid = {39820407},
issn = {1574-6941},
}
@article {pmid39817738,
year = {2025},
author = {Wittlinger, J-P and Castejón, N and Hausmann, B and Berry, D and Schnorr, SL},
title = {Shewanella is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm Eisenia fetida.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0206924},
doi = {10.1128/aem.02069-24},
pmid = {39817738},
issn = {1098-5336},
abstract = {Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil. To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (pfa), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome of Eisenia fetida, its compost-based dietary source, and the resultant castings. This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, including Shewanellaceae, and Planctomycetota, including Gemmataceae within the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed amplicon sequence variants (ASVs) belonging primarily to Shewanella. Intriguingly, the 20C PUFAs were identified only in gut soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate that Shewanella can explain PUFA enrichment in the gut environment because of the pfa gene presence detected via PfaA-KS sequence data.IMPORTANCEPrior research has demonstrated that earthworm microbiomes can potentially harbor polyunsaturated fatty acids (PUFAs) that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analyses to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especially Shewanella, activated through the gut ecosystem.},
}
@article {pmid39813101,
year = {2025},
author = {Shan, Y and Hao, H and He, J and Hu, N and Liu, P and Zhan, M and Jiao, W and Yin, Y},
title = {Thermal Enhanced Electrokinetic Bacterial Transport in Porous Media.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c07954},
pmid = {39813101},
issn = {1520-5851},
abstract = {Soil bacterial communities are crucial to various ecosystem services, with significant implications for environmental processes and human health. Delivering functional bacterial strains to target locations enhances the preferred ecological features. However, the delivery process is often constrained by limited bacterial transport through low-permeability soil. Although electrokinetics breaks the bottleneck of bacterial transport in thin porous media, its efficiency remains limited. Here, we tested the hypothesis that thermal effects enhance electrokinetic transport by shifting the net force acting on the bacterium. We found that heating significantly increased electrokinetic transport by 2.75-fold at 1 V cm[-1] through porous media. Thermal enhancement mechanisms were interpreted by the heating shift of net force integrating matrix attractive and electrokinetic forces and verified by the Quartz Crystal Microbalance with Dissipation Monitoring (QCMD) observed adhesion rigidity shift. Thermal-dependent parameters liquid viscosity and dielectric constant were the primary contributors to the net force shift. Their variations reduce the attractive force and augment the electrokinetic forces, resulting in lower adhesion rigidity and enhanced bacterial transport. A mechanism-based approach interlinking electric field strength, thermal effect, and collision efficiency was established to facilitate the application of thermally enhanced electrokinetic bacterial transport. These findings provide new prospects for improving bacterial transport, hence optimizing soil ecosystem functions.},
}
@article {pmid39811355,
year = {2025},
author = {Paredes Contreras, BV and Vermelho, AB and Casanova, L and de Alencar Santos Lage, C and Spindola Vilela, CL and da Silva Cardoso, V and Pacheco Arge, LW and Cardoso-Rurr, JS and Correa, SS and Passos De Mansoldo, FR and Pinheiro Pereira Reis-Mansur, MC and Alves da Silva, E and Schultz, J and Rosado, AS},
title = {Enhanced UV-B photoprotection activity of carotenoids from the novel Arthrobacter sp. strain LAPM80 isolated from King George Island, Antarctica.},
journal = {Heliyon},
volume = {11},
number = {1},
pages = {e41400},
pmid = {39811355},
issn = {2405-8440},
abstract = {Antarctica's harsh environmental conditions, characterized by high levels of ultraviolet (UV) radiation, pose challenges for microorganisms. To survive in these extreme cold regions with heightened UV exposure, microorganisms employ various adaptive strategies, including photoprotective carotenoid synthesis. Carotenoids are garnering attention in the skin health industry because of their UV photoprotection potential, given the direct relationship between UV exposure and skin burns, and cancer. Also, there is a growing demand for natural and environmentally friendly photoprotectors, such as microbial-based products, in opposition to synthetic photoprotective agents with known adverse effects. In this study, we assessed the carotenoid-producing abilities of Actinomycetota strains from Antarctic Peninsula soils and the photoprotective carotenoid action on UV irradiation resistance. Among 20 evaluated strains, one exhibited significant carotenoid production and it was identified through genomic analysis as a likely novel Arthrobacter sp. strain, LAPM80. This strain's genome revealed the presence of genes coding for the biosynthesis of decaprenoxanthin C50 carotenoid. The LAPM80 strain exhibited enhanced resistance against UV-B irradiation, correlating with increased total carotenoid production in its stationary growth phase. Chemical characterization of the carotenoid extract identified major components as C50 carotenoids, probably decaprenoxanthin and/or sarcinaxanthin. Scanning electron microscopy revealed minimal surface changes in bacteria during carotenoid-rich phase after UV-B irradiation exposure. These findings highlight the likely ability of LAPM80 strain's C50 carotenoids to improve UV-B iiradiation resistance, indicating their potential for developing natural photoprotective compounds for the dermo-cosmetic industry.},
}
@article {pmid39808188,
year = {2025},
author = {Nguyen, MP and Lehosmaa, K and Martz, F and Koskimäki, JJ and Toth, K and Ahonen, SHK and Häggman, H and Pirttilä, AM},
title = {Dynamics of fungal endophytic communities in bilberry (Vaccinium myrtillus L.) fruits through development is shaped by host phenolic compounds.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {1},
pages = {},
doi = {10.1093/femsec/fiae168},
pmid = {39808188},
issn = {1574-6941},
support = {//Finnish Cultural Foundation/ ; //European Regional Development Fund/ ; 240208//Alfred Kordelin Foundation/ ; },
mesh = {*Fruit/microbiology ; *Vaccinium myrtillus/microbiology ; *Endophytes/genetics/isolation &amp; purification/classification/metabolism ; *Fungi/genetics/classification/isolation &amp; purification/growth &amp; development ; *Phenols/metabolism ; *Mycobiome ; },
abstract = {The physical and chemical properties of wild berry fruits change dramatically during development, and the ripe berries host species-specific endophytic communities. However, the development of fungal endophytic communities during berry ripening is unknown. We studied bilberries (Vaccinium myrtillus L.), valuable natural resources in northern Europe and richest sources of phenolic compounds, to characterize dynamics of the fungal communities over fruit developmental stages (raw, veraison, and ripe). Our focus was to examine the changes in the fruit phenolic compounds associated with the fungal community structure using liquid chromatography-mass spectrometry for phenolic compounds and high-throughput sequencing technology targeting the internal transcribed spacer 2 ribosomal DNA region for endophytic fungi. We found that the fungal diversity increased with the ripening stages. The fungal profile changed dramatically through fruit development, and the veraison stage was a transition stage, where the core mycobiome of fruits changed. The fungal community structure and abundance of the most dominant genera in raw and ripe stages, Monilinia and Cladosporium, respectively, were driven by the bilberry phenolic profile. We conclude that sampling time, tissue age, and phenolic compounds play important roles in the development of fruit fungal community. Moreover, phenolic compounds could be the host's strategy to recruit beneficial microbes.},
}
@article {pmid39807875,
year = {2025},
author = {Schloss, PD},
title = {phylotypr: an R package for classifying DNA sequences.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0114424},
doi = {10.1128/mra.01144-24},
pmid = {39807875},
issn = {2576-098X},
abstract = {The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.},
}
@article {pmid39806487,
year = {2025},
author = {Dieppa-Colón, E and Martin, C and Kosmopoulos, JC and Anantharaman, K},
title = {Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {5},
pmid = {39806487},
issn = {2524-6372},
support = {T32GM135066/GM/NIGMS NIH HHS/United States ; R35GM143024/GM/NIGMS NIH HHS/United States ; R35GM143024/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.<br><br>RESULTS: Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster them, taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution.<br><br>CONCLUSION: Given that prophages are particularly overlooked and merit increased attention due to their vital implications for microbiomes and their hosts, we created Prophage-DB to advance our understanding of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.},
}
@article {pmid39805038,
year = {2025},
author = {Wei, L and Van Beeck, W and Hanlon, M and DiCaprio, E and Marco, ML},
title = {Lacto-Fermented Fruits and Vegetables: Bioactive Components and Effects on Human Health.},
journal = {Annual review of food science and technology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-food-052924-070656},
pmid = {39805038},
issn = {1941-1421},
abstract = {Lacto-fermented fruits and vegetables (FVs) such as kimchi, sauerkraut, and fermented olives and nonalcoholic juices have a long history as dietary staples. Herein, the production steps and microbial ecology of lacto-fermented FVs are discussed alongside findings from human and laboratory studies investigating the health benefits of these foods. Lacto-fermented FVs are enriched in bioactive compounds, including lactic and acetic acids, phenolic compounds, amino acid derivatives such as indole-3-lactic acid, phenyl-lactic acid, γ-aminobutyric acid, and bacteriocins, and beneficial live microbes. At least 11 human studies have been performed on kimchi, whereas others have been investigated in only one or two trials. Besides exploring the health benefits, it is imperative to ensure that these foods made either commercially or at home have minimal risk for foodborne illness and exposure to undesired compounds like biogenic amines. Development of starter-culture strains and production protocols can lead to lacto-fermented FVs designed for specific health benefits.},
}
@article {pmid39804671,
year = {2025},
author = {Broderick, CM and Benucci, GMN and Bachega, LR and Miller, GD and Evans, SE and Hawkes, CV},
title = {Long-term climate establishes functional legacies by altering microbial traits.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf005},
pmid = {39804671},
issn = {1751-7370},
abstract = {Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.},
}
@article {pmid39799671,
year = {2025},
author = {Mo, Y and Abdolahpur Monikh, F and Jaffer, YD and Mugani, R and Ionescu, D and Chen, G and Yang, J and Grossart, HP},
title = {Effects of tire wear particles on freshwater bacterial-fungal community dynamics and subsequent elemental cycles using microcosms.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137062},
doi = {10.1016/j.jhazmat.2024.137062},
pmid = {39799671},
issn = {1873-3336},
abstract = {Ecological impacts of tire wear particles (TWPs) on microbial communities and biogeochemical cycles in freshwater remain largely unknown. Here, we conducted a microcosm experiment to investigate interactions between the overlying water and sediment without and with TWPs addition in a rural vs. urban lake system. Our results revealed the degree of change in microbial community diversity in water is higher than that in sediment following TWPs addition. For bacterial communities, TWPs addition changed their composition in the water, but only little in the sediment. For fungal communities, TWPs addition changed their composition both in water and sediments. Furthermore, in water, TWPs addition increased network complexity between bacteria-bacteria, fungi-fungi and bacteria-fungi in the urban system but reduced it in the rural one. In contrast, TWPs presence did not significantly change network complexity among microbial communities in the sediment of both lakes. Isotope labeling analysis uncovered that based on a short-term (6 hours) incubation experiment, TWPs addition did not significantly change carbon nor nitrogen cycling in the water. Yet, certain changes could be observed, especially in the long-term experiment (1 month), indicating that TWPs pollution has the potential to impact elemental cycling and thus ecosystem functions by altering microbial communities. Our results provide new insights into TWPs-induced ecological effects on microorganisms and potential biogeochemical consequences in a rural vs. urban lakes.},
}
@article {pmid39798462,
year = {2025},
author = {Kovarova, A and Prole, G and Farrell, ML and Maguire, M and Murphy, LC and Chueiri, A and O'Connor, L and Miliotis, G and Morris, D and Burke, LP},
title = {Antimicrobial resistant Enterobacterales of clinical importance in mute swans.},
journal = {The Science of the total environment},
volume = {961},
number = {},
pages = {178400},
doi = {10.1016/j.scitotenv.2025.178400},
pmid = {39798462},
issn = {1879-1026},
abstract = {Urban water environments, including canals, harbours and estuaries are susceptible to contamination with antimicrobials and drug-resistant bacteria through domestic and industrial wastewater discharges and storm water overflows. There is potential for wildlife using these waters to acquire and transmit drug-resistant bacteria and antimicrobial resistance genes (ARGs) of clinical importance. This study aimed to assess clinically important drug-resistant bacteria in urban waterfowl, particularly mute swans. Faecal samples were collected from 17 mute swans in the Greater Dublin Area, Ireland during July, August, October, and November of 2022. Samples were swabbed directly onto agars to select for carbapenem resistant, Extended-spectrum Beta-lactamase (ESBL)-producing, ciprofloxacin resistant and colistin resistant bacteria. Isolates identified by MALDI-TOF as Enterobacterales were tested for susceptibility to a panel of 16 antimicrobials and real-time PCR was employed to detect cefotaximase and carbapenemase genes (CRGs). Drug-resistant isolates were characterised by Whole Genome Sequencing (WGS), including long read sequencing for carbapenemase and mobile colistin resistance (mcr) gene-producing Enterobacterales isolates. Eleven of seventeen (65 %) swan samples were positive for the resistant organism(s) (n = 35), comprising Escherichia coli (n = 32; 82 %) and other Enterobacterales (n = 3). Twenty E. coli (63 %) produced ESBL, with 16/20 (80 %) identified as positive for blaCTX-M-group 1 enzymes, comprising CTX-M-15 (n = 13), CTX-M-55 (n = 2) and CTX-M-1 (n = 1) and 4/20 (20 %) positive for blaCTX-M-group 9 enzymes CTX-M-27 (n = 2) and CTX-M-9 (n = 2). Three E. coli isolates were phenotypically ertapenem resistant, one of which was an ST4450 isolate which carried plasmid encoded blaOXA-181 and blaCMY-141 with blaCTX-M-15 identified chromosomally. One colistin resistant E. coli bore the mcr-1 gene chromosomally. Bioinformatic analysis revealed high-risk pathogenic ESBL E. coli clones including ST38 (n = 3), ST69 (n = 3), and ST131 (n = 2). The study indicates mute swans are a reservoir for drug-resistant Enterobacterales and ARGs of clinical importance and may be a useful sentinel species for antimicrobial resistance (AMR) surveillance in wildlife.},
}
@article {pmid39798088,
year = {2025},
author = {Stefanic, P and Stare, E and Floccari, VA and Kovac, J and Hertel, R and Rocha, U and Kovács, &#xc1;T and Mandić-Mulec, I and Strube, ML and Dragoš, A},
title = {Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales.},
journal = {Cell reports},
volume = {44},
number = {1},
pages = {115197},
doi = {10.1016/j.celrep.2024.115197},
pmid = {39798088},
issn = {2211-1247},
abstract = {Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database and riverbank soil isolates reveal prophages primarily related to mobile genetic elements in laboratory strains. Distinct and previously unknown prophages in local isolates prompt an investigation into factors shaping prophage presence, with phylogenetic relatedness predicting the prophage repertoire slightly better than geographical origin. Data also show that prophages exhibit strong co-occurrence and exclusion patterns within genomes. Laboratory experiments indicate that most predicted prophages are cryptic, as they are not induced under DNA-damaging conditions. Importantly, stress responses increase with the number of predicted prophages, suggesting their influence on host physiology. This study highlights the diversity, integration patterns, and potential roles of prophages in B. subtilis, shedding light on bacterial genome evolution and phage-host dynamics.},
}
@article {pmid39797436,
year = {2025},
author = {Shopen Gochev, C and Demory, D and Lopes Dos Santos, A and Carlson, MCG and Gutiérrez-Rodríguez, A and Weitz, JS and Lindell, D},
title = {Cold Surface Waters of the Sub-Antarctic Pacific Ocean Support High Cyanophage Abundances and Infection Levels.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70031},
doi = {10.1111/1462-2920.70031},
pmid = {39797436},
issn = {1462-2920},
support = {2679/20//Israel Science Foundation/ ; 639682//Simons Foundation/ ; 721231//Simons Foundation/ ; 721254//Simons Foundation/ ; },
mesh = {Pacific Ocean ; *Seawater/virology/microbiology ; *Bacteriophages/isolation &amp; purification ; *Cold Temperature ; Cyanobacteria/virology ; Synechococcus/virology ; Prochlorococcus/virology ; Antarctic Regions ; },
abstract = {Cyanobacterial distributions are shaped by abiotic factors including temperature, light and nutrient availability as well as biotic factors such as grazing and viral infection. In this study, we investigated the abundances of T4-like and T7-like cyanophages and the extent of picocyanobacterial infection in the cold, high-nutrient-low-chlorophyll, sub-Antarctic waters of the southwest Pacific Ocean during austral spring. Synechococcus was the dominant picocyanobacterium, ranging from 4.7 × 10[3] to 1.2 × 10[5] cells∙mL[-1], while Prochlorococcus abundances were relatively low overall, ranging from 1.0 × 10[3] to 3.9 × 10[4] cells∙mL[-1]. Using taxon-specific, single-virus and single-cell polony methods, we found that cyanophages were on average 15-fold, and up to 50-fold, more abundant than cyanobacteria in these waters. T4-like cyanophages (ranging from 1.7 × 10[5] to 6.5 × 10[5] phage·mL[-1]) were 2.7-fold more abundant than T7-like cyanophages (ranging from 3.1 × 10[4] to 2.8 × 10[5] phage·mL[-1]). Picocyanobacteria were primarily infected by T4-like cyanophages with more Synechococcus (4.8%-12.1%) infected than Prochlorococcus (2.5%-6.2%), whereas T7-like cyanophages infected less than 1% of both genera. These infection levels translated to daily mortality in the range of 5.7%-26.2% and 2.9%-14.3% of the standing stock of Synechococcus and Prochlorococcus, respectively. Our findings suggest that T4-like cyanophages are significant agents of cyanobacterial mortality in the cold, low-iron, sub-Antarctic waters of the South Pacific Ocean.},
}
@article {pmid39794865,
year = {2025},
author = {Passarelli-Araujo, H and Venancio, TM and Hanage, WP},
title = {Relating ecological diversity to genetic discontinuity across bacterial species.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {8},
pmid = {39794865},
issn = {1474-760X},
mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; Genetic Variation ; Phylogeny ; Mycobacterium tuberculosis/genetics ; Machine Learning ; Evolution, Molecular ; Biodiversity ; },
abstract = {BACKGROUND: Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring the degree to which bacterial diversity exists as a continuum or sorted into discrete and readily defined species remains a challenge in microbial ecology. Here, we aim to quantify the genetic discontinuity (δ) and investigate how this metric is related to ecology.<br><br>RESULTS: We harness a dataset comprising 210,129 genomes to systematically explore genetic discontinuity patterns across several distantly related species, finding clear breakpoints which vary depending on the taxa in question. By delving into pangenome characteristics, we uncover a significant association between pangenome saturation and genetic discontinuity. Closed pangenomes are associated with more pronounced breaks, exemplified by Mycobacterium tuberculosis. Additionally, through a machine learning approach, we detect key features such as gene conservation patterns and functional annotations that significantly impact genetic discontinuity prediction.<br><br>CONCLUSIONS: Our study clarifies bacterial genetic patterns and their ecological impacts, enhancing the delineation of species boundaries and deepening our understanding of microbial diversity.},
}
@article {pmid39794276,
year = {2025},
author = {Tang, L and Manefield, M},
title = {Aeration promotes Proteobacteria over Firmicutes in macerated food waste resulting in superior anaerobic digestion efficiency.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf001},
pmid = {39794276},
issn = {1574-6968},
abstract = {Aeration is a common pretreatment method to enhance biogas production via anaerobic digestion of waste organic feedstocks such as unused food. While impacts on downstream anaerobic digestion have been intensively investigated, the consequence of aeration on the microbial community in food waste has not been characterised. Food waste has a low pH resulting from the dominance of lactic acid bacteria within the Firmicutes phylum. This excludes other phylotypes with a higher potential to hydrolyse complex biopolymers in food waste. In this study we reveal that aeration of macerated food waste results in a dramatic shift away from Firmicutes towards dominance of Proteobacteria that are better known for extracellular enzyme production. Given that hydrolysis is the rate limiting step in anaerobic digestion, this explains why aeration improves the efficiency of biogas production from food waste. The discovery that Proteobacteria dominate microbial communities in aerated food waste opens up opportunities to manipulate extracellular enzyme production through gene expression mechanisms common among Proteobacteria such as quorum sensing.},
}
@article {pmid39792461,
year = {2025},
author = {Tan, G and LeCates, CN and Simpson, A and Holtzen, S and Parris, DJ and Stewart, FJ and Stockton, A and , },
title = {Amplicon Sequencing Reveals Diversity in Spatially Separated Microbial Communities in the Icelandic Mars Analog Environment Mælifellssandur.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2023.0124},
pmid = {39792461},
issn = {1557-8070},
abstract = {Exploration missions to Mars rely on landers or rovers to perform multiple analyses over geographically small sampling regions, while landing site selection is done using large-scale but low-resolution remote-sensing data. Utilizing Earth analog environments to estimate small-scale spatial and temporal variation in key geochemical signatures and biosignatures will help mission designers ensure future sampling strategies meet mission science goals. Icelandic lava fields can serve as Mars analog sites due to conditions that include low nutrient availability, temperature extremes, desiccation, and isolation from anthropogenic contamination. This work reports analysis of samples collected using methods analogous to those of planetary missions to characterize microbial communities at different spatial scales in Mælifellssandur, Iceland, an environment with homogeneity at "remote imaging" resolution (overall temperature, apparent moisture content, and regolith grain size). Although microbial richness did not vary significantly among samples, the phylogenetic composition of the sediment microbiome differed significantly among sites separated by 100 m, which suggests distinct microbial signatures despite apparent homogeneity from remote observations. This work highlights the importance of considering microenvironments in future life-detection missions to extraterrestrial planetary bodies.},
}
@article {pmid39792290,
year = {2025},
author = {Foffi, R and Brumley, DR and Peaudecerf, FJ and Stocker, R and Słomka, J},
title = {Slower swimming promotes chemotactic encounters between bacteria and small phytoplankton.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {2},
pages = {e2411074122},
doi = {10.1073/pnas.2411074122},
pmid = {39792290},
issn = {1091-6490},
support = {PZ00P2_202188//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; ANR-22-CPJ2-0015-01//Agence Nationale de la Recherche (ANR)/ ; GBMF9197//Gordon and Betty Moore Foundation (GBMF)/ ; 542395FY22//Simons Foundation (SF)/ ; 205321_207488//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; CRSII5-186422//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 955910//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; },
mesh = {*Phytoplankton/physiology ; *Chemotaxis/physiology ; Bacteria/metabolism ; Bacterial Physiological Phenomena ; Models, Biological ; },
abstract = {Chemotaxis enables marine bacteria to increase encounters with phytoplankton cells by reducing their search times, provided that bacteria detect noisy chemical gradients around phytoplankton. Gradient detection depends on bacterial phenotypes and phytoplankton size: large phytoplankton produce spatially extended but shallow gradients, whereas small phytoplankton produce steeper but spatially more confined gradients. To date, it has remained unclear how phytoplankton size and bacterial swimming speed affect bacteria's gradient detection ability and search times for phytoplankton. Here, we compute an upper bound on the increase in bacterial encounter rate with phytoplankton due to chemotaxis over random motility alone. We find that chemotaxis can substantially decrease search times for small phytoplankton, but this advantage is highly sensitive to variations in bacterial phenotypes or phytoplankton leakage rates. By contrast, chemotaxis toward large phytoplankton cells reduces the search time more modestly, but this benefit is more robust to variations in search or environmental parameters. Applying our findings to marine phytoplankton communities, we find that, in productive waters, chemotaxis toward phytoplankton smaller than 2 μm provides little to no benefit, but can decrease average search times for large phytoplankton (∼20 μm) from 2 wk to 2 d, an advantage that is robust to variations and favors bacteria with higher swimming speeds. By contrast, in oligotrophic waters, chemotaxis can reduce search times for picophytoplankton (∼1 μm) up to 10-fold, from a week to half a day, but only for bacteria with low swimming speeds and long sensory timescales. This asymmetry may promote the coexistence of diverse search phenotypes in marine bacterial populations.},
}
@article {pmid39789151,
year = {2025},
author = {Frasca, S and Alabiso, A and D'Andrea, MM and Migliore, L},
title = {Uncovering the Fungal Community Composition of Alive and Dead Posidonia oceanica Matte.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {170},
pmid = {39789151},
issn = {1432-184X},
mesh = {*Alismatales/microbiology ; Ascomycota/genetics/classification/metabolism/growth &amp; development ; Mycobiome ; Fungi/genetics/classification/metabolism/isolation &amp; purification ; DNA, Fungal/genetics ; Seawater/microbiology ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; Phylogeny ; },
abstract = {Posidonia oceanica retains a large amount of carbon within its belowground recalcitrant structure, the 'matte,' which is characterized by low oxygen availability and biodegradation. Fungi may play a pivotal role in carbon sequestration within the matte, even if little/no information is available. To fill this gap, we profiled fungal communities from the upper and lower layers of alive and dead matte, by using an ITS2-5.8S rDNA metabarcoding approach. The study was conducted in a shallow coastal stretch of the Aegean Sea (Crete). Then, 184 operational taxonomic units were identified, predominantly belonging to Ascomycota, in alive and dead matte. Nevertheless, their composition significantly differed: the host-specific Posidoniomyces atricolor was dominant in alive but not in dead matte, while fast-growing saprotrophs, potentially accelerating the decomposition rate, increased in dead matte. These findings lay the groundwork for future investigations on the possible increase of biodegradation under the changing environmental conditions.},
}
@article {pmid39788196,
year = {2025},
author = {Kim, YT and Huang, YP and Ozturk, G and Hahn, J and Taha, AY and Wang, A and Barile, D and Mills, DA},
title = {Characterization of Bifidobacterium bifidum growth and metabolism on whey protein phospholipid concentrate.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25885},
pmid = {39788196},
issn = {1525-3198},
abstract = {Whey protein phospholipid concentrate (WPPC) is a co-product generated during the manufacture of whey protein isolate. WPPC is depleted of simple sugars but contains numerous glycoconjugates embedded in the milk fat globule membrane, suggesting this fraction may serve as a carbon source for growth of bifidobacteria commonly enriched in breast fed infants. In this work, we demonstrate that WPPC can serve as a sole carbon source for the growth of Bifidobacterium bifidum, a species common to the breastfed infant and routinely used as a probiotic. Growth on WPPC fractions resulted in expression of key extracellular glycosyl hydrolases in B. bifidum associated with the catabolism of glycoproteins. Interestingly, this included induction of fucosidase genes in B. bifidum linked to catabolism of fucosylated human milk oligosaccharides even though the WPPC glycan possesses little fucose. Additional growth studies revealed that WPPC-glycan components N-acetylglucosamine or N-acetylgalactosamine were required for pre-activation of B. bifidum toward rapid growth on the fucosylated human milk oligosaccharides. Growth on WPPC fractions also resulted in expression of extracellular sialidases in B. bifidum which promoted a consistent release of sialic acid, a well-known component of bovine milk oligosaccharides and glycoconjugates with potential impacts on gut microbial ecology and host cognition. These studies suggest WPPC may serve as a promising bioactive component to facilitate probiotic activity for use in infant formulas and other synbiotic applications.},
}
@article {pmid39787750,
year = {2025},
author = {Zhang, S and Wang, J and Liu, Z and Xia, X and Wu, X and Li, X and Liu, Y and Xu, Z and Marzadri, A and McDowell, WH and Cai, Y and Yang, Z},
title = {Temperature has an enhanced role in sediment N2O and N2 fluxes in wider rivers.},
journal = {Water research},
volume = {273},
number = {},
pages = {123095},
doi = {10.1016/j.watres.2025.123095},
pmid = {39787750},
issn = {1879-2448},
abstract = {Riverine N2O and N2 fluxes, key components of the global nitrogen budget, are known to be influenced by river size (often represented by average river width), yet the specific mechanisms behind these effects remain unclear. This study examined how environmental and microbial factors influenced sediment N2O and N2 fluxes across rivers with varying widths (2.8 to 2,000 m) in China. Sediment acted as sources of both N2O and N2 emissions, with both N2 (0.2 to 20.8 mmol m[-2] d[-1]) and N2O fluxes (0.7-54.2 μmol m[-2] d[-1]) decreasing significantly as river width increased. N2 fluxes were positively correlated with denitrifying bacterial abundance, whereas N2O fluxes, when normalized by the abundance of denitrifying bacteria, were negatively correlated with the abundance of N2O-reducing microbes. Water physicochemical factors, particularly temperature and nitrate, were more important drivers of these fluxes than sediment factors. Nitrate significantly increased denitrifying bacterial abundance, whereas higher temperatures enhanced cell-specific activity. Lower N2O and N2 emissions in wider rivers were attributed to decreased denitrifying microbial abundance and lower denitrification rates, in addition to the commonly assumed reduction in exogenous N2O and N2 inputs. Rolling regression analysis showed that nitrate concentration had a stronger effect on sediment N2O and N2 fluxes in narrower rivers, whereas temperature was more influential in wider rivers. This difference is attributed to more stable nitrate concentrations and decreased nitrogen removal efficiency in wider rivers, while temperature variation remained consistent across all river widths. Beyond sediments, temperature had a greater effect on excess N2O concentrations than nitrate in the overlying water of wider rivers (>165 m), highlighting its broader impact. This study provides new biogeochemical insights into how river width influences sediment N2O and N2 fluxes and highlights the importance of incorporating temperature into flux predictions, particularly for wider rivers.},
}
@article {pmid39786593,
year = {2025},
author = {Xu, Y and Liang, J and Qin, L and Niu, T and Liang, Z and Li, Z and Chen, B and Zhou, J and Yu, K},
title = {The Dynamics of Symbiodiniaceae and Photosynthetic Bacteria Under High-Temperature Conditions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {169},
pmid = {39786593},
issn = {1432-184X},
support = {42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; },
mesh = {*Photosynthesis ; *Symbiosis ; *Anthozoa/microbiology/physiology ; China ; *Hot Temperature ; *Dinoflagellida/physiology ; Animals ; *Seasons ; Bacteria/classification/metabolism/genetics ; Cyanobacteria/physiology ; Chlorophyll A/metabolism ; },
abstract = {Coral thermal tolerance is intimately linked to their symbiotic relationships with photosynthetic microorganisms. However, the potential compensatory role of symbiotic photosynthetic bacteria in supporting Symbiodiniaceae photosynthesis under extreme summer temperatures remains largely unexplored. Here, we examined the seasonal variations in Symbiodiniaceae and photosynthetic bacterial community structures in Pavona decussata corals from Weizhou Island, Beibu Gulf, China, with particular emphasis on the role of photosynthetic bacteria under elevated temperature conditions. Our results revealed that Symbiodiniaceae density and Chlorophyll a concentration were lowest during the summer and highest in the winter. Notably, the summer bacterial community was predominately composed of the proteorhodopsin bacterium BD 1-7 _clade, alongside a significant increase in Cyanobacteria, particularly Synechococcus_CC9902 and Cyanobium_PCC-6307, which represented 61.85% and 31.48% of the total Cyanobacterial community, respectively. In vitro experiments demonstrated that Cyanobacteria significantly enhanced Symbiodiniaceae photosynthetic efficiency under high-temperature conditions. These findings suggest that the increased abundance of photosynthetic bacteria during summer may mitigate the adverse physiological effects of reduced Symbiodiniaceae density, thereby contributing to coral stability. Our study highlights a potential synergistic interaction between Symbiodiniaceae and photosynthetic bacteria, emphasizing the importance of understanding these dynamic interactions in sustaining coral resilience against environmental stress, although further research is necessary to establish their role in preventing coral bleaching.},
}
@article {pmid39786575,
year = {2024},
author = {McNeal, R and Wells, JD and Tomberlin, JK},
title = {Bernard Greenberg: a legacy in medical, veterinary, and forensic entomology.},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjae158},
pmid = {39786575},
issn = {1938-2928},
abstract = {Bernard Greenberg was a ground-breaking scientist in the worlds of medical-veterinary and forensic entomology, studying the ability of flies to serve as a vector of human and other vertebrate pathogens. His work also extended beyond these topics, creating key studies on flies and their associated microbial ecology. These efforts led to numerous research publications and two books on flies and their associated microorganisms. Greenberg served a pioneering role in establishing the field of forensic entomology in the USA later in his career, publishing key papers and a book that are highly cited to this day. We present a review of Dr Greenberg's scientific contributions concerning flies and disease, insect/microbe interactions, and insects as forensic indicators.},
}
@article {pmid39779689,
year = {2025},
author = {Cottin, A and Dequiedt, S and Djemiel, C and Prévost-Bouré, NC and Tripied, J and Lelièvre, M and Terreau, L and Régnier, T and Karimi, B and Jolivet, C and Bispo, A and Saby, N and Maron, PA and Ranjard, L and Terrat, S},
title = {Harmonized Datasets of microbiological parameters from a French national-scale soil monitoring survey.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {34},
pmid = {39779689},
issn = {2052-4463},
support = {2021PRE00370//Conseil r&#xe9;gional de Bourgogne-Franche-Comt&#xe9; (Regional Council of Burgundy)/ ; },
abstract = {Microbiological datasets and associated environmental parameters from the French soil quality monitoring network (RMQS) offer an opportunity for long-term and large-scale soil quality monitoring. Soils supply important ecosystem services e.g. carbon dynamics/storage or mineral element recycling, supported by the soil microbial diversity (bacteria, archaea and fungi). Based on the 2,240 sites of the 2000-2015 RMQS, molecular tools were applied to characterize soil microbiota. Soil DNA analysis yielded molecular microbial biomass for 2,168 sites, bacterial and fungal qPCR for 2,073 sites, and high-throughput amplicon sequencing of targeted 16S rDNA bacterial and archaeal genes for 1,842 sites. All these datasets were partially or completely unavailable, so raw results files from RMQS microbiological studies were harmonized and published in a Dataverse repository to facilitate their reusability. Altogether, these datasets allow for in-depth studies of soil microbial ecology and biogeography, and will be updated with fungal datasets and the second currently ongoing monitoring campaign (2016-2027).},
}
@article {pmid39779584,
year = {2025},
author = {Roy, A and Ray, S},
title = {Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39779584},
issn = {1559-0305},
abstract = {Nine homologous Cold Shock Proteins (Csps) have been recognized in the E.coli Cold Shock Domain gene family. These Csps function as RNA chaperones. This study aims to establish the evolutionary relationships among these genes by identifying and classifying their paralogous counterparts. It focuses on the physicochemical, structural, and functional analysis of the genes to explore the phylogeny of the Csp gene family. Computational tools were employed for protein molecular modeling, conformational analysis, functional studies, and duplication-divergence assessments. The research also examined amino acid conservation, protein mutations, domain-motif patterns, and evolutionary residue communities to better understand residual interactions, evolutionary coupling, and co-evolution. H33, M5, W11 and F53 residues were highly conserved within the protein family. It was further seen that residues M5, G17, G58, G61, P62, A64, V67 were intolerant to any kind of mutation whereas G3, D40, G41, Y42, S44, T54, T68, S69 were most tolerable towards substitutions. The study of residue communities displayed that the strongest residue coupling was observed in N13, F18, S27, F31, and W11. It was observed that all the gene pairs except CspF/CspH had new motifs generated over time. It was ascertained that all the gene pairs underwent asymmetric expression divergence after duplication. The Ka/ Ks ratio also revealed that all residues undertook neutral and purifying selection pressure. New functions were seen to develop in gene pairs evident from generation of new motifs. The discovery of new motifs and functions in Csps highlights their adaptive versatility, crucial for E. coli's resilience to environmental stressors and valuable for understanding bacterial stress response mechanisms. These findings will pave the way for future investigations into Csp evolution, with potential applications in microbial ecology and antimicrobial strategy development.},
}
@article {pmid39779304,
year = {2025},
author = {Diakaki, M and Jimenez, BA and de Lange, E and Butterbach, P and van der Heijden, L and Köhl, J and de Boer, W and Postma, J},
title = {Spinach Seed Microbiome Characteristics Linked to Suppressiveness Against Globisporangium ultimum Damping-Off.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf004},
pmid = {39779304},
issn = {1574-6941},
abstract = {Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesised that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (ITS1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process in turn could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.},
}
@article {pmid39777550,
year = {2025},
author = {Byers, AK and Wakelin, SA and Condron, L and Black, A},
title = {Land Use Change Disrupts the Network Complexity and Stability of Soil Microbial Carbon Cycling Genes Across an Agricultural Mosaic Landscape.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {167},
pmid = {39777550},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Carbon Cycle ; New Zealand ; *Agriculture ; *Soil/chemistry ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; Carbon/metabolism ; Gene Regulatory Networks ; Forests ; Ecosystem ; },
abstract = {To understand the effects of agricultural land use change and management on soil carbon (C) cycling, it is crucial to examine how these changes can influence microbial soil C cycling. Network analysis can offer insights into the structure, complexity, and stability of the soil microbiome in response to environmental disturbances, including land use change. Using SparCC-based co-occurrence networks, we studied how land use change impacts the connectivity, complexity, and stability of microbial C-cycling gene networks across an agricultural mosaic landscape in Canterbury, New Zealand. The most densely connected networks were found in land uses that were under the most intensive agricultural management, or under naturally regenerating vegetation. The microbial C-cycling gene networks from both land uses presented high network connectivity, low modularity, and a low proportion of negative gene interactions. In contrast, microbial C-cycling genes from native forests, which had the most stable and undisturbed plant cover, had the lowest network connectivity, highest modularity, and a greater proportion of negative gene interactions. Although the differences in total soil C content between land uses were small, the large effects of land use on the network structure of microbial C-cycling genes may have important implications for long-term microbial soil C cycling. Furthermore, this research highlights the value of using microbial network analysis to study the metabolic gene interactions shaping the functional structure of soil microbial communities in a manner not typically captured by more traditional forms of microbial diversity analysis.},
}
@article {pmid39777152,
year = {2024},
author = {Liao, H and Wang, X and Wang, X and Zhang, M and Zhang, Y and Huang, S and Wang, H and Jin, H and Wang, J and Li, X and Yan, J and Schubert, T and Löffler, FE and Yang, Y},
title = {Organohalide respiration: retrospective and perspective through bibliometrics.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1490849},
doi = {10.3389/fmicb.2024.1490849},
pmid = {39777152},
issn = {1664-302X},
abstract = {Organohalide-respiring bacteria (OHRB) play a pivotal role in the transformation of organohalogens in diverse environments. This bibliometric analysis provides a timely overview of OHRB research trends and identifies knowledge gaps. Publication numbers have steadily increased since the process was discovered in 1982, with fluctuations in total citations and average citations per publication. The past decade witnessed a peak in publications, underscoring heightened research activity and extensive collaboration. Thematic analysis identified two primary research foci: mechanistic exploration of OHRB and their interplay with environmental factors. Future research should prioritize elucidating the roles OHRB's play in biogeochemical cycling, utilizing synthetic biology tools for enhanced biotransformation, deciphering OHRB's ecological interactions, unraveling their evolutionary pathways, and investigating dehalogenation capabilities in other microorganisms, including archaea. These research directions promise to advance our understanding of microbially-driven organohalide transformations, microbial ecology, and genetic engineering potential, ultimately informing natural organohalide cycling and environmental management strategies.},
}
@article {pmid39775407,
year = {2025},
author = {Sun, X and Armstrong, M and Moradi, A and Bhattacharya, R and Antão-Geraldes, AM and Munthali, E and Grossart, HP and Matsuzaki, SS and Kangur, K and Dunalska, JA and Stockwell, JD and Borre, L},
title = {Impacts of climate-induced drought on lake and reservoir biodiversity and ecosystem services: A review.},
journal = {Ambio},
volume = {},
number = {},
pages = {},
pmid = {39775407},
issn = {1654-7209},
support = {RGPIN-2019-04315//Natural Sciences and Engineering Research Council of Canada/ ; 1638679//U.S. National Science Foundation (NSF) Macrosystems Biology Program/ ; 722518//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 722518//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 722518//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; LA/P/0007/2020//SusTEC/ ; PRG 1266//Estonian Research Council/ ; JPMEERF20232002//Environmental Restoration and Conservation Agency/ ; 1702991//National Science Foundation/ ; UIDB/00690/2020//CIMO/ ; UIDP/00690/2020//CIMO/ ; PIDDAC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
abstract = {Intensifying extreme droughts are altering lentic ecosystems and disrupting services provisioning. Unfortunately, drought research often lacks a holistic and intersectoral consideration of drought impacts, which can limit relevance of the insights for adaptive management. This literature review evaluated the current state of lake and reservoir extreme drought research in relation to biodiversity and three ecosystem services. The study findings demonstrated that few articles linked or discussed drought implications with one or more ecosystem services, instead focusing primarily on biodiversity. Drought effects on biodiversity varied among species and taxonomic groups. In the limited literature that included ecosystem service provisioning, droughts had a general negative effect. Drinking water supply can decrease and become more costly. Decreasing water flow and volume can reduce hydropower generation. Degraded water quality can also impact recreation. Future intersectoral collaborations and research on intensifying droughts should support adaptive management efforts in mitigating drought impacts.},
}
@article {pmid39774713,
year = {2025},
author = {Dobrzyński, J and Kulkova, I and Jakubowska, Z and Wróbel, B},
title = {Non-native PGPB Consortium Altered the Rhizobacterial Community and Slightly Stimulated the Growth of Winter Oilseed Rape (Brassica napus L.) Under Field Conditions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {168},
pmid = {39774713},
issn = {1432-184X},
support = {DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; },
mesh = {*Brassica napus/microbiology/growth &amp; development ; *Soil Microbiology ; Pseudomonas/growth &amp; development/metabolism ; Plant Roots/microbiology/growth &amp; development ; Phosphorus/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; Nitrogen/metabolism ; Rhizosphere ; Microbial Consortia ; Indoleacetic Acids/metabolism ; Microbiota ; Azotobacter/growth &amp; development/metabolism ; },
abstract = {Plant growth-promoting bacteria (PGPB) are among the most promising alternatives to mineral fertilizers. However, little is known about the effects of applied bacteria on the native microbiota, including the rhizobacterial community, which plays a crucial role in bacteria-plant interactions. Therefore, this study is aimed at assessing the effects of PGPB not only on plants but also, importantly, on the native rhizobacterial community of winter oilseed rape. The bacterial consortium, consisting of Pseudomonas sp. KR227 and Azotobacter PBC1 (P2A), slightly promoted plant growth, increasing the root weight by 21.95% and seed yield by 18.94%. This likely results from its ability to produce indole-3-acetic acid (IAA), solubilize phosphorus, and fix nitrogen, as indicated by a 35.76% increase in N-NH4 and a 35.05% increase in available phosphorus (AP). The introduced PGPB altered the rhizobacterial community of rapeseed, increasing the relative abundance of the phylum Proteobacteria and the genus Pseudomonas while decreasing the relative abundance of phylum Verrucomicrobiota (3 weeks after inoculation). Moreover, Proteobacteria were positively correlated with AP, while Verrucomicrobiota were correlated with N-NH4. At the genus level, Flavobacterium and Pseudomonas were positively correlated with AP, whereas Candidatus Udaeobacter showed a positive correlation with N-NH4 and a negative correlation with pH. Importantly, the P2A consortium did not significantly affect the diversity of native rapeseed rhizobacteria. These findings suggest that the tested P2A consortium has potential as a biostimulant in rapeseed cultivation.},
}
@article {pmid39774673,
year = {2025},
author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F},
title = {Author Correction: Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {453},
doi = {10.1038/s41467-024-55458-6},
pmid = {39774673},
issn = {2041-1723},
}
@article {pmid39772705,
year = {2025},
author = {Zhou, J and Liu, Z and Wang, S and Li, J and Zhang, L and Liao, Z},
title = {A novel framework unveiling the importance of heterogeneous selection and drift on the community structure of symbiotic microbial indicator taxa across altitudinal gradients in amphibians.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0419223},
doi = {10.1128/spectrum.04192-23},
pmid = {39772705},
issn = {2165-0497},
abstract = {UNLABELLED: Existing analytical frameworks for community assembly have a noticeable knowledge gap, lacking a comprehensive assessment of the relative contributions of individual or grouped microbial distinct sampling units (DSUs) and distinct taxonomic units (DTUs) to each mechanism. Here, we propose a comprehensive framework for identifying DTUs/DSUs that remarkably contribute to the various mechanisms sustaining microbial community structure. Amphibian symbiotic microbes along an altitudinal gradient from Sichuan Province, China, were employed to examine the proposed statistical framework. In different altitude groups, we found that heterogeneous selection governed the community structure of symbiotic microbes across DSUs, while stochastic processes tended to increase with altitude. For DTUs at phylum and family levels, drift emerged as the dominant mechanism driving the community structure in the most symbiotic microbial taxa, while heterogeneous selection governs the most dominant or indicator taxa. Notably, the relative contribution of heterogeneous selection was significantly positively correlated with the relative abundance and niche breadth of taxa, and negatively correlated with drift. We also detected that community assembly processes remarkably regulate the structure of symbiotic microbial communities and their correlation with environmental variables. Altogether, our modeling framework is a robust and valuable tool that further enlarges our insight into microbiota community assembly.<br><br>IMPORTANCE: Distinguishing the drivers regulating microbial community assembly is essential in microbial ecology. We propose a novel modeling framework to partition the relative contributions of each individual or group of microbial DSUs and DTUs into different underpinning mechanisms. An empirical study on amphibian symbiotic microbes notably enlarges insight into community assembly patterns in the herpetological symbiotic ecosystem and demonstrates that the proposed statistical framework is an informative and sturdy tool to quantify microbial assembly processes at both levels of DSUs and DTUs. More importantly, our proposed modeling framework can provide in-depth insights into microbiota community assembly within the intricate tripartite host-environment-microbe relationship.},
}
@article {pmid39772204,
year = {2024},
author = {Obong'o, BO and Ogutu, FO and Hurley, SK and Okiko, GM and Mahony, J},
title = {Exploring the Microbial Ecology of Water in Sub-Saharan Africa and the Potential of Bacteriophages in Water Quality Monitoring and Treatment to Improve Its Safety.},
journal = {Viruses},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/v16121897},
pmid = {39772204},
issn = {1999-4915},
mesh = {Africa South of the Sahara ; *Bacteriophages/physiology ; *Water Quality ; *Water Microbiology ; *Water Purification/methods ; Bacteria/virology ; Humans ; Food Safety/methods ; Biodegradation, Environmental ; },
abstract = {Access to safe water and food is a critical issue in sub-Saharan Africa, where microbial contamination poses significant health risks. Conventional water treatment and food preservation methods have limitations in addressing water safety, particularly for antibiotic-resistant bacteria and other pathogenic microorganisms. This review explores the potential application of bacteriophages as an innovative solution for water treatment and food safety in the region. Bacteriophages specifically infect bacteria and offer a targeted approach to reducing bacterial load, including multidrug-resistant strains, without the drawbacks of chemical disinfectants. This review also highlights the advantages of phage bioremediation, including its specificity, adaptability, and minimal environmental impact. It also discusses various case studies demonstrating its efficacy in different water systems. Additionally, we underscore the need for further research and the development of region-specific phage applications to improve water quality and public health outcomes in sub-Saharan Africa. By integrating bacteriophage strategies into water treatment and food production, the region can address critical microbial threats, mitigate the spread of antimicrobial resistance, and advance global efforts toward ensuring safe water for all.},
}
@article {pmid39771075,
year = {2024},
author = {Tapia, Y and Salazar, O and Seguel, O and Suazo-Hernández, J and Urdiales-Flores, D and Aponte, H and Urdiales, C},
title = {Optimizing Heavy Metal Uptake in Carpobrotus aequilaterus Through Electrokinetic Treatment: A Comprehensive Study on Phytoremediation from Mine Tailings.},
journal = {Toxics},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/toxics12120860},
pmid = {39771075},
issn = {2305-6304},
support = {3220201//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; },
abstract = {Copper mining drives economic growth, with the global demand expected to reach 120 million metric tons annually by 2050. However, mining produces tailings containing heavy metals (HMs), which poses environmental risks. This study investigated the efficacy of phytoremediation (Phy) combined with electrokinetic treatment (EKT) to increase metal uptake in Carpobrotus aequilaterus grown in tailings from the Metropolitan Region of Chile. The plants were exposed to varying voltages and treatment durations. In the control (no EKT), the root metal contents were Fe (1008.41 mg/kg) > Cu (176.38 mg/kg) > Mn (103.73 mg/kg) > Zn (30.26 mg/kg), whereas in the shoots, the order was Mn (48.69 mg/kg) > Cu (21.14 mg/kg) > Zn (17.67 mg/kg) > Fe (27.32 mg/kg). The optimal EKT (15 V for 8 h) significantly increased metal uptake, with roots accumulating Fe (5997.24 mg kg[-1]) > Mn (672 mg kg[-1]) > Cu (547.68 mg kg[-1]) > Zn (90.99 mg kg[-1]), whereas shoots contained Fe (1717.95 mg kg[-1]) > Mn (930 mg kg[-1]) > Cu (219.47 mg kg[-1]) > Zn (58.48 mg kg[-1]). Although EKT enhanced plant growth and biomass, higher voltages stressed the plants. Longer treatments were more effective, suggesting that EK-Phy is a promising method for remediating metal-contaminated tailings.},
}
@article {pmid39770685,
year = {2024},
author = {Han, Y and He, J and Li, M and Peng, Y and Jiang, H and Zhao, J and Li, Y and Deng, F},
title = {Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122482},
pmid = {39770685},
issn = {2076-2607},
support = {SQ2023YFE0102739//National Key Research and Development Program of China/ ; 2022A1515110819//Youth project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; 32170430//National Natural Science Foundation of China/ ; },
abstract = {Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio's high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing's ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications.},
}
@article {pmid39770645,
year = {2024},
author = {Neviani, E},
title = {The Natural Whey Starter Used in the Production of Grana Padano and Parmigiano Reggiano PDO Cheeses: A Complex Microbial Community.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122443},
pmid = {39770645},
issn = {2076-2607},
abstract = {Natural whey starter (NWS) is an undefined complex culture used in the production of Grana Padano and Parmigiano Reggiano PDO cheeses. The aim of this review is to discuss, in light of the latest research results, the role of NWS as a primary player in the cheese-making process, considering the microbial community scenario. NWS is traditionally produced by fermenting part of the whey collected at the end of a previous cheese-making process. The method used to produce NWS, based on the back-slopping principle, favors the selection of a microbiota composed mainly of thermophilic lactic acid bacteria. This method of preparation induces the survival of several different species and biotypes. The presence of such a mixture of strains facilitates the development of a natural starter characterized by a remarkable ability to adapt to non-standardized cheese-making parameters. NWS is a microbial community whose activity is not simply the result of the sum of the activities of individual microorganisms, but rather the activity of the community as a whole, in which each individual bacterial cell responds to the presence of the others. According to this traditional protocol, the NWS becomes the 'microbiological bond' between cheeses over time.},
}
@article {pmid39770585,
year = {2024},
author = {Heczko, PB and Giemza, M and Ponikiewska, W and Strus, M},
title = {Importance of Lactobacilli for Human Health.},
journal = {Microorganisms},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/microorganisms12122382},
pmid = {39770585},
issn = {2076-2607},
support = {RPMP.01.02.01-12-0413/17.//The National Centre for Research and Development/ ; },
abstract = {As an extraordinarily diverse group of bacteria, lactobacilli are now classified into several genera, many of which still include "Lactobacillus" in their names. Despite their names, this group of lactic acid bacteria comprises microorganisms that are crucial for human health, especially during the early development of the human microbiota and immune system. The interactions between lactobacilli and components of the mucosal immunity lead to its shaping and development, which is possibly considered a prime mover in the advancement of the human immune system. Although much of the evidence backing the pivotal role of lactobacilli in maintaining human health comes from studies on probiotics aiming to elucidate the mechanisms of their functional activities and studies on mucosal immunity in germ-free mice, it is justifiable to extend observations on the properties of the individual probiotic Lactobacillus that are related to health benefits onto other strains sharing common characteristics of the species. In this review, we will discuss the acquisition, presence, and functions of lactobacilli in different human microbiota throughout their whole life, including those arising in the amnion and their interactions with mucosal and immune cells. Examples of immune system modulation by probiotic lactobacilli include their colonic competition for available nutrients, interference with colonization sites, competition for binding sites on gut epithelial cells, bacteriocin production, reduction of colonic pH, and nonspecific stimulation of the immune system.},
}
@article {pmid39770454,
year = {2024},
author = {Atazhanova, GA and Levaya, YK and Badekova, KZ and Ishmuratova, MY and Smagulov, MK and Ospanova, ZO and Smagulova, EM},
title = {Inhibition of the Biofilm Formation of Plant Streptococcus mutans.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/ph17121613},
pmid = {39770454},
issn = {1424-8247},
support = {&#x410;&#x420;23488250//MINISTRY OF SCIENCE AND HIGHER EDUCATION OF REPUBLIC OF KAZAKHSTAN/ ; },
abstract = {This review is devoted to a systematic analysis of studies aimed at investigating plant extracts, essential oils and phytochemical compounds capable of inhibiting Streptococcus mutans biofilm formation. This paper investigates the effect of extracts, essential oils and individual plant compounds on inhibiting the biofilm formation of Streptococcus mutans, one of the major pathogens responsible for the development of dental caries. Using cultural microbiology and molecular biology techniques, the authors describe the mechanisms by which plant samples reduce Streptococcus mutans adhesion and growth. The results show that several plant components have antibacterial properties, contributing to the reduction of Streptococcus mutans colony numbers and inhibiting the synthesis of extract-exopolysaccharide matrices required for biofilm formation. This work highlights the potential of botanicals in inhibiting Streptococcus mutans biofilm formation, which can be applied as natural antimicrobial agents in the prevention and treatment of dental diseases. Views on the use of these plant extracts and their components in dental preparations such as toothpastes, rinses and gels aimed at preventing dental caries are evaluated. The review shows the relevance of the research to optimizing the use of plant extracts, essential oils, individual compounds and their active actions in the control of Streptococcus mutans biofilms.},
}
@article {pmid39769364,
year = {2024},
author = {Grzyb, T and Szulc, J},
title = {Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
doi = {10.3390/ijms252413601},
pmid = {39769364},
issn = {1422-0067},
mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Phosphorus/metabolism ; Nitrogen/metabolism ; Symbiosis ; Nutrients/metabolism ; },
abstract = {While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.},
}
@article {pmid39768235,
year = {2024},
author = {Riekeles, M and Santos, B and Youssef, SA and Schulze-Makuch, D},
title = {Viability and Motility of Escherichia coli Under Elevated Martian Salt Stresses.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/life14121526},
pmid = {39768235},
issn = {2075-1729},
support = {Scholarship for Max Riekeles//Friedrich-Ebert-Stiftung e.V./ ; },
abstract = {This study investigates the effects of three Martian-relevant salts-sodium chlorate, sodium perchlorate, and sodium chloride-on the viability and motility of Escherichia coli, a model organism for understanding microbial responses to environmental stress. These salts are abundant on Mars and play a crucial role in forming brines, one of the few sources of stable liquid water on the planet. We analyze the survivability under different salt concentrations using colony plating. Additionally, we perform a semi-automated motility analysis, analyzing microbial speeds and motility patterns. Our results show that sodium perchlorate is the most toxic, followed by sodium chlorate, with sodium chloride being the least harmful. Both survivability and motility are affected by salt concentration and exposure time. Notably, we observe a short-lived increase in motility at certain concentrations, particularly under sodium chlorate and sodium perchlorate stress, despite rapid declines in cell viability, suggesting a stress response mechanism. Given that motility might enhance an organism's ability to navigate harsh and variable environments, it holds promise as a key biosignature in the search for life on Mars.},
}
@article {pmid39764393,
year = {2024},
author = {Russo, CJ and Husain, K and Murugan, A},
title = {Soft Modes as a Predictive Framework for Low Dimensional Biological Systems across Scales.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {39764393},
issn = {2331-8422},
abstract = {All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments show that their response to perturbations is surprisingly low-dimensional: confined to only a few stereotyped changes out of the many possible. Here, we explore a unifying dynamical systems framework - soft modes - to explain and analyze low-dimensionality in biology, from molecules to eco-systems. We argue that this one framework of soft modes makes non-trivial predictions that generalize classic ideas from developmental biology to disparate systems, namely: phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.},
}
@article {pmid39762141,
year = {2025},
author = {Nguyen, PN and Rehan, SM},
title = {Supporting wild bee development with a bacterial symbiont.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae317},
pmid = {39762141},
issn = {1365-2672},
abstract = {AIMS: Wild bees foster diverse microbiota that may determine survival success of developing larvae. Here, we compare survivorship and microbial communities of Ceratina calcarata small carpenter bees reared from eggs across three treatments: maternally collected control provisions with diverse microbiota, sterile provisions, and probiotic provisions supplemented with a beneficial symbiont, Apilactobacillus kunkeei.<br><br>METHODS AND RESULTS: Survival probability and adult masses differed across treatments, with the probiotic treatment resulting in highest survivorship and masses. By comparing the bacterial (16S rRNA), fungal (ITS), and plant (rbcL) communities of adults reared across treatments, we characterized distinct microbial communities across each that suggest the microbiome may be sensitive to microbial succession and competition.<br><br>CONCLUSIONS: We describe positive implications for the usage of probiotics on wild bees. Furthermore, the sensitivity of bee microbiota's relationships to their host, floral resources, and the environment suggests that holistic approaches best encapsulate the complex network of interactions between bees and their microbes.},
}
@article {pmid39760916,
year = {2025},
author = {García-Bodelón, &#xc1; and Baković, N and Cano, E and Useros, F and Lara, E and González-Miguéns, R},
title = {Predators in the Dark: Metabarcoding Reveals Arcellinida Communities Associated with Bat Guano, Endemic to Dinaric Karst in Croatia.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {166},
pmid = {39760916},
issn = {1432-184X},
support = {PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; Garant&#xed;a Juvenil CM 2021//Comunidad de Madrid (Spain)/ ; Garant&#xed;a Juvenil CM 2021//Comunidad de Madrid (Spain)/ ; Class: UP/I-612-07/21-48/170, Ref. No.: 517-10-1-1-21-3, 16.07.2021//Croatian Ministry of Economy and Sustainable Development/ ; },
mesh = {Croatia ; Animals ; *Chiroptera/microbiology ; *Caves/microbiology ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; Chironomidae/genetics ; Feces/microbiology ; Electron Transport Complex IV/genetics/analysis ; Geologic Sediments/microbiology ; Phylogeny ; },
abstract = {Karst caves, formed from the dissolution of soluble rocks, are characterized by the absence of photosynthetic activity and low levels of organic matter. Organisms evolve under these particular conditions, which causes high levels of endemic biodiversity in both macroorganism and microbes. Recent research has highlighted the presence of testate amoebae (Arcellinida) group in cave environments. This study investigates the diversity of Arcellinida in Dinaric karstic caves in Croatia, a global diversity hotspot, focusing on the influence of bat guano on community structure. Sediment samples were collected from two independent hydrosystems, and a metabarcoding approach was used to assess Arcellinida diversity at specific and intraspecific levels, using Arcellinid-specific primers to amplify the mitochondrial cytochrome oxidase subunit I (COI) region. Results reveal a significant impact of guano on both specific and intraspecific diversity of Arcellinida. Communities in guano-rich sites displayed higher diversity, abundance, and the presence of unique OTUs and genetic variants not observed in other habitats, highlighting the crucial role of bats as ecosystem engineers. In contrast, sites without guano hosted communities with low abundance and reduced biodiversity. These differences suggest the existence of guano-associated Arcellinida communities. This study provides new insights into the biodiversity of subterranean ecosystems and the ecological roles of Arcellinida in karstic environments.},
}
@article {pmid39760871,
year = {2025},
author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE},
title = {Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {165},
pmid = {39760871},
issn = {1432-184X},
mesh = {*Polygalacturonase/metabolism ; *Soil Microbiology ; *Rhizosphere ; Fungi/enzymology/metabolism/isolation &amp; purification/classification/genetics ; Aspergillus/metabolism/enzymology/isolation &amp; purification ; Egypt ; Fungal Proteins/metabolism ; },
abstract = {Microorganisms are preferred as an enzyme source due to their short lifespan, high production rate, affordability, and absence of harmful chemicals in enzymes generated from plant and animal sources. Fungi communities are biological factories for many bioactive compounds such as the important industrial enzyme pectinase. The current study dealt with production, optimization, purification, biocompatibility, and application of fungal pectinase obtained from five plant rhizospheres (banana, jarawa, lemon, tomato, and wheat) at Fayoum Governorate, Egypt. The highest pectinase degrading index (PDI) was scored for FB5, FJ2, and FW1 isolates. Pectinase production was also examined quantitively and the highest output of 1603.67, 1311.22, and 1264.83 U/ml was gained by FB5, FJ1, and FW1 fungal isolates, respectively. The most active pectinase-producing fungi were identified as Aspergillus niveus strain AUMC1624, A. niger strain AUMC16245, and A. brasiliensis strain AUMC16244, respectively. For pectinase production optimization, one factor at a time (OFAT) protocol was applied and revealed that A. niger, A. niveus, and A. brasiliensis reached maximum pectinase levels at 1% pectin after 5, 7, and 7 days, at 40, 45, and 45 °C, respectively. Obtained pectinases were partially purified using ammonium sulfate precipitation (ASP) and organic solvent precipitation (OSP) methods. The highest activity using the ASP method scored at 40-60% saturation with A. niger. The thermostability characterization of A. niger pectinase was reached with relative activities of 61.7, 69.0, 99.9, 91.3, and 90.6% at temperatures ranging between 30 and 70 °C. pH optimized at pH 5-7. The enzyme's molecular weight was approximately 30 kDa. The GC-mass analysis of pectinase end products included acetic acid ethyl ester, hexadecane carbonsaure methylase, and hexadecenoic acid. The biocompatibility was examined using a human skin cell line (HFb-4) for the first time, with a minimal half concentration (IC50) of 151.86 ± 0.76 U/ml. The biocompatible pectinase was applied as a clothes bioscouring agent with different concentrations of 1893.52 U/ml achieving the highest bioscouring with 20.0%.},
}
@article {pmid39760805,
year = {2025},
author = {Willemsen, A and Manzano-Marín, A and Horn, M},
title = {Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts.},
journal = {Genome biology and evolution},
volume = {17},
number = {1},
pages = {},
doi = {10.1093/gbe/evae271},
pmid = {39760805},
issn = {1759-6653},
support = {//European Union's Horizon 2020 research and innovation programme/ ; 891572//Marie Sklodowska-Curie/ ; 101039843//European Union/ ; //European Research Council Executive Agency/ ; //Austrian Science Fund/ ; },
mesh = {*Giant Viruses/genetics ; *Codon Usage ; *Amoeba/virology/genetics ; Genome, Protozoan ; Host Specificity ; Phylogeny ; Acanthamoeba/virology/genetics ; },
abstract = {The need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents 6 high-quality amoeba genomes from known and potential giant virus hosts belonging to 2 distinct eukaryotic clades: Amoebozoa and Discoba. We employ their genomic data to investigate the predictability of giant virus host range. Using a combination of long- and short-read sequencing, we obtained highly contiguous and complete genomes of Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba terricola, Naegleria clarki, Vermamoeba vermiformis, and Willaertia magna, contributing to the collection of sequences for the eukaryotic tree of life. We found that the 6 amoebae have distinct codon usage patterns and that, contrary to other virus groups, giant viruses often have different and even opposite codon usage with their known hosts. Conversely, giant viruses with matching codon usage are frequently not known to infect or replicate in these hosts. Interestingly, analyses of integrated viral sequences in the amoeba host genomes reveal potential novel virus-host associations. Matching of codon usage preferences is often used to predict virus-host pairs. However, with the broad-scale analyses performed in this study, we demonstrate that codon usage alone appears to be a poor predictor of host range for giant viruses infecting amoeba. We discuss the potential strategies that giant viruses employ to ensure high viral fitness in nonmatching hosts. Moreover, this study emphasizes the need for more high-quality protist genomes. Finally, the amoeba genomes presented in this study set the stage for future experimental studies to better understand how giant viruses interact with different host species.},
}
@article {pmid39753761,
year = {2025},
author = {Peng, Z and van der Heijden, MGA and Liu, Y and Li, X and Pan, H and An, Y and Gao, H and Qi, J and Gao, J and Qian, X and Tiedje, JM and Wei, G and Jiao, S},
title = {Agricultural subsoil microbiomes and functions exhibit lower resistance to global change than topsoils in Chinese agroecosystems.},
journal = {Nature food},
volume = {},
number = {},
pages = {},
pmid = {39753761},
issn = {2662-1355},
abstract = {Soils play a critical role in supporting agricultural production. Subsoils, below 20 cm, underpin fundamental agroecosystem sustainability traits including soil carbon storage, climate regulation and water provision. However, little is known about the ecological stability of subsoils in response to global change. Here we conducted a microcosm experiment to determine whether subsoils were more sensitive to global changes across 40 agricultural ecosystems in China, in combination with a multiple global change factor experiment and an in situ field study. We found that subsoils exhibited greater fluctuation in species diversity, community composition, and complexity of microbial networks and ecosystem functions than topsoils, indicating lower resistance to global changes. Soil biodiversity was a major driver of ecosystem resistance, surpassing climate and soil parameters. A reciprocal microorganism transplant experiment showed that microorganisms isolated from the topsoil are more resistant to global changes than those from subsoil. Our study emphasizes that subsoil ecosystems are sensitive to global changes, underscoring the importance of including subsoils in predictions of agricultural sustainability and crop productivity under changing environmental conditions.},
}
@article {pmid39752189,
year = {2025},
author = {Bloomfield, SJ and Hildebrand, F and Zomer, AL and Palau, R and Mather, AE},
title = {Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications.},
journal = {Microbial genomics},
volume = {11},
number = {1},
pages = {},
doi = {10.1099/mgen.0.001337},
pmid = {39752189},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Food Microbiology ; Metagenome ; Bacteria/genetics/classification/isolation &amp; purification ; Salmonella/genetics/isolation &amp; purification/classification ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/isolation &amp; purification/classification ; },
abstract = {A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including Escherichia coli, Klebsiella/Raoultella spp., Salmonella spp. and Vibrio spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.},
}
@article {pmid39745433,
year = {2024},
author = {Grüterich, L and Woodhouse, JN and Mueller, P and Tiemann, A and Ruscheweyh, H-J and Sunagawa, S and Grossart, H-P and Streit, WR},
title = {Assessing environmental gradients in relation to dark CO2 fixation in estuarine wetland microbiomes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0217724},
doi = {10.1128/aem.02177-24},
pmid = {39745433},
issn = {1098-5336},
abstract = {UNLABELLED: The rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2-fixing microorganisms are preventing some of the CO2 from entering the atmosphere. Yet, the controls of dark CO2 fixation are rarely studied in situ. Here, we examined the gene and transcript abundance of key genes involved in microbial CO2 fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO2 fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood-Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood-Ljungdahl pathway was favored by reducing, O2-poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to a few bacterial phyla, namely, Desulfobacterota, Methylomirabilota, Nitrospirota, Chloroflexota, and Pseudomonadota.<br><br>IMPORTANCE: The increasing concentration of atmospheric CO2 has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO2 fixation by soil microbes (a.k.a. dark CO2 fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO2-fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO2 fixation and its potential role in the global climate system.},
}
@article {pmid39745058,
year = {2025},
author = {Doyle, RT and Grieves, LA and Gerstein, AC},
title = {Microbial ecology and evolution.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2024-0192},
pmid = {39745058},
issn = {1480-3275},
}
@article {pmid39744675,
year = {2024},
author = {Mathers, AJ and Li, TJX and He, Q and Narendra, S and Stoesser, N and Eyre, DW and Walker, AS and Barry, KE and Castañeda-Barba, S and Huang, FW and Parikh, H and Kotay, S and Crook, DW and Reidys, C},
title = {Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir.},
journal = {npj antimicrobials and resistance},
volume = {2},
number = {1},
pages = {50},
pmid = {39744675},
issn = {2731-8745},
abstract = {Mobile genetic elements are key to the global emergence of antibiotic resistance. We successfully reconstructed the complete bacterial genome and plasmid assemblies of isolates sharing the same bla KPC carbapenemase gene to understand evolution over time in six confined hospital drains over five years. From 82 isolates we identified 14 unique strains from 10 species with 113 bla KPC-carrying plasmids across 16 distinct replicon types. To assess dynamic gene movement, we introduced the 'Composite-Sample Complex', a novel mathematical approach to using probability to capture the directional movement of antimicrobial resistance genes. The Composite Sample Complex accounts for the co-occurrence of both plasmids and chromosomes within an isolate, and highlights likely gene donors and recipients. From the validated model, we demonstrate frequent transposition events of bla KPC from plasmids to other plasmids, as well as integration into the bacterial chromosome within specific drains. We present a novel approach to estimate the directional movement of antimicrobial resistance via gene mobilization.},
}
@article {pmid39744400,
year = {2024},
author = {Bradbury, ES and Holland-Moritz, H and Gill, A and Havrilla, CA},
title = {Plant and soil microbial composition legacies following indaziflam herbicide treatment.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1450633},
pmid = {39744400},
issn = {1664-302X},
abstract = {Land stewards in dryland ecosystems across the western U.S. face challenges to manage the exotic grass Bromus tectorum (cheatgrass), which is a poor forage, is difficult to remove, and increases risk of catastrophic fire. Managers may consider using indaziflam (Rejuvra™), a relatively new pre-emergent herbicide, which may reduce cheatgrass cover within drylands. However, few studies have explored the effects of indaziflam on non-target organisms. We tested how indaziflam application impacted cover and biomass of native and exotics within the plant community and composition and diversity of the soil microbiome by comparing untreated and treated arid shrubland sites in Boulder County, Colorado, USA. We found that indaziflam application decreased cheatgrass cover by as much as 80% and increased native plant cover by the same amount. Indaziflam application also was associated with increased soil nitrate (NO3 [-]), decreased soil organic matter, and had a significant effect on the composition of the soil microbiome. Microbial community composition was significantly related to soil NO3 [-], soil organic matter, soil pH, and native species and cheatgrass biomass. An indicator species analysis suggested that indaziflam application shifted microbial communities. In untreated sites, ammonia-oxidizing bacteria Nitrosomonadaceae and nitrogen-digesting Opitutaceae and the fungi Articulospora proliferata were found. While in treated sites, ammonia-oxidizing archaea which are associated with intact drylands, Nitrososphaeraceae and toxin digesters and acidic-soil species Sphingomonas and Acidimicrobiia were significantly associated. Overall, these results demonstrate that indaziflam application can increase native plant recruitment, while also affecting soil properties and the soil microbiome. The findings from this study can be used to inform decision-making during dryland restoration planning process as indaziflam use may have benefits and unknown long-term consequences for the biogeochemistry and microbial ecology of the system.},
}
@article {pmid39742975,
year = {2024},
author = {Dougherty, PE and Pedersen, MS and Forero-Junco, LM and Carstens, AB and Raaijmakers, JM and Riber, L and Hansen, LH},
title = {Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks.},
journal = {Virus research},
volume = {},
number = {},
pages = {199524},
doi = {10.1016/j.virusres.2024.199524},
pmid = {39742975},
issn = {1872-7492},
abstract = {The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.},
}
@article {pmid39742000,
year = {2024},
author = {Ford, SE and Slater, GF and Engel, K and Warr, O and Lollar, GS and Brady, A and Neufeld, JD and Lollar, BS},
title = {Deep terrestrial indigenous microbial community dominated by Candidatus Frackibacter.},
journal = {Communications earth &amp; environment},
volume = {5},
number = {1},
pages = {795},
doi = {10.1038/s43247-024-01966-8},
pmid = {39742000},
issn = {2662-4435},
abstract = {Characterizing deep subsurface microbial communities informs our understanding of Earth's biogeochemistry as well as the search for life beyond the Earth. Here we characterized microbial communities within the Kidd Creek Observatory subsurface fracture water system with mean residence times of hundreds of millions to over one billion years. 16S rRNA analysis revealed that biosamplers well isolated from the mine environment were dominated by a putatively anaerobic and halophilic bacterial species from the Halobacteroidaceae family, Candidatus Frackibacter. Contrastingly, biosamplers and biofilms exposed to the mine environment contained aerobic Sphingomonas taxa. δ[13]C values of phospholipid fatty acids and putative functional predictions derived from 16S rRNA gene profiles, imply Candidatus Frackibacter may use carbon derived from ancient carbon-rich layers common in these systems. These results indicate that Candidatus Frackibacter is not unique to hydraulically fracked sedimentary basins but rather may be indigenous to a wide range of deep, saline groundwaters hosted in carbon-rich rocks.},
}
@article {pmid39741633,
year = {2024},
author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y},
title = {A real-world pharmacovigilance study of Sorafenib based on the FDA Adverse Event Reporting System.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1442765},
doi = {10.3389/fphar.2024.1442765},
pmid = {39741633},
issn = {1663-9812},
abstract = {AIMS: The primary objective of this study was to closely monitor and identify adverse events (AEs) associated with Sorafenib, a pharmacological therapeutic agent used to treat hepatocellular carcinoma, renal cell carcinoma, and thyroid cancer. The ultimate goal was to optimize patient safety and provide evidence-based guidance for the appropriate use of this drug.<br><br>METHODS: Reports from the FDA Adverse Event Reporting System (FAERS) database were comprehensively collected and analyzed, covering the first quarter of 2004 to the first quarter of 2024. Disproportionality analysis was performed using robust algorithms for effective data mining to quantify the signals associated with Sorafenib-related AEs.<br><br>RESULTS: In total, we identifued 18,624 patients (82,857 AEs in the Sorafenib population) from the collected reports and examined, the occurrence of Sorafenib-induced AEs in 26 organ systems. The study results revealed the presence of the expected AEs, including Diarrhoea, Palmar-plantar erythrodysaesthesia syndrome, Hepatocellular carcinoma, Fatigue, and Rash, which was consistent with the information provided in the drug insert. In addition, unexpected significant AEs, such as Gait inability, Palmoplantar keratoderma and Hyperkeratosis were observed at the preferred term (PT) level. These findings suggest the potential occurrence of adverse reactions not currently documented in drug descriptions.<br><br>CONCLUSION: This study successfully detected new and unforeseen signals associated with Sorafenib-related AEs related to Sorafenib administration, providing important insights into the complex correlations between AEs and Sorafenib use. The results of this study emphasize the critical importance of continuous and vigilant surveillance for the timely identification and effective management of AEs to improve the overall patient safety and wellbeing in the context of Sorafenib therapy.},
}
@article {pmid39739109,
year = {2024},
author = {Rovira-Alsina, L and Romans-Casas, M and Perona-Vico, E and Ceballos-Escalera, A and Balaguer, MD and Bañeras, L and Puig, S},
title = {Microbial Electrochemical Technologies: Sustainable Solutions for Addressing Environmental Challenges.},
journal = {Advances in biochemical engineering/biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39739109},
issn = {0724-6145},
abstract = {Addressing global challenges of waste management demands innovative approaches to turn biowaste into valuable resources. This chapter explores the potential of microbial electrochemical technologies (METs) as an alternative opportunity for biowaste valorisation and resource recovery due to their potential to address limitations associated with traditional methods. METs leverage microbial-driven oxidation and reduction reactions, enabling the conversion of different feedstocks into energy or value-added products. Their versatility spans across gas, food, water and soil streams, offering multiple solutions at different technological readiness levels to advance several sustainable development goals (SDGs) set out in the 2030 Agenda. By critically examining recent studies, this chapter uncovers challenges, optimisation strategies, and future research directions for real-world MET implementations. The integration of economic perspectives with technological developments provides a comprehensive understanding of the opportunities and demands associated with METs in advancing the circular economy agenda, emphasising their pivotal role in waste minimisation, resource efficiency promotion, and closed-loop system renovation.},
}
@article {pmid39738334,
year = {2024},
author = {Ahadi, R and Bouket, AC and Alizadeh, A and Masigol, H and Grossart, HP},
title = {Globisporangium tabrizense sp. nov., Globisporangium mahabadense sp. nov., and Pythium bostanabadense sp. nov. (Oomycota), three new species from Iranian aquatic environments.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {31701},
pmid = {39738334},
issn = {2045-2322},
mesh = {Iran ; *Phylogeny ; *Pythium/genetics/isolation &amp; purification ; Oomycetes/genetics/classification/isolation &amp; purification ; Cucumis sativus/microbiology ; },
abstract = {During a survey on the biodiversity of oomycetes in aquatic environments in northwest Iran (East Azarbaijan and West Azarbaijan provinces), three Pythium and four Globisporangium isolates were recovered from agricultural water pools and irrigation canals, respectively. Through a polyphasic approach combining morphology and phylogenetic analysis using the nuclear rDNA ITS1-5.8 S-ITS2 (ITS) and partial sequences of the cytochrome c oxidase subunit I and II (COX1 and COX2), three novel species were identified namely Globisporangium tabrizense sp. nov., G. mahabadense sp. nov., and Pythium bostanabadense sp. nov. Furthermore, experiments confirmed the pathogenicity of all identified species on cucumber seedlings, suggesting a pathogenic lifestyle also in aquatic systems. Our research contributes to a better understanding of the diversity, host range and distribution of oomycetes genera Globisporangium and Pythium in northwestern Iran. Detailed morphological descriptions and illustrations are provided for all species.},
}
@article {pmid39605409,
year = {2024},
author = {Alexander, AM and Loo, HQ and Askew, L and Raghuram, V and Read, TD and Goldberg, JB},
title = {Intraspecific Diversity of Staphylococcus aureus Populations Isolated from Cystic Fibrosis Respiratory Infections.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39605409},
issn = {2692-8205},
abstract = {Chronic bacterial infections are often polymicrobial, comprising multiple bacterial species or variants of the same species. Because chronic infections may last for decades, they have the potential to generate high levels of intraspecific variation through within-host diversification over time, and the potential for superinfections to occur through the introduction of multiple pathogen populations to the ongoing infection. Traditional methods for identifying infective agents generally involve isolating one single colony from a given sample, usually after selecting for a specific pathogen or antibiotic resistance profile. Isolating a recognized virulent or difficult to treat pathogen is an important part of informing clinical treatment and correlative research; however, these reductive methods alone, do not provide researchers or healthcare providers with the potentially important perspective on the true pathogen population structure and dynamics over time. To begin to address this limitation, in this study, we compare findings on Staphylococcus aureus single colonies versus and pools of colonies taken from fresh sputum samples from three patients with cystic fibrosis to isolates collected from the same sputum samples and processed by the clinical microbiology laboratory. Phenotypic and genotypic analysis of isolated S. aureus populations revealed coexisting lineages in two of three sputum samples as well as population structures that were not reflected in the single colony isolates. Altogether, our observations presented here demonstrate that clinically relevant diversity can be missed with standard sampling methods when assessing chronic infections. More broadly, this work outlines the potential impact that comprehensive population-level sampling may have for both research efforts and more effective treatment practices.},
}
@article {pmid39737770,
year = {2025},
author = {Rawstern, AH and Hernandez, DJ and Afkhami, ME},
title = {Central Taxa Are Keystone Microbes During Early Succession.},
journal = {Ecology letters},
volume = {28},
number = {1},
pages = {e70031},
doi = {10.1111/ele.70031},
pmid = {39737770},
issn = {1461-0248},
support = {DEB-1922521//National Science Foundation/ ; DEB-2030060//National Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; Biodiversity ; Bacteria/classification/genetics ; Ecosystem ; },
abstract = {Microorganisms underpin numerous ecosystem processes and support biodiversity globally. Yet, we understand surprisingly little about what structures environmental microbiomes, including how to efficiently identify key players. Microbiome network theory predicts that highly connected hubs act as keystones, but this has never been empirically tested in nature. Combining culturing, sequencing, networks and field experiments, we isolated 'central' (highly connected, hub taxa), 'intermediate' (moderately connected), and 'peripheral' (weakly/unconnected) microbes and experimentally evaluated their effects on soil microbiome assembly during early succession in nature. Central early colonisers significantly (1) enhanced biodiversity (35%-40% richer communities), (2) reshaped trajectories of microbiome assembly and (3) increased recruitment of additional influential microbes by > 60%. In contrast, peripheral microbes did not increase diversity and were transient taxa, minimally affected by the presence of other microbes. This work elucidates fundamental principles of network theory in microbial ecology and demonstrates for the first time in nature that central microbes act as keystone taxa.},
}
@article {pmid39736538,
year = {2024},
author = {Radjasa, OK and Steven, R and Natanael, Y and Nugrahapraja, H and Radjasa, SK and Kristianti, T and Moeis, MR and Trinugroho, JP and Suharya, HB and Rachmatsyah, AO and Dwijayanti, A and Putri, MR and de Fretes, CE and Siallagan, ZL and Fadli, M and Opier, RDA and Farahyah, JD and Rahmawati, V and Rizanti, M and Humaira, Z and Prihatmanto, AS and Hananto, ND and Susanto, RD and Chahyadi, A and Elfahmi, and Priharto, N and Kamarisima, and Dwivany, FM},
title = {From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1259},
pmid = {39736538},
issn = {1471-2164},
mesh = {*Lycopene/metabolism ; Indonesia ; *Genome, Bacterial ; Bioprospecting ; Genomics/methods ; Phylogeny ; Multigene Family ; Peptide Synthases/genetics/metabolism ; Whole Genome Sequencing ; Carotenoids/metabolism ; Actinobacteria/genetics/metabolism ; },
abstract = {BACKGROUND: The marine environment boasts distinctive physical, chemical, and biological characteristics. While numerous studies have delved into the microbial ecology and biological potential of the marine environment, exploration of genetically encoded, deep-sea sourced secondary metabolites remains scarce. This study endeavors to investigate marine bioproducts derived from deep-sea water samples at a depth of 1,000 m in the Java Trench, Indonesia, utilizing both culture-dependent and whole-genome sequencing methods.<br><br>RESULTS: Our efforts led to the successful isolation and cultivation of a bacterium Priestia flexa JT4 from the water samples, followed by comprehensive genome sequencing. The resultant high-quality draft genome, approximately 4&#xa0;Mb, harbored 5185 coding sequences (CDSs). Notably, 61.97% of these CDSs were inadequately characterized, presenting potential novel CDSs. This study is the first to identify the "open-type" (&#x3b1;&#x2009;<&#x2009;1) pangenome within the genus Priestia. Moreover, our analysis uncovered eight biosynthetic gene clusters (BGCs) using the common genome mining pipeline, antiSMASH. Two non-ribosomal peptide synthetase (NRPS) BGCs within these clusters exhibited the potential to generate novel biological compounds. Noteworthy is the confirmation that the terpene BGC in P. flexa JT4 can produce lycopene, a compound in substantial industrial demand. The presence of lycopene in the P. flexa JT4 cells was verified using Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) in multiple reaction modes.<br><br>CONCLUSIONS: This study highlights the bioprospecting opportunity to explore novel bioproducts and lycopene compounds from P. flexa JT4. It marks the pioneering exploration of deep-sea bacterium bioprospecting in Indonesia, seeking to unveil novel bioproducts and lycopene compounds through a genome mining approach.},
}
@article {pmid39736196,
year = {2024},
author = {Wong, JWH and Balskus, EP},
title = {Small molecules as modulators of phage-bacteria interactions.},
journal = {Current opinion in chemical biology},
volume = {84},
number = {},
pages = {102566},
doi = {10.1016/j.cbpa.2024.102566},
pmid = {39736196},
issn = {1879-0402},
abstract = {Bacteriophages (phages) play a critical role in microbial ecology and evolution. Their interactions with bacteria are influenced by a complex network of chemical signals derived from a wide range of sources including both endogenous bacterial metabolites and exogenous environmental compounds. In this review, we highlight two areas where small molecules play a pivotal role in modulating phage behaviors. First, we discuss how temperate phages respond to various chemical cues that influence the lysis-lysogeny decision, describing recent advances in our understanding of noncanonical cues. Second, we examine the diverse array of small molecules that disrupt phage infection, potentially serving as bacterial defense strategies against their long-standing competitors. Collectively, this growing body of research highlights the intricate molecular mechanisms governing phage-bacteria dynamics, offering new perspectives on the chemical language shaping microbial communities.},
}
@article {pmid39732620,
year = {2024},
author = {Berrios, L and Ansell, TB and Dahlberg, PD and Peay, KG},
title = {Standardizing experimental approaches to investigate interactions between bacteria and ectomycorrhizal fungi.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuae035},
pmid = {39732620},
issn = {1574-6976},
abstract = {Bacteria and ectomycorrhizal fungi (EcMF) represent two of the most dominant plant root-associated microbial groups on Earth, and their interactions continue to gain recognition as significant factors that shape forest health and resilience. Yet we currently lack a focused review that explains the state of bacteria-EcMF interaction research in the context of experimental approaches and technological advancements. To these ends, we illustrate the utility of studying bacteria-EcMF interactions, detail outstanding questions, outline research priorities in the field, and provide a suite of approaches that can be used to promote experimental reproducibility, field advancement, and collaboration. Though this review centers on the ecology of bacteria, EcMF, and trees, it by default offers experimental and conceptual insights that can be adapted to various subfields of microbiology and microbial ecology.},
}
@article {pmid39732444,
year = {2024},
author = {Correa, SS and Schultz, J and Huntington, B and Naschberger, A and Rosado, AS},
title = {Carboxysomes: The next frontier in biotechnology and sustainable solutions.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108511},
doi = {10.1016/j.biotechadv.2024.108511},
pmid = {39732444},
issn = {1873-1899},
abstract = {Some bacteria possess microcompartments that function as protein-based organelles. Bacterial microcompartments (BMCs) sequester enzymes to optimize metabolic reactions. Several BMCs have been characterized to date, including carboxysomes and metabolosomes. Genomic analysis has identified novel BMCs and their loci, often including genes for signature enzymes critical to their function, but further characterization is needed to confirm their roles. Among the various BMCs, carboxysomes, which are found in cyanobacteria and some chemoautotrophic bacteria, and are most extensively investigated. These self-assembling polyhedral proteinaceous BMCs are essential for carbon fixation. Carboxysomes encapsulate the enzymes RuBisCo and carbonic anhydrase, which increase the carbon fixation rate in the cell and decrease the oxygenation rate by RuBisCo. The ability of carboxysomes to concentrate carbon dioxide in crops and industrially relevant microorganisms renders them attractive targets for carbon assimilation bioengineering. Thus, carboxysome characterization is the first step toward developing carboxysome-based applications. Therefore, this review comprehensively explores carboxysome morphology, physiology, and biochemistry. It also discusses recent advances in microscopy and complementary techniques for isolating and characterizing this versatile class of prokaryotic organelles.},
}
@article {pmid39731630,
year = {2024},
author = {Fluch, M and Corretto, E and Feldhaar, H and Schuler, H},
title = {Seasonal Changes in the Gut Microbiota of Halyomorpha halys.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {164},
pmid = {39731630},
issn = {1432-184X},
mesh = {Animals ; *Seasons ; *Gastrointestinal Microbiome ; *Heteroptera/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; Pantoea/isolation &amp; purification/physiology/genetics/classification ; Phylogeny ; },
abstract = {The gut microbiome plays an important role in insect evolution and ecology. Bacteria support the host's nutrition and defense and therefore play an important role in the fitness of the host. Halyomorpha halys is one of the most important invasive pest species in the world. Native to North-Eastern Asia, this Pentatomid bug has recently invaded North America and Europe, causing significant damage to agricultural production. Although an increasing number of studies investigated the biology of this pest species, little is known about the composition of its gut microbiota. Like many other Pentatomid species, H. halys harbors a primary symbiont called "Candidatus Pantoea carbekii," which produces vitamins and essential amino acids for the host. However, information about the presence of other bacteria is currently lacking. Therefore, we investigated the gut microbiota of H. halys individuals, which were collected in the field across the year using a high-throughput 16S rRNA gene metabarcoding approach. Our results revealed 3309 different ASVs associated with H. halys, with Pantoea being the most abundant symbiont, present in almost all individuals. Additionally, many individuals harbor Commensalibacter, a genus of acetic acid bacterial symbionts. Besides these two predominant taxa, we show a high diversity of microorganisms associated with H. halys with seasonal fluctuations, highlighting a dynamic microbiota that might influence the biology of this species.},
}
@article {pmid39730790,
year = {2024},
author = {Struniawski, K and Kozera, R and Trzciński, P and Marasek-Ciołakowska, A and Sas-Paszt, L},
title = {Extreme learning machine for identifying soil-dwelling microorganisms cultivated on agar media.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {31034},
pmid = {39730790},
issn = {2045-2322},
support = {BIOSTRATEG3/344433/16/NCBR/2018//Narodowe Centrum Bada&#x144; i Rozwoju/ ; },
mesh = {*Soil Microbiology ; *Machine Learning ; Agar/chemistry ; Soil/chemistry ; Image Processing, Computer-Assisted/methods ; Culture Media ; },
abstract = {The aim of this research is to create an automated system for identifying soil microorganisms at the genera level based on raw microscopic images of monocultural colonies grown in laboratory environment. The examined genera are: Fusarium, Trichoderma, Verticillium, Purpureolicillium and Phytophthora. The proposed pipeline deals with unprocessed microscopic images, avoiding additional sample marking or coloration. The methodology includes several stages: image preprocessing, segmenting images to isolate microorganisms from the background, calculating features related to image color and texture for classification. Using an extensive dataset of 2866 images from the National Institute of Horticultural Research in Skierniewice the Extreme Learning Machine model was trained and validated. The model showcases high accuracy and computational efficiency compared to other Machine Learning state-of-the art methods e.g. CatBoost, Random Forest or Convolutional Neural Networks. Statistical techniques, including Multivariate Analysis of Variance were employed to confirm significant differences among the datasets, enhancing the model's robustness. Nevertheless, Shapley Additive Explanations values provided transparency into the model's decision-making process. This approach has the potential to improve early detection and management of soil pathogens, promoting sustainable agriculture and demonstrating machine learning's potential in environmental monitoring, microbial ecology or industrial microbiology.},
}
@article {pmid39730187,
year = {2024},
author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z},
title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279825.124},
pmid = {39730187},
issn = {1549-5469},
abstract = {Metagenomics, particularly genome-resolved metagenomics, has significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies due to the lack of comprehensive reference genome databases and robust bioinformatics tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass although a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than one thousand rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for in-depth study of GI tract eukaryotes.},
}
@article {pmid39730090,
year = {2024},
author = {Vinh, NT and Kim, NK and Lee, SH and Trinh, HP and Park, HD},
title = {Gene abundance and microbial syntrophy as key drivers of anaerobic digestion revealed through 16S rRNA gene and metagenomic analysis.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {144028},
doi = {10.1016/j.chemosphere.2024.144028},
pmid = {39730090},
issn = {1879-1298},
abstract = {Genes in microorganisms influence the biological processes in anaerobic digestion (AD). However, key genes involved in the four metabolic steps (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) remain largely unexplored. This study investigated the abundance and distribution of key functional genes in full-scale anaerobic digesters processing food waste (FWDs) and municipal wastewater (MWDs) through 16S rRNA gene and shotgun metagenomic analysis. Our results revealed that FWDs exhibited a higher abundance of key genes in the metabolic steps, despite having significantly lower microbial diversity compared to MWDs. Pathways and genes associated with syntrophic oxidation of acetate (SAO) and butyrate (SBO) were more present in FWDs. SAO potentially used both the conventional reversed Wood-Ljungdahl pathway and its integration with the glycine cleavage system in FWDs, which complements pathways for acetate oxidation under ammonia stress conditions. Similarly, genes associated with SBO (atoB and croR) were notably more prevalent in FWDs compared to MWDs with an 8.4-fold and 108-fold increase, respectively, indicating the adaptation of SBO bacteria to convert butyrate into acetate. The higher abundance of key genes in FWDs was driven by microbes adapting to the feedstock compositions with higher levels of substrate content, volatile fatty acids, and ammonia. This study quantified the genes central to AD metabolism and uncovered the contributions of microbial diversity, gene abundance, syntrophy, and feedstock characteristics to the functionality of AD processes. These findings enhance understanding of the microbial ecology in AD and provide a foundation for developing innovative strategies to enhance biogas production and waste management.},
}
@article {pmid39726151,
year = {2024},
author = {Nieland, MA and Lacy, P and Allison, SD and Bhatnagar, JM and Doroski, DA and Frey, SD and Greaney, K and Hobbie, SE and Kuebbing, SE and Lewis, DB and McDaniel, MD and Perakis, SS and Raciti, SM and Shaw, AN and Sprunger, CD and Strickland, MS and Templer, PH and Vietorisz, C and Ward, EB and Keiser, AD},
title = {Nitrogen Deposition Weakens Soil Carbon Control of Nitrogen Dynamics Across the Contiguous United States.},
journal = {Global change biology},
volume = {30},
number = {12},
pages = {e70016},
doi = {10.1111/gcb.70016},
pmid = {39726151},
issn = {1365-2486},
support = {1831944//Division of Environmental Biology/ ; SC0020382//Biological and Environmental Research/ ; 1845417//National Science Foundation/ ; 2045135//Division of Earth Sciences/ ; //University of Massachusetts Amherst/ ; },
mesh = {*Soil/chemistry ; United States ; *Carbon/metabolism/analysis ; *Nitrogen/metabolism/analysis ; *Soil Microbiology ; *Nitrification ; Forests ; Biomass ; },
abstract = {Anthropogenic nitrogen (N) deposition is unequally distributed across space and time, with inputs to terrestrial ecosystems impacted by industry regulations and variations in human activity. Soil carbon (C) content normally controls the fraction of mineralized N that is nitrified (ƒnitrified), affecting N bioavailability for plants and microbes. However, it is unknown whether N deposition has modified the relationships among soil C, net N mineralization, and net nitrification. To test whether N deposition alters the relationship between soil C and net N transformations, we collected soils from coniferous and deciduous forests, grasslands, and residential yards in 14 regions across the contiguous United States that vary in N deposition rates. We quantified rates of net nitrification and N mineralization, soil chemistry (soil C, N, and pH), and microbial biomass and function (as beta-glucosidase (BG) and N-acetylglucosaminidase (NAG) activity) across these regions. Following expectations, soil C was a driver of ƒnitrified across regions, whereby increasing soil C resulted in a decline in net nitrification and ƒnitrified. The ƒnitrified value increased with lower microbial enzymatic investment in N acquisition (increasing BG:NAG ratio) and lower active microbial biomass, providing some evidence that heterotrophic microbial N demand controls the ammonium pool for nitrifiers. However, higher total N deposition increased ƒnitrified, including for high soil C sites predicted to have low ƒnitrified, which decreased the role of soil C as a predictor of ƒnitrified. Notably, the drop in contemporary atmospheric N deposition rates during the 2020 COVID-19 pandemic did not weaken the effect of N deposition on relationships between soil C and ƒnitrified. Our results suggest that N deposition can disrupt the relationship between soil C and net N transformations, with this change potentially explained by weaker microbial competition for N. Therefore, past N inputs and soil C should be used together to predict N dynamics across terrestrial ecosystems.},
}
@article {pmid39725503,
year = {2025},
author = {Belanche, A and Bannink, A and Dijkstra, J and Durmic, Z and Garcia, F and Santos, FG and Huws, S and Jeyanathan, J and Lund, P and Mackie, RI and McAllister, TA and Morgavi, DP and Muetzel, S and Pitta, DW and Yáñez-Ruiz, DR and Ungerfeld, EM},
title = {Feed additives for methane mitigation: A guideline to uncover the mode of action of antimethanogenic feed additives for ruminants.},
journal = {Journal of dairy science},
volume = {108},
number = {1},
pages = {375-394},
doi = {10.3168/jds.2024-25046},
pmid = {39725503},
issn = {1525-3198},
mesh = {*Methane ; Animals ; *Animal Feed ; *Ruminants ; *Rumen/metabolism ; Diet/veterinary ; },
abstract = {This publication aims to provide guidelines of the knowledge required and the potential research to be conducted in order to understand the mode of action of antimethanogenic feed additives (AMFA). In the first part of the paper, we classify AMFA into 4 categories according to their mode of action: (1) lowering dihydrogen (H2) production; (2) inhibiting methanogens; (3) promoting alternative H2-incorporating pathways; and (4) oxidizing methane (CH4). The second part of the paper presents questions that guide the research to identify the mode of action of an AMFA on the rumen CH4 production from 5 different perspectives: (1) microbiology; (2) cell and molecular biochemistry; (3) microbial ecology; (4) animal metabolism; and (5) cross-cutting aspects. Recommendations are provided to address various research questions within each perspective, along with examples of how aspects of the mode of action of AMFA have been elucidated before. In summary, this paper offers timely and comprehensive guidelines to better understand and reveal the mode of action of current and emerging AMFA.},
}
@article {pmid39725195,
year = {2024},
author = {Xu, W and Lam, C and Wang, Y and Hei Wan, S and Hang Ho, P and Myung, J and Yung, CCM},
title = {Temporal succession of marine microbes drives plastisphere community convergence in subtropical coastal waters.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125572},
doi = {10.1016/j.envpol.2024.125572},
pmid = {39725195},
issn = {1873-6424},
abstract = {Marine plastic pollution is a pervasive environmental issue, with microplastics serving as novel substrates for microbial colonization in aquatic ecosystems. This study investigates the succession of plastisphere communities on four common plastic types (polyethylene, polypropylene, polyethylene terephthalate, and polystyrene) in subtropical coastal waters of Hong Kong SAR. Over a 42-day period, we analysed the temporal development of microbial communities using a three-domain universal metabarcoding method. Our results reveal that temporal succession is a stronger driver of community structure than plastic type, with prokaryotic communities converging across different plastics as biofilms mature. Despite this convergence, plastisphere communities remain distinct from planktonic communities throughout the experiment, suggesting that plastics create unique ecological niches in marine environments. We observed differences in diversity patterns and community composition among prokaryotic, eukaryotic, and chloroplastic communities, highlighting the importance of multi-domain analyses in plastisphere research. Functional predictions suggest potential roles of prokaryotic communities in biogeochemical cycling and possible pathogenicity, highlighting the ecological and public health implications of plastisphere formation. This study provides valuable insights into the dynamics of microbial colonization across domains on marine plastics and enhances our understanding of how these anthropogenic substrates influence microbial ecology in marine ecosystems.},
}
@article {pmid39724890,
year = {2024},
author = {Kusradze, I and Rcheulishvili, O and Karumidze, N and Rigvava, S and Rcheulishvili, A and Goliadze, R and Kamashidze, L and Chipurupalli, A and Metreveli, N and Goderdzishvili, M},
title = {PHAGE-BACTERIA INTERACTIONS UNDER METAL STRESS: A STUDY OF THE NOVEL STENOTROPHOMONAS MALTOPHILIA PHAGE VB_STM18.},
journal = {Georgian medical news},
volume = {},
number = {355},
pages = {117-122},
pmid = {39724890},
issn = {1512-0112},
mesh = {*Stenotrophomonas maltophilia/virology/drug effects ; *Cadmium/toxicity ; *Bacteriophages ; Biodegradation, Environmental ; Stress, Physiological/drug effects ; },
abstract = {Stenotrophomonas maltophilia is a highly adaptable gram-negative bacteria, demonstrating resilience in metal-contaminated environment, which makes it a key subject for understanding microbial survival under heavy metal stress. This study investigates the effects of cadmium ions (Cd[2+]) on the growth dynamics, cadmium uptake, and bacteriophage vB_Stm18-host interactions, with implications for environmental microbiology and applied biotechnology. Growth analysis revealed that S. maltophilia tolerates Cd[2+] at 0.01 g/L, although exposure prolonged the lag phase by 3 hours. Despite the initial growth inhibition, the bacterium adapted and achieved control-like growth levels by 18 hours. Bioaccumulation assays showed progressive cadmium uptake, reaching 1876 µg/g at 24 hours, highlighting its potential for bioremediation. The influence of Cd[2+] on phage vB_Stm18's life cycle was assessed through adsorption efficiency and burst size measurements. Short-term exposure to Cd[2+] caused minimal reductions in adsorption efficiency (97% vs. 98% in control) but significantly decreased the burst size to 17 particles per infected cell. Prolonged exposure exacerbated these effects, with adsorption efficiency decreasing to 58% and burst size dropping to 6 particles per infected cell, after 18 hours of pre-incubation. These findings suggest that cadmium alters bacterial surface structures, intracellular processes and disrupts phage replication and release. Therefore, this study sheds light on the molecular interplay between environmental pollutants and microbial systems providing valuable insights into microbial ecology in metal-contaminated habitats as well as informing strategies for optimizing phage therapy and bioremediation under heavy metal stress.},
}
@article {pmid39724159,
year = {2024},
author = {Ulbrich, J and Jobe, NE and Jones, DS and Kieft, TL},
title = {Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {163},
pmid = {39724159},
issn = {1432-184X},
support = {NCKRI-NMT Internal Seed Grant Program//National Cave and Karst Research Institute/ ; },
mesh = {*Caves ; *Parks, Recreational ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Bacteria/genetics/classification/isolation &amp; purification/virology ; *RNA, Ribosomal, 16S/genetics ; California ; Metagenome ; Phylogeny ; Virome ; Biodiversity ; },
abstract = {Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.},
}
@article {pmid39723821,
year = {2024},
author = {Sanchez, VA and Renner, T and Baker, LJ and Hendry, TA},
title = {Genome evolution following an ecological shift in nectar-dwelling Acinetobacter.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0101024},
doi = {10.1128/msphere.01010-24},
pmid = {39723821},
issn = {2379-5042},
abstract = {UNLABELLED: The bacterial genus Acinetobacter includes species found in environmental habitats like soil and water, as well as taxa adapted to be host-associated or pathogenic. High genetic diversity may allow for this habitat flexibility, but the specific genes underlying switches between habitats are poorly understood. One lineage of Acinetobacter has undergone a substantial habitat change by evolving from a presumed soil-dwelling ancestral state to thrive in floral nectar. Here, we compared the genomes of floral-dwelling and pollinator-associated Acinetobacter, including newly described species, with genomes from relatives found in other environments to determine the genomic changes associated with this ecological shift. Following one evolutionary origin of floral nectar adaptation, nectar-dwelling Acinetobacter taxa have undergone reduction in genome size compared with relatives and have experienced dynamic gene gains and losses as they diversified. Gene content changes suggest a shift to metabolism of monosaccharides rather than diverse carbohydrates, and scavenging of nitrogen sources, which we predict to be beneficial in nectar environments. Gene gains appear to result from duplication events, evolutionary divergence, and horizontal gene transfer. Most notably, nectar-dwelling Acinetobacter acquired the ability to degrade pectin from plant pathogens, and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritionally unbalanced habitat of nectar. These results identify the genomic changes and traits coinciding with a dramatic habitat switch from soil to floral nectar.<br><br>IMPORTANCE: Many bacteria, including the genus Acinetobacter, commonly evolve to exploit new habitats. However, the genetic changes that underlie habitat switches are often unknown. Floral nectar is home to specialized microbes that can grow in this nutritionally unbalanced habitat. Several specialized Acinetobacter species evolved from soil-dwelling relatives to become common and abundant in floral nectar. Here, we investigate the genomic adaptations required to successfully colonize a novel habitat like floral nectar. We performed comparative genomics analyses between nectar-dwelling Acinetobacter and Acinetobacter species from other environments, like soil and water. We find that although gene loss coincided with the switch to living in nectar, gains of specific genes from other bacteria may have been particularly important for this ecological change. Acinetobacter living in nectar gained genes for degrading pectin, a plant polysaccharide, which may improve access to nutrients in their environment. These findings shed light on how evolutionary novelty evolves in bacteria.},
}
@article {pmid39723138,
year = {2024},
author = {Xie, S and Ma, J and Lu, Z},
title = {Bacteroides thetaiotaomicron enhances oxidative stress tolerance through rhamnose-dependent mechanisms.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1505218},
pmid = {39723138},
issn = {1664-302X},
abstract = {This study probes into the unique metabolic responses of Bacteroides thetaiotaomicron (B. thetaiotaomicron), a key player in the gut microbiota, when it metabolizes rhamnose rather than typical carbohydrates. Known for its predominant role in the Bacteroidetes phylum, B. thetaiotaomicron efficiently breaks down poly- and mono-saccharides into beneficial short-chain fatty acids (SCFAs), crucial for both host health and microbial ecology balance. Our research focused on how this bacterium's SCFA production differ when utilizing various monosaccharides, with an emphasis on the oxidative stress responses triggered by rhamnose consumption. Notably, rhamnose use results in unique metabolic byproducts, including substantial quantities of 1,2-propanediol, which differs significantly from those produced during glucose metabolism. Our research reveals that rhamnose consumption is associated with a reduction in reactive oxygen species (ROS), signifying improved resistance to oxidative stress compared to other sugars. This effect is attributed to specific gene expressions within the rhamnose metabolic pathway. Notably, overexpression of the rhamnose metabolism regulator RhaR in B. thetaiotaomicron enhances its survival in oxygen-rich conditions by reducing hydrogen peroxide production. This reduction is linked to decreased expression of pyruvate:ferredoxin oxidoreductase (PFOR). In contrast, experiments with a rhaR-deficient strain demonstrated that the absence of RhaR causes B. thetaiotaomicron cells growing on rhamnose to produce ROS at rates comparable to cells grown on glucose, therefore, losing their advantage in oxidative resistance. Concurrently, the expression of PFOR is no longer suppressed. These results indicate that when B. thetaiotaomicron is cultured in a rhamnose-based medium, RhaR can restrain the expression of PFOR. Although PFOR is not a primary contributor to intracellular ROS production, its sufficient inhibition does reduce ROS levels to certain extent, consequently improving the bacterium's resistance to oxidative stress. It highlights the metabolic flexibility and robustness of microbes in handling diverse metabolic challenges and oxidative stress in gut niches through the consumption of alternative carbohydrates.},
}
@article {pmid39721552,
year = {2024},
author = {IJdema, F and Lievens, S and Smets, R and Poma, G and Van Der Borght, M and Lievens, B and De Smet, J},
title = {Modulating the fatty acid composition of black soldier fly larvae via substrate fermentation.},
journal = {Animal : an international journal of animal bioscience},
volume = {19},
number = {1},
pages = {101383},
doi = {10.1016/j.animal.2024.101383},
pmid = {39721552},
issn = {1751-732X},
abstract = {Black soldier fly larvae (BSFL, Hermetia illucens) contain high amounts of proteins and essential amino acids and are therefore an appropriate feed source. However, they lack essential fatty acids (FAs), specifically ω-3 and ω-6, making them a less desirable feed choice for aquaculture. The aim of this study was to increase the ω-3 and ω-6 FA concentrations in BSFL by manipulating the FA composition in their rearing substrate. Specifically, the potential of substrate fermentation using the ω-3 and ω-6 FA-producing fungus Mortierella alpina was assessed. Fermentation of two agricultural side streams (wheat bran (WB) and WB with distiller's dried grains with solubles (DDGS)) increased substrate total crude fat concentration by 2.1 - 4.6%, as well as the concentration of several essential FAs, including the ω-6 FAs arachidonic acid (from less than 0.2 mg/g fat to a maximum of 44.2 mg/g fat) and gamma-linolenic acid (from less than 1.2 mg/g fat to a maximum of 45.8 mg/g fat and the ω-3 FA eicosapentaenoic acid (EPA) (from less than 0.7 mg/g fat to a maximum of 49.9 mg/g fat). Rearing BSFL on feeds from such fermented substrates resulted in similar changes in larval FA composition, specifically a higher concentration of EPA (from less than 0.2 mg/g fat to a maximum of 26.6 mg/g fat in the larvae fed on fermented diets), however, larval growth was reduced. Feeds made from fermented substrates were prone to stickiness and dehydration, possibly limiting larval movement and feeding, thereby affecting larval growth. Furthermore, proximate analysis of the substrates revealed sugar depletion after fermentation, which could be detrimental for larval growth and illustrate important attention points going forward. This study shows that fermentation of agricultural side streams WB and a mixture of WB with DDGS with Mortierella alpina alters their FA profile, increasing their ω-3 and ω-6 FA concentrations and that of BSFL fed with those substrates. Therefore, these results suggest that BSFL with tailor-made FA profiles for a specific application could be successfully produced.},
}
@article {pmid39716780,
year = {2024},
author = {Quevedo-Caraballo, S and de Vega, C and Lievens, B and Fukami, T and Álvarez-Pérez, S},
title = {Tiny but mighty? Overview of a decade of research on nectar bacteria.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20369},
pmid = {39716780},
issn = {1469-8137},
support = {//Agentschap Innoveren en Ondernemen/ ; //Fonds Wetenschappelijk Onderzoek/ ; //KU Leuven/ ; PIPF-2023/ECO-29442//Consejer&#xed;a de Educaci&#xf3;n, Ciencia y Universidades, Comunidad de Madrid/ ; CNS2022-135237//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PID2022-136719NB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; RYC2018-023847-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; //Complutense University of Madrid, Spain/ ; DEB 1737758//Directorate for Biological Sciences/ ; //ESF Investing in your future/ ; },
abstract = {An emerging focus of research at the intersection of botany, zoology, and microbiology is the study of floral nectar as a microbial habitat, referred to as the nectar microbiome, which can alter plant-pollinator interactions. Studies on these microbial communities have primarily focused on yeasts, and it was only about a decade ago that bacteria began to be studied as widespread inhabitants of floral nectar. This review aims to give an overview of the current knowledge on nectar bacteria, with emphasis on evolutionary origin, dispersal mode, effects on nectar chemistry and plant-animal interactions, community assembly, agricultural applications, and their use as model systems in ecological research. We further outline gaps in our understanding of the ecological significance of these microorganisms, their response to environmental changes, and the potential cascading effects.},
}
@article {pmid39715919,
year = {2024},
author = {Jiang, ZB and Zhang, H and Tian, JJ and Guo, HH and Zhou, LR and Ma, XL},
title = {The Microbial Diversity of Biological Moss Crust: Application in Saline-Alkali Soil Management.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {162},
pmid = {39715919},
issn = {1432-184X},
support = {82160672//the National Natural Science Foundation of China/ ; 2022AAC05041 and 2023AAC05048//Outstanding Youth Program of Ningxia Natural Science Foundation/ ; 2021BEB04019//the Key R&amp;D Projects in Ningxia/ ; 2021AAC03210 and 2019AAC03113//the Ningxia Natural Science Foundation/ ; },
mesh = {*Soil/chemistry ; *Soil Microbiology ; *Bryophyta/microbiology ; China ; Biodiversity ; Alkalies/analysis ; Salinity ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chlorophyll/analysis ; },
abstract = {Soil salinization poses a substantial threat to global food security, particularly under the influence of climate change, and is recognized as one of the most urgent challenges in land degradation. This study aims to elucidate the challenges associated with managing arid and semi-arid saline-alkali lands in China's Ningxia province and propose feasible solutions. To assess moss crust colonization, we measured changes in organic matter and chlorophyll levels. Additionally, we investigated the impact of an interlayer composed of Goji berry root bark using liquid chromatography-mass spectrometry analysis, biological enzyme activity analysis, and metagenomic sequencing. A total of 45 endophytes were isolated from the moss crust. The most significant colonization of moss crusts was observed when the Goji berry root bark was used as the interlayer, resulting in a significant increase in chlorophyll content. Several responses were identified as pivotal factors facilitating moss crust growth when the Goji berry root bark was used as the interlayer. In saline-alkali soil, the Goji berry root bark interlayer increased the activities of sucrase, urease, and alkaline phosphatase. Metagenomic data analysis revealed variations in the relative abundance of microorganisms at the phylum level, although these differences were not statistically significant. Evaluation of the impact of physical isolation and moss crust transplantation on the ecological restoration of saline-alkali soil using liquid chromatography-tandem mass spectrometry and metagenomic sequencing indicated that the Goji berry root bark as a physical isolation method promotes moss crust colonization in saline-alkali soil and increases soil organic matter and nutrient elements, offering valuable insights for the ecological management of saline-alkali land and serving as a reference for future research in this field.},
}
@article {pmid39714209,
year = {2024},
author = {Payne, PE and Knobbe, LN and Chanton, P and Zaugg, J and Mortazavi, B and Mason, OU},
title = {Uncovering novel functions of the enigmatic, abundant, and active Anaerolineae in a salt marsh ecosystem.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0116224},
doi = {10.1128/msystems.01162-24},
pmid = {39714209},
issn = {2379-5077},
abstract = {Anaerolineae, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novel Anaerolineae metagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representing Anaerolineales, Promineifilales, JAAYZQ01, B4-G1, JAFGEY01, UCB3, and Caldilineales orders. Metagenome and metatranscriptome reads were mapped to annotated MAGs, revealing nearly all Anaerolineae encoded and transcribed genes required for oxidation of carbon compounds ranging from simple sugars to complex polysaccharides, fermentation, and carbon fixation. Furthermore, the majority of Anaerolineae expressed genes involved in anaerobic and aerobic respiration and secondary metabolite production. The data revealed that the belowground salt marsh Anaerolineae in the rhizosphere are important players in carbon cycling, including degradation of simple carbon compounds and more recalcitrant plant material, such as cellulose, using a diversity of electron acceptors and represent an unexplored reservoir of novel secondary metabolites.IMPORTANCEGiven that coastal salt marshes are recognized as biogeochemical hotspots, it is fundamentally important to understand the functional role of the microbiome in this ecosystem. In particular, Anaerolineae are abundant members of the salt marsh rhizosphere and have been identified as core microbes, suggesting they play an important functional role. Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an 'omics-based approach, we determined that Anaerolineae are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. Surprisingly, Anaerolineae encoded and transcribed genes involved in aerobic respiration, which was unexpected given the reduced nature of the salt marsh rhizosphere. Finally, the majority of Anaerolineae appear to be involved in secondary metabolite production, suggesting that this group represents an unexplored reservoir of novel and important secondary metabolites.},
}
@article {pmid39714150,
year = {2024},
author = {Beizman-Magen, Y and Orevi, T and Kashtan, N},
title = {Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0200424},
doi = {10.1128/aem.02004-24},
pmid = {39714150},
issn = {1098-5336},
abstract = {Antibiotic secretion plays a pivotal role in bacterial interference competition; yet, the impact of environmental hydration conditions on such competition is not well understood. Here, we investigate how hydration conditions affect interference competition among bacteria, studying the interactions between the antibiotic-producing Bacillus velezensis FZB42 and two bacterial strains susceptible to its antibiotics: Xanthomonas euvesicatoria 85-10 and Pseudomonas syringae DC3000. Our results show that wet-dry cycles significantly modify the response of the susceptible bacteria to both the supernatant and cells of the antibiotic-producing bacteria, compared to constantly wet conditions. Notably, X. euvesicatoria shows increased protection against both the cells and supernatants of B. velezensis under wet-dry cycles, while P. syringae cells become more susceptible under wet-dry cycles. In addition, we observed a reciprocal interaction between P. syringae and B. velezensis, where P. syringae inhibits B. velezensis under wet conditions. Our findings highlight the important role of hydration conditions in shaping bacterial interference competition, providing valuable insights into the microbial ecology of water-unsaturated surfaces, with implications for applications such as biological control of plant pathogens and mitigating antibiotic resistance.IMPORTANCEOur study reveals that hydration conditions, particularly wet-dry cycles, significantly influence antibiotic-mediated competition between bacterial species. We revealed that the effectiveness of antibiotics produced by Bacillus velezensis against two susceptible bacterial species: Xanthomonas and Pseudomonas varies based on these hydration conditions. Unlike traditional laboratory environments, many real-world habitats, such as soil, plant surfaces, and even animal skin, undergo frequent wet-dry cycles. These conditions affect bacterial competition dynamics and outcomes, with wet-dry cycles providing increased protection for some bacteria while making others more susceptible. Our findings highlight the importance of considering environmental hydration when studying microbial interactions and developing biological control strategies. This research has important implications for improving agricultural practices and understanding natural microbial ecosystems.},
}
@article {pmid39711055,
year = {2024},
author = {Mant, D and Orevi, T and Kashtan, N},
title = {Impact of micro-habitat fragmentation on microbial population growth dynamics.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae256},
pmid = {39711055},
issn = {1751-7370},
abstract = {Microbial communities thrive in virtually every habitat on Earth and are essential to the function of diverse ecosystems. Most microbial habitats are not spatially continuous and well-mixed, but rather composed, at the microscale, of many isolated or semi-isolated local patches of different sizes, resulting in partitioning of microbial populations into discrete local populations. The impact of this spatial fragmentation on population dynamics is not well-understood. Here, we study how such variably sized micro-habitat patches affect the growth dynamics of clonal microbial populations and how dynamics in individual patches dictate those of the metapopulation. To investigate this, we developed the μ-SPLASH, an ecology-on-a-chip platform, enabling the culture of microbes in microscopic landscapes comprised of thousands of microdroplets, with a wide range of sizes. Using the μ-SPLASH, we cultured the model bacteria E. coli and based on time-lapse microscopy, analyzed the population dynamics within thousands of individual droplets. Our results reveal that growth curves substantially vary with droplet size. Although growth rates generally increase with drop size, reproductive success and the time to approach carrying capacity, display non-monotonic patterns. Combining μ-SPLASH experiments with computational modeling, we show that these patterns result from both stochastic and deterministic processes, and demonstrate the roles of initial population density, patchiness, and patch size distribution in dictating the local and metapopulation dynamics. This study reveals basic principles that elucidate the effects of habitat fragmentation and population partitioning on microbial population dynamics. These insights deepen our understanding of natural microbial communities and have significant implications for microbiome engineering.},
}
@article {pmid39710833,
year = {2024},
author = {Bullington, JA and Langenfeld, K and Phaneuf, JR and Boehm, AB and Francis, CA},
title = {Microbial Community of a Sandy Beach Subterranean Estuary is Spatially Heterogeneous and Impacted by Winter Waves.},
journal = {Environmental microbiology},
volume = {26},
number = {12},
pages = {e70009},
doi = {10.1111/1462-2920.70009},
pmid = {39710833},
issn = {1462-2920},
support = {2024504//National Science Foundation, Understanding the Rules of Life: Microbiome Theory and Mechanisms (URoL:MTM)/ ; //Stanford McGee and Levorsen Research Grant/ ; //ARCO Stanford Graduate Fellowship/ ; },
mesh = {*Microbiota/genetics ; *Estuaries ; *Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Bathing Beaches ; California ; *Seawater/microbiology ; Archaea/genetics/classification ; Phylogeny ; },
abstract = {Subterranean estuaries (STEs) are critical ecosystems at the interface of meteoric groundwater and subsurface seawater that are threatened by sea level rise. To characterize the influence of tides and waves on the STE microbial community, we collected porewater samples from a high-energy beach STE at Stinson Beach, California, USA, over the two-week neap-spring tidal transition during both a wet and dry season. The microbial community, analyzed by 16S rRNA gene (V4) amplicon sequencing, clustered according to consistent physicochemical features found within STEs. The porewater community harbored relatively abundant Proteobacteria, Verrucomicrobiota, and Bacteroidota, as well as members of the archaeal DPANN superphylum and bacterial Candidate Phyla Radiation (CPR). Tidal conditions were not associated with microbial community composition; however, a wave overtopping event significantly impacted the beach microbiome. As a baseline for environmental change, our results elucidate the unique dynamics of a STE microbiome with unprecedented temporal resolution, highlighting the transport of cellular material through beach porewater due to waves.},
}
@article {pmid39710772,
year = {2024},
author = {Ali, A and Zhong, X and Wang, Q and Xu, H},
title = {Use of a broad β-diversity for bioassessment of salinity stress on community homogeneity in marine environments.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39710772},
issn = {1614-7499},
support = {31672308//The Natural Science Foundation of China/ ; 41076089//The Natural Science Foundation of China/ ; ZR2022QD065//Youth Project of the Natural Science Foundation of Shandong Province, China/ ; },
abstract = {To determine the feasibility of β-diversity measures to evaluate the impact of salinity stress on community homogeneity in marine environments, a 1-month bioassay was conducted using the protozoan assemblage as the test community. The test samples were collected using the slide method in coastal waters of the Yellow Sea, northern China. Five treatments were designed according to a salinity gradient of 9, 19, 29, 39, and 49 PSU. The homogeneity of the test community showed significant variability in both composition and abundance patterns among five treatments. The multivariate dispersion measure on compositional data was linearly associated with the salinity stress compared to those on abundance alone or in combination with occurrence. The traditional β-diversity index represented a different behavior from that of the multivariate dispersion measures. These findings suggest that the composition-based multivariate dispersion may be a useful tool to evaluate the global salinity stress on community homogeneity in marine ecosystems.},
}
@article {pmid39709274,
year = {2024},
author = {Kerkar, AU and Sutherland, KR and Thompson, AW},
title = {Non-viral predators of marine picocyanobacteria.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.11.010},
pmid = {39709274},
issn = {1878-4380},
abstract = {The Earth's most abundant photosynthetic cells, the picocyanobacteria - Prochlorococcus and Synechococcus - play a fundamental global role in aquatic ecosystems. The success of these picocyanobacteria is interpreted through a cross-scale systems framework that integrates bottom-up controls on growth (e.g., nutrients and light), diversity, and the selective pressures and response to predation. While viral predators are well studied and experimentally tractable, the diverse non-viral predators of picocyanobacteria are disconnected from this framework and experimentally challenging, leaving a major gap in understanding the picocyanobacteria. This review presents existing research on non-viral picocyanobacterial predators and promising research frontiers that will expand knowledge of the ecology and evolution of these crucial microorganisms.},
}
@article {pmid39708482,
year = {2024},
author = {Zhao, H and Hu, X and Guan, S and Cai, J and Li, W and Zhang, D and Feng, Y and Zhu, W and Marzorati, M and Li, B and Zhang, X and Tian, J},
title = {Capilliposide A alleviates DSS-induced colitis by regulating the intestinal flora and its metabolites of origin.},
journal = {International immunopharmacology},
volume = {146},
number = {},
pages = {113858},
doi = {10.1016/j.intimp.2024.113858},
pmid = {39708482},
issn = {1878-1705},
abstract = {Ulcerative colitis is a chronic idiopathic inflammatory disease that impacts the mucous membrane of the colon. Lately, the incidence and prevalence of UC has been increasing globally. However, there are significant side effects of existing drugs for UC intervention. Accordingly, there is a pressing demand to explore novel bioactive substances for addressing UC. Natural product saponins have attracted great attention due to their obvious anti-colitis potential. Capilliposide A is a triterpenoid saponin, which is derived from Lysimachia capillipes Hemsl., exhibits good anti-inflammatory activity. Nonetheless, the impact and mechanism of CPS-A on ulcerative colitis remains obscure. This study aimed to investigate the therapeutic effects of CPS-A on the dextran sulphate sodium induced colitis mouse model and explore its mechanism. The efficacy and safety of CPS-A were evaluated in a well-established dextran sodium sulfate (DSS)-induced colitis mice model. Disease progression was monitored via clinical symptoms, histopathological examination, quantification of inflammatory cytokines, and epithelial barrier function evaluation. Plasma samples and intestinal contents were collected for non-targeted metabolomics and 16sRNA sequencing, respectively, to jointly evaluate the mechanism of action. CPS-A alleviated colitis by improving weight, Disease activity index score, histopathology, goblet cell, colon length, and expression of inflammatory factors. Moreover, CPS-A effectively preserved the integrity of the intestinal barrier by enhancing the expression of tight junction proteins and mucin in the colonic tissue of mice. Furthermore, CPS-A exerted a regulatory effect on the composition of the gut microbiota, promoting bacterial richness and diversity. It not only suppressed the abundance of detrimental bacteria while enhancing the abundance of advantageous bacteria, but also modulated the metabolites derived from the intestinal flora. Importantly, correlation analysis shows that these indicators are highly correlated. This study revealed that CPS-A exhibits a favorable therapeutic efficacy against colitis, primarily attributed to its ability to modulate the gut microbiota their associated metabolites as the key mechanisms of action.},
}
@article {pmid39708146,
year = {2024},
author = {Zhao, L and Zhang, S and Li, J and Zhang, C and Xiao, R and Bai, X and Xu, H and Zhang, F},
title = {Unveiling Diversity and Function: Venom-Associated Microbes in Two Spiders, Heteropoda venatoria and Chilobrachys guangxiensis.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {156},
pmid = {39708146},
issn = {1432-184X},
mesh = {Animals ; *Spiders/microbiology/physiology ; *Spider Venoms ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Apoptosis ; Symbiosis ; Humans ; Cell Line, Tumor ; High-Throughput Nucleotide Sequencing ; Anti-Inflammatory Agents/pharmacology ; },
abstract = {Spiders are natural predators of agricultural pests, primarily due to the potent venom in their venom glands. Spider venom is compositionally complex and holds research value. This study analyzes the diversity of symbiotic bacteria in spider venom glands and venom, as well as the biological activity of culturable symbiotic bacteria. Focusing on the venom glands and venom of Heteropoda venatoria and Chilobrachys guangxiensis, we identified a diverse array of microorganisms. High-throughput sequencing detected 2151 amplicon sequence variants (ASVs), spanning 31 phyla, 75 classes, and 617 genera. A total of 125 strains of cultivable bacteria were isolated. Using the Oxford cup method, crude extracts from 46 of these strains exhibited inhibitory effects against at least one indicator bacterium. MTT (Thiazolyl blue) assays revealed that the crude extracts from 43 strains had inhibitory effects on tumor cell line MGC-803 growth. Additionally, DAPI (4',6-diamidino-2'-phenylindole) staining and flow cytometry were employed to detect cell apoptosis. The anti-inflammatory activity of nine bacterial strains was assessed using a NO assay kit and enzyme-linked immunosorbent assay (ELISA). This study further investigated the biological activity of venom, exploring the relationship between the venom and the functional activity of venom-associated bacteria.},
}
@article {pmid39708144,
year = {2024},
author = {Quevedo-Caraballo, S and Roldán, A and Álvarez-Pérez, S},
title = {Demethylation Inhibitor Fungicides Have a Significantly Detrimental Impact on Population Growth and Composition of Nectar Microbial Communities.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {160},
pmid = {39708144},
issn = {1432-184X},
support = {PIPF-2023/ECO-29442//Consejer&#xed;a de Educaci&#xf3;n, Ciencia y Universidades, Comunidad de Madrid/ ; RYC2018-023847-I, CNS2022-135237//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {*Fungicides, Industrial/pharmacology ; *Plant Nectar ; *Microbiota/drug effects ; Bacteria/classification/drug effects/isolation &amp; purification/genetics ; Demethylation ; Fungi/drug effects/classification/isolation &amp; purification ; Metschnikowia/drug effects ; Flowers/microbiology/growth &amp; development ; },
abstract = {Demethylation inhibitor (DMI) fungicides are a mainstay of modern agriculture due to their widespread use for crop protection against plant-pathogenic fungi. However, DMI residues can disperse and persist in the environment, potentially affecting non-target fungi. Previous research has demonstrated that DMIs and other fungicides inhibit yeast growth in floral nectar microbial communities and decrease fungal richness and diversity of exposed flowers with no apparent effect on bacteria. Nevertheless, the effect of DMIs on the population growth of different species of nectar inhabitants and the dynamics of these microbial communities remains understudied. To address these issues, in this study we created synthetic microbial communities including yeasts (Metschnikowia reukaufii and Metschnikowia pulcherrima) and bacteria (Rosenbergiella epipactidis and Comamonas sp.) and propagated them in culture media containing different DMIs (imazalil, propiconazole, and prothioconazole) at different doses or no fungicide. Our results showed that DMIs have a significant impact on some of the most common microbial inhabitants of floral nectar by favoring the growth of bacteria over yeasts. Furthermore, habitat generalists such as M. pulcherrima and Comamonas sp. were more impacted by the presence of fungicides than the nectar specialists M. reukaufii and R. epipactidis, especially upon dispersal across habitat patches. Future research should determine if the patterns observed in the present study hold true for other species of nectar microbes and explore the interaction between growth limitation due to fungicide presence, dispersal limitation, and other mechanisms involved in community assembly in floral nectar.},
}
@article {pmid39708139,
year = {2024},
author = {Zhao, Z and Liu, S and Jiang, S and Zhang, D and Sha, Z},
title = {Diversity and Potential Metabolic Characteristics of Culturable Copiotrophic Bacteria That Can Grow on Low-Nutrient Medium in Zhenbei Seamount in the South China Sea.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {157},
pmid = {39708139},
issn = {1432-184X},
support = {LSKJ202203102//the Science and Technology Innovation Project of Laoshan Laboratory/ ; XDB42000000//the Strategic Priority Research Program of Chinese Academy of Sciences/ ; 42221005//the NSFC Innovative Group Grant/ ; 42376143//the National Natural Science Foundation of China/ ; },
mesh = {*Seawater/microbiology ; China ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification/growth &amp; development ; Gammaproteobacteria/metabolism/genetics/isolation &amp; purification/classification/growth &amp; development ; Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Nitrates/metabolism ; Culture Media/chemistry ; Nutrients/metabolism ; Alphaproteobacteria/metabolism/genetics/isolation &amp; purification/classification/growth &amp; development ; Vibrio/metabolism/genetics/isolation &amp; purification/growth &amp; development/classification ; },
abstract = {Oligotrophs are predominant in nutrient-poor environments, but copiotrophic bacteria may tolerate conditions of low energy and can also survive and thrive in these nutrient-limited conditions. In the present study, we isolated 648 strains using a dilution plating method after enrichment for low-nutrient conditions. We collected 150 seawater samples at 21 stations in different parts of the water column at the Zhenbei Seamount in the South China Sea. The 648 isolated copiotrophic strains that could grow on low-nutrient medium were in 21 genera and 42 species. A total of 99.4% (644/648) of the bacteria were in the phylum Pseudomonadota, with 73.3% (472/644) in the class Gammaproteobacteria and 26.7% (172/644) in the class Alphaproteobacteria. Among the 42 representative isolates, Pseudoalteromonas arabiensis, Roseibium aggregatum, and Vibrio neocaledonicus were present in all layers of seawater and at almost all of the stations. Almost half of these species (20/42) contained genes that performed nitrate reduction, with confirmation by nitrate reduction testing. These isolates also contained genes that functioned in sulfur metabolism, including sulfate reduction, thiosulfate oxidation, thiosulfate disproportionation, and dimethylsulfoniopropionate degradation. GH23, CBM50, GT4, GT2, and GT51 were the main carbohydrate-active enzymes (CAZymes), and these five enzymes were present in all or almost all of the isolated strains. The most abundant classes of CAZymes were those associated with the degradation of chitin, starch, and cellulose. Collectively, our study of marine copiotrophic bacteria capable of growing on low-nutrient medium demonstrated the diversity of these species and their potential metabolic characteristics.},
}
@article {pmid39708121,
year = {2024},
author = {Grisnik, M and Walker, DM},
title = {Bat Cutaneous Microbial Assemblage Functional Redundancy Across a Host-Mediated Disturbance.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {161},
pmid = {39708121},
issn = {1432-184X},
support = {32801-00803//Tennessee Wildlife Resources Agency,United States/ ; },
mesh = {*Chiroptera/microbiology ; Animals ; *Seasons ; *Bacteria/genetics/classification/isolation &amp; purification ; *Skin/microbiology ; *Microbiota ; Ascomycota/genetics/physiology ; Ecosystem ; },
abstract = {Understanding the processes and factors that influence the structure of host-associated microbial assemblages has been a major area of research as these assemblages play a role in host defense against pathogens. Previous work has found that bacterial taxa within bat cutaneous microbial assemblages have antifungal capabilities against the emerging fungal pathogen, Pseudogymnoascus destructans. However, our understanding of natural fluctuations in these cutaneous microbial assemblages over time due to shifts in host habitat is lacking. The objective of this work was to understand how the taxonomic and functional bat cutaneous microbial assemblage responds to seasonal shifts in host habitat. We hypothesized that at the community level, there will be turnover in taxonomic structure but functional redundancy across seasons. On a finer scale, we hypothesized that there will be differences in the relative abundance of functional genes that code for select pathways across seasons. Results showed that, on a broad scale, the bat cutaneous microbial assemblage is seasonally taxonomically dynamic but functionally redundant. Additionally, although there was almost complete taxonomic turnover between winter and summer bat microbial assemblages, there was no difference in assemblage structure across winters. This functional redundancy was also observed at finer scales, with no differences in the abundance of genes within pathways of hypothesized importance across seasons or winters. Taken together, results suggest species sorting mechanisms correlated with shifts in host habitat use, drive taxonomic but not functional host-associated cutaneous microbial community assembly.},
}
@article {pmid39708106,
year = {2024},
author = {Singh, S and Singh, AK and Pradhan, B and Tripathi, S and Kumar, KS and Chand, S and Rout, PR and Shahid, MK},
title = {Harnessing Trichoderma Mycoparasitism as a Tool in the Management of Soil Dwelling Plant Pathogens.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {158},
pmid = {39708106},
issn = {1432-184X},
mesh = {*Trichoderma/physiology ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; Pest Control, Biological/methods ; Agriculture/methods ; Plants/microbiology ; Biological Control Agents ; Soil/chemistry ; },
abstract = {Maintaining and enhancing agricultural productivity for food security while preserving the ecology and environment from the harmful effects of toxicants is the main challenge in modern monoculture farming systems. Microbial biological agents can be a promising substitute for traditional synthetic pesticides to manage plant diseases. Trichoderma spp. are soil-dwelling ascomycete fungi and are common biocontrol agents against diverse phytopathogens. Trichoderma-based biocontrol techniques can regulate and control soil-borne plant diseases through mechanisms such as mycoparasitism, the production of antibiotics and hydrolytic enzymes, rhizo-sphere competence, the effective competition for available resources, induction of plant resistance and facilitation of plant growth. Numerous secondary metabolites produced by Trichoderma spp. are reported to prevent the development of soil-borne plant disease. Thus, Trichoderma spp. may have direct and indirect biological impacts on the targeted plant pathogens. Furthermore, this review discusses the convenient implications and challenges of applying Trichoderma-based strategies in agricultural settings. Overall, the assessment underscores the potential of Trichoderma as a sustainable and effective tool for mitigating soil-borne pathogens, highlighting avenues for future research and applications.},
}
@article {pmid39708073,
year = {2024},
author = {Han, GH and Yu, J and Kang, MJ and Park, MJ and Noh, CH and Kim, YJ and Kwon, KK},
title = {Correction to: Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {159},
doi = {10.1007/s00248-024-02478-w},
pmid = {39708073},
issn = {1432-184X},
}
@article {pmid39708062,
year = {2024},
author = {Nonthijun, P and Tanunchai, B and Schroeter, SA and Wahdan, SFM and Alves, EG and Hilke, I and Buscot, F and Schulze, ED and Disayathanoowat, T and Purahong, W and Noll, M},
title = {Feels Like Home: A Biobased and Biodegradable Plastic Offers a Novel Habitat for Diverse Plant Pathogenic Fungi in Temperate Forest Ecosystems.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {155},
pmid = {39708062},
issn = {1432-184X},
mesh = {*Forests ; *Fungi/genetics/metabolism/classification ; *Biodegradable Plastics/metabolism ; *Trees/microbiology ; Soil Microbiology ; Plant Diseases/microbiology ; Biodegradation, Environmental ; Ecosystem ; Soil/chemistry ; Plant Leaves/microbiology ; },
abstract = {Poly(butylene succinate-co-adipate) (PBSA), a biodegradable plastic, is significantly colonized and degraded by soil microbes under natural field conditions, especially by fungal plant pathogens, raising concerns about potential economic losses. This study hypothesizes that the degradation of biodegradable plastics may increase the presence and abundance of plant pathogens by serving as an additional carbon source, ultimately posing a risk to forest ecosystems. We investigated (i) fungal plant pathogens during the exposure of PBSA in European broadleaved and coniferous forests (two forest types), with a specific focus on potential risk to tree health, and (ii) the response of such fungi to environmental factors, including tree species, soil pH, nutrient availability, moisture content, and the physicochemical properties of leaf litter layer. Next-generation sequencing (NGS) revealed that PBSA harbored a total of 318 fungal plant pathogenic amplicon sequence variants (ASVs) belonging to 108 genera. Among the identified genera (Alternaria, Nectria, Phoma, Lophodermium, and Phacidium), some species have been reported as causative agents of tree diseases. Plenodomus was present in high relative abundances on PBSA, which have not previously been associated with disease in broadleaved and coniferous forests. Furthermore, the highest number of fungal plant pathogens were detected at 200 days of PBSA exposure (112 and 99 fungal plant pathogenic ASV on PBSA degraded under Q. robur and F. sylvatic-dominated forest, respectively), which was double compared mature leaves and needles from the same forest sites. These findings suggest that PBSA attracts fungal plant pathogens in forests as an additional carbon source, potentially leading to increased disease outbreaks and disrupting the stability of forest ecosystems. The fungal plant pathogenic community compositions were mainly shaped by forest type, PBSA exposure time, site locations, leaf litter layer water content, and N:P ratio from leaf litter layer in both forest types. This study provides valuable insights into the potential risks posed by biodegradable plastic degradation in forests after 200 and 400 days of exposure, respectively. Further comprehensive evaluations of their effects on tree health and ecosystems, ideally on a long-term basis, are needed. These evaluations should include integrating microbial investigation, soil health monitoring, and ecosystem interaction assessments. Nevertheless, it should be noted that our interpretation of plant pathogens is solely based on high-throughput sequencing, bioinformatics, and annotation tools.},
}
@article {pmid39703713,
year = {2024},
author = {Sheng, Y and Zeng, X and Zhao, L and Li, Y},
title = {Editorial: Microbial involvement in biogeochemical cycling and contaminant transformations at land-water ecotones.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1525521},
pmid = {39703713},
issn = {1664-302X},
}
@article {pmid39701829,
year = {2024},
author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM},
title = {An interdisciplinary perspective of the built-environment microbiome.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae166},
pmid = {39701829},
issn = {1574-6941},
abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.},
}
@article {pmid39701529,
year = {2024},
author = {Firkins, JL and Henderson, EL and Duan, H and Pope, PB},
title = {International Symposium on Ruminant Physiology: Current perspective on rumen microbial ecology to improve fiber digestibility.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25863},
pmid = {39701529},
issn = {1525-3198},
abstract = {Although cellulose has received the most attention, further research is needed for a complete comprehension of other fiber components in forage and nonforage fiber sources corresponding with the array of enzymes needed for depolymerization and resulting fermentation of sugars. The carbohydrate-active enzymes (CAZymes) have been described in detail herein, although new information will no doubt accumulate in the future. Known CAZymes are attributed to taxa that are easily detected via 16S rRNA gene profiling techniques, but such approaches have limitations. We describe how closely related species or strains expand into different niches depending on diet and the dynamic availability of remaining fibrous substrates. Moreover, expression of CAZymes and other enzymes such as in fermentation pathways can shift among strains and even within strains over time of incubation. We describe unique fibrolytic components of bacteria, protozoa, and fungi while emphasizing the development of consortia that efficiently increase neutral detergent fiber degradability (NDFD). For example, more powerful genome-centric functional omics approaches combined with expanded bioinformatics and network analyses are needed to expand our current understanding of ruminal function and the bottlenecks that lead to among-study variation in NDFD. Specific examples highlighted include our lack of fundamental understanding why starch limits NDFD, whereas moderate inclusion of rumen-degraded protein, certain supplemental fatty acids (especially palmitic), and supplemental sugars sometimes stimulates NDFD. Current and future research must uncover deeper complexity in the rumen microbiome through a combination of approaches described herein to be followed by validation using novel cultivation studies and, ultimately, NDFD measured in vivo for integration with ruminant productivity traits.},
}
@article {pmid39699229,
year = {2024},
author = {Anuforo, PC and Würz, B and Wick, LY and Kallies, R},
title = {Draft genome sequences of Pseudomonas chengduensis strain BW1 and Sphingobium sp. strain MK2 isolated from oil sands process-affected water.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0067724},
doi = {10.1128/mra.00677-24},
pmid = {39699229},
issn = {2576-098X},
abstract = {Draft genomes of two phenanthrene-degrading bacterial isolates from oil sands process-affected water (OSPW) in Alberta, Canada were sequenced. Both isolates grew in close association on agar plates and were difficult to obtain axenically. They represent novel Pseudomonas chengduensis and Sphingobium sp. strains with genomes of 5.5 and 4.1 Mbases length, respectively.},
}
@article {pmid39699221,
year = {2024},
author = {Lustermans, JJM and Sereika, M and Burdorf, LDW and Albertsen, M and Schramm, A and Marshall, IPG},
title = {Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0125924},
doi = {10.1128/msystems.01259-24},
pmid = {39699221},
issn = {2379-5077},
abstract = {UNLABELLED: Cable bacteria, filamentous sulfide oxidizers that live in sulfidic sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remain mostly uninvestigated. Here, we elucidate the electron exchange capabilities of the bacterial community by coupling metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria over 155 days. We identified candidate flocking bacteria as bacteria containing genes for motility and extracellular electron transfer including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Based on these criteria, 22 MAGs were from candidate flockers, which constituted 21.4% of all 103 MAGs. Of the candidate flocking bacteria, 42.1% expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of metabolically versatile taxonomic groups: 18 genera spread across nine phyla. Our data suggest that cable bacteria in freshwater sediments engage in electric relationships with diverse exoelectrogenic microbes. This community, found in deeper anoxic sediment layers, is involved in sulfur, carbon, and metal (in particular Fe) cycling and indirectly utilizes oxygen here by extracellularly transferring electrons to cable bacteria.<br><br>IMPORTANCE: Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor "shortcut" to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.},
}
@article {pmid39698295,
year = {2024},
author = {Bovio-Winkler, P and Cabezas, A and Etchebehere, C},
title = {Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae050},
pmid = {39698295},
issn = {2730-6151},
abstract = {The phylum Chloroflexota has been found to exhibit high abundance in the microbial communities from wastewater treatment plants (WWTPs) in both aerobic and anaerobic systems. However, its metabolic role has not been fully explored due to the lack of cultured isolates. To address this gap, we use publicly available metagenome datasets from both activated sludge (AS) and methanogenic (MET) full-scale wastewater treatment reactors to assembled genomes. Using this strategy, 264 dereplicated, medium- and high-quality metagenome-assembled genomes (MAGs) classified within Chloroflexota were obtained. Taxonomic classification revealed that AS and MET reactors harbored distinct Chloroflexota families. Nonetheless, the majority of the annotated MAGs (166 MAGs with >85% completeness and < 5% contamination) shared most of the metabolic potential features, including the ability to degrade simple sugars and complex polysaccharides, fatty acids and amino acids, as well as perform fermentation of different products. While Chloroflexota MAGs from MET reactors showed the potential for strict fermentation, MAGs from AS harbored the potential for facultatively aerobic metabolism. Metabolic reconstruction of Chloroflexota members from AS unveiled their versatile metabolism and suggested a primary role in hydrolysis, carbon removal and involvement in nitrogen cycling, thus establishing them as fundamental components of the ecosystem. Microbial reference genomes are essential resources for understanding the potential functional role of uncultured organisms in WWTPs. Our study provides a comprehensive genome catalog of Chloroflexota for future analyses aimed at elucidating their role in these ecosystems.},
}
@article {pmid39697668,
year = {2024},
author = {Roy, A and Ghosh, A and Bhadury, P},
title = {Delving deep into the draft genome of Mangrovibacter sp. SLW1, isolated from Sundarbans mangrove.},
journal = {Access microbiology},
volume = {6},
number = {8},
pages = {},
pmid = {39697668},
issn = {2516-8290},
abstract = {Mangrovibacter sp. SLW1, a Gram-negative, aerobic, motile bacterium, was isolated from mangrove litterfall in Sundarbans mangrove. The draft genome is 5.5 Mbp in size with 49.45 mol% guanine-cytosine (GC) content. The linear chromosome of the bacterium consists of 27 contigs with 7339 coding sequences. The detailed in silico analyses of the genome of Mangrovibacter sp. SLW1 provide information on ecological adaptation. The genome is a reservoir for multiple heavy metals and metalloid resistance gene clusters as well as exhibit metabolic capabilities for utilization of a wide range of carbohydrates. It also encodes for tris-catecholate siderophore and can regulate uptake of iron thereby may influence plant growth such as mangrove vegetation.},
}
@article {pmid39695543,
year = {2024},
author = {Qin, K and Qing, J and Wang, Q and Li, Y},
title = {Epidemiological shifts in chronic kidney disease: a 30-year global and regional assessment.},
journal = {BMC public health},
volume = {24},
number = {1},
pages = {3519},
pmid = {39695543},
issn = {1471-2458},
support = {82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; },
mesh = {Humans ; *Renal Insufficiency, Chronic/epidemiology/mortality ; Male ; Incidence ; *Global Health/statistics &amp; numerical data ; Female ; Middle Aged ; Adult ; Prevalence ; Aged ; *Global Burden of Disease ; Risk Factors ; Disability-Adjusted Life Years ; Adolescent ; Young Adult ; Quality-Adjusted Life Years ; },
abstract = {BACKGROUND: Chronic kidney disease (CKD) presents a growing global health challenge, with significant variability in disease burden across different regions and countries. This study aimed to analyze the trends in incidence, prevalence, mortality, and disability-adjusted life years (DALYs) for CKD from 1990 to 2019, utilizing data from the Global Burden of Disease Study.<br><br>METHODS: We conducted an in-depth study on the global and age-standardized incidence, prevalence, mortality, and DALYs of CKD, and assessed trends over a 30-year period. Additionally, we explored the associations between healthcare access and quality (HAQ), the Socio-Demographic Index (SDI), and CKD. Furthermore, we conducted a detailed analysis of six risk factors closely related to CKD, and based on these findings, provided strong evidence for enhancing the management of CKD.<br><br>RESULTS: In 2019, there were 18,986,903 cases of CKD, with an average annual percent change (AAPC) of 1.82 (95% CI&#x2009;=&#x2009;1.8 to 1.82) in incidence since 1990. The age-standardized incidence rate increased from 192.45 per 100,000 in 1990 to 233.65 per 100,000 in 2019. Prevalence also rose, with a total of 69,729,430 cases in 2019 and an AAPC of 1.19 (95% CI&#x2009;=&#x2009;1.19 to 1.2). Mortality and DALYs have increased correspondingly, with the mortality rate reaching 18.29 per 100,000 and total DALYs at 41,538,592 in 2019. The analysis showed that higher HAQ levels are associated with better outcomes in terms of lower mortality and DALY rates, whereas lower HAQ levels correlate with poorer outcomes. In addition, high fasting plasma glucose and high systolic blood pressure are the main contributors to CKD-related deaths, with their population attributable fraction&#xa0;(PAF) significantly decreasing as the SDI decreases.<br><br>CONCLUSION: The burden of CKD has significantly increased over the past three decades, influenced by demographic changes and variations in healthcare quality and access. Effective public health strategies and improvements in healthcare delivery are needed to address the disparities in CKD outcomes globally.},
}
@article {pmid39695352,
year = {2025},
author = {Moore, M and Whittington, HD and Knickmeyer, R and Azcarate-Peril, MA and Bruno-Bárcena, JM},
title = {Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2440120},
doi = {10.1080/19490976.2024.2440120},
pmid = {39695352},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Bacteria/metabolism/classification/isolation &amp; purification/genetics ; Feces/microbiology ; Lactose/metabolism ; Dietary Fiber/metabolism ; Oligosaccharides/metabolism ; Amino Sugars ; },
abstract = {Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL[-1]) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.},
}
@article {pmid39694113,
year = {2024},
author = {Van Peteghem, L and Matassa, S and Sakarika, M},
title = {Fueling the protein transition: Can waste-derived ethanol enable efficient and high-quality microbial protein production?.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131990},
doi = {10.1016/j.biortech.2024.131990},
pmid = {39694113},
issn = {1873-2976},
abstract = {Meeting the protein needs of a growing population will require significant resources. In this context, microbial protein (MP) offers a nutritious and versatile protein source from recovered resources. This meta-analysis of over 100 studies examines the efficiency and nutritional quality of MP production using ethanol. Ethanol, a feedstock derived from CO2 and biological waste, is used by various microorganisms, and has an established role in the food sector. Results show that ethanol-based MP production is technically feasible for food applications, reaching biomass concentrations of 14-230 g/L and productivities of 11-13 g/L/h. The protein content of MP correlates with productivity, and the nutritional quality of ethanol-grown MP matches common sources like pork and tofu. Lastly, operational choices affect the techno-economic feasibility of using waste-derived ethanol and other recovered resources. This meta-analysis highlights the potential of ethanol-grown MP, though further research is needed to close existing knowledge gaps.},
}
@article {pmid39693383,
year = {2024},
author = {Arrington, EC and Tarn, J and Kivenson, V and Nunn, BL and Liu, RM and Paul, BG and Valentine, DL},
title = {Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae247},
pmid = {39693383},
issn = {1751-7370},
abstract = {Aqueous-soluble hydrocarbons dissolve into the ocean's interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partially partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning of two free-living Cycloclasticus strains recovered from seawater incubations with n-pentane and distinguish them as an open ocean variant and a seep-proximal variant, each with distinct capabilities for hydrocarbon catabolism. Comparative metagenomic analysis indicates the variant more frequently observed further from natural seeps encodes more general pathways for hydrocarbon consumption, including short-chain alkanes, aromatics, and long-chain alkanes, and also possesses redox versatility in the form of respiratory nitrate reduction and thiosulfate oxidation; in contrast, the seep variant specializes in short-chain alkanes and relies strictly on oxygen as the terminal electron acceptor. Both variants observed in our work were dominant ecotypes of Cycloclasticus observed during the Deepwater Horizon disaster, a conclusion supported by 16S rRNA gene analysis and read-recruitment of sequences collected from the submerged oil plume during active flow. A comparative genomic analysis of Cycloclasticus across various ecosystems suggests distinct strategies for hydrocarbon transformations among each clade. Our findings suggest Cycloclasticus is a versatile and opportunistic consumer of hydrocarbons and may have a greater role in the cycling of sulfur and nitrogen, thus contributing broad ecological impact to various ecosystems globally.},
}
@article {pmid39693347,
year = {2024},
author = {Sun, X and Buchanan, PJ and Zhang, IH and San Roman, M and Babbin, AR and Zakem, EJ},
title = {Ecological dynamics explain modular denitrification in the ocean.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {52},
pages = {e2417421121},
doi = {10.1073/pnas.2417421121},
pmid = {39693347},
issn = {1091-6490},
support = {LS-FMME-00871981//Simons Foundation (SF)/ ; OCE-2138890 and OCE-2142998//NSF (NSF)/ ; N/A//MIT School of Science MathWorks Science Fellowship/ ; 2125142//NSF (NSF)/ ; },
mesh = {*Denitrification/physiology ; *Oceans and Seas ; *Ecosystem ; Seawater/microbiology/chemistry ; Nitrogen/metabolism ; Nitrous Oxide/metabolism ; Oxygen/metabolism ; Bacteria/metabolism ; },
abstract = {Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO3[-]→NO2[-]→NO→N2O→N2), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain subsets ("modules") of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when organic matter (OM) limits growth, which explains the viability of populations respiring NO2[-] and N2O in a NO3[-]-filled ocean. Results predict denitrifier community succession along environmental gradients: Pathway length increases as the limiting substrate shifts from OM to N, suggesting a niche for the short NO3[-]→NO2[-] module in free-living, OM-limited communities, and for the complete pathway in organic particle-associated communities, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3[-]→NO2[-] module. Results also capture observations that NO3[-] is the dominant source of N2O. Our framework advances the mechanistic understanding of the relationship between microbial ecology and N loss in the ocean and can be extended to other processes and environments.},
}
@article {pmid39692747,
year = {2024},
author = {Wallace, EJ and O'Dwyer, J and Dolan, EB and Burke, LP and Wylie, R and Bellavia, G and Straino, S and Cianfarani, F and Ciotti, G and Serini, S and Calviello, G and Roche, ET and Mitra, T and Duffy, GP},
title = {Actuation-Mediated Compression of a Mechanoresponsive Hydrogel by Soft Robotics to Control Release of Therapeutic Proteins.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2401744},
doi = {10.1002/advs.202401744},
pmid = {39692747},
issn = {2198-3844},
support = {713690//Horizon 2020/ ; 812865//Horizon 2020/ ; GOIPD/2020/157//Irish Research Council/ ; 13/RC/2073/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {Therapeutic proteins, the fastest growing class of pharmaceuticals, are subject to rapid proteolytic degradation in vivo, rendering them inactive. Sophisticated drug delivery systems that maintain protein stability, prolong therapeutic effects, and reduce administration frequency are urgently required. Herein, a mechanoresponsive hydrogel is developed contained within a soft robotic drug delivery (SRDD) device. In a step-change from previously reported systems, pneumatic actuation of this system releases the cationic therapeutic protein Vascular Endothelial Growth Factor (VEGF) in a bioactive form which is required for therapeutic angiogenesis, the growth of new blood vessels, in numerous clinical conditions. The ability of the SRDD device to release bioactive VEGF in a spatiotemporal manner from the hydrogel is tested in diabetic rats - a model in which angiogenesis is difficult to stimulate. Daily actuation of the SRDD device in the diabetic rat model significantly increased cluster of differentiation 31+ (CD31+) blood vessel number (p = 0.0335) and the diameter of alpha-smooth muscle actin+ (α-SMA+) blood vessels (p = 0.0025) compared to passive release of VEGF from non-actuated devices. The SRDD device combined with the mechanoresponsive hydrogel offers the potential to deliver an array of bioactive therapeutics in a spatiotemporal manner to mimic their natural release in vivo.},
}
@article {pmid39691821,
year = {2024},
author = {Ghosh, A and Bhambra, SK and Chandrasekaran, R and Bhadury, P},
title = {Genome description of a potentially new species of Streptomyces isolated from the Indian Sundarbans mangrove.},
journal = {Access microbiology},
volume = {6},
number = {12},
pages = {},
pmid = {39691821},
issn = {2516-8290},
abstract = {A potentially new species of Streptomyces was isolated from station 177 of the Sundarbans Seasonal Time Series in the Indian Sundarbans mangrove. The isolate was cultured from a sediment sample on TYS medium of salinity 15. Sequencing and annotation of the 16S rRNA showed 100% identity against S. laurentii NPS17 against GenBank/ENA/DDBJ. Annotation of the whole genome against the GTDB database showed closest identity with S. terrae SKN60 and belongs to the same clade as S. roseicoloratus TRM44457T and S. laurentii ATCC 31255. The genome is ~7.2 Mb and has a G+C% of 73%. The average amino acid identity was 85.01% with S. roseicoloratus and 80.34% with S. roseolus. The assembly reflected the presence of all essential genes and had 19 biosynthetic gene clusters predicted.},
}
@article {pmid39689568,
year = {2024},
author = {Sumerta, IN and Ruan, X and Howell, K},
title = {The forgotten wine: Understanding palm wine fermentation and composition.},
journal = {International journal of food microbiology},
volume = {429},
number = {},
pages = {111022},
doi = {10.1016/j.ijfoodmicro.2024.111022},
pmid = {39689568},
issn = {1879-3460},
abstract = {Palm wine is an alcoholic beverage that has existed for centuries and has important economic and socio-culture values in many tropical and sub-tropical countries. Lesser known than other types of wines, palm wine is made by spontaneous fermentation of palm sap by naturally occurring microbial communities. The palm sap ecosystem has unique microbial composition and diversity, which determines the composition of the eventual wine and is likely affected by geographical distinctiveness. While these features are well understood in grape and rice wine, these features have not been understood in palm wine. Here, we gather information of microbial communities and metabolite profiles from published studies, covering a wide range of methodologies and regions to better understand the causal links between the principal microbial species and major metabolites of palm wine. We assessed palm wine quality across production regions and local practices to provide general characteristics of palm wine and identify specific regional information. These will provide better understandings to the function of microbial communities and metabolite diversity, the contribution of regional variations and to ensure product quality in this unique, yet overlooked, fermented beverage.},
}
@article {pmid39689238,
year = {2024},
author = {Yang, Q and Defoirdt, T},
title = {Weak selection for resistance to quorum sensing inhibition during multiple host infection cycles.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae251},
pmid = {39689238},
issn = {1751-7370},
abstract = {Quorum sensing inhibition is a promising novel approach to control bacterial infections. However, it is not clear whether quorum sensing inhibition will impose selective pressure for the spread of resistance against quorum sensing inhibition in pathogen populations. Previous research tried to answer this question by using synthetic growth media, and this revealed that whether or not resistance will spread completely depends on the environment in which it is studied. Therefore, the spread of resistance should be studied in the environment where it ultimately matters: in vivo during infection of a host. Here, using quorum sensing inhibitor-susceptible and -resistant mimics, we show that resistance to quorum sensing inhibition does not spread in host-associated populations of Vibrio campbellii during up to 35 cycles of infection and transmission if the initial frequency of the resistance is low in the pathogen population, whereas it further increases to 100% if it is already prevalent. However, even in the latter case, the resistance spreads at a slower pace than resistance to antibiotics spreads under the same conditions.},
}
@article {pmid39689178,
year = {2024},
author = {Li, G and Liu, T and Xie, W and Liu, Z and Li, H and Whalen, JK and Jousset, A and Wei, Z},
title = {Metabolites limiting predator growth wane with prey biodiversity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {52},
pages = {e2410210121},
doi = {10.1073/pnas.2410210121},
pmid = {39689178},
issn = {1091-6490},
support = {32201399//MOST | National Natural Science Foundation of China (NSFC)/ ; 32171640//MOST | National Natural Science Foundation of China (NSFC)/ ; KYQN2023048//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; 2022YFD1500302//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Animals ; *Biodiversity ; *Nematoda/physiology ; *Food Chain ; *Predatory Behavior/physiology ; Microbiota/physiology ; Bacteria/metabolism/classification ; Soil Microbiology ; },
abstract = {Predator-prey interactions are a major driver of microbiome dynamics, but remain difficult to predict. While several prey traits potentially impact resistance to predation, their effects in a multispecies context remain unclear. Here, we leverage synthetic bacterial communities of varying complexity to identify traits driving palatability for nematodes, a main consumer of bacteria in soil. We assessed trophic interactions between four nematode species and 122 bacterial isolates, across a gradient of prey biodiversity ranging from single species to 50 species. Nematode size, a proxy for prey palatability, varied strongly with prey community composition and could be predicted by metabolic and morphological properties of the prey. However, the influence of prey traits on predators depended on biodiversity. Secondary metabolites drove palatability in monoculture, but this effect vanished under increasing prey biodiversity, where prey size became the dominant predictors of nematode size. Although idiosyncratic properties are often emphasized in the literatures, our results suggest that in biodiverse assemblages, the composition of available prey and their traits are more reliable predictors of predator-prey interactions. This study offers valuable insights into microbial ecology in the context of predator-prey interactions, as cryptic microbial responses can be guided by deductions based on generalizable biological traits.},
}
@article {pmid39687379,
year = {2024},
author = {Lee, D and Oliveira, FCC and Conant, RT and Kim, M},
title = {Microbial community assembly across agricultural soil mineral mesocosms revealed by 16S rRNA gene amplicon sequencing data.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {111125},
doi = {10.1016/j.dib.2024.111125},
pmid = {39687379},
issn = {2352-3409},
abstract = {Increasing atmospheric carbon dioxide (CO2) concentrations are impacting the global climate, resulting in significant interest in soil carbon sequestration as a mitigation strategy. While recognized that mineral-associated organic matter (MAOM) in soils is mainly formed through microbial activity, our understanding of microbial-derived MAOM formation processes remains limited due to the complexity of the soil environment. To gain insights into this issue, we incubated fresh soil samples for 45 days with one of three mineral additions: Sand, Kaolinite+Sand, or Illite+Sand. 16S rRNA V3/V4 gene amplicon sequencing was then conducted on samples using an Illumina NextSeq 2000 flow cell. The reads were analyzed and taxonomically assigned with QIIME2 v2023.5.1 and SILVA 138. The dataset has been made publicly available through NCBI GenBank under BioProject ID PRJNA1124235. This dataset is important and useful as it provides valuable insights into the interactions between soil minerals and microbial communities, which can inform strategies for enhancing soil carbon sequestration and mitigating climate change. Moreover, it serves as a crucial reference for future studies, offering a foundational understanding of microbial dynamics in soil systems and guiding further research in microbial ecology and carbon cycling.},
}
@article {pmid39683937,
year = {2024},
author = {Liu, S and Teng, L and Ping, J},
title = {Graphitic Carbon Nitride Confers Bacterial Tolerance to Antibiotics in Wastewater Relating to ATP Depletion.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {23},
pages = {},
doi = {10.3390/molecules29235780},
pmid = {39683937},
issn = {1420-3049},
support = {62105175//National Natural Science Foundation of China/ ; ZR2021QF058//Natural Science Foundation of Shandong Province/ ; 2022PY036//The Education and Industry Integration Pilot Project of Qilu University of Technology/ ; 432413/01090//Start-up fund of Tianjin Renai College/ ; },
mesh = {*Graphite/chemistry ; *Wastewater/microbiology/chemistry ; *Anti-Bacterial Agents/pharmacology ; *Adenosine Triphosphate/metabolism ; Nitrogen Compounds/chemistry ; Staphylococcus aureus/drug effects ; Ofloxacin/pharmacology ; Drug Resistance, Bacterial/drug effects ; Reactive Oxygen Species/metabolism ; Microbial Sensitivity Tests ; Water Purification/methods ; },
abstract = {Graphitic carbon nitride (C3N4) is a kind of visible light-responsive photocatalyst that has been of great interest in wastewater treatment. However, its environmental impact and biological effect remains to be elucidated. This study investigated the effect of C3N4 nanosheets on bacterial abundance and antibiotic tolerance in wastewater. Interestingly, as compared to the wastewater containing the antibiotic ofloxacin alone, the wastewater containing both ofloxacin and C3N4 had much higher numbers of total living bacteria, but lower levels of the ofloxacin-resistant bacteria and the ofloxacin-resistant gene qnrS. The model bacterium Staphylococcus aureus was then used to explore the mechanism of C3N4-induced antibiotic tolerance. The nanosheets neither adsorbed the antibiotic nor promoted drug efflux, uncovering that drug adsorption and efflux were not involved in antibiotic tolerance. Further investigations revealed that the nanosheets, like arsenate and menadione, drastically reduced ATP levels and induced the production of reactive oxygen species for enhanced antibiotic tolerance. This study revealed an antibiotic-tolerating mechanism associated with C3N4-induced ATP depletion, and shed a light on the effect of photocatalysts on microbial ecology during their application in wastewater treatment.},
}
@article {pmid39682491,
year = {2024},
author = {Suriyasathaporn, W and Kongkaew, A and Intanon, M and Srithanasuwan, A and Saipinta, D and Pangprasit, N and Thongtharb, A and Chuasakhonwilai, A and Chaisri, W},
title = {Non-aureus Staphylococci Cause the Spontaneous Cure or Persistent Infection of Major Bovine Mastitis Pathogens in the Murine Mammary Glands.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/ani14233526},
pmid = {39682491},
issn = {2076-2615},
support = {FF66/017//The Fundamental Fund, Chiang Mai University/ ; },
abstract = {The microbial ecology in mastitis involves the interactions between bacteria and the mammary gland environment. Poor mastitis control, for which understanding these microbial relationships is crucial, increases the risk of mastitis and co-infections. The aim of this study was to determine the pathogenesis and bacterial ecology of murine mammary glands following intramammary infection (IMI) with S. aureus (AU), S. agalactiae (SA), and four isolates of selected non-aureus staphylococci (NAS), as well as co-infections of AU or SA with NAS. Selected NAS demonstrated resistance to growth inhibition after co-culture with AU and SA and were proven to be protective in vitro against AU and SA. Both single infections and co-infections of AU, SA, two selected isolates of S. hominis (NAS1 and NAS2), and two selected isolates of S. chromogens (NAS3 and NAS4) were injected into the murine mammary glands at 10[5] CFU/mL. After 72 h of inoculation, the results showed that AU, AU-NAS2, and AU-NAS3 expressed severe inflammation with clinical signs of mastitis. The persistence of AU was found for AU, NAS3, and AU-NAS3, whereas the persistence of SA was found for SA-NAS1, SA-NAS3, and SA-NAS, although single SA could not persist. Interestingly, NAS2 in both the single- and co-IMIs with AU or SA resulted in a spontaneous cure 72 h after the IMI. In conclusion, some NAS have beneficial results because they can eliminate S. aureus and S. agalactiae, but some NAS have negative effects because they can support persistent S. agalactiae infection. These results may be used to explain both the advantages and disadvantages of NAS on farms with poor mastitis control. In addition, the beneficial S. hominis may initiate natural live antibiotics and reduce antibiotic resistance problems.},
}
@article {pmid39681734,
year = {2024},
author = {Rajendran, D and Vinayagam, S and Sekar, K and Bhowmick, IP and Sattu, K},
title = {Symbiotic Bacteria: Wolbachia, Midgut Microbiota in Mosquitoes and Their Importance for Vector Prevention Strategies.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {154},
pmid = {39681734},
issn = {1432-184X},
mesh = {*Wolbachia/physiology ; Animals ; *Symbiosis ; *Gastrointestinal Microbiome ; *Mosquito Vectors/microbiology ; Culicidae/microbiology ; Mosquito Control/methods ; },
abstract = {Mosquito-borne illnesses pose a significant threat to eradication under existing vector management measures. Chemo-based vector control strategies (use of insecticides) raise a complication of resistance and environmental pollution. Biological control methods are an alternative approach to overcoming this complication arising from insecticides. The mosquito gut microbiome is essential to supporting the factors that involve metabolic regulation and metamorphic development (from juvenile to adult), as well as the induction of an immune response. The induced immune response includes the JAK-STAT, IMD, and Toll pathways due to the microbial interaction with the midgut cells (MG cells) that prevent disease transmission to humans. The aforementioned sequel to the review provides information about endosymbiont Wolbachia, which contaminates insect cells, including germline and somatic cytoplasm, and inhibits disease-causing pathogen development and transmission by competing for resources within the cell. Moreover, it reduces the host population via cytoplasmic incompatibility (CI), feminization, male killing, and parthenogenesis. Furthermore, the Cif factor in Wolbachia is responsible for CI induction that produces inviable cells with the translocating systems and the embryonic defect-causing protein factor, WalE1 (WD0830), which manipulates the host actin. This potential of Wolbachia can be used to design a paratransgenic system to control vectors in the field. An extracellular symbiotic bacterium such as Asaia, which is grown in the growth medium, is used to transfer lethal genes within itself. Besides, the genetically transferred symbiotic bacteria infect the wild mosquito population and are easily manifold. So, it might be suitable for vector control strategies in the future.},
}
@article {pmid39681034,
year = {2024},
author = {Fu, Y and Hu, F and Wang, F and Xu, M and Jia, Z and Amelung, W and Mei, Z and Han, X and Virta, M and Jiang, X and Tiedje, JM},
title = {Field-based evidence for the prevalence of soil antibiotic resistomes under long-term antibiotic-free fertilization.},
journal = {Environment international},
volume = {195},
number = {},
pages = {109202},
doi = {10.1016/j.envint.2024.109202},
pmid = {39681034},
issn = {1873-6750},
abstract = {Growing evidence suggests that the use of manure containing residual antibiotics universally leads to an increase in soil antibiotic resistance genes (ARGs). However, there is limited understanding of the influence of long-term antibiotic-free fertilization and the differences between antibiotic-free manure and chemical fertilizer on soil ARGs. This study aimed to quantify the assembly patterns of the antibiotic resistome by in situ probing bacterial community and environmental variations in field soils that have been subjected to long-term exposure to chemical fertilizer and/or manure from animals without antibiotic amendments. Long-term fertilization slightly impacts the diversity of antibiotic resistomes, with 85.5 % of total ARGs and mobile genetic elements (MGEs) being common across all treatment types, while significantly increasing their abundances from 0.68 to a maximum of 0.90 copies/16S rRNA. The rise in ARG abundances was less pronounced when using antibiotic-free manure compared to chemical fertilizer, particularly for Rank Ⅱ ARGs. However, when antibiotic-free manure and chemical fertilizer were combined, a significant increase in nutrients (such as available nitrogen and organic matter) and MGEs occurred, leading to the enrichment of soil microbial populations, especially in certain resistant species, and Rank Ⅰ and Ⅱ ARGs. Despite the influence of various factors like bacterial communities, soil properties, heavy metals, and MGEs, the MGEs had the most significant standardized effects on shaping ARGs through both direct and indirect pathways. Our findings indicates that while of antibiotic-free manure can lower the risk of antibiotic residues and promote sustainable farming practices, it may not fully eliminate the prevalence of ARGs, highlighting the need for more comprehensive strategies to address antibiotic resistance in agriculture rather than simply prohibiting the use of antibiotics.},
}
@article {pmid39680930,
year = {2024},
author = {Li, XY and Zhu, CW and Chen, S and Xiang, Q and Lu, C and Lin, XY and Chen, QL},
title = {Elevated CO2 Increased Antibiotic Resistomes in Seed Endophytes: Evidence from a Free-Air CO2 Enrichment (FACE) Experiment.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c09625},
pmid = {39680930},
issn = {1520-5851},
abstract = {Climate warming affects antibiotic resistance genes (ARGs) in soil and the plant microbiome, including seed endophytes. Seeds act as vectors for ARG dissemination in the soil-plant system, but the impact of elevated CO2 on seed resistomes remains poorly understood. Here, a free-air CO2 enrichment system was used to examine the impact of elevated CO2 on seed-associated ARGs and seed endophytic bacteria and fungi. Results indicated that elevated CO2 levels significantly increased the relative abundance of seed ARGs and mobile genetic elements (MGEs), especially those related to beta-lactam resistance and MGEs. Increased CO2 levels also influenced the composition of seed bacterial and fungal communities and the complexity of bacteria-fungi interactions. Fungi were more sensitive to changes in the CO2 level than bacteria, with deterministic processes playing a greater role in fungal community assembly. Co-occurrence network analysis revealed a stronger correlation between fungi and ARGs compared to bacteria. The structure equation model (SEM) showed that elevated CO2 directly influenced seed resistomes by altering bacterial composition and indirectly through bacteria-fungi interactions. Together, our work offers new insights into the effects of elevated CO2 on antibiotic resistomes in the seed endosphere, highlighting their increased dissemination potential within soil-plant systems and the associated health risks in a changing environment.},
}
@article {pmid39680691,
year = {2024},
author = {Yang, JC and Lagishetty, V and Aja, E and Arias-Jayo, N and Chang, C and Hauer, M and Katzka, W and Zhou, Y and Sedighian, F and Koletic, C and Liang, F and Dong, TS and Situ, J and Troutman, R and Buri, H and Bhute, S and Simpson, CA and Braun, J and Jacob, N and Jacobs, JP},
title = {Biogeographical distribution of gut microbiome composition and function is partially recapitulated by fecal transplantation into germ-free mice.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae250},
pmid = {39680691},
issn = {1751-7370},
abstract = {Fecal microbiota transplantation has been vital for establishing whether host phenotypes can be conferred through the microbiome. However, whether the existing microbial ecology along the mouse gastrointestinal tract can be recapitulated in germ-free mice colonized with stool remains unknown. We first identified microbes and their predicted functions specific to each of six intestinal regions in three cohorts of specific pathogen-free mice spanning two facilities. Of these region-specific microbes, the health-linked genus Akkermansia was consistently enriched in the lumen of the small intestine compared to the colon. Predictive functional modeling on 16S rRNA gene amplicon sequencing data recapitulated in shotgun sequencing data revealed increased microbial central metabolism, lipolytic fermentation, and cross-feeding in the small intestine, whereas butyrate synthesis was colon-enriched. Neuroactive compound metabolism also demonstrated regional specificity, including small intestine-enriched gamma-aminobutyric acid degradation and colon-enriched tryptophan degradation. Specifically, the jejunum and ileum stood out as sites with high predicted metabolic and neuromodulation activity. Differences between luminal and mucosal microbiomes within each site of the gastrointestinal tract were largely facility-specific, though there were a few consistent patterns in microbial metabolism in specific pathogen-free mice. These included luminal enrichment of central metabolism and cross-feeding within both the small intestine and the colon, and mucosal enrichment of butyrate synthesis within the colon. Across three cohorts of germ-free mice colonized with mice or human stool, compositional and functional region specificity were inconsistently reproduced. These results underscore the importance of investigating the spatial variation of the gut microbiome to better understand its impact on host physiology.},
}
@article {pmid39679708,
year = {2024},
author = {Liu, Z and Jiang, C and Yin, Z and Ibrahim, IA and Zhang, T and Wen, J and Zhou, L and Jiang, G and Li, L and Yang, Z and Huang, Y and Yang, Z and Gu, Y and Meng, D and Yin, H},
title = {Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0102824},
doi = {10.1128/aem.01028-24},
pmid = {39679708},
issn = {1098-5336},
abstract = {UNLABELLED: Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.<br><br>IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.},
}
@article {pmid39679616,
year = {2024},
author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D},
title = {Gut microbiota genome features associated with brain injury in extremely premature infants.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2410479},
doi = {10.1080/19490976.2024.2410479},
pmid = {39679616},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Genome, Bacterial ; Cohort Studies ; },
abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.},
}
@article {pmid39675658,
year = {2024},
author = {Yan, R and Xu, X and Niu, Y and Ying, S and Cai, J and Chen, R and Gu, Y and Kan, H},
title = {Microbial Diversity and Environmental Determinants at Shanghai Hongqiao Railway Station: A Comprehensive Microbial Assessment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125534},
doi = {10.1016/j.envpol.2024.125534},
pmid = {39675658},
issn = {1873-6424},
abstract = {The COVID-19 pandemic has underscored the importance of indoor environmental management in transportation hubs, which are critical for pathogen transmission due to high foot traffic. However, research has primarily focused on subways, with limited studies on train stations. In this study, samples were collected at the Shanghai Hongqiao Railway Station in winter, spring, and summer. Microbial DNA was extracted from collected indoor surfaces and ambient air samples and then analyzed through high-throughput 16S rRNA gene sequencing. Alongside sample collection, environmental data were recorded. Alpha diversity was greatest in winter, followed by summer, and least in spring within the train station environment. Surface samples exhibited higher alpha diversity compared to air samples, with no notable difference between indoor and outdoor air. Beta diversity showed significant variation across seasons and locations, with seasonal changes more pronounced than spatial ones, primarily due to differences between air and surface samples rather than indoor and outdoor environments. Key determinants of microbial community structure included CO2, temperature, illuminance, and passenger volume. The microbial community in train stations originates from various sources, with contributions from both natural elements (like wastewater/sludge, soil, and plants) and human sources (such as gastrointestinal, oral, and dermal flora). This study highlights the microbial ecology of train stations, emphasizing the need for microbial surveillance and management in transportation settings.},
}
@article {pmid39673336,
year = {2024},
author = {Liu, J and He, Y and Qiu, Z and Fahad, S and Zhao, S and Zhu 朱, M&#x58a8;},
title = {Erysiphe russellii Causing Powdery Mildew on Oxalis corniculata L. in Central China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-10-24-2249-PDN},
pmid = {39673336},
issn = {0191-2917},
abstract = {Oxalis corniculata L. (Creeping woodsorrel) is a perennial plant of the genus Oxalis in Oxalidaceae family, which has the high ornamental and medicinal value. Extracts of creeping woodsorrel are used as antioxidants and cholinesterase inhibitors and for anti-inflammatory, antiseptic, analgesic, antirheumatic ache, and antimicrobial purposes (Leporatti et al. 2003). In June 2024, powdery mildew was found on the leaves of Creeping woodsorrel in Xinxiang City, Henan Province, China (113.925°E, 35.294°N). About 100 plants were examined and 80 % were infected with disease symptoms, i.e. curling and senescence. The white masses were on the both sides of plant leaves covering up to 90% of the leaves area. The slightly or straight curved conidiophores (n = 50) were 68 to 99× 6 to 12 μm in size and consisted of foot cells, shorter cells and singly conidia. The ellipsoidal to oval conidia (n =50), were 26 to 10 ×11 to 5 μm in size and had a length/width ratio of 1.6 to 2.2. These morphological characteristics were similar to the previously reported Creeping woodsorrel powdery mildew fungus, Erysiphe russellii (Thuong et al. 2017; Takamatsu et al. 2015). Following previously described methods (White et al. 1990; Bradshaw et al. 2022; Zhu et al. 2022), the ITS (ribosomal transcribed spacer), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), RPB2 (RNA polymerase II), GS (glutamine synthetase) and CAM (calmodulin) gene regions of three isolates were amplified with specific primers ITS1/ITS4 (ITS1 5'-TCCGTAGGTGAACCTGCGG-3'; ITS4 5'-TCCTCCGCTTATTGATATGC-3'), PMGAPDH1/PMGAPDH3R (PMGAPDH1 5'-GGAATGGCTATGCGTGTACC-3'; PMGAPDH3R 5'-CCCCATTCGTTGTCGTACCATG-3'), CAM1/CAM4R (CAM1 5'-CTTTGCATCATGAGTTGGAC-3'; CAM4R 5'-GGCTCGAAAAATGAAAGATACCG-3'), Rpb2_4/Rpb2_6R (Rpb2_4 5'-GCAAGCTCAACTGCTGGTG-3'; Rpb2_6R 5'-TCCAGCGATGTGCTGTTGG-3'), GSPM2/GSPM3R (GSPM2 5'-CCAATCAGTTACTGTTTGTTCCC-3'; GSPM3R 5'-GGACTTCCTGATATTATGCC3'). Sanger sequencing results showed that each sequence of the three isolates were the same. Then sequences of one isolate were uploaded in GenBank (Accession No. PQ044579, PQ149219, PQ149220, PQ149221and PQ149222, respectively). The sequences were 100% identical to those of a previously reported E russellii on O. corniculata (Thuong et al. 2017; Takamatsu et al. 2015). The pathogen and the previously reported E russellii are clustered in the same branch in the phylogenetic tree (Thuong et al. 2017; Takamatsu et al. 2015). The pathogenicity was tested according to the method previously described (Zhu et al. 2021). By blowing conidia on infected leaves with pressurized air, the fungus was inoculated onto the leaves of three healthy plants (three-month-old), with three uninoculated plants (three-month-old) treated as controls. The infected plants and the control plants were placed in the culture room with the temperature 23 °C, humidity 50% and light/Dark 16/8 h, respectively. 10-12 days post inoculation, the leaves of the inoculated plants showed signs and symptoms of powdery mildew, while the control group was unaffected. The pathogen of the infected plant disease was re-examined by morphological characteristics and was similar to the original fungus. The pathogenicity tests were repeated three times and same results were obtained. Therefore, the pathogen was identified and confirmed as E russellii (isolate ER-ZM2024). Previously, E russellii was reported on Oxalis corniculata L. in Japan and Korea (Thuong et al. 2017; Takamatsu et al. 2015). To the best our knowledge, this is the first report of powdery mildew caused by E russellii on O. corniculata L. in central China. This identification of E russellii on O. corniculata L. provides a new perspective for the study of the disease. The results of this study provide the sequences of E russellii for further phylogenetic analysis.},
}
@article {pmid39665561,
year = {2024},
author = {Unzueta-Martínez, A and Girguis, PR},
title = {Taxonomic diversity and functional potential of microbial communities in oyster calcifying fluid.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0109424},
doi = {10.1128/aem.01094-24},
pmid = {39665561},
issn = {1098-5336},
abstract = {UNLABELLED: Creating and maintaining an appropriate chemical environment is essential for biomineralization, the process by which organisms precipitate minerals to form their shells or skeletons, yet the mechanisms involved in maintaining calcifying fluid chemistry are not fully defined. In particular, the role of microorganisms in facilitating or hindering animal biomineralization is poorly understood. Here, we investigated the taxonomic diversity and functional potential of microbial communities inhabiting oyster calcifying fluid. We used shotgun metagenomics to survey calcifying fluid microbial communities from three different oyster harvesting sites. There was a striking consistency in taxonomic composition across the three collection sites. We also observed archaea and viruses that had not been previously identified in oyster calcifying fluid. Furthermore, we identified microbial energy-conserving metabolisms that could influence the host's calcification, including genes involved in sulfate reduction and denitrification that are thought to play pivotal roles in inorganic carbon chemistry and calcification in microbial biofilms. These findings provide new insights into the taxonomy and functional capacity of oyster calcifying fluid microbiomes, highlighting their potential contributions to shell biomineralization, and contribute to a deeper understanding of the interplay between microbial ecology and biogeochemistry that could potentially bolster oyster calcification.<br><br>IMPORTANCE: Previous research has underscored the influence of microbial metabolisms in carbonate deposition throughout the geological record. Despite the ecological importance of microbes to animals and inorganic carbon transformations, there have been limited studies characterizing the potential role of microbiomes in calcification by animals such as bivalves. Here, we use metagenomics to investigate the taxonomic diversity and functional potential of microbial communities in calcifying fluids from oysters collected at three different locations. We show a diverse microbial community that includes bacteria, archaea, and viruses, and we discuss their functional potential to influence calcifying fluid chemistry via reactions like sulfate reduction and denitrification. We also report the presence of carbonic anhydrase and urease, both of which are critical in microbial biofilm calcification. Our findings have broader implications in understanding what regulates calcifying fluid chemistry and consequentially the resilience of calcifying organisms to 21st century acidifying oceans.},
}
@article {pmid39660837,
year = {2024},
author = {Lewin, GR},
title = {mSphere of Influence: How the single cell contributes to the collective.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0043124},
doi = {10.1128/msphere.00431-24},
pmid = {39660837},
issn = {2379-5042},
abstract = {Gina Lewin works in the field of microbial ecology, with a focus on the human microbiota. In this mSphere of Influence article, she reflects on how two papers describing bacterial single-cell RNA-seq-"Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing" by S. B. Blattman, W. Jiang, P. Oikonomou, and S. Tavazoie (Nat Microbiol 5:1192-1201, 2020, https://doi.org/10.1038/s41564-020-0729-6) and "Microbial single-cell RNA sequencing by split-pool barcoding" by A. Kuchina, L. M. Brettner, L. Paleologu, C. M. Roco, et al. (Science 371:eaba5257, 2021, https://doi.org/10.1126/science.aba5257)-impacted her work by developing a new approach to study how single cells of bacteria contribute to ecosystem-level processes.},
}
@article {pmid39659497,
year = {2024},
author = {Ritsch, M and Brait, N and Harvey, E and Marz, M and Lequime, S},
title = {Endogenous viral elements: insights into data availability and accessibility.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae099},
pmid = {39659497},
issn = {2057-1577},
abstract = {Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR ('findable, accessible, interoperable, and reusable') principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host-virus interactions and their evolutionary history.},
}
@article {pmid39657855,
year = {2024},
author = {Gu, Z and He, L and Liu, T and Xing, M and Feng, L and Luo, G},
title = {Exploring Strategies for Kitchen Waste Treatment and Remediation from the Perspectives of Microbial Ecology and Genomics.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {143925},
doi = {10.1016/j.chemosphere.2024.143925},
pmid = {39657855},
issn = {1879-1298},
abstract = {Nowadays, the rapid growth of population has led to a substantial increase in kitchen waste and wasted sludge. Kitchen waste is rich in organic matter, including lignocellulose. Synergistic treatment involving kitchen waste and wasted sludge can enhance treatment process. Vermicomposting can facilitate microbial activities on organic matter. Nevertheless, the underlying mechanisms remain unclear. In this study, metagenomics was used to analyze microbial functional genes in vermicomposting. Redundancy analysis found that TOC, TN and DTN adversely affect earthworm growth and reproduction. The relative abundance of Bacteroidetes and Firmicutes were increased with earthworms, thereby potentially augmenting lignocellulose degradation. The predominant functional genes included amino acid, carbohydrate, and inorganic ion conversion and metabolism. Metagenomics analysis demonstrated that GH1, GH3, GH5, GH6, GH9, GH12, GH44, GH48 and GH74, GT41, GT4, GT2, and GT51 were dominant. Furthermore, there was higher abundance of carbohydrate-active enzymes in the vermicomposting, particularly during the later phases (30-45 days). Co-occurrence network revealed that Cellvibrio in the vermicomposting exhibited a relatively dense positive correlation with other microbial groups. The findings elucidated the mechanism of vermicomposting as a promising approach for managing kitchen waste and wasted sludge.},
}
@article {pmid39657789,
year = {2024},
author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, &#xc1;T and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH},
title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1115},
pmid = {39657789},
issn = {1362-4962},
support = {KICH1.LWV04.21.013//NWO/ ; 101000392//Horizon 2020/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; 547394769//German Research Foundation/ ; //University of Sydney/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; IM230100154//Australian Research Council Industry Fellowship/ ; //Hans Fischer Society/ ; //UK Government Department for Environment, Food &amp; Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 101072485//Horizon Europe Marie Sk&#x142;odowska-Curie/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; 101117891-MeDiSyn//ERC Starting/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; //Department of Biotechnology/ ; //National Agri-Food Biotechnology Institute/ ; 101087181//EU/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; 2021YFA0909500//National Key Research and Development Program of China/ ; 32170080//National Natural Science Foundation of China/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 21K06336//KAKENHI/ ; 21/07038-0//S&#xe3;o Paulo Research Foundation/ ; VI.Veni.202.130//NWO Talent/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 222676//USDA Evans-Allen Research/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; //University of Illinois/ ; 802736//European Union Horizon 2020/ ; 735867//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; //NWO Merian/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101066127//European Union/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; K12 GM068524/GM/NIGMS NIH HHS/United States ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Alexander von Humboldt-Stiftung/ ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; NE/T010959/1//Signals in the Soil/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; 495740318//German Research Foundation/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; 101072485//European Union's Horizon/ ; //European Regional Development Fund/ ; 802736//European Union's Horizon 2020/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; //Swiss Federal Government/ ; PS00349981//Fulbright/ ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; DM60066//Italian Ministry of Research/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; NA22NOS4200050//NERRS/ ; BB/V005723/2//BBSRC/ ; 1347411//CONAHCYT/ ; T32GM136583/NH/NIH HHS/United States ; 101130799//European Union's Horizon/ ; CFB 2.0//Novo Nordisk Foundation/ ; //Basic Science Research Program/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; //Werner Siemens Foundation/ ; OCENW.XL21.XL21.088//NWO-XL/ ; DNRF137//Danish National Research Foundation/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; CBET-2032243//U.S. National Science Foundation/ ; //Delta Stewardship Council Delta Science Program/ ; //European Union's Horizon 2020 Research/ ; 852600//Innovation Program ERC St/ ; 101072485//European Union's Horizon Europe/ ; //Conahcyt Mexico International PhD Studentship/ ; //Strathclyde University Global Research Scholarship/ ; 3141-00013A//Innovation Fund Denmark/ ; K445/2022//Leibniz Association/ ; 23/01956-2//S&#xe3;o Paulo Research Foundation/ ; DGE 2241144//NSF GRFP/ ; 024.004.014//MiCRop Consortium/ ; CF22-1239//Carlsberg Foundation/ ; 102022750//SINTEF/ ; 102029187//SEP AGREE/ ; 102024676-14//POS BIOINFO 2024/ ; 101106349//Marie Sklodowska-Curie/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //National Research Fund of Ukraine/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; //German Academic Scholarship Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; //Department of Biotechnology/ ; //University Grants Commission/ ; PROYEXCEL_00012//Spanish "Junta de Andaluc&#xed;a"/ ; GNT2021638//National Health and Medical Research Council/ ; DP230102668//Australian Research Council Discovery Project/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 865738/ERC_/European Research Council/International ; T32-GM136629//Chemical-Biology Interface Training/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 757173//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; //Horizon Europe Marie Sk&#x142;odowska-Curie Actions Postdoctoral Fellowship/ ; 101099528//European Innovation Council/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; //Swedish Pharmaceutical Society PostDoc/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; //Saarland University/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; AUFF-E-2022-9-42//AUFF/ ; 101055020-COMMUNITY//ERC Advanced/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; 10.55776/P 34036//Austrian Science Fund/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; },
abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.},
}
@article {pmid39651958,
year = {2024},
author = {Werlang, CA and Sahoo, JK and Cárcarmo-Oyarce, G and Stevens, C and Uzun, D and Putnik, R and Hasturk, O and Choi, J and Kaplan, DL and Ribbeck, K},
title = {Selective Biofilm Inhibition through Mucin-Inspired Engineering of Silk Glycopolymers.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.4c12945},
pmid = {39651958},
issn = {1520-5126},
abstract = {Mucins are key components of innate immune defense and possess remarkable abilities to manage pathogenic microbes while supporting beneficial ones and maintaining microbial homeostasis at mucosal surfaces. Their unique properties have garnered significant interest in developing mucin-inspired materials as novel therapeutic strategies for selectively controlling pathogens without disrupting the overall microbial ecology. However, natural mucin production is challenging to scale, driving the need for simpler materials that reproduce mucin's bioactivity. In this work, we generated silk-based glycopolymers with different monosaccharides (GalNAc, GlcNAc, NeuNAc, GlcN, and GalN) and different grafting densities. Using the oral cavity as a model system, we treated in vitro cultures of pathogenic Streptococcus mutans and commensal Streptococcus sanguinis with our glycopolymers, finding that silk-tethered GalNAc uniquely prevented biofilm formation without affecting overall bacterial growth of either species. This relatively simple material reproduced mucin's virulence-neutralizing effects while maintaining biocompatibility. These mucin-inspired materials represent a valuable tool for preventing infection-related harm and offer a strategy for the domestication of pathogens in other environments.},
}
@article {pmid39651889,
year = {2024},
author = {Wang, J and Schamp, CN and Hudson, LK and Chaggar, HK and Bryan, DW and Garman, KN and Radosevich, M and Denes, TG},
title = {Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0171224},
doi = {10.1128/spectrum.01712-24},
pmid = {39651889},
issn = {2165-0497},
abstract = {UNLABELLED: Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis (n = 8; n represents the number of distinct strains), L. monocytogenes (n = 3), "Listeria swaminathanii" (Lsw) (n = 1), Listeria marthii (n = 1), and Listeria booriae (n = 1). Most strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated (P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens.<br><br>IMPORTANCE: As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.},
}
@article {pmid39644970,
year = {2024},
author = {Tumeo, A and McDonagh, F and Kovarova, A and Ryan, K and Clarke, C and Miliotis, G},
title = {Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2024.11.018},
pmid = {39644970},
issn = {2213-7173},
abstract = {OBJECTIVES: While Escherichia coli phylogroup-A is typically associated with commensal strains, some isolates can harbour virulence and exhibit multidrug-resistant (MDR) phenotypes. We report the draft genome of a rare instance of carbapenem, fosfomycin and colistin resistant E. coli phylogroup-A, isolated as part of routine screening of a human patient in a clinical setting in Ireland.<br><br>METHODS: E. coli E230738 was identified using MALDI-ToF/MS. Antibiotic susceptibility testing was performed using the Sensitire-EUMDRXXF plate. Whole-genome-sequencing was conducted with NextSeq1000, and genomic analysis identified antibiotic-resistance-genes (ARGs) and virulence-factors (VFs). Phylogenetic analysis was performed using whole-genome-multilocus-sequence-typing (wgMLST).<br><br>RESULTS: E. coli E230738 genome was identified to belong to phylogroup-A/ST10 complex and to harbour 63 ARGs (17 acquired). Resistance to beta-lactams, including carbapenems and cephalosporins was likely due to predicted chromosomal blaNDM-5. Colistin resistance appeared associated with acquired mcr-1.1. Despite lacking fosfomycin-inactivating-enzymes, fosfomycin resistance was observed, possibly due to efflux pumps. 47 chromosomal VFs were identified, involved in adhesion and iron acquisition amongst others. Plasmid replicons associated with the spread of MDR genes such as IncHI2/HI2A were detected. Phylogenetic analysis showed the closest relative being a strain from the UK differing by 851 genes.<br><br>CONCLUSION: This is a first detected instance of a blaNDM-5 and mcr-1.1 co-occurring in E. coli in Ireland. The MDR profile of E. coli E230738 highlights the growing public health threat posed by the dissemination of MDR E. coli lineages with limited treatment options and underscores the need for clinical screening coupled with genomic surveillance to better understand evolving MDR patterns in E. coli.},
}
@article {pmid39642168,
year = {2024},
author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M},
title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012627},
doi = {10.1371/journal.pcbi.1012627},
pmid = {39642168},
issn = {1553-7358},
abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.},
}
@article {pmid39641603,
year = {2024},
author = {Grimm, H and Lorenz, J and Straub, D and Joshi, P and Shuster, J and Zarfl, C and Muehe, EM and Kappler, A},
title = {Nitrous oxide is the main product during nitrate reduction by a novel lithoautotrophic iron(II)-oxidizing culture from an organic-rich paddy soil.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0126224},
doi = {10.1128/aem.01262-24},
pmid = {39641603},
issn = {1098-5336},
abstract = {Microbial nitrate reduction coupled to iron(II) oxidation (NRFeOx) occurs in paddy soils due to high levels of dissolved iron(II) and regular application of nitrogen fertilizer. However, to date, there is no lithoautotrophic NRFeOx isolate or enrichment culture available from this soil environment. Thus, resulting impacts on greenhouse gas emissions during nitrate reduction (i.e., nitrous oxide [N2O]) and on toxic metalloid (i.e., arsenic) mobility can hardly be investigated. We enriched a lithoautotrophic NRFeOx culture, culture HP (Huilongpu paddy, named after its origin), from a paddy soil (Huilongpu Town, China), which was dominated by Gallionella (71%). The culture reduced 0.45 to 0.63 mM nitrate and oxidized 1.76 to 2.31 mM iron(II) within 4 days leading to N2O as the main N-product (62%-88% N2O-N of total reduced NO3[-]-N). Nitrite was present as an intermediate at a maximum of 0.16 ± 0.1 mM. Cells were associated with, but mostly not encrusted by, poorly crystalline iron(III) minerals (ferrihydrite). Culture HP performed best below an iron(II) threshold of 2.5-3.5 mM and in a pH range of 6.50-7.05. In the presence of 100 µM arsenite, only 0%-18% of iron(II) was oxidized. Due to low iron(II) oxidation, arsenite was not immobilized. However, the proportion of N2O-N of total reduced NO3[-]-N decreased from 77% to 30%. Our results indicate that lithoautotrophic NRFeOx occurs even in organic-rich paddy soils, resulting in denitrification and subsequent N2O emissions. The obtained novel enrichment culture allows us to study the impact of lithoautotrophic NRFeOx on arsenic mobility and N2O emissions in paddy soils.IMPORTANCEPaddy soils are naturally rich in iron(II) and regularly experience nitrogen inputs due to fertilization. Nitrogen fertilization increases nitrous oxide emissions as it is an intermediate product during nitrate reduction. Microorganisms can live using nitrate and iron(II) as electron acceptor and donor, respectively, but mostly require an organic co-substrate. By contrast, microorganisms that only rely on nitrate, iron(II), and CO2 could inhabit carbon-limited ecological niches. So far, no isolate or consortium of lithoautotrophic iron(II)-oxidizing, nitrate-reducing microorganisms has been obtained from paddy soil. Here, we describe a lithoautotrophic enrichment culture, dominated by a typical iron(II)-oxidizer (Gallionella), that oxidized iron(II) and reduced nitrate to nitrous oxide, negatively impacting greenhouse gas dynamics. High arsenic concentrations were toxic to the culture but decreased the proportion of nitrous oxide of the total reduced nitrate. Our results suggest that autotrophic nitrate reduction coupled with iron(II) oxidation is a relevant, previously overlooked process in paddy soils.},
}
@article {pmid39637856,
year = {2024},
author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA},
title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.10.069},
pmid = {39637856},
issn = {1879-0445},
abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.},
}
@article {pmid39637512,
year = {2024},
author = {Wilkie, I and Orellana, LH},
title = {Elusive marine Verrucomicrobiota: Seasonally abundant members of the novel genera Seribacter and Chordibacter specialize in degrading sulfated glycans.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {1},
pages = {126562},
doi = {10.1016/j.syapm.2024.126562},
pmid = {39637512},
issn = {1618-0984},
abstract = {Members of the phylum Verrucomicrobiota play a significant role in various ecosystems, yet they are underrepresented in databases due to their comparatively lower abundance and isolation challenges. The use of cultivation-independent approaches has unveiled their hidden diversity and specialized metabolic capabilities, yet many of these populations remain uncharacterized. In this study, we focus on members of the family MB11C04 associated with North Sea spring blooms. Our analyses revealed recurrent MB11C04 populations with increased abundance in the late stages of spring blooms over ten-years. By examining their genomic content, we identified specialized genetic features for the degradation of complex polysaccharides, particularly sulfated and fucose-rich compounds, suggesting their role in utilizing organic matter during the collapse of the bloom. Furthermore, we describe two novel genera each with a novel species (Seribacter gen. Nov., Chordibacter gen. Nov.) in accordance with the SeqCode initiative based on high quality metagenome-assembled genomes. We also propose a new name for the family MB11C04, Seribacteraceae. Our findings shed light on the ecological significance and metabolic potential of Verrucomicrobiota populations in spring bloom events.},
}
@article {pmid39633812,
year = {2024},
author = {Bauchinger, F and Seki, D and Berry, D},
title = {Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1454634},
pmid = {39633812},
issn = {1664-302X},
abstract = {Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa. These results suggest that keystone taxa may have stabilizing properties in a subset of community members rather than global effects. The work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance.},
}
@article {pmid39633134,
year = {2024},
author = {Han, GH and Yu, J and Kang, MJ and Park, MJ and Noh, CH and Kim, YJ and Kwon, KK},
title = {Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {153},
pmid = {39633134},
issn = {1432-184X},
support = {20210469//Ministry of Oceans and Fisheries/ ; },
mesh = {Animals ; Republic of Korea ; *Microbiota ; *Skin/microbiology ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Gills/microbiology ; Biological Evolution ; Species Specificity ; },
abstract = {Phylosymbiosis is defined as the relationship in which the microbiome recapitulates the phylogeny of the host and has been demonstrated in a variety of terrestrial organisms, although it has been understudied in fish, the most phylogenetically diverse vertebrate. Given that the species-specificity of fish microbiomes was detected in multiple body parts and differed by body parts, we assumed that the phylogenetic reflection of the microbiome would differ across body parts. Thus, we analyze the difference of phylosymbiotic relationships in the microbial communities found in three body parts (skin, gills, and intestine) of seven wild fish species from four families (Labridae, Sebastidae, Sparidae, and Rajidae) via 16S rRNA gene amplicon sequencing. Fishes were purchased at Docheon port market in Tongyeong City, Korea and were transported to nearby research institutes for aliveness. Mantel tests using dissimilarity values of microbiomes and hosts' divergence times showed that the differences in microbial communities in all three body parts were related to the hosts' divergence time. This pattern was the most pronounced in the skin. Furthermore, fishes from the same family showed similar bacterial compositions on their skins and gills, with clear differences depending on the family, with the exception of Labridae. These results suggest that the skin microbiome is particularly vulnerable to evolutionary pressures. We hypothesized that the evolution of the fish immune system and the difference in feeding habits induced the stronger phylosymbiotic signal in the skin. Collectively, this dataset will be useful for understanding the fish microbiome and give insights into phylosymbiosis of aquatic animals across body parts.},
}
@article {pmid39633061,
year = {2024},
author = {Paduano, S and Marchesi, I and Valeriani, F and Frezza, G and Facchini, MC and Romano Spica, V and Bargellini, A},
title = {Characterization by 16S Amplicon Sequencing of Bacterial Communities Overall and During the Maturation Process of Peloids in Two Spas of an Italian Thermal Complex.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {152},
pmid = {39633061},
issn = {1432-184X},
mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; Italy ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Clay/chemistry ; Biodiversity ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Mineral Waters/microbiology ; Phylogeny ; },
abstract = {Peloids are made by mixing clay materials with thermo-mineral waters, enriched with organic substances from microorganisms during maturation. Their beneficial properties may depend on clay minerals, water characteristics, and microbial components, although strong evidence is lacking. Next Generation Sequencing (NGS) allows a comprehensive approach to studying the entire microbial community, including cultivable and uncultivable bacteria. Our study aims to characterize, by NGS, the bacterial community overall and during the maturation process of thermal muds in two spas (A-B) of an Italian thermal complex. Peloids were produced from sulfurous-bromine-iodine thermal water and clay material: natural mud for spa A and sterile clay for spa B. Thermal waters and peloids at different maturation stages (2/4/6 months) were analyzed for microbiome characterization by 16S amplicon sequencing. Biodiversity profiles showed a low level of similarity between peloids and water used for their maturation. Peloids from spa A showed greater microbial richness than those from spa B, suggesting that natural mud with an existing bacterial community leads to greater biodiversity than sterile clay. Genera involved in sulfur metabolism were prevalent in both spas, as expected considering peloids matured in sulfide-rich water. For all three maturation stages, the prevalent genera were Thiobacillus and Pelobacter in spa A and Thiobacillus, Thauera, Pelobacter, and Desulfuromonas in spa B. Richness and diversity indices showed that the community seemed to stabilize after 2-4 months. The 16S amplicon sequencing to study bacterial communities enables the identification of a biological signature that characterizes a specific thermal matrix, defining its therapeutic and cosmetic properties. The bacterial composition of peloids is affected by the thermal water and the type of clay material used in their formulation and maturation.},
}
@article {pmid39632307,
year = {2024},
author = {Delmoitié, B and Sakarika, M and Rabaey, K and De Wever, H and Regueira, A},
title = {Tailoring non-axenic lactic acid fermentation from cheese whey permeate targeting a flexible lactic acid platform.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123529},
doi = {10.1016/j.jenvman.2024.123529},
pmid = {39632307},
issn = {1095-8630},
abstract = {Lactic acid (LA) is an important biobased platform chemical, with potential applications in synthetising a wide range of chemical products or serving as feedstock for various bioprocesses. Industrial LA production via pure culture fermentation is characterized by high operational costs and utilizes food-grade sugars, thereby reducing the feasibility of LA applications. In this context, our research focussed on valorising the largest dairy side stream, cheese whey permeate, through the use of mixed microbial communities. We evaluated the effect of different operational parameters (temperature, pH and hydraulic retention time) in non-axenic fermentations on productivity, yield, concentration, optical purity, and community. Our findings revealed that operating at mildly thermophilic conditions (45 °C) resulted in highly selective LA production, and significantly augmented the LA yield, and productivity, compared to higher temperatures (50-55 °C). In addition, operating at circumneutral pH conditions (6.0-6.5) led to significantly increased the LA fermentation performance compared to the conventional acid pH conditions (≤5.5). This led to an unprecedented LA productivity of 27.4 g/L/h with a LA yield of 70.0% which is 2.5 times higher compared to previous reported maximum. Additionally, varying pH levels influenced the optical purity of LA: we achieved an optical L-LA purity of 98.3% at pH 6.0-6.5, and an optical D-LA purity of 91.3% at a pH of 5.5. A short hydraulic retention time of less than 12 h was crucial for selective LA production. This process also yielded a microbial biomass composed of 90.3-98.6% Lactobacillus delbrueckii, which could be potentially valorised as probiotic or protein ingredient in food or feed products. Our work shows that by careful selection of operational conditions, the overall performance can be significantly increased compared to the state-of-the-art. These results highlight the potential of non-sterile LA fermentation and show that careful selection of simple reactor operation parameters can maximize process performance. A preliminary assessment suggests that valorising EU cheese whey permeate could increase LA and poly-LA production by 40 and 125 times, respectively. This could also lead to the production of 4,000 kton protein-rich biomass, potentially reducing CO2 emissions linked to EU food and feed production by 4.87% or 2.77% respectively.},
}
@article {pmid39629059,
year = {2024},
author = {Pecsi, EL and Forbes, S and Guillemette, F},
title = {Organic Matter Composition as a Driver of Soil Bacterial Responses to Pig Carcass Decomposition in a Canadian Continental Climate.},
journal = {Journal of geophysical research. Biogeosciences},
volume = {129},
number = {12},
pages = {e2024JG008355},
pmid = {39629059},
issn = {2169-8953},
abstract = {Organic by-products are released into the surrounding soil during the terrestrial decomposition of animal remains. The affected area, known as the Cadaver Decomposition Island (CDI), can undergo biochemical changes that contribute to landscape heterogeneity. Soil bacteria are highly sensitive to labile inputs, but it is unknown how they respond to shifts in dissolved organic matter (DOM) quantity and quality resulting from animal decomposition. We aimed to evaluate the relationship between soil DOM composition and bacterial activity/function in CDIs under a Canadian temperate continental climate. This was studied in soils surrounding adult pig carcasses (n = 3) that were surface deposited within a mixed forested environment (Trois-Rivières, Québec) in June 2019. Using fluorescence spectroscopy and dissolved organic carbon analyses, we detected a pulse of labile protein-like DOM during the summer season (day 55). This was found to be an important driver of heightened soil bacterial respiration, cell abundance and potential carbohydrate metabolism. These bacterial disturbances persisted into the cooler autumn season (day 156) and led to the gradual transformation of labile DOM inputs into microbially sourced humic-like compounds. By the spring (day 324), DOM quantities and bacterial measures almost recovered, but DOM quality remained distinct from surrounding vegetal humic signals. All observed effects were spatially constrained to the topsoil (A-horizon) and within 20 cm laterally from the carcasses. These findings provide valuable insight into CDI organic matter cycling within a cold-climate ecosystem. Repeated CDI studies will however be required to capture the changing dynamics resulting from increasing global temperatures.},
}
@article {pmid39628456,
year = {2024},
author = {Sinclair, JS and Buchner, D and Gessner, MO and Müller, J and Pauls, SU and Stoll, S and Welti, EAR and Bässler, C and Buse, J and Dziock, F and Enss, J and Hörren, T and Künast, R and Li, Y and Marten, A and Morkel, C and Richter, R and Seibold, S and Sorg, M and Twietmeyer, S and Weis, D and Weisser, W and Wiggering, B and Wilmking, M and Zotz, G and Frenzel, M and Leese, F and Haase, P},
title = {Effects of land cover and protected areas on flying insect diversity.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {e14425},
doi = {10.1111/cobi.14425},
pmid = {39628456},
issn = {1523-1739},
support = {//Hessisches Landesamt f&#xfc;r Umwelt und Geologie/ ; //LOEWE Centre for Translational Biodiversity Genomics/ ; 871128//EU Horizon project eLTER PLUS/ ; },
abstract = {Widespread insect losses are a critical global problem. Mitigating this problem requires identifying the principal drivers across different taxa and determining which insects are covered by protected areas. However, doing so is hindered by missing information on most species owing to extremely high insect diversity and difficulties in morphological identification. To address this knowledge gap, we used one of the most comprehensive insect DNA metabarcoding data sets assembled (encompassing 31,846 flying insect species) in which data were collected from a network of 75 Malaise traps distributed across Germany. Collection sites encompass gradients of land cover, weather, and climate, along with differences in site protection status, which allowed us to gain broader insights into how insects respond to these factors. We examined changes in total insect biomass, species richness, temporal turnover, and shifts in the composition of taxa, key functional groups (pollinators, threatened species, and invasive species), and feeding traits. Lower insect biomass generally equated to lower richness of all insects and higher temporal turnover, suggesting that biomass loss translates to biodiversity loss and less stable communities. Spatial variability in insect biomass and composition was primarily driven by land cover, rather than weather or climate change. As vegetation and land-cover heterogeneity increased, insect biomass increased by 50% in 2019 and 56% in 2020 and total species richness by 58% and 33%, respectively. Similarly, areas with low-vegetation habitats exhibited the highest richness of key taxa, including pollinators and threatened species, and the widest variety of feeding traits. However, these habitats tended to be less protected despite their higher diversity. Our results highlight the value of heterogeneous low vegetation for promoting overall insect biomass and diversity and that better protection of insects requires improved protection and management of unforested areas, where many biodiversity hotspots and key taxa occur.},
}
@article {pmid39624182,
year = {2024},
author = {Wirth, JS and Katz, LS and Williams, GM and Chen, JC},
title = {primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other.},
journal = {Journal of open source software},
volume = {9},
number = {101},
pages = {},
pmid = {39624182},
issn = {2475-9066},
abstract = {In both molecular epidemiology and microbial ecology, it is useful to be able to categorize specific strains of microorganisms in either an ingroup or an outgroup in a given population, e.g. to distinguish a pathogenic strain of interest from its non-virulent relatives. An "ingroup" refers to a group of microbes that are the primary focus of study or interest. Conversely, an "outgroup" consists of microbes that are closely-related to, but have evolved separately from, the ingroup. While whole genome sequencing and downstream phylogenetic analyses can be employed to do this, these techniques are often slow and can be resource intensive. Additionally, the laboratory would have to sequence the whole genome to use these tools to determine whether or not a new sample is part of the ingroup or outgroup. Alternatively, polymerase chain reaction (PCR) can be used to amplify regions of genetic material that are specific to the strain(s) of interest. PCR is faster, less expensive, and more accessible than whole genome sequencing, so having a PCR-based approach can accelerate the detection of specific strain(s) of microbes and facilitate diagnoses and/or population studies.},
}
@article {pmid39621250,
year = {2024},
author = {Lin, X and Lin, C and Li, X and Yao, F and Guo, X and Wang, M and Zeng, M and Yuan, Y and Xie, Q and Huang, X and Jiao, X},
title = {Gut Microbiota Dysbiosis Facilitates Susceptibility to Bloodstream Infection.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {39621250},
issn = {1976-3794},
support = {201224106490150//Shantou Science and Technology Project/ ; },
abstract = {To study the role of intestinal flora in the development of bloodstream infections (BSIs). 42 patients and 19 healthy controls (HCs) were screened into the study and their intestinal flora was measured by 16S rRNA gene sequencing. The bacterial diversity was significantly lower in the BSI group compared with that in the HCs (P < 0.001), and beta diversity was significantly differentiated between the two groups (PERMANOVA, P = 0.001). The four keystone species [Roseburia, Faecalibacterium, Prevotella, and Enterococcus (LDA > 4)] differed significantly between the two groups. Dysbiosis of fecal microbial ecology is a common condition present in patients with BSI. The proliferation of certain pathogens or reduction of SCFA-producing bacteria would cause susceptibility to BSI.},
}
@article {pmid39619625,
year = {2024},
author = {Sakarika, M and Matassa, S and Carvajal-Arroyo, JM and Ganigué, R},
title = {Editorial: Microbial biorefineries for a more sustainable, circular economy.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {12},
number = {},
pages = {1512756},
doi = {10.3389/fbioe.2024.1512756},
pmid = {39619625},
issn = {2296-4185},
}
@article {pmid39612478,
year = {2024},
author = {Zhao, Y and Ran, W and Xu, W and Song, Y},
title = {ITS amplicon sequencing revealed that rare taxa of tea rhizosphere fungi are closely related to the environment and provide feedback on tea tree diseases.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0188924},
doi = {10.1128/spectrum.01889-24},
pmid = {39612478},
issn = {2165-0497},
abstract = {The rhizospheres of plants and soil microorganisms are intricately interconnected. Tea trees are cultivated extensively on the karst plateau of Guizhou Province, China; however, the understanding of the interactions among fungal communities, community taxa, and diseases impacting tea tree in the soil rhizosphere is limited. Our aim is to offer insights for the advancement of modern agriculture in ecologically fragile karst tea gardens, as well as microbiomics concepts for green and sustainable environmental development. This study utilized the internal transcribed spacer high-throughput sequencing technology to explore the symbiotic relationship between rhizosphere fungi and plant disease feedback in multiple tea estates across the Guizhou Plateau. The ecological preferences and environmental thresholds of fungi were investigated via environmental variables. Furthermore, a correlation was established between different taxa and individual soil functions. Research has indicated that tea leaf blight disrupts symbiotic connections among fungal groups. For various taxa, we found that numerous taxa consistently maintained core positions within the community, whereas rare taxa were able to stabilize due to a high proportion of positive effects. Additionally, abundant taxa presented a wider range of environmental feedback, whereas the rare taxon diversity presented a stronger positive association with the soil Z score. This study contributes to our understanding of the importance of rare taxa in plant rhizosphere soil processes. Emphasis should be placed on the role of rare taxa in pest and disease control within green agriculture while also strengthening systematic development and biogeographical research related to rare taxa in this region.IMPORTANCEIn this study, based on internal transcribed spacer high-throughput sequencing, fungal communities in the rhizosphere soil of tea trees and their interactions with the environment in karst areas were reported, and the symbiotic relationships of different fungal taxa and their feedback to the environment were described in detail by using the knowledge of microbial ecology. On this basis, it was found that tea tree diseases affect the symbiotic relationships of fungal taxa. At the same time, we found that rare taxa have stronger cooperative relationships in response to environmental changes and explored their participation in soil processes based on fungal trait sets. This study will provide basic data for the development of modern agriculture in tea gardens and theoretical basis for the sustainable prevention and control of tea tree diseases.},
}
@article {pmid39611982,
year = {2024},
author = {Kou, Z and Liu, J and Tohti, G and Zhu, X and Zheng, B and Zhu, Y and Zhang, W},
title = {Distinct Bacterial Communities Within the Nonrhizosphere, Rhizosphere, and Endosphere of Ammodendron bifolium Under Winter Condition in the Takeermohuer Desert.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {151},
pmid = {39611982},
issn = {1432-184X},
support = {2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; },
mesh = {*Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil Microbiology ; *Desert Climate ; *Seasons ; Plant Roots/microbiology ; Soil/chemistry ; Microbiota ; },
abstract = {Due to human activities and severe climatic conditions, the population of Ammodendron bifolium, an excellent sand-fixing plant, has gradually decreased in the Takeermohuer Desert. The plant-associated bacteria community can enhance its survival in harsh environments. However, the understanding of A. bifolium-associated bacterial community is still unclear during the harsh winter. We investigated the bacterial community structure from the A. bifolium rhizosphere and nonrhizosphere at different depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) and from endosphere (i.e., root endosphere and stem endosphere) in winter. At the same time, we analyzed the impact of different compartments and soil factors on the bacterial community structure. Studies have shown that the A. bifolium rhizosphere exhibits higher levels of SOM (soil organic matter), SOC (soil organic carbon), SAN (soil alkaline nitrogen), and SAK (soil available potassium) compared with the nonrhizosphere. The dominant bacterial phyla were Proteobacteria (19.6%), Cyanobacteria (15.9%), Actinobacteria (13.6%), Acidobacteria (9.0%), and Planctomycetota (5.7%) in the desert. Proteobacteria (24.0-30.2%) had the highest relative abundance in rhizosphere, Actinobacteria (18.3-22.6%) had the highest relative abundance in nonrhizosphere, and Cyanobacteria had the highest relative abundance in endosphere. At the genus level, the relative abundance of Pseudomonas (1.2%) in the root endosphere was the highest and the other genera were mostly unclassified. The Chao1 and PD_whole_tree indices showed that the diversity of the bacterial communities decreased from nonrhizosphere, rhizosphere, root endosphere to stem endosphere. Co-occurrence network analyses identified Proteobacteria and Actinobacteria as key species across the three compartments. Additionally, unique keystone species like Cyanobacteria, Verrucomicrobiota, and Desulfobacterota were found only in the endosphere. The bacterial community in the rhizosphere was influenced by factors such as EC (electrical conductivity), STC (soil total carbon), SOM, SOC, STN (soil total nitrogen), SAN, STP (soil total phosphorus), and SAK, while that of the nonrhizosphere was mainly influenced by pH, C/N (STC/STN), SAP, and distance. The study highlighted differences in bacterial community composition, diversity, and influencing factors across the three compartments, which can provide a better understanding of the association/interactions between A. bifolium and bacterial communities and lay a foundation for revealing its adaptability in winter.},
}
@article {pmid39611949,
year = {2024},
author = {Makumbi, JP and Leareng, SK and Pierneef, RE and Makhalanyane, TP},
title = {Synergizing Ecotoxicology and Microbiome Data Is Key for Developing Global Indicators of Environmental Antimicrobial Resistance.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {150},
pmid = {39611949},
issn = {1432-184X},
support = {UID 110717//National Research Foundation of South Africa/ ; UID 110717//National Research Foundation of South Africa/ ; },
mesh = {*Microbiota/drug effects ; Humans ; *Ecotoxicology ; Animals ; Risk Assessment ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Public Health ; Drug Resistance, Microbial ; },
abstract = {The One Health concept recognises the interconnectedness of humans, plants, animals and the environment. Recent research strongly supports the idea that the environment serves as a significant reservoir for antimicrobial resistance (AMR). However, the complexity of natural environments makes efforts at AMR public health risk assessment difficult. We lack sufficient data on key ecological parameters that influence AMR, as well as the primary proxies necessary for evaluating risks to human health. Developing environmental AMR 'early warning systems' requires models with well-defined parameters. This is necessary to support the implementation of clear and targeted interventions. In this review, we provide a comprehensive overview of the current tools used globally for environmental AMR human health risk assessment and the underlying knowledge gaps. We highlight the urgent need for standardised, cost-effective risk assessment frameworks that are adaptable across different environments and regions to enhance comparability and reliability. These frameworks must also account for previously understudied AMR sources, such as horticulture, and emerging threats like climate change. In addition, integrating traditional ecotoxicology with modern 'omics' approaches will be essential for developing more comprehensive risk models and informing targeted AMR mitigation strategies.},
}
@article {pmid39611829,
year = {2024},
author = {Hameed, A and McDonagh, F and Sengupta, P and Miliotis, G and Sivabalan, SKM and Szydlowski, L and Simpson, A and Singh, NK and Rekha, PD and Raman, K and Venkateswaran, K},
title = {Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0137624},
doi = {10.1128/spectrum.01376-24},
pmid = {39611829},
issn = {2165-0497},
abstract = {UNLABELLED: During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genome sequencing and phylogenomic analyses revealed a close genetic relationship among two strains from Mars 2020 cleanroom floors (179-C4-2-HS, 179-J1A1-HS), one strain from the Agave plant (AT2.8), and another strain from wheat-associated soil (V4I25). All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566[T], delineating new phylogenetic branches within the genus. Detailed molecular analyses, including gyrB (90.2%), ANI (86.4%), average amino acid identity (87.8%) phylogenies, digital DNA-DNA hybridization (32.6%), and percentage of conserved proteins (77.7%) indicated significant divergence from N. niacini NBRC 15566[T]. Consequently, these strains have been designated Neobacillus driksii sp. nov., with the type strain 179-C4-2-HS[T] (DSM 115941[T] = NRRL B-65665[T]). N. driksii grew at 4°C to 45°C, pH range of 6.0 to 9.5, and 0.5% to 5% NaCl. The major cellular fatty acids are iso-C15:0 and anteiso-C15:0. The dominant polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. Metagenomic analysis within NASA cleanrooms revealed that N. driksii is scarce (17 out of 236 samples). Genes encoding the biosynthesis pathway for lasso peptides were identified in all N. driksii strains and are not commonly found in other Neobacillus species, except in 7 out of 26 recognized species. This study highlights the unique metabolic capabilities of N. driksii, underscoring their potential in antimicrobial research and biotechnology.<br><br>IMPORTANCE: The microbial surveillance of the Mars 2020 assembly cleanroom led to the isolation of novel N. driksii with potential applications in cleanroom environments, such as hospitals, pharmaceuticals, semiconductors, and aeronautical industries. N. driksii genomes were found to possess genes responsible for producing lasso peptides, which are crucial for antimicrobial defense, communication, and enzyme inhibition. Isolation of N. driksii from cleanrooms, Agave plants, and dryland wheat soils, suggested niche-specific ecology and resilience under various environmentally challenging conditions. The discovery of potent antimicrobial agents from novel N. driksii underscores the importance of genome mining and the isolation of rare microorganisms. Bioactive gene clusters potentially producing nicotianamine-like siderophores were found in N. driksii genomes. These siderophores can be used for bioremediation to remove heavy metals from contaminated environments, promote plant growth by aiding iron uptake in agriculture, and treat iron overload conditions in medical applications.},
}
@article {pmid39611809,
year = {2024},
author = {Mermans, F and Chatzigiannidou, I and Teughels, W and Boon, N},
title = {Quantifying synthetic bacterial community composition with flow cytometry: efficacy in mock communities and challenges in co-cultures.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0100924},
doi = {10.1128/msystems.01009-24},
pmid = {39611809},
issn = {2379-5077},
abstract = {Determination of bacterial community composition in synthetic communities is critical for understanding microbial systems. The community composition is typically determined through bacterial plating or through PCR-based methods, which can be labor-intensive, expensive, or prone to bias. Simultaneously, flow cytometry has been suggested as a cheap and fast alternative. However, since the technique captures the phenotypic state of bacterial cells, accurate determination of community composition could be affected when bacteria are co-cultured. We investigated the performance of flow cytometry for quantifying oral synthetic communities and compared it to the performance of strain specific qPCR and 16S rRNA gene amplicon sequencing. Therefore, axenic cultures, mock communities and co-cultures of oral bacteria were prepared. Random forest classifiers trained on flow cytometry data of axenic cultures were used to determine the composition of the synthetic communities, as well as strain specific qPCR and 16S rRNA gene amplicon sequencing. Flow cytometry was shown to have a lower average root mean squared error and outperformed the PCR-based methods in even mock communities (flow cytometry: 0.11 ± 0.04; qPCR: 0.26 ± 0.09; amplicon sequencing: 0.15 ± 0.01). When bacteria were co-cultured, neither flow cytometry, strain-specific qPCR, nor 16S rRNA gene amplicon sequencing resulted in similar community composition. Performance of flow cytometry was decreased compared with mock communities due to changing phenotypes. Finally, discrepancies between flow cytometry and strain-specific qPCR were found. These findings highlight the challenges ahead for quantifying community composition in co-cultures by flow cytometry.IMPORTANCEQuantification of bacterial composition in synthetic communities is crucial for understanding and steering microbial interactions. Traditional approaches like plating, strain-specific qPCR, and amplicon sequencing are often labor-intensive and expensive and limit high-throughput experiments. Recently, flow cytometry has been suggested as a swift and cheap alternative for quantifying communities and has been successfully demonstrated on simple bacterial mock communities. However, since flow cytometry measures the phenotypic state of cells, measurements can be affected by differing phenotypes. Especially, changing phenotypes resulting from co-culturing bacteria can have a profound effect on the applicability of the technique in this context. This research illustrates the feasibility and challenges of flow cytometry for the determination of community structure in synthetic mock communities and co-cultures.},
}
@article {pmid39609949,
year = {2024},
author = {Almela, P and Elser, JJ and Giersch, JJ and Hotaling, S and Rebbeck, V and Hamilton, TL},
title = {Laboratory Experiments Suggest a Limited Impact of Increased Nitrogen Deposition on Snow Algae Blooms.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70052},
doi = {10.1111/1758-2229.70052},
pmid = {39609949},
issn = {1758-2229},
support = {2113783//National Science Foundation/ ; 2113784//National Science Foundation/ ; },
mesh = {*Nitrogen/metabolism/analysis ; *Snow/chemistry ; *Phosphorus/metabolism/analysis ; *Eutrophication ; *Biomass ; },
abstract = {Snow algal blooms decrease snow albedo and increase local melt rates. However, the causes behind the size and frequency of these blooms are still not well understood. One factor likely contributing is nutrient availability, specifically nitrogen and phosphorus. The nutrient requirements of the taxa responsible for these blooms are not known. Here, we assessed the growth of three commercial strains of snow algae under 24 different nutrient treatments that varied in both absolute and relative concentrations of nitrogen and phosphorus. After 38 days of incubation, we measured total biomass and cell size and estimated their effective albedo reduction surface. Snow algal strains tended to respond similarly and achieved bloom-like cell densities over a wide range of nutrient conditions. However, the molar ratio of nitrogen to phosphorus at which maximum biomass was achieved was between 4 and 7. Our data indicate a high requirement for phosphorus for snow algae and highlights phosphorus availability as a critical factor influencing the frequency and extent of snow algae blooms and their potential contribution to snow melt through altered albedo. Snow algae can thrive across a range of nitrogen (N) and phosphorus (P) conditions, with a higher P requirement for optimal growth. Our study suggests that increased N deposition may have a limited impact on snow algae bloom occurrence and size, emphasising P as a key factor influencing these blooms and their potential to accelerate snow melt by lowering albedo.},
}
@article {pmid39609930,
year = {2024},
author = {Paquette, AJ and Bhatnagar, S and Vadlamani, A and Gillis, T and Khot, V and Novotnik, B and De la Hoz Siegler, H and Strous, M and Rattray, JE},
title = {Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {98},
pmid = {39609930},
issn = {2524-6372},
abstract = {BACKGROUND: Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.<br><br>RESULTS: Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.<br><br>CONCLUSIONS: Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.},
}
@article {pmid39608606,
year = {2024},
author = {Young Lee, J and Hyeon Jo, Y and Hee Kim, T and Eun Lee, S and Seo Hong, E and Sun Kang, T},
title = {Microbial and Sensory Characteristics of Traditional Watery Kimchi (Dongchimi) Fortified with Probiotics.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100422},
doi = {10.1016/j.jfp.2024.100422},
pmid = {39608606},
issn = {1944-9097},
abstract = {Dongchimi, a traditional Korean watery kimchi, relies on complex interactions among diverse lactic acid bacteria (LAB) to maintain its freshness and quality. Recently, dongchimi has gained attention as a health-promoting food due to its content of probiotics and prebiotics. In this study, six probiotic strains were employed into dongchimi fermentation, and its sensory and microbial characteristics were evaluated. The LAB-enriched dongchimi demonstrated superior sensory preference (63%) and significantly higher LAB counts (average 5.2 × 10[7] CFU/ml) compared to traditional dongchimi. Furthermore, microbial diversity between the LAB-enriched and traditional dongchimi was analyzed during the fermentation process using both culture-dependent Sanger sequencing and culture-independent metabarcoding techniques, employing 16S ribosomal RNA gene sequences. Lactiplantibacillus plantarum was identified as the dominant probiotic strain in both types of dongchimi, while other probiotics, including Bifidobacterium bifidum, B. animalis, Limosilactobacillus Fermentum, and Heyndrickxia coagulans, were exclusively detected in the LAB-enriched dongchimi. In conclusion, Lactiplanti. plantarum and Limosi. Fermentum were identified as the most effective probiotics for dongchimi fermentation. These results offer critical insights into the microbial ecology and probiotic strains essential for optimizing synbiotic dongchimi, thereby reinforcing health claims related to probiotics and prebiotics.},
}
@article {pmid39605469,
year = {2024},
author = {Woodruff, GC and Moser, KA and Wang, J},
title = {The Bacteria of a Fig Microcommunity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.22.624729},
pmid = {39605469},
issn = {2692-8205},
abstract = {UNLABELLED: Understanding the biotic drivers of diversity is a major goal of microbial ecology. One approach towards tackling this issue is to interrogate relatively simple communities that are easy to observe and perturb. Figs (syconia) of the genus Ficus represent such a system. Here, we describe the microbial communities of Ficus septica figs, which are associated with the nematode Caenorhabditis inopinata (the sister species of the C. elegans genetic model system). In 2019, 38 Ficus septica figs (across 12 plants in Taiwan) were dissected, and metadata such as foundress wasp number and nematode occupancy were collected for each fig. Suspensions derived from interior fig material and fig surface washes were prepared for 16S microbial metabarcoding. Over 3,000 OTUs were detected, and microbial communities were dominated by members of Proteobacteria , Bacteroidota , and Actinobacteriota . Although microbial communities of fig exteriors and interiors can be distinguished, levels of microbial alpha diversity were comparable across these areas of the fig. Nematodes likewise had no detectable impact on microbial alpha diversity, although nematodes were associated with a modest change in microbial community composition. A handful of OTUs (associated with the genera Kosokonia , Ochobactrum , and Stenotrophomonas) revealed potential differential abundance among figs varying in nematode occupancy. Additionally, foundress wasp number was negatively correlated with microbial alpha diversity. These findings set the stage for future studies that directly test the role of nematode and wasp occupancy on microbial communities, as well as investigations that probe nematode-microbe interactions through laboratory experiments. Taken together, these results constitute a fundamental step in characterizing the natural microbial communities of figs and Caenorhabditis nematodes.<br><br>IMPORTANCE: Unraveling why different species live in different places is a longstanding open question in ecology, and it is clear that interspecific interactions among species are a major contributor to species distributions. Ficus figs are a useful system for ecological studies because they are relatively simple microcosms where characterizing animal community composition of multiple samples is straightforward. Additionally, Caenorhabditis inopinata , a close relative of the C. elegans genetic model system, thrives in Ficus septica figs. Here, we tie 16S microbial metabarcoding to nematode and wasp occupancy data to understand the causes of bacterial community composition in F. septica figs. We found that microbial composition, but not total diversity, varies among fig surface and interiors. Likewise, we found that nematode occupancy impacts microbial composition but not alpha diversity. Moreover, we show that as the number of foundress wasps increases, the microbial alpha diversity decreases. Finally, we identified OTUs that are potentially associated with nematode occupancy. Taken together, these results represent a key step in describing a microcommunity wherein ecological genetic hypotheses can be tested, as well as one that can potentially reveal the roles of uncharacterized genes in established model systems.},
}
@article {pmid39604741,
year = {2024},
author = {de Freitas, AS and Carlos, FS and Martins, GL and Monteiro, GGTN and Roesch, LFW},
title = {Bacterial Resilience and Community Shifts Under 11 Draining-Flooding Cycles in Rice Soils.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {149},
pmid = {39604741},
issn = {1432-184X},
mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Floods ; *Soil/chemistry ; Brazil ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Ecosystem ; },
abstract = {Flooded rice cultivation, accounting for 75% of global rice production, significantly influences soil redox potential, element speciation, pH, and nutrient availability, presenting challenges such as extensive water usage and altered soil properties. This study investigates bacterial community dynamics in rice soils subjected to repeated draining and flooding in Rio Grande do Sul, Brazil. We demonstrate that bacterial communities exhibit remarkable resilience (the capacity to recover after being altered by a disturbance) but cannot remain stable after long-term exposure to environmental changes. The beta diversity analysis revealed four distinct community states after 11 draining/flooding cycles, indicating resilience over successive environment changes. However, the consistent environmental disturbance reduced microbial resilience, causing the bacterial community structure to shift over time. Those differences were driven by substitutions of taxa and functions and not by the loss of diversity. Notable shifts included a decline in Acidobacteria and an increase in Proteobacteria and Chloroflexi. Increased Verrucomicrobia abundance corresponded with lower pH levels. Functional predictions suggested dynamic metabolic responses, with increased nitrification during drained cycles and a surge in fermenters after the sixth cycle. Despite cyclic disturbances, bacterial communities exhibit resilience, contributing to stable ecosystem functioning in flooded rice soils. These findings enhance our understanding of microbial adaptation, providing insights into sustainable rice cultivation and soil management practices.},
}
@article {pmid39603473,
year = {2024},
author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T},
title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131878},
doi = {10.1016/j.biortech.2024.131878},
pmid = {39603473},
issn = {1873-2976},
abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %∼74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.},
}
@article {pmid39601575,
year = {2024},
author = {Maguire, M and Serna, C and Montero Serra, N and Kovarova, A and O'Connor, L and Cahill, N and Hooban, B and DeLappe, N and Brennan, W and Devane, G and Cormican, M and Morris, D and Coughlan, SC and Miliotis, G and Gonzalez-Zorn, B and Burke, LP},
title = {Spatiotemporal and genomic analysis of carbapenem resistance elements in Enterobacterales from hospital inpatients and natural water ecosystems of an Irish city.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0090424},
doi = {10.1128/spectrum.00904-24},
pmid = {39601575},
issn = {2165-0497},
abstract = {Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control of infections are complicated due to the inter-species spread of carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids and transposons. Due to wastewater discharges, urban water ecosystems represent a known reservoir of CPE. However, the dynamics of carbapenemase-bearing MGE dissemination between Enterobacterales in humans and environmental waters are poorly understood. We carried out whole-genome sequencing, combining short- and long-sequencing reads to enable complete characterization of CPE isolated from patients, wastewaters, and natural waters between 2018 and 2020 in Galway, Ireland. Isolates were selected based on their carriage of Class A blaKPC-2 (n = 6), Class B blaNDM-5 (n = 12), and Class D blaOXA-48 (n = 21) CEGs. CEGs were plasmid-borne in all but two isolates. OXA-48 dissemination was associated with a 64 kb IncL plasmid (62%), in a broad range of Enterobacterales isolates from both niches. Conversely, blaKPC-2 and blaNDM-5 genes were usually carried on larger and more variable multireplicon IncF plasmids in Klebsiella pneumoniae and Escherichia coli, respectively. In every isolate, each CEG was surrounded by a gene-specific common genetic environment which constituted part, or all, of a transposable element that was present in both plasmids and the bacterial chromosome. Transposons Tn1999 and Tn4401 were associated with blaOXA-48 and blaKPC-2, respectively, while blaNDM-5 was associated with variable IS26 bound composite transposons, usually containing a class 1 integron.IMPORTANCESince 2018, the Irish National Carbapenemase-Producing Enterobacterales (CPE) Reference Laboratory Service at University Hospital Galway has performed whole-genome sequencing on suspected and confirmed CPE from clinical specimens as well as patient and environmental screening isolates. Understanding the dynamics of CPE and carbapenemase-encoding gene encoding mobile genetic element (MGE) flux between human and environmental reservoirs is important for One Health surveillance of these priority organisms. We employed hybrid assembly approaches for improved resolution of CPE genomic surveillance, typing, and plasmid characterization. We analyzed a diverse collection of human (n = 17) and environmental isolates (n = 22) and found common MGE across multiple species and in different ecological niches. The conjugation ability and frequency of a subset of these plasmids were demonstrated to be affected by the presence or absence of necessary conjugation genes and by plasmid size. We characterize several MGE at play in the local dissemination of carbapenemase genes. This may facilitate their future detection in the clinical laboratory.},
}
@article {pmid39601521,
year = {2024},
author = {Atkinson, CGF and Kerns, KA and Hendrickson, EL and He, X and Bor, B and McLean, JS},
title = {Complete genome of Nanosynbacter sp. strain BB002, isolated and cultivated from a site of periodontal disease.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0063724},
doi = {10.1128/mra.00637-24},
pmid = {39601521},
issn = {2576-098X},
abstract = {Nanosynbacter sp. strain BB002, was isolated from the human oral cavity on its basibiont bacterial host Actinomyces sp. oral taxon 171 strain F0337, related to Actinomyces oris. As a member of the Saccharibacteria within the candidate phylum radiation group (CPR), its reduced genome facilitates the survival as an ultrasmall (<0.2 μm) epibiont.},
}
@article {pmid39597739,
year = {2024},
author = {Sun, X and Liu, Y and He, L and Kuang, Z and Dai, S and Hua, L and Jiang, Q and Wei, T and Ye, P and Zeng, H},
title = {Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112350},
pmid = {39597739},
issn = {2076-2607},
support = {2023NSFSC1262//the Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2024-19//Sichuan Innovation Team of the Chinese National Modern Agriculture Industry Technology System/ ; CARS-21-21//National Chinese Medicinal Materials Technology System/ ; 2022ZZCX078//Sichuan Provincial Finance Independent Innovation Project/ ; },
abstract = {Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.},
}
@article {pmid39597685,
year = {2024},
author = {Zhang, K and Chen, X and Shi, X and Yang, Z and Yang, L and Liu, D and Yu, F},
title = {Endophytic Bacterial Community, Core Taxa, and Functional Variations Within the Fruiting Bodies of Laccaria.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112296},
pmid = {39597685},
issn = {2076-2607},
support = {202205AD160036//the Yunnan Technology Innovation/ ; 42077072//the National Natural Science Foundation of Management Practices China/ ; },
abstract = {Macrofungi do not exist in isolation but establish symbiotic relationships with microorganisms, particularly bacteria, within their fruiting bodies. Herein, we examined the fruiting bodies' bacteriome of seven species of the genus Laccaria collected from four locations in Yunnan, China. By analyzing bacterial diversity, community structure, and function through 16S rRNA sequencing, we observed the following: (1) In total, 4,840,291 high-quality bacterial sequences obtained from the fruiting bodies were grouped into 16,577 amplicon sequence variants (ASVs), and all samples comprised 23 shared bacterial ASVs. (2) The Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex was found to be the most abundant and presumably coexisting bacterium. (3) A network analysis revealed that endophytic bacteria formed functional groups, which were dominated by the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Novosphingobium, and Variovorax. (4) The diversity, community structure, and dominance of ecological functions (chemoheterotrophy and nitrogen cycling) among endophytic bacteria were significantly shaped by geographic location, habitat, and fungal genotype, rather than fruiting body type. (5) A large number of the endophytic bacteria within Laccaria are bacteria that promote plant growth; however, some pathogenic bacteria that pose a threat to human health might also be present. This research advances our understanding of the microbial ecology of Laccaria and the factors shaping its endophytic bacterial communities.},
}
@article {pmid39597671,
year = {2024},
author = {Skliros, D and Kostakou, M and Kokkari, C and Tsertou, MI and Pavloudi, C and Zafeiropoulos, H and Katharios, P and Flemetakis, E},
title = {Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112281},
pmid = {39597671},
issn = {2076-2607},
support = {5010932//Operational Program Fisheries and Maritime 2014-2020/ ; },
abstract = {The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.},
}
@article {pmid39597543,
year = {2024},
author = {Wu, D and He, X and Lu, Y and Gao, Z and Chong, Y and Hong, J and Wu, J and Deng, W and Xi, D},
title = {Effects of Different Dietary Combinations on Blood Biochemical Indicators and Rumen Microbial Ecology in Wenshan Cattle.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112154},
pmid = {39597543},
issn = {2076-2607},
abstract = {With the continuous optimization of feed ingredients in livestock production, barley has garnered significant attention as a potential substitute for corn in feed. This study aims to investigate the effects of replacing part of the corn and soybean meal with barley, wheat bran, and rapeseed meal on Wenshan cattle, focusing on the rumen microbial community, blood physiological and biochemical indicators, and growth traits. Through an intensive feeding experiment with two different dietary ratios, we found that adding barley to the diet significantly reduced the host's blood lipid concentration and significantly increased the height, body length, heart girth, and average daily weight gain of Wenshan cattle. Analysis of the rumen microbial community structure showed that the addition of barley significantly affected the relative abundance of Firmicutes, Proteobacteria, and Bacteroidetes, with the relative abundance of Spirochaetes being significantly lower than that of the control group (p < 0.05). The dominant bacterial groups mainly included Acinetobacter, Solibacillus, and Lysinibacillus. In summary, this study reveals the potential of different feed ingredient ratios involving barley, wheat bran, and rapeseed meal in the production performance of Wenshan cattle. By regulating blood physiology and improving the rumen micro-ecological structure, it provides new scientific evidence for optimizing livestock and poultry feeding management strategies. Future research will further explore the optimal application ratio of barley under different feeding conditions and its long-term impact on animal health and production performance.},
}
@article {pmid39597512,
year = {2024},
author = {Banerji, A and Brinkman, NE and Davis, B and Franklin, A and Jahne, M and Keely, SP},
title = {Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112121},
pmid = {39597512},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.},
}
@article {pmid39596705,
year = {2024},
author = {Moraes, BDGC and Martins, RCR and Fonseca, JVDS and Franco, LAM and Pereira, GCO and Bartelli, TF and Cortes, MF and Scaccia, N and Santos, CF and Musqueira, PT and Otuyama, LJ and Pylro, VS and Mariano, L and Rocha, V and Witkin, SS and Sabino, E and Guimaraes, T and Costa, SF},
title = {Impact of Exogenous Lactiplantibacillus plantarum on the Gut Microbiome of Hematopoietic Stem Cell Transplantation Patients Colonized by Multidrug-Resistant Bacteria: An Observational Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/antibiotics13111010},
pmid = {39596705},
issn = {2079-6382},
support = {FAPESP//001/ ; },
abstract = {Background:Lactiplantibacillus plantarum can inhibit the growth of multidrug-resistant organisms (MDROs) and modulate the gut microbiome. However, data on hematopoietic stem cell transplantation (HSCT) are scarce. Aim: In an observational study, we assessed the impact of L. plantarum on the modulation of the gut microbiome in HSCT patients colonized by MDROs. Methods: Participants were allocated to an intervention group (IG = 22) who received capsules of L. plantarum (5 × 10[9] CFU) twice per day until the onset of neutropenia or a control group (CG = 20). The V4 region of the 16S bacterial rRNA gene was sequenced in 87 stool samples from a subset of 33 patients (IG = 20 and CG = 13). The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) program was used to predict metagenome functions. Results:L. plantarum demonstrated an average 86% (±11%) drug-target engagement at 43 (±29) days of consumption and was deemed safe, well-tolerated, and associated with an increase in the abundance of the Lactobacillales (p < 0.05). A significant increase in Lactococcus and a reduction in Turicibacter (p < 0.05) were identified on the second week of L. plantarum use. Although Enterococcus abundance had a greater rise in the CG (p = 0.07), there were no significant differences concerning the Gram-negative MDROs. No serious adverse effects were reported in the IG. We observed a greater, non-significant pyruvate fermentation to propanoate I (p = 0.193) relative abundance in the IG compared with the CG. L. plantarum use was safe and tolerable by HSCT patients. Conclusions: While L. plantarum is safe and may impact Enterococcus and Turicibacter abundance, it showed no impact on Gram-negative MDRO abundance in HSCT patients.},
}
@article {pmid39592542,
year = {2024},
author = {Kaur, T and Devi, R and Negi, R and Kour, H and Singh, S and Khan, SS and Kumari, C and Kour, D and Chowdhury, S and Kapoor, M and Rai, AK and Rustagi, S and Shreaz, S and Yadav, AN},
title = {Macronutrients-availing microbiomes: biodiversity, mechanisms, and biotechnological applications for agricultural sustainability.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39592542},
issn = {1874-9356},
abstract = {Nitrogen, phosphorus, and potassium are the three most essential micronutrients which play major roles in plant survivability by being a structural or non-structural component of the cell. Plants acquire these nutrients from soil in the fixed (NO3[¯], NH4[+]) and solubilized forms (K[+], H2PO4[-] and HPO4[2-]). In soil, the fixed and solubilized forms of nutrients are unavailable or available in bare minimum amounts; therefore, agrochemicals were introduced. Agrochemicals, mined from the deposits or chemically prepared, have been widely used in the agricultural farms over the decades for the sake of higher production of the crops. The excessive use of agrochemicals has been found to be deleterious for humans, as well as the environment. In the environment, agrochemical usage resulted in soil acidification, disturbance of microbial ecology, and eutrophication of aquatic and terrestrial ecosystems. A solution to such devastating agro-input was found to be substituted by macronutrients-availing microbiomes. Macronutrients-availing microbiomes solubilize and fix the insoluble form of nutrients and convert them into soluble forms without causing any significant harm to the environment. Microbes convert the insoluble form to the soluble form of macronutrients (nitrogen, phosphorus, and potassium) through different mechanisms such as fixation, solubilization, and chelation. The microbiomes having capability of fixing and solubilizing nutrients contain some specific genes which have been reported in diverse microbial species surviving in different niches. In the present review, the biodiversity, mechanism of action, and genomics of different macronutrients-availing microbiomes are presented.},
}
@article {pmid39587399,
year = {2024},
author = {Trevathan-Tackett, SM and Kepfer-Rojas, S and Malerba, M and Macreadie, PI and Djukic, I and Zhao, J and Young, EB and York, PH and Yeh, SC and Xiong, Y and Winters, G and Whitlock, D and Weaver, CA and Watson, A and Visby, I and Tylkowski, J and Trethowan, A and Tiegs, S and Taylor, B and Szpikowski, J and Szpikowska, G and Strickland, VL and Stivrins, N and Sousa, AI and Sinutok, S and Scheffel, WA and Santos, R and Sanderman, J and Sánchez-Carrillo, S and Sanchez-Cabeza, JA and Rymer, KG and Ruiz-Fernandez, AC and Robroek, BJM and Roberts, T and Ricart, AM and Reynolds, LK and Rachlewicz, G and Prathep, A and Pinsonneault, AJ and Pendall, E and Payne, R and Ozola, I and Onufrock, C and Ola, A and Oberbauer, SF and Numbere, AO and Novak, AB and Norkko, J and Norkko, A and Mozdzer, TJ and Morgan, P and Montemayor, DI and Martin, CW and Malone, SL and Major, M and Majewski, M and Lundquist, CJ and Lovelock, CE and Liu, S and Lin, HJ and Lillebo, A and Li, J and Kominoski, JS and Khuroo, AA and Kelleway, JJ and Jinks, KI and Jerónimo, D and Janousek, C and Jackson, EL and Iribarne, O and Hanley, T and Hamid, M and Gupta, A and Guariento, RD and Grudzinska, I and da Rocha Gripp, A and González Sagrario, MA and Garrison, LM and Gagnon, K and Gacia, E and Fusi, M and Farrington, L and Farmer, J and de Assis Esteves, F and Escapa, M and Domańska, M and Dias, ATC and de Los Santos, CB and Daffonchio, D and Czyryca, PM and Connolly, RM and Cobb, A and Chudzińska, M and Christiaen, B and Chifflard, P and Castelar, S and Carneiro, LS and Cardoso-Mohedano, JG and Camden, M and Caliman, A and Bulmer, RH and Bowen, J and Boström, C and Bernal, S and Berges, JA and Benavides, JC and Barry, SC and Alatalo, JM and Al-Haj, AN and Adame, MF},
title = {Climate Effects on Belowground Tea Litter Decomposition Depend on Ecosystem and Organic Matter Types in Global Wetlands.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02116},
pmid = {39587399},
issn = {1520-5851},
abstract = {Patchy global data on belowground litter decomposition dynamics limit our capacity to discern the drivers of carbon preservation and storage across inland and coastal wetlands. We performed a global, multiyear study in over 180 wetlands across 28 countries and 8 macroclimates using standardized litter as measures of "recalcitrant" (rooibos tea) and "labile" (green tea) organic matter (OM) decomposition. Freshwater wetlands and tidal marshes had the highest tea mass remaining, indicating a greater potential for carbon preservation in these ecosystems. Recalcitrant OM decomposition increased with elevated temperatures throughout the decay period, e.g., increase from 10 to 20 °C corresponded to a 1.46-fold increase in the recalcitrant OM decay rate constant. The effect of elevated temperature on labile OM breakdown was ecosystem-dependent, with tidally influenced wetlands showing limited effects of temperature compared with freshwater wetlands. Based on climatic projections, by 2050 wetland decay constants will increase by 1.8% for labile and 3.1% for recalcitrant OM. Our study highlights the potential for reduction in belowground OM in coastal and inland wetlands under increased warming, but the extent and direction of this effect at a large scale is dependent on ecosystem and OM characteristics. Understanding local versus global drivers is necessary to resolve ecosystem influences on carbon preservation in wetlands.},
}
@article {pmid39587087,
year = {2024},
author = {Whalen, ED and Grandy, AS and Geyer, KM and Morrison, EW and Frey, SD},
title = {Microbial trait multifunctionality drives soil organic matter formation potential.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10209},
pmid = {39587087},
issn = {2041-1723},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism ; *Carbon/metabolism ; Biomass ; Organic Chemicals/metabolism ; },
abstract = {Soil microbes are a major source of organic residues that accumulate as soil organic matter, the largest terrestrial reservoir of carbon on Earth. As such, there is growing interest in determining the microbial traits that drive soil organic matter formation and stabilization; however, whether certain microbial traits consistently predict soil organic matter accumulation across different functional pools (e.g., total vs. stable soil organic matter) is unresolved. To address these uncertainties, we incubated individual species of fungi in soil organic matter-free model soils, allowing us to directly relate the physiological, morphological, and biochemical traits of fungi to their soil organic matter formation potentials. We find that the formation of different soil organic matter functional pools is associated with distinct fungal traits, and that 'multifunctional' species with intermediate investment across this key grouping of traits (namely, carbon use efficiency, growth rate, turnover rate, and biomass protein and phenol contents) promote soil organic matter formation, functional complexity, and stability. Our results highlight the limitations of categorical trait-based frameworks that describe binary trade-offs between microbial traits, instead emphasizing the importance of synergies among microbial traits for the formation of functionally complex soil organic matter.},
}
@article {pmid39586934,
year = {2024},
author = {Rong, X and Liu, X and Du, F and Aanderud, ZT and Zhang, Y},
title = {Biocrusts Mediate the Niche Distribution and Diversity of Ammonia-Oxidizing Microorganisms in the Gurbantunggut Desert, Northwestern China.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {148},
pmid = {39586934},
issn = {1432-184X},
support = {2022TSYCCX0007//the Xinjiang Tianshan Youth Talent Top Project/ ; 2022D01D083//the Key Fund Projects of the Natural Science Foundation of Xinjiang/ ; U2003214//the National Natural Science Foundation of China/ ; },
mesh = {*Archaea/genetics/metabolism/classification ; *Desert Climate ; *Ammonia/metabolism ; *Soil Microbiology ; China ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Oxidation-Reduction ; Soil/chemistry ; Biodiversity ; Ecosystem ; Seasons ; Microbiota ; Nitrification ; },
abstract = {Biological soil crusts (biocrusts) play pivotal ecological roles in regulating nitrogen cycling within desert ecosystems. While acknowledging the essential role played by ammonia-oxidizing microorganisms in nitrogen transformation, there remains a paucity of understanding concerning how disturbances to biocrusts impact the diversity and spatial distribution patterns among ammonia oxidizer communities within temperate deserts. This investigation delved into assessing how 4 years' worth of removing biocrust influenced niche differentiation between nitrifying archaea and bacteria while also examining its effects on shaping community structures of predominant ammonia-oxidizing archaea (AOA) within the Gurbantunggut Desert soils. Despite notable variations in abundance of ammonia-oxidizing microbes across distinct soil depths throughout different seasons, it became apparent that removing biocrust significantly altered both the abundance and niche pattern for AOA alongside their bacterial counterparts during winter and summer periods. Notably dominating over their bacterial counterparts within desert soils, AOA displayed their highest archaeal to bacterial amoA gene copy ratio (6549-fold higher) at a soil depth of 5-10 cm during summer. Moreover, substantial impacts were observed upon AOA diversity along with compositional changes following such perturbation events. The aftermath saw an emergence of more diffuse yet dynamic AOA communities, especially noticeable amidst winter when nitrogen and water limitations were relatively alleviated. In summary, our findings underscore how interactions between biocrust coverages alongside factors like soil temperature, total carbon content, or NO3[-]_N concentrations govern niches occupied by ammoxidation communities whilst influencing assemblage processes too. The sensitivity shown by dominant AOAs towards biocrust removal further underscores how biocrust coverage influences nitrogen transformation processes while potentially involving other communities and functions in desert ecosystems.},
}
@article {pmid39585925,
year = {2024},
author = {Richards, TA and Eme, L and Archibald, JM and Leonard, G and Coelho, SM and de Mendoza, A and Dessimoz, C and Dolezal, P and Fritz-Laylin, LK and Gabaldón, T and Hampl, V and Kops, GJPL and Leger, MM and Lopez-Garcia, P and McInerney, JO and Moreira, D and Muñoz-Gómez, SA and Richter, DJ and Ruiz-Trillo, I and Santoro, AE and Sebé-Pedrós, A and Snel, B and Stairs, CW and Tromer, EC and van Hooff, JJE and Wickstead, B and Williams, TA and Roger, AJ and Dacks, JB and Wideman, JG},
title = {Reconstructing the last common ancestor of all eukaryotes.},
journal = {PLoS biology},
volume = {22},
number = {11},
pages = {e3002917},
doi = {10.1371/journal.pbio.3002917},
pmid = {39585925},
issn = {1545-7885},
abstract = {Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.},
}
@article {pmid39583547,
year = {2024},
author = {Yang, X and Gänzle, M and Wang, R},
title = {Editorial: How the application of antimicrobial hurdles in meat processing facilities shapes microbial ecology.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1501925},
pmid = {39583547},
issn = {1664-302X},
}
@article {pmid39348267,
year = {2024},
author = {Clegg, T and Pawar, S},
title = {Variation in thermal physiology can drive the temperature-dependence of microbial community richness.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.84662},
pmid = {39348267},
issn = {2050-084X},
support = {NERC QMEE Centre for Doctoral Training NE/P012345/1//Natural Environment Research Council/ ; RF-2020-653\2//Leverhulme Trust/ ; NE/M020843/1//NERC Natural Environment Research Council/ ; NE/S000348/1//NERC Natural Environment Research Council/ ; },
mesh = {*Temperature ; *Microbiota/physiology ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Bacterial Physiological Phenomena ; },
abstract = {Predicting how species diversity changes along environmental gradients is an enduring problem in ecology. In microbes, current theories tend to invoke energy availability and enzyme kinetics as the main drivers of temperature-richness relationships. Here, we derive a general empirically-grounded theory that can explain this phenomenon by linking microbial species richness in competitive communities to variation in the temperature-dependence of their interaction and growth rates. Specifically, the shape of the microbial community temperature-richness relationship depends on how rapidly the strength of effective competition between species pairs changes with temperature relative to the variance of their growth rates. Furthermore, it predicts that a thermal specialist-generalist tradeoff in growth rates alters coexistence by shifting this balance, causing richness to peak at relatively higher temperatures. Finally, we show that the observed patterns of variation in thermal performance curves of metabolic traits across extant bacterial taxa is indeed sufficient to generate the variety of community-level temperature-richness responses observed in the real world. Our results provide a new and general mechanism that can help explain temperature-diversity gradients in microbial communities, and provide a quantitative framework for interlinking variation in the thermal physiology of microbial species to their community-level diversity.},
}
@article {pmid39578630,
year = {2024},
author = {Barber, DG and Child, HT and Joslin, GR and Wierzbicki, L and Tennant, RK},
title = {Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28934},
pmid = {39578630},
issn = {2045-2322},
support = {CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; },
mesh = {*Metagenomics/methods ; *Soil Microbiology ; Soil/chemistry ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Metagenomic analysis has enabled insights into soil community structure and dynamics. Long-read sequencing for metagenomics can enhance microbial ecology by improving taxonomic classification, genome assembly, and functional annotation. However, protocols for purifying high-molecular weight DNA from soil are not yet optimised. We used a statistical design of experiments approach to enhance mechanical lysis of soil samples, increasing the length of purified DNA fragments. Low energy input into mechanical lysis improved DNA integrity, resulting in longer sequenced reads. Our optimized settings of 4 m s[-1] for 10 s increased fragment length by 70% compared to the manufacturer's recommendations. Longer reads from low intensity lysis produced longer contiguous sequences after assembly, potentially improving a range of down-stream analyses. Importantly, there was minimal bias exhibited in the microbial community composition due to lysis efficiency variations. We therefore propose a framework for improving the fragment lengths of DNA purified from diverse soil types, improving soil science research with long-read sequencing.},
}
@article {pmid39572704,
year = {2024},
author = {Li, J and Göbel, F and Hsu, HY and Koch, JN and Hager, N and Flegler, WA and Tanabe, TS and Dahl, C},
title = {YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1548},
pmid = {39572704},
issn = {2399-3642},
support = {Da 351/8-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/13-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/14-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Signal Transduction ; *Bacterial Proteins/metabolism/genetics ; *Gene Expression Regulation, Bacterial ; Biological Transport ; },
abstract = {Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. SoxT1A mutants are sulfur oxidation-negative despite high transcription levels of sulfur oxidation genes, showing that SoxT1A delivers sulfur to the cytoplasm for its further oxidation. SoxT1B serves as a signal transduction unit for the transcriptional repressor SoxR, as SoxT1B mutants are sulfur oxidation-negative due to low transcription unless SoxR is also absent. Thus, SoxT1A and SoxT1B play essential but distinct roles in oxidative sulfur metabolism and its regulation.},
}
@article {pmid39572621,
year = {2024},
author = {Rabenhorst, SHB and Ferrasi, AC and Barboza, MMO and Melo, VMM},
title = {Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28890},
pmid = {39572621},
issn = {2045-2322},
support = {07939716/2020//Funda&#xe7;&#xe3;o Cearense de Apoio ao Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Humans ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/microbiology/pathology ; *Stomach Neoplasms/microbiology/pathology ; *Gastritis/microbiology/pathology ; Virulence ; *Gastric Mucosa/microbiology/pathology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Metaplasia/microbiology ; Adult ; Gastrointestinal Microbiome ; },
abstract = {Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.},
}
@article {pmid39572453,
year = {2024},
author = {Méndez, A and Sanmartín, P and Balboa, S and Trueba-Santiso, A},
title = {Environmental Proteomics Elucidates Phototrophic Biofilm Responses to Ornamental Lighting on Stone-built Heritage.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {147},
pmid = {39572453},
issn = {1432-184X},
support = {04_IN606D_2021_2598528//Programa de Doutoramento Industrial - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; RYC2020-029987-I//Ram&#xf3;n y Cajal contract - Spanish State Research Agency (AEI)/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; },
mesh = {*Biofilms/radiation effects/growth &amp; development ; *Proteomics ; Light ; Phototrophic Processes ; Cyanobacteria/metabolism/radiation effects/physiology ; Chlorophyta/radiation effects/metabolism/physiology ; Proteome ; Lighting ; },
abstract = {Recent studies are showing that some lights suitable for illuminating the urban fabric (i.e. that do not include the red, green and blue sets of primary colours) may halt biological colonisation on monuments, mainly that caused by phototrophic subaerial biofilms (SABs), which may exacerbate the biodeterioration of substrates. However, the light-triggered mechanisms that cause changes in the growth of the phototrophs remain unknown. Environmental proteomics could be used to provide information about the changes in the SAB metabolism under stress inflicted by nocturnal lighting. Here, laboratory-produced SABs, composed of Chlorophyta, Streptophyta and Cyanobacteriota, were subjected to three types of lighting used for monuments: cool white, warm white and amber + green (potentially with a biostatic effect). A control without light (i.e. darkness) was also included for comparison. The nocturnal lighting impaired the capacity of the SABs to decompose superoxide radicals and thus protect themselves from oxidative stress. Cool white and warm white light both strongly affected the proteomes of the SABs and reduced the total peptide content, with the extent of the reduction depending on the genera of the organisms involved. Analysis of the photo-damaging effect of amber + green light on the biofilm metabolism revealed a negative impact on photosystems I and II and production of photosystem antenna protein-like, as well as a triggering effect on protein metabolism (synthesis, folding and degradation). This research provides, for the first-time, a description of the proteomic changes induced by lighting on SABs colonising illuminated monuments in urban areas.},
}
@article {pmid39571806,
year = {2024},
author = {Graham, A and Thorn, C and McDonagh, M and O'Donnell, C and Nolan, S and Kirwan, SF and O'Connor, S and Nzeteu, CO and Montoya, ACV and Bartle, A and Hall, A and Abberton, C and Friel, R and Waters, SM and O'Flaherty, V},
title = {Development and in-vitro assessment of novel oxygen-releasing feed additives to reduce enteric ruminant methane emissions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177598},
doi = {10.1016/j.scitotenv.2024.177598},
pmid = {39571806},
issn = {1879-1026},
abstract = {Ruminant livestock contribute significantly to global methane production and mitigation of which is of utmost importance. Feed additives represent a cost-effective means of achieving this. A potential target for such additives is rumen Oxidative Reduction Potential (ORP), a parameter which influences CH4 production rates, with methanogenesis occurring optimally at ORPs below -300 mV. Thus, a controlled elevation of rumen ORP represents a potentially benign means of methanogen suppression. This research involved assessing a range of oxygen-releasing compounds for their ability to increase rumen ORP and inhibit methanogenesis, using the in-vitro rumen simulation technique (RUSITEC). Seven potential CH4 inhibitors were tested in a 21-day trial monitoring biogas volume, CH4 content, ORP, digestibility, ammonia, and volatile fatty acids concentration. The additives evaluated included: liquid peroxide (H2O2) and urea hydrogen peroxide (UHP), as well as slower reacting species (calcium and magnesium peroxide), in addition to encapsulated liquid H2O2 for controlled, slow release. Consistent CH4 reductions of >50 % were observed from all additives. Reduced neutral detergent fibre (NDF) digestibility and a reduction in total volatile fatty acids (VFAs) was observed for some treatments, but MgO2 and encapsulated H2O2 reduced CH4 volume by 62 % and 58 %, respectively, and had no detrimental effects on digestibility (p > 0.05) or on VFA production. Ex-situ ORP measurements demonstrated significant increases in ORP upon addition of the additives, with MgO2 and encapsulated H2O2 inducing a more moderate effect suggesting a controlled additive release was achieved with the slow-release format of encapsulated liquid H2O2. Thus, potential slow-release forms deemed suitable to progress to bolus or pellet format in-vivo were identified and could enable a longer-lasting suppression of methanogens within the rumen, facilitating application in both intensive and pasture-based production systems.},
}
@article {pmid39571521,
year = {2024},
author = {Zuo, J and Yang, S and Grossart, HP and Xiao, P and Zhang, H and Sun, R and Li, G and Jiang, H and Zhao, Q and Jiao, M and Cheng, Y and Wang, Z and Geng, R and Ma, Z and Li, R},
title = {Sequential decline in cyanobacterial, total prokaryotic, and eukaryotic responses to backward flow in a river connected to Lake Taihu.},
journal = {Water research},
volume = {269},
number = {},
pages = {122784},
doi = {10.1016/j.watres.2024.122784},
pmid = {39571521},
issn = {1879-2448},
abstract = {River ecosystems face escalating challenges due to altered flow regimes from human activities, such as urbanization with hydrological modifications. Understanding the role of microbial communities for ecosystems with changing flow regimes is still incomplete and remains at the frontier of aquatic microbial ecology. In particular, influences of riverine backward flow on the aquatic biota remain largely unknown. Therefore, we examined the impact of backward flow on the cyanobacterial, total prokaryotic, and eukaryotic communities in the Changdougang River, which naturally flows into Lake Taihu, through environmental DNA metabarcoding. We analyzed the differences in community diversity, assembly, and ecological network stability among groups under backward, weak, and forward flow direction conditions. Non-metric multidimensional scaling showed higher variations in communities of groups across flow direction conditions than seasonal groups. Variations in alpha and beta diversity showed that cyanobacterial and total prokaryotic communities experienced strong homogenization under backward flow conditions, whereas the ecological uniqueness of the eukaryotic community decreased. Assembly of the three flow-related communities was primarily governed by drift and dispersal limitation in stochastic processes. However, in the cyanobacterial community, homogeneous selection in deterministic processes increased from 22.79 % to 42.86 % under backward flow, aligning with trends observed in the checkerboard score (C-score). More importantly, the topological properties of ecological networks and the degree of average variation revealed higher stability in the cyanobacterial community compared to total prokaryotic and eukaryotic communities. Considering the variations in cohesion, the network stability in the cyanobacterial community decreased under backward flow. Our findings emphasize the distinct and sequentially diminishing responses of cyanobacterial, total prokaryotic, and eukaryotic communities to backward flowing rivers. This knowledge is crucial for maintaining ecological health of rivers, assessing the complex ecological impacts on hydrological engineering, and formulating sustainable water management strategies.},
}
@article {pmid39570409,
year = {2024},
author = {Xu, H and Zhang, Y and Fan, D and Meng, S and Fan, L and Song, C and Qiu, L and Li, D and Fang, L and Liu, Z and Bing, X},
title = {Influences of Community Coalescence on the Assembly of Bacterial Communities of the Small-Scale Complex Aquatic System from the Perspective of Bacterial Transmission, Core Taxa, and Co-occurrence Patterns.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {145},
pmid = {39570409},
issn = {1432-184X},
support = {2023JBFR01//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; CARS-46//the earmarked fund for CARS/ ; 2023TD18//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; },
mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Aquaculture ; *Rhizosphere ; *Feces/microbiology ; Animals ; Biofilms ; Fishes/microbiology ; Water Microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Recirculating aquaculture and aquaponics are considered sustainable aquaculture models playing important roles in animal-derived protein supply. In these aquaculture systems, microorganisms are crucial for the system stability. The community coalescence by mixing substances and microorganisms from various microhabitats under hydraulic forces is important for shaping the bacterial communities in these small-scale complex systems. However, the influences of community coalescence on bacterial communities remain rarely revealed in these systems. In this study, aquaponics (APS) and recirculating aquaculture (RAS) systems were set up to explore the bacterial community coalescence across different microhabitats, including water, fish feces, biofilter biofilms, and plant rhizosphere environment. Our results showed that diversity and compositions varied across different microhabitats in both systems. However, bacterial transmissions across these microhabitats differed between systems. The core microbiome of the RAS and APS were formed under community coalescence with the highest contribution of bacterial taxa derived from the fish feces. Nevertheless, the plant rhizosphere bacterial community also contributed to the core microbiome of the APS. Furthermore, the core taxa showed a higher average degree than the other nodes in the bacterial community networks in all microhabitats except for the plant rhizosphere environment, implying the important roles of core taxa in maintaining these bacterial community networks. Our results provide new insights into the assembly of bacterial communities under community coalescence in the artificial aquatic ecosystems comprising complex microhabitats, which is vital for developing microbial solutions for regulating the microbial communities to improve system performance in the future.},
}
@article {pmid39570377,
year = {2024},
author = {Jensen, IC and Schramm, A and Offenberg, J},
title = {Fungus Fighters: Wood Ants (Formica polyctena) and Their Associated Microbes Inhibit Plant Pathogenic Fungi.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {146},
pmid = {39570377},
issn = {1432-184X},
support = {NNF21OC0071665//Novo Nordisk Fonden/ ; NNF21OC0071665//Novo Nordisk Fonden/ ; 34009-19-1562//Internationalt Center for Forskning i &#xd8;kologisk Jordbrug og F&#xf8;devaresystemer/ ; },
mesh = {*Ants/microbiology/physiology ; Animals ; *Plant Diseases/microbiology/prevention &amp; control ; Malus/microbiology ; Fungi/physiology/classification ; Antibiosis ; Bacteria/classification/drug effects/isolation &amp; purification ; Ascomycota/physiology/drug effects ; },
abstract = {Plant diseases cost the global economy billions of US dollars every year. The problem has mainly been addressed by using chemical pesticides, but recently, the use of ants has shown promising effects against plant pathogens. However, the mechanisms accounting for these effects have not yet been determined. One possible explanation is antimicrobial microorganisms associated with ants. Through controlled laboratory experiments, we investigated the inhibitory effects of wood ants (Formica polyctena) and their associated microorganisms against economically important plant pathogenic fungi. All live ants, extracts from crushed ants, and extracts from washed ants significantly inhibited the apple brown rot (Monilinia fructigena) while yielding the growth of other microbes. Furthermore, all investigated wood ants transferred microorganisms to their surroundings within 10 s when walking across a surface. We isolated the most dominant microorganisms deposited by walking ants and from washed ant extracts (i.e., strains likely found on the surface of ants), resulting in four bacterial cultures and one yeast. Two of these isolates, strain I3 (most closely related to Pseudomonas sichuanensis and P. entomophila) and strain I1b (most closely related to Bacillus mycoides), showed inhibitory effects against apple brown rot and apple scab (Venturia inaequalis), while strain I3 also inhibited gray mold (Botrytis cinerea) and Fusarium head blight (Fusarium graminearum). These results suggest that wood ants have potential as biological control agents against commercially relevant plant pathogens, and that their inhibitory effect might be at least partially caused by antibiotic compounds produced by their associated microorganisms.},
}
@article {pmid39568064,
year = {2024},
author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB},
title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on Southern African dryland soil microbial communities.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae157},
pmid = {39568064},
issn = {1574-6941},
abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggest that they are functionally stable, and that they could be functional even under harsher conditions, such as those expected with climate change.},
}
@article {pmid39567391,
year = {2024},
author = {Vezina, B and Cooper, HB and Wisniewski, JA and Parker, MH and Jenney, AWJ and Holt, KE and Wyres, KL},
title = {Wild-Type Domestication: Loss of Intrinsic Metabolic Traits Concealed by Culture in Rich Media.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {144},
pmid = {39567391},
issn = {1432-184X},
support = {DP200103364//Australian Research Council/ ; DP200103364//Australian Research Council/ ; APP1176192//National Health and Medical Research Council/ ; },
mesh = {*Klebsiella pneumoniae/genetics/metabolism/growth &amp; development ; *Culture Media/chemistry ; *Genome, Bacterial ; Histidine/metabolism ; Mutation ; Whole Genome Sequencing ; },
abstract = {Bacteria are typically isolated on rich media to maximise isolation success, removing them from their native evolutionary context. This eliminates selection pressures, enabling otherwise deleterious genomic events to accumulate. Here, we present a cautionary tale of these 'quiet mutations' which can persist unnoticed in bacterial culture lines. We used a combination of microbiological culture (standard and minimal media conditions), whole genome sequencing and metabolic modelling to investigate putative Klebsiella pneumoniae L-histidine auxotrophs. Additionally, we used genome-scale metabolic modelling to predict auxotrophies among completed public genomes (n = 2637). Two sub-populations were identified within a K. pneumoniae frozen stock, differing in their ability to grow in the absence of L-histidine. These sub-populations were the same 'strain', separated by eight single nucleotide variants and an insertion sequence-mediated deletion of the L-histidine biosynthetic operon. The His[-] sub-population remained undetected for > 10 years despite its inclusion in independent laboratory experiments. Genome-scale metabolic models predicted 0.8% public genomes contained ≥ 1 auxotrophy, with purine/pyrimidine biosynthesis and amino acid metabolism most frequently implicated. We provide a definitive example of the role of standard rich media culture conditions in obscuring biologically relevant mutations (i.e. nutrient auxotrophies) and estimate the prevalence of such auxotrophies using public genome collections. While the prevalence is low, it is not insignificant given the thousands of K. pneumoniae that are isolated for global surveillance and research studies each year. Our data serve as a pertinent reminder that rich-media culturing can cause unnoticed wild-type domestication.},
}
@article {pmid39567372,
year = {2024},
author = {Issifu, S and Acharya, P and Kaur-Bhambra, J and Gubry-Rangin, C and Rasche, F},
title = {Biological Nitrification Inhibitors with Antagonistic and Synergistic Effects on Growth of Ammonia Oxidisers and Soil Nitrification.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {143},
pmid = {39567372},
issn = {1432-184X},
support = {RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; URF150571//Royal Society University Research Fellowship/ ; },
mesh = {*Nitrification ; *Soil Microbiology ; *Ammonia/metabolism ; *Soil/chemistry ; Archaea/metabolism/drug effects/growth &amp; development ; Oxidation-Reduction ; Rhizosphere ; Bacteria/metabolism/drug effects/growth &amp; development ; },
abstract = {Biological nitrification inhibition (BNI) refers to the plant-mediated process in which nitrification is inhibited through rhizospheric release of diverse metabolites. While it has been assumed that interactive effects of these metabolites shape rhizosphere processes, including BNI, there is scant evidence supporting this claim. Hence, it was a primary objective to assess the interactive effects of selected metabolites, including caffeic acid (CA), vanillic acid (VA), vanillin (VAN), syringic acid (SA), and phenylalanine (PHE), applied as single and combined compounds, against pure cultures of various ammonia-oxidising bacteria (AOB, Nitrosomonas europaea, Nitrosospira multiformis, Nitrosospira tenuis, Nitrosospira briensis) and archaea (AOA, Nitrososphaera viennensis), as well as soil nitrification. Additionally, benzoic acid (BA) was examined as a novel biological nitrification inhibitor. All metabolites, except SA, tested as single compounds, achieved varied levels of inhibition of microbial growth, with CA exhibiting the highest inhibitory potential. Similarly, all metabolites applied as single compounds, except PHE, inhibited soil nitrification by up to 62%, with BA being the most potent. Inhibition of tested nitrifying microbes was also observed when compounds were assessed in combination. The combinations VA + PH, VA + CA, and VA + VAN exhibited synergism against N. tenuis and N. briensis, while others showed antagonism against N. europaea, N. multiformis, and N. viennensis. Although all combinations suppressed soil nitrification, their interactions against soil nitrification revealed antagonism. Our findings indicate that both antagonism and synergism are possible in rhizospheric interactions involving BNI metabolites, resulting in growth inhibition of nitrifiers and suppression of soil nitrification.},
}
@article {pmid39565130,
year = {2024},
author = {Yu, C and Yu, M and Ma, R and Wei, S and Jin, M and Jiao, N and Zheng, Q and Zhang, R and Feng, X},
title = {A novel Alteromonas phage with tail fiber containing six potential iron-binding domains.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0093424},
doi = {10.1128/spectrum.00934-24},
pmid = {39565130},
issn = {2165-0497},
abstract = {Viruses play a vital role in regulating microbial communities, contributing to biogeochemical cycles of carbon, nitrogen, and essential metals. Alteromonas is widespread and plays an essential role in marine microbial ecology. However, there is limited knowledge about the interactions of Alteromonas and its viruses (alterophages). This study isolated a novel podovirus, vB_AmeP-R22Y (R22Y), which infects Alteromonas marina SW-47 (T). Phylogenetic analysis suggested that R22Y represented a novel viral genus within the Schitoviridae family. R22Y exhibited a broad host range and a relatively large burst size, exerting an important impact on the adaptability and dynamics of host populations. Two auxiliary metabolic genes, encoding Acyl carrier protein and AAA domain-containing protein, were predicted in R22Y, which may potentially assist in host fatty acid metabolism and VB12 biosynthesis, respectively. Remarkably, the prediction of the R22Y tail fiber structure revealed six conserved histidine residues (HxH motifs) that could potentially bind iron ions, suggesting that alterophages may function as organic iron-binding ligands in the marine environment. Our isolation and characterization of R22Y complements the Trojan Horse hypothesis, proposes the possible role of alterophages for marine iron biogeochemical cycling, and provides new insights into phage-host interactions in the iron-limited ocean.IMPORTANCEIron (Fe), as an essential micronutrient, is often a limiting factor for microbial growth in marine ecosystems. The Trojan Horse hypothesis suggests that iron in the phage tail fibers is recognized by the host's siderophore-bound iron receptor, enabling the phage to attach and initiate infection. The potential role of phages as iron-binding ligands has significant implications for oceanic trace metal biogeochemistry. In this study, we isolated a new phage R22Y with the potential to bind iron ions, using Alteromonas, a major siderophore producer, as the host. The tail fiber structure of R22Y exhibits six conserved HxH motifs, suggesting that each phage could potentially bind up to 36 iron ions. R22Y may contribute to colloidal organically complexed dissolved iron in the marine environment. This finding provides further insights into the Trojan Horse hypothesis, suggesting that alterophages may act as natural iron-binding ligands in the marine environment.},
}
@article {pmid39563404,
year = {2024},
author = {Chari, NR and Muratore, TJ and Frey, SD and Winters, CL and Martinez, G and Taylor, BN},
title = {Long-Term Soil Warming Drives Different Belowground Responses in Arbuscular Mycorrhizal and Ectomycorrhizal Trees.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17550},
doi = {10.1111/gcb.17550},
pmid = {39563404},
issn = {1365-2486},
support = {DEB-1456610//National Science Foundation/ ; DEB-1832110//National Science Foundation/ ; },
mesh = {*Mycorrhizae/physiology ; *Trees/microbiology/physiology/growth &amp; development ; *Soil/chemistry ; *Plant Roots/microbiology ; *Global Warming ; Biomass ; Soil Microbiology ; Carbon/metabolism/analysis ; Nitrogen/metabolism/analysis ; Climate Change ; Temperature ; },
abstract = {The ability of trees to acquire soil nutrients under future climate conditions will influence forest composition and function in a warmer world. Rarely are multiple belowground carbon allocation pathways measured simultaneously in large global change experiments, restricting our understanding of how trees may shift their allocation of resources to different nutrient acquisition mechanisms under future climates. Leveraging a 20-year soil warming experiment, we show that ectomycorrhizal (EM) trees reduce mycorrhizal colonization and root exudation while increasing fine root biomass, while arbuscular mycorrhizal (AM) trees largely maintained their belowground carbon allocation patterns in warmer soils. We suggest that AM trees may be better adapted to thrive under global warming due to higher rates of nitrogen mineralization in warmer soils and the ability of their mycorrhizal symbiont to acquire mineralized inorganic nutrients, whereas EM trees may need to alter their belowground carbon allocation patterns to remain competitive as global temperatures rise.},
}
@article {pmid39561700,
year = {2024},
author = {Partida-Martínez, LP},
title = {Laila P. Partida-Martínez.},
journal = {Current biology : CB},
volume = {34},
number = {22},
pages = {R1121-R1122},
doi = {10.1016/j.cub.2024.09.085},
pmid = {39561700},
issn = {1879-0445},
mesh = {*Symbiosis ; Fungi/physiology ; Plants/microbiology ; History, 21st Century ; History, 20th Century ; },
abstract = {Interview with Laila Partida-Martínez, who studies microbial ecology, fungal-bacterial symbioses and plant-microbe interactions at the Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav).},
}
@article {pmid39561304,
year = {2024},
author = {Vargas Ribera, PR and Kim, N and Venbrux, M and Álvarez-Pérez, S and Rediers, H},
title = {Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0302954},
pmid = {39561304},
issn = {1932-6203},
mesh = {*Agrobacterium tumefaciens/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Agrobacterium/genetics ; Genome, Bacterial ; DNA, Bacterial/genetics ; },
abstract = {Rhizogenic Agrobacterium, the causative agent of hairy root disease (HRD), is known for its high phenotypic and genetic diversity. The taxonomy of rhizogenic agrobacteria has undergone several changes in the past and is still somewhat controversial. While the classification of Agrobacterium strains was initially mainly based on phenotypic properties and the symptoms they induced on plants, more and more genetic information has been used along the years to infer Agrobacterium taxonomy. This has led to the definition of the so-called Agrobacterium tumefaciens species complex (Atsc), which comprises several genomospecies. Interestingly, the rhizogenic Agrobacterium strains are found in several of these genomospecies. Nevertheless, even up until today Agrobacterium strains, and in particular rhizogenic agrobacteria, are prone to misclassification and considerable confusion in literature. In this study, we evaluated different phylogenetic analysis approaches for their use to improve Agrobacterium taxonomy and tried to gain more insight in the classification of strains into this complex genus, with a particular focus on rhizogenic agrobacteria. The genome sequence analysis of 580 assemblies, comprising Agrobacterium, Allorhizobium and Rhizobium strains demonstrated that phylogenies based on single marker genes, such as the commonly used 16S rRNA and recA gene, do not provide sufficient resolution for proper delineation of the different genomospecies within the Atsc. Our results revealed that (in silico) multi-locus sequences analysis (MLSA) in combination with average nucleotide identity (ANIb) at a 94.0% threshold delineates genomospecies accurately and efficiently. Additionally, this latter approach permitted the identification of two new candidate genomospecies.},
}
@article {pmid39560406,
year = {2024},
author = {Ye, Y-Q and Ye, M-Q and Zhang, X-Y and Huang, Y-Z and Zhou, Z-Y and Feng, Y-J and Du, Z-J},
title = {Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota, and the environmental distribution and ecogenomics of Gaopeijiales ord. nov.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0053524},
doi = {10.1128/msystems.00535-24},
pmid = {39560406},
issn = {2379-5077},
abstract = {The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of Gemmatimonadota from marine environment have been described; thus, little is known about the physiology and metabolism of members of the marine lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to Gemmatimonadota were isolated from marine sediments collected from Xiaoshi Island in Weihai, China, using an aerobic enrichment method. The integrated results of phylogenetic and phenotypic characteristics supported that these four strains represent one novel species in a novel genus, for which the name Gaopeijia maritima gen. nov., sp. nov. is proposed, as the first representative of novel taxa, Gaopeijiales ord. nov., Gaopeijiaceae fam. nov. in the class Longimicrobiia. Gaopeijiales was detected in 22,884 out of 95,549 amplicon data sets, mainly from soil. However, the highest mean relative abundances were in sponge (0.7%) and marine sediment (0.35%), showing salt-related character. Most of the Gaopeijiales subgroups potentially belong to the rare bacterial biosphere. The aerobic enrichment in this study could significantly increase the relative abundance of Gaopeijiales (from 0.37% to 2.6%). Furthermore, the metabolic capabilities inferred from high-quality representative Gaopeijiales genomes/MAGs suggest that this group primarily performs chemoorganoheterotrophic metabolism with facultatively anaerobic characteristics and possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed in the four novel strains.IMPORTANCEDespite rapid advances in molecular and sequencing technologies, obtaining pure cultures remains a crucial research goal in microbiology, as it is essential for a deeper understanding of microbial metabolism. Gemmatimonadota is a widespread but rarely cultured bacterial phylum. Currently, there are only six cultured strains of this interesting group, all isolated from non-marine environments. Little is known about the physiology and metabolism of members of the marine lineages. Here we isolated and characterized four novel marine strains, and proposed a new order Gaopeijiales within Gemmatimonadota. Furthermore, the global distribution, environmental preference, and metabolic potential of Gaopeijiales are analyzed using public data. Our work enriches the resources available for the under-represented phylum Gemmatimonadota and provides insights into the physiological and metabolic characteristics of the marine lineage (Gaopeijiales) through culturology and omics.},
}
@article {pmid39558480,
year = {2024},
author = {Zechner, EL and Kienesberger, S},
title = {Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2430423},
pmid = {39558480},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/metabolism/genetics/classification/drug effects ; Animals ; *Host Microbial Interactions ; Mutagens/metabolism ; Polyketides/metabolism/pharmacology ; Enterotoxins/metabolism ; Peptides ; },
abstract = {The human intestinal tract is densely colonized by a microbial community that is subject to intense competition. Bacteria in this complex habitat seek to outcompete their neighbors for nutrients and eliminate competitors with antibacterial toxins. Antagonism can be mediated by diverse effectors including toxic proteins and small molecule inhibitors that are released extracellularly or delivered by specialized secretion systems to targeted cells. Two prototypical microbiota-derived enterotoxins, colibactin and tilimycin, and the newly discovered family of indolimines represent an expanding group of non-proteinaceous small molecules which specifically target DNA. In addition to cell killing, they generate mutations and genome instability in intoxicated microbes and host cells alike. They have been studied in detail because of their direct toxicity to human cells and important etiological roles in intestinal pathologies. Increasing evidence, however, reveals that these commensal genotoxins are also mediators of interbacterial antagonism, which impacts gut microbial ecology. In this review, we illustrate the functional versatility of commensal genotoxins in the gut ecosystem.},
}
@article {pmid39557685,
year = {2024},
author = {Mai, N and Foysal, MJ and Timms, VJ and Pearson, LA and Romanis, CS and Mills, TJT and Powell, JR and Neilan, BA},
title = {Seasonal and Spatial Dynamics of Fungal Leaf Endophytes in Eucalyptus crebra (Narrow-Leaved Ironbark).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {142},
pmid = {39557685},
issn = {1432-184X},
support = {CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; FF0883440//Australian Research Council/ ; },
mesh = {*Eucalyptus/microbiology ; *Seasons ; *Endophytes/isolation &amp; purification/classification/genetics ; *Plant Leaves/microbiology ; *Fungi/classification/isolation &amp; purification/genetics ; Biodiversity ; Ascomycota/genetics/isolation &amp; purification ; Basidiomycota/isolation &amp; purification/genetics/classification ; },
abstract = {Fungal endophytes play an important role in improving the health and productivity of native and cultivated plant species. Despite their ecological and industrial importance, few eucalypt species have been studied in terms of their endophyte communities. We examined the seasonal and spatial dynamics of fungal leaf endophytes in the model species, Eucalyptus crebra (narrow-leaved ironbark), using ITS-based amplicon sequencing. Alpha and beta diversity analyses revealed significantly higher species richness in summer compared to autumn and spring. Similarly, two-way ANOVA analysis showed significantly higher species diversity in summer compared to autumn (observed p < 0.001, Chao1 p < 0.005) and spring (observed p < 0.005, Chao1 p < 0.005). No difference in Shannon index was observed among different canopy levels across the season. Beta-diversity showed differences in fungal composition across the seasons and at various canopy levels based on unweighted UniFrac distance metric (PERMANOVA season p < 0.001, canopy p < 0.05), signifying distinct separation of fungi based on presence-absence. Ascomycota was the most abundant and diverse phylum and was present throughout the year. In contrast, Basidiomycota was only observed during cooler and drier seasons. Neofusicoccum was the most abundant genus, but distribution fluctuated significantly across the seasons. Pestalotiopsis and Neopestalotiopsis were most abundant in the low leaf canopy, whereas Pseudosydowia was most abundant in the high canopy. This study indicates that the diversity and abundance of endophytic fungi in the leaves of healthy E. crebra trees fluctuate seasonally and across canopy levels. The data generated can be used as a baseline for assessing and potentially modulating the health of E. crebra and other important Eucalyptus spp.},
}
@article {pmid39551884,
year = {2024},
author = {Mamo, Z and Abera, S and Tafesse, M},
title = {Taxonomic and functional profiling of microbial community in municipal solid waste dumpsite.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {12},
pages = {384},
pmid = {39551884},
issn = {1573-0972},
support = {EN-1/17-1/18//Addis Ababa Science and Technology University/ ; },
mesh = {*Solid Waste ; *Bacteria/classification/genetics/metabolism ; *Waste Disposal Facilities ; *Microbiota ; *Metagenomics ; Phylogeny ; Refuse Disposal ; Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; },
abstract = {Understanding the microbial ecology of landfills is crucial for improving waste management strategies and utilizing the potential of these microbial communities for biotechnological applications. This study aimed to conduct a comprehensive taxonomic and functional profiling of the microbial community present in the Addis Ababa municipal solid waste dumpsite using a shotgun metagenomics sequencing approach. The taxonomic analysis of the sample revealed the significant presence of bacteria, with the Actinomycetota (56%), Pseudomonadota (23%), Bacillota (3%), and Chloroflexota (3%) phyla being particularly abundant. The most abundant KEGG categories were carbohydrates metabolism, membrane transport, signal transduction, and amino acid metabolism. The biodegradation and metabolism of xenobiotics, as well as terpenoids and polyketides, were also prevalent. Moreover, the Comprehensive Antibiotic Resistance Database (CARD) identified 52 antibiotic resistance gene (ARG) subtypes belonging to 14 different drug classes, with the highest abundances observed for glycopeptide, phosphonic acid, and multidrug resistance genes. Actinomycetota was the dominant phylum harboring ARGs, followed by Pseudomonadota and Chloroflexota. This study offers valuable insights into the taxonomic and functional diversity of the microbial community in the Addis Ababa municipal solid waste dumpsite. It sheds light on the widespread presence of metabolically versatile microbes, antibiotic resistance genes, mobile genetic elements, and pathogenic bacteria. This understanding can contribute to the creation of efficient waste management strategies and the investigation of possible biotechnological uses for these microbial communities.},
}
@article {pmid39551202,
year = {2024},
author = {Duran, C and Bouchard, A and Agogué, H and Dupuy, C and Duran, R and Cravo-Laureau, C},
title = {Importance of eukaryotes in shaping microbial benthic communities in Charente-maritime marshes, France.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177523},
doi = {10.1016/j.scitotenv.2024.177523},
pmid = {39551202},
issn = {1879-1026},
abstract = {Marshes are wetlands known for providing major ecosystem services in terms of water quality and human activities. These ecosystem services are mainly provided by marshes' benthic community, composed of prokaryotes (bacteria and archaea) but also of eukaryotes (micro-eukaryotes and meiofauna). The aim of this study is to (1) assess the environmental parameters affecting benthic community composition in marshes, (2) highlight the associations between organisms from the three domains of life, and (3) determine the parameters controlling these associations. Hence, benthic communities of eight different marshes from three typologies (salted, brackish and freshwater) and four seasons (autumn 2020, spring 2021, summer 2021 and autumn 2021) were assessed. This study revealed three main drivers of community composition. First, salinity drives the community composition illustrated by the differences observed between the three typologies of marshes. Relative abundance of Nitrososphaeria, Halobacteria, Bacillariophyceae, Conoidasida and nematodes increased with salinity while methanogenic archaea, Chlorophyceae and copepod's relative abundance decreased. The second driver is the physical-chemistry of the site, particularly nutrients. The season is the last driver of community composition, seasonal pattern varying for each site within a typology. LEfSe analyses defined biomarkers of typology and season, among which many prokaryotes involved in the nitrogen cycle and photosynthetic micro-eukaryotes where present in different co-occurrence networks, highlighting the importance of nitrogen cycle in marshes. Co-occurrence networks revealed several connections between organisms of the three domains of life, particularly between prokaryotes and photosynthetic eukaryotes. This study illustrates thus the importance of holistic approaches in microbial ecology for revealing a comprehensive view of the whole microbial interactions occurring in complex ecosystems.},
}
@article {pmid39549623,
year = {2024},
author = {White, CA and Antell, EH and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, WQ and Alvarez-Cohen, L},
title = {Life history strategies determine response to SRT driven crash in anammox bioreactors.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122727},
doi = {10.1016/j.watres.2024.122727},
pmid = {39549623},
issn = {1879-2448},
abstract = {Anaerobic ammonium oxidation (anammox) is a biological process often applied in wastewater treatment plants for nitrogen removal from highly concentrated side-stream effluents from anaerobic digesters. However, they are vulnerable to process instability prompted by operational shocks and microbial community imbalances, resulting in lengthy recovery times. These issues are further compounded by a lack of understanding of how sustained press disturbances influence the microbial ecology of the system. Here we investigate the response and recovery of an anammox membrane bioreactor to a solids retention time (SRT)-induced reactor crash using 16S rRNA gene and shotgun metagenomic sequencing. We observed a strong selection of bacterial groups based on reproduction strategies, with the Orders Rhodospirillales and Sphingobacteriales increasing from 1.0 % and 11.9 % prior to the crash to 31.9 % and 18.1 % during the crash respectively. The Orders Brocadiales and Anaerolineales decreased from 17.3 % and 28.3 % to 7.3 % and 1.4 % over the same time period, respectively. Metagenomic and metatranscriptomic analyses revealed differential crash responses in metabolically distinct groups of bacteria, with increased expression of genes for extracellular carbohydrate active enzymes, peptidases and membrane transporters. Following the crash, the reactor recovered to its prior state of nitrogen removal performance and pathway analysis demonstrated increased expression of genes related to exopolysaccharide biosynthesis and quorum sensing during the reactor recovery period. This study highlights the effects of reactor perturbations on microbial community dynamics in anammox bioreactors and provides insight into potential recovery mechanisms from severe disturbance.},
}
@article {pmid39549075,
year = {2024},
author = {de la Sovera, V and Bovio-Winkler, P and Zinola, G and Etchebehere, C},
title = {Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {519},
pmid = {39549075},
issn = {1432-0614},
support = {SNI//ANII/ ; SNI//ANII/ ; SNI//ANII/ ; (II/FVF/2019/121).//Carlos Vaz Ferreira/ ; },
mesh = {*Methane/metabolism ; *Biomass ; *Bioreactors/microbiology ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Archaea/genetics/metabolism/classification ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Microbiota ; Biodegradation, Environmental ; },
abstract = {Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed. KEY POINTS: • The applied methodology was successful to obtain biomass suitable to perform BMP assays. • The microbial community was resilient to external biomass addition. • Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.},
}
@article {pmid39546027,
year = {2024},
author = {Khamespanah, E and Asad, S and Vanak, Z and Mehrshad, M},
title = {Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {141},
pmid = {39546027},
issn = {1432-184X},
mesh = {*Carbon-Sulfur Lyases/genetics/metabolism ; *Metagenomics ; *Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation &amp; purification/metabolism ; Archaea/genetics/enzymology/classification ; Groundwater/microbiology ; Metagenome ; Seawater/microbiology ; },
abstract = {The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.},
}
@article {pmid39545996,
year = {2024},
author = {Scheelings, TF and Van, TTH and Moore, RJ and Skerratt, LF},
title = {Location Matters: Variations in Cloacal Microbiota Composition of Spatially Separated Freshwater Turtles.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {140},
pmid = {39545996},
issn = {1432-184X},
mesh = {Animals ; *Turtles/microbiology ; *Cloaca/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Fresh Water/microbiology ; Australia ; Gastrointestinal Microbiome ; Biodiversity ; },
abstract = {The gut microbiota of vertebrates is malleable and may be shaped by both intrinsic and extrinsic factors. Here, the effect that geography has on the cloacal microbiota of two species of Australian freshwater chelonians, eastern longneck turtle (Chelodina longicollis) and Macquarie River turtle (Emydura macquarii), captured from waterbodies with different levels of anthropogenic pressure was investigated. We analysed the microbiota composition, structure and diversity through 16S rRNA gene amplicon sequencing. It was hypothesised that animals from less disturbed environments would harbour a more diverse cloacal microbial population. The cloacal microbiotas from 93 turtles (C. longicollis n = 78; E. macquarii n = 15), from five locations, were analysed. For both species, the most predominant phylum was Proteobacteria. Cloacal microbiota alpha diversity varied significantly between the C. longicollis from all locations, but no differences were found for E. macquarii. In C. longicollis, turtles from wetlands within the centre of Melbourne had the lowest alpha diversity metrics, while the highest alpha diversity values were seen in turtles captured from an undisturbed rural waterbody. Beta diversity, obtained by weighted UniFrac distance, showed significant differences between locations of capture for both species of turtles in this investigation. For C. longicollis, 87 biomarkers were identified responsible for explaining differences between locations, and in E. macquarii, 42 biomarkers were found. This is the first study to explore the cloacal microbiota composition of the eastern longneck turtle and gives greater insight into microbial community structures in Macquarie River turtles. Our study demonstrated that cloacal microbiota composition of freshwater turtles was significantly influenced by locality and that disrupted environments may reduce microbial diversity in C. longicollis. Interestingly, we discovered that the effects of location contrasted significantly between species for alpha diversity with differences discovered for C. longicollis but not E. macquarii. However, for both species, beta diversity was notably influenced by habitat type. These results highlight the need to interpret chelonian microbiota data in the context of geography and human disturbance of the environment.},
}
@article {pmid39545729,
year = {2024},
author = {Beaudry, MS and Bhuiyan, MIU and Glenn, TC},
title = {Enriching the future of public health microbiology with hybridization bait capture.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0006822},
doi = {10.1128/cmr.00068-22},
pmid = {39545729},
issn = {1098-6618},
abstract = {SUMMARYPublic health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.},
}
@article {pmid39544963,
year = {2024},
author = {Wong, HL and Bulzu, PA and Ghai, R and Chiriac, MC and Salcher, MM},
title = {Ubiquitous genome streamlined Acidobacteriota in freshwater environments.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae124},
pmid = {39544963},
issn = {2730-6151},
abstract = {Acidobacteriota are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an Acidobacteriota genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia. UBA12189 has small genome sizes (<1.4 Mbp), low GC content, and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to a 300-m depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis. When compared to other genome-streamlined bacteria such as Nanopelagicales and Methylopumilus, genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur, and nitrogen metabolisms, limited numbers of membrane transporters, as well as a higher degree of auxotrophy for various amino acids, vitamins, and reduced sulfur. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, complete biosynthesis pathways for heme and vitamin K2, cbb3-type cytochrome c oxidases, and heme-requiring enzymes. These genes may give a selective advantage during the genome streamlining process. We propose the new genus Acidiparvus, with two new species named "A. lacustris" and "A. fluvialis". Acidiparvus is the first described genome-streamlined lineage under the phylum Acidobacteriota, which is a free-living, slow-growing scavenger in freshwater environments.},
}
@article {pmid39543974,
year = {2024},
author = {Gonsiorczyk, T and Hupfer, M and Hilt, S and Gessner, MO},
title = {Rapid Eutrophication of a Clearwater Lake: Trends and Potential Causes Inferred From Phosphorus Mass Balance Analyses.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17575},
doi = {10.1111/gcb.17575},
pmid = {39543974},
issn = {1365-2486},
mesh = {*Eutrophication ; *Lakes/chemistry ; *Phosphorus/analysis ; *Geologic Sediments/analysis/chemistry ; *Seasons ; Environmental Monitoring/methods ; },
abstract = {Many clearwater lakes increasingly show symptoms of eutrophication, but the underlying causes are largely unknown. We combined long-term water chemistry data, multi-year sediment trap measurements, sediment analyses and simple mass balance models to elucidate potential causes of eutrophication of a deep temperate clearwater lake, where total phosphorus (TP) concentrations quadrupled within a decade, accompanied by expanding hypolimnetic anoxia. Discrepancies between modeled and empirically determined P inputs suggest that the observed sharp rise in TP was driven by internal processes. The magnitude of seasonal variation in TP greatly increased at the same time, both in surface and deep water, partly decoupled from deep water oxygen conditions. A positive correlation between annual P loss from the upper water column and hypolimnetic P accumulation could hint at a short-circuited P cycle involving lateral TP transport from shallow-water zones and deposition and release from sediments in deep water. This hypothesis is also supported by P budgets for the upper 20 m during stable summer stratification, suggesting that sediments in shallow lake areas acted as a P net source until 2018. These changes are potentially related to shifts in submerged macrophytes from wintergreen charophyte meadows (Nitellopsis obtusa) to annual free-floating hornwort (Ceratophyllum demersum) and to increased sulfide formation, promoting iron fixation in the sediments. Iron bound to sulfur is unavailable for binding P, resulting in a positive feedback between P release in shallow lake areas, primary productivity, macrophyte community structure and redox-dependent sediment biogeochemistry. Overall, our results suggest that relationships more complex than the commonly invoked increase in internal P release under increasingly anoxic conditions can drive rapid lake eutrophication. Since the proportion of littoral areas is typically large even in deep stratified lakes, littoral processes may contribute more frequently to the rapid lake eutrophication trends observed around the world than is currently recognized.},
}
@article {pmid39541983,
year = {2024},
author = {Urtecho, G and Moody, T and Huang, Y and Sheth, RU and Richardson, M and Descamps, HC and Kaufman, A and Lekan, O and Zhang, Z and Velez-Cortes, F and Qu, Y and Cohen, L and Ricaurte, D and Gibson, TE and Gerber, GK and Thaiss, CA and Wang, HH},
title = {Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.},
journal = {Cell systems},
volume = {15},
number = {11},
pages = {1002-1017.e4},
doi = {10.1016/j.cels.2024.10.007},
pmid = {39541983},
issn = {2405-4720},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Fecal Microbiota Transplantation/methods ; Mice, Inbred C57BL ; Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Mammals/microbiology ; Feces/microbiology ; },
abstract = {While fecal microbiota transplantation (FMT) has been shown to be effective in reversing gut dysbiosis, we lack an understanding of the fundamental processes underlying microbial engraftment in the mammalian gut. Here, we explored a murine gut colonization model leveraging natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of FMT. We identified a natural "super-donor" consortium that robustly engrafts into diverse recipients and resists reciprocal colonization. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 h, followed by a slower emergence of late colonizers over 15-30 days. Moreover, engraftment was localized to distinct compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization suggested engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally dependent manner. A record of this paper's transparent peer review process is included in the supplemental information.},
}
@article {pmid39541852,
year = {2024},
author = {Wang, Q and Wang, M and Yang, Q and Feng, L and Zhang, H and Wang, R and Wang, R},
title = {The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122776},
doi = {10.1016/j.watres.2024.122776},
pmid = {39541852},
issn = {1879-2448},
abstract = {Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.},
}
@article {pmid39540979,
year = {2024},
author = {Frew, A and Aguilar-Trigueros, CA},
title = {Increasing Phylogenetic Clustering of Arbuscular Mycorrhizal Fungal Communities in Roots Explains Enhanced Plant Growth and Phosphorus Uptake.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {139},
pmid = {39540979},
issn = {1432-184X},
support = {DE220100479//Australian Research Council/ ; },
mesh = {*Mycorrhizae/genetics/physiology ; *Phosphorus/metabolism ; *Plant Roots/microbiology/growth &amp; development ; *Phylogeny ; *Symbiosis ; *Sorghum/microbiology/growth &amp; development ; Soil Microbiology ; Mycobiome ; Biomass ; Plant Development ; },
abstract = {Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.},
}
@article {pmid39537004,
year = {2024},
author = {Bernetti, A and Barili, S and Sannino, C and Mugnai, G and Borruso, L and Pinchuk, I and Pezzolla, D and Turchetti, B and Gigliotti, G and Buzzini, P},
title = {Selective response of soil bacterial and fungal taxa to biodegradable polymers.},
journal = {Environmental research},
volume = {264},
number = {Pt 1},
pages = {120344},
doi = {10.1016/j.envres.2024.120344},
pmid = {39537004},
issn = {1096-0953},
abstract = {Biodegradable mulching films offer an eco-friendly alternative to petroleum-based plastics in agriculture, but their effects on soil parameters are not well understood. A microcosm experiment (20 °C, 75% field capacity) investigated the impact of two doses (0.021% and 1% w/w) of a biodegradable polymer on soil chemical and microbiological properties over a year. The 1% dose significantly (p < 0.05) increased CO2 emissions, water-extractable organic C, and hydrolytic activity. A significant (p < 0.05) effect on microbial alpha- and beta-diversity was noted only during short- and medium-term incubations. In contrast, a taxon-related response was found for both bacterial and fungal taxa affecting the abundance of the genera Aquicella, Cellvibrio, Bacillus, Ramlibacter, and Saccharibacteria genera incertae sedis among bacteria, and Malassezia, Orbilia, and Rhodotorula among fungi (including both yeast and filamentous lifestyles). Microbial functions revealed a greater impact on fungal communities compared to bacterial ones. However, after one year of exposition, only a marginal effect on the abundance of both bacterial and fungal functional groups was found in the microcosms. A significantly higher concentration of tightly bound exopolysaccharides in the presence of 1% biodegradable polymer at the start of the experiment suggested their key role in microbial degradation of bioplastics via biofilm formation.},
}
@article {pmid39536049,
year = {2024},
author = {Zhao, Y and Cordero, OX and Tikhonov, M},
title = {Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.},
journal = {PLoS computational biology},
volume = {20},
number = {11},
pages = {e1012590},
doi = {10.1371/journal.pcbi.1012590},
pmid = {39536049},
issn = {1553-7358},
abstract = {Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.},
}
@article {pmid39524341,
year = {2024},
author = {Dzialo, MC and Arumugam, S and Piampongsant, S and Cool, L and Vanderaa, C and Herrera-Malaver, B and Opsomer, T and Dehaen, W and Wenseleers, T and Roncoroni, M and Alawamleh, A and Wäckers, F and Lievens, B and Hansson, BS and Voordeckers, K and Sachse, S and Verstrepen, KJ},
title = {Drosophila suzukii and Drosophila melanogaster prefer distinct microbial and plant aroma compounds in a complex fermented matrix.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111141},
pmid = {39524341},
issn = {2589-0042},
abstract = {Volatile aroma compounds are important chemical cues for insects. Behavioral responses to specific odors differ strongly between insect species, and the exact causative molecules are often unknown. Beer is frequently used in insect traps because it combines hundreds of plant and microbial aromas that attract many insects. Here, we analyzed responses of the pest fruit fly Drosophila suzukii and benign Drosophila melanogaster to beers with different chemical compositions. Using extensive chemical and behavioral assays, we identified ecologically relevant chemicals that influence drosophilid behavior and that induce different odor-evoked activity patterns in the antennal lobe of the two species obtained by functional imaging. Specific mixes of compounds increased the species-specificity and sex-specificity of lures in both laboratory and greenhouse settings. Together, our study shows how examining insect responses to highly complex natural mixtures of aroma compounds provides insight into insect-specific behavioral responses and also opens avenues for improved pest control.},
}
@article {pmid39535358,
year = {2024},
author = {Tidimalo, C and Maximiliano, O and Karen, J and Lebre, PH and Bernard, O and Michelle, G and Oagile, D and Cowan, DA},
title = {Microbial diversity in the arid and semi-arid soils of Botswana.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70044},
pmid = {39535358},
issn = {1758-2229},
support = {//PhD bursary for Tidimalo Coetzee from the University of Botswana/ ; //Oppenheimer Foundation/ ; 674-AA-2010-A1//United States Agency for International Development/ ; //University of Pretoria for postdoctoral support/ ; },
mesh = {*Soil Microbiology ; Botswana ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; *Biodiversity ; Microbiota/genetics ; Phylogeny ; Hydrogen-Ion Concentration ; DNA, Bacterial/genetics ; },
abstract = {To date, little research has been conducted on the landscape-scale distribution of soil microbial communities and the factors driving their community structures in the drylands of Africa. We investigated the influence of landscape-scale variables on microbial community structure and diversity across different ecological zones in Botswana. We used amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacers (ITS) and a suite of environmental parameters to determine drivers of microbial community structure. Bacterial communities were dominated by Actinomycetota (21.1%), Pseudomonadota (15.9%), and Acidobacteriota (10.9%). The dominant fungal communities were Ascomycota (57.3%) and Basidiomycota (7.5%). Soil pH, mean annual precipitation, total organic carbon, and soil ions (calcium and magnesium) were the major predictors of microbial community diversity and structure. The co-occurrence patterns of bacterial and fungal communities were influenced by soil pH, with network-specific fungi-bacteria interactions observed. Potential keystone taxa were identified for communities in the different networks. Most of these interactions were between microbial families potentially involved in carbon cycling, suggesting functional redundancy in these soils. Our findings highlight the significance of soil pH in determining the landscape-scale structure of microbial communities in Botswana's dryland soils.},
}
@article {pmid39532738,
year = {2024},
author = {Fu, M and Liu, Y and Li, S and Yan, D and Liu, P and Liu, Y and Ji, M},
title = {The Spatial Dynamics of Diazotrophs in the Forefield of Three Tibetan Glaciers.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {138},
pmid = {39532738},
issn = {1432-184X},
support = {42171138//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; },
mesh = {*Ice Cover/microbiology ; Tibet ; *Soil Microbiology ; *Nitrogen Fixation ; Soil/chemistry ; Nitrogen/metabolism ; Ecosystem ; Bacteria/classification/metabolism/genetics/isolation &amp; purification/enzymology ; Nitrogen-Fixing Bacteria/metabolism/classification/isolation &amp; purification/genetics ; Phylogeny ; Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Nitrogen is often a limiting nutrient for microbial communities and plants in glacier forefields. Nitrogen-fixing microorganisms (diazotrophs) play an important role in providing bioavailable nitrogen, with their composition determining the nitrogen-fixating capacities. This study investigates the spatial and temporal dynamics of diazotrophs in the forefields of three Tibetan glaciers: Qiangyong, Kuoqionggangri, and Longxiazailongba. We collected soil samples from recently deglaciated barren grounds, and also along an ecosystem succession transect at Kuoqionggangri glacier, encompassing barren ground, herb steppe, legume steppe, and alpine meadow ecosystems. Our finding revealed abundant and diverse diazotrophs in the recently deglaciated barren ground. They are taxonomically affiliated with anaerobic Bradyrhizobium, Desulfobulbus, and Pelobacter, which may be relics from subglacial sediments. The vegetated soils (herb steppe, legume steppe, and alpine meadow) were dominated by phototrophic Nostoc and Anabaena, as well as symbiotic Sinorhizobium. Soil physicochemical parameters, such as soil organic carbon, pH, and nitrate ion, significantly influenced diazotroph community structure. This study highlights the critical role of diazotrophs in mitigating nitrogen limitation during early ecosystem development in glacier forefields. Understanding the distribution and ecological drivers of diazotrophs in these rapidly changing environments provides insights into biogeochemical cycling and ecosystem resilience under climate change.},
}
@article {pmid39528791,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39528791},
issn = {1740-1534},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
}
@article {pmid39528727,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39528727},
issn = {2058-5276},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
}
@article {pmid39528652,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {npj biodiversity},
volume = {3},
number = {1},
pages = {34},
pmid = {39528652},
issn = {2731-4243},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.},
}
@article {pmid39528617,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1466},
pmid = {39528617},
issn = {2399-3642},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.},
}
@article {pmid39528577,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {122},
pmid = {39528577},
issn = {2055-5008},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.},
}
@article {pmid39528441,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9637},
pmid = {39528441},
issn = {2041-1723},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.},
}
@article {pmid39528211,
year = {2024},
author = {Jang, J and Park, J and Hwang, CY and Gim, Y and Park, KT and Yoon, YJ and Seo, M and Lee, BY},
title = {Selective transmission of airborne bacterial communities from the ocean to the atmosphere over the Northern Pacific Ocean.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177462},
doi = {10.1016/j.scitotenv.2024.177462},
pmid = {39528211},
issn = {1879-1026},
abstract = {This study simultaneously measured the taxonomic diversity of bacterial communities in both seawater and PM2.5 aerosol samples collected from the Northern Pacific Ocean during a cruise covering 7724 km between 37°N 126°E and 58°N 179°E. The relative abundance of Proteobacteria, Cyanobacteria, and Firmicutes were found to be more prevalent in aerosol samples (39 ± 16 %, 5.1 ± 1.9 %, and 3.2 ± 1.7 %, respectively) than in seawater samples (26 ± 9 %, 3.8 ± 1.7 %, and 0.02 ± 0.09 %, respectively). The preferential aerosolization of bacterial communities such as Proteobacteria and Firmicutes was likely to be accompanied by a terrestrial origin and high hydrophobicity. Cyanobacteria could undergo increased aerosolization, possibly because of their smaller size in the significantly higher salinity open ocean (32.8 ± 0.14 PSU) compared to those in lower salinity coastal areas (31.3 ± 1.4 PSU). The results of this study indicated that bacterial properties substantially affect their transfer from the ocean to the atmosphere, possibly influencing climate change and public health.},
}
@article {pmid39527614,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39527614},
issn = {1751-7370},
}
@article {pmid39527081,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Falcao Salles, J and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Adoukè Agbodjato, N and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {11},
pages = {},
pmid = {39527081},
issn = {1574-6941},
abstract = {Injecting H2 in deep underground to store this energy carrier will produce artificial subsurface lithoautotrophic microbial ecosystems that modify the taxonomic diversity of indigenous microbial communities and their metabolic activities.},
}
@article {pmid39526991,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Falcao Salles, J and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0141624},
doi = {10.1128/msystems.01416-24},
pmid = {39526991},
issn = {2379-5077},
}
@article {pmid39526896,
year = {2024},
author = {Wei, F and Jiang, H and Zhu, C and Zhong, L and Lin, Z and Wu, Y and Song, L},
title = {The co-fermentation of whole-grain black barley and quinoa improves murine cognitive impairment induced by a high-fat diet via altering gut microbial ecology and suppressing neuroinflammation.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo02704c},
pmid = {39526896},
issn = {2042-650X},
abstract = {A high-fat diet (HFD) is associated with various adverse health outcomes, including cognitive impairment and an elevated risk of neurodegenerative conditions. This relationship is partially attributed to the influence of an HFD on the gut microbiota. The objective of this research was to evaluate the neuroprotective benefits of co-fermented black barley and quinoa with Lactobacillus (FG) against cognitive impairments triggered by an HFD and to investigate the microbiota-gut-brain axis mechanisms involved. C57BL/6J mice were randomized into four groups: the normal control group (NC, n = 10), the high-fat diet group (HFD, n = 10), the high-fat diet group supplemented with FG (HFG, 10 mL per kg BW, n = 10), and the high-fat diet group supplemented with Lactobacillus (HFL, 10 mL per kg BW, n = 10). Our results showed that the FG intervention enhanced the behavioral and locomotor skills of the mice, elevated the levels of dopamine (DA) and norepinephrine (NPI) in brain tissues, and alleviated synaptic ultrastructural damage in the hippocampus. Furthermore, FG intervention was observed to exert a protective effect on both the blood-brain barrier and the colonic barrier, as evidenced by an increase in the mRNA levels of Zona occludens-1 (ZO-1), Claudin-4, and Occludin in the hippocampus and colon. These beneficial effects may be attributed to FG's regulation of gut microbiota dysbiosis, which involves the restoration of intestinal flora diversity, reduction of the Firmicutes/Bacteroidetes (F/B) ratio, and a decrease in the levels of pro-inflammatory bacteria such as s_Escherichia coli E and g_Escherichia; moreover, there was an increase in the abundances of anti-inflammatory bacteria, such as s_Bacteroides thetaiotaomicron and s_Parabacteroides goldsteinii. Metagenomic analysis revealed that the FG treatment downregulated the lipopolysaccharide (LPS) pathway and upregulated neurotransmitter biosynthetic pathways. These probiotic effects of FG resulted in reduced production and "leakage" of LPS and decreased mRNA expression of Toll-like receptor 4 (Tlr4), cluster of differentiation 14 (CD14), and myeloid differentiation factor 88 (Myd88) in hippocampal and colon tissues. Consequently, a reduction was observed in the levels of inflammatory cytokines in the serum, hippocampus, and colon, along with suppression of the immunoreactivity of microglia and astrocytes. Our results suggest that FG may serve as an intervention strategy for preventing cognitive impairments caused by an HFD.},
}
@article {pmid39526802,
year = {2024},
author = {Schiml, VC and Walter, JM and Hagen, LH and Varnai, A and Bergaust, LL and De Leon, AVP and Elsgaard, L and Bakken, LR and Arntzen, M&#xd8;},
title = {Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0174224},
doi = {10.1128/aem.01742-24},
pmid = {39526802},
issn = {1098-5336},
abstract = {UNLABELLED: Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs). However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to identify microbial drivers for lignocellulose transformation in woodchip bioreactors and their active enzymes. Our findings highlight a microbial community enriched for (ligno)cellulose-degrading denitrifiers with key players from the taxa Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota). A wide substrate specificity is observed among the many expressed carbohydrate-active enzymes (CAZymes) including PULs from Bacteroidetes. This suggests a broad degradation of lignocellulose subfractions, including enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.<br><br>IMPORTANCE: Freshwater ecosystems face significant threats from agricultural runoff, which can lead to eutrophication and subsequent degradation of water quality. One solution to mitigate this issue is using denitrifying woodchip bioreactors (WBRs), where microorganisms convert nitrate into nitrogen gases utilizing lignocellulose as a carbon source. Despite the well-documented polysaccharide-degrading strategies in various systems, the mechanisms employed by denitrifying microorganisms in WBRs remain largely unexplored. This study fills a critical knowledge gap by revealing the degrading strategies of denitrifying microbial communities in WBRs. By integrating state-of-the-art techniques, we have identified key microbial drivers including Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota) playing significant roles in lignocellulose transformation and showcasing a broad substrate specificity and complex metabolic capability. Our findings advance the understanding of microbial ecology in WBRs and by revealing the enzymatic activities, this research may inform efforts to improve water quality, protect aquatic ecosystems, and reduce greenhouse gas emissions from WBRs.},
}
@article {pmid39520764,
year = {2025},
author = {Rodriguez-Caturla, MY and Margalho, LP and Graça, JS and Pia, AKR and Xavier, VL and Noronha, MF and Cabral, L and Lemos-Junior, WJF and Castillo, CJC and SantˈAna, AS},
title = {Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage.},
journal = {International journal of food microbiology},
volume = {427},
number = {},
pages = {110955},
doi = {10.1016/j.ijfoodmicro.2024.110955},
pmid = {39520764},
issn = {1879-3460},
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Hydrogen-Ion Concentration ; Vacuum ; Cattle ; Animals ; *Red Meat/microbiology ; *Food Packaging/methods ; *Food Microbiology ; *Food Storage ; Bacteria/metabolism/growth &amp; development/classification/genetics/isolation &amp; purification ; Metabolome ; Brazil ; RNA, Ribosomal, 16S/genetics ; },
abstract = {This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4-5.8, 5.8-6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC-MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4-5.8 and 5.8-6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.},
}
@article {pmid39520558,
year = {2024},
author = {Boadella, J and Butturini, A and Doménech-Pascual, A and Freixinos, Z and Perujo, N and Urmeneta, J and Vidal, A and Romaní, AM},
title = {Microbial Life in Playa-Lake Sediments: Adapted Structure, Plastic Function to Extreme Water Activity Variations.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {137},
pmid = {39520558},
issn = {1432-184X},
support = {PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; 2020 FISDU 00465//Catalan Government Ministry of Business and Knowledge, Area of Universities and Research/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; *Biofilms/growth &amp; development ; *Salinity ; *Bacteria/classification/genetics/metabolism ; Biomass ; Droughts ; Water ; },
abstract = {Saline shallow lakes in arid and semi-arid regions frequently undergo drying episodes, leading to significant variations in salinity and water availability. Research on the impacts of salinity and drought on the structure and function of biofilms in hypersaline shallow lakes is limited. This study aimed to understand the potential changes of biofilms in playa-lake sediments during the drying process. Sediments were sampled at different depths (surface, subsurface) and hydrological periods (wet, retraction, and dry), which included a decrease in water activity (aw, the availability of water for microbial use) from 0.99 to 0.72. aw reduction caused a greater effect on functional variables compared to structural variables, indicating the high resistance of the studied biofilms to changes in salinity and water availability. Respiration and hydrolytic extracellular enzyme activities exhibited higher values under high aw, while phenol oxidase activity and prokaryote biomass increased at lower aw. This shift occurred at both depths but was more pronounced at the surface, possibly due to the more extreme conditions (up to 0.7 aw). The increased levels of extracellular polymeric substances and carotenoids developed at low aw may help protect microorganisms in high salinity and drought environments. However, these harsh conditions may interfere with the activity of hydrolytic enzymes and their producers, while promoting the growth of resistant prokaryotes and their capacity to obtain C and N sources from recalcitrant compounds. The resilience of biofilms in hypersaline lakes under extreme conditions is given by their resistant biochemichal structure and the adaptability of their microbial functioning.},
}
@article {pmid39516195,
year = {2024},
author = {Speth, DR and Zeller, LM and Graf, JS and Overholt, WA and Küsel, K and Milucka, J},
title = {Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9682},
pmid = {39516195},
issn = {2041-1723},
mesh = {*Symbiosis ; *Phylogeny ; *Denitrification ; Metagenome ; Aerobiosis ; Ciliophora/genetics/metabolism ; Groundwater/microbiology ; Gammaproteobacteria/genetics/metabolism ; Germany ; Electron Transport Complex IV/genetics/metabolism ; California ; Genome, Bacterial ; },
abstract = {The endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we report four complete, circular metagenome assembled genomes (cMAGs) representing respiratory endosymbionts inhabiting groundwater in California, Ohio, and Germany. These cMAGs form two lineages comprising a monophyletic clade within the uncharacterized gammaproteobacterial order UBA6186, enabling evolutionary analysis of their key protein complexes. Strikingly, all four cMAGs encode a cytochrome cbb3 oxidase, which indicates that these endosymbionts have the capacity for aerobic respiration. Accordingly, we detect these respiratory endosymbionts in diverse habitats worldwide, thus further expanding the ecological scope of this respiratory symbiosis.},
}
@article {pmid39513042,
year = {2024},
author = {Park, KJ and Gao, Y},
title = {Gut-brain axis and neurodegeneration: mechanisms and therapeutic potentials.},
journal = {Frontiers in neuroscience},
volume = {18},
number = {},
pages = {1481390},
pmid = {39513042},
issn = {1662-4548},
abstract = {This paper reviews the effects of gut microbiota in regulating neurodegenerative diseases through controlling gut-brain axis. Specific microbial populations and their metabolites (short-chain fatty acids and tryptophan derivatives) regulate neuroinflammation, neurogenesis and neural barrier integrity. We then discuss ways by which these insights lead to possible interventions - probiotics, prebiotics, dietary modification, and fecal microbiota transplantation (FMT). We also describe what epidemiological and clinical studies have related certain microbiota profiles with the courses of neurodegenerative diseases and how these impact the establishment of microbiome-based diagnostics and individualized treatment options. We aim to guide microbial ecology research on this key link to neurodegenerative disorders and also to highlight collaborative approaches to manage neurological health by targeting microbiome-related factors.},
}
@article {pmid39511174,
year = {2024},
author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F},
title = {Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9628},
pmid = {39511174},
issn = {2041-1723},
support = {NNF22OC0071609//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; ERC-RA-0020//Helmholtz Association/ ; 101059607//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 12471341//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Oxidation-Reduction ; Anaerobiosis ; *Archaea/metabolism/genetics ; *Butanes/metabolism ; *Carbon Dioxide/metabolism ; Oxidoreductases/metabolism/genetics ; Kinetics ; Alkanes/metabolism ; Thermodynamics ; },
abstract = {Microbial formation and oxidation of volatile alkanes in anoxic environments significantly impacts biogeochemical cycles on Earth. The discovery of archaea oxidizing volatile alkanes via deeply branching methyl-coenzyme M reductase variants, dubbed alkyl-CoM reductases (ACR), prompted the hypothesis of archaea-catalysed alkane formation in nature (alkanogenesis). A combination of metabolic modelling, anaerobic physiology assays, and isotope labeling of Candidatus Syntrophoarchaeum archaea catalyzing the anaerobic oxidation of butane (AOB) show a back flux of CO2 to butane, demonstrating reversibility of the entire AOB pathway. Back fluxes correlate with thermodynamics and kinetics of the archaeal catabolic system. AOB reversibility supports a biological formation of butane, and generally of higher volatile alkanes, helping to explain the presence of isotopically light alkanes and deeply branching ACR genes in sedimentary basins isolated from gas reservoirs.},
}
@article {pmid39509969,
year = {2024},
author = {Aparicio, S and Ríos-Mejía, A and Gallardo-Mejías, JP and Robles, &#xc1; and Borrás, L},
title = {Microalgae-bacteria consortia dynamics in a long term operated membrane-coupled high-rate algal pond (MHRAP).},
journal = {Journal of environmental management},
volume = {371},
number = {},
pages = {123186},
doi = {10.1016/j.jenvman.2024.123186},
pmid = {39509969},
issn = {1095-8630},
abstract = {Traditional activated sludge-based technologies have significant drawbacks, including high energy requirements and greenhouse gas emissions. Microalgae-based processes offer a promising, low-cost, and environmentally friendly alternative. However, the knowledge of treatment systems based on microalgae-bacteria consortia is limited, and even more so is their microbial composition and its relationship with operational parameters. Thus, this study explores the dynamics of microalgae-bacteria consortia in a long-term operated membrane-coupled high-rate algal pond (MHRAP) for wastewater treatment. For this, a pilot-scale MHRAP plant, located in a wastewater treatment plant in Valencia (Spain), was monitored under various hydraulic retention times (HRT) and wastewater influents: i) effluent from a primary settler and ii) effluent form pre-treatment. The biomass retention time was kept constant at 6 days. The composition of the bacterial community was studied through 16S rDNA sequencing, while 18S rDNA sequencing was used to study the microalgae. The results indicate that shorter HRTs significantly increased bacterial diversity, but not eukarya. Principal Co-ordinates Analysis (PCoA) revealed that the HRT and the incoming wastewater quality control the type of the bacterial populations. However, this effect was not observed in eukaryotic organisms. The dominant microalgae genera identified were Desmodesmus and Coelastrella, with Coelastrella becoming more prevalent at shorter HRTs. For bacteria, Verrumicrobiota dominated (18-56%) at high HRT while Proteobacteria was dominant (28-44%) at HRTs below 6 days. The changes observed in the bacterial composition, including the ammonia oxidizing bacteria (AOB) community (mainly Nitrosomonas), suggest that photo-inhibition could be taking place. The nitrite oxidizing bacteria (NOB) community was dominated by Nitrospira and Candidatus Nitrotoga. Operational parameters such as light intensity, pH, and nitrite concentration were found to significantly influence the microbial community structure. Higher light intensity and alkaline pH favored the growth of Desmodesmus, while Coelastrella thrived under lower HRTs. Bacterial diversity plays a crucial role in the treatment process, while microalgae primarily support aerobic bacterial processes by providing oxygen. These findings contribute to a deeper understanding of the complex biological processes in microalgae-bacteria consortia and offer insights into improving wastewater treatment technologies.},
}
@article {pmid39508609,
year = {2024},
author = {Xue, S-J and Liu, J and Zhao, F-Y and Zhang, X-T and Zhu, Z-Q and Zhang, J-Y},
title = {Spatio-temporal distribution and biotechnological potential of culturable yeasts in the intertidal sediments and seawater of Aoshan Bay, China.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0157024},
doi = {10.1128/aem.01570-24},
pmid = {39508609},
issn = {1098-5336},
abstract = {Marine yeasts play a crucial role in marine microbial ecology, facilitating the biogeochemical cycling of carbon and nitrogen in marine ecosystems, while also serving as important reservoirs of bioactive compounds with extensive applications in pharmaceuticals, agriculture, and various industries. Intertidal flats, characterized by their complex ecological dynamics, are postulated to harbor a wealth of yeast resources. This study employed a culture-dependent approach to assess the diversity, spatio-temporal distribution, and biotechnological potential of yeast communities residing within the intertidal sediments and seawater of Aoshan Bay. A total of 392 yeast strains were identified from 20 distinct genera, encompassing 43 recognized species and four candidate novel species. Notably, 17 of these species were identified as novel occurrences in marine environments, underscoring the rich yeast biodiversity of the Aoshan Bay ecosystem, with Candida emerging as the dominant genus in both sedimentary and aqueous habitats. Yeast community composition exhibited significant spatial and temporal variation, with peak diversity and abundance observed in autumn, the subtidal zone, and the surface soil layer. No clear pattern, however, emerged linking these shifts to specific changes in community composition, highlighting the complex interactions between microbial communities, environmental variables, and anthropogenic disturbance. Although several yeast species isolated here have been previously recognized for their biotechnological potential, their diverse and abundant extracellular enzyme profiles were characterized, further highlighting their crucial role in organic matter decomposition and nutrient cycling within the tidal ecosystem, as well as their potential applicability in the food, fine chemical, textile, and pharmaceutical industries.IMPORTANCEThis study presents groundbreaking insights into the yeast diversity of Aoshan Bay, offering invaluable information on their spatial and temporal distribution patterns, as well as their biotechnological potential in the tidal environment. The findings reveal that the eutrophic intertidal flat is a rich repository of yeasts with abundant extracellular enzymatic activity and an important role in nutrient cycling and decomposition processes. Also, these yeasts serve as crucial indicators of ecosystem health and function and are excellent candidates for biotechnological and industrial applications. Collectively, this study not only expands our knowledge of the diversity and distribution of intertidal yeasts but also highlights their promising potential for biotechnological applications.},
}
@article {pmid39505133,
year = {2024},
author = {Hu, Y and Song, Y and Cai, J and Chao, J and Gong, Y and Jiang, X and Shao, K and Tang, X and Gao, G},
title = {Stronger biogeographical pattern of bacterioplankton communities than biofilm communities along a riverine ecosystem: A local scale study of the Kaidu river in the arid and semi-arid northwest of China.},
journal = {Environmental research},
volume = {264},
number = {Pt 1},
pages = {120294},
doi = {10.1016/j.envres.2024.120294},
pmid = {39505133},
issn = {1096-0953},
abstract = {Although the biogeographical pattern and mechanisms underlying microbial assembly have been well-explored in lentic ecosystems, the relevant scenarios in lotic ecosystems remain poorly understood. By sequencing the bacterial communities in bacterioplankton and biofilm, our study detected their distance-decay relationship (DDR), and the balance between deterministic and stochastic processes, along the Kaidu river in an arid and semi-arid region of northwest China. Our results revealed that bacterioplankton and biofilm had significantly contrasting community structures. The bacterioplankton communities showed a gradually decreasing trend in alpha-diversity from the headwater to the river mouth, contrasting with the alpha-diversity of biofilm communities which was constant along the river length. Both bacterioplankton and biofilm showed significant DDRs along the 500-km river corridor with the slope of the bacterioplankton DDR being steeper than that of the biofilm DDR, which implies a stronger biogeography of bacterioplankton than biofilm. Relative to biofilm communities, the species interactions formed a denser and more complex network in the bacterioplankton communities than in the biofilm communities. Our results also revealed that there was a transition of community assembly from deterministic to stochastic processes upstream to downstream, although both the bacterioplankton and biofilm communities were mainly regulated by deterministic processes within the entire river. All these empirical results expand our knowledge of microbial ecology in an arid and semi-arid lotic ecosystem.},
}
@article {pmid39503489,
year = {2024},
author = {Teixeira, GM and Cordeiro Montanari, GC and Nicoletto, MLA and da Silva, DV and Noriler, SA and de Oliveira, JP and da Silva Rodrigues, MV and Sipoli Sanches, D and de Padua Pereira, U and Nunes da Rocha, U and Oliveira, AGd},
title = {Draft genome of Bacillus velezensis CMRP6330, a suitable biocontrol agent for disease management in crops.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0065724},
doi = {10.1128/mra.00657-24},
pmid = {39503489},
issn = {2576-098X},
abstract = {As a biological alternative to managing diseases in crop production, we highlight the Bacillus velezensis strain LABIM41 (CMRP6330). Its genome, composed of 3,970,959 bp, possesses a rich metabolic machinery and a wide range of molecules with different biological activities and roles in its symbiotic relationship with its plant hosts.},
}
@article {pmid39502209,
year = {2024},
author = {Kipkoech, R and Takase, M and Ahogle, AMA and Ocholla, G},
title = {Analysis of properties of biodiesel and its development and promotion in Ghana.},
journal = {Heliyon},
volume = {10},
number = {20},
pages = {e39078},
pmid = {39502209},
issn = {2405-8440},
abstract = {The increasing global population and the challenges associated with fossil fuel has led to a surge in energy demand, necessitating research on renewable and environmentally friendly energy sources. Biodiesel, is produced from biomass materials like vegetable oil and fats, is a promising alternative. Transesterification is a principal method used in biodiesel production, as it is simple, versatile, and efficient. Biodiesel offers several advantages, including emissions, lubricity, and safety, making it a sustainable fuel option and its properties conforms to the international standards. However, it has lower energy content, cold weather performance issues, and slightly reduced engine power compared to petroleum diesel. The choice of biodiesel feedstock depends on its properties, with jatropha oil and other feedstocks being potential in Ghana. Research on biodiesel in Ghana is still in early stages and the Ghanaian government's policy aims to replace 10 % of petroleum fuel with biofuel by 2020 and 20 % by 2030, but these goals have not been achieved due to barriers. Despite these challenges, the government and stakeholders in the biofuel industry are working to optimize the biodiesel sector for sustainability, efficiency, and scalability. Innovative cultivation techniques and low-cost oil extraction methods are required, necessitating interdisciplinary research collaborations. By capitalizing on these opportunities and implementing targeted interventions, Ghana can become a regional leader in sustainable biodiesel production.},
}
@article {pmid39501667,
year = {2024},
author = {You, Z and Zhang, X and Huang, S and Chen, D and Zhu, Y and Li, G and Chen, X},
title = {The Influence of Skin Microbial Ecology on γδ T Cell Immune Pathways in Allergic Dermatitis Models in Mice.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jleuko/qiae244},
pmid = {39501667},
issn = {1938-3673},
abstract = {Atopic dermatitis (AD) is a complex disease influenced by alterations in the skin microbiome and immune dysregulation. Despite the recognized role of these factors, the specific pathways by which distinct microbial populations affect skin immunity remain insufficiently understood. On a molecular level, the pathogenesis of AD involves critical cytokines such as IL-4, IL-17, interferon-γ (IFN-γ), and IL-10, which contribute to the imbalance in T helper (Th) cell responses. Importantly, gamma-delta (γδ) T cells, which produce these cytokines and infiltrate affected epithelial cells in AD, have been underexplored. This study seeks to alleviate AD symptoms in mice by adjusting both peripheral and local immune environments through the transplantation of skin microbiota. By employing 16S rRNA sequencing, we characterized the skin microbiome of the mouse model. Our results demonstrate that microbiota intervention significantly reduces skin thickening and serum IgE levels in DNFB-induced AD mice. Additionally, changes in skin microbiota modulated immune cell dynamics, restoring the Th1/Th2 balance and leading to clinical improvement. These findings highlight the critical role of skin microbiota in shaping immune responses, positioning microbiota-based therapies as a potential treatment for AD.},
}
@article {pmid39501615,
year = {2024},
author = {Prost-Boxoen, L and Bafort, Q and Van de Vloet, A and Almeida-Silva, F and Paing, YT and Casteleyn, G and D'hondt, S and De Clerck, O and Van de Peer, Y},
title = {Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
pmid = {39501615},
issn = {1469-8137},
support = {833522//H2020 European Research Council/ ; 833522/ERC_/European Research Council/International ; I001621N//European Marine Biological Resource Centre Belgium/ ; 11H0426N//Fonds Wetenschappelijk Onderzoek/ ; G0C0116N//Fonds Wetenschappelijk Onderzoek/ ; BOF.MET.2021.0005.01//Bijzonder Onderzoeksfonds UGent/ ; 1168420N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.},
}
@article {pmid39500284,
year = {2024},
author = {Arrigan, D and Kothe, CI and Oliverio, A and Evans, JD and Wolfe, BE},
title = {Novel fermentations integrate traditional practice and rational design of fermented-food microbiomes.},
journal = {Current biology : CB},
volume = {34},
number = {21},
pages = {R1094-R1108},
doi = {10.1016/j.cub.2024.09.047},
pmid = {39500284},
issn = {1879-0445},
mesh = {*Fermented Foods/microbiology ; *Fermentation ; *Microbiota ; *Food Microbiology/methods ; Humans ; },
abstract = {Fermented foods and beverages have been produced around the world for millennia, providing humans with a range of gastronomic, cultural, health, and scientific benefits. Building on these traditional forms, a convergence of factors, including culinary innovation, globalization, shifts in consumer preferences, and advances in microbiome sciences, has led to the emergence of so-called 'novel fermentations'. In this review, we define novel fermentation as the confluence of traditional food practices and rational microbiome design. Using principles of microbial ecology and evolution, we develop a microbiological framework that outlines several strategies for producing and characterizing novel fermentations, including switching substrates, engrafting target species, assembling whole-community chimeras, and generating novel phenotypes. A subsequent analysis of existing traditional ferments points to gaps in 'fermentation space' where novel ferments could potentially be produced using new combinations of microbes and food substrates. We highlight some important safety and sociocultural issues presented by the repurposing and modification of microbes from traditional ferments that fermented-food producers and microbiologists need to address.},
}
@article {pmid39499580,
year = {2024},
author = {Zhang, X and Zhang, XX and Ma, L},
title = {New Horizons in Micro/Nanoplastic-Induced Oxidative Stress: Overlooked Free Radical Contributions and Microbial Metabolic Dysregulations in Anaerobic Digestion.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c08865},
pmid = {39499580},
issn = {1520-5851},
abstract = {Excessive production of reactive oxygen species (ROS) induced by micro/nanoplastics (MPs/NPs) is highly toxic to microbes. However, the mechanisms underlying ROS generation and metabolic regulation within anaerobic guilds remain poorly understood. In this study, we investigated the effects of environmentally relevant levels of polypropylene (PP)-MPs/NPs on oxidative stress and microbial ecology during anaerobic digestion (AD). Electron paramagnetic resonance spectroscopy revealed that PP-MPs/NPs elevated the concentrations of environmentally persistent free radicals (EPFRs) and derived hydroxyl radicals ([•]OH). EPFRs were identified as the primary contributors to [•]OH generation, as evidenced by a high Spearman correlation coefficient (r = 0.884, p < 0.001) and free radical-quenching studies. The formation of [•]OH enhanced ROS production by 86.2-100.9%, resulting in decreased cellular viability and methane production (by 37.5-50.5%) at 100 mg/g TS PP-MPs/NPs. Genome-centric metagenomic and metatranscriptomic analyses suggested that PP-MPs/NPs induced the reassembly of community structures, re-evolution of functional traits, and remodeling of interspecies interactions. Specifically, PP-MPs/NPs induced a shift in methanogen consortia from hydrogenotrophic Methanofollis sp. to acetoclastic and hydrogenotrophic Methanothrix soehngenii, primarily because of the latter's diverse ingestion patterns, electron bifurcation complexes, and ROS-scavenging abilities. Downregulation of genes associated with antioxidative defense systems (i.e., sodN, katA, and osmC) and ROS-driven redox signal transduction pathways (c-di-AMP and phosphorylation signaling pathways) provided insights into the mechanisms underlying ROS-induced microbial metabolic dysregulation. Our findings enhance the understanding of microbial ecological and metabolic traits under MPs/NPs stressors, facilitating the control of MPs/NPs toxicity and the stabilization of AD processes.},
}
@article {pmid39498487,
year = {2024},
author = {Dooley, KD and Henry, LP and Bergelson, J},
title = {Impact of timing on the invasion of synthetic bacterial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae220},
pmid = {39498487},
issn = {1751-7370},
abstract = {Microbial communities regularly experience ecological invasions that can lead to changes in composition and function. Factors thought to impact susceptibility to invasions, such as diversity and resource use, vary over the course of community assembly. We used synthetic bacterial communities to evaluate the success and impact of invasions occurring at different times during the community assembly process. Fifteen distinct communities were subjected to each of three bacterial invaders at the initial assembly of the community ("initial invasion"), 24 hours into community assembly ("early invasion"), when the community was still undergoing transient dynamics, and 7 days into community assembly ("late invasion"), once the community had settled into its final composition. Communities were passaged daily and characterized through sequencing after reaching a stable composition. Invasions often failed to persist over time, particularly in higher richness communities. However, invasions had their largest effect on composition when they occurred before a community had settled into a stable composition. We found instances where an invader was ultimately excluded yet had profound and long-lasting effects on invaded communities. Invasion outcome was positively associated with lower community richness and resource use efficiency by the community, which varied throughout assembly. Our results demonstrate that microbial communities experiencing transient community dynamics are more affected by, and in some instances prone to, invasion, a finding relevant to efforts to modify the composition of microbial communities.},
}
@article {pmid39498135,
year = {2024},
author = {Gu, Y and Meng, D and Liu, Z and Zhang, M and Yang, Z and Yin, H and Liang, Y and Xiao, N},
title = {Biotic and abiotic properties mediating sediment microbial diversity and function in a river-lake continuum.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1479670},
pmid = {39498135},
issn = {1664-302X},
abstract = {A river-lake system plays an important role in water management by providing long-term and frequent water diversions. However, hydrological connectivity in the system can have a profound effect on sediment microbial communities through pH, nutrient concentrations, and benthos invertebrates. Consequently, identifying the key environmental factors and their driving mechanisms is vital for microbial adaptation strategies to extreme environments. In this study, we analyzed the significant difference in sediment bacterial and fungal community structures and diversity indices among Dongting Lake and its tributary rivers, which worked as a typical river-connected lake ecosystem. There were significant differences in biotic and abiotic environments in the sediment habitats of Dongting Lake and its tributary rivers. Random forest analysis revealed that pH and Mollusca were found to be the most important abiotic and biotic variables for predicting both bacterial and fungal community structures, respectively. The beta diversity decomposition analyses showed that the bacterial and fungal community compositional dissimilarities among different sections were dominated by species replacement processes, with more than half of the OTUs in each section being unique. Notably, both biotic and abiotic factors affected the number and the relative abundance of these bacterial and fungal unique OTUs, leading to changes in community composition. Mollusca, pH, TP, NO3-N, and NH4-N were negatively related to the relative abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Ascomycota, while Annelida and ORP were positively related to the relative abundance of Actinobacteria and Gemmatimonadetes. Additionally, PICRUSt analysis revealed that the functional dissimilarity among lakes and rivers was strengthened in unique species compared to all species in bacterial and fungal communities, and the changes of functional types helped to improve the habitat environment in the main Dongting Lake and promote the process of microbial growth. From our results, the role of macrozoobenthos and physicochemical characteristics in driving the sediment microbial community spatial variations became clear, which contributed to further understanding of the river-lake ecosystem.},
}
@article {pmid39497067,
year = {2024},
author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD},
title = {Removal of sequencing adapter contamination improves microbial genome databases.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1033},
pmid = {39497067},
issn = {1471-2164},
mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; },
abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.},
}
@article {pmid39496952,
year = {2024},
author = {Djotan, AKG and Matsushita, N and Fukuda, K},
title = {Within-Site Variations in Soil Physicochemical Properties Explained the Spatiality and Cohabitation of Arbuscular Mycorrhizal Fungi in the Roots of Cryptomeria Japonica.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {136},
pmid = {39496952},
issn = {1432-184X},
support = {JP22H02382//Japan Society for the Promotion of Science/ ; },
mesh = {*Mycorrhizae/classification ; *Soil/chemistry ; *Soil Microbiology ; *Cryptomeria/microbiology ; *Plant Roots/microbiology ; Japan ; Phosphorus/analysis ; Forests ; Hydrogen-Ion Concentration ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) live in a community in the roots of host plants. Still, the patterns and factors that drive their spatiality and cohabitation remain uncovered, particularly that of trees in planted forests, which we aimed to clarify in Cryptomeria japonica, a major plantation tree in Japan. We analyzed 65 paired root and soil samples of Cryptomeria japonica trees collected from 11 microsite (MS) plots at two environmentally different forest sites in central Japan and measured soil pH, total phosphorus (TP), C, N, and the carbon-to-nitrogen ratio. Root AMF communities were recovered using Illumina's next-generation amplicon sequencing targeting the small subunit of ribosomal DNA. We detected more than 500 AMF OTUs at each site but only three belonging to Dominikia, Rhizophagus, and Sclerocystis were dominant in the roots of C. japonica, detected each at an average relative abundance higher than 20%. Two showed negatively correlated spatial distributions and different associations with soil pH. Similarly, the physicochemical properties at MSs significantly determined the AMF assemblages in the roots of C. japonica. Dominikia, Rhizophagus, and Sclerocystis coexist in the roots of C. japonica where soil physicochemical properties, particularly pH, determine their spatial dynamic, turnovers, and cohabitation patterns. These findings highlight the importance of simultaneous colonization of plants by multiple AMF.},
}
@article {pmid39496518,
year = {2024},
author = {Khaleque, HN and Fathollahzadeh, H and Kaksonen, AH and Valdés, J and Vergara, E and Holmes, DS and Watkin, ELJ},
title = {Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {12},
pages = {},
pmid = {39496518},
issn = {1574-6941},
support = {//Curtin University/ ; //CSIRO/ ; },
mesh = {*Phosphates/metabolism ; *Carbon/metabolism ; *Nitrogen/metabolism ; *Genome, Bacterial ; Citric Acid Cycle/genetics ; Genomics ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; },
abstract = {In-depth comparative genomic analysis was conducted to predict carbon, nitrogen, and phosphate assimilation pathways in the halotolerant, acidophilic genus Acidihalobacter. The study primarily aimed to understand how the metabolic capabilities of each species can determine their roles and effects on the microbial ecology of their unique saline and acidic environments, as well as in their potential application to saline water bioleaching systems. All four genomes encoded the genes for the complete tricarboxylic acid cycle, including 2-oxoglutarate dehydrogenase, a key enzyme absent in obligate chemolithotrophic acidophiles. Genes for a unique carboxysome shell protein, csoS1D, typically found in halotolerant bacteria but not in acidophiles, were identified. All genomes contained lactate and malate utilization genes, but only A. ferrooxydans DSM 14175T contained genes for the metabolism of propionate. Genes for phosphate assimilation were present, though organized differently across species. Only A. prosperus DSM 5130T and A. aeolianus DSM 14174T genomes contained nitrogen fixation genes, while A. ferrooxydans DSM 14175T and A. yilgarnensis DSM 105917T possessed genes for urease transporters and respiratory nitrate reductases, respectively. The findings suggest that all species can fix carbon dioxide but can also potentially utilize exogenous carbon sources and that the non-nitrogen-fixing species rely on alternative nitrogen assimilation mechanisms.},
}
@article {pmid39494810,
year = {2024},
author = {Malik, M and Das, S and Paul, P and Chakraborty, P and Roy, R and Maity, A and Das, A and Dasgupta, M and Trivedi, S and Tribedi, P},
title = {Cuminaldehyde in combination with tetracycline shows promising antibiofilm activity against drug-resistant Pseudomonas aeruginosa.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-20},
doi = {10.1080/08927014.2024.2422874},
pmid = {39494810},
issn = {1029-2454},
abstract = {Pseudomonas aeruginosa, an opportunistic pathogen often causes biofilm-linked infections. A combinatorial approach involving tetracycline (antibiotic) and cuminaldehyde (phytochemical) was explored to combat this infectious pathogen. The results showed that both tetracycline and cuminaldehyde individually demonstrated antibacterial effects. However, when the compounds were applied together, there was a significant increase in their antimicrobial potential. The determined fractional inhibitory concentration index of 0.43 indicated a synergistic interaction between the two compounds. Furthermore, a series of experiments demonstrated that the combined application of cuminaldehyde and tetracycline could lead to a significant enhancement of their antibiofilm potential. This enhanced antibiofilm potential was attributed to the accumulation of reactive oxygen species and increased cell membrane permeability. Besides, this combinatorial application reduced the secretion of various virulence factors from P. aeruginosa. Therefore, this combined approach holds promise for effectively treating P. aeruginosa biofilms.},
}
@article {pmid39493671,
year = {2024},
author = {Kleikamp, HBC and van der Zwaan, R and van Valderen, R and van Ede, JM and Pronk, M and Schaasberg, P and Allaart, MT and van Loosdrecht, MCM and Pabst, M},
title = {NovoLign: metaproteomics by sequence alignment.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae121},
pmid = {39493671},
issn = {2730-6151},
abstract = {Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. We assessed the NovoLign pipeline for taxonomic coverage and false positive annotations using a wide range of in silico and experimental data, including pure reference strains, laboratory enrichment cultures, synthetic communities, and environmental microbial communities. In summary, we present NovoLign, a de novo metaproteomics pipeline that employs large-scale sequence alignment to enable rapid taxonomic profiling, evaluation of database searching outcomes, and the creation of reference sequence databases. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.},
}
@article {pmid39491387,
year = {2023},
author = {González-Alonso, V and Pradal, I and Wardhana, YR and Cnockaert, M and Wieme, AD and Vandamme, P and De Vuyst, L},
title = {Microbial ecology and metabolite dynamics of backslopped triticale sourdough productions and the impact of scale.},
journal = {International journal of food microbiology},
volume = {408},
number = {},
pages = {110445},
doi = {10.1016/j.ijfoodmicro.2023.110445},
pmid = {39491387},
issn = {1879-3460},
abstract = {Triticale (X Triticosecale Wittmack) is a hybrid of wheat (Triticum aestivum L.) and rye (Secale cereale L.), combining the positive attributes of both cereals. However, it has not been exploited for sourdough production yet. Further, the effect of scale on sourdough production has not been investigated systematically up to now. The aims of the present study were to assess the microbial ecology and metabolomic output of eleven spontaneously fermented, backslopped sourdough productions made with triticale flour on a scale of 100, 200, 500, and 1000 g. The acidification profile [pH and total titratable acidity (TTA)], microbial diversity (culture-dependent and culture-independent), metabolite dynamics, and appropriate correlations were determined. After ten fermentation steps, different species of Lactobacillaceae were prevalent in the mature sourdoughs, in particular Latilactobacillus curvatus, Limosilactobacillus fermentum, and Pediococcus pentosaceus. The microbial diversity could be traced back to the grains and was also present in the milling fractions (flour, bran, and shorts). Furthermore, thanks to the use of Illumina-based high-throughput sequencing and an amplicon sequence variant (ASV) approach, the presence of undesirable bacterial groups (bacilli, clostridia, and enterobacteria) during the initial steps of the backslopping cycle was revealed, as well as a finetuned taxonomic diversity of the LAB genera involved. Small sourdough productions (100 and 200 g) selected for a lower species diversity and reached a stable consortium faster than large ones (500 and 1000 g). Although a comparable final pH of 3.6-4.0 was obtained, the TTA of small sourdoughs was lower than that of large ones. Regarding the metabolic output, the simultaneous production of mannitol and erythritol, beyond ethanol and glycerol, could be linked to sourdoughs in which Liml. fermentum was the sole LAB species present. Further, the use of the arginine deiminase pathway by P. pentosaceus and Liml. fermentum was obvious. An appropriate extraction method followed by liquid injection gas chromatography coupled to triple quadrupole tandem mass spectrometry allowed the quantification of interesting volatile organic compounds, such as ethyl lactate. These findings support the inclusion of triticale as a viable alternative to wheat or rye for the production of sourdoughs that can be integrated into bread-making production schemes.},
}
@article {pmid39482450,
year = {2024},
author = {Gao, L and Rao, MPN and Liu, YH and Wang, PD and Lian, ZH and Abdugheni, R and Jiang, HC and Jiao, JY and Shurigin, V and Fang, BZ and Li, WJ},
title = {SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {135},
pmid = {39482450},
issn = {1432-184X},
support = {2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2022D01A154//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022B0202110001//Key-Area Research and Development Programof Guangdong Province/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Salinity ; *Archaea/genetics/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Geologic Sediments/microbiology ; Phylogeny ; Desert Climate ; Ecosystem ; },
abstract = {Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.},
}
@article {pmid39480531,
year = {2024},
author = {Dobrzyński, J and Naziębło, A},
title = {Paenibacillus as a Biocontrol Agent for Fungal Phytopathogens: Is P. polymyxa the Only One Worth Attention?.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {134},
pmid = {39480531},
issn = {1432-184X},
mesh = {*Plant Diseases/microbiology/prevention &amp; control ; *Paenibacillus/physiology/metabolism ; *Paenibacillus polymyxa/physiology ; Biological Control Agents ; Fusarium/physiology ; Colletotrichum/physiology/growth &amp; development ; Pest Control, Biological ; Rhizoctonia/physiology/growth &amp; development ; Botrytis/growth &amp; development/physiology ; Fungi/physiology ; },
abstract = {Control of fungal phytopathogens is a significant challenge in modern agriculture. The widespread use of chemical fungicides to control these pathogens often leads to environmental and food contamination. An eco-friendly alternative that can help reduce reliance on these chemicals is plant growth-promoting bacteria (PGPB), particularly those of the genus Paenibacillus, which appear to be highly effective. The review aims to summarize the existing knowledge on the potential of Paenibacillus spp. as fungal biocontrol agents, identify knowledge gaps, and answer whether other species of the genus Paenibacillus, in addition to Paenibacillus polymyxa, can also be effective biocontrol agents. Paenibacillus spp. can combat plant phytopathogens through various mechanisms, including the production of lipopeptides (such as fusaricidin, paenimyxin, and pelgipeptin), the induction of systemic resistance (ISR), hydrolytic enzymes (chitinase, cellulase, and glucanase), and volatile organic compounds. These properties enable Paenibacillus strains to suppress the growth of fungi such as Fusarium oxysporum, F. solani, Rhizoctonia solani, Botrytis cinerea, or Colletotrichum gloeosporioides. Notably, several strains of Paenibacillus, including P. polymyxa, P. illinoisensis KJA-424, P. lentimorbus B-30488, and P. elgii JCK1400, have demonstrated efficacy in controlling fungal diseases in plants. Importantly, many formulations with Paenibacillus strains have already been patented, and some are commercially available, but most of them contain only P. polymyxa. Nevertheless, considering the data presented in this review, we believe that other strains from the Paenibacillus genus (besides P. polymyxa) will also be commercialized and used in plant protection in the future. Importantly, there is still limited information regarding their impact on the native microbiota, particularly from the metataxonomic and metagenomic perspectives. Expanding knowledge in this area could enhance the effectiveness of biocontrol agents containing Paenibacillus spp., ensuring safe and sustainable use of biological fungicides.},
}
@article {pmid39488271,
year = {2024},
author = {Allen, J and Sire, M and Belouard, N and Gorzerino, C and Coutellec, MA and Mony, C and Pannard, A and Piscart, C},
title = {Could landscape ecology principles apply at the microscale? A metabarcoding approach on Trichoptera larvae-associated microbial diversity.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {177304},
doi = {10.1016/j.scitotenv.2024.177304},
pmid = {39488271},
issn = {1879-1026},
mesh = {Animals ; *Larva ; *Microbiota ; *Insecta ; *DNA Barcoding, Taxonomic ; *Bacteria/classification/genetics ; Fungi ; Biodiversity ; Ecology ; Diatoms ; Ecosystem ; Environmental Monitoring/methods ; },
abstract = {Landscape heterogeneity is known as a major factor of community structure and composition. Whether this effect of the landscape extends at different scales and particularly at the relevant scale for microorganisms remained to be determined. We used the cases produced by aquatic larvae of Trichoptera, which assemble organic or mineral particles, as naturally replicated experimental systems representing structured substrates to determine the effect of landscape structuration on microbial communities. A metabarcoding approach was used to characterise fungal, bacterial and diatom communities on cases produced by six Trichoptera species and related unstructured organic and mineral substrates. The structuration of the particles constituting the cases was also determined as a measure of microscale landscape. Structured substrates harboured communities of diatoms, fungi and bacteria that differed from those found on unstructured substrates. Microbial communities also differed between organic and mineral substrates. We found a higher microbial diversity on structured substrates than on unstructured substrates. The heterogeneity of the microscale landscape also affected bacterial and fungal communities within cases. These results highlight the importance of microscale landscape structuration for microbial diversity and demonstrate that approaches of landscape ecology could be downscaled to the microscale.},
}
@article {pmid39488149,
year = {2024},
author = {Németh, Z and Svigruha, R and Ács, A and Farkas, A and Tapolczai, K and Elekes, K and Fodor, I and Pirger, Z},
title = {Developmental, behavioral, and biochemical effects of chronic exposure to sublethal concentrations of organic UV-filter compounds on a freshwater model species.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {277},
number = {},
pages = {107134},
doi = {10.1016/j.aquatox.2024.107134},
pmid = {39488149},
issn = {1879-1514},
abstract = {The prevalence of organic/chemical UV-filter compounds in aquatic ecosystems represents a growing environmental issue. The long-term toxicity risks of many UV-filters at environmentally relevant concentrations to aquatic biota are still less studied, especially in the case of invertebrates. This study was designed to evaluate the chronic toxicity of avobenzone (AVO), octocrylene (OCTO), and octinoxate (OCTI), three UV-filters which frequently occur in the aquatic environment, to the water flea (Daphnia magna) at an environmentally relevant concentration of 200 ng l[-1] in a 21-day exposure. Potential alterations in the growth, reproduction, and heart rate were continuously monitored during the treatments. Filtration rate, swimming, and the state of the antioxidant- and metabolic functions were evaluated at the end of exposures. Avobenzone significantly increased the reproductive output, heart rate, and filtration rate, while evoked a significant decrease of swimming behavior, and inhibited the activity of catalase (CAT) and glutathione S-transferase (GST) enzymes. The body size, reproduction, heart rate, and superoxide dismutase (SOD) activity were significantly increased whereas the activity of GST and CAT was significantly reduced by OCTO. OCTI significantly increased reproduction, heart rate, CAT and SOD activity but significantly decreased the swimming behavior. Our results confirmed that chronic exposure to organic UV-filters even at environmentally relevant concentrations affect basic physiological traits and cellular defense pathways in D. magna. Highlighting, our observations revealed previously unknown physiological changes (e.g., altered heart rate, filtration rate, SOD activity) caused by the investigated UV-filter compounds. Future research is to be aimed at investigating the mixture effects of these compounds and at the understanding of the potential cellular and molecular mechanisms underlying the changes induced.},
}
@article {pmid39485000,
year = {2024},
author = {Kortekaas Krohn, I and Callewaert, C and Belasri, H and De Pessemier, B and Diez Lopez, C and Mortz, CG and O'Mahony, L and Pérez-Gordo, M and Sokolowska, M and Unger, Z and Untersmayr, E and Homey, B and Gomez-Casado, C},
title = {The influence of lifestyle and environmental factors on host resilience through a homeostatic skin microbiota: An EAACI Task Force Report.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16378},
pmid = {39485000},
issn = {1398-9995},
support = {//European Academy of Allergy and Clinical Immunology/ ; },
abstract = {Human skin is colonized with skin microbiota that includes commensal bacteria, fungi, arthropods, archaea and viruses. The composition of the microbiota varies at different anatomical locations according to changes in body temperature, pH, humidity/hydration or sebum content. A homeostatic skin microbiota is crucial to maintain epithelial barrier functions, to protect from invading pathogens and to interact with the immune system. Therefore, maintaining homeostasis holds promise to be an achievable goal for microbiome-directed treatment strategies as well as a prophylactic strategy to prevent the development of skin diseases, as dysbiosis or disruption of homeostatic skin microbiota is associated with skin inflammation. A healthy skin microbiome is likely modulated by genetic as well as environmental and lifestyle factors. In this review, we aim to provide a complete overview of the lifestyle and environmental factors that can contribute to maintaining the skin microbiome healthy. Awareness of these factors could be the basis for a prophylactic strategy to prevent the development of skin diseases or to be used as a therapeutic approach.},
}
@article {pmid39482383,
year = {2024},
author = {Gaborieau, B and Vaysset, H and Tesson, F and Charachon, I and Dib, N and Bernier, J and Dequidt, T and Georjon, H and Clermont, O and Hersen, P and Debarbieux, L and Ricard, JD and Denamur, E and Bernheim, A},
title = {Prediction of strain level phage-host interactions across the Escherichia genus using only genomic information.},
journal = {Nature microbiology},
volume = {9},
number = {11},
pages = {2847-2861},
pmid = {39482383},
issn = {2058-5276},
support = {R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ANR-19-AMRB-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-AMRB-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-20-CE92-0048//Agence Nationale de la Recherche (French National Research Agency)/ ; DEQ20161136698//Fondation pour la Recherche M&#xe9;dicale (Foundation for Medical Research in France)/ ; },
mesh = {*Host Specificity ; *Bacteriophages/genetics/physiology/classification ; *Genomics/methods ; Algorithms ; Escherichia coli/virology/genetics ; Phage Therapy ; Escherichia/genetics/virology ; Genome, Bacterial/genetics ; Genome, Viral/genetics ; Host-Pathogen Interactions ; ROC Curve ; Host Microbial Interactions ; },
abstract = {Predicting bacteriophage infection of specific bacterial strains promises advancements in phage therapy and microbial ecology. Whether the dynamics of well-established phage-host model systems generalize to the wide diversity of microbes is currently unknown. Here we show that we could accurately predict the outcomes of phage-bacteria interactions at the strain level in natural isolates from the genus Escherichia using only genomic data (area under the receiver operating characteristic curve (AUROC) of 86%). We experimentally established a dataset of interactions between 403 diverse Escherichia strains and 96 phages. Most interactions are explained by adsorption factors as opposed to antiphage systems which play a marginal role. We trained predictive algorithms and pinpoint poorly predicted interactions to direct future research efforts. Finally, we established a pipeline to recommend tailored phage cocktails, demonstrating efficiency on 100 pathogenic E. coli isolates. This work provides quantitative insights into phage-host specificity and supports the use of predictive algorithms in phage therapy.},
}
@article {pmid39481794,
year = {2024},
author = {Li, X and Li, Y and Wang, Y and Liu, Y and Riaz, L and Wang, Q and Zeng, X and Qin, Z and Irfan, M and Yang, Q},
title = {Methodology comparison of environmental sediment fungal community analysis.},
journal = {Environmental research},
volume = {263},
number = {Pt 3},
pages = {120260},
doi = {10.1016/j.envres.2024.120260},
pmid = {39481794},
issn = {1096-0953},
abstract = {Fungi play important roles in ecosystems. Analyzing fungal communities in environments has long been a challenge due to the large difference in compositions retrieved using different methods or sequencing regions, obscuring the true abundance and species information. Our study aimed to compare and determine more accurate approach for evaluating fungal populations in river sediment. To achieve this, different primer sets in the internal transcribed spacer (ITS) (ITS5/ITS1R, ITS1F/ITS2), 18S rRNA gene (0817F/1196R) for High-throughput sequencing (HTS), metagenomic shotgun sequencing (MS) directly from environmental samples, and HTS using ITS primers for the fungal samples collected from plate cultivation were used to characterize the fungal communities. We calculated diversity index and used FungalTraits to analyze methods preferences for fungal species. The study revealed that when analyzing the fungal species directly from environmental samples, amplification and sequencing of ITS region demonstrated more accuracy than MS and 18S rRNA gene sequencing methods, but displayed significant primer preference. Over 30 % fungal species from HTS after plate cultivation were not present in HTS from the environmental samples. NMDS analysis demonstrated significant disparities in species diversity among different methods, suggesting potential complementarity between them. Over 85% species identified by HTS using ITS primers belonged to filamentous fungi, while the MS mostly identified yeast (62%). Therefore, to get more accurate fungal community information in sediment, multiple methods were recommended by using cultivation, molecular biological methods dependent on PCR techniques like ITS1F/ITS2 primer for HTS and PCR independent method such as metagenomic shotgun sequencing techniques.},
}
@article {pmid39476778,
year = {2024},
author = {Li, J and Sun, Y and Zhang, Q and Liu, S and Liu, P and Zhang, XX},
title = {Unveiling the potential role of virus-encoded polyphosphate kinases in enhancing phosphorus removal in activated sludge systems.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122678},
doi = {10.1016/j.watres.2024.122678},
pmid = {39476778},
issn = {1879-2448},
abstract = {While microbial phosphate removal in activated sludge (AS) systems has been extensively studied, the role of viruses in this process remains largely unexplored. In this study, we identified 149 viral auxiliary metabolic genes associated with phosphorus cycling from 2,510 viral contigs (VCs) derived from AS systems. Notably, polyphosphate kinase 1 (ppk1) and polyphosphate kinase 2 (ppk2) genes, which are primarily responsible for phosphate removal, were found in five unclassified VCs. These genes exhibited conserved protein structures and active catalytic sites, indicating a pivotal role of viruses in enhancing phosphorus removal. Phylogenetic analysis demonstrated a close relationship between viral ppk genes and their bacterial counterparts, suggesting the occurrence of horizontal gene transfer. Furthermore, experimental assays validated that viral ppk genes enhanced host phosphate removal capabilities. VCs carrying ppk genes were observed across diverse ecological and geographical contexts, suggesting their potential to bolster host functions in varied environmental and nutrient settings, spanning natural and engineered systems. These findings uncover a previously underappreciated mechanism by which viruses enhance phosphate removal in wastewater treatment plants. Overall, our study highlights the potential for leveraging virus-encoded genes to improve the efficiency of biological phosphorus removal processes, offering new insights into the microbial ecology of AS systems and the role of viruses in biogeochemical cycling.},
}
@article {pmid39472801,
year = {2024},
author = {Valiei, A and Dickson, AM and Aminian-Dehkordi, J and Mofrad, MRK},
title = {Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {441},
pmid = {39472801},
issn = {1471-2180},
mesh = {*Bacteria/metabolism/classification/growth &amp; development/genetics ; *Biofilms/growth &amp; development ; Humans ; *Gastrointestinal Microbiome ; Microbial Interactions ; Bacterial Physiological Phenomena ; Models, Biological ; Kinetics ; Symbiosis ; Ecosystem ; Nutrients/metabolism ; },
abstract = {Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces. One example is gut mucosal communities, where dense, closely packed communities develop under the concurrent influence of nutrient transport from the lumen and fluid-mediated detachment of bacteria. In this study, we model a mucosal niche through a coupled agent-based and finite-volume modeling approach. This methodology enables us to model bacterial interactions affected by nutrient release from various sources while adjusting individual bacterial kinetics. We explored how the dispersion and abundance of bacteria are influenced by biochemical kinetics in different types of metabolic interactions, with a particular focus on the trade-off between growth rate and yield. Our findings demonstrate that in competitive scenarios, higher growth rates result in a larger share of the niche space. In contrast, growth yield plays a critical role in neutralism, commensalism, and mutualism interactions. When bacteria are introduced sequentially, they cause distinct spatiotemporal effects, such as deeper niche colonization in commensalism and mutualism scenarios driven by species intermixing effects, which are enhanced by high growth yields. Moreover, sub-ecosystem interactions dictate the dynamics of three-species communities, sometimes yielding unexpected outcomes. Competitive, fast-growing bacteria demonstrate robust colonization abilities, yet they face challenges in displacing established mutualistic systems. Bacteria that develop a cooperative relationship with existing species typically obtain niche residence, regardless of their growth rates, although higher growth yields significantly enhance their abundance. Our results underscore the importance of bacterial niche dynamics in shaping community properties and succession, highlighting a new approach to manipulating microbial systems.},
}
@article {pmid39470240,
year = {2024},
author = {Dumann, G and Rohland, O and Abdel-Glil, MY and Allen, RJ and Bauer, M and Busch, A},
title = {Draft genomes of the bile duct microbiome strains Klebsiella pneumoniae and Enterococcus lactis isolated from bilioenteric drainages with biofilm-forming abilities.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0020224},
doi = {10.1128/mra.00202-24},
pmid = {39470240},
issn = {2576-098X},
abstract = {We describe the genetic properties of two strains isolated from the elusive bile duct microbiome from solid organ transplant patients. Bacterial strains Enterococcus lactis (MS-STENT-08-E-001) and Klebsiella pneumoniae (MS-STENT-01-M-001) were isolated from the biofilms of bile duct catheters.},
}
@article {pmid39468827,
year = {2024},
author = {Flores, JN and Lubin, JB and Silverman, MA},
title = {The case for microbial intervention at weaning.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2414798},
pmid = {39468827},
issn = {1949-0984},
support = {R01 DK133453/DK/NIDDK NIH HHS/United States ; T32 GM008562/GM/NIGMS NIH HHS/United States ; },
mesh = {*Weaning ; *Gastrointestinal Microbiome ; Humans ; Animals ; *Probiotics/administration &amp; dosage ; Host Microbial Interactions ; Diet ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Intestines/microbiology/immunology ; },
abstract = {Weaning, the transition from a milk-based diet to solid food, coincides with the most significant shift in gut microbiome composition in the lifetime of most mammals. Notably, this period also marks a "window of opportunity" where key components of the immune system develop, and host-microbe interactions shape long-term immune homeostasis thereby influencing the risk of autoimmune and inflammatory diseases. This review provides a comprehensive analysis of the changes in nutrition, microbiota, and host physiology that occur during weaning. We explore how these weaning-associated processes differ across species, lifestyles, and regions of the intestine. Using prinicples of microbial ecology, we propose that the weaning transition is an optimal period for microbiome-targeted therapeutic interventions. Additionally, we suggest that replicating features of the weaning microbiome in adults could promote the successful engraftment of probiotics. Finally, we highlight key research areas that could deepen our understanding of the complex relationships between diet, commensal microbes, and the host, informing the development of more effective microbial therapies.},
}
@article {pmid39468208,
year = {2024},
author = {Ilicic, D and Woodhouse, J and Karsten, U and Schimani, K and Zimmermann, J and Grossart, HP},
title = {Chytrid fungi infecting Arctic microphytobenthic communities under varying salinity conditions.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {25821},
pmid = {39468208},
issn = {2045-2322},
mesh = {Arctic Regions ; *Salinity ; *Chytridiomycota/genetics/isolation &amp; purification ; Diatoms/microbiology/genetics ; Mycobiome ; Ecosystem ; Biodiversity ; Food Chain ; },
abstract = {This study aimed to investigate the presence and diversity of fungal parasites in Arctic coastal microphytobenthic communities. These communities represent a key component in the functioning of Arctic trophic food webs. Fungal parasites, particularly Chytridiomycota (chytrids), play significant roles by controlling microalgal bloom events, impacting genetic diversity, modifying microbial interactions, and accelerating nutrient and energy transfer to higher trophic levels. In the context of rapid Arctic warming and increased glacier meltwater, which significantly affects these communities, we used high-throughput sequencing to explore fungal community composition. Our results show that chytrids dominate fungal communities in Arctic benthic habitats and that the overall fungal diversity is primarily influenced by the salinity gradient. Chytrid representation is positively correlated with the presence of potential benthic diatom (Surirella, Nitzschia, Navicula) and green algae (Ulvophyceae) hosts, while microscopic observations provide further evidence for the presence of active chytrid infections.},
}
@article {pmid39467902,
year = {2024},
author = {Awais, M and Xiang, Y and Shah, N and Bilal, H and Yang, D and Hu, H and Li, T and Ji, X and Li, H},
title = {Unraveling the Role of Contaminants Reshaping the Microflora in Zea mays Seeds from Heavy Metal-Contaminated and Pristine Environment.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {133},
pmid = {39467902},
issn = {1432-184X},
support = {KUST-AN2023006Y//Kunming University of Science and Technology Plan Project/ ; KUST-AN2023006Y//Kunming University of Science and Technology Plan Project/ ; 42267059//National Natural Science Foundation of China/ ; SKLEG2023216//State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences/ ; },
mesh = {*Zea mays/microbiology ; *Metals, Heavy/analysis ; *Seeds/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; China ; *Soil Pollutants/analysis ; *Fungi/genetics/classification/isolation &amp; purification/drug effects ; *Microbiota/drug effects ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Heavy metal (HM) contaminants are the emerging driving force for reshaping the microflora of plants by eradicating the non-tolerance and non-resistant microbes via their lethal effects. Seeds served as a prime source of ancestral microbial diversity hereditary transfer from generation to generation. However, the problem arises when they got exposed to metal contamination, does metal pollutant disrupt the delicate balance of microbial communities within seeds and lead to shifts in their microflora across generations. In this study, the endophytic community within Zea mays seeds was compared across three distinct regions in Yunnan province, China: a HM-contaminated site Ayika (AK), less-contaminated site Sanduoduo (SD), and a non-contaminated Site Dali (DL). High-throughput sequencing techniques were employed to analyze the microbial communities. A total of 492,177 high-quality reads for bacterial communities and 1,001,229 optimized sequences for fungal communities were obtained. These sequences were assigned to 502 and 239 operational taxonomic units (OTUs) for bacteria and fungi, respectively. A higher diversity was recorded in AK samples than in SD and DL. Microbial community structure analysis showed higher diversity and significant fluctuation in specific taxa abundance in the metal-polluted samples exhibiting higher response of microbial flora to HM. In AK samples, bacterial genera such as Gordonia and Burkholderia-Caballeronia-Paraburkholderia were dominant, while in SD Pseudomonas and Streptomyces were dominant. Among the fungal taxa, Fusarium, Saccharomycopsis, and Lecanicillium were prevalent in HM-contaminated sites. Our finding revealed the influential effect of HM contaminants on reshaping the seed microbiome of the Zea mays, showing both the resilience of certain important microbial taxa as well the shifts in the diversity in the contaminated and pristine conditions. The knowledge will benefit to develop effective soil remediation, reclamation, and crop management techniques, and eventually assisting in the extenuation of metal pollution's adverse effects on plant health and agricultural productivity.},
}
@article {pmid39460615,
year = {2024},
author = {Wen, J and Zhang, H and Chu, D and Chen, X and Feng, J and Wang, Y and Liu, G and Zhang, Y and Li, Y and Ning, K},
title = {Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae966},
pmid = {39460615},
issn = {1362-4962},
support = {32071465//National Natural Science Foundation of China/ ; 2023YFA1800900//National Key Research and Development Program of China/ ; },
abstract = {Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced DeepInverton, a deep learning model that identifies invertons across a broad phylogenetic spectrum without using sequencing reads. By analyzing 68 733 bacterial genomes and 9382 metagenomes, we have uncovered over 200 000 nonredundant invertons and have also highlighted their abundance in pathogens. Additionally, we identified a post-Cambrian Explosion increase of invertons, paralleling species diversification. Furthermore, we revealed that invertons regulate diverse functions, including antimicrobial resistance and biofilm formation, underscoring their role in environmental adaptation. Notably, the majority of inverton identifications by DeepInverton have been confirmed by the in vitro experiments. The comprehensive inverton profiles have deepened our understanding of invertons at pan-genome and pan-metagenome scales, enabling a broad spectrum of applications in microbial ecology and synthetic biology.},
}
@article {pmid39454273,
year = {2024},
author = {Xun, F and Feng, M and Zhao, C and Luo, W and Han, X and Ci, Z and Yin, Y and Wang, R and Wu, QL and Grossart, HP and Xing, P},
title = {Epilimnetic oligotrophication increases contribution of oxic methane production to atmospheric methane flux from stratified lakes.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122602},
doi = {10.1016/j.watres.2024.122602},
pmid = {39454273},
issn = {1879-2448},
abstract = {Although considerable attention has been paid to the effects of eutrophication on aquatic methane (CH4) emissions to the atmosphere, the ecosystem-level effects of oligotrophication/re-oligotrophication on aquatic CH4 production and subsequent ecological responses remain to be elucidated. It has been hypothesized that dissolved inorganic phosphorus (DIP)-deficient conditions drive the ecosystem to utilize poorly bioavailable organic phosphorus for biomass formation, thereby generating CH4 as a by-product. To test this hypothesis, a mass balance approach was used to estimate in situ oxic methane production (OMP) in an oligotrophic, deep Lake Fuxian. The isotopic signature of dissolved [13]C-CH4, the potential substrates for OMP, and the phnJ/phnD genes associated with microbial demethylation of organic phosphorus compounds were analyzed. Our results indicate that CH4 accumulation was maximal in the surface mixed layer (SML, i.e., Epilimnion) during lake stratification, and ∼ 86 % of the total CH4 flux to the atmosphere was due to OMP. Decomposition of methylphosphonate (MPn) by Alphaproteobacteria (genera Sphingomonas and Mesorhizobium) contributed significantly to OMP. Furthermore, water temperature (Temp), chlorophyll a (Chla), and DIP were the most critical predictors of water OMP potential. Meta-analysis of currently available global data showed that OMP had a negative exponential distribution with DIP (OMP = 2.0 e[-0.71DIP], R[2] = 0.57, p < 0.05). DIP concentrations below a threshold of 3.40 ∼ 9.35 μg P L[-1] triggered OMP processes and increased the atmospheric CH4 emissions. Under future warming scenarios, stratification and catchment management induced oligotrophication or re-oligotrophication may systematically affect the biogeochemical cycling of phosphorus and the OMP contribution to CH4 emission in stratified lakes.},
}
@article {pmid39452361,
year = {2024},
author = {Kiewra, D and Dyczko, D and Žákovská, A and Nejezchlebova, H},
title = {Prevalence of Borrelia and Rickettsia in Ixodes ricinus from Chosen Urban and Protected Areas in Poland and the Czech Republic.},
journal = {Insects},
volume = {15},
number = {10},
pages = {},
pmid = {39452361},
issn = {2075-4450},
abstract = {(1) Background: Ixodes ricinus is responsible for the spreading of medically important pathogens. Monitoring the level of tick infection in various areas is essential for determining the potential tick-born risk. This study aimed to detect Borrelia spp. and Rickettsia spp. in I. ricinus ticks collected in urban and protected areas both in Poland and the Czech Republic. (2) Methods: Ticks were collected by flagging in the years 2016-2017. Borrelia spp. was detected using nested PCR targeting the flaB gene and Rickettsia spp. using nested PCR targeting gltA. (3) Results: In total, DNA of Borrelia spp. was detected in 25.9% of samples. Ticks collected in Poland were more infected compared to the Czech Republic and ticks collected in protected areas were more infected with Borrelia spp. than ticks collected in urban areas. The RFLP analysis showed the occurrence of B. afzelii and B. garinii in both countries, and additionally B. valaisiana, B. burgdorferi s.s., and B. miyamotoi in Poland. Rickettsia spp. was detected in 17.4% of I. ricinus, with comparable infection level in both countries; however, regional differences were observed. (4) Conclusion: The regional differences in Borrelia spp. and Rickettsia spp. prevalence in I. ricinus indicate the complexity of factors influencing the level of infection and underline the need for adaptation public health surveillance strategies in each region.},
}
@article {pmid39450335,
year = {2024},
author = {Hodžić, A and Veinović, G and Alić, A and Seki, D and Kunert, M and Nikolov, G and Sukara, R and Šupić, J and Tomanović, S and Berry, D},
title = {A metalloprotease secreted by an environmentally acquired gut bacterium hinders Borrelia afzelii colonization in Ixodes ricinus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1476266},
pmid = {39450335},
issn = {2235-2988},
mesh = {*Ixodes/microbiology ; Animals ; *Borrelia burgdorferi Group/genetics/metabolism ; *Gastrointestinal Microbiome ; *Metalloproteases/metabolism ; Bacillus cereus/enzymology/metabolism/genetics ; Lyme Disease/microbiology ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Although the importance of the microbiome in the context of tick biology and vector competence has recently come into a broader research focus, the field is still in its infancy and the complex ecological interactions between the tick residential bacteria and pathogens are obscure. Here, we show that an environmentally acquired gut bacterium has the potential to impair Borrelia afzelii colonization within the tick vector through a secreted metalloprotease. Oral introduction of either Bacillus cereus LTG-1 isolate or its purified enhancin (BcEnhancin) protein significantly reduces B. afzelii burden in the guts of Ixodes ricinus ticks. This effect is attributed to the ability of BcEnhancin to degrade a glycan-rich peritrophic matrix (PM), which is a gut protective barrier essential for Borrelia survival. Our study highlights the importance of the gut microbiome in determining tick vector competence and provides a deeper mechanistic insight into the complex network of interactions between Borrelia, the tick, and the tick microbiome.},
}
@article {pmid39450162,
year = {2024},
author = {Nenciarini, S and Rivero, D and Ciccione, A and Amoriello, R and Cerasuolo, B and Pallecchi, M and Bartolucci, GL and Ballerini, C and Cavalieri, D},
title = {Impact of cooperative or competitive dynamics between the yeast Saccharomyces cerevisiae and lactobacilli on the immune response of the host.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1399842},
pmid = {39450162},
issn = {1664-3224},
mesh = {Humans ; *Saccharomyces cerevisiae/immunology ; *Gastrointestinal Microbiome/immunology ; *Lactobacillus/immunology ; Probiotics ; Animals ; Microbial Interactions/immunology ; Dysbiosis/immunology ; },
abstract = {Fungi and bacteria can be found coexisting in a wide variety of environments. The combination of their physical and molecular interactions can result in a broad range of outcomes for each partner, from competition to cooperative relationships. Most of these interactions can also be found in the human gastrointestinal tract. The gut microbiota is essential for humans, helping the assimilation of food components as well as the prevention of pathogen invasions through host immune system modulation and the production of beneficial metabolites such as short-chain fatty acids (SCFAs). Several factors, including changes in diet habits due to the progressive Westernization of the lifestyle, are linked to the onset of dysbiosis statuses that impair the correct balance of the gut environment. It is therefore crucial to explore the interactions between commensal and diet-derived microorganisms and their influence on host health. Investigating these interactions through co-cultures between human- and fermented food-derived lactobacilli and yeasts led us to understand how the strains' growth yield and their metabolic products rely on the nature and concentration of the species involved, producing either cooperative or competitive dynamics. Moreover, single cultures of yeasts and lactobacilli proved to be ideal candidates for developing immune-enhancing products, given their ability to induce trained immunity in blood-derived human monocytes in vitro. Conversely, co-cultures as well as mixtures of yeasts and lactobacilli have been shown to induce an anti-inflammatory response on the same immune cells in terms of cytokine profiles and activation surface markers, opening new possibilities in the design of probiotic and dietary therapies.},
}
@article {pmid39449043,
year = {2024},
author = {Zhai, X and Gobbi, A and Kot, W and Krych, L and Nielsen, DS and Deng, L},
title = {A single-stranded based library preparation method for virome characterization.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {219},
pmid = {39449043},
issn = {2049-2618},
mesh = {*Virome/genetics ; *Genome, Viral/genetics ; *Gastrointestinal Microbiome/genetics ; *Gene Library ; Humans ; DNA, Viral/genetics ; DNA, Single-Stranded/genetics ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: The gut virome is an integral component of the gut microbiome, playing a crucial role in maintaining gut health. However, accurately depicting the entire gut virome is challenging due to the inherent diversity of genome types (dsDNA, ssDNA, dsRNA, and ssRNA) and topologies (linear, circular, or fragments), with subsequently biases associated with current sequencing library preparation methods. To overcome these problems and improve reproducibility and comparability across studies, universal or standardized virome sequencing library construction methods are highly needed in the gut virome study.<br><br>RESULTS: We repurposed the ligation-based single-stranded library (SSLR) preparation method for virome studies. We demonstrate that the SSLR method exhibits exceptional efficiency in quantifying viral DNA genomes (both dsDNA and ssDNA) and outperforms existing double-stranded (Nextera) and single-stranded (xGen, MDA&#x2009;+&#x2009;Nextera) library preparation approaches in terms of minimal amplification bias, evenness of coverage, and integrity of assembling viral genomes. The SSLR method can be utilized for the simultaneous library preparation of both DNA and RNA viral genomes. Furthermore, the SSLR method showed its ability to capture highly modified phage genomes, which were often lost using other library preparation approaches.<br><br>CONCLUSION: We introduce and improve a fast, simple, and efficient ligation-based single-stranded DNA library preparation for gut virome study. This method is compatible with Illumina sequencing platforms and only requires ligation reagents within 3-h library preparation, which is similar or even better than the advanced library preparation method (xGen). We hope this method can be further optimized, validated, and widely used to make gut virome study more comparable and reproducible. Video Abstract.},
}
@article {pmid39448159,
year = {2025},
author = {Diaz, M and Aird, H and Le Viet, T and Gutiérrez, AV and Larke-Mejia, N and Omelchenko, O and Moragues-Solanas, L and Fritscher, J and Som, N and McLauchlin, J and Hildebrand, F and Jørgensen, F and Gilmour, M},
title = {Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes.},
journal = {Food microbiology},
volume = {125},
number = {},
pages = {104649},
doi = {10.1016/j.fm.2024.104649},
pmid = {39448159},
issn = {1095-9998},
mesh = {*Listeria monocytogenes/genetics/isolation &amp; purification/growth &amp; development/classification ; *Fast Foods/microbiology ; Food Microbiology ; Microbiota ; Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; Environmental Microbiology ; Metagenomics ; Pseudomonas fluorescens/genetics/isolation &amp; purification/growth &amp; development/classification ; Food Contamination/analysis ; },
abstract = {Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to its remarkable ability to persist through safety control efforts, posing a subsequent health threat to consumers. Understanding the microbial communities coexisting with L. monocytogenes in food processing environments provides insights into its persistence mechanisms. We investigated the microbial communities on non-food contact surfaces in a facility producing ready-to-eat foods, known to harbour a ST121 L. monocytogenes strain over multiple years. A 10-week sampling period was coordinated with the company and public health authorities. Metagenomic analysis revealed a stable microbial composition dominated by Pseudomonas fluorescens. While highly related populations were present in high-care production zones, distinctive taxa characteristic of specific areas were observed (e.g., Sphingomonas aerolata). Although Listeria spp. were not detected in metagenomes, they were detected in cultured samples, suggesting low relative abundance in factory settings. The findings suggest that a stable resident microbiota, with distinct adaptations to different areas within the factory, was selected for by their collective ability to survive control efforts in this environment. Listeria spp. was a member of this microbial community, albeit at low abundance, and may likewise benefit from the mutualism of the overall microbial community.},
}
@article {pmid39446706,
year = {2024},
author = {Shinfuku, MS and Domeignoz-Horta, LA and Choudoir, MJ and Frey, SD and Mitchell, MF and Ranjan, R and DeAngelis, KM},
title = {Seasonal effects of long-term warming on ecosystem function and bacterial diversity.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0311364},
pmid = {39446706},
issn = {1932-6203},
mesh = {*Seasons ; *Soil Microbiology ; *Biodiversity ; *Bacteria/classification/genetics ; *Ecosystem ; *Climate Change ; Soil/chemistry ; Global Warming ; },
abstract = {Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness.},
}
@article {pmid39445507,
year = {2024},
author = {Liu, L and Zhang, X and Schorn, S and Doda, T and Kang, M and Bouffard, D and Kirillin, G and Milucka, J and Shi, X and Grossart, HP},
title = {Strong Subseasonal Variability of Oxic Methane Production Challenges Methane Budgeting in Freshwater Lakes.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {44},
pages = {19690-19701},
doi = {10.1021/acs.est.4c07413},
pmid = {39445507},
issn = {1520-5851},
mesh = {*Methane ; *Lakes ; Seasons ; Environmental Monitoring ; Fresh Water ; },
abstract = {Methane (CH4) accumulation in the well-oxygenated lake epilimnion enhances the diffusive atmospheric CH4 emission. Both lateral transport and in situ oxic methane production (OMP) have been suggested as potential sources. While the latter has been recently supported by increasing evidence, quantifying the exact contribution of OMP to atmospheric emissions remains challenging. Based on a large high-resolution field data set collected during 2019-2020 in the deep stratified Lake Stechlin and on three-dimensional hydrodynamic modeling, we improved existing CH4 budgets by resolving each component of the mass balance model at a seasonal scale and therefore better constrained the residual OMP. All terms in our model showed a large temporal variability at scales from intraday to seasonal, and the modeled OMP was most sensitive to the surface CH4 flux estimates. Future efforts are needed to reduce the uncertainties in estimating OMP rates using the mass balance approach by increasing the frequency of atmospheric CH4 flux measurements.},
}
@article {pmid39442306,
year = {2024},
author = {Wen, X and Xiang, L and Harindintwali, JD and Wang, Y and He, C and Fu, Y and Wei, S and Hashsham, SA and Jiang, J and Jiang, X and Wang, F},
title = {Mitigating risks from atrazine drift to soybeans through foliar pre-spraying with a degrading bacterium.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136224},
doi = {10.1016/j.jhazmat.2024.136224},
pmid = {39442306},
issn = {1873-3336},
abstract = {Herbicides play a crucial role in managing weeds in agriculture, ensuring the productivity and quality of crops. However, herbicide drift poses a significant threat to sensitive plants, necessitating the consideration of ecosystem-based solutions to address this issue. In this study, foliar pre-spraying of atrazine-degrading Paenarthrobacter sp. AT5 was proposed as a new approach to mitigate the risks associated with atrazine drift on soybeans. Exposure to atrazine reduced chlorophyll levels and disturbed the antioxidant system and metabolic processes in soybean leaves, ultimately causing leaves to turn yellow. However, by pre-spraying, strain AT5 successfully colonized the surface of soybean leaves and mitigated the harmful effects of atrazine. This was achieved by slowing down atrazine absorption, expediting its reduction (half-life decreased from 2.22 d to 0.86 d), altering its degradation pathway (enhancing hydroxylation while weakening alkylation), and enhancing the interaction within phyllosphere bacteria communities. This study introduces a new approach that is both eco-friendly and user-friendly for reducing the risks of herbicide drift to sensitive crops, hence promoting the development of mixed cropping.},
}
@article {pmid39440978,
year = {2024},
author = {Soto Ocaña, J and Friedman, ES and Keenan, O and Bayard, NU and Ford, E and Tanes, C and Munneke, MJ and Beavers, WN and Skaar, EP and Bittinger, K and Zemel, BS and Wu, GD and Zackular, JP},
title = {Metal availability shapes early life microbial ecology and community succession.},
journal = {mBio},
volume = {15},
number = {11},
pages = {e0153424},
pmid = {39440978},
issn = {2150-7511},
support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; R01DK107565, P30DK050306//HHS | National Institutes of Health (NIH)/ ; R35GM138369//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; UL1 TR001878/TR/NCATS NIH HHS/United States ; R01DK107565//HHS | National Institutes of Health (NIH)/ ; R01 DK107565/DK/NIDDK NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Metals/metabolism ; *Leukocyte L1 Antigen Complex/metabolism/analysis ; Bacteria/metabolism/classification/genetics ; Breast Feeding ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Infant, Newborn ; Microbiota ; Infant Formula ; },
abstract = {The gut microbiota plays a critical role in human health and disease. Microbial community assembly and succession early in life are influenced by numerous factors. In turn, assembly of this microbial community is known to influence the host, including immune system development, and has been linked to outcomes later in life. To date, the role of host-mediated nutritional immunity and metal availability in shaping microbial community assembly and succession early in life has not been explored in depth. Using a human infant cohort, we show that the metal-chelating protein calprotectin is highly abundant in infants. Taxa previously shown to be successful early colonizers of the infant gut, such as Enterococcus, Enterobacteriaceae, and Bacteroides, are highly resistant to experimental metal starvation in culture. Lactobacillus, meanwhile, is highly susceptible to metal restriction, pointing to a possible mechanism by which host-mediated metal limitation shapes the fitness of early colonizing taxa in the infant gut. We further demonstrate that formula-fed infants harbor markedly higher levels of metals in their gastrointestinal tract compared to breastfed infants. Formula-fed infants with high levels of metals harbor distinct microbial communities compared to breastfed infants, with higher levels of Enterococcus, Enterobacter, and Klebsiella, taxa which show increased resistance to the toxic effects of high metal concentrations. These data highlight a new paradigm in microbial community assembly and suggest an unappreciated role for nutritional immunity and dietary metals in shaping the earliest colonization events of the microbiota.IMPORTANCEEarly life represents a critical window for microbial colonization of the human gastrointestinal tract. Surprisingly, we still know little about the rules that govern the successful colonization of infants and the factors that shape the success of early life microbial colonizers. In this study, we report that metal availability is an important factor in the assembly and succession of the early life microbiota. We show that the host-derived metal-chelating protein, calprotectin, is highly abundant in infants and successful early life colonizers can overcome metal restriction. We further demonstrate that feeding modality (breastmilk vs formula) markedly impacts metal levels in the gut, potentially influencing microbial community succession. Our work suggests that metals, a previously unexplored aspect of early life ecology, may play a critical role in shaping the early events of microbiota assembly in infants.},
}
@article {pmid39440963,
year = {2024},
author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K},
title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.},
journal = {mSystems},
volume = {9},
number = {11},
pages = {e0068224},
pmid = {39440963},
issn = {2379-5077},
support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; },
abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.<br><br>IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.},
}
@article {pmid39437908,
year = {2024},
author = {Yang, X and Chen, N and Yu, H and Liu, X and Feng, Y and Xing, D and Tian, Y},
title = {Applying machine learning and genetic algorithms accelerated for optimizing ethanol production.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {177027},
doi = {10.1016/j.scitotenv.2024.177027},
pmid = {39437908},
issn = {1879-1026},
mesh = {*Ethanol/metabolism ; *Machine Learning ; *Algorithms ; Zea mays ; Fermentation ; Neural Networks, Computer ; Biofuels ; },
abstract = {Corn straws can produce bioethanol via simultaneous saccharification and co-fermentation (SSCF). However, identifying optimal combinations of operating parameters from numerous possibilities through a cost-effective strategy to improve SSCF efficiency and yield remains challenging. The eXtreme Gradient Boost (XGB) and deep neural network (DNN) models were constructed to accurately predict ethanol yield from only five input variables, achieving >83 % accuracy. Subsequently, the XGB and the DNN models were merged with the genetic algorithm (GA) as the new optimization strategies. Experimental validation showed that the new strategy optimize the efficiency and yield of the SSCF ethanol production system quickly and accurately. Moreover, the potential optimization mechanism was investigated through the comprehensive interpretability analysis for XGB and the microbial ecology analysis. Enzyme Solution Volume (61.7 %) dominated, followed by time (12.9 %), substrate concentration (10.4 %), temperature (7.7 %), and inoculum volume (7.3 %). This efficient and accurate algorithm design strategy can significantly reduce the time required to optimize biochemical systems.},
}
@article {pmid39436938,
year = {2024},
author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP},
title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012530},
pmid = {39436938},
issn = {1553-7358},
mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; },
abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.},
}
@article {pmid39436933,
year = {2024},
author = {Di Nezio, F and Ong, ILH and Riedel, R and Goshal, A and Dhar, J and Roman, S and Storelli, N and Sengupta, A},
title = {Synergistic phenotypic adaptations of motile purple sulphur bacteria Chromatium okenii during lake-to-laboratory domestication.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0310265},
pmid = {39436933},
issn = {1932-6203},
mesh = {*Lakes/microbiology ; *Phenotype ; *Adaptation, Physiological ; Chromatiaceae/physiology ; Microscopy, Atomic Force ; },
abstract = {Isolating microorganisms from natural environments for cultivation under optimized laboratory settings has markedly improved our understanding of microbial ecology. Artificial growth conditions often diverge from those in natural ecosystems, forcing wild isolates into distinct selective pressures, resulting in diverse eco-physiological adaptations mediated by modification of key phenotypic traits. For motile microorganisms we still lack a biophysical understanding of the relevant traits emerging during domestication and their mechanistic interplay driving short-to-long-term microbial adaptation under laboratory conditions. Using microfluidics, atomic force microscopy, quantitative imaging, and mathematical modeling, we study phenotypic adaptation of Chromatium okenii, a motile phototrophic purple sulfur bacterium from meromictic Lake Cadagno, grown under laboratory conditions over multiple generations. Our results indicate that naturally planktonic C. okenii leverage shifts in cell-surface adhesive interactions, synergistically with changes in cell morphology, mass density, and distribution of intracellular sulfur globules, to suppress their swimming traits, ultimately switching to a sessile lifeform. A computational model of cell mechanics confirms the role of such phenotypic shifts in suppressing the planktonic lifeform. By investigating key phenotypic traits across different physiological stages of lab-grown C. okenii, we uncover a progressive loss of motility during the early stages of domestication, followed by concomitant deflagellation and enhanced surface attachment, ultimately driving the transition of motile sulfur bacteria to a sessile state. Our results establish a mechanistic link between suppression of motility and surface attachment via phenotypic changes, underscoring the emergence of adaptive fitness under laboratory conditions at the expense of traits tailored for natural environments.},
}
@article {pmid39436423,
year = {2024},
author = {Hirota, A and Kouduka, M and Fukuda, A and Miyakawa, K and Sakuma, K and Ozaki, Y and Ishii, E and Suzuki, Y},
title = {Biofilm Formation on Excavation Damaged Zone Fractures in Deep Neogene Sedimentary Rock.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {132},
pmid = {39436423},
issn = {1432-184X},
mesh = {*Biofilms/growth &amp; development ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; Phylogeny ; Groundwater/microbiology ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Gammaproteobacteria/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; },
abstract = {Deep underground galleries are used to access the deep biosphere in addition to mining and other engineering applications, such as geological disposal of radioactive waste. Fracture networks developed in the excavation damaged zone (EDZ) are concerned with accelerating mass transport, where microbial colonization might be possible due to the availability of space and nutrients. In this study, microbial biofilms at EDZ fractures were investigated by drilling from a 350-m-deep gallery and subsequent borehole logging at the Horonobe Underground Research Laboratory (URL). By using microscopic and spectroscopic techniques, the dense colonization of microbial cells was demonstrated at the surfaces of the EDZ fractures with high hydraulic conductivity. 16S rRNA gene sequence analysis revealed the dominance of gammaproteobacterial lineages, the cultivated members of which are aerobic methanotrophs. The near-complete genomes from Horonobe groundwater, affiliated with the methanotrophic lineages, were fully equipped with genes involved in aerobic methanotrophy. Although the mediation of aerobic methanotrophy remains to be demonstrated, microbial O2 production was supported by the presence of genes in the near-complete genomes, such as catalase and superoxide dismutase that produce O2 from reactive oxygen species and a nitric oxide reductase gene with the substitutions of amino acids in motifs. It is concluded that the EDZ fractures provide energetically favorable subsurface habitats for microorganisms.},
}
@article {pmid39435521,
year = {2024},
author = {Muratore, TJ and Knorr, MA and Simpson, MJ and Stephens, RB and Phillips, RP and Frey, SD},
title = {Response of Root Respiration to Warming and Nitrogen Addition Depends on Tree Species.},
journal = {Global change biology},
volume = {30},
number = {10},
pages = {e17530},
doi = {10.1111/gcb.17530},
pmid = {39435521},
issn = {1365-2486},
support = {DEB-1456610//National Science Foundation/ ; DEB-1832110//National Science Foundation/ ; 2106096//National Science Foundation/ ; Hatch NH-00701//New Hampshire Agricultural Experiment Station/ ; //Natural Sciences and Engineering Research Council (NSERC) of Canada/ ; },
mesh = {*Plant Roots/metabolism/growth &amp; development ; *Nitrogen/metabolism ; *Acer/physiology/metabolism/growth &amp; development ; *Quercus/physiology/metabolism ; Soil/chemistry ; Global Warming ; Biomass ; Carbon Dioxide/metabolism ; Trees/growth &amp; development/metabolism/physiology ; },
abstract = {Roots contribute a large fraction of CO2 efflux from soils, yet the extent to which global change factors affect root-derived fluxes is poorly understood. We investigated how red maple (Acer rubrum) and red oak (Quercus rubra) root biomass and respiration respond to long-term (15 years) soil warming, nitrogen addition, or their combination in a temperate forest. We found that ecosystem root respiration was decreased by 40% under both single-factor treatments (nitrogen addition or warming) but not under their combination (heated × nitrogen). This response was driven by the reduction of mass-specific root respiration under warming and a reduction in maple root biomass in both single-factor treatments. Mass-specific root respiration rates for both species acclimated to soil warming, resulting in a 43% reduction, but were not affected by N addition or the combined heated × N treatment. Notably, the addition of nitrogen to warmed soils alleviated thermal acclimation and returned mass-specific respiration rates to control levels. Oak roots contributed disproportionately to ecosystem root respiration despite the decrease in respiration rates as their biomass was maintained or enhanced under warming and nitrogen addition. In contrast, maple root respiration rates were consistently higher than oak, and this difference became critical in the heated × nitrogen treatment, where maple root biomass increased, contributing significantly more CO2 relative to single-factor treatments. Our findings highlight the importance of accounting for the root component of respiration when assessing soil carbon loss in response to global change and demonstrate that combining warming and N addition produces effects that cannot be predicted by studying these factors in isolation.},
}
@article {pmid39435438,
year = {2024},
author = {Michalska-Smith, M and Schlatter, DC and Pombubpa, N and Castle, SC and Grandy, AS and Borer, ET and Seabloom, EW and Kinkel, LL},
title = {Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1452534},
pmid = {39435438},
issn = {1664-302X},
abstract = {Plants serve as critical links between above- and below-ground microbial communitites, both influencing and being influenced by microbes in these two realms. Below-ground microbial communities are expected to respond to soil resource environments, which are mediated by the roots of plants that can, in turn, be influenced by the above-ground community of foliar endophytes. For instance, diverse plant communities deposit more, and more diverse, nutrients into the soil, and this deposition is often increased when foliar pathogens are removed. Differences in soil resources can alter soil microbial composition and phenotypes, including inhibitory capacity, resource use, and antibiotic resistance. In this work, we consider plots differing in plant richness and application of foliar fungicide, evaluating consequences on soil resource levels and root-associated Streptomyces phenotypes. Soil carbon, nitrogen, phosphorus, potassium, and organic matter were greater in samples from polyculture than monoculture, yet this increase was surprisingly offset when foliar fungal communities were disrupted. We find that Streptomyces phenotypes varied more between richness plots-with the Streptomyces from polyculture showing lower inhibitory capacity, altered resource-use profiles, and greater antibiotic resistance-than between subplots with/without foliar fungicide. Where foliar fungicide affected phenotypes, it did so differently in polyculture than in monoculture, for instance decreasing niche width and overlap in monoculture while increasing them in polyculture. No differences in phenotype were correlated with soil nutrient levels, suggesting the need for further research looking more closely at soil resource diversity and particular compounds that were found to differ between treatments.},
}
@article {pmid39435044,
year = {2024},
author = {Gruseck, R and Palatinszky, M and Wagner, M and Hofmann, T and Zumstein, M},
title = {Quantification of guanidine in environmental samples using benzoin derivatization and LC-MS analysis.},
journal = {MethodsX},
volume = {13},
number = {},
pages = {102972},
pmid = {39435044},
issn = {2215-0161},
abstract = {The recent discovery of guanidine-dependent riboswitches in many microbes raised interest in the biological function and metabolism of this nitrogen-rich compound. However, very little is known about the concentrations of guanidine in the environment. Several methods have been published for quantifying guanidine and guanidino compounds in human urine and blood, often relying on derivatization followed by fluorescence detection. We adapted this analytical approach using benzoin as the derivatization agent to sensitively and selectively quantify guanidine in environmental samples, thereby facilitating future research on the biological and environmental roles of guanidine. This adapted method was applied to human urine, raw wastewater, and biological growth media as relevant matrices. Our liquid chromatography-tandem mass spectrometry analyses of the derivatized solutions identified a different major derivatization product than previously reported. This product was consistently observed across various substrates (guanidine, methylguanidine, and arginine) and derivatization agents (benzoin and anisoin). We observed a constant background signal, restricting our analyses to a lower limit of quantification of 50 nM. Despite this limitation, our method allowed for the quantification of guanidine concentrations significantly lower than those reported in previous derivatization-based studies.•Selective and sensitive detection of guanidine by LC-MS.•Method development and validation for robust detection of guanidine in environmental samples.•Reduction of sample preparation steps and reduced usage of toxic chemicals compared to previous methods.},
}
@article {pmid39432984,
year = {2024},
author = {Sun, Y and Wang, N and Zhong, X and Xu, G},
title = {Can microplastics variability drive the colonization dynamics of periphytic protozoan fauna in marine environments?.},
journal = {Marine pollution bulletin},
volume = {209},
number = {Pt A},
pages = {117148},
doi = {10.1016/j.marpolbul.2024.117148},
pmid = {39432984},
issn = {1879-3363},
abstract = {In recent years, microplastics have become a global environmental hot topic of concern. To explore the effects of different concentrations of microplastics on colonization dynamics of periphytic protozoan fauna, a 21-day study was conducted in temperature-controlled circulation systems. Periphytic protozoan communities were used as test organisms and exposed to five concentrations of MPs: 0, 1, 5, 25, and 125 mg l[-1], identification and enumeration were conducted on days 3, 5, 7, 10, 14 and 21. The results showed that the colonization dynamics were driven by MPs and significantly shifted at concentrations over 5 mg l[-1]. However, a notable decline in maximum species richness and abundance was observed in the high concentrations of microplastic, along with significant deviations in colonization patterns from the control group (0 mg l[-1]). Therefore, it is suggested that the colonization dynamics of periphytic protozoa can serve as a bioindicator for assessing microplastic concentrations in marine environments.},
}
@article {pmid39432094,
year = {2024},
author = {Shafana Farveen, M and Narayanan, R},
title = {Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review.},
journal = {Archives of microbiology},
volume = {206},
number = {11},
pages = {441},
pmid = {39432094},
issn = {1432-072X},
mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Proteomics ; Genomics ; Microbial Consortia ; },
abstract = {Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.},
}
@article {pmid39431865,
year = {2024},
author = {Daly, SE and Feng, J and Daeschel, D and Kovac, J and Snyder, AB},
title = {The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments.},
journal = {mSystems},
volume = {9},
number = {11},
pages = {e0062024},
pmid = {39431865},
issn = {2379-5077},
support = {2022-67017-36289//U.S. Department of Agriculture (USDA)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics/classification ; Food Microbiology ; Food Handling ; Dairying ; Dairy Products/microbiology ; },
abstract = {Accurate knowledge of the microbiota collected from surfaces in food processing environments is important for food quality and safety. This study assessed discrepancies in taxonomic composition and alpha and beta diversity values generated from eight different bioinformatic workflows for the analysis of 16S rRNA gene sequences extracted from the microbiota collected from surfaces in dairy processing environments. We found that the microbiota collected from environmental surfaces varied widely in density (0-9.09 log10 CFU/cm[2]) and Shannon alpha diversity (0.01-3.40). Consequently, depending on the sequence analysis method used, characterization of low-abundance genera (i.e., below 1% relative abundance) and the number of genera identified (114-173 genera) varied considerably. Some low-abundance genera, including Listeria, varied between the amplicon sequence variant (ASV) and operational taxonomic unit (OTU) methods. Centered log-ratio transformation inflated alpha and beta diversity values compared to rarefaction. Furthermore, the ASV method also inflated alpha and beta diversity values compared to the OTU method (P < 0.05). Therefore, for sparse, uneven, low-density data sets, the OTU method and rarefaction are better for taxonomic and ecological characterization of surface microbiota.IMPORTANCECulture-dependent environmental monitoring programs are used by the food industry to identify foodborne pathogens and spoilage biota on surfaces in food processing environments. The use of culture-independent 16S rRNA amplicon sequencing to characterize this surface microbiota has been proposed as a tool to enhance environmental monitoring. However, there is no consensus on the most suitable bioinformatic analyses to accurately capture the diverse levels and types of bacteria on surfaces in food processing environments. Here, we quantify the impact of different bioinformatic analyses on the results and interpretation of 16S rRNA amplicon sequences collected from three cultured dairy facilities in New York State. This study provides guidance for the selection of appropriate 16S rRNA analysis procedures for studying environmental microbiota in dairy processing environments.},
}
@article {pmid39430784,
year = {2024},
author = {Li, X and Wang, Q and Wu, F and Ye, Z and Li, Y},
title = {Association between advanced lung cancer inflammation index and chronic kidney disease: a cross-sectional study.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1430471},
pmid = {39430784},
issn = {2296-861X},
abstract = {BACKGROUND: Chronic kidney disease (CKD) is one of the common chronic diseases, and malnutrition and inflammation play a key role in the development of CKD. The advanced lung cancer inflammation index (ALI) is a novel index of nutrition and inflammation, and its association with CKD has not yet been clarified. The aim of this study was to explore the potential association between ALI and CKD.<br><br>METHODS: We conducted a cross-sectional survey using data extracted from the National Health and Nutrition Examination Survey (NHANES, 2003-2018). Weighted multivariate logistic regression was used to assess the association between ALI and CKD, and smoothed curve fitting and threshold effect analyses were used to describe the nonlinear association between ALI and CKD. Subgroup analyses were performed to further assess the influence of other covariates on the relationship between ALI and CKD.<br><br>RESULTS: A total of 39,469 adult participants were included in the study, of whom 7,204 (18.25%) were diagnosed with CKD. After adjusting for multiple confounders, we found a significant negative correlation between ALI and CKD (OR&#x2009;=&#x2009;0.93; 95%CI, 0.91-0.95; p&#x2009;<&#x2009;0.0001). The risk of CKD tended to decrease with increasing quartiles of ALI. Smoothed curve fitting showed an L-shaped negative correlation between ALI and CKD. Threshold analysis showed a saturation effect of ALI at the inflection point of 55.09. Subgroup analyses and interaction tests showed that this negative association was maintained across age, sex, race, BMI, diabetes, hypertension, cardiovascular disease, and cancer subgroups (P for interaction >0.05).<br><br>CONCLUSION: Our findings suggest a significant correlation between ALI and CKD in the US adult population. However, more large-scale prospective studies are still needed to further confirm our findings.},
}
@article {pmid39430052,
year = {2025},
author = {Qin, K and Wang, Q and Qing, J and Li, Y and Gong, H and Zha, Z and Zhou, B and Li, Y},
title = {Analysis of mutations in Chinese patients with polycystic kidney disease by targeted exome sequencing.},
journal = {Genes &amp; diseases},
volume = {12},
number = {1},
pages = {101246},
pmid = {39430052},
issn = {2352-3042},
}
@article {pmid39425011,
year = {2024},
author = {Sánchez, V and Baumann, A and Kromm, F and Yergaliyev, T and Brandt, A and Scholda, J and Kopp, F and Camarinha-Silva, A and Bergheim, I},
title = {Oral supplementation of choline attenuates the development of alcohol-related liver disease (ALD).},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {30},
number = {1},
pages = {181},
pmid = {39425011},
issn = {1528-3658},
mesh = {Animals ; *Choline/administration &amp; dosage/metabolism ; *Liver Diseases, Alcoholic/metabolism/etiology/prevention &amp; control/pathology/drug therapy ; *Dietary Supplements ; Mice ; Female ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Liver/metabolism/drug effects/pathology ; Administration, Oral ; Permeability ; Ethanol/adverse effects ; Disease Models, Animal ; },
abstract = {BACKGROUND: Chronic alcohol intake is associated with alterations of choline metabolism in various tissues. Here, we assessed if an oral choline supplementation attenuated the development of alcohol-related liver disease (ALD) in mice.<br><br>METHODS: Female C57BL/6&#xa0;J mice (n&#x2009;=&#x2009;8/group) were either pair-fed a liquid control diet, or a Lieber DeCarli liquid diet (5% ethanol)&#x2009;&#xb1;&#x2009;2.7&#xa0;g choline/kg diet for 29&#xa0;days. Liver damage, markers of intestinal permeability and intestinal microbiota composition were determined. Moreover, the effects of choline on ethanol-induced intestinal permeability were assessed in an ex vivo model.<br><br>RESULTS: ALD development as determined by liver histology and assessing markers of inflammation (e.g., nitric oxide, interleukin 6 and 4-hydroxynonenal protein adducts) was attenuated by the supplementation of choline. Intestinal permeability in small intestine being significantly higher in ethanol-fed mice was at the level of controls in ethanol-fed mice receiving choline. In contrast, no effects of the choline supplementation were found on intestinal microbiota composition. Choline also significantly attenuated the ethanol-induced intestinal barrier dysfunction in small intestinal tissue ex vivo, an effect almost entirely abolished by the choline oxidase inhibitor dimbunol.<br><br>CONCLUSION: Our results suggest that an oral choline supplementation attenuates the development of ALD in mice and is related to a protection from intestinal barrier dysfunction.},
}
@article {pmid39423562,
year = {2024},
author = {Dal Bello, M and Abreu, CI},
title = {Temperature structuring of microbial communities on a global scale.},
journal = {Current opinion in microbiology},
volume = {82},
number = {},
pages = {102558},
doi = {10.1016/j.mib.2024.102558},
pmid = {39423562},
issn = {1879-0364},
abstract = {Temperature is a fundamental physical constraint regulating key aspects of microbial life. Protein binding, membrane fluidity, central dogma processes, and metabolism are all tightly controlled by temperature, such that growth rate profiles across taxa and environments follow the same general curve. An open question in microbial ecology is how the effects of temperature on individual traits scale up to determine community structure and function at planetary scales. Here, we review recent theoretical and experimental efforts to connect physiological responses to the outcome of species interactions, the assembly of microbial communities, and their function as temperature changes. We identify open questions in the field and define a roadmap for future studies.},
}
@article {pmid39423289,
year = {2024},
author = {Steensen, K and Séneca, J and Bartlau, N and Yu, XA and Hussain, FA and Polz, MF},
title = {Prophages in Vibrio.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae202},
pmid = {39423289},
issn = {1751-7370},
abstract = {Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to constitute the most abundant and ecologically relevant group of phages that can integrate their genome into the host chromosome, it is becoming increasingly clear that other prophages are widespread. Here, we show that prophages derived from filamentous and tailless phages with genome sizes below 16 kb make up the majority of prophages in marine bacteria of the genus Vibrio. To estimate prophage prevalence unaffected by database biases, we combined comparative genomics and chemical induction of 58 diverse Vibrio cyclitrophicus isolates, resulting in 107 well-curated prophages. Complemented with computationally predicted prophages, we obtained 1,158 prophages from 931 naturally co-existing strains of the family Vibrionaceae. Prophages resembling tailless and filamentous phages predominated, accounting for 80% of all prophages in V. cyclitrophicus and 60% across the Vibrionaceae. In our experimental model, prophages of all three viral realms actively replicated upon induction indicating their ability to transfer to new hosts. Indeed, prophages were rapidly gained and lost, as suggested by variable prophage content between closely related V. cyclitrophicus. Prophages related to filamentous and tailless phages were integrated into only three genomic locations and restored the function of their integration site. Despite their small size, they contained highly diverse accessory genes that may contribute to host fitness, such as phage defense systems. We propose that, like their well-studied tailed equivalent, tailless and filamentous temperate phages are active and highly abundant drivers of host ecology and evolution in marine Vibrio, which have been largely overlooked.},
}
@article {pmid39419992,
year = {2024},
author = {Mei, S and Wang, M and Salles, JF and Hackl, T},
title = {Diverse rhizosphere-associated Pseudomonas genomes from along a Wadden Island salt marsh transition zone.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1140},
pmid = {39419992},
issn = {2052-4463},
support = {[2020]596//China Scholarship Council (CSC)/ ; },
mesh = {*Rhizosphere ; *Pseudomonas/genetics ; *Soil Microbiology ; *Wetlands ; *Genome, Bacterial ; Artemisia/genetics/microbiology ; Biodiversity ; },
abstract = {Soil microbes are key drivers of ecosystem processes promoting nutrient cycling, system productivity, and resilience. While much is known about the roles of microbes in established systems, their impact on soil development and the successional transformation over time remains poorly understood. Here, we provide 67 diverse, rhizosphere-associated Pseudomonas draft genomes from an undisturbed salt march primary succession spanning >100 years of soil development. Pseudomonas are cosmopolitan bacteria with a significant role in plant establishment and growth. We obtained isolates associated with Limonium vulgare and Artemisia maritima, two typical salt marsh perennial plants with roles in soil stabilization, salinity regulation, and biodiversity support. We anticipate that our data, in combination with the provided physiochemical measurements, will help identify genomic signatures associated with the different selective regimes along the successional stages, such as varying soil complexity, texture, and nutrient availability. Such findings would advance our understanding of Pseudomonas' role in natural soil ecosystems and provide the basis for a better understanding of the roles of microbes throughout ecosystem transformations.},
}
@article {pmid39419884,
year = {2024},
author = {Mohammed, FA and Abu-Hussien, SH and Dougdoug, NKE and Koutb, N and Korayem, AS},
title = {Streptomyces fradiae Mitigates the Impact of Potato Virus Y by Inducing Systemic Resistance in Two Egyptian Potato (Solanum tuberosum L.) Cultivars.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {131},
pmid = {39419884},
issn = {1432-184X},
mesh = {*Solanum tuberosum/virology/microbiology ; *Streptomyces/isolation &amp; purification/physiology/genetics ; *Potyvirus/physiology ; *Plant Diseases/virology/microbiology ; *Disease Resistance ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this study, the impact of culture media filtrate of QD3 actinobacterial isolate on two potato cultivars, Spunta and Diamond, infected with potato virus Y (PVY) was investigated. Various parameters, including infection percentage, PVY virus infectivity, disease severity scoring, PVY optical density, photosynthetic and defense-related biochemical markers, enzymatic profiling, phenolic compounds, proline content, salicylic acid levels, and growth and yield parameters, were assessed to elucidate the potential of the QD3 actinobacterial isolate culture filtrate in mitigating PVY-induced damage. The physiological and biochemical characteristics of the QD3 actinobacterial isolate, including its salinity tolerance, pH preferences, and metabolic traits, were investigated. Molecular identification via 16S rRNA gene sequencing confirmed its classification as Streptomyces fradiae QD3, and it was deposited in GenBank with the gene accession number MN160630. Distinct responses between Spunta and Diamond cultivars, with Spunta displaying greater resistance to PVY infection. Notably, pre-infection foliar application of the QD3 filtrate significantly reduced disease symptoms and virus infection in both cultivars. For post-PVY infection, the QD3 filtrate effectively mitigated disease severity and the PVY optical density. Furthermore, the QD3 filtrate positively influenced photosynthetic pigments, enzymatic antioxidant activities, and key biochemical components associated with plant defense mechanisms. Gas chromatography‒mass spectrometry (GC‒MS) analysis revealed palmitic acid (hexadecanoic acid, methyl ester) and oleic acid (9-octadecanoic acid, methyl ester) as the most prominent compounds, with retention times of 23.23 min and 26.41 min, representing 53.27% and 23.25%, respectively, of the total peak area as primary unsaturated fatty acids and demonstrating antiviral effects against plant viruses. Cytotoxicity assays on normal human skin fibroblasts (HSFs) revealed the safety of QD3 metabolites, with low discernible toxicity at high concentrations, reinforcing their potential as safe and effective interventions. The phytotoxicity results indicate that all the seeds presented high germination rates of approximately 95-98%, suggesting that the treatment conditions had no phytotoxic effect on the Brassica oleracea (broccoli) seeds, Lactuca sativa (lettuce) seeds, and Eruca sativa (arugula or rocket) seeds. Overall, the results of this study suggest that the S. fradiae filtrate has promising anti-PVY properties, influencing various physiological, biochemical, and molecular aspects in potato cultivars. These findings provide valuable insights into potential strategies for managing PVY infections in potato crops, emphasizing the importance of Streptomyces-derived interventions in enhancing plant health and crop protection.},
}
@article {pmid39419230,
year = {2024},
author = {Siebert, C and Ionescu, D and Mallast, U and Merchel, S and Merkel, B and Möller, P and Pavetich, S and Pohl, T and Rödiger, T and Yechieli, Y},
title = {A new type of submarine chimneys built of halite.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {176752},
doi = {10.1016/j.scitotenv.2024.176752},
pmid = {39419230},
issn = {1879-1026},
abstract = {In contrast to the subaquatic sulphide and carbonate chimneys, which are known from Mid Ocean Ridges and abyssal submarine volcanoes, chimneys built of salts have not been described yet. Here we present such halite chimneys as a new form of cold-water smokers in hypersaline environments. The here described structures rise up from the bottom of the Dead Sea and result from the submarine discharge of saturated halite-dissolution brines into the salt lake, which is at halite saturation and holds remarkable chloride excess. At the interface with the lake brine, halite precipitates instantaneously, forming chimneys up to several meters in height. The brines leading to the formation of these chimneys vary in composition, while their generation processes are similar. Fresh groundwater from surrounding aquifers enters the saline lake sediments and considerably leaches halite in the adjacencies of the lake. Simultaneously, it mixes with ancient brines before it emerges from the lake floor. The distinct differences in composition between the Dead Sea and the emerging chimney brines lead to the instantaneous crystallisation of halite and few other mineral phases. The chimney structure result from the buoyancy flow of the chimney brines, which are less dense then the ambient Dead Sea. The chimneys indicate intense cavitation of massive halite bodies in the subsurface of the Dead Sea environment, a process that leads to increasing formation of hazardous sinkholes. Since chimneys are proven in shallow water but may be expected in deeper parts too, they are comfortably mappable by echo-sounding or aerial imaging. They thus provide in the Dead Sea as in any likewise setting a potent predictive tool to locate dangerous subsurface cavitation and hence areas that are at risk of collapse in the near future.},
}
@article {pmid39419211,
year = {2024},
author = {Santos-Silva, L and Roque, WF and de Moura, JM and Mello, IS and de Carvalho, LAL and Pinheiro, DG and Bouzan, RS and Brescovit, AD and de Andrade, RLT and da Silva, GF and Battirola, LD and Soares, MA},
title = {Toxic metals in Amazonian soil modify the bacterial community associated with Diplopoda.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {176915},
doi = {10.1016/j.scitotenv.2024.176915},
pmid = {39419211},
issn = {1879-1026},
mesh = {*Soil Pollutants/toxicity ; Animals ; *Bacteria/drug effects/classification ; *Microbiota/drug effects ; Arthropods/drug effects ; Soil Microbiology ; Cadmium/toxicity ; Brazil ; Mercury/toxicity/metabolism ; Soil/chemistry ; Environmental Monitoring ; Rainforest ; },
abstract = {Toxic metal pollution in the Amazon is a serious problem that reduces the quality of water, soil, air, and consequently alters communities of fauna, flora, and microbiota, harming human health and well-being. Our aim was to determine the impact of toxic metals on the structure of the bacterial community associated with Diplopoda in the Amazon rainforest. Animals were kept in microcosms contaminated with cadmium (50 mg.kg[-1]), mercury (35 mg.kg[-1]) and no toxic metal (control). The intestinal and molting chamber microbiota were accessed by culture-dependent and culture-independent methods (16S metabarcoding). The cultivated strains were identified, and their functional traits evaluated: secretion of enzymes, growth at different pH, resistance to metals and antibiotics, and ability to reduce toxic effects of metals on plants. Our research described Brachyurodesmus albus, a new species of Diplopoda. We obtained 177 isolates distributed in 35 genera and 61 species of bacteria (Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota) associated with the gut and molting chamber of B. albus. Metabarcoding data provided a more robust access to the bacterial community, resulting in 24 phyla, 561 genera and 6792 ASVs. The presence of metal Cd and Hg alters the composition and abundance of bacteria associated with B. albus (PERMANOVA p < 0.05). The microhabitat (gut and molting chamber) harbours bacterial communities that differ in composition and abundance (PERMANOVA p < 0.05). The presence of Cd and Hg alters important metabolic pathways related to the prokaryotic defense system; antimicrobial resistance genes, endocytosis and secretion system, estimated by PICRUSt. Bacteria selected with high resistance to Cd and Hg buffer the toxic effect of metals on tomato seedlings. This work describes B. albus and concludes that its diverse bacterial microbiota is altered by soil contamination by toxic metals, as well as being an important repository for prospecting strains to be applied in bioremediation programs.},
}
@article {pmid39419002,
year = {2024},
author = {Meroz, N and Livny, T and Toledano, G and Sorokin, Y and Tovi, N and Friedman, J},
title = {Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species.},
journal = {Cell systems},
volume = {15},
number = {10},
pages = {930-940.e5},
doi = {10.1016/j.cels.2024.09.007},
pmid = {39419002},
issn = {2405-4720},
mesh = {*Biological Evolution ; Microbial Interactions/physiology ; Adaptation, Physiological ; Mutation ; Bacteria/genetics/metabolism ; Evolution, Molecular ; },
abstract = {Evolution often follows similar trajectories in replicate populations, suggesting that it may be predictable. However, populations are naturally embedded in multispecies communities, and the extent to which evolution is contingent on the specific species interacting with the focal population is still largely unexplored. Here, we study adaptations in strains of 11 different species, experimentally evolved both in isolation and in various pairwise co-cultures. Although partner-specific effects are detectable, evolution was mostly shared between strains evolved with different partners; similar changes occurred in strains' growth abilities, in community properties, and in about half of the repeatedly mutated genes. This pattern persisted even in species pre-adapted to the abiotic conditions. These findings indicate that evolution may not always depend strongly on the biotic environment, making predictions regarding coevolutionary dynamics less challenging than previously thought. A record of this paper's transparent peer review process is included in the supplemental information.},
}
@article {pmid39418776,
year = {2024},
author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M},
title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.},
journal = {Multiple sclerosis and related disorders},
volume = {92},
number = {},
pages = {105936},
doi = {10.1016/j.msard.2024.105936},
pmid = {39418776},
issn = {2211-0356},
abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.<br><br>METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.<br><br>RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the &#x3b1;-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.<br><br>CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.},
}
@article {pmid39418385,
year = {2024},
author = {Lien, YW and Amendola, D and Lee, KS and Bartlau, N and Xu, J and Furusawa, G and Polz, MF and Stocker, R and Weiss, GL and Pilhofer, M},
title = {Mechanism of bacterial predation via ixotrophy.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6719},
pages = {eadp0614},
doi = {10.1126/science.adp0614},
pmid = {39418385},
issn = {1095-9203},
mesh = {*Bacterial Adhesion ; *Bacteroidetes/physiology/ultrastructure ; Cryoelectron Microscopy ; Single-Cell Analysis ; *Type VI Secretion Systems/metabolism/ultrastructure ; *Vibrio/physiology/ultrastructure ; *Flagella/ultrastructure ; },
abstract = {Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.},
}
@article {pmid39417884,
year = {2024},
author = {Mircea, C and Rusu, I and Levei, EA and Cristea, A and Gridan, IM and Zety, AV and Banciu, HL},
title = {The Fungal Side of the Story: Saprotrophic- vs. Symbiotrophic-Predicted Ecological Roles of Fungal Communities in Two Meromictic Hypersaline Lakes from Romania.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {130},
pmid = {39417884},
issn = {1432-184X},
support = {PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P1-1.1-PD-2021-0634//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; },
mesh = {*Lakes/microbiology ; Romania ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; *Salinity ; *Mycobiome ; RNA, Ribosomal, 18S/genetics ; Biodiversity ; Geologic Sediments/microbiology ; Soil Microbiology ; DNA, Fungal/genetics ; Phylogeny ; },
abstract = {Over three-quarters of Earth's surface exhibits extreme environments where life thrives under harsh physicochemical conditions. While prokaryotes have often been investigated in these environments, only recent studies have revealed the remarkable adaptability of eukaryotes, in particular fungi. This study explored the mycobiota of two meromictic hypersaline lakes, Ursu and Fără Fund, in Transylvania (Romania). The intrinsic and extrinsic fungal diversity was assessed using amplicon sequencing of environmental DNA samples from sediments, water columns, surrounding soils, and an associated rivulet. The fungal communities, illustrated by the 18S rRNA gene and ITS2 region, exhibited contrasting patterns between the lakes. The ITS2 region assessed better than the 18S rRNA gene the fungal diversity. The ITS2 data showed that Ascomycota was the most abundant fungal group identified in both lakes, followed by Aphelidiomycota, Chytridiomycota, and Basidiomycota. Despite similar α-diversity levels, significant differences in fungal community structure were observed between the lakes, correlated with salinity, total organic carbon, total nitrogen, and ammonium. Taxonomic profiling revealed depth-specific variations, with Saccharomycetes prevalent in Ursu Lake's deeper layers and Lecanoromycetes prevalent in the Fără Fund Lake. The functional annotation using FungalTraits revealed diverse ecological roles within the fungal communities. Lichenized fungi were dominant in Fără Fund Lake, while saprotrophs were abundant in Ursu Lake. Additionally, wood and soil saprotrophs, along with plant pathogens, were more prevalent in the surrounding soils, rivulet, and surface water layers. A global overview of the trophic relations in each studied niche was impossible to establish due to the unconnected graphs corresponding to the trophic interactions of the analyzed fungi. Plotting the unweighted connected subgraphs at the genus level suggests that salinity made the studied niches similar for the identified taxa. This study shed light on the understudied fungal diversity, distribution, and ecological functions in hypersaline environments.},
}
@article {pmid39415203,
year = {2024},
author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH},
title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {198},
pmid = {39415203},
issn = {2049-2618},
support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; },
mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; },
abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.<br><br>RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.<br><br>CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.},
}
@article {pmid39414684,
year = {2024},
author = {Siqueira, JS and de Carvalho, LAL and Santos, CHB and Frezarin, ET and Pinheiro, DG and Nicodemo, D and Desoignies, N and Rigobelo, EC},
title = {Influence of Growth Support on the Diversity, Composition, and Functionality of Microbial Communities Associated with Tillandsia recurvata.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {129},
pmid = {39414684},
issn = {1432-184X},
mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; Fungi/classification/genetics/isolation &amp; purification/physiology ; Biodiversity ; Trees/microbiology ; Soil Microbiology ; },
abstract = {Tillandsia recurvata is an epiphytic plant commonly found in tropical regions and colonizes tree trunks, fences, and power wires. This plant plays an important role in interacting with trees, sharing microorganisms, and performing specific functions in the process of tree colonization. The objective of this study was to evaluate and compare the microbiomes of T. recurvata collected from two different locations (trees and fences) and two plant tissues (leaves and roots). The hypothesis of this study was that the microbiome of T. recurvata is composed of microorganisms that would provide nutritional support to compensate for the lack of nutrients in a particular growth support. The results showed significant differences in microbial diversity between trees and fences, with trees exhibiting higher richness and more complex microbial networks. Proteobacteria was the most prevalent bacterial phylum, with Actinobacteria and Sphingomonas also playing key roles in nitrogen fixation and plant growth. Fungal communities were similar across locations, with Ascomycota and Basidiomycota being predominant, but Paraconiothyrium and Nigrospora showed significant differences in abundance between trees and fences. Functional analysis indicated similar metabolic profiles across leaf and root samples, with key functions for T. recurvata including carbohydrate and amino acid metabolism, stress control, and biofertilization.},
}
@article {pmid39411441,
year = {2024},
author = {Pardo-Esté, C and Cortés, J and Castro-Severyn, J and Pérez, V and Henriquez-Aedo, K and Cuadros, F and Yañez, C and Cuadros-Orellana, S and Dorador, C and Molina, V and Eissler, Y and Paquis, P and Jeffrey, WH and Pozo, P and Pérez, PA and Hengst, MB},
title = {Secondary metabolites with antimicrobial activity produced by thermophilic bacteria from a high-altitude hydrothermal system.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1477458},
pmid = {39411441},
issn = {1664-302X},
abstract = {Thermophilic microorganisms possess several adaptations to thrive in high temperature, which is reflected as biosynthesis of proteins and thermostable molecules, isolation and culture represent a great methodological challenge, therefore High throughput sequencing enables screening of the whole bacterial genome for functional potential, providing rapid and cost-effective information to guide targeted cultures for the identification and characterization of novel natural products. In this study, we isolated two thermophilic bacterial strains corresponding to Bacillus LB7 and Streptomyces LB8, from the microbial mats in the Atacama Desert. By combining genome mining, targeted cultures and biochemical characterization, we aimed to identify their capacity to synthesize bioactive compounds with antimicrobial properties. Additionally, we determined the capability to produce bioactive compounds under controlled in vitro assays and detected by determining their masses by Thin-Layer Chromatography/Mass Spectrometry (TLC/MS). Overall, both isolates can produce antimicrobial (e.g., Myxalamide C by-product) and antioxidants (e.g. Dihydroxymandelic Acid, Amide biotine and Flavone by-products) compounds. Bacillus LB7 strain possesses a more diverse repertoire with 51.95% of total metabolites unmatched, while Streptomyces LB8 favors mainly antioxidants, but has over 70% of unclassified compounds, highlighting the necessity to study and elucidate the structure of novel compounds. Based on these results, we postulate that the uncultured or rare cultured thermophiles inhabiting high-altitude hydrothermal ecosystems in the Atacama Desert offer a promising opportunity to the study of novel microbial bioactive compounds.},
}
@article {pmid39411429,
year = {2024},
author = {Xiao, P and Wu, Y and Zuo, J and Grossart, HP and Sun, R and Li, G and Jiang, H and Cheng, Y and Wang, Z and Geng, R and Zhang, H and Ma, Z and Yan, A and Li, R},
title = {Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1479158},
pmid = {39411429},
issn = {1664-302X},
abstract = {INTRODUCTION: In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&amp;ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.<br><br>METHODS: Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.<br><br>RESULTS AND DISCUSSION: This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.},
}
@article {pmid39409485,
year = {2024},
author = {Jechow, A and Bumberger, J and Palm, B and Remmler, P and Schreck, G and Ogashawara, I and Kiel, C and Kohnert, K and Grossart, HP and Singer, GA and Nejstgaard, JC and Wollrab, S and Berger, SA and Hölker, F},
title = {Characterizing and Implementing the Hamamatsu C12880MA Mini-Spectrometer for Near-Surface Reflectance Measurements of Inland Waters.},
journal = {Sensors (Basel, Switzerland)},
volume = {24},
number = {19},
pages = {},
pmid = {39409485},
issn = {1424-8220},
support = {Leibniz Competition No. K45/2017 (CONNECT-Connectivity and synchronization of lake ecosystems in space and time)//Leibniz Association/ ; IGB Frontiers project (2017)//Leibniz Institute of Freshwater Ecology and Inland Fisheries/ ; },
abstract = {In recent decades, inland water remote sensing has seen growing interest and very strong development. This includes improved spatial resolution, increased revisiting times, advanced multispectral sensors and recently even hyperspectral sensors. However, inland waters are more challenging than oceanic waters due to their higher complexity of optically active constituents and stronger adjacency effects due to their small size and nearby vegetation and built structures. Thus, bio-optical modeling of inland waters requires higher ground-truthing efforts. Large-scale ground-based sensor networks that are robust, self-sufficient, non-maintenance-intensive and low-cost could assist this otherwise labor-intensive task. Furthermore, most existing sensor systems are rather expensive, precluding their employability. Recently, low-cost mini-spectrometers have become widely available, which could potentially solve this issue. In this study, we analyze the characteristics of such a mini-spectrometer, the Hamamatsu C12880MA, and test it regarding its application in measuring water-leaving radiance near the surface. Overall, the measurements performed in the laboratory and in the field show that the system is very suitable for the targeted application.},
}
@article {pmid39406893,
year = {2024},
author = {Ioannou, A and Berkhout, MD and Geerlings, SY and Belzer, C},
title = {Akkermansia muciniphila: biology, microbial ecology, host interactions and therapeutic potential.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39406893},
issn = {1740-1534},
abstract = {Akkermansia muciniphila is a gut bacterium that colonizes the gut mucosa, has a role in maintaining gut health and shows promise for potential therapeutic applications. The discovery of A. muciniphila as an important member of our gut microbiome, occupying an extraordinary niche in the human gut, has led to new hypotheses on gut health, beneficial microorganisms and host-microbiota interactions. This microorganism has established a unique position in human microbiome research, similar to its role in the gut ecosystem. Its unique traits in using mucin sugars and mechanisms of action that can modify host health have made A. muciniphila a subject of enormous attention from multiple research fields. A. muciniphila is becoming a model organism studied for its ability to modulate human health and gut microbiome structure, leading to commercial products, a genetic model and possible probiotic formulations. This Review provides an overview of A. muciniphila and Akkermansia genus phylogeny, ecophysiology and diversity. Furthermore, the Review discusses perspectives on ecology, strategies for harnessing beneficial effects of A. muciniphila for human mucosal metabolic and gut health, and its potential as a biomarker for diagnostics and prognostics.},
}
@article {pmid39406702,
year = {2024},
author = {Wegner, H and Roitman, S and Kupczok, A and Braun, V and Woodhouse, JN and Grossart, HP and Zehner, S and Béjà, O and Frankenberg-Dinkel, N},
title = {Identification of Shemin pathway genes for tetrapyrrole biosynthesis in bacteriophage sequences from aquatic environments.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8783},
pmid = {39406702},
issn = {2041-1723},
support = {FR1487/16-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 143/18//Israel Science Foundation (ISF)/ ; },
mesh = {*Tetrapyrroles/biosynthesis/metabolism ; *Bacteriophages/genetics/metabolism ; Escherichia coli/genetics/virology/metabolism ; 5-Aminolevulinate Synthetase/genetics/metabolism ; Amino Acid Sequence ; Heme/metabolism/biosynthesis ; Aminolevulinic Acid/metabolism ; Phylogeny ; Fresh Water/virology ; Biosynthetic Pathways/genetics ; },
abstract = {Tetrapyrroles such as heme, chlorophyll, and vitamin B12 are essential for various metabolic pathways. They derive from 5-aminolevulinic acid (5-ALA), which can be synthesized by a single enzyme (5-ALA synthase or AlaS, Shemin pathway) or by a two-enzyme pathway. The genomes of some bacteriophages from aquatic environments carry various tetrapyrrole biosynthesis genes. Here, we analyze available metagenomic datasets and identify alaS homologs (viral alaS, or valaS) in sequences corresponding to marine and freshwater phages. The genes are found individually or as part of complete or truncated three-gene loci encoding heme-catabolizing enzymes. Amino-acid sequence alignments and three-dimensional structure prediction support that the valaS sequences likely encode functional enzymes. Indeed, we demonstrate that is the case for a freshwater phage valaS sequence, as it can complement an Escherichia coli 5-ALA auxotroph, and an E. coli strain overexpressing the gene converts the typical AlaS substrates glycine and succinyl-CoA into 5-ALA. Thus, our work identifies valaS as an auxiliary metabolic gene in phage sequences from aquatic environments, further supporting the importance of tetrapyrrole metabolism in bacteriophage biology.},
}
@article {pmid39404095,
year = {2024},
author = {Leleiwi, I and Kokkinias, K and Kim, Y and Baniasad, M and Shaffer, M and Sabag-Daigle, A and Daly, RA and Flynn, RM and Wysocki, VH and Ahmer, BMM and Borton, MA and Wrighton, KC},
title = {Gut microbiota carbon and sulfur metabolisms support Salmonella infections.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39404095},
issn = {1751-7370},
support = {T32GM132057//NIH Predoctoral Training/ ; DE-SC0021350//DOE/ ; R01AI143288//NIH NIAID/ ; R01 AI143288/AI/NIAID NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Sulfur/metabolism ; *Carbon/metabolism ; *Salmonella typhimurium/genetics ; Feces/microbiology ; Mice, Inbred C57BL ; Salmonella Infections/microbiology ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Salmonella Infections, Animal/microbiology ; Female ; },
abstract = {Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for seven members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that support Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.},
}
@article {pmid39404077,
year = {2024},
author = {Ellington, AJ and Walters, K and Christner, BC and Fox, S and Bonfantine, K and Walker, C and Lampman, P and Vuono, DC and Strickland, M and Lambert, K and Kobziar, LN},
title = {Dispersal of microbes from grassland fire smoke to soils.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39404077},
issn = {1751-7370},
support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; 2039531//National Science Foundation/ ; P20GM103408//National Institute of General Medical Sciences of the National Institutes of Health/ ; },
mesh = {*Soil Microbiology ; *Smoke ; *Grassland ; *Soil/chemistry ; Bacteria/classification/isolation &amp; purification/radiation effects ; Microbiota ; Wildfires ; Fires ; Biomass ; Poaceae/microbiology ; Carbon/analysis/metabolism ; },
abstract = {Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of subjects including agriculture, restoration, plant disease, and biodiversity.},
}
@article {pmid39402079,
year = {2024},
author = {Ashraf, H and Dikarlo, P and Masia, A and Zarbo, IR and Solla, P and Ijaz, UZ and Sechi, LA},
title = {Mycobacterium avium subspecies paratuberculosis (MAP) infection, and its impact on gut microbiome of individuals with multiple sclerosis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24027},
pmid = {39402079},
issn = {2045-2322},
support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Mycobacterium avium subsp. paratuberculosis/isolation &amp; purification ; *Paratuberculosis/microbiology ; *Multiple Sclerosis/microbiology ; Female ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Middle Aged ; },
abstract = {The microbial ecology of Mycobacterium avium subspecies paratuberculosis infections (MAP) within the context of Multiple Sclerosis (MS) is largely an unexplored topic in the literature. Thus, we have characterized the compositional and predicted functional differences of the gut microbiome between MS patients with MAP (MAP+) and without (MAP-) infection. This was done in the context of exposome differences (through self-reported filled questionnaires), principally in anthropometric and sociodemographic patterns to gain an understanding of the gut microbiome dynamics. 16S rRNA microbiome profiling of faecal samples (n = 69) was performed for four groups, which differed by disease and MAP infection: healthy cohort (HC) MAP-; HC MAP+ ; MS MAP-; and MS MAP+ . Using a dynamic strategy, with MAP infection and time of sampling as occupancy models, we have recovered the core microbiome for both HC and MS individuals. Additional application of neutral modeling suggests key genera that are under selection pressure by the hosts. These include members of the phyla Actinobacteriota, Bacteroidota, and Firmicutes. As several subjects provided multiple samples, a Quasi Conditional Association Test that incorporates paired-nature of samples found major differences in Archaea. To consolidate treatment groups, confounders, microbiome, and the disease outcome parameters, a mediation analysis is performed for MS cohort. This highlighted certain genera i.e., Sutterella, Akkermansia, Bacteriodes, Gastranaerophilales, Alistipes, Balutia, Faecalibacterium, Lachnospiraceae, Anaerostipes, Ruminococcaceae, Eggerthellaceae and Clostridia-UCG-014 having mediatory effect using disease duration as an outcome and MAP infection as a treatment group. Our analyses indicate that the gut microbiome may be an important target for dietary and lifestyle intervention in MS patients with and without MAP infection.},
}
@article {pmid39401449,
year = {2024},
author = {Ahmerkamp, S and Pacherres, CO and Mosshammer, M and Godefroid, M and Wind-Hansen, M and Kuypers, M and Behrendt, L and Koren, K and Kühl, M},
title = {Novel Approach for Lifetime-Proportional Luminescence Imaging Using Frame Straddling.},
journal = {ACS sensors},
volume = {9},
number = {10},
pages = {5531-5540},
pmid = {39401449},
issn = {2379-3694},
mesh = {*Luminescent Measurements/methods ; Luminescence ; Oxygen/chemistry ; },
abstract = {Optode-based chemical imaging is a rapidly evolving field that has substantially enhanced our understanding of the role of microenvironments and chemical gradients in biogeochemistry, microbial ecology, and biomedical sciences. Progress in sensor chemistry has resulted in a broadened spectrum of analytes, alongside enhancements in sensor performance (e.g., sensitivity, brightness, and photostability). However, existing imaging techniques are often costly, challenging to implement, and limited in their recording speed. Here we use the "frame-straddling" technique, originally developed for particle image velocimetry for imaging the O2-dependent, integrated luminescence decay of optical O2 sensor materials. The method synchronizes short excitation pulses and camera exposures to capture two frames at varying brightness, where the first excitation pulse occurs at the end of the exposure of the first frame and the second excitation pulse at the beginning of the second frame. Here the first frame truncates the luminescence decay, whereas the second frame fully captures it. The difference between the frames quantifies the integral of the luminescence decay curve, which is proportional to the luminescence lifetime, at time scales below one millisecond. Short excitation pulses avoid depopulation of the ground state of luminophores, resulting in a linear Stern-Volmer response with increasing concentrations of the quencher (O2), which can be predicted through a simple model. This methodology is compatible with a wide range of camera systems, making it a versatile tool for various optode based chemical imaging applications. We showcase the utility of frame straddling in measuring O2 dynamics around algae and by observing O2 scavenging sodium dithionite particles sinking through oxygenated water.},
}
@article {pmid39399973,
year = {2024},
author = {Simpson, A and Wood-Charlson, EM and Smith, M and Koch, BJ and Beilsmith, K and Kimbrel, JA and Kellom, M and Hunter, CI and Walls, RL and Schriml, LM and Wilhelm, RC},
title = {MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {39399973},
issn = {2047-217X},
support = {IND90024429//USDA/ ; //Purdue University/ ; //Lawrence Berkeley National Laboratory/ ; },
mesh = {*Isotope Labeling/methods ; Reproducibility of Results ; Microbiota/genetics ; Metadata ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; },
abstract = {DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.},
}
@article {pmid39398475,
year = {2024},
author = {Kumar, G and Bhadury, P},
title = {Dataset of metagenomic profiles of human gut microbiome from frozen fecal samples sequenced using Illumina and ONT chemistries.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110961},
pmid = {39398475},
issn = {2352-3409},
abstract = {The data presented in this study are metagenomic profiles of human gut microbiome deduced from frozen fecal samples using two different sequencing chemistries namely, Illumina and Oxford Nanopore Technologies (ONT). The generated data is obtained from genomic DNA extracted from frozen fecal samples collected from a healthy individual on Day 3, Day 5, Day 9, Day 12, and Day 30, in addition to Day 1 (unfrozen). The metagenomic sequence data have been deposited at NCBI SRA as BioProject PRJNA827663. The taxonomic annotation undertaken using MG-RAST showed relative abundance of bacteria represented by different taxonomic levels varied significantly based on two sequencing chemistries. There was distinct temporal variation in the relative abundance of bacteria at different taxonomic levels based on the day of extraction of genomic DNA. This dataset can be used to study differences in functional profiles of human gut microbiome using different sequencing technologies. Moreover, generated data can aid in selection of most appropriate sequencing chemistry to study future human gut microbiome studies based on the appropriate preservation method of fecal samples.},
}
@article {pmid39397203,
year = {2024},
author = {Liu, K and Yan, Q and Guo, X and Wang, W and Zhang, Z and Ji, M and Wang, F and Liu, Y},
title = {Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment : Bacterial Communities in Glacial Lakes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {128},
pmid = {39397203},
issn = {1432-184X},
support = {ANSO-CR-KP-2021-04//the Key Collaborative Research Program of the Alliance of International Science Organizations/ ; 42330410//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; },
mesh = {*Lakes/microbiology ; *Geologic Sediments/microbiology ; *Ice Cover/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; Microbiota ; Ecosystem ; Tibet ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; },
abstract = {Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.},
}
@article {pmid39388223,
year = {2024},
author = {Alcaraz, CM and Séneca, J and Kunert, M and Pree, C and Sudo, M and Petersen, JM},
title = {Sulfur-oxidizing symbionts colonize the digestive tract of their lucinid hosts.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39388223},
issn = {1751-7370},
mesh = {Animals ; *Symbiosis ; *Bivalvia/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Tract/microbiology ; *Gills/microbiology ; *Sulfur/metabolism ; *In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; },
abstract = {Like many marine invertebrates, marine lucinid clams have an intimate relationship with beneficial sulfur-oxidizing bacteria located within specialized gill cells known as bacteriocytes. Most previous research has focused on the symbionts in the gills of these (and other) symbiotic bivalves, often assuming that the symbionts only persistently colonize the gills, at least in the adult stage. We used 16S rRNA gene sequencing and digital polymerase chain reaction with symbiont-specific primers targeting the soxB gene on the foot, mantle, visceral mass, and gills of the lucinid clam Loripes orbiculatus. We also used fluorescence in situ hybridization with symbiont-specific probes to examine symbiont distribution at the level of the whole holobiont. Despite 40 years of research on these symbioses, we detected previously unknown populations of symbiont cells in several organs, including the digestive tract. As in the well-studied gills, symbionts in the digestive tract may be housed within host cells. A 14-month starvation experiment without hydrogen sulfide to power symbiont metabolism caused a larger reduction in symbiont numbers in the gills compared to the visceral mass, raising the possibility that symbionts in the digestive tract are persistent and may have a distinct physiology and role in the symbiosis compared with the gill symbionts. Our results highlight the unexpectedly complex relationships between marine lucinid clams and their symbionts and challenge the view that chemosynthetic symbionts are restricted to the gills of these hosts.},
}
@article {pmid39387587,
year = {2024},
author = {Akob, DM and Oates, AE and Girguis, PR and Badgley, BD and Cooper, VS and Poretsky, RS and Tierney, BT and Litchman, E and Whitaker, RJ and Whiteson, KL and Metcalf, CJE and , },
title = {Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology.},
journal = {mSphere},
volume = {9},
number = {11},
pages = {e0030724},
pmid = {39387587},
issn = {2379-5042},
mesh = {*Biodiversity ; *Ecology ; *Microbiology ; *Societies, Scientific ; United States ; Biological Evolution ; Humans ; Microbiota ; },
abstract = {The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind and Earth. To that end, EEB is developing new transdisciplinary tools to analyze these ecologically critical, complex microbial communities. The American Society for Microbiology's Council on Microbial Sciences hosted a virtual retreat in 2023 to discuss the trajectory of EEB both within the Society and microbiology writ large. The retreat emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The maximal potential impact of EEB will not be achieved without contributions from disparate fields that unite diverse technologies and data sets. In turn, this level of transdisciplinary efforts requires actively encouraging "broad" research, spanning inclusive global collaborations that incorporate both scientists and the public. Together, the American Society for Microbiology and EEB are poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.},
}
@article {pmid39387577,
year = {2024},
author = {Beck, KL and Haiminen, N and Agarwal, A and Carrieri, AP and Madgwick, M and Kelly, J and Pylro, V and Kawas, B and Wiedmann, M and Ganda, E},
title = {Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production.},
journal = {mSystems},
volume = {9},
number = {11},
pages = {e0084024},
pmid = {39387577},
issn = {2379-5077},
support = {#PEN04752, #PEN04731//U.S. Department of Agriculture (USDA)/ ; },
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Milk/microbiology/chemistry ; Animals ; Food Microbiology/methods ; Microbiota/genetics ; Algorithms ; Principal Component Analysis ; Machine Learning ; },
abstract = {UNLABELLED: The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection could be a valuable approach to be used in food systems. These methods could be used to identify ingredients that deviate from their typical microbial composition, which could indicate food fraud or safety issues. The objective of this study was to assess the feasibility of using shotgun sequencing data as input into anomaly detection algorithms using fluid milk as a model system. Contrastive principal component analysis (PCA), cluster-based methods, and explainable artificial intelligence (AI) were evaluated for the detection of two anomalous sample classes using longitudinal metagenomic profiling of fluid milk compared to baseline (BL) samples collected under comparable circumstances. Traditional methods (alpha and beta diversity, clustering-based contrastive PCA, multidimensional scaling, and dendrograms) failed to differentiate anomalous sample classes; however, explainable AI was able to classify anomalous vs baseline samples and indicate microbial drivers in association with antibiotic use. We validated the potential for explainable AI to classify different milk sources using larger publicly available fluid milk 16S rDNA sequencing data sets and demonstrated that explainable AI is able to differentiate between milk storage methods, processing stages, and seasons. Our results indicate that the application of artificial intelligence continues to hold promise in the realm of microbiome data analysis and could present further opportunities for downstream analytic automation to aid in food safety and quality.<br><br>IMPORTANCE: We evaluated the feasibility of using untargeted metagenomic sequencing of raw milk for detecting anomalous food ingredient content with artificial intelligence methods in a study specifically designed to test this hypothesis. We also show through analysis of publicly available fluid milk microbial data that our artificial intelligence approach is able to successfully predict milk in different stages of processing. The approach could potentially be applied in the food industry for safety and quality control.},
}
@article {pmid39387551,
year = {2024},
author = {Halbrook, S and Wilber, W and Barrow, ME and Farrer, EC},
title = {Bacterial community response to novel and repeated disturbances.},
journal = {Environmental microbiology reports},
volume = {16},
number = {5},
pages = {e70022},
pmid = {39387551},
issn = {1758-2229},
support = {LEQSF(2017-20)-RD-A-14//Louisiana Board of Regents/ ; //Tulane University/ ; DEB-2141922//National Science Foundation/ ; },
mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; Salinity ; Microbiota ; Ecosystem ; Biodiversity ; },
abstract = {Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past disturbances can alter microbial community structure and their response to subsequent disturbance events, but it remains unclear if the same recovery patterns persist after long-term exposure to stress. Here, we compare bacterial community composition in a community that experienced 2 years of monthly salinity addition disturbances with a community that has not experienced salinity additions. We then track the response and recovery to an additional salinity addition based on past disturbance exposure. We tested the following hypotheses: first, communities with a repeated disturbance history will have a different community composition than communities without a disturbance history; second, communities exposed to repeated disturbances will undergo a different recovery trajectory than communities experiencing a novel disturbance. We find that repeated disturbances alter community composition and affect community response and recovery to a subsequent disturbance after 2 years, primarily through increased resistance. This work enhances our understanding of microbial temporal dynamics and suggests that novel disturbances may pose a threat to microbial community structure and function.},
}
@article {pmid39392836,
year = {2024},
author = {Daisley, BA and Allen-Vercoe, E},
title = {Microbes as medicine.},
journal = {Annals of the New York Academy of Sciences},
volume = {1541},
number = {1},
pages = {63-82},
pmid = {39392836},
issn = {1749-6632},
support = {950-232131//Canada Research Chairs/ ; PDF-402947//Natural Sciences and Engineering Research Council of Canada/ ; //Natural Sciences and Engineering Research Council of Canada/ ; 2023//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Humans ; *Probiotics/therapeutic use ; *Microbiota/drug effects/physiology ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Precision Medicine/methods ; Animals ; },
abstract = {Over the last two decades, advancements in sequencing technologies have significantly deepened our understanding of the human microbiome's complexity, leading to increased concerns about the detrimental effects of antibiotics on these intricate microbial ecosystems. Concurrently, the rise in antimicrobial resistance has intensified the focus on how beneficial microbes can be harnessed to treat diseases and improve health and offer potentially promising alternatives to traditional antibiotic treatments. Here, we provide a comprehensive overview of both established and emerging microbe-centric therapies, from probiotics to advanced microbial ecosystem therapeutics, examine the sophisticated ways in which microbes are used medicinally, and consider their impacts on microbiome homeostasis and health outcomes through a microbial ecology lens. In addition, we explore the concept of rewilding the human microbiome by reintroducing "missing microbes" from nonindustrialized societies and personalizing microbiome modulation to fit individual microbial profiles-highlighting several promising directions for future research. Ultimately, the advancements in sequencing technologies combined with innovative microbial therapies and personalized approaches herald a new era in medicine poised to address antibiotic resistance and improve health outcomes through targeted microbiome management.},
}
@article {pmid39392487,
year = {2024},
author = {Legeay, J and Basiru, S and Ziami, A and Errafii, K and Hijri, M},
title = {Response of Alternaria and Fusarium Species to Low Precipitation in a Drought-Tolerant Plant in Morocco.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {127},
pmid = {39392487},
issn = {1432-184X},
support = {Project AS-85//OPC Africa and OCP Innovation/ ; },
mesh = {Morocco ; *Fusarium/physiology/isolation &amp; purification/classification ; *Droughts ; *Alternaria/physiology/classification ; *Plant Roots/microbiology ; *Rain ; Soil Microbiology ; Mycobiome ; Rhizosphere ; },
abstract = {The plant mycobiome plays a crucial role in the host life cycle, influencing both healthy and diseased states, and is essential for plant tolerance to drought. In this study, we used ITS metabarcoding to investigate the fungal community of the drought-resistant plant Malva sylvestris L. in Morocco along a gradient of precipitation, encompassing subhumid and semi-arid environments. We sampled three biotopes: rhizosphere, bulk soil, and root endosphere. Our findings revealed an absence of beta-diversity differences between bulk soil and rhizosphere, indicating that the plant does not selectively influence its rhizosphere mycobiome. Additionally, ASVs belonging to the genus Alternaria represented up to 30% of reads in the plant's roots and correlated with drought (p = 0.006), indicating a potential role for this fungal genus in mitigating drought, possibly as part of the dark septate endophyte group. Root staining and microscopic observation revealed extensive colonization by fungal hyphae and microsclerotia-like structures. Furthermore, ASVs identified as Fusarium equiseti were also correlated with low precipitation and recognized as a hub taxon in the roots. However, it remains uncertain whether this species is pathogenic or beneficial to the plant. These insights contribute to our understanding of the plant mycobiome's role in drought tolerance and highlight the importance of specific fungal taxa in supporting plant health under varying environmental conditions. Future research should focus on characterizing these taxa's functional roles and their interactions with the host plant to further elucidate their contributions to drought resistance.},
}
@article {pmid39390291,
year = {2024},
author = {Delzenne, NM and Bindels, LB and Neyrinck, AM and Walter, J},
title = {The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39390291},
issn = {1740-1534},
abstract = {Dietary fibres constitute a heterogeneous class of nutrients that are key in the prevention of various chronic diseases. Most dietary fibres are fermented by the gut microbiome and may, thereby, modulate the gut microbial ecology and metabolism, impacting human health. Dietary fibres may influence the occurrence of specific bacterial taxa, with this effect varying between individuals. The effect of dietary fibres on microbial diversity is a matter of debate. Most intervention studies with dietary fibres in the context of obesity and related metabolic disorders reveal the need for an accurate assessment of the microbiome to better understand the variable response to dietary fibres. Epidemiological studies confirm that a high dietary fibre intake is strongly associated with a reduced occurrence of many types of cancer. However, there is a need to determine the impact of intervention with specific dietary fibres on cancer risk, therapy efficacy and toxicity, as well as in cancer cachexia. In this Review, we summarize the mechanisms by which the gut microbiome can mediate the physiological benefits of dietary fibres in the contexts of obesity, cardiometabolic diseases and cancer, their incidence being clearly linked to low dietary fibre intake.},
}
@article {pmid39389280,
year = {2024},
author = {Lima, M and Muddana, C and Xiao, Z and Bandyopadhyay, A and Wangikar, PP and Pakrasi, HB and Tang, YJ},
title = {The new chassis in the flask: Advances in Vibrio natriegens biotechnology research.},
journal = {Biotechnology advances},
volume = {77},
number = {},
pages = {108464},
doi = {10.1016/j.biotechadv.2024.108464},
pmid = {39389280},
issn = {1873-1899},
abstract = {Biotechnology has been built on the foundation of a small handful of well characterized and well-engineered organisms. Recent years have seen a breakout performer gain attention as a new entrant into the bioengineering toolbox: Vibrio natriegens. This review covers recent research efforts into making V. natriegens a biotechnology platform, using a large language model (LLM) and knowledge graph to expedite the literature survey process. Scientists have made advancements in research pertaining to the fundamental metabolic characteristics of V. natriegens, development and characterization of synthetic biology tools, systems biology analysis and metabolic modeling, bioproduction and metabolic engineering, and microbial ecology. Each of these subcategories has relevance to the future of V. natriegens for bioengineering applications. In this review, we cover these recent advancements and offer context for the impact they may have on the field, highlighting benefits and drawbacks of using this organism. From examining the recent bioengineering research, it appears that V. natriegens is on the precipice of becoming a platform bacterium for the future of biotechnology.},
}
@article {pmid39386005,
year = {2024},
author = {Lin, X and Waring, K and Ghezzi, H and Tropini, C and Tyson, J and Ziels, RM},
title = {High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.},
journal = {PNAS nexus},
volume = {3},
number = {10},
pages = {pgae411},
pmid = {39386005},
issn = {2752-6542},
abstract = {Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms are commonly employed for high-throughput applications of SSU rRNA amplicon sequencing, but at the cost of poor taxonomic classification due to limited fragment lengths. The Oxford Nanopore Technologies (ONT) platform can sequence full-length SSU rRNA genes, but its lower raw-read accuracy has so-far limited accurate taxonomic classification and de novo feature generation. Here, we present a sequencing workflow, termed ssUMI, that combines unique molecular identifier (UMI)-based error correction with newer (R10.4+) ONT chemistry and sample barcoding to enable high throughput near full-length SSU rRNA (e.g. 16S rRNA) amplicon sequencing. The ssUMI workflow generated near full-length 16S rRNA consensus sequences with 99.99% mean accuracy using a minimum subread coverage of 3×, surpassing the accuracy of Illumina short reads. The consensus sequences generated with ssUMI were used to produce error-free de novo sequence features with no false positives with two microbial community standards. In contrast, Nanopore raw reads produced erroneous de novo sequence features, indicating that UMI-based error correction is currently necessary for high-accuracy microbial profiling with R10.4+ ONT sequencing chemistries. We showcase the cost-competitive scalability of the ssUMI workflow by sequencing 87 time-series wastewater samples and 27 human gut samples, obtaining quantitative ecological insights that were missed by short-read amplicon sequencing. ssUMI, therefore, enables accurate and low-cost full-length 16S rRNA amplicon sequencing on Nanopore, improving accessibility to high-resolution microbiome science.},
}
@article {pmid39383960,
year = {2024},
author = {Goswami, V and Deepika, S and Sharma, P and Kothamasi, D},
title = {Recycling steel slag as fertiliser proxy in agriculture is good circular economy but disrupts plant microbial symbioses in the soil.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176750},
doi = {10.1016/j.scitotenv.2024.176750},
pmid = {39383960},
issn = {1879-1026},
mesh = {*Agriculture/methods ; *Fertilizers ; *Mycorrhizae/physiology ; *Soil Microbiology ; *Symbiosis ; Steel ; Hordeum/microbiology ; Recycling ; Soil/chemistry ; },
abstract = {Modern agriculture depends on synthetic fertilisers to ensure food security but their manufacture and use accounts for ~5 % of the global greenhouse gas emissions. Achieving climate change targets therefore requires alternatives, that while maintaining crop productivity, reduce emissions across the lifecycle of fertiliser utilisation. Steel slag, a nutrient-rich by-product of steel manufacture, offers a viable alternative. Being substantially cheaper than fertilisers, it is economically attractive for farmers, particularly in low-middle income countries of the Global South. However, slag application in agriculture poses risk of pollutant transfer to the human food chain and disruption of key plant-microbe symbioses like the arbuscular mycorrhizal fungi (AMF). Here, using barley as a model crop, we tested the suitability of slag as a fertiliser proxy. Mycorrhizal and non-mycorrhizal barley were grown in soils ameliorated with slag in concentrations of 0, 2, 5 and 10 t ha[-1]. We analysed slag-mycorrhiza interaction and their combined effects on crop yield and risks to human nourishment. Slag increased grain yield by respective 32 and 21 % in mycorrhizal and non-mycorrhizal barley. Grain concentration of metal pollutants in mycorrhizal and non-mycorrhizal barley fertilised with slag were within the WHO recommended limits. But slag reduced mycorrhizal colonisation in barley roots and extraradical hyphal spread in the soil. The consequent decline in symbiont function lowered AMF-mediated plant nutrient uptake and increased mineral losses in leachates. AMF are keystone species of the soil microbiome. Loss of AMF function presents long-term ecological consequences for agriculture and necessitates a careful evaluation of slag application to soil.},
}
@article {pmid39382725,
year = {2024},
author = {Wang, L and Liu, Z and Bres, C and Jin, G and Fanin, N},
title = {Coniferous Tree Species Identity and Leaf Aging Alter the Composition of Phyllosphere Communities Through Changes in Leaf Traits.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {126},
pmid = {39382725},
issn = {1432-184X},
support = {2572021AW30//Fundamental Research Funds for the Central Universities/ ; 2022YFD2201100//National Key R &amp; D Program of China/ ; 2572022DS13//the Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Plant Leaves/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Trees/microbiology/growth &amp; development ; Fungi/classification/genetics/physiology/isolation &amp; purification ; Pinus/microbiology/growth &amp; development ; Abies/microbiology ; Picea/microbiology/growth &amp; development ; Biodiversity ; Tracheophyta/microbiology ; },
abstract = {Phyllosphere microorganisms are essential for plant growth and health. Although there are an increasing number of studies showing that the composition of phyllosphere communities varies among different plant species, it remains unclear whether and how their bacterial and fungal community composition predictably varies with plant traits and leaf age. In this study, we used high-throughput sequencing to explore the diversity and composition of phyllosphere communities in needles of different ages (originating from different cohorts) for three evergreen coniferous species (Pinus koraiensis, Picea koraiensis, and Abies nephrolepis). Our results indicated that Gammaproteobacteria (bacteria) and Dothideomycetes (fungi) were dominant in newly formed needles, whereas Actinobacteria (bacteria) and Eurotiomycetes (fungi) were dominant in perennial needles. Tree species identity and needle age were the main factors explaining the variations of the α diversity (species richness of phyllosphere communities) and β diversity (dissimilarity among phyllosphere communities). In particular, we found that leaf dry matter content, leaf mass per area, and total phosphorus content emerged as key predictors of composition and diversity of phyllosphere microbial communities, underscoring the major influence of tree species identity and needle age on phyllosphere communities through changes in plant functional traits. Finally, we found that the interaction between tree species identity and needle age also contributed significantly to explaining the diversity and composition of phyllosphere communities, probably because differences in plant functional traits or environmental conditions between new and perennial needles depend on tree growth rates and resource acquisition strategies. These findings provide new insights into the mechanisms of community assembly among different evergreen tree species and offer a better understanding of the interactions between plant traits and phyllosphere microorganisms during needle aging.},
}
@article {pmid39382674,
year = {2024},
author = {Murray, MLH and Dopheide, A and Leonard, J and Padamsee, M and Schwendenmann, L},
title = {Phyllosphere of Agathis australis Leaves and the Impact of the Soil-Borne Pathogen Phytophthora agathidicida.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {125},
pmid = {39382674},
issn = {1432-184X},
mesh = {*Plant Leaves/microbiology ; *Phytophthora/isolation &amp; purification/genetics ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; New Zealand ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Combretaceae/microbiology ; },
abstract = {Leaf surface microbial communities play an important role in forest ecosystems and are known to be affected by environmental and host conditions, including diseases impacting the host. Phytophthora agathidicida is a soil-borne pathogen that causes severe disease (kauri dieback) in one of New Zealand's endemic trees, Agathis australis (kauri). This research characterised the microbial communities of the A. australis phyllosphere (i.e. leaf surface) using modern molecular techniques and explored the effects of P. agathidicida on those communities. Fresh leaves were collected from trees where P. agathidicida was and was not detected in the soil and characterisation of the leaf surface microbial community was carried out via high-throughput amplicon sequencing of the internal transcribed spacer (ITS) and 16S ribosomal RNA regions. Nutrients in leaf leachates were also measured to identify other possible drivers of microbial diversity. The dominant phyllosphere microbial phylum was Proteobacteria followed by Acidobacteria. The phyllosphere microbial richness of A. agathis associated with P. agathidicida-infected soils was found to be generally lower than where the pathogen was not detected for both prokaryote (bacterial) and fungal phyla. Leaf leachate pH as well as boron and silicon had significant associations with bacterial and fungal community structure. These findings contribute to the development of a comprehensive understanding of A. australis leaf surface microbial communities and the effects of the soil pathogen P. agathidicida on those communities.},
}
@article {pmid39382297,
year = {2024},
author = {Eigemann, F and Hoffmann, J and Schampera, C and Liu, S and Bolaños, LM and Heemeyer, M and Carlson, CA and Giovannoni, S and Hellweger, FL},
title = {Emergent ecology in a microscale model of the surface ocean.},
journal = {mBio},
volume = {15},
number = {11},
pages = {e0237224},
pmid = {39382297},
issn = {2150-7511},
support = {BIOS-SCOPE//Simons Foundation (SF)/ ; //North-German Supercomputing Alliance/ ; },
mesh = {*Phytoplankton/metabolism/physiology ; *Oceans and Seas ; *Ecosystem ; *Seawater/microbiology/chemistry ; Bacteria/metabolism/genetics ; Models, Biological ; Chemotaxis ; Bacterial Physiological Phenomena ; Carbon/metabolism ; Cyanobacteria/metabolism/physiology/growth &amp; development ; Ecology ; },
abstract = {Microbial processes operate at the microscale, which is not resolved by existing ecosystem models. Here, we present a novel model that simulates a 1 mL three-dimensional cube using a hybrid Lagrangian-Eulerian approach, at ecologically relevant timescales. The model simulates individual microbes, including three phytoplankton size classes with healthy, senescent, and dead lifecycle stages; copiotrophic and oligotrophic heterotrophic bacteria; and dissolved organic matter at 50 µm resolution. Diffusion, shear, sedimentation, chemotaxis, and attachment processes are explicitly resolved. The emerging quantitative representation of the ecosystem shows that (1) copiotrophs grow mostly attached to eukaryotic phytoplankters and get almost all of their carbon from them vs. oligotrophs that grow on exudates and lysates of cyanobacteria; (2) contrasting diel patterns in substrate appearance in the phycosphere vs. ambient water and growth of particle-associated copiotrophs vs. free-living oligotrophs; (3) attached bacteria reduce carbon flux from the phycosphere, lowering chemotactic efficiency toward eukaryotes below that toward cyanobacteria; (4) shear reduces chemotactic efficiency and fitness of the copiotroph; and (5) the main benefit of chemotaxis is to locate attachment partners. These patterns are consistent with available observations. Our study provides insights into the microscale ecology of marine bacteria, and the open-source code is a tool for further research in this area.IMPORTANCEA large amount of global CO2 fixation is performed by marine phytoplankton, and a substantial fraction of that is released as dissolved organic carbon and further processed by heterotrophic bacteria. The interaction between phytoplankton and bacteria, i.e., the carbon flux between them, is therefore an important process in the global carbon and climate system. Some bacteria have developed specialized behavioral traits, like swimming and attachment, to increase their carbon acquisition. These interactions occur at the micrometer scale, for example, the immediate vicinity of phytoplankters (the phycosphere), but existing biogeochemical models typically only simulate down to the 1 meter vertical or ~100 kilometer horizontal scale. We present a new microscale model and use it to predict fluxes and other features in the surface ocean. The model makes important predictions about the fluxes between various types of phytoplankton and bacteria and the role of behavioral traits, and it provides a basis and tool for further research in this area.},
}
@article {pmid39381885,
year = {2024},
author = {Witzgall, K and Hesse, BD and Pacay-Barrientos, NL and Jansa, J and Seguel, O and Oses, R and Buegger, F and Guigue, J and Rojas, C and Rousk, K and Grams, TEE and Pietrasiak, N and Mueller, CW},
title = {Soil carbon and nitrogen cycling at the atmosphere-soil interface: Quantifying the responses of biocrust-soil interactions to global change.},
journal = {Global change biology},
volume = {30},
number = {10},
pages = {e17519},
doi = {10.1111/gcb.17519},
pmid = {39381885},
issn = {1365-2486},
support = {MU3021/6-2//Deutsche Forschungsgemeinschaft/ ; EAR-2012475//National Science Foundation (NSF)/ ; },
mesh = {*Soil/chemistry ; *Climate Change ; *Nitrogen Cycle ; *Soil Microbiology ; *Carbon Cycle ; *Droughts ; *Atmosphere/chemistry ; Carbon/metabolism/analysis ; Carbon Dioxide/metabolism/analysis ; Nitrogen/metabolism/analysis ; Ecosystem ; },
abstract = {In drylands, where water scarcity limits vascular plant growth, much of the primary production occurs at the soil surface. This is where complex macro- and microbial communities, in an intricate bond with soil particles, form biological soil crusts (biocrusts). Despite their critical role in regulating C and N cycling in dryland ecosystems, there is limited understanding of the fate of biologically fixed C and N from biocrusts into the mineral soil, or how climate change will affect C and N fluxes between the atmosphere, biocrusts, and subsurface soils. To address these gaps, we subjected biocrust-soil systems to experimental warming and drought under controlled laboratory conditions, monitored CO2 fluxes, and applied dual isotopic labeling pulses ([13]CO2 and [15]N2). This allowed detailed quantification of elemental pathways into specific organic matter (OM) pools and microbial biomass via density fractionation and phospholipid fatty acid analyses. While biocrusts modulated CO2 fluxes regardless of the temperature regime, drought severely limited their photosynthetic C uptake to the extent that the systems no longer sustained net C uptake. Furthermore, the effect of biocrusts extended into the underlying 1 cm of mineral soil, where C and N accumulated as mineral-associated OM (MAOM<63μm). This was strongly associated with increased relative dominance of fungi, suggesting that fungal hyphae facilitate the downward C and N translocation and subsequent MAOM formation. Most strikingly, however, these pathways were disrupted in systems exposed to warming, where no effects of biocrusts on the elemental composition of the underlying soil nor on MAOM were determined. This was further associated with reduced net biological N fixation under combined warming and drought, highlighting how changing climatic conditions diminish some of the most fundamental ecosystem functions of biocrusts, with detrimental repercussions for C and N cycling and the persistence of soil organic matter pools in dryland ecosystems.},
}
@article {pmid39380680,
year = {2024},
author = {Karavaeva, V and Sousa, FL},
title = {Navigating the archaeal frontier: insights and projections from bioinformatic pipelines.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1433224},
pmid = {39380680},
issn = {1664-302X},
abstract = {Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.},
}
@article {pmid39379763,
year = {2024},
author = {Peng, Z and Xu, Z and Tong, H and Xing, Y and Luo, Z and Wu, Y and Yu, Z},
title = {Leaf Rust Pathogens on Hypericum pseudohenryi: Describing Melampsora danbaensis sp. nov. and M. hyperici-pseudohenryi sp. nov. from China.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {122},
pmid = {39379763},
issn = {1432-184X},
support = {2023YFC2604800-03//National Key Research and Development Program of China/ ; },
mesh = {China ; *Hypericum/microbiology/classification ; *Phylogeny ; *Plant Diseases/microbiology ; *Plant Leaves/microbiology ; *Basidiomycota/classification/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; Spores, Fungal ; },
abstract = {Based on morphological and phylogenetic evidence, two novel species of Melampsora were discovered on Hypericum pseudohenryi in China and have been thoroughly characterized. One of these species, designated as M. danbaensis, exhibits distinct features such as aecia of Uredo-type, typically appearing in gregarious or grouped arrangements, and presenting a shallowly pulvinate structure. Aeciospores exhibit tremendous variations in size, ranging in shape from globose to ellipsoidal and bearing pronounced verrucose texture. Telia resemble crusts one-spore deep, covering nearly the entire abaxial leaf surface, with sessile teliospores reaching sizes of up to 65.8 µm, and exhibiting a clavate to cylindrical shape. Another species, designated as M. hyperici-pseudohenryi, is distinguished by Uredo-type uredinia, which are hypophyllous, scattered or grouped, and interspersed with numerous paraphyses. Its urediniospores tend to be globose, ellipsoidal or obovoid, echinulate, and are accompanied by clavate to capitate paraphyses reaching lengths up to 77.6 µm. Phylogenetically, both species form a novel monophyletic clade within the Melampsora genus, with robust support demonstrated by a high Maximum likelihood bootstrap support (MLBS) value of 100% and a Bayesian posterior probability (BPP) of 1. This study enriches our understanding of the diversity and geographical distribution of Melampsora species that infect Hypericum plants in China.},
}
@article {pmid39379709,
year = {2024},
author = {Larrouy, JL and Ridgway, HJ and Dhami, MK and Jones, EE},
title = {Improvement in Microbiota Recovery Using Cas-9 Digestion of Mānuka Plastid and Mitochondrial DNA.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {124},
pmid = {39379709},
issn = {1432-184X},
support = {C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Plastids/genetics ; *DNA, Mitochondrial/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Lamiales/microbiology/genetics ; CRISPR-Cas Systems ; DNA, Bacterial/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; Sequence Analysis, DNA ; },
abstract = {Understanding host-microbe interactions in planta is an expanding area of research. Amplicon sequencing of the 16S rRNA gene is a powerful and common method to study bacterial communities associated with plants. However, the co-amplification of mitochondrial and plastid 16S rRNA genes by universal primers impairs the sensitivity and performance of 16S rRNA sequencing. In 2020, a new method, Cas-16S-seq, was reported in the literature to remove host contamination for profiling the microbiota in rice, a well-studied domestic plant, by engineering RNA-programmable Cas9 nuclease in 16S rRNA sequencing. For the first time, we tested the efficiency and applicability of the Cas-16S-seq method on foliage, flowers, and seed of a non-domesticated wild plant for which there is limited genomic information, Leptospermum scoparium (mānuka). Our study demonstrated the efficiency of the Cas-16S-seq method for L. scoparium in removing host contamination in V4-16S amplicons. An increase of 46% in bacterial sequences was found using six guide RNAs (gRNAs), three gRNAs targeting the mitochondrial sequence, and three gRNAs targeting the chloroplast sequence of L. scoparium in the same reaction. An increase of 72% in bacterial sequences was obtained by targeting the mitochondrial and chloroplast sequences of L. scoparium in the same sample at two different steps of the library preparation (DNA and 1st step PCR). The number of OTUs (operational taxonomic units) retrieved from soil samples was consistent when using the different methods (Cas-16S-seq and 16S-seq) indicating that the Cas-16S-seq implemented for L. scoparium did not introduce bias to microbiota profiling. Our findings provide a valuable tool for future studies investigating the bacterial microbiota of L. scoparium in addition to evaluating an important tool in the plant microbiota research on other non-domesticated wild species.},
}
@article {pmid39379544,
year = {2024},
author = {Bastidas Navarro, M and Balseiro, E and Modenutti, B},
title = {Lake Bacterial Communities in North Patagonian Andes: The Effect of the Nothofagus pumilio Treeline.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {123},
pmid = {39379544},
issn = {1432-184X},
support = {PICT 2015-2138//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2017-1940//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2018-1563//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Cyanobacteria/genetics/classification ; Microbiota ; Nitrogen/analysis ; Carbon/analysis/metabolism ; Phosphorus/analysis ; Biodiversity ; Altitude ; Trees/microbiology ; Argentina ; },
abstract = {One of the most noticeable environmental discontinuities in mountains is the transition that exists in vegetation below and above the treeline. In the North Patagonian Andean lakes (between 900 and 1950 m a.s.l.), we analyzed the bacterial community composition of lakes in relation to surrounding vegetation (erected trees, krummholz belt, and bare rocks), dissolved organic carbon (DOC), and total dissolved nutrients (nitrogen, TDN and phosphorus, TDP). We observed a decrease in DOC, TDP, and TDN concentrations with altitude, reflecting shifts in the source inputs entering the lakes by runoff. Cluster analysis based on bacterial community composition showed a segregation of the lakes below treeline, from those located above. This first cluster was characterized by the cyanobacteria Cyanobium PCC-6307, while in the krummholz belt and bare rocks, bacterial communities were dominated by Actinobacteria hgcl-clade and Proteobacteria (Sandarakinorhabdus and Rhodovarius), with the presence of pigments such as actinorhodopsin, carotenoids, and bacteriochlorophyll a. The net relatedness index (NRI), which considers the community phylogenetic dispersion, showed that lakes located on bare rocks were structured by environmental filtering, while communities of lakes below treeline were structured by species interactions such as competition. Beta-diversity was higher among lakes below than among lakes located above the treeline. The contribution of species turnover was more important than nestedness. Our study brings light on how bacterial communities may respond to changes in the surrounding vegetation, highlighting the importance of evaluating different aspects of community structure to understand metacommunity organization.},
}
@article {pmid39378744,
year = {2024},
author = {Zhu, T and Li, S and Tao, C and Chen, W and Chen, M and Zong, Z and Wang, Y and Li, Y and Yan, B},
title = {Understanding the mechanism of microplastic-associated antibiotic resistance genes in aquatic ecosystems: Insights from metagenomic analyses and machine learning.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122570},
doi = {10.1016/j.watres.2024.122570},
pmid = {39378744},
issn = {1879-2448},
abstract = {The pervasive presence of microplastics (MPs) in aquatic systems facilitates the transmission of antibiotic resistance genes (ARGs), thereby posing risks to ecosystems and human well-being. However, owing to variations in environmental backgrounds and the limited scope of research subjects, studies on ARGs in MPs lack unified conclusions, particularly regarding whether different types of MPs selectively promote ARG enrichment. Analysing large-scale datasets can better encompass broad spatiotemporal scales and diverse samples, facilitating a more extensive exploration of the complex ecological relationships between MPs and ARGs. The present study integrated existing metagenomic datasets to conduct a comprehensive risk assessment and comparative analysis of resistance groups across various MPs. In addition, we endeavoured to elucidate potential associations between ARGs and bacterial taxa, as well as MP structural features, using machine learning (ML) methods. The findings of our research highlight the pivotal role of MP type in shaping plastispheres, accounting for 9.56 % of the biotic variation (Adonis index) and explaining 18.59 % of the ARG variance. Compared to conventional MPs, biodegradable MPs, such as polyhydroxyalkanoates (PHA) and polylactic acid (PLA), exhibit lower species uniformity and diversity but pose a higher risk of ARG occurrence. These ML approaches effectively forecasted ARG abundance by using the bacterial taxa and molecular structure descriptors (MDs) of MPs (average R[2]tra = 0.882, R[2]test = 0.759). Feature analysis showed that MDs associated with lipophilicity, solubility, toxicity, and surface potential significantly influenced the relative abundance of ARGs in the plastispheres. The interpretable multiple linear regression (MLR) model, particularly notable, elucidated a linear relationship between bacterial genera and ARGs, offering promise for identifying potential ARG hosts. This study offers novel insights into ARG dynamics and ecological risks within aquatic plastispheres, highlighting the importance of comprehensive MP monitoring initiatives.},
}
@article {pmid39377576,
year = {2024},
author = {Woldetsadik, YA and Lazinski, DW and Camilli, A},
title = {A Vibrio cholerae anti-phage system depletes nicotinamide adenine dinucleotide to restrict virulent bacteriophages.},
journal = {mBio},
volume = {15},
number = {11},
pages = {e0245724},
pmid = {39377576},
issn = {2150-7511},
support = {AI055058//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; GM139772//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R37 AI055058/AI/NIAID NIH HHS/United States ; R01 AI055058/AI/NIAID NIH HHS/United States ; R21 AI147658/AI/NIAID NIH HHS/United States ; T32 GM139772/GM/NIGMS NIH HHS/United States ; AI147658//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*NAD/metabolism ; *Bacteriophages/genetics/physiology ; *Vibrio cholerae/virology/genetics ; Virulence ; Bacterial Proteins/genetics/metabolism ; Genomic Islands ; Virus Replication ; },
abstract = {Bacteria and their predatory viruses (bacteriophages or phages) are in a perpetual molecular arms race. This has led to the evolution of numerous phage defensive systems in bacteria that are still being discovered, as well as numerous ways of interference or circumvention on the part of phages. Here, we identify a unique molecular battle between the classical biotype of Vibrio cholerae and virulent phages ICP1, ICP2, and ICP3. We show that classical biotype strains resist almost all isolates of these phages due to a 25-kb genomic island harboring several putative anti-phage systems. We observed that one of these systems, Nezha, encoding SIR2-like and helicase proteins, inhibited the replication of all three phages. Bacterial SIR2-like enzymes degrade the essential metabolic coenzyme nicotinamide adenine dinucleotide (NAD[+]), thereby preventing replication of the invading phage. In support of this mechanism, we identified one phage isolate, ICP1_2001, which circumvents Nezha by encoding two putative NAD[+] regeneration enzymes. By restoring the NAD[+] pool, we hypothesize that this system antagonizes Nezha without directly interacting with its proteins and should be able to antagonize other anti-phage systems that deplete NAD[+].IMPORTANCEBacteria and phages are in a perpetual molecular arms race, with bacteria evolving an extensive arsenal of anti-phage systems and phages evolving mechanisms to overcome these systems. This study identifies a previously uncharacterized facet of the arms race between Vibrio cholerae and its phages. We identify an NAD[+]-depleting anti-phage defensive system called Nezha, potent against three virulent phages. Remarkably, one phage encodes proteins that regenerate NAD[+] to counter the effects of Nezha. Without Nezha, the NAD[+] regeneration genes are detrimental to the phage. Our study provides new insight into the co-evolutionary dynamics between bacteria and phages and informs the microbial ecology and phage therapy fields.},
}
@article {pmid39376571,
year = {2024},
author = {Qian, C and Hui, J and Peng, Z and Sun, X and Zhang, J},
title = {Mucosal microbiota characterization in gastric cancer identifies immune-activated-related transcripts relevant gastric microbiome signatures.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1435334},
pmid = {39376571},
issn = {1664-3224},
mesh = {Humans ; *Stomach Neoplasms/immunology/microbiology/genetics/mortality ; *Gastric Mucosa/microbiology/immunology/metabolism ; Female ; *Tumor Microenvironment/immunology ; Male ; Middle Aged ; *Gastrointestinal Microbiome/immunology/genetics ; Aged ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/immunology/genetics ; Adult ; },
abstract = {Tumor microenvironment (TME) immune cells and gastric mucosal microbiome constitute two vital elements of tumor tissue. Increasing evidence has elucidated their clinicopathological significance in predicting outcomes and therapeutic efficacy. However, comprehensive characterization of immune cell-associated microbiome signatures in the TME is still in the early stages of development. Here, we characterized the gastric mucosa microbiome and its associations with immune-activated related transcripts (IATs) in 170 GC tumor tissues and matched non-tumor tissues using 16s rRNA gene sequencing and quantitative reverse transcription-PCR. Microbial diversity and richness were significantly higher in GC tumor tissues than in non-tumor tissues. Differences in microbial composition between the groups were evident, with Firmicutes, Proteobacteria, Bacteroidota, Campilobacterota, Actinobacteria, Fusobacteriota, Verrucomicrobiota, Acidobacteriota, and Cyanobacteria being the dominant phyla in the gastric mucosal microbiota. Microbial interaction network analysis revealed distinctive centralities of oral bacteria (such as Fusobacterium, Porphyromonas, Prevotella, etc.) in both tumor and normal mucosae networks, suggesting their significant influence on GC microbial ecology. Furthermore, we analyzed the expression of IATs (CXCL9, CXCL10, GZMA, GZMB, PRF1, CD8A, IFNG, TBX2, and TNF) and characterized IAT-relevant gastric microbiome signatures in GC patients. Our results showed that the expression of CXCL9, CXCL10, GZMA, GZMB, PRF1 and IFNG was significantly higher in tumor tissues than in adjacent normal tissues in GC patients. Notably, high expression of IATs in tumor tissues was associated with improved survival in GC patients and could serve as a powerful predictor for disease-free survival. Additionally, analysis of IAT levels and mucosal microbiota diversity revealed a correlation between higher IAT expression and increased microbiota richness and evenness in the IATs [high] group, suggesting potential interactions between mucosal microbiota and tumor immunopathology. Spearman correlation analysis showed positive associations between IAT expression and specific mucosal bacterial species. Notably, Akkermansia muciniphila demonstrated potential involvement in modulating GZMB expression in the GC mucosal microenvironment. These findings underscore the importance of mucosal microbiota alterations in GC and suggest potential therapeutic targets focusing on modulating the tumor microbiota for improved clinical outcomes. The detailed characterization of these elements has profound implications for both treatment and survival prediction in GC. We observed that microbial diversity and richness were significantly higher in GC tumor tissues compared to non-tumor tissues. These differences highlight the unique microbial landscape of GC tumors and suggest that the microbiome could influence tumor development and progression. Importantly, our study demonstrated that high expression levels of IATs in GC tumor tissues were associated with improved patient survival. This suggests that IATs not only reflect immune activation but also serve as valuable biomarkers for predicting disease-free survival. The potential of IATs as predictive markers underscores their utility in guiding therapeutic strategies and personalizing treatment approaches. Moreover, the correlation between higher IAT expression and increased microbiota richness and evenness suggests that a diverse and balanced microbiome may enhance immune responses and contribute to better clinical outcomes. These findings highlight the critical need to consider mucosal microbiota alterations in GC management. Targeting the tumor microbiota could emerge as a promising therapeutic strategy, potentially leading to more effective treatments and improved patient outcomes. Understanding and modulating the microbiome's role in GC opens new avenues for innovative therapeutic interventions and personalized medicine.},
}
@article {pmid39375832,
year = {2024},
author = {Obiol, A and Del Campo, J and de Vargas, C and Mahé, F and Massana, R},
title = {How marine are Marine Stramenopiles (MAST)? A cross-system evaluation.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {11},
pages = {},
pmid = {39375832},
issn = {1574-6941},
support = {PID2019-108457RB-I00//Spanish Ministry of Science and Innovation/ ; EUR2022-134047//GENEXLAB/ ; PID2022-137508NB-I00//EPIC/ ; CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; },
mesh = {*Phylogeny ; *Seawater/microbiology ; *Stramenopiles/genetics/classification ; Aquatic Organisms/genetics ; Biodiversity ; Ecosystem ; Sequence Analysis, DNA ; Genes, rRNA ; },
abstract = {Marine Stramenopiles (MAST) were first described two decades ago through ribosomal RNA gene (rRNA gene) sequences from marine surveys of microbial eukaryotes. MAST comprise several independent lineages at the base of the Stramenopiles. Despite their prevalence in the ocean, the majority of MAST diversity remains uncultured. Previous studies, mainly in marine environments, have explored MAST's cell morphology, distribution, trophic strategies, and genomics using culturing-independent methods. In comparison, less is known about their presence outside marine habitats. Here, we analyse the extensive EukBank dataset to assess the extent to which MAST can be considered marine protists. Additionally, by incorporating newly available rRNA gene sequences, we update Stramenopiles phylogeny, identifying three novel MAST lineages. Our results indicate that MAST are primarily marine with notable exceptions within MAST-2 and MAST-12, where certain subclades are prevalent in freshwater and soil habitats. In the marine water column, only a few MAST species, particularly within clades -1, -3, -4, and -7, dominate and exhibit clear latitudinal distribution patterns. Overall, the massive sequencing dataset analysed in our study confirms and partially expands the previously described diversity of MASTs groups and underscores the predominantly marine nature of most of these uncultured lineages.},
}
@article {pmid39366327,
year = {2024},
author = {Xu, J and Li, X and Xi, C and Weir, MH},
title = {Development of a machine learning model to support low cost real-time Legionella monitoring in premise plumbing systems.},
journal = {Water research},
volume = {267},
number = {},
pages = {122510},
doi = {10.1016/j.watres.2024.122510},
pmid = {39366327},
issn = {1879-2448},
abstract = {Legionella pneumophila (L. pneumophila) is a pathogenic bacterium primarily known for causing Legionnaires' Disease which is known for high mortality rates, particularly in the elderly. With caseloads continuing to increase, further research is needed to improve our understanding of optimized sampling schema and safe limits of L. pneumophila, in part to target improved treatment options and realistic population-level risk modeling. Particularly in healthcare and other high-risk locations these become crucial and time sensitive needs. Therefore, we conceptualized this research as a means of incorporating easily measured physiochemical water quality parameters and generalization of the unique ecology of building water systems to build a computational model that can allow for more rapid and accurate decision making. This research uses the specific machine learning (ML) method called statistical learning theory to incorporate concentration of host cells, such as native amoeba, and physiochemical water quality parameters to estimate the probability of observing ranges of Legionella gene copy concentrations. Using data from previously published research on Legionella prevalence in a large building, our ML method trains the model on the relative impacts of physiochemical parameters on likely amoeba host cell occurrences. The model is expanded to estimate host cell concentrations using correlations and regressions operated through LASSO algorithms. After categorization variables from these results are then used to inform a logistic regression to provide an estimate of the probability of Legionella gene copy concentration ranges. In summary, conventional results generated by logistic regression and multiple linear regression quantified the associations among ecological conditions in the water and ability to predict a likely range of Legionella concentration in a management focused way. Further, two ML methods, PCA and LASSO, demonstrated feasibility in accurate real-time monitoring of Legionella through physiochemical indicators as evidenced with good accuracy of predictions based for validation results. Furthermore results demonstrate the vital need to account for the impact of water quality on building on host cells, and via their quantified water microbial ecology, not just Legionella concentrations.},
}
@article {pmid39365014,
year = {2024},
author = {Arnold, ND and Paper, M and Fuchs, T and Ahmad, N and Jung, P and Lakatos, M and Rodewald, K and Rieger, B and Qoura, F and Kandawa-Schulz, M and Mehlmer, N and Brück, TB},
title = {High-quality genome of a novel Thermosynechococcaceae species from Namibia and characterization of its protein expression patterns at elevated temperatures.},
journal = {MicrobiologyOpen},
volume = {13},
number = {5},
pages = {e70000},
pmid = {39365014},
issn = {2045-8827},
support = {031B0838B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031A305A//Bundesministerium f&#xfc;r Wirtschaft und Energie/ ; //Bayerisches Staatsministerium f&#xfc;r Umwelt und Verbraucherschutz/ ; },
mesh = {Namibia ; *Cyanobacteria/genetics/classification/metabolism ; *Genome, Bacterial ; *Phylogeny ; *Hot Springs/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/genetics/metabolism ; Hot Temperature ; Sequence Analysis, DNA ; Proteome/analysis ; DNA, Bacterial/genetics ; },
abstract = {Thermophilic cyanobacteria thrive in extreme environments, making their thermoresistant enzymes valuable for industrial applications. Common habitats include hot springs, which act as evolutionary accelerators for speciation due to geographical isolation. The family Thermosynechococcaceae comprises thermophilic cyanobacteria known for their ability to thrive in high-temperature environments. These bacteria are notable for their photosynthetic capabilities, significantly contributing to primary production in extreme habitats. Members of Thermosynechococcaceae exhibit unique adaptations that allow them to perform photosynthesis efficiently at elevated temperatures, making them subjects of interest for studies on microbial ecology, evolution, and potential biotechnological applications. In this study, the genome of a thermophilic cyanobacterium, isolated from a hot spring near Okahandja in Namibia, was sequenced using a PacBio Sequel IIe long-read platform. Cultivations were performed at elevated temperatures of 40, 50, and 55°C, followed by proteome analyses based on the annotated genome. Phylogenetic investigations, informed by the 16S rRNA gene and aligned nucleotide identity (ANI), suggest that the novel cyanobacterium is a member of the family Thermosynechococcaceae. Furthermore, the new species was assigned to a separate branch, potentially representing a novel genus. Whole-genome alignments supported this finding, revealing few conserved regions and multiple genetic rearrangement events. Additionally, 129 proteins were identified as differentially expressed in a temperature-dependent manner. The results of this study broaden our understanding of cyanobacterial adaptation to extreme environments, providing a novel high-quality genome of Thermosynechococcaceae cyanobacterium sp. Okahandja and several promising candidate proteins for expression and characterization studies.},
}
@article {pmid39364584,
year = {2024},
author = {Buchner, D and Sinclair, JS and Ayasse, M and Beermann, AJ and Buse, J and Dziock, F and Enss, J and Frenzel, M and Hörren, T and Li, Y and Monaghan, MT and Morkel, C and Müller, J and Pauls, SU and Richter, R and Scharnweber, T and Sorg, M and Stoll, S and Twietmeyer, S and Weisser, WW and Wiggering, B and Wilmking, M and Zotz, G and Gessner, MO and Haase, P and Leese, F},
title = {Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14023},
doi = {10.1111/1755-0998.14023},
pmid = {39364584},
issn = {1755-0998},
support = {//Hessisches Landesamt f&#xfc;r Naturschutz, Umwelt und Geologie/ ; 871128//EU Horizon 2020 project eLTER PLUS/ ; //Landes-Offensive zur Entwicklung Wissenschaftlich-&#xf6;konomischer Exzellenz of the German federal State of Hesse/ ; },
abstract = {Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large-scale and long-term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.},
}
@article {pmid39361898,
year = {2024},
author = {Ramoneda, J and Hoffert, M and Stallard-Olivera, E and Casamayor, EO and Fierer, N},
title = {Leveraging genomic information to predict environmental preferences of bacteria.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39361898},
issn = {1751-7370},
support = {OPP 2133684//US National Science Foundation/ ; AEROSMIC PID2021-127701NB-I00//European Regional Development Fund/ ; //Spanish Agency of Research/ ; PID2023-151209NA-I00//Spanish Agency of Research/ ; 2022-BP-00050//Generalitat de Catalunya/ ; P2EZP3_199849/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Bacteria/genetics/classification ; Genome, Bacterial ; Genomics ; Environment ; Bacterial Physiological Phenomena ; },
abstract = {Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies constrain our ability to predict how assemblages will shift in response to global change factors, design effective probiotics, or guide cultivation efforts. We need innovative approaches that take advantage of expanding genome databases to accurately infer the environmental preferences of bacteria and validate the accuracy of these inferences. By doing so, we can broaden our quantitative understanding of the environmental preferences of the majority of bacterial taxa that remain uncharacterized. With this perspective, we highlight why it is important to infer environmental preferences from genomic information and discuss the range of potential strategies for doing so. In particular, we highlight concrete examples of how both cultivation-independent and cultivation-dependent approaches can be integrated with genomic data to develop predictive models. We also emphasize the limitations and pitfalls of these approaches and the specific knowledge gaps that need to be addressed to successfully expand our understanding of the environmental preferences of bacteria.},
}
@article {pmid39360821,
year = {2024},
author = {Han, S and Kim, S and Sedlacek, CJ and Farooq, A and Song, C and Lee, S and Liu, S and Brüggemann, N and Rohe, L and Kwon, M and Rhee, S-K and Jung, M-Y},
title = {Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.},
journal = {mBio},
volume = {15},
number = {11},
pages = {e0216924},
pmid = {39360821},
issn = {2150-7511},
support = {2019R1A6A1A10072987//National Research Foundation of Korea (NRF)/ ; 2021R1C1C1008303//National Research Foundation of Korea (NRF)/ ; 2022R1A4A503144711//National Research Foundation of Korea (NRF)/ ; ZK74//Austrian Science Fund (FWF)/ ; 2023RIS-009//Regional Innovation Strategy (RIS)/ ; },
mesh = {*Ammonia/metabolism ; *Oxidation-Reduction ; *Archaea/genetics/metabolism/classification ; *Nitrification ; *Phylogeny ; Genome, Archaeal ; Adaptation, Physiological ; Genomics ; },
abstract = {UNLABELLED: Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems.<br><br>IMPORTANCE: Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.},
}
@article {pmid39360459,
year = {2024},
author = {Li, X and Leizeaga, A and Rousk, J and Zhou, S and Hugelius, G and Manzoni, S},
title = {Recovery of Soil Microbial Metabolism After Rewetting Depends on Interacting Environmental Conditions and Changes in Functional Groups and Life History Strategies.},
journal = {Global change biology},
volume = {30},
number = {10},
pages = {e17522},
doi = {10.1111/gcb.17522},
pmid = {39360459},
issn = {1365-2486},
support = {101001608//H2020 European Research Council/ ; KAW 2017.0171//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; //Schmidt Sciences, LLC/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; *Fungi/physiology/metabolism ; *Climate Change ; Bacteria/metabolism/growth &amp; development ; Microbiota ; Hydrogen-Ion Concentration ; },
abstract = {Climate change is causing an intensification of soil drying and rewetting events, altering microbial functioning and potentially destabilizing soil organic carbon. After rewetting, changes in microbial community carbon use efficiency (CUE), investment in life history strategies, and fungal to bacterial dominance co-occur. Still, we have yet to generalize what drives these dynamic responses. Here, we collated 123 time series of microbial community growth (G, sum of fungal and bacterial growth, evaluated by leucine and acetate incorporation, respectively) and respiration (R) after rewetting and calculated CUE = G/(G + R). First, we characterized CUE recovery by two metrics: maximum CUE and time to maximum CUE. Second, we translated microbial growth and respiration data into microbial investments in life history strategies (high yield (Y), resource acquisition (A), and stress tolerance (S)). Third, we characterized the temporal change in fungal to bacterial dominance. Finally, the metrics describing the CUE recovery, investment in life history strategies, and fungal to bacterial dominance after rewetting were explained by environmental factors and microbial properties. CUE increased after rewetting as fungal dominance declined, but the maximum CUE was explained by the CUE under moist conditions, rather than specific environmental factors. In contrast, higher soil pH and carbon availability accelerated the decline of microbial investment in stress tolerance and fungal dominance. We conclude that microbial CUE recovery is mostly driven by the shifting microbial community composition and the metabolic capacity of the community, whereas changes in microbial investment in life history strategies and fungal versus bacterial dominance depend on soil pH and carbon availability.},
}
@article {pmid39360321,
year = {2024},
author = {MacGregor, H and Fukai, I and Ash, K and Arkin, AP and Hazen, TC},
title = {Potential applications of microbial genomics in nuclear non-proliferation.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1410820},
pmid = {39360321},
issn = {1664-302X},
abstract = {As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.},
}
@article {pmid39359935,
year = {2024},
author = {Li, Y and Li, Z and Zheng, S and Xu, X},
title = {Probiotics in the management of radiation-induced oral mucositis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1477143},
pmid = {39359935},
issn = {2235-2988},
mesh = {*Probiotics/therapeutic use ; Humans ; *Stomatitis/etiology/microbiology/therapy/prevention &amp; control ; *Radiation Injuries/therapy ; *Dysbiosis ; Microbiota ; Head and Neck Neoplasms/radiotherapy ; Radiotherapy/adverse effects ; Mouth/microbiology ; Quality of Life ; },
abstract = {Oral mucositis is a common and debilitating oral complication in head and neck cancer patients undergoing radiotherapy, resulting in diminished quality of life and potential treatment disruptions. Oral microbiota has long been recognized as a contributing factor in the initiation and progression of radiation-induced oral mucositis (RIOM). Numerous studies have indicated that the radiation-induced oral microbial dysbiosis promotes the occurrence and severity of oral mucositis. Therefore, approaches that modulate oral microbial ecology are promising for the management of RIOM. Probiotics as a relatively predicable and safe measure that modulates microecology have garnered significant interest. In this review, we discussed the correlation between RIOM and oral microbiota, with a particular focus on the efficacy of probiotics in the control of RIOM, in order to provide novel paradigm for the management of this disease.},
}
@article {pmid39358950,
year = {2024},
author = {Zhang, J and Qin, L and Chang, Y and He, Y and Zhao, W and Zhao, Y and Ding, Y and Gao, J and Zhao, X},
title = {One-Pot Assay for Rapid Detection of Stenotrophomonas maltophilia by RPA-CRISPR/Cas12a.},
journal = {ACS synthetic biology},
volume = {13},
number = {10},
pages = {3400-3412},
doi = {10.1021/acssynbio.4c00481},
pmid = {39358950},
issn = {2161-5063},
mesh = {*Stenotrophomonas maltophilia/genetics ; *CRISPR-Cas Systems/genetics ; Nucleic Acid Amplification Techniques/methods ; Recombinases/metabolism/genetics ; DNA, Bacterial/genetics ; CRISPR-Associated Proteins/genetics ; Endodeoxyribonucleases/genetics ; Bacterial Proteins ; },
abstract = {Stenotrophomonas maltophilia (S. maltophilia, SMA) is a common opportunistic pathogen that poses a serious threat to the food industry and human health. Traditional detection methods for SMA are time-consuming, have low detection rates, require complex and expensive equipment and professional technical personnel for operation, and are unsuitable for on-site detection. Therefore, establishing an efficient on-site detection method has great significance in formulating appropriate treatment strategies and ensuring food safety. In the present study, a rapid one-pot detection method was established for SMA using a combination of Recombinase Polymerase Amplification (RPA) and CRISPR/Cas12a, referred to as ORCas12a-SMA (one-pot RPA-CRISPR/Cas12a platform). In the ORCas12a-SMA detection method, all components were added into a single tube simultaneously to achieve one-pot detection and address the problems of nucleic acid cross-contamination and reduced sensitivity caused by frequent cap opening during stepwise detection. The ORCas12a-SMA method could detect at least 3 × 10° copies·μL[-1] of SMA genomic DNA within 30 min at 37 °C. Additionally, this method exhibited sensitivity compared to the typical two-step RPA-CRISPR/Cas12a method. Overall, the ORCas12a-SMA detection offered the advantages of rapidity, simplicity, high sensitivity and specificity, and decreased need for complex large-scale instrumentation. This assay is the first application of the one-pot platform based on the combination of RPA and CRISPR/Cas12a in SMA detection and is highly suitable for point-of-care testing. It helps reduce losses in the food industry and provides assistance in formulating timely and appropriate antimicrobial treatment plans.},
}
@article {pmid39358586,
year = {2024},
author = {de Lorenzo, V and Baquero, F and Aguilar, A},
title = {Carlos Asensio and the dawn of molecular microbial ecology.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39358586},
issn = {1618-1905},
support = {CL6-2021-UE 101060625//Horizon 2020 Framework Programme/ ; Y2020/TCS- 6555//Comunidad de Madrid/ ; },
abstract = {At near 50 years of the discovery of microcins, this article highlights the pivotal-but under-recognised-influence of Spanish biochemist Carlos Asensio (1925-1982) in contemporary microbiology, featuring the epistemological, sociological, and cultural impact of his scientific achievements. At a time when the intestinal microbiome is central to current biomedical research, it is due to emphasise his role in the establishment of new scientific fields that are now considered fundamental. Despite his premature death at the peak of his conceptual and experimental creativity, many of his ideas about microbial communication in complex communities inspired a generation of researchers and opened new topics reach to this day. Asensio was also a trailblazer in Spain, advocating for fundamental research within the socio-economic context of his time. He foresaw the shift towards what is now termed the knowledge-based bioeconomy, recognised the need for multidisciplinary research teams, and advocated integration science into societal and political agendas. These facets became evident during his research on microcins, low molecular weight bioactive compounds produced by enterobacteria. These molecules were hypothesised as mediators of microbial interactions in the human gut and were considered potential new antibiotics and even antitumoral agents. His research mobilised young talent and attracted unprecedented resources in Spain during the late 1970s-early 1980s. It underscored the medical value of microbial ecology and exemplified the benefits of collaboration between academia and industry. Asensio played a pivotal role in the emergence of molecular microbial ecology as a research discipline and its foundational and applied significance in biotechnology.},
}
@article {pmid39358432,
year = {2024},
author = {Zhi, W and Li, A and Wang, Q and Yuan, X and Qing, J and Zhang, C and Wang, Y and Li, Y},
title = {Safety and efficacy assessment of fecal microbiota transplantation as an adjunctive treatment for IgA nephropathy: an exploratory clinical trial.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22935},
pmid = {39358432},
issn = {2045-2322},
support = {82170716//National Science Foundation of China/ ; },
mesh = {Humans ; *Glomerulonephritis, IGA/therapy ; Male ; Female ; Adult ; *Fecal Microbiota Transplantation/methods/adverse effects ; *Gastrointestinal Microbiome ; Middle Aged ; Treatment Outcome ; Cytokines/blood/metabolism ; },
abstract = {To assess the safety and efficacy of fecal microbiota transplantation (FMT) as an adjunctive therapeutic intervention for IgA nephropathy (IgAN). Fifteen patients with IgA nephropathy were recruited based on inclusion and exclusion criteria and underwent FMT using enteric microbial capsules. Clinical indicators, intestinal microbiota and metabolomic profiles, as well as changes in serum immune cells and cytokines, were monitored before and after FMT. No severe adverse reactions were observed in the subjects. After FMT, there was a reduction in the 24-h urinary protein quantification in subjects. The relative abundances of Phocaeicola_vulgatus, Bacteroides_uniformis, Prevotella_copri, Phocaeicola_dorei, Bacteroides_ovatus, Bacteroides_xylanisolvens, Parabacteroides _distasonis, Bifidobacterium_pseudocatenulatum, Bacteroides_sp._HF-162, and Bifidobacterium_longum changed after FMT. In terms of intestinal metabolites, the levels of acylcarnitine18:0 (ACar.18:0), cotinine, N-arachidonoyl-L-serine, phosphatidylcholine (PC. (18:3e/22:6)), serotonin, and fumagillin showed significant changes. Flow cytometry analysis showed the absolute count of plasma B cells decreased in subjects, and this change correlated with alterations in the intestinal microbiota and metabolites. This study preliminarily evaluates the safety and efficacy of FMT in patients with IgAN. No significant adverse reactions were observed, and the administration of FMT alongside ACEI/ARB therapy was effective in reducing urinary protein levels in patients with IgAN, a process that may be associated with B-cell immunity.},
}
@article {pmid39357457,
year = {2024},
author = {Olavarria, K and Sousa, DZ},
title = {Thermodynamic tools for more efficient biotechnological processes: an example in poly-(3-hydroxybutyrate) production from carbon monoxide.},
journal = {Current opinion in biotechnology},
volume = {90},
number = {},
pages = {103212},
doi = {10.1016/j.copbio.2024.103212},
pmid = {39357457},
issn = {1879-0429},
abstract = {Modern biotechnology requires the integration of several disciplines, with thermodynamics being a crucial one. Experimental approaches frequently used in biotechnology, such as rewiring of metabolic networks or culturing of micro-organisms in engineered environments, can benefit from the application of thermodynamic tools. In this paper, we provide an overview of several thermodynamic tools that are useful for the design and optimization of biotechnological processes, and we demonstrate their potential application in the production of poly-(3-hydroxybutyrate) (PHB) from carbon monoxide (CO). We discuss how these tools can aid in the design of metabolic engineering strategies, the calculation of expected yields, the assessment of the thermodynamic feasibility of the targeted conversions, the identification of potential thermodynamic bottlenecks, and the selection of genetic engineering targets. Although we illustrate these tools using the specific example of PHB production from CO, they can be applied to other substrates and products.},
}
@article {pmid39357161,
year = {2024},
author = {Wan, W and Grossart, HP and Zhang, W and Xiong, X and Yuan, W and Liu, W and Yang, Y},
title = {Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria.},
journal = {Water research},
volume = {267},
number = {},
pages = {122516},
doi = {10.1016/j.watres.2024.122516},
pmid = {39357161},
issn = {1879-2448},
abstract = {Elucidating the influences of ecological restoration measure of lakeshore vegetation removal on water quality and biological community is an important but underestimated subject. We adopted molecular and statistical tools to estimate ecological restoration performance in a plateau lake receiving vegetation removal and simultaneously investigated variabilities of bacterial communities in water and sediment. Significant decreases in lake trophic level and algal bloom degree followed notable decreases in water total nitrogen and total phosphorus after vegetation removal. Non-significant changes in sediment nutrients accompanied remarkable variabilities of abundance and composition of nutrient-cycling functional genes (NCFGs) of sediment bacteria. Taxonomic and phylogenetic α-diversities, functional redundancies, and dispersal potentials of bacteria in water and sediment decreased after vegetation removal, and community successions of water and sediment bacteria were separately significant and non-significant. There were opposite changes in ecological attributes of bacteria in water and sediment in response to vegetation removal, including niche breadth, species replacement, richness difference, community complexity, and community stability. Species replacement rather than richness difference affected more on taxonomic β-diversities of bacteria in water and sediment before and after vegetation removal, and determinism rather than stochasticity dominated bacterial community assemblage. Our results highlighted vegetation removal mitigated algal bloom and affected differently on landscapes of water and sediment bacteria. These findings point to dominant ecological mechanisms underlying landscape shifts in water and sediment bacteria in a disturbed lake receiving vegetation removal and have the potential to guide lake ecological restoration.},
}
@article {pmid39353102,
year = {2024},
author = {He, J and Castilla-Alcantara, JC and Ortega-Calvo, JJ and Harms, H and Wick, LY},
title = {DC Electric Fields Promote Biodegradation of Waterborne Naphthalene in Biofilter Systems.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {41},
pages = {18234-18243},
pmid = {39353102},
issn = {1520-5851},
mesh = {*Biodegradation, Environmental ; Filtration ; Electricity ; Water Pollutants, Chemical/metabolism ; Naphthalenes/metabolism ; },
abstract = {Biofiltration is a simple and low-cost method for the cleanup of contaminated water. However, the reduced availability of dissolved chemicals to surface-attached degrader bacteria may limit its efficient use at certain hydraulic loadings. When a direct current (DC) electric field is applied to an immersed packed bed, it invokes electrokinetic processes, such as electroosmotic water flow (EOF). EOF is a surface-charge-induced plug-flow-shaped movement of pore fluids. It acts at a nanometer distance above surfaces and allows the change of microscale pressure-driven flow profiles and, hence, the availability of dissolved contaminants to microbial degraders. In laboratory percolation columns, we assessed the effects of a weak DC electric field (E = 0.5 V·cm[-1]) on the biodegradation of waterborne naphthalene (NAH) by surface-attached Pseudomonas fluorescens LP6a. To vary NAH bioavailability, we used different NAH concentrations (C0 = 2.7, 5.1, or 7.8 × 10[-5] mol·L[-1]) and Darcy velocities typical for biofiltration (U¯ = 0.2-1.2 × 10[-4] m·s[-1]). In DC-free controls, we observed higher specific degradation rates (qc) at higher NAH concentrations. The qc depended on U¯, suggesting bioavailability restrictions depending on the hydraulic residence times. DC fields consistently increased qc and resulted in linearly increasing benefits up to 55% with rising hydraulic loadings relative to controls. We explain these biodegradation benefits by EOF-altered microscale flow profiles allowing for better NAH provision to bacteria attached to the collectors even though the EOF was calculated to be 100-800 times smaller than bulk water flow. Our data suggest that electrokinetic approaches may give rise to future technical applications that allow regulating biodegradation, for example, in response to fluctuating hydraulic loadings.},
}
@article {pmid39354222,
year = {2024},
author = {Suzuki, Y and Webb, SJ and Kouduka, M and Kobayashi, H and Castillo, J and Kallmeyer, J and Moganedi, K and Allwright, AJ and Klemd, R and Roelofse, F and Mapiloko, M and Hill, SJ and Ashwal, LD and Trumbull, RB},
title = {Subsurface Microbial Colonization at Mineral-Filled Veins in 2-Billion-Year-Old Mafic Rock from the Bushveld Igneous Complex, South Africa.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {116},
pmid = {39354222},
issn = {1432-184X},
support = {AB0502//Astrobiology Center Program of National Institutes of Natural Sciences (NINS)/ ; },
mesh = {South Africa ; *Bacteria/isolation &amp; purification/classification ; Geologic Sediments/microbiology ; Minerals/analysis/metabolism ; Clay/chemistry ; Soil Microbiology ; },
abstract = {Recent advances in subsurface microbiology have demonstrated the habitability of multi-million-year-old igneous rocks, despite the scarce energy supply from rock-water interactions. Given the minimal evolution coupled with exceedingly slow metabolic rates in subsurface ecosystems, spatiotemporally stable igneous rocks can sustain microbes over geological time scales. This study investigated a 2-billion-year-old mafic rock in the Bushveld Igneous Complex, South Africa, where ultradeep drilling is being executed by the International Continental Scientific Drilling Program (ICDP). New procedures were successfully developed to simultaneously detect indigenous and contaminant microbial cells in a drill core sample. Precision rock sectioning coupled with infrared, fluorescence, and electron microscopy imaging of the rock section with submicron resolution revealed microbial colonization in veins filled with clay minerals. The entry and exit of microbial cells in the veins are severely limited by tight packing with clay minerals, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Igneous Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.},
}
@article {pmid39354152,
year = {2024},
author = {Freire-Zapata, V and Holland-Moritz, H and Cronin, DR and Aroney, S and Smith, DA and Wilson, RM and Ernakovich, JG and Woodcroft, BJ and Bagby, SC and , and , and Rich, VI and Sullivan, MB and Stegen, JC and Tfaily, MM},
title = {Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.},
journal = {Nature microbiology},
volume = {9},
number = {11},
pages = {2892-2908},
pmid = {39354152},
issn = {2058-5276},
support = {DE-SC0021349//DOE | SC | Biological and Environmental Research (BER)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; },
mesh = {*Permafrost/microbiology ; *Greenhouse Gases/metabolism/analysis ; *Microbiota ; *Methane/metabolism ; *Metagenomics ; *Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; Sweden ; Ecosystem ; Soil Microbiology ; },
abstract = {Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO2 and CH4 porewater variations. Our study showcases insights gained by using feature-level data and microorganism-metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.},
}
@article {pmid39350412,
year = {2024},
author = {Khan, A and Abass, S and Nizami, SAI and Shariq, M and Zahiruddin, S and Parveen, B and Parveen, R},
title = {The Gut Health Revolution: Herbs and Dietary Phytochemicals in Balancing Gut Microbiota for Optimal Human Health.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010313921240923125946},
pmid = {39350412},
issn = {1873-4316},
abstract = {The gut microbiota is a varied population of microorganisms that live in the human gastrointestinal system. Emerging research emphasizes the importance of this microbial ecology in general health and its influence on a variety of disorders. The review explores the synergy between herbal treatment and traditional medicine, emphasizing their cultural significance and therapeutic benefits. It delves into the intricate relationship between herbal remedies, traditional healing practices, and their sustained usage over centuries. The review highlights the pivotal role of the gut microbiota in herbal medicine, elucidating how treatments influence the gastrointestinal microorganisms, impacting overall health. Dietary phytochemicals are underscored for their significance in herbal medicine and nutritional well-being, along with the interdependence of plant extracts and botanicals. The investigation explores the molecular connections between phytoconstituents and gut microbiota, aiming to deepen the understanding of herbal medicine's tailored approach to specific health challenges. The summary concludes by emphasizing herbal treatments' unique ability to regulate gut flora, contributing to overall gastrointestinal wellbeing. In closing, the review provides a concise overview, serving as a valuable resource for integrative medicine research, with recommendations for future exploration of herbal medicine's potential in healthcare.},
}
@article {pmid39349736,
year = {2024},
author = {Karačić, S and Suarez, C and Hagelia, P and Persson, F and Modin, O and Martins, PD and Wilén, BM},
title = {Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22742},
pmid = {39349736},
issn = {2045-2322},
mesh = {*Oxidation-Reduction ; *Manganese/metabolism ; *Iron/metabolism ; *Construction Materials/microbiology ; Corrosion ; *Biofilms/growth &amp; development ; Nitrogen/metabolism ; Sulfur/metabolism ; Steel/chemistry ; Bacteria/metabolism/genetics ; Hydrogen-Ion Concentration ; },
abstract = {The deterioration of fibre-reinforced sprayed concrete was studied in the Oslofjord subsea tunnel (Norway). At sites with intrusion of saline groundwater resulting in biofilm growth, the concrete exhibited significant concrete deterioration and steel fibre corrosion. Using amplicon sequencing and shotgun metagenomics, the microbial taxa and surveyed potential microbial mechanisms of concrete degradation at two sites over five years were identified. The concrete beneath the biofilm was investigated with polarised light microscopy, scanning electron microscopy and X-ray diffraction. The oxic environment in the tunnel favoured aerobic oxidation processes in nitrogen, sulfur and metal biogeochemical cycling as evidenced by large abundances of metagenome-assembled genomes (MAGs) with potential for oxidation of nitrogen, sulfur, manganese and iron, observed mild acidification of the concrete, and the presence of manganese- and iron oxides. These results suggest that autotrophic microbial populations involved in the cycling of several elements contributed to the corrosion of steel fibres and acidification causing concrete deterioration.},
}
@article {pmid39349195,
year = {2024},
author = {Cheng, X and Zhao, R and Bodelier, PLE and Song, Y and Yang, K and Tuovinen, OH and Wang, H},
title = {Differential response of subterranean microbiome to exogenous organic matter input in a cave ecosystem.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176584},
doi = {10.1016/j.scitotenv.2024.176584},
pmid = {39349195},
issn = {1879-1026},
mesh = {*Microbiota ; *Caves/microbiology ; Soil Microbiology ; Bacteria/metabolism ; Fungi ; Ecosystem ; Climate Change ; },
abstract = {As a recurrent climatic phenomenon in the context of climate change, extreme rainstorms induce vertical translocation of organic matter and increase moisture content in terrestrial ecosystems. However, it remains unclear whether heavy rainstorms can impact microbial communities in the deep biosphere by modulating organic matter input. In this study, we present findings on the different responses of bacterial and fungal communities in a subsurface cave to rainstorms and moisture variations through field surveys and microcosm experiments. During periods of rainstorms, the influx of dissolved organic matter (DOM) from soil overlying the cave into cave sediments significantly enhanced the correlation between core bacteria and environmental factors, particularly fluorescence spectral indices. The resource utilization of core bacteria was diminished, while the functional diversity of core fungi remained relatively unaltered. We also performed simulated experiments with restricted external DOM inputs, in which DOM content was observed to decrease and microbial diversity increase in response to artificially increased moisture content (MC). The niche breadth of core bacteria decreased and became more closely associated with DOM as the MC increased, while the niche breadth of core fungi remained predominantly unchanged. Compared to fungi, cave bacteria exhibited higher sensitivity towards variations in DOM. The core microbiome can efficiently utilize the available organic matter and participate in nitrogen- and sulfur-related metabolic processes. The study systematically revealed distinct microbial responses to rainstorm events, thereby providing valuable insights for future investigations into energy utilization within deep biospheres.},
}
@article {pmid39349071,
year = {2024},
author = {Toporowska, M and Żebracki, K and Mazur, A and Mazur-Marzec, H and Šulčius, S and Alzbutas, G and Lukashevich, V and Dziga, D and Mieczan, T},
title = {Biodegradation of microcystins by microbiota of duckweed Spirodelapolyrhiza.},
journal = {Chemosphere},
volume = {366},
number = {},
pages = {143436},
doi = {10.1016/j.chemosphere.2024.143436},
pmid = {39349071},
issn = {1879-1298},
mesh = {*Microcystins/metabolism ; *Biodegradation, Environmental ; *Microbiota ; *Araceae/metabolism ; Tandem Mass Spectrometry ; Cyanobacteria/metabolism/genetics ; Bacteria/metabolism/genetics/classification ; },
abstract = {Cyanobacteria-produced allelochemicals, including hepatotoxic microcystins (MCs), exert an inhibitory effect on macrophyte growth. However, the role of macrophyte-associated bacteria and algae (macrophyte microbiota) in mitigating these immediate negative effects of cyanotoxins remains poorly understood. In this paper, we analyzed the biodegradation of microcystin-RR, MC-LR, and MC-LF by microbiota of the macrophyte Spirodela polyrhiza. The biodegradation of two MC variants was observed and LC-MS/MS analysis allowed identifying the degradation products of MC-RR (m/z 1011, 984, 969, 877, 862, 820, and 615) and MC-LR (m/z 968 and 953), including eight previously unreported products. No degradation products of MC-LF were detected, suggesting its stability and resistance under experimental conditions. NGS-based profiling of microbial consortia revealed no major differences in bacterial community composition across experimental treatments. Taxa previously reported as capable of MC degradation have been found in S. polyrhiza microbiota. Furthermore, the presence of genes encoding putative microcystinase homologues and the formation of new linear intermediates suggest a biochemical pathway that is similar, but not identical to previously reported. The ability of aquatic plant microbiota to biodegrade MCs holds environmental significance, and further studies in this field are required.},
}
@article {pmid39346682,
year = {2024},
author = {Child, HT and Wierzbicki, L and Joslin, GR and Tennant, RK},
title = {Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.},
journal = {Access microbiology},
volume = {6},
number = {9},
pages = {},
pmid = {39346682},
issn = {2516-8290},
abstract = {Metagenomics has been transformative in our understanding of the diversity and function of soil microbial communities. Applying long read sequencing to whole genome shotgun metagenomics has the potential to revolutionise soil microbial ecology through improved taxonomic classification, functional characterisation and metagenome assembly. However, optimisation of robust methods for long read metagenomics of environmental samples remains undeveloped. In this study, Oxford Nanopore sequencing using samples from five commercially available soil DNA extraction kits was compared across four soil types, in order to optimise read length and reproducibility for comparative long read soil metagenomics. Average extracted DNA lengths varied considerably between kits, but longer DNA fragments did not translate consistently into read lengths. Highly variable decreases in the length of resulting reads from some kits were associated with poor classification rate and low reproducibility in microbial communities identified between technical repeats. Replicate samples from other kits showed more consistent conversion of extracted DNA fragment size into read length and resulted in more congruous microbial community representation. Furthermore, extraction kits showed significant differences in the community representation and structure they identified across all soil types. Overall, the QIAGEN DNeasy PowerSoil Pro Kit displayed the best suitability for reproducible long-read WGS metagenomic sequencing, although further optimisation of DNA purification and library preparation may enable translation of higher molecular weight DNA from other kits into longer read lengths. These findings provide a novel insight into the importance of optimising DNA extraction for achieving replicable results from long read metagenomic sequencing of environmental samples.},
}
@article {pmid39346007,
year = {2024},
author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ},
title = {Quantifying microbial DNA in metagenomes improves microbial trait estimation.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae111},
pmid = {39346007},
issn = {2730-6151},
abstract = {Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.},
}
@article {pmid39340684,
year = {2024},
author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Richard, JI and Perveen, K and Bukhari, NA and Glick, BR and Sayyed, RZ and Mastinu, A},
title = {Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {120},
pmid = {39340684},
issn = {1432-184X},
mesh = {Animals ; *Solanum lycopersicum/microbiology/parasitology ; *Soil Microbiology ; *Rhizosphere ; *Bacillus/genetics/physiology ; *Plant Roots/microbiology/parasitology ; *Pest Control, Biological ; Plant Diseases/parasitology/prevention &amp; control/microbiology ; Trichoderma/physiology/genetics ; Tylenchoidea/physiology ; Microbiota ; Antinematodal Agents/pharmacology ; Biological Control Agents/pharmacology ; Bacteria/genetics/classification ; },
abstract = {The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.},
}
@article {pmid39340560,
year = {2024},
author = {Charalampous, G and Kormas, KA and Antoniou, E and Kalogerakis, N and Gontikaki, E},
title = {Distinct Communities of Bacteria and Unicellular Eukaryotes in the Different Water Masses of Cretan Passage Water Column (Eastern Mediterranean Sea).},
journal = {Current microbiology},
volume = {81},
number = {11},
pages = {381},
pmid = {39340560},
issn = {1432-0991},
support = {1874//Hellenic Foundation for Research and Innovation/ ; 1510//Hellenic Foundation for Research and Innovation/ ; },
mesh = {Mediterranean Sea ; *Bacteria/classification/genetics/isolation &amp; purification ; *Eukaryota/classification/genetics/isolation &amp; purification ; *Seawater/microbiology ; *Microbiota ; *RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Phylogeny ; Ecosystem ; },
abstract = {Elucidating marine microbiota diversity and dynamics holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation. This work aims to contribute in the understanding of microbial ecology and networking in one of the world's most understudied marine regions, the Eastern Mediterranean Sea. High-throughput 16S and 18S rRNA gene sequencing analysis was applied to study the diversity of bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage during two seasonally-different sampling expeditions. We assumed that microbial associations differ between the surface and deepwater masses and created co-occurrence networks to evaluate this hypothesis. Our results unveiled vertical variations in both bacterial and unicellular eukaryotic diversity with species fluctuations indicative of seasonality being recorded in the surface water mass. Heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling were enriched in the deepest water layers. Moreover, surface waters presented a higher number of microbial associations indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean. Overall, our data provide insight in a heavily stressed, yet underexplored, marine area that requires further research to unravel the ecological roles of marine microbes. To our knowledge, this is the first study that combines molecular biology tools to provide data on both planktic prokaryotes and unicellular eukaryotes across the different water masses in this marine region of the Eastern Mediterranean basin.},
}
@article {pmid39340556,
year = {2024},
author = {Fernandez de Landa, G and Alberoni, D and Braglia, C and Baffoni, L and Fernandez de Landa, M and Revainera, PD and Quintana, S and Zumpano, F and Maggi, MD and Di Gioia, D},
title = {The Gut Microbiome of Two Wild Bumble Bee Species Native of South America: Bombus pauloensis and Bombus bellicosus.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {121},
pmid = {39340556},
issn = {1432-184X},
support = {777760//European Commission/ ; 777760//European Commission/ ; 777760//European Commission/ ; 777760//European Commission/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Nosema/physiology/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; South America ; },
abstract = {South America is populated by a wide range of bumble bee species that represent an important source of biodiversity, supporting pollination services in natural and agricultural ecosystems. These pollinators provide unique specific microbial niches, populated by a wide number of microorganisms such as symbionts, environmental opportunistic bacteria, and pathogens. Recently, it was demonstrated how microbial populations are shaped by trophic resources and environmental conditions but also by anthropogenic pressure, which strongly affects microbes' functionality. This study is focused on the impact of different land uses (natural reserve, agroecosystem, and suburban) on the gut microbiome composition of two South American bumble bees, Bombus pauloensis and Bombus bellicosus. Gut microbial DNA extracted from collected bumble bees was sequenced on the Illumina MiSeq platform and correlated with land use. Nosema ceranae load was analyzed with qPCR and correlated with microbiome data. Significant differences in gut microbiome composition between the two wild bumble bee species were highlighted, with notable variations in α- and β-diversity across study sites. Bombus bellicosus showed a high abundance of Pseudomonas, a genus that includes environmental saprobes, and was found to be the second major taxa populating the gut microbiome, probably indicating the vulnerability of this host to environmental pollution. Pathogen analysis unveils a high prevalence of N. ceranae, with B. bellicosus showing higher susceptibility. Finally, Gilliamella exhibited a negative correlation with N. ceranae, suggesting a potential protective role of this commensal taxon. Our findings underscore the importance of considering microbial dynamics in pollinator conservation strategies, highlighting potential interactions between gut bacteria and pathogens in shaping bumble bee health.},
}
@article {pmid39340548,
year = {2024},
author = {Radouane, N and Errafii, K and Mouhib, S and Mhand, KA and Legeay, J and Hijri, M},
title = {Potential Plant-To-Plant Transmission: Shared Endophytic Bacterial Community Between Ziziphus lotus and Its Parasite Cuscuta epithymum.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {119},
pmid = {39340548},
issn = {1432-184X},
support = {Projects AS-77 and AS-85//OCP Group/ ; },
mesh = {*Cuscuta/physiology/microbiology/genetics ; *Ziziphus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Endophytes/genetics/physiology/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; Host-Parasite Interactions ; DNA, Bacterial/genetics ; },
abstract = {Microbiota associated with host-parasite relationships offer an opportunity to explore interactions among plants, parasites, and microbes, thereby contributing to the overall complexity of community structures. The dynamics of ecological interactions between parasitic plants and their hosts in arid environments remain largely understudied, especially in Africa. This study aimed to examine the bacterial communities of Cuscuta epithymum L. (clover dodder), an epiphytic parasitic plant, and its host, Ziziphus lotus L. (jujuba), in an arid environment. Our goal was to uncover the ecological complexities of microbial communities within the framework of plant-plant interactions. We conducted a comprehensive analysis of the bacterial composition and diversity within populations of the C. epithymum parasite, the infected- and non-infected jujuba host, and their interface at the shoots of the host. This involved amplicon sequencing, targeting the V5-V6 regions of the 16S rRNA gene. A total of 5680 amplicon sequence variants (ASVs) were identified, with Pseudomonadota, Bacillota, and Actinobacteriota being prevalent phyla. Among the bacterial communities, three genera were dominant: Cutibacterium, Staphylococcus, and Acinetobacter. Interestingly, analyses of alpha-diversity (p = 0.3 for Shannon index and p = 0.5 for Simplon index) and beta-diversity (PERMANOVA, with p-values of 0.6 and 0.3) revealed no significant differences between Cuscuta-infected and non-infected jujube shrubs, suggesting a shared shoot endophytic bacteriome. This finding advances our comprehension of microbial communities linked to plant-parasite interactions in the arid environments of Africa. Further research on various hosts is required to confirm plant-to-plant bacterial transmission through Cuscuta infection. Additionally, studies on functional diversity, cytology, ecophysiology and the mechanisms by which bacterial communities transferred between host and parasite are necessary.},
}
@article {pmid39338505,
year = {2024},
author = {Shah, H and Trivedi, M and Gurjar, T and Sahoo, DK and Jergens, AE and Yadav, VK and Patel, A and Pandya, P},
title = {Decoding the Gut Microbiome in Companion Animals: Impacts and Innovations.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
pmid = {39338505},
issn = {2076-2607},
abstract = {The changing notion of "companion animals" and their increasing global status as family members underscores the dynamic interaction between gut microbiota and host health. This review provides a comprehensive understanding of the intricate microbial ecology within companion animals required to maintain overall health and prevent disease. Exploration of specific diseases and syndromes linked to gut microbiome alterations (dysbiosis), such as inflammatory bowel disease, obesity, and neurological conditions like epilepsy, are highlighted. In addition, this review provides an analysis of the various factors that impact the abundance of the gut microbiome like age, breed, habitual diet, and microbe-targeted interventions, such as probiotics. Detection methods including PCR-based algorithms, fluorescence in situ hybridisation, and 16S rRNA gene sequencing are reviewed, along with their limitations and the need for future advancements. Prospects for longitudinal investigations, functional dynamics exploration, and accurate identification of microbial signatures associated with specific health problems offer promising directions for future research. In summary, it is an attempt to provide a deeper insight into the orchestration of multiple microbial species shaping the health of companion animals and possible species-specific differences.},
}
@article {pmid39338496,
year = {2024},
author = {Denux, M and Armenteros, M and Weber, L and Miller, CA and Sántha, K and Apprill, A},
title = {Coral Reef Water Microbial Communities of Jardines de la Reina, Cuba.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
pmid = {39338496},
issn = {2076-2607},
abstract = {Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean's 'Crown Jewel' reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms.},
}
@article {pmid39338466,
year = {2024},
author = {Lauzon, J and Caron, D and Lazar, CS},
title = {The Saint-Leonard Urban Glaciotectonic Cave Harbors Rich and Diverse Planktonic and Sedimentary Microbial Communities.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
pmid = {39338466},
issn = {2076-2607},
support = {RGPIN-2019-06670//Natural Sciences and Engineering Research Council/ ; },
abstract = {The terrestrial subsurface harbors unique microbial communities that play important biogeochemical roles and allow for studying a yet unknown fraction of the Earth's biodiversity. The Saint-Leonard cave in Montreal City (Canada) is of glaciotectonic origin. Its speleogenesis traces back to the withdrawal of the Laurentide Ice Sheet 13,000 years ago, during which the moving glacier dislocated the sedimentary rock layers. Our study is the first to investigate the microbial communities of the Saint-Leonard cave. By using amplicon sequencing, we analyzed the taxonomic diversity and composition of bacterial, archaeal and eukaryote communities living in the groundwater (0.1 µm- and 0.2 µm-filtered water), in the sediments and in surface soils. We identified a microbial biodiversity typical of cave ecosystems. Communities were mainly shaped by habitat type and harbored taxa associated with a wide variety of lifestyles and metabolic capacities. Although we found evidence of a geochemical connection between the above soils and the cave's galleries, our results suggest that the community assembly dynamics are driven by habitat selection rather than dispersal. Furthermore, we found that the cave's groundwater, in addition to being generally richer in microbial taxa than sediments, contained a considerable diversity of ultra-small bacteria and archaea.},
}
@article {pmid39338465,
year = {2024},
author = {Cruz, LG and Shen, FT and Chen, CP and Chen, WC},
title = {Dose Effect of Polyethylene Microplastics Derived from Commercial Resins on Soil Properties, Bacterial Communities, and Enzymatic Activity.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
pmid = {39338465},
issn = {2076-2607},
support = {MOST 110-2313-B-005-015-//National Science and Technology Council/ ; },
abstract = {Soils are the largest reservoir of microplastics (MPs) on earth. Since MPs can remain in soils for a very long time, their effects are magnified. In this study, different concentrations of polyethylene (PE) MPs derived from commercial resins (0%, 1%, 7%, and 14%, represented as MP_0, MP_1, MP_7, and MP_14) were added to soils to assess the changes in the soils' chemical properties, enzyme activities, and bacterial communities during a 70-day incubation period. The results show that PE MP treatments with low concentrations differed from other treatments in terms of exchangeable Ca and Mg, whereas at high concentrations, the pH and availability of phosphate ions differed. Fluorescein diacetate (FDA), acid phosphatase (ACP), and N-acetyl-β-d-glucosaminidase (NAG) enzyme activities exhibited a dose-related trend with the addition of the PE MPs; however, the average FDA and ACP activities were significantly affected only by MP_14. Changes in the microbial communities were observed at both the phylum and family levels with all PE MP treatments. It was revealed that even a low dosage of PE MPs in soils can affect the functional microbes, and a greater impact is observed on those that can survive in polluted environments with limited resources.},
}
@article {pmid39338425,
year = {2024},
author = {Lyu, G and Hu, J and Ma, J},
title = {Variation in Bacterial and Fungal Communities in Soils from Three Major Apple Pear (Pyrus bretschneideri Rehd.) Orchards.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
pmid = {39338425},
issn = {2076-2607},
support = {41571304//National Natural Science Foundation of China/ ; },
abstract = {Microbial communities are closely related to the overall health and quality of soil, but studies on microbial ecology in apple pear orchard soils are limited. In the current study, 28 soil samples were collected from three apple pear orchards, and the composition and structure of fungal and bacterial communities were investigated by high-throughput sequencing. The molecular ecological network showed that the keystone taxa of bacterial communities were Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Nitrospirae, and Chloroflexi, and the keystone taxon of fungal communities was Ascomycota. Mantel tests showed that soil texture and pH were important factors shaping soil bacterial and fungal communities, and soil water soluble organic carbon (WSOC) and nitrate nitrogen (NO3[-]-N) were also closely related to soil bacterial communities. Canonical correspondence analysis (CCA) and variation partition analysis (VPA) revealed that geographic distance, soil texture, pH, and other soil properties could explain 10.55%, 13.5%, and 19.03% of the overall variation in bacterial communities, and 11.61%, 13.03%, and 20.26% of the overall variation in fungal communities, respectively. The keystone taxa of bacterial and fungal communities in apple pear orchard soils and their strong correlation with soil properties could provide useful clues toward sustainable management of orchards.},
}
@article {pmid39338386,
year = {2024},
author = {Galinytė, D and Bernatoniene, J and Žilius, M and Rysevaitė-Kyguolienė, K and Savickas, A and Karosienė, J and Briedis, V and Pauža, DH and Savickienė, N},
title = {In Vitro Study of Cyano-Phycocyanin Release from Hydrogels and Ex Vivo Study of Skin Penetration.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {17},
number = {9},
pages = {},
pmid = {39338386},
issn = {1424-8247},
abstract = {BACKGROUND: This study explored the most suitable materials for incorporating cyano-phycocyanin (C-PC) into hydrogels, focusing on maintaining the C-PC's long-term structural integrity and stabilityNext, the release of C-PC from the hydrogels and its skin penetration were investigated.<br><br>METHODS: A series of 1% (w/w) C-PC hydrogels was prepared using various gelling agents and preservatives. Spectrophotometric measurements compared the amount of C-PC in the hydrogels to the initially added amount. After selecting the most suitable gelling agent and preservative, two C-PC hydrogels, with and without propylene glycol (PG) (Sigma-Aldrich, St. Louis, MO, USA), were produced for further testing. In vitro release studies utilized modified Franz-type diffusion cells, while ex vivo skin-permeation studies employed Bronaugh-type cells and human skin. Confocal laser scanning microscopy analyzed C-PC accumulation in the skin.<br><br>RESULTS: The findings demonstrated that sodium alginate (Sigma-Aldrich, St. Louis, MO, USA), hydroxyethyl cellulose (HEC) (Sigma-Aldrich, St. Louis, MO, USA), and Soligel[TM] (Givaudan, Vernier, Switzerland) are effective biopolymers for formulating hydrogels while maintaining C-PC stability. After 6 h, C-PC release from the hydrogel containing PG was approximately 10% or 728.07 (&#xb1;19.35) &#x3bc;g/cm[2], significantly higher than the nearly 7% or 531.44 (&#xb1;26.81) &#x3bc;g/cm[2] release from the hydrogel without PG (p < 0.05). The ex vivo qualitative skin-permeation study indicated that PG enhances C-PC penetration into the outermost skin layer.<br><br>CONCLUSION: PG's ability to enhance the release of C-PC from the hydrogel, coupled with its capacity to modify the skin barrier ex vivo, facilitates the penetration of C-PC into the stratum corneum.},
}
@article {pmid39335049,
year = {2024},
author = {Afonso, L and Grzegorczyk, KG and Salomão, JM and Basso, KR and Alves, LC and Silva, MCD and Chryssafidis, AL and Gionco-Cano, B and Yamada-Ogatta, SF and Andrade, G},
title = {Fluopsin C Promotes Biofilm Removal of XDR Acinetobacter baumannii and Presents an Additive Effect with Polymyxin B on Planktonic Cells.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {39335049},
issn = {2079-6382},
support = {439754/2018-6//National Council for Scientific and Technological Development/ ; 406016/2022-4//National Council for Scientific and Technological Development/ ; },
abstract = {Acinetobacter baumannii emerged as one of the most important pathogens for the development of new antimicrobials due to the worldwide detection of isolates resistant to all commercial antibiotics, especially in nosocomial infections. Biofilm formation enhances A. baumannii survival by impairing antimicrobial action, being an important target for new antimicrobials. Fluopsin C (FlpC) is an organocupric secondary metabolite with broad-spectrum antimicrobial activity. This study aimed to evaluate the antibiofilm activity of FlpC in established biofilms of extensively drug-resistant A. baumannii (XDRAb) and the effects of its combination with polymyxin B (PolB) on planktonic cells. XDRAb susceptibility profiles were determined by Vitek 2 Compact, disk diffusion, and broth microdilution. FlpC and PolB interaction was assessed using the microdilution checkerboard method and time-kill kinetics. Biofilms of XDRAb characterization and removal by FlpC exposure were assessed by biomass staining with crystal violet. Confocal Laser Scanning Microscopy was used to determine the temporal removal of the biofilms using DAPI, and cell viability using live/dead staining. The minimum inhibitory concentration (MIC) of FlpC on XDRAb was 3.5 µg mL[-1]. Combining FlpC + PolB culminated in an additive effect, increasing bacterial susceptibility to both antibiotics. FlpC-treated 24 h biofilms reached a major biomass removal of 92.40 ± 3.38% (isolate 230) using 7.0 µg mL[-1] FlpC. Biomass removal occurred significantly over time through the dispersion of the extracellular matrix and decreasing cell number and viability. This is the first report of FlpC's activity on XDRAb and the compound showed a promissory response on planktonic and sessile cells, making it a candidate for the development of a new antimicrobial product.},
}
@article {pmid39332295,
year = {2024},
author = {Tapia, N and Gallardo-Bustos, C and Rojas, C and Vargas, IT},
title = {Long-term evaluation of soil-based bioelectrochemical green roof systems for greywater treatment.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122643},
doi = {10.1016/j.jenvman.2024.122643},
pmid = {39332295},
issn = {1095-8630},
mesh = {*Soil/chemistry ; *Bioelectric Energy Sources ; Water Purification/methods ; Waste Disposal, Fluid/methods ; Biological Oxygen Demand Analysis ; },
abstract = {Water scarcity has generated the need to identify new sources. Due to its low organic contaminant load, greywater reuse has emerged as a potential alternative. Moreover, the search for decentralized treatment systems in urban areas has prompted research on using green roofs for greywater treatment. However, the performance of organic matter removal is limited by the type of substrate and height of the growing media. Bioelectrochemical systems (BESs) improve treatment performance by providing an additional electron acceptor (the electrode). In this study, nine reactors under three different conditions, i.e., open circuit (OC), microbial fuel cell (MFC), and microbial electrolysis cell (MEC), were built to evaluate the treatment of synthetic greywater in a substrate-growing medium composed of perlite and coconut fiber and operated in batch-cycle mode for 397 days. The results suggested that using BESs enables greywater treatment and the removal of pollutants to levels that allow their reuse for irrigation. Furthermore, electrical conductivity was reduced from 732.4 ± 41.2 μS/cm[2] in OC to 637.32 ± 22.73 μS/cm[2] and 543.15 ± 19.69 μS/cm[2] in MEC and MFC, respectively. The soluble chemical oxygen demand in the latter treatments reached 76% removal, compared to levels above the OC, which only reached approximately 67%. Microbial community analysis revealed differences, mainly in the cathodes, showing a higher development of Flavobacterium, Azospirillum, and Zoogloea in MFCs, which could explain the higher levels of organic matter removal in the other conditions, suggesting that the BES could produce an enrichment of beneficial bacterial groups for treatment. Therefore, implementing BESs in green roofs enables sustainable long-term greywater treatment.},
}
@article {pmid39331293,
year = {2024},
author = {Bianchelli, J and Sagua, MI and Quiroga, MP and Nuozzi, G and Fernández, J and Schiaffino, MR},
title = {Temporal dynamics of Legionella (Proteobacteria, Legionellaceae) in two Pampean shallow lakes from Argentina.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {49},
pages = {59058-59070},
pmid = {39331293},
issn = {1614-7499},
support = {PICT 0891-2017//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICTO 00006-2019//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; SIB 2053-2022//Universidad Nacional del Noroeste de la Provincia de Buenos Aires/ ; },
mesh = {Argentina ; *Lakes/microbiology ; *Legionella/genetics ; Water Microbiology ; Real-Time Polymerase Chain Reaction ; },
abstract = {Aquatic systems have traditionally played a key role in the development of human life, providing multiple ecosystem services to society and being a reservoir for a wide biodiversity of organisms. Among them, bacteria belonging to Legionella stand out, mainly because they are of great interest both in the field of microbial ecology and public health, since some of them turn out to be pathogenic for humans. The aim of this work was to study the monthly temporal dynamics of Legionella spp. and its relationship with the environmental variables measured in two Pampean shallow lakes (Gómez and Carpincho, Buenos Aires Province, Argentina). The analysis was carried out using a quantitative approach by real-time polymerase chain reaction (qPCR) and a non-quantitative approach using bacterial diversity data obtained by next-generation sequencing (NGS), using the Illumina MiSeq platform. Our results showed that the overall Legionella abundance was very high in the studied Pampean shallow lakes. Notably, fluctuations in dissolved organic carbon and temperature influenced the dynamics shifts in Legionella abundances. Correlation analyses between Legionella reads from NGS and copy numbers obtained through qPCR revealed positive relationships, unveiling distinctions attributable to the diverse sequence processing algorithms employed in the analysis of NGS data.},
}
@article {pmid39330355,
year = {2024},
author = {Abbà, S and Valentini, B and Stefanini, I},
title = {Fungal Identifier (FId): An Updated Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach to Ease Ascomycetous Yeast Isolates' Identification in Ecological Studies.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {39330355},
issn = {2309-608X},
support = {RGP0060/2021//HFSP/ ; 20225SXSHY//PRIN 2022/ ; },
abstract = {Culturomics has been temporarily exceeded by the advent of omics approaches such as metabarcoding and metagenomics. However, despite improving our knowledge of microbial population composition, both metabarcoding and metagenomics are not suitable for investigating and experimental testing inferences about microbial ecological roles and evolution. This leads to a recent revival of culturomics approaches, which should be supported by improvements in the available tools for high-throughput microbial identification. This study aimed to update the classical PCR-RFLP approach in light of the currently available knowledge on yeast genomics. We generated and analyzed a database including more than 1400 ascomycetous yeast species, each characterized by PCR-RFLP profiles obtained with 143 different endonucleases. The results allowed for the in silico evaluation of the performance of the tested endonucleases in the yeast species' identification and the generation of FId (Fungal Identifier), an online freely accessible tool for the identification of yeast species according to experimentally obtained PCR-RFLP profiles.},
}
@article {pmid39328926,
year = {2024},
author = {Duque-Granda, D and Vivero-Gómez, RJ and Junca, H and Cadavid-Restrepo, G and Moreno-Herrera, CX},
title = {Interaction and effects of temperature preference under a controlled environment on the diversity and abundance of the microbiome in Lutzomyia longipalpis (Diptera: Psychodidae).},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {44},
number = {},
pages = {e00857},
pmid = {39328926},
issn = {2215-017X},
abstract = {Characterization of the temperature effects on the abundance and richness of the microbiota of Lutzomyia longipalpis, insect vector of Leishmania infantum in America, is an aspect of pivotal importance to understand the interactions between temperature, bacteria, and Leishmania infection. We developed and used a customized device with a temperature gradient (21-34 °C) to assess the temperature preferences of wild females of Lu. longipalpis collected in a rural area (Ricaurte, Cundinamarca, Colombia). Each replicate consisted of 50 females exposed to the gradient for an hour. At the end of the exposure time, insects were collected and separated by the temperature ranges selected varying from 21 °C to 34 °C. They were organized in 17 pools from which total DNA extracts were obtained, and samples were subjected to 16S rRNA amplicon sequencing analyzes. The most abundant phyla across the different temperature ranges were Proteobacteria (17.22-90.73 %), Firmicutes (5.99-77.21 %) and Actinobacteria (1.56-59.85 %). Results also showed an abundance (30 % to 57.36 %) of Pseudomonas (mainly at temperatures of 21-29 °C and 34 °C) that decreased to 6.55 %-13.20 % at temperatures of 31-33 °C, while Bacillus increase its abundance to 67.24 % at 29-33 °C. Serratia also had a greater representation (49.79 %), specifically in sand flies recovered at 25-27 °C. No significant differences were found at α-diversity level when comparing richness using the Shannon-Wiener, Simpson, and Chao1 indices, while β-diversity differences were found using the Bray-Curtis index (F-value of 3.5073, p-value < 0.013, R-squared of 0,4889), especially in the groups of Lu. longipalpis associated at higher temperatures (29-33 °C). It was also possible to detect the presence of endosymbionts such as Spiroplasma and Arsenophonus in the range of 29-33 °C. Rickettsia was only detected in Lu. longipalpis sand flies recovered between 25-27 °C. It was possible to characterize Lu. longipalpis microbiota in response to intraspecific temperature preferences and observe changes in bacterial communities and endosymbionts at different ranges of said environmental variable, which may be important in its vector competence and environmental plasticity to adapt to new climate change scenarios.},
}
@article {pmid39327479,
year = {2024},
author = {Tavaddod, S and Dawson, A and Allen, RJ},
title = {Bacterial aggregation triggered by low-level antibiotic-mediated lysis.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {90},
pmid = {39327479},
issn = {2055-5008},
support = {682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; BB/R012415/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; 682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; *Escherichia coli/drug effects/genetics ; *Bacteriolysis/drug effects ; Biofilms/drug effects/growth &amp; development ; Microbial Sensitivity Tests ; },
abstract = {Suspended bacterial aggregates play a central role in ocean biogeochemistry, industrial processes and probably many clinical infections - yet the factors that trigger aggregation remain poorly understood, as does the relationship between suspended aggregates and surface-attached biofilms. Here we show that very low doses of cell-wall targeting antibiotic, far below the minimal inhibitory concentration, can trigger aggregation of Escherichia coli cells. This occurs when a few cells lyse, releasing extracellular DNA - thus, cell-to-cell variability in antibiotic response leads to population-level aggregation. Although lysis-triggered aggregation echoes known trigger mechanisms for surface-attached biofilms, these aggregates may have different ecological implications since they do not show increased biofilm-forming potential or increased antibiotic resistance. Our work contributes to understanding the nature of bacterial aggregates and the factors that trigger their formation, and the possible consequences of widespread low-dose antibiotic exposure in the environment and in the body.},
}
@article {pmid39327101,
year = {2024},
author = {Goldman, AD and Fournier, GP},
title = {The very early evolution of biological complexity.},
journal = {Trends in genetics : TIG},
volume = {40},
number = {11},
pages = {912-913},
doi = {10.1016/j.tig.2024.09.001},
pmid = {39327101},
issn = {0168-9525},
mesh = {*Biological Evolution ; Phylogeny ; Evolution, Molecular ; },
abstract = {All extant life is descended from a common ancestor, which, despite being very ancient, appears to have been a complex cellular organism. A new study by Moody et al. shows that this ancestor was not only a complex cell, but also lived within a microbial ecology likely inhabited by other complex cells.},
}
@article {pmid39326062,
year = {2024},
author = {Sun, X and Favier, A and Folmar, J and Pyenson, NC and Sanchez, A and Rebolleda-Gómez, M},
title = {Metabolic Plasticity Shapes Microbial Communities across a Temperature Gradient.},
journal = {The American naturalist},
volume = {204},
number = {4},
pages = {381-399},
doi = {10.1086/731997},
pmid = {39326062},
issn = {1537-5323},
mesh = {*Temperature ; *Microbiota ; Bacteria/metabolism ; Fermentation ; Carbon/metabolism ; Ecosystem ; },
abstract = {AbstractA central challenge in community ecology is understanding and predicting the effects of abiotic factors on community assembly. In particular, microbial communities play a central role in the ecosystem, but we do not understand how changing factors like temperature are going to affect community composition or function. In this article, we studied the self-assembly of multiple communities in synthetic environments to understand changes in microbial community composition based on metabolic responses of different functional groups along a temperature gradient. In many microbial communities, different microbial functional groups coexist through the partitioning of carbon sources in an emergent trophic structure (cross-feeding). In this system, respirofermentative bacteria display a preference for the sugars supplied as the only carbon source but secrete secondary carbon sources (organic acids) that are more efficiently consumed by obligate respirators. As a consequence of this trophic structure, the metabolic plasticity of the respirofermenters has downstream consequences for the relative abundance of respirators across temperatures. We found that the effects of different temperatures on microbial composition can largely be described by an increase in fermentation by-products with increasing temperatures from the respirofermentative bacteria. This research highlights the importance of metabolic plasticity and metabolic trade-offs in predicting species interactions and community dynamics across abiotic gradients.},
}
@article {pmid39321934,
year = {2024},
author = {Liu, YC and Ramiro-Garcia, J and O'Connor, S and Paulo, LM and Maria Braguglia, C and Cristina Gagliano, M and O'Flaherty, V},
title = {Microbial community response to temperature reduction during anaerobic treatment of long chain fatty acids-containing wastewater.},
journal = {Bioresource technology},
volume = {413},
number = {},
pages = {131529},
doi = {10.1016/j.biortech.2024.131529},
pmid = {39321934},
issn = {1873-2976},
mesh = {*Wastewater/microbiology/chemistry ; Anaerobiosis ; *Fatty Acids/metabolism ; *Bioreactors ; *Temperature ; Bacteria/metabolism ; Water Purification/methods ; Biomass ; Microbiota/physiology ; },
abstract = {Acclimating mesophilic biomass to low temperatures have been used to start-up psychrophilic anaerobic reactors, but limited microbial information is available during the acclimation. To investigate microbial responses to temperature reductions, duplicate lab-scale anaerobic digestion (AD) reactors were operated for 166 days, with the temperature being reduced from 37°C to 15°C, using synthetic long chain fatty acid (LCFA)-containing wastewater as the feedstock. The acclimated biomass at 15°C exhibited efficient removal of organic matter (total COD>75%, soluble COD>88%, and LCFA>99%). Temperature reductions lead to significant reductions in microbiome diversity. Fermentative bacteria were highly dynamic and functional redundant during temperature reductions. Smithella was the dominant syntrophic bacteria involved in LCFA degradation coupled with Methanothrix and Methanocorpusculum at 15°C. Membrane modifications and compatible cellular solutes production were triggered by temperature reductions as microbial response to cold stress. This study provided molecular insights in microbial acclimation to low temperatures for psychrophilic AD.},
}
@article {pmid39319483,
year = {2024},
author = {Rasmussen, KL and Thieringer, PH and Nevadomski, S and Martinez, AM and Dawson, KS and Corsetti, FA and Zheng, XY and Lv, Y and Chen, X and Celestian, AJ and Berelson, WM and Rollins, NE and Spear, JR},
title = {Living to Lithified: Construction and Preservation of Silicified Biomarkers.},
journal = {Geobiology},
volume = {22},
number = {5},
pages = {1-30},
doi = {10.1111/gbi.12620},
pmid = {39319483},
issn = {1472-4669},
support = {/NASA/NASA/United States ; //Geological Society of America/ ; },
mesh = {*Biomarkers/analysis ; Cyanobacteria/metabolism ; Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism ; Hot Springs/microbiology/chemistry ; },
abstract = {Whole microorganisms are rarely preserved in the fossil record but actively silicifying environments like hot springs provide an opportunity for microbial preservation, making silicifying environments critical for the study of microbial life through time on Earth and possibly other planetary bodies. Yet, the changes that biosignatures may undergo through lithification and burial remain unconstrained. At Steep Cone Geyser in Yellowstone National Park, we collected microbial material from (1) the living system across the active outflows, (2) the silicified areas adjacent to flows, and (3) lithified and buried material to assess the preservation of biosignatures and their changes across the lithification transect. Five biofabrics, built predominantly by Cyanobacteria Geitlerinema, Pseudanabaenaceae, and Leptolyngbya with some filamentous anoxygenic phototrophs contributions, were identified and tracked from the living system through the process of silicification/lithification. In the living systems, δ[30]Si values decrease from +0.13‰ in surficial waters to -2‰ in biomat samples, indicating a kinetic isotope effect potentially induced by increased association with actively growing biofabrics. The fatty acids C16:1 and iso-C14:0 and the hydrocarbon C17:0 were disentangled from confounding signals and determined to be reliable lipid biosignatures for living biofabric builders and tenant microorganisms. Builder and tenant microbial biosignatures were linked to specific Cyanobacteria, anoxygenic phototrophs, and heterotrophs, which are prominent members of the living communities. Upon lithification and burial, silicon isotopes of silicified biomass began to re-equilibrate, increasing from δ[30]Si -2‰ in living biomats to -0.55‰ in lithified samples. Active endolithic microbial communities were identified in lithified samples and were dominated by Cyanobacteria, heterotrophic bacteria, and fungi. Results indicate that distinct microbial communities build and inhabit silicified biofabrics through time and that microbial biosignatures shift over the course of lithification. These findings improve our understanding of how microbial communities silicify, the biomarkers they retain, and transitionary impacts that may occur through lithification and burial.},
}
@article {pmid39317790,
year = {2024},
author = {Knorr, MA and Contosta, AR and Morrison, EW and Muratore, TJ and Anthony, MA and Stoica, I and Geyer, KM and Simpson, MJ and Frey, SD},
title = {Unexpected sustained soil carbon flux in response to simultaneous warming and nitrogen enrichment compared with single factors alone.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
pmid = {39317790},
issn = {2397-334X},
abstract = {Recent observations document that long-term soil warming in a temperate deciduous forest leads to significant soil carbon loss, whereas chronic soil nitrogen enrichment leads to significant soil carbon gain. Most global change experiments like these are single factor, investigating the impacts of one stressor in isolation of others. Because warming and ecosystem nitrogen enrichment are happening concurrently in many parts of the world, we designed a field experiment to test how these two factors, alone and in combination, impact soil carbon cycling. Here, we show that long-term continuous soil warming or nitrogen enrichment when applied alone followed the predicted response, with warming resulting in significant soil carbon loss and nitrogen fertilization tending towards soil carbon gain. The combination treatment showed an unanticipated response, whereby soil respiratory carbon loss was significantly higher than either single factor alone, but without a concomitant decline in soil carbon storage. Observations suggest that when soils are exposed to both factors simultaneously, plant carbon inputs to the soil are enhanced, counterbalancing soil carbon loss and helping maintain soil carbon stocks near control levels. This has implications for both atmospheric CO2 emissions and soil fertility and shows that coupling two important global change drivers results in a distinctive response that was not predicted by the behaviour of the single factors in isolation.},
}
@article {pmid39311575,
year = {2024},
author = {Han, C-J and Huang, J-P and Chiang, M-R and Jean, OSM and Nand, N and Etebari, K and Shelomi, M},
title = {The hindgut microbiota of coconut rhinoceros beetles (Oryctes rhinoceros) in relation to their geographical populations.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {10},
pages = {e0098724},
pmid = {39311575},
issn = {1098-5336},
support = {MOST-109-2311-B-002-016-MY3//National Science and Technology Council (NSTC)/ ; 111L7822,112L7814,113L7801//Ministry of Education, Taiwan/ ; },
mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Symbiosis ; Bacteria/classification/genetics/isolation &amp; purification ; Cocos/microbiology ; Genetic Variation ; },
abstract = {The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a palm tree pest capable of rapidly expanding its population in new territories. Previous studies identified a digestive symbiosis between CRB and its gut microbes. However, no research compared the genetic variation of CRBs with their hindgut microbiota on a global scale. This study aims to investigate the genetic divergence of CRB and the compositional variation of CRB's microbiota across different geographical locations, and explore the association between them and their predicted functional profiles and environmental data. The research reveals a distinct and consistent microbial community within local populations, but it varies across different geographical populations. The microbial functional profiles linked to the production of digestive enzymes, including cellulases and ligninases, are nonetheless globally conserved. This suggests that CRBs employ specific mechanisms to select and maintain microbes with functional benefits, contributing to host adaptability, stress tolerance, and fitness. The CRB microbial communities did not appear to recapitulate the genetic variation of their hosts. Rather than depend on obligate symbionts, CRBs seem to establish similar digestive associations with whatever environmentally acquired microbes are available wherever they are, aiding them in successfully establishing after invading a new location.IMPORTANCECoconut rhinoceros beetles (CRBs) are notorious pests on Arecaceae plants, posing destructive threats to countries highly reliant on coconut, oil palm, and date palm as economic crops. In the last century, CRBs have rapidly expanded their presence to territories that were once free of these beetles. The United States, for instance, has officially designated CRBs as invasive and alien pests. Given their remarkable ability to swiftly adapt to new environments, their gut microbes may play a crucial role in this process. While the microbiota of CRBs vary depending on geographical location, these beetles consistently exhibit a functionally identical digestive association with locally acquired microbes. This underscores the significance of CRB-microbe association in shaping the adaptive strategies of this agricultural pest.},
}
@article {pmid39311333,
year = {2024},
author = {Deo, R and Lakra, U and Ojha, M and Nigam, VK and Sharma, SR},
title = {Exopolysaccharides in microbial interactions: signalling, quorum sensing, and community dynamics.},
journal = {Natural product research},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/14786419.2024.2405867},
pmid = {39311333},
issn = {1478-6427},
abstract = {Microbial interactions within diverse ecosystems are intricately governed by the dynamic interplay of exopolysaccharides (EPSs) produced by microorganisms. This review delves into the multifaceted roles of EPS in microbial signalling, quorum sensing (QS), and community dynamics, highlighting their significance in orchestrating cooperative behaviours and shaping community structures. EPSs serve as pivotal signalling molecules, influencing chemical communication and promoting intricate interactions among microorganisms. The integration of EPS into QS mechanisms adds an additional layer of complexity, allowing microorganisms to assess population density and synchronise communal responses. Furthermore, EPSs actively contribute to community dynamics by influencing spatial organisation, adhesion, and resistance to environmental stressors. By providing comprehensive knowledge of EPS dynamics, this review offers valuable insights into microbial ecology, serving as a foundational resource for future research. It will benefit the research community by advancing our understanding of microbial ecosystems, with broad applications in biotechnology, environmental science, and beyond.},
}
@article {pmid39297874,
year = {2024},
author = {Castledine, M and Pennycook, J and Newbury, A and Lear, L and Erdos, Z and Lewis, R and Kay, S and Sanders, D and Sünderhauf, D and Buckling, A and Hesse, E and Padfield, D},
title = {Characterizing a stable five-species microbial community for use in experimental evolution and ecology.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {9},
pages = {},
pmid = {39297874},
issn = {1465-2080},
mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Ecology ; Biological Evolution ; Microbial Interactions ; },
abstract = {Model microbial communities are regularly used to test ecological and evolutionary theory as they are easy to manipulate and have fast generation times, allowing for large-scale, high-throughput experiments. A key assumption for most model microbial communities is that they stably coexist, but this is rarely tested experimentally. Here we report the (dis)assembly of a five-species microbial community from a metacommunity of soil microbes that can be used for future experiments. Using reciprocal invasion-from-rare experiments we show that all species can coexist and we demonstrate that the community is stable for a long time (~600 generations). Crucially for future work, we show that each species can be identified by their plate morphologies, even after >1 year in co-culture. We characterise pairwise species interactions and produce high-quality reference genomes for each species. This stable five-species community can be used to test key questions in microbial ecology and evolution.},
}
@article {pmid39303870,
year = {2024},
author = {McDonagh, F and Tumeo, A and Murray, EK and Hallahan, B and Miliotis, G},
title = {Complete genome of Escherichia coli sequence type 73 with acquired blaTEM-1 and high genotypic virulence load identified in human saliva.},
journal = {Journal of global antimicrobial resistance},
volume = {39},
number = {},
pages = {149-152},
doi = {10.1016/j.jgar.2024.08.011},
pmid = {39303870},
issn = {2213-7173},
abstract = {OBJECTIVES: Escherichia coli sequence type (ST) 73 is a pandemic lineage of the ExPEC (Extraintestinal Pathogenic E. coli) family associated with conserved virulence. We report the complete genome of a genomically hypervirulent E. coli ST73 strain isolated from the oral cavity of a patient with a diagnosis of treatment resistant schizophrenia and receiving clozapine treatment.<br><br>METHODS: E. coli strain GABEEC132 underwent second and third generation sequencing with Illumina and Oxford-Nanopore-Technologies (ONT) platforms. Antibiotic resistance genes (ARGs) and virulence factors (VFs) were bioinformatically identified using the NCBI-AMR-Finder-Plus database and Virulence-Factors-database (VFDB), respectively. To contextualize the genome within a broader epidemiological framework, phylogenetic analysis was conducted using representative genomes of E. coli ST73 O6:H1 (n = 55).<br><br>RESULTS: E. coli strain GABEEC132 was identified as possessing the O6:H1 serotype and classified within the B2 phylogroup. The strain exhibited a high genomic virulence load, encoding for 194 VFs. Additionally, it encoded three ARGs, including an acquired blaTEM-1 located on a rep_cluster_2350 8 237 Kb mobilisable plasmid, presenting phenotypic resistance to ampicillin and piperacillin.<br><br>CONCLUSION: This report provides novel insights into the oral prevalence of genotypically hypervirulent and drug-resistant E. coli ST73, a pandemic lineage.},
}
@article {pmid39301056,
year = {2024},
author = {Smith, L and Fullerton, H and Moyer, CL},
title = {Complex hydrothermal vent microbial mat communities used to assess primer selection for targeted amplicon surveys from Kama'ehuakanaloa Seamount.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18099},
pmid = {39301056},
issn = {2167-8359},
mesh = {*Hydrothermal Vents/microbiology ; *Archaea/genetics/isolation &amp; purification ; *Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; DNA Primers/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The microbiota of hydrothermal vents has been widely implicated in the dynamics of oceanic biogeochemical cycling. Lithotrophic organisms utilize reduced chemicals in the vent effluent for energy, which fuels carbon fixation, and their metabolic byproducts can then support higher trophic levels and high-biomass ecosystems. However, despite the important role these microorganisms play in our oceans, they are difficult to study. Most are resistant to culturing in a lab setting, so culture-independent methods are necessary to examine community composition. Targeted amplicon surveying has become the standard practice for assessing the structure and diversity of hydrothermal vent microbial communities. Here, the performance of primer pairs targeting the V3V4 and V4V5 variable regions of the SSU rRNA gene was assessed for use on environmental samples from microbial mats surrounding Kama'ehuakanaloa Seamount, an iron-dominated hydrothermal vent system. Using the amplicon sequence variant (ASV) approach to taxonomic identification, the structure and diversity of microbial communities were elucidated, and both primer pairs generated robust data and comparable alpha diversity profiles. However, several distinct differences in community composition were identified between primer sets, including differential relative abundances of both bacterial and archaeal phyla. The primer choice was determined to be a significant driver of variation among the taxonomic profiles generated. Based on the higher quality of the raw sequences generated and on the breadth of abundant taxa found using the V4V5 primer set, it is determined as the most efficacious primer pair for whole-community surveys of microbial mats at Kama'ehuakanaloa Seamount.},
}
@article {pmid39303138,
year = {2024},
author = {Boukheloua, R and Mukherjee, I and Park, H and Šimek, K and Kasalický, V and Ngochera, M and Grossart, HP and Picazo-Mozo, A and Camacho, A and Cabello-Yeves, PJ and Rodriguez-Valera, F and Callieri, C and Andrei, AS and Pernthaler, J and Posch, T and Alfreider, A and Sommaruga, R and Hahn, MW and Sonntag, B and López-García, P and Moreira, D and Jardillier, L and Lepère, C and Biderre-Petit, C and Bednarska, A and Ślusarczyk, M and Tóth, VR and Banciu, HL and Kormas, K and Orlić, S and Šantić, D and Muyzer, G and Herlemann, DPR and Tammert, H and Bertilsson, S and Langenheder, S and Zechmeister, T and Salmaso, N and Storelli, N and Capelli, C and Lepori, F and Lanta, V and Vieira, HH and Kostanjšek, F and Kabeláčová, K and Chiriac, MC and Haber, M and Shabarova, T and Fernandes, C and Rychtecký, P and Znachor, P and Szőke-Nagy, T and Layoun, P and Wong, HL and Kavagutti, VS and Bulzu, PA and Salcher, MM and Piwosz, K and Ghai, R},
title = {Global freshwater distribution of Telonemia protists.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39303138},
issn = {1751-7370},
support = {20-12496X//Grant Agency of the Czech Republic/ ; 017/2022/P//GAJU/ ; 2021/03/Y/NZ8/00076//National Science Centre/ ; },
mesh = {*Fresh Water/microbiology/parasitology ; *Phylogeny ; *RNA, Ribosomal, 18S/genetics ; *In Situ Hybridization, Fluorescence ; Metagenome ; Lakes/microbiology/parasitology ; Biodiversity ; Metagenomics ; },
abstract = {Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remain unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analyzed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10%-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.},
}
@article {pmid39302483,
year = {2024},
author = {Nelson, K and Schloter, M},
title = {Special Collection on Pollution, Bioremediation, and the Environment.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {118},
pmid = {39302483},
issn = {1432-184X},
mesh = {*Biodegradation, Environmental ; *Environmental Pollution ; },
}
@article {pmid39299325,
year = {2024},
author = {Ren, W and Ren, G and Kuramae, EE and Bodelier, PLE and Chen, S and Teng, Y and Luo, Y},
title = {Mode of application of sulfonated graphene modulated bioavailable heavy metal contents and microbial community composition in long-term heavy metal contaminated soil.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176295},
doi = {10.1016/j.scitotenv.2024.176295},
pmid = {39299325},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Soil Pollutants/metabolism/analysis ; *Graphite ; *Metals, Heavy/analysis/metabolism ; *Microbiota/drug effects ; *Biodegradation, Environmental ; Soil/chemistry ; Bacteria/metabolism ; Cadmium/metabolism/analysis ; },
abstract = {Nanomaterials are increasingly recognized for their potential in soil remediation. However, their impact on soil microbial communities in contaminated soil remains poorly understood. In this study, we investigated the dynamic effects of sulfonated graphene (SG) following one-time or repeated applications on heavy metal availability and soil microbial communities in long-term heavy metal-contaminated soil over 180 days. Our findings revealed that one-time SG application at 30 mg kg[-1] significantly increased the bioavailable cadmium (Cd) and copper (Cu) contents by approximately 30 %-40 % after 2 and 180 days. Repeated SG applications, however, displayed no significant influence on heavy metal availability. One-time SG application, coupled with the increased available Cd, induced significant enrichment of some specific functional bacterial genera involved in glycan biosynthesis metabolism and biosynthesis of other secondary metabolites, thereby decreasing the available contents of heavy metals after 90 days. However, the shifts in bacterial community structure and function were subsequently partially recovered after 180 days. Conversely, repeated SG treatments led to minimal alterations after 90 days while leading to similar shifts in the bacterial community at 60 mg kg[-1] after 180 days. The fungal community structure remained largely unaltered across all SG treatments. Intriguingly, SG treatments substantially stimulated fungal biomass, with the stimulation degree dependent on SG dosage. These results provide valuable insights for developing phytoremediation strategies, suggesting tailored SG applications during specific growth phases to optimize remediation efficiency.},
}
@article {pmid39298326,
year = {2024},
author = {Gordon, JI and Barratt, MJ and Hibberd, MC and Rahman, M and Ahmed, T},
title = {Establishing human microbial observatory programs in low- and middle-income countries.},
journal = {Annals of the New York Academy of Sciences},
volume = {1540},
number = {1},
pages = {13-20},
doi = {10.1111/nyas.15224},
pmid = {39298326},
issn = {1749-6632},
support = {//Fondazione Internazionale Premio Balzan/ ; //Bill and Melinda Gates Foundation/ ; /NH/NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Humans ; *Developing Countries ; Global Health ; *Microbiota ; },
abstract = {Studies of the human microbiome are progressing rapidly but have largely focused on populations living in high-income countries. With increasing evidence that the microbiome contributes to the pathogenesis of diseases that affect infants, children, and adults in low- and middle-income countries (LMICs), and with profound and rapid ongoing changes occurring in our lifestyles and biosphere, understanding the origins of and developing microbiome-directed therapeutics for treating a number of global health challenges requires the development of programs for studying human microbial ecology in LMICs. Here, we discuss how the establishment of long-term human microbial observatory programs in selected LMICs could provide one timely approach.},
}
@article {pmid39296299,
year = {2024},
author = {Wang, X and Li, H and Yang, Y and Wu, Z and Wang, Z and Li, D and Xia, W and Zou, S and Liu, Y and Wang, F},
title = {Geographic and environmental impacts on gut microbiome in Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1452101},
pmid = {39296299},
issn = {1664-302X},
abstract = {INTRODUCTION: Gut microbiome plays a crucial role in the health of wild animals. Their structural and functional properties not only reflect the host's dietary habits and habitat conditions but also provide essential support for ecological adaptation in various environments.<br><br>METHODS: This study investigated the gut microbiome of Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita) across different geographic regions using 16S rRNA gene and metagenomic sequencing.<br><br>RESULTS: Results showed distinct clustering patterns in gut microbiota based on geographic location. Soil had an insignificant impact on host gut microbiome. Himalayan langurs from mid-altitude regions exhibited higher levels of antibiotic resistance genes associated with multidrug resistance, while Xizang macaques from high-altitude regions showed a broader range of resistance genes. Variations in carbohydrate-active enzymes and KEGG pathways indicated unique metabolic adaptations to different environments.<br><br>DISCUSSION: These findings provide valuable insights into the health and conservation of these primates and the broader implications of microbial ecology and functional adaptations in extreme conditions.},
}
@article {pmid39296290,
year = {2024},
author = {Wang, Z and Gao, Z and Yu, Y and Li, H and Luo, W and Ji, Z and Ding, H},
title = {New insights into the structure and function of microbial communities in Maxwell Bay, Antarctica.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1463144},
pmid = {39296290},
issn = {1664-302X},
abstract = {The microbial communities inhabiting polar ecosystems, particularly in Maxwell Bay, Antarctica, play a pivotal role in nutrient cycling and ecosystem dynamics. However, the diversity of these microbial communities remains underexplored. In this study, we aim to address this gap by investigating the distribution, environmental drivers, and metabolic potential of microorganisms in Maxwell Bay. We analyzed the prokaryotic and eukaryotic microbiota at 11 stations, revealing distinctive community structures and diverse phylum dominance by using high-throughput sequencing. Spatial analysis revealed a significant impact of longitude on microbial communities, with microeukaryotes exhibiting greater sensitivity to spatial factors than microprokaryotes. We constructed co-occurrence networks to explore the stability of microbial communities, indicating the complexity and stability of microprokaryotic communities compared with those of microeukaryotes. Our findings suggest that the microeukaryotic communities in Maxwell Bay are more susceptible to disturbances. Additionally, this study revealed the spatial correlations between microbial communities, diversity, and environmental variables. Redundancy analysis highlighted the significance of pH and dissolved oxygen in shaping microprokaryotic and microeukaryotic communities, indicating the anthropogenic influence near the scientific research stations. Functional predictions using Tax4Fun2 and FUNGuild revealed the metabolic potential and trophic modes of the microprokaryotic and microeukaryotic communities, respectively. Finally, this study provides novel insights into the microbial ecology of Maxwell Bay, expanding the understanding of polar microbiomes and their responses to environmental factors.},
}
@article {pmid39294302,
year = {2024},
author = {Sousa, LGV and Novak, J and França, A and Muzny, CA and Cerca, N},
title = {Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia Strongly Influence Each Other's Transcriptome in Triple-Species Biofilms.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {117},
pmid = {39294302},
issn = {1432-184X},
support = {R01AI146065-01A1//National Institute of Allergy and Infectious Diseases/ ; UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2020.04912.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL57/2016/CP1377/CT0032//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; R01 AI146065/AI/NIAID NIH HHS/United States ; },
mesh = {*Biofilms/growth &amp; development ; *Gardnerella vaginalis/genetics ; *Transcriptome ; *Prevotella/genetics/physiology ; Female ; Humans ; Vaginosis, Bacterial/microbiology ; Vagina/microbiology ; },
abstract = {Bacterial vaginosis (BV), the most common vaginal infection worldwide, is characterized by the development of a polymicrobial biofilm on the vaginal epithelium. While Gardnerella spp. have been shown to have a prominent role in BV, little is known regarding how other species can influence BV development. Thus, we aimed to study the transcriptome of Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia, when growing in triple-species biofilms. Single and triple-species biofilms were formed in vitro, and RNA was extracted and sent for sequencing. cDNA libraries were prepared and sequenced. Quantitative PCR analysis (qPCR) was performed on the triple-species biofilms to evaluate the biofilm composition. The qPCR results revealed that the triple-species biofilms were mainly composed by G. vaginalis and P. bivia was the species with the lowest percentage. The RNA-sequencing analysis revealed a total of 432, 126, and 39 differentially expressed genes for G. vaginalis, F. vaginae, and P. bivia, respectively, when growing together. Gene ontology enrichment of G. vaginalis downregulated genes revealed several functions associated with metabolism, indicating a low metabolic activity of G. vaginalis when growing in polymicrobial biofilms. This work highlighted that the presence of 3 different BV-associated bacteria in the biofilm influenced each other's transcriptome and provided insight into the molecular mechanisms that enhanced the virulence potential of polymicrobial consortia. These findings will contribute to understand the development of incident BV and the interactions occurring within the biofilm.},
}
@article {pmid39290267,
year = {2024},
author = {Zhang, K and Zhang, Q and Qiu, H and Ma, Y and Hou, N and Zhang, J and Kan, C and Han, F and Sun, X and Shi, J},
title = {The complex link between the gut microbiome and obesity-associated metabolic disorders: Mechanisms and therapeutic opportunities.},
journal = {Heliyon},
volume = {10},
number = {17},
pages = {e37609},
pmid = {39290267},
issn = {2405-8440},
abstract = {Microbial interactions are widespread and important processes that support the link between disease and microbial ecology. The gut microbiota is a major source of microbial stimuli that can have detrimental or beneficial effects on human health. It is also an endocrine organ that maintains energy homeostasis and host immunity. Obesity is a highly and increasingly prevalent metabolic disease and the leading cause of preventable death worldwide. An imbalance in the gut microbiome is associated with several diseases including obesity-related metabolic disorders. This review summarizes the complex association between the gut microbiome and obesity-associated metabolic diseases and validates the role and mechanisms of ecological dysregulation in the gut in obesity-associated metabolic disorders. Therapies that could potentially alleviate obesity-associated metabolic diseases by modulating the gut microbiota are discussed.},
}
@article {pmid39288091,
year = {2024},
author = {Liu, X and Salles, JF},
title = {Drivers and consequences of microbial community coalescence.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39288091},
issn = {1751-7370},
support = {//China Scholarship Council and the European Research Council/ ; },
mesh = {*Microbiota ; *Ecosystem ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Microbial communities are undergoing unprecedented dispersion and amalgamation across diverse ecosystems, thereby exerting profound and pervasive influences on microbial assemblages and ecosystem dynamics. This review delves into the phenomenon of community coalescence, offering an ecological overview that outlines its four-step process and elucidates the intrinsic interconnections in the context of community assembly. We examine pivotal mechanisms driving community coalescence, with a particular emphasis on elucidating the fates of both source and resident microbial communities and the consequential impacts on the ecosystem. Finally, we proffer recommendations to guide researchers in this rapidly evolving domain, facilitating deeper insights into the ecological ramifications of microbial community coalescence.},
}
@article {pmid39287748,
year = {2024},
author = {Kujawska, M and Neuhaus, K and Huptas, C and Jiménez, E and Arboleya, S and Schaubeck, M and Hall, LJ},
title = {Exploring the Potential Probiotic Properties of Bifidobacterium breve DSM 32583-A Novel Strain Isolated from Human Milk.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {39287748},
issn = {1867-1314},
abstract = {Human milk is the best nutrition for infants, providing optimal support for the developing immune system and gut microbiota. Hence, it has been used as source for probiotic strain isolation, including members of the genus Bifidobacterium, in an effort to provide beneficial effects to infants who cannot be exclusively breastfed. However, not all supplemented bifidobacteria can effectively colonise the infant gut, nor confer health benefits to the individual infant host; therefore, new isolates are needed to develop a range of dietary products for this specific age group. Here, we investigated the beneficial potential of Bifidobacterium breve DSM 32583 isolated from human milk. We show that in vitro B. breve DSM 32583 exhibited several characteristics considered fundamental for beneficial bacteria, including survival in conditions simulating those present in the digestive tract, adherence to human epithelial cell lines, and inhibition of growth of potentially pathogenic microorganisms. Its antibiotic resistance patterns were comparable to those of known beneficial bifidobacterial strains, and its genome did not contain plasmids nor virulence-associated genes. These results suggest that B. breve DSM 32583 is a potential probiotic candidate.},
}
@article {pmid39287688,
year = {2024},
author = {Demin, K and Prazdnova, E and Kulikov, M and Mazanko, M and Gorovtsov, A},
title = {Alternative agar substitutes for culturing unculturable microorganisms.},
journal = {Archives of microbiology},
volume = {206},
number = {10},
pages = {405},
pmid = {39287688},
issn = {1432-072X},
support = {SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; },
mesh = {*Agar/chemistry ; *Culture Media/chemistry ; *Polysaccharides, Bacterial/metabolism ; *Bacteria/growth &amp; development/metabolism/drug effects ; Gels/chemistry ; },
abstract = {Gelling agents are necessary for the preparation of solid or semisolid media. For more than a hundred years, agar has been the primary gelling agent. However, a substantial body of evidence has accumulated suggesting that agar-based media inhibit the growth of many microbial species through the generation of reactive oxygen species (ROS), toxic organic contaminants, or competitive exclusion effects. In this review we have compiled the largest amount of data to date on the use of various gelling agents in microbial isolation and cultivation, with the particular emphasis on rare microbe isolation cases. Our analysis suggested that microbial-derived compounds (especially gellan gum), as gelling agents, are superior to agar in their ability to isolate and maintain either new or known microbial species. We analyzed the reasons behind this success and concluded that there are phylum-level differences in microbial responses to the changes in conditions from natural to the laboratory conditions (with respect to gelling agent usage). Consequently, we hypothesize that at least partial success of microbial-derived gelling agents lies in the recreation of the natural microenvironment conditions (which we address as the "familiarity of conditions" hypothesis). Finally, we present a list of recommendations and suggestions for further microbial ecology studies.},
}
@article {pmid39287374,
year = {2024},
author = {Vinogradova, E and Mukhanbetzhanov, N and Nurgaziyev, M and Jarmukhanov, Z and Aipova, R and Sailybayeva, A and Bekbossynova, M and Kozhakhmetov, S and Kushugulova, A},
title = {Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0058524},
pmid = {39287374},
issn = {2379-5077},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Urbanization ; Male ; Female ; Kazakhstan/epidemiology ; *Diet ; Adult ; Rural Population/statistics &amp; numerical data ; Middle Aged ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Urban Population/statistics &amp; numerical data ; Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Young Adult ; },
abstract = {UNLABELLED: This study provides a comprehensive assessment of how urban-rural divides influence gut microbial diversity and composition across the distinct geographical landscapes of Kazakhstan, elucidating the intricate interplay between lifestyle, environment, and gut microbiome. In this prospective cohort study, we enrolled 651 participants from urban centers and rural settlements across Kazakhstan, following ethical approval and informed consent. Comprehensive demographic, dietary, and stool sample data were collected. 16S rRNA gene sequencing and shotgun metagenomics techniques were employed to delineate the intricate patterns of the gut microbiome. A rigorous statistical framework dissected the interplay between urbanization gradients, geography, dietary lifestyles, and microbial dynamics. Our findings demonstrate a stark microbial divide between urban and rural gut ecosystems. The study found significant differences in gut microbiome diversity and composition between urban and rural populations in Kazakhstan. Urban microbiomes exhibited reduced diversity, higher Firmicutes/Bacteroidetes ratios, and increased prevalence of genera Coprococcus and Parasutterella. In contrast, rural populations had greater microbial diversity and abundance of Ligilactobacillus, Sutterella, and Paraprevotella. Urbanization also influenced dietary patterns, with urban areas consuming more salt, cholesterol, and protein, while rural areas had diets richer in carbohydrates and fiber. The study also identified distinct patterns in the prevalence of antibiotic resistance genes and virulence factors between urban and rural gut microbiomes. This study sheds light on how urbanization may be deeply involved in shaping the intricate mosaic of the gut microbiome across Kazakhstan's diverse geographical and dietary landscapes, underscoring the complex interplay between environmental exposures, dietary lifestyles, and the microbial residents inhabiting our intestines.<br><br>IMPORTANCE: The study examined gut microbiome composition across diverse geographical locations in Kazakhstan, spanning urban centers and rural settlements. This allows for thoroughly investigating how urbanization gradients and geographic factors shape the gut microbiome. The study's examination of the gut resistome and prevalence of virulence-associated genes provide essential insights into the public health implications of urbanization-driven microbiome alterations. Collecting comprehensive demographic, dietary, and stool sample data enables the researchers to better understand the relationships between urbanization, nutritional patterns, and gut microbiome composition. The findings have important implications for understanding how urbanization-driven microbiome changes may impact human health and well-being, paving the way for tailored interventions to restore a balanced gut microbial ecology.},
}
@article {pmid39283121,
year = {2024},
author = {Machado, DT and Dias, BdC and Cayô, R and Gales, AC and Marques de Carvalho, F and Vasconcelos, ATR},
title = {Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation.},
journal = {Microbiology spectrum},
volume = {12},
number = {11},
pages = {e0211324},
pmid = {39283121},
issn = {2165-0497},
support = {E-26/210.012/2020//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 88887.677436/2022-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 402659/2018-0,443805/2018-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; OPP1193112//Bill and Melinda Gates Foundation (GF)/ ; 88887.508687/2020-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 302023/2024-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 307915/2022-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 312066/2019-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; E-26/201.046/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; },
mesh = {Animals ; *Spores, Bacterial/genetics/growth &amp; development ; *Phylogeny ; *Metagenome ; *Genome, Bacterial/genetics ; *Firmicutes/genetics/classification ; Humans ; Cattle ; Swine ; Gastrointestinal Microbiome/genetics ; Vertebrates/microbiology ; Poultry/microbiology ; },
abstract = {Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia (Borkfalkiaceae, Lachnospiraceae, Monoglobaceae, and Oscillospiraceae families) and Bacilli (Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia, Bacilli, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia, Bacilli, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.},
}
@article {pmid39282566,
year = {2024},
author = {Abdelshafy Mohamad, OA and Liu, YH and Huang, Y and Kuchkarova, N and Dong, L and Jiao, JY and Fang, BZ and Ma, JB and Hatab, S and Li, WJ},
title = {Metabonomic analysis to identify exometabolome changes underlying antifungal and growth promotion mechanisms of endophytic Actinobacterium Streptomyces albidoflavus for sustainable agriculture practice.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1439798},
pmid = {39282566},
issn = {1664-302X},
abstract = {In recent years, there has been an increasing focus on microbial ecology and its possible impact on agricultural production, owing to its eco-friendly nature and sustainable use. The current study employs metabolomics technologies and bioinformatics approaches to identify changes in the exometabolome of Streptomyces albidoflavus B24. This research aims to shed light on the mechanisms and metabolites responsible for the antifungal and growth promotion strategies, with potential applications in sustainable agriculture. Metabolomic analysis was conducted using Q Exactive UPLC-MS/MS. Our findings indicate that a total of 3,840 metabolites were identified, with 137 metabolites exhibiting significant differences divided into 61 up and 75 downregulated metabolites based on VIP >1, |FC| >1, and p < 0.01. The interaction of S. albidoflavus B24 monoculture with the co-culture demonstrated a stronger correlation coefficient. The Principal Component Analysis (PCA) demonstrates that PCA1 accounted for 23.36%, while PCA2 accounted for 20.28% distinction. OPLS-DA score plots indicate significant separation among different groups representing (t1) 24% as the predicted component (to1) depicts 14% as the orthogonal component. According to the findings of this comprehensive study, crude extracts from S. albidoflavus demonstrated varying abilities to impede phytopathogen growth and enhance root and shoot length in tested plants. Through untargeted metabolomics, we discovered numerous potential molecules with antagonistic activity against fungal phytopathogens among the top 10 significant metabolites with the highest absolute log2FC values. These include Tetrangulol, 4-Hydroxybenzaldehyde, and Cyclohexane. Additionally, we identified plant growth-regulating metabolites such as N-Succinyl-L-glutamate, Nicotinic acid, L-Aspartate, and Indole-3-acetamide. The KEGG pathway analysis has highlighted these compounds as potential sources of antimicrobial properties. The inhibitory effect of S. albidoflavus crude extracts on pathogen growth is primarily attributed to the presence of specific gene clusters responsible for producing cyclic peptides such as ansamycins, porphyrin, alkaloid derivatives, and neomycin. Overall, it is apparent that crude extracts from S. albidoflavus exhibited varying abilities to inhibit the growth of three phytopathogens and enhancement in both root and shoot length of tested plants. This research enhances our understanding of how secondary metabolites contribute to growth promotion and biocontrol, supporting ecosystem sustainability and resilience while boosting productivity in sustainable agriculture.},
}
@article {pmid39282232,
year = {2024},
author = {Taylor, T and Daksa, J and Shimels, MZ and Etalo, DW and Thiombiano, B and Walmsey, A and Chen, AJ and Bouwmeester, HJ and Raaijmakers, JM and Brady, SM and Kawa, D},
title = {Evaluating Mechanisms of Soil Microbiome Suppression of Striga Infection in Sorghum.},
journal = {Bio-protocol},
volume = {14},
number = {17},
pages = {e5058},
pmid = {39282232},
issn = {2331-8325},
abstract = {The root parasitic weed Striga hermonthica has a devastating effect on sorghum and other cereal crops in Sub-Saharan Africa. Available Striga management strategies are rarely sufficient or not widely accessible or affordable. Identification of soil- or plant-associated microorganisms that interfere in the Striga infection cycle holds potential for development of complementary biological control measures. Such inoculants should be preferably based on microbes native to the regions of their application. We developed a method to assess microbiome-based soil suppressiveness to Striga with a minimal amount of field-collected soil. We previously used this method to identify the mechanisms of microbe-mediated suppression of Striga infection and to test individual microbial strains. Here, we present protocols to assess the functional potential of the soil microbiome and individual bacterial taxa that adversely affect Striga parasitism in sorghum via three major known suppression mechanisms. These methods can be further extended to other Striga hosts and other root parasitic weeds. Key features • This protocol provides a detailed description of the methods used in Kawa et al. [1]. • This protocol is optimized to assess soil suppressiveness to Striga infection by using natural field-collected soil and the same soil sterilized by gamma-radiation. • This protocol is optimized to test bacterial (and not fungal) isolates. • This protocol can be easily extended to other host-parasite-microbiome systems.},
}
@article {pmid39277779,
year = {2024},
author = {Boltz, JP and Rittmann, BE},
title = {Microbial ecology of nitrate-, selenate-, selenite-, and sulfate-reducing bacteria in a H2-driven bioprocess.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {11},
pages = {},
pmid = {39277779},
issn = {1574-6941},
mesh = {*Nitrates/metabolism ; *Sulfates/metabolism ; *Bioreactors/microbiology ; *Selenic Acid/metabolism ; *Hydrogen/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development/classification ; *Selenious Acid/metabolism ; *Oxidation-Reduction ; Wastewater/microbiology ; Selenium Compounds/metabolism ; Biofilms/growth &amp; development ; Autotrophic Processes ; },
abstract = {A hydrogen (H2)-based membrane biofilm reactor (H2-MBfR) can reduce electron acceptors nitrate (NO3-), selenate (SeO42-), selenite (HSeO3-), and sulfate (SO42-), which are in wastewaters from coal mining and combustion. This work presents a model to describe a H2-driven microbial community comprised of hydrogenotrophic and heterotrophic bacteria that respire NO3-, SeO42-, HSeO3-, and SO42-. The model provides mechanistic insights into the interactions between autotrophic and heterotrophic bacteria in a microbial community that is founded on H2-based autotrophy. Simulations were carried out for a range of relevant solids retention times (SRT; 0.1-20 days) and with adequate H2-delivery capacity to reduce all electron acceptors. Bacterial activity began at an ∼0.6-day SRT, when hydrogenotrophic denitrifiers began to accumulate. Selenate-reducing and selenite-reducing hydrogenotrophs became established next, at SRTs of ∼1.2 and 2 days, respectively. Full NO3-, SeO42-, and HSeO3- reductions were complete by an SRT of ∼5 days. SO42- reduction began at an SRT of ∼10 days and was complete by ∼15 days. The desired goal of reducing NO3-, SeO42-, and HSeO3-, but not SO42-, was achievable within an SRT window of 5-10 days. Autotrophic hydrogenotrophs dominated the active biomass, but nonactive solids were a major portion of the solids, especially for an SRT ≥ 5 days.},
}
@article {pmid39267336,
year = {2024},
author = {Du, X and Guo, Y and Zhao, X and Zhang, L and Fan, R and Li, Y},
title = {METTL3-mediated TIM1 promotes macrophage M1 polarization and inflammation through IGF2BP2-dependent manner.},
journal = {Journal of biochemical and molecular toxicology},
volume = {38},
number = {10},
pages = {e23845},
doi = {10.1002/jbt.23845},
pmid = {39267336},
issn = {1099-0461},
support = {20210302124578//This study was supported by the Shanxi Province Basic Research Program Project/ ; },
mesh = {Humans ; *Macrophages/metabolism ; *Inflammation/metabolism/pathology/genetics ; *Hepatitis A Virus Cellular Receptor 1/metabolism/genetics ; *Methyltransferases/metabolism/genetics ; *RNA-Binding Proteins/metabolism/genetics ; THP-1 Cells ; Lipopolysaccharides/pharmacology ; },
abstract = {Macrophage polarization and inflammation may play an important role in the development of sepsis. T-cell immunoglobulin mucin 1 (TIM1) has been demonstrated to promote macrophage inflammatory responses. However, whether TIM1 regulates macrophage polarization and inflammation to affect sepsis development remains unclear. Human monocytic leukemia cell line was induced into macrophages, followed by stimulated with LPS and IL-4 to induce M1 polarization and M2 polarization. The expression levels of TIM1, methyltransferase 3 (METTL3), and insulin like growth factor 2 mRNA binding protein 2 (IGF2BP2) were examined by qRT-PCR and western blot. IL-6, IL-1β, and TNF-α levels were tested by ELISA. CD86[+]cell rate was analyzed by flow cytometry. The m[6]A methylation level of TIM1 was assessed by MeRIP assay. The interaction of between TIM1 and METTL3 or IGF2BP2 was assessed by dual-luciferase reporter assay and RIP assay. TIM1 knockdown repressed LPS-induced macrophage M1 polarization and inflammation. In terms of mechanism, METTL3 promoted TIM1 expression through m[6]A modification, and this modification could be recognized by IGF2BP2. Besides, knockdown of METTL3/IGF2BP2 suppressed LPS-induced macrophage M1 polarization and inflammation, while this effect could be eliminated by TIM1 overexpression. METTL3/IGF2BP2/TIM1 axis promoted macrophage M1 polarization and inflammation, which might provide potential target for sepsis treatment.},
}
@article {pmid39273112,
year = {2024},
author = {Druker, S and Sicsic, R and Ravid, S and Scheinin, S and Raz, T},
title = {Reproductive Tract Microbial Transitions from Late Gestation to Early Postpartum Using 16S rRNA Metagenetic Profiling in First-Pregnancy Heifers.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273112},
issn = {1422-0067},
mesh = {Female ; Animals ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Cattle ; *Postpartum Period ; *Vagina/microbiology ; *Microbiota/genetics ; *Uterus/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; },
abstract = {Studies in recent years indicate that reproductive tract microbial communities are crucial for shaping mammals' health and reproductive outcomes. Following parturition, uterine bacterial contamination often occurs due to the open cervix, which may lead to postpartum uterine inflammatory diseases, especially in primiparous individuals. However, investigations into spatio-temporal microbial transitions in the reproductive tract of primigravid females remain limited. Our objective was to describe and compare the microbial community compositions in the vagina at late gestation and in the vagina and uterus at early postpartum in first-pregnancy heifers. Three swab samples were collected from 33 first-pregnancy Holstein Friesian heifers: one vaginal sample at gestation day 258 ± 4, and vaginal and uterine samples at postpartum day 7 ± 2. Each sample underwent 16S rRNA V4 region metagenetic analysis via Illumina MiSeq, with bioinformatics following Mothur MiSeq SOP. The reproductive tract bacterial communities were assigned to 1255 genus-level OTUs across 30 phyla. Dominant phyla, accounting for approximately 90% of the communities, included Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria. However, the results revealed distinct shifts in microbial composition between the prepartum vagina (Vag-pre), postpartum vagina (Vag-post), and postpartum uterus (Utr-post). The Vag-pre and Utr-post microbial profiles were the most distinct. The Utr-post group had lower relative abundances of Proteobacteria but higher abundances of Bacteroidetes, Fusobacteria, and Tenericutes compared to Vag-pre, while Vag-post displayed intermediate values for these phyla, suggesting a transitional profile. Additionally, the Utr-post group exhibited lower bacterial richness and diversity compared to both Vag-pre and Vag-post. The unsupervised probabilistic Dirichlet Multinomial Mixtures model identified two distinct community types: most Vag-pre samples clustered into one type and Utr-post samples into another, while Vag-post samples were distributed evenly between the two. LEfSe analysis revealed distinct microbial profiles at the genus level. Overall, specific microbial markers were associated with anatomical and temporal transitions, revealing a dynamic microbial landscape during the first pregnancy and parturition. These differences highlight the complexity of these ecosystems and open new avenues for research in reproductive biology and microbial ecology.},
}
@article {pmid39272492,
year = {2024},
author = {Nerini, M and Russo, A and Decorosi, F and Meriggi, N and Viti, C and Cavalieri, D and Marvasi, M},
title = {A Microbial Phenomics Approach to Determine Metabolic Signatures to Enhance Seabream Sparus aurata Traceability, Differentiating between Wild-Caught and Farmed.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {17},
pages = {},
pmid = {39272492},
issn = {2304-8158},
support = {2/SSL/16/TO-1/ICR/21/TO//Regione Toscana with the project PO FEAMP 2014-2020 - Misura 1.39 SSL FLAG Costa degli Etrusch/ ; },
abstract = {BACKGROUND: The need for efficient and simplified techniques for seafood traceability is growing. This study proposes the Biolog EcoPlate assay as an innovative method for assessing wild and farmed Sparus aurata traceability, offering advantages over other molecular techniques in terms of technical simplicity.<br><br>METHODS: The Biolog EcoPlate assay, known for its high-throughput capabilities in microbial ecology, was utilized to evaluate the functional diversity of microbial communities from various organs of S. aurata (seabream) from the Mediterranean area. Samples were taken from the anterior and posterior gut, cloaca swabs and gills to distinguish between farmed and wild-caught individuals. The analysis focused on color development in OmniLog Units for specific carbon sources at 48 h.<br><br>RESULTS: Gills provided the most accurate clusterization of sample origin. The assay monitored the development of color for carbon sources such as &#x3b1;-cyclodextrin, D-cellobiose, glycogen, &#x3b1;-D-lactose, L-threonine and L-phenylalanine. A mock experiment using principal component analysis (PCA) successfully identified the origin of a blind sample. Shannon and Simpson indexes were used to statistically assess the diversity, reflecting the clusterization of different organ samples; Conclusions: The Biolog EcoPlate assay proves to be a quick, cost-effective method for discriminate S. aurata traceability (wild vs. farmed), demonstrating reliable reproducibility and effective differentiation between farmed and wild-caught seabream.},
}
@article {pmid39268533,
year = {2024},
author = {Wilson, T and Siddiqi, M and Xi, Y and LaPointe, G},
title = {Tracking the microbial communities from the farm to the processing facility of a washed-rind cheese operation.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1404795},
pmid = {39268533},
issn = {1664-302X},
abstract = {Milk residue and the accompanying biofilm accumulation in milking systems can compromise the microbial quality of milk and the downstream processes of cheese production. Over a six-month study, the microbial ecosystems of milk (n = 24), tap water (n = 24) and environmental swabs (n = 384) were cultured by plating decimal dilutions to obtain viable counts of total aerobic mesophilic lactose-utilizing bacteria (lactose-M17), lactic acid bacteria (MRS), yeasts and molds (Yeast, Glucose, Chloramphenicol (YGC) medium). Viable aerobic lactose-M17 plate counts of milk remained well below 4.7 log CFU/ml over five of the months, except for 1 week in November where milk at the facility exceeded 5 log CFU/ml. Swab samples of the farm milking equipment showed consistent viable counts after sanitation, while the bulk tank swabs contained the lowest counts. Viable counts from swabs of the facility were generally below the detection limit in the majority of samples with occasional residual contamination on some food contact surfaces. Extracted DNA was amplified using primers targeting the V3-V4 region of the 16S rRNA gene, and the amplicons were sequenced by MiSeq to determine the shared microbiota between the farm and the processing facility (8 genera). Culture independent analysis of bacterial taxa in milk, water and residual contamination after sanitation with swab samples revealed the shared and distinct microbiota between the sample types of both facilities. Amplicon sequence variants (ASVs) of the V3-V4 region of the 16S rRNA gene revealed that the microbiota of milk samples had lower diversity than water or environmental swabs (279 ASVs compared to 3,444 in water and 8,747 in environmental swabs). Brevibacterium and Yaniella (both Actinomycetota) were observed in all sampling types. Further studies will include whole genome sequencing of Brevibacterium spp. isolates to determine their functionality and diversity within the system.},
}
@article {pmid39266780,
year = {2024},
author = {Cao, X and Li, M and Wu, X and Fan, S and Lin, L and Xu, L and Zhang, X and Zhou, F},
title = {Gut fungal diversity across different life stages of the onion fly Delia antiqua.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {115},
pmid = {39266780},
issn = {1432-184X},
mesh = {Animals ; *Diptera/microbiology/growth &amp; development ; *Fungi/classification/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; *Larva/microbiology/growth &amp; development ; Male ; Female ; Pupa/microbiology/growth &amp; development ; Biodiversity ; Life Cycle Stages ; Mycobiome ; },
abstract = {A significant number of microorganisms inhabit the intestinal tract or the body surface of insects. While the majority of research on insect microbiome interaction has mainly focused on bacteria, of late multiple studies have been acknowledging the importance of fungi and have started reporting the fungal communities as well. In this study, high-throughput sequencing was used to compare the diversity of intestinal fungi in Delia antiqua (Diptera: Anthomyiidae) at different growth stages, and effect of differential fungi between adjacent life stages on the growth and development of D. antiqua was investigated. The results showed that there were significant differences in the α and β diversity of gut fungal communities between two adjacent growth stages. Among the dominant fungi, genera Penicillium and Meyerozyma and family Cordycipitaceae had higher abundances. Cordycipitaceae was mainly enriched in the pupal and adult (male and female) stages, Penicillium was mainly enriched in the pupal, 2nd instar and 3rd instar larval stages, and Meyerozyma was enriched in the pupal stage. Only three fungal species were found to differ between two adjacent growth stages. These three fungal species including Fusarium oxysporum, Meyerozyma guilliermondii and Penicillium roqueforti generally inhibited the growth and development of D. antiqua, with only P. roqueforti promoting the growth and development of female insects. This study will provide theoretical support for the search for new pathogenic microorganisms for other fly pests control and the development of new biological control strategies for fly pests.},
}
@article {pmid39264951,
year = {2024},
author = {Pfennig, T and Kullmann, E and Zavřel, T and Nakielski, A and Ebenhöh, O and Červený, J and Bernát, G and Matuszyńska, AB},
title = {Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012445},
pmid = {39264951},
issn = {1553-7358},
mesh = {*Photosynthesis/physiology ; *Synechocystis/metabolism/physiology ; *Light ; *Models, Biological ; Computational Biology ; Carbon Dioxide/metabolism ; Carbon Cycle/physiology ; Phycobilisomes/metabolism ; Computer Simulation ; },
abstract = {Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.},
}
@article {pmid39264809,
year = {2024},
author = {Boverhoff, D and Kool, J and Pijnacker, R and Ducarmon, QR and Zeller, G and Shetty, S and Sie, S and Mulder, AC and van der Klis, F and Franz, E and Mughini-Gras, L and van Baarle, D and Fuentes, S},
title = {Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands.},
journal = {Cell reports},
volume = {43},
number = {9},
pages = {114729},
doi = {10.1016/j.celrep.2024.114729},
pmid = {39264809},
issn = {2211-1247},
mesh = {Netherlands ; Humans ; *Feces/microbiology ; Adult ; Aged ; Middle Aged ; Adolescent ; Child, Preschool ; Aged, 80 and over ; Child ; Infant ; Male ; Female ; Young Adult ; Infant, Newborn ; Longevity ; Gastrointestinal Microbiome/genetics ; Microbiota ; },
abstract = {Defining what constitutes a healthy microbiome throughout our lives remains an ongoing challenge. Understanding to what extent host and environmental factors can influence it has been the primary motivation for large population studies worldwide. Here, we describe the fecal microbiome of 3,746 individuals (0-87 years of age) in a nationwide study in the Netherlands, in association with extensive questionnaires. We validate previous findings, such as infant-adult trajectories, and explore the collective impact of our variables, which explain over 40% of the variation in microbiome composition. We identify associations with less explored factors, particularly those ethnic related, which show the largest impact on the adult microbiome composition, diversity, metabolic profiles, and CAZy (carbohydrate-active enzyme) repertoires. Understanding the sources of microbiome variability is crucial, given its potential as a modifiable target with therapeutic possibilities. With this work, we aim to serve as a foundational element for the design of health interventions and fundamental research.},
}
@article {pmid39264366,
year = {2024},
author = {Yüksel, E and Voragen, AGJ and Kort, R},
title = {The pectin metabolizing capacity of the human gut microbiota.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/10408398.2024.2400235},
pmid = {39264366},
issn = {1549-7852},
abstract = {The human gastrointestinal microbiota, densely populated with a diverse array of microorganisms primarily from the bacterial phyla Bacteroidota, Bacillota, and Actinomycetota, is crucial for maintaining health and physiological functions. Dietary fibers, particularly pectin, significantly influence the composition and metabolic activity of the gut microbiome. Pectin is fermented by gut bacteria using carbohydrate-active enzymes (CAZymes), resulting in the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which provide various health benefits. The gastrointestinal microbiota has evolved to produce CAZymes that target different pectin components, facilitating cross-feeding within the microbial community. This review explores the fermentation of pectin by various gut bacteria, focusing on the involved transport systems, CAZyme families, SCFA synthesis capacity, and effects on microbial ecology in the gut. It addresses the complexities of the gut microbiome's response to pectin and highlights the importance of microbial cross-feeding in maintaining a balanced and diverse gut ecosystem. Through a systematic analysis of pectinolytic CAZyme production, this review provides insights into the enzymatic mechanisms underlying pectin degradation and their broader implications for human health, paving the way for more targeted and personalized dietary strategies.},
}
@article {pmid39264291,
year = {2024},
author = {Jones, BS and DeWitt, ME and Wenner, JJ and Sanders, JW},
title = {Lyme Disease Under-Ascertainment During the COVID-19 Pandemic in the United States: Retrospective Study.},
journal = {JMIR public health and surveillance},
volume = {10},
number = {},
pages = {e56571},
pmid = {39264291},
issn = {2369-2960},
mesh = {Humans ; *Lyme Disease/epidemiology ; *COVID-19/epidemiology ; United States/epidemiology ; North Carolina/epidemiology ; Retrospective Studies ; Pandemics ; Bayes Theorem ; },
abstract = {BACKGROUND: The COVID-19 pandemic resulted in a massive disruption in access to care and thus passive, hospital- and clinic-based surveillance programs. In 2020, the reported cases of Lyme disease were the lowest both across the United States and North Carolina in recent years. During this period, human contact patterns began to shift with higher rates of greenspace utilization and outdoor activities, putting more people into contact with potential vectors and associated vector-borne diseases. Lyme disease reporting relies on passive surveillance systems, which were likely disrupted by changes in health care-seeking behavior during the pandemic.<br><br>OBJECTIVE: This study aimed to quantify the likely under-ascertainment of cases of Lyme disease during the COVID-19 pandemic in the United States and North Carolina.<br><br>METHODS: We fitted publicly available, reported Lyme disease cases for both the United States and North Carolina prior to the year 2020 to predict the number of anticipated Lyme disease cases in the absence of the pandemic using a Bayesian modeling approach. We then compared the ratio of reported cases divided by the predicted cases to quantify the number of likely under-ascertained cases. We then fitted geospatial models to further quantify the spatial distribution of the likely under-ascertained cases and characterize spatial dynamics at local scales.<br><br>RESULTS: Reported cases of Lyme Disease were lower in 2020 in both the United States and North Carolina than prior years. Our findings suggest that roughly 14,200 cases may have gone undetected given historical trends prior to the pandemic. Furthermore, we estimate that only 40% to 80% of Lyme diseases cases were detected in North Carolina between August 2020 and February 2021, the peak months of the COVID-19 pandemic in both the United States and North Carolina, with prior ascertainment rates returning to normal levels after this period. Our models suggest both strong temporal effects with higher numbers of cases reported in the summer months as well as strong geographic effects.<br><br>CONCLUSIONS: Ascertainment rates of Lyme disease were highly variable during the pandemic period both at national and subnational scales. Our findings suggest that there may have been a substantial number of unreported Lyme disease cases despite an apparent increase in greenspace utilization. The use of counterfactual modeling using spatial and historical trends can provide insight into the likely numbers of missed cases. Variable ascertainment of cases has implications for passive surveillance programs, especially in the trending of disease morbidity and outbreak detection, suggesting that other methods may be appropriate for outbreak detection during disturbances to these passive surveillance systems.},
}
@article {pmid39260494,
year = {2024},
author = {Ejaz, MR and Badr, K and Hassan, ZU and Al-Thani, R and Jaoua, S},
title = {Metagenomic approaches and opportunities in arid soil research.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {176173},
doi = {10.1016/j.scitotenv.2024.176173},
pmid = {39260494},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Metagenomics ; *Soil/chemistry ; Desert Climate ; Microbiota ; },
abstract = {Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.},
}
@article {pmid39259499,
year = {2024},
author = {Schwab, ST and Bühler, LY and Schleheck, D and Nelson, TF and Mecking, S},
title = {Correlation of Enzymatic Depolymerization Rates with the Structure of Polyethylene-Like Long-Chain Aliphatic Polyesters.},
journal = {ACS macro letters},
volume = {13},
number = {10},
pages = {1245-1250},
pmid = {39259499},
issn = {2161-1653},
abstract = {Long-chain aliphatic polyesters are emerging sustainable materials that exhibit polyethylene-like properties while being amenable to chemical recycling and biodegradation. However, varying polyester chemical structures results in markedly different degradation rates, which cannot be predicted from commonly correlated bulk polyester properties, such as polymer melting temperature. To elucidate these structure-degradability relationships, long-chain polyesters varying in their monomer composition and crystallinity were subjected to enzymatic hydrolysis, the rates of which were quantified via detection of formed monomers. Copolymers with poorly water-soluble, long-chain diol monomers (e.g., 1,18-octadecanediol) demonstrated strongly reduced depolymerization rates compared to copolymers with shorter chain length diol monomers. This was illustrated by, e.g., the 20× faster hydrolysis of PE-4,18, consisting of 1,4-butanediol and 1,18-octadecanedicarboxylic acid monomers, relative to PE-18,4. The insoluble long-chain diol monomer released upon hydrolysis was proposed to remain attached to the bulk polymer surface, decreasing the accessibility of the remaining ester bonds to enzymes for further hydrolysis. Tuning of polyester crystallinity via the introduction of branched monomers led to variable hydrolysis rates, which increased by an order of magnitude when crystallinity decreased from 72% to 45%. The results reported enables the informed design of polyester structures with balanced material properties and amenability to depolymerization.},
}
@article {pmid39259393,
year = {2024},
author = {Berlow, M and Mesa, M and Creek, M and Duarte, JG and Carpenter, E and Phinizy, B and Andonian, K and Dlugosch, KM},
title = {Plant G × Microbial E: Plant Genotype Interaction with Soil Bacterial Community Shapes Rhizosphere Composition During Invasion.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {113},
pmid = {39259393},
issn = {1432-184X},
support = {1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 2023-67012-40306//USDA/ ; 2023-67013-40169//USDA/ ; 2023-67013-40169//USDA/ ; },
mesh = {*Soil Microbiology ; *Rhizosphere ; *Introduced Species ; *Genotype ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Centaurea/microbiology/genetics ; Plant Roots/microbiology ; California ; Soil/chemistry ; },
abstract = {It is increasingly recognized that different genetic variants of hosts can uniquely shape their microbiomes. Invasive species often evolve in their introduced ranges, but little is known about the potential for their microbial associations to change during invasion as a result. We asked whether host genotype (G), microbial environment (E), or their interaction (G × E) affected the composition and diversity of host-associated microbiomes in Centaurea solstitialis (yellow starthistle), a Eurasian plant that is known to have evolved novel genotypes and phenotypes and to have altered microbial interactions, in its severe invasion of CA, USA. We conducted an experiment in which native and invading plant genotypes were inoculated with native and invaded range soil microbial communities. We used amplicon sequencing to characterize rhizosphere bacteria in both the experiment and the field soils from which they were derived. We found that native and invading plant genotypes accumulated different microbial associations at the family level in each soil community, often counter to differences in family abundance between soil communities. Root associations with potentially beneficial Streptomycetaceae were particularly interesting, as these were more abundant in the invaded range field soil and accumulated on invading genotypes. We also found that bacterial diversity is higher in invaded soils, but that invading genotypes accumulated a lower diversity of bacteria and unique microbial composition in experimental inoculations, relative to native genotypes. Thus variation in microbial associations of invaders was driven by the interaction of plant G and microbial E, and rhizosphere microbial communities appear to change in composition in response to host evolution during invasion.},
}
@article {pmid39259373,
year = {2024},
author = {Zhang, K and Tan, X and Zhang, Q},
title = {Nutritional Quality of Basal Resource in Stream Food Webs Increased with Light Reduction-Implications for Riparian Revegetation.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {114},
pmid = {39259373},
issn = {1432-184X},
support = {Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; },
mesh = {*Rivers/microbiology/chemistry ; *Food Chain ; *Fatty Acids, Unsaturated/analysis/metabolism ; *Light ; Cyanobacteria/metabolism/growth &amp; development ; Chlorophyta/metabolism/growth &amp; development ; Diatoms/metabolism/growth &amp; development ; Nutritive Value ; },
abstract = {Biofilms are considered a basal resource with high nutritional quality in stream food webs, as periphytic algae are abundant of polyunsaturated fatty acids (PUFAs). PUFAs are essential for growth and reproduction of consumers who cannot or have very limited capacity to biosynthesize. Yet, how the nutritional quality based on PUFA of basal food sources changes with light intensity remains unclear. We conducted a manipulative experiment in mesocosms to explore the response and mechanisms of nutritional quality to shading, simulating riparian restoration. We found a significant increase in PUFA% (including arachidonic acid, ARA) under shading conditions. The increased PUFA is caused by the algal community succession from Cyanobacteria and Chlorophyta to Bacillariophyta which is abundant of PUFA (especially eicosapentaenoic acid, EPA; docosahexaenoic acid, DHA). On the other hand, shading increased PUFA via upregulating enzymes such as Δ12 desaturase (FAD2, EC:1.14.19.6) and 3-ketoacyl-CoA synthase (KCS, EC:2.3.1.199) in the biosynthesis of unsaturated fatty acid elongation pathways. Our findings imply that riparian reforestation by decreasing light intensity increases the nutritional quality of basal resources in streams, which may enhance transfer of good quality carbon to consumers in higher trophic levels through bottom-up effects.},
}
@article {pmid39258201,
year = {2024},
author = {Iliopoulou, S and Kourteli, M and Damialis, A and Kapsanaki-Gotsi, E and Pyrri, I},
title = {Air mycobiome in the National Library of Greece following relocation to novel premises.},
journal = {Heliyon},
volume = {10},
number = {16},
pages = {e36362},
pmid = {39258201},
issn = {2405-8440},
abstract = {The aim of this work was to study the diversity and spatiotemporal fluctuations of airborne fungi in the National Library of Greece after its relocation from the Vallianeio historic building in the center of Athens to entirely new premises at the Stavros Niarchos Foundation Cultural Center, and also to compare the fungal aerosol in between the two sites. The air mycobiota were studied by a volumetric culture-based method, during the year 2019 in order to assess their diversity and abundance and to compare with those previously reported in the historic building. Twenty-eight genera of filamentous fungi were recovered indoors and 17 outdoors, in addition to yeasts registered as a group. The number of fungal genera recovered was almost similar in both premises, whereas seventeen genera indoors were identical, dominated by Penicillium, Cladosporium and Aspergillus. The mean daily fungal concentration was found to be 66 CFU m[-3] indoors and 927 CFU m[-3] outdoors in the new location vs 293 and 428 CFU m[-] [3] indoors and 707 and 648 CFU m[-] [3] outdoors in the previous one. The mean daily concentration indoors was consistently and significantly lower (P < 0.05) in the new building than in the historic one, although it was higher outdoors. The indoor/outdoor ratio for the total fungi was 0.07 in the new vs 0.41 and 0.66 in the previous one and reveals a superior indoor air quality in the new site. Air temperature and occupancy had a statistically significant impact on the concentration of indoor fungi. The remarkably reduced concentration of the mycobiota in the new premises indicated a considerable decline in fungal burden, mainly due to technological excellency of the facility and continuous preventive measures to ensure an enhanced indoor air quality in the National Library of Greece. This case study provides a paradigm about upgrading of indoor air after re-establishment of a facility in another setting.},
}
@article {pmid39256405,
year = {2024},
author = {Gan, L and Zheng, J and Xu, WH and Lin, J and Liu, J and Zhang, Y and Wu, Z and Lv, Z and Jia, Y and Guo, Q and Chen, S and Liu, C and Defoirdt, T and Qin, Q and Liu, Y},
title = {Author Correction: Deciphering the virulent Vibrio harveyi causing spoilage in muscle of aquatic crustacean Litopenaeus vannamei.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21131},
doi = {10.1038/s41598-024-71652-4},
pmid = {39256405},
issn = {2045-2322},
}
@article {pmid39256399,
year = {2024},
author = {Huang, WRH and Braam, C and Kretschmer, C and Villanueva, SL and Liu, H and Ferik, F and van der Burgh, AM and Boeren, S and Wu, J and Zhang, L and Nürnberger, T and Wang, Y and Seidl, MF and Evangelisti, E and Stuttmann, J and Joosten, MHAJ},
title = {Author Correction: Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7910},
doi = {10.1038/s41467-024-52322-5},
pmid = {39256399},
issn = {2041-1723},
}
@article {pmid39255667,
year = {2024},
author = {Mei, Z and Wang, F and Fu, Y and Liu, Y and Hashsham, SA and Wang, Y and Harindintwali, JD and Dou, Q and Virta, M and Jiang, X and Deng, Y and Zhang, T and Tiedje, JM},
title = {Biofilm enhanced the mitigations of antibiotics and resistome in sulfadiazine and trimethoprim co-contaminated soils.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135721},
pmid = {39255667},
issn = {1873-3336},
support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; },
mesh = {*Sulfadiazine/pharmacology ; *Biofilms/drug effects ; *Trimethoprim/pharmacology ; *Soil Pollutants/toxicity ; *Anti-Bacterial Agents/pharmacology ; *Soil Microbiology ; *Manure/microbiology ; Arthrobacter/genetics/drug effects/metabolism ; Charcoal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; },
abstract = {Reducing antibiotic levels in soil ecosystems is vital to curb the dissemination of antimicrobial resistance genes (ARGs) and mitigate global health threats. However, gaps persist in understanding how antibiotic resistome can be suppressed during antibiotic degradation. Herein, we investigate the efficacy of a biochar biofilm incorporating antibiotics-degrading bacterial strain (Arthrobacter sp. D2) to mitigate antibiotic resistome in non-manured and manure-amended soils with sulfadiazine (SDZ) and trimethoprim (TMP) contamination. Results show that biofilm enhanced SDZ degradation by 83.0% within three days and increased TMP attenuation by 55.4% over 60 days in non-manured soils. In the non-manured black soil, the relative abundance of ARGs increased initially after biofilm inoculation. However, by day 30, it decreased by 20.5% compared to the controls. Moreover, after 7 days, biofilm reduced TMP by 38.5% in manured soils and decreased the total ARG abundance by 19.0%. Thus, while SDZ degradation did not increase sulfonamide resistance genes, TMP dissipation led to a proliferation of insertion sequences and related TMP resistance genes. This study underscores the importance of antibiotic degradation in reducing related ARGs while cautioning against the potential proliferation and various ARGs transfer by resistant microorganisms.},
}
@article {pmid39254334,
year = {2024},
author = {Lyng, M and Þórisdóttir, B and Sveinsdóttir, SH and Hansen, ML and Jelsbak, L and Maróti, G and Kovács, &#xc1;T},
title = {Taxonomy of Pseudomonas spp. determines interactions with Bacillus subtilis.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0021224},
pmid = {39254334},
issn = {2379-5077},
support = {DNRF137//Danmarks Grundforskningsfond (DNRF)/ ; NNF19SA0059360//Novo Nordisk Fonden (NNF)/ ; NNF19OC0055625//Novo Nordisk Fonden (NNF)/ ; PhD fellowship//Technical University of Denmark/ ; },
mesh = {*Pseudomonas/physiology ; *Bacillus subtilis/physiology ; *Soil Microbiology ; *Microbial Interactions/physiology ; Rhizosphere ; },
abstract = {UNLABELLED: Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila, and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini. Using such a non-inhibiting isolate, Pseudomonas P9_31, which increased B. subtilis pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.<br><br>IMPORTANCE: There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other's growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720 Pseudomonas isolates, and their impact on the biofilm formation of Bacillus subtilis was tested. The aim was to determine whether a majority of Pseudomonas will promote or inhibit the biofilms of B. subtilis in the co-cultures. This study reports that Pseudomonas taxonomy is a good predictor of interaction outcome, and only a minority of Pseudomonas isolates promote Bacillus biofilm establishment.},
}
@article {pmid39252061,
year = {2024},
author = {Trego, A and O'Sullivan, S and O'Flaherty, V and Collins, G and Ijaz, UZ},
title = {Individual methanogenic granules are whole-ecosystem replicates with reproducible responses to environmental cues.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {68},
pmid = {39252061},
issn = {2524-6372},
support = {3C-BIOTECH 261330/ERC_/European Research Council/International ; 3C-BIOTECH 261330/ERC_/European Research Council/International ; 3C-BIOTECH 261330/ERC_/European Research Council/International ; TC/2014/0016//Enterprise Ireland/ ; 14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 17/CDA/4658/SFI_/Science Foundation Ireland/Ireland ; NE/L011956/1//Natural Environment Research Council/ ; },
abstract = {BACKGROUND: In this study, individual methanogenic (anaerobic), granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates were sourced from a lab-scale, engineered, biological wastewater treatment system, were size-separated, and the largest granules were individually subjected to controlled environmental cues in micro-batch reactors (μBRs).<br><br>RESULTS: Individual granules were identical with respect to the structure of the active community based on cDNA analysis. Additionally, it was observed that the active microbial community of individual granules, at the depth of 16S rRNA gene sequencing, produced reproducible responses to environmental changes in pH, temperature, substrate, and trace-metal supplementation. We identified resilient and susceptible taxa associated with each environmental condition tested, as well as selected specialists, whose niche preferences span the entire trophic chain required for the complete anaerobic degradation of organic matter.<br><br>CONCLUSIONS: We found that single anaerobic granules can be considered highly-replicated whole-ecosystems with potential usefulness for the field of microbial ecology. Additionally, they act as the smallest whole-community unit within the meta-community of an engineered bioreactor. When subjected to various environmental cues, anaerobic granules responded reproducibly allowing for rare or unique opportunities for high-throughput studies testing whole-community responses to a wide range of environmental conditions.},
}
@article {pmid39250422,
year = {2024},
author = {Vijay, S and Bao, NLH and Vinh, DN and Nhat, LTH and Thu, DDA and Quang, NL and Trieu, LPT and Nhung, HN and Ha, VTN and Thai, PVK and Ha, DTM and Lan, NH and Caws, M and Thwaites, GE and Javid, B and Thuong, NT},
title = {Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates from a longitudinal study.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39250422},
issn = {2050-084X},
support = {10.35802/207487/WT_/Wellcome Trust/United Kingdom ; R21 AI169005/AI/NIAID NIH HHS/United States ; R21AI169005//National Institute of Allergy and Infectious Diseases/ ; 10.35802/106680/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 10.35802/206724/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Rifampin/pharmacology ; *Mycobacterium tuberculosis/drug effects/genetics ; *Isoniazid/pharmacology ; Longitudinal Studies ; *Microbial Sensitivity Tests ; Humans ; *Antitubercular Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Tuberculosis, Multidrug-Resistant/microbiology/drug therapy ; Tuberculosis/microbiology/drug therapy ; },
abstract = {Antibiotic tolerance in Mycobacterium tuberculosis reduces bacterial killing, worsens treatment outcomes, and contributes to resistance. We studied rifampicin tolerance in isolates with or without isoniazid resistance (IR). Using a minimum duration of killing assay, we measured rifampicin survival in isoniazid-susceptible (IS, n=119) and resistant (IR, n=84) isolates, correlating tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs), and isoniazid-resistant mutations. Longitudinal IR isolates were analyzed for changes in rifampicin tolerance and genetic variant emergence. The median time for rifampicin to reduce the bacterial population by 90% (MDK90) increased from 1.23 days (IS) and 1.31 days (IR) to 2.55 days (IS) and 1.98 days (IR) over 15-60 days of incubation, indicating fast and slow-growing tolerant sub-populations. A 6 log10-fold survival fraction classified tolerance as low, medium, or high, showing that IR is linked to increased tolerance and faster growth (OR = 2.68 for low vs. medium, OR = 4.42 for low vs. high, p-trend = 0.0003). High tolerance in IR isolates was associated with rifampicin treatment in patients and genetic microvariants. These findings suggest that IR tuberculosis should be assessed for high rifampicin tolerance to optimize treatment and prevent the development of multi-drug-resistant tuberculosis.},
}
@article {pmid39249553,
year = {2024},
author = {Morimura, H and Ishigami, K and Sato, T and Sone, T and Kikuchi, Y},
title = {Geographical, Seasonal, and Growth-Related Dynamics of Gut Microbiota in a Grapevine Pest, Apolygus spinolae (Heteroptera: Miridae).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {112},
pmid = {39249553},
issn = {1432-184X},
support = {22KJ0057//Japan Society for the Promotion of Science/ ; 21K20579//Japan Society for the Promotion of Science/ ; S-3-7//Northern Advancement Center for Science and Technology/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Vitis/microbiology ; *Heteroptera/microbiology/growth &amp; development ; *Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; *Symbiosis ; Japan ; Nymph/microbiology/growth &amp; development ; },
abstract = {A number of insects are associated with gut symbiotic microorganisms, wherein symbiotic partners play pivotal metabolic roles for each other such as nutrient supplementation, diet degradation, and pesticide detoxification. Despite the ecological and evolutionary importance of gut microbial communities in insects, their diversity and dynamics remain unclear in many species. The green plant bug Apolygus spinolae, a notorious grapevine pest in Japan, damages grape shoots and severely reduces grape berry yield and quality. The plant bug possesses a simple tubular gut housing ~ 10[4] bacteria. Here, we investigated geographic, seasonal, and growth-related dynamics of gut microbiota by high-throughput sequencing in 82 individuals (11 nymphs and 71 adults) from five locations in Hokkaido, Japan. In plant bugs, gut microbiota changed dynamically depending on region, season, and developmental stage. Among the gut bacteria, Serratia was consistently and abundantly detected and was significantly affected by seasonal changes. In addition, Caballeronia, known as a specific symbiont in some stinkbug species, was abundantly detected, especially in insects collected in late summer despite A. spinolae complete lack of midgut crypts known as symbiotic organ harboring Caballeronia in other stinkbug species. Considering their prevalence among host bug populations, it is possible these gut microorganisms play a pivotal role in the adaptation of the green plant bug to grapevine fields, although further confirmation through rearing experiments is needed.},
}
@article {pmid39248572,
year = {2024},
author = {Sivaloganathan, DM and Wan, X and Leon, G and Brynildsen, MP},
title = {Loss of Gre factors leads to phenotypic heterogeneity and cheating in Escherichia coli populations under nitric oxide stress.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0222924},
pmid = {39248572},
issn = {2150-7511},
support = {CBET-1453325//National Science Foundation (NSF)/ ; PGSD3 - 516782 - 2018//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; Focused Research Team award on Precision Antibiotics//Princeton University (PU)/ ; },
mesh = {*Escherichia coli/genetics/metabolism/drug effects ; *Escherichia coli Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Hydrogen Peroxide/pharmacology/metabolism/toxicity ; *Nitric Oxide/metabolism ; Phenotype ; Stress, Physiological ; Transcription Factors/genetics/metabolism ; Transcriptional Elongation Factors/metabolism/genetics ; },
abstract = {Nitric oxide (·NO) is one of the toxic metabolites that bacteria can be exposed to within phagosomes. Gre factors, which are also known as transcript cleavage factors or transcription elongation factors, relieve back-tracked transcription elongation complexes by cleaving nascent RNAs, which allows transcription to resume after stalling. Here we discovered that loss of both Gre factors in Escherichia coli, GreA and GreB, significantly compromised ·NO detoxification due to ·NO-induced phenotypic heterogeneity in ΔgreAΔgreB populations, which did not occur in wild-type cultures. Under normal culturing conditions, both wild-type and ΔgreAΔgreB synthesized transcripts uniformly, whereas treatment with ·NO led to bimodal transcript levels in ΔgreAΔgreB that were unimodal in wild-type. Interestingly, exposure to another toxic metabolite of phagosomes, hydrogen peroxide (H2O2), produced analogous results. Furthermore, we showed that loss of Gre factors led to cheating under ·NO stress where transcriptionally deficient cells benefited from the detoxification activities of the transcriptionally proficient subpopulation. Collectively, these results show that loss of Gre factor activities produces phenotypic heterogeneity under ·NO and H2O2 stress that can yield cheating between subpopulations.IMPORTANCEToxic metabolite stress occurs in a broad range of contexts that are important to human health, microbial ecology, and biotechnology, whereas Gre factors are highly conserved throughout the bacterial kingdom. Here we discovered that loss of Gre factors in E. coli leads to phenotypic heterogeneity under ·NO and H2O2 stress, which we further show with ·NO results in cheating between subpopulations. Collectively, these data suggest that Gre factors play a role in coping with toxic metabolite stress, and that loss of Gre factors can produce cheating between neighbors.},
}
@article {pmid39248476,
year = {2024},
author = {Maitra, P and Hrynkiewicz, K and Szuba, A and Niestrawska, A and Mucha, J},
title = {The effects of Pinus sylvestris L. geographical origin on the community and co-occurrence of fungal and bacterial endophytes in a common garden experiment.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0080724},
pmid = {39248476},
issn = {2165-0497},
mesh = {*Pinus sylvestris/microbiology ; *Endophytes/classification/isolation &amp; purification/genetics/physiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/isolation &amp; purification/genetics/physiology ; *Plant Roots/microbiology ; *Microbiota ; Seasons ; Phylogeny ; Biodiversity ; },
abstract = {UNLABELLED: Below-ground microorganisms, particularly endophytes, are pivotal for plant establishment and functioning through nutrient acquisition and enhancing resistance to abiotic and biotic stresses. The impact of host plant origin within a species on the composition and interaction networks of root endophytic fungi and bacteria has been less explored compared with plant phylogeny and biological distance. This study investigates the effect of geographic origin on the fungal and bacterial microbiomes of Pinus sylvestris L. root endophytes. Roots from plants grown in a common garden, originating from six locations, were harvested in two distinct seasons. Fungal and bacterial microbiomes were analyzed using Illumina MiSeq sequencing. The operational taxonomic unit (OTU) richness of endophytic fungi and bacteria showed no significant variation due to tree origin or season. However, the Shannon diversity index for endophytic fungi was seasonally influenced. The composition of endophytic fungal and bacterial communities was affected by both tree origin and season, correlating with host root biochemical parameters, such as starch, total non-structural carbohydrates, carbon, nitrogen, and climatic factors, such as mean annual precipitation and temperature. Moreover, the abundance of specific endophytic fungi and bacteria varied across different P. sylvestris origins, depending on the season. The complexity of the co-occurrence networks of fungal and bacterial endophytes within P. sylvestris also differed by geographical origin and season. This study highlights the significant role of biochemical and climatic factors associated with tree origin in shaping interactions with endophytic communities, potentially affecting plant health and adaptability across diverse environments.<br><br>IMPORTANCE: This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine (Pinus sylvestris). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant-microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems.},
}
@article {pmid39248406,
year = {2024},
author = {Yuan, X and Qing, J and Zhi, W and Wu, F and Yan, Y and Li, Y},
title = {Gut and respiratory microbiota landscapes in IgA nephropathy: a cross-sectional study.},
journal = {Renal failure},
volume = {46},
number = {2},
pages = {2399749},
pmid = {39248406},
issn = {1525-6049},
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology ; Cross-Sectional Studies ; Male ; Female ; Adult ; *Gastrointestinal Microbiome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Machine Learning ; Case-Control Studies ; Bacteria/isolation &amp; purification/classification/genetics ; Microbiota ; Young Adult ; },
abstract = {BACKGROUND: IgA nephropathy (IgAN) is intimately linked to mucosal immune responses, with nasopharyngeal and intestinal lymphoid tissues being crucial for its abnormal mucosal immunity. The specific pathogenic bacteria in these sites associated with IgAN, however, remain elusive. Our study employs 16S rRNA sequencing and machine learning (ML) approaches to identify specific pathogenic bacteria in these locations and to investigate common pathogens that may exacerbate IgAN.<br><br>METHODS: In this cross-sectional analysis, we collected pharyngeal swabs and stool specimens from IgAN patients and healthy controls. We applied 16SrRNA sequencing to identify differential microbial populations. ML algorithms were then used to classify IgAN based on these microbial differences. Spearman correlation analysis was employed to link key bacteria with clinical parameters.<br><br>RESULTS: We observed a reduced microbial diversity in IgAN patients compared to healthy controls. In the gut microbiota of IgAN patients, increases in Bacteroides, Escherichia-Shigella, and Parabacteroides, and decreases in Parasutterella, Dialister, Faecalibacterium, and Subdoligranulum were notable. In the respiratory microbiota, increases in Neisseria, Streptococcus, Fusobacterium, Porphyromonas, and Ralstonia, and decreases in Prevotella, Leptotrichia, and Veillonella were observed. Post-immunosuppressive therapy, Oxalobacter and Butyricoccus levels were significantly reduced in the gut, while Neisseria and Actinobacillus levels decreased in the respiratory tract. Veillonella and Fusobacterium appeared to influence IgAN through dual immune loci, with Fusobacterium abundance correlating with IgAN severity.<br><br>CONCLUSIONS: This study revealing that changes in flora structure could provide important pathological insights for identifying therapeutic targets, and ML could facilitate noninvasive diagnostic methods for IgAN.},
}
@article {pmid39247694,
year = {2024},
author = {Nasher, F and Wren, BW},
title = {Unravelling mechanisms of bacterial recognition by Acanthamoeba: insights into microbial ecology and immune responses.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1405133},
pmid = {39247694},
issn = {1664-302X},
abstract = {Acanthamoeba, are ubiquitous eukaryotic microorganisms, that play a pivotal role in recognizing and engulfing various microbes during predation, offering insights into microbial dynamics and immune responses. An intriguing observation lies in the apparent preference of Acanthamoeba for Gram-negative over Gram-positive bacteria, suggesting potential differences in the recognition and response mechanisms to bacterial prey. Here, we comprehensively review pattern recognition receptors (PRRs) and microbe associated molecular patterns (MAMPs) that influence Acanthamoeba interactions with bacteria. We analyze the molecular mechanisms underlying these interactions, and the key finding of this review is that Acanthamoeba exhibits an affinity for bacterial cell surface appendages that are decorated with carbohydrates. Notably, this parallels warm-blooded immune cells, underscoring a conserved evolutionary strategy in microbial recognition. This review aims to serve as a foundation for exploring PRRs and MAMPs. These insights enhance our understanding of ecological and evolutionary dynamics in microbial interactions and shed light on fundamental principles governing immune responses. Leveraging Acanthamoeba as a model organism, provides a bridge between ecological interactions and immunology, offering valuable perspectives for future research.},
}
@article {pmid39247294,
year = {2024},
author = {Grimm, H and Drabesch, S and Nicol, A and Straub, D and Joshi, P and Zarfl, C and Planer-Friedrich, B and Muehe, EM and Kappler, A},
title = {Arsenic immobilization and greenhouse gas emission depend on quantity and frequency of nitrogen fertilization in paddy soil.},
journal = {Heliyon},
volume = {10},
number = {16},
pages = {e35706},
pmid = {39247294},
issn = {2405-8440},
abstract = {Nitrogen (N) fertilization in paddy soils decreases arsenic mobility and methane emissions. However, it is unknown how quantity and frequency of N fertilization affects the interlinked redox reactions of iron(II)-driven denitrification, iron mineral (trans-)formation with subsequent arsenic (im-)mobilization, methane and nitrous oxide emissions, and how this links to microbiome composition. Thus, we incubated paddy soil from Vercelli, Italy, over 129 days and applied nitrate fertilizer at different concentrations (control: 0, low: ∼35, medium: ∼100, high: ∼200 mg N kg[-1] soil[-1]) once at the beginning and after 49 days. In the high N treatment, nitrate reduction was coupled to oxidation of dissolved and solid-phase iron(II), while naturally occurring arsenic was retained on iron minerals due to suppression of reductive iron(III) mineral dissolution. In the low N treatment, 40 μg L[-1] of arsenic was mobilized into solution after nitrate depletion, with 69 % being immobilized after a second nitrate application. In the non-fertilized control, concentrations of dissolved arsenic were as high as 76 μg L[-1], driven by mobilization of 36 % of the initial mineral-bound arsenic. Generally, N fertilization led to 1.5-fold higher total GHG emissions (sum of CO2, CH4 and N2O as CO2 equivalents), 158-fold higher N2O, and 7.5-fold lower CH4 emissions compared to non-fertilization. On day 37, Gallionellaceae, Comamonadaceae and Rhodospirillales were more abundant in the high N treatment compared to the non-fertilized control, indicating their potential role as key players in nitrate reduction coupled to iron(II) oxidation. The findings underscore the dual effect of N fertilization, immobilizing arsenic in the short-term (low/medium N) or long-term (high N), while simultaneously increasing N2O and lowering CH4 emissions. This highlights the significance of both the quantity and frequency of N fertilizer application in paddy soils.},
}
@article {pmid39244747,
year = {2024},
author = {Bayer, B and Liu, S and Louie, K and Northen, TR and Wagner, M and Daims, H and Carlson, CA and Santoro, AE},
title = {Metabolite release by nitrifiers facilitates metabolic interactions in the ocean.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39244747},
issn = {1751-7370},
mesh = {*Seawater/microbiology ; *Nitrification ; Oceans and Seas ; Nitrites/metabolism ; Heterotrophic Processes ; Microbial Interactions ; Metabolome ; Coculture Techniques ; Ammonia/metabolism ; },
abstract = {Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which organic compounds are released by nitrifiers and potentially available to heterotrophs, we characterized the exo- and endometabolomes of the ammonia-oxidizing archaeon Nitrosopumilus adriaticus CCS1 and the nitrite-oxidizing bacterium Nitrospina gracilis Nb-211. Nitrifier endometabolome composition was not a good predictor of exometabolite availability, indicating that metabolites were predominately released by mechanisms other than cell death/lysis. Although both nitrifiers released labile organic compounds, N. adriaticus preferentially released amino acids, particularly glycine, suggesting that its cell membranes might be more permeable to small, hydrophobic amino acids. We further initiated co-culture systems between each nitrifier and a heterotrophic alphaproteobacterium, and compared exometabolite and transcript patterns of nitrifiers grown axenically to those in co-culture. In particular, B vitamins exhibited dynamic production and consumption patterns in nitrifier-heterotroph co-cultures. We observed an increased production of vitamin B2 and the vitamin B12 lower ligand dimethylbenzimidazole by N. adriaticus and N. gracilis, respectively. In contrast, the heterotroph likely produced vitamin B5 in co-culture with both nitrifiers and consumed the vitamin B7 precursor dethiobiotin when grown with N. gracilis. Our results indicate that B vitamins and their precursors could play a particularly important role in governing specific metabolic interactions between nitrifiers and heterotrophic microbes in the ocean.},
}
@article {pmid39244369,
year = {2024},
author = {Baptista, RC and Ferrocino, I and Pavani, M and Guerreiro, TM and Câmara, AA and Lang, &#xc9; and Dos Santos, JLP and Catharino, RR and Alves Filho, EG and Rodrigues, S and de Brito, ES and Caturla, MYR and Sant'Ana, AS and Cocolin, L},
title = {Microbiota diversity of three Brazilian native fishes during ice and frozen storage.},
journal = {Food microbiology},
volume = {124},
number = {},
pages = {104617},
doi = {10.1016/j.fm.2024.104617},
pmid = {39244369},
issn = {1095-9998},
mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Volatile Organic Compounds/analysis/metabolism ; *Food Storage ; *Fishes/microbiology ; Brazil ; *Seafood/microbiology/analysis ; *RNA, Ribosomal, 16S/genetics ; *Freezing ; Ice ; Food Microbiology ; Biodiversity ; Female ; },
abstract = {This study aimed to assess the bacterial microbiota involved in the spoilage of pacu (Piaractus mesopotamics), patinga (female Piaractus mesopotamics x male Piaractus brachypomus), and tambacu (female Colossoma macropomum × male Piaractus mesopotamics) during ice and frozen storage. Changes in the microbiota of three fish species (N = 22) during storage were studied through 16S rRNA amplicon-based sequencing and correlated with volatile organic compounds (VOCs) and metabolites assessed by nuclear magnetic resonance (NMR). Storage conditions (time and temperature) affected the microbiota diversity in all fish samples. Fish microbiota comprised mainly of Pseudomonas sp., Brochothrix sp., Acinetobacter sp., Bacillus sp., Lactiplantibacillus sp., Kocuria sp., and Enterococcus sp. The relative abundance of Kocuria, P. fragi, L. plantarum, Enterococcus, and Acinetobacter was positively correlated with the metabolic pathways of ether lipid metabolism while B. thermosphacta and P. fragi were correlated with metabolic pathways involved in amino acid metabolism. P. fragi was the most prevalent spoilage bacteria in both storage conditions (ice and frozen), followed by B. thermosphacta. Moreover, the relative abundance of identified Bacillus strains in fish samples stored in ice was positively correlated with the production of VOCs (1-hexanol, nonanal, octenol, and 2-ethyl-1-hexanol) associated with off-flavors. [1]H NMR analysis confirmed that amino acids, acetic acid, and ATP degradation products increase over (ice) storage, and therefore considered chemical spoilage index of fish fillets.},
}
@article {pmid39243903,
year = {2024},
author = {Macedo Silva, JR and Petra de Oliveira Barros, V and Terceiro, PS and Nunes de Oliveira, &#xcd; and Francisco da Silva Moura, O and Duarte de Freitas, J and Crispim, AC and Maciel Melo, VM and Thompson, FL and Maraschin, M and Landell, MF},
title = {Brazilian mangrove sediments as a source of biosurfactant-producing yeast Pichia pseudolambica for bioremediation.},
journal = {Chemosphere},
volume = {365},
number = {},
pages = {143285},
doi = {10.1016/j.chemosphere.2024.143285},
pmid = {39243903},
issn = {1879-1298},
mesh = {*Surface-Active Agents/metabolism ; *Biodegradation, Environmental ; Brazil ; *Pichia/metabolism ; *Geologic Sediments/microbiology/chemistry ; Surface Tension ; Wetlands ; Hydrocarbons/metabolism ; },
abstract = {This work highlights the biosurfactant production potential of yeasts from mangroves in northeastern Brazil. The biosurfactants were evaluated by their emulsifying capacity (EI24), with 6 isolates showing values between 50% and 62%. Surfactant properties from crude extract were measured using drop collapse, oil displacement, Parafilm® M, surface tension and critical micellar concentration tests. The effects of temperature, salinity, pH, and the ability to emulsify different hydrocarbons were analyzed, showing a promising potential of the yeast species investigated to tolerance to high temperatures and acidic pH, in addition to emulsifying different sources of hydrocarbons with environmental impact. It is important to note that the Pichia pseudolambica isolates showed a remarkable ability to reduce the surface tension of water, from 70.82 mN/m to 36.47 mN/m. In addition, the critical micellar concentration (CMC) values ranged from 7 to 16 mg/mL, highlighting the promising surfactant activity of these isolates for future applications. It was identified that the biosurfactant adhered to the yeast cell wall, and FTIR and 1H NMR spectroscopy analysis was carried out on the yeast biomass and its post-sonication supernatant. The results indicate the presence of characteristic functional groups and peaks found in biosurfactants of a glycolipid nature. Taking together the results reveals the promising potential of biosurfactant biosynthesis of P. pseudolambica yeast, a trait not reported in the literature so far for this species. P. pseudolambica presents a relevant metabolic potential for alternative substrate use and resilience to adverse conditions that could enable it to produce biosurfactants for the biotechnological remediation of areas contaminated by oil derivatives. The metabolic properties herein investigated, together with their presence in Brazilian mangroves, make P. pseudolambica an emerging candidate for developing industrial processes and sustainable strategies for the recovery of ecosystems impacted by oil spills, being positioned as a sustainable alternative to conventional surfactants.},
}
@article {pmid39243542,
year = {2024},
author = {Song, Y and Zhang, Z and Liu, Y and Peng, F and Feng, Y},
title = {Enhancement of anaerobic treatment of antibiotic pharmaceutical wastewater through the development of iron-based and carbon-based materials: A critical review.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135514},
doi = {10.1016/j.jhazmat.2024.135514},
pmid = {39243542},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/chemistry ; *Wastewater/chemistry ; Anaerobiosis ; *Iron/chemistry ; *Water Pollutants, Chemical/chemistry ; Carbon/chemistry ; Waste Disposal, Fluid/methods ; Biodegradation, Environmental ; Water Purification/methods ; },
abstract = {The extensive use of antibiotics has created an urgent need to address antibiotic wastewater treatment, posing significant challenges for environmental protection and public health. Recent advances in the efficacy and mechanisms of conductive materials (CMs) for enhancing the anaerobic biological treatment of antibiotic pharmaceutical wastewater are reviewed. For the first time, the focus is on the various application forms of iron-based and carbon-based CMs in strengthening the anaerobic methanogenic system. This includes the use of single CMs such as zero-valent iron (ZVI), magnetite, biochar (BC), activated carbon (AC), and graphene (GP), as well as iron-based and carbon-based composite CMs with diverse structures. These structures include mixed, surface-loaded, and core-shell combinations, reflecting the development of CMs. Iron-based and carbon-based CMs promote the rapid removal of antibiotics through adsorption and enhanced biodegradation. They also mitigate the inhibitory effects of toxic pollutants on microbial activity and reduce the expression of antibiotic resistance genes (ARGs). Additionally, as effective electron carriers, these CMs enrich microorganisms with direct interspecies electron transfer (DIET) functions, accelerate interspecies electron transfer, and facilitate the conversion of organic matter into methane. Finally, this review proposes the use of advanced molecular detection technologies to clarify microbial ecology and metabolic mechanisms, along with microscopic characterization techniques for the modification of CMs. These methods can provide more direct evidence to analyze the mechanisms underlying the cooperative anaerobic treatment of refractory organic wastewater by CMs and microorganisms.},
}
@article {pmid39239791,
year = {2024},
author = {Fouad, AM and Abo-Al-Ela, HG and Negm, EA and Abdelhaseib, M and Alian, A and Abdelsater, N and Said, REM and Anwar, FAS and Assar, DH and Mohamed, SA},
title = {Impact of Polyonchobothrium magnum on health and gut microbial ecology of African catfish (Clarias gariepinus): Insights from morphological, molecular, and microbiological analyses.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e14013},
doi = {10.1111/jfd.14013},
pmid = {39239791},
issn = {1365-2761},
abstract = {Parasites pose significant challenges to aquaculture and fisheries industries. Our study focuses on the Polyonchobothrium magnum and African catfish to address a potential health issue in aquaculture, explore host-parasite interactions that can help develop effective management practices to ensure fish health and industry sustainability. P. magnum was isolated from the stomach of African catfish (Clarias gariepinus) as the primary site of infection, with a prevalence of 10%. Most affected fish were heavily infected (8 out of 10). Infection was confirmed by sequencing the PCR-targeted region of the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene, along with light and scanning electron microscopes. The parasite had an elongated scolex with deep bothria, a prominent apical disc wider than the scolex itself, and a four-lobed appearance. The scolex contained a central rostellum divided into two semicircles, bearing 26-30 hooks, with an average of 28. The apical disc had large hooks arranged in four quadrants, with 6-8 hooks each, averaging 7 per quadrant. No neck was observed. Phylogenetic analysis of our sequence showed a 100% match with isolates from Guangzhou, China. In infected fish, the anterior kidney showed increased expression levels of nuclear factor kappa B and lysozyme, but decreased levels of in major histocompatibility complex antigen II. Plasma analysis revealed a significant drop in superoxide dismutase, a rise in interleukin-1 beta, and lower IgM levels compared to non-infected controls. Non-infected fish displayed greater gut microbiota diversity, with dominant families including Moraxellaceae, Enterobacteriaceae, Fusobacteriaceae, and Caulobacteraceae, and prevalent genera such as Acinetobacter, Cetobacterium, and Brevundimonas. In contrast, infected fish exhibited very low diversity, with significantly higher proportions of Enterobacteriaceae (45.99%) and Aeromonadaceae (41.79%) compared to non-infected fish, which had 13.76% and 3.64% respectively. Cetobacterium somerae was prevalent in non-infected fish, while infected fish harboured Aeromonas fluvialis, Plesiomonas shigelloides, and Gallaecimonas xiamenensis. Overall, P. magnum disrupted the immune status and gut microbiota of the host, thereby impacting its health.},
}
@article {pmid39236824,
year = {2024},
author = {Guo, Q and Xiao, Y and Zhu, Y and Korpelainen, H and Li, C},
title = {Selenium availability in tea: Unraveling the role of microbiota assembly and functions.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {175995},
doi = {10.1016/j.scitotenv.2024.175995},
pmid = {39236824},
issn = {1879-1026},
mesh = {*Selenium/metabolism/analysis ; *Microbiota ; *Camellia sinensis/metabolism ; *Soil Microbiology ; Tea ; Soil/chemistry ; Soil Pollutants/metabolism/analysis ; Bacteria/metabolism ; },
abstract = {Tea (Camellia sinensis (L.) O. Kuntze) plants have a strong ability to accumulate selenium (Se). However, the question of how tea plants affect Se availability has received little attention. In this study, five tea cultivars, including Soubei (SB), Aolǜ (AL), Longjing43 (LJ), Zhaori (ZR) and Fenglǜ (FL), were chosen for the study. Quantitative Microbial Ecology Chip and high-throughput sequencing were used to explore the effects of five tea cultivars on soil functions, microbial community structures and Se availability. The results showed that the total soil Se content in the FL garden was lower compared to LJ and SB gardens, whereas available Se was highest in the FL garden. Based on the Bray-Curtis distances, tea cultivar was the main factor affecting bacterial and fungal community structures. The abundance of functional genes concerning carbon, nitrogen, phosphorus and sulfur cycling processes varied among tea gardens. The higher soil NH4[+] and NO3[-] contents, and higher abundance of functional genes like nifH, amoA1 and narG, whereas lower total nitrogen in the FL garden than in the AL and LJ tea gardens demonstrated that the FL tea plants induced microbes to accelerate soil nitrogen cycling processes. Dominant microbes that positively related with functional genes like nifH, narG, and amoA1 were also positively related with the available Se content. In conclusion, tea cultivars could regulate soil functions through affecting microbial community structures and then affecting the soil Se availability. The soil nitrogen cycle processes are suggested to be closely related with Se transformation in tea gardens.},
}
@article {pmid39236233,
year = {2024},
author = {Richards, L and Cremin, K and Coates, M and Vigor, F and Schäfer, P and Soyer, OS},
title = {Ammonia leakage can underpin nitrogen-sharing among soil microorganisms.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39236233},
issn = {1751-7370},
support = {//Gordon and Betty Moore Foundation/ ; //Midlands Integrative Biosciences Training Partnership/ ; P3141153//Baden-W&#xfc;rttemberg Stiftung/ ; },
mesh = {*Ammonia/metabolism ; *Soil Microbiology ; *Nitrogen/metabolism ; *Nitrates/metabolism ; *Bacillus subtilis/metabolism/growth &amp; development/genetics ; Soil/chemistry ; Microbial Interactions ; Hydrogen-Ion Concentration ; Ammonium Compounds/metabolism ; },
abstract = {Soil microbial communities host a large number of microbial species that support important ecological functions such as biogeochemical cycling and plant nutrition. The extent and stability of these functions are affected by inter-species interactions among soil microorganisms, yet the different mechanisms underpinning microbial interactions in the soil are not fully understood. Here, we study the extent of nutrient-based interactions among two model, plant-supporting soil microorganisms, the fungi Serendipita indica, and the bacteria Bacillus subtilis. We found that S. indica is unable to grow with nitrate - a common nitrogen source in the soil - but this inability could be rescued, and growth restored in the presence of B. subtilis. We demonstrate that this effect is due to B. subtilis utilising nitrate and releasing ammonia, which can be used by S. indica. We refer to this type of mechanism as ammonia mediated nitrogen sharing (N-sharing). Using a mathematical model, we demonstrated that the pH dependent equilibrium between ammonia (NH3) and ammonium (NH+4) results in an inherent cellular leakiness, and that reduced amonnium uptake or assimilation rates could result in higher levels of leaked ammonia. In line with this model, a mutant B. subtilis - devoid of ammonia uptake - showed higher S. indica growth support in nitrate media. These findings highlight that ammonia based N-sharing can be a previously under-appreciated mechanism underpinning interaction among soil microorganisms and could be influenced by microbial or abiotic alteration of pH in microenvironments.},
}
@article {pmid39235751,
year = {2025},
author = {Lemée, P and Bridier, A},
title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2852},
number = {},
pages = {289-309},
pmid = {39235751},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; },
abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.},
}
@article {pmid39235736,
year = {2025},
author = {Islam, DT and Mobasser, S and Kotaru, S and Telli, AE and Telli, N and Cupples, AM and Hashsham, SA},
title = {Electrochemical Detection of Nucleic Acids Using Three-Dimensional Graphene Screen-Printed Electrodes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2852},
number = {},
pages = {47-64},
pmid = {39235736},
issn = {1940-6029},
mesh = {*Graphite/chemistry ; *Electrodes ; *Electrochemical Techniques/methods/instrumentation ; *Biosensing Techniques/methods/instrumentation ; Nucleic Acids/analysis ; Humans ; DNA/analysis ; },
abstract = {Electrochemical approaches, along with miniaturization of electrodes, are increasingly being employed to detect and quantify nucleic acid biomarkers. Miniaturization of the electrodes is achieved through the use of screen-printed electrodes (SPEs), which consist of one to a few dozen sets of electrodes, or by utilizing printed circuit boards. Electrode materials used in SPEs include glassy carbon (Chiang H-C, Wang Y, Zhang Q, Levon K, Biosensors (Basel) 9:2-11, 2019), platinum, carbon, and graphene (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015). There are numerous modifications to the electrode surfaces as well (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015). These approaches offer distinct advantages, primarily due to their demonstrated superior limit of detection without amplification. Using the SPEs and potentiostats, we can detect cells, proteins, DNA, and RNA concentrations in the nanomolar (nM) to attomolar (aM) range. The focus of this chapter is to describe the basic approach adopted for the use of SPEs for nucleic acid measurement.},
}
@article {pmid39235733,
year = {2025},
author = {Williams, MR and Telli, AE and Telli, N and Islam, DT and Hashsham, SA},
title = {Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2852},
number = {},
pages = {3-17},
pmid = {39235733},
issn = {1940-6029},
mesh = {*Nucleic Acid Amplification Techniques/methods ; *Food Microbiology/methods ; Animals ; *Milk/microbiology ; *Salmonella/genetics/isolation &amp; purification ; *DNA, Bacterial/genetics/isolation &amp; purification ; *Polymerase Chain Reaction/methods ; Foodborne Diseases/microbiology ; Escherichia coli/genetics/isolation &amp; purification ; Molecular Diagnostic Techniques/methods ; Swine ; },
abstract = {The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection of Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.},
}
@article {pmid39234658,
year = {2024},
author = {King, WL and Hayward, RJ and Goebel, M and Fleishman, SM and Bauerle, TL and Bell, TH},
title = {Getting to the root of root-microbe interactions.},
journal = {Science progress},
volume = {107},
number = {3},
pages = {368504241278783},
pmid = {39234658},
issn = {2047-7163},
mesh = {Ecosystem ; Microbiota/physiology ; *Plant Roots/microbiology/metabolism ; Plants/microbiology/metabolism ; *Soil Microbiology ; },
abstract = {Microbial relationships with roots influence many ecosystem functions and nutrient fluxes, including their sometimes-profound effects on plant health and productivity. Fine roots were often classified with a diameter less than 2 mm, but fine roots under that size perform distinct functional roles in the environment. Importantly, two broad functional categories of fine roots are absorptive and transportive, with absorptive fine roots acting as metabolic hotspots for root activity. In two of our recent studies, we have shown that several microbial community characteristics differ between absorptive and transportive fine roots, including composition, abundance, and function, as well as the root metabolome. This highlights a growing recognition within microbial ecology that we must consider fine-scale environmental variability, such as root physiology and morphology, when interpreting microbial patterns. In this commentary, we summarize the findings of our latest article, further speculate on some of these patterns, and suggest future studies for examining decomposition and applying cutting-edge single-cell sequencing techniques.},
}
@article {pmid39234547,
year = {2024},
author = {Marshall, IPG},
title = {Electromicrobiological concentration cells are an overlooked potential energy conservation mechanism for subsurface microorganisms.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1407868},
pmid = {39234547},
issn = {1664-302X},
abstract = {Thermodynamics has predicted many different kinds of microbial metabolism by determining which pairs of electron acceptors and donors will react to produce an exergonic reaction (a negative net change in Gibbs free energy). In energy-limited environments, such as the deep subsurface, such an approach can reveal the potential for unexpected or counter-intuitive energy sources for microbial metabolism. Up until recently, these thermodynamic calculations have been carried out with the assumption that chemical species appearing on the reactant and product side of a reaction formula have a constant concentration, and thus do not count towards net concentration changes and the overall direction of the reaction. This assumption is reasonable considering microorganisms are too small (~1 μm) for any significant differences in concentration to overcome diffusion. However, recent discoveries have demonstrated that the reductive and oxidative halves of reactions can be separated by much larger distances, from millimetres to centimetres via conductive filamentous bacteria, mineral conductivity, and biofilm conductivity. This means that the concentrations of reactants and products can indeed be different, and that concentration differences can contribute to the net negative change in Gibbs free energy. It even means that the same redox reaction, simultaneously running in forward and reverse, can drive energy conservation, in an ElectroMicrobiological Concentration Cell (EMCC). This paper presents a model to investigate this phenomenon and predict under which circumstances such concentration-driven metabolism might take place. The specific cases of oxygen concentration cells, sulfide concentration cells, and hydrogen concentration cells are examined in more detail.},
}
@article {pmid39233440,
year = {2024},
author = {Hosseiniyan Khatibi, SM and Dimaano, NG and Veliz, E and Sundaresan, V and Ali, J},
title = {Exploring and exploiting the rice phytobiome to tackle climate change challenges.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101078},
doi = {10.1016/j.xplc.2024.101078},
pmid = {39233440},
issn = {2590-3462},
abstract = {The future of agriculture is uncertain under the current climate change scenario. Climate change directly and indirectly affects the biotic and abiotic elements that control agroecosystems, jeopardizing the safety of the world's food supply. A new area that focuses on characterizing the phytobiome is emerging. The phytobiome comprises plants and their immediate surroundings, involving numerous interdependent microscopic and macroscopic organisms that affect the health and productivity of plants. Phytobiome studies primarily focus on the microbial communities associated with plants, which are referred to as the plant microbiome. The development of high-throughput sequencing technologies over the past 10 years has dramatically advanced our understanding of the structure, functionality, and dynamics of the phytobiome; however, comprehensive methods for using this knowledge are lacking, particularly for major crops such as rice. Considering the impact of rice production on world food security, gaining fresh perspectives on the interdependent and interrelated components of the rice phytobiome could enhance rice production and crop health, sustain rice ecosystem function, and combat the effects of climate change. Our review re-conceptualizes the complex dynamics of the microscopic and macroscopic components in the rice phytobiome as influenced by human interventions and changing environmental conditions driven by climate change. We also discuss interdisciplinary and systematic approaches to decipher and reprogram the sophisticated interactions in the rice phytobiome using novel strategies and cutting-edge technology. Merging the gigantic datasets and complex information on the rice phytobiome and their application in the context of regenerative agriculture could lead to sustainable rice farming practices that are resilient to the impacts of climate change.},
}
@article {pmid39233079,
year = {2024},
author = {Zhang, G and Guo, Z and Ke, Y and Li, H and Xiao, X and Lin, D and Lin, L and Wang, Y and Liu, J and Lu, H and Hong, H and Yan, C},
title = {Comparative analysis of size-fractional eukaryotic microbes in subtropical riverine systems inferred from 18S rRNA gene V4 and V9 regions.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {175972},
doi = {10.1016/j.scitotenv.2024.175972},
pmid = {39233079},
issn = {1879-1026},
mesh = {*RNA, Ribosomal, 18S/genetics ; *Rivers/microbiology ; *Eukaryota/genetics ; Microbiota/genetics ; Ecosystem ; Environmental Monitoring/methods ; },
abstract = {Eukaryotic microbes play key ecological roles in riverine ecosystems. Amplicon sequencing has greatly facilitated the identification and characterization of eukaryotic microbial communities. Currently, 18S rRNA gene V4 and V9 hypervariable regions are widely used for sequencing eukaryotic microbes. Identifying optimal regions for the profiling of size-fractional eukaryotic microbial communities is critical for microbial ecological studies. In this study, we spanned three rivers with typical natural-human influenced transition gradients to evaluate the performance of the 18S rRNA gene V4 and V9 hypervariable regions for sequencing size-fractional eukaryotic microbes (>180 μm, 20-180 μm, 5-20 μm, 3-5 μm, 0.8-3 μm). Our comparative analysis revealed that amplicon results depend on the specific species and microbial size. The V9 region was most effective for detecting a broad taxonomic range of species. The V4 region was superior to the V9 region for the identification of microbes in the minor 3 μm and at the family and genus levels, especially for specific microbial groups, such as Labyrinthulomycetes. However, the V9 region was more effective for studies of diverse eukaryotic groups, including Archamoebae, Heterolobosea, and Microsporidia, and various algae, such as Haptophyta, Florideophycidae, and Bangiales. Our results highlight the importance of accounting for potential misclassifications when employing both V4 and V9 regions for the identification of microbial sequences. The use of optimal regions for amplification could enhance the utility of amplicon sequencing in environmental studies. The insights gained from this work will aid future studies that employ amplicon-based identification approaches for the characterization of eukaryotic microbial communities and contribute to our understanding of microbial ecology within aquatic systems.},
}
@article {pmid39231820,
year = {2024},
author = {Song, X and Li, J and Xiong, Z and Sha, H and Wang, G and Liu, Q and Zeng, T},
title = {Effects of Detoxifying Substances on Uranium Removal by Bacteria Isolated from Mine Soils: Performance, Mechanisms, and Bacterial Communities.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {111},
pmid = {39231820},
issn = {1432-184X},
support = {52170164//National Natural Science Foundation of China/ ; 2022RC1184//Science and Technology Innovation Program of Hunan Province of China/ ; },
mesh = {*Uranium/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/genetics/isolation &amp; purification/classification ; *Mining ; *Biodegradation, Environmental ; Acyl-Butyrolactones/metabolism ; Glutathione/metabolism ; Soil Pollutants, Radioactive/metabolism ; },
abstract = {In this study, we investigated the effect of detoxifying substances on U(VI) removal by bacteria isolated from mine soil. The results demonstrated that the highest U(VI) removal efficiency (85.6%) was achieved at pH 6.0 and a temperature of 35 °C, with an initial U(VI) concentration of 10 mg/L. For detoxifying substances, signaling molecules acyl homoserine lactone (AHLs, 0.1 µmol/L), anthraquinone-2, 6-disulfonic acid (AQDS, 1 mmol/L), reduced glutathione (GSH, 0.1 mmol/L), selenium (Se, 1 mg/L), montmorillonite (MT, 1 g/L), and ethylenediaminetetraacetic acid (EDTA, 0.1 mmol/L) substantially enhanced the bacterial U(VI) removal by 34.9%, 37.4%, 54.5%, 35.1%, 32.8%, and 47.8% after 12 h, respectively. This was due to the alleviation of U(VI) toxicity in bacteria through detoxifying substances, as evidenced by lower malondialdehyde (MDA) content and higher superoxide dismutase (SOD) and catalase (CAT) activities for bacteria exposed to U(VI) and detoxifying substances, compared to those exposed to U(VI) alone. FTIR results showed that hydroxyl, carboxyl, phosphorus, and amide groups participated in the U(VI) removal. After exposure to U(VI), the relative abundances of Chryseobacterium and Stenotrophomonas increased by 48.5% and 12.5%, respectively, suggesting their tolerance ability to U(VI). Gene function prediction further demonstrated that the detoxifying substances AHLs alleviate U(VI) toxicity by influencing bacterial metabolism. This study suggests the potential application of detoxifying substances in the U(VI)-containing wastewater treatment through bioremediation.},
}
@article {pmid39230264,
year = {2024},
author = {Rodriguez-Gonzalez, RA and Balacheff, Q and Debarbieux, L and Marchi, J and Weitz, JS},
title = {Metapopulation model of phage therapy of an acute Pseudomonas aeruginosa lung infection.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0017124},
pmid = {39230264},
issn = {2379-5077},
support = {R01 AI146592/AI/NIAID NIH HHS/United States ; //Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACYT)/ ; },
mesh = {*Pseudomonas aeruginosa/virology ; *Phage Therapy/methods ; *Pseudomonas Infections/therapy/immunology ; Animals ; Mice ; Bacteriophages/physiology ; Lung/microbiology/immunology/virology ; Models, Biological ; Mice, Inbred C57BL ; Humans ; Drug Resistance, Multiple, Bacterial ; },
abstract = {UNLABELLED: Infections caused by multidrug resistant (MDR) pathogenic bacteria are a global health threat. Bacteriophages ("phage") are increasingly used as alternative or last-resort therapeutics to treat patients infected by MDR bacteria. However, the therapeutic outcomes of phage therapy may be limited by the emergence of phage resistance during treatment and/or by physical constraints that impede phage-bacteria interactions in vivo. In this work, we evaluate the role of lung spatial structure on the efficacy of phage therapy for Pseudomonas aeruginosa infections. To do so, we developed a spatially structured metapopulation network model based on the geometry of the bronchial tree, including host innate immune responses and the emergence of phage-resistant bacterial mutants. We model the ecological interactions between bacteria, phage, and the host innate immune system at the airway (node) level. The model predicts the synergistic elimination of a P. aeruginosa infection due to the combined effects of phage and neutrophils, given the sufficient innate immune activity and efficient phage-induced lysis. The metapopulation model simulations also predict that MDR bacteria are cleared faster at distal nodes of the bronchial tree. Notably, image analysis of lung tissue time series from wild-type and lymphocyte-depleted mice revealed a concordant, statistically significant pattern: infection intensity cleared in the bottom before the top of the lungs. Overall, the combined use of simulations and image analysis of in vivo experiments further supports the use of phage therapy for treating acute lung infections caused by P. aeruginosa, while highlighting potential limits to therapy in a spatially structured environment given impaired innate immune responses and/or inefficient phage-induced lysis.<br><br>IMPORTANCE: Phage therapy is increasingly employed as a compassionate treatment for severe infections caused by multidrug-resistant (MDR) bacteria. However, the mixed outcomes observed in larger clinical studies highlight a gap in understanding when phage therapy succeeds or fails. Previous research from our team, using in vivo experiments and single-compartment mathematical models, demonstrated the synergistic clearance of acute P. aeruginosa pneumonia by phage and neutrophils despite the emergence of phage-resistant bacteria. In fact, the lung environment is highly structured, prompting the question of whether immunophage synergy explains the curative treatment of P. aeruginosa when incorporating realistic physical connectivity. To address this, we developed a metapopulation network model mimicking the lung branching structure to assess phage therapy efficacy for MDR P. aeruginosa pneumonia. The model predicts the synergistic elimination of P. aeruginosa by phage and neutrophils but emphasizes potential challenges in spatially structured environments, suggesting that higher innate immune levels may be required for successful bacterial clearance. Model simulations reveal a spatial pattern in pathogen clearance where P. aeruginosa are cleared faster at distal nodes of the bronchial tree than in primary nodes. Interestingly, image analysis of infected mice reveals a concordant and statistically significant pattern: infection intensity clears in the bottom before the top of the lungs. The combined use of modeling and image analysis supports the application of phage therapy for acute P. aeruginosa pneumonia while emphasizing potential challenges to curative success in spatially structured in vivo environments, including impaired innate immune responses and reduced phage efficacy.},
}
@article {pmid39229495,
year = {2024},
author = {Li, L and Chen, S and Xue, X and Chen, J and Tian, J and Huo, L and Zhang, T and Zeng, X and Su, S},
title = {Purifying selection drives distinctive arsenic metabolism pathways in prokaryotic and eukaryotic microbes.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae106},
pmid = {39229495},
issn = {2730-6151},
abstract = {Microbes play a crucial role in the arsenic biogeochemical cycle through specific metabolic pathways to adapt to arsenic toxicity. However, the different arsenic-detoxification strategies between prokaryotic and eukaryotic microbes are poorly understood. This hampers our comprehension of how microbe-arsenic interactions drive the arsenic cycle and the development of microbial methods for remediation. In this study, we utilized conserved protein domains from 16 arsenic biotransformation genes (ABGs) to search for homologous proteins in 670 microbial genomes. Prokaryotes exhibited a wider species distribution of arsenic reduction- and arsenic efflux-related genes than fungi, whereas arsenic oxidation-related genes were more prevalent in fungi than in prokaryotes. This was supported by significantly higher acr3 (arsenite efflux permease) expression in bacteria (upregulated 3.72-fold) than in fungi (upregulated 1.54-fold) and higher aoxA (arsenite oxidase) expression in fungi (upregulated 5.11-fold) than in bacteria (upregulated 2.05-fold) under arsenite stress. The average values of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (dN/dS) of homologous ABGs were higher in archaea (0.098) and bacteria (0.124) than in fungi (0.051). Significant negative correlations between the dN/dS of ABGs and species distribution breadth and gene expression levels in archaea, bacteria, and fungi indicated that microbes establish the distinct strength of purifying selection for homologous ABGs. These differences contribute to the distinct arsenic metabolism pathways in prokaryotic and eukaryotic microbes. These observations facilitate a significant shift from studying individual or several ABGs to characterizing the comprehensive microbial strategies of arsenic detoxification.},
}
@article {pmid39226184,
year = {2024},
author = {Zhai, Z and Yang, Y and Chen, S and Wu, Z},
title = {Long-Term Exposure to Polystyrene Microspheres and High-Fat Diet-Induced Obesity in Mice: Evaluating a Role for Microbiota Dysbiosis.},
journal = {Environmental health perspectives},
volume = {132},
number = {9},
pages = {97002},
pmid = {39226184},
issn = {1552-9924},
mesh = {Animals ; *Dysbiosis/microbiology ; Mice ; *Obesity/microbiology ; *Diet, High-Fat ; *Mice, Inbred C57BL ; *Microspheres ; *Polystyrenes/toxicity ; *Gastrointestinal Microbiome/drug effects ; Male ; Microplastics/toxicity ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Microplastics (MPs) have become a global environmental problem, emerging as contaminants with potentially alarming consequences. However, long-term exposure to polystyrene microspheres (PS-MS) and its effects on diet-induced obesity are not yet fully understood.<br><br>OBJECTIVES: We aimed to investigate the effect of PS-MS exposure on high-fat diet (HFD)-induced obesity and underlying mechanisms.<br><br>METHODS: In the present study, C57BL/6J mice were fed a normal diet (ND) or a HFD in the absence or presence of PS-MS via oral administration for 8 wk. Antibiotic depletion of the microbiota and fecal microbiota transplantation (FMT) were performed to assess the influence of PS-MS on intestinal microbial ecology. We performed 16S rRNA sequencing to dissect microbial discrepancies and investigated the dysbiosis-associated intestinal integrity and inflammation in serum.<br><br>RESULTS: Compared with HFD mice, mice fed the HFD with PS-MS exhibited higher body weight, liver weight, metabolic dysfunction-associated steatotic liver disease (MASLD) activity scores, and mass of white adipose tissue, as well as higher blood glucose and serum lipid concentrations. Furthermore, 16S rRNA sequencing of the fecal microbiota revealed that mice fed the HFD with PS-MS had greater &#x3b1;-diversity and greater relative abundances of Lachnospiraceae, Oscillospiraceae, Bacteroidaceae, Akkermansiaceae, Marinifilaceae, Deferribacteres, and Desulfovibrio, but lower relative abundances of Atopobiaceae, Bifidobacterium, and Parabacteroides. Mice fed the HFD with PS-MS exhibited lower expression of MUC2 mucin and higher levels of lipopolysaccharide and inflammatory cytokines [tumor necrosis factor-&#x3b1; (TNF-&#x3b1;), interleukin-6 (IL-6), IL-1&#x3b2;, and IL-17A] in serum. Correlation analyses revealed that differences in the microbial flora of mice exposed to PS-MS were associated with obesity. Interestingly, microbiota-depleted mice did not show the same PS-MS-associated differences in Muc2 and Tjp1 expression in the distal colon, expression of inflammatory cytokines in serum, or obesity outcomes between HFD and HFD + PS-MS. Importantly, transplantation of feces from HFD + PS-MS mice to microbiota-depleted HFD-fed mice resulted in a lower expression of mucus proteins, higher expression of inflammatory cytokines, and obesity outcomes, similar to the findings in HFD + PS-MS mice.<br><br>CONCLUSIONS: Our findings provide a new gut microbiota-driven mechanism for PS-MS-induced obesity in HFD-fed mice, suggesting the need to reevaluate the adverse health effects of MPs commonly found in daily life, particularly in susceptible populations. https://doi.org/10.1289/EHP13913.},
}
@article {pmid39224076,
year = {2024},
author = {McMillan, AS and Theriot, CM},
title = {Bile acids impact the microbiota, host, and C. difficile dynamics providing insight into mechanisms of efficacy of FMTs and microbiota-focused therapeutics.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2393766},
pmid = {39224076},
issn = {1949-0984},
support = {R35 GM149222/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bile Acids and Salts/metabolism ; Humans ; *Fecal Microbiota Transplantation ; *Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Animals ; },
abstract = {Clostridioides difficile is a major nosocomial pathogen, causing significant morbidity and mortality worldwide. Antibiotic usage, a major risk factor for Clostridioides difficile infection (CDI), disrupts the gut microbiota, allowing C. difficile to proliferate and cause infection, and can often lead to recurrent CDI (rCDI). Fecal microbiota transplantation (FMT) and live biotherapeutic products (LBPs) have emerged as effective treatments for rCDI and aim to restore colonization resistance provided by a healthy gut microbiota. However, much is still unknown about the mechanisms mediating their success. Bile acids, extensively modified by gut microbes, affect C. difficile's germination, growth, and toxin production while also shaping the gut microbiota and influencing host immune responses. Additionally, microbial interactions, such as nutrient competition and cross-feeding, contribute to colonization resistance against C. difficile and may contribute to the success of microbiota-focused therapeutics. Bile acids as well as other microbial mediated interactions could have implications for other diseases being treated with microbiota-focused therapeutics. This review focuses on the intricate interplay between bile acid modifications, microbial ecology, and host responses with a focus on C. difficile, hoping to shed light on how to move forward with the development of new microbiota mediated therapeutic strategies to combat rCDI and other intestinal diseases.},
}
@article {pmid39222062,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: coverage-based analysis for identification of microbiome.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
pmid = {39222062},
issn = {1477-4054},
support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; },
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}
@article {pmid39221110,
year = {2024},
author = {Mohr, AE and Jasbi, P and van Woerden, I and Chi, J and Gu, H and Bruening, M and Whisner, CM},
title = {Microbial Ecology and Metabolism of Emerging Adulthood: Gut Microbiome Insights from a College Freshman Cohort.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {1-23},
pmid = {39221110},
issn = {2993-3935},
support = {DP5 OD017910/OD/NIH HHS/United States ; T32 DK137525/DK/NIDDK NIH HHS/United States ; },
abstract = {The human gut microbiome (GM) undergoes dynamic changes throughout life, transitioning from infancy to adulthood. Despite improved understanding over the past years about how genetics, lifestyle, and the external environment impact the GM, limited research has explored the GM's evolution during late-stage adolescence, especially among college students. This study addresses this gap by investigating the longitudinal dynamics of fecal microbial, functional, and metabolomic signatures in a diverse group of first-year, dormitory-housed college students. A total of 485 stool samples from 246 participants were analyzed, identifying four primary GM community types, predominantly led by Bacteroides (66.8% of samples), as well as Blautia and Prevotella. The Prevotella/Bacteroides (P/B) ratio emerged as a robust GM composition indicator, predictively associated with 15 metabolites. Notably, higher P/B ratios correlated negatively with p-cresol sulfate and cholesterol sulfate, implying potential health implications, while positively correlating with kynurenic acid. Distinct GM transition and stability patterns were found from a detailed longitudinal subset of 93 participants over an academic year. Parasutterella and the Ruminococcus gnavus group exhibited positive associations with compositional variability, whereas Faecalibacterium and Eubacterium ventriosum group displayed negative associations, the latter suggesting stabilizing roles in the GM. Most notably, nearly half of the longitudinal cohort experienced GM community shifts, emphasizing long-term GM adaptability. Comparing individuals with stable community types to those undergoing transitions, we observed significant differences in microbial composition and diversity, signifying substantial shifts in the microbiota during transitions. Although diet-related variables contributed to some observed variance, diet did not independently predict the probability of switching between community types within the study's timeframe via multi-state Markov modeling. Furthermore, exploration of stability within dynamic microbiomes among the longitudinal cohort experiencing shifts in community types revealed that microbiome taxa at the genus level exhibited significantly higher total variance than estimated functional and fecal metabolomic features. This suggests tight control of function and metabolism, despite community shifting. Overall, this study highlights the dynamic nature of the late-stage adolescent GM, the role of core taxa, metabolic pathways, the fecal metabolome, and lifestyle and dietary factors, contributing to our understanding of GM assembly and potential health implications during this life phase.},
}
@article {pmid39218095,
year = {2024},
author = {Anedda, E and Alexa, EA and Farrell, ML and Croffie, M and Madigan, G and Morris, D and Burgess, CM},
title = {Comparison of antimicrobial resistant Enterobacterales isolates from the dairy production environment in low and high zinc containing regions.},
journal = {The Science of the total environment},
volume = {953},
number = {},
pages = {175905},
doi = {10.1016/j.scitotenv.2024.175905},
pmid = {39218095},
issn = {1879-1026},
mesh = {*Zinc/analysis ; *Enterobacteriaceae/drug effects ; *Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Dairying ; Drug Resistance, Bacterial/genetics ; Ireland ; Animals ; Milk/microbiology ; Cattle ; Soil Pollutants/analysis ; },
abstract = {Heavy metals occur naturally in the environment, and their concentration varies in soil across different regions. However, the presence of heavy metals may influence the antimicrobial resistance (AMR) in bacterial populations. Therefore, the objective of this study was to investigate and characterise the antimicrobial resistance profiles of Enterobacterales in soil and bovine milk filters from high and low zinc-containing regions in Ireland. In total, 50 soil samples and 29 milk filters were collected from two geographic locations with varying soil zinc concentrations. Samples were cultured for the enumeration and detection of Enterobacterales. Specifically, extended-spectrum beta-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales were isolated using selective media. Species identification was performed using MALDI-TOF. The phenotypic resistance profiles of selected Enterobacterales were determined by disk diffusion testing, following EUCAST and CLSI criteria; while, the genotypic resistance profiles of the same isolates were determined by whole genome sequencing (WGS). Heavy metal concentrations were also measured for all soil samples. A total of 40 antimicrobial resistant Enterobacterales were identified in soil (n = 31) and milk filters (n = 9). The predominant species detected in the high zinc-containing region was Escherichia coli in both sample types (soil n = 10, milk filters n = 2), while in the low zinc-containing region Serratia fonticola was predominant in soil samples (n = 8) and E. coli in milk filters (n = 4). Ten E. coli isolates identified from soil samples in the high zinc-containing region were multidrug resistant, showing resistance to all the antimicrobials tested, except for carbapenems. The WGS findings confirmed the phenotypic resistance results. Moreover, zinc resistance-associated genes and genes encoding for efflux pumps were identified. The current study revealed distinct phenotypic resistance profiles of Enterobacterales in low and high zinc-containing regions, and highlighted the benefit of utilising milk filters for AMR surveillance in dairy production.},
}
@article {pmid39216241,
year = {2024},
author = {Liao, X and Hou, L and Zhang, L and Grossart, HP and Liu, K and Liu, J and Chen, Y and Liu, Y and Hu, A},
title = {Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135675},
doi = {10.1016/j.jhazmat.2024.135675},
pmid = {39216241},
issn = {1873-3336},
mesh = {*Rivers/microbiology ; *Altitude ; *Microbiota/drug effects ; *Drug Resistance, Microbial/genetics ; Ecosystem ; Bacteria/genetics/drug effects/classification ; Geologic Sediments/microbiology ; Viruses/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Ice Cover/microbiology ; China ; },
abstract = {The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.},
}
@article {pmid39215820,
year = {2024},
author = {Thompson, C and Silva, R and Gibran, FZ and Bacha, L and de Freitas, MAM and Thompson, M and Landuci, F and Tschoeke, D and Zhang, XH and Wang, X and Zhao, W and Gatts, PV and de Almeida, MG and de Rezende, CE and Thompson, F},
title = {The Abrolhos Nominally Herbivorous Coral Reef Fish Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare Have Similarities in Feeding But Species-Specific Microbiomes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {110},
pmid = {39215820},
issn = {1432-184X},
mesh = {Animals ; *Coral Reefs ; *RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Herbivory ; Species Specificity ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; Perciformes/microbiology ; Diet/veterinary ; },
abstract = {Coral reefs rely heavily on reef fish for their health, yet overfishing has resulted in their decline, leading to an increase in fast-growing algae and changes in reef ecosystems, a phenomenon described as the phase-shift. A clearer understanding of the intricate interplay between herbivorous, their food, and their gut microbiomes could enhance reef health. This study examines the gut microbiome and isotopic markers (δ[13]C and δ[15]N) of four key nominally herbivorous reef fish species (Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare) in the Southwestern Atlantic's Abrolhos Reef systems. Approximately 16.8 million 16S rRNA sequences were produced for the four fish species, with an average of 317,047 ± 57,007 per species. Bacteria such as Proteobacteria, Firmicutes, and Cyanobacteria were prevalent in their microbiomes. These fish show unique microbiomes that result from co-diversification, diet, and restricted movement. Coral-associated bacteria (Endozoicomonas, Rhizobia, and Ruegeria) were found in abundance in the gut contents of the parrotfish species Sc. trispinosus and Sp. axillare. These parrotfishes could aid coral health by disseminating such beneficial bacteria across the reef. Meanwhile, Kyphosus sp. predominantly had Pirellulaceae and Rhodobacteraceae. Four fish species had a diet composed of turf components (filamentous Cyanobacteria) and brown algae (Dictyopteris). They also had similar isotopic niches, suggesting they shared food sources. A significant difference was observed between the isotopic signature of fish muscular gut tissue and gut contents, pointing to the role that host genetics and gut microbes play in differentiating fish tissues.},
}
@article {pmid39215735,
year = {2024},
author = {Paulo, LM and Liu, YC and Castilla-Archilla, J and Ramiro-Garcia, J and Hughes, D and Mahony, T and Holohan, BC and Wilmes, P and O'Flaherty, V},
title = {Full-scale study on high-rate low-temperature anaerobic digestion of agro-food wastewater: process performances and microbial community.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {90},
number = {4},
pages = {1239-1249},
pmid = {39215735},
issn = {0273-1223},
support = {14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; TC/2014/0016//Enterprise Ireland/ ; },
mesh = {*Bioreactors ; Anaerobiosis ; *Wastewater ; *Waste Disposal, Fluid/methods ; Temperature ; Biological Oxygen Demand Analysis ; Bacteria/metabolism/classification ; Biofuels ; Industrial Waste ; },
abstract = {The fast-growing global population has led to a substantial increase in food production, which generates large volumes of wastewater during the process. Despite most industrial wastewater being discharged at lower ambient temperatures (<20 °C), majority of the high-rate anaerobic reactors are operated at mesophilic temperatures (>30 °C). High-rate low-temperature anaerobic digestion (LtAD) has proven successful in treating industrial wastewater both at laboratory and pilot scales, boasting efficient organic removal and biogas production. In this study, we demonstrated the feasibility of two full-scale high-rate LtAD bioreactors treating meat processing and dairy wastewater, and the microbial communities in both reactors were examined. Both reactors exhibited rapid start-up, achieving considerable chemical oxygen demand (COD) removal efficiencies (total COD removal >80%) and generating high-quality biogas (CH4% in biogas >75%). Long-term operations (6-12 months) underscored the robustness of LtAD bioreactors even during winter periods (average temperature <12 °C), as evidenced by sustained high COD removal rates (total COD removal >80%). The stable performance was underpinned by a resilient microbial community comprising active acetoclastic methanogens, hydrolytic, and fermentative bacteria. These findings underscore the feasibility of high-rate low-temperature anaerobic wastewater treatment, offering promising solutions to the zero-emission wastewater treatment challenge.},
}
@article {pmid39212186,
year = {2024},
author = {Junker Mentzel, CM and Hui, Y and Hammerich, TMS and Klug-Dambmann, M and Liu, Y and Zachariassen, LF and Hansen, LH and Aslampaloglou, A and Kiersgaard, M and Nielsen, DS and Hansen, AK and Krych, L},
title = {Low-gainer diet-induced obese microbiota transplanted mice exhibit increased fighting.},
journal = {Clinical and translational science},
volume = {17},
number = {9},
pages = {e13906},
pmid = {39212186},
issn = {1752-8062},
support = {//LIFEPHARM/ ; //Novo Nordisk A/S/ ; //Center for Applied Laboratory Animal Research/ ; },
mesh = {Animals ; Male ; *Obesity/microbiology/etiology ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation ; *Mice, Inbred C57BL ; *Diet, High-Fat/adverse effects ; *Weight Gain ; Mice ; Disease Models, Animal ; Leptin/blood/metabolism ; Feces/microbiology ; },
abstract = {Weight gain variation is a great challenge in diet-induced obesity studies since low-gainer animals are of limited experimental value. The inbred C57BL/6 (B6) mice are frequently used models due to their genetic homogeneity and susceptibility to diet-induced obesity (DIO). The aim of this study is to investigate if the gut microbiota (GM) influences the fraction of low weight gainers in DIO studies. A total of 100 male B6 mice (donor population) were fed a high-fat diet for 14 weeks and divided into the study groups high gainer (HG) and low gainer (LG) based on their weight gain. Subsequently, fecal matter transplantation (FMT) was done on germ-free B6 mice with GM from HG and LG donors (FMT population). LG (13.35 ± 2.5 g) and HG (25.52 ± 2.0 g) animals were identified by the weight gain from week 1 to week 12. Interestingly, the start weight of the LG (20.36 ± 1.4 g) and HG (21.59 ± 0.7 g) groups differed significantly. Transplanting LG or HG fecal matter to germ-free mice resulted in significant differences in weight gain between HG and LG, as well as differences in serum leptin levels and epididymal fat pad weight. A clear LG-specific GM composition could not be distinguished by 16S rRNA gene amplicon sequencing. Surprisingly, significantly more fighting was recorded in LG groups of both donor populations and when transplanted to germ-free mice. The HG and LG phenotypes could be transferred to germ-free mice. The increased fighting in the LG group in both studies suggests not only that the tendency to fight can be transferred by FMT in these mice, but also that fighting should be prevented in DIO studies to minimize the number of LG animals.},
}
@article {pmid39214074,
year = {2024},
author = {Letourneau, J and Carrion, VM and Zeng, J and Jiang, S and Osborne, OW and Holmes, ZC and Fox, A and Epstein, P and Tan, CY and Kirtley, M and Surana, NK and David, LA},
title = {Interplay between particle size and microbial ecology in the gut microbiome.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39214074},
issn = {1751-7370},
support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; 2016-IDG-1013//North Carolina Biotechnology Center/ ; N00014-18-1-2616//Office of Naval Research/ ; 1R01DK116187/NH/NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; Animals ; *Feces/microbiology ; Mice ; *Particle Size ; Adult ; Male ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; Diet ; Young Adult ; Mice, Inbred C57BL ; Mastication ; Middle Aged ; },
abstract = {Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is known about what drives FPS in the human gut. Here, we analyzed FPS by laser diffraction across a total of 76 individuals and found FPS to be strongly individualized. Contrary to our initial hypothesis, a behavioral intervention with 41 volunteers designed to increase chewing efficiency did not impact FPS. Dietary patterns could also not be associated with FPS. Instead, we found evidence that human and mouse gut microbiomes shaped FPS. Fecal samples from germ-free and antibiotic-treated mice exhibited increased FPS relative to colonized mice. In humans, markers of longer transit time were correlated with smaller FPS. Gut microbiota diversity and composition were also associated with FPS. Finally, ex vivo culture experiments using human fecal microbiota from distinct donors showed that differences in microbiota community composition can drive variation in particle size. Together, our results support an ecological model in which the human gut microbiome plays a key role in reducing the size of food particles during digestion. This finding has important implications for our understanding of energy extraction and subsequent uptake in gastrointestinal tract. FPS may therefore be viewed as an informative functional readout, providing new insights into the metabolic state of the gut microbiome.},
}
@article {pmid39211880,
year = {2024},
author = {Schluter, J and Matheis, F and Ebina, W and Jogia, W and Sullivan, AP and Gordon, K and Fanega de la Cruz, E and Victory-Hays, ME and Heinly, MJ and Diefenbach, CS and Peled, JU and Foster, KR and Levitt, A and McLaughlin, E},
title = {A randomized controlled trial of postbiotic administration during antibiotic treatment increases microbiome diversity and enriches health associated taxa.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.25.24311015},
pmid = {39211880},
abstract = {Antibiotic-induced microbiome injury, defined as a reduction of ecological diversity and obligate anaerobe taxa, is associated with negative health outcomes in hospitalized patients, and healthy individuals who received antibiotics in the past are at higher risk for autoimmune diseases. No interventions are currently available that effectively target the microbial ecosystem in the gut to prevent this negative collateral damage of antibiotics. Here, we present the results from a single-center, randomized placebo-controlled trial involving 32 patients who received an oral, fermentation-derived postbiotic alongside oral antibiotic therapy for gastrointestinal (GI)-unrelated infections. Postbiotics comprise complex mixtures of metabolites produced by bacteria during fermentation and other processes, which can mediate microbial ecology. Bacterial ecosystem alpha diversity, quantified by the inverse Simpson index, during the end of the antibiotic course was significantly higher (+40%) across the 16 postbiotic-treated patients compared with the 16 patients who received a placebo, and the postbiotic was well-tolerated. Secondary analyses of 157 stool samples collected longitudinally revealed that the increased diversity was driven by enrichment in health-associated microbial genera: obligate anaerobe Firmicutes, in particular taxa belonging to the Lachnospiraceae family, were higher in treated patients; conversely, Escherichia/Shigella abundances, which comprise pathobionts and antimicrobial-resistant strains, were reduced in postbiotic-treated patients at the end of their antibiotic course and up to 10 days later. Taken together, these results indicate that postbiotic co-administration during antibiotic therapy could support a health-associated gut microbiome community and may reduce antibiotic-induced microbiome injury.},
}
@article {pmid39204682,
year = {2024},
author = {Andreata, MFL and Afonso, L and Niekawa, ETG and Salomão, JM and Basso, KR and Silva, MCD and Alves, LC and Alarcon, SF and Parra, MEA and Grzegorczyk, KG and Chryssafidis, AL and Andrade, G},
title = {Microbial Fertilizers: A Study on the Current Scenario of Brazilian Inoculants and Future Perspectives.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {16},
pages = {},
pmid = {39204682},
issn = {2223-7747},
abstract = {The increasing need for sustainable agricultural practices, combined with the demand for enhanced crop productivity, has led to a growing interest in utilizing microorganisms for biocontrol of diseases and pests, as well as for growth promotion. In Brazilian agriculture, the use of plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting fungi (PGPF) has become increasingly prevalent, with a corresponding rise in the number of registered microbial inoculants each year. PGPR and PGPF occupy diverse niches within the rhizosphere, playing a crucial role in soil nutrient cycling and influencing a wide range of plant physiological processes. This review examines the primary mechanisms employed by these microbial agents to promote growth, as well as the strategy of co-inoculation to enhance product efficacy. Furthermore, we provide a comprehensive analysis of the microbial inoculants currently available in Brazil, detailing the microorganisms accessible for major crops, and discuss the market's prospects for the research and development of novel products in light of current challenges faced in the coming years.},
}
@article {pmid39203927,
year = {2024},
author = {Govaert, M and Rotsaert, C and Vannieuwenhuyse, C and Duysburgh, C and Medlin, S and Marzorati, M and Jarrett, H},
title = {Survival of Probiotic Bacterial Cells in the Upper Gastrointestinal Tract and the Effect of the Surviving Population on the Colonic Microbial Community Activity and Composition.},
journal = {Nutrients},
volume = {16},
number = {16},
pages = {},
pmid = {39203927},
issn = {2072-6643},
support = {Not applicable//Heights/ ; },
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; *Colon/microbiology ; *Upper Gastrointestinal Tract/microbiology ; Microbial Viability ; Bacteria/growth &amp; development ; Fatty Acids, Volatile/metabolism ; },
abstract = {Many health-promoting effects have been attributed to the intake of probiotic cells. However, it is important that probiotic cells arrive at the site of their activity in a viable state in order to exert their beneficial effects. Careful selection of the appropriate probiotic formulation is therefore required as mainly the type of probiotic species/strain and the administration strategy may affect survival of the probiotic cells during the upper gastrointestinal (GIT) passage. Therefore, the current study implemented Simulator of the Human Microbial Ecosystem (SHIME[®]) technology to investigate the efficacy of different commercially available probiotic formulations on the survival and culturability of probiotic bacteria during upper GIT passage. Moreover, Colon-on-a-Plate (CoaP™) technology was applied to assess the effect of the surviving probiotic bacteria on the gut microbial community (activity and composition) of three human donors. Significantly greater survival and culturability rates were reported for the delayed-release capsule formulation (>50%) as compared to the powder, liquid, and standard capsule formulations (<1%) (p < 0.05), indicating that the delayed-release capsule was most efficacious in delivering live bacteria cells. Indeed, administration of the delayed-release capsule probiotic digest resulted in enhanced production of SCFAs and shifted gut microbial community composition towards beneficial bacterial species. These results thus indicate that careful selection of the appropriate probiotic formulation and administration strategy is crucial to deliver probiotic cells in a viable state at the site of their activity (distal ileum and colon).},
}
@article {pmid39203578,
year = {2024},
author = {Yan, Y and Shi, Z and Wang, C and Jin, Z and Yin, J and Zhu, G},
title = {Viral Diversity and Ecological Impact of DNA Viruses in Dominant Tick Species in China.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203578},
issn = {2076-2607},
support = {RCYJ2012//Basic Scientific Research Funds of Hangzhou Medical College/ ; },
abstract = {Ticks are blood-feeding ectoparasites that also transmit various pathogens, posing severe risks to human and animal health. DNA viruses play a crucial role in the microbial ecology of ticks, but their distribution and ecological significance remain largely undetermined. Here, we assembled an extensive catalog encompassing 4320 viral operational taxonomic units (vOTUs) from six main dominant tick species in China, of which 94.8% have not been found in any other environment. To bridge the knowledge gap in tick DNA virus research and provide a crucial resource platform, we developed the Tick DNA Virus Database. This database includes the vOTUs that are known to cause diseases. Most of the predicted vOTUs are associated with dominant bacterial and archaeal phyla. We identified 105 virus-encoded putative auxiliary metabolic genes (AMGs) that are involved in host metabolism and environmental adaptation, potentially influencing ticks through both top-down and bottom-up mechanisms. The identification of microbial communities and antibiotic resistance in wild tick species suggests that wild ticks are reservoirs of antibiotic resistance and potential spreaders of antibiotic resistance. These findings reveal the potential role of tick viruses in ecosystems, highlighting the importance of monitoring tick microbiomes to address global public health challenges.},
}
@article {pmid39203418,
year = {2024},
author = {Barazetti, AR and Dealis, ML and Basso, KR and Silva, MCD and Alves, LDC and Parra, MEA and Simionato, AS and Cely, MVT and Macedo, AL and Silva, DB and Andrade, G},
title = {Evaluation of Resistance Induction Promoted by Bioactive Compounds of Pseudomonas aeruginosa LV Strain against Asian Soybean Rust.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203418},
issn = {2076-2607},
abstract = {Pseudomonas are known as higher producers of secondary metabolites with antimicrobial properties and plant growth promoters, including resistance induction. These mechanisms should be an alternative to pesticide use in crop production. Phakopsora pachyrhizi causes Asian soybean rust, representing a high loss of yield around the world. The objective of this paper was to evaluate the application of secondary metabolites produced by Pseudomonas aeruginosa LV strain from the semi-purified fraction F4A in soybean plants to induce plant resistance against P. pachyrhizi in field conditions. The experimental design was performed in randomized blocks with three replicates using two F4A doses (1 and 10 μg mL[-1]) combined or not with fungicides (Unizeb Gold[®] or Sphere Max[®]). The control treatment, with Uni + Sph, saponins, flavonoids, and sphingolipids, showed higher intensities in the plants. In contrast, plants treated with the F4A fraction mainly exhibited fatty acid derivatives and some non-identified compounds with nitrogen. Plants treated with Sphere Max[®], with or without F4A10, showed higher intensities of glycosylated flavonoids, such as kaempferol, luteolin, narigenin, and apigenin. Plants treated with F4A showed higher intensities of genistein and fatty acid derivatives. These increases in flavonoid compound biosynthesis and antioxidant properties probably contribute to the protection against reactive oxygen species (ROS).},
}
@article {pmid39203403,
year = {2024},
author = {Al-Tarshi, M and Dobretsov, S and Al-Belushi, M},
title = {Bacterial Communities across Multiple Ecological Niches (Water, Sediment, Plastic, and Snail Gut) in Mangrove Habitats.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203403},
issn = {2076-2607},
support = {RC/GRG-AGR/FISH/22/01//Ministry of Higher Education, Research and Innovation/ ; RC/GRG-AGR/FISH/22/01//Sultan Qaboos University/ ; },
abstract = {Microbial composition across substrates in mangroves, particularly in the Middle East, remains unclear. This study characterized bacterial communities in sediment, water, Terebralia palustris snail guts, and plastic associated with Avicennia marina mangrove forests in two coastal lagoons in the Sea of Oman using 16S rDNA gene MiSeq sequencing. The genus Vibrio dominated all substrates except water. In the gut of snails, Vibrio is composed of 80-99% of all bacterial genera. The water samples showed a different pattern, with the genus Sunxiuqinia being dominant in both Sawadi (50.80%) and Qurum (49.29%) lagoons. There were significant differences in bacterial communities on different substrata, in particular plastic. Snail guts harbored the highest number of unique Operational Taxonomic Units (OTUs) in both lagoons, accounting for 30.97% OTUs in Sawadi and 28.91% OTUs in Qurum, compared to other substrates. Plastic in the polluted Sawadi lagoon with low salinity harbored distinct genera such as Vibrio, Aestuariibacter, Zunongwangia, and Jeotgalibacillus, which were absent in the Qurum lagoon with higher salinity and lower pollution. Sawadi lagoon exhibited higher species diversity in sediment and plastic substrates, while Qurum lagoon demonstrated lower species diversity. The principal component analysis (PCA) indicates that environmental factors such as salinity, pH, and nutrient levels significantly influence bacterial community composition across substrates. Variations in organic matter and potential anthropogenic influences, particularly from plastics, further shape bacterial communities. This study highlights the complex microbial communities in mangrove ecosystems, emphasizing the importance of considering multiple substrates in mangrove microbial ecology studies. The understanding of microbial dynamics and anthropogenic impacts is crucial for shaping effective conservation and management strategies in mangrove ecosystems, particularly in the face of environmental changes.},
}
@article {pmid39200461,
year = {2024},
author = {Han, D and Yang, Y and Guo, Z and Dai, S and Jiang, M and Zhu, Y and Wang, Y and Yu, Z and Wang, K and Rong, C and Yu, Y},
title = {A Review on the Interaction of Acetic Acid Bacteria and Microbes in Food Fermentation: A Microbial Ecology Perspective.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {16},
pages = {},
pmid = {39200461},
issn = {2304-8158},
support = {32200012//National Natural Science Foundation of China/ ; 22KJB180016//Basic Science Research Program for Higher Education Institutions in Jiangsu Province (Natural Science)/ ; },
abstract = {In fermented foods, acetic acid bacteria (AAB), kinds of bacteria with a long history of utilization, contribute to safety, nutritional, and sensory properties primarily through acetic acid fermentation. AAB are commonly found in various fermented foods such as vinegar, sour beer, fermented cocoa and coffee beans, kefir beverages, kombucha, and sourdough. They interact and cooperate with a variety of microorganisms, resulting in the formation of diverse metabolites and the production of fermented foods with distinct flavors. Understanding the interactions between AAB and other microbes is crucial for effectively controlling and utilizing AAB in fermentation processes. However, these microbial interactions are influenced by factors such as strain type, nutritional conditions, ecological niches, and fermentation duration. In this review, we examine the relationships and research methodologies of microbial interactions and interaction studies between AAB and yeasts, lactic acid bacteria (LAB), and bacilli in different food fermentation processes involving these microorganisms. The objective of this review is to identify key interaction models involving AAB and other microorganisms. The insights gained will provide scientific guidance for the effective utilization of AAB as functional microorganisms in food fermentation processes.},
}
@article {pmid39198281,
year = {2024},
author = {He, Z and Smets, BF and Dechesne, A},
title = {Mating Assay: Plating Below a Cell Density Threshold is Required for Unbiased Estimation of Plasmid Conjugation Frequency of RP4 Transfer Between E. coli Strains.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {109},
pmid = {39198281},
issn = {1432-184X},
support = {0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; PhD Scholarship//Sino-Danish Center/ ; PhD Scholarship//Sino-Danish Center/ ; },
mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *Plasmids/genetics ; Gene Transfer, Horizontal ; },
abstract = {Mating assays are common laboratory experiments for measuring the conjugation frequency, i.e. efficiency at which a plasmid transfers from a population of donor cells to a population of recipient cells. Selective plating remains a widely used quantification method to enumerate transconjugants at the end of such assays. However, conjugation frequencies may be inaccurately estimated because plasmid transfer can occur on transconjugant-selective plates rather than only during the intended mating duration. We investigated the influence of cell density on this phenomenon. We conducted mating experiments with IncPα plasmid RP4 harbored in Escherichia coli at a fixed cell density and mating conditions, inoculated a serial dilution of the mating mixture on transconjugant-selective plates or in transconjugant-selective broth, and compared the results to a model of cell-to-cell distance distribution. Our findings suggest that irrespective of the mating mode (liquid vs solid), the enumeration of transconjugants becomes significantly biased if the plated cell density exceeds 28 Colony Forming Unit (CFU)/mm[2] (or 1.68•10[5] CFU/standard 9 cm Petri dish). This threshold is determined with a 95% confidence interval of ± 4 CFU/mm[2] (± 2.46•10[4] CFU/standard 9 cm Petri dish). Liquid mating assays were more sensitive to this bias because the conjugation frequency of RP4 is several orders of magnitude lower in suspension compared to surface mating. Therefore, if selective plating is used, we recommend to plate at this density threshold and that negative controls are performed where donors and recipients are briefly mixed before plating at the same dilutions as for the actual mating assay. As an alternative, a liquid enumeration method can be utilized to increase the signal-to-noise ratio and allow for more accurate enumeration of transconjugants.},
}
@article {pmid39197278,
year = {2024},
author = {Peng, C and Wang, Y and Sha, X and Li, M and Wang, X and Wang, J and Wang, Y and Liu, C and Wang, L},
title = {Adverse effect of TWPs on soil fungi and the contribution of benzothiazole rubber additives.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135574},
doi = {10.1016/j.jhazmat.2024.135574},
pmid = {39197278},
issn = {1873-3336},
mesh = {*Benzothiazoles ; *Soil Microbiology ; *Fungi/drug effects ; *Rubber ; *Soil Pollutants/toxicity/analysis ; Biomass ; },
abstract = {Tire wear particles (TWPs) pollution is widely present in soil, especially in areas severely affected by traffic. Herein, regular variation of fungal biomass with TWPs was found in soils with different distances from the highway. In addition, the concentrations of benzothiazole compounds (BTHs), an important class of rubber vulcanization accelerators, were found to be positively correlated to the TWPs abundance. Sixty days' soil microcosm experiments were conducted to further confirm the adverse effect of TWPs and BTHs on soil fungi. TWPs spiking at 1000 mg/kg, a detectable level in the roadside, resulted in significant reduction of biomass and significant changes of soil fungal community structure, with Eurotium and Polyporales being the sensitive species. BTH+ 2-hydroxybenzothiazole (OHBT) (the dominant BTHs in soil) spiking at 200 ng/kg, the dose equivalent to 1000 mg/kg TWPs pollution, also caused a similar magnitude of soil fungal biomass reduction. Adonis demonstrated no significant difference of fungal community structure between TWPs and BTH+OHBT spiked soil, suggesting the adverse effect of TWPs on soil fungi may be explained by the act of BTHs. Pure culture using the representative soil fungi Eurotium and Polyporales also confirmed that BTHs were the main contributors to the adverse effect of TWPs on soil fungi.},
}
@article {pmid39196435,
year = {2024},
author = {Tenore, A and Russo, F and Jacob, J and Grattepanche, JD and Buttaro, B and Klapper, I},
title = {A Mathematical Model of Diel Activity and Long Time Survival in Phototrophic Mixed-Species Subaerial Biofilms.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {10},
pages = {123},
pmid = {39196435},
issn = {1522-9602},
support = {1951532//National Science Foundation/ ; 2325170//National Science Foundation/ ; },
mesh = {*Biofilms/growth &amp; development ; *Models, Biological ; *Mathematical Concepts ; *Phototrophic Processes/physiology ; *Cyanobacteria/physiology/metabolism ; *Computer Simulation ; Biomass ; Heterotrophic Processes/physiology ; Microbial Interactions/physiology ; Bacterial Physiological Phenomena ; },
abstract = {Subaerial biofilms (SAB) are intricate microbial communities living on terrestrial surfaces, of interest in a variety of contexts including cultural heritage preservation, microbial ecology, biogeochemical cycling, and biotechnology. Here we propose a mathematical model aimed at better understanding the interplay between cyanobacteria and heterotrophic bacteria, common microbial SAB constituents, and their mutual dependence on local environmental conditions. SABs are modeled as thin mixed biofilm-liquid water layers sitting on stone. A system of ordinary differential equations regulates the dynamics of key SAB components: cyanobacteria, heterotrophs, polysaccharides and decayed biomass, as well as cellular levels of organic carbon, nitrogen and energy. These components are interconnected through a network of energetically dominant metabolic pathways, modeled with limitation terms reflecting the impact of biotic and abiotic factors. Daily cylces of temperature, humidity, and light intensity are considered as input model variables that regulate microbial activity by influencing water availability and metabolic kinetics. Relevant physico-chemical processes, including pH regulation, further contribute to a description of the SAB ecology. Numerical simulations explore the dynamics of SABs in a real-world context, revealing distinct daily activity periods shaped by water activity and light availability, as well as longer time scale survivability conditions. Results also suggest that heterotrophs could play a substantial role in decomposing non-volatile carbon compounds and regulating pH, thus influencing the overall composition and stability of the biofilm.},
}
@article {pmid39196422,
year = {2024},
author = {Toloza-Moreno, DL and Yockteng, R and Pérez-Zuñiga, JI and Salinas-Castillo, C and Caro-Quintero, A},
title = {Implications of Domestication in Theobroma cacao L. Seed-Borne Microbial Endophytes Diversity.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {108},
pmid = {39196422},
issn = {1432-184X},
mesh = {*Cacao/microbiology ; *Endophytes/genetics/classification/isolation &amp; purification/physiology ; *Seeds/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *Domestication ; Microbiota ; Fungi/genetics/classification/isolation &amp; purification ; Genotype ; Biodiversity ; },
abstract = {The study of plant-microbe interactions is a rapidly growing research field, with increasing attention to the role of seed-borne microbial endophytes in protecting the plant during its development from abiotic and biotic stresses. Recent evidence suggests that seed microbiota is crucial in establishing the plant microbial community, affecting its composition and structure, and influencing plant physiology and ecology. For Theobroma cacao L., the diversity and composition of vertically transmitted microbes have yet to be addressed in detail. We explored the composition and diversity of seed-borne endophytes in cacao pods of commercial genotypes (ICS95, IMC67), recently liberated genotypes from AGROSAVIA (TCS01, TCS19), and landraces from Tumaco (Colombia) (AC9, ROS1, ROS2), to evaluate microbial vertical transmission and establishment in various tissues during plant development. We observed a higher abundance of Pseudomonas and Pantoea genera in the landraces and AGROSAVIA genotypes, while the commercial genotypes presented a higher number of bacteria species but in low abundance. In addition, all the genotypes and plant tissues showed a high percentage of fungi of the genus Penicillium. These results indicate that domestication in cacao has increased bacterial endophyte diversity but has reduced their abundance. We isolated some of these seed-borne endophytes to evaluate their potential as growth promoters and found that Bacillus, Pantoea, and Pseudomonas strains presented high production of indole acetic acid and ACC deaminase activity. Our results suggest that cacao domestication could lead to the loss of essential bacteria for seedling establishment and development. This study improves our understanding of the relationship and interaction between perennial plants and seed-borne microbiota.},
}
@article {pmid39193431,
year = {2024},
author = {Ding, J and Cui, X and Wang, X and Zhai, F and Wang, L and Zhu, L},
title = {Multi-omics analysis of gut microbiota and metabolites reveals contrasting profiles in domestic pigs and wild boars across urban environments.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1450306},
pmid = {39193431},
issn = {1664-302X},
abstract = {The gut microbiota plays a crucial role in host health and metabolism. This study explores the differences in gut microbiota and metabolites between domestic pigs (DP) and wild boars (WB) in urban environments. We analyzed gut microbial composition, metabolic profiles, virome composition, antibiotic resistance genes (ARGs), and human pathogenic bacteria (HPB) in both DP and WB. Our results revealed that DP exhibited a higher Firmicutes/Bacteroidetes ratio and were enriched in bacterial genera associated with domestication and modern feeding practices. Metabolomic analysis showed distinct profiles, with WB significantly enriched in the Pantothenate and CoA biosynthesis pathway, highlighting dietary and environmental influences on host metabolism. Additionally, DP had a distinct gut virome composition, particularly enriched in lytic phages of the Chaseviridae family. ARG analysis indicated a higher abundance of tetracycline resistance genes in DP, likely due to antibiotic use in pig farms. Furthermore, variations in HPB composition underscored potential health risks associated with contact with pig feces. These findings provide valuable insights into the microbial ecology of domestic pigs and wild boars, emphasizing the importance of these comparisons in identifying zoonotic pathogen transmission pathways and managing antibiotic resistance. Continued research in this area is essential for developing effective strategies to mitigate public health risks and promote sustainable livestock management practices.},
}
@article {pmid39191402,
year = {2024},
author = {Aoun, N and Georgoulis, SJ and Avalos, JK and Grulla, KJ and Miqueo, K and Tom, C and Lowe-Power, TM},
title = {A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia.},
journal = {mBio},
volume = {15},
number = {10},
pages = {e0032324},
pmid = {39191402},
issn = {2150-7511},
support = {Hatch #1023861,Award# 1030618//USDA | National Institute of Food and Agriculture (NIFA)/ ; //Hellman Foundation (The Hellman Foundation)/ ; },
mesh = {*Type VI Secretion Systems/genetics/metabolism ; *Phylogeny ; *Genome, Bacterial ; *Ralstonia solanacearum/genetics/metabolism ; *Evolution, Molecular ; Plant Diseases/microbiology ; Bacterial Toxins/genetics/metabolism ; Burkholderiaceae/genetics/metabolism/classification ; Multigene Family ; Ralstonia/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; },
abstract = {Soilborne Ralstonia solanacearum species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and Paracidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters ("aux" clusters) across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.IMPORTANCEWe explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the Ralstonia solanacearum species complex. We discovered that most Ralstonia wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of Ralstonia pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the Ralstonia toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of Ralstonia wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of Ralstonia pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.},
}
@article {pmid39190978,
year = {2024},
author = {Xu, M and Wang, F and Stedtfeld, RD and Fu, Y and Xiang, L and Sheng, H and Li, Z and Hashsham, SA and Jiang, X and Tiedje, JM},
title = {Transfer of antibiotic resistance genes from soil to rice in paddy field.},
journal = {Environment international},
volume = {191},
number = {},
pages = {108956},
doi = {10.1016/j.envint.2024.108956},
pmid = {39190978},
issn = {1873-6750},
mesh = {*Oryza/genetics ; *Soil Microbiology ; *Fertilizers ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Animals ; Agriculture ; Swine ; Composting ; Genes, Bacterial ; },
abstract = {The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.},
}
@article {pmid39189736,
year = {2024},
author = {Wang, L and Ducoste, JJ and de Los Reyes, FL},
title = {Perturbations to common gardens of anaerobic co-digesters reveal relationships between functional resilience and microbial community composition.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {9},
pages = {e0029824},
pmid = {39189736},
issn = {1098-5336},
support = {15-05-U//North Carolina Water Resources Research Institute/ ; CBET 1805666//National Science Foundation (NSF)/ ; },
mesh = {*Microbiota/physiology ; *Bioreactors/microbiology ; Anaerobiosis ; *Methane/metabolism ; Bacteria/metabolism/classification/genetics ; },
abstract = {We report the relationship between enrichment of adapted populations and enhancement of community functional resilience in methanogenic bioreactors. Although previous studies have shown the positive effects of acclimation, this work directly investigated the relationships between microbiome dynamics and performance of anaerobic co-digesting reactors in response to different levels of an environmental perturbation (loading of grease interceptor waste [GIW]). Using the methanogenic microbiome from a full-scale digester, we developed eight sets of microbial communities in triplicate using different feed sources. These substrate-specific microbiomes were then exposed to three independent disturbance events of low-, mid- and high-GIW loading rates. This approach allowed us to directly attribute differences in community responses to differences in community composition. Despite identical inocula, environment (digester operation, substrate loading rate, and feeding patterns) and general whole-community function (methane production and effluent quality) during the cultivation period, different substrates led to different microbial community assemblies. Lipid pre-acclimation led to enrichment of a pool of specialized populations, along with thriving of sub-dominant communities. The enrichment of these populations improved functional resilience and process performance when exposed to a low level of lipid-rich perturbation compared with less-acclimated communities. At higher levels of perturbation, the communities were not able to recover methanogenesis, indicating a loading limit to the resilience response. This study extends our current understanding of environmental perturbations, feed-specific adaptation, and functional resilience in methanogenic bioreactors.IMPORTANCEThis study demonstrates, for the first time for GIW co-digestion, how applying similar perturbations to different microbial communities was used to directly identify the causal relationships between microbial community, function, and environment in triplicate anaerobic microbiomes. We evaluated the impact of feed-specific adaptation on methanogenic microbiomes and demonstrated how microbiomes can be influenced to improve their functional (methanogenic) resilience to GIW inhibition. These findings demonstrate how an ecological framework can help improve a biological engineering application, and more specifically, increase the potential of anaerobic co-digestion for converting wastes to energy.},
}
@article {pmid39188310,
year = {2024},
author = {Berrios, L and Venturini, AM and Ansell, TB and Tok, E and Johnson, W and Willing, CE and Peay, KG},
title = {Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae104},
pmid = {39188310},
issn = {2730-6151},
abstract = {Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.},
}
@article {pmid39187952,
year = {2024},
author = {Stryker, J and White, E and Díaz-Almeyda, E and Sidoti, B and Oberle, B},
title = {Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e16396},
doi = {10.1002/ajb2.16396},
pmid = {39187952},
issn = {1537-2197},
abstract = {PREMISE: Up to half of tropical forest plant species grow on other plants. Lacking access to soils, vascular epiphytes have unique adaptations for mineral nutrition. Among the most distinctive is the tank growth form of certain large bromeliads, which absorb nutrients that are cycled by complex microbial communities in water trapped among their overlapping leaf bases. However, tanks form only after years of growth by juvenile plants, which must acquire nutrients differently. Understanding how nutrient dynamics change during tank bromeliad development can provide key insights into the role of microorganisms in the maintenance of tropical forest biodiversity.<br><br>METHODS: We evaluated variations in plant morphology, growth, foliar nitrogen physiology, and phyllosphere bacterial communities along a size gradient spanning the transition to tank formation in the threatened species Tillandsia utriculata.<br><br>RESULTS: Sequential morphological and growth phases coincided with the transition to tank formation when the longest leaf on plants was between 14 and 19&#x2009;cm. Before this point, foliar ammonium concentrations were very high, but after, leaf segments absorbed significantly more nitrate. Leaf-surface bacterial communities tracked ontogenetic changes in plant morphology and nitrogen metabolism, with less-diverse communities in tankless plants distinguished by a high proportion of taxa implicated in ureolysis, nitrogen fixation, and methanotrophy, whereas nitrate reduction characterized communities on individuals that could form a tank.<br><br>CONCLUSIONS: Coupled changes in plant morphology, physiology, and microbiome function facilitate the transition between alternative nutritional modes in tank bromeliads. Comparing bromeliads across life stages and habitats may illuminate how nitrogen-use varies across scales.},
}
@article {pmid39182301,
year = {2024},
author = {Peruzzo, A and Petrin, S and Boscolo Anzoletti, A and Mancin, M and Di Cesare, A and Sabatino, R and Lavagnolo, MC and Beggio, G and Baggio, G and Danesi, P and Barco, L and Losasso, C},
title = {The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135567},
doi = {10.1016/j.jhazmat.2024.135567},
pmid = {39182301},
issn = {1873-3336},
mesh = {*Agriculture ; *Soil Microbiology ; *Sewage/microbiology ; *Bacteria/genetics ; Soil/chemistry ; Composting ; Metagenomics ; Fertilizers ; },
abstract = {In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.},
}
@article {pmid39180136,
year = {2024},
author = {Khadem, S and Berry, D and Al-Khlifeh, E},
title = {Climate influences the gut eukaryome of wild rodents in the Great Rift Valley of Jordan.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {358},
pmid = {39180136},
issn = {1756-3305},
mesh = {Animals ; Jordan/epidemiology ; Mice ; *Gastrointestinal Microbiome ; *Feces/parasitology/microbiology ; *Climate ; Eukaryota/classification/isolation &amp; purification/genetics ; Animals, Wild/parasitology ; RNA, Ribosomal, 18S/genetics ; Rodentia/microbiology/parasitology ; Biodiversity ; Murinae/parasitology ; },
abstract = {BACKGROUND: The mammalian gut microbiome includes a community of eukaryotes with significant taxonomic and functional diversity termed the eukaryome. The molecular analysis of eukaryotic diversity in microbiomes of wild mammals is still in its early stages due to the recent emergence of interest in this field. This study aimed to fill this knowledge gap by collecting data on eukaryotic species found in the intestines of wild rodents. Because little is known about the influence of climate on the gut eukaryome, we compared the composition of the gut eukaryotes in two rodent species, Mus musculus domesticus and Acomys cahirinus, which inhabit a transect crossing a temperate and tropical zone on the Jordanian side of the Great Rift Valley (GRV).<br><br>METHODS: We used high-throughput amplicon sequencing targeting the 18S rRNA gene in fecal samples from rodents to identify eukaryotic organisms, their relative abundance, and their potential for pathogenicity.<br><br>RESULTS: Nematodes and protozoa were the most prevalent species in the eukaryome communities, whereas fungi made up 6.5% of the total. Sixty percent of the eukaryotic ASVs belonged to taxa that included known pathogens. Eighty percent of the rodents were infected with pinworms, specifically Syphacia obvelata. Eukaryotic species diversity differed significantly between bioclimatic zones (p&#x2009;=&#x2009;0.001). Nippostrongylus brasiliensis and Aspiculuris tetraptera were found to be present exclusively in the Sudanian zone rodents. This area has not reported any cases of Trichuris infections. Yet, Capillaria infestations were unique to the Mediterranean region, while Trichuris vulpis infestations were also prevalent in the Mediterranean and Irano-Turanian regions.<br><br>CONCLUSIONS: This study highlights the importance of considering host species diversity and environmental factors when studying eukaryome composition in wild mammals. These data will be valuable as a reference to eukaryome study.},
}
@article {pmid39178936,
year = {2024},
author = {Anedda, E and Ekhlas, D and Alexa, E and Farrell, ML and Gaffney, MT and Madigan, G and Morris, D and Burgess, CM},
title = {Characterization of antimicrobial resistant Enterobacterales isolated from spinach and soil following zinc amendment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {361},
number = {},
pages = {124774},
doi = {10.1016/j.envpol.2024.124774},
pmid = {39178936},
issn = {1873-6424},
mesh = {*Spinacia oleracea/microbiology ; *Soil Microbiology ; *Zinc/pharmacology ; *Enterobacteriaceae/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; *Soil Pollutants ; Soil/chemistry ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antimicrobial resistant bacteria can occur in the primary food production environment. The emergence and dissemination of antimicrobial resistance (AMR) in the environment can be influenced by several factors, including the presence of heavy metals. The aim of this study was to examine the presence and characteristics of antimicrobial resistant Enterobacterales in soils and spinach grown in soils with and without zinc amendment. A total of 160 samples (92 soil and 68 spinach) were collected from two locations, in which some plots had been amended with zinc. Samples were cultured on selective agars for detection of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL), carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales. Samples were also cultured for enumeration of total Enterobacterales. Isolates were identified by MALDI-TOF. Antimicrobial susceptibility testing was carried out in accordance with EUCAST and CLSI criteria. The whole genome sequence (WGS) of selected isolates was determined. Inductively coupled plasma atomic emission spectrometry was also performed on soil samples in order to measure the concentration of zinc. In total 20 antimicrobial resistant Enterobacterales were isolated from the soil (n = 8) and spinach samples (n = 12). In both sample types, Serratia fonticola (n = 16) was the dominant species, followed by Escherichia coli (n = 1), Citrobacter freundii (n = 1) and Morganella morganii (n = 1) detected in spinach samples, and Enterobacter cloacae (n = 1) detected in a soil sample. The WGS identified genes conferring resistance to different antimicrobials in agreement with the phenotypic results; 14 S. fonticola isolates were confirmed as ESBL producers and harboured the blaFONA gene. Genes that encoded for zinc resistance and multidrug efflux pumps, transporters that can target both antimicrobials and heavy metals, were also identified. Overall, the findings of this study suggest the presence of zinc did not influence the AMR Enterobacterales in soil or spinach samples.},
}
@article {pmid39178591,
year = {2024},
author = {Gao, FZ and Hu, LX and Liu, YS and Qiao, LK and Chen, ZY and Su, JQ and He, LY and Bai, H and Zhu, YG and Ying, GG},
title = {Unveiling the overlooked small-sized microbiome in river ecosystems.},
journal = {Water research},
volume = {265},
number = {},
pages = {122302},
doi = {10.1016/j.watres.2024.122302},
pmid = {39178591},
issn = {1879-2448},
mesh = {*Rivers/microbiology ; *Microbiota ; *Ecosystem ; Metagenomics ; Bacteria/genetics ; },
abstract = {Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment.},
}
@article {pmid39175749,
year = {2024},
author = {Peña-Salinas, ME and Speth, DR and Utter, DR and Spelz, RM and Lim, S and Zierenberg, R and Caress, DW and Núñez, PG and Vázquez, R and Orphan, VJ},
title = {Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa 'ja 'ag hydrothermal vent fields in the Pescadero Basin, Gulf of California.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17724},
pmid = {39175749},
issn = {2167-8359},
mesh = {*Hydrothermal Vents/microbiology ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Seawater/microbiology/chemistry ; California ; Bacteria/genetics/classification ; },
abstract = {Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa 'ja 'ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.},
}
@article {pmid39175056,
year = {2024},
author = {Sbardellati, DL and Vannette, RL},
title = {Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {155},
pmid = {39175056},
issn = {2049-2618},
support = {2023-67011-40501//U.S. Department of Agriculture/ ; 1929516//National Science Foundation/ ; },
mesh = {Bees/virology/microbiology ; Animals ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Virome ; *Metagenome ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Gastrointestinal Tract/microbiology/virology ; },
abstract = {BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.<br><br>RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.<br><br>CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.},
}
@article {pmid39174521,
year = {2024},
author = {Foulquier, A and Datry, T and Corti, R and von Schiller, D and Tockner, K and Stubbington, R and Gessner, MO and Boyer, F and Ohlmann, M and Thuiller, W and Rioux, D and Miquel, C and Albariño, R and Allen, DC and Altermatt, F and Arce, MI and Arnon, S and Banas, D and Banegas-Medina, A and Beller, E and Blanchette, ML and Blessing, J and Boëchat, IG and Boersma, K and Bogan, M and Bonada, N and Bond, N and Brintrup, K and Bruder, A and Burrows, R and Cancellario, T and Canhoto, C and Carlson, S and Cid, N and Cornut, J and Danger, M and de Freitas Terra, B and De Girolamo, AM and Del Campo, R and Díaz Villanueva, V and Dyer, F and Elosegi, A and Febria, C and Figueroa Jara, R and Four, B and Gafny, S and Gómez, R and Gómez-Gener, L and Guareschi, S and Gücker, B and Hwan, J and Jones, JI and Kubheka, PS and Laini, A and Langhans, SD and Launay, B and Le Goff, G and Leigh, C and Little, C and Lorenz, S and Marshall, J and Martin Sanz, EJ and McIntosh, A and Mendoza-Lera, C and Meyer, EI and Miliša, M and Mlambo, MC and Morais, M and Moya, N and Negus, P and Niyogi, D and Pagán, I and Papatheodoulou, A and Pappagallo, G and Pardo, I and Pařil, P and Pauls, SU and Polášek, M and Rodríguez-Lozano, P and Rolls, RJ and Sánchez-Montoya, MM and Savić, A and Shumilova, O and Sridhar, KR and Steward, A and Taleb, A and Uzan, A and Valladares, Y and Vander Vorste, R and Waltham, NJ and Zak, DH and Zoppini, A},
title = {Unravelling large-scale patterns and drivers of biodiversity in dry rivers.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7233},
pmid = {39174521},
issn = {2041-1723},
support = {869226 (DRYvER)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)/ ; },
mesh = {*Biodiversity ; *Rivers/microbiology ; Animals ; Fungi/classification/genetics ; Geologic Sediments/microbiology ; Bacteria/classification/genetics ; Invertebrates/classification ; DNA Barcoding, Taxonomic ; Plants/classification ; Archaea/classification/genetics ; },
abstract = {More than half of the world's rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.},
}
@article {pmid39172818,
year = {2024},
author = {Frazier, AN and Belk, AD and Beck, MR and Koziel, JA},
title = {Impact of methane mitigation strategies on the native ruminant microbiome: A protocol for a systematic review and meta-analysis.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308914},
pmid = {39172818},
issn = {1932-6203},
mesh = {*Methane/metabolism ; *Ruminants/microbiology ; Animals ; *Microbiota ; *Systematic Reviews as Topic ; *RNA, Ribosomal, 16S/genetics ; *Meta-Analysis as Topic ; },
abstract = {Recently, research has investigated the role of the ruminant native microbiome, and the role microbes play in methane (CH4) production and mitigation. However, the variation across microbiome studies makes implementing impactful strategies difficult. The first objective of this study is to identify, summarize, compile, and discuss the current literature on CH4 mitigation strategies and how they interact with the native ruminant microbiome. The second objective is to perform a meta-analysis on the identified16S rRNA sequencing data. A literature search using Web of Science, Scopus, AGRIS, and Google Scholar will be implemented. Eligible criteria will be defined using PICO (population, intervention, comparator, and outcomes) elements. Two independent reviewers will be utilized for both the literature search and data compilation. Risk of bias will be assessed using the Cochrane Risk Bias 2.0 tool. Publicly available 16S rRNA amplicon gene sequencing data will be downloaded from NCBI Sequence Read Archive, European Nucleotide Archive or similar database using appropriate extraction methods. Data processing will be performed using QIIME2 following a standardized protocol. Meta-analyses will be performed on both alpha and beta diversity as well as taxonomic analyses. Alpha diversity metrics will be tested using a Kruskal-Wallis test with a Benjamini-Hochberg multiple testing correction. Beta diversity will be statistically tested using PERMANOVA testing with multiple test corrections. Hedge's g standardized mean difference statistic will be used to calculate fixed and random effects model estimates using a 95% confidence interval. Heterogeneity between studies will be assessed using the I2 statistic. Potential publication bias will be further assessed using Begg's correlation test and Egger's regression test. The GRADE approach will be used to assess the certainty of evidence. The following protocol will be used to guide future research and meta-analyses for investigating CH4 mitigation strategies and ruminant microbial ecology. The future work could be used to enhance livestock management techniques for GHG control. This protocol is registered in Open Science Framework (https://osf.io/vt56c) and available in the Systematic Reviews for Animals and Food (https://www.syreaf.org/contact).},
}
@article {pmid39171106,
year = {2024},
author = {Pi, X and Du, Z and Teng, W and Fu, H and Hu, L and Li, J and Ding, J and Yang, X and Zhang, Y},
title = {Characteristics of stachyose-induced effects on gut microbiota and microbial metabolites in vitro associated with obesity in children.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1411374},
pmid = {39171106},
issn = {2296-861X},
abstract = {Childhood obesity presents a serious health concern associated with gut microbiota alterations. Dietary interventions targeting the gut microbiota have emerged as promising strategies for managing obesity in children. This study aimed to elucidate the impact of stachyose (STS) supplementation on the gut microbiota composition and metabolic processes in obese children. Fecal samples were collected from 40 obese children (20 boys and 20 girls) aged between 6 and 15 and in vitro fermentation was conducted with or without the addition of STS, respectively, followed by 16S rRNA amplicon sequencing and analysis of short-chain fatty acids (SCFAs) and gases. Notably, our results revealed that STS supplementation led to significant alterations in gut microbiota composition, including an increase in the abundance of beneficial bacteria such as Bifidobacterium and Faecalibacterium, and a decrease in harmful bacteria including Escherichia-Shigella, Parabacteroides, Eggerthella, and Flavonifractor. Moreover, STS supplementation resulted in changes in SCFAs production, with significant increases in acetate levels and reductions in propionate and propionate, while simultaneously reducing the generation of gases such as H2S, H2, and NH3. The Area Under the Curve (AUC)-Random Forest algorithm and PICRUSt 2 were employed to identify valuable biomarkers and predict associations between the gut microbiota, metabolites, and metabolic pathways. The results not only contribute to the elucidation of STS's modulatory effects on gut microbiota but also underscore its potential in shaping metabolic activities within the gastrointestinal environment. Furthermore, our study underscores the significance of personalized nutrition interventions, particularly utilizing STS supplementation, in the management of childhood obesity through targeted modulation of gut microbial ecology and metabolic function.},
}
@article {pmid39168311,
year = {2024},
author = {MacGibeny, MA and Adjei, S and Pyle, H and Bunick, CG and Ghannoum, M and Grada, A and Harris-Tryon, T and Tyring, SK and Kong, HH},
title = {The Human Skin Microbiome in Health: CME Part 1.},
journal = {Journal of the American Academy of Dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaad.2024.07.1498},
pmid = {39168311},
issn = {1097-6787},
abstract = {Human skin is home to a myriad of microorganisms, including bacteria, viruses, fungi, and mites, many of which are considered commensal microbes that aid in maintaining the overall homeostasis or steady-state condition of the skin and contribute to skin health. Our understanding of the complexities of the skin's interaction with its microorganisms is evolving. This knowledge is based primarily on in vitro and animal studies, and more work is needed to understand how this knowledge relates to humans. Here, we introduce the concept of the skin microbiome and discuss skin microbial ecology, some intrinsic factors with potential influence on the human skin microbiome, and possible microbiome-host interactions. The second article of this two-part CME series describes how microbiome alterations may be associated with skin disease, how medications can affect the microbiome, and what microbiome-based therapies are under investigation.},
}
@article {pmid39165397,
year = {2024},
author = {Jacob, M and Thomas, PK and Giebel, HA and Billerbeck, S and Simon, M and Striebel, M and Dlugosch, L},
title = {Cross-domain diversity effects: linking diatom species richness, intraspecific richness, and biomass production to host-associated bacterial diversity.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae046},
pmid = {39165397},
issn = {2730-6151},
abstract = {Interactions between bacteria and microalgae are important for the functioning of aquatic ecosystems, yet interactions based on the biodiversity of these two taxonomic domains have been scarcely studied. Specifically, it is unclear whether a positive biodiversity-productivity relationship in phytoplankton is largely facilitated by niche partitioning among the phytoplankton organisms themselves or whether associated bacterial communities play an additional role in modifying these diversity effects. Moreover, the effects of intraspecific diversity in phytoplankton communities on bacterial community diversity have not been tested. To address these points, we factorially manipulated both species and intraspecific richness of three diatoms to test the effects of diatom species/strain diversity on biomass production and bacterial diversity in algae-bacteria communities. The results show that diatom intraspecific diversity has significant positive effects on culture biomass and the diversity of the associated free-living bacterial community (0.2-3 μm size fraction), which are comparable in magnitude to species diversity effects. However, there were little to no effects of diatom diversity on host-associated bacterial diversity (>3 μm size fraction), or of bacterial diversity on biomass production. These results suggest a decoupling of bacterial diversity from the diatom diversity-productivity relationship and provide early insights regarding the relations between diversity across domains in aquatic ecosystems.},
}
@article {pmid39165109,
year = {2024},
author = {Gloder, G and Bourne, ME and Cuny, MAC and Verreth, C and Crauwels, S and Dicke, M and Poelman, EH and Jacquemyn, H and Lievens, B},
title = {Caterpillar-parasitoid interactions: species-specific influences on host microbiome composition.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {10},
pages = {},
pmid = {39165109},
issn = {1574-6941},
support = {G.0961.19//Flemish Fund for Scientific Research/ ; },
mesh = {Animals ; *Larva/microbiology ; *Microbiota ; *Butterflies/microbiology/parasitology ; *Host-Parasite Interactions ; Wolbachia/genetics ; Species Specificity ; Nosema/pathogenicity ; Wasps/microbiology ; Bacteria/classification/genetics/growth &amp; development ; },
abstract = {There is increasing evidence that host-parasitoid interactions can have a pronounced impact on the microbiome of host insects, but it is unclear to what extent this is caused by the host and/or parasitoid. Here, we compared the internal and external microbiome of caterpillars of Pieris brassicae and Pieris rapae parasitized by Cotesia glomerata or Cotesia rubecula with nonparasitized caterpillars. Additionally, we investigated the internal and external microbiome of the parasitoid larvae. Both internal and external bacterial densities were significantly higher for P. brassicae than P. rapae, while no differences were found between parasitized and nonparasitized caterpillars. In contrast, parasitism significantly affected the composition of the internal and external microbiome of the caterpillars and the parasitoid larvae, but the effects were dependent on the host and parasitoid species. Irrespective of host species, a Wolbachia species was exclusively found inside caterpillars parasitized by C. glomerata, as well as in the corresponding developing parasitoid larvae. Similarly, a Nosema species was abundantly present inside parasitized caterpillars and the parasitoid larvae, but this was independent of the host and the parasitoid species. We conclude that parasitism has pronounced effects on host microbiomes, but the effects depend on both the host and parasitoid species.},
}
@article {pmid39163484,
year = {2024},
author = {Dede, B and Reeves, EP and Walter, M and Bach, W and Amann, R and Meyerdierks, A},
title = {Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39163484},
issn = {1751-7370},
support = {EXC-309-49926684//Deutsche Forschungsgemeinschaft/ ; //Norwegian Research Council/ ; 179560//University of Bergen Centre for Geobiology/ ; //Max Planck Society/ ; },
mesh = {*Hydrothermal Vents/microbiology ; Atlantic Ocean ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Chemoautotrophic Growth ; *Seawater/microbiology ; Microbiota ; Hydrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; Oxidation-Reduction ; In Situ Hybridization, Fluorescence ; Carbon Dioxide/metabolism ; },
abstract = {Hydrothermal vent systems release reduced chemical compounds that act as an important energy source in the deep sea. Chemolithoautotrophic microbes inhabiting hydrothermal plumes oxidize these compounds, in particular, hydrogen and reduced sulfur, to obtain the energy required for CO2 fixation. Here, we analysed the planktonic communities of four hydrothermal systems located along the Mid-Atlantic Ridge: Irinovskoe, Semenov-2, Logatchev-1, and Ashadze-2, by combining long-read 16S rRNA gene analysis, fluorescence in situ hybridization, meta-omics, and thermodynamic calculations. Sulfurimonas and SUP05 dominated the microbial communities in these hydrothermal plumes. Investigation of Sulfurimonas and SUP05 MAGs, and their gene transcription in plumes indicated a niche partitioning driven by hydrogen and sulfur. In addition to sulfur and hydrogen oxidation, a novel SAR202 clade inhabiting the plume, here referred to as genus Carboxydicoccus, harbours the capability for CO oxidation and CO2 fixation via reverse TCA cycle. Both pathways were also highly transcribed in other hydrogen-rich plumes, including the Von Damm vent field. Carboxydicoccus profundi reached up to 4% relative abundance (1.0 x 103 cell ml- 1) in Irinovskoe non-buoyant plume and was also abundant in non-hydrothermally influenced deep-sea metagenomes (up to 5 RPKM). Therefore, CO, which is probably not sourced from the hydrothermal fluids (1.9-5.8 μM), but rather from biological activities within the rising fluid, may serve as a significant energy source in hydrothermal plumes. Taken together, this study sheds light on the chemolithoautotrophic potential of the bacterial community in Mid-Atlantic Ridge plumes.},
}
@article {pmid39162854,
year = {2024},
author = {Joshi, S and Pham, K and Moe, L and McNees, R},
title = {Exploring the Microbial Diversity and Composition of Three Cigar Product Categories.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {107},
pmid = {39162854},
issn = {1432-184X},
mesh = {*Tobacco Products ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Biodiversity ; Phylogeny ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; },
abstract = {Cigars and cigarillos are emerging as popular tobacco alternatives to cigarettes. However, these products may be equally harmful to human health than cigarettes and are associated with similar adverse health effects. We used 16S rRNA gene amplicon sequencing to extensively characterize the microbial diversity and investigate differences in microbial composition across 23 different products representing three different cigar product categories: filtered cigar, cigarillo, and large cigar. High throughput sequencing of the V4 hypervariable region of the 16 s rRNA gene revealed 2124 Operational Taxonomic Units (OTUs). Our findings showed that the three categories of cigars differed significantly in observed richness and Shannon diversity, with filtered cigars exhibiting lower diversity compared to large cigars and cigarillos. We also found a shared and unique microbiota among different product types. Firmicutes was the most abundant phylum in all product categories, followed by Actinobacteria. Among the 16 genera shared across all product types were Bacillus, Staphylococcus, Pseudomonas, and Pantoea. Nine genera were exclusively shared by large cigars and cigarillos and an additional thirteen genera were exclusive to filtered cigars. Analysis of individual cigar products showed consistent microbial composition across replicates for most large cigars and cigarillos while filtered cigars showed more inter-product variability. These findings provide important insights into the microbial diversity of the different cigar product types.},
}
@article {pmid39162497,
year = {2024},
author = {Chatzigiannidou, I and Heyse, J and Props, R and Rubbens, P and Mermans, F and Teughels, W and Van de Wiele, T and Boon, N},
title = {Real-time flow cytometry to assess qualitative and quantitative responses of oral pathobionts during exposure to antiseptics.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0095524},
pmid = {39162497},
issn = {2165-0497},
support = {G0B2719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 1221020N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G020119//Fonds Wetenschappelijk Onderzoek (FWO)/ ; },
mesh = {*Flow Cytometry/methods ; *Anti-Infective Agents, Local/pharmacology ; *Chlorhexidine/pharmacology ; Humans ; *Bacteria/drug effects ; *Triclosan/pharmacology ; Cetylpyridinium/pharmacology ; Microbial Sensitivity Tests/methods ; Mouth/microbiology ; Periodontitis/microbiology ; },
abstract = {UNLABELLED: Antiseptics are widely used in oral healthcare to prevent or treat oral diseases, such as gingivitis and periodontitis. However, the incidence of bacteria being tolerant to standard antiseptics has sharply increased over the last few years. This stresses the urgency for surveillance against tolerant organisms, as well as the discovery of novel antimicrobials. Traditionally, susceptibility to antimicrobials is assessed by broth micro-dilution or disk diffusion assays, both of which are time-consuming, labor-intensive, and provide limited information on the mode of action of the antimicrobials. The abovementioned limitations highlight the need for the development of new methods to monitor and further understand antimicrobial susceptibility. In this study, we used real-time flow cytometry, combined with membrane permeability staining, as a quick and sensitive technology to study the quantitative and qualitative responses of two oral pathobionts to different concentrations of chlorhexidine (CHX), cetylpyridinium chloride (CPC), or triclosan. Apart from the real-time monitoring of cell damage, we further applied a phenotypic fingerprinting method to differentiate between the bacterial subpopulations that arose due to treatment. We quantified the pathobiont damage rate of different antiseptics at different concentrations within 15 minutes of exposure and identified the conditions under which the bacteria were most susceptible. Moreover, we detected species-specific and treatment-specific phenotypic subpopulations. This proves that real-time flow cytometry can provide information on the susceptibility of different microorganisms in a short time frame while differentiating between antiseptics and thus could be a valuable tool in the discovery of novel antimicrobial compound, while at the same time deciphering their mode of action.<br><br>IMPORTANCE: With increasing evidence that microorganisms are becoming more tolerant to standard antimicrobials, faster and more accessible antimicrobial susceptibility testing methods are needed. However, traditional susceptibility assays are laborious and time-consuming. To overcome the abovementioned limitations, we introduce a novel approach to define antimicrobial susceptibility in a much shorter time frame with the use of real-time flow cytometry. Furthermore, phenotypic fingerprinting analysis can be applied on the data to study the way antiseptics affect the bacterial cell morphology over time and, thus, gain information on the mode of action of a certain compound.},
}
@article {pmid39162262,
year = {2024},
author = {Liu, M and Li, Q and Xu, W and Wang, L and Wu, F and Tan, L and Li, L and Zhang, G},
title = {Characterization of water microbiota and their relationship with resident oysters during an oyster mortality event.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0288123},
pmid = {39162262},
issn = {2165-0497},
support = {2022YFD2400304//National Key R&amp;D Program of China/ ; 2022LZGC015//Key Research and Development Program of Shandong/ ; ZFJH202309//Key Research and Development Program of Shandong/ ; CARS-49//Earmarked Fund for CARS/ ; },
mesh = {Animals ; *Microbiota/physiology ; *Ostreidae/microbiology ; *Water Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Seawater/microbiology ; Cyanobacteria/genetics/physiology/growth &amp; development ; Temperature ; },
abstract = {Microorganisms are vital for the health of marine invertebrates, and their assembly is driven by both deterministic and stochastic factors that regulate residents (innate to the host) and transients (from ambient water). However, the role of water microbiota and the significance of deterministic and stochastic processes in aquatic hosts facing mortality threats are largely unknown. This study examines the shifts in water microbiota during an oyster mortality event using amplicon sequencing and compared with those of resident oysters to disentangle the balance of the deterministic and stochastic factors involved. Water temperature and dissolved oxygen significantly shape the microbial community with a distinct monthly pattern, and Cyanobacteria blooms might exacerbate oyster mortality. The comparative analysis of microbial communities in oysters and water revealed that ≤ 21% of the genera were shared between oysters and water, implying that water microbiota cannot easily transfer into oysters. Furthermore, these shared genera had different functions, with oysters more involved in promoting host digestion and nutrient acquisition and water bacteria enriched more in functions promoting their own growth and survival. These findings illustrate that oysters may possess specific selection or barrier mechanisms that permit a small percentage of transients, controlled by stochastic factors and having a minimal effect on oyster mortality, to enter, whereas the majority of oyster microbiota are residents governed by deterministic factors. Consequently, oysters exhibit some plasticity in their symbiotic microbiota, enabling them to maintain microbial homeostasis and adapt to complex microbial surroundings. This may be a shared mechanism among marine invertebrates for survival in complex marine environments.IMPORTANCEPacific oysters are widely cultured and play vital ecological roles. However, the summer mortality hinders sustainable oyster farming. Untangling causative mechanisms of oyster mortality is a complex task due to the intricate "interactome" involving environmental factors, hosts, and pathogens. Interactions between hosts and microorganisms offer an ideal avenue for investigating the truth. We systematically investigated the microbial community in water and resident oysters during a summer mortality event and proposed that the assembly of oyster microbiota is primarily governed by deterministic processes independent of mortality. Pathogens mainly originate from resident members of the oyster microbiota, with a limited influence from the microbial community in the water. Additionally, environmental degraders, such as Cyanobacteria blooms, cannot be overlooked as a contributing factor of oyster mortality. This study evaluated the weight of deterministic and stochastic factors in microbial assembly during an oyster mortality event and greatly broadened our understanding of the "interactome" through the interaction between oysters and water in microbiota.},
}
@article {pmid39161630,
year = {2024},
author = {Blázquez, M and Pérez-Vargas, I and Garrido-Benavent, I and Villar-dePablo, M and Turégano, Y and Frías-López, C and Sánchez-Gracia, A and de Los Ríos, A and Gasulla, F and Pérez-Ortega, S},
title = {Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group.},
journal = {Persoonia},
volume = {52},
number = {},
pages = {44-93},
pmid = {39161630},
issn = {0031-5850},
abstract = {Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation. Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages. In order to use the Ramalina decipiens group as a model system it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry and geographic origin). We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi. Citation: Blázquez M, Pérez-Vargas I, Garrido-Benavent I, et al. 2024. Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group. Persoonia 52: 44-93. https://doi.org/10.3767/persoonia.2024.52.03 .},
}
@article {pmid39160591,
year = {2024},
author = {Lee, H and Hwang, K and Cho, A and Kim, S and Kim, M and Morgan-Kiss, R and Priscu, JC and Kim, KM and Kim, OS},
title = {Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {60},
pmid = {39160591},
issn = {2524-6372},
support = {PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; OPP 1637708//National Science Foundation/ ; OPP 1637708//National Science Foundation/ ; },
abstract = {BACKGROUND: Lake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney.<br><br>RESULTS: Lake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus.<br><br>CONCLUSIONS: The vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column.},
}
@article {pmid39159439,
year = {2024},
author = {Dos Santos, A and Schultz, J and Almeida Trapp, M and Modolon, F and Romanenko, A and Kumar Jaiswal, A and Gomes, L and Rodrigues-Filho, E and Rosado, AS},
title = {Investigating Polyextremophilic Bacteria in Al Wahbah Crater, Saudi Arabia: A Terrestrial Model for Life on Saturn's Moon Enceladus.},
journal = {Astrobiology},
volume = {24},
number = {8},
pages = {824-838},
doi = {10.1089/ast.2024.0017},
pmid = {39159439},
issn = {1557-8070},
mesh = {Saudi Arabia ; *Exobiology/methods ; *Extraterrestrial Environment ; Genome, Bacterial/genetics ; Mars ; Bacteria/genetics/isolation &amp; purification ; Phylogeny ; },
abstract = {The study of extremophilic microorganisms has sparked interest in understanding extraterrestrial microbial life. Such organisms are fundamental for investigating life forms on Saturn's icy moons, such as Enceladus, which is characterized by potentially habitable saline and alkaline niches. Our study focused on the salt-alkaline soil of the Al Wahbah crater in Saudi Arabia, where we identified microorganisms that could be used as biological models to understand potential life on Enceladus. The search involved isolating 48 bacterial strains, sequencing the genomes of two thermo-haloalkaliphilic strains, and characterizing them for astrobiological application. A deeper understanding of the genetic composition and functional capabilities of the two novel strains of Halalkalibacterium halodurans provided valuable insights into their survival strategies and the presence of coding genes and pathways related to adaptations to environmental stressors. We also used mass spectrometry with a molecular network approach, highlighting various classes of molecules, such as phospholipids and nonproteinogenic amino acids, as potential biosignatures. These are essential features for understanding life's adaptability under extreme conditions and could be used as targets for biosignatures in upcoming missions exploring Enceladus' orbit. Furthermore, our study reinforces the need to look at new extreme environments on Earth that might contribute to the astrobiology field.},
}
@article {pmid39158314,
year = {2024},
author = {Guéneau, V and Jiménez, G and Castex, M and Briandet, R},
title = {Insights into the genomic and phenotypic characteristics of Bacillus spp. strains isolated from biofilms in broiler farms.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {9},
pages = {e0066324},
pmid = {39158314},
issn = {1098-5336},
support = {2020/0548//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; },
mesh = {*Biofilms/growth &amp; development ; Animals ; *Bacillus/genetics/isolation &amp; purification/physiology/classification ; *Chickens/microbiology ; Farms ; Phenotype ; Bacillus subtilis/genetics/physiology/isolation &amp; purification ; Genome, Bacterial ; Bacillus licheniformis/genetics/physiology ; Genomics ; },
abstract = {The characterization of surface microbiota living in biofilms within livestock buildings has been relatively unexplored, despite its potential impact on animal health. To enhance our understanding of these microbial communities, we characterized 11 spore-forming strains isolated from two commercial broiler chicken farms. Sequencing of the strains revealed them to belong to three species Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis. Genomic analysis revealed the presence of antimicrobial resistance genes and genes associated with antimicrobial secretion specific to each species. We conducted a comprehensive characterization of the biofilm formed by these strains under various conditions, and we revealed significant structural heterogeneity across the different strains. A macro-colony interaction model was employed to assess the compatibility of these strains to coexist in mixed biofilms. We identified highly competitive B. velezensis strains, which cannot coexist with other Bacillus spp. Using confocal laser scanning microscopy along with a specific dye for extracellular DNA, we uncovered the importance of extracellular DNA for the formation of B. licheniformis biofilms. Altogether, the results highlight the heterogeneity in both genome and biofilm structure among Bacillus spp. isolated from biofilms present within livestock buildings.IMPORTANCELittle is known about the microbial communities that develop on farms in direct contact with animals. Nonpathogenic strains of Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis were found in biofilm samples collected from surfaces in contact with animals. Significant genetic and phenotypic diversity was described among these Bacillus strains. The strains do not possess mobile antibiotic resistance genes in their genomes and have a strong capacity to form structured biofilms. Among these species, B. velezensis was noted for its high competitiveness compared with the other Bacillus spp. Additionally, the importance of extracellular DNA in the formation of B. licheniformis biofilms was observed. These findings provide insights for the management of these surface microbiota that can influence animal health, such as the use of competitive strains to minimize the establishment of undesirable bacteria or enzymes capable of specifically deconstructing biofilms.},
}
@article {pmid39157765,
year = {2024},
author = {de Santana, CO and Spealman, P and Oliveira, E and Gresham, D and de Jesus, T and Chinalia, F},
title = {Prokaryote communities along a source-to-estuary river continuum in the Brazilian Atlantic Forest.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17900},
pmid = {39157765},
issn = {2167-8359},
mesh = {Brazil ; *Rivers/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Forests ; Estuaries ; Biodiversity ; Archaea/genetics/classification/isolation &amp; purification ; Microbiota ; },
abstract = {The activities of microbiomes in river sediments play an important role in sustaining ecosystem functions by driving many biogeochemical cycles. However, river ecosystems are frequently affected by anthropogenic activities, which may lead to microbial biodiversity loss and/or changes in ecosystem functions and related services. While parts of the Atlantic Forest biome stretching along much of the eastern coast of South America are protected by governmental conservation efforts, an estimated 89% of these areas in Brazil are under threat. This adds urgency to the characterization of prokaryotic communities in this vast and highly diverse biome. Here, we present prokaryotic sediment communities in the tropical Juliana River system at three sites, an upstream site near the river source in the mountains (Source) to a site in the middle reaches (Valley) and an estuarine site near the urban center of Ituberá (Mangrove). The diversity and composition of the communities were compared at these sites, along with environmental conditions, the former by using qualitative and quantitative analyses of 16S rRNA gene amplicons. While the communities included distinct populations at each site, a suite of core taxa accounted for the majority of the populations at all sites. Prokaryote diversity was highest in the sediments of the Mangrove site and lowest at the Valley site. The highest number of genera exclusive to a given site was found at the Source site, followed by the Mangrove site, which contained some archaeal genera not present at the freshwater sites. Copper (Cu) concentrations were related to differences in communities among sites, but none of the other environmental factors we determined was found to have a significant influence. This may be partly due to an urban imprint on the Mangrove site by providing organic carbon and nutrients via domestic effluents.},
}
@article {pmid39155010,
year = {2024},
author = {Wong, LC and Rodenburg, U and Leite, RR and Korthals, GW and Pover, J and Koerten, H and Kuramae, EE and Bodelier, PLE},
title = {Exploring microbial diversity and interactions for asbestos modifying properties.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175577},
doi = {10.1016/j.scitotenv.2024.175577},
pmid = {39155010},
issn = {1879-1026},
mesh = {*Biodegradation, Environmental ; *Bacteria/metabolism/classification ; Fungi/metabolism ; Asbestos ; Soil Microbiology ; Iron/metabolism ; Asbestos, Serpentine ; },
abstract = {Asbestos poses a substantial environmental health risk, and biological treatment offers a promising approach to mitigate its impact by altering its chemical composition. However, the dynamics of microbial co-inoculation in asbestos bioremediation remain poorly understood. This study investigates the effect of microbial single cultures and co-cultures on modifying crocidolite and chrysotile fibers, focusing on the extraction of iron and magnesium. Seventy bacterial and eighty-three fungal strains were isolated from five diverse sites, characterized phylogenetically using the 16S rRNA gene and ITS region, respectively, and assessed for siderophore and organic acid production. Most bacterial strains were identified as Pseudomonas, while Penicillium predominated among fungal strains. Ten bacterial and 25 fungal strains were found to produce both organic compounds. Four microbial co-cultures (one bacterium-bacterium, two fungus-bacterium, and one fungus-fungus) exhibiting synergistic effects in plate assays, alongside their respective single cultures, were incubated with crocidolite and chrysotile. ICP-OES analysis revealed that in crocidolite, the co-culture HRF19-HRB12 removed more iron than their single cultures, while Penicillium TPF36 showed the highest iron removal. The co-culture of two Pseudomonas strains (HRB12-RB5) exhibited the highest magnesium concentration in the supernatant. In chrysotile, the co-culture HRB12-RB5 removed more iron than their individual cultures, with Penicillium TFSF27 exhibiting the highest iron concentration in the solution. Penicillium TFSF27 and the co-culture TFSF27-TPF36 demonstrated the highest magnesium removal. SEM-XRMA analysis showed a significant reduction in iron and magnesium content, confirming elemental extraction from the fibers' structure. This study significantly broadens the range of microbial strains capable of modifying asbestos fibers and underscores the potential of microbial co-cultures in asbestos remediation.},
}
@article {pmid39150265,
year = {2024},
author = {Longhi, G and Lugli, GA and Tarracchini, C and Fontana, F and Bianchi, MG and Carli, E and Bussolati, O and van Sinderen, D and Turroni, F and Ventura, M},
title = {From raw milk cheese to the gut: investigating the colonization strategies of Bifidobacterium mongoliense.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {9},
pages = {e0124424},
pmid = {39150265},
issn = {1098-5336},
support = {PE00000003//National Recovery and Resilience Plan (NRRP)/ ; SFI/12/RC/2273a//Irish Government's National Development Plan/ ; SFI/12/RC/2273b//Irish Government's National Development Plan/ ; },
mesh = {*Cheese/microbiology ; *Bifidobacterium/genetics/metabolism/growth &amp; development ; Humans ; *Milk/microbiology ; *Gastrointestinal Microbiome ; Animals ; Italy ; },
abstract = {The microbial ecology of raw milk cheeses is determined by bacteria originating from milk and milk-producing animals. Recently, it has been shown that members of the Bifidobacterium mongoliense species may become transmitted along the Parmigiano Reggiano cheese production chain and ultimately may colonize the consumer intestine. However, there is a lack of knowledge regarding the molecular mechanisms that mediate the interaction between B. mongoliense and the human gut. Based on 128 raw milk cheeses collected from different Italian regions, we isolated and characterized 10 B. mongoliense strains. Comparative genomics allowed us to unveil the presence of enzymes required for the degradation of sialylated host-glycans in B. mongoliense, corroborating the appreciable growth on de Man-Rogosa-Sharpe (MRS) medium supplemented with 3'-sialyllactose (3'-SL) or 6'-sialyllactose (6'-SL). The B. mongoliense BMONG18 was chosen, due to its superior ability to utilize 3'-SL and mucin as representative strain, to investigate its behavior when co-inoculated with other bifidobacterial species. Conversely, members of other bifidobacterial species did not appear to benefit from the presence of BMONG18, highlighting a competitive scenario for nutrient acquisition. Transcriptomic data of BMONG18 reveal no significant differences in gene expression when cultivated in a gut simulating medium (GSM), regardless of whether cheese was included or not. Furthermore, BMONG18 was shown to exhibit high adhesion capabilities to HT29-MTX human cells, in line with its colonization ability of a human host.IMPORTANCEFermented foods are nourishments produced through controlled microbial growth that play an essential role in worldwide human nutrition. Research interest in fermented foods has increased since the 80s, driven by growing awareness of their potential health benefits beyond mere nutritional content. Bifidobacterium mongoliense, previously identified throughout the production process of Parmigiano Reggiano cheese, was found to be capable of establishing itself in the intestines of its consumers. Our study underscores molecular mechanisms through which this bifidobacterial species, derived from food, interacts with the host and other gut microbiota members.},
}
@article {pmid39150230,
year = {2024},
author = {Li, J and Yang, X and Zhang, X and Zhang, L},
title = {Effects and mechanisms of microbial ecology and diversity on phytoremediation of cadmium-contaminated soil under the influence of biodegradable organic acids.},
journal = {International journal of phytoremediation},
volume = {26},
number = {14},
pages = {2392-2403},
doi = {10.1080/15226514.2024.2391025},
pmid = {39150230},
issn = {1549-7879},
mesh = {*Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Cadmium/metabolism ; *Bacillus megaterium/metabolism ; *Soil Microbiology ; *Lolium/metabolism ; Rhizosphere ; Citric Acid/metabolism ; Bacteria/metabolism ; },
abstract = {In recent years, heavy metal pollution has become a global environmental problem and poses a great threat to the health of people and ecosystems. Therefore, strategies for the effective remediation of Cd from contaminated soil are urgently needed. In this study, ryegrass was utilized as a remediation plant, and its remediation potential was enhanced through the application of Citric Acid (CA) in conjunction with Bacillus megaterium (B. megaterium). The P3 treatment (CA + Bacillus megaterium) exhibited a significantly higher efficiency in promoting cadmium extraction by ryegrass, resulting in a 1.79-fold increase in shoot cadmium accumulation compared to the control group (CK) with no Bacillus megaterium or CA. Moreover, the P3 treatment led to an increased abundance of Actinobacteriota, Acidobacteriota, and Patescibacteria in the rhizosphere. The concentration of amino derivatives (such as betaine, sulfolithocholylglycine, N-alpha-acetyl-lysine, glycocholic acid, arginyl-threonine) showed significant upregulation following the P3 treatment. In summary, this study proposes a viable approach for phytoremediation of soil contaminated with cadmium by harnessing the mobilizing abilities of soil bacteria.},
}
@article {pmid39148674,
year = {2024},
author = {Dyczko, D and Błażej, P and Kiewra, D},
title = {The influence of forest habitat type on Ixodes ricinus infections with Rickettsia spp. in south-western Poland.},
journal = {Current research in parasitology &amp; vector-borne diseases},
volume = {6},
number = {},
pages = {100200},
pmid = {39148674},
issn = {2667-114X},
abstract = {This study investigates the prevalence of Rickettsia spp. in Ixodes ricinus tick populations in different forest habitat types (broadleaf forest, mixed broadleaf and coniferous forest, and coniferous forest) in south-western Poland. During the survey periods from April to June 2018 and 2019 a total of 494 I. ricinus ticks, including 374 nymphs, 60 females and 60 males, were tested for Rickettsia infections by nested PCR targeting the gltA gene. The overall infection rate was 42.3%; however, we observed statistically significant year-to-year variation. Infection rates varied between tick developmental stages and were significantly influenced by forest habitat type. As assessed by a generalized linear mixed model (GLMM), the highest infection rates were observed in mixed broadleaf and coniferous forests, while coniferous forests had a significant negative effect on infection prevalence. DNA sequencing of selected samples confirmed the predominance of Rickettsia helvetica (91.2%) and less frequent Rickettsia monacensis (8.8%). This study suggests that the forest habitat types can influence Rickettsia spp. infection in tick populations; however, a comprehensive understanding of all factors influencing the level of infection requires future study.},
}
@article {pmid39143010,
year = {2024},
author = {Ozbayram, EG and Kleinsteuber, S and Sträuber, H and Schroeder, BG and da Rocha, UN and Corrêa, FB and Harms, H and Nikolausz, M},
title = {Three-domain microbial communities in the gut of Pachnoda marginata larvae: A comparative study revealing opposing trends in gut compartments.},
journal = {Environmental microbiology reports},
volume = {16},
number = {4},
pages = {e13324},
pmid = {39143010},
issn = {1758-2229},
mesh = {Animals ; *Larva/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Eukaryota/classification/genetics/isolation &amp; purification ; Phylogeny ; Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {This study aimed to examine the bacterial, methanogenic archaeal, and eukaryotic community structure in both the midgut and hindgut of Pachnoda marginata larvae using an amplicon sequencing approach. The goal was to investigate how various diets and the soil affect the composition of these three-domain microbial communities within the gut of insect larvae. The results indicated a notable variation in the microbial community composition among the gut compartments. The majority of the bacterial community in the hindgut was composed of Ruminococcaceae and Christensenellaceae. Nocardiaceae, Microbacteriaceae, and Lachnospiraceae were detected in midgut samples from larvae feeding on the leaf diet, whereas Sphingomonadaceae, Rhodobacteraceae, and Promicromonasporaceae dominated the bacterial community of midgut of larvae feeding on the straw diet. The diet was a significant factor that influenced the methanogenic archaeal and eukaryotic community patterns. The methanogenic communities in the two gut compartments significantly differed from each other, with the midgut communities being more similar to those in the soil. A higher diversity of methanogens was observed in the midgut samples of both diets compared to the hindgut. Overall, the microbiota of the hindgut was more host-specific, while the assembly of the midgut was more influenced by the environmental microorganisms.},
}
@article {pmid39142044,
year = {2024},
author = {Battulga, B and Nakayama, M and Matsuoka, S and Kondo, T and Atarashi-Andoh, M and Koarashi, J},
title = {Dynamics and functions of microbial communities in the plastisphere in temperate coastal environments.},
journal = {Water research},
volume = {264},
number = {},
pages = {122207},
doi = {10.1016/j.watres.2024.122207},
pmid = {39142044},
issn = {1879-2448},
mesh = {*Biofilms ; *Bacteria/genetics/classification ; Fungi/genetics ; Microbiota ; Microplastics ; Japan ; Geologic Sediments/microbiology ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Microbial attachment and biofilm formation on microplastics (MPs <5 mm in size) in the environment have received growing attention. However, there is limited knowledge of microbial function and their effect on the properties and behavior of MPs in the environment. In this study, microbial communities in the plastisphere were explored to understand microbial ecology as well as their impact on aquatic ecosystems. Using the amplicon sequencing of 16S and internal transcribed spacer (ITS) genes, we uncovered the composition and diversity of bacterial and fungal communities in samples of MPs (fiber, film, foam, and fragment), surface water, bottom sediment, and coastal sand in two contrasting coastal areas of Japan. Differences in microbial diversity and taxonomic composition were detected depending on sample type (MPs, water, sediment, and sand) and the research site. Although relatively higher bacterial and fungal gene counts were determined in MP fragments and foams from the research sites, there were no significant differences in microbial community composition depending on the morphotypes of MPs. Given the colonization by hydrocarbon-degrading communities and the presence of pathogens on MPs, the complex processes of microbial taxa influence the characteristics of MP-associated biofilms, and thus, the properties of MPs. This study highlights the metabolic functions of microbes in MP-associated biofilms, which could be key to uncovering the true impact of plastic debris on the global ecosystem.},
}
@article {pmid39141295,
year = {2024},
author = {Turbant, F and Blache, A and Węgrzyn, G and Achouak, W and Wien, F and Arluison, V},
title = {Use of Synchrotron Radiation Circular Dichroism to Analyze the Interaction and Insertion of Proteins into Bacterial Outer Membrane Vesicles.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2843},
number = {},
pages = {73-94},
pmid = {39141295},
issn = {1940-6029},
mesh = {*Circular Dichroism/methods ; *Synchrotrons ; *Bacterial Outer Membrane Proteins/chemistry/metabolism ; Bacterial Outer Membrane/metabolism/chemistry ; Protein Structure, Secondary ; Lipid Bilayers/metabolism/chemistry ; },
abstract = {Circular dichroism (CD) is a spectroscopic technique commonly used for the analysis of proteins. Particularly, it allows the determination of protein secondary structure content in various media, including the membrane environment. In this chapter, we present how CD applications can be used to analyze the interaction of proteins with bacterial outer membrane vesicles (OMVs). Most CD studies characterizing the structure of proteins inserted into membranes rely on artificial lipid bilayers, mimicking natural membranes. Nevertheless, these artificial models lack the important features of the true membrane, especially for the outer membrane of Gram-negative bacteria. These features include lipid diversity, glycosylation, and asymmetry. Here, we show how to analyze the interactions of proteins, either integral or peripheral, with OMVs in solution and with supported membranes of OMVs, using conventional CD and orientated circular dichroism (OCD). We explain how to decipher the spectroscopic signals to obtain information on the molecular structure of the protein upon its interaction with an OMV and through its potential insertion into an OMV membrane.},
}
@article {pmid39141097,
year = {2024},
author = {Papazachariou, V and Fernández-Juárez, V and Parfrey, LW and Riemann, L},
title = {Nitrogen Fixation and Microbial Communities Associated with Decomposing Seagrass Leaves in Temperate Coastal Waters.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {106},
pmid = {39141097},
issn = {1432-184X},
mesh = {*Nitrogen Fixation ; *Plant Leaves/microbiology ; *Seawater/microbiology/chemistry ; *Microbiota ; *Zosteraceae/microbiology/metabolism ; Nitrogen/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Denmark ; Cyanobacteria/metabolism/genetics/classification/isolation &amp; purification ; },
abstract = {Seagrass meadows play pivotal roles in coastal biochemical cycles, with nitrogen fixation being a well-established process associated with living seagrass. Here, we tested the hypothesis that nitrogen fixation is also associated with seagrass debris in Danish coastal waters. We conducted a 52-day in situ experiment to investigate nitrogen fixation (proxied by acetylene reduction) and dynamics of the microbial community (16S rRNA gene amplicon sequencing) and the nitrogen fixing community (nifH DNA/RNA amplicon sequencing) associated with decomposing Zostera marina leaves. The leaves harboured distinct microbial communities, including distinct nitrogen fixers, relative to the surrounding seawater and sediment throughout the experiment. Nitrogen fixation rates were measurable on most days, but highest on days 3 (dark, 334.8 nmol N g[-1] dw h[-1]) and 15 (light, 194.6 nmol N g[-1] dw h[-1]). Nitrogen fixation rates were not correlated with the concentration of inorganic nutrients in the surrounding seawater or with carbon:nitrogen ratios in the leaves. The composition of nitrogen fixers shifted from cyanobacterial Sphaerospermopsis to heterotrophic genera like Desulfopila over the decomposition period. On the days with highest fixation, nifH RNA gene transcripts were mainly accounted for by cyanobacteria, in particular by Sphaerospermopsis and an unknown taxon (order Nostocales), alongside Proteobacteria. Our study shows that seagrass debris in temperate coastal waters harbours substantial nitrogen fixation carried out by cyanobacteria and heterotrophic bacteria that are distinct relative to the surrounding seawater and sediments. This suggests that seagrass debris constitutes a selective environment where degradation is affected by the import of nitrogen via nitrogen fixation.},
}
@article {pmid39140100,
year = {2024},
author = {Crous, PW and Jurjević, &#x17d; and Balashov, S and De la Peña-Lastra, S and Mateos, A and Pinruan, U and Rigueiro-Rodríguez, A and Osieck, ER and Altés, A and Czachura, P and Esteve-Raventós, F and Gunaseelan, S and Kaliyaperumal, M and Larsson, E and Luangsa-Ard, JJ and Moreno, G and Pancorbo, F and Piątek, M and Sommai, S and Somrithipol, S and Asif, M and Delgado, G and Flakus, A and Illescas, T and Kezo, K and Khamsuntorn, P and Kubátová, A and Labuda, R and Lavoise, C and Lebel, T and Lueangjaroenkit, P and Maciá-Vicente, JG and Paz, A and Saba, M and Shivas, RG and Tan, YP and Wingfield, MJ and Aas, T and Abramczyk, B and Ainsworth, AM and Akulov, A and Alvarado, P and Armada, F and Assyov, B and Avchar, R and Avesani, M and Bezerra, JL and Bhat, JD and Bilański, P and Bily, DS and Boccardo, F and Bozok, F and Campos, JC and Chaimongkol, S and Chellappan, N and Costa, MM and Dalecká, M and Darmostuk, V and Daskalopoulos, V and Dearnaley, J and Dentinger, BTM and De Silva, NI and Dhotre, D and Carlavilla, JR and Doungsa-Ard, C and Dovana, F and Erhard, A and Ferro, LO and Gallegos, SC and Giles, CE and Gore, G and Gorfer, M and Guard, FE and Hanson, S&#xc5; and Haridev, P and Jankowiak, R and Jeffers, SN and Kandemir, H and Karich, A and Kisło, K and Kiss, L and Krisai-Greilhuber, I and Latha, KPD and Lorenzini, M and Lumyong, S and Manimohan, P and Manjón, JL and Maula, F and Mazur, E and Mesquita, NLS and Młynek, K and Mongkolsamrit, S and Morán, P and Murugadoss, R and Nagarajan, M and Nalumpang, S and Noisripoom, W and Nosalj, S and Novaes, QS and Nowak, M and Pawłowska, J and Peiger, M and Pereira, OL and Pinto, A and Plaza, M and Polemis, E and Polhorský, A and Ramos, DO and Raza, M and Rivas-Ferreiro, M and Rodriguez-Flakus, P and Ruszkiewicz-Michalska, M and Sánchez, A and Santos, A and Schüller, A and Scott, PA and Şen, I and Shelke, D and Śliwa, L and Solheim, H and Sonawane, H and Strašiftáková, D and Stryjak-Bogacka, M and Sudsanguan, M and Suwannarach, N and Suz, LM and Syme, K and Taşkın, H and Tennakoon, DS and Tomka, P and Vaghefi, N and Vasan, V and Vauras, J and Wiktorowicz, D and Villarreal, M and Vizzini, A and Wrzosek, M and Yang, X and Yingkunchao, W and Zapparoli, G and Zervakis, GI and Groenewald, JZ},
title = {Fungal Planet description sheets: 1614-1696.},
journal = {Fungal systematics and evolution},
volume = {13},
number = {},
pages = {183-440},
pmid = {39140100},
issn = {2589-3831},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Baobabopsis sabindy in leaves of Eragrostis spartinoides, Cortinarius magentiguttatus among deep leaf litter, Laurobasidium azarandamiae from uredinium of Puccinia alyxiae on Alyxia buxifolia, Marasmius pseudoelegans on well-rotted twigs and litter in mixed wet sclerophyll and subtropical rainforest. Bolivia, Favolaschia luminosa on twigs of Byttneria hirsuta, Lecanora thorstenii on bark, in savannas with shrubs and trees. Brazil, Asterina costamaiae on leaves of Rourea bahiensis, Purimyces orchidacearum (incl. Purimyces gen. nov.) as root endophyte on Cattleya locatellii. Bulgaria, Monosporascus bulgaricus and Monosporascus europaeus isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. Finland, Inocybe undatolacera on a lawn, near Betula pendula. France, Inocybe querciphila in humus of mixed forest. Germany, Arrhenia oblongispora on bare soil attached to debris of herbaceous plants and grasses. Greece, Tuber aereum under Quercus coccifera and Acer sempervirens. India, Alfoldia lenyadriensis from the gut of a Platynotus sp. beetle, Fulvifomes subramanianii on living Albizzia amara, Inosperma pavithrum on soil, Phylloporia parvateya on living Lonicera sp., Tropicoporus maritimus on living Peltophorum pterocarpum. Indonesia, Elsinoe atypica on leaf of Eucalyptus pellita. Italy, Apiotrichum vineum from grape wine, Cuphopyllus praecox among grass. Madagascar, Pisolithus madagascariensis on soil under Intsia bijuga. Netherlands, Cytosporella calamagrostidis and Periconia calamagrostidicola on old leaves of Calamagrostis arenaria, Hyaloscypha caricicola on leaves of Carex sp., Neoniesslia phragmiticola (incl. Neoniesslia gen. nov.) on leaf sheaths of standing dead culms of Phragmites australis, Neptunomyces juncicola on culms of Juncus maritimus, Zenophaeosphaeria calamagrostidis (incl. Zenophaeosphaeria gen. nov.) on culms of Calamagrostis arenaria. Norway, Hausneria geniculata (incl. Hausneria gen. nov.) from a gallery of Dryocoetes alni on Alnus incana. Pakistan, Agrocybe auriolus on leaf litter of Eucalyptus camaldulensis, Rhodophana rubrodisca in nutrient-rich loamy soil with Morus alba. Poland, Cladosporium nubilum from hypersaline brine, Entomortierella ferrotolerans from soil at mines and postmining sites, Pseudopezicula epiphylla from sooty mould community on Quercus robur, Quixadomyces sanctacrucensis from resin of Pinus sylvestris, Szafranskia beskidensis (incl. Szafranskia gen. nov.) from resin of Abies alba. Portugal, Ascocoryne laurisilvae on degraded wood of Laurus nobilis, Hygrocybe madeirensis in laurel forests, Hygrocybula terracocta (incl. Hygrocybula gen. nov.) on mossy areas of laurel forests planted with Cryptomeria japonica. Republic of Kenya, Penicillium gorferi from a sterile chicken feather embedded in a soil sample. Slovakia, Cerinomyces tatrensis on bark of Pinus mugo, Metapochonia simonovicovae from soil. South Africa, Acremonium agapanthi on culms of Agapanthus praecox, Alfaria elegiae on culms of Elegia ebracteata, Beaucarneamyces stellenboschensis (incl. Beaucarneamyces gen. nov.) on dead leaves of Beaucarnea stricta, Gardeniomyces kirstenboschensis (incl. Gardeniomyces gen. nov.) rotting fruit of Gardenia thunbergia, Knufia dianellae on dead leaves of Dianella caerulea, Lomaantha quercina on twigs of Quercus suber. Melanina restionis on dead leaves of Restio duthieae, Microdochium buffelskloofinum on seeds of Eragrostis cf. racemosa, Thamnochortomyces kirstenboschensis (incl. Thamnochortomyces gen. nov.) on culms of Thamnochortus fraternus, Tubeufia hagahagana on leaves of Hypoxis angustifolia, Wingfieldomyces cypericola on dead leaves of Cyperus papyrus. Spain, Geastrum federeri in soil under Quercus suber and Q. canariensis, Geastrum nadalii in calcareous soil under Juniperus, Quercus, Cupressus, Pinus and Robinia, Hygrocybe garajonayensis in laurel forests, Inocybe cistophila on acidic soil under Cistus ladanifer, Inocybe sabuligena in a mixed Quercus ilex subsp. ballota/Juniperus thurifera open forest, Mycena calongei on mossy bark base of Juniperus oxycedrus, Rhodophana ulmaria on soil in Ulmus minor forest, Tuber arriacaense in soil under Populus pyramidalis, Volvariella latispora on grassy soils in a Quercus ilex ssp. rotundifolia stand. Sweden, Inocybe iota in alpine heath on calcareous soil. Thailand, Craterellus maerimensis and Craterellus sanbuakwaiensis on laterite and sandy soil, Helicocollum samlanense on scale insects, Leptosporella cassiae on dead twigs of Cassia fistula, Oxydothis coperniciae on dead leaf of Copernicia alba, Russula mukdahanensis on soil, Trechispora sangria on soil, Trechispora sanpatongensis on soil. Türkiye, Amanita corylophila in a plantation of Corylus avellana. Ukraine, Pararthrophiala adonis (incl. Pararthrophiala gen. nov.) on dead stems of Adonis vernalis. USA, Cladorrhinum carnegieae from Carnegiea gigantea, Dematipyriformia americana on swab from basement wall, Dothiora americana from outside air, Dwiroopa aeria from bedroom air, Lithohypha cladosporioides from hospital swab, Macroconia verruculosa on twig of Ilex montana, associated with black destroyed ascomycetous fungus and Biatora sp., Periconia floridana from outside air, Phytophthora fagacearum from necrotic leaves and shoots of Fagus grandifolia, Queenslandipenidiella californica on wood in crawlspace. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Jurjević Z, Balashov S, De la Peña-Lastra S, Mateos A, Pinruan U, Rigueiro-Rodríguez A, Osieck ER, Altés A, Czachura P, Esteve-Raventós F, Gunaseelan S, Kaliyaperumal M, Larsson E, Luangsa-ard JJ, Moreno G, Pancorbo F, Piątek M, Sommai S, Somrithipol S, Asif M, Delgado G, Flakus A, Illescas T, Kezo K, Khamsuntorn P, Kubátová A, Labuda R, Lavoise C, Lebel T, Lueangjaroenkit P, Maciá-Vicente JG, Paz A, Saba M, Shivas RG, Tan YP, Wingfield MJ, Aas T, Abramczyk B, Ainsworth AM, Akulov A, Alvarado P, Armada F, Assyov B, Avchar R, Avesani M, Bezerra JL, Bhat JD, Bilański P, Bily DS, Boccardo F, Bozok F, Campos JC, Chaimongkol S, Chellappan N, Costa MM, Dalecká M, Darmostuk V, Daskalopoulos V, Dearnaley J, Dentinger BTM, De Silva NI, Dhotre D, Carlavilla JR, Doungsa-ard C, Dovana F, Erhard A, Ferro LO, Gallegos SC, Giles CE, Gore G, Gorfer M, Guard FE, Hanson S-A, Haridev P, Jankowiak R, Jeffers SN, Kandemir H, Karich A, Kisło K, Kiss L, Krisai-Greilhuber I, Latha KPD, Lorenzini M, Lumyong S, Manimohan P, Manjón JL, Maula F, Mazur E, Mesquita NLS, Młynek K, Mongkolsamrit S, Morán P, Murugadoss R, Nagarajan M, Nalumpang S, Noisripoom W, Nosalj S, Novaes QS, Nowak M, Pawłowska J, Peiger M, Pereira OL, Pinto A, Plaza M, Polemis E, Polhorský A, Ramos DO, Raza M, Rivas-Ferreiro M, Rodriguez-Flakus P, Ruszkiewicz-Michalska M, Sánchez A, Santos A, Schüller A, Scott PA, Şen İ, Shelke D, Śliwa L, Solheim H, Sonawane H, Strašiftáková D, Stryjak-Bogacka M, Sudsanguan M, Suwannarach N, Suz LM, Syme K, Taşkın H, Tennakoon DS, Tomka P, Vaghefi N, Vasan V, Vauras J, Wiktorowicz D, Villarreal M, Vizzini A, Wrzosek M, Yang X, Yingkunchao W, Zapparoli G, Zervakis GI, Groenewald JZ (2024). Fungal Planet description sheets: 1614-1696. Fungal Systematics and Evolution 13: 183-440. doi: 10.3114/fuse.2024.13.11.},
}
@article {pmid39136489,
year = {2024},
author = {Brar, G and Floden, M and McFrederick, Q and Rajamohan, A and Yocum, G and Bowsher, J},
title = {Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {9},
pages = {e0207623},
pmid = {39136489},
issn = {1098-5336},
support = {RII Track-2 FEC18268341826834//National Science Foundation (NSF)/ ; IOS-1557940//National Science Foundation (NSF)/ ; ARS 3060-21220-032-00D//U.S. Department of Agriculture (USDA)/ ; ARS 3060-21220-032-00D//U.S. Department of Agriculture (USDA)/ ; },
mesh = {Animals ; Bees/microbiology/growth &amp; development ; *Gastrointestinal Microbiome ; *Larva/microbiology/growth &amp; development ; *Pollen/microbiology ; Female ; Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; Lactobacillaceae/genetics/growth &amp; development/physiology/isolation &amp; purification ; },
abstract = {Social bees have been extensively studied for their gut microbial functions, but the significance of the gut microbiota in solitary bees remains less explored. Solitary bee, Megachile rotundata females provision their offspring with pollen from various plant species, harboring a diverse microbial community that colonizes larvae guts. The Apilactobacillus is the most abundant microbe, but evidence concerning the effects of Apilactobacillus and other provision microbes on growth and survival are lacking. We hypothesized that the presence of Apilactobacillus in abundance would enhance larval and prepupal development, weight, and survival, while the absence of intact microbial communities was expected to have a negative impact on bee fitness. We reared larvae on pollen provisions with naturally collected microbial communities (Natural pollen) or devoid of microbial communities (Sterile pollen). We also assessed the impact of introducing Apilactobacillus micheneri by adding it to both types of pollen provisions. Feeding larvae with sterile pollen + A. micheneri led to the highest mortality rate, followed by natural pollen + A. micheneri, and sterile pollen. Larval development was significantly delayed in groups fed with sterile pollen. Interestingly, larval and prepupal weights did not significantly differ across treatments compared to natural pollen-fed larvae. 16S rRNA gene sequencing found a dominance of Sodalis, when A. micheneri was introduced to natural pollen. The presence of Sodalis with abundant A. micheneri suggests potential crosstalk between both, shaping bee nutrition and health. Hence, this study highlights that the reliance on nonhost-specific environmental bacteria may not impact fitness of M. rotundata.IMPORTANCEThis study investigates the impact of environmentally acquired gut microbes of solitary bee fitness with insights into the microbial ecology of bee and their health. While the symbiotic microbiome is well-studied in social bees, the role of environmental acquired microbiota in solitary bees remains unclear. Assessing this relationship in a solitary pollinator, the leaf-cutting bee, Megachile rotundata, we discovered that this bee species does not depend on the diverse environmental bacteria found in pollen for either its larval growth or survival. Surprisingly, high concentrations of the most abundant pollen bacteria, Apilactobacillus micheneri did not consistently benefit bee fitness, but caused larval mortality. Our findings also suggest an interaction between Apilactobacillus and the Sodalis and perhaps their role in bee nutrition. Hence, this study provides significant insights that contribute to understanding the fitness, conservation, and pollination ecology of other solitary bee species in the future.},
}
@article {pmid39133233,
year = {2024},
author = {Kwiatkowska, K and Ormaniec, P},
title = {Microbial Succession on Microplastics in Wastewater Treatment Plants: Exploring the Complexities of Microplastic-Microbiome Interactions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {105},
pmid = {39133233},
issn = {1432-184X},
mesh = {*Microplastics/analysis ; *Wastewater/microbiology/chemistry ; *Biofilms ; *Microbiota ; *Sewage/microbiology/chemistry ; Waste Disposal, Fluid ; Water Pollutants, Chemical/analysis ; Bacteria/classification/metabolism ; Plastics/chemistry ; },
abstract = {Despite some effectiveness of wastewater treatment processes, microplastics accumulate in sewage sludge and their further use may contribute to the release of plastic microplastics into the environment. There is an urgent need to reduce the amount of microplastics in sewage sludge. Plastic particles serve as solid substrates for various microorganisms, promoting the formation of microbial biofilms with different metabolic activities. The biofilm environment associated with microplastics will determine the efficiency of treatment processes, especially biological methods, and the mechanisms of organic compound conversion. A significant source of microplastics is the land application of sewage sludge from wastewater treatment plants. The detrimental impact of microplastics affects soil enzymatic activity, soil microorganisms, flora, fauna, and plant production. This review article summarizes the development of research related to microplastics and discusses the issue of microplastic introduction from sewage sludge. Given that microplastics can contain complex composite polymers and form a plastisphere, further research is needed to understand their potential environmental impact, pathogenicity, and the characteristics of biofilms in wastewater treatment systems. The article also discusses the physicochemical properties of microplastics in wastewater treatment plants and their role in biofilm formation. Then, the article explained the impact of these properties on the possibility of the formation of biofilms on their surface due to the peculiar structure of microorganisms and also characterized what factors enable the formation of specific plastisphere in wastewater treatment plants. It highlights the urgent need to understand the basic information about microplastics to assess environmental toxicity more rationally, enabling better pollution control and the development of regulatory standards to manage microplastics entering the environment.},
}
@article {pmid39132685,
year = {2024},
author = {Ye, D and Liu, Y and Li, J and Zhou, J and Cao, J and Wu, Y and Wang, X and Fang, Y and Ye, X and Zou, J and Ma, Q},
title = {Competitive dynamics and balance between Streptococcus mutans and commensal streptococci in oral microecology.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/1040841X.2024.2389386},
pmid = {39132685},
issn = {1549-7828},
abstract = {Dental caries, as a biofilm-related disease, is closely linked to dysbiosis in microbial ecology within dental biofilms. Beyond its impact on oral health, bacteria within the oral cavity pose systemic health risks by potentially entering the bloodstream, thereby increasing susceptibility to bacterial endocarditis, among other related diseases. Streptococcus mutans, a principal cariogenic bacterium, possesses virulence factors crucial to the pathogenesis of dental caries. Its ability to adhere to tooth surfaces, produce glucans for biofilm formation, and metabolize sugars into lactic acid contributes to enamel demineralization and the initiation of carious lesions. Its aciduricity and ability to produce bacteriocins enable a competitive advantage, allowing it to thrive in acidic environments and dominate in changing oral microenvironments. In contrast, commensal streptococci, such as Streptococcus sanguinis, Streptococcus gordonii, and Streptococcus salivarius, act as primary colonizers and compete with S. mutans for adherence sites and nutrients during biofilm formation. This competition involves the production of alkali, peroxides, and antibacterial substances, thereby inhibiting S. mutans growth and maintaining microbial balance. This dynamic interaction influences the balance of oral microbiota, with disruptions leading to shifts in microbial composition that are marked by rapid increases in S. mutans abundance, contributing to the onset of dental caries. Thus, understanding the dynamic interactions between commensal and pathogenic bacteria in oral microecology is important for developing effective strategies to promote oral health and prevent dental caries. This review highlights the roles and competitive interactions of commensal bacteria and S. mutans in oral microecology, emphasizing the importance of maintaining oral microbial balance for health, and discusses the pathological implications of perturbations in this balance.},
}
@article {pmid39128495,
year = {2024},
author = {De Pessemier, B and López, CD and Taelman, S and Verdonck, M and Chen, Y and Stockman, A and Lambert, J and Van de Wiele, T and Callewaert, C},
title = {Comparative Whole Metagenome Analysis in Lesional and Nonlesional Scalp Areas of Patients with Psoriasis Capitis and Healthy Individuals.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2024.07.020},
pmid = {39128495},
issn = {1523-1747},
abstract = {Psoriasis is an immune-mediated inflammatory disorder, where the majority of the patients suffer from psoriasis capitis or scalp psoriasis. Current therapeutics remain ineffective to treat scalp lesions. In this study, we present a whole-metagenome characterization of the scalp microbiome in psoriasis capitis. We investigated how changes in the homeostatic cutaneous microbiome correlate with the condition and identified metagenomic biomarkers (taxonomic, functional, virulence factors, antimicrobial resistance genes) that could partly explain its emergence. Within this study, 83 top and back scalp samples from healthy individuals and 64 lesional and nonlesional scalp samples from subjects with untreated psoriasis capitis were analyzed. Using qPCR targeting the 16S and 18S ribosomal RNA genes, we found a significant decrease in microbial load within scalp regions affected by psoriasis compared with that in their nonlesional counterparts. Metagenomic analysis revealed that psoriatic lesions displayed significant lower Cutibacterium species (including C. modestum, C. namnetense, C. granulosum, C. porci), along with an elevation in Staphylococcus aureus. A heightened relative presence of efflux pump protein-encoding genes was detected, suggesting potential antimicrobial resistance mechanisms. These mechanisms are known to specifically target human antimicrobial peptides (including cathelicidin LL-37), which are frequently encountered within psoriasis lesions. These shifts in microbial community dynamics may contribute to psoriasis disease pathogenesis.},
}
@article {pmid39126446,
year = {2024},
author = {Izumi, H},
title = {Abundances of ectomycorrhizal exploration types show the type-dependent temporal dynamics over the seasons-a controlled growth container experiment.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39126446},
issn = {1618-1905},
abstract = {Ectomycorrhizas are ubiquitous symbiotic associations between host trees and soil fungi. While the seasonal changes of the taxonomic community structure of ectomycorrhizal fungi have been studied extensively, the temporal dynamics of ectomycorrhizal exploration types which have been proposed for elucidating the functional roles of ectomycorrhizas have not been fully examined. The purpose of the study is to test the hypothesis of whether the abundance of the exploration types in the hosts with different phenology shows different temporal patterns over the seasons. Two host species, deciduous Quercus acutissima and evergreen Q. glauca, were planted in growth containers with natural forest soils and were grown in single or combined species treatment, under similar environmental conditions and in shared soil spore banks of the ectomycorrhizal fungi. The ectomycorrhizal exploration types that occurred on these two host species in two different treatments were observed for two growing seasons. The observed exploration types, namely contact, short-distance, and long-distance type as well as the overall abundance of the ectomycorrhizas showed distinct temporal patterns although no specific response to the host seasonal phenology was found. The abundances of the contact type showed no relation to the seasons whereas those of the short- and the long-distance type increased with time. The formation of the long-distance type was strongly influenced by the host species treatments while that of the other two types was not so. Therefore, the different exploration types demonstrate distinct temporal patterns depending on the types but no specific seasonal responses.},
}
@article {pmid39123264,
year = {2024},
author = {Rothrock, MJ and Zwirzitz, B and Al Hakeem, WG and Oladeinde, A and Guard, JY and Li, X},
title = {16S amplicon-based microbiome biomapping of a commercial broiler hatchery.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {46},
pmid = {39123264},
issn = {2524-4671},
abstract = {Hatcheries, where eggs from multiple breeder farms are incubated and hatched before being sent to different broiler farms, represent a nexus point in the commercial production of broilers in the United States. Considering all downstream microbial quality and safety aspects of broiler production (live production, processing, consumer use) can be potentially affected by the hatchery, a better understanding of microbial ecology within commercial hatcheries is essential. Therefore, a commercial broiler hatchery was biomapped using 16S rRNA amplicon-based microbiome analyses of four sample type categories (Air, Egg, Water, Facility) across five different places in the pre-hatch, hatch, and post-hatch areas. While distinct microbiota were found for each sample type category and hatchery area, microbial community analyses revealed that Egg microbiota trended towards clustering with the facility-related samples when moving from the prehatch to post-hatch areas, highlighting the potential effect of the hatchery environment in shaping the pre-harvest broiler-related microbiota. Prevalence analyses revealed 20 ASVs (Core20) present in the core microbiota of all sample types and areas, with each ASV possessing a unique distribution throughout the hatchery. Interestingly, three Enterobacteriaceae ASVs were in the Core20, including Salmonella. Subsequent analyses showed that Salmonella, while a minor prehatch and hatch Core20ASV, dominated the Enterobacteriaceae niche and total microbiota in the chick pad feces in the post-hatch area of the hatchery, and the presence of this Salmonella ASV in the post-hatch feces was associated with swabs of breakroom tables. These findings highlight the complexity of commercial hatchery microbiota, including identifying chick pad feces and breakroom tables as potentially important sampling or disinfection targets for hatchery managers to focus their Salmonella mitigation efforts to reduce loads entering live production farms.},
}
@article {pmid39122657,
year = {2024},
author = {Brenzinger, K and Glatter, T and Hakobyan, A and Meima-Franke, M and Zweers, H and Liesack, W and Bodelier, PLE},
title = {Exploring modes of microbial interactions with implications for methane cycling.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {9},
pages = {},
pmid = {39122657},
issn = {1574-6941},
support = {5535/1-1//DFG/ ; 870.15.073/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Methane/metabolism ; *Microbial Interactions ; *Volatile Organic Compounds/metabolism ; *Carbon Dioxide/metabolism ; Methylomonas/metabolism/genetics ; Proteomics ; Proteome ; Heterotrophic Processes ; Oxygenases/metabolism/genetics ; },
abstract = {Methanotrophs are the sole biological sink of methane. Volatile organic compounds (VOCs) produced by heterotrophic bacteria have been demonstrated to be a potential modulating factor of methane consumption. Here, we identify and disentangle the impact of the volatolome of heterotrophic bacteria on the methanotroph activity and proteome, using Methylomonas as model organism. Our study unambiguously shows how methanotrophy can be influenced by other organisms without direct physical contact. This influence is mediated by VOCs (e.g. dimethyl-polysulphides) or/and CO2 emitted during respiration, which can inhibit growth and methane uptake of the methanotroph, while other VOCs had a stimulating effect on methanotroph activity. Depending on whether the methanotroph was exposed to the volatolome of the heterotroph or to CO2, proteomics revealed differential protein expression patterns with the soluble methane monooxygenase being the most affected enzyme. The interaction between methanotrophs and heterotrophs can have strong positive or negative effects on methane consumption, depending on the species interacting with the methanotroph. We identified potential VOCs involved in the inhibition while positive effects may be triggered by CO2 released by heterotrophic respiration. Our experimental proof of methanotroph-heterotroph interactions clearly calls for detailed research into strategies on how to mitigate methane emissions.},
}
@article {pmid39122033,
year = {2024},
author = {de Menezes, AB and Gashchak, S and Wood, MD and Beresford, NA},
title = {Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone.},
journal = {The Science of the total environment},
volume = {950},
number = {},
pages = {175381},
doi = {10.1016/j.scitotenv.2024.175381},
pmid = {39122033},
issn = {1879-1026},
mesh = {*Wildfires ; *Chernobyl Nuclear Accident ; *Soil Microbiology ; *Microbiota ; *Soil Pollutants, Radioactive/analysis ; Radiation Monitoring ; Soil/chemistry ; Bacteria/classification ; Ukraine ; Forests ; },
abstract = {There is considerable uncertainty regarding radiation's effects on biodiversity in natural complex ecosystems typically subjected to multiple environmental disturbances and stresses. In this study we characterised the relationships between soil microbial communities and estimated total absorbed dose rates to bacteria, grassy vegetation and trees in the Red Forest region of the Chornobyl Exclusion Zone. Samples were taken from sites of contrasting ecological histories and along burn and no burn areas following a wildfire. Estimated total absorbed dose rates to bacteria reached levels one order of magnitude higher than those known to affect bacteria in laboratory studies. Sites with harsher ecological conditions, notably acidic pH and low soil moisture, tended to have higher radiation contamination levels. No relationship between the effects of fire and radiation were observed. Microbial groups that correlated with high radiation sites were mostly classified to taxa associated with high environmental stress habitats or stress resistance traits. Distance-based linear models and co-occurrence analysis revealed that the effects of radiation on the soil microbiome were minimal. Hence, the association between high radiation sites and specific microbial groups is more likely a result of the harsher ecological conditions in these sites, rather than due to radiation itself. In this study, we provide a starting point for understanding the relationship between soil microbial communities and estimated total absorbed radiation dose rates to different components of an ecosystem highly contaminated with radiation. Our results suggest that soil microbiomes adapted to natural soil conditions are more likely to be resistant to ionising radiation than expected from laboratory studies, which demonstrates the importance of assessing the impact of ionising radiation on soil microbial communities under field conditions.},
}
@article {pmid39119822,
year = {2024},
author = {West, NJ and Landa, M and Obernosterer, I},
title = {Differential association of key bacterial groups with diatoms and Phaeocystis spp. during spring blooms in the Southern Ocean.},
journal = {MicrobiologyOpen},
volume = {13},
number = {4},
pages = {e1428},
pmid = {39119822},
issn = {2045-8827},
support = {LEFE-CYBER//Centre National de la Recherche Scientifique/ ; //Institut Polaire Fran&#xe7;ais Paul Emile Victor/ ; 10-BLAN-0614//Agence Nationale de la Recherche/ ; },
mesh = {*Diatoms/classification ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Haptophyta/classification/growth &amp; development ; Phytoplankton/classification/growth &amp; development ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Seasons ; },
abstract = {Interactions between phytoplankton and heterotrophic bacteria significantly influence the cycling of organic carbon in the ocean, with many of these interactions occurring at the micrometer scale. We explored potential associations between specific phytoplankton and bacteria in two size fractions, 0.8-3 µm and larger than 3 µm, at three naturally iron-fertilized stations and one high nutrient low chlorophyll station in the Southern Ocean. The composition of phytoplankton and bacterial communities was determined by sequencing the rbcL gene and 16S rRNA gene from DNA and RNA extracts, which represent presence and potential activity, respectively. Diatoms, particularly Thalassiosira, contributed significantly to the DNA sequences in the larger size fractions, while haptophytes were dominant in the smaller size fraction. Correlation analysis between the most abundant phytoplankton and bacterial operational taxonomic units revealed strong correlations between Phaeocystis and picoeukaryotes with SAR11, SAR116, Magnetospira, and Planktomarina. In contrast, most Thalassiosira operational taxonomic units showed the highest correlations with Polaribacter, Sulfitobacteria, Erythrobacter, and Sphingobium, while Fragilariopsis, Haslea, and Thalassionema were correlated with OM60, Fluviicola, and Ulvibacter. Our in-situ observations suggest distinct associations between phytoplankton and bacterial taxa, which could play crucial roles in nutrient cycling in the Southern Ocean.},
}
@article {pmid39118147,
year = {2024},
author = {Xiong, Y and Mueller, RS and Feng, S and Guo, X and Pan, C},
title = {Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {148},
pmid = {39118147},
issn = {2049-2618},
support = {R01 AT011618/AT/NCCIH NIH HHS/United States ; R01AT011618/NH/NIH HHS/United States ; },
mesh = {*Proteomics/methods ; *Isotope Labeling ; *Algorithms ; Escherichia coli/metabolism ; Carbon Isotopes/metabolism ; Tandem Mass Spectrometry/methods ; Proteome ; },
abstract = {BACKGROUND: Proteomic stable isotope probing (SIP) is used in microbial ecology to trace a non-radioactive isotope from a labeled substrate into de novo synthesized proteins in specific populations that are actively assimilating and metabolizing the substrate in a complex microbial community. The Sipros algorithm is used in proteomic SIP to identify variably labeled proteins and quantify their isotopic enrichment levels (atom%) by performing enrichment-resolved database searching.<br><br>RESULTS: In this study, Sipros was upgraded to improve the labeled protein identification, isotopic enrichment quantification, and database searching speed. The new Sipros 4 was compared with the existing Sipros 3, Calisp, and MetaProSIP in terms of the number of identifications and the accuracy and precision of atom% quantification on both the peptide and protein levels using standard E. coli cultures with 1.07 atom%, 2 atom%, 5 atom%, 25 atom%, 50 atom%, and 99 atom% [13]C enrichment. Sipros 4 outperformed Calisp and MetaProSIP across all samples, especially in samples with&#x2009;&#x2265;&#x2009;5 atom% [13]C labeling. The computational speed on Sipros 4 was&#x2009;>&#x2009;20 times higher than Sipros 3 and was on par with the overall speed of Calisp- and MetaProSIP-based pipelines. Sipros 4 also demonstrated higher sensitivity for the detection of labeled proteins in two [13]C-SIP experiments on a real-world soil community. The labeled proteins were used to trace [13]C from [13]C-methanol and [13]C-labeled plant exudates to the consuming soil microorganisms and their newly synthesized proteins.<br><br>CONCLUSION: Overall, Sipros 4 improved the quality of the proteomic SIP results and reduced the computational cost of SIP database searching, which will make proteomic SIP more useful and accessible to the border community. Video Abstract.},
}
@article {pmid39113789,
year = {2024},
author = {Strik, DPBTB and Ganigue, R},
title = {Editorial: Microbial chain elongation-carbon recovering biorefineries for the circular economy.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {12},
number = {},
pages = {1448975},
pmid = {39113789},
issn = {2296-4185},
}
@article {pmid39113100,
year = {2024},
author = {Nieto, EE and Jurburg, SD and Steinbach, N and Festa, S and Morelli, IS and Coppotelli, BM and Chatzinotas, A},
title = {DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {146},
pmid = {39113100},
issn = {2049-2618},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Soil Pollutants/metabolism ; *Biodegradation, Environmental ; *RNA, Ribosomal, 16S/genetics ; *RNA, Ribosomal, 18S/genetics ; *Bacteria/metabolism/classification/genetics ; Biomass ; Carbon Isotopes/metabolism ; Food Chain ; Polycyclic Aromatic Hydrocarbons/metabolism ; Isotope Labeling ; },
abstract = {BACKGROUND: Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a [13]C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation.<br><br>RESULTS: Inoculation effectively increased PAH removal in the&#xa0;short-term, but not in&#xa0;the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of [13]C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil.<br><br>CONCLUSION: Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.},
}
@article {pmid39110233,
year = {2024},
author = {Wei, L and Wang, Y and Li, N and Zhao, N and Xu, S},
title = {Bacteria-Like Gaiella Accelerate Soil Carbon Loss by Decomposing Organic Matter of Grazing Soils in Alpine Meadows on the Qinghai-Tibet Plateau.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {104},
pmid = {39110233},
issn = {1432-184X},
support = {2023-ZJ-767//Qinghai Province Applied Basic Research Program/ ; 2023-ZJ-767//Qinghai Province Applied Basic Research Program/ ; LHZX-2020-02//Joint Special Project of Sanjiangyuan National Park/ ; LHZX-2020-02//Joint Special Project of Sanjiangyuan National Park/ ; },
mesh = {*Soil Microbiology ; Tibet ; *Carbon/metabolism/analysis ; *Soil/chemistry ; *Grassland ; Animals ; Carbon Sequestration ; Herbivory ; Bacteria/metabolism/classification ; },
abstract = {The alpine meadows of the Qinghai-Tibet Plateau have significant potential for storing soil carbon, which is important to global carbon sequestration. Grazing is a major threat to its potential for carbon sequestration. However, grazing poses a major threat to this potential by speeding up the breakdown of organic matter in the soil and releasing carbon, which may further lead to positive carbon-climate change feedback and threaten ecological security. Therefore, in order to accurately explore the driving mechanism and regulatory factors of soil organic matter decomposition in grazing alpine meadows on the Qinghai-Tibet Plateau, we took the grazing sample plots of typical alpine meadows as the research object and set up grazing intensities of different life cycles, aiming to explore the relationship and main regulatory factors of grazing on soil organic matter decomposition and soil microorganisms. The results show the following: (1) soil microorganisms, especially Acidobacteria and Acidobacteria, drove the decomposition of organic matter in the soil, thereby accelerating the release of soil carbon, which was not conducive to soil carbon sequestration in grassland; (2) the grazing triggering effect formed a positive feedback with soil microbial carbon release, accelerating the decomposition of organic matter and soil carbon loss; and (3) the grazing ban and light grazing were more conducive to slowing down soil organic matter decomposition and increasing soil carbon sequestration.},
}
@article {pmid39109653,
year = {2024},
author = {Corich, L and Losasso, C and Meneghel, A and Blarasin, FI and Basaglia, G and Corich, MA},
title = {The first case of urosepsis caused by Corynebacterium aurimucosum in an immunocompetent patient.},
journal = {Future microbiology},
volume = {19},
number = {11},
pages = {963-970},
pmid = {39109653},
issn = {1746-0921},
mesh = {Humans ; *Corynebacterium/isolation &amp; purification/genetics/pathogenicity/classification ; Aged ; Female ; *Corynebacterium Infections/microbiology/diagnosis/drug therapy ; *Sepsis/microbiology/drug therapy ; *Urinary Tract Infections/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Non-diphtheroid Corynebacterium sepsis is rare and has affected only immunocompromised or particularly predisposed patients so far. We present the first case of urosepsis caused by Corynebacterium aurimucosum in a 67-year-old woman, without any known immunodeficiencies and in absence of any immunosuppressive therapy, admitted to the hospital for fever and acute dyspnea. This work suggests a new approach in evaluating the isolation of Corynebacteria, especially if isolated from blood. In particular, it highlights the potential infectious role of C. aurimucosum (often considered a contaminant and only rarely identified as an etiological agent of infections) and its clinical consequences, detailing also interesting aspects about its microbiological diagnosis and relative therapy and clarifying contrasting data of literature.},
}
@article {pmid39109421,
year = {2024},
author = {Alfahl, Z and Biggins, S and Higgins, O and Chueiri, A and Smith, TJ and Morris, D and O'Dwyer, J and Hynds, PD and Burke, LP and O'Connor, L},
title = {A rapid on-site loop-mediated isothermal amplification technology as an early warning system for the detection of Shiga toxin-producing Escherichia coli in water.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {8},
pages = {},
pmid = {39109421},
issn = {1465-2080},
mesh = {*Nucleic Acid Amplification Techniques/methods ; *Shiga-Toxigenic Escherichia coli/genetics/isolation &amp; purification ; *Water Microbiology ; Molecular Diagnostic Techniques/methods/instrumentation ; Sensitivity and Specificity ; Rivers/microbiology ; Shiga Toxin 1/genetics ; Groundwater/microbiology ; },
abstract = {Shiga toxin-producing Escherichia coli (STEC) is an important waterborne pathogen capable of causing serious gastrointestinal infections with potentially fatal complications, including haemolytic-uremic syndrome. All STEC serogroups harbour genes that encode at least one Shiga toxin (stx1 and/or stx2), which constitute the primary virulence factors of STEC. Loop-mediated isothermal amplification (LAMP) enables rapid real-time pathogen detection with a high degree of specificity and sensitivity. The aim of this study was to develop and validate an on-site portable diagnostics workstation employing LAMP technology to permit rapid real-time STEC detection in environmental water samples. Water samples (n=28) were collected from groundwater wells (n=13), rivers (n=12), a turlough (n=2) and an agricultural drain (n=1) from the Corrib catchment in Galway. Water samples (100 ml) were passed through a 0.22 µm filter, and buffer was added to elute captured cells. Following filtration, eluates were tested directly using LAMP assays targeting stx1, stx2 and E. coli phoA genes. The portable diagnostics workstation was used in field studies to demonstrate the on-site testing capabilities of the instrument. Real-time PCR assays targeting stx1 and stx2 genes were used to confirm the results. The limit of detection for stx1, stx2 and phoA LAMP assays were 2, 2 and 6 copies, respectively. Overall, stx1, stx2 and phoA genes were detected by LAMP in 15/28 (53.6 %), 9/28 (32.2 %) and 24/28 (85.7 %) samples, respectively. For confirmation, the LAMP results for stx1 and stx2 correlated perfectly (100 %) with those obtained using PCR. The portable diagnostics workstation exhibited high sensitivity throughout the on-site operation, and the average time from sample collection to final result was 40 min. We describe a simple, transferable and efficient diagnostic technology for on-site molecular analysis of various water sources. This method allows on-site testing of drinking water, enabling evidence-based decision-making by public health and water management authorities.},
}
@article {pmid39109205,
year = {2024},
author = {Zhu, L and Chen, L and Lin, B and Xu, Y and Dong, W and Lv, Y and Tang, J and Zhang, G and Zhang, L and Yang, S and Yang, Q and Chen, S},
title = {Deciphering the microbial succession and color formation mechanism of "green-covering and red-heart" Guanyin Tuqu.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1412503},
pmid = {39109205},
issn = {1664-302X},
abstract = {"Green-covering and red-heart" Guanyin Tuqu (GRTQ), as a type of special fermentation starter, is characterized by the "green-covering" formed on the surface of Guanyin Tuqu (SQ) and the "red-heart" in the center of Guanyin Tuqu (CQ). However, the mechanisms that promote temporal succession in the GRTQ microbial ecology and the formation of "green-covering and red-heart" characteristics remain unclear. Herein, we correlated the temporal profiles of microbial community succession with the main environmental variables (temperature, moisture, and acidity) and spatial position (center and surface) in GRTQ throughout fermentation. According to the results of high-throughput sequencing and culture-dependent methods, the microbial communities in the CQ and SQ demonstrated functional complementarity. For instance, the bacterial richness index of the CQ was greater than that of SQ, and the fungal richness index of the SQ was greater than that of CQ at the later stage of fermentation. Furthermore, Saccharomycopsis, Saccharomyces, Aspergillus, Monascus, Lactobacillus, Bacillus, Rhodanobacter, and Chitinophaga were identified as the dominant microorganisms in the center, while the surface was represented by Saccharomycopsis, Aspergillus, Monascus, Lactobacillus, Acetobacter, and Weissella. By revealing the physiological characteristics of core microorganisms at different spatial positions of GRTQ, such as Aspergillus clavatus and Monascus purpureus, as well as their interactions with environmental factors, we elucidated the color formation mechanism behind the phenomenon of "green" outside and "red" inside. This study provides fundamental information support for optimizing the production process of GRTQ.},
}
@article {pmid39107417,
year = {2024},
author = {Cordovez, V and Carrión, VJ and Rivas Torres, G and Ortiz, DA and Cabrera, W and Balian, H and Vivanco, AK and Pérez-Jaramillo, JE and Chaves, J and Pazmiño, DA and van 't Hof, P and Raaijmakers, JM},
title = {Darwin's expedition revisited to reveal the evolution of plant-microbe interactions on Galápagos.},
journal = {Nature microbiology},
volume = {9},
number = {8},
pages = {1903-1905},
pmid = {39107417},
issn = {2058-5276},
support = {GSC fund 17150//Universidad San Francisco de Quito (USFQ)/ ; },
mesh = {*Plants/microbiology ; Ecuador ; *Biological Evolution ; Host-Pathogen Interactions ; Plant Diseases/microbiology ; },
}
@article {pmid39106714,
year = {2024},
author = {Qing, J and Li, C and Zhi, H and Zhang, L and Wu, J and Li, Y},
title = {Exploring macrophage heterogeneity in IgA nephropathy: Mechanisms of renal impairment and current therapeutic targets.},
journal = {International immunopharmacology},
volume = {140},
number = {},
pages = {112748},
doi = {10.1016/j.intimp.2024.112748},
pmid = {39106714},
issn = {1878-1705},
mesh = {*Glomerulonephritis, IGA/metabolism/immunology ; Humans ; *Macrophages/immunology/metabolism ; Kidney/pathology/metabolism/immunology ; Male ; Female ; Glomerular Filtration Rate ; Adult ; Single-Cell Analysis ; },
abstract = {The lack of understanding of the mechanism of renal injury in IgA nephropathy (IgAN) hinders the development of personalized treatment plans and targeted therapies. Improved insight into the cause of renal dysfunction in IgAN is necessary to enhance the effectiveness of strategies for slowing the progression of the disease. This study examined single cell RNA sequencing (scRNA seq) and bulk-RNA seq data and found that the gene expression of renal intrinsic cells (RIC) was significantly changed in patients with renal impairment, with a primary focus on energy metabolism. We discovered a clear metabolic reprogramming of RIC during renal function impairment (RF) using the 'scMetabolism' package, which manifested as a weakening of oxidative phosphorylation, alterations in fatty acid metabolism, and changes in glycolysis. Cellular communication analysis revealed that communication between macrophages (Ma) and RIC became more active and impacted cell function through the ligand-receptor-transcription factor (L-R-TF) axis in patients with RF. Our studies showed a notable upsurge in the expression of gene CLU and the infiltration of CLU[+] Ma in patients with RF. CLU is a multifunctional protein, extensively involved in processes such as cell apoptosis and immune responses. Data obtained from the Nephroseq V5 database and multiplex immunohistochemistry (mIHC) were used to validate the findings, which were found to be robustly correlated with estimated glomerular filtration rate (eGFR) of the IgAN patients, as demonstrated by linear regression (LR). This study provides new insights into the cellular and molecular changes that occur in IgAN during renal impairment, revealing that elevated expression of CLU and CLU[+] Ma percolation are common features in patients with RF. These findings offer potential targets and strategies for personalized management and targeted therapy of IgAN.},
}
@article {pmid39106212,
year = {2024},
author = {Pottie, I and Vázquez Fernández, R and Van de Wiele, T and Briers, Y},
title = {Phage lysins for intestinal microbiome modulation: current challenges and enabling techniques.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2387144},
pmid = {39106212},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Bacteriophages/physiology ; Animals ; *Endopeptidases/metabolism ; Bacteria/genetics/metabolism/virology/classification ; Probiotics ; Anti-Bacterial Agents/pharmacology ; Bacterial Infections/microbiology/drug therapy/therapy ; Viral Proteins/metabolism/genetics ; Peptidoglycan/metabolism ; },
abstract = {The importance of the microbiota in the intestinal tract for human health has been increasingly recognized. In this perspective, microbiome modulation, a targeted alteration of the microbial composition, has gained interest. Phage lysins, peptidoglycan-degrading enzymes encoded by bacteriophages, are a promising new class of antibiotics currently under clinical development for treating bacterial infections. Due to their high specificity, lysins are considered microbiome-friendly. This review explores the opportunities and challenges of using lysins as microbiome modulators. First, the high specificity of endolysins, which can be further modulated using protein engineering or targeted delivery methods, is discussed. Next, obstacles and possible solutions to assess the microbiome-friendliness of lysins are considered. Finally, lysin delivery to the intestinal tract is discussed, including possible delivery methods such as particle-based and probiotic vehicles. Mapping the hurdles to developing lysins as microbiome modulators and identifying possible ways to overcome these hurdles can help in their development. In this way, the application of these innovative antimicrobial agents can be expanded, thereby taking full advantage of their characteristics.},
}
@article {pmid39105581,
year = {2024},
author = {Zhu, Y-X and Yang, T-Y and Deng, J-H and Yin, Y and Song, Z-R and Du, Y-Z},
title = {Stochastic processes drive divergence of bacterial and fungal communities in sympatric wild insect species despite sharing a common diet.},
journal = {mSphere},
volume = {9},
number = {8},
pages = {e0038624},
pmid = {39105581},
issn = {2379-5042},
support = {BK20231330//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; },
mesh = {Animals ; *Insecta/microbiology ; *Fungi/classification/genetics ; *Microbiota ; *Sympatry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Stochastic Processes ; *Diet ; Mycobiome ; Citrus/microbiology ; },
abstract = {UNLABELLED: Arthropods harbor complex microbiota that play a pivotal role in host fitness. While multiple factors, like host species and diet, shape microbiota in arthropods, their impact on community assembly in wild insects remains largely unknown. In this study, we surveyed bacterial and fungal community assembly in nine sympatric wild insect species that share a common citrus fruit diet. Source tracking analysis suggested that these insects acquire some bacteria and fungi from the citrus fruit with varying degrees. Although sharing a common diet led to microbiota convergence, the diversity, composition, and network of both bacterial and fungal communities varied significantly among surveyed insect groups. Null model analysis indicated that stochastic processes, particularly dispersal limitation and drift, are primary drivers of structuring insect bacterial and fungal communities. Importantly, the influence of each community assembly process varied strongly depending on the host species. Thus, we proposed a speculative view that the host specificity of the microbiome and mycobiome assembly is widespread in wild insects despite sharing the same regional species pool. Overall, this research solidifies the importance of host species in shaping microbiomes and mycobiomes, providing novel insights into their assembly mechanisms in wild insects.<br><br>IMPORTANCE: Since the microbiome has been shown to impact insect fitness, a mechanistic understanding of community assembly has potentially significant applications but remains largely unexplored. In this paper, we investigate bacterial and fungal community assembly in nine sympatric wild insect species that share a common diet. The main findings indicate that stochastic processes drive the divergence of microbiomes and mycobiomes in nine sympatric wild insect species. These findings offer novel insights into the assembly mechanisms of microbiomes and mycobiomes in wild insects.},
}
@article {pmid39103310,
year = {2024},
author = {Liu, J and Xu, G and Zhao, S and He, J},
title = {Plastisphere Microbiomes Respiring Persistent Organohalide Pollutants.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {33},
pages = {14740-14752},
doi = {10.1021/acs.est.4c02251},
pmid = {39103310},
issn = {1520-5851},
mesh = {*Microbiota ; Plastics ; Persistent Organic Pollutants/metabolism ; Bacteria/metabolism ; Halogenated Diphenyl Ethers/metabolism ; Biodegradation, Environmental ; },
abstract = {Plastics are invading nearly all ecosystems on earth, acting as emerging repositories for toxic organic pollutants and thereby imposing substantial threats to ecological integrity. The colonization of plastics by microorganisms, forming the plastisphere, has garnered attention due to its potential influence on biogeochemical cycles. However, the capability of plastisphere microorganisms to attenuate organohalide pollutants remains to be evaluated. This study revealed that the plastisphere, collected from coastal ecosystems, harbors unique microbiomes, while the natural accumulation of organohalide pollutants on plastics may favor the proliferation of organohalide-respiring bacteria (OHRB). Laboratory tests further elucidated the high potential of plastisphere microbiota to reductively dehalogenate a variety of organohalide pollutants. Notably, over 70% tested plastisphere completely debrominated tetrabromobisphenol A (TBBPA) and polybrominated diphenyl ethers (PBDEs) to nonhalogenated products, whereas polychlorinated biphenyls (PCBs) were converted to lower congeners under anaerobic conditions. Dehalococcoides, Dehalogenimonas, and novel Dehalococcoidia populations might contribute to the observed dehalogenation based on their growth during incubation and positive correlations with the quantity of halogens removed. Intriguingly, large fractions of these OHRB populations were identified in a lack of the currently known TBBPA/PBDEs/PCBs reductive dehalogenase (RDase) genes, suggesting the presence of novel RDase genes. Microbial community analyses identified organohalides as a crucial factor in determining the composition, diversity, interaction, and assembly of microbes derived from the plastisphere. Collectively, this study underscores the overlooked roles of the plastisphere in the natural attenuation of persistent organohalide pollutants and sheds light on the unignorable impacts of organohalide compounds on the microbial ecology of the plastisphere.},
}
@article {pmid39101559,
year = {2024},
author = {Brar, NK and Dhariwal, A and Shekhar, S and Junges, R and Hakansson, AP and Petersen, FC},
title = {HAMLET, a human milk protein-lipid complex, modulates amoxicillin induced changes in an ex vivo biofilm model of the oral microbiome.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1406190},
pmid = {39101559},
issn = {1664-302X},
abstract = {Challenges from infections caused by biofilms and antimicrobial resistance highlight the need for novel antimicrobials that work in conjunction with antibiotics and minimize resistance risk. In this study we investigated the composite effect of HAMLET (human alpha-lactalbumin made lethal to tumor cells), a human milk protein-lipid complex and amoxicillin on microbial ecology using an ex vivo oral biofilm model with pooled saliva samples. HAMLET was chosen due to its multi-targeted antimicrobial mechanism, together with its synergistic effect with antibiotics on single species pathogens, and low risk of resistance development. The combination of HAMLET and low concentrations of amoxicillin significantly reduced biofilm viability, while each of them alone had little or no impact. Using a whole metagenomics approach, we found that the combination promoted a remarkable shift in overall microbial composition compared to the untreated samples. A large proportion of the bacterial species in the combined treatment were Lactobacillus crispatus, a species with probiotic effects, whereas it was only detected in a minor fraction in untreated samples. Although resistome analysis indicated no major shifts in alpha-diversity, the results showed the presence of TEM beta-lactamase genes in low proportions in all treated samples but absence in untreated samples. Our study illustrates HAMLET's capability to alter the effects of amoxicillin on the oral microbiome and potentially favor the growth of selected probiotic bacteria when in combination. The findings extend previous knowledge on the combined effects of HAMLET and antibiotics against target pathogens to include potential modulatory effects on polymicrobial biofilms of human origin.},
}
@article {pmid39101364,
year = {2024},
author = {Elias Masiques, N and Vossen, E and De Vrieze, J and De Smet, S and Van Hecke, T},
title = {The formation of sulfur metabolites during in vitro gastrointestinal digestion of fish, white meat and red meat is affected by the addition of fructo-oligosaccharides.},
journal = {Food &amp; function},
volume = {15},
number = {17},
pages = {8729-8739},
doi = {10.1039/d4fo00928b},
pmid = {39101364},
issn = {2042-650X},
mesh = {Animals ; *Fermentation ; *Oligosaccharides/metabolism ; *Red Meat/analysis ; Cattle ; *Digestion ; Swine ; *Chickens ; Fishes/metabolism ; Gastrointestinal Tract/metabolism ; Sulfur/metabolism ; Meat/analysis ; Humans ; Fatty Acids, Volatile/metabolism ; Ammonia/metabolism ; },
abstract = {The formation of sulfur metabolites during large intestinal fermentation of red meat may affect intestinal health. In this study, four muscle sources with varying heme-Fe content (beef, pork, chicken and salmon), with or without fructo-oligosaccharides (FOS), were exposed to an in vitro gastrointestinal digestion and fermentation model, after which the formation of sulfur metabolites, protein fermentation metabolites, and short (SCFA) and branched (BCFA) chain fatty acids was assessed. When FOS were present during muscle fermentation, levels of SCFA (+54%) and H2S (+36%) increased, whereas levels of CS2 (-37%), ammonia (-60%) and indole (-30%) decreased, and the formation of dimethyl sulfides and phenol was suppressed. Red meat fermentation was not accompanied by higher H2S formation, but beef ferments tended to contain 33 to 49% higher CS2 levels compared to the ferments of other muscle sources. In conclusion, there is a greater effect on sulfur fermentation by the addition of FOS to the meats, than the intrinsic heme-Fe content of meat.},
}
@article {pmid39098418,
year = {2024},
author = {Zhang, M and Duan, T and Luo, Y and Zhang, H and Li, W and Wang, X and Han, J},
title = {Impact mechanisms of various surfactants on the biodegradation of phenanthrene in soil: Bioavailability and microbial community responses.},
journal = {The Science of the total environment},
volume = {950},
number = {},
pages = {175225},
doi = {10.1016/j.scitotenv.2024.175225},
pmid = {39098418},
issn = {1879-1026},
mesh = {*Phenanthrenes/metabolism ; *Surface-Active Agents/metabolism ; *Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Soil Microbiology ; Soil/chemistry ; Biological Availability ; Microbiota/drug effects ; Polysorbates ; Glycolipids ; },
abstract = {The present study was conducted to systematically explore the mechanisms underlying the impact of various surfactants (CTAB, SDBS, Tween 80 and rhamnolipid) at different doses (10, 100 and 1000 mg/kg) on the biodegradation of a model polycyclic aromatic hydrocarbon (PAH) by indigenous soil microorganisms, focusing on bioavailability and community responses. The cationic surfactant CTAB inhibited the biodegradation of phenanthrene within the whole tested dosage range by decreasing its bioavailability and adversely affecting soil microbial communities. Appropriate doses of SDBS (1000 mg/kg), Tween 80 (100, 1000 mg/kg) and rhamnolipid at all amendment levels promoted the transformation of phenanthrene from the very slow desorption fraction (Fvslow) to bioavailable fractions (rapid and slow desorption fractions, Frapid and Fslow), assessed via Tenax extraction. However, only Tween 80 and rhamnolipid at these doses significantly improved both the rates and extents of phenanthrene biodegradation by 22.1-204.3 and 38.4-76.7 %, respectively, while 1000 mg/kg SDBS had little effect on phenanthrene removal. This was because the inhibitory effects of anionic surfactant SDBS, especially at high doses, on the abundance, diversity and activity of soil microbial communities surpassed the bioavailability enhancement in dominating biodegradation. In contrast, the nonionic surfactant Tween 80 and biosurfactant rhamnolipid enhanced the bioavailability of phenanthrene for degradation and also that to specific degrading bacterial genera, which stimulated their growth and increased the abundance of the related nidA degradation gene. Moreover, they promoted the total microbial/bacterial biomass, community diversity and polyphenol oxidase activity by providing available substrates and nutrients. These findings contribute to the design of suitable surfactant types and dosages for mitigating the environmental risk of PAHs and simultaneously benefiting microbial ecology in soil through bioremediation.},
}
@article {pmid39095861,
year = {2024},
author = {Anthony, WE and Allison, SD and Broderick, CM and Chavez Rodriguez, L and Clum, A and Cross, H and Eloe-Fadrosh, E and Evans, S and Fairbanks, D and Gallery, R and Gontijo, JB and Jones, J and McDermott, J and Pett-Ridge, J and Record, S and Rodrigues, JLM and Rodriguez-Reillo, W and Shek, KL and Takacs-Vesbach, T and Blanchard, JL},
title = {From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {56},
pmid = {39095861},
issn = {2524-6372},
support = {DE-AC05-76RL01830//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 89233218CNA000001//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; },
abstract = {Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.},
}
@article {pmid39095500,
year = {2024},
author = {},
title = {Bringing microbial ecology into focus.},
journal = {Nature microbiology},
volume = {9},
number = {8},
pages = {1901-1902},
pmid = {39095500},
issn = {2058-5276},
mesh = {*Ecology ; Microbiota ; Humans ; Bacteria/genetics/classification/metabolism ; },
}
@article {pmid39095499,
year = {2024},
author = {Carreira, C and Lønborg, C and Acharya, B and Aryal, L and Buivydaite, Z and Borim Corrêa, F and Chen, T and Lorenzen Elberg, C and Emerson, JB and Hillary, L and Khadka, RB and Langlois, V and Mason-Jones, K and Netherway, T and Sutela, S and Trubl, G and Wa Kang'eri, A and Wang, R and White, RA and Winding, A and Zhao, T and Sapkota, R},
title = {Integrating viruses into soil food web biogeochemistry.},
journal = {Nature microbiology},
volume = {9},
number = {8},
pages = {1918-1928},
pmid = {39095499},
issn = {2058-5276},
support = {NNF21OC0072586//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 36223//Villum Fonden (Villum Foundation)/ ; 1127-00033B//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; },
mesh = {*Soil Microbiology ; *Food Chain ; *Viruses/genetics/classification/isolation &amp; purification ; *Soil/chemistry ; *Microbiota ; Animals ; Plants/virology/microbiology ; Ecosystem ; Bacteria/virology/metabolism/genetics ; },
abstract = {The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. We highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.},
}
@article {pmid39094415,
year = {2024},
author = {Song, Y and Cao, X and Li, SA and Li, Z and Grossart, HP and Ma, H},
title = {Human activities-impacted lake dissolved organic matter (DOM) affects phycosphere microbial diversity and DOM diversification via carbon metabolism.},
journal = {Journal of environmental management},
volume = {367},
number = {},
pages = {122011},
doi = {10.1016/j.jenvman.2024.122011},
pmid = {39094415},
issn = {1095-8630},
mesh = {*Lakes/microbiology ; *Carbon/metabolism ; Humans ; Benzopyrans ; Bacteria/metabolism ; },
abstract = {Photosynthetic carbon sequestration and microbial carbon metabolism are major processes of algae-bacteria interactions, affecting pollutant degradation as well as fundamental biogeochemical cycles in aquatic systems. Human-induced land-use changes greatly alter the molecular composition and input of terrestrial dissolved organic matter (DOM) in inland lakes. However, how the origin of DOM leads to varying effects on phycosphere microbial communities or molecular composition of DOM, e.g., via carbon metabolism, has been little studied in freshwater. Here, we incubated the cyanobacterium Microcystis aeruginosa and a bacterial community from natural lakes to establish an alga-bacteria model system. This allowed us to investigate how DOM from different sources affects phycosphere microbial diversity and DOM diversification. We showed that Suwannee River fulvic acid (SRFA), Suwannee River natural organic matter (SRNOM) and cropland lake DOM promote algal growth, whereas DOM from an urban lake inhibits algal growth. Algal metabolites and DOM together shaped the chemotaxis response of phycosphere communities. High-resolution mass spectrometry analysis demonstrated that DOM chemo-diversity tended to become uniform after interactions of diverse DOM sources with the algae-bacteria symbiosis system. Molecular thermodynamic analysis of DOM based on a substrate-explicit model further verified that microbial interactions render DOM less bioavailable and thus increase recalcitrant DOM formation. Metabolome analysis uncovered that DOM addition intensifies metabolic pathways related to labile and recalcitrant DOM utilization (mainly lignin/carboxyl-rich alicyclic molecule (CRAM)-like DOM, unsaturated hydrocarbon), whereby cofactor and vitamin metabolism represented an extremely strong activity in all metabolic pathways. Our results highlight covariation and interactions of DOM with microbial metabolism at the molecular level and expands our understanding of microbially mediated DOM shaping aquatic carbon cycling.},
}
@article {pmid39088119,
year = {2024},
author = {Ferreira, P and Benabderrahim, MA and Hamza, H and Marchesini, A and Rejili, M and Castro, J and Tavares, RM and Costa, D and Sebastiani, F and Lino-Neto, T},
title = {Exploring the Influence of Date Palm Cultivars on Soil Microbiota.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {103},
pmid = {39088119},
issn = {1432-184X},
support = {2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {*Soil Microbiology ; *Phoeniceae/microbiology/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; Genotype ; Plant Roots/microbiology ; Soil/chemistry ; },
abstract = {Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses.},
}
@article {pmid39087852,
year = {2024},
author = {Wu, T and Bafort, Q and Mortier, F and Almeida-Silva, F and Natran, A and Van de Peer, Y},
title = {The immediate metabolomic effects of whole-genome duplication in the greater duckweed, Spirodela polyrhiza.},
journal = {American journal of botany},
volume = {111},
number = {8},
pages = {e16383},
pmid = {39087852},
issn = {1537-2197},
support = {833522/ERC_/European Research Council/International ; },
mesh = {*Araceae/genetics/metabolism ; *Genome, Plant ; *Metabolomics ; *Gene Duplication ; Metabolome ; Polyploidy ; Biomass ; },
abstract = {PREMISE: In plants, whole-genome duplication (WGD) is a common mutation with profound evolutionary potential. Given the costs associated with a superfluous genome copy, polyploid establishment is enigmatic. However, in the right environment, immediate phenotypic changes following WGD can facilitate establishment. Metabolite abundances are the direct output of the cell's regulatory network and determine much of the impact of environmental and genetic change on the phenotype. While it is well known that an increase in the bulk amount of genetic material can increase cell size, the impact of gene dosage multiplication on the metabolome remains largely unknown.<br><br>METHODS: We used untargeted metabolomics on four genetically distinct diploid-neoautotetraploid pairs of the greater duckweed, Spirodela polyrhiza, to investigate how WGD affects metabolite abundances per cell and per biomass.<br><br>RESULTS: Autopolyploidy increased metabolite levels per cell, but the response of individual metabolites varied considerably. However, the impact on metabolite level per biomass was restricted because the increased cell size reduced the metabolite concentration per cell. Nevertheless, we detected both quantitative and qualitative effects of WGD on the metabolome. Many effects were strain-specific, but some were shared by all four strains.<br><br>CONCLUSIONS: The nature and impact of metabolic changes after WGD depended strongly on the genotype. Dosage effects have the potential to alter the plant metabolome qualitatively and quantitatively, but were largely balanced out by the reduction in metabolite concentration due to an increase in cell size in this species.},
}
@article {pmid39085652,
year = {2024},
author = {Brinch, C and Otani, S and Munk, P and van den Beld, M and Franz, E and Aarestrup, FM},
title = {Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {102},
pmid = {39085652},
issn = {1432-184X},
support = {NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; },
mesh = {Denmark ; *Sewage/microbiology ; *Vibrio cholerae/genetics/isolation &amp; purification/classification ; Genome, Bacterial ; Wastewater/microbiology ; Cholera/microbiology/epidemiology ; },
abstract = {We report the discovery of a persistent presence of Vibrio cholerae at very low abundance in the inlet of a single wastewater treatment plant in Copenhagen, Denmark at least since 2015. Remarkably, no environmental or locally transmitted clinical case of V. cholerae has been reported in Denmark for more than 100 years. We, however, have recovered a near-complete genome out of 115 metagenomic sewage samples taken over the past 8 years, despite the extremely low relative abundance of one V. cholerae read out of 500,000 sequenced reads. Due to the very low relative abundance, routine screening of the individual samples did not reveal V. cholerae. The recovered genome lacks the gene responsible for cholerae toxin production, but although this strain may not pose an immediate public health risk, our finding illustrates the importance, challenges, and effectiveness of wastewater-based pathogen surveillance.},
}
@article {pmid39085298,
year = {2024},
author = {Vidal-Verdú, &#xc0; and Torrent, D and Iglesias, A and Latorre-Pérez, A and Abendroth, C and Corbín-Agustí, P and Peretó, J and Porcar, M},
title = {The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {65},
pmid = {39085298},
issn = {2055-5008},
support = {ACIF/2021/110//Generalitat Valenciana (Regional Government of Valencia)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Coleoptera/microbiology ; Metagenomics/methods ; Phylogeny ; Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; },
abstract = {Insect gut microbiomes play a crucial role in the insect development and are shaped, among other factors, by the specialized insect diet habits as well as the morphological structure of the gut. Rose chafers (Pachnoda spp.; Coleoptera: Scarabaeidae) have a highly differentiated gut characterized by a pronounced hindgut dilation which resembles a miniaturized rumen. Specifically, the species Pachnoda marginata has not been previously studied in detail in terms of microbial ecology. Here, we show a fine scale study of the highly compartmentalized gut of P. marginata by using amplicon and metagenomic sequencing to shed light on the bacterial, archaeal and fungal communities thriving in each section of the gut. We found a microbial gradient along the gut from aerobic (foregut) to strictly anaerobic communities (hindgut). In addition, we have characterized interesting biological activities and metabolic pathways of gut microbial communities related to cellulose degradation, methane production and sulfate reduction. Taken together, our results reveal the highly diverse microbial community and the potential of P. marginata gut as a source of industrially relevant microbial diversity.},
}
@article {pmid39083238,
year = {2024},
author = {Romano, I and Ventorino, V and Schettino, M and Magaraci, G and Pepe, O},
title = {Changes in Soil Microbial Communities Induced by Biodegradable and Polyethylene Mulch Residues Under Three Different Temperatures.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {101},
pmid = {39083238},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Biodegradation, Environmental ; *Temperature ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Fungi/genetics/metabolism/classification ; *Polyethylene ; *Microbiota ; *Soil/chemistry ; Biodegradable Plastics/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Mulching is a common method increasing crop yield and achieving out-of-season production; nevertheless, their removal poses a significant environmental danger. In this scenario, the use of biodegradable plastic mulches comes up as a solution to increase the sustainability of this practice, as they can be tilled in soil without risk for the environment. In this context, it is important to study the microbial response to this practice, considering their direct involvement in plastic biodegradation. This study evaluated the biodegradation of three commercial mulch residues: one conventional non-biodegradable mulch versus two biodegradable ones (white and black compostable Mater-Bi mulches). The experiment was conducted under three incubation temperatures (room temperature 20-25 °C, 30 °C, and 45 °C) for a 6-month trial using fallow agricultural soil. Soil without plastic mulch residues was used as a control. White mater-bi biodegradable mulch residues showed higher degradation rates up to 88.90% at 30 °C, and up to 69.15% at room temperature. Furthermore, incubation at 45 °C determines the absence of degradation for all types of mulch considered. Moreover, bacterial alpha diversity was primarily influenced by plastic type and temperature, while fungal populations were mainly affected by temperature. Beta diversity was impacted by all experimental variables. Predicted functional genes crucial for degrading complex substrates, including those encoding hydrolases, cutinases, cellobiosidases, and lipases, were derived from 16S rRNA gene sequencing data. Cluster analysis based on predicted enzyme-encoding gene abundance revealed two clusters, mainly linked to sampling time. Finally, core microbiome analysis identified dominant bacterial and fungal taxa in various soil-plastic ecosystems during degradation, pinpointing species potentially involved in plastic breakdown. The present study allows an assessment of how different temperatures affect the degradation of mulch residues in soil, providing important insights for different climatic growing zones. It also fills a gap in the literature by directly comparing the effects of biodegradable and polyethylene mulches on soil microbial communities.},
}
@article {pmid39081364,
year = {2024},
author = {Schmitz, DA and Wechsler, T and Mignot, I and Kümmerli, R},
title = {Predicting bacterial interaction outcomes from monoculture growth and supernatant assays.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae045},
pmid = {39081364},
issn = {2730-6151},
abstract = {How to derive principles of community dynamics and stability is a central question in microbial ecology. Bottom-up experiments, in which a small number of bacterial species are mixed, have become popular to address it. However, experimental setups are typically limited because co-culture experiments are labor-intensive and species are difficult to distinguish. Here, we use a four-species bacterial community to show that information from monoculture growth and inhibitory effects induced by secreted compounds can be combined to predict the competitive rank order in the community. Specifically, integrative monoculture growth parameters allow building a preliminary competitive rank order, which is then adjusted using inhibitory effects from supernatant assays. While our procedure worked for two different media, we observed differences in species rank orders between media. We then parameterized computer simulations with our empirical data to show that higher order species interactions largely follow the dynamics predicted from pairwise interactions with one important exception. The impact of inhibitory compounds was reduced in higher order communities because their negative effects were spread across multiple target species. Altogether, we formulated three simple rules of how monoculture growth and supernatant assay data can be combined to establish a competitive species rank order in an experimental four-species community.},
}
@article {pmid39081075,
year = {2024},
author = {Bontemps, Z and Paranjape, K and Guy, L},
title = {Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts.},
journal = {FEMS microbiology reviews},
volume = {48},
number = {4},
pages = {},
pmid = {39081075},
issn = {1574-6976},
support = {F23-0260//Helge Ax:son Johnsons Foundation/ ; //NSERC/ ; },
mesh = {*Symbiosis ; *Host Microbial Interactions/physiology ; *Biological Evolution ; Gammaproteobacteria/genetics/physiology/classification ; Animals ; Bacteria/genetics/classification ; Ecosystem ; },
abstract = {Interactions between eukaryotic hosts and their bacterial symbionts drive key ecological and evolutionary processes, from regulating ecosystems to the evolution of complex molecular machines and processes. Over time, endosymbionts generally evolve reduced genomes, and their relationship with their host tends to stabilize. However, host-bacteria relationships may be heavily influenced by environmental changes. Here, we review these effects on one of the most ancient and diverse endosymbiotic groups, formed by-among others-Legionellales, Francisellaceae, and Piscirickettsiaceae. This group is referred to as Deep-branching Intracellular Gammaproteobacteria (DIG), whose last common ancestor presumably emerged about 2 Ga ago. We show that DIGs are globally distributed, but generally at very low abundance, and are mainly identified in aquatic biomes. Most DIGs harbour a type IVB secretion system, critical for host-adaptation, but its structure and composition vary. Finally, we review the different types of microbial interactions that can occur in diverse environments, with direct or indirect effects on DIG populations. The increased use of omics technologies on environmental samples will allow a better understanding of host-bacterial interactions and help unravel the definition of DIGs as a group from an ecological, molecular, and evolutionary perspective.},
}
@article {pmid39080099,
year = {2024},
author = {Tiusanen, M and Becker-Scarpitta, A and Wirta, H},
title = {Distinct Communities and Differing Dispersal Routes in Bacteria and Fungi of Honey Bees, Honey, and Flowers.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {100},
pmid = {39080099},
issn = {1432-184X},
support = {201801360//Koneen S&#xe4;&#xe4;ti&#xf6;/ ; },
mesh = {Bees/microbiology ; Animals ; *Flowers/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/isolation &amp; purification/genetics ; *Honey/microbiology/analysis ; *Microbiota ; Finland ; Pollination ; DNA Barcoding, Taxonomic ; Seasons ; },
abstract = {Microbiota, the communities of microbes on and in organisms or organic matter, are essential for the functioning of ecosystems. How microbes are shared and transmitted delineates the formation of a microbiota. As pollinators forage, they offer a route to transfer microbes among the flowering plants, themselves, and their nests. To assess how the two components of the microbiota, bacteria and fungi, in pollination communities are shared and transferred, we focused on the honey bee Apis mellifera and collected honey bee, honey (representing the hive microbiota), and flower samples three times during the summer in Finland. We identified the bacteria and fungi by DNA metabarcoding. To determine the impact of honey bees' flower choices on the honey bee and hive microbiota, we identified also plant DNA in honey. The bacterial communities of honey bees, honey, and flowers all differ greatly from each other, while the fungal communities of honey bees and honey are very similar, yet different from flowers. The time of the summer and the sampling area influence all these microbiota. For flowers, the plant identity impacts both bacterial and fungal communities' composition the most. For the dispersal pathways of bacteria to honey bees, they are acquired directly from the honey and indirectly from flowers through the honey, while fungi are directly transmitted to honey bees from flowers. Overall, the distinctiveness of the microbiota of honey bees, honey, and the surrounding flowers suggests the sharing of microbes among them occurs but plays a minor role for the established microbiota.},
}
@article {pmid39079336,
year = {2024},
author = {Zhang, Y and Li, X and Ren, A and Yao, M and Chen, C and Zhang, H and van der Meer, W and Liu, G},
title = {Impacts of water treatments on bacterial communities of biofilm and loose deposits in drinking water distribution systems.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108893},
doi = {10.1016/j.envint.2024.108893},
pmid = {39079336},
issn = {1873-6750},
mesh = {*Biofilms/growth &amp; development/drug effects ; *Drinking Water/microbiology ; *Water Purification/methods ; *Water Supply ; *Bacteria ; Water Microbiology ; },
abstract = {Treated drinking water is delivered to customers through drinking water distribution systems (DWDSs). Although studies have focused on exploring the microbial ecology of DWDSs, knowledge about the effects of different water treatments on the bacterial community of biofilm and loose deposits in DWDS is limited. This study assessed the effects of additional treatments on the bacterial communities developed in 10 months' old pilot DWDSs. The results showed a similar bacterial community in the pipe-wall biofilm, which was dominated by Novosphingobium spp. (20-82 %) and Sphingomonas spp. (11-53 %), regardless of the treatment applied. The bacterial communities that were retained in the distribution systems (including pipe-wall biofilm and loose deposits) were similar to the particle-associated bacteria (PAB) in the corresponding supply water. The additional treatments showed clear effects of the removal and/or introduction of particles. The genera Aeromonas spp., Clostridium spp., Legionella spp., and Pseudomonas spp., which contain opportunistic pathogenic species, were only detected among the PAB in ion exchange system. Our study demonstrated that the biofilm community is consistent across treatments, and the contribution from bacteria in loose deposits is important but can be controlled by removing particles. These findings offer more insight into the origin and development of microbial ecology in DWDSs and suggest paths for further research on the possibility of managing the microbial ecology in distribution systems.},
}
@article {pmid39079302,
year = {2024},
author = {Zhou, W and Huang, D and Chen, S and Wang, G and Li, R and Xu, W and Lei, Y and Xiao, R and Yin, L and Chen, H and Li, F},
title = {Microplastic dilemma: Assessing the unexpected trade-offs between biodegradable and non-biodegradable forms on plant health, cadmium uptake, and sediment microbial ecology.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135240},
doi = {10.1016/j.jhazmat.2024.135240},
pmid = {39079302},
issn = {1873-3336},
mesh = {*Cadmium/metabolism/toxicity ; *Microplastics/toxicity/metabolism ; *Soil Microbiology ; *Geologic Sediments/microbiology/chemistry ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; Plant Roots/metabolism/microbiology ; Biodegradable Plastics/metabolism ; Plants/metabolism ; Plant Development/drug effects ; },
abstract = {Despite extensive substitution of biodegradable plastics (BPs) for conventional plastics (CPs), research on their environmental ecological consequences as microplastics (MPs) is scarce. This study aimed to fill this gap by investigating the impacts of six prototypical MPs (categorized into BMPs and CMPs) on plant growth, cadmium (Cd) translocation, and bacterial communities in contaminated sediments. Results showed both BMPs and CMPs hindered plant development; yet interestingly, BMPs provoked more pronounced physiological and biochemical changes alongside increased oxidative stress due to reactive oxygen species accumulation. Notably, most MP types promoted the absorption of Cd by plant roots potentially via a "dilution effect". BMPs also induced larger shifts in soil microbial metabolic functions compared to CMPs. Ramlibacter was identified as a key biomarker distinguishing BMPs from CMPs, with link to multiple N metabolic pathways and N assimilation. This study offers novel insights into intricate biochemical mechanisms and environmental chemistry behaviors underpinning MP-Cd interactions within the plant-microbe-sediment system, emphasizing BMPs' higher potential ecological risks based on their significant effects on plant health and microbial ecology. This work contributes to enhancing the comprehensive understanding of their ecological implications and potential threats to environmental security.},
}
@article {pmid39077993,
year = {2024},
author = {Jirsová, D and Wideman, JG},
title = {Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39077993},
issn = {1751-7370},
support = {2119963//National Science Foundation/ ; GBMF9201//Gordon and Betty Moore Foundation/ ; CZ.02.01.01/00/22_010/0008117//VEDA FELLOWSHIPS within the Operational program Jan Amos Komensky/ ; },
mesh = {Biological Evolution ; *Heterotrophic Processes ; Phylogeny ; Plastids/genetics ; *Stramenopiles/classification/genetics ; },
abstract = {Stramenopiles represent a significant proportion of aquatic and terrestrial biota. Most biologists can name a few, but these are limited to the phototrophic (e.g. diatoms and kelp) or parasitic species (e.g. oomycetes, Blastocystis), with free-living heterotrophs largely overlooked. Though our attention is slowly turning towards heterotrophs, we have only a limited understanding of their biology due to a lack of cultured models. Recent metagenomic and single-cell investigations have revealed the species richness and ecological importance of stramenopiles-especially heterotrophs. However, our lack of knowledge of the cell biology and behaviour of these organisms leads to our inability to match species to their particular ecological functions. Because photosynthetic stramenopiles are studied independently of their heterotrophic relatives, they are often treated separately in the literature. Here, we present stramenopiles as a unified group with shared synapomorphies and evolutionary history. We introduce the main lineages, describe their important biological and ecological traits, and provide a concise update on the origin of the ochrophyte plastid. We highlight the crucial role of heterotrophs and mixotrophs in our understanding of stramenopiles with the goal of inspiring future investigations in taxonomy and life history. To understand each of the many diversifications within stramenopiles-towards autotrophy, osmotrophy, or parasitism-we must understand the ancestral heterotrophic flagellate from which they each evolved. We hope the following will serve as a primer for new stramenopile researchers or as an integrative refresher to those already in the field.},
}
@article {pmid39074063,
year = {2024},
author = {Nyathi, M and Dhlamini, Z and Ncube, T},
title = {Cloning Cellulase Genes from Victoria Falls Rainforest Decaying Logs Metagenome.},
journal = {Polish journal of microbiology},
volume = {73},
number = {3},
pages = {343-348},
pmid = {39074063},
issn = {2544-4646},
mesh = {*Cellulase/genetics/metabolism ; *Metagenome ; *Rainforest ; Soil Microbiology ; Cloning, Molecular ; Hydrogen-Ion Concentration ; Escherichia coli/genetics ; Temperature ; Metagenomics ; Bacteria/genetics/classification/enzymology/isolation &amp; purification ; },
abstract = {The Victoria Falls rainforest is a protected site whose forest floors harbor a host of cellulolytic microorganisms involved in biomass degradation. This study collected decaying logs and soil from the rainforest for bioprospecting cellulases from their metagenomes. Metagenomic DNA was isolated from the compound sample. Degenerate cellulase primers were used to amplify cellulase genes in the metagenome. The resulting amplicons cloned into Z-competent Escherichia coli DH5α were analyzed by functional screening for the production of cellulase extracellularly. Functional screening of the clones resulted in one clone (Clone-i) testing positive for extracellular cellulase production. Submerged fermentation of Clone-i was carried out for cellulase production. The cellulases were characterized to determine their activity's optimum pH and temperature. The diversity of the cellulases produced by Clone-i was determined. Clone-i's optimum enzyme activity was observed after 72 hours of incubation at 50°C and pH 5. Clone-i produced 80% more exoglucanases as compared to endoglucanases. The cellulolytic Clone-i' isolate shows Victoria Falls rainforest's potential as an enzyme bioprospecting site, reflecting that metagenomics is a valuable tool in microbial ecology.},
}
@article {pmid39073401,
year = {2024},
author = {Williams, SE and Varliero, G and Lurgi, M and Stach, JEM and Race, PR and Curnow, P},
title = {Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {7},
pages = {},
pmid = {39073401},
issn = {1465-2080},
mesh = {*Porifera/microbiology ; *Microbiota ; *Archaea/classification/genetics/isolation &amp; purification ; Animals ; Atlantic Ocean ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; },
abstract = {Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.},
}
@article {pmid39073317,
year = {2024},
author = {Bahri, S and Bouazizi, S and Nahdi, A and Mlika, M and Hamdi, M and Jameleddine, S},
title = {Insights on the Tunisian Prickly Pear Molasses as a Potential Antifibrotic and Antioxidant Candidate against Lung Fibrosis.},
journal = {Chemistry &amp; biodiversity},
volume = {21},
number = {11},
pages = {e202401030},
doi = {10.1002/cbdv.202401030},
pmid = {39073317},
issn = {1612-1880},
support = {//Tunisian Ministry of Higher Education/ ; //Scientific Research/ ; },
mesh = {Animals ; *Antioxidants/pharmacology/chemistry ; *Rats, Wistar ; Rats ; *Pulmonary Fibrosis/drug therapy/chemically induced/metabolism/pathology ; *Molasses ; Male ; Bleomycin ; Oxidative Stress/drug effects ; Pyrus/chemistry ; Tunisia ; Antifibrotic Agents/pharmacology/chemistry ; Disease Models, Animal ; Lung/drug effects/pathology/metabolism ; },
abstract = {Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial disease leading to pulmonary damage and respiratory failure. We aimed to investigate the effect of prickly pear molasses (PPM) on an experimental model of pulmonary fibrosis induced by bleomycin (BLM) in Wistar rat. Animals were divided into 5 groups: the control group (G1), the BLM group (G2) and three groups (G3, G4, G5) receiving a single intra-tracheal injection of BLM (4 mg/kg) and PPM (at 2, 4.5 and10 %) that was introduced into the diet one week before BLM injection and continued for 3 weeks. Our phytochemical results revealed significant polyphenol and flavonoid content. LCMS analysis revealed the presence of Sinapinic acid, t-ferulic acid, t-cinnamic acid, Caffeic acid, gallic acid and vallinic acid among others. Our histological study revealed significant decrease in collagen deposition in the groups of rats treated with 4.5 % and 10 % molasses compared to BLM group. Oxidative stress in pulmonary tissues was investigated using catalase (CAT), superoxide dismutase (SOD), and malondialdehyde (MDA) assays. Treatment with PPM normalized the disturbance in the level of these oxidative markers in G3,G4, G5 compared to G2. In conclusion, PPM exhibit antifibrotic and antioxidant activities in BLM model of lung fibrosis.},
}
@article {pmid39073180,
year = {2024},
author = {Bielčik, M and Schlägel, UE and Schäfer, M and Aguilar-Trigueros, CA and Lakovic, M and Sosa-Hernández, MA and Hammer, EC and Jeltsch, F and Rillig, MC},
title = {Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {99},
number = {6},
pages = {2211-2233},
doi = {10.1111/brv.13119},
pmid = {39073180},
issn = {1469-185X},
support = {GRK 2118//Deutsche Forschungsgemeinschaft/ ; SCHL 2259/1-1.//Deutsche Forschungsgemeinschaft/ ; 100619639//Fachagentur Nachwachsende Rohstoffe/ ; },
mesh = {*Fungi/physiology ; *Ecosystem ; Models, Biological ; },
abstract = {Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.},
}
@article {pmid39071402,
year = {2024},
author = {Dieppa-Colón, E and Martin, C and Anantharaman, K},
title = {Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39071402},
issn = {2692-8205},
support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.<br><br>RESULTS: Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster and taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution.<br><br>CONCLUSION: Prophages are particularly overlooked in viral ecology and merit increased attention due to their vital implications for microbiomes and their hosts. Here, we created Prophage-DB to advance our comprehension of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.},
}
@article {pmid39066818,
year = {2024},
author = {Castellano-Hinojosa, A and Tortosa, G and Fernández-Zambrano, A and Correa-Galeote, D and Bedmar, EJ and Medina-Sánchez, JM},
title = {Strong Saharan Dust Deposition Events Alter Microbial Diversity and Composition in Sediments of High-Mountain Lakes of Sierra Nevada (Spain).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {99},
pmid = {39066818},
issn = {1432-184X},
support = {A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; PID2020-118872RB-I00//MICIN/AEI/10.13039/501100011033/ ; LifeWatch-2019-10-UGR-01//Ministry of Science and Innovation through the FEDER funds from the Spanish Pluriregional Operational Program 2014-2020 (POPE), LifeWatch-ERIC action line/ ; },
mesh = {*Geologic Sediments/microbiology/chemistry ; *Lakes/microbiology/chemistry ; *Dust/analysis ; Spain ; *Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification ; Microbiota ; Africa, Northern ; },
abstract = {Mediterranean high-mountain lakes are being increasingly affected by strong Saharan dust deposition events. However, the ecological impacts of these severe atmospheric episodes remain largely unknown. We examined the effects of a strong Saharan dust intrusion to the Iberian Peninsula in 2022 on the physicochemical parameters and prokaryotic communities in sediments of nine high-mountain lakes of Sierra Nevada (Spain) located above 2800 m.a.s.l and in different orientations (north vs. south). A previous year (2021), with lower Saharan dust deposition with respect to 2022, was used for interannual comparisons. The strong dust deposition to the high-mountain lakes resulted in a significant increase in sediment nutrient availability which was linked to changes in the composition of prokaryotic communities. Decreases in alpha diversity and changes in beta diversity of prokaryotic communities were mainly observed in lakes located in the south compared to the north orientation likely because the former was more affected by the atmospheric dust deposition episode. Dust intrusion to the high-mountain lakes resulted in significant changes in the relative abundance of specific genera involved in important nutrient cycling processes such as phosphate solubilization, nitrogen fixation, nitrification, and denitrification. Saharan dust deposition also increased predicted microbial functionality in all lakes. Our findings show that severe atmospheric dust inputs to remote high-mountain lakes of Sierra Nevada can have significant biogeochemical and biodiversity consequences through changes in nutrient availability and prokaryotic communities in sediments of these freshwater ecosystems. This information contributes to understanding how Mediterranean high-mountain lakes of Sierra Nevada face strong intrusions of Saharan dust and their ecological consequences.},
}
@article {pmid39065051,
year = {2024},
author = {Du, W and Li, J and Zhang, G and Yu, K and Liu, S},
title = {Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River.},
journal = {Microorganisms},
volume = {12},
number = {7},
pages = {},
pmid = {39065051},
issn = {2076-2607},
support = {52100171//National Natural Science Foundation of China/ ; BYESS2023103//Young Elite Scientist Sponsorship Program by Beijing Association for Science and Technology/ ; },
abstract = {Bacteria and archaea are foundational life forms on Earth and play crucial roles in the development of our planet's biological hierarchy. Their interactions influence various aspects of life, including eukaryotic cell biology, molecular biology, and ecological dynamics. However, the coexistence network patterns of these microorganisms within natural river ecosystems, vital for nutrient cycling and environmental health, are not well understood. To address this knowledge gap, we systematically explored the non-random coexistence patterns of planktonic bacteria and archaea in the 6000-km stretch of the Yangtze River by using high-throughput sequencing technology. By analyzing the O/R ratio, representing the divergence between observed (O%) and random (R%) co-existence incidences, and the module composition, we found a preference of both bacteria and archaea for intradomain associations over interdomain associations. Seasons notably influenced the co-existence of bacteria and archaea, and archaea played a more crucial role in spring as evidenced by their predominant presence of interphyla co-existence and more species as keystone ones. The autumn network was characterized by a higher node or edge number, greater graph density, node degree, degree centralization, and nearest neighbor degree, indicating a more complex and interconnected structure. Landforms markedly affected microbial associations, with more complex networks and more core species found in plain and non-source areas. Distance-decay analysis suggested the importance of geographical distance in shaping bacteria and archaea co-existence patterns (more pronounced in spring). Natural, nutrient, and metal factors, including water temperature, NH4[+]-N, Fe, Al, and Ni were identified as crucial determinants shaping the co-occurrence patterns. Overall, these findings revealed the dynamics of prokaryotic taxa coexistence patterns in response to varying environmental conditions and further contributed to a broader understanding of microbial ecology in freshwater biogeochemical cycling.},
}
@article {pmid39065031,
year = {2024},
author = {Sapp, PA and Townsend, JR and Kirby, TO and Govaert, M and Duysburgh, C and Verstrepen, L and Marzorati, M and Marshall, TM and Esposito, R},
title = {AG1[®], a Novel Synbiotic, Maintains Gut Barrier Function following Inflammatory Challenge in a Caco-2/THP1-Blue™ Co-Culture Model.},
journal = {Microorganisms},
volume = {12},
number = {7},
pages = {},
pmid = {39065031},
issn = {2076-2607},
support = {n/a//Athletic Greens International (Carson City, NV 89701)/ ; },
abstract = {Nutritional interventions to reduce gastrointestinal (GI) permeability are of significant interest to physically active adults and those experiencing chronic health conditions. This in vitro study was designed to assess the impact of AG1, a novel synbiotic, on GI permeability following an inflammatory challenge. Interventions [AG1 (vitamins/minerals, pre-/probiotics, and phytonutrients) and control (control medium)] were fed separately into a human GI tract model (stomach, small intestine, and colon). In the colonic phase, the GI contents were combined with fecal inocula from three healthy human donors. GI permeability was evaluated with transepithelial electrical resistance (TEER) in a Caco-2 (apical)/THP1-Blue™ (basolateral) co-culture model. The apical side received sodium butyrate (positive control) or Caco-2 complete medium (negative control) during baseline testing. In the 24 h experiment, the apical side received colonic simulation isolates from the GI model, and the basolateral side was treated with Caco-2 complete medium, then 6 h treatment with lipopolysaccharide. TEER was assessed at 0 h and 24 h, and inflammatory markers were measured at 30 h in triplicate. Paired samples t-tests were used to evaluate endpoint mean difference (MD) for AG1 vs. control. TEER was higher for AG1 (mean ± SD: 99.89 ± 1.32%) vs. control (mean ± SD: 92.87 ± 1.22%) following activated THP1-induced damage [MD: 7.0% (p < 0.05)]. AG1 maintained TEER similar to the level of the negative control [-0.1% (p = 0.02)]. No differences in inflammatory markers were observed. These in vitro data suggest that acute supplementation with AG1 might stimulate protective effects on GI permeability. These changes may be driven by SCFA production due to the pre-/probiotic properties of AG1, but more research is needed.},
}
@article {pmid39062734,
year = {2024},
author = {Zhang, H and Li, S and Zhou, S and Guo, W and Chen, P and Li, Y and Wu, W},
title = {Divergence of Phyllosphere Microbial Community Assemblies and Components of Volatile Organic Compounds between the Invasive Sphagneticola trilobata, the Native Sphagneticola calendulacea and Their Hybrids, and Its Implications for Invasiveness.},
journal = {Genes},
volume = {15},
number = {7},
pages = {},
pmid = {39062734},
issn = {2073-4425},
support = {2023KCXTD017//Guangdong Province University Innovative Team Project: Innovation and Development Application of Ornamental Plant Germplasm with Lingnan Characteristics/ ; },
mesh = {*Volatile Organic Compounds/metabolism ; *Microbiota ; *Introduced Species ; Brassicaceae/microbiology/genetics ; China ; },
abstract = {Closely-related plant groups with distinct microbiomes, chemistries and ecological characteristics represent tractable models to explore mechanisms shaping species spread, competitive dynamics and community assembly at the interface of native and introduced ranges. We investigated phyllosphere microbial communities, volatile organic compound (VOC) compositions, and potential interactions among introduced S. trilobata, native S. calendulacea and their hybrid in South China. S. trilobata exhibited higher α diversity but significantly different community composition compared to the native and hybrid groups. However, S. calendulacea and the hybrid shared certain microbial taxa, suggesting potential gene flow or co-existence. The potent antimicrobial VOC profile of S. trilobata, including unique compounds like p-cymene (13.33%), likely contributes to its invasion success. The hybrid's intermediate microbial and VOC profiles suggest possible consequences for species distribution, genetic exchange, and community assembly in heterogeneous environments. This hybrid deserves further study as both an opportunity for and threat to diversity maintenance. These differentiating yet connected plant groups provide insight into ecological and evolutionary dynamics shaping microbiome structure, species co-occurrence and competitive outcomes during biological exchange and habitat transformation. An interdisciplinary approach combining chemical and microbial ecology may reveal mechanisms underlying community stability and change, informing management of species spread in a globalized world.},
}
@article {pmid39061809,
year = {2024},
author = {Hriňová, K and Dlapová, J and Kubala, B and Kormanová, &#x13d; and Levarski, Z and Struhárňanská, E and Turňa, J and Stuchlík, S},
title = {Production of Reverse Transcriptase and DNA Polymerase in Bacterial Expression Systems.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {11},
number = {7},
pages = {},
pmid = {39061809},
issn = {2306-5354},
support = {APVV-17-0333//Slovak Research and Development Agency/ ; APVV-21-0215//Slovak Research and Development Agency/ ; APVV-21-0227//Slovak Research and Development Agency/ ; APVV-22-0161//Slovak Research and Development Agency/ ; },
abstract = {DNA amplification and reverse transcription enzymes have proven to be invaluable in fast and reliable diagnostics and research applications because of their processivity, specificity, and robustness. Our study focused on the production of mutant Taq DNA polymerase and mutant M-MLV reverse transcriptase in the expression hosts Vibrio natriegens and Escherichia coli under various expression conditions. We also examined nonspecific extracellular production in V. natriegens. Intracellularly, M-MLV was produced in V. natriegens at the level of 11% of the total cell proteins (TCPs) compared with 16% of TCPs in E. coli. We obtained a soluble protein that accounted for 11% of the enzyme produced in V. natriegens and 22% of the enzyme produced in E. coli. Taq pol was produced intracellularly in V. natriegens at the level of 30% of TCPs compared with 26% of TCPs in E. coli. However, Taq pol was almost non-soluble in E. coli, whereas in V. natriegens, we obtained a soluble protein that accounted for 23% of the produced enzyme. We detected substantial extracellular production of Taq pol. Thus, V. natriegens is a suitable alternative host with the potential for production of recombinant proteins.},
}
@article {pmid39060935,
year = {2024},
author = {Baptista, MS and Lee, CK and Monteiro, MR and Torgo, L and Cary, SC and Magalhães, C},
title = {Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {52},
pmid = {39060935},
issn = {2524-6372},
abstract = {BACKGROUND: Isolating the effects of deterministic variables (e.g., physicochemical conditions) on soil microbial communities from those of neutral processes (e.g., dispersal) remains a major challenge in microbial ecology. In this study, we disturbed soil microbial communities of two McMurdo Dry Valleys of Antarctica exhibiting distinct microbial biogeographic patterns, both devoid of aboveground biota and different in macro- and micro-physicochemical conditions. We modified the availability of water, nitrogen, carbon, copper ions, and sodium chloride salts in a laboratory-based experiment and monitored the microbial communities for up to two months. Our aim was to mimic a likely scenario in the near future, in which similar selective pressures will be applied to both valleys. We hypothesized that, given their unique microbial communities, the two valleys would select for different microbial populations when subjected to the same disturbances.<br><br>RESULTS: The two soil microbial communities, subjected to the same disturbances, did not respond similarly as reflected in both 16S rRNA genes and transcripts. Turnover of the two microbial communities showed a contrasting response to the same environmental disturbances and revealed different potentials for adaptation to change. These results suggest that the heterogeneity between these microbial communities, reflected in their strong biogeographic patterns, was maintained even when subjected to the same selective pressure and that the 'rare biosphere', at least in these samples, were deeply divergent and did not act as a reservoir for microbiota that enabled convergent responses to change in environmental conditions.<br><br>CONCLUSIONS: Our findings strongly support the occurrence of endemic microbial communities that show a structural resilience to environmental disturbances, spanning a wide range of physicochemical conditions. In the highly arid and nutrient-limited environment of the Dry Valleys, these results provide direct evidence of microbial biogeographic patterns that can shape the communities' response in the face of future environmental changes.},
}
@article {pmid39059201,
year = {2024},
author = {Bai, X and Samari-Kermani, M and Schijven, J and Raoof, A and Dinkla, IJT and Muyzer, G},
title = {Enhancing slow sand filtration for safe drinking water production: interdisciplinary insights into Schmutzdecke characteristics and filtration performance in mini-scale filters.},
journal = {Water research},
volume = {262},
number = {},
pages = {122059},
doi = {10.1016/j.watres.2024.122059},
pmid = {39059201},
issn = {1879-2448},
mesh = {*Filtration ; *Drinking Water/microbiology ; *Water Purification/methods ; *Sand ; *Escherichia coli ; Silicon Dioxide/chemistry ; Biofilms ; },
abstract = {The demand for safe drinking water is constantly challenged by increasing biohazards. One widely used solution is implementing indoor-operated slow sand filtration (SSF) as one of the final barriers in water production. SSF has gained popularity due to its low energy consumption and efficient removal of biohazards, especially microorganisms, without using chemicals. SSF involves both physical-chemical and biological removal, particularly in the "Schmutzdecke", which is a biofilm-like layer on the sand bed surface. To achieve the optimal performance of SSF, a systematic understanding of the influence of SSF operating parameters on the Schmutzdecke development and filter filtration performance is required. Our study focused on three operational parameters, i.e., sand material, sand size, and the addition of an inoculum (suspension of matured Schmutzdecke), on the mini-scale filters. The effects of these parameters on the Schmutzdecke development and SSF removal performance were studied by biochemical analyses and 16S amplicon sequencing, together with spiking experiments with Escherichia coli (E. coli) in the mini-scale filters. Our results indicate that the mini-scale filters successfully developed Schmutzdeckes and generated bacterial breakthrough curves efficiently. The sand size and material were found to have an impact on Schmutzdecke's development. The addition of inoculum to new filters did not induce significant changes in the microbial community composition of the Schmutzdecke, but we observed positive effects of faster Schmutzdecke development and better removal performance in some inoculated filters. Our study highlights the value of mini-scale filters for SSF studies, which provide insights into Schmutzdecke microbial ecology and bacterial removal with significantly reduced requirements of materials and effort as compared to larger-scale filters. We found that operational parameters have a greater impact on the Schmutzdecke biochemical characteristics and removal performances than on the microbial community composition. This suggests that Schmutzdecke characteristics may provide more reliable predictors of SSF removal performance, which could help to improve safe drinking water production.},
}
@article {pmid39055957,
year = {2024},
author = {Zhang, Y and Gan, G and Li, Y and Li, W and Jiang, Y and Wang, P and Hu, J and Wang, N and Quan, X and Liu, J and Raza, W and Xu, Y and Hohmann, P and Jousset, A and Wang, Y and Shen, Q and Jiang, G and Wei, Z},
title = {Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants.},
journal = {iScience},
volume = {27},
number = {7},
pages = {110319},
pmid = {39055957},
issn = {2589-0042},
abstract = {The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt caused by Ralstonia solanacearum. We first identified disease-suppressive and disease-conducive rhizosphere microbiome in a susceptible tomato recipient. Using a non-destructive rhizobox and 16S rRNA amplicon sequencing, we monitored the dynamics of both microbiome types during the eggplant development. Most differences were observed at the early stage and then diminished over time. The suppressive microbiome maintained a higher proportion of initial community members throughout eggplant development and exhibited stronger deterministic processes in the early stage, underscoring the importance of plant selection in recruiting protective microbes for rhizosphere immunity. Our study sheds light on the development of microbiome-based strategies for plant disease management and resistance breeding.},
}
@article {pmid39052866,
year = {2024},
author = {},
title = {Correction to: Alpine soil microbial ecology in a changing world.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {8},
pages = {},
doi = {10.1093/femsec/fiae085},
pmid = {39052866},
issn = {1574-6941},
}
@article {pmid39052865,
year = {2024},
author = {Vuilleumier, S and Barthelmebs, L and Corcoll, N and Hery, M and G Karpouzas, D and Wick, LY},
title = {Editorial: thematic issue on microbial ecotoxicology.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {8},
pages = {},
pmid = {39052865},
issn = {1574-6941},
mesh = {*Ecotoxicology ; },
}
@article {pmid39051617,
year = {2024},
author = {Pluym, T and Waegenaar, F and De Gusseme, B and Boon, N},
title = {Microbial drinking water monitoring now and in the future.},
journal = {Microbial biotechnology},
volume = {17},
number = {7},
pages = {e14532},
pmid = {39051617},
issn = {1751-7915},
support = {1S02022N//Fonds Wetenschappelijk Onderzoek/ ; 1S26823N//Fonds Wetenschappelijk Onderzoek/ ; S006221N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {*Drinking Water/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; Humans ; Water Microbiology ; Environmental Monitoring/methods ; },
abstract = {Over time, humanity has addressed microbial water contamination in various ways. Historically, individuals resorted to producing beer to combat the issue. Fast forward to the 19th century, and we witnessed a scientific approach by Robert Koch. His groundbreaking gelatine plating method aimed to identify and quantify bacteria, with a proposed limit of 100 colony-forming units per millilitre (CFU/mL) to avoid Cholera outbreaks. Despite considerable advancements in plating techniques through experimentation with media compositions and growth temperatures, the reliance on a century-old method for water safety remains the state-of-the-art. Even though most countries succeed in producing qualitative water at the end of the production centres, it is difficult to control, and guarantee, the same quality during distribution. Rather than focusing solely on specific sampling points, we propose a holistic examination of the entire water network to ensure comprehensive safety. Current practices leave room for uncertainties, especially given the low concentrations of pathogens. Innovative methods like flow cytometry and flow cytometric fingerprinting offer the ability to detect changes in the microbiome of drinking water. Additionally, molecular techniques and emerging sequencing technologies, such as third-generation sequencing (MinION), mark a significant leap forward, enhancing detection limits and emphasizing the identification of unwanted genes rather than the unwanted bacteria/microorganisms itself. Over the last decades, there has been the realization that the drinking water distribution networks are complex ecosystems that, beside bacteria, comprise of viruses, protozoans and even isopods. Sequencing techniques to find eukaryotic DNA are necessary to monitor the entire microbiome of the drinking water distribution network. Or will artificial intelligence, big data and machine learning prove to be the way to go for (microbial) drinking water monitoring? In essence, it is time to transcend century-old practices and embrace modern technologies to ensure the safety of our drinking water from production to consumption.},
}
@article {pmid39047455,
year = {2024},
author = {Blair, MF and Vaidya, R and Salazar-Benites, G and Bott, CB and Pruden, A},
title = {Relating microbial community composition to treatment performance in an ozone-biologically active carbon filtration potable reuse treatment train.},
journal = {Water research},
volume = {262},
number = {},
pages = {122091},
doi = {10.1016/j.watres.2024.122091},
pmid = {39047455},
issn = {1879-2448},
mesh = {*Ozone ; *Water Purification/methods ; *Filtration ; Microbiota ; Charcoal/chemistry ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Treatment trains that couple ozone (O3) with biologically active carbon (BAC) filtration are of interest as a lower cost, more sustainable, membrane-free approach to water reuse. However, little is known about the microbial communities that are the fundamental drivers of O3-BAC treatment. The objective of this study was to demonstrate microbial community profiling as a diagnostic tool for assessing the functionality, biological stability, and resilience of coupled physical, chemical, advanced oxidative and biological processes employed in water reuse treatment. We utilized 16S rRNA gene amplicon sequencing to profile the bacterial microbiota over time throughout a potable reuse train employing coagulation, flocculation, sedimentation, ozonation, BAC filtration, granular activated carbon (GAC) adsorption, and UV disinfection. A distinct baseline microbiota was associated with each stage of treatment (ANOSIM, p < 0.05, r-stat = 0.52), each undergoing succession with time and operational shifts. Ozonation resulted in the sharpest shifts (i.e., 83.3 % average change in Genus level relative abundances, when adjusted O3:TOC ratio > 1), and also variance, in microbial community composition. Adjustment in O3:TOC ratios, temperature, filter-aid polymer, monochloramine quenching agent, and empty-bed contact time also resulted in measurable changes in the baseline microbial community composition of individual processes, but to a lesser degree. Of these, supplementation of nitrogen and phosphorus resulted in the strongest bifurcation, especially in the microbial communities inhabiting the BAC (ANOSIM: p < 0.05, BAC5 r-stat = 0.32; BAC10 r-stat = 0.54) and GAC (ANOSIM: p < 0.05, GAC10 r-stat = 0.54; GAC20 r-stat = 0.63) units. Additionally, we found that the BAC microbial community was responsive to an inoculation of microbially active media, which resulted in improved TOC removal. The findings of this study improve understanding of bacterial dynamics occurring in advanced water treatment trains and can inform improved system design and operation.},
}
@article {pmid39046569,
year = {2024},
author = {Chen, X and Zhang, W and Geng, M and Shen, J and Wang, J},
title = {Carbon and Nutrient Limitations of Microbial Metabolism in Xingkai Lake, China: Abiotic and Biotic Drivers.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {97},
pmid = {39046569},
issn = {1432-184X},
support = {42230507//National Natural Science Foundation of China/ ; 42225708//National Natural Science Foundation of China/ ; },
mesh = {*Lakes/microbiology/chemistry ; China ; *Carbon/metabolism ; *Phosphorus/metabolism/analysis ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Fungi/metabolism/classification ; *Nitrogen/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; Nutrients/metabolism/analysis ; },
abstract = {Microbial communities are crucial for water quality and biogeochemical cycling in freshwaters. Microbes secrete extracellular enzymes to decompose organic matter for their needs of nutrients and scarce elements. Yet, there is a lack of knowledge on microbial metabolic limitations in freshwaters, especially in lake sediments. Here, we examined the carbon, nitrogen, and phosphorus-acquiring extracellular enzyme activities and the bacterial and fungal communities of 30 sediments across Xingkai Lake, the largest freshwater lake in Northeast Asia. We further analyzed the microbial metabolic limitations via extracellular enzyme stoichiometry and explored the direct and indirect effects of abiotic and biotic factors on the limitations. We found that microbial metabolisms were primarily limited by phosphorus in Xingkai Lake. For instance, microbial carbon and phosphorus limitations were closely correlated to abiotic factors like water depth, total dissolved solids, sediment total carbon, and conductivity. The metabolic limitations were also affected by biotic factors, such as showing positive relationships with the alpha and beta diversity of bacteria, and with the beta diversity of fungi. In addition, community compositions of bacteria and fungi were mainly correlated to abiotic factors such as total carbon and dissolved organic carbon, respectively. Collectively, microbial metabolic limitations were affected directly or indirectly by abiotic factors and microbial communities. Our findings indicate that microbial metabolic limitations are not only driven by bacteria and fungi but also by abiotic factors such as water depth and total nitrogen, and thus provide empirical evidence for effective management of freshwater lakes under climate warming and intensified human activities.},
}
@article {pmid39046558,
year = {2024},
author = {Xie, G and Sun, C and Gong, Y and Luo, W and Tang, X},
title = {Beyond the Bloom: Unraveling the Diversity, Overlap, and Stability of Free-Living and Particle-Attached Bacterial Communities in a Cyanobacteria-Dominated Hypereutrophic Lake.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {96},
pmid = {39046558},
issn = {1432-184X},
support = {WGKQ2022032//West Anhui University/ ; 41971062//National Natural Science Foundation of China/ ; },
mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics/classification ; *Eutrophication ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; Seasons ; Ecosystem ; China ; },
abstract = {In aquatic ecosystems with low nutrient levels, organic aggregates (OAs) act as nutrient hotspots, hosting a diverse range of microbial species compared to those in the water column. Lake eutrophication, marked by intensified and prolonged cyanobacterial blooms, significantly impacts material and energy cycling processes, potentially altering the ecological traits of both free-living (FL) and particle-attached (PA) bacteria. However, the extent to which observed patterns of FL and PA bacterial diversity, community assembly, and stability extend to hypereutrophic lakes remains understudied. To address this gap, we investigated bacterial diversity, composition, assembly processes, and stability within hypereutrophic Lake Xingyun. Our results revealed that FL bacterial communities exhibited higher α-diversity than PA counterparts, coupled with discernible taxonomic compositions. Both bacterial communities showed distinct seasonality, influenced by cyanobacterial bloom intensity. Environmental factors accounted for 71.1% and 54.2% of the variation among FL and PA bacteria, respectively. The assembly of the PA bacterial community was predominantly stochastic, while FL assembly was more deterministic. The FL network demonstrated greater stability, complexity, and negative interactions, indicative of competitive relationships, while the PA network showed a prevalence of positive correlations, suggesting mutualistic interactions. Importantly, these findings differ from observations in oligotrophic, mesotrophic, and eutrophic lakes. Overall, this research provides valuable insights into the interplay among bacterial fractions, enhancing our understanding of nutrient status and cyanobacterial blooms in shaping bacterial communities.},
}
@article {pmid39046491,
year = {2024},
author = {Soto-Cortés, E and Marroquín-Rodríguez, M and Basanta, MD and Maldonado-López, Y and Parra-Olea, G and Rebollar, EA},
title = {Host Species and Environment Shape the Skin Microbiota of Mexican Axolotls.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {98},
pmid = {39046491},
issn = {1432-184X},
support = {CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; IN205521//PAPIIT/UNAM/ ; },
mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Mexico ; *Fungi/classification/isolation &amp; purification/genetics ; Ambystoma mexicanum/microbiology ; Host Specificity ; Environment ; Biodiversity ; },
abstract = {Skin microbiomes in amphibians are complex systems that can be influenced by biotic and abiotic factors. In this study, we examined the effect of host species and environmental conditions on the skin bacterial and fungal microbiota of four obligate paedomorphic salamander species, commonly known as axolotls (Ambystoma andersoni, A. dumerilii, A. mexicanum, and A. taylori), all of them endemic to the Trans-Mexican Volcanic Belt. We found that despite their permanent aquatic lifestyle, these species present a host-specific skin microbiota that is distinct from aquatic communities. We identified skin-associated taxa that were unique to each host species and that differentiated axolotl species based on alpha and beta diversity metrics. Moreover, we identified a set of microbial taxa that were shared across hosts with high relative abundances across skin samples. Specifically, bacterial communities were dominated by Burkholderiales and Pseudomonadales bacterial orders and Capnodiales and Pleosporales fungal orders. Host species and environmental variables collectively explained more microbial composition variation in bacteria (R2 = 0.46) in comparison to fungi (R2 = 0.2). Our results contribute to a better understanding of the factors shaping the diversity and composition of skin microbial communities in Ambystoma. Additional studies are needed to disentangle the effects of specific host associated and environmental factors that could influence the skin microbiome of these endangered species.},
}
@article {pmid39043275,
year = {2024},
author = {Fernández-Blanco, C and Pereira, A and Veiga, MC and Kennes, C and Ganigué, R},
title = {Comprehensive comparative study on n-caproate production by Clostridium kluyveri: batch vs. continuous operation modes.},
journal = {Bioresource technology},
volume = {408},
number = {},
pages = {131138},
doi = {10.1016/j.biortech.2024.131138},
pmid = {39043275},
issn = {1873-2976},
mesh = {*Ethanol/metabolism ; *Clostridium kluyveri/metabolism ; *Caproates/metabolism ; Batch Cell Culture Techniques ; Bioreactors ; Fermentation ; Acetates/metabolism ; Oxidation-Reduction ; },
abstract = {Recently, there has been notable interest in researching and industrially producing medium-chain carboxylic acids (MCCAs) like n-caproate and n-caprylate via chain elongation process. This study presents a comprehensive assessment of the behavior and MCCA production profiles of Clostridium kluyveri in batch and continuous modes, at different ethanol:acetate molar ratios (1.5:1, 3.5:1 and 5.5:1). The highest n-caproate concentration, 12.9 ± 0.67 g/L (92.9 ± 1.39 % MCCA selectivity), was achieved in batch mode at a 3.5:1 ratio. Interestingly, higher ratios favored batch mode selectivity over continuous mode when this was equal or higher to 3.5:1. Steady state operation yielded the highest n-caproate (9.5 ± 0.13 g/L) and n-caprylate (0.35 ± 0.020 g/L) concentrations at the 3.5:1 ratio. Increased ethanol:acetate ratios led to a higher excessive ethanol oxidation (EEO) in both operational modes, potentially limiting n-caproate production and selectivity, especially at the 5.5:1 ratio. Overall, this study reports the efficient MCCA production of both batch and continuous modes by C. kluyveri.},
}
@article {pmid39043163,
year = {2024},
author = {DeWitt, ME and Sanders, JW},
title = {Tropical Diseases in the United States: Beyond Poverty - Advancing an Ecological Framework in Tropical Medicine.},
journal = {The American journal of tropical medicine and hygiene},
volume = {111},
number = {3},
pages = {449-451},
pmid = {39043163},
issn = {1476-1645},
mesh = {*Tropical Medicine ; Humans ; *Poverty ; United States/epidemiology ; },
}
@article {pmid39039555,
year = {2024},
author = {Wang, D and Liu, L and Xu, X and Wang, C and Wang, Y and Deng, Y and Zhang, T},
title = {Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {134},
pmid = {39039555},
issn = {2049-2618},
mesh = {*Bacteriophages/genetics/classification/physiology/isolation &amp; purification ; *Sewage/virology/microbiology ; *Wastewater/virology/microbiology ; *Bacteria/virology/genetics/classification ; Biofilms ; Metagenomics ; Water Purification/methods ; Microbiota ; },
abstract = {BACKGROUND: Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.<br><br>RESULTS: We uncovered distinct distribution&#xa0;patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as&#xa0;potentially host abundance- or phage/host ratio-driven phage population changes.<br><br>CONCLUSIONS: The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. Video Abstract.},
}
@article {pmid39039015,
year = {2024},
author = {Vanharanta, M and Santoro, M and Villena-Alemany, C and Piiparinen, J and Piwosz, K and Grossart, HP and Labrenz, M and Spilling, K},
title = {Microbial remineralization processes during postspring-bloom with excess phosphate available in the northern Baltic Sea.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {8},
pages = {},
pmid = {39039015},
issn = {1574-6941},
support = {731065//European Commission/ ; 2021/03/Y/NZ8/00076//National Science Centre, Poland/ ; GR1540/37-1//DFG/ ; },
mesh = {*Seawater/microbiology/chemistry ; *Phosphates/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development ; *Phosphorus/metabolism ; *Carbon/metabolism ; *Nitrogen/metabolism ; Finland ; Oceans and Seas ; Eutrophication ; Heterotrophic Processes ; },
abstract = {The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2-3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis.},
}
@article {pmid39030648,
year = {2024},
author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE},
title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {50},
pmid = {39030648},
issn = {2524-6372},
support = {2016/23699-8; 2018/14892-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.},
}
@article {pmid39030520,
year = {2024},
author = {Joo, M and Nam, S},
title = {Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {268},
pmid = {39030520},
issn = {1471-2180},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Adolescent ; *RNA, Ribosomal, 16S/genetics ; *Obesity/microbiology/immunology ; Female ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Inflammatory Bowel Diseases/microbiology/immunology ; Crohn Disease/microbiology/immunology ; Colitis, Ulcerative/microbiology/immunology ; Dysbiosis/microbiology ; Prevotella/genetics/classification/isolation &amp; purification ; Faecalibacterium prausnitzii/genetics ; Feces/microbiology ; },
abstract = {BACKGROUND: Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of studies investigating the association between gut microbiome and gastrointestinal (GI) diseases in adolescents.<br><br>METHOD: We obtained 16S rRNA-seq datasets for gut microbiome analysis from 202 adolescents, comprising ulcerative colitis (UC), Crohn's disease (CD), obesity (Ob), and healthy controls (HC). We utilized Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to acquire Operational Taxonomic Units (OTUs). Subsequently, we analyzed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) terms and pathway enrichment for the identified OTUs.<br><br>RESULTS: In this study, we investigated the difference between the gut microbiomes in adolescents with GI diseases and those in healthy adolescents using 202 samples of 16S rRNA sequencing data. The distribution of the six main gut microbiota (i.e., unclassified Dorea, unclassified Lachnospiraceae, unclassified Ruminococcus, Faecalibacterium prausnitzii, Prevotella copri, unclassified Sutterella) was different based on the status of obesity and inflammatory diseases. Dysbiosis was observed within Lachnospiraceae in adolescents with inflammatory diseases (i.e., UC and CD), and in adolescents with obesity within Prevotella and Sutterella. More specifically, our results showed that the relative abundance of Faecalibacterium prausnitzii and unclassified Lachnospiraceae was more than 10% and 8% higher, respectively, in the UC group compared to the CD, Ob, and HC groups. Additionally, the Ob group had over 20% and over 3% higher levels of Prevotella copri and unclassified Sutterella, respectively, compared to the UC, CD, and HC groups. Also, inspecting associations between the six specific microbiota and KO terms, we found that the six microbiota -relating KO terms were associated with NOD-like receptor signaling. These six taxa differences may affect the immune system and inflammatory response by affecting NOD-like receptor signaling in the host during critical adolescence.<br><br>CONCLUSION: In this study, we discovered that dysbiosis of the microbial community had varying degrees of influence on the inflammatory and immune response pathways in adolescents with inflammatory diseases and obesity.},
}
@article {pmid39030408,
year = {2024},
author = {Gilbert, JA and Hartmann, EM},
title = {The indoors microbiome and human health.},
journal = {Nature reviews. Microbiology},
volume = {22},
number = {12},
pages = {742-755},
pmid = {39030408},
issn = {1740-1534},
mesh = {Humans ; *Microbiota ; Air Microbiology ; Air Pollution, Indoor ; Built Environment ; },
abstract = {Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.},
}
@article {pmid39029405,
year = {2024},
author = {Kozaeva, E and Eida, AA and Gunady, EF and Dangl, JL and Conway, JM and Brophy, JA},
title = {Roots of synthetic ecology: microbes that foster plant resilience in the changing climate.},
journal = {Current opinion in biotechnology},
volume = {88},
number = {},
pages = {103172},
doi = {10.1016/j.copbio.2024.103172},
pmid = {39029405},
issn = {1879-0429},
mesh = {*Microbiota/physiology ; *Climate Change ; *Plants/microbiology ; Plant Development ; Ecosystem ; Synthetic Biology ; Ecology ; Plant Roots/microbiology ; },
abstract = {Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant-microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.},
}
@article {pmid39025292,
year = {2024},
author = {Guo, X and Zhao, W and Yin, D and Mei, Z and Wang, F and Tiedje, J and Ling, S and Hu, S and Xu, T},
title = {Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124566},
doi = {10.1016/j.envpol.2024.124566},
pmid = {39025292},
issn = {1873-6424},
mesh = {*Zebrafish/genetics ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Sulfonamides/pharmacology ; *Aspirin/pharmacology ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; Sulfamethoxazole/pharmacology ; Water Pollutants, Chemical ; Bacteria/genetics/drug effects ; },
abstract = {Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.},
}
@article {pmid39021442,
year = {2024},
author = {Bowers, RM and Gonzalez-Pena, V and Wardhani, K and Goudeau, D and Blow, MJ and Udwary, D and Klein, D and Vill, AC and Brito, IL and Woyke, T and Malmstrom, RR and Gawad, C},
title = {scMicrobe PTA: near complete genomes from single bacterial cells.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae085},
pmid = {39021442},
issn = {2730-6151},
support = {DP2 CA239145/CA/NCI NIH HHS/United States ; },
abstract = {Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.},
}
@article {pmid39021414,
year = {2024},
author = {Marin, C and Migura-García, L and Rodríguez, JC and Ventero, MP and Pérez-Gracia, MT and Vega, S and Tort-Miró, C and Marco-Fuertes, A and Lorenzo-Rebenaque, L and Montoro-Dasi, L},
title = {Swine farm environmental microbiome: exploring microbial ecology and functionality across farms with high and low sanitary status.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1401561},
pmid = {39021414},
issn = {2297-1769},
abstract = {INTRODUCTION: Stringent regulations in pig farming, such as antibiotic control and the ban on certain additives and disinfectants, complicate disease control efforts. Despite the evolution of microbial communities inside the house environment, they maintain stability over the years, exhibiting characteristics specific to each type of production and, in some cases, unique to a particular company or farm production type. In addition, some infectious diseases are recurrent in specific farms, while other farms never present these diseases, suggesting a connection between the presence of these microorganisms in animals or their environment. Therefore, the aim of this study was to characterise environmental microbiomes of farms with high and low sanitary status, establishing the relationships between both, health status, environmental microbial ecology and its functionality.<br><br>METHODS: For this purpose, 6 pig farms were environmentally sampled. Farms were affiliated with a production company that handle the majority of the pigs slaughtered in Spain. This study investigated the relationship among high health and low health status farms using high throughput 16S rRNA gene sequencing. In addition, to identify ecologically relevant functions and potential pathogens based on the 16S rRNA gene sequences obtained, functional Annotation with PROkaryotic TAXa (FAPROTAX) was performed.<br><br>RESULTS AND DISCUSSION: This study reveals notable differences in microbial communities between farms with persistent health issues and those with good health outcomes, suggesting a need for protocols tailored to address specific challenges. The variation in microbial populations among farms underscores the need for specific and eco-friendly cleaning and disinfection protocols. These measures are key to enhancing the sustainability of livestock farming, ensuring safer products and boosting competitive edge in the market.},
}
@article {pmid39019971,
year = {2024},
author = {Grafmüller, J and Möllmer, J and Muehe, EM and Kammann, CI and Kray, D and Schmidt, HP and Hagemann, N},
title = {Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16555},
pmid = {39019971},
issn = {2045-2322},
mesh = {*Charcoal/chemistry ; *Fertilizers ; *Crops, Agricultural/growth &amp; development ; *Minerals/chemistry ; Nitrogen/chemistry ; Brassica/growth &amp; development ; Soil/chemistry ; Nutrients ; Agriculture/methods ; Magnesium/chemistry ; },
abstract = {Mechanized biochar field application remains challenging due to biochar's poor flowability and bulk density. Granulation of biochar with fertilizer provides a product ready for application with well-established machinery. However, it's unknown whether granulated biochar-based fertilizers (gBBF) are as effective as co-application of non-granulated biochar with fertilizer. Here, we compared a gBBF with a mineral compound fertilizer (control), and with a non-granulated biochar that was co-applied at a rate of 1.1 t ha[-1] with the fertilizer in a white cabbage greenhouse pot trial. Half the pots received heavy rain simulation treatments to investigate nutrient leaching. Crop yields were not significantly increased by biochar without leaching compared to the control. With leaching, cabbage yield increased with gBBF and biochar-co-application by 14% (p > 0.05) and 34% (p < 0.05), respectively. Nitrogen leaching was reduced by 26-35% with both biochar amendments. Biochar significantly reduced potassium, magnesium, and sulfur leaching. Most nitrogen associated with gBBF was released during the trial and the granulated biochar regained its microporosity. Enriching fertilizers with biochar by granulation or co-application can improve crop yields and decrease nutrient leaching. While the gBBF yielded less biomass compared to biochar co-application, improved mechanized field application after granulation could facilitate the implementation of biochar application in agriculture.},
}
@article {pmid39018765,
year = {2024},
author = {Bittleston, LS},
title = {Connecting microbial community assembly and function.},
journal = {Current opinion in microbiology},
volume = {80},
number = {},
pages = {102512},
doi = {10.1016/j.mib.2024.102512},
pmid = {39018765},
issn = {1879-0364},
mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; Biodiversity ; Humans ; },
abstract = {Microbial ecology is moving away from purely descriptive analyses to experiments that can determine the underlying mechanisms driving changes in community assembly and function. More species-rich microbial communities generally have higher functional capabilities depending on if there is positive selection of certain species or complementarity among different species. When building synthetic communities or laboratory enrichment cultures, there are specific choices that can increase the number of species able to coexist. Higher resource complexity or the addition of physical niches are two of the many factors leading to greater biodiversity and associated increases in functional capabilities. We can use principles from community ecology and knowledge of microbial physiology to generate improved microbiomes for use in medicine, agriculture, or environmental management.},
}
@article {pmid39017940,
year = {2024},
author = {Kim, YS and Yun, HS and Lee, JH and Lee, KL and Choi, JS and Won, DH and Kim, YJ and Kim, HS and Yoon, HS},
title = {Comparison of Metabarcoding and Microscopy Methodologies to Analyze Diatom Communities in Five Estuaries Along the Southern Coast of the Korean Peninsula.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {95},
pmid = {39017940},
issn = {1432-184X},
support = {2016R1A6A1A05011910//National Research Foundation of Korea/ ; 2016R1A6A1A05011910//National Research Foundation of Korea/ ; 2021R1I1A205551711//National Research Foundation of Korea/ ; },
mesh = {*Diatoms/classification/growth &amp; development ; *DNA Barcoding, Taxonomic ; *Microscopy/methods ; *Estuaries ; Republic of Korea ; Biodiversity ; Phylogeny ; Ecosystem ; },
abstract = {The study of microalgal communities is critical for understanding aquatic ecosystems. These communities primarily comprise diatoms (Heterokontophyta), with two methods commonly used to study them: Microscopy and metabarcoding. However, these two methods often deliver different results; thus, their suitability for analyzing diatom communities is frequently debated and evaluated. This study used these two methods to analyze the diatom communities in identical water samples and compare the results. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that species belonging to the orders Bacillariales and Naviculales (class Bacillariophyceae) are the most diverse. In the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species (Nitzschia frustulum, Nitzschia inconspicua, Nitzschia intermedia, Navicula gregaria, Navicula perminuta, Navicula recens, Navicula sp.) belonging to the Bacillariaceae and Naviculaceae families. The results of the two methods differed in identifying diatom species in the communities and analyzing their structural characteristics. These results are consistent with the fact that diatoms belonging to the genera Nitzschia and Navicula are abundant in the communities; furthermore, only the Illumina MiSeq data showed the abundance of the Melosira and Entomoneis genera. The results obtained from microscopy were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, to analyze diatom communities effectively and accurately, these two methods should be combined.},
}
@article {pmid39012154,
year = {2024},
author = {Salazar-Jaramillo, L and de la Cuesta-Zuluaga, J and Chica, LA and Cadavid, M and Ley, RE and Reyes, A and Escobar, JS},
title = {Gut microbiome diversity within Clostridia is negatively associated with human obesity.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0062724},
pmid = {39012154},
issn = {2379-5077},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Adult ; Female ; Cross-Sectional Studies ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Body Mass Index ; },
abstract = {UNLABELLED: Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production.<br><br>IMPORTANCE: The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.},
}
@article {pmid39012115,
year = {2024},
author = {Luyt, NA and de Witt, RN and Divol, B and Patterton, HG and Setati, ME and Taillandier, P and Bauer, FF},
title = {Physical cell-cell contact elicits specific transcriptomic responses in wine yeast species.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0057223},
pmid = {39012115},
issn = {2165-0497},
support = {UID85055//National Research Foundation (NRF)/ ; UID83471//National Research Foundation (NRF)/ ; },
mesh = {*Wine/microbiology ; *Saccharomyces cerevisiae/genetics/metabolism ; *Transcriptome ; *Fermentation ; *Gene Expression Regulation, Fungal ; Saccharomycetales/genetics/metabolism ; Gene Expression Profiling ; Vitis/microbiology/genetics ; Cell Wall/metabolism/genetics ; Fungal Proteins/genetics/metabolism ; Microbial Interactions ; },
abstract = {Fermenting grape juice provides a habitat for a well-mapped and evolutionarily relevant microbial ecosystem consisting of many natural or inoculated strains of yeasts and bacteria. The molecular nature of many of the ecological interactions within this ecosystem remains poorly understood, with the partial exception of interactions of a metabolic nature such as competition for nutrients and production of toxic metabolites/peptides. Data suggest that physical contact between species plays a significant role in the phenotypic outcome of interspecies interactions. However, the molecular nature of the mechanisms regulating these phenotypes remains unknown. Here, we present a transcriptomic analysis of physical versus metabolic contact between two wine relevant yeast species, Saccharomyces cerevisiae and Lachancea thermotolerans. The data show that these species respond to the physical presence of the other species. In S. cerevisiae, physical contact results in the upregulation of genes involved in maintaining cell wall integrity, cell wall structural components, and genes involved in the production of H2S. In L. thermotolerans, HSP stress response genes were the most significantly upregulated gene family. Both yeasts downregulated genes belonging to the FLO family, some of which play prominent roles in cellular adhesion. qPCR analysis indicates that the expression of some of these genes is regulated in a species-specific manner, suggesting that yeasts adjust gene expression to specific biotic challenges or interspecies interactions. These findings provide fundamental insights into yeast interactions and evolutionary adaptations of these species to the wine ecosystem.IMPORTANCEWithin the wine ecosystem, yeasts are the most relevant contributors to alcoholic fermentation and wine organoleptic characteristics. While some studies have described yeast-yeast interactions during alcoholic fermentation, such interactions remain ill-defined, and little is understood regarding the molecular mechanisms behind many of the phenotypes observed when two or more species are co-cultured. In particular, no study has investigated transcriptional regulation in response to physical interspecies cell-cell contact, as opposed to the generally better understood/characterized metabolic interactions. These data are of direct relevance to our understanding of microbial ecological interactions in general while also creating opportunities to improve ecosystem-based biotechnological applications such as wine fermentation. Furthermore, the presence of competitor species has rarely been considered an evolutionary biotic selection pressure. In this context, the data reveal novel gene functions. This, and further such analysis, is likely to significantly enlarge the genome annotation space.},
}
@article {pmid39011025,
year = {2024},
author = {Alam, M and Pandit, B and Moin, A and Iqbal, UN},
title = {Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture.},
journal = {Indian journal of microbiology},
volume = {64},
number = {2},
pages = {343-366},
pmid = {39011025},
issn = {0046-8991},
abstract = {Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.},
}
@article {pmid39010847,
year = {2024},
author = {Qing, J and Zhang, L and Li, C and Li, Y},
title = {Mendelian randomization analysis revealed that albuminuria is the key factor affecting socioeconomic status in CKD patients.},
journal = {Renal failure},
volume = {46},
number = {2},
pages = {2367705},
doi = {10.1080/0886022X.2024.2367705},
pmid = {39010847},
issn = {1525-6049},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Albuminuria ; *Renal Insufficiency, Chronic/complications ; *Social Class ; *Glomerular Filtration Rate ; },
abstract = {Previous studies indicate a strong correlation between the incidence of chronic kidney disease (CKD) and lower economic status. However, these studies often struggle to delineate a clear cause-effect relationship, leaving healthcare providers uncertain about how to manage kidney disease in a way that improves patients' financial outcomes. Our study aimed to explore and establish a causal relationship between CKD and socioeconomic status, identifying critical influencing factors. We utilized summary meta-analysis data from the CKDGen Consortium and UK Biobank. Genetic variants identified from these sources served as instrumental variables (IVs) to estimate the association between CKD and socioeconomic status. The presence or absence of CKD, estimated glomerular filtration rate (eGFR), and albuminuria were used as exposures, while income and regional deprivation were analyzed as outcomes. We employed the R packages 'TwoSampleMR' and 'Mendelianrandomization' to conduct both univariable and multivariable Mendelian randomization (MR) analyses, assessing for potential pleiotropy and heterogeneity. Our univariable MR analysis revealed a significant causal relationship between high levels of albuminuria and lower income (OR = 0.84, 95% CI: 0.73-0.96, p = 0.013), with no significant pleiotropy detected. In the multivariable MR analysis, both CKD (OR = 0.867, 95% CI: 0.786-0.957, p = 0.0045) and eGFR (OR = 0.065, 95% CI: 0.010-0.437, p = 0.0049) exhibited significant effects on income. This study underscores that higher albuminuria levels in CKD patients are associated with decreased income and emphasizes the importance of effective management and treatment of albuminuria in CKD patients to mitigate both social and personal economic burdens.},
}
@article {pmid39008123,
year = {2024},
author = {Núñez-Muñoz, LA and Sánchez-García, ME and Calderón-Pérez, B and De la Torre-Almaraz, R and Ruiz-Medrano, R and Xoconostle-Cázares, B},
title = {Metagenomic Analysis of Rhizospheric Bacterial Community of Citrus Trees Expressing Phloem-Directed Antimicrobials.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {93},
pmid = {39008123},
issn = {1432-184X},
support = {SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; CF-2023-G-231//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; },
mesh = {*Rhizosphere ; *Phloem/microbiology/metabolism ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; *Plant Diseases/microbiology ; *Citrus/microbiology ; Plants, Genetically Modified/microbiology/genetics ; Phylogeny ; Metagenomics ; Muramidase/metabolism/genetics ; Plant Proteins/genetics/metabolism ; beta-Defensins/genetics ; RNA, Ribosomal, 16S/genetics ; Anti-Infective Agents/pharmacology/metabolism ; Citrus sinensis/microbiology ; Plant Roots/microbiology ; },
abstract = {Huanglongbing, also known as citrus greening, is currently the most devastating citrus disease with limited success in prevention and mitigation. A promising strategy for Huanglongbing control is the use of antimicrobials fused to a carrier protein (phloem protein of 16 kDa or PP16) that targets vascular tissues. This study investigated the effects of genetically modified citrus trees expressing Citrus sinensis PP16 (CsPP16) fused to human lysozyme and β-defensin-2 on the soil microbiome diversity using 16S amplicon analysis. The results indicated that there were no significant alterations in alpha diversity, beta diversity, phylogenetic diversity, differential abundance, or functional prediction between the antimicrobial phloem-overexpressing plants and the control group, suggesting minimal impact on microbial community structure. However, microbiota diversity analysis revealed distinct bacterial assemblages between the rhizosphere soil and root environments. This study helps to understand the ecological implications of crops expressing phloem-targeted antimicrobials for vascular disease management, with minimal impact on soil microbiota.},
}
@article {pmid39008061,
year = {2024},
author = {Helmy, KG and Abu-Hussien, SH},
title = {Root Rot Management in Common Bean (Phaseolus vulgaris L.) Through Integrated Biocontrol Strategies using Metabolites from Trichoderma harzianum, Serratia marcescens, and Vermicompost Tea.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {94},
pmid = {39008061},
issn = {1432-184X},
mesh = {*Phaseolus/microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; *Serratia marcescens/physiology/metabolism ; *Rhizoctonia/physiology ; *Plant Roots/microbiology ; Biological Control Agents/pharmacology ; Pest Control, Biological ; Antibiosis ; Hypocreales/physiology/metabolism ; Egypt ; Composting ; Soil Microbiology ; },
abstract = {Common bean (Phaseolus vulgaris L.) is an essential food staple and source of income for small-holder farmers across Africa. However, yields are greatly threatened by fungal diseases like root rot induced by Rhizoctonia solani. This study aimed to evaluate an integrated approach utilizing vermicompost tea (VCT) and antagonistic microbes for effective and sustainable management of R. solani root rot in common beans. Fourteen fungal strains were first isolated from infected common bean plants collected across three Egyptian governorates, with R. solani being the most virulent isolate with 50% dominance. Subsequently, the antagonistic potential of vermicompost tea (VCT), Serratia sp., and Trichoderma sp. was assessed against this destructive pathogen. Combinations of 10% VCT and the biocontrol agent isolates displayed potent inhibition of R. solani growth in vitro, prompting in planta testing. Under greenhouse conditions, integrated applications of 5 or 10% VCT with Serratia marcescens, Trichoderma harzianum, or effective microorganisms (EM1) afforded up to 95% protection against pre- and post-emergence damping-off induced by R. solani in common bean cv. Giza 6. Similarly, under field conditions, combining VCT with EM1 (VCT + EM1) or Trichoderma harzianum (VCT + Trichoderma harzianum) substantially suppressed disease severity by 65.6% and 64.34%, respectively, relative to untreated plants. These treatments also elicited defense enzyme activity and distinctly improved growth parameters including 136.68% and 132.49% increases in pod weight per plant over control plants. GC-MS profiling of Trichoderma harzianum, Serratia marcescens, and vermicompost tea (VCT) extracts revealed unique compounds dominated by cyclic pregnane, fatty acid methyl esters, linoleic acid derivatives, and free fatty acids like oleic, palmitic, and stearic acids with confirmed biocontrol and plant growth-promoting activities. The results verify VCT-mediated delivery of synergistic microbial consortia as a sustainable platform for integrated management of debilitating soil-borne diseases, enhancing productivity and incomes for smallholder bean farmers through regeneration of soil health. Further large-scale validation can pave the adoption of this climate-resilient approach for securing food and nutrition security.},
}
@article {pmid39007602,
year = {2024},
author = {Jensen, N and Maldonado-Gomez, M and Krishnakumar, N and Weng, C-Y and Castillo, J and Razi, D and Kalanetra, K and German, JB and Lebrilla, CB and Mills, DA and Taft, DH},
title = {Dietary fiber monosaccharide content alters gut microbiome composition and fermentation.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {8},
pages = {e0096424},
pmid = {39007602},
issn = {1098-5336},
support = {R01DK124193//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; F32HD093185//HHS | National Institutes of Health (NIH)/ ; //Mars (Mars Incorporated)/ ; F32 HD093185/HD/NICHD NIH HHS/United States ; R01 DK124193/DK/NIDDK NIH HHS/United States ; //Gut Microbiome Yogurt and Probiotics Fellowship/ ; //Bill and Melinda Gates Foundation (GF)/ ; },
mesh = {*Fermentation ; *Gastrointestinal Microbiome ; *Dietary Fiber/metabolism ; *Monosaccharides/metabolism/analysis ; Animals ; *Bacteria/classification/metabolism/genetics ; Feces/microbiology/chemistry ; Fatty Acids, Volatile/metabolism ; },
abstract = {UNLABELLED: Members of the mammalian gut microbiota metabolize diverse complex carbohydrates that are not digested by the host, which are collectively labeled "dietary fiber." While the enzymes and transporters that each strain uses to establish a nutrient niche in the gut are often exquisitely specific, the relationship between carbohydrate structure and microbial ecology is imperfectly understood. The present study takes advantage of recent advances in complex carbohydrate structure determination to test the effects of fiber monosaccharide composition on microbial fermentation. Fifty-five fibers with varied monosaccharide composition were fermented by a pooled feline fecal inoculum in a modified MiniBioReactor array system over a period of 72 hours. The content of the monosaccharides glucose and xylose was significantly associated with the reduction of pH during fermentation, which was also predictable from the concentrations of the short-chain fatty acids lactic acid, propionic acid, and the signaling molecule indole-3-acetic acid. Microbiome diversity and composition were also predictable from monosaccharide content and SCFA concentration. In particular, the concentrations of lactic acid and propionic acid correlated with final alpha diversity and were significantly associated with the relative abundance of several of the genera, including Lactobacillus and Dubosiella. Our results suggest that monosaccharide composition offers a generalizable method to compare any dietary fiber of interest and uncover links between diet, gut microbiota, and metabolite production.<br><br>IMPORTANCE: The survival of a microbial species in the gut depends on the availability of the nutrients necessary for that species to survive. Carbohydrates in the form of non-host digestible fiber are of particular importance, and the set of genes possessed by each species for carbohydrate consumption can vary considerably. Here, differences in the monosaccharides that are the building blocks of fiber are considered for their impact on both the survival of different species of microbes and on the levels of microbial fermentation products produced. This work demonstrates that foods with similar monosaccharide content will have consistent effects on the survival of microbial species and on the production of microbial fermentation products.},
}
@article {pmid39003240,
year = {2024},
author = {Vass, M and Székely, AJ and Carlsson-Graner, U and Wikner, J and Andersson, A},
title = {Microeukaryote community coalescence strengthens community stability and elevates diversity.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {8},
pages = {},
pmid = {39003240},
issn = {1574-6941},
support = {2018-05973//Swedish Research Council/ ; },
mesh = {*Biodiversity ; *Diatoms/growth &amp; development ; *Fungi/genetics/classification/growth &amp; development ; Rivers/microbiology ; Seawater/microbiology ; Ciliophora/growth &amp; development/genetics ; Cercozoa/genetics/growth &amp; development ; Microbiota ; Eukaryota/growth &amp; development ; },
abstract = {Mixing of entire microbial communities represents a frequent, yet understudied phenomenon. Here, we mimicked estuarine condition in a microcosm experiment by mixing a freshwater river community with a brackish sea community and assessed the effects of both environmental and community coalescences induced by varying mixing processes on microeukaryotic communities. Signs of shifted community composition of coalesced communities towards the sea parent community suggest asymmetrical community coalescence outcome, which, in addition, was generally less impacted by environmental coalescence. Community stability, inferred from community cohesion, differed among river and sea parent communities, and increased following coalescence treatments. Generally, community coalescence increased alpha diversity and promoted competition from the introduction (or emergence) of additional (or rare) species. These competitive interactions in turn had community stabilizing effect as evidenced by the increased proportion of negative cohesion. The fate of microeukaryotes was influenced by mixing ratios and frequencies (i.e. one-time versus repeated coalescence). Namely, diatoms were negatively impacted by coalescence, while fungi, ciliates, and cercozoans were promoted to varying extents, depending on the mixing ratios of the parent communities. Our study suggests that the predictability of coalescence outcomes was greater when the sea parent community dominated the final community, and this predictability was further enhanced when communities collided repeatedly.},
}
@article {pmid39003046,
year = {2025},
author = {Lamprea Pineda, PA and Demeestere, K and Alvarado-Alvarado, AA and Devlieghere, F and Boon, N and Van Langenhove, H and Walgraeve, C},
title = {Degradation of gaseous hydrocarbons in aerated stirred bioreactors inoculated with Rhodococcus erythropolis: Effect of the carbon source and SIFT-MS method development.},
journal = {Journal of environmental sciences (China)},
volume = {147},
number = {},
pages = {268-281},
doi = {10.1016/j.jes.2023.10.020},
pmid = {39003046},
issn = {1001-0742},
mesh = {*Rhodococcus/metabolism ; *Bioreactors/microbiology ; *Biodegradation, Environmental ; *Hydrocarbons/metabolism ; Carbon/metabolism ; Air Pollutants/metabolism/analysis ; Mass Spectrometry ; Toluene/metabolism ; Xylenes/metabolism ; Butanes/metabolism ; Benzene Derivatives ; Pentanes ; },
abstract = {The study of microbial hydrocarbons removal is of great importance for the development of future bioremediation strategies. In this study, we evaluated the removal of a gaseous mixture containing toluene, m-xylene, ethylbenzene, cyclohexane, butane, pentane, hexane and heptane in aerated stirred bioreactors inoculated with Rhodococcus erythropolis and operated under non-sterile conditions. For the real-time measurement of hydrocarbons, a novel systematic approach was implemented using Selected-Ion Flow Tube Mass Spectrometry (SIFT-MS). The effect of the carbon source (∼9.5 ppmv) on (i) the bioreactors' performance (BR1: dosed with only cyclohexane as a single hydrocarbon versus BR2: dosed with a mixture of the 8 hydrocarbons) and (ii) the evolution of microbial communities over time were investigated. The results showed that cyclohexane reached a maximum removal efficiency (RE) of 53% ± 4% in BR1. In BR2, almost complete removal of toluene, m-xylene and ethylbenzene, being the most water-soluble and easy-to-degrade carbon sources, was observed. REs below 32% were obtained for the remaining compounds. By exposing the microbial consortium to only the five most recalcitrant hydrocarbons, REs between 45% ± 5% and 98% ± 1% were reached. In addition, we observed that airborne microorganisms populated the bioreactors and that the type of carbon source influenced the microbial communities developed. The abundance of species belonging to the genus Rhodococcus was below 10% in all bioreactors at the end of the experiments. This work provides fundamental insights to understand the complex behavior of gaseous hydrocarbon mixtures in bioreactors, along with a systematic approach for the development of SIFT-MS methods.},
}
@article {pmid39002491,
year = {2024},
author = {Meroz, N and Livny, T and Friedman, J},
title = {Quantifying microbial interactions: concepts, caveats, and applications.},
journal = {Current opinion in microbiology},
volume = {80},
number = {},
pages = {102511},
doi = {10.1016/j.mib.2024.102511},
pmid = {39002491},
issn = {1879-0364},
mesh = {*Microbial Interactions ; Ecosystem ; Microbiota ; Bacteria/metabolism/genetics ; },
abstract = {Microbial communities are fundamental to every ecosystem on Earth and hold great potential for biotechnological applications. However, their complex nature hampers our ability to study and understand them. A common strategy to tackle this complexity is to abstract the community into a network of interactions between its members - a phenomenological description that captures the overall effects of various chemical and physical mechanisms that underpin these relationships. This approach has proven useful for numerous applications in microbial ecology, including predicting community dynamics and stability and understanding community assembly and evolution. However, care is required in quantifying and interpreting interactions. Here, we clarify the concept of an interaction and discuss when interaction measurements are useful despite their context-dependent nature. Furthermore, we categorize different approaches for quantifying interactions, highlighting the research objectives each approach is best suited for.},
}
@article {pmid39001714,
year = {2024},
author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ},
title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39001714},
issn = {1751-7370},
support = {GBMF9741//Gordon and Betty Moore Foundation/ ; 714774//European Union's Horizon 2020 Research and Innovation Programme/ ; /ERC_/European Research Council/International ; 947317//European Union's Horizon 2020 Research and Innovation Programme/ ; 735929LPI//Simons Foundation/ ; FL150100038//Australian Research Council Laureate Fellowship/ ; 812811//Simons Foundation/ ; 101087081//European Union's Horizon Europe ERA Chair Program/ ; URF150571//Royal Society University Research Fellowship/ ; },
mesh = {*Phylogeny ; *Archaea/genetics/classification ; Bacteria/genetics/classification ; Evolution, Molecular ; Genome, Bacterial ; Symbiosis ; Ecology ; },
abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.},
}
@article {pmid38995161,
year = {2024},
author = {Seixas, MH and Munroe, JS and Eggleston, EM},
title = {Bacterial diversity and geomicrobiology of Winter Wonderland ice cave, Utah, USA.},
journal = {MicrobiologyOpen},
volume = {13},
number = {4},
pages = {e1426},
pmid = {38995161},
issn = {2045-8827},
support = {//Middlebury College/ ; },
mesh = {Utah ; *Bacteria/classification/genetics/isolation &amp; purification ; *Caves/microbiology ; *Ice ; Soil Microbiology ; Biodiversity ; Microscopy, Electron, Scanning ; Seasons ; Water Microbiology ; },
abstract = {The Winter Wonderland ice cave, located at an elevation of 3140 m above sea level in the Uinta Mountains of northern Utah, USA, maintains a constant sub-zero temperature. Seasonal snowmelt and rain enter the cave, freeze on the surface of the existing ice, and contribute to a 3-m-thick layered ice mass. This ice mass contains organic matter and cryogenic cave carbonates (CCCs) that date back centuries. In this study, samples of ice, liquid water, and exposed CCCs were collected to examine the bacterial communities within the cave and to determine if these communities vary spatially and between sample types. Flow cytometry showed that cell counts are an order of magnitude higher in liquid water samples than in ice. Epifluorescence microscopy and scanning electron microscopy imaging revealed potential coccoid and bacillus microbial morphologies in water samples and putative cells or calcite spherules in the CCCs. The diversity of bacteria associated with soil, identified through sequence-based analysis, supports the hypothesis that water enters the cave by filtering through soil and bedrock. A differential abundance of bacterial taxa was observed between sample types, with the greatest diversity found in CCCs. This supports a geomicrobiological framework where microbes aggregate in the water, sink into a concentrated layer, and precipitate out of the ice with the CCCs, thereby reducing the cell counts in the ice. These CCCs may provide essential nutrients for the bacteria or could themselves be products of biomineralization.},
}
@article {pmid38995046,
year = {2024},
author = {Gibson, C and Jauffur, S and Guo, B and Frigon, D},
title = {Activated sludge microbial community assembly: the role of influent microbial community immigration.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {8},
pages = {e0059824},
pmid = {38995046},
issn = {1098-5336},
support = {RGPIN-2016-06498, STPGP-521349-18//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; McGill Engineering Doctoral Award//Faculty of Engineering, McGill University (Faculty of Engineering, McGill)/ ; },
mesh = {*Sewage/microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Wastewater/microbiology ; Waste Disposal, Fluid/methods ; },
abstract = {Wastewater treatment plants (WWTPs) are host to diverse microbial communities and receive a constant influx of microbes from influent wastewater. However, the impact of immigrants on the structure and activities of the activated sludge (AS) microbial community remains unclear. To gain insight on this phenomenon known as perpetual community coalescence, the current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the microbial populations to reveal the fundamental mechanisms involved in immigration between sewers and AS-WWTP. The immigration dynamics of heterotrophs were analyzed by harvesting wastewater biomass solids from three different sewer systems and adding to synthetic wastewater. Immigrating influent populations were observed to contribute up to 14% of the sequencing reads in the AS. By modeling the net growth rate of taxa, it was revealed that immigrants primarily exhibited low or negative net growth rates. By developing a protocol to reproducibly grow AS-WWTP communities in the lab, we have laid down the foundational principles for the testing of operational factors creating community variations with low noise and appropriate replication. Understanding the processes that drive microbial community diversity and assembly is a key question in microbial ecology. In the future, this knowledge can be used to manipulate the structure of microbial communities and improve system performance in WWTPs.IMPORTANCEIn biological wastewater treatment processes, the microbial community composition is essential in the performance and stability of the system. This study developed a reproducible protocol to investigate the impact of influent immigration (or perpetual coalescence of the sewer and activated sludge communities) with appropriate reproducibility and controls, allowing intrinsic definitions of core and immigrant populations to be established. The method developed herein will allow sequential manipulative experiments to be performed to test specific hypothesis and optimize wastewater treatment processes to meet new treatment goals.},
}
@article {pmid38993674,
year = {2024},
author = {Huang, C and Liu, D and Yang, S and Huang, Y and Wei, X and Zhang, P and Lin, J and Xu, B and Liu, Y and Guo, D and Li, Y and Li, J and Zhang, H},
title = {Effect of time-restricted eating regimen on weight loss is mediated by gut microbiome.},
journal = {iScience},
volume = {27},
number = {7},
pages = {110202},
pmid = {38993674},
issn = {2589-0042},
abstract = {Time-restricted eating (TRE) is a promising obesity management strategy, but weight-loss efficacy varies among participants, and the underlying mechanism is unclear. The study aimed to investigate the role of gut microbiota in weight-loss response during long-term TRE intervention. We analyzed data from 51 obese adults in a 12-month TRE program, categorizing them into distinct weight loss groups (DG) and moderate weight loss groups (MG) based on their TRE responses. Shotgun metagenomic sequencing analysis revealed a significant increase in species closely associated with weight loss effectiveness and metabolic parameter changes in the DG group. Pathways related to fatty acid biosynthesis, glycogen biosynthesis, and nucleotide metabolism were reduced in the DG group and enhanced in the MG group. Next, we identified nine specific species at baseline that contributed better responses to TRE intervention and significant weight loss. Collectively, gut microbiota contributes to responsiveness heterogeneity in TRE and can predict weight-loss effectiveness.},
}
@article {pmid38992757,
year = {2024},
author = {Zeng, X and Liu, Y and Wang, Q and Ma, H and Li, X and Wang, Q and Yang, Q},
title = {Tanning wastewater restructured nitrogen-transforming bacteria communities and promoted N2O emissions in receiving river riparian sediments.},
journal = {Environmental research},
volume = {260},
number = {},
pages = {119580},
doi = {10.1016/j.envres.2024.119580},
pmid = {38992757},
issn = {1096-0953},
mesh = {*Rivers/microbiology/chemistry ; *Wastewater/microbiology/chemistry/analysis ; *Geologic Sediments/microbiology/chemistry ; *Nitrogen/analysis ; *Tanning ; Water Pollutants, Chemical/analysis ; Bacteria ; Denitrification ; Nitrous Oxide/analysis ; },
abstract = {Physicochemical and toxicological characterization of leather tanning wastewater has been widely documented. However, few reports have examined the response of denitrification N2 and N2O emissions in riparian sediments of tannery wastewater-receiving rivers. In this study, [15]N-nitrate labeling was used to reveal the effects of tanning wastewater on denitrification N2 and N2O emission in a wastewater-receiving river (the old Mang River, OMR). OMR riparian sediments were highly polluted with total organic carbon (93.39 mg/kg), total nitrogen (5.00 g/kg) and heavy metals; specifically, Cr, Zn, Cd, and Pb were found at concentrations 47.3, 5.8, 1.6, 4.3, and 2.8 times that in a nearby parallel river without tanning wastewater input (the new Mang River, NMR), respectively. The denitrification N2 emission rates (0.0015 nmol N · g[-1] h[-1]) of OMR riparian sediments were significantly reduced by 2.5 times compared with those from the NMR (p < 0.05), but the N2O emission rates (0.31 nmol N · g[-1] h[-1]) were significantly increased (4.1 times, p < 0.05). Although the dominant nitrogen-transforming bacteria phylum was Proteobacteria in the riparian sediments of both rivers, 11 nitrogen-transforming bacteria genera in the OMR were found to be significantly enriched; five of these were related to pollutant degradation based on linear discriminant analysis (LDA >3). The average activity of the electron transport system in the OMR was 6.3 times lower than that of the NMR (p < 0.05). Among pollution factors, heavy metal complex pollution was the dominant factor driving variations in N2O emissions, microbial community structure, and electron transport system activity. These results provide a new understanding and reference for the treatment of tanning wastewater-receiving rivers.},
}
@article {pmid38987492,
year = {2024},
author = {Ng, MS and Soon, N and Afiq-Rosli, L and Kunning, I and Mana, RR and Chang, Y and Wainwright, BJ},
title = {Highly Diverse Symbiodiniaceae Types Hosted by Corals in a Global Hotspot of Marine Biodiversity.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {92},
pmid = {38987492},
issn = {1432-184X},
mesh = {*Anthozoa/microbiology ; Animals ; *Biodiversity ; *Dinoflagellida/genetics/classification/physiology ; *Symbiosis ; *Coral Reefs ; Papua New Guinea ; Phylogeny ; High-Throughput Nucleotide Sequencing ; },
abstract = {Symbiotic dinoflagellates in the genus Symbiodiniaceae play vital roles in promoting resilience and increasing stress tolerance in their coral hosts. While much of the world's coral succumb to the stresses associated with increasingly severe and frequent thermal bleaching events, live coral cover in Papua New Guinea (PNG) remains some of the highest reported globally despite the historically warm waters surrounding the country. Yet, in spite of the high coral cover in PNG and the acknowledged roles Symbiodiniaceae play within their hosts, these communities have not been characterized in this global biodiversity hotspot. Using high-throughput sequencing of the ITS2 rDNA gene, we profiled the endosymbionts of four coral species, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta, and Porites lutea, across six sites in PNG. Our findings reveal patterns of Cladocopium and Durusdinium dominance similar to other reefs in the Coral Triangle, albeit with much greater intra- and intergenomic variation. Host- and site-specific variations in Symbiodiniaceae type profiles were observed across collection sites, appearing to be driven by environmental conditions. Notably, the extensive intra- and intergenomic variation, coupled with many previously unreported sequences, highlight PNG as a potential hotspot of symbiont diversity. This work represents the first characterization of the coral-symbiont community structure in the PNG marine biodiversity hotspot, serving as a baseline for future studies.},
}
@article {pmid38987022,
year = {2024},
author = {Litchman, E and Villéger, S and Zinger, L and Auguet, JC and Thuiller, W and Munoz, F and Kraft, NJB and Philippot, L and Violle, C},
title = {Refocusing the microbial rare biosphere concept through a functional lens.},
journal = {Trends in ecology &amp; evolution},
volume = {39},
number = {10},
pages = {923-936},
doi = {10.1016/j.tree.2024.06.005},
pmid = {38987022},
issn = {1872-8383},
mesh = {*Microbiota ; Ecosystem ; Biodiversity ; },
abstract = {The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions.},
}
@article {pmid38985714,
year = {2024},
author = {Ugwuanyi, IR and Steele, A and Glamoclija, M},
title = {Microbial Ecology of an Arctic Travertine Geothermal Spring: Implications for Biosignature Preservation and Astrobiology.},
journal = {Astrobiology},
volume = {24},
number = {7},
pages = {734-753},
doi = {10.1089/ast.2023.0130},
pmid = {38985714},
issn = {1557-8070},
mesh = {Arctic Regions ; *Exobiology ; *Hot Springs/microbiology/chemistry ; Mars ; Silicon Dioxide/chemistry ; Svalbard ; Carbonates/chemistry/analysis ; Microbiota ; Temperature ; Biofilms ; },
abstract = {Jotun springs in Svalbard, Norway, is a rare warm environment in the Arctic that actively forms travertine. In this study, we assessed the microbial ecology of Jotun's active (aquatic) spring and dry spring transects. We evaluated the microbial preservation potential and mode, as well as the astrobiological relevance of the travertines to marginal carbonates mapped at Jezero Crater on Mars (the Mars 2020 landing site). Our results revealed that microbial communities exhibited spatial dynamics controlled by temperature, fluid availability, and geochemistry. Amorphous carbonates and silica precipitated within biofilm and on the surface of filamentous microorganisms. The water discharged at the source is warm, with near neutral pH, and undersaturated in silica. Hence, silicification possibly occurred through cooling, dehydration, and partially by a microbial presence or activities that promote silica precipitation. CO2 degassing and possible microbial contributions induced calcite precipitation and travertine formation. Jotun revealed that warm systems that are not very productive in carbonate formation may still produce significant carbonate buildups and provide settings favorable for fossilization through silicification and calcification. Our findings suggest that the potential for amorphous silica precipitation may be essential for Jezero Crater's marginal carbonates because it significantly increases the preservation potential of putative martian organisms.},
}
@article {pmid38983631,
year = {2024},
author = {Hawes, I and García-Maldonado, JQ and Falcón, LI},
title = {Editorial: Exploring microbial mat communities in extreme environments.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1440619},
doi = {10.3389/fmicb.2024.1440619},
pmid = {38983631},
issn = {1664-302X},
}
@article {pmid38982970,
year = {2024},
author = {Jiang, J and Xiang, X and Zhou, Q and Zhou, L and Bi, X and Khanal, SK and Wang, Z and Chen, G and Guo, G},
title = {Optimization of a Novel Engineered Ecosystem Integrating Carbon, Nitrogen, Phosphorus, and Sulfur Biotransformation for Saline Wastewater Treatment Using an Interpretable Machine Learning Approach.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {29},
pages = {12989-12999},
doi = {10.1021/acs.est.4c03160},
pmid = {38982970},
issn = {1520-5851},
mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Sulfur/metabolism ; *Machine Learning ; *Wastewater/chemistry ; *Carbon/metabolism ; Biotransformation ; Ecosystem ; Waste Disposal, Fluid/methods ; Denitrification ; },
abstract = {The denitrifying sulfur (S) conversion-associated enhanced biological phosphorus removal (DS-EBPR) process for treating saline wastewater is characterized by its unique microbial ecology that integrates carbon (C), nitrogen (N), phosphorus (P), and S biotransformation. However, operational instability arises due to the numerous parameters and intricates bacterial interactions. This study introduces a two-stage interpretable machine learning approach to predict S conversion-driven P removal efficiency and optimize DS-EBPR process. Stage one utilized the XGBoost regression model, achieving an R[2] value of 0.948 for predicting sulfate reduction (SR) intensity from anaerobic parameters with feature engineering. Stage two involved the CatBoost classification and regression model integrating anoxic parameters with the predicted SR values for predicting P removal, reaching an accuracy of 94% and an R[2] value of 0.93, respectively. This study identified key environmental factors, including SR intensity (20-45 mg S/L), influent P concentration (<9.0 mg P/L), mixed liquor volatile suspended solids (MLVSS)/mixed liquor suspended solids (MLSS) ratio (0.55-0.72), influent C/S ratio (0.5-1.0), anoxic reaction time (5-6 h), and MLSS concentration (>6.50 g/L). A user-friendly graphic interface was developed to facilitate easier optimization and control. This approach streamlines the determination of optimal conditions for enhancing P removal in the DS-EBPR process.},
}
@article {pmid38982962,
year = {2024},
author = {Sbibih, Y and Saddari, A and Alla, I and Abdesselami, O and Ben Moussa, C and Ezrari, S and Benaissa, E and Ben Lahlou, Y and Elouennass, M and Maleb, A},
title = {Microbial ecology of protective isolation room: Air and Surfaces.},
journal = {La Tunisie medicale},
volume = {102},
number = {7},
pages = {394-398},
pmid = {38982962},
issn = {2724-7031},
mesh = {Humans ; *Air Microbiology ; *Cross Infection/prevention &amp; control/epidemiology/microbiology ; Prospective Studies ; Patients' Rooms/organization &amp; administration/statistics &amp; numerical data ; Patient Isolation/methods ; Hospitals, University ; Immunocompromised Host ; Tunisia/epidemiology ; },
abstract = {INTRODUCTION: Healthcare-associated infections pose a significant public health burden, leading to morbidity, mortality, prolonged hospital stays, and substantial social and economic costs. Immunocompromised patients are at a heightened risk of nosocomial infections.<br><br>AIM: This prospective study conducted at Mohammed VI University Hospital of Oujda aimed to assess the microbial ecology of surfaces and air in an immunosuppressed patient room compared to a double hospitalization room.<br><br>METHODS: Microbiological air purity tests were conducted employing both the sedimentation method and the collision method with the assistance of Microflow Alpha. The sedimentation method used Mueller Hinton with 5% human blood, facilitating the free fall of contaminated dust particles. The collection program employed was set for 10 minutes per 1 m3. For surface sampling, swabs were taken from a 25 cm2 surface. The swabs were immediately forwarded to the Microbiology Laboratory. We carried out both macroscopic and microscopic identification of colonies, followed by definitive biochemical identification using the BD phoenixTM system. Antibiotic susceptibility was assessed through agar diffusion on Muller Hinton medium coupled with the determination of the minimum inhibitory concentration.<br><br>RESULTS: The results revealed a decreased bacterial count within the protective isolation room, in contrast to the standard hospital room. We noted the predominance of coagulase-negative Staphylococcus spp and Bacillus spp. Staphylococcus aureus and Aspergillus spp, common pathogens in healthcare-associated infections, were notably absent in the protective isolation room. The findings underline the pivotal role of hospital environments in the transmission of healthcare-associated infections.<br><br>CONCLUSION: The protective isolation room demonstrated effective control of microbial contamination, with fewer and less resistant germs. The study highlighted the significance of air treatment systems in preventing the spread of opportunistic infections. Our study underscored the critical role of microbiological cleanliness in preventing nosocomial infections.},
}
@article {pmid38982749,
year = {2024},
author = {Schrecengost, A and Rotterová, J and Poláková, K and Čepička, I and Beinart, RA},
title = {Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38982749},
issn = {1751-7370},
support = {//Simons Foundation Early Career Investigator in Marine Microbial Ecology and Evolution Award/ ; 1330406//United States National Science Foundation EPSCoR Track II Cooperative Agreement Award/ ; 23-06004S//Czech Science Foundation/ ; OIA-1655221//National Science Foundation EPSCoR/ ; //Vini&#x10d;n&#xe1; Microscopy Core Facility/ ; LM2023050//MEYS CR/ ; 1919588//National Science Foundation Major Research Instrumentation/ ; },
mesh = {*Symbiosis ; *Ciliophora/classification/genetics/physiology ; *Phylogeny ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 18S/genetics ; DNA, Archaeal/genetics/chemistry ; Sequence Analysis, DNA ; Seawater/microbiology/parasitology ; },
abstract = {Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the ubiquity of these symbioses in anoxic habitats, patterns of symbiont specificity and fidelity are not well known. We surveyed two unrelated, commonly found groups of anaerobic ciliates, the Plagiopylea and Metopida, isolated from anoxic marine sediments. We sequenced host 18S rRNA and symbiont 16S rRNA marker genes as well as the symbiont internal transcribed spacer region from our cultured ciliates to identify hosts and their associated methanogenic symbionts. We found that marine ciliates from both of these co-occurring, divergent groups harbor closely related yet distinct intracellular archaea within the Methanocorpusculum genus. The symbionts appear to be stable at the host species level, but at higher taxonomic levels, there is evidence that symbiont replacements have occurred. Gaining insight into this unique association will deepen our understanding of the complex transmission modes of marine microbial symbionts, and the mutualistic microbial interactions occurring across domains of life.},
}
@article {pmid38980056,
year = {2024},
author = {Henson, MW and Thrash, JC},
title = {Microbial ecology of northern Gulf of Mexico estuarine waters.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0131823},
pmid = {38980056},
issn = {2379-5077},
support = {Simons Investigator in Aquatic Microbial Ecology Award//Simons Foundation (SF)/ ; Marine Microbiology Postdoctoral Fellowship//Simons Foundation (SF)/ ; LEQSF[2014-2017]-RDA-06//Louisiana Board of Regents (LBR)/ ; Lerner Gray grant//American Museum of Natural History (AMNH)/ ; Gulf Research Program Early Career Research Fellowship//National Academies of Sciences, Engineering, and Medicine (NASEM)/ ; LEEC Grant//Louisiana Department of Fish and Wildlife/ ; },
mesh = {Gulf of Mexico ; *Estuaries ; Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology/chemistry ; Louisiana ; Microbiota ; Water Microbiology ; Ecosystem ; Salinity ; },
abstract = {Estuarine and coastal ecosystems are of high economic and ecological importance, owing to their diverse communities and the disproportionate role they play in carbon cycling, particularly in carbon sequestration. Organisms inhabiting these environments must overcome strong natural fluctuations in salinity, nutrients, and turbidity, as well as numerous climate change-induced disturbances such as land loss, sea level rise, and, in some locations, increasingly severe tropical cyclones that threaten to disrupt future ecosystem health. The northern Gulf of Mexico (nGoM) along the Louisiana coast contains dozens of estuaries, including the Mississippi-Atchafalaya River outflow, which dramatically influence the region due to their vast upstream watershed. Nevertheless, the microbiology of these estuaries and surrounding coastal environments has received little attention. To improve our understanding of microbial ecology in the understudied coastal nGoM, we conducted a 16S rRNA gene amplicon survey at eight sites and multiple time points along the Louisiana coast and one inland swamp spanning freshwater to high brackish salinities, totaling 47 duplicated Sterivex (0.2-2.7 µm) and prefilter (>2.7 µm) samples. We cataloged over 13,000 Amplicon Sequence ariants (ASVs) from common freshwater and marine clades such as SAR11 (Alphaproteobacteria), Synechococcus (Cyanobacteria), and acI and Candidatus Actinomarina (Actinobacteria). We observed correlations with freshwater or marine habitats in many organisms and characterized a group of taxa with specialized distributions across brackish water sites, supporting the hypothesis of an endogenous brackish-water community. Additionally, we observed brackish-water associations for several aquatic clades typically considered marine or freshwater taxa, such as SAR11 subclade II, SAR324, and the acI Actinobacteria. The data presented here expand the geographic coverage of microbial ecology in estuarine communities, help delineate the native and transitory members of these environments, and provide critical aquatic microbiological baseline data for coastal and estuarine sites in the nGoM.IMPORTANCEEstuarine and coastal waters are diverse ecosystems influenced by tidal fluxes, interconnected wetlands, and river outflows, which are of high economic and ecological importance. Microorganisms play a pivotal role in estuaries as "first responders" and ecosystem architects, yet despite their ecological importance, they remain underrepresented in microbial studies compared to open ocean environments. This leads to substantial knowledge gaps that are important for understanding global biogeochemical cycling and making decisions about conservation and management strategies in these environments. Our study makes key contributions to the microbial ecology of estuarine and coastal habitats in the northern Gulf of Mexico. Our microbial community data support the concept of a globally distributed, core brackish microbiome and emphasize previously underrecognized brackish-water taxa. Given the projected worsening of land loss, oil spills, and natural disasters in this region, our results will serve as important baseline data for researchers investigating the microbial communities found across estuaries.},
}
@article {pmid38980052,
year = {2024},
author = {Flinkstrom, Z and Bryson, S and Candry, P and Winkler, M-KH},
title = {Metagenomic clustering links specific metabolic functions to globally relevant ecosystems.},
journal = {mSystems},
volume = {9},
number = {8},
pages = {e0057324},
pmid = {38980052},
issn = {2379-5077},
support = {DE-SC0020356//U.S. Department of Energy (DOE)/ ; },
mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Ecosystem ; Cluster Analysis ; Microbiota/genetics ; },
abstract = {UNLABELLED: Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome's functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute's Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data.<br><br>IMPORTANCE: Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome's metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.},
}
@article {pmid38979877,
year = {2024},
author = {Overgaard, CK and Jamy, M and Radutoiu, S and Burki, F and Dueholm, MKD},
title = {Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.},
journal = {Molecular ecology resources},
volume = {24},
number = {7},
pages = {e13991},
doi = {10.1111/1755-0998.13991},
pmid = {38979877},
issn = {1755-0998},
support = {9041-00236B//Danmarks Frie Forskningsfond/ ; 2021-04055//Vetenskapsr&#xe5;det/ ; 101044505/ERC_/European Research Council/International ; },
mesh = {*Eukaryota/genetics/classification ; *Computational Biology/methods ; *Benchmarking ; *High-Throughput Nucleotide Sequencing/methods ; *rRNA Operon/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Phylogeny ; },
abstract = {The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operon clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing strategies (PacBio circular consensus sequencing and two Nanopore approaches using unique molecular identifiers) and three tools for resolving amplicons sequence variants (ASVs) (USEARCH, VSEARCH, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essentially error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples, which enables us to identify previously undescribed microeukaryotic lineages.},
}
@article {pmid38974332,
year = {2024},
author = {Johnston, JT and Quoc, BN and Abrahamson, B and Candry, P and Ramon, C and Cash, KJ and Saccomano, SC and Samo, TJ and Ye, C and Weber, PK and Winkler, MH and Mayali, X},
title = {Increasing aggregate size reduces single-cell organic carbon incorporation by hydrogel-embedded wetland microbes.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae086},
pmid = {38974332},
issn = {2730-6151},
abstract = {Microbial degradation of organic carbon in sediments is impacted by the availability of oxygen and substrates for growth. To better understand how particle size and redox zonation impact microbial organic carbon incorporation, techniques that maintain spatial information are necessary to quantify elemental cycling at the microscale. In this study, we produced hydrogel microspheres of various diameters (100, 250, and 500 μm) and inoculated them with an aerobic heterotrophic bacterium isolated from a freshwater wetland (Flavobacterium sp.), and in a second experiment with a microbial community from an urban lacustrine wetland. The hydrogel-embedded microbial populations were incubated with [13]C-labeled substrates to quantify organic carbon incorporation into biomass via nanoSIMS. Additionally, luminescent nanosensors enabled spatially explicit measurements of oxygen concentrations inside the microspheres. The experimental data were then incorporated into a reactive-transport model to project long-term steady-state conditions. Smaller (100 μm) particles exhibited the highest microbial cell-specific growth per volume, but also showed higher absolute activity near the surface compared to the larger particles (250 and 500 μm). The experimental results and computational models demonstrate that organic carbon availability was not high enough to allow steep oxygen gradients and as a result, all particle sizes remained well-oxygenated. Our study provides a foundational framework for future studies investigating spatially dependent microbial activity in aggregates using isotopically labeled substrates to quantify growth.},
}
@article {pmid38973247,
year = {2024},
author = {Akay, C and Ulrich, N and Rocha, U and Ding, C and Adrian, L},
title = {Sequential Anaerobic-Aerobic Treatment Enhances Sulfamethoxazole Removal: From Batch Cultures to Observations in a Large-Scale Wastewater Treatment Plant.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {28},
pages = {12609-12620},
pmid = {38973247},
issn = {1520-5851},
mesh = {*Sulfamethoxazole/metabolism ; *Wastewater/chemistry ; Anaerobiosis ; Waste Disposal, Fluid ; Water Pollutants, Chemical/metabolism ; Aerobiosis ; },
abstract = {Sulfamethoxazole (SMX) passes through conventional wastewater treatment plants (WWTPs) mainly unaltered. Under anoxic conditions sulfate-reducing bacteria can transform SMX but the fate of the transformation products (TPs) and their prevalence in WWTPs remain unknown. Here, we report the anaerobic formation and aerobic degradation of SMX TPs. SMX biotransformation was observed in nitrate- and sulfate-reducing enrichment cultures. We identified 10 SMX TPs predominantly showing alterations in the heterocyclic and N[4]-arylamine moieties. Abiotic oxic incubation of sulfate-reducing culture filtrates led to further degradation of the major anaerobic SMX TPs. Upon reinoculation under oxic conditions, all anaerobically formed TPs, including the secondary TPs, were degraded. In samples collected at different stages of a full-scale municipal WWTP, anaerobically formed SMX TPs were detected at high concentrations in the primary clarifier and digested sludge units, where anoxic conditions were prevalent. Contrarily, their concentrations were lower in oxic zones like the biological treatment and final effluent. Our results suggest that anaerobically formed TPs were eliminated in the aerobic treatment stages, consistent with our observations in batch biotransformation experiments. More generally, our findings highlight the significance of varying redox states determining the fate of SMX and its TPs in engineered environments.},
}
@article {pmid38971962,
year = {2024},
author = {Zhang, W and Zhang, F and Wu, Y and Liu, J and Fahad, S and Li, Z and Zhao, S and Qiu, Z and Zhu 朱, M&#x58a8;},
title = {Powdery Mildew of Xanthium strumarium Caused by Podosphaera xanthii in central China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-05-24-1062-PDN},
pmid = {38971962},
issn = {0191-2917},
abstract = {Xanthium strumarium, known as cocklebur, is an annual herb and has been used in traditional Chinese medicine. In October 2020, powdery mildew-like disease signs and symptoms were observed on X. strumarium grown in a crop field, Xinxiang city, Henan Province, China (35.36076° N, 113.93467° E). The specimen (PX-XS2023) was stored in Xinxiang Key Laboratory of Plant Stress Biology. White colonies in irregular or coalesced circular shaped-lesions were abundant on both ad- and abaxial surfaces of leaves and covered up to 99 % of the leaf area. Some of the infected leaves were senesced. More than 70 % of plants (n = 130) exhibited these signs and symptoms. Conidiophores were straight or slightly curved, 55 to 160 × 11 to 13 μm composed of foot-cells, shorter cells and conidia. Conidia were ellipsoid to oval, 29 to 40 × 14 to 20 μm (n = 50), with a length/width ration of 2.0 to 2.5, containing fibrosin bodies. Dark brown to black chasmothecia were found on infected leaves. The appendages were mycelium-shaped and at the base of scattered or gregarious chasmothecia (n = 50, 70 to 120 μm in diameter). Asci were 55 to 80 × 50 to 65 μm (n=30). These morphological characteristics were consistent with those of Podosphaera xanthii (Braun and Cook 2012). The internal transcribed spacer (ITS) region and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) region of the fungus (PX-XS2023) were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022) according to a previously reported method (Zhu et al. 2022). The resulting sequences were respectively deposited into GenBank (Accession No. MW300956 and PP236083). BLASTn analysis indicated that the sequences were respectively 99.82 % (564/565) and 100% (272/272) identical to P. xanthii (MT260063 and ON075658). The phylogenetic analysis indicated that the strain PX-XS2023 and P. xanthii were clustered into a same branch. Therefore, the causal agent of powdery mildew on X. strumarium was P. xanthii. To conduct pathogenicity assays, mature leaves of five healthy X. strumarium (height in 50 centimeters) were inoculated with fungal conidia by gently pressing surfaces of infested leaves onto leaves of healthy plants (Zhu et al. 2020). Five untreated plants served as controls. The controls and inoculated plants were separately maintained in greenhouses (humidity, 60%; light/dark, 16 h/8 h; temperature, 18°C). Eight days post-inoculation, signs of powdery mildew were detectable on inoculated plants, however, the controls were asymptomatic. Thus, the fungal pathogen was morphologically and molecularly identified and confirmed as P. xanthii. This powdery mildew caused by P. xanthii was previously reported on X. strumarium in Korea, Russia and India (Farr and Rossman, 2021). In addition, P. xanthii was recorded on X. strumarium in Xinjiang Province, China (Tai 1979). However, this is the first report of P. xanthii on X. strumarium in central China, where is around 3000 km away from Xinjiang Province with geographically differences. The sudden presence of powdery mildew caused by P. xanthii may adversely affect plant health and thus reduce medical value of X. strumarium. Therefore, the identification and confirmation of P. xanthii infecting X. strumarium enhance the knowledge on the hosts of this pathogen in China and will provide fundamental information for disease control in the future.},
}
@article {pmid38969462,
year = {2024},
author = {Chen, Y and Zhou, H and Gao, H and Su, Z and Li, X and Qi, P and Li, T and Hu, C and Li, Z and Bi, Z and Xing, X and Yang, J and Chen, C and Ma, K and Chen, J},
title = {Comprehensive comparison of water quality risk and microbial ecology between new and old cast iron pipe distribution systems.},
journal = {Journal of environmental sciences (China)},
volume = {146},
number = {},
pages = {55-66},
doi = {10.1016/j.jes.2023.05.020},
pmid = {38969462},
issn = {1001-0742},
mesh = {*Iron ; *Water Quality ; *Biofilms ; Corrosion ; *Water Supply ; Water Microbiology ; Drinking Water/microbiology/chemistry ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Water Pollutants, Chemical/analysis ; Trihalomethanes/analysis ; },
abstract = {The effects of cast iron pipe corrosion on water quality risk and microbial ecology in drinking water distribution systems (DWDSs) were investigated. It was found that trihalomethane (THMs) concentration and antibiotic resistance genes (ARGs) increased sharply in the old DWDSs. Under the same residual chlorine concentration conditions, the adenosine triphosphate concentration in the effluent of old DWDSs (Eff-old) was significantly higher than that in the effluent of new DWDSs. Moreover, stronger bioflocculation ability and weaker hydrophobicity coexisted in the extracellular polymeric substances of Eff-old, meanwhile, iron particles could be well inserted into the structure of the biofilms to enhance the mechanical strength and stability of the biofilms, hence enhancing the formation of THMs. Old DWDSs significantly influenced the microbial community of bulk water and triggered stronger microbial antioxidant systems response, resulting in higher ARGs abundance. Corroded cast iron pipes induced a unique interaction system of biofilms, chlorine, and corrosion products. Therefore, as the age of cast iron pipes increases, the fluctuation of water quality and microbial ecology should be paid more attention to maintain the safety of tap water.},
}
@article {pmid38969457,
year = {2024},
author = {Chen, SC and Musat, F and Richnow, HH and Krüger, M},
title = {Microbial diversity and oil biodegradation potential of northern Barents Sea sediments.},
journal = {Journal of environmental sciences (China)},
volume = {146},
number = {},
pages = {283-297},
doi = {10.1016/j.jes.2023.12.010},
pmid = {38969457},
issn = {1001-0742},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Biodegradation, Environmental ; Arctic Regions ; *Microbiota ; Petroleum/metabolism ; Bacteria/classification/metabolism/genetics ; Archaea/metabolism/classification/genetics ; Water Pollutants, Chemical/analysis/metabolism ; Biodiversity ; },
abstract = {The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.},
}
@article {pmid38969451,
year = {2024},
author = {Ma, B and Zheng, L and Xie, B and Ma, L and Jia, M and Xie, C and Hu, C and Ulbricht, M and Wei, Y},
title = {Sustainable wastewater treatment and reuse in space.},
journal = {Journal of environmental sciences (China)},
volume = {146},
number = {},
pages = {237-240},
doi = {10.1016/j.jes.2023.08.023},
pmid = {38969451},
issn = {1001-0742},
mesh = {*Wastewater ; *Waste Disposal, Fluid/methods ; *Water Purification/methods ; Space Flight ; },
abstract = {Exploring the vast extraterrestrial space is an inevitable trend with continuous human development. Water treatment and reuse are crucial in the limited and closed space that is available in spaceships or long-term use space bases that will be established in the foreseeable future. Dedicated water treatment technologies have experienced iterative development for more than 60 years since the first manned spaceflight was successfully launched. Herein, we briefly review the related wastewater characteristics and the history of water treatment in space stations, and we focus on future challenges and perspectives, aiming at providing insights for optimizing wastewater treatment technologies and closing the water cycle in future.},
}
@article {pmid38968348,
year = {2024},
author = {Miettinen, TP and Gomez, AL and Wu, Y and Wu, W and Usherwood, TR and Hwang, Y and Roller, BRK and Polz, MF and Manalis, SR},
title = {Cell size, density, and nutrient dependency of unicellular algal gravitational sinking velocities.},
journal = {Science advances},
volume = {10},
number = {27},
pages = {eadn8356},
pmid = {38968348},
issn = {2375-2548},
mesh = {*Cell Size ; *Nutrients/metabolism ; Gravitation ; Phytoplankton/physiology/metabolism ; Photosynthesis ; Microalgae/metabolism ; },
abstract = {Eukaryotic phytoplankton, also known as algae, form the basis of marine food webs and drive marine carbon sequestration. Algae must regulate their motility and gravitational sinking to balance access to light at the surface and nutrients in deeper layers. However, the regulation of gravitational sinking remains largely unknown, especially in motile species. Here, we quantify gravitational sinking velocities according to Stokes' law in diverse clades of unicellular marine microalgae to reveal the cell size, density, and nutrient dependency of sinking velocities. We identify a motile algal species, Tetraselmis sp., that sinks faster when starved due to a photosynthesis-driven accumulation of carbohydrates and a loss of intracellular water, both of which increase cell density. Moreover, the regulation of cell sinking velocities is connected to proliferation and can respond to multiple nutrients. Overall, our work elucidates how cell size and density respond to environmental conditions to drive the vertical migration of motile algae.},
}
@article {pmid38965531,
year = {2024},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {148},
pmid = {38965531},
issn = {1741-7007},
support = {Intramural Research Program//U.S. National Library of Medicine/ ; },
mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; },
abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.<br><br>RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.<br><br>CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.},
}
@article {pmid38964855,
year = {2024},
author = {Zhao, F and Wang, B and Cui, Q and Wu, Y},
title = {Genetically modified indigenous Pseudomonas aeruginosa drove bacterial community to change positively toward microbial enhanced oil recovery applications.},
journal = {Journal of applied microbiology},
volume = {135},
number = {7},
pages = {},
doi = {10.1093/jambio/lxae168},
pmid = {38964855},
issn = {1365-2672},
support = {31700117//National Natural Science Foundation of China/ ; 6096//Qufu Normal University/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/metabolism ; *Petroleum/metabolism ; *Surface-Active Agents/metabolism ; Biodegradation, Environmental ; Bacteria/genetics/metabolism/classification ; Hydrocarbons/metabolism ; Microbiota ; },
abstract = {AIMS: Microbial enhanced oil recovery (MEOR) is cost-effective and eco-friendly for oil exploitation. Genetically modified biosurfactants-producing high-yield strains are promising for ex-situ MEOR. However, can they survive and produce biosurfactants in petroleum reservoirs for in-situ MEOR? What is their effect on the native bacterial community?<br><br>METHODS AND RESULTS: A genetically modified indigenous biosurfactants-producing strain Pseudomonas aeruginosa PrhlAB was bioaugmented in simulated reservoir environments. Pseudomonas aeruginosa PrhlAB could stably colonize in simulated reservoirs. Biosurfactants (200&#xa0;mg l-1) were produced in simulated reservoirs after bio-augmenting strain PrhlAB. The surface tension of fluid was reduced to 32.1 mN m-1. Crude oil was emulsified with an emulsification index of 60.1%. Bio-augmenting strain PrhlAB stimulated the MEOR-related microbial activities. Hydrocarbon-degrading bacteria and biosurfactants-producing bacteria were activated, while the hydrogen sulfide-producing bacteria were inhibited. Bio-augmenting P. aeruginosa PrhlAB reduced the diversity of bacterial community, and gradually simplified the species composition. Bacteria with oil displacement potential became dominant genera, such as Shewanella, Pseudomonas, and Arcobacter.<br><br>CONCLUSIONS: Culture-based and sequence-based analyses reveal that genetically modified biosurfactants-producing strain P. aeruginosa PrhlAB are promising for in-situ MEOR as well.},
}
@article {pmid38962127,
year = {2024},
author = {Lange, E and Kranert, L and Krüger, J and Benndorf, D and Heyer, R},
title = {Microbiome modeling: a beginner's guide.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1368377},
pmid = {38962127},
issn = {1664-302X},
abstract = {Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.},
}
@article {pmid38960913,
year = {2024},
author = {Bischof, PSP and Bartolomaeus, TUP and Löber, U and Bleidorn, C},
title = {Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {91},
pmid = {38960913},
issn = {1432-184X},
support = {F01KI1909A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {Animals ; *Diptera/microbiology ; *Larva/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic ; Kelp/microbiology ; },
abstract = {Coelopidae (Diptera), known as kelp flies, exhibit an ecological association with beached kelp and other rotting seaweeds. This unique trophic specialization necessitates significant adaptations to overcome the limitations of an algal diet. We aimed to investigate whether the flies' microbiome could be one of these adaptive mechanisms. Our analysis focused on assessing composition and diversity of adult and larval microbiota of the kelp fly Coelopa frigida. Feeding habits of the larvae of this species have been subject of numerous studies, with debates whether they directly consume kelp or primarily feed on associated bacteria. By using a 16S rRNA metabarcoding approach, we found that the larval microbiota displayed considerably less diversity than adults, heavily dominated by only four operational taxonomic units (OTUs). Phylogenetic placement recovered the most dominant OTU of the larval microbiome, which is the source of more than half of all metabarcoding sequence reads, as an undescribed genus of Orbaceae (Gammaproteobacteria). Interestingly, this OTU is barely found among the 15 most abundant taxa of the adult microbiome, where it is responsible for less than 2% of the metabarcoding sequence reads. The other three OTUs dominating the larval microbiome have been assigned as Psychrobacter (Gammaproteobacteria), Wohlfahrtiimonas (Gammaproteobacteria), and Cetobacterium (Fusobacteriota). Moreover, we also uncovered a distinct shift in the functional composition between the larval and adult stages, where our taxonomic profiling suggests a significant decrease in functional diversity in larval samples. Our study offers insights into the microbiome dynamics and functional composition of Coelopa frigida.},
}
@article {pmid38960411,
year = {2024},
author = {Mafune, KK and Kasson, MT and Winkler, MH},
title = {Building blocks toward sustainable biofertilizers: variation in arbuscular mycorrhizal spore germination when immobilized with diazotrophic bacteria in biodegradable hydrogel beads.},
journal = {Journal of applied microbiology},
volume = {135},
number = {7},
pages = {},
doi = {10.1093/jambio/lxae167},
pmid = {38960411},
issn = {1365-2672},
support = {2021 postdoctoral//Washington Research Foundation/ ; //Mycological Society of America/ ; 2023-67013-4017//National Institute of Food and Agriculture/ ; },
mesh = {*Mycorrhizae/physiology ; *Spores, Fungal/growth &amp; development ; *Hydrogels ; *Azospirillum brasilense/metabolism ; *Fertilizers/analysis ; Alginates ; },
abstract = {AIM: We investigated whether there was interspecies and intraspecies variation in spore germination of 12 strains of arbuscular mycorrhizal fungi when co-entrapped with the diazotrophic plant growth-promoting bacteria, Azospirillum brasilense Sp7 in alginate hydrogel beads.<br><br>METHODS AND RESULTS: Twelve Rhizophagus irregularis, Rhizophagus intraradices, and Funneliformis mosseae strains were separately combined with a live culture of Azospirillum brasilense Sp7. Each fungal-bacterial consortia was supplemented with sodium alginate to a 2% concentration (v/v) and cross-linked in calcium chloride (2%&#xa0;w/v) to form biodegradable hydrogel beads. One hundred beads from each combination (total of 1200) were fixed in solidified modified Strullu and Romand media. Beads were observed for successful spore germination and bacterial growth over 14 days. In all cases, successful growth of A. brasilense was observed. For arbuscular mycorrhizal fungi, interspecies variation in spore germination was observed, with R. intraradices having the highest germination rate (64.3%), followed by R. irregularis (45.5%) and F. mosseae (40.3%). However, a difference in intraspecies germination was only observed among strains of R. irregularis and F. mosseae. Despite having varying levels of germination, even the strains with the lowest potential were still able to establish with the plant host Brachypodium distachyon in a model system.<br><br>CONCLUSIONS: Arbuscular mycorrhizal spore germination varied across strains when co-entrapped with a diazotrophic plant growth-promoting bacteria. This demonstrates that hydrogel beads containing a mixed consortium hold potential as a sustainable biofertilizer and that compatibility tests remain an important building block when aiming to create a hydrogel biofertilizer that encases a diversity of bacteria and fungi. Moving forward, further studies should be conducted to test the efficacy of these hydrogel biofertilizers on different crops across varying climatic conditions in order to optimize their potential.},
}
@article {pmid38959887,
year = {2024},
author = {Perruzza, L and Rezzonico Jost, T and Raneri, M and Gargari, G and Palatella, M and De Ponte Conti, B and Seehusen, F and Heckmann, J and Viemann, D and Guglielmetti, S and Grassi, F},
title = {Protection from environmental enteric dysfunction and growth improvement in malnourished newborns by amplification of secretory IgA.},
journal = {Cell reports. Medicine},
volume = {5},
number = {7},
pages = {101639},
pmid = {38959887},
issn = {2666-3791},
support = {INV-004078/GATES/Bill &amp; Melinda Gates Foundation/United States ; },
mesh = {Animals ; *Immunoglobulin A, Secretory/metabolism ; *Malnutrition/immunology ; Mice ; Female ; *Gastrointestinal Microbiome ; Animals, Newborn ; Humans ; Apyrase/metabolism ; Infant, Newborn ; },
abstract = {Environmental enteric dysfunction (EED) is a condition associated with malnutrition that can progress to malabsorption and villous atrophy. Severe EED results in linear growth stunting, slowed neurocognitive development, and unresponsiveness to oral vaccines. Prenatal exposure to malnutrition and breast feeding by malnourished mothers replicates EED. Pups are characterized by deprivation of secretory IgA (SIgA) and altered development of the gut immune system and microbiota. Extracellular ATP (eATP) released by microbiota limits T follicular helper (Tfh) cell activity and SIgA generation in Peyer's patches (PPs). Administration of a live biotherapeutic releasing the ATP-degrading enzyme apyrase to malnourished pups restores SIgA levels and ameliorates stunted growth. SIgA is instrumental in improving the growth and intestinal immune competence of mice while they are continuously fed a malnourished diet. The analysis of microbiota composition suggests that amplification of endogenous SIgA may exert a dominant function in correcting malnourishment dysbiosis and its consequences on host organisms, irrespective of the actual microbial ecology.},
}
@article {pmid38958675,
year = {2024},
author = {Dendooven, L and Pérez-Hernández, V and Navarro-Pérez, G and Tlalmis-Corona, J and Navarro-Noya, YE},
title = {Spatial and Temporal Shifts of Endophytic Bacteria in Conifer Seedlings of Abies religiosa (Kunth) Schltdl. &amp; Cham.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {90},
pmid = {38958675},
issn = {1432-184X},
support = {591213//Consejo Nacional de Humanidades Ciencia y Tecnolog&#xed;a (CONAHCyT)/ ; INFR-2015-01-253217//Consejo Nacional de Humanidades Ciencia y Tecnolog&#xed;a (CONAHCyT)/ ; },
mesh = {*Seedlings/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *Endophytes/classification/isolation &amp; purification/physiology/genetics ; *RNA, Ribosomal, 16S/genetics ; *Abies/microbiology ; *Plant Roots/microbiology ; Soil Microbiology ; Biodiversity ; Microbiota ; DNA, Bacterial/genetics ; },
abstract = {Endophytes play an important role in plant development, survival, and establishment, but their temporal dynamics in young conifer plants are still largely unknown. In this study, the bacterial community was determined by metabarcoding of the 16S rRNA gene in the rhizoplane, roots, and aerial parts of 1- and 5-month-old seedlings of natural populations of Abies religiosa (Kunth) Schltdl. &amp; Cham. In 1-month-old seedlings, Pseudomonas dominated aerial parts (relative abundance 71.6%) and roots (37.9%). However, the roots exhibited significantly higher bacterial species richness than the aerial parts, with the dissimilarity between these plant sections mostly explained by the loss of bacterial amplification sequence variants. After 5 months, Mucilaginibacter dominated in the rhizoplane (9.0%), Streptomyces in the roots (12.2%), and Pseudomonas in the aerial parts (18.1%). The bacterial richness and community structure differed significantly between the plant sections, and these variations were explained mostly by 1-for-1 substitution. The relative abundance of putative metabolic pathways significantly differed between the plant sections at both 1 and 5 months. All the dominant bacterial genera (e.g., Pseudomonas and Burkholderia-Caballeronia-Paraburkholderia) have been reported to have plant growth-promoting capacities and/or antagonism against pathogens, but what defines their role for plant development has still to be determined. This investigation improves our understanding of the early plant-bacteria interactions essential for natural regeneration of A. religiosa forest.},
}
@article {pmid38955825,
year = {2024},
author = {Pan, H and Wattiez, R and Gillan, D},
title = {Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.},
journal = {Current microbiology},
volume = {81},
number = {8},
pages = {257},
pmid = {38955825},
issn = {1432-0991},
support = {No.2023-BSBA-024//Joint Funds of the Natural Science Foundation of Liaoning Province of China/ ; },
mesh = {*Soil Microbiology ; *Proteomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; Fungi/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; Computational Biology/methods ; },
abstract = {Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.},
}
@article {pmid38955821,
year = {2024},
author = {Weisse, T and Pröschold, T and Kammerlander, B and Sonntag, B and Schicker, L},
title = {Numerical and Thermal Response of the Bacterivorous Ciliate Colpidium kleini, a Species Potentially at Risk of Extinction by Rising Water Temperatures.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {89},
pmid = {38955821},
issn = {1432-184X},
support = {10.55776/P32714//Austrian Science Fund/ ; DOC fForte 22883//&#xd6;sterreichischen Akademie der Wissenschaften/ ; },
mesh = {*Ciliophora/physiology/growth &amp; development/classification/isolation &amp; purification ; Lakes/microbiology/parasitology ; Temperature ; Phylogeny ; Extinction, Biological ; Bacteria/classification/isolation &amp; purification/genetics ; },
abstract = {We investigated the food-dependent growth and thermal response of the freshwater ciliate Colpidium kleini using numerical response (NR) experiments. This bacterivorous ciliate occurs in lotic water and the pelagial of lakes and ponds. The C. kleini strain used in this work was isolated from a small alpine lake and identified by combining detailed morphological inspections with molecular phylogeny. Specific growth rates (rmax) were measured from 5 to 21 °C. The ciliate did not survive at 22 °C. The threshold bacterial food levels (0.3 - 2.2 × 10[6] bacterial cells mL[-1]) matched the bacterial abundance in the alpine lake from which C. kleini was isolated. The food threshold was notably lower than previously reported for C. kleini and two other Colpidium species. The threshold was similar to levels reported for oligotrich and choreotrich ciliates if expressed in terms of bacterial biomass (0.05 - 0.43 mg C L[-1]). From the NR results, we calculated physiological mortality rates at zero food concentration. The mean mortality (0.55 ± 0.17 d[-1]) of C. kleini was close to the mean estimate obtained for other planktonic ciliates that do not encyst. We used the data obtained by the NR experiments to fit a thermal performance curve (TPC). The TPC yielded a temperature optimum at 17.3 °C for C. kleini, a maximum upper thermal tolerance limit of 21.9 °C, and a thermal safety margin of 4.6 °C. We demonstrated that combining NR with TPC analysis is a powerful tool to predict better a species' fitness in response to temperature and food.},
}
@article {pmid38954336,
year = {2024},
author = {Benammar, L and Menasria, T and Dibi, AR},
title = {Deciphering the geochemical influences on bacterial diversity and communities among two Algerian hot springs.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {32},
pages = {44848-44862},
pmid = {38954336},
issn = {1614-7499},
mesh = {*Hot Springs/microbiology ; Algeria ; *Bacteria ; *RNA, Ribosomal, 16S ; Biodiversity ; Archaea ; },
abstract = {Northeastern Algeria boasts numerous hot springs, yet these hydrothermal sites remain largely unexplored for their microbial ecology. The present study explores the bacterial abundance and diversity within two distinct Algerian hot springs (Hammam Saïda and Hammam Debagh) and investigates the link between the prevailing bacteria with geochemical parameters. High-throughput 16S rRNA gene sequencing of water and sediment samples revealed a bacterial dominance of 99.85-91.16% compared to Archaea (0.14-0.66%) in both springs. Interestingly, Saïda hot spring, characterized by higher temperatures and sodium content, harbored a community dominated by Pseudomonadota (51.13%), whereas Debagh, a Ca-Cl-SO4 type spring, was primarily populated by Bacillota with 55.33%. Bacteroidota displayed even distribution across both sites. Additional phyla, including Chloroflexota, Deinococcota, Cyanobacteriota, and Chlorobiota, were also present. Environmental factors, particularly temperature, sodium, potassium, and alkalinity, significantly influenced bacterial diversity and composition. These findings shed light on the interplay between distinct microbial communities and their associated geochemical properties, providing valuable insights for future research on biogeochemical processes in these unique ecosystems driven by distinct environmental conditions, including potential applications in bioremediation and enzyme discovery.},
}
@article {pmid38952448,
year = {2024},
author = {Aqueel, R and Badar, A and Ijaz, UZ and Malik, KA},
title = {Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1381883},
pmid = {38952448},
issn = {1664-302X},
abstract = {Biotic stresses, such as plant viruses, e.g., cotton leaf curl virus (CLCuV), can alter root-associated and leaf-associated microbial diversities in plants. There are complex ecological dynamics at play, with each microbe contributing to a multitude of biotic and abiotic interactions, thus deciding the stability of the plant's ecosystem in response to the disease. Deciphering these networks of interactions is a challenging task. The inferential research in microbiome is also at a nascent stage, often constrained by the underlying analytical assumptions and the limitations with respect to the depth of sequencing. There is also no real consensus on network-wide statistics to identify the influential microbial players in a network. Guided by the latest developments in network science, including recently published metrics such as Integrated View of Influence (IVI) and some other centrality measures, this study provides an exposé of the most influential nodes in the rhizospheric and phyllospheric microbial networks of the cotton leaf curl disease (CLCuD) susceptible, partially tolerant, and resistant cotton varieties. It is evident from our results that the CLCuD-resistant Gossypium arboreum possesses an equal share of keystone species, which helps it to withstand ecological pressures. In the resistant variety, the phyllosphere harbors the most influential nodes, whereas in the susceptible variety, they are present in the rhizosphere. Based on hubness score, spreading score, and IVI, the top 10 occurring keystone species in the FDH-228 (resistant) variety include Actinokineospora, Cohnella, Thermobacillus, Clostridium, Desulfofarcimen, and MDD-D21. Elusimicrobia, Clostridium-sensu-stricto_12, Candidatus woesebacteria, and Dyella were identified as the most influential nodes in the PFV-1 (partially tolerant) variety. In the PFV-2 (susceptible) variety, the keystone species were identified as Georginia, Nesterenkonia, Elusimicrobia MVP-88, Acetivibrio, Tepedisphaerales, Chelatococcus, Nitrosospira, and RCP2-54. This concept deciphers the diseased and healthy plant's response to viral disease, which may be microbially mediated.},
}
@article {pmid38949619,
year = {2024},
author = {Jibrin, MO and Sharma, A and Mavian, CN and Timilsina, S and Kaur, A and Iruegas-Bocardo, F and Potnis, N and Minsavage, GV and Coutinho, TA and Creswell, TC and Egel, DS and Francis, DM and Kebede, M and Miller, SA and Montelongo, MJ and Nikolaeva, E and Pianzzola, MJ and Pruvost, O and Quezado-Duval, AM and Ruhl, GE and Shutt, VM and Maynard, E and Maeso, DC and Siri, MI and Trueman, CL and Salemi, M and Vallad, GE and Roberts, PD and Jones, JB and Goss, EM},
title = {Phylodynamic Insights into Global Emergence and Diversification of the Tomato Pathogen Xanthomonas hortorum pv. gardneri.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {37},
number = {10},
pages = {712-720},
doi = {10.1094/MPMI-04-24-0035-R},
pmid = {38949619},
issn = {0894-0282},
mesh = {*Solanum lycopersicum/microbiology ; *Plant Diseases/microbiology ; *Xanthomonas/genetics/pathogenicity ; *Phylogeny ; *Genetic Variation ; Genome, Bacterial ; },
abstract = {The emergence of plant pathogens is often associated with waves of unique evolutionary and epidemiological events. Xanthomonas hortorum pv. gardneri is one of the major pathogens causing bacterial spot disease of tomatoes. After its first report in the 1950s, there were no formal reports on this pathogen until the 1990s, despite active global research on the pathogens that cause tomato and pepper bacterial spot disease. Given the recently documented global distribution of X. hortorum pv. gardneri, our objective was to examine genomic diversification associated with its emergence. We sequenced the genomes of X. hortorum pv. gardneri strains collected in eight countries to examine global population structure and pathways of emergence using phylodynamic analysis. We found that strains isolated post-1990 group by region of collection and show minimal impact of recombination on genetic variation. A period of rapid geographic expansion in X. hortorum pv. gardneri is associated with acquisition of a large plasmid conferring copper tolerance by horizontal transfer and coincides with the burgeoning hybrid tomato seed industry through the 1980s. The ancestry of X. hortorum pv. gardneri is consistent with introduction to hybrid tomato seed production and dissemination during the rapid increase in trade of hybrid seeds. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
}
@article {pmid38946903,
year = {2024},
author = {Malfent, F and Zehl, M and Kirkegaard, RH and Oberhofer, M and Zotchev, SB},
title = {Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1408479},
pmid = {38946903},
issn = {1664-302X},
abstract = {Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces spp. were isolated from the rare and endangered traditional medicinal plant Leontopodium nivale ssp. alpinum, also known as Edelweiss. In the search for novel natural products, nine endophytic Streptomyces spp. from Edelweiss were investigated via genome sequencing and analysis, followed by fermentation in different media and investigation of secondary metabolomes. A total of 214 secondary metabolite biosynthetic gene clusters (BGCs), of which 35 are presumably unique, were identified by the bioinformatics tool antiSMASH in the genomes of these isolates. LC-MS analyses of the secondary metabolomes of these isolates revealed their potential to produce both known and presumably novel secondary metabolites, whereby most of the identified molecules could be linked to their cognate BGCs. This work sets the stage for further investigation of endophytic streptomycetes from Edelweiss aimed at the discovery and characterization of novel bioactive natural products.},
}
@article {pmid38946328,
year = {2024},
author = {Langlois, GA},
title = {Past-President address: My journey in microbial ecology-footprints in the sand, island hopping, supply chains, and technology bridges.},
journal = {The Journal of eukaryotic microbiology},
volume = {71},
number = {4},
pages = {e13037},
doi = {10.1111/jeu.13037},
pmid = {38946328},
issn = {1550-7408},
mesh = {*Ecology ; Eukaryota/physiology ; History, 20th Century ; History, 21st Century ; },
abstract = {This paper highlights and honors the connectivity among protistan researchers, using my own research journey as a backdrop, with attention to the supply chain of ideas, supporters, and other influencers who helped to shape and guide my career by sharing their ideas, protocols, skills, and enthusiasm. In looking back at the journey, the supply chain in my career has also included changes in the conceptual framework for my research studies, converging with a continuous flow of ideas and support from colleagues and mentors. To illustrate the complex map of ideas and supporters, this paper will examine technological advances, paradigm shifts in ecological constructs, geographical considerations, breakthroughs in peritrich biology, and the importance of an integrated perspective as we navigate the changing realities of today's scientific challenges.},
}
@article {pmid38946115,
year = {2024},
author = {Zayed, N and Vertommen, R and Simoens, K and Bernaerts, K and Boon, N and Srivastava, MG and Braem, A and Van Holm, W and Castro, AB and Teughels, W},
title = {How well do antimicrobial mouth rinses prevent dysbiosis in an in vitro periodontitis biofilm model?.},
journal = {Journal of periodontology},
volume = {95},
number = {9},
pages = {880-891},
doi = {10.1002/JPER.23-0674},
pmid = {38946115},
issn = {1943-3670},
mesh = {*Biofilms/drug effects ; Humans ; *Dysbiosis/prevention &amp; control ; *Mouthwashes/pharmacology/therapeutic use ; *Periodontitis/prevention &amp; control/microbiology ; Microscopy, Electron, Scanning ; Chlorhexidine/pharmacology/analogs &amp; derivatives/therapeutic use ; Interleukin-8 ; In Vitro Techniques ; Anti-Infective Agents/pharmacology/therapeutic use ; Durapatite ; Anti-Infective Agents, Local/pharmacology/therapeutic use ; Microbiota/drug effects ; },
abstract = {BACKGROUND: Periodontal diseases are associated with dysbiosis in the oral microbial communities. Managing oral biofilms is therefore key for preventing these diseases. Management protocols often include over-the-counter antimicrobial mouth rinses, which lack data on their effects on the oral microbiome's ecology, bacterial composition, metabolic activity, and dysbiosis resilience. This study examined the efficacy of antimicrobial mouth rinses to halt dysbiosis in in vitro oral biofilms under periodontitis-simulating conditions.<br><br>METHODS: Multispecies oral biofilms were grown on hydroxyapatite discs (HADs) and rinsed daily with one of six mouth rinses. Positive and negative controls were included. After three rinses, biofilms were analyzed with viability quantitative polymerase chain reaction and visualized using scanning electron microscopy. Supernatants of rinsed biofilms were used for metabolic activity analysis. In addition, human oral keratinocytes were exposed to rinsed biofilms to assess their inflammatory response. All outputs were analyzed for correlation using Spearman coefficient.<br><br>RESULTS: Product-related changes were observed in the rinsed biofilms. Three of the six tested mouth rinses could significantly prevent dysbiosis with &#x2265;30% reduction in pathobiont abundance relative to the control. These biofilms had lower metabolic activity, and the exposed human oral keratinocyte produced less interleukin-8. Interleukin-8 production correlated to both pathobiont quantity and the metabolic activity of the biofilms.<br><br>CONCLUSION: Some mouth rinses could support biofilm resilience and stop dysbiosis evolution in the biofilm model, with a clear product-related effect. Such mouth rinses can be considered for patients under maintenance/supportive periodontal therapy to prevent/delay disease recurrence. Others are more useful for different periodontal therapy stages.},
}
@article {pmid38945268,
year = {2024},
author = {Tom, WA and Judy, JV and Kononoff, PJ and Fernando, SC},
title = {Influence of empirically derived filtering parameters, amplicon sequence variant, and operational taxonomic unit pipelines on assessing rumen microbial diversity.},
journal = {Journal of dairy science},
volume = {107},
number = {11},
pages = {9209-9234},
doi = {10.3168/jds.2023-24479},
pmid = {38945268},
issn = {1525-3198},
mesh = {Animals ; *Rumen/microbiology ; Cattle ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; },
abstract = {Microbes play an important role in human and animal health, as well as animal productivity. The host microbial interactions within ruminants play a critical role in animal health and productivity and provide up to 70% of the animal's energy needs in the form of fermentation products. As such, many studies have investigated microbial community composition to understand the microbial community changes and factors that affect microbial colonization and persistence. Advances in next-generation sequencing technologies and the low cost of sequencing have led many studies to use 16S rDNA-based analysis tools for interrogation of microbiomes at a much finer scale than traditional culturing. However, methods that rely on single base pair differences for bacterial taxa clustering may inflate or underestimate diversity, leading to inaccurate identification of bacterial diversity. Therefore, in this study, we sequenced mock communities of known membership and abundance to establish filtration parameters to reduce the inflation of microbial diversity due to PCR and sequencing errors. Additionally, we evaluated the effect of the resulting filtering parameters proposed using established bioinformatic pipelines on a study consisting of Holstein and Jersey cattle to identify breed and treatment effects on the bacterial community composition and the impact of filtering on global microbial community structure analysis and results. Filtration resulted in a sharp reduction in bacterial taxa identified, yet retain most sequencing data (retaining >79% of sequencing reads) when analyzed using 3 different microbial analysis pipelines (DADA2, Mothur, USEARCH). After filtration, conclusions from α-diversity and β-diversity tests showed very similar results across all analysis methods. The mock community-based filtering parameters proposed in this study help provide a more realistic estimation of bacterial diversity. Additionally, filtration reduced the variation between microbiome analysis methods and helped to identify microbial community differences that could have been missed due to the large animal-to-animal variation observed in the unfiltered data. As such, we believe the new filtering parameters described in this study will help to obtain diversity estimates that are closer to realistic values, improve the ability to detecting microbial community differences, and help to better understand microbial community changes in 16S rDNA-based studies.},
}
@article {pmid38943017,
year = {2024},
author = {Pires, CS and Costa, L and Barbosa, SG and Sequeira, JC and Cachetas, D and Freitas, JP and Martins, G and Machado, AV and Cavaleiro, AJ and Salvador, AF},
title = {Microplastics Biodegradation by Estuarine and Landfill Microbiomes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {88},
pmid = {38943017},
issn = {1432-184X},
support = {UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2023.01617.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; },
mesh = {*Biodegradation, Environmental ; *Microbiota ; *Microplastics/metabolism ; *Waste Disposal Facilities ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Water Pollutants, Chemical/metabolism ; Polyesters/metabolism ; Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Estuaries ; Polyethylene/metabolism ; Polyethylene Terephthalates/metabolism ; },
abstract = {Plastic pollution poses a worldwide environmental challenge, affecting wildlife and human health. Assessing the biodegradation capabilities of natural microbiomes in environments contaminated with microplastics is crucial for mitigating the effects of plastic pollution. In this work, we evaluated the potential of landfill leachate (LL) and estuarine sediments (ES) to biodegrade polyethylene (PE), polyethylene terephthalate (PET), and polycaprolactone (PCL), under aerobic, anaerobic, thermophilic, and mesophilic conditions. PCL underwent extensive aerobic biodegradation with LL (99 ± 7%) and ES (78 ± 3%) within 50-60 days. Under anaerobic conditions, LL degraded 87 ± 19% of PCL in 60 days, whereas ES showed minimal biodegradation (3 ± 0.3%). PE and PET showed no notable degradation. Metataxonomics results (16S rRNA sequencing) revealed the presence of highly abundant thermophilic microorganisms assigned to Coprothermobacter sp. (6.8% and 28% relative abundance in anaerobic and aerobic incubations, respectively). Coprothermobacter spp. contain genes encoding two enzymes, an esterase and a thermostable monoacylglycerol lipase, that can potentially catalyze PCL hydrolysis. These results suggest that Coprothermobacter sp. may be pivotal in landfill leachate microbiomes for thermophilic PCL biodegradation across varying conditions. The anaerobic microbial community was dominated by hydrogenotrophic methanogens assigned to Methanothermobacter sp. (21%), pointing at possible syntrophic interactions with Coprothermobacter sp. (a H2-producer) during PCL biodegradation. In the aerobic experiments, fungi dominated the eukaryotic microbial community (e.g., Exophiala (41%), Penicillium (17%), and Mucor (18%)), suggesting that aerobic PCL biodegradation by LL involves collaboration between fungi and bacteria. Our findings bring insights on the microbial communities and microbial interactions mediating plastic biodegradation, offering valuable perspectives for plastic pollution mitigation.},
}
@article {pmid38942024,
year = {2024},
author = {Harder, CB and Miyauchi, S and Virágh, M and Kuo, A and Thoen, E and Andreopoulos, B and Lu, D and Skrede, I and Drula, E and Henrissat, B and Morin, E and Kohler, A and Barry, K and LaButti, K and Salamov, A and Lipzen, A and Merényi, Z and Hegedüs, B and Baldrian, P and Stursova, M and Weitz, H and Taylor, A and Koriabine, M and Savage, E and Grigoriev, IV and Nagy, LG and Martin, F and Kauserud, H},
title = {Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations.},
journal = {Cell genomics},
volume = {4},
number = {7},
pages = {100586},
pmid = {38942024},
issn = {2666-979X},
mesh = {*Genome, Fungal/genetics ; *Agaricales/genetics ; Phylogeny ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Plants/microbiology/genetics ; },
abstract = {Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.},
}
@article {pmid38940921,
year = {2024},
author = {Picariello, E and De Nicola, F},
title = {Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {86},
pmid = {38940921},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Fagus/microbiology ; *Quercus/microbiology ; *Forests ; *Microbiota ; *Soil/chemistry ; *Seasons ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Biodiversity ; Forestry ; Trees/microbiology ; Ecosystem ; },
abstract = {Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.},
}
@article {pmid38940862,
year = {2024},
author = {Ljaljević Grbić, M and Dimkić, I and Janakiev, T and Kosel, J and Tavzes, &#x10c; and Popović, S and Knežević, A and Legan, L and Retko, K and Ropret, P and Unković, N},
title = {Uncovering the Role of Autochthonous Deteriogenic Biofilm Community: Rožanec Mithraeum Monument (Slovenia).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {87},
pmid = {38940862},
issn = {1432-184X},
support = {451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; },
mesh = {*Biofilms ; *Lichens/microbiology/physiology ; *Calcium Carbonate ; Slovenia ; Ascomycota/physiology ; Mycobiome ; },
abstract = {The primary purpose of the study, as part of the planned conservation work, was to uncover all aspects of autochthonous biofilm pertaining to the formation of numerous deterioration symptoms occurring on the limestone Rožanec Mithraeum monument in Slovenia. Using state-of-the-art sequencing technologies combining mycobiome data with observations made via numerous light and spectroscopic (FTIR and Raman) microscopy analyses pointed out to epilithic lichen Gyalecta jenensis and its photobiont, carotenoid-rich Trentepohlia aurea, as the origin of salmon-hued pigmented alterations of limestone surface. Furthermore, the development of the main deterioration symptom on the monument, i.e., biopitting, was instigated by the formation of typical endolithic thalli and ascomata of representative Verrucariaceae family (Verrucaria sp.) in conjunction with the oxalic acid-mediated dissolution of limestone. The domination of lichenized fungi, as the main deterioration agents, both on the relief and surrounding limestone, was additionally supported by the high relative abundance of lichenized and symbiotroph groups in FUNGuild analysis. Obtained results not only upgraded knowledge of this frequently occurring but often overlooked group of extremophilic stone heritage deteriogens but also provided a necessary groundwork for the development of efficient biocontrol formulation applicable in situ for the preservation of similarly affected limestone monuments.},
}
@article {pmid38940768,
year = {2024},
author = {Baroncelli, R and Cobo-Díaz, JF and Benocci, T and Peng, M and Battaglia, E and Haridas, S and Andreopoulos, W and LaButti, K and Pangilinan, J and Lipzen, A and Koriabine, M and Bauer, D and Le Floch, G and Mäkelä, MR and Drula, E and Henrissat, B and Grigoriev, IV and Crouch, JA and de Vries, RP and Sukno, SA and Thon, MR},
title = {Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {38940768},
issn = {2047-217X},
mesh = {*Colletotrichum/genetics/pathogenicity ; *Transcriptome ; *Genome, Fungal ; *Evolution, Molecular ; Phylogeny ; Adaptation, Physiological/genetics ; Gene Expression Profiling/methods ; Plant Diseases/microbiology/genetics ; },
abstract = {BACKGROUND: Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes.<br><br>RESULTS: Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation.<br><br>CONCLUSIONS: These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.},
}
@article {pmid38940583,
year = {2024},
author = {Xie, G and Sun, C and Luo, W and Gong, Y and Tang, X},
title = {Distinct ecological niches and community dynamics: understanding free-living and particle-attached bacterial communities in an oligotrophic deep lake.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0071424},
pmid = {38940583},
issn = {1098-5336},
support = {41971062, 42371065//MOST | National Natural Science Foundation of China (NSFC)/ ; WGKQ2022032//West Anhui University ()/ ; },
mesh = {*Lakes/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; China ; *Microbiota ; Ecosystem ; Seasons ; },
abstract = {Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher α- and β-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. Cyanobium, Comamonadaceae, and Roseomonas were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems.IMPORTANCEUnderstanding the diversity of microbial communities, their assembly mechanisms, and their responses to environmental changes is fundamental to the study of aquatic microbial ecology. Oligotrophic deep-water lakes are fragile ecosystems with limited nutrient resources, rendering them highly susceptible to environmental fluctuations. Examining different bacterial types within these lakes offers valuable insights into the intricate mechanisms governing community dynamics and adaptation strategies across various scales. In our investigation of oligotrophic deep freshwater Lake Fuxian in China, we explored the seasonal and vertical dynamics of two bacterial types: free-living (FL) and particle-attached (PA). Our findings unveiled distinct patterns in the diversity, composition, and putative functions of these bacteria, all shaped by environmental factors. Understanding these subtleties provides insight into bacterial interactions, thereby influencing the overall ecosystem functioning. Ultimately, our research illuminates the adaptation and roles of FL and PA bacteria within these unique lake environments, contributing significantly to our broader comprehension of ecosystem stability and health.},
}
@article {pmid38939048,
year = {2024},
author = {Shi, Q and Sun, L and Gao, J and Li, F and Chen, D and Shi, T and Tan, Y and Chang, H and Liu, X and Kang, J and Lu, F and Huang, Z and Zhao, H},
title = {Effects of sodium lauryl sulfate and postbiotic toothpaste on oral microecology.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2372224},
pmid = {38939048},
issn = {2000-2297},
abstract = {The diversity and delicate balance of the oral microbiome contribute to oral health, with its disruption leading to oral and systemic diseases. Toothpaste includes elements like traditional additives such as sodium lauryl sulfate (SLS) as well as novel postbiotics derived from probiotics, which are commonly employed for maintaining oral hygiene and a healthy oral cavity. However, the response of the oral microbiota to these treatments remains poorly understood. In this study, we systematically investigated the impact of SLS, and toothpaste containing postbiotics (hereafter, postbiotic toothpaste) across three systems: biofilms, animal models, and clinical populations. SLS was found to kill bacteria in both preformed biofilms (mature biofilms) and developing biofilms (immature biofilms), and disturbed the microbial community structure by increasing the number of pathogenic bacteria. SLS also destroyed periodontal tissue, promoted alveolar bone resorption, and enhanced the extent of inflammatory response level. The postbiotic toothpaste favored bacterial homeostasis and the normal development of the two types of biofilms in vitro, and attenuated periodontitis and gingivitis in vivo via modulation of oral microecology. Importantly, the postbiotic toothpaste mitigated the adverse effects of SLS when used in combination, both in vitro and in vivo. Overall, the findings of this study describe the impact of toothpaste components on oral microflora and stress the necessity for obtaining a comprehensive understanding of oral microbial ecology by considering multiple aspects.},
}
@article {pmid38938005,
year = {2024},
author = {Chaudhary, DK and Kim, SE and Park, HJ and Kim, KH},
title = {Unveiling the Bacterial Community across the Stomach, Hepatopancreas, Anterior Intestine, and Posterior Intestine of Pacific Whiteleg Shrimp.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {6},
pages = {1260-1269},
pmid = {38938005},
issn = {1738-8872},
mesh = {Animals ; *Penaeidae/microbiology ; *Hepatopancreas/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Republic of Korea ; *Intestines/microbiology ; Phylogeny ; Stomach/microbiology ; Biodiversity ; Aquaculture ; DNA, Bacterial/genetics ; },
abstract = {The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.},
}
@article {pmid38937989,
year = {2024},
author = {Wu, H and Mu, C and Li, X and Fan, W and Shen, L and Zhu, W},
title = {Breed-Driven Microbiome Heterogeneity Regulates Intestinal Stem Cell Proliferation via Lactobacillus-Lactate-GPR81 Signaling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {11},
number = {33},
pages = {e2400058},
pmid = {38937989},
issn = {2198-3844},
support = {32030104//National Natural Science Foundation of China/ ; 2022YFD1300402//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Cell Proliferation/physiology ; *Stem Cells/metabolism/cytology ; *Lactobacillus/metabolism/genetics ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Swine ; *Lactic Acid/metabolism ; Signal Transduction/physiology ; Wnt Signaling Pathway/physiology/genetics ; Jejunum/microbiology/metabolism/cytology ; Obesity/metabolism/microbiology ; Intestinal Mucosa/metabolism/microbiology/cytology ; },
abstract = {Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome-wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus-dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β-catenin signaling. Experiments using in-house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β-catenin signaling in a GPR81-dependent manner to promote ISC-mediated epithelial proliferation. However, heat-killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus-lactate-GPR81 axis, a key mechanism bridging breed-driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis.},
}
@article {pmid38936927,
year = {2024},
author = {Shen, CL and Wankhade, UD and Shankar, K and Najjar, RS and Feresin, RG and Elmassry, MM and Dufour, JM and Kaur, G and Chintapalli, SV and Piccolo, BD and Dunn, DM and Cao, JJ},
title = {Effects of Statin and Annatto-extracted Tocotrienol Supplementation on Glucose Homeostasis, Bone Microstructure, and Gut Microbiota Composition in Obese Mice.},
journal = {In vivo (Athens, Greece)},
volume = {38},
number = {4},
pages = {1557-1570},
pmid = {38936927},
issn = {1791-7549},
support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Tocotrienols/pharmacology/administration &amp; dosage ; Mice ; *Homeostasis/drug effects ; *Obesity/drug therapy/metabolism ; Male ; *Dietary Supplements ; *Bone and Bones/drug effects/metabolism/pathology ; *Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology ; *Diet, High-Fat/adverse effects ; Bixaceae/chemistry ; Mice, Obese ; Plant Extracts/pharmacology/administration &amp; dosage ; Glucose/metabolism ; Mice, Inbred C57BL ; Insulin Resistance ; Blood Glucose ; Disease Models, Animal ; Liver/drug effects/metabolism/pathology ; Biomarkers ; Carotenoids ; },
abstract = {BACKGROUND/AIM: This study examined the effects of tocotrienols (TT) in conjunction with statin on glucose homeostasis, bone microstructure, gut microbiome, and systemic and liver inflammatory markers in obese C57BL/6J mice.<br><br>MATERIALS AND METHODS: Forty male C57BL/6J mice were fed a high-fat diet (HFD) and assigned into four groups in a 2 (no statin vs. 120 mg statin/kg diet)&#xd7;2 (no TT vs. 400 mg TT/kg diet) factorial design for 14 weeks.<br><br>RESULTS: Statin and TT improved glucose tolerance only when each was given alone, and only statin supplementation decreased insulin resistance. Consistently, only statin supplementation decreased serum insulin levels and HOMA-IR. Pancreatic insulin was also increased with statin treatment. Statin and TT, alone or in combination, reduced the levels of serum IL-6, but only TT attenuated the increased serum leptin levels induced by a HFD. Statin supplementation increased bone area/total area and connectivity density at LV-4, while TT supplementation increased bone area/total area and trabecular number, but decreased trabecular separation at the distal femur. Statin supplementation, but not TT, reduced hepatic inflammatory cytokine gene expression. Neither TT supplementation nor statin supplementation statistically altered microbiome species evenness or richness. However, they altered the relative abundance of certain microbiome species. Most notably, both TT and statin supplementation increased the relative abundance of Lachnospiraceae UCG-006.<br><br>CONCLUSION: TT and statin collectively benefit bone microstructure, glucose homeostasis, and microbial ecology in obese mice. Such changes may be, in part, associated with suppression of inflammation in the host.},
}
@article {pmid38936916,
year = {2024},
author = {Morikawa, T and Paudel, D and Uehara, O and Ariwansa, D and Kobayashi, Y and Yang, J and Yoshida, K and Abiko, Y},
title = {Effects of Laurus nobilis Leaf Extract (LAURESH[®]) on Oral and Gut Microbiota Diversity in Mice.},
journal = {In vivo (Athens, Greece)},
volume = {38},
number = {4},
pages = {1758-1766},
pmid = {38936916},
issn = {1791-7549},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Plant Leaves/chemistry ; Mice ; *Plant Extracts/pharmacology ; *Laurus/chemistry ; *RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Biodiversity ; Feces/microbiology ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; Male ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND/AIM: The leaves of Laurus nobilis have been used for culinary purposes for many years and have recently been shown to have beneficial effects on human health by altering microbiota composition. However, the effects of L. nobilis on the diversity of microbiomes in the oral cavity and gut remain unknown. Therefore, in this study, we examined the effects of an extract of L. nobilis on the diversity of microbiomes in the oral cavity and gut in mice.<br><br>MATERIALS AND METHODS: C57BL/6J mice were randomly divided into two groups and fed a standard diet (SD) and a standard diet containing 5% LAURESH[&#xae;], a laurel extract (SDL). After 10 weeks, oral swabs and fecal samples were collected. The bacterial DNA extracted from the oral swabs and feces was used for microbiota analysis using 16S rRNA sequencing. The sequencing data were analyzed using the Quantitative Insights into Microbial Ecology 2 in the DADA2 pipeline and 16S rRNA database.<br><br>RESULTS: The &#x3b1;-diversity of the oral microbiome was significantly greater in the SDL group than in the SD group. The &#x3b2;-diversity of the oral microbiome was also significantly different between the groups. Moreover, the taxonomic abundance analysis showed that five bacteria in the gut were significantly different among the groups. Furthermore, the SDL diet increased the abundance of beneficial gut bacteria, such as Akkermansia sp.<br><br>CONCLUSION: Increased diversity of the oral microbiome and proportion of Akkermansia sp. in the gut microbiome induced by L. nobilis consumption may benefit oral and gut health.},
}
@article {pmid38936824,
year = {2024},
author = {Chen, YC and Destouches, L and Cook, A and Fedorec, AJH},
title = {Synthetic microbial ecology: engineering habitats for modular consortia.},
journal = {Journal of applied microbiology},
volume = {135},
number = {7},
pages = {},
doi = {10.1093/jambio/lxae158},
pmid = {38936824},
issn = {1365-2672},
support = {EP/W524335/1//Engineering and Physical Sciences Research Council/ ; BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Microbial Consortia ; *Synthetic Biology/methods ; *Microbiota ; *Ecosystem ; Ecology ; },
abstract = {Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.},
}
@article {pmid38935596,
year = {2024},
author = {O'Brien, JM and Blais, N and Butler, C and White, N and Bustead, A and Figler, C and Wells, M and Anderson, G and Yuhas, A and Ernakovich, JG},
title = {Ten "simple" rules for non-Indigenous researchers engaging Indigenous communities in Arctic research.},
journal = {PLoS computational biology},
volume = {20},
number = {6},
pages = {e1012093},
pmid = {38935596},
issn = {1553-7358},
mesh = {Arctic Regions ; Humans ; *Indigenous Peoples ; Research Personnel ; },
}
@article {pmid38935504,
year = {2024},
author = {Luo, S and Zhang, X and Zhou, X},
title = {Temporospatial dynamics and host specificity of honeybee gut bacteria.},
journal = {Cell reports},
volume = {43},
number = {7},
pages = {114408},
doi = {10.1016/j.celrep.2024.114408},
pmid = {38935504},
issn = {2211-1247},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; *Host Specificity ; *Bacteria/genetics ; Host Microbial Interactions/physiology ; },
abstract = {Honeybees are important pollinators worldwide, with their gut microbiota playing a crucial role in maintaining their health. The gut bacteria of honeybees consist of primarily five core lineages that are spread through social interactions. Previous studies have provided a basic understanding of the composition and function of the honeybee gut microbiota, with recent advancements focusing on analyzing diversity at the strain level and changes in bacterial functional genes. Research on honeybee gut microbiota across different regions globally has provided insights into microbial ecology. Additionally, recent findings have shed light on the mechanisms of host specificity of honeybee gut bacteria. This review explores the temporospatial dynamics in honeybee gut microbiota, discussing the reasons and mechanisms behind these fluctuations. This synopsis provides insights into host-microbe interactions and is invaluable for honeybee health.},
}
@article {pmid38935220,
year = {2024},
author = {Parra, B and Lutz, VT and Brøndsted, L and Carmona, JL and Palomo, A and Nesme, J and Van Hung Le, V and Smets, BF and Dechesne, A},
title = {Characterization and Abundance of Plasmid-Dependent Alphatectivirus Bacteriophages.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {85},
pmid = {38935220},
issn = {1432-184X},
support = {101026675//European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant/ ; 002200000279//VRID Postdoctorado from Vicerrector&#xed;a de Investigaci&#xf3;n y Desarrollo, Universidad de Concepci&#xf3;n/ ; P-PhanFARE (23046)//Villum Fonden/ ; },
mesh = {*Plasmids/genetics ; *Wastewater/virology/microbiology ; *Bacteriophages/genetics/isolation &amp; purification/physiology/classification ; Genome, Viral ; Escherichia coli/virology/genetics ; Host Specificity ; Pseudomonas putida/virology/genetics ; Salmonella enterica/virology/genetics ; Phylogeny ; },
abstract = {Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since conjugative plasmids of the incompatibility group P (IncP) are ubiquitous mobile genetic elements that often carry ARG and are broad-host-range, they are important targets to prevent the dissemination of AMR. Plasmid-dependent phages infect plasmid-carrying bacteria by recognizing components of the conjugative secretion system as receptors. We sought to isolate plasmid-dependent phages from wastewater using an avirulent strain of Salmonella enterica carrying the conjugative IncP plasmid pKJK5. Irrespective of the site, we only obtained bacteriophages belonging to the genus Alphatectivirus. Eleven isolates were sequenced, their genomes analyzed, and their host range established using S. enterica, Escherichia coli, and Pseudomonas putida carrying diverse conjugative plasmids. We confirmed that Alphatectivirus are abundant in domestic and hospital wastewater using culture-dependent and culture-independent approaches. However, these results are not consistent with their low or undetectable occurrence in metagenomes. Therefore, overall, our results emphasize the importance of performing phage isolation to uncover diversity, especially considering the potential of plasmid-dependent phages to reduce the spread of ARG carried by conjugative plasmids, and to help combat the AMR crisis.},
}
@article {pmid38933974,
year = {2024},
author = {Rezende, GS and Rocha, FI and Funnicelli, MIG and Malavazi, I and Crauwels, S and Brandao, MM and Cunha, AF},
title = {Metabarcoding analysis reveals an interaction among distinct groups of bacteria associated with three different varietals of grapes used for wine production in Brazil.},
journal = {Heliyon},
volume = {10},
number = {11},
pages = {e32283},
pmid = {38933974},
issn = {2405-8440},
abstract = {Grapes are globally popular with wine production being one of the most well-known uses of grapes worldwide. Brazil has a growing wine industry, and the Serra Gaúcha region is a significant contributor to the country's wine production. Nonetheless, other states are increasing their relevance in this segment. Environmental factors and the soil microbiome (bacteria and fungi) heavily influence grape quality, shaping the crucial "terroir" for wines. Here, soil quality was assessed through nutrient analysis and bacteria microbial diversity, which could significantly impact grape health and final wine attributes. Soil samples from São Paulo's vineyards, focusing on Syrah, Malbec, and Cabernet Sauvignon, underwent chemical and microbial analysis via 16S rRNA metabarcoding and highlighted significant differences in soil composition between vineyards. Statistical analyses including PCA and CAP showcased region-based separation and intricate associations between microbiota, region, and grape variety. Correlation analysis pinpointed microbial genera linked to specific soil nutrients. Random Forest analysis identified abundant bacterial genera per grape variety and the Network analysis revealed varied co-occurrence patterns, with Cabernet Sauvignon exhibiting complex microbial interactions. This study unveils complex relationships between soil microbiota, nutrients, and diverse grape varieties in distinct vineyard regions. Understanding how these specific microorganisms are associated with grapes can improve vineyard management, grape quality, and wine production. It can also potentially optimize soil health, bolster grapevine resilience against pests and diseases, and contribute to the unique character of wines known as terroir.},
}
@article {pmid38933028,
year = {2024},
author = {Stemple, B and Gulliver, D and Sarkar, P and Tinker, K and Bibby, K},
title = {Metagenome-assembled genomes provide insight into the metabolic potential during early production of Hydraulic Fracturing Test Site 2 in the Delaware Basin.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1376536},
pmid = {38933028},
issn = {1664-302X},
abstract = {Demand for natural gas continues to climb in the United States, having reached a record monthly high of 104.9 billion cubic feet per day (Bcf/d) in November 2023. Hydraulic fracturing, a technique used to extract natural gas and oil from deep underground reservoirs, involves injecting large volumes of fluid, proppant, and chemical additives into shale units. This is followed by a "shut-in" period, during which the fracture fluid remains pressurized in the well for several weeks. The microbial processes that occur within the reservoir during this shut-in period are not well understood; yet, these reactions may significantly impact the structural integrity and overall recovery of oil and gas from the well. To shed light on this critical phase, we conducted an analysis of both pre-shut-in material alongside production fluid collected throughout the initial production phase at the Hydraulic Fracturing Test Site 2 (HFTS 2) located in the prolific Wolfcamp formation within the Permian Delaware Basin of west Texas, USA. Specifically, we aimed to assess the microbial ecology and functional potential of the microbial community during this crucial time frame. Prior analysis of 16S rRNA sequencing data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. Here, we performed a metagenomic analysis of produced water sampled on Day 33 of production. This analysis yielded three high-quality metagenome-assembled genomes (MAGs), one of which was a Clostridia draft genome closely related to the recently classified Petromonas tenebris. This draft genome likely represents the dominant Clostridia species observed in our 16S rRNA profile. Annotation of the MAGs revealed the presence of genes involved in critical metabolic processes, including thiosulfate reduction, mixed acid fermentation, and biofilm formation. These findings suggest that this microbial community has the potential to contribute to well souring, biocorrosion, and biofouling within the reservoir. Our research provides unique insights into the early stages of production in one of the most prolific unconventional plays in the United States, with important implications for well management and energy recovery.},
}
@article {pmid38932970,
year = {2024},
author = {Ponce, MA and Maille, JM and Stoll, I and James, A and Bruce, A and Kim, TN and Scully, ED and Morrison, WR},
title = {Microbial vectoring capacity by internal- and external-infesting stored product insects after varying dispersal periods between novel food patches: An underestimated risk.},
journal = {Ecology and evolution},
volume = {14},
number = {6},
pages = {e11368},
pmid = {38932970},
issn = {2045-7758},
abstract = {Understanding the ability of internal- and external-infesting stored product insects to vector microbes is important for estimating the relative risk that insects pose to postharvest commodities as they move between habitat patches and in the landscape. Thus, the aim of the current study was to evaluate and compare the microbial growth in novel food patches at different dispersal periods by different populations of Sitophilus oryzae (e.g., internal-infesting) and Lasioderma serricorne (e.g., external-infesting). Adults of both species collected from laboratory colonies or field-captured populations were either placed immediately in a novel food patch, or given a dispersal period of 24 or 72 h in a sterilized environment before entering a surrogate food patch. Vectored microbes in new food patches were imaged after 3 or 5 days of foraging, and microbial growth was processed using ImageJ while fungal species were identified through sequencing the ITS4/5 ribosomal subunit. We found that increasing dispersal time resulted in multiple-fold reductions in microbial growth surrogate food patches by L. serricorne but not S. oryzae. This was likely attributable to higher mobility by S. oryzae than L. serricorne. A total of 20 morphospecies were identified from 13 genera among the 59 sequences, with a total of 23% and 16% classified as Aspergillus and Penicillium spp. Our data suggest that there is a persistent risk of microbial contamination by both species, which has important food safety implications at food facilities.},
}
@article {pmid38930577,
year = {2024},
author = {Hernández-Zulueta, J and Rubio-Bueno, S and Zamora-Tavares, MDP and Vargas-Ponce, O and Rodríguez-Troncoso, AP and Rodríguez-Zaragoza, FA},
title = {Metabarcoding the Bacterial Assemblages Associated with Toxopneustes roseus in the Mexican Central Pacific.},
journal = {Microorganisms},
volume = {12},
number = {6},
pages = {},
pmid = {38930577},
issn = {2076-2607},
abstract = {The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin Toxopneustes roseus and its relationship with environmental variables will contribute to understanding the species' physiology and ecology. We collected sea urchins from coral ecosystems at six sites in the MCP during the summer and winter for two consecutive years. The spatial scale represented the most important variation in the T. roseus bacteriome, particularly because of Isla Isabel National Park (PNII). Likewise, spatial differences correlated with habitat structure variables, mainly the sponge and live coral cover. The PNII exhibited highly diverse bacterial assemblages compared to other sites, characterized by families associated with diseases and environmental stress (Saprospiraceae, Flammeovirgaceae, and Xanthobacteraceae). The remaining five sites presented a constant spatiotemporal pattern, where the predominance of the Campylobacteraceae and Helicobacteraceae families was key to T. roseus' holobiont. However, the dominance of certain bacterial families, such as Enterobacteriaceae, in the second analyzed year suggests that Punto B and Islas e islotes de Bahía Chamela Sanctuary were exposed to sewage contamination. Overall, our results improve the understanding of host-associated bacterial assemblages in specific time and space and their relationship with the environmental condition.},
}
@article {pmid38928853,
year = {2024},
author = {Tata, A and Massaro, A and Miano, B and Petrin, S and Antonelli, P and Peruzzo, A and Pezzuto, A and Favretti, M and Bragolusi, M and Zacometti, C and Losasso, C and Piro, R},
title = {A Snapshot, Using a Multi-Omic Approach, of the Metabolic Cross-Talk and the Dynamics of the Resident Microbiota in Ripening Cheese Inoculated with Listeria innocua.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {38928853},
issn = {2304-8158},
support = {RC IZSVe 11/2018//Ministero della Salute/ ; },
abstract = {Raw milk cheeses harbor complex microbial communities. Some of these microorganisms are technologically essential, but undesirable microorganisms can also be present. While most of the microbial dynamics and cross-talking studies involving interaction between food-derived bacteria have been carried out on agar plates in laboratory-controlled conditions, the present study evaluated the modulation of the resident microbiota and the changes of metabolite production directly in ripening raw milk cheese inoculated with Listeria innocua strains. Using a proxy of the pathogenic Listeria monocytogenes, we aimed to establish the key microbiota players and chemical signals that characterize Latteria raw milk cheese over 60 days of ripening time. The microbiota of both the control and Listeria-inoculated cheeses was analyzed using 16S rRNA targeted amplicon sequencing, while direct analysis in real time mass spectrometry (DART-HRMS) was applied to investigate the differences in the metabolic profiles of the cheeses. The diversity analysis showed the same microbial diversity trend in both the control cheese and the inoculated cheese, while the taxonomic analysis highlighted the most representative genera of bacteria in both the control and inoculated cheese: Lactobacillus and Streptococcus. On the other hand, the metabolic fingerprints revealed that the complex interactions between resident microbiota and L. innocua were governed by continuously changing chemical signals. Changes in the amounts of small organic acids, hydroxyl fatty acids, and antimicrobial compounds, including pyroglutamic acid, hydroxy-isocaproic acid, malic acid, phenyllactic acid, and lactic acid, were observed over time in the L. innocua-inoculated cheese. In cheese that was inoculated with L. innocua, Streptococcus was significantly correlated with the volatile compounds carboxylbenzaldheyde and cyclohexanecarboxylic acid, while Lactobacillus was positively correlated with some volatile and flavor compounds (cyclohexanecarboxylic acid, pyroxidal acid, aminobenzoic acid, and vanillic acid). Therefore, we determined the metabolic markers that characterize a raw milk cheese inoculated with L. innocua, the changes in these markers with the ripening time, and the positive correlation of flavor and volatile compounds with the resident microbiota. This multi-omics approach could suggest innovative food safety strategies based on the enhanced management of undesirable microorganisms by means of strain selection in raw matrices and the addition of specific antimicrobial metabolites to prevent the growth of undesirable microorganisms.},
}
@article {pmid38928813,
year = {2024},
author = {Vale, ADS and Pereira, CMT and De Dea Lindner, J and Rodrigues, LRS and Kadri, NKE and Pagnoncelli, MGB and Kaur Brar, S and Soccol, CR and Pereira, GVM},
title = {Exploring Microbial Influence on Flavor Development during Coffee Processing in Humid Subtropical Climate through Metagenetic-Metabolomics Analysis.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
pmid = {38928813},
issn = {2304-8158},
support = {440343/2022-4//National Council for Scientific and Technological Development/ ; },
abstract = {Research into microbial interactions during coffee processing is essential for developing new methods that adapt to climate change and improve flavor, thus enhancing the resilience and quality of global coffee production. This study aimed to investigate how microbial communities interact and contribute to flavor development in coffee processing within humid subtropical climates. Employing Illumina sequencing for microbial dynamics analysis, and high-performance liquid chromatography (HPLC) integrated with gas chromatography-mass spectrometry (GC-MS) for metabolite assessment, the study revealed intricate microbial diversity and associated metabolic activities. Throughout the fermentation process, dominant microbial species included Enterobacter, Erwinia, Kluyvera, and Pantoea from the prokaryotic group, and Fusarium, Cladosporium, Kurtzmaniella, Leptosphaerulina, Neonectria, and Penicillium from the eukaryotic group. The key metabolites identified were ethanol, and lactic, acetic, and citric acids. Notably, the bacterial community plays a crucial role in flavor development by utilizing metabolic versatility to produce esters and alcohols, while plant-derived metabolites such as caffeine and linalool remain stable throughout the fermentation process. The undirected network analysis revealed 321 interactions among microbial species and key substances during the fermentation process, with Enterobacter, Kluyvera, and Serratia showing strong connections with sugar and various volatile compounds, such as hexanal, benzaldehyde, 3-methylbenzaldehyde, 2-butenal, and 4-heptenal. These interactions, including inhibitory effects by Fusarium and Cladosporium, suggest microbial adaptability to subtropical conditions, potentially influencing fermentation and coffee quality. The sensory analysis showed that the final beverage obtained a score of 80.83 ± 0.39, being classified as a specialty coffee by the Specialty Coffee Association (SCA) metrics. Nonetheless, further enhancements in acidity, body, and aftertaste could lead to a more balanced flavor profile. The findings of this research hold substantial implications for the coffee industry in humid subtropical regions, offering potential strategies to enhance flavor quality and consistency through controlled fermentation practices. Furthermore, this study contributes to the broader understanding of how microbial ecology interplays with environmental factors to influence food and beverage fermentation, a topic of growing interest in the context of climate change and sustainable agriculture.},
}
@article {pmid38927252,
year = {2024},
author = {Huang, Y and Chen, Y and Xie, H and Feng, Y and Chen, S and Bao, B},
title = {Effects of Inducible Nitric Oxide Synthase (iNOS) Gene Knockout on the Diversity, Composition, and Function of Gut Microbiota in Adult Zebrafish.},
journal = {Biology},
volume = {13},
number = {6},
pages = {},
pmid = {38927252},
issn = {2079-7737},
support = {2022YFD2400103//the National Key R&amp;D Program of China/ ; 2021N3016//the Regional Development Project of Fujian/ ; },
abstract = {The gut microbiota constitutes a complex ecosystem that has an important impact on host health. In this study, genetically engineered zebrafish with inducible nitric oxide synthase (iNOS or NOS2) knockout were used as a model to investigate the effects of nos2a/nos2b gene single knockout and nos2 gene double knockout on intestinal microbiome composition and function. Extensive 16S rRNA sequencing revealed substantial changes in microbial diversity and specific taxonomic abundances, yet it did not affect the functional structure of the intestinal tissues. Notably, iNOS-deficient zebrafish demonstrated a decrease in Vibrio species and an increase in Aeromonas species, with more pronounced effects observed in double knockouts. Further transcriptomic analysis of the gut in double iNOS knockout zebrafish indicated significant alterations in immune-related and metabolic pathways, including the complement and PPAR signaling pathways. These findings underscore the crucial interplay between host genetics and gut microbiota, indicating that iNOS plays a key role in modulating the gut microbial ecology, host immune system, and metabolic responses.},
}
@article {pmid38926469,
year = {2024},
author = {Martin, LC and O'Hare, MA and Ghielmetti, G and Twesigomwe, D and Kerr, TJ and Gumbo, R and Buss, PE and Kitchin, N and Hemmings, SMJ and Miller, MA and Goosen, WJ},
title = {Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14768},
pmid = {38926469},
issn = {2045-2322},
support = {S007355//American Association of Zoo Veterinarians/ ; 86949//National Research Foundation, South Africa/ ; MND200409511840//National Research Foundation/ ; /WT_/Wellcome Trust/United Kingdom ; 222941/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; S005651//American Association of Zoo Veterinarians/ ; PMDS22052113333//National Research Foundation/ ; },
mesh = {Animals ; *Elephants/microbiology/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Respiratory System/microbiology ; Animals, Zoo/microbiology ; Sequence Analysis, DNA/methods ; Animals, Wild/microbiology ; Phylogeny ; },
abstract = {Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.},
}
@article {pmid38926391,
year = {2024},
author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A},
title = {Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5412},
pmid = {38926391},
issn = {2041-1723},
support = {1545756//National Science Foundation (NSF)/ ; 2004751//National Science Foundation (NSF)/ ; 2125798//National Science Foundation (NSF)/ ; 4813//Water Research Foundation (WRF)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Sewage/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/metabolism ; Water Purification/methods ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid/methods ; Drug Resistance, Bacterial/genetics ; Selection, Genetic ; },
abstract = {Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.},
}
@article {pmid38923208,
year = {2024},
author = {Bosch, J and Lebre, PH and Marais, E and Maggs-Kölling, G and Cowan, DA},
title = {Kinetics and pathways of sub-lithic microbial community (hypolithon) development.},
journal = {Environmental microbiology reports},
volume = {16},
number = {3},
pages = {e13290},
pmid = {38923208},
issn = {1758-2229},
support = {//University of Pretoria/ ; 113308//National Research Foundation/ ; 137954//National Research Foundation/ ; 95565//National Research Foundation/ ; },
mesh = {*Soil Microbiology ; *Cyanobacteria/genetics/isolation &amp; purification/growth &amp; development/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Desert Climate ; Namibia ; Kinetics ; Phylogeny ; DNA, Bacterial/genetics ; Soil/chemistry ; },
abstract = {Type I hypolithons are microbial communities dominated by Cyanobacteria. They adhere to the underside of semi-translucent rocks in desert pavements, providing them with a refuge from the harsh abiotic stresses found on the desert soil surface. Despite their crucial role in soil nutrient cycling, our understanding of their growth rates and community development pathways remains limited. This study aimed to quantify the dynamics of hypolithon formation in the pavements of the Namib Desert. We established replicate arrays of sterile rock tiles with varying light transmission in two areas of the Namib Desert, each with different annual precipitation regimes. These were sampled annually over 7 years, and the samples were analysed using eDNA extraction and 16S rRNA gene amplicon sequencing. Our findings revealed that in the zone with higher precipitation, hypolithon formation became evident in semi-translucent rocks 3 years after the arrays were set up. This coincided with a Cyanobacterial 'bloom' in the adherent microbial community in the third year. In contrast, no visible hypolithon formation was observed at the array set up in the hyper-arid zone. This study provides the first quantitative evidence of the kinetics of hypolithon development in hot desert environments, suggesting that development rates are strongly influenced by precipitation regimes.},
}
@article {pmid38922748,
year = {2024},
author = {Pérez-Pazos, E and Beidler, KV and Narayanan, A and Beatty, BH and Maillard, F and Bancos, A and Heckman, KA and Kennedy, PG},
title = {Fungi rather than bacteria drive early mass loss from fungal necromass regardless of particle size.},
journal = {Environmental microbiology reports},
volume = {16},
number = {3},
pages = {e13280},
pmid = {38922748},
issn = {1758-2229},
support = {SCW1632//Department of Energy Office of Biological and Environmental Research Genomic Science Program/ ; 2038293//National Science Foundation/ ; },
mesh = {*Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development/metabolism ; *Particle Size ; Fungi/growth &amp; development/classification/genetics/physiology ; Soil Microbiology ; Hydrogen-Ion Concentration ; Ascomycota/growth &amp; development/physiology ; },
abstract = {Microbial necromass is increasingly recognized as an important fast-cycling component of the long-term carbon present in soils. To better understand how fungi and bacteria individually contribute to the decomposition of fungal necromass, three particle sizes (>500, 250-500, and <250 μm) of Hyaloscypha bicolor necromass were incubated in laboratory microcosms inoculated with individual strains of two fungi and two bacteria. Decomposition was assessed after 15 and 28 days via necromass loss, microbial respiration, and changes in necromass pH, water content, and chemistry. To examine how fungal-bacterial interactions impact microbial growth on necromass, single and paired cultures of bacteria and fungi were grown in microplates containing necromass-infused media. Microbial growth was measured after 5 days through quantitative PCR. Regardless of particle size, necromass colonized by fungi had higher mass loss and respiration than both bacteria and uninoculated controls. Fungal colonization increased necromass pH, water content, and altered chemistry, while necromass colonized by bacteria remained mostly unaltered. Bacteria grew significantly more when co-cultured with a fungus, while fungal growth was not significantly affected by bacteria. Collectively, our results suggest that fungi act as key early decomposers of fungal necromass and that bacteria may require the presence of fungi to actively participate in necromass decomposition.},
}
@article {pmid38922446,
year = {2024},
author = {Filek, K and Vuković, BB and Žižek, M and DiBello, A and Kanjer, L and Trotta, A and Corrente, M and Bosak, S},
title = {Correction to: Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {84},
doi = {10.1007/s00248-024-02405-z},
pmid = {38922446},
issn = {1432-184X},
}
@article {pmid38921731,
year = {2024},
author = {Wang, C and Defoirdt, T and Rajkovic, A},
title = {The Effect of Caco-2 Cells on Sporulation and Enterotoxin Expression by Foodborne Clostridium perfringens.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
pmid = {38921731},
issn = {2076-0817},
support = {201808630020//China Scholarship Council/ ; BOF20/BAS/120//Special Research Fund of Ghent University/ ; 1506419N//Research Foundation - Flanders/ ; },
abstract = {Clostridium perfringens enterotoxin (Cpe)-producing strains cause gastrointestinal infections in humans and account for the second-largest number of all foodborne outbreaks caused by bacterial toxins. The Cpe toxin is only produced during sporulation; this process might be affected when C. perfringens comes into contact with host cells. The current study determined how the cpe expression levels and spore formation changed over time during co-culture with Caco-2 cells (as a model of intestinal epithelial cells). In co-culture with Caco-2 cells, total C. perfringens cell counts first decreased and then remained more or less stable, whereas spore counts were stable over the whole incubation period. The cpe mRNA level in the co-culture with Caco-2 cells increased more rapidly than in the absence of Caco-2 cells (3.9-fold higher levels in coculture than in the absence of Caco-2 cells after 8 h of incubation). Finally, we found that cpe expression is inhibited by a cue released by Caco-2 cells (8.3-fold lower levels in the presence of supernatants of Caco-2 cells than in the absence of the supernatants after 10 h of incubation); as a consequence, the increased expression in co-culture with Caco-2 cells must be caused by a factor associated with the Caco-2 cells.},
}
@article {pmid38920365,
year = {2024},
author = {Givati, S and Forchielli, E and Aharonovich, D and Barak, N and Weissberg, O and Belkin, N and Rahav, E and Segrè, D and Sher, D},
title = {Diversity in the utilization of different molecular classes of dissolved organic matter by heterotrophic marine bacteria.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0025624},
pmid = {38920365},
issn = {1098-5336},
support = {RGP0020/2016//Human Frontier Science Program (HFSP)/ ; NSFOCE-BSF 1635070//United States-Israel Binational Science Foundation (BSF)/ ; 1786/20//Israel Science Foundation (ISF)/ ; },
mesh = {*Seawater/microbiology ; *Heterotrophic Processes ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Mediterranean Sea ; Microbiota ; Amino Acids/metabolism ; Organic Chemicals/metabolism ; },
abstract = {UNLABELLED: Heterotrophic marine bacteria utilize and recycle dissolved organic matter (DOM), impacting biogeochemical cycles. It is currently unclear to what extent distinct DOM components can be used by different heterotrophic clades. Here, we ask how a natural microbial community from the Eastern Mediterranean Sea (EMS) responds to different molecular classes of DOM (peptides, amino acids, amino sugars, disaccharides, monosaccharides, and organic acids) comprising much of the biomass of living organisms. Bulk bacterial activity increased after 24 h for all treatments relative to the control, while glucose and ATP uptake decreased or remained unchanged. Moreover, while the per-cell uptake rate of glucose and ATP decreased, that of Leucin significantly increased for amino acids, reflecting their importance as common metabolic currencies in the marine environment. Pseudoalteromonadaceae dominated the peptides treatment, while different Vibrionaceae strains became dominant in response to amino acids and amino sugars. Marinomonadaceae grew well on organic acids, and Alteromonadaseae on disaccharides. A comparison with a recent laboratory-based study reveals similar peptide preferences for Pseudoalteromonadaceae, while Alteromonadaceae, for example, grew well in the lab on many substrates but dominated in seawater samples only when disaccharides were added. We further demonstrate a potential correlation between the genetic capacity for degrading amino sugars and the dominance of specific clades in these treatments. These results highlight the diversity in DOM utilization among heterotrophic bacteria and complexities in the response of natural communities.<br><br>IMPORTANCE: A major goal of microbial ecology is to predict the dynamics of natural communities based on the identity of the organisms, their physiological traits, and their genomes. Our results show that several clades of heterotrophic bacteria each grow in response to one or more specific classes of organic matter. For some clades, but not others, growth in a complex community is similar to that of isolated strains in laboratory monoculture. Additionally, by measuring how the entire community responds to various classes of organic matter, we show that these results are ecologically relevant, and propose that some of these resources are utilized through common uptake pathways. Tracing the path between different resources to the specific microbes that utilize them, and identifying commonalities and differences between different natural communities and between them and lab cultures, is an important step toward understanding microbial community dynamics and predicting how communities will respond to perturbations.},
}
@article {pmid38918384,
year = {2024},
author = {Dueholm, MKD and Andersen, KS and Korntved, AC and Rudkjøbing, V and Alves, M and Bajón-Fernández, Y and Batstone, D and Butler, C and Cruz, MC and Davidsson, &#xc5; and Erijman, L and Holliger, C and Koch, K and Kreuzinger, N and Lee, C and Lyberatos, G and Mutnuri, S and O'Flaherty, V and Oleskowicz-Popiel, P and Pokorna, D and Rajal, V and Recktenwald, M and Rodríguez, J and Saikaly, PE and Tooker, N and Vierheilig, J and De Vrieze, J and Wurzbacher, C and Nielsen, PH},
title = {MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5361},
pmid = {38918384},
issn = {2041-1723},
support = {Dark Matter and grant 13351//Villum Fonden (Villum Foundation)/ ; 6111-00617 A//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; },
mesh = {*Archaea/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; *Bacteria/genetics/classification/metabolism ; *Microbiota/genetics ; *Biodiversity ; *Phylogeny ; Wastewater/microbiology ; Bioreactors/microbiology ; Methane/metabolism ; Sequence Analysis, DNA ; },
abstract = {Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.},
}
@article {pmid38918217,
year = {2024},
author = {Duong, HL and Paufler, S and Harms, H and Maskow, T and Schlosser, D},
title = {Biocalorimetry-aided monitoring of fungal pretreatment of lignocellulosic agricultural residues.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {394},
pmid = {38918217},
issn = {1432-0614},
support = {911 Program//B&#x1ed9; Gi&#xe1;o d&#x1ee5;c v&#xe0; &#xd0;&#xe0;o t&#x1ea1;o/ ; },
mesh = {*Lignin/metabolism ; *Triticum/microbiology/chemistry ; *Fungi/metabolism ; Fermentation ; Hydrolysis ; Agriculture/methods ; },
abstract = {The present study aimed to investigate whether and how non-invasive biocalorimetric measurements could serve for process monitoring of fungal pretreatment during solid-state fermentation (SSF) of lignocellulosic agricultural residues such as wheat straw. Seven filamentous fungi representing different lignocellulose decay types were employed. Water-soluble sugars being immediately available after fungal pretreatment and those becoming water-extractable after enzymatic digestion of pretreated wheat straw with hydrolysing (hemi)cellulases were considered to constitute the total bioaccessible sugar fraction. The latter was used to indicate the success of pretreatments and linked to corresponding species-specific metabolic heat yield coefficients (YQ/X) derived from metabolic heat flux measurements during fungal wheat straw colonisation. An YQ/X range of about 120 to 140 kJ/g was seemingly optimal for pretreatment upon consideration of all investigated fungi and application of a non-linear Gaussian fitting model. Upon exclusion from analysis of the brown-rot basidiomycete Gloeophyllum trabeum, which differs from all other here investigated fungi in employing extracellular Fenton chemistry for lignocellulose decomposition, a linear relationship where amounts of total bioaccessible sugars were suggested to increase with increasing YQ/X values was obtained. It remains to be elucidated whether an YQ/X range being optimal for fungal pretreatment could firmly be established, or if the sugar accessibility for post-treatment generally increases with increasing YQ/X values as long as "conventional" enzymatic, i.e. (hemi)cellulase-based, lignocellulose decomposition mechanisms are operative. In any case, metabolic heat measurement-derived parameters such as YQ/X values may become very valuable tools supporting the assessment of the suitability of different fungal species for pretreatment of lignocellulosic substrates. KEY POINTS: • Biocalorimetry was used to monitor wheat straw pretreatment with seven filamentous fungi. • Metabolic heat yield coefficients (YQ/X) seem to indicate pretreatment success. • YQ/X values may support the selection of suitable fungal strains for pretreatment.},
}
@article {pmid38917910,
year = {2024},
author = {Gao, Y and Heng, S and Wang, J and Liu, Z and Liu, Y and Chen, B and Han, Y and Li, W and Lu, X and Zhen, G},
title = {Bioelectrochemically altering microbial ecology in upflow anaerobic sludge blanket to enhance methanogenesis fed with high-sulfate methanolic wastewater.},
journal = {Bioresource technology},
volume = {406},
number = {},
pages = {131026},
doi = {10.1016/j.biortech.2024.131026},
pmid = {38917910},
issn = {1873-2976},
mesh = {*Wastewater/microbiology ; *Methanol/metabolism ; *Methane/metabolism ; *Sulfates/metabolism ; *Sewage/microbiology ; Anaerobiosis ; Bioreactors/microbiology ; Electrodes ; },
abstract = {A bioelectrochemical upflow anaerobic sludge blanket (BE-UASB) was constructed and compared with the traditional UASB to investigate the role of bioelectrocatalysis in modulating methanogenesis and sulfidogensis involved within anaerobic treatment of high-sulfate methanolic wastewater (COD/SO4[2-] ratio ≤ 2). Methane production rate for BE-UASB was 1.4 times higher than that of the single UASB, while SO4[2-] removal stabilized at 16.7%. Bioelectrocatalysis selectively enriched key functional anaerobes and stimulated the secretion of extracellular polymeric substances, especially humic acids favoring electron transfer, thereby accelerating the electroactive biofilms development of electrodes. Methanomethylovorans was the dominant genus (35%) to directly convert methanol to CH4. Methanobacterium as CO2 electroreduction methane-producing archaea appeared only on electrodes. Acetobacterium exhibited anode-dependence, which provided acetate for sulfate-reducing bacteria (norank Syntrophobacteraceae and Desulfomicrobium) through synergistic coexistence. This study confirmed that BE-UASB regulated the microbial ecology to achieve efficient removal and energy recovery of high-sulfate methanolic wastewater.},
}
@article {pmid38917500,
year = {2024},
author = {Zhang, D and Calmanovici, B and Marican, H and Reisser, J and Summers, S},
title = {The assembly and ecological roles of biofilms attached to plastic debris of Ashmore reef.},
journal = {Marine pollution bulletin},
volume = {205},
number = {},
pages = {116651},
doi = {10.1016/j.marpolbul.2024.116651},
pmid = {38917500},
issn = {1879-3363},
mesh = {*Biofilms ; *Plastics ; Australia ; Microbiota ; Seawater/microbiology ; Coral Reefs ; Bacteria ; Waste Products ; },
abstract = {Plastic pollution in the ocean is a global environmental hazard aggravated by poor management of plastic waste and growth of annual plastic consumption. Microbial communities colonizing the plastic's surface, the plastisphere, has gained global interest resulting in numerous efforts to characterize the plastisphere. However, there are insufficient studies deciphering the underlying metabolic processes governing the function of the plastisphere and the plastic they reside upon. Here, we collected plastic and seawater samples from Ashmore Reef in Australia to examine the planktonic microbes and plastic associated biofilm (PAB) to investigate the ecological impact, pathogenic potential, and plastic degradation capabilities of PAB in Ashmore Reef, as well as the role and impact of bacteriophages on PAB. Using high-throughput metagenomic sequencing, we demonstrated distinct microbial communities between seawater and PAB. Similar numbers of pathogenic bacteria were found in both sample types, yet plastic and seawater select for different pathogen populations. Virulence Factor analysis further illustrated stronger pathogenic potential in PAB, highlighting the pathogenicity of environmental PAB. Furthermore, functional analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed xenobiotic degradation and fatty acid degradation to be enriched in PABs. In addition, construction of metagenome-assembled genomes (MAG) and functional analysis further demonstrated the presence of a complete Polyethylene (PE) degradation pathway in multiple Proteobacteria MAGs, especially in Rhodobacteriaceae sp. Additionally, we identified viral population presence in PAB, revealing the key role of bacteriophages in shaping these communities within the PAB. Our result provides a comprehensive overview of the various ecological processes shaping microbial community on marine plastic debris.},
}
@article {pmid38916294,
year = {2024},
author = {Chadwick, GL and Dury, GA and Nayak, DD},
title = {Physiological and transcriptomic response to methyl-coenzyme M reductase limitation in Methanosarcina acetivorans.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0222023},
pmid = {38916294},
issn = {1098-5336},
support = {//Searle Scholars Program (SSP)/ ; Beckman Young Investigator Award//Arnold and Mabel Beckman Foundation (AMBF)/ ; Simons Early Career Investigator in Marine Microbial Ecology and Evolution//Simons Foundation (SF)/ ; Packard Fellowship in Science and Engineering//David and Lucile Packard Foundation (PF)/ ; Chan-Zuckerberg Biohub - San Francisco Investigator//Chan Zuckerberg Initiative (CZI)/ ; 5T32GM06698-14//HHS | National Institutes of Health (NIH)/ ; //Adolph C. and Mary Sprague Miller Institute for Basic Research in Science, University of California Berkeley (MIBRS)/ ; },
mesh = {*Methanosarcina/genetics/enzymology/metabolism ; *Oxidoreductases/metabolism/genetics ; *Transcriptome ; Methane/metabolism ; Archaeal Proteins/genetics/metabolism ; Gene Expression Regulation, Archaeal ; Operon ; },
abstract = {UNLABELLED: Methyl-coenzyme M reductase (MCR) catalyzes the final step of methanogenesis, the microbial metabolism responsible for nearly all biological methane emissions to the atmosphere. Decades of biochemical and structural research studies have generated detailed insights into MCR function in vitro, yet very little is known about the interplay between MCR and methanogen physiology. For instance, while it is routinely stated that MCR catalyzes the rate-limiting step of methanogenesis, this has not been categorically tested. In this study, to gain a more direct understanding of MCR's control on the growth of Methanosarcina acetivorans, we generate a strain with an inducible mcr operon on the chromosome, allowing for careful control of MCR expression. We show that MCR is not growth rate-limiting in substrate-replete batch cultures. However, through careful titration of MCR expression, growth-limiting state(s) can be obtained. Transcriptomic analysis of M. acetivorans experiencing MCR limitation reveals a global response with hundreds of differentially expressed genes across diverse functional categories. Notably, MCR limitation leads to strong induction of methylsulfide methyltransferases, likely due to insufficient recycling of metabolic intermediates. In addition, the mcr operon is not transcriptionally regulated, i.e., it is constitutively expressed, suggesting that the overabundance of MCR might be beneficial when cells experience nutrient limitation or stressful conditions. Altogether, we show that there is a wide range of cellular MCR concentrations that can sustain optimal growth, suggesting that other factors such as anabolic reactions might be rate-limiting for methanogenic growth.<br><br>IMPORTANCE: Methane is a potent greenhouse gas that has contributed to ca. 25% of global warming in the post-industrial era. Atmospheric methane is primarily of biogenic origin, mostly produced by microorganisms called methanogens. Methyl-coenzyme M reductase (MCR) catalyzes methane formatio in methanogens. Even though MCR comprises ca. 10% of the cellular proteome, it is hypothesized to be growth-limiting during methanogenesis. In this study, we show that Methanosarcina acetivorans cells grown in substrate-replicate batch cultures produce more MCR than its cellular demand for optimal growth. The tools outlined in this study can be used to refine metabolic models of methanogenesis and assay lesions in MCR in a higher-throughput manner than isolation and biochemical characterization of pure protein.},
}
@article {pmid38915372,
year = {2024},
author = {Levi, EE and Jeppesen, E and Nejstgaard, JC and Davidson, TA},
title = {Chlorophyll-a determinations in mesocosms under varying nutrient and temperature treatments: in-situ fluorescence sensors versus in-vitro measurements.},
journal = {Open research Europe},
volume = {4},
number = {},
pages = {69},
pmid = {38915372},
issn = {2732-5121},
abstract = {Harmful algal blooms (HABs) are a significant threat to freshwater ecosystems, and monitoring for changes in biomass is therefore important. Fluorescence in-situ sensors enable rapid and high frequency real-time data collection and have been widely used to determine chlorophyll- a (Chla) concentrations that are used as an indicator of the total algal biomass. However, conversion of fluorescence to equivalent Chla concentrations is often complicated due to biofouling, phytoplankton composition and the type of equipment used. Here, we validated measurements from 24 Chla and 12 phycocyanin (cyanobacteria indicator) fluorescence in-situ sensors (Cyclops-7F, Turner Designs) against spectrophotometrically (in-vitro) determined Chla and tested a data-cleaning procedure for eliminating data errors and impacts of non-photochemical quenching. The test was done across a range of freshwater plankton communities in 24 mesocosms (i.e. experimental tanks) with a 2x3 (high and low nutrient x ambient, IPCC-A2 and IPCC-A2+50% temperature scenarios) factorial design. For most mesocosms (tanks), we found accurate (r [2] ≥ 0.7) calibration of in-situ Chla fluorescence data using simple linear regression. An exception was tanks with high in-situ phycocyanin fluorescence, for which multiple regressions were employed, which increased the explained variance by >16%. Another exception was the low Chla concentration tanks (r [2] < 0.3). Our results also show that the high frequency in-situ fluorescence data recorded the timing of sudden Chla variations, while less frequent in-vitro sampling sometimes missed these or, when recorded, the duration of changes was inaccurately determined. Fluorescence in-situ sensors are particularly useful to detect and quantify sudden phytoplankton biomass variations through high frequency measurements, especially when using appropriate data-cleaning methods and accounting for factors that can impact the fluorescence readings. Nevertheless, corroborating these data with in-vitro Chla assessments would provide additional validation for the early warnings provided by sensor data.},
}
@article {pmid38912052,
year = {2024},
author = {Goldman, SL and Sanders, JG and Sprockett, DD and Landers, A and Yan, W and Moeller, AH},
title = {Hackflex library preparation enables low-cost metagenomic profiling.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae075},
pmid = {38912052},
issn = {2730-6151},
support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; T32 AI145821/AI/NIAID NIH HHS/United States ; },
abstract = {Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/μL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.},
}
@article {pmid38910491,
year = {2024},
author = {Kommana, G and Hupfer, M and Woodhouse, JN and Grossart, HP and Goldhammer, T},
title = {Reduced greenhouse gas emissions from particulate organic matter degradation in iron-enriched sediments.},
journal = {Environmental science. Processes &amp; impacts},
volume = {26},
number = {7},
pages = {1227-1244},
doi = {10.1039/d4em00185k},
pmid = {38910491},
issn = {2050-7895},
mesh = {*Geologic Sediments/chemistry ; *Greenhouse Gases/analysis ; *Iron ; Particulate Matter/analysis ; Germany ; Air Pollutants/analysis ; Environmental Monitoring ; Biodegradation, Environmental ; Water Pollutants, Chemical/analysis ; },
abstract = {Iron (Fe) plays an important role in the biogeochemical cycling of carbon and nutrients in aquatic systems. Reactive Fe phases can interact with organic carbon and facilitate the removal of carbon from the biogeochemical cycle; however, this important ecosystem function is often strongly controlled by Fe availability. Due to pollution from lignite mining in the Lusatian province in Northeast Germany, large amounts of iron and sulfate are released into the fluvial-lacustrine system of the Spree River. It was hypothesized that the input of freshly precipitated iron oxyhydroxides from mining areas (e.g., ferrihydrite) alter the biodegradation of particulate organic matter (POM) in downstream lacustrine sediments. To investigate the Fe-dependent degradation of POM, slurries mimicking iron-polluted sediments (85 mg Fe per g, 116 mg Fe per g, and 149 mg Fe per g dry weight) were incubated with plankton or leaf POM under anoxic and oxic headspace conditions, and CO2 and CH4 emissions, water chemistry, and stable isotopes of dissolved inorganic carbon were measured. The experiments revealed that (i) with an increasing Fe content, the CO2 and CH4 emissions were gradually reduced, (ii) CO2 and CH4 production was higher during plankton degradation than during leaf decomposition, and (iii) under oxic conditions, CO2 production was higher and CH4 production was lower when compared to the treatments under anoxic conditions. These findings demonstrate that while benthic mineralization of fresh POM typically releases greenhouse gases into the water column, the availability of iron oxyhydroxides can contribute to reduced greenhouse gas emissions from sediments. This is of considerable relevance for future carbon budgets of similar mining-affected, iron-polluted fluvial-lacustrine river systems.},
}
@article {pmid38909617,
year = {2024},
author = {Kullberg, RFJ and Wikki, I and Haak, BW and Kauko, A and Galenkamp, H and Peters-Sengers, H and Butler, JM and Havulinna, AS and Palmu, J and McDonald, D and Benchraka, C and Abdel-Aziz, MI and Prins, M and Maitland van der Zee, AH and van den Born, BJ and Jousilahti, P and de Vos, WM and Salomaa, V and Knight, R and Lahti, L and Nieuwdorp, M and Niiranen, T and Wiersinga, WJ},
title = {Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies.},
journal = {The Lancet. Microbe},
volume = {5},
number = {9},
pages = {100864},
doi = {10.1016/S2666-5247(24)00079-X},
pmid = {38909617},
issn = {2666-5247},
mesh = {Humans ; Middle Aged ; Adult ; *Hospitalization/statistics &amp; numerical data ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Aged ; Finland/epidemiology ; *Butyrates/metabolism ; *RNA, Ribosomal, 16S/genetics/analysis ; Netherlands/epidemiology ; Young Adult ; *Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Adolescent ; Communicable Diseases/microbiology/epidemiology ; Cohort Studies ; Risk Factors ; },
abstract = {BACKGROUND: Microbiota alterations are common in patients hospitalised for severe infections, and preclinical models have shown that anaerobic butyrate-producing gut bacteria protect against systemic infections. However, the relationship between microbiota disruptions and increased susceptibility to severe infections in humans remains unclear. We investigated the relationship between gut microbiota and the risk of future infection-related hospitalisation in two large population-based cohorts.<br><br>METHODS: In this observational microbiome study, gut microbiota were characterised using 16S rRNA gene sequencing in independent population-based cohorts from the Netherlands (HELIUS study; derivation cohort) and Finland (FINRISK 2002 study; validation cohort). HELIUS was conducted in Amsterdam, Netherlands, and included adults (aged 18-70 years at inclusion) who were randomly sampled from the municipality register of Amsterdam. FINRISK 2002 was conducted in six regions in Finland and is a population survey that included a random sample of adults (aged 25-74 years). In both cohorts, participants completed questionnaires, underwent a physical examination, and provided a faecal sample at inclusion (Jan 3, 2013, to Nov 27, 2015, for HELIUS participants and Jan 21 to April 19, 2002, for FINRISK participants. For inclusion in our study, a faecal sample needed to be provided and successfully sequenced, and national registry data needed to be available. Primary predictor variables were microbiota composition, diversity, and relative abundance of butyrate-producing bacteria. Our primary outcome was hospitalisation or mortality due to any infectious disease during 5-7-year follow-up after faecal sample collection, based on national registry data. We examined associations between microbiota and infection risk using microbial ecology and Cox proportional hazards.<br><br>FINDINGS: We profiled gut microbiota from 10&#x2009;699 participants (4248 [39&#xb7;7%] from the derivation cohort and 6451&#xa0;[60&#xb7;3%] from the validation cohort). 602 (5&#xb7;6%) participants (152 [3&#xb7;6%] from the derivation cohort; 450 [7&#xb7;0%] from the validation cohort) were hospitalised or died due to infections during follow-up. Gut microbiota composition of these participants differed from those without hospitalisation for infections (derivation p=0&#xb7;041; validation p=0&#xb7;0002). Specifically, higher relative abundance of butyrate-producing bacteria was associated with a reduced risk of hospitalisation for infections (derivation cohort cause-specific hazard ratio 0&#xb7;75 [95% CI 0&#xb7;60-0&#xb7;94] per 10% increase in butyrate producers, p=0&#xb7;013; validation cohort 0&#xb7;86 [0&#xb7;77-0&#xb7;96] per 10% increase, p=0&#xb7;0077). These associations remained unchanged following adjustment for demographics, lifestyle, antibiotic exposure, and comorbidities.<br><br>INTERPRETATION: Gut microbiota composition, specifically colonisation with butyrate-producing bacteria, was associated with protection against hospitalisation for infectious diseases in the general population across two independent European cohorts. Further studies should investigate whether modulation of the microbiome can reduce the risk of severe infections.<br><br>FUNDING: Amsterdam UMC, Porticus, National Institutes of Health, Netherlands Organisation for Health Research and Development (ZonMw), and Leducq Foundation.},
}
@article {pmid38906896,
year = {2024},
author = {Schorn, S and Graf, JS and Littmann, S and Hach, PF and Lavik, G and Speth, DR and Schubert, CJ and Kuypers, MMM and Milucka, J},
title = {Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {5293},
pmid = {38906896},
issn = {2041-1723},
mesh = {*Methane/metabolism ; *Lakes/microbiology ; *Oxidation-Reduction ; Anaerobiosis ; Methylococcaceae/metabolism/genetics ; Metagenomics ; Oxygen/metabolism ; },
abstract = {Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d[-1]. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity.},
}
@article {pmid38904568,
year = {2024},
author = {Ganier, C and Callewaert, C and Matos, TR and Sonkoly, E and Dyring-Andersen, B and Rajan, N},
title = {Young ESDR: Engaging and Nurturing the Next-Generation Skin Research Community.},
journal = {The Journal of investigative dermatology},
volume = {144},
number = {11},
pages = {2349-2350},
doi = {10.1016/j.jid.2024.05.004},
pmid = {38904568},
issn = {1523-1747},
}
@article {pmid38902915,
year = {2024},
author = {Kerr, BJ and Anderson, CL and Pearce, SC and Schweer, WP},
title = {Dietary isoacids effects on growth, nitrogen, and energy digestibility, and fecal volatile fatty acids and microbial ecology in finishing pigs.},
journal = {Journal of animal science},
volume = {102},
number = {},
pages = {},
pmid = {38902915},
issn = {1525-3163},
mesh = {Animals ; *Feces/chemistry/microbiology ; *Animal Feed/analysis ; *Digestion/drug effects ; *Diet/veterinary ; *Fatty Acids, Volatile/metabolism ; Female ; *Nitrogen/metabolism ; *Animal Nutritional Physiological Phenomena ; Swine/growth &amp; development ; Energy Metabolism/drug effects ; },
abstract = {Isoacids are branched ketoacids which when fed to ruminants have been shown to enhance the growth of fiber-digesting organisms. Ninety finishing gilts were individually fed dietary treatments consisting of diet type: corn-soybean meal (CSBM), a diet containing 40% distillers dried grains with solubles (DDGS), or a diet containing 40% sugar beet pulp (SBP); in combination with either no feed additive (CNT), the addition of 0.50% isobutyrate (IB), or the addition of a 0.88% mix of isobutyrate, isovalerate, and 2-methylbutyrate (MX). Gilts consumed an average of 2.171 kg/d over the 28-d trial. On d 26, fresh fecal samples were collected for determination of apparent total tract digestibility (ATTD) of gross energy (GE) and nitrogen (N), determination of fecal volatile fatty acids (VFA), and evaluation of microbial ecology. There was no interaction between diet type and isoacid addition, and no main effect of isoacid or diet type on alpha or Shannon microbial diversity measures (P > 0.05). There was no interaction between isoacid addition and diet type, and no main effect of isoacid addition on microbial beta diversity (P > 0.05), but differences were observed in microbial beta diversity due to diet type (P ≤ 0.05). There was no interaction between diet type and isoacid addition observed in fecal VFA concentrations (P > 0.05), with only minor differences in fecal VFA concentrations noted due to isoacid addition (P ≤ 0.05). The interaction between diet type and isoacid addition on ATTD of dietary GE and N (P ≤ 0.01) was large because the addition of IB did not affect the ATTD of GE or N in pigs fed the CSBM diet, but increased ATTD of GE and N in pigs fed diets containing DDGS and decreased the ATTD of GE and N in pigs fed diets containing SBP. In contrast, adding a blend of isoacids (i.e., MX) reduced the ATTD of GE and N, regardless of diet type. There was no interaction between diet type and isoacid addition, and no effect of isoacid addition was observed on pig performance (P > 0.05). Diet type did not affect average daily gain (P > 0.05), but pigs fed diets containing DDGS or SBP consumed less feed (P = 0.01) and exhibited greater GF ratios compared to pigs fed the low-fiber CSBM diet (P ≤ 0.05). In conclusion, there was little to no effect of isoacid addition on microbial ecology, fecal VFA concentrations, ATTD of GE or N, or pig performance, but the improvement in ATTD of GE and N in pigs fed diets containing DDGS when IB was added warrants further investigation.},
}
@article {pmid38896653,
year = {2024},
author = {Elliott, JFK and McLeod, DV and Taylor, TB and Westra, ER and Gandon, S and Watson, BNJ},
title = {Conditions for the spread of CRISPR-Cas immune systems into bacterial populations.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38896653},
issn = {1751-7370},
support = {BB/T008741/1//Biotechnology and Biological Sciences Research Council SWBio DTP/ ; DH150169//Royal Society Dorothy Hodgkin Fellowship/ ; NE/S001921/1//Natural Environment Research Council/ ; BB/X010600/1//Biotechnology and Biological Sciences Research Council Discovery Fellowship/ ; },
mesh = {*CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Bacteria/genetics/virology/classification ; Pseudomonas aeruginosa/virology/genetics/immunology ; Gene Transfer, Horizontal ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Bacteria contain a wide variety of innate and adaptive immune systems which provide protection to the host against invading genetic material, including bacteriophages (phages). It is becoming increasingly clear that bacterial immune systems are frequently lost and gained through horizontal gene transfer. However, how and when new immune systems can become established in a bacterial population have remained largely unstudied. We developed a joint epidemiological and evolutionary model that predicts the conditions necessary for the spread of a CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) immune system into a bacterial population lacking this system. We found that whether bacteria carrying CRISPR-Cas will spread (increase in frequency) into a bacterial population depends on the abundance of phages and the difference in the frequency of phage resistance mechanisms between bacteria carrying a CRISPR-Cas immune system and those not (denoted as ${f}
_{\Delta }
$). Specifically, the abundance of cells carrying CRISPR-Cas will increase if there is a higher proportion of phage resistance (either via CRISPR-Cas immunity or surface modification) in the CRISPR-Cas-possessing population than in the cells lacking CRISPR-Cas. We experimentally validated these predictions in a model using Pseudomonas aeruginosa PA14 and phage DMS3vir. Specifically, by varying the initial ratios of different strains of bacteria that carry alternative forms of phage resistance, we confirmed that the spread of cells carrying CRISPR-Cas through a population can be predicted based on phage density and the relative frequency of resistance phenotypes. Understanding which conditions promote the spread of CRISPR-Cas systems helps to predict when and where these defences can become established in bacterial populations after a horizontal gene transfer event, both in ecological and clinical contexts.},
}
@article {pmid38896454,
year = {2024},
author = {Zhang, Y and Quensen, J and Chen, B and Li, H and Tiedje, J and Sun, W and Qian, X},
title = {Paenalcaligenes faecalis sp. nov., a novel species of the family Alcaligenaceae isolated from chicken faeces.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {6},
pages = {},
doi = {10.1099/ijsem.0.006429},
pmid = {38896454},
issn = {1466-5034},
mesh = {Animals ; *Base Composition ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Chickens/microbiology ; *Feces/microbiology ; *DNA, Bacterial/genetics ; *Nucleic Acid Hybridization ; *Bacterial Typing Techniques ; *Sequence Analysis, DNA ; *Alcaligenaceae/genetics/classification/isolation &amp; purification ; Fatty Acids ; Genome, Bacterial ; },
abstract = {A Gram-negative, motile, rod-shaped aerobic and alkalogenic bacterium, designated as strain YLCF04[T], was isolated from chicken faeces. Its growth was optimal at 28 °C (range, 10-40 °C), pH 8 (range, pH 6-9) and in 1 % (w/v) NaCl (range, 0-10 %). It was classified to the genus Paenalcaligenes and was most closely related to Paenalcaligenes hominis CCUG 53761A[T] (97.5 % similarity) based on 16S rRNA gene sequence analysis. Average nucleotide identity and digital DNA-DNA hybridization values between YLCF04[T] and P. hominis CCUG 53761A[T] were 76.3 and 18.2 %, respectively. Strain YLCF04[T] has a genome size of 2.7 Mb with DNA G+C content of 46.3 mol%. Based on its phylogenetic, genomic, phenotypic and biochemical characteristics, strain YLCF04[T] represents a novel species of the genus Paenalcaligenes, for which the name Paenalcaligenes faecalis sp. nov. is proposed. The type strain is YLCF04[T] (=CCTCC AB 2022359[T]= KCTC 92789[T]).},
}
@article {pmid38895568,
year = {2024},
author = {Puente-Sánchez, F and Macías-Pérez, LA and Campbell, KL and Royo-Llonch, M and Balagué, V and Sánchez, P and Tamames, J and Mundy, CJ and Pedrós-Alió, C},
title = {Bacterioplankton taxa compete for iron along the early spring-summer transition in the Arctic Ocean.},
journal = {Ecology and evolution},
volume = {14},
number = {6},
pages = {e11546},
pmid = {38895568},
issn = {2045-7758},
abstract = {Microbial assemblages under the sea ice of the Dease Strait, Canadian Arctic, were sequenced for metagenomes of a small size fraction (0.2-3 μm). The community from early March was typical for this season, with Alpha- and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes. Toward summer, Bacteroidetes, and particularly the genus Polaribacter, became increasingly dominant, followed by the Gammaproteobacteria. Analysis of genes responsible for microbial acquisition of iron showed an abundance of ABC transporters for divalent cations and ferrous iron. The most abundant transporters, however, were the outer membrane TonB-dependent transporters of iron-siderophore complexes. The abundance of iron acquisition genes suggested this element was essential for the microbial assemblage. Interestingly, Gammaproteobacteria were responsible for most of the siderophore synthesis genes. On the contrary, Bacteroidetes did not synthesize siderophores but accounted for most of the transporters, suggesting a role as cheaters in the competition for siderophores as public goods. This cheating ability of the Bacteroidetes may have contributed to their dominance in the summer.},
}
@article {pmid38894967,
year = {2024},
author = {Zou, C and Yi, X and Li, H and Bizic, M and Berman-Frank, I and Gao, K},
title = {Correlation of methane production with physiological traits in Trichodesmium IMS 101 grown with methylphosphonate at different temperatures.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1396369},
pmid = {38894967},
issn = {1664-302X},
abstract = {The diazotrophic cyanobacterium Trichodesmium has been recognized as a potentially significant contributor to aerobic methane generation via several mechanisms including the utilization of methylphophonate (MPn) as a source of phosphorus. Currently, there is no information about how environmental factors regulate methane production by Trichodesmium. Here, we grew Trichodesmium IMS101 at five temperatures ranging from 16 to 31°C, and found that its methane production rates increased with rising temperatures to peak (1.028 ± 0.040 nmol CH4 μmol POC[-1] day[-1]) at 27°C, and then declined. Its specific growth rate changed from 0.03 ± 0.01 d[-1] to 0.34 ± 0.02 d[-1], with the optimal growth temperature identified between 27 and 31°C. Within the tested temperature range the Q10 for the methane production rate was 4.6 ± 0.7, indicating a high sensitivity to thermal changes. In parallel, the methane production rates showed robust positive correlations with the assimilation rates of carbon, nitrogen, and phosphorus, resulting in the methane production quotients (molar ratio of carbon, nitrogen, or phosphorus assimilated to methane produced) of 227-494 for carbon, 40-128 for nitrogen, and 1.8-3.4 for phosphorus within the tested temperature range. Based on the experimental data, we estimated that the methane released from Trichodesmium can offset about 1% of its CO2 mitigation effects.},
}
@article {pmid38892722,
year = {2024},
author = {Thompson, RS and Bowers, SJ and Vargas, F and Hopkins, S and Kelley, T and Gonzalez, A and Lowry, CA and Dorrestein, PC and Vitaterna, MH and Turek, FW and Knight, R and Wright, KP and Fleshner, M},
title = {A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Produces Dynamic and Reproducible Changes in the Gut Microbial Ecosystem in Male Rats.},
journal = {Nutrients},
volume = {16},
number = {11},
pages = {},
pmid = {38892722},
issn = {2072-6643},
support = {N00014-15-1-2809//Office of Naval Research/ ; },
mesh = {Animals ; *Prebiotics ; Male ; *Gastrointestinal Microbiome/drug effects ; *Rats, Sprague-Dawley ; *Oligosaccharides/pharmacology/administration &amp; dosage ; *Glucans ; Rats ; Bile Acids and Salts/metabolism ; Feces/microbiology ; Bacteria/classification/metabolism ; RNA, Ribosomal, 16S ; Diet/methods ; },
abstract = {Despite substantial evidence supporting the efficacy of prebiotics for promoting host health and stress resilience, few experiments present evidence documenting the dynamic changes in microbial ecology and fecal microbially modified metabolites over time. Furthermore, the literature reports a lack of reproducible effects of prebiotics on specific bacteria and bacterial-modified metabolites. The current experiments examined whether consumption of diets enriched in prebiotics (galactooligosaccharides (GOS) and polydextrose (PDX)), compared to a control diet, would consistently impact the gut microbiome and microbially modified bile acids over time and between two research sites. Male Sprague Dawley rats were fed control or prebiotic diets for several weeks, and their gut microbiomes and metabolomes were examined using 16S rRNA gene sequencing and untargeted LC-MS/MS analysis. Dietary prebiotics altered the beta diversity, relative abundance of bacterial genera, and microbially modified bile acids over time. PICRUSt2 analyses identified four inferred functional metabolic pathways modified by the prebiotic diet. Correlational network analyses between inferred metabolic pathways and microbially modified bile acids revealed deoxycholic acid as a potential network hub. All these reported effects were consistent between the two research sites, supporting the conclusion that dietary prebiotics robustly changed the gut microbial ecosystem. Consistent with our previous work demonstrating that GOS/PDX reduces the negative impacts of stressor exposure, we propose that ingesting a diet enriched in prebiotics facilitates the development of a health-promoting gut microbial ecosystem.},
}
@article {pmid38892504,
year = {2024},
author = {Duysburgh, C and Govaert, M and Guillemet, D and Marzorati, M},
title = {Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties.},
journal = {Nutrients},
volume = {16},
number = {11},
pages = {},
pmid = {38892504},
issn = {2072-6643},
mesh = {*Prebiotics ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Gum Arabic/pharmacology ; *Dietary Fiber/pharmacology ; Dietary Supplements ; Colon/microbiology/metabolism/drug effects ; Fermentation ; Bacteria/drug effects/classification ; },
abstract = {Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine).},
}
@article {pmid38891933,
year = {2024},
author = {Carpio, LE and Olivares, M and Benítez-Paez, A and Serrano-Candelas, E and Barigye, SJ and Sanz, Y and Gozalbes, R},
title = {Comparative Binding Study of Gliptins to Bacterial DPP4-like Enzymes for the Treatment of Type 2 Diabetes Mellitus (T2DM).},
journal = {International journal of molecular sciences},
volume = {25},
number = {11},
pages = {},
pmid = {38891933},
issn = {1422-0067},
support = {reference INNTAL32/19/002, INNTA3/2021/16 and INNTA3/2022/20//Agencia Valenciana de la innovaci&#xf3;/ ; grant PID2020-119536RB-I00//Spanish Ministry of Science, Innovation and Universities (MCIU)/ ; APOTIP/2021/035//Generalitat Valenciana/ ; CEX2021-001189-S/MCIU/AEI/10.13039/501100011033//Spanish Government MCIU/AEI/ ; },
mesh = {Humans ; Bacteria/metabolism ; Bacterial Proteins/metabolism/chemistry ; Binding Sites ; *Diabetes Mellitus, Type 2/metabolism/drug therapy ; *Dipeptidyl Peptidase 4/metabolism/chemistry ; *Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Gastrointestinal Microbiome ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; },
abstract = {The role of the gut microbiota and its interplay with host metabolic health, particularly in the context of type 2 diabetes mellitus (T2DM) management, is garnering increasing attention. Dipeptidyl peptidase 4 (DPP4) inhibitors, commonly known as gliptins, constitute a class of drugs extensively used in T2DM treatment. However, their potential interactions with gut microbiota remain poorly understood. In this study, we employed computational methodologies to investigate the binding affinities of various gliptins to DPP4-like homologs produced by intestinal bacteria. The 3D structures of DPP4 homologs from gut microbiota species, including Segatella copri, Phocaeicola vulgatus, Bacteroides uniformis, Parabacteroides merdae, and Alistipes sp., were predicted using computational modeling techniques. Subsequently, molecular dynamics simulations were conducted for 200 ns to ensure the stability of the predicted structures. Stable structures were then utilized to predict the binding interactions with known gliptins through molecular docking algorithms. Our results revealed binding similarities of gliptins toward bacterial DPP4 homologs compared to human DPP4. Specifically, certain gliptins exhibited similar binding scores to bacterial DPP4 homologs as they did with human DPP4, suggesting a potential interaction of these drugs with gut microbiota. These findings could help in understanding the interplay between gliptins and gut microbiota DPP4 homologs, considering the intricate relationship between the host metabolism and microbial communities in the gut.},
}
@article {pmid38890249,
year = {2024},
author = {Plewa-Tutaj, K and Krzyściak, P and Dobrzycka, A},
title = {Mycological air contamination level and biodiversity of airborne fungi isolated from the zoological garden air - preliminary research.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {30},
pages = {43066-43079},
pmid = {38890249},
issn = {1614-7499},
support = {2022/06/X/NZ8/00430//National Science Center, Poland/ ; },
mesh = {*Air Microbiology ; *Fungi/isolation &amp; purification/classification ; *Biodiversity ; Animals ; *Environmental Monitoring ; Gardens ; Animals, Zoo/microbiology ; },
abstract = {The aim of this paper was to evaluate the degree of mycological air contamination and determine the taxonomic diversity of airborne fungi residing in the air of 20 different animal facilities in a zoological garden. The concentrations of fungi in the zoological garden were measured using a MAS-100 air sampler. The collected microorganisms were identified using the combination of molecular and morphological methods. The fungal concentration ranged from 50 to 3.65 × 10[4] CFU/m[3] during the whole study. The quantitative analysis of the fungal aerosol showed that the obtained concentration values were lower than the recommended permissible limits (5 × 10[4] CFU/m[3] for fungi). Environmental factors, including temperature and relative humidity, exerted a varying effect on the presence and concentration of isolated fungi. Relative humidity was shown to correlate positively with the concentration of fungal spores in the air of the facilities studied (rho = 0.57, p < 0.0021). In parallel, no significant correlation was established between temperature and total fungal concentration (rho = - 0.1, p < 0.2263). A total of 112 fungal strains belonging to 50 species and 10 genera were isolated. Penicillium was the dominant genera, including 58.9% of total fungal strains, followed by Aspergillus 25.89%, Cladosporium 3.57%, Talaromyces 3.57%, Mucor 1.78%, Schizophyllum 1.78%, Syncephalastrum 0.89%, Alternaria 0.89%, Absidia 0.89%, and Cunninghamella 0.89%. Our preliminary studies provide basic information about the fungal concentrations, as well as their biodiversity in zoological garden. Further studies are needed to generate additional data from long-term sampling in order to increase our understanding of airborne fungal composition in the zoological garden.},
}
@article {pmid38888768,
year = {2024},
author = {Sanderson, H and White, AP},
title = {Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2813},
number = {},
pages = {19-37},
pmid = {38888768},
issn = {1940-6029},
mesh = {*Salmonella/genetics ; Humans ; *Genomics/methods ; *Salmonella Infections/microbiology/epidemiology ; *Phylogeny ; *Genome, Bacterial ; *Molecular Epidemiology/methods ; Virulence Factors/genetics ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; },
abstract = {Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.},
}
@article {pmid38888737,
year = {2024},
author = {Sagar, A and Rai, S and Sharma, S and Perveen, K and Bukhari, NA and Sayyed, RZ and Mastinu, A},
title = {Molecular Characterization Reveals Biodiversity and Biopotential of Rhizobacterial Isolates of Bacillus Spp.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {83},
pmid = {38888737},
issn = {1432-184X},
mesh = {*Bacillus/isolation &amp; purification/genetics/metabolism ; *Soil Microbiology ; *Biodiversity ; India ; Plant Roots/microbiology ; Cicer/microbiology/growth &amp; development ; Solanum lycopersicum/microbiology/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Phylogeny ; Antibiosis ; Siderophores/metabolism ; Indoleacetic Acids/metabolism ; },
abstract = {Bacillus species appearas the most attractive plant growth-promoting rhizobacteria (PGPR) and alternative to synthetic chemical pesticides. The present study examined the antagonistic potential of spore forming-Bacilli isolated from organic farm soil samples of Allahabad, India. Eighty-seven Bacillus strains were isolated and characterized based on their morphological, plant growth promoting traits and molecular characteristics. The diversity analysis used 16S-rDNA, BOX-element, and enterobacterial repetitive intergenic consensus. Two strains, PR30 and PR32, later identified as Bacillus sp., exhibited potent in vitro antagonistic activity against Ralstonia solanaceorum. These isolates produced copious amounts of multiple PGP traits, such as indole-3-acetic acid (40.0 and 54.5 μg/mL), phosphate solubilization index (PSI) (4.4 and 5.3), ammonia, siderophore (3 and 4 cm), and 1-aminocyclopropane-1-carboxylate deaminase (8.1and 9.2 μM/mg//h) and hydrogen cyanide. These isolates were subjected to the antibiotic sensitivity test. The two potent isolates based on the higher antagonistic and the best plant growth-promoting ability were selected for plant growth-promoting response studies in tomatoe, broccoli, and chickpea. In the pot study, Bacillus subtilis (PR30 and PR31) showed significant improvement in seed germination (27-34%), root length (20-50%), shoot length (20-40%), vigor index (50-75%), carotenoid content (0.543-1.733), and lycopene content (2.333-2.646 mg/100 g) in tomato, broccoli, and chickpea. The present study demonstrated the production of multiple plant growth-promoting traits by the isolates and their potential as effective bioinoculants for plant growth promotion and biocontrol of phytopathogens.},
}
@article {pmid38886127,
year = {2024},
author = {Piwosz, K and Villena-Alemany, C and Całkiewicz, J and Mujakić, I and Náhlík, V and Dean, J and Koblížek, M},
title = {Response of aerobic anoxygenic phototrophic bacteria to limitation and availability of organic carbon.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {7},
pages = {},
pmid = {38886127},
issn = {1574-6941},
support = {2021/03/Y/NZ8/00076//National Science Centre, Poland/ ; },
mesh = {*Carbon/metabolism ; *Phototrophic Processes ; Heterotrophic Processes ; Lakes/microbiology ; Bacteria, Aerobic/metabolism/growth &amp; development ; Light ; Ecosystem ; Bacteria/metabolism/growth &amp; development/genetics ; },
abstract = {Aerobic anoxygenic phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, enhancing their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light (near-infrared light, λ > 800 nm) conditions to elucidate how they profit from photoheterotrophy. We found that AAP bacteria induce photoheterotrophic metabolism under carbon limitation, but they overcompete heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. Interestingly, recalcitrant (lignin) or low-energy (acetate) carbon sources inhibited the growth of AAP bacteria, especially in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria in pelagic environments.},
}
@article {pmid38884913,
year = {2024},
author = {Obregón-Gutierrez, P and Aragón, V and Correa-Fiz, F},
title = {Analysis of the Nasal Microbiota in Healthy and Diseased Pigs.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2815},
number = {},
pages = {93-113},
pmid = {38884913},
issn = {1940-6029},
mesh = {Animals ; *Microbiota/genetics ; Swine/microbiology ; *RNA, Ribosomal, 16S/genetics ; Nose/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Swine Diseases/microbiology ; Sequence Analysis, DNA/methods ; },
abstract = {Massive sequencing of a fragment of 16S rRNA gene allows the characterization of bacterial communities in different body sites: the microbiota. Nasal microbiota can be analyzed by DNA extraction from nasal swabs, amplification of the specific fragment of interest, and posterior sequencing. The raw sequences obtained need to go through a computational process to check their quality and then assign the taxonomy. Here, we will describe the complete process from sampling to get the microbial diversity of nasal microbiota in health and disease.},
}
@article {pmid38878412,
year = {2024},
author = {Zheng, P and Mao, A and Meng, S and Yu, F and Zhang, S and Lun, J and Li, J and Hu, Z},
title = {Assembly mechanism of microbial community under different seasons in Shantou sea area.},
journal = {Marine pollution bulletin},
volume = {205},
number = {},
pages = {116550},
doi = {10.1016/j.marpolbul.2024.116550},
pmid = {38878412},
issn = {1879-3363},
mesh = {*Seasons ; *Microbiota ; *Seawater/microbiology ; Bacteria/classification ; Phylogeny ; Biodiversity ; China ; Oceans and Seas ; },
abstract = {Coastal areas are often affected by a variety of climates, and microbial composition patterns are conducive to adaptation to these environments. In this study, the composition and pattern of microbial communities in the Shantou sea from four seasons were analyzed. The diversity of microbial community was significant differences under different seasons (p < 0.01). Meanwhile, dissolved oxygen levels, temperature were key factors to shift microbial communities. The assembly mechanism of microbial communities was constructed by the iCAMP (Infer community assembly mechanism by the phylogenetic bin-based null). Interestingly, the analyses revealed that drift was the predominant driver of this process (44.5 %), suggesting that microbial community assembly in this setting was dominated by stochastic processes. For example, Vibrio was found to be particularly susceptible to stochastic processes, indicating that the pattern of bacterial community was governed by stochastic processes. Thus, these results offering novel insight into the regulation of microbial ecology in marine environments.},
}
@article {pmid38876584,
year = {2024},
author = {Kothe, CI and Carøe, C and Mazel, F and Zilber, D and Cruz-Morales, P and Mohellibi, N and Evans, JD},
title = {Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {189},
number = {},
pages = {114490},
doi = {10.1016/j.foodres.2024.114490},
pmid = {38876584},
issn = {1873-7145},
mesh = {*Fermentation ; *Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Taste ; Fermented Foods/microbiology ; Microbiota ; Japan ; Metagenomics ; },
abstract = {Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators' sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of Staphylococccus epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.},
}
@article {pmid38876281,
year = {2024},
author = {Ponce-Jahen, SJ and Valenzuela, EI and Rangel-Mendez, JR and Sánchez-Carrillo, S and Cervantes, FJ},
title = {Anoxic nitrification with carbon-based materials as terminal electron acceptors.},
journal = {Bioresource technology},
volume = {406},
number = {},
pages = {130961},
doi = {10.1016/j.biortech.2024.130961},
pmid = {38876281},
issn = {1873-2976},
mesh = {*Nitrification ; *Carbon/chemistry ; Electrons ; Graphite/chemistry ; Phylogeny ; Oxidation-Reduction ; Ammonium Compounds/metabolism ; Anaerobiosis ; Nitrates/metabolism ; Bacteria/metabolism ; },
abstract = {This study investigates the potential of humic substances (HS) and graphene oxide (GO), as extracellular electron acceptors (EEA) for nitrification, aiming to explore alternatives to sustain this process in wastewater treatment systems. Experimental results demonstrate the conversion of ammonium to nitrate (up to 87 % of conversion) coupled to the reduction of either HS or GO by anaerobic consortia. Electron balance confirmed the contribution of HS and GO to ammonium oxidation. Tracer analysis in incubations performed with [15]NH4[+] demonstrated [15]NO3[-] as the main product with a minor fraction ending as [29]N2. Phylogenetic analysis identified Firmicutes, Euryarchaeota, and Chloroflexi as the microbial lineages potentially involved in anoxic nitrification linked to HS reduction. This study introduces a new avenue for research in which carbon-based materials with electron-accepting capacity may support the anoxic oxidation of ammonium, for instance in bioelectrochemical systems in which carbon-based anodes could support this novel process.},
}
@article {pmid38874336,
year = {2024},
author = {Tomazelli, D and Klauberg-Filho, O and Mendes, LW and Goss-Souza, D},
title = {The impact of land-use changes and management intensification on bacterial communities in the last decade: a review.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0030924},
pmid = {38874336},
issn = {1098-5336},
support = {1/CX/CSRD VA/United States ; },
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Brazil ; *Agriculture/methods ; *Microbiota ; Biodiversity ; Soil/chemistry ; },
abstract = {In the last decade, advances in soil bacterial ecology have contributed to increasing agricultural production. Brazil is the world leading agriculture producer and leading soil biodiversity reservoir. Meanwhile, there is still a significant gap in the knowledge regarding the soil microscopic life and its interactions with agricultural practices, and the replacement of natural vegetation by agroecosystems is yet to be unfolded. Through high throughput DNA sequencing, scientists are now exploring the complexity of soil bacterial communities and their relationship with soil and environmental characteristics. This study aimed to investigate the progress of bacterial ecology studies in Brazil over the last 10 years, seeking to understand the effect of the conversion of natural vegetation in agricultural systems on the diversity and structure of the soil microbial communities. We conducted a systematic search for scientific publication databases. Our systematic search has matched 62 scientific articles from three different databases. Most of the studies were placed in southeastern and northern Brazil, with no records of studies about microbial ecology in 17 out of 27 Brazilian states. Out of the 26 studies that examined the effects of replacing natural vegetation with agroecosystems, most authors concluded that changes in soil pH and vegetation cover replacement were the primary drivers of shifts in microbial communities. Understanding the ecology of the bacteria inhabiting Brazilian soils in agroecosystems is paramount for developing more efficient soil management strategies and cleaner agricultural technologies.},
}
@article {pmid38873612,
year = {2024},
author = {Pulvirenti, F and Giufrè, M and Pentimalli, TM and Camilli, R and Milito, C and Villa, A and Sculco, E and Cerquetti, M and Pantosti, A and Quinti, I},
title = {Oropharyngeal microbial ecosystem perturbations influence the risk for acute respiratory infections in common variable immunodeficiency.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1371118},
pmid = {38873612},
issn = {1664-3224},
mesh = {Humans ; *Common Variable Immunodeficiency/microbiology/immunology/complications ; *Oropharynx/microbiology ; Male ; Female ; Middle Aged ; Adult ; *Respiratory Tract Infections/microbiology/immunology ; *Dysbiosis ; Microbiota ; Prospective Studies ; Aged ; RNA, Ribosomal, 16S/genetics ; Acute Disease ; Bacteria/classification/genetics ; Case-Control Studies ; },
abstract = {BACKGROUND: The respiratory tract microbiome is essential for human health and well-being and is determined by genetic, lifestyle, and environmental factors. Patients with Common Variable Immunodeficiency (CVID) suffer from respiratory and intestinal tract infections, leading to chronic diseases and increased mortality rates. While CVID patients' gut microbiota have been analyzed, data on the respiratory microbiome ecosystem are limited.<br><br>OBJECTIVE: This study aims to analyze the bacterial composition of the oropharynx of adults with CVID and its link with clinical and immunological features and risk for respiratory acute infections.<br><br>METHODS: Oropharyngeal samples from 72 CVID adults and 26 controls were collected in a 12-month prospective study. The samples were analyzed by metagenomic bacterial 16S ribosomal RNA sequencing and processed using the Quantitative Insights Into Microbial Ecology (QIME) pipeline. Differentially abundant species were identified and used to build a dysbiosis index. A machine learning model trained on microbial abundance data was used to test the power of microbiome alterations to distinguish between healthy individuals and CVID patients.<br><br>RESULTS: Compared to controls, the oropharyngeal microbiome of CVID patients showed lower alpha- and beta-diversity, with a relatively increased abundance of the order Lactobacillales, including the family Streptococcaceae. Intra-CVID analysis identified age >45 years, COPD, lack of IgA, and low residual IgM as associated with a reduced alpha diversity. Expansion of Haemophilus and Streptococcus genera was observed in patients with undetectable IgA and COPD, independent from recent antibiotic use. Patients receiving azithromycin as antibiotic prophylaxis had a higher dysbiosis score. Expansion of Haemophilus and Anoxybacillus was associated with acute respiratory infections within six months.<br><br>CONCLUSIONS: CVID patients showed a perturbed oropharynx microbiota enriched with potentially pathogenic bacteria and decreased protective species. Low residual levels of IgA/IgM, chronic lung damage, anti antibiotic prophylaxis contributed to respiratory dysbiosis.},
}
@article {pmid38873164,
year = {2024},
author = {Rodríguez-Cruz, UE and Castelán-Sánchez, HG and Madrigal-Trejo, D and Eguiarte, LE and Souza, V},
title = {Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1369263},
pmid = {38873164},
issn = {1664-302X},
abstract = {A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the "Archaean Domes" (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5-9.8) and high salinity (5.28% to saturation).},
}
@article {pmid38870896,
year = {2024},
author = {de la Cuesta-Zuluaga, J and Boldt, L and Maier, L},
title = {Response, resistance, and recovery of gut bacteria to human-targeted drug exposure.},
journal = {Cell host &amp; microbe},
volume = {32},
number = {6},
pages = {786-793},
doi = {10.1016/j.chom.2024.05.009},
pmid = {38870896},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects ; Xenobiotics/pharmacology ; Symbiosis ; Gastrointestinal Tract/microbiology/drug effects ; Drug Resistance, Bacterial ; Host Microbial Interactions/drug effects ; },
abstract = {Survival strategies of human-associated microbes to drug exposure have been mainly studied in the context of bona fide pathogens exposed to antibiotics. Less well understood are the survival strategies of non-pathogenic microbes and host-associated commensal communities to the variety of drugs and xenobiotics to which humans are exposed. The lifestyle of microbial commensals within complex communities offers a variety of ways to adapt to different drug-induced stresses. Here, we review the responses and survival strategies employed by gut commensals when exposed to drugs-antibiotics and non-antibiotics-at the individual and community level. We also discuss the factors influencing the recovery and establishment of a new community structure following drug exposure. These survival strategies are key to the stability and resilience of the gut microbiome, ultimately influencing the overall health and well-being of the host.},
}
@article {pmid38869727,
year = {2024},
author = {Dyczko, D and Krysmann, A and Kolanek, A and Borczyk, B and Kiewra, D},
title = {Bacterial pathogens in Ixodes ricinus collected from lizards Lacerta agilis and Zootoca vivipara in urban areas of Wrocław, SW Poland- preliminary study.},
journal = {Experimental &amp; applied acarology},
volume = {93},
number = {2},
pages = {409-420},
pmid = {38869727},
issn = {1572-9702},
mesh = {Animals ; Female ; Male ; *Anaplasma/isolation &amp; purification/genetics ; *Borrelia/isolation &amp; purification/genetics ; Cities ; *Ixodes/microbiology/physiology ; Larva/microbiology/physiology ; *Lizards/parasitology/microbiology ; Nymph/microbiology/physiology ; Poland ; *Rickettsia/genetics/isolation &amp; purification ; },
abstract = {The aim of this study was to determine the level of infection of Ixodes ricinus ticks with pathogens (Borrelia spp., Rickettsia spp., and Anaplasma spp.) collected from Lacerta agilis and Zootoca vivipara lizards in the urban areas of Wrocław (SW Poland). The study was carried out in July-August 2020. Lizards were caught by a noose attached to a pole or by bare hands, identified by species, and examined for the presence of ticks. Each lizard was then released at the site of capture. Ticks were removed with tweezers, identified by species using keys, and molecular tests were performed for the presence of pathogens. From 28 lizards (17 specimens of Z. vivipara and 11 specimens of L. agilis) a total of 445 ticks, including 321 larvae and 124 nymphs, identified as I. ricinus were collected. A larger number of ticks were obtained from L. agilis compared to Z. vivipara. Molecular tests for the presence of pathogens were performed on 445 specimens of I. ricinus. The nested PCR method for the fla gene allowed the detection of Borrelia spp. in 9.4% of ticks, and it was higher in ticks from L. agilis (12.0%) than from Z. vivipara (1.0%). The RFLP method showed the presence of three species, including two belonging to the B. burgdorferi s.l. complex (B. lusitaniae and B. afzelii), and B. miyamotoi. The overall level of infection of Rickettsia spp. was 19.3%, including 27.2% in ticks collected from Z. vivipara and 17.0% from L. agilis. Sequencing of randomly selected samples confirmed the presence of R. helvetica. DNA of Anaplasma spp. was detected only in one pool of larvae collected from L. agilis, and sample sequencing confirmed the presence of (A) phagocytophilum. The research results indicate the important role of lizards as hosts of ticks and their role in maintaining pathogens in the environment including urban agglomeration as evidenced by the first recorded presence of (B) miyamotoi and (A) phagocytophilum in I. ricinus ticks collected from L. agilis. However, confirmation of the role of sand lizards in maintaining (B) miyamotoi and A. phagocytophilum requires more studies and sampling of lizard tissue.},
}
@article {pmid38868805,
year = {2024},
author = {Riello, GBC and da Silva, PM and da Silva Oliveira, FA and de Oliveira, RTG and da Silva, FER and da Frota França, IG and Melo, VMM and Miyajima, F and Pinheiro, RF and Danielle S, M},
title = {Gut Microbiota Composition Correlates with Disease Severity in Myelodysplastic Syndrome.},
journal = {International journal of hematology-oncology and stem cell research},
volume = {18},
number = {2},
pages = {192-201},
pmid = {38868805},
issn = {2008-3009},
abstract = {The myelodysplastic syndrome (MDS) is a heterogeneous group of clonal disorders of hematopoietic progenitor cells related to ineffective hematopoiesis and an increased risk of transformation to acute myelogenous leukemia. MDS is divided into categories, namely lineage dysplasia (MDS-SLD), MDS with ring sideroblasts (MDS-RS), MDS with multilineage dysplasia (MDS-MLD), MDS with excess blasts (MDS-EB). The International Prognostic Classification System (IPSS) ranks the patients as very low, low, intermediate, high, and very high based on disease evolution and survival rates. Evidence points to toll-like receptor (TLR) abnormal signaling as an underlying mechanism of this disease, providing a link between MDS and immune dysfunction. Microbial signals, such as lipopolysaccharides from gram-negative bacteria, can activate or suppress TLRs. Therefore, we hypothesized that MDS patients present gut microbiota alterations associated with disease subtypes and prognosis. To test this hypothesis, we sequenced the 16S rRNA gene from fecal samples of 30 MDS patients and 16 healthy elderly controls. We observed a negative correlation between Prevotella spp. and Akkermansia spp. in MDS patients compared with the control group. High-risk patients presented a significant increase in the genus Prevotella spp. compared to the other risk categories. There was a significant reduction in the abundance of the genus Akkermansia spp. in high-risk patients compared with low- and intermediate-risk. There was a significant decrease in the genus Ruminococcus spp. in MDS-EB patients compared with controls. Our findings show a new association between gut dysbiosis and higher-risk MDS, with a predominance of gram-negative bacteria.},
}
@article {pmid38868511,
year = {2024},
author = {Li, M and Hu, J and Wei, Z and Jousset, A and Pommier, T and Yu, X and Xu, Y and Shen, Q},
title = {Synthetic microbial communities: Sandbox and blueprint for soil health enhancement.},
journal = {iMeta},
volume = {3},
number = {1},
pages = {e172},
pmid = {38868511},
issn = {2770-596X},
abstract = {We summarize here the use of SynComs in improving various dimensions of soil health, including fertility, pollutant removal, soil-borne disease suppression, and soil resilience; as well as a set of useful guidelines to assess and understand the principles for designing SynComs to enhance soil health. Finally, we discuss the next stages of SynComs applications, including highly diverse and multikingdom SynComs targeting several functions simultaneously.},
}
@article {pmid38867105,
year = {2024},
author = {Mahjoubi, M and Cherif, H and Aliyu, H and Chouchane, H and Cappello, S and Neifar, M and Mapelli, F and Souissi, Y and Borin, S and Cowan, DA and Cherif, A},
title = {Brucella pituitosa strain BU72, a new hydrocarbonoclastic bacterium through exopolysaccharide-based surfactant production.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38867105},
issn = {1618-1905},
abstract = {Hydrocarbon and heavy metal pollution are amongst the most severe and prevalent environmental problems due to their toxicity and persistence. Bioremediation using microorganisms is considered one of the most effective ways to treat polluted sites. In the present study, we unveil the bioremediation potential of Brucella pituitosa strain BU72. Besides its ability to grow on multiple hydrocarbons as the sole carbon source and highly tolerant to several heavy metals, BU72 produces different exopolysaccharide-based surfactants (EBS) when grown with glucose or with crude oil as sole carbon source. These EBS demonstrated particular and specific functional groups as determined by Fourier transform infrared (FTIR) spectral analysis that showed a strong absorption peak at 3250 cm[-1] generated by the -OH group for both EBS. The FTIR spectra of the produced EBS revealed major differences in functional groups and protein content. To better understand the EBS production coupled with the degradation of hydrocarbons and heavy metal resistance, the genome of strain BU72 was sequenced. Annotation of the genome revealed multiple genes putatively involved in EBS production pathways coupled with resistance to heavy metals genes such as arsenic tolerance and cobalt-zinc-cadmium resistance. The genome sequence analysis showed the potential of BU72 to synthesise secondary metabolites and the presence of genes involved in plant growth promotion. Here, we describe the physiological, metabolic, and genomic characteristics of Brucella pituitosa strain BU72, indicating its potential as a bioremediation agent.},
}
@article {pmid38865907,
year = {2024},
author = {Wang, L and Lee, E and Barlaz, MA and de Los Reyes, FL},
title = {Linking microbial population dynamics in anaerobic bioreactors to food waste type and decomposition stage.},
journal = {Waste management (New York, N.Y.)},
volume = {186},
number = {},
pages = {77-85},
doi = {10.1016/j.wasman.2024.06.004},
pmid = {38865907},
issn = {1879-2456},
mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; Refuse Disposal/methods ; Solid Waste/analysis ; Bacteria/metabolism/genetics/classification ; Vegetables/microbiology ; Methane/metabolism ; Fruit/microbiology ; Garbage ; Food Loss and Waste ; },
abstract = {A key question in anaerobic microbial ecology is how microbial communities develop over different stages of waste decomposition and whether these changes are specific to waste types. We destructively sampled over time 26 replicate bioreactors cultivated on fruit/vegetable waste (FVW) and meat waste (MW) based on pre-defined waste components and composition. To characterize community shifts, we examined 16S rRNA genes from both the leachate and solid fractions of the waste. Waste decomposition occurred faster in FVW than MW, as accumulation of ammonia in MW reactors led to inhibition of methanogenesis. We identified population succession during different stages of waste decomposition and linked specific populations to different waste types. Community analyses revealed underrepresentation of methanogens in the leachate fractions, emphasizing the importance of consistent and representative sampling when characterizing microbial communities in solid waste.},
}
@article {pmid38861460,
year = {2024},
author = {Wutkowska, M and Tláskal, V and Bordel, S and Stein, LY and Nweze, JA and Daebeler, A},
title = {Leveraging genome-scale metabolic models to understand aerobic methanotrophs.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38861460},
issn = {1751-7370},
support = {21-17322M//Czech Science Foundation/ ; },
mesh = {*Methane/metabolism ; Oxidation-Reduction ; Aerobiosis ; Metabolic Networks and Pathways/genetics ; Models, Biological ; },
abstract = {Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.},
}
@article {pmid38860973,
year = {2024},
author = {Deehan, EC and Zhang, Z and Nguyen, NK and Perez-Muñoz, ME and Cole, J and Riva, A and Berry, D and Prado, CM and Walter, J},
title = {Adaptation to tolerate high doses of arabinoxylan is associated with fecal levels of Bifidobacterium longum.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2363021},
pmid = {38860973},
issn = {1949-0984},
support = {741623/ERC_/European Research Council/International ; },
mesh = {*Xylans/metabolism ; Humans ; *Feces/microbiology/chemistry ; Male ; Female ; *Dietary Fiber/metabolism ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Bifidobacterium longum/metabolism ; Adult ; Dietary Supplements/analysis ; Fermentation ; Aged ; Adaptation, Physiological ; },
abstract = {Dietary fiber supplements are a strategy to close the 'fiber gap' and induce targeted modulations of the gut microbiota. However, higher doses of fiber supplements cause gastrointestinal (GI) symptoms that differ among individuals. What determines these inter-individual differences is insufficiently understood. Here we analyzed findings from a six-week randomized controlled trial that evaluated GI symptoms to corn bran arabinoxylan (AX; n = 15) relative to non-fermentable microcrystalline cellulose (MCC; n = 16) at efficacious supplement doses of 25 g/day (females) or 35 g/day (males) in adults with excess weight. Self-reported flatulence, bloating, and stomach aches were evaluated weekly. Bacterial taxa involved in AX fermentation were identified by bioorthogonal non-canonical amino acid tagging. Associations between GI symptoms, fecal microbiota features, and diet history were systematically investigated. AX supplementation increased symptoms during the first three weeks relative to MCC (p < 0.05, Mann-Whitney tests), but subjects 'adapted' with symptoms reverting to baseline levels toward the end of treatment. Symptom adaptations were individualized and correlated with the relative abundance of Bifidobacterium longum at baseline (rs = 0.74, p = 0.002), within the bacterial community that utilized AX (rs = 0.69, p = 0.006), and AX-induced shifts in acetate (rs = 0.54, p = 0.039). Lower baseline consumption of animal-based foods and higher whole grains associated with less severity and better adaptation. These findings suggest that humans do 'adapt' to tolerate efficacious fiber doses, and this process is linked to their microbiome and dietary factors known to interact with gut microbes, providing a basis for the development of strategies for improved tolerance of dietary fibers.},
}
@article {pmid38860825,
year = {2024},
author = {Paillet, T and Lamy-Besnier, Q and Figueroa, C and Petit, M-A and Dugat-Bony, E},
title = {Dynamics of the viral community on the surface of a French smear-ripened cheese during maturation and persistence across production years.},
journal = {mSystems},
volume = {9},
number = {7},
pages = {e0020124},
pmid = {38860825},
issn = {2379-5077},
mesh = {*Cheese/microbiology/virology ; *Bacteriophages/genetics/isolation &amp; purification ; Bacteria/virology/genetics/isolation &amp; purification ; Microbiota ; Food Microbiology ; France ; Metagenomics ; Virome ; },
abstract = {The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development of different microbial groups such as lactic acid bacteria, fungi, and ripening bacteria. Recent studies indicate that a viral community, mainly composed of bacteriophages, also represents a common and substantial part of the cheese microbiome. However, the composition of this community, its temporal variations, and associations between bacteriophages and their hosts remain poorly characterized. Here, we studied a French smear-ripened cheese by both viral metagenomics and 16S metabarcoding approaches to assess both the succession of phages and bacterial communities on the cheese surface during cheese ripening and their temporal variations in ready-to-eat cheeses over the years of production. We observed a clear transition of the phage community structure during ripening with a decreased relative abundance of viral species (vOTUs) associated with Lactococcus phages, which were replaced by vOTUs associated with phages infecting ripening bacteria such as Brevibacterium, Glutamicibacter, Pseudoalteromonas, and Vibrio. The dynamics of the phage community was strongly associated with bacterial successions observed on the cheese surface. Finally, while some variations in the distribution of phages were observed in ready-to-eat cheeses produced at different dates spanning more than 4 years of production, the most abundant phages were detected throughout. This result revealed the long-term persistence of the dominant phages in the cheese production environment. Together, these findings offer novel perspectives on the ecology of bacteriophages in smear-ripened cheese and emphasize the significance of incorporating bacteriophages in the microbial ecology studies of fermented foods.IMPORTANCEThe succession of diverse microbial populations is critical for ensuring the production of high-quality cheese. We observed a temporal succession of phages on the surface of a smear-ripened cheese, with new phage communities showing up when ripening bacteria start covering this surface. Interestingly, the final phage community of this cheese is also consistent over large periods of time, as the same bacteriophages were found in cheese products from the same manufacturer made over 4 years. This research highlights the importance of considering these bacteriophages when studying the microbial life of fermented foods like cheese.},
}
@article {pmid38858788,
year = {2024},
author = {Silva, DP and Villela, HDM and Santos, HF and Duarte, GAS and Ribeiro, JR and Ghizelini, AM and Vilela, CLS and Rosado, PM and Fazolato, CS and Santoro, EP and Carmo, FL and Ximenes, DS and Soriano, AU and Rachid, CTCC and Thurber, RLV and Peixoto, RS},
title = {Correction: Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {105},
pmid = {38858788},
issn = {2049-2618},
}
@article {pmid38857239,
year = {2024},
author = {Martinez-Villegas, L and Lado, P and Klompen, H and Wang, S and Cummings, C and Pesapane, R and Short, SM},
title = {The microbiota of Amblyomma americanum reflects known westward expansion.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0304959},
pmid = {38857239},
issn = {1932-6203},
mesh = {Animals ; *Microbiota ; Female ; Male ; *Amblyomma/microbiology ; United States ; Ixodidae/microbiology ; },
abstract = {Amblyomma americanum, a known vector of multiple tick-borne pathogens, has expanded its geographic distribution across the United States in the past decades. Tick microbiomes may play a role shaping their host's life history and vectorial capacity. Bacterial communities associated with A. americanum may reflect, or enable, geographic expansion and studying the microbiota will improve understanding of tick-borne disease ecology. We examined the microbiota structure of 189 adult ticks collected in four regions encompassing their historical and current geographic distribution. Both geographic region of origin and sex were significant predictors of alpha diversity. As in other tick models, within-sample diversity was low and uneven given the presence of dominant endosymbionts. Beta diversity analyses revealed that bacterial profiles of ticks of both sexes collected in the West were significantly different from those of the Historic range. Biomarkers were identified for all regions except the historical range. In addition, Bray-Curtis dissimilarities overall increased with distance between sites. Relative quantification of ecological processes showed that, for females and males, respectively, drift and dispersal limitation were the primary drivers of community assembly. Collectively, our findings highlight how microbiota structural variance discriminates the western-expanded populations of A. americanum ticks from the Historical range. Spatial autocorrelation, and particularly the detection of non-selective ecological processes, are indicative of geographic isolation. We also found that prevalence of Ehrlichia chaffeensis, E. ewingii, and Anaplasma phagocytophilum ranged from 3.40-5.11% and did not significantly differ by region. Rickettsia rickettsii was absent from our samples. Our conclusions demonstrate the value of synergistic analysis of biogeographic and microbial ecology data in investigating range expansion in A. americanum and potentially other tick vectors as well.},
}
@article {pmid38855766,
year = {2024},
author = {Tong, L and Jun, L and He, J and Min, Y and Guoqing, D and Yuting, H and Huaxing, Z and Huan, W and Tingshuang, P},
title = {Differences in environmental microbial community responses under rice-crab co-culture and crab monoculture models under cyanobacterial bloom.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1327520},
pmid = {38855766},
issn = {1664-302X},
abstract = {Cyanobacterial blooms (CBs) present significant challenges to Chinese mitten crab (CMC) culture, posing hazards to the aquatic microbial ecology. However, the current focus on the microbial ecological changes within the CMC culture system under the influence of CBs is somewhat insufficient. There's an urgent need to analyze the microbial ecosystem of the CMC culture system under CBs. This study employed 16S rRNA gene amplicon sequencing to investigate the dynamics of the environmental microbial community in both the rice-crab co-culture (RC) and crab monoculture (CM) models. The results revealed that cyanobacteria reached high levels in the CM water in July, while they began to increase in the RC water in August. Notably, OTU147 (uncultured bacterium g_Planktothrix NIVA-CYA 15), identified as the dominant taxon associated with CBs, showed a significant linear relationship with TP, NO2 [-]-N, and the N:P ratio. TP, TN, NO2 [-]-N, and CODMn had a more pronounced impact on the structure of bacterial communities and cyanobacterial taxa in the water. The bacterial community structure involved in carbon metabolism displayed temporal succession in the water. The co-occurrence network of the bacterial community primarily consisted of Chloroflexi, Proteobacteria, and Firnicutes in the sediment, and Actinobacteria, Proteobacteria, Chloroflexi, and Bacteroidota in the water. In contrast, the co-occurrence network included different peripheral species in the sediment and water. Keystone species were predominantly represented by OTU22 (uncultured actinobacterium g_ hgcI clade) and OTU12 (uncultured Opitutae bacterium g_ norank) in the RC water, and by OTU25 (uncultured bacterium g_ Limnohabitans) in the CM water. TP, TN, NO2 [-]-N, and CODMn were identified as the primary environmental factors influencing these keystone taxa within the culture water. In conclusion, this study on the microbial ecology of the CMC culture system under the influence of CBs provides valuable insights that can be instrumental in subsequent management efforts.},
}
@article {pmid38852236,
year = {2024},
author = {Xu, Y and Yu, Z and Liu, C and Hu, Y and Zhang, J and Liu, J and Chen, X and Liu, J and Wang, G and Liu, X and Jin, J and Li, Y},
title = {Variability in soybean yield responses to elevated atmospheric CO2: Insights from non-structural carbohydrate remobilisation during seed filling.},
journal = {Plant physiology and biochemistry : PPB},
volume = {213},
number = {},
pages = {108802},
doi = {10.1016/j.plaphy.2024.108802},
pmid = {38852236},
issn = {1873-2690},
mesh = {*Glycine max/metabolism/growth &amp; development/drug effects/physiology ; *Carbon Dioxide/metabolism/pharmacology ; *Photosynthesis/drug effects ; *Carbohydrate Metabolism ; *Seeds/metabolism/growth &amp; development/drug effects ; },
abstract = {The increasing atmospheric CO2 concentration (e[CO2]) has mixed effects on soybean most varieties' yield. This study elucidated the effect of e[CO2] on soybean yield and the underlying mechanisms related to photosynthetic capacity, non-structural carbohydrate (NSC) accumulation, and remobilisation. Four soybean cultivars were cultivated in open-top chambers at two CO2 levels. Photosynthesis rates were determined from R2 to R6. Plants were sampled at R5 and R8 to determine carbohydrate concentrations. There were significant variations in yield responses among the soybean cultivars under e[CO2], from no change in DS1 to a 22% increase in SN14. DS1 and SN14 had the smallest and largest increase, respectively, in daily carbon assimilation capacity. Under e[CO2], DS1, MF5, and XHJ had an increase in Ci, at which point the transition from Rubisco-limited to ribulose-1,5-bisphosphate regeneration-limited photosynthesis occurred, in contrast with SN14. Thus, the cultivars might have distinct mechanisms that enhance photosynthesis under e[CO2] conditions. A positive correlation was between daily carbon assimilation response to e[CO2] and soybean yield, emphasising the importance of enhanced photosynthate accumulation before the R5 stage in determining yield response to e[CO2]. E[CO2] significantly influenced NSC accumulation in vegetative organs at R5, with variation among cultivars. There was enhanced NSC remobilisation during seed filling, indicating cultivar-specific responses to the remobilisation of sucrose and soluble sugars, excluding sucrose and starch. A positive correlation was between leaf and stem NSC remobilisation and yield response to e[CO2], emphasising the role of genetic differences in carbohydrate remobilisation mechanisms in determining soybean yield variation under elevated CO2 levels.},
}
@article {pmid38849711,
year = {2024},
author = {Doménech-Pascual, A and Carrasco-Barea, L and Gich, F and Boadella, J and Freixinos Campillo, Z and Gómez Cerezo, R and Butturini, A and Romaní, AM},
title = {Differential response of bacteria and fungi to drought on the decomposition of Sarcocornia fruticosa woody stems in a saline stream.},
journal = {Environmental microbiology},
volume = {26},
number = {6},
pages = {e16661},
doi = {10.1111/1462-2920.16661},
pmid = {38849711},
issn = {1462-2920},
support = {PID2021-123735OB-C2/MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RTI2018-097950-B-C2//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PCI2020-120702-2/AEI/10.13039/501.100.011.033//Agencia Estatal de Investigaci&#xf3;n/ ; 2021 FISDU 00297//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; },
mesh = {*Droughts ; *Bacteria/metabolism/classification ; *Fungi/metabolism ; *Rivers/microbiology ; *Salinity ; *Plant Stems/microbiology/metabolism ; Ecosystem ; },
abstract = {Inland saline ecosystems suffer multiple stresses (e.g., high radiation, salinity, water scarcity) that may compromise essential ecosystem functions such as organic matter decomposition. Here, we investigated the effects of drought on microbial colonization and decomposition of Sarcocornia fruticosa woody stems across different habitats in a saline watershed: on the dry floodplain, submerged in the stream channel and at the shoreline (first submerged, then emerged). Unexpectedly, weight loss was not enhanced in the submerged stems, while decomposition process differed between habitats. On the floodplain, it was dominated by fungi and high cellulolytic activity; in submerged conditions, a diverse community of bacteria and high ligninolytic activity dominated; and, on the shoreline, enzyme activities were like submerged conditions, but with a fungal community similar to the dry conditions. Results indicate distinct degradation paths being driven by different stress factors: strong water scarcity and photodegradation in dry conditions, and high salinity and reduced oxygen in wet conditions. This suggests that fungi are more resistant to drought, and bacteria to salinity. Overall, in saline watersheds, variations in multiple stress factors exert distinct environmental filters on bacteria and fungi and their role in the decomposition of plant material, affecting carbon cycling and microbial interactions.},
}
@article {pmid38849299,
year = {2024},
author = {Papazlatani, C and Garbeva, P and Huerta Lwanga, E},
title = {Effect of microplastic pollution on the gut microbiome of anecic and endogeic earthworms.},
journal = {FEMS microbiology letters},
volume = {371},
number = {},
pages = {},
pmid = {38849299},
issn = {1574-6968},
mesh = {*Oligochaeta/microbiology/drug effects ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Bacteria/classification/drug effects/isolation &amp; purification/genetics ; Soil Pollutants/toxicity ; Soil Microbiology ; },
abstract = {Microplastic (MP) pollution constitutes an emerging type of pollution threatening both aquatic and terrestrial ecosystems. The impact on aquatic ecosystems has been extensively studied, but the effect on terrestrial ecosystems and their inhabitants is mostly underexplored. In this study, we explored the effect of MP pollution on gut bacterial microbiome of endogeic (Aporrectodea caliginosa) and anecic (Lumbricus terrestris) earthworms. The experiments were performed in sandy soil with 0.2% of low-density polyethylene MPs (LDPE MPs). We observed that the endogeic earthworms had 100% survival, while anecic earthworms survived 25 days in the control (i.e. in absence of MPs) and 21 days in the treatment with LDPE MPs. The main driver of shifts in the diversity and composition of the bacterial communities in the gut of tested earthworms was the lifestyle of the worms, followed by the presence of MPs. The bacterial microbiome diversity was significantly different among the two types of earthworms, and the highest bacterial diversity was found in the gut of the endogeic earthworms. The effect of MPs on gut bacterial microbiome was clearly observed in the changes in the relative abundance of several phyla and families of the bacterial communities in both types of earthworms, although it was most evident in the anecic earthworms. The Actinobacteriota, Proteobacteria, and Firmicutes were the main groups enhanced in the MP treatments, suggesting enrichment of the bacterial communities with potential plastic degraders.},
}
@article {pmid38844497,
year = {2024},
author = {Serra Moncadas, L and Hofer, C and Bulzu, PA and Pernthaler, J and Andrei, AS},
title = {Author Correction: Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4830},
doi = {10.1038/s41467-024-49328-4},
pmid = {38844497},
issn = {2041-1723},
}
@article {pmid38842339,
year = {2024},
author = {Kortenbosch, HH and van Leuven, F and van den Heuvel, C and Schoustra, SE and Zwaan, BJ and Snelders, E},
title = {Catching some air: a method to spatially quantify aerial triazole resistance in Aspergillus fumigatus.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0027124},
pmid = {38842339},
issn = {1098-5336},
support = {GROEN.2019.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; },
mesh = {*Aspergillus fumigatus/drug effects/genetics ; *Drug Resistance, Fungal ; *Air Microbiology ; *Triazoles/pharmacology ; *Antifungal Agents/pharmacology ; Spores, Fungal/drug effects/genetics ; Environmental Monitoring/methods ; },
abstract = {Airborne triazole-resistant spores of the human fungal pathogen Aspergillus fumigatus are a significant human health problem as the agricultural use of triazoles has been selecting for cross-resistance to life-saving clinical triazoles. However, how to quantify exposure to airborne triazole-resistant spores remains unclear. Here, we describe a method for cost-effective wide-scale outdoor air sampling to measure both spore abundance as well as antifungal resistance fractions. We show that prolonged outdoor exposure of sticky seals placed in delta traps, when combined with a two-layered cultivation approach, can regionally yield sufficient colony-forming units (CFUs) for the quantitative assessment of aerial resistance levels at a spatial scale that was up to now unfeasible. When testing our method in a European pilot sampling 12 regions, we demonstrate that there are significant regional differences in airborne CFU numbers, and the triazole-resistant fraction of airborne spores is widespread and varies between 0 and 0.1 for itraconazole (∼4 mg/L) and voriconazole (∼2 mg/L). Our efficient and accessible air sampling protocol opens up extensive options for fine-scale spatial sampling and surveillance studies of airborne A. fumigatus.IMPORTANCEAspergillus fumigatus is an opportunistic fungal pathogen that humans and other animals are primarily exposed to through inhalation. Due to the limited availability of antifungals, resistance to the first choice class of antifungals, the triazoles, in A. fumigatus can make infections by this fungus untreatable and uncurable. Here, we describe and validate a method that allows for the quantification of airborne resistance fractions and quick genotyping of A. fumigatus TR-types. Our pilot study provides proof of concept of the suitability of the method for use by citizen-scientists for large-scale spatial air sampling. Spatial air sampling can open up extensive options for surveillance, health-risk assessment, and the study of landscape-level ecology of A. fumigatus, as well as investigating the environmental drivers of triazole resistance.},
}
@article {pmid38840338,
year = {2024},
author = {Olson, EG and Dittoe, DK and Micciche, AC and Stock, DA and Rubinelli, PM and Rothrock, MJ and Ricke, SC},
title = {Microbiome analyses of poultry feeds: Part II. Comparison of different poultry feeds.},
journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes},
volume = {59},
number = {8},
pages = {448-482},
doi = {10.1080/03601234.2024.2361596},
pmid = {38840338},
issn = {1532-4109},
mesh = {Animals ; *Animal Feed/analysis ; *Poultry/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Chickens/microbiology ; Microbiota ; },
abstract = {Within the realm of poultry feed mill operations, the persistent concern over microbial feed quality necessitates the establishment of a robust baseline for enhancing and sustaining the standards of commercial feeds. This dual-phase investigation, comprising Parts I, was previously published, and the current study presented here as Part II aimed to illuminate this baseline using 16S rRNA gene sequencing. In Part II, nine distinct commercial poultry feeds formulated as starters, growers, starter/growers, or supplements, the selected feeds underwent genomic DNA extraction, amplification with custom dual-indexed primers, and subsequent Illumina MiSeq sequencing. Through data analysis in QIIME2-2021.4 and R Studio, the study unveils alpha (Kruskal-Wallis) and beta (ANOSIM) diversity, taxonomic differences (ANCOM), and core microbiomes (core_members), deeming main and pairwise effects statistically significant at p < 0.05 and Q < 0.05. Notably, the investigation identified 30% common core microbial members across the nine feed types, shedding light on potential foodborne poultry pathogens such as Helicobacter and Campylobacter. Probiotic-associated feeds exhibited distinct microbial communities, emphasizing the need to explore their impact on the early poultry gastrointestinal tract (GIT) further.},
}
@article {pmid38840053,
year = {2024},
author = {Ullah, I and Ullah, S and Amin, F and Al-Hawadi, JS and Okla, MK and Alaraidh, IA and AbdElgawad, H and Liu, K and Harrison, MT and Saud, S and Hassan, S and Nawaz, T and Zhu, M and Liu, H and Fahad, S},
title = {Germination responses of Lens Culiunaris L. seeds to osmotic potentials at cardinal temperatures using hydrothermal time model.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {502},
pmid = {38840053},
issn = {1471-2229},
mesh = {*Germination/physiology ; *Seeds/physiology/growth &amp; development ; *Lens Plant/physiology/growth &amp; development ; *Temperature ; Water/metabolism ; Models, Biological ; Osmotic Pressure ; },
abstract = {BACKGROUND: Lentil is a significant legume that are consumed as a staple food and have a significant economic impact around the world. The purpose of the present research on lentil was to assess the hydrothermal time model's capacity to explain the dynamics of Lens culinaris L. var. Markaz-09 seed germination, as well as to ascertain the germination responses at various sub-optimal temperatures (T) and water potentials (Ψ). In order to study lentil seed germination (SG) behavior at variable water potentials (Ψs) and temperatures (Ts). A lab experiment employing the hydrothermal time model was created. Seeds were germinated at six distinct temperatures: 15 [0]С, 20 [0]С, 25 [0]С, 30 [0]С, 35 [0]С, and 40 [0]С, with five Ψs of 0, -0.3, -0.6, -0.9, and - 1.2 MPa in a PEG-6000 (Polyethylene glycol 6000) solution.<br><br>RESULTS: The results indicated that the agronomic parameters like Germination index (GI), Germination energy (GE), Timson germination index (TGI), were maximum in 25 [0]C at (-0.9&#xa0;MPa) and lowest at 40 [0]C in 0&#xa0;MPa. On other hand, mean germination time (MGT) value was highest at 15 [0]C in -1.2&#xa0;MPa and minimum at 40 [0]C in (-0.6&#xa0;MPa) while Mean germination rate (MGR) was maximum at 40 [0]C in (0&#xa0;MPa) and minimum at 15 [0]C in (-0.6&#xa0;MPa).<br><br>CONCLUSIONS: The HTT model eventually defined the germination response of Lens culinaris L. var. Markaz-09 (Lentil) for all Ts and &#x3a8;s, allowing it to be employed as a predictive tool in Lens culinaris L. var. Markaz-09 (Lentil) seed germination simulation models.},
}
@article {pmid38839775,
year = {2024},
author = {Ray, K and Basak, SK and Giri, CK and Kotal, HN and Mandal, A and Chatterjee, K and Saha, S and Biswas, B and Mondal, S and Das, I and Ghosh, A and Bhadury, P and Joshi, R},
title = {Ecological restoration at pilot-scale employing site-specific rationales for small-patch degraded mangroves in Indian Sundarbans.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {12952},
pmid = {38839775},
issn = {2045-2322},
support = {BT/PR7501/BCE/8/982/2013//Department of Biotechnology, Government of India; Science and Engineering Research Board, Department of Science and Technology, Government of India/ ; File No. BT/PR30531/BCE/8/1496/2018//Department of Biotechnology, Government of India; Science and Engineering Research Board, Department of Science and Technology, Government of India/ ; EMR/2016/005262//Department of Biotechnology, Government of India; Science and Engineering Research Board, Department of Science and Technology, Government of India/ ; },
mesh = {*Wetlands ; India ; *Conservation of Natural Resources/methods ; Ecosystem ; Environmental Restoration and Remediation/methods ; Pilot Projects ; Bayes Theorem ; },
abstract = {To date, degraded mangrove ecosystem restoration accomplished worldwide primarily aligns towards rehabilitation with monotypic plantations, while ecological restoration principles are rarely followed in these interventions. However, researchers admit that most of these initiatives' success rate is not appreciable often. An integrative framework of ecological restoration for degraded mangroves where site-specific observations could be scientifically rationalized, with co-located reference pristine mangroves as the target ecosystem to achieve is currently distinctively lacking. Through this experimental scale study, we studied the suitability of site-specific strategies to ecologically restore degraded mangrove patches vis-à-vis the conventional mono-species plantations in a highly vulnerable mangrove ecosystem in Indian Sundarbans. This comprehensive restoration framework was trialed in small discrete degraded mangrove patches spanning ~ 65 ha. Site-specific key restoration components applied are statistically validated through RDA analyses and Bayesian t-tests. 25 quantifiable metrics evaluate the restoration success of a ~ 3 ha degraded mangrove patch with Ridgeline distribution, Kolmogorov-Smirnov (K-S) tests, and Mahalanobis Distance (D[2]) measure to prove the site's near-equivalence to pristine reference in multiple ecosystem attributes. This restoration intervention irrevocably establishes the greater potential of this framework in the recovery of ecosystem functions and self-sustenance compared to that of predominant monoculture practices for vulnerable mangroves.},
}
@article {pmid38839017,
year = {2024},
author = {Ruan, SY and Luo, HW and Tang, XR and Qi, JY},
title = {Effects of 3-year organic farming management on soil antibiotic resistant genes and virulence factors in a double rice cropping system.},
journal = {The Science of the total environment},
volume = {944},
number = {},
pages = {173722},
doi = {10.1016/j.scitotenv.2024.173722},
pmid = {38839017},
issn = {1879-1026},
mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Organic Agriculture/methods ; *Virulence Factors/genetics ; China ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; },
abstract = {Investigating the antibiotic resistance genes (ARGs) and virulence factors (VFs) within soil microbial communities is crucial for understanding microbial ecology and the evolution of antibiotic resistance. However, the study of ARGs, VFs, and their predominant microbial hosts in soils under varying rice production management practices remains largely underexplored. To this end, a three-year field experiment was conducted under organic management within a double rice cropping system in South China. The study revealed that, in contrast to conventional management (CK), organic farming practices did not significantly alter the total reads of ARGs and VFs. However, there was a notable alteration in the ARGs abundance at the antibiotic class level, such as an increase (P < 0.05) in the abundance of Multidrug ARGs (by 1.7 %) and a decrease (P < 0.05) in Rifamycin (by 17.5 %) and Fosfomycin ARGs (by 15.3 %). Furthermore, a significant shift in VFs was observed under organic farming compared to CK, characterized by an increase (P < 0.05) in offensive VFs and a decrease (P < 0.05) in nonspecific VFs and the regulation of virulence-associated genes. Key microbial taxa identified as influencing ARGs and VFs in the tested soil samples, e.g., Proteobacteria. The findings highlight the need for more detailed attention to soil ecology within organic rice production systems in South China, particularly concerning the significant alterations observed in ARGs and VFs.},
}
@article {pmid38839005,
year = {2024},
author = {David, GM and Pimentel, IM and Rehsen, PM and Vermiert, AM and Leese, F and Gessner, MO},
title = {Multiple stressors affecting microbial decomposer and litter decomposition in restored urban streams: Assessing effects of salinization, increased temperature, and reduced flow velocity in a field mesocosm experiment.},
journal = {The Science of the total environment},
volume = {943},
number = {},
pages = {173669},
doi = {10.1016/j.scitotenv.2024.173669},
pmid = {38839005},
issn = {1879-1026},
mesh = {*Rivers/chemistry/microbiology ; *Salinity ; Biodegradation, Environmental ; Ecosystem ; Plant Leaves ; Alnus ; Temperature ; Environmental Monitoring ; },
abstract = {A multitude of anthropogenic stressors impact biological communities and ecosystem processes in urban streams. Prominent among them are salinization, increased temperature, and altered flow regimes, all of which can affect microbial decomposer communities and litter decomposition, a fundamental ecosystem process in streams. Impairments caused by these stressors individually or in combination and recovery of communities and ecosystem processes after release from these stressors are not well understood. To improve our understanding of multiple stressors impacts we performed an outdoor stream mesocosm experiment with 64 experimental units to assess the response of microbial litter decomposers and decomposition. The three stressors we applied in a full-factorial design were increased salinity (NaCl addition, 0.53 mS cm[-1] above ambient), elevated temperature (3.5 °C above ambient), and reduced flow velocity (3.5 vs 14.2 cm s[-1]). After two weeks of stressor exposure (first sampling) and two subsequent weeks of recovery (second sampling), we determined leaf-associated microbial respiration, fungal biomass, and the sporulation activity and community composition of aquatic hyphomycetes in addition to decomposition rates of black alder (Alnus glutinosa) leaves confined in fine-mesh litter bags. Microbial colonization of the litter was accompanied by significant mass loss in all mesocosms. However, there was little indication that mass loss, microbial respiration, fungal biomass, sporulation rate or community composition of aquatic hyphomycetes was strongly affected by either single stressors or their interactions. Two exceptions were temperature effects on sporulation and decomposition rate. Similarly, no notable differences among mesocosms were observed after the recovery phase. These results suggest that microbial decomposers and leaf litter decomposition are either barely impaired by exposure to the tested stressors at the levels applied in our experiment, or that communities in restored urban streams are well adapted to cope with these stressor levels.},
}
@article {pmid38832805,
year = {2024},
author = {Freitas, ASd and Zagatto, LFG and Rocha, GS and Pellegrinetti, TA and Alves, LdCM and Lara, VMd and Mandro, JA and Martins, GL and Muniz, AW and Hanada, RE and Würdig Roesch, LF and Tsai, SM},
title = {Bacterial genomes recovered from litter's metagenomes in Amazonian Dark Earths.},
journal = {Microbiology resource announcements},
volume = {13},
number = {7},
pages = {e0042224},
pmid = {38832805},
issn = {2576-098X},
support = {2021/10.626-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 314806/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 01.02.016301.00293/2021//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas (FAPEAM)/ ; 2020/08927-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; },
abstract = {Here, we report 27 metagenome-assembled bacterial genomes (MAGs) from litter samples of a secondary forest located in Brazil over an Amazonian Dark Earth pool. The data set includes members from the phyla Pseudomonadata (14 MAGs), Actinomycetota (7 MAGs), Bacteroidota (4 MAGs), Bacillota (1 MAG), and Bdellovibrionota (1 MAG).},
}
@article {pmid38831142,
year = {2024},
author = {Chen, D and Tian, C and Yuan, H and Zhai, W and Chang, Z},
title = {Nitrogen Removal Performance and Microbial Community Structure of IMTA Ponds (Apostistius japonicus-Penaeus japonicus-Ulva).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {82},
pmid = {38831142},
issn = {1432-184X},
support = {2023YFD2401704//National Key Research and Development Program of China/ ; CARS-48//Agriculture Research System of China/ ; No.2023TD50//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; },
mesh = {*Nitrogen/metabolism ; *Aquaculture ; *Denitrification ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Ponds/microbiology ; *Microbiota ; Animals ; *Penaeidae/microbiology ; *Nitrous Oxide/metabolism/analysis ; Geologic Sediments/microbiology ; Oxidation-Reduction ; Ammonium Compounds/metabolism ; },
abstract = {Denitrification and anaerobic ammonium oxidation (anammox) are key processes for nitrogen removal in aquaculture, reducing the accumulated nitrogen nutrients to nitrogen gas or nitrous oxide gas. Complete removal of nitrogen from aquaculture systems is an important measure to solve environmental pollution. In order to evaluate the nitrogen removal potential of marine aquaculture ponds, this study investigated the denitrification and anammox rates, the flux of nitrous oxide (N2O) at the water-air interface, the sediment microbial community structure, and the gene expression associated with the nitrogen removal process in integrated multi-trophic aquaculture (IMTA) ponds (Apostistius japonicus-Penaeus japonicus-Ulva) with different culture periods. The results showed that the denitrification and anammox rates in sediments increased with the increase of cultivation periods and depth, and there was no significant difference in nitrous oxide gas flux at the water-air interface between different cultivation periods (p > 0.05). At the genus and phylum levels, the abundance of microorganisms related to nitrogen removal reactions in sediments changed significantly with the increase of cultivation period and depth, and was most significantly affected by the concentration of particulate organic nitrogen (PON) in sediments. The expression of denitrification gene (narG, nirS, nosZ) in surface sediments was significantly higher than that in deep sediments (p < 0.05), and was negatively correlated with denitrification rate. All samples had a certain anammox capacity, but no known anammox bacteria were found in the microbial diversity detection, and the expression of gene (hzsB) related to the anammox process was extremely low, which may indicate the existence of an unknown anammox bacterium. The data of this study showed that the IMTA culture pond had a certain potential for nitrogen removal, and whether it could make a contribution to reducing the pollution of culture wastewater still needed additional practice and evaluation, and also provided a theoretical basis for the nitrogen removal research of coastal mariculture ponds.},
}
@article {pmid38830709,
year = {2024},
author = {Mugani, R and El Khalloufi, F and Kasada, M and Redouane, EM and Haida, M and Aba, RP and Essadki, Y and Zerrifi, SEA and Herter, SO and Hejjaj, A and Aziz, F and Ouazzani, N and Azevedo, J and Campos, A and Putschew, A and Grossart, HP and Mandi, L and Vasconcelos, V and Oudra, B},
title = {Monitoring of toxic cyanobacterial blooms in Lalla Takerkoust reservoir by satellite imagery and microcystin transfer to surrounding farms.},
journal = {Harmful algae},
volume = {135},
number = {},
pages = {102631},
doi = {10.1016/j.hal.2024.102631},
pmid = {38830709},
issn = {1878-1470},
mesh = {*Microcystins/metabolism/analysis ; *Harmful Algal Bloom ; *Microcystis/physiology/growth &amp; development ; *Satellite Imagery ; *Environmental Monitoring/methods ; Cyanobacteria/physiology/growth &amp; development ; Indonesia ; Synechococcus/physiology ; Lakes/microbiology ; },
abstract = {Cyanobacterial harmful algal blooms (CyanoHABs) threaten public health and freshwater ecosystems worldwide. In this study, our main goal was to explore the dynamics of cyanobacterial blooms and how microcystins (MCs) move from the Lalla Takerkoust reservoir to the nearby farms. We used Landsat imagery, molecular analysis, collecting and analyzing physicochemical data, and assessing toxins using HPLC. Our investigation identified two cyanobacterial species responsible for the blooms: Microcystis sp. and Synechococcus sp. Our Microcystis strain produced three MC variants (MC-RR, MC-YR, and MC-LR), with MC-RR exhibiting the highest concentrations in dissolved and intracellular toxins. In contrast, our Synechococcus strain did not produce any detectable toxins. To validate our Normalized Difference Vegetation Index (NDVI) results, we utilized limnological data, including algal cell counts, and quantified MCs in freeze-dried Microcystis bloom samples collected from the reservoir. Our study revealed patterns and trends in cyanobacterial proliferation in the reservoir over 30 years and presented a historical map of the area of cyanobacterial infestation using the NDVI method. The study found that MC-LR accumulates near the water surface due to the buoyancy of Microcystis. The maximum concentration of MC-LR in the reservoir water was 160 µg L[-1]. In contrast, 4 km downstream of the reservoir, the concentration decreased by a factor of 5.39 to 29.63 µgL[-1], indicating a decrease in MC-LR concentration with increasing distance from the bloom source. Similarly, the MC-YR concentration decreased by a factor of 2.98 for the same distance. Interestingly, the MC distribution varied with depth, with MC-LR dominating at the water surface and MC-YR at the reservoir outlet at a water depth of 10 m. Our findings highlight the impact of nutrient concentrations, environmental factors, and transfer processes on bloom dynamics and MC distribution. We emphasize the need for effective management strategies to minimize toxin transfer and ensure public health and safety.},
}
@article {pmid38830413,
year = {2024},
author = {Kerfahi, D and Dong, K and Tripathi, B and Adams, JM},
title = {Global comparison shows that soil bacterial communities in extreme pH soils are more structured by deterministic processes.},
journal = {The Science of the total environment},
volume = {942},
number = {},
pages = {173662},
doi = {10.1016/j.scitotenv.2024.173662},
pmid = {38830413},
issn = {1879-1026},
mesh = {*Soil Microbiology ; Hydrogen-Ion Concentration ; *Soil/chemistry ; *Bacteria ; Microbiota ; },
abstract = {A major aim of microbial ecology is the search for basic 'rules' that dominate variation in microbial communities. An earlier comparison of several soil successional series showed that pH explained variation in the relative importance of stochastic versus deterministic processes in bacterial communities. In neutral pH soils, bacterial communities were more strongly influenced by stochastic processes than in low or high pH soils. Here, we took a broad level approach to attempt a more definitive answer of whether soil pH dominates bacterial community structuring using the global database of 237 samples. The beta-NTI showed that at both a global and continental scale, samples with low pH were dominated by deterministic processes, while in samples at around neutral pH, stochastic processes dominated. At high pH, stochasticity dominated on the global scale, but on several continents, the beta-NTI showed determinism predominating. Overall, it appears that bacterial community structuring is strongly and predictably affected by pH, with the most consistent difference observed between determinism at low pH and stochasticity at neutral pH. There is a need for hypothesis testing to explain why this trend exists. It is possible that at low pH, there is a greater selection for consortia to exploit resources, which leads to more predictable, deterministic combinations of species co-occurring. Additionally, the high energy demands for homeostasis and the constraints from the lack of available nutrient resources may impose greater niche-based competition, resulting in more deterministic community structuring at low pH.},
}
@article {pmid38829422,
year = {2024},
author = {Jurado, V and Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Sanchez-Moral, S and Saiz-Jimenez, C},
title = {Gypsum Cave Biofilm Communities are Strongly Influenced by Bat- And Arthropod-Related Fungi.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {80},
pmid = {38829422},
issn = {1432-184X},
mesh = {*Caves/microbiology ; *Chiroptera/microbiology/physiology ; Animals ; *Biofilms ; *Fungi/classification/physiology/genetics/isolation &amp; purification ; *Arthropods/microbiology ; *Calcium Sulfate ; Spain ; Biodiversity ; Mycobiome ; Soil Microbiology ; },
abstract = {The Gypsum Karst of Sorbas, Almeria, southeast Spain, includes a few caves whose entrances are open and allow the entry and roosting of numerous bats. Caves are characterized by their diversity of gypsum speleothems, such as stalactites, coralloids, gypsum crusts, etc. Colored biofilms can be observed on the walls of most caves, among which the Covadura and C3 caves were studied. The objective was to determine the influence that bat mycobiomes may have on the fungal communities of biofilms. The results indicate that the fungi retrieved from white and yellow biofilms in Covadura Cave (Ascomycota, Mortierellomycota, Basidiomycota) showed a wide diversity, depending on their location, and were highly influenced by the bat population, the guano and the arthropods that thrive in the guano, while C3 Cave was more strongly influenced by soil- and arthropod-related fungi (Ascomycota, Mortierellomycota), due to the absence of roosting bats.},
}
@article {pmid38829379,
year = {2024},
author = {Gwokyalya, R and Herren, JK and Weldon, CW and Ndlela, S and Gichuhi, J and Ongeso, N and Wairimu, AW and Ekesi, S and Mohamed, SA},
title = {Shaping the Microbial Landscape: Parasitoid-Driven Modifications of Bactrocera dorsalis Microbiota.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {81},
pmid = {38829379},
issn = {1432-184X},
mesh = {Animals ; *Tephritidae/microbiology/parasitology ; *Wasps/microbiology/physiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Larva/microbiology/parasitology/growth &amp; development ; *RNA, Ribosomal, 16S/genetics ; Fungi/genetics/physiology ; Host-Parasite Interactions ; Microbiota ; Dysbiosis/microbiology/parasitology ; },
abstract = {Koinobiont endoparasitoids regulate the physiology of their hosts through altering host immuno-metabolic responses, processes which function in tandem to shape the composition of the microbiota of these hosts. Here, we employed 16S rRNA and ITS amplicon sequencing to investigate whether parasitization by the parasitoid wasps, Diachasmimorpha longicaudata (Ashmaed) (Hymenoptera: Braconidae) and Psyttalia cosyrae (Wilkinson) (Hymenoptera: Braconidae), induces gut dysbiosis and differentially alter the gut microbial (bacteria and fungi) communities of an important horticultural pest, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae). We further investigated the composition of bacterial communities of adult D. longicaudata and P. cosyrae to ascertain whether the adult parasitoids and parasitized host larvae share microbial taxa through transmission. We demonstrated that parasitism by D. longicaudata induced significant gut perturbations, resulting in the colonization and increased relative abundance of pathogenic gut bacteria. Some pathogenic bacteria like Stenotrophomonas and Morganella were detected in both the guts of D. longicaudata-parasitized B. dorsalis larvae and adult D. longicaudata wasps, suggesting a horizontal transfer of microbes from the parasitoid to the host. The bacterial community of P. cosyrae adult wasps was dominated by Arsenophonus nasoniae, whereas that of D. longicaudata adults was dominated by Paucibater spp. and Pseudomonas spp. Parasitization by either parasitoid wasp was associated with an overall reduction in fungal diversity and evenness. These findings indicate that unlike P. cosyrae which is avirulent to B. dorsalis, parasitization by D. longicaudata induces shifts in the gut bacteriome of B. dorsalis larvae to a pathobiont-dominated community. This mechanism possibly enhances its virulence against the pest, further supporting its candidacy as an effective biocontrol agent of this frugivorous tephritid fruit fly pest.},
}
@article {pmid38828615,
year = {2024},
author = {Ramirez-Puebla, ST and Mark Welch, JL and Borisy, GG},
title = {Improved Visualization of Oral Microbial Consortia.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345241251784},
doi = {10.1177/00220345241251784},
pmid = {38828615},
issn = {1544-0591},
support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; },
abstract = {Bacteria on the tongue dorsum (TD) form consortia tens to hundreds of microns in diameter organized around a core of epithelial cells. Whole-mount preparations have been instrumental in revealing their organization and specific microbial associations. However, their thickness and intricate 3-dimensional complexity present challenges for a comprehensive spatial analysis. To overcome these challenges, we employed a complementary approach: embedding in hydrophilic plastic followed by sectioning and postsectioning labeling. Samples were labeled by hybridization with multiplexed fluorescent oligonucleotide probes and visualized by spectral imaging and linear unmixing. Application of this strategy to TD biofilms improved the visualization of bacteria that were difficult to resolve in whole-mount imaging. Actinomyces, previously detected as patches, became resolved at the single-cell level. The filamentous taxa Leptotrichia and Lachnospiraceae, located at the core of the consortium, were regularly visualized whereas previously they were rarely detected when using whole mounts. Streptococcus salivarius, heterogeneously detected in whole mounts, were regularly and homogenously observed. Two-dimensional images provide valuable information about the organization of bacterial biofilms. However, they offer only a single plane of view for objects that can extend to hundreds of microns in thickness, and information obtained from such images may not always reflect the complexity of a 3-dimensional object. We combined serial physical sectioning with optical sectioning to facilitate the 3-dimensional reconstruction of consortia, spanning over 100 µm in thickness. Our work showcases the use of hydrophilic plastic embedding and sectioning for examining the structure of TD biofilms through spectral imaging fluorescence in situ hybridization. The result was improved visualization of important members of the human oral microbiome. This technique serves as a complementary method to the previously employed whole-mount analysis, offering its own set of advantages and limitations. Addressing the spatial complexity of bacterial consortia demands a multifaceted approach for a comprehensive and effective analysis.},
}
@article {pmid38827504,
year = {2024},
author = {Gupta, VVSR and Tiedje, JM},
title = {Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales.},
journal = {mLife},
volume = {3},
number = {1},
pages = {21-41},
pmid = {38827504},
issn = {2770-100X},
abstract = {The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.},
}
@article {pmid38827283,
year = {2024},
author = {Viladomat Jasso, M and García-Ulloa, M and Zapata-Peñasco, I and Eguiarte, LE and Souza, V},
title = {Metagenomic insight into taxonomic composition, environmental filtering and functional redundancy for shaping worldwide modern non-lithifying microbial mats.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17412},
pmid = {38827283},
issn = {2167-8359},
mesh = {*Metagenomics ; Archaea/genetics/classification ; Mexico ; Bacteria/genetics/classification ; Ecosystem ; Microbiota/genetics ; Metagenome ; Geologic Sediments/microbiology ; },
abstract = {Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics.},
}
@article {pmid38825932,
year = {2024},
author = {Li, SQ and Song, Y and Zhou, F and Chen, MY and Chen, LG and Zhou, JP},
title = {[Primary biliary cholangitis and autoimmune hepatitis overlap syndrome complicated with skin and soft tissue infection of lower limb during corticosteroids treatment: a case report].},
journal = {Zhonghua nei ke za zhi},
volume = {63},
number = {6},
pages = {618-620},
doi = {10.3760/cma.j.cn112138-20231030-00263},
pmid = {38825932},
issn = {0578-1426},
mesh = {Humans ; Adrenal Cortex Hormones/adverse effects ; Cholangitis/chemically induced ; *Hepatitis, Autoimmune/etiology/drug therapy ; Liver Cirrhosis, Biliary/drug therapy/complications ; Lower Extremity ; },
}
@article {pmid38820701,
year = {2024},
author = {Wang, Z and Fu, X and Kuramae, EE},
title = {Insight into farming native microbiome by bioinoculant in soil-plant system.},
journal = {Microbiological research},
volume = {285},
number = {},
pages = {127776},
doi = {10.1016/j.micres.2024.127776},
pmid = {38820701},
issn = {1618-0623},
mesh = {*Soil Microbiology ; *Microbiota/physiology ; *Soil/chemistry ; *Agriculture/methods ; Bacteria/classification/metabolism/isolation &amp; purification/genetics ; Crops, Agricultural/microbiology ; Plants/microbiology ; Microbial Interactions ; },
abstract = {Applying beneficial microorganisms (BM) as bioinoculants presents a promising soil-amendment strategy while impacting the native microbiome, which jointly alters soil-plant performance. Leveraging the untapped potential of native microbiomes alongside bioinoculants may enable farmers to sustainably regulate soil-plant systems via natural bioresources. This review synthesizes literature on native microbiome responses to BMs and their interactive effects on soil and plant performance. We highlight that native microbiomes harbor both microbial "helpers" that can improve soil fertility and plant productivity, as well as "inhibitors" that hinder these benefits. To harness the full potential of resident microbiome, it is crucial to elucidate their intricate synergistic and antagonistic interplays with introduced BMs and clarify the conditions that facilitate durable BM-microbiome synergies. Hence, we indicate current challenges in predicting these complex microbial interactions and propose corresponding strategies for microbiome breeding via BM bioinoculant. Overall, fully realizing the potential of BMs requires clarifying their interactions with native soil microbiomes and judiciously engineering microbiome to harness helpful microbes already present within agroecosystems.},
}
@article {pmid38819559,
year = {2024},
author = {Sanchez, FB and Sato Guima, SE and Setubal, JC},
title = {How to Obtain and Compare Metagenome-Assembled Genomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2802},
number = {},
pages = {135-163},
pmid = {38819559},
issn = {1940-6029},
mesh = {*Metagenome/genetics ; *Metagenomics/methods ; Software ; Computational Biology/methods ; Databases, Genetic ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; },
abstract = {Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation methods are devised. Thanks to improvements and cost reductions of DNA sequencing technologies and growing interest in microbial ecology, the rise in number of MAGs in genome repositories has been exponential. This chapter covers the basics of MAG retrieval and processing and provides a practical step-by-step guide using a real dataset and state-of-the-art tools for MAG analysis and comparison.},
}
@article {pmid38819147,
year = {2024},
author = {Sumner, DY},
title = {Oxygenation of Earth's atmosphere induced metabolic and ecologic transformations recorded in the Lomagundi-Jatuli carbon isotopic excursion.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {6},
pages = {e0009324},
pmid = {38819147},
issn = {1098-5336},
mesh = {*Earth, Planet ; *Atmosphere/chemistry ; *Carbon Isotopes/analysis/metabolism ; Oxygen/metabolism ; Methane/metabolism ; Bacteria/metabolism/genetics/classification ; Cyanobacteria/metabolism/genetics ; },
abstract = {The oxygenation of Earth's atmosphere represents the quintessential transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution; molecular clock models indicate the diversification and ecological expansion of respiratory metabolisms in the several hundred million years following atmospheric oxygenation. Across this same interval, the geological record preserves [13]C enrichment in some carbonate rocks, called the Lomagundi-Jatuli excursion (LJE). By combining data from geologic and genomic records, a self-consistent metabolic evolution model emerges for the LJE. First, fermentation and methanogenesis were major processes remineralizing organic carbon before atmospheric oxygenation. Once an ozone layer formed, shallow water and exposed environments were shielded from UVB/C radiation, allowing the expansion of cyanobacterial primary productivity. High primary productivity and methanogenesis led to preferential removal of [12]C into organic carbon and CH4. Extreme and variable [13]C enrichments in carbonates were caused by [13]C-depleted CH4 loss to the atmosphere. Through time, aerobic respiration diversified and became ecologically widespread, as did other new metabolisms. Respiration displaced fermentation and methanogenesis as the dominant organic matter remineralization processes. As CH4 loss slowed, dissolved inorganic carbon in shallow environments was no longer highly [13]C enriched. Thus, the loss of extreme [13]C enrichments in carbonates marks the establishment of a new microbial mat ecosystem structure, one dominated by respiratory processes distributed along steep redox gradients. These gradients allowed the exchange of metabolic by-products among metabolically diverse organisms, providing novel metabolic opportunities. Thus, the microbially induced oxygenation of Earth's atmosphere led to the transformation of microbial ecosystems, an archetypal example of planetary microbiology.IMPORTANCEThe oxygenation of Earth's atmosphere represents the most extensive known chemical transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution by providing oxidants independent of the sites of photosynthesis. Thus, the evolutionary changes during this interval and their effects on planetary-scale biogeochemical cycles are fundamental to our understanding of the interdependencies among genomes, organisms, ecosystems, elemental cycles, and Earth's surface chemistry through time.},
}
@article {pmid38819146,
year = {2024},
author = {Tang, S and Wu, G and Liu, Y and Xue, B and Zhang, S and Zhang, W and Jia, Y and Xie, Q and Liang, C and Wang, L and Heng, H and Wei, W and Shi, X and Hu, Y and Yang, J and Zhao, L and Wang, X and Zhao, L and Yuan, H},
title = {Guild-level signature of gut microbiome for diabetic kidney disease.},
journal = {mBio},
volume = {15},
number = {7},
pages = {e0073524},
pmid = {38819146},
issn = {2150-7511},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetic Nephropathies/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Metagenomics ; Adult ; Aged ; *Metagenome ; },
abstract = {UNLABELLED: Current microbiome signatures for chronic diseases such as diabetic kidney disease (DKD) are mainly based on low-resolution taxa such as genus or phyla and are often inconsistent among studies. In microbial ecosystems, bacterial functions are strain specific, and taxonomically different bacteria tend to form co-abundance functional groups called guilds. Here, we identified guild-level signatures for DKD by performing in-depth metagenomic sequencing and conducting genome-centric and guild-based analysis on fecal samples from 116 DKD patients and 91 healthy subjects. Redundancy analysis on 1,543 high-quality metagenome-assembled genomes (HQMAGs) identified 54 HQMAGs that were differentially distributed among the young healthy control group, elderly healthy control group, early-stage DKD patients (EDG), and late-stage DKD patients (LDG). Co-abundance network analysis classified the 54 HQMAGs into two guilds. Compared to guild 2, guild 1 contained more short-chain fatty acid biosynthesis genes and fewer genes encoding uremic toxin indole biosynthesis, antibiotic resistance, and virulence factors. Guild indices, derived from the total abundance of guild members and their diversity, delineated DKD patients from healthy subjects and between different severities of DKD. Age-adjusted partial Spearman correlation analysis showed that the guild indices were correlated with DKD disease progression and with risk indicators of poor prognosis. We further validated that the random forest classification model established with the 54 HQMAGs was also applicable for classifying patients with end-stage renal disease and healthy subjects in an independent data set. Therefore, this genome-level, guild-based microbial analysis strategy may identify DKD patients with different severity at an earlier stage to guide clinical interventions.<br><br>IMPORTANCE: Traditionally, microbiome research has been constrained by the reliance on taxonomic classifications that may not reflect the functional dynamics or the ecological interactions within microbial communities. By transcending these limitations with a genome-centric and guild-based analysis, our study sheds light on the intricate and specific interactions between microbial strains and diabetic kidney disease (DKD). We have unveiled two distinct microbial guilds with opposite influences on host health, which may redefine our understanding of microbial contributions to disease progression. The implications of our findings extend beyond mere association, providing potential pathways for intervention and opening new avenues for patient stratification in clinical settings. This work paves the way for a paradigm shift in microbiome research in DKD and potentially other chronic kidney diseases, from a focus on taxonomy to a more nuanced view of microbial ecology and function that is more closely aligned with clinical outcomes.},
}
@article {pmid38818274,
year = {2023},
author = {Fu, Y and Dou, Q and Smalla, K and Wang, Y and Johnson, TA and Brandt, KK and Mei, Z and Liao, M and Hashsham, SA and Schäffer, A and Smidt, H and Zhang, T and Li, H and Stedtfeld, R and Sheng, H and Chai, B and Virta, M and Jiang, X and Wang, F and Zhu, YG and Tiedje, JM},
title = {Gut microbiota research nexus: One Health relationship between human, animal, and environmental resistomes.},
journal = {mLife},
volume = {2},
number = {4},
pages = {350-364},
pmid = {38818274},
issn = {2770-100X},
abstract = {The emergence and rapid spread of antimicrobial resistance is of global public health concern. The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes (ARGs). In this review, we describe the reservoirs of gut ARGs and their dynamics in both animals and humans, use the One Health perspective to track the transmission of ARG-containing bacteria between humans, animals, and the environment, and assess the impact of antimicrobial resistance on human health and socioeconomic development. The gut resistome can evolve in an environment subject to various selective pressures, including antibiotic administration and environmental and lifestyle factors (e.g., diet, age, gender, and living conditions), and interventions through probiotics. Strategies to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic resistance. With the help of effective measures taken at the national, local, personal, and intestinal management, it will also result in preventing or minimizing the spread of infectious diseases. This review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.},
}
@article {pmid38818270,
year = {2023},
author = {Liu, J and Xu, G and Zhao, S and He, J},
title = {Resilience and functional redundancy of methanogenic digestion microbiome safeguard recovery of methanogenesis activity under the stress induced by microplastics.},
journal = {mLife},
volume = {2},
number = {4},
pages = {378-388},
pmid = {38818270},
issn = {2770-100X},
abstract = {Microplastics and nanoplastics are emerging pollutants that substantially influence biological element cycling in natural ecosystems. Plastics are also prevalent in sewage, and they accumulate in waste-activated sludge (WAS). However, the impacts of plastics on the methanogenic digestion of WAS and the underpinning microbiome remain underexplored, particularly during long-term operation. In this study, we found that short-term exposure to individual microplastics and nanoplastics (polyethylene, polyvinyl chloride, polystyrene, and polylactic acid) at a low concentration (10 particles/g sludge) slightly enhanced methanogenesis by 2.1%-9.0%, whereas higher levels (30-200 particles/g sludge) suppressed methanogenesis by 15.2%-30.1%. Notably, the coexistence of multiple plastics, particularly at low concentrations, showed synergistic suppression of methanogenesis. Unexpectedly, methanogenesis activity completely recovered after long-term exposure to plastics, despite obvious suppression of methanogenesis by initial plastic exposure. The inhibition of methanogenesis by plastics could be attributed to the stimulated generation of reactive oxygen species. The stress induced by plastics dramatically decreased the relative abundance of methanogens but showed marginal influence on putative hydrolytic and fermentation populations. Nonetheless, the digestion sludge microbiome exhibited resilience and functional redundancy, contributing to the recovery of methanogenesis during the long-term operation of digesters. Plastics also increased the complexity, modularity, and negative interaction ratios of digestion sludge microbiome networks, but their influence on community assembly varied. Interestingly, a unique plastisphere was observed, the networks and assembly of which were distinct from the sludge microbiome. Collectively, the comprehensive evaluation of the influence of microplastics and nanoplastics on methanogenic digestion, together with the novel ecological insights, contribute to better understanding and manipulating this engineered ecosystem in the face of increasing plastic pollution.},
}
@article {pmid38817815,
year = {2023},
author = {Wu, L and Yang, Y and Ning, D and Gao, Q and Yin, H and Xiao, N and Zhou, BY and Chen, S and He, Q and Zhou, J},
title = {Assessing mechanisms for microbial taxa and community dynamics using process models.},
journal = {mLife},
volume = {2},
number = {3},
pages = {239-252},
pmid = {38817815},
issn = {2770-100X},
abstract = {Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer-resource model with a neutral model in stochastic differential equations. Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer-resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.},
}
@article {pmid38816803,
year = {2024},
author = {Saeed, S and Ullah, S and Amin, F and Al-Hawadi, JS and Okla, MK and Alaraidh, IA and AbdElgawad, H and Liu, K and Harrison, MT and Saud, S and Hassan, S and Nawaz, T and Zhu, M and Liu, H and Khan, MA and Fahad, S},
title = {Salicylic acid and Tocopherol improve wheat (Triticum aestivum L.) Physio-biochemical and agronomic features grown in deep sowing stress: a way forward towards sustainable production.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {477},
pmid = {38816803},
issn = {1471-2229},
mesh = {*Triticum/growth &amp; development/metabolism/drug effects ; *Salicylic Acid/pharmacology/metabolism ; *Tocopherols/metabolism ; *Germination/drug effects ; Seeds/drug effects/growth &amp; development ; Antioxidants/metabolism ; Stress, Physiological ; Sustainable Development ; Chlorophyll/metabolism ; },
abstract = {BACKGROUND: The rate of germination and other physiological characteristics of seeds that are germinating are impacted by deep sowing. Based on the results of earlier studies, conclusions were drawn that deep sowing altered the physio-biochemical and agronomic characteristics of wheat (Triticum aestivum L.).<br><br>RESULTS: In this study, seeds of wheat were sown at 2 (control) and 6&#xa0;cm depth and the impact of exogenously applied salicylic acid and tocopherol (Vitamin-E) on its physio-biochemical and agronomic features was assessed. As a result, seeds grown at 2&#xa0;cm depth witnessed an increase in mean germination time, germination percentage, germination rate index, germination energy, and seed vigor index. In contrast, 6&#xa0;cm deep sowing resulted in negatively affecting all the aforementioned agronomic characteristics. In addition, deep planting led to a rise in MDA, glutathione reductase, and antioxidants enzymes including APX, POD, and SOD concentration. Moreover, the concentration of chlorophyll a, b, carotenoids, proline, protein, sugar, hydrogen peroxide, and agronomic attributes was boosted significantly with exogenously applied salicylic acid and tocopherol under deep sowing stress.<br><br>CONCLUSIONS: The results of the study showed that the depth of seed sowing has an impact on agronomic and physio-biochemical characteristics and that the negative effects of deep sowing stress can be reduced by applying salicylic acid and tocopherol to the leaves.},
}
@article {pmid38816227,
year = {2024},
author = {Carrillo-Barragan, P},
title = {Clean your own house first: integrating sustainability into microbiology labs.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {7},
pages = {},
pmid = {38816227},
issn = {1574-6941},
support = {//University of Basel/ ; },
mesh = {*Laboratories ; Environmental Microbiology ; Sustainable Development ; Microbiology ; Conservation of Natural Resources ; },
abstract = {Microbiology laboratories are pivotal hubs for exploring the potential of microorganisms and addressing global challenges. Particularly, Environmental Microbiology facilities hold substantial influence in advancing knowledge and capabilities crucial for achieving the United Nations Sustainable Development Goals. This raises the imperative of integrating sustainable practices to mitigate the environmental impact of research activities and foster a culture of responsibility. Such an approach not only aligns with global sustainability objectives but also catalyses innovative, eco-conscious methodologies in scientific research aimed at tackling pressing environmental issues. Concerns regarding the environmental footprint of laboratory practices have stimulated innovative improvements within the scientific community, ranging from resource-efficient initiatives to the management of essential commodities like water and energy. This perspective discusses specific areas where microbiology laboratories can enhance their sustainability efforts, drawing on reports and case studies of pioneering groups. Additionally, it explores potential collaborators to support these endeavours and emphasises the pivotal role of early career researchers in driving this transition. By initiating discussions and sparking curiosity within the environmental microbial community, this commentary seeks to propel the microbial ecology field toward a greener future, starting from within the laboratory environment.},
}
@article {pmid38814337,
year = {2024},
author = {Filek, K and Vuković, BB and Žižek, M and Kanjer, L and Trotta, A and Di Bello, A and Corrente, M and Bosak, S},
title = {Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {79},
pmid = {38814337},
issn = {1432-184X},
support = {UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; },
mesh = {Animals ; *Turtles/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; Microbiota ; Cloaca/microbiology ; Mycobiome ; Biodiversity ; Gastrointestinal Microbiome ; Biofilms ; },
abstract = {Research on microbial communities associated with wild animals provides a valuable reservoir of knowledge that could be used for enhancing their rehabilitation and conservation. The loggerhead sea turtle (Caretta caretta) is a globally distributed species with its Mediterranean population categorized as least concern according to the IUCN Red List of Threatened Species as a result of robust conservation efforts. In our study, we aimed to further understand their biology in relation to their associated microorganisms. We investigated epi- and endozoic bacterial and endozoic fungal communities of cloaca, oral mucosa, carapace biofilm. Samples obtained from 18 juvenile, subadult, and adult turtles as well as 8 respective enclosures, over a 3-year period, were analysed by amplicon sequencing of 16S rRNA gene and ITS2 region of nuclear ribosomal gene. Our results reveal a trend of decreasing diversity of distal gut bacterial communities with the age of turtles. Notably, Tenacibaculum species show higher relative abundance in juveniles than in adults. Differential abundances of taxa identified as Tenacibaculum, Moraxellaceae, Cardiobacteriaceae, and Campylobacter were observed in both cloacal and oral samples in addition to having distinct microbial compositions with Halioglobus taxa present only in oral samples. Fungal communities in loggerheads' cloaca were diverse and varied significantly among individuals, differing from those of tank water. Our findings expand the known microbial diversity repertoire of loggerhead turtles, highlighting interesting taxa specific to individual body sites. This study provides a comprehensive view of the loggerhead sea turtle bacterial microbiota and marks the first report of distal gut fungal communities that contributes to establishing a baseline understanding of loggerhead sea turtle holobiont.},
}
@article {pmid38814057,
year = {2024},
author = {Chen, M and Grégoire, DS and Bain, JG and Blowes, DW and Hug, LA},
title = {Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {6},
pages = {e0014324},
pmid = {38814057},
issn = {1098-5336},
support = {ORF-RE09-061//Ontario Research Fund - Research Excellence/ ; //Canada Research Chairs (Chaires de recherche du Canada)/ ; //Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
mesh = {*Mining ; *Sulfur/metabolism ; *Iron/metabolism ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Copper/metabolism/analysis ; *Nickel/metabolism ; Ontario ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Biodegradation, Environmental ; },
abstract = {The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.},
}
@article {pmid38812552,
year = {2024},
author = {Zhu, W and Chang, L and Zhang, M and Chen, Q and Sui, L and Shen, C and Jiang, J},
title = {Microbial diversity in mountain-dwelling amphibians: The combined effects of host and climatic factors.},
journal = {iScience},
volume = {27},
number = {6},
pages = {109907},
pmid = {38812552},
issn = {2589-0042},
abstract = {Comprehending the determinants of host-associated microbiota is pivotal in microbial ecology. Yet, the links between climatic factors and variations in host-associated microbiota necessitate further clarification. Mountain-dwelling amphibians, with limited dispersal abilities, serve as valuable models for addressing these questions. Our study, using 126 amphibian-associated microbial samples (64 gut and 62 skin) and 101 environmental microbial samples (51 soil and 50 water) from the eastern Tibetan Plateau, revealed host factors as primary drivers of the variations in host-associated microbiota. However, climatic factors contributed to additional variations in gut microbial beta-diversity and skin microbial function. Water microbiota were identified as a significant contributor to the amphibian-associated microbiomes, with their climate-driven variations mediating an indirect association between the variations in climatic factors and host-associated microbiota. These findings extend our understanding of the assembly of host-associated microbiota in amphibians, emphasizing the significance of microbiota in evaluating the impact of climate change on animals.},
}
@article {pmid38812371,
year = {2024},
author = {Liu, J and Wu, Y and Zhang, W and Fahad, S and Qiu, Z and Zhu 朱, M&#x58a8;},
title = {Podosphaera xanthii Causing Powdery Mildew on Salvia farinacea in Central China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-03-24-0591-PDN},
pmid = {38812371},
issn = {0191-2917},
abstract = {Salvia farinacea, commonly referred as mealycup sage, is a perennial herbaceous plant belonging to the Salvia genus of the Lamiaceae family. It originates from the Mediterranean region, North America, and Europe and is globally cultivated due to its appealing and captivating flowers. Moreover, mealycup sage is utilized as traditional Chinese medicinal plant for treatment of cardiovascular diseases (Li et al. 2018). In October 2023, powdery mildew-like symptoms were observed on Salvia farinacea plants cultivated in a garden located in Xinxiang City, Henan Province, China (113.93, 35.29). The leaves were covered with white and thin masses of mycelia, conidiophores and conidia of the fungus. About 100 plants were checked and 90 % were infected. There were a large number of white colonies with irregular or continuous round lesions on the adaxial and abaxial surfaces of the leaves, covering approximately 80% of the leaf area. The slightly or straight curved conidiophores (n = 30) were 46 to 145× 8 to 11 μm in size and consisted of foot cells, shorter cells and conidia. The ellipsoidal to oval conidia (n = 30), containing fibrosin bodies, were 24 to 35 × 12 to 19 μm in size and had a length/width ratio of 1.8 to 2.1. No chasmothecia were observed on leaves. These morphological features were consistent with those of Podosphaera xanthii (Braun and Cook 2012). Following the previously described method (White et al. 1990; Bradshaw et al. 2022; Zhu et al. 2022a), the sequences of ITS and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regions were amplified with specific primers ITS1/ITS4 (ITS1 5'-TCCGTAGGTGAACCTGCGG-3' ; ITS4 5'-TCCTCCGCTTATTGATATGC-3') and PMGAPDH1/PMGAPDH3R (PMGAPDH1 5'-GGAATGGCTATGCGTGTACC-3'; PMGAPDH3R 5'-CCCCATTCGTTGTCGTACCATG-3'), and the resulting sequences were uploaded in GenBank (Accession No. OR761885 and PP236082, respectively). BLASTn analysis showed that the sequence shared 560/565 (99%) and 272/272 (100%) homology with P. xanthii (MW301281) on Impatiens balsamina (Zhu et al. 2022b) and with P. xanthii (ON075658) on Cucumis melo (Bradshaw et al. 2022), respectively. The phylogenetic analysis clearly illustrated that the collected isolate of P. xanthii clustered in the same clade. The pathogenicity was tested according to the method previously described (Zhu et al. 2021). The fungus was inoculated onto the leaf surfaces of three healthy plants by blowing conidia from infected leaves with pressurized air. Non-inoculated plants were treated as control. Both the control and inoculated plants were separately placed in growth chambers under 60% humidity; light/dark, 16 h/8 h; and a temperature of 18°C. After a period of 12-15 days, the leaves of the inoculated plants exhibited signs of powdery mildew, whereas the control group remained unaffected. Therefore, the fungal pathogen was identified and confirmed as P. xanthii (isolate PXSF202310). Previously, P. xanthii was reported on Impatiens balsamina and S. farinacea from China and Korea (Zhu et al. 2021; Choi et al. 2022). As far as we know, this is the first documentation of P. xanthii on S. farinacea in central China. The presence of P. xanthii can lead to a deterioration in plant health and stunted growth, thereby negatively impacting both the decorative and medicinal value of S. farinacea. The recognition of P. xanthii on S. farinacea enhances our comprehension of this pathogen hosts and provides fundamental information for forthcoming disease control studies.},
}
@article {pmid38812269,
year = {2024},
author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Munoz, F and Tenllado, &#xc1; and Vinyeta, M and Le Roux, X and Vasseur, F},
title = {Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana.},
journal = {The New phytologist},
volume = {243},
number = {2},
pages = {620-635},
doi = {10.1111/nph.19870},
pmid = {38812269},
issn = {1469-8137},
support = {ANR-17-CE02-0018-01//Agence Nationale de la Recherche/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft/ ; ERC-StG-2014-639706-CONSTRAINTS/ERC_/European Research Council/International ; ERC-StG-2020-949843/ERC_/European Research Council/International ; },
mesh = {*Arabidopsis/genetics/metabolism/microbiology ; *Nitrogen Cycle ; *Soil Microbiology ; *Biomass ; Nitrogen/metabolism ; Soil/chemistry ; Genotype ; Nitrification ; Denitrification ; Ecosystem ; },
abstract = {In natural systems, different plant species have been shown to modulate specific nitrogen (N) cycling processes so as to meet their N demand, thereby potentially influencing their own niche. This phenomenon might go beyond plant interactions with symbiotic microorganisms and affect the much less explored plant interactions with free-living microorganisms involved in soil N cycling, such as nitrifiers and denitrifiers. Here, we investigated variability in the modulation of soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), and their ratio (NEA : DEA), across 193 Arabidopsis thaliana accessions. We studied the genetic and environmental determinants of such plant-soil interactions, and effects on plant biomass production in the next generation. We found that NEA, DEA, and NEA : DEA varied c. 30-, 15- and 60-fold, respectively, among A. thaliana genotypes and were related to genes linked with stress response, flowering, and nitrate nutrition, as well as to soil parameters at the geographic origin of the analysed genotypes. Moreover, plant-mediated N cycling activities correlated with the aboveground biomass of next-generation plants in home vs away nonautoclaved soil, suggesting a transgenerational impact of soil biotic conditioning on plant performance. Altogether, these findings suggest that nutrient-based plant niche construction may be much more widespread than previously thought.},
}
@article {pmid38811807,
year = {2024},
author = {Eliette, AS and Elodie, B and Arnaud, M and Tiffany, R and Aymé, S and Pascal, P},
title = {Idiosyncratic invasion trajectories of human bacterial pathogens facing temperature disturbances in soil microbial communities.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {12375},
pmid = {38811807},
issn = {2045-2322},
support = {773830//European Commission One Health EJP/ ; 773830//European Commission One Health EJP/ ; 773830//European Commission One Health EJP/ ; },
mesh = {*Soil Microbiology ; *Listeria monocytogenes/physiology ; Humans ; *Microbiota ; Klebsiella pneumoniae/physiology ; Temperature ; Biodiversity ; },
abstract = {Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze-thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities.},
}
@article {pmid38810265,
year = {2024},
author = {Li, C and Wang, L and Tong, C and Li, H and Qin, Z and Zeng, X and Chang, Y and Li, M and Yang, Q},
title = {Molecular Insights into the Defense of Dioscorea opposita Cultivar Tiegun Callus Against Pathogenic and Endophytic Fungal Infection Through Transcriptome Analysis.},
journal = {Phytopathology},
volume = {114},
number = {8},
pages = {1893-1903},
doi = {10.1094/PHYTO-04-24-0125-R},
pmid = {38810265},
issn = {0031-949X},
mesh = {*Dioscorea/microbiology/genetics ; *Alternaria/physiology/pathogenicity ; *Plant Diseases/microbiology/immunology ; *Endophytes/physiology/genetics ; Penicillium/genetics/physiology/pathogenicity ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Transcriptome ; },
abstract = {Dioscorea opposita cultivar Tiegun is an economically important crop with high nutritional and medicinal value. Plants can activate complex and diverse defense mechanisms after infection by pathogenic fungi. Moreover, endophytic fungi can also trigger the plant immune system to resist pathogen invasion. However, the study of the effects of endophytic fungi on plant infection lags far behind that of pathogenic fungi, and the underlying mechanism is not fully understood. Here, the black spot pathogen Alternaria alternata and the endophytic fungus Penicillium halotolerans of Tiegun were identified and used to infect calli. The results showed that A. alternata could cause more severe membrane lipid peroxidation, whereas P. halotolerans could rapidly increase the activity of the plant antioxidant enzymes superoxide dismutase, peroxidase, and catalase; thus, the degree of damage to the callus caused by P. halotolerans was weaker than that caused by A. alternata. RNA sequencing analysis revealed that various plant defense pathways, such as phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and the mitogen-activated protein kinase signaling pathway, play important roles in triggering the plant immune response during fungal infection. Furthermore, the tryptophan metabolism, betalain biosynthesis, fatty acid degradation, flavonoid biosynthesis, tyrosine metabolism, and isoquinoline alkaloid biosynthesis pathways may accelerate the infection of pathogenic fungi, and the ribosome biogenesis pathway in eukaryotes may retard the damage caused by endophytic fungi. This study lays a foundation for exploring the infection mechanism of yam pathogens and endophytic fungi and provides insight for effective fungal disease control in agriculture.},
}
@article {pmid38808529,
year = {2024},
author = {Demircan, T and Gül, S and Taşçı, EA},
title = {Can Microbiome Modulate Regenerative Capacity? A Comparative Microbiome Study Reveals a Dominant Presence of Flavobacteriaceae in Blastema Tissue During Axolotl Limb Regeneration.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {6},
pages = {291-302},
doi = {10.1089/omi.2024.0075},
pmid = {38808529},
issn = {1557-8100},
mesh = {Animals ; *Regeneration ; *Microbiota/genetics ; *Ambystoma mexicanum/microbiology/physiology ; *RNA, Ribosomal, 16S/genetics ; *Extremities/microbiology ; Phylogeny ; },
abstract = {The axolotl (Ambystoma mexicanum) is renowned for its remarkable regenerative capabilities, which are not diminished by the transition from a neotenic to a metamorphic state. This study explored the microbiome dynamics in axolotl limb regeneration by examining the microbial communities present in neotenic and metamorphic axolotls at two critical stages of limb regeneration: pre-amputation and during blastema formation. Utilizing 16S rRNA amplicon sequencing, we investigated the variations in microbiome profiles associated with different developmental and regenerative states. Our findings reveal a distinct separation in the microbiome profiles of neotenic and metamorphic samples, with a clear demarcation in microbial composition at both the phylum and genus levels. In neotenic 0DPA samples, Proteobacteria and Firmicutes were the most abundant, whereas in neotenic 7DPA samples, Proteobacteria and Bacteroidetes dominated. Conversely, metamorphic samples displayed a higher abundance of Firmicutes and Bacteroidetes at 0DPA and Proteobacteria and Firmicutes at 7DPA. Alpha and beta diversity analyses, along with dendrogram construction, demonstrated significant variations within and between the sample groups, suggesting a strong influence of both developmental stage and regenerative state on the microbiome. Notably, Flavobacterium and Undibacterium emerged as distinctive microbial entities in neotenic 7DPA samples, highlighting potential key players in the microbial ecology of regeneration. These findings suggest that the axolotl's microbiome is dynamically responsive to blastema formation, and they underscore the potential influence of microbial communities on the regeneration process. This study lays the groundwork for future research into the mechanisms by which the microbiome may modulate regenerative capacity.},
}
@article {pmid38806848,
year = {2024},
author = {Banchi, E and Manna, V and Muggia, L and Celussi, M},
title = {Marine Fungal Diversity and Dynamics in the Gulf of Trieste (Northern Adriatic Sea).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {78},
pmid = {38806848},
issn = {1432-184X},
mesh = {*Seawater/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Biodiversity ; *RNA, Ribosomal, 18S/genetics/analysis ; Mycobiome ; DNA, Fungal/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; DNA, Ribosomal Spacer/genetics/analysis ; Ascomycota/genetics/classification/isolation &amp; purification ; },
abstract = {Fungi contribute to different important ecological processes, including decomposition of organic matter and nutrient cycling, but in the marine environment the main factors influencing their diversity and dynamics at the spatial and temporal levels are still largely unclear. In this study, we performed DNA metabarcoding on seawater sampled monthly over a year and a half in the Gulf of Trieste (northern Adriatic Sea), targeting the internal transcribed spacer (ITS) and the 18S rRNA gene regions. The fungal communities were diverse, very dynamic, and belonged predominantly to marine taxa. Samples could be clustered in two groups, mainly based on the high (> 30%) or low relative proportion of the ascomycetes Parengyodontium album, which emerged as a key taxon in this area. Dissolved and particulate organic C:N ratio played important roles in shaping the mycoplankton assemblages, suggesting that differently bioavailable organic matter pools may be utilized by different consortia. The proportion of fungal over total reads was 31% for ITS and 0.7% for 18S. ITS had the highest taxonomic resolution but low power to detect early divergent fungal lineages. Our results on composition, distribution, and environmental drivers extended our knowledge of the structure and function of the mycobiome of coastal waters.},
}
@article {pmid38806738,
year = {2024},
author = {Wissner, JL and Parada-Fabián, JC and Márquez-Velázquez, NA and Escobedo-Hinojosa, W and Gaudêncio, SP and Prieto-Davó, A},
title = {Diversity and Bioprospection of Gram-positive Bacteria Derived from a Mayan Sinkhole.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {77},
pmid = {38806738},
issn = {1432-184X},
support = {POSTDOC//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; POSTDOC//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; LA/P/0140/2020//FCT-Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia, IP/ ; PAIP 5000-9149//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico, Facultad de Qu&#xed;mica/ ; A1-S-10785//Consejo Nacional de Ciencia Humanidades y Tecnolog&#xed;a (CONAHCyT) Ciencia B&#xe1;sica/ ; },
mesh = {*Geologic Sediments/microbiology ; Mexico ; *Biodiversity ; *Gram-Positive Bacteria/isolation &amp; purification/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; Bioprospecting ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Seawater/microbiology ; },
abstract = {Water-filled sinkholes known locally as cenotes, found on the Yucatán Peninsula, have remarkable biodiversity. The primary objective of this study was to explore the biotechnological potential of Gram-positive cultivable bacteria obtained from sediment samples collected at the coastal cenote Pol-Ac in Yucatán, Mexico. Specifically, the investigation aimed to assess production of hydrolytic enzymes and antimicrobial compounds. 16 S rRNA gene sequencing led to the identification of 49 Gram-positive bacterial isolates belonging to the phyla Bacillota (n = 29) and Actinomycetota (n = 20) divided into the common genera Bacillus and Streptomyces, as well as the genera Virgibacillus, Halobacillus, Metabacillus, Solibacillus, Neobacillus, Rossellomorea, Nocardiopsis and Corynebacterium. With growth at 55ºC, 21 of the 49 strains were classified as moderately thermotolerant. All strains were classified as halotolerant and 24 were dependent on marine water for growth. Screening for six extracellular hydrolytic enzymes revealed gelatinase, amylase, lipase, cellulase, protease and chitinase activities in 93.9%, 67.3%, 63.3%, 59.2%, 59.2% and 38.8%, of isolated strains, respectively. The genes for polyketide synthases type I, were detected in 24 of the strains. Of 18 strains that achieved > 25% inhibition of growth in the bacterial pathogen Staphylococcus aureus ATCC 6538, 4 also inhibited growth in Escherichia coli ATCC 35,218. Isolates Streptomyces sp. NCA_378 and Bacillus sp. NCA_374 demonstrated 50-75% growth inhibition against at least one of the two pathogens tested, along with significant enzymatic activity across all six extracellular enzymes. This is the first comprehensive report on the biotechnological potential of Gram-positive bacteria isolated from sediments in the cenotes of the Yucatán Peninsula.},
}
@article {pmid38805423,
year = {2024},
author = {Fournier, C and Fiedler, A and Weidele, M and Kautz, H and Schleheck, D},
title = {Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0303937},
pmid = {38805423},
issn = {1932-6203},
mesh = {*Filtration/instrumentation/methods ; *Plankton/genetics ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Lakes/microbiology ; Phylogeny ; Biomass ; },
abstract = {Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.},
}
@article {pmid38804464,
year = {2024},
author = {Lappan, R and Thakar, J and Molares Moncayo, L and Besser, A and Bradley, JA and Goordial, J and Trembath-Reichert, E and Greening, C},
title = {The atmosphere: a transport medium or an active microbial ecosystem?.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38804464},
issn = {1751-7370},
support = {RGY0058/2022//Human Frontier Science Program/ ; },
mesh = {*Atmosphere ; *Ecosystem ; Microbiota ; Air Microbiology ; Biodiversity ; Bacteria/metabolism/classification/growth &amp; development ; },
abstract = {The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.},
}
@article {pmid38804108,
year = {2024},
author = {Ochoa-Hueso, R and Eldridge, DJ and Berdugo, M and Trivedi, P and Sokoya, B and Cano-Díaz, C and Abades, S and Alfaro, F and Bamigboye, AR and Bastida, F and Blanco-Pastor, JL and de Los Rios, A and Durán, J and Geisen, S and Grebenc, T and Illán, JG and Liu, YR and Makhalanyane, TP and Mamet, S and Molina-Montenegro, MA and Moreno, JL and Nahberger, TU and Peñaloza-Bojacá, GF and Plaza, C and Rey, A and Rodríguez, A and Siebe, C and Singh, BK and Teixido, AL and Torres-Díaz, C and Wang, L and Wang, J and Wang, J and Zaady, E and Zhou, X and Zhou, XQ and Tedersoo, L and Delgado-Baquerizo, M},
title = {Unearthing the soil-borne microbiome of land plants.},
journal = {Global change biology},
volume = {30},
number = {5},
pages = {e17295},
doi = {10.1111/gcb.17295},
pmid = {38804108},
issn = {1365-2486},
support = {LRB17\1019//British Ecological Society/ ; J4-1766//Slovenian Research Agency/ ; GOPC-CA-20-0001//Junta de Andaluc&#xed;a/ ; P20_00323//Junta de Andaluc&#xed;a/ ; EMC21_00207//Junta de Andaluc&#xed;a/ ; GO2022-01//Junta de Andaluc&#xed;a/ ; PID2019-106004RA-I00//Spanish Ministry of Science and Innovation/ ; PID2020-115813RA-I00//Spanish Ministry of Science and Innovation/ ; TED2021-130908B-C41//Spanish Ministry of Science and Innovation/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; *Embryophyta ; Biodiversity ; Soil/chemistry ; },
abstract = {Plant-soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change.},
}
@article {pmid38804043,
year = {2024},
author = {Owens, LA and Thurber, MI and Goldberg, TL},
title = {CRISPR-Cas9-mediated host signal reduction for 18S metabarcoding of host-associated eukaryotes.},
journal = {Molecular ecology resources},
volume = {24},
number = {6},
pages = {e13980},
pmid = {38804043},
issn = {1755-0998},
support = {R01 AG049395/AG/NIA NIH HHS/United States ; T32 AI007414/AI/NIAID NIH HHS/United States ; 1R21AI163592-01/HI/NHLBI NIH HHS/United States ; T32AI007414/HI/NHLBI NIH HHS/United States ; 1R01AG049395-01/HI/NHLBI NIH HHS/United States ; R21 AI163592/AI/NIAID NIH HHS/United States ; },
mesh = {*CRISPR-Cas Systems ; *Eukaryota/genetics ; *DNA Barcoding, Taxonomic/methods ; *RNA, Ribosomal, 18S/genetics ; Metagenomics/methods ; Humans ; Animals ; },
abstract = {Metabarcoding-based methods for identification of host-associated eukaryotes have the potential to revolutionize parasitology and microbial ecology, yet significant technical challenges remain. In particular, highly abundant host reads can mask the presence of less-abundant target organisms, especially for sample types rich in host DNA (e.g., blood and tissues). Here, we present a new CRISPR-Cas9-mediated approach designed to reduce host signal by selective amplicon digestion, thus enriching clinical samples for eukaryotic endosymbiont sequences during metabarcoding. Our method achieves a nearly 76% increased efficiency in host signal reduction compared with no treatment and a nearly 60% increased efficiency in host signal reduction compared with the most commonly used published method. Furthermore, the application of our method to clinical samples allows for the detection of parasite infections that would otherwise have been missed.},
}
@article {pmid38802328,
year = {2024},
author = {Fu, Y and Hu, F and Wang, F and Xu, M and Jia, Z and Amelung, W and Mei, Z and Han, X and Virta, M and Jiang, X and Tiedje, JM},
title = {Distinct Assembly Patterns of Soil Antibiotic Resistome Revealed by Land-Use Changes over 30 Years.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {23},
pages = {10216-10226},
doi = {10.1021/acs.est.3c10423},
pmid = {38802328},
issn = {1520-5851},
mesh = {*Soil/chemistry ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; },
abstract = {Compared with the ever-growing information about the anthropogenic discharge of nutrients, metals, and antibiotics on the disturbance of antibiotic resistance genes (ARGs), less is known about how the potential natural stressors drive the evolutionary processes of antibiotic resistance. This study examined how soil resistomes evolved and differentiated over 30 years in various land use settings with spatiotemporal homogeneity and minimal human impact. We found that the contents of soil organic carbon, nitrogen, soil microbial biomass, and bioavailable heavy metals, as well as related changes in the antibiotic resistome prevalence including diversity and abundance, declined in the order of grassland > cropland > bareland. Sixty-nine remaining ARGs and 14 mobile genetic elements (MGEs) were shared among three land uses. Multiple factors (i.e., soil properties, heavy metals, bacterial community, and MGEs) contributed to the evolutionary changes of the antibiotic resistome, wherein the resistome profile was dominantly driven by MGEs from both direct and indirect pathways, supported by a partial least-squares path model analysis. Our results suggest that pathways to mitigate ARGs in soils can coincide with land degradation processes, posing a challenge to the common goal of managing our environment sustainably.},
}
@article {pmid38801800,
year = {2024},
author = {Oesterle, I and Ayeni, KI and Ezekiel, CN and Berry, D and Rompel, A and Warth, B},
title = {Insights into the early-life chemical exposome of Nigerian infants and potential correlations with the developing gut microbiome.},
journal = {Environment international},
volume = {188},
number = {},
pages = {108766},
doi = {10.1016/j.envint.2024.108766},
pmid = {38801800},
issn = {1873-6750},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Nigeria ; *Milk, Human/chemistry/microbiology ; Infant ; Female ; *Feces/microbiology/chemistry ; Exposome ; Xenobiotics/analysis ; Infant, Newborn ; RNA, Ribosomal, 16S ; Environmental Pollutants/analysis ; Adult ; Male ; },
abstract = {Early-life exposure to natural and synthetic chemicals can impact acute and chronic health conditions. Here, a suspect screening workflow anchored on high-resolution mass spectrometry was applied to elucidate xenobiotics in breast milk and matching stool samples collected from Nigerian mother-infant pairs (n = 11) at three time points. Potential correlations between xenobiotic exposure and the developing gut microbiome, as determined by 16S rRNA gene amplicon sequencing, were subsequently explored. Overall, 12,192 and 16,461 features were acquired in the breast milk and stool samples, respectively. Following quality control and suspect screening, 562 and 864 features remained, respectively, with 149 of these features present in both matrices. Taking advantage of 242 authentic reference standards measured for confirmatory purposes of food bio-actives and toxicants, 34 features in breast milk and 68 features in stool were identified and semi-quantified. Moreover, 51 and 78 features were annotated with spectral library matching, as well as 416 and 652 by in silico fragmentation tools in breast milk and stool, respectively. The analytical workflow proved its versatility to simultaneously determine a diverse panel of chemical classes including mycotoxins, endocrine-disrupting chemicals (EDCs), antibiotics, plasticizers, perfluorinated alkylated substances (PFAS), and pesticides, although it was originally optimized for polyphenols. Spearman rank correlation of the identified features revealed significant correlations between chemicals of the same classification such as polyphenols. One-way ANOVA and differential abundance analysis of the data obtained from stool samples revealed that molecules of plant-based origin elevated as complementary foods were introduced to the infants' diets. Annotated compounds in the stool, such as tricetin, positively correlated with the genus Blautia. Moreover, vulgaxanthin negatively correlated with Escherichia-Shigella. Despite the limited sample size, this exploratory study provides high-quality exposure data of matched biospecimens obtained from mother-infant pairs in sub-Saharan Africa and shows potential correlations between the chemical exposome and the gut microbiome.},
}
@article {pmid38801423,
year = {2024},
author = {Ramírez-Pool, JA and Calderón-Pérez, B and Ruiz-Medrano, R and Ortiz-Castro, R and Xoconostle-Cazares, B},
title = {Bacillus Strains as Effective Biocontrol Agents Against Phytopathogenic Bacteria and Promoters of Plant Growth.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {76},
pmid = {38801423},
issn = {1432-184X},
mesh = {*Bacillus/physiology ; *Arabidopsis/microbiology/growth &amp; development ; *Plant Diseases/prevention &amp; control/microbiology ; Quorum Sensing ; Chromobacterium/physiology/growth &amp; development ; Biological Control Agents/pharmacology ; Plant Development ; Seedlings/microbiology/growth &amp; development ; Soil Microbiology ; },
abstract = {Modern crop production relies on the application of chemical pesticides and fertilizers causing environmental and economic challenges. In response, less environmentally impactful alternatives have emerged such as the use of beneficial microorganisms. These microorganisms, particularly plant growth-promoting bacteria (PGPB), have demonstrated their ability to enhance plant growth, protect against various stresses, and reduce the need for chemical inputs. Among the PGPB, Bacillus species have garnered attention due to their adaptability and commercial potential. Recent reports have highlighted Bacillus strains as biocontrol agents against phytopathogenic bacteria while concurrently promoting plant growth. We also examined Bacillus plant growth-promoting abilities in Arabidopsis thaliana seedlings. In this study, we assessed the potential of various Bacillus strains to control diverse phytopathogenic bacteria and inhibit quorum sensing using Chromobacterium violaceum as a model system. In conclusion, our results suggest that bacteria of the genus Bacillus hold significant potential for biotechnological applications. This includes developments aimed at reducing agrochemical use, promoting sustainable agriculture, and enhancing crop yield and protection.},
}
@article {pmid38801001,
year = {2024},
author = {Timmis, K and Hallsworth, JE and McGenity, TJ and Armstrong, R and Colom, MF and Karahan, ZC and Chavarría, M and Bernal, P and Boyd, ES and Ramos, JL and Kaltenpoth, M and Pruzzo, C and Clarke, G and López-Garcia, P and Yakimov, MM and Perlmutter, J and Greening, C and Eloe-Fadrosh, E and Verstraete, W and Nunes, OC and Kotsyurbenko, O and Nikel, PI and Scavone, P and Häggblom, MM and Lavigne, R and Le Roux, F and Timmis, JK and Parro, V and Michán, C and García, JL and Casadevall, A and Payne, SM and Frey, J and Koren, O and Prosser, JI and Lahti, L and Lal, R and Anand, S and Sood, U and Offre, P and Bryce, CC and Mswaka, AY and Jores, J and Kaçar, B and Blank, LM and Maaßen, N and Pope, PB and Banciu, HL and Armitage, J and Lee, SY and Wang, F and Makhalanyane, TP and Gilbert, JA and Wood, TK and Vasiljevic, B and Soberón, M and Udaondo, Z and Rojo, F and Tamang, JP and Giraud, T and Ropars, J and Ezeji, T and Müller, V and Danbara, H and Averhoff, B and Sessitsch, A and Partida-Martínez, LP and Huang, W and Molin, S and Junier, P and Amils, R and Wu, XL and Ron, E and Erten, H and de Martinis, ECP and Rapoport, A and Öpik, M and Pokatong, WDR and Stairs, C and Amoozegar, MA and Serna, JG},
title = {A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society.},
journal = {Microbial biotechnology},
volume = {17},
number = {5},
pages = {e14456},
pmid = {38801001},
issn = {1751-7915},
mesh = {*Microbiology/education ; Humans ; Biotechnology ; },
abstract = {EXECUTIVE SUMMARY: Microbes are all pervasive in their distribution and influence on the functioning and well-being of humans, life in general and the planet. Microbially-based technologies contribute hugely to the supply of important goods and services we depend upon, such as the provision of food, medicines and clean water. They also offer mechanisms and strategies to mitigate and solve a wide range of problems and crises facing humanity at all levels, including those encapsulated in the sustainable development goals (SDGs) formulated by the United Nations. For example, microbial technologies can contribute in multiple ways to decarbonisation and hence confronting global warming, provide sanitation and clean water to the billions of people lacking them, improve soil fertility and hence food production and develop vaccines and other medicines to reduce and in some cases eliminate deadly infections. They are the foundation of biotechnology, an increasingly important and growing business sector and source of employment, and the centre of the bioeconomy, Green Deal, etc. But, because microbes are largely invisible, they are not familiar to most people, so opportunities they offer to effectively prevent and solve problems are often missed by decision-makers, with the negative consequences this entrains. To correct this lack of vital knowledge, the International Microbiology Literacy Initiative-the IMiLI-is recruiting from the global microbiology community and making freely available, teaching resources for a curriculum in societally relevant microbiology that can be used at all levels of learning. Its goal is the development of a society that is literate in relevant microbiology and, as a consequence, able to take full advantage of the potential of microbes and minimise the consequences of their negative activities. In addition to teaching about microbes, almost every lesson discusses the influence they have on sustainability and the SDGs and their ability to solve pressing problems of societal inequalities. The curriculum thus teaches about sustainability, societal needs and global citizenship. The lessons also reveal the impacts microbes and their activities have on our daily lives at the personal, family, community, national and global levels and their relevance for decisions at all levels. And, because effective, evidence-based decisions require not only relevant information but also critical and systems thinking, the resources also teach about these key generic aspects of deliberation. The IMiLI teaching resources are learner-centric, not academic microbiology-centric and deal with the microbiology of everyday issues. These span topics as diverse as owning and caring for a companion animal, the vast range of everyday foods that are produced via microbial processes, impressive geological formations created by microbes, childhood illnesses and how they are managed and how to reduce waste and pollution. They also leverage the exceptional excitement of exploration and discovery that typifies much progress in microbiology to capture the interest, inspire and motivate educators and learners alike. The IMiLI is establishing Regional Centres to translate the teaching resources into regional languages and adapt them to regional cultures, and to promote their use and assist educators employing them. Two of these are now operational. The Regional Centres constitute the interface between resource creators and educators-learners. As such, they will collect and analyse feedback from the end-users and transmit this to the resource creators so that teaching materials can be improved and refined, and new resources added in response to demand: educators and learners will thereby be directly involved in evolution of the teaching resources. The interactions between educators-learners and resource creators mediated by the Regional Centres will establish dynamic and synergistic relationships-a global societally relevant microbiology education ecosystem-in which creators also become learners, teaching resources are optimised and all players/stakeholders are empowered and their motivation increased. The IMiLI concept thus embraces the principle of teaching societally relevant microbiology embedded in the wider context of societal, biosphere and planetary needs, inequalities, the range of crises that confront us and the need for improved decisioning, which should ultimately lead to better citizenship and a humanity that is more sustainable and resilient.<br><br>ABSTRACT: The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us-individuals/communities/nations/the human world-and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI. HERE, WE PRESENT: our concept of how microbiology literacy may be achieved and the rationale underpinning it; the type of teaching resources being created to realise the concept and the framing of microbial activities treated in these resources in the context of sustainability, societal needs and responsibilities and decision-making; and the key role of Regional Centres that will translate the teaching resources into local languages, adapt them according to local cultural needs, interface with regional educators and develop and serve as hubs of microbiology literacy education networks. The topics featuring in teaching resources are learner-centric and have been selected for their inherent relevance, interest and ability to excite and engage. Importantly, the resources coherently integrate and emphasise the overarching issues of sustainability, stewardship and critical thinking and the pervasive interdependencies of processes. More broadly, the concept emphasises how the multifarious applications of microbial activities can be leveraged to promote human/animal, plant, environmental and planetary health, improve social equity, alleviate humanitarian deficits and causes of conflicts among peoples and increase understanding between peoples (Microbial Biotechnology, 2023, 16(6), 1091-1111). Importantly, although the primary target of the freely available (CC BY-NC 4.0) IMiLI teaching resources is schoolchildren and their educators, they and the teaching philosophy are intended for all ages, abilities and cultural spectra of learners worldwide: in university education, lifelong learning, curiosity-driven, web-based knowledge acquisition and public outreach. The IMiLI teaching resources aim to promote development of a global microbiology education ecosystem that democratises microbiology knowledge.},
}
@article {pmid38799067,
year = {2024},
author = {Vargas-Sánchez, M and Alcocer, J and Puche, E and Sánchez-Carrillo, S},
title = {Abiotic processes control carbon dioxide dynamics in temperate karst lakes.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17393},
pmid = {38799067},
issn = {2167-8359},
mesh = {*Lakes/chemistry ; *Carbon Dioxide/analysis/metabolism ; Spain ; *Seasons ; Environmental Monitoring/methods ; Carbon Cycle ; Phytoplankton/metabolism ; },
abstract = {Inland waters are crucial in the carbon cycle, contributing significantly to the global CO2 fluxes. Carbonate lakes may act as both sources and sinks of CO2 depending on the interactions between the amount of dissolved inorganic carbon (DIC) inputs, lake metabolisms, and geochemical processes. It is often difficult to distinguish the dominant mechanisms driving CO2 dynamics and their effects on CO2 emissions. This study was undertaken in three groundwater-fed carbonate-rich lakes in central Spain (Ruidera Lakes), severely polluted with nitrates from agricultural overfertilization. Diel and seasonal (summer and winter) changes in CO2 concentration (CCO2) DIC, and CO2 emissions-(FCO2)-, as well as physical and chemical variables, including primary production and phytoplanktonic chlorophyll-a were measured. In addition, δ[13]C-DIC, δ[13]C-CO2 in lake waters, and δ[13]C of the sedimentary organic matter were measured seasonally to identify the primary CO2 sources and processes. While the lakes were consistently CCO2 supersaturated and FCO2 was released to the atmosphere during both seasons, the highest CCO2 and DIC were in summer (0.36-2.26 µmol L[-1]). Our results support a strong phosphorus limitation for primary production in these lakes, which impinges on CO2 dynamics. External DIC inputs to the lake waters primarily drive the CCO2 and, therefore, the FCO2. The δ[13]C-DIC signatures below -12‰ confirmed the primary geogenic influence on DIC. As also suggested by the high values on the calcite saturation index, the Miller-Tans plot revealed that the CO2 source in the lakes was close to the signature provided by the fractionation of δ[13]C-CO2 from calcite precipitation. Therefore, the main contribution behind the CCO2 values found in these karst lakes should be attributed to the calcite precipitation process, which is temperature-dependent according to the seasonal change observed in δ[13]C-DIC values. Finally, co-precipitation of phosphate with calcite could partly explain the observed low phytoplankton production in these lakes and the impact on the contribution to increasing greenhouse gas emissions. However, as eutrophication increases and the soluble reactive phosphorus (SRP) content increases, the co-precipitation of phosphate is expected to be progressively inhibited. These thresholds must be assessed to understand how the CO3[2-] ions drive lake co-precipitation dynamics. Carbonate regions extend over 15% of the Earth's surface but seem essential in the CO2 dynamics at a global scale.},
}
@article {pmid38798771,
year = {2024},
author = {Mahalak, KK and Liu, L and Bobokalonov, J and Narrowe, AB and Firrman, J and Bittinger, K and Hu, W and Jones, SM and Moustafa, AM},
title = {Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota in vitro.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1304045},
pmid = {38798771},
issn = {2296-861X},
abstract = {INTRODUCTION: Studies have shown that a diet high in fiber and prebiotics has a positive impact on human health due largely to the fermentation of these compounds by the gut microbiota. One underutilized source of fiber may be rice bran, a waste product of rice processing that is used most frequently as an additive to livestock feed but may be a good source of fibers and other phenolic compounds as a human diet supplement. Previous studies focused on specific compounds extracted from rice bran showed that soluble fibers extracted from rice bran can improve glucose response and reduce weight gain in mouse models. However, less is known about changes in the human gut microbiota in response to regular rice bran consumption.<br><br>METHODS: In this study, we used a Simulator of the Human Intestinal Microbial Ecology (SHIME&#xae;) to cultivate the human gut microbiota of 3 different donors in conditions containing either soluble or insoluble fiber fractions from rice bran. Using 16S rRNA amplicon sequencing and targeted metabolomics via Gas Chromatography-Mass Spectrometry, we explored how gut microbial communities developed provided different supplemental fiber sources.<br><br>RESULTS: We found that insoluble and soluble fiber fractions increased short-chain fatty acid production, indicating that both fractions were fermented. However, there were differences in response between donors, for example the gut microbiota from donor 1 increased acetic acid production with both fiber types compared with control; whereas for donors 2 and 3, butanoic acid production increased with ISF and SF supplementation. Both soluble and insoluble rice bran fractions increased the abundance of Bifidobacterium and Lachnospiraceae taxa.<br><br>DISCUSSION: Overall, analysis of the effect of soluble and insoluble rice bran fractions on the human in vitro gut microbiota and the metabolites produced revealed individually variant responses to these prebiotics.},
}
@article {pmid38798271,
year = {2024},
author = {Almeida-Silva, F and Prost-Boxoen, L and Van de Peer, Y},
title = {hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors.},
journal = {The New phytologist},
volume = {243},
number = {2},
pages = {811-819},
pmid = {38798271},
issn = {1469-8137},
support = {833522/ERC_/European Research Council/International ; 833522//H2020 European Research Council/ ; 11H0426N//Fonds Wetenschappelijk Onderzoek/ ; BOF.MET.2021.0005.01//Bijzonder Onderzoeksfonds UGent/ ; },
mesh = {*Software ; *Hybridization, Genetic ; *Gene Expression Profiling ; *Oryza/genetics ; *Transcriptome/genetics ; Gossypium/genetics ; Hybrid Vigor/genetics ; Gene Expression Regulation, Plant ; Plant Roots/genetics ; Polyploidy ; },
abstract = {Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).},
}
@article {pmid38794902,
year = {2024},
author = {Fricker, AD and Yao, T and Lindemann, SR and Flores, GE},
title = {Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {7},
pages = {},
pmid = {38794902},
issn = {1574-6941},
support = {SC1 GM136546/GM/NIGMS NIH HHS/United States ; SC1GM136546/NH/NIH HHS/United States ; },
mesh = {Humans ; *Mucins/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Microbial Consortia ; *Fermentation ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome ; Akkermansia/metabolism ; Desulfovibrio/metabolism/genetics/classification ; Bacteroides/metabolism/genetics/classification/growth &amp; development ; },
abstract = {Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor's communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.},
}
@article {pmid38792792,
year = {2024},
author = {Jiao, F and Qian, L and Wu, J and Zhang, D and Zhang, J and Wang, M and Sui, X and Zhang, X},
title = {Diversity and Composition of Soil Acidobacterial Communities in Different Temperate Forest Types of Northeast China.},
journal = {Microorganisms},
volume = {12},
number = {5},
pages = {},
pmid = {38792792},
issn = {2076-2607},
support = {LBH-Q21167//Heilongjiang Province Postdoctoral Research Start-up Fund Project/ ; },
abstract = {To gain an in-depth understanding of the diversity and composition of soil Acidobacteria in five different forest types in typical temperate forest ecosystems and to explore their relationship with soil nutrients. The diversity of soil Acidobacteria was determined by high-throughput sequencing technology. Soil Acidobacteria's alpha-diversity index and soil nutrient content differed significantly among different forest types. β-diversity and the composition of soil Acidobacteria also varied across forest types. Acidobacterial genera, such as Acidobacteria_Gp1, Acidobacteria_Gp4, and Acidobacteria_Gp17, play key roles in different forests. The RDA analyses pointed out that the soil pH, available nitrogen (AN), carbon to nitrogen (C/N) ratio, available phosphorus (AP), total carbon (TC), and total phosphorus (TP) were significant factors affecting soil Acidobacteria in different forest types. In this study, the diversity and composition of soil Acidobacteria under different forest types in a temperate forest ecosystem were analyzed, revealing the complex relationship between them and soil physicochemical properties. These findings not only enhance our understanding of soil microbial ecology but also provide important guidance for ecological conservation and restoration strategies for temperate forest ecosystems.},
}
@article {pmid38790992,
year = {2024},
author = {Roszkowska, P and Klimczak, E and Ostrycharz, E and Rączka, A and Wojciechowska-Koszko, I and Dybus, A and Cheng, YH and Yu, YH and Mazgaj, S and Hukowska-Szematowicz, B},
title = {Small Intestinal Bacterial Overgrowth (SIBO) and Twelve Groups of Related Diseases-Current State of Knowledge.},
journal = {Biomedicines},
volume = {12},
number = {5},
pages = {},
pmid = {38790992},
issn = {2227-9059},
abstract = {The human gut microbiota creates a complex microbial ecosystem, characterized by its high population density, wide diversity, and complex interactions. Any imbalance of the intestinal microbiome, whether qualitative or quantitative, may have serious consequences for human health, including small intestinal bacterial overgrowth (SIBO). SIBO is defined as an increase in the number of bacteria (10[3]-10[5] CFU/mL), an alteration in the bacterial composition, or both in the small intestine. The PubMed, Science Direct, Web of Science, EMBASE, and Medline databases were searched for studies on SIBO and related diseases. These diseases were divided into 12 groups: (1) gastrointestinal disorders; (2) autoimmune disease; (3) cardiovascular system disease; (4) metabolic disease; (5) endocrine disorders; (6) nephrological disorders; (7) dermatological diseases; (8) neurological diseases (9); developmental disorders; (10) mental disorders; (11) genetic diseases; and (12) gastrointestinal cancer. The purpose of this comprehensive review is to present the current state of knowledge on the relationships between SIBO and these 12 disease groups, taking into account risk factors and the causal context. This review fills the evidence gap on SIBO and presents a biological-medical approach to the problem, clearly showing the groups and diseases having a proven relationship with SIBO, as well as indicating groups within which research should continue to be expanded.},
}
@article {pmid38790880,
year = {2024},
author = {Ding, Y and Wang, L and Wang, H and Li, H},
title = {Dynamic Succession of Natural Microbes during the Ecolly Grape Growth under Extremely Simplified Eco-Cultivation.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
pmid = {38790880},
issn = {2304-8158},
support = {LYNJ202110//research and application of key technologies for sustainable development of wine industry/ ; },
abstract = {The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included Gibberella, Alternaria, Filobasidium, Naganishia, Ascochyta, Apiotrichum, Comoclathris, and Aureobasidium, and the dominant bacterial genera mainly contained Sediminibacterium, Ralstonia, Pantoea, Bradyrhizobium, Brevundimonas, Mesorhizobium, Planococcus, and Planomicrobium. In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry.},
}
@article {pmid38790838,
year = {2024},
author = {Ayed, L and M'hir, S and Nuzzolese, D and Di Cagno, R and Filannino, P},
title = {Harnessing the Health and Techno-Functional Potential of Lactic Acid Bacteria: A Comprehensive Review.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
pmid = {38790838},
issn = {2304-8158},
abstract = {This review examines the techno-functional properties of lactic acid bacteria (LABs) in the food industry, focusing on their potential health benefits. We discuss current findings related to the techno-functionality of LAB, which includes acidification, proteolytic and lipolytic features, and a variety of other biochemical activities. These activities include the production of antimicrobial compounds and the synthesis of exopolysaccharides that improve food safety and consumer sensory experience. LABs are also known for their antioxidant abilities, which help reduce oxidative reactions in foods and improve their functional properties. In addition, LABs' role as probiotics is known for their promising effects on gut health, immune system modulation, cholesterol control, and general wellbeing. Despite these advantages, several challenges hinder the effective production and use of probiotic LABs, such as maintaining strain viability during storage and transport as well as ensuring their efficacy in the gastrointestinal tract. Our review identifies these critical barriers and suggests avenues for future research.},
}
@article {pmid38788571,
year = {2024},
author = {Liu, J and Zhao, R and Feng, J and Fu, W and Cao, L and Zhang, J and Lei, Y and Liang, J and Lin, L and Li, X and Li, B},
title = {Bacterial assembly and succession patterns in conventional and advanced drinking water systems: From source to tap.},
journal = {Journal of hazardous materials},
volume = {473},
number = {},
pages = {134613},
doi = {10.1016/j.jhazmat.2024.134613},
pmid = {38788571},
issn = {1873-3336},
mesh = {*Drinking Water/microbiology ; *Bacteria/classification/genetics/metabolism ; *Water Purification/methods ; *Water Microbiology ; Halogenation ; Filtration ; Biodiversity ; Water Supply ; },
abstract = {Bacteria are pivotal to drinking water treatment and public health. However, the mechanisms of bacterial assembly and their impact on species coexistence remain largely unexplored. This study explored the assembly and succession of bacterial communities in two full-scale drinking water systems over one year. We observed a decline in bacterial biomass, diversity, and co-occurrence network complexity along the treatment processes, except for the biological activated carbon filtration stage. The conventional plant showed higher bacterial diversity than the advanced plant, despite similar bacterial concentrations and better removal efficiency. The biological activated carbon filter exhibited high phylogenetic diversity, indicating enhanced bacterial metabolic functionality for organic matter removal. Chlorination inactivated most bacteria but favored some chlorination-resistant and potentially pathogenic species, such as Burkholderia, Bosea, Brevundimonas, and Acinetobacter. Moreover, the spatiotemporal dynamics of the bacterial continuum were primarily driven by stochastic processes, explaining more than 78% of the relative importance. The advanced plant's bacterial community was less influenced by dispersal limitation and more by homogeneous selection. The stochastic process regulated bacterial diversity and influenced the complexity of the species co-occurrence network. These findings deepen our understanding of microbial ecological mechanisms and species interactions, offering insights for enhancing hygienic safety in drinking water systems.},
}
@article {pmid38786909,
year = {2024},
author = {Jawień, P and Pfitzner, WP and Schaffner, F and Kiewra, D},
title = {Mosquitoes (Diptera: Culicidae) of Poland: An Update of Species Diversity and Current Challenges.},
journal = {Insects},
volume = {15},
number = {5},
pages = {},
pmid = {38786909},
issn = {2075-4450},
abstract = {This article presents the current state of knowledge of mosquito species (Diptera: Culicidae) occurring in Poland. In comparison to the most recently published checklists (1999 and 2007), which listed 47 mosquito species, four species (Aedes japonicus, Anopheles daciae, Anopheles hyrcanus, and Anopheles petragnani) are added to the Polish fauna. Our new checklist of Polish mosquito fauna includes 51 species of mosquitoes from five genera: Aedes (30), Anopheles (8), Coquillettidia (1), Culiseta (7), and Culex (5). Aspects of the ecology and biology of the Polish mosquito fauna, with particular emphasis on newly recorded species, are discussed.},
}
@article {pmid38786897,
year = {2024},
author = {Dyczko, D and Plewa-Tutaj, K and Kiewra, D},
title = {Entomopathogenic Fungi in Forest Habitats of Ixodes ricinus.},
journal = {Insects},
volume = {15},
number = {5},
pages = {},
pmid = {38786897},
issn = {2075-4450},
abstract = {(1) Background: In addition to the microclimate, host availability, and tick microbiota, soil environmental microorganisms can affect tick populations. This study aimed to (1) determine the presence and diversity of entomopathogenic fungi (EF) in forests, where ticks are abundant, and (2) estimate the effectiveness of the isolated EF strains against Ixodes ricinus. (2) Methods: EF were isolated using the trap insect method from soil collected from tick sites. A bioassay was used to estimate the effectiveness of EF against ticks. (3) Results: The presence of EF was found in all tested forest habitat types. A total of 53 strains belonging to the genera Metarhizium, Beauveria, and Isaria were isolated. All the six strains subjected to the bioassay showed potential efficacy against both adult and nymphal stages of I. ricinus; however, the strains differed in their effectiveness. The most effective isolate against I. ricinus was the soil environmental strain of Metarhizium anisopliae. (4) Conclusion: The study indicates that tick habitats can be the source of entomopathogenic fungi, which have a lethal effect on ticks, as demonstrated in preliminary laboratory tests with I. ricinus. However, for practical use, extensive field tests and further research on application methods and long-term effects are necessary to develop effective and sustainable tick management strategies.},
}
@article {pmid38782346,
year = {2024},
author = {Liu, Y and Delgado-Baquerizo, M and Bing, H and Wang, Y and Wang, J and Chen, J and Qiu, S and Zhu, H and Wu, Y and Fang, L and Chang, R},
title = {Warming-induced shifts in alpine soil microbiome: An ecosystem-scale study with environmental context-dependent insights.},
journal = {Environmental research},
volume = {255},
number = {},
pages = {119206},
doi = {10.1016/j.envres.2024.119206},
pmid = {38782346},
issn = {1096-0953},
mesh = {*Soil Microbiology ; *Microbiota ; Tibet ; Soil/chemistry ; Global Warming ; Ecosystem ; Altitude ; Climate Change ; },
abstract = {Climate warming is a pressing global issue with substantial impacts on soil health and function. However, the influence of environmental context on the responses of soil microorganisms to warming remains largely elusive, particularly in alpine ecosystems. This study examined the responses of the soil microbiome to in situ experimental warming across three elevations (3850 m, 4100 m, and 4250 m) in the meadow of Gongga Mountain, eastern Tibetan Plateau. Our findings demonstrate that soil microbial diversity is highly resilient to warming, with significant impacts observed only at specific elevations. Furthermore, the influence of warming on the composition of the soil microbial community is also elevation-dependent, underscoring the importance of local environmental context in shaping microbial evolution in alpine soils under climate warming. Notably, we identified soil moisture at 3850 m and carbon-to-nitrogen ratio at 4250 m as indirect predictors regulating the responses of microbial diversity to warming at specific elevations. These findings underscore the paramount importance of considering pre-existing environmental conditions in predicting the response of alpine soil microbiomes to climate warming. Our study provides novel insights into the intricate interactions between climate warming, soil microbiome, and environmental context in alpine ecosystems, illuminating the complex mechanisms governing soil microbial ecology in these fragile and sensitive environments.},
}
@article {pmid38781750,
year = {2024},
author = {Bouchali, R and Mandon, C and Danty-Berger, E and Géloën, A and Marjolet, L and Youenou, B and Pozzi, ACM and Vareilles, S and Galia, W and Kouyi, GL and Toussaint, JY and Cournoyer, B},
title = {Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns.},
journal = {International journal of hygiene and environmental health},
volume = {260},
number = {},
pages = {114391},
doi = {10.1016/j.ijheh.2024.114391},
pmid = {38781750},
issn = {1618-131X},
mesh = {*Rain ; Humans ; *Microbiota ; *Water Microbiology ; *Cities ; *Bacteria/isolation &amp; purification/classification/genetics ; *Environmental Monitoring/methods ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.},
}
@article {pmid38780093,
year = {2024},
author = {Beaver, RC and Neufeld, JD},
title = {Microbial ecology of the deep terrestrial subsurface.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38780093},
issn = {1751-7370},
support = {//Nuclear Waste Management Organization/ ; //Ontario Research Fund: Research Excellence/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Archaea/classification/isolation &amp; purification/metabolism ; *Bacteria/classification/isolation &amp; purification/metabolism/genetics ; *Soil Microbiology ; Microbiota ; Ecosystem ; },
abstract = {The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.},
}
@article {pmid38779669,
year = {2024},
author = {Kou, Z and Liu, K and Qiao, Z and Wang, Y and Li, Y and Li, Y and Yu, X and Han, W},
title = {The alterations of oral, airway and intestine microbiota in chronic obstructive pulmonary disease: a systematic review and meta-analysis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1407439},
pmid = {38779669},
issn = {1664-3224},
mesh = {*Pulmonary Disease, Chronic Obstructive/microbiology ; Humans ; *Gastrointestinal Microbiome ; Mouth/microbiology ; Microbiota ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Increasing evidence indicates the microbial ecology of chronic obstructive pulmonary disease (COPD) is intricately associated with the disease's status and severity, and distinct microbial ecological variations exist between COPD and healthy control (HC). This systematic review and meta-analysis aimed to summarize microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota of different stages of COPD and HC to make comparisons.<br><br>METHODS: A comprehensive systematic literature search was conducted in PubMed, Embase, the Web of Science, and the Cochrane Library databases to identify relevant English articles on the oral, airway, and intestine microbiota in COPD published between 2003 and 8 May 2023. Information on microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota was collected for comparison between different stages of COPD and HC.<br><br>RESULTS: A total of 20 studies were included in this review, involving a total of 337 HC participants, 511 COPD patients, and 154 AECOPD patients. We observed that no significant differences in alpha diversity between the participant groups, but beta diversity was significantly different in half of the included studies. Compared to HC, Prevotella, Streptococcus, Actinomyces, and Veillonella of oral microbiota in SCOPD were reduced at the genus level. Most studies supported that Haemophilus, Lactobacillus, and Pseudomonas were increased, but Veillonella, Prevotella, Actinomyces, Porphyromonas, and Atopobium were decreased at the genus level in the airway microbiota of SCOPD. However, the abundance of Haemophilus, Lactobacillus and Pseudomonas genera exhibited an increase, whereas Actinomyces and Porphyromonas showed a decrease in the airway microbiota of AECOPD compared to HC. And Lachnospira of intestine microbiota in SCOPD was reduced at the genus level.<br><br>CONCLUSION: The majority of published research findings supported that COPD exhibited decreased alpha diversity compared to HC. However, our meta-analysis does not confirm it. In order to further investigate the characteristics and mechanisms of microbiome in the oral-airway- intestine axis of COPD patients, larger-scale and more rigorous studies are needed.<br><br>PROSPERO (https://www.crd.york.ac.uk/prospero/), identifier CRD42023418726.},
}
@article {pmid38779326,
year = {2024},
author = {Mellouk, A and Mahmood, T and Jlali, M and Vieco-Saiz, N and Michel, V and Cozannet, P and Ozbek, S and Mercier, Y and Devillard, E and Consuegra, J},
title = {Potential of guar gum as a leaky gut model in broilers: Digestibility, performance, and microbiota responses.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {17},
number = {},
pages = {177-187},
pmid = {38779326},
issn = {2405-6383},
abstract = {Diet is a major modulator of animal resilience and its three pillars: host's immune response, gut microbiota, and intestinal barrier. In the present study, we endeavour to delineate a challenging condition aimed to degrade these pillars and elucidate its impact on broiler performance and nutrient digestibility. To attain this objective, we opted to use guar gum (GG) as a source of galactomannan. A series of three in vivo experiments were conducted employing conventional or semi-purified diets, supplemented with or without GG during the grower phase (14-28 d). Our findings demonstrate a substantial decline in animal performance metrics such as body weight (reduced by 29%, P < 0.001), feed intake (decreased by 12%, P < 0.001), and feed conversion ratio (up to 58% increase, P < 0.001) in the presence of GG at 2%. The supplementation of a semi-purified diet with incremental doses of GG resulted in a linear reduction (P < 0.001) in the apparent total tract digestibility of dry matter and apparent metabolisable energy. Additionally, a marked reduction in ileal endogenous losses, as well as apparent and standardised digestibility of all amino acids with varying proportions (P < 0.05), was observed. These alterations were accompanied by disrupted gut integrity assessed by fluorescein isothiocyanate-dextran (FITC-d) (P < 0.001) as well as an inflammatory status characterised by elevated levels of acute-phase proteins, namely orosomucoid and serum amyloid A in the sera (P = 0.03), and increased mRNA expression levels of IL-1, IL-6, IL-8, Inos, and K203 genes in the ileum, along with a decrease in IgA levels in the gut lumen (P < 0.05). Microbial ecology and activity were characterised by reduced diversity and richness (Shannon index, P = 0.005) in the presence of GG. Consequently, our results revealed diminished levels of short-chain fatty acids (P = 0.01) and their producer genera, such as Clostridium_XIVa and Blautia, in the gut caeca, coupled with excessive accumulation of lactate (17-fold increase, P < 0.01) in the presence of GG at 2%. In addition to providing a more comprehensive characterisation of the GG supplementation as a leaky gut model, our results substantiate a thorough understanding of the intricate adjustments and interplay between the intestinal barrier, immune response, and microbiota. Furthermore, they underscore the significance of feed components in modulating these dynamics.},
}
@article {pmid38779128,
year = {2024},
author = {Eckmann, CA and Bachy, C and Wittmers, F and Strauss, J and Blanco-Bercial, L and Vergin, KL and Parsons, RJ and Kudela, RM and Johnson, R and Bolaños, LM and Giovannoni, SJ and Carlson, CA and Worden, AZ},
title = {Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae.},
journal = {Communications earth &amp; environment},
volume = {5},
number = {1},
pages = {266},
pmid = {38779128},
issn = {2662-4435},
abstract = {Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delineate seasonal stability periods more ecologically relevant than seasons defined by calendar dates. During winter mixing, tiny prasinophytes dominated by Class II comprise 46 ± 24% of eukaryotic algal (plastid-derived) 16S rRNA V1-V2 amplicons, specifically Ostreococcus Clade OII, Micromonas commoda, and Bathycoccus calidus. In contrast, Class VII are rare and Classes I and VI peak during warm stratified periods when surface eukaryotic phytoplankton abundances are low. Seasonality underpins a reservoir of genetic diversity from multiple prasinophyte classes during warm periods that harbor ephemeral taxa. Persistent Class II sub-species dominating the winter/spring bloom period retreat to the deep chlorophyll maximum in summer, poised to seed the mixed layer upon winter convection, exposing a mechanism for initiating high abundances at bloom onset. Comparisons to tropical oceans reveal broad distributions of the dominant sub-species herein. This unparalleled window into temporal and spatial niche partitioning of picoeukaryotic primary producers demonstrates how key prasinophytes prevail in warm oceans.},
}
@article {pmid38775958,
year = {2024},
author = {Starr, K and Montesanto, F and Perisho, E and Aluthge, N and Pegg, M and Fernando, SC},
title = {Gut Microbial Composition of Cyprinella lutrensis (Red Shiner) and Notropis stramineus (Sand Shiner): Insights from Wild Fish Populations.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {75},
pmid = {38775958},
issn = {1432-184X},
support = {20-121 &amp; 18-176//Nebraska Environmental Trust/ ; 20-121 &amp; 18-176//Nebraska Environmental Trust/ ; NC 1189//National Institute of Food and Agriculture/ ; 2022-33522-38219//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/isolation &amp; purification/genetics ; *Cyprinidae/microbiology ; *Rivers/microbiology ; RNA, Ribosomal, 16S/genetics ; Nebraska ; },
abstract = {The gut microbiome is a highly intricate ecosystem that exerts a pivotal influence on the host's physiology. Characterizing fish microbiomes is critical to understanding fish physiology and health, but little is known about the ecology and colonization dynamics of microorganisms inhabiting fish species. In this study, we investigated the bacterial communities of two small-bodied fish species, Cyprinella lutrensis (red shiner) and Notropis stramineus (sand shiner), two fish species where gut microbiomes have not been investigated previously and surrounding waters, collected from rivers in Nebraska, USA. Our study focused on evaluating microbial diversity in small-bodied fish and identifying autochthonous microbes present within these species irrespective of location to better understand bacterial community composition and possible roles of such bacterial species. Our results revealed that both red shiner and sand shiner exhibited gut bacterial communities dominated by typical bacterial phyla found in freshwater fish. The phylum Bacteroidota was minimally abundant in both species and significantly lower in relative abundance compared to the surrounding water microbial community. Furthermore, we found that the gut microbiomes of red shiner and sand shiner differed from the microbial community in the surrounding water, suggesting that these fish species contain host-associated bacterial species that may provide benefits to the host such as nutrient digestion and colonization resistance of environmental pathogens. The fish gut bacterial communities were sensitive to environmental conditions such as turbidity, dissolved oxygen, temperature, and total nitrogen. Our findings also show bacterial community differences between fish species; although they shared notable similarities in bacterial taxa at phyla level composition, ASV level analysis of bacterial taxa displayed compositional differences. These findings contribute to a better understanding of the gut bacterial composition of wild, freshwater, small-bodied fish and highlight the influence of intrinsic (host) and environmental factors on shaping the bacterial composition.},
}
@article {pmid38773211,
year = {2024},
author = {Fischer, FC and Schulze-Makuch, D and Heinz, J},
title = {Microbial preference for chlorate over perchlorate under simulated shallow subsurface Mars-like conditions.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11537},
pmid = {38773211},
issn = {2045-2322},
support = {455070607//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Perchlorates/metabolism ; *Mars ; *Chlorates/metabolism ; *Extraterrestrial Environment ; Aspergillus niger/metabolism ; Saccharomycetales/metabolism ; Water/chemistry ; Microbial Viability ; },
abstract = {The Martian surface and shallow subsurface lacks stable liquid water, yet hygroscopic salts in the regolith may enable the transient formation of liquid brines. This study investigated the combined impact of water scarcity, UV exposure, and regolith depth on microbial survival under Mars-like environmental conditions. Both vegetative cells of Debaryomyces hansenii and Planococcus halocryophilus, alongside with spores of Aspergillus niger, were exposed to an experimental chamber simulating Martian environmental conditions (constant temperatures of about - 11 °C, low pressure of approximately 6 mbar, a CO2 atmosphere, and 2 h of daily UV irradiation). We evaluated colony-forming units (CFU) and water content at three different regolith depths before and after exposure periods of 3 and 7 days, respectively. Each organism was tested under three conditions: one without the addition of salts to the regolith, one containing sodium chlorate, and one with sodium perchlorate. Our results reveal that the residual water content after the exposure experiments increased with regolith depth, along with the organism survival rates in chlorate-containing and salt-free samples. The survival rates of the three organisms in perchlorate-containing regolith were consistently lower for all organisms and depths compared to chlorate, with the most significant difference being observed at a depth of 10-12 cm, which corresponds to the depth with the highest residual water content. The postulated reason for this is an increase in the salt concentration at this depth due to the freezing of water, showing that for these organisms, perchlorate brines are more toxic than chlorate brines under the experimental conditions. This underscores the significance of chlorate salts when considering the habitability of Martian environments.},
}
@article {pmid38773116,
year = {2024},
author = {Huang, WRH and Braam, C and Kretschmer, C and Villanueva, SL and Liu, H and Ferik, F and van der Burgh, AM and Boeren, S and Wu, J and Zhang, L and Nürnberger, T and Wang, Y and Seidl, MF and Evangelisti, E and Stuttmann, J and Joosten, MHAJ},
title = {Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4339},
pmid = {38773116},
issn = {2041-1723},
support = {201706990001//China Scholarship Council (CSC)/ ; E032-2017-01 55851//CONCYTEC | Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica (Cienciactiva)/ ; },
mesh = {*Nicotiana/immunology/microbiology/genetics/metabolism ; *Plant Proteins/metabolism/genetics ; *Plant Immunity/genetics ; *Protein Serine-Threonine Kinases/metabolism/genetics ; *Plant Diseases/microbiology/immunology ; Phytophthora/pathogenicity ; Protein Kinases/metabolism/genetics ; Phosphorylation ; Gene Expression Regulation, Plant ; Reactive Oxygen Species/metabolism ; Signal Transduction ; },
abstract = {Cell-surface receptors form the front line of plant immunity. The leucine-rich repeat (LRR)-receptor-like kinases SOBIR1 and BAK1 are required for the functionality of the tomato LRR-receptor-like protein Cf-4, which detects the secreted effector Avr4 of the pathogenic fungus Fulvia fulva. Here, we show that the kinase domains of SOBIR1 and BAK1 directly phosphorylate each other and that residues Thr522 and Tyr469 of the kinase domain of Nicotiana benthamiana SOBIR1 are required for its kinase activity and for interacting with signalling partners, respectively. By knocking out multiple genes belonging to different receptor-like cytoplasmic kinase (RLCK)-VII subfamilies in N. benthamiana:Cf-4, we show that members of RLCK-VII-6, -7, and -8 differentially regulate the Avr4/Cf-4-triggered biphasic burst of reactive oxygen species. In addition, members of RLCK-VII-7 play an essential role in resistance against the oomycete pathogen Phytophthora palmivora. Our study provides molecular evidence for the specific roles of RLCKs downstream of SOBIR1/BAK1-containing immune complexes.},
}
@article {pmid38772810,
year = {2024},
author = {Zai, X and Cordovez, V and Zhu, F and Zhao, M and Diao, X and Zhang, F and Raaijmakers, JM and Song, C},
title = {C4 cereal and biofuel crop microbiomes.},
journal = {Trends in microbiology},
volume = {32},
number = {11},
pages = {1119-1131},
doi = {10.1016/j.tim.2024.04.008},
pmid = {38772810},
issn = {1878-4380},
mesh = {*Biofuels/microbiology ; *Microbiota/physiology ; *Edible Grain/microbiology ; *Crops, Agricultural/microbiology ; Setaria Plant/genetics/microbiology ; Climate Change ; },
abstract = {Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.},
}
@article {pmid38771894,
year = {2024},
author = {Van Hee, S and Alınç, T and Weldegergis, BT and Dicke, M and Colazza, S and Peri, E and Jacquemyn, H and Cusumano, A and Lievens, B},
title = {Differential effects of plant-beneficial fungi on the attraction of the egg parasitoid Trissolcus basalis in response to Nezara viridula egg deposition.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0304220},
pmid = {38771894},
issn = {1932-6203},
mesh = {Animals ; *Beauveria/physiology ; *Capsicum/parasitology/microbiology ; *Wasps/physiology ; *Oviposition ; Volatile Organic Compounds/metabolism ; Female ; Trichoderma/physiology ; Host-Parasite Interactions ; Ovum ; Herbivory ; },
abstract = {There is increasing evidence that plant-associated microorganisms play important roles in defending plants against insect herbivores through both direct and indirect mechanisms. While previous research has shown that these microbes can modify the behaviour and performance of insect herbivores and their natural enemies, little is known about their effect on egg parasitoids which utilize oviposition-induced plant volatiles to locate their hosts. In this study, we investigated how root inoculation of sweet pepper (Capsicum annuum) with the plant-beneficial fungi Beauveria bassiana ARSEF 3097 or Trichoderma harzianum T22 influences the olfactory behaviour of the egg parasitoid Trissolcus basalis following egg deposition by its host Nezara viridula. Olfactometer assays showed that inoculation by T. harzianum significantly enhanced the attraction of the egg parasitoid, while B. bassiana had the opposite effect. However, no variation was observed in the chemical composition of plant volatiles. Additionally, fitness-related traits of the parasitoids (wasp body size) were not altered by any of the two fungi, suggesting that fungal inoculation did not indirectly affect host quality. Altogether, our results indicate that plant inoculation with T. harzianum T22 can be used to enhance attraction of egg parasitoids, which could be a promising strategy in manipulating early plant responses against pest species and improving sustainable crop protection. From a more fundamental point of view, our findings highlight the importance of taking into account the role of microorganisms when studying the intricate interactions between plants, herbivores and their associated egg parasitoids.},
}
@article {pmid38771538,
year = {2024},
author = {Song, S and Sun, Z and Xu, G and Xu, H},
title = {Continuous warming drives the colonization dynamics of periphytic ciliate fauna in marine environments.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {25},
pages = {37326-37336},
pmid = {38771538},
issn = {1614-7499},
support = {31672308//The Natural Science Foundation of China/ ; 41076089//The Natural Science Foundation of China/ ; },
mesh = {*Ciliophora/physiology ; *Global Warming ; *Ecosystem ; Temperature ; },
abstract = {In order to evaluate the influence of global warming on the ecosystem processes in marine environments, the changes in colonization dynamics of periphytic microbiota were studied using the periphytic ciliate communities as the test organism fauna under a continuous warming gradient of 22℃ (control), 25℃, 28℃, 31℃, and 34 ℃. The results demonstrated that (1) the test ciliate communities generally showed a similar temporal pattern in within the colonization process under the water temperatures from 22 up to 28℃; however, (2) the colonization dynamics were significantly changed, and the fitness of colonization curves to the MacArthur-Wilson model equation was failed under the temperature increased by 6 ℃, and (3) the loading or assimilative capacity of the test aquatic ecosystem was decreased with the increase of water temperature. Therefore, this study suggests that continuous warming may significantly drive the colonization dynamics of periphytic ciliates in marine ecosystems.},
}
@article {pmid38771339,
year = {2024},
author = {Jiao, Y and Zhang, G and Ai, X and Wang, X},
title = {Comparison of the Effects of LDPE and PBAT Film Residues on Soil Microbial Ecology.},
journal = {Current microbiology},
volume = {81},
number = {7},
pages = {185},
pmid = {38771339},
issn = {1432-0991},
support = {52200109//National Natural Science Foundation of China/ ; 202102310278//State Scholarship Fund and the Key R&amp;D and Promotion Project of Henan Province/ ; },
mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Polyethylene/chemistry ; Polyesters/metabolism ; Soil/chemistry ; Soil Pollutants/analysis ; Microbiota ; },
abstract = {The plastic film is extensively applied with limited recycling, leading to the long-run residue accumulation in soil, which offers a distinctive habitat for microorganisms, and creates a plastisphere. In this study, traditional low-density polyethylene (LDPE) plastic film and biodegradable polybutylene adipate terephthalate (PBAT) plastic film materials were selected to test their effects on soil microbial ecology. Based on high-throughput sequencing, compared to the soil environment, the alpha-diversity of bacterial communities in plastisphere was lower, and the abundance of Actinobacteria increased. Plastic film residues, as bacterial habitats, exhibited greater heterogeneity and harbor unique bacterial communities. The communities were distinguished between plastisphere and soil environment by means of a random-forest (RF) machine-learning model. Prominent distinctions emerged among bacterial functions between soil environment and plastisphere, especially regarding organics degradation. The neutral model and null model indicated that the constitution of bacterial communities was dominated by random processes except in LDPE plastisphere. The bacterial co-occurrence network of the plastisphere exhibited higher complexity and modularity. This study contributes to our comprehending of characteristics of plastisphere bacterial communities in soil environment and the associated ecological risks of plastic film residues accumulation.},
}
@article {pmid38771320,
year = {2024},
author = {Wang, Y and Zou, Q},
title = {Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {74},
pmid = {38771320},
issn = {1432-184X},
support = {62102269, 62373080//National Natural Science Foundation of China/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Fungi/genetics/classification/physiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; *Adaptation, Physiological ; Ecosystem ; Bacterial Physiological Phenomena ; },
abstract = {Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.},
}
@article {pmid38765607,
year = {2024},
author = {Wu, S and Qu, Z and Chen, D and Wu, H and Caiyin, Q and Qiao, J},
title = {Deciphering and designing microbial communities by genome-scale metabolic modelling.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {1990-2000},
pmid = {38765607},
issn = {2001-0370},
abstract = {Microbial communities are shaped by the complex interactions among organisms and the environment. Genome-scale metabolic models (GEMs) can provide deeper insights into the complexity and ecological properties of various microbial communities, revealing their intricate interactions. Many researchers have modified GEMs for the microbial communities based on specific needs. Thus, GEMs need to be comprehensively summarized to better understand the trends in their development. In this review, we summarized the key developments in deciphering and designing microbial communities using different GEMs. A timeline of selected highlights in GEMs indicated that this area is evolving from the single-strain level to the microbial community level. Then, we outlined a framework for constructing GEMs of microbial communities. We also summarized the models and resources of static and dynamic community-level GEMs. We focused on the role of external environmental and intracellular resources in shaping the assembly of microbial communities. Finally, we discussed the key challenges and future directions of GEMs, focusing on the integration of GEMs with quorum sensing mechanisms, microbial ecology interactions, machine learning algorithms, and automatic modeling, all of which contribute to consortia-based applications in different fields.},
}
@article {pmid38763283,
year = {2024},
author = {Liu, S and Shi, Y and Chen, J and Zhang, Z and Cao, H and Li, W and Ye, M},
title = {Interspecific barrier effect driven by heavy metals makes soil bacterial functional assembly more stochastic.},
journal = {Environmental research},
volume = {253},
number = {},
pages = {119153},
doi = {10.1016/j.envres.2024.119153},
pmid = {38763283},
issn = {1096-0953},
mesh = {*Soil Microbiology ; *Metals, Heavy/toxicity/analysis ; *Soil Pollutants/toxicity/analysis ; *Bacteria/genetics/classification/drug effects ; China ; Stochastic Processes ; Microbiota/drug effects ; },
abstract = {Residual heavy metals in soils will destroy microbial community stability and influence its aggregation. However, exploring microbial ecology under heavy-metal stress still requires a conjoint analysis of bacterial interspecies communication and the community diversity maintenance mechanism. In this study, soil samples were collected from a heavy-metal-contaminated site in China to investigate the ecological response of indigenous microbial communities through high-throughput sequencing. Results showed that bacterial taxa and functions generated unusual decoupling phenomena. There were no significant differences in the diversity of species with the increase in concentration of heavy metals (Hg, Se, and Cr), but the functional diversity was lost. Also, the average niche breadth of bacterial species increased from 1.70 to 2.28, but community stability declined and the species assembly was always a deterministic process (NST <0.5). After the bacterial functional assembly changed from a stochastic process to a deterministic process (NST <0.5), it was transformed into a stochastic process (NST >0.5) again under the stress of high-concentration heavy metals, indicating that the collective stress resistance of bacterial communities changed from positive mutation into passive functional propagation. The research results can provide new insight into understanding the adaptive evolution of communities and ecosystem restoration under the stress of soil heavy metals.},
}
@article {pmid38762502,
year = {2024},
author = {Awala, SI and Gwak, JH and Kim, Y and Jung, MY and Dunfield, PF and Wagner, M and Rhee, SK},
title = {Nitrous oxide respiration in acidophilic methanotrophs.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4226},
pmid = {38762502},
issn = {2041-1723},
mesh = {*Nitrous Oxide/metabolism ; *Methane/metabolism ; Hydrogen-Ion Concentration ; Oxidoreductases/metabolism/genetics ; Oxygen/metabolism ; Oxidation-Reduction ; Anaerobiosis ; Methanol/metabolism ; Hydrogen/metabolism ; Oxygenases/metabolism/genetics ; },
abstract = {Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.},
}
@article {pmid38762482,
year = {2024},
author = {Min, K and Glowacki, AJ and Bosma, ML and McGuire, JA and Tian, S and McAdoo, K and DelSasso, A and Fourre, T and Gambogi, RJ and Milleman, J and Milleman, KR},
title = {Quantitative analysis of the effects of essential oil mouthrinses on clinical plaque microbiome: a parallel-group, randomized trial.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {578},
pmid = {38762482},
issn = {1472-6831},
mesh = {Humans ; *Mouthwashes/therapeutic use ; *Oils, Volatile/therapeutic use/pharmacology ; *Dental Plaque/microbiology ; *Microbiota/drug effects ; Adult ; *Gingivitis/microbiology/prevention &amp; control ; Male ; Female ; Anti-Infective Agents, Local/therapeutic use ; Salicylates/therapeutic use ; Young Adult ; Middle Aged ; Drug Combinations ; Terpenes ; },
abstract = {BACKGROUND: The rich diversity of microorganisms in the oral cavity plays an important role in the maintenance of oral health and development of detrimental oral health conditions. Beyond commonly used qualitative microbiome metrics, such as relative proportions or diversity, both the species-level identification and quantification of bacteria are key to understanding clinical disease associations. This study reports the first-time application of an absolute quantitative microbiome analysis using spiked DNA standards and shotgun metagenome sequencing to assess the efficacy and safety of product intervention on dental plaque microbiome.<br><br>METHODS: In this parallel-group, randomized clinical trial, essential oil mouthrinses, including LISTERINE&#xae; Cool Mint Antiseptic (LCM), an alcohol-containing prototype mouthrinse (ACPM), and an alcohol-free prototype mouthrinse (AFPM), were compared against a hydroalcohol control rinse on clinical parameters and the oral microbiome of subjects with moderate gingivitis. To enable a sensitive and clinically meaningful measure of bacterial abundances, species were categorized according to their associations with oral conditions based on published literature and quantified using known amounts of spiked DNA standards.<br><br>RESULTS: Multivariate analysis showed that both LCM and ACPM shifted the dysbiotic microbiome composition of subjects with gingivitis to a healthier state after 4 weeks of twice-daily use, resembling the composition of subjects with clinically healthy oral conditions recruited for observational reference comparison at baseline. The essential oil-containing mouthrinses evaluated in this study showed statistically significant reductions in clinical gingivitis and plaque measurements when compared to the hydroalcohol control rinse after 6 weeks of use.<br><br>CONCLUSIONS: By establishing a novel quantitative method for microbiome analysis, this study sheds light on the mechanisms of LCM mouthrinse efficacy on oral microbial ecology, demonstrating that repeated usage non-selectively resets a gingivitis-like oral microbiome toward that of a healthy oral cavity.<br><br>TRIAL REGISTRATION: The trial was registered on ClinicalTrials.gov on 10/06/2021. The registration number is NCT04921371.},
}
@article {pmid38761763,
year = {2024},
author = {Wang, Z and Lü, C and Wang, Y and Gomes, RL and Clarke, CJ and Gomes, HI},
title = {Zero-valent iron (ZVI) facilitated in-situ selenium (Se) immobilization and its recovery by magnetic separation: Mechanisms and implications for microbial ecology.},
journal = {Journal of hazardous materials},
volume = {473},
number = {},
pages = {134591},
doi = {10.1016/j.jhazmat.2024.134591},
pmid = {38761763},
issn = {1873-3336},
mesh = {*Selenium/chemistry ; *Iron/chemistry ; *Water Pollutants, Chemical/chemistry ; *Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism/genetics ; Biodegradation, Environmental ; RNA, Ribosomal, 16S/genetics ; Magnetic Phenomena ; },
abstract = {Selenium (Se(VI)) is environmentally toxic. One of the most popular reducing agents for Se(VI) remediation is zero-valent iron (ZVI). However, most ZVI studies were carried out in water matrices, and the recovery of reduced Se has not been investigated. A water-sediment system constructed using natural sediment was employed here to study in-situ Se remediation and recovery. A combined effect of ZVI and unacclimated microorganisms from natural sediment was found in Se(VI) removal in the water phase with a removal efficiency of 92.7 ± 1.1% within 7 d when 10 mg L[-1] Se(VI) was present. Soluble Se(VI) was removed from the water and precipitated to the sediment phase (74.8 ± 0.1%), which was enhanced by the addition of ZVI (83.3 ± 0.3%). The recovery proportion of the immobilized Se was 34.2 ± 0.1% and 92.5 ± 0.2% through wet and dry magnetic separation with 1 g L[-1] ZVI added, respectively. The 16 s rRNA sequencing revealed the variations in the microbial communities in response to ZVI and Se, which the magnetic separation could potentially mitigate in the long term. This study provides a novel technique to achieve in-situ Se remediation and recovery by combining ZVI reduction and magnetic separation.},
}
@article {pmid38760758,
year = {2024},
author = {Min, K and Bosma, ML and John, G and McGuire, JA and DelSasso, A and Milleman, J and Milleman, KR},
title = {Quantitative analysis of the effects of brushing, flossing, and mouthrinsing on supragingival and subgingival plaque microbiota: 12-week clinical trial.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {575},
pmid = {38760758},
issn = {1472-6831},
mesh = {Humans ; *Dental Plaque/microbiology ; *Gingivitis/microbiology ; *Mouthwashes/therapeutic use ; Female ; *Microbiota/drug effects ; Adult ; *Toothbrushing/methods ; Male ; *Dental Devices, Home Care ; Single-Blind Method ; Middle Aged ; Salicylates/therapeutic use ; Drug Combinations ; Terpenes/therapeutic use/pharmacology ; Bacterial Load/drug effects ; Anti-Infective Agents, Local/therapeutic use ; Young Adult ; },
abstract = {BACKGROUND: Translational microbiome research using next-generation DNA sequencing is challenging due to the semi-qualitative nature of relative abundance data. A novel method for quantitative analysis was applied in this 12-week clinical trial to understand the mechanical vs. chemotherapeutic actions of brushing, flossing, and mouthrinsing against the supragingival dental plaque microbiome. Enumeration of viable bacteria using vPCR was also applied on supragingival plaque for validation and on subgingival plaque to evaluate interventional effects below the gingival margin.<br><br>METHODS: Subjects with gingivitis were enrolled in a single center, examiner-blind, virtually supervised, parallel group controlled clinical trial. Subjects with gingivitis were randomized into brushing only (B); brushing and flossing (BF); brushing and rinsing with Listerine&#xae; Cool Mint&#xae; Antiseptic (BA); brushing and rinsing with Listerine&#xae; Cool Mint&#xae; Zero (BZ); or brushing, flossing, and rinsing with Listerine&#xae; Cool Mint&#xae; Zero (BFZ). All subjects brushed twice daily for 1&#xa0;min with a sodium monofluorophosphate toothpaste and a soft-bristled toothbrush. Subjects who flossed used unflavored waxed dental floss once daily. Subjects assigned to mouthrinses rinsed twice daily. Plaque specimens were collected at the baseline visit and after 4 and 12 weeks of intervention. Bacterial cell number quantification was achieved by adding reference amounts of DNA controls to plaque samples prior to DNA extraction, followed by shallow shotgun metagenome sequencing.<br><br>RESULTS: 286 subjects completed the trial. The metagenomic data for supragingival plaque showed significant reductions in Shannon-Weaver diversity, species richness, and total and categorical bacterial abundances (commensal, gingivitis, and malodor) after 4 and 12 weeks for the BA, BZ, and BFZ groups compared to the B group, while no significant differences were observed between the B and BF groups. Supragingival plaque vPCR further validated these results, and subgingival plaque vPCR demonstrated significant efficacy for the BFZ intervention only.<br><br>CONCLUSIONS: This publication reports on a successful application of a quantitative method of microbiome analysis in a clinical trial demonstrating the sustained and superior efficacy of essential oil mouthrinses at controlling dental plaque compared to mechanical methods. The quantitative microbiological data in this trial also reinforce the safety and mechanism of action of EO mouthrinses against plaque microbial ecology and highlights the importance of elevating EO mouthrinsing as an integral part of an oral hygiene regimen.<br><br>TRIAL REGISTRATION: The trial was registered on ClinicalTrials.gov on 31/10/2022. The registration number is NCT05600231.},
}
@article {pmid38758374,
year = {2024},
author = {Nie, X and Zhao, Z and Zhang, X and Bastías, DA and Nan, Z and Li, C},
title = {Endophytes Alleviate Drought-Derived Oxidative Damage in Achnatherum inebrians Plants Through Increasing Antioxidants and Regulating Host Stress Responses.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {73},
pmid = {38758374},
issn = {1432-184X},
support = {31772665//The National Nature Science Foundation of China/ ; jbky-2022-ey21//The Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Endophytes/metabolism/physiology ; *Antioxidants/metabolism ; *Oxidative Stress ; *Droughts ; *Epichloe/physiology/genetics/metabolism ; Gene Expression Regulation, Plant ; Stress, Physiological ; },
abstract = {Endophytes generally increase antioxidant contents of plants subjected to environmental stresses. However, the mechanisms by which endophytes alter the accumulation of antioxidants in plant tissues are not entirely clear. We hypothesized that, in stress situations, endophytes would simultaneously reduce oxidative damage and increase antioxidant contents of plants and that the accumulation of antioxidants would be a consequence of the endophyte ability to regulate the expression of plant antioxidant genes. We investigated the effects of the fungal endophyte Epichloë gansuensis (C.J. Li &amp; Nan) on oxidative damage, antioxidant contents, and expression of representative genes associated with antioxidant pathways in Achnatherum inebrians (Hance) Keng plants subjected to low (15%) and high (60%) soil moisture conditions. Gene expression levels were measured using RNA-seq. As expected, the endophyte reduced the oxidative damage by 17.55% and increased the antioxidant contents by 53.14% (on average) in plants subjected to low soil moisture. In line with the accumulation of antioxidants in plant tissues, the endophyte increased the expression of most plant genes associated with the biosynthesis of antioxidants (e.g., MIOX, crtB, gpx) while it reduced the expression of plant genes related to the metabolization of antioxidants (e.g., GST, PRODH, ALDH). Our findings suggest that endophyte ability of increasing antioxidant contents in plants may reduce the oxidative damage caused by stresses and that the fungal regulation of plant antioxidants would partly explain the accumulation of these compounds in plant tissues.},
}
@article {pmid38756954,
year = {2024},
author = {Wang, F and Xiang, L and Sze-Yin Leung, K and Elsner, M and Zhang, Y and Guo, Y and Pan, B and Sun, H and An, T and Ying, G and Brooks, BW and Hou, D and Helbling, DE and Sun, J and Qiu, H and Vogel, TM and Zhang, W and Gao, Y and Simpson, MJ and Luo, Y and Chang, SX and Su, G and Wong, BM and Fu, TM and Zhu, D and Jobst, KJ and Ge, C and Coulon, F and Harindintwali, JD and Zeng, X and Wang, H and Fu, Y and Wei, Z and Lohmann, R and Chen, C and Song, Y and Sanchez-Cid, C and Wang, Y and El-Naggar, A and Yao, Y and Huang, Y and Cheuk-Fung Law, J and Gu, C and Shen, H and Gao, Y and Qin, C and Li, H and Zhang, T and Corcoll, N and Liu, M and Alessi, DS and Li, H and Brandt, KK and Pico, Y and Gu, C and Guo, J and Su, J and Corvini, P and Ye, M and Rocha-Santos, T and He, H and Yang, Y and Tong, M and Zhang, W and Suanon, F and Brahushi, F and Wang, Z and Hashsham, SA and Virta, M and Yuan, Q and Jiang, G and Tremblay, LA and Bu, Q and Wu, J and Peijnenburg, W and Topp, E and Cao, X and Jiang, X and Zheng, M and Zhang, T and Luo, Y and Zhu, L and Li, X and Barceló, D and Chen, J and Xing, B and Amelung, W and Cai, Z and Naidu, R and Shen, Q and Pawliszyn, J and Zhu, YG and Schaeffer, A and Rillig, MC and Wu, F and Yu, G and Tiedje, JM},
title = {Emerging contaminants: A One Health perspective.},
journal = {Innovation (Cambridge (Mass.))},
volume = {5},
number = {4},
pages = {100612},
pmid = {38756954},
issn = {2666-6758},
support = {P42 ES027706/ES/NIEHS NIH HHS/United States ; },
abstract = {Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.},
}
@article {pmid38756730,
year = {2024},
author = {Akashi, M and Takemura, M and Suzuki, S},
title = {Continuous year-round isolation of giant viruses from brackish shoreline soils.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1402690},
pmid = {38756730},
issn = {1664-302X},
abstract = {Giant viruses, categorized under Nucleocytoviricota, are believed to exist ubiquitously in natural environments. However, comprehensive reports on isolated giant viruses remain scarce, with limited information available on unrecoverable strains, viral proliferation sites, and natural hosts. Previously, the author highlighted Pandoravirus hades, Pandoravirus persephone, and Mimivirus sp. styx, isolated from brackish water soil, as potential hotspots for giant virus multiplication. This study presents findings from nearly a year of monthly sampling within the same brackish water region after isolating the three aforementioned strains. This report details the recurrent isolation of a wide range of giant viruses. Each month, four soil samples were randomly collected from an approximately 5 × 10 m plot, comprising three soil samples and one water sample containing sediment from the riverbed. Acanthamoeba castellanii was used as a host for virus isolation. These efforts consistently yielded at least one viral species per month, culminating in a total of 55 giant virus isolates. The most frequently isolated species was Mimiviridae (24 isolates), followed by Marseilleviridae (23 isolates), Pandoravirus (6 isolates), and singular isolates of Pithovirus and Cedratvirus. Notably, viruses were not consistently isolated from any of the four samples every month, with certain sites yielding no viruses. Cluster analysis based on isolate numbers revealed that soil samples from May and water and sediment samples from January produced the highest number of viral strains. These findings underscore brackish coastal soil as a significant site for isolating numerous giant viruses, highlighting the non-uniform distribution along coastlines.},
}
@article {pmid38755460,
year = {2024},
author = {Flores-Almaraz, VS and Truong, C and Hernández-Oaxaca, D and Reyes-Galindo, V and Mastretta-Yanes, A and Jaramillo-Correa, JP and Salas-Lizana, R},
title = {Foliar mycobiome remains unaltered under urban air-pollution but differentially express stress-related genes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {72},
pmid = {38755460},
issn = {1432-184X},
support = {grant 778409//CONAHCyT Becas Nacionales/ ; grant 308488//CONAHCYT FORDECYT-PRONACES/ ; grant 308488//CONAHCYT FORDECYT-PRONACES/ ; grant 308488//CONAHCYT FORDECYT-PRONACES/ ; Project 319083//CONAHCyT PRONACES Sistemas Socioecol&#xf3;gicos 2021/ ; Project 319083//CONAHCyT PRONACES Sistemas Socioecol&#xf3;gicos 2021/ ; Project 319083//CONAHCyT PRONACES Sistemas Socioecol&#xf3;gicos 2021/ ; },
mesh = {*Mycobiome ; *Fungi/genetics/classification/isolation &amp; purification ; *Plant Leaves/microbiology ; Mexico ; *Air Pollution/adverse effects ; Ozone ; Stress, Physiological ; Cities ; },
abstract = {Air pollution caused by tropospheric ozone contributes to the decline of forest ecosystems; for instance, sacred fir, Abies religiosa (Kunth) Schltdl. &amp; Cham. forests in the peri-urban region of Mexico City. Individual trees within these forests exhibit variation in their response to ozone exposure, including the severity of visible symptoms in needles. Using RNA-Seq metatranscriptomic data and ITS2 metabarcoding, we investigated whether symptom variation correlates with the taxonomic and functional composition of fungal mycobiomes from needles collected in this highly polluted area in the surroundings of Mexico City. Our findings indicate that ozone-related symptoms do not significantly correlate with changes in the taxonomic composition of fungal mycobiomes. However, genes coding for 30 putative proteins were differentially expressed in the mycobiome of asymptomatic needles, including eight genes previously associated with resistance to oxidative stress. These results suggest that fungal communities likely play a role in mitigating the oxidative burst caused by tropospheric ozone in sacred fir. Our study illustrates the feasibility of using RNA-Seq data, accessible from global sequence repositories, for the characterization of fungal communities associated with plant tissues, including their gene expression.},
}
@article {pmid38755154,
year = {2024},
author = {Schmider, T and Hestnes, AG and Brzykcy, J and Schmidt, H and Schintlmeister, A and Roller, BRK and Teran, EJ and Söllinger, A and Schmidt, O and Polz, MF and Richter, A and Svenning, MM and Tveit, AT},
title = {Physiological basis for atmospheric methane oxidation and methanotrophic growth on air.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4151},
pmid = {38755154},
issn = {2041-1723},
support = {295910//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; 315129//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; },
mesh = {*Methane/metabolism ; *Oxidation-Reduction ; *Carbon Monoxide/metabolism ; *Hydrogen/metabolism ; Atmosphere/chemistry ; Air ; Nitrogen/metabolism ; Greenhouse Gases/metabolism ; },
abstract = {Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane. Still, the physiological basis allowing atmMOB to grow on air is not well understood. Here we assess the ability and strategies of seven methanotrophic species to grow with air as sole energy, carbon, and nitrogen source. Four species, including three outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, carbon monoxide, and hydrogen during 12 months of growth on air. These four species exhibited distinct substrate preferences implying the existence of multiple metabolic strategies to grow on air. The estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance in atmMOB and other aerobic microorganisms. Moreover, the atmMOB also covered their nitrogen requirements from air. During growth on air, the atmMOB decreased investments in biosynthesis while increasing investments in trace gas oxidation. Furthermore, we confirm that a high apparent specific affinity for methane is a key characteristic of atmMOB. Our work shows that atmMOB grow on the trace concentrations of methane, carbon monoxide, and hydrogen present in air and outlines the metabolic strategies that enable atmMOB to mitigate greenhouse gases.},
}
@article {pmid38755019,
year = {2024},
author = {Vaccalluzzo, A and Pino, A and Grimaldi, RL and Caggia, C and Cianci, S and Randazzo, CL},
title = {Lacticaseibacillus rhamnosus TOM 22.8 (DSM 33500) is an effective strategy for managing vaginal dysbiosis, rising the lactobacilli population.},
journal = {Journal of applied microbiology},
volume = {135},
number = {5},
pages = {},
doi = {10.1093/jambio/lxae110},
pmid = {38755019},
issn = {1365-2672},
support = {//Uriach/ ; },
mesh = {Female ; Humans ; *Probiotics/administration &amp; dosage/therapeutic use ; *Lacticaseibacillus rhamnosus ; *Dysbiosis/microbiology ; *Vagina/microbiology ; Adult ; Middle Aged ; Young Adult ; Quality of Life ; Lactobacillus ; Vaginosis, Bacterial/microbiology/drug therapy ; },
abstract = {AIM: The present study is a single-centre, randomized, controlled clinical trial aimed to evaluate the effectiveness of the probiotic Lacticaseibacillus rhamnosus TOM 22.8 (DSM 33500) strain, orally administrated, to treat vaginal dysbiosis.<br><br>METHODS AND RESULTS: Overall, 80 women, with signs and symptoms of vaginal dysbiosis, were enrolled and allocated to the treatment group (A, n=60), who took 1 capsule of the probiotic strain for 10 consecutive days, or the non-treatment group (B, n=20), who did not receive any treatment. Clinical (vaginal signs and symptoms; pH of the vaginal fluid; Amsel criteria; Nugent score; Lactobacillary grade) and microbiological examinations were performed at baseline (T0), 10 days (T1), and 30 (T2) days after the oral administration of the probiotic TOM 22.8 strain. The latter resulted in a restoration of the physiological pH, accompanied by remission or attenuation of clinical signs and symptoms as well as the improvement of the quality of life (QoL). Microbiological data revealed a significant reduction of potentially pathogenic bacteria.<br><br>CONCLUSION: The administration of the L. rhamnosus TOM 22.8 probiotic strain could be proposed as an effective strategy for the treatment of vaginal dysbiosis.},
}
@article {pmid38754710,
year = {2024},
author = {Thomé, PC and Wolinska, J and Van Den Wyngaert, S and Reñé, A and Ilicic, D and Agha, R and Grossart, HP and Garcés, E and Monaghan, MT and Strassert, JFH},
title = {Phylogenomics including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum.},
journal = {Molecular phylogenetics and evolution},
volume = {197},
number = {},
pages = {108103},
doi = {10.1016/j.ympev.2024.108103},
pmid = {38754710},
issn = {1095-9513},
mesh = {*Phylogeny ; *Chytridiomycota/genetics/classification ; *Phytoplankton/genetics/classification ; Genomics ; },
abstract = {Parasitism is the most common lifestyle on Earth and has emerged many times independently across the eukaryotic tree of life. It is frequently found among chytrids (Chytridiomycota), which are early-branching unicellular fungi that feed osmotrophically via rhizoids as saprotrophs or parasites. Chytrids are abundant in most aquatic and terrestrial environments and fulfil important ecosystem functions. As parasites, they can have significant impacts on host populations. They cause global amphibian declines and influence the Earth's carbon cycle by terminating algal blooms. To date, the evolution of parasitism within the chytrid phylum remains unclear due to the low phylogenetic resolution of rRNA genes for the early diversification of fungi, and because few parasitic lineages have been cultured and genomic data for parasites is scarce. Here, we combine transcriptomics, culture-independent single-cell genomics and a phylogenomic approach to overcome these limitations. We newly sequenced 29 parasitic taxa and combined these with existing data to provide a robust backbone topology for the diversification of Chytridiomycota. Our analyses reveal multiple independent lifestyle transitions between parasitism and saprotrophy among chytrids and multiple host shifts by parasites. Based on these results and the parasitic lifestyle of other early-branching holomycotan lineages, we hypothesise that the chytrid last common ancestor was a parasite of phytoplankton.},
}
@article {pmid38754295,
year = {2024},
author = {Verstraete, W},
title = {Nitrogen and me - How little did we, and do we know about "stikstof - azote - nitrogen"?.},
journal = {Water research},
volume = {258},
number = {},
pages = {121687},
doi = {10.1016/j.watres.2024.121687},
pmid = {38754295},
issn = {1879-2448},
mesh = {Humans ; *Agriculture ; Fertilizers ; History, 20th Century ; *Nitrogen ; },
abstract = {This retrospective article reflects on the complex and evolving relationship between humans and nitrogen over several decades. Raised on a Flemish farm, the author's early experiences with nitrogen in agriculture - both its benefits and dangers - laid the foundation for a lifelong interest in this element. The article traverses a broad range of topics related to nitrogen, highlighting its critical role in various historical, agricultural, environmental, and industrial contexts. The narrative begins with a historical overview of nitrogen's role in agriculture and warfare. The development of industrial processes like the Haber and Ostwald methods transformed nitrogen into a key ingredient for both fertilizers and explosives. The dual nature of nitrogen - as a life-giver in agriculture and a destructive component in warfare and also in biodiversity - is an important theme. The article delves into the environmental impacts of nitrogen, particularly in the context of modern agriculture and industrialization. Issues like fertilization, water contamination, and the challenges of managing nitrogenous waste highlight the complex interplay between human activities and environmental health. Technological advancements are explored, including the development of bioaugmentation methods and the potential of genetic engineering in optimizing nitrogen fixation. Throughout the narrative, personal anecdotes are weaved with scientific information, offering a unique perspective on the historical and contemporary challenges of managing nitrogen. The discussion extends to the broader implications of nitrogen management in the context of sustainability, climate change, and global food security and its overall regulatory space. All these considerations call for a re-evaluation of our relationship with nitrogen, advocating for innovative solutions and systemic thinking to address the multifaceted challenges posed by this essential, yet often problematic element.},
}
@article {pmid38752760,
year = {2024},
author = {Barnett, SE and Shade, A},
title = {Seven years of microbial community metagenomes from temperate soils affected by an ongoing coal seam fire.},
journal = {Microbiology resource announcements},
volume = {13},
number = {6},
pages = {e0019824},
pmid = {38752760},
issn = {2576-098X},
support = {1749544//National Science Foundation (NSF)/ ; },
abstract = {We examined the dynamics of soil microbiomes under heat press disturbance from an underground coal mine fire in Centralia, PA. Here, we present metagenomic sequencing and assembly data from soil microbiomes across seven consecutive years at repeatedly sampled fire-affected sites along with unaffected reference sites.},
}
@article {pmid38750737,
year = {2024},
author = {Kaijser, W and Lorenz, AW and Brauer, VS and Burfeid-Castellanos, A and David, GM and Nuy, JK and Baikova, D and Beszteri, B and Gillmann, SM and Kiesel, J and Mayombo, NAS and Peters, K and Rettig, K and Rolauffs, P and Haase, P and Hering, D},
title = {Differential associations of five riverine organism groups with multiple stressors.},
journal = {The Science of the total environment},
volume = {934},
number = {},
pages = {173105},
doi = {10.1016/j.scitotenv.2024.173105},
pmid = {38750737},
issn = {1879-1026},
mesh = {*Rivers/microbiology ; *Environmental Monitoring ; Animals ; *Biodiversity ; Fungi ; Diatoms/physiology ; Invertebrates/physiology ; Fishes ; Bacteria/classification ; Water Pollutants, Chemical/analysis ; },
abstract = {The decline of river and stream biodiversity results from multiple simultaneous occuring stressors, yet few studies explore responses explore responses across various taxonomic groups at the same locations. In this study, we address this shortcoming by using a coherent data set to study the association of nine commonly occurring stressors (five chemical, one morphological and three hydraulic) with five taxonomic groups (bacteria, fungi, diatoms, macro-invertebrates and fish). According to studies on single taxonomic groups, we hypothesise that gradients of chemical stressors structure community composition of all taxonomic groups, while gradients of hydraulic and morphological stressors are mainly related to larger organisms such as benthic macro-invertebrates and fish. Organisms were sampled over two years at 20 sites in two catchments: a recently restored urban lowland catchment (Boye) and a moderately disturbed rural mountainous catchment (Kinzig). Dissimilarity matrices were computed for each taxonomic group within a catchment. Taxonomic dissimilarities between sites were linked to stressor dissimilarities using multivariable Generalized Linear Mixed Models. Stressor gradients were longer in the Boye, but did in contrast to the Kinzig not cover low stress intensities. Accordingly, responses of the taxonomic groups were stronger in the Kinzig catchment than in the recently restored Boye catchment. The discrepancy between catchments underlines that associations to stressors strongly depend on which part of the stressor gradient is covered in a catchment. All taxonomic groups were related to conductivity. Bacteria, fungi and macro-invertebrates change with dissolved oxygen, and bacteria and fungi with total nitrogen. Morphological and hydraulic stressors had minor correlations with bacteria, fungi and diatoms, while macro-invertebrates were strongly related to fine sediment and discharge, and fish to high flow peaks. The results partly support our hypotheses about the differential associations of the different taxonomic groups with the stressors.},
}
@article {pmid38750646,
year = {2024},
author = {Huusko, K and Manninen, OH and Myrsky, E and Stark, S},
title = {Soil fungal and bacterial communities reflect differently tundra vegetation state transitions and soil physico-chemical properties.},
journal = {The New phytologist},
volume = {243},
number = {1},
pages = {407-422},
doi = {10.1111/nph.19808},
pmid = {38750646},
issn = {1469-8137},
support = {323504//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/physiology ; *Bacteria/classification ; *Tundra ; Finland ; Chemical Phenomena ; Plants/microbiology ; },
abstract = {Strong disturbances may induce ecosystem transitions into new alternative states that sustain through plant-soil interactions, such as the transition of dwarf shrub-dominated into graminoid-dominated vegetation by herbivory in tundra. Little evidence exists on soil microbial communities in alternative states, and along the slow process of ecosystem return into the predisturbance state. We analysed vegetation, soil microbial communities and activities as well as soil physico-chemical properties in historical reindeer enclosures in northernmost Finland in the following plot types: control heaths in the surrounding tundra; graminoid-dominated; 'shifting'; and recovered dwarf shrub-dominated vegetation inside enclosures. Soil fungal communities followed changes in vegetation, whereas bacterial communities were more affected by soil physico-chemical properties. Graminoid plots were characterized by moulds, pathotrophs and dark septate endophytes. Ericoid mycorrhizal and saprotrophic fungi were typical for control and recovered plots. Soil microbial communities inside the enclosures showed historical contingency, as their spatial variation was high in recovered plots despite the vegetation being more homogeneous. Self-maintaining feedback loops between plant functional types, soil microbial communities, and carbon and nutrient mineralization act effectively to stabilize alternative vegetation states, but once predisturbance vegetation reestablishes itself, soil microbial communities and physico-chemical properties return back towards their predisturbance state.},
}
@article {pmid38749545,
year = {2024},
author = {Sato, Y},
title = {Transcriptome analysis: a powerful tool to understand individual microbial behaviors and interactions in ecosystems.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {88},
number = {8},
pages = {850-856},
doi = {10.1093/bbb/zbae064},
pmid = {38749545},
issn = {1347-6947},
support = {17H04716//Japan Society for the Promotion of Science/ ; JPMJFR2174//Japan Science and Technology Agency/ ; },
mesh = {*Ecosystem ; *Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Transcriptome ; Microbiota/genetics ; Bacteria/genetics/metabolism/classification ; Microbial Interactions/genetics ; Metagenome ; },
abstract = {Transcriptome analysis is a powerful tool for studying microbial ecology, especially individual microbial functions in an ecosystem and their interactions. With the development of high-throughput sequencing technology, great progress has been made in analytical methods for microbial communities in natural environments. 16S rRNA gene amplicon sequencing (ie microbial community structure analysis) and shotgun metagenome analysis have been widely used to determine the composition and potential metabolic capability of microorganisms in target environments without requiring culture. However, even if the types of microorganisms present and their genes are known, it is difficult to determine what they are doing in an ecosystem. Gene expression analysis (transcriptome analysis; RNA-seq) is a powerful tool to address these issues. The history and basic information of gene expression analysis, as well as examples of studies using this method to analyze microbial ecosystems, are presented.},
}
@article {pmid38749241,
year = {2024},
author = {Kutralam-Muniasamy, G and Shruti, VC and Pérez-Guevara, F},
title = {Plastisphere-hosted viruses: A review of interactions, behavior, and effects.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134533},
doi = {10.1016/j.jhazmat.2024.134533},
pmid = {38749241},
issn = {1873-3336},
mesh = {*Viruses ; Plastics ; Virus Physiological Phenomena ; Biofilms ; Ecosystem ; Microplastics ; },
abstract = {Microbial communities, including bacteria, diatoms, and fungi, colonize plastic surfaces, forming biofilms known as the "plastisphere." Recent research has revealed that plastispheres also host a wide range of viruses, sparking interest in microbial ecology and virology. This shared habitat allows viruses to replicate, interact, infect, and spread, potentially impacting the environment and human health. Consequently, viruses attached to microplastics are now recognized to have broad effects on cellular and immune responses. However, the ecology and implications of viruses hosted in plastisphere habitats remain poorly understood, highlighting their fundamental importance as a subject of study. This review explores various pathways for virus attachment to plastispheres, factors influencing these interactions, their impacts within plastisphere and host-associated environments, and associated issues. It also summarizes current research and identifies knowledge gaps. We anticipate that this paper will help improve our predictive understanding of plastisphere viruses in natural settings and emphasizes the need for more research in real-world environments to advance the field.},
}
@article {pmid38748252,
year = {2024},
author = {Perez-Bou, L and Gonzalez-Martinez, A and Cabrera, JJ and Juarez-Jimenez, B and Rodelas, B and Gonzalez-Lopez, J and Correa-Galeote, D},
title = {Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {71},
pmid = {38748252},
issn = {1432-184X},
mesh = {*DNA Primers/genetics ; *Real-Time Polymerase Chain Reaction/methods ; *Wastewater/microbiology ; *Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects/isolation &amp; purification/classification ; },
abstract = {The high prevalence of antibiotic resistant bacteria (ARB) in several environments is a great concern threatening human health. Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including aadA and aadB (conferring resistance to aminoglycosides); ampC, blaTEM, blaSHV, and mecA (resistance to beta-lactams); dfrA1 (resistance to trimethoprim); ermB (resistance to macrolides); fosA (resistance to fosfomycin); qnrS (resistance to quinolones); and tetA(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade > 70%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs' biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (> 90%), good linearity of the standard curve (R[2] > 0.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.},
}
@article {pmid38747602,
year = {2024},
author = {Sudo, M and Osvatic, J and Taylor, JD and Dufour, SC and Prathep, A and Wilkins, LGE and Rattei, T and Yuen, B and Petersen, JM},
title = {SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers.},
journal = {mSystems},
volume = {9},
number = {6},
pages = {e0113523},
pmid = {38747602},
issn = {2379-5077},
support = {VRG14-021//Vienna Science and Technology Fund (WWTF)/ ; Grant-DOI 10.55776/DOC69//Austrian Science Fund (FWF) DocFunds/ ; 802494//EC | European Research Council (ERC)/ ; SEP-210693430//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; 10.55776/COE7//University of Vienna/ ; },
mesh = {Animals ; Adaptation, Physiological/genetics ; Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Hydrothermal Vents/microbiology ; Multigene Family ; *Oxidation-Reduction ; Phylogeny ; *Sulfides/metabolism ; Sulfur/metabolism ; *Symbiosis/genetics ; Bivalvia ; },
abstract = {Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of soxY in these genomes, with up to five distinct copies per genome. Symbionts harboring only the "canonical" soxY were typically ecological "specialists" that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent soxY genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the soxY gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.IMPORTANCESulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological "specialists," and some are "generalists," but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be "generalists," revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.},
}
@article {pmid38747384,
year = {2024},
author = {Tanabe, TS and Bach, E and D'Ermo, G and Mohr, MG and Hager, N and Pfeiffer, N and Guiral, M and Dahl, C},
title = {A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex.},
journal = {Protein science : a publication of the Protein Society},
volume = {33},
number = {6},
pages = {e5014},
pmid = {38747384},
issn = {1469-896X},
support = {57388731//Deutscher Akademischer Austauschdienst/Hubert Curien Procope program/ ; 40444VM//Deutscher Akademischer Austauschdienst/Hubert Curien Procope program/ ; //Studienstiftung des Deutschen Volkes/ ; 351/13-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Sulfurtransferases/metabolism/chemistry/genetics ; *Oxidoreductases/metabolism/chemistry ; *Bacterial Proteins/metabolism/chemistry/genetics ; },
abstract = {A heterodisulfide reductase-like complex (sHdr) and novel lipoate-binding proteins (LbpAs) are central players of a wide-spread pathway of dissimilatory sulfur oxidation. Bioinformatic analysis demonstrate that the cytoplasmic sHdr-LbpA systems are always accompanied by sets of sulfur transferases (DsrE proteins, TusA, and rhodaneses). The exact composition of these sets may vary depending on the organism and sHdr system type. To enable generalizations, we studied model sulfur oxidizers from distant bacterial phyla, that is, Aquificota and Pseudomonadota. DsrE3C of the chemoorganotrophic Alphaproteobacterium Hyphomicrobium denitrificans and DsrE3B from the Gammaproteobacteria Thioalkalivibrio sp. K90mix, an obligate chemolithotroph, and Thiorhodospira sibirica, an obligate photolithotroph, are homotrimers that donate sulfur to TusA. Additionally, the hyphomicrobial rhodanese-like protein Rhd442 exchanges sulfur with both TusA and DsrE3C. The latter is essential for sulfur oxidation in Hm. denitrificans. TusA from Aquifex aeolicus (AqTusA) interacts physiologically with AqDsrE, AqLbpA, and AqsHdr proteins. This is particularly significant as it establishes a direct link between sulfur transferases and the sHdr-LbpA complex that oxidizes sulfane sulfur to sulfite. In vivo, it is unlikely that there is a strict unidirectional transfer between the sulfur-binding enzymes studied. Rather, the sulfur transferases form a network, each with a pool of bound sulfur. Sulfur flux can then be shifted in one direction or the other depending on metabolic requirements. A single pair of sulfur-binding proteins with a preferred transfer direction, such as a DsrE3-type protein towards TusA, may be sufficient to push sulfur into the sink where it is further metabolized or needed.},
}
@article {pmid38746754,
year = {2024},
author = {Shan, Z and Chen, H and Deng, Y and He, D and Ren, L},
title = {An abrupt regime shift of bacterioplankton community from weak to strong thermal pollution in a subtropical bay.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1395583},
pmid = {38746754},
issn = {1664-302X},
abstract = {Thermal pollution from the cooling system of the nuclear power plants greatly changes the environmental and the ecological conditions of the receiving marine water body, but we know little about their impact on the steady-state transition of marine bacterioplankton communities. In this study, we used high-throughput sequencing based on the 16S rRNA gene to investigate the impact of the thermal pollution on the bacterioplankton communities in a subtropical bay (the Daya Bay). We observed that thermal pollution from the cooling system of the nuclear power plant caused a pronounced thermal gradient ranging from 19.6°C to 24.12°C over the whole Daya Bay. A temperature difference of 4.5°C between the northern and southern parts of the bay led to a regime shift in the bacterioplankton community structure. In the three typical scenarios of regime shifts, the steady-state transition of bacterioplankton community structure in response to temperature increasing was more likely consistent with an abrupt regime shift rather than a smooth regime or a discontinuous regime model. Water temperature was a decisive factor on the regime shift of bacterioplankton community structure. High temperature significantly decreased bacterioplankton diversity and shifted its community compositions. Cyanobium and Synechococcus of Cyanobacteria, NS5 marine group of Bacteroidota, and Vibrio of Gammaproteobacteria were found that favored high temperature environments. Furthermore, the increased water temperature significantly altered the community assembly of bacterioplankton in Daya Bay, with a substantial decrease in the proportion of drift and others, and a marked increase in the proportion of homogeneous selection. In summary, we proposed that seawater temperature increasing induced by the thermal pollution resulted in an abrupt regime shift of bacterioplankton community in winter subtropical bay. Our research might broad our understanding of marine microbial ecology under future conditions of global warming.},
}
@article {pmid38746391,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Krulilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: Coverage-based Analysis for Identification of Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38746391},
issn = {2692-8205},
support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; },
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}
@article {pmid38740585,
year = {2024},
author = {Bin, X and Wang, P and Shen, Y and Xiang, X and Jafir, M and Wan, X},
title = {Investigation of Fungal Community Structure in the Gut of the Stag Beetle Dorcus hopei (Coleoptera; Lucanidae): Comparisons Among Developmental Stages.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {70},
pmid = {38740585},
issn = {1432-184X},
support = {31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Coleoptera/microbiology/growth &amp; development ; *Larva/growth &amp; development/microbiology ; *Fungi/genetics/classification/physiology ; *Gastrointestinal Microbiome ; Pupa/growth &amp; development/microbiology ; Mycobiome ; Biodiversity ; Symbiosis ; High-Throughput Nucleotide Sequencing ; },
abstract = {Stag beetles, recognized as common saproxylic insects, are valued for their vibrant coloration and distinctive morphology. These beetles play a crucial ecological role in decomposition and nutrient cycling, serving as a vital functional component in ecosystem functioning. Although previous studies have confirmed that stag beetles are predominantly fungivores, the fluctuations in their intestinal fungal communities at different developmental stages remain poorly understood. In the current study, high-throughput sequencing was employed to investigate the dynamic changes within intestinal fungal communities at various developmental stages in the stag beetle Dorcus hopei. Results showed that microbial diversity was higher during the larval stage than during the pupal and adult stages. Furthermore, significant differences were identified in the composition of the intestinal fungal communities across the larval, pupal, and adult stages, suggesting that developmental transitions may be crucial factors contributing to variations in fungal community composition and diversity. Dominant genera included Candida, Scheffersomyces, Phaeoacremonium, and Trichosporon. Functional predictions indicated a greater diversity and relative abundance of endosymbiotic fungi in the larval gut, suggesting a potential dependency of larvae on beneficial gut fungi for nutrient acquisition. Additionally, the application of abundance-based β-null deviation and niche width analyses revealed that the adult gut exerted a stronger selection pressure on its fungal community, favoring certain taxa. This selection process culminates in a more robust co-occurrence network of fungal communities within the adult gut, thereby enhancing their adaptability to environmental fluctuations. This study advances our understanding of the intestinal fungal community structure in stag beetles, providing a crucial theoretical foundation for the development of saproxylic beetle resources, biomass energy utilization, plastic degradation strategies, and beetle conservation efforts.},
}
@article {pmid38740197,
year = {2024},
author = {Ibrahim, SS and Ionescu, D and Grossart, HP},
title = {Tapping into fungal potential: Biodegradation of plastic and rubber by potent Fungi.},
journal = {The Science of the total environment},
volume = {934},
number = {},
pages = {173188},
doi = {10.1016/j.scitotenv.2024.173188},
pmid = {38740197},
issn = {1879-1026},
mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Fungi/metabolism ; *Rubber/metabolism ; Polyurethanes ; },
abstract = {Plastic polymers are present in most aspects of routine daily life. Their increasing leakage into the environment poses a threat to environmental, animal, and human health. These polymers are often resistant to microbial degradation and are predicted to remain in the environment for tens to hundreds of years. Fungi have been shown to degrade complex polymers and are considered good candidates for bioremediation (biological pollutant reduction) of plastics. Therefore, we screened 18 selected fungal strains for their ability to degrade polyurethane (PU), polyethylene (PE), and tire rubber. As a proxy for plastic polymer mineralization, we quantified O2 consumption and CO2 production in an enclosed biodegradation system providing plastic as the sole carbon source. In contrast to most studies we demonstrated that the tested fungi attach to, and colonize the different plastic polymers without any pretreatment of the plastics and in the absence of sugars, which were suggested essential for priming the degradation process. Functional polymer groups identified by Fourier-transform infrared spectroscopy (FTIR), and changes in fungal morphology as seen in light and scanning electron microscopy (SEM) were used as indicators of fungal adaptation to growth on PU as a substrate. Thereby, SEM analysis revealed new morphological structures and deformation of the cell wall of several fungal strains when colonizing PU and utilizing this plastic polymer for cell growth. Strains of Fusarium, Penicillium, Botryotinia cinerea EN41, and Trichoderma demonstrated a high potential to degrade PU, rubber, and PE. Growing on PU, over 90 % of the O2 was consumed in <14 days with 300-500 ppm of CO2 generated in parallel. Our study highlights a high bioremediation potential of some fungal strains to efficiently degrade plastic polymers, largely dependent on plastic type.},
}
@article {pmid38739959,
year = {2024},
author = {Kazmi, SSUH and Tayyab, M and Pastorino, P and Barcelò, D and Yaseen, ZM and Grossart, HP and Khan, ZH and Li, G},
title = {Decoding the molecular concerto: Toxicotranscriptomic evaluation of microplastic and nanoplastic impacts on aquatic organisms.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134574},
doi = {10.1016/j.jhazmat.2024.134574},
pmid = {38739959},
issn = {1873-3336},
mesh = {*Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Aquatic Organisms/drug effects/genetics ; Animals ; *Transcriptome/drug effects ; Nanoparticles/toxicity/chemistry ; },
abstract = {The pervasive and steadily increasing presence of microplastics/nanoplastics (MPs/NPs) in aquatic environments has raised significant concerns regarding their potential adverse effects on aquatic organisms and their integration into trophic dynamics. This emerging issue has garnered the attention of (eco)toxicologists, promoting the utilization of toxicotranscriptomics to unravel the responses of aquatic organisms not only to MPs/NPs but also to a wide spectrum of environmental pollutants. This review aims to systematically explore the broad repertoire of predicted molecular responses by aquatic organisms, providing valuable intuitions into complex interactions between plastic pollutants and aquatic biota. By synthesizing the latest literature, present analysis sheds light on transcriptomic signatures like gene expression, interconnected pathways and overall molecular mechanisms influenced by various plasticizers. Harmful effects of these contaminants on key genes/protein transcripts associated with crucial pathways lead to abnormal immune response, metabolic response, neural response, apoptosis and DNA damage, growth, development, reproductive abnormalities, detoxification, and oxidative stress in aquatic organisms. However, unique challenge lies in enhancing the fingerprint of MPs/NPs, presenting complicated enigma that requires decoding their specific impact at molecular levels. The exploration endeavors, not only to consolidate existing knowledge, but also to identify critical gaps in understanding, push forward the frontiers of knowledge about transcriptomic signatures of plastic contaminants. Moreover, this appraisal emphasizes the imperative to monitor and mitigate the contamination of commercially important aquatic species by MPs/NPs, highlighting the pivotal role that regulatory frameworks must play in protecting all aquatic ecosystems. This commitment aligns with the broader goal of ensuring the sustainability of aquatic resources and the resilience of ecosystems facing the growing threat of plastic pollutants.},
}
@article {pmid38736980,
year = {2024},
author = {Ahmad, R and Liaquat, M and Sammi, S and Al-Hawadi, JS and Jahangir, M and Mumtaz, A and Khan, I and Okla, MK and Alaraidh, IA and AbdElgawad, H and Liu, K and Harrison, MT and Saud, S and Hassan, S and Nawaz, T and Zhu, M and Liu, H and Adnan, M and Sadiq, A and Rahman, TU and Asghari, BH and Fahad, S},
title = {Physicochemical and nutritional profiles of wild adlay (Coix lacryma-jobi Linn) accessions by GC, FTIR, and spectrophotometer.},
journal = {Food chemistry: X},
volume = {22},
number = {},
pages = {101418},
pmid = {38736980},
issn = {2590-1575},
abstract = {Purpose of current study was to determine physicochemical, triglyceride composition, and functional groups of wild adlay accessions (brown, black, yellow, grey, green, off white, and purple) to find out its scope as cereal crop. Triglycerides, minerals and functional groups were determined through Gas chromatography, spectrophotometer and Fourier Transform Infrared (FTIR) spectrophotometer respectively. Results revealed variation among bulk densities, specific densities, percent empty spaces, and corresponding grain counts per 10 g of sample are useful in distinguishing brown, black, yellow, grey, green, off white, and purple wild adlay accessions. Specific density and grain count per 10 g sample was significantly related. No statistical relationship exists among the pronounced physical characteristics. Brown adlay expressed the highest protein, fat, and fiber contents 15.82%, 4.76% and 2.37% respectively. Protein, fat, ash, and fiber percent contents were found comparable to cultivated adlay. Spectrophotometric analysis revealed macro elements including phosphorus, potassium, calcium, and sodium in the range 0.3% - 2.2% and micro elements boron, iron, copper, zinc, and manganese in the range 1.6 mg/kg - 20.8 mg/kg. Gas chromatography showed polyunsaturated fatty acids (PUFA) constitute the primary fraction (39% ± 7.2) of wild adlay triglycerides. Linoleic and palmitic acids were present as prominent fatty acids, 43.5% ±1.4 and 26.3% ±1.4 respectively. Infra-red frequencies distinguished functional groups in narrow band and fingerprint region of protein in association with out of plane region leading to structural differences among adlay accessions. Comparison of major distinguishing vibrational frequencies among different flours indicated black adlay containing highest functional groups appeared promising for varietal development.},
}
@article {pmid38734822,
year = {2024},
author = {Breedt, G and Korsten, L and Gokul, JK},
title = {Influence of Soil Phosphate on Rhizobacterial Performance in Affecting Wheat Yield.},
journal = {Current microbiology},
volume = {81},
number = {7},
pages = {170},
pmid = {38734822},
issn = {1432-0991},
mesh = {*Triticum/microbiology/growth &amp; development ; *Phosphates/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Rhizosphere ; Fertilizers/analysis ; Paenibacillus/metabolism/genetics/growth &amp; development ; Phosphorus/metabolism ; },
abstract = {As a primary nutrient in agricultural soils, phosphorus plays a crucial but growth-limiting role for plants due to its complex interactions with various soil elements. This often results in excessive phosphorus fertilizer application, posing concerns for the environment. Agri-research has therefore shifted focus to increase fertilizer-use efficiency and minimize environmental impact by leveraging plant growth-promoting rhizobacteria. This study aimed to evaluate the in-field incremental effect of inorganic phosphate concentration (up to 50 kg/ha/P) on the ability of two rhizobacterial isolates, Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29), from the previous Breedt et al. (Ann Appl Biol 171:229-236, 2017) study on maize in enhancing the yield of commercially grown Duzi® cultivar wheat. Results obtained from three seasons of field trials revealed a significant relationship between soil phosphate concentration and the isolates' effectiveness in improving wheat yield. Rhizospheric samples collected at flowering during the third season, specifically to assess phosphatase enzyme activity at the different soil phosphate levels, demonstrated a significant decrease in soil phosphatase activity when the phosphorus rate reached 75% for both isolates. Furthermore, in vitro assessments of inorganic phosphate solubilization by both isolates at five increments of tricalcium phosphate-amended Pikovskaya media found that only isolate T19 was capable of solubilizing tricalcium at concentrations exceeding 3 mg/ml. The current study demonstrates the substantial influence of inorganic phosphate on the performance of individual rhizobacterial isolates, highlighting that this is an essential consideration when optimizing these isolates to increase wheat yield in commercial cultivation.},
}
@article {pmid38733792,
year = {2024},
author = {Musat, F and Kjeldsen, KU and Rotaru, AE and Chen, SC and Musat, N},
title = {Archaea oxidizing alkanes through alkyl-coenzyme M reductases.},
journal = {Current opinion in microbiology},
volume = {79},
number = {},
pages = {102486},
doi = {10.1016/j.mib.2024.102486},
pmid = {38733792},
issn = {1879-0364},
mesh = {*Alkanes/metabolism ; *Archaea/enzymology/genetics/metabolism ; *Oxidation-Reduction ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; Electron Transport ; Archaeal Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; Bacteria/enzymology/genetics/metabolism/classification ; },
abstract = {This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.},
}
@article {pmid38730059,
year = {2024},
author = {Kimura, K and Okuro, T},
title = {Cyanobacterial Biocrust on Biomineralized Soil Mitigates Freeze-Thaw Effects and Preserves Structure and Ecological Functions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {69},
pmid = {38730059},
issn = {1432-184X},
support = {JPMJSA1906//Science and Technology Research Partnership for Sustainable Development/ ; JP22H01310//Japan Society for the Promotion of Science/ ; JPMEERF20205001//Environment Research and Technology Development Fund/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Freezing ; *Cyanobacteria/metabolism/chemistry ; Carbonates/chemistry/metabolism ; Ecosystem ; Sporosarcina/metabolism/growth &amp; development ; },
abstract = {Biocrust inoculation and microbially induced carbonate precipitation (MICP) are tools used in restoring degraded arid lands. It remains unclear whether the ecological functions of the two tools persist when these methods are combined and subjected to freeze-thaw (FT) cycles. We hypothesized a synergetic interaction between MICP treatment and biocrust under FT cycles, which would allow both components to retain their ecological functions. We grew cyanobacterial (Nostoc commune) biocrusts on bare soil and on MICP (Sporosarcina pasteurii)-treated soil, subjecting them to repeated FT cycles simulating the Mongolian climate. Generalized linear modeling revealed that FT cycling did not affect physical structure or related functions but could increase the productivity and reduce the nutrient condition of the crust. The results confirm the high tolerance of MICP-treated soil and biocrust to FT cycling. MICP treatment + biocrust maintained higher total carbohydrate content under FT stress. Our study indicates that biocrust on biomineralized soil has a robust enough structure to endure FT cycling during spring and autumn and to promote restoration of degraded lands.},
}
@article {pmid38729708,
year = {2024},
author = {Garcia-Gutierrez, E and Monteoliva García, G and Bodea, I and Cotter, PD and Iguaz, A and Garre, A},
title = {A secondary model for the effect of pH on the variability in growth fitness of Listeria innocua strains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {186},
number = {},
pages = {114314},
doi = {10.1016/j.foodres.2024.114314},
pmid = {38729708},
issn = {1873-7145},
mesh = {*Listeria/growth &amp; development/classification ; Hydrogen-Ion Concentration ; *Food Microbiology ; Models, Biological ; Colony Count, Microbial ; Risk Assessment ; },
abstract = {Variability in microbial growth is a keystone of modern Quantitative Microbiological Risk Assessment (QMRA). However, there are still significant knowledge gaps on how to model variability, with the most common assumption being that variability is constant. This is implemented by an error term (with constant variance) added on top of the secondary growth model (for the square root of the growth rate). However, this may go against microbial ecology principles, where differences in growth fitness among bacterial strains would be more prominent in the vicinity of the growth limits than at optimal growth conditions. This study coins the term "secondary models for variability", evaluating whether they should be considered in QMRA instead of the constant strain variability hypothesis. For this, 21 strains of Listeria innocua were used as case study, estimating their growth rate by the two-fold dilution method at pH between 5 and 10. Estimates of between-strain variability and experimental uncertainty were obtained for each pH using mixed-effects models, showing the lowest variability at optimal growth conditions, increasing towards the growth limits. Nonetheless, the experimental uncertainty also increased towards the extremes, evidencing the need to analyze both sources of variance independently. A secondary model was thus proposed, relating strain variability and pH conditions. Although the modelling approach certainly has some limitations that would need further experimental validation, it is an important step towards improving the description of variability in QMRA, being the first model of this type in the field.},
}
@article {pmid38728984,
year = {2024},
author = {Yuan, Y and Zhang, G and Fang, H and Peng, S and Xia, Y and Wang, F},
title = {The ecology of the sewer systems: Microbial composition, function, assembly, and network in different spatial locations.},
journal = {Journal of environmental management},
volume = {359},
number = {},
pages = {121107},
doi = {10.1016/j.jenvman.2024.121107},
pmid = {38728984},
issn = {1095-8630},
mesh = {*Sewage/microbiology ; RNA, Ribosomal, 16S/genetics ; Wastewater/microbiology ; Ecology ; Corrosion ; Microbiota ; },
abstract = {Microbial induced concrete corrosion (MICC) is the primary deterioration affecting global sewers. Disentangling ecological mechanisms in the sewer system is meaningful for implementing policies to protect sewer pipes using trenchless technology. It is necessary to understand microbial compositions, interaction networks, functions, alongside assembly processes in sewer microbial communities. In this study, sewer wastewater samples and microbial samples from the upper part (UP), middle part (MP) and bottom part (BP) of different pipes were collected for 16S rRNA gene amplicon analysis. It was found that BP harbored distinct microbial communities and the largest proportion of unique species (1141) compared to UP and MP. The community in BP tended to be more clustered. Furthermore, significant differences in microbial functions existed in different spatial locations, including the carbon cycle, nitrogen cycle and sulfur cycle. Active microbial sulfur cycling indicated the corrosion risk of MICC. Among the environmental factors, the oxidation‒reduction potential drove changes in BP, while sulfate managed changes in UP and BP. Stochasticity dominated community assembly in the sewer system. Additionally, the sewer microbial community exhibited numerous positive links. BP possessed a more complex, modular network with higher modularity. These deep insights into microbial ecology in the sewer system may guide engineering safety and disaster prevention in sewer infrastructure.},
}
@article {pmid38728226,
year = {2024},
author = {Ma, T and Rothschild, J and Halabeya, F and Zilman, A and Milstein, JN},
title = {Mechanics limits ecological diversity and promotes heterogeneity in confined bacterial communities.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {20},
pages = {e2322321121},
pmid = {38728226},
issn = {1091-6490},
support = {RGPIN-2019-06520//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; RGPIN-2022-04909//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 207-2019-2020-Q4-00576//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
mesh = {*Escherichia coli/physiology ; Models, Biological ; Biodiversity ; Ecosystem ; },
abstract = {Multispecies bacterial populations often inhabit confined and densely packed environments where spatial competition determines the ecological diversity of the community. However, the role of mechanical interactions in shaping the ecology is still poorly understood. Here, we study a model system consisting of two populations of nonmotile Escherichia coli bacteria competing within open, monolayer microchannels. The competitive dynamics is observed to be biphasic: After seeding, either one strain rapidly fixates or both strains orient into spatially stratified, stable communities. We find that mechanical interactions with other cells and local spatial constraints influence the resulting community ecology in unexpected ways, severely limiting the overall diversity of the communities while simultaneously allowing for the establishment of stable, heterogeneous populations of bacteria displaying disparate growth rates. Surprisingly, the populations have a high probability of coexisting even when one strain has a significant growth advantage. A more coccus morphology is shown to provide a selective advantage, but agent-based simulations indicate this is due to hydrodynamic and adhesion effects within the microchannel and not from breaking of the nematic ordering. Our observations are qualitatively reproduced by a simple Pólya urn model, which suggests the generality of our findings for confined population dynamics and highlights the importance of early colonization conditions on the resulting diversity and ecology of bacterial communities. These results provide fundamental insights into the determinants of community diversity in dense confined ecosystems where spatial exclusion is central to competition as in organized biofilms or intestinal crypts.},
}
@article {pmid38727217,
year = {2024},
author = {Thomas, MJN and Brockhurst, MA and Coyte, KZ},
title = {What makes a temperate phage an effective bacterial weapon?.},
journal = {mSystems},
volume = {9},
number = {6},
pages = {e0103623},
pmid = {38727217},
issn = {2379-5077},
support = {/WT_/Wellcome Trust/United Kingdom ; BB/T014342/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 220243/Z/20/Z//Wellcome Trust (WT)/ ; 226047/Z/22/Z//Wellcome Trust (WT)/ ; },
mesh = {*Lysogeny ; *Pseudomonas aeruginosa/virology ; Bacteriophages/genetics/physiology ; },
abstract = {UNLABELLED: Temperate bacteriophages (phages) are common features of bacterial genomes and can act as self-amplifying biological weapons, killing susceptible competitors and thus increasing the fitness of their bacterial hosts (lysogens). Despite their prevalence, however, the key characteristics of an effective temperate phage weapon remain unclear. Here, we use systematic mathematical analyses coupled with experimental tests to understand what makes an effective temperate phage weapon. We find that effectiveness is controlled by phage life history traits-in particular, the probability of lysis and induction rate-but that the optimal combination of traits varies with the initial frequency of a lysogen within a population. As a consequence, certain phage weapons can be detrimental when their hosts are rare yet beneficial when their hosts are common, while subtle changes in individual life history traits can completely reverse the impact of an individual phage weapon on lysogen fitness. We confirm key predictions of our model experimentally, using temperate phages isolated from the clinically relevant Liverpool epidemic strain of Pseudomonas aeruginosa. Through these experiments, we further demonstrate that nutrient availability can also play a critical role in driving frequency-dependent patterns in phage-mediated competition. Together, these findings highlight the complex and context-dependent nature of temperate phage weapons and the importance of both ecological and evolutionary processes in shaping microbial community dynamics more broadly.<br><br>IMPORTANCE: Temperate bacteriophages-viruses that integrate within bacterial DNA-are incredibly common within bacterial genomes and can act as powerful self-amplifying weapons. Bacterial hosts that carry temperate bacteriophages can thus gain a fitness advantage within a given niche by killing competitors. But what makes an effective phage weapon? Here, we first use a simple mathematical model to explore the factors determining bacteriophage weapon utility. Our models suggest that bacteriophage weapons are nuanced and context-dependent; an individual bacteriophage may be beneficial or costly depending upon tiny changes to how it behaves or the bacterial community it inhabits. We then confirm these mathematical predictions experimentally, using phages isolated from cystic fibrosis patients. But, in doing so, we also find that another factor-nutrient availability-plays a key role in shaping bacteriophage-mediated competition. Together, our results provide new insights into how temperate bacteriophages modulate bacterial communities.},
}
@article {pmid38726295,
year = {2024},
author = {Casero, JJD and Rovedder, APM and Vargas, LK},
title = {Editorial: Plant-microbe interactions in forest ecosystems, volume II.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1414383},
pmid = {38726295},
issn = {1664-462X},
}
@article {pmid38724726,
year = {2024},
author = {Bobonis, J and Yang, ALJ and Voogdt, CGP and Typas, A},
title = {TAC-TIC, a high-throughput genetics method to identify triggers or blockers of bacterial toxin-antitoxin systems.},
journal = {Nature protocols},
volume = {19},
number = {8},
pages = {2231-2249},
pmid = {38724726},
issn = {1750-2799},
mesh = {*Toxin-Antitoxin Systems/genetics ; *Escherichia coli/genetics ; Bacterial Toxins/genetics/metabolism ; Bacteriophages/genetics ; High-Throughput Screening Assays/methods ; Conjugation, Genetic ; },
abstract = {Toxin-antitoxin systems (TAs) are abundant in bacterial chromosomes and can arrest growth under stress, but usually remain inactive. TAs have been increasingly implicated in halting the growth of infected bacteria from bacteriophages or foreign genetic elements[1,2] to protect the population (abortive infection, Abi). The vast diversity and abundance of TAs and other Abi systems[3] suggest they play an important immunity role, yet what allows them to sense attack remains largely enigmatic. Here, we describe a method called toxin activation-inhibition conjugation (TAC-TIC), which we used to identify gene products that trigger or block the toxicity of phage-defending tripartite retron-TAs[4]. TAC-TIC employs high-density arrayed mobilizable gene-overexpression libraries, which are transferred into cells carrying the full TA system or only its toxic component, on inducible vectors. The double-plasmid transconjugants are then pinned on inducer-containing agar plates and their colony fitness is quantified to identify gene products that trigger a TA to inhibit growth (TAC), or that block it from acting (TIC). TAC-TIC is optimized for the Singer ROTOR pinning robot, but can also be used with other robots or manual pinners, and allows screening tens of thousands of genes against any TA or Abi (with toxicity) within a week. Finally, we present a dual conjugation donor/cloning strain (Escherichia coli DATC), which accelerates the construction of TAC-TIC gene-donor libraries from phages, enabling the use of TAC-TIC for identifying TA triggers and antidefense mechanisms in phage genomes.},
}
@article {pmid38723661,
year = {2024},
author = {Tschitschko, B and Esti, M and Philippi, M and Kidane, AT and Littmann, S and Kitzinger, K and Speth, DR and Li, S and Kraberg, A and Tienken, D and Marchant, HK and Kartal, B and Milucka, J and Mohr, W and Kuypers, MMM},
title = {Rhizobia-diatom symbiosis fixes missing nitrogen in the ocean.},
journal = {Nature},
volume = {630},
number = {8018},
pages = {899-904},
pmid = {38723661},
issn = {1476-4687},
mesh = {Carbon/metabolism ; *Diatoms/metabolism/physiology ; *Nitrogen/metabolism ; *Nitrogen Fixation ; *Oceans and Seas ; Photosynthesis ; Phylogeny ; *Rhizobium/classification/metabolism/physiology ; *Seawater/microbiology/chemistry ; *Symbiosis ; Cyanobacteria/isolation &amp; purification/metabolism ; Atlantic Ocean ; },
abstract = {Nitrogen (N2) fixation in oligotrophic surface waters is the main source of new nitrogen to the ocean[1] and has a key role in fuelling the biological carbon pump[2]. Oceanic N2 fixation has been attributed almost exclusively to cyanobacteria, even though genes encoding nitrogenase, the enzyme that fixes N2 into ammonia, are widespread among marine bacteria and archaea[3-5]. Little is known about these non-cyanobacterial N2 fixers, and direct proof that they can fix nitrogen in the ocean has so far been lacking. Here we report the discovery of a non-cyanobacterial N2-fixing symbiont, 'Candidatus Tectiglobus diatomicola', which provides its diatom host with fixed nitrogen in return for photosynthetic carbon. The N2-fixing symbiont belongs to the order Rhizobiales and its association with a unicellular diatom expands the known hosts for this order beyond the well-known N2-fixing rhizobia-legume symbioses on land[6]. Our results show that the rhizobia-diatom symbioses can contribute as much fixed nitrogen as can cyanobacterial N2 fixers in the tropical North Atlantic, and that they might be responsible for N2 fixation in the vast regions of the ocean in which cyanobacteria are too rare to account for the measured rates.},
}
@article {pmid38722447,
year = {2024},
author = {Hu, Y and Cai, J and Song, Y and Li, G and Gong, Y and Jiang, X and Tang, X and Shao, K and Gao, G},
title = {Sediment DNA Records the Critical Transition of Bacterial Communities in the Arid Lake.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {68},
pmid = {38722447},
issn = {1432-184X},
support = {2019YFA0607100//Key Technologies Research and Development Program/ ; U2003205//National Natural Science Foundation of China/ ; 2022xjkk1504//The third Xinjiang Scientific Expedition/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; China ; *DNA, Bacterial/genetics ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Microbiota ; },
abstract = {It is necessary to predict the critical transition of lake ecosystems due to their abrupt, non-linear effects on social-economic systems. Given the promising application of paleolimnological archives to tracking the historical changes of lake ecosystems, it is speculated that they can also record the lake's critical transition. We studied Lake Dali-Nor in the arid region of Inner Mongolia because of the profound shrinking the lake experienced between the 1300 s and the 1600 s. We reconstructed the succession of bacterial communities from a 140-cm-long sediment core at 4-cm intervals and detected the critical transition. Our results showed that the historical trajectory of bacterial communities from the 1200 s to the 2010s was divided into two alternative states: state1 from 1200 to 1300 s and state2 from 1400 to 2010s. Furthermore, in the late 1300 s, the appearance of a tipping point and critical slowing down implied the existence of a critical transition. By using a multi-decadal time series from the sedimentary core, with general Lotka-Volterra model simulations, local stability analysis found that bacterial communities were the most unstable as they approached the critical transition, suggesting that the collapse of stability triggers the community shift from an equilibrium state to another state. Furthermore, the most unstable community harbored the strongest antagonistic and mutualistic interactions, which may imply the detrimental role of interaction strength on community stability. Collectively, our study showed that sediment DNA can be used to detect the critical transition of lake ecosystems.},
}
@article {pmid38722171,
year = {2024},
author = {Stice, SP and Jan, H-H and Chen, H-C and Nwosu, L and Shin, GY and Weaver, S and Coutinho, T and Kvitko, BH and Baltrus, DA},
title = {Erratum for Stice et al., "Pantailocins: phage-derived bacteriocins from Pantoea ananatis and Pantoea stewartii subsp. indologenes".},
journal = {Applied and environmental microbiology},
volume = {90},
number = {6},
pages = {e0062924},
doi = {10.1128/aem.00629-24},
pmid = {38722171},
issn = {1098-5336},
}
@article {pmid38718505,
year = {2024},
author = {Liu, S and Zhang, Z and Zhao, C and Zhang, M and Han, F and Hao, J and Wang, X and Shan, X and Zhou, W},
title = {Nonlinear responses of biofilm bacteria to alkyl-chain length of parabens by DFT calculation.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134460},
doi = {10.1016/j.jhazmat.2024.134460},
pmid = {38718505},
issn = {1873-3336},
mesh = {*Parabens/chemistry/toxicity ; *Biofilms/drug effects ; Bacteria/drug effects ; Density Functional Theory ; Quorum Sensing/drug effects ; },
abstract = {Parabens can particularly raise significant concerns regarding the disruption of microbial ecology due to their antimicrobial properties. However, the responses of biofilm bacteria to diverse parabens with different alkyl-chain length remains unclear. Here, theoretical calculations and bioinformatic analysis were performed to decipher the influence of parabens varying alkyl-chain lengths on the biofilm bacteria. Our results showed that the disturbances in bacterial community did not linearly response to the alkyl-chain length of parabens, and propylparaben (PrP), with median chain length, had more severe impact on bacterial community. Despite the fact that paraben lethality linearly increased with chain length, the PrP had a higher chemical reactions potential than parabens with shorter or longer alkyl-chain. The chemical reactions potential was critical in the nonlinear responses of bacterial community to alkyl-chain length of parabens. PrP could impose selective pressure to disturb the bacterial community, because it had a more profound contribution to deterministic assembly process. Furthermore, N-acyl-homoserine lactones was also significantly promoted under PrP exposure, confirming that PrP could affect the bacterial community by influencing the quorum-sensing system. Overall, our study reveals the nonlinear responses of bacterial communities to the alkyl-chain lengths of parabens and provides insightful perspectives for the better regulation of parabens. ENVIRONMENTAL IMPLICATION: Parabens are recognized as emerging organic pollutants, which specially raise great concerns due to their antimicrobial properties disturbing microbial ecology. However, few study have addressed the relationship between bacterial community responses and the molecular structural features of parabens with different alkyl-chain length. This investigation revealed nonlinear responses of the bacterial community to the alkyl-chain length of parabens through DFT calculation and bioinformatic analysis and identified the critical roles of chemical reactions potential in nonlinear responses of bacterial community. Our results benefit the precise evaluation of ecological hazards posed by parabens and provide useful insights for better regulation of parabens.},
}
@article {pmid38714759,
year = {2024},
author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R},
title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.},
journal = {Nature microbiology},
volume = {9},
number = {5},
pages = {1152-1156},
pmid = {38714759},
issn = {2058-5276},
support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; },
mesh = {*Spectrum Analysis, Raman/methods ; *Internet ; Humans ; Databases, Factual ; },
}
@article {pmid38712704,
year = {2024},
author = {Vandermaesen, J and Daly, AJ and Mawarda, PC and Baetens, JM and De Baets, B and Boon, N and Springael, D},
title = {Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship.},
journal = {Ecology letters},
volume = {27},
number = {5},
pages = {e14433},
doi = {10.1111/ele.14433},
pmid = {38712704},
issn = {1461-0248},
support = {266039//EU FP7/ ; G0D0322N//Fonds Wetenschappelijk Onderzoek/ ; BELSPO P7/25//Belgian Science Policy (BELSPO)/ ; },
mesh = {*Microbiota ; Benzamides ; Microbial Interactions ; Phyllobacteriaceae/physiology ; Groundwater/microbiology ; Biodiversity ; },
abstract = {The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.},
}
@article {pmid38712077,
year = {2024},
author = {Letourneau, J and Carrion, VM and Jiang, S and Osborne, OW and Holmes, ZC and Fox, A and Epstein, P and Tan, CY and Kirtley, M and Surana, NK and David, LA},
title = {Interplay between particle size and microbial ecology in the gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38712077},
issn = {2692-8205},
support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; },
abstract = {Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is known about what drives FPS in the human gut. Here, we analyzed FPS by laser diffraction across a total of 76 individuals and found FPS to be strongly individualized. Surprisingly, a behavioral intervention with 41 volunteers designed to increase chewing efficiency did not impact FPS. Dietary patterns could also not be associated with FPS. Instead, we found evidence that mammalian and human gut microbiomes shaped FPS. Fecal samples from germ-free and antibiotic-treated mice exhibited increased FPS relative to colonized mice. In humans, markers of longer transit time were correlated with smaller FPS. Gut microbiota diversity and composition were also associated with FPS. Finally, ex vivo culture experiments using human fecal microbiota from distinct donors showed that differences in microbiota community composition can drive variation in particle size. Together, our results support an ecological model in which the human gut microbiome plays a key role in reducing the size of food particles during digestion, and that the microbiomes of individuals vary in this capacity. These new insights also suggest FPS in humans to be governed by processes beyond those found in other mammals and emphasize the importance of gut microbiota in shaping their own abiotic environment.},
}
@article {pmid38711157,
year = {2024},
author = {Jurburg, SD and Blowes, SA and Shade, A and Eisenhauer, N and Chase, JM},
title = {Synthesis of recovery patterns in microbial communities across environments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {79},
pmid = {38711157},
issn = {2049-2618},
support = {FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Microbiota ; *Soil Microbiology ; *Bayes Theorem ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; Mammals/microbiology ; Biodiversity ; Water Microbiology ; },
abstract = {BACKGROUND: Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns.<br><br>RESULTS: To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50&#xa0;days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle.<br><br>CONCLUSIONS: This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract.},
}
@article {pmid38710359,
year = {2024},
author = {Lambert, S and Vercauteren, M and Catarino, AI and Li, Y and Van Landuyt, J and Boon, N and Everaert, G and De Rijcke, M and Janssen, CR and Asselman, J},
title = {Aerosolization of micro- and nanoplastics via sea spray: Investigating the role of polymer type, size, and concentration, and potential implications for human exposure.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {351},
number = {},
pages = {124105},
doi = {10.1016/j.envpol.2024.124105},
pmid = {38710359},
issn = {1873-6424},
mesh = {*Aerosols ; Humans ; *Microplastics/analysis ; *Seawater/chemistry ; *Plastics ; *Particle Size ; Polymers/chemistry ; Air Pollutants/analysis ; Inhalation Exposure/statistics &amp; numerical data ; Environmental Monitoring/methods ; Environmental Exposure ; Nanoparticles ; },
abstract = {Micro- and nanoplastics (MNPs) can enter the atmosphere via sea spray aerosols (SSAs), but the effects of plastic characteristics on the aerosolization process are unclear. Furthermore, the importance of the transport of MNPs via these SSAs as a possible new exposure route for human health remains unknown. The aim of this study was two-fold: (1) to examine if a selection of factors affects aerosolization processes of MNPs, and (2) to estimate human exposure to MNPs via aerosols inhalation. A laboratory-based bubble bursting mechanism, simulating the aerosolization process at sea, was used to investigate the influence of MNP as well as seawater characteristics. To determine the potential human exposure to microplastics via inhalation of SSAs, the results of the laboratory experiments were extrapolated to the field based on sea surface microplastic concentrations and the volume of inhaled aerosols. Enrichment seemed to be influenced by MNP size, concentration and polymer type. With higher enrichment for smaller particles and denser polymers. Experiments with different concentrations showed a larger range of variability but nonetheless lower concentrations seemed to result in higher enrichment, presumably due to lower aggregation. In addition to the MNP characteristics, the type of seawater used seemed to influence the aerosolization process. Our human exposure estimate to microplastic via inhalation of sea spray aerosols shows that in comparison with reported inhaled concentrations in urban and indoor environments, this exposure route seems negligible for microplastics. Following the business-as-usual scenario on plastic production, the daily plastic inhalation in coastal areas in 2100 is estimated to increase but remain far below 1 particle per day. This study shows that aerosolization of MNPs is a new plastic transport pathway to be considered, but in terms of human exposure it seems negligible compared to other more important sources of MNPs, based on current reported environmental concentrations.},
}
@article {pmid38708804,
year = {2024},
author = {Burr, DJ and Drauschke, J and Kanevche, K and Kümmel, S and Stryhanyuk, H and Heberle, J and Perfumo, A and Elsaesser, A},
title = {Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {20},
number = {36},
pages = {e2400289},
doi = {10.1002/smll.202400289},
pmid = {38708804},
issn = {1613-6829},
support = {462858357//Deutsche Forschungsgemeinschaft/ ; Freigeist//Volkswagen Foundation/ ; 50WB1623//Bundesministerium f&#xfc;r Wirtschaft und Energie/ ; 50WB2023//Bundesministerium f&#xfc;r Wirtschaft und Energie/ ; },
mesh = {Spectroscopy, Fourier Transform Infrared/methods ; *Carbon Isotopes/chemistry ; Microscopy, Atomic Force ; Isotope Labeling/methods ; Nanotechnology/methods ; Escherichia coli/metabolism/growth &amp; development ; Glucose/metabolism ; },
abstract = {This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of [13]C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of [13]C-[13]C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.},
}
@article {pmid38707845,
year = {2024},
author = {Rivas-Santisteban, J and Yubero, P and Robaina-Estévez, S and González, JM and Tamames, J and Pedrós-Alió, C},
title = {Quantifying microbial guilds.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae042},
pmid = {38707845},
issn = {2730-6151},
abstract = {The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.},
}
@article {pmid38706006,
year = {2024},
author = {Liew, KJ and Shahar, S and Shamsir, MS and Shaharuddin, NB and Liang, CH and Chan, KG and Pointing, SB and Sani, RK and Goh, KM},
title = {Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {29},
pmid = {38706006},
issn = {2524-6372},
support = {FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; 4J549//UTM QuickWin grant/ ; 4J549//UTM QuickWin grant/ ; T2EP30123-0028//Singapore Ministry of Education ARC Tier 2 fund/ ; 1736255, 1849206, and 1920954//National Science Foundation/ ; },
abstract = {BACKGROUND: Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism.<br><br>RESULTS: Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures.<br><br>CONCLUSIONS: This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.},
}
@article {pmid38705066,
year = {2024},
author = {Shao, YH and Wu, JH and Chen, HW},
title = {Comammox Nitrospira cooperate with anammox bacteria in a partial nitritation-anammox membrane bioreactor treating low-strength ammonium wastewater at high loadings.},
journal = {Water research},
volume = {257},
number = {},
pages = {121698},
doi = {10.1016/j.watres.2024.121698},
pmid = {38705066},
issn = {1879-2448},
mesh = {*Bioreactors/microbiology ; *Wastewater/microbiology ; *Ammonium Compounds/metabolism ; Bacteria/metabolism ; Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; },
abstract = {Research has revealed that comammox Nitrospira and anammox bacteria engage in dynamic interactions in partial nitritation-anammox reactors, where they compete for ammonium and nitrite or comammox Nitrospria supply nitrite to anammox bacteria. However, two gaps in the literature are present: the know-how to manipulate the interactions to foster a stable and symbiotic relationship and the assessment of how effective this partnership is for treating low-strength ammonium wastewater at high hydraulic loads. In this study, we employed a membrane bioreactor designed to treat synthetic ammonium wastewater at a concentration of 60 mg N/L, reaching a peak loading of 0.36 g N/L/day by gradually reducing the hydraulic retention time to 4 hr. Throughout the experiment, the reactor achieved an approximately 80 % nitrogen removal rate through strategically adjusting intermittent aeration at every stage. Notably, the genera Ca. Kuenena, Nitrosomonas, and Nitrospira collectively constituted approximately 40 % of the microbial community. Under superior intermittent aeration conditions, the expression of comammox amoA was consistently higher than that of Nitrospira nxrB and AOB amoA in the biofilm, despite the higher abundance of Nitrosomonas than comammox Nitrospira, implying that the biofilm environment is favorable for fostering cooperation between comammox and anammox bacteria. We then assessed the in situ activity of comammox Nitrospira in the reactor by selectively suppressing Nitrosomonas using 1-octyne, thereby confirming that comammox Nitrospira played the primary role in facilitating the nitritation (33.1 % of input ammonium) rather than complete nitrification (7.3 % of input ammonium). Kinetic analysis revealed a specific ammonia-oxidizing rate 5.3 times higher than the nitrite-oxidizing rate in the genus Nitrospira, underscoring their critical role in supplying nitrite. These findings provide novel insights into the cooperative interplay between comammox Nitrospira and anammox bacteria, potentially reshaping the management of nitrogen cycling in engineered environments, and aiding the development of microbial ecology-driven wastewater treatment technologies.},
}
@article {pmid38703220,
year = {2024},
author = {Zhao, L and Zhang, S and Xiao, R and Zhang, C and Lyu, Z and Zhang, F},
title = {Diversity and Functionality of Bacteria Associated with Different Tissues of Spider Heteropoda venatoria Revealed through Integration of High-Throughput Sequencing and Culturomics Approaches.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {67},
pmid = {38703220},
issn = {1432-184X},
mesh = {Animals ; *Spiders/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing ; *RNA, Ribosomal, 16S/genetics ; Female ; Gastrointestinal Microbiome ; Humans ; Phylogeny ; Biodiversity ; Anti-Bacterial Agents/pharmacology ; Pesticides ; },
abstract = {Spiders host a diverse range of bacteria in their guts and other tissues, which have been found to play a significant role in their fitness. This study aimed to investigate the community diversity and functional characteristics of spider-associated bacteria in four tissues of Heteropoda venatoria using HTS of the 16S rRNA gene and culturomics technologies, as well as the functional verification of the isolated strains. The results of HTS showed that the spider-associated bacteria in different tissues belonged to 34 phyla, 72 classes, 170 orders, 277 families, and 458 genera. Bacillus was found to be the most abundant bacteria in the venom gland, silk gland, and ovary, while Stenotrophomonas, Acinetobacter, and Sphingomonas were dominant in the gut microbiota. Based on the amplicon sequencing results, 21 distinct cultivation conditions were developed using culturomics to isolate bacteria from the ovary, gut, venom gland, and silk gland. A total of 119 bacterial strains, representing 4 phyla and 25 genera, with Bacillus and Serratia as the dominant genera, were isolated. Five strains exhibited high efficiency in degrading pesticides in the in vitro experiments. Out of the 119 isolates, 28 exhibited antibacterial activity against at least one of the tested bacterial strains, including the pathogenic bacteria Staphylococcus aureus, Acinetobacter baumanii, and Enterococcus faecalis. The study also identified three strains, GL312, PL211, and PL316, which exhibited significant cytotoxicity against MGC-803. The crude extract from the fermentation broth of strain PL316 was found to effectively induce apoptosis in MGC-803 cells. Overall, this study offers a comprehensive understanding of the bacterial community structure associated with H. venatoria. It also provides valuable insights into discovering novel antitumor natural products for gastric cancer and xenobiotic-degrading bacteria of spiders.},
}
@article {pmid38702804,
year = {2024},
author = {Das, R and Mishra, P and Mishra, B and Jha, R},
title = {Effect of in ovo feeding of xylobiose and xylotriose on plasma immunoglobulin, cecal metabolites production, microbial ecology, and metabolic pathways in broiler chickens.},
journal = {Journal of animal science and biotechnology},
volume = {15},
number = {1},
pages = {62},
pmid = {38702804},
issn = {1674-9782},
abstract = {BACKGROUND: Dietary supplementation of xylooligosaccharides (XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites. But no study investigated and compared the effect of in ovo feeding of xylobiose (XOS2) and xylotriose (XOS3) in chickens. This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens. A total of 144 fertilized chicken eggs were divided into three groups: a) non-injected control (CON), b) XOS2, and c) XOS3. On the 17[th] embryonic day, the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac. After hatching, the chicks were raised for 21 d. Blood was collected on d 14 to measure plasma immunoglobulin. Cecal digesta were collected for measuring short-chain fatty acids (SCFA) on d 14 and 21, and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21.<br><br>RESULTS: The results were considered significantly different at P&#x2009;<&#x2009;0.05. ELISA quantified plasma IgA and IgG on d 14 chickens, revealing no differences among the treatments. Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d&#xa0;21. However, the SCFA concentrations were lower in the XOS3 than in the CON group on d 21. The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7, and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON. There was a reduction in the relative abundance of genus Clostridium sensu stricto&#xa0;1&#xa0;in the XOS2 compared to the CON on d 7 and the genus Ruminococcus torques in both XOS2 and XOS3 groups compared to the CON on d 21. The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation I and L-histidine degradation I pathways, which contribute to improved gut health, respectively, in the microbiome on d 7. In contrast, on d 21, the XOS2 and XOS3 groups enriched the thiamin salvage II, L-isoleucine biosynthesis IV, and O-antigen building blocks biosynthesis (E. coli) pathways, which are indicative of improved gut health. Unlike the XOS3 and CON, the microbiome enriched the pathways associated with energy enhancement, including flavin biosynthesis I, sucrose degradation III, and Calvin-Benson-Bassham cycle pathways, in the XOS2 group on d 21.<br><br>CONCLUSION: In ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels. The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups. The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.},
}
@article {pmid38700528,
year = {2024},
author = {Purahong, W and Ji, L and Wu, YT},
title = {Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {66},
pmid = {38700528},
issn = {1432-184X},
support = {MOST 107-2311-B-020-002//Ministry of Science and Technology, Taiwan/ ; },
mesh = {*Mycobiome ; *Wood/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Forests ; Tropical Climate ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Biodiversity ; },
abstract = {Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.},
}
@article {pmid38700397,
year = {2024},
author = {Havlena, ZE and Hose, LD and DuChene, HR and Baker, GM and Powell, JD and Labrado, AL and Brunner, B and Jones, DS},
title = {Origin and modern microbial ecology of secondary mineral deposits in Lehman Caves, Great Basin National Park, NV, USA.},
journal = {Geobiology},
volume = {22},
number = {3},
pages = {e12594},
doi = {10.1111/gbi.12594},
pmid = {38700397},
issn = {1472-4669},
support = {80NSSC20K0619//NASA Exobiology/ ; //Rocky Mountain Association of Geologists/ ; },
mesh = {*Caves/microbiology ; *Minerals/analysis ; *Bacteria/classification/metabolism ; Nevada ; Archaea/metabolism ; Geologic Sediments/microbiology/chemistry ; Parks, Recreational ; RNA, Ribosomal, 16S/genetics ; Sulfuric Acids ; Phylogeny ; Microbiota ; Calcium Sulfate/chemistry ; Microscopy, Electron, Scanning ; },
abstract = {Lehman Caves is an extensively decorated high desert cave that represents one of the main tourist attractions in Great Basin National Park, Nevada. Although traditionally considered a water table cave, recent studies identified abundant speleogenetic features consistent with a hypogenic and, potentially, sulfuric acid origin. Here, we characterized white mineral deposits in the Gypsum Annex (GA) passage to determine whether these secondary deposits represent biogenic minerals formed during sulfuric acid corrosion and explored microbial communities associated with these and other mineral deposits throughout the cave. Powder X-ray diffraction (pXRD), scanning electron microscopy with electron dispersive spectroscopy (SEM-EDS), and electron microprobe analyses (EPMA) showed that, while most white mineral deposits from the GA contain gypsum, they also contain abundant calcite, silica, and other phases. Gypsum and carbonate-associated sulfate isotopic values of these deposits are variable, with δ[34]SV-CDT between +9.7‰ and +26.1‰, and do not reflect depleted values typically associated with replacement gypsum formed during sulfuric acid speleogenesis. Petrographic observations show that the sulfates likely co-precipitated with carbonate and SiO2 phases. Taken together, these data suggest that the deposits resulted from later-stage meteoric events and not during an initial episode of sulfuric acid speleogenesis. Most sedimentary and mineral deposits in Lehman Caves have very low microbial biomass, with the exception of select areas along the main tour route that have been impacted by tourist traffic. High-throughput 16S rRNA gene amplicon sequencing showed that microbial communities in GA sediments are distinct from those in other parts of the cave. The microbial communities that inhabit these oligotrophic secondary mineral deposits include OTUs related to known ammonia-oxidizing Nitrosococcales and Thaumarchaeota, as well as common soil taxa such as Acidobacteriota and Proteobacteria. This study reveals microbial and mineralogical diversity in a previously understudied cave and expands our understanding of the geomicrobiology of desert hypogene cave systems.},
}
@article {pmid38697936,
year = {2024},
author = {Nair, GR and Kooverjee, BB and de Scally, S and Cowan, DA and Makhalanyane, TP},
title = {Changes in nutrient availability substantially alter bacteria and extracellular enzymatic activities in Antarctic soils.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {6},
pages = {},
pmid = {38697936},
issn = {1574-6941},
support = {UID 110717//National Research Foundation of South Africa/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Nitrogen/metabolism ; *Bacteria/genetics/enzymology/metabolism ; *Nutrients/metabolism ; *Soil/chemistry ; *Microbiota ; *Carbon/metabolism ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting in meltwater run-off and the mobilization of surface nutrients. Yet, the short-term effects of altered nutrient regimes on the diversity and function of soil microbiota in polyextreme environments such as Antarctica, remains poorly understood. We studied these effects by constructing soil microcosms simulating augmented carbon, nitrogen, and moisture. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatments. Other treatments led to a shift in the relative abundances of these microbial assemblages although the distributional patterns were random. Only nitrogen treatment appeared to lead to distinct community structural patterns, with increases in abundance of Proteobacteria (Gammaproteobateria) and a decrease in Verrucomicrobiota (Chlamydiae and Verrucomicrobiae).The effects of extracellular enzyme activities and soil parameters on changes in microbial taxa were also significant following nitrogen addition. Structural equation modeling revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms, supporting evidence of microbial resilience to nutrient increases. In contrast with studies suggesting that these communities may be resistant to change, Antarctic soil microbiota responded rapidly to augmented nutrient regimes.},
}
@article {pmid38697548,
year = {2024},
author = {Hendry, MJ and Kirk, L and Warner, J and Shaw, S and Peyton, BM and Schmeling, E and Barbour, SL},
title = {Selenate bioreduction in a large in situ field trial.},
journal = {The Science of the total environment},
volume = {933},
number = {},
pages = {172869},
doi = {10.1016/j.scitotenv.2024.172869},
pmid = {38697548},
issn = {1879-1026},
mesh = {*Water Pollutants, Chemical/metabolism/analysis ; *Selenic Acid/metabolism ; *Biodegradation, Environmental ; British Columbia ; Coal Mining ; Selenium/metabolism/analysis ; Mining ; },
abstract = {Removing selenium (Se) from mine effluent is a common challenge. A long-term, in situ experiment was conducted to bioremediate large volumes (up to 7500 m[c] d[-1]) of Se(VI)-contaminated water (mean 87 μg L[-1]) by injecting the water into a saturated waste rock fill (SRF) at a coal mining operation in Elk Valley, British Columbia, Canada. To stimulate/maintain biofilm growth in the SRF, labile organic carbon (methanol) and nutrients were added to the water prior to its injection. A conservative tracer (Br[-]) was also added to track the migration of injected water across the SRF, identify wells with minimal dilution and used to quantify the extent of bioreduction. The evolution of the Se species through the SRF was monitored in time and space for 201 d. Selenium concentrations of <3.8 μg L[-1] were attained in monitoring wells located 38 m from the injection wells after 114 to 141 d of operation. Concentrations of Se species in water samples from complementary long-term (351-498 d) column experiments using influent Se(VI) concentrations of 1.0 mg L[-1] were consistent with the results of the in situ experiment. Solid samples collected at the completion of the column experiments confirmed the presence of indigenous Se-reducing bacteria and that the sequestered Se was present as insoluble Se(0), likely in Se-S ring compounds. Based on the success of this ongoing bioremediation experiment, this technology is being applied at other mine sites.},
}
@article {pmid38696469,
year = {2024},
author = {Freilich, MA and Poirier, C and Dever, M and Alou-Font, E and Allen, J and Cabornero, A and Sudek, L and Choi, CJ and Ruiz, S and Pascual, A and Farrar, JT and Johnston, TMS and D'Asaro, EA and Worden, AZ and Mahadevan, A},
title = {3D intrusions transport active surface microbial assemblages to the dark ocean.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {19},
pages = {e2319937121},
pmid = {38696469},
issn = {1091-6490},
support = {N00014-16-1-3130//DOD | USN | Office of Naval Research (ONR)/ ; GBMF 3788//Gordon and Betty Moore Foundation (GBMF)/ ; Dimensions 2230811//National Science Foundation (NSF)/ ; N/A//DOD | National Defense Science and Engineering Graduate (NDSEG)/ ; Martin Fellowship//MIT | Environmental Solutions Initiative, Massachusetts Institute of Technology (ESI)/ ; Montrym Fund//MIT | Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology (EAPS, MIT)/ ; N00014-18-1-2416//DOD | USN | Office of Naval Research (ONR)/ ; N00014-18-1-2139//DOD | USN | Office of Naval Research (ONR)/ ; N00014-18-1-2431//DOD | USN | Office of Naval Research (ONR)/ ; },
mesh = {*Seawater/microbiology/chemistry ; *Bacteria/metabolism ; *Oceans and Seas ; Carbon/metabolism ; Carbon Cycle ; Chlorophyll/metabolism ; Ecosystem ; Phytoplankton/metabolism ; Seasons ; Biomass ; Microbiota/physiology ; Oxygen/metabolism ; },
abstract = {Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.},
}
@article {pmid38695873,
year = {2024},
author = {Roh, H and Kannimuthu, D},
title = {Genomic and Transcriptomic Diversification of Flagellin Genes Provides Insight into Environmental Adaptation and Phylogeographic Characteristics in Aeromonas hydrophila.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {65},
pmid = {38695873},
issn = {1432-184X},
mesh = {*Flagellin/genetics ; *Aeromonas hydrophila/genetics/physiology ; *Transcriptome ; Phylogeography ; Adaptation, Physiological/genetics ; Phylogeny ; Biofilms/growth &amp; development ; },
abstract = {Aeromonas hydrophila is an opportunistic motile pathogen with a broad host range, infecting both terrestrial and aquatic animals. Environmental and geographical conditions exert selective pressure on both geno- and phenotypes of pathogens. Flagellin, directly exposed to external environments and containing important immunogenic epitopes, may display significant variability in response to external conditions. In this study, we conducted a comparative analysis of ~ 150 A. hydrophila genomes, leading to the identification of six subunits of the flagellin gene (fla-1 to fla-4, flaA, and flaB). Individual strains harbored different composition of flagellin subunits and copies. The composition of subunits showed distinct patterns depending on environmental sources. Strains from aquatic environments were mainly comprised of fla-1 to fla-4 subunits, while terrestrial strains predominated in groups harboring flaA and flaB subunits. Each flagellin showed varying levels of expression, with flaA and flaB demonstrating significantly higher expression compared to others. One of the chemotaxis pathways that control flagellin movement through a two-component system was significantly upregulated in flaA(+ 1)/flaB(+ 1) group, whereas flaA and flaB showed different transcriptomic expressions. The genes positively correlated with flaA expression were relevant to biofilm formation and bacterial chemotaxis, but flaB showed a negative correlation with the genes in ABC transporters and quorum sensing pathway. However, the expression patterns of fla-2 to fla-4 were identical. This suggests various types of flagellin subunits may have different biological functions. The composition and expression levels of flagellin subunits could provide valuable insights into the adaptation of A. hydrophila and the differences among strains in response to various external environments.},
}
@article {pmid38694807,
year = {2024},
author = {Sumithra, TG and Sharma, SRK and Suresh, G and Gop, AP and Surya, S and Gomathi, P and Anil, MK and Sajina, KA and Reshma, KJ and Ebeneezar, S and Narasimapallavan, I and Gopalakrishnan, A},
title = {Mechanistic insights into the early life stage microbiota of silver pompano (Trachinotus blochii).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1356828},
pmid = {38694807},
issn = {1664-302X},
abstract = {INTRODUCTION: Deep investigations of host-associated microbiota can illuminate microbe-based solutions to improve production in an unprecedented manner. The poor larval survival represents the critical bottleneck in sustainable marine aquaculture practices. However, little is known about the microbiota profiles and their governing eco-evolutionary processes of the early life stages of marine teleost, impeding the development of suitable beneficial microbial management strategies. The study provides first-hand mechanistic insights into microbiota and its governing eco-evolutionary processes in early life stages of a tropical marine teleost model, Trachinotus blochii.<br><br>METHODS: The microbiota profiles and their dynamics from the first day of hatching till the end of metamorphosis and that of fingerling's gut during the routine hatchery production were studied using 16S rRNA amplicon-based high-throughput sequencing. Further, the relative contributions of various external factors (rearing water, live feed, microalgae, and formulated feed) to the microbiota profiles at different ontogenies was also analyzed.<br><br>RESULTS: A less diverse but abundant core microbial community (~58% and 54% in the whole microbiota and gut microbiota, respectively) was observed throughout the early life stages, supporting 'core microbiota' hypothesis. Surprisingly, there were two well-differentiated clusters in the whole microbiota profiles, &#x2264;10 DPH (days post-hatching) and&#x2009;>&#x2009;10 DPH samples. The levels of microbial taxonomic signatures of stress indicated increased stress in the early stages, a possible explanation for increased mortality during early life stages. Further, the results suggested an adaptive mechanism for establishing beneficial strains along the ontogenetic progression. Moreover, the highly transient microbiota in the early life stages became stable along the ontogenetic progression, hypothesizing that the earlier life stages will be the best window to influence the microbiota. The egg microbiota also crucially affected the microbial community. Noteworthily, both water and the feed microbiota significantly contributed to the early microbiota, with the feed microbiota having a more significant contribution to fish microbiota. The results illustrated that rotifer enrichment would be the optimal medium for the early larval microbiota manipulations.<br><br>CONCLUSION: The present study highlighted the crucial foundations for the microbial ecology of T. blochii during early life stages with implications to develop suitable beneficial microbial management strategies for sustainable mariculture production.},
}
@article {pmid38694752,
year = {2024},
author = {Brame, JE and Liddicoat, C and Abbott, CA and Edwards, RA and Robinson, JM and Gauthier, NE and Breed, MF},
title = {The macroecology of butyrate-producing bacteria via metagenomic assessment of butyrate production capacity.},
journal = {Ecology and evolution},
volume = {14},
number = {5},
pages = {e11239},
pmid = {38694752},
issn = {2045-7758},
abstract = {Butyrate-producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short-chain fatty acid butyrate. However, the macroecological influences on their biogeographical distribution remain poorly resolved. Here we aimed to characterise their global distribution together with key explanatory climatic, geographical and physicochemical variables. We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic (n = 13,078) and Australia-wide soil 16S rRNA (n = 1331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations. The highest median BPC scores were found in anoxic and fermentative environments, including the human (BPC = 2.99) and non-human animal gut (BPC = 2.91), and in some plant-soil systems (BPC = 2.33). Within plant-soil systems, roots (BPC = 2.50) and rhizospheres (BPC = 2.34) had the highest median BPC scores. Among soil samples, geographical and climatic variables had the strongest overall effects on BPC scores (variable importance score range = 0.30-0.03), with human population density also making a notable contribution (variable importance score = 0.20). Higher BPC scores were in soils from seasonally productive sandy rangelands, temperate rural residential areas and sites with moderate-to-high soil iron concentrations. Abundances of butyrate-producing bacteria in outdoor soils followed complex ecological patterns influenced by geography, climate, soil chemistry and hydrological fluctuations. These new macroecological insights further our understanding of the ecological patterns of outdoor butyrate-producing bacteria, with implications for emerging microbially focused ecological and human health policies.},
}
@article {pmid38691424,
year = {2024},
author = {Xiong, X and Othmer, HG and Harcombe, WR},
title = {Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38691424},
issn = {1751-7370},
support = {R01 GM121498/GM/NIGMS NIH HHS/United States ; R01-GM121498/NH/NIH HHS/United States ; },
mesh = {*Escherichia coli/drug effects/genetics/growth &amp; development ; *Anti-Bacterial Agents/pharmacology ; *Symbiosis ; *Salmonella enterica/drug effects/genetics ; Coculture Techniques ; Microbial Interactions ; Ampicillin/pharmacology ; Drug Resistance, Bacterial ; },
abstract = {Antibiotic persistence (heterotolerance) allows a subpopulation of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity. Tracking ampicillin-induced death for bacteria on agar surfaces, we found that E. coli forms up to 55 times more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence of S. enterica, the presence of cross-feeding, average nutrient starvation, or spontaneous resistant mutations. Time-series fluorescent microscopy revealed increased cell-to-cell variation in E. coli lag time in the mutualistic co-culture. Furthermore, we discovered that an E. coli cell can survive antibiotic killing if the nearby S. enterica cells on which it relies die first. In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially structured interactions during antibiotic treatment and understanding microbial community resilience more broadly.},
}
@article {pmid38691215,
year = {2024},
author = {Tokash-Peters, AG and Niyonzima, JD and Kayirangwa, M and Muhayimana, S and Tokash, IW and Jabon, JD and Lopez, SG and Kearns, PJ and Woodhams, DC},
title = {Mosquito Microbiomes of Rwanda: Characterizing Mosquito Host and Microbial Communities in the Land of a Thousand Hills.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {64},
pmid = {38691215},
issn = {1432-184X},
support = {DGE 1249946//Directorate for Biological Sciences/ ; 1950051//Directorate for Biological Sciences/ ; 1947684//National Science Foundation/ ; 1947684//National Science Foundation/ ; },
mesh = {Rwanda ; Animals ; *Microbiota ; *Culicidae/microbiology ; *Wolbachia/genetics/isolation &amp; purification/classification ; *Bacteria/classification/genetics/isolation &amp; purification ; Mosquito Vectors/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Serratia/genetics/isolation &amp; purification/classification ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Mosquitoes are a complex nuisance around the world and tropical countries bear the brunt of the burden of mosquito-borne diseases. Rwanda has had success in reducing malaria and some arboviral diseases over the last few years, but still faces challenges to elimination. By building our understanding of in situ mosquito communities in Rwanda at a disturbed, human-occupied site and at a natural, preserved site, we can build our understanding of natural mosquito microbiomes toward the goal of implementing novel microbial control methods. Here, we examined the composition of collected mosquitoes and their microbiomes at two diverse sites using Cytochrome c Oxidase I sequencing and 16S V4 high-throughput sequencing. The majority (36 of 40 species) of mosquitoes captured and characterized in this study are the first-known record of their species for Rwanda but have been characterized in other nations in East Africa. We found significant differences among mosquito genera and among species, but not between mosquito sexes or catch method. Bacteria of interest for arbovirus control, Asaia, Serratia, and Wolbachia, were found in abundance at both sites and varied greatly by species.},
}
@article {pmid38691135,
year = {2024},
author = {Salem, MA and Nour El-Din, HT and Hashem, AM and Aziz, RK},
title = {Genome-Scale Investigation of the Regulation of azoR Expression in Escherichia coli Using Computational Analysis and Transposon Mutagenesis.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {63},
pmid = {38691135},
issn = {1432-184X},
mesh = {*DNA Transposable Elements/genetics ; *Gene Expression Regulation, Bacterial ; *Escherichia coli Proteins/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; *Nitroreductases/genetics/metabolism ; NADH, NADPH Oxidoreductases/genetics/metabolism ; Mutagenesis ; Genome, Bacterial ; Computational Biology ; Mutagenesis, Insertional ; },
abstract = {Bacterial azoreductases are enzymes that catalyze the reduction of ingested or industrial azo dyes. Although azoreductase genes have been well identified and characterized, the regulation of their expression has not been systematically investigated. To determine how different factors affect the expression of azoR, we extracted and analyzed transcriptional data from the Gene Expression Omnibus (GEO) resource, then confirmed computational predictions by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results showed that azoR expression was lower with higher glucose concentration, agitation speed, and incubation temperature, but higher at higher culture densities. Co-expression and clustering analysis indicated ten genes with similar expression patterns to azoR: melA, tpx, yhbW, yciK, fdnG, fpr, nfsA, nfsB, rutF, and chrR (yieF). In parallel, constructing a random transposon library in E. coli K-12 and screening 4320 of its colonies for altered methyl red (MR)-decolorizing activity identified another set of seven genes potentially involved in azoR regulation. Among these genes, arsC, relA, plsY, and trmM were confirmed as potential azoR regulators based on the phenotypic decolorization activity of their transposon mutants, and the expression of arsC and relA was confirmed, by qRT-PCR, to significantly increase in E. coli K-12 in response to different MR concentrations. Finally, the significant decrease in azoR transcription upon transposon insertion in arsC and relA (as compared to its expression in wild-type E. coli) suggests their probable involvement in azoR regulation. In conclusion, combining in silico analysis and random transposon mutagenesis suggested a set of potential regulators of azoR in E. coli.},
}
@article {pmid38690316,
year = {2024},
author = {Rivera-Lopez, EO and Nieves-Morales, R and Melendez-Martinez, G and Paez-Diaz, JA and Rodriguez-Carrio, SM and Rodriguez-Ramos, J and Morales-Valle, L and Rios-Velazquez, C},
title = {Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing.},
journal = {Data in brief},
volume = {54},
number = {},
pages = {110421},
pmid = {38690316},
issn = {2352-3409},
abstract = {The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.},
}
@article {pmid38688974,
year = {2024},
author = {Morigasaki, S and Matsui, M and Ohtsu, I and Doi, Y and Kawano, Y and Nakai, R and Iwasaki, W and Hayashi, H and Takaya, N},
title = {Temporal and fertilizer-dependent dynamics of soil bacterial communities in buckwheat fields under long-term management.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9896},
pmid = {38688974},
issn = {2045-2322},
support = {JP19H05688//Japan Society for the Promotion of Science/ ; JP19H05683//Japan Society for the Promotion of Science/ ; JP19H05679//Japan Society for the Promotion of Science/ ; },
mesh = {*Fagopyrum ; *Soil Microbiology ; *Fertilizers ; *Bacteria/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; Microbiota ; Nitrogen/metabolism/analysis ; Agriculture/methods ; },
abstract = {This study integrated bacterial community and soil chemicals to characterize the soil ecosystem in an open upland field managed by six controlled fertilizer programs using the minimum amount of pesticides. Amplicon sequencing the 16S rRNA gene revealed that inorganic nitrogen fertilizer and compost altered the diversity and structure of the soil bacterial community throughout buckwheat (Fagopyrum esculentum Moench 'Hitachiakisoba') cultivation. The bacterial community comprised three clusters that contained bacteria that are prevalent in soils fertilized with nitrogen (cluster 1, 340 taxa), without nitrogen and compost (cluster 2, 234 taxa), and with compost-fertilized (cluster 3, 296 taxa). Cluster 2 contained more taxa in Actinobacteriota and less in Acidobacteriota, and cluster 3 contained more taxa in Gemmatimonadota compared with the other clusters. The most frequent taxa in cluster 1 were within the Chloroflexi phylum. The bacterial community structure correlated with soil chemical properties including pH, total organic carbon, SO4[2-], soluble Ca[2+]. A co-occurrence network of bacterial taxa and chemicals identified key bacterial groups comprising the center of a community network that determined topology and dynamics of the network. Temporal dynamics of the bacterial community structure indicated that Burkholderiales were associated with buckwheat ripening, indicating plant-bacteria interaction in the ecosystem.},
}
@article {pmid38688113,
year = {2024},
author = {Ghani, MI and Yi, B and Rehmani, MS and Wei, X and Siddiqui, JA and Fan, R and Liu, Y and El-Sheikh, MA and Chen, X and Ahmad, P},
title = {Potential of melatonin and Trichoderma harzianum inoculation in ameliorating salt toxicity in watermelon: Insights into antioxidant system, leaf ultrastructure, and gene regulation.},
journal = {Plant physiology and biochemistry : PPB},
volume = {211},
number = {},
pages = {108639},
doi = {10.1016/j.plaphy.2024.108639},
pmid = {38688113},
issn = {1873-2690},
mesh = {*Citrullus/microbiology/drug effects/metabolism ; *Melatonin/pharmacology ; *Antioxidants/metabolism ; *Plant Leaves/drug effects/metabolism ; *Gene Expression Regulation, Plant/drug effects ; Salt Stress ; Hypocreales ; Photosynthesis/drug effects ; Oxidative Stress/drug effects ; },
abstract = {Melatonin (MT) is an extensively studied biomolecule with dual functions, serving as an antioxidant and a signaling molecule. Trichoderma Harzianum (TH) is widely recognized for its effectiveness as a biocontrol agent against many plant pathogens. However, the interplay between seed priming and MT (150 μm) in response to NaCl (100 mM) and its interaction with TH have rarely been investigated. This study aimed to evaluate the potential of MT and TH, alone and in combination, to mitigate salt stress (SS) in watermelon plants. The findings of this study revealed a significant decline in the morphological, physiological, and biochemical indices of watermelon seedlings exposed to SS. However, MT and TH treatments reduced the negative impact of salt stress. The combined application of MT and TH exerted a remarkable positive effect by increasing the growth, photosynthetic and gas exchange parameters, chlorophyll fluorescence indices, and ion balance (decreasing Na[+] and enhancing K[+]). MT and TH effectively alleviated oxidative injury by inhibiting hydrogen peroxide formation in saline and non-saline environments, as established by reduced lipid peroxidation and electrolyte leakage. Moreover, oxidative injury induced by SS on the cells was significantly mitigated by regulation of the antioxidant system, AsA-GSH-related enzymes, the glyoxalase system, augmentation of osmolytes, and activation of several genes involved in the defense system. Additionally, the reduction in oxidative damage was examined by chloroplast integrity via transmission electron microscopy (TEM). Overall, the results of this study provide a promising contribution of MT and TH in safeguarding the watermelon crop from oxidative damage induced by salt stress.},
}
@article {pmid38685217,
year = {2024},
author = {Liu, Z and Zhang, J and Fan, C and Sun, S and An, X and Sun, Y and Gao, T and Zhang, D},
title = {Influence of Bacillus subtilis strain Z-14 on microbial ecology of cucumber rhizospheric vermiculite infested with fusarium oxysporum f. sp. cucumerinum.},
journal = {Pesticide biochemistry and physiology},
volume = {201},
number = {},
pages = {105875},
doi = {10.1016/j.pestbp.2024.105875},
pmid = {38685217},
issn = {1095-9939},
mesh = {*Fusarium/genetics/physiology ; *Cucumis sativus/microbiology ; *Rhizosphere ; *Bacillus subtilis/genetics/physiology/metabolism ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; Aluminum Silicates ; Plant Roots/microbiology ; },
abstract = {Fusarium oxysporum (FO) is a typical soil-borne pathogenic fungus, and the cucumber wilt disease caused by F. oxysporum f. sp. cucumerinum (FOC) seriously affects crop yield and quality. Vermiculite is increasingly being used as a culture substrate; nevertheless, studies exploring the effectiveness and mechanisms of biocontrol bacteria in this substrate are limited. In this study, vermiculite was used as a culture substrate to investigate the control effect of Bacillus subtilis strain Z-14 on cucumber wilt and the rhizospheric microecology, focusing on colonization ability, soil microbial diversity, and rhizosphere metabolome. Pot experiments showed that Z-14 effectively colonized the cucumber roots, achieving a controlled efficacy of 61.32% for wilt disease. It significantly increased the abundance of Bacillus and the expression of NRPS and PKS genes, while reducing the abundance of FO in the rhizosphere. Microbial diversity sequencing showed that Z-14 reduced the richness and diversity of the rhizosphere bacterial community, increased the richness and diversity of the fungal community, and alleviated the effect of FO on the community structure of the cucumber rhizosphere. The metabolomics analysis revealed that Z-14 affected ABC transporters, amino acid synthesis, and the biosynthesis of plant secondary metabolites. Additionally, Z-14 increased the contents of phenylacetic acid, capsidol, and quinolinic acid, all of which were related to the antagonistic activity in the rhizosphere. Z-14 exhibited a significant control effect on cucumber wilt and influenced the microflora and metabolites in rhizospheric vermiculite, providing a theoretical basis for further understanding the control effect and mechanism of cucumber wilt in different culture substrates.},
}
@article {pmid38684474,
year = {2024},
author = {Cohen, Y and Johnke, J and Abed-Rabbo, A and Pasternak, Z and Chatzinotas, A and Jurkevitch, E},
title = {Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {6},
pages = {},
pmid = {38684474},
issn = {1574-6941},
support = {CH 731/2-1//Deutsche Forschungsgemeinschaft/ ; 1583/12//Israel Science Foundation/ ; },
mesh = {*Sewage/microbiology ; *Microbiota ; *Rivers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Water Microbiology ; Bdellovibrio/genetics/metabolism ; },
abstract = {Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics and functions of the microbial communities in highly sewage-impacted rivers is limited, in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem, we show, using 16S and 18S rRNA gene-based community analysis and targeted qPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Hydrolyzers of organics compounds, as well as nitrogen and phosphorus recyclers were lacking, pointing at reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio and like organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify, while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.},
}
@article {pmid38683238,
year = {2024},
author = {Cowan, DA and Albers, SV and Antranikian, G and Atomi, H and Averhoff, B and Basen, M and Driessen, AJM and Jebbar, M and Kelman, Z and Kerou, M and Littlechild, J and Müller, V and Schönheit, P and Siebers, B and Vorgias, K},
title = {Extremophiles in a changing world.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {2},
pages = {26},
pmid = {38683238},
issn = {1433-4909},
mesh = {*Extremophiles/metabolism/physiology ; Sustainable Development ; Adaptation, Physiological ; Extreme Environments ; Biotechnology ; },
abstract = {Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.},
}
@article {pmid38683223,
year = {2024},
author = {Kunzler, M and Schlechter, RO and Schreiber, L and Remus-Emsermann, MNP},
title = {Hitching a Ride in the Phyllosphere: Surfactant Production of Pseudomonas spp. Causes Co-swarming of Pantoea eucalypti 299R.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {62},
pmid = {38683223},
issn = {1432-184X},
mesh = {*Pantoea/genetics/metabolism/physiology/growth &amp; development ; *Pseudomonas/metabolism/genetics/growth &amp; development/physiology ; *Surface-Active Agents/metabolism ; },
abstract = {Here, we demonstrate the beneficial effect of surfactant-producing pseudomonads on Pantoea eucalypti 299R. We conducted a series of experiments in environments of increasing complexity. P. eucalypti 299R (Pe299R), and Pseudomonas sp. FF1 (Pff1) or Pe299R and surfactant-production deficient Pseudomonas sp. FF1::ΔviscB (Pff1ΔviscB) were co-inoculated in broth, on swarming agar plates, and on plants. In broth, there were no differences in the growth dynamics of Pe299R when growing in the presence of Pff1 or Pff1ΔviscB. By contrast, on swarming agar plates, Pe299R was able to co-swarm with Pff1 which led to a significant increase in Pe299R biomass compared to Pe299R growing with Pff1ΔviscB or in monoculture. Finally in planta, and using the single-cell bioreporter for reproductive success (CUSPER), we found a temporally distinct beneficial effect of Pff1 on co-inoculated Pe299R subpopulations that did not occur in the presence of Pff1ΔviscB. We tested three additional surfactant-producing pseudomonads and their respective surfactant knockout mutants on PE299R on swarming agar showing similar results. This led us to propose a model for the positive effect of surfactant production during leaf colonization. Our results indicate that co-motility might be common during leaf colonization and adds yet another facet to the already manyfold roles of surfactants.},
}
@article {pmid38682902,
year = {2024},
author = {Song, H-S and Lee, N-R and Kessell, AK and McCullough, HC and Park, S-Y and Zhou, K and Lee, D-Y},
title = {Kinetics-based inference of environment-dependent microbial interactions and their dynamic variation.},
journal = {mSystems},
volume = {9},
number = {5},
pages = {e0130523},
pmid = {38682902},
issn = {2379-5077},
support = {2020R1A2C2007192//National Research Foundation of Korea (NRF)/ ; 32136-05-1- HD050//MAFRA | Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET)/ ; //Nebraska Tobacco Settlement Biomedical Research Development Fund (NTSBRDF)/ ; 2125155//National Science Foundation (NSF)/ ; 2021R1F1A1064592//National Research Foundation of Korea (NRF)/ ; },
mesh = {*Microbial Interactions/physiology ; Kinetics ; *Escherichia coli/metabolism ; Models, Biological ; Environment ; },
abstract = {Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental understanding of how microbial interactions are driven by environmental factors, significantly limiting our capability to predict and engineer community dynamics and function. To address this issue, we propose a novel theoretical framework that allows us to represent interspecies interactions as an explicit function of environmental variables (such as substrate concentrations) by combining growth kinetics and a generalized Lotka-Volterra model. A synergistic integration of these two complementary models leads to the prediction of alterations in interspecies interactions as the outcome of dynamic balances between positive and negative influences of microbial species in mixed relationships. The effectiveness of our method was experimentally demonstrated using a synthetic consortium of two Escherichia coli mutants that are metabolically dependent (due to an inability to synthesize essential amino acids) but competitively grow on a shared substrate. The analysis of the E. coli binary consortium using our model not only showed how interactions between the two amino acid auxotrophic mutants are controlled by the dynamic shifts in limiting substrates but also enabled quantifying previously uncharacterizable complex aspects of microbial interactions, such as asymmetry in interactions. Our approach can be extended to other ecological systems to model their environment-dependent interspecies interactions from growth kinetics.IMPORTANCEModeling environment-controlled interspecies interactions through separate identification of positive and negative influences of microbes in mixed relationships is a new capability that can significantly improve our ability to understand, predict, and engineer the complex dynamics of microbial communities. Moreover, the prediction of microbial interactions as a function of environmental variables can serve as valuable benchmark data to validate modeling and network inference tools in microbial ecology, the development of which has often been impeded due to the lack of ground truth information on interactions. While demonstrated against microbial data, the theory developed in this work is readily applicable to general community ecology to predict interactions among macroorganisms, such as plants and animals, as well as microorganisms.},
}
@article {pmid38680790,
year = {2024},
author = {García, FM and Guerrero, SIB and la Peña, CG and Gutiérrez, DRA and Rodríguez, QKS and Herrera, CAM and Paniagua, FV and Velásquez, CD and Montoya, AC and Núñez, LMV},
title = {Bacteria in the blood of healthy stray dogs infested by ticks in northern Mexico.},
journal = {Journal of advanced veterinary and animal research},
volume = {11},
number = {1},
pages = {132-138},
pmid = {38680790},
issn = {2311-7710},
abstract = {OBJECTIVE: The objectives of this study were to determine the richness, abundance, and diversity of bacteria in stray dogs (Canis lupus familiaris) infested by ticks in Comarca Lagunera, northern Mexico, and to establish their pathogenic and or/zoonotic potential.<br><br>MATERIALS AND METHODS: Blood samples from 12 dogs were collected, and their deoxyribonucleic acid was extracted. The V3-V4 region of the 16S ribosomal ribunocleic acid gene was amplified by polymerase chain reaction. Next-generation sequencing (NGS) was performed on a MiSeq Illumina platform, and the data were analyzed using quantitative insights into microbial ecology.<br><br>RESULTS: The operational taxonomic units resulted in 23 phyla, 54 classes, 89 orders, 189 families, 586 genera, and 620 bacterial species; among them, 64 species and/or bacterial genera with pathogenic or zoonotic potential were identified, some of which have been reported in the literature as relevant to public health (Anaplasma phagocytophilum, Brucella spp., Clostridium spp., Corynebacterium affermentants, Cutibacterium spp., Dietzia spp., Ehrlichia canis, Fusobacterium necrophorum, Leptotrichia spp., Mycobacterium spp., Paracoccus spp., and Roseomonas gilardii).<br><br>CONCLUSION: This research offers relevant information on the prevalence of tick-borne diseases as well as other potential zoonotic diseases in the blood of stray dogs parasitized by ticks in northern Mexico. New molecular biology and massive NGS techniques may play an important role in the study and documentation of bacterial profiles from animals in close proximity to humans.},
}
@article {pmid38679176,
year = {2024},
author = {Guo, Z and Ma, XS and Ni, SQ},
title = {Journey of the swift nitrogen transformation: Unveiling comammox from discovery to deep understanding.},
journal = {Chemosphere},
volume = {358},
number = {},
pages = {142093},
doi = {10.1016/j.chemosphere.2024.142093},
pmid = {38679176},
issn = {1879-1298},
mesh = {*Nitrogen/metabolism ; *Ammonia/metabolism ; *Bacteria/metabolism/genetics ; *Oxidation-Reduction ; *Nitrogen Cycle ; Nitrification ; Ecosystem ; },
abstract = {COMplete AMMonia OXidizer (comammox) refers to microorganisms that have the function of oxidizing NH4[+] to NO3[-] alone. The discovery of comammox overturned the two-step theory of nitrification in the past century and triggered many important scientific questions about the nitrogen cycle in nature. This comprehensive review delves into the origin and discovery of comammox, providing a detailed account of its detection primers, clades metabolic variations, and environmental factors. An in-depth analysis of the ecological niche differentiation among ammonia oxidizers was also discussed. The intricate role of comammox in anammox systems and the relationship between comammox and nitrogen compound emissions are also discussed. Finally, the relationship between comammox and anammox is displayed, and the future research direction of comammox is prospected. This review reveals the metabolic characteristics and distribution patterns of comammox in ecosystems, providing new perspectives for understanding nitrogen cycling and microbial ecology. Additionally, it offers insights into the potential application value and prospects of comammox.},
}
@article {pmid38678007,
year = {2024},
author = {Wang, X and Tang, Y and Yue, X and Wang, S and Yang, K and Xu, Y and Shen, Q and Friman, VP and Wei, Z},
title = {The role of rhizosphere phages in soil health.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {5},
pages = {},
pmid = {38678007},
issn = {1574-6941},
support = {2022YFC3501501//National Key Research and Development Program of China/ ; 42325704//National Natural Science Foundation of China/ ; //Nanjing Agricultural University/ ; },
mesh = {*Soil Microbiology ; *Rhizosphere ; *Bacteriophages/genetics ; *Microbiota ; *Bacteria/virology/genetics ; Gene Transfer, Horizontal ; Plants/microbiology/virology ; Ecosystem ; },
abstract = {While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.},
}
@article {pmid38676557,
year = {2024},
author = {Glasl, B and Luter, HM and Damjanovic, K and Kitzinger, K and Mueller, AJ and Mahler, L and Engelberts, JP and Rix, L and Osvatic, JT and Hausmann, B and Séneca, J and Daims, H and Pjevac, P and Wagner, M},
title = {Co-occurring nitrifying symbiont lineages are vertically inherited and widespread in marine sponges.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae069},
pmid = {38676557},
issn = {1751-7370},
support = {T 1218//Austrian Science Fund/ ; },
mesh = {Animals ; *Porifera/microbiology ; *Symbiosis ; *Nitrification ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Phylogeny ; *Ammonia/metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Metagenome ; },
abstract = {Ammonia-oxidizing archaea and nitrite-oxidizing bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification-the aerobic oxidation of ammonia to nitrite and further to nitrate-and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterize two novel nitrifying symbiont lineages, Candidatus Nitrosokoinonia and Candidatus Nitrosymbion in the marine sponge Coscinoderma matthewsi using a combination of molecular tools, in situ visualization, and physiological rate measurements. Both represent a new genus in the ammonia-oxidizing archaeal class Nitrososphaeria and the nitrite-oxidizing bacterial order Nitrospirales, respectively. Furthermore, we show that larvae of this viviparous sponge are densely colonized by representatives of Ca. Nitrosokoinonia and Ca. Nitrosymbion indicating vertical transmission. In adults, the representatives of both symbiont genera are located extracellularly in the mesohyl. Comparative metagenome analyses and physiological data suggest that ammonia-oxidizing archaeal symbionts of the genus Ca. Nitrosokoinonia strongly rely on endogenously produced nitrogenous compounds (i.e. ammonium, urea, nitriles/cyanides, and creatinine) rather than on exogenous ammonium sources taken up by the sponge. Additionally, the nitrite-oxidizing bacterial symbionts of the genus Ca. Nitrosymbion may reciprocally support the ammonia-oxidizers with ammonia via the utilization of sponge-derived urea and cyanate. Comparative analyses of published environmental 16S rRNA gene amplicon data revealed that Ca. Nitrosokoinonia and Ca. Nitrosymbion are widely distributed and predominantly associated with marine sponges and corals, suggesting a broad relevance of our findings.},
}
@article {pmid38675977,
year = {2024},
author = {Król, N and Chitimia-Dobler, L and Dobler, G and Kiewra, D and Czułowska, A and Obiegala, A and Zajkowska, J and Juretzek, T and Pfeffer, M},
title = {Identification of New Microfoci and Genetic Characterization of Tick-Borne Encephalitis Virus Isolates from Eastern Germany and Western Poland.},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
pmid = {38675977},
issn = {1999-4915},
support = {61508669//Pfizer (Germany)/ ; },
mesh = {*Encephalitis Viruses, Tick-Borne/genetics/classification/isolation &amp; purification ; Animals ; Poland ; Germany/epidemiology ; *Phylogeny ; *Encephalitis, Tick-Borne/virology/epidemiology ; Humans ; Ixodes/virology ; },
abstract = {(1) Background: Tick-borne encephalitis (TBE) is the most important tick-borne viral disease in Eurasia, although effective vaccines are available. Caused by the tick-borne encephalitis virus (TBEV, syn. Orthoflavivirus encephalitidis), in Europe, it is transmitted by ticks like Ixodes ricinus and Dermacentor reticulatus. TBEV circulates in natural foci, making it endemic to specific regions, such as southern Germany and northeastern Poland. Our study aimed to identify new TBEV natural foci and genetically characterize strains in ticks in previously nonendemic areas in Eastern Germany and Western Poland. (2) Methods: Ticks were collected from vegetation in areas reported by TBE patients. After identification, ticks were tested for TBEV in pools of a maximum of 10 specimens using real-time RT-PCR. From the positive TBEV samples, E genes were sequenced. (3) Results: Among 8400 ticks from 19 sites, I. ricinus (n = 4784; 56.9%) was predominant, followed by D. reticulatus (n = 3506; 41.7%), Haemaphysalis concinna (n = 108; 1.3%), and I. frontalis (n = 2; <0.1%). TBEV was detected in 19 pools originating in six sites. The phylogenetic analyses revealed that TBEV strains from Germany and Poland clustered with other German strains, as well as those from Finland and Estonia. (4) Conclusions: Although there are still only a few cases are reported from these areas, people spending much time outdoors should consider TBE vaccination.},
}
@article {pmid38674735,
year = {2024},
author = {Isokpehi, RD and Kim, Y and Krejci, SE and Trivedi, VD},
title = {Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
pmid = {38674735},
issn = {2076-2607},
support = {U41 HG006941/HG/NHGRI NIH HHS/United States ; U41HG006941/NH/NIH HHS/United States ; },
abstract = {Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.},
}
@article {pmid38674704,
year = {2024},
author = {Wang, H and Pijl, A and Liu, B and Wamelink, W and Korthals, GW and Costa, OYA and Kuramae, EE},
title = {A Comparison of Different Protocols for the Extraction of Microbial DNA Inhabiting Synthetic Mars Simulant Soil.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
pmid = {38674704},
issn = {2076-2607},
abstract = {Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl radicals through cationic redox cycling may interfere with DNA extraction. This study evaluated different protocols for extracting microbial DNA from Mars Global Simulant (MGS-1), a Mars simulant soil. Two commercial kits were tested: the FastDNA SPIN Kit for soil ("MP kit") and the DNeasy PowerSoil Pro Kit ("PowerSoil kit"). MGS-1 was incubated with living soil for five weeks, and DNA was extracted from aliquots using the kits. After extraction, the DNA was quantified with a NanoDrop spectrophotometer and used as the template for 16S rRNA gene amplicon sequencing and qPCR. The MP kit was the most efficient, yielding approximately four times more DNA than the PowerSoil kit. DNA extracted using the MP kit with 0.5 g soil resulted in 28,642-37,805 16S rRNA gene sequence reads and 30,380-42,070 16S rRNA gene copies, whereas the 16S rRNA gene could not be amplified from DNA extracted using the PowerSoil kit. We suggest that the FastDNA SPIN Kit is the best option for studying microbial communities in Mars simulant soils.},
}
@article {pmid38672854,
year = {2024},
author = {Daval, C and Tran, T and Verdier, F and Martin, A and Alexandre, H and Grandvalet, C and Tourdot-Maréchal, R},
title = {Identification of Key Parameters Inducing Microbial Modulation during Backslopped Kombucha Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {38672854},
issn = {2304-8158},
support = {PO FEDER-FSE Bourgogne 2014/2020//European Regional Development Fund/ ; },
abstract = {The aim of this study was to assess the impact of production parameters on the reproducibility of kombucha fermentation over several production cycles based on backslopping. Six conditions with varying oxygen accessibility (specific interface surface) and initial acidity (through the inoculation rate) of the cultures were carried out and compared to an original kombucha consortium and a synthetic consortium assembled from yeasts and bacteria isolated from the original culture. Output parameters monitored were microbial populations, biofilm weight, key physico-chemical parameters and metabolites. Results highlighted the existence of phases in microbial dynamics as backslopping cycles progressed. The transitions between phases occurred faster for the synthetic consortium compared to the original kombucha. This led to microbial dynamics and fermentative kinetics that were reproducible over several cycles but that could also deviate and shift abruptly to different behaviors. These changes were mainly induced by an increase in the Saccharomyces cerevisiae population, associated with an intensification of sucrose hydrolysis, sugar consumption and an increase in ethanol content, without any significant acceleration in the rate of acidification. The study suggests that the reproducibility of kombucha fermentations relies on high biodiversity to slow down the modulations of microbial dynamics induced by the sustained rhythm of backslopping cycles.},
}
@article {pmid38670213,
year = {2024},
author = {Sun, Y and Du, P and Li, H and Zhou, K and Shou, L and Chen, J and Meng Li, },
title = {Prokaryotic community assembly patterns and nitrogen metabolic potential in oxygen minimum zone of Yangtze Estuary water column.},
journal = {Environmental research},
volume = {252},
number = {Pt 3},
pages = {119011},
doi = {10.1016/j.envres.2024.119011},
pmid = {38670213},
issn = {1096-0953},
mesh = {*Estuaries ; China ; *Nitrogen/metabolism/analysis ; *Oxygen/metabolism/analysis ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S ; Nitrogen Cycle ; },
abstract = {It is predicted that oxygen minimum zones (OMZs) in the ocean will expand as a consequence of global warming and environmental pollution. This will affect the overall microbial ecology and microbial nitrogen cycle. As one of the world's largest alluvial estuaries, the Yangtze Estuary has exhibited a seasonal OMZ since the 1980s. In this study, we have uncovered the microbial composition, the patterns of community assembly and the potential for microbial nitrogen cycling within the water column of the Yangtze Estuary, with a particular focus on OMZ. Based on the 16 S rRNA gene sequencing, a specific spatial variation in the composition of prokaryotic communities was observed for each water layer, with the Proteobacteria (46.1%), Bacteroidetes (20.3%), and Cyanobacteria (10.3%) dominant. Stochastic and deterministic processes together shaped the community assembly in the water column. Further, pH was the most important environmental factor influencing prokaryotic composition in the surface water, followed by silicate, PO4[3-], and distance offshore (p < 0.05). Water depth, NH4[+], and PO4[3-] were the main factors in the bottom water (p < 0.05). At last, species analysis and marker gene annotation revealed candidate nitrogen cycling performers, and a rich array of nitrogen cycling potential in the bottom water of the Yangtze Estuary. The determined physiochemical parameters and potential for nitrogen respiration suggested that organic nitrogen and NO3[-] (or NO2[-]) are the preferred nitrogen sources for microorganisms in the Yangtze Estuary OMZ. These findings are expected to advance research on the ecological responses of estuarine oxygen minimum zones (OMZs) to future global climate perturbations.},
}
@article {pmid38668461,
year = {2024},
author = {Takács, E and Lázár, D and Siakwa, A and Klátyik, S and Mörtl, M and Kocsányi, L and Barócsi, A and Lenk, S and Lengyel, E and Székács, A},
title = {Ecotoxicological Evaluation of Safener and Antimicrobial Additives in Isoxaflutole-Based Herbicide Formulations.},
journal = {Toxics},
volume = {12},
number = {4},
pages = {},
pmid = {38668461},
issn = {2305-6304},
support = {NVKP_16-1-2016-0049//Hungarian National Research, Development and Innovation Office within the National Com-petitiveness and Excellence Program/ ; NKFIH-3524-1/2022//National Research, Development and Innovation Fund by the Hungarian Ministry of Culture and Innovation/ ; TKP2021-NVA-22//Thematic Excellence Program 2021, National Defense, National Security Sub-Program/ ; },
abstract = {The environmental load by isoxaflutole and its formulated herbicide products has increasingly become apparent because, after the ban of atrazine, isoxaflutole has become its replacement active ingredient (a.i.). Obtaining information regarding the fate of this a.i. in environmental matrices and its ecotoxicological effects on aquatic organisms is essential for the risk assessment of the herbicide. In this study, the effects of Merlin Flexx- and Merlin WG75 formulated isoxaflutole-based herbicide products and two selected additives (cyprosulfamide safener and 1,2-benzisothiazol-3(2H)-one antimicrobial agent) were investigated on Raphidocelis subcapitata in growth inhibition assays. In ecotoxicological tests, two conventional (optical density and chlorophyll-a content) and two induced fluorescence-based (Fv*/Fp: efficiency of the photosystem PSII and Rfd* changes in the observed ratio of fluorescence decrease) endpoints were determined by UV-spectrophotometer and by our FluoroMeter Module, respectively. Furthermore, dissipation of isoxaflutole alone and in its formulated products was examined by an HPLC-UV method. In ecotoxicological assays, the fluorescence-based Rfd* was observed as the most sensitive endpoint. In this study, the effects of the safener cyprosulfamide and the antimicrobial agent 1,2-benzisothiazol-3(2H)-one on R. subcapitata is firstly reported. The results indicated that the isoxaflutole-equivalent toxicity of the mixture of the isoxaflutole-safener-antimicrobial agent triggered lower toxicity (EC50 = 2.81 ± 0.22 mg/L) compared to the individual effect of the a.i. (EC50 = 0.02 ± 0.00 mg/L). The Merlin Flexx formulation (EC50 = 27.04 ± 1.41 mg/L) was found to be approximately 50-fold less toxic than Merlin WG75, which can be explained by the different chemical characteristics and quantity of additives in them. The additives influenced the dissipation of the a.i. in Z8 medium, as the DT50 value decreased by approximately 1.2- and 3.5-fold under light and dark conditions, respectively.},
}
@article {pmid38668249,
year = {2024},
author = {Plewa-Tutaj, K and Twarużek, M and Kosicki, R and Soszczyńska, E},
title = {Analysis of Mycotoxins and Cytotoxicity of Airborne Molds Isolated from the Zoological Garden-Screening Research.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
pmid = {38668249},
issn = {2076-0817},
support = {DEC390 2022/06/X/NZ8/00430//National Science Centre, Poland/ ; },
abstract = {OBJECTIVE: The objective of this paper was to assess the airborne mold contamination, secondary metabolite profiles, and cytotoxicity of the dominant fungal species isolated from the air in selected rooms at a Zoological Garden.<br><br>MATERIALS AND METHODS: Fungal concentrations were measured with MAS-100 air samplers. The collected airborne fungi were identified using a combination of morphological and molecular methods. The cytotoxicity of 84 strains belonging to two Penicillium and Aspergillus genera was determined using the quantitative colorimetric MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium salt) assay. The mycotoxins were detected using high-performance liquid chromatography (HPLC) with a mass spectrometry detector.<br><br>RESULTS: The ITS gene was amplified and sequenced to identify the 132 species. For mycotoxicological and cytotoxicity analyses, 52 Penicillium isolates and 32 Aspergillus representatives were selected. Cytotoxicity was confirmed in 97.6% of cases analyzed. Using the LC-MS/MS method, 42 out of 84 strains produced at least one of the following toxins: ochratoxin A, ochratoxin B, patulin, gliotoxin, roquefortine C, griseofulvin, sterigmatocystin, fumonisin B2, moniliformin, and mycophenolic acid.<br><br>CONCLUSIONS: Analytical methods for assessing the presence of mycotoxins in fungal isolates collected directly from the air have proven to be an effective tool. Our research provides new information on the occurrence of potentially toxin-producing molds within a zoo.},
}
@article {pmid38665977,
year = {2023},
author = {Crous, PW and Costa, MM and Kandemir, H and Vermaas, M and Vu, D and Zhao, L and Arumugam, E and Flakus, A and Jurjević, &#x17d; and Kaliyaperumal, M and Mahadevakumar, S and Murugadoss, R and Shivas, RG and Tan, YP and Wingfield, MJ and Abell, SE and Marney, TS and Danteswari, C and Darmostuk, V and Denchev, CM and Denchev, TT and Etayo, J and Gené, J and Gunaseelan, S and Hubka, V and Illescas, T and Jansen, GM and Kezo, K and Kumar, S and Larsson, E and Mufeeda, KT and Piątek, M and Rodriguez-Flakus, P and Sarma, PVSRN and Stryjak-Bogacka, M and Torres-Garcia, D and Vauras, J and Acal, DA and Akulov, A and Alhudaib, K and Asif, M and Balashov, S and Baral, HO and Baturo-Cieśniewska, A and Begerow, D and Beja-Pereira, A and Bianchinotti, MV and Bilański, P and Chandranayaka, S and Chellappan, N and Cowan, DA and Custódio, FA and Czachura, P and Delgado, G and De Silva, NI and Dijksterhuis, J and Dueñas, M and Eisvand, P and Fachada, V and Fournier, J and Fritsche, Y and Fuljer, F and Ganga, KGG and Guerra, MP and Hansen, K and Hywel-Jones, N and Ismail, AM and Jacobs, CR and Jankowiak, R and Karich, A and Kemler, M and Kisło, K and Klofac, W and Krisai-Greilhuber, I and Latha, KPD and Lebeuf, R and Lopes, ME and Lumyong, S and Maciá-Vicente, JG and Maggs-Kölling, G and Magistà, D and Manimohan, P and Martín, MP and Mazur, E and Mehrabi-Koushki, M and Miller, AN and Mombert, A and Ossowska, EA and Patejuk, K and Pereira, OL and Piskorski, S and Plaza, M and Podile, AR and Polhorský, A and Pusz, W and Raza, M and Ruszkiewicz-Michalska, M and Saba, M and Sánchez, RM and Singh, R and Śliwa, L and Smith, ME and Stefenon, VM and Strasiftáková, D and Suwannarach, N and Szczepańska, K and Telleria, MT and Tennakoon, DS and Thines, M and Thorn, RG and Urbaniak, J and van der Vegte, M and Vasan, V and Vila-Viçosa, C and Voglmayr, H and Wrzosek, M and Zappelini, J and Groenewald, JZ},
title = {Fungal Planet description sheets: 1550-1613.},
journal = {Persoonia},
volume = {51},
number = {},
pages = {280-417},
pmid = {38665977},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale insect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps poecilometigena on Poecilometis sp. Bolivia, Lecanora menthoides on sandstone, in open semi-desert montane areas, Sticta monlueckiorum corticolous in a forest, Trichonectria epimegalosporae on apothecia of corticolous Megalospora sulphurata var. sulphurata, Trichonectria puncteliae on the thallus of Punctelia borreri. Brazil, Catenomargarita pseudocercosporicola (incl. Catenomargarita gen. nov.) hyperparasitic on Pseudocercospora fijiensis on leaves of Musa acuminata, Tulasnella restingae on protocorms and roots of Epidendrum fulgens. Bulgaria, Anthracoidea umbrosae on Carex spp. Croatia, Hymenoscyphus radicis from surface-sterilised, asymptomatic roots of Microthlaspi erraticum, Orbilia multiserpentina on wood of decorticated branches of Quercus pubescens. France, Calosporella punctatispora on dead corticated twigs of Aceropalus. French West Indies (Martinique), Eutypella lechatii on dead corticated palm stem. Germany, Arrhenia alcalinophila on loamy soil. Iceland, Cistella blauvikensis on dead grass (Poaceae). India, Fulvifomes maritimus on living Peltophorum pterocarpum, Fulvifomes natarajanii on dead wood of Prosopis juliflora, Fulvifomes subazonatus on trunk of Azadirachta indica, Macrolepiota bharadwajii on moist soil near the forest, Narcissea delicata on decaying elephant dung, Paramyrothecium indicum on living leaves of Hibiscus hispidissimus, Trichoglossum syamviswanathii on moist soil near the base of a bamboo plantation. Iran, Vacuiphoma astragalicola from stem canker of Astragalus sarcocolla. Malaysia, Neoeriomycopsis fissistigmae (incl. Neoeriomycopsidaceae fam. nov.) on leaf spots on flower Fissistigma sp. Namibia, Exophiala lichenicola lichenicolous on Acarospora cf. luederitzensis. Netherlands, Entoloma occultatum on soil, Extremus caricis on dead leaves of Carex sp., Inocybe pseudomytiliodora on loamy soil. Norway, Inocybe guldeniae on calcareous soil, Inocybe rupestroides on gravelly soil. Pakistan, Hymenagaricus brunneodiscus on soil. Philippines, Ophiocordyceps philippinensis parasitic on Asilus sp. Poland, Hawksworthiomyces ciconiae isolated from Ciconia ciconia nest, Plectosphaerella vigrensis from leaf spots on Impatiens noli-tangere, Xenoramularia epitaxicola from sooty mould community on Taxus baccata. Portugal, Inocybe dagamae on clay soil. Saudi Arabia, Diaporthe jazanensis on branches of Coffea arabica. South Africa, Alternaria moraeae on dead leaves of Moraea sp., Bonitomyces buffels-kloofinus (incl. Bonitomyces gen. nov.) on dead twigs of unknown tree, Constrictochalara koukolii on living leaves of Itea rhamnoides colonised by a Meliola sp., Cylindromonium lichenophilum on Parmelina tiliacea, Gamszarella buffelskloofina (incl. Gamszarella gen. nov.) on dead insect, Isthmosporiella africana (incl. Isthmosporiella gen. nov.) on dead twigs of unknown tree, Nothoeucasphaeria buffelskloofina (incl. Nothoeucasphaeria gen. nov.), on dead twigs of unknown tree, Nothomicrothyrium beaucarneae (incl. Nothomicrothyrium gen. nov.) on dead leaves of Beaucarnea stricta, Paramycosphaerella proteae on living leaves of Protea caffra, Querciphoma foliicola on leaf litter, Rachicladosporium conostomii on dead twigs of Conostomium natalense var. glabrum, Rhamphoriopsis synnematosa on dead twig of unknown tree, Waltergamsia mpumalanga on dead leaves of unknown tree. Spain, Amanita fulvogrisea on limestone soil, in mixed forest, Amanita herculis in open Quercus forest, Vuilleminia beltraniae on Cistus symphytifolius. Sweden, Pachyella pulchella on decaying wood on sand-silt riverbank. Thailand, Deniquelata cassiae on dead stem of Cassia fistula, Stomiopeltis thailandica on dead twigs of Magnolia champaca. Ukraine, Circinaria podoliana on natural limestone outcrops, Neonematogonum carpinicola (incl. Neonematogonum gen. nov.) on dead branches of Carpinus betulus. USA, Exophiala wilsonii water from cooling tower, Hygrophorus aesculeticola on soil in mixed forest, and Neocelosporium aereum from air in a house attic. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Costa MM, Kandemir H, et al. 2023. Fungal Planet description sheets: 1550-1613. Persoonia 51: 280-417. doi: 10.3767/persoonia.2023.51.08.},
}
@article {pmid38664322,
year = {2024},
author = {Vincent, J and Tenore, A and Mattei, MR and Frunzo, L},
title = {Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {6},
pages = {63},
pmid = {38664322},
issn = {1522-9602},
support = {861088//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; },
mesh = {*Biofilms/growth &amp; development ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Mathematical Concepts ; *Models, Biological ; *Models, Genetic ; Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; },
abstract = {In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.},
}
@article {pmid38663208,
year = {2024},
author = {Ceballos-Escalera, A and Pous, N and Bañeras, L and Balaguer, MD and Puig, S},
title = {Advancing towards electro-bioremediation scaling-up: On-site pilot plant for successful nitrate-contaminated groundwater treatment.},
journal = {Water research},
volume = {256},
number = {},
pages = {121618},
doi = {10.1016/j.watres.2024.121618},
pmid = {38663208},
issn = {1879-2448},
mesh = {*Groundwater/chemistry ; *Nitrates/metabolism ; *Biodegradation, Environmental ; *Water Pollutants, Chemical ; Pilot Projects ; *Water Purification/methods ; Denitrification ; Spain ; Bioreactors ; },
abstract = {The potential of nitrate electro-bioremediation has been fully demonstrated at the laboratory scale, although it has not yet been fully implemented due to the challenges associated with scaling-up bioelectrochemical reactors and their on-site operation. This study describes the initial start-up and subsequent stable operation of an electro-bioremediation pilot plant for the treatment of nitrate-contaminated groundwater on-site (Navata site, Spain). The pilot plant was operated under continuous flow mode for 3 months, producing an effluent suitable for drinking water in terms of nitrates and nitrites (<50 mg NO3[-] L[-1]; 0 mg NO2[-] L[-1]). A maximum nitrate removal rate of 0.9 ± 0.1 kg NO3[-] m[-3] d[-1] (efficiency 82 ± 18 %) was achieved at a cathodic hydraulic retention time (HRTcat) of 2.0 h with a competitive energy consumption of 4.3 ± 0.4 kWh kg[-1] NO3[-]. Under these conditions, the techno-economic analysis estimated an operational cost of 0.40 € m[-3]. Simultaneously, microbiological analyses revealed structural heterogeneity in the reactor, with denitrification functionality concentrated predominantly from the centre to the upper section of the reactor. The most abundant groups were Pseudomonadaceae, Rhizobiaceae, Gallionellaceae, and Xanthomonadaceae. In conclusion, this pilot plant represents a significant advancement in implementing this technology on a larger scale, validating its effectiveness in terms of nitrate removal and cost-effectiveness. Moreover, the results validate the electro-bioremediation in a real environment and encourage further investigation of its potential as a water treatment.},
}
@article {pmid38662665,
year = {2024},
author = {Hulatt, CJ and Suzuki, H and Détain, A and Wijffels, RH and Leya, T and Posewitz, MC},
title = {The genome of the Arctic snow alga Limnomonas spitsbergensis (Chlamydomonadales).},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {7},
pages = {},
pmid = {38662665},
issn = {2160-1836},
support = {749910//Marie Sk&#x142;odowska-Curie Individual Fellowship/ ; //European Union's Horizon 2020/ ; //Posewitz lab/ ; //Colorado School of Mines/ ; //National Center for Genome Resources/ ; NN9634K//UNINETT Sigma-2 Compute Infrastructure/ ; },
mesh = {Arctic Regions ; *Snow/microbiology ; *Molecular Sequence Annotation ; Phylogeny ; Chlorophyta/genetics ; Genomics/methods ; },
abstract = {Snow algae are a diverse group of extremophilic microeukaryotes found on melting polar and alpine snowfields. They play an important role in the microbial ecology of the cryosphere, and their propagation on snow and ice surfaces may in part accelerate climate-induced melting of these systems. High-quality snow algae genomes are needed for studies on their unique physiology, adaptive mechanisms, and genome evolution under multiple forms of stress, including cold temperatures and intense sunlight. Here, we assembled and annotated the genome of Limnomonas spitsbergensis, a cryophilic biciliate green alga originally isolated from melting snow on Svalbard, in the Arctic. The L. spitsbergensis genome assembly is based primarily on the use of PacBio long reads and secondly Illumina short reads, with an assembly size of 260.248 Mb in 124 contigs. A combination of 3 alternative annotation strategies was used including protein homology, RNA-seq evidence, and PacBio full-length transcript isoforms. The best merged set of annotations identified 18,277 protein-coding genes, which were 95.2% complete based on Benchmarking Universal Single-Copy Orthologs analysis. We also provide the annotated mitogenome, which is a relatively large 77.942 kb circular mapping sequence containing extensive repeats. The L. spitsbergensis genome will provide a new resource for research on snow algae adaptation, behavior, and natural selection in unique, low-temperature terrestrial environments that are under threat from climate change.},
}
@article {pmid38662575,
year = {2024},
author = {Liu, X and Salles, JF},
title = {Bridging ecological assembly process and community stability upon bacterial invasions.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38662575},
issn = {1751-7370},
mesh = {*Soil Microbiology ; *Escherichia coli/genetics ; *Microbiota ; Ecosystem ; Microbial Interactions ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Understanding the link between microbial community stability and assembly processes is crucial in microbial ecology. Here, we investigated whether the impact of biotic disturbances would depend on the processes controlling community assembly. For that, we performed an experiment using soil microcosms in which microbial communities assembled through different processes were invaded by Escherichia coli. We show that the ecological assembly process of the resident community plays a significant role in invader-resident competition, invader survival, and compositional stability of the resident community. Specifically, the resident communities primarily assembled through stochastic processes were more susceptible to invader survival. Besides, E. coli invasion acts as a biotic selection pressure, leading to competition between the invader and resident taxa, suppressing the stochasticity in the resident community. Taken together, this study provides empirical evidence for the interpretation of microbial community assemblage on their (potential) ecosystem functions and services, such as the prevention of pathogen establishment and the pathogenic states of soil microbiomes.},
}
@article {pmid38662080,
year = {2024},
author = {Ezhumalai, G and Arun, M and Manavalan, A and Rajkumar, R and Heese, K},
title = {A Holistic Approach to Circular Bioeconomy Through the Sustainable Utilization of Microalgal Biomass for Biofuel and Other Value-Added Products.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {61},
pmid = {38662080},
issn = {1432-184X},
mesh = {*Microalgae/metabolism/growth &amp; development ; *Biofuels ; *Biomass ; Cyanobacteria/metabolism ; Seaweed/metabolism ; Carbon Dioxide/metabolism ; },
abstract = {Emissions from transportation and industry primarily cause global warming, leading to floods, glacier melt, and rising seas. Widespread greenhouse gas emissions and resulting global warming pose significant risks to the environment, economy, and society. The need for alternative fuels drives the development of third-generation feedstocks: microalgae, seaweed, and cyanobacteria. These microalgae offer traits like rapid growth, high lipid content, non-competition with human food, and growth on non-arable land using brackish or waste water, making them promising for biofuel. These unique phototrophic organisms use sunlight, water, and carbon dioxide (CO2) to produce biofuels, biochemicals, and more. This review delves into the realm of microalgal biofuels, exploring contemporary methodologies employed for lipid extraction, significant value-added products, and the challenges inherent in their commercial-scale production. While the cost of microalgae bioproducts remains high, utilizing wastewater nutrients for cultivation could substantially cut production costs. Furthermore, this review summarizes the significance of biocircular economy approaches, which encompass the utilization of microalgal biomass as a feed supplement and biofertilizer, and biosorption of heavy metals and dyes. Besides, the discussion extends to the in-depth analysis and future prospects on the commercial potential of biofuel within the context of sustainable development. An economically efficient microalgae biorefinery should prioritize affordable nutrient inputs, efficient harvesting techniques, and the generation of valuable by-products.},
}
@article {pmid38661241,
year = {2024},
author = {Xiong, H and Zhang, X and Zeng, H and Xie, S and Yi, S},
title = {Experience of diet in patients with inflammatory bowel disease: A thematic synthesis of qualitative studies.},
journal = {Journal of clinical nursing},
volume = {33},
number = {8},
pages = {3283-3293},
doi = {10.1111/jocn.17186},
pmid = {38661241},
issn = {1365-2702},
mesh = {Humans ; *Inflammatory Bowel Diseases/diet therapy/psychology ; *Qualitative Research ; *Diet/psychology/methods ; Adult ; Male ; Female ; Middle Aged ; },
abstract = {AIM: To synthesise the dietary expesriences of patients with inflammatory bowel disease by reviewing relevant qualitative studies.<br><br>BACKGROUND: Diet plays a crucial role in the development and progression of inflammatory bowel disease (IBD). There is no specific diet that can be recommended for all patients. We conducted a synthesis of qualitative studies to gain a comprehensive understanding of the dietary management experience of patients with IBD, aiming to provide better dietary guidance in the future.<br><br>DESIGN: A qualitative synthesis was conducted following the Thomas and Harden method and reported following the ENTREQ statement.<br><br>METHODS: Qualitative studies were systematically searched in five electronic databases: PubMed, PsycINFO, Embase, CINAHL, and Web of Science. There was no time limit for publication, and all database searches were up to 10 May, 2023. The Joanna Briggs Institute Qualitative Assessment and Review Instrument was utilised to appraise the quality of the included studies. Data for inclusion in articles were extracted and analysed using a thematic synthesis method.<br><br>RESULTS: Six studies involving 119 patients were eventually included. The studies were conducted in six different countries. Four major themes were identified: the diet of patients with IBD is completely different from the normal one; manage symptoms and live with the disease by modifying diet; psychological adjustment to eating (be frustrated; worried and afraid; feel ashamed; growth and resilience); barriers and challenges (barriers from perceived social support; conflicts between diet and nutrition; challenges from food hedonism and cravings).<br><br>CONCLUSIONS: Patients with IBD highlighted the distinction between their diet and the normal diet. Dietary modifications were used as a way to manage symptoms and live with the disease. In addition to physical symptoms, patients experienced diet-related psychological changes. Dietary modifications in patients with IBD encounters difficulties and challenges, necessitating prompt guidance and intervention. (1) The implementation of dietary modifications in patients with IBD encounters numerous obstacles and complexities, necessitating prompt guidance and intervention.<br><br>No patient or public contribution.<br><br>REGISTRATION: The protocol was registered with PROSPERO (CRD42023391545).},
}
@article {pmid38660030,
year = {2024},
author = {Lourenço, KS and Suleiman, AKA and Pijl, A and Dimitrov, MR and Cantarella, H and Kuramae, EE},
title = {Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments.},
journal = {MethodsX},
volume = {12},
number = {},
pages = {102699},
pmid = {38660030},
issn = {2215-0161},
abstract = {In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).},
}
@article {pmid38659931,
year = {2024},
author = {Prochera, A and Muppirala, AN and Kuziel, GA and Soualhi, S and Shepherd, A and Sun, L and Issac, B and Rosenberg, HJ and Karim, F and Perez, K and Smith, KH and Archibald, TH and Rakoff-Nahoum, S and Hagen, SJ and Rao, M},
title = {Enteric glia regulate Paneth cell secretion and intestinal microbial ecology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38659931},
issn = {2692-8205},
support = {K08 DK110532/DK/NIDDK NIH HHS/United States ; P50 HD105351/HD/NICHD NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 DK135707/DK/NIDDK NIH HHS/United States ; R01 DK130836/DK/NIDDK NIH HHS/United States ; },
abstract = {Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions [1]. To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express PLP1 in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1[+] cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1[+] glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.},
}
@article {pmid38658559,
year = {2024},
author = {Chen, KH and Feng, J and Bodelier, PLE and Yang, Z and Huang, Q and Delgado-Baquerizo, M and Cai, P and Tan, W and Liu, YR},
title = {Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3471},
pmid = {38658559},
issn = {2041-1723},
support = {32071595//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371731//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177022//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methane/metabolism ; *Oryza/metabolism/microbiology ; *Denitrification ; *Soil Microbiology ; *Oxidation-Reduction ; China ; *Soil/chemistry ; Aerobiosis ; Bacteria/metabolism/genetics/classification ; Nitrous Oxide/metabolism ; Phylogeny ; Carbon Isotopes/metabolism ; Metagenome ; },
abstract = {Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and [13]CH4-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH4 oxidation in supporting denitrification. Our results reveal positive relationships between CH4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, [13]CH4-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating [13]C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of [13]C-metagenome-assembled genomes and [13]C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH4 oxidation, for the coupling of CH4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.},
}
@article {pmid38658525,
year = {2024},
author = {Arthofer, P and Panhölzl, F and Delafont, V and Hay, A and Reipert, S and Cyran, N and Wienkoop, S and Willemsen, A and Sifaoui, I and Arberas-Jiménez, I and Schulz, F and Lorenzo-Morales, J and Horn, M},
title = {A giant virus infecting the amoeboflagellate Naegleria.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3307},
pmid = {38658525},
issn = {2041-1723},
support = {P37198-B//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 891572//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 101039843//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Genome, Viral/genetics ; *Giant Viruses/genetics/classification/ultrastructure/isolation &amp; purification/physiology ; *Naegleria/genetics/virology ; Naegleria fowleri/genetics/isolation &amp; purification ; Phylogeny ; Humans ; },
abstract = {Giant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.},
}
@article {pmid38657743,
year = {2024},
author = {Atasoy, M and Scott, WT and Regueira, A and Mauricio-Iglesias, M and Schaap, PJ and Smidt, H},
title = {Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches.},
journal = {Biotechnology advances},
volume = {73},
number = {},
pages = {108363},
doi = {10.1016/j.biotechadv.2024.108363},
pmid = {38657743},
issn = {1873-1899},
mesh = {Bioreactors/microbiology ; *Fatty Acids, Volatile/metabolism ; Kinetics ; *Metabolic Networks and Pathways ; Models, Biological ; *Microbiota ; },
abstract = {In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach has evolved beyond its traditional role in energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic acid, and butyric acid. VFAs hold great potential for various industries and biobased applications due to their versatile properties. Despite increasing global demand, over 90% of VFAs are currently produced synthetically from petrochemicals. Realizing the potential of large-scale biobased VFA production from waste streams offers significant eco-friendly opportunities but comes with several key challenges. These include low VFA production yields, unstable acid compositions, complex and expensive purification methods, and post-processing needs. Among these, production yield and acid composition stand out as the most critical obstacles impacting economic viability and competitiveness. This paper seeks to offer a comprehensive view of combining complementary modeling approaches, including kinetic and microbial modeling, to understand the workings of microbial communities and metabolic pathways in VFA production, enhance production efficiency, and regulate acid profiles through the integration of omics and bioreactor data.},
}
@article {pmid38657507,
year = {2024},
author = {Fu, Y and Jia, F and Su, J and Xu, X and Zhang, Y and Li, X and Jiang, X and Schäffer, A and Virta, M and Tiedje, JM and Wang, F},
title = {Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134252},
doi = {10.1016/j.jhazmat.2024.134252},
pmid = {38657507},
issn = {1873-3336},
mesh = {Animals ; *Ursidae/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; *Diet ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.},
}
@article {pmid38657451,
year = {2024},
author = {Guo, D and Tian, K and Peng, X and Liu, S and Xu, X and Tian, W},
title = {Cadmium/zinc stresses and plant cultivation influenced soil microflora: a pot experiment conducted in field.},
journal = {Ecotoxicology and environmental safety},
volume = {277},
number = {},
pages = {116384},
doi = {10.1016/j.ecoenv.2024.116384},
pmid = {38657451},
issn = {1090-2414},
mesh = {*Soil Microbiology ; *Cadmium/toxicity ; *Zinc/toxicity ; *Soil Pollutants/toxicity ; *Rhizosphere ; *Biodegradation, Environmental ; *Fungi/drug effects ; *Bacteria/drug effects/genetics ; Soil/chemistry ; Microbiota/drug effects ; Metals, Heavy/toxicity ; Stress, Physiological ; },
abstract = {It's of great challenge to address for heavy metal-contaminated soil. Once the farmland is contaminated with heavy metals, the microbial ecology of the plant rhizosphere will change, which in turn impacts crop productivity and quality. However, few studies have explored the effects of heavy metals on plant rhizosphere microbes in farmland and the role that plant cultivation plays in such a phytoremediation practice. In this study, the impacts of comfrey (Symphytum officinale L.) cultivation and the stresses of cadmium/zinc (Cd/Zn) on rhizosphere soil microflora were examined. Microbial DNA was collected from soils to evaluate the prevalence of bacteria and fungi communities in rhizosphere soils. High-throughput 16 S rRNA sequencing was used to determine the diversity of the bacterial and fungal communities. The results showed that growing comfrey on polluted soils reduced the levels of Cd and Zn from the vertical profile. Both the comfrey growth and Cd/Zn stresses affected the community of rhizosphere microorganisms (bacteria or fungi). Additionally, the analysis of PCoA and NMDS indicated that the cultivation of comfrey significantly changed the bacterial composition and structure of unpolluted soil. Comfrey cultivation in polluted and unpolluted soils did not result in much variance in the fungi's species composition, but the fungal compositions of the two-type soils were noticeably different. This work provided a better understanding of the impacts of Cd/Zn stresses and comfrey cultivation on rhizosphere microbial community, as well as new insight into phytoremediation of heavy metal-contaminated soils.},
}
@article {pmid38655503,
year = {2024},
author = {Horstmann, L and Lipus, D and Bartholomäus, A and Arens, F and Airo, A and Ganzert, L and Zamorano, P and Schulze-Makuch, D and Wagner, D},
title = {Persistent microbial communities in hyperarid subsurface habitats of the Atacama Desert: Insights from intracellular DNA analysis.},
journal = {PNAS nexus},
volume = {3},
number = {4},
pages = {pgae123},
pmid = {38655503},
issn = {2752-6542},
abstract = {Desert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under the absence of regular precipitation, microorganisms are the main ecological component mediating nutrient fluxes by using soil components, like minerals and salts, and atmospheric gases as a source for energy and water. While most of the previous studies on microbial ecology of desert environments have focused on surface environments, little is known about microbial life in deeper sediment layers. Our study is extending the limited knowledge about microbial communities within the deeper subsurface of the hyperarid core of the Atacama Desert. By employing intracellular DNA extraction and subsequent 16S rRNA sequencing of samples collected from a soil pit in the Yungay region of the Atacama Desert, we unveiled a potentially viable microbial subsurface community residing at depths down to 4.20 m. In the upper 80 cm of the playa sediments, microbial communities were dominated by Firmicutes taxa showing a depth-related decrease in biomass correlating with increasing amounts of soluble salts. High salt concentrations are possibly causing microbial colonization to cease in the lower part of the playa sediments between 80 and 200 cm depth. In the underlying alluvial fan deposits, microbial communities reemerge, possibly due to gypsum providing an alternative water source. The discovery of this deeper subsurface community is reshaping our understanding of desert soils, emphasizing the need to consider subsurface environments in future explorations of arid ecosystems.},
}
@article {pmid38654537,
year = {2024},
author = {Zhu 朱墨, M and Zhang, W and Duan, X and Yan, S and Cai, Y and Gong, S and Fahad, S and Qiu, Z},
title = {Biocontrol Potential of Cladosporium sphaerospermum Against the Wheat Powdery Mildew Fungus Blumeria graminis f. sp. tritici.},
journal = {Plant disease},
volume = {108},
number = {10},
pages = {2983-2988},
doi = {10.1094/PDIS-02-24-0433-SC},
pmid = {38654537},
issn = {0191-2917},
mesh = {*Ascomycota/physiology ; *Cladosporium/physiology ; *Triticum/microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; Spores, Fungal/physiology ; Pest Control, Biological ; Biomass ; },
abstract = {Cladosporium spp. are known to be mycoparasites and inhibit phytopathogenic fungi. However, so far, little information is available on the impact of Cladosporium spp. on powdery mildews. Based on the morphological characteristics and molecular analysis, C. sphaerospermum was identified as a mycoparasite on the wheat powdery mildew fungus Blumeria graminis f. sp. tritici (Bgt), recently named B. graminis s. str. C. sphaerospermum was capable of preventing colony formation and conidial distribution of Bgt. The biomasses of Bgt notably decreased by 1.3, 2.2, 3.6, and 3.8 times at 2, 4, 6, and 8 days postinoculation (dpi), respectively. In addition, biomasses of C. sphaerospermum at 2, 4, 6, and 8 dpi significantly increased to 5.6, 13.9, 18.2, and 67.3 times, respectively. In vitro, C. sphaerospermum exudates significantly impaired appressorial formation of Bgt. Thus, C. sphaerospermum acts as a potential biological control agent by suppressing the formation, distribution, and development of Bgt conidia and is a viable alternative for managing the wheat powdery mildew. These results suggest that C. sphaerospermum is an antagonistic parasite of the wheat powdery mildew fungus and, hence, provide new knowledge about the biological control of phytopathogenic fungi.},
}
@article {pmid38653968,
year = {2024},
author = {Serra Moncadas, L and Hofer, C and Bulzu, PA and Pernthaler, J and Andrei, AS},
title = {Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3421},
pmid = {38653968},
issn = {2041-1723},
support = {PZ00P3_193240//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Fresh Water/microbiology ; *Phylogeny ; *Adaptation, Physiological/genetics ; Metagenomics/methods ; Evolution, Molecular ; Genome Size ; Proteome/genetics/metabolism ; },
abstract = {The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.},
}
@article {pmid38653406,
year = {2024},
author = {Wu, T and Ding, J and Zhao, YJ and Ding, L and Zang, Y and Sun, HJ and Zhong, L and Pang, JW and Li, Y and Ren, NQ and Yang, SS},
title = {Microplastics shaped performance, microbial ecology and community assembly in simultaneous nitrification, denitrification and phosphorus removal process.},
journal = {The Science of the total environment},
volume = {929},
number = {},
pages = {172651},
doi = {10.1016/j.scitotenv.2024.172651},
pmid = {38653406},
issn = {1879-1026},
mesh = {*Nitrification ; *Denitrification ; *Phosphorus/metabolism ; *Water Pollutants, Chemical/metabolism/analysis ; *Waste Disposal, Fluid/methods ; *Microplastics ; Wastewater ; Microbiota ; },
abstract = {The widespread use of microplastics (MPs) has led to an increase in their discharge to wastewater treatment plants. However, the knowledge of impact of MPs on macro-performance and micro-ecology in simultaneous nitrification, denitrification, and phosphorus removal (SNDPR) systems is limited, hampering the understanding of potential risks posed by MPs. This study firstly comprehensively investigated the performance, species interactions, and community assembly under polystyrene (PS) and polyvinyl chloride (PVC) exposure in SNDPR systems. The results showed under PS (1, 10 mg/L) and PVC (1, 10 mg/L) exposure, total nitrogen removal was reduced by 3.38-10.15 %. PS and PVC restrained the specific rates of nitrite and nitrate reduction (SNIRR, SNRR), as well as the activities of nitrite and nitrate reductase enzymes (NIR, NR). The specific ammonia oxidation rate (SAOR) and activity of ammonia oxidase enzyme (AMO) were reduced only at 10 mg/L PVC. PS and PVC enhanced the size of co-occurrence networks, niche breadth, and number of key species while decreasing microbial cooperation by 5.85-13.48 %. Heterogeneous selection dominated microbial community assembly, and PS and PVC strengthened the contribution of stochastic processes. PICRUSt prediction further revealed some important pathways were blocked by PS and PVC. Together, the reduced TN removal under PS and PVC exposure can be attributed to the inhibition of SAOR, SNRR, and SNIRR, the restrained activities of NIR, NR, and AMO, the changes in species interactions and community assembly mechanisms, and the suppression of some essential metabolic pathways. This paper offers a new perspective on comprehending the effects of MPs on SNDPR systems.},
}
@article {pmid38651910,
year = {2024},
author = {Rodríguez-Ramos, J and Nicora, CD and Purvine, SO and Borton, MA and McGivern, BB and Hoyt, DW and Lipton, MS and Wrighton, KC},
title = {Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments.},
journal = {Microbiology resource announcements},
volume = {13},
number = {6},
pages = {e0003324},
pmid = {38651910},
issn = {2576-098X},
support = {P30 CA016058/CA/NCI NIH HHS/United States ; Award 1781//Joint Genome Institute Large-scale sequencing award/ ; DE-AC05-76RL01830//Office of Biological and Environmental Research/ ; DE-SC0018170//Subsurface Biogeochemical Research program/ ; },
abstract = {Rivers are critical ecosystems that impact global biogeochemical cycles. Nonetheless, a mechanistic understanding of river microbial metabolisms and their influences on geochemistry is lacking. Here, we announce metaproteomes of river sediments that are paired with metagenomes and metabolites, enabling an understanding of the microbial underpinnings of river respiration.},
}
@article {pmid38648266,
year = {2024},
author = {Ramoneda, J and Fan, K and Lucas, JM and Chu, H and Bissett, A and Strickland, MS and Fierer, N},
title = {Ecological relevance of flagellar motility in soil bacterial communities.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38648266},
issn = {1751-7370},
support = {P2EZP3_199849/SNSF_/Swiss National Science Foundation/Switzerland ; 2131837//US National Science Foundation/ ; },
mesh = {*Flagella/genetics/physiology ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics ; Bacterial Physiological Phenomena ; Carbon/metabolism ; Soil/chemistry ; Metagenome ; Genome, Bacterial ; },
abstract = {Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.},
}
@article {pmid38648112,
year = {2024},
author = {Temple, C and Blouin, AG and Boezen, D and Botermans, M and Durant, L and De Jonghe, K and de Koning, P and Goedefroit, T and Minet, L and Steyer, S and Verdin, E and Zwart, M and Massart, S},
title = {Biological Characterization of Physostegia Chlorotic Mottle Virus, an Emergent Virus Infecting Vegetables in Diversified Production Systems.},
journal = {Phytopathology},
volume = {114},
number = {7},
pages = {1680-1688},
doi = {10.1094/PHYTO-06-23-0194-R},
pmid = {38648112},
issn = {0031-949X},
mesh = {*Plant Diseases/virology ; *Hemiptera/virology ; *Vegetables/virology ; Solanum lycopersicum/virology ; Animals ; Switzerland ; Insect Vectors/virology ; Crops, Agricultural/virology ; Host Specificity ; },
abstract = {In 2014, Physostegia chlorotic mottle virus (PhCMoV) was discovered in Austria in Physostegia virginiana. Subsequent collaborative efforts established a link between the virus and severe fruit symptoms on important crops such as tomato, eggplant, and cucumber across nine European countries. Thereafter, specific knowledge gaps, which are crucial to assess the risks PhCMoV can pose for production and how to manage it, needed to be addressed. In this study, the transmission, prevalence, and disease severity of PhCMoV were examined. This investigation led to the identification of PhCMoV presence in a new country, Switzerland. Furthermore, our research indicates that the virus was already present in Europe 30 years ago. Bioassays demonstrated PhCMoV can result in up to 100% tomato yield losses depending on the phenological stage of the plant at the time of infection. PhCMoV was found to naturally infect 12 new host plant species across eight families, extending its host range to 21 plant species across 15 plant families. The study also identified a polyphagous leafhopper (genus Anaceratagallia) as a natural vector of PhCMoV. Overall, PhCMoV was widespread in small-scale diversified vegetable farms in Belgium where tomato is grown in soil under tunnels, occurring in approximately one-third of such farms. However, outbreaks were sporadic and were associated at least once with the cultivation in tomato tunnels of perennial plants that can serve as a reservoir host for the virus and its vector. To further explore this phenomenon and manage the virus, studying the ecology of the vector would be beneficial.},
}
@article {pmid38647288,
year = {2024},
author = {Waegenaar, F and García-Timermans, C and Van Landuyt, J and De Gusseme, B and Boon, N},
title = {Impact of operational conditions on drinking water biofilm dynamics and coliform invasion potential.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {5},
pages = {e0004224},
pmid = {38647288},
issn = {1098-5336},
support = {1S02022N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; S006221N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; },
mesh = {*Biofilms/growth &amp; development ; *Drinking Water/microbiology ; *Enterobacteriaceae/physiology/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Water Quality ; Water Purification ; Water Microbiology ; Water Supply ; },
abstract = {UNLABELLED: Biofilms within drinking water distribution systems serve as a habitat for drinking water microorganisms. However, biofilms can negatively impact drinking water quality by causing water discoloration and deterioration and can be a reservoir for unwanted microorganisms. In this study, we investigated whether indicator organisms for drinking water quality, such as coliforms, can settle in mature drinking water biofilms. Therefore, a biofilm monitor consisting of glass rings was used to grow and sample drinking water biofilms. Two mature drinking water biofilms were characterized by flow cytometry, ATP measurements, confocal laser scanning microscopy, and 16S rRNA sequencing. Biofilms developed under treated chlorinated surface water supply exhibited lower cell densities in comparison with biofilms resulting from treated groundwater. Overall, the phenotypic as well as the genotypic characteristics were significantly different between both biofilms. In addition, the response of the biofilm microbiome and possible biofilm detachment after minor water quality changes were investigated. Limited changes in pH and free chlorine addition, to simulate operational changes that are relevant for practice, were evaluated. It was shown that both biofilms remained resilient. Finally, mature biofilms were prone to invasion of the coliform, Serratia fonticola. After spiking low concentrations (i.e., ±100 cells/100 mL) of the coliform to the corresponding bulk water samples, the coliforms were able to attach and get established within the mature biofilms. These outcomes emphasize the need for continued research on biofilm detachment and its implications for water contamination in distribution networks.<br><br>IMPORTANCE: The revelation that even low concentrations of coliforms can infiltrate into mature drinking water biofilms highlights a potential public health concern. Nowadays, the measurement of coliform bacteria is used as an indicator for fecal contamination and to control the effectiveness of disinfection processes and the cleanliness and integrity of distribution systems. In Flanders (Belgium), 533 out of 18,840 measurements exceeded the established norm for the coliform indicator parameter in 2021; however, the source of microbial contamination is mostly unknown. Here, we showed that mature biofilms, are susceptible to invasion of Serratia fonticola. These findings emphasize the importance of understanding and managing biofilms in drinking water distribution systems, not only for their potential to influence water quality, but also for their role in harboring and potentially disseminating pathogens. Further research into biofilm detachment, long-term responses to operational changes, and pathogen persistence within biofilms is crucial to inform strategies for safeguarding drinking water quality.},
}
@article {pmid38646773,
year = {2024},
author = {Weng, LY and Luan, DD and Zhou, DP and Guo, QG and Wang, GZ and Zhang, JL},
title = {Improving crop health by synthetic microbial communities: Progress and prospects.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {3},
pages = {847-857},
doi = {10.13287/j.1001-9332.202403.028},
pmid = {38646773},
issn = {1001-9332},
mesh = {*Crops, Agricultural/growth &amp; development/microbiology ; *Microbiota ; *Rhizosphere ; Soil Microbiology ; Synthetic Biology/methods ; Agriculture/methods ; },
abstract = {Crop health directly affects yields and food security. At present, agrochemicals such as fertilizers and pesticides are mainly used in agricultural production to promote crop health. However, long-term excessive utilization of agrochemicals will damage the ecological environment of farmlands and increase the safety risk of agricultural products. It is urgent to explore efficient and environment-friendly agricultural products. Rhizosphere microbiome are considered as the second genome of plants, which are closely related to crop health. Understanding the key functional microbes, microbe-microbe interactions, and plant-microbe interactions are fundamental for exploring the potential of beneficial microbes in promoting crop health. However, due to the heterogeneity and complexity of the natural environment, stimulating the function of indigenous microorganisms remains uncertain. Synthetic microbial community (SynCom) is an artificial combination of two or more different strain isolates of microorganisms, with different taxonomic, genetic, or functional characteristic. Because of the advantages of maintaining species diversity and community stability, SynCom has been widely applied in the fields of human health, environmental governance and industrial production, and may also have great potential in promoting crop health. We summarized the concept and research status of SynCom, expounded the principles and methods of constructing SynCom, and analyzed the research on the promotion of crop health by exploring the mechanism of plant-microbe interactions, promoting plant growth and development, and improving stress resistance. Finally, we envisaged the future prospects to guide the using SynCom to improve crop health.},
}
@article {pmid38643981,
year = {2024},
author = {Haller, F and Jimenez, K and Baumgartner, M and Lang, M and Klotz, A and Jambrich, M and Busslinger, G and Müllauer, L and Khare, V and Gasche, C},
title = {Nfe2l2/NRF2 Deletion Attenuates Tumorigenesis and Increases Bacterial Diversity in a Mouse Model of Lynch Syndrome.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {17},
number = {7},
pages = {311-324},
doi = {10.1158/1940-6207.CAPR-23-0478},
pmid = {38643981},
issn = {1940-6215},
support = {P32302FW//Austrian Science Fund (FWF)/ ; },
mesh = {Animals ; *NF-E2-Related Factor 2/metabolism/genetics ; Mice ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/pathology/metabolism ; *MutS Homolog 2 Protein/genetics/metabolism ; Humans ; *Mice, Inbred C57BL ; *Disease Models, Animal ; Carcinogenesis/genetics/pathology ; Mice, Knockout ; Female ; Intestinal Mucosa/pathology/metabolism/microbiology ; Male ; },
abstract = {Lynch syndrome (LS) is the most prevalent heritable form of colorectal cancer. Its early onset and high lifetime risk for colorectal cancer emphasize the necessity for effective chemoprevention. NFE2L2 (NRF2) is often considered a potential druggable target, and many chemopreventive compounds induce NRF2. However, although NRF2 counteracts oxidative stress, it is also overexpressed in colorectal cancer and may promote tumorigenesis. In this study, we evaluated the role of NRF2 in the prevention of LS-associated neoplasia. We found increased levels of NRF2 in intestinal epithelia of mice with intestinal epithelium-specific Msh2 deletion (MSH2ΔIEC) compared with C57BL/6 (wild-type) mice, as well as an increase in downstream NRF2 targets NAD(P)H dehydrogenase (quinone 1) and glutamate-cysteine ligase catalytic subunit. Likewise, NRF2 levels were increased in human MSH2-deficient LS tumors compared with healthy human controls. In silico analysis of a publicly accessible RNA sequencing LS dataset also found an increase in downstream NRF2 targets. Upon crossing MSH2ΔIEC with Nrf2null (MSH2ΔIECNrf2null) mice, we unexpectedly found reduced tumorigenesis in MSH2ΔIECNrf2null mice compared with MSH2ΔIEC mice after 40 weeks, which occurred despite an increase in oxidative damage in MSH2ΔIECNrf2null mice. The loss of NRF2 impaired proliferation as seen by Ki67 intestinal staining and in organoid cultures. This was accompanied by diminished WNT/β-catenin signaling, but apoptosis was unaffected. Microbial α-diversity increased over time with the loss of NRF2 based upon 16S rRNA gene amplicon sequencing of murine fecal samples. Altogether, we show that NRF2 protein levels are increased in MSH2 deficiency and associated neoplasia, but the loss of NRF2 attenuates tumorigenesis. Activation of NRF2 may not be a feasible strategy for chemoprevention in LS. Prevention Relevance: Patients with LS have an early onset and high lifetime risk for colorectal cancer. In this study, we show that NRF2 protein levels are increased in MSH2 deficiency and associated neoplasia, but the loss of NRF2 attenuates tumorigenesis. This suggests that NRF2 may not be a tumor suppressor in this specific context.},
}
@article {pmid38643524,
year = {2024},
author = {Mishra, S and Zhang, X and Yang, X},
title = {Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition.},
journal = {Microbiological research},
volume = {284},
number = {},
pages = {127726},
doi = {10.1016/j.micres.2024.127726},
pmid = {38643524},
issn = {1618-0623},
mesh = {Bacteria/genetics/classification/metabolism ; Metagenomics ; Microbiota/physiology ; *Plant Development ; *Plant Roots/microbiology ; *Plants/microbiology ; *Rhizosphere ; *Soil Microbiology ; },
abstract = {Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.},
}
@article {pmid38642761,
year = {2024},
author = {Wu, WF and Li, XY and Chen, SC and Jin, BJ and Wu, CY and Li, G and Sun, CL and Zhu, YG and Lin, XY},
title = {Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities.},
journal = {The Science of the total environment},
volume = {929},
number = {},
pages = {172622},
doi = {10.1016/j.scitotenv.2024.172622},
pmid = {38642761},
issn = {1879-1026},
mesh = {*Oryza/microbiology ; *Fertilizers ; *Nitrogen ; *Fungi/physiology ; Mycobiome ; Agriculture ; Microbiota ; Plant Leaves/microbiology ; },
abstract = {The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.},
}
@article {pmid38638900,
year = {2024},
author = {Yang, W and Li, X and Yan, H and Sun, Y and Wu, D and Du, Y and Luo, Y},
title = {Recruitment of beneficial cucumber rhizosphere microbes mediated by amino acid secretion induced by biocontrol Bacillus subtilis isolate 1JN2.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1379566},
pmid = {38638900},
issn = {1664-302X},
abstract = {INTRODUCTION: At present, the use of beneficial microorganisms to control cucumber Fusarium wilt is a widely used method, and the rhizosphere microecological reset is one of the mechanisms involved. However, how biocontrol strains reshape cucumber rhizosphere microecology remains to be further studied.<br><br>METHODS: The composition changes of cucumber root exudates induced by biocontrol strain 1JN2, the microbial ecology of cucumber rhizosphere and the colonization ability of biocontrol strain 1JN2 in cucumber rhizosphere were analyzed through UHPLC-MS/MS analysis, Illumina high-throughput sequencing and SEM, respectively.<br><br>RESULTS: First, cucumber plants treated with biocontrol Bacillus 1JN2 reduced the disease severity of Fusarium wilt by 60%. Significant changes in cucumber root exudates were found after 1JN2 inoculation and the contents of four amino acids including glutamine, tryptophan, glycine and glutamic acid were significantly increased. Second, It was found that the bacterial diversity in the rhizosphere of cucumber was significantly increased in both the strain treatment group and the amino acid mixture treatment group, The number of Bacillus was the largest in all dominant populations, exceeded 20% in all treatment groups. The bacteria of Hydrogenispora and Vicinamibacteria were significantly increased after treatment.<br><br>DISCUSSION: Overall, the results demonstrated that amino acid substances in cucumber root exudates induced by biocontrol strain 1JN2 can shift the cucumber root microenvironment and prevent the occurrence of Fusarium wilt disease.},
}
@article {pmid38638570,
year = {2024},
author = {Verbeelen, T and Fernandez, CA and Nguyen, TH and Gupta, S and Leroy, B and Wattiez, R and Vlaeminck, SE and Leys, N and Ganigué, R and Mastroleo, F},
title = {Radiotolerance of N-cycle bacteria and their transcriptomic response to low-dose space-analogue ionizing irradiation.},
journal = {iScience},
volume = {27},
number = {5},
pages = {109596},
pmid = {38638570},
issn = {2589-0042},
abstract = {The advancement of regenerative life support systems (RLSS) is crucial to allow long-distance space travel. Within the Micro-Ecological Life Support System Alternative (MELiSSA), efficient nitrogen recovery from urine and other waste streams is vital to produce liquid fertilizer to feed food and oxygen production in subsequent photoautotrophic processes. This study explores the effects of ionizing radiation on nitrogen cycle bacteria that transform urea to nitrate. In particular, we assess the radiotolerance of Comamonas testosteroni, Nitrosomonas europaea, and Nitrobacter winogradskyi after exposure to acute γ-irradiation. Moreover, a comprehensive whole transcriptome analysis elucidates the effects of spaceflight-analogue low-dose ionizing radiation on the individual axenic strains and on their synthetic community o. This research sheds light on how the spaceflight environment could affect ureolysis and nitrification processes from a transcriptomic perspective.},
}
@article {pmid38636749,
year = {2024},
author = {Xu, Y and Niu, C and Liang, S and Guo, J and Li, K and Zhang, J and Li, J and Jin, Y and Bai, J and Dai, J and Lu, C},
title = {An inulin-based glycovesicle for pathogen-targeted drug delivery to ameliorate salmonellosis.},
journal = {International journal of biological macromolecules},
volume = {267},
number = {Pt 2},
pages = {131656},
doi = {10.1016/j.ijbiomac.2024.131656},
pmid = {38636749},
issn = {1879-0003},
mesh = {Animals ; *Inulin/pharmacology/chemistry ; Mice ; *Anti-Bacterial Agents/pharmacology/chemistry ; *Salmonella Infections/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; Drug Delivery Systems ; Levofloxacin/pharmacology ; Micelles ; Drug Carriers/chemistry ; Nanoparticles/chemistry ; },
abstract = {The gut microbiota plays a significant role in the pathogenesis and remission of inflammatory bowel disease. However, conventional antibiotic therapies may alter microbial ecology and lead to dysbiosis of the gut microbiome, which greatly limits therapeutic efficacy. To address this challenge, novel nanomicelles that couple inulin with levofloxacin via disulfide bonds for the treatment of salmonellosis were developed in this study. Owing to their H2S-responsiveness, the nanomicelles can target the inflamed colon and rapidly release levofloxacin to selectively fight against enteric pathogens. Moreover, the embedded inulin can serve as prebiotic fiber to increase the amount of Bifidobacteria and Lactobacilli in mice with salmonellosis, thus maintaining the intestinal mechanical barrier and regulating the balance of the intestinal flora. Therefore, multifunctional nanomicelles had a better curative effect than pure levofloxacin on ameliorating inflammation in vivo. The pathogen-targeted glycovesicle represents a promising drug delivery platform to maximize the efficacy of antibacterial drugs for the treatment of inflammatory bowel disease.},
}
@article {pmid38636461,
year = {2024},
author = {Zafar, H and Saier, MH},
title = {An Insider's Perspective about the Pathogenic Relevance of Gut Bacterial Transportomes.},
journal = {Microbial physiology},
volume = {34},
number = {1},
pages = {133-141},
pmid = {38636461},
issn = {2673-1673},
support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteria/metabolism/pathogenicity ; Animals ; Biological Transport ; Bacterial Proteins/metabolism ; Host Microbial Interactions/physiology ; Carrier Proteins/metabolism ; Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: The gut microbiome is integral to host health, hosting complex interactions between the host and numerous microbial species in the gastrointestinal tract. Key among the molecular mechanisms employed by gut bacteria are transportomes, consisting of diverse transport proteins crucial for bacterial adaptation to the dynamic, nutrient-rich environment of the mammalian gut. These transportomes facilitate the movement of a wide array of molecules, impacting both the host and the microbial community.<br><br>SUMMARY: This communication explores the significance of transportomes in gut bacteria, focusing on their role in nutrient acquisition, competitive interactions among microbes, and potential pathogenicity. It delves into the transportomes of key gut bacterial species like E. coli, Salmonella, Bacteroides, Lactobacillus, Clostridia, and Bifidobacterium, examining the functions of predicted transport proteins. The overview synthesizes recent research efforts, highlighting how these transportomes influence host-microbe interactions and contribute to the microbial ecology of the gut.<br><br>KEY MESSAGES: Transportomes are vital for the survival and adaptation of bacteria in the gut, enabling the import and export of various nutrients and molecules. The complex interplay of transport proteins not only supports bacterial growth and competition but also has implications for host health, potentially contributing to pathogenic processes. Understanding the pathogenic potential of transportomes in major gut bacterial species provides insights into gut health and disease, offering avenues for future research and therapeutic strategies.},
}
@article {pmid38634861,
year = {2024},
author = {Lee, HJ and Whang, KS},
title = {Falsiroseomonas oryziterrae sp. nov., and Falsiroseomonas oryzae sp. nov., isolated from rice paddy soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {4},
pages = {},
doi = {10.1099/ijsem.0.006349},
pmid = {38634861},
issn = {1466-5034},
mesh = {*Oryza ; Base Composition ; Cardiolipins ; Fatty Acids/chemistry ; Phosphatidylethanolamines ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Amino Acids ; Nucleotides ; Phosphatidylcholines ; Phosphatidylglycerols ; Soil ; },
abstract = {Three Gram-stain-negative, aerobic, non-motile and coccobacilli-shaped bacterial strains, designated as NPKOSM-4[T], NPKOSM-8 and MO-31[T], were isolated from rice paddy soil. They had 96.5-100 % 16S rRNA gene sequence similarity to each other, and strains NPKOSM-4[T] and NPKOSM-8 showed 100 % 16S rRNA gene sequence similarity, confirming that they were the same species. Comparative analysis of 16S rRNA genes with closely related type strains showed that three isolates were most closely related to Falsiroseomonas terricola EM0302[T] (96.1-97.8 %), Falsiroseomonas wooponensis WW53[T] (95.51-96.3 %) and Falsiroseomonas bella CQN31[T] (96.0-96.5 %), respectively. The genomes of strains NPKOSM-4[T] and MO-31[T] consisted of 4 632 875 and 6 455 771 bps, respectively, with 72.0 and 72.1 mol% G+C content. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strains NPKOSM-4[T] and MO-31[T] and type strains of Falsiroseomonas species were lower than the cut-offs (≥95 % for ANI, ≥95-96 % for AAI and ≥ 70 % for dDDH) required to define a bacterial species. The major fatty acids of strains NPKOSM-4[T], NPKOSM-8 and MO-31[T] were C18 : 1 ω7c and C18 : 1 2-OH (<10 %) and the predominant quinone was Q-10. The polar lipids of strain NPKOSM-4[T] were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and three unidentified aminolipids. The polar lipid profiles of strain MO-31[T] contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminolipid and three unidentified lipids. Based on their distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, strains NPKOSM-4[T], NPKOSM-8 and MO-31[T] are considered to represent two novel species of the genus Falsiroseomonas, for which the names Falsiroseomonas oryziterrae sp. nov. [to accommodate strains NPKOSM-4[T] (= KACC 22135[T]=JCM 34745[T]), NPKOSM-8 (=KACC 22134=JCM 34746)] and Falsiroseomonas oryzae sp. nov. [to accommodate strain MO-31[T] (= KACC 22465[T]=JCM 35532[T])] are proposed.},
}
@article {pmid38634692,
year = {2024},
author = {Zimmermann, J and Piecyk, A and Sieber, M and Petersen, C and Johnke, J and Moitinho-Silva, L and Künzel, S and Bluhm, L and Traulsen, A and Kaleta, C and Schulenburg, H},
title = {Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life.},
journal = {mBio},
volume = {15},
number = {5},
pages = {e0001224},
pmid = {38634692},
issn = {2150-7511},
support = {261376515//Deutsche Forschungsgemeinschaft (DFG)/ ; 261376515//Deutsche Forschungsgemeinschaft (DFG)/ ; 261376515//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Host Microbial Interactions ; Gastrointestinal Tract/microbiology ; Microbiota ; },
abstract = {UNLABELLED: The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function.<br><br>IMPORTANCE: The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host's lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.},
}
@article {pmid38634606,
year = {2024},
author = {Vandepol, NS and Shade, A},
title = {Is everything everywhere? A hands-on activity to engage undergraduates with key concepts in quantitative microbial biogeography.},
journal = {Journal of microbiology &amp; biology education},
volume = {25},
number = {2},
pages = {e0017023},
pmid = {38634606},
issn = {1935-7877},
support = {1749544//National Science Foundation/ ; //The Michigan State University Certification in College Teaching within the Graduate School in partnership with the College of Natural Sciences/ ; //The French Centre National de la Recherche Scientifique (CNRS)/ ; },
abstract = {The ubiquity and ease with which microbial cells disperse over space is a key concept in microbiology, especially in microbial ecology. The phenomenon prompted Baas Becking's famous "everything is everywhere" statement that now acts as the null hypothesis in studies that test the dispersal limitation of microbial taxa. Despite covering the content in lectures, exam performance indicated that the concepts of dispersal and biogeography challenged undergraduate students in an upper-level Microbial Ecology course. Therefore, we iteratively designed a hands-on classroom activity to supplement the lecture content and reinforce fundamental microbial dispersal and biogeography concepts while also building quantitative reasoning and teamwork skills. In a class period soon after the lecture, the students formed three-to-five-person teams to engage in the activity, which included a hands-on dispersal simulation and worksheet to guide discussion. The simulation involved stepwise neutral immigration or emigration and then environmental selection on a random community of microbial taxa represented by craft poms. The students recorded the results at each step as microbial community data. A field guide was provided to identify the taxonomy based on the pom phenotype and a reference to each taxon's preferred environmental niches. The worksheet guided a reflection of student observations during the simulation. It also sharpened quantitative thinking by prompting the students to summarize and visualize their and other teams' microbial community data and then to compare the observed community distributions to the idealized expectation given only selection without dispersal. We found that the activity improved student performance on exam questions and general student satisfaction and comfort with the biogeography concepts. Activity instructions and a list of needed materials are included for instructors to reproduce for their classrooms.},
}
@article {pmid38632086,
year = {2024},
author = {Chen, H and Zwaenepoel, A and Van de Peer, Y},
title = {wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {5},
pages = {},
pmid = {38632086},
issn = {1367-4811},
support = {3G032219//Research Foundation-Flanders/ ; //Ghent University/ ; },
mesh = {*Polyploidy ; *Genome, Plant ; *Gene Duplication ; *Phylogeny ; Evolution, Molecular ; Software ; Genomics/methods ; },
abstract = {MOTIVATION: Major improvements in sequencing technologies and genome sequence assembly have led to a huge increase in the number of available genome sequences. In turn, these genome sequences form an invaluable source for evolutionary, ecological, and comparative studies. One kind of analysis that has become routine is the search for traces of ancient polyploidy, particularly for plant genomes, where whole-genome duplication (WGD) is rampant.<br><br>RESULTS: Here, we present a major update of a previously developed tool wgd, namely wgd v2, to look for remnants of ancient polyploidy, or WGD. We implemented novel and improved previously developed tools to (a) construct KS age distributions for the whole-paranome (collection of all duplicated genes in a genome), (b) unravel intragenomic and intergenomic collinearity resulting from WGDs, (c) fit mixture models to age distributions of gene duplicates, (d) correct substitution rate variation for phylogenetic placement of WGDs, and (e) date ancient WGDs via phylogenetic dating of WGD-retained gene duplicates. The applicability and feasibility of wgd v2 for the identification and the relative and absolute dating of ancient WGDs is demonstrated using different plant genomes.<br><br>wgd v2 is open source and available at https://github.com/heche-psb/wgd.},
}
@article {pmid38631226,
year = {2024},
author = {Rubin-Blum, M and Makovsky, Y and Rahav, E and Belkin, N and Antler, G and Sisma-Ventura, G and Herut, B},
title = {Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea.},
journal = {Marine environmental research},
volume = {198},
number = {},
pages = {106497},
doi = {10.1016/j.marenvres.2024.106497},
pmid = {38631226},
issn = {1879-0291},
mesh = {Mediterranean Sea ; *Archaea/genetics/metabolism ; *Seawater/microbiology ; *Bacteria/metabolism/genetics/classification ; *Microbiota ; Carbon/metabolism ; Salts ; Methane/metabolism ; },
abstract = {Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼10[6] cell ml[-1]) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L[-1] d[-1] ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.},
}
@article {pmid38630182,
year = {2024},
author = {Nithyapriya, S and Sundaram, L and Eswaran, SUD and Perveen, K and Alshaikh, NA and Sayyed, RZ and Mastinu, A},
title = {Purification and Characterization of Desferrioxamine B of Pseudomonas fluorescens and Its Application to Improve Oil Content, Nutrient Uptake, and Plant Growth in Peanuts.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {60},
pmid = {38630182},
issn = {1432-184X},
support = {RSP2024R358//King Saud University/ ; },
mesh = {*Arachis ; Deferoxamine ; *Pseudomonas fluorescens ; India ; RNA, Ribosomal, 16S/genetics ; Nutrients ; Siderophores ; Iron ; Soil ; },
abstract = {Microorganisms produce siderophores, which are low-molecular-weight iron chelators when iron availability is limited. The present analyzed the role of LNPF1 as multifarious PGPR for improving growth parameters and nutrient content in peanut and soil nutrients. Such multifarious PGPR strains can be used as effective bioinoculants for peanut farming. In this work, rhizosphere bacteria from Zea mays and Arachis hypogaea plants in the Salem area of Tamil Nadu, India, were isolated and tested for biochemical attributes and characteristics that stimulate plant growth, such as the production of hydrogen cyanide, ammonia (6 µg/mL), indole acetic acid (76.35 µg/mL), and solubilizing phosphate (520 µg/mL). The 16S rRNA gene sequences identified the isolate LNPF1 as Pseudomonas fluorescens with a similarity percentage of 99% with Pseudomonas sp. Isolate LNPF1 was evaluated for the production of siderophore. Siderophore-rich supernatant using a Sep Pack C18 column and Amberlite-400 Resin Column (λmax 264) produced 298 mg/L and 50 mg/L of siderophore, respectively. The characterization of purified siderophore by TLC, HPLC, FTIR, and 2D-NMR analysis identified the compound as desferrioxamine, a hydroxamate siderophore. A pot culture experiment determined the potential of LNPF1 to improve iron and oil content and photosynthetic pigments in Arachis hypogaea L. and improve soil nutrient content. Inoculation of A. hypogea seeds with LNPF1 improved plant growth parameters such as leaf length (60%), shoot length (22%), root length (54.68%), fresh weight (47.28%), dry weight (37%), and number of nuts (66.66) compared to the control (untreated seeds). This inoculation also improved leaf iron content (43.42), short iron content (38.38%), seed iron (46.72%), seed oil (31.68%), carotenoid (64.40%), and total chlorophyll content (98.%) compared to control (untreated seeds). Bacterized seeds showed a substantial increase in nodulation (61.65%) and weight of individual nodules (95.97) vis-à-vis control. The results of the present study indicated that P. fluorescens might be utilized as a potential bioinoculant to improve growth, iron content, oil content, number of nuts and nodules of Arachishypogaea L., and enrich soil nutrients.},
}
@article {pmid38629830,
year = {2024},
author = {Castro, AE and Montecillo, AD and Villanueva, RMD and Obusan, MCM},
title = {Bacterial community profiles of select tributaries of Laguna Lake in the Philippines.},
journal = {Microbiology resource announcements},
volume = {13},
number = {5},
pages = {e0116123},
pmid = {38629830},
issn = {2576-098X},
abstract = {Laguna Lake is known for its ecological, economic, and cultural importance. Effects of urbanization and accumulation of emerging pollutants have been associated with its water quality; however, the microbial ecology of its tributaries remains to be explored. We report bacterial community profiles from shotgun metagenomes of its select tributary waters.},
}
@article {pmid38628677,
year = {2024},
author = {Kim, M and Park, T and Park, C and Baek, YC and Cho, A and Lee, HG and Kim, E and Bok, EY and Jung, YH and Hur, TY and Do, YJ},
title = {Impact of rumen cannulation surgery on rumen microbiota composition in Hanwoo steers.},
journal = {Journal of animal science and technology},
volume = {66},
number = {2},
pages = {353-365},
pmid = {38628677},
issn = {2055-0391},
abstract = {Rumen cannulation is a surgical technique used to collect rumen contents from ruminants. However, rumen cannulation surgery may potentially impact the composition of the rumen microbiota. This study aimed to examine the longitudinal alterations in the rumen microbiota composition of Hanwoo steers after cannulation surgery. In this study, eight Hanwoo steers were used; four steers underwent rumen cannulation surgery (cannulation group), while the remaining four were left intact (control group). Rumen samples were collected from all eight steers using the stomach tubing method on the day before surgery (day 0) and on postoperative days 1, 4, 7, 10, 14, 17, 21, 24, and 28, resulting in 80 samples (10 timepoints × 8 animals). The microbiota of all 80 samples were analyzed using 16S rRNA gene amplicon sequencing with Quantitative Insights into Microbial Ecology version 2 (QIIME2). There were no significant differences (p > 0.05) in all major phyla and most major genera representing at least 0.5% of total sequences across all 80 samples between the control and cannulation groups on the preoperative and postoperative days. However, while the alpha diversity indices did not differ (p > 0.05) between the two groups on the preoperative day, they significantly differed (p < 0.05) between the two groups on the postoperative days. Further, the overall microbial distribution based on both unweighted and weighted principal coordinate analysis plots significantly differed (p < 0.05) between the two groups on both the preoperative and postoperative days. Orthogonal polynomial contrasts indicated that major genera and microbial diversity in the cannulation group decreased following surgery but returned to their initial states by postoperative day 28. In conclusion, this study demonstrates that rumen cannulation surgery affects some major taxa and microbial diversity, suggesting that the rumen cannulation method can alter the composition of rumen microbiota in Hanwoo steers.},
}
@article {pmid38627476,
year = {2024},
author = {Ridley, RS and Conrad, RE and Lindner, BG and Woo, S and Konstantinidis, KT},
title = {Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8798},
pmid = {38627476},
issn = {2045-2322},
support = {2136146//National Science Foundation/ ; },
mesh = {Humans ; *Multiomics ; *Plastics ; Polymers ; Biotransformation ; Biodegradation, Environmental ; },
abstract = {Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.},
}
@article {pmid38626537,
year = {2024},
author = {Ali, A and Wang, N and Wang, Q and Xu, G and Xu, H},
title = {An approach to evaluating seasonal responses to acute toxicity of antibiotic nitrofurazone on periphytic ciliated protist communities in marine environments.},
journal = {European journal of protistology},
volume = {94},
number = {},
pages = {126081},
doi = {10.1016/j.ejop.2024.126081},
pmid = {38626537},
issn = {1618-0429},
mesh = {*Seasons ; *Nitrofurazone/pharmacology ; *Ciliophora/drug effects ; China ; Water Pollutants, Chemical/toxicity ; Anti-Bacterial Agents/pharmacology ; Seawater ; },
abstract = {Periphytic protists including ciliates are the primary components of microbial communities in which they play a vital role in the progression of food webs by moving resources from lower to higher trophic levels. However, the toxic effects of veterinary antibiotics on periphytic protists across four seasons are minimally understood. Therefore, in this study, a 1-year survey was conducted with the antibiotic nitrofurazone (NFZ) applied at concentrations of 0.0, 1.5, 3.0, 6.0, and 12.0 mg/L. Samples of protist communities were collected using microscope glass slides during four seasons in the coastal waters of the Yellow Sea, Qingdao, northern China. The abundance of protists dropped with an increase in NFZ concentrations, and almost all species were dead at a concentration of 12.0 mg/L. The 12 h-LC50 values of NFZ for the protist biota were similar among the four seasons, despite significant seasonal variability in the community structure. The present results suggest that the periphytic protist biota may be used as a biomarker for assessing the ecotoxicity of NFZ in marine environments regardless of the year season.},
}
@article {pmid38625060,
year = {2024},
author = {Garvin, ZK and Abades, SR and Trefault, N and Alfaro, FD and Sipes, K and Lloyd, KG and Onstott, TC},
title = {Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38625060},
issn = {1751-7370},
support = {/NASA/NASA/United States ; //Astrobiology Early Career Collaboration Award/ ; //High Meadows Environmental Institute at Princeton University/ ; //Walbridge Fund Graduate Award/ ; G110-21-W8189//W.M. Keck Foundation/ ; 1170995//National Fund for Scientific and Technological Development/ ; //National Science Foundation/ ; 2121637//Frontier Research in Earth Sciences/ ; 2151015//Division of Ocean Sciences/ ; },
mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Desert Climate ; *Hot Springs/microbiology ; *Oxidation-Reduction ; Carbon Monoxide/metabolism ; Hydrogen/metabolism ; Microbiota ; Altitude ; Soil/chemistry ; },
abstract = {High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing their impact on trace gas-oxidizers in the surrounding soils. We assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy/carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.},
}
@article {pmid38624181,
year = {2024},
author = {Manck, LE and Coale, TH and Stephens, BM and Forsch, KO and Aluwihare, LI and Dupont, CL and Allen, AE and Barbeau, KA},
title = {Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38624181},
issn = {1751-7370},
support = {OCE-1026607//NSF/ ; DGE-1144086//NSF/ ; 729162//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; OCE-1558453//NSF/ ; OCE-1756884//NSF/ ; 970820//Simons Collaboration on Principles of Microbial Ecosystems/ ; OCE-1558841//NSF/ ; },
mesh = {*Iron/metabolism ; *Carbon/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Seawater/microbiology ; California ; *Heterotrophic Processes ; Microbiota ; },
abstract = {Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.},
}
@article {pmid38622815,
year = {2024},
author = {Riquelme Del Río, B and Sepulveda-Jauregui, A and Salas-Rabaza, JA and Mackenzie, R and Thalasso, F},
title = {Fine-Scale Spatial Variability of Greenhouse Gas Emissions From a Subantarctic Peatland Bog.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {17},
pages = {7393-7402},
pmid = {38622815},
issn = {1520-5851},
mesh = {*Greenhouse Gases/analysis ; *Wetlands ; *Methane/analysis ; Carbon Dioxide/analysis ; Soil/chemistry ; Ecosystem ; Sphagnopsida ; Environmental Monitoring ; },
abstract = {Peatlands are recognized as crucial greenhouse gas sources and sinks and have been extensively studied. Their emissions exhibit high spatial heterogeneity when measured on site using flux chambers. However, the mechanism by which this spatial variability behaves on a very fine scale remains unclear. This study investigates the fine-scale spatial variability of greenhouse gas emissions from a subantarctic Sphagnum peatland bog. Using a recently developed skirt chamber, methane emissions and ecosystem respiration (as carbon dioxide) were measured at a submeter scale resolution, at five specific 3 × 3 m plots, which were examined across the site throughout a single campaign during the Austral summer season. The results indicated that methane fluxes were significantly less homogeneously distributed compared with ecosystem respiration. Furthermore, we established that the spatial variation scale, i.e., the minimum spatial domain over which notable changes in methane emissions and ecosystem respiration occur, was <0.56 m[2]. Factors such as ground height relative to the water table and vegetation coverage were analyzed. It was observed that Tetroncium magellanicum exhibited a notable correlation with higher methane fluxes, likely because of the aerenchymatous nature of this species, facilitating gas transport. This study advances understanding of gas exchange patterns in peatlands but also emphasizes the need for further efforts for characterizing spatial dynamics at a very fine scale for precise greenhouse gas budget assessment.},
}
@article {pmid38621490,
year = {2024},
author = {Cheng, J and Robles-Lecompte, A and McKenna, AM and Chang, NB},
title = {Deciphering linkages between DON and the microbial community for nitrogen removal using two green sorption media in a surface water filtration system.},
journal = {Chemosphere},
volume = {357},
number = {},
pages = {142042},
doi = {10.1016/j.chemosphere.2024.142042},
pmid = {38621490},
issn = {1879-1298},
mesh = {*Nitrogen/metabolism ; *Filtration/methods ; Water Pollutants, Chemical/metabolism/analysis ; Water Purification/methods ; Biodegradation, Environmental ; Denitrification ; Adsorption ; Microbiota ; Florida ; Aluminum Oxide/chemistry ; Waste Disposal, Fluid/methods ; },
abstract = {The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 T FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.},
}
@article {pmid38619794,
year = {2024},
author = {Van Holm, W and Zayed, N and Lauwens, K and Saghi, M and Axelsson, J and Aktan, MK and Braem, A and Simoens, K and Vanbrabant, L and Proost, P and Van Holm, B and Maes, P and Boon, N and Bernaerts, K and Teughels, W},
title = {Oral Biofilm Composition, Dissemination to Keratinocytes, and Inflammatory Attenuation Depend on Probiotic and Synbiotic Strain Specificity.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {38619794},
issn = {1867-1314},
support = {C24/17/086//KU Leuven/ ; C16/17/010//KU Leuven/ ; C16/17/010//KU Leuven/ ; C24/17/086//KU Leuven/ ; G091218N//Fonds Wetenschappelijk Onderzoek/ ; G091218N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {Several inflammatory diseases are characterized by a disruption in the equilibrium between the host and its microbiome. Due to the increase in resistance, the use of antibiotics for the widespread, nonspecific killing of microorganisms is at risk. Pro-microbial approaches focused on stimulating or introducing beneficial species antagonistic toward pathobionts may be a viable alternative for restoring the host-microbiome equilibrium. Unfortunately, not all potential probiotic or synbiotic species and even subspecies (to strain level) are equally effective for the designated pathology, leading to conflicting accounts of their efficacy. To assess the extent of these species- and strain-specific effects, 13 probiotic candidates were evaluated for their probiotic and synbiotic potential with glycerol on in vitro oral biofilms, dissemination from biofilms to keratinocytes, and anti-inflammatory activity. Species- and strain-specific effects and efficacies were observed in how they functioned as probiotics or synbiotics by influencing oral pathobionts and commensals within biofilms and affected the dissemination of pathobionts to keratinocytes, ranging from ineffective strains to strains that reduced pathobionts by 3 + log. In addition, a minority of the candidates exhibited the ability to mitigate the inflammatory response of LPS-stimulated monocytes. For a comprehensive assessment of probiotic therapy for oral health, a judicious selection of fully characterized probiotic strains that are specifically tailored to the designated pathology is required. This approach aims to challenge the prevailing perception of probiotics, shifting the focus away from "form over function." Rather than using unproven, hypothetical probiotic strains from known genera or species, one should choose strains that are actually functional in resolving the desired pathology before labelling them probiotics.},
}
@article {pmid38619730,
year = {2024},
author = {Zhu, H and Li, S and Wu, Z and Xiong, X and Lin, P and Liu, B and He, D and Liu, G},
title = {Diversity Patterns of Eukaryotic Phytoplankton in the Medog Section of the Yarlung Zangbo River.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {59},
pmid = {38619730},
issn = {1432-184X},
mesh = {*Ecosystem ; *Rivers ; Biodiversity ; Biomass ; Phytoplankton ; },
abstract = {As one of the important biodiversity conservation areas in China, the ecosystem in the lower reaches of the Yarlung Zangbo River is fragile, and is particularly sensitive to global changes. To reveal the diversity pattern of phytoplankton, the metabarcode sequencing was employed in the Medog section of the lower reaches of the Yarlung Zangbo River during autumn 2019 in present study. The phytoplankton assemblies can be significantly divided into the main stem and the tributaries; there are significant differences in the phytoplankton biomass, alpha and beta diversity between the main stem and the tributaries. While both the main stem and the tributaries are affected by dispersal limitation, the phytoplankton assemblages in the entire lower reaches are primarily influenced by heterogeneous selection. Community dissimilarity and assembly process were significantly correlated with turbidity, electrical conductivity, and nitrogen nutrition. The tributaries were the main source of the increase in phytoplankton diversity in the lower reaches of the Yarlung Zangbo River. Such diversity pattern of phytoplankton in the lower reach may be caused by the special habitat in Medog, that is, the excessive flow velocity, and the significant spatial heterogeneity in physical and chemical factors between stem and tributaries. Based on the results and conclusions obtained in present study, continuous long-term monitoring is essential to assess and quantify the impact of global changes on phytoplankton.},
}
@article {pmid38618866,
year = {2024},
author = {Zha, Z and Wang, R and Wang, Q and Chen, F and Ye, Z and Li, Y},
title = {A fast and efficient liquid chromatography-tandem mass spectrometry method for measuring l- and d-amino acids in the urine of patients with immunoglobulin A nephropathy.},
journal = {Biomedical chromatography : BMC},
volume = {38},
number = {6},
pages = {e5866},
doi = {10.1002/bmc.5866},
pmid = {38618866},
issn = {1099-0801},
support = {82170716//National Science Foundation of China/ ; 81870333//National Science Foundation of China/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; //College Science and Technology Innovation Project of Shanxi Education Department/ ; },
mesh = {Humans ; *Tandem Mass Spectrometry/methods ; *Amino Acids/urine ; *Glomerulonephritis, IGA/urine ; Chromatography, Liquid/methods ; Male ; Adult ; Female ; Middle Aged ; Reproducibility of Results ; Biomarkers/urine ; Stereoisomerism ; Linear Models ; Case-Control Studies ; Young Adult ; },
abstract = {Immunoglobulin nephropathy (IgAN) stands as the most prevalent primary glomerular nephropathy globally, typically diagnosed through an invasive renal biopsy. Emerging research suggests the significant involvement of chiral amino acids in kidney disease progression. This study introduces a nonderivative LC-tandem mass spectrometry approach, offering efficient separation outcomes within 15 min for identifying chiral amino acids in human urine samples. Subsequently, using this method, the analysis of l- and d-amino acids in the urine of both patients with IgAN and healthy individuals was conducted. Fourteen d-amino acids and 20 l-amino acids were identified in the urine samples obtained from 17 patients with IgAN and 21 healthy individuals. The results indicated notable variances in the concentrations of both l- and d-amino acids between the IgAN and healthy control groups. In contrast to the healthy group, the IgAN group exhibited higher mean urine concentrations of most l-amino acids and lower concentrations of d-amino acids. Furthermore, correlations between amino acids and clinical markers were investigated. These results propose a novel method for monitoring trace amino acids in urine samples and introduce a new concept for potential markers of IgAN.},
}
@article {pmid38617439,
year = {2024},
author = {Ogaya, Y and Kadota, T and Hamada, M and Nomura, R and Nakano, K},
title = {Characterization of the unique oral microbiome of children harboring Helicobacter pylori in the oral cavity.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2339158},
pmid = {38617439},
issn = {2000-2297},
abstract = {OBJECTIVE: Helicobacter pylori infection is acquired in childhood via the oral cavity, although its relationship with the characteristics of the oral microbiome has not been elucidated. In this study, we performed comprehensive analysis of the oral microbiome in children and adults with or without H. pylori in the oral cavity.<br><br>METHODS: Bacterial DNA was extracted from 41 adult and 21 child saliva specimens, and H. pylori was detected using PCR. 16S rRNA gene amplification was performed for next-generation sequencing. Bioinformatic analyses were conducted using Quantitative Insights into Microbial Ecology 2 (QIIME 2).<br><br>RESULTS: Faith's phylogenetic diversity analysis showed a significant difference between H. pylori-negative adult and child specimens in terms of &#x3b1;-diversity (p&#x2009;<&#x2009;0.05), while no significant difference was observed between H. pylori-positive adult and child specimens. There was also a significant difference in &#x3b2;-diversity between H. pylori-positive and negative child specimens (p&#x2009;<&#x2009;0.05). Taxonomic analysis at the genus level revealed that Porphyromonas was the only bacterium that was significantly more abundant in both H. pylori-positive adults and children than in corresponding negative specimens (p&#x2009;<&#x2009;0.01 and p&#x2009;<&#x2009;0.05, respectively).<br><br>CONCLUSION: These results suggest unique oral microbiome characteristics in children with H. pylori infection in the oral cavity.},
}
@article {pmid38613756,
year = {2024},
author = {Costa, JL and Silva, LG and Veras, STS and Gavazza, S and Florencio, L and Motteran, F and Kato, MT},
title = {Use of nitrate, sulphate, and iron (III) as electron acceptors to improve the anaerobic degradation of linear alkylbenzene sulfonate: effects on removal potential and microbiota diversification.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38613756},
issn = {1614-7499},
support = {APQ-0603-3.07/14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; CAPES-PrInt//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; finance code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; process number 88887.467533/2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {Linear alkylbenzene sulfonate (LAS) is a synthetic anionic surfactant that is found in certain amounts in wastewaters and even in water bodies, despite its known biodegradability. This study aimed to assess the influence of nitrate, sulphate, and iron (III) on LAS anaerobic degradation and biomass microbial diversity. Batch reactors were inoculated with anaerobic biomass, nutrients, LAS (20 mg L[-1]), one of the three electron acceptors, and ethanol (40 mg L[-1]) as a co-substrate. The control treatments, with and without co-substrate, showed limited LAS biodegradation efficiencies of 10 ± 2% and 0%, respectively. However, when nitrate and iron (III) were present without co-substrate, biodegradation efficiencies of 53 ± 4% and 75 ± 3% were achieved, respectively, which were the highest levels observed. Clostridium spp. was prominent in all treatments, while Alkaliphilus spp. and Bacillus spp. thrived in the presence of iron, which had the most significant effect on LAS biodegradation. Those microorganisms were identified as crucial in affecting the LAS anaerobic degradation. The experiments revealed that the presence of electron acceptors fostered the development of a more specialised microbiota, especially those involved in the LAS biodegradation. A mutual interaction between the processes of degradation and adsorption was also shown.},
}
@article {pmid38613638,
year = {2024},
author = {Cai, Y and Chen, Z and Chen, E and Zhang, D and Wei, T and Sun, M and Lian, Y},
title = {Succinic Acid Ameliorates Concanavalin A-Induced Hepatitis by Altering the Inflammatory Microenvironment and Expression of BCL-2 Family Proteins.},
journal = {Inflammation},
volume = {},
number = {},
pages = {},
pmid = {38613638},
issn = {1573-2576},
support = {2021J05278//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//The Health Science Foundation of Fujian Youth Program/ ; 82303109//National Natural Science Foundation of China/ ; 2022J05299//Natural Science Foundation of Fujian Province, China/ ; 2021B002//Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China/ ; },
abstract = {Autoimmune hepatitis (AIH) is a severe immune-mediated inflammatory liver disease that currently lacks feasible drug treatment methods. Our study aimed to evaluate the protective effect of succinic acid against AIH and provide a reliable method for the clinical treatment of AIH. We performed an in vivo study of the effects of succinic acid on concanavalin A (ConA)-induced liver injury in mice. We examined liver transaminase levels, performed hematoxylin and eosin (HE) staining, and observed apoptotic phenotypes in mice. We performed flow cytometry to detect changes in the number of neutrophils and monocytes, and used liposomes to eliminate the liver Kupffer cells and evaluate their role. We performed bioinformatics analysis, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and western blotting to detect mitochondrial apoptosis-induced changes in proteins from the B-cell lymphoma 2(Bcl-2) family. Succinic acid ameliorated ConA-induced AIH in a concentration-dependent manner, as reflected in the survival curve. HE and TUNEL staining and terminal deoxynucleotidyl transferase dUTP nick end labeling revealed decreased alanine transaminase and aspartate aminotransferase levels, and reduced liver inflammation and apoptosis. RT-qPCR and enzyme-linked immunosorbent assay revealed that succinic acid significantly reduced liver pro-inflammatory cytokine levels. Flow cytometry revealed significantly decreased levels of liver neutrophils. Moreover, the protective effect of succinic acid disappeared after the Kupffer cells were eliminated, confirming their important role in the effect. Bioinformatics analysis, RT-qPCR, and western blotting showed that succinic acid-induced changes in proteins from the Bcl-2 family involved mitochondrial apoptosis, indicating the molecular mechanism underlying the protective effect of succinic acid. Succinic acid ameliorated ConA-induced liver injury by regulating immune balance, inhibiting pro-inflammatory factors, and promoting anti-apoptotic proteins in the liver. This study provides novel insights into the biological functions and therapeutic potential of succinic acid in the treatment of autoimmune liver injury.},
}
@article {pmid38606974,
year = {2024},
author = {Cardoso, PM and Hill, LJ and Villela, HDM and Vilela, CLS and Assis, JM and Rosado, PM and Rosado, JG and Chacon, MA and Majzoub, ME and Duarte, GAS and Thomas, T and Peixoto, RS},
title = {Localization and symbiotic status of probiotics in the coral holobiont.},
journal = {mSystems},
volume = {9},
number = {5},
pages = {e0026124},
pmid = {38606974},
issn = {2379-5077},
support = {FCC/1/1976-40-01,BAS/1/1095-01-0//King Abdullah University of Science and Technology (KAUST)/ ; },
mesh = {*Anthozoa/microbiology/physiology ; *Symbiosis/physiology ; Animals ; *Probiotics/pharmacology ; In Situ Hybridization, Fluorescence ; Halomonas/physiology ; Microbiota/physiology ; },
abstract = {UNLABELLED: Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome.<br><br>IMPORTANCE: Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.},
}
@article {pmid38602612,
year = {2024},
author = {Xie, Y and Fan, Y and Su, M and Wang, Y and Zhang, G},
title = {Characteristics of the oral microbiota in patients with primary Sjögren's syndrome.},
journal = {Clinical rheumatology},
volume = {43},
number = {6},
pages = {1939-1947},
pmid = {38602612},
issn = {1434-9949},
support = {2019-106-21//Shantou Medical Health Science and Technology Plan/ ; A2019244//Medical Science Research Foundation of Guangdong Province/ ; },
mesh = {Humans ; *Sjogren's Syndrome/microbiology ; Female ; Middle Aged ; *Saliva/microbiology ; *Microbiota ; Male ; Adult ; *Mouth/microbiology ; *RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; High-Throughput Nucleotide Sequencing ; Dental Plaque/microbiology ; Dental Caries/microbiology ; },
abstract = {OBJECTIVE: Primary Sjögren's syndrome (pSS) is an autoimmune disease with unknown etiology that is considered to be related to environmental and genetic factors. The aim of this study was to clarify the oral microflora characteristics of pSS patients and to reveal the connection between oral bacterial composition and dental caries using a high-throughput sequencing technique.<br><br>METHODS: Thirty-five pSS patients and 20 healthy controls were enrolled in this study. We collected saliva and plaque samples from pSS patients and saliva samples from healthy controls. We used 16S ribosomal DNA (16S rDNA) high-throughput sequencing targeting the V3-V4 hypervariable region to determine the composition and structure of the microbiota in the three sample sets. Finally, bioinformatics analyses, including the diversity of the microbiota, species differences, and functional prediction were performed.<br><br>RESULTS: In the alpha diversity and beta diversity analysis, the Chao1 (P&#x2009;<&#x2009;0.01), observed species (P&#x2009;<&#x2009;0.01), and PD whole tree indices (P&#x2009;<&#x2009;0.01) were significantly lower in the saliva and plaque samples of pSS patients than in the saliva samples of healthy controls, but the Shannon (P&#x2009;<&#x2009;0.01) and Simpson indices (P&#x2009;<&#x2009;0.01) were significantly higher in the healthy controls, and their total diversity significantly differed. In the main flora composition at the genus level (top 10), we identified Prevotella and Veillonella as more enriched in the saliva of pSS patients and Fusobacterium, Actinomyces, and Leptotrichia as more enriched in the plaque of pSS patients. Predictive functional analysis showed that the oral microbiota of pSS patients was related to translation, metabolism of cofactors and vitamins, and nucleotide metabolism.<br><br>CONCLUSIONS: The oral microbial ecology of patients with pSS is dysregulated, resulting in a decrease in overall diversity. Prevotella and Veillonella may be related to pSS, while Fusobacterium, Actinomyces, and Leptotrichia may be related to dental caries in pSS patients. Key Points &#x2022; This study revealed differences in the oral microbial composition of patients with pSS compared to healthy controls. &#x2022; We included a plaque group of pSS patients to identify the microbiota related to pSS and dental caries. &#x2022; Prevotella and Veillonella may contribute to pSS, and Fusobacterium, Actinomyces, and Leptotrichia are associated with dental caries in pSS patients.},
}
@article {pmid38602532,
year = {2024},
author = {Xing, H and Chen, W and Liu, Y and Cahill, JF},
title = {Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {58},
pmid = {38602532},
issn = {1432-184X},
support = {31670531 and 32071645//National Natural Science Foundation of China/ ; 2022JBGS04 and 2023JBGS06//Research Project of Baishanzu National Park/ ; },
mesh = {China ; Forests ; Gamma Rays ; *Microbiota ; *Mycorrhizae ; Soil ; },
abstract = {Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.},
}
@article {pmid38602492,
year = {2024},
author = {Machushynets, NV and Al Ayed, K and Terlouw, BR and Du, C and Buijs, NP and Willemse, J and Elsayed, SS and Schill, J and Trebosc, V and Pieren, M and Alexander, FM and Cochrane, SA and Liles, MR and Medema, MH and Martin, NI and van Wezel, GP},
title = {Discovery and Derivatization of Tridecaptin Antibiotics with Altered Host Specificity and Enhanced Bioactivity.},
journal = {ACS chemical biology},
volume = {19},
number = {5},
pages = {1106-1115},
pmid = {38602492},
issn = {1554-8937},
mesh = {*Anti-Bacterial Agents/pharmacology/chemistry ; *Pseudomonas aeruginosa/drug effects ; Humans ; *Microbial Sensitivity Tests ; Host Specificity ; Drug Discovery ; Lipopeptides/pharmacology/chemistry ; Peptides ; },
abstract = {The prevalence of multidrug-resistant (MDR) pathogens combined with a decline in antibiotic discovery presents a major challenge for health care. To refill the discovery pipeline, we need to find new ways to uncover new chemical entities. Here, we report the global genome mining-guided discovery of new lipopeptide antibiotics tridecaptin A5 and tridecaptin D, which exhibit unusual bioactivities within their class. The change in the antibacterial spectrum of Oct-TriA5 was explained solely by a Phe to Trp substitution as compared to Oct-TriA1, while Oct-TriD contained 6 substitutions. Metabolomic analysis of producer Paenibacillus sp. JJ-21 validated the predicted amino acid sequence of tridecaptin A5. Screening of tridecaptin analogues substituted at position 9 identified Oct-His9 as a potent congener with exceptional efficacy against Pseudomonas aeruginosa and reduced hemolytic and cytotoxic properties. Our work highlights the promise of tridecaptin analogues to combat MDR pathogens.},
}
@article {pmid38598334,
year = {2024},
author = {Wei, X and Tsai, MS and Liang, L and Jiang, L and Hung, CJ and Jelliffe-Pawlowski, L and Rand, L and Snyder, M and Jiang, C},
title = {Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114078},
doi = {10.1016/j.celrep.2024.114078},
pmid = {38598334},
issn = {2211-1247},
mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota/genetics ; *Lactobacillus/genetics ; Adhesins, Bacterial/genetics ; Ethnicity/genetics ; Adult ; Evolution, Molecular ; Pregnancy ; Selection, Genetic ; Biological Evolution ; },
abstract = {The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.},
}
@article {pmid38593340,
year = {2024},
author = {Suárez-Moo, P and Prieto-Davó, A},
title = {Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications.},
journal = {MicrobiologyOpen},
volume = {13},
number = {2},
pages = {e1407},
pmid = {38593340},
issn = {2045-8827},
support = {//Consejo Nacional de Humanidades Ciencias y Tecnolog&#xed;as (CONAHCYT), M&#xe9;xico project A1-S-10785 (APD) and postdoctoral fellowship (362331) (PSM)/ ; },
mesh = {Bacteria/genetics ; Metagenome ; *Microbiota ; Multigene Family ; *Bacillaceae/genetics ; *Biological Products ; Biosynthetic Pathways/genetics ; },
abstract = {Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.},
}
@article {pmid38593079,
year = {2024},
author = {Zhong, Q and Liao, B and Liu, J and Shen, W and Wang, J and Wei, L and Ma, Y and Dong, PT and Bor, B and McLean, JS and Chang, Y and Shi, W and Cen, L and Wu, M and Liu, J and Li, Y and He, X and Le, S},
title = {Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {16},
pages = {e2319790121},
pmid = {38593079},
issn = {1091-6490},
support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 GM110243/GM/NIGMS NIH HHS/United States ; R01 AI087946/AI/NIAID NIH HHS/United States ; R01 GM124378/GM/NIGMS NIH HHS/United States ; R01 AI152421/AI/NIAID NIH HHS/United States ; R01 DE030943/DE/NIDCR NIH HHS/United States ; R01 AI132818/AI/NIAID NIH HHS/United States ; R01 DE031274/DE/NIDCR NIH HHS/United States ; S10 OD023603/OD/NIH HHS/United States ; },
mesh = {Humans ; *Bacteriophages/physiology ; Symbiosis ; Bacteria/genetics ; },
abstract = {Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, the factors influencing the long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members of the human oral microbiome. These ultrasmall bacteria form episymbiotic relationships with their host bacteria and impact their physiology. Here, we showed that during surface-associated growth, a human oral Saccharibacteria isolate (named TM7x) protects its host bacterium, a Schaalia odontolytica strain (named XH001) against lytic phage LC001 predation. RNA-Sequencing analysis identified in XH001 a gene cluster with predicted functions involved in the biogenesis of cell wall polysaccharides (CWP), whose expression is significantly down-regulated when forming a symbiosis with TM7x. Through genetic work, we experimentally demonstrated the impact of the expression of this CWP gene cluster on bacterial-phage interaction by affecting phage binding. In vitro coevolution experiments further showed that the heterogeneous populations of TM7x-associated and TM7x-free XH001, which display differential susceptibility to LC001 predation, promote bacteria and phage coexistence. Our study highlights the tripartite interaction between the bacterium, episymbiont, and phage. More importantly, we present a mechanism, i.e., episymbiont-mediated modulation of gene expression in host bacteria, which impacts their susceptibility to phage predation and contributes to the formation of "source-sink" dynamics between phage and bacteria in biofilm, promoting their long-term coexistence within the human microbiome.},
}
@article {pmid38591008,
year = {2024},
author = {Kang, M and Liu, L and Grossart, HP},
title = {Spatio-temporal variations of methane fluxes in sediments of a deep stratified temperate lake.},
journal = {iScience},
volume = {27},
number = {4},
pages = {109520},
pmid = {38591008},
issn = {2589-0042},
abstract = {Spatio-temporal variability of sediment-mediated methane (CH4) production in freshwater lakes causes large uncertainties in predicting global lake CH4 emissions under different climate change and eutrophication scenarios. We conducted extensive sediment incubation experiments to investigate CH4 fluxes in Lake Stechlin, a deep, stratified temperate lake. Our results show contrasting spatial patterns in CH4 fluxes between littoral and profundal sites. The littoral sediments, ∼33% of the total sediment surface area, contributed ∼86.9% of the annual CH4 flux at the sediment-water interface. Together with sediment organic carbon quality, seasonal stratification is responsible for the striking spatial difference in sediment CH4 production between littoral and profundal zones owing to more sensitive CH4 production than oxidation to warming. While profundal sediments produce a relatively small amount of CH4, its production increases markedly as anoxia spreads in late summer. Our measurements indicate that future lake CH4 emissions will increase due to climate warming and concomitant hypoxia/anoxia.},
}
@article {pmid38589480,
year = {2024},
author = {Sanchis Pla, L and van Gestel, J},
title = {Exploring the microbial savanna: predator-prey interactions in the soil.},
journal = {Molecular systems biology},
volume = {20},
number = {5},
pages = {477-480},
pmid = {38589480},
issn = {1744-4292},
support = {101116560//ERC Starting Grant/ ; },
mesh = {*Soil Microbiology ; Grassland ; Animals ; Food Chain ; Predatory Behavior ; Soil/chemistry ; },
abstract = {Soils host complex multi-trophic communities with diverse, mostly microbial, predator and prey species, including numerous bacterivorous protists and bacterial prey. The molecular mechanisms underlying microbial predator-prey interactions have thus far mainly been explored using reductionist methods, outside the soil environment and independent from the broader life history strategies that microbes display in soils. In this Comment, we advocate for an integrative research approach, combining molecular systems biology and microbial ecology, to investigate how predator-prey interactions shape microbial life history strategies and thereby population dynamics in natural soil communities.},
}
@article {pmid38587642,
year = {2024},
author = {Srinivasan, S and Jnana, A and Murali, TS},
title = {Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {56},
pmid = {38587642},
issn = {1432-184X},
support = {CRG/2022/003227//Science and Engineering Research Board/ ; },
mesh = {Humans ; *Microbial Interactions ; *Microbiota ; Microbial Consortia ; Coculture Techniques ; Community Networks ; },
abstract = {Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.},
}
@article {pmid38587527,
year = {2024},
author = {Garcia Mendez, DF and Egan, S and Wist, J and Holmes, E and Sanabria, J},
title = {Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {57},
pmid = {38587527},
issn = {1432-184X},
support = {FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Bioreactors ; Feces ; },
abstract = {Understanding the intricate ecological interactions within the gut microbiome and unravelling its impact on human health is a challenging task. Bioreactors are valuable tools that have contributed to our understanding of gut microbial ecology. However, there is a lack of studies describing and comparing the microbial diversity cultivated in these models. This knowledge is crucial for refining current models to reflect the gastrointestinal microbiome accurately. In this study, we analysed the microbial diversity of 1512 samples from 18 studies available in public repositories that employed cultures performed in batches and various bioreactor models to cultivate faecal microbiota. Community structure comparison between samples using t-distributed stochastic neighbour embedding and the Hellinger distance revealed a high variation between projects. The main driver of these differences was the inter-individual variation between the donor faecal inocula. Moreover, there was no overlap in the structure of the microbial communities between studies using the same bioreactor platform. In addition, α-diversity analysis using Hill numbers showed that highly complex bioreactors did not exhibit higher diversities than simpler designs. However, analyses of five projects in which the samples from the faecal inoculum were also provided revealed an amplicon sequence variants enrichment in bioreactors compared to the inoculum. Finally, a comparative analysis of the taxonomy of the families detected in the projects and the GMRepo database revealed bacterial families exclusively found in the bioreactor models. These findings highlight the potential of bioreactors to enrich low-abundance microorganisms from faecal samples, contributing to uncovering the gut microbial "dark matter".},
}
@article {pmid38585661,
year = {2024},
author = {Hill, LJ and Messias, CSMA and Vilela, CLS and Garritano, AN and Villela, HDM and do Carmo, FL and Thomas, T and Peixoto, RS},
title = {Bacteria associated with the in hospite Symbiodiniaceae's phycosphere.},
journal = {iScience},
volume = {27},
number = {4},
pages = {109531},
pmid = {38585661},
issn = {2589-0042},
abstract = {Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.},
}
@article {pmid38585291,
year = {2023},
author = {Hobusch, U and Scheuch, M and Heuckmann, B and Hodžić, A and Hobusch, GM and Rammel, C and Pfeffer, A and Lengauer, V and Froehlich, DE},
title = {One Health Education Nexus: enhancing synergy among science-, school-, and teacher education beyond academic silos.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1337748},
pmid = {38585291},
issn = {2296-2565},
mesh = {Humans ; Ecosystem ; *One Health ; *Teacher Training ; Students ; Schools ; Health Education ; Educational Status ; },
abstract = {INTRODUCTION: The fact that the daily lives of billions of people were affected by the medical, social, and political aspects of the SARS-CoV-2 pandemic shows the need to anchor the understanding of One Health in society. Hence, promoting awareness and deepening the understanding of the interrelation between human health, animal health, and ecosystems must be accomplished through quality education, as advocated by UN Sustainable Development Goal 4. The often-questioned and discussed measures taken by governments to control the global pandemic between 2020 and 2023 can be seen as an opportunity to meet the educational needs of civil society solutions in multi-stakeholder settings between public, universities, and schools.<br><br>METHODS: This paper focuses on the integration of One Health principles in educational frameworks, particularly within the context of the higher education teaching framework "Teaching Clinic." This master-level course in the domain of pre-service teacher education serves as a potent vehicle for facilitating One Health Education, bridging the gap between research, higher education, and schools. Through the presentation of two case studies, this article demonstrates how the Teaching Clinic approach fosters interdisciplinary perspectives and provides a dynamic learning environment for pre-service teachers, as well as for pupils involved in the educational process.<br><br>RESULTS: In both cases, the integration of educational One Health school teaching-learning settings effectively enhanced pupils' understanding of complex topics and engaged them in active learning experiences. Pre-service teachers played a crucial role in developing, implementing, and evaluating these interventions. In Case I, pupils demonstrated proficiency in analyzing data and evaluating mathematical models, while in Case II, the chosen instructional approach facilitated One Health knowledge acquisition and enjoyment among pupils. These results underscore the potential of the One Health Teaching Clinic as a valuable educational framework for enhancing teaching and learning outcomes for pre-service teachers and fostering pupil engagement in socio-scientific One Health-related topics.<br><br>DISCUSSION: The discussion delves into the significance of breaking down disciplinary silos and the crucial role of teacher education in promoting a holistic approach to education, emphasizing the intersectionality of One Health Education and Education for Sustainable Development. This article underpins the significance of collaborative efforts across multiple (scientific) disciplines and across secondary and tertiary education levels to reach a nexus. Moreover, it emphasizes the alignment of this approach with the 2030 Agenda, Education for Sustainable Development, and Sustainable Development Goals, highlighting the potential for collective action toward a more sustainable future.},
}
@article {pmid38581683,
year = {2024},
author = {Loos, D and Filho, APDC and Dutilh, BE and Barber, AE and Panagiotou, G},
title = {A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114046},
doi = {10.1016/j.celrep.2024.114046},
pmid = {38581683},
issn = {2211-1247},
mesh = {*Soil Microbiology ; *Fungi/genetics/classification ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Humans ; Biodiversity ; Genomics/methods ; Phylogeny ; },
abstract = {Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.},
}
@article {pmid38581020,
year = {2024},
author = {Douillard, FP and Derman, Y and Jian, C and Korpela, K and Saxén, H and Salonen, A and de Vos, WM and Korkeala, H and Lindström, M},
title = {Case report: Aberrant fecal microbiota composition of an infant diagnosed with prolonged intestinal botulism.},
journal = {Gut pathogens},
volume = {16},
number = {1},
pages = {20},
pmid = {38581020},
issn = {1757-4749},
abstract = {BACKGROUND: Intestinal botulism is primarily reported in small babies as a condition known as infant botulism. The condition results from the ingestion of environmental or foodborne spores of botulinum neurotoxin (BoNT) producing Clostridia, usually Clostridium botulinum, and subsequent spore germination into active botulinum neurotoxinogenic cultures in the gut. It is generally considered that small babies are susceptible to C. botulinum colonization because of their immature gut microbiota. Yet, it is poorly understood which host factors contribute to the clinical outcome of intestinal botulism. We previously reported a case of infant botulism where the infant recovered clinically in six weeks but continued to secrete C. botulinum cells and/or BoNT in the feces for seven months.<br><br>CASE PRESENTATION: To further understand the microbial ecology behind this exceptionally long-lasting botulinum neurotoxinogenic colonization, we characterized the infant fecal microbiota using 16S rRNA gene amplicon sequencing over the course of disease and recovery. C. botulinum could be detected in the infant fecal samples at low levels through the acute phase of the disease and three months after recovery. Overall, we observed a temporal delay in the maturation of the infant fecal microbiota associated with a persistently high-level bifidobacterial population and a low level of Lachnospiraceae, Bacteroidaceae and Ruminococcaceae compared to healthy infants over time.<br><br>CONCLUSION: This study brings novel insights into the infant fecal composition associated with intestinal botulism and provides a basis for a more systematic analysis of the gut microbiota of infants diagnosed with botulism. A better understanding of the gut microbial ecology associated with infant botulism may support the development of prophylactic strategies against this life-threatening disease in small babies.},
}
@article {pmid38579997,
year = {2024},
author = {Cao, Y and Li, Y and Jia, L and Wang, Q and Niu, T and Yang, Q and Wang, Q and Zeng, X and Wang, R and Yue, L},
title = {Long-term and combined heavy-metal contamination forms a unique microbiome and resistome: A case study in a Yellow River tributary sediments.},
journal = {Environmental research},
volume = {252},
number = {Pt 1},
pages = {118861},
doi = {10.1016/j.envres.2024.118861},
pmid = {38579997},
issn = {1096-0953},
mesh = {*Metals, Heavy/toxicity/analysis ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Microbiota/drug effects ; *Water Pollutants, Chemical/analysis/toxicity ; China ; Environmental Monitoring ; Bacteria/genetics/drug effects ; },
abstract = {Microorganisms have developed mechanisms to adapt to environmental stress, but how microbial communities adapt to long-term and combined heavy-metal contamination under natural environmental conditions remains unclear. Specifically, this study analyzed the characteristics of heavy metal composition, microbial community, and heavy metal resistance genes (MRGs) in sediments along Mang River, a tributary of the Yellow River, which has been heavily polluted by industrial production for more than 40 years. The results showed that the concentrations of Cr, Zn, Pb, Cu and As in most sediments were higher than the ambient background values. Bringing the heavy metals speciation and concentration into the risk evaluation method, two-thirds of the sediment samples were at or above the moderate risk level, and the ecological risk of combined heavy metals in the sediments decreased along the river stream. The high ecological risk of heavy metals affected the microbial community structure, metabolic pathways and MRG distribution. The formation of a HM-resistant microbiome possibly occurred through the spread of insertion sequences (ISs) carrying multiple MRGs, the types of ISs carrying MRGs outnumber those of plasmids, and the quantity of MRGs on ISs is also higher than that on plasmids. These findings could improve our understanding of the adaptation mechanism of microbial communities to long-term combined heavy metal contamination.},
}
@article {pmid38578091,
year = {2024},
author = {Morrison, BH and Jones, JL and Dzwonkowski, B and Krause, JW},
title = {Tracking Vibrio: population dynamics and ecology of Vibrio parahaemolyticus and V. vulnificus in an Alabama estuary.},
journal = {Microbiology spectrum},
volume = {12},
number = {5},
pages = {e0367423},
pmid = {38578091},
issn = {2165-0497},
support = {U19 FD005923/FD/FDA HHS/United States ; #5U19FD005923-04//HHS | U.S. Food and Drug Administration (FDA)/ ; },
mesh = {*Vibrio parahaemolyticus/isolation &amp; purification/growth &amp; development ; *Vibrio vulnificus/isolation &amp; purification/growth &amp; development ; *Estuaries ; Alabama ; Population Dynamics ; Salinity ; Vibrio Infections/microbiology/epidemiology ; Seawater/microbiology ; Water Microbiology ; },
abstract = {UNLABELLED: Vibrio is a genus of halophilic, gram-negative bacteria found in estuaries around the globe. Integral parts of coastal cultures often involve contact with vectors of pathogenic Vibrio spp. (e.g., consuming raw shellfish). High rates of mortality from certain Vibrio spp. infections demonstrate the need for an improved understanding of Vibrio spp. dynamics in estuarine regions. Our study assessed meteorological, hydrographic, and biological correlates of Vibrio parahaemolyticus and V. vulnificus at 10 sites in the Eastern Mississippi Sound System (EMSS) from April to October 2019. During the sampling period, median abundances of V. parahaemolyticus and V. vulnificus were 2.31 log MPN/L and 2.90 log MPN/L, respectively. Vibrio spp. dynamics were largely driven by site-based variation, with sites closest to freshwater inputs having the highest abundances. The E-W wind scalar, which affects Ekman transport, was a novel Vibrio spp. correlate observed. A potential salinity effect on bacterial-particle associations was identified, where V. vulnificus was associated with larger particles in conditions outside of their optimal salinity. Additionally, V. vulnificus abundances were correlated to those of harmful algal species that did not dominate community chlorophyll. Correlates from this study may be used to inform the next iteration of regionally predictive Vibrio models and may lend additional insight to Vibrio spp. ecology in similar systems.<br><br>IMPORTANCE: Vibrio spp. are bacteria found in estuaries worldwide; some species can cause illness and infections in humans. Relationships between Vibrio spp. abundance, salinity, and temperature are well documented, but correlations to other environmental parameters are less understood. This study identifies unique correlates (e.g., E-W wind scalar and harmful algal species) that could potentially inform the next iteration of predictive Vibrio models for the EMSS region. Additionally, these correlates may allow existing environmental monitoring efforts to be leveraged in providing data inputs for future Vibrio risk models. An observed correlation between salinity and V. vulnificus/particle-size associations suggests that predicted environmental changes may affect the abundance of Vibrio spp. in certain reservoirs, which may alter which vectors present the greatest vibrio risk.},
}
@article {pmid38575035,
year = {2024},
author = {Zheng, W and Wu, Q and Guo, X and Zhou, P and Wu, J and Yan, W},
title = {Rocky desertification succession alters soil microbial communities and survival strategies in the karst context.},
journal = {The Science of the total environment},
volume = {927},
number = {},
pages = {172171},
doi = {10.1016/j.scitotenv.2024.172171},
pmid = {38575035},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Microbiota ; *Fungi ; *Soil/chemistry ; Archaea/genetics/physiology ; Ecosystem ; Conservation of Natural Resources ; },
abstract = {Rocky desertification is one of the most ecological problems in the karst context. Although extensive research has been conducted to explore how to restore and protect, the responses of soil fungi and archaea to rocky desertification succession remain limited. Here, four grades of rocky desertification in a karst ecosystem were selected, amplicon sequencing analysis was conducted to investigate fungal and archaeal community adaptation in response to rocky desertification succession. Our findings revealed that the diversity and community structure of fungi and archaea in soils declined with the aggravation of rocky desertification. As the rocky desertification succession intensified, microbial interactions shifted from cooperation to competition. Microbial survival strategies were K-strategist and r-strategist dominated in the early and late stages of succession, respectively. Additionally, the driving factors affecting microorganisms have shifted from vegetation diversity to soil properties as the intensification of rocky desertification. Collectively, our study highlighted that plant diversity and soil properties play important roles on soil microbiomes in fragile karst ecosystems and that environmental factors induced by human activities might still be the dominant factor exacerbating rocky desertification, which could significantly enrich our understanding of microbial ecology within karst ecosystems.},
}
@article {pmid38574431,
year = {2024},
author = {Cunha, ICMD and Silva, AVRD and Boleta, EHM and Pellegrinetti, TA and Zagatto, LFG and Zagatto, SDSS and Chaves, MG and Mendes, R and Patreze, CM and Tsai, SM and Mendes, LW},
title = {The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype.},
journal = {Microbiological research},
volume = {283},
number = {},
pages = {127706},
doi = {10.1016/j.micres.2024.127706},
pmid = {38574431},
issn = {1618-0623},
mesh = {*Rhizosphere ; Plants/microbiology ; Bacteria/genetics ; *Microbiota ; Soil/chemistry ; Phenotype ; Soil Microbiology ; Plant Roots/microbiology ; },
abstract = {Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.},
}
@article {pmid38571798,
year = {2024},
author = {Rani, V and Horváth, Z and Nejstgaard, JC and Fierpasz, &#xc1; and Pálffy, K and Vad, CF},
title = {Food density drives diet shift of the invasive mysid shrimp, Limnomysis benedeni.},
journal = {Ecology and evolution},
volume = {14},
number = {4},
pages = {e11202},
pmid = {38571798},
issn = {2045-7758},
abstract = {Understanding the diet preferences and food selection of invasive species is crucial to better predict their impact on community structure and ecosystem functioning. Limnomysis benedeni, a Ponto-Caspian invasive mysid shrimp, is one of the most successful invaders in numerous European river and lake ecosystems. While existing studies suggest potentially strong trophic impact due to high predation pressure on native plankton communities, little is known of its food selectivity between phyto- and zooplankton, under different food concentrations. Here, we therefore investigated the feeding selectivity of L. benedeni on two commonly occurring prey organisms in freshwaters, the small rotifer zooplankton Brachionus calyciflorus together with the microphytoplankton Cryptomonas sp. present in increasing densities. Our results demonstrated a clear shift in food selection, with L. benedeni switching from B. calyciflorus to Cryptomonas sp. already when the two prey species were provided in equal biomasses. Different functional responses were observed for the two food types, indicating somewhat different foraging mechanisms for each food type. These findings provide experimental evidence on the feeding flexibility of invasive mysid shrimps and potential implications for trophic interactions in invaded ecosystems.},
}
@article {pmid38567263,
year = {2023},
author = {Crous, PW and Osieck, ER and Shivas, RG and Tan, YP and Bishop-Hurley, SL and Esteve-Raventós, F and Larsson, E and Luangsa-Ard, JJ and Pancorbo, F and Balashov, S and Baseia, IG and Boekhout, T and Chandranayaka, S and Cowan, DA and Cruz, RHSF and Czachura, P and De la Peña-Lastra, S and Dovana, F and Drury, B and Fell, J and Flakus, A and Fotedar, R and Jurjević, &#x17d; and Kolecka, A and Mack, J and Maggs-Kölling, G and Mahadevakumar, S and Mateos, A and Mongkolsamrit, S and Noisripoom, W and Plaza, M and Overy, DP and Piątek, M and Sandoval-Denis, M and Vauras, J and Wingfield, MJ and Abell, SE and Ahmadpour, A and Akulov, A and Alavi, F and Alavi, Z and Altés, A and Alvarado, P and Anand, G and Ashtekar, N and Assyov, B and Banc-Prandi, G and Barbosa, KD and Barreto, GG and Bellanger, JM and Bezerra, JL and Bhat, DJ and Bilański, P and Bose, T and Bozok, F and Chaves, J and Costa-Rezende, DH and Danteswari, C and Darmostuk, V and Delgado, G and Denman, S and Eichmeier, A and Etayo, J and Eyssartier, G and Faulwetter, S and Ganga, KGG and Ghosta, Y and Goh, J and Góis, JS and Gramaje, D and Granit, L and Groenewald, M and Gulden, G and Gusmão, LFP and Hammerbacher, A and Heidarian, Z and Hywel-Jones, N and Jankowiak, R and Kaliyaperumal, M and Kaygusuz, O and Kezo, K and Khonsanit, A and Kumar, S and Kuo, CH and Læssøe, T and Latha, KPD and Loizides, M and Luo, SM and Maciá-Vicente, JG and Manimohan, P and Marbach, PAS and Marinho, P and Marney, TS and Marques, G and Martín, MP and Miller, AN and Mondello, F and Moreno, G and Mufeeda, KT and Mun, HY and Nau, T and Nkomo, T and Okrasińska, A and Oliveira, JPAF and Oliveira, RL and Ortiz, DA and Pawłowska, J and Pérez-De-Gregorio, M&#xc0; and Podile, AR and Portugal, A and Privitera, N and Rajeshkumar, KC and Rauf, I and Rian, B and Rigueiro-Rodríguez, A and Rivas-Torres, GF and Rodriguez-Flakus, P and Romero-Gordillo, M and Saar, I and Saba, M and Santos, CD and Sarma, PVSRN and Siquier, JL and Sleiman, S and Spetik, M and Sridhar, KR and Stryjak-Bogacka, M and Szczepańska, K and Taşkın, H and Tennakoon, DS and Thanakitpipattana, D and Trovão, J and Türkekul, I and van Iperen, AL and van 't Hof, P and Vasquez, G and Visagie, CM and Wingfield, BD and Wong, PTW and Yang, WX and Yarar, M and Yarden, O and Yilmaz, N and Zhang, N and Zhu, YN and Groenewald, JZ},
title = {Fungal Planet description sheets: 1478-1549.},
journal = {Persoonia},
volume = {50},
number = {},
pages = {158-310},
pmid = {38567263},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Aschersonia mackerrasiae on whitefly, Cladosporium corticola on bark of Melaleuca quinquenervia, Penicillium nudgee from soil under Melaleuca quinquenervia, Pseudocercospora blackwoodiae on leaf spot of Persoonia falcata, and Pseudocercospora dalyelliae on leaf spot of Senna alata. Bolivia, Aspicilia lutzoniana on fully submersed siliceous schist in high-mountain streams, and Niesslia parviseta on the lower part and apothecial discs of Erioderma barbellatum on a twig. Brazil, Cyathus bonsai on decaying wood, Geastrum albofibrosum from moist soil with leaf litter, Laetiporus pratigiensis on a trunk of a living unknown hardwood tree species, and Scytalidium synnematicum on dead twigs of unidentified plant. Bulgaria, Amanita abscondita on sandy soil in a plantation of Quercus suber. Canada, Penicillium acericola on dead bark of Acer saccharum, and Penicillium corticola on dead bark of Acer saccharum. China, Colletotrichum qingyuanense on fruit lesion of Capsicum annuum. Denmark, Helminthosphaeria leptospora on corticioid Neohypochnicium cremicolor. Ecuador (Galapagos), Phaeosphaeria scalesiae on Scalesia sp. Finland, Inocybe jacobssonii on calcareous soils in dry forests and park habitats. France, Cortinarius rufomyrrheus on sandy soil under Pinus pinaster, and Periconia neominutissima on leaves of Poaceae. India, Coprinopsis fragilis on decaying bark of logs, Filoboletus keralensis on unidentified woody substrate, Penicillium sankaranii from soil, Physisporinus tamilnaduensis on the trunk of Azadirachta indica, and Poronia nagaraholensis on elephant dung. Iran, Neosetophoma fici on infected leaves of Ficus elastica. Israel, Cnidariophoma eilatica (incl. Cnidariophoma gen. nov.) from Stylophora pistillata. Italy, Lyophyllum obscurum on acidic soil. Namibia, Aureobasidium faidherbiae on dead leaf of Faidherbia albida, and Aureobasidium welwitschiae on dead leaves of Welwitschia mirabilis. Netherlands, Gaeumannomycella caricigena on dead culms of Carex elongata, Houtenomyces caricicola (incl. Houtenomyces gen. nov.) on culms of Carex disticha, Neodacampia ulmea (incl. Neodacampia gen. nov.) on branch of Ulmus laevis, Niesslia phragmiticola on dead standing culms of Phragmites australis, Pseudopyricularia caricicola on culms of Carex disticha, and Rhodoveronaea nieuwwulvenica on dead bamboo sticks. Norway, Arrhenia similis half-buried and moss-covered pieces of rotting wood in grass-grown path. Pakistan, Mallocybe ahmadii on soil. Poland, Beskidomyces laricis (incl. Beskidomyces gen. nov.) from resin of Larix decidua ssp. polonica, Lapidomyces epipinicola from sooty mould community on Pinus nigra, and Leptographium granulatum from a gallery of Dendroctonus micans on Picea abies. Portugal, Geoglossum azoricum on mossy areas of laurel forest areas planted with Cryptomeria japonica, and Lunasporangiospora lusitanica from a biofilm covering a biodeteriorated limestone wall. Qatar, Alternaria halotolerans from hypersaline sea water, and Alternaria qatarensis from water sample collected from hypersaline lagoon. South Africa, Alfaria thamnochorti on culm of Thamnochortus fraternus, Knufia aloeicola on Aloe gariepensis, Muriseptatomyces restionacearum (incl. Muriseptatomyces gen. nov.) on culms of Restionaceae, Neocladosporium arctotis on nest of cases of bag worm moths (Lepidoptera, Psychidae) on Arctotis auriculata, Neodevriesia scadoxi on leaves of Scadoxus puniceus, Paraloratospora schoenoplecti on stems of Schoenoplectus lacustris, Tulasnella epidendrea from the roots of Epidendrum × obrienianum, and Xenoidriella cinnamomi (incl. Xenoidriella gen. nov.) on leaf of Cinnamomum camphora. South Korea, Lemonniera fraxinea on decaying leaves of Fraxinus sp. from pond. Spain, Atheniella lauri on the bark of fallen trees of Laurus nobilis, Halocryptovalsa endophytica from surface-sterilised, asymptomatic roots of Salicornia patula, Inocybe amygdaliolens on soil in mixed forest, Inocybe pityusarum on calcareous soil in mixed forest, Inocybe roseobulbipes on acidic soils, Neonectria borealis from roots of Vitis berlandieri × Vitis rupestris, Sympoventuria eucalyptorum on leaves of Eucalyptus sp., and Tuber conchae from soil. Sweden, Inocybe bidumensis on calcareous soil. Thailand, Cordyceps sandindaengensis on Lepidoptera pupa, buried in soil, Ophiocordyceps kuchinaraiensis on Coleoptera larva, buried in soil, and Samsoniella winandae on Lepidoptera pupa, buried in soil. Taiwan region (China), Neophaeosphaeria livistonae on dead leaf of Livistona rotundifolia. Türkiye, Melanogaster anatolicus on clay loamy soils. UK, Basingstokeomyces allii (incl. Basingstokeomyces gen. nov.) on leaves of Allium schoenoprasum. Ukraine, Xenosphaeropsis corni on recently dead stem of Cornus alba. USA, Nothotrichosporon aquaticum (incl. Nothotrichosporon gen. nov.) from water, and Periconia philadelphiana from swab of coil surface. Morphological and culture characteristics for these new taxa are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Shivas RG, et al. 2023. Fungal Planet description sheets: 1478-1549. Persoonia 50: 158- 310. https://doi.org/10.3767/persoonia.2023.50.05.},
}
@article {pmid38562743,
year = {2024},
author = {Matz, LM and Shah, NS and Porterfield, L and Stuyck, OM and Jochum, MD and Kayed, R and Taglialatela, G and Urban, RJ and Buffington, SA},
title = {Microbial determinants of dementia risk in subjects of Mexican descent with type 2 diabetes living in South Texas.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {38562743},
support = {T32 AG067952/AG/NIA NIH HHS/United States ; UL1 TR001439/TR/NCATS NIH HHS/United States ; },
abstract = {Type 2 diabetes (T2D) is a common forerunner of neurodegeneration and dementia, including Alzheimer's Disease (AD), yet the underlying mechanisms remain unresolved. Individuals of Mexican descent living in South Texas have increased prevalence of comorbid T2D and early onset AD, despite low incidence of the predisposing APOE-e4 variant and an absence of the phenotype among relatives residing in Mexico - suggesting a role for environmental factors in coincident T2D and AD susceptibility. Here, in a small clinical trial, we show dysbiosis of the human gut microbiome could contribute to neuroinflammation and risk for AD in this population. Divergent Gastrointestinal Symptom Rating Scale (GSRS) responses, despite no differences in expressed dietary preferences, provided the first evidence for altered gut microbial ecology among T2D subjects (sT2D) versus population-matched healthy controls (HC). Metataxonomic 16S rRNA sequencing of participant stool revealed a decrease in alpha diversity of sT2D versus HC gut communities and identified BMI as a driver of gut community structure. Linear discriminant analysis effect size (LEfSe) identified a significant decrease in the relative abundance of the short-chain fatty acid-producing taxa Lachnospiraceae, Faecalibacterium, and Alistipes and an increase in pathobionts Escherichia-Shigella, Enterobacter, and Clostridia innocuum among sT2D gut microbiota, as well as differentially abundant gene and metabolic pathways. These results suggest characterization of the gut microbiome of individuals with T2D could identify key actors among "disease state" microbiota which may increase risk for or accelerate the onset of neurodegeneration. Furthermore, they identify candidate microbiome-targeted approaches for prevention and treatment of neuroinflammation in AD.},
}
@article {pmid38562476,
year = {2024},
author = {Zhang, R and Zhang, H and Yang, C and Li, H and Wu, J},
title = {Effects of water stress on nutrients and enzyme activity in rhizosphere soils of greenhouse grape.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1376849},
pmid = {38562476},
issn = {1664-302X},
abstract = {In grape cultivation, incorrect water regulation will lead to significant water wastage, which in turn will change soil structure and disrupt soil nutrient cycling processes. This study aimed to investigate the effects of different water regulation treatments [by setting moderate water stress (W1), mild water stress (W2), and adequate water availability (CK)] on soil physical-chemical properties and enzyme activity in greenhouse grape during the growing season. The result showed that the W2 treatment had a negative impact on the build-up of dissolved organic carbon (DOC), nitrate nitrogen (NO3-N), and available phosphorus (AP). Throughout the reproductive period, the W1 and W2 treatments decreased the soil's microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) contents, and MBC was more vulnerable to water stress. During the growth period, the trends of urease, catalase, and sucrase activities in different soil depth were ranked as 10-20 cm > 0-10 cm > 20-40 cm. The urease activity in 0-10 cm soil was suppressed by both W1 and W2 treatments, while the invertase activity in various soil layers under W1 treatment differed substantially. The W1 treatment also reduced the catalase activity in the 20-40 cm soil layer in the grape growth season. These findings suggested that W2 treatment can conserve water and enhance microbial ecology of greenhouse grape soils. Therefore, W2 treatment was the most effective water regulation measure for local greenhouse grape cultivation.},
}
@article {pmid38562261,
year = {2024},
author = {Zünd, JN and Plüss, S and Mujezinovic, D and Menzi, C and von Bieberstein, PR and de Wouters, T and Lacroix, C and Leventhal, GE and Pugin, B},
title = {A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae035},
pmid = {38562261},
issn = {2730-6151},
abstract = {The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.},
}
@article {pmid38555787,
year = {2024},
author = {Mugani, R and El Khalloufi, F and Redouane, EM and Haida, M and Aba, RP and Essadki, Y and El Amrani Zerrifi, S and Hejjaj, A and Ouazzani, N and Campos, A and Grossart, HP and Mandi, L and Vasconcelos, V and Oudra, B},
title = {Unlocking the potential of bacterioplankton-mediated microcystin degradation and removal: A bibliometric analysis of sustainable water treatment strategies.},
journal = {Water research},
volume = {255},
number = {},
pages = {121497},
doi = {10.1016/j.watres.2024.121497},
pmid = {38555787},
issn = {1879-2448},
abstract = {Microcystins (MCs) constitute a significant threat to human and environmental health, urging the development of effective removal methods for these toxins. In this review, we explore the potential of MC-degrading bacteria as a solution for the removal of MCs from water. The review insights into the mechanisms of action employed by these bacteria, elucidating their ability to degrade and thus remove MCs. After, the review points out the influence of the structural conformation of MCs on their removal, particularly their stability at different water depths within different water bodies. Then, we review the crucial role played by the production of MCs in ensuring the survival and safeguarding of the enzymatic activities of Microcystis cells. This justifies the need for developing effective and sustainable methods for removing MCs from aquatic ecosystems, given their critical ecological function and potential toxicity to humans and animals. Thereafter, challenges and limitations associated with using MC-degrading bacteria in water treatment are discussed, emphasizing the need for further research to optimize the selection of bacterial strains used for MCs biodegradation. The interaction of MCs-degrading bacteria with sediment particles is also crucial for their toxin removal potential and its efficiency. By presenting critical information, this review is a valuable resource for researchers, policymakers, and stakeholders involved in developing sustainable and practical approaches to remove MCs. Our review highlights the potential of various applications of MC-degrading bacteria, including multi-soil-layering (MSL) technologies. It emphasizes the need for ongoing research to optimize the utilization of MC-degrading bacteria in water treatment, ultimately ensuring the safety and quality of water sources. Moreover, this review highlights the value of bibliometric analyses in revealing research gaps and trends, providing detailed insights for further investigations. Specifically, we discuss the importance of employing advanced genomics, especially combining various OMICS approaches to identify and optimize the potential of MCs-degrading bacteria.},
}
@article {pmid38555472,
year = {2024},
author = {Pan, J and Zhang, Z and Li, Y and Yu, J and You, Z and Li, C and Wang, S and Zhu, M and Ren, F and Zhang, X and Sun, Y and Wang, S},
title = {A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {3},
pages = {},
pmid = {38555472},
issn = {1477-4054},
support = {2022FY101100//Science &amp; Technology Fundamental Resources Investigation Program/ ; 62325308//National Science Fund for Distinguished Young Scholars of China/ ; 32170114//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Deep Learning ; Pattern Recognition, Automated ; Neural Networks, Computer ; Algorithms ; Bacteria ; },
abstract = {Predicting interactions between microbes and hosts plays critical roles in microbiome population genetics and microbial ecology and evolution. How to systematically characterize the sophisticated mechanisms and signal interplay between microbes and hosts is a significant challenge for global health risks. Identifying microbe-host interactions (MHIs) can not only provide helpful insights into their fundamental regulatory mechanisms, but also facilitate the development of targeted therapies for microbial infections. In recent years, computational methods have become an appealing alternative due to the high risk and cost of wet-lab experiments. Therefore, in this study, we utilized rich microbial metagenomic information to construct a novel heterogeneous microbial network (HMN)-based model named KGVHI to predict candidate microbes for target hosts. Specifically, KGVHI first built a HMN by integrating human proteins, viruses and pathogenic bacteria with their biological attributes. Then KGVHI adopted a knowledge graph embedding strategy to capture the global topological structure information of the whole network. A natural language processing algorithm is used to extract the local biological attribute information from the nodes in HMN. Finally, we combined the local and global information and fed it into a blended deep neural network (DNN) for training and prediction. Compared to state-of-the-art methods, the comprehensive experimental results show that our model can obtain excellent results on the corresponding three MHI datasets. Furthermore, we also conducted two pathogenic bacteria case studies to further indicate that KGVHI has excellent predictive capabilities for potential MHI pairs.},
}
@article {pmid38555095,
year = {2024},
author = {Brame, JE and Warbrick, I and Heke, D and Liddicoat, C and Breed, MF},
title = {Short-term passive greenspace exposures have little effect on nasal microbiomes: A cross-over exposure study of a Māori cohort.},
journal = {Environmental research},
volume = {252},
number = {Pt 1},
pages = {118814},
doi = {10.1016/j.envres.2024.118814},
pmid = {38555095},
issn = {1096-0953},
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Air Microbiology ; Air Pollutants/analysis ; Bacteria/genetics/classification/isolation &amp; purification ; Cohort Studies ; Cross-Over Studies ; Environmental Exposure ; Maori People ; *Microbiota ; New Zealand ; *Nose/microbiology ; Parks, Recreational ; RNA, Ribosomal, 16S/analysis ; },
abstract = {Indigenous health interventions have emerged in New Zealand aimed at increasing people's interactions with and exposure to macro and microbial diversity. Urban greenspaces provide opportunities for people to gain such exposures. However, the dynamics and pathways of microbial transfer from natural environments onto a person remain poorly understood. Here, we analysed bacterial 16S rRNA amplicons in air samples (n = 7) and pre- and post-exposure nasal samples (n = 238) from 35 participants who had 30-min exposures in an outdoor park. The participants were organised into two groups: over eight days each group had two outdoor park exposures and two indoor office exposures, with a cross-over study design and washout days between exposure days. We investigated the effects of participant group, location (outdoor park vs. indoor office), and exposures (pre vs. post) on the nasal bacterial community composition and three key suspected health-associated bacterial indicators (alpha diversity, generic diversity of Gammaproteobacteria, and read abundances of butyrate-producing bacteria). The participants had distinct nasal bacterial communities, but these communities did not display notable shifts in composition following exposures. The community composition and key health bacterial indicators were stable throughout the trial period, with no clear or consistent effects of group, location, or exposure. We conclude that 30-min exposure periods to urban greenspaces are unlikely to create notable changes in the nasal microbiome of visitors, which contrasts with previous research. Our results suggest that longer exposures or activities that involves closer interaction with microbial rich ecological components (e.g., soil) are required for greenspace exposures to result in noteworthy changes in the nasal microbiome.},
}
@article {pmid38554019,
year = {2024},
author = {Hohagen, M and Sánchez, L and Herbst, AJ and Kählig, H and Shin, JW and Berry, D and Del Favero, G and Kleitz, F},
title = {MANNosylation of Mesoporous Silica Nanoparticles Modifies TLR4 Localization and NF-κB Translocation in T24 Bladder Cancer Cells.},
journal = {Advanced healthcare materials},
volume = {13},
number = {17},
pages = {e2304150},
pmid = {38554019},
issn = {2192-2659},
support = {//University of Vienna/ ; IBS-R004//Institute for Basic Science/ ; },
mesh = {Humans ; *Toll-Like Receptor 4/metabolism ; *Silicon Dioxide/chemistry ; *Nanoparticles/chemistry ; *NF-kappa B/metabolism ; *Urinary Bladder Neoplasms/metabolism/pathology ; *Mannose/chemistry ; Cell Line, Tumor ; Bacterial Adhesion/drug effects ; Caveolin 1/metabolism ; Porosity ; Lipopolysaccharides ; },
abstract = {D-mannose is widely used as non-antibiotic treatment for bacterial urinary tract infections. This application is based on a well-studied mechanism of binding to the type 1 bacterial pili and, therefore, blocking bacteria adhesion to the uroepithelial cells. To implement D-mannose into carrier systems, the mechanism of action of the sugar in the bladder environment is also relevant and requires investigation. Herein, two different MANNosylation strategies using mesoporous silica nanoparticles (MSNs) are described. The impact of different chemical linkers on bacterial adhesion and bladder cell response is studied via confocal microscopy imaging of the MSN interactions with the respective organisms. Cytotoxicity is assessed and the expression of Toll-like receptor 4 (TLR4) and caveolin-1 (CAV-1), in the presence or absence of simulated infection with bacterial lipopolysaccharide (LPS), is evaluated using the human urinary bladder cancer cell line T24. Further, localisation of the transcription factor NF-κB due to the MANNosylated materials is examined over time. The results show that MANNosylation modifies bacterial adhesion to the nanomaterials and significantly affects TLR4, caveolin-1, and NF-κB in bladder cells. These elements are essential components of the inflammatory cascade/pathogens response during urinary tract infections. These findings demonstrate that MANNosylation is a versatile tool to design hybrid nanocarriers for targeted biomedical applications.},
}
@article {pmid38553666,
year = {2024},
author = {Ma, ZS},
title = {Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {137},
pmid = {38553666},
issn = {1471-2105},
mesh = {Animals ; Humans ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome ; Biodiversity ; Sequence Analysis, DNA ; Metagenomics/methods ; },
abstract = {BACKGROUND: Metagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and enabled the high-profile human microbiome and earth microbiome projects. The terminology-change from microbes to microbiomes signals that our capability to count and classify microbes (microbiomes) has achieved the same or similar level as we can for the biomes (macrobiomes) of plants and animals (macrobes). While the traditional investigations of macrobiomes have usually been conducted through naturalists' (Linnaeus &amp; Darwin) naked eyes, and aerial and satellite images (remote-sensing), the large-scale investigations of microbiomes have been made possible by DNA-sequencing-based metagenomic technologies. Two major types of metagenomic sequencing technologies-amplicon sequencing and whole-genome (shotgun sequencing)-respectively generate two contrastingly different categories of metagenomic reads (data)-OTU (operational taxonomic unit) tables representing microorganisms and OMU (operational metagenomic unit), a new term coined in this article to represent various cluster units of metagenomic genes.<br><br>RESULTS: The ecological science of microbiomes based on the OTU representing microbes has been unified with the classic ecology of macrobes (macrobiomes), but the unification based on OMU representing metagenomes has been rather limited. In a previous series of studies, we have demonstrated the applications of several classic ecological theories (diversity, composition, heterogeneity, and biogeography) to the studies of metagenomes. Here I push the envelope for the unification of OTU and OMU again by demonstrating the applications of metacommunity assembly and ecological networks to the metagenomes of human gut microbiomes. Specifically, the neutral theory of biodiversity (Sloan's near neutral model), Ning et al.stochasticity framework, core-periphery network, high-salience skeleton network, special trio-motif, and positive-to-negative ratio are applied to analyze the OMU tables from whole-genome sequencing technologies, and demonstrated with seven human gut metagenome datasets from the human microbiome project.<br><br>CONCLUSIONS: All of the ecological theories demonstrated previously and in this article, including diversity, composition, heterogeneity, stochasticity, and complex network analyses, are equally applicable to OMU metagenomic analyses, just as to OTU analyses. Consequently, I strongly advocate the unification of OTU/OMU (microbiomes) with classic ecology of plants and animals (macrobiomes) in the context of medical ecology.},
}
@article {pmid38552803,
year = {2024},
author = {Petra de Oliveira Barros, V and Macedo Silva, JR and Maciel Melo, VM and Terceiro, PS and Nunes de Oliveira, I and Duarte de Freitas, J and Francisco da Silva Moura, O and Xavier de Araújo-Júnior, J and Erlanny da Silva Rodrigues, E and Maraschin, M and Thompson, FL and Landell, MF},
title = {Biosurfactants production by marine yeasts isolated from zoanthids and characterization of an emulsifier produced by Yarrowia lipolytica LMS 24B.},
journal = {Chemosphere},
volume = {355},
number = {},
pages = {141807},
doi = {10.1016/j.chemosphere.2024.141807},
pmid = {38552803},
issn = {1879-1298},
mesh = {*Yarrowia/metabolism ; Surface-Active Agents/chemistry ; Kerosene ; *Petroleum/analysis ; Hydrocarbons/metabolism ; Carbon/metabolism ; Biodegradation, Environmental ; },
abstract = {The present study investigates the potential for biosurfactant production of 19 marine yeast species obtained from zoanthids. Using the emulsification index test to screen the samples produced by the marine yeasts, we verified that five isolates exhibited an emulsification index ≥50%. Additional tests were performed on such isolates, including oil displacement, drop collapse, Parafilm M assay, and surface tension measurement. The tolerance of produced biosurfactants for environmental conditions was also analyzed, especially considering the media's temperature, pH, and salinity. Moreover, the surfactant's ability to emulsify different hydrocarbon sources and to metabolize kerosene as the sole carbon source was evaluated in vitro. Our results demonstrate that yeast biosurfactants can emulsify hydrocarbon sources under different physicochemical conditions and metabolize kerosene as a carbon source. Considering the Yarrowia lipolytica LMS 24B as the yeast model for biosurfactant production from the cell's wall biomass, emulsification indexes of 61.2% were obtained, even at a high temperature of 120 °C. Furthermore, the Fourier-transform middle infrared spectroscopy (FTIR) analysis of the biosurfactant's chemical composition revealed the presence of distinct functional groups assigned to a glycoprotein complex. Considering the status of developing new bioproducts and bioprocesses nowadays, our findings bring a new perspective to biosurfactant production by marine yeasts, especially Y. lipolytica LMS 24B. In particular, the presented results validate the relevance of marine environments as valuable sources of genetic resources, i.e., yeast strains capable of metabolizing and emulsifying petroleum derivatives.},
}
@article {pmid38549428,
year = {2024},
author = {Männistö, MK and Ahonen, SHK and Ganzert, L and Tiirola, M and Stark, S and Häggblom, MM},
title = {Bacterial and fungal communities in sub-Arctic tundra heaths are shaped by contrasting snow accumulation and nutrient availability.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {4},
pages = {},
pmid = {38549428},
issn = {1574-6941},
support = {252323//Academy of Finland/ ; OCE 2129351//National Science Foundation/ ; },
mesh = {*Ecosystem ; *Mycobiome ; Snow ; Tundra ; Bacteria/genetics ; Soil/chemistry ; Seasons ; Climate Change ; Nutrients ; Arctic Regions ; },
abstract = {Climate change is affecting winter snow conditions significantly in northern ecosystems but the effects of the changing conditions for soil microbial communities are not well-understood. We utilized naturally occurring differences in snow accumulation to understand how the wintertime subnivean conditions shape bacterial and fungal communities in dwarf shrub-dominated sub-Arctic Fennoscandian tundra sampled in mid-winter, early, and late growing season. Phospholipid fatty acid (PLFA) and quantitative PCR analyses indicated that fungal abundance was higher in windswept tundra heaths with low snow accumulation and lower nutrient availability. This was associated with clear differences in the microbial community structure throughout the season. Members of Clavaria spp. and Sebacinales were especially dominant in the windswept heaths. Bacterial biomass proxies were higher in the snow-accumulating tundra heaths in the late growing season but there were only minor differences in the biomass or community structure in winter. Bacterial communities were dominated by members of Alphaproteobacteria, Actinomycetota, and Acidobacteriota and were less affected by the snow conditions than the fungal communities. The results suggest that small-scale spatial patterns in snow accumulation leading to a mosaic of differing tundra heath vegetation shapes bacterial and fungal communities as well as soil carbon and nutrient availability.},
}
@article {pmid38549276,
year = {2024},
author = {Gao, J and Chen, L and Wang, J and Zhao, W and Zhang, J and Qin, Z and Wang, M and Chen, X and Li, M and Yang, Q},
title = {Response of the Symbiotic Microbial Community of Dioscorea opposita Cultivar Tiegun to Root-Knot Nematode Infection.},
journal = {Plant disease},
volume = {108},
number = {8},
pages = {2472-2483},
doi = {10.1094/PDIS-01-24-0169-RE},
pmid = {38549276},
issn = {0191-2917},
mesh = {Animals ; *Dioscorea/microbiology/parasitology ; *Plant Roots/microbiology/parasitology ; *Plant Diseases/parasitology/microbiology ; *Soil Microbiology ; *Symbiosis ; *Tylenchoidea/physiology ; *Rhizosphere ; *Microbiota ; Bacteria/classification/genetics/isolation &amp; purification ; Nematoda/physiology/microbiology ; },
abstract = {Yam is an important medicinal and edible dual-purpose plant with high economic value. However, nematode damage severely affects its yield and quality. One of the major effects of nematode infestations is the secondary infection of pathogenic bacteria or fungi through entry wounds made by the nematodes. Understanding the response of the symbiotic microbial community of yam plants to nematodes is crucial for controlling such a disease. In this study, we investigated the rhizosphere and how endophytic microbiomes shift after nematode infection during the tuber expansion stage in the Dioscorea opposita Thunb. cultivar Tiegun. Our results revealed that soil depth affected the abundance of nematodes, and the relative number of Meloidogyne incognita was higher in the diseased soil at a depth of 16 to 40 cm than those at a depth of 0 to 15 and 41 to 70 cm. The abundance of and interactions among soil microbiota members were significantly correlated with root-knot nematode (RKN) parasitism at various soil depths. However, the comparison of the microbial α-diversity and composition between healthy and diseased rhizosphere soil showed no difference. Compared with healthy soils, the co-occurrence networks of M. incognita-infested soils included a higher ratio of positive correlations linked to plant health. In addition, we detected a higher abundance of certain taxonomic groups belonging to Chitinophagaceae and Xanthobacteraceae in the rhizosphere of RKN-infested plants. The nematodes, besides causing direct damage to plants, also possess the ability to act synergistically with other pathogens, especially Ramicandelaber and Fusarium, leading to the development of disease complexes. In contrast to soil samples, RKN parasitism specifically had a significant effect on the composition and assembly of the root endophytic microbiota. The RKN colonization impacted a wide variety of endophytic microbiomes, including Pseudomonas, Sphingomonas, Rhizobium, Neocosmospora, and Fusarium. This study revealed the relationship between RKN disease and changes in the rhizosphere and endophytic microbial community, which may provide novel insights that help improve biological management of yam RKNs.},
}
@article {pmid38548725,
year = {2024},
author = {Giordano, N and Gaudin, M and Trottier, C and Delage, E and Nef, C and Bowler, C and Chaffron, S},
title = {Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2721},
pmid = {38548725},
issn = {2041-1723},
support = {862923//European Commission (EC)/ ; },
mesh = {*Ecosystem ; Phylogeny ; *Bacteria/genetics ; Aquatic Organisms/genetics ; Oceans and Seas ; },
abstract = {Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integrated Tara Oceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across diverse phylogenetic distances. Identified co-active communities include species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling reveals a higher potential for interaction within co-active communities and points towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may act as joint mechanisms shaping bacterioplankton community assembly in the global ocean surface.},
}
@article {pmid38548158,
year = {2024},
author = {Yang, S and Zuo, J and Grossart, HP and Dai, G and Liu, J and Song, L and Gan, N},
title = {Evaluating microcystinase A-based approach on microcystins degradation during harvested cyanobacterial blooms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {348},
number = {},
pages = {123878},
doi = {10.1016/j.envpol.2024.123878},
pmid = {38548158},
issn = {1873-6424},
mesh = {Microcystins/metabolism ; Reproducibility of Results ; *Cyanobacteria/metabolism ; *Microcystis/metabolism ; Biomass ; },
abstract = {Addressing notorious and worldwide Microcystis blooms, mechanical algae harvesting is an effective emergency technology for bloom mitigation and removal of nutrient loads in waterbodies. However, the absence of effective methods for removal of cyanobacterial toxins, e.g., microcystins (MCs), poses a challenge to recycle the harvested Microcystis biomass. In this study, we therefore introduced a novel approach, the "captured biomass-MlrA enzymatic MC degradation", by enriching microcystinase A (MlrA) via fermentation and spraying it onto salvaged Microcystis slurry to degrade all MCs. After storing the harvested Microcystis slurry, a rapid release of extracellular MCs occurred within the initial 8 h, reaching a peak concentration of 5.33 μg/mL at 48 h during the composting process. Upon spraying the recombinant MlrA crude extract (about 3.36 U) onto the Microcystis slurry in a ratio of 0.1% (v/v), over 95% of total MCs were degraded within a 24-h period. Importantly, we evaluated the reliability and safety of using MlrA extracts to degrade MCs. Results showed that organic matter/nutrient contents, e.g. soluble proteins, polysaccharides, phycocyanin and carotenoids, were not significantly altered. Furthermore, the addition of MlrA extracts did not significantly change the bacterial community composition and diversity in the Microcystis slurry, indicating that the MlrA extracts did not increase the risk of pathogenic bacteria. Our study provides an effective and promising method for the pre-treatment of harvested Microcystis biomass, highlighting an ecologically sustainable framework for addressing Microcystis blooms.},
}
@article {pmid38547998,
year = {2024},
author = {Li, Y and Schütte, W and Dekeukeleire, M and Janssen, C and Boon, N and Asselman, J and Lebeer, S and Spacova, I and De Rijcke, M},
title = {The immunostimulatory activity of sea spray aerosols: bacteria and endotoxins activate TLR4, TLR2/6, NF-κB and IRF in human cells.},
journal = {The Science of the total environment},
volume = {927},
number = {},
pages = {171969},
doi = {10.1016/j.scitotenv.2024.171969},
pmid = {38547998},
issn = {1879-1026},
mesh = {Humans ; *NF-kappa B/metabolism ; *Aerosols ; *Endotoxins ; Toll-Like Receptor 4/metabolism ; Interferon Regulatory Factors/metabolism ; Toll-Like Receptor 2/metabolism ; Bacteria ; Air Pollutants ; Belgium ; Immunity, Innate ; },
abstract = {Frequent exposure to sea spray aerosols (SSA) containing marine microorganisms and bioactive compounds may influence human health. However, little is known about potential immunostimulation by SSA exposure. This study focuses on the effects of marine bacteria and endotoxins in SSA on several receptors and transcription factors known to play a key role in the human innate immune system. SSA samples were collected in the field (Ostend, Belgium) or generated in the lab using a marine aerosol reference tank (MART). Samples were characterized by their sodium contents, total bacterial counts, and endotoxin concentrations. Human reporter cells were exposed to SSA to investigate the activation of toll-like receptor 4 (TLR4) in HEK-Blue hTLR4 cells and TLR2/6 in HEK-Blue hTLR2/6 cells, as well as the activation of nuclear factor kappa B (NF-κB) and interferon regulatory factors (IRF) in THP1-Dual monocytes. These responses were then correlated to the total bacterial counts and endotoxin concentrations to explore dose-effect relationships. Field SSA contained from 3.0 × 10[3] to 6.0 × 10[5] bacteria/m[3] air (averaging 2.0 ± 1.9 × 10[5] bacteria/m[3] air) and an endotoxin concentration ranging from 7 to 1217 EU/m[3] air (averaging 389 ± 434 EU/m[3] air). In contrast, MART SSA exhibited elevated levels of total bacterial count (from 2.0 × 10[5] to 2.4 × 10[6], averaging 7.3 ± 5.5 × 10[5] cells/m[3] air) and endotoxin concentration from 536 to 2191 (averaging 1310 ± 513 EU/m[3] air). SSA samples differentially activated TLR4, TLR2/6, NF-κB and IRF. These immune responses correlated dose-dependently with the total bacterial counts, endotoxin levels, or both. This study sheds light on the immunostimulatory potential of SSA and its underlying mechanisms, highlighting the need for further research to deepen our understanding of the health implications of SSA exposure.},
}
@article {pmid38546802,
year = {2024},
author = {Stephenson, MM and Coleman, ME and Azzolina, NA},
title = {Trends in Burdens of Disease by Transmission Source (USA, 2005-2020) and Hazard Identification for Foods: Focus on Milkborne Disease.},
journal = {Journal of epidemiology and global health},
volume = {14},
number = {3},
pages = {787-816},
pmid = {38546802},
issn = {2210-6014},
mesh = {Humans ; *Foodborne Diseases/epidemiology ; United States/epidemiology ; *Disease Outbreaks/statistics &amp; numerical data ; Animals ; *Milk/microbiology ; Cost of Illness ; Hazard Analysis and Critical Control Points/methods ; Food Microbiology ; },
abstract = {BACKGROUND: Robust solutions to global, national, and regional burdens of communicable and non-communicable diseases, particularly related to diet, demand interdisciplinary or transdisciplinary collaborations to effectively inform risk analysis and policy decisions.<br><br>OBJECTIVE: U.S. outbreak data for 2005-2020 from all transmission sources were analyzed for trends in the burden of infectious disease and foodborne outbreaks.<br><br>METHODS: Outbreak data from 58 Microsoft Access[&#xae;] data tables were structured using systematic queries and pivot tables for analysis by transmission source, pathogen, and date. Trends were examined using graphical representations, smoothing splines, Spearman's rho rank correlations, and non-parametric testing for trend. Hazard Identification was conducted based on the number and severity of illnesses.<br><br>RESULTS: The evidence does not support increasing trends in the burden of infectious foodborne disease, though strongly increasing trends were observed for other transmission sources. Morbidity and mortality were dominated by person-to-person transmission; foodborne and other transmission sources accounted for small portions of the disease burden. Foods representing the greatest hazards associated with the four major foodborne bacterial diseases were identified. Fatal foodborne disease was dominated by fruits, vegetables, peanut butter, and pasteurized dairy.<br><br>CONCLUSION: The available evidence conflicts with assumptions of zero risk for pasteurized milk and increasing trends in the burden of illness for raw milk. For future evidence-based risk management, transdisciplinary risk analysis methodologies are essential to balance both communicable and non-communicable diseases and both food safety and food security, considering scientific, sustainable, economic, cultural, social, and political factors to support health and wellness for humans and ecosystems.},
}
@article {pmid38544331,
year = {2024},
author = {Wang, C and Defoirdt, T and Rajkovic, A},
title = {The impact of indole and mucin on sporulation, biofilm formation, and enterotoxin production in foodborne Clostridium perfringens.},
journal = {Journal of applied microbiology},
volume = {135},
number = {4},
pages = {},
doi = {10.1093/jambio/lxae083},
pmid = {38544331},
issn = {1365-2672},
support = {201808630020//China Scholarship Council/ ; BOF20/BAS/120//Ghent University/ ; 1506419N//Research Foundation Flanders/ ; },
mesh = {*Clostridium perfringens/genetics ; *Enterotoxins/genetics ; Mucins/metabolism ; Spores, Bacterial ; Biofilms ; },
abstract = {AIMS: Indole and mucin are compounds found in the host environment as they are produced by the host or by the host-associated microbiota. This study investigated whether indole and mucin impact Clostridium perfringens growth and sporulation, as well as enterotoxin production and biofilm formation.<br><br>METHODS AND RESULTS: There was no impact on growth of Cl. perfringens for up to 400&#xa0;&#xb5;M indole and 240&#xa0;mg/l mucin, and neither indole nor mucin affected sporulation. Reverse-transcriptase qPCR showed that mucin strongly upregulated the expression of Cl. perfringens enterotoxin (up to 121-fold increase), whereas indole had a much more modest effect (2-fold). This was also reflected in increased Cl. perfringens enterotoxin levels in mucin-treated Cl. perfringens (as assessed by a reversed passive latex agglutination assay). Finally, mucin and indole significantly increased biofilm formation of Cl. perfringens, although the effect size was relatively small (less than 1.5 fold).<br><br>CONCLUSION: These results indicate that Cl. perfringens can sense its presence in a host environment by responding to mucin, and thereby markedly increased enterotoxin production.},
}
@article {pmid38543583,
year = {2024},
author = {Pandey, S and Blache, A and Achouak, W},
title = {Insights into Bacterial Extracellular Vesicle Biogenesis, Functions, and Implications in Plant-Microbe Interactions.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543583},
issn = {2076-2607},
abstract = {Plant-microbe interactions play a crucial role in shaping plant health and survival. In recent years, the role of extracellular vesicles (EVs) in mediating intercellular communication between plants and microbes has emerged as an intriguing area of research. EVs serve as important carriers of bioactive molecules and genetic information, facilitating communication between cells and even between different organisms. Pathogenic bacteria leverage extracellular vesicles (EVs) to amplify their virulence, exploiting their cargo rich in toxins and virulence factors. Conversely, beneficial microbes initiate EV secretion to stimulate plant immune responses and nurture symbiotic relationships. The transfer of EV-packed small RNAs (sRNAs) has been demonstrated to facilitate the modulation of immune responses. Furthermore, harnessing the potential of EVs holds promise for the development of innovative diagnostic tools and sustainable crop protection strategies. This review highlights the biogenesis and functions of EVs in bacteria and their importance in plant defense, and paves the way for future research in this exciting field.},
}
@article {pmid38543493,
year = {2024},
author = {Heczko, P},
title = {Editorial for Special Issue "Effects of Probiotics on Health".},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543493},
issn = {2076-2607},
abstract = {Since 1987, when Professor Sherwood Gorbach discovered, characterized, and commercialized the first probiotic Lactobacillus rhamnosus GG, a total of over 17,000 publications have been indexed in PubMed under "probiotic" and "health", which is an extensive amount of research on the specific bacteria and yeasts defined as "live microorganisms that, when administered in adequate amounts, exert a health benefit on the host" [...].},
}
@article {pmid38543484,
year = {2024},
author = {Rosa-Masegosa, A and Rodriguez-Sanchez, A and Gorrasi, S and Fenice, M and Gonzalez-Martinez, A and Gonzalez-Lopez, J and Muñoz-Palazon, B},
title = {Microbial Ecology of Granular Biofilm Technologies for Wastewater Treatment: A Review.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543484},
issn = {2076-2607},
abstract = {Nowadays, the discharge of wastewater is a global concern due to the damage caused to human and environmental health. Wastewater treatment has progressed to provide environmentally and economically sustainable technologies. The biological treatment of wastewater is one of the fundamental bases of this field, and the employment of new technologies based on granular biofilm systems is demonstrating success in tackling the environmental issues derived from the discharge of wastewater. The granular-conforming microorganisms must be evaluated as functional entities because their activities and functions for removing pollutants are interconnected with the surrounding microbiota. The deep knowledge of microbial communities allows for the improvement in system operation, as the proliferation of microorganisms in charge of metabolic roles could be modified by adjustments to operational conditions. This is why engineering must consider the intrinsic microbiological aspects of biological wastewater treatment systems to obtain the most effective performance. This review provides an extensive view of the microbial ecology of biological wastewater treatment technologies based on granular biofilms for mitigating water pollution.},
}
@article {pmid38543271,
year = {2024},
author = {Srivastava, MG and Kamarudin, NHN and Aktan, MK and Zheng, K and Zayed, N and Yongabi, D and Wagner, P and Teughels, W and Boccaccini, AR and Braem, A},
title = {pH-Triggered Controlled Release of Chlorhexidine Using Chitosan-Coated Titanium Silica Composite for Dental Infection Prevention.},
journal = {Pharmaceutics},
volume = {16},
number = {3},
pages = {},
pmid = {38543271},
issn = {1999-4923},
support = {STG/17/024, C32/18/059//KU Leuven/ ; },
abstract = {Peri-implantitis is a growing pathological concern for dental implants which aggravates the occurrence of revision surgeries. This increases the burden on both hospitals and the patients themselves. Research is now focused on the development of materials and accompanying implants designed to resist biofilm formation. To enhance this endeavor, a smart method of biofilm inhibition coupled with limiting toxicity to the host cells is crucial. Therefore, this research aims to establish a proof-of-concept for the pH-triggered release of chlorhexidine (CHX), an antiseptic commonly used in mouth rinses, from a titanium (Ti) substrate to inhibit biofilm formation on its surface. To this end, a macroporous Ti matrix is filled with mesoporous silica (together referred to as Ti/SiO2), which acts as a diffusion barrier for CHX from the CHX feed side to the release side. To limit release to acidic conditions, the release side of Ti/SiO2 is coated with crosslinked chitosan (CS), a pH-responsive and antimicrobial natural polymer. Scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM/EDX) and Fourier transform infrared (FTIR) spectroscopy confirmed successful CS film formation and crosslinking on the Ti/SiO2 disks. The presence of the CS coating reduced CHX release by 33% as compared to non-coated Ti/SiO2 disks, thus reducing the antiseptic exposure to the environment in normal conditions. Simultaneous differential scanning calorimetry and thermogravimetric analyzer (SDT) results highlighted the thermal stability of the crosslinked CS films. Quartz crystal microbalance with dissipation monitoring (QCM-D) indicated a clear pH response for crosslinked CS coatings in an acidic medium. This pH response also influenced CHX release through a Ti/SiO2/CS disk where the CHX release was higher than the average trend in the neutral medium. Finally, the antimicrobial study revealed a significant reduction in biofilm formation for the CS-coated samples compared to the control sample using viability quantitative polymerase chain reaction (v-qPCR) measurements, which were also corroborated using SEM imaging. Overall, this study investigates the smart triggered release of pharmaceutical agents aimed at inhibiting biofilm formation, with potential applicability to implant-like structures.},
}
@article {pmid38542054,
year = {2024},
author = {Barathan, M and Ng, SL and Lokanathan, Y and Ng, MH and Law, JX},
title = {Unseen Weapons: Bacterial Extracellular Vesicles and the Spread of Antibiotic Resistance in Aquatic Environments.},
journal = {International journal of molecular sciences},
volume = {25},
number = {6},
pages = {},
pmid = {38542054},
issn = {1422-0067},
support = {DIP-2023-011//National University of Malaysia/ ; FF-2021-518//Faculty of Medicine, Universiti Kebangsaan Malaysia/ ; },
mesh = {*Ecosystem ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Multiple, Bacterial ; *Extracellular Vesicles ; Genes, Bacterial ; },
abstract = {This paper sheds light on the alarming issue of antibiotic resistance (ABR) in aquatic environments, exploring its detrimental effects on ecosystems and public health. It examines the multifaceted role of antibiotic use in aquaculture, agricultural runoff, and industrial waste in fostering the development and dissemination of resistant bacteria. The intricate interplay between various environmental factors, horizontal gene transfer, and bacterial extracellular vesicles (BEVs) in accelerating the spread of ABR is comprehensively discussed. Various BEVs carrying resistance genes like blaCTX-M, tetA, floR, and sul/I, as well as their contribution to the dominance of multidrug-resistant bacteria, are highlighted. The potential of BEVs as both a threat and a tool in combating ABR is explored, with promising strategies like targeted antimicrobial delivery systems and probiotic-derived EVs holding significant promise. This paper underscores the urgency of understanding the intricate interplay between BEVs and ABR in aquatic environments. By unraveling these unseen weapons, we pave the way for developing effective strategies to mitigate the spread of ABR, advocating for a multidisciplinary approach that includes stringent regulations, enhanced wastewater treatment, and the adoption of sustainable practices in aquaculture.},
}
@article {pmid38539868,
year = {2024},
author = {M'hir, S and Ayed, L and De Pasquale, I and Fanizza, E and Tlais, AZA and Comparelli, R and Verni, M and Latronico, R and Gobbetti, M and Di Cagno, R and Filannino, P},
title = {Comparison of Milk Kefirs Obtained from Cow's, Ewe's and Goat's Milk: Antioxidant Role of Microbial-Derived Exopolysaccharides.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
pmid = {38539868},
issn = {2076-3921},
abstract = {Different types of milk are used in the production of milk kefir, but little information is available on the release of potentially antioxidant exopolysaccharides (EPS). The aim of this study was to investigate whether the microbial dynamics and EPS release are dependent on the milk substrate. In our study, the inoculated microbial consortium was driven differently by each type of milk (cow, ewe, and goat). This was evident in the sugar consumption, organic acid production, free amino release, and EPS production. The amount and the composition of the secreted EPS varied depending on the milk type, with implications for the structure and functional properties of the EPS. The low EPS yield in ewe's milk was associated with a higher lactic acid production and thus with the use of carbon sources oriented towards energy production. Depending on the milk used as substrate, the EPS showed different monosaccharide and FT-IR profiles, microstructures, and surface morphologies. These differences affected the antiradical properties and reducing power of the EPS. In particular, EPS extracted from cow's milk had a higher antioxidant activity than other milk types, and the antioxidant activity was concentration dependent.},
}
@article {pmid38539229,
year = {2024},
author = {Villena-Alemany, C and Mujakić, I and Fecskeová, LK and Woodhouse, J and Auladell, A and Dean, J and Hanusová, M and Socha, M and Gazulla, CR and Ruscheweyh, HJ and Sunagawa, S and Silva Kavagutti, V and Andrei, A&#x15e; and Grossart, HP and Ghai, R and Koblížek, M and Piwosz, K},
title = {Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {65},
pmid = {38539229},
issn = {2049-2618},
support = {19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 2021/03/Y/NZ8/00076//Polska Akademia Nauk/ ; },
mesh = {*Phototrophic Processes ; *Lakes/microbiology ; Bacteria/genetics ; Biomass ; Bacteria, Aerobic/genetics/metabolism ; Phytoplankton/genetics ; },
abstract = {BACKGROUND: Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Despite their substantial contribution to bacterial biomass, microbial food webs, and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across 3 years in a temperate, meso-oligotrophic freshwater lake.<br><br>RESULTS: AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM genes, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource, we demonstrated that the majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. AAP community presented an indigenous freshwater nature characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment.<br><br>CONCLUSIONS: Our findings highlight the substantial contribution of AAP bacteria to the carbon flow and ecological dynamics of lakes and unveil a recurrent and dynamic seasonal succession of the AAP community. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom. We suggest a potential role of AAP bacteria within the context of the PEG model and their consideration in further ecological models.},
}
@article {pmid38537828,
year = {2024},
author = {Madge Pimentel, I and Baikova, D and Buchner, D and Burfeid Castellanos, A and David, GM and Deep, A and Doliwa, A and Hadžiomerović, U and Mayombo, NAS and Prati, S and Spyra, MA and Vermiert, AM and Beisser, D and Dunthorn, M and Piggott, JJ and Sures, B and Tiegs, SD and Leese, F and Beermann, AJ},
title = {Assessing the response of an urban stream ecosystem to salinization under different flow regimes.},
journal = {The Science of the total environment},
volume = {926},
number = {},
pages = {171849},
doi = {10.1016/j.scitotenv.2024.171849},
pmid = {38537828},
issn = {1879-1026},
mesh = {Animals ; *Ecosystem ; *Rivers ; Invertebrates/physiology ; Fresh Water ; Sodium Chloride ; },
abstract = {Urban streams are exposed to a variety of anthropogenic stressors. Freshwater salinization is a key stressor in these ecosystems that is predicted to be further exacerbated by climate change, which causes simultaneous changes in flow parameters, potentially resulting in non-additive effects on aquatic ecosystems. However, the effects of salinization and flow velocity on urban streams are still poorly understood as multiple-stressor experiments are often conducted at pristine rather than urban sites. Therefore, we conducted a mesocosm experiment at the Boye River, a recently restored stream located in a highly urbanized area in Western Germany, and applied recurrent pulses of salinity along a gradient (NaCl, 9 h daily of +0 to +2.5 mS/cm) in combination with normal and reduced current velocities (20 cm/s vs. 10 cm/s). Using a comprehensive assessment across multiple organism groups (macroinvertebrates, eukaryotic algae, fungi, parasites) and ecosystem functions (primary production, organic-matter decomposition), we show that flow velocity reduction has a pervasive impact, causing community shifts for almost all assessed organism groups (except fungi) and inhibiting organic-matter decomposition. Salinization affected only dynamic components of community assembly by enhancing invertebrate emigration via drift and reducing fungal reproduction. We caution that the comparatively small impact of salt in our study can be due to legacy effects from past salt pollution by coal mining activities >30 years ago. Nevertheless, our results suggest that urban stream management should prioritize the continuity of a minimum discharge to maintain ecosystem integrity. Our study exemplifies a holistic approach for the assessment of multiple-stressor impacts on streams, which is needed to inform the establishment of a salinity threshold above which mitigation actions must be taken.},
}
@article {pmid38537819,
year = {2024},
author = {Tobias-Hünefeldt, SP and van Beusekom, JEE and Russnak, V and Dähnke, K and Streit, WR and Grossart, HP},
title = {Seasonality, rather than estuarine gradient or particle suspension/sinking dynamics, determines estuarine carbon distributions.},
journal = {The Science of the total environment},
volume = {926},
number = {},
pages = {171962},
doi = {10.1016/j.scitotenv.2024.171962},
pmid = {38537819},
issn = {1879-1026},
mesh = {*Carbon/analysis ; Dissolved Organic Matter ; *Greenhouse Gases/analysis ; Estuaries ; Particulate Matter/analysis ; Rivers ; },
abstract = {Estuaries are important components of the global carbon cycle; exchanging carbon between aquatic, atmospheric, and terrestrial environments, representing important loci for blue carbon storage and greenhouse gas emissions. However, how estuarine gradients affect sinking/suspended particles, and dissolved organic matter dynamic interactions remains unexplored. We fractionated suspended/sinking particles to assess and characterise carbon fate differences. We investigated bacterial colonisation (SYBR Green I) and exopolymer concentrations (TEP/CSP) with microscopy staining techniques. C/H/N and dry weight analysis identified particle composition differences. Meanwhile, nutrient and carbon analysis, and excitation and emission matrix evaluations with a subsequent parallel factor (PARAFAC) analysis characterised dissolved organic matter. The lack of clear salinity driven patterns in our study are presumably due to strong mixing forces and high particle heterogeneity along the estuary, with only density differences between suspended and sinking particles. Elbe estuary particles' organic portion is made up of marine-like (sinking) and terrestrial-like (suspended) signatures. Salinity did not have a significant role in microbial degradation and carbon composition, although brackish estuary portions were more biologically active. Indicative of increased degradation rates, leading to decreased greenhouse gas emissions, which are especially relevant for estuaries, with their disproportionate greenhouse gas emissions. Bacterial colonisation decreased seawards, indicative of decreased degradation, and shifts in microbial community composition and functions. Our findings span diverse strands of research, concerning steady carbon contributions from both marine and terrestrial sources, carbon aromaticity, humification index, and bioavailability. Their integration highlights the importance of the Elbe estuary as a model system, providing robust information for future policy decisions affecting dissolved and particulate matter dynamics within the Elbe Estuary.},
}
@article {pmid38537644,
year = {2024},
author = {Kawa, D and Thiombiano, B and Shimels, MZ and Taylor, T and Walmsley, A and Vahldick, HE and Rybka, D and Leite, MFA and Musa, Z and Bucksch, A and Dini-Andreote, F and Schilder, M and Chen, AJ and Daksa, J and Etalo, DW and Tessema, T and Kuramae, EE and Raaijmakers, JM and Bouwmeester, H and Brady, SM},
title = {The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {113971},
pmid = {38537644},
issn = {2211-1247},
mesh = {*Sorghum/microbiology/metabolism ; *Striga/physiology ; *Plant Roots/microbiology/metabolism/parasitology ; *Microbiota ; *Soil Microbiology ; Metabolome ; Plant Diseases/microbiology/parasitology ; },
abstract = {Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.},
}
@article {pmid38537571,
year = {2024},
author = {Jing, J and Garbeva, P and Raaijmakers, JM and Medema, MH},
title = {Strategies for tailoring functional microbial synthetic communities.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38537571},
issn = {1751-7370},
mesh = {*Microbiota ; Soil/chemistry ; Soil Microbiology ; Microbial Interactions ; },
abstract = {Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.},
}
@article {pmid38535593,
year = {2024},
author = {Cristino, S and Pascale, MR and Marino, F and Derelitto, C and Salaris, S and Orsini, M and Squarzoni, S and Grottola, A and Girolamini, L},
title = {Characterization of a Novel Species of Legionella Isolated from a Healthcare Facility: Legionella resiliens sp. nov.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
pmid = {38535593},
issn = {2076-0817},
abstract = {Two Legionella-like isolates, 8cVS16[T] and 9fVS26, were isolated from a water distribution system (WDS) in a healthcare facility. Cells were Gram- and Ziehl Neelsen-stain-negative, rod-shaped, motile, and exhibited a blue-white fluorescence under Wood's lamp at 365 nm. The strains grew in a range of 32-37 °C on BCYE with L-cysteine (Cys+), GVPC, and MWY agar medium, with a positive reaction for oxidase, catalase, and gelatinase. The dominant fatty acids were summed features 3 (C16:1ω7c/C16:1ω6c) (27.7%), C16:0 iso (17.5%), and C16:0 (16.3%), and Q13 as the major ubiquinone. The mip and rpoB gene sequences showed a similarity of 96.7% and 92.4%, with L. anisa (ATCC 35292[T]). The whole genomes sequencing (WGS) performed displayed a GC content of 38.21 mol% for both. The digital DNA-DNA hybridization (dDDH) analysis demonstrated the separation of the two strains from the phylogenetically most related L. anisa (ATCC 35292[T]), with ≤43% DNA-DNA relatedness. The Average Nucleotide Identity (ANI) between the two strains and L. anisa (ATCC 35292[T]) was 90.74%, confirming that the two isolates represent a novel species of the genus Legionella. The name proposed for this species is Legionella resiliens sp. nov., with 8cVS16[T] (=DSM 114356[T] = CCUG 76627[T]) as the type strain.},
}
@article {pmid38531380,
year = {2024},
author = {Skinner, JP and Palar, S and Allen, C and Raderstorf, A and Blake, P and Morán Reyes, A and Berg, RN and Muse, C and Robles, A and Hamdan, N and Chu, MY and Delgado, AG},
title = {Acetylene Tunes Microbial Growth During Aerobic Cometabolism of Trichloroethene.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {14},
pages = {6274-6283},
pmid = {38531380},
issn = {1520-5851},
mesh = {*Trichloroethylene/metabolism ; Acetylene/metabolism ; Biodegradation, Environmental ; Bacteria/metabolism ; Biomass ; *Groundwater ; },
abstract = {Microbial aerobic cometabolism is a possible treatment approach for large, dilute trichloroethene (TCE) plumes at groundwater contaminated sites. Rapid microbial growth and bioclogging pose a persistent problem in bioremediation schemes. Bioclogging reduces soil porosity and permeability, which negatively affects substrate distribution and contaminant treatment efficacy while also increasing the operation and maintenance costs of bioremediation. In this study, we evaluated the ability of acetylene, an oxygenase enzyme-specific inhibitor, to decrease biomass production while maintaining aerobic TCE cometabolism capacity upon removal of acetylene. We first exposed propane-metabolizing cultures (pure and mixed) to 5% acetylene (v v[-1]) for 1, 2, 4, and 8 d and we then verified TCE aerobic cometabolic activity. Exposure to acetylene overall decreased biomass production and TCE degradation rates while retaining the TCE degradation capacity. In the mixed culture, exposure to acetylene for 1-8 d showed minimal effects on the composition and relative abundance of TCE cometabolizing bacterial taxa. TCE aerobic cometabolism and incubation conditions exerted more notable effects on microbial ecology than did acetylene. Acetylene appears to be a viable approach to control biomass production that may lessen the likelihood of bioclogging during TCE cometabolism. The findings from this study may lead to advancements in aerobic cometabolism remediation technologies for dilute plumes.},
}
@article {pmid38530469,
year = {2024},
author = {Maraci, &#xd6; and Antonatou-Papaioannou, A and Jünemann, S and Schneeberger, K and Schulze, M and Scheffler, I and Caspers, BA},
title = {Bats, Bacteria, and Bat Smell V.2.0: Repeatable Sex-Specific Differences in Scent Organ Microbiota.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {55},
pmid = {38530469},
issn = {1432-184X},
support = {SCHN 1584/2-1//Deutsche Forschungsgemeinschaft/ ; SCHN 1584/2-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Male ; Female ; Odorants ; Smell ; *Chiroptera ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Bacteria ; Pheromones/metabolism ; *Microbiota/genetics ; },
abstract = {Reproducibility is a fundamental principle in science, ensuring reliable and valid findings. However, replication studies are scarce, particularly in ecology, due to the emphasis on novelty for publication. We explored the possibility of replicating original findings in the field of microbial and chemical ecology by conducting a conceptual replication of a previous study analysing the sex-specific differences in the microbial communities inhabiting the wing sacs, a scent organ with crucial functions in olfactory communication, of greater sac-winged bat (Saccopteryx bilineata). In the original study, the skin swabs from the antebrachial wing sacs of the males and wing sac rudiments of the females were analysed using culture-dependent methods to test sex-specific differences. The authors demonstrated that males have lower microbial richness and different microbial composition than females. We attempted to reproduce these findings using 16S rRNA sequencing, which offers improved accuracy in pinpointing microbial members than culture-dependent methods because of advanced statistical methods. Our study validated the original study's findings: Males had a lower microbial richness, and the community composition differed between the sexes. Furthermore, in the current study, males had an increased abundance of bacteria that might potentially be involved in odour production and degradation of malodorous substances and antimicrobial production. Our conceptual replication study corroborated that microbes can play a role in shaping their host's olfactory phenotype and consequently influence sexual selection. Furthermore, the current study emphasises the importance of replication efforts and hopefully encourages a culture that values replication studies in scientific practice.},
}
@article {pmid38528797,
year = {2024},
author = {Avila Santos, AP and de Almeida, BLS and Bonidia, RP and Stadler, PF and Stefanic, P and Mandic-Mulec, I and Rocha, U and Sanches, DS and de Carvalho, ACPLF},
title = {BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification.},
journal = {RNA biology},
volume = {21},
number = {1},
pages = {1-12},
pmid = {38528797},
issn = {1555-8584},
mesh = {*Deep Learning ; RNA, Untranslated/genetics ; Algorithms ; RNA ; Neural Networks, Computer ; },
abstract = {The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification. This study presents BioDeepFuse, a hybrid deep learning framework integrating convolutional neural networks (CNN) or bidirectional long short-term memory (BiLSTM) networks with handcrafted features for enhanced accuracy. This framework employs a combination of k-mer one-hot, k-mer dictionary, and feature extraction techniques for input representation. Extracted features, when embedded into the deep network, enable optimal utilization of spatial and sequential nuances of ncRNA sequences. Using benchmark datasets and real-world RNA samples from bacterial organisms, we evaluated the performance of BioDeepFuse. Results exhibited high accuracy in ncRNA classification, underscoring the robustness of our tool in addressing complex ncRNA sequence data challenges. The effective melding of CNN or BiLSTM with external features heralds promising directions for future research, particularly in refining ncRNA classifiers and deepening insights into ncRNAs in cellular processes and disease manifestations. In addition to its original application in the context of bacterial organisms, the methodologies and techniques integrated into our framework can potentially render BioDeepFuse effective in various and broader domains.},
}
@article {pmid38526664,
year = {2024},
author = {Roy, R and Paul, P and Chakraborty, P and Malik, M and Das, S and Chatterjee, S and Maity, A and Dasgupta, M and Sarker, RK and Sarkar, S and Das Gupta, A and Tribedi, P},
title = {Cuminaldehyde and Tobramycin Forestall the Biofilm Threats of Staphylococcus aureus: A Combinatorial Strategy to Evade the Biofilm Challenges.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {38526664},
issn = {1559-0291},
support = {R&amp;D/2020/F2//The Neotia University/ ; },
abstract = {Staphylococcus aureus, an opportunistic Gram-positive pathogen, is known for causing various infections in humans, primarily by forming biofilms. The biofilm-induced antibiotic resistance has been considered a significant medical threat. Combinatorial therapy has been considered a reliable approach to combat antibiotic resistance by using multiple antimicrobial agents simultaneously, targeting bacteria through different mechanisms of action. To this end, we examined the effects of two molecules, cuminaldehyde (a natural compound) and tobramycin (an antibiotic), individually and in combination, against staphylococcal biofilm. Our experimental observations demonstrated that cuminaldehyde (20 μg/mL) in combination with tobramycin (0.05 μg/mL) exhibited efficient reduction in biofilm formation compared to their individual treatments (p < 0.01). Additionally, the combination showed an additive interaction (fractional inhibitory concentration value 0.66) against S. aureus. Further analysis revealed that the effective combination accelerated the buildup of reactive oxygen species (ROS) and increased the membrane permeability of the bacteria. Our findings also specified that the cuminaldehyde in combination with tobramycin efficiently reduced biofilm-associated pathogenicity factors of S. aureus, including fibrinogen clumping ability, hemolysis property, and staphyloxanthin production. The selected concentrations of tobramycin and cuminaldehyde demonstrated promising activity against the biofilm development of S. aureus on catheter models without exerting antimicrobial effects. In conclusion, the combination of tobramycin and cuminaldehyde presented a successful strategy for combating staphylococcal biofilm-related healthcare threats. This combinatorial approach holds the potential for controlling biofilm-associated infections caused by S. aureus.},
}
@article {pmid38524670,
year = {2023},
author = {Yount, TA and Murtha, AN and Cecere, AG and Miyashiro, TI},
title = {Quorum sensing facilitates interpopulation signaling by Vibrio fischeri within the light organ of Euprymna scolopes.},
journal = {Israel journal of chemistry},
volume = {63},
number = {5-6},
pages = {},
pmid = {38524670},
issn = {0021-2148},
support = {R01 GM129133/GM/NIGMS NIH HHS/United States ; },
abstract = {Quorum sensing is an intercellular signaling mechanism that enables bacterial cells to coordinate population-level behaviors. How quorum sensing functions in natural habitats remains poorly understood. Vibrio fischeri is a bacterial symbiont of the Hawaiian bobtail squid Euprymna scolopes and depends on LuxI/LuxR quorum sensing to produce the symbiotic trait of bioluminescence. A previous study demonstrated that animals emit light when co-colonized by a Δlux mutant, which lacks several genes within the lux operon that are necessary for bioluminescence production, and a LuxI[-] mutant, which cannot synthesize the quorum signaling molecule N-3-oxohexanoyl-homoserine lactone. Here, we build upon that observation and show that populations of LuxI[-] feature elevated promoter activity for the lux operon. We find that population structures comprising of Δlux and LuxI[-] are attenuated within the squid, but a wild-type strain enables the LuxI[-] strain type to be maintained in vivo. These experimental results support a model of interpopulation signaling, which provides basic insight into how quorum sensing functions within the natural habitats found within a host.},
}
@article {pmid38521905,
year = {2024},
author = {Wu, J and Lv, Y and Hao, P and Zhang, Z and Zheng, Y and Chen, E and Fan, Y},
title = {Immunological profile of lactylation-related genes in Crohn's disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {300},
pmid = {38521905},
issn = {1479-5876},
support = {82300630//National Natural Science Foundation of China/ ; 2022GGB011//Project of Young and Middle-aged Backbone Talents Cultivation/ ; 2021J011329//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//Health Science Foundation of Fujian Youth Program/ ; },
mesh = {Humans ; *Crohn Disease/genetics ; Databases, Factual ; Lactic Acid ; Sequence Analysis, RNA ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a disease characterized by intestinal immune dysfunction, often accompanied by metabolic abnormalities. Disturbances in lactate metabolism have been found in the intestine of patients with CD, but studies on the role of lactate and related Lactylation in the pathogenesis of CD are still unknown.<br><br>METHODS: We identified the core genes associated with Lactylation by downloading and merging three CD-related datasets (GSE16879, GSE75214, and GSE112366) from the GEO database, and analyzed the functions associated with the hub genes and the correlation between their expression levels and immune infiltration through comprehensive analysis. We explored the Lactylation levels of different immune cells using single-cell data and further analyzed the differences in Lactylation levels between inflammatory and non-inflammatory sites.<br><br>RESULTS: We identified six Lactylation-related hub genes that are highly associated with CD. Further analysis revealed that these six hub genes were highly correlated with the level of immune cell infiltration. To further clarify the effect of Lactylation on immune cells, we analyzed single-cell sequencing data of immune cells from inflammatory and non-inflammatory sites in CD patients and found that there were significant differences in the levels of Lactylation between different types of immune cells, and that the levels of Lactylation were significantly higher in immune cells from inflammatory sites.<br><br>CONCLUSIONS: These results suggest that Lactylation-related genes and their functions are closely associated with changes in inflammatory cells in CD patients.},
}
@article {pmid38519354,
year = {2024},
author = {, and Jurburg, SD and Álvarez Blanco, MJ and Chatzinotas, A and Kazem, A and König-Ries, B and Babin, D and Smalla, K and Cerecetto, V and Fernandez-Gnecco, G and Covacevich, F and Viruel, E and Bernaschina, Y and Leoni, C and Garaycochea, S and Terra, JA and Fresia, P and Figuerola, ELM and Wall, LG and Covelli, JM and Agnello, AC and Nieto, EE and Festa, S and Dominici, LE and Allegrini, M and Zabaloy, MC and Morales, ME and Erijman, L and Coniglio, A and Cassán, FD and Nievas, S and Roldán, DM and Menes, R and Jauri, PV and Marrero, CS and Massa, AM and Revetria, MAM and Fernández-Scavino, A and Pereira-Mora, L and Martínez, S and Frene, JP},
title = {Datathons: fostering equitability in data reuse in ecology.},
journal = {Trends in microbiology},
volume = {32},
number = {5},
pages = {415-418},
doi = {10.1016/j.tim.2024.02.010},
pmid = {38519354},
issn = {1878-4380},
mesh = {Argentina ; *Biodiversity ; *Ecology ; *Microbiota ; Uruguay ; },
abstract = {Approaches to rapidly collecting global biodiversity data are increasingly important, but biodiversity blind spots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to date and formed collaborative consortia for microbiome data synthesis.},
}
@article {pmid38518769,
year = {2024},
author = {Pristner, M and Wasinger, D and Seki, D and Klebermaß-Schrehof, K and Berger, A and Berry, D and Wisgrill, L and Warth, B},
title = {Neuroactive metabolites and bile acids are altered in extremely premature infants with brain injury.},
journal = {Cell reports. Medicine},
volume = {5},
number = {4},
pages = {101480},
pmid = {38518769},
issn = {2666-3791},
mesh = {Infant, Newborn ; Infant ; Humans ; *Infant, Extremely Premature ; Chromatography, Liquid/methods ; *Bile Acids and Salts ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; },
abstract = {The gut microbiome is associated with pathological neurophysiological evolvement in extremely premature infants suffering from brain injury. The exact underlying mechanism and its associated metabolic signatures in infants are not fully understood. To decipher metabolite profiles linked to neonatal brain injury, we investigate the fecal and plasma metabolome of samples obtained from a cohort of 51 extremely premature infants at several time points, using liquid chromatography (LC)-high-resolution mass spectrometry (MS)-based untargeted metabolomics and LC-MS/MS-based targeted analysis for investigating bile acids and amidated bile acid conjugates. The data are integrated with 16S rRNA gene amplicon gut microbiome profiles as well as patient cytokine, growth factor, and T cell profiles. We find an early onset of differentiation in neuroactive metabolites between infants with and without brain injury. We detect several bacterially derived bile acid amino acid conjugates in plasma and feces. These results provide insights into the early-life metabolome of extremely premature infants.},
}
@article {pmid38516656,
year = {2024},
author = {Brait, N and Hackl, T and Morel, C and Exbrayat, A and Gutierrez, S and Lequime, S},
title = {A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {vead088},
pmid = {38516656},
issn = {2057-1577},
abstract = {Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.},
}
@article {pmid38514851,
year = {2024},
author = {Silva, DEO and Costa, RM and Campos, JR and Rocha, SMB and de Araujo Pereira, AP and Melo, VMM and Oliveira, FAS and de Alcantara Neto, F and Mendes, LW and Araujo, ASF},
title = {Short-term restoration practices change the bacterial community in degraded soil from the Brazilian semiarid.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6845},
pmid = {38514851},
issn = {2045-2322},
mesh = {*Soil ; RNA, Ribosomal, 16S/genetics ; Brazil ; *Bacteria/genetics ; Acidobacteria/genetics ; Soil Microbiology ; },
abstract = {Land degradation by deforestation adversely impacts soil properties, and long-term restoration practices have been reported to potentially reverse these effects, particularly on soil microorganisms. However, there is limited knowledge regarding the short-term effects of restoration on the soil bacterial community in semiarid areas. This study evaluates the bacterial community in soils experiencing degradation (due to slash-and-burn deforestation) and restoration (utilizing stone cordons and revegetation), in comparison to a native soil in the Brazilian semiarid region. Three areas were selected: (a) under degradation; (b) undergoing short-term restoration; and (c) a native area, and the bacterial community was assessed using 16S rRNA sequencing on soil samples collected during both dry and rainy seasons. The dry and rainy seasons exhibited distinct bacterial patterns, and native sites differed from degraded and restoration sites. Chloroflexi and Proteobacteria phyla exhibited higher prevalence in degraded and restoration sites, respectively, while Acidobacteria and Actinobacteria were more abundant in sites undergoing restoration compared to degraded sites. Microbial connections varied across sites and seasons, with an increase in nodes observed in the native site during the dry season, more edges and positive connections in the restoration site, and a higher occurrence of negative connections in the degradation site during the rainy season. Niche occupancy analysis revealed that degradation favored specialists over generalists, whereas restoration exhibited a higher prevalence of generalists compared to native sites. Specifically, degraded sites showed a higher abundance of specialists in contrast to restoration sites. This study reveals that land degradation impacts the soil bacterial community, leading to differences between native and degraded sites. Restoring the soil over a short period alters the status of the bacterial community in degraded soil, fostering an increase in generalist microbes that contribute to enhanced soil stability.},
}
@article {pmid38512483,
year = {2024},
author = {Zhan, Y and Wang, E and Zhou, Y and He, G and Lv, P and Wang, L and Zhou, T and Miao, X and Chen, C and Li, Q},
title = {Facilitating Effects of Reductive Soil Disinfestation on Soil Health and Physiological Properties of Panax ginseng.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {54},
pmid = {38512483},
issn = {1432-184X},
mesh = {Soil/chemistry ; *Panax ; Agriculture/methods ; *Microbiota ; *Mycobiome ; Soil Microbiology ; },
abstract = {Chemical soil fumigation (CSF) and reductive soil disinfestation (RSD) have been proven to be effective agricultural strategies to improve soil quality, restructure microbial communities, and promote plant growth in soil degradation remediation. However, it is still unclear how RSD and CSF ensure soil and plant health by altering fungal communities. Field experiments were conducted to investigate the effects of CSF with chloropicrin, and RSD with animal feces on soil properties, fungal communities and functional composition, and plant physiological characteristics were evaluated. Results showed that RSD and CSF treatment improved soil properties, restructured fungal community composition and structure, enhanced fungal interactions and functions, and facilitated plant growth. There was a significant increase in OM, AN, and AP contents in the soil with both CSF and RSD treatments compared to CK. Meanwhile, compared with CK and CSF, RSD treatment significantly increased biocontrol Chaetomium relative abundance while reducing pathogenic Neonectria relative abundance, indicating that RSD has strong inhibition potential. Furthermore, the microbial network of RSD treatment was more complex and interconnected, and the functions of plant pathogens, and animal pathogen were decreased. Importantly, RSD treatment significantly increased plant SOD, CAT, POD activity, SP, Ca, Zn content, and decreased MDA, ABA, Mg, K, and Fe content. In summary, RSD treatment is more effective than CSF treatment, by stimulating the proliferation of probiotic communities to further enhance soil health and plant disease resistance.},
}
@article {pmid38509266,
year = {2024},
author = {Djotan, AKG and Matsushita, N and Fukuda, K},
title = {Year-round dynamics of arbuscular mycorrhizal fungi communities in the roots and surrounding soils of Cryptomeria japonica.},
journal = {Mycorrhiza},
volume = {34},
number = {1-2},
pages = {119-130},
pmid = {38509266},
issn = {1432-1890},
support = {JP22H02382//Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Mycorrhizae/genetics ; Soil/chemistry ; Ecosystem ; *Cryptomeria/genetics ; Plant Roots/microbiology ; Soil Microbiology ; Trees ; DNA, Fungal/genetics ; Fungi/genetics ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) live simultaneously inside and outside of host plant roots for a functional mycorrhizal symbiosis. Still, the year-round dynamics and relationships between soil properties and AMF communities of trees in forest ecosystems remain unclear. We collected paired root and soil samples of the same Cryptomeria japonica trees at two forest sites (five trees at each site) every 2 months over a year. Total DNA was extracted from roots and soil separately and soil physicochemical properties were measured. With Illumina's next-generation amplicon sequencing targeting the small subunit of fungal ribosomal DNA, we clarified seasonal dynamics of soil properties and AMF communities. Soil pH and total phosphorus showed significant seasonality while total carbon, nitrogen, and C/N did not. Only pH was a good predictor of the composition and dynamics of the AMF community. The total AMF community (roots + soil) showed significant seasonality because of variation from May to September. Root and soil AMF communities were steady year-round, however, with similar species richness but contained significantly different AMF assemblages in any sampling month. Despite the weak seasonality in the communities, the top two dominant OTUs showed significant but different shifts between roots and soils across seasons with strong antagonistic relationships. In conclusion, few dominant AMF taxa are dynamically shifting between the roots and soils of C. japonica to respond to seasonal and phenological variations in their microhabitats. AMF inhabiting forest ecosystems may have high environmental plasticity to sustain a functional symbiosis regardless of seasonal variations that occur in the soil.},
}
@article {pmid38508742,
year = {2024},
author = {Nishimura, Y and Yamada, K and Okazaki, Y and Ogata, H},
title = {DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics.},
journal = {Microbes and environments},
volume = {39},
number = {1},
pages = {},
pmid = {38508742},
issn = {1347-4405},
mesh = {*Software ; *User-Computer Interface ; Sequence Alignment ; Genomics ; Genome ; },
abstract = {With the explosion of available genomic information, comparative genomics has become a central approach to understanding microbial ecology and evolution. We developed DiGAlign (https://www.genome.jp/digalign/), a web server that provides versatile functionality for comparative genomics with an intuitive interface. It allows the user to perform the highly customizable visualization of a synteny map by simply uploading nucleotide sequences of interest, ranging from a specific region to the whole genome landscape of microorganisms and viruses. DiGAlign will serve a wide range of biological researchers, particularly experimental biologists, with multifaceted features that allow the rapid characterization of genomic sequences of interest and the generation of a publication-ready figure.},
}
@article {pmid38508273,
year = {2024},
author = {O'Donnell, C and Thorn, C and Roskam, E and Friel, R and Kirwan, SF and Waters, SM and O'Flaherty, V},
title = {Novel oxidising feed additives reduce in vitro methane emissions using the rumen simulation technique.},
journal = {The Science of the total environment},
volume = {926},
number = {},
pages = {171808},
doi = {10.1016/j.scitotenv.2024.171808},
pmid = {38508273},
issn = {1879-1026},
mesh = {Animals ; Female ; *Rumen ; *Propionates/metabolism ; Methane/metabolism ; Magnesium Oxide/metabolism ; Diet ; Silage/analysis ; Ruminants ; Acetates/metabolism ; Oxygen/metabolism ; Animal Feed/analysis ; Fermentation ; Digestion ; Lactation ; },
abstract = {Enteric methane (CH4) produced by ruminant livestock is a potent greenhouse gas and represents significant energy loss for the animal. The novel application of oxidising compounds as antimethanogenic agents with future potential to be included in ruminant feeds, was assessed across two separate experiments in this study. Low concentrations of oxidising agents, namely urea hydrogen peroxide (UHP) with and without potassium iodide (KI), and magnesium peroxide (MgO2), were investigated for their effects on CH4 production, total gas production (TGP), volatile fatty acid (VFA) profiles, and nutrient disappearance in vitro using the rumen simulation technique. In both experiments, the in vitro diet consisted of 50:50 grass silage:concentrate on a dry matter basis. Treatment concentrations were based on the amount of oxygen delivered and expressed in terms of fold concentration. In Experiment 1, four treatments were tested (Control, 1× UHP + KI, 1× UHP, and 0.5× UHP + KI), and six treatments were assessed in Experiment 2 (Control, 0.5× UHP + KI, 0.5× UHP, 0.25× UHP + KI, 0.25× UHP, and 0.12× MgO2). All treatments in this study had a reducing effect on CH4 parameters. A dose-dependent reduction of TGP and CH4 parameters was observed, where treatments delivering higher levels of oxygen resulted in greater CH4 suppression. 1× UHP + KI reduced TGP by 28 % (p = 0.611), CH4% by 64 % (p = 0.075) and CH4 mmol/g digestible organic matter by 71 % (p = 0.037). 0.12× MgO2 reduced CH4 volume by 25 % (p > 0.05) without affecting any other parameters. Acetate-to-propionate ratios were reduced by treatments in both experiments (p < 0.01). Molar proportions of acetate and butyrate were reduced, while propionate and valerate were increased in UHP treatments. High concentrations of UHP affected the degradation of neutral detergent fibre in the forage substrate. Future in vitro work should investigate alternative slow-release oxygen sources aimed at prolonging CH4 suppression.},
}
@article {pmid38508106,
year = {2024},
author = {Luo, Y and Pang, J and Pan, S and Wang, J and Jiang, X and Xu, Q and Zhang, H and Ruan, C and Ren, J and Zhang, C and Shi, J},
title = {Penicillium oxalicum SL2-enhanced nanoscale zero-valent iron effectively reduces Cr(VI) and shifts soil microbiota.},
journal = {Journal of hazardous materials},
volume = {469},
number = {},
pages = {134058},
doi = {10.1016/j.jhazmat.2024.134058},
pmid = {38508106},
issn = {1873-3336},
mesh = {*Chromium/analysis/metabolism ; *Environmental Restoration and Remediation ; Iron ; *Penicillium ; Soil ; Urease ; *Water Pollutants, Chemical/analysis ; },
abstract = {Most current researches focus solely on reducing soil chromium availability. It is difficult to reduce soil Cr(VI) concentration below 5.0 mg kg[-1] using single remediation technology. This study introduced a sustainable soil Cr(VI) reduction and stabilization system, Penicillium oxalicum SL2-nanoscale zero-valent iron (nZVI), and investigated its effect on Cr(VI) reduction efficiency and microbial ecology. Results showed that P. oxalicum SL2-nZVI effectively reduced soil total Cr(VI) concentration from 187.1 to 3.4 mg kg[-1] within 180 d, and remained relatively stable at 360 d. The growth curve of P. oxalicum SL2 and microbial community results indicated that γ-ray irradiation shortened the adaptation time of P. oxalicum SL2 and facilitated its colonization in soil. P. oxalicum SL2 colonization activated nZVI and its derivatives, and increased soil iron bioavailability. After restoration, the negative effect of Cr(VI) on soil microorganisms was markedly alleviated. Cr(VI), Fe(II), bioavailable Cr/Fe, Eh, EC and urease (SUE) were the key environmental factors of soil microbiota. Notably, Penicillium significantly stimulated the growth of urease-positive bacteria, Arthrobacter, Pseudarthrobacter, and Microvirga, synergistically reducing soil chromium availability. The combination of P. oxalicum SL2 and nZVI is expected to form a green, economical and long-lasting Cr(VI) reduction stabilization strategy.},
}
@article {pmid38507071,
year = {2024},
author = {Martin-Pozas, T and Nováková, A and Jurado, V and Cuezva, S and Fernandez-Cortes, A and Saiz-Jimenez, C and Sanchez-Moral, S},
title = {A Second Fungal Outbreak in Castañar Cave, Spain, Discloses the Fragility of Subsurface Ecosystems.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {53},
pmid = {38507071},
issn = {1432-184X},
support = {PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114978GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114978GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {*Fungi/genetics ; Spain/epidemiology ; *Ecosystem ; Caves/microbiology ; Disease Outbreaks ; },
abstract = {Castañar is a cave with strict visitor control measures since it was open to public visits in 2003. However, in recent years, the cave suffered two fungal outbreaks, the first in 2008 and controlled by cleaning the contaminated sediments and subsequent closure of the cave until 2014. The cave was reopened but limited to a maximum of 450 visitors/year. Despite these restrictions on visit, the cave experienced a second outbreak in 2021, originating from the installation of a steel grating walkway, aiming at protecting the ground sediments from the visitors' footsteps. Here, we conducted an analysis using Next-Generation Sequencing and culture-dependent techniques to investigate the fungal communities related to the second outbreak and compare with those present before the cave suffered the outbreak. The results show that the most abundant fungi involved in the 2021 outbreak were already detected in 2020, and even in 2008 and 2009, although the main species that originating both outbreaks were different, likely due to the different carbon sources introduced into the cave.},
}
@article {pmid38506907,
year = {2024},
author = {Sun, P and Wu, Y and Guo, M and Zhu, M and Zhang, L and Zhang, J and Li, Z},
title = {First Report of Powdery Mildew caused by Erysiphe astragali on Sphaerophysa salsula.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-02-24-0334-PDN},
pmid = {38506907},
issn = {0191-2917},
abstract = {Sphaerophysa salsula (Pall.) DC., also known as Yang Liao Pao, belongs to the Leguminosae family and is the only existing species in the Sphaerophysa genus. S. salsula is tolerance to cold, high salt, and alkaline soil, it is widely cultivated in China as a forage crop, and used as a Chinese folk medicine to treat hypertension (Ma et al., 2002). In 2023, signs and symptoms similar to powdery mildew were found on S. salsula planted in Tumd left (40.515°N, 110.424°E), Baotou City, Inner Mongolia Autonomous Region, China. The white powdery substance covered 90% of the leaf area, and the infected plants showed weak growth and senescence. More than 80% of plants (n=200) had these powdery mildew-like symptoms. Hyphal appressoria are solitary, conidiophores have few branches and septa. Conidia are cylindrical to clavate, 25-32 μm long and 8-15 μm wide (n=30), conidia form single subapical germ tubes, straight to curved-sinuous, with swollen apex or distinctly lobed conidial appressorium. Based on these morphological characteristics, the fungus was tentatively identified as an Erysiphe sp. (Schmidt and Braun 2020). Fungal structures were isolated from diseased leaves, and genomic DNA of the pathogen was extracted using the method described by Zhu et al. (2022). The internal transcribed spacer (ITS) region was amplified by PCR using the primers PMITS1/PMITS2 (Cunnington et al. 2003) and the amplicon sequenced by Invitrogen (Shanghai, China). The powdery mildew strain, named as KMD (GenBank accession no.: PP267067), showed an identity of 100% (645/645bp) with Erysiphe astragali, a powdery mildew reported on Astragalus glycyphyllos in Golestan, Iran (GenBank: OP806834) and identity of 99.6% (643/645bp) with Erysiphe astragali (GenBank: MW142495), a powdery mildew reported on A. scaberrimus in Inner Mongolia, China (Sun et al. 2023). Pathogenicity tests were conducted by brushing the conidia from infected S. salsula leaves onto leaves of four healthy plants, while four control plants were brushed in the same manner. All the treated plants were placed in separate growth chambers maintained at 19°C and 65% humidity, with a 16 h light/8 h dark photoperiod. Nine days after inoculation, the treated plants showed powdery mildew symptoms, while the control plants remained asymptomatic. The same results were obtained for two repeated pathogenicity experiments. The powdery mildew fungus was reisolated and identified as E. astragali based on morphological and molecular analysis, thereby fulfilling Koch's postulates. No report on the occurrence of powdery mildew on S. salsula plants has been found previously. The occurrence of this destructive powdery mildew may adversely affect the cultivation of S. salsula. Identifying the pathogen of powdery mildew will support future efforts to control and manage powdery mildew on S. salsula.},
}
@article {pmid38502221,
year = {2024},
author = {Saati-Santamaría, Z and Flores-Félix, JD and Igual, JM and Velázquez, E and García-Fraile, P and Martínez-Molina, E},
title = {Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host.},
journal = {Journal of molecular evolution},
volume = {92},
number = {2},
pages = {169-180},
pmid = {38502221},
issn = {1432-1432},
support = {SA293P18//Junta de Castilla y Le&#xf3;n/ ; },
mesh = {*Fatty Acids ; Phylogeny ; *Plants/genetics ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {The bacterial strain SECRCQ15[T] was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15[T], we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15[T] genome. We also found that singletons of F. quinoae SECRCQ15[T] are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.},
}
@article {pmid38500703,
year = {2024},
author = {Dreyling, L and Penone, C and Schenk, NV and Schmitt, I and Dal Grande, F},
title = {Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae012},
pmid = {38500703},
issn = {2730-6151},
abstract = {Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.},
}
@article {pmid38499207,
year = {2024},
author = {Kodama, T and Takehara, T},
title = {Molecular Genealogy of Metabolic-associated Hepatocellular Carcinoma.},
journal = {Seminars in liver disease},
volume = {44},
number = {2},
pages = {147-158},
pmid = {38499207},
issn = {1098-8971},
support = {JP23ama221410,JP23ck0106793,JP23fk0210131//Japan Agency for Medical Research and Development/ ; JP23ama221410//Japan Agency for Medical Research and Development/ ; JP23ck0106793//Japan Agency for Medical Research and Development/ ; JP23fk0210131//Japan Agency for Medical Research and Development/ ; },
mesh = {Humans ; *Carcinoma, Hepatocellular/genetics ; *Liver Neoplasms/genetics ; *Tumor Microenvironment ; *Genetic Predisposition to Disease ; Animals ; Non-alcoholic Fatty Liver Disease/genetics ; Lipid Metabolism/genetics ; Insulin Resistance ; Membrane Proteins/genetics ; Diabetes Mellitus, Type 2/genetics ; Oxidative Stress ; Obesity/genetics/complications ; Risk Factors ; Polymorphism, Single Nucleotide ; Acyltransferases/genetics ; Adaptor Proteins, Signal Transducing ; Phospholipases A2, Calcium-Independent ; },
abstract = {This review examines the latest epidemiological and molecular pathogenic findings of metabolic-associated hepatocellular carcinoma (HCC). Its increasing prevalence is a significant concern and reflects the growing burden of obesity and metabolic diseases, including metabolic dysfunction-associated steatotic liver disease, formerly known as nonalcoholic fatty liver disease, and type 2 diabetes. Metabolic-associated HCC has unique molecular abnormality and distinctive gene expression patterns implicating aberrations in bile acid, fatty acid metabolism, oxidative stress, and proinflammatory pathways. Furthermore, a notable frequency of single nucleotide polymorphisms in genes such as patatin-like phospholipase domain-containing 3, transmembrane 6 superfamily member 2, glucokinase regulator, and membrane-bound O-acyltransferase domain-containing 7 has been observed. The tumor immune microenvironment of metabolic-associated HCC is characterized by unique phenotypes of macrophages, neutrophils, and T lymphocytes. Additionally, the pathogenesis of metabolic-associated HCC is influenced by abnormal lipid metabolism, insulin resistance, and dysbiosis. In conclusion, deciphering the intricate interactions among metabolic processes, genetic predispositions, inflammatory responses, immune regulation, and microbial ecology is imperative for the development of novel therapeutic and preventative measures against metabolic-associated HCC.},
}
@article {pmid38498218,
year = {2024},
author = {Greipel, E and Nagy, K and Csákvári, E and Dér, L and Galajda, P and Kutasi, J},
title = {Chemotactic Interactions of Scenedesmus sp. and Azospirillum brasilense Investigated by Microfluidic Methods.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {52},
pmid = {38498218},
issn = {1432-184X},
mesh = {*Azospirillum brasilense ; *Scenedesmus/metabolism ; Microfluidics ; Oxaloacetic Acid/metabolism ; Plant Growth Regulators/metabolism ; Plants/metabolism ; },
abstract = {The use of algae for industrial, biotechnological, and agricultural purposes is spreading globally. Scenedesmus species can play an essential role in the food industry and agriculture due to their favorable nutrient content and plant-stimulating properties. Previous research and the development of Scenedesmus-based foliar fertilizers raised several questions about the effectiveness of large-scale algal cultivation and the potential effects of algae on associative rhizobacteria. In the microbiological practice applied in agriculture, bacteria from the genus Azospirillum are one of the most studied plant growth-promoting, associative, nitrogen-fixing bacteria. Co-cultivation with Azospirillum species may be a new way of optimizing Scenedesmus culturing, but the functioning of the co-culture system still needs to be fully understood. It is known that Azospirillum brasilense can produce indole-3-acetic acid, which could stimulate algae growth as a plant hormone. However, the effect of microalgae on Azospirillum bacteria is unclear. In this study, we investigated the behavior of Azospirillum brasilense bacteria in the vicinity of Scenedesmus sp. or its supernatant using a microfluidic device consisting of physically separated but chemically coupled microchambers. Following the spatial distribution of bacteria within the device, we detected a positive chemotactic response toward the microalgae culture. To identify the metabolites responsible for this behavior, we tested the chemoeffector potential of citric acid and oxaloacetic acid, which, according to our HPLC analysis, were present in the algae supernatant in 0.074 mg/ml and 0.116 mg/ml concentrations, respectively. We found that oxaloacetic acid acts as a chemoattractant for Azospirillum brasilense.},
}
@article {pmid38497641,
year = {2024},
author = {Dean, CJ and Peña-Mosca, F and Ray, T and Wehri, TJ and Sharpe, K and Antunes, AM and Doster, E and Fernandes, L and Calles, VF and Bauman, C and Godden, S and Heins, B and Pinedo, P and Machado, VS and Caixeta, LS and Noyes, NR},
title = {Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infections in primiparous cows under organic directives.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {4},
pages = {e0223423},
pmid = {38497641},
issn = {1098-5336},
mesh = {Female ; Cattle ; Animals ; Staphylococcus aureus/genetics ; Metagenome ; Case-Control Studies ; *Mastitis, Bovine/epidemiology/microbiology ; *Staphylococcal Infections/epidemiology/veterinary/microbiology ; Milk/microbiology ; Mammary Glands, Animal/microbiology ; },
abstract = {UNLABELLED: The primary objective of this study was to identify associations between the prepartum teat apex microbiome and the presence of Staphylococcus aureus intramammary infections (IMI) in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on five organic dairy farms. Cases had higher odds of having S. aureus metagenomic DNA on the teat apex prior to parturition compared to controls (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in the abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93), and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Genes encoding for Microcin B17 AMPs were the most prevalent on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of genes encoding for Microcin B17 was also higher in cases compared to controls (LFC 0.26).<br><br>IMPORTANCE: Intramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes the detection of genomic features such as genes that encode for AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role prepartum teat apex microbiome dynamics play in IMI risk.},
}
@article {pmid38494494,
year = {2024},
author = {Liu, X and Salles, JF},
title = {Lose-lose consequences of bacterial community-driven invasions in soil.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {57},
pmid = {38494494},
issn = {2049-2618},
mesh = {*Soil ; Soil Microbiology ; Bacteria/genetics/metabolism ; *Microbiota ; },
abstract = {BACKGROUND: Community-driven invasion, also known as community coalescence, occurs widely in natural ecosystems. Despite that, our knowledge about the process and mechanisms controlling community-driven invasion in soil ecosystems is lacking. Here, we performed a set of coalescence experiments in soil microcosms and assessed impacts up to 60 days after coalescence by quantifying multiple traits (compositional, functional, and metabolic) of the invasive and coalescent communities.<br><br>RESULTS: Our results showed that coalescences significantly triggered changes in the resident community's succession trajectory and functionality (carbohydrate metabolism), even when the size of the invasive community is small (~&#x2009;5% of the resident density) and 99% of the invaders failed to survive. The invasion impact was mainly due to the high suppression of constant residents (65% on average), leading to a lose-lose situation where both invaders and residents suffered with coalescence. Our results showed that surviving residents could benefit from the coalescence, which supports the theory of "competition-driven niche segregation" at the microbial community level. Furthermore, the result showed that both short- and long-term coalescence effects were predicted by similarity and unevenness indexes of compositional, functional, and metabolic traits of invasive communities. This indicates the power of multi-level traits in monitoring microbial community succession. In contrast, the varied importance of different levels of traits suggests that competitive processes depend on the composition of the invasive community.<br><br>CONCLUSIONS: Our results shed light on the process and consequence of community coalescences and highlight that resource competition between invaders and residents plays a critical role in soil microbial community coalescences. These findings provide valuable insights for understanding and predicting soil microbial community succession in frequently disturbed natural and agroecosystems. Video Abstract.},
}
@article {pmid38493536,
year = {2024},
author = {Mekonnen, YT and Savini, F and Indio, V and Seguino, A and Giacometti, F and Serraino, A and Candela, M and De Cesare, A},
title = {Systematic review on microbiome-related nutritional interventions interfering with the colonization of foodborne pathogens in broiler gut to prevent contamination of poultry meat.},
journal = {Poultry science},
volume = {103},
number = {5},
pages = {103607},
pmid = {38493536},
issn = {1525-3171},
mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome ; *Poultry Diseases/prevention &amp; control/microbiology ; Meat/analysis ; Probiotics/administration &amp; dosage/pharmacology ; Animal Feed/analysis ; Food Microbiology ; Foodborne Diseases/veterinary/prevention &amp; control/microbiology ; Diet/veterinary ; },
abstract = {This systematic review aimed to compile the available body of knowledge about microbiome-related nutritional interventions contributing to improve the chicken health and having an impact on the reduction of colonization by foodborne pathogens in the gut. Original research articles published between 2012 and 2022 were systematically searched in Scopus and PubMed. A total of 1,948 articles were retrieved and 140 fulfilled the inclusion criteria. Overall, 73 papers described 99 interventions against colonization by Escherichia coli and related organisms; 10 papers described 15 interventions against Campylobacter spp.; 36 papers described 54 interventions against Salmonella; 40 papers described 54 interventions against Clostridium perfringens. A total of 197 microbiome-related interventions were identified as effective against one or more of the listed pathogens and included probiotics (n = 80), prebiotics (n = 23), phytobiotics (n = 25), synbiotics (n = 12), organic acids (n = 12), enzymes (n = 4), essential oils (n = 14) and combination of these (n = 27). The identified interventions were mostly administered in the feed (173/197) or through oral gavage (11/197), in the drinking water (7/197), in ovo (2/197), intra amniotic (2/197), in fresh or reused litter (1/197) or both in the feed and water (1/197). The interventions enhanced the beneficial microbial communities in the broiler gut as Lactic acid bacteria, mostly Lactobacillus spp., or modulated multiple microbial populations. The mechanisms promoting the fighting against colonization by foodborne pathogens included competitive exclusion, production of short chain fatty acids, decrease of gut pH, restoration of the microbiome after dysbiosis events, promotion of a more stable microbial ecology, expression of genes improving the integrity of intestinal mucosa, enhancing of mucin production and improvement of host immune response. All the studies extracted from the literature described in vivo trials but performed on a limited number of animals under experimental settings. Moreover, they detailed the effect of the intervention on the chicken gut without details on further impact on poultry meat safety.},
}
@article {pmid38493186,
year = {2024},
author = {Wu, L and Wang, XW and Tao, Z and Wang, T and Zuo, W and Zeng, Y and Liu, YY and Dai, L},
title = {Data-driven prediction of colonization outcomes for complex microbial communities.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2406},
pmid = {38493186},
issn = {2041-1723},
support = {U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; RF1 AG067744/AG/NIA NIH HHS/United States ; K25 HL166208/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; Feces/microbiology ; *Enterococcus faecium ; Microbial Interactions ; Enterococcus faecalis ; },
abstract = {Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.},
}
@article {pmid38492828,
year = {2024},
author = {Malik, M and Das, S and Chakraborty, P and Paul, P and Roy, R and Das Gupta, A and Sarkar, S and Chatterjee, S and Maity, A and Dasgupta, M and Sarker, RK and Tribedi, P},
title = {Application of cuminaldehyde and ciprofloxacin for the effective control of biofilm assembly of Pseudomonas aeruginosa: A combinatorial study.},
journal = {Microbial pathogenesis},
volume = {190},
number = {},
pages = {106624},
doi = {10.1016/j.micpath.2024.106624},
pmid = {38492828},
issn = {1096-1208},
mesh = {*Biofilms/drug effects ; *Ciprofloxacin/pharmacology ; *Pseudomonas aeruginosa/drug effects/physiology ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Benzaldehydes/pharmacology ; *Reactive Oxygen Species/metabolism ; Virulence Factors ; Cymenes/pharmacology ; Drug Synergism ; Cell Membrane Permeability/drug effects ; Humans ; },
abstract = {Pseudomonas aeruginosa is widely associated with biofilm-mediated antibiotic resistant chronic and acute infections which constitute a persistent healthcare challenges. Addressing this threat requires exploration of novel therapeutic strategies involving the combination of natural compounds and conventional antibiotics. Hence, our study has focused on two compounds; cuminaldehyde and ciprofloxacin, which were strategically combined to target the biofilm challenge of P. aeruginosa. The minimum inhibitory concentration (MIC) of cuminaldehyde and ciprofloxacin was found to be 400 μg/mL and 0.4 μg/mL, respectively. Moreover, the fractional inhibitory concentration index (FICI = 0.62) indicated an additive interaction prevailed between cuminaldehyde and ciprofloxacin. Subsequently, sub-MIC doses of cuminaldehyde (25 μg/mL) and ciprofloxacin (0.05 μg/mL) were selected for an array of antibiofilm assays which confirmed their biofilm inhibitory potential without exhibiting any antimicrobial activity. Furthermore, selected doses of the mentioned compounds could manage biofilm on catheter surface by inhibiting and disintegrating existing biofilm. Additionally, the test combination of the mentioned compounds reduced virulence factors secretion, accumulated reactive oxygen species and increased cell-membrane permeability. Thus, the combination of cuminaldehyde and ciprofloxacin demonstrates potential in combating biofilm-associated Pseudomonal threats.},
}
@article {pmid38492604,
year = {2024},
author = {Zhao, S and Zheng, Q and Wang, H and Fan, X},
title = {Nitrogen in landfills: Sources, environmental impacts and novel treatment approaches.},
journal = {The Science of the total environment},
volume = {924},
number = {},
pages = {171725},
doi = {10.1016/j.scitotenv.2024.171725},
pmid = {38492604},
issn = {1879-1026},
abstract = {Nitrogen (N) accumulation in landfills is a pressing environmental concern due to its diverse sources and significant environmental impacts. However, there is relatively limited attention and research focus on N in landfills as it is overshadowed by other more prominent pollutants. This study comprehensively examines the sources of N in landfills, including food waste contributing to 390 million tons of N annually, industrial discharges, and sewage treatment plant effluents. The environmental impacts of N in landfills are primarily manifested in N2O emissions and leachate with high N concentrations. To address these challenges, this study presents various mitigation and management strategies, including N2O reduction measures and novel NH4[+] removal techniques, such as electrochemical technologies, membrane separation processes, algae-based process, and other advanced oxidation processes. However, a more in-depth understanding of the complexities of N cycling in landfills is required, due to the lack of long-term monitoring data and the presence of intricate interactions and feedback mechanisms. To ultimately achieve optimized N management and minimized adverse environmental impacts in landfill settings, future prospects should emphasize advancements in monitoring and modeling technologies, enhanced understanding of microbial ecology, implementation of circular economy principles, application of innovative treatment technologies, and comprehensive landfill design and planning.},
}
@article {pmid38491554,
year = {2024},
author = {Xu, G and Zhao, S and Rogers, MJ and Chen, C and He, J},
title = {Global prevalence of organohalide-respiring bacteria dechlorinating polychlorinated biphenyls in sewage sludge.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {54},
pmid = {38491554},
issn = {2049-2618},
support = {R-302-000-198720//Ng Teng Fong Charitable Foundation (NTFCF)/ ; MOE-00003301//The Ministry of Education, Singapore/ ; },
mesh = {Humans ; *Polychlorinated Biphenyls/analysis ; Sewage ; *Chloroflexi/genetics ; Prevalence ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; *Environmental Pollutants/analysis ; Geologic Sediments/microbiology ; },
abstract = {BACKGROUND: Massive amounts of sewage sludge are generated during biological sewage treatment and are commonly subjected to anaerobic digestion, land application, and landfill disposal. Concurrently, persistent organic pollutants (POPs) are frequently found in sludge treatment and disposal systems, posing significant risks to both human health and wildlife. Metabolically versatile microorganisms originating from sewage sludge are inevitably introduced to sludge treatment and disposal systems, potentially affecting the fate of POPs. However, there is currently a dearth of comprehensive assessments regarding the capability of sewage sludge microbiota from geographically disparate regions to attenuate POPs and the underpinning microbiomes.<br><br>RESULTS: Here we report the global prevalence of organohalide-respiring bacteria (OHRB) known for their capacity to attenuate POPs in sewage sludge, with an occurrence frequency of ~50% in the investigated samples (605 of 1186). Subsequent laboratory tests revealed microbial reductive dechlorination of polychlorinated biphenyls (PCBs), one of the most notorious categories of POPs, in 80 out of 84 sludge microcosms via various pathways. Most chlorines were removed from the para- and meta-positions of PCBs; nevertheless, ortho-dechlorination of PCBs also occurred widely, although to lower extents. Abundances of several well-characterized OHRB genera (Dehalococcoides, Dehalogenimonas, and Dehalobacter) and uncultivated Dehalococcoidia lineages increased during incubation and were positively correlated with PCB dechlorination, suggesting their involvement in dechlorinating PCBs. The previously identified PCB reductive dehalogenase (RDase) genes pcbA4 and pcbA5 tended to coexist in most sludge microcosms, but the low ratios of these RDase genes to OHRB abundance also indicated the existence of currently undescribed RDases in sewage sludge. Microbial community analyses revealed a positive correlation between biodiversity and PCB dechlorination activity although there was an apparent threshold of community co-occurrence network complexity beyond which dechlorination activity decreased.<br><br>CONCLUSIONS: Our findings that sludge microbiota exhibited nearly ubiquitous dechlorination of PCBs indicate widespread and nonnegligible impacts of sludge microbiota on the fate of POPs in sludge treatment and disposal systems. The existence of diverse OHRB also suggests sewage sludge as an alternative source to obtain POP-attenuating consortia and calls for further exploration of OHRB populations in sewage sludge. Video Abstract.},
}
@article {pmid38488929,
year = {2024},
author = {Dayang Najwa, AB and Elexson, N and Dalene, L and Teng, ST},
title = {Vibrio Species and Cyanobacteria: Understanding Their Association in Local Shrimp Farm Using Canonical Correspondence Analysis (CCA).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {51},
pmid = {38488929},
issn = {1432-184X},
mesh = {Animals ; *Vibrio ; *Cyanobacteria ; Ponds ; Water ; Aquaculture ; *Vibrio parahaemolyticus ; *Penaeidae/microbiology ; },
abstract = {In aquatic environments, Vibrio and cyanobacteria establish varying relationships influenced by environmental factors. To investigate their association, this study spanned 5 months at a local shrimp farm, covering the shrimp larvae stocking cycle until harvesting. A total of 32 samples were collected from pond A (n = 6), pond B (n = 6), effluent (n = 10), and influent (n = 10). Vibrio species and cyanobacteria density were observed, and canonical correspondence analysis (CCA) assessed their correlation. CCA revealed a minor correlation (p = 0.847, 0.255, 0.288, and 0.304) between Vibrio and cyanobacteria in pond A, pond B, effluent, and influent water, respectively. Notably, Vibrio showed a stronger correlation with pH (6.14-7.64), while cyanobacteria correlated with pH, salinity (17.4-24 ppt), and temperature (30.8-31.5 °C), with salinity as the most influential factor. This suggests that factors beyond cyanobacteria influence Vibrio survival. Future research could explore species-specific relationships, regional dynamics, and multidimensional landscapes to better understand Vibrio-cyanobacteria connections. Managing water parameters may prove more efficient in controlling vibriosis in shrimp farms than targeting cyanobacterial populations.},
}
@article {pmid38488280,
year = {2024},
author = {Giacomini, JJ and Torres-Morales, J and Tang, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {12},
number = {4},
pages = {e0401723},
pmid = {38488280},
issn = {2165-0497},
support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; Aggregatibacter/physiology ; Phylogeny ; *Ecosystem ; *Haemophilus/genetics ; Mouth ; },
abstract = {UNLABELLED: Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility.<br><br>IMPORTANCE: Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.},
}
@article {pmid38485445,
year = {2024},
author = {Harris, TD and Reinl, KL and Azarderakhsh, M and Berger, SA and Berman, MC and Bizic, M and Bhattacharya, R and Burnet, SH and Cianci-Gaskill, JA and Domis, LNS and Elfferich, I and Ger, KA and Grossart, HF and Ibelings, BW and Ionescu, D and Kouhanestani, ZM and Mauch, J and McElarney, YR and Nava, V and North, RL and Ogashawara, I and Paule-Mercado, MCA and Soria-Píriz, S and Sun, X and Trout-Haney, JV and Weyhenmeyer, GA and Yokota, K and Zhan, Q},
title = {What makes a cyanobacterial bloom disappear? A review of the abiotic and biotic cyanobacterial bloom loss factors.},
journal = {Harmful algae},
volume = {133},
number = {},
pages = {102599},
doi = {10.1016/j.hal.2024.102599},
pmid = {38485445},
issn = {1878-1470},
mesh = {*Cyanobacteria/physiology ; *Harmful Algal Bloom ; },
abstract = {Cyanobacterial blooms present substantial challenges to managers and threaten ecological and public health. Although the majority of cyanobacterial bloom research and management focuses on factors that control bloom initiation, duration, toxicity, and geographical extent, relatively little research focuses on the role of loss processes in blooms and how these processes are regulated. Here, we define a loss process in terms of population dynamics as any process that removes cells from a population, thereby decelerating or reducing the development and extent of blooms. We review abiotic (e.g., hydraulic flushing and oxidative stress/UV light) and biotic factors (e.g., allelopathic compounds, infections, grazing, and resting cells/programmed cell death) known to govern bloom loss. We found that the dominant loss processes depend on several system specific factors including cyanobacterial genera-specific traits, in situ physicochemical conditions, and the microbial, phytoplankton, and consumer community composition. We also address loss processes in the context of bloom management and discuss perspectives and challenges in predicting how a changing climate may directly and indirectly affect loss processes on blooms. A deeper understanding of bloom loss processes and their underlying mechanisms may help to mitigate the negative consequences of cyanobacterial blooms and improve current management strategies.},
}
@article {pmid38485438,
year = {2024},
author = {Woodhouse, JN and Burford, MA and Neilan, BA and Jex, A and Tichkule, S and Sivonen, K and Fewer, DP and Grossart, HP and Willis, A},
title = {Long-term stability of the genome structure of the cyanobacterium, Dolichospermum in a deep German lake.},
journal = {Harmful algae},
volume = {133},
number = {},
pages = {102600},
doi = {10.1016/j.hal.2024.102600},
pmid = {38485438},
issn = {1878-1470},
support = {/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics ; Phytoplankton ; Biomass ; Phosphorus ; },
abstract = {Dolichospermum is a cyanobacterial genus commonly associated with toxic blooms in lakes and brackish water bodies worldwide, and is a long-term resident of Lake Stechlin, northeastern Germany. In recent decades, shifts in the phosphorus loading and phytoplankton species composition have seen increased biomass of Dolichospermum during summer blooms from 1998, peaking around 2005, and declining after 2020. Cyanobacteria are known to rapidly adapt to new environments, facilitated by genome adaptation. To investigate the changes in genomic features that may have occurred in Lake Stechlin Dolichospermum during this time of increased phosphorus loading and higher biomass, whole genome sequence analysis was performed on samples of ten akinetes isolated from ten, 1 cm segments of a sediment core, representing a ∼45-year period from 1970 to 2017. Comparison of these genomes with genomes of extant isolates revealed a clade of Dolichospermum that clustered with the ADA-6 genus complex, with remarkable genome stability, without gene gain or loss events in response to recent environmental changes. The genome characteristics indicate that this species is suited to a deep-chlorophyll maximum, including additional light-harvesting and phosphorus scavenging genes. Population SNP analysis revealed two sub-populations that shifted in dominance as the lake transitioned between oligotrophic and eutrophic conditions. Overall, the results show little change within the population, despite diversity between extant populations from different geographic locations and the in-lake changes in phosphorus concentrations.},
}
@article {pmid38484962,
year = {2024},
author = {Fang, X and Colina Blanco, AE and Christl, I and Le Bars, M and Straub, D and Kleindienst, S and Planer-Friedrich, B and Zhao, FJ and Kappler, A and Kretzschmar, R},
title = {Simultaneously decreasing arsenic and cadmium in rice by soil sulfate and limestone amendment under intermittent flooding.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {347},
number = {},
pages = {123786},
doi = {10.1016/j.envpol.2024.123786},
pmid = {38484962},
issn = {1873-6424},
mesh = {Cadmium/analysis ; *Arsenic/analysis ; Calcium Carbonate ; Soil ; *Oryza ; Sulfates ; Clay ; Sulfur Oxides ; Sand ; *Soil Pollutants/analysis ; *Oxides ; *Calcium Compounds ; },
abstract = {Water management in paddy soils can effectively reduce the soil-to-rice grain transfer of either As or Cd, but not of both elements simultaneously due to the higher mobility of As under reducing and Cd under oxidizing soil conditions. Limestone amendment, the common form of liming, is well known for decreasing Cd accumulation in rice grown on acidic soils. Sulfate amendment was suggested to effectively decrease As accumulation in rice, especially under intermittent soil flooding. To study the unknown effects of combined sulfate and limestone amendment under intermittent flooding for simultaneously decreasing As and Cd in rice, we performed a pot experiment using an acidic sandy loam paddy soil. We also included a clay loam paddy soil to study the role of soil texture in low-As rice production under intermittent flooding. We found that liming not only decreased rice Cd concentrations but also greatly decreased dimethylarsenate (DMA) accumulation in rice. We hypothesize that this is due to suppressed sulfate reduction, As methylation, and As thiolation by liming in the sulfate-amended soil and a higher share of deprotonated DMA at higher pH which is taken up less readily than protonated DMA. Decreased gene abundance of potential soil sulfate-reducers by liming further supported our hypothesis. Combined sulfate and limestone amendment to the acidic sandy loam soil produced rice with 43% lower inorganic As, 72% lower DMA, and 68% lower Cd compared to the control soil without amendment. A tradeoff between soil aeration and water availability was observed for the clay loam soil, suggesting difficulties to decrease As in rice while avoiding plant water stress under intermittent flooding in fine-textured soils. Our results suggest that combining sulfate amendment, liming, and intermittent flooding can help to secure rice safety when the presence of both As and Cd in coarse-textured soils is of concern.},
}
@article {pmid38483479,
year = {2024},
author = {Mermans, F and De Baets, H and García-Timermans, C and Teughels, W and Boon, N},
title = {Unlocking the mechanism of action: a cost-effective flow cytometry approach for accelerating antimicrobial drug development.},
journal = {Microbiology spectrum},
volume = {12},
number = {4},
pages = {e0393123},
pmid = {38483479},
issn = {2165-0497},
support = {G0B2719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; },
mesh = {Humans ; *Cephalothin ; Flow Cytometry ; Cost-Benefit Analysis ; *Anti-Infective Agents/pharmacology ; Drug Development ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antimicrobial resistance is one of the greatest challenges to global health. While the development of new antimicrobials can combat resistance, low profitability reduces the number of new compounds brought to market. Elucidating the mechanism of action is crucial for developing new antimicrobials. This can become expensive as there are no universally applicable pipelines. Phenotypic heterogeneity of microbial populations resulting from antimicrobial treatment can be captured through flow cytometric fingerprinting. Since antimicrobials are classified into limited groups, the mechanism of action of known compounds can be used for predictive modeling. We demonstrate a cost-effective flow cytometry approach for determining the mechanism of action of new compounds. Cultures of Actinomyces viscosus and Fusobacterium nucleatum were treated with different antimicrobials and measured by flow cytometry. A Gaussian mixture mask was applied over the data to construct phenotypic fingerprints. Fingerprints were used to assess statistical differences between mechanism of action groups and to train random forest classifiers. Classifiers were then used to predict the mechanism of action of cephalothin. Statistical differences were found among the different mechanisms of action groups. Pairwise comparison showed statistical differences for 35 out of 45 pairs for A. viscosus and for 32 out of 45 pairs for F. nucleatum after 3.5 h of treatment. The best-performing random forest classifier yielded a Matthews correlation coefficient of 0.92 and the mechanism of action of cephalothin could be successfully predicted. These findings suggest that flow cytometry can be a cheap and fast alternative for determining the mechanism of action of new antimicrobials.IMPORTANCEIn the context of the emerging threat of antimicrobial resistance, the development of novel antimicrobials is a commonly employed strategy to combat resistance. Elucidating the mechanism of action of novel compounds is crucial in this development but can become expensive, as no universally applicable pipelines currently exist. We present a novel flow cytometry-based approach capable of determining the mechanism of action swiftly and cost-effectively. The workflow aims to accelerate drug discovery and could help facilitate a more targeted approach for antimicrobial treatment of patients.},
}
@article {pmid38481338,
year = {2024},
author = {Sun, J and Zhao, J and Liu, M and Li, J and Cheng, J and Li, W and Yuan, M and Xiao, S and Xue, C},
title = {SreC-dependent adaption to host iron environments regulates the transition of trophic stages and developmental processes of Curvularia lunata.},
journal = {Molecular plant pathology},
volume = {25},
number = {3},
pages = {e13444},
pmid = {38481338},
issn = {1364-3703},
support = {31271992//National Natural Science Foundation of China/ ; 2022JH2/101300168//Liaoning Provincial Applied Basic Program/ ; },
mesh = {*Iron/metabolism ; *Fungal Proteins/genetics/metabolism ; Virulence ; *Curvularia ; },
abstract = {Plant pathogens are challenged by host-derived iron starvation or excess during infection, but the mechanism of plant pathogens rapidly adapting to the dynamic host iron environments to assimilate iron for invasion and colonization remains largely unexplored. Here, we found that the GATA transcription factor SreC in Curvularia lunata is required for virulence and adaption to the host iron excess environment. SreC directly binds to the ATGWGATAW element in an iron-dependent manner to regulate the switch between different iron assimilation pathways, conferring adaption to host iron environments in different trophic stages of C. lunata. SreC also regulates the transition of trophic stages and developmental processes in C. lunata. SreC-dependent adaption to host iron environments is essential to the infectious growth and survival of C. lunata. We also demonstrate that CgSreA (a SreC orthologue) plays a similar role in Colletotrichum graminicola. We conclude that Sre mediates adaption to the host iron environment during infection, and the function is conserved in hemibiotrophic fungi.},
}
@article {pmid38480488,
year = {2024},
author = {Munley, JA and Kelly, LS and Park, G and Drury, SK and Gillies, GS and Coldwell, PS and Kannan, KB and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM},
title = {Acute emergence of the intestinal pathobiome after postinjury pneumonia.},
journal = {The journal of trauma and acute care surgery},
volume = {97},
number = {1},
pages = {65-72},
pmid = {38480488},
issn = {2163-0763},
support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; T32 GM008721/GM/NIGMS NIH HHS/United States ; T32 HL160491/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; *Rats, Sprague-Dawley ; Female ; Male ; Rats ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Sex Factors ; Disease Models, Animal ; Sepsis/microbiology ; Pneumonia/microbiology/etiology ; },
abstract = {BACKGROUND: Previous preclinical studies have demonstrated sex-specific alterations in the gut microbiome following traumatic injury or sepsis alone; however, the impact of host sex on dysbiosis in the setting of postinjury sepsis acutely is unknown. We hypothesized that multicompartmental injury with subsequent pneumonia would result in host sex-specific dysbiosis.<br><br>METHODS: Male and proestrus female Sprague-Dawley rats (n = 8/group) were subjected to either multicompartmental trauma (PT) (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofracture), PT plus 2-hour daily restraint stress (PT/RS), PT with postinjury day 1 Pseudomonas aeruginosa pneumonia (PT-PNA), PT/RS with pneumonia (PT/RS-PNA), or naive controls. Fecal microbiome was measured on days 0 and 2 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology 2 bioinformatics analyses. Microbial &#x3b1;-diversity was assessed using Chao1 (number of different unique species) and Shannon (species richness and evenness) indices. &#x3b2;-diversity was assessed using principal coordinate analysis. Significance was defined as p < 0.05.<br><br>RESULTS: All groups had drastic declines in the Chao1 (&#x3b1;-diversity) index compared with naive controls (p < 0.05). Groups PT-PNA and PT/RS-PNA resulted in different &#x3b2;-diversity arrays compared with uninfected counterparts (PT, PT/RS) (p = 0.001). Postinjury sepsis cohorts showed a loss of commensal bacteria along with emergence of pathogenic bacteria, with blooms of Proteus in PT-PNA and Escherichia-Shigella group in PT/RS-PNA compared with other cohorts. At day 2, PT-PNA resulted in &#x3b2;-diversity, which was unique between males and females (p = 0.004). Microbiome composition in PT-PNA males was dominated by Anaerostipes and Parasuterella , whereas females had increased Barnesiella and Oscillibacter . The PT/RS males had an abundance of Gastranaerophilales and Muribaculaceae .<br><br>CONCLUSION: Multicompartmental trauma complicated by sepsis significantly diminishes diversity and alters microbial composition toward a severely dysbiotic state early after injury, which varies between males and females. These findings highlight the role of sex in postinjury sepsis and the pathobiome, which may influence outcomes after severe trauma and sepsis.},
}
@article {pmid38477597,
year = {2024},
author = {Miliotis, G and Sengupta, P and Hameed, A and Chuvochina, M and McDonagh, F and Simpson, AC and Parker, CW and Singh, NK and Rekha, PD and Morris, D and Raman, K and Kyrpides, NC and Hugenholtz, P and Venkateswaran, K},
title = {Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.},
journal = {mBio},
volume = {15},
number = {4},
pages = {e0018124},
pmid = {38477597},
issn = {2150-7511},
support = {FutureCare Seed Fund//University of Galway (NUI Galway)/ ; 2012 Space Biology NNH12ZTT001N grant no. 19-12829-26//National Aeronautics and Space Administration (NASA)/ ; DP220100900//Australian Research Council Discovery Project/ ; //U.S. Department of Energy Joint Genome Institute, DOE Office of Science User Facility, U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; },
mesh = {Humans ; *Fatty Acids/analysis ; *Ceftazidime ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Nucleic Acid Hybridization ; Spores/chemistry ; Nucleotides ; DNA ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; },
abstract = {UNLABELLED: A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HS[T], exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HS[T] is most closely related to Virgibacillus halophilus 5B73C[T], sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HS[T] is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HS[T] = DSM 115946[T] = NRRL B-65666[T]), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73C[T] = DSM 21623[T] = JCM 21758[T] = KCTC 13935[T]). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6[T] = DSM 22952[T] = CCM 7714[T]). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known β-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins.<br><br>IMPORTANCE: The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.},
}
@article {pmid38476936,
year = {2024},
author = {Dittoe, DK and Feye, KM and Ovall, C and Thompson, HA and Ricke, SC},
title = {Exploiting the microbiota of organic and inorganic acid-treated raw poultry products to improve shelf-life.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1348159},
pmid = {38476936},
issn = {1664-302X},
abstract = {INTRODUCTION: Targeted amplicon sequencing of the 16S rRNA delineates the complex microbial interactions that occur during food spoilage, providing a tool to intensively screen microbiota response to antimicrobial processing aids and interventions. The current research determines the microbiota and spoilage indicator (total aerobes and lactic acid bacteria; LAB) response to inorganic and organic antimicrobial intervention use on the shelf-life of fresh, never-frozen, skin-on, bone-in chicken wings.<br><br>METHODS: Wings (n=200) were sourced from local processor and either not treated (NT) or treated with 15-s dips of tap water (TW), organic (peracetic acid; PAA), inorganic acids (sodium bisulfate; SBS), and their combination (SBS + PAA). Wings were stored (4&#xb0;C) and rinsed in neutralizing Buffered Peptone Water (BPW) for 1 min on d 0, 7, 14, and 21 post-treatment. Spoilage indicators, aerobic mesophiles and LAB, were quantified from rinsates. Genomic DNA of d 14 and 21 rinsates were extracted, and V4 of 16S rRNA gene was sequenced. Sequences were analyzed using QIIME2.2019.7. APC and LAB counts were reported as Log10 CFU/g of chicken and analyzed in R Studio as a General Linear Model using ANOVA. Pairwise differences were determined using Tukey's HSD (P&#xa3;0.05).<br><br>RESULTS: Spoilage was indicated for all products by day 21 according to APC counts (>7 Log10 CFU/g); however, wings treated with SBS and SBS + PAA demonstrated a 7-day extended shelf-life compared to those treated with NT, TW, or PAA. The interaction of treatment and time impacted the microbial diversity and composition (p < 0.05), with those treated with SBS having a lower richness and evenness compared to those treated with the controls (NT and TW; p < 0.05, Q < 0.05). On d 14, those treated with SBS and SBS + PAA had lower relative abundance of typical spoilage population while having a greater relative abundance of Bacillus spp. (~70 and 50% of population; ANCOM p < 0.05). By d 21, the Bacillus spp. populations decreased below 10% of the population among those treated with SBS and SBS + PAA.<br><br>DISCUSSION: Therefore, there are differential effects on the microbial community depending on the chemical intervention used with organic and inorganic acids, impacting the microbial ecology differently.},
}
@article {pmid38476935,
year = {2024},
author = {Indong, RA and Park, JM and Hong, JK and Lyou, ES and Han, T and Hong, JK and Lee, TK and Lee, JI},
title = {A simple protocol for cultivating the bacterivorous soil nematode Caenorhabditis elegans in its natural ecology in the laboratory.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1347797},
pmid = {38476935},
issn = {1664-302X},
abstract = {The complex interplay between an animal and its surrounding environment requires constant attentive observation in natural settings. Moreover, how ecological interactions are affected by an animal's genes is difficult to ascertain outside the laboratory. Genetic studies with the bacterivorous nematode Caenorhabditis elegans have elucidated numerous relationships between genes and functions, such as physiology, behaviors, and lifespan. However, these studies use standard laboratory culture that does not reflect C. elegans true ecology. C. elegans is found growing in nature and reproduced in large numbers in soils enriched with rotting fruit or vegetation, a source of abundant and diverse microbes that nourish the thriving populations of nematodes. We developed a simple mesocosm we call soil-fruit-natural-habitat that simulates the natural ecology of C. elegans in the laboratory. Apples were placed on autoclaved potted soils, and after a soil microbial solution was added, the mesocosm was subjected to day-night, temperature, and humidity cycling inside a growth chamber. After a period of apple-rotting, C elegans were added, and the growing worm population was observed. We determined optimal conditions for the growth of C. elegans and then performed an ecological succession experiment observing worm populations every few days. Our data showed that the mesocosm allows abundant growth and reproduction of C. elegans that resembles populations of the nematode found in rotting fruit in nature. Overall, our study presents a simple protocol that allows the cultivation of C. elegans in a natural habitat in the laboratory for a broad group of scientists to study various aspects of animal and microbial ecology.},
}
@article {pmid38475926,
year = {2024},
author = {Suarez, C and Rosenqvist, T and Dimitrova, I and Sedlacek, CJ and Modin, O and Paul, CJ and Hermansson, M and Persson, F},
title = {Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {51},
pmid = {38475926},
issn = {2049-2618},
support = {2018-01423//Svenska Forskningsr&#xe5;det Formas/ ; 2019-00432//Svenska Forskningsr&#xe5;det Formas/ ; 2019-00432//Svenska Forskningsr&#xe5;det Formas/ ; 2018-01423//Svenska Forskningsr&#xe5;det Formas/ ; 2020-01905//Svenska Forskningsr&#xe5;det Formas/ ; ZK74//Austrian Science Fund/ ; },
mesh = {*Ammonia ; *Anaerobic Ammonia Oxidation ; Phylogeny ; Sewage/microbiology ; Bacteria ; Bioreactors/microbiology ; Nitrogen ; Biofilms ; Oxidation-Reduction ; },
abstract = {BACKGROUND: Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert ammonium to nitrogen gas. Little is known about how these biofilm communities develop, and whether knowledge about the assembly of biofilms in natural communities can be applied to PNA biofilms.<br><br>RESULTS: We followed the start-up of a full-scale PNA moving bed biofilm reactor for 175 days using shotgun metagenomics. Environmental filtering likely restricted initial biofilm colonization, resulting in low phylogenetic diversity, with the initial microbial community comprised mainly of Proteobacteria. Facilitative priority effects allowed further biofilm colonization, with the growth of initial aerobic colonizers promoting the arrival and growth of anaerobic taxa like methanogens and anammox bacteria. Among the early colonizers were known 'oligotrophic' ammonia oxidizers including comammox Nitrospira and Nitrosomonas cluster 6a AOB. Increasing the nitrogen load in the bioreactor allowed colonization by 'copiotrophic' Nitrosomonas cluster 7 AOB and resulted in the exclusion of the initial ammonia- and nitrite oxidizers.<br><br>CONCLUSIONS: We show that complex dynamic processes occur in PNA microbial communities before a stable bioreactor process is achieved. The results of this study not only contribute to our knowledge about biofilm assembly and PNA bioreactor start-up but could also help guide strategies for the successful implementation of PNA bioreactors. Video Abstract.},
}
@article {pmid38471203,
year = {2024},
author = {Malinowski, N and Morgan, MJ and Wylie, J and Walsh, T and Domingos, S and Metcalfe, S and Kaksonen, AH and Barnhart, EP and Mueller, R and Peyton, BM and Puzon, GJ},
title = {Prokaryotic microbial ecology as an ecosurveillance tool for eukaryotic pathogen colonisation: Meiothermus and Naegleria fowleri.},
journal = {Water research},
volume = {254},
number = {},
pages = {121426},
doi = {10.1016/j.watres.2024.121426},
pmid = {38471203},
issn = {1879-2448},
mesh = {*Naegleria fowleri ; Prospective Studies ; *Drinking Water ; Bacteria ; Biofilms ; },
abstract = {Naegleria fowleri has been detected in drinking water distribution systems (DWDS) in Australia, Pakistan and the United States and is the causative agent of the highly fatal disease primary amoebic meningoencephalitis. Previous small scale field studies have shown that Meiothermus may be a potential biomarker for N. fowleri. However, correlations between predictive biomarkers in small sample sizes often breakdown when applied to larger more representative datasets. This study represents one of the largest and most rigorous temporal investigations of Naegleria fowleri colonisation in an operational DWDS in the world and measured the association of Meiothermus and N. fowleri over a significantly larger space and time in the DWDS. A total of 232 samples were collected from five sites over three-years (2016-2018), which contained 29 positive N. fowleri samples. Two specific operational taxonomic units assigned to M. chliarophilus and M. hypogaeus, were significantly associated with N. fowleri presence. Furthermore, inoculation experiments demonstrated that Meiothermus was required to support N. fowleri growth in field-collected biofilms. This validates Meiothermus as prospective biological tool to aid in the identification and surveillance of N. fowleri colonisable sites.},
}
@article {pmid38470030,
year = {2024},
author = {Tittes, C and Nijland, J and Schoentag, AMC and Hackl, T and Di Cianni, N and Marchfelder, A and Quax, TEF},
title = {Development of a genetic system for Haloferax gibbonsii LR2-5, model host for haloarchaeal viruses.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {4},
pages = {e0012924},
pmid = {38470030},
issn = {1098-5336},
support = {//Deutsche Forschungsgemeinschaft (DFG)/ ; //EC | European Research Council (ERC)/ ; },
mesh = {*Haloferax/genetics ; Gene Deletion ; *Haloferax volcanii/genetics/metabolism ; Promoter Regions, Genetic ; *Viruses/genetics ; *Archaeal Proteins/genetics ; },
abstract = {UNLABELLED: Archaeal viruses are among the most enigmatic members of the virosphere, and their diverse morphologies raise many questions about their infection mechanisms. The study of molecular mechanisms underlying virus-host interactions hinges upon robust model organisms with a system for gene expression and deletion. Currently, there are only a limited number of archaea that have associated viruses and have a well-developed genetic system. Here, we report the development of a genetic system for the euryarchaeon Haloferax gibbonsii LR2-5. This strain can be infected by multiple viruses and is a model for the study of virus-host interactions. We created a Hfx. gibbonsii LR2-5 ∆pyrE strain, resulting in uracil auxotrophy, which could be used as a selection marker. An expression plasmid carrying a pyrE gene from the well-established Haloferax volcanii system was tested for functionality. Expression of a GFP-MinD fusion under a tryptophan inducible promoter was fully functional and showed similar cellular localization as in Hfx. volcanii. Thus, the plasmids of the Hfx. volcanii system can be used directly for the Hfx. gibbonsii LR2-5 genetic system, facilitating the transfer of tools between the two. Finally, we tested for the functionality of gene deletions by knocking out two genes of the archaeal motility structure, the archaellum. These deletion mutants were as expected non-motile and the phenotype of one deletion could be rescued by the expression of the deleted archaellum gene from a plasmid. Thus, we developed a functional genetic toolbox for the euryarchaeal virus host Hfx. gibbonsii LR2-5, which will propel future studies on archaeal viruses.<br><br>IMPORTANCE: Species from all domains of life are infected by viruses. In some environments, viruses outnumber their microbial hosts by a factor of 10, and viruses are the most important predators of microorganisms. While much has been discovered about the infection mechanisms of bacterial and eukaryotic viruses, archaeal viruses remain understudied. Good model systems are needed to study their virus-host interactions in detail. The salt-loving archaeon Haloferax gibbonsii LR2-5 has been shown to be infected by a variety of different viruses and, thus, is an excellent model to study archaeal viruses. By establishing a genetic system, we have significantly expanded the toolbox for this model organism, which will fuel our understanding of infection strategies of the underexplored archaeal viruses.},
}
@article {pmid38467467,
year = {2024},
author = {Powell, ME and McCoy, SJ},
title = {Divide and conquer: Spatial and temporal resource partitioning structures benthic cyanobacterial mats.},
journal = {Journal of phycology},
volume = {60},
number = {2},
pages = {254-272},
doi = {10.1111/jpy.13443},
pmid = {38467467},
issn = {1529-8817},
support = {DGE-2040435//National Science Foundation/ ; OCE-2239425//National Science Foundation/ ; },
mesh = {*Ecosystem ; *Cyanobacteria/metabolism ; Sulfur/metabolism ; Carbon/metabolism ; },
abstract = {Benthic cyanobacterial mats are increasing in abundance worldwide with the potential to degrade ecosystem structure and function. Understanding mat community dynamics is thus critical for predicting mat growth and proliferation and for mitigating any associated negative effects. Carbon, nitrogen, and sulfur cycling are the predominant forms of nutrient cycling discussed within the literature, while metabolic cooperation and viral interactions are understudied. Although many forms of nutrient cycling in mats have been assessed, the links between niche dynamics, microbial interactions, and nutrient cycling are not well described. Here, we present an updated review on how nutrient cycling and microbial community interactions in mats are structured by resource partitioning via spatial and temporal heterogeneity and succession. We assess community interactions and nutrient cycling at both intramat and metacommunity scales. Additionally, we present ideas and recommendations for research in this area, highlighting top-down control, boundary layers, and metabolic cooperation as important future directions.},
}
@article {pmid38466433,
year = {2024},
author = {Ważny, R and Jędrzejczyk, RJ and Rozpądek, P and Domka, A and Tokarz, KM and Janicka, M and Turnau, K},
title = {Bacteria Associated with Spores of Arbuscular Mycorrhizal Fungi Improve the Effectiveness of Fungal Inocula for Red Raspberry Biotization.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {50},
pmid = {38466433},
issn = {1432-184X},
mesh = {*Mycorrhizae/physiology ; *Rubus ; Spores, Fungal ; Plants/microbiology ; Bacteria ; Chlorophyll ; Water ; },
abstract = {Intensive crop production leads to the disruption of the symbiosis between plants and their associated microorganisms, resulting in suboptimal plant productivity and lower yield quality. Therefore, it is necessary to improve existing methods and explore modern, environmentally friendly approaches to crop production. One of these methods is biotization, which involves the inoculation of plants with appropriately selected symbiotic microorganisms which play a beneficial role in plant adaptation to the environment. In this study, we tested the possibility of using a multi-microorganismal inoculum composed of arbuscular mycorrhizal fungi (AMF) and AMF spore-associated bacteria for biotization of the red raspberry. Bacteria were isolated from the spores of AMF, and their plant growth-promoting properties were tested. AMF inocula were supplemented with selected bacterial strains to investigate their effect on the growth and vitality of the raspberry. The investigations were carried out in the laboratory and on a semi-industrial scale in a polytunnel where commercial production of seedlings is carried out. In the semi-industrial experiment, we tested the growth parameters of plants and physiological response of the plant to temporary water shortage. We isolated over fifty strains of bacteria associated with spores of AMF. Only part of them showed plant growth-promoting properties, and six of these (belonging to the Paenibacillus genus) were used for the inoculum. AMF inoculation and co-inoculation of AMF and bacteria isolated from AMF spores improved plant growth and vitality in both experimental setups. Plant dry weight was improved by 70%, and selected chlorophyll fluorescence parameters (the contribution of light to primary photochemistry and fraction of reaction centre chlorophyll per chlorophyll of the antennae) were increased. The inoculum improved carbon assimilation, photosynthetic rate, stomatal conductance and transpiration after temporary water shortage. Raspberry biotization with AMF and bacteria associated with spores has potential applications in horticulture where ecological methods based on plant microorganism interaction are in demand.},
}
@article {pmid38465733,
year = {2024},
author = {Javourez, U and Matassa, S and Vlaeminck, SE and Verstraete, W},
title = {Ruminations on sustainable and safe food: Championing for open symbiotic cultures ensuring resource efficiency, eco-sustainability and affordability.},
journal = {Microbial biotechnology},
volume = {17},
number = {3},
pages = {e14436},
pmid = {38465733},
issn = {1751-7915},
mesh = {Animals ; *Ruminants ; *Biotechnology ; Fermentation ; Animal Feed ; Costs and Cost Analysis ; },
abstract = {Microbes are powerful upgraders, able to convert simple substrates to nutritional metabolites at rates and yields surpassing those of higher organisms by a factor of 2 to 10. A summary table highlights the superior efficiencies of a whole array of microbes compared to conventionally farmed animals and insects, converting nitrogen and organics to food and feed. Aiming at the most resource-efficient class of microbial proteins, deploying the power of open microbial communities, coined here as 'symbiotic microbiomes' is promising. For instance, a production train of interest is to develop rumen-inspired technologies to upgrade fibre-rich substrates, increasingly available as residues from emerging bioeconomy initiatives. Such advancements offer promising perspectives, as currently only 5%-25% of the available cellulose is recovered by ruminant livestock systems. While safely producing food and feed with open cultures has a long-standing tradition, novel symbiotic fermentation routes are currently facing much higher market entrance barriers compared to axenic fermentation. Our global society is at a pivotal juncture, requiring a shift towards food production systems that not only embrace the environmental and economic sustainability but also uphold ethical standards. In this context, we propose to re-examine the place of spontaneous or natural microbial consortia for safe future food and feed biotech developments, and advocate for intelligent regulatory practices. We stress that reconsidering symbiotic microbiomes is key to achieve sustainable development goals and defend the need for microbial biotechnology literacy education.},
}
@article {pmid38465465,
year = {2024},
author = {Van Goethem, MW and Marasco, R and Hong, PY and Daffonchio, D},
title = {The antibiotic crisis: On the search for novel antibiotics and resistance mechanisms.},
journal = {Microbial biotechnology},
volume = {17},
number = {3},
pages = {e14430},
pmid = {38465465},
issn = {1751-7915},
support = {//King Abdullah University of Science and Technology (KAUST)/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Ecosystem ; Bacteria/genetics ; Drug Resistance, Microbial ; Agriculture ; },
abstract = {In the relentless battle for human health, the proliferation of antibiotic-resistant bacteria has emerged as an impending catastrophe of unprecedented magnitude, potentially driving humanity towards the brink of an unparalleled healthcare crisis. The unyielding advance of antibiotic resistance looms as the foremost threat of the 21st century in clinical, agricultural and environmental arenas. Antibiotic resistance is projected to be the genesis of the next global pandemic, with grim estimations of tens of millions of lives lost annually by 2050. Amidst this impending calamity, our capacity to unearth novel antibiotics has languished, with the past four decades marred by a disheartening 'antibiotic discovery void'. With nearly 80% of our current antibiotics originating from natural or semi-synthetic sources, our responsibility is to cast our investigative nets into uncharted ecological niches teeming with microbial strife, the so-called 'microbial oases of interactions'. Within these oases of interactions, where microorganisms intensively compete for space and nutrients, a dynamic and ever-evolving microbial 'arms race' is constantly in place. Such a continuous cycle of adaptation and counter-adaptation is a fundamental aspect of microbial ecology and evolution, as well as the secrets to unique, undiscovered antibiotics, our last bastion against the relentless tide of resistance. In this context, it is imperative to invest in research to explore the competitive realms, like the plant rhizosphere, biological soil crusts, deep sea hydrothermal vents, marine snow and the most modern plastisphere, in which competitive interactions are at the base of the microorganisms' struggle for survival and dominance in their ecosystems: identify novel antibiotic by targeting microbial oases of interactions could represent a 'missing piece of the puzzle' in our fight against antibiotic resistance.},
}
@article {pmid38461750,
year = {2024},
author = {Michielsen, S and Vercelli, GT and Cordero, OX and Bachmann, H},
title = {Spatially structured microbial consortia and their role in food fermentations.},
journal = {Current opinion in biotechnology},
volume = {87},
number = {},
pages = {103102},
doi = {10.1016/j.copbio.2024.103102},
pmid = {38461750},
issn = {1879-0429},
mesh = {*Fermentation ; *Microbial Consortia/physiology ; *Food Microbiology ; },
abstract = {Microbial consortia are important for the fermentation of foods. They bring combined functionalities to the fermented product, but stability and product consistency of fermentations with complex consortia can be hard to control. Some of these consortia, such as water- and milk-kefir and kombucha, grow as multispecies aggregates or biofilms, in which micro-organisms taking part in a fermentation cascade are spatially organized. The spatial organization of micro-organisms in these aggregates can impact what metabolic interactions are realized in the consortia, ultimately affecting the growth dynamics and evolution of microbes. A better understanding of such spatially structured communities is of interest from the perspective of microbial ecology and biotechnology, as multispecies aggregates can be used to valorize energy-rich substrates, such as plant-based substrates or side streams from the food industry.},
}
@article {pmid38458948,
year = {2024},
author = {Fu, S and Wang, Q and Wang, R and Zhang, Y and Lan, R and He, F and Yang, Q},
title = {Corrigendum to "Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment" [Sci. Total Environ. 820 (2022) 153286].},
journal = {The Science of the total environment},
volume = {922},
number = {},
pages = {171434},
doi = {10.1016/j.scitotenv.2024.171434},
pmid = {38458948},
issn = {1879-1026},
}
@article {pmid38457521,
year = {2024},
author = {Colombi, E and Bertels, F and Doulcier, G and McConnell, E and Pichugina, T and Sohn, KH and Straub, C and McCann, HC and Rainey, PB},
title = {Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {11},
pages = {e2309263121},
pmid = {38457521},
issn = {1091-6490},
support = {MAU1709//Royal Society of New Zealand | Marsden Fund (Royal Society of New Zealand Marsden Fund)/ ; SFB1182 Project C4//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Phylogeny ; *Conjugation, Genetic ; *Gene Transfer, Horizontal/genetics ; Biological Evolution ; DNA Transposable Elements/genetics ; },
abstract = {Integrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness. Most ICEs characterized to date encode readily observable phenotypes contributing to symbiosis, pathogenicity, and antimicrobial resistance, yet the majority of ICEs carry genes of unknown function. Recent observations of rapid acquisition of ICEs in a pandemic lineage of Pseudomonas syringae pv. actinidae led to investigation of the structural and functional diversity of these elements. Fifty-three unique ICE types were identified across the P. syringae species complex. Together they form a distinct family of ICEs (PsICEs) that share a distant relationship to ICEs found in Pseudomonas aeruginosa. PsICEs are defined by conserved backbone genes punctuated by an array of accessory cargo genes, are highly recombinogenic, and display distinct evolutionary histories compared to their bacterial hosts. The most common cargo is a recently disseminated 16-kb mobile genetic element designated Tn6212. Deletion of Tn6212 did not alter pathogen growth in planta, but mutants displayed fitness defects when grown on tricarboxylic acid (TCA) cycle intermediates. RNA-seq analysis of a set of nested deletion mutants showed that a Tn6212-encoded LysR regulator has global effects on chromosomal gene expression. We show that Tn6212 responds to preferred carbon sources and manipulates bacterial metabolism to maximize growth.},
}
@article {pmid38453959,
year = {2024},
author = {Guerrero-Egido, G and Pintado, A and Bretscher, KM and Arias-Giraldo, LM and Paulson, JN and Spaink, HP and Claessen, D and Ramos, C and Cazorla, FM and Medema, MH and Raaijmakers, JM and Carrión, VJ},
title = {bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2072},
pmid = {38453959},
issn = {2041-1723},
mesh = {*Genome, Bacterial/genetics ; *Pseudomonas syringae/genetics ; Workflow ; Genomics/methods ; },
abstract = {Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE (https://github.com/Carrion-lab/bacLIFE) a streamlined computational workflow for genome annotation, large-scale comparative genomics, and prediction of lifestyle-associated genes (LAGs). As a proof of concept, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, which led to the identification of hundreds of genes potentially associated with a plant pathogenic lifestyle. Site-directed mutagenesis of 14 of these predicted LAGs of unknown function, followed by plant bioassays, showed that 6 predicted LAGs are indeed involved in the phytopathogenic lifestyle of Burkholderia plantarii and Pseudomonas syringae pv. phaseolicola. These 6 LAGs encompassed a glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases and hypothetical proteins. Collectively, our results highlight bacLIFE as an effective computational tool for prediction of LAGs and the generation of hypotheses for a better understanding of bacteria-host interactions.},
}
@article {pmid38452350,
year = {2024},
author = {Boutin, S and Lussier, E and Laforest-Lapointe, I},
title = {Investigating the spatiotemporal dynamics of apple tree phyllosphere bacterial and fungal communities across cultivars in orchards.},
journal = {Canadian journal of microbiology},
volume = {70},
number = {6},
pages = {238-251},
doi = {10.1139/cjm-2023-0215},
pmid = {38452350},
issn = {1480-3275},
mesh = {*Malus/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Plant Leaves/microbiology ; Spatio-Temporal Analysis ; Biodiversity ; Mycobiome ; Flowers/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The phyllosphere, a reservoir of diverse microbial life associated with plant health, harbors microbial communities that are subject to various complex ecological processes acting at multiple scales. In this study, we investigated the determinants of the spatiotemporal variation in bacterial and fungal communities within the apple tree phyllosphere, employing 16S and ITS amplicon sequencing. Our research assessed the impact of key factors-plant compartment, site, time, and cultivar-on the composition and diversity of leaf and flower microbial communities. Our analyses, based on samples collected from three cultivars in three orchards in 2022, revealed that site and time are the strongest drivers of apple tree phyllosphere microbial communities. Conversely, plant compartment and cultivar exhibited minor roles in explaining community composition and diversity. Predominantly, bacterial communities comprised Hymenobacter (25%) and Sphingomonas (10%), while the most relatively abundant fungal genera included Aureobasidium (27%) and Sporobolomyces (10%). Additionally, our results show a gradual decrease in alpha-diversity throughout the growth season. These findings emphasize the necessity to consider local microbial ecology dynamics in orchards, especially as many groups worldwide aim for the development of biocontrol strategies (e.g., by manipulating plant-microbe interactions). More research is needed to improve our understanding of the determinants of time and site-specific disparities within apple tree phyllosphere microbial communities across multiple years, locations, and cultivars.},
}
@article {pmid38452018,
year = {2024},
author = {Du, Z and Behrens, SF},
title = {Effect of target gene sequence evenness and dominance on real-time PCR quantification of artificial sulfate-reducing microbial communities.},
journal = {PloS one},
volume = {19},
number = {3},
pages = {e0299930},
pmid = {38452018},
issn = {1932-6203},
mesh = {Real-Time Polymerase Chain Reaction/methods ; Phylogeny ; Reproducibility of Results ; *Sulfates ; *Microbiota/genetics ; },
abstract = {Quantitative real-time PCR of phylogenetic and functional marker genes is among the most commonly used techniques to quantify the abundance of microbial taxa in environmental samples. However, in most environmental applications, the approach is a rough assessment of population abundance rather than an exact absolute quantification method because of PCR-based estimation biases caused by multiple factors. Previous studies on these technical issues have focused on primer or template sequence features or PCR reaction conditions. However, how target gene sequence characteristics (e.g., evenness and dominance) in environmental samples affect qPCR quantifications has not been well studied. Here, we compared three primer sets targeting the beta subunit of the dissimilatory sulfite reductase (dsrB) to investigate qPCR quantification performance under different target gene sequence evenness and dominance conditions using artificial gBlock template mixtures designed accordingly. Our results suggested that the qPCR quantification performance of all tested primer sets was determined by the comprehensive effect of the target gene sequence evenness and dominance in environmental samples. Generally, highly degenerate primer sets have equivalent or better qPCR quantification results than a more target-specific primer set. Low template concentration in this study (~105 copies/L) will exaggerate the qPCR quantification results difference among tested primer sets. Improvements to the accuracy and reproducibility of qPCR assays for gene copy number quantification in environmental microbiology and microbial ecology studies should be based on prior knowledge of target gene sequence information acquired by metagenomic analysis or other approaches, careful selection of primer sets, and proper reaction conditions optimization.},
}
@article {pmid38450400,
year = {2024},
author = {Duarte, RDC and Iannetta, PPM and Gomes, AM and Vasconcelos, MW},
title = {More than a meat- or synthetic nitrogen fertiliser-substitute: a review of legume phytochemicals as drivers of 'One Health' via their influence on the functional diversity of soil- and gut-microbes.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1337653},
pmid = {38450400},
issn = {1664-462X},
abstract = {Legumes are essential to healthy agroecosystems, with a rich phytochemical content that impacts overall human and animal well-being and environmental sustainability. While these phytochemicals can have both positive and negative effects, legumes have traditionally been bred to produce genotypes with lower levels of certain plant phytochemicals, specifically those commonly termed as 'antifeedants' including phenolic compounds, saponins, alkaloids, tannins, and raffinose family oligosaccharides (RFOs). However, when incorporated into a balanced diet, such legume phytochemicals can offer health benefits for both humans and animals. They can positively influence the human gut microbiome by promoting the growth of beneficial bacteria, contributing to gut health, and demonstrating anti-inflammatory and antioxidant properties. Beyond their nutritional value, legume phytochemicals also play a vital role in soil health. The phytochemical containing residues from their shoots and roots usually remain in-field to positively affect soil nutrient status and microbiome diversity, so enhancing soil functions and benefiting performance and yield of following crops. This review explores the role of legume phytochemicals from a 'one health' perspective, examining their on soil- and gut-microbial ecology, bridging the gap between human nutrition and agroecological science.},
}
@article {pmid38448699,
year = {2024},
author = {Tao, F and Houlton, BZ and Frey, SD and Lehmann, J and Manzoni, S and Huang, Y and Jiang, L and Mishra, U and Hungate, BA and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Wang, YP and Ahrens, B and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y},
title = {Reply to: Model uncertainty obscures major driver of soil carbon.},
journal = {Nature},
volume = {627},
number = {8002},
pages = {E4-E6},
pmid = {38448699},
issn = {1476-4687},
mesh = {*Uncertainty ; },
}
@article {pmid38446847,
year = {2024},
author = {Koslová, A and Hackl, T and Bade, F and Sanchez Kasikovic, A and Barenhoff, K and Schimm, F and Mersdorf, U and Fischer, MG},
title = {Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {11},
pages = {e2314606121},
pmid = {38446847},
issn = {1091-6490},
support = {5734//Gordon and Betty Moore Foundation (GBMF)/ ; ALTF 1150-2018//European Molecular Biology Organization (EMBO)/ ; },
mesh = {Humans ; Virophages ; *Giant Viruses/genetics ; *Stramenopiles/genetics ; *Virus Diseases ; Antiviral Agents ; },
abstract = {Endogenous viral elements (EVEs) are common genetic passengers in various protists. Some EVEs represent viral fossils, whereas others are still active. The marine heterotrophic flagellate Cafeteria burkhardae contains several EVE types related to the virophage mavirus, a small DNA virus that parasitizes the lytic giant virus CroV. We hypothesized that endogenous virophages may act as an antiviral defense system in protists, but no protective effect of virophages in wild host populations has been shown so far. Here, we tested the activity of virophage EVEs and studied their impact on giant virus replication. We found that endogenous mavirus-like elements (EMALEs) from globally distributed Cafeteria populations produced infectious virus particles specifically in response to CroV infection. However, reactivation was stochastic, often inefficient, and poorly reproducible. Interestingly, only one of eight EMALE types responded to CroV infection, implying that other EMALEs may be linked to different giant viruses. We isolated and cloned several reactivated virophages and characterized their particles, genomes, and infection dynamics. All tested virophages inhibited the production of CroV during coinfection, thereby preventing lysis of the host cultures in a dose-dependent manner. Comparative genomics of different C. burkhardae strains revealed that inducible EMALEs are common and are not linked to specific geographic locations. We demonstrate that naturally occurring virophage EVEs reactivate upon giant virus infection, thus providing a striking example that eukaryotic EVEs can become active under specific conditions. Moreover, our results support the hypothesis that virophages can act as an adaptive antiviral defense system in protists.},
}
@article {pmid38441415,
year = {2024},
author = {Lee, HJ and Hwang, JS and Lee, EK and Whang, KS},
title = {Erythrobacter oryzae sp. nov., isolated from rice paddy soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {3},
pages = {},
doi = {10.1099/ijsem.0.006287},
pmid = {38441415},
issn = {1466-5034},
mesh = {*Sphingomonadaceae ; *Oryza ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Fatty Acids/chemistry ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; },
abstract = {Two novel bacterial strains, designated as COR-2[T] and CR-8, were isolated from paddy soil. These isolates were aerobic, Gram-stain-negative, non-spore-forming, non-motile, rod-shaped, and formed orange-coloured colonies. Phylogenetic analysis based on 16S rRNA gene sequences showed that two strains formed a clear phylogenetic lineage with the genus Erythrobacter. Strains COR-2[T] and CR-8 showed 99.9 % 16S rRNA gene sequence similarity. Both strains had the highest 16S rRNA gene similarity of 99.1-99.7 % to Erythrobacter colymbi TPW-24[T], Erythrobacter donghaensis SW-132[T] and Erythrobacter tepidarius DSM 10594[T], respectively. The genome of strain COR-2[T] comprised 3 559 918 bp and the genomic DNA G + C content was 67.7 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain COR-2[T] and its closely related species of the genus Erythrobacter were 79.3-85.5% and 24.1-29.1 %, respectively. The major respiratory quinone was Q-10, while the major fatty acids were C18 : 1 ω7c and C17 : 1 ω6c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids and eight unidentified lipids. Based on phylogenetic and phenotypic considerations, the two strains [COR-2[T] (type strain; = KACC 22941[T]=JCM 35529[T]) and CR-8 (= KACC 22945=JCM 35530)] are considered to represent novel species of the genus Erythrobacter, for which the name Erythrobacter oryzae sp. nov. is proposed.},
}
@article {pmid38440286,
year = {2024},
author = {Zeng, L and Noeparvar, P and Burne, RA and Glezer, BS},
title = {Genetic characterization of glyoxalase pathway in oral streptococci and its contribution to interbacterial competition.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2322241},
pmid = {38440286},
issn = {2000-2297},
support = {R01 DE012236/DE/NIDCR NIH HHS/United States ; },
abstract = {OBJECTIVES: To analyze contributions to microbial ecology of Reactive Electrophile Species (RES), including methylglyoxal, generated during glycolysis.<br><br>METHODS: Genetic analyses were performed on the glyoxalase pathway in Streptococcus mutans (SM) and Streptococcus sanguinis (SS), followed by phenotypic assays and transcription analysis.<br><br>RESULTS: Deleting glyoxalase I (lguL) reduced RES tolerance to a far greater extent in SM than in SS, decreasing the competitiveness of SM against SS. Although SM displays a greater RES tolerance than SS, lguL-null mutants of either species showed similar tolerance; a finding consistent with the ability of methylglyoxal to induce the expression of lguL in SM, but not in SS. A novel paralogue of lguL (named gloA2) was identified in most streptococci. SM mutant &#x2206;gloA2SM showed little change in methylglyoxal tolerance yet a significant growth defect and increased autolysis on fructose, a phenotype reversed by the addition of glutathione, or by the deletion of a fructose: phosphotransferase system (PTS) that generates fructose-1-phosphate (F-1-P).<br><br>CONCLUSIONS: Fructose contributes to RES generation in a PTS-specific manner, and GloA2 may be required to degrade certain RES derived from F-1-P. This study reveals the critical roles of RES in fitness and interbacterial competition and the effects of PTS in modulating RES metabolism.},
}
@article {pmid38439944,
year = {2024},
author = {Ma, H and Liu, J and Mo, L and Arias-Giraldo, LM and Xiang, M and Liu, X},
title = {Wild plant species with broader precipitation niches exhibit stronger host selection in rhizosphere microbiome assembly.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycad015},
pmid = {38439944},
issn = {2730-6151},
abstract = {Plants actively recruit microbes from the soil, forming species-specific root microbiomes. However, their relationship with plant adaptations to temperature and precipitation remains unclear. Here we examined the host-selected and conserved microbiomes of 13 native plant species in the Xilingol steppe, Inner Mongolia, a semi-arid region in China. By calculating the global precipitation and temperature niches of these plants, considering plant phylogenetic distances, and analyzing functional traits, we found that these factors significantly influenced the rhizosphere microbiome assembly. We further quantified the strength of host selection and observed that plants with wider precipitation niches exhibited greater host selection strength in their rhizosphere microbiome assembly and higher rhizosphere bacterial diversity. In general, the rhizosphere microbiome showed a stronger link to plant precipitation niches than temperature niches. Haliangium exhibited consistent responsiveness to host characteristics. Our findings offer novel insights into host selection effects and the ecological determinants of wild plant rhizosphere microbiome assembly, with implications for steering root microbiomes of wild plants and understanding plant-microbiome evolution.},
}
@article {pmid38436268,
year = {2024},
author = {Wang, Q and Cole, JR},
title = {Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification.},
journal = {Microbiology resource announcements},
volume = {13},
number = {4},
pages = {e0106323},
pmid = {38436268},
issn = {2576-098X},
abstract = {The RDP Classifier is one of the most popular machine learning approaches for taxonomic classification due to its robustness and relatively high accuracy. Both the RDP taxonomy and RDP Classifier have been updated to incorporate newly described taxa and recent changes to prokaryotic nomenclature.},
}
@article {pmid38436256,
year = {2024},
author = {Ling, J and Hryckowian, AJ},
title = {Re-framing the importance of Group B Streptococcus as a gut-resident pathobiont.},
journal = {Infection and immunity},
volume = {92},
number = {9},
pages = {e0047823},
pmid = {38436256},
issn = {1098-5522},
support = {R35 GM150996/GM/NIGMS NIH HHS/United States ; R35GM150996//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; DGE-2137424//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; 1U48DP006383//UW-Madison Prevention Research Center/ ; Gift//Judy L. and Sal A. Troia/ ; },
mesh = {*Streptococcus agalactiae ; Humans ; *Streptococcal Infections/microbiology ; *Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/microbiology ; Animals ; },
abstract = {Streptococcus agalactiae (Group B Streptococcus, GBS) is a Gram-positive bacterial species that causes disease in humans across the lifespan. While antibiotics are used to mitigate GBS infections, it is evident that antibiotics disrupt human microbiomes (which can predispose people to other diseases later in life), and antibiotic resistance in GBS is on the rise. Taken together, these unintended negative impacts of antibiotics highlight the need for precision approaches for minimizing GBS disease. One possible approach involves selectively depleting GBS in its commensal niches before it can cause disease at other body sites or be transmitted to at-risk individuals. One understudied commensal niche of GBS is the adult gastrointestinal (GI) tract, which may predispose colonization at other body sites in individuals at risk for GBS disease. However, a better understanding of the host-, microbiome-, and GBS-determined variables that dictate GBS GI carriage is needed before precise GI decolonization approaches can be developed. In this review, we synthesize current knowledge of the diverse body sites occupied by GBS as a pathogen and as a commensal. We summarize key molecular factors GBS utilizes to colonize different host-associated niches to inform future efforts to study GBS in the GI tract. We also discuss other GI commensals that are pathogenic in other body sites to emphasize the broader utility of precise de-colonization approaches for mitigating infections by GBS and other bacterial pathogens. Finally, we highlight how GBS treatments could be improved with a more holistic understanding of GBS enabled by continued GI-focused study.},
}
@article {pmid38430754,
year = {2024},
author = {Yan, X and Li, S and Abdullah Al, M and Mo, Y and Zuo, J and Grossart, HP and Zhang, H and Yang, Y and Jeppesen, E and Yang, J},
title = {Community stability of free-living and particle-attached bacteria in a subtropical reservoir with salinity fluctuations over 3 years.},
journal = {Water research},
volume = {254},
number = {},
pages = {121344},
doi = {10.1016/j.watres.2024.121344},
pmid = {38430754},
issn = {1879-2448},
mesh = {*Ecosystem ; Salinity ; Lakes/microbiology ; Bacteria/genetics ; *Microbiota/physiology ; Aquatic Organisms ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Changes in salinity have a profound influence on ecological services and functions of inland freshwater ecosystems, as well as on the shaping of microbial communities. Bacterioplankton, generally classified into free-living (FL) and particle-attached (PA) forms, are main components of freshwater ecosystems and play key functional roles for biogeochemical cycling and ecological stability. However, there is limited knowledge about the responses of community stability of both FL and PA bacteria to salinity fluctuations. Here, we systematically explored changes in community stability of both forms of bacteria based on high-frequency sampling in a shallow urban reservoir (Xinglinwan Reservoir) in subtropical China for 3 years. Our results indicated that (1) salinity was the strongest environmental factor determining FL and PA bacterial community compositions - rising salinity increased the compositional stability of both bacterial communities but decreased their α-diversity. (2) The community stability of PA bacteria was significantly higher than that of FL at high salinity level with low salinity variance scenarios, while the opposite was found for FL bacteria, i.e., their stability was higher than PA bacteria at low salinity level with high variance scenarios. (3) Both bacterial traits (e.g., bacterial genome size and interaction strength of rare taxa) and precipitation-induced factors (e.g., changes in salinity and particle) likely contributed collectively to differences in community stability of FL and PA bacteria under different salinity scenarios. Our study provides additional scientific basis for ecological management, protection and restoration of urban reservoirs under changing climatic and environmental conditions.},
}
@article {pmid38430049,
year = {2024},
author = {Barnett, SE and Shade, A},
title = {Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance.},
journal = {Ecology letters},
volume = {27},
number = {3},
pages = {e14393},
doi = {10.1111/ele.14393},
pmid = {38430049},
issn = {1461-0248},
support = {1749544//National Science Foundation/ ; },
mesh = {Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Resilience, Psychological ; Soil Microbiology ; Bacteria/genetics ; *Microbiota/physiology ; },
abstract = {Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute to functions. This study leverages a 7-year time series of a 60-year-old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the 'whole' bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall structural resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.},
}
@article {pmid38427046,
year = {2024},
author = {Alvarenga, DO and Priemé, A and Rousk, K},
title = {The Feather Moss Hylocomium splendens Affects the Transcriptional Profile of a Symbiotic Cyanobacterium in Relation to Acquisition and Turnover of Key Nutrients.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {49},
pmid = {38427046},
issn = {1432-184X},
support = {947719/ERC_/European Research Council/International ; },
mesh = {Symbiosis ; Nitrogen Fixation ; *Bryopsida/genetics/metabolism/microbiology ; *Bryophyta ; *Cyanobacteria/metabolism ; Amino Acids/metabolism ; },
abstract = {Moss-cyanobacteria symbioses were proposed to be based on nutrient exchange, with hosts providing C and S while bacteria provide N, but we still lack understanding of the underlying molecular mechanisms of their interactions. We investigated how contact between the ubiquitous moss Hylocomium splendens and its cyanobiont affects nutrient-related gene expression of both partners. We isolated a cyanobacterium from H. splendens and co-incubated it with washed H. splendens shoots. Cyanobacterium and moss were also incubated separately. After 1 week, we performed acetylene reduction assays to estimate N2 fixation and RNAseq to evaluate metatranscriptomes. Genes related to N2 fixation and the biosynthesis of several amino acids were up-regulated in the cyanobiont when hosted by the moss. However, S-uptake and the biosynthesis of the S-containing amino acids methionine and cysteine were down-regulated in the cyanobiont while the degradation of selenocysteine was up-regulated. In contrast, the number of differentially expressed genes in the moss was much lower, and almost no transcripts related to nutrient metabolism were affected. It is possible that, at least during the early stage of this symbiosis, the cyanobiont receives few if any nutrients from the host in return for N, suggesting that moss-cyanobacteria symbioses encompass relationships that are more plastic than a constant mutualist flow of nutrients.},
}
@article {pmid38426066,
year = {2024},
author = {Yue, Y and Hao, H and Wang, Q and Xiao, T and Zhang, Y and Chen, Q and Chen, H and Zhang, J},
title = {Dynamics of the soil microbial community associated with Morchella cultivation: diversity, assembly mechanism and yield prediction.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1345231},
pmid = {38426066},
issn = {1664-302X},
abstract = {INTRODUCTION: The artificial cultivation of morels has been a global research focus owing to production variability. Understanding the microbial ecology in cultivated soil is essential to increase morel yield and alleviate pathogen harm.<br><br>METHODS: A total of nine Morchella cultivation experiments in four soil field types, forest, paddy, greenhouse, and orchard in Shanghai city were performed to determine the potential ecological relationship between Morchella growth and soil microbial ecology.<br><br>RESULTS: Generally, significant variation was observed in the soil microbial diversity and composition between the different experimental field types. The niche width analysis indicated that the bacterial habitat niche breadth was significantly greater than the fungal community width, which was further confirmed by a null model that revealed that homogeneous selection could explain 46.26 and 53.64% of the variance in the bacterial and fungal assemblies, respectively. Moreover, the neutral community model revealed that stochastic processes dominate the bacterial community in forests and paddies and both the bacterial and fungal communities in orchard crops, whereas deterministic processes mostly govern the fungal community in forests and paddies and both the bacterial and the fungal communities in greenhouses. Furthermore, co-occurrence patterns were constructed, and the results demonstrated that the dynamics of the soil microbial community are related to fluctuations in soil physicochemical characteristics, especially soil potassium. Importantly, structural equation modeling further demonstrated that the experimental soil type significantly affects the potassium content of the soil, which can directly or indirectly promote Morchella yield by inhibiting soil fungal richness.<br><br>DISCUSSION: This was the first study to predict morel yield through soil potassium fertilizer and soil fungal community richness, which provides new insights into deciphering the importance of microbial ecology in morel agroecosystems.},
}
@article {pmid38425054,
year = {2024},
author = {Law, SR and Mathes, F and Paten, AM and Alexandre, PA and Regmi, R and Reid, C and Safarchi, A and Shaktivesh, S and Wang, Y and Wilson, A and Rice, SA and Gupta, VVSR},
title = {Life at the borderlands: microbiomes of interfaces critical to One Health.},
journal = {FEMS microbiology reviews},
volume = {48},
number = {2},
pages = {},
pmid = {38425054},
issn = {1574-6976},
support = {//CSIRO/ ; },
mesh = {Animals ; Humans ; *One Health ; *Microbiota ; Biological Evolution ; Soil Microbiology ; Plants/microbiology ; },
abstract = {Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.},
}
@article {pmid38424049,
year = {2024},
author = {Zhong, ZP and Du, J and Köstlbacher, S and Pjevac, P and Orlić, S and Sullivan, MB},
title = {Viral potential to modulate microbial methane metabolism varies by habitat.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1857},
pmid = {38424049},
issn = {2041-1723},
support = {3790//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 1759874//National Science Foundation (NSF)/ ; 1829831//National Science Foundation (NSF)/ ; NA//OSU | Byrd Polar and Climate Research Center, Ohio State University (Byrd Polar and Climate Research Center of The Ohio State University)/ ; },
mesh = {Animals ; Methane/metabolism ; Ecosystem ; *Viruses/genetics ; Metagenome ; *Euryarchaeota/genetics ; },
abstract = {Methane is a potent greenhouse gas contributing to global warming. Microorganisms largely drive the biogeochemical cycling of methane, yet little is known about viral contributions to methane metabolism (MM). We analyzed 982 publicly available metagenomes from host-associated and environmental habitats containing microbial MM genes, expanding the known MM auxiliary metabolic genes (AMGs) from three to 24, including seven genes exclusive to MM pathways. These AMGs are recovered on 911 viral contigs predicted to infect 14 prokaryotic phyla including Halobacteriota, Methanobacteriota, and Thermoproteota. Of those 24, most were encoded by viruses from rumen (16/24), with substantially fewer by viruses from environmental habitats (0-7/24). To search for additional MM AMGs from an environmental habitat, we generate metagenomes from methane-rich sediments in Vrana Lake, Croatia. Therein, we find diverse viral communities, with most viruses predicted to infect methanogens and methanotrophs and some encoding 13 AMGs that can modulate host metabolisms. However, none of these AMGs directly participate in MM pathways. Together these findings suggest that the extent to which viruses use AMGs to modulate host metabolic processes (e.g., MM) varies depending on the ecological properties of the habitat in which they dwell and is not always predictable by habitat biogeochemical properties.},
}
@article {pmid38423404,
year = {2024},
author = {Das, S and Malik, M and Dastidar, DG and Roy, R and Paul, P and Sarkar, S and Chakraborty, P and Maity, A and Dasgupta, M and Gupta, AD and Chatterjee, S and Sarker, RK and Maiti, D and Tribedi, P},
title = {Piperine, a phytochemical prevents the biofilm city of methicillin-resistant Staphylococcus aureus: A biochemical approach to understand the underlying mechanism.},
journal = {Microbial pathogenesis},
volume = {189},
number = {},
pages = {106601},
doi = {10.1016/j.micpath.2024.106601},
pmid = {38423404},
issn = {1096-1208},
mesh = {Humans ; *Methicillin-Resistant Staphylococcus aureus ; Anti-Bacterial Agents/pharmacology/metabolism ; *Staphylococcal Infections ; Biofilms ; Phytochemicals/pharmacology ; DNA/metabolism ; Microbial Sensitivity Tests ; *Alkaloids ; *Piperidines ; *Benzodioxoles ; *Polyunsaturated Alkamides ; },
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA), a drug-resistant human pathogen causes several nosocomial as well as community-acquired infections involving biofilm machinery. Hence, it has gained a wide interest within the scientific community to impede biofilm-induced MRSA-associated health complications. The current study focuses on the utilization of a natural bioactive compound called piperine to control the biofilm development of MRSA. Quantitative assessments like crystal violet, total protein recovery, and fluorescein-di-acetate (FDA) hydrolysis assays, demonstrated that piperine (8 and 16 μg/mL) could effectively compromise the biofilm formation of MRSA. Light and scanning electron microscopic image analysis confirmed the same. Further investigation revealed that piperine could reduce extracellular polysaccharide production by down-regulating the expression of icaA gene. Besides, piperine could reduce the cell-surface hydrophobicity of MRSA, a crucial factor of biofilm formation. Moreover, the introduction of piperine could interfere with microbial motility indicating the interaction of piperine with the quorum-sensing components. A molecular dynamics study showed a stable binding between piperine and AgrA protein (regulator of quorum sensing) suggesting the possible meddling of piperine in quorum-sensing of MRSA. Additionally, the exposure to piperine led to the accumulation of intracellular reactive oxygen species (ROS) and potentially heightened cell membrane permeability in inhibiting microbial biofilm formation. Besides, piperine could reduce the secretion of diverse virulence factors from MRSA. Further exploration revealed that piperine interacted with extracellular DNA (e-DNA), causing disintegration by weakening the biofilm architecture. Conclusively, this study suggests that piperine could be a potential antibiofilm molecule against MRSA-associated biofilm infections.},
}
@article {pmid38419638,
year = {2024},
author = {Boase, K and Santini, T and Watkin, E},
title = {Microbes of biotechnological importance in acidic saline lakes in the Yilgarn Craton, Western Australia.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1308797},
pmid = {38419638},
issn = {1664-302X},
abstract = {Acidic salt lakes are environments that harbor an array of biologically challenging conditions. Through 16S rRNA, 18S rRNA, and ITS amplicon sequencing of eight such lakes across the Yilgarn Craton of Western Australia, we aim to understand the microbial ecology of these lakes with a focus on iron- and sulfur-oxidizing and reducing microorganisms that have theoretical application in biomining industries. In spite of the biological challenges to life in these lakes, the microbial communities were highly diverse. Redundancy analysis of soil samples revealed sulfur, ammonium, organic carbon, and potassium were significant diversities of the microbial community composition. The most abundant microbes with a hypothetical application in biomining include the genus 9 M32 of the Acidithiobacillus family, Alicyclobacillus and Acidiphilium, all of which are possible iron- and/or sulfur-oxidizing bacteria. It is evident through this study that these lakes harbor multiple organisms with potential in biomining industries that should be exploited and studied further.},
}
@article {pmid38412470,
year = {2024},
author = {Shi, TL and Jia, KH and Bao, YT and Nie, S and Tian, XC and Yan, XM and Chen, ZY and Li, ZC and Zhao, SW and Ma, HY and Zhao, Y and Li, X and Zhang, RG and Guo, J and Zhao, W and El-Kassaby, YA and Müller, N and Van de Peer, Y and Wang, XR and Street, NR and Porth, I and An, X and Mao, JF},
title = {High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.},
journal = {Plant physiology},
volume = {195},
number = {1},
pages = {652-670},
pmid = {38412470},
issn = {1532-2548},
support = {2022YFD2200103//National Key R&amp;D Program of China/ ; 32171816//National Natural Science Foundation of China/ ; },
mesh = {*Populus/genetics ; *Alleles ; *Genome, Plant/genetics ; Gene Expression Regulation, Plant ; Haplotypes/genetics ; Hybridization, Genetic ; Machine Learning ; },
abstract = {Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.},
}
@article {pmid38411098,
year = {2024},
author = {Moreno, CM and Bernish, M and Meyer, MG and Li, Z and Waite, N and Cohen, NR and Schofield, O and Marchetti, A},
title = {Molecular physiology of Antarctic diatom natural assemblages and bloom event reveal insights into strategies contributing to their ecological success.},
journal = {mSystems},
volume = {9},
number = {3},
pages = {e0130623},
pmid = {38411098},
issn = {2379-5077},
support = {PLR1440435//National Science Foundation (NSF)/ ; OPP1745036//National Science Foundation (NSF)/ ; },
mesh = {*Diatoms/genetics ; Antarctic Regions ; Phytoplankton/genetics ; Oceans and Seas ; Plankton/metabolism ; Iron/metabolism ; },
abstract = {UNLABELLED: The continental shelf of the Western Antarctic Peninsula (WAP) is a highly variable system characterized by strong cross-shelf gradients, rapid regional change, and large blooms of phytoplankton, notably diatoms. Rapid environmental changes coincide with shifts in plankton community composition and productivity, food web dynamics, and biogeochemistry. Despite the progress in identifying important environmental factors influencing plankton community composition in the WAP, the molecular basis for their survival in this oceanic region, as well as variations in species abundance, metabolism, and distribution, remains largely unresolved. Across a gradient of physicochemical parameters, we analyzed the metabolic profiles of phytoplankton as assessed through metatranscriptomic sequencing. Distinct phytoplankton communities and metabolisms closely mirrored the strong gradients in oceanographic parameters that existed from coastal to offshore regions. Diatoms were abundant in coastal, southern regions, where colder and fresher waters were conducive to a bloom of the centric diatom, Actinocyclus. Members of this genus invested heavily in growth and energy production; carbohydrate, amino acid, and nucleotide biosynthesis pathways; and coping with oxidative stress, resulting in uniquely expressed metabolic profiles compared to other diatoms. We observed strong molecular evidence for iron limitation in shelf and slope regions of the WAP, where diatoms in these regions employed iron-starvation induced proteins, a geranylgeranyl reductase, aquaporins, and urease, among other strategies, while limiting the use of iron-containing proteins. The metatranscriptomic survey performed here reveals functional differences in diatom communities and provides further insight into the environmental factors influencing the growth of diatoms and their predicted response to changes in ocean conditions.<br><br>IMPORTANCE: In the Southern Ocean, phytoplankton must cope with harsh environmental conditions such as low light and growth-limiting concentrations of the micronutrient iron. Using metratranscriptomics, we assessed the influence of oceanographic variables on the diversity of the phytoplankton community composition and on the metabolic strategies of diatoms along the Western Antarctic Peninsula, a region undergoing rapid climate change. We found that cross-shelf differences in oceanographic parameters such as temperature and variable nutrient concentrations account for most of the differences in phytoplankton community composition and metabolism. We opportunistically characterized the metabolic underpinnings of a large bloom of the centric diatom Actinocyclus in coastal waters of the WAP. Our results indicate that physicochemical differences from onshore to offshore are stronger than between southern and northern regions of the WAP; however, these trends could change in the future, resulting in poleward shifts in functional differences in diatom communities and phytoplankton blooms.},
}
@article {pmid38411061,
year = {2024},
author = {Zhang, Y and Deng, Y and Wang, C and Li, S and Lau, FTK and Zhou, J and Zhang, T},
title = {Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants.},
journal = {mSystems},
volume = {9},
number = {3},
pages = {e0133323},
pmid = {38411061},
issn = {2379-5077},
support = {T21-604/19-R//Hong Kong Theme Based Research Scheme/ ; GRF17206120//Hong Kong General Research Fund/ ; DEMP-2017-03//Hong Kong DSD/ ; },
mesh = {Wastewater ; Sewage/microbiology ; Hong Kong/epidemiology ; Bacteria/genetics ; *Water Purification ; *Environmental Pollutants ; },
abstract = {UNLABELLED: Wastewater treatment plants (WWTPs) are indispensable biotechnology facilities for modern cities and play an essential role in modern urban infrastructure by employing microorganisms to remove pollutants in wastewater, thus protecting public health and the environment. This study conducted a 13-month bacterial community survey of six full-scale WWTPs in Hong Kong with samples of influent, activated sludge (AS), and effluent to explore their synchronism and asynchronism of bacterial community. Besides, we compared AS results of six Hong Kong WWTPs with data from 1,186 AS amplicon data in 269 global WWTPs and a 9-year metagenomic sequencing survey of a Hong Kong WWTP. Our results showed the compositions of bacterial communities varied and the bacterial community structure of AS had obvious differences across Hong Kong WWTPs. The co-occurrence analysis identified 40 pairs of relationships that existed among Hong Kong WWTPs to show solid associations between two species and stochastic processes took large proportions for the bacterial community assembly of six WWTPs. The abundance and distribution of the functional bacteria in worldwide and Hong Kong WWTPs were examined and compared, and we found that ammonia-oxidizing bacteria had more diversity than nitrite-oxidizing bacteria. Besides, Hong Kong WWTPs could make great contributions to the genome mining of microbial dark matter in the global "wanted list." Operational parameters had important effects on OTUs' abundance, such as the temperature to the genera of Tetrasphaera, Gordonia and Nitrospira. All these results obtained from this study can deepen our understanding of the microbial ecology in WWTPs and provide foundations for further studies.<br><br>IMPORTANCE: Wastewater treatment plants (WWTPs) are an indispensable component of modern cities, as they can remove pollutants in wastewater to prevent anthropogenic activities. Activated sludge (AS) is a fundamental wastewater treatment process and it harbors a highly complex microbial community that forms the main components and contains functional groups. Unveiling "who is there" is a long-term goal of the research on AS microbiology. High-throughput sequencing provides insights into the inventory diversity of microbial communities to an unprecedented level of detail. At present, the analysis of communities in WWTPs usually comes from a specific WWTP and lacks comparisons and verification among different WWTPs. The wide-scale and long-term sampling project and research in this study could help us evaluate the AS community more accurately to find the similarities and different results for different WWTPs in Hong Kong and other regions of the world.},
}
@article {pmid38410391,
year = {2024},
author = {Duysburgh, C and Miclotte, L and Green, JB and Watts, KT and Sardi, MI and Chakrabarti, A and Khafipour, E and Marzorati, M},
title = {Saccharomyces cerevisiae derived postbiotic alters gut microbiome metabolism in the human distal colon resulting in immunomodulatory potential in vitro.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1358456},
pmid = {38410391},
issn = {1664-302X},
abstract = {The yeast-based postbiotic EpiCor is a well-studied formulation, consisting of a complex mixture of bioactive molecules. In clinical studies, EpiCor postbiotic has been shown to reduce intestinal symptoms in a constipated population and support mucosal defense in healthy subjects. Anti-inflammatory potential and butyrogenic properties have been reported in vitro, suggesting a possible link between EpiCor's gut modulatory activity and immunomodulation. The current study used a standardized in vitro gut model, the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), to obtain a deeper understanding on host-microbiome interactions and potential microbiome modulation following repeated EpiCor administration. It was observed that EpiCor induced a functional shift in carbohydrate fermentation patterns in the proximal colon environment. Epicor promoted an increased abundance of Bifidobacterium in both the proximal and distal colon, affecting overall microbial community structure. Co-occurrence network analysis at the phylum level provided additional evidence of changes in the functional properties of microbial community promoted by EpiCor, increasing positive associations between Actinobacteria with microbes belonging to the Firmicutes phylum. These results, together with a significant increase in butyrate production provide additional support of EpiCor benefits to gut health. Investigation of host-microbiome interactions confirmed the immunomodulatory potential of the applied test product. Specific microbial alterations were observed in the distal colon, with metabotyping indicating that specific metabolic pathways, such as bile acid and tryptophan metabolism, were affected following EpiCor supplementation. These results, especially considering many effects were seen distally, further strengthen the position of EpiCor as a postbiotic with health promoting functionality in the gut, which could be further assessed in vivo.},
}
@article {pmid38409540,
year = {2024},
author = {Xu, T and Novotny, A and Zamora-Terol, S and Hambäck, PA and Winder, M},
title = {Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {48},
pmid = {38409540},
issn = {1432-184X},
support = {2016-04685//Swedish Research Council/ ; 2016-04685//Swedish Research Council/ ; },
mesh = {Animals ; Zooplankton/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; *Rotifera ; },
abstract = {In aquatic ecosystems, zooplankton-associated bacteria potentially have a great impact on the structure of ecosystems and trophic networks by providing various metabolic pathways and altering the ecological niche of host species. To understand the composition and drivers of zooplankton gut microbiota, we investigated the associated microbial communities of four zooplankton genera from different seasons in the Baltic Sea using the 16S rRNA gene. Among the 143 ASVs (amplified sequence variants) observed belonging to heterotrophic bacteria, 28 ASVs were shared across all zooplankton hosts over the season, and these shared core ASVs represented more than 25% and up to 60% of relative abundance in zooplankton hosts but were present at low relative abundance in the filtered water. Zooplankton host identity had stronger effects on bacterial composition than seasonal variation, with the composition of gut bacterial communities showing host-specific clustering patterns. Although bacterial compositions and dominating core bacteria were different between zooplankton hosts, higher gut bacteria diversity and more bacteria contributing to the temporal variation were found in Temora and Pseudocalanus, compared to Acartia and Synchaeta. Diet diatom and filamentous cyanobacteria negatively correlated with gut bacteria diversity, but the difference in diet composition did not explain the dissimilarity of gut bacteria composition, suggesting a general effect of diet on the inner conditions in the zooplankton gut. Synchaeta maintained high stability of gut bacterial communities with unexpectedly low bacteria-bacteria interactions as compared to the copepods, indicating host-specific regulation traits. Our results suggest that the patterns of gut bacteria dynamics are host-specific and the variability of gut bacteria is not only related to host taxonomy but also related to host behavior and life history traits.},
}
@article {pmid38408899,
year = {2024},
author = {Banerjee, A and Ghosh, A and Saha, B and Bhadury, P and De, P},
title = {Surface Charge-Switchable Antifouling Block Copolymer with Bacteriostatic Properties.},
journal = {Langmuir : the ACS journal of surfaces and colloids},
volume = {40},
number = {10},
pages = {5314-5325},
doi = {10.1021/acs.langmuir.3c03771},
pmid = {38408899},
issn = {1520-5827},
mesh = {*Biofouling/prevention &amp; control ; Proteins/metabolism ; Cations/chemistry ; Cell Membrane/metabolism ; Polymers/chemistry ; Surface Properties ; },
abstract = {Zwitterionic polymers are an emerging family of effective, low-fouling materials that can withstand unintended interactions with biological systems while exhibiting enhanced activity in bacterial matrix deterioration and biofilm eradication. Herein, we modularly synthesized an amphiphilic block copolymer, ZABCP, featuring potential bacteriostatic properties composed of a charge-switchable polyzwitterionic segment and a redox-sensitive pendant disulfide-labeled polymethacrylate block. The leucine-appended polyzwitterionic segment with alternatively positioned cationic amine and anionic carboxylate functionalities undergoes charge alterations (+ve → 0 → -ve) on pH variation. By introducing appropriate amphiphilicity, ZABCP forms distinct vesicles with redox-sensitive bilayer membranes and zwitterionic shielding coronas, enabling switching of surface charge. ZABCP vesicles exhibit 180 ± 20 nm hydrodynamic diameter, and its charge switching behavior in response to pH was confirmed by the change of zeta potential value from -23 to +36 mV. The binding interaction between ZABCP vesicles with lysozyme and pepsin proteins strengthens when the surface charge shifts from neutral (pH 7.4) to either anionic or cationic. This surface-charge-switchable phenomenon paves the way for implementing cationic ZABCP vesicles for bacterial cell growth inhibition, which is shown by the pronounced transition of cellular morphology, including clustering, aggregation, or elongation as well as membrane disruption for both Bacillus subtilis (Gram-positive) and Escherichia coli (Gram-negative). Such enhanced bacteriostatic activity could be ascribed to a strong electrostatic interaction between cationic vesicles and negatively charged bacterial membranes, leading to cell membrane disruption. Overall, this study provides a tailor-made approach to adopt low-fouling properties and potential bacteriostatic activity using zwitterionic polymers through precise control of pH.},
}
@article {pmid38407642,
year = {2024},
author = {Wang, Y and Xue, D and Chen, X and Qiu, Q and Chen, H},
title = {Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {47},
pmid = {38407642},
issn = {1432-184X},
support = {2022376//the Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//the Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; QNTS202201//the Youth Innovation Program of CIB/ ; 42001093//the National Natural Science Foundation of China/ ; 2019QZKK0304//the Second Tibetan Plateau Scientific Expedition/ ; },
mesh = {*Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Sphagnopsida ; Bacteria/genetics ; Carbon ; Nitrogen ; Nutrients ; },
abstract = {Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the [13]C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.},
}
@article {pmid38407587,
year = {2024},
author = {Kempraj, V and Auth, J and Cha, DH and Mason, CJ},
title = {Impact of Larval Food Source on the Stability of the Bactrocera dorsalis Microbiome.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {46},
pmid = {38407587},
issn = {1432-184X},
support = {2040-22430-028-000-D//USDA ARS/ ; 2040-43000-018-000-D//USDA ARS/ ; 2040-22430-028-000-D//USDA ARS/ ; 60-2040-3-003//Animal and Plant Health Inspection Service/ ; },
mesh = {Humans ; Female ; Animals ; Larva ; RNA, Ribosomal, 16S/genetics ; *Fruit ; *Tephritidae ; },
abstract = {Bacterial symbionts are crucial to the biology of Bactrocera dorsalis. With larval diet (fruit host) being a key factor that determines microbiome composition and with B. dorsalis using more than 400 fruits as hosts, it is unclear if certain bacterial symbionts are preserved and are passed on to B. dorsalis progenies despite changes in larval diet. Here, we conducted a fly rearing experiment to characterize diet-induced changes in the microbiome of female B. dorsalis. In order to explicitly investigate the impacts of larval diet on the microbiome, including potential stable bacterial constituents of B. dorsalis, we performed 16S rRNA sequencing on the gut tissues of teneral female flies reared from four different host fruits (guava, mango, papaya, and rose apple) infested using a single cohort of wild B. dorsalis that emerged from tropical almond (mother flies). Although B. dorsalis-associated microbiota were predominantly shaped by the larval diet, some major bacterial species from the mother flies were retained in progenies raised on different larval diets. With some variation, Klebsiella (ASV 1 and 2), Morganella (ASV 3), and Providencia (ASV 6) were the major bacterial symbionts that were stable and made up 0.1-80% of the gut and ovipositor microbiome of female teneral flies reared on different host fruits. Our results suggest that certain groups of bacteria are stably associated with female B. dorsalis across larval diets. These findings provide a basis for unexplored research on symbiotic bacterial function in B. dorsalis and may aid in the development of novel management techniques against this devastating pest of horticultural importance.},
}
@article {pmid38405409,
year = {2024},
author = {Hoffbeck, C and Middleton, DMRL and Lamar, SK and Keall, SN and Nelson, NJ and Taylor, MW},
title = {Gut microbiome of the sole surviving member of reptile order Rhynchocephalia reveals biogeographic variation, influence of host body condition and a substantial core microbiota in tuatara across New Zealand.},
journal = {Ecology and evolution},
volume = {14},
number = {2},
pages = {e11073},
pmid = {38405409},
issn = {2045-7758},
abstract = {Tuatara are the sole extant species in the reptile order Rhynchocephalia. They are ecologically and evolutionarily unique, having been isolated geographically for ~84 million years and evolutionarily from their closest living relatives for ~250 million years. Here we report the tuatara gut bacterial community for the first time. We sampled the gut microbiota of translocated tuatara at five sanctuaries spanning a latitudinal range of ~1000 km within Aotearoa New Zealand, as well as individuals from the source population on Takapourewa (Stephens Island). This represents a first look at the bacterial community of the order Rhynchocephalia and provides the opportunity to address several key hypotheses, namely that the tuatara gut microbiota: (1) differs from those of other reptile orders; (2) varies among geographic locations but is more similar at sites with more similar temperatures and (3) is shaped by tuatara body condition, parasitism and ambient temperature. We found significant drivers of the microbiota in sampling site, tuatara body condition, parasitism and ambient temperature, suggesting the importance of these factors when considering tuatara conservation. We also derived a 'core' community of shared bacteria across tuatara at many sites, despite their geographic range and isolation. Remarkably, >70% of amplicon sequence variants could not be assigned to known genera, suggesting a largely undescribed gut bacterial community for this ancient host species.},
}
@article {pmid38403716,
year = {2024},
author = {Nayman, EI and Schwartz, BA and Polmann, M and Gumabong, AC and Nieuwdorp, M and Cickovski, T and Mathee, K},
title = {Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {4585},
pmid = {38403716},
issn = {2045-2322},
support = {09150182010020//ZONMW-VICI/ ; },
mesh = {Humans ; Female ; Ethnicity ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/epidemiology ; Adenosine Deaminase ; Minority Groups ; Intercellular Signaling Peptides and Proteins ; Fatty Acids, Volatile ; },
abstract = {Gut microbiota, or the collection of diverse microorganisms in a specific ecological niche, are known to significantly impact human health. Decreased gut microbiota production of short-chain fatty acids (SCFAs) has been implicated in type 2 diabetes mellitus (T2DM) disease progression. Most microbiome studies focus on ethnic majorities. This study aims to understand how the microbiome differs between an ethnic majority (the Dutch) and minority (the South-Asian Surinamese (SAS)) group with a lower and higher prevalence of T2DM, respectively. Microbiome data from the Healthy Life in an Urban Setting (HELIUS) cohort were used. Two age- and gender-matched groups were compared: the Dutch (n = 41) and SAS (n = 43). Microbial community compositions were generated via DADA2. Metrics of microbial diversity and similarity between groups were computed. Biomarker analyses were performed to determine discriminating taxa. Bacterial co-occurrence networks were constructed to examine ecological patterns. A tight microbiota cluster was observed in the Dutch women, which overlapped with some of the SAS microbiota. The Dutch gut contained a more interconnected microbial ecology, whereas the SAS network was dispersed, i.e., contained fewer inter-taxonomic correlational relationships. Bacteroides caccae, Butyricicoccus, Alistipes putredinis, Coprococcus comes, Odoribacter splanchnicus, and Lachnospira were enriched in the Dutch gut. Haemophilus, Bifidobacterium, and Anaerostipes hadrus discriminated the SAS gut. All but Lachnospira and certain strains of Haemophilus are known to produce SCFAs. The Dutch gut microbiome was distinguished from the SAS by diverse, differentially abundant SCFA-producing taxa with significant cooperation. The dynamic ecology observed in the Dutch was not detected in the SAS. Among several potential gut microbial biomarkers, Haemophilus parainfluenzae likely best characterizes the ethnic minority group, which is more predisposed to T2DM. The higher prevalence of T2DM in the SAS may be associated with the gut dysbiosis observed.},
}
@article {pmid38402967,
year = {2024},
author = {Zhou, P and Li, D and Zhang, C and Ping, Q and Wang, L and Li, Y},
title = {Comparison of different sewage sludge pretreatment technologies for improving sludge solubilization and anaerobic digestion efficiency: A comprehensive review.},
journal = {The Science of the total environment},
volume = {921},
number = {},
pages = {171175},
doi = {10.1016/j.scitotenv.2024.171175},
pmid = {38402967},
issn = {1879-1026},
mesh = {Anaerobiosis ; *Sewage/microbiology ; *Ultrasonics ; Methane/chemistry ; Hydrolysis ; Waste Disposal, Fluid ; Bioreactors ; },
abstract = {Anaerobic digestion (AD) of sewage sludge reduces organic solids and produces methane, but the complex nature of sludge, especially the difficulty in solubilization, limits AD efficiency. Pretreatments, by destroying sludge structure and promoting disintegration and hydrolysis, are valuable strategies to enhance AD performance. There is a plethora of reviews on sludge pretreatments, however, quantitative comparisons from multiple perspectives across different pretreatments remain scarce. This review categorized various pretreatments into three groups: Physical (ultrasonic, microwave, thermal hydrolysis, electric decomposition, and high pressure homogenization), chemical (acid, alkali, Fenton, calcium peroxide, and ozone), and biological (microaeration, exogenous bacteria, and exogenous hydrolase) pretreatments. The optimal conditions of various pretreatments and their impacts on enhancing AD efficiency were summarized; the effects of different pretreatments on microbial community in the AD system were comprehensively compared. The quantitative comparison based on dissolution degree of COD (DDCOD) indicted that the sludge solubilization performance is in the order of physical, chemical, and biological pretreatments, although with each below 40 % DDCOD. Biological pretreatment, particularly microaeration and exogenous bacteria, excel in AD enhancement. Pretreatments alter microbial ecology, favoring Firmicutes and Methanosaeta (acetotrophic methanogens) over Proteobacteria and Methanobacterium (hydrogenotrophic methanogens). Most pretreatments have unfavorable energy and economic outcomes, with electric decomposition and microaeration being exceptions. On the basis of the overview of the above pretreatments, a full energy and economy assessment for sewage sludge treatment was suggested. Finally, challenges associated with sludge pretreatments and AD were analyzed, and future research directions were proposed. This review may broaden comprehension of sludge pretreatments and AD, and provide an objective basis for the selection of sludge pretreatment technologies.},
}
@article {pmid38402751,
year = {2024},
author = {Rosenqvist, T and Chan, S and Ahlinder, J and Salomonsson, EN and Suarez, C and Persson, KM and Rådström, P and Paul, CJ},
title = {Inoculation with adapted bacterial communities promotes development of full scale slow sand filters for drinking water production.},
journal = {Water research},
volume = {253},
number = {},
pages = {121203},
doi = {10.1016/j.watres.2024.121203},
pmid = {38402751},
issn = {1879-2448},
mesh = {*Drinking Water ; *Water Purification/methods ; Bacteria/genetics ; *Microbiota ; Firmicutes ; Filtration/methods ; Silicon Dioxide/chemistry ; },
abstract = {Gravity-driven filtration through slow sand filters (SSFs) is one of the oldest methods for producing drinking water. As water passes through a sand bed, undesired microorganisms and chemicals are removed by interactions with SSF biofilm and its resident microbes. Despite their importance, the processes through which these microbial communities form are largely unknown, as are the factors affecting these processes. In this study, two SSFs constructed using different sand sources were compared to an established filter and observed throughout their maturation process. One SSF was inoculated through addition of sand scraped from established filters, while the other was not inoculated. The operational and developing microbial communities of SSFs, as well as their influents and effluents, were studied by sequencing of 16S ribosomal rRNA genes. A functional microbial community resembling that of the established SSF was achieved in the inoculated SSF, but not in the non-inoculated SSF. Notably, the non-inoculated SSF had significantly (p < 0.01) higher abundances of classes Armatimonadia, Elusimicrobia, Fimbriimonadia, OM190 (phylum Planctomycetota), Parcubacteria, Vampirivibrionia and Verrucomicrobiae. Conversely, it had lower abundances of classes Anaerolineae, Bacilli, bacteriap25 (phylum Myxococcota), Blastocatellia, Entotheonellia, Gemmatimonadetes, lineage 11b (phylum Elusimicrobiota), Nitrospiria, Phycisphaerae, subgroup 22 (phylum Acidobacteriota) and subgroup 11 (phylum Acidobacteriota). Poor performance of neutral models showed that the assembly and dispersal of SSF microbial communities was mainly driven by selection. The temporal turnover of microbial species, as estimated through the scaling exponent of the species-time relationship, was twice as high in the non-inoculated filter (0.946 ± 0.164) compared to the inoculated filter (0.422 ± 0.0431). This study shows that the addition of an inoculum changed the assembly processes within SSFs. Specifically, the rate at which new microorganisms were observed in the biofilm was reduced. The reduced temporal turnover may be driven by inoculating taxa inhibiting growth, potentially via secondary metabolite production. This in turn would allow the inoculation community to persist and contribute to SSF function.},
}
@article {pmid38402201,
year = {2024},
author = {Zhu, H and Li, M and Bi, D and Yang, H and Gao, Y and Song, F and Zheng, J and Xie, R and Zhang, Y and Liu, H and Yan, X and Kong, C and Zhu, Y and Xu, Q and Wei, Q and Qin, H},
title = {Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1688},
pmid = {38402201},
issn = {2041-1723},
support = {81972221//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 81801564//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 81902422//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 82072634//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
mesh = {Animals ; Humans ; Mice ; Carcinogenesis/genetics ; *Colorectal Neoplasms/pathology ; *Fusobacterium nucleatum/genetics ; Proto-Oncogene Proteins p21(ras)/genetics ; RNA Helicases ; },
abstract = {Fusobacterium nucleatum (F. nucleatum) promotes intestinal tumor growth and its relative abundance varies greatly among patients with CRC, suggesting the presence of unknown, individual-specific effectors in F. nucleatum-dependent carcinogenesis. Here, we identify that F. nucleatum is enriched preferentially in KRAS p.G12D mutant CRC tumor tissues and contributes to colorectal tumorigenesis in Villin-Cre/Kras[G12D+/-] mice. Additionally, Parabacteroides distasonis (P. distasonis) competes with F. nucleatum in the G12D mouse model and human CRC tissues with the KRAS mutation. Orally gavaged P. distasonis in mice alleviates the F. nucleatum-dependent CRC progression. F. nucleatum invades intestinal epithelial cells and binds to DHX15, a protein of RNA helicase family expressed on CRC tumor cells, mechanistically involving ERK/STAT3 signaling. Knock out of Dhx15 in Villin-Cre/Kras[G12D+/-] mice attenuates the CRC phenotype. These findings reveal that the oncogenic effect of F. nucleatum depends on somatic genetics and gut microbial ecology and indicate that personalized modulation of the gut microbiota may provide a more targeted strategy for CRC treatment.},
}
@article {pmid38401719,
year = {2024},
author = {Martin-Pozas, T and Cuezva, S and Fernandez-Cortes, A and Gonzalez-Pumariega, M and Elez, J and Duarte, E and de la Rasilla, M and Canaveras, JC and Saiz-Jimenez, C and Sanchez-Moral, S},
title = {Adaptive response of prokaryotic communities to extreme pollution flooding in a Paleolithic rock art cave (Pindal Cave, northern Spain).},
journal = {The Science of the total environment},
volume = {921},
number = {},
pages = {171137},
doi = {10.1016/j.scitotenv.2024.171137},
pmid = {38401719},
issn = {1879-1026},
mesh = {Animals ; Cattle ; *Ecosystem ; Spain ; Floods ; Prokaryotic Cells ; *Microbiota ; Nitrogen ; Mammals ; },
abstract = {A flood event affecting Pindal Cave, a UNESCO World Heritage site, introduced a substantial amount of external sediments and waste into the cave. This event led to the burial of preexisting sediments, altering the biogeochemical characteristics of the cave ecosystem by introducing heightened levels of organic matter, nitrogen compounds, phosphorus, and heavy metals. The sediments included particulate matter and waste from a cattle farm located within the water catchment area of the cavity, along with diverse microorganisms, reshaping the cave microbial community. This study addresses the ongoing influence of a cattle farm on the cave ecosystem and aims to understand the adaptive responses of the underground microbial community to the sudden influx of waste allochthonous material. Here, we show that the flood event had an immediate and profound effect on the cave microbial community, marked by a significant increase in methanogenic archaea, denitrifying bacteria, and other microorganisms commonly associated with mammalian intestinal tracts. Furthermore, our findings reveal that one year after the flood, microorganisms related to the flood decreased, while the increase in inorganic forms of ammonium and nitrate suggests potential nitrification, aligning with increased abundances of corresponding functional genes involved in nitrogen cycling. The results reveal that the impact of pollution was neither recent nor isolated, and it was decisive in stopping livestock activity near the cave. The influence of the cattle farm has persisted since its establishment over the impluvium area, and this influence endures even a year after the flood. Our study emphasizes the dynamic interplay between natural events, anthropogenic activities, and microbial communities, offering insights into the resilience of cave ecosystems. Understanding microbial adaptation in response to environmental disturbances, as demonstrated in this cave ecosystem, has implications for broader ecological studies and underscores the importance of considering temporal dynamics in conservation efforts.},
}
@article {pmid38401169,
year = {2024},
author = {Vieira, HH and Bulzu, PA and Kasalický, V and Haber, M and Znachor, P and Piwosz, K and Ghai, R},
title = {Isolation of a widespread giant virus implicated in cryptophyte bloom collapse.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38401169},
issn = {1751-7370},
support = {20-12496X//Grant Agency of the Czech Republic/ ; GACR 23-06806S//Grant Agency of the Czech Republic/ ; 22-33245S//Czech Science Foundation/ ; 2021/03/Y/NZ8/00076//National Science Centre/ ; },
mesh = {Humans ; *Giant Viruses ; Phytoplankton ; Cryptophyta/genetics ; Eukaryota ; *Viruses ; },
abstract = {Photosynthetic cryptophytes are ubiquitous protists that are major participants in the freshwater phytoplankton bloom at the onset of spring. Mortality due to change in environmental conditions and grazing have been recognized as key factors contributing to bloom collapse. In contrast, the role of viral outbreaks as factors terminating phytoplankton blooms remains unknown from freshwaters. Here, we isolated and characterized a cryptophyte virus contributing to the annual collapse of a natural cryptophyte spring bloom population. This viral isolate is also representative for a clade of abundant giant viruses (phylum Nucleocytoviricota) found in freshwaters all over the world.},
}
@article {pmid38400045,
year = {2024},
author = {Johnson, ML and Zwart, MP},
title = {Robust Approaches to the Quantitative Analysis of Genome Formula Variation in Multipartite and Segmented Viruses.},
journal = {Viruses},
volume = {16},
number = {2},
pages = {},
pmid = {38400045},
issn = {1999-4915},
support = {016.Vidi.171.061/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Viruses/genetics ; Genome, Viral ; Biological Evolution ; },
abstract = {When viruses have segmented genomes, the set of frequencies describing the abundance of segments is called the genome formula. The genome formula is often unbalanced and highly variable for both segmented and multipartite viruses. A growing number of studies are quantifying the genome formula to measure its effects on infection and to consider its ecological and evolutionary implications. Different approaches have been reported for analyzing genome formula data, including qualitative description, applying standard statistical tests such as ANOVA, and customized analyses. However, these approaches have different shortcomings, and test assumptions are often unmet, potentially leading to erroneous conclusions. Here, we address these challenges, leading to a threefold contribution. First, we propose a simple metric for analyzing genome formula variation: the genome formula distance. We describe the properties of this metric and provide a framework for understanding metric values. Second, we explain how this metric can be applied for different purposes, including testing for genome-formula differences and comparing observations to a reference genome formula value. Third, we re-analyze published data to illustrate the applications and weigh the evidence for previous conclusions. Our re-analysis of published datasets confirms many previous results but also provides evidence that the genome formula can be carried over from the inoculum to the virus population in a host. The simple procedures we propose contribute to the robust and accessible analysis of genome-formula data.},
}
@article {pmid38399791,
year = {2024},
author = {Stroeva, AR and Klyukina, AA and Vidishcheva, ON and Poludetkina, EN and Solovyeva, MA and Pyrkin, VO and Gavirova, LA and Birkeland, NK and Akhmanov, GG and Bonch-Osmolovskaya, EA and Merkel, AY},
title = {Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea.},
journal = {Microorganisms},
volume = {12},
number = {2},
pages = {},
pmid = {38399791},
issn = {2076-2607},
support = {20-54-20001//Russian Foundation for Basic Research/ ; },
abstract = {The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results-correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers.},
}
@article {pmid38395561,
year = {2024},
author = {Aswathi, KN and Shirke, A and Praveen, A and Murthy, PS},
title = {Functioning of Saccharomyces cerevisiae in honey coffee (Coffea canephora) and their effect on metabolites, volatiles and flavor profiles.},
journal = {Food research international (Ottawa, Ont.)},
volume = {180},
number = {},
pages = {114092},
doi = {10.1016/j.foodres.2024.114092},
pmid = {38395561},
issn = {1873-7145},
mesh = {Saccharomyces cerevisiae/metabolism ; *Coffea/chemistry ; *Honey ; *Yeast, Dried ; Sugars/metabolism ; },
abstract = {Post-harvesting and microbial activity of coffee play a critical role in the metabolites and the sensory quality of the brew. The pulped natural/honey coffee process is an improvised semi-dry technique consisting of prolonged fermentation of depulped coffee beans excluding washing steps. The starter culture application in coffee industry plays an important role to enhance the cup quality. This work focuses on the fermentation of pulped natural/honey Robusta coffee with a starter culture (Saccharomyces cerevisiae MTCC 173) and the identification of fermentation patterns through [1]H NMR, microbial ecology, volatomics and organoleptics of brew. Fermentation was accelerated by yeast populace (10 cfu log/mL) for 192 h. Principal compound analysis performed on [1]H NMR led to the investigation of metabolites such as sugars, alkaloids, alcohols, organic acids and amino acids. Detection of some sugars and organic acids represented that the starter cultures imparted few metabolic changes during the process. A major activity of sugars in fermentation with 83.3 % variance in PC 1 and 16.7 % in PC 2 was observed. The chemical characteristics such as carbohydrates (41.88 ± 0.77 mg/g), polyphenols (34.16 ± 0.79 mg/g), proteins (58.54 ± 0.66 mg/g), caffeine (26.54 ± 0.06 mg/g), and CGA (21.83 ± 0.04 mg/g) were also evaluated. The heatmap-based visualization of GC-MS accorded characterization of additional 5 compounds in treated (T) coffee contributing to sweet, fruity and caramelly odor notes compared to untreated (UT). The sensory outlines 72.5 in T and 70.5 in UT scores. Preparation of honey coffee with Saccharomyces cerevisiae is the first report, which modulated the flavor and quality of coffee.},
}
@article {pmid38395158,
year = {2024},
author = {Li, XM and Hu, HF and Chen, SC},
title = {Artificial light at night causes community instability of bacterial community in urban soils.},
journal = {The Science of the total environment},
volume = {921},
number = {},
pages = {171129},
doi = {10.1016/j.scitotenv.2024.171129},
pmid = {38395158},
issn = {1879-1026},
mesh = {*Ecosystem ; *Soil ; Light Pollution ; Environment ; Bacteria ; Light ; },
abstract = {Urban soils host diverse bacteria crucial for ecosystem functions and urban health. As urbanization rises, artificial light at night (ALAN) imposes disturbances on soil ecosystems, yet how ALAN affects the structure and stability of soil bacterial community remains unclear. Here we coupled a short-term incubation experiment, community profiling, network analysis, and in situ field survey to assess the ecological impacts of ALAN. We showed that ALAN influenced bacterial compositions and shifted the bacterial network to a less stable phase, altering denitrification potential. Such transition in community stability probably resulted from an ALAN-induced decrease in competition and/or an increase in facilitation, in line with the Stress Gradient Hypothesis. Similar destabilizing effects were also detected in bacterial networks in multiple urban soils subjected to different levels of ALAN stress, supporting the action of ALAN on naturally-occurring soil bacterial communities. Overall, our findings highlight ALAN as a new form of anthropogenic stress that jeopardizes the stability of soil bacterial community, which would facilitate ecological projection of expanding ALAN exposure.},
}
@article {pmid38393401,
year = {2024},
author = {Minahan, NT and Chen, CH and Chuang, YC and Tsai, KH and Shen, WC and Guo, YL},
title = {Fungal Spore Richness and Abundance of Allergenic Taxa: Comparing a Portable Impactor and Passive Trap Indoors and Outdoors in an Urban Setting.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {45},
pmid = {38393401},
issn = {1432-184X},
mesh = {*Allergens ; Spores, Fungal/genetics ; *Fungi/genetics ; Air Microbiology ; Environmental Monitoring ; },
abstract = {Fungal spores are common airborne allergens, and fungal richness has been implicated in allergic disease. Amplicon sequencing of environmental DNA from air samples is a promising method to estimate fungal spore richness with semi-quantification of hundreds of taxa and can be combined with quantitative PCR to derive abundance estimates. However, it remains unclear how the choice of air sampling method influences these estimates. This study compared active sampling with a portable impactor and passive sampling with a passive trap over different durations to estimate fungal spore richness and the abundance of allergenic taxa. Air sampling was conducted indoors and outdoors at 12 residences, including repeated measurements with a portable impactor and passive traps with 1-day and 7-day durations. ITS2 amplicon sequence data were transformed to spore equivalents estimated by quantitative PCR, repeated active samples were combined, and abundance-based rarefaction was performed to standardize sample coverage for estimation of genus-level richness and spore abundance. Rarefied fungal richness was similar between methods indoors but higher for passive traps with a 7-day duration outdoors. Rarefied abundance of allergenic genera was similar between methods but some genera had lower abundance for passive traps with a 1-day duration, which differed indoors and outdoors indicating stochasticity in the collection of spores on collocated samplers. This study found that similar estimates of fungal spore richness and abundance of allergenic taxa can be obtained using a portable impactor or a passive trap within one day and that increased passive sample duration provides limited additional information.},
}
@article {pmid38391651,
year = {2024},
author = {Hoffstadt, K and Nikolausz, M and Krafft, S and Bonatelli, ML and Kumar, V and Harms, H and Kuperjans, I},
title = {Optimization of the Ex Situ Biomethanation of Hydrogen and Carbon Dioxide in a Novel Meandering Plug Flow Reactor: Start-Up Phase and Flexible Operation.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {11},
number = {2},
pages = {},
pmid = {38391651},
issn = {2306-5354},
support = {KESW-1-2-032A-B//European Regional Development Fund (ERDF)/ ; },
abstract = {With the increasing use of renewable energy resources for the power grid, the need for long-term storage technologies, such as power-to-gas systems, is growing. Biomethanation provides the opportunity to store energy in the form of the natural gas-equivalent biomethane. This study investigates a novel plug flow reactor that employs a helical static mixer for the biological methanation of hydrogen and carbon dioxide. In tests, the reactor achieved an average methane production rate of 2.5 LCH4LR∗d (methane production [LCH4] per liter of reactor volume [LR] per day [d]) with a maximum methane content of 94%. It demonstrated good flexibilization properties, as repeated 12 h downtimes did not negatively impact the process. The genera Methanothermobacter and Methanobacterium were predominant during the initial phase, along with volatile organic acid-producing, hydrogenotrophic, and proteolytic bacteria. The average ratio of volatile organic acid to total inorganic carbon increased to 0.52 ± 0.04, while the pH remained stable at an average of pH 8.1 ± 0.25 from day 32 to 98, spanning stable and flexible operation modes. This study contributes to the development of efficient flexible biological methanation systems for sustainable energy storage and management.},
}
@article {pmid38388537,
year = {2024},
author = {Faller, L and Leite, MFA and Kuramae, EE},
title = {Enhancing phosphate-solubilising microbial communities through artificial selection.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1649},
pmid = {38388537},
issn = {2041-1723},
mesh = {*Phosphates ; Ecosystem ; Soil Microbiology ; Agriculture ; Soil ; *Microbiota/genetics ; },
abstract = {Microbial communities, acting as key drivers of ecosystem processes, harbour immense potential for sustainable agriculture practices. Phosphate-solubilising microorganisms, for example, can partially replace conventional phosphate fertilisers, which rely on finite resources. However, understanding the mechanisms and engineering efficient communities poses a significant challenge. In this study, we employ two artificial selection methods, environmental perturbation, and propagation, to construct phosphate-solubilising microbial communities. To assess trait transferability, we investigate the community performance in different media and a hydroponic system with Chrysanthemum indicum. Our findings reveal a distinct subset of phosphate-solubilising bacteria primarily dominated by Klebsiella and Enterobacterales. The propagated communities consistently demonstrate elevated levels of phosphate solubilisation, surpassing the starting soil community by 24.2% in activity. The increased activity of propagated communities remains consistent upon introduction into the hydroponic system. This study shows the efficacy of community-level artificial selection, particularly through propagation, as a tool for successfully modifying microbial communities to enhance phosphate solubilisation.},
}
@article {pmid38385702,
year = {2024},
author = {Zhao, Y and Ling, N and Liu, X and Li, C and Jing, X and Hu, J and Rui, J},
title = {Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {3},
pages = {e0007024},
pmid = {38385702},
issn = {1098-5336},
support = {41771293//MOST | National Natural Science Foundation of China (NSFC)/ ; 42277100//MOST | National Natural Science Foundation of China (NSFC)/ ; 20JR5RA308//Outstanding Youth Foundation of Gansu Province/ ; lzujbky-2019-ct01//Fundamental Research Funds for Central Universities of China/ ; lzujbky-2022-ct04//Fundamental Research Funds for Central Universities of China/ ; },
mesh = {*Bacteria/genetics ; *Soil/chemistry ; Ammonia ; Nitrification ; Oxidation-Reduction ; Soil Microbiology ; Archaea/genetics ; Phylogeny ; },
abstract = {Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.},
}
@article {pmid38380980,
year = {2024},
author = {Van Gerrewey, T and Navarrete, O and Vandecruys, M and Perneel, M and Boon, N and Geelen, D},
title = {Bacterially enhanced plant-growing media for controlled environment agriculture.},
journal = {Microbial biotechnology},
volume = {17},
number = {2},
pages = {e14422},
pmid = {38380980},
issn = {1751-7915},
support = {HBC.2017.0209//Agentschap Innoveren en Ondernemen/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Agriculture ; *Bacteria/genetics ; Plants/genetics ; Soil/chemistry ; Plant Roots/microbiology ; Soil Microbiology ; },
abstract = {Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.},
}
@article {pmid38380088,
year = {2024},
author = {Savaglia, V and Lambrechts, S and Tytgat, B and Vanhellemont, Q and Elster, J and Willems, A and Wilmotte, A and Verleyen, E and Vyverman, W},
title = {Geology defines microbiome structure and composition in nunataks and valleys of the Sør Rondane Mountains, East Antarctica.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1316633},
pmid = {38380088},
issn = {1664-302X},
abstract = {Understanding the relation between terrestrial microorganisms and edaphic factors in the Antarctic can provide insights into their potential response to environmental changes. Here we examined the composition of bacterial and micro-eukaryotic communities using amplicon sequencing of rRNA genes in 105 soil samples from the Sør Rondane Mountains (East Antarctica), differing in bedrock or substrate type and associated physicochemical conditions. Although the two most widespread taxa (Acidobacteriota and Chlorophyta) were relatively abundant in each sample, multivariate analysis and co-occurrence networks revealed pronounced differences in community structure depending on substrate type. In moraine substrates, Actinomycetota and Cercozoa were the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble substrates, Cyanobacteriota and Metazoa were the dominant bacterial and eukaryotic taxa. However, at lower taxonomic level, a distinct differentiation was observed within the Cyanobacteriota phylum depending on substrate type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans were relatively abundant according to the 18S rRNA dataset, even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet ("Dry Valley"). Overall, our study shows that different substrate types support distinct microbial communities, and that mineral soil diversity is a major determinant of terrestrial microbial diversity in inland Antarctic nunataks and valleys.},
}
@article {pmid38378706,
year = {2024},
author = {Papin, M and Philippot, L and Breuil, MC and Bru, D and Dreux-Zigha, A and Mounier, A and Le Roux, X and Rouard, N and Spor, A},
title = {Survival of a microbial inoculant in soil after recurrent inoculations.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {4177},
pmid = {38378706},
issn = {2045-2322},
support = {ANR-20-CE02-0014//Agence Nationale de la Recherche/ ; },
mesh = {*Agricultural Inoculants ; Soil ; Nitrates ; Agriculture ; *Pseudomonas fluorescens ; Soil Microbiology ; },
abstract = {Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (10[6] and 10[8] cfu.g soil[-1]). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.},
}
@article {pmid38376218,
year = {2024},
author = {Kridler, MR and Viney, IA and Custer, JM and Schlottman, B and Bartelme, R and Carini, P},
title = {Draft genome sequences of Arthrobacter sp. AZCC_0090 and Mycobacterium sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona.},
journal = {Microbiology resource announcements},
volume = {13},
number = {3},
pages = {e0108923},
pmid = {38376218},
issn = {2576-098X},
support = {IOS-2141605//National Science Foundation (NSF)/ ; DGE-2137419//National Science Foundation (NSF)/ ; //Technology and Research Initiative Fund-WEES/ ; },
abstract = {Here, we present the genomes of two soil actinobacteria: Arthrobacter sp. strain AZCC_0090 and Mycobacterium sp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern Arizona, USA.},
}
@article {pmid38376179,
year = {2024},
author = {Bisesi, AT and Möbius, W and Nadell, CD and Hansen, EG and Bowden, SD and Harcombe, WR},
title = {Bacteriophage specificity is impacted by interactions between bacteria.},
journal = {mSystems},
volume = {9},
number = {3},
pages = {e0117723},
pmid = {38376179},
issn = {2379-5077},
support = {IOS-2019304//National Science Foundation (NSF)/ ; IOS-2017879//National Science Foundation (NSF)/ ; BB/V011464/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Bacteriophages/physiology ; Bacteria ; Escherichia coli/physiology ; Bacterial Physiological Phenomena ; Symbiosis ; },
abstract = {UNLABELLED: Predators play a central role in shaping community structure, function, and stability. The degree to which bacteriophage predators (viruses that infect bacteria) evolve to be specialists with a single bacterial prey species versus generalists able to consume multiple types of prey has implications for their effect on microbial communities. The presence and abundance of multiple bacterial prey types can alter selection for phage generalists, but less is known about how interactions between prey shape predator specificity in microbial systems. Using a phenomenological mathematical model of phage and bacterial populations, we find that the dominant phage strategy depends on prey ecology. Given a fitness cost for generalism, generalist predators maintain an advantage when prey species compete, while specialists dominate when prey are obligately engaged in cross-feeding interactions. We test these predictions in a synthetic microbial community with interacting strains of Escherichia coli and Salmonella enterica by competing a generalist T5-like phage able to infect both prey against P22vir, an S. enterica-specific phage. Our experimental data conform to our modeling expectations when prey species are competing or obligately mutualistic, although our results suggest that the in vitro cost of generalism is caused by a combination of biological mechanisms not anticipated in our model. Our work demonstrates that interactions between bacteria play a role in shaping ecological selection on predator specificity in obligately lytic bacteriophages and emphasizes the diversity of ways in which fitness trade-offs can manifest.<br><br>IMPORTANCE: There is significant natural diversity in how many different types of bacteria a bacteriophage can infect, but the mechanisms driving this diversity are unclear. This study uses a combination of mathematical modeling and an in vitro system consisting of Escherichia coli, Salmonella enterica, a T5-like generalist phage, and the specialist phage P22vir to highlight the connection between bacteriophage specificity and interactions between their potential microbial prey. Mathematical modeling suggests that competing bacteria tend to favor generalist bacteriophage, while bacteria that benefit each other tend to favor specialist bacteriophage. Experimental results support this general finding. The experiments also show that the optimal phage strategy is impacted by phage degradation and bacterial physiology. These findings enhance our understanding of how complex microbial communities shape selection on bacteriophage specificity, which may improve our ability to use phage to manage antibiotic-resistant microbial infections.},
}
@article {pmid38376167,
year = {2024},
author = {Hegarty, B and Riddell V, J and Bastien, E and Langenfeld, K and Lindback, M and Saini, JS and Wing, A and Zhang, J and Duhaime, M},
title = {Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods.},
journal = {mSystems},
volume = {9},
number = {3},
pages = {e0110523},
pmid = {38376167},
issn = {2379-5077},
support = {DGE1256260, 2055455, DGE134012//National Science Foundation (NSF)/ ; NA17OAR4320152//DOC | National Oceanic and Atmospheric Administration (NOAA)/ ; Blue Sky Initiative//College of Engineering, University of Michigan/ ; },
mesh = {*Benchmarking ; Ecosystem ; *Viruses ; Metagenomics/methods ; Databases, Nucleic Acid ; },
abstract = {UNLABELLED: Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral identification tools. However, the effectiveness of this strategy is unknown. Here, we benchmarked combinations of six widely used informatics tools for viral identification and analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, and Kaiju), called "rulesets." Rulesets were tested against mock metagenomes composed of taxonomically diverse sequence types and diverse aquatic metagenomes to assess the effects of the degree of viral enrichment and habitat on tool performance. We found that six rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, Padj ≥ 0.05]. Each contained VirSorter2, and five used our "tuning removal" rule designed to remove non-viral contamination. While DeepVirFinder, VIBRANT, and VirSorter were each found once in these high-accuracy rulesets, they were not found in combination with each other: combining tools does not lead to optimal performance. Our validation suggests that the MCC plateau at 0.77 is partly caused by inaccurate labeling within reference sequence databases. In aquatic metagenomes, our highest MCC ruleset identified more viral sequences in virus-enriched (44%-46%) than in cellular metagenomes (7%-19%). While improved algorithms may lead to more accurate viral identification tools, this should be done in tandem with careful curation of sequence databases. We recommend using the VirSorter2 ruleset and our empirically derived tuning removal rule. Our analysis provides insight into methods for in silico viral identification and will enable more robust viral identification from metagenomic data sets.<br><br>IMPORTANCE: The identification of viruses from environmental metagenomes using informatics tools has offered critical insights in microbial ecology. However, it remains difficult for researchers to know which tools optimize viral recovery for their specific study. In an attempt to recover more viruses, studies are increasingly combining the outputs from multiple tools without validating this approach. After benchmarking combinations of six viral identification tools against mock metagenomes and environmental samples, we found that these tools should only be combined cautiously. Two to four tool combinations maximized viral recovery and minimized non-viral contamination compared with either the single-tool or the five- to six-tool ones. By providing a rigorous overview of the behavior of in silico viral identification strategies and a pipeline to replicate our process, our findings guide the use of existing viral identification tools and offer a blueprint for feature engineering of new tools that will lead to higher-confidence viral discovery in microbiome studies.},
}
@article {pmid38373802,
year = {2024},
author = {O'Hara, E and Zaheer, R and Andrés-Lasheras, S and McAllister, TA and Gruninger, RJ},
title = {Evaluating the liver abscess microbiota of beef cattle during a reduction in tylosin supplementation shows differences according to abscess size and fraction.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {4},
pages = {},
pmid = {38373802},
issn = {1574-6941},
support = {//Agriculture and Agri-Food Canada/ ; //Genome Alberta/ ; ANH.02.19//Beef Cattle Research Council/ ; },
mesh = {Cattle ; Animals ; Tylosin/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Liver Abscess/veterinary/epidemiology/microbiology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Dietary Supplements/analysis ; *Microbiota ; Animal Feed/analysis ; },
abstract = {Liver abscesses (LA) resulting from bacterial infection in cattle pose a significant global challenge to the beef and dairy industries. Economic losses from liver discounts at slaughter and reduced animal performance drive the need for effective mitigation strategies. Tylosin phosphate supplementation is widely used to reduce LA occurrence, but concerns over antimicrobial overuse emphasize the urgency to explore alternative approaches. Understanding the microbial ecology of LA is crucial to this, and we hypothesized that a reduced timeframe of tylosin delivery would alter LA microbiomes. We conducted 16S rRNA sequencing to assess severe liver abscess bacteriomes in beef cattle supplemented with in-feed tylosin. Our findings revealed that shortening tylosin supplementation did not notably alter microbial communities. Additionally, our findings highlighted the significance of sample processing methods, showing differing communities in bulk purulent material and the capsule-adhered material. Fusobacterium or Bacteroides ASVs dominated LA, alongside probable opportunistic gut pathogens and other microbes. Moreover, we suggest that liver abscess size correlates with microbial community composition. These insights contribute to our understanding of factors impacting liver abscess microbial ecology and will be valuable in identifying antibiotic alternatives. They underscore the importance of exploring varied approaches to address LA while reducing reliance on in-feed antibiotics.},
}
@article {pmid38373396,
year = {2024},
author = {Jaber, D and Younes, N and Khalil, E and Albsoul-Younes, A and Zawiah, M and Al-Bakri, AG},
title = {Studying Microbial Ecology of Diabetic Foot Infections: Significance of PCR Analysis for Prudent Antimicrobial Stewardship.},
journal = {The international journal of lower extremity wounds},
volume = {},
number = {},
pages = {15347346241230288},
doi = {10.1177/15347346241230288},
pmid = {38373396},
issn = {1552-6941},
abstract = {This study presents a comprehensive investigation into the microbial ecology of diabetic foot infections (DFIs), using molecular-polymerase chain reaction (PCR) analysis to accurately identify the causative agents. One hundred DFI patients were recruited and classified using the Depth Extent Phase and Associated Etiology (DEPA) score according to their severity. Results revealed polymicrobial infections in 75% of cases, predominantly featuring Staphylococcus epidermidis (83%) and Staphylococcus aureus (63%). Importantly, 20% of samples exhibited facultative anaerobes Bacteroides fragilis or Clostridium perfringens, exclusively in high DEPA score ulcers. Candida albicans coinfection was identified in 19.2% of cases, underscoring the need for mycological evaluation. Empirical antimicrobial therapy regimens were tailored to DEPA severity, yet our findings highlighted a potential gap in methicillin-resistant Staphylococcus aureus (MRSA) coverage. Despite an 88% prevalence of methicillin-resistant Staphylococci, vancomycin usage was suboptimal. This raises concerns about the underestimation of MRSA risk and the need for tailored antibiotic guidelines. Our study demonstrates the efficacy of molecular-PCR analysis in identifying diverse microbial communities in DFIs, influencing targeted antibiotic choices. The results advocate for refined antimicrobial guidelines, considering regional variations in microbial patterns and judiciously addressing multidrug-resistant strains. This research contributes crucial insights for optimizing DFIs management and helps the physicians to have a fast decision in selection the suitable antibiotic for each patient and to decrease the risk of bacterial resistance from the improper use of broad-spectrum empirical therapies.},
}
@article {pmid38370212,
year = {2024},
author = {Taherkhani, H and KavianFar, A and Aminnezhad, S and Lanjanian, H and Ahmadi, A and Azimzadeh, S and Masoudi-Nejad, A},
title = {Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome.},
journal = {Heliyon},
volume = {10},
number = {4},
pages = {e24775},
pmid = {38370212},
issn = {2405-8440},
abstract = {In microbiome studies, the diversity and types of microbes have been extensively explored; however, the significance of microbial ecology is equally paramount. The comprehension of metabolic interactions among the wide array of microorganisms in the lung microbiota is indispensable for understanding chronic pulmonary disease and for the development of potent treatments. In this investigation, metabolic networks were simulated, and ecological theory was employed to assess the diagnosis of COPD, subsequently suggesting innovative treatment strategies for COPD exacerbation. Lung sputum 16S rRNA paired-end data from 112 COPD patients were utilized, and a supervised machine-learning algorithm was applied to identify taxa associated with sex and mortality. Subsequently, an OTU table with Greengenes 99 % dataset was generated. Finally, the interactions between bacterial species were analyzed using a simulated metabolic network. A total of 1781 OTUs and 1740 bacteria at the genus level were identified. We employed an additional dataset to validate our analyses. Notably, among the more abundant genera, Pseudomonas was detected in females, while Lactobacillus was detected in males. Additionally, a decrease in bacterial diversity was observed during COPD exacerbation, and mortality was associated with the high abundance of the Staphylococcus and Pseudomonas genera. Moreover, an increase in Proteobacteria abundance was observed during COPD exacerbations. In contrast, COPD patients exhibited decreased levels of Firmicutes and Bacteroidetes. Significant connections between microbial ecology and bacterial diversity in COPD patients were discovered, highlighting the critical role of microbial ecology in the understanding of COPD. Through the simulation of metabolic interactions among bacteria, the observed dysbiosis in COPD was elucidated. Furthermore, the prominence of anaerobic bacteria in COPD patients was revealed to be influenced by parasitic relationships. These findings have the potential to contribute to improved clinical management strategies for COPD patients.},
}
@article {pmid38367872,
year = {2024},
author = {Tuts, L and Rasschaert, G and Heyndrickx, M and Boon, N and Eppinger, R and Becue, I},
title = {Detection of antibiotic residues in groundwater with a validated multiresidue UHPLC-MS/MS quantification method.},
journal = {Chemosphere},
volume = {352},
number = {},
pages = {141455},
doi = {10.1016/j.chemosphere.2024.141455},
pmid = {38367872},
issn = {1879-1298},
mesh = {Animals ; Humans ; Anti-Bacterial Agents/analysis ; Chromatography, High Pressure Liquid/methods ; Tandem Mass Spectrometry/methods ; Lactams, Macrocyclic/analysis ; Sulfanilamide/analysis ; Chloramphenicol/analysis ; Sulfonamides/analysis ; Lincosamides ; Pleuromutilins ; *Groundwater ; Macrolides/analysis ; *Drug Residues/analysis ; },
abstract = {The occurrence of antibiotic residues in the environment has received considerable attention because of their potential to select for bacterial resistance. The overuse of antibiotics in human medicine and animal production results in antibiotic residues entering the aquatic environment, but concentrations are currently not well determined. This study investigates the occurrence of antibiotics in groundwater in areas strongly related to agriculture and the antibiotic treatment of animals. A multiresidue method was validated according to EU Regulation 2021/808, to allow (semi-)quantitative analysis of 78 antibiotics from 10 different classes: β-lactams, sulfonamides, tetracyclines, lincosamides, amphenicols, (fluoro)quinolones, macrolides, pleuromutilins, ansamycins and diaminopyrimidines using ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). This method was used to test different storage conditions of these water samples during a stability study over a period of 2 weeks. Sulfonamides, lincosamides and pleuromutilins were the most stable. Degradation was most pronounced for β-lactam antibiotics, macrolides and ansamycins. To maintain stability, storage of samples at -18 °C is preferred. With the validated method, antibiotic residues were detected in groundwater, sampled from regions associated with intensive livestock farming in Flanders (Belgium). Out of 50 samples, 14% contained at least one residue. Concentrations were low, ranging from < LOD to 0.03 μg/L. Chloramphenicol, oxolinic acid, tetracycline and sulfonamides (sulfadiazine, sulfadoxine, sulfamethazine and sulfisoxazole) were detected. This study presents a new method for the quantification of antibiotic residues, which was applied to investigate the presence of antibiotic residues in groundwater in Flanders.},
}
@article {pmid38367838,
year = {2024},
author = {González-Feijoo, R and Santás-Miguel, V and Arenas-Lago, D and Álvarez-Rodríguez, E and Núñez-Delgado, A and Arias-Estévez, M and Pérez-Rodríguez, P},
title = {Effectiveness of cork and pine bark powders as biosorbents for potentially toxic elements present in aqueous solution.},
journal = {Environmental research},
volume = {250},
number = {},
pages = {118455},
doi = {10.1016/j.envres.2024.118455},
pmid = {38367838},
issn = {1096-0953},
mesh = {*Pinus/chemistry ; *Quercus/chemistry ; *Plant Bark/chemistry ; Adsorption ; *Water Pollutants, Chemical/analysis/chemistry ; Powders/chemistry ; Hydrogen-Ion Concentration ; Metals, Heavy/analysis/chemistry ; },
abstract = {Cork oak and pine bark, two of the most prolific byproducts of the European forestry sector, were assessed as biosorbents for eliminating potentially toxic elements (PTEs) from water-based solutions. Our research suggests that bioadsorption stands out as a viable and environmental eco-friendly technology, presenting a sustainable method for the extraction of PTEs from polluted water sources. This study aimed to evaluate and compare the efficiency of cork powder and pine bark powder as biosorbents. Specifically, the adsorption of Fe, Cu, Zn, Cd, Ni, Pb and Sn at equilibrium were studied through batch experiments by varying PTEs concentrations, pH, and ionic strength. Results from adsorption-desorption experiments demonstrate the remarkable capacity of both materials to retain the studied PTE. Cork powder and pine bark powder exhibited the maximum retention capacity for Fe and Cd, while they performed poorly for Pb and Sn, respectively. Nevertheless, pine bark showed a slightly lower retention capacity than cork. Increasing the pH resulted in cork showing the highest adsorption for Zn and the lowest for Sn, while for pine bark, Cd was the most adsorbed, and Sn was the least adsorbed, respectively. The highest adsorption of both materials occurred at pH 3.5-5, depending on the PTE tested. The ionic strength also influenced the adsorption of the various PTEs for both materials, with decreased adsorption as ionic strength increased. The findings suggest that both materials could be effective for capturing and eliminating the examined PTEs, albeit with different efficiencies. Remarkably, pine bark demonstrated superior adsorption capabilities, which were observed to vary based on the specific element and the experimental conditions. These findings contribute to elucidating the bio-adsorption potential of these natural materials, specifically their suitability in mitigating PTEs pollution, and favoring the recycling and revalorization of byproducts that might otherwise be considered residue.},
}
@article {pmid38367043,
year = {2024},
author = {LeBlanc, NR and Harrigian, FC},
title = {Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {44},
pmid = {38367043},
issn = {1432-184X},
support = {2038-22430-003-000-D//Agricultural Research Service/ ; },
mesh = {Soil/chemistry ; Soil Microbiology ; *Composting ; *Fusarium ; Bacteria/genetics ; Sequence Analysis ; },
abstract = {The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.},
}
@article {pmid38366262,
year = {2024},
author = {Wang, J and Zhu, YG and Tiedje, JM and Ge, Y},
title = {Global biogeography and ecological implications of cobamide-producing prokaryotes.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38366262},
issn = {1751-7370},
support = {42307162//National Natural Science Foundation of China/ ; 2019QZKK0308//Second Tibetan Plateau Scientific Expedition and Research Program/ ; DBI-1759892//US National Science Foundation/ ; //Institute for Cyber-Enabled Research at Michigan State University/ ; },
mesh = {*Cobamides ; Metagenome ; *Microbiota ; Soil ; },
abstract = {Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.},
}
@article {pmid38365962,
year = {2024},
author = {Paes da Costa, D and das Graças Espíndola da Silva, T and Sérgio Ferreira Araujo, A and Prudêncio de Araujo Pereira, A and William Mendes, L and Dos Santos Borges, W and Felix da França, R and Alberto Fragoso de Souza, C and Alves da Silva, B and Oliveira Silva, R and Valente de Medeiros, E},
title = {Soil fertility impact on recruitment and diversity of the soil microbiome in sub-humid tropical pastures in Northeastern Brazil.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {3919},
pmid = {38365962},
issn = {2045-2322},
mesh = {*Soil ; RNA, Ribosomal, 16S/genetics/metabolism ; Brazil ; Bacteria ; *Microbiota/genetics ; Soil Microbiology ; },
abstract = {Soil fertility is key point to pastures systems and drives the microbial communities and their functionality. Therefore, an understanding of the interaction between soil fertility and microbial communities can increase our ability to manage pasturelands and maintain their soil functioning and productivity. This study probed the influence of soil fertility on microbial communities in tropical pastures in Brazil. Soil samples, gathered from the top 20 cm of twelve distinct areas with diverse fertility levels, were analyzed via 16S rRNA sequencing. The soils were subsequently classified into two categories, namely high fertility (HF) and low fertility (LF), using the K-Means clustering. The random forest analysis revealed that high fertility (HF) soils had more bacterial diversity, predominantly Proteobacteria, Nitrospira, Chloroflexi, and Bacteroidetes, while Acidobacteria increased in low fertility (LF) soils. High fertility (HF) soils exhibited more complex network interactions and an enrichment of nitrogen-cycling bacterial groups. Additionally, functional annotation based on 16S rRNA varied between clusters. Microbial groups in HF soil demonstrated enhanced functions such as nitrate reduction, aerobic ammonia oxidation, and aromatic compound degradation. In contrast, in the LF soil, the predominant processes were ureolysis, cellulolysis, methanol oxidation, and methanotrophy. Our findings expand our knowledge about how soil fertility drives bacterial communities in pastures.},
}
@article {pmid38365802,
year = {2024},
author = {Fenibo, EO and Nkuna, R and Matambo, T},
title = {Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {3866},
pmid = {38365802},
issn = {2045-2322},
mesh = {RNA, Ribosomal, 16S/genetics/metabolism ; Niger ; *Soil Pollutants/metabolism ; Soil Microbiology ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Microbiota/genetics ; *Petroleum/metabolism ; Hydrocarbons/metabolism ; Soil/chemistry ; DNA/metabolism ; },
abstract = {Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.},
}
@article {pmid38365260,
year = {2024},
author = {Díez-Vives, C and Riesgo, A},
title = {High compositional and functional similarity in the microbiome of deep-sea sponges.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365260},
issn = {1751-7370},
support = {100010434//'la Caixa' Foundation/ ; PID2019-105769GB-I00//Spanish Ministry of Science and Innovation/ ; 796011//Marie Sk&#x142;odowska-Curie Individual Fellowships Grant Agreement/ ; },
mesh = {Animals ; Bacteria/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; *Microbiota ; Water/metabolism ; *Porifera ; },
abstract = {Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.},
}
@article {pmid38365254,
year = {2024},
author = {Layoun, P and López-Pérez, M and Haro-Moreno, JM and Haber, M and Thrash, JC and Henson, MW and Kavagutti, VS and Ghai, R and Salcher, MM},
title = {Flexible genomic island conservation across freshwater and marine Methylophilaceae.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365254},
issn = {1751-7370},
support = {19-23469S//Czech Science Foundation/ ; KA131//University of South Bohemia, Faculty of Science, Department of Ecosystem Biology/ ; 116/2019/P//Grant Agency of the University of South Bohemia in &#x10c;esk&#xe9; Bud&#x11b;jovice/ ; },
mesh = {*Methylophilaceae ; Genome, Bacterial ; Genomic Islands ; Phylogeny ; Lakes ; },
abstract = {The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater "Ca. Methylopumilus" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 "Ca. Methylopumilus" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.},
}
@article {pmid38365250,
year = {2024},
author = {Sher, AW and Aufrecht, JA and Herrera, D and Zimmerman, AE and Kim, YM and Munoz, N and Trejo, JB and Paurus, VL and Cliff, JB and Hu, D and Chrisler, WB and Tournay, RJ and Gomez-Rivas, E and Orr, G and Ahkami, AH and Doty, SL},
title = {Dynamic nitrogen fixation in an aerobic endophyte of Populus.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365250},
issn = {1751-7370},
support = {#50774//Environmental Molecular Sciences Laboratory/ ; //United States Department of Energy Office of Science/ ; DE-SC0021137//Office of Biological and Environmental Research/ ; },
mesh = {*Nitrogen Fixation/physiology ; *Populus/genetics/metabolism ; Endophytes/genetics ; Oxidoreductases/genetics ; In Situ Hybridization, Fluorescence ; Nitrogenase/genetics/metabolism ; Nitrogen ; },
abstract = {Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.},
}
@article {pmid38365248,
year = {2024},
author = {Gottel, NR and Hill, MS and Neal, MJ and Allard, SM and Zengler, K and Gilbert, JA},
title = {Biocontrol in built environments to reduce pathogen exposure and infection risk.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365248},
issn = {1751-7370},
support = {UCSD 2223669//NSF ENG-EPSRC EFRI ELiS/ ; 80NSSC19K1604//NASA ROSBIO/ ; },
mesh = {Humans ; *Microbiota ; Bacteria/genetics ; *Bacillus ; Anti-Bacterial Agents ; Built Environment ; },
abstract = {The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.},
}
@article {pmid38365244,
year = {2024},
author = {Yu, XA and McLean, C and Hehemann, JH and Angeles-Albores, D and Wu, F and Muszyński, A and Corzett, CH and Azadi, P and Kujawinski, EB and Alm, EJ and Polz, MF},
title = {Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365244},
issn = {1751-7370},
support = {DE-SC0008743//United States Department of Energy/ ; DE-SC0015662//United States Department of Energy/ ; },
mesh = {Bacteria/genetics ; *Seaweed ; *Microbiota ; },
abstract = {Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.},
}
@article {pmid38365240,
year = {2024},
author = {Shen, L and Liu, Y and Chen, L and Lei, T and Ren, P and Ji, M and Song, W and Lin, H and Su, W and Wang, S and Rooman, M and Pucci, F},
title = {Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365240},
issn = {1751-7370},
support = {U21A20176//National Natural Science Foundation of China/ ; 2019QZKK0503//Second Tibetan Plateau Scientific Expedition and Research/ ; 92251304//National Natural Science Foundation of China/ ; swzy202008//Open Project Fund of Anhui Provincial Key Laboratory of Protection and Utilization of Important Biological Resources/ ; 2022AH010012//Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics/ ; },
mesh = {*Exiguobacterium ; *Extremophiles ; Genomics ; Phylogeny ; Proteins ; },
abstract = {Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.},
}
@article {pmid38365232,
year = {2024},
author = {Zheng, Y and Wang, B and Gao, P and Yang, Y and Xu, B and Su, X and Ning, D and Tao, Q and Li, Q and Zhao, F and Wang, D and Zhang, Y and Li, M and Winkler, MH and Ingalls, AE and Zhou, J and Zhang, C and Stahl, DA and Jiang, J and Martens-Habbena, W and Qin, W},
title = {Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365232},
issn = {1751-7370},
support = {548565//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; //Florida Agricultural Experiment Station Hatch project/ ; //National Natural Science Foundation of China/ ; 2020Z01//Shanghai Sheshan National Geophysical Observatory/ ; 20200925173954005//Stable Support Plan Program of Shenzhen Natural Science Fund/ ; ZDSYS201802081843490//Southern University of Science and Technology/ ; //Shenzhen Key Laboratory of Marine Archaea Geo-Omics/ ; 2020KCXTD023//the Innovation Team Project of Universities/ ; //National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities of China/ ; 92051114//National Natural Science Foundation of China/ ; },
mesh = {*Archaea ; *Ammonia/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.},
}
@article {pmid38363394,
year = {2024},
author = {Duan, Y and Li, Y and Zhao, J and Zhang, J and Luo, C and Jia, R and Liu, X},
title = {Changes in Microbial Composition During the Succession of Biological Soil Crusts in Alpine Hulun Buir Sandy Land, China.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {43},
pmid = {38363394},
issn = {1432-184X},
mesh = {Ecosystem ; Soil ; Sand ; Soil Microbiology ; *Lichens ; *Cyanobacteria ; *Microbiota ; Nitrogen ; Phosphorus ; China ; },
abstract = {Biological soil crusts (biocrusts) are considered "desert ecosystem engineers" because they play a vital role in the restoration and stability maintenance of deserts, including those cold sandy land ecosystems at high latitudes, which are especially understudied. Microorganisms participate in the formation and succession of biocrusts, contributing to soil properties' improvement and the stability of soil aggregates, and thus vegetation development. Accordingly, understanding the composition and successional characteristics of microorganisms is a prerequisite for analyzing the ecological functions of biocrusts and related applications. Here, the Hulun Buir Sandy Land region in northeastern China-lying at the highest latitude of any sandy land in the country-was selected for study. Through a field investigation and next-generation sequencing (Illumina MiSeq PE300 Platform), our goal was to assess the shifts in diversity and community composition of soil bacteria and fungi across different stages during the succession of biocrusts in this region, and to uncover the main factors involved in shaping their soil microbial community. The results revealed that the nutrient enrichment capacity of biocrusts for available nitrogen, total nitrogen, total phosphorus, total content of water-soluble salt, available potassium, soil organic matter, and available phosphorus was progressively enhanced by the succession of cyanobacterial crusts to lichen crusts and then to moss crusts. In tandem, soil bacterial diversity increased as biocrust succession proceeded but fungal diversity decreased. A total of 32 bacterial phyla and 11 fungal phyla were identified, these also known to occur in other desert ecosystems. Among those taxa, the relative abundance of Proteobacteria and Cyanobacteria significantly increased and decreased, respectively, along the cyanobacterial crust-lichen-moss crust successional gradient. However, for Actinobacteria, Chloroflexi, and Acidobacteria their changed relative abundance was significantly hump-shaped, increasing in the shift from cyanobacterial crust to lichen crust, and then decreasing as lichen crust shifted to moss crust. In this process, the improved soil properties effectively enhanced soil bacterial and fungal community composition. Altogether, these findings broaden our understanding about how soil microbial properties can change during the succession of biocrusts in high-latitude, cold sandy land ecosystems.},
}
@article {pmid38362164,
year = {2024},
author = {Pasciullo Boychuck, S and Brenner, LJ and Gagorik, CN and Schamel, JT and Baker, S and Tran, E and vonHoldt, BM and Koepfli, KP and Maldonado, JE and DeCandia, AL},
title = {The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine-scale differentiation across host species and island populations.},
journal = {Ecology and evolution},
volume = {14},
number = {2},
pages = {e11017},
pmid = {38362164},
issn = {2045-7758},
abstract = {California's Channel Islands are home to two endemic mammalian carnivores: island foxes (Urocyon littoralis) and island spotted skunks (Spilogale gracilis amphiala). Although it is rare for two insular terrestrial carnivores to coexist, these known competitors persist on both Santa Cruz Island and Santa Rosa Island. We hypothesized that examination of their gut microbial communities would provide insight into the factors that enable this coexistence, as microbial symbionts often reflect host evolutionary history and contemporary ecology. Using rectal swabs collected from island foxes and island spotted skunks sampled across both islands, we generated 16S rRNA amplicon sequencing data to characterize their gut microbiomes. While island foxes and island spotted skunks both harbored the core mammalian microbiome, host species explained the largest proportion of variation in the dataset. We further identified intraspecific variation between island populations, with greater differentiation observed between more specialist island spotted skunk populations compared to more generalist island fox populations. This pattern may reflect differences in resource utilization following fine-scale niche differentiation. It may further reflect evolutionary differences regarding the timing of intraspecific separation. Considered together, this study contributes to the growing catalog of wildlife microbiome studies, with important implications for understanding how eco-evolutionary processes enable the coexistence of terrestrial carnivores-and their microbiomes-in island environments.},
}
@article {pmid38361649,
year = {2024},
author = {Parks, M and Lee, JS and Camua, K and Hollender, E},
title = {Turtle species and ecology drive carapace microbiome diversity in three seasonally interconnected wetland habitats.},
journal = {Access microbiology},
volume = {6},
number = {1},
pages = {},
pmid = {38361649},
issn = {2516-8290},
abstract = {Different species of freshwater turtles exhibit primary behaviours ranging from aerial basking to benthic bottom-walking, cycle between wet and dry conditions at different time intervals, and undertake short-distance overland movements between aquatic habitats. These behaviours in turn may impact the accumulation of microbes on external shell surfaces of turtles and provide novel niches for differentiation of microbial communities. We assessed microbial diversity using 16S and 18S rRNA metabarcoding on carapace surfaces of six species of freshwater turtles residing in three adjacent and seasonally interconnected wetland habitats in southeast Oklahoma (United States). Communities were highly diverse, with nearly 4200 prokaryotic and 500 micro-eukaryotic amplicon sequence variants recovered, and included taxa previously reported as common or differentially abundant on turtle shells. The 16S rRNA alpha diversity tended to be highest for two species of benthic turtles, while 18S rRNA alpha diversity was highest for two basking and one shallow-water benthic species. Beta diversity of communities was more strongly differentiated by turtle species than by collection site, and ordination patterns were largely reflective of turtle species' primary habits (i.e. benthic, basking, or benthic-basking). Our data support that freshwater turtles could play a role in microbial ecology and evolution in freshwater habitats and warrant additional exploration including in areas with high native turtle diversity and inter-habitat turtle movements.},
}
@article {pmid38357595,
year = {2024},
author = {Fickling, NW and Abbott, CA and Brame, JE and Cando-Dumancela, C and Liddicoat, C and Robinson, JM and Breed, MF},
title = {Light-dark cycles may influence in situ soil bacterial networks and diurnally-sensitive taxa.},
journal = {Ecology and evolution},
volume = {14},
number = {2},
pages = {e11018},
pmid = {38357595},
issn = {2045-7758},
abstract = {Soil bacterial taxa have important functional roles in ecosystems (e.g. nutrient cycling, soil formation, plant health). Many factors influence their assembly and regulation, with land cover types (e.g. open woodlands, grasslands), land use types (e.g. nature reserves, urban green space) and plant-soil feedbacks being well-studied factors. However, changes in soil bacterial communities in situ over light-dark cycles have received little attention, despite many plants and some bacteria having endogenous circadian rhythms that could influence soil bacterial communities. We sampled surface soils in situ across 24-h light-dark cycles (at 00:00, 06:00, 12:00, 18:00) at two land cover types (remnant vegetation vs. cleared, grassy areas) and applied 16S rRNA amplicon sequencing to investigate changes in bacterial communities. We show that land cover type strongly affected soil bacterial diversity, with soils under native vegetation expressing 15.4%-16.4% lower alpha diversity but 4.9%-10.6% greater heterogeneity than soils under cleared vegetation. In addition, we report time-dependent and site-specific changes in bacterial network complexity and between 598-922 ASVs showing significant changes in relative abundance across times. Native site node degree (bacterial interactions) at the phylum level was 16.0% higher in the early morning than in the afternoon/evening. Our results demonstrate for the first time that light-dark cycles have subtle yet important effects on soil bacterial communities in situ and that land cover influences these dynamics. We provide a new view of soil microbial ecology and suggest that future studies should consider the time of day when sampling soil bacteria.},
}
@article {pmid38356049,
year = {2024},
author = {van Bergeijk, DA and Augustijn, HE and Elsayed, SS and Willemse, J and Carrión, VJ and Du, C and Urem, M and Grigoreva, LV and Cheprasov, MY and Grigoriev, S and Jansen, H and Wintermans, B and Budding, AE and Spaink, HP and Medema, MH and van Wezel, GP},
title = {Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000-year-old mammoth.},
journal = {Environmental microbiology},
volume = {26},
number = {2},
pages = {e16589},
doi = {10.1111/1462-2920.16589},
pmid = {38356049},
issn = {1462-2920},
support = {//Universiteit Leiden/ ; 101055020-COMMUNITY//European Research Council/International ; 948770-DECIPHER//European Research Council/International ; },
mesh = {Animals ; Phylogeny ; *Mammoths ; Genomics ; *Streptomyces/genetics ; *Actinomycetales ; Feces ; },
abstract = {Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.},
}
@article {pmid38356037,
year = {2024},
author = {Xian, WD and Ding, J and Chen, J and Qu, W and Cao, P and Tang, C and Liu, X and Zhang, Y and Li, JL and Wang, P and Li, WJ and Wang, J},
title = {Distinct Assembly Processes Structure Planktonic Bacterial Communities Among Near- and Offshore Ecosystems in the Yangtze River Estuary.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {42},
pmid = {38356037},
issn = {1432-184X},
mesh = {*Ecosystem ; *Rivers/microbiology ; Plankton/genetics ; Estuaries ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Water ; },
abstract = {The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.},
}
@article {pmid38354254,
year = {2024},
author = {Doré, H and Eisenberg, AR and Junkins, EN and Leventhal, GE and Ganesh, A and Cordero, OX and Paul, BG and Valentine, DL and O'Malley, MA and Wilbanks, EG},
title = {Targeted hypermutation of putative antigen sensors in multicellular bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {9},
pages = {e2316469121},
pmid = {38354254},
issn = {1091-6490},
support = {W911NF-19-2-0026//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; W911NF-19-D-0001//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; 508543//Joint Genome Institute (JGI)/ ; },
mesh = {*Bacteria/genetics ; Archaea/genetics ; Metagenome ; Retroelements ; *Bacteriophages/genetics ; },
abstract = {Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remain elusive. We find that 82% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci capable of generating 10[282] different combinations of target proteins. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1's DGR target genes are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In Thiohalocapsa PB-PSB1 and other bacteria hosting this lineage of cellular DGRs, the diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified targets act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia, though this remains to be experimentally tested. These findings could have implications for understanding the evolution of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans.},
}
@article {pmid38351424,
year = {2024},
author = {Morelle, J and Bastos, A and Frankenbach, S and Frommlet, JC and Campbell, DA and Lavaud, J and Serôdio, J},
title = {The Photoprotective Behavior of a Motile Benthic Diatom as Elucidated from the Interplay Between Cell Motility and Physiological Responses to a Light Microgradient Using a Novel Experimental Setup.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {40},
pmid = {38351424},
issn = {1432-184X},
mesh = {*Diatoms/physiology ; Photosynthesis ; Chlorophyll ; Light ; Cell Movement ; },
abstract = {It has long been hypothesized that benthic motile pennate diatoms use phototaxis to optimize photosynthesis and minimize photoinhibitory damage by adjusting their position within vertical light gradients in coastal benthic sediments. However, experimental evidence to test this hypothesis remains inconclusive, mainly due to methodological difficulties in studying cell behavior and photosynthesis over realistic spatial microscale gradients of irradiance and cell position. In this study, a novel experimental approach was developed and used to test the hypothesis of photosynthesis optimization through motility, based on the combination of single-cell in vivo chlorophyll fluorometry and microfluidic chips. The approach allows the concurrent study of behavior and photosynthetic activity of individual cells of the epipelic diatom species Craspedostauros britannicus exposed to a light microgradient of realistic dimensions, simulating the irradiance and distance scales of light microgradients in benthic sediments. Following exposure to light, (i) cells explored their light environment before initiating light-directed motility; (ii) cells used motility to lower their light dose, when exposed to the highest light intensities; and (iii) motility was combined with reversible non-photochemical quenching, to allow cells to avoid photoinhibition. The results of this proof-of-concept study not only strongly support the photoprotective nature of photobehavior in the studied species but also revealed considerable variability in how individual cells reacted to a light microgradient. The experimental setup can be readily applied to study motility and photosynthetic light responses of other diatom species or natural assemblages, as well as other photoautotrophic motile microorganisms, broadening the toolset for experimental microbial ecology research.},
}
@article {pmid38351266,
year = {2024},
author = {Arbulu, S and Kjos, M},
title = {Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {41},
pmid = {38351266},
issn = {1432-184X},
support = {101029099//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 296906//Norges Forskningsr&#xe5;d/ ; },
mesh = {*Bacteriocins/pharmacology ; Biofilms ; Bacteria ; Peptides ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.},
}
@article {pmid38348184,
year = {2024},
author = {Wang, W and Dong, Y and Guo, W and Zhang, X and Degen, AA and Bi, S and Ding, L and Chen, X and Long, R},
title = {Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1301258},
pmid = {38348184},
issn = {1664-302X},
abstract = {Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.},
}
@article {pmid38346660,
year = {2024},
author = {Durán-Viseras, A and Lindner, BG and Hatt, JK and Lai, A and Wallace, R and Ginn, O and Brown, J and Konstantinidis, KT},
title = {Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities.},
journal = {The Science of the total environment},
volume = {920},
number = {},
pages = {170772},
doi = {10.1016/j.scitotenv.2024.170772},
pmid = {38346660},
issn = {1879-1026},
mesh = {Humans ; Animals ; Poultry ; Soil ; Metagenome ; Chickens ; Water ; *Microbiota ; *Anti-Infective Agents ; Anti-Bacterial Agents ; Metagenomics ; },
abstract = {In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.},
}
@article {pmid38345372,
year = {2024},
author = {Campbell, BC and Greenfield, P and Barnhart, EP and Gong, S and Midgley, DJ and Paulsen, IT and George, SC},
title = {Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams.},
journal = {mBio},
volume = {15},
number = {3},
pages = {e0173523},
pmid = {38345372},
issn = {2150-7511},
mesh = {*Coal/microbiology ; Carbon/metabolism ; Methane/metabolism ; *Deltaproteobacteria/metabolism ; },
abstract = {Biogenic methane in subsurface coal seam environments is produced by diverse consortia of microbes. Although this methane is useful for global energy security, it remains unclear which microbes can liberate carbon from the coal. Most of this carbon is relatively resistant to biodegradation, as it is contained within aromatic rings. Thus, to explore for coal-degrading taxa in the subsurface, this study reconstructed relevant metagenome-assembled genomes (MAGs) from coal seams by using a key genomic marker for the anaerobic degradation of monoaromatic compounds as a guide: the benzoyl-CoA reductase gene (bcrABCD). Three MAGs were identified with this genetic potential. The first represented a novel taxon from the Krumholzibacteriota phylum, which this study is the first to describe. This Krumholzibacteriota MAG contained a full set of genes for benzoyl-CoA dearomatization, in addition to other genes for anaerobic catabolism of monoaromatics. Analysis of Krumholzibacteriota MAGs from other environments revealed that this genetic potential may be common, and thus, Krumholzibacteriota may be important organisms for the liberation of recalcitrant carbon in a broad range of environments. Moreover, the assembly and characterization of two Syntrophorhabdus aromaticivorans MAGs from different continents and a Syntrophaceae sp. MAG implicate the Deltaproteobacteria class in coal seam monoaromatic degradation. Each of these taxa are potential rate-limiting organisms for subsurface coal-to-methane biodegradation. Their description here provides some understanding of their function within the coal seam microbiome and will help inform future efforts in coal bed methane stimulation, anoxic bioremediation of organic pollutants, and assessments of anoxic, subsurface carbon cycling and emissions.IMPORTANCESubsurface coal seams are highly anoxic, oligotrophic environments, where the main source of carbon is "locked away" within aromatic rings. Despite these challenges, many coal seams accumulate biogenic methane, implying that the coal seam microbiome is "unlocking" this carbon source in situ. For over two decades, researchers have endeavored to understand which organisms perform these processes. This study provides the first descriptions of organisms with this genetic potential from the coal seam environment. Here, we report metagenomic insights into carbon liberation from aromatic molecules and the degradation pathways involved and describe a Krumholzibacteriota, two Syntrophorhabdus aromaticivorans, and a Syntrophaceae MAG that contain this genetic potential. This is also the first time that the Krumholzibacteriota phylum has been implicated in anaerobic dearomatization of aromatic hydrocarbons. This potential is identified here in numerous MAGs from other terrestrial and marine subsurface habitats, implicating the Krumholzibacteriota in carbon-cycling processes across a broad range of environments.},
}
@article {pmid38344937,
year = {2024},
author = {Ugolini, GS and Wang, M and Secchi, E and Pioli, R and Ackermann, M and Stocker, R},
title = {Microfluidic approaches in microbial ecology.},
journal = {Lab on a chip},
volume = {24},
number = {5},
pages = {1394-1418},
pmid = {38344937},
issn = {1473-0189},
mesh = {Animals ; *Microfluidics/methods ; *Ecology ; },
abstract = {Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.},
}
@article {pmid38344169,
year = {2024},
author = {Pertierra, LR and Varliero, G and Barbosa, A and Biersma, EM and Convey, P and Chown, SL and Cowan, D and De Los Rios, A and Escribano-Alvarez, P and Fontaneto, D and Fraser, C and Harris, M and Hughes, K and Griffiths, H and le Roux, P and Liu, XP and Lynch, H and Majewska, R and Martinez, PA and Molina-Montenegro, M and Olalla-Tarraga, MA and Peck, L and Quesada, A and Ronquillo, C and Ropert-Coudert, Y and Sancho, L and Terauds, A and Vianna, J and Wilmotte, A and Hortal, J and Greve, M},
title = {TerrANTALife 1.0 Biodiversity data checklist of known Antarctic terrestrial and freshwater life forms.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e106199},
pmid = {38344169},
issn = {1314-2828},
abstract = {BACKGROUND: Incomplete species inventories for Antarctica represent a key challenge for comprehensive ecological research and conservation in the region. Additionally, data required to understand population dynamics, rates of evolution, spatial ranges, functional traits, physiological tolerances and species interactions, all of which are fundamental to disentangle the different functional elements of Antarctic biodiversity, are mostly missing. However, much of the fauna, flora and microbiota in the emerged ice-free land of the continent have an uncertain presence and/or unresolved status, with entire biodiversity compendia of prokaryotic groups (e.g. bacteria) being missing. All the available biodiversity information requires consolidation, cross-validation, re-assessment and steady systematic inclusion in order to create a robust catalogue of biodiversity for the continent.<br><br>NEW INFORMATION: We compiled, completed and revised eukaryotic species inventories present in terrestrial and freshwater ecosystems in Antarctica in a new living database: terrANTALife (version 1.0). The database includes the first integration in a compendium for many groups of eukaryotic microorganisms. We also introduce a first catalogue of amplicon sequence variants (ASVs) of prokaryotic biodiversity. Available compendia and literature to date were searched for Antarctic terrestrial and freshwater species, integrated, taxonomically harmonised and curated by experts to create comprehensive checklists of Antarctic organisms. The final inventories comprises 470 animal species (including vertebrates, free-living invertebrates and parasites), 306 plants (including all Viridiplantae: embryophytes and green algae), 997 fungal species and 434 protists (sensu lato). We also provide a first account for many groups of microorganisms, including non-lichenised fungi and multiple groups of eukaryotic unicellular species (Stramenophila, Alveolata and Rhizaria (SAR), Chromists and Amoeba), jointly referred to as "protists". In addition, we identify 1753 bacterial (obtained from 348117 ASVs) and 34 archaeal genera (from 1848 ASVs), as well as, at least, 14 virus families. We formulate a basic tree of life in Antarctica with the main lineages listed in the region and their "known-accepted-species" numbers.},
}
@article {pmid38343862,
year = {2024},
author = {Lin, H and Chen, Y and Abror, G and Price, M and Morris, A and Sun, J and Palella, F and Chew, KW and Brown, TT and Rinaldo, CR and Peddada, SD},
title = {The effect of sexual behavior on HIV-1 seroconversion is mediated by the gut microbiome and proinflammatory cytokines.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {38343862},
issn = {2693-5015},
support = {S10 OD023402/OD/NIH HHS/United States ; U01 HL146208/HL/NHLBI NIH HHS/United States ; ZIA ES103390/ImNIH/Intramural NIH HHS/United States ; },
abstract = {The association between HIV-1 seroconversion and gut dysbiosis is well documented, and its association with sexual activity is also widely recognized. However, it is not known whether the gut dysbiosis mediates the effects of high-risk sexual behavior on HIV-1 seroconversion. In this report we focused on men who engaged in high-risk sexual behavior where they had receptive anal intercourse with multiple men. We demonstrate that proinflammatory cytokines, sCD14 and sCD163, and gut microbiota mediate the effects of this high-risk sexual behavior on subsequent HIV seroconversion. We discovered changes in the gut microbial ecology, prior to seroconversion, both in terms of the composition as well as inter-relationships among the commensal species. Furthermore, these changes correlate with future HIV seroconversion. Specifically, as the number of sexual partners increased, we discovered in a "dose-response" manner, a decrease in the abundance of commensal and short-chain fatty acid-producing species, A. muciniphila, B. caccae, B. fragilis, B. uniformis, Bacteroides spp., Butyricimonas spp., and Odoribacter spp, and an increase in proinflammatory species Dehalobacterium spp. and Methanobrevibacter spp. These changes were also observed among subsequent HIV seroconverters. Interestingly, we also discovered a reduction in correlations among these commensal and short-chain fatty acid producing bacteria in a "dose-response" manner with the number of sexual partners. Our mediation analysis not only provides a conceptual model for the disease process but also provides clues for future clinical interventions that will manipulate the gut microbiota to treat high-risk subjects to prevent HIV seroconversion.},
}
@article {pmid38338599,
year = {2024},
author = {Bodie, AR and Wythe, LA and Dittoe, DK and Rothrock, MJ and O'Bryan, CA and Ricke, SC},
title = {Alternative Additives for Organic and Natural Ready-to-Eat Meats to Control Spoilage and Maintain Shelf Life: Current Perspectives in the United States.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
pmid = {38338599},
issn = {2304-8158},
abstract = {Food additives are employed in the food industry to enhance the color, smell, and taste of foods, increase nutritional value, boost processing efficiency, and extend shelf life. Consumers are beginning to prioritize food ingredients that they perceive as supporting a healthy lifestyle, emphasizing ingredients they deem acceptable as alternative or "clean-label" ingredients. Ready-to-eat (RTE) meat products can be contaminated with pathogens and spoilage microorganisms after the cooking step, contributing to food spoilage losses and increasing the risk to consumers for foodborne illnesses. More recently, consumers have advocated for no artificial additives or preservatives, which has led to a search for antimicrobials that meet these demands but do not lessen the safety or quality of RTE meats. Lactates and diacetates are used almost universally to extend the shelf life of RTE meats by reducing spoilage organisms and preventing the outgrowth of the foodborne pathogen Listeria monocytogenes. These antimicrobials applied to RTE meats tend to be broad-spectrum in their activities, thus affecting overall microbial ecology. It is to the food processing industry's advantage to target spoilage organisms and pathogens specifically.},
}
@article {pmid38337180,
year = {2024},
author = {Finn, DR},
title = {A metagenomic alpha-diversity index for microbial functional biodiversity.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {3},
pages = {},
pmid = {38337180},
issn = {1574-6941},
support = {522758166//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Metagenome ; *Biodiversity ; RNA, Ribosomal ; Ecosystem ; },
abstract = {Alpha-diversity indices are an essential tool for describing and comparing biodiversity. Microbial ecologists apply indices originally intended for, or adopted by, macroecology to address questions relating to taxonomy (conserved marker) and function (metagenome-based data). In this Perspective piece, I begin by discussing the nature and mathematical quirks important for interpreting routinely employed alpha-diversity indices. Secondly, I propose a metagenomic alpha-diversity index (MD) that measures the (dis)similarity of protein-encoding genes within a community. MD has defined limits, whereby a community comprised mostly of similar, poorly diverse protein-encoding genes pulls the index to the lower limit, while a community rich in divergent homologs and unique genes drives it toward the upper limit. With data acquired from an in silico and three in situ metagenome studies, I derive MD and typical alpha-diversity indices applied to taxonomic (ribosomal rRNA) and functional (all protein-encoding) genes, and discuss their relationships with each other. Not all alpha-diversity indices detect biological trends, and taxonomic does not necessarily follow functional biodiversity. Throughout, I explain that protein Richness and MD provide complementary and easily interpreted information, while probability-based indices do not. Finally, considerations regarding the unique nature of microbial metagenomic data and its relevance for describing functional biodiversity are discussed.},
}
@article {pmid38332550,
year = {2024},
author = {Louw, NL and Wolfe, BE and Uricchio, LH},
title = {A phylogenomic perspective on interspecific competition.},
journal = {Ecology letters},
volume = {27},
number = {2},
pages = {e14359},
doi = {10.1111/ele.14359},
pmid = {38332550},
issn = {1461-0248},
support = {1942063//National Science Foundation/ ; 2021362//National Science Foundation/ ; },
mesh = {Phylogeny ; *Genome ; *Genomics ; Biological Evolution ; Phenotype ; },
abstract = {Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbour trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harbouring phylogenetic signal and demonstrate its application through a proof-of-principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions.},
}
@article {pmid38332365,
year = {2024},
author = {Amaral, RR and Love, RM and Braga, T and Souza Côrtes, MI and Rachid, CTCC and Rôças, IN and Siqueira, JF},
title = {Impact of root canal preparation using two single-file systems on the intra-radicular microbiome of teeth with primary apical periodontitis.},
journal = {Clinical oral investigations},
volume = {28},
number = {2},
pages = {139},
pmid = {38332365},
issn = {1436-3771},
mesh = {Humans ; *Root Canal Preparation ; Dental Pulp Cavity/microbiology ; Root Canal Therapy ; *Periapical Periodontitis/microbiology ; Bacteria ; },
abstract = {OBJECTIVES: This study aimed to describe the effects of two single-file systems on the diversity of the endodontic microbiome of teeth with primary asymptomatic apical periodontitis.<br><br>MATERIALS AND METHODS: The root canals from single-rooted teeth with apical periodontitis were prepared using either the Reciproc Blue (RB) or the XP-endo Shaper (XPS) instrument system. The latter was followed by a supplementary step with the XP-endo Finisher (XPF) instrument. For irrigation, 5.25% sodium hypochlorite was used. Root canal samples were taken at the baseline (S1), after preparation (S2), and after the supplementary step (S3). DNA was extracted and subjected to high-throughput sequencing using the MiSeq Illumina platform.<br><br>RESULTS: Samples from 10 teeth from the RB and 7 from the XPS group were subjected to DNA sequencing. Initial samples differed significantly from post-preparation samples in bacterial diversity, with no significant difference when comparing the two instrument systems. The most dominant phyla in S2 were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria. The same phyla were found to dominate baseline samples and samples taken after using XPF, but with differences in the ranking of the most dominant ones. At the genus level, the most dominant genera identified after RB instrumentation were Bacteroidaceae [G-1], Fusobacterium, and Staphylococcus, while the most dominant genera after XPS instrumentation were Fusobacterium and Porphyromonas. These genera were also dominant in the initial samples.<br><br>CONCLUSIONS: Both treatment protocols had measurable effects on the root canal microbial diversity, with no significant differences between them. Most of the dominant taxa involved in the primary infection and probably in the aetiology of apical periodontitis were eliminated or substantially reduced.<br><br>CLINICAL RELEVANCE: The most dominant taxa that persisted after instrumentation were Fusobacterium, Porphyromonas, Staphylococcus, and Bacteroidaceae [G-1].},
}
@article {pmid38332161,
year = {2024},
author = {McDougall, FK and Speight, N and Funnell, O and Boardman, WSJ and Power, ML},
title = {Dynamics of Antimicrobial Resistance Carriage in Koalas (Phascolarctos Cinereus) and Pteropid Bats (Pteropus Poliocephalus) Before, During and After Wildfires.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {39},
pmid = {38332161},
issn = {1432-184X},
mesh = {Humans ; Animals ; *Chiroptera ; *Wildfires ; *Phascolarctidae ; Anti-Bacterial Agents/pharmacology ; Australia ; Drug Resistance, Bacterial/genetics ; Animals, Wild ; },
abstract = {In the 2019-2020 summer, wildfires decimated the Australian bush environment and impacted wildlife species, including koalas (Phascolarctos cinereus) and grey headed flying fox pups (Pteropid bats, Pteropus poliocephalus). Consequently, hundreds of koalas and thousands of bat pups entered wildlife hospitals with fire-related injuries/illness, where some individuals received antimicrobial therapy. This study investigated the dynamics of antimicrobial resistance (AMR) in pre-fire, fire-affected and post-fire koalas and Pteropid bat pups. PCR and DNA sequencing were used to screen DNA samples extracted from faeces (koalas and bats) and cloacal swabs (koalas) for class 1 integrons, a genetic determinant of AMR, and to identify integron-associated antibiotic resistance genes. Class 1 integrons were detected in 25.5% of koalas (68 of 267) and 59.4% of bats (92 of 155). Integrons contained genes conferring resistance to aminoglycosides, trimethoprim and beta-lactams. Samples were also screened for blaTEM (beta-lactam) resistance genes, which were detected in 2.6% of koalas (7 of 267) and 25.2% of bats (39 of 155). Integron occurrence was significantly higher in fire-affected koalas in-care compared to wild pre-fire koalas (P < 0.0001). Integron and blaTEM occurrence were not significantly different in fire-affected bats compared to pre-fire bats (P > 0.05), however, their occurrence was significantly higher in fire-affected bats in-care compared to wild fire-affected bats (P < 0.0001 and P = 0.0488 respectively). The observed shifts of AMR dynamics in wildfire-impacted species flags the need for judicious antibiotic use when treating fire-affected wildlife to minimise unwanted selective pressure and negative treatment outcomes associated with carriage of resistance genes and antibiotic resistant bacteria.},
}
@article {pmid38331994,
year = {2024},
author = {Tao, X and Yang, Z and Feng, J and Jian, S and Yang, Y and Bates, CT and Wang, G and Guo, X and Ning, D and Kempher, ML and Liu, XJA and Ouyang, Y and Han, S and Wu, L and Zeng, Y and Kuang, J and Zhang, Y and Zhou, X and Shi, Z and Qin, W and Wang, J and Firestone, MK and Tiedje, JM and Zhou, J},
title = {Experimental warming accelerates positive soil priming in a temperate grassland ecosystem.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1178},
pmid = {38331994},
issn = {2041-1723},
support = {DE-SC0004601//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020163//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0010570//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; 41825016//National Natural Science Foundation of China (National Science Foundation of China)/ ; EF-2025558//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-2129235//NSF | BIO | Division of Environmental Biology (DEB)/ ; },
mesh = {*Ecosystem ; *Grassland ; Soil ; Carbon ; Climate Change ; },
abstract = {Unravelling biosphere feedback mechanisms is crucial for predicting the impacts of global warming. Soil priming, an effect of fresh plant-derived carbon (C) on native soil organic carbon (SOC) decomposition, is a key feedback mechanism that could release large amounts of soil C into the atmosphere. However, the impacts of climate warming on soil priming remain elusive. Here, we show that experimental warming accelerates soil priming by 12.7% in a temperate grassland. Warming alters bacterial communities, with 38% of unique active phylotypes detected under warming. The functional genes essential for soil C decomposition are also stimulated, which could be linked to priming effects. We incorporate lab-derived information into an ecosystem model showing that model parameter uncertainty can be reduced by 32-37%. Model simulations from 2010 to 2016 indicate an increase in soil C decomposition under warming, with a 9.1% rise in priming-induced CO2 emissions. If our findings can be generalized to other ecosystems over an extended period of time, soil priming could play an important role in terrestrial C cycle feedbacks and climate change.},
}
@article {pmid38331428,
year = {2024},
author = {Lee Díaz, AS and Minchev, Z and Raaijmakers, JM and Pozo, MJ and Garbeva, P},
title = {Impact of bacterial and fungal inoculants on the resident rhizosphere microbiome and the volatilome of tomato plants under leaf herbivory stress.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {2},
pages = {},
pmid = {38331428},
issn = {1574-6941},
support = {765290//European Union/ ; },
mesh = {*Agricultural Inoculants ; *Solanum lycopersicum ; Rhizosphere ; Herbivory ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; },
abstract = {Various studies have addressed the impact of microbial inoculants on the composition of the resident microbiome. How microbial inoculants impact plant metabolism and interact with the resident rhizobiota under herbivory stress remains elusive. Here, we investigated the impact of two bacterial and two fungal inoculants, inoculated as single species and as a synthetic community, on the rhizosphere microbiome and volatilome of tomato plants (Solanum lycopersicum) comparing nonstress conditions to exposed to leaf herbivory by Spodoptera exigua. Based on amplicon sequencing analysis, rhizobacterial community composition was significantly affected by all four inoculants and the magnitude of this effect was dependent on herbivory stress. Fungal community composition was altered by the microbial inoculants but independent of herbivory stress. The rhizosphere volatilome was impacted by the microbial inoculation and differences between treatments were evened under herbivory stress. Each microbial inoculant caused unique changes in the volatilome of stressed plants but also shared similar responses, in particular the enhanced production of dimethyl disulfide and benzothiazole. In conclusion, the introduction of microbial inoculants in the tomato rhizosphere caused unique as well as common changes in the rhizosphere microbiome and volatilome, but these changes were minor compared to the microbiome changes induced by herbivory stress.},
}
@article {pmid38329329,
year = {2024},
author = {Amill, F and Gauthier, J and Rautio, M and Derome, N},
title = {Characterization of gill bacterial microbiota in wild Arctic char (Salvelinus alpinus) across lakes, rivers, and bays in the Canadian Arctic ecosystems.},
journal = {Microbiology spectrum},
volume = {12},
number = {3},
pages = {e0294323},
pmid = {38329329},
issn = {2165-0497},
support = {//UL | Sentinelle Nord, Universit&#xe9; Laval (Sentinel North)/ ; //Canada First Research Excellence Fund (CFREF)/ ; //Polar Knowledge Canada (PKC)/ ; },
mesh = {Animals ; Bays ; Canada ; Dysbiosis ; Gills ; *Lakes ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Trout/genetics/metabolism ; Water/metabolism ; },
abstract = {Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (Salvelinus alpinus), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors. For this purpose, a total of 140 adult anadromous individuals were collected from rivers, lakes, and bays belonging to five Inuit communities located in four distinct hydrologic basins in the Canadian Arctic (Nunavut and Nunavik) during spring (May) and autumn (August). Various environmental factors were collected, including latitudes, water and air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, and chlorophyll-a concentration. The taxonomic distribution of transcriptionally active taxa within the gill microbiota was quantified by 16S rRNA gene transcripts sequencing. The results showed differential bacterial activity between the different geographical locations, explained by latitude, salinity, and, to a lesser extent, air temperature. Network analysis allowed the detection of a potential dysbiosis signature (i.e., bacterial imbalance) in fish gill microbiota from Duquet Lake in the Hudson Strait and the system Five Mile Inlet connected to the Hudson Bay, both showing the lowest alpha diversity and connectivity between taxa.IMPORTANCEThis paper aims to decipher the complex relationship between Arctic char (Salvelinus alpinus) and its symbiotic microbial consortium in gills. This salmonid is widespread in the Canadian Arctic and is the main protein and polyunsaturated fatty acids source for Inuit people. The influence of environmental parameters on gill microbiota in wild populations remains poorly understood. However, assessing the Arctic char's active gill bacterial community is essential to look for potential pathogens or dysbiosis that could threaten wild populations. Here, we concluded that Arctic char gill microbiota was mainly influenced by latitude and air temperature, the latter being correlated with water temperature. In addition, a dysbiosis signature detected in gill microbiota was potentially associated with poor fish health status recorded in these disturbed environments. With those results, we hypothesized that rapid climate change and increasing anthropic activities in the Arctic might profoundly disturb Arctic char gill microbiota, affecting their survival.},
}
@article {pmid38328439,
year = {2024},
author = {Jaeger, JW and Brandt, A and Gui, W and Yergaliyev, T and Hernández-Arriaga, A and Muthu, MM and Edlund, K and Elashy, A and Molinaro, A and Möckel, D and Sarges, J and Halibasic, E and Trauner, M and Kahles, F and Rolle-Kampczyk, U and Hengstler, J and Schneider, CV and Lammers, T and Marschall, HU and von Bergen, M and Camarinha-Silva, A and Bergheim, I and Trautwein, C and Schneider, KM},
title = {Microbiota modulation by dietary oat beta-glucan prevents steatotic liver disease progression.},
journal = {JHEP reports : innovation in hepatology},
volume = {6},
number = {3},
pages = {100987},
pmid = {38328439},
issn = {2589-5559},
abstract = {BACKGROUND &amp; AIMS: Changes in gut microbiota in metabolic dysfunction-associated steatotic liver disease (MASLD) are important drivers of disease progression towards fibrosis. Therefore, reversing microbial alterations could ameliorate MASLD progression. Oat beta-glucan, a non-digestible polysaccharide, has shown promising therapeutic effects on hyperlipidemia associated with MASLD, but its impact on gut microbiota and most importantly MASLD-related fibrosis remains unknown.<br><br>METHODS: We performed detailed metabolic phenotyping, including assessments of body composition, glucose tolerance, and lipid metabolism, as well as comprehensive characterization of the gut-liver axis in a western-style diet (WSD)-induced model of MASLD and assessed the effect of a beta-glucan intervention on early and advanced liver disease. Gut microbiota were modulated using broad-spectrum antibiotic treatment.<br><br>RESULTS: Oat beta-glucan supplementation did not affect WSD-induced body weight gain or glucose intolerance and the metabolic phenotype remained largely unaffected. Interestingly, oat beta-glucan dampened MASLD-related inflammation, which was associated with significantly reduced monocyte-derived macrophage infiltration and fibroinflammatory gene expression, as well as strongly reduced fibrosis development. Mechanistically, this protective effect was not mediated by changes in bile acid composition or signaling, but was dependent on gut microbiota and was lost upon broad-spectrum antibiotic treatment. Specifically, oat beta-glucan partially reversed unfavorable changes in gut microbiota, resulting in an expansion of protective taxa, including Ruminococcus, and Lactobacillus followed by reduced translocation of Toll-like receptor ligands.<br><br>CONCLUSIONS: Our findings identify oat beta-glucan as a highly efficacious food supplement that dampens inflammation and fibrosis development in diet-induced MASLD. These results, along with its favorable dietary profile, suggest that it may be a cost-effective and well-tolerated approach to preventing MASLD progression and should be assessed in clinical studies.<br><br>IMPACT AND IMPLICATIONS: Herein, we investigated the effect of oat beta-glucan on the gut-liver axis and fibrosis development in a mouse model of metabolic dysfunction-associated steatotic liver disease (MASLD). Beta-glucan significantly reduced inflammation and fibrosis in the liver, which was associated with favorable shifts in gut microbiota that protected against bacterial translocation and activation of fibroinflammatory pathways. Together, oat beta-glucan may be a cost-effective and well-tolerated approach to prevent MASLD progression and should be assessed in clinical studies.},
}
@article {pmid38327124,
year = {2024},
author = {Rudzki, EN and Antonson, ND and Jones, TM and Schelsky, WM and Trevelline, BK and Hauber, ME and Kohl, KD},
title = {Host avian species and environmental conditions influence the microbial ecology of brood parasitic brown-headed cowbird nestlings: What rules the roost?.},
journal = {Molecular ecology},
volume = {33},
number = {6},
pages = {e17289},
doi = {10.1111/mec.17289},
pmid = {38327124},
issn = {1365-294X},
support = {1953226//US National Science Foundation/ ; 2026836//US National Science Foundation/ ; 2139321//US National Science Foundation/ ; 2305848//US National Science Foundation/ ; },
mesh = {Animals ; *Parasites ; RNA, Ribosomal, 16S/genetics ; Nesting Behavior ; *Passeriformes ; },
abstract = {The role of species interactions, as well as genetic and environmental factors, all likely contribute to the composition and structure of the gut microbiome; however, disentangling these independent factors under field conditions represents a challenge for a functional understanding of gut microbial ecology. Avian brood parasites provide unique opportunities to investigate these questions, as brood parasitism results in parasite and host nestlings being raised in the same nest, by the same parents. Here we utilized obligate brood parasite brown-headed cowbird nestlings (BHCO; Molothrus ater) raised by several different host passerine species to better understand, via 16S rRNA sequencing, the microbial ecology of brood parasitism. First, we compared faecal microbial communities of prothonotary warbler nestlings (PROW; Protonotaria citrea) that were either parasitized or non-parasitized by BHCO and communities among BHCO nestlings from PROW nests. We found that parasitism by BHCO significantly altered both the community membership and community structure of the PROW nestling microbiota, perhaps due to the stressful nest environment generated by brood parasitism. In a second dataset, we compared faecal microbiotas from BHCO nestlings raised by six different host passerine species. Here, we found that the microbiota of BHCO nestlings was significantly influenced by the parental host species and the presence of an inter-specific nestmate. Thus, early rearing environment is important in determining the microbiota of brood parasite nestlings and their companion nestlings. Future work may aim to understand the functional effects of this microbiota variability on nestling performance and fitness.},
}
@article {pmid38325783,
year = {2024},
author = {Wang, B and Hu, K and Li, C and Zhang, Y and Hu, C and Liu, Z and Ding, J and Chen, L and Zhang, W and Fang, J and Zhang, H},
title = {Geographic distribution of bacterial communities of inland waters in China.},
journal = {Environmental research},
volume = {249},
number = {},
pages = {118337},
doi = {10.1016/j.envres.2024.118337},
pmid = {38325783},
issn = {1096-0953},
mesh = {China ; *Bacteria/genetics/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/analysis/genetics ; Biodiversity ; Water Microbiology ; Fresh Water/microbiology ; },
abstract = {Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.},
}
@article {pmid38325494,
year = {2024},
author = {Forsmark, B and Bizjak, T and Nordin, A and Rosenstock, NP and Wallander, H and Gundale, MJ},
title = {Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition.},
journal = {The Science of the total environment},
volume = {918},
number = {},
pages = {170741},
doi = {10.1016/j.scitotenv.2024.170741},
pmid = {38325494},
issn = {1879-1026},
mesh = {*Nitrogen/analysis ; Soil ; Carbon ; Forests ; *Microbiota ; Soil Microbiology ; },
abstract = {Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha[-1] yr[-1]) and high (50 kg N ha[-1] yr[-1]) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available.},
}
@article {pmid38325456,
year = {2024},
author = {Redouane, EM and Núñez, A and Achouak, W and Barakat, M and Alex, A and Martins, JC and Tazart, Z and Mugani, R and Zerrifi, SEA and Haida, M and García, AM and Campos, A and Lahrouni, M and Oufdou, K and Vasconcelos, V and Oudra, B},
title = {Microcystin influence on soil-plant microbiota: Unraveling microbiota modulations and assembly processes in the rhizosphere of Vicia faba.},
journal = {The Science of the total environment},
volume = {918},
number = {},
pages = {170634},
doi = {10.1016/j.scitotenv.2024.170634},
pmid = {38325456},
issn = {1879-1026},
mesh = {*Vicia faba ; Soil ; Microcystins/toxicity ; Rhizosphere ; *Cyanobacteria ; *Microbiota ; Soil Microbiology ; Plant Roots/metabolism ; },
abstract = {Microcystins (MCs) are frequently detected in cyanobacterial bloom-impacted waterbodies and introduced into agroecosystems via irrigation water. They are widely known as phytotoxic cyanotoxins, which impair the growth and physiological functions of crop plants. However, their impact on the plant-associated microbiota is scarcely tackled and poorly understood. Therefore, we aimed to investigate the effect of MCs on microbiota-inhabiting bulk soil (BS), root adhering soil (RAS), and root tissue (RT) of Vicia faba when exposed to 100 μg L[-1] MCs in a greenhouse pot experiment. Under MC exposure, the structure, co-occurrence network, and assembly processes of the bacterial microbiota were modulated with the greatest impact on RT-inhabiting bacteria, followed by BS and, to a lesser extent, RAS. The analyses revealed a significant decrease in the abundances of several Actinobacteriota-related taxa within the RT microbiota, including the most abundant and known genus of Streptomyces. Furthermore, MCs significantly increased the abundance of methylotrophic bacteria (Methylobacillus, Methylotenera) and other Proteobacteria-affiliated genera (e.g., Paucibacter), which are supposed to degrade MCs. The co-occurrence network of the bacterial community in the presence of MCs was less complex than the control network. In MC-exposed RT, the turnover in community composition was more strongly driven by deterministic processes, as proven by the beta-nearest taxon index. Whereas in MC-treated BS and RAS, both deterministic and stochastic processes can influence community assembly to some extent, with a relative dominance of deterministic processes. Altogether, these results suggest that MCs may reshape the structure of the microbiota in the soil-plant system by reducing bacterial taxa with potential phytobeneficial traits and increasing other taxa with the potential capacity to degrade MCs.},
}
@article {pmid38324120,
year = {2024},
author = {Scaini, A and Mulligan, J and Berg, H and Brangarí, A and Bukachi, V and Carenzo, S and Chau Thi, D and Courtney-Mustaphi, C and Ekblom, A and Fjelde, H and Fridahl, M and Hansson, A and Hicks, L and Höjer, M and Juma, B and Kain, JH and Kariuki, RW and Kim, S and Lane, P and Leizeaga, A and Lindborg, R and Livsey, J and Lyon, SW and Marchant, R and McConville, JR and Munishi, L and Nilsson, D and Olang, L and Olin, S and Olsson, L and Rogers, PM and Rousk, J and Sandén, H and Sasaki, N and Shoemaker, A and Smith, B and Thai Huynh Phuong, L and Varela Varela, A and Venkatappa, M and Vico, G and Von Uexkull, N and Wamsler, C and Wondie, M and Zapata, P and Zapata Campos, MJ and Manzoni, S and Tompsett, A},
title = {Pathways from research to sustainable development: Insights from ten research projects in sustainability and resilience.},
journal = {Ambio},
volume = {53},
number = {4},
pages = {517-533},
pmid = {38324120},
issn = {1654-7209},
support = {2016-06359//Vetenskapsr&#xe5;det/ ; 2016-06355//Vetenskapsr&#xe5;det/ ; 2016-06297//Vetenskapsr&#xe5;det/ ; 2016-06300//Vetenskapsr&#xe5;det/ ; 2016-06327//Vetenskapsr&#xe5;det/ ; 2016-06329//Vetenskapsr&#xe5;det/ ; 2016-06334//Vetenskapsr&#xe5;det/ ; 2016-06289//Vetenskapsr&#xe5;det/ ; 2016-06313//Vetenskapsr&#xe5;det/ ; 2016-06389//Vetenskapsr&#xe5;det/ ; },
mesh = {Humans ; *Resilience, Psychological ; },
abstract = {Drawing on collective experience from ten collaborative research projects focused on the Global South, we identify three major challenges that impede the translation of research on sustainability and resilience into better-informed choices by individuals and policy-makers that in turn can support transformation to a sustainable future. The three challenges comprise: (i) converting knowledge produced during research projects into successful knowledge application; (ii) scaling up knowledge in time when research projects are short-term and potential impacts are long-term; and (iii) scaling up knowledge across space, from local research sites to larger-scale or even global impact. Some potential pathways for funding agencies to overcome these challenges include providing targeted prolonged funding for dissemination and outreach, and facilitating collaboration and coordination across different sites, research teams, and partner organizations. By systematically documenting these challenges, we hope to pave the way for further innovations in the research cycle.},
}
@article {pmid38322759,
year = {2023},
author = {Yang, X and Narvaez-Bravo, C and Zhang, P},
title = {Driving forces shaping the microbial ecology in meat packing plants.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1333696},
pmid = {38322759},
issn = {1664-302X},
abstract = {Meat production is a complex system, continually receiving animals, water, air, and workers, all of which serve as carriers of bacteria. Selective pressures involved in different meat processing stages such as antimicrobial interventions and low temperatures, may promote the accumulation of certain residential microbiota in meat cutting facilities. Bacteria including human pathogens from all these sources can contaminate meat surfaces. While significant advancements have been made in enhancing hygienic standards and pathogen control measures in meat plants, resulting in a notable reduction in STEC recalls and clinical cases, STEC still stands as a predominant contributor to foodborne illnesses associated with beef and occasionally with pork. The second-and third-generation sequencing technology has become popular in microbiota related studies and provided a better image of the microbial community in the meat processing environments. In this article, we reviewed the potential factors influencing the microbial ecology in commercial meat processing facilities and conducted a meta-analysis on the microbiota data published in the last 10 years. In addition, the mechanisms by which bacteria persist in meat production environments have been discussed with a focus on the significant human pathogen E. coli O157:H7 and generic E. coli, an indicator often used for the hygienic condition in food production.},
}
@article {pmid38319112,
year = {2024},
author = {Guo, J and Ning, H and Li, Y and Xu, Q and Shen, Q and Ling, N and Guo, S},
title = {Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice.},
journal = {mBio},
volume = {15},
number = {3},
pages = {e0273323},
pmid = {38319112},
issn = {2150-7511},
support = {32372808//National Natural Science Foundation of China (NSFC)/ ; 41977080//National Natural Science Foundation of China (NSFC)/ ; U2003210//National Natural Science Foundation of China (NSFC)/ ; 202206193000001, 20220816113416001//Shenzhen Science and Technology Program/ ; JCYJ20230807111217035//Shenzhen Science and Technology Program/ ; 2019QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; },
mesh = {*Oryza ; *Microbiota ; Bacteria ; Fungi ; Plant Roots/microbiology ; Soil Microbiology ; Rhizosphere ; Soil/chemistry ; },
abstract = {UNLABELLED: The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.<br><br>IMPORTANCE: The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.},
}
@article {pmid38317822,
year = {2024},
author = {Kop, LFM and Koch, H and Jetten, MSM and Daims, H and Lücker, S},
title = {Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycad017},
pmid = {38317822},
issn = {2730-6151},
abstract = {The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.},
}
@article {pmid38317643,
year = {2024},
author = {Vlasselaer, L and Crauwels, S and Lievens, B and De Coninck, B},
title = {Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {3},
pages = {},
pmid = {38317643},
issn = {1574-6941},
support = {HBC.2020.3181//VLAIO/ ; },
mesh = {Lactuca ; *Phytophthora/genetics ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Microbiota/genetics ; Rhizosphere ; Flavobacterium/genetics ; Soil Microbiology ; },
abstract = {Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.},
}
@article {pmid38315121,
year = {2024},
author = {Han, K and Li, J and Yang, D and Zhuang, Q and Zeng, H and Rong, C and Yue, J and Li, N and Gu, C and Chen, L and Chen, C},
title = {Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.},
journal = {Microbiology spectrum},
volume = {12},
number = {3},
pages = {e0360223},
pmid = {38315121},
issn = {2165-0497},
support = {2021YFF0703805//MOST | National Key Research and Development Program of China (NKPs)/ ; 82102447//MOST | National Natural Science Foundation of China (NSFC)/ ; DFL20191801//Beijing Hospital Authority/ ; Z201100005520040//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; QML20230701//Beijing Hospitals Authority Youth Programme/ ; },
mesh = {Animals ; Humans ; Mice ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Bacteria/genetics ; DNA ; },
abstract = {Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.},
}
@article {pmid38313259,
year = {2024},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38313259},
issn = {2692-8205},
abstract = {Microbiomes are generally characterized by high diversity of coexisting microbial species and strains that remains stable within a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis obtained, namely, pure competition, host-parasite relationship and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environments. These findings show that basic phenomena that are universal in microbial communities, environmental variation and HGT, provide for stabilization of microbial diversity and ecological complexity.},
}
@article {pmid38312729,
year = {2024},
author = {Wang, Y and Long, C and Yin, L and Liu, R and Liao, Y and He, G and Liu, Z},
title = {Effects of simulated acid rain on hydrochemical factors and microbial community structure in red soil aquifers.},
journal = {RSC advances},
volume = {14},
number = {7},
pages = {4482-4491},
pmid = {38312729},
issn = {2046-2069},
abstract = {Acid rain can lower the pH of groundwater and affect its hydrogeochemistry and microbial ecology. However, the effects of acid rain on the hydrogeochemistry and microbial ecology of red soil groundwater systems in southern China are poorly understood. Previous research had mainly investigated the sources and patterns of groundwater acidification, but not the microbial mechanisms that contribute to this process and their associations with hydrochemical factors. To address this knowledge gap, we conducted a soil column experiment to simulate the infiltration of acid rain through various filter materials (coarse, medium, and fine sand) and to examine the hydrochemical and microbial features of the infiltrate, which can reveal how simulated acid rain (pH 3.5-7.0) alters the hydrochemistry and microbial community composition in red soil aquifers. The results showed that the pH of the leachate decreased due to simulated acid rain, and that the leaching efficiency of nitrogen and metal ions was influenced by the particle size of the filter media. Illumina 16S rRNA gene sequencing revealed that the leachate was dominated by Proteobacteria, Patescibacteria, Actinobacteria, and Acidobacteria, with Proteobacteria accounting for 67.04-74.69% of the bacterial community and containing a high proportion of nitrifying and denitrifying bacteria. Additionally, several genera with heavy metal tolerance, such as Burkholderia-Caballeronia-Paraburkholderia, Delftia, Methylversatilis, Aquicella, and Ralstonia, were widely distributed in the leachate, indicating the strong adaptive capacity of the microbial population. A correlation analysis between the hydrochemical factors and the microbial community structure revealed that pH was the most influential factor, followed by NO2[-]-N, Fe, Al, Cu, Mn, and others. These results indicate that acidification modifies the hydrochemical conditions of the aquifer, creating an environment that is unfavorable for microbial growth and survival. However, some microorganisms may acquire resistance genes to cope with environmental changes.},
}
@article {pmid38311160,
year = {2024},
author = {Guo, M and Shang, X and Ma, Y and Zhang, K and Zhang, L and Zhou, Y and Gong, Z and Miao, R},
title = {Biochars assisted phytoremediation of polycyclic aromatic hydrocarbons contaminated agricultural soil: Dynamic responses of functional genes and microbial community.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {345},
number = {},
pages = {123476},
doi = {10.1016/j.envpol.2024.123476},
pmid = {38311160},
issn = {1873-6424},
mesh = {*Polycyclic Aromatic Hydrocarbons/analysis ; Soil/chemistry ; Biodegradation, Environmental ; *Soil Pollutants/analysis ; Soil Microbiology ; Bacteria/genetics/metabolism ; *Microbiota ; *Charcoal ; },
abstract = {A biochar-intensified phytoremediation experiment was designed to investigate the dynamic effects of different biochars on polycyclic aromatic hydrocarbon (PAH) removal in ryegrass rhizosphere contaminated soil. Maize and wheat straw biochar pyrolyzed at 300 °C and 500 °C were amended into PAH-contaminated soil, and then ryegrass (Lolium multiflorum L.) was planted for 90 days. Spearman's correlations among PAH removal, enzyme activity, abundance of PAH-ring hydroxylating dioxygenase (PAH-RHDα), and fungal and bacterial community structure were analyzed to elucidate the microbial degradation mechanisms during the combined remediation process. The results showed that 500 °C wheat straw biochar had higher surface area and more nutrients, and significantly accelerated the phytoremediation of PAHs (62.5 %), especially for high molecular weight PAH in contaminated soil. The activities of urease and dehydrogenase and the abundance of total and PAH-degrading bacteria, which improved with time by biochar and ryegrass, had a positive correlation with the removal rate of PAHs. Biochar enhanced the abundance of gram-negative (GN) PAH-RHDα genes. The GN PAH-degraders, Sphingomonas, bacteriap25, Haliangium, and Dongia may play vital roles in PAH degradation in biochar-amended rhizosphere soils. Principal coordinate analysis indicated that biochar led to significant differences in fungal community structures before 30 days, while the diversity of the bacterial community composition depended on planting ryegrass after 60 days. These findings imply that the structural reshaping of microbial communities results from incubation time and the selection of biochar and ryegrass in PAH-contaminated soils. Applying 500 °C wheat straw biochar could enhance the rhizoremediation of PAH-contaminated soil and benefit the soil microbial ecology.},
}
@article {pmid38307852,
year = {2024},
author = {Jimonet, P and Druart, C and Blanquet-Diot, S and Boucinha, L and Kourula, S and Le Vacon, F and Maubant, S and Rabot, S and Van de Wiele, T and Schuren, F and Thomas, V and Walther, B and Zimmermann, M and , },
title = {Gut Microbiome Integration in Drug Discovery and Development of Small Molecules.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {52},
number = {4},
pages = {274-287},
doi = {10.1124/dmd.123.001605},
pmid = {38307852},
issn = {1521-009X},
mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Drug Discovery ; Drug Interactions ; },
abstract = {Human microbiomes, particularly in the gut, could have a major impact on the efficacy and toxicity of drugs. However, gut microbial metabolism is often neglected in the drug discovery and development process. Medicen, a Paris-based human health innovation cluster, has gathered more than 30 international leading experts from pharma, academia, biotech, clinical research organizations, and regulatory science to develop proposals to facilitate the integration of microbiome science into drug discovery and development. Seven subteams were formed to cover the complementary expertise areas of 1) pharma experience and case studies, 2) in silico microbiome-drug interaction, 3) in vitro microbial stability screening, 4) gut fermentation models, 5) animal models, 6) microbiome integration in clinical and regulatory aspects, and 7) microbiome ecosystems and models. Each expert team produced a state-of-the-art report of their respective field highlighting existing microbiome-related tools at every stage of drug discovery and development. The most critical limitations are the growing, but still limited, drug-microbiome interaction data to produce predictive models and the lack of agreed-upon standards despite recent progress. In this paper we will report on and share proposals covering 1) how microbiome tools can support moving a compound from drug discovery to clinical proof-of-concept studies and alert early on potential undesired properties stemming from microbiome-induced drug metabolism and 2) how microbiome data can be generated and integrated in pharmacokinetic models that are predictive of the human situation. Examples of drugs metabolized by the microbiome will be discussed in detail to support recommendations from the working group. SIGNIFICANCE STATEMENT: Gut microbial metabolism is often neglected in the drug discovery and development process despite growing evidence of drugs' efficacy and safety impacted by their interaction with the microbiome. This paper will detail existing microbiome-related tools covering every stage of drug discovery and development, current progress, and limitations, as well as recommendations to integrate them into the drug discovery and development process.},
}
@article {pmid38305149,
year = {2024},
author = {Mukhia, S and Kumar, A and Kumar, R},
title = {Bacterial community distribution and functional potentials provide key insights into their role in the ecosystem functioning of a retreating Eastern Himalayan glacier.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {3},
pages = {},
pmid = {38305149},
issn = {1574-6941},
support = {45/17/2020-/BIO/BMS//Indian Council of Medical Research/ ; DBT/JRF/BET-17/I/2017/AL/367//Department of Biotechnology/ ; DST/INSPIRE/04/2014/001280//Department of Science and Technology/ ; SRG/2019/001071//Science and Engineering Research Board/ ; },
mesh = {*Ecosystem ; Ice Cover ; Metagenomics ; Bacteria ; Metagenome ; *Microbiota ; Proteobacteria/genetics ; Sulfur/metabolism ; },
abstract = {Himalayan glaciers are receding at an exceptional rate, perturbing the local biome and ecosystem processes. Understanding the microbial ecology of an exclusively microbe-driven biome provides insights into their contributions to the ecosystem functioning through biogeochemical fluxes. Here, we investigated the bacterial communities and their functional potential in the retreating East Rathong Glacier (ERG) of Sikkim Himalaya. Amplicon-based taxonomic classification revealed the dominance of the phyla Proteobacteria, Bacteroidota, and candidate Patescibacteria in the glacial sites. Further, eight good-quality metagenome-assembled genomes (MAGs) of Proteobacteria, Patescibacteria, Acidobacteriota, and Choloflexota retrieved from the metagenomes elucidated the microbial contributions to nutrient cycling. The ERG MAGs showed aerobic respiration as a primary metabolic feature, accompanied by carbon fixation and complex carbon degradation potentials. Pathways for nitrogen metabolism, chiefly dissimilatory nitrate reduction and denitrification, and a complete sulphur oxidation enzyme complex for sulphur metabolism were identified in the MAGs. We observed that DNA repair and oxidative stress response genes complemented with osmotic and periplasmic stress and protein chaperones were vital for adaptation against the intense radiation and stress conditions of the extreme Himalayan niche. Current findings elucidate the microbiome and associated functional potentials of a vulnerable glacier, emphasizing their significant ecological roles in a changing glacial ecosystem.},
}
@article {pmid38305133,
year = {2024},
author = {Ramakodi, MP},
title = {Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data.},
journal = {FEMS microbiology letters},
volume = {371},
number = {},
pages = {},
doi = {10.1093/femsle/fnae009},
pmid = {38305133},
issn = {1574-6968},
mesh = {RNA, Ribosomal, 18S/genetics ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor = 0.950; P-value = 4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.},
}
@article {pmid38303015,
year = {2024},
author = {Mejías-Molina, C and Pico-Tomàs, A and Martínez-Puchol, S and Itarte, M and Torrell, H and Canela, N and Borrego, CM and Corominas, L and Rusiñol, M and Bofill-Mas, S},
title = {Wastewater-based epidemiology applied at the building-level reveals distinct virome profiles based on the age of the contributing individuals.},
journal = {Human genomics},
volume = {18},
number = {1},
pages = {10},
pmid = {38303015},
issn = {1479-7364},
support = {202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; 202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; 202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; 202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; ICRA-ENV 2017 SGR 1124//Consolidated Research Group grants/ ; ICRA-ENV 2017 SGR 1124//Consolidated Research Group grants/ ; },
mesh = {Humans ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; Virome/genetics ; *Viruses/genetics ; *Virus Diseases ; },
abstract = {BACKGROUND: Human viruses released into the environment can be detected and characterized in wastewater. The study of wastewater virome offers a consolidated perspective on the circulation of viruses within a population. Because the occurrence and severity of viral infections can vary across a person's lifetime, studying the virome in wastewater samples contributed by various demographic segments can provide valuable insights into the prevalence of viral infections within these segments. In our study, targeted enrichment sequencing was employed to characterize the human virome in wastewater at a building-level scale. This was accomplished through passive sampling of wastewater in schools, university settings, and nursing homes in two cities in Catalonia. Additionally, sewage from a large urban wastewater treatment plant was analysed to serve as a reference for examining the collective excreted human virome.<br><br>RESULTS: The virome obtained from influent wastewater treatment plant samples showcased the combined viral presence from individuals of varying ages, with astroviruses and human bocaviruses being the most prevalent, followed by human adenoviruses, polyomaviruses, and papillomaviruses. Significant variations in the viral profiles were observed among the different types of buildings studied. Mamastrovirus 1 was predominant in school samples, salivirus and human polyomaviruses JC and BK in the university settings while nursing homes showed a more balanced distribution of viral families presenting papillomavirus and picornaviruses and, interestingly, some viruses linked to immunosuppression.<br><br>CONCLUSIONS: This study shows the utility of building-level wastewater-based epidemiology as an effective tool for monitoring the presence of viruses circulating within specific age groups. It provides valuable insights for public health monitoring and epidemiological studies.},
}
@article {pmid38302681,
year = {2024},
author = {Wdowiak-Wróbel, S and Kalita, M and Palusińska-Szysz, M and Marek-Kozaczuk, M and Sokołowski, W and Coutinho, TA},
title = {Pantoea trifolii sp. nov., a novel bacterium isolated from Trifolium rubens root nodules.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2698},
pmid = {38302681},
issn = {2045-2322},
support = {PL-RPA2/07/TRIFOMIKRO/2019//Narodowe Centrum Bada&#x144; i Rozwoju/ ; POL180702349288//National Research Foundation/ ; },
mesh = {Sequence Analysis, DNA ; *Pantoea/genetics ; *Trifolium/genetics ; RNA, Ribosomal, 16S/genetics ; DNA ; Phylogeny ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Bacterial Typing Techniques ; Nucleic Acid Hybridization ; },
abstract = {A novel bacterium, designated strain MMK2[T], was isolated from a surface-sterilised root nodule of a Trifolium rubens plant growing in south-eastern Poland. Cells were Gram negative, non-spore forming and rod shaped. The strain had the highest 16S rRNA gene sequence similarity with P. endophytica (99.4%), P. leporis (99.4%) P. rwandensis (98.8%) and P. rodasii (98.45%). Phylogenomic analysis clearly showed that strain MMK2[T] and an additional strain, MMK3, should reside in the genus Pantoea and that they were most closely related to P. endophytica and P. leporis. Genome comparisons showed that the novel strain shared 82.96-93.50% average nucleotide identity and 26.2-53. 2% digital DNA:DNA hybridization with closely related species. Both strains produced siderophores and were able to solubilise phosphates. The MMK2[T] strain was also able to produce indole-3-acetic acid. The tested strains differed in their antimicrobial activity, but both were able to inhibit the growth of Sclerotinia sclerotiorum 10Ss01. Based on the results of the phenotypic, phylogenomic, genomic and chemotaxonomic analyses, strains MMK2[T] and MMK3 belong to a novel species in the genus Pantoea for which the name Pantoea trifolii sp. nov. is proposed with the type strain MMK2[T] (= DSM 115063[T] = LMG 33049[T]).},
}
@article {pmid38302544,
year = {2024},
author = {Prasoodanan P K, V and Kumar, S and Dhakan, DB and Waiker, P and Saxena, R and Sharma, VK},
title = {Metagenomic exploration of Andaman region of the Indian Ocean.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2717},
pmid = {38302544},
issn = {2045-2322},
mesh = {Indian Ocean ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; Metagenome ; *Microbiota/genetics ; Water ; Seawater ; },
abstract = {Ocean microbiome is crucial for global biogeochemical cycles and primary productivity. Despite numerous studies investigating the global ocean microbiomes, the microbiome composition of the Andaman region of the Indian Ocean remains largely unexplored. While this region harbors pristine biological diversity, the escalating anthropogenic activities along coastal habitats exert an influence on the microbial ecology and impact the aquatic ecosystems. We investigated the microbiome composition in the coastal waters of the Andaman Islands by 16S rRNA gene amplicon and metagenomic shotgun sequencing approaches and compared it with the Tara Oceans Consortium. In the coastal waters of the Andaman Islands, a significantly higher abundance and diversity of Synechococcus species was observed with a higher abundance of photosynthesis pigment-related genes to adapt to variable light conditions and nutrition. In contrast, Prochlorococcus species showed higher abundance in open ocean water samples of the Indian Ocean region, with a relatively limited functional diversity. A higher abundance of antibiotic-resistance genes was also noted in the coastal waters region. We also updated the ocean microbiome gene catalog with 93,172 unique genes from the Andaman coastal water microbiome. This study provides valuable insights into the Indian Ocean microbiome and supplements the global marine microbial ecosystem studies.},
}
@article {pmid38299778,
year = {2024},
author = {León-Sobrino, C and Ramond, JB and Coclet, C and Kapitango, RM and Maggs-Kölling, G and Cowan, DA},
title = {Temporal dynamics of microbial transcription in wetted hyperarid desert soils.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {3},
pages = {},
pmid = {38299778},
issn = {1574-6941},
support = {113308//University of Pretoria/ ; },
mesh = {*Ecosystem ; Soil ; Desert Climate ; Soil Microbiology ; *Microbiota/genetics ; Water ; RNA, Messenger ; },
abstract = {Rainfall is rare in hyperarid deserts but, when it occurs, it triggers large biological responses essential for the long-term maintenance of the ecosystem. In drylands, microbes play major roles in nutrient cycling, but their responses to short-lived opportunity windows are poorly understood. Due to its ephemeral nature, mRNA is ideally suited to study microbiome dynamics upon abrupt changes in the environment. We analyzed microbial community transcriptomes after simulated rainfall in a Namib Desert soil over 7 days. Using total mRNA from dry and watered plots we infer short-term functional responses in the microbiome. A rapid two-phase cycle of activation and return to basal state was completed in a short period. Motility systems activated immediately, whereas competition-toxicity increased in parallel to predator taxa and the drying of soils. Carbon fixation systems were downregulated, and reactivated upon return to a near-dry state. The chaperone HSP20 was markedly regulated by watering across all major bacteria, suggesting a particularly important role in adaptation to desiccated ecosystems. We show that transcriptomes provide consistent and high resolution information on microbiome processes in a low-biomass environment, revealing shared patterns across taxa. We propose a structured dispersal-predation dynamic as a central driver of desert microbial responses to rainfall.},
}
@article {pmid38297006,
year = {2024},
author = {Maza-Márquez, P and Lee, MD and Bebout, BM},
title = {Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2561},
pmid = {38297006},
issn = {2045-2322},
mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/genetics ; Phylogeny ; Viruses/genetics ; *Microbiota ; },
abstract = {In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.},
}
@article {pmid38296863,
year = {2024},
author = {Bååth, E and Kritzberg, ES},
title = {Temperature Adaptation of Aquatic Bacterial Community Growth Is Faster in Response to Rising than to Falling Temperature.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {38},
pmid = {38296863},
issn = {1432-184X},
mesh = {Temperature ; *Cold Temperature ; *Lakes ; Bacteria/metabolism ; Seasons ; },
abstract = {Bacteria are key organisms in energy and nutrient cycles, and predicting the effects of temperature change on bacterial activity is important in assessing global change effects. A changing in situ temperature will affect the temperature adaptation of bacterial growth in lake water, both long term in response to global change, and short term in response to seasonal variations. The rate of adaptation may, however, depend on whether temperature is increasing or decreasing, since bacterial growth and turnover scale with temperature. Temperature adaptation was studied for winter (in situ temperature 2.5 °C) and summer communities (16.5 °C) from a temperate lake in Southern Sweden by exposing them to a temperature treatment gradient between 0 and 30 °C in ~ 5 °C increments. This resulted mainly in a temperature increase for the winter and a decrease for the summer community. Temperature adaptation of bacterial community growth was estimated as leucine incorporation using a temperature Sensitivity Index (SI, log growth at 35 °C/4 °C), where higher values indicate adaptation to higher temperatures. High treatment temperatures resulted in higher SI within days for the winter community, resulting in an expected level of community adaptation within 2 weeks. Adaptation for the summer community was also correlated to treatment temperature, but the rate of adaption was slower. Even after 5 weeks, the bacterial community had not fully adapted to the lowest temperature conditions. Thus, during periods of increasing temperature, the bacterial community will rapidly adapt to function optimally, while decreasing temperature may result in long periods of non-optimal functioning.},
}
@article {pmid38294246,
year = {2024},
author = {Kashani, M and Engle, MA and Kent, DB and Gregston, T and Cozzarelli, IM and Mumford, AC and Varonka, MS and Harris, CR and Akob, DM},
title = {Illegal dumping of oil and gas wastewater alters arid soil microbial communities.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {2},
pages = {e0149023},
pmid = {38294246},
issn = {1098-5336},
support = {//DOI | U.S. Geological Survey (USGS)/ ; },
mesh = {*Wastewater ; Soil Microbiology ; Soil/chemistry ; Phylogeny ; Desert Climate ; *Microbiota ; Hydrocarbons ; },
abstract = {The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.},
}
@article {pmid38293374,
year = {2024},
author = {Choi, YJ and Lim, JY and Kang, MJ and Choi, JY and Yang, JH and Chung, YB and Park, SH and Min, SG and Lee, MA},
title = {Changes in bacterial composition and metabolite profiles during kimchi fermentation with different garlic varieties.},
journal = {Heliyon},
volume = {10},
number = {2},
pages = {e24283},
pmid = {38293374},
issn = {2405-8440},
abstract = {Garlic, a key ingredient in kimchi, is an indispensable source of lactic acid bacteria, which are essential for fermentation. This study explored the effects of various garlic varieties on kimchi fermentation, focusing on changes in microbial communities and metabolite profiles. We observed that the type of garlic used did not significantly alter the microbial community. However, the presence of garlic itself made a significant difference. Specifically, kimchi with garlic showed higher abundance of Leuconostoc and Weissella, which are bacteria primarily responsible for kimchi fermentation. Additionally, kimchi containing garlic had increased levels of mannitol and fructose, which significantly influence taste; however, lactic acid and putrescine levels were decreased. Therefore, the addition of garlic directly contributes to the flavor profile of kimchi. Sixty-two metabolites were identified using gas chromatography and mass spectrometry. The variety of garlic added influenced the metabolite profiles of kimchi, particularly in the later stages of fermentation. These profiles were categorized based on the garlic's origin, whether from southern or northern ecotypes (R[2]X = 0.933, R[2]Y = 0.986, Q[2] = 0.878). These findings confirm that both the presence and the variety of garlic significantly impact the microbial ecology and metabolites during kimchi fermentation, underscoring its essential role in the process.},
}
@article {pmid38293109,
year = {2024},
author = {Leleiwi, I and Kokkinias, K and Kim, Y and Baniasad, M and Shaffer, M and Sabag-Daigle, A and Daly, RA and Flynn, RM and Wysocki, VH and Ahmer, BMM and Borton, MA and Wrighton, KC},
title = {Gut microbiome carbon and sulfur metabolisms support Salmonella during pathogen infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.01.16.575907},
pmid = {38293109},
issn = {2692-8205},
abstract = {Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and an ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting the microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, here we performed multi-omics approaches on fecal microbial communities from untreated and Salmonella -infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. This data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella- induced inflammation significantly reduced the diversity of transcriptionally active members in the gut microbiome, yet increased gene expression was detected for 7 members, with Luxibacter and Ligilactobacillus being the most active. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst transcriptionally active members. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that supports Salmonella respiration. Advancement of pathobiome understanding beyond inferences from prior amplicon-based approaches can hold promise for infection mitigation, with the active community outlined here offering intriguing organismal and metabolic therapeutic targets.},
}
@article {pmid38289133,
year = {2024},
author = {Op De Beeck, M and Troein, C and Peterson, C and Tunlid, A and Persson, P},
title = {Elucidating fungal decomposition of organic matter at sub-micrometer spatial scales using optical photothermal infrared (O-PTIR) microspectroscopy.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {2},
pages = {e0148923},
pmid = {38289133},
issn = {1098-5336},
support = {2020-04293//Vetenskapsr&#xe5;det (VR)/ ; 2021-05188//Vetenskapsr&#xe5;det (VR)/ ; },
mesh = {*Basidiomycota ; *Mycorrhizae ; Hyphae ; Cellulose ; Spectrophotometry, Infrared/methods ; },
abstract = {In microbiological studies, a common goal is to link environmental factors to microbial activities. Both environmental factors and microbial activities are typically derived from bulk samples. It is becoming increasingly clear that such bulk environmental parameters poorly represent the microscale environments microorganisms experience. Using infrared (IR) microspectroscopy, the spatial distribution of chemical compound classes can be visualized, making it a useful tool for studying the interactions between microbial cells and their microenvironments. The spatial resolution of conventional IR microspectroscopy has been limited by the diffraction limit of IR light. The recent development of optical photothermal infrared (O-PTIR) microspectroscopy has pushed the spatial resolution of IR microspectroscopy beyond this diffraction limit, allowing the distribution of chemical compound classes to be visualized at sub-micrometer spatial scales. To examine the potential and limitations of O-PTIR microspectroscopy to probe the interactions between fungal cells and their immediate environments, we imaged the decomposition of cellulose films by cells of the ectomycorrhizal fungus Paxillus involutus and compared O-PTIR results using conventional IR microspectroscopy. Whereas the data collected with conventional IR microspectroscopy indicated that P. involutus has only a very limited ability to decompose cellulose films, O-PTIR data suggested that the ability of P. involutus to decompose cellulose was substantial. Moreover, the O-PTIR method enabled the identification of a zone located outside the fungal hyphae where the cellulose was decomposed by oxidation. We conclude that O-PTIR can provide valuable new insights into the abilities and mechanisms by which microorganisms interact with their surrounding environments.IMPORTANCEInfrared (IR) microspectroscopy allows the spatial distribution of chemical compound classes to be visualized. The use of conventional IR microspectroscopy in microbiological studies has been restricted by limited spatial resolution. Recent developments in laser technology have enabled a new class of IR microspectroscopy instruments to be developed, pushing the spatial resolution beyond the diffraction limit of IR light to approximately 500 nm. This improved spatial resolution now allows microscopic observations of changes in chemical compounds to be made, making IR microspectroscopy a useful tool to investigate microscale changes in chemistry that are caused by microbial activity. We show these new possibilities using optical photothermal infrared microspectroscopy to visualize the changes in cellulose substrates caused by oxidation by the ectomycorrhizal fungus Paxillus involutus at the interface between individual fungal hyphae and cellulose substrates.},
}
@article {pmid38289092,
year = {2024},
author = {Bontemps, Z and Moënne-Loccoz, Y and Hugoni, M},
title = {Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave.},
journal = {mSystems},
volume = {9},
number = {2},
pages = {e0123323},
pmid = {38289092},
issn = {2379-5077},
support = {//DRAC Nouvelle Aquitaine/ ; },
mesh = {*Coloring Agents ; *Microbiota ; Caves ; },
abstract = {Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.},
}
@article {pmid38286834,
year = {2024},
author = {Wang, X and Liu, Y and Qing, C and Zeng, J and Dong, J and Xia, P},
title = {Analysis of diversity and function of epiphytic bacterial communities associated with macrophytes using a metagenomic approach.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {37},
pmid = {38286834},
issn = {1432-184X},
mesh = {*Ecosystem ; Lakes ; Metagenome ; Bacteria/genetics/metabolism ; *Potamogetonaceae/genetics/microbiology ; Nitrogen/metabolism ; },
abstract = {Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions of epiphytic bacterial communities adhering to various submerged macrophytes remain largely unexplored. In this study, we employed a metagenomic approach to investigate the diversity and function of epiphytic bacterial communities associated with six submerged macrophytes: Ceratophyllum demersum, Hydrilla verticillata, Myriophyllum verticillatum, Potamogeton lucens, Stuckenia pectinata, and Najas marina. The results revealed that the predominant epiphytic bacterial species for each plant type included Pseudomonas spp., Microbacterium spp., and Stenotrophomonas rhizophila. Multiple comparisons and linear discriminant analysis effect size indicated a significant divergence in the community composition of epiphytic bacteria among the six submerged macrophytes, with 0.3-1% of species uniquely identified. Epiphytic bacterial richness associated with S. pectinata significantly differed from that of both C. demersum and H. verticillata, although no significant differences were observed in diversity and evenness. Functionally, notable variations were observed in the relative abundances of genes associated with carbon, nitrogen, and phosphorus cycling within epiphytic bacterial communities on the submerged macrophyte hosts. Among these communities, H. verticillata exhibited enrichment in genes related to the 3-hydroxypropionate bicycle and nitrogen assimilation, translocation, and denitrification. Conversely, M. verticillatum showcased enrichment in genes linked to the reductive citric acid cycle (Arnon-Buchanan cycle), reductive pentose phosphate cycle (Calvin cycle), polyphosphate degradation, and organic nitrogen metabolism. In summary, our findings offer valuable insights into the diversity and function of epiphytic bacteria on submerged macrophyte leaves, shedding light on their roles in lake ecosystems.},
}
@article {pmid38286067,
year = {2024},
author = {Lamprea-Pineda, PA and Demeestere, K and González-Cortés, JJ and Boon, N and Devlieghere, F and Van Langenhove, H and Walgraeve, C},
title = {Addition of (bio)surfactants in the biofiltration of hydrophobic volatile organic compounds in air.},
journal = {Journal of environmental management},
volume = {353},
number = {},
pages = {120132},
doi = {10.1016/j.jenvman.2024.120132},
pmid = {38286067},
issn = {1095-8630},
mesh = {Humans ; Surface-Active Agents/chemistry ; *Volatile Organic Compounds ; Hexanes ; Polysorbates ; Cyclohexanes ; *Saponins ; Filtration/methods ; },
abstract = {The removal of volatile organic compounds (VOCs) in air is of utmost importance to safeguard both environmental quality and human well-being. However, the low aqueous solubility of hydrophobic VOCs results in poor removal in waste gas biofilters (BFs). In this study, we evaluated the addition of (bio)surfactants in three BFs (BF1 and BF2 mixture of compost and wood chips (C + WC), and BF3 filled with expanded perlite) to enhance the removal of cyclohexane and hexane from a polluted gas stream. Experiments were carried out to select two (bio)surfactants (i.e., Tween 80 and saponin) out of five (sodium dodecyl sulfate (SDS), Tween 80, surfactin, rhamnolipid and saponin) from a physical-chemical (i.e., decreasing VOC gas-liquid partitioning) and biological (i.e., the ability of the microbial consortium to grow on the (bio)surfactants) point of view. The results show that adding Tween 80 at 1 critical micelle concentration (CMC) had a slight positive effect on the removal of both VOCs, in BF1 (e.g., 7.0 ± 0.6 g cyclohexane m[-3] h[-1], 85 ± 2% at 163 s; compared to 6.7 ± 0.4 g cyclohexane m[-3] h[-1], 76 ± 2% at 163 s and 0 CMC) and BF2 (e.g., 4.3 ± 0.4 g hexane m[-3] h[-1], 27 ± 2% at 82 s; compared to 3.1 ± 0.7 g hexane m[-3] h[-1], 16 ± 4% at 82 s and 0 CMC), but a negative effect in BF3 at either 1, 3 and 9 CMC (e.g., 2.4 ± 0.4 g hexane m[-3] h[-1], 30 ± 4% at 163 s and 1 CMC; compared to 4.6 ± 1.0 g hexane m[-3] h[-1], 43 ± 8% at 163 s and 0 CMC). In contrast, the performance of all BFs improved with the addition of saponin, particularly at 3 CMC. Notably, in BF3, the elimination capacity (EC) and removal efficiency (RE) doubled for both VOCs (i.e., 9.1 ± 0.6 g cyclohexane m[-3] h[-1], 49 ± 3%; 4.3 ± 0.3 g hexane m[-3] h[-1], 25 ± 3%) compared to no biosurfactant addition (i.e., 4.5 ± 0.4 g cyclohexane m[-3] h[-1], 23 ± 3%; hexane 2.2 ± 0.5 g m[-3] h[-1], 10 ± 2%) at 82 s. Moreover, the addition of the (bio)surfactants led to a shift in the microbial consortia, with a different response in BF1-BF2 compared to BF3. This study evaluates for the first time the use of saponin in BFs, it demonstrates that cyclohexane and hexane RE can be improved by (bio)surfactant addition, and it provides recommendations for future studies in this field.},
}
@article {pmid38282644,
year = {2024},
author = {Schauberger, C and Thamdrup, B and Lemonnier, C and Trouche, B and Poulain, J and Wincker, P and Arnaud-Haond, S and Glud, RN and Maignien, L},
title = {Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycad005},
pmid = {38282644},
issn = {2730-6151},
abstract = {Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. depth = 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one-third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. Although community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life = 125-419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor.},
}
@article {pmid38281398,
year = {2024},
author = {Van Peteghem, L and Sakarika, M and Matassa, S and Pikaar, I and Ganigué, R and Rabaey, K},
title = {Corrigendum to "Towards new carbon-neutral food systems: Combining carbon capture and utilization with microbial protein production" [Bioresour. Technol. 349 (2022) 126853].},
journal = {Bioresource technology},
volume = {395},
number = {},
pages = {130362},
doi = {10.1016/j.biortech.2024.130362},
pmid = {38281398},
issn = {1873-2976},
}
@article {pmid38280409,
year = {2024},
author = {Yao, S and Swanson, CS and Cheng, Z and He, Q and Yuan, H},
title = {Alternating polarity as a novel strategy for building synthetic microbial communities capable of robust Electro-Methanogenesis.},
journal = {Bioresource technology},
volume = {395},
number = {},
pages = {130374},
doi = {10.1016/j.biortech.2024.130374},
pmid = {38280409},
issn = {1873-2976},
mesh = {RNA, Ribosomal, 16S/genetics ; Biofuels ; Charcoal ; Bayes Theorem ; *Microbiota ; *Euryarchaeota/genetics ; Methane ; },
abstract = {Electro-methanogenic microbial communities can produce biogas with high efficiency and have attracted extensive research interest. In this study an alternating polarity strategy was developed to build electro-methanogenic communities. In two-chamber bioelectrochemical systems amended with activated carbon, the electrode potential was alternated between +0.8 V and -0.4 V vs. standard hydrogen electrode every three days. Cumulative biogas production under alternating polarity increased from 45 L/L/kg-activated carbon after start-up to 125 L/L/kg after the 4th enrichment, significantly higher than that under intermittent cathode (-0.4 V/open circuit), continuous cathode (-0.4 V), and open circuit. The communities assembled under alternating polarity were electroactive and structurally different from those assembled under other conditions. One Methanobacterium population and two Geobacter populations were consistently abundant and active in the communities. Their 16S rRNA was up-regulated by electrode potentials. Bayesian networks inferred close associations between these populations. Overall, electro-methanogenic communities have been successfully assembled with alternating polarity.},
}
@article {pmid38279257,
year = {2024},
author = {Córdova-Espinoza, MG and González-Vázquez, R and Barron-Fattel, RR and Gónzalez-Vázquez, R and Vargas-Hernández, MA and Albores-Méndez, EM and Esquivel-Campos, AL and Mendoza-Pérez, F and Mayorga-Reyes, L and Gutiérrez-Nava, MA and Medina-Quero, K and Escamilla-Gutiérrez, A},
title = {Aptamers: A Cutting-Edge Approach for Gram-Negative Bacterial Pathogen Identification.},
journal = {International journal of molecular sciences},
volume = {25},
number = {2},
pages = {},
pmid = {38279257},
issn = {1422-0067},
mesh = {Humans ; *Aptamers, Nucleotide ; SELEX Aptamer Technique ; Gram-Negative Bacteria/genetics ; Bacteria ; *Communicable Diseases ; },
abstract = {Early and accurate diagnoses of pathogenic microorganisms is essential to correctly identify diseases, treating infections, and tracking disease outbreaks associated with microbial infections, to develop precautionary measures that allow a fast and effective response in epidemics and pandemics, thus improving public health. Aptamers are a class of synthetic nucleic acid molecules with the potential to be used for medical purposes, since they can be directed towards any target molecule. Currently, the use of aptamers has increased because they are a useful tool in the detection of specific targets. We present a brief review of the use of aptamers to detect and identify bacteria or even some toxins with clinical importance. This work describes the advances in the technology of aptamers, with the purpose of providing knowledge to develop new aptamers for diagnoses and treatment of different diseases caused by infectious microorganisms.},
}
@article {pmid38278954,
year = {2024},
author = {Ma, X and Vanneste, S and Chang, J and Ambrosino, L and Barry, K and Bayer, T and Bobrov, AA and Boston, L and Campbell, JE and Chen, H and Chiusano, ML and Dattolo, E and Grimwood, J and He, G and Jenkins, J and Khachaturyan, M and Marín-Guirao, L and Mesterházy, A and Muhd, DD and Pazzaglia, J and Plott, C and Rajasekar, S and Rombauts, S and Ruocco, M and Scott, A and Tan, MP and Van de Velde, J and Vanholme, B and Webber, J and Wong, LL and Yan, M and Sung, YY and Novikova, P and Schmutz, J and Reusch, TBH and Procaccini, G and Olsen, JL and Van de Peer, Y},
title = {Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment.},
journal = {Nature plants},
volume = {10},
number = {2},
pages = {240-255},
pmid = {38278954},
issn = {2055-0278},
support = {833522/ERC_/European Research Council/International ; },
mesh = {*Alismatales/genetics ; *Zosteraceae/genetics ; Ecosystem ; },
abstract = {We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.},
}
@article {pmid38278226,
year = {2024},
author = {Sabrekov, AF and Semenov, MV and Terentieva, IE and Krasnov, GS and Kharitonov, SL and Glagolev, MV and Litti, YV},
title = {Anaerobic methane oxidation is quantitatively important in deeper peat layers of boreal peatlands: Evidence from anaerobic incubations, in situ stable isotopes depth profiles, and microbial communities.},
journal = {The Science of the total environment},
volume = {916},
number = {},
pages = {170213},
doi = {10.1016/j.scitotenv.2024.170213},
pmid = {38278226},
issn = {1879-1026},
mesh = {*Carbon Dioxide/analysis ; Anaerobiosis ; Methane/metabolism ; Soil ; RNA, Ribosomal, 16S ; Acetates ; *Microbiota ; Isotopes ; },
abstract = {Boreal peatlands store most of their carbon in layers deeper than 0.5 m under anaerobic conditions, where carbon dioxide and methane are produced as terminal products of organic matter degradation. Since the global warming potential of methane is much greater than that of carbon dioxide, the balance between the production rates of these gases is important for future climate predictions. Herein, we aimed to understand whether anaerobic methane oxidation (AMO) could explain the high CO2/CH4 anaerobic production ratios that are widely observed for the deeper peat layers of boreal peatlands. Furthermore, we quantified the metabolic pathways of methanogenesis to examine whether hydrogenotrophic methanogenesis is a dominant methane production pathway for the presumably recalcitrant deeper peat. To assess the CH4 cycling in deeper peat, we combined laboratory anaerobic incubations with a pathway-specific inhibitor, in situ depth patterns of stable isotopes in CH4, and 16S rRNA gene amplicon sequencing for three representative boreal peatlands in Western Siberia. We found up to a 69 % reduction in CH4 production due to AMO, which largely explained the high CO2/CH4 anaerobic production ratios and the in situ depth-related patterns of δ[13]C and δD in methane. The absence of acetate accumulation after inhibiting acetotrophic methanogenesis and the presence of sulfate- and nitrate-reducing anaerobic acetate oxidizers in the deeper peat indicated that these microorganisms use SO4[2-] and NO3[-] as electron acceptors. Acetotrophic methanogenesis dominated net CH4 production in the deeper peat, accounting for 81 ± 13 %. Overall, anaerobic oxidation is quantitatively important for the methane cycle in the deeper layers of boreal peatlands, affecting both methane and its main precursor concentrations.},
}
@article {pmid38276724,
year = {2024},
author = {Hassan, Z and Westerhoff, HV},
title = {Arsenic Contamination of Groundwater Is Determined by Complex Interactions between Various Chemical and Biological Processes.},
journal = {Toxics},
volume = {12},
number = {1},
pages = {},
pmid = {38276724},
issn = {2305-6304},
abstract = {At a great many locations worldwide, the safety of drinking water is not assured due to pollution with arsenic. Arsenic toxicity is a matter of both systems chemistry and systems biology: it is determined by complex and intertwined networks of chemical reactions in the inanimate environment, in microbes in that environment, and in the human body. We here review what is known about these networks and their interconnections. We then discuss how consideration of the systems aspects of arsenic levels in groundwater may open up new avenues towards the realization of safer drinking water. Along such avenues, both geochemical and microbiological conditions can optimize groundwater microbial ecology vis-à-vis reduced arsenic toxicity.},
}
@article {pmid38275746,
year = {2023},
author = {Seppi, M and Pasqualini, J and Facchin, S and Savarino, EV and Suweis, S},
title = {Emergent Functional Organization of Gut Microbiomes in Health and Diseases.},
journal = {Biomolecules},
volume = {14},
number = {1},
pages = {},
pmid = {38275746},
issn = {2218-273X},
mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis ; *Microbiota ; Metagenome ; Metagenomics ; },
abstract = {Continuous and significant progress in sequencing technologies and bioinformatics pipelines has revolutionized our comprehension of microbial communities, especially for human microbiomes. However, most studies have focused on studying the taxonomic composition of the microbiomes and we are still not able to characterize dysbiosis and unveil the underlying ecological consequences. This study explores the emergent organization of functional abundances and correlations of gut microbiomes in health and disease. Leveraging metagenomic sequences, taxonomic and functional tables are constructed, enabling comparative analysis. First, we show that emergent taxonomic and functional patterns are not useful to characterize dysbiosis. Then, through differential abundance analyses applied to functions, we reveal distinct functional compositions in healthy versus unhealthy microbiomes. In addition, we inquire into the functional correlation structure, revealing significant differences between the healthy and unhealthy groups, which may significantly contribute to understanding dysbiosis. Our study demonstrates that scrutinizing the functional organization in the microbiome provides novel insights into the underlying state of the microbiome. The shared data structure underlying the functional and taxonomic compositions allows for a comprehensive macroecological examination. Our findings not only shed light on dysbiosis, but also underscore the importance of studying functional interrelationships for a nuanced understanding of the dynamics of the microbial community. This research proposes a novel approach, bridging the gap between microbial ecology and functional analyses, promising a deeper understanding of the intricate world of the gut microbiota and its implications for human health.},
}
@article {pmid38274012,
year = {2023},
author = {Ulčar, B and Regueira, A and Podojsteršek, M and Boon, N and Ganigué, R},
title = {Why do lactic acid bacteria thrive in chain elongation microbiomes?.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {11},
number = {},
pages = {1291007},
pmid = {38274012},
issn = {2296-4185},
abstract = {Efficient waste management is necessary to transition towards a more sustainable society. An emerging trend is to use mixed culture biotechnology to produce chemicals from organic waste. Insights into the metabolic interactions between community members and their growth characterization are needed to mediate knowledge-driven bioprocess development and optimization. Here, a granular sludge bioprocess for the production of caproic acid through sugar-based chain elongation metabolism was established. Lactic acid and chain-elongating bacteria were identified as the two main functional guilds in the granular community. The growth features of the main community representatives (isolate Limosilactobacillus musocae G03 for lactic acid bacteria and type strain Caproiciproducens lactatifermentans for chain-elongating bacteria) were characterized. The measured growth rates of lactic acid bacteria (0.051 ± 0.005 h[-1]) were two times higher than those of chain-elongating bacteria (0.026 ± 0.004 h[-1]), while the biomass yields of lactic acid bacteria (0.120 ± 0.005 g biomass/g glucose) were two times lower than that of chain-elongating bacteria (0.239 ± 0.007 g biomass/g glucose). This points towards differential growth strategies, with lactic acid bacteria resembling that of a r-strategist and chain-elongating bacteria resembling that of a K-strategist. Furthermore, the half-saturation constant of glucose for L. mucosae was determined to be 0.35 ± 0.05 g/L of glucose. A linear trend of caproic acid inhibition on the growth of L. mucosae was observed, and the growth inhibitory caproic acid concentration was predicted to be 13.6 ± 0.5 g/L, which is the highest reported so far. The pre-adjustment of L. mucosae to 4 g/L of caproic acid did not improve the overall resistance to it, but did restore the growth rates at low caproic acid concentrations (1-4 g/L) to the baseline values (i.e., growth rate at 0 g/L of caproic acid). High resistance to caproic acid enables lactic acid bacteria to persist and thrive in the systems intended for caproic acid production. Here, insights into the growth of two main functional guilds of sugar-based chain elongation systems are provided which allows for a better understanding of their interactions and promotes future bioprocess design and optimization.},
}
@article {pmid38273535,
year = {2024},
author = {Lewis, ASL and Lau, MP and Jane, SF and Rose, KC and Be'eri-Shlevin, Y and Burnet, SH and Clayer, F and Feuchtmayr, H and Grossart, HP and Howard, DW and Mariash, H and Delgado Martin, J and North, RL and Oleksy, I and Pilla, RM and Smagula, AP and Sommaruga, R and Steiner, SE and Verburg, P and Wain, D and Weyhenmeyer, GA and Carey, CC},
title = {Anoxia begets anoxia: A positive feedback to the deoxygenation of temperate lakes.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17046},
doi = {10.1111/gcb.17046},
pmid = {38273535},
issn = {1365-2486},
support = {//College of Science Roundtable at Virginia Tech/ ; //Cornell Atkinson Center for Sustainability, Cornell University/ ; GR1540/37-1//Deutsche Forschungsgemeinschaft/ ; //EMALCSA Chair/ ; //Institute for Critical Technology and Applied Science/ ; //Leibniz-Institut f&#xfc;r Gew&#xe4;sser&#xf6;kologie und Binnenfischerei/ ; //LTSER Platform Tyrolean Alps (LTER-Austria)/ ; C01X2205//Ministry of Business, Innovation and Employment/ ; //Missouri Department of Natural Resources/ ; 1737424//National Science Foundation/ ; 1753639//National Science Foundation/ ; 1754265//National Science Foundation/ ; 1840995//National Science Foundation/ ; 1933016//National Science Foundation/ ; 2019528//National Science Foundation/ ; 2048031//National Science Foundation/ ; NE/R016429/1//Natural Environment Research Council/ ; //Oak Ridge National Laboratory/ ; 2020-01091//Svenska Forskningsr&#xe5;det Formas/ ; 2020-03222//Vetenskapsr&#xe5;det/ ; //Water Power Technologies Office/ ; },
mesh = {Humans ; *Lakes ; Chlorophyll A/analysis ; *Environmental Monitoring/methods ; Feedback ; Hypoxia ; Phosphorus/analysis ; Oxygen ; Eutrophication ; },
abstract = {Declining oxygen concentrations in the deep waters of lakes worldwide pose a pressing environmental and societal challenge. Existing theory suggests that low deep-water dissolved oxygen (DO) concentrations could trigger a positive feedback through which anoxia (i.e., very low DO) during a given summer begets increasingly severe occurrences of anoxia in following summers. Specifically, anoxic conditions can promote nutrient release from sediments, thereby stimulating phytoplankton growth, and subsequent phytoplankton decomposition can fuel heterotrophic respiration, resulting in increased spatial extent and duration of anoxia. However, while the individual relationships in this feedback are well established, to our knowledge, there has not been a systematic analysis within or across lakes that simultaneously demonstrates all of the mechanisms necessary to produce a positive feedback that reinforces anoxia. Here, we compiled data from 656 widespread temperate lakes and reservoirs to analyze the proposed anoxia begets anoxia feedback. Lakes in the dataset span a broad range of surface area (1-126,909 ha), maximum depth (6-370 m), and morphometry, with a median time-series duration of 30 years at each lake. Using linear mixed models, we found support for each of the positive feedback relationships between anoxia, phosphorus concentrations, chlorophyll a concentrations, and oxygen demand across the 656-lake dataset. Likewise, we found further support for these relationships by analyzing time-series data from individual lakes. Our results indicate that the strength of these feedback relationships may vary with lake-specific characteristics: For example, we found that surface phosphorus concentrations were more positively associated with chlorophyll a in high-phosphorus lakes, and oxygen demand had a stronger influence on the extent of anoxia in deep lakes. Taken together, these results support the existence of a positive feedback that could magnify the effects of climate change and other anthropogenic pressures driving the development of anoxia in lakes around the world.},
}
@article {pmid38273527,
year = {2024},
author = {Fontaine, S and Abbadie, L and Aubert, M and Barot, S and Bloor, JMG and Derrien, D and Duchene, O and Gross, N and Henneron, L and Le Roux, X and Loeuille, N and Michel, J and Recous, S and Wipf, D and Alvarez, G},
title = {Plant-soil synchrony in nutrient cycles: Learning from ecosystems to design sustainable agrosystems.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17034},
doi = {10.1111/gcb.17034},
pmid = {38273527},
issn = {1365-2486},
support = {ANR-20-PCA-0006//ANR/ ; //European Union/ ; //INRAE-CNRS/ ; //ISITE Clermont-Ferrand/ ; },
mesh = {Humans ; *Soil ; *Ecosystem ; Agriculture ; Plants ; Carbon ; },
abstract = {Redesigning agrosystems to include more ecological regulations can help feed a growing human population, preserve soils for future productivity, limit dependency on synthetic fertilizers, and reduce agriculture contribution to global changes such as eutrophication and warming. However, guidelines for redesigning cropping systems from natural systems to make them more sustainable remain limited. Synthetizing the knowledge on biogeochemical cycles in natural ecosystems, we outline four ecological systems that synchronize the supply of soluble nutrients by soil biota with the fluctuating nutrient demand of plants. This synchrony limits deficiencies and excesses of soluble nutrients, which usually penalize both production and regulating services of agrosystems such as nutrient retention and soil carbon storage. In the ecological systems outlined, synchrony emerges from plant-soil and plant-plant interactions, eco-physiological processes, soil physicochemical processes, and the dynamics of various nutrient reservoirs, including soil organic matter, soil minerals, atmosphere, and a common market. We discuss the relative importance of these ecological systems in regulating nutrient cycles depending on the pedoclimatic context and on the functional diversity of plants and microbes. We offer ideas about how these systems could be stimulated within agrosystems to improve their sustainability. A review of the latest advances in agronomy shows that some of the practices suggested to promote synchrony (e.g., reduced tillage, rotation with perennial plant cover, crop diversification) have already been tested and shown to be effective in reducing nutrient losses, fertilizer use, and N2 O emissions and/or improving biomass production and soil carbon storage. Our framework also highlights new management strategies and defines the conditions for the success of these nature-based practices allowing for site-specific modifications. This new synthetized knowledge should help practitioners to improve the long-term productivity of agrosystems while reducing the negative impact of agriculture on the environment and the climate.},
}
@article {pmid38273522,
year = {2024},
author = {Lí, JT and Hicks, LC and Brangarí, AC and Tájmel, D and Cruz-Paredes, C and Rousk, J},
title = {Subarctic winter warming promotes soil microbial resilience to freeze-thaw cycles and enhances the microbial carbon use efficiency.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17040},
doi = {10.1111/gcb.17040},
pmid = {38273522},
issn = {1365-2486},
support = {202006100130//Distinguished International Students Scholarship/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; 2022-01478//Svenska Forskningsr&#xe5;det Formas/ ; 2020-03858//Vetenskapsr&#xe5;det/ ; 2020-04083//Vetenskapsr&#xe5;det/ ; 4.3-2021-00164//Vetenskapsr&#xe5;det/ ; },
mesh = {*Soil Microbiology ; Seasons ; Soil/chemistry ; Carbon ; *Resilience, Psychological ; Climate Change ; },
abstract = {Climate change is predicted to cause milder winters and thus exacerbate soil freeze-thaw perturbations in the subarctic, recasting the environmental challenges that soil microorganisms need to endure. Historical exposure to environmental stressors can facilitate the microbial resilience to new cycles of that same stress. However, whether and how such microbial memory or stress legacy can modulate microbial responses to cycles of frost remains untested. Here, we conducted an in situ field experiment in a subarctic birch forest, where winter warming resulted in a substantial increase in the number and intensity of freeze-thaw events. After one season of winter warming, which raised mean surface and soil (-8 cm) temperatures by 2.9 and 1.4°C, respectively, we investigated whether the in situ warming-induced increase in frost cycles improved soil microbial resilience to an experimental freeze-thaw perturbation. We found that the resilience of microbial growth was enhanced in the winter warmed soil, which was associated with community differences across treatments. We also found that winter warming enhanced the resilience of bacteria more than fungi. In contrast, the respiration response to freeze-thaw was not affected by a legacy of winter warming. This translated into an enhanced microbial carbon-use efficiency in the winter warming treatments, which could promote the stabilization of soil carbon during such perturbations. Together, these findings highlight the importance of climate history in shaping current and future dynamics of soil microbial functioning to perturbations associated with climate change, with important implications for understanding the potential consequences on microbial-mediated biogeochemical cycles.},
}
@article {pmid38272989,
year = {2024},
author = {Laanbroek, HJ and Rains, MC and Verhoeven, JTA and Whigham, DF},
title = {The effect of intentional summer flooding for mosquito control on the nitrogen dynamics of impounded Avicennia germinans mangrove forests.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2165},
pmid = {38272989},
issn = {2045-2322},
mesh = {*Wetlands ; *Avicennia ; Ecosystem ; Mosquito Control ; Nitrogen/analysis ; Plant Breeding ; Forests ; Soil/chemistry ; },
abstract = {Coastal wetlands such as mangrove forests are breeding grounds for nuisance-causing insects. Rotational Impoundment Management (RIM) for mosquito control involves annual summer inundation of impounded mangrove forests with estuarine water during the summer half year. However, in addition to controlling mosquitos, RIM may change biogeochemical pathways. This study set out to investigate how RIM quantitatively affects physicochemical soil characteristics and potential nitrifying and denitrifying activities (PNA and PDA), which are key in the global nitrogen cycle. Before and after the implementation of RIM, soil samples were collected annually in habitats differing in size and abundance of black mangroves (Avicennia germinans) in an impoundment with RIM and in an adjacent impoundment with a more open connection to the lagoon. Compared to the non-managed impoundment, soil moisture content, total nitrogen and PDA increased, while salinity decreased after the start of annual summer flooding, but only in the dwarf habitat. In the sparse and dense habitats, total nitrogen and PDA increased independently of summer flooding, whereas soil moisture content and salinity were not affected by RIM. Labile organic nitrogen increased only in the RIM impoundment, irrespective of the habitat type. PNA was generally not affected with time, except in the dwarf habitat in the absence of intentional summer flooding where it increased. Changes in the non-managed impoundment adjacent to the RIM impoundment demonstrate the importance of groundwater exchange in linked ecosystems. The consequences of interventions in the management of mangrove impoundments and adjacent forests for the nitrogen budget are discussed.},
}
@article {pmid38271645,
year = {2024},
author = {De Bondt, Y and Verdonck, C and Brandt, MJ and De Vuyst, L and Gänzle, MG and Gobbetti, M and Zannini, E and Courtin, CM},
title = {Wheat Sourdough Breadmaking: A Scoping Review.},
journal = {Annual review of food science and technology},
volume = {15},
number = {1},
pages = {265-282},
doi = {10.1146/annurev-food-110923-034834},
pmid = {38271645},
issn = {1941-1421},
mesh = {*Bread/microbiology ; *Fermentation ; *Triticum ; Food Handling ; Humans ; Food Microbiology ; Taste ; Nutritive Value ; },
abstract = {Using sourdough in breadmaking can enhance bread's shelf-life and flavor compared to exclusive baker's yeast use and is believed to increase its nutritional quality and healthiness. Previous research established insight into the microbial ecology of sourdough, but the link between leavening agent use, processing, and bread quality remains elusive. However, such knowledge is key for standardization, research on the health benefits, and the definition of sourdough bread. In this systematic scoping review, we analyzed 253 studies and identified large variations in the type and amount of leavening agent, fermentation conditions, and bread quality (specific loaf volume and acidification). The interrelation between these elements and their effect on the extent of fermentation is discussed, together with issues preventing proper comparison of breadmaking procedures. With this review, we want to contribute to the dialogue concerning the definition of sourdough-type bread products and the research into the health benefits attributed to them.},
}
@article {pmid38267517,
year = {2024},
author = {Acuña, JJ and Rilling, JI and Inostroza, NG and Zhang, Q and Wick, LY and Sessitsch, A and Jorquera, MA},
title = {Variovorax sp. strain P1R9 applied individually or as part of bacterial consortia enhances wheat germination under salt stress conditions.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2070},
pmid = {38267517},
issn = {2045-2322},
support = {1221228//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 1201386//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; },
mesh = {*Triticum ; Salt Stress ; Plant Development ; Salt Tolerance ; *Comamonadaceae ; *Magnesium ; *Radioisotopes ; },
abstract = {Endophytes isolated from extremophile plants are interesting microbes for improving the stress tolerance of agricultural plants. Here, we isolated and characterized endophytic bacteria showing plant growth-promoting (PGP) traits from plants in two extreme Chilean biomes (Atacama Desert and Chilean Patagonia). Forty-two isolates were characterized as both halotolerant auxin producers (2-51 mg L[-1]) and 1-aminocyclopropane-1-carboxylate (ACC)-degrading bacteria (15-28 µmol αKB mg protein[-1] h[-1]). The most efficient isolates were tested as single strains, in dual and triple consortia, or in combination with previously reported PGP rhizobacteria (Klebsiella sp. 27IJA and 8LJA) for their impact on the germination of salt-exposed (0.15 M and 0.25 M NaCl) wheat seeds. Interestingly, strain P1R9, identified as Variovorax sp., enhanced wheat germination under salt stress conditions when applied individually or as part of bacterial consortia. Under salt stress, plants inoculated with dual consortia containing the strain Variovorax sp. P1R9 showed higher biomass (41%) and reduced lipid peroxidation (33-56%) than uninoculated plants. Although the underlying mechanisms remain elusive, our data suggest that the application of Variovorax sp. P1R9, alone or as a member of PGP consortia, may improve the salt stress tolerance of wheat plants.},
}
@article {pmid38265481,
year = {2024},
author = {He, B and Li, Q and Zou, S and Bai, X and Li, W and Chen, Y},
title = {Dynamic Changes of Soil Microbial Communities During the Afforestation of Pinus Armandii in a Karst Region of Southwest China.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {36},
pmid = {38265481},
issn = {1432-184X},
support = {Qiankehe Jichu-ZK [2021] 231//the Project of Guizhou Science and Technology Fund/ ; Bikelianhe [2023] 10 and 24//the Project of Bijie Science and Technology Fund/ ; Bikelianhe [2023] 10 and 24//the Project of Bijie Science and Technology Fund/ ; Bkhzdzx [2021]1//Bijie Science and Technology Major Project/ ; Bikelianhezi Guigongcheng [2021] 8//the Opening Fund for Guizhou Province Key Laboratory of Ecological Protection and Restoration of Typical Plateau Wetlands/ ; [2022]096//the Technology Top Talent Project in Department of Education of Guizhou Province/ ; Qianjiaohe KY [2022]120 and 123//the Support Plan for Young Science and Technology talents of Guizhou Province Education Department/ ; },
mesh = {*Microbiota ; *Mycobiome ; China ; *Pinus ; Soil ; },
abstract = {Clarifying the response of soil microbial communities to vegetation restoration is essential to comprehend biogeochemical processes and ensure the long-term viability of forest development. To assess the variations in soil microbial communities throughout the growth of Pinus armandii plantations in the karst region, we utilized the "space instead of time" approach and selected four P. armandii stands with ages ranging from 10 to 47 years, along with a grassland control. The microbial community structure was determined by conducting Illumina sequencing of the 16 S rRNA gene and the ITS gene, respectively. The results demonstrated that afforestation with P. armandii significantly influenced soil microbial communities, as indicated by notable differences in bacterial and fungal composition and diversity between the plantations and the control. However, soil microbe diversity did not display significant variation across stand ages. Moreover, the bacterial community exhibited higher responsiveness to age gradients compared to the fungal community. Soil physicochemical factors play a critical role in elucidating microbial diversity and community composition variations during restoration processes. TN, AN, TP, AP, SOC, AK, and pH were the most significant influencing factors for the composition of bacterial community, while TC, SOC, pH, and TCa were the most significant influencing factors for the composition of fungal community. Our findings indicate substantial changes in soil bacterial and fungal communities across successive stages of development. Additionally, the changes in dominant bacteria and fungi characteristics across the age gradient were primarily attributed to variations in the prevailing soil conditions and chemical factors.},
}
@article {pmid38261090,
year = {2024},
author = {Deschamps, C and Denis, S and Humbert, D and Priymenko, N and Chalancon, S and De Bodt, J and Van de Wiele, T and Ipharraguerre, I and Alvarez-Acero, I and Achard, C and Apper, E and Blanquet-Diot, S},
title = {Canine Mucosal Artificial Colon: development of a new colonic in vitro model adapted to dog sizes.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {166},
pmid = {38261090},
issn = {1432-0614},
mesh = {Dogs ; Animals ; *Ecosystem ; Colon ; *Actinobacteria ; Ammonia ; Anaerobiosis ; },
abstract = {Differences in dog breed sizes are an important determinant of variations in digestive physiology, mainly related to the large intestine. In vitro gut models are increasingly used as alternatives to animal experiments for technical, cost, societal, and regulatory reasons. Up to now, only one in vitro model of the canine colon incorporates the dynamics of different canine gut regions, yet no adaptations exist to reproduce size-related digestive parameters. To address this limitation, we developed a new model of the canine colon, the CANIne Mucosal ARtificial COLon (CANIM-ARCOL), simulating main physiochemical (pH, transit time, anaerobiosis), nutritional (ileal effluent composition), and microbial (lumen and mucus-associated microbiota) parameters of this ecosystem and adapted to three dog sizes (i.e., small under 10 kg, medium 10-30 kg, and large over 30 kg). To validate the new model regarding microbiota composition and activities, in vitro fermentations were performed in bioreactors inoculated with stools from 13 dogs (4 small, 5 medium, and 4 large). After a stabilization period, microbiota profiles clearly clustered depending on dog size. Bacteroidota and Firmicutes abundances were positively correlated with dog size both in vitro and in vivo, while opposite trends were observed for Actinobacteria and Proteobacteria. As observed in vivo, microbial activity also increased with dog size in vitro, as evidenced from gas production, short-chain fatty acids, ammonia, and bile acid dehydroxylation. In line with the 3R regulation, CANIM-ARCOL could be a relevant platform to assess bilateral interactions between food and pharma compounds and gut microbiota, capturing inter-individual or breed variabilities. KEY POINTS: • CANIM-ARCOL integrates main canine physicochemical and microbial colonic parameters • Gut microbiota associated to different dog sizes is accurately maintained in vitro • The model can help to move toward personalized approach considering dog body weight.},
}
@article {pmid38261068,
year = {2024},
author = {Pei, P and Aslam, M and Wang, H and Ye, P and Li, T and Liang, H and Lin, Q and Chen, W and Du, H},
title = {Diversity and ecological function of urease-producing bacteria in the cultivation environment of Gracilariopsis lemaneiformis.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {35},
pmid = {38261068},
issn = {1432-184X},
support = {2022fjscq02//the Open Program of Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province/ ; 2022fjscq02//the Open Program of Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province/ ; 41976125//the National Natural Science Foundation of China/ ; 42206116//the Natural Science Foundation of China grants/ ; 2022KCXTD008//the Program for University Innovation Team of Guangdong Province/ ; 2018KCXTD012//the Team Project of Department of Education of Guangdong Province/ ; },
mesh = {*Urease ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Seaweed ; Nitrogen ; Urea ; },
abstract = {Urease-producing bacteria (UPB) provide inorganic nitrogen for primary producers by hydrolyzing urea, and play an important role in marine nitrogen cycle. However, there is still an incomplete understanding of UPB and their ecological functions in the cultivation environment of the red macroalgae Gracilariopsis lemaneiformis. This study comprehensively analyzed the diversity of culturable UPB and explored their effects on urea uptake by G. lemaneiformis. A total of 34 isolates belonging to four main bacterial phyla i.e. (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) were identified through 16S rRNA sequencing and were screened for UPB by urea agar chromogenic medium assay and ureC gene cloning. Our data revealed that only 8 strains contained urease. All of these UPB exhibited different urease activities, which were determined by the Berthelot reaction colorimetry assay. Additionally, the UPB strain (G13) isolated from G. lemaneiformis with higher urease activity was selected for co-culture with G. lemaneiformis to explore its role in promoting or inhibiting nitrogen uptake by macroalgae. The results showed a significant increase in urea consumption in the culture medium and the total cellular nitrogen in G. lemaneiformis in the UPB-co culture group compared to the sterile group. This suggests that the selected UPB strain positively influences nitrogen uptake by G. lemaneiformis. Similarly, isotopic assays revealed that the δ[15]N content of G. lemaneiformis was significantly higher in the UPB-co culture than in the control group, where δ[15]N-urea was the only nitrogen source in the culture medium. This indicates that the UPB helped G. lemaneiformis to absorb more nitrogen from urea. Moreover, the highest content of δ[15]N was found in G. lemaneiformis with epiphytic bacteria compared to sterilized (i.e. control), showing that epiphytic bacteria, along with UPB, have a compound effect in helping G. lemaneiformis absorb more nitrogen from urea. Taken together, these results provide unique insight into the ecological role of UPB and suggest that urease from macroalgae environment-associated bacteria might be an important player in marine nitrogen cycling.},
}
@article {pmid38261023,
year = {2024},
author = {Herren, P and Dunn, AM and Meyling, NV and Savio, C and Hesketh, H},
title = {Effect of CO2 Concentrations on Entomopathogen Fitness and Insect-Pathogen Interactions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {34},
pmid = {38261023},
issn = {1432-184X},
support = {859850//Horizon 2020 Framework Programme/ ; },
mesh = {Animals ; *Carbon Dioxide ; Insecta ; Larva ; *Bacillus thuringiensis ; Biological Control Agents ; },
abstract = {Numerous insect species and their associated microbial pathogens are exposed to elevated CO2 concentrations in both artificial and natural environments. However, the impacts of elevated CO2 on the fitness of these pathogens and the susceptibility of insects to pathogen infections are not well understood. The yellow mealworm, Tenebrio molitor, is commonly produced for food and feed purposes in mass-rearing systems, which increases risk of pathogen infections. Additionally, entomopathogens are used to control T. molitor, which is also a pest of stored grains. It is therefore important to understand how elevated CO2 may affect both the pathogen directly and impact on host-pathogen interactions. We demonstrate that elevated CO2 concentrations reduced the viability and persistence of the spores of the bacterial pathogen Bacillus thuringiensis. In contrast, conidia of the fungal pathogen Metarhizium brunneum germinated faster under elevated CO2. Pre-exposure of the two pathogens to elevated CO2 prior to host infection did not affect the survival probability of T. molitor larvae. However, larvae reared at elevated CO2 concentrations were less susceptible to both pathogens compared to larvae reared at ambient CO2 concentrations. Our findings indicate that whilst elevated CO2 concentrations may be beneficial in reducing host susceptibility in mass-rearing systems, they may potentially reduce the efficacy of the tested entomopathogens when used as biological control agents of T. molitor larvae. We conclude that CO2 concentrations should be carefully selected and monitored as an additional environmental factor in laboratory experiments investigating insect-pathogen interactions.},
}
@article {pmid38260895,
year = {2023},
author = {Tan, H and Du, XH and Bonito, G and Masaphy, S},
title = {Editorial: Morels: physiology, genetics, and interactions with the environment.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1352719},
pmid = {38260895},
issn = {1664-302X},
}
@article {pmid38260330,
year = {2024},
author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA},
title = {A toxic environment selects for specialist microbiome in poison frogs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38260330},
issn = {2692-8205},
support = {DP2 HD102042/HD/NICHD NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; },
abstract = {Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate microbiome community composition. In poison frogs within the family Dendrobatidae, the skin microbiome is exposed to the alkaloids that the frogs sequester from their diet and use for defense. Given the demonstrated antimicrobial effects of these poison frog alkaloids, these compounds may be structuring the skin microbial community. To test this, we first characterized microbial communities from chemically defended and closely related non-defended frogs from Ecuador. Then we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of a single frog species. In both the field and lab experiments, we found that alkaloid-exposed microbiomes are more species rich and phylogenetically diverse, with an increase in rare taxa. To better understand the strain-specific behavior in response to alkaloids, we cultured microbial strains from poison frog skin and found the majority of strains exhibited either enhanced growth or were not impacted by the addition of DHQ. Additionally, stable isotope tracing coupled to nanoSIMS suggests that some of these strains are able to metabolize DHQ. Taken together, these data suggest that poison frog chemical defenses open new niches for skin-associated microbes with specific adaptations, including the likely metabolism of alkaloids, that enable their survival in this toxic environment. This work helps expand our understanding of how exposure to exogenous compounds like alkaloids can impact host microbiomes.},
}
@article {pmid38259105,
year = {2024},
author = {Hoang, DQ and Wilson, LR and Scheftgen, AJ and Suen, G and Currie, CR},
title = {Disturbance-diversity relationships of microbial communities change based on growth substrate.},
journal = {mSystems},
volume = {9},
number = {2},
pages = {e0088723},
pmid = {38259105},
issn = {2379-5077},
support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria ; Cellulose ; Glucose ; },
abstract = {Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances and how those responses can vary is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that the community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticcacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticcacaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (1.95-7.33 Hill 1 diversity) that peaks at the intermediate disturbance frequency treatment or one disturbance every 3 days. Communities grown on glucose, however, ranged from 1.63 to 5.19 Hill 1 diversity with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency and may potentially explain the variety of diversity-disturbance relationships observed in microbial systems.IMPORTANCEA generalizable diversity-disturbance relationship (DDR) of microbial communities remains a contentious topic. Various microbial systems have different DDRs. Rather than finding support or refuting specific DDRs, we investigated the underlying factors that lead to different DDRs. In this study, we measured a cellulose-enriched microbial community's response to a range of disturbance frequencies from high to low, across two different substrates: cellulose and glucose. We demonstrate that the community displays a unimodal DDR when grown on cellulose and a monotonically increasing DDR when grown on glucose. Our findings suggest that the same community can display different DDRs. These results suggest that the range of DDRs we observe across different microbial systems may be due to the nutritional resources microbial communities can access and the interactions between bacteria and their environment.},
}
@article {pmid38259093,
year = {2024},
author = {Fadum, JM and Borton, MA and Daly, RA and Wrighton, KC and Hall, EK},
title = {Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics.},
journal = {mSystems},
volume = {9},
number = {2},
pages = {e0105923},
pmid = {38259093},
issn = {2379-5077},
support = {P30 CA046934/CA/NCI NIH HHS/United States ; },
mesh = {*Ecosystem ; Nitrates/analysis ; Lakes/chemistry ; Organic Chemicals ; *Ammonium Compounds ; Water ; Nitrogen ; },
abstract = {Nitrogen (N) availability is one of the principal drivers of primary productivity across aquatic ecosystems. However, the microbial communities and emergent metabolisms that govern N cycling in tropical lakes are both distinct from and poorly understood relative to those found in temperate lakes. This latitudinal difference is largely due to the warm (>20°C) temperatures of tropical lake anoxic hypolimnions (deepest portion of a stratified water column), which result in unique anaerobic metabolisms operating without the temperature constraints found in lakes at temperate latitudes. As such, tropical hypolimnions provide a platform for exploring microbial membership and functional diversity. To better understand N metabolism in warm anoxic waters, we combined measurements of geochemistry and water column thermophysical structure with genome-resolved metatranscriptomic analyses of the water column microbiome in Lake Yojoa, Honduras. We sampled above and below the oxycline in June 2021, when the water column was stratified, and again at the same depths and locations in January 2022, when the water column was mixed. We identified 335 different lineages and significantly different microbiome membership between seasons and, when stratified, between depths. Notably, nrfA (indicative of dissimilatory nitrate reduction to ammonium) was upregulated relative to other N metabolism genes in the June hypolimnion. This work highlights the taxonomic and functional diversity of microbial communities in warm and anoxic inland waters, providing insight into the contemporary microbial ecology of tropical ecosystems as well as inland waters at higher latitudes as water columns continue to warm in the face of global change.IMPORTANCEIn aquatic ecosystems where primary productivity is limited by nitrogen (N), whether continuously, seasonally, or in concert with additional nutrient limitations, increased inorganic N availability can reshape ecosystem structure and function, potentially resulting in eutrophication and even harmful algal blooms. Whereas microbial metabolic processes such as mineralization and dissimilatory nitrate reduction to ammonium increase inorganic N availability, denitrification removes bioavailable N from the ecosystem. Therefore, understanding these key microbial mechanisms is critical to the sustainable management and environmental stewardship of inland freshwater resources. This study identifies and characterizes these crucial metabolisms in a warm, seasonally anoxic ecosystem. Results are contextualized by an ecological understanding of the study system derived from a multi-year continuous monitoring effort. This unique data set is the first of its kind in this largely understudied ecosystem (tropical lakes) and also provides insight into microbiome function and associated taxa in warm, anoxic freshwaters.},
}
@article {pmid38256774,
year = {2024},
author = {Reyes-Ardila, WL and Rugeles-Silva, PA and Duque-Zapata, JD and Vélez-Martínez, GA and Tarazona Pulido, L and Cardona Tobar, KM and Díaz Gallo, SA and Muñoz Flórez, JE and Díaz-Ariza, LA and López-Alvarez, D},
title = {Exploring Genomics and Microbial Ecology: Analysis of Bidens pilosa L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
pmid = {38256774},
issn = {2223-7747},
support = {FP44842-221-2018//Pontificia Universidad Javeriana/ ; FP44842-221-2018//Ministry of Science, Technology, and Innovation, the Ministry of National Education/ ; FP44842-221-2018//Ministry of Industry, Commerce and Tourism/ ; FP44842-221-2018//ICETEX/ ; FP44842-221-2018//Ministry of National Education/ ; },
abstract = {Bidens pilosa L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented to analyze genetic diversity and population structure, and metabarcoding to examine microbial composition in soils from Palmira, Sibundoy, and Bogotá, Colombia. A total of 2,984,123 loci and 3485 single nucleotide polymorphisms (SNPs) were identified, revealing a genetic variation of 12% between populations and 88% within individuals, and distributing the population into three main genetic groups, FST = 0.115 (p < 0.001) and FIT = 0.013 (p > 0.05). In the soil analysis, significant correlations were found between effective cation exchange capacity (ECEC) and apparent density, soil texture, and levels of Mg and Fe, as well as negative correlations between ECEC and Mg, and Mg, Fe, and Ca. Proteobacteria and Ascomycota emerged as the predominant bacterial and fungal phyla, respectively. Analyses of alpha, beta, and multifactorial diversity highlight the influence of ecological and environmental factors on these microbial communities, revealing specific patterns of clustering and association between bacteria and fungi in the studied locations.},
}
@article {pmid38254227,
year = {2024},
author = {Gul, F and Herrema, H and Davids, M and Keating, C and Nasir, A and Ijaz, UZ and Javed, S},
title = {Gut microbial ecology and exposome of a healthy Pakistani cohort.},
journal = {Gut pathogens},
volume = {16},
number = {1},
pages = {5},
pmid = {38254227},
issn = {1757-4749},
support = {NE/L011956/1//Natural Environment Research Council/ ; EP/P029329/1//Engineering and Physical Sciences Research Council/ ; },
abstract = {BACKGROUND: Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC).<br><br>METHODS: 16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through [Formula: see text] test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment.<br><br>RESULTS: A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history.<br><br>CONCLUSIONS: This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings.},
}
@article {pmid38253620,
year = {2024},
author = {Zeng, J and Xie, C and Huang, Z and Cho, CH and Chan, H and Li, Q and Ashktorab, H and Smoot, DT and Wong, SH and Yu, J and Gong, W and Liang, C and Xu, H and Chen, H and Liu, X and Wu, JCY and Ip, M and Gin, T and Zhang, L and Chan, MTV and Hu, W and Wu, WKK},
title = {LOX-1 acts as an N[6]-methyladenosine-regulated receptor for Helicobacter pylori by binding to the bacterial catalase.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {669},
pmid = {38253620},
issn = {2041-1723},
mesh = {Animals ; Humans ; Mice ; *Adenosine/analogs &amp; derivatives ; Catalase/metabolism ; *Helicobacter Infections/metabolism ; *Helicobacter pylori/metabolism ; RNA, Messenger/genetics ; *Scavenger Receptors, Class E/genetics ; },
abstract = {The role of N[6]-methyladenosine (m[6]A) modification of host mRNA during bacterial infection is unclear. Here, we show that Helicobacter pylori infection upregulates host m[6]A methylases and increases m[6]A levels in gastric epithelial cells. Reducing m[6]A methylase activity via hemizygotic deletion of methylase-encoding gene Mettl3 in mice, or via small interfering RNAs targeting m[6]A methylases, enhances H. pylori colonization. We identify LOX-1 mRNA as a key m[6]A-regulated target during H. pylori infection. m[6]A modification destabilizes LOX-1 mRNA and reduces LOX-1 protein levels. LOX-1 acts as a membrane receptor for H. pylori catalase and contributes to bacterial adhesion. Pharmacological inhibition of LOX-1, or genetic ablation of Lox-1, reduces H. pylori colonization. Moreover, deletion of the bacterial catalase gene decreases adhesion of H. pylori to human gastric sections. Our results indicate that m[6]A modification of host LOX-1 mRNA contributes to protection against H. pylori infection by downregulating LOX-1 and thus reducing H. pylori adhesion.},
}
@article {pmid38251984,
year = {2024},
author = {Shoemaker, WR and Grilli, J},
title = {Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {38251984},
issn = {2050-084X},
support = {2010885//National Science Foundation/ ; },
mesh = {Logistic Models ; Phylogeny ; *Biological Evolution ; Biodiversity ; *Microbiota ; },
abstract = {The structure and diversity of microbial communities are intrinsically hierarchical due to the shared evolutionary history of their constituents. This history is typically captured through taxonomic assignment and phylogenetic reconstruction, sources of information that are frequently used to group microbes into higher levels of organization in experimental and natural communities. Connecting community diversity to the joint ecological dynamics of the abundances of these groups is a central problem of community ecology. However, how microbial diversity depends on the scale of observation at which groups are defined has never been systematically examined. Here, we used a macroecological approach to quantitatively characterize the structure and diversity of microbial communities among disparate environments across taxonomic and phylogenetic scales. We found that measures of biodiversity at a given scale can be consistently predicted using a minimal model of ecology, the Stochastic Logistic Model of growth (SLM). This result suggests that the SLM is a more appropriate null-model for microbial biodiversity than alternatives such as the Unified Neutral Theory of Biodiversity. Extending these within-scale results, we examined the relationship between measures of biodiversity calculated at different scales (e.g. genus vs. family), an empirical pattern previously evaluated in the context of the Diversity Begets Diversity (DBD) hypothesis (Madi et al., 2020). We found that the relationship between richness estimates at different scales can be quantitatively predicted assuming independence among community members, demonstrating that the DBD can be sufficiently explained using the SLM as a null model of ecology. Contrastingly, only by including correlations between the abundances of community members (e.g. as the consequence of interactions) can we predict the relationship between estimates of diversity at different scales. The results of this study characterize novel microbial patterns across scales of organization and establish a sharp demarcation between recently proposed macroecological patterns that are not and are affected by ecological interactions.},
}
@article {pmid38251877,
year = {2024},
author = {Schloss, PD},
title = {Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses.},
journal = {mSphere},
volume = {9},
number = {2},
pages = {e0035423},
pmid = {38251877},
issn = {2379-5042},
support = {R01 CA215574/CA/NCI NIH HHS/United States ; U01 CA264071/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; },
abstract = {UNLABELLED: Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is "inadmissible" because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses.<br><br>IMPORTANCE: Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.},
}
@article {pmid38248928,
year = {2023},
author = {Masigol, H and Retter, A and Pourmoghaddam, MJ and Amini, H and Taheri, SR and Mostowfizadeh-Ghalamfarsa, R and Kimiaei, M and Grossart, HP},
title = {Opening Pandora's Box: Neglected Biochemical Potential of Permafrost-Associated Fungal Communities in a Warming Climate.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
pmid = {38248928},
issn = {2309-608X},
support = {DFG GR1540/37-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Permafrost, a vast storage reservoir of frozen organic matter, is rapidly thawing due to climate change, releasing previously preserved carbon into the environment. This phenomenon has significant consequences for microbial communities, including fungi, inhabiting permafrost-associated regions. In this review, we delve into the intricate interplay between permafrost thawing and fungal diversity and functionality with an emphasis on thermokarst lakes. We explore how the release of organic carbon from thawing permafrost alters the composition and activities of fungal communities, emphasizing the potential for shifts in taxonomic diversity and functional gene expression. We discuss the formation of thermokarst lakes, as an example of permafrost thaw-induced ecological disruptions and their impact on fungal communities. Furthermore, we analyze the repercussions of these changes, including effects on nutrient cycling, plant productivity, and greenhouse gas (GHG) emissions. By elucidating the multifaceted relationship between permafrost thaw and aquatic fungi, this review provides valuable insights into the ecological consequences of ongoing climate change in permafrost-affected regions.},
}
@article {pmid38248338,
year = {2024},
author = {Kirby, TO and Sapp, PA and Townsend, JR and Govaert, M and Duysburgh, C and Marzorati, M and Marshall, TM and Esposito, R},
title = {AG1[®] Induces a Favorable Impact on Gut Microbial Structure and Functionality in the Simulator of Human Intestinal Microbial Ecosystem[®] Model.},
journal = {Current issues in molecular biology},
volume = {46},
number = {1},
pages = {557-569},
pmid = {38248338},
issn = {1467-3045},
support = {N/A//Athletic Greens International/ ; },
abstract = {Modulation of the human gut microbiome has become an area of interest in the nutraceutical space. We explored the effect of the novel foundational nutrition supplement AG1[®] on the composition of human microbiota in an in vitro experimental design. Employing the Simulator of Human Intestinal Microbial Ecosystem (SHIME[®]) model, AG1[®] underwent digestion, absorption, and subsequent colonic microenvironment simulation under physiologically relevant conditions in healthy human fecal inocula. Following 48 h of colonic simulation, the gut microbiota were described using shallow shotgun, whole genome sequencing. Metagenomic data were used to describe changes in community structure (alpha diversity, beta diversity, and changes in specific taxa) and community function (functional heterogeneity and changes in specific bacterial metabolic pathways). Results showed no significant change in alpha diversity, but a significant effect of treatment and donor and an interaction between the treatment and donor effect on structural heterogeneity likely stemming from the differential enrichment of eight bacterial taxa. Similar findings were observed for community functional heterogeneity likely stemming from the enrichment of 20 metabolic pathways characterized in the gene ontology term database. It is logical to conclude that an acute dose of AG1 has significant effects on gut microbial composition that may translate into favorable effects in humans.},
}
@article {pmid38246125,
year = {2024},
author = {Mahony, J},
title = {Biological and bioinformatic tools for the discovery of unknown phage-host combinations.},
journal = {Current opinion in microbiology},
volume = {77},
number = {},
pages = {102426},
doi = {10.1016/j.mib.2024.102426},
pmid = {38246125},
issn = {1879-0364},
mesh = {*Bacteriophages/genetics ; Artificial Intelligence ; Computational Biology ; *Microbiota ; Metagenomics ; },
abstract = {The field of microbial ecology has been transformed by metagenomics in recent decades and has culminated in vast datasets that facilitate the bioinformatic dissection of complex microbial communities. Recently, attention has turned from defining the microbiota composition to the interactions and relationships that occur between members of the microbiota. Within complex microbiota, the identification of bacteriophage-host combinations has been a major challenge. Recent developments in artificial intelligence tools to predict protein structure and function as well as the relationships between bacteria and their infecting bacteriophages allow a strategic approach to identifying and validating phage-host relationships. However, biological validation of these predictions remains essential and will serve to improve the existing predictive tools. In this review, I provide an overview of the most recent developments in both bioinformatic and experimental approaches to predicting and experimentally validating unknown phage-host combinations.},
}
@article {pmid38244618,
year = {2024},
author = {Yalçın, G and Yıldız, D and Calderó-Pascual, M and Yetim, S and Şahin, Y and Parakatselaki, ME and Avcı, F and Karakaya, N and Ladoukakis, ED and Berger, SA and Ger, KA and Jeppesen, E and Beklioğlu, M},
title = {Quality matters: Response of bacteria and ciliates to different allochthonous dissolved organic matter sources as a pulsed disturbance in shallow lakes.},
journal = {The Science of the total environment},
volume = {916},
number = {},
pages = {170140},
doi = {10.1016/j.scitotenv.2024.170140},
pmid = {38244618},
issn = {1879-1026},
mesh = {Animals ; *Ecosystem ; *Lakes/microbiology ; Dissolved Organic Matter ; Bacteria ; Biomass ; Plankton ; },
abstract = {Shallow lake ecosystems are particularly prone to disturbances such as pulsed dissolved organic matter (allochthonous-DOM; hereafter allo-DOM) loadings from catchments. However, the effects of allo-DOM with contrasting quality (in addition to quantity) on the planktonic communities of microbial loop are poorly understood. To determine the impact of different qualities of pulsed allo-DOM disturbance on the coupling between bacteria and ciliates, we conducted a mesocosm experiment with two different allo-DOM sources added to mesocosms in a single-pulse disturbance event: Alder tree leaf extract, a more labile (L) source and HuminFeed® (HF), a more recalcitrant source. Allo-DOM sources were used as separate treatments and in combination (HFL) relative to the control without allo-DOM additions (C). Our results indicate that the quality of allo-DOM was a major regulator of planktonic microbial community biomass and/or composition through which both bottom-up and top-down forces were involved. Bacteria biomass showed significant nonlinear responses in L and HFL with initial increases followed by decreases to pre-pulse conditions. Ciliate biomass was significantly higher in L compared to all other treatments. In terms of composition, bacterivore ciliate abundance was significantly higher in both L and HFL treatments, mainly driven by the bacterial biomass increase in the same treatments. GAMM models showed negative interaction between metazoan zooplankton biomass and ciliates, but only in the L treatment, indicating top-down control on ciliates. Ecosystem stability analyses revealed overperformance, high resilience and full recovery of bacteria in the HFL and L treatments, while ciliates showed significant shift in compositional stability in HFL and L with incomplete taxonomic recovery. Our study highlights the importance of allo-DOM quality shaping the response within the microbial loop not only through triggering different scenarios in biomass, but also the community composition, stability, and species interactions (top-down and bottom-up) in bacteria and plankton.},
}
@article {pmid38244196,
year = {2024},
author = {Truter, M and Koopman, JE and Jordaan, K and Tsamkxao, LO and Cowan, DA and Underdown, SJ and Ramond, JB and Rifkin, RF},
title = {Documenting the diversity of the Namibian Ju|'hoansi intestinal microbiome.},
journal = {Cell reports},
volume = {43},
number = {2},
pages = {113690},
doi = {10.1016/j.celrep.2024.113690},
pmid = {38244196},
issn = {2211-1247},
mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; Prevotella ; *Saccharomycetales ; },
abstract = {We investigate the bacterial and fungal composition and functionality of the Ju|'hoansi intestinal microbiome (IM). The Juǀ'hoansi are a hunter-gatherer community residing in northeastern Namibia. They formerly subsisted by hunting and gathering but have been increasingly exposed to industrial dietary sources, medicines, and lifestyle features. They present an opportunity to study the evolution of the human IM in situ, from a predominantly hunter-gatherer to an increasingly Western urban-forager-farmer lifestyle. Their bacterial IM resembles that of typical hunter-gatherers, being enriched for genera such as Prevotella, Blautia, Faecalibacterium, Succinivibrio, and Treponema. Fungal IM inhabitants include animal pathogens and plant saprotrophs such as Fusarium, Issatchenkia, and Panellus. Our results suggest that diet and culture exert a greater influence on Ju|'hoansi IM composition than age, self-identified biological sex, and medical history. The Ju|'hoansi exhibit a unique core IM composition that diverges from the core IMs of other populations.},
}
@article {pmid38244160,
year = {2024},
author = {Wang, N and Wang, Q and Song, S and Sun, Z and Zhao, A and Ali, A and Xu, G and Zhong, X and Wang, F and Xu, H},
title = {Microplastics drive community dynamics of periphytic protozoan fauna in marine environments.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {9},
pages = {13327-13334},
pmid = {38244160},
issn = {1614-7499},
support = {31672308//The Natural Science Foundation of China/ ; 41076089//The Natural Science Foundation of China/ ; ZR2022QD065//the Youth Project of the Natural Science Foundation of Shandong Province, China/ ; },
mesh = {Ecosystem ; Biodiversity ; Environmental Monitoring ; Microplastics ; Plastics ; *Ciliophora/physiology ; *Water Pollutants, Chemical/toxicity ; },
abstract = {The pollution of microplastics (MPs) to the marine environment has become a widespread focus of attention. To assess MP-induced ecotoxicity on marine ecosystems, periphytic protozoan communities were used as test organisms and exposed to five concentrations of MPs: 0, 1, 5, 25, and 125 mg l[-1]. Protozoan samples were collected using microscope slides from coastal waters of the Yellow Sea, northern China. A total of 13 protozoan species were identified and represented different tolerance to MP-induced ecotoxicity. Inhibition effects of MPs on the test protozoan communities were clearly shown in terms of both the species richness and individual abundance and followed linear relationships to MP concentrations. The community patterns were driven by MPs and significantly shifted at concentrations over 5 mg l[-1]. Our findings demonstrated that MPs may induce the community-level ecotoxic response of periphytic protozoan fauna and followed significant community dynamics. Thus, it is suggested that periphytic protozoan fauna may be used as useful community-based test model organisms for evaluating MP-induced ecotoxicity in marine environments.},
}
@article {pmid38243487,
year = {2023},
author = {Saintillan, D},
title = {Dispersion of run-and-tumble microswimmers through disordered media.},
journal = {Physical review. E},
volume = {108},
number = {6-1},
pages = {064608},
doi = {10.1103/PhysRevE.108.064608},
pmid = {38243487},
issn = {2470-0053},
abstract = {Understanding the transport properties of microorganisms and self-propelled particles in porous media has important implications for human health as well as microbial ecology. In free space, most microswimmers perform diffusive random walks as a result of the interplay of self-propulsion and orientation decorrelation mechanisms such as run-and-tumble dynamics or rotational diffusion. In an unstructured porous medium, collisions with the microstructure result in a decrease in the effective spatial diffusivity of the particles from its free-space value. Here, we analyze this problem for a simple model system consisting of noninteracting point particles performing run-and-tumble dynamics through a two-dimensional disordered medium composed of a random distribution of circular obstacles, in the absence of Brownian diffusion or hydrodynamic interactions. The particles are assumed to collide with the obstacles as hard spheres and subsequently slide on the obstacle surface with no frictional resistance while maintaining their orientation, until they either escape or tumble. We show that the variations in the long-time diffusivity can be described by a universal dimensionless hindrance function f(ϕ,Pe) of the obstacle area fraction ϕ and Péclet number Pe, or ratio of the swimmer run length to the obstacle size. We analytically derive an asymptotic expression for the hindrance function valid for dilute media (Peϕ≪1), and its extension to denser media is obtained using stochastic simulations. As we explain, the model is also easily generalized to describe dispersion in three dimensions.},
}
@article {pmid38241807,
year = {2024},
author = {Wang, D and Han, I and McCullough, K and Klaus, S and Lee, J and Srinivasan, V and Li, G and Wang, ZL and Bott, CB and McQuarrie, J and Stinson, BM and deBarbadillo, C and Dombrowski, P and Barnard, J and Gu, AZ},
title = {Side-Stream Enhanced Biological Phosphorus Removal (S2EBPR) enables effective phosphorus removal in a pilot-scale A-B stage shortcut nitrogen removal system for mainstream municipal wastewater treatment.},
journal = {Water research},
volume = {251},
number = {},
pages = {121050},
doi = {10.1016/j.watres.2023.121050},
pmid = {38241807},
issn = {1879-2448},
mesh = {*Sewage ; Denitrification ; Phosphorus/metabolism ; Rivers ; Nitrogen ; RNA, Ribosomal, 16S ; Phylogeny ; Nitrites ; Pilot Projects ; Bioreactors ; *Water Purification/methods ; Polyphosphates/metabolism ; Carbon ; },
abstract = {While the adsorption/bio-oxidation (A/B) process has been widely studied for carbon capture and shortcut nitrogen (N) removal, its integration with enhanced biological phosphorus (P) removal (EBPR) has been considered challenging and thus unexplored. Here, full-scale pilot testing with an integrated system combining A-stage high-rate activated sludge with B-stage partial (de)nitrification/anammox and side-stream EBPR (HRAS-P(D)N/A-S2EBPR) was conducted treating real municipal wastewater. The results demonstrated that, despite the relatively low influent carbon load, the B-stage P(D)N-S2EBPR system could achieve effective P removal performance, with the carbon supplement and redirection of the A-stage sludge fermentate to the S2EBPR. The novel process configuration design enabled a system shift in carbon flux and distribution for efficient EBPR, and provided unique selective factors for ecological niche partitioning among different key functionally relevant microorganisms including polyphosphate accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). The combined nitrite from B-stage to S2EBPR and aerobic-anoxic conditions in our HRAS-P(D)N/A-S2EBPR system promoted DPAOs for simultaneous internal carbon-driven denitrification via nitrite and P removal. 16S rRNA gene-based oligotyping analysis revealed high phylogenetic microdiversity within the Accumulibacter population and discovered coexistence of certain oligotypes of Accumulibacter and Competibacter correlated with efficient P removal. Single-cell Raman micro-spectroscopy-based phenotypic profiling showed high phenotypic microdiversity in the active PAO community and the involvement of unidentified PAOs and internal carbon-accumulating organisms that potentially played an important role in system performance. This is the first pilot study to demonstrate that the P(D)N-S2EBPR system could achieve shortcut N removal and influent carbon-independent EBPR simultaneously, and the results provided insights into the effects of incorporating S2EBPR into A/B process on metabolic activities, microbial ecology, and resulted system performance.},
}
@article {pmid38236289,
year = {2024},
author = {Bergman, I and Lindström, ES and Sassenhagen, I},
title = {Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {33},
pmid = {38236289},
issn = {1432-184X},
support = {146-300-188//Olle Engkvists Stiftelse/ ; 146-300-188//Olle Engkvists Stiftelse/ ; },
mesh = {Ecosystem ; *Microalgae ; Semen ; Carbon ; *Ciliophora ; Lakes ; },
abstract = {The freshwater raphidophyte Gonyostomum semen forms extensive summer blooms in northern European humic lakes. The development of these blooms might be facilitated by a lack of natural top-down control, as few zooplankton species are able to prey on these large algal cells (up to 100 μm) that expel trichocysts upon physical stress. In this study, we describe a small ciliate species (< 17 μm) that preys on G. semen by damaging the cell membrane until cytoplasm and organelles spill out. Sequencing of clonal cultures of the ciliate tentatively identified it as the prostomatid species Urotricha pseudofurcata. Grazing experiments illustrated that feeding by U. cf. pseudofurcata can significantly reduce cell concentrations of the microalga. However, differences in cell size and growth rate between two investigated ciliate strains resulted in noticeably different grazing pressure. Environmental sequencing data from five different lakes supported potential interactions between the two species. Urotricha cf. pseudofurcata might, thus, play an important role in aquatic ecosystems that are regularly dominated by G. semen, reducing the abundance of this bloom-forming microalga and enabling transfer of organic carbon to higher trophic levels.},
}
@article {pmid38236100,
year = {2023},
author = {Singh, A and Sharma, P and Singh, A and Agarwal, C and Patel M, G and Ganapathy, K},
title = {RELEVANCE FOR DIAGNOSIS, THERAPY, AND STRATEGIES OF GUT MICROBES DYSBIOSIS IN CHRONIC KIDNEY DISEASE: A SYSTEMATIC REVIEW.},
journal = {Georgian medical news},
volume = {},
number = {344},
pages = {57-63},
pmid = {38236100},
issn = {1512-0112},
mesh = {Humans ; Animals ; Rats ; Dysbiosis/diagnosis ; *Gastrointestinal Microbiome ; Quality of Life ; Inflammation ; *Renal Insufficiency, Chronic/complications/diagnosis/therapy ; },
abstract = {Dysbiosis and weakened gastrointestinal barrier function have been identified as potential regulators of Chronic Kidney Disease (CKD). The complex connection among gut micro biota and CKD is provided in this study, with particular attention to how inflammation contributes to the CKD path physiology. It establishes the inverse association between CKD and gut microbial dysbiosis by exploring the collision of CKD about the organization and capabilities of the gut micro biota. The possibility of new diagnostic tools in measuring the dynamic changes within the gut microbial ecology illustrates the importance of accurately diagnosing gut micro biota abnormalities in CKD. Additionally, the study explores the targeted medicines that focus on gut micro biota in CKD. Using data from both human clinical trials and rat models, the study demonstrates the variety of therapeutic approaches and their ability to limit the rate of development of CKD and its accompanying problems. The study we performed was based on the Preferred Reporting Items for Systematic reviews and Meta Analyses (PRISMA) approach. The findings show the significance of investigating the relationship between gut micro biota and CKD, paving up the possibility for new therapeutic strategies to improve the patient outcomes and quality of life. The present understanding of CKD-induced modifications to the gut micro biota and the ensuing effects on gastrointestinal health, emphasizing studies, will be highlighted in this review.},
}
@article {pmid38236032,
year = {2024},
author = {Hozalski, RM and Zhao, X and Kim, T and LaPara, TM},
title = {On-site filtration of large sample volumes improves the detection of opportunistic pathogens in drinking water distribution systems.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {2},
pages = {e0165823},
pmid = {38236032},
issn = {1098-5336},
support = {M.L. 2018 Chp. 214 Art. 4 Sec. 02 Subd. 04f//Minnesota Environment and Natural Resources Trust Fund (ENRTF)/ ; },
mesh = {*Drinking Water/microbiology ; *Legionella pneumophila ; Propidium/*analogs &amp; derivatives ; *Mycobacterium/genetics ; Water Microbiology ; Water Supply ; *Legionella/genetics ; *Azides ; },
abstract = {In this study, we compared conventional vacuum filtration of small volumes through disc membranes (effective sample volumes for potable water: 0.3-1.0 L) with filtration of high volumes using ultrafiltration (UF) modules (effective sample volumes for potable water: 10.6-84.5 L) for collecting bacterial biomass from raw, finished, and tap water at seven drinking water systems. Total bacteria, Legionella spp., Legionella pneumophila, Mycobacterium spp., and Mycobacterium avium complex in these samples were enumerated using both conventional quantitative PCR (qPCR) and viability qPCR (using propidium monoazide). In addition, PCR-amplified gene fragments were sequenced for microbial community analysis. The frequency of detection (FOD) of Legionella spp. in finished and tap water samples was much greater using UF modules (83% and 77%, respectively) than disc filters (24% and 33%, respectively). The FODs for Mycobacterium spp. in raw, finished, and tap water samples were also consistently greater using UF modules than disc filters. Furthermore, the number of observed operational taxonomic units and diversity index values for finished and tap water samples were often substantially greater when using UF modules as compared to disc filters. Conventional and viability qPCR yielded similar results, suggesting that membrane-compromised cells represented a minor fraction of total bacterial biomass. In conclusion, our research demonstrates that large-volume filtration using UF modules improved the detection of opportunistic pathogens at the low concentrations typically found in public drinking water systems and that the majority of bacteria in these systems appear to be viable in spite of disinfection with free chlorine and/or chloramine.IMPORTANCEOpportunistic pathogens, such as Legionella pneumophila, are a growing public health concern. In this study, we compared sample collection and enumeration methods on raw, finished, and tap water at seven water systems throughout the State of Minnesota, USA. The results showed that on-site filtration of large water volumes (i.e., 500-1,000 L) using ultrafiltration membrane modules improved the frequency of detection of relatively rare organisms, including opportunistic pathogens, compared to the common approach of filtering about 1 L using disc membranes. Furthermore, results from viability quantitative PCR (qPCR) with propidium monoazide were similar to conventional qPCR, suggesting that membrane-compromised cells represent an insignificant fraction of microorganisms. Results from these ultrafiltration membrane modules should lead to a better understanding of the microbial ecology of drinking water distribution systems and their potential to inoculate premise plumbing systems with opportunistic pathogens where conditions are more favorable for their growth.},
}
@article {pmid38235197,
year = {2023},
author = {Meesters, C and Weldegergis, BT and Dicke, M and Jacquemyn, H and Lievens, B},
title = {Limited effects of plant-beneficial fungi on plant volatile composition and host-choice behavior of Nesidiocoris tenuis.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1322719},
pmid = {38235197},
issn = {1664-462X},
abstract = {Biological control using plant-beneficial fungi has gained considerable interest as a sustainable method for pest management, by priming the plant for enhanced defense against pathogens and insect herbivores. However, despite promising outcomes, little is known about how different fungal strains mediate these beneficial effects. In this study, we evaluated whether inoculation of tomato seeds with the plant-beneficial fungi Beauveria bassiana ARSEF 3097, Metarhizium brunneum ARSEF 1095 and Trichoderma harzianum T22 affected the plant's volatile organic compound (VOC) profile and the host-choice behavior of Nesidiocoris tenuis, an emerging pest species in NW-European tomato cultivation, and the related zoophytophagous biocontrol agent Macrolophus pygmaeus. Results indicated that fungal inoculation did not significantly alter the VOC composition of tomato plants. However, in a two-choice cage assay where female insects were given the option to select between control plants and fungus-inoculated plants, N. tenuis preferred control plants over M. brunneum-inoculated plants. Nearly 72% of all N. tenuis individuals tested chose the control treatment. In all other combinations tested, no significant differences were found for none of the insects. We conclude that inoculation of tomato with plant-beneficial fungi had limited effects on plant volatile composition and host-choice behavior of insects. However, the observation that N. tenuis was deterred from the crop when inoculated with M. brunneum and attracted to non-inoculated plants may provide new opportunities for future biocontrol based on a push-pull strategy.},
}
@article {pmid38234383,
year = {2022},
author = {Tan, YP and Bishop-Hurley, SL and Shivas, RG and Cowan, DA and Maggs-Kölling, G and Maharachchikumbura, SSN and Pinruan, U and Bransgrove, KL and De la Peña-Lastra, S and Larsson, E and Lebel, T and Mahadevakumar, S and Mateos, A and Osieck, ER and Rigueiro-Rodríguez, A and Sommai, S and Ajithkumar, K and Akulov, A and Anderson, FE and Arenas, F and Balashov, S and Bañares, &#xc1; and Berger, DK and Bianchinotti, MV and Bien, S and Bilański, P and Boxshall, AG and Bradshaw, M and Broadbridge, J and Calaça, FJS and Campos-Quiroz, C and Carrasco-Fernández, J and Castro, JF and Chaimongkol, S and Chandranayaka, S and Chen, Y and Comben, D and Dearnaley, JDW and Ferreira-Sá, AS and Dhileepan, K and Díaz, ML and Divakar, PK and Xavier-Santos, S and Fernández-Bravo, A and Gené, J and Guard, FE and Guerra, M and Gunaseelan, S and Houbraken, J and Janik-Superson, K and Jankowiak, R and Jeppson, M and Jurjević, &#x17d; and Kaliyaperumal, M and Kelly, LA and Kezo, K and Khalid, AN and Khamsuntorn, P and Kidanemariam, D and Kiran, M and Lacey, E and Langer, GJ and López-Llorca, LV and Luangsa-Ard, JJ and Lueangjaroenkit, P and Lumbsch, HT and Maciá-Vicente, JG and Mamatha Bhanu, LS and Marney, TS and Marqués-Gálvez, JE and Morte, A and Naseer, A and Navarro-Ródenas, A and Oyedele, O and Peters, S and Piskorski, S and Quijada, L and Ramírez, GH and Raja, K and Razzaq, A and Rico, VJ and Rodríguez, A and Ruszkiewicz-Michalska, M and Sánchez, RM and Santelices, C and Savitha, AS and Serrano, M and Leonardo-Silva, L and Solheim, H and Somrithipol, S and Sreenivasa, MY and Stępniewska, H and Strapagiel, D and Taylor, T and Torres-Garcia, D and Vauras, J and Villarreal, M and Visagie, CM and Wołkowycki, M and Yingkunchao, W and Zapora, E and Groenewald, JZ and Crous, PW},
title = {Fungal Planet description sheets: 1436-1477.},
journal = {Persoonia},
volume = {49},
number = {},
pages = {261-350},
pmid = {38234383},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Colletotrichum araujiae on leaves, stems and fruits of Araujia hortorum. Australia, Agaricus pateritonsus on soil, Curvularia fraserae on dying leaf of Bothriochloa insculpta, Curvularia millisiae from yellowing leaf tips of Cyperus aromaticus, Marasmius brunneolorobustus on well-rotted wood, Nigrospora cooperae from necrotic leaf of Heteropogon contortus, Penicillium tealii from the body of a dead spider, Pseudocercospora robertsiorum from leaf spots of Senna tora, Talaromyces atkinsoniae from gills of Marasmius crinis-equi and Zasmidium pearceae from leaf spots of Smilaxglyciphylla. Brazil, Preussia bezerrensis from air. Chile, Paraconiothyrium kelleni from the rhizosphere of Fragaria chiloensis subsp. chiloensis f. chiloensis. Finland, Inocybe udicola on soil in mixed forest with Betula pendula, Populus tremula, Picea abies and Alnus incana. France, Myrmecridium normannianum on dead culm of unidentified Poaceae. Germany, Vexillomyces fraxinicola from symptomless stem wood of Fraxinus excelsior. India, Diaporthe limoniae on infected fruit of Limonia acidissima, Didymella naikii on leaves of Cajanus cajan, and Fulvifomes mangroviensis on basal trunk of Aegiceras corniculatum. Indonesia, Penicillium ezekielii from Zea mays kernels. Namibia, Neocamarosporium calicoremae and Neocladosporium calicoremae on stems of Calicorema capitata, and Pleiochaeta adenolobi on symptomatic leaves of Adenolobus pechuelii. Netherlands, Chalara pteridii on stems of Pteridium aquilinum, Neomackenziella juncicola (incl. Neomackenziella gen. nov.) and Sporidesmiella junci from dead culms of Juncus effusus. Pakistan, Inocybe longistipitata on soil in a Quercus forest. Poland, Phytophthora viadrina from rhizosphere soil of Quercus robur, and Septoria krystynae on leaf spots of Viscum album. Portugal (Azores), Acrogenospora stellata on dead wood or bark. South Africa, Phyllactinia greyiae on leaves of Greyia sutherlandii and Punctelia anae on bark of Vachellia karroo. Spain, Anteaglonium lusitanicum on decaying wood of Prunus lusitanica subsp. lusitanica, Hawksworthiomyces riparius from fluvial sediments, Lophiostoma carabassense endophytic in roots of Limbarda crithmoides, and Tuber mohedanoi from calcareus soils. Spain (Canary Islands), Mycena laurisilvae on stumps and woody debris. Sweden, Elaphomyces geminus from soil under Quercus robur. Thailand, Lactifluus chiangraiensis on soil under Pinus merkusii, Lactifluus nakhonphanomensis and Xerocomus sisongkhramensis on soil under Dipterocarpus trees. Ukraine, Valsonectria robiniae on dead twigs of Robinia hispida. USA, Spiralomyces americanus (incl. Spiralomyces gen. nov.) from office air. Morphological and culture characteristics are supported by DNA barcodes. Citation: Tan YP, Bishop-Hurley SL, Shivas RG, et al. 2022. Fungal Planet description sheets: 1436-1477. Persoonia 49: 261-350. https://doi.org/10.3767/persoonia.2022.49.08.},
}
@article {pmid38232435,
year = {2024},
author = {Cagri Ozturk, R and Feyzioglu, AM and Capkin, E and Yildiz, I and Altinok, I},
title = {Effects of environmental parameters on spatial and temporal distribution of marine microbial communities in the southern Black Sea.},
journal = {Marine environmental research},
volume = {195},
number = {},
pages = {106344},
doi = {10.1016/j.marenvres.2024.106344},
pmid = {38232435},
issn = {1879-0291},
mesh = {*Seawater/chemistry ; RNA, Ribosomal, 16S/genetics ; Black Sea ; Bacteria/genetics ; *Microbiota ; Water ; },
abstract = {The Black Sea is a unique environment with strong and permanent vertical stratification, with a thin layer of oxic zone above and a permanent anoxic zone below. Few high-throughput genomic surveys have been conducted to examine microbiota in the Black Sea. Yet, there is no study on the seasonal and vertical variation in microbial community compositions, driving forces and mechanisms of community assembly. In this study, seasonal, vertical, and spatial microbial assemblages were studied in terms of diversity, abundance, and community structure using 16S rRNA metabarcoding. 16S rRNA metabarcoding confirmed seasonal changes in microbial communities and the presence of distinct microbial groups among different water layers. Taxa belonging to Cyanobiaceae contributed a large fraction of the total biomass and were the most abundant autotrophic bacteria found across the whole water column, including hydrogen sulfide-containing anoxic zone. Temperature, salinity, water density, conductivity, light, chlorophyll-a, O2, NO3, NH3, PO4, Si, and H2S had a significant influence on the vertical bacterial community assemblages. The copper mine discharge system at 180 m did not affect microbial community structure and composition. Temperature seemed to be a primary factor in the variance between shallow depths. In conclusion, the lack of light, low dissolved oxygen levels, and low temperature do not restrict microbial diversity, as proven by the higher diversity observed in deeper zones. Wastewater in Black Sea region may be discharged into the Black Sea to depth of 180 m or deeper without impacting microbial ecology.},
}
@article {pmid38229613,
year = {2023},
author = {Pavan, S and Gorthi, SP and Prabhu, AN and Das, B and Mutreja, A and Vasudevan, K and Shetty, V and Ramamurthy, T and Ballal, M},
title = {Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson's Disease from India.},
journal = {Annals of Indian Academy of Neurology},
volume = {26},
number = {6},
pages = {908-916},
pmid = {38229613},
issn = {0972-2327},
abstract = {OBJECTIVES: Recent advancement in understanding neurological disorders has revealed the involvement of dysbiosis of the gut microbiota in the pathophysiology of Parkinson's disease (PD). We sequenced microbial DNA using fecal samples collected from PD cases and healthy controls (HCs) to evaluate the role of gut microbiota.<br><br>METHODS: Full-length bacterial 16S rRNA gene sequencing of fecal samples was performed using amplified polymerase chain reaction (PCR) products on the GridION Nanopore sequencer. Sequenced data were analyzed using web-based tools BugSeq and MicrobiomeAnalyst.<br><br>RESULTS: We found that certain bacterial families like Clostridia UCG 014, Cristensenellaceae, and Oscillospiraceae are higher in abundance, and Lachinospiracea, Coriobacteriaceae and genera associated with short-chain fatty acid production, Faecalibacterium, Fusicatenibacter, Roseburia and Blautia, are lower in abundance among PD cases when compared with the HC. Genus Akkermansia, Dialister, Bacteroides, and Lachnospiraceae NK4A136 group positively correlated with constipation in PD.<br><br>CONCLUSION: Observations from this study support the other global research on the PD gut microbiome background and provide fresh insight into the gut microbial composition of PD patients from a south Indian population. We report a higher abundance of Clostridia UCG 014 group, previously not linked to PD.},
}
@article {pmid38228918,
year = {2024},
author = {Alonso, A and Boyero, L and Solla, A and Ferreira, V},
title = {Dieback and Replacement of Riparian Trees May Impact Stream Ecosystem Functioning.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {32},
pmid = {38228918},
issn = {1432-184X},
mesh = {*Ecosystem ; Trees ; Rivers/microbiology ; Biomass ; Nitrogen ; Plant Leaves/microbiology ; *Alnus/microbiology ; },
abstract = {Alders are nitrogen (N)-fixing riparian trees that promote leaf litter decomposition in streams through their high-nutrient leaf litter inputs. While alders are widespread across Europe, their populations are at risk due to infection by the oomycete Phytophthora ×alni, which causes alder dieback. Moreover, alder death opens a space for the establishment of an aggressive N-fixing invasive species, the black locust (Robinia pseudoacacia). Shifts from riparian vegetation containing healthy to infected alder and, eventually, alder loss and replacement with black locust may alter the key process of leaf litter decomposition and associated microbial decomposer assemblages. We examined this question in a microcosm experiment comparing three types of leaf litter mixtures: one representing an original riparian forest composed of healthy alder (Alnus lusitanica), ash (Fraxinus angustifolia), and poplar (Populus nigra); one with the same species composition where alder had been infected by P. ×alni; and one where alder had been replaced with black locust. The experiment lasted six weeks, and every two weeks, microbially driven decomposition, fungal biomass, reproduction, and assemblage structure were measured. Decomposition was highest in mixtures with infected alder and lowest in mixtures with black locust, reflecting differences in leaf nutrient concentrations. Mixtures with alder showed distinct fungal assemblages and higher sporulation rates than mixtures with black locust. Our results indicate that alder loss and its replacement with black locust may alter key stream ecosystem processes and assemblages, with important changes already occurring during alder infection. This highlights the importance of maintaining heathy riparian forests to preserve proper stream ecosystem functioning.},
}
@article {pmid38228915,
year = {2024},
author = {Iqbal, Z and Ahmad, M and Raza, MA and Hilger, T and Rasche, F},
title = {Phosphate-Solubilizing Bacillus sp. Modulate Soil Exoenzyme Activities and Improve Wheat Growth.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {31},
pmid = {38228915},
issn = {1432-184X},
mesh = {*Phosphates ; Triticum/microbiology ; *Bacillus ; Soil ; Phosphorus ; Bacillus subtilis ; Soil Microbiology ; },
abstract = {Phosphorus (P) is a vital mineral nutrient in agriculture and its deficiency results in reduced growth, yield, and grain quality in cereals. Much of the applied P in agriculture becomes fixed in soils, limiting its accessibility to plants. Thus, investigating sustainable strategies to release fixed P resources and enhance plant uptake is crucial. This study explored how plant-associated bacteria employ phosphate solubilizing mechanisms to improve P availability. The growth patterns of four bacterial strains, namely Bacillus subtilis ZE15 and ZR3, along with Bacillus megaterium ZE32 and ZR19, were examined in Pikovskaya's broth culture with and without the addition of insoluble phosphorus (P). In the absence of P amendment, most strains reached a stationary growth phase by the fourth day. However, their responses diverged when exposed to P-amended media. Particularly, ZE15 demonstrated the highest P solubilization capability, achieving up to 130 µg mL[-1] solubilization in vitro. All strains produced organic acids in Pikovskaya's broth culture. A comparison of the influence of Ca3(PO4)2 revealed significantly greater organic acid quantities in the presence of insoluble P. Notably, strain ZE15 exhibited the highest phosphate esterase activity (3.65 nmol g[-1] dry matter), while strain ZE32 showed the highest ß-D glucosidase activity (2.81 nmol g[-1] dry matter) in the presence of insoluble P. The ability of Bacillus species to solubilize P in combination with increased exoenzyme activity in the rhizosphere could be used in future studies to support P uptake through enhanced solubilization and mineralization.},
}
@article {pmid38225668,
year = {2024},
author = {Terzin, M and Laffy, PW and Robbins, S and Yeoh, YK and Frade, PR and Glasl, B and Webster, NS and Bourne, DG},
title = {The road forward to incorporate seawater microbes in predictive reef monitoring.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {5},
pmid = {38225668},
issn = {2524-6372},
abstract = {Marine bacterioplankton underpin the health and function of coral reefs and respond in a rapid and sensitive manner to environmental changes that affect reef ecosystem stability. Numerous meta-omics surveys over recent years have documented persistent associations of opportunistic seawater microbial taxa, and their associated functions, with metrics of environmental stress and poor reef health (e.g. elevated temperature, nutrient loads and macroalgae cover). Through positive feedback mechanisms, disturbance-triggered heterotrophic activity of seawater microbes is hypothesised to drive keystone benthic organisms towards the limit of their resilience and translate into shifts in biogeochemical cycles which influence marine food webs, ultimately affecting entire reef ecosystems. However, despite nearly two decades of work in this space, a major limitation to using seawater microbes in reef monitoring is a lack of a unified and focused approach that would move beyond the indicator discovery phase and towards the development of rapid microbial indicator assays for (near) real-time reef management and decision-making. By reviewing the current state of knowledge, we provide a comprehensive framework (defined as five phases of research and innovation) to catalyse a shift from fundamental to applied research, allowing us to move from descriptive to predictive reef monitoring, and from reactive to proactive reef management.},
}
@article {pmid38224372,
year = {2024},
author = {Syiemiong, D and Rabha, J},
title = {Unveiling nature's treasures: actinobacteria from Meghalaya's mining sites as sources of bioactive compounds.},
journal = {Archives of microbiology},
volume = {206},
number = {2},
pages = {64},
pmid = {38224372},
issn = {1432-072X},
mesh = {*Actinobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria ; *Actinomycetales ; *Nocardia ; },
abstract = {Coal and sillimanite mining sites present unique ecological niches favoring the growth of actinobacteria, a group of Gram-positive bacteria known for producing a wide array of bioactive compounds. Isolating these bacteria from such environments could unveil novel compounds with potential biotechnological applications. This study involved the isolation of actinobacteria from two mining sites in Meghalaya, India. The dominant genera from both sites were Streptomyces, Amycolatopsis, Nocardia, and Streptosporangium. Metabolic pathway prediction from 16S rRNA gene revealed several pathways beneficial for plant growth. Exploration of biosynthetic genes indicated a prevalence of the type-II polyketide synthase gene. Sequencing the ketosynthase-alpha domain of the gene led to predictions of various bioactive secondary metabolites. Around 44% of the isolates demonstrated antimicrobial properties, with some also displaying plant growth-promoting traits. Amycolatopsis SD-15 exhibited promising results in planta when tested on tomato plants. These findings highlight the potential of actinobacteria from Meghalaya's mining sites across medical, agricultural, and industrial domains.},
}
@article {pmid38223759,
year = {2024},
author = {Liu, B and Lee, CW and Bong, CW and Wang, AJ},
title = {Investigating Escherichia coli habitat transition from sediments to water in tropical urban lakes.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16556},
pmid = {38223759},
issn = {2167-8359},
mesh = {*Escherichia coli ; *Lakes/microbiology ; Water Microbiology ; Water Quality ; Ecosystem ; },
abstract = {BACKGROUND: Escherichia coli is a commonly used faecal indicator bacterium to assess the level of faecal contamination in aquatic habitats. However, extensive studies have reported that sediment acts as a natural reservoir of E. coli in the extraintestinal environment. E. coli can be released from the sediment, and this may lead to overestimating the level of faecal contamination during water quality surveillance. Thus, we aimed to investigate the effects of E. coli habitat transition from sediment to water on its abundance in the water column.<br><br>METHODS: This study enumerated the abundance of E. coli in the water and sediment at five urban lakes in the Kuala Lumpur-Petaling Jaya area, state of Selangor, Malaysia. We developed a novel method for measuring habitat transition rate of sediment E. coli to the water column, and evaluated the effects of habitat transition on E. coli abundance in the water column after accounting for its decay in the water column.<br><br>RESULTS: The abundance of E. coli in the sediment ranged from below detection to 12,000 cfu g[-1], and was about one order higher than in the water column (1 to 2,300 cfu mL[-1]). The habitat transition rates ranged from 0.03 to 0.41 h[-1]. In contrast, the E. coli decay rates ranged from 0.02 to 0.16 h[-1]. In most cases (>80%), the habitat transition rates were higher than the decay rates in our study.<br><br>DISCUSSION: Our study provided a possible explanation for the persistence of E. coli in tropical lakes. To the best of our knowledge, this is the first quantitative study on habitat transition of E. coli from sediments to water column.},
}
@article {pmid38218325,
year = {2024},
author = {Eberhardt, N and Santamarina, BG and Enghardt, ML and Rohland, O and Hussain, I and Tannert, A and Thieme, L and Rubio, I and Jürgen Rödel, and Bettina Löffler, and Arndt, HD and Bauer, M and Busch, A},
title = {The effects of photoactivated ciprofloxacin and bile acids on biofilms on bile duct catheters.},
journal = {International journal of antimicrobial agents},
volume = {63},
number = {4},
pages = {107086},
doi = {10.1016/j.ijantimicag.2024.107086},
pmid = {38218325},
issn = {1872-7913},
mesh = {Humans ; *Ciprofloxacin/pharmacology ; *Bile Acids and Salts/pharmacology ; Pilot Projects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Biofilms ; Bile Ducts ; Catheters ; Escherichia coli ; },
abstract = {OBJECTIVES: This study examined the potential of a novel photoactivatable ciprofloxacin to act against bacterial infections and microbiomes related to biliary diseases. It also evaluated treatment by combining the impact of bile acids and antibiotics on biofilms. Innovative strategies were evaluated to address the elusive bile duct microbiome resulting in biofilm-related infections linked to biliary catheters. The healthy biliary system is considered sterile, but bile microbiomes can occur in disease, and these correlate with hepatobiliary diseases. Causes include biofilms that form on internal-external biliary drainage catheters. These biliary catheters were used to noninvasively study the otherwise elusive bile microbiome for a pilot study.<br><br>METHODS: A new photoactivatable antibiotic was tested for efficacy against human-derived pathogenic bacterial isolates - Salmonella enterica and Escherichia coli - and catheter-derived bile duct microbiomes. In addition, the effect of bile acids on the antibiotic treatment of biofilms was quantified using crystal violet staining, confocal laser scanning microscopy, and biofilm image analysis. Two novel approaches for targeting biliary biofilms were tested.<br><br>RESULTS: A photoactivated antibiotic based on ciprofloxacin showed efficacy in preventing biofilm formation and reducing bacterial viability without harming eukaryotic cells. Furthermore, combination treatment of antibiotics with bile acids, such as ursodesoxycholic acid, mildly influenced biofilm biomass but reduced bacterial survival within biofilms.<br><br>CONCLUSION: Bile acids, in addition to their endocrine and paracrine functions, may enhance antibiotic killing of bacterial biofilms compared with antibiotics alone. These approaches hold promise for treating biliary infections such as cholangitis.},
}
@article {pmid38217646,
year = {2024},
author = {Blache, A and Achouak, W},
title = {Extraction and Purification of Outer Membrane Vesicles and Their Associated RNAs.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2741},
number = {},
pages = {11-24},
pmid = {38217646},
issn = {1940-6029},
mesh = {*Gram-Negative Bacteria/genetics ; Escherichia coli/genetics ; RNA, Bacterial/genetics/metabolism ; Bacterial Outer Membrane Proteins/genetics/metabolism ; *Extracellular Vesicles/metabolism ; },
abstract = {Outer membrane vesicles (OMVs), produced by Gram negative-bacteria and sRNAs, are key players in cell-to-cell communication and interactions of bacteria with the environment. OMVs act as information carriers and encapsulate various molecules such as proteins, lipids, metabolites, and RNAs. OMVs and sRNAs play a broad range of functions from pathogenesis to stress resistance, to biofilm formation and both mediate interkingdom signaling. Various studies indicate that there is a mechanism of intercellular communication mediated by OMV-derived bacterial RNAs that is conserved among certain bacterial species. Here we describe methods for the extraction and purification of vesicles produced by Gram-negative bacteria, such as Pseudomonas brassicacearum and Escherichia coli, and address methods for the extraction of OMVs-derived sRNA and techniques for the analysis of sRNAs.},
}
@article {pmid38217094,
year = {2024},
author = {Garuglieri, E and Marasco, R and Odobel, C and Chandra, V and Teillet, T and Areias, C and Sánchez-Román, M and Vahrenkamp, V and Daffonchio, D},
title = {Searching for microbial contribution to micritization of shallow marine sediments.},
journal = {Environmental microbiology},
volume = {26},
number = {2},
pages = {e16573},
doi = {10.1111/1462-2920.16573},
pmid = {38217094},
issn = {1462-2920},
support = {OSR#4097//King Abdullah University of Science and Technology/ ; },
mesh = {*Geologic Sediments/chemistry ; Carbonates ; Calcium Carbonate ; *Microbiota ; },
abstract = {Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.},
}
@article {pmid38216372,
year = {2024},
author = {Pogoreutz, C and Ziegler, M},
title = {Frenemies on the reef? Resolving the coral-Endozoicomonas association.},
journal = {Trends in microbiology},
volume = {32},
number = {5},
pages = {422-434},
doi = {10.1016/j.tim.2023.11.006},
pmid = {38216372},
issn = {1878-4380},
mesh = {Animals ; *Anthozoa/microbiology/physiology ; *Coral Reefs ; Microbiota ; Phylogeny ; *Symbiosis ; },
abstract = {Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum.},
}
@article {pmid38214516,
year = {2024},
author = {Weller, DL and Murphy, CM and Love, TMT and Danyluk, MD and Strawn, LK},
title = {Methodological differences between studies confound one-size-fits-all approaches to managing surface waterways for food and water safety.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {2},
pages = {e0183523},
pmid = {38214516},
issn = {1098-5336},
support = {2019-51181-30016//U.S. Department of Agriculture (USDA)/ ; //VT | Virginia Agricultural Experiment Station, Virginia Polytechnic Institute and State University (VAES)/ ; },
mesh = {*Escherichia coli ; Environmental Microbiology ; Salmonella ; *Listeria ; Food ; Food Microbiology ; Food Safety ; },
abstract = {Even though differences in methodology (e.g., sample volume and detection method) have been shown to affect observed microbial water quality, multiple sampling and laboratory protocols continue to be used for water quality monitoring. Research is needed to determine how these differences impact the comparability of findings to generate best management practices and the ability to perform meta-analyses. This study addresses this knowledge gap by compiling and analyzing a data set representing 2,429,990 unique data points on at least one microbial water quality target (e.g., Salmonella presence and Escherichia coli concentration). Variance partitioning analysis was used to quantify the variance in likelihood of detecting each pathogenic target that was uniquely and jointly attributable to non-methodological versus methodological factors. The strength of the association between microbial water quality and select methodological and non-methodological factors was quantified using conditional forest and regression analysis. Fecal indicator bacteria concentrations were more strongly associated with non-methodological factors than methodological factors based on conditional forest analysis. Variance partitioning analysis could not disentangle non-methodological and methodological signals for pathogenic Escherichia coli, Salmonella, and Listeria. This suggests our current perceptions of foodborne pathogen ecology in water systems are confounded by methodological differences between studies. For example, 31% of total variance in likelihood of Salmonella detection was explained by methodological and/or non-methodological factors, 18% was jointly attributable to both methodological and non-methodological factors. Only 13% of total variance was uniquely attributable to non-methodological factors for Salmonella, highlighting the need for standardization of methods for microbiological water quality testing for comparison across studies.IMPORTANCEThe microbial ecology of water is already complex, without the added complications of methodological differences between studies. This study highlights the difficulty in comparing water quality data from projects that used different sampling or laboratory methods. These findings have direct implications for end users as there is no clear way to generalize findings in order to characterize broad-scale ecological phenomenon and develop science-based guidance. To best support development of risk assessments and guidance for monitoring and managing waters, data collection and methods need to be standardized across studies. A minimum set of data attributes that all studies should collect and report in a standardized way is needed. Given the diversity of methods used within applied and environmental microbiology, similar studies are needed for other microbiology subfields to ensure that guidance and policy are based on a robust interpretation of the literature.},
}
@article {pmid38212738,
year = {2024},
author = {Varliero, G and Lebre, PH and Adams, B and Chown, SL and Convey, P and Dennis, PG and Fan, D and Ferrari, B and Frey, B and Hogg, ID and Hopkins, DW and Kong, W and Makhalanyane, T and Matcher, G and Newsham, KK and Stevens, MI and Weigh, KV and Cowan, DA},
title = {Biogeographic survey of soil bacterial communities across Antarctica.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {9},
pmid = {38212738},
issn = {2049-2618},
support = {310030_215119/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Humans ; Antarctic Regions ; Phylogeny ; *Soil ; *Cyanobacteria ; Biodiversity ; Soil Microbiology ; },
abstract = {BACKGROUND: Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs.<br><br>RESULTS: Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs.<br><br>CONCLUSIONS: Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.},
}
@article {pmid38212192,
year = {2024},
author = {Ayeni, KI and Berry, D and Ezekiel, CN and Warth, B},
title = {Enhancing microbiome research in sub-Saharan Africa.},
journal = {Trends in microbiology},
volume = {32},
number = {2},
pages = {111-115},
doi = {10.1016/j.tim.2023.11.003},
pmid = {38212192},
issn = {1878-4380},
mesh = {Humans ; Africa South of the Sahara ; *Microbiota ; },
abstract = {While there are lighthouse examples of microbiome research in sub-Saharan Africa (SSA), a significant proportion of local researchers face several challenges. Here, we highlight prevailing issues limiting microbiome research in SSA and suggest potential technological, societal, and research-based solutions. We emphasize the need for considerable investment in infrastructures, training, and appropriate funding to democratize modern technologies with a view to providing useful data to improve human health.},
}
@article {pmid38211751,
year = {2024},
author = {Busch, A and Roy, S and Helbing, DL and Colic, L and Opel, N and Besteher, B and Walter, M and Bauer, M and Refisch, A},
title = {Gut microbiome in atypical depression.},
journal = {Journal of affective disorders},
volume = {349},
number = {},
pages = {277-285},
doi = {10.1016/j.jad.2024.01.060},
pmid = {38211751},
issn = {1573-2517},
mesh = {Humans ; Depression ; *Depressive Disorder, Major/diagnosis ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Recent studies showed that immunometabolic dysregulation is related to unipolar major depressive disorder (MDD) and that it more consistently maps to MDD patients endorsing an atypical symptom profile, characterized by energy-related symptoms including increased appetite, weight gain, and hypersomnia. Despite the documented influence of the microbiome on immune regulation and energy homeostasis, studies have not yet investigated microbiome differences among clinical groups in individuals with MDD.<br><br>METHODS: Fifteen MDD patients with atypical features according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5)-5, forty-four MDD patients not fulfilling the DSM-5 criteria for the atypical subtype, and nineteen healthy controls were included in the study. Participants completed detailed clinical assessment and stool samples were collected. Samples were sequenced for the prokaryotic 16S rRNA gene, in the V3-V4 variable regions. Only samples with no antibiotic exposure in the previous 12&#xa0;months and a minimum of >2000 quality-filtered reads were included in the analyses.<br><br>RESULTS: There were no statistically significant differences in alpha- and beta-diversity between the MDD groups and healthy controls. However, within the atypical MDD group, there was an increase in the Verrucomicrobiota phylum, with Akkermansia as the predominant bacterial genus.<br><br>LIMITATIONS: Cross-sectional data, modest sample size, and significantly increased body mass index in the atypical MDD group.<br><br>CONCLUSIONS: There were no overall differences among the investigated groups. However, differences were found at several taxonomic levels. Studies in larger longitudinal samples with relevant confounders are needed to advance the understanding of the microbial influences on the clinical heterogeneity of depression.},
}
@article {pmid38206365,
year = {2024},
author = {Reyes-Reyes, EM and Brown, J and Trial, MD and Chinnasamy, D and Wiegand, JP and Bradford, D and Brinton, RD and Rodgers, KE},
title = {Vivaria housing conditions expose sex differences in brain oxidation, microglial activation, and immune system states in aged hAPOE4 mice.},
journal = {Experimental brain research},
volume = {242},
number = {3},
pages = {543-557},
pmid = {38206365},
issn = {1432-1106},
support = {P01 AG026572/AG/NIA NIH HHS/United States ; P30 AG072980/AG/NIA NIH HHS/United States ; R01 AG057931/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; Mice ; Animals ; Female ; Male ; Aged ; Infant ; *Apolipoprotein E4/genetics/metabolism ; Microglia/pathology ; *Alzheimer Disease/genetics ; Housing Quality ; Sex Characteristics ; CD8-Positive T-Lymphocytes/metabolism/pathology ; Brain/metabolism ; Immune System/metabolism/pathology ; Mice, Transgenic ; },
abstract = {Apolipoprotein E ε4 allele (APOE4) is the predominant genetic risk factor for late-onset Alzheimer's disease (AD). APOE4 mouse models have provided advances in the understanding of disease pathogenesis, but unaccounted variables like rodent housing status may hinder translational outcomes. Non-sterile aspects like food and bedding can be major sources of changes in rodent microflora. Alterations in intestinal microbial ecology can cause mucosal barrier impairment and increase pro-inflammatory signals. The present study examined the role of sterile and non-sterile food and housing on redox indicators and the immune status of humanized-APOE4 knock-in mice (hAPOe4). hAPOE4 mice were housed under sterile conditions until 22 months of age, followed by the transfer of a cohort of mice to non-sterile housing for 2 months. At 24 months of age, the redox/immunologic status was evaluated by flow cytometry/ELISA. hAPOE4 females housed under non-sterile conditions exhibited: (1) higher neuronal and microglial oxygen radical production and (2) lower CD68[+] microglia (brain) and CD8[+] T cells (periphery) compared to sterile-housed mice. In contrast, hAPOE4 males in non-sterile housing exhibited: (1) higher MHCII[+] microglia and CD11b[+]CD4[+] T cells (brain) and (2) higher CD11b[+]CD4[+] T cells and levels of lipopolysaccharide-binding protein and inflammatory cytokines in the periphery relative to sterile-housed mice. This study demonstrated that sterile vs. non-sterile housing conditions are associated with the activation of redox and immune responses in the brain and periphery in a sex-dependent manner. Therefore, housing status may contribute to variable outcomes in both the brain and periphery.},
}
@article {pmid38868338,
year = {2023},
author = {Wan, W and Grossart, HP and He, D and Liu, W and Wang, S and Yang, Y},
title = {Differentiation strategies for planktonic bacteria and eukaryotes in response to aggravated algal blooms in urban lakes.},
journal = {iMeta},
volume = {2},
number = {1},
pages = {e84},
pmid = {38868338},
issn = {2770-596X},
abstract = {Aggravated algal blooms potentially decreased environmental heterogeneity. Different strategies of planktonic bacteria and eukaryotes in response to aggravated algal blooms. Environmental constraints of plankton showed different patterns over time.},
}
@article {pmid38818334,
year = {2023},
author = {Zhu, YG and Zhu, D and Rillig, MC and Yang, Y and Chu, H and Chen, QL and Penuelas, J and Cui, HL and Gillings, M},
title = {Ecosystem Microbiome Science.},
journal = {mLife},
volume = {2},
number = {1},
pages = {2-10},
pmid = {38818334},
issn = {2770-100X},
abstract = {The microbiome contributes to multiple ecosystem functions and services through its interactions with a complex environment and other organisms. To date, however, most microbiome studies have been carried out on individual hosts or particular environmental compartments. This greatly limits a comprehensive understanding of the processes and functions performed by the microbiome and its dynamics at an ecosystem level. We propose that the theory and tools of ecosystem ecology be used to investigate the connectivity of microorganisms and their interactions with the biotic and abiotic environment within entire ecosystems and to examine their contributions to ecosystem services. Impacts of natural and anthropogenic stressors on ecosystems will likely cause cascading effects on the microbiome and lead to unpredictable outcomes, such as outbreaks of emerging infectious diseases or changes in mutualistic interactions. Despite enormous advances in microbial ecology, we are yet to study microbiomes of ecosystems as a whole. Doing so would establish a new framework for microbiome study: Ecosystem Microbiome Science. The advent and application of molecular and genomic technologies, together with data science and modeling, will accelerate progress in this field.},
}
@article {pmid38868331,
year = {2023},
author = {Li, C and Jin, L and Zhang, C and Li, S and Zhou, T and Hua, Z and Wang, L and Ji, S and Wang, Y and Gan, Y and Liu, J},
title = {Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress.},
journal = {iMeta},
volume = {2},
number = {1},
pages = {e79},
pmid = {38868331},
issn = {2770-596X},
abstract = {Global changes such as seawater intrusion and freshwater resource salinization increase environmental stress imposed on the aquatic microbiome. A strong predictive understanding of the responses of the aquatic microbiome to environmental stress will help in coping with the "gray rhino" events in the environment, thereby contributing to an ecologically sustainable future. Considering that microbial ecological networks are tied to the stability of ecosystem functioning and that abundant and rare biospheres with different biogeographic patterns are important drivers of ecosystem functioning, the roles of abundant and rare biospheres in maintaining ecological networks need to be clarified. Here we showed that, with the increasing salinity stress induced by the freshwater-to-seawater transition, the microbial diversity reduced significantly and the taxonomic structure experienced a strong succession. The complexity and stability of microbial ecological networks were diminished by the increasing stress. The composition of the microorganisms supporting the networks underwent sharp turnovers during the freshwater-to-seawater transition, with the abundant biosphere behaving more robustly than the rare biosphere. Notably, the abundant biosphere played a much more important role than the rare biosphere in stabilizing ecological networks under low-stress environments, but the difference between their relative importance narrowed significantly with the increasing stress, suggesting that the environmental stress weakened the "Matthew effect" in the microbial world. With in-depth insights into the aquatic microbial ecology under stress, our findings highlight the importance of adjusting conservation strategies for the abundant and rare biospheres to maintain ecosystem functions and services in response to rising environmental stress.},
}
@article {pmid38868349,
year = {2023},
author = {Fu, S and Wang, R and Xu, Z and Zhou, H and Qiu, Z and Shen, L and Yang, Q},
title = {Metagenomic sequencing combined with flow cytometry facilitated a novel microbial risk assessment framework for bacterial pathogens in municipal wastewater without cultivation.},
journal = {iMeta},
volume = {2},
number = {1},
pages = {e77},
pmid = {38868349},
issn = {2770-596X},
abstract = {A workflow that combined metagenomic sequencing with flow cytometry was developed. The absolute abundance of pathogens was accurately estimated in mock communities and real samples. Metagenome-assembled genomes binned from metagenomic data set is robust in phylogenetic analysis and virulence profiling.},
}
@article {pmid38665803,
year = {2023},
author = {Schilling, OS and Nagaosa, K and Schilling, TU and Brennwald, MS and Sohrin, R and Tomonaga, Y and Brunner, P and Kipfer, R and Kato, K},
title = {Revisiting Mt Fuji's groundwater origins with helium, vanadium and environmental DNA tracers.},
journal = {Nature water},
volume = {1},
number = {1},
pages = {60-73},
pmid = {38665803},
issn = {2731-6084},
abstract = {Known locally as the water mountain, for millennia Japan's iconic Mt Fuji has provided safe drinking water to millions of people via a vast network of groundwater and freshwater springs. Groundwater, which is recharged at high elevations, flows down Fuji's flanks within three basaltic aquifers, ultimately forming countless pristine freshwater springs among Fuji's foothills. Here we challenge the current conceptual model of Fuji being a simple system of laminar groundwater flow with little to no vertical exchange between its three aquifers. This model contrasts strongly with Fuji's extreme tectonic instability due to its unique location on top of the only known continental trench-trench-trench triple junction, its complex geology and its unusual microbial spring water communities. On the basis of a unique combination of microbial environmental DNA, vanadium and helium tracers, we provide evidence for prevailing deep circulation and a previously unknown deep groundwater contribution to Fuji's freshwater springs. The most substantial deep groundwater upwelling has been found along Japan's most tectonically active region, the Fujikawa-kako Fault Zone. Our findings broaden the hydrogeological understanding of Fuji and demonstrate the vast potential of combining environmental DNA, on-site noble gas and trace element analyses for groundwater science.},
}
@article {pmid38665197,
year = {2023},
author = {Simister, RL and Iulianella Phillips, BP and Wickham, AP and Cayer, EM and Hart, CJR and Winterburn, PA and Crowe, SA},
title = {DNA sequencing, microbial indicators, and the discovery of buried kimberlites.},
journal = {Communications earth &amp; environment},
volume = {4},
number = {1},
pages = {387},
pmid = {38665197},
issn = {2662-4435},
abstract = {Population growth and technological advancements are placing growing demand on mineral resources. New and innovative exploration technologies that improve detection of deeply buried mineralization and host rocks are required to meet these demands. Here we used diamondiferous kimberlite ore bodies as a test case and show that DNA amplicon sequencing of soil microbial communities resolves anomalies in microbial community composition and structure that reflect the surface expression of kimberlites buried under 10 s of meters of overburden. Indicator species derived from laboratory amendment experiments were employed in an exploration survey in which the species distributions effectively delineated the surface expression of buried kimberlites. Additional indicator species derived directly from field observations improved the blind discovery of kimberlites buried beneath similar overburden types. Application of DNA sequence-based analyses of soil microbial communities to mineral deposit exploration provides a powerful illustration of how genomics technologies can be leveraged in the discovery of critical new resources.},
}
@article {pmid38665180,
year = {2023},
author = {Naz, N and Harandi, BF and Newmark, J and Kounaves, SP},
title = {Microbial growth in actual martian regolith in the form of Mars meteorite EETA79001.},
journal = {Communications earth &amp; environment},
volume = {4},
number = {1},
pages = {381},
pmid = {38665180},
issn = {2662-4435},
abstract = {Studies to understand the growth of organisms on Mars are hampered by the use of simulants to duplicate martian mineralogy and chemistry. Even though such materials are improving, no terrestrial simulant can replace a real martian sample. Here we report the use of actual martian regolith, in the form of Mars meteorite EETA79001 sawdust, to demonstrate its ability to support the growth of four microorganisms, E. coli. Eucapsis sp., Chr20-20201027-1, and P. halocryophilus, for up to 23 days under terrestrial conditions using regolith:water ratios from 4:1 to 1:10. If the EETA79001 sawdust is widely representative of regolith on the martian surface, our results imply that microbial life under appropriate conditions could have been present on Mars in the past and/or today in the subsurface, and that the regolith does not contain any bactericidal agents. The results of our study have implications not only for putative martian microbial life but also for building bio-sustainable human habitats on Mars.},
}
@article {pmid38867909,
year = {2022},
author = {Zhu, YX and Yang, R and Wang, XY and Wen, T and Gong, MH and Shen, Y and Xu, JY and Zhao, DS and Du, YZ},
title = {Gut microbiota composition in the sympatric and diet-sharing Drosophila simulans and Dicranocephalus wallichii bowringi shaped largely by community assembly processes rather than regional species pool.},
journal = {iMeta},
volume = {1},
number = {4},
pages = {e57},
pmid = {38867909},
issn = {2770-596X},
abstract = {Clarifying the mechanisms underlying microbial community assembly from regional microbial pools is a central issue of microbial ecology, but remains largely unexplored. Here, we investigated the gut bacterial and fungal microbiome assembly processes and potential sources in Drosophila simulans and Dicranocephalus wallichii bowringi, two wild, sympatric insect species that share a common diet of waxberry. While some convergence was observed, the diversity, composition, and network structure of the gut microbiota significantly differed between these two host species. Null model analyses revealed that stochastic processes (e.g., drift, dispersal limitation) play a principal role in determining gut microbiota from both hosts. However, the strength of each ecological process varied with the host species. Furthermore, the source-tracking analysis showed that only a minority of gut microbiota within D. simulans and D. wallichii bowringi are drawn from a regional microbial pool from waxberries, leaves, or soil. Results from function prediction implied that host species-specific gut microbiota might arise partly through host functional requirement and specific selection across host-microbiota coevolution. In conclusion, our findings uncover the importance of community assembly processes over regional microbial pools in shaping sympatric insect gut microbiome structure and function.},
}
@article {pmid38818216,
year = {2022},
author = {Guo, X and Yuan, M and Lei, J and Shi, Z and Zhou, X and Li, J and Deng, Y and Yang, Y and Wu, L and Luo, Y and Tiedje, JM and Zhou, J},
title = {Climate warming restructures seasonal dynamics of grassland soil microbial communities.},
journal = {mLife},
volume = {1},
number = {3},
pages = {245-256},
pmid = {38818216},
issn = {2770-100X},
abstract = {Soil microbial community's responses to climate warming alter the global carbon cycle. In temperate ecosystems, soil microbial communities function along seasonal cycles. However, little is known about how the responses of soil microbial communities to warming vary when the season changes. In this study, we investigated the seasonal dynamics of soil bacterial community under experimental warming in a temperate tall-grass prairie ecosystem. Our results showed that warming significantly (p = 0.001) shifted community structure, such that the differences of microbial communities between warming and control plots increased nonlinearly (R [2] = 0.578, p = 0.021) from spring to winter. Also, warming significantly (p < 0.050) increased microbial network complexity and robustness, especially during the colder seasons, despite large variations in network size and complexity in different seasons. In addition, the relative importance of stochastic processes in shaping the microbial community decreased by warming in fall and winter but not in spring and summer. Our study indicates that climate warming restructures the seasonal dynamics of soil microbial community in a temperate ecosystem. Such seasonality of microbial responses to warming may enlarge over time and could have significant impacts on the terrestrial carbon cycle.},
}
@article {pmid39295780,
year = {2022},
author = {Mesnage, R and Calatayud, M and Duysburgh, C and Marzorati, M and Antoniou, MN},
title = {Alterations in infant gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME technology.},
journal = {Gut microbiome (Cambridge, England)},
volume = {3},
number = {},
pages = {e6},
pmid = {39295780},
issn = {2632-2897},
abstract = {Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. We describe the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology. SHIME microbiota culture was undertaken in the presence of a concentration of 100-mg/L glyphosate and the same glyphosate equivalent concentration of Roundup. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large-scale disturbances, including an increased abundance of long-chain polyunsaturated fatty acids. Changes in bacterial composition measured by qPCR and 16S rRNA suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota.},
}
@article {pmid38234686,
year = {2022},
author = {Crous, PW and Boers, J and Holdom, D and Osieck, ER and Steinrucken, TV and Tan, YP and Vitelli, JS and Shivas, RG and Barrett, M and Boxshall, AG and Broadbridge, J and Larsson, E and Lebel, T and Pinruan, U and Sommai, S and Alvarado, P and Bonito, G and Decock, CA and De la Peña-Lastra, S and Delgado, G and Houbraken, J and Maciá-Vicente, JG and Raja, HA and Rigueiro-Rodríguez, A and Rodríguez, A and Wingfield, MJ and Adams, SJ and Akulov, A and Al-Hidmi, T and Antonín, V and Arauzo, S and Arenas, F and Armada, F and Aylward, J and Bellanger, JM and Berraf-Tebbal, A and Bidaud, A and Boccardo, F and Cabero, J and Calledda, F and Corriol, G and Crane, JL and Dearnaley, JDW and Dima, B and Dovana, F and Eichmeier, A and Esteve-Raventós, F and Fine, M and Ganzert, L and García, D and Torres-Garcia, D and Gené, J and Gutiérrez, A and Iglesias, P and Istel, &#x141; and Jangsantear, P and Jansen, GM and Jeppson, M and Karun, NC and Karich, A and Khamsuntorn, P and Kokkonen, K and Kolařík, M and Kubátová, A and Labuda, R and Lagashetti, AC and Lifshitz, N and Linde, C and Loizides, M and Luangsa-Ard, JJ and Lueangjaroenkit, P and Mahadevakumar, S and Mahamedi, AE and Malloch, DW and Marincowitz, S and Mateos, A and Moreau, PA and Miller, AN and Molia, A and Morte, A and Navarro-Ródenas, A and Nebesářová, J and Nigrone, E and Nuthan, BR and Oberlies, NH and Pepori, AL and Rämä, T and Rapley, D and Reschke, K and Robicheau, BM and Roets, F and Roux, J and Saavedra, M and Sakolrak, B and Santini, A and Ševčíková, H and Singh, PN and Singh, SK and Somrithipol, S and Spetik, M and Sridhar, KR and Starink-Willemse, M and Taylor, VA and van Iperen, AL and Vauras, J and Walker, AK and Wingfield, BD and Yarden, O and Cooke, AW and Manners, AG and Pegg, KG and Groenewald, JZ},
title = {Fungal Planet description sheets: 1383-1435.},
journal = {Persoonia},
volume = {48},
number = {},
pages = {261-371},
pmid = {38234686},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Agaricus albofoetidus, Agaricus aureoelephanti and Agaricus parviumbrus on soil, Fusarium ramsdenii from stem cankers of Araucaria cunninghamii, Keissleriella sporoboli from stem of Sporobolus natalensis, Leptosphaerulina queenslandica and Pestalotiopsis chiaroscuro from leaves of Sporobolus natalensis, Serendipita petricolae as endophyte from roots of Eriochilus petricola, Stagonospora tauntonensis from stem of Sporobolus natalensis, Teratosphaeria carnegiei from leaves of Eucalyptus grandis × E. camaldulensis and Wongia ficherai from roots of Eragrostis curvula. Canada, Lulworthia fundyensis from intertidal wood and Newbrunswickomyces abietophilus (incl. Newbrunswickomyces gen. nov.) on buds of Abies balsamea. Czech Republic, Geosmithia funiculosa from a bark beetle gallery on Ulmus minor and Neoherpotrichiella juglandicola (incl. Neoherpotrichiella gen. nov.) from wood of Juglans regia. France, Aspergillus rouenensis and Neoacrodontium gallica (incl. Neoacrodontium gen. nov.) from bore dust of Xestobium rufovillosum feeding on Quercus wood, Endoradiciella communis (incl. Endoradiciella gen. nov.) endophytic in roots of Microthlaspi perfoliatum and Entoloma simulans on soil. India, Amanita konajensis on soil and Keithomyces indicus from soil. Israel, Microascus rothbergiorum from Stylophora pistillata. Italy, Calonarius ligusticus on soil. Netherlands, Appendopyricularia juncicola (incl. Appendopyricularia gen. nov.), Eriospora juncicola and Tetraploa juncicola on dead culms of Juncus effusus, Gonatophragmium physciae on Physcia caesia and Paracosmospora physciae (incl. Paracosmospora gen. nov.) on Physcia tenella, Myrmecridium phragmitigenum on dead culm of Phragmites australis, Neochalara lolae on stems of Pteridium aquilinum, Niesslia nieuwwulvenica on dead culm of undetermined Poaceae, Nothodevriesia narthecii (incl. Nothodevriesia gen. nov.) on dead leaves of Narthecium ossifragum and Parastenospora pini (incl. Parastenospora gen. nov.) on dead twigs of Pinus sylvestris. Norway, Verticillium bjoernoeyanum from sand grains attached to a piece of driftwood on a sandy beach. Portugal, Collybiopsis cimrmanii on the base of living Quercus ilex and amongst dead leaves of Laurus and herbs. South Africa, Paraproliferophorum hyphaenes (incl. Paraproliferophorum gen. nov.) on living leaves of Hyphaene sp. and Saccothecium widdringtoniae on twigs of Widdringtonia wallichii. Spain, Cortinarius dryosalor on soil, Cyphellophora endoradicis endophytic in roots of Microthlaspi perfoliatum, Geoglossum lauri-silvae on soil, Leptographium gemmatum from fluvial sediments, Physalacria auricularioides from a dead twig of Castanea sativa, Terfezia bertae and Tuber davidlopezii in soil. Sweden, Alpova larskersii, Inocybe alpestris and Inocybe boreogodeyi on soil. Thailand, Russula banwatchanensis, Russula purpureoviridis and Russula lilacina on soil. Ukraine, Nectriella adonidis on overwintered stems of Adonis vernalis. USA, Microcyclus jacquiniae from living leaves of Jacquinia keyensis and Penicillium neoherquei from a minute mushroom sporocarp. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Boers J, Holdom D, et al. 2022. Fungal Planet description sheets: 1383-1435. Persoonia 48: 261-371. https://doi.org/10.3767/persoonia.2022.48.08.},
}
@article {pmid38868712,
year = {2022},
author = {Xi, J and Lei, B and Liu, YX and Ding, Z and Liu, J and Xu, T and Hou, L and Han, S and Qian, X and Ma, Y and Xue, Q and Gao, J and Gu, J and Tiedje, JM and Lin, Y},
title = {Microbial community roles and chemical mechanisms in the parasitic development of Orobanche cumana.},
journal = {iMeta},
volume = {1},
number = {3},
pages = {e31},
pmid = {38868712},
issn = {2770-596X},
abstract = {Orobanche cumana Wallr. is a holoparasite weed that extracts water and nutrients from its host the sunflower, thereby causing yield reductions and quality losses. However, the number of O. cumana parasites in the same farmland is distinctly different. The roots of some hosts have been heavily parasitized, while others have not been parasitized. What are the factors contributing to this phenomenon? Is it possible that sunflower interroot microorganisms are playing a regulatory role in this phenomenon? The role of the microbial community in this remains unclear. In this study, we investigated the rhizosphere soil microbiome for sunflowers with different degrees of O. cumana parasitism, that is, healthy, light infection, moderate infection, and severe infection on the sunflower roots. The microbial structures differed significantly according to the degree of parasitism, where Xanthomonadaceae was enriched in severe infections. Metagenomic analyses revealed that amino acid, carbohydrate, energy, and lipid metabolism were increased in the rhizosphere soils of severely infected sunflowers, which were attributed to the proliferation of Lysobacter. Lysobacter antibioticus (HX79) was isolated and its capacity to promote O. cumana seed germination and increase the germ tube length was confirmed by germination and pot experiments. Cyclo(Pro-Val), an active metabolite of strain HX79, was identified and metabolomic and molecular docking approaches confirmed it was responsible for promoting O. cumana seed germination and growth. And we found that Pseudomonas mandelii HX1 inhibited the growth of O. cumana in the host rhizosphere soil. Our findings clarify the role of rhizosphere microbiota in regulating the parasite O. cumana to possibly facilitate the development of a new weed suppression strategy.},
}
@article {pmid39131681,
year = {2022},
author = {Movva, R and Murtaza, N and Giri, R and Png, CW and Davies, J and Alabbas, S and Oancea, I and O'Cuiv, P and Morrison, M and Begun, J and Florin, TH},
title = {Successful Manipulation of the Gut Microbiome to Treat Spontaneous and Induced Murine Models of Colitis.},
journal = {Gastro hep advances},
volume = {1},
number = {3},
pages = {359-374},
pmid = {39131681},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: There is clinical interest in the sustainability or otherwise of prebiotic, microbial, and antibiotic treatments to both prevent and treat inflammatory bowel diseases. This study examined the role of antibiotic manipulation of the gut microbiome to treat spontaneous and induced murine models of colitis.<br><br>METHODS: Symptomatic, histological, molecular, and microbial ecology and bioinformatic readouts were used to study the effect of a 10-day antibiotic cocktail and then follow-up over 2 months in the spontaneous Winnie colitis mouse preclinical model of ulcerative colitis and also the indirect antibiotic and Winnie microbiotic gavage effects in an acute dextran sodium sulfate-induced colitis model in wild-type mice.<br><br>RESULTS: The antibiotics elicited a striking reduction in both colitis symptoms and blinded histological colitis scores, together with a convergence of the microbial taxonomy of the spontaneous colitis and wild-type control mice, toward a taxonomic phenotype usually considered to be dysbiotic. The improvement in colitis was sustained over the following 8 weeks although the microbial taxonomy changed. In&#xa0;vitro, fecal waters from the antibiotic-treated colitis and wild-type mice suppressed the inflammatory tenor of colonic epithelial cells, and gavaged cecal slurries from these mice moderated the acute induced colitis.<br><br>CONCLUSION: The results clearly show the possibility of a sustained remission of colitis by microbial manipulation, which is relevant to clinical management of inflammatory bowel diseases. The beneficial effects appeared to depend on the microbial metabolome rather than its taxonomy.},
}
@article {pmid38647867,
year = {2022},
author = {Dzulkarnain, ELN and Audu, JO and Wan Dagang, WRZ and Abdul-Wahab, MF},
title = {Microbiomes of biohydrogen production from dark fermentation of industrial wastes: current trends, advanced tools and future outlook.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {16},
pmid = {38647867},
issn = {2197-4365},
support = {MyBrainSC scholarship//Ministry of Higher Education, Malaysia/ ; 05G24//Universiti Teknologi Malaysia/ ; 09G86//Universiti Teknologi Malaysia/ ; },
abstract = {Biohydrogen production through dark fermentation is very attractive as a solution to help mitigate the effects of climate change, via cleaner bioenergy production. Dark fermentation is a process where organic substrates are converted into bioenergy, driven by a complex community of microorganisms of different functional guilds. Understanding of the microbiomes underpinning the fermentation of organic matter and conversion to hydrogen, and the interactions among various distinct trophic groups during the process, is critical in order to assist in the process optimisations. Research in biohydrogen production via dark fermentation is currently advancing rapidly, and various microbiology and molecular biology tools have been used to investigate the microbiomes. We reviewed here the different systems used and the production capacity, together with the diversity of the microbiomes used in the dark fermentation of industrial wastes, with a special emphasis on palm oil mill effluent (POME). The current challenges associated with biohydrogen production were also included. Then, we summarised and discussed the different molecular biology tools employed to investigate the intricacy of the microbial ecology associated with biohydrogen production. Finally, we included a section on the future outlook of how microbiome-based technologies and knowledge can be used effectively in biohydrogen production systems, in order to maximise the production output.},
}
@article {pmid38867731,
year = {2022},
author = {Jiao, S and Chu, H and Zhang, B and Wei, X and Chen, W and Wei, G},
title = {Linking soil fungi to bacterial community assembly in arid ecosystems.},
journal = {iMeta},
volume = {1},
number = {1},
pages = {e2},
pmid = {38867731},
issn = {2770-596X},
abstract = {Revealing the roles of biotic factors in driving community assembly, which is crucial for the understanding of biodiversity and ecosystem functions, is a fundamental but infrequently investigated subject in microbial ecology. Here, combining a cross-biome observational study with an experimental microcosm study, we provided evidence to reveal the major roles of biotic factors (i.e., soil fungi and cross-kingdom species associations) in determining soil bacterial biogeography and community assembly in complex terrestrial ecosystems of the arid regions of northwest China. The results showed that the soil fungal richness mediates the balance of assembly processes of bacterial communities, and stochastic assembly processes decreased with increasing fungal richness. Our results further suggest that the predicted increase in aridity conditions due to climate change will reduce bacterial α-diversity, particularly in desert soils and subsurface layer, and induce more negative species associations. Together, our study represents a significant advance in linking soil fungi to the mechanisms underlying bacterial biogeographic patterns and community assembly in arid ecosystems under climate aridity and land-use change scenarios.},
}
@article {pmid38202384,
year = {2023},
author = {Wang, B and Sun, M and Wang, Y and Yan, T and Li, Y and Wu, X and Wang, Y and Zhuang, W},
title = {Cadmium-Tolerant Bacterium Strain Cdb8-1 Contributed to the Remediation of Cadmium Pollution through Increasing the Growth and Cadmium Uptake of Chinese Milk Vetch (Astragalus sinicus L.) in Cadmium-Polluted Soils.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {1},
pages = {},
pmid = {38202384},
issn = {2223-7747},
support = {32271916//National Natural Science Foundation of China/ ; JSPKLB202211//Independent Scientific Research Project of Institute of Botany, Jiangsu Province, and Chinese Academy of Sciences/ ; },
abstract = {Cadmium (Cd) pollution has attracted global attention because it not only jeopardizes soil microbial ecology and crop production, but also threatens human health. As of now, microbe-assisted phytoremediation has proven to be a promising approach for the revegetation of Cd-contaminated soil. Therefore, it is important to find such tolerant microorganisms. In the present study, we inoculated a bacteria strain tolerant to Cd, Cdb8-1, to Cd-contaminated soils and then explored the effects of Cdb8-1 inoculation on the performance of the Chinese milk vetch. The results showed plant height, root length, and fresh and dry weight of Chinese milk vetch grown in Cdb8-1-inoculated soils increased compared to the non-inoculated control group. The inoculation of Cd-contaminated soils with Cdb8-1 also enhanced their antioxidant defense system and decreased the H2O2 and malondialdehyde (MDA) contents, which alleviated the phytotoxicity of Cd. The inoculation of Cdb8-1 in Cd-contaminated soils attenuated the contents of total and available Cd in the soil and augmented the BCF and TF of Chinese milk vetch, indicating that the combined application of Cd-tolerant bacteria Cdb8-1 and Chinese milk vetch is a potential solution to Cd-contaminated soils.},
}
@article {pmid38200027,
year = {2024},
author = {Verbeelen, T and Fernandez, CA and Nguyen, TH and Gupta, S and Aarts, R and Tabury, K and Leroy, B and Wattiez, R and Vlaeminck, SE and Leys, N and Ganigué, R and Mastroleo, F},
title = {Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity.},
journal = {NPJ microgravity},
volume = {10},
number = {1},
pages = {3},
pmid = {38200027},
issn = {2373-8065},
support = {4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; },
abstract = {Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLife[TM] PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.},
}
@article {pmid38199186,
year = {2024},
author = {Truong, D and Changey, F and Rondags, E and Framboisier, X and Etienne, M and Guedon, E},
title = {Evaluation of short-circuited electrodes in combination with dark fermentation for promoting biohydrogen production process.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {157},
number = {},
pages = {108631},
doi = {10.1016/j.bioelechem.2023.108631},
pmid = {38199186},
issn = {1878-562X},
mesh = {Fermentation ; *Manure ; *Bioreactors ; Hydrogen ; Electrodes ; },
abstract = {Short-circuited electrodes, in combination with dark fermentation, were evaluated in a biohydrogen production process. The system is based on an innovative design of a non-compartmented electromicrobial bioreactor with a conductive tubular membrane as cathode and a graphite felt as anode. In particular, the electrode specialization occurred when the bioreactor was inoculated with manure as the whole medium and when a vacuum was applied in the tubular membrane, for allowing continuous extraction of gaseous species (H2, CH4, CO2) from the bioreactor. This specialization of the electrodes as anode and cathode was further confirmed by microbial ecology analysis of biofilms and by cyclic voltammetry measurements. In these experimental conditions, the potential of the electrochemical system (short-circuited electrodes) reached values as low as -320 mV vs. SHE, associated with a significant bioH2 production. Moreover, a higher bioH2 production occurred and a potential of the electrochemical system as low as -429 mV vs SHE was temporarily observed, when additional heat treatments of the whole manure were applied in order to remove methanogen microorganisms (i.e., hydrogen consumers). In the bioreactor, the higher production of bioH2 would be promoted by electrofermentation from the current flow observed between short-circuited anode and cathode.},
}
@article {pmid38193259,
year = {2024},
author = {De Paepe, E and Plekhova, V and Vangeenderhuysen, P and Baeck, N and Bullens, D and Claeys, T and De Graeve, M and Kamoen, K and Notebaert, A and Van de Wiele, T and Van Den Broeck, W and Vanlede, K and Van Winckel, M and Vereecke, L and Elliott, C and Cox, E and Vanhaecke, L},
title = {Integrated gut metabolome and microbiome fingerprinting reveals that dysbiosis precedes allergic inflammation in IgE-mediated pediatric cow's milk allergy.},
journal = {Allergy},
volume = {79},
number = {4},
pages = {949-963},
doi = {10.1111/all.16005},
pmid = {38193259},
issn = {1398-9995},
support = {//Fonds Wetenschappelijk Onderzoek/ ; //Bijzonder Onderzoeksfonds UGent/ ; },
mesh = {Humans ; Child ; Child, Preschool ; Cattle ; Female ; Mice ; Animals ; *Milk Hypersensitivity ; Dysbiosis ; RNA, Ribosomal, 16S ; *Microbiota ; Inflammation ; Allergens ; Lactoglobulins ; Immunoglobulin E ; Metabolome ; },
abstract = {BACKGROUND: IgE-mediated cow's milk allergy (IgE-CMA) is one of the first allergies to arise in early childhood and may result from exposure to various milk allergens, of which β-lactoglobulin (BLG) and casein are the most important. Understanding the underlying mechanisms behind IgE-CMA is imperative for the discovery of novel biomarkers and the design of innovative treatment and prevention strategies.<br><br>METHODS: We report a longitudinal in&#xa0;vivo murine model, in which two mice strains (BALB/c and C57Bl/6) were sensitized to BLG using either cholera toxin or an oil emulsion (n&#x2009;=&#x2009;6 per group). After sensitization, mice were challenged orally, their clinical signs monitored, antibody (IgE and IgG1) and cytokine levels (IL-4 and IFN-&#x3b3;) measured, and fecal samples subjected to metabolomics. The results of the murine models were further extrapolated to fecal microbiome-metabolome data from our population of IgE-CMA (n&#x2009;=&#x2009;22) and healthy (n&#x2009;=&#x2009;23) children (Trial: NCT04249973), on which polar metabolomics, lipidomics and 16S rRNA metasequencing were performed. In&#xa0;vitro gastrointestinal digestions and multi-omics corroborated the microbial origin of proposed metabolic changes.<br><br>RESULTS: During mice sensitization, we observed multiple microbially derived metabolic alterations, most importantly bile acid, energy and tryptophan metabolites, that preceded allergic inflammation. We confirmed microbial dysbiosis, and its associated effect on metabolic alterations in our patient cohort, through in&#xa0;vitro digestions and multi-omics, which was accompanied by metabolic signatures of low-grade inflammation.<br><br>CONCLUSION: Our results indicate that gut dysbiosis precedes allergic inflammation and nurtures a chronic low-grade inflammation in children on elimination diets, opening important new opportunities for future prevention and treatment strategies.},
}
@article {pmid38191744,
year = {2024},
author = {Nawata, K and Kadoya, A and Suzuki, S},
title = {Persistence of Marine Bacterial Plasmid in the House Fly (Musca domestica): Marine-Derived Antimicrobial Resistance Genes Have a Chance of Invading the Human Environment.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {30},
pmid = {38191744},
issn = {1432-184X},
support = {KAKENHI 20H00633//Japanese Society of Promotion of Science/ ; Endowed Chair Program//The Sumitomo Electric Industries Group Corporate Social Responsibility Foundation/ ; },
mesh = {Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; *Houseflies ; Angiotensin Receptor Antagonists ; Escherichia coli/genetics ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Enterobacteriaceae/genetics ; *Anti-Infective Agents ; },
abstract = {The house fly is known to be a vector of antibiotic-resistant bacteria (ARB) in animal farms. It is also possible that the house fly contributes to the spread of ARB and antibiotic resistance genes (ARGs) among various environments. We hypothesized that ARB and ARGs present in marine fish and fishery food may gain access to humans via the house fly. We show herein that pAQU1, a marine bacterial ARG-bearing plasmid, persists in the house fly intestine for 5 days after fly ingestion of marine bacteria. In the case of Escherichia coli bearing the same plasmid, the persistence period exceeded 7 days. This interval is sufficient for transmission to human environments, meaning that the house fly is capable of serving as a vector of marine-derived ARGs. Time course monitoring of the house fly intestinal microflora showed that the initial microflora was occupied abundantly with Enterobacteriaceae. Experimentally ingested bacteria dominated the intestinal environment immediately following ingestion; however, after 72 h, the intestinal microflora recovered to resemble that observed at baseline, when diverse genera of Enterobacteriaceae were seen. Given that pAQU1 in marine bacteria and E. coli were detected in fly excrement (defined here as any combination of feces and regurgitated material) at 7 days post-bacterial ingestion, we hypothesize that the house fly may serve as a vector for transmission of ARGs from marine items and fish to humans via contamination with fly excrement.},
}
@article {pmid38191681,
year = {2024},
author = {de Pontes, JS and Oehl, F and Pereira, CD and de Toledo Machado, CT and Coyne, D and da Silva, DKA and Maia, LC},
title = {Heterogeneity in Arbuscular Mycorrhizal Fungi and Plant Communities of the Brazilian Cerrado, Transitional Areas toward the Caatinga, and the Atlantic Forest.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {29},
pmid = {38191681},
issn = {1432-184X},
mesh = {*Mycorrhizae/genetics ; Brazil ; Forests ; Rainforest ; *Microbiota ; Soil ; },
abstract = {The Cerrado is the most diverse tropical savanna worldwide and the second-largest biome in South America. The objective of this study was to understand the heterogeneity and dynamics of arbuscular mycorrhizal fungi (AMF) in different types of natural Cerrado vegetation and areas that are transitioning to dryer savannas or tropical rainforests and to elucidate the driving factors responsible for the differences between these ecosystems. Twenty-one natural sites were investigated, including typical Cerrado forest, typical Caatinga, Atlantic Rainforest, transitions between Cerrado and Caatinga, Cerrado areas near Caatinga or rainforest, and Carrasco sites. Spores were extracted from the soils, counted, and morphologically analyzed. In total, 82 AMF species were detected. AMF species richness varied between 36 and 51, with the highest richness found in the area transitioning between Cerrado and Caatinga, followed by areas of Cerrado close to Caatinga and typical Cerrado forest. The types of Cerrado vegetation and the areas transitioning to the Caatinga shared the highest numbers of AMF species (32-38). Vegetation, along with chemical and physical soil parameters, affected the AMF communities, which may also result from seasonal rainfall patterns. The Cerrado has a great AMF diversity and is, consequently, a natural refuge for AMF. The plant and microbial communities as well as the diversity of habitats require urgent protection within the Cerrado, as it represents a key AMF hotspot.},
}
@article {pmid38190944,
year = {2024},
author = {Kim, G and Yang, H and Lee, J and Cho, KS},
title = {Comparative analysis of hydrogen production and bacterial communities in mesophilic and thermophilic consortia using multiple inoculum sources.},
journal = {Chemosphere},
volume = {350},
number = {},
pages = {141144},
doi = {10.1016/j.chemosphere.2024.141144},
pmid = {38190944},
issn = {1879-1298},
mesh = {Fermentation ; *Food ; *Refuse Disposal ; Bacteria ; Hydrogen ; Bioreactors ; },
abstract = {This study investigates the hydrogen (H2) production performance and bacterial communities in mesophilic (37 °C) and thermophilic (50 °C) H2-producing consortia derived from different inoculum sources and utilizing food waste as a substrate. This study found notable variations in H2 production characteristics among these consortia. Among the mesophilic consortia (MC), the W-MC obtained with wetland (W) as the inoculum source exhibited the highest hydrogen production (3900 mL·L[-1] and 117 mL·L[-1]·h[-1]), while among the thermophilic consortia (TC), the FP-TC obtained with forest puddle sediment (FP) as the inoculum source showed the highest performance (2112 mL·L[-1] and 127 mL·L[-1]·h[-1]). This study reveals that the choice of inoculum source plays a crucial role in determining hydrogen production efficiency. Furthermore, the bacterial community analysis demonstrated varying microbial diversity and richness in different inoculum sources. Clostridium, a well-known H2-producing bacterium, was found in both mesophilic and thermophilic consortia and showed a positive correlation with H2 production. Other bacteria, such as Sporanaerobacter, Caproiciproducens, and Caldibacillus, also exhibited significant correlations with H2 production, suggesting their potential roles in the process. The study highlights the complex interactions between bacterial communities and hydrogen production performance, shedding light on the critical factors influencing this renewable energy source. Overall, this study contributes to our understanding of the microbial ecology and the factors affecting hydrogen production in different temperature conditions, which can have practical implications for optimizing biohydrogen production processes using organic waste substrates.},
}
@article {pmid38190786,
year = {2024},
author = {Zhao, A and Wang, Q and Xu, H and Xu, G},
title = {Effects of continuous warming on homogeneity of periphytic protozoan fauna in marine ecosystems.},
journal = {Marine pollution bulletin},
volume = {199},
number = {},
pages = {116017},
doi = {10.1016/j.marpolbul.2023.116017},
pmid = {38190786},
issn = {1879-3363},
mesh = {*Ecosystem ; *Environmental Biomarkers ; Temperature ; },
abstract = {As a powerful biological indicator, multivariate dispersion in a community is widely used to evaluate the biological evaluation of environmental heterogeneity. To investigate the effects of persistent warming on microbial fauna in marine environments, the periphytic protozoan communities were used as test organisms and incubated in five temperature-controlled circulation system at 22 (control), 25, 28, 31 and 34 °C, respectively. The results showed that (1) there was a clear variation in species occurrence, and the α-/γ-diversity measures decreased with the increase of temperatures; (2) the compositional pattern was significantly driven by the persistent warming compared to community pattern from species-abundance data; and (3) both traditional β-diversity and multivariate dispersion measures on species compositional matrix were significantly correlative with changes in the temperature. Therefore, it is suggested that continuous temperature fluctuations have a greater impact on homogeneity of species composition of protozoan communities than that of their community structure.},
}
@article {pmid38187389,
year = {2023},
author = {Roland, MM and Peacock, TE and Hall, N and Mohammed, AD and Ball, R and Jolly, A and Alexeev, S and Dopkins, N and Nagarkatti, M and Nagarkatti, P and Kubinak, JL},
title = {B-cell-specific MhcII regulates microbiota composition in a primarily IgA-independent manner.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1253674},
pmid = {38187389},
issn = {1664-3224},
support = {P20 GM103641/GM/NIGMS NIH HHS/United States ; R01 AI155887/AI/NIAID NIH HHS/United States ; R56 AI162986/AI/NIAID NIH HHS/United States ; S10 OD032271/OD/NIH HHS/United States ; },
mesh = {Animals ; Mice ; Antilymphocyte Serum ; B-Lymphocytes ; Homeodomain Proteins/genetics ; *Immunoglobulin A ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Genes, MHC Class II ; },
abstract = {BACKGROUND: The expression of major histocompatibility complex class II (MhcII) molecules on B cells is required for the development of germinal centers (GCs) in lymphoid follicles; the primary sites for the generation of T-cell-dependent (TD) antibody responses. Peyer's patches (PPs) are secondary lymphoid tissues (SLOs) in the small intestine (SI) that give rise to high-affinity, TD antibodies (mainly immunoglobulin A (IgA)) generated against the microbiota. While several studies have demonstrated that MhcII antigen presentation by other immune cells coordinate TD IgA responses and regulate microbiota composition, whether or not B-cell-specific MhcII influences gut microbial ecology is unknown.<br><br>METHODS: Here, we developed a novel Rag1 [-/-] adoptive co-transfer model to answer this question. In this model, Rag1 [-/-] mice were reconstituted with na&#xef;ve CD4[+] T cells and either MhcII-sufficient or MhcII-deficient na&#xef;ve B cells. Subsequent to this, resulting shifts in microbiota composition was characterized via 16S rRNA gene sequencing of SI-resident and fecal bacterial communities.<br><br>RESULTS: Results from our experiments indicate that SLO development and reconstitution of an anti-commensal TD IgA response can be induced in Rag1 [-/-] mice receiving T cells and MhcII-sufficient B cells, but not in mice receiving T cells and MhcII-deficient B cells. Results from our 16S experiments confirmed that adaptive immunity is a relevant host factor shaping microbial ecology in the gut, and that its impact was most pronounced on SI-resident bacterial communities.<br><br>CONCLUSION: Our data also clearly establishes that MhcII-mediated cognate interactions between B cells and T cells regulates this effect by maintaining species richness in the gut, which is a phenotype commonly associated with good health. Finally, contrary to expectations, our experimental results indicate that IgA was not responsible for driving any of the effects on the microbiota ascribed to the loss of B cell-specific MhcII. Collectively, results from our experiments support that MhcII-mediated antigen presentation by B cells regulates microbiota composition and promotes species richness through an IgA-independent mechanism.},
}
@article {pmid38185942,
year = {2024},
author = {Zayed, N and Munjaković, H and Aktan, MK and Simoens, K and Bernaerts, K and Boon, N and Braem, A and Pamuk, F and Saghi, M and Van Holm, W and Fidler, A and Gašperšič, R and Teughels, W},
title = {Electrolyzed Saline Targets Biofilm Periodontal Pathogens In Vitro.},
journal = {Journal of dental research},
volume = {103},
number = {3},
pages = {243-252},
doi = {10.1177/00220345231216660},
pmid = {38185942},
issn = {1544-0591},
mesh = {Humans ; *Interleukin-8 ; Dysbiosis ; Biofilms ; *Anti-Infective Agents ; Inflammation ; },
abstract = {Preventing the development and recurrence of periodontal diseases often includes antimicrobial mouthrinses to control the growth of the periodontal pathogens. Most antimicrobials are nonselective, targeting the symbiotic oral species as well as the dysbiosis-inducing ones. This affects the overall microbial composition and metabolic activity and consequently the host-microbe interactions, which can be detrimental (associated with inflammation) or beneficial (health-associated). Consequently, guiding the antimicrobial effect for modulating the microbial composition to a health-associated one should be considered. For such an approach, this study investigated electrolyzed saline as a novel rinse. Electrolyzed saline was prepared from sterile saline using a portable electrolysis device. Multispecies oral homeostatic and dysbiotic biofilms were grown on hydroxyapatite discs and rinsed daily with electrolyzed saline (EOS). Corresponding positive (NaOCl) and negative (phosphate-buffered saline) controls were included. After 3 rinses, biofilms were analyzed with viability quantitative polymerase chain reaction and scanning electron microscopy. Supernatants of rinsed biofilms were used for metabolic activity analysis (high-performance liquid chromatography) through measuring organic acid content. In addition, human oral keratinocytes (HOKs) were exposed to EOS to test biocompatibility (cytotoxicity and inflammation induction) and also to rinsed biofilms to assess their immunogenicity after rinsing. Rinsing the dysbiotic biofilms with EOS could reduce the counts of the pathobionts (>3 log10 Geq/mm[2] reduction) and avert biofilm dysbiosis (≤1% pathobiont abundance), leading to the dominance of commensal species (≥99%), which altered both biofilm metabolism and interleukin 8 (IL-8) induction in HOKs. EOS had no harmful effects on homeostatic biofilms. The scanning electron micrographs confirmed the same. In addition, tested concentrations of EOS did not have any cytotoxic effects and did not induce IL-8 production in HOKs. EOS showed promising results for diverting dysbiosis in in vitro rinsed biofilms and controlling key periopathogens, with no toxic effects on commensal species or human cells. This novel rinsing should be considered for clinical applications.},
}
@article {pmid38185393,
year = {2024},
author = {Wang, L and Zheng, M and Liu, J and Jin, Z and Wang, C and Gao, M and Zhang, H and Zhang, X and Xia, X},
title = {LDLa containing C-type lectin mediates phagocytosis of V.anguillarum and regulates immune effector genes in shrimp.},
journal = {Fish &amp; shellfish immunology},
volume = {145},
number = {},
pages = {109361},
doi = {10.1016/j.fsi.2024.109361},
pmid = {38185393},
issn = {1095-9947},
mesh = {Animals ; Lectins, C-Type/genetics ; Phagocytosis ; *Bacterial Infections ; Receptors, Pattern Recognition/genetics ; Bacteria/metabolism ; Crustacea/metabolism ; *Penaeidae ; Immunity, Innate/genetics ; Hemocytes ; Arthropod Proteins/genetics ; },
abstract = {C-type lectins (CTLs) function as pattern recognition receptors (PRRs) by recognizing invading microorganisms, thereby triggering downstream immune events against infected pathogens. In this study, a novel CTL containing a low-density lipoprotein receptor class A (LDLa) domain was obtained from Litopenaeus vannamei, designed as LvLDLalec. Stimulation by the bacterial pathogen Vibrio anguillarum (V. anguillarum) resulted in remarkable up-regulation of LvLDLalec, as well as release of LvLDLalec into hemolymph. The rLvLDLalec protein possessed broad-spectrum bacterial binding and agglutinating activities, as well as hemocyte attachment ability. Importantly, LvLDLalec facilitated the bacterial clearance in shrimp hemolymph and protected shrimp from bacterial infection. Further studies revealed that LvLDLalec promoted hemocytes phagocytosis against V. anguillarum and lysosomes were involved in the process. Meanwhile, LvLDLalec participated in humoral immunity through activating and inducing nuclear translocation of Dorsal to regulate phagocytosis-related genes and antimicrobial peptides (AMPs) genes, thereby accelerated the removal of invading pathogens in vivo and improved the survival rate of L. vannamei. These results unveil that LvLDLalec serves as a PRR participate in cellular and humoral immunity exerting opsonin activity to play vital roles in the immune regulatory system of L. vannamei.},
}
@article {pmid38182675,
year = {2024},
author = {Zhou, Y and Meng, F and Ochieng, B and Xu, J and Zhang, L and Kimirei, IA and Feng, M and Zhu, L and Wang, J},
title = {Climate and Environmental Variables Drive Stream Biofilm Bacterial and Fungal Diversity on Tropical Mountainsides.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {28},
pmid = {38182675},
issn = {1432-184X},
mesh = {*Rivers ; Tanzania ; Bacteria/genetics ; Biofilms ; *Microbiota ; },
abstract = {High mountain freshwater systems are particularly sensitive to the impacts of global warming and relevant environmental changes. Microorganisms contribute substantially to biogeochemical processes, yet their distribution patterns and driving mechanism in alpine streams remain understudied. Here, we examined the bacterial and fungal community compositions in stream biofilm along the elevational gradient of 745-1874 m on Mt. Kilimanjaro and explored their alpha and beta diversity patterns and the underlying environmental drivers. We found that the species richness and evenness monotonically increased towards higher elevations for bacteria, while were non-significant for fungi. However, both bacterial and fungal communities showed consistent elevational distance-decay relationships, i.e., the dissimilarity of assemblage composition increased with greater elevational differences. Bacterial alpha diversity patterns were mainly affected by chemical variables such as total nitrogen and phosphorus, while fungi were affected by physical variables such as riparian shading and stream width. Notably, climatic variables such as mean annual temperature strongly affected the elevational succession of bacterial and fungal community compositions. Our study is the first exploration of microbial biodiversity and their underlying driving mechanisms for stream ecosystems in tropical alpine regions. Our findings provide insights on the response patterns of tropical aquatic microbial community composition and diversity under climate change.},
}
@article {pmid38181473,
year = {2024},
author = {Zhao, A and Zhong, X and Xu, H and Xu, G},
title = {Continuous warming shifts the community pattern of periphytic protozoan fauna in marine environments.},
journal = {Marine pollution bulletin},
volume = {199},
number = {},
pages = {116016},
doi = {10.1016/j.marpolbul.2023.116016},
pmid = {38181473},
issn = {1879-3363},
mesh = {*Ecosystem ; Environmental Monitoring/methods ; *Ciliophora ; Food Chain ; Environmental Biomarkers ; Biodiversity ; },
abstract = {Protozoan fauna is playing an important role in the functioning of microbial food webs by transferring the flux of material and energy from low to high tropic levels in marine ecosystems. To assess effects of elevated temperature on the marine ecosystem, periphytic protozoan communities were used as the test microbial fauna, and were incubated in a temperature-controlled circulation system in a successive temperature gradient of 22 (control), 25, 28, 31 and 34 °C. The results showed that: (1) the test microbial fauna was shifted in both species composition and community structure; (2) the average taxonomic distinctness represented a clear decreasing trend, (3) while the variation in taxonomic distinctness significantly increased with increase of water temperature; and (4) the community pattern was significantly departed from an expectation when temperature increased by 12 °C. These results suggested that Protozoa may be used as a useful bioindicator of global warming in marine ecosystems.},
}
@article {pmid38179971,
year = {2024},
author = {Price, CE and Valls, RA and Ramsey, AR and Loeven, NA and Jones, JT and Barrack, KE and Schwartzman, JD and Royce, DB and Cramer, RA and Madan, JC and Ross, BD and Bliska, J and O'Toole, GA},
title = {Intestinal Bacteroides modulates inflammation, systemic cytokines, and microbial ecology via propionate in a mouse model of cystic fibrosis.},
journal = {mBio},
volume = {15},
number = {2},
pages = {e0314423},
pmid = {38179971},
issn = {2150-7511},
support = {R01 ES033988/ES/NIEHS NIH HHS/United States ; P30 DK117469/DK/NIDDK NIH HHS/United States ; R35 GM142685/GM/NIGMS NIH HHS/United States ; T32 HL134598/HL/NHLBI NIH HHS/United States ; T32 AI007363/AI/NIAID NIH HHS/United States ; },
mesh = {Child ; Infant ; Humans ; Mice ; Animals ; *Cystic Fibrosis/complications ; Cystic Fibrosis Transmembrane Conductance Regulator ; Propionates ; Bacteroides/genetics ; Caco-2 Cells ; Inflammation/complications ; Disease Models, Animal ; Dysbiosis/complications ; Escherichia coli ; },
abstract = {Persons with cystic fibrosis (CF), starting in early life, show intestinal microbiome dysbiosis characterized in part by a decreased relative abundance of the genus Bacteroides. Bacteroides is a major producer of the intestinal short chain fatty acid propionate. We demonstrate here that cystic fibrosis transmembrane conductance regulator-defective (CFTR-/-) Caco-2 intestinal epithelial cells are responsive to the anti-inflammatory effects of propionate. Furthermore, Bacteroides isolates inhibit the IL-1β-induced inflammatory response of CFTR-/- Caco-2 intestinal epithelial cells and do so in a propionate-dependent manner. The introduction of Bacteroides-supplemented stool from infants with cystic fibrosis into the gut of Cftr[F508del] mice results in higher propionate in the stool as well as the reduction in several systemic pro-inflammatory cytokines. Bacteroides supplementation also reduced the fecal relative abundance of Escherichia coli, indicating a potential interaction between these two microbes, consistent with previous clinical studies. For a Bacteroides propionate mutant in the mouse model, pro-inflammatory cytokine KC is higher in the airway and serum compared with the wild-type (WT) strain, with no significant difference in the absolute abundance of these two strains. Taken together, our data indicate the potential multiple roles of Bacteroides-derived propionate in the modulation of systemic and airway inflammation and mediating the intestinal ecology of infants and children with CF. The roles of Bacteroides and the propionate it produces may help explain the observed gut-lung axis in CF and could guide the development of probiotics to mitigate systemic and airway inflammation for persons with CF.IMPORTANCEThe composition of the gut microbiome in persons with CF is correlated with lung health outcomes, a phenomenon referred to as the gut-lung axis. Here, we demonstrate that the intestinal microbe Bacteroides decreases inflammation through the production of the short-chain fatty acid propionate. Supplementing the levels of Bacteroides in an animal model of CF is associated with reduced systemic inflammation and reduction in the relative abundance of the opportunistically pathogenic group Escherichia/Shigella in the gut. Taken together, these data demonstrate a key role for Bacteroides and microbially produced propionate in modulating inflammation, gut microbial ecology, and the gut-lung axis in cystic fibrosis. These data support the role of Bacteroides as a potential probiotic in CF.},
}
@article {pmid38179905,
year = {2024},
author = {Huffines, JT and Boone, RL and Kiedrowski, MR},
title = {Temperature influences commensal-pathogen dynamics in a nasal epithelial cell co-culture model.},
journal = {mSphere},
volume = {9},
number = {1},
pages = {e0058923},
pmid = {38179905},
issn = {2379-5042},
support = {P30 DK072482/DK/NIDDK NIH HHS/United States ; T32 GM008111/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Temperature ; Coculture Techniques ; *Staphylococcus aureus ; Dysbiosis ; *Sinusitis/microbiology ; Epithelial Cells/microbiology ; Inflammation ; Chronic Disease ; },
abstract = {Chronic rhinosinusitis (CRS) is an inflammatory disease of the paranasal sinuses, and microbial dysbiosis associated with CRS is thought to be a key driver of host inflammation that contributes to disease progression. Staphylococcus aureus is a common upper respiratory tract (URT) pathobiont associated with higher carriage rates in CRS populations, where S. aureus-secreted toxins can be identified in CRS tissues. Although many genera of bacteria colonize the URT, few account for the majority of sequencing reads. These include S. aureus and several species belonging to the genus Corynebacterium, including Corynebacterium propinquum and Corynebacterium pseudodiphtheriticum, which are observed at high relative abundance in the healthy URT. Studies have examined bacterial interactions between major microbionts of the URT and S. aureus, but few have done so in the context of a healthy versus diseased URT environment. Here, we examine the role of temperature in commensal, pathogen, and epithelial dynamics using an air-liquid interface cell culture model mimicking the nasal epithelial environment. Healthy URT temperatures change from the nares to the nasopharynx and are increased during disease. Temperatures representative of the healthy URT increase persistence and aggregate formation of commensal C. propinquum and C. pseudodiphtheriticum, reduce S. aureus growth, and lower epithelial cytotoxicity compared to higher temperatures correlating with the diseased CRS sinus. Dual-species colonization revealed species-specific interactions between Corynebacterium species and S. aureus dependent on temperature. Our findings suggest URT mucosal temperature plays a significant role in mediating polymicrobial and host-bacterial interactions that may exacerbate microbial dysbiosis in chronic URT diseases.IMPORTANCEChronic rhinosinusitis is a complex inflammatory disease with a significant healthcare burden. Although presence of S. aureus and microbial dysbiosis are considered mediators of inflammation in CRS, no studies have examined the influence of temperature on S. aureus interactions with the nasal epithelium and the dominant genus of the healthy URT, Corynebacterium. Interactions between Corynebacterium species and S. aureus have been documented in several studies, but none to date have examined how environmental changes in the URT may alter their interactions with the epithelium or each other. This study utilizes a polarized epithelial cell culture model at air-liquid interface to study the colonization and spatial dynamics of S. aureus and clinical isolates of Corynebacterium from people with CRS to characterize the role temperature has in single- and dual-species dynamics on the nasal epithelium.},
}
@article {pmid38179459,
year = {2023},
author = {Parsons, RJ and Liu, S and Longnecker, K and Yongblah, K and Johnson, C and Bolaños, LM and Comstock, J and Opalk, K and Kido Soule, MC and Garley, R and Carlson, CA and Temperton, B and Bates, NR},
title = {Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1287477},
pmid = {38179459},
issn = {1664-302X},
abstract = {Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L[-1] of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.},
}
@article {pmid38175304,
year = {2024},
author = {Marčiulynas, A and Menkis, A},
title = {Long-term Dynamics of Fungal Communities Inhabiting Decaying Stumps of Quercus robur.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {27},
pmid = {38175304},
issn = {1432-184X},
mesh = {*Mycobiome ; *Quercus ; High-Throughput Nucleotide Sequencing ; Trees ; Wood ; },
abstract = {We studied the diversity, composition, and long-term dynamics of wood-inhabiting fungi in Quercus robur stumps left after commercial tree harvesting in Lithuania. Sampling of wood was carried out at three sites and from stumps, which were 10-, 20-, 30-, 40-, and 50-year-old. DNA was isolated from wood samples and fungal communities analyzed using high-throughput sequencing. Results showed that stump age had a limited effect on fungal diversity. The development of fungal communities in oak stums was found to be a slow process as fungal communities remained similar for decades, while larger changes were only detected in older stumps. The most common fungi were Eupezizella sp. (18.4%), Hyphodontia pallidula (12.9%), Mycena galericulata (8.3%), and Lenzites betulinus (7.1%). Fistulina hepatica, which is a red-listed wood-decay oak fungus, was also detected at a low relative abundance in stump wood. In the shortage of suitable substrate, oak stumps may provide habitats for long-term survival of different fungal species, including red-listed and oak-related fungi.},
}
@article {pmid38175217,
year = {2024},
author = {Grandhay, C and Prétot, E and Klaba, V and Celle, H and Normand, AC and Bertrand, X and Grenouillet, F},
title = {Yeast Biodiversity of Karst Waters: Interest of Four Culture Media and an Improved MALDI-TOF MS Database.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {26},
pmid = {38175217},
issn = {1432-184X},
mesh = {Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Culture Media ; *Drinking Water ; Biodiversity ; },
abstract = {Karst aquifers are a significant source of drinking water and highly vulnerable to pollution and microbial contamination. Microbiological regulations for the quality of drinking water mostly focus on bacterial levels and lack guidance concerning fungal contamination. Moreover, there is no standardised microbial analysis methodology for identifying fungi in water. Our main objective was to establish the most effective culture and identification methodology to examine yeast diversity in karst waters. We assessed the comparative efficacy of four culture media (CHROMagar Candida, dichloran glycerol 18% [DG18], dichloran rose Bengal chloramphenicol [DRBC], and SYMPHONY agar) for yeast isolation from karst water samples. Furthermore, we investigated the comprehensiveness of databases used in MALDI-TOF mass spectrometry (MALDI-TOF MS) for identifying environmental yeast species. In total, we analysed 162 water samples, allowing the identification of 2479 yeast isolates. We demonstrate that a combination of four culture media, each with distinct specifications, more efficiently covers a wide range of yeast species in karst water than a combination of only two or three. Supplementation of a MALDI-TOF MS database is also critical for analysing environmental microbial samples and improved the identification of yeast biodiversity. This study is an initial step towards standardising the analysis of fungal biodiversity in karst waters, enabling a better understanding of the significance of this environmental reservoir in relation to public health.},
}
@article {pmid38172411,
year = {2024},
author = {Kankonkar, HT and Khandeparker, RS},
title = {Halotolerant Bacteria from Genus Nesterenkonia sandarakina VSA9 as a Potential Polyhydroxyalkanoate Producer.},
journal = {Current microbiology},
volume = {81},
number = {1},
pages = {53},
pmid = {38172411},
issn = {1432-0991},
mesh = {*Polyhydroxyalkanoates ; Phylogeny ; *Micrococcaceae/metabolism ; Bacteria/genetics/metabolism ; Acyltransferases/metabolism ; },
abstract = {Nesterenkonia sandarakina VSA9 pigmented bacteria isolated from Sargassum is being reported to produce polyhydroxyalkanoates (PHA) deduced through detecting the presence of pha C gene using the molecular method. The PHA synthase gene was of type I which has been concluded from the phylogenetic tree and multiple sequence analysis. The amino acid analysis of pha C gene confirms the involvement of the lipase box having a sequence of G-Y-C-I-G-G with cysteine as the active center of the PHA synthase. Homology modeling predicted the 3D protein structure which is similar to the PHA synthase of Chromobacterium sp. USM2. The solvent extract of N. sandarakina VSA9 showed the presence of Carotenoid compound with maximum wavelength at 475 nm. The study's findings could have far-reaching implications, contributing to advancements in the biotechnology, industrial processes, and sustainable practices. The simultaneous production of carotenoids and PHAs by N. sandarakina VSA9 presents exciting opportunities for the development of innovative and environmentally friendly applications.},
}
@article {pmid38171425,
year = {2024},
author = {Gao, T and Tian, H and Xiang, L and Wang, Z and Fu, Y and Shi, J and Wen, X and Jiang, X and He, W and Hashsham, SA and Wang, F},
title = {Characteristics of bacterial community and extracellular enzymes in response to atrazine application in black soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {343},
number = {},
pages = {123286},
doi = {10.1016/j.envpol.2023.123286},
pmid = {38171425},
issn = {1873-6424},
mesh = {*Atrazine/analysis ; Soil ; Soil Microbiology ; *Herbicides/analysis ; Bacteria/metabolism ; *Soil Pollutants/analysis ; Biomarkers/metabolism ; Biodegradation, Environmental ; },
abstract = {The ecological functioning of black soil largely depends on the activities of various groups of microorganisms. However, little is known about how atrazine, a widely used herbicide with known harmful effects on the environment, influences the microbial ecology of black soil, and the extracellular enzymes related to the carbon, nitrogen and phosphorus cycles. Here, we evaluated the change in extracellular enzymes and bacterial community characteristics in black soil after exposure to various concentrations of atrazine. Low concentrations of applied atrazine (10 - 20 mg kg[-1]) were almost completely degraded after 120 days. At high concentrations (80 - 100 mg kg[-1]), about 95% of the applied atrazine was degraded over the same period. Additionally, linear fitting of data indicated that the total enzymatic activity index (TEI) and bacterial α-diversity index were negatively correlated with atrazine applied concentration. The atrazine had a greater effect on bacterial beta diversity after 120 days, which differentiated species clusters treated with low and high atrazine concentrations. Soil bacterial community structure and function were affected by atrazine, especially at high atrazine concentrations (80 - 100 mg kg[-1]). Key microorganisms such as Sphingomonas and Nocardioides were identified as biomarkers for atrazine dissipation. Functional prediction indicated that most metabolic pathways might be involved in atrazine dissipation. Overall, the findings enhance our understanding of the factors driving atrazine degradation in black soil and supports the use of biomarkers as indicators of atrazine dissipation.},
}
@article {pmid38171124,
year = {2024},
author = {Soni, K and Kothamasi, D and Chandra, R},
title = {Municipal wastewater treatment plant showing a potential reservoir for clinically relevant MDR bacterial strains co-occurrence of ESBL genes and integron-integrase genes.},
journal = {Journal of environmental management},
volume = {351},
number = {},
pages = {119938},
doi = {10.1016/j.jenvman.2023.119938},
pmid = {38171124},
issn = {1095-8630},
mesh = {Humans ; beta-Lactamases/genetics ; Integrons/genetics ; Integrases ; Bacteria ; Anti-Bacterial Agents/pharmacology ; Escherichia coli ; Wastewater ; *Bacillus ; *Water Purification ; Drug Resistance, Multiple ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Municipal wastewater treatment plants (MWWTPs) are a milieu for co-occurrence of multiple antibiotic resistance genes (ARGs). This facilitates mixing and genetic exchange; and promotes dissemination of multidrug resistance (MDR) to wastewater bacterial communities which is hazardous for the effluent receiving environment. This study investigated the co-occurrence of extended-spectrum beta-lactamase (ESBL) genes (blaTEM, blaCTX-M, blaSHV, blaOXA), and integron-integrase genes (intI1, intI2, intI3) in MDR bacteria isolated from the Bharwara MWWTP in Lucknow, India. Thirty-one MDR bacterial colonies resistant to three or more antibiotics were isolated from three treatment stages of this MWWTP. Six of these: Staphylococcus aureus, Serratia marcescens, Salmonella enterica, Shigella sonnei, Escherichia coli, and Bacillus sp. Had co-occurrence of ESBL and integron-integrase genes. These six isolates were examined for the occurrence of MDR efflux genes (qacA, acrB) and ARGs (aac(3)-1, qnrA1, tetA, vanA) and tested for resistance against 12 different antibiotics. The highest resistance was against penicillin-G (100%) and lowest for chloramphenicol (16.66%). Bacillus sp. Isolate BWKRC6 had the highest co-occurrence of antibiotic resistance-determining genes and was resistant to all the 12 antibiotics tested. The co-occurrence of ESBL, integron-integrase, antibiotic resistance-determining and MDR efflux genes in bacteria isolated from the Bharwara MWWTP indicates that the wastewaters of this treatment plant may have become a hotspot for MDR bacteria and may present human and environmental health hazards. Therefore, there is need for a rapid action to limit the spread of this threat. Public regulatory authorities must urgently implement measures to prevent MWWTPs becoming reservoirs for evolution of antibiotic resistance genes and development of antibiotic resistance.},
}
@article {pmid38169617,
year = {2023},
author = {Song, W and Wu, F and Yan, Y and Li, Y and Wang, Q and Hu, X and Li, Y},
title = {Gut microbiota landscape and potential biomarker identification in female patients with systemic lupus erythematosus using machine learning.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1289124},
pmid = {38169617},
issn = {2235-2988},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Lupus Erythematosus, Systemic/diagnosis ; Biomarkers ; Machine Learning ; },
abstract = {OBJECTIVES: Systemic Lupus Erythematosus (SLE) is a complex autoimmune disease that disproportionately affects women. Early diagnosis and prevention are crucial for women's health, and the gut microbiota has been found to be strongly associated with SLE. This study aimed to identify potential biomarkers for SLE by characterizing the gut microbiota landscape using feature selection and exploring the use of machine learning (ML) algorithms with significantly dysregulated microbiotas (SDMs) for early identification of SLE patients. Additionally, we used the SHapley Additive exPlanations (SHAP) interpretability framework to visualize the impact of SDMs on the risk of developing SLE in females.<br><br>METHODS: Stool samples were collected from 54 SLE patients and 55 Negative Controls (NC) for microbiota analysis using 16S rRNA sequencing. Feature selection was performed using Elastic Net and Boruta on species-level taxonomy. Subsequently, four ML algorithms, namely logistic regression (LR), Adaptive Boosting (AdaBoost), Random Forest (RF), and eXtreme gradient boosting (XGBoost), were used to achieve early identification of SLE with SDMs. Finally, the best-performing algorithm was combined with SHAP to explore how SDMs affect the risk of developing SLE in females.<br><br>RESULTS: Both alpha and beta diversity were found to be different in SLE group. Following feature selection, 68 and 21 microbiota were retained in Elastic Net and Boruta, respectively, with 16 microbiota overlapping between the two, i.e., SDMs for SLE. The four ML algorithms with SDMs could effectively identify SLE patients, with XGBoost performing the best, achieving Accuracy, Sensitivity, Specificity, Positive Predictive Value, Negative Predictive Value, and AUC values of 0.844, 0.750, 0.938, 0.923, 0.790, and 0.930, respectively. The SHAP interpretability framework showed a complex non-linear relationship between the relative abundance of SDMs and the risk of SLE, with Escherichia_fergusonii having the largest SHAP value.<br><br>CONCLUSIONS: This study revealed dysbiosis in the gut microbiota of female SLE patients. ML classifiers combined with SDMs can facilitate early identification of female patients with SLE, particularly XGBoost. The SHAP interpretability framework provides insight into the impact of SDMs on the risk of SLE and may inform future scientific treatment for SLE.},
}
@article {pmid38169416,
year = {2024},
author = {Kim, K and Jinno, C and Li, X and Bravo, D and Cox, E and Ji, P and Liu, Y},
title = {Impact of an oligosaccharide-based polymer on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic E. coli.},
journal = {Journal of animal science and biotechnology},
volume = {15},
number = {1},
pages = {1},
pmid = {38169416},
issn = {1674-9782},
support = {W4002 and NC1202//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Our previous study has reported that supplementation of oligosaccharide-based polymer enhances gut health and disease resistance of pigs infected with enterotoxigenic E. coli (ETEC) F18 in a manner similar to carbadox. The objective of this study was to investigate the impacts of oligosaccharide-based polymer or antibiotic on the host metabolic profiles and colon microbiota of weaned pigs experimentally infected with ETEC F18.<br><br>RESULTS: Multivariate analysis highlighted the differences in the metabolic profiles of serum and colon digesta which were predominantly found between pigs supplemented with oligosaccharide-based polymer and antibiotic. The relative abundance of metabolic markers of immune responses and nutrient metabolisms, such as amino acids and carbohydrates, were significantly differentiated between the oligosaccharide-based polymer and antibiotic groups (q&#x2009;<&#x2009;0.2 and fold change&#x2009;>&#x2009;2.0). In addition, pigs in antibiotic had a reduced (P&#x2009;<&#x2009;0.05) relative abundance of Lachnospiraceae and Lactobacillaceae, whereas had greater (P&#x2009;<&#x2009;0.05) Clostridiaceae and Streptococcaceae in the colon digesta on d 11 post-inoculation (PI) compared with d 5 PI.<br><br>CONCLUSIONS: The impact of oligosaccharide-based polymer on the metabolic and microbial profiles of pigs is not fully understood, and further exploration is needed. However, current research suggest that various mechanisms are involved in the enhanced disease resistance and performance in ETEC-challenged pigs by supplementing this polymer.},
}
@article {pmid38167150,
year = {2024},
author = {Alahmad, A and Harir, M and Fochesato, S and Tulumello, J and Walker, A and Barakat, M and Ndour, PMS and Schmitt-Kopplin, P and Cournac, L and Laplaze, L and Heulin, T and Achouak, W},
title = {Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {1},
pmid = {38167150},
issn = {2049-2618},
support = {ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; },
mesh = {*Pennisetum/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Plant Roots/microbiology ; *Microbiota ; Soil/chemistry ; Plants/microbiology ; Exudates and Transudates ; Soil Microbiology ; Rhizosphere ; },
abstract = {BACKGROUND: The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four distinct lines with contrasting soil aggregation abilities.<br><br>RESULTS: Utilizing 16S rRNA gene and ITS metabarcoding for microbiota profiling, coupled with FTICR-MS metabonomic analysis of metabolite composition in distinct plant compartments and root exudates, we revealed substantial disparities in microbial diversity and interaction networks. The &#xdf;-NTI analysis highlighted bacterial rhizosphere turnover driven primarily by deterministic processes, showcasing prevalent homogeneous selection in root tissue (RT) and root-adhering soil (RAS). Conversely, fungal communities were more influenced by stochastic processes. In bulk soil assembly, a combination of deterministic and stochastic mechanisms shapes composition, with deterministic factors exerting a more pronounced role. Metabolic profiles across shoots, RT, and RAS in different pearl millet lines mirrored their soil aggregation levels, emphasizing the impact of inherent plant traits on microbiota composition and unique metabolic profiles in RT and exudates. Notably, exclusive presence of antimicrobial compounds, including DIMBOA and H-DIMBOA, emerged in root exudates and RT of low aggregation lines.<br><br>CONCLUSIONS: This research underscores the pivotal influence of root exudates in shaping the root-associated microbiota composition across pearl millet lines, entwined with their soil aggregation capacities. These findings underscore the interconnectedness of root exudates and microbiota, which jointly shape rhizosheath structure, deepening insights into soil-plant-microbe interactions and ecological processes shaping rhizosphere microbial communities. Deciphering plant-microbe interactions and their contribution to soil aggregation and microbiota dynamics holds promise for the advancement of sustainable agricultural strategies. Video Abstract.},
}
@article {pmid38166159,
year = {2024},
author = {Chen, X and He, C and Zhang, Q and Bayakmetov, S and Wang, X},
title = {Modularized Design and Construction of Tunable Microbial Consortia with Flexible Topologies.},
journal = {ACS synthetic biology},
volume = {13},
number = {1},
pages = {183-194},
pmid = {38166159},
issn = {2161-5063},
support = {R01 EB031893/EB/NIBIB NIH HHS/United States ; R01 GM131405/GM/NIGMS NIH HHS/United States ; },
mesh = {*Microbial Consortia/genetics ; *Bacteria/genetics ; },
abstract = {Complex and fluid bacterial community compositions are critical to diversity, stability, and function. However, quantitative and mechanistic descriptions of the dynamics of such compositions are still lacking. Here, we develop a modularized design framework that allows for bottom-up construction and the study of synthetic bacterial consortia with different topologies. We showcase the microbial consortia design and building process by constructing amensalism and competition consortia using only genetic circuit modules to engineer different strains to form the community. Functions of modules and hosting strains are validated and quantified to calibrate dynamic parameters, which are then directly fed into a full mechanistic model to accurately predict consortia composition dynamics for both amensalism and competition without further fitting. More importantly, such quantitative understanding successfully identifies the experimental conditions to achieve coexistence composition dynamics. These results illustrate the process of both computationally and experimentally building up bacteria consortia complexity and hence achieve robust control of such fluid systems.},
}
@article {pmid38165515,
year = {2024},
author = {Fowler, AE and McFrederick, QS and Adler, LS},
title = {Pollen Diet Diversity does not Affect Gut Bacterial Communities or Melanization in a Social and Solitary Bee Species.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {25},
doi = {10.1007/s00248-023-02323-6},
pmid = {38165515},
issn = {1432-184X},
support = {GNE19-200-33243//Northeast SARE/ ; AFRI-2018-08591//U.S. Department of Agriculture/ ; },
mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Diet/veterinary ; Medicago sativa ; Pollen ; },
abstract = {Pollinators face many stressors, including reduced floral diversity. A low-diversity diet can impair organisms' ability to cope with additional stressors, such as pathogens, by altering the gut microbiome and/or immune function, but these effects are understudied for most pollinators. We investigated the impact of pollen diet diversity on two ecologically and economically important generalist pollinators, the social bumble bee (Bombus impatiens) and the solitary alfalfa leafcutter bee (Megachile rotundata). We experimentally tested the effect of one-, two-, or three-species pollen diets on gut bacterial communities in both species, and the melanization immune response in B. impatiens. Pollen diets included dandelion (Taraxacum officinale), staghorn sumac (Rhus typhina), and hawthorn (Crataegus sp.) alone, each pair-wise combination, or a mix of all three species. We fed bees their diet for 7 days and then dissected out guts and sequenced 16S rRNA gene amplicons to characterize gut bacterial communities. To assess melanization in B. impatiens, we inserted microfilament implants into the bee abdomen and measured melanin deposition on the implant. We found that pollen diet did not influence gut bacterial communities in M. rotundata. In B. impatiens, pollen diet composition, but not diversity, affected gut bacterial richness in older, but not newly-emerged bees. Pollen diet did not affect the melanization response in B. impatiens. Our results suggest that even a monofloral, low-quality pollen diet such as dandelion can support diverse gut bacterial communities in captive-reared adults of these bee species. These findings shed light on the effects of reduced diet diversity on bee health.},
}
@article {pmid38165150,
year = {2024},
author = {Kanchongkittiphon, W and Nopnipa, S and Mathuranyanon, R and Nonthabenjawan, N and Sritournok, S and Manuyakorn, W and Wanapaisan, P},
title = {Characterization of gut microbiome profile in children with confirmed wheat allergy.},
journal = {Asian Pacific journal of allergy and immunology},
volume = {},
number = {},
pages = {},
doi = {10.12932/AP-080623-1626},
pmid = {38165150},
issn = {0125-877X},
abstract = {BACKGROUND: Food allergies pose serious health risks, including life-threatening anaphylactic reactions, increased morbidity, and reduced quality of life. Wheat allergy is a common concern in Asia. There is growing interest in understanding the potential association between dysregulation of the gut microbiome and the development of food allergies.<br><br>OBJECTIVE: This study aimed to explore the gut microbiome of Thai children with wheat allergy and its potential association with allergic responses.<br><br>METHODS: Microbial abundance was assessed using Quantitative Insights into Microbial Ecology 2 (QIIME2) microbiome analysis based on 16S rDNA data. The correlation between microbial richness and relevant parameters was evaluated using the Spearman correlation analysis. Additionally, the microbial community functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2).<br><br>RESULTS: The gut microbiome analysis revealed significant differences between the two groups at the phylum and genus levels. Firmicutes (p = 0.012) and Verrucomicrobia (p < 0.001) were enriched in wheat-allergic children, whereas specific gut microbes such as Megamonas (p = 0.04), Romboutsia (p < 0.001), Fusobacterium (p < 0.001), Clostridium senso stricto1 (p < 0.001), and Turicibacter (p < 0.001) were more abundant in healthy children. Anaerostripes (p = 0.011), Erysipelatoclostridium (p < 0.001), Prevotella 2 (p < 0.001), Ruminiclostridium 5 (p < 0.001), and Clostridium innnocuum (p < 0.001) were enriched in children with a confirmed wheat allergy. Functional analysis indicated disparities in the pathways related to arginine and polyamine biosynthesis.<br><br>CONCLUSION: These findings offer valuable insights into the gut microbiome of children with wheat allergy and its potential impact on symptom severity, laying the groundwork for further research and interventions aimed at addressing this health concern.},
}
@article {pmid38163403,
year = {2024},
author = {Dufour, OK and Hoffman, E and Sleith, RS and Katz, LA and Weiner, AKM and Sehein, TR},
title = {Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing.},
journal = {European journal of protistology},
volume = {92},
number = {},
pages = {126049},
pmid = {38163403},
issn = {1618-0429},
support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; },
mesh = {*Amoeba/genetics ; Ecosystem ; Wetlands ; Phylogeny ; *Amoebozoa ; *Lobosea ; New England ; },
abstract = {Testate amoebae (order Arcellinida) are abundant in freshwater ecosystems, including low pH bogs and fens. Within these environments, Arcellinida are considered top predators in microbial food webs and their tests are useful bioindicators of paleoclimatic changes and anthropogenic pollutants. Accurate species identifications and characterizations of diversity are important for studies of paleoclimate, microbial ecology, and environmental change; however, morphological species definitions mask cryptic diversity, which is a common phenomenon among microbial eukaryotes. Lineage-specific primers recently designed to target Arcellinida for amplicon sequencing successfully captured a poorly-described yet diverse fraction of the microbial eukaryotic community. Here, we leveraged the application of these newly-designed primers to survey the diversity of Arcellinida in four low-pH New England bogs and fens, investigating variation among bogs (2018) and then across seasons and habitats within two bogs (2019). Three OTUs represented 66% of Arcellinida reads obtained across all habitats surveyed. 103 additional OTUs were present in lower abundance with some OTUs detected in only one sampling location, suggesting habitat specificity. By establishing a baseline for Arcellinida diversity, we provide a foundation to monitor key taxa in habitats that are predicted to change with increasing anthropogenic pressure and rapid climate change.},
}
@article {pmid38162520,
year = {2023},
author = {Capeding, MRZ and Phee, LCM and Ming, C and Noti, M and Vidal, K and Le Carrou, G and Frézal, A and Moll, JM and Vogt, JK and Myers, PN and Nielsen, BH and Boulangé, CL and Samuel, TM and Berger, B and Cercamondi, CI},
title = {Safety, efficacy, and impact on gut microbial ecology of a Bifidobacterium longum subspecies infantis LMG11588 supplementation in healthy term infants: a randomized, double-blind, controlled trial in the Philippines.},
journal = {Frontiers in nutrition},
volume = {10},
number = {},
pages = {1319873},
pmid = {38162520},
issn = {2296-861X},
abstract = {INTRODUCTION: Bifidobacterium longum subspecies infantis (B. infantis) may play a key role in infant gut development. This trial evaluated safety, tolerability, and efficacy of B. infantis LMG11588 supplementation.<br><br>METHODS: This randomized, placebo-controlled, double-blind study conducted in the Philippines included healthy breastfed and/or formula-fed infants (14-21&#x2009;days old) randomized for 8&#x2009;weeks to a control group (CG; n&#x2009;=&#x2009;77), or any of two B. infantis experimental groups (EGs): low (Lo-EG; 1*10[8] CFU/day; n&#x2009;=&#x2009;75) or high dose (Hi-EG; 1.8*10[10] CFU/day; n&#x2009;=&#x2009;76). Primary endpoint was weight gain; secondary endpoints included stooling patterns, gastrointestinal symptoms, adverse events, fecal microbiome, biomarkers, pH, and organic acids.<br><br>RESULTS: Non-inferiority in weight gain was demonstrated for Hi-EG and Lo-EG vs. CG. Overall, probiotic supplementation promoted mushy-soft stools, fewer regurgitation episodes, and increased fecal acetate production, which was more pronounced in the exclusively breastfed infants (EBF) and positively correlated with B. infantis abundance. In EBF, fecal pro-inflammatory cytokines (IL-1 beta, IL-8) were reduced. Strain-level metagenomic analysis allowed attributing the increased abundance of B. infantis in EGs versus CG, to LMG11588 probiotic colonization. Colonization by autochthonous B. infantis strains was similar between groups.<br><br>DISCUSSION: B. infantis LMG11588 supplementation was associated with normal infant growth, was safe and well-tolerated and promoted a Bifidobacterium-rich microbiota driven by B. infantis LMG11588 colonization without disturbing the natural dispersal of autochthonous B. infantis strains. In EBF, supplementation stimulated microbial metabolic activity and beneficially modulated enteric inflammation.},
}
@article {pmid38162026,
year = {2023},
author = {Modolon, F and Schultz, J and Duarte, G and Vilela, CLS and Thomas, T and Peixoto, RS},
title = {In situ devices can culture the microbial dark matter of corals.},
journal = {iScience},
volume = {26},
number = {12},
pages = {108374},
pmid = {38162026},
issn = {2589-0042},
abstract = {Most microorganisms found in environmental samples have never been cultured and can often only be explored through molecular or microscopic approaches. Here, we adapt the use of in situ diffusion-based devices to culture "yet-to-be-cultured" microorganisms associated with coral mucus and compare this with a traditional culturing method. The culturability of microorganisms associated with mucus of the coral Pocillopora damicornis increased by 420% and 570% with diffusion growth chambers and microwell chip devices, respectively, compared with the traditional method tested. The obtained cultures represent up to 64.4% of the total diversity of amplicon sequence variants (ASVs) found in the mucus of the coral P. damicornis. In addition, some previously uncultured microorganisms, such as members of the family Nitrosopumilaceae and halophilic/halotolerant bacteria were cultured. Our results validate alternative microbial culturing strategies to culture coral-associated microorganisms, while significantly increasing the culturability of previous microbial dark matter.},
}
@article {pmid38159169,
year = {2023},
author = {Wang, G and Wang, X and Yang, Z and Wang, S and Li, W and Shang, S and Luo, Y and Wang, L},
title = {Effects of Fusarium solani on the Growth and Development of Anoplophora glabripennis Larvae.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {23},
pmid = {38159169},
issn = {1432-184X},
mesh = {Animals ; Larva/microbiology ; *Coleoptera/microbiology ; *Fusarium ; },
abstract = {Anoplophora glabripennis (Asian longhorned beetle) is a wood-boring pest that can inhabit a wide range of healthy deciduous host trees in native and non-native habitats. Lignocellulose degradation plays a major role in the acquisition of nutrients during the growth and development of A. glabripennis larvae. In this study, the lignocellulose degradation capacity of Fusarium solani, a fungal symbiont of A. glabripennis, was investigated in fermentation culture and in four host tree species. The impact of F. solani on larval growth and survival parameters was assessed. Fermentation culture demonstrated continuous and stable production of lignocellulolytic enzymes over the cultivation period. Furthermore, F. solani was able to degrade host tree lignocellulose, as shown by decreased soluble sugar and cellulose contents and an increase in protein content. No significant differences in larval survival were observed in larvae fed with or without F. solani. However, weight and head capsule width were higher in larvae fed on F. solani, and gut lignocellulose activities were elevated in fed larvae. Our results indicate a role for F. solani in the predigestion of lignocellulose during the colonization and parasitic stages of A. glabripennis larval development, and also the F. solani an important symbiotic partner to A. glabripennis, lowering barriers to colonization and development in a range of habitats.},
}
@article {pmid38159125,
year = {2023},
author = {Hao, Z and Wang, Q and Wang, J and Deng, Y and Yan, Z and Tian, L and Jiang, H},
title = {Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {24},
pmid = {38159125},
issn = {1432-184X},
support = {51839011//National Natural Science Foundation of China/ ; },
mesh = {*Water ; Nitrates ; *Microbiota/genetics ; Metagenome ; Nitrogen/metabolism ; },
abstract = {Drastic changes in hydrological conditions within floodplain ecosystems create distinct microbial habitats. However, there remains a lack of exploration regarding the variations in microbial function potentials across the flooding and drought seasons. In this study, metagenomics and environmental analyses were employed in floodplains that experience hydrological variations across four seasons. Analysis of functional gene composition, encompassing nitrogen, carbon, and sulfur metabolisms, revealed apparent differences between the flooding and drought seasons. The primary environmental drivers identified were water level, overlying water depth, submergence time, and temperature. Specific modules, e.g., the hydrolysis of β-1,4-glucosidic bond, denitrification, and dissimilatory/assimilatory nitrate reduction to ammonium, exhibited higher relative abundance in summer compared to winter. It is suggested that cellulose degradation was potentially coupled with nitrate reduction during the flooding season. Phylogenomic analysis of metagenome-assembled genomes (MAGs) unveiled that the Desulfobacterota lineage possessed abundant nitrogen metabolism genes supported by pathway reconstruction. Variation of relative abundance implied its environmental adaptability to both the wet and dry seasons. Furthermore, a novel order was found within Methylomirabilota, containing nitrogen reduction genes in the MAG. Overall, this study highlights the crucial role of hydrological factors in modulating microbial functional diversity and generating genomes with abundant nitrogen metabolism potentials.},
}
@article {pmid38157893,
year = {2024},
author = {Guarin, TC and Li, L and Haak, L and Teel, L and Pagilla, KR},
title = {Contaminants of emerging concern reduction and microbial community characterization across a three-barrier advanced water treatment system.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {169637},
doi = {10.1016/j.scitotenv.2023.169637},
pmid = {38157893},
issn = {1879-1026},
mesh = {Charcoal/chemistry ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/chemistry ; *Water Purification/methods ; Filtration/methods ; *Ozone/chemistry ; *Drinking Water ; },
abstract = {This research investigated the removal of contaminants of emerging concern (CECs) and characterized the microbial community across an advanced water treatment (AWT) train consisting of Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF), Ozone-Biological Activated Carbon Filtration (O3/BAC), Granular Activated Carbon filtration, Ultraviolet Disinfection, and Cartridge Filtration (GAC/UV/CF). The AWT train successfully met the goals of CECs and bulk organics removal. The microbial community at each treatment step of the AWT train was characterized using 16S rRNA sequencing on the Illumina MiSeq platform generated from DNA extracted from liquid and solid (treatment media) samples taken along the treatment train. Differences in the microbial community structure were observed. The dominant operational taxonomic units (OTU) decreased along the treatment train, but the treatment steps did impact the microbial community composition downstream of each unit process. These results provide insights into microbial ecology in advanced water treatment systems, which are influenced and shaped by each treatment step, the microbial community interactions, and their potential metabolic contribution to CECs degradation.},
}
@article {pmid38157796,
year = {2024},
author = {Wang, L and Nabi, F and Yi, W and Wang, D and Zhu, Y and Jiang, X},
title = {Low-dose thiram exposure elicits dysregulation of the gut microbial ecology in broiler chickens.},
journal = {Ecotoxicology and environmental safety},
volume = {270},
number = {},
pages = {115879},
doi = {10.1016/j.ecoenv.2023.115879},
pmid = {38157796},
issn = {1090-2414},
mesh = {Animals ; Thiram/toxicity ; Chickens/genetics ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Fungicides, Industrial/toxicity ; Bacteria/genetics ; },
abstract = {Thiram, a typical fungicide pesticide, is widely used in agricultural production. The presence of thiram residues is not only due to over-utilization, but is also primarily attributed to long-term accumulation. However, there is a paucity of information regarding the impact of prolonged utilization of thiram at low doses on the gut microbiota, particularly with respect to gut fungi. Our objective is to explore the effect of thiram on broilers from the perspective of gut microbiota, which includes both bacteria and fungi. We developed a long-term low-dose thiram model to simulate thiram residue and employed 16 S rRNA and ITS gene sequencing to investigate the diversity and profile of gut microbiota between group CC (normal diet) and TC (normal diet supplemented with 5 mg/kg thiram). The results revealed that low doses of thiram had a detrimental effect on broiler's growth performance, resulting in an approximate reduction of 669.33 g in their final body weight at day 45. Our findings indicated that low-dose thiram had a negative impact on the gut bacterial composition, leading to a notable reduction in the abundance of Merdibacter, Paenibacillus, Macrococcus, Fournierella, and Anaeroplasma (p < 0.05) compared to the CC group. Conversely, the relative level of Myroides was significantly increased (p < 0.05) in response to thiram exposure. In gut fungi, thiram significantly enhanced the diversity and richness of gut fungal populations (p < 0.05), as evidenced by the notable increase in alpha indices, i.e. ACE (CC: 346.49 ± 117.27 vs TC: 787.27 ± 379.14, p < 0.05), Chao 1 (CC: 317.63 ± 69.13 vs TC: 504.85 ± 104.50, p < 0.05), Shannon (CC: 1.28 ± 1.19 vs TC: 5.39 ± 2.66, p < 0.05), Simpson (CC: 0.21 ± 0.21 vs TC: 0.78 ± 0.34, p < 0.05). Furthermore, the abundance of Ascomycota, Kickxellomycota, and Glomeromycota were significantly increased (p < 0.05) by exposure to thiram, conversely, the level of Basidiomycota was decreased (p < 0.05) in the TC group compared to the CC group. Overall, this study demonstrated that low doses of thiram induced significant changes in the composition and abundance of gut microbiota in broilers, with more pronounced changes observed in the gut fungal community as compared to the gut bacterial community. Importantly, our findings further emphasize the potential risks associated with low dose thiram exposure and have revealed a novel discovery indicating that significant alterations in gut fungi may serve as the crucial factor contributing to the detrimental effects exerted by thiram residues.},
}
@article {pmid38157058,
year = {2023},
author = {Chowaniec, K and Styburski, J and Kozioł, S and Pisańska, Z and Skubała, K},
title = {Dune Blowouts as Microbial Hotspots and the Changes of Overall Microbial Activity and Photosynthetic Biomass Along with Succession of Biological Soil Crusts.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {22},
pmid = {38157058},
issn = {1432-184X},
support = {U1U/W18/NO/28.34//Faculty of Biology, Jagiellonian University/ ; },
mesh = {Biomass ; *Ecosystem ; *Soil ; Soil Microbiology ; Desert Climate ; },
abstract = {Biological soil crust (BSC) constitutes a consortium of cyanobacteria, algae, lichen, mosses, and heterotrophic microorganisms, forming a miniature ecosystem within the uppermost soil layer. The biomass of different organisms forming BSC and their activity changes along with succession. Previous studies focused primarily on BSC in hyper-arid/arid regions, whereas the ecophysiology of BSC in temperate climates is still not well recognized. In order to determine changes in overall microbial activity and photosynthetic biomass in BSC at different stages of the succession of inland sandy grasslands, we analyzed dehydrogenase activity and determined the content of photosynthetic pigments. We also compared these parameters between BSC developed on the dune ridges and aeolian blowouts in the initial stage of succession. Our study revealed a significant increase in both photosynthetic biomass and overall microbial activity in BSC as the succession of inland shifting sands progresses. We found that chl a concentration in BSC could be considered a useful quantitative indicator of both the presence of photoautotrophs and the degree of soil crust development in warm-summer humid continental climates. The photosynthetic biomass was closely related to increased microbial activity in BSC, which suggests that photoautotrophs constitute a major BSC component. Dune blowouts constitute environmental niches facilitating the development of BSC, compared to dune ridges. High biomass of microorganisms in the dune blowouts may be associated with a high amount of organic material and more favorable moisture conditions. We conclude that deflation fields are key places for keeping a mosaic of habitats in the area of shifting sands and can be a reservoir of microorganisms supporting further settlement of dune slopes by BSC.},
}
@article {pmid38156301,
year = {2023},
author = {Wani, AK and Ahmad, S and Américo-Pinheiro, JHP and Tizro, N and Singh, R},
title = {Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study.},
journal = {Iranian journal of microbiology},
volume = {15},
number = {6},
pages = {723-733},
pmid = {38156301},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51'51″N 75°32'07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics.<br><br>MATERIALS AND METHODS: In the present study, physiochemical parameters including temperature (65-75&#xb0;C), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis.<br><br>RESULTS: Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs).<br><br>CONCLUSION: The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries.},
}
@article {pmid38153618,
year = {2023},
author = {Xiong, L and Li, Y and Zeng, K and Wei, Y and Li, H and Ji, X},
title = {Revealing viral diversity in the Napahai plateau wetland based on metagenomics.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {3},
pmid = {38153618},
issn = {1572-9699},
support = {32160294, 42267059//National Natural Science Foundation of China/ ; },
mesh = {*Wetlands ; Ecosystem ; Phylogeny ; China ; *Bacteriophages ; },
abstract = {We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.},
}
@article {pmid38153543,
year = {2023},
author = {Ciric, M and Šaraba, V and Budin, C and de Boer, T and Nikodinovic-Runic, J},
title = {Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {21},
pmid = {38153543},
issn = {1432-184X},
support = {870292//EU Horizon 2020 Research and Innovation Programme - BioICEP/ ; 451-03-47/2023-01/200042//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; },
mesh = {Humans ; Polyurethanes ; *Comamonadaceae ; DNA, Ribosomal ; *Groundwater ; Pseudomonas ; Suppuration ; },
abstract = {Plastic waste is a global environmental burden and long-lasting plastic polymers, including ubiquitous and toxic polyurethanes (PUs), rapidly accumulate in the water environments. In this study, samples were collected from the three alkaline groundwater occurrences in the geotectonic regions of the Pannonian basin of northern Serbia (Torda and Slankamen Banja) and Inner Dinarides of western Serbia (Mokra Gora) with aim to isolate and identify bacteria with plastic- and lignocellulose-degrading potential, that could be applied to reduce the burden of environmental plastic pollution. The investigated occurrences belong to cold, mildly alkaline (pH: 7.6-7.9) brackish and hyperalkaline (pH: 11.5) fresh groundwaters of the SO4 - Na + K, Cl - Na + K and OH, Cl - Ca, Na + K genetic type. Full-length 16S rDNA sequencing, using Oxford Nanopore sequencing device, was performed with DNA extracted from colonies obtained by cultivation of all groundwater samples, as well as with DNA extracted directly from one groundwater sample. The most abundant genera belong to Pseudomonas, Acidovorax, Kocuria and Methylotenera. All screened isolates (100%) had the ability to grow on at least 3 of the tested plastic and lignocellulosic substrates, with 53.9% isolates degrading plastic substrate Impranil® DLN-SD (SD), a model compound for PUs degradation. Isolates degrading SD that were identified by partial 16S rDNA sequencing belong to the Stenotrophomonas, Pseudomonas, Paraburkholderia, Aeromonas, Vibrio and Acidovorax genera. Taking into account that plastics, including commonly produced PUs, are widespread in groundwater, identification of PUs-degrading bacteria may have potential applications in bioremediation of groundwater polluted with this polymer.},
}
@article {pmid38151633,
year = {2024},
author = {Paulino, PG and Abuin-Denis, L and Maitre, A and Piloto-Sardiñas, E and Obregon, D and Santos, HA and Cabezas-Cruz, A},
title = {Dissecting the impact of Anaplasma phagocytophilum infection on functional networks and community stability of the tick microbiome.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {27},
number = {4},
pages = {1205-1218},
pmid = {38151633},
issn = {1618-1905},
support = {E-26/211.312/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 313753/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; SGCE - RAPPORT No 0300//Collectivit&#xe9; de Corse/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; },
mesh = {*Anaplasma phagocytophilum/physiology/genetics ; Animals ; *Ixodes/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; Ehrlichiosis/microbiology ; Nymph/microbiology ; Gastrointestinal Microbiome/physiology ; },
abstract = {CONTEXT: Pathogens can manipulate microbial interactions to ensure survival, potentially altering the functional patterns and microbiome assembly. The present study investigates how Anaplasma phagocytophilum infection affects the functional diversity, composition, and assembly of the Ixodes scapularis microbiome, with a focus on high central pathways-those characterized by elevated values in centrality metrics such as eigenvector, betweenness, and degree measures, in the microbial community.<br><br>METHODS: Using previously published data from nymphs' gut V4 region's amplicons of bacterial 16S rRNA, we predicted the functional diversity and composition in control and A. phagocytophilum-infected ticks and inferred co-occurrence networks of taxa and ubiquitous pathways in each condition to associate the high central pathways to the microbial community assembly.<br><br>RESULTS: Although no differences were observed concerning pathways richness and diversity, there was a significant impact on taxa and functional assembly when ubiquitous pathways in each condition were filtered. Moreover, a notable shift was observed in the microbiome's high central functions. Specifically, pathways related to the degradation of nucleosides and nucleotides emerged as the most central functions in response to A. phagocytophilum infection. This finding suggests a reconfiguration of functional relationships within the microbial community, potentially influenced by the pathogen's limited metabolic capacity. This limitation implies that the tick microbiome may provide additional metabolic resources to support the pathogen's functional needs.<br><br>CONCLUSIONS: Understanding the metabolic interactions within the tick microbiome can enhance our knowledge of pathogen colonization mechanisms and uncover new disease control and prevention strategies. For example, certain pathways that were more abundant or highly central during infection may represent potential targets for microbiota-based vaccines.},
}
@article {pmid38148858,
year = {2023},
author = {Khan, A and Singh, AV and Gautam, SS and Agarwal, A and Punetha, A and Upadhayay, VK and Kukreti, B and Bundela, V and Jugran, AK and Goel, R},
title = {Microbial bioformulation: a microbial assisted biostimulating fertilization technique for sustainable agriculture.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1270039},
pmid = {38148858},
issn = {1664-462X},
abstract = {Addressing the pressing issues of increased food demand, declining crop productivity under varying agroclimatic conditions, and the deteriorating soil health resulting from the overuse of agricultural chemicals, requires innovative and effective strategies for the present era. Microbial bioformulation technology is a revolutionary, and eco-friendly alternative to agrochemicals that paves the way for sustainable agriculture. This technology harnesses the power of potential microbial strains and their cell-free filtrate possessing specific properties, such as phosphorus, potassium, and zinc solubilization, nitrogen fixation, siderophore production, and pathogen protection. The application of microbial bioformulations offers several remarkable advantages, including its sustainable nature, plant probiotic properties, and long-term viability, positioning it as a promising technology for the future of agriculture. To maintain the survival and viability of microbial strains, diverse carrier materials are employed to provide essential nourishment and support. Various carrier materials with their unique pros and cons are available, and choosing the most appropriate one is a key consideration, as it substantially extends the shelf life of microbial cells and maintains the overall quality of the bioinoculants. An exemplary modern bioformulation technology involves immobilizing microbial cells and utilizing cell-free filters to preserve the efficacy of bioinoculants, showcasing cutting-edge progress in this field. Moreover, the effective delivery of bioformulations in agricultural fields is another critical aspect to improve their overall efficiency. Proper and suitable application of microbial formulations is essential to boost soil fertility, preserve the soil's microbial ecology, enhance soil nutrition, and support crop physiological and biochemical processes, leading to increased yields in a sustainable manner while reducing reliance on expensive and toxic agrochemicals. This manuscript centers on exploring microbial bioformulations and their carrier materials, providing insights into the selection criteria, the development process of bioformulations, precautions, and best practices for various agricultural lands. The potential of bioformulations in promoting plant growth and defense against pathogens and diseases, while addressing biosafety concerns, is also a focal point of this study.},
}
@article {pmid38148389,
year = {2023},
author = {Petrović, M and Janakiev, T and Grbić, ML and Unković, N and Stević, T and Vukićević, S and Dimkić, I},
title = {Insights into Endophytic and Rhizospheric Bacteria of Five Sugar Beet Hybrids in Terms of Their Diversity, Plant-Growth Promoting, and Biocontrol Properties.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {19},
pmid = {38148389},
issn = {1432-184X},
mesh = {*Beta vulgaris ; Plant Development ; Bacillus subtilis ; Endophytes ; Plant Roots/microbiology ; Phosphates ; },
abstract = {Sugar beet is the most important crop for sugar production in temperate zones. The plant microbiome is considered an important factor in crop productivity and health. Here, we investigated the bacterial diversity of seeds, roots, and rhizosphere of five sugar beet hybrids named Eduarda (ED), Koala (KO), Tibor (T), Tajfun (TF), and Cercospora-resistant (C). A culture-independent next-generation sequencing approach was used for the further investigation of seed-borne endophytes. Hybrid-associated bacteria were evaluated for their plant growth-promoting (PGP) characteristics, antagonistic activity towards Cercospora beticola and several Fusarium strains in dual culture assays, and drought and salinity tolerance. High-throughput sequencing revealed that the Proteobacteria phylum was most dominant in the seeds of all hybrids, followed by Cyanobacteria and Actinobacteriota. The predominant genus in all hybrids was Pantoea, followed by Pseudomonas, Acinetobacter, Chalicogloea, Corynebacterium, Enterobacter, Enterococcus, Glutamicibacter, Kosakonia, and Marinilactibacillus. Unique genera in the hybrids were Pleurocapsa and Arthrobacter (T), Klebsiella (TF), Apibacter (ED), and Alloscardovia (KO). The genera that were most represented in one hybrid were Weissella and Staphylococcus (TF); Streptococcus (T); Gardnerella, Prevotella, and Rothia (KO); and Gilliamella, Lactobacillus, and Snodgrassella (ED). Thirty-two bacteria out of 156 isolates from the rhizosphere, roots, and seeds were selected with respect to various plant growth-promoting activities in vitro, i.e., nitrogen fixation, phosphate solubilization, siderophore production, indole-3-acetic acid production, 1-aminocyclopropane-1-carboxylic acid deaminase activity, hydrogen cyanide production, exoenzymatic activity (amylase, protease, lipase, cellulase, xylanase, mannanases, gelatinase, and pectinase), mitigation of environmental stresses, and antifungal activity. Mixta theicola KO3-44, Providencia vermicola ED3-10, Curtobacterium pusillum ED2-6, and Bacillus subtilis KO3-18 had the highest potential to promote plant growth due to their multiple abilities (nitrogen fixation, phosphate solubilization, production of siderophores, and IAA). The best antagonistic activity towards phytopathogenic fungi was found for Bacillus velezensis C3-19, Paenibacillus polymyxa C3-36 and Bacillus halotolerans C3-16/2.1. Only four isolates B. velezensis T2-23, B. subtilis T3-4, B. velezensis ED2-2, and Bacillus halotolerans C3-16/2.1 all showed enzymatic activity, with the exception of xylanase production. B. halotolerans C3-16/2.1 exhibited the greatest tolerance to salinity, while two B. subtilis strains (C3-62 and TF2-1) grew successfully at the maximum concentration of PEG. The current study demonstrates that sugar beet-associated bacteria have a wide range of beneficial traits and are therefore highly promising for the formulation of biological control and PGP agents.},
}
@article {pmid38148362,
year = {2023},
author = {Ofek, T and Trabelcy, B and Izhaki, I and Halpern, M},
title = {Vibrio cholerae O1 Inhabit Intestines and Spleens of Fish in Aquaculture Ponds.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {20},
pmid = {38148362},
issn = {1432-184X},
support = {2728/17//the India-Israel Joint UGC-ISF/ ; 2015103//the United States-Israel Binational Science Foundation, BSF/ ; },
mesh = {Animals ; *Vibrio cholerae O1 ; Cholera Toxin ; Ponds ; Spleen ; *Cholera/epidemiology ; Intestines ; Fishes ; },
abstract = {Vibrio cholerae is the causative agent of cholera, an acute diarrheal disease that spreads locally and globally in epidemics and pandemics. Although it was discovered that fish harbor V. cholerae strains in their intestines, most investigations revealed non-toxic V. cholerae serogroups in fish. Due to the rarity of toxigenic V. cholerae serogroups, it is difficult to cultivate these strains from environmental samples. Hence, here we aimed to uncover evidence of the occurrence of toxigenic V. cholerae in the intestines and spleens of various fish species. By using molecular detection tools, we show that V. cholerae O1 and strains positive for the cholera toxin inhabit both healthy and diseased fish intestines and spleens, suggesting that fish may serve as intermediate vectors of toxigenic V. cholerae. No significant differences were found between the abundance of toxigenic V. cholerae (either O1 or cholera toxin positive strains) in the healthy and the diseased fish intestines or spleens. In conclusion, a variety of fish species may serve as potential vectors and reservoirs of toxigenic V. cholerae as they form a link between the other reservoirs of V. cholerae (chironomids, copepods, and waterbirds). Similarly, they may aid in the spread of this bacterium between water bodies.},
}
@article {pmid38147140,
year = {2023},
author = {Lee, H and Chaudhary, DK and Lim, OB and Kim, DU},
title = {Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov., isolated from forest soil.},
journal = {Archives of microbiology},
volume = {206},
number = {1},
pages = {42},
pmid = {38147140},
issn = {1432-072X},
support = {NIBR202203112//National Institute of Biological Resources/ ; },
mesh = {Phylogeny ; *Cardiolipins ; Forests ; *Paenibacillus/genetics ; DNA ; },
abstract = {During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38[T] and TW40[T]. Both strains were catalase positive and oxidase negative. Strains TW38[T] and TW40[T] demonstrated growth within a temperature range of 10-37 °C and 18-37 °C, respectively, and thrived within a pH range of 5.5-9.0 and 6.0-8.0, respectively. Both strains grew at 0-2.0% (w/v) NaCl concentrations. The phylogenetic analysis indicated that strains TW38[T] and TW40[T] affiliated to the genus Paenibacillus, with the closest neighbors being Paenibacillus montanisoli RA17[T] (98.6%) and Paenibacillus arachidis E3[T] (95.4%), respectively. In both strains, the sole respiratory quinone was MK-7, the signature fatty acid was antiso-C15:0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The digital DNA-DNA hybridization and the average nucleotide identity values between TW38[T], TW40[T], and closest reference strains were < 29.0% and < 85.0%, respectively. The DNA G+C content of TW38[T] and TW40[T] was 54.5% and 57.1%, respectively. In general, the phylogenetic, genomics, chemotaxonomic, and phenotypic data support the differentiation of TW38[T] and TW40[T] from other closest members of the genus Paenibacillus. Thus, we conclude both strains TW38[T] and TW40[T] represent novel species of the genus Paenibacillus, for which the name Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov. are proposed, respectively. The type strain of Paenibacillus silvisoli is TW38[T] (= KCTC 43468[T] = NBRC 116015[T]) and type strain of Paenibacillus humicola is TW40[T] (= KCTC 43469[T] = NBRC 116016[T]).},
}
@article {pmid38146666,
year = {2024},
author = {Sveen, TR and Viketoft, M and Bengtsson, J and Bahram, M},
title = {Core taxa underpin soil microbial community turnover during secondary succession.},
journal = {Environmental microbiology},
volume = {26},
number = {1},
pages = {e16561},
doi = {10.1111/1462-2920.16561},
pmid = {38146666},
issn = {1462-2920},
support = {2021-03724//The Swedish Research Council/ ; //The Swedish University of Agricultural Sciences (early career grant)/ ; 2020-00807//The Swedish Research Council Formas/ ; },
mesh = {*Soil ; Phylogeny ; Soil Microbiology ; Forests ; *Microbiota/genetics ; Bacteria/genetics ; Grassland ; },
abstract = {Understanding the processes that underpin the community assembly of bacteria is a key challenge in microbial ecology. We studied soil bacterial communities across a large-scale successional gradient of managed and abandoned grasslands paired with mature forest sites to disentangle drivers of community turnover and assembly. Diversity partitioning and phylogenetic null-modelling showed that bacterial communities in grasslands remain compositionally stable following abandonment and secondary succession but they differ markedly from fully afforested sites. Zeta diversity analyses revealed the persistence of core microbial taxa that both reflected and differed from whole-scale community turnover patterns. Differences in soil pH and C:N were the main drivers of community turnover between paired grassland and forest sites and the variability of pH within successional stages was a key factor related to the relative dominance of deterministic assembly processes. Our results indicate that grassland microbiomes could be compositionally resilient to abandonment and secondary succession and that the major changes in microbial communities between grasslands and forests occur fairly late in the succession when trees have established as the dominant vegetation. We also show that core taxa may show contrasting responses to management and abandonment in grasslands.},
}
@article {pmid38146049,
year = {2024},
author = {Santos, LRC and Barros, PSDR and Monteiro, DA and Tabosa, JN and de Melo, AF and de Lyra, MDCCP and Oliveira, JRS and Fernandes Júnior, PI and de Freitas, ADS and Rachid, CTCDC},
title = {Influences of plant organ, genotype, and cultivation site on the endophytic bacteriome of maize (Zea mays L.) in the semi-arid region of Pernambuco, Brazil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {55},
number = {1},
pages = {789-797},
pmid = {38146049},
issn = {1678-4405},
mesh = {*Zea mays/microbiology ; Brazil ; Endophytes/genetics ; Bacteria/genetics ; *Actinomycetales ; Genotype ; Plant Roots/microbiology ; },
abstract = {Endophytic bacteria play a crucial role in plant development and adaptation, and the knowledge of how endophytic bacteria assemblage is influenced by cultivation site and plant genotype is an important step to achieve microbiome manipulation. This work aimed to study the roots and stems of endophytic bacteriome of four maize genotypes cultivated in two regions of the semi-arid region of Pernambuco - Brazil. Our hypothesis is that the endophytic community assemblage will be influenced by plant genotypes and cultivation region. Metabarcoding sequencing data revealed significant differences in alfa diversity in function of both factors, genotypes, and maize organs. Beta diversity analysis showed that the bacterial communities differ mainly in function of the plant organ. The most abundant genera found in the samples were Leifsonia, Bacillus, Klebsiella, Streptomyces, and Bradyrhizobium. To understand ecological interactions within each compartment, we constructed co-occurrence network for each organ. This analysis revealed important differences in network structure and complexity and suggested that Leifsonia (the main genera found) had distinct ecological roles depending on the plant organ. Our data showed that root endophytic maize bacteria would be influenced by cultivation site, but not by genotype. We believe that, collectively, our data not only characterize the bacteriome associated with this plant and how different factors shape it, but also increase the knowledge to select potential bacteria for bioinoculant production.},
}
@article {pmid38143001,
year = {2024},
author = {Shi, B and Cheng, X and Jiang, S and Pan, J and Zhu, D and Lu, Z and Jiang, Y and Liu, C and Guo, H and Xie, J},
title = {Unveiling the power of COD/N on constructed wetlands in a short-term experiment: Exploring microbiota co-occurrence patterns and assembly dynamics.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {169568},
doi = {10.1016/j.scitotenv.2023.169568},
pmid = {38143001},
issn = {1879-1026},
mesh = {*Denitrification ; Wetlands ; Biological Oxygen Demand Analysis ; Nitrification ; *Microbiota ; Nitrogen/chemistry ; Water ; Waste Disposal, Fluid/methods ; },
abstract = {Constructed wetlands (CWs) are a cost-effective and environmentally friendly wastewater treatment technology. The influent chemical oxygen demand (COD)/nitrogen (N) ratio (CNR) plays a crucial role in microbial activity and purification performance. However, the effects of CNR changes on microbial diversity, interactions, and assembly processes in CWs are not well understood. In this study, we conducted comprehensive mechanistic experiments to investigate the response of CWs to changes in influent CNR, focusing on the effluent, rhizosphere, and substrate microbiota. Our goal is to provide new insights into CW management by integrating microbial ecology and environmental engineering perspectives. We constructed two groups of horizontal subsurface flow constructed wetlands (HFCWs) and set up three influent CNRs to analyse the microbial responses and nutrient removal. The results indicated that increasing influent CNR led to a decrease in microbial α-diversity and niche width. Genera involved in nitrogen removal and denitrification, such as Rhodobacter, Desulfovibrio, and Zoogloea, were enriched under medium/high CNR conditions, resulting in higher nitrate (NO3[-]-N) removal (up to 99 %) than that under lower CNR conditions (<60 %). Environmental factors, including water temperature (WT), pH, and phosphorus (P), along with CNR-induced COD and NO3[-]-N play important roles in microbial succession in HFCWs. The genus Nitrospira, which is involved in nitrification, exhibited a significant negative correlation (p < 0.05) with WT, COD, and P. Co-occurrence network analysis revealed that increasing influent CNR reduced the complexity of the network structure and increased microbial competition. Analysis using null models demonstrated that the microbial community assembly in HFCWs was primarily driven by stochastic processes under increasing influent CNR conditions. Furthermore, HFCWs with more stochastic microbial communities exhibited better denitrification performance (NO3[-]-N removal). Overall, this study enhances our understanding of nutrient removal, microbial co-occurrence, and assembly mechanisms in CWs under varying influent CNRs.},
}
@article {pmid38140550,
year = {2023},
author = {Vickos, U and Camasta, M and Grandi, N and Scognamiglio, S and Schindler, T and Belizaire, MRD and Lango-Yaya, E and Koyaweda, GW and Senzongo, O and Pounguinza, S and Estimé, KKJF and N'yetobouko, S and Gadia, CLB and Feiganazoui, DA and Le Faou, A and Orsini, M and Perno, CF and Zinzula, L and Rafaï, CD},
title = {COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome.},
journal = {Viruses},
volume = {15},
number = {12},
pages = {},
pmid = {38140550},
issn = {1999-4915},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Humans ; *SARS-CoV-2/genetics ; Proteome ; *COVID-19/epidemiology ; Central African Republic/epidemiology ; Phylogeny ; Genomics ; Antiviral Agents ; },
abstract = {Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African countries. Information about COVID-19 in Africa has been limited and contradictory, and thus regional studies are important. On this premise, we conducted a genomic surveillance study about COVID-19 lineages circulating in Bangui, Central African Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints in Bangui from 2 to 22 July 2021. Fifty-three samples tested positive for SARS-CoV-2, and viral genomes were sequenced to look for the presence of different viral strains. We performed phylogenetic analysis and described the lineage landscape of SARS-CoV-2 circulating in the CAR along 15 months of pandemics and in Africa during the study period, finding the Delta variant as the predominant Variant of Concern (VoC). The deduced aminoacidic sequences of structural and non-structural genes were determined and compared to reference and reported isolates from Africa. Despite the limited number of positive samples obtained, this study provides valuable information about COVID-19 evolution at the regional level and allows for a better understanding of SARS-CoV-2 circulation in the CAR.},
}
@article {pmid38139130,
year = {2023},
author = {Popov, IV and Popov, IV and Krikunova, AA and Lipilkina, TA and Derezina, TN and Chikindas, ML and Venema, K and Ermakov, AM},
title = {Gut Microbiota Composition of Insectivorous Synanthropic and Fructivorous Zoo Bats: A Direct Metagenomic Comparison.},
journal = {International journal of molecular sciences},
volume = {24},
number = {24},
pages = {},
pmid = {38139130},
issn = {1422-0067},
support = {23-14-00316//Russian Science Foundation/ ; Agreement 075-10-2021-093, Project [IMB-2102]//Ministry of Science and Higher Education of the Russian Federation/ ; //K.V. was supported by the Dutch Province of Limburg with a grant to the Centre for Healthy Eating &amp; Food Innovation (HEFI) of Maastricht University-campus Venlo/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Chiroptera ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Bacteria/genetics ; },
abstract = {Bats are natural reservoirs for many emerging viral diseases. That is why their virome is widely studied. But at the same time, studies of their bacterial gut microbiota are limited, creating a degree of uncertainty about the role of bats in global microbial ecology. In this study, we analyzed gut microbiota of insectivorous Nyctalus noctula and Vespertilio murinus from rehabilitation centers from Rostov-on-Don and Moscow, respectively, and fructivorous Carollia perspicillata from the Moscow Zoo based on V3-V4 16S rRNA metagenomic sequencing. We revealed that microbial diversity significantly differs between the insectivorous and fructivorous species studied, while the differences between N. noctula and V. murinus are less pronounced, which shows that bats' gut microbiota is not strictly species-specific and depends more on diet type. In the gut microbiota of synanthropic bats, we observed bacteria that are important for public health and animal welfare such as Bacteroides, Enterobacter, Clostridiaceae, Enterococcus, Ureaplasma, Faecalibacterium, and Helicobacter, as well as some lactic acid bacteria such as Pediococcus, Lactobacillus, Lactococcus, and Weisella. All these bacteria, except for Bacteroides and Weisella, were significantly less abundant in C. perspicillata. This study provides a direct metagenomic comparison of synanthropic insectivorous and zoo fructivorous bats, suggesting future directions for studying these animals' role in microbial ecology.},
}
@article {pmid38138049,
year = {2023},
author = {Lourenço, KS and Cantarella, H and Kuramae, EE},
title = {Carbon and Nutrients from Organic Residues Modulate the Dynamics of Prokaryotic and Fungal Communities.},
journal = {Microorganisms},
volume = {11},
number = {12},
pages = {},
pmid = {38138049},
issn = {2076-2607},
abstract = {Inputs of carbon (C) and nutrients from organic residues may select specific microbes and shape the soil microbial community. However, little is known about the abiotic filtering of the same residues with different nutrient concentrations applied to the soil. In our study, we explored how applying organic residue, vinasse, as fertilizer in its natural state (V) versus its concentrated form (CV) impacts soil microbiota. We conducted two field experiments, evaluating soil prokaryotic and fungal communities over 24 and 45 days with vinasse (V or CV) plus N fertilizer. We used 16S rRNA gene and ITS amplicon sequencing. Inorganic N had no significant impact on bacterial and fungal diversity compared to the control. However, the varying concentrations of organic C and nutrients in vinasse significantly influenced the soil microbiome structure, with smaller effects observed for V compared to CV. Prokaryotic and fungal communities were not correlated (co-inertia: RV coefficient = 0.1517, p = 0.9708). Vinasse did not change the total bacterial but increased the total fungal abundance. A higher C input enhanced the prokaryotic but reduced the fungal diversity. Our findings highlight vinasse's role as an abiotic filter shaping soil microbial communities, with distinct effects on prokaryotic and fungal communities. Vinasse primarily selects fast-growing microorganisms, shedding light on the intricate dynamics between organic residues, nutrient concentrations, and soil microbes.},
}
@article {pmid38137974,
year = {2023},
author = {Pérez, G and Krause, SMB and Bodelier, PLE and Meima-Franke, M and Pitombo, L and Irisarri, P},
title = {Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils.},
journal = {Microorganisms},
volume = {11},
number = {12},
pages = {},
pmid = {38137974},
issn = {2076-2607},
support = {CSIC-4562//Comisi&#xf3;n Sectorial de Investigaci&#xf3;n Cient&#xed;fica/ ; POS_EXT_2016_1_133774//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; 32050410288//National Science Foundation of China 568 (NSFC), International (Regional) Cooperation and Exchange Program/ ; },
abstract = {Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria-methanotrophs and their respective traits.},
}
@article {pmid38136731,
year = {2023},
author = {Balcha, ES and Gómez, F and Gemeda, MT and Bekele, FB and Abera, S and Cavalazzi, B and Woldesemayat, AA},
title = {Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {12},
pages = {},
pmid = {38136731},
issn = {2079-6382},
abstract = {The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the β-lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with β-lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance.},
}
@article {pmid38133854,
year = {2024},
author = {Chatterjee, S and Paul, P and Chakraborty, P and Das, S and Das Gupta, A and Roy, R and Malik, M and Sarkar, S and Sarker, RK and Tribedi, P},
title = {Combinatorial application of cuminaldehyde and gentamicin shows enhanced antimicrobial and antibiofilm action on Pseudomonas aeruginosa.},
journal = {Folia microbiologica},
volume = {69},
number = {4},
pages = {823-834},
pmid = {38133854},
issn = {1874-9356},
mesh = {*Biofilms/drug effects ; *Pseudomonas aeruginosa/drug effects/physiology ; *Gentamicins/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Benzaldehydes/pharmacology ; Cymenes/pharmacology ; Virulence Factors ; Drug Synergism ; Humans ; },
abstract = {The emergence of biofilm-induced drug tolerance poses a critical challenge to public healthcare management. Pseudomonas aeruginosa, a gram-negative opportunistic bacterium, is involved in various biofilm-associated infections in human hosts. Towards this direction, in the present study, a combinatorial approach has been explored as it is a demonstrably effective strategy for managing microbial infections. Thus, P. aeruginosa has been treated with cuminaldehyde (a naturally occurring phytochemical) and gentamicin (an aminoglycoside antibiotic) in connection to the effective management of the biofilm challenges. It was also observed that the test molecules could show increased antimicrobial activity against P. aeruginosa. A fractional inhibitory concentration index (FICI) of 0.65 suggested an additive interaction between cuminaldehyde and gentamicin. Besides, a series of experiments such as crystal violet assay, estimation of extracellular polymeric substance (EPS), and microscopic images indicated that an enhanced antibiofilm activity was obtained when the selected compounds were applied together on P. aeruginosa. Furthermore, the combination of the selected compounds was found to reduce the secretion of virulence factors from P. aeruginosa. Taken together, this study suggested that the combinatorial application of cuminaldehyde and gentamicin could be considered an effective approach towards the control of biofilm-linked infections caused by P. aeruginosa.},
}
@article {pmid38133759,
year = {2024},
author = {Hidalgo, J and Artetxe, U and Becerril, JM and Gómez-Sagasti, MT and Epelde, L and Vilela, J and Garbisu, C},
title = {Biological remediation treatments improve the health of a mixed contaminated soil before significantly reducing contaminant levels.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {4},
pages = {6010-6024},
pmid = {38133759},
issn = {1614-7499},
support = {Project Phy2SUDOE - SOE4/P5/E1021//Interreg/ ; AGL 2015-64481-C2-1-R//Ministerio de Econom&#xed;a y Competitividad/ ; AGL2016-76592-R//Ministerio de Econom&#xed;a y Competitividad/ ; UPV/EHU-GV IT-1648-22//Eusko Jaurlaritza/ ; },
mesh = {Sewage ; *Soil Pollutants/analysis ; Biodegradation, Environmental ; Soil ; *Polychlorinated Biphenyls ; Soil Microbiology ; },
abstract = {The remediation of mixed contaminated soil is challenging as it often requires actions to minimize metal-induced risks while degrading organic contaminants. Here, the effectiveness of different bioremediation strategies, namely, rhizoremediation with native plant species, mycoremediation with Pleurotus ostreatus spent mushroom substrate, and biostimulation with organic by-products (i.e., composted sewage sludge and spent mushroom substrate), for the recovery of a mixed contaminated soil from an abandoned gravel pit was studied. The combination of biostimulation and rhizoremediation led to the most significant increase in soil health, according to microbial indicator values. The application of composted sewage sludge led to the highest reduction in anthracene and polychlorinated biphenyls concentrations. None of the strategies managed to decrease contamination levels below regulatory limits, but they did enhance soil health. It was concluded that the biological remediation treatments improved soil functioning in a short time, before the concentration of soil contaminants was significantly reduced.},
}
@article {pmid38127978,
year = {2023},
author = {Liuu, S and Nepelska, M and Pfister, H and Gamelas Magalhaes, J and Chevalier, G and Strozzi, F and Billerey, C and Maresca, M and Nicoletti, C and Di Pasquale, E and Pechard, C and Bardouillet, L and Girardin, SE and Boneca, IG and Doré, J and Blottière, HM and Bonny, C and Chene, L and Cultrone, A},
title = {Identification of a muropeptide precursor transporter from gut microbiota and its role in preventing intestinal inflammation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {52},
pages = {e2306863120},
pmid = {38127978},
issn = {1091-6490},
support = {FP7/2007-2013//European community's Seventh Framework Programme/ ; FP7/2007-2013//European community's Seventh framework Programme/ ; },
mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; Peptidoglycan/metabolism ; Intestines/pathology ; Inflammation/metabolism ; Membrane Transport Proteins/metabolism ; Anti-Inflammatory Agents/metabolism ; Dextran Sulfate ; *Colitis/metabolism ; Disease Models, Animal ; Colon/metabolism ; Mice, Inbred C57BL ; },
abstract = {The gut microbiota is a considerable source of biologically active compounds that can promote intestinal homeostasis and improve immune responses. Here, we used large expression libraries of cloned metagenomic DNA to identify compounds able to sustain an anti-inflammatory reaction on host cells. Starting with a screen for NF-κB activation, we have identified overlapping clones harbouring a heterodimeric ATP-binding cassette (ABC)-transporter from a Firmicutes. Extensive purification of the clone's supernatant demonstrates that the ABC-transporter allows for the efficient extracellular accumulation of three muropeptide precursor, with anti-inflammatory properties. They induce IL-10 secretion from human monocyte-derived dendritic cells and proved effective in reducing AIEC LF82 epithelial damage and IL-8 secretion in human intestinal resections. In addition, treatment with supernatants containing the muropeptide precursor reduces body weight loss and improves histological parameters in Dextran Sulfate Sodium (DSS)-treated mice. Until now, the source of peptidoglycan fragments was shown to come from the natural turnover of the peptidoglycan layer by endogenous peptidoglycan hydrolases. This is a report showing an ABC-transporter as a natural source of secreted muropeptide precursor and as an indirect player in epithelial barrier strengthening. The mechanism described here might represent an important component of the host immune homeostasis.},
}
@article {pmid38126787,
year = {2024},
author = {Walsh, C and Stallard-Olivera, E and Fierer, N},
title = {Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology.},
journal = {mBio},
volume = {15},
number = {2},
pages = {e0205023},
pmid = {38126787},
issn = {2150-7511},
support = {Graduate Research Assistantship//Cooperative Institute for Research in Environmental Sciences (CIRES)/ ; },
mesh = {*Machine Learning ; Algorithms ; *Microbiota ; },
abstract = {Due to the complex nature of microbiome data, the field of microbial ecology has many current and potential uses for machine learning (ML) modeling. With the increased use of predictive ML models across many disciplines, including microbial ecology, there is extensive published information on the specific ML algorithms available and how those algorithms have been applied. Thus, our goal is not to summarize the breadth of ML models available or compare their performances. Rather, our goal is to provide more concrete and actionable information to guide microbial ecologists in how to select, run, and interpret ML algorithms to predict the taxa or genes associated with particular sample categories or environmental gradients of interest. Such microbial data often have unique characteristics that require careful consideration of how to apply ML models and how to interpret the associated results. This review is intended for practicing microbial ecologists who may be unfamiliar with some of the intricacies of ML models. We provide examples and discuss common opportunities and pitfalls specific to applying ML models to the types of data sets most frequently collected by microbial ecologists.},
}
@article {pmid38125540,
year = {2023},
author = {Dhivahar, J and Parthasarathy, A and Krishnan, K and Kovi, BS and Pandian, GN},
title = {Bat-associated microbes: Opportunities and perils, an overview.},
journal = {Heliyon},
volume = {9},
number = {12},
pages = {e22351},
pmid = {38125540},
issn = {2405-8440},
abstract = {The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.},
}
@article {pmid38115223,
year = {2024},
author = {Euler, S and Jeffrey, LC and Maher, DT and Johnston, SG and Sugimoto, R and Tait, DR},
title = {Microbiome mediating methane and nitrogen transformations in a subterranean estuary.},
journal = {Environmental microbiology},
volume = {26},
number = {1},
pages = {e16558},
doi = {10.1111/1462-2920.16558},
pmid = {38115223},
issn = {1462-2920},
support = {DE180100535//Australian Research Council/ ; },
mesh = {*Greenhouse Gases ; Estuaries ; Methane ; Dissolved Organic Matter ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Ammonium Compounds ; },
abstract = {Subterranean estuaries (STEs) are important coastal biogeochemical reactors facilitating unique niches for microbial communities. A common approach in determining STE greenhouse gas and nutrient fluxes is to use terrestrial endmembers, not accounting for microbially mediated transformations throughout the STE. As such, the microbial ecology and spatial distribution of specialists that cycle compounds in STEs remain largely underexplored. In this study, we applied 16S rRNA amplicon sequencing with paired biogeochemical characterisations to spatially evaluate microbial communities transforming greenhouse gases and nutrients in an STE. We show that methanogens are most prevalent at the terrestrial end (up to 2.81% relative abundance) concomitant to the highest porewater methane, carbon dioxide and dissolved organic carbon concentrations (0.41 ± 0.02 μM, 273.31 ± 6.05 μM and 0.51 ± 0.02 mM, respectively). Lower ammonium concentrations corresponded with abundant nitrifying and ammonia-oxidising prokaryotes in the mixing zone (up to 11.65% relative abundance). Methane, ammonium and dissolved organic carbon concentrations all decreased by >50% from the terrestrial to the oceanic end of the 15 m transect. This study highlights the STE's hidden microbiome zonation, as well as the importance of accounting for microbial transformations mitigating nutrient and greenhouse gas fluxes to the coastal ecosystems.},
}
@article {pmid38114339,
year = {2024},
author = {Sutherland, WJ and Bennett, C and Brotherton, PNM and Butchart, SHM and Butterworth, HM and Clarke, SJ and Esmail, N and Fleishman, E and Gaston, KJ and Herbert-Read, JE and Hughes, AC and James, J and Kaartokallio, H and Le Roux, X and Lickorish, FA and Newport, S and Palardy, JE and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Primack, RB and Primack, WE and Schloss, IR and Spalding, MD and Ten Brink, D and Tew, E and Timoshyna, A and Tubbs, N and Watson, JEM and Wentworth, J and Wilson, JD and Thornton, A},
title = {A horizon scan of global biological conservation issues for 2024.},
journal = {Trends in ecology &amp; evolution},
volume = {39},
number = {1},
pages = {89-100},
doi = {10.1016/j.tree.2023.11.001},
pmid = {38114339},
issn = {1872-8383},
mesh = {*Ecosystem ; *Biodiversity ; Conservation of Natural Resources ; Forecasting ; Food ; },
abstract = {We present the results of our 15th horizon scan of novel issues that could influence biological conservation in the future. From an initial list of 96 issues, our international panel of scientists and practitioners identified 15 that we consider important for societies worldwide to track and potentially respond to. Issues are novel within conservation or represent a substantial positive or negative step-change with global or regional extents. For example, new sources of hydrogen fuel and changes in deep-sea currents may have profound impacts on marine and terrestrial ecosystems. Technological advances that may be positive include benchtop DNA printers and the industrialisation of approaches that can create high-protein food from air, potentially reducing the pressure on land for food production.},
}
@article {pmid38112791,
year = {2023},
author = {Yue, Y and Yang, Z and Wang, F and Chen, X and Huang, Y and Ma, J and Cai, L and Yang, M},
title = {Effects of Cascade Reservoirs on Spatiotemporal Dynamics of the Sedimentary Bacterial Community: Co-occurrence Patterns, Assembly Mechanisms, and Potential Functions.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {18},
pmid = {38112791},
issn = {1432-184X},
mesh = {*Ecosystem ; Biodiversity ; Fresh Water ; Rivers/microbiology ; *Microbiota ; Bacteria/genetics ; China ; Nitrogen ; },
abstract = {Dam construction as an important anthropogenic activity significantly influences ecological processes in altered freshwater bodies. However, the effects of multiple cascade dams on microbial communities have been largely overlooked. In this study, the spatiotemporal distribution, co-occurrence relationships, assembly mechanisms, and functional profiles of sedimentary bacterial communities were systematically investigated in 12 cascade reservoirs across two typical karst basins in southwest China over four seasons. A significant spatiotemporal heterogeneity was observed in bacterial abundance and diversity. Co-occurrence patterns in the Wujiang Basin exhibited greater edge counts, graph density, average degree, robustness, and reduced modularity, suggesting more intimate and stronger ecological interactions among species than in the Pearl River Basin. Furthermore, Armatimonadota and Desulfobacterota, identified as keystone species, occupied a more prominent niche than the dominant species. A notable distance-decay relationship between geographical distance and community dissimilarities was identified in the Pearl River Basin. Importantly, in the Wujiang Basin, water temperature emerged as the primary seasonal variable steering the deterministic process of bacterial communities, whereas 58.5% of the explained community variance in the neutral community model (NCM) indicated that stochastic processes governed community assembly in the Pearl River Basin. Additionally, principal component analysis (PCA) revealed more pronounced seasonal dynamics in nitrogen functional compositions than spatial variation in the Wujiang Basin. Redundancy analysis (RDA) results indicated that in the Wujiang Basin, environmental factors and in Pearl River Basin, geographical distance, reservoir age, and hydraulic retention time (HRT), respectively, influenced the abundance of nitrogen-related genes. Notably, these findings offer novel insights: building multiple cascade reservoirs could lead to a cascading decrease in biodiversity and resilience in the river-reservoir ecosystem.},
}
@article {pmid38112441,
year = {2024},
author = {Foxall, RL and Means, J and Marcinkiewicz, AL and Schillaci, C and DeRosia-Banick, K and Xu, F and Hall, JA and Jones, SH and Cooper, VS and Whistler, CA},
title = {Inoviridae prophage and bacterial host dynamics during diversification, succession, and Atlantic invasion of Pacific-native Vibrio parahaemolyticus.},
journal = {mBio},
volume = {15},
number = {1},
pages = {e0285123},
pmid = {38112441},
issn = {2150-7511},
support = {R/SFA-4//UNH | New Hampshire Sea Grant, University of New Hampshire (NHSG)/ ; R-HCE-3//UNH | New Hampshire Sea Grant, University of New Hampshire (NHSG)/ ; R/SFA-13//UNH | New Hampshire Sea Grant, University of New Hampshire (NHSG)/ ; NH00698//UNH | COLSA | New Hampshire Agricultural Experiment Station (NHAES)/ ; NH00625//UNH | COLSA | New Hampshire Agricultural Experiment Station (NHAES)/ ; NH00658//UNH | COLSA | New Hampshire Agricultural Experiment Station (NHAES)/ ; },
mesh = {Prophages ; *Vibrio parahaemolyticus/genetics ; Inoviridae ; Ecosystem ; Bacteria ; *Bacteriophages/genetics ; },
abstract = {An understanding of the processes that contribute to the emergence of pathogens from environmental reservoirs is critical as changing climate precipitates pathogen evolution and population expansion. Phylogeographic analysis of Vibrio parahaemolyticus hosts combined with the analysis of their Inoviridae phage resolved ambiguities of diversification dynamics which preceded successful Atlantic invasion by the epidemiologically predominant ST36 lineage. It has been established experimentally that filamentous phage can limit host recombination, but here, we show that phage loss is linked to rapid bacterial host diversification during epidemic spread in natural ecosystems alluding to a potential role for ubiquitous inoviruses in the adaptability of pathogens. This work paves the way for functional analyses to define the contribution of inoviruses in the evolutionary dynamics of environmentally transmitted pathogens.},
}
@article {pmid38111463,
year = {2024},
author = {Li, C and Gillings, MR and Zhang, C and Chen, Q and Zhu, D and Wang, J and Zhao, K and Xu, Q and Leung, PH and Li, X and Liu, J and Jin, L},
title = {Ecology and risks of the global plastisphere as a newly expanding microbial habitat.},
journal = {Innovation (Cambridge (Mass.))},
volume = {5},
number = {1},
pages = {100543},
pmid = {38111463},
issn = {2666-6758},
abstract = {Plastic offers a new niche for microorganisms, the plastisphere. The ever-increasing emission of plastic waste makes it critical to understand the microbial ecology of the plastisphere and associated effects. Here, we present a global fingerprint of the plastisphere, analyzing samples collected from freshwater, seawater, and terrestrial ecosystems. The plastisphere assembles a distinct microbial community that has a clearly higher heterogeneity and a more deterministically dominated assembly compared to natural habitats. New coexistence patterns-loose and fragile networks with mostly specialist linkages among microorganisms that are rarely found in natural habitats-are seen in the plastisphere. Plastisphere microbiomes generally have a great potential to metabolize organic compounds, which could accelerate carbon turnover. Microorganisms involved in the nitrogen cycle are also altered in the plastisphere, especially in freshwater plastispheres, where a high abundance of denitrifiers may increase the release of nitrite (aquatic toxicant) and nitrous oxide (greenhouse gas). Enrichment of animal, plant, and human pathogens means that the plastisphere could become an increasingly mobile reservoir of harmful microorganisms. Our findings highlight that if the trajectory of plastic emissions is not reversed, the expanding plastisphere could pose critical planetary health challenges.},
}
@article {pmid38110747,
year = {2023},
author = {Steinberger, Y and Doniger, T and Applebaum, I and Sherman, C and Rotbart, N},
title = {Effects of Vineyard Agro-management Practices on Soil Bacterial Community Composition, and Diversity.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {17},
pmid = {38110747},
issn = {1432-184X},
mesh = {Humans ; *Soil/chemistry ; Farms ; Soil Microbiology ; Agriculture ; Bacteria/genetics ; *Microbiota ; },
abstract = {Changes in land use strongly affect soil biological and physico-chemical structure and characteristics, which are strongly related to agricultural conversion of natural habitats to man-made usage. These are among the most important and not always beneficial changes, affecting loss of habitats. In Golan Heights basaltic soils, vineyards are currently a driving force in land-use change. Such changes could have an important effect on soil microbial community that play an important role in maintaining stable functioning of soil ecosystems. This study investigated the microbial communities in five different agro-managements using molecular tools that can clarify the differences in microbial community structure and function. Significant differences in soil microbial community composition were found. However, no differences in alpha diversity or functionality were found between the treatments. To the best of our knowledge, this is the first report indicating that the bacterial community in different agro-managements provide an insight into the potential function of a vineyard system.},
}
@article {pmid38110491,
year = {2023},
author = {Elsayed, SS and van der Heul, HU and Xiao, X and Nuutila, A and Baars, LR and Wu, C and Metsä-Ketelä, M and van Wezel, GP},
title = {Unravelling key enzymatic steps in C-ring cleavage during angucycline biosynthesis.},
journal = {Communications chemistry},
volume = {6},
number = {1},
pages = {281},
pmid = {38110491},
issn = {2399-3669},
support = {16439//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
abstract = {Angucyclines are type II polyketide natural products, often characterized by unusual structural rearrangements through B- or C-ring cleavage of their tetracyclic backbone. While the enzymes involved in B-ring cleavage have been extensively studied, little is known of the enzymes leading to C-ring cleavage. Here, we unravel the function of the oxygenases involved in the biosynthesis of lugdunomycin, a highly rearranged C-ring cleaved angucycline derivative. Targeted deletion of the oxygenase genes, in combination with molecular networking and structural elucidation, showed that LugOI is essential for C12 oxidation and maintaining a keto group at C6 that is reduced by LugOII, resulting in a key intermediate towards C-ring cleavage. An epoxide group is then inserted by LugOIII, and stabilized by the novel enzyme LugOV for the subsequent cleavage. Thus, for the first time we describe the oxidative enzymatic steps that form the basis for a wide range of rearranged angucycline natural products.},
}
@article {pmid38108886,
year = {2023},
author = {Morrill, A and Forbes, MR and Vesterinen, EJ and Tamminen, M and Sääksjärvi, IE and Kaunisto, KM},
title = {Molecular Characterisation of Faecal Bacterial Assemblages Among Four Species of Syntopic Odonates.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {16},
pmid = {38108886},
issn = {1432-184X},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Ecology ; Feces ; Host Specificity ; *Odonata ; },
abstract = {Factors such as host species, phylogeny, diet, and both timing and location of sampling are thought to influence the composition of gut-associated bacteria in insects. In this study, we compared the faecal-associated bacterial taxa for three Coenagrion and one Enallagma damselfly species. We expected high overlap in representation of bacterial taxa due to the shared ecology and diet of these species. Using metabarcoding based on the 16S rRNA gene, we identified 1513 sequence variants, representing distinct bacterial 'taxa'. Intriguingly, the damselfly species showed somewhat different magnitudes of richness of ZOTUs, ranging from 480 to 914 ZOTUs. In total, 921 (or 60.8% of the 1513) distinct ZOTUs were non-shared, each found only in one species, and then most often in only a single individual. There was a surfeit of these non-shared incidental ZOTUs in the Enallagma species accounting for it showing the highest bacterial richness and accounting for a sample-wide pattern of more single-species ZOTUs than expected, based on comparisons to the null model. Future studies should address the extent to which faecal bacteria represent non-incidental gut bacteria and whether abundant and shared taxa are true gut symbionts. Pictures of odonates adopted from Norske Art databank under Creative Commons License (CC BY 4.0).},
}
@article {pmid38107863,
year = {2023},
author = {Vandeweyer, D and Bruno, D and Bonelli, M and IJdema, F and Lievens, B and Crauwels, S and Casartelli, M and Tettamanti, G and De Smet, J},
title = {Bacterial biota composition in gut regions of black soldier fly larvae reared on industrial residual streams: revealing community dynamics along its intestinal tract.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1276187},
pmid = {38107863},
issn = {1664-302X},
abstract = {Some insect species have gained attention as efficient bioconverters of low-value organic substrates (i.e., residual streams) into high-value biomass. Black soldier fly (BSF) (Hermetia illucens) larvae are particularly interesting for bioconversion due to their ability to grow on a wide range of substrates, including low-value industrial residual streams. This is in part due to the plasticity of the gut microbiota of polyphagous insects, like BSF. Gut microbiota composition varies depending on rearing substrates, via a mechanism that might support the recruitment of microorganisms that facilitate digestion of a specific substrate. At the same time, specific microbial genera do persist on different substrates via unknown mechanisms. This study aimed to offer insights on this microbial plasticity by investigating how the composition of the bacterial community present in the gut of BSF larvae responds to two industrial residual streams: swill (a mixture of catering and supermarket leftovers) and distiller's dried grains with solubles. The bacterial biota composition of substrates, whole larvae at the beginning of the rearing period and at harvest, rearing residues, and larval gut regions were investigated through 16S rRNA gene sequencing. It was observed that both substrate and insect development influenced the bacterial composition of the whole larvae. Zooming in on the gut regions, there was a clear shift in community composition from a higher to a lower diversity between the anterior/middle midgut and the posterior midgut/hindgut, indicating a selective pressure occurring in the middle midgut region. Additionally, the abundance of the bacterial biota was always high in the hindgut, while its diversity was relatively low. Even more, the bacterial community in the hindgut was found to be relatively more conserved over the different substrates, harboring members of the BSF core microbiota. We postulate a potential role of the hindgut as a reservoir for insect-associated microbes. This warrants further research on that underexplored region of the intestinal tract. Overall, these findings contribute to our understanding of the bacterial biota structure and dynamics along the intestinal tract, which can aid microbiome engineering efforts to enhance larval performance on (industrial) residual streams.},
}
@article {pmid38105519,
year = {2024},
author = {Pinto, S and Benincà, E and Galazzo, G and Jonkers, D and Penders, J and Bogaards, JA},
title = {Heterogeneous associations of gut microbiota with Crohn's disease activity.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2292239},
pmid = {38105519},
issn = {1949-0984},
mesh = {Humans ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome ; Inflammation ; Bacteria/genetics ; Bacteroidetes ; },
abstract = {The multi-factorial involvement of gut microbiota with Crohn's disease (CD) necessitates robust analysis to uncover possible associations with particular microbes. CD has been linked to specific bacteria, but reported associations vary widely across studies. This inconsistency may result from heterogeneous associations across individual patients, resulting in no apparent or only weak relationships with the means of bacterial abundances. We investigated the relationship between bacterial relative abundances and disease activity in a longitudinal cohort of CD patients (n = 57) and healthy controls (n = 15). We applied quantile regression, a statistical technique that allows investigation of possible relationships outside the mean response. We found several significant and mostly negative associations with CD, especially in lower quantiles of relative abundance on family or genus level. Associations found by quantile regression deviated from the mean response in relative abundances of Coriobacteriaceae, Pasteurellaceae, Peptostreptococcaceae, Prevotellaceae, and Ruminococcaceae. For the family Streptococcaceae we found a significant elevation in relative abundance for patients experiencing an exacerbation relative to those who remained without self-reported symptoms or measurable inflammation. Our analysis suggests that specific bacterial families are related to CD and exacerbation, but associations vary between patients due to heterogeneity in disease course, medication history, therapy response, gut microbiota composition and historical contingency. Our study underscores that microbial diversity is reduced in the gut of CD patients, but suggests that the process of diversity loss is rather irregular with respect to specific taxonomic groups. This novel insight may advance our ecological understanding of this complex disease.},
}
@article {pmid38103698,
year = {2024},
author = {Yuan, J and Yang, L and Yu, P and Tang, N and Liu, L and Wang, W and Wang, P and Yang, Q and Guo, S and Li, J},
title = {Comparison and development of scanning electron microscope techniques for delicate plant tissues.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {340},
number = {},
pages = {111963},
doi = {10.1016/j.plantsci.2023.111963},
pmid = {38103698},
issn = {1873-2259},
mesh = {Microscopy, Electron, Scanning ; *Plants ; Temperature ; *Water ; },
abstract = {Cell deformation often occurs during sample preparation and imaging with scanning electron microscope (SEM), especially with delicate samples, which influences the accuracy of the results. Here we investigate the influence of several preparation methods on cell deformation, using water content and tissue hardness as indicators to classify "delicate" samples of plant species. The degree of deformation in samples resulting from five preparation methods was measured at the tissue and single-cell levels, revealing that a cryo- and methanol-fixation produced lower degrees of tissue dimension deformation and better preservation of cell shape for delicate samples, while for harder tissues, other preparation methods for a dehydrated specimen are also suitable. Stability and image quality of delicate samples could be improved with the application of a cryo-protectant combined with a lower cryo-stage temperature, e.g. - 30 °C. We show that the sample stability under the beam was improved by combining larger sample size and cryo-stage application. Furthermore, the influence of adaxial and abaxial tissue surfaces, the accelerating voltage, and sputter coating time on sample stability and image quality was evaluated. Our study is valuable for artifact reduction and easy application of SEM.},
}
@article {pmid38102317,
year = {2023},
author = {Modra, H and Ulmann, V and Gersl, M and Babak, V and Konecny, O and Hubelova, D and Caha, J and Kudelka, J and Falkinham, JO and Pavlik, I},
title = {River Sediments Downstream of Villages in a Karstic Watershed Exhibited Increased Numbers and Higher Diversity of Nontuberculous Mycobacteria.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {15},
pmid = {38102317},
issn = {1432-184X},
mesh = {*Nontuberculous Mycobacteria ; *Rivers ; Prevalence ; Water Quality ; Phosphorus ; },
abstract = {The impact of residential villages on the nontuberculous mycobacteria (NTM) in streams flowing through them has not been studied in detail. Water and sediments of streams are highly susceptible to anthropogenic inputs such as surface water flows. This study investigated the impact of seven residential villages in a karst watershed on the prevalence and species spectrum of NTM in water and sediments. Higher NTM species diversity (i.e., 19 out of 28 detected) was recorded downstream of the villages and wastewater treatment plants (WWTPs) compared to sampling sites upstream (i.e., 5). Significantly, higher Zn and lower silicon concentrations were detected in sediments inside the village and downstream of the WWTP's effluents. Higher phosphorus concentration in sediment was downstream of WWTPs compared to other sampling sites. The effluent from the WWTPs had a substantial impact on water quality parameters with significant increases in total phosphorus, anions (Cl[-]and N-NH3[-]), and cations (Na[+] and K[+]). The results provide insights into NTM numbers and species diversity distribution in a karst watershed and the impact of urban areas. Although in this report the focus is on the NTM, it is likely that other water and sediment microbes will be influenced as well.},
}
@article {pmid38098978,
year = {2023},
author = {Gonzalez, OA and Kirakodu, SS and Ebersole, JL},
title = {DAMPs and alarmin gene expression patterns in aging healthy and diseased mucosal tissues.},
journal = {Frontiers in oral health},
volume = {4},
number = {},
pages = {1320083},
pmid = {38098978},
issn = {2673-4842},
support = {P20 GM103538/GM/NIGMS NIH HHS/United States ; P40 RR003640/RR/NCRR NIH HHS/United States ; },
abstract = {INTRODUCTION: Periodontitis is delineated by a dysbiotic microbiome at sites of lesions accompanied by a dysregulated persistent inflammatory response that undermines the integrity of the periodontium. The interplay of the altered microbial ecology and warning signals from host cells would be a critical feature for maintaining or re-establishing homeostasis in these tissues.<br><br>METHODS: This study used a nonhuman primate model (Macaca mulatta) with naturally-occurring periodontitis (n&#x2009;=&#x2009;34) and experimental ligature-induced periodontitis (n&#x2009;=&#x2009;36) to describe the features of gene expression for an array of damage-associate molecular patterns (DAMPs) or alarmins within the gingival tissues. The animals were age stratified into: &#x2264;3 years (Young), 7-12 years (Adolescent), 12-15 years (Adult) and 17-23 years (Aged). Gingival tissue biopsies were examined via microarray. The analysis focused on 51 genes representative of the DAMPs/alarmins family of host cell warning factors and 18 genes associated with tissue destructive processed in the gingival tissues. Bacterial plaque samples were collected by curette sampling and 16S rRNA gene sequences used to describe the oral microbiome.<br><br>RESULTS: A subset of DAMPs/alarmins were expressed in healthy and naturally-occurring periodontitis tissues in the animals and suggested local effects on gingival tissues leading to altered levels of DAMPs/alarmins related to age and disease. Significant differences from adult healthy levels were most frequently observed in the young and adolescent animals with few representatives in this gene array altered in the healthy aged gingival tissues. Of the 51 target genes, only approximately &#x2153; were altered by &#x2265;1.5-fold in any of the age groups of animals during disease, with those increases observed during disease initiation. Distinctive positive and negative correlations were noted with the DAMP/alarmin gene levels and comparative expression changes of tissue destructive molecules during disease across the age groups. Finally, specific correlations of DAMP/alarmin genes and relative abundance of particular microbes were observed in health and resolution samples in younger animals, while increased correlations during disease in the older groups were noted.<br><br>CONCLUSIONS: Thus, using this human-like preclinical model of induced periodontitis, we demonstrated the dynamics of the activation of the DAMP/alarmin warning system in the gingival tissues that showed some specific differences based on age.},
}
@article {pmid38098078,
year = {2023},
author = {Huete-Stauffer, TM and Logares, R and Ansari, MI and Røstad, A and Calleja, ML and Morán, XAG},
title = {Increased prokaryotic diversity in the Red Sea deep scattering layer.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {87},
pmid = {38098078},
issn = {2524-6372},
support = {CCF-2017/2018//King Abdullah University of Science and Technology/ ; RYC-2013-12554//Ministerio de Econom&#xed;a y Competitividad/ ; },
abstract = {BACKGROUND: The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450-600 m.<br><br>RESULTS: Despite the general consensus of homogeneous conditions in the mesopelagic layer, we observed variability in physico-chemical variables (oxygen, inorganic nutrients, DOC) in the depth profiles. We also identified distinct seasonal indicator prokaryotes inhabiting the DSL, representing between 2% (in spring) to over 10% (in winter) of total 16S rRNA gene sequences. The dominant indicator groups were Alteromonadales in winter, Vibrionales in spring and Microtrichales in summer. Using multidimensional scaling analysis, the DSL samples showed divergence from the surrounding mesopelagic layers and were distributed according to depth (47% of variance explained). We identified the sources of diversity that contribute to the DSL by analyzing the detailed profiles of spring, where 3 depths were sampled in the mesopelagic. On average, 7% was related to the epipelagic, 34% was common among the other mesopelagic waters and 38% was attributable to the DSL, with 21% of species being unique to this layer.<br><br>CONCLUSIONS: We conclude that the mesopelagic physico-chemical properties shape a rather uniform prokaryotic community, but that the 200&#xa0;m deep DSL contributes uniquely and in a high proportion to the diversity of the Red Sea mesopelagic.},
}
@article {pmid38097563,
year = {2023},
author = {Riva, A and Rasoulimehrabani, H and Cruz-Rubio, JM and Schnorr, SL and von Baeckmann, C and Inan, D and Nikolov, G and Herbold, CW and Hausmann, B and Pjevac, P and Schintlmeister, A and Spittler, A and Palatinszky, M and Kadunic, A and Hieger, N and Del Favero, G and von Bergen, M and Jehmlich, N and Watzka, M and Lee, KS and Wiesenbauer, J and Khadem, S and Viernstein, H and Stocker, R and Wagner, M and Kaiser, C and Richter, A and Kleitz, F and Berry, D},
title = {Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {8210},
pmid = {38097563},
issn = {2041-1723},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P27831-B28//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 741623//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Inulin/metabolism ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria ; Prebiotics ; },
abstract = {Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin. 16S rRNA gene amplicon sequencing of sorted cells revealed that the ability to bind inulin was widespread in the microbiota. We further evaluate which taxa are metabolically stimulated by inulin and find that diverse taxa from the phyla Firmicutes and Actinobacteria respond to inulin, and several isolates of these taxa can degrade inulin. Incubation with another prebiotic, xylooligosaccharides (XOS), in contrast, shows a more robust bifidogenic effect. Interestingly, the Coriobacteriia Eggerthella lenta and Gordonibacter urolithinfaciens are indirectly stimulated by the inulin degradation process, expanding our knowledge of inulin-responsive bacteria.},
}
@article {pmid38096695,
year = {2024},
author = {Wang, Q and Sun, Z and Song, S and Ali, A and Xu, H},
title = {Can salinity variability drive the colonization dynamics of periphytic protozoan fauna in marine environments?.},
journal = {Marine pollution bulletin},
volume = {198},
number = {},
pages = {115882},
doi = {10.1016/j.marpolbul.2023.115882},
pmid = {38096695},
issn = {1879-3363},
mesh = {*Biodiversity ; Environmental Monitoring ; Salinity ; *Ciliophora ; Logistic Models ; Ecosystem ; },
abstract = {To investigate effects of salinity variability on colonization dynamics of periphytic protozoan fauna, a 21-day study was conducted in temperature-controlled circulation systems (TCCSs). Periphytic protozoan communities were incubated using glass slides as artificial substrata in five TCCS aquaria with a large-scale salinity gradient of 9, 19, 29 (control), 39, and 49 PSU, respectively. The colonization dynamics were observed on days 3, 5, 7, 10, 14, and 21. The colonization dynamics were well fitted to the MacArthur-Wilson and logistic model equations in colonization and growth curves in all five treatments, respectively. However, the maximum species richness and abundance were reduced, and the colonization patterns were significantly shifted in four treatments with salinity changed by 20 PSU compared to the control (29 PSU). Thus, it is suggested that the large-scale salinity variability may reduce the species richness significantly and affect colonization dynamics of periphytic protozoan fauna in marine environments.},
}
@article {pmid38095470,
year = {2024},
author = {Guo, Q and Gong, L},
title = {Compared with pure forest, mixed forest alters microbial diversity and increases the complexity of interdomain networks in arid areas.},
journal = {Microbiology spectrum},
volume = {12},
number = {1},
pages = {e0264223},
pmid = {38095470},
issn = {2165-0497},
support = {2021XJKK0900//the third comprehensive scientific investigtion project in xinjiang/ ; },
mesh = {*Soil Microbiology ; Forests ; Trees ; *Microbiota ; Soil/chemistry ; },
abstract = {The results provide a comparative study of the response of soil microbial ecology to the afforestation of different tree species and deepen the understanding of the factors controlling soil microbial community structure.},
}
@article {pmid38095319,
year = {2024},
author = {Forman-Ankjaer, B and Hvid-Jensen, F and Kobel, CM and Greve, T},
title = {Short communication: first case of bacteraemia caused by Dielma fastidiosa in a patient hospitalized with diverticulitis.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {132},
number = {2},
pages = {130-133},
doi = {10.1111/apm.13367},
pmid = {38095319},
issn = {1600-0463},
mesh = {Humans ; Phylogeny ; Likelihood Functions ; *Bacteremia/diagnosis ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Diverticulitis ; },
abstract = {Dielma fastidiosa is a gram-negative, anaerobic rod belonging to the family Erysipelotrichaceae. D. fastidiosa has previously been isolated in human stool samples as part of the commensal flora; however, prior to this case, it has never been identified as a human pathogen. We present the first case of bacteraemia with D. fastidiosa. Bacterial growth in the blood culture bottle was detected by the automated blood culture system BacT/ALERT 3D. Culturing was performed, and bacterial colonies were identified as D. fastidiosa using MALDI-TOF MS. A subsequent whole-genome sequencing using Illumina NovaSeq was performed, and a phylogenetic tree depicting all available sequences of D. fastidiosa was generated. The reference MALDI-TOF spectrum and species identification was compared with the previously published spectrum. Whole-genome sequencing confirmed the tentative MALDI-TOF species identification. Notably, the maximum-likelihood-based phylogenetic analysis placed the D. fastidiosa isolate from this clinical case within the known variation of the eight publicly available sequences of this species. We identified D. fastidiosa by whole-genome sequencing followed by maximum-likelihood analysis as a possible pathogen in this case of bacteraemia in a patient hospitalized with diverticulitis.},
}
@article {pmid38094622,
year = {2023},
author = {Ollison, GA and Hu, SK and Hopper, JV and Stewart, BP and Beatty, JL and Caron, DA},
title = {Physiology governing diatom vs. dinoflagellate bloom and decline in coastal Santa Monica Bay.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1287326},
pmid = {38094622},
issn = {1664-302X},
abstract = {Algal blooms on the Southern California coast are typically dominated by diatom and dinoflagellate taxa, and are governed by their physiological responses to environmental cues; however, we lack a predictive understanding of the environmental controls underlying the establishment and persistence of these distinct bloom events. In this study, we examined gene expression among the numerically dominant diatom and dinoflagellate taxa during spring upwelling bloom events to compare the physiological underpinnings of diatom vs. dinoflagellate bloom dynamics. Diatoms, which bloomed following upwelling events, expressed genes related to dissolved inorganic nitrogen utilization, and genes related to the catabolism of chitin that may have prolonged their bloom duration following nitrogen depletion. Conversely, dinoflagellates bloomed under depleted inorganic nitrogen conditions, exhibited less variation in transcriptional activity, and expressed few genes associated with dissolved inorganic nutrients during their bloom. Dinoflagellate profiles exhibited evidence of proteolysis and heterotrophy that may have enabled them to bloom to high abundances under depleted inorganic nutrients. Taken together, diatom and dinoflagellate transcriptional profiles illustrated guild-specific physiologies that are tuned to respond to and thrive under distinct environmental "windows of opportunity."},
}
@article {pmid38091083,
year = {2023},
author = {Perez-Bou, L and Muñoz-Palazon, B and Gonzalez-Lopez, J and Gonzalez-Martinez, A and Correa-Galeote, D},
title = {Deciphering the Role of WWTPs in Cold Environments as Hotspots for the Dissemination of Antibiotic Resistance Genes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {14},
pmid = {38091083},
issn = {1432-184X},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater ; Waste Disposal, Fluid ; Genes, Bacterial/genetics ; Ecosystem ; Drug Resistance, Microbial/genetics ; Sewage/microbiology ; },
abstract = {Cold environments are the most widespread extreme habitats in the world. However, the role of wastewater treatment plants (WWTPs) in the cryosphere as hotspots in antibiotic resistance dissemination has not been well established. Hence, a snapshot of the resistomes of WWTPs in cold environments, below 5 °C, was provided to elucidate their role in disseminating antibiotic resistance genes (ARGs) to the receiving waterbodies. The resistomes of two natural environments from the cold biosphere were also determined. Quantitative PCR analysis of the aadA, aadB, ampC, blaSHV, blaTEM, dfrA1, ermB, fosA, mecA, qnrS, and tetA(A) genes indicated strong prevalences of these genetic determinants in the selected environments, except for the mecA gene, which was not found in any of the samples. Notably, high abundances of the aadA, ermB, and tetA(A) genes were found in the influents and activated sludge, highlighting that WWTPs of the cryosphere are critical hotspots for disseminating ARGs, potentially worsening the resistance of bacteria to some of the most commonly prescribed antibiotics. Besides, the samples from non-disturbed cold environments had large quantities of ARGs, although their ARG profiles were highly dissimilar. Hence, the high prevalences of ARGs lend support to the fact that antibiotic resistance is a common issue worldwide, including environmentally fragile cold ecosystems.},
}
@article {pmid38088973,
year = {2023},
author = {Liu, ZS and Wang, KH and Cai, M and Yang, ML and Wang, XK and Ma, HL and Yuan, YH and Wu, LH and Li, DF and Liu, SJ},
title = {Agromyces chromiiresistens sp. nov., Novosphingobium album sp. nov., Sphingobium arseniciresistens sp. nov., Sphingomonas pollutisoli sp. nov., and Salinibacterium metalliresistens sp. nov.: five new members of Microbacteriaceae and Sphingomonadaceae from polluted soil.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1289110},
pmid = {38088973},
issn = {1664-302X},
abstract = {There are many unidentified microbes in polluted soil needing to be explored and nominated to benefit the study of microbial ecology. In this study, a taxonomic research was carried out on five bacterial strains which were isolated and cultivated from polycyclic aromatic hydrocarbons, and heavy metals polluted soil of an abandoned coking plant. Phylogenetical analysis showed that they belonged to the phyla Proteobacteria and Actinobacteria, and their 16S rRNA gene sequence identities were lower than 98.5% to any known and validly nominated bacterial species, suggesting that they were potentially representing new species. Using polyphasic taxonomic approaches, the five strains were classified as new species of the families Microbacteriaceae and Sphingomonadaceae. Genome sizes of the five strains ranged from 3.07 to 6.60 Mb, with overall DNA G+C contents of 63.57-71.22 mol%. The five strains had average nucleotide identity of 72.38-87.38% and digital DNA-DNA hybridization of 14.0-34.2% comparing with their closely related type strains, which were all below the thresholds for species delineation, supporting these five strains as novel species. Based on the phylogenetic, phylogenomic, and phenotypic characterizations, the five novel species are proposed as Agromyces chromiiresistens (type strain H3Y2-19a[T] = CGMCC 1.61332[T]), Salinibacterium metalliresistens (type strain H3M29-4[T] = CGMCC 1.61335T), Novosphingobium album (type strain H3SJ31-1[T] = CGMCC 1.61329[T]), Sphingomonas pollutisoli (type strain H39-1-10[T] = CGMCC 1.61325[T]), and Sphingobium arseniciresistens (type strain H39-3-25[T] = CGMCC 1.61326[T]). Comparative genome analysis revealed that the species of the family Sphingomonadaceae represented by H39-1-10[T], H39-3-25[T], and H3SJ31-1[T] possessed more functional protein-coding genes for the degradation of aromatic pollutants than the species of the family Microbacteriaceae represented by H3Y2-19a[T] and H3M29-4[T]. Furthermore, their capacities of resisting heavy metals and metabolizing aromatic compounds were investigated. The results indicated that strains H3Y2-19a[T] and H39-3-25[T] were robustly resistant to chromate (VI) and/or arsenite (III). Strains H39-1-10[T] and H39-3-25[T] grew on aromatic compounds, including naphthalene, as carbon sources even in the presence of chromate (VI) and arsenite (III). These features reflected their adaptation to the polluted soil environment.},
}
@article {pmid38088573,
year = {2024},
author = {Lücking, G and Albrecht, K and Märtlbauer, E and Schauer, K},
title = {Draft genome sequences of two thermophilic, spore-forming Aeribacillus pallidus strains isolated from dairy products.},
journal = {Microbiology resource announcements},
volume = {13},
number = {1},
pages = {e0089623},
pmid = {38088573},
issn = {2576-098X},
abstract = {The presence of thermophilic spore-forming bacteria is challenging in industrial food processing. The presented genome sequences of Aeribacillus pallidus, isolated from raw milk and cocoa powder, provide insights into how to prevent damage to minimally processed foods and products with extended shelf life, such as milk products.},
}
@article {pmid38087672,
year = {2024},
author = {Effenberger, M and Grander, C and Hausmann, B and Enrich, B and Pjevac, P and Zoller, H and Tilg, H},
title = {Apelin and the gut microbiome: Potential interaction in human MASLD.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {56},
number = {6},
pages = {932-940},
doi = {10.1016/j.dld.2023.11.023},
pmid = {38087672},
issn = {1878-3562},
mesh = {Humans ; *Apelin/blood ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Case-Control Studies ; Aged ; *Carcinoma, Hepatocellular/microbiology/blood ; *Liver Cirrhosis/microbiology/blood ; Liver Neoplasms/microbiology ; Apelin Receptors/metabolism ; Cytokines/blood ; Feces/microbiology/chemistry ; Adult ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading cause of chronic liver disease with increasing numbers worldwide. Adipokines like apelin (APLN) can act as key players in the complex pathophysiology of MASLD.<br><br>AIMS: Investigating the role of APLN in MASLD.<br><br>METHODS: Fecal and blood samples were collected in a MASLD cohort and healthy controls (HC). MASLD patients with liver fibrosis and MASLD-associated hepatocellular carcinoma (HCC) were included into the study. Systemic concentration of Apelin, Apelin receptor (APLNR) and circulating cytokines were measured in serum samples.<br><br>RESULTS: Apelin concentration correlated with the Fib-4 score and was elevated in MASLD patients (mild fibrosis, mF (Fib-4 <3.25) and severe fibrosis, sF (Fib-4 >3.25)) as well as in MASLD-associated HCC patients compared to HC. In accordance APLNR and circulating cytokines were also elevated in mF and sF. In contrast apelin levels were negatively associated with liver survival at three and five years. Changes in taxa composition at phylum level showed an increase of Enterobactericae, Prevotellaceae and Lactobacillaceae in patients with sF compared to mF. We could also observe an association between apelin concentrations and bacterial lineages (phyla).<br><br>CONCLUSIONS: Circulating apelin is associated with liver fibrosis and HCC. In addition, there might exist an interaction between systemic apelin and the gut microbiome.},
}
@article {pmid38087002,
year = {2023},
author = {Montaño-Salazar, S and Quintanilla, E and Sánchez, JA},
title = {Microbial shifts associated to ENSO-derived thermal anomalies reveal coral acclimation at holobiont level.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {22049},
pmid = {38087002},
issn = {2045-2322},
mesh = {Animals ; *Anthozoa/microbiology ; El Nino-Southern Oscillation ; Biodiversity ; Acclimatization ; Cold Temperature ; Bacteria ; Coral Reefs ; },
abstract = {The coral microbiome conforms a proxy to study effects of changing environmental conditions. However, scarce information exists regarding microbiome dynamics and host acclimation in response to environmental changes associated to global-scale disturbances. We assessed El Niño Southern Oscillation (ENSO)-derived thermal anomalies shifts in the bacterial microbiome of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) from the remote island of Malpelo in the Tropical Eastern Pacific. Malpelo is a hot spot of biodiversity and lacks direct coastal anthropogenic impacts. We evaluated the community composition and predicted functional profiles of the microbiome during 2015, 2017 and 2018, including different phases of ENSO cycle. The bacterial community diversity and composition between the warming and cooling phase were similar, but differed from the neutral phase. Relative abundances of different microbiome core members such as Endozoicomonas and Mycoplasma mainly drove these differences. An acclimated coral holobiont is suggested not just to warm but also to cold stress by embracing similar microbiome shifts and functional redundancy that allow maintaining coral's viability under thermal stress. Responses of the microbiome of unperturbed sea fans such as P. cairnsi in Malpelo could be acting as an extended phenotype facilitating the acclimation at the holobiont level.},
}
@article {pmid38086476,
year = {2024},
author = {Zhang, M and Zhao, B and Yan, Y and Cheng, Z and Li, Z and Han, L and Sun, Y and Zheng, Y and Xia, Y},
title = {Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {169203},
doi = {10.1016/j.scitotenv.2023.169203},
pmid = {38086476},
issn = {1879-1026},
mesh = {Metagenome ; *Arsenic/analysis ; Carbon/metabolism ; *Microbiota ; Bacteria/metabolism ; Geologic Sediments/chemistry ; },
abstract = {The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d[-1] and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.},
}
@article {pmid38085721,
year = {2023},
author = {Coleman, ME and Oscar, TP and Negley, TL and Stephenson, MM},
title = {Suppression of pathogens in properly refrigerated raw milk.},
journal = {PloS one},
volume = {18},
number = {12},
pages = {e0289249},
pmid = {38085721},
issn = {1932-6203},
mesh = {Humans ; Animals ; Milk ; Food Microbiology ; Pilot Projects ; Colony Count, Microbial ; Salmonella ; *Escherichia coli O157 ; *Listeria monocytogenes ; },
abstract = {Conflicting claims exist regarding pathogen growth in raw milk. A small pilot study was designed to provide definitive data on trends for pathogen growth and decline in raw bovine milk hygienically produced for direct human consumption. An independent laboratory conducted the study, monitoring growth and decline of pathogens inoculated into raw milk. Raw milk samples were inoculated with foodborne pathogens (Campylobacter, E. coli O157:H7, Listeria monocytogenes, or Salmonella) at lower (<162 colony forming units (CFU) per mL) and higher levels (<8,300 CFU/mL). Samples were stored at 4.4°C and quantified over time after inoculation (days 0, 3, 6, 9, 12, and 14) by standard culture-based methods. Statistical analysis of trends using the Mann-Kendall Trend Test and Analysis of Variance were conducted for 48 time series observations. Evidence of pathogen growth was documented for L. monocytogenes in 8 of 12 replicates (P = 0.001 to P = 0.028). Analysis of variance confirmed significant increases for L. monocytogenes at both initial levels in week 2. No evidence of growth was documented over 14 days for the three pathogens predominantly associated with raw milk outbreaks in the US (Campylobacter, E. coli O157:H7, and Salmonella). Further research is needed to characterize parameters for pathogen growth and decline to support re-assessment of risks that were based on incorrect assumptions about interactions of pathogens with the raw milk microbiota.},
}
@article {pmid38082204,
year = {2024},
author = {Li, X and Yu, S and Cheng, Z and Chang, X and Yun, Y and Jiang, M and Chen, X and Wen, X and Li, H and Zhu, W and Xu, S and Xu, Y and Wang, X and Zhang, C and Wu, Q and Hu, J and Lin, Z and Aury, JM and Van de Peer, Y and Wang, Z and Zhou, X and Wang, J and Lü, P and Zhang, L},
title = {Origin and evolution of the triploid cultivated banana genome.},
journal = {Nature genetics},
volume = {56},
number = {1},
pages = {136-142},
pmid = {38082204},
issn = {1546-1718},
support = {833522//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Musa/genetics ; *Fusarium/genetics ; Triploidy ; Plant Breeding ; Transcription Factors/genetics ; Plant Diseases/genetics ; },
abstract = {Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas.},
}
@article {pmid38082143,
year = {2023},
author = {Botero Rute, LM and Caro-Quintero, A and Acosta-González, A},
title = {Enhancing the Conventional Culture: the Evaluation of Several Culture Media and Growth Conditions Improves the Isolation of Ruminal Bacteria.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {13},
pmid = {38082143},
issn = {1432-184X},
mesh = {Cattle ; Animals ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Rumen/microbiology ; Bacteria ; *Microbiota ; },
abstract = {The rumen microbiota is critical in cattle digestion. Still, its low cultivability makes it difficult to study its ecological function and biotechnological potential. To improve the recovery of ruminal microorganisms, this study combined the evaluation of several cultivation parameters with metabarcoding analysis. The parameters tested comprised eight media cultures, three sample dilutions (10[-2], 10[-6], 10[-12]), and two incubation times (3 and 7 days). Bacterial populations were determined through Illumina sequencing of 16S rRNA from three biological replicates. The results indicate that none of the culture media recovered all rumen populations and that there was an altered relative abundance of the dominant phyla. In the rumen, Bacteroidetes and Firmicutes comprised 75% and 15% of the relative abundance, respectively, while in the culture media, these were 15% and 60%, respectively. Principal coordinate analysis (PCoA) of the bacterial community revealed significant shifts in population composition due to dilution, with 10[-2] and 10[-6] dilutions clustered closely while the 10[-12] dilution differed markedly. In contrast, incubation duration did not influence population diversity. According to the results, two media, CAN and KNT, were selected based on their ability to recover more similar populations compared to the rumen sample. The metataxonomic study showed that CAN media had consistent reproducibility over time, while KNT showed enrichment of different taxa due to the use of rumen fluid as a substrate. From these, 64 pure cultures were obtained and 54 were identified through 16S rRNA gene sequencing. Being Streptococcus the most frequently isolated genus, this prevalence contrasts with the liquid media composition, underscoring the importance of refining single colony isolation strategies. Although no culture medium could replicate the native rumen bacterial population perfectly, our findings highlight the potential of CAN and KNT media in recovering populations that are more closely aligned to natural rumen conditions. In conclusion, our study emphasizes the importance of integrating molecular approaches in selecting suitable cultivation media and parameters to depict rumen bacteria accurately.},
}
@article {pmid38078767,
year = {2024},
author = {Smith, AB and Specker, JT and Hewlett, KK and Scoggins, TR and Knight, M and Lustig, AM and Li, Y and Evans, KM and Guo, Y and She, Q and Christopher, MW and Garrett, TJ and Moustafa, AM and Van Tyne, D and Prentice, BM and Zackular, JP},
title = {Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection.},
journal = {mBio},
volume = {15},
number = {1},
pages = {e0165623},
pmid = {38078767},
issn = {2150-7511},
support = {K22 AI137220/AI/NIAID NIH HHS/United States ; R21 AI164018/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; R03 AI168491/AI/NIAID NIH HHS/United States ; L40 AI147162/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Clostridioides difficile ; Enterococcus faecalis ; *Clostridium Infections/microbiology ; Bacteria ; *Gastrointestinal Microbiome ; },
abstract = {Clostridioides difficile and Enterococcus faecalis are two pathogens of great public health importance. Both bacteria colonize the human gastrointestinal tract where they are known to interact in ways that worsen disease outcomes. We show that the damage associated with C. difficile infection (CDI) releases nutrients that benefit E. faecalis. One particular nutrient, heme, allows E. faecalis to use oxygen to generate energy and grow better in the gut. Understanding the mechanisms of these interspecies interactions could inform therapeutic strategies for CDI.},
}
@article {pmid38078555,
year = {2024},
author = {Zhang, X and Dai, H and Huang, Y and Liu, K and Li, X and Zhang, S and Fu, S and Jiao, S and Chen, C and Dong, B and Yang, Z and Cui, Y and Li, H and Liu, S},
title = {Species pool, local assembly processes: Disentangling the mechanisms determining bacterial α- and β-diversity during forest secondary succession.},
journal = {Molecular ecology},
volume = {33},
number = {4},
pages = {e17241},
doi = {10.1111/mec.17241},
pmid = {38078555},
issn = {1365-294X},
support = {31700383//Natural Science Foundation of China/ ; 31800375//Natural Science Foundation of China/ ; 31930078//Natural Science Foundation of China/ ; 32071556//Natural Science Foundation of China/ ; U1904204//Natural Science Foundation of China/ ; 222300420036//Natural Science Foundation of Henan Province/ ; //the Fundamental Research Funds of Northwest A&amp;F University/ ; QCYRCXM-2022-347//the high-level innovation and entrepreneurship talent project of Qinchuangyuan/ ; },
mesh = {*Biodiversity ; Forests ; Ecology ; *Microbiota ; Bacteria/genetics ; Soil ; Ecosystem ; },
abstract = {Across ecology, and particularly within microbial ecology, there is limited understanding how the generation and maintenance of diversity. Although recent work has shown that both local assembly processes and species pools are important in structuring microbial communities, the relative contributions of these mechanisms remain an important question. Moreover, the roles of local assembly processes and species pools are drastically different when explicitly considering the potential for saturation or unsaturation, yet this issue is rarely addressed. Thus, we established a conceptual model that incorporated saturation theory into the microbiological domain to advance the understanding of mechanisms controlling soil bacterial diversity during forest secondary succession. Conceptual model hypotheses were tested by coupling soil bacterial diversity, local assembly processes and species pools using six different forest successional chronosequences distributed across multiple climate zones. Consistent with the unsaturated case proposed in our conceptual framework, we found that species pool consistently affected α-diversity, even while local assembly processes on local richness operate. In contrast, the effects of species pool on β-diversity disappeared once local assembly processes were taken into account, and changes in environmental conditions during secondary succession led to shifts in β-diversity through mediation of the strength of heterogeneous selection. Overall, this study represents one of the first to demonstrate that most local bacterial communities might be unsaturated, where the effect of species pool on α-diversity is robust to the consideration of multiple environmental influences, but β-diversity is constrained by environmental selection.},
}
@article {pmid38076468,
year = {2024},
author = {Nikita, R and Ghosh, A and Yash, and Kumar, C and Mandal, A and Saini, N and Dubey, SK and Gogoi, K and Rajts, F and Belton, B and Bhadury, P},
title = {Dataset of biological community structure in Deepor Beel using eDNA approach-A RAMSAR wetland of Assam, India.},
journal = {Data in brief},
volume = {52},
number = {},
pages = {109786},
pmid = {38076468},
issn = {2352-3409},
abstract = {Deepor Beel, located in the state of Assam in India, is a Wetland of International Importance with a Wildlife Sanctuary and is the only RAMSAR site in the state. Though of invaluable ecological significance, the wetland is facing anthropogenic stressors, leading to rapid degradation of ecological health. In December 2022, surface water was collected from six stations of Deepor Beel to elucidate biological communities using the eDNA approach. At the time of sampling, in-situ environmental parameters were measured in triplicates. The dissolved nutrients and concentrations of metals and metalloids were estimated using UV-Vis Spectrophotometry and ICP-MS approaches respectively. The study revealed a high concentration of dissolved nitrate in the surface water. High-throughput sequencing using Nanopore sequencing chemistry in a MinION platform indicated the overwhelming abundance of Moraxellaceae (Prokaryotes) and Eumetazoa (Eukaryotes). The abundance of Cyprinidae were also encountered in the studied wetland reflecting the biodiversity of fish populations. High nitrate along with elucidated microbial signals are crucial to designate ecological health status of Deeper Beel. This study is aimed at generating baseline information to aid long-term monitoring and restoration of the Deepor Beel as well as the first comprehensive assessment of a RAMSAR Site located in northeast of India.},
}
@article {pmid38075488,
year = {2024},
author = {Wang, X and Guo, K and Rabaey, K and Prévoteau, A},
title = {(Bio)electrochemistry for the environment, ready for ignition?.},
journal = {Environmental science and ecotechnology},
volume = {17},
number = {},
pages = {100336},
pmid = {38075488},
issn = {2666-4984},
}
@article {pmid38073168,
year = {2023},
author = {Kumar, G and Bhadury, P},
title = {Exploring the influences of geographical variation on sequence signatures in the human gut microbiome.},
journal = {Journal of genetics},
volume = {102},
number = {},
pages = {},
pmid = {38073168},
issn = {0973-7731},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Firmicutes/genetics ; Bacteroidetes/genetics ; Geography ; },
abstract = {Geography shapes the structure and function of human gut microbiomes. In this study, we have explored the available human gut microbiome 16S rRNA sequence datasets of cohorts representing large geographical gradients. The 16S rRNA sequences representing V3-V4 as well as V4 regions generated using Illumina sequencing chemistry in the MiSeq platform encompassing the United States of America, Chile, South Africa, Kuwait, and Malaysia were subjected to in-depth computational biology analyses. Firmicutes and Bacteroidetes were the most dominant phyla present in all studied cohorts but Actinobacteria was exclusively present in high abundance in cohorts from Malaysia (15.99%). The relative abundance of five families, namely Bacteroidaceae, Ruminococcaceae, Prevotellaceae, Clostridiaceae, and Eubacteriaceae were highest representing the studied cohorts. The permutational multivariate analysis of variance (PERMANOVA) showed that the dissimilarity in the gut microbiome structure of cohorts representing studied countries was significant (R[2] = 0.28, P<0.001). The calculated Firmicutes to Bacteroidetes (F : B) ratio was found to be lowest in cohorts from South Africa (1.11) and Chile (0.95). The cohorts from South Africa exhibited the highest alpha diversity based on Hill numbers at q=0, whereas at q=1 and 2, cohorts from Malaysia had the highest alpha diversity. The beta diversity analysis revealed that cohorts from Chile formed a distinct cluster among all the studied geographical locations. For the first time, the study also showed that cohorts from Malaysia representing short geographical distances exhibited distinct intrapopulation differences in the gut microbiome and may not be influenced by cultural and genetic factors.},
}
@article {pmid38072930,
year = {2023},
author = {Sakarika, M and Kerckhof, FM and Van Peteghem, L and Pereira, A and Van Den Bossche, T and Bouwmeester, R and Gabriels, R and Van Haver, D and Ulčar, B and Martens, L and Impens, F and Boon, N and Ganigué, R and Rabaey, K},
title = {The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions.},
journal = {Microbial cell factories},
volume = {22},
number = {1},
pages = {254},
pmid = {38072930},
issn = {1475-2859},
support = {CO2PERATE//Agentschap Innoveren en Ondernemen/ ; HBC.2019.2601//Agentschap Innoveren en Ondernemen/ ; HBC.2018.0188//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2205//Agentschap Innoveren en Ondernemen/ ; 1286824N//Fonds Wetenschappelijk Onderzoek/ ; 1S27821N//Fonds Wetenschappelijk Onderzoek/ ; BOF19/STA/044//Universiteit Gent/ ; },
mesh = {Biomass ; *Amino Acids ; *Proteome ; Cysteine ; Cell Size ; },
abstract = {BACKGROUND: It is increasingly recognized that conventional food production systems are not able to meet the globally increasing protein needs, resulting in overexploitation and depletion of resources, and environmental degradation. In this context, microbial biomass has emerged as a promising sustainable protein alternative. Nevertheless, often no consideration is given on the fact that the cultivation conditions affect the composition of microbial cells, and hence their quality and nutritional value. Apart from the properties and nutritional quality of the produced microbial food (ingredient), this can also impact its sustainability. To qualitatively assess these aspects, here, we investigated the link between substrate availability, growth rate, cell composition and size of Cupriavidus necator and Komagataella phaffii.<br><br>RESULTS: Biomass with decreased nucleic acid and increased protein content was produced at low growth rates. Conversely, high rates resulted in larger cells, which could enable more efficient biomass harvesting. The proteome allocation varied across the different growth rates, with more ribosomal proteins at higher rates, which could potentially affect the techno-functional properties of the biomass. Considering the distinct amino acid profiles established for the different cellular components, variations in their abundance impacts the product quality leading to higher cysteine and phenylalanine content at low growth rates. Therefore, we hint that costly external amino acid supplementations that are often required to meet the nutritional needs could be avoided by carefully applying conditions that enable targeted growth rates.<br><br>CONCLUSION: In summary, we demonstrate tradeoffs between nutritional quality and production rate, and we discuss the microbial biomass properties that vary according to the growth conditions.},
}
@article {pmid38072911,
year = {2023},
author = {Arnolds, KL and Higgins, RC and Crandall, J and Li, G and Linger, JG and Guarnieri, MT},
title = {Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {12},
pmid = {38072911},
issn = {1432-184X},
support = {DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; },
mesh = {*Ecosystem ; Saccharomyces cerevisiae/genetics ; Soil Microbiology ; *Microbiota ; Soil ; Risk Assessment ; },
abstract = {Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.},
}
@article {pmid38072409,
year = {2023},
author = {Ide, H and Ishii, K and Takahashi, Y and Fujitani, H and Tsuneda, S},
title = {Effects of Co-existing Heterotrophs on Physiology of and Nitrogen Metabolism in Autotrophic Nitrite-oxidizing Candidatus Nitrotoga.},
journal = {Microbes and environments},
volume = {38},
number = {4},
pages = {},
pmid = {38072409},
issn = {1347-4405},
mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Gallionellaceae/metabolism ; Nitrogen/metabolism ; },
abstract = {Interactions between autotrophic nitrifiers and heterotrophs have attracted considerable attention in microbial ecology. However, the mechanisms by which heterotrophs affect the physiological activity of and nitrogen metabolism in autotrophic nitrite oxidizers remain unclear. We herein focused on nitrite-oxidizing Candidatus Nitrotoga and compared an axenic culture including only Ca. Nitrotoga with a co-culture of both Ca. Nitrotoga and Acidovorax in physiological experiments and transcriptomics. In the co-culture with Acidovorax, nitrite consumption by Ca. Nitrotoga was promoted, and some genes relevant to nitrogen metabolism in Ca. Nitrotoga were highly expressed. These results provide insights into the mechanisms by which co-existing heterotrophs affect autotrophic nitrifiers.},
}
@article {pmid38070605,
year = {2024},
author = {Suman, J and Sredlova, K and Fraraccio, S and Jerabkova, M and Strejcek, M and Kabickova, H and Cajthaml, T and Uhlik, O},
title = {Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase.},
journal = {Chemosphere},
volume = {349},
number = {},
pages = {140909},
doi = {10.1016/j.chemosphere.2023.140909},
pmid = {38070605},
issn = {1879-1298},
mesh = {Animals ; *Polychlorinated Biphenyls/metabolism ; Hydroxylation ; Mixed Function Oxygenases/metabolism ; Bacteria/metabolism ; },
abstract = {Monohydroxylated PCBs (OH-PCBs) are an (eco)toxicologically significant group of compounds, as they arise from the oxidation of polychlorinated biphenyls (PCBs) and, at the same time, may exert even more severe toxic effects than their parent PCB molecules. Despite having been widely detected in environmental samples, plants, and animals, information on the fate of OH-PCBs in the environment is scarce, including on the enzymatic machinery behind their degradation. To date, only a few bacterial taxa capable of OH-PCB transformation have been reported. In this study, we aimed to obtain a deeper insight into the transformation of OH-PCBs in soil bacteria and isolated a Pseudomonas sp. strain P1B16 based on its ability to use o-phenylphenol (2-PP) which, when exposed to the Delor 103-derived OH-PCB mixture, depleted a wide spectrum of mono-, di, and trichlorinated OH-PCBs. In the P1B16 genome, a region designated as hbp was identified, which bears a set of putative genes involved in the transformation of OH-PCBs, namely hbpA encoding for a putative flavin-dependent 2-hydroxybiphenyl monooxygenase, hbpC (2,3-dihydroxybiphenyl-1,2-dioxygenase), hbpD (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase), and the transcriptional activator-encoding gene hbpR. The hbpA coding sequence was heterologously expressed, purified, and its substrate specificity was investigated towards the Delor 103-derived OH-PCB mixture, individual OH-PCBs, and multiple (chlorinated) phenolics. Apart from 2-PP and 2-chlorophenol, HbpA was also demonstrated to transform a range of OH-PCBs, including a 3-hydroxy-2,2',4',5,5'-pentachlorobiphenyl. Importantly, this is the first direct evidence of HbpA homologs being involved in the degradation of OH-PCBs. Moreover, using a P1B16-based biosensor strain, the specific induction of hbp genes by 2-PP, 3-phenylphenol, 4-phenylphenol, and the OH-PCB mixture was demonstrated. This study provides direct evidence on the specific enzymatic machinery responsible for the transformation of OH-PCBs in bacteria, with many implications in ecotoxicology, environmental restoration, and microbial ecology in habitats burdened with PCB contamination.},
}
@article {pmid38070053,
year = {2024},
author = {Deng, W and Bai, NE and Qi, FL and Yang, XY and She, R and Xiao, W},
title = {Temporal dynamics of the microbial heterogeneity-diversity relationship in microcosmic systems.},
journal = {Oecologia},
volume = {204},
number = {1},
pages = {35-46},
pmid = {38070053},
issn = {1432-1939},
support = {32371557//National Natural Science Foundation of China/ ; 2019QZKK2002//Second Tibetan Plateau Scientifc Expedition and Research Program/ ; },
mesh = {Animals ; *Biodiversity ; *Plants ; Ecosystem ; },
abstract = {Spatial heterogeneity significantly enhances biodiversity, representing one of the ecology's most enduring paradigms. However, many studies have found decreasing, humped, and neutral correlations between spatial heterogeneity and biodiversity (heterogeneity-diversity relationships, HDR). These findings have pushed this widely accepted theory back into controversy. Microbial HDR research has lagged compared to that of plants and animals. Nevertheless, microbes have features that add a temporal-scale perspective to HDR research that is critical to understanding patterns of HDR. In this study, 157 microcosms with different types spatial heterogeneity were set up to map the HDR of microorganisms and their temporal dynamics using high-throughput sequencing techniques. The results show that the following: 1. Spatial heterogeneity can significantly alter microbial diversity in microcosmic systems. Changes in microbial diversity, in turn, lead to changes in environmental conditions. These changes caused microorganisms to exhibit increasing, decreasing, humped, U-shaped, and neutral HDR patterns. 2. The emergence of HDR patterns is characterized by temporal dynamics. Additionally, the HDR patterns generated by spatial structural and compositional heterogeneity exhibit inconsistent emergence times. These results suggest that the temporal dynamics of HDR may be one of the reasons for the coexistence of multiple patterns in previous studies. The feedback regulation between spatial heterogeneity-biodiversity-environmental conditions is an essential reason for the temporally dynamics of HDR patterns. All future ecological studies should pay attention to the temporal dynamic patterns of ecological factors.},
}
@article {pmid38067489,
year = {2023},
author = {Singh, SK and Shrivastava, S and Mishra, AK and Kumar, D and Pandey, VK and Srivastava, P and Pradhan, B and Behera, BC and Bahuguna, A and Baek, KH},
title = {Friedelin: Structure, Biosynthesis, Extraction, and Its Potential Health Impact.},
journal = {Molecules (Basel, Switzerland)},
volume = {28},
number = {23},
pages = {},
pmid = {38067489},
issn = {1420-3049},
mesh = {Humans ; *Triterpenes/chemistry ; Anti-Inflammatory Agents ; Antioxidants/pharmacology ; Phytochemicals ; },
abstract = {Pharmaceutical companies are investigating more source matrices for natural bioactive chemicals. Friedelin (friedelan-3-one) is a pentacyclic triterpene isolated from various plant species from different families as well as mosses and lichen. The fundamental compounds of these friedelane triterpenoids are abundantly found in cork tissues and leaf materials of diverse plant genera such as Celastraceae, Asteraceae, Fabaceae, and Myrtaceae. They possess many pharmacological effects, including anti-inflammatory, antioxidant, anticancer, and antimicrobial activities. Friedelin also has an anti-insect effect and the ability to alter the soil microbial ecology, making it vital to agriculture. Ultrasound, microwave, supercritical fluid, ionic liquid, and acid hydrolysis extract friedelin with reduced environmental impact. Recently, the high demand for friedelin has led to the development of CRISPR/Cas9 technology and gene overexpression plasmids to produce friedelin using genetically engineered yeast. Friedelin with low cytotoxicity to normal cells can be the best phytochemical for the drug of choice. The review summarizes the structural interpretation, biosynthesis, physicochemical properties, quantification, and various forms of pharmacological significance.},
}
@article {pmid38067008,
year = {2023},
author = {Popov, IV and Berezinskaia, IS and Popov, IV and Martiusheva, IB and Tkacheva, EV and Gorobets, VE and Tikhmeneva, IA and Aleshukina, AV and Tverdokhlebova, TI and Chikindas, ML and Venema, K and Ermakov, AM},
title = {Cultivable Gut Microbiota in Synanthropic Bats: Shifts of Its Composition and Diversity Associated with Hibernation.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {23},
pages = {},
pmid = {38067008},
issn = {2076-2615},
support = {23-14-00316//Russian Science Foundation/ ; agreement 075-10-2021-093, Project [IMB-2102]//Ministry of Science and Higher Education of the Russian Federation/ ; K.V. was supported by the Dutch Province of Limburg with a grant to the Centre for Healthy Eating &amp; Food Innovation (HEFI) of Maastricht University-campus Venlo.//Centre for Healthy Eating &amp; Food Innovation (HEFI)/ ; },
abstract = {The role of bats in the global microbial ecology no doubt is significant due to their unique immune responses, ability to fly, and long lifespan, all contributing to pathogen spread. Some of these animals hibernate during winter, which results in the altering of their physiology. However, gut microbiota shifts during hibernation is little studied. In this research, we studied cultivable gut microbiota composition and diversity of Nyctalus noctula before, during, and after hibernation in a bat rehabilitation center. Gut microorganisms were isolated on a broad spectrum of culture media, counted, and identified with mass spectrometry. Linear modeling was used to investigate associations between microorganism abundance and N. noctula physiological status, and alpha- and beta-diversity indexes were used to explore diversity changes. As a result, most notable changes were observed in Serratia liquefaciens, Hafnia alvei, Staphylococcus sciuri, and Staphylococcus xylosus, which were significantly more highly abundant in hibernating bats, while Citrobacter freundii, Klebsiella oxytoca, Providencia rettgeri, Citrobacter braakii, and Pedicoccus pentosaceus were more abundant in active bats before hibernation. The alpha-diversity was the lowest in hibernating bats, while the beta-diversity differed significantly among all studied periods. Overall, this study shows that hibernation contributes to changes in bat cultivable gut microbiota composition and diversity.},
}
@article {pmid38066493,
year = {2023},
author = {Shuanglian, Y and Huiling, Z and Xunting, L and Yifang, D and Yufen, L and Shanshan, X and Lijuan, S and Yunpeng, L},
title = {Establishment and validation of early prediction model for hypertriglyceridemic severe acute pancreatitis.},
journal = {Lipids in health and disease},
volume = {22},
number = {1},
pages = {218},
pmid = {38066493},
issn = {1476-511X},
support = {3502Z20204007//Xiamen Key Programs of Medicine and Health/ ; 3502Z20199172//Xiamen Priority Programs of Medicine and Health/ ; 2023zsyyhlky-010//Nursing research Programs of Zhongshan Hospital Xiamen University/ ; },
mesh = {Humans ; *Pancreatitis/diagnosis ; Severity of Illness Index ; Acute Disease ; Ascites ; Retrospective Studies ; Prognosis ; Biomarkers ; C-Reactive Protein ; *Hypertriglyceridemia ; },
abstract = {BACKGROUND: The prevalence of hypertriglyceridaemia-induced acute pancreatitis (HTG-AP) is increasing due to improvements in living standards and dietary changes. However, currently, there is no clinical multifactor scoring system specific to HTG-AP. This study aimed to screen the predictors of HTG-SAP and combine several indicators to establish and validate a visual model for the early prediction of HTG-SAP.<br><br>METHODS: The clinical data of 266 patients with HTG-SAP were analysed. Patients were classified into severe (N&#x2009;=&#x2009;42) and non-severe (N&#x2009;=&#x2009;224) groups according to the Atlanta classification criteria. Several statistical analyses, including one-way analysis, least absolute shrinkage with selection operator (LASSO) regression model, and binary logistic regression analysis, were used to evaluate the data.<br><br>RESULTS: The univariate analysis showed that several factors showed no statistically significant differences, including the number of episodes of pancreatitis, abdominal pain score, and several blood diagnostic markers, such as lactate dehydrogenase (LDH), serum calcium (Ca[2+]), C-reactive protein (CRP), and the incidence of pleural effusion, between the two groups (P&#x2009;<&#x2009;0.000). LASSO regression analysis identified six candidate predictors: CRP, LDH, Ca[2+], procalcitonin (PCT), ascites, and Balthazar computed tomography grade. Binary logistic regression multivariate analysis showed that CRP, LDH, Ca[2+], and ascites were independent predictors of HTG-SAP, and the area under the curve (AUC) values were 0.886, 0.893, 0.872, and 0.850, respectively. The AUC of the newly established HTG-SAP model was 0.960 (95% confidence interval: 0.936-0.983), which was higher than that of the bedside index for severity in acute pancreatitis (BISAP) score, modified CT severity index, Ranson score, and Japanese severity score (JSS) CT grade (AUC: 0.794, 0.796, 0.894 and 0.764, respectively). The differences were significant (P&#x2009;<&#x2009;0.01), except for the JSS prognostic indicators (P&#x2009;=&#x2009;0.130). The Hosmer-Lemeshow test showed that the predictive results of the model were highly consistent with the actual situation (P&#x2009;>&#x2009;0.05). The decision curve analysis plot suggested that clinical intervention can benefit patients when the model predicts that they are at risk for developing HTG-SAP.<br><br>CONCLUSIONS: CRP, LDH, Ca[2+], and ascites are independent predictors of HTG-SAP. The prediction model constructed based on these indicators has a high accuracy, sensitivity, consistency, and practicability in predicting HTG-SAP.},
}
@article {pmid38065941,
year = {2023},
author = {Zhou, Y and Yang, Z and Liu, J and Li, X and Wang, X and Dai, C and Zhang, T and Carrión, VJ and Wei, Z and Cao, F and Delgado-Baquerizo, M and Li, X},
title = {Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {8126},
pmid = {38065941},
issn = {2041-1723},
mesh = {Soil ; *Microbiota ; *Fabaceae ; Arachis ; Rhizosphere ; Crop Production ; Soil Microbiology ; Plant Roots ; },
abstract = {It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.},
}
@article {pmid38063370,
year = {2024},
author = {Tamames, J and Jiménez-Lalana, D and Redondo, &#xc1; and Martínez-García, S and de Los Rios, A},
title = {In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day.},
journal = {Molecular ecology resources},
volume = {24},
number = {2},
pages = {e13909},
doi = {10.1111/1755-0998.13909},
pmid = {38063370},
issn = {1755-0998},
mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Spain ; },
abstract = {We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the-art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands. Also, we did a two-day sampling campaign of marine waters in which the results obtained on the first day guided the experimental design of the second day. We demonstrate that it is possible to generate metagenomic information in less than one day, making it feasible to obtain taxonomic and functional profiles fast and efficiently, even in field conditions. This capacity can be used in the further to perform real-time functional and taxonomic monitoring of microbial communities in remote areas.},
}
@article {pmid38060022,
year = {2023},
author = {Abu Bakar, N and Lau, BYC and González-Aravena, M and Smykla, J and Krzewicka, B and Karsani, SA and Alias, SA},
title = {Geographical Diversity of Proteomic Responses to Cold Stress in the Fungal Genus Pseudogymnoascus.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {11},
pmid = {38060022},
issn = {1432-184X},
support = {Postgraduate sponsorship//Majlis Amanah Rakyat/ ; HICoE grant (IOES-2014G)//Ministry of Higher Education, Malaysia/ ; UMRP (RP026A-18SUS)//Universiti Malaya/ ; },
mesh = {*Cold-Shock Response ; Proteomics ; *Ascomycota ; Soil Microbiology ; Soil ; Antarctic Regions ; Cold Temperature ; },
abstract = {In understanding stress response mechanisms in fungi, cold stress has received less attention than heat stress. However, cold stress has shown its importance in various research fields. The following study examined the cold stress response of six Pseudogymnoascus spp. isolated from various biogeographical regions through a proteomic approach. In total, 2541 proteins were identified with high confidence. Gene Ontology enrichment analysis showed diversity in the cold stress response pathways for all six Pseudogymnoascus spp. isolates, with metabolic and translation-related processes being prominent in most isolates. 25.6% of the proteins with an increase in relative abundance were increased by more than 3.0-fold. There was no link between the geographical origin of the isolates and the cold stress response of Pseudogymnoascus spp. However, one Antarctic isolate, sp3, showed a distinctive cold stress response profile involving increased flavin/riboflavin biosynthesis and methane metabolism. This Antarctic isolate (sp3) was also the only one that showed decreased phospholipid metabolism in cold stress conditions. This work will improve our understanding of the mechanisms of cold stress response and adaptation in psychrotolerant soil microfungi, with specific attention to the fungal genus Pseudogymnoascus.},
}
@article {pmid38059790,
year = {2023},
author = {Martinez-Gutierrez, CA and Uyeda, JC and Aylward, FO},
title = {A timeline of bacterial and archaeal diversification in the ocean.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {38059790},
issn = {2050-084X},
support = {IIBR-2141862//National Science Foundation/ ; Early Career Award in Marine Microbial Ecology and Evolution//Simons Foundation/ ; },
mesh = {*Archaea/genetics ; Phylogeny ; *Cyanobacteria ; Oxygen ; Oceans and Seas ; Seawater/microbiology ; },
abstract = {Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.},
}
@article {pmid38057381,
year = {2023},
author = {Oliveira, FR and Lansac-Tôha, FM and Meira, BR and Progênio, M and Velho, LFM},
title = {Influence of Ecological Multiparameters on Facets of β-Diversity of Freshwater Plankton Ciliates.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {10},
pmid = {38057381},
issn = {1432-184X},
mesh = {*Ecosystem ; Plankton ; Phylogeny ; Fresh Water ; Biodiversity ; *Ciliophora ; Water ; },
abstract = {Understanding the relative importance of the factors that drive global patterns of biodiversity is among the major topics of ecological and biogeographic research. In freshwater bodies, spatial, temporal, abiotic, and biotic factors are important structurers of these ecosystems and can trigger distinct responses according to the facet of biodiversity considered. The objective was to evaluate how different facets of β-diversity (taxonomic, functional, and phylogenetic) based on data from the planktonic ciliate community of a Neotropical floodplain, are influenced by temporal, spatial, abiotic, and biotic factors. The research was conducted in the upper Paraná River floodplain between the years 2010 and 2020 in different water bodies. All predictors showed significant importance on the facets of β-diversity, except the abiotic predictors on species composition data, for the taxonomic facet. The functional and phylogenetic facets were mostly influenced by abiotic, biotic, and spatial factors. For temporal predictors, results showed influence on taxonomic (structure and composition data) and functional (structure data) facets. Also, a fraction of shared explanation between the temporal and abiotic components was observed for the distinct facets. Significant declines in β-diversity in continental ecosystems have been evidenced, especially those with drastic implications for ecosystemic services. Therefore, the preservation of a high level of diversity in water bodies, also involving phylogenetic and functional facets, should be a priority in conservation plans and goals, to ensure the maintenance of important ecological processes involving ciliates.},
}
@article {pmid38055943,
year = {2023},
author = {Rodríguez, MA and Fernández, LA and Daisley, BA and Reynaldi, FJ and Allen-Vercoe, E and Thompson, GJ},
title = {Probiotics and in-hive fermentation as a source of beneficial microbes to support the gut microbial health of honey bees.},
journal = {Journal of insect science (Online)},
volume = {23},
number = {6},
pages = {},
pmid = {38055943},
issn = {1536-2442},
support = {//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas Buenos Aires/ ; //Global Affairs Canada Emerging Leaders/ ; //Americas Scholarship Program/ ; //Mar&#xed;a Agustina Rodr&#xed;guez/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Anti-Bacterial Agents/immunology/pharmacology/therapeutic use ; *Beekeeping/methods ; *Bees/drug effects/immunology/microbiology ; *Fermentation/immunology ; *Gastrointestinal Microbiome/immunology ; *Probiotics/pharmacology/therapeutic use ; },
abstract = {Managed populations of honey bees (Apis mellifera Linnaeus; Hymenoptera: Apidae) are regularly exposed to infectious diseases. Good hive management including the occasional application of antibiotics can help mitigate infectious outbreaks, but new beekeeping tools and techniques that bolster immunity and help control disease transmission are welcome. In this review, we focus on the applications of beneficial microbes for disease management as well as to support hive health and sustainability within the apicultural industry. We draw attention to the latest advances in probiotic approaches as well as the integration of fermented foods (such as water kefir) with disease-fighting properties that might ultimately be delivered to hives as an alternative or partial antidote to antibiotics. There is substantial evidence from in vitro laboratory studies that suggest beneficial microbes could be an effective method for improving disease resistance in honey bees. However, colony level evidence is lacking and there is urgent need for further validation via controlled field trials experimentally designed to test defined microbial compositions against specific diseases of interest.},
}
@article {pmid38054947,
year = {2024},
author = {Knight, T and Sureka, S},
title = {A New Paradigm for Threat Agnostic Biodetection: Biological Intelligence (BIOINT).},
journal = {Health security},
volume = {22},
number = {1},
pages = {31-38},
pmid = {38054947},
issn = {2326-5108},
mesh = {Humans ; *Intelligence ; },
}
@article {pmid38054712,
year = {2024},
author = {Schloss, PD},
title = {Waste not, want not: revisiting the analysis that called into question the practice of rarefaction.},
journal = {mSphere},
volume = {9},
number = {1},
pages = {e0035523},
pmid = {38054712},
issn = {2379-5042},
support = {R01 CA215574/CA/NCI NIH HHS/United States ; U01 CA264071/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Computer Simulation ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {In 2014, McMurdie and Holmes published the provocatively titled "Waste not, want not: why rarefying microbiome data is inadmissible." The claims of their study have significantly altered how microbiome researchers control for the unavoidable uneven sequencing depths that are inherent in modern 16S rRNA gene sequencing. Confusion over the distinction between the definitions of rarefying and rarefaction continues to cloud the interpretation of their results. More importantly, the authors made a variety of problematic choices when designing and analyzing their simulations. I identified 11 factors that could have compromised the results of the original study. I reproduced the original simulation results and assessed the impact of those factors on the underlying conclusion that rarefying data is inadmissible. Throughout, the design of the original study made choices that caused rarefying and rarefaction to appear to perform worse than they truly did. Most important were the approaches used to assess ecological distances, the removal of samples with low sequencing depth, and not accounting for conditions where sequencing effort is confounded with treatment group. Although the original study criticized rarefying for the arbitrary removal of valid data, repeatedly rarefying data many times (i.e., rarefaction) incorporates all the data. In contrast, it is the removal of rare taxa that would appear to remove valid data. Overall, I show that rarefaction is the most robust approach to control for uneven sequencing effort when considered across a variety of alpha and beta diversity metrics.IMPORTANCEOver the past 10 years, the best method for normalizing the sequencing depth of samples characterized by 16S rRNA gene sequencing has been contentious. An often cited article by McMurdie and Holmes forcefully argued that rarefying the number of sequence counts was "inadmissible" and should not be employed. However, I identified a number of problems with the design of their simulations and analysis that compromised their results. In fact, when I reproduced and expanded upon their analysis, it was clear that rarefaction was actually the most robust approach for controlling for uneven sequencing effort across samples. Rarefaction limits the rate of falsely detecting and rejecting differences between treatment groups. Far from being "inadmissible", rarefaction is a valuable tool for analyzing microbiome sequence data.},
}
@article {pmid38054526,
year = {2023},
author = {Altaisaikhan, A and Yoshihara, K and Hata, T and Miyata, N and Asano, Y and Suematsu, T and Kadota, Y and Sudo, N},
title = {Dietary supplementation with 1-kestose induces altered locomotor activity and increased striatal dopamine levels with a change in gut microbiota in male mice.},
journal = {Physiological reports},
volume = {11},
number = {23},
pages = {e15882},
pmid = {38054526},
issn = {2051-817X},
support = {JP20H04106//KAKENHI/ ; JP23K18276//KAKENHI/ ; 2020-192//Smoking Research Foundation (SRF)/ ; },
mesh = {Mice ; Animals ; Male ; *Dopamine ; *Gastrointestinal Microbiome ; Trisaccharides ; Prebiotics ; },
abstract = {1-Kestose (KES), a dietary fiber and prebiotic carbohydrate, benefits various physiological functions. This study aimed to examine whether diets supplemented with KES over three consecutive generations could significantly affect some host physiological aspects, including behavioral phenotypes and gut microbial ecology. Mice that received KES-supplemented diets for three generations demonstrated increased activity compared with those fed diets lacking KES. Furthermore, the KES group showed increased striatal dopamine (DA) and serotonin (5-HT) levels. The observed increase in DA levels within the striatum was positively correlated with locomotor activity in the KES group but not in the control (CON) group. The α-diversities were significantly lower in the KES group compared to the CON group. The three-dimensional principal coordinate analysis revealed a substantial distinction between the KES and CON groups across each generation. At the genus level, most gut microbiota genera exhibited lower abundances in the KES group than in the CON group, except for Bifidobacteria and Akkermansia. Spearman's rank-order analysis indicated significant negative correlations between the striatal DA levels and α-diversity values. These findings suggest that prolonged supplementation with KES may stimulate increased locomotor activity along with elevated striatal DA levels, which are potentially associated with KES-induced alterations in the gut microbiota.},
}
@article {pmid38053549,
year = {2023},
author = {Song, W and Li, H and Zhou, Y and Liu, X and Li, Y and Wang, M and Li, DD and Tu, Q},
title = {Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1291242},
pmid = {38053549},
issn = {1664-302X},
abstract = {A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.},
}
@article {pmid38053159,
year = {2023},
author = {Costa, LSAS and de Faria, MR and Chiaramonte, JB and Mendes, LW and Sepo, E and de Hollander, M and Fernandes, JMC and Carrión, VJ and Bettiol, W and Mauchline, TH and Raaijmakers, JM and Mendes, R},
title = {Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {85},
pmid = {38053159},
issn = {2524-6372},
support = {BB/N016246/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X010953/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen.<br><br>RESULTS: The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides.<br><br>CONCLUSION: Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.},
}
@article {pmid38049781,
year = {2023},
author = {Thapa, S and Zhou, S and O'Hair, J and Al Nasr, K and Ropelewski, A and Li, H},
title = {Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach.},
journal = {BMC biotechnology},
volume = {23},
number = {1},
pages = {51},
pmid = {38049781},
issn = {1472-6750},
support = {2018-38821-27737//USDA-NIFA/ ; 2018-38821-27737//USDA-NIFA/ ; 2018-38821-27737//USDA-NIFA/ ; OCI 1053575//NSF/ ; },
mesh = {Animals ; *Cellulase/metabolism ; Metagenome ; Goats/genetics/metabolism/microbiology ; Rumen/metabolism/microbiology ; Escherichia coli/genetics ; Bacteria ; *Cellulases/genetics ; Cellulose ; },
abstract = {BACKGROUND: Goat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis of cellulose and hemi-cellulose into fermentable sugar for biofuel and other value-added biochemical production. Even though, the limited understanding of rumen microbial genetic diversity and the absence of effective screening culture methods have impeded the full utilization of these potential enzymes. In this study, we applied culture independent metagenomics sequencing approach to isolate, and identify microbial communities in goat rumen, meanwhile, clone and functionally characterize novel cellulase and xylanase genes in goat rumen bacterial communities.<br><br>RESULTS: Bacterial DNA samples were extracted from goat rumen fluid. Three genomic libraries were sequenced using Illumina HiSeq 2000 for paired-end 100-bp (PE100) and Illumina HiSeq 2500 for paired-end 125-bp (PE125). A total of 435gb raw reads were generated. Taxonomic analysis using Graphlan revealed that Fibrobacter, Prevotella, and Ruminococcus are the most abundant genera of bacteria in goat rumen. SPAdes assembly and prodigal annotation were performed. The contigs were also annotated using the DOE-JGI pipeline. In total, 117,502 CAZymes, comprising endoglucanases, exoglucanases, beta-glucosidases, xylosidases, and xylanases, were detected in all three samples. Two genes with predicted cellulolytic/xylanolytic activities were cloned and expressed in E. coli BL21(DE3). The endoglucanases and xylanase enzymatic activities of the recombinant proteins were confirmed using substrate plate assay and dinitrosalicylic acid (DNS) analysis. The 3D structures of endoglucanase A and endo-1,4-beta xylanase was predicted using the Swiss Model. Based on the 3D structure analysis, the two enzymes isolated from goat's rumen metagenome are unique with only 56-59% similarities to those homologous proteins in protein data bank (PDB) meanwhile, the structures of the enzymes also displayed greater stability, and higher catalytic activity.<br><br>CONCLUSIONS: In summary, this study provided the database resources of bacterial metagenomes from goat's rumen fluid, including gene sequences with annotated functions and methods for gene isolation and over-expression of cellulolytic enzymes; and a wealth of genes in the metabolic pathways affecting food and nutrition of ruminant animals.},
}
@article {pmid38047964,
year = {2023},
author = {Guo, D and Ge, J and Tang, Z and Tian, B and Li, W and Li, C and Xu, L and Luo, J},
title = {Dynamic Gut Microbiota of Apolygus lucorum Across Different Life Stages Reveals Potential Pathogenic Bacteria for Facilitating the Pest Management.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {9},
pmid = {38047964},
issn = {1432-184X},
mesh = {Adult ; Animals ; Humans ; *Gastrointestinal Microbiome ; Firmicutes ; Proteobacteria ; China ; Nymph ; Serratia/genetics ; },
abstract = {Insect's gut microbiota has diverse effects on their fitness, and a comprehensive understanding of gut microbiota functions requires analyzing its diversity. Apolygus lucorum is a highly destructive pest that threatens many economically important crops in China. This study investigated the gut microbiota of A. lucorum across its life cycle using both culture-dependent and culture-independent methods. A total of 87 gut bacterial isolates were identified, belonging to 4 phyla, 27 families, and 45 genera, while Miseq sequencing detected 91 amplicon sequence variants (ASVs) assigned to 5 phyla, 28 families, and 39 genera. Proteobacteria and Firmicutes were the predominant phyla, with Staphylococcus and Serratia as the major genera. There were significant differences in the relative abundance of these genera between the nymph and adult stages. Staphylococcus was significantly more abundant in nymphs than it in adults, while Serratia was significantly more abundant in sexually mature adults than in other developmental stages. Notably, Serratia is a common opportunistic pathogen in many insects. Injecting the gut-dominant isolate Serratia marcescens verified its high pathogenicity. Additionally, immune indicators of the bug at different developmental stages supported the hypothesis that Serratia is a pathogen of A. lucorum. This study provides a foundation for understanding the role of gut bacteria in the life history of A. lucorum and developing new pest control strategies based on microbes.},
}
@article {pmid38047636,
year = {2023},
author = {Hill, MS and Gilbert, JA},
title = {Microbiology of the built environment: harnessing human-associated built environment research to inform the study and design of animal nests and enclosures.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {87},
number = {4},
pages = {e0012121},
pmid = {38047636},
issn = {1098-5557},
mesh = {Animals ; Humans ; *Built Environment ; *Environmental Microbiology ; },
abstract = {SUMMARYOver the past decade, hundreds of studies have characterized the microbial communities found in human-associated built environments (BEs). These have focused primarily on how the design and use of our built spaces have shaped human-microbe interactions and how the differential selection of certain taxa or genetic traits has influenced health outcomes. It is now known that the more removed humans are from the natural environment, the greater the risk for the development of autoimmune and allergic diseases, and that indoor spaces can be harsh, selective environments that can increase the emergence of antimicrobial-resistant and virulent phenotypes in surface-bound communities. However, despite the abundance of research that now points to the importance of BEs in determining human-microbe interactions, only a fraction of non-human animal structures have been comparatively explored. It is here, in the context of human-associated BE research, that we consider the microbial ecology of animal-built natural nests and burrows, as well as artificial enclosures, and point to areas of primary interest for future research.},
}
@article {pmid38047236,
year = {2023},
author = {Lupatelli, CA and Attard, A and Kuhn, ML and Cohen, C and Thomen, P and Noblin, X and Galiana, E},
title = {Automated high-content image-based characterization of microorganism behavioral diversity and distribution.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {5640-5649},
pmid = {38047236},
issn = {2001-0370},
abstract = {Microorganisms have evolved complex systems to respond to environmental signals. Gradients of particular molecules and elemental ions alter the behavior of microbes and their distribution within their environment. Microdevices coupled with automated image-based methods are now employed to analyze the instantaneous distribution and motion behaviors of microbial species in controlled environments at small temporal scales, mimicking, to some extent, macro conditions. Such technologies have so far been adopted for investigations mainly on individual species. Similar versatile approaches must now be developed for the characterization of multiple and complex interactions between a microbial community and its environment. Here, we provide a comprehensive step-by-step method for the characterization of species-specific behavior in a synthetic mixed microbial suspension in response to an environmental driver. By coupling accessible microfluidic devices with automated image analysis approaches, we evaluated the behavioral response of three morphologically different telluric species (Phytophthora parasitica, Vorticella microstoma, Enterobacter aerogenes) to a potassium gradient driver. Using the TrackMate plug-in algorithm, we performed morphometric and then motion analyses to characterize the response of each microbial species to the driver. Such an approach enabled to confirm the different morphological features of the three species and simultaneously characterize their specific motion in reaction to the driver and their co-interaction dynamics. By increasing the complexity of suspensions, this approach could be integrated in a framework for phenotypic analysis in microbial ecology research, helping to characterize how key drivers influence microbiota assembly at microbiota host-environment interfaces.},
}
@article {pmid38042956,
year = {2023},
author = {Alfonso, S and Mente, E and Fiocchi, E and Manfrin, A and Dimitroglou, A and Papaharisis, L and Barkas, D and Toomey, L and Boscarato, M and Losasso, C and Peruzzo, A and Stefani, A and Zupa, W and Spedicato, MT and Nengas, I and Lembo, G and Carbonara, P},
title = {Growth performance, gut microbiota composition, health and welfare of European sea bass (Dicentrarchus labrax) fed an environmentally and economically sustainable low marine protein diet in sea cages.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {21269},
pmid = {38042956},
issn = {2045-2322},
support = {Grant no. 817737//European Union's Horizon 2020 research and innovation programme/ ; },
mesh = {Animals ; *Bass/metabolism ; *Gastrointestinal Microbiome ; Diet ; Fish Oils/metabolism ; Fatty Acids/metabolism ; Diet, Protein-Restricted ; Animal Feed/analysis ; },
abstract = {The large use of fish meal/fish oil in carnivorous fish feeds is the main concern regarding environmental sustainability of aquaculture. Here, we evaluated the effects of an innovative diet, designed to be (1) environmentally sustainable by lowering the marine protein content while being (2) cost effective by using sustainable alternative raw materials with acceptable cost and produced on an industrial scale, on growth performance, gut microbiota composition, health and welfare of European sea bass (Dicentrarchus labrax), a key species of the Mediterranean marine aquaculture, reared in sea cages. Results show that the specific growth rate of fish fed the low marine protein diet was significantly lower than those fed conventional diet (0.67% vs 0.69%). Fatty acid profile of fillets from fish fed a low marine protein diet presented significant lower n-6 and higher n-3 content when compared to conventional ones. Then, a significant increase in the abundance of Vibrio and reduction of Photobacterium were found in the gut of fish fed with the low marine protein diet but effects on sea bass health needs further investigation. Finally, no major health and welfare alterations for fish fed the low marine protein diet were observed, combined with a potential slight benefit related to humoral immunity. Overall, these results suggest that despite the low marine protein diet moderately affects growth performance, it nevertheless may enhance environmental and economic sustainability of the sea bass aquaculture.},
}
@article {pmid38040657,
year = {2023},
author = {Baril, X and Constant, P},
title = {Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {12},
pages = {},
pmid = {38040657},
issn = {1574-6941},
support = {RGPIN-2018-05262//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Carbon/metabolism ; *Hydrogenase/genetics/metabolism ; Oxidation-Reduction ; Soil ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Hydrogen/metabolism ; Bacteria ; *Microbiota ; Cellulose/metabolism ; Sucrose/metabolism ; },
abstract = {High-affinity H2-oxidizing bacteria (HA-HOB) thriving in soil are responsible for the most important sink of atmospheric H2. Their activity increases with soil organic carbon content, but the incidence of different carbohydrate fractions on the process has received little attention. Here we tested the hypothesis that carbon amendments impact HA-HOB activity and diversity differentially depending on their recalcitrance and their concentration. Carbon sources (sucrose, starch, cellulose) and application doses (0, 0.1, 1, 3, 5% Ceq soildw-1) were manipulated in soil microcosms. Only 0.1% Ceq soildw-1 cellulose treatment stimulated the HA-HOB activity. Sucrose amendments induced the most significant changes, with an abatement of 50% activity at 1% Ceq soildw-1. This was accompanied with a loss of bacterial and fungal alpha diversity and a reduction of high-affinity group 1 h/5 [NiFe]-hydrogenase gene (hhyL) abundance. A quantitative classification framework was elaborated to assign carbon preference traits to 16S rRNA gene, ITS and hhyL genotypes. The response was uneven at the taxonomic level, making carbon preference a difficult trait to predict. Overall, the results suggest that HA-HOB activity is more susceptible to be stimulated by low doses of recalcitrant carbon, while labile carbon-rich environment is an unfavorable niche for HA-HOB, inducing catabolic repression of hydrogenase.},
}
@article {pmid38038797,
year = {2024},
author = {Mustaq, S and Moin, A and Pandit, B and Tiwary, BK and Alam, M},
title = {Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications.},
journal = {Folia microbiologica},
volume = {69},
number = {1},
pages = {17-32},
pmid = {38038797},
issn = {1874-9356},
mesh = {Humans ; *Phyllobacteriaceae/genetics ; Phylogeny ; Bacteria/genetics ; *Fabaceae/microbiology ; Nitrogen/metabolism ; DNA, Bacterial/metabolism ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; },
abstract = {The family Phyllobacteriaceae is a heterogeneous assemblage of more than 146 species of bacteria assigned to its existing 18 genera. Phylogenetic analyses have shown great phylogenetic diversity and also suggested about incorrect classification of several species that need to be reassessed for their proper phylogenetic classification. However, almost 50% of the family members belong to the genus Mesorhizobium only, of which the majority are symbiotic nitrogen fixers associated with different legumes. Other major genera are Phyllobacterium, Nitratireductor, Aquamicrobium, and Aminobacter. Nitrogen-fixing, legume nodulating members are present in Aminobacter and Phyllobacterium as well. Aquamicrobium spp. can degrade environmental pollutants, like 2,4-dichlorophenol, 4-chloro-2-methylphenol, and 4-chlorophenol. Chelativorans, Pseudaminobacter, Aquibium, and Oricola are the other genera that contain multiple species having diverse metabolic capacities, the rest being single-membered genera isolated from varied environments. In addition, heavy metal and antibiotic resistance, chemolithoautotrophy, poly-β-hydroxybutyrate storage, cellulase production, etc., are the other notable characteristics of some of the family members. In this report, we have comprehensively reviewed each of the species of the family Phyllobacteriaceae in their eco-physiological aspects and found that the family is rich with ecologically and metabolically highly diverse bacteria having great potential for human welfare and environmental clean-up.},
}
@article {pmid38036921,
year = {2023},
author = {Gallardo-Becerra, L and Cervantes-Echeverría, M and Cornejo-Granados, F and Vazquez-Morado, LE and Ochoa-Leyva, A},
title = {Perspectives in Searching Antimicrobial Peptides (AMPs) Produced by the Microbiota.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {8},
pmid = {38036921},
issn = {1432-184X},
support = {Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; },
mesh = {Humans ; *Antimicrobial Cationic Peptides/genetics/pharmacology ; Antimicrobial Peptides ; Bacteria/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; },
abstract = {Changes in the structure and function of the microbiota are associated with various human diseases. These microbial changes can be mediated by antimicrobial peptides (AMPs), small peptides produced by the host and their microbiota, which play a crucial role in host-bacteria co-evolution. Thus, by studying AMPs produced by the microbiota (microbial AMPs), we can better understand the interactions between host and bacteria in microbiome homeostasis. Additionally, microbial AMPs are a new source of compounds against pathogenic and multi-resistant bacteria. Further, the growing accessibility to metagenomic and metatranscriptomic datasets presents an opportunity to discover new microbial AMPs. This review examines the structural properties of microbiota-derived AMPs, their molecular action mechanisms, genomic organization, and strategies for their identification in any microbiome data as well as experimental testing. Overall, we provided a comprehensive overview of this important topic from the microbial perspective.},
}
@article {pmid38036897,
year = {2023},
author = {Hernández-Pelegrín, L and Ros, VID and Herrero, S and Crava, CM},
title = {Non-retroviral Endogenous Viral Elements in Tephritid Fruit Flies Reveal Former Viral Infections Not Related to Known Circulating Viruses.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {7},
pmid = {38036897},
issn = {1432-184X},
mesh = {Animals ; RNA, Small Interfering/genetics/metabolism ; *Viruses/genetics ; *RNA Viruses/genetics ; *Virus Diseases ; *Diptera ; },
abstract = {A wide variety of insect-specific non-retroviral RNA viruses specifically infect insects. During viral infection, fragments of viral sequences can integrate into the host genomes creating non-retroviral endogenous viral elements (nrEVEs). Although the exact function of nrEVEs is so far unknown, some studies suggest that nrEVEs may interfere with virus replication by producing PIWI-interacting RNAs (piRNAs) that recognize and degrade viral RNAs through sequence complementarity. In this article, we identified the nrEVEs repertoire of ten species within the dipteran family Tephritidae (true fruit flies), which are considered a major threat to agriculture worldwide. Our results suggest that each of these species contains nrEVEs, although in limited numbers, and that nrEVE integration may have occurred both before and after speciation. Furthermore, the majority of nrEVEs originated from viruses with negative single-stranded RNA genomes and represent structural viral functions. Notably, these nrEVEs exhibit low similarity to currently known circulating viruses. To explore the potential role of nrEVEs, we investigated their transcription pattern and the production of piRNAs in different tissues of Ceratitis capitata. We successfully identified piRNAs that are complementary to the sequence of one nrEVE in C. capitata, thereby highlighting a potential link between nrEVEs and the piRNA pathway. Overall, our results provide valuable insights into the comparative landscape of nrEVEs in true fruit flies, contributing to the understanding of the intimate relation between fruit flies and their past and present viral pathogens.},
}
@article {pmid38033596,
year = {2023},
author = {Zhang, M and Kong, Z and Fu, H and Shu, X and Xue, Q and Lai, H and Guo, Q},
title = {Rhizosphere microbial ecological characteristics of strawberry root rot.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1286740},
pmid = {38033596},
issn = {1664-302X},
abstract = {INTRODUCTION: Strawberry (Fragaria × ananassa Duch.) holds a preeminent position among small fruits globally due to its delectable fruits and significant economic value. However, strawberry cultivation is hampered by various plant diseases, hindering the sustainable development of the strawberry industry. The occurrence of plant diseases is closely linked to imbalance in rhizosphere microbial community structure.<br><br>METHODS: In the present study, a systematic analysis of the differences and correlations among non-culturable microorganisms, cultivable microbial communities, and soil nutrients in rhizosphere soil, root surface soil, and non-rhizosphere soil of healthy and diseased strawberry plants affected by root rot was conducted. The goal was to explore the relationship between strawberry root rot occurrence and rhizosphere microbial community structure.<br><br>RESULTS: According to the results, strawberry root rot altered microbial community diversity, influenced fungal community composition in strawberry roots, reduced microbial interaction network stability, and enriched more endophytic-phytopathogenic bacteria and saprophytic bacteria. In addition, the number of bacteria isolated from the root surface soil of diseased plants was significantly higher than that of healthy plants.<br><br>DISCUSSION: In summary, the diseased strawberry plants changed microbial community diversity, fungal species composition, and enriched functional microorganisms significantly, in addition to reshaping the microbial co-occurrence network. The results provide a theoretical basis for revealing the microecological mechanism of strawberry root rot and the ecological prevention and control of strawberry root rot from a microbial ecology perspective.},
}
@article {pmid38033562,
year = {2023},
author = {Farmer, M and Rajasabhai, R and Tarpeh, W and Tyo, K and Wells, G},
title = {Meta-omic profiling reveals ubiquity of genes encoding for the nitrogen-rich biopolymer cyanophycin in activated sludge microbiomes.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1287491},
pmid = {38033562},
issn = {1664-302X},
abstract = {Recovering nitrogen (N) from municipal wastewater is a promising approach to prevent nutrient pollution, reduce energy use, and transition toward a circular N bioeconomy, but remains a technologically challenging endeavor. Existing N recovery techniques are optimized for high-strength, low-volume wastewater. Therefore, developing methods to concentrate dilute N from mainstream wastewater will bridge the gap between existing technologies and practical implementation. The N-rich biopolymer cyanophycin is a promising candidate for N bioconcentration due to its pH-tunable solubility characteristics and potential for high levels of accumulation. However, the cyanophycin synthesis pathway is poorly explored in engineered microbiomes. In this study, we analyzed over 3,700 publicly available metagenome assembled genomes (MAGs) and found that the cyanophycin synthesis gene cphA was ubiquitous across common activated sludge bacteria. We found that cphA was present in common phosphorus accumulating organisms (PAO) Ca. 'Accumulibacter' and Tetrasphaera, suggesting potential for simultaneous N and P bioconcentration in the same organisms. Using metatranscriptomic data, we confirmed the expression of cphA in lab-scale bioreactors enriched with PAO. Our findings suggest that cyanophycin synthesis is a ubiquitous metabolic activity in activated sludge microbiomes. The possibility of combined N and P bioconcentration could lower barriers to entry for N recovery, since P concentration by PAO is already a widespread biotechnology in municipal wastewater treatment. We anticipate this work to be a starting point for future evaluations of combined N and P bioaccumulation, with the ultimate goal of advancing widespread adoption of N recovery from municipal wastewater.},
}
@article {pmid38030916,
year = {2023},
author = {Mlewski, EC and Saona, LA and Boidi, FJ and Chiappero, MF and Vaieretti, MV and Soria, M and Farías, ME and Izquierdo, AE},
title = {Exploring Soil Bacterial Diversity in Relation to Edaphic Physicochemical Properties of High-altitude Wetlands from Argentine Puna.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {6},
pmid = {38030916},
issn = {1432-184X},
support = {PICT 2018-4129//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; },
mesh = {Humans ; *Ecosystem ; Wetlands ; Soil/chemistry ; Altitude ; Bacteria/genetics ; *Microbiota ; Soil Microbiology ; },
abstract = {High Andean wetlands, particularly those known as vegas or bofedales, are essential conservation ecosystems due to their significant contribution to ecosystem services. The soil microbial communities in these ecosystems play a crucial role in fundamental processes such as decomposition and nutrient cycling, sustaining life in the region. However, at present, these microbial communities are poorly understood. In order to contribute to this knowledge, we aimed to characterize and compare the microbial communities from soils of seven Argentine Puna vegas and to analyze their association with soil physicochemical characteristics. Proteobacteria (Gamma and Alphaproteobacteria) was the dominant phylum across all vegas, followed in abundance by Actinobacteriota, Desulfobacterota, and Chloroflexi. Furthermore, the abundance of specific bacterial families and genera varied significantly between the vegas; some of them can be associated with plant growth-promoting bacteria such as Rhodomicrobium in La Quebradita and Quebrada del Diablo, Bacillus in Antofalla and Las Quinuas. Laguna Negra showed no shared ASVs with abundance in genera such as Sphingomonas and Pseudonocardia. The studied vegas also differed in their soil physicochemical properties; however, associations between the composition of microbial communities with the edaphic parameters measured were not found. These results suggest that other environmental factors (e.g., geographic, climatic, and plant communities' characteristics) could determine soil microbial diversity patterns. Further investigations are needed to be focused on understanding the composition and function of microorganisms in the soil associated with specific vegetation types in these high-altitude wetlands, which will provide valuable insights into the ecological dynamics of these ecosystems for conservation strategies.},
}
@article {pmid38030815,
year = {2023},
author = {Zhang, N and Zhu, W and Zhang, S and Liu, T and Gong, L and Wang, Z and Zhang, W and Cui, Y and Wu, Q and Li, J and Yu, H and El-Omar, EM and Hao, J and Lu, W},
title = {A Novel Bifidobacterium/Klebsiella Ratio in Characterization Analysis of the Gut and Bile Microbiota of CCA Patients.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {5},
pmid = {38030815},
issn = {1432-184X},
mesh = {Humans ; Bifidobacterium/genetics ; Klebsiella/genetics ; RNA, Ribosomal, 16S/genetics ; Bile ; *Gastrointestinal Microbiome ; *Microbiota ; Firmicutes/genetics ; Bacteroidetes/genetics ; Feces/microbiology ; },
abstract = {Cholangiocarcinoma (CCA) is a serious health problem worldwide. The gut and bile microbiota have not been clearly characterized in patients with CCA, and better noninvasive diagnostic approaches for CCA need to be established. The aim of this study was to investigate the characteristics of the gut and bile microbiota in CCA patients. Forty-two CCA patients and 16 healthy normal controls (HNCs) were enrolled. DNA was extracted from fecal and bile samples and subjected to 16S rRNA gene analysis. We found that there were significant differences in the species diversity, structure, and composition of the microbial communities between the CCA group and the HNC grouAt the phylum level, compared with that in the HNC group, the relative abundance of Firmicutes and Actinobacteriota was significantly decreased in the CCA group, whereas Proteobacteria and Bacteroidota were significantly enriched. The Firmicutes/Bacteroidota (F/B) ratio significantly decreased in the CCA group compared to the HNC grouThe relative abundance of Klebsiella in the CCA group was significantly higher than that in the HNC group, while the relative abundance of Bifidobacterium was significantly decreased. The Bifidobacterium/Klebsiella (B/K) ratio was established as a novel biomarker and was found to be significantly decreased in the CCA group compared with the HNC grouOur findings provide evidence supporting the use of Klebsiella and Bifidobacterium as noninvasive intestinal microbiomarkers for improving the diagnosis of CCA.},
}
@article {pmid38029116,
year = {2023},
author = {Ouamba, AJK and Gagnon, M and Varin, T and Chouinard, PY and LaPointe, G and Roy, D},
title = {Phylogenetic variation in raw cow milk microbiota and the impact of forage combinations and use of silage inoculants.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1175663},
pmid = {38029116},
issn = {1664-302X},
abstract = {INTRODUCTION: The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk.<br><br>METHODS: We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells.<br><br>RESULTS AND DISCUSSION: Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated by Enterobacteriaceae, Microbacteriaceae, Beijerinckiaceae, and Sphingomonadaceae, the GL and GLICI communities showed high proportions of Leuconostocaceae and Acetobacteraceae, respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated by Enterobacteriaceae and other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.},
}
@article {pmid38029109,
year = {2023},
author = {Crosby, KC and Rojas, M and Sharma, P and Johnson, MA and Mazloom, R and Kvitko, BH and Smits, THM and Venter, SN and Coutinho, TA and Heath, LS and Palmer, M and Vinatzer, BA},
title = {Genomic delineation and description of species and within-species lineages in the genus Pantoea.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1254999},
pmid = {38029109},
issn = {1664-302X},
support = {R25 GM072767/GM/NIGMS NIH HHS/United States ; },
abstract = {As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.},
}
@article {pmid38029094,
year = {2023},
author = {Semenov, M and Li, H and Luo, Y and Deng, Y and Kuzyakov, Y},
title = {Editorial: Microbial regulation of soil carbon cycling in terrestrial ecosystems.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1295624},
pmid = {38029094},
issn = {1664-302X},
}
@article {pmid38029079,
year = {2023},
author = {Koepper, S and Clark, KF and McClure, JT and Revie, CW and Stryhn, H and Thakur, KK},
title = {Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1245818},
pmid = {38029079},
issn = {1664-302X},
abstract = {The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.},
}
@article {pmid38026034,
year = {2023},
author = {Gjini, E and Madec, S},
title = {Towards a mathematical understanding of invasion resistance in multispecies communities.},
journal = {Royal Society open science},
volume = {10},
number = {11},
pages = {231034},
pmid = {38026034},
issn = {2054-5703},
abstract = {Multispecies community composition and dynamics are key to health and disease across biological systems, a prominent example being microbial ecosystems. Explaining the forces that govern diversity and resilience in the microbial consortia making up our body's defences remains a challenge. In this, theoretical models are crucial, to bridge the gap between species dynamics and underlying mechanisms and to develop analytic insight. Here we propose a replicator equation framework to model multispecies dynamics where an explicit notion of invasion resistance of a system emerges and can be studied explicitly. For illustration, we derive the conceptual link between such replicator equation and N microbial species' growth and interaction traits, stemming from micro-scale environmental modification. Within this replicator framework, mean invasion fitness arises, evolves dynamically, and may undergo critical predictable shifts with global environmental changes. This mathematical approach clarifies the key role of this resident system trait for invader success, and highlights interaction principles among N species that optimize their collective resistance to invasion. We propose this model based on the replicator equation as a powerful new avenue to study, test and validate mechanisms of invasion resistance and colonization in multispecies microbial ecosystems and beyond.},
}
@article {pmid38026022,
year = {2023},
author = {Tarnowski, MJ and Varliero, G and Scown, J and Phelps, E and Gorochowski, TE},
title = {Soil as a transdisciplinary research catalyst: from bioprospecting to biorespecting.},
journal = {Royal Society open science},
volume = {10},
number = {11},
pages = {230963},
pmid = {38026022},
issn = {2054-5703},
abstract = {The vast microbial biodiversity of soils is beginning to be observed and understood by applying modern DNA sequencing techniques. However, ensuring this potentially valuable information is used in a fair and equitable way remains a challenge. Here, we present a public engagement project that explores this topic through collaborative research of soil microbiomes at six urban locations using nanopore-based DNA sequencing. The project brought together researchers from the disciplines of synthetic biology, environmental humanities and microbial ecology, as well as school students aged 14-16 years old, to gain a broader understanding of views on the use of data from the environment. Discussions led to the transformation of 'bioprospecting', a metaphor with extractive connotations which is often used to frame environmental DNA sequencing studies, towards a more collaborative approach-'biorespecting'. This shift in terminology acknowledges that genetic information contained in soil arises as a result of entire ecosystems, including the people involved in its creation. Therefore, any use of sequence information should be accountable to the ecosystems from which it arose. As knowledge can arise from ecosystems and communities, science and technology should acknowledge this link and reciprocate with care and benefit-sharing to help improve the wellbeing of future generations.},
}
@article {pmid38023904,
year = {2023},
author = {Fu, X and Huang, Y and Fu, Q and Qiu, Y and Zhao, J and Li, J and Wu, X and Yang, Y and Liu, H and Yang, X and Chen, H},
title = {Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1252821},
pmid = {38023904},
issn = {1664-462X},
abstract = {Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health.},
}
@article {pmid38016221,
year = {2024},
author = {Zhang, X and Wang, Y and Jiao, P and Zhang, M and Deng, Y and Jiang, C and Liu, XW and Lou, L and Li, Y and Zhang, XX and Ma, L},
title = {Microbiome-functionality in anaerobic digesters: A critical review.},
journal = {Water research},
volume = {249},
number = {},
pages = {120891},
doi = {10.1016/j.watres.2023.120891},
pmid = {38016221},
issn = {1879-2448},
mesh = {Anaerobiosis ; *Bioreactors/microbiology ; *Microbiota ; Methane/metabolism ; Metabolic Networks and Pathways ; },
abstract = {Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.},
}
@article {pmid38015286,
year = {2023},
author = {Liu, D and Wei, L},
title = {Epigenetic Regulation in Response to CO2 Fluctuation in Marine Microalga Nannochloropsis oceanica.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {4},
pmid = {38015286},
issn = {1432-184X},
mesh = {*Carbon Dioxide ; Epigenesis, Genetic ; Histones/genetics ; *Microalgae/genetics ; Adaptation, Physiological ; Carbon ; },
abstract = {Microalgae often undergo different CO2 experiment in their habitat. To adapt to low CO2, carbon concentrating mechanism (CCM) could be launched in majority of microalgae and CCM are regulated at RNA level are well known. However, epigenetic modifications and their potential regulation of the transcription of masked genes at the genome level in response to CO2 fluctuation remain unclear. Here epigenetic regulation in response to CO2 fluctuation and epigenome-association with phenotypic plasticity of CCM are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that lysine butyrylation (Kbu) and histone H3K9m2 modifications were present in N. oceanica IMET1. Moreover, Kbu modification positively regulated gene expression. In response to CO2 fluctuation, there were 5,438 and 1,106 genes regulated by Kbu and H3K9m2 in Nannochloropsis, respectively. Gained or lost histone methylations were closely associated with activating or repressing gene expressions. Differential modifications were mainly enriched in carbon fixation, photorespiration, photosynthesis, and lipid metabolism etc. Massive genome-wide epigenetic reprogramming was observed after N. oceanica cells shifted from high CO2 to low CO2. Particularly, we firstly noted that the transcription of the key low CO2 responsive carbonic anhydrase (CA5), a key component involved in CCM stress signaling, was potentially regulated by bivalent Kbu-H3K9m2 modifications in microalgae. This study provides novel insights into the relationship between gene transcription and epigenetic modification in Nannochloropsis, which will lay foundation on genetic improvement of CCM at epigenetic level.},
}
@article {pmid38008827,
year = {2023},
author = {Zhu, YL and Huang, YJ and Nuerhamanti, N and Bai, XY and Wang, HN and Zhu, XY and Zhang, W},
title = {The Composition and Diversity of the Rhizosphere Bacterial Community of Ammodendron bifolium Growing in the Takeermohuer Desert Are Different from Those in the Nonrhizosphere.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {2},
pmid = {38008827},
issn = {1432-184X},
support = {32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
mesh = {*Ecosystem ; Rhizosphere ; Bacteria/genetics ; Proteobacteria ; Acidobacteria ; *Fabaceae ; Soil/chemistry ; Plants ; Nitrogen ; Soil Microbiology ; },
abstract = {Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing sand dunes) and endangered plant in the Takeermohuer Desert, and the bacterial community associated with this plant rhizosphere is still unclear. In this study, we investigated the composition and diversity of the bacterial community from the A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using culture and high-throughput sequencing methods. We preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. The results showed that the high-salinity Takeermohuer Desert has an oligotrophic environment, while the A. bifolium rhizosphere exhibited a relatively nutrient-rich environment due to higher contents of soil organic matter (SOM) and soil alkaline nitrogen (SAN) than bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phylum level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in the rhizosphere, and those of Firmicutes (9.8%) and Chloroflexi (6.9%) were relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genera were Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD_whole_tree indices in the rhizosphere soil were significantly higher than those in the bulk soil at the same soil depth and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in the Takeermohuer Desert were the phyla Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi. Furthermore, the major edaphic factors affecting the rhizosphere bacterial community were electrical conductivity (EC), SOM, soil total nitrogen (STN), SAN, and soil available potassium (SAK), while the major edaphic factors affecting the bacterial community in bulk soil were distance and ratio of carbon to nitrogen (C/N). We concluded that the A. bifolium rhizosphere bacterial community is different from that of the nonrhizosphere in composition, structure, diversity, and driving factors, which may improve our understanding of the relationship between plant and bacterial communities and lay a theoretical foundation for A. bifolium species conservation in desert ecosystems.},
}
@article {pmid38008821,
year = {2023},
author = {Fuster, M and Ruiz, T and Lamarque, A and Coulon, M and Legrand, B and Sabart, M and Latour, D and Mallet, C},
title = {Cyanosphere Dynamic During Dolichospermum Bloom: Potential Roles in Cyanobacterial Proliferation.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {3},
pmid = {38008821},
issn = {1432-184X},
mesh = {*Cyanobacteria/genetics ; *Microcystis ; *Microbiota ; Cell Proliferation ; Lakes ; Eutrophication ; },
abstract = {Under the effect of global change, management of cyanobacterial proliferation becomes increasingly pressing. Given the importance of interactions within microbial communities in aquatic ecosystems, a handful of studies explored the potential relations between cyanobacteria and their associated bacterial community (i.e., cyanosphere). Yet, most of them specifically focused on the ubiquitous cyanobacteria Microcystis, overlooking other genera. Here, based on 16s rDNA metabarcoding analysis, we confirmed the presence of cyanosphere representing up to 30% of the total bacterial community diversity, during bloom episode of another preponderant cyanobacterial genus, Dolichospermum. Moreover, we highlighted a temporal dynamic of this cyanosphere. A sPLS-DA model permits to discriminate three important dates and 220 OTUs. With their affiliations, we were able to show how these variations potentially imply a turnover in ecological functions depending on bloom phases. Although more studies are necessary to quantify the impacts of these variations, we argue that cyanosphere can have an important, yet underestimated, role in the modulation of cyanobacterial blooms.},
}
@article {pmid38006200,
year = {2023},
author = {Houldcroft, CJ and Underdown, S},
title = {Infectious disease in the Pleistocene: Old friends or old foes?.},
journal = {American journal of biological anthropology},
volume = {182},
number = {4},
pages = {513-531},
doi = {10.1002/ajpa.24737},
pmid = {38006200},
issn = {2692-7691},
support = {//Oxford Brookes University/ ; },
mesh = {Animals ; Humans ; Friends ; *Hominidae ; *Communicable Diseases/epidemiology ; Genome ; DNA ; },
abstract = {The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.},
}
@article {pmid38004650,
year = {2023},
author = {Aponte, H and Sulbaran-Bracho, Y and Mondaca, P and Vidal, C and Pérez, R and Meier, S and Cornejo, P and Rojas, C},
title = {Biochemical, Catabolic, and PGP Activity of Microbial Communities and Bacterial Strains from the Root Zone of Baccharis linearis in a Mediterranean Mine Tailing.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004650},
issn = {2076-2607},
support = {3210752//FONDECYT/ ; InES19-FRO19101//MINEDUC/ ; },
abstract = {The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroResp[TM] system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs.},
}
@article {pmid38001901,
year = {2023},
author = {Macedo-Viñas, M and Lucas, A},
title = {Evolution of Microbial Flora Colonizing Burn Wounds during Hospitalization in Uruguay.},
journal = {Biomedicines},
volume = {11},
number = {11},
pages = {},
pmid = {38001901},
issn = {2227-9059},
abstract = {(1) Background: Infections are a main cause of morbidity and mortality among burn patients. The spectrum of microorganisms depends on the epidemiological context and treatment practices. We aimed to describe the evolution of microbial flora colonizing burn wounds among patients hospitalized during 15 or more days at the National Burn Center in 2015. (2) Methods: Demographic data, length of stay, total body surface area burn, and status at discharge were collected from electronic records and culture results from the laboratory database. (3) Results: Among 98 included patients, 87 were colonized. The mean length of stay was 39 days overall and 16 days in the ICU. Acinetobacter spp., Enterococcus spp., and Staphylococcus aureus predominated. Fifty-six patients harbored multidrug-resistant bacteria and had a significantly greater TBSA. The mean time to colonization was 6 days overall and 14 days for multidrug-resistant bacteria; it was significantly longer for methicillin-resistant S. aureus than for methicillin-susceptible S. aureus. (4) Conclusions: This is the first report describing the dynamics of microbial colonization of burn wounds in Uruguay. Similarities were found with reports elsewhere, but early colonization with yeasts and the absence of Streptococcus pyogenes were unique. Each burn center needs to monitor its microbial ecology to tailor their antimicrobial strategies effectively.},
}
@article {pmid38000643,
year = {2024},
author = {Jiang, M and Khunjar, W and Li, A and Chandran, K},
title = {Divergent microbial structure still results in convergent microbial function during arrested anaerobic digestion of food waste at different hydraulic retention times.},
journal = {Bioresource technology},
volume = {393},
number = {},
pages = {130069},
doi = {10.1016/j.biortech.2023.130069},
pmid = {38000643},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Food Loss and Waste ; Food ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; Bioreactors ; Fatty Acids, Volatile/metabolism ; Methane ; },
abstract = {In this study, two arrested anaerobic digestion bioreactors, fed with food waste, operated under different hydraulic retention times (HRTs) exhibited similar total volatile fatty acid (VFA) yields (p = 0.09). 16S rRNA gene sequencing revealed distinct microbial structure (p = 0.02) at the two HRTs. However, between the two HRTs, there were no differences in potential (DNA) and extant (mRNA) functionality for the production of acetic (AA)-, propionic (PA)-, butyric (BA)- and valeric-acid (VA), as indicated by the metagenome and metatranscriptome data, respectively. The highest potential and extant functionality for PA production in the reactor microbiomes mirrored the highest abundance of PA in the reactor effluents. Meta-omics analysis of BA production indicated possible metabolite exchange across different community members. Notably, the basis for similar VFA production performance observed under the HRTs tested lies in the community-level redundancy in convergent acidification functions and pathways, rather than trends in community-level structure alone.},
}
@article {pmid38000642,
year = {2024},
author = {Wu, K and Leliveld, T and Zweers, H and Rijnaarts, H and Langenhoff, A and Fernandes, TV},
title = {Impact of mixed microalgal and bacterial species on organic micropollutants removal in photobioreactors under natural light.},
journal = {Bioresource technology},
volume = {393},
number = {},
pages = {130083},
doi = {10.1016/j.biortech.2023.130083},
pmid = {38000642},
issn = {1873-2976},
mesh = {Photobioreactors/microbiology ; *Microalgae ; *Chlorella ; Sewage ; Bacteria ; Biomass ; },
abstract = {Single microalgae species are effective at the removal of various organic micropollutants (OMPs), however increased species diversity might enhance this removal. Sixteen OMPs were added to 2 continuous photobioreactors, one inoculated with Chlorella sorokiniana and the other with a microalgal-bacterial community, for 112 d under natural light. Three media were sequentially used in 3 Periods: I) synthetic sewage (d 0-28), II) 10x diluted anaerobically digested black water (AnBW) (d 28-94) and III) 5x diluted AnBW (d 94-112). Twelve OMPs were removed > 30 %, while 4 were < 10 % removed. Removal efficiencies were similar for 9 OMPs, yet the mixed community showed a 2-3 times higher removal capacity (µg OMP/g dry weight) than C. sorokiniana during Period II pseudo steady state. The removal decreased drastically in Period III due to overgrowth of filamentous green algae. This study shows for the first time how microbial community composition and abundance are key for OMPs removal.},
}
@article {pmid37999395,
year = {2023},
author = {Hernanz-Torrijos, M and Ortega, MJ and Úbeda, B and Bartual, A},
title = {Polyunsaturated Aldehydes Profile in the Diatom Cyclotella cryptica Is Sensitive to Changes in Its Phycosphere Bacterial Assemblages.},
journal = {Marine drugs},
volume = {21},
number = {11},
pages = {},
pmid = {37999395},
issn = {1660-3397},
support = {RTI2018-101272-B-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Plan Propio UCA 2022-2023//University of C&#xe1;diz/ ; },
mesh = {*Diatoms/chemistry ; Aldehydes/pharmacology/chemistry ; Oceans and Seas ; Bacteria ; Marine Biology ; },
abstract = {Diatoms are responsible for the fixation of ca. 20% of the global CO2 and live associated with bacteria that utilize the organic substances produced by them. Current research trends in marine microbial ecology show which diatom and bacteria interact mediated through the production and exchange of infochemicals. Polyunsaturated aldehydes (PUA) are organic molecules released by diatoms that are considered to have infochemical properties. In this work, we investigated the possible role of PUA as a mediator in diatom-bacteria interactions. To this end, we compare the PUA profile of a newly isolated oceanic PUA producer diatom, Cyclotella cryptica, co-cultured with and without associated bacteria at two phosphate availability conditions. We found that the PUA profile of C. cryptica cultured axenically was different than its profile when it was co-cultured with autochthonous (naturally associated) and non-autochthonous bacteria (unnaturally inoculated). We also observed that bacterial presence significantly enhanced diatom growth and that C. cryptica modulated the percentage of released PUA in response to the presence of bacteria, also depending on the consortium type. Based on our results, we propose that this diatom could use released PUA as a specific organic matter sign to attract beneficial bacteria for constructing its own phycosphere, for more beneficial growth.},
}
@article {pmid37997641,
year = {2024},
author = {Tájmel, D and Cruz-Paredes, C and Rousk, J},
title = {Heat wave-induced microbial thermal trait adaptation and its reversal in the Subarctic.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17032},
doi = {10.1111/gcb.17032},
pmid = {37997641},
issn = {1365-2486},
support = {9036-00004B//Danmarks Frie Forskningsfond/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; 2020-04083//Vetenskapsr&#xe5;det/ ; 4.3-2021-00164//Vetenskapsr&#xe5;det/ ; },
mesh = {*Ecosystem ; *Hot Temperature ; Soil Microbiology ; Climate Change ; Temperature ; Soil/chemistry ; Carbon ; },
abstract = {Climate change predictions suggest that arctic and subarctic ecosystems will be particularly affected by rising temperatures and extreme weather events, including severe heat waves. Temperature is one of the most important environmental factors controlling and regulating microbial decomposition in soils; therefore, it is critical to understand its impact on soil microorganisms and their feedback to climate warming. We conducted a warming experiment in a subarctic birch forest in North Sweden to test the effects of summer heat waves on the thermal trait distributions that define the temperature dependences for microbial growth and respiration. We also determined the microbial temperature dependences 10 and 12 months after the heat wave simulation had ended to investigate the persistence of the thermal trait shifts. As a result of warming, the bacterial growth temperature dependence shifted to become warm-adapted, with a similar trend for fungal growth. For respiration, there was no shift in the temperature dependence. The shifts in thermal traits were not accompanied by changes in α- or β-diversity of the microbial community. Warming increased the fungal-to-bacterial growth ratio by 33% and decreased the microbial carbon use efficiency by 35%, and both these effects were caused by the reduction in moisture the warming treatments caused, while there was no evidence that substrate depletion had altered microbial processes. The warm-shifted bacterial thermal traits were partially restored within one winter but only fully recovered to match ambient conditions after 1 year. To conclude, a summer heat wave in the Subarctic resulted in (i) shifts in microbial thermal trait distributions; (ii) lower microbial process rates caused by decreased moisture, not substrate depletion; and (iii) no detectable link between the microbial thermal trait shifts and community composition changes.},
}
@article {pmid37994377,
year = {2024},
author = {Lyche Solheim, A and Gundersen, H and Mischke, U and Skjelbred, B and Nejstgaard, JC and Guislain, ALN and Sperfeld, E and Giling, DP and Haande, S and Ballot, A and Moe, SJ and Stephan, S and Walles, TJW and Jechow, A and Minguez, L and Ganzert, L and Hornick, T and Hansson, TH and Stratmann, CN and Järvinen, M and Drakare, S and Carvalho, L and Grossart, HP and Gessner, MO and Berger, SA},
title = {Lake browning counteracts cyanobacteria responses to nutrients: Evidence from phytoplankton dynamics in large enclosure experiments and comprehensive observational data.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17013},
doi = {10.1111/gcb.17013},
pmid = {37994377},
issn = {1365-2486},
support = {603378, 226273//European Union FP7/ ; 731065//European Union H2020/ ; 01LC1501, 033L041B//German Federal Ministry of Education and Research/ ; GE 1775/2-1//German Research Foundation/ ; K45/2017, SAW-2015-IGB-1//Leibniz Association/ ; //Morsa River Basin authority, Norway/ ; },
mesh = {*Phytoplankton ; Lakes/microbiology ; Humic Substances ; Eutrophication ; *Cyanobacteria ; Nutrients ; Phosphorus/analysis ; China ; },
abstract = {Lakes worldwide are affected by multiple stressors, including climate change. This includes massive loading of both nutrients and humic substances to lakes during extreme weather events, which also may disrupt thermal stratification. Since multi-stressor effects vary widely in space and time, their combined ecological impacts remain difficult to predict. Therefore, we combined two consecutive large enclosure experiments with a comprehensive time-series and a broad-scale field survey to unravel the combined effects of storm-induced lake browning, nutrient enrichment and deep mixing on phytoplankton communities, focusing particularly on potentially toxic cyanobacterial blooms. The experimental results revealed that browning counteracted the stimulating effect of nutrients on phytoplankton and caused a shift from phototrophic cyanobacteria and chlorophytes to mixotrophic cryptophytes. Light limitation by browning was identified as the likely mechanism underlying this response. Deep-mixing increased microcystin concentrations in clear nutrient-enriched enclosures, caused by upwelling of a metalimnetic Planktothrix rubescens population. Monitoring data from a 25-year time-series of a eutrophic lake and from 588 northern European lakes corroborate the experimental results: Browning suppresses cyanobacteria in terms of both biovolume and proportion of the total phytoplankton biovolume. Both the experimental and observational results indicated a lower total phosphorus threshold for cyanobacterial bloom development in clearwater lakes (10-20 μg P L[-1]) than in humic lakes (20-30 μg P L[-1]). This finding provides management guidance for lakes receiving more nutrients and humic substances due to more frequent extreme weather events.},
}
@article {pmid37991947,
year = {2023},
author = {Arya, S and George, AB and O'Dwyer, JP},
title = {Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {48},
pages = {e2307313120},
pmid = {37991947},
issn = {1091-6490},
support = {376199//Simons Foundation (SF)/ ; },
mesh = {*Microbiota ; *Machine Learning ; },
abstract = {Microbiome engineering offers the potential to leverage microbial communities to improve outcomes in human health, agriculture, and climate. To translate this potential into reality, it is crucial to reliably predict community composition and function. But a brute force approach to cataloging community function is hindered by the combinatorial explosion in the number of ways we can combine microbial species. An alternative is to parameterize microbial community outcomes using simplified, mechanistic models, and then extrapolate these models beyond where we have sampled. But these approaches remain data-hungry, as well as requiring an a priori specification of what kinds of mechanisms are included and which are omitted. Here, we resolve both issues by introducing a mechanism-agnostic approach to predicting microbial community compositions and functions using limited data. The critical step is the identification of a sparse representation of the community landscape. We then leverage this sparsity to predict community compositions and functions, drawing from techniques in compressive sensing. We validate this approach on in silico community data, generated from a theoretical model. By sampling just [Formula: see text]1% of all possible communities, we accurately predict community compositions out of sample. We then demonstrate the real-world application of our approach by applying it to four experimental datasets and showing that we can recover interpretable, accurate predictions on composition and community function from highly limited data.},
}
@article {pmid37991578,
year = {2023},
author = {Liu, HH and Chen, L and Shao, HB and Gao, S and Hong, XY and Bing, XL},
title = {Environmental Factors and the Symbiont Cardinium Influence the Bacterial Microbiome of Spider Mites Across the Landscape.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {1},
pmid = {37991578},
issn = {1432-184X},
support = {32001905 and 32020103011//National Natural Science Foundation of China/ ; 32001905 and 32020103011//National Natural Science Foundation of China/ ; 2022YFC2601000//National Key Research and Development Program of China/ ; BK20211213//Natural Science Foundation of Jiangsu Province/ ; KJQN202110//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; Animals ; *Tetranychidae ; RNA, Ribosomal, 16S/genetics ; Bacteroidetes/genetics ; *Arthropods ; *Microbiota ; },
abstract = {Microbes play a key role in the biology, ecology, and evolution of arthropods. Despite accumulating data on microbial communities in arthropods that feed on plants using piercing-sucking mouthparts, we still lack a comprehensive understanding of the composition and assembly factors of the microbiota, particularly in field-collected spider mites. Here, we applied 16S rRNA amplicon sequencing to investigate the characters of the bacterial community in 140 samples representing 420 mite individuals, belonging to eight Tetranychus species (Acari: Tetranychidae) collected from 26 sites in China. The results showed that the bacterial composition of spider mites varied significantly among different species, locations, and plants. The environment showed a significant influence on the bacterial community of spider mites, with different relative contributions. Latitude and precipitation were found to be the main factors influencing the bacterial community composition. The dissimilarity of bacterial community and geographical distance between mite locations were significantly correlated. The assembly of spider mite bacterial communities seemed to be mainly influenced by stochastic processes. Furthermore, the symbiont Cardinium was found to be important in shaping the microbiota of many Tetranychus species. The relative abundance of Cardinium was > 50% in T. viennensis, T. urticae G, T. urticae R, and T. turkestani. Removing Cardinium reads from our analysis significantly changed Shannon diversity index and weighted beta diversity in these species. Altogether, this study provides novel insights into bacterial diversity patterns that contribute to our knowledge of the symbiotic relationships between arthropods and their bacterial communities.},
}
@article {pmid37989722,
year = {2024},
author = {Yuan, M and Na, M and Hicks, LC and Rousk, J},
title = {Limiting resources for soil microbial growth in climate change simulation treatments in the subarctic.},
journal = {Ecology},
volume = {105},
number = {1},
pages = {e4210},
doi = {10.1002/ecy.4210},
pmid = {37989722},
issn = {1939-9170},
support = {KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; 2020-03858//The Swedish Research Council Vetenskapsr&#xe5;det/ ; 2020-04083//The Swedish Research Council Vetenskapsr&#xe5;det/ ; 4.3-2021-00164//Swedish Research Council's/ ; },
mesh = {*Ecosystem ; *Climate Change ; Soil ; Soil Microbiology ; Tundra ; Arctic Regions ; Plants ; Carbon ; Nitrogen ; Bacteria ; },
abstract = {The microbial use of resources to sustain life and reproduce influences for example, decomposition and plant nutrient provisioning. The study of "limiting factors" has shed light on the interaction between plants and their environment. Here, we investigated whether carbon (C), nitrogen (N), or phosphorus (P) was limiting for soil microorganisms in a subarctic tundra heath, and how changes in resource availability associated with climate change affected this. We studied samples in which changes in resource availability due to climate warming were simulated by the addition of birch litter and/or inorganic N. To these soils, we supplied factorial C (as glucose), N (as NH4 NO3), and P (as KH2 PO4 /K2 HPO4) additions ("limiting factor assays," LFA), to determine the limiting factors. The combination of C and P induced large growth responses in all soils and, combined with a systematic tendency for growth increases by C, this suggested that total microbial growth was primarily limited by C and secondarily by P. The C limitation was alleviated by the field litter treatment and strengthened by N fertilization. The microbial growth response to the LFA-C and LFA-P addition was strongest in the field-treatment that combined litter and N addition. We also found that bacteria were closer to P limitation than fungi. Our results suggest that, under a climate change scenario, increased C availability resulting from Arctic greening, treeline advance, and shrubification will reduce the microbial C limitation, while increased N availability resulting from warming will intensify the microbial C limitation. Our results also suggest that the synchronous increase of both C and N availability might lead to a progressive P limitation of microbial growth, primarily driven by bacteria being closer to P limitation. These shifts in microbial resource limitation might lead to a microbial targeting of the limiting element from organic matter, and also trigger competition for nutrients between plants and microorganisms, thus modulating the productivity of the ecosystem.},
}
@article {pmid37987191,
year = {2023},
author = {Garbisu, C and Alkorta, I},
title = {A case for the importance of following antibiotic resistant bacteria throughout the soil food web.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {12},
pages = {e2300153},
doi = {10.1002/bies.202300153},
pmid = {37987191},
issn = {1521-1878},
support = {PID2020-116495RB-I00//MCIN/AEI/10.13039/501100011033/ ; IT1578-22//Basque Government/ ; //JRL Environmental Antibiotic Resistance/ ; },
mesh = {Animals ; *Soil ; *Bacteria/genetics ; Manure/microbiology ; Food Chain ; Ecosystem ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Genes, Bacterial ; },
abstract = {It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.},
}
@article {pmid37986012,
year = {2023},
author = {Basbas, C and Garzon, A and Schlesener, C and van Heule, M and Profeta, R and Weimer, BC and Silva-Del-Rio, N and Byrne, BA and Karle, B and Aly, SS and Lima, FS and Pereira, RV},
title = {Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {59},
pmid = {37986012},
issn = {2524-4671},
abstract = {BACKGROUND: The goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial California dairy farms using shotgun metagenomics. A set subset of 95 intrauterine swab samples, taken from a larger selection of 307 individual cow samples previously collected, were examined for α and β diversity and differential abundance associated with metritis. Cows within 21 days post-partum were categorized into one of three clinical groups during sample collection: control (CT, n = 32), defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge; metritis (MET, n = 33), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; and purulent discharge cows (PUS, n = 31), defined as a non-fetid purulent or mucopurulent vaginal discharge.<br><br>RESULTS: All three clinical groups (CT, MET, and PUS) were highly diverse, with the top 12 most abundant genera accounting for 10.3%, 8.8%, and 10.1% of mean relative abundance, respectively. The &#x3b1; diversity indices revealed a lower diversity from samples collected from MET and PUS when compared to CT cows. PERMANOVA statistical testing revealed a significant difference (P adjusted&#x2009;<&#x2009;0.01) in the diversity of genera between CT and MET samples (R2&#x2009;=&#x2009;0.112, P&#x2009;=&#x2009;0.003) and a non-significant difference between MET and PUS samples (R2&#x2009;=&#x2009;0.036, P&#x2009;=&#x2009;0.046). ANCOM-BC analysis revealed that from the top 12 most abundant genera, seven genera were increased in the natural log fold change (LFC) of abundance in MET when compared to CT samples: Bacteroides, Clostridium, Fusobacterium, Phocaeicola, Porphyromonas, Prevotella, and Streptococcus. Two genera, Dietzia and Microbacterium, were decreased in natural LFC of abundance when comparing MET (regardless of treatment) and CT, while no changes in natural LFC of abundance were observed for Escherichia, Histophilus, and Trueperella.<br><br>CONCLUSIONS: The results presented here, are the current deepest shotgun metagenomic analyses conducted on the bovine uterine microbiome to date (mean of 256,425 genus-level reads per sample). Our findings support that uterine samples from cows without metritis (CT) had increased &#x3b1;-diversity but decreased &#x3b2;-diversity when compared to metritis or PUS cows, characteristic of dysbiosis. In summary, our findings highlight that MET cows have an increased abundance of Bacteroides, Porphyromonas, and Fusobacterium when compared to CT and PUS, and support the need for further studies to better understand their potential causal role in metritis pathogenesis.},
}
@article {pmid37984648,
year = {2024},
author = {Bhattarai, B and Bhattacharjee, AS and Coutinho, FH and Goel, R},
title = {Investigating the viral ecology and contribution to the microbial ecology in full-scale mesophilic anaerobic digesters.},
journal = {Chemosphere},
volume = {349},
number = {},
pages = {140743},
doi = {10.1016/j.chemosphere.2023.140743},
pmid = {37984648},
issn = {1879-1298},
mesh = {Anaerobiosis ; *Bioreactors/microbiology ; *Methane/metabolism ; Bacteria/metabolism ; Sewage ; },
abstract = {In an attempt to assess the diversity of viruses and their potential to modulate the metabolism of functional microorganisms in anaerobic digesters, we collected digestate from three mesophilic anaerobic digesters in full-scale wastewater treatment plants treating real municipal wastewater. The reads were analyzed using bioinformatics algorithms to elucidate viral diversity, identify their potential role in modulating the metabolism of functional microorganisms, and provide essential genomic information for the potential use of virus-mediated treatment in controlling the anaerobic digester microbiome. We found that Siphoviridae was the dominant family in mesophilic anaerobic digesters, followed by Myoviridae and Podoviridae. Lysogeny was prevalent in mesophilic anaerobic digesters as the majority of metagenome-assembled genomes contained at least one viral genome within them. One virus within the genome of an acetoclastic methanogen (Methanothrix soehngenii) was observed with a gene (fwdE) acquired via lateral transfer from hydrogenotrophic methanogens. The virus-mediated acquisition of fwdE gene enables possibility of mixotrophic methanogenesis in Methanothrix soehngenii. This evidence highlighted that lysogeny provides fitness advantage to methanogens in anaerobic digesters by adding flexibility to changing substrates. Similarly, we found auxiliary metabolic genes, such as cellulase and alpha glucosidase, of bacterial origin responsible for sludge hydrolysis in viruses. Additionally, we discovered novel viral genomes and provided genomic information on viruses infecting acidogenic, acetogenic, and pathogenic bacteria that can potentially be used for virus-mediated treatment to deal with the souring problem in anaerobic digesters and remove pathogens from biosolids before land application. Collectively, our study provides a genome-level understanding of virome in conjunction with the microbiome in anaerobic digesters that can be used to optimize the anaerobic digestion process for efficient biogas generation.},
}
@article {pmid37982643,
year = {2023},
author = {Lo, H-Y and Wink, K and Nitz, H and Kästner, M and Belder, D and Müller, JA and Kaster, A-K},
title = {scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling.},
journal = {mSystems},
volume = {8},
number = {6},
pages = {e0099823},
pmid = {37982643},
issn = {2379-5077},
mesh = {Workflow ; *Genomics/methods ; *Microfluidics/methods ; },
abstract = {A central question in microbial ecology is which member of a community performs a particular metabolism. Several sophisticated isotope labeling techniques are available for analyzing the metabolic function of populations and individual cells in a community. However, these methods are generally either insufficiently sensitive or throughput-limited and thus have limited applicability for the study of complex environmental samples. Here, we present a novel approach that combines highly sensitive radioisotope tracking, microfluidics, high-throughput sorting, and single-cell genomics to simultaneously detect and identify individual microbial cells based solely on their in situ metabolic activity, without prior information on community structure.},
}
@article {pmid37981701,
year = {2023},
author = {Sadeghi, J and Chaganti, SR and Johnson, TB and Heath, DD},
title = {Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {258},
pmid = {37981701},
issn = {2049-2618},
mesh = {Animals ; Phylogeny ; *Microbiota/genetics ; Fishes ; *Gastrointestinal Microbiome/genetics ; Water ; },
abstract = {BACKGROUND: While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation.<br><br>RESULTS: We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes.<br><br>CONCLUSIONS: Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.},
}
@article {pmid37980777,
year = {2023},
author = {Acosta, DJ and Alper, HS},
title = {Advances in enzymatic and organismal technologies for the recycling and upcycling of petroleum-derived plastic waste.},
journal = {Current opinion in biotechnology},
volume = {84},
number = {},
pages = {103021},
doi = {10.1016/j.copbio.2023.103021},
pmid = {37980777},
issn = {1879-0429},
mesh = {Mutation ; *Petroleum ; Polymers ; Recycling ; Plastics ; },
abstract = {Biological catalysts are emerging with the capability to depolymerize a wide variety of plastics. Improving and discovering these catalysts has leveraged a range of tools, including microbial ecology studies, high-throughput selections, and computationally guided mutational studies. In this review, we discuss the prospects for biological solutions to plastic recycling and upcycling with a focus on major advances in polyethylene terephthalate depolymerization, expanding the range of polymers with known biological catalysts, and the utilization of derived products. We highlight several recent improvements in enzymes and reaction properties, the discovery of a wide variety of novel plastic-depolymerizing biocatalysts, and how depolymerization products can be utilized in recycling and upcycling.},
}
@article {pmid37979870,
year = {2024},
author = {Xiao, Z and Lu, C and Wu, Z and Li, X and Ding, K and Zhu, Z and Han, R and Zhao, J and Ge, T and Li, G and Zhu, YG},
title = {Continuous cropping disorders of eggplants (Solanum melongena L.) and tomatoes (Solanum lycopersicum L.) in suburban agriculture: Microbial structure and assembly processes.},
journal = {The Science of the total environment},
volume = {909},
number = {},
pages = {168558},
doi = {10.1016/j.scitotenv.2023.168558},
pmid = {37979870},
issn = {1879-1026},
mesh = {*Solanum lycopersicum ; *Solanum melongena ; Soil Microbiology ; Agriculture ; Bacteria/genetics ; Soil/chemistry ; Rhizosphere ; },
abstract = {Deciphering the intricate relationships between microorganisms and plants remains a formidable challenge in plant microbial ecology, an area that holds promise for optimizing microbial interventions to enhance stress resilience and agricultural yields. In our investigation, we procured samples during 2019 and 2022 from a suburban agricultural greenhouse. Our study delineated the composition of bacterial and fungal communities across various ecological niches-namely, the rhizosphere soil, bulk soil, and phyllosphere of healthy, Ralstonia solanacearum-infected, and dead eggplants and tomatoes. The structure and composition of both fungal and bacterial communities change significantly under the influence of the host genotype across all samples. In the tomato or eggplant groups, bacterial wilt exerts a more pronounced impact on the bacterial community than on the fungal community. We speculate that the rhizosphere of healthy eggplants and tomatoes harbored more antibiotic-producing (e.g., Amycolatopsis and Penicillium) and biocontrol (e.g., Bacillus) strains, which can lead to have lower absolute abundance of R. solanacearum. In the context of R. solanacearum invasion, deterministic processes were responsible for shaping 70.67 % and 80.63 % of the bacterial community assembly in the rhizosphere of eggplants and tomatoes, respectively. Deterministic processes dominated the assembly of fungal communities in the rhizosphere of R. solanacearum-infected eggplants, whereas the opposite was true in the tomatoes. Homogeneous selection emerged as the predominant force governing the bacterial community assembly in the rhizospheres of R. solanacearum-infected eggplants and tomatoes. The bacterial co-occurrence networks in healthy rhizosphere soil were characterized by reduced vulnerability and enhanced stability (i.e., robustness index) and complexity (i.e., cohesion index), compared to their infected counterparts. In summary, complex microbial networks in rhizosphere soils are more resistant to invasion by soil-borne pathogens. The dynamics of bacterial interactions and community assembly processes are pivotal for effective microbiome management and offer predictive insights into the ecological ramifications of R. solanacearum invasions.},
}
@article {pmid37977011,
year = {2023},
author = {Scaria, SS and Balasubramanian, B and Dandin, VS and Meyyazhagan, A and Pappuswamy, M and Sattanathan, G and Liu, WC and Kadanthottu Sebastian, J and Park, S},
title = {Review on impacts of micro- and nano-plastic on aquatic ecosystems and mitigation strategies.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {265},
number = {},
pages = {106759},
doi = {10.1016/j.aquatox.2023.106759},
pmid = {37977011},
issn = {1879-1514},
mesh = {Animals ; Humans ; *Ecosystem ; Microplastics/toxicity ; Plastics/toxicity ; *Water Pollutants, Chemical/toxicity ; Food Chain ; },
abstract = {The rapid proliferation of microplastics (MPs) and nanoplastics (NPs) in our environment presents a formidable hazard to both biotic and abiotic components. These pollutants originate from various sources, including commercial production and the breakdown of larger plastic particles. Widespread contamination of the human body, agroecosystems, and animals occurs through ingestion, entry into the food chain, and inhalation. Consequently, the imperative to devise innovative methods for MPs and NPs remediation has become increasingly apparent. This review explores the current landscape of strategies proposed to mitigate the escalating threats associated with plastic waste. Among the array of methods in use, microbial remediation emerges as a promising avenue for the decomposition and reclamation of MPs and NPs. In response to the growing concern, numerous nations have already implemented or are in the process of adopting regulations to curtail MPs and NPs in aquatic habitats. This paper aims to address this gap by delving into the environmental fate, behaviour, transport, ecotoxicity, and management of MPs and NPs particles within the context of nanoscience, microbial ecology, and remediation technologies. Key findings of this review encompass the intricate interdependencies between MPs and NPs and their ecosystems. The ecological impact, from fate to ecotoxicity, is scrutinized in light of the burgeoning environmental imperative. As a result, this review not only provides an encompassing understanding of the ecological ramifications of MPs and NPs but also highlights the pressing need for further research, innovation, and informed interventions.},
}
@article {pmid37976624,
year = {2023},
author = {Liu, S and Lin, Y and Liu, T and Xu, X and Wang, J and Chen, Q and Sun, W and Dang, C and Ni, J},
title = {Planktonic/benthic Bathyarchaeota as a "gatekeeper" enhance archaeal nonrandom co-existence and deterministic assembling in the Yangtze River.},
journal = {Water research},
volume = {247},
number = {},
pages = {120829},
doi = {10.1016/j.watres.2023.120829},
pmid = {37976624},
issn = {1879-2448},
mesh = {Humans ; *Archaea/genetics ; *Plankton ; Geologic Sediments/microbiology ; Rivers/microbiology ; Water ; Carbon ; RNA, Ribosomal, 16S ; Phylogeny ; DNA, Archaeal ; },
abstract = {Archaea, the third proposed domain of life, mediate carbon and nutrient cycling in global natural habitats. Compared with bacteria, our knowledge about archaeal ecological modes in large freshwater environments subject to varying natural and human factors is limited. By metabarcoding analysis of 303 samples, we provided the first integrate biogeography about archaeal compositions, co-existence networks, and assembling processes within a 6000 km continuum of the Yangtze River. Our study revealed that, among the major phyla, water samples owned a higher proportion of Thaumarchaeota (62.8%), while sediments had higher proportions of Euryarchaeota (33.4%) and Bathyarchaeota (18.8%). A decline of polarization in phylum abundance profile was observed from plateau/mountain/hill to basin/plain areas, which was attributed to the increase of nutrients and metals. Planktonic and benthic Bathyarchaeota tended to co-occur with both major (e.g., methanogens or Thermoplasmata) and minor (e.g., Asgard or DPANN) taxa in the non-random networks, harboring the highest richness and abundances of keystone species and contributing the most positively to edge number, node degree, and nearest neighbor degree. Furthermore, we noted significantly positive contributions of Bathyarchaeota abundance and network complexity to the dominance of deterministic process in archaeal assembly (water: 65.3%; sediments: 92.6%), since higher carbon metabolic versatility of Bathyarchaeota would benefit archaeal symbiotic relations. Stronger deterministic assembling was identified at the lower-reach plain, and higher concentrations of ammonium and aluminum separately functioning as nutrition and agglomerator were the main environmental drivers. We lastly found that the Three Gorges Dam caused a simultaneous drop of benthic Bathyarchaeota abundance, network co-existence, and deterministic effects immediately downstream due to riverbed erosion as a local interference. These findings highlight that Bathyarchaeota are a "gatekeeper" to promote fluvial archaeal diversity, stability, and predictability under varying macroscopic and microscopic factors, expanding our knowledge about microbial ecology in freshwater biogeochemical cycling globally.},
}
@article {pmid37975506,
year = {2023},
author = {Lequime, S},
title = {The sociality continuum of viruses: a commentary on Leeks et al. 2023.},
journal = {Journal of evolutionary biology},
volume = {36},
number = {11},
pages = {1568-1570},
doi = {10.1111/jeb.14247},
pmid = {37975506},
issn = {1420-9101},
mesh = {*Onions ; *Viruses/genetics ; Evolution, Molecular ; },
}
@article {pmid37974054,
year = {2023},
author = {Minnebo, Y and De Paepe, K and Raes, J and Van de Wiele, T},
title = {Eating patterns contribute to shaping the gut microbiota in the mucosal simulator of the human intestinal microbial ecosystem.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {12},
pages = {},
doi = {10.1093/femsec/fiad149},
pmid = {37974054},
issn = {1574-6941},
support = {30770923//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Feeding Behavior ; Colon/microbiology ; Feces/microbiology ; },
abstract = {Eating patterns, i.e. meal frequency and circadian timing of meals, are often modified in weight loss and metabolic healing strategies. However, in-depth research into the effects on the gut microbiome remains scarce, particularly across various colon regions and niches. We identified eating patterns to contribute in shaping the in vitro gut biomass production, metabolism, and microbial community compositions by subjecting four faecal microbiomes to a pattern that is standardized for a dynamic gut model (feeding at 09, 17, and 01 h), a typical Western (breakfast, lunch, and dinner at 09, 13, and 19 h, respectively), and a time-restricted pattern (single meal at 09 h). While eating patterns moderately affected the microbiome (2.4% and 1.8% significant variation in proportional and quantitative microbial compositions, respectively), significant changes were noted in the time-restricted pattern, including increased Bacteroides, Butyricicoccus, Dialister, and Faecalibacterium abundances. Sampling every 4 h revealed no significant circadian fluctuations in biomass production, microbial community compositions, or functionality. Longer fasting times favoured the growth of slower-growing species, such as Akkermansia, Dialister, and Parasutterella over faster-growers, such as Pseudomonas and Stenotrophomonas. Our findings illustrate the importance of recording and considering eating patterns as a gut microbiome determinant in in vivo and in vitro dietary intervention studies.},
}
@article {pmid37973932,
year = {2023},
author = {Feliu-Paradeda, L and Puig, S and Bañeras, L},
title = {Design and validation of a multiplex PCR method for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20073},
pmid = {37973932},
issn = {2045-2322},
support = {PCI2019-111932-2//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2021 FISDU00132//Generalitat de Catalunya/ ; UdG-AG-575//Universitat de Girona/ ; },
mesh = {*Clostridium acetobutylicum/genetics ; *Clostridium cellulovorans/genetics ; Multiplex Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Clostridium/genetics ; Butanols ; 1-Butanol ; Fermentation ; },
abstract = {Co-cultures of clostridia with distinct physiological properties have emerged as an alternative to increase the production of butanol and other added-value compounds from biomass. The optimal performance of mixed tandem cultures may depend on the stability and fitness of each species in the consortium, making the development of specific quantification methods to separate their members crucial. In this study, we developed and tested a multiplex qPCR method targeting the 16S rRNA gene for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans in co-cultures. Designed primer pairs and probes could specifically quantify the three Clostridium species with no cross-reactions thus allowing significant changes in their growth kinetics in the consortia to be detected and correlated with productivity. The method was used to test a suitable medium composition for simultaneous growth of the three species. We show that higher alcohol productions were obtained when combining C. carboxidivorans and C. acetobutylicum compared to individual cultures, and further improved (> 90%) in the triplet consortium. Altogether, the methodology could be applied to fermentation processes targeting butanol productions from lignocellulosic feedstocks with a higher substrate conversion efficiency.},
}
@article {pmid37971428,
year = {2023},
author = {Silcocks, M and Chang, X and Thuong Thuong, NT and Qin, Y and Minh Ha, DT and Khac Thai, PV and Vijay, S and Anh Thu, DD and Ngoc Ha, VT and Ngoc Nhung, H and Huu Lan, N and Quynh Nhu, NT and Edwards, D and Nath, A and Pham, K and Duc Bang, N and Hong Chau, TT and Thwaites, G and Heemskerk, AD and Chuen Khor, C and Teo, YY and Inouye, M and Ong, RT-H and Caws, M and Holt, KE and Dunstan, SJ},
title = {Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam.},
journal = {Microbiology spectrum},
volume = {11},
number = {6},
pages = {e0256223},
pmid = {37971428},
issn = {2165-0497},
support = {/WT_/Wellcome Trust/United Kingdom ; U19 AI162583/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Antitubercular Agents/pharmacology/therapeutic use ; Beijing ; Vietnam/epidemiology ; Genotype ; *Tuberculosis, Multidrug-Resistant/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Mutation ; },
abstract = {Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.},
}
@article {pmid37971255,
year = {2023},
author = {Martínez-Alvarez, L and Ramond, J-B and Vikram, S and León-Sobrino, C and Maggs-Kölling, G and Cowan, DA},
title = {With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {12},
pages = {e0062923},
pmid = {37971255},
issn = {1098-5336},
support = {113308//National Research Foundation (NRF)/ ; },
mesh = {*Bacteria/genetics ; Desert Climate ; Soil Microbiology ; Sodium Chloride ; *Microbiota ; },
abstract = {The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.},
}
@article {pmid37970641,
year = {2023},
author = {Spencer-Williams, I and Meyer, M and DePas, W and Elliott, E and Haig, SJ},
title = {Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking-Water-Associated Pathogens in a Full-Scale Drinking Water Distribution System.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {48},
pages = {20360-20369},
pmid = {37970641},
issn = {1520-5851},
mesh = {*Drinking Water/microbiology ; RNA, Ribosomal, 16S/genetics ; Corrosion ; Nontuberculous Mycobacteria/genetics ; Phosphates ; Water Microbiology ; },
abstract = {Increases in phosphate availability in drinking water distribution systems (DWDSs) from the use of phosphate-based corrosion control strategies may result in nutrient and microbial community composition shifts in the DWDS. This study assessed the year-long impacts of full-scale DWDS orthophosphate addition on both the microbial ecology and density of drinking-water-associated pathogens that infect the immunocompromised (DWPIs). Using 16S rRNA gene amplicon sequencing and droplet digital PCR, drinking water microbial community composition and DWPI density were examined. Microbial community composition analysis suggested significant compositional changes after the orthophosphate addition. Significant increases in total bacterial density were observed after orthophosphate addition, likely driven by a 2 log 10 increase in nontuberculous mycobacteria (NTM). Linear effect models confirmed the importance of phosphate addition with phosphorus concentration explaining 17% and 12% of the variance in NTM and L. pneumophila density, respectively. To elucidate the impact of phosphate on NTM aggregation, a comparison of planktonic and aggregate fractions of NTM cultures grown at varying phosphate concentrations was conducted. Aggregation assay results suggested that higher phosphate concentrations cause more disaggregation, and the interaction between phosphate and NTM is species specific. This work reveals new insight into the consequences of orthophosphate application on the DWDS microbiome and highlights the importance of proactively monitoring the DWDS for DWPIs.},
}
@article {pmid37970497,
year = {2023},
author = {Lee, JH and Kim, S and Kim, ES and Keum, GB and Doo, H and Kwak, J and Pandey, S and Cho, JH and Ryu, S and Song, M and Cho, JH and Kim, S and Kim, HB},
title = {Comparative analysis of the pig gut microbiome associated with the pig growth performance.},
journal = {Journal of animal science and technology},
volume = {65},
number = {4},
pages = {856-864},
pmid = {37970497},
issn = {2055-0391},
abstract = {There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.},
}
@article {pmid37968548,
year = {2024},
author = {Naidoo, Y and Pierneef, RE and Cowan, DA and Valverde, A},
title = {Characterization of the soil resistome and mobilome in Namib Desert soils.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {27},
number = {4},
pages = {967-975},
pmid = {37968548},
issn = {1618-1905},
mesh = {*Soil Microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Desert Climate ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Gene Transfer, Horizontal ; Soil/chemistry ; Genes, Bacterial ; Interspersed Repetitive Sequences ; },
abstract = {The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.},
}
@article {pmid37968339,
year = {2023},
author = {Sadiq, FA and De Reu, K and Steenackers, H and Van de Walle, A and Burmølle, M and Heyndrickx, M},
title = {Dynamic social interactions and keystone species shape the diversity and stability of mixed-species biofilms - an example from dairy isolates.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {118},
pmid = {37968339},
issn = {2730-6151},
support = {101025683//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 35906//Villum Fonden (Villum Foundation)/ ; },
abstract = {Identifying interspecies interactions in mixed-species biofilms is a key challenge in microbial ecology and is of paramount importance given that interactions govern community functionality and stability. We previously reported a bacterial four-species biofilm model comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus that were isolated from the surface of a dairy pasteuriser after cleaning and disinfection. These bacteria produced 3.13-fold more biofilm mass compared to the sum of biofilm masses in monoculture. The present study confirms that the observed community synergy results from dynamic social interactions, encompassing commensalism, exploitation, and amensalism. M. lacticum appears to be the keystone species as it increased the growth of all other species that led to the synergy in biofilm mass. Interactions among the other three species (in the absence of M. lacticum) also contributed towards the synergy in biofilm mass. Biofilm inducing effects of bacterial cell-free-supernatants were observed for some combinations, revealing the nature of the observed synergy, and addition of additional species to dual-species combinations confirmed the presence of higher-order interactions within the biofilm community. Our findings provide understanding of bacterial interactions in biofilms which can be used as an interaction-mediated approach for cultivating, engineering, and designing synthetic bacterial communities.},
}
@article {pmid37966591,
year = {2024},
author = {Heinrichs, ME and Piedade, GJ and Popa, O and Sommers, P and Trubl, G and Weissenbach, J and Rahlff, J},
title = {Breaking the Ice: A Review of Phages in Polar Ecosystems.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2738},
number = {},
pages = {31-71},
pmid = {37966591},
issn = {1940-6029},
mesh = {*Bacteriophages ; Ecosystem ; Biomass ; Biological Evolution ; Cell Death ; *Viroids ; },
abstract = {Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.},
}
@article {pmid37966223,
year = {2023},
author = {Liu, S and Greenhut, IV and Heist, EP and Heist, MR and Moe, LA},
title = {Bacterial community dynamics during distilled spirit fermentation: influence of mash recipes and fermentation processes.},
journal = {Microbiology spectrum},
volume = {11},
number = {6},
pages = {e0162423},
pmid = {37966223},
issn = {2165-0497},
mesh = {*Saccharomyces cerevisiae ; Fermentation ; *Ethanol ; Bacteria/genetics ; Sugars ; },
abstract = {Production of ethanol from sugars and yeast is an ancient, ostensibly simple process. The source of sugars varies depending on the desired product and can include fruits, vegetables, molasses, honey, or grains, among other things. The source of yeast can be natural in the case of spontaneous ferments, but dry yeast addition is typical for large-scale fermentations. While the polymicrobial nature of some alcoholic fermentations is appreciated (e.g., for wine), most grain-based ethanol producers view microbes, apart from the added yeast, as "contaminants" meant to be controlled in order to maximize efficiency of ethanol production per unit of sugar. Nonetheless, despite rigorous cleaning-in-place measures and cooking the mash, bacteria are routinely cultured from these fermentations. We now know that bacteria can contribute to fermentation efficiency on an industrial scale, yet nothing is known about the makeup and stability of microbial communities in distilled spirit fermentations. The work here establishes the roles of mash recipes and distillery practices in microbial community assembly and dynamics over the course of fermentation. This represents an important first step in appreciating the myriad roles of bacteria in the production of distilled spirits.},
}
@article {pmid37966203,
year = {2023},
author = {Miliotis, G and McDonagh, F and Singh, NK and O'Connor, L and Tuohy, A and Morris, D and Venkateswaran, K},
title = {Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station.},
journal = {Microbiology spectrum},
volume = {11},
number = {6},
pages = {e0189723},
pmid = {37966203},
issn = {2165-0497},
support = {2021_ECRAward//University of Galway (NUI Galway)/ ; Space Biology NNH12ZTT001N grant no. 19-12829-26//National Aeronautics and Space Administration (NASA)/ ; },
mesh = {Humans ; *Space Flight ; Bacteria/genetics ; Klebsiella/genetics ; Plasmids ; Genomics ; Klebsiella pneumoniae/genetics ; },
abstract = {The International Space Station (ISS) is a unique, hermetically sealed environment, subject to environmental pressures not encountered on Earth, including microgravity and radiation (cosmic ionising/UV). While bacteria's adaptability during spaceflight remains elusive, recent research suggests that it may be species and even clone-specific. Considering the documented spaceflight-induced suppression of the human immune system, a deper understanding of the genomics of potential human pathogens in space could shed light on species and lineages of medical astromicrobiological significance. In this study, we used hybrid assembly methods and comparative genomics to deliver a comprehensive genomic characterization of 10 Klebsiella isolates retrieved from the ISS. Our analysis unveiled that Klebsiella quasipneumoniae ST138 demonstrates both spatial and temporal persistence aboard the ISS, showing evidence of genomic divergence from its Earth-based ST138 lineage. Moreover, we characterized plasmids from Klebsiella species of ISS origin, which harbored genes for disinfectant resistance and enhanced thermotolerance, suggestin possible adaptive advantages. Furthermore, we identified a mobile genetic element containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the "high-risk" ST101 clone. Our work provides insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the dynamics of potential pathogenic bacteria in such environments.},
}
@article {pmid37965618,
year = {2023},
author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN},
title = {Sediment microbiome diversity and functional profiles of unprotected arid-tropical natural wetlands in South Africa revealed by shotgun metagenomics data.},
journal = {Data in brief},
volume = {51},
number = {},
pages = {109726},
pmid = {37965618},
issn = {2352-3409},
abstract = {The Limpopo province, located in the arid-tropical region in northeastern South Africa, is renowned for its diverse natural wetlands, some of which are currently unprotected. These wetlands play a crucial role in preserving biodiversity, purifying water, controlling floods, and supporting agricultural production for rural communities. Unfortunately, human activities such as agricultural effluents, run-offs, domestic wastewater, and plastics pollution, along with the impacts of climate change, are mounting pressures on these ecosystems. However, there is limited information on the microbial ecology of natural wetlands in this region, considering the changing anthropogenic activities. The data presented represents the first report on the microbial and functional diversity of sediment microbiomes associated with unprotected arid-tropical natural wetlands in South Africa. Metagenomic shotgun sequencing was performed on sediment samples from ten different wetlands using the Illumina NextSeq 2000 platform. Taxonomic profiling of 328,625,930 high-quality sequencing reads using the MetaPhlAn v3.0 pipeline revealed that Bacteria were the most abundant kingdom (54.5 %), followed by Viruses (0.40 %), Archaea (0.01 %), and Eukaryota (0.36 %). Among bacteria, the most prevalent taxa belonged to the phylum Proteobacteria, particularly the classes Gammaproteobacteria and Betaproteobacteria, which accounted for 83 % of bacterial sequences. The Terrabacteria group, consisting of the phyla Firmicutes and Actinobacteria, made up 3 % of the bacterial population. The abundance of these top bacterial taxa varied across different wetland samples, both at the genus and species levels. In addition, hierarchical clustering based on Bray-Curtis dissimilarity distances of fungal, protist, archaea, and virus species showed distinct clustering of sediment samples from different wetlands. Functional annotation of the metagenomes identified 1224-1702 enzyme classes, 84,833-198,397 gene families, and 280-400 pathways across the various wetland sediments. The data provide crucial baseline information on the microbial and functional diversity of sediment communities in arid tropical wetlands. This knowledge will contribute to a better understanding of these unique environments and can aid in their management and conservation efforts in rural South Africa.},
}
@article {pmid37964521,
year = {2023},
author = {Brunetti, AE and Lyra, ML and Monteiro, JPC and Zurano, JP and Baldo, D and Haddad, CFB and Moeller, AH},
title = {Convergence of gut microbiota in myrmecophagous amphibians.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2011},
pages = {20232223},
pmid = {37964521},
issn = {1471-2954},
support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; Biological Evolution ; *Microbiota ; Mammals/microbiology ; Anura ; RNA, Ribosomal, 16S ; },
abstract = {The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.},
}
@article {pmid37961388,
year = {2023},
author = {Karim, S and Zenzal, TJ and Beati, L and Sen, R and Adegoke, A and Kumar, D and Downs, LP and Keko, M and Nussbaum, A and Becker, DJ and Moore, FR},
title = {Ticks without borders: Microbial communities of immature Neotropical tick species parasitizing migratory landbirds along northern Gulf of Mexico.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37961388},
issn = {2692-8205},
support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; },
abstract = {The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can lead to the emergence of novel tick-borne pathogens or the re-emergence of previously eradicated ones. This study assessed the prevalence of exotic tick species parasitizing resident, short-distance, and long-distance songbirds during spring and autumn at stopover sites in the northern Gulf of Mexico using the mitochondrial 12S rDNA gene. Birds were captured for tick collection from six different sites from late August to early November in both 2018 and 2019. The highest number of ticks were collected in the 2019 season. Most ticks were collected off the Yellow-breasted Chat (Icteria virens) and Common Yellowthroat (Geothlypis trichas), and 54% of the total ticks collected were from Grand Chenier, LA. A high throughput 16S ribosomal RNA sequencing approach was followed to characterize the microbial communities and identify pathogenic microbes in all tick samples. Tick microbial communities, diversity, and community structure were determined using quantitative insight into microbial ecology (QIIME). The sparse correlations for compositional data (SparCC) approach was then used to construct microbial network maps and infer microbial correlations. A total of 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre was the most abundant tick genus and species, respectively. Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant bacteria include the pathogenic Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma. BLAST analysis and phylogenetic reconstruction of the Rickettsia sequences revealed the highest similarities to pathogenic spotted and non-spotted fever groups, including R. buchneri, R. conorii, R. prowazekii, R. bellii, R. australis, R. parkeri, R. monacensis, and R. monteiroi. Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also observed a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium. Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing means dispersal distances from 421-5003 kilometers. These findings strongly highlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.},
}
@article {pmid37959068,
year = {2023},
author = {Bettera, L and Levante, A and Bancalari, E and Bottari, B and Cirlini, M and Neviani, E and Gatti, M},
title = {Lacticaseibacillus Strains Isolated from Raw Milk: Screening Strategy for Their Qualification as Adjunct Culture in Cheesemaking.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {21},
pages = {},
pmid = {37959068},
issn = {2304-8158},
support = {FIL-Quota Incentivante//University of Parma/ ; },
abstract = {The microbial ecology fundamentals of raw milk and long-ripened cheeses consist of a complex interaction between starter lactic acid bacteria (SLAB) and non-starter LAB (NSLAB). Although NSLAB aromatic properties are paramount, other phenotypic traits need to be considered for their use as adjunct cultures, such as the capability to endure technological parameters encountered during cheesemaking. The present study focused on the isolation and characterization of NSLAB from spontaneously fermented raw cow's milk coming from 20 dairies that produce Grana Padano PDO cheese. From 122 isolates, the screening process selected the 10 most diverse strains belonging to Lacticaseibacillus spp. to be phenotypically characterized. The strains were tested for their growth performance in milk in combination with the application of technological stresses, for their ability to produce volatile compounds after their growth in milk, and for their ability to use different nutrient sources and resist chemicals. The complex characterization qualified the strains 5959_Lbparacasei and 5296_Lbparacasei as the best candidates to be used as adjunct strains in the production of raw milk and long-ripened cheeses, provided that antibiotic resistance is measured before their employment. Other strains with interesting aromatic capabilities but lower heat resistance were 5293_Lbparacasei, 5649_Lbparacasei and 5780_Lbparacasei, which could be candidates as adjunct strains for uncooked cheese production.},
}
@article {pmid37957741,
year = {2023},
author = {Moldovan, OT and Carrell, AA and Bulzu, PA and Levei, E and Bucur, R and Sitar, C and Faur, L and Mirea, IC and Șenilă, M and Cadar, O and Podar, M},
title = {The gut microbiome mediates adaptation to scarce food in Coleoptera.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {80},
pmid = {37957741},
issn = {2524-6372},
support = {R01 DE024463/DE/NIDCR NIH HHS/United States ; R01DE024463/NH/NIH HHS/United States ; },
abstract = {Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles' microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibula, adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineages Spiroplasma or Wolbachia. All beetles had relatively high levels of fermentative Carnobacterium and Vagococcus involved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.},
}
@article {pmid37956766,
year = {2024},
author = {Dong, CD and Huang, CP and Chen, CW and Hung, CM},
title = {The remediation of marine sediments containing polycyclic aromatic hydrocarbons by peroxymonosulfate activated with Sphagnum moss-derived biochar and its benthic microbial ecology.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {341},
number = {},
pages = {122912},
doi = {10.1016/j.envpol.2023.122912},
pmid = {37956766},
issn = {1873-6424},
mesh = {*Sphagnopsida ; *Polycyclic Aromatic Hydrocarbons ; Peroxides ; Carbon ; Geologic Sediments/chemistry ; },
abstract = {This research was to study the efficiency of Sphagnum moss-derived biochar (SMBC) in removing polycyclic aromatic hydrocarbons (PAHs) from marine sediment using a peroxymonosulfate (PMS)-based carbon-advanced oxidation process (PMS-CAOPs). Sphagnum moss-derived biochar (SMBC) was generated via a simple thermochemical process for PMS activation toward enhancing decontamination of sediments. At pH 6, the SMBC/PMS system achieved a PAH removal efficiency exceeding 78% in 12 h reaction time. Moreover, PAHs of 6-, 5-, 4-, 3-, and 2-ring structures exhibited 98%, 74%, 68%, 85%, and 91%, of removal, respectively. The SMBC activation of PMS generated both radicals (SO4[•-] and HO•) and nonradical ([1]O2), species responsible for PAHs degradation, attributed primarily to inherent iron and carbon moieties. The significant PAHs degradation efficiency showcased by the SMBC/PMS process holds promise for augmenting the performance of indigenous benthic microbial activity in sediment treatment contexts. The response of sediment microbial communities to PAH-induced stress was particularly associated with the Proteobacteria phylum, specifically the Sulfurovum genus. The findings of the present study highlight the efficacy of environmentally benign reactive radical/nonradical-based PMS-CAOP using pristine carbon materials, offering a sustainable strategy for sediment treatment.},
}
@article {pmid37956735,
year = {2024},
author = {Cohen, E and Azriel, S and Auster, O and Gal, A and Mikhlin, S and Crauwels, S and Rahav, G and Gal-Mor, O},
title = {A new Salmonella enterica serovar that was isolated from a wild sparrow presents a distinct genetic, metabolic and virulence profile.},
journal = {Microbes and infection},
volume = {26},
number = {3},
pages = {105249},
doi = {10.1016/j.micinf.2023.105249},
pmid = {37956735},
issn = {1769-714X},
mesh = {Animals ; Mice ; *Salmonella enterica/genetics ; Salmonella typhimurium/genetics ; Serogroup ; *Salmonella Infections, Animal/microbiology ; *Sparrows ; Virulence/genetics ; *Arsenic ; },
abstract = {Salmonella enterica is a ubiquitous and clinically-important bacterial pathogen, able to infect and cause different diseases in a wide range of hosts. Here, we report the isolation and characterization of a new S. enterica serovar (13,23:i:-; S. Tirat-Zvi), belonging to the Havana supper-lineage that was isolated from a wild house sparrow (Passer domesticus) in Israel. Whole genome sequencing and complete assembly of its genome indicated a plasmid-free, 4.7 Mb genome that carries the Salmonella pathogenicity islands 1-6, 9, 19 and an integrative and conjugative element (ICE), encoding arsenic resistance genes. Phenotypically, S. Tirat-Zvi isolate TZ282 was motile, readily formed biofilm, more versatile in carbon source utilization than S. Typhimurium and highly tolerant to arsenic, but impaired in host cell invasion. In-vivo infection studies indicated that while S. Tirat-Zvi was able to infect and cause an acute inflammatory enterocolitis in young chicks, it was compromised in mice colonization and did not cause an inflammatory colitis in mice compared to S. Typhimurium. We suggest that these phenotypes reflect the distinctive ecological niche of this new serovar and its evolutionary adaptation to passerine birds, as a permissive host. Moreover, these results further illuminate the genetic, phenotypic and ecological diversity of S. enterica pathovars.},
}
@article {pmid37956179,
year = {2023},
author = {Sauters, TJC and Roth, C and Murray, D and Sun, S and Floyd Averette, A and Onyishi, CU and May, RC and Heitman, J and Magwene, PM},
title = {Amoeba predation of Cryptococcus: A quantitative and population genomic evaluation of the accidental pathogen hypothesis.},
journal = {PLoS pathogens},
volume = {19},
number = {11},
pages = {e1011763},
pmid = {37956179},
issn = {1553-7374},
support = {R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; R01 AI133654/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Humans ; Mice ; *Amoeba/microbiology ; Metagenomics ; Predatory Behavior ; *Cryptococcus neoformans/genetics ; *Cryptococcosis/genetics/microbiology ; },
abstract = {The "Amoeboid Predator-Fungal Animal Virulence Hypothesis" posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor Bzp4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions.},
}
@article {pmid37954239,
year = {2023},
author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D},
title = {Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1258775},
pmid = {37954239},
issn = {1664-302X},
abstract = {Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse Acomys cahirinus and the house mouse Mus musculus, in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the D-loop sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano-Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano-Turanian, and Sudanian regions. The phyla Firmicutes and Bacteroidetes were highly abundant, and Deferribacterota, Cyanobacteria and Proteobacteria were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV.},
}
@article {pmid37951257,
year = {2024},
author = {Ye, J and Li, J and Li, L and Zhang, S and Chen, J and Zhu, D and Zhang, C and Xie, B and Zhang, B and Hou, K},
title = {Trends in global ambient fine particulate matter pollution and diabetes mortality rates attributable to it in the 1990-2019: 30 years systematic analysis of global burden of disease.},
journal = {The Science of the total environment},
volume = {908},
number = {},
pages = {168358},
doi = {10.1016/j.scitotenv.2023.168358},
pmid = {37951257},
issn = {1879-1026},
mesh = {Humans ; Particulate Matter ; Global Burden of Disease ; *Diabetes Mellitus/epidemiology ; Environmental Pollution ; Environmental Exposure ; *Air Pollution ; Quality-Adjusted Life Years ; },
abstract = {AIM: To analyze the trends in ambient fine particulate matter pollution (PM2.5) and the age-standardized mortality rate (ASMR) of diabetes attributable to it from 1990 to 2019 by region, country, and socio-economic development status.<br><br>METHODS: The main data, including the summary exposure value (SEV) of ambient PM2.5 and the ASMR of diabetes due to ambient PM2.5, was collected from the Global Burden of Disease 2019 database. The socio-demographic index (SDI) was employed for assessing a particular region or country's degree of socio-economic development. Joinpoint regression analysis was used to assess the changes of ambient PM2.5 and ASMR of diabetes attributable to it.<br><br>RESULTS: Globally, the SEV of ambient PM2.5 increased from 15.65&#xa0;&#x3bc;g/m[3] in 1990 to 26.22&#xa0;&#x3bc;g/m[3] in 2019, with an annual average percent change (AAPC) of 1.788 (95&#xa0;% CI 1.687-1.889) &#x3bc;g/m[3]. The ASMR of diabetes attributable to ambient PM2.5 increased from 1.57 per 100,000 population in 1990 to 2.47 per 100.000 population in 2019 (AAPC&#xa0;=&#xa0;1.569 [95&#xa0;% CI 1.42-1.718]). Most regions and countries had an increase of SEV of ambient PM2.5 and ASMR of diabetes attributable to ambient PM2.5. The largest increase of SEV of ambient PM2.5 was observed in South Asia (AAPC&#xa0;=&#xa0;3.556 [95&#xa0;% CI 3.329-3.875]), while the largest increase of ASMR of diabetes was in Central Asia (AAPC&#xa0;=&#xa0;5.170 [95%CI 4.696-5.647]). Moreover, the increase of SEV of ambient PM2.5 and ASMR of diabetes attributable to it were positively associated with SDI in low SDI countries (SDI&#xa0;<&#xa0;0.46), whereas the opposite result was observed when SDI&#xa0;&#x2265;&#xa0;0.46.<br><br>CONCLUSION: From 1990 to 2019, the population's exposure to ambient PM2.5 and ASMR of diabetes attributable to it increased generally, especially in low-middle SDI regions. Ambient PM2.5 remains a threat to global health. Greater investment in ambient PM2.5 and the mortality attributable to it are needed.},
}
@article {pmid37950563,
year = {2023},
author = {White, A and Giannetto, M and Mulla, L and Del Rosario, A and Lim, T and Culver, E and Timmer, M and Bushell, J and Lambert, MR and Hernández-Gómez, O},
title = {Bacterial communities of the threatened Western Pond Turtle may be impacted by land use.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {12},
pages = {},
doi = {10.1093/femsec/fiad143},
pmid = {37950563},
issn = {1574-6941},
support = {//David H. Smith Postdoctoral Fellowship/ ; //Association of Zoos and Aquariums Saving Animals From Extinction Western Pond Turtle Range-wide Conservation Coalition Grant/ ; //Northern California Herpetological Society/ ; },
mesh = {Animals ; *Turtles/microbiology ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Fresh Water ; },
abstract = {As semi-aquatic species that use both terrestrial and aquatic habitats, freshwater turtles and their microbial communities are especially sensitive to the impacts of habitat disturbance. In this study, we use 16S rRNA amplicon sequencing to characterize the shell and cloacal bacterial communities of turtles in the San Francisco Bay Area. We captured western pond turtles (Actinemys/Emys marmorata) across eight sites located in urban and rural environments, along with invasive red-eared sliders (Trachemys scripta elegans). We assessed differences in western pond turtle bacterial communities diversity/composition between shell and cloacal samples and evaluated how alpha/beta diversity metrics were influenced by habitat quality. We found phylum-level bacterial taxonomic turnover in the bacterial communities of western pond turtles relative to the host tissue substrate samples. Our findings indicate that location identity elicits a high degree of lower-level (i.e. species/genus) bacterial taxonomic turnover. Further, we found that samples originating from good quality habitat had poorer shell bacterial communities but more diverse cloacal ones. The shell bacterial communities of red-eared sliders overlapped with those western pond turtles suggesting the existence of microbial dispersal between these two species. Our results add to our current understanding of turtle symbiont microbial ecology by establishing patterns of bacterial symbiont variation in an urban to rural gradient.},
}
@article {pmid37942081,
year = {2023},
author = {Han, X and Beck, K and Bürgmann, H and Frey, B and Stierli, B and Frossard, A},
title = {Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1279041},
pmid = {37942081},
issn = {1664-302X},
abstract = {Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.},
}
@article {pmid37941937,
year = {2023},
author = {Zhang, H and Wei, T and Li, Q and Fu, L and He, L and Wang, Y},
title = {Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16257},
pmid = {37941937},
issn = {2167-8359},
mesh = {DNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Water ; *Microbiota/genetics ; Sulfates ; },
abstract = {Our knowledge on biogeochemistry and microbial ecology of marine blue holes is limited due to challenges in collecting multilayered water column and oxycline zones. In this study, we collected samples from 16 water layers in Yongle blue hole (YBH) located in the South China Sea using the in situ microbial filtration and fixation (ISMIFF) apparatus. The microbial communities based on 16S rRNA metagenomic reads for the ISMIFF samples showed high microbial diversity and consistency among samples with similar dissolved oxygen levels. At the same depth of the anoxic layer, the ISMIFF samples were dominated by sulfate-reducing bacteria from Desulfatiglandales (17.96%). The sulfide concentration is the most significant factor that drives the division of microbial communities in YBH, which might support the prevalence of sulfate-reducing microorganisms in the anoxic layers. Our results are different from the microbial community structures of a Niskin sample of this study and the reported samples collected in 2017, in which a high relative abundance of Alteromonadales (26.59%) and Thiomicrospirales (38.13%), and Arcobacteraceae (11.74%) was identified. We therefore demonstrate a new profile of microbial communities in YBH probably due to the effect of sampling and molecular biological methods, which provides new possibilities for further understanding of the material circulation mechanism of blue holes and expanding anoxic marine water zones under global warming.},
}
@article {pmid37941395,
year = {2022},
author = {Blumberg, K and Miller, M and Ponsero, A and Hurwitz, B},
title = {Ontology-driven analysis of marine metagenomics: what more can we learn from our data?.},
journal = {GigaScience},
volume = {12},
number = {},
pages = {},
pmid = {37941395},
issn = {2047-217X},
mesh = {*Ecology ; *Microbiota/genetics ; Metagenome ; Metagenomics ; },
abstract = {BACKGROUND: The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data.<br><br>RESULTS: Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments.<br><br>CONCLUSIONS: In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.},
}
@article {pmid37938301,
year = {2022},
author = {McDaniel, EA and van Steenbrugge, JJM and Noguera, DR and McMahon, KD and Raaijmakers, JM and Medema, MH and Oyserman, BO},
title = {TbasCO: trait-based comparative 'omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {111},
pmid = {37938301},
issn = {2730-6151},
support = {MCB-1518130//National Science Foundation (NSF)/ ; MCB-1518130//National Science Foundation (NSF)/ ; },
abstract = {A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.},
}
@article {pmid37934729,
year = {2023},
author = {Vasileiou, D and Karapiperis, C and Baltsavia, I and Chasapi, A and Ahrén, D and Janssen, PJ and Iliopoulos, I and Promponas, VJ and Enright, AJ and Ouzounis, CA},
title = {CGG toolkit: Software components for computational genomics.},
journal = {PLoS computational biology},
volume = {19},
number = {11},
pages = {e1011498},
pmid = {37934729},
issn = {1553-7358},
mesh = {Reproducibility of Results ; *Genomics/methods ; *Software ; Computational Biology/methods ; Genome ; },
abstract = {Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release.},
}
@article {pmid37934609,
year = {2023},
author = {Qiao, N and Gaur, G and Modesto, M and Chinnici, F and Scarafile, D and Borruso, L and Marin, AC and Spiezio, C and Valente, D and Sandri, C and Gänzle, MG and Mattarelli, P},
title = {Physiological and genomic characterization of Lactiplantibacillus plantarum isolated from Indri indri in Madagascar.},
journal = {Journal of applied microbiology},
volume = {134},
number = {11},
pages = {},
doi = {10.1093/jambio/lxad255},
pmid = {37934609},
issn = {1365-2672},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Canada Research Chairs/ ; //China Scholarship Council/ ; },
mesh = {Animals ; *Indriidae/metabolism ; Madagascar ; Coumaric Acids/metabolism ; *Lactobacillus plantarum/genetics/metabolism ; Genomics ; *Anti-Infective Agents/metabolism ; },
abstract = {AIMS: Indri indri is a lemur of Madagascar which is critically endangered. The analysis of the microbial ecology of the intestine offers tools to improve conservation efforts. This study aimed to achieve a functional genomic analysis of three Lactiplantibacillus plantarum isolates from indris.<br><br>METHODS AND RESULTS: Samples were obtained from 18 indri; 3 isolates of Lp. plantarum were obtained from two individuals. The three isolates were closely related to each other, with <10 single nucleotide polymorphisms, suggesting that the two individuals shared diet-associated microbes. The genomes of the three isolates were compared to 96 reference strains of Lp. plantarum. The three isolates of Lp. plantarum were not phenotypically resistant to antibiotics but shared all 17 genes related to antimicrobial resistance that are part of the core genome of Lp. plantarum. The genomes of the three indri isolates of Lp. plantarum also encoded for the 6 core genome genes coding for enzymes related to metabolism of hydroxybenzoic and hydroxycinnamic acids. The phenotype for metabolism of hydroxycinnamic acids by indri isolates of Lp. plantarum matched the genotype.<br><br>CONCLUSIONS: Multiple antimicrobial resistance genes and gene coding for metabolism of phenolic compounds were identified in the genomes of the indri isolates, suggesting that Lp. plantarum maintains antimicrobial resistance in defense of antimicrobial plant secondary pathogens and that their metabolism by intestinal bacteria aids digestion of plant material by primate hosts.},
}
@article {pmid37933257,
year = {2023},
author = {Ochoa-Sánchez, M and Acuña Gomez, EP and Moreno, L and Moraga, CA and Gaete, K and Eguiarte, LE and Souza, V},
title = {Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16290},
pmid = {37933257},
issn = {2167-8359},
mesh = {Animals ; *Spheniscidae ; RNA, Ribosomal, 16S ; *Microbiota ; Soil ; },
abstract = {Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.},
}
@article {pmid37932283,
year = {2023},
author = {Simpson, AC and Sengupta, P and Zhang, F and Hameed, A and Parker, CW and Singh, NK and Miliotis, G and Rekha, PD and Raman, K and Mason, CE and Venkateswaran, K},
title = {Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {19207},
pmid = {37932283},
issn = {2045-2322},
support = {R01 MH117406/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Prevalence ; Phenotype ; *Paenibacillus/genetics ; Fatty Acids/analysis ; DNA ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; },
abstract = {With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10[T] (= NRRL B-65660[T] = DSM 115933[T]), Leifsonia virtsii F6_8S_P_1A[T] (= NRRL B-65661[T] = DSM 115931[T]), Leifsonia williamsii F6_8S_P_1B[T] (= NRRL B-65662[T] = DSM 115932[T]), Paenibacillus vandeheii F6_3S_P_1C[T] (= NRRL B-65663[T] = DSM 115940[T]), and Sporosarcina highlanderae F6_3S_P_2[T] (= NRRL B-65664[T] = DSM 115943[T]). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.},
}
@article {pmid37931689,
year = {2024},
author = {Álvarez-Pérez, S and Lievens, B and de Vega, C},
title = {Floral nectar and honeydew microbial diversity and their role in biocontrol of insect pests and pollination.},
journal = {Current opinion in insect science},
volume = {61},
number = {},
pages = {101138},
doi = {10.1016/j.cois.2023.101138},
pmid = {37931689},
issn = {2214-5753},
mesh = {Animals ; *Plant Nectar ; *Pollination ; Insecta ; Carbohydrates ; Ecosystem ; },
abstract = {Sugar-rich plant-related secretions, such as floral nectar and honeydew, that are commonly used as nutrient sources by insects and other animals, are also the ecological niche for diverse microbial communities. Recent research has highlighted the great potential of nectar and honeydew microbiomes in biological pest control and improved pollination, but the exploitation of these microbiomes requires a deep understanding of their community dynamics and plant-microbe-insect interactions. Additionally, the successful application of microbes in crop fields is conditioned by diverse ecological, legal, and ethical challenges that should be taken into account. In this article, we provide an overview of the nectar and honeydew microbiomes and discuss their potential applications in sustainable agricultural practices.},
}
@article {pmid37931135,
year = {2023},
author = {Naik, AT and Kamensky, KM and Hellum, AM and Moisander, PH},
title = {Disturbance frequency directs microbial community succession in marine biofilms exposed to shear.},
journal = {mSphere},
volume = {8},
number = {6},
pages = {e0024823},
pmid = {37931135},
issn = {2379-5042},
support = {N00014220-1-2170//DOD | USN | Office of Naval Research (ONR)/ ; Multi-Institutional Collaborative Seed Funding//University of Massachusetts Dartmouth (UMD)/ ; N00014-16-1-3051//Michigan State University (MSU)/ ; },
mesh = {*Biofilms ; *Microbiota ; Prokaryotic Cells ; },
abstract = {Disturbances are major drivers of community succession in many microbial systems; however, relatively little is known about marine biofilm community succession, especially under antifouling disturbance. Antifouling technologies exert strong local disturbances on marine biofilms, and resulting biomass losses can be accompanied by shifts in biofilm community composition and succession. We address this gap in knowledge by bridging microbial ecology with antifouling technology development. We show that disturbance by shear can strongly alter marine biofilm community succession, acting as a selective filter influenced by frequency of exposure. Examining marine biofilm succession patterns with and without shear revealed stable associations between key prokaryotic and eukaryotic taxa, highlighting the importance of cross-domain assessment in future marine biofilm research. Describing how compounded top-down and bottom-up disturbances shape the succession of marine biofilms is valuable for understanding the assembly and stability of these complex microbial communities and predicting species invasiveness.},
}
@article {pmid37926855,
year = {2023},
author = {Minnebo, Y and Delbaere, K and Goethals, V and Raes, J and Van de Wiele, T and De Paepe, K},
title = {Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {240},
pmid = {37926855},
issn = {2049-2618},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Butyrates/metabolism ; Nutrients ; Fermentation ; Carbohydrates ; Feces/microbiology ; },
abstract = {BACKGROUND: Transit time is an important modulator of the human gut microbiome. The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research. We singled out gut transit time in an unprecedented in vitro approach by subjecting faecal microbial communities from six individuals with either short, medium or long in vivo transit times, to three different colonic transit times of 21, 32 and 63 h in the validated human gut in vitro model, SHIME.<br><br>RESULTS: Transit time was identified as the single most important driver of microbial cell concentrations (52%), metabolic activity (45%) and quantitative (24%) and proportional (22%) community composition. Deceleration of transit was characterised by a significant decrease of specific Bifidobacterium and Veillonella spp. and increase of specific fibre degrading bacteria and nutrient specialists, such as Bacteroides, Prevotella, Ruminococcus, Bilophila and Akkermansia spp. These microbial communities reached a higher population density and net carbohydrate fermentation, leading to an increased SCFA production at longer transit times. In contrast, the carbohydrate-to-biomass production efficiency was increased at shorter transits, particularly in well-adapted faecal microbiomes from donors with short in vivo transit. Said adaptation was also reflected in the carbohydrate-to-SCFA conversion efficiency which varied with donor, but also colon region and SCFA chain length. A long transit time promoted propionate production, whereas butyrate production and butyrate producers were selectively enriched in the proximal colon at medium transit time.<br><br>CONCLUSION: Microbial growth rates and nutrient utilisation efficiency mediate the species-specific gut microbiota response to in vitro transit time variation, which is the main driver of in vitro microbial load, metabolism and community composition. Given the in vivo transit time variation within and between individuals, the personalisation of in vitro transit time based on in vivo data is required to accurately study intra- and inter-individual differences in gut microbiome structure, functionality and interactions with host and environmental modulators. Video Abstract.},
}
@article {pmid37925991,
year = {2023},
author = {Chen, C and Li, P and Yin, M and Wang, J and Sun, Y and Ju, W and Liu, L and Li, ZH},
title = {Deciphering characterization of seasonal variations in microbial communities of marine ranching: Diversity, co-occurrence network patterns, and assembly processes.},
journal = {Marine pollution bulletin},
volume = {197},
number = {},
pages = {115739},
doi = {10.1016/j.marpolbul.2023.115739},
pmid = {37925991},
issn = {1879-3363},
mesh = {Seasons ; *Microbiota ; Temperature ; Microbial Consortia ; Bacteria ; },
abstract = {Offshore coastal marine ranching ecosystems are one of the most productive ecosystems. The results showed that the composition and structure of the microbial communities varied considerably with the season. Co-occurrence network analysis demonstrated that the microbial network was more complex in summer and positively correlated links (cooperative or symbiotic) were dominated in autumn and winter. Null model indicated that the ecological processes of the bacterial communities were mainly governed by deterministic processes (mainly homogeneous selection) in summer. For microeukaryotic communities, assembly processes were more regulated by stochastic processes in all seasons. For rare taxa, assembly processes were regulated by stochastic processes and were not affected by seasonality. Changes in water temperature due to seasonal variations were the main, but not the only, environmental factor driving changes in microbial communities. This study will improve the understanding of offshore coastal ecosystems through the perspective of microbial ecology.},
}
@article {pmid37925029,
year = {2024},
author = {Ghosh, A and Yash, and Kumar, C and Bhadury, P},
title = {Cascading effects of trace metals enrichment on phytoplankton communities of the River Ganga in South Asia.},
journal = {Chemosphere},
volume = {347},
number = {},
pages = {140607},
doi = {10.1016/j.chemosphere.2023.140607},
pmid = {37925029},
issn = {1879-1298},
mesh = {Phytoplankton ; Rivers ; Ecosystem ; Asia, Southern ; *Arsenic/toxicity ; *Diatoms ; *Trace Elements/pharmacology ; Iron/pharmacology ; },
abstract = {Globally freshwater ecosystems and associated biota including phytoplankton communities are at extreme risk from trace metal pollution originating from geogenic as well as from anthropogenic sources such as release of untreated industrial effluents. In the present study influence of iron- and arsenic-enrichments on structure and metabolism of phytoplankton communities of River Ganga, one of the largest rivers of South Asia, was assessed under laboratory-based microcosm experiments. Surface water samples were collected and subsequently enriched with higher than recommended concentrations of iron (10 mg/L) and arsenic (10 μg/L). The set-up comprised of nine containers of 25 L volume with three containers each for iron- and arsenic-enrichment and was maintained for 30 days. Trace metal enrichment rapidly changed the phytoplankton community structure and chemistry of nutrients uptake. Iron-enrichment prompted diatom blooms comprising of Thalassiosira, succeeded by green algae Coelastrum. Arsenic-enrichment maintained cyanobacteria for longer time-spans compared to the control and iron-enriched containers but significantly lesser abundance of diatoms. Variations in community composition was also reflected in nutrient uptake rates with silicate release in the arsenic-enriched containers at the end of the experiment. Changes in macronutrient dynamics also altered genus growth rates wherein both iron- and arsenic appeared to lower the death rate of Thalassosira but stimulated growth of other genera including Skeletonema and Pandorina. Iron appeared to influence lesser number of genera compared to arsenic which altered growth rates of both diatoms and green algae. This consequently influenced the gross primary productivity values which lowered both in the iron- and arsenic-enriched containers compared to the control owing to decrease in phytoplankton diversity. Iron appeared to drive phytoplankton communities toward a less general and more specialized composition with high abundance of selective species comprising of small diatoms such as Thalassiosira, whereas arsenic appears to select for green algal enrichment in freshwater ecosystems.},
}
@article {pmid37920817,
year = {2023},
author = {Talavera-Marcos, S and Parras-Moltó, M and Aguirre de Cárcer, D},
title = {Leveraging phylogenetic signal to unravel microbiome function and assembly rules.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {5165-5173},
pmid = {37920817},
issn = {2001-0370},
abstract = {Clarifying the general rules behind microbial community assembly will foster the development of microbiome-based technological solutions. Here, we study microbial community assembly through a computational analysis of phylogenetic core groups (PCGs): discrete portions of the bacterial phylogeny with high prevalence in the ecosystem under study. We first show that the existence of PCGs was a predominant feature of the varied set of microbial ecosystems studied. Then, we re-analyzed an in vitro experimental dataset using a PCG-based approach, drawing only from its community composition data and from publicly available genomic databases. Using mainly genome scale metabolic models and population dynamics modeling, we obtained ecological insights on metabolic niche structure and population dynamics comparable to those gained after canonical experimentation. Thus, leveraging phylogenetic signal to help unravel microbiome function and assembly rules offers a potential avenue to gain further insight on Earth's microbial ecosystems.},
}
@article {pmid37920261,
year = {2023},
author = {Poirier, S and Coeuret, G and Champomier-Vergès, MC and Desmonts, MH and Werner, D and Feurer, C and Frémaux, B and Guillou, S and Luong, NM and Rué, O and Loux, V and Zagorec, M and Chaillou, S and , },
title = {Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1286661},
pmid = {37920261},
issn = {1664-302X},
abstract = {BACKGROUND: The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics.<br><br>METHODS: Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers.<br><br>RESULTS: Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism.<br><br>CONCLUSION: We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.},
}
@article {pmid37920009,
year = {2023},
author = {Yuan, X and Song, W and Li, Y and Wang, Q and Qing, J and Zhi, W and Han, H and Qin, Z and Gong, H and Hou, G and Li, Y},
title = {Using Bayesian networks with tabu algorithm to explore factors related to chronic kidney disease with mental illness: A cross-sectional study.},
journal = {Mathematical biosciences and engineering : MBE},
volume = {20},
number = {9},
pages = {16194-16211},
doi = {10.3934/mbe.2023723},
pmid = {37920009},
issn = {1551-0018},
mesh = {Humans ; Cross-Sectional Studies ; Bayes Theorem ; Algorithms ; *Renal Insufficiency, Chronic/epidemiology ; *Mental Disorders/epidemiology ; },
abstract = {While Bayesian networks (BNs) offer a promising approach to discussing factors related to many diseases, little attention has been poured into chronic kidney disease with mental illness (KDMI) using BNs. This study aimed to explore the complex network relationships between KDMI and its related factors and to apply Bayesian reasoning for KDMI, providing a scientific reference for its prevention and treatment. Data was downloaded from the online open database of CHARLS 2018, a population-based longitudinal survey. Missing values were first imputed using Random Forest, followed by propensity score matching (PSM) for class balancing regarding KDMI. Elastic Net was then employed for variable selection from 18 variables. Afterwards, the remaining variables were included in BNs model construction. Structural learning of BNs was achieved using tabu algorithm and the parameter learning was conducted using maximum likelihood estimation. After PSM, 427 non-KDMI cases and 427 KDMI cases were included in this study. Elastic Net identified 11 variables significantly associated with KDMI. The BNs model comprised 12 nodes and 24 directed edges. The results suggested that diabetes, physical activity, education levels, sleep duration, social activity, self-report on health and asset were directly related factors for KDMI, whereas sex, age, residence and Internet access represented indirect factors for KDMI. BN model not only allows for the exploration of complex network relationships between related factors and KDMI, but also could enable KDMI risk prediction through Bayesian reasoning. This study suggests that BNs model holds great prospects in risk factor detection for KDMI.},
}
@article {pmid37919394,
year = {2023},
author = {Dougherty, PE and Nielsen, TK and Riber, L and Lading, HH and Forero-Junco, LM and Kot, W and Raaijmakers, JM and Hansen, LH},
title = {Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria.},
journal = {The ISME journal},
volume = {17},
number = {12},
pages = {2415-2425},
pmid = {37919394},
issn = {1751-7370},
support = {NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 801199//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; },
mesh = {*Prophages/genetics ; *Triticum ; Bacteria/genetics ; },
abstract = {Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and diversity in 63 Erwinia and Pseudomonas strains isolated from flag leaves of wheat grown in a single field. Introducing and validating Virion Induction Profiling Sequencing (VIP-Seq), we identify and quantify the activity of 120 spontaneously induced prophages, discovering that some phyllosphere bacteria produce more than 10[8] virions/mL in overnight cultures, with significant induction also observed in planta. Sequence analyses and plaque assays reveal E. aphidicola prophages contribute a majority of intraspecies genetic diversity and divide their bacterial hosts into antagonistic factions engaged in widespread microbial warfare, revealing the importance of prophage-mediated microdiversity. When comparing spontaneously active prophages with predicted prophages we also find insertion sequences are strongly correlated with non-active prophages. In conclusion, we discover widespread and largely unknown prophage diversity and function in phyllosphere bacteria.},
}
@article {pmid37914532,
year = {2023},
author = {Ray, AE and Tribbia, DZ and Cowan, DA and Ferrari, BC},
title = {Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {87},
number = {4},
pages = {e0004823},
pmid = {37914532},
issn = {1098-5557},
support = {FT170100341, DP220103430//Department of Education and Training | Australian Research Council (ARC)/ ; 4406//Department of the Environment and Energy | Australian Antarctic Division (AAD)/ ; },
mesh = {*Carbon Monoxide/metabolism ; *Gases ; Hydrogen/metabolism ; Soil ; Methane/metabolism ; Water ; },
abstract = {Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.},
}
@article {pmid37914126,
year = {2024},
author = {Abkar, L and Moghaddam, HS and Fowler, SJ},
title = {Microbial ecology of drinking water from source to tap.},
journal = {The Science of the total environment},
volume = {908},
number = {},
pages = {168077},
doi = {10.1016/j.scitotenv.2023.168077},
pmid = {37914126},
issn = {1879-1026},
mesh = {*Drinking Water/analysis ; Water Supply ; *Water Purification/methods ; Sanitary Engineering ; Public Health ; Water Microbiology ; },
abstract = {As drinking water travels from its source, through various treatment processes, hundreds to thousands of kilometres of distribution network pipes, to the taps in private homes and public buildings, it is exposed to numerous environmental changes, as well as other microbes living in both water and on surfaces. This review aims to identify the key locations and factors that are associated with changes in the drinking water microbiome throughout conventional urban drinking water systems from the source to the tap water. Over the past 15 years, improvements in cultivation-independent methods have enabled studies that allow us to answer such questions. As a result, we are beginning to move towards predicting the impacts of disturbances and interventions resulting ultimately in management of drinking water systems and microbial communities rather than mere observation. Many challenges still exist to achieve effective management, particularly within the premise plumbing environment, which exhibits diverse and inconsistent conditions that may lead to alterations in the microbiota, potentially presenting public health risks. Finally, we recommend the establishment of global collaborative projects on the drinking water microbiome that will enhance our current knowledge and lead to tools for operators and researchers alike to improve global access to high-quality drinking water.},
}
@article {pmid37909775,
year = {2023},
author = {Mason, G and Footer, MJ and Rojas, ER},
title = {Mechanosensation induces persistent bacterial growth during bacteriophage predation.},
journal = {mBio},
volume = {14},
number = {6},
pages = {e0276622},
pmid = {37909775},
issn = {2150-7511},
support = {R35 GM143057/GM/NIGMS NIH HHS/United States ; 5R35GM143057-02//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Escherichia coli/virology/growth &amp; development ; *Bacteriophages/physiology/growth &amp; development ; },
abstract = {Bacteria and bacteriophage form one of the most important predator-prey relationships on earth, yet how the long-term stability of this ecological interaction is achieved is unclear. Here, we demonstrate that Escherichia coli can rapidly grow during bacteriophage predation if they are doing so in spatially confined environments. This discovery revises our understanding of bacteria-bacteriophage population dynamics in many real-world environments where bacteria grow in confinement, such as the gut and the soil. Additionally, this result has clear implications for the potential of bacteriophage therapy and the role of mechanosensation during bacterial pathogenesis.},
}
@article {pmid37909659,
year = {2024},
author = {Quiroga, MV and Stegen, JC and Mataloni, G and Cowan, D and Lebre, PH and Valverde, A},
title = {Microdiverse bacterial clades prevail across Antarctic wetlands.},
journal = {Molecular ecology},
volume = {33},
number = {1},
pages = {e17189},
doi = {10.1111/mec.17189},
pmid = {37909659},
issn = {1365-294X},
support = {PICT 2016-2517//ANPCyT - Argentina/ ; PICT 2020-3113//ANPCyT - Argentina/ ; //European Union/ ; //Instituto Ant&#xe1;rtico Argentino - Direcci&#xf3;n Nacional del Ant&#xe1;rtico/ ; CLU-2019-05 IRNASA/CSIC//Junta de Castilla y Le&#xf3;n/ ; //NRF - South Africa/ ; Contract DE-AC05-76RL01830 -JCS//U.S. Department of Energy-BER program/ ; },
mesh = {Phylogeny ; Antarctic Regions ; *Wetlands ; Bacteria/genetics ; *Microbiota ; },
abstract = {Antarctica's extreme environmental conditions impose selection pressures on microbial communities. Indeed, a previous study revealed that bacterial assemblages at the Cierva Point Wetland Complex (CPWC) are shaped by strong homogeneous selection. Yet which bacterial phylogenetic clades are shaped by selection processes and their ecological strategies to thrive in such extreme conditions remain unknown. Here, we applied the phyloscore and feature-level βNTI indexes coupled with phylofactorization to successfully detect bacterial monophyletic clades subjected to homogeneous (HoS) and heterogenous (HeS) selection. Remarkably, only the HoS clades showed high relative abundance across all samples and signs of putative microdiversity. The majority of the amplicon sequence variants (ASVs) within each HoS clade clustered into a unique 97% sequence similarity operational taxonomic unit (OTU) and inhabited a specific environment (lotic, lentic or terrestrial). Our findings suggest the existence of microdiversification leading to sub-taxa niche differentiation, with putative distinct ecotypes (consisting of groups of ASVs) adapted to a specific environment. We hypothesize that HoS clades thriving in the CPWC have phylogenetically conserved traits that accelerate their rate of evolution, enabling them to adapt to strong spatio-temporally variable selection pressures. Variable selection appears to operate within clades to cause very rapid microdiversification without losing key traits that lead to high abundance. Variable and homogeneous selection, therefore, operate simultaneously but on different aspects of organismal ecology. The result is an overall signal of homogeneous selection due to rapid within-clade microdiversification caused by variable selection. It is unknown whether other systems experience this dynamic, and we encourage future work evaluating the transferability of our results.},
}
@article {pmid37903921,
year = {2023},
author = {Jansson, JK and McClure, R and Egbert, RG},
title = {Soil microbiome engineering for sustainability in a changing environment.},
journal = {Nature biotechnology},
volume = {41},
number = {12},
pages = {1716-1728},
pmid = {37903921},
issn = {1546-1696},
mesh = {*Soil ; *Microbiota/genetics ; Soil Microbiology ; Synthetic Biology ; Biotechnology ; },
abstract = {Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.},
}
@article {pmid37902333,
year = {2023},
author = {van der Meij, A and Elsayed, SS and Du, C and Willemse, J and Wood, TM and Martin, NI and Raaijmakers, JM and van Wezel, GP},
title = {The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {11},
pages = {e0123923},
pmid = {37902333},
issn = {1098-5336},
support = {14221//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; },
mesh = {*Plant Growth Regulators ; *Amino Acids ; Anti-Bacterial Agents ; Hormones ; },
abstract = {Microorganisms that live on or inside plants can influence plant growth and health. Among the plant-associated bacteria, streptomycetes play an important role in defense against plant diseases, but the underlying mechanisms are not well understood. Here, we demonstrate that the plant hormones jasmonic acid (JA) and methyl jasmonate directly affect the life cycle of streptomycetes by modulating antibiotic synthesis and promoting faster development. Moreover, the plant hormones specifically stimulate the synthesis of the polyketide antibiotic actinorhodin in Streptomyces coelicolor. JA is then modified in the cell by amino acid conjugation, thereby quenching toxicity. Collectively, these results provide new insight into the impact of a key plant hormone on diverse phenotypic responses of streptomycetes.},
}
@article {pmid37901816,
year = {2023},
author = {Li, Y and Hou, Y and Hou, Q and Long, M and Wang, Z and Rillig, MC and Liao, Y and Yong, T},
title = {Soil microbial community parameters affected by microplastics and other plastic residues.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1258606},
pmid = {37901816},
issn = {1664-302X},
abstract = {INTRODUCTION: The impact of plastics on terrestrial ecosystems is receiving increasing attention. Although of great importance to soil biogeochemical processes, how plastics influence soil microbes have yet to be systematically studied. The primary objectives of this study are to evaluate whether plastics lead to divergent responses of soil microbial community parameters, and explore the potential driving factors.<br><br>METHODS: We performed a meta-analysis of 710 paired observations from 48 published articles to quantify the impact of plastic on the diversity, biomass, and functionality of soil microbial communities.<br><br>RESULTS AND DISCUSSION: This study indicated that plastics accelerated soil organic carbon loss (effect size&#x2009;=&#x2009;-0.05, p&#x2009;=&#x2009;0.004) and increased microbial functionality (effect size&#x2009;=&#x2009;0.04, p&#x2009;=&#x2009;0.003), but also reduced microbial biomass (effect size&#x2009;=&#x2009;-0.07, p&#x2009;<&#x2009;0.001) and the stability of co-occurrence networks. Polyethylene significantly reduced microbial richness (effect size&#x2009;=&#x2009;-0.07, p&#x2009;<&#x2009;0.001) while polypropylene significantly increased it (effect size&#x2009;=&#x2009;0.17, p&#x2009;<&#x2009;0.001). Degradable plastics always had an insignificant effect on the microbial community. The effect of the plastic amount on microbial functionality followed the "hormetic dose-response" model, the infection point was about 40&#x2009;g/kg. Approximately 3564.78&#x2009;&#x3bc;m was the size of the plastic at which the response of microbial functionality changed from positive to negative. Changes in soil pH, soil organic carbon, and total nitrogen were significantly positively correlated with soil microbial functionality, biomass, and richness (R[2]&#x2009;=&#x2009;0.04-0.73, p&#x2009;<&#x2009;0.05). The changes in microbial diversity were decoupled from microbial community structure and functionality. We emphasize the negative impacts of plastics on soil microbial communities such as microbial abundance, essential to reducing the risk of ecological surprise in terrestrial ecosystems. Our comprehensive assessment of plastics on soil microbial community parameters deepens the understanding of environmental impacts and ecological risks from this emerging pollution.},
}
@article {pmid37897125,
year = {2023},
author = {Seppey, CVW and Cabrol, L and Thalasso, F and Gandois, L and Lavergne, C and Martinez-Cruz, K and Sepulveda-Jauregui, A and Aguilar-Muñoz, P and Astorga-España, MS and Chamy, R and Dellagnezze, BM and Etchebehere, C and Fochesatto, GJ and Gerardo-Nieto, O and Mansilla, A and Murray, A and Sweetlove, M and Tananaev, N and Teisserenc, R and Tveit, AT and Van de Putte, A and Svenning, MM and Barret, M},
title = {Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes.},
journal = {Environmental microbiology},
volume = {25},
number = {12},
pages = {3364-3386},
doi = {10.1111/1462-2920.16526},
pmid = {37897125},
issn = {1462-2920},
support = {Project MATCH C16B03//ECOS sud CONICYT/ ; grant no. 256132/H30//ECOS sud CONICYT/ ; project METHANOBASE (ELAC2014_DCC-0092)//ERANet-LAC program/ ; //French Ministries of Foreign Affairs and International Development (MAEDI)/ ; //German Federal Ministry of Education and Research, WISNA program/ ; grant no. 277238//Mexican National Council for Science and Technology (CONACYT)/ ; //National Education, Superior Education and Research (MENESR)/ ; MillenniumScienceInitiativeProgram-ICN2021_002//Chilean National Agency of Research and Development (ANID)/ ; },
mesh = {*Microbiota/genetics ; *Euryarchaeota/genetics ; Wetlands ; Soil/chemistry ; Methane ; },
abstract = {Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.},
}
@article {pmid37895286,
year = {2023},
author = {Aboushaala, K and Wong, AYL and Barajas, JN and Lim, P and Al-Harthi, L and Chee, A and Forsyth, CB and Oh, CD and Toro, SJ and Williams, FMK and An, HS and Samartzis, D},
title = {The Human Microbiome and Its Role in Musculoskeletal Disorders.},
journal = {Genes},
volume = {14},
number = {10},
pages = {},
pmid = {37895286},
issn = {2073-4425},
support = {R21 AR079679/AR/NIAMS NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Bacteria ; *Musculoskeletal Diseases ; Oxygen ; },
abstract = {Musculoskeletal diseases (MSDs) are characterized as injuries and illnesses that affect the musculoskeletal system. MSDs affect every population worldwide and are associated with substantial global burden. Variations in the makeup of the gut microbiota may be related to chronic MSDs. There is growing interest in exploring potential connections between chronic MSDs and variations in the composition of gut microbiota. The human microbiota is a complex community consisting of viruses, archaea, bacteria, and eukaryotes, both inside and outside of the human body. These microorganisms play crucial roles in influencing human physiology, impacting metabolic and immunological systems in health and disease. Different body areas host specific types of microorganisms, with facultative anaerobes dominating the gastrointestinal tract (able to thrive with or without oxygen), while strict aerobes prevail in the nasal cavity, respiratory tract, and skin surfaces (requiring oxygen for development). Together with the immune system, these bacteria have coevolved throughout time, forming complex biological relationships. Changes in the microbial ecology of the gut may have a big impact on health and can help illnesses develop. These changes are frequently impacted by lifestyle choices and underlying medical disorders. The potential for safety, expenses, and efficacy of microbiota-based medicines, even with occasional delivery, has attracted interest. They are, therefore, a desirable candidate for treating MSDs that are chronic and that may have variable progression patterns. As such, the following is a narrative review to address the role of the human microbiome as it relates to MSDs.},
}
@article {pmid37894228,
year = {2023},
author = {Jech, SD and Day, N and Barger, NN and Antoninka, A and Bowker, MA and Reed, S and Tucker, C},
title = {Cultivating Resilience in Dryland Soils: An Assisted Migration Approach to Biological Soil Crust Restoration.},
journal = {Microorganisms},
volume = {11},
number = {10},
pages = {},
pmid = {37894228},
issn = {2076-2607},
support = {RC18-1322//Department of Defense Strategic Environmental Research and Development Program/ ; NA//Canyonlands Research Center/ ; NA//Wildlife Conservation Society Climate Adaptation Fund/ ; },
abstract = {Land use practices and climate change have driven substantial soil degradation across global drylands, impacting ecosystem functions and human livelihoods. Biological soil crusts, a common feature of dryland ecosystems, are under extensive exploration for their potential to restore the stability and fertility of degraded soils through the development of inoculants. However, stressful abiotic conditions often result in the failure of inoculation-based restoration in the field and may hinder the long-term success of biocrust restoration efforts. Taking an assisted migration approach, we cultivated biocrust inocula sourced from multiple hot-adapted sites (Mojave and Sonoran Deserts) in an outdoor facility at a cool desert site (Colorado Plateau). In addition to cultivating inoculum from each site, we created an inoculum mixture of biocrust from the Mojave Desert, Sonoran Desert, and Colorado Plateau. We then applied two habitat amelioration treatments to the cultivation site (growth substrate and shading) to enhance soil stability and water availability and reduce UV stress. Using marker gene sequencing, we found that the cultivated mixed inoculum comprised both local- and hot-adapted cyanobacteria at the end of cultivation but had similar cyanobacterial richness as each unmixed inoculum. All cultivated inocula had more cyanobacterial 16S rRNA gene copies and higher cyanobacterial richness when cultivated with a growth substrate and shade. Our work shows that it is possible to field cultivate biocrust inocula sourced from different deserts, but that community composition shifts toward that of the cultivation site unless habitat amelioration is employed. Future assessments of the function of a mixed inoculum in restoration and its resilience in the face of abiotic stressors are needed to determine the relative benefit of assisted migration compared to the challenges and risks of this approach.},
}
@article {pmid37883861,
year = {2024},
author = {Zhang, X and Luther, AK and Rabaey, K and Prévoteau, A},
title = {Periodic polarization duty cycle tunes performance and adhesion of anodic electroactive biofilms.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {155},
number = {},
pages = {108581},
doi = {10.1016/j.bioelechem.2023.108581},
pmid = {37883861},
issn = {1878-562X},
mesh = {*Geobacter ; Biofilms ; Electrodes ; Carbon ; *Bioelectric Energy Sources ; },
abstract = {Periodic polarization can improve the performance of anodic electroactive biofilms (EABs). The impact of the half-period duration was previously investigated at constant duty cycle (50%), i.e., the proportion of a period during which the electrode is polarized. Here, we cultured eight EABs on glassy carbon electrodes at four different duty cycles (50%, 67%, 80% and 91%) by varying the time interval under open circuit conditions, while keeping the polarization duration at 10 s. The shorter duty cycles slightly slowed initial growth but produced EABs generating higher faradaic currents. The total charge recovery over 38 days increased with decreasing duty cycles from 0.53 kC.cm[-2] (duty cycle of 91%) to 1.65 kC.cm[-2] (50%). EABs with the shortest duty cycle fully detached twice from the electrode surface, but detachments were quickly followed by the formation of more efficient EABs. We then carried out controlled removal of some aged and low current-producing EABs by applying a 30 s cathodic current (H2 evolution at -15 mA.cm[-2]) and observed the subsequent rapid development of fresh EABs displaying better electrochemical performance. Our results illustrate that well-chosen dynamic controls of electrode potentials can substantially improve the average current production of EABs, or allow a simple replacement of underperforming EABs.},
}
@article {pmid37878053,
year = {2023},
author = {Maisnam, P and Jeffries, TC and Szejgis, J and Bristol, D and Singh, BK and Eldridge, DJ and Horn, S and Chieppa, J and Nielsen, UN},
title = {Severe Prolonged Drought Favours Stress-Tolerant Microbes in Australian Drylands.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3097-3110},
pmid = {37878053},
issn = {1432-184X},
support = {DP150104199; DP190101968//Australian Research Council/ ; },
mesh = {Humans ; Ecosystem ; Droughts ; Soil Microbiology ; Australia ; Soil/chemistry ; Bacteria/genetics ; *Chytridiomycota ; *Microbiota ; },
abstract = {Drylands comprise one-third of Earth's terrestrial surface area and support over two billion people. Most drylands are projected to experience altered rainfall regimes, including changes in total amounts and fewer but larger rainfall events interspersed by longer periods without rain. This transition will have ecosystem-wide impacts but the long-term effects on microbial communities remain poorly quantified. We assessed belowground effects of altered rainfall regimes (+ 65% and -65% relative to ambient) at six sites in arid and semi-arid Australia over a period of three years (2016-2019) coinciding with a significant natural drought event (2017-2019). Microbial communities differed significantly among semi-arid and arid sites and across years associated with variation in abiotic factors, such as pH and carbon content, along with rainfall. Rainfall treatments induced shifts in microbial community composition only at a subset of the sites (Milparinka and Quilpie). However, differential abundance analyses revealed that several taxa, including Acidobacteria, TM7, Gemmatimonadates and Chytridiomycota, were more abundant in the wettest year (2016) and that their relative abundance decreased in drier years. By contrast, the relative abundance of oligotrophic taxa such as Actinobacteria, Alpha-proteobacteria, Planctomycetes, and Ascomycota and Basidiomycota, increased during the prolonged drought. Interestingly, fungi were shown to be more sensitive to the prolonged drought and to rainfall treatment than bacteria with Basidiomycota mostly dominant in the reduced rainfall treatment. Moreover, correlation network analyses showed more positive associations among stress-tolerant dominant taxa following the drought (i.e., 2019 compared with 2016). Our result indicates that such stress-tolerant taxa play an important role in how whole communities respond to changes in aridity. Such knowledge provides a better understanding of microbial responses to predicted increases in rainfall variability and the impact on the functioning of semi-arid and arid ecosystems.},
}
@article {pmid37878052,
year = {2023},
author = {Chen, M and Su, S and Zhang, C and Zhu, J and Feng, W and Chen, H and Jiang, J and Lu, Z and Liu, W and Gan, J},
title = {The Role of Biogeography in Shaping Intestinal Flora and Influence on Fatty Acid Composition in Red Swamp Crayfish (Procambarus clarkii).},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3111-3127},
pmid = {37878052},
issn = {1432-184X},
mesh = {Animals ; *Gastrointestinal Microbiome ; Astacoidea/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Fatty Acids ; },
abstract = {Intestinal microbiota plays an important role in promoting digestion, metabolism, and immunity. Intestinal microbiota and fatty acids are important indicators to evaluate the health and nutritional composition of Procambarus clarkii. They have been shown to be strongly influence by environmental and genetic factors. However, it is not clear whether environmental factors have a greater impact on the intestinal microbiota and fatty acid composition of crayfish. The link between the intestinal microbial communities and fatty acid (FA) compositions of red swamp crayfish from different geographical has not yet been studied. Thus, the current paper focuses on the influence of different environments on the fatty acids in muscles of crayfish and the possible existence between gut microbiota and fatty acids. Therefore, in this study, we compared the fatty acid compositions and intestinal microbiota of five crayfish populations from different geographical locations. The results were further analyzed to determine whether there is a relationship between geographical location, fatty acid compositions and intestinal microbiota. The gut microbial communities of the crayfish populations were characterized using 16S rRNA high-throughput gene sequencing. The results showed that there were significant differences in FA compositions of crayfish populations from different geographical locations. A similar trend was observed in the gut microbiome, which also varied significantly according to geographic location. Interestingly, the analysis revealed that there was a relationship between fatty acid compositions and intestinal microbes, revealed by alpha diversity analysis and cluster analysis. However, further studies of the interactions between the P. clarkii gut microbiota and biochemical composition are needed, which will ultimately reveal the complexity of microbial ecosystems with potential applications in aquaculture and species conservation.},
}
@article {pmid37877729,
year = {2023},
author = {Eng, AY and Narayanan, A and Alster, CJ and DeAngelis, KM},
title = {Thermal adaptation of soil microbial growth traits in response to chronic warming.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {11},
pages = {e0082523},
pmid = {37877729},
issn = {1098-5336},
support = {DEB-1749206, DEB-1832110//National Science Foundation (NSF)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {*Soil ; *Global Warming ; Soil Microbiology ; Climate Change ; Biomass ; },
abstract = {Soils are the largest terrestrial carbon sink and the foundation of our food, fiber, and fuel systems. Healthy soils are carbon sinks, storing more carbon than they release. This reduces the amount of carbon dioxide released into the atmosphere and buffers against climate change. Soil microbes drive biogeochemical cycling and contribute to soil health through organic matter breakdown, plant growth promotion, and nutrient distribution. In this study, we determined how soil microbial growth traits respond to long-term soil warming. We found that bacterial isolates from warmed plots showed evidence of adaptation of optimum growth temperature. This suggests that increased microbial biomass and growth in a warming world could result in greater carbon storage. As temperatures increase, greater microbial activity may help reduce the soil carbon feedback loop. Our results provide insight on how atmospheric carbon cycling and soil health may respond in a warming world.},
}
@article {pmid37877306,
year = {2023},
author = {Zhu, B and Gu, H and He, J and Li, F and Yu, J and Liu, W and Chen, Q and Lai, Y and Yu, S},
title = {The impact of smash-ridge tillage on agronomic traits of tobacco plants, soil enzymatic activity, microbial community structure, and functional diversity.},
journal = {Plant signaling &amp; behavior},
volume = {18},
number = {1},
pages = {2260640},
pmid = {37877306},
issn = {1559-2324},
mesh = {*Soil/chemistry ; Nicotiana/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Agriculture/methods ; *Microbiota ; },
abstract = {Smash-ridge tillage is a novel cultivation technique that significantly influences the quality of arable land and crop yield. In this study, we employed high-throughput 16S rRNA sequencing and Biolog-ECO methods to systematically investigate the impact of smash-ridge tillage on soil microbial community structure and functional diversity. The results demonstrate that both ST30 and ST50 treatments significantly enhance the average plant height, average plant diameter, average fresh root weight, stem fresh weight, and leaf area of tobacco plants, with the ST50 treatment exhibiting superior performance. Furthermore, both ST30 and ST50 treatments exhibit significantly higher soil enzyme activity and microbial community diversity compared to the CK treatment. They also improve the soil microbial utilization of carbon sources. Additionally, the ST50-treated soil samples demonstrate 15 microbial functional pathways that exceed those of the CK and ST30 treatments. In conclusion, the Smash-ridge tillage treatment at a depth of 50 cm yields more favorable results. This study provides a theoretical foundation for enhancing soil quality in Smash-ridge tillage by elucidating the mechanisms through which it impacts soil microbial ecology.},
}
@article {pmid37875737,
year = {2023},
author = {Dahl, SA and Seifert, J and Camarinha-Silva, A and Cheng, YC and Hernández-Arriaga, A and Hudler, M and Windisch, W and König, A},
title = {Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3082-3096},
pmid = {37875737},
issn = {1432-184X},
mesh = {Animals ; Rumen/microbiology ; *Deer ; Forests ; Bacteria ; Nutrients ; *Microbiota ; },
abstract = {Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer's rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.},
}
@article {pmid37875201,
year = {2024},
author = {Chen, S and Kuramae, EE and Jia, Z and Liu, B},
title = {Stable isotope probing reveals compositional and functional shifts in active denitrifying communities along the soil profile in an intensive agricultural area.},
journal = {The Science of the total environment},
volume = {907},
number = {},
pages = {167968},
doi = {10.1016/j.scitotenv.2023.167968},
pmid = {37875201},
issn = {1879-1026},
mesh = {*Soil ; *Nitrates/analysis ; Agriculture ; DNA ; Isotopes ; Denitrification ; Soil Microbiology ; },
abstract = {Denitrifying microbial communities in the vadose zone play an essential role in eliminating the nitrate leached from agricultural practices. This nitrate could otherwise contaminate groundwater and threaten public health. Here, we utilized stable isotope probing combined with amplicon sequencing and functional gene quantification to inspect the composition and function of heterotrophic denitrifying microorganisms along a 9-m soil profile in an intensive agricultural area. Dramatic differences in the composition of the active denitrifiers were uncovered between the surface soil and deep layers of the vadose zone. The main denitrifying bacterial taxa identified from [13]C-DNA fractions were Pseudomonadaceae (Pseudomonas), Rhodocyclaceae (Azoarcus), and Burkholderiaceae in the surface soil (0-0.2 m), and were Pseudomonadaceae (Pseudomonas), Burkholderiaceae, Bacillaceae (Bacillus), and Paenibacillaceae (Ammoniphilus) in the deep layers (0.5-9.0 m). Analysis of the functional genes (nirS, nirK, and nosZ) in isotope-labeled DNA revealed an upward nos/nir ratio with increasing soil depth, which may account for the higher nitrous oxide emission potential in the surface soil, as compared to the deeper sand-rich, low organic carbon layers. This study improves our understanding of active denitrifying microbes in the vadose zone and helps in developing techniques to reduce nitrate pollution in groundwater.},
}
@article {pmid37874854,
year = {2023},
author = {George, AB and O'Dwyer, J},
title = {Universal abundance fluctuations across microbial communities, tropical forests, and urban populations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {44},
pages = {e2215832120},
pmid = {37874854},
issn = {1091-6490},
support = {376199//Simons Foundation (SF)/ ; 220020439//James S. McDonnell Foundation (JSMF)/ ; },
mesh = {Humans ; Urban Population ; *Forests ; Population Dynamics ; *Microbiota ; Cities ; },
abstract = {The growth of complex populations, such as microbial communities, forests, and cities, occurs over vastly different spatial and temporal scales. Although research in different fields has developed detailed, system-specific models to understand each individual system, a unified analysis of different complex populations is lacking; such an analysis could deepen our understanding of each system and facilitate cross-pollination of tools and insights across fields. Here, we use a shared framework to analyze time-series data of the human gut microbiome, tropical forest, and urban employment. We demonstrate that a single, three-parameter model of stochastic population dynamics can reproduce the empirical distributions of population abundances and fluctuations in all three datasets. The three parameters characterizing a species measure its mean abundance, deterministic stability, and stochasticity. Our analysis reveals that, despite the vast differences in scale, all three systems occupy a similar region of parameter space when time is measured in generations. In other words, although the fluctuations observed in these systems may appear different, this difference is primarily due to the different physical timescales associated with each system. Further, we show that the distribution of temporal abundance fluctuations is described by just two parameters and derive a two-parameter functional form for abundance fluctuations to improve risk estimation and forecasting.},
}
@article {pmid37871765,
year = {2024},
author = {Brandt, A and Csarmann, K and Hernández-Arriaga, A and Baumann, A and Staltner, R and Halilbasic, E and Trauner, M and Camarinha-Silva, A and Bergheim, I},
title = {Antibiotics attenuate diet-induced nonalcoholic fatty liver disease without altering intestinal barrier dysfunction.},
journal = {The Journal of nutritional biochemistry},
volume = {123},
number = {},
pages = {109495},
doi = {10.1016/j.jnutbio.2023.109495},
pmid = {37871765},
issn = {1873-4847},
mesh = {Male ; Mice ; Animals ; *Non-alcoholic Fatty Liver Disease/etiology/metabolism ; Liver/metabolism ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice, Inbred C57BL ; Diet/adverse effects ; Inflammation/metabolism ; *Gastrointestinal Diseases ; Fructose/metabolism ; Diet, High-Fat ; },
abstract = {To date the role of the alterations of intestinal microbiota in the development of intestinal barrier dysfunction in settings of nonalcoholic fatty liver disease (NAFLD) has not been fully understood. Here, we assessed the effect of antibiotics on development of NAFLD and their impact on intestinal barrier dysfunction. Male C57BL/6J mice were either pair-fed a liquid control diet (C) or fat- and fructose-rich diet (FFr) +/- antibiotics (AB, ampicillin/vancomycin/metronidazole/gentamycin) for 7 weeks. Fasting blood glucose was determined and markers of liver damage, inflammation, intestinal barrier function, and microbiota composition were assessed. The development of hepatic steatosis with early signs of inflammation found in FFr-fed mice was significantly abolished in FFr+AB-fed mice. Also, while prevalence of bacteria in feces was not detectable and TLR4 ligand levels in portal plasma were at the level of controls in FFr+AB-fed mice, impairments of intestinal barrier function like an increased permeation of xylose and iNOS protein levels persisted to a similar extent in both FFr-fed groups irrespective of AB use. Exposure of everted small intestinal tissue sacs of naïve mice to fructose resulted in a significant increase in tissue permeability and loss of tight junction proteins, being not affected by the presence of AB, whereas the concomitant treatment of tissue sacs with the NOS inhibitor aminoguanidine attenuated these alterations. Taken together, our data suggest that intestinal barrier dysfunction in diet-induced NAFLD in mice may not be predominantly dependent on changes in intestinal microbiota but rather that fructose-induced alterations of intestinal NO-homeostasis might be critically involved.},
}
@article {pmid37866247,
year = {2023},
author = {Kleikamp, HBC and Grouzdev, D and Schaasberg, P and van Valderen, R and van der Zwaan, R and Wijgaart, RV and Lin, Y and Abbas, B and Pronk, M and van Loosdrecht, MCM and Pabst, M},
title = {Metaproteomics, metagenomics and 16S rRNA sequencing provide different perspectives on the aerobic granular sludge microbiome.},
journal = {Water research},
volume = {246},
number = {},
pages = {120700},
doi = {10.1016/j.watres.2023.120700},
pmid = {37866247},
issn = {1879-2448},
mesh = {*Sewage/chemistry ; RNA, Ribosomal, 16S/genetics ; Bioreactors ; *Microbiota ; Metagenome ; Metagenomics/methods ; },
abstract = {The tremendous progress in sequencing technologies has made DNA sequencing routine for microbiome studies. Additionally, advances in mass spectrometric techniques have extended conventional proteomics into the field of microbial ecology. However, systematic studies that provide a better understanding of the complementary nature of these 'omics' approaches, particularly for complex environments such as wastewater treatment sludge, are urgently needed. Here, we describe a comparative metaomics study on aerobic granular sludge from three different wastewater treatment plants. For this, we employed metaproteomics, whole metagenome, and 16S rRNA amplicon sequencing to study the same granule material with uniform size. We furthermore compare the taxonomic profiles using the Genome Taxonomy Database (GTDB) to enhance the comparability between the different approaches. Though the major taxonomies were consistently identified in the different aerobic granular sludge samples, the taxonomic composition obtained by the different omics techniques varied significantly at the lower taxonomic levels, which impacts the interpretation of the nutrient removal processes. Nevertheless, as demonstrated by metaproteomics, the genera that were consistently identified in all techniques cover the majority of the protein biomass. The established metaomics data and the contig classification pipeline are publicly available, which provides a valuable resource for further studies on metabolic processes in aerobic granular sludge.},
}
@article {pmid37860776,
year = {2023},
author = {Yitbarek, S and Guittar, J and Knutie, SA and Ogbunugafor, CB},
title = {Deconstructing taxa x taxa xenvironment interactions in the microbiota: A theoretical examination.},
journal = {iScience},
volume = {26},
number = {10},
pages = {107875},
pmid = {37860776},
issn = {2589-0042},
abstract = {A major objective of microbial ecology is to identify how the composition of microbial taxa shapes host phenotypes. However, most studies focus on pairwise interactions and ignore the potentially significant effects of higher-order microbial interactions.Here, we quantify the effects of higher-order interactions among taxa on host infection risk. We apply our approach to an in silico dataset that is built to resemble a population of insect hosts with gut-associated microbial communities at risk of infection from an intestinal parasite across a breadth of nutrient environmental contexts.We find that the effect of higher-order interactions is considerable and can change appreciably across environmental contexts. Furthermore, we show that higher-order interactions can stabilize community structure thereby reducing host susceptibility to parasite invasion.Our approach illustrates how incorporating the effects of higher-order interactions among gut microbiota across environments can be essential for understanding their effects on host phenotypes.},
}
@article {pmid37858824,
year = {2024},
author = {Niu, S and Xie, J and Wang, G and Li, Z and Zhang, K and Li, H and Xia, Y and Tian, J and Yu, E and Xie, W and Gong, W},
title = {Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system.},
journal = {The Science of the total environment},
volume = {907},
number = {},
pages = {167913},
doi = {10.1016/j.scitotenv.2023.167913},
pmid = {37858824},
issn = {1879-1026},
mesh = {Wastewater ; Bacteria ; *Microbiota ; Aquaculture ; *Water Purification ; },
abstract = {Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.},
}
@article {pmid37855643,
year = {2023},
author = {Villabona, N and Moran, N and Hammer, T and Reyes, A},
title = {Conserved, yet disruption-prone, gut microbiomes in neotropical bumblebees.},
journal = {mSphere},
volume = {8},
number = {6},
pages = {e0013923},
pmid = {37855643},
issn = {2379-5042},
support = {R35 GM131738/GM/NIGMS NIH HHS/United States ; },
mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota ; Ecology ; },
abstract = {Social bees are an important model for the ecology and evolution of gut microbiomes. These bees harbor ancient, specific, and beneficial gut microbiomes and are crucial pollinators. However, most of the research has concentrated on managed honeybees and bumblebees in the temperate zone. Here we used 16S rRNA gene sequencing to characterize gut microbiomes in wild neotropical bumblebee communities from Colombia. We also analyzed drivers of microbiome structure across our data and previously published data from temperate bumblebees. Our results show that lineages of neotropical bumblebees not only retained their ancient gut bacterial symbionts during dispersal from North America but also are prone to major disruption, a shift that is strongly associated with parasite infection. Finally, we also found that microbiomes are much more strongly structured by host phylogeny than by geography, despite the very different environmental conditions and plant communities in the two regions.},
}
@article {pmid37852481,
year = {2024},
author = {Zammit, I and Badia, S and Mejías-Molina, C and Rusiñol, M and Bofill-Mas, S and Borrego, CM and Corominas, L},
title = {Zooming in to the neighborhood level: A year-long wastewater-based epidemiology monitoring campaign for COVID-19 in small intraurban catchments.},
journal = {The Science of the total environment},
volume = {907},
number = {},
pages = {167811},
doi = {10.1016/j.scitotenv.2023.167811},
pmid = {37852481},
issn = {1879-1026},
mesh = {Humans ; *COVID-19/epidemiology ; SARS-CoV-2 ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; },
abstract = {In recent years, wastewater-based epidemiology (WBE) has emerged as a valuable and cost-effective tool for monitoring the prevalence of COVID-19. Large-scale monitoring efforts have been implemented in numerous countries, primarily focusing on sampling at the entrance of wastewater treatment plants (WWTPs) to cover a large population. However, sampling at a finer spatial scale, such as at the neighborhood level (NGBs), pose new challenges, including the absence of composite sampling infrastructure and increased uncertainty due to the dynamics of small catchments. This study aims to investigate the feasibility and accuracy of WBE when deployed at the neighborhood level (sampling in sewers) compared to the city level (sampling at the entrance of a WWTP). To achieve this, we deployed specific WBE sampling stations at the intraurban scale within three NGBs in Barcelona, Spain. The study period covers the 5th and the 6th waves of COVID-19 in Spain, spanning from March 2021 to March 2022, along with the WWTP downstream from the NGBs. The results showed a strong correlation between the dynamics of COVID-19 clinical cases and wastewater SARS-CoV-2 loads at both the NGB and city levels. Notably, during the 5th wave, which was dominated by the Delta SARS-CoV-2 variant, wastewater loads were higher than during the 6th wave (Omicron variant), despite a lower number of clinical cases recorded during the 5th wave. The correlations between wastewater loads and clinical cases at the NGB level were stronger than at the WWTP level. However, the early warning potential varied across neighborhoods and waves, with some cases showing a one-week early warning and others lacking any significant early warning signal. Interestingly, the prevalence of COVID-19 did not exhibit major differences among NGBs with different socioeconomic statuses.},
}
@article {pmid37848722,
year = {2023},
author = {Rizaludin, MS and Garbeva, P and Zwart, M and Hu, J},
title = {Microbial volatiles mediate bacterial evolutionary dynamics.},
journal = {The ISME journal},
volume = {17},
number = {12},
pages = {2144-2146},
pmid = {37848722},
issn = {1751-7370},
}
@article {pmid37844340,
year = {2023},
author = {Li, Z and Ma, H and Hong, Z and Zhang, T and Cao, M and Cui, F and Grossart, HP},
title = {Phytoplankton interspecific interactions modified by symbiotic fungi and bacterial metabolites under environmentally relevant hydrogen peroxide concentrations stress.},
journal = {Water research},
volume = {246},
number = {},
pages = {120739},
doi = {10.1016/j.watres.2023.120739},
pmid = {37844340},
issn = {1879-2448},
mesh = {Phytoplankton ; Hydrogen Peroxide/pharmacology ; Symbiosis ; *Chlorella vulgaris ; *Cyanobacteria ; *Microcystis/metabolism ; Water ; Fungi ; Microcystins/metabolism ; },
abstract = {Hydrogen peroxide (H2O2), which accumulates in water and triggers oxidative stress for aquatic microbes, has been shown to have profound impacts on planktonic microbial community dynamics including cyanobacterial bloom formation. Yet, potential effects of H2O2 on interspecific relationships of phytoplankton-microbe symbiotic interactions remain unclear. Here, we investigated effects of environmentally relevant H2O2 concentrations on interspecific microbial relationships in algae-microbe symbiosis. Microbes play a crucial role in the competition between M. aeruginosa and Chlorella vulgaris at low H2O2 concentrations (∼400 nM), in which fungi and bacteria protect Microcystis aeruginosa from oxidative stress. Moreover, H2O2 stimulated the synthesis and release of extracellular microcystin-LR from Microcystis aeruginosa, while intracellular microcystin-LR concentrations remained at a relatively constant level. In the presence of H2O2, loss of organoheterocyclic compounds, organic acids and ketones contributed to the growth of M. aeruginosa, but the reduction of vitamins inhibited it. Regulation of interspecific relationships by H2O2 is achieved by its action on fungal species and bacterial secretory metabolites. This study explored the response of phytoplankton interspecific relationships in symbiotic phytoplankton-microbe interactions to environmentally relevant H2O2 concentrations stress, providing a theoretical basis for understanding the formation of harmful-algae blooming and impact of photochemical properties of water on aquatic ecological safety and stability.},
}
@article {pmid37843656,
year = {2023},
author = {Znamínko, M and Falteisek, L and Vrbická, K and Klímová, P and Christiansen, JR and Jørgensen, CJ and Stibal, M},
title = {Methylotrophic Communities Associated with a Greenland Ice Sheet Methane Release Hotspot.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3057-3067},
pmid = {37843656},
issn = {1432-184X},
support = {A32524//Hartmann Fonden/ ; 0135-00229B//Danish Independent Research Fund/ ; LL2004 'MARCH4G'//Czech Ministry of Education, Youth and Sports/ ; },
mesh = {Greenland ; *Ice Cover/microbiology ; *Methane/analysis ; Climate ; Seasons ; },
abstract = {Subglacial environments provide conditions suitable for the microbial production of methane, an important greenhouse gas, which can be released from beneath the ice as a result of glacial melting. High gaseous methane emissions have recently been discovered at Russell Glacier, an outlet of the southwestern margin of the Greenland Ice Sheet, acting not only as a potential climate amplifier but also as a substrate for methane consuming microorganisms. Here, we describe the composition of the microbial assemblage exported in meltwater from the methane release hotspot at Russell Glacier and its changes over the melt season and as it travels downstream. We found that a substantial part (relative abundance 27.2% across the whole dataset) of the exported assemblage was made up of methylotrophs and that the relative abundance of methylotrophs increased as the melt season progressed, likely due to the seasonal development of the glacial drainage system. The methylotrophs were dominated by representatives of type I methanotrophs from the Gammaproteobacteria; however, their relative abundance decreased with increasing distance from the ice margin at the expense of type II methanotrophs and/or methylotrophs from the Alphaproteobacteria and Betaproteobacteria. Our results show that subglacial methane release hotspot sites can be colonized by microorganisms that can potentially reduce methane emissions.},
}
@article {pmid37843655,
year = {2023},
author = {Sudhakari, PA and Ramisetty, BCM},
title = {An Eco-evolutionary Model on Surviving Lysogeny Through Grounding and Accumulation of Prophages.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3068-3081},
pmid = {37843655},
issn = {1432-184X},
mesh = {Humans ; Lysogeny ; Prophages/genetics ; Escherichia coli/genetics ; *Superinfection/genetics ; Wastewater ; *Bacteriophages/genetics ; Genome, Bacterial ; },
abstract = {Temperate phages integrate into the bacterial genomes propagating along with the bacterial genomes. Multiple phage elements, representing diverse prophages, are present in most bacterial genomes. The evolutionary events and the ecological dynamics underlying the accumulation of prophage elements in bacterial genomes have yet to be understood. Here, we show that the local wastewater had 7% of lysogens (hosting mitomycin C-inducible prophages), and they showed resistance to superinfection by their corresponding lysates. Genomic analysis of four lysogens and four non-lysogens revealed the presence of multiple prophages (belonging to Myoviridae and Siphoviridae) in both lysogens and non-lysogens. For large-scale comparison, 2180 Escherichia coli genomes isolated from various sources across the globe and 523 genomes specifically isolated from diverse wastewaters were analyzed. A total of 15,279 prophages were predicted among 2180 E. coli genomes and 2802 prophages among 523 global wastewater isolates, with a mean of ~ 5 prophages per genome. These observations indicate that most putative prophages are relics of past bacteria-phage conflicts; they are "grounded" prophages that cannot excise from the bacterial genome. Prophage distribution analysis based on the sequence homology suggested the random distribution of E. coli prophages within and between E. coli clades. The independent occurrence pattern of these prophages indicates extensive horizontal transfers across the genomes. We modeled the eco-evolutionary dynamics to reconstruct the events that could have resulted in the prophage accumulation accounting for infection, superinfection immunity, and grounding. In bacteria-phage conflicts, the bacteria win by grounding the prophage, which could confer superinfection immunity.},
}
@article {pmid37836513,
year = {2023},
author = {Perreau, C and Thabuis, C and Verstrepen, L and Ghyselinck, J and Marzorati, M},
title = {Ex Vivo Colonic Fermentation of NUTRIOSE[®] Exerts Immuno-Modulatory Properties and Strong Anti-Inflammatory Effects.},
journal = {Nutrients},
volume = {15},
number = {19},
pages = {},
pmid = {37836513},
issn = {2072-6643},
support = {//Roquette/ ; },
mesh = {Humans ; *Dextrins ; Fermentation ; *Lipopolysaccharides/metabolism ; Caco-2 Cells ; Colon/metabolism ; Fatty Acids, Volatile/metabolism ; Immunity ; Anti-Inflammatory Agents/pharmacology/metabolism ; },
abstract = {NUTRIOSE[®] (Roquette, Lestrem, France) is a resistant dextrin with well-established prebiotic effects. This study evaluated the indirect effects of pre-digested NUTRIOSE[®] on host immune response and gut barrier integrity. Fecal samples from eight healthy donors were inoculated in a Colon-on-a-plate[®] system (ProDigest, Ghent, Belgium) with or without NUTRIOSE[®] supplementation. Following 48 h fermentation, colonic suspensions were tested in a Caco-2/THP1-Blue™ co-culture system to determine their effects on gut barrier activity (transepithelial electrical resistance) and immune response following lipopolysaccharide stimulation. Additionally, changes in short-chain fatty acid levels (SCFA) and microbial community composition following a 48 h fermentation in the Colon-on-a-plate[®] system were measured. Across all donors, immune-mediated intestinal barrier damage was significantly reduced with NUTRIOSE[®]-supplemented colonic suspensions versus blank. Additionally, IL-6 and IL-10 levels were significantly increased, and the level of the neutrophil chemoattractant IL-8 was significantly decreased with NUTRIOSE[®]-supplemented colonic suspensions versus blank in the co-culture models following lipopolysaccharide stimulation. These beneficial effects of NUTRIOSE[®] supplementation were likely due to increased acetate and propionate levels and the enrichment of SCFA-producing bacteria. NUTRIOSE[®] was well fermented by the colonic bacteria of all eight donors and had protective effects on inflammation-induced disruption of the intestinal epithelial barrier and strong anti-inflammatory effects.},
}
@article {pmid37833155,
year = {2023},
author = {Munley, JA and Kelly, LS and Park, G and Gillies, GS and Pons, EE and Kannan, KB and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM},
title = {Sex-specific intestinal dysbiosis persists after multicompartmental injury.},
journal = {Surgery},
volume = {174},
number = {6},
pages = {1453-1462},
doi = {10.1016/j.surg.2023.08.023},
pmid = {37833155},
issn = {1532-7361},
support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; },
mesh = {Female ; Male ; Rats ; Animals ; Rats, Sprague-Dawley ; *Dysbiosis/etiology ; RNA, Ribosomal, 16S ; *Multiple Trauma ; Computational Biology ; },
abstract = {BACKGROUND: Preclinical studies of the gut microbiome after severe traumatic injury have demonstrated severe dysbiosis in males, with sex-specific microbial differences up to 2 days after injury. However, the impact of host sex on injury-driven dysbiosis over time remains unknown. We hypothesized that sex-specific differences in intestinal microbiome diversity and composition after traumatic injury with and without stress would persist after 7 days.<br><br>METHODS: Male and proestrus female Sprague-Dawley rats (n&#xa0;= 8/group) were subjected to either polytrauma (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), polytrauma plus chronic restraint stress, or na&#xef;ve controls. The fecal microbiome was measured on days 0, 3, and 7 using 16S rRNA sequencing and Quantitative Insights into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity (Chao1 and Shannon indices) and beta-diversity were assessed. Analyses were performed in GraphPad and "R," with significance defined as P < .05.<br><br>RESULTS: Polytrauma and polytrauma plus chronic restraint stress reduced alpha-diversity (Chao1, Shannon) within 3 days postinjury, which persisted up to day 7 in both sexes; polytrauma and polytrauma plus chronic restraint stress females had significantly decreased Chao1 compared to male counterparts at day 7 (P&#xa0;= .02). At day 7, the microbiome composition in polytrauma females had higher proportion of Mucispirillum, whereas polytrauma plus chronic restraint stress males demonstrated elevated abundance of Ruminococcus and Akkermansia.<br><br>CONCLUSION: Multicompartmental trauma induces intestinal dysbiosis that is sex-specific with persistence of decreased diversity and unique "pathobiome" signatures in females after 1 week. These findings underline sex as an important biological variable that may influence variable host-specific responses and outcomes after severe trauma and critical illness. This underscores the need to consider precision medicine strategies to ameliorate these outcomes.},
}
@article {pmid37831075,
year = {2023},
author = {Xu, H and Xiao, Q and Dai, Y and Chen, D and Zhang, C and Jiang, Y and Xie, J},
title = {Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3043-3056},
pmid = {37831075},
issn = {1432-184X},
mesh = {*Rivers/chemistry ; *Carbon Sequestration ; Dissolved Organic Matter ; Leucine/metabolism ; Multiomics ; Carbon/metabolism ; Bacteria/genetics/metabolism ; Water/metabolism ; },
abstract = {Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.},
}
@article {pmid37830797,
year = {2023},
author = {Stapelfeldt, HRD and Lanclos, VC and Henson, MW and Thrash, JC},
title = {Draft genome sequence of the BAL58 Betaproteobacteria representative strain LSUCC0117.},
journal = {Microbiology resource announcements},
volume = {12},
number = {11},
pages = {e0062023},
pmid = {37830797},
issn = {2576-098X},
support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; OCE-1945279//National Science Foundation (NSF)/ ; },
abstract = {Here, we present the draft genome sequence of strain LSUCC0117, a representative of the abundant aquatic BAL58 Betaproteobacteria group which we isolated from a coastal site in the northern Gulf of Mexico. The genome is estimated at over 99% complete, with a genome size of 2,687,225 bp.},
}
@article {pmid37828283,
year = {2023},
author = {Kothamasi, D and Vermeylen, S and Deepika, S},
title = {Are ecological processes that select beneficial traits in agricultural microbes nature's intellectual property rights?.},
journal = {Nature biotechnology},
volume = {41},
number = {10},
pages = {1381-1384},
pmid = {37828283},
issn = {1546-1696},
support = {894188//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; },
mesh = {*Intellectual Property ; *Agriculture ; Bacteria ; },
}
@article {pmid37823651,
year = {2023},
author = {Tran, WC and Sullivan, B and Kitzmiller, CE and Choudoir, M and Simoes, R and Dayarathne, N and DeAngelis, KM},
title = {Draft genome sequence of Paenibacillus sp. strain RC67, an isolate from a long-term forest soil warming experiment in Petersham, Massachusetts.},
journal = {Microbiology resource announcements},
volume = {12},
number = {11},
pages = {e0037323},
pmid = {37823651},
issn = {2576-098X},
support = {DEB-1749206, DEB-1456610, DEB-1832210//National Science Foundation (NSF)/ ; },
abstract = {Paenibacillus sp. strain RC67 was isolated from the Harvard Forest long-term soil warming experiment. The assembled genome is a single contig with 7,963,753 bp and 99.4% completion. Genome annotation suggests that the isolate is of a novel bacterial species.},
}
@article {pmid37822474,
year = {2023},
author = {Callewaert, C and Pezavant, M and Vandaele, R and Meeus, B and Vankrunkelsven, E and Van Goethem, P and Plumacker, A and Misset, B and Darcis, G and Piret, S and De Vleeschouwer, L and Staelens, F and Van Varenbergh, K and Tombeur, S and Ottevaere, A and Montag, I and Vandecandelaere, P and Jonckheere, S and Vandekerckhove, L and Tobback, E and Wieers, G and Marot, JC and Anseeuw, K and D'Hoore, L and Tuyls, S and De Tavernier, B and Catteeuw, J and Lotfi, A and Melnik, A and Aksenov, A and Grandjean, D and Stevens, M and Gasthuys, F and Guyot, H},
title = {Sniffing out safety: canine detection and identification of SARS-CoV-2 infection from armpit sweat.},
journal = {Frontiers in medicine},
volume = {10},
number = {},
pages = {1185779},
pmid = {37822474},
issn = {2296-858X},
abstract = {Detection dogs were trained to detect SARS-CoV-2 infection based on armpit sweat odor. Sweat samples were collected using cotton pads under the armpits of negative and positive human patients, confirmed by qPCR, for periods of 15-30 min. Multiple hospitals and organizations throughout Belgium participated in this study. The sweat samples were stored at -20°C prior to being used for training purposes. Six dogs were trained under controlled atmosphere conditions for 2-3 months. After training, a 7-day validation period was conducted to assess the dogs' performances. The detection dogs exhibited an overall sensitivity of 81%, specificity of 98%, and an accuracy of 95%. After validation, training continued for 3 months, during which the dogs' performances remained the same. Gas chromatography/mass spectrometry (GC/MS) analysis revealed a unique sweat scent associated with SARS-CoV-2 positive sweat samples. This scent consisted of a wide variety of volatiles, including breakdown compounds of antiviral fatty acids, skin proteins and neurotransmitters/hormones. An acceptability survey conducted in Belgium demonstrated an overall high acceptability and enthusiasm toward the use of detection dogs for SARS-CoV-2 detection. Compared to qPCR and previous canine studies, the detection dogs have good performances in detecting SARS-CoV-2 infection in humans, using frozen sweat samples from the armpits. As a result, they can be used as an accurate pre-screening tool in various field settings alongside the PCR test.},
}
@article {pmid37821698,
year = {2023},
author = {Pavlopoulos, GA and Baltoumas, FA and Liu, S and Selvitopi, O and Camargo, AP and Nayfach, S and Azad, A and Roux, S and Call, L and Ivanova, NN and Chen, IM and Paez-Espino, D and Karatzas, E and , and Iliopoulos, I and Konstantinidis, K and Tiedje, JM and Pett-Ridge, J and Baker, D and Visel, A and Ouzounis, CA and Ovchinnikov, S and Buluç, A and Kyrpides, NC},
title = {Unraveling the functional dark matter through global metagenomics.},
journal = {Nature},
volume = {622},
number = {7983},
pages = {594-602},
pmid = {37821698},
issn = {1476-4687},
support = {DP5 OD026389/OD/NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; },
mesh = {Cluster Analysis ; *Metagenome/genetics ; *Metagenomics/methods ; *Proteins/chemistry/classification/genetics ; Databases, Protein ; Protein Conformation ; *Microbiology ; },
abstract = {Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities[1,2]. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database[3]. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.},
}
@article {pmid37821652,
year = {2023},
author = {Yost, RT and Fowler, AE and Adler, LS},
title = {Gut Transplants from Bees Fed an Antipathogenic Pollen Diet Do Not Confer Pathogen Resistance to Recipients.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3133-3137},
pmid = {37821652},
issn = {1432-184X},
support = {2128221//National Science Foundation/ ; NE2001//U.S. Department of Agriculture/ ; },
mesh = {Bees ; Animals ; Pollen ; Diet/veterinary ; *Microbiota ; *Gastrointestinal Microbiome ; Crithidia ; *Biological Products ; },
abstract = {Pollinators are threatened by diverse stressors, including microbial pathogens such as Crithidia bombi. Consuming sunflower pollen dramatically reduces C. bombi infection in the bumble bee Bombus impatiens, but the mechanism behind this medicinal effect is unclear. We asked whether diet mediates resistance to C. bombi through changes in the gut microbiome. We hypothesized that sunflower pollen changes the gut microbiome, which in turn reduces Crithidia infection. To test this, we performed a gut transplant experiment. We fed donor bees either a sunflower pollen treatment or buckwheat pollen as a control treatment and then inoculated recipient bees with homogenized guts from either sunflower-fed or buckwheat-fed donor bees. All recipient bees were then fed a wildflower pollen diet. Two days after the transplant, we infected recipients with C. bombi, and 2 days later, we provided another donor gut transplant. To quantify infection, we performed both fecal screens and dissections of the recipient bees. We found no significant differences in C. bombi infection intensity or presence between bees that received sunflower-fed microbiomes versus buckwheat-fed microbiomes. This suggests that sunflower pollen's effects on pathogen resistance are not mediated by gut microbiota.},
}
@article {pmid37820474,
year = {2023},
author = {Ma, L and Roman, M and Alhadidi, A and Jia, M and Martini, F and Xue, Y and Verliefde, A and Gutierrez, L and Cornelissen, E},
title = {Fate of organic micropollutants during brackish water desalination for drinking water production in decentralized capacitive electrodialysis.},
journal = {Water research},
volume = {245},
number = {},
pages = {120625},
doi = {10.1016/j.watres.2023.120625},
pmid = {37820474},
issn = {1879-2448},
mesh = {*Drinking Water ; *Water Purification ; Sodium Chloride ; Ions ; Adsorption ; Saline Waters ; },
abstract = {Capacitive electrodialysis (CED) is an emerging and promising desalination technology for decentralized drinking water production. Brackish water, often used as a drinking water source, may contain organic micropollutants (OMPs), thus raising environmental and health concerns. This study investigated the transport of OMPs in a fully-functional decentralized CED system for drinking water production under realistic operational conditions. Eighteen environmentally-relevant OMPs (20 µg L[-1]) with different physicochemical properties (charge, size, hydrophobicity) were selected and added to the feed water. The removal of OMPs was significantly lower than that of salts (∼94%), mainly due to their lower electrical mobility and higher steric hindrance. The removal of negatively-charged OMPs reached 50% and was generally higher than that of positively-charged OMPs (31%), whereas non-charged OMPs were barely transported. Marginal adsorption of OMPs was found under moderate water recovery (50%), in contrast to significant adsorption of charged OMPs under high water recovery (80%). The five-month operation demonstrated that the CED system could reliably produce water with low salt ions and TOC concentrations, meeting the respective WHO requirements. The specific energy consumption of the CED stack under 80% water recovery was 0.54 kWh m[-3], which is competitive to state-of-the-art RO, ED, and emerging MCDI in brackish water desalination. Under this condition, the total OPEX was 2.43 € m[-3], of which the cost of membrane replacement contributed significantly. Although the CED system proved to be a robust, highly adaptive, and fully automated technology for decentralized drinking water production, it was not highly efficient in removing OMPs, especially non-charged OMPs.},
}
@article {pmid37819096,
year = {2023},
author = {Khot, V and Strous, M and Dong, X and Kiesser, AK},
title = {Viral diversity and dynamics and CRISPR-Cas-mediated immunity in a robust alkaliphilic cyanobacterial consortium.},
journal = {Microbiology spectrum},
volume = {11},
number = {6},
pages = {e0221723},
pmid = {37819096},
issn = {2165-0497},
support = {//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Canada First Research Excellence Fund (CFREF)/ ; //Alberta Innovates (AI)/ ; Alberta Graduate Excellence//Government of Alberta (Alberta Government)/ ; Faculty of Graduate Studies Doctoral Scholarship//University of Calgary (U of C)/ ; },
mesh = {CRISPR-Cas Systems ; *Cyanobacteria/genetics ; *Viruses ; },
abstract = {Biotechnology applications utilizing the function of microbial communities have become increasingly important solutions as we strive for sustainable applications. Although viral infections are known to have a significant impact on microbial turnover and nutrient cycling, viral dynamics have remained largely overlooked in these engineered communities. Predatory perturbations to the functional stability of these microbial biotechnology applications must be investigated in order to design more robust applications. In this study, we closely examine virus-microbe dynamics in a model microbial community used in a biotechnology application. Our findings suggest that viral dynamics change significantly with environmental conditions and that microbial immunity may play an important role in maintaining functional stability. We present this study as a comprehensive template for other researchers interested in exploring predatory dynamics in engineered microbial communities.},
}
@article {pmid37819078,
year = {2023},
author = {Svet, L and Parijs, I and Isphording, S and Lories, B and Marchal, K and Steenackers, HP},
title = {Competitive interactions facilitate resistance development against antimicrobials.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {10},
pages = {e0115523},
pmid = {37819078},
issn = {1098-5336},
mesh = {*Anti-Infective Agents/pharmacology ; Biofilms ; Bacteria/genetics ; Phenotype ; Sulfathiazoles/pharmacology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates Pseudomonas rhodesiae and Raoultella terrigena influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of P. rhodesiae. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in P. rhodesiae. Whereas P. rhodesiae was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of R. terrigena was thus required for P. rhodesiae to acquire resistance, the resistance mechanisms did not depend on the presence of R. terrigena. Whole genome sequencing of resistant P. rhodesiae clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance.IMPORTANCEAntimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.},
}
@article {pmid37818230,
year = {2023},
author = {Grander, C and Meyer, M and Steinacher, D and Claudel, T and Hausmann, B and Pjevac, P and Grabherr, F and Oberhuber, G and Grander, M and Brigo, N and Jukic, A and Schwärzler, J and Weiss, G and Adolph, TE and Trauner, M and Tilg, H},
title = {24-Norursodeoxycholic acid ameliorates experimental alcohol-related liver disease and activates hepatic PPARγ.},
journal = {JHEP reports : innovation in hepatology},
volume = {5},
number = {11},
pages = {100872},
pmid = {37818230},
issn = {2589-5559},
support = {P 29379/FWF_/Austrian Science Fund FWF/Austria ; P 33070/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {BACKGROUND &amp; AIMS: Alcohol-related liver disease (ALD) is a global healthcare challenge with limited treatment options. 24-Norursodeoxycholic acid (NorUDCA) is a synthetic bile acid with anti-inflammatory properties in experimental and human cholestatic liver diseases. In the present study, we explored the efficacy of norUDCA in experimental ALD.<br><br>METHODS: NorUDCA was tested in a preventive and therapeutic setting in an experimental ALD model (Lieber-DeCarli diet enriched with ethanol). Liver disease was phenotypically evaluated using histology and biochemical methods, and anti-inflammatory properties and peroxisome proliferator-activated receptor gamma activation by norUDCA were evaluated in cellular model systems.<br><br>RESULTS: NorUDCA administration ameliorated ethanol-induced liver injury, reduced hepatocyte death, and reduced the expression of hepatic pro-inflammatory cytokines including tumour necrosis factor (Tnf), Il-1&#x3b2;, Il-6, and Il-10. NorUDCA shifted hepatic macrophages towards an anti-inflammatory M2 phenotype. Further, norUDCA administration altered the composition of the intestinal microbiota, specifically increasing the abundance of Roseburia, Enterobacteriaceae, and Clostridum spp. In a&#xa0;therapeutic model, norUDCA also ameliorated ethanol-induced liver injury. Moreover, norUDCA suppressed lipopolysaccharide-induced IL-6 expression in human peripheral blood mononuclear cells and evoked peroxisome proliferator-activated receptor gamma activation.<br><br>CONCLUSIONS: NorUDCA ameliorated experimental ALD, protected against hepatic inflammation, and affected gut microbial commensalism. NorUDCA could serve as a novel therapeutic agent in the future management of patients with ALD.<br><br>IMPACT AND IMPLICATIONS: Alcohol-related liver disease is a global healthcare concern with limited treatment options. 24-Norursodeoxycholic acid (NorUDCA) is a modified bile acid, which was proven to be effective in human cholestatic liver diseases. In the present study, we found a protective effect of norUDCA in experimental alcoholic liver disease. For patients with ALD, norUDCA could be a potential new treatment option.},
}
@article {pmid37816903,
year = {2023},
author = {Abdolahpur Monikh, F and Baun, A and Hartmann, NB and Kortet, R and Akkanen, J and Lee, JS and Shi, H and Lahive, E and Uurasjärvi, E and Tufenkji, N and Altmann, K and Wiesner, Y and Grossart, HP and Peijnenburg, W and Kukkonen, JVK},
title = {Exposure protocol for ecotoxicity testing of microplastics and nanoplastics.},
journal = {Nature protocols},
volume = {18},
number = {11},
pages = {3534-3564},
pmid = {37816903},
issn = {1750-2799},
support = {965367//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 964766//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Humans ; *Microplastics/analysis/toxicity ; Plastics/toxicity ; *Water Pollutants, Chemical/analysis/chemistry/toxicity ; },
abstract = {Despite the increasing concern about the harmful effects of micro- and nanoplastics (MNPs), there are no harmonized guidelines or protocols yet available for MNP ecotoxicity testing. Current ecotoxicity studies often use commercial spherical particles as models for MNPs, but in nature, MNPs occur in variable shapes, sizes and chemical compositions. Moreover, protocols developed for chemicals that dissolve or form stable dispersions are currently used for assessing the ecotoxicity of MNPs. Plastic particles, however, do not dissolve and also show dynamic behavior in the exposure medium, depending on, for example, MNP physicochemical properties and the medium's conditions such as pH and ionic strength. Here we describe an exposure protocol that considers the particle-specific properties of MNPs and their dynamic behavior in exposure systems. Procedure 1 describes the top-down production of more realistic MNPs as representative of MNPs in nature and particle characterization (e.g., using thermal extraction desorption-gas chromatography/mass spectrometry). Then, we describe exposure system development for short- and long-term toxicity tests for soil (Procedure 2) and aquatic (Procedure 3) organisms. Procedures 2 and 3 explain how to modify existing ecotoxicity guidelines for chemicals to target testing MNPs in selected exposure systems. We show some examples that were used to develop the protocol to test, for example, MNP toxicity in marine rotifers, freshwater mussels, daphnids and earthworms. The present protocol takes between 24 h and 2 months, depending on the test of interest and can be applied by students, academics, environmental risk assessors and industries.},
}
@article {pmid37816747,
year = {2023},
author = {Rahlff, J and Esser, SP and Plewka, J and Heinrichs, ME and Soares, A and Scarchilli, C and Grigioni, P and Wex, H and Giebel, HA and Probst, AJ},
title = {Marine viruses disperse bidirectionally along the natural water cycle.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {6354},
pmid = {37816747},
issn = {2041-1723},
mesh = {*Ecosystem ; Water Cycle ; Seawater/analysis ; *Viruses/genetics ; Aerosols/analysis ; },
abstract = {Marine viruses in seawater have frequently been studied, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2% of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols collected at ~2 m height above sea level and rain. Viruses detected in rain and these aerosols showed a significantly higher percent G/C base content compared to marine viruses. CRISPR spacer matches of marine prokaryotes to foreign viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization, adaptations, and dispersal support transmission of viruses along the natural water cycle.},
}
@article {pmid37816673,
year = {2023},
author = {Byers, AK and Condron, LM and O'Callaghan, M and Waller, L and Dickie, IA and Wakelin, SA},
title = {Plant species identity and plant-induced changes in soil physicochemistry-but not plant phylogeny or functional traits - shape the assembly of the root-associated soil microbiome.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {11},
pages = {},
pmid = {37816673},
issn = {1574-6941},
mesh = {*Soil Microbiology ; Phylogeny ; Soil ; *Microbiota ; Bacteria/genetics ; Plants/microbiology ; Plant Roots/microbiology ; Rhizosphere ; },
abstract = {The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly.},
}
@article {pmid37814279,
year = {2023},
author = {Liu, W and Liu, H and Wang, Y and Zhao, Z and Balasubramanian, B and Jha, R},
title = {Effects of Enteromorpha prolifera polysaccharides on growth performance, intestinal barrier function and cecal microbiota in yellow-feathered broilers under heat stress.},
journal = {Journal of animal science and biotechnology},
volume = {14},
number = {1},
pages = {132},
pmid = {37814279},
issn = {1674-9782},
support = {32002196//National Nature Science Foundation of China/ ; },
abstract = {BACKGROUND: Global warming leading to heat stress (HS) is becoming a major challenge for broiler production. This study aimed to explore the protective effects of seaweed (Enteromorpha prolifera) polysaccharides (EPS) on the intestinal barrier function, microbial ecology, and performance of broilers under HS. A total of 144 yellow-feathered broilers (male, 56 days old) with 682.59 ± 7.38 g were randomly assigned to 3 groups: 1) TN (thermal neutral zone, 23.6 ± 1.8 °C), 2) HS (heat stress, 33.2 ± 1.5 °C for 10 h/d), and 3) HSE (HS + 0.1% EPS). Each group contained 6 replicates with 8 broilers per replicate. The study was conducted for 4 weeks; feed intake and body weights were measured at the end of weeks 2 and 4. At the end of the feeding trial, small intestine samples were collected for histomorphology, antioxidant, secretory immunoglobulin A (sIgA) content, apoptosis, gene and protein expression analysis; cecal contents were also collected for microbiota analysis based on 16S rDNA sequencing.<br><br>RESULTS: Dietary EPS promoted the average daily gain (ADG) of broilers during 3-4 weeks of HS (P&#x2009;<&#x2009;0.05). At the end of HS on broilers, the activity of total superoxide dismutase (T-SOD), glutathione S-transferase (GST), and the content of sIgA in jejunum were improved by EPS supplementation (P&#x2009;<&#x2009;0.05). Besides, dietary EPS reduced the epithelial cell apoptosis of jejunum and ileum in heat-stressed broilers (P&#x2009;<&#x2009;0.05). Addition of EPS in HS group broilers' diet upregulated the relative mRNA expression of Occludin, ZO-1, &#x3b3;-GCLc and IL-10 of the jejunum (P&#x2009;<&#x2009;0.05), whereas downregulated the relative mRNA expression of NF-&#x3ba;B p65, TNF-&#x3b1; and IL-1&#x3b2; of the jejunum (P&#x2009;<&#x2009;0.05). Dietary EPS increased the protein expression of Occludin and ZO-1, whereas it reduced the protein expression of NF-&#x3ba;B p65 and MLCK (P&#x2009;<&#x2009;0.01) and tended to decrease the protein expression of TNF-&#x3b1; (P&#x2009;=&#x2009;0.094) in heat-stressed broilers. Furthermore, the proportions of Bacteroides and Oscillospira among the three groups were positively associated with jejunal apoptosis and pro-inflammatory cytokine expression (P&#x2009;<&#x2009;0.05) and negatively correlated with jejunal Occludin level (P&#x2009;<&#x2009;0.05). However, the proportions of Lactobacillus, Barnesiella, Subdoligranulum, Megasphaera, Collinsella, and Blautia among the three groups were positively related to ADG (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: EPS can be used as a feed additive in yellow-feathered broilers. It effectively improves growth performance and alleviates HS-induced intestinal injury by relieving inflammatory damage and improving the tight junction proteins expression. These beneficial effects may be related to inhibiting NF-&#x3ba;B/MLCK signaling pathway activation and regulation of cecal microbiota.},
}
@article {pmid37813267,
year = {2024},
author = {Biagioli, F and Coleine, C and Delgado-Baquerizo, M and Feng, Y and Saiz-Jimenez, C and Selbmann, L},
title = {Outdoor climate drives diversity patterns of dominant microbial taxa in caves worldwide.},
journal = {The Science of the total environment},
volume = {906},
number = {},
pages = {167674},
doi = {10.1016/j.scitotenv.2023.167674},
pmid = {37813267},
issn = {1879-1026},
mesh = {Caves/microbiology ; Bacteria/metabolism ; *Microbiota ; Geography ; *Mycobiome ; },
abstract = {The cave microbiota is assumed to be shaped by indoor microclimate, biotic and abiotic factors, which are largely dependent from outside environmental conditions; however, this knowledge is available at local or regional scales only. To address this knowledge gap, we reanalyzed over 1050 bacterial and fungal communities of caves worldwide, and found that outdoor temperature and rainfall play a critical role in explaining differences in microbial diversity patterns of global caves, selecting specific dominant taxa across gradients of growing aridity conditions with arid climate leading to a reduction in total cave microbial diversity. Moreover, we found that fungal (from 186 to 1908 taxa) and bacterial (from 467 to 1619 taxa) diversity increased under temperate-tropical and temperate-continental climatic regions, respectively, highlighting an opposite preference for the two microbial compartments. We hypothesized that outdoor geographical, climatic variables and lithology are critical epistatic drivers in assembling microbial communities and their dominant taxa, whose ecological responses could be useful to predict the fate of these subterranean environments in the context of climate change. Our work elucidates the intimate connection between caves microbiota and surface ecosystems highlighting the sensitivity of cave microbial communities to climatic changes and environmental degradation. This work also provides a natural benchmark for the biogeographic information for caves globally and for protection strategies aiming at conservation of underground environments.},
}
@article {pmid37812012,
year = {2023},
author = {Kocurek, B and Ramachandran, P and Grim, CJ and Morin, P and Howard, L and Ottesen, A and Timme, R and Leonard, SR and Rand, H and Strain, E and Tadesse, D and Pettengill, JB and Lacher, DW and Mammel, M and Jarvis, KG},
title = {Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities.},
journal = {Microbiology spectrum},
volume = {11},
number = {6},
pages = {e0148223},
pmid = {37812012},
issn = {2165-0497},
mesh = {Humans ; *Listeria monocytogenes/genetics ; Food Microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Seafood ; },
abstract = {In developed countries, the human diet is predominated by food commodities, which have been manufactured, processed, and stored in a food production facility. Little is known about the application of metagenomic sequencing approaches for detecting foodborne pathogens, such as L. monocytogenes, and characterizing microbial diversity in food production ecosystems. In this work, we investigated the utility of 16S rRNA amplicon and quasimetagenomic sequencing for the taxonomic and phylogenetic classification of Listeria culture enrichments of environmental swabs collected from dairy and seafood production facilities. We demonstrated that single-nucleotide polymorphism (SNP) analyses of L. monocytogenes metagenome-assembled genomes (MAGs) from quasimetagenomic data sets can achieve similar resolution as culture isolate whole-genome sequencing. To further understand the impact of genome coverage on MAG SNP cluster resolution, an in silico downsampling approach was employed to reduce the percentage of target pathogen sequence reads, providing an initial estimate of required MAG coverage for subtyping resolution of L. monocytogenes.},
}
@article {pmid37812006,
year = {2023},
author = {Phillips, EK and Shaffer, JMC and Henson, MW and Coelho, JT and Martin, MO and Thrash, JC},
title = {Genome sequences of four agarolytic bacteria from the Bacteroidia and Gammaproteobacteria.},
journal = {Microbiology resource announcements},
volume = {12},
number = {11},
pages = {e0066723},
pmid = {37812006},
issn = {2576-098X},
support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; OCE-1945279, EF-2125191//National Science Foundation (NSF)/ ; },
abstract = {Here we present the genomes of four marine agarolytic bacteria belonging to the Bacteroidota and Proteobacteria. Two genomes are closed and two are in draft form, but all are at least 99% complete and offer new opportunities to study agar-degradation in marine bacteria.},
}
@article {pmid37811990,
year = {2023},
author = {He, D and Yao, X and Zhang, P and Liu, W and Huang, J and Sun, H and Wang, N and Zhang, X and Wang, H and Zhang, H and Ao, X and Xie, F},
title = {Effects of continuous cropping on fungal community diversity and soil metabolites in soybean roots.},
journal = {Microbiology spectrum},
volume = {11},
number = {6},
pages = {e0178623},
pmid = {37811990},
issn = {2165-0497},
support = {LJKZ0678//Project of Scientific Research in Education Department of Liaoning Province, China/ ; 22-318-2-05//Project of Science and technology of Shenyang, China/ ; LJKZ0630//Project of Scientific Research in Education Department of Liaoning province, China/ ; },
mesh = {*Soil ; *Mycobiome ; Glycine max ; Rhizosphere ; Soil Microbiology ; Crops, Agricultural/microbiology ; },
abstract = {Soybean yield can be affected by soybean soil fungal communities in different tillage patterns. Soybean is an important food crop with great significance worldwide. Continuous cultivation resulted in soil nutrient deficiencies, disordered metabolism of root exudates, fungal pathogen accumulation, and an altered microbial community, which brought a drop in soybean output. In this study, taking the soybean agroecosystem in northeast China, we revealed the microbial ecology and soil metabolites spectrum, especially the diversity and composition of soil fungi and the correlation of pathogenic fungi, and discussed the mechanisms and the measures of alleviating the obstacles.},
}
@article {pmid37810791,
year = {2023},
author = {McKenney, EA and Nichols, LM and Alvarado, S and Hardy, S and Kemp, K and Polmanteer, R and Shoemaker, A and Dunn, RR},
title = {Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16163},
pmid = {37810791},
issn = {2167-8359},
mesh = {*Flour/microbiology ; RNA, Ribosomal, 16S/genetics ; Fermentation ; *Bacteria/genetics ; Lactobacillus/genetics ; },
abstract = {The microbial fermentation behind sourdough bread is among our oldest technologies, yet there are many opportunities for sourdough science to learn from traditional bakers. We analyzed 16S rRNA sequences in R to assess the bacterial community structure and performance of 40 starters grown from 10 types of flour over 14 days, and identified six distinct stages of succession. At each stage, bacterial taxa correlate with determinants of bread quality including pH, rise, and aromatic profile. Day 1 starter cultures were dominated by microorganisms commonly associated with plants and flour, and by aromas similar to toasted grain/cereal. Bacterial diversity peaked from days 2-6 as taxa shifted from opportunistic/generalist bacteria associated with flour inputs, toward specialized climax bacterial communities (days 10-14) characterized by acid-tolerant taxa and fruity (p < 3.03e-03), sour (p < 1.60e-01), and fermented (p < 1.47e-05) aromas. This collection of traits changes predictably through time, regardless of flour type, highlighting patterns of bacterial constraints and dynamics that are conserved across systems and scales. Yet, while sourdough climax communities exhibit similar markers of maturity (i.e., pH ≤ 4 and enriched in Lactobacillus (mean abundance 48.1%), Pediococcus (mean abundance 22.7%), and/or Gluconobacter (mean abundance 19.1%)), we also detected specific taxa and aromas associated with each type of flour. Our results address important ecological questions about the relationship between community structure and starter performance, and may enable bakers to deliberately select for specific sourdough starter and bread characteristics.},
}
@article {pmid37807043,
year = {2023},
author = {Hayes, MG and Langille, MGI and Gu, H},
title = {Cross-study analyses of microbial abundance using generalized common factor methods.},
journal = {BMC bioinformatics},
volume = {24},
number = {1},
pages = {380},
pmid = {37807043},
issn = {1471-2105},
support = {CGS-M Alexander Graham Bell Scholarship//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/05108-2017//Natural Sciences and Engineering Research Council of Canada/ ; Scotia Scholars Award//Nova Scotia Health Research Foundation/ ; },
mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; Genomics ; Computational Biology/methods ; },
abstract = {BACKGROUND: By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results.<br><br>RESULTS: We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space.<br><br>CONCLUSIONS: By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability, and recommend a particular implementation.},
}
@article {pmid37805972,
year = {2023},
author = {Pandit, B and Moin, A and Mondal, A and Banik, A and Alam, M},
title = {Characterization of a biofilm-forming, amylase-producing, and heavy-metal-bioremediating strain Micrococcus sp. BirBP01 isolated from oligotrophic subsurface lateritic soil.},
journal = {Archives of microbiology},
volume = {205},
number = {11},
pages = {351},
pmid = {37805972},
issn = {1432-072X},
mesh = {Micrococcus/genetics/metabolism ; Soil ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Metals, Heavy/metabolism ; Bacteria/genetics ; Biofilms ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; },
abstract = {Lateritic soil is the reddish to brown-colored soil composed mainly of iron or aluminium oxides, hydroxides, or oxyhydroxides. Information on bacteria that inhabit this soil type, their ecological role, and metabolic potential are scarce. We have isolated and partially characterized a bacterial strain BirBP01 from a lead, calcium, and magnesium-rich, oligotrophic subsurface lateritic soil-sample collected from 12-feet deep horizon of a laterite mining pit in Birbhum district, India. The isolate is a biofilm-forming, Gram-positive bacterium having a sarcinae arrangement, mesophilic, slightly alkaliphilic, able to produce amylase, and resistant against multiple heavy-metals. BirBP01 has the ability to bioremediate 51% of Pb, 30% of Zn, and 22% of Cu through biosorption, possibly into the biofilm matrix. The bioremediating ability of the bacterium alleviated the inhibitory effect of heavy-metals on the germination of chickpea (Cicer arietinum L.) seeds. 16S rRNA gene-based phylogenetic analysis revealed that BirBP01 is a member of the genus Micrococcus. It showed more than 99% identity of the 16S rRNA gene sequence, and clustered within the same branch of the phylogenetic tree, with strains of M. yunnanensis, M. endophyticus, and M. luteus. The ability to produce amylase, and bioremediate heavy-metals signify that Micrococcus sp. BirBP01 could be potentially a good candidate for industrial applications, and to clean up heavy-metal contaminated sites.},
}
@article {pmid37804686,
year = {2024},
author = {Çömlekcioğlu, U and Jezierska, S and Opsomer, G and Pascottini, OB},
title = {Uterine microbial ecology and disease in cattle: A review.},
journal = {Theriogenology},
volume = {213},
number = {},
pages = {66-78},
doi = {10.1016/j.theriogenology.2023.09.016},
pmid = {37804686},
issn = {1879-3231},
mesh = {Female ; Cattle ; Animals ; Dysbiosis/veterinary ; *Cattle Diseases/prevention &amp; control/microbiology ; Uterus/microbiology ; *Endometritis/veterinary ; Bacteria ; *Uterine Diseases/veterinary/microbiology ; },
abstract = {Due to the critical contribution of the uterine-associated microbiota in reproductive health, physiology, and performance, culture-independent methods have been increasingly employed to unravel key aspects of microbial ecology in the uterus of cattle. Nowadays, we know that bacterial diversity is crucial to maintain uterine health, however, there is still no consensus on the exact composition of a healthy uterine microbiota (or eubiosis). Generally, loss of bacterial diversity (or dysbiosis) contributes to the development of uterine infections, associated with increased relative abundances of Bacteroides, Fusobacterium, Trueperella, and Porphyromonas. Uterine infections are highly prevalent and gravely influence the profitability of cattle operations, animal welfare, and public health. Thus, understanding the dynamics of uterine microbial ecology is essential to develop effective strategies focused on preventing and mitigating the adverse effects of uterine dysbiosis as well as assisting in the process of restoring the core, healthy uterine microbiota. The aim of this review is to summarize research conducted in the microbial ecology of bovine uteri. We discuss the origin of the uterine microflora of healthy cows and the factors influencing its composition. In addition, we review the biology of specific pathogens that are known to increase in abundance during the occurrence of uterine disease. Lastly, we provide an overview of the bacterial biofilm in the bovine endometrium, and we briefly summarize the rationale for the use of probiotics to prevent uterine disease in cattle.},
}
@article {pmid37803760,
year = {2023},
author = {Tadielo, LE and Dos Santos, EAR and Possebon, FS and Schmiedt, JA and Juliano, LCB and Cerqueira-Cézar, CK and de Oliveira, JP and Sampaio, ANDCE and Melo, PRL and Caron, EFF and Pinto, JPAN and Bersot, LDS and Pereira, JG},
title = {Characterization of microbial ecology, Listeria monocytogenes, and Salmonella sp. on equipment and utensil surfaces in Brazilian poultry, pork, and dairy industries.},
journal = {Food research international (Ottawa, Ont.)},
volume = {173},
number = {Pt 2},
pages = {113422},
doi = {10.1016/j.foodres.2023.113422},
pmid = {37803760},
issn = {1873-7145},
mesh = {Animals ; Swine ; *Listeria monocytogenes ; Poultry ; Food Microbiology ; Dairying ; *Pork Meat ; Brazil ; RNA, Ribosomal, 16S ; *Red Meat ; Escherichia coli ; Salmonella/genetics ; },
abstract = {This study aimed to evaluate the level of counting by indicator microorganisms, identify the microbial ecology, detect Listeria monocytogenes and Salmonella sp., and determine the presence of virulence genes and biofilm formation. A total of 480 samples were collected from the surfaces of the equipment and utensils using sterile swabs for the detection of L. monocytogenes and Salmonella sp. and counting mesophilic aerobes, Enterobacteriaceae, Escherichia coli, and Pseudomonas sp. The microbial ecology was evaluated by sequencing the 16S rRNA gene. Genes for virulence and biofilm formation were analyzed and adhesion capacity was evaluated for L. monocytogenes and Salmonella sp. The mesophilic aerobe count was the highest in the dairy processing facility, followed by the pork and poultry slaughterhouses. L. monocytogenes was detected in all facilities, with the highest detection in the pork slaughterhouse, followed by the poultry and dairy facilities. Salmonella sp. was only detected in the dairy. Isolates of L. monocytogenes and Salmonella sp. showed poor adhesion to polystyrene surfaces, virulence genes, and biofilm formation. The frequent contaminants in the slaughterhouses were Pseudomonas, Acinetobacter, and Aeromonas in poultry, Acinetobacter, Pseudomonas, and Brevundimonas in pork, and Pseudomonas, Kocuria, and Staphylococcus in dairy. Our results provide useful information to understand the microbiological risks associated with contamination.},
}
@article {pmid37803713,
year = {2023},
author = {Podduturi, R and da Silva David, G and da Silva, RJ and Hyldig, G and Jørgensen, NOG and Agerlin Petersen, M},
title = {Characterization and finding the origin of off-flavor compounds in Nile tilapia cultured in net cages in hydroelectric reservoirs, São Paulo State, Brazil.},
journal = {Food research international (Ottawa, Ont.)},
volume = {173},
number = {Pt 2},
pages = {113375},
doi = {10.1016/j.foodres.2023.113375},
pmid = {37803713},
issn = {1873-7145},
mesh = {Animals ; *Cichlids ; Brazil ; *Volatile Organic Compounds ; Naphthols/analysis/chemistry ; },
abstract = {An increasing demand for fish products has led to an intensive aquaculture production in Brazil, and cultivation of fish constituted 860 × 10[3] tons in 2022, contributing to the 87% of total fish consumption. Nile tilapia constitutes almost half of the aquaculture production, and most tilapia farms use floating net cages. One of the major constraints of intensive fish production is production of off-flavors. Release of nutrients by the fish leads to deterioration of the water quality and stimulates growth of microorganisms, also including off-flavor producing species. The objective of this study was to determine levels of taste and odor compounds (geosmin, 2-MIB and a selection of volatile compounds) and their impact on the flavor quality of Nile tilapia produced in net cages in reservoirs in São Paulo State, Brazil. GC-MS analysis of fish and water from six different farms showed concentrations of geosmin in the water from 1 to 8 ng/L, while geosmin in fish flesh ranged from 40 to 750 ng/kg. The level of 2-MIB in water was 2 to 25 ng/L, and 0 to 800 ng/kg fish. The GC-MS analysis also revealed presence of more than 100 volatile organic compounds in the fish flesh, consisting of aldehydes, alcohols, benzene derivatives, hydrocarbons, ketones and few other compounds. Geosmin and 2-MIB related flavor notes were detected in all fish by a sensory panel, and a high correlation between the chemical and sensory analyses was found. The potential impact of the volatile organic compounds on the fish flavor is discussed. Analysis of the water quality in the reservoirs indicated that levels of geosmin and 2-MIB levels were highly influenced by the nutrient levels in the water.},
}
@article {pmid37802356,
year = {2024},
author = {Sarkodie, EK and Jiang, L and Li, K and Guo, Z and Yang, J and Shi, J and Peng, Y and Wu, X and Huang, S and Deng, Y and Jiang, H and Liu, H and Liu, X},
title = {The influence of cysteine in transformation of Cd fractionation and microbial community structure and functional profile in contaminated paddy soil.},
journal = {The Science of the total environment},
volume = {906},
number = {},
pages = {167535},
doi = {10.1016/j.scitotenv.2023.167535},
pmid = {37802356},
issn = {1879-1026},
mesh = {Humans ; Cadmium/analysis ; Cysteine ; Soil/chemistry ; *Microbiota ; Sulfur ; Nitrogen ; *Soil Pollutants/analysis ; *Oryza ; },
abstract = {Remediating cadmium (Cd) contaminated paddy soil is vital for agroecology, food safety, and human health. Soil washing is more feasible to reduce remediation method due to its high efficiency. However, green, low-cost and more efficient washing agents are still required. In this study, we investigated the ability of cysteine as a washing agent for soil washing to remove Cd from contaminated paddy soil. Through a batch experiment, we evaluated the removal efficiency of cysteine as a washing agent by comparing their removal rate with that of a microbial inoculant and sulphuric acid as other washing agents. The transformation of Cd fractionation and microbial community structure and functional profile in paddy soils after cysteine leaching was studied by using sequential extraction and high-throughput sequencing. Results showed that cysteine had better efficiency in the removal of Cd from paddy soil in comparison to sulphuric acid and the microbial inoculant, and could achieve a maximum removal rate of 97 % Cd in paddy soil. Cysteine decreased the proportion of Cd in the exchangeable fraction, carbonate bound fraction, iron and manganese bound fraction, and organic matter bound fraction and was best for the removal of the residual fraction, which contributed to its higher Cd removal ability. Considering the economic benefits of the reagents used, cysteine was shown to be economically feasible for use as a leaching agent. In addition, cysteine could significantly increase the relative abundance of Thermochromatium, Sideroxydans, Streptacidiphilus, and Frankia which promoted the nitrogen and sulfur metabolism in the paddy soil. In summary, this study revealed that cysteine was readily available, cheap, non-toxic, highly efficient, and even has fertilizing properties, making it eco-friendly and ideal for remediation of Cd-contaminated paddy soils. Besides, the health of paddy soils would also benefit from cysteine's promotion of microbial nitrogen and sulfur metabolism.},
}
@article {pmid37800904,
year = {2023},
author = {Ettinger, CL and Wu-Woods, J and Kurbessoian, T and Brown, DJ and Souza Pacheco, Id and Vindiola, BG and Walling, LL and Atkinson, PW and Byrne, FJ and Redak, R and Stajich, JE},
title = {Geographical survey of the mycobiome and microbiome of Southern California glassy-winged sharpshooters.},
journal = {mSphere},
volume = {8},
number = {5},
pages = {e0026723},
pmid = {37800904},
issn = {2379-5042},
mesh = {Animals ; *Mycobiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Hemiptera/microbiology ; Geography ; },
abstract = {The glassy-winged sharpshooter, Homalodisca vitripennis Germar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the plant pathogen, Xylella fastidiosa. While studies have focused on X. fastidiosa or known symbionts of H. vitripennis, little work has been done at the scale of the microbiome (the bacterial community) or mycobiome (the fungal community). Here, we characterize the mycobiome and the microbiome of H. vitripennis across Southern California and explore correlations with captivity and host insecticide resistance status. Using high-throughput sequencing of the ribosomal internal transcribed spacer 1 region and the 16S rRNA gene to profile the mycobiome and microbiome, respectively, we found that while the H. vitripennis mycobiome significantly varied across Southern California, the microbiome did not. We also observed a significant difference in both the mycobiome and microbiome between captive and wild H. vitripennis. Finally, we found that the mycobiome, but not the microbiome, was correlated with insecticide resistance status in wild H. vitripennis. This study serves as a foundational look at the H. vitripennis mycobiome and microbiome across Southern California. Future work should explore the putative link between microbes and insecticide resistance status and investigate whether microbial communities should be considered in H. vitripennis management practices. IMPORTANCE The glassy-winged sharpshooter is an invasive leafhopper that feeds on the xylem of plants and transmits the devastating pathogen, Xylella fastidiosa, resulting in significant economic damage to California's agricultural system. While studies have focused on this pathogen or obligate symbionts of the glassy-winged sharpshooter, there is limited knowledge of the bacterial and fungal communities that make up its microbiome and mycobiome. To address this knowledge gap, we explored the composition of the mycobiome and the microbiome of the glassy-winged sharpshooter across Southern California and identified differences associated with geography, captivity, and host insecticide resistance status. Understanding sources of variation in the microbial communities associated with the glassy-winged sharpshooter is an important consideration for developing management strategies to control this invasive insect. This study is a first step toward understanding the role microbes may play in the glassy-winged sharpshooter's resistance to insecticides.},
}
@article {pmid37799598,
year = {2023},
author = {Wang, H and Yan, B and Wu, Y and Yin, M and Wang, M and Fu, C},
title = {Microbial community diversity and potential functionality in response to dam construction along the Three Gorge Reservoir, China.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1218806},
pmid = {37799598},
issn = {1664-302X},
abstract = {River and reservoir bacterial communities are the most basic part of river biomes and ecosystem structure, and play an important role in river biological processes. Yet, it remains unclear how highly regulated dam reservoirs affect both soil and sediment bacterial communities. A temporal distribution pattern of bacterial communities was investigated using Illumina MiSeq sequencing in a transition section of the Three Gorges Reservoir (TGR). In total, 106,682 features belong to the bacteria kingdom, encompassing 95 phyla, 228 classes, 514 orders, 871 families, 1959 genera, and 3,053 species. With water level regulation, Shannon diversity index, and observed species differed significantly, with no significant difference in Simpson evenness. Both in the high water level period (October) and the low water level period (June), Proteobacteria, Acidobacteri, and Chloroflexi were the most abundant phyla. Whereas, based on PCA plots and Circos plot, the microbial community structure has changed significantly. LEfSe method was used to identify the classified bacterial taxa with significant abundance differences between the low water level and high water level periods. KOs (KEGG Orthology) pathway enrichment analysis were conducted to investigate functional and related metabolic pathways in groups. To some extent, it can be inferred that water level regulation affects community growth by affecting the metabolism of the microbial community.},
}
@article {pmid37798675,
year = {2023},
author = {Avila Santos, AP and Kabiru Nata'ala, M and Kasmanas, JC and Bartholomäus, A and Keller-Costa, T and Jurburg, SD and Tal, T and Camarinha-Silva, A and Saraiva, JP and Ponce de Leon Ferreira de Carvalho, AC and Stadler, PF and Sipoli Sanches, D and Rocha, U},
title = {The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {48},
pmid = {37798675},
issn = {2524-4671},
abstract = {BACKGROUND: Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward. We created the Animal-Associated Metagenome Metadata Database (AnimalAssociatedMetagenomeDB - AAMDB) to facilitate the identification and reuse of publicly available non-human, animal-associated metagenomic data, and metadata. Further, we used the AAMDB to (i) annotate common and scientific names of the species; (ii) determine the fraction of vertebrates and invertebrates; (iii) study their biogeography; and (iv) specify whether the animals were wild, pets, livestock or used for medical research.<br><br>RESULTS: We manually selected metagenomes associated with non-human animals from SRA and MG-RAST. &#xa0;Next, we standardized and curated 51 metadata attributes (e.g., host, compartment, geographic coordinates, and country). The AAMDB version 1.0 contains 10,885 metagenomes associated with 165 different species from 65 different countries.&#xa0;From the collected metagenomes, 51.1% were recovered from animals associated with medical research or grown for human consumption (i.e., mice, rats, cattle, pigs, and poultry). Further, we observed an over-representation of animals collected in temperate regions (89.2%) and a lower representation of samples from the polar zones, with only 11 samples in total. The most common genus among invertebrate animals was Trichocerca (rotifers).<br><br>CONCLUSION: Our work may guide host species selection in novel animal-associated metagenome research, especially in biodiversity and conservation studies. The data available in our database will allow scientists to perform meta-analyses and test new hypotheses (e.g., host-specificity, strain heterogeneity, and biogeography of animal-associated metagenomes), leveraging existing data. The AAMDB WebApp is a user-friendly interface that is publicly available at https://webapp.ufz.de/aamdb/ .},
}
@article {pmid37796897,
year = {2023},
author = {Diao, M and Dyksma, S and Koeksoy, E and Ngugi, DK and Anantharaman, K and Loy, A and Pester, M},
title = {Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction.},
journal = {FEMS microbiology reviews},
volume = {47},
number = {5},
pages = {},
pmid = {37796897},
issn = {1574-6976},
support = {P 31996-B/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Oxidation-Reduction ; *Bacteria/metabolism ; *Archaea/metabolism ; Sulfates/metabolism ; Sulfites/metabolism ; Sulfur/metabolism ; Phylogeny ; },
abstract = {Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.},
}
@article {pmid37794496,
year = {2023},
author = {Lühken, R and Becker, N and Dyczko, D and Sauer, FG and Kliemke, K and Schmidt-Chanasit, J and Rydzanicz, K},
title = {First record of Anopheles (Anopheles) hyrcanus (Pallas 1771) (Diptera: Culicidae) in Poland.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {345},
pmid = {37794496},
issn = {1756-3305},
support = {BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {Animals ; *Culicidae ; *Anopheles/parasitology ; Poland ; Mosquito Vectors ; Climate ; Europe ; },
abstract = {The spatial distribution of mosquito species in the course of globalization and climate warming is highly dynamic. Different studies have demonstrated the spread and establishment of thermophilic mosquito species, potentially increasing the prevalence of 'nuisance' mosquitoes and the local transmission of pathogens. Here we report the first recorded sampling of Anopheles hyrcanus in Wrocław, southwest Poland. This is the most northern detection of this species to date in Europe. Future spread and population development of this potential vector of malaria parasites, viruses or zoonotic helminths, such as Dirofilaria spp., must be monitored carefully. Potential factors underlying the spread of this species are discussed.},
}
@article {pmid37794421,
year = {2023},
author = {Xiang, S and Chen, Z and Dai, Z and Wang, F},
title = {Global burden of lower respiratory infections attributable to secondhand smoke among children under 5 years of age, 2010-2019: a systematic analysis of the global burden of disease study 2019.},
journal = {BMC public health},
volume = {23},
number = {1},
pages = {1920},
pmid = {37794421},
issn = {1471-2458},
mesh = {Humans ; Child ; Child, Preschool ; Global Burden of Disease ; *Tobacco Smoke Pollution/adverse effects ; Quality-Adjusted Life Years ; *Respiratory Tract Infections/epidemiology ; Risk Factors ; Global Health ; },
abstract = {BACKGROUND: Epidemiological trends of lower respiratory infections (LRIs) attributable to secondhand smoke (SHS) among children under 5 years since smoking bans have been increasingly applied globally remain unclear. Here, we aimed to estimate the spatiotemporal trends of the global, regional, and national burden of LRIs attributable to SHS among children under 5 years old between 2010 and 2019.<br><br>METHODS: Data on the deaths, and disability adjusted life years (DALYs) of the disease burden was retrieved from the Global Burden of Disease (GBD) 2019 for 204 countries and territories between 2010 and 2019. The rates per 100,000 population, along with 95% uncertainty intervals, as well as population-attributable fraction (PAF) was presented for each estimate.<br><br>RESULTS: In 2019, an estimated 6.94% (3.80-10.12%) of under-5 LRIs deaths were attributable to SHS globally, with an under-5 mortality rate of 7.02 per 100,000, a decrease of 5.77% since 2010. Similarly, 6.95% (3.81-10.13%) of LRIs DALYs were due to SHS among children under 5 years, with a rate in under-5s of 619.36 DALYs per 100,000, and also a 5.77% decrease since 2010. Azerbaijan, Turkmenistan, and Papua New Guinea showed the highest under-5 mortality and DALYs burden rates of LRIs attributable to SHS in 2019. In contrast, the PAF was stagnant over the past ten years and there is even a year-on-year upward trend in South Asia. Nationally, in 2019, Bosnia and Herzegovina, Armenia, and Montenegro showed the highest PAFSHS of LRIs burden among children under 5 years of age. In addition, the burden was heavier in children under 1 year of age and was significantly negatively associated with sociodemographic index.<br><br>CONCLUSIONS: SHS remains a risk factor that cannot be ignored for LRIs burden worldwide. Hence, governments and health systems should continue to take steps to reduce SHS pollution among young children to mitigate this burden.},
}
@article {pmid37794084,
year = {2023},
author = {Hettiarachchi, A and Cnockaert, M and Joossens, M and Gekière, A and Meeus, I and Vereecken, NJ and Michez, D and Smagghe, G and Vandamme, P},
title = {The wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta microbiota are host specific and dominated by endosymbionts and environmental microorganisms.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3013-3026},
pmid = {37794084},
issn = {1432-184X},
mesh = {Bees ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Mycobiome ; Bacteria ; *Spiroplasma ; },
abstract = {We characterized the microbial communities of the crop, midgut, hindgut, and ovaries of the wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta through 16S rRNA gene and ITS2 amplicon sequencing and a large-scale isolation campaign. The bacterial communities of these bees were dominated by endosymbionts of the genera Wolbachia and Spiroplasma. Bacterial and yeast genera representing the remaining predominant taxa were linked to an environmental origin. While only a single sampling site was examined for Andrena vaga, Anthophora plumipes, and Colletes cunicularius, and two sampling sites for Osmia cornuta, the microbiota appeared to be host specific: bacterial, but not fungal, communities generally differed between the analyzed bee species, gut compartments and ovaries. This may suggest a selective process determined by floral and host traits. Many of the gut symbionts identified in the present study are characterized by metabolic versatility. Whether they exert similar functionalities within the bee gut and thus functional redundancy remains to be elucidated.},
}
@article {pmid37794025,
year = {2023},
author = {Li, X and Chen, D and Carrión, VJ and Revillini, D and Yin, S and Dong, Y and Zhang, T and Wang, X and Delgado-Baquerizo, M},
title = {Author Correction: Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {6188},
doi = {10.1038/s41467-023-41564-4},
pmid = {37794025},
issn = {2041-1723},
}
@article {pmid37792090,
year = {2023},
author = {Rippel, TM and Wimp, GM},
title = {Succession of Fungal Communities and Their Functional Profiles in a Decaying Foundation Species.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3003-3012},
pmid = {37792090},
issn = {1432-184X},
mesh = {*Mycobiome ; Ecosystem ; Fungi/physiology ; Soil Microbiology ; Plant Leaves/microbiology ; Biomass ; Plants ; Soil ; },
abstract = {Dead plant biomass from foundation plant species is fundamental for the survival of coastal salt marshes because dead biomass aids in the vertical accretion of the ecosystem. Fungi regulate the decomposition of dead biomass, and thus play an essential role for marsh survival. Despite their importance, little is known about the compositional and functional changes of fungal communities in plant matter throughout senescence and litter decomposition. Here, we analyzed how fungal communities and their functionality change in the foundation plant species Spartina patens, which builds vast amounts of dead plant biomass (thatch) on the soil surface. We analyzed the chemical and fungal properties of live biomass, standing dead biomass (dead biomass shortly after senescence), upper thatch (top layer of litter on the soil surface), and lower thatch (bottom layer of litter on the soil surface) during September and November of 2021. We found that the chemical and fungal properties of different S. patens biomass types followed a predictable litter decomposition pattern. Notably, live biomass, standing dead biomass, upper thatch, and lower thatch all hosted unique fungal communities and litter chemistry. Functional groups present in live biomass (pathogens, epiphytes, and mycoparasites) were lost during senescence and later replaced by diverse saprotrophs. The abundance of lignocellulose saprotrophs increased throughout decomposition, with the highest abundance occurring in lower thatch. These results suggest a predictable succession of fungal communities through the senescence and decomposition of the foundation species S. patens. Our study highlights the diversity of fungal communities in a disappearing foundation species.},
}
@article {pmid37792089,
year = {2023},
author = {Sun, J and Zhou, H and Cheng, H and Chen, Z and Yang, J and Wang, Y and Jing, C},
title = {Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3027-3042},
pmid = {37792089},
issn = {1432-184X},
mesh = {*Bacteria/genetics ; *Manganese ; Geologic Sediments/microbiology ; Nickel ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Cobalt ; },
abstract = {Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.},
}
@article {pmid37791342,
year = {2023},
author = {Kamiya, S},
title = {Microbial ecology between Clostridioides difficile and gut microbiota.},
journal = {Bioscience of microbiota, food and health},
volume = {42},
number = {4},
pages = {229-235},
pmid = {37791342},
issn = {2186-6953},
abstract = {Clostridioides difficile colonizes a polymicrobial environment in the intestine and is a causative agent for antibiotic-associated diarrhea (AAD) and pseudomembranous colitis (PMC). The most important virulence factors of C. difficile are bacterial toxins, and three toxins (toxin A, toxin B, and binary toxin) are produced by toxigenic strains. Other virulence factors include spores, flagella, capsules, biofilms, hydrolytic enzymes and adhesins. C. difficile infection (CDI) is specifically diagnosed by anaerobic culture and toxin detection by either nucleic acid amplification test (NAAT) or enzyme-linked immunosorbent assay (ELISA). For treatment of CDI, metronidazole, vancomycin and fidaxomicin are used based on the severity of CDI. Mutual interaction between C. difficile and gut microbiota is associated with pathogenesis of CDI, and decreased microbial diversity with altered gut microbiome was detected in CDI patients. Restoration of certain gut microbiota is considered to be potentially effective for the prevention and treatment of CDI, and an ideal goal for CDI patients is restoration of the gut microbiota to a healthy state. Fecal microbiota transplantation (FMT) is a highly successful method of microbiome restoration and has been reported to be effective for the prevention of recurrent CDI. In addition, approaches to restoring the gut microbiota by using probioitcs and live biotherapeutic products (LBPs) are currently being studied to examine the effect on CDI. Further microbial ecological research on C. difficile and gut microbiota could lead to a better understanding of the pathogenesis and treatment of CDI.},
}
@article {pmid37783827,
year = {2023},
author = {Skwara, A and Gowda, K and Yousef, M and Diaz-Colunga, J and Raman, AS and Sanchez, A and Tikhonov, M and Kuehn, S},
title = {Statistically learning the functional landscape of microbial communities.},
journal = {Nature ecology &amp; evolution},
volume = {7},
number = {11},
pages = {1823-1833},
pmid = {37783827},
issn = {2397-334X},
support = {R01 GM151538/GM/NIGMS NIH HHS/United States ; T32 GM150375/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; Biomass ; Soil ; Models, Theoretical ; },
abstract = {Microbial consortia exhibit complex functional properties in contexts ranging from soils to bioreactors to human hosts. Understanding how community composition determines function is a major goal of microbial ecology. Here we address this challenge using the concept of community-function landscapes-analogues to fitness landscapes-that capture how changes in community composition alter collective function. Using datasets that represent a broad set of community functions, from production/degradation of specific compounds to biomass generation, we show that statistically inferred landscapes quantitatively predict community functions from knowledge of species presence or absence. Crucially, community-function landscapes allow prediction without explicit knowledge of abundance dynamics or interactions between species and can be accurately trained using measurements from a small subset of all possible community compositions. The success of our approach arises from the fact that empirical community-function landscapes appear to be not rugged, meaning that they largely lack high-order epistatic contributions that would be difficult to fit with limited data. Finally, we show that this observation holds across a wide class of ecological models, suggesting community-function landscapes can be efficiently inferred across a broad range of ecological regimes. Our results open the door to the rational design of consortia without detailed knowledge of abundance dynamics or interactions.},
}
@article {pmid37782571,
year = {2023},
author = {Schnyder, E and Bodelier, PLE and Hartmann, M and Henneberger, R and Niklaus, PA},
title = {Experimental erosion of microbial diversity decreases soil CH4 consumption rates.},
journal = {Ecology},
volume = {104},
number = {12},
pages = {e4178},
doi = {10.1002/ecy.4178},
pmid = {37782571},
issn = {1939-9170},
support = {144065 to Pascal A. Niklaus.//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Ecosystem ; *Soil ; Bacteria/genetics ; Biodiversity ; Wetlands ; Methane ; Soil Microbiology ; },
abstract = {Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4) cycle by removing atmospheric CH4 and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution-to-extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 10[1] -10[7] -fold, preincubated under a high CH4 atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.},
}
@article {pmid37779539,
year = {2022},
author = {Caparrós, E and Cenit, MC and Muriel, J and Benítez-Páez, A and Moreno, MV and González-Delgado, P and Rubio, G and Sanz, Y and Fernández, J},
title = {Intestinal microbiota is modified in pediatric food protein-induced enterocolitis syndrome.},
journal = {The journal of allergy and clinical immunology. Global},
volume = {1},
number = {4},
pages = {217-224},
pmid = {37779539},
issn = {2772-8293},
abstract = {BACKGROUND: Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated food hypersensitivity that affects the gastrointestinal system, especially in children, who often present with more severe clinical manifestations than adults do. Although its pathogenesis is poorly understood and biomarkers are still lacking, scientific evidence suggests that gut microbiota may play an important role in the development of FPIES.<br><br>OBJECTIVE: We aimed to compare the composition of gut microbiota in children with FPIES with that in age- and sex-matched healthy controls.<br><br>METHODS: We analyzed the gut microbiota profiles in fecal samples of 17 patients with FPIES (case patients) and 12 age-matched healthy children (controls) by tag sequencing of the 16S ribosomal RNA gene hypervariable V4-V5 regions. Subjects' sociodemographic, clinical, and food diary variables were described and compared between groups by using inferential statistical tests. Nonparametric linear discriminant analysis was performed for intestinal microbiota data.<br><br>RESULTS: Patients with confirmed cases FPIES (n&#xa0;= 17; average patient age, 7.5&#xa0;&#xb1; 3.2 years) and controls without FPIES or any atopy (n&#xa0;= 12, average patient age, 6.9&#xa0;&#xb1; 2.7 years) were included. Fish was the main FPIES-inducing allergen in 65% of the cases. The patients with FPIES showed higher proportions of Lachnospiraceae spp (P&#xa0;< .0286) and a lower proportion of Ruminococcaceae spp (P&#xa0;< .0066), Lactobacillaceae spp (P&#xa0;< .0075), and Leuconostocaceae spp (P&#xa0;< .0173) than the controls.<br><br>CONCLUSIONS: Our data clearly show a different gut microbial signature in patients with FPIES, suggesting a new potential avenue for aiding the diagnosis and clinical management of FPIES. Larger studies are needed to confirm these results.},
}
@article {pmid37778560,
year = {2024},
author = {Buenaño-Vargas, C and Gagliano, MC and Paulo, LM and Bartle, A and Graham, A and van Veelen, HPJ and O'Flaherty, V},
title = {Acclimation of microbial communities to low and moderate salinities in anaerobic digestion.},
journal = {The Science of the total environment},
volume = {906},
number = {},
pages = {167470},
doi = {10.1016/j.scitotenv.2023.167470},
pmid = {37778560},
issn = {1879-1026},
mesh = {*Wastewater ; Anaerobiosis ; Sewage/microbiology ; Waste Disposal, Fluid ; Salinity ; Bioreactors/microbiology ; Bacteria ; *Microbiota ; },
abstract = {In recent years anaerobic digestion (AD) has been investigated as suitable biotechnology to treat wastewater at elevated salinities. However, when starting up AD reactors with inocula that are not adapted to salinity, low concentrations of sodium (Na[+]) in the influent can already cause disintegration of microbial aggregates and wash-out. This study investigated biomass acclimation to 5 g Na[+/]L of two different non-adapted inocula in two lab-scale hybrid expanded granular sludge bed (EGSB)-anaerobic filter (AF) reactors fed with synthetic wastewater. After an initial biomass disintegration, new aggregates were formed relatively fast (i.e., after 95 days of operation), indicating microbial community adaptation. The newly formed microbial aggregates accumulated Na[+] at the expense of calcium (Ca[2+]), but this did not hamper biomass retention or process performance. The hybrid reactor configuration, including a pumice stone filter in the upper section, and the low up-flow velocities applied, were key features for retaining the biomass within the system. This reactor configuration can be easily applied and represents a low-cost alternative for acclimating biomass to saline effluents, even in existing digesters. When the acclimated biomass was transferred from EGSB to an up-flow anaerobic sludge blanket (UASB) reactor configuration also fed with saline synthetic wastewater, more dense aggregates in the form of granules were obtained. The performances of the UASB inoculated with the acclimated biomass were comparable to another reactor seeded with saline-adapted granular sludge from a full-scale plant. Regardless of the inoculum origin, a defined core microbiome of Bacteria (Thermovirga, Bacteroidetes vadinHA17, Blvii28 wastewater-sludge group, Mesotoga, and Synergistaceae) and Archaea (Methanosaeta and Methanobacterium) was detected, highlighting the importance of these microbial groups in developing halotolerance and maintaining AD process stability.},
}
@article {pmid37778079,
year = {2023},
author = {Sabach, O and Buhnik-Rosenblau, K and Kesten, I and Freilich, S and Freilich, S and Kashi, Y},
title = {The rise of the sourdough: Genome-scale metabolic modeling-based approach to design sourdough starter communities with tailored-made properties.},
journal = {International journal of food microbiology},
volume = {407},
number = {},
pages = {110402},
doi = {10.1016/j.ijfoodmicro.2023.110402},
pmid = {37778079},
issn = {1879-3460},
mesh = {Saccharomyces cerevisiae/genetics/metabolism ; Fermentation ; *Lactobacillales/metabolism ; *Yeast, Dried ; Bacteria ; Pediococcus ; Bread/microbiology ; Flour/microbiology ; Food Microbiology ; },
abstract = {Sourdough starters harbor microbial consortia that benefit the final product's aroma and volume. The complex nature of these spontaneously developed communities raises challenges in predicting the fermentation phenotypes. Herein, we demonstrated for the first time in this field the potential of genome-scale metabolic modeling (GEMs) in the study of sourdough microbial communities. Broad in-silico modeling of microbial growth was applied on communities composed of yeast (Saccharomyces cerevisiae) and different Lactic Acid Bacteria (LAB) species, which mainly predominate in sourdough starters. Simulations of model-represented communities associated specific bacterial compositions with sourdough phenotypes. Based on ranking the phenotypic performances of different combinations, Pediococcus spp. - Lb. sakei group members were predicted to have an optimal effect considering the increase in S. cerevisiae growth abilities and overall CO2 secretion rates. Flux Balance Analysis (FBA) revealed mutual relationships between the Pediococcus spp. - Lb. sakei group members and S. cerevisiae through bidirectional nutrient dependencies, and further underlined that these bacteria compete with the yeast over nutrients to a lesser extent than the rest LAB species. Volatile compounds (VOCs) production was further modeled, identifying species-specific and community-related VOCs production profiles. The in-silico models' predictions were validated by experimentally building synthetic sourdough communities and assessing the fermentation phenotypes. The Pediococcus spp. - Lb. sakei group was indeed associated with increased yeast cell counts and fermentation rates, demonstrating a 25 % increase in the average leavening rates during the first 10 fermentation hours compared to communities with a lower representation of these group members. Overall, these results provide a possible novel strategy towards the de-novo design of sourdough starter communities with tailored-made characterizations, including a shortened leavening period.},
}
@article {pmid37778064,
year = {2023},
author = {Niu, G and Wang, R and Zhou, H and Yang, J and Lu, X and Han, X and Huang, J},
title = {Nitrogen addition and mowing had only weak interactive effects on macronutrients in plant-soil systems of a typical steppe in Inner Mongolia.},
journal = {Journal of environmental management},
volume = {347},
number = {},
pages = {119121},
doi = {10.1016/j.jenvman.2023.119121},
pmid = {37778064},
issn = {1095-8630},
mesh = {*Ecosystem ; *Soil ; Nitrogen ; Plants ; China ; Nutrients ; Grassland ; },
abstract = {Effective management of macronutrients is pivotal in the optimization and provisioning of ecosystem services in grassland areas, particularly in degraded grasslands. In such instances where mowing and nitrogen (N) fertilization have emerged as predominant management strategies, nutrient management is especially important. However, the precise effects of these concurrent practices on the distribution of macronutrients in plant-soil systems remain unclear. Here we evaluated the effects of 12 years of N addition (2, 10, and 50 g N m[-2] year[-1]) and mowing on the concentrations and pools of six macronutrients (i.e., N; phosphorus P; sulfur S, calcium Ca, magnesium Mg, and potassium K) in three plant components (aboveground plants, litter, and belowground roots) at the community level and in the soil in a typical steppe in Inner Mongolia. Our results revealed that N addition generally raised the N concentration in the entire plant-soil system, regardless of whether plots were mowed. Higher N addition (10 and 50 g N m[-2] year[-1]) also led to higher concentrations of P (+22%, averaging two N addition rates), S (+16%), K (+22%), Ca (+22%), and Mg (+24%) in plants but lower concentrations of these nutrients in the litter. Similar decreases in K (-9%), Ca (-46%), and Mg (-8%) were observed in the roots. In light of the observed increases in vegetation biomass and the lack of pronounced changes in soil bulk density, we found that the ecosystem N enrichment resulted in increased pools of all measured macronutrients in plants, litter, and roots (with the exception of Ca in the roots) while concurrently decreased the pools of P (-20%, averaging two higher N addition rates), S (-12%), K (-10%), Ca (-37%), and Mg (-19%) in the soil, with no obvious effect of the mowing practice. Overall, mowing exhibited a very limited capacity to alleviate the effects of long-term N addition on macronutrients in the plant-soil system. These findings highlight the importance of considering the distribution of macronutrients across distinct plant organs and the dynamic nutrient interplay between plants and soil, particularly in the context of long-term fertilization and mowing practices, when formulating effective grassland management strategies.},
}
@article {pmid37777451,
year = {2023},
author = {Tsirigotaki, M and Galanakis, E},
title = {Impact of vaccines on Staphylococcus aureus colonization: A systematic review and meta-analysis.},
journal = {Vaccine},
volume = {41},
number = {44},
pages = {6478-6487},
doi = {10.1016/j.vaccine.2023.09.034},
pmid = {37777451},
issn = {1873-2518},
abstract = {BACKGROUND: Concerns regarding vaccine effects on microbial ecology have led to interest in the non-targeted effects of vaccinations.<br><br>OBJECTIVES: To systematically review the literature related to the impact of vaccines on S. aureus carriage.<br><br>METHODS: We conducted a systematic search of MEDLINE, Scopus and clinical trials.gov for studies that assessed vaccine effects on S. aureus carriage in children and adults using predefined inclusion and exclusion criteria. Generic inverse variance meta-analysis was done using random-effects models.<br><br>RESULTS: Of 1,686 studies screened, 34 were eligible for inclusion, of which 22 were observational and 12 randomized controlled studies (RCTs). 88.2% (30/34) provided data on pneumococcal conjugate vaccines (PCV), 23.5% on influenza vaccines (8/34), 6% on other vaccines (2/34) and 20.6% on more than one vaccine (7/34). Most studies tested nasopharyngeal specimens (82.3%, 28/34). Among children aged more than 18-24&#xa0;months, evidence suggested no effect of PCV on S. aureus colonization [2 RCTs, pooled OR 1.09 (95% CI 0.94-1.25), p 0.25; 7 observational studies, pooled OR: 1.02 (95% CI 0.83-1.25), p 0.86]. A transient increase in S. aureus carriage in PCV-vaccinated infants 9-15&#xa0;months was shown [2 RCTs, pooled OR 1.11 (95% CI 1.00-1.23), p 0.06; 4 observational studies, pooled OR 1.64 (95% CI 1.00-2.68), p 0.05]. A reduction in S. aureus carriage was observed after influenza vaccination [4 observational studies; OR 0.85 (95% CI 0.78-0.94), p 0.0001]. Based on the Grading of Recommendations Assessment, Development and Evaluation, the quality of evidence was considered low for randomized and very low for non-randomized trials.<br><br>CONCLUSION: Evidence did not suggest long-term effects of pneumococcal vaccinations on S. aureus nasopharyngeal carriage in children, however transient niche changes may occur in infants. Influenza vaccination was related to decreased rates of S. aureus carriage. Data regarding other vaccines is scarce. Further research and ongoing surveillance are needed to monitor colonization changes.},
}
@article {pmid37775010,
year = {2023},
author = {Shen, Z and Yu, B and Shao, K and Gao, G and Tang, X},
title = {Warming reduces microeukaryotic diversity, network complexity and stability.},
journal = {Environmental research},
volume = {238},
number = {Pt 2},
pages = {117235},
doi = {10.1016/j.envres.2023.117235},
pmid = {37775010},
issn = {1096-0953},
mesh = {*Ecosystem ; *Climate Change ; Analysis of Variance ; Temperature ; },
abstract = {Unraveling how climate warming affects microorganisms and the underlying mechanisms has been a hot topic in climate change and microbial ecology. To date, many studies have reported microbial responses to climate warming, especially in soil ecosystems, however, knowledge of how warming influences microeukaryotic diversity, network complexity and stability in lake ecosystems, in particular the possible underlying mechanisms, is largely unknown. To address this gap, we conducted 20 mesocosms spanning five temperature scenarios (26 °C, 27.5 °C, 29 °C, 30.5 °C, and 32 °C) in Lake Bosten, a hotspot for studying climate change, and investigated microeukaryotic communities using 18S rRNA gene sequencing. Our results demonstrated that warming, time, and their interactions significantly reduced microeukaryotic α-diversity (two-way ANOVA: P＜0.01). Although warming did not significantly affect microeukaryotic community structure (ANOSIM: P＞0.05), it enhanced species turnover. Microeukaryotic networks exhibited distinct co-occurrence patterns and topological properties across temperature scenarios. Warming reduced network complexity and stability, as well as altered species interactions. Collectively, these findings are likely to have implications for ecological management of lake ecosystems, in particular semi-arid and arid regions, and for predicting ecological consequences of climate change.},
}
@article {pmid37769814,
year = {2023},
author = {Zinzula, L and Scholz, J and Nagy, I and Di Guardo, G and Orsini, M},
title = {Biophysical characterization of the cetacean morbillivirus haemagglutinin glycoprotein.},
journal = {Virus research},
volume = {336},
number = {},
pages = {199231},
pmid = {37769814},
issn = {1872-7492},
abstract = {Cetacean morbillivirus (CeMV) is an enveloped, non-segmented, negative-stranded RNA virus that infects marine mammals, spreading across species and causing lethal disease outbreaks worldwide. Among the eight proteins encoded by the CeMV genome, the haemagglutinin (H) glycoprotein is responsible for the virus attachment to host cell receptors. CeMV H represents an attractive target for antiviral and diagnostic research, yet the elucidation of the molecular mechanisms underlying its role in infection and inter-species transmission was hampered thus far due to the unavailability of recombinant versions of the protein. Here we present the cloning, expression and purification of a recombinant CeMV H ectodomain (rH-ecto), providing an initial characterization of its biophysical and structural properties. Sodium dodecyl sulphate - polyacrylamide gel electrophoresis (PAGE) combined to Western blot analysis and periodic acid Schiff assay showed that CeMV rH-ecto is purifiable at homogeneity from insect cells as a secreted, soluble and glycosylated protein. Miniaturized differential scanning fluorimetry, Blue Native PAGE and size exclusion chromatography coupled to multiangle light scattering revealed that CeMV rH-ecto is globularly folded, thermally stable and exists in solution in the oligomeric states of dimer and multiple of dimers. Furthermore, negative stain electron microscopy single particle analysis allowed us to delineate a low-resolution molecular architecture of the CeMV rH-ecto dimer, which recapitulates native assemblies from other morbilliviral H proteins, such as those from measles virus and canine distemper virus. This set of experiments by orthogonal techniques validates the CeMV rH-ecto as an experimental model for future biochemical studies on its structure and functions.},
}
@article {pmid37774017,
year = {2023},
author = {Wielscher, M and Pfisterer, K and Samardzic, D and Balsini, P and Bangert, C and Jäger, K and Buchberger, M and Selitsch, B and Pjevac, P and Willinger, B and Weninger, W},
title = {The phageome in normal and inflamed human skin.},
journal = {Science advances},
volume = {9},
number = {39},
pages = {eadg4015},
pmid = {37774017},
issn = {2375-2548},
mesh = {Humans ; *Virome ; Skin/microbiology ; *Microbiota ; Metagenome ; Bacteria/genetics ; DNA, Viral/genetics ; },
abstract = {Dysbiosis of skin microbiota drives the progression of atopic dermatitis (AD). The contribution of bacteriophages to bacterial community compositions in normal and inflamed skin is unknown. Using shotgun metagenomics from skin swabs of healthy individuals and patients with AD, we found 13,586 potential viral contiguous DNA sequences, which could be combined into 164 putative viral genomes including 133 putative phages. The Shannon diversity index for the viral metagenome-assembled genomes (vMAGs) did not correlate with AD. In total, we identified 28 vMAGs that differed significantly between normal and AD skin. Quantitative polymerase chain reaction validation of three complete vMAGs revealed their independence from host bacterium abundance. Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology.},
}
@article {pmid37771751,
year = {2023},
author = {Arikawa, K and Hosokawa, M},
title = {Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {4508-4518},
pmid = {37771751},
issn = {2001-0370},
abstract = {Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.},
}
@article {pmid37771273,
year = {2023},
author = {Staller, K and Olén, O and Söderling, J and Roelstraete, B and Törnblom, H and Kuo, B and Nguyen, LH and Ludvigsson, JF},
title = {Antibiotic use as a risk factor for irritable bowel syndrome: Results from a nationwide, case-control study.},
journal = {Alimentary pharmacology &amp; therapeutics},
volume = {58},
number = {11-12},
pages = {1175-1184},
doi = {10.1111/apt.17736},
pmid = {37771273},
issn = {1365-2036},
support = {K23DK120945/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Humans ; *Irritable Bowel Syndrome/drug therapy/epidemiology/diagnosis ; Case-Control Studies ; Anti-Bacterial Agents/adverse effects ; Risk Factors ; Sweden/epidemiology ; },
abstract = {BACKGROUND: The microbiome plays an important role in the pathophysiology of irritable bowel syndrome (IBS). Antibiotic use can fundamentally alter gut microbial ecology. We examined the association of antibiotic use with IBS in a large population-based investigation.<br><br>METHODS: A case-control study with prospectively collected data on 29,111 adult patients diagnosed with IBS in Sweden between 2007 and 2016 matched with 135,172 controls. Using a comprehensive histopathology cohort, the Swedish Patient Register, and the Prescribed Drug Register, we identified all consecutive cases of IBS in addition to cumulative antibiotic dispensations accrued until 1&#x2009;year prior to IBS (exclusionary period) for cases and time of matching for up to five general population controls matched on the basis of age, sex, country and calendar year. Conditional logistic regression estimated multivariable-adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for the risk of IBS.<br><br>RESULTS: Patients with IBS (n&#x2009;=&#x2009;29,111) were more likely than controls (n&#x2009;=&#x2009;135,172) to have used antibiotics up to 1&#x2009;year prior to diagnosis (74.9% vs. 57.8%). After multivariable adjustment, this translated to a more than twofold increased odds of IBS (OR 2.21, 95% CI 2.14-2.28) that did not differ according to age, sex, year of IBS diagnosis or IBS subtype. Compared to none, 1-2 (OR 1.67, 95% CI 1.61-1.73) and &#x2265;3 antibiotics dispensations (OR 3.36, 95% CI 3.24-3.49) were associated with increased odds of IBS (p for trend <0.001) regardless of the antibiotic class.<br><br>CONCLUSIONS: Prior antibiotics use was associated with an increased odds of IBS with the highest risk among people with multiple antibiotics dispensations.},
}
@article {pmid37768303,
year = {2023},
author = {Kiewra, D and Krysmann, A},
title = {Interactions between hard ticks (Ixodidae) and bacterial tick-borne pathogens.},
journal = {Annals of parasitology},
volume = {69},
number = {1},
pages = {7-16},
doi = {10.17420/ap6901.502},
pmid = {37768303},
issn = {2299-0631},
mesh = {Animals ; Humans ; *Ixodidae ; *Tick-Borne Diseases ; *Rickettsia/genetics ; *Ticks ; Europe ; *Ixodes ; },
abstract = {In Europe, ticks are particularly important vectors of pathogens known as tick-borne pathogens (TBP). TBP can influence hosts, including domestic animals and humans as well as ticks. This review focuses on interactions between hard ticks and medically and veterinary significant bacterial pathogens i.e. Borrelia burgdorferi s.l., Anaplasma spp, and Rickettsia spp. The interactions between ticks and bacteria include among others the impact on gene expression and tick behaviour. Infection with TBP may influence tick salivary proteins and midgut receptors. Infection with B. burgdorferi s.l. changes the bahaviour of the tick allowing them for longer questing and increased mobility, while A. phagocytophilum increases survive in low temperatures by upregulating the expression of antifreeze glycoprotein (IAFGP). Whereas Rickettsia spp. increases ticks attraction towards the 900 MHz electromagnetic field.},
}
@article {pmid37768099,
year = {2023},
author = {Ghesquière, J and Simoens, K and Koos, E and Boon, N and Teughels, W and Bernaerts, K},
title = {Spatiotemporal monitoring of a periodontal multispecies biofilm model: demonstration of prebiotic treatment responses.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {10},
pages = {e0108123},
pmid = {37768099},
issn = {1098-5336},
mesh = {Humans ; *Bacteria ; Streptococcus gordonii/physiology ; Fusobacterium nucleatum ; Streptococcus sanguis ; Streptococcus oralis ; Biofilms ; *Periodontitis ; Arginine/metabolism ; Porphyromonas gingivalis/physiology ; },
abstract = {Biofilms are complex polymicrobial communities which are often associated with human infections such as the oral disease periodontitis. Studying these complex communities under controlled conditions requires in vitro biofilm model systems that mimic the natural environment as close as possible. This study established a multispecies periodontal model in the drip flow biofilm reactor in order to mimic the continuous flow of nutrients at the air-liquid interface in the oral cavity. The design is engineered to enable real-time characterization. A community of five bacteria, Streptococcus gordonii-GFPmut3*, Streptococcus oralis-GFPmut3*, Streptococcus sanguinis-pVMCherry, Fusobacterium nucleatum, and Porphyromonas gingivalis-SNAP26 is visualized using two distinct fluorescent proteins and the SNAP-tag. The biofilm in the reactor develops into a heterogeneous, spatially uniform, dense, and metabolically active biofilm with relative cell abundances similar to those in a healthy individual. Metabolic activity, structural features, and bacterial composition of the biofilm remain stable from 3 to 6 days. As a proof of concept for our periodontal model, the 3 days developed biofilm is exposed to a prebiotic treatment with L-arginine. Multifaceted effects of L-arginine on the oral biofilm were validated by this model setup. L-arginine showed to inhibit growth and incorporation of the pathogenic species and to reduce biofilm thickness and volume. Additionally, L-arginine is metabolized by Streptococcus gordonii-GFPmut3* and Streptococcus sanguinis-pVMCherry, producing high levels of ornithine and ammonium in the biofilm. In conclusion, our drip flow reactor setup is promising in studying spatiotemporal behavior of a multispecies periodontal community.ImportancePeriodontitis is a multifactorial chronic inflammatory disease in the oral cavity associated with the accumulation of microorganisms in a biofilm. Not the presence of the biofilm as such, but changes in the microbiota (i.e., dysbiosis) drive the development of periodontitis, resulting in the destruction of tooth-supporting tissues. In this respect, novel treatment approaches focus on maintaining the health-associated homeostasis of the resident oral microbiota. To get insight in dynamic biofilm responses, our research presents the establishment of a periodontal biofilm model including Streptococcus gordonii, Streptococcus oralis, Streptococcus sanguinis, Fusobacterium nucleatum, and Porphyromonas gingivalis. The added value of the model setup is the combination of simulating continuously changing natural mouth conditions with spatiotemporal biofilm profiling using non-destructive characterization tools. These applications are limited for periodontal biofilm research and would contribute in understanding treatment mechanisms, short- or long-term exposure effects, the adaptation potential of the biofilm and thus treatment strategies.},
}
@article {pmid37767604,
year = {2023},
author = {Bustos-Lobato, L and Rus, MJ and Saúco, C and Simon-Soro, A},
title = {Oral microbial biomap in the drought environment: Sjogren's syndrome.},
journal = {Molecular oral microbiology},
volume = {38},
number = {5},
pages = {400-407},
doi = {10.1111/omi.12435},
pmid = {37767604},
issn = {2041-1014},
mesh = {Humans ; *Sjogren's Syndrome/microbiology ; Droughts ; Ecosystem ; Saliva/microbiology ; },
abstract = {Sjogren's syndrome (SS) is an autoimmune disease that affects primarily the salivary glands, making perturbations in the oral ecosystem and potential factors of salivary flow that influence the onset and development of the disease. The oral cavity contains diverse microorganisms that inhabit various niches such as the oral microbial "biomap." It does not seem specific enough to establish a characteristic microbiome, given the diversity of clinical manifestations, variable rates of salivary secretion, and influential risk factors in patients with SS. This review discusses the biogeography of the oral microbiome in patients with SS such as saliva, tongue, tooth, mucosa, and gum. The microorganisms that were more abundant in the different oral niches were Gram-positive species, suggesting a higher survival of cell wall bacteria in this arid oral environment. Reduced salivary flow appears not to be linked to the cause of dysbiosis alone but influences host-associated risk factors. However, much work remains to be done to establish the role of the microbiome in the etiopathogenesis of autoimmune diseases such as SS. Future studies of the microbiome in autoimmunity will shed light on the role of specific microorganisms that have never been linked before with SS.},
}
@article {pmid37767299,
year = {2023},
author = {Cai, J and Pan, R and Lin, J and Liu, J and Zhang, L and Wen, X and Chen, X and Zhang, X},
title = {Improved EfficientNet for corn disease identification.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1224385},
pmid = {37767299},
issn = {1664-462X},
abstract = {INTRODUCTION: Corn is one of the world's essential crops, and the presence of corn diseases significantly affects both the yield and quality of corn. Accurate identification of corn diseases in real time is crucial to increasing crop yield and improving farmers' income. However, in real-world environments, the complexity of the background, irregularity of the disease region, large intraclass variation, and small interclass variation make it difficult for most convolutional neural network models to achieve disease recognition under such conditions. Additionally, the low accuracy of existing lightweight models forces farmers to compromise between accuracy and real-time.<br><br>METHODS: To address these challenges, we propose FCA-EfficientNet. Building upon EfficientNet, the fully-convolution-based coordinate attention module allows the network to acquire spatial information through convolutional structures. This enhances the network's ability to focus on disease regions while mitigating interference from complex backgrounds. Furthermore, the adaptive fusion module is employed to fuse image information from different scales, reducing interference from the background in disease recognition. Finally, through multiple experiments, we have determined the network structure that achieves optimal performance.<br><br>RESULTS: Compared to other widely used deep learning models, this proposed model exhibits outstanding performance in terms of accuracy, precision, recall, and F1 score. Furthermore, the model has a parameter count of 3.44M and Flops of 339.74M, which is lower than most lightweight network models. We designed and implemented a corn disease recognition application and deployed the model on an Android device with an average recognition speed of 92.88ms, which meets the user's needs.<br><br>DISCUSSION: Overall, our model can accurately identify corn diseases in realistic environments, contributing to timely and effective disease prevention and control.},
}
@article {pmid37766415,
year = {2023},
author = {Bohórquez-Herrera, J and Abad Matías, ID and Gutiérrez Castañeda, CG},
title = {Impact of different environmental pollution processes on bacterial key-indicators in tropical rivers: scoping review.},
journal = {FEMS microbiology letters},
volume = {370},
number = {},
pages = {},
doi = {10.1093/femsle/fnad098},
pmid = {37766415},
issn = {1574-6968},
support = {//Universidad de Cartagena/ ; },
abstract = {Freshwater ecosystems are an essential resource for human use and natural populations, but they are exposed to different sources of man-made pollution. This study analyses how different environmental pollution processes influence the structure of bacterial communities in tropical rivers. A scoping review was performed to characterize the bacterial communities in freshwater ecosystems in tropical regions that have been reported to be associated with pollution of different kinds. The statistical analyses allowed us to categorize the genera found into three large groups (pollution generalists, middle types, and pollution specialists) according to the types of pollutants with which they were associated. The results show that Escherichia has a greater association with fecal contamination, while Enterococcus is more associated with domestic wastewater and organic and synthetic chemicals. The present study proposes Streptomyces as a potential indicator of waters with microbial contamination, as well as some other genera as possible indicators of waters with heavy metal contamination.},
}
@article {pmid37760211,
year = {2023},
author = {Verstrepen, L and Calatayud-Arroyo, M and Duysburgh, C and De Medts, J and Ekmay, RD and Marzorati, M},
title = {Amino Acid Digestibility of Different Formulations of Torula Yeast in an In Vitro Porcine Gastrointestinal Digestion Model and Their Protective Effects on Barrier Function and Inflammation in a Caco-2/THP1Co-Culture Model.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {18},
pages = {},
pmid = {37760211},
issn = {2076-2615},
support = {//Arbiom Inc./ ; },
abstract = {Single-cell protein from torula yeast (Cyberlindnera jadinii) grown on lignocellulosic biomass has been proven to be an excellent alternative protein source for animal feed. This study aimed to evaluate the amino acid (AA) digestibility by estimating intestinal absorption from three yeast-based ingredients, produced by cultivating C. jadinii on hydrolysate, using either mixed woody species (drum- (WDI) or spray-dried (WSI)) or corn dextrose (drum-dried (DDI)) as the carbon source. Further, the protective effect of intestinal digests on activated THP1-Blue™-induced epithelial damage and cytokine profile was evaluated. Total protein content from these three ingredients ranged from 34 to 45%, while the AA dialysis showed an estimated bioaccessibility between 41 and 58%, indicating good digestibility of all test products. A protective effect against epithelial-induced damage was observed for two of the three tested products. Torula yeast cultivated on wood and drum-dried (WDI) and torula yeast cultivated on wood and spray-dried (WSI) significantly increased transepithelial electrical resistance (TEER) values (111-147%, p < 0.05), recovering the epithelial barrier from the inflammation-induced damage in a dose-dependent manner. Further, WSI digests significantly reduced IL8 (250.8 ± 28.1 ng/mL), IL6 (237.9 ± 1.8 pg/mL) and TNF (2797.9 ± 216.3 pg/mL) compared to the blank control (IL8 = 485.7 ± 74.4 ng/mL, IL6 = 478.7 ± 58.9 pg/mL; TNF = 4273.5 ± 20.9 pg/mL) (p < 0.05). These results align with previous in vivo studies, supporting torula yeast-based ingredients as a high-quality protein source for pigs, protecting the intestinal barrier from inflammatory damage, and reducing the pro-inflammatory response. We provided novel insights into the mechanisms behind the health improvement of pigs fed on torula yeast-based ingredients, with potential applications for designing nutritional interventions to recover intestinal homeostasis during critical production periods, such as weaning.},
}
@article {pmid37756318,
year = {2023},
author = {Zhang, X and Yao, C and Zhang, B and Tan, W and Gong, J and Wang, GY and Zhao, J and Lin, X},
title = {Dynamics of Benthic Nitrate Reduction Pathways and Associated Microbial Communities Responding to the Development of Seasonal Deoxygenation in a Coastal Mariculture Zone.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {40},
pages = {15014-15025},
doi = {10.1021/acs.est.3c03994},
pmid = {37756318},
issn = {1520-5851},
mesh = {Nitrates/analysis ; Chlorophyll A ; Seasons ; Organic Chemicals ; *Ammonium Compounds ; Nitrogen/analysis ; *Microbiota ; Oxygen ; Denitrification ; },
abstract = {Intensive mariculture activities result in eutrophication and enhance coastal deoxygenation. Deoxygenation profoundly influences nitrate reduction processes and further the fate of nitrogen (N) in coastal systems. Herein, [15]N isotope labeling, real-time PCR, and high-throughput sequencing techniques were jointly used to investigate the participation and seasonal dynamics of sediment nitrate reduction pathways and the succession of functional microbial communities during the development of seasonal deoxygenation in a coastal aquaculture zone. Denitrification dominated benthic nitrate reduction (46.26-80.91%). Both denitrification and dissimilatory nitrate reduction to ammonium were significantly enhanced by summer deoxygenation (dissolved oxygen levels fell to 2.94 ± 0.28 mg L[-1]), while anammox remained unchanged. The abundance of the nitrous oxide reductase gene nosZ increased during deoxygenation. The community of the nosZ gene was sensitive to deoxygenation, with Azospirillum and Ruegeria accounting for the majority. Pelobacter was overwhelming in the nrfA gene (encoding dissimilatory nitrite reductase) community, which was less affected by deoxygenation. The variations of benthic nitrate reduction processes were driven by bottom water oxygen combined with temperature, chlorophyll a, and microbial gene abundances and community compositions. Our results implicated that seasonal oxygen-deficient zones could be substantial N sinks of coastal ecosystems and important for N balance. Effective management measures need to be developed to avoid further exacerbation of coastal deoxygenation and maintain the sustainable development of mariculture.},
}
@article {pmid37755230,
year = {2023},
author = {Bareia, T and Pollak, S and Guler, P and Puyesky, S and Eldar, A},
title = {Major distinctions between the two oligopeptide permease systems of Bacillus subtilis with respect to signaling, development and evolutionary divergence.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {9},
pages = {},
pmid = {37755230},
issn = {1465-2080},
mesh = {*Bacillus subtilis/genetics ; Biological Evolution ; *Biological Phenomena ; Signal Transduction ; Oligopeptides ; },
abstract = {Oligopeptide-permeases (Opps) are used by bacteria to import short peptides. In addition to their metabolic benefit, imported short peptides are used in many Gram-positive bacteria as signalling molecules of the RRNPP super-family of quorum-sensing systems, making Opps an integral part of cell–cell communication. In some Gram-positive bacteria there exist multiple Opps and the relative importance of those to RRNPP quorum sensing are not fully clear. Specifically, in Bacillus subtilis , the Gram-positive model species, there exist two homologous oligopeptide permeases named Opp and App. Previous work showed that the App system is mutated in lab strain 168 and its recovery partially complements an Opp mutation for several developmental processes. Yet, the nature of the impact of App on signalling and development in wild-type strains, where both permeases are active was not studied. Here we re-examine the impact of the two permease systems. We find that App has a minor contribution to biofilm formation, surfactin production and phage infection compared to the effect of Opp. This reduced effect is also reflected in its lower ability to import the signals of four different Rap-Phr RRNPP systems. Further analysis of the App system revealed that, unlike Opp, some App genes have undergone horizontal transfer, resulting in two distinct divergent alleles of this system in B. subtilis strains. We found that both alleles were substantially better adapted than the Opp system to import an exogenous RRNPP signal of the Bacillus cereus group PlcR-PapR system. In summary, we find that the App system has only a minor role in signalling but may still be crucial for the import of other peptides.},
}
@article {pmid37754985,
year = {2023},
author = {Marsaux, B and Moens, F and Marzorati, M and Van de Wiele, T},
title = {The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME[®] Model.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {9},
pages = {},
pmid = {37754985},
issn = {2309-608X},
support = {812969//Marie Sklodowska-Curie/ ; BOF22/GOA/031//UGent special research fund/ ; },
abstract = {From the estimated 2.2 to 3.8 million fungal species existing on Earth, only a minor fraction actively colonizes the human gastrointestinal tract. In fact, these fungi only represent 0.1% of the gastrointestinal biosphere. Despite their low abundance, fungi play dual roles in human health-both beneficial and detrimental. Fungal infections are often associated with bacterial dysbiosis following antibiotic use, yet our understanding of gut fungi-bacteria interactions remains limited. Here, we used the SHIME[®] gut model to explore the colonization of human fecal-derived fungi across gastrointestinal compartments. We accounted for the high inter-individual microbial diversity by using fecal samples from healthy adults, healthy babies, and Crohn's disease patients. Using quantitative Polymerase Chain Reaction and targeted next-generation sequencing, we demonstrated that SHIME[®]-colonized mycobiomes change upon loss of transient colonizers. In addition, SHIME[®] reactors from Crohn's disease patients contained comparable bacterial levels as healthy adults but higher fungal concentrations, indicating unpredictable correlations between fungal levels and total bacterial counts. Our findings rather link higher bacterial α-diversity to limited fungal growth, tied to colonization resistance. Hence, while healthy individuals had fewer fungi engrafting the colonic reactors, low α-diversity in impaired (Crohn's disease patients) or immature (babies) microbiota was associated with greater fungal abundance. To validate, antibiotic-treated healthy colonic microbiomes demonstrated increased fungal colonization susceptibility, and bacterial taxa that were negatively correlated with fungal expansion were identified. In summary, fungal colonization varied individually and transiently, and bacterial resistance to fungal overgrowth was more related with specific bacterial genera than total bacterial load. This study sheds light on fungal-bacterial dynamics in the human gut.},
}
@article {pmid37754764,
year = {2023},
author = {Barbosa, C and Tamayo-Leiva, J and Alcorta, J and Salgado, O and Daniele, L and Morata, D and Díez, B},
title = {Effects of hydrogeochemistry on the microbial ecology of terrestrial hot springs.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0024923},
pmid = {37754764},
issn = {2165-0497},
abstract = {Temperature, pH, and hydrochemistry of terrestrial hot springs play a critical role in shaping thermal microbial communities. However, the interactions of biotic and abiotic factors at this terrestrial-aquatic interface are still not well understood on a global scale, and the question of how underground events influence microbial communities remains open. To answer this, 11 new samples obtained from the El Tatio geothermal field were analyzed by 16S rRNA amplicon sequencing (V4 region), along with 191 samples from previous publications obtained from the Taupo Volcanic Zone, the Yellowstone Plateau Volcanic Field, and the Eastern Tibetan Plateau, with their temperature, pH, and major ion concentration. Microbial alpha diversity was lower in acid-sulfate waters, and no significant correlations were found with temperature. However, moderate correlations were observed between chemical parameters such as pH (mostly constrained to temperatures below 70°C), SO4 [2-] and abundances of members of the phyla Armatimonadota, Deinococcota, Chloroflexota, Campilobacterota, and Thermoplasmatota. pH and SO4 [2-] gradients were explained by phase separation of sulfur-rich hydrothermal fluids and oxidation of reduced sulfur in the steam phase, which were identified as key processes shaping these communities. Ordination and permutational analysis of variance showed that temperature, pH, and major element hydrochemistry explain only 24% of the microbial community structure. Therefore, most of the variance remained unexplained, suggesting that other environmental or biotic factors are also involved and highlighting the environmental complexity of the ecosystem and its great potential to test niche theory ecological associated questions. IMPORTANCE This is the first approach to investigate whether geothermal processes could have an influence on the ecology of thermal microbial communities on a global scale. In addition to temperature and pH, microbial communities are structured by sulfate concentrations, which depends on the tectono-magmatic settings (such as the depth of magmatic chambers) and the local settings (such as the availability of a confining layer separating NaCl waters from steam after phase separation) and the possibility of mixing with more diluted fluids. Comparison of microbial communities from different geothermal areas by homogeneous sequence processing showed that no significant geographic distance decay was detected on the microbial communities according to Bray-Curtis, Jaccard, unweighted, and weighted Unifrac similarity/dissimilarity indices. Instead, an ancient potential divergence in the same taxonomic groups is suggested between globally distant thermal zones.},
}
@article {pmid37754664,
year = {2023},
author = {Djemiel, C and Dequiedt, S and Bailly, A and Tripied, J and Lelièvre, M and Horrigue, W and Jolivet, C and Bispo, A and Saby, N and Valé, M and Maron, P-A and Ranjard, L and Terrat, S},
title = {Biogeographical patterns of the soil fungal:bacterial ratio across France.},
journal = {mSphere},
volume = {8},
number = {5},
pages = {e0036523},
pmid = {37754664},
issn = {2379-5042},
mesh = {Humans ; *Soil/chemistry ; *Environmental Biomarkers ; Soil Microbiology ; Bacteria/genetics ; France ; Carbon ; },
abstract = {Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.},
}
@article {pmid37752280,
year = {2023},
author = {Dong, M and Kuramae, EE and Zhao, M and Li, R and Shen, Q and Kowalchuk, GA},
title = {Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {104},
pmid = {37752280},
issn = {2730-6151},
support = {41977044//National Natural Science Foundation of China (National Science Foundation of China)/ ; 202006850020//China Scholarship Council (CSC)/ ; },
abstract = {Soil aggregates contain distinct physio-chemical properties across different size classes. These differences in micro-habitats support varied microbial communities and modulate the effect of plant on microbiome, which affect soil functions such as disease suppression. However, little is known about how the residents of different soil aggregate size classes are impacted by plants throughout their growth stages. Here, we examined how tomato plants impact soil aggregation and bacterial communities within different soil aggregate size classes. Moreover, we investigated whether aggregate size impacts the distribution of soil pathogen and their potential inhibitors. We collected samples from different tomato growth stages: before-planting, seedling, flowering, and fruiting stage. We measured bacterial density, community composition, and pathogen abundance using qPCR and 16 S rRNA gene sequencing. We found the development of tomato growth stages negatively impacted root-adhering soil aggregation, with a gradual decrease of large macro-aggregates (1-2 mm) and an increase of micro-aggregates (<0.25 mm). Additionally, changes in bacterial density and community composition varied across soil aggregate size classes. Furthermore, the pathogen exhibited a preference to micro-aggregates, while macro-aggregates hold a higher abundance of potential pathogen-inhibiting taxa and predicted antibiotic-associated genes. Our results indicate that the impacts of tomatoes on soil differ for different soil aggregate size classes throughout different plant growth stages, and plant pathogens and their potential inhibitors have different habitats within soil aggregate size classes. These findings highlight the importance of fine-scale heterogeneity of soil aggregate size classes in research on microbial ecology and agricultural sustainability, further research focuses on soil aggregates level could help identify candidate tax involved in suppressing pathogens in the virtual micro-habitats.},
}
@article {pmid37750468,
year = {2023},
author = {Wang, Z and Ishii, S and Novak, PJ},
title = {Quantification of depth-dependent microbial growth in encapsulated systems.},
journal = {Microbial biotechnology},
volume = {16},
number = {11},
pages = {2094-2104},
pmid = {37750468},
issn = {1751-7915},
mesh = {In Situ Hybridization, Fluorescence ; *Biofilms ; *Alginates ; },
abstract = {Encapsulated systems have been widely used in environmental applications to selectively retain and protect microorganisms. The permeable matrix used for encapsulation, however, limits the accessibility of existing analytical methods to study the behaviour of the encapsulated microorganisms. Here, we present a novel method that overcomes these limitations and enables direct observation and enumeration of encapsulated microbial colonies over a range of spatial and temporal scales. The method involves embedding, cross-sectioning, and analysing the system via fluorescence in situ hybridization and retains the structure of encapsulants and the morphology of encapsulated colonies. The major novelty of this method lies in its ability to distinguish between, and subsequently analyse, multiple microorganisms within a single encapsulation matrix across depth. Our results demonstrated the applicability and repeatability of this method with alginate-encapsulated pure (Nitrosomonas europaea) and enrichment cultures (anammox enrichment). The use of this method can potentially reveal interactions between encapsulated microorganisms and their surrounding matrix, as well as quantitatively validate predictions from mathematical models, thereby advancing our understanding of microbial ecology in encapsulated or even biofilm systems and facilitating the optimization of these systems.},
}
@article {pmid37749300,
year = {2023},
author = {Mueller, AJ and Daebeler, A and Herbold, CW and Kirkegaard, RH and Daims, H},
title = {Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales.},
journal = {The ISME journal},
volume = {17},
number = {11},
pages = {2123-2133},
pmid = {37749300},
issn = {1751-7370},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Bacteria ; Ammonia/metabolism ; Nitrification ; Genomics ; Phylogeny ; },
abstract = {Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named "Ca. Nitronereus thalassa", represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, "Ca. Nitronereus thalassa" harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, "Ca. Nitronereus thalassa" appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.},
}
@article {pmid37748600,
year = {2023},
author = {Lamprea Pineda, PA and Demeestere, K and González-Cortés, JJ and Alvarado-Alvarado, AA and Boon, N and Devlieghere, F and Van Langenhove, H and Walgraeve, C},
title = {Effect of inoculum type, packing material and operational conditions on the biofiltration of a mixture of hydrophobic volatile organic compounds in air.},
journal = {The Science of the total environment},
volume = {904},
number = {},
pages = {167326},
doi = {10.1016/j.scitotenv.2023.167326},
pmid = {37748600},
issn = {1879-1026},
mesh = {*Volatile Organic Compounds/analysis ; Filtration/methods ; Hexanes ; Biodegradation, Environmental ; Cyclohexanes ; Toluene ; *Air Pollutants/analysis ; Bioreactors/microbiology ; },
abstract = {The emission of volatile organic compounds (VOCs) into the atmosphere causes negative environmental and health effects. Biofiltration is known to be an efficient and cost-effective treatment technology for the removal of VOCs in waste gas streams. However, little is known on the removal of VOC mixtures and the effect of operational conditions, particularly for hydrophobic VOCs, and on the microbial populations governing the biofiltration process. In this study, we evaluated the effect of inoculum type (acclimated activated sludge (A-AS) versus Rhodococcus erythropolis) and packing material (mixture of compost and wood chips (C + WC) versus expanded perlite) on the removal of a mixture of hydrophobic VOCs (toluene, cyclohexane and hexane) in three biofilters (BFs), i.e., BF1: C + WC and R. erythropolis; BF2: C + WC and A-AS; and BF3: expanded perlite and R. erythropolis. The BFs were operated for 374 days at varying inlet loads (ILs) and empty bed residence times (EBRTs). The results showed that the VOCs were removed in the following order: toluene > cyclohexane > hexane, which corresponds to their air-water partitioning coefficient and thus bioavailability of each VOC. Toluene is the most hydrophilic VOC, while hexane is the most hydrophobic. BF2 outperformed BF1 and BF3 in each operational phase, with average maximum elimination capacities (ECmax) of 21 ± 3 g toluene m[-3] h[-1] (removal efficiency (RE): 100 %; EBRT: 82 s), 11 ± 2 g cyclohexane m[-3] h[-1] (RE: 86 ± 6 %; EBRT: 163 s) and 6.2 ± 0.9 g hexane m[-3] h[-1] (RE: 96 ± 4 %; EBRT: 245 s). Microbial analysis showed that despite having different inocula, the genera Rhodococcus, Mycobacterium and/or Pseudonocardia dominated in all BFs but at different relative abundances. This study provides new insights into the removal of difficult-to-degrade VOC mixtures with limited research to date on biofiltration.},
}
@article {pmid37748072,
year = {2023},
author = {Maegele, I and Rupp, S and Özbek, S and Guse, A and Hambleton, EA and Holstein, TW},
title = {A predatory gastrula leads to symbiosis-independent settlement in Aiptasia.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {40},
pages = {e2311872120},
pmid = {37748072},
issn = {1091-6490},
mesh = {Animals ; *Sea Anemones ; Symbiosis ; Gastrula ; *Anthozoa ; *Asteraceae ; *Dinoflagellida ; Larva ; },
abstract = {The planula larvae of the sea anemone Aiptasia have so far not been reported to complete their life cycle by undergoing metamorphosis into adult forms. This has been a major obstacle in their use as a model for coral-dinoflagellate endosymbiosis. Here, we show that Aiptasia larvae actively feed on crustacean nauplii, displaying a preference for live prey. This feeding behavior relies on functional stinging cells, indicative of complex neuronal control. Regular feeding leads to significant size increase, morphological changes, and efficient settlement around 14 d postfertilization. Surprisingly, the presence of dinoflagellate endosymbionts does not affect larval growth or settlement dynamics but is crucial for sexual reproduction. Our findings finally close Aiptasia's life cycle and highlight the functional nature of its larvae, as in Haeckel's Gastrea postulate, yet reveal its active carnivory, thus contributing to our understanding of early metazoan evolution.},
}
@article {pmid37747940,
year = {2023},
author = {Murali, R and Yu, H and Speth, DR and Wu, F and Metcalfe, KS and Crémière, A and Laso-Pèrez, R and Malmstrom, RR and Goudeau, D and Woyke, T and Hatzenpichler, R and Chadwick, GL and Connon, SA and Orphan, VJ},
title = {Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea.},
journal = {PLoS biology},
volume = {21},
number = {9},
pages = {e3002292},
pmid = {37747940},
issn = {1545-7885},
mesh = {*Archaea ; Anaerobiosis ; *Sulfates/metabolism ; Geologic Sediments/microbiology ; Bacteria/genetics ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.},
}
@article {pmid37746209,
year = {2022},
author = {Yamaguchi, S and Fujioka, T and Yoshimi, A and Kumagai, T and Umemura, M and Abe, K and Machida, M and Kawai, K},
title = {Discovery of a gene cluster for the biosynthesis of novel cyclic peptide compound, KK-1, in Curvularia clavata.},
journal = {Frontiers in fungal biology},
volume = {3},
number = {},
pages = {1081179},
pmid = {37746209},
issn = {2673-6128},
abstract = {KK-1, a cyclic depsipeptide with 10 residues produced by a filamentous fungus Curvularia clavata BAUA-2787, is a promising pesticide active compound with high activity against many plant pathogens, especially Botrytis cinerea. As a first step toward the future mass production of KK-1 through synthetic biological approaches, we aimed to identify the genes responsible for the KK-1 biosynthesis. To achieve this, we conducted whole genome sequencing and transcriptome analysis of C. clavata BAUA-2787 to predict the KK-1 biosynthetic gene cluster. We then generated the overexpression and deletion mutants for each cluster gene using our originally developed transformation system for this fungus, and analyzed the KK-1 production and the cluster gene expression levels to confirm their involvement in KK-1 biosynthesis. As a result of these, a region of approximately 71 kb was found, containing 10 open reading frames, which were co-induced during KK-1 production, as a biosynthetic gene cluster. These include kk1B, which encodes nonribosomal peptide synthetase with a domain structure that is consistent with the structural features of KK-1, and kk1F, which encodes a transcription factor. The overexpression of kk1F increased the expression of the entire cluster genes and, consequently, improved KK-1 production, whereas its deletion decreased the expression of the entire cluster genes and almost eliminated KK-1 production, demonstrating that the protein encoded by kk1F regulates the expressions of the other nine cluster genes cooperatively as the pathway-specific transcription factor. Furthermore, the deletion of each cluster gene caused a reduction in KK-1 productivity, indicating that each gene is involved in KK-1 production. The genes kk1A, kk1D, kk1H, and kk1I, which showed a significant decrease in KK-1 productivity due to deletion, were presumed to be directly involved in KK-1 structure formation, including the biosynthesis of the constituent residues. kk1C, kk1E, kk1G, and kk1J, which maintained a certain level of KK-1 productivity despite deletion, were possibly involved in promoting or assisting KK-1 production, such as extracellular transportation and the removal of aberrant units incorporated into the peptide chain.},
}
@article {pmid37746167,
year = {2022},
author = {Koizumi, A and Miyazawa, K and Ogata, M and Takahashi, Y and Yano, S and Yoshimi, A and Sano, M and Hidaka, M and Nihira, T and Nakai, H and Kimura, S and Iwata, T and Abe, K},
title = {Cleavage of α-1,4-glycosidic linkages by the glycosylphosphatidylinositol-anchored α-amylase AgtA decreases the molecular weight of cell wall α-1,3-glucan in Aspergillus oryzae.},
journal = {Frontiers in fungal biology},
volume = {3},
number = {},
pages = {1061841},
pmid = {37746167},
issn = {2673-6128},
abstract = {Aspergillus fungi contain α-1,3-glucan with a low proportion of α-1,4-glucan as a major cell wall polysaccharide. Glycosylphosphatidylinositol (GPI)-anchored α-amylases are conserved in Aspergillus fungi. The GPI-anchored α-amylase AmyD in Aspergillus nidulans has been reported to directly suppress the biosynthesis of cell wall α-1,3-glucan but not to degrade it in vivo. However, the detailed mechanism of cell wall α-1,3-glucan biosynthesis regulation by AmyD remains unclear. Here we focused on AoAgtA, which is encoded by the Aspergillus oryzae agtA gene, an ortholog of the A. nidulans amyD gene. Similar to findings in A. nidulans, agtA overexpression in A. oryzae grown in submerged culture decreased the amount of cell wall α-1,3-glucan and led to the formation of smaller hyphal pellets in comparison with the wild-type strain. We analyzed the enzymatic properties of recombinant (r)AoAgtA produced in Pichia pastoris and found that it degraded soluble starch, but not linear bacterial α-1,3-glucan. Furthermore, rAoAgtA cleaved 3-α-maltotetraosylglucose with a structure similar to the predicted boundary structure between the α-1,3-glucan main chain and a short spacer composed of α-1,4-linked glucose residues in cell wall α-1,3-glucan. Interestingly, rAoAgtA randomly cleaved only the α-1,4-glycosidic bonds of 3-α-maltotetraosylglucose, indicating that AoAgtA may cleave the spacer in cell wall α-1,3-glucan. Consistent with this hypothesis, heterologous overexpression of agtA in A. nidulans decreased the molecular weight of cell wall α-1,3-glucan. These in vitro and in vivo properties of AoAgtA suggest that GPI-anchored α-amylases can degrade the spacer α-1,4-glycosidic linkages in cell wall α-1,3-glucan before its insolubilization, and this spacer cleavage decreases the molecular weight of cell wall α-1,3-glucan in vivo.},
}
@article {pmid37746119,
year = {2023},
author = {Tamano, K and Brown, DW and Yoshimi, A},
title = {Editorial: The use of metabolic engineering techniques to increase the productivity of primary and secondary metabolites within filamentous fungi.},
journal = {Frontiers in fungal biology},
volume = {4},
number = {},
pages = {1178290},
pmid = {37746119},
issn = {2673-6128},
}
@article {pmid37744927,
year = {2023},
author = {Frates, ES and Spietz, RL and Silverstein, MR and Girguis, P and Hatzenpichler, R and Marlow, JJ},
title = {Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1235906},
pmid = {37744927},
issn = {1664-302X},
abstract = {Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.},
}
@article {pmid37744490,
year = {2023},
author = {Petrin, S and Orsini, M and Massaro, A and Olsen, JE and Barco, L and Losasso, C},
title = {Phenotypic and genotypic antimicrobial resistance correlation and plasmid characterization in Salmonella spp. isolates from Italy reveal high heterogeneity among serovars.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1221351},
pmid = {37744490},
issn = {2296-2565},
mesh = {Animals ; Humans ; Serogroup ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Phenotype ; Salmonella/genetics ; Italy ; Aminoglycosides ; },
abstract = {INTRODUCTION: The spread of antimicrobial resistance among zoonotic pathogens such as Salmonella is a serious health threat, and mobile genetic elements (MGEs) carrying antimicrobial resistance genes favor this phenomenon. In this work, phenotypic antimicrobial resistance to commonly used antimicrobials was studied, and the antimicrobial resistance genes (ARGs) and plasmid replicons associated with the resistances were determined.<br><br>METHODS: Eighty-eight Italian Salmonella enterica strains (n&#x2009;=&#x2009;88), from human, animal and food sources, isolated between 2009 and 2019, were selected to represent serovars with different frequency of isolation in human cases of salmonellosis. The presence of plasmid replicons was also investigated.<br><br>RESULTS AND DISCUSSION: Resistances to sulphonamides (23.9%), ciprofloxacin (27.3%), ampicillin (29.5%), and tetracycline (32.9%) were the most found phenotypes. ARGs identified in the genomes correlated with the phenotypical results, with blaTEM-1B, sul1, sul2, tetA and tetB genes being frequently identified. Point mutations in gyrA and parC genes were also detected, in addition to many different aminoglycoside-modifying genes, which, however, did not cause phenotypic resistance to aminoglycosides. Many genomes presented plasmid replicons, however, only a limited number of ARGs were predicted to be located on the contigs carrying these replicons. As an expectation of this, multiple ARGs were identified on contigs with IncQ1 plasmid replicon in strains belonging to the monophasic variant of Salmonella Typhimurium. In general, high variability in ARGs and plasmid replicons content was observed among isolates, highlighting a high level of heterogeneity in Salmonella enterica. Irrespective of the serovar., many of the ARGs, especially those associated with critically and highly important antimicrobials for human medicine were located together with plasmid replicons, thus favoring their successful dissemination.},
}
@article {pmid37737949,
year = {2023},
author = {Li, X and Chen, S and Zhao, L and Zeng, X and Liu, Y and Li, C and Yang, Q},
title = {Effect of lactic acid bacteria by different concentrations of copper based on non-target metabolomic analysis.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {49},
pages = {107568-107579},
pmid = {37737949},
issn = {1614-7499},
mesh = {Animals ; Humans ; *Copper/chemistry ; *Lactobacillales ; Bacteria ; Intestines ; Mammals ; },
abstract = {Copper (Cu) is an essential element for mammals, but excess intake can have detrimental health consequences. However, Cu is no longer present in the "Limit of Contaminants in Foods" promulgated in 2022. The potential impact of different Cu (II) concentrations on human health remains unclear. In this study, a strain of lactic acid bacteria (LAB), namely, Lactiplantibacillus plantarum CICC 23121 (L23121), was selected as a prebiotic indicator strain to indirectly assess the effects of food-limited Cu (II) concentrations (issued by Tolerance limit of copper in foods in 1994) on the functions of intestinal microbes. We used non-target metabolomics, automatic growth curve detector, scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR) to investigate the effects of Cu (II) on L23121. The study revealed shows that the 50% minimum inhibitory concentration (MIC50) of Cu (II) for most lactic acid bacteria was 4 mg/L. At low Cu (II) concentrations (≤ 4 mg/L), the pentose phosphate pathway and pyrimidine metabolism of the lactic acid bacteria were affected, resulting in a decrease in the content of beneficial secondary metabolites and a significant decrease in the cell activity. As Cu (II) concentrations increase (≥ 6 mg/L), the key amino acid and lipid metabolisms were affected, leading to the inhibition of growth and primary metabolite production of the bacteria. Under high concentration of Cu (II) (6 mg/L), the surface adhesion of the bacteria was distorted and covered with significantly large particles, and the functional groups of the cells were significantly shifted. As a probiotic, the abundance of lactic acid bacteria in the intestine is significantly reduced, which will inevitably seriously damage intestinal homeostasis. Thus, to protect human intestinal microbes' health, it is recommended to limit the concentration of Cu in food to less than 4 mg/L.},
}
@article {pmid37737839,
year = {2023},
author = {Lee, HJ and Whang, KS},
title = {Oryzibacter oryziterrae gen. nov., sp. nov., isolated from rice paddy soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.006033},
pmid = {37737839},
issn = {1466-5034},
mesh = {*Oryza ; Base Composition ; Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Soil ; },
abstract = {A novel Gram-stain-negative, aerobic, motile and pleomorphic rod-shaped bacterial strain, designated COJ-58[T], was isolated from rice paddy soil. Strain COJ-58[T] grew optimally at 20-30 °C, at pH 5.0-8.0 and with 0-1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain COJ-58[T] forms a distinct lineage within the family Pleomorphomonadaceae, with highest similarity to Pleomorphomonas carboxyditropha SVCO-16[T] (95.9 %), Pleomorphomonas koreensis Y9[T] (95.8 %), Pleomorphomonas oryzae F-7[T] (95.7 %) and Pleomorphomonas diazotrophica R5-392[T] (95.6 %), respectively. The average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity and percentage of conserved proteins values between the genomes of strain COJ-58[T] and its closely related taxa are ≤77.2 %, ≤21.6 %, ≤68.3 % and ≤61.3 %, respectively. The genome size of strain COJ-58[T] is 4.9 Mb and the genomic DNA G + C content is 63.7 mol%. The major fatty acids are C18 : 1 ω7c, C16 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I). The differential phenotypic and genotypic characteristics of strain COJ-58[T] indicate that it represents a novel genus and species, for which the name Oryzibacter oryziterrae gen. nov., sp. nov. is proposed, with strain COJ-58[T] (=KACC 22108[T]=JCM 34744[T]) as the type strain.},
}
@article {pmid37737625,
year = {2023},
author = {Turner, TL and Mitra, SD and Kochan, TJ and Pincus, NB and Lebrun-Corbin, M and Cheung, BH and Gatesy, SW and Afzal, T and Nozick, SH and Ozer, EA and Hauser, AR},
title = {Taxonomic characterization of Pseudomonas hygromyciniae sp. nov., a novel species discovered from a commercially purchased antibiotic.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0183821},
pmid = {37737625},
issn = {2165-0497},
support = {K24 AI104831/AI/NIAID NIH HHS/United States ; R01 AI118257/AI/NIAID NIH HHS/United States ; R21 AI153953/AI/NIAID NIH HHS/United States ; R21 AI164254/AI/NIAID NIH HHS/United States ; },
abstract = {In an attempt to identify novel bacterial species, microbiologists have examined a wide range of environmental niches. We describe the serendipitous discovery of a novel gram-negative bacterial species from a different type of extreme niche: a purchased vial of antibiotic. The vial of antibiotic hygromycin B was found to be factory contaminated with a bacterial species, which we designate Pseudomonas hygromyciniae sp. nov. The proposed novel species belongs to the P. fluorescens complex and is most closely related to P. brenneri, P. proteolytica, and P. fluorescens. The type strain Pseudomonas hygromyciniae sp. nov. strain SDM007[T] (SDM007[T]) harbors a novel 250 kb megaplasmid which confers resistance to hygromycin B and contains numerous other genes predicted to encode replication and conjugation machinery. SDM007[T] grows in hygromycin concentrations of up to 5 mg/mL but does not use the antibiotic as a carbon or nitrogen source. While unable to grow at 37°C ruling out its ability to infect humans, it grows and survives at temperatures between 4 and 30°C. SDM007[T] can infect plants, as demonstrated by the lettuce leaf model, and is highly virulent in the Galleria mellonella infection model but is unable to infect mammalian A549 cells. These findings indicate that commercially manufactured antibiotics represent another extreme environment that may support the growth of novel bacterial species. IMPORTANCE Physical and biological stresses in extreme environments may select for bacteria not found in conventional environments providing researchers with the opportunity to not only discover novel species but to uncover new enzymes, biomolecules, and biochemical pathways. This strategy has been successful in harsh niches such as hot springs, deep ocean trenches, and hypersaline brine pools. Bacteria belonging to the Pseudomonas species are often found to survive in these unusual environments, making them relevant to healthcare, food, and manufacturing industries. Their ability to survive in a variety of environments is mainly due to the high genotypic and phenotypic diversity displayed by this genus. In this study, we discovered a novel Pseudomonas sp. from a desiccated environment of a sealed antibiotic bottle that was considered sterile. A close genetic relationship with its phylogenetic neighbors reiterated the need to use not just DNA-based tools but also biochemical characteristics to accurately classify this organism.},
}
@article {pmid37737001,
year = {2023},
author = {Bernadus, JBB and Pelealu, J and Kandou, GD and Pinaria, AG and Mamahit, JME and Tallei, TE},
title = {Metagenomic Insight into the Microbiome and Virome Associated with Aedes aegypti Mosquitoes in Manado (North Sulawesi, Indonesia).},
journal = {Infectious disease reports},
volume = {15},
number = {5},
pages = {549-563},
pmid = {37737001},
issn = {2036-7430},
abstract = {The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the microbial community entailed an assessment of taxa abundance and diversity using Kraken version 2.1.2. The study delineated the prevalence of dominant bacterial phyla, including Proteobacteria, with varying abundance of Firmicutes, Bacteroidota, and Actinobacteria, and notable occurrence of Tenericutes. Furthermore, the presence of the fungal phylum Ascomycota was also detected. Among the identified barcodes, Barcode04 emerged as the most abundant and diverse, while Barcode06 exhibited greater evenness. Barcode03, 05, and 07 displayed moderate richness and diversity. Through an analysis of the relative abundance, a spectrum of viruses within Ae. aegypti populations was unveiled, with Negarnaviricota constituting the most prevalent phylum, followed by Nucleocytoviricota, Uroviricota, Artverviricota, Kitrinoviricota, Peploviricota, Phixviricota, and Cossaviricota. The presence of Negarnaviricota viruses raises pertinent public health concerns. The presence of other viral phyla underscores the intricate nature of virus-mosquito interactions. The analysis of viral diversity provides valuable insights into the range of viruses carried by Ae. aegypti. The community exhibits low biodiversity, with a few dominant species significantly influencing its composition. This has implications for healthcare and ecological management, potentially simplifying control measures but also posing risks if the dominant species are harmful. This study enriches our comprehension of the microbiome and virome associated with Ae. aegypti mosquitoes, emphasizing the importance of further research to fully comprehend their ecological significance and impact on public health. The findings shed light on the microbial ecology of Ae. aegypti, offering potential insights into mosquito biology, disease transmission, and strategies for vector control. Future studies should endeavor to establish specific associations with Ae. aegypti, elucidate the functional roles of the identified microbial and viral species, and investigate their ecological implications.},
}
@article {pmid37725513,
year = {2023},
author = {Yang, J and Bowring, JZ and Krusche, J and Lehmann, E and Bejder, BS and Silva, SF and Bojer, MS and Grunert, T and Peschel, A and Ingmer, H},
title = {Cross-species communication via agr controls phage susceptibility in Staphylococcus aureus.},
journal = {Cell reports},
volume = {42},
number = {9},
pages = {113154},
doi = {10.1016/j.celrep.2023.113154},
pmid = {37725513},
issn = {2211-1247},
mesh = {Humans ; Staphylococcus aureus/metabolism ; *Bacteriophages/metabolism ; Staphylococcus/metabolism ; Glycosyltransferases/metabolism ; *Staphylococcal Infections ; Bacterial Proteins/metabolism ; Quorum Sensing ; },
abstract = {Bacteria use quorum sensing (QS) to coordinate group behavior in response to cell density, and some bacterial viruses (phages) also respond to QS. In Staphylococcus aureus, the agr-encoded QS system relies on accumulation of auto-inducing cyclic peptides (AIPs). Other staphylococci also produce AIPs of which many inhibit S. aureus agr. We show that agr induction reduces expression of tarM, encoding a glycosyltransferase responsible for α-N-acetylglucosamine modification of the major S. aureus phage receptor, the wall teichoic acids. This allows lytic phage Stab20 and related phages to infect and kill S. aureus. However, in mixed communities, producers of inhibitory AIPs like S. haemolyticus, S. caprae, and S. pseudintermedius inhibit S. aureus agr, thereby impeding phage infection. Our results demonstrate that cross-species interactions dramatically impact phage susceptibility. These interactions likely influence microbial ecology and impact the efficacy of phages in medical and biotechnological applications such as phage therapy.},
}
@article {pmid37725094,
year = {2023},
author = {Rossetto Marcelino, V},
title = {The value of connections.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37725094},
issn = {2050-084X},
mesh = {*Gastrointestinal Microbiome ; },
abstract = {High proportions of gut bacteria that produce their own food can be an indicator for poor gut health.},
}
@article {pmid37724869,
year = {2023},
author = {Leroux, N and Sylvain, FE and Holland, A and Luis Val, A and Derome, N},
title = {Gut microbiota of an Amazonian fish in a heterogeneous riverscape: integrating genotype, environment, and parasitic infections.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0275522},
pmid = {37724869},
issn = {2165-0497},
abstract = {A number of key factors can structure the gut microbiota of fish such as environment, diet, health state, and genotype. Mesonauta festivus, an Amazonian cichlid, is a relevant model organism to study the relative contribution of these factors on the community structure of fish gut microbiota. M. festivus has well-studied genetic populations and thrives in rivers with drastically divergent physicochemical characteristics. Here, we collected 167 fish from 12 study sites and used 16S and 18S rRNA metabarcoding approaches to characterize the gut microbiome structure of M. festivus. These data sets were analyzed in light of the host fish genotypes (genotyping-by-sequencing) and an extensive characterization of environmental physico-chemical parameters. We explored the relative contribution of environmental dissimilarity, the presence of parasitic taxa, and phylogenetic relatedness on structuring the gut microbiota. We documented occurrences of Nyctotherus sp. infecting a fish and linked its presence to a dysbiosis of the host gut microbiota. Moreover, we detected the presence of helminths which had a minor impact on the gut microbiota of their host. In addition, our results support a higher impact of the phylogenetic relatedness between fish rather than environmental similarity between sites of study on structuring the gut microbiota for this Amazonian cichlid. Our study in a heterogeneous riverscape integrates a wide range of factors known to structure fish gut microbiomes. It significantly improves understanding of the complex relationship between fish, their parasites, their microbiota, and the environment. IMPORTANCE The gut microbiota is known to play important roles in its host immunity, metabolism, and comportment. Its taxonomic composition is modulated by a complex interplay of factors that are hard to study simultaneously in natural systems. Mesonauta festivus, an Amazonian cichlid, is an interesting model to simultaneously study the influence of multiple variables on the gut microbiota. In this study, we explored the relative contribution of the environmental conditions, the presence of parasitic infections, and the genotype of the host on structuring the gut microbiota of M. festivus in Amazonia. Our results highlighted infections by a parasitic ciliate that caused a disruption of the gut microbiota and by parasitic worms that had a low impact on the microbiota. Finally, our results support a higher impact of the genotype than the environment on structuring the microbiota for this fish. These findings significantly improve understanding of the complex relationship among fish, their parasites, their microbiota, and the environment.},
}
@article {pmid37724866,
year = {2023},
author = {van der Loos, LM and De Coninck, L and Zell, R and Lequime, S and Willems, A and De Clerck, O and Matthijnssens, J},
title = {Highly divergent CRESS DNA and picorna-like viruses associated with bleached thalli of the green seaweed Ulva.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0025523},
pmid = {37724866},
issn = {2165-0497},
abstract = {Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a substantial impact on the ecology and aquaculture of seaweeds, but surprisingly little is known about virus diversity in macroalgal hosts. Using metagenomic sequencing, we characterized viral communities associated with healthy and bleached specimens of the commercially important green seaweed Ulva. We identified 20 putative new and divergent viruses, of which the majority belonged to the Circular Rep-Encoding Single-Stranded (CRESS) DNA viruses [single-stranded (ss)DNA genomes], Durnavirales [double-stranded (ds)RNA], and Picornavirales (ssRNA). Other newly identified RNA viruses were related to the Ghabrivirales, the Mitoviridae, and the Tombusviridae. Bleached Ulva samples contained particularly high viral read numbers. While reads matching assembled CRESS DNA viruses and picorna-like viruses were nearly absent from the healthy Ulva samples (confirmed by qPCR), they were very abundant in the bleached specimens. Therefore, bleaching in Ulva could be caused by one or a combination of the identified viruses but may also be the result of another causative agent or abiotic stress, with the viruses simply proliferating in already unhealthy seaweed tissue. This study highlights how little we know about the diversity and ecology of seaweed viruses, especially in relation to the health and diseases of the algal host, and emphasizes the need to better characterize the algal virosphere. IMPORTANCE Green seaweeds of the genus Ulva are considered a model system to study microbial interactions with the algal host. Remarkably little is known, however, about viral communities associated with green seaweeds, especially in relation to the health of the host. In this study, we characterized the viral communities associated with healthy and bleached Ulva. Our findings revealed the presence of 20 putative novel viruses associated with Ulva, encompassing both DNA and RNA viruses. The majority of these viruses were found to be especially abundant in bleached Ulva specimens. This is the first step toward understanding the role of viruses in the ecology and aquaculture of this green seaweed.},
}
@article {pmid37723328,
year = {2023},
author = {Sasi, R and Suchithra, TV},
title = {Wastewater microbial diversity versus molecular analysis at a glance: a mini-review.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {54},
number = {4},
pages = {3033-3039},
pmid = {37723328},
issn = {1678-4405},
mesh = {*Wastewater ; Phylogeny ; *Microbiota ; Genomics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Bioreactors/microbiology ; Sewage/microbiology ; },
abstract = {Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.},
}
@article {pmid37723166,
year = {2023},
author = {Ye, H and Borusak, S and Eberl, C and Krasenbrink, J and Weiss, AS and Chen, SC and Hanson, BT and Hausmann, B and Herbold, CW and Pristner, M and Zwirzitz, B and Warth, B and Pjevac, P and Schleheck, D and Stecher, B and Loy, A},
title = {Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5533},
pmid = {37723166},
issn = {2041-1723},
mesh = {Humans ; Animals ; Mice ; *Affect ; Bile Acids and Salts ; *Salmonella enterica ; Taurine ; Sulfur ; },
abstract = {Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.},
}
@article {pmid37722685,
year = {2023},
author = {Jacobovitz, MR and Hambleton, EA and Guse, A},
title = {Unlocking the Complex Cell Biology of Coral-Dinoflagellate Symbiosis: A Model Systems Approach.},
journal = {Annual review of genetics},
volume = {57},
number = {},
pages = {411-434},
doi = {10.1146/annurev-genet-072320-125436},
pmid = {37722685},
issn = {1545-2948},
support = {/ERC_/European Research Council/International ; },
mesh = {Animals ; *Anthozoa/genetics ; Symbiosis/genetics ; Ecosystem ; *Dinoflagellida/genetics ; Systems Analysis ; },
abstract = {Symbiotic interactions occur in all domains of life, providing organisms with resources to adapt to new habitats. A prime example is the endosymbiosis between corals and photosynthetic dinoflagellates. Eukaryotic dinoflagellate symbionts reside inside coral cells and transfer essential nutrients to their hosts, driving the productivity of the most biodiverse marine ecosystem. Recent advances in molecular and genomic characterization have revealed symbiosis-specific genes and mechanisms shared among symbiotic cnidarians. In this review, we focus on the cellular and molecular processes that underpin the interaction between symbiont and host. We discuss symbiont acquisition via phagocytosis, modulation of host innate immunity, symbiont integration into host cell metabolism, and nutrient exchange as a fundamental aspect of stable symbiotic associations. We emphasize the importance of using model systems to dissect the cellular complexity of endosymbiosis, which ultimately serves as the basis for understanding its ecology and capacity to adapt in the face of climate change.},
}
@article {pmid37719127,
year = {2023},
author = {Castañeda-Molina, Y and Marulanda-Moreno, SM and Saldamando-Benjumea, C and Junca, H and Moreno-Herrera, CX and Cadavid-Restrepo, G},
title = {Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15916},
pmid = {37719127},
issn = {2167-8359},
mesh = {Animals ; Spodoptera ; Larva ; *Bacillus thuringiensis/genetics ; Endotoxins ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; },
abstract = {BACKGROUND: Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest.<br><br>METHODS: The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain.<br><br>RESULTS: Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.},
}
@article {pmid37717747,
year = {2023},
author = {Farrell, ML and Chueiri, A and Maguire, M and Kovářová, A and Miliotis, G and O'Connor, L and McDonagh, F and Duane, S and Cormican, M and Devane, G and Tuohy, A and DeLappe, N and De Bock, F and Burke, LP and Morris, D},
title = {Longitudinal carriage of antimicrobial resistant Enterobacterales in healthy individuals in Ireland - Assessing the impact of recreational water use on duration of carriage.},
journal = {The Science of the total environment},
volume = {905},
number = {},
pages = {167100},
doi = {10.1016/j.scitotenv.2023.167100},
pmid = {37717747},
issn = {1879-1026},
mesh = {Humans ; *Escherichia coli/genetics ; Enterobacteriaceae/genetics ; Ireland/epidemiology ; beta-Lactamases/genetics ; Feces ; *Anti-Infective Agents ; Anti-Bacterial Agents ; },
abstract = {The increasing prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales (ESBL-PE) and carbapenemase-producing Enterobacterales (CPE) is a major public health concern worldwide. Despite the associated risk of infection from gut colonisation with a resistant Enterobacterales, the incidence and duration of carriage in healthy individuals is poorly studied. This "persistence study" is the first in Ireland to assess the longitudinal carriage of ESBL-PE and CPE in healthy individuals. A cohort of 45 participants, 22 of whom were colonised with ESBL-PE, was recruited from a recently completed point prevalence study that investigated colonisation in recreational water users (WU) versus controls. Six bi-monthly faecal samples per participant were analysed for CPE and ESBL-PE over one year and the relationship between persistent colonisation and exposure to natural waters was investigated. For 11 of 45 participants (24.4 %) ESBL-E. coli (ESBL-EC) was detected in at least one sample. Genomic analysis revealed that six participants harboured the same ESBL-EC strains as identified in the preceding study. ESBL-EC persisted in the gut for a median duration of 10.3 months (range 4-23 months), consistent with previous research. Five participants (11.1 %) carried ESBL-EC for the entire study year. The carbapenemase gene blaIMI-2 was detected once. Colonisation was higher in water users during the non-bathing season (n = 10, November 2021-April 2022), than during the bathing season (n = 5, May 2022-September 2022) [relative risk 1.99 (95 % CI 0.34-11.71)]. However, overall WU were less likely to be colonised with ESBL-EC than controls (19 % vs 25 % respectively, RR 0.76, CI 0.24-2.34). Further research is warranted to better understand the factors influencing the persistence of gut colonisation with ESBL-EC and CPE and to what extent bathing water quality impacts colonisation for those regularly exposed.},
}
@article {pmid37717325,
year = {2023},
author = {Sandeep, R and Muscolino, JF and Macêdo, WV and Piculell, M and Christensson, M and Poulsen, JS and Nielsen, JL and Vergeynst, L},
title = {Effect of biofilm thickness on the activity and community composition of phosphorus accumulating bacteria in a moving bed biofilm reactor.},
journal = {Water research},
volume = {245},
number = {},
pages = {120599},
doi = {10.1016/j.watres.2023.120599},
pmid = {37717325},
issn = {1879-2448},
abstract = {Can biofilms enhance the rates of phosphorus removal in wastewater treatment? In order to narrow the scientific gap on the effect of biofilm thickness on the activity and microbial community of phosphorus-accumulating bacteria, this study investigated biofilms of 30 to 1000 µm thickness in a moving bed biofilm reactor. Measurements on 5 different biofilm carriers showed that biomass-specific phosphorus release and uptake rates increased as a function of biofilm thickness for biofilms thinner than about 110 µm but were lower for thicker biofilms of about 550-1000 µm. The reduced phosphorus uptake and release rates in the thickest biofilms can result from substrate mass transfer limitations whereas the low activity in the thinnest biofilms can be related to a too high turnover rate in the biofilm due to heterotrophic growth. Additionally, the microbial ecology of the different biofilms confirms the observed phosphorus uptake and release rates. The results from the full-length 16S rRNA gene sequencing of the bacterial community showed that the thicker biofilms were characterized by higher relative abundance (40-58%) of potential phosphorus accumulating genera Zoogloea, Acinetobacter, Dechloromonas and Ca. Accumulibacter. In contrast, the thinner biofilms were dominated by the genus Ferribacterium (34-60%), which might be competing with phosphorus-accumulating bacteria as indicated by the relatively high acetate uptake rates in the thinner biofilms. It is concluded that there is an optimal biofilm thickness of 100-500 µm, at which the phosphorus accumulating bacteria have the highest activity.},
}
@article {pmid37715042,
year = {2023},
author = {Candry, P and Chadwick, GL and Caravajal-Arroyo, JM and Lacoere, T and Winkler, MH and Ganigué, R and Orphan, VJ and Rabaey, K},
title = {Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities.},
journal = {The ISME journal},
volume = {17},
number = {11},
pages = {2014-2022},
pmid = {37715042},
issn = {1751-7370},
mesh = {*Carboxylic Acids ; *Biofilms ; Bacteria ; Lactic Acid ; Sugars ; },
abstract = {Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150-500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of [15]N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.},
}
@article {pmid37713796,
year = {2023},
author = {Cai, X and Hu, Y and Zhou, S and Meng, D and Xia, S and Wang, H},
title = {Unraveling bacterial and eukaryotic communities in secondary water supply systems: Dynamics, assembly, and health implications.},
journal = {Water research},
volume = {245},
number = {},
pages = {120597},
doi = {10.1016/j.watres.2023.120597},
pmid = {37713796},
issn = {1879-2448},
mesh = {Water ; Eukaryota ; Bacteria ; Water Supply ; *Amoeba ; *Microbiota ; },
abstract = {Secondary water supply systems (SWSSs) are crucial water supply infrastructures for high-rise buildings in metropolitan cities. In recent years, they have garnered public attention due to increased microbial risks. However, our understanding of SWSS microbial ecology, particularly concerning the composition of eukaryotes and the underlying mechanisms driving microbial dynamics and assembly in SWSSs, remains elusive. Herein, we conducted a comprehensive investigation on both eukaryotes and bacteria along the water transportation pathway and across various microbial habitats (water, biofilm, and sediment) in SWSSs. Sequencing results revealed that eukaryotes within SWSSs predominantly consist of protists (average abundance: 31.23%) and metazoans (20.91%), while amoebae accounted for 4.71% of the total. During water transportation from the distribution mains to taps, both bacterial and eukaryotic communities exhibited significant community shifts, and higher degrees of variation were observed for eukaryotic community among different locations within SWSSs. The normalized stochasticity ratio (NST) analysis demonstrated that bacterial community assembly was governed by stochastic processes, while eukaryotic community assembly was primarily shaped by deterministic processes. Within SWSS tanks, bacterial communities significantly varied across water, biofilm, and sediment, whereas eukaryotic communities showed minor differences among these habitats. The co-occurrence networks analysis revealed that tank biofilm and sediment harbored more eukaryote-bacterium linkages than water, suggesting biofilm and sediment might be hotspots for inter-kingdom interactions. We also applied FEAST analysis to track the source of tap water microbiota, results of which showed that household-tap bacteria mainly originated from tank water. In contrast, tank biofilm was identified as the primary microbial source to eukaryotes in household tap water. Additionally, engineering factors such as tank materials significantly affected amoeba community, and the SWSS configuration was found to influence Legionella and Mycobacterium abundances in SWSSs. Overall, results of our study shed light on the microbial ecology in SWSS and provide insights into SWSS management and health risk control.},
}
@article {pmid37712979,
year = {2023},
author = {Li, Y and Yang, H and Su, Y and Gong, X and Yao, B and Cheng, L},
title = {Phosphorus Coupled with High Nitrogen Addition Exerts a Great Influence on Soil Bacterial Community in a Semiarid Grassland.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2993-3002},
pmid = {37712979},
issn = {1432-184X},
mesh = {*Ecosystem ; *Soil/chemistry ; Grassland ; Nitrogen/chemistry ; Phosphorus ; Bacteria/genetics ; Soil Microbiology ; China ; },
abstract = {Nitrogen (N) and phosphorus (P) addition, either individually or in combination, has been demonstrated to enhance plant productivity in grassland ecosystems. Soil bacterial community, which is the driver of litter decomposition and nutrient cycling, is assumed to control responses of terrestrial ecosystem structure and function to N and P addition. Using a high-throughput Illumina MiSeq sequencing platform, we conducted a 9-year field experiment of N (0, 5, 10, and 20 g N m[-2] yr[-1]) and P (0 and 10 g P m[-2] yr[-1]) additions in the Inner Mongolian steppes to elucidate long-term effects of N and P addition on soil bacterial richness, diversity and composition. We found that N addition reduced the relative abundance of Acidobacteria, Chloroflexi, and Nitrospirae, while increased that of Bacteroides. The results showed that the bacterial biomarker was enriched in P addition treatments, either individually or combined with N addition. Both N and P addition altered the bacterial community structure, while only N addition greatly decreased bacterial richness and diversity. More importantly, we showed that all of these effects were most significant in N3P treatment (20 g N m[-2] yr[-1] and 10 g P m[-2] yr[-1]), implying that P coupled with a high-level N addition exerted a great influence on soil bacterial community. Structural equation models revealed that N and P addition had a great direct effect on soil bacterial community and an indirect effect on it mainly by changing the litter biomass. Our findings highlighted that severe niche differentiation was induced by P along with a high-level N, further emphasizing the importance of simultaneously evaluating response of soil bacterial community to N and P addition, especially in the context of increasing anthropogenic nutrient additions.},
}
@article {pmid37711620,
year = {2023},
author = {Rosel-Pech, C and Pinto-Cardoso, S and Chávez-Torres, M and Montufar, N and Osuna-Padilla, I and Ávila-Ríos, S and Reyes-Terán, G and Aguirre-Alvarado, C and Matías Juan, NA and Pérez-Lorenzana, H and Vázquez-Rosales, JG and Bekker-Méndez, VC},
title = {Distinct fecal microbial signatures are linked to sex and chronic immune activation in pediatric HIV infection.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1244473},
pmid = {37711620},
issn = {1664-3224},
mesh = {Adult ; Child ; Humans ; Female ; Male ; *HIV Infections ; RNA, Ribosomal, 16S/genetics ; *Aging, Premature ; Anti-Bacterial Agents ; Disease Progression ; },
abstract = {INTRODUCTION: Our understanding of HIV-associated gut microbial dysbiosis in children perinatally-infected with HIV (CLWH) lags behind that of adults living with HIV. Childhood represents a critical window for the gut microbiota. Any disturbances, including prolonged exposure to HIV, antiretroviral drugs, and antibiotics are likely to have a significant impact on long-term health, resulting in a less resilient gut microbiome. The objective of our study was to characterize the gut microbiota in CLWH, and compare it with HIV-unexposed and -uninfected children.<br><br>METHODS: We enrolled 31 children aged 3 to 15 years; 15 were CLWH and 16 were HUU. We assessed dietary patterns and quality; quantified soluble and cellular markers of HIV disease progression by flow cytometry, enzyme-linked immunosorbent and multiplex-bead assays, and profiled the gut microbiota by 16S rRNA sequencing. We explored relationships between the gut microbiota, antibiotic exposure, dietary habits, soluble and cellular markers and host metadata.<br><br>RESULTS: Children had a Western-type diet, their median health eating index score was 67.06 (interquartile range 58.76-74.66). We found no discernable impact of HIV on the gut microbiota. Alpha diversity metrics did not differ between CLWH and HUU. Sex impacted the gut microbiota (R-squared= 0.052, PERMANOVA p=0.024). Male children had higher microbial richness compared with female children. Two taxa were found to discriminate female from male children independently from HIV status: Firmicutes for males, and Bacteroides for females. Markers of HIV disease progression were comparable between CLWH and HUU, except for the frequency of exhausted CD4+ T cells (PD-1+) which was increased in CLWH (p=0.0024 after adjusting for confounders). Both the frequency of exhausted CD4+ and activated CD4+ T cells (CD38+ HLADR+) correlated positively with the relative abundance of Proteobacteria (rho=0.568. false discovery rate (FDR)-adjusted p= 0.029, and rho=0.62, FDR-adjusted p=0.0126, respectively).<br><br>CONCLUSION: The gut microbiota of CLWH appears similar to that of HUU, and most markers of HIV disease progression are normalized with long-term ART, suggesting a beneficial effect of the latter on the gut microbial ecology. The relationship between exhausted and activated CD4+ T cells and Proteobacteria suggests a connection between the gut microbiome, and premature aging in CLWH.},
}
@article {pmid37711139,
year = {2023},
author = {Vijay, S and Nair, RR and Sharan, D and Jakkala, K and Ajitkumar, P},
title = {Percoll discontinuous density gradient centrifugation method for the fractionation of the subpopulations of Mycobacterium smegmatis and Mycobacterium tuberculosis from in vitro cultures.},
journal = {MethodsX},
volume = {11},
number = {},
pages = {102344},
pmid = {37711139},
issn = {2215-0161},
abstract = {Bacterial populations in the in vitro laboratory cultures, environment, and patients contain metabolically different subpopulations that respond differently to stress agents, including antibiotics, and emerge as stress tolerant or resistant strains. To contain the emergence of such strains, it is important to study the features of the metabolic status and response of the subpopulations to stress agents. For this purpose, an efficient method is required for the fractionation and isolation of the subpopulations from the cultures. Here we describe in detail the manual setting up of a simple, easy-to-do, reproducibly robust Percoll discontinuous density gradient centrifugation for the fractionation of subpopulations of short-sized cells (SCs) and normal/long-sized cells (NCs) from Mycobacterium smegmatis and Mycobacterium tuberculosis cultures, which we had reported earlier. About 90-98% enrichment was obtained respectively for SCs and NCs for M. smegmatis and 69-67% enrichment was obtained respectively for the SCs and NCs for M. tuberculosis.•The Percoll discontinuous density gradient centrifugation helps the fractionation and isolation of mycobacterial subpopulations that differ in density.•The method offers a consistently reproducible high enrichment of the subpopulations of SCs and NCs from the in vitro cultures of M. smegmatis and M. tuberculosis.•Our earlier reports on the consistency in the differential response of the subpopulations, enriched using the method, to oxidative, nitrite, and antibiotic stress proves its validity.},
}
@article {pmid37708771,
year = {2023},
author = {Sentenac, H and Loyau, A and Zoccarato, L and Jassey, VEJ and Grossart, HP and Schmeller, DS},
title = {Biofilm community composition is changing in remote mountain lakes with a relative increase in potentially toxigenic algae.},
journal = {Water research},
volume = {245},
number = {},
pages = {120547},
doi = {10.1016/j.watres.2023.120547},
pmid = {37708771},
issn = {1879-2448},
abstract = {Mountain lakes provide clear drinking water to humankind but are strongly impacted by global change. Benthic biofilms are crucial for maintaining water quality in these oligotrophic lakes, yet little is known about the effects of global change on mountain biofilm communities. By combining analyses of metabarcoding data on 16S and 18S rRNA genes with climatic and environmental data, we investigated global change effects on the composition of biofilm prokaryotic and micro-eukaryotic assemblages in a five-year monitoring program of 26 Pyrenean lakes (2016-2020). Using time-decay relationships and within-lake dissimilarity modelling, we show that the composition of both prokaryotic and micro-eukaryotic biofilm communities significantly shifted and their biodiversity declined from 2016 to 2020. In particular, analyses of temporal trends with linear mixed models indicated an increase in the richness and relative abundance of cyanobacteria, including potentially toxigenic cyanobacteria, and a concomitant decrease in diatom richness and relative abundance. While these compositional shifts may be due to several drivers of global change acting simultaneously on mountain lake biota, water pH and hardness were, from our data, the main environmental variables associated with changes for both prokaryotic and micro-eukaryotic assemblages. Water pH and hardness increased in our lakes over the study period, and are known to increase in Pyrenean lakes due to the intensification of rock weathering as a result of climate change. Given predicted climate trends and if water pH and hardness do cause some changes in benthic biofilms, those changes might be further exacerbated in the future. Such biofilm compositional shifts may induce cascading effects in mountain food webs, threatening the resilience of the entire lake ecosystem. The rise in potentially toxigenic cyanobacteria also increases intoxication risks for humans, pets, wild animals, and livestock that use mountain lakes. Therefore, our study has implications for water quality, ecosystem health, public health, as well as local economies (pastoralism, tourism), and highlights the possible impacts of global change on mountain lakes.},
}
@article {pmid37708391,
year = {2023},
author = {Ionescu, D and Volland, JM and Contarini, PE and Gros, O},
title = {Genomic Mysteries of Giant Bacteria: Insights and Implications.},
journal = {Genome biology and evolution},
volume = {15},
number = {9},
pages = {},
pmid = {37708391},
issn = {1759-6653},
mesh = {*Genomics ; Bacteria/genetics ; Archaea/genetics ; Biological Evolution ; *Pentaerythritol Tetranitrate ; },
abstract = {Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2-3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.},
}
@article {pmid37705860,
year = {2024},
author = {Mills, S and Trego, AC and Prevedello, M and De Vrieze, J and O'Flaherty, V and Lens, PNL and Collins, G},
title = {Unifying concepts in methanogenic, aerobic, and anammox sludge granulation.},
journal = {Environmental science and ecotechnology},
volume = {17},
number = {},
pages = {100310},
pmid = {37705860},
issn = {2666-4984},
abstract = {The retention of dense and well-functioning microbial biomass is crucial for effective pollutant removal in several biological wastewater treatment technologies. High solids retention is often achieved through aggregation of microbial communities into dense, spherical aggregates known as granules, which were initially discovered in the 1980s. These granules have since been widely applied in upflow anaerobic digesters for waste-to-energy conversions. Furthermore, granular biomass has been applied in aerobic wastewater treatment and anaerobic ammonium oxidation (anammox) technologies. The mechanisms underpinning the formation of methanogenic, aerobic, and anammox granules are the subject of ongoing research. Although each granule type has been extensively studied in isolation, there has been a lack of comparative studies among these granulation processes. It is likely that there are some unifying concepts that are shared by all three sludge types. Identifying these unifying concepts could allow a unified theory of granulation to be formed. Here, we review the granulation mechanisms of methanogenic, aerobic, and anammox granular sludge, highlighting several common concepts, such as the role of extracellular polymeric substances, cations, and operational parameters like upflow velocity and shear force. We have then identified some unique features of each granule type, such as different internal structures, microbial compositions, and quorum sensing systems. Finally, we propose that future research should prioritize aspects of microbial ecology, such as community assembly or interspecies interactions in individual granules during their formation and growth.},
}
@article {pmid37702500,
year = {2023},
author = {Deng, T and He, Z and Xu, M and Dong, M and Guo, J and Sun, G and Huang, H},
title = {Species' functional traits and interactions drive nitrate-mediated sulfur-oxidizing community structure and functioning.},
journal = {mBio},
volume = {14},
number = {5},
pages = {e0156723},
pmid = {37702500},
issn = {2150-7511},
mesh = {*Ecosystem ; Nitrates ; *Microbiota ; Sulfur ; Phenotype ; Oxidation-Reduction ; },
abstract = {Understanding the processes and mechanisms governing microbial community assembly and their linkages to ecosystem functioning has long been a core issue in microbial ecology. An in-depth insight still requires combining with analyses of species' functional traits and microbial interactions. Our study showed how species' functional traits and interactions determined microbial community structure and functions by a well-controlled laboratory experiment with nitrate-mediated sulfur oxidation systems using high-throughput sequencing and culture-dependent technologies. The results provided solid evidences that species' functional traits and interactions were the intrinsic factors determining community structure and function. More importantly, our study established quantitative links between community structure and function based on species' functional traits and interactions, which would have important implications for the design and synthesis of microbiomes with expected functions.},
}
@article {pmid37695394,
year = {2023},
author = {Wei, N and Tan, J},
title = {Correction to: Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2869},
doi = {10.1007/s00248-023-02300-z},
pmid = {37695394},
issn = {1432-184X},
}
@article {pmid37692385,
year = {2023},
author = {Fan, R and Liu, Y and Bin, Y and Huang, J and Yi, B and Tang, X and Li, Y and Cai, Y and Yang, Z and Yang, M and Song, J and Pan, Q and Liu, Z and Ghani, MI and Hu, X and Chen, X},
title = {Identification of Colletotrichum aenigma as the new causal agent of leaf blight disease on Aucuba japonica Thunb., and screenings of effective fungicides for its sustainable management.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1222844},
pmid = {37692385},
issn = {1664-302X},
abstract = {Aucuba japonica Thunb is an evergreen woody ornamental plant with significant economic and ecological values. It also produces aucubin, showing a variety of biological activities. It is widely planted in the southwest region of China, including karst landscape areas in Guizhou Province. In January 2022, a serious leaf blight disease was observed on the leaves of A. japonica in the outdoor gardens of Guizhou University, Guiyang, Guizhou, China. The causal agent was identified as Colletotrichum aenigma through amplification and sequencing of the internal transcribed spacer (ITS) region, translation of the chitin synthase (CHS) and actin (ACT) genes, and morphological characterizations. Koch's postulates were confirmed by its pathogenicity on healthy leaves, including re-isolation and identification. To our knowledge, this is the first report of C. aenigma causing leaf blight on A. japonica worldwide. To identify pathogen characteristics that could be utilized for future disease management, the effects of temperature and light on mycelial growth, conidia production, and conidial germination, and the effects of humidity on conidial germination were studied. Optimal temperatures for mycelial growth of C. aenigma BY827 were 25-30°C, while 15°C and 35°C were favorable for conidia production. Concurrently, alternating 10-h light and 14-h dark, proved to be beneficial for mycelial growth and conidial germination. Additionally, conidial germination was enhanced at 90% humidity. In vitro screenings of ten chemical pesticides to assess their efficacy in suppressing C. aenigma representative strain BY827. Among them, difenoconazole showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 0.0148 μg/ml. Subsequently, field experiment results showed that difenoconazole had the highest control efficiency on A. japonica leaf blight (the decreasing rate of disease incidence and decreasing rate of disease index were 44.60 and 47.75%, respectively). Interestingly, we discovered that C. aenigma BY827 may develop resistance to mancozeb, which is not reported yet among Colletotrichum spp. strains. In conclusion, our study provided new insights into the causal agent of A. japonica leaf blight, and the effective fungicides evaluated provided an important basis and potential resource for the sustainable control of A. japonica leaf blight caused by C. aenigma in the field.},
}
@article {pmid37692384,
year = {2023},
author = {Mermans, F and Mattelin, V and Van den Eeckhoudt, R and García-Timermans, C and Van Landuyt, J and Guo, Y and Taurino, I and Tavernier, F and Kraft, M and Khan, H and Boon, N},
title = {Opportunities in optical and electrical single-cell technologies to study microbial ecosystems.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1233705},
pmid = {37692384},
issn = {1664-302X},
abstract = {New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.},
}
@article {pmid37692382,
year = {2023},
author = {Amon, CER and Fossou, RK and Ebou, AET and Koua, DK and Kouadjo, CG and Brou, YC and Voko Bi, DRR and Cowan, DA and Zézé, A},
title = {The core bacteriobiome of Côte d'Ivoire soils across three vegetation zones.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1220655},
pmid = {37692382},
issn = {1664-302X},
abstract = {The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d'Ivoire. 45 surface soil samples were collected from Côte d'Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d'Ivoire, provides insights into the distribution of bacterial taxa in Côte d'Ivoire soils, and the findings may serve as biological indicator for land management in Côte d'Ivoire.},
}
@article {pmid37691494,
year = {2023},
author = {Mödl, B and Awad, M and Zwolanek, D and Scharf, I and Schwertner, K and Milovanovic, D and Moser, D and Schmidt, K and Pjevac, P and Hausmann, B and Krauß, D and Mohr, T and Svinka, J and Kenner, L and Casanova, E and Timelthaler, G and Sibilia, M and Krieger, S and Eferl, R},
title = {Defects in microvillus crosslinking sensitize to colitis and inflammatory bowel disease.},
journal = {EMBO reports},
volume = {24},
number = {10},
pages = {e57084},
pmid = {37691494},
issn = {1469-3178},
support = {DOC 59-833//Austrian Science Fund (FWF)/ ; P35069-B//Austrian Science Fund (FWF)/ ; P32900-B//Austrian Science Fund (FWF)/ ; P33430//Austrian Science Fund (FWF)/ ; ERC-2015-AdG TNT-Tumors 694883//EC | European Research Council (ERC)/ ; 766214//EC | Horizon 2020 Framework Programme (H2020)/ ; },
mesh = {Animals ; Mice ; *Microvilli/metabolism/pathology ; Humans ; *Inflammatory Bowel Diseases/metabolism/pathology/genetics ; *Intestinal Mucosa/metabolism/pathology ; Colitis/chemically induced/metabolism/pathology/genetics ; Cadherins/metabolism/genetics ; Mice, Knockout ; Enterocytes/metabolism/pathology ; Disease Models, Animal ; Dextran Sulfate ; Epithelial Cells/metabolism/pathology ; Permeability ; Mice, Inbred C57BL ; },
abstract = {Intestinal epithelial cells are covered by the brush border, which consists of densely packed microvilli. The Intermicrovillar Adhesion Complex (IMAC) links the microvilli and is required for proper brush border organization. Whether microvillus crosslinking is involved in the intestinal barrier function or colitis is currently unknown. We investigate the role of microvillus crosslinking in colitis in mice with deletion of the IMAC component CDHR5. Electron microscopy shows pronounced brush border defects in CDHR5-deficient mice. The defects result in severe mucosal damage after exposure to the colitis-inducing agent DSS. DSS increases the permeability of the mucus layer and brings bacteria in direct contact with the disorganized brush border of CDHR5-deficient mice. This correlates with bacterial invasion into the epithelial cell layer which precedes epithelial apoptosis and inflammation. Single-cell RNA sequencing data of patients with ulcerative colitis reveals downregulation of CDHR5 in enterocytes of diseased areas. Our results provide experimental evidence that a combination of microvillus crosslinking defects with increased permeability of the mucus layer sensitizes to inflammatory bowel disease.},
}
@article {pmid37690780,
year = {2023},
author = {Cantu-Jungles, TM and Hamaker, BR},
title = {Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber.},
journal = {The Journal of nutrition},
volume = {153},
number = {11},
pages = {3156-3163},
doi = {10.1016/j.tjnut.2023.09.001},
pmid = {37690780},
issn = {1541-6100},
mesh = {*Gastrointestinal Microbiome ; Health Promotion ; Motivation ; Dietary Fiber/pharmacology ; *Microbiota ; },
abstract = {Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.},
}
@article {pmid37689957,
year = {2023},
author = {Wang, S and De Paepe, K and Van de Wiele, T and Fu, X and Wang, S and Zhang, B and Huang, Q},
title = {Starch-entrapped microspheres enhance gut microbiome-mediated anti-obesity effects of resistant starch in high-fat diet induced obese C57BL/6J mice.},
journal = {Food research international (Ottawa, Ont.)},
volume = {172},
number = {},
pages = {113215},
doi = {10.1016/j.foodres.2023.113215},
pmid = {37689957},
issn = {1873-7145},
mesh = {Animals ; Mice ; Mice, Inbred C57BL ; *Resistant Starch ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Dysbiosis ; Microspheres ; Obesity ; Starch/pharmacology ; Amylose ; },
abstract = {The prevalence of obesity is growing worldwide and has been extensively linked to gut microbiota dysbiosis. In addition to exercise and physical activity, fiber-rich foods may be a first-line prophylactic to manage obesity. This study investigated in vivo dietary intervention with high-amylose maize starch (HAMS) and starch-entrapped microspheres (MS) to treat high-fat diet induced metabolic disorder and gut microbiome dysbiosis in mice. MS more efficiently controlled body weight as well as adipose tissue mass compared to HAMS. Furthermore, MS significantly reduced blood glucose, insulin, lipid and pro-inflammatory cytokine levels compared to the high-fat diet, while the effects of HAMS were less pronounced. The MS-altered gut microbiota composition favoring Streptococcaceae, Bacilli, Firmicutes and unclassified Clostridiales was predicted to promote fatty acid, pantothenate and Coenzyme A biosynthesis. In line with this, elevated fecal short chain fatty acid (SCFA), in particular, propionate concentration was observed in MS-fed mice. Our study provides novel insights into the mechanistic action of MS on intestinal homeostasis, providing a basis for future dietary therapeutic applications.},
}
@article {pmid37688636,
year = {2023},
author = {Garrido, AG and Machado, LF and Pereira, CM and Abrantes, DP and Calderon, EN and Zilberberg, C},
title = {Marine Heatwave Caused Differentiated Dysbiosis in Photosymbiont Assemblages of Corals and Hydrocorals During El Niño 2015/2016.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2959-2969},
pmid = {37688636},
issn = {1432-184X},
mesh = {Animals ; *Anthozoa ; El Nino-Southern Oscillation ; Dysbiosis ; Coral Reefs ; Climate Change ; },
abstract = {Reef corals have been threatened by climate change, with more frequent and intense bleaching events leading to extensive coral mortality and loss of coral cover worldwide. In the face of this, the corals' photosymbiont assemblages have received special attention as a key to better understand the bleaching process and its recovery. To assess the effects of thermal anomalies, the coral Mussismilia harttii and the hydrocoral Millepora alcicornis were monitored through the El Niño 2015/2016 at a Southwestern Atlantic (SWA) coral reef. A severe bleaching event (57% of colonies bleached) was documented, triggered by a < 3 °C-week heatwave, but no mortality was detected. The hydrocoral was more susceptible than the scleractinian, displaying bleaching symptoms earlier and experiencing a longer and more intense bleaching event. The composition of photosymbionts in the M. alcicornis population was affected only at the rare biosphere level (< 5% relative abundance), with the emergence of new symbionts after bleaching. Conversely, a temporary dysbiosis was observed in the M. harttii population, with one of the dominant symbiodiniaceans decreasing in relative abundance at the peak of the bleaching, which negatively affected the total β-diversity. After colonies' complete recovery, symbiodiniaceans' dominances returned to normal levels in both hosts. These results highlight critical differences in how the two coral species cope with bleaching and contribute to the understanding of the role of photosymbionts throughout the bleaching-recovery process.},
}
@article {pmid37687396,
year = {2023},
author = {Galinytė, D and Balčiūnaitė-Murzienė, G and Karosienė, J and Morudov, D and Naginienė, R and Baranauskienė, D and Šulinskienė, J and Kudlinskienė, I and Savickas, A and Savickienė, N},
title = {Determination of Heavy Metal Content: Arsenic, Cadmium, Mercury, and Lead in Cyano-Phycocyanin Isolated from the Cyanobacterial Biomass.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {17},
pages = {},
pmid = {37687396},
issn = {2223-7747},
abstract = {Cyano-phycocyanin (C-PC) is a light-absorbing biliprotein found in cyanobacteria, commonly known as blue-green algae. Due to its antioxidative, anti-inflammatory, and anticancer properties, this protein is a promising substance in medicine and pharmaceuticals. However, cyanobacteria tend to bind heavy metals from the environment, making it necessary to ensure the safety of C-PC for the development of pharmaceutical products, with C-PC isolated from naturally collected cyanobacterial biomass. This study aimed to determine the content of the most toxic heavy metals, arsenic (As), cadmium (Cd), mercury (Hg), and lead (Pb) in C-PC isolated from different cyanobacterial biomasses collected in the Kaunas Lagoon during 2019-2022, and compare them with the content of heavy metals in C-PC isolated from cultivated Spirulina platensis (S. platensis). Cyanobacteria of Aphanizomenon flos-aquae (A. flos-aquae) dominated the biomass collected in 2019, while the genus Microcystis dominated the biomasses collected in the years 2020 and 2022. Heavy metals were determined using inductively coupled plasma mass spectrometry (ICP-MS). ICP-MS analysis revealed higher levels of the most investigated heavy metals (Pb, Cd, and As) in C-PC isolated from the biomass with the dominant Microcystis spp. compared to C-PC isolated from the biomass with the predominant A. flos-aquae. Meanwhile, C-PC isolated from cultivated S. platensis exhibited lower concentrations of As and Pb than C-PC isolated from naturally collected cyanobacterial biomass.},
}
@article {pmid37687181,
year = {2023},
author = {Tom, A and Jacob, J and Mathews, M and Rajagopal, R and Alfarhan, A and Barcelo, D and Narayanankutty, A},
title = {Synthesis of Bis-Chalcones and Evaluation of Its Effect on Peroxide-Induced Cell Death and Lipopolysaccharide-Induced Cytokine Production.},
journal = {Molecules (Basel, Switzerland)},
volume = {28},
number = {17},
pages = {},
pmid = {37687181},
issn = {1420-3049},
mesh = {*Antioxidants/pharmacology ; *Chalcones/pharmacology ; Lipopolysaccharides/pharmacology ; Cell Death ; Peroxides ; Cytokines ; },
abstract = {Plant secondary metabolites are important sources of biologically active compounds with wide pharmacological potentials. Among the different classes, the chalcones form integral pharmacologically active agents. Natural chalcones and bis-chalcones exhibit high antioxidant and anti-inflammatory properties in various experiments. Studies are also underway to explore more biologically active bis-chalcones by chemical synthesis of these compounds. In this study, the effects of six synthetic bis-chalcones were evaluated in intestinal epithelial cells (IEC-6); further, the anti-inflammatory potentials were studied in lipopolysaccharide-induced cytokine production in macrophages. The synthesized bis-chalcones differ from each other first of all by the nature of the aromatic cores (functional group substitution, and their position) and by the size of a central alicycle. The exposure of IEC-6 cells to peroxide radicals reduced the cell viability; however, pre-treatment with the bis-chalcones improved the cell viability in these cells. The mechanism of action was observed to be the increased levels of glutathione and antioxidant enzyme activities. Further, these bis-chalcones also inhibited the LPS-stimulation-induced inflammatory cytokine production in RAW 264.7 macrophages. Overall, the present study indicated the cytoprotective and anti-inflammatory abilities of synthetic bis-chalcones.},
}
@article {pmid37684546,
year = {2023},
author = {Liu, N and Huang, Z and Fang, Y and Dong, Z},
title = {Impacts of Thermal Drainage on Bacterial Diversity and Community Construction in Tianwan Nuclear Power Plant.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2981-2992},
pmid = {37684546},
issn = {1432-184X},
mesh = {*Ecosystem ; *Nuclear Power Plants ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Drainage ; Carbon ; },
abstract = {As one of the low-carbon and high-efficient energy sources, nuclear power is developing vigorously to alleviate the crisis of global climate warming and realize carbon neutrality goals. Meanwhile, the ecological effect of thermal drainage in the nuclear power plant is significantly remarkable, which environmental assessment system has not yet referred to microorganisms. The rapid response of microbial diversity and community structure to environmental changes is crucial for ecosystem stability. This study investigated the bacterial diversity, community construction, and the co-occurrence patterns by 16S rRNA gene amplicon sequencing among gradient warming regions in Tianwan Nuclear Power Plant. The alpha diversity of the high warming region was the lowest in summer, which was dominated by Proteobacteria, whereas the highest bacterial diversity presented in high warming regions in winter, which harbored higher proportions of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The spatial distribution of bacterial communities showed clear separation especially in summer. Strong correlations were between community compositions and environmental factors, such as salinity, DO, TN, and temperature in summer. Furthermore, remarkable seasonality in bacterial co-occurrence patterns was discovered: the robustness of the bacterial co-occurrence network was promoted in winter, while the complexity and robustness were decreased in summer due to the warming of thermal drainage. These findings reveal the potential factors underpinning the influence of thermal drainage on bacterial community structure, which make it possible to predict the ecological effect of the nuclear power plants by exploring how the microbial assembly is likely to respond to the temperature and other environmental changes.},
}
@article {pmid37684545,
year = {2023},
author = {Huang, R and Tang, C and Zhao, Y and Liu, L and Chen, J and Shi, Z and Yan, Z},
title = {Unveiling the Biochar-Respiratory Growth of Methanosarcina acetivorans Involving Extracellular Polymeric Substances.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2970-2980},
pmid = {37684545},
issn = {1432-184X},
support = {22008142//National Natural Science Foundation of China/ ; ZR2022YQ31//Natural Science Foundation of Shandong Province/ ; BK20200232//Natural Science Foundation of Jiangsu Province/ ; Qilu Youth Talent Program//Shandong University/ ; },
mesh = {*Methanosarcina/genetics ; *Extracellular Polymeric Substance Matrix ; Electron Transport ; Methane ; },
abstract = {Biochar can be applied to diverse natural and engineered anaerobic systems. Biochar plays biogeochemical roles during its production, storage, and environmental dynamics, one of which is related to the global methane flux governed by methanotrophs and methanogens. Our understanding of relevant mechanisms is currently limited to the roles of biochar in methanotrophic growth, but less is known about the roles of biochar in methanogenic growth. Here, we demonstrated that biochar enhanced the methanogenic growth of a model methanogen, Methanosarcina acetivorans, and the role of biochar as an electron acceptor during methanogenic growth was confirmed, which is referred to as biochar-respiratory growth. The biochar-respiratory growth of M. acetivorans promoted the secretion of extracellular polymeric substances (EPS) with augmented electron transfer capabilities, and the removal of EPS significantly attenuated extracellular electron transfer. Identification and quantification of prosthetic cofactors for EPS suggest an important role of flavin and F420 in extracellular electron transfer. Transcriptomic analysis provided additional insights into the biochar-respiratory growth of M. acetivorans, showing that there was a positive response in transcriptional regulation to the favorable growth environment provided by biochar, which stimulated global methanogenesis. Our results shed more light on the in situ roles of biochar in the ecophysiology of methanogens in diverse anaerobic environments.},
}
@article {pmid37682693,
year = {2024},
author = {Wilberts, L and Vuts, J and Caulfield, JC and Thomas, G and Withall, DM and Wäckers, F and Birkett, MA and Jacquemyn, H and Lievens, B},
title = {Effects of root inoculation of entomopathogenic fungi on olfactory-mediated behavior and life-history traits of the parasitoid Aphidius ervi (Haliday) (Hymenoptera: Braconidae).},
journal = {Pest management science},
volume = {80},
number = {2},
pages = {307-316},
doi = {10.1002/ps.7762},
pmid = {37682693},
issn = {1526-4998},
support = {1S79919N//Fonds Wetenschappelijk Onderzoek/ ; C24E/19/052//KU Leuven/ ; BB/X010953/1//Growing Health Institute Strategic Programme funded by the Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/OS/CP/000001//Industrial Strategy Challenge Fund funded by the Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Animals ; *Parasites ; Pest Control, Biological ; *Wasps/physiology ; Plants ; Nicotiana ; *Aphids/physiology ; *Capsicum ; },
abstract = {BACKGROUND: Although most biological control programs use multiple biological agents to manage pest species, to date only a few programs have combined the use of agents from different guilds. Using sweet pepper (Capsicum annuum L.), the entomopathogenic fungus Akanthomyces muscarius ARSEF 5128, the tobacco peach aphid Myzus persicae var. nicotianae and the aphid parasitoid Aphidius ervi as the experimental model, we explored whether root inoculation with an entomopathogenic fungus is compatible with parasitoid wasps for enhanced biocontrol of aphids.<br><br>RESULTS: In dual-choice behavior experiments, A. ervi was significantly attracted to the odor of M. persicae-infested C. annuum plants that had been inoculated with A. muscarius, compared to noninoculated infested plants. There was no significant difference in attraction to the odor of uninfested plants. Myzus persicae-infested plants inoculated with A. muscarius emitted significantly higher amounts of indole, (E)-nerolidol, (3E,7E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene and one unidentified terpene compared to noninoculated infested plants. Coupled gas chromatography-electroantennography, using the antennae of A. ervi, confirmed the physiological activity of these elevated compounds. Inoculation of plants with A. muscarius did not affect parasitism rate nor parasitoid longevity, but significantly increased the speed of mummy formation in parasitized aphids on fungus-inoculated plants.<br><br>CONCLUSION: Our data suggest that root inoculation of C. annuum with A. muscarius ARSEF 5128 alters the olfactory-mediated behavior of parasitoids, but has little effect on parasitism efficiency or life-history parameters. However, increased attraction of parasitoids towards M. persicae-infested plants when inoculated by entomopathogenic fungi can accelerate host localization and hence improve biocontrol efficacy. &#xa9; 2023 Society of Chemical Industry.},
}
@article {pmid37680522,
year = {2023},
author = {You, Y and Zhang, W and Cai, M and Guo, Q and Wang, J and Cai, Y and Lin, J},
title = {Discovery of fecal microbial signatures in patients with ankylosing spondylitis.},
journal = {Archives of rheumatology},
volume = {38},
number = {2},
pages = {217-229},
pmid = {37680522},
issn = {2618-6500},
abstract = {OBJECTIVES: This study aimed to investigate the characteristics of the gut microbiota in Chinese patients with ankylosing spondylitis (AS) and healthy controls in Quanzhou aiming to explore the correlation between microbiome changes and AS activities.<br><br>PATIENTS AND METHODS: In this study, high-throughput sequencing of the gene of 16S ribosomal RNA (16S rRNA) in fecal samples from 40 AS patients and 40 healthy controls, for a total of 80 participants (70 males, 10 females; mean age 33.7&#xb1;10.7 years; range, 15 to 58 years), was conducted between January 2018 and January 2019. Alpha and beta diversity were analyzed using the QIIME (Quantitative Insights Into Microbial Ecology) software, and differences were analyzed using Student's t-test, linear discriminant analysis coupled with effect size and Metastats. Finally, a correlation network was constructed using Pearson's analysis.<br><br>RESULTS: The alpha index values of the AS group were not significantly different from those of the control group. At the genus level, eight genera, Ruminiclostridium_9, Fusicatenibacter, Adlercreutzia, CAG-56, Intestinimonas, Lachnospira, Bacteroides, and Pseudoflavonifractor, were significantly enriched in patients with AS, whereas the abundance of uncultured_bacterium_f_Saccharimonadaceae, Prevotella_7, uncultured_bacterium_f_ Enterobacteriaceae, Cronobacter, Prevotellaceae_NK3B31_group, and Weissella were significantly decreased in patients with AS. In addition, diseaserelated gut microbial communities were detected in patients with AS.<br><br>CONCLUSION: We found differences in the gut microbiome between the patients with AS and controls and identified potential disease activity-related bacterial communities.},
}
@article {pmid37676325,
year = {2023},
author = {Sun, P and Wang, M and Zheng, W and Li, S and Zhu, X and Chai, X and Zhao, S},
title = {Unbalanced diets enhance the complexity of gut microbial network but destabilize its stability and resistance.},
journal = {Stress biology},
volume = {3},
number = {1},
pages = {20},
pmid = {37676325},
issn = {2731-0450},
abstract = {Stability is a fundamental ecological property of the gut microbiota and is associated with host health. Numerous studies have shown that unbalanced dietary components disturb the gut microbial composition and thereby contribute to the onset and progression of disease. However, the impact of unbalanced diets on the stability of the gut microbiota is poorly understood. In the present study, four-week-old mice were fed a plant-based diet high in refined carbohydrates or a high-fat diet for four weeks to simulate a persistent unbalanced diet. We found that persistent unbalanced diets significantly reduced the gut bacterial richness and increased the complexity of bacterial co-occurrence networks. Furthermore, the gut bacterial response to unbalanced diets was phylogenetically conserved, which reduced network modularity and enhanced the proportion of positive associations between community taxon, thereby amplifying the co-oscillation of perturbations among community species to destabilize gut microbial communities. The disturbance test revealed that the gut microbiota of mice fed with unbalanced diets was less resistant to antibiotic perturbation and pathogenic bacteria invasion. This study may fill a gap in the mechanistic understanding of the gut microbiota stability in response to diet and provide new insights into the gut microbial ecology.},
}
@article {pmid37676037,
year = {2023},
author = {Danevčič, T and Spacapan, M and Dragoš, A and Kovács, &#xc1;T and Mandic-Mulec, I},
title = {DegQ is an important policing link between quorum sensing and regulated adaptative traits in Bacillus subtilis.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0090823},
pmid = {37676037},
issn = {2165-0497},
abstract = {Quorum sensing (QS) is a widespread bacterial communication system that controls important adaptive traits in a cell density-dependent manner. However, mechanisms by which QS-regulated traits are linked within the cell and mechanisms by which these links affect adaptation are not well understood. In this study, Bacillus subtilis was used as a model bacterium to investigate the link between the ComQXPA QS system, DegQ, surfactin and protease production in planktonic and biofilm cultures. The work tests two alternative hypotheses predicting that hypersensitivity of the QS signal-deficient mutant (comQ::kan) to exogenously added ComX, resulting in increased surfactin production, is linked to an additional genetic locus, or alternatively, to overexpression of the ComX receptor ComP. Results are in agreement with the first hypothesis and show that the P srfAA hypersensitivity of the comQ::kan mutant is linked to a 168 strain-specific mutation in the P degQ region. Hence, the markerless ΔcomQ mutant lacking this mutation is not overresponsive to ComX. Such hyper-responsiveness is specific for the P srfAA and not detected in another ComX-regulated promoter, the P aprE , which is under the positive control by DegQ. Our results suggest that DegQ by exerting differential effect on P srfAA and P aprE acts as a policing mechanism and the intracellular link, which guards the cell from an overinvestment into surfactin production. IMPORTANCE DegQ levels are known to regulate surfactin synthesis and extracellular protease production, and DegQ is under the control of the ComX-dependent QS. DegQ also serves as an important policing link between these QS-regulated processes, preventing overinvestment in these costly processes. This work highlights the importance of DegQ, which acts as the intracellular link between ComX production and the response by regulating extracellular degradative enzyme synthesis and surfactin production.},
}
@article {pmid37675430,
year = {2023},
author = {Edwards, J and Hoffbeck, C and West, AG and Pas, A and Taylor, MW},
title = {16S rRNA gene-based microbiota profiles from diverse avian faeces are largely independent of DNA preservation and extraction method.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1239167},
pmid = {37675430},
issn = {1664-302X},
abstract = {The avian gut microbiota has been the subject of considerable recent attention, with potential implications for diverse fields such as the poultry industry, microbial ecology, and conservation. Faecal microbiotas are frequently used as a non-invasive proxy for the gut microbiota, however the extraction of high-quality microbial DNA from avian faeces has often proven challenging. Here we aimed to evaluate the performance of two DNA preservation methods (95% ethanol and RNAlater) and five extraction approaches (IndiSpin Pathogen Kit, QIAamp PowerFecal Pro DNA Kit, MicroGEM PrepGEM Bacteria Kit, ZymoBIOMICS DNA Miniprep Kit, and an in-house phase separation-based method) for studying the avian gut microbiota. Systematic testing of the efficacy of these approaches on faecal samples from an initial three avian species (chicken, ostrich, and the flightless parrot kākāpō) revealed substantial differences in the quality, quantity and integrity of extracted DNA, but negligible influence of applied method on 16S rRNA gene-based microbiota profiles. Subsequent testing with a selected combination of preservation and extraction method on 10 further phylogenetically and ecologically diverse avian species reiterated the efficacy of the chosen approach, with bacterial community structure clustering strongly by technical replicates for a given avian species. Our finding that marked differences in extraction efficacy do not appear to influence 16S rRNA gene-based bacterial community profiles provides an important foundation for ongoing research on the avian gut microbiota.},
}
@article {pmid37674014,
year = {2023},
author = {Cornish, CM and Bergholz, P and Schmidt, K and Sweetman, J},
title = {How Benthic Sediment Microbial Communities Respond to Glyphosate and Its Metabolite: a Microcosm Experiment.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2949-2958},
pmid = {37674014},
issn = {1432-184X},
mesh = {RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/analysis ; *Herbicides/pharmacology ; *Microbiota ; Glyphosate ; },
abstract = {Glyphosate is the most commonly used agricultural herbicide in the world. In aquatic ecosystems, glyphosate often adsorbs to benthic substrates or is metabolized and degraded by microorganisms. The effects of glyphosate on microbial communities vary widely as microorganisms respond differently to exposure. To help understand the impacts of glyphosate on the sediment microbiome, we conducted a microcosm experiment examining the responses of benthic sediment microbial communities to herbicide treatments. Sediments from a prairie pothole wetland were collected, and 16S rRNA gene sequencing was used to analyze community composition 2-h and 14-days after a single treatment of low (0.07 ppm), medium (0.7 ppm), or high (7 ppm) glyphosate, aminomethylphosphonic acid (glyphosate metabolite), or a glyphosate-based commercial formula. We found no significant differences in microbial community composition across treatments, concentration levels, or day of sampling. These findings suggest that microbial species in the Prairie Pothole Region of North America may be tolerant to glyphosate exposure.},
}
@article {pmid37671861,
year = {2023},
author = {Roller, BRK and Hellerschmied, C and Wu, Y and Miettinen, TP and Gomez, AL and Manalis, SR and Polz, MF},
title = {Single-cell mass distributions reveal simple rules for achieving steady-state growth.},
journal = {mBio},
volume = {14},
number = {5},
pages = {e0158523},
pmid = {37671861},
issn = {2150-7511},
support = {Life Sciences Project Award-572792//Simons Foundation (SF)/ ; },
mesh = {Reproducibility of Results ; Cell Division ; *Bacteria ; Culture Media ; Biomass ; },
abstract = {Microbiologists have watched clear liquid turn cloudy for over 100 years. While the cloudiness of a culture is proportional to its total biomass, growth rates from optical density measurements are challenging to interpret when cells change size. Many bacteria adjust their size at different steady-state growth rates, but also when shifting between starvation and growth. Optical density cannot disentangle how mass is distributed among cells. Here, we use single-cell mass measurements to demonstrate that a population of cells in batch culture achieves a stable mass distribution for only a short period of time. Achieving steady-state growth in rich medium requires low initial biomass concentrations and enough time for individual cell mass accumulation and cell number increase via cell division to balance out. Steady-state growth is important for reliable cell mass distributions and experimental reproducibility. We discuss how mass variation outside of steady-state can impact physiology, ecology, and evolution experiments.},
}
@article {pmid37669892,
year = {2023},
author = {Hellal, J and Lise, B and Annette, B and Aurélie, C and Giulia, C and Simon, C and Cristiana, CL and Caroline, C and Nicolas, G and Marina, H and Fabrice, ML and Jean, M and Soizic, M and Carmen, P and Stéphane, P and Agnès, R and Stéphane, V},
title = {Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {10},
pages = {},
pmid = {37669892},
issn = {1574-6941},
mesh = {Ecotoxicology ; *Environmental Pollutants/toxicity ; Environmental Pollution ; *Environmental Restoration and Remediation ; Risk Assessment ; },
abstract = {Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.},
}
@article {pmid37668400,
year = {2023},
author = {Du, H and Pan, J and Zhang, C and Yang, X and Wang, C and Lin, X and Li, J and Liu, W and Zhou, H and Yu, X and Mo, S and Zhang, G and Zhao, G and Qu, W and Jiang, C and Tian, Y and He, Z and Liu, Y and Li, M},
title = {Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0157723},
pmid = {37668400},
issn = {2165-0497},
abstract = {As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.},
}
@article {pmid37668159,
year = {2023},
author = {Van den Eeckhoudt, R and Christiaens, AS and Ceyssens, F and Vangalis, V and Verstrepen, KJ and Boon, N and Tavernier, F and Kraft, M and Taurino, I},
title = {Full-electric microfluidic platform to capture, analyze and selectively release single cells.},
journal = {Lab on a chip},
volume = {23},
number = {19},
pages = {4276-4286},
doi = {10.1039/d3lc00645j},
pmid = {37668159},
issn = {1473-0189},
mesh = {*Microfluidics ; Automation ; Cell Movement ; Cell Size ; *Dielectric Spectroscopy ; Saccharomyces cerevisiae ; },
abstract = {Current single-cell technologies require large and expensive equipment, limiting their use to specialized labs. In this paper, we present for the first time a microfluidic device which demonstrates a combined method for full-electric cell capturing, analyzing, and selectively releasing with single-cell resolution. All functionalities are experimentally demonstrated on Saccharomyces cerevisiae. Our microfluidic platform consists of traps centered around a pair of individually accessible coplanar electrodes, positioned under a microfluidic channel. Using this device, we validate our novel Two-Voltage method for trapping single cells by positive dielectrophoresis (pDEP). Cells are attracted to the trap when a high voltage (VH) is applied. A low voltage (VL) holds the already trapped cell in place without attracting additional cells, allowing full control over the number of trapped cells. After trapping, the cells are analyzed by broadband electrochemical impedance spectroscopy. These measurements allow the detection of single cells and the extraction of cell parameters. Additionally, these measurements show a strong correlation between average phase change and cell size, enabling the use of our system for size measurements in biological applications. Finally, our device allows selectively releasing trapped cells by turning off the pDEP signal in their trap. The experimental results show the techniques potential as a full-electric single-cell analysis tool with potential for miniaturization and automation which opens new avenues towards small-scale, high throughput single-cell analysis and sorting lab-on-CMOS devices.},
}
@article {pmid37667323,
year = {2023},
author = {Rodríguez-Pastor, R and Hasik, AZ and Knossow, N and Bar-Shira, E and Shahar, N and Gutiérrez, R and Zaman, L and Harrus, S and Lenski, RE and Barrick, JE and Hawlena, H},
title = {Bartonella infections are prevalent in rodents despite efficient immune responses.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {315},
pmid = {37667323},
issn = {1756-3305},
support = {DEB-1813069//National Science Foundation/ ; 1391/15//Israel Science Foundation/ ; },
mesh = {Animals ; *Bartonella Infections/epidemiology/veterinary ; *Bartonella ; Immunoglobulin G ; Kinetics ; Immunity ; },
abstract = {BACKGROUND: Pathogens face strong selection from host immune responses, yet many host populations support pervasive pathogen populations. We investigated this puzzle in a model system of Bartonella and rodents from Israel's northwestern Negev Desert. We chose to study this system because, in this region, 75-100% of rodents are infected with Bartonella at any given time, despite an efficient immunological response. In this region, Bartonella species circulate in three rodent species, and we tested the hypothesis that at least one of these hosts exhibits a waning immune response to Bartonella, which allows reinfections.<br><br>METHODS: We inoculated captive animals of all three rodent species with the same Bartonella strain, and we quantified the bacterial dynamics and Bartonella-specific immunoglobulin G antibody kinetics over a period of 139&#xa0;days after the primary inoculation, and then for 60&#xa0;days following reinoculation with the same strain.<br><br>RESULTS: Contrary to our hypothesis, we found a strong, long-lasting immunoglobulin G antibody response, with protective immunological memory in all three rodent species. That response prevented reinfection upon exposure of the rodents to the same Bartonella strain.<br><br>CONCLUSIONS: This study constitutes an initial step toward understanding how the interplay between traits of Bartonella and their hosts influences the epidemiological dynamics of these pathogens in nature.},
}
@article {pmid37667132,
year = {2023},
author = {Lv, H and Li, X and He, D and Chen, X and Liu, M and Lan, Y and Zhao, J and Wang, H and Yan, Z},
title = {Genotype-Controlled Vertical Transmission Exerts Selective Pressure on Community Assembly of Salvia miltiorrhiza.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2934-2948},
pmid = {37667132},
issn = {1432-184X},
mesh = {*Salvia miltiorrhiza/genetics/metabolism ; Fungi/genetics ; Endophytes/genetics ; *Microbiota/genetics ; Soil ; Seedlings ; Plant Roots/microbiology ; },
abstract = {The plant's endophytic fungi play an important role in promoting host development and metabolism. Studies have shown that the factors affecting the assembly of the endophyte community mainly include host genotype, vertical transmission, and soil origin. However, we do not know the role of vertically transmitted endohytic fungi influences on the host-plant's endophytic community assembly. Salvia miltiorrhiza from three production areas were used as research objects; we constructed three production area genotypes of S. miltiorrhiza regenerated seedlings simultaneously. Based on high-throughput sequencing, we analyzed the effects of genotype, soil origin, and vertical transmission on endophytic fungal communities. The results show that the community of soil origins significantly affected the endophytic fungal community in the regenerated seedlings of S. miltiorrhiza. The influence of genotype on community composition occurs through a specific mechanism. Genotype may selectively screen certain communities into the seed, thereby exerting selection pressure on the community composition process of offspring. As the number of offspring increases gradually, the microbiota, controlled by genotype and transmitted vertically, stabilizes, ultimately resulting in a significant effect of genotype on community composition.Furthermore, we observed that the taxa influencing the active ingredients are also selected as the vertically transmitted community. Moreover, the absence of an initial vertically transmitted community in S. miltiorrhiza makes it more vulnerable to infection by pathogenic fungi. Therefore, it is crucial to investigate and comprehend the selection model of the vertically transmitted community under varying genotypes and soil conditions. This research holds significant implications for enhancing the quality and yield of medicinal plants and economic crops.},
}
@article {pmid37666974,
year = {2023},
author = {Lin, Q and Li, L and De Vrieze, J and Li, C and Fang, X and Li, X},
title = {Functional conservation of microbial communities determines composition predictability in anaerobic digestion.},
journal = {The ISME journal},
volume = {17},
number = {11},
pages = {1920-1930},
pmid = {37666974},
issn = {1751-7370},
mesh = {Anaerobiosis ; *Microbiota ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal ; Bioreactors ; Microbial Consortia/genetics ; },
abstract = {A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be predicted and explained, especially in microorganism-driven systems. We addressed this challenge by monitoring microbial community responses to the periodic addition of the same feedstock throughout anaerobic digestion, a typical microorganism-driven system where microorganisms degrade and transform the feedstock. The immediate and delayed response consortia were assemblages of microorganisms whose abundances significantly increased on the first or third day after feedstock addition. The immediate response consortia were more predictable than the delayed response consortia and showed a reproducible and predictable order-level composition across multiple feedstock additions. These results stood in both present (16 S rRNA gene) and potentially active (16 S rRNA) microbial communities and in different feedstocks with different biodegradability and were validated by simulation modeling. Despite substantial species variability, the immediate response consortia aligned well with the reproducible CH4 production, which was attributed to the conservation of expressed functions by the response consortia throughout anaerobic digestion, based on metatranscriptomic data analyses. The high species variability might be attributed to intraspecific competition and contribute to biodiversity maintenance and functional redundancy. Our results demonstrate reproducible and predictable microbial community responses and their importance in stabilizing system functions.},
}
@article {pmid37664629,
year = {2023},
author = {Simon, LM and Flocco, C and Burkart, F and Methner, A and Henke, D and Rauer, L and Müller, CL and Vogel, J and Quaisser, C and Overmann, J and Simon, S},
title = {Microbial fingerprints reveal interaction between museum objects, curators, and visitors.},
journal = {iScience},
volume = {26},
number = {9},
pages = {107578},
pmid = {37664629},
issn = {2589-0042},
abstract = {Microbial communities reside at the interface between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To investigate this, we selected objects from the Museum für Naturkunde and the Pergamonmuseum in Berlin, Germany, varying in material and size. Using swabs, we collected 126 samples from natural and cultural heritage objects, which were analyzed through 16S rRNA sequencing. By comparing the microbial composition of touched and untouched objects, we identified a microbial signature associated with human skin microbes. Applying this signature to cultural heritage objects, we identified areas with varying degrees of exposure to human contact on the Ishtar gate and Sam'al gate lions. Furthermore, we differentiated objects touched by two different individuals. Our findings demonstrate that the microbiome of museum objects provides insights into the level of human contact, crucial for conservation, heritage science, and potentially provenance research.},
}
@article {pmid37662195,
year = {2023},
author = {Hoang, DQ and Wilson, LR and Scheftgen, AJ and Suen, G and Currie, CR},
title = {Disturbance-Diversity Relationships of Microbial Communities Change Based on Growth Substrate.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37662195},
issn = {2692-8205},
support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; },
abstract = {Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances, and how those responses can vary, is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source, and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticaccacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticaccaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants, and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (0.67-1.99 Shannon diversity and 1.38-5.25 Inverse Simpson diversity) that peak at the intermediate disturbance frequency treatment, or 1 disturbance every 3 days. Communities grown on glucose, however, ranged from 0.49-1.43 Shannon diversity and 1.37- 3.52 Inverse Simpson with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency, and may potentially explain the variety of diversity-disturbance relationships observed in microbial ecosystems.},
}
@article {pmid37658881,
year = {2023},
author = {Owashi, Y and Minami, T and Kikuchi, T and Yoshida, A and Nakano, R and Kageyama, D and Adachi-Hagimori, T},
title = {Microbiome of Zoophytophagous Biological Control Agent Nesidiocoris tenuis.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2923-2933},
pmid = {37658881},
issn = {1432-184X},
mesh = {Humans ; Animals ; Biological Control Agents ; *Hemiptera/genetics ; RNA, Ribosomal, 16S/genetics ; *Rickettsia/genetics ; *Spiroplasma ; *Wolbachia/genetics ; *Microbiota ; Symbiosis ; },
abstract = {Many insects are associated with endosymbionts that influence the feeding, reproduction, and distribution of their hosts. Although the small green mirid, Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae), a zoophytophagous predator that feeds on plants as well as arthropods, is a globally important biological control agent, its microbiome has not been sufficiently studied. In the present study, we assessed the microbiome variation in 96 N. tenuis individuals from 14 locations throughout Japan, based on amplicon sequencing of the 16S ribosomal RNA gene. Nine major bacteria associated with N. tenuis were identified: Rickettsia, two strains of Wolbachia, Spiroplasma, Providencia, Serratia, Pseudochrobactrum, Lactococcus, and Stenotrophomonas. Additionally, a diagnostic PCR analysis for three typical insect reproductive manipulators, Rickettsia, Wolbachia, and Spiroplasma, was performed on a larger sample size (n = 360) of N. tenuis individuals; the most prevalent symbiont was Rickettsia (69.7%), followed by Wolbachia (39.2%) and Spiroplasma (6.1%). Although some symbionts were co-infected, their prevalence did not exhibit any specific tendency, such as a high frequency in specific infection combinations. The infection frequency of Rickettsia was significantly correlated with latitude and temperature, while that of Wolbachia and Spiroplasma was significantly correlated with host plants. The predominance of these bacteria and the absence of obligate symbionts suggested that the N. tenuis microbiome is typical for predatory arthropods rather than sap-feeding insects. Rickettsia and Wolbachia were vertically transmitted rather than horizontally transmitted from the prey. The functional validation of each symbiont would be warranted to develop N. tenuis as a biological control agent.},
}
@article {pmid37659544,
year = {2023},
author = {Kazmi, SSUH and Saqib, HSA and Pastorino, P and Grossart, HP and Yaseen, ZM and Abualreesh, MH and Liu, W and Wang, Z},
title = {Influence of the antibiotic nitrofurazone on community dynamics of marine periphytic ciliates: Evidence from community-based bioassays.},
journal = {The Science of the total environment},
volume = {904},
number = {},
pages = {166687},
doi = {10.1016/j.scitotenv.2023.166687},
pmid = {37659544},
issn = {1879-1026},
mesh = {*Ecosystem ; Nitrofurazone/toxicity ; Anti-Bacterial Agents/toxicity ; Environmental Monitoring ; Biodiversity ; *Ciliophora ; },
abstract = {Marine periphytic ciliates play a pivotal role in shaping coastal ecosystems dynamics, thereby acting as robust biological indicators of aquatic ecosystem health and functionality. However, the understanding of the effects of veterinary antibiotics on composition and structure of periphytic ciliate communities remains limited. Therefore, this research investigates the influence of the veterinary antibiotic nitrofurazone on the community dynamics of marine periphytic ciliates through bioassay experiments conducted over a one-year cycle. Various concentrations of nitrofurazone were administered to the tested ciliate assemblages, and subsequent changes in community composition, abundance, and diversity were quantitatively analyzed. The research revealed significant alterations in periphytic ciliate communities following exposure to nitrofurazone. Concentration-dependent (0-8 mg L[-1]) decrease in ciliates abundance, accompanied by shifts in species composition, community structure, and community patterns were observed. Comprehensive assessment of diversity metrics indicated significant changes in species richness and evenness in the presence of nitrofurazone, potentially disrupting the stability of ciliate communities. Furthermore, nitrofurazone significantly influenced the community structure of ciliates in all seasons (winter: R[2] = 0.489; spring: R[2] = 0.666; summer: R[2] = 0.700, autumn: R[2] = 0.450), with high toxic potential in treatments 4 and 8 mg L[-1]. Differential abundances of ciliates varied across seasons and nitrofurazone treatments, some orders like Pleurostomatida were consistently affected, while others (i.e., Strombidida and Philasterida) showed irregular distributions or were evenly affected (e.g., Urostylida and Synhymeniida). Retrieved contrasting patterns between nitrofurazone and community responses underscore the broad response repertoire exhibited by ciliates to antibiotic exposure, suggesting potential cascading effects on associated ecological processes in the periphyton community. These findings significantly enhance the understanding of the ecological impacts of nitrofurazone on marine periphytic ciliate communities, emphasizing the imperative for vigilant monitoring and regulation of veterinary antibiotics to protect marine ecosystem health and biodiversity. Further research is required to explore the long-term effects of nitrofurazone exposure and evaluate potential strategies to reduce the ecological repercussions of antibiotics in aquatic environments, with a particular focus on nitrofurazone.},
}
@article {pmid37659520,
year = {2023},
author = {Schulz, G and van Beusekom, JEE and Jacob, J and Bold, S and Schöl, A and Ankele, M and Sanders, T and Dähnke, K},
title = {Low discharge intensifies nitrogen retention in rivers - A case study in the Elbe River.},
journal = {The Science of the total environment},
volume = {904},
number = {},
pages = {166740},
doi = {10.1016/j.scitotenv.2023.166740},
pmid = {37659520},
issn = {1879-1026},
mesh = {*Rivers ; *Nitrates/analysis ; Ecosystem ; Environmental Monitoring/methods ; Nitrogen/analysis ; Eutrophication ; Harmful Algal Bloom ; Water ; },
abstract = {Eutrophication due to excessive nutrient inputs is a major threat to coastal ecosystems worldwide, causing harmful algae blooms, seagrass loss and hypoxia. Decisions to combat eutrophication in the North Sea were made in the 1980s. Despite significant improvements during recent decades, high nitrogen loads and resulting eutrophication problems remain. In this study, long-term changes in nitrogen inputs to the Elbe Estuary (Germany) were characterized based on nitrogen data provided by the Elbe River Basin Community from 1985 to 2019. Additionally, surface water samples were taken at the weir separating the river from the estuary from 2011 to 2021 to characterize dissolved inorganic nitrogen concentrations and nitrate stable isotope composition. The findings suggest a close coupling of river discharge with the riverine nitrogen cycle. Nitrogen loads decreased disproportionately with decreasing discharge. This decrease is due to intensified nitrogen retention in the Elbe catchment, which can double nitrogen retention compared to average discharge conditions. Phytoplankton growth was enhanced by long residence times and high light availability at low water levels. This suggests that the recent decreases in nitrogen loads in the Elbe River were not only a result of management measures in the catchment but were also amplified by a recent long-lasting drought in the catchment. Based on projections from the Intergovernmental Panel on Climate Change, more frequent and extensive droughts are anticipated, which may lead to future seasonal shifts to nitrate limitation in the lower Elbe River.},
}
@article {pmid37658593,
year = {2023},
author = {Ahmmed, MK and Bhowmik, S and Ahmmed, F and Giteru, SG and Islam, SS and Hachem, M and Hussain, MA and Kanwugu, ON and Agyei, D and Defoirdt, T},
title = {Utilisation of probiotics for disease management in giant freshwater prawn (Macrobrachium rosenbergii): Administration methods, antagonistic effects and immune response.},
journal = {Journal of fish diseases},
volume = {46},
number = {12},
pages = {1321-1336},
doi = {10.1111/jfd.13850},
pmid = {37658593},
issn = {1365-2761},
support = {//Bijzonder Onderzoeksfonds UGent/ ; //University of Otago/ ; //Ural Federal University/ ; },
mesh = {Animals ; *Palaemonidae ; *Fish Diseases ; *Probiotics/therapeutic use ; Fresh Water ; Immunity ; Disease Management ; },
abstract = {The giant freshwater prawn (Macrobrachium rosenbergii) is a high-yielding prawn variety well-received worldwide due to its ability to adapt to freshwater culture systems. Macrobrachium rosenbergii is an alternative to shrimp typically obtained from marine and brackish aquaculture systems. However, the use of intensive culture systems can lead to disease outbreaks, particularly in larval and post-larval stages, caused by pathogenic agents such as viruses, bacteria, fungi, yeasts and protozoans. White tail disease (viral), white spot syndrome (viral) and bacterial necrosis are examples of economically significant diseases. Given the increasing antibiotic resistance of disease-causing microorganisms, probiotics have emerged as promising alternatives for disease control. Probiotics are live active microbes that are introduced into a target host in an adequate number or dose to promote its health. In the present paper, we first discuss the diseases that occur in M. rosenbergii production, followed by an in-depth discussion on probiotics. We elaborate on the common methods of probiotics administration and explain the beneficial health effects of probiotics as immunity enhancers. Moreover, we discuss the antagonistic effects of probiotics on pathogenic microorganisms. Altogether, this paper provides a comprehensive overview of disease control in M. rosenbergii aquaculture through the use of probiotics, which could enhance the sustainability of prawn culture.},
}
@article {pmid37657296,
year = {2023},
author = {Fu, S and Zhang, Y and Wang, R and Qiu, Z and Song, W and Yang, Q and Shen, L},
title = {A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens.},
journal = {Journal of environmental management},
volume = {345},
number = {},
pages = {118737},
doi = {10.1016/j.jenvman.2023.118737},
pmid = {37657296},
issn = {1095-8630},
mesh = {*Metagenome ; *Drinking Water ; Phylogeny ; Anti-Bacterial Agents ; Risk Management ; },
abstract = {Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.},
}
@article {pmid37656873,
year = {2023},
author = {Cantoran, A and Maillard, F and Baldrian, P and Kennedy, PG},
title = {Defining a core microbial necrobiome associated with decomposing fungal necromass.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {9},
pages = {},
doi = {10.1093/femsec/fiad098},
pmid = {37656873},
issn = {1574-6941},
mesh = {Animals ; Carbon ; Ecosystem ; Forests ; *Mycobiome ; *Mycorrhizae ; },
abstract = {Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.},
}
@article {pmid37656196,
year = {2023},
author = {Fagre, AC and Islam, A and Reeves, WK and Kading, RC and Plowright, RK and Gurley, ES and McKee, CD},
title = {Bartonella Infection in Fruit Bats and Bat Flies, Bangladesh.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2910-2922},
pmid = {37656196},
issn = {1432-184X},
mesh = {Animals ; Phylogeny ; Bangladesh/epidemiology ; *Chiroptera ; Genetic Variation ; *Bartonella Infections/epidemiology/veterinary/microbiology ; *Bartonella/genetics ; DNA ; },
abstract = {Bats harbor diverse intracellular Bartonella bacteria, but there is limited understanding of the factors that influence transmission over time. Investigation of Bartonella dynamics in bats could reveal general factors that control transmission of multiple bat-borne pathogens, including viruses. We used molecular methods to detect Bartonella DNA in paired bat (Pteropus medius) blood and bat flies in the family Nycteribiidae collected from a roost in Faridpur, Bangladesh between September 2020 and January 2021. We detected high prevalence of Bartonella DNA in bat blood (35/55, 64%) and bat flies (59/60, 98%), with sequences grouping into three phylogenetic clades. Prevalence in bat blood increased over the study period (33% to 90%), reflecting an influx of juvenile bats in the population and an increase in the prevalence of bat flies. Discordance between infection status and the clade/genotype of detected Bartonella was also observed in pairs of bats and their flies, providing evidence that bat flies take blood meals from multiple bat hosts. This evidence of bat fly transfer between hosts and the changes in Bartonella prevalence during a period of increasing nycteribiid density support the role of bat flies as vectors of bartonellae. The study provides novel information on comparative prevalence and genetic diversity of Bartonella in pteropodid bats and their ectoparasites, as well as demographic factors that affect Bartonella transmission and potentially other bat-borne pathogens.},
}
@article {pmid37655448,
year = {2023},
author = {Wang, Y and Li, Q and Zhang, J and Liu, P and Zheng, H and Chen, L and Wang, Z and Tan, C and Zhang, M and Zhang, H and Miao, W and Wang, Y and Xuan, X and Yi, G and Wang, P},
title = {Ring1a protects against colitis through regulating mucosal immune system and colonic microbial ecology.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2251646},
pmid = {37655448},
issn = {1949-0984},
mesh = {Animals ; Mice ; *Colitis/genetics/microbiology ; *Gastrointestinal Microbiome ; Immune System ; Metronidazole/pharmacology ; Prevotella/genetics ; },
abstract = {Inflammatory bowel disease (IBD) represents a prominent chronic immune-mediated inflammatory disorder, yet its etiology remains poorly comprehended, encompassing intricate interactions between genetics, immunity, and the gut microbiome. This study uncovers a novel colitis-associated risk gene, namely Ring1a, which regulates the mucosal immune response and intestinal microbiota. Ring1a deficiency exacerbates colitis by impairing the immune system. Concomitantly, Ring1a deficiency led to a Prevotella genus-dominated pathogenic microenvironment, which can be horizontally transmitted to co-housed wild type (WT) mice, consequently intensifying dextran sodium sulfate (DSS)-induced colitis. Furthermore, we identified a potential mechanism linking the altered microbiota in Ring1aKO mice to decreased levels of IgA, and we demonstrated that metronidazole administration could ameliorate colitis progression in Ring1aKO mice, likely by reducing the abundance of the Prevotella genus. We also elucidated the immune landscape of DSS colitis and revealed the disruption of intestinal immune homeostasis associated with Ring1a deficiency. Collectively, these findings highlight Ring1a as a prospective candidate risk gene for colitis and suggest metronidazole as a potential therapeutic option for clinically managing Prevotella genus-dominated colitis.},
}
@article {pmid37655346,
year = {2023},
author = {Gutierrez, T and Liu, H},
title = {Editorial: Rising stars in aquatic microbiology: 2022.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1265720},
doi = {10.3389/fmicb.2023.1265720},
pmid = {37655346},
issn = {1664-302X},
}
@article {pmid37653502,
year = {2023},
author = {Zehentner, B and Scherer, S and Neuhaus, K},
title = {Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {243},
pmid = {37653502},
issn = {1471-2180},
mesh = {*Escherichia coli O157/genetics ; Transcription Initiation Site ; *Enterohemorrhagic Escherichia coli ; Cell Cycle ; Culture Media ; },
abstract = {Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well new intergenic (orphan) TSS, not associated with known genes. Previously, it was hypothesized that many such signals represent noise or pervasive transcription, not associated with a biological function. Here, a modified Cappable-seq protocol allows determining the primary transcriptome of the enterohemorrhagic E. coli O157:H7 EDL933 (EHEC). We used four different growth media, both in exponential and stationary growth phase, replicated each thrice. This yielded 19,975 EHEC canonical and non-canonical TSS, which reproducibly occurring in three biological replicates. This questions the hypothesis of experimental noise or pervasive transcription. Accordingly, conserved promoter motifs were found upstream indicating proper TSSs. More than 50% of 5,567 canonical and between 32% and 47% of 10,355 non-canonical TSS were differentially expressed in different media and growth phases, providing evidence for a potential biological function also of non-canonical TSS. Thus, reproducible and environmentally regulated expression suggests that a substantial number of the non-canonical TSSs may be of unknown function rather than being the result of noise or pervasive transcription.},
}
@article {pmid37653010,
year = {2023},
author = {Gralka, M and Pollak, S and Cordero, OX},
title = {Genome content predicts the carbon catabolic preferences of heterotrophic bacteria.},
journal = {Nature microbiology},
volume = {8},
number = {10},
pages = {1799-1808},
pmid = {37653010},
issn = {2058-5276},
mesh = {*Carbon/metabolism ; Bacteria ; Heterotrophic Processes ; *Microbiota/genetics ; Genomics ; },
abstract = {Heterotrophic bacteria-bacteria that utilize organic carbon sources-are taxonomically and functionally diverse across environments. It is challenging to map metabolic interactions and niches within microbial communities due to the large number of metabolites that could serve as potential carbon and energy sources for heterotrophs. Whether their metabolic niches can be understood using general principles, such as a small number of simplified metabolic categories, is unclear. Here we perform high-throughput metabolic profiling of 186 marine heterotrophic bacterial strains cultured in media containing one of 135 carbon substrates to determine growth rates, lag times and yields. We show that, despite high variability at all levels of taxonomy, the catabolic niches of heterotrophic bacteria can be understood in terms of their preference for either glycolytic (sugars) or gluconeogenic (amino and organic acids) carbon sources. This preference is encoded by the total number of genes found in pathways that feed into the two modes of carbon utilization and can be predicted using a simple linear model based on gene counts. This allows for coarse-grained descriptions of microbial communities in terms of prevalent modes of carbon catabolism. The sugar-acid preference is also associated with genomic GC content and thus with the carbon-nitrogen requirements of their encoded proteome. Our work reveals how the evolution of bacterial genomes is structured by fundamental constraints rooted in metabolism.},
}
@article {pmid37652144,
year = {2023},
author = {Low, KE and Tingley, JP and Klassen, L and King, ML and Xing, X and Watt, C and Hoover, SER and Gorzelak, M and Abbott, DW},
title = {Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates.},
journal = {Biotechnology advances},
volume = {69},
number = {},
pages = {108245},
doi = {10.1016/j.biotechadv.2023.108245},
pmid = {37652144},
issn = {1873-1899},
mesh = {Animals ; *Carbohydrates/chemistry ; Carbohydrate Metabolism ; Agriculture ; Soil/chemistry ; *Microbiota ; },
abstract = {Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.},
}
@article {pmid37650927,
year = {2023},
author = {Ho, HVN and Dunigan, DD and Salsbery, ME and Agarkova, IV and Al Ameeli, Z and Van Etten, JL and DeLong, JP},
title = {Viral Chemotaxis of Paramecium Bursaria Altered by Algal Endosymbionts.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2904-2909},
pmid = {37650927},
issn = {1432-184X},
support = {1736030//Directorate for Biological Sciences/ ; },
mesh = {*Paramecium ; Chemotaxis ; *Phycodnaviridae ; Symbiosis ; },
abstract = {Chemotaxis is widespread across many taxa and often aids resource acquisition or predator avoidance. Species interactions can modify the degree of movement facilitated by chemotaxis. In this study, we investigated the influence of symbionts on Paramecium bursaria's chemotactic behavior toward chloroviruses. To achieve this, we performed choice experiments using chlorovirus and control candidate attractors (virus stabilization buffer and pond water). We quantified the movement of Paramecia grown with or without algal and viral symbionts toward each attractor. All Paramecia showed some chemotaxis toward viruses, but cells without algae and viruses showed the most movement toward viruses. Thus, the endosymbiotic algae (zoochlorellae) appeared to alter the movement of Paramecia toward chloroviruses, but it was not clear that ectosymbiotic viruses (chlorovirus) also had this effect. The change in behavior was consistent with a change in swimming speed, but a change in attraction remains possible. The potential costs and benefits of chemotactic movement toward chloroviruses for either the Paramecia hosts or its symbionts remain unclear.},
}
@article {pmid37649628,
year = {2023},
author = {Levante, A and Bertani, G and Marrella, M and Mucchetti, G and Bernini, V and Lazzi, C and Neviani, E},
title = {The microbiota of Mozzarella di Bufala Campana PDO cheese: a study across the manufacturing process.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1196879},
pmid = {37649628},
issn = {1664-302X},
abstract = {INTRODUCTION: Mozzarella di Bufala Campana PDO cheese (MBC) is a globally esteemed Italian cheese. The traditional cheesemaking process of MBC relies on natural whey starter culture, water buffalo's milk, and the local agroecosystem.<br><br>METHODS: In this study, the microbial ecology of intermediate samples of MBC production, coming from two dairies with slightly different cheesemaking technology (dairy M large producer, and dairy C medium-small), was investigated using 16S rRNA amplicon sequencing. This research aimed to provide insights into the dynamics of microbial consortia involved in various cheesemaking steps.<br><br>RESULTS AND DISCUSSION: All samples, except for raw buffalo milk, exhibited a core microbiome predominantly composed of Streptococcus spp. and Lactobacillus spp., albeit with different ratios between the two genera across the two MBC producers. Notably, the microbiota of the brine from both dairies, analyzed using 16S amplicon sequencing for the first time, was dominated by the Lactobacillus and Streptococcus genera, while only dairy C showed the presence of minor genera such as Pediococcus and Lentilactobacillus. Intriguingly, the final mozzarella samples from both producers displayed an inversion in the dominance of Lactobacillus spp. over Streptococcus spp. in the microbiota compared to curd samples, possibly attributable to the alleviation of thermal stress following the curd stretching step. In conclusion, the different samples from the two production facilities did not exhibit significant differences in terms of the species involved in MBC cheesemaking. This finding confirms that the key role in the MBC cheesemaking process lies with a small-sized microbiome primarily composed of Streptococcus and Lactobacillus spp.},
}
@article {pmid37649327,
year = {2024},
author = {Mariën, Q and Regueira, A and Ganigué, R},
title = {Steerable isobutyric and butyric acid production from CO2 and H2 by Clostridium luticellarii.},
journal = {Microbial biotechnology},
volume = {17},
number = {1},
pages = {e14321},
pmid = {37649327},
issn = {1751-7915},
support = {ERDF (UE)//Galician Competitive Research Group/ ; GRC ED431C 2021/37//Galician Competitive Research Group/ ; BOF19/STA/044//Bijzonder Onderzoeksfonds UGent/ ; 1SC5722N//Fonds Wetenschappelijk Onderzoek/ ; ED481B-2021-012//Xunta de Galicia/ ; },
mesh = {Butyric Acid/metabolism ; *Isobutyrates ; *Carbon Dioxide ; Acetic Acid ; Fermentation ; *Clostridium ; },
abstract = {Clostridium luticellarii is a recently discovered acetogen that is uniquely capable of producing butyric and isobutyric acid from various substrates (e.g. methanol), but it is unclear which factors influence its (iso)butyric acid production from H2 and CO2 . We aimed to investigate the autotrophic metabolism of C. luticellarii by identifying the necessary growth conditions and examining the effects of pH and metabolite levels on product titers and selectivity. Results show that autotrophic growth of C. luticellarii requires the addition of complex nutrient sources and the absence of shaking conditions. Further experiments combined with thermodynamic calculations identified pH as a key parameter governing the direction of metabolic fluxes. At circumneutral pH (~6.5), acetic acid is the sole metabolic end product but C. luticellarii possesses the unique ability to co-oxidize organic acids such as valeric acid under high H2 partial pressures (>1 bar). Conversely, mildly acidic pH (≤5.5) stimulates the production of butyric and isobutyric acid while partly halting the oxidation of organic acids. Additionally, elevated acetic acid concentrations stimulated butyric and isobutyric acid production up to a combined selectivity of 53 ± 3%. Finally, our results suggest that isobutyric acid is produced by a reversible isomerization of butyric acid, but valeric and caproic acid are not isomerized. These combined insights can inform future efforts to optimize and scale-up the production of valuable chemicals from CO2 using C. luticellarii.},
}
@article {pmid37643688,
year = {2023},
author = {McEvoy, N and O'Connor, A and McDonagh, F and Lonappan, AM and Farrell, ML and Kovarova, A and Burke, L and Ryan, K and Hallahan, B and Miliotis, G},
title = {Complete genome of an inhibitor-resistant blaTEM-30 encoding Escherichia coli sequence type 127 isolate identified in human saliva with a high genotypic virulence load.},
journal = {Journal of global antimicrobial resistance},
volume = {35},
number = {},
pages = {44-47},
doi = {10.1016/j.jgar.2023.08.014},
pmid = {37643688},
issn = {2213-7173},
mesh = {Humans ; *Escherichia coli ; Virulence/genetics ; *Escherichia coli Infections ; Phylogeny ; Saliva ; Virulence Factors/genetics ; Genotype ; Anti-Bacterial Agents/pharmacology ; },
abstract = {OBJECTIVES: Escherichia coli sequence type (ST) 127 is a pandemic lineage that belongs to the extraintestial pathogenic (ExPEC) family, mainly associated with urinary tract infections and bloodstream infections. Here, we report the complete genome of an E. coli ST 127 isolate which was identified in the saliva of a patient with treatment-resistant schizophrenia (TRS) exhibiting no signs of infection. The objective of this work is to determine the mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and virulence factors (VFs) that contribute to the pathogenicity of such ST127 isolates.<br><br>METHODS: Whole-genome sequencing (WGS) of isolate GABEEC10 was performed using DNABseq and Nanopore MinION platforms. Hybrid assembly of GABEEC10 was conducted with Unicycler v. 0.5.0. and annotated using PROKKA v1.14.5. Comparative genomics and phylogenomics were conducted using average nucleotide identity (ANI) and approximately-maximum-likelihood phylogenetic inference. ARGs, VFs, and serotyping were identified with Abricate v1.0.0 using CARD, vfdb, and EcOH databases, respectively.<br><br>RESULTS: Escherichia coli salivary isolate GABEEC10 was identified to belong to phylogroup B2 and have a serotype of O6 H31 with a total genome length of 4,940,530 bp and a mean guanine-cytosine (GC) content of 50.40 %. GABEEC10 was identified to have a highly virulent genotype with the presence of 84 VFs in addition to 44 ARGs, including an acquired blaTEM-30. The strain was identified to additionally carry four mobilisable plasmids.<br><br>CONCLUSION: We report the complete genome of E. coli GABAEEC10 that can be used for gaining insights into the pathogenicity, drug resistance mechanisms, and dissemination patterns of the emerging pandemic lineage ST 127.},
}
@article {pmid37640259,
year = {2023},
author = {Ikeda, T and Ogawa, T and Aono, T},
title = {Dethiobiotin uptake and utilization by bacteria possessing bioYB operon.},
journal = {Research in microbiology},
volume = {174},
number = {8},
pages = {104131},
doi = {10.1016/j.resmic.2023.104131},
pmid = {37640259},
issn = {1769-7123},
mesh = {*Biotin/metabolism ; Biological Transport ; *Operon ; Bacteria/genetics/metabolism ; },
abstract = {Biotin is an essential vitamin for all organisms. Some bacteria cannot synthesize biotin and live by acquiring biotin from the environment. Bacterial biotin transporters (BioY) are classified into three mechanistic types. The first forms the BioMNY complex with ATPase (BioM) and transmembrane protein (BioN). The second relies on a promiscuous energy coupling module. The third functions independently. One-third of bioY genes spread in bacteria cluster with bioM and bioN on the genomes, and the rest does not. Interestingly, some bacteria have the bioY gene clustering with bioB gene, which encodes biotin synthase, an enzyme that converts dethiobiotin to biotin, on their genome. This bioY-bioB cluster is observed even though these bacteria cannot synthesize biotin. Azorhizobium caulinodans ORS571, a rhizobium of tropical legume Sesbania rostrata, is one of such bacteria. In this study using this bacterium, we demonstrated that the BioY linked to BioB could transport not only biotin but also dethiobiotin, and the combination of BioY and BioB contributed to the growth of A. caulinodans ORS571 in a biotin-deficient but dethiobiotin-sufficient environment. We propose that such environment universally exists in the natural world, and the identification of such environment will be a new subject in the field of microbial ecology.},
}
@article {pmid37639796,
year = {2023},
author = {Mei, Z and Fu, Y and Wang, F and Xiang, L and Hu, F and Harindintwali, JD and Wang, M and Virta, M and Hashsham, SA and Jiang, X and Tiedje, JM},
title = {Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves.},
journal = {Journal of hazardous materials},
volume = {460},
number = {},
pages = {132388},
doi = {10.1016/j.jhazmat.2023.132388},
pmid = {37639796},
issn = {1873-3336},
mesh = {Humans ; *Sodium Chloride ; *Anti-Bacterial Agents/pharmacology ; Plant Leaves ; Soil ; Vegetables ; Magnetic Phenomena ; },
abstract = {Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.},
}
@article {pmid37637623,
year = {2023},
author = {Ratna, HVK and Jeyaraman, M and Yadav, S and Jeyaraman, N and Nallakumarasamy, A},
title = {Is Dysbiotic Gut the Cause of Low Back Pain?.},
journal = {Cureus},
volume = {15},
number = {7},
pages = {e42496},
pmid = {37637623},
issn = {2168-8184},
abstract = {Low back pain (LBP) is the foremost cause of disability that affects the day-to-day activities of millions of people worldwide. The putative trigger of LBP is linked to the gut microbiome (GM) and its dysbiotic environment. With the concept of GM, various disease pathogenesis has been revisited with plausible crosstalks and micromolecular mimicry. In the normal intervertebral disc (IVD), Firmicutes and Actinobacteria were found in abundance. The blood-disc barrier protects IVD from systemic infection, resists inflammation, and halts the immune surveillance of the inner aspects of IVD. The insights into microbial ecology will broaden our horizons in GM and IVD degeneration in LBP cases. However, an improved understanding of GM and back pain has to be explored in large-scale individuals with varied timescales to validate the above findings. The role of GM (diet, prebiotics, probiotics, and fecal microbiota transplantation) in pain modulation can form novel therapies in cases of LBP.},
}
@article {pmid37637134,
year = {2023},
author = {White, C and Antell, E and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, W and Alvarez-Cohen, L},
title = {Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1243410},
pmid = {37637134},
issn = {1664-302X},
abstract = {Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4[+]:NO2[-], where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4[+]:NO2[-] ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4[+]:NO2[-] ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4[+]:NO2[-] ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.},
}
@article {pmid37637113,
year = {2023},
author = {Huang, J and Li, J and Zhou, W and Cheng, Y and Li, J},
title = {Effect of different rice transplanting patterns on microbial community in water, sediment, and Procambarus clarkii intestine in rice-crayfish system.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1233815},
pmid = {37637113},
issn = {1664-302X},
abstract = {Although the microbial ecology of integrated rice-crayfish farming systems is receiving increasing attention with the expanding application area in China, the effects of rice transplanting patterns on the microbial community of water, sediment and Procambarus clarkii intestine in rice-crayfish system has yet to be determined. This study explored the microbial community present in water, sediment and intestine samples from three transplant patterns (rice crayfish with wide-narrow row transplanting, rice-crayfish with normal transplanting and pond-crayfish, abbreviated as RC-W, RC, and PC, respectively) using high-throughput sequencing. The results showed that the dominant microbial taxa from sediment, surrounding water, and intestine at phylum level were Proteobacteria, Chloroflexi, Cyanobacteria, Actinobacteria, Bacteroidetes. The patterns of rice transplanting had significant effects on microbial biodiversity and species composition in surrounding water. The OTUs community richness of water under RC group was significantly higher than that of PC group and RC-W group. The OTU relative abundance of top 10 operational taxonomic units had significantly different (p < 0.05) in the water samples from the three groups. The intestinal OTU community richness of Procambarus clarkii in the three groups was positively correlated with the community richness of water. The proximity between intestinal and water samples in PCA diagram indicated that their species composition was more similar. The results also showed that rice transplanting patterns can affect intestinal microbial biodiversity of Procambarus clarkii and the intestinal microbial biodiversity correlated with water bodies. Although the intestinal microbial diversity of crayfish in RC-W group was lower than that in RC group, the relative abundance of potential pathogenic bacteria, such as Vibrio, Aeromonas, in intestine of the crayfish in the RC-W group was significantly decreased under rice wide-narrow row transplanting model. Redundancy analysis revealed that environmental parameters, such as pH, DO, nitrate, which regulate the composition of microbial community structures. This study provides an understanding for microbial response to different rice transplanting pattern in rice-crayfish farming system.},
}
@article {pmid37635954,
year = {2024},
author = {Romans-Casas, M and Feliu-Paradeda, L and Tedesco, M and Hamelers, HVM and Bañeras, L and Balaguer, MD and Puig, S and Dessì, P},
title = {Selective butyric acid production from CO2 and its upgrade to butanol in microbial electrosynthesis cells.},
journal = {Environmental science and ecotechnology},
volume = {17},
number = {},
pages = {100303},
pmid = {37635954},
issn = {2666-4984},
abstract = {Microbial electrosynthesis (MES) is a promising carbon utilization technology, but the low-value products (i.e., acetate or methane) and the high electric power demand hinder its industrial adoption. In this study, electrically efficient MES cells with a low ohmic resistance of 15.7 mΩ m[2] were operated galvanostatically in fed-batch mode, alternating periods of high CO2 and H2 availability. This promoted acetic acid and ethanol production, ultimately triggering selective (78% on a carbon basis) butyric acid production via chain elongation. An average production rate of 14.5 g m[-2] d[-1] was obtained at an applied current of 1.0 or 1.5 mA cm[-2], being Megasphaera sp. the key chain elongating player. Inoculating a second cell with the catholyte containing the enriched community resulted in butyric acid production at the same rate as the previous cell, but the lag phase was reduced by 82%. Furthermore, interrupting the CO2 feeding and setting a constant pH2 of 1.7-1.8 atm in the cathode compartment triggered solventogenic butanol production at a pH below 4.8. The efficient cell design resulted in average cell voltages of 2.6-2.8 V and a remarkably low electric energy requirement of 34.6 kWhel kg[-1] of butyric acid produced, despite coulombic efficiencies being restricted to 45% due to the cross-over of O2 and H2 through the membrane. In conclusion, this study revealed the optimal operating conditions to achieve energy-efficient butyric acid production from CO2 and suggested a strategy to further upgrade it to valuable butanol.},
}
@article {pmid37635262,
year = {2023},
author = {Zhai, X and Castro-Mejía, JL and Gobbi, A and Aslampaloglou, A and Kot, W and Nielsen, DS and Deng, L},
title = {The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {193},
pmid = {37635262},
issn = {2049-2618},
mesh = {Humans ; *Bacteriophages/genetics ; DNA, Bacterial ; Feces ; Metagenome ; RNA ; },
abstract = {BACKGROUND: There is an increasing interest in investigating the human gut virome for its influence on the gut bacterial community and its putative influence on the trajectory towards health or disease. Most gut virome studies are based on sequencing of stored fecal samples. However, relatively little is known about how conventional storage buffers and storage conditions affect the infectivity of bacteriophages and influence the downstream metavirome sequencing.<br><br>RESULTS: We demonstrate that the infectivity and genome recovery rate of different spiked bacteriophages (T4, c2 and Phi X174) are variable and highly dependent on storage buffers. Regardless of the storage temperature and timespan, all tested phages immediately lost 100% (DNA/RNA Shield) or more than 90% (StayRNA and RNAlater) of their infectivity. Generally, in SM buffer at 4&#xa0;&#xb0;C phage infectivity was preserved for up to 30 days and phage DNA integrity was maintained for up to 100&#xa0;days. While in CANVAX, the most effective buffer, all spiked phage genomes were preserved for at least 100&#xa0;days. Prolonged storage time (500&#xa0;days) at -&#xa0;80&#xa0;&#xb0;C impacted viral diversity differently in the different buffers. Samples stored in CANVAX or DNA/RNA Shield buffer had the least shifts in metavirome composition, after prolonged storage, but they yielded more contigs classified as "uncharacterised". Moreover, in contrast to the SM buffer, these storage buffers yielded a higher fraction of bacterial DNA in metavirome-sequencing libraries. We demonstrated that the latter was due to inactivation of the DNases employed to remove extra-cellular DNA during virome extraction. The latter could be partly avoided by employing additional washing steps prior to virome extraction.<br><br>CONCLUSION: Fecal sample storage buffers and storage conditions (time and temperature) strongly influence bacteriophage infectivity and viral composition as determined by plaque assay and metavirome sequencing. The choice of buffer had a larger effect than storage temperature and storage time on the quality of the viral sequences and analyses. Based on these results, we recommend storage of fecal virome samples at in SM buffer at 4&#xa0;&#xb0;C for the isolation of viruses and at -&#xa0;80&#xa0;&#xb0;C for metagenomic applications if practically feasible (i.e., access to cold storage). For fecal samples stored in other buffers, samples should be cleared of these buffers before viral extraction and sequencing. Video Abstract.},
}
@article {pmid37635076,
year = {2024},
author = {Barman, D and Dkhar, MS},
title = {Purification and characterization of moderately thermostable raw-starch digesting α-amylase from endophytic Streptomyces mobaraensis DB13 associated with Costus speciosus.},
journal = {The Journal of general and applied microbiology},
volume = {69},
number = {6},
pages = {293-300},
doi = {10.2323/jgam.2023.08.001},
pmid = {37635076},
issn = {1349-8037},
mesh = {*alpha-Amylases/metabolism/chemistry/isolation &amp; purification ; *Streptomyces/enzymology ; *Enzyme Stability ; *Starch/metabolism ; Hydrogen-Ion Concentration ; *Molecular Weight ; Kinetics ; *Temperature ; Endophytes/enzymology/metabolism/genetics ; Substrate Specificity ; Bacterial Proteins/metabolism/chemistry/isolation &amp; purification/genetics ; Electrophoresis, Polyacrylamide Gel ; },
abstract = {Endophytic actinobacteria are known to produce various enzymes with potential industrial applications. Alpha-amylase is an important class of industrial enzyme with a multi-dimensional utility. The present experiment was designed to characterize a moderately thermostable α-amylase producing endophytic Streptomyces mobaraensis DB13 isolated from Costus speciosus (J. Koenig) Sm. The enzyme was purified using 60% ammonium sulphate precipitation, dialysis, and Sephadex G-100 column chromatography. Based on 12% SDS-PAGE, the molecular weight of the purified α-amylase was estimated to be 55 kDa. The maximum α-amylase activity was achieved at pH 7.0, 50°C and it retained 80% of its activity at both pH 7.0 and 8.0 after incubation for 2 h. The α-mylase activity is strongly enhanced by Ca[2+], Mg[2+], and inhibited by Ba[2+]. The activity remains stable in the presence of Tween-80, SDS, PMSF, and Triton X-100; however, β-mercaptoethanol, EDTA, and H2O2 reduced the activity. The kinetic parameters Km and Vmax values for this α-amylase were calculated as 2.53 mM and 29.42 U/mL respectively. The α-amylase had the ability to digest various raw starches at a concentration of 10 mg/mL at pH 7.0, 50°C, where maize and rice are the preferred substrates. The digestion starts after 4 h of incubation, which reaches maximum after 48 h of incubation. These results suggest that S. mobaraensis DB13 is a potential source of moderately thermostable α-amylase enzyme, that effciently hydrolyzes raw starch. It suggesting that this α-amylase is a promising candidate to be use for industrial purposes.},
}
@article {pmid37633274,
year = {2023},
author = {Pérez-Cobas, AE and Ginevra, C and Rusniok, C and Jarraud, S and Buchrieser, C},
title = {The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia.},
journal = {Cell reports. Medicine},
volume = {4},
number = {9},
pages = {101167},
pmid = {37633274},
issn = {2666-3791},
mesh = {Humans ; *Pneumonia, Bacterial/diagnosis ; Respiratory System ; *Coinfection ; Dysbiosis ; *Microbiota ; },
abstract = {Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co-infections. The RTM structure is defined by a "commensal" cluster associated with a healthy RTM and a "pathogen" enriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.},
}
@article {pmid37633148,
year = {2024},
author = {Guo, T and Wang, T and Chen, L and Zheng, B},
title = {Whole-grain highland barley premade biscuit prepared by hot-extrusion 3D printing: Printability and nutritional assessment.},
journal = {Food chemistry},
volume = {432},
number = {},
pages = {137226},
doi = {10.1016/j.foodchem.2023.137226},
pmid = {37633148},
issn = {1873-7072},
mesh = {*Nutrition Assessment ; *Hordeum ; Functional Food ; Corn Oil ; Printing, Three-Dimensional ; },
abstract = {In this study, to explore the possibility of applying whole-grain highland barley (HB) in functional food, HB premade biscuit was created by hot-extrusion 3D printing (HEP) for the first time, and its printability and nutritional functions were evaluated. The rheology results showed 20% (w/w) HB suspension with 9% corn oil addition had better printability due to the formation of a structure with higher elasticity and stronger resistance to deformation. Moreover, the obtained premade biscuit had lower predicted glycemic index (pGI) and starch digestibility. Meanwhile, in vivo experiment results showed it could affect the glycolipid metabolism, ameliorate the high fat diet (HFD)-induced metabolic disorders and maintain the balance of the gut microbial ecology. This could be attributed to the decrease in Firmicutes/Bacteroidetes ratio and the proliferation of propionate-producing probiotics, especially Veilonella, Weissella and Desulfovibrio. Overall, this study could provide basic data and innovative approaches to prepare nutritional whole-grain foods.},
}
@article {pmid37632540,
year = {2023},
author = {Seward, J and Bräuer, S and Beckett, P and Roy-Léveillée, P and Emilson, E and Watmough, S and Basiliko, N},
title = {Recovery of Smelter-Impacted Peat and Sphagnum Moss: a Microbial Perspective.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2894-2903},
pmid = {37632540},
issn = {1432-184X},
mesh = {Ecosystem ; *Sphagnopsida ; Soil/chemistry ; *Metals, Heavy ; Ontario ; },
abstract = {Peatlands store approximately one-half of terrestrial soil carbon and one-tenth of non-glacial freshwater. Some of these important ecosystems are located near heavy metal emitting smelters. To improve the understanding of smelter impacts and potential recovery after initial pollution controls in the 1970s (roughly 50 years of potential recovery), we sampled peatlands along a distance gradient of 134 km from a smelter in Sudbury, Ontario, Canada, an area with over a century of nickel (Ni) and copper (Cu) mining activity. This work is aimed at evaluating potential shifts in bacterial and archaeal community structures in Sphagnum moss and its underlying peat within smelter-impacted poor fens. In peat, total Ni and Cu concentrations were higher (0.062-0.067 and 0.110-0.208 mg/g, respectively) at sites close to the smelter and exponentially dropped with distance from the smelter. This exponential decrease in Ni concentrations was also observed in Sphagnum. 16S rDNA amplicon sequencing showed that peat and Sphagnum moss host distinct microbiomes with peat accommodating a more diverse community structure. The microbiomes of Sphagnum were dominated by Proteobacteria (62.5%), followed by Acidobacteria (11.9%), with no observable trends with distance from the smelter. Dominance of Acidobacteria (32.4%) and Proteobacteria (29.6%) in peat was reported across all sites. No drift in taxonomy was seen across the distance gradient or from the reference sites, suggesting a potential microbiome recovery toward that of the reference peatlands microbiomes after decades of pollution controls. These results advance the understanding of peat and Sphagnum moss microbiomes, as well as depict the sensitivities and the resilience of peatland ecosystems.},
}
@article {pmid37630470,
year = {2023},
author = {Won, S and Shin, C and Kang, HY},
title = {Potential Self-Attenuation of Arsenic by Indigenous Microorganisms in the Nakdong River.},
journal = {Microorganisms},
volume = {11},
number = {8},
pages = {},
pmid = {37630470},
issn = {2076-2607},
support = {NRF- 2020R1I1A3068585//National Research Foundation of Korea/ ; },
abstract = {The toxic element arsenic (As) has become the major focus of global research owing to its harmful effects on human health, resulting in the establishment of several guidelines to prevent As contamination. The widespread industrial use of As has led to its accumulation in the environment, increasing the necessity to develop effective remediation technologies. Among various treatments, such as chemical, physical, and biological treatments, used to remediate As-contaminated environments, biological methods are the most economical and eco-friendly. Microbial oxidation of arsenite (As(III)) to arsenate (As(V)) is a primary detoxification strategy for As remediation as it reduces As toxicity and alters its mobility in the environment. Here, we evaluated the self-detoxification potential of microcosms isolated from Nakdong River water by investigating the autotrophic and heterotrophic oxidation of As(III) to As(V). Experimental data revealed that As(III) was oxidized to As(V) during the autotrophic and heterotrophic growth of river water microcosms. However, the rate of oxidation was significantly higher under heterotrophic conditions because of the higher cell growth and density in an organic-matter-rich environment compared to that under autotrophic conditions without the addition of external organic matter. At an As(III) concentration > 5 mM, autotrophic As(III) oxidation remained incomplete, even after an extended incubation time. This inhibition can be attributed to the toxic effect of the high contaminant concentration on bacterial growth and the acidification of the growth medium with the oxidation of As(III) to As(V). Furthermore, we isolated representative pure cultures from both heterotrophic- and autotrophic-enriched cultures. The new isolates revealed new members of As(III)-oxidizing bacteria in the diversified bacterial community. This study highlights the natural process of As attenuation within river systems, showing that microcosms in river water can detoxify As under both organic-matter-rich and -deficient conditions. Additionally, we isolated the bacterial strains HTAs10 and ATAs5 from the microcosm which can be further investigated for potential use in As remediation systems. Our findings provide insights into the microbial ecology of As(III) oxidation in river ecosystems and provide a foundation for further investigations into the application of these bacteria for bioremediation.},
}
@article {pmid37624441,
year = {2023},
author = {Pinheiro Alves de Souza, Y and Schloter, M and Weisser, W and Schulz, S},
title = {Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2882-2893},
pmid = {37624441},
issn = {1432-184X},
mesh = {Biomass ; *Soil ; Soil Microbiology ; Bacteria/genetics ; Archaea/genetics ; *Microbiota ; },
abstract = {Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.},
}
@article {pmid37624156,
year = {2023},
author = {Cao, Y and Wang, R and Liu, Y and Li, Y and Jia, L and Yang, Q and Zeng, X and Li, X and Wang, Q and Wang, R and Riaz, L},
title = {Improved Calculations of Heavy Metal Toxicity Coefficients for Evaluating Potential Ecological Risk in Sediments Based on Seven Major Chinese Water Systems.},
journal = {Toxics},
volume = {11},
number = {8},
pages = {},
pmid = {37624156},
issn = {2305-6304},
support = {U1904205//Key Project of the National Natural Science Foundation of China-Henan Joint Fund/ ; NSFC 42277409//National Natural Science Foundation of China/ ; 22B180006//Educational Commission of the Henan Province of China/ ; 21A180014//Key Project of Natural Science of the Education Department of Henan Province of China/ ; 212102110322//Science and Technology Project of Henan Province/ ; },
abstract = {Several methods have been used to assess heavy metal contamination in sediments. However, an assessment that considers both composite heavy metal speciation and concentration is necessary to accurately study ecological risks. This study improved the potential ecological risk index method and calculated the toxicity coefficients of seven heavy metals: Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn). The newly calculated toxicity coefficients were validated by using previously published heavy metal distribution data of the Henan section of the Yellow River. The calculation procedure is based on the principle that the abundance of heavy metals in the environment and their bioavailable forms affect the toxicity of heavy metals. The toxicity coefficients for the seven heavy metals were calculated as follows: As = 10, Cd = 20, Cr = 5, Cu = 2, Ni = 5, Pb = 5, Zn = 1. Ecological risk assessment of the Henan section of the Yellow River using the improved toxicity coefficients revealed that the ecological risk of Cd and total heavy metals is higher than previous calculations, reaching the strength and moderate risk levels, respectively. The improved potential ecological risk index method is more sensitive to heavy metal pollution and thus provides a better indication of ecological risk. This is a necessary improvement to provide more accurate pollution assessments.},
}
@article {pmid37620628,
year = {2023},
author = {Chen, X and Li, Q and Chen, D and Zhao, L and Xiao, C},
title = {Restoration Measures of Fencing after Tilling Guided Succession of Grassland Soil Microbial Community Structure to Natural Grassland in the Sanjiangyuan Agro-pasture Ecotone of the Qinghai-Tibetan Plateau.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2870-2881},
pmid = {37620628},
issn = {1432-184X},
support = {2019QZKK040104//the Second Tibetan Plateau Scientific Expedition and Research (STEP) Program/ ; 2021FY100705//the Special Project on National Science and Technology Basic Resources Investigation of China/ ; 31770501//the National Natural Science Foundation of China/ ; },
mesh = {*Soil/chemistry ; Grassland ; Tibet ; Soil Microbiology ; Plants ; *Microbiota ; },
abstract = {In the fragile Sanjiangyuan (SJY) agro-pasture ecotone of the Qinghai-Tibetan Plateau (QTP), planting and fencing have been used to alleviate grassland degradation and to provide high-quality grass seeds for the implementation of the project of "grain for green". The soil microbe is the major driving factor in maintaining plant productivity and soil nutrient cycling. However, few studies have explored the effects of planting and fencing on soil microorganisms in the SJY agro-pasture ecotone. We explored the effects of tilling (TG) and fencing after tilling (FTG) on soil microbial communities to reveal the effects of restoration measures on soil microbes and to provide a reference in assessing and improving ecosystem structure. The results showed that restoration measures increased soil microbial species diversity and significantly changed their community structure. We found, the microbial composition was more complex under FTG, and its fungal variability was higher and more similar to that of natural grassland. Additionally, restoration measures resulted in fungal co-occurrence network was more edges, higher density, larger diameter and more positive interactions. This was due to the management of the vegetation-soil microenvironment by FTG inducing a differentiation of microbial community structure. In summary, the implementation of FTG could change the microenvironment in the SJY agro-pasture ecotone, so that variation in the structure of microbial community tended toward that of natural grassland, and increased the stability of microbial co-occurrence network, which was more obvious in the fungal community. HIGHLIGHTS: • Restoration measures have changed the vegetation characteristics and soil microenvironment. • Fencing after tilling (FTG) has brought the microenvironment closer to natural grassland. • FTG significantly increased microbial unique ASVs. The number of fungal unique ASVs was similar to that of natural grassland. • FTG resulted in changes in microbial community structure towards natural grasslands and increased the stability of the microbial co-occurrence network, which was more apparent in the fungal community.},
}
@article {pmid37620398,
year = {2023},
author = {De Micco, V and Amitrano, C and Mastroleo, F and Aronne, G and Battistelli, A and Carnero-Diaz, E and De Pascale, S and Detrell, G and Dussap, CG and Ganigué, R and Jakobsen, &#xd8;M and Poulet, L and Van Houdt, R and Verseux, C and Vlaeminck, SE and Willaert, R and Leys, N},
title = {Plant and microbial science and technology as cornerstones to Bioregenerative Life Support Systems in space.},
journal = {NPJ microgravity},
volume = {9},
number = {1},
pages = {69},
pmid = {37620398},
issn = {2373-8065},
abstract = {Long-term human space exploration missions require environmental control and closed Life Support Systems (LSS) capable of producing and recycling resources, thus fulfilling all the essential metabolic needs for human survival in harsh space environments, both during travel and on orbital/planetary stations. This will become increasingly necessary as missions reach farther away from Earth, thereby limiting the technical and economic feasibility of resupplying resources from Earth. Further incorporation of biological elements into state-of-the-art (mostly abiotic) LSS, leading to bioregenerative LSS (BLSS), is needed for additional resource recovery, food production, and waste treatment solutions, and to enable more self-sustainable missions to the Moon and Mars. There is a whole suite of functions crucial to sustain human presence in Low Earth Orbit (LEO) and successful settlement on Moon or Mars such as environmental control, air regeneration, waste management, water supply, food production, cabin/habitat pressurization, radiation protection, energy supply, and means for transportation, communication, and recreation. In this paper, we focus on air, water and food production, and waste management, and address some aspects of radiation protection and recreation. We briefly discuss existing knowledge, highlight open gaps, and propose possible future experiments in the short-, medium-, and long-term to achieve the targets of crewed space exploration also leading to possible benefits on Earth.},
}
@article {pmid37619629,
year = {2023},
author = {Wang, SH and Yuan, SW and Che, FF and Wan, X and Wang, YF and Yang, DH and Yang, HJ and Zhu, D and Chen, P},
title = {Strong bacterial stochasticity and fast fungal turnover in Taihu Lake sediments, China.},
journal = {Environmental research},
volume = {237},
number = {Pt 2},
pages = {116954},
doi = {10.1016/j.envres.2023.116954},
pmid = {37619629},
issn = {1096-0953},
abstract = {Understanding the assembly and turnover of microbial communities is crucial for gaining insights into the diversity and functioning of lake ecosystems, a fundamental and central issue in microbial ecology. The ecosystem of Taihu Lake has been significantly jeopardized due to urbanization and industrialization. In this study, we examined the diversity, assembly, and turnover of bacterial and fungal communities in Taihu Lake sediment. The results revealed strong bacterial stochasticity and fast fungal turnover in the sediment. Significant heterogeneity was observed among all sediment samples in terms of environmental factors, especially ORP, TOC, and TN, as well as microbial community composition and alpha diversity. For instance, the fungal richness index exhibited an approximate 3-fold variation. Among the environmental factors, TOC, TN, and pH had a more pronounced influence on the bacterial community composition compared to the fungal community composition. Interestingly, species replacement played a dominant role in microbial beta diversity, with fungi exhibiting a stronger pattern. In contrast, stochastic processes governed the community assembly of both bacteria and fungi, but were more pronounced for bacteria (R[2] = 0.7 vs. 0.5). These findings deepen the understanding of microbial assembly and turnover in sediments under environmental stress and provide essential insights for maintaining the multifunctionality of lake ecosystems.},
}
@article {pmid37615431,
year = {2023},
author = {Armour, CR and Sovacool, KL and Close, WL and Topçuoğlu, BD and Wiens, J and Schloss, PD},
title = {Machine learning classification by fitting amplicon sequences to existing OTUs.},
journal = {mSphere},
volume = {8},
number = {5},
pages = {e0033623},
pmid = {37615431},
issn = {2379-5042},
support = {R01 CA215574/CA/NCI NIH HHS/United States ; R01CA215574/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Algorithms ; *Microbiota/genetics ; },
abstract = {The ability to use 16S rRNA gene sequence data to train machine learning classification models offers the opportunity to diagnose patients based on the composition of their microbiome. In some applications, the taxonomic resolution that provides the best models may require the use of de novo operational taxonomic units (OTUs) whose composition changes when new data are added. We previously developed a new reference-based approach, OptiFit, that fits new sequence data to existing de novo OTUs without changing the composition of the original OTUs. While OptiFit produces OTUs that are as high quality as de novo OTUs, it is unclear whether this method for fitting new sequence data into existing OTUs will impact the performance of classification models relative to models trained and tested only using de novo OTUs. We used OptiFit to cluster sequences into existing OTUs and evaluated model performance in classifying a dataset containing samples from patients with and without colonic screen relevant neoplasia (SRN). We compared the performance of this model to standard methods including de novo and database-reference-based clustering. We found that using OptiFit performed as well or better in classifying SRNs. OptiFit can streamline the process of classifying new samples by avoiding the need to retrain models using reclustered sequences. IMPORTANCE There is great potential for using microbiome data to aid in diagnosis. A challenge with de novo operational taxonomic unit (OTU)-based classification models is that 16S rRNA gene sequences are often assigned to OTUs based on similarity to other sequences in the dataset. If data are generated from new patients, the old and new sequences must be reclustered to OTUs and the classification model retrained. Yet there is a desire to have a single, validated model that can be widely deployed. To overcome this obstacle, we applied the OptiFit clustering algorithm to fit new sequence data to existing OTUs allowing for reuse of the model. A random forest model implemented using OptiFit performed as well as the traditional reassign and retrain approach. This result shows that it is possible to train and apply machine learning models based on OTU relative abundance data that do not require retraining or the use of a reference database.},
}
@article {pmid37614461,
year = {2023},
author = {Kandeel, SA and Megahed, AA},
title = {Editorial: Infectious diseases, microbial ecology, and antimicrobial resistance dynamics in food animals.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1266980},
pmid = {37614461},
issn = {2297-1769},
}
@article {pmid37610498,
year = {2023},
author = {Wei, N and Tan, J},
title = {Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2858-2868},
pmid = {37610498},
issn = {1432-184X},
support = {030869//Holden Arboretum/ ; LEQSF(2023-26)-RD-A-14//Louisiana Board of Regents/ ; 10635//Gordon and Betty Moore Foundation/ ; },
mesh = {*Microbiota/genetics ; Bacteria/genetics ; *Araceae/microbiology ; },
abstract = {To understand how microbiota influence plant populations in nature, it is important to examine the biogeographic distribution of plant-associated microbiomes and the underlying mechanisms. However, we currently lack a fundamental understanding of the biogeography of plant microbiomes across populations and the environmental and host genetic factors that shape their distribution. Leveraging the broad distribution and extensive genetic variation in duckweeds (the Lemna species complex), we identified key factors that governed plant microbiome diversity and compositional variation geographically. In line with the microbial biogeography of free-living microbiomes, we observed higher bacterial richness in temperate regions relative to lower latitudes in duckweed microbiomes (with 10% higher in temperate populations). Our analyses revealed that higher temperature and sodium concentration in aquatic environments showed a negative impact on duckweed bacterial richness, whereas temperature, precipitation, pH, and concentrations of phosphorus and calcium, along with duckweed genetic variation, influenced the biogeographic variation of duckweed bacterial community composition. Analyses of plant microbiome assembly processes further revealed that niche-based selection played an important role (26%) in driving the biogeographic variation of duckweed bacterial communities, alongside the contributions of dispersal limitation (33%) and drift (39%). These findings add significantly to our understanding of host-associated microbial biogeography and provide important insights for predicting plant microbiome vulnerability and resilience under changing climates and intensifying anthropogenic activities.},
}
@article {pmid37608162,
year = {2023},
author = {Fecchio, A and Bell, JA and Williams, EJ and Dispoto, JH and Weckstein, JD and de Angeli Dutra, D},
title = {Co-infection with Leucocytozoon and Other Haemosporidian Parasites Increases with Latitude and Altitude in New World Bird Communities.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2838-2846},
pmid = {37608162},
issn = {1432-184X},
support = {DEB-1503804//National Science Foundation/ ; },
mesh = {Animals ; *Parasites ; *Coinfection/veterinary ; Bayes Theorem ; Altitude ; *Bird Diseases/epidemiology/parasitology ; Birds ; *Haemosporida ; Prevalence ; },
abstract = {Establishing how environmental gradients and host ecology drive spatial variation in infection rates and diversity of pathogenic organisms is one of the central goals in disease ecology. Here, we identified the predictors of concomitant infection and lineage richness of blood parasites in New Word bird communities. Our multi-level Bayesian models revealed that higher latitudes and elevations played a determinant role in increasing the probability of a bird being co-infected with Leucocytozoon and other haemosporidian parasites. The heterogeneity in both single and co-infection rates was similarly driven by host attributes and temperature, with higher probabilities of infection in heavier migratory host species and at cooler localities. Latitude, elevation, host body mass, migratory behavior, and climate were also predictors of Leucocytozoon lineage richness across the New World avian communities, with decreasing parasite richness at higher elevations, rainy and warmer localities, and in heavier and resident host species. Increased parasite richness was found farther from the equator, confirming a reverse Latitudinal Diversity Gradient pattern for this parasite group. The increased rates of Leucocytozoon co-infection and lineage richness with increased latitude are in opposition with the pervasive assumption that pathogen infection rates and diversity are higher in tropical host communities.},
}
@article {pmid37607924,
year = {2023},
author = {Li, X and Chen, D and Carrión, VJ and Revillini, D and Yin, S and Dong, Y and Zhang, T and Wang, X and Delgado-Baquerizo, M},
title = {Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5090},
pmid = {37607924},
issn = {2041-1723},
mesh = {*Fusariosis ; *Microbiota ; *Fusarium ; Metagenome ; Hydrogen-Ion Concentration ; },
abstract = {Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.},
}
@article {pmid37607131,
year = {2023},
author = {Klapper, FA and Kiel, C and Bellstedt, P and Vyverman, W and Pohnert, G},
title = {Structure Elucidation of the First Sex-Inducing Pheromone of a Diatom.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {62},
number = {43},
pages = {e202307165},
doi = {10.1002/anie.202307165},
pmid = {37607131},
issn = {1521-3773},
support = {FWO G001521N, BOF/GOA No. 01G01715//European Marine Biological Resource Centre Belgium/ ; Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Diatoms are abundant unicellular microalgae, responsible for ≈20 % of global photosynthetic CO2 fixation. Nevertheless, we know little about fundamental aspects of their biology, such as their sexual reproduction. Pheromone-mediated chemical communication is crucial for successful mating. An attraction pheromone was identified in the diatom Seminavis robusta, but metabolites priming cells for sex and synchronizing search and mating behavior remained elusive. These sex-inducing pheromones (SIP) induce cell cycle arrest and trigger the production of the attraction pheromone. Here we describe the challenging structure elucidation of an S. robusta SIP. Guided by metabolomics, a candidate metabolite was identified and elucidated by labeling experiments, NMR, ESI MS[n] analyses, and chemical transformations. The use of negative ion mode MS was essential to decipher the unprecedented hydroxyproline and β-sulfated aspartate-containing cyclic heptapeptide that acts in femtomolar concentrations.},
}
@article {pmid37606945,
year = {2023},
author = {Ricks, KD and Ricks, NJ and Yannarell, AC},
title = {Patterns of Plant Salinity Adaptation Depend on Interactions with Soil Microbes.},
journal = {The American naturalist},
volume = {202},
number = {3},
pages = {276-287},
doi = {10.1086/725393},
pmid = {37606945},
issn = {1537-5323},
mesh = {Humans ; *Salinity ; Acclimatization ; *Infertility ; Phenotype ; Soil ; },
abstract = {AbstractAs plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum, collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution.},
}
@article {pmid37606696,
year = {2023},
author = {Theodorescu, M and Bucur, R and Bulzu, PA and Faur, L and Levei, EA and Mirea, IC and Cadar, O and Ferreira, RL and Souza-Silva, M and Moldovan, OT},
title = {Environmental Drivers of the Moonmilk Microbiome Diversity in Some Temperate and Tropical Caves.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2847-2857},
pmid = {37606696},
issn = {1432-184X},
mesh = {*Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota ; Proteobacteria/genetics ; },
abstract = {Moonmilk is a cave deposit that was used for medical and cosmetic purposes and has lately raised interest for its antimicrobial potential. We studied five moonmilk samples from four caves with different microclimatic conditions, two temperate in north-western and northern Romania (Ferice, Fața Apei, and Izvorul Tăușoarelor caves) and one tropical in Minas Gerais, Brazil (Nestor Cave). The physicochemical and mineralogical analyses confirmed the presence of calcite and dolomite as the main phase in the moonmilk. A 16S rRNA gene-based metabarcoding approach showed the most abundant bacteria phyla Proteobacteria, GAL15, Actinobacteriota, and Acidobacteriota. The investigated caves differed in the dominant orders of bacteria, with the highest distance between the Romanian and Nestor Cave samples. Climate and, implicitly, the soil microbiome can be responsible for some differences we found between all the samples. However, other factors can be involved in shaping the moonmilk microbiome, as differences were found between samples in the same cave (Ferice). In our five moonmilk samples, 1 phylum, 70 orders (~ 36%), and 252 genera (~ 47%) were unclassified, which hints at the great potential of cave microorganisms for future uses.},
}
@article {pmid37604894,
year = {2023},
author = {Utzeri, VJ and Cilli, E and Fontani, F and Zoboli, D and Orsini, M and Ribani, A and Latorre, A and Lissovsky, AA and Pillola, GL and Bovo, S and Gruppioni, G and Luiselli, D and Fontanesi, L},
title = {Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13635},
pmid = {37604894},
issn = {2045-2322},
mesh = {Animals ; *DNA, Ancient ; Phylogeny ; *Lagomorpha ; Biological Evolution ; Archaeology ; },
abstract = {Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.},
}
@article {pmid37604501,
year = {2023},
author = {Kuzyk, SB and Messner, K and Plouffe, J and Ma, X and Wiens, K and Yurkov, V},
title = {Diverse aerobic anoxygenic phototrophs synthesize bacteriochlorophyll in oligotrophic rather than copiotrophic conditions, suggesting ecological niche.},
journal = {Environmental microbiology},
volume = {25},
number = {11},
pages = {2653-2665},
doi = {10.1111/1462-2920.16482},
pmid = {37604501},
issn = {1462-2920},
mesh = {Humans ; *Bacteriochlorophylls ; Phylogeny ; Bacteria, Aerobic/genetics ; Ecosystem ; Photosynthesis ; *Alphaproteobacteria ; },
abstract = {While investigating aerobic anoxygenic phototrophs (AAP) from Lake Winnipeg's bacterial community, over 500 isolates were obtained. Relatives of 20 different species were examined simultaneously, identifying conditions for optimal growth or pigment production to determine features that may unify this group of phototrophs. All were distributed among assorted α-Proteobacterial families including Erythrobacteraceae, Sphingomonadaceae, Sphingosinicellaceae, Acetobacteraceae, Methylobacteriaceae, and Rhodobacteraceae. Major phenotypic characteristics matched phylogenetic association, including pigmentation, morphology, metal transformations, tolerances, lipid configurations, and enzyme activities, which distinctly separated each taxonomic family. While varying pH and temperature had a limited independent impact on pigment production, bacteriochlorophyll synthesis was distinctly promoted under low nutrient conditions, whereas copiotrophy repressed its production but enhanced carotenoid yield. New AAP diversity was also reported by revealing strains related to non-phototrophic Rubellimicrobium and Sphingorhabdus, as well as spread throughout Roseomonas, Sphingomonas, and Methylobacterium/Methylorubrum, which previously only had a few known photosynthetic members. This study exemplified the overwhelming diversity of AAP in a single aquatic environment, confirming cultivation continues to be of importance in microbial ecology to discover functionality in both new and previously reported cohorts of bacteria as specific laboratory conditions were required to promote aerobic bacteriochlorophyll production.},
}
@article {pmid37603734,
year = {2023},
author = {Lee, H and Bloxham, B and Gore, J},
title = {Resource competition can explain simplicity in microbial community assembly.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {35},
pages = {e2212113120},
pmid = {37603734},
issn = {1091-6490},
mesh = {*Ecology ; Laboratories ; *Microbiota ; },
abstract = {Predicting the composition and diversity of communities is a central goal in ecology. While community assembly is considered hard to predict, laboratory microcosms often follow a simple assembly rule based on the outcome of pairwise competitions. This assembly rule predicts that a species that is excluded by another species in pairwise competition cannot survive in a multispecies community with that species. Despite the empirical success of this bottom-up prediction, its mechanistic origin has remained elusive. In this study, we elucidate how this simple pattern in community assembly can emerge from resource competition. Our geometric analysis of a consumer-resource model shows that trio community assembly is always predictable from pairwise outcomes when one species grows faster than another species on every resource. We also identify all possible trio assembly outcomes under three resources and find that only two outcomes violate the assembly rule. Simulations demonstrate that pairwise competitions accurately predict trio assembly with up to 100 resources and the assembly of larger communities containing up to twelve species. We then further demonstrate accurate quantitative prediction of community composition using the harmonic mean of pairwise fractions. Finally, we show that cross-feeding between species does not decrease assembly rule prediction accuracy. Our findings highlight that simple community assembly can emerge even in ecosystems with complex underlying dynamics.},
}
@article {pmid37601377,
year = {2023},
author = {Flocco, CG and Methner, A and Burkart, F and Geppert, A and Overmann, J},
title = {Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1197837},
pmid = {37601377},
issn = {1664-302X},
abstract = {Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.},
}
@article {pmid37597041,
year = {2023},
author = {Cleary, DFR and de Voogd, NJ and Stuij, TM and Swierts, T and Oliveira, V and Polónia, ARM and Louvado, A and Gomes, NCM and Coelho, FJRC},
title = {A Study of Sponge Symbionts from Different Light Habitats.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2819-2837},
pmid = {37597041},
issn = {1432-184X},
mesh = {Animals ; Biodiversity ; Phylogeny ; Bacteria/genetics ; Seawater/microbiology ; *Microbiota ; Water ; *Porifera ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.},
}
@article {pmid37594520,
year = {2023},
author = {Martínez, LT and Marchant, M and Díaz, RTA and Arrojo, M&#xc1; and Muñoz, P},
title = {Benthic Foraminifera as Pollution Biomarkers: a Morphological Approach.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2802-2818},
pmid = {37594520},
issn = {1432-184X},
support = {1130511//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 170124//Fondo de Equipamiento Cient&#xed;fico y Tecnol&#xf3;gico/ ; },
mesh = {*Water Pollutants, Chemical/analysis ; Geologic Sediments/chemistry ; *Foraminifera/chemistry ; Environmental Monitoring/methods ; *Metals, Heavy/toxicity/analysis ; Biomarkers ; },
abstract = {Coastal areas are often intervened by anthropic activities, which increase the contamination of toxic agents such as heavy metals. This causes adverse morphological effects on benthic microorganisms, such as foraminifera. This group is one of the most susceptible to environmental deterioration, so they can be used as pollution biomarkers by identifying shell abnormalities. Therefore, 28 sediment samples from northern Chile were analyzed, calculating the Abnormality Index-FAI and its spatio-temporal distributions in benthic foraminifera, as well as the minimum and maximum abnormality percentages and their relationship with heavy metal concentrations, using a generalized non-linear model and a principal component analysis. The results indicated a proportion of abnormal shells within the ranges described for polluted areas conditions, revealing environmental stress conditions. This reflected a change in the environmental conditions in the most recent sediments of the bay. The highest FAI values were observed to the southwest of the bay, caused by the local current system. The species Bolivina seminuda, Buliminella elegantissima, and Epistominella exigua presented a greater number of deformities, allowing them to be used as contamination biomarkers. A significant correlation was found between Ti, Mn, Ni, Va, and Ba with decreased chamber sizes, wrong coiling, scars, and number of abnormality types. This suggests the effect of the particular geochemical conditions of the area on the heavy metals that cause toxic effects on foraminifera. These analyses are an efficient tool for identifying the effects of environmental stress before they occur in higher organisms, mitigating the environmental impact on marine biodiversity.},
}
@article {pmid37594170,
year = {2023},
author = {Hambleton, EA},
title = {How corals get their nutrients.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37594170},
issn = {2050-084X},
mesh = {Animals ; *Nutrients ; *Anthozoa ; Cell Wall ; },
abstract = {Algae living inside corals provide sugars for their host by digesting their own cell walls.},
}
@article {pmid37590550,
year = {2022},
author = {de Almeida, OGG and De Martinis, ECP},
title = {Multitargeted Analyses are Instrumental for Microbial Ecology Studies.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {187},
pages = {},
doi = {10.3791/64789},
pmid = {37590550},
issn = {1940-087X},
}
@article {pmid37586176,
year = {2023},
author = {Bai, X and Dinkla, IJT and Muyzer, G},
title = {Shedding light on the total and active core microbiomes in slow sand filters for drinking water production.},
journal = {Water research},
volume = {243},
number = {},
pages = {120404},
doi = {10.1016/j.watres.2023.120404},
pmid = {37586176},
issn = {1879-2448},
mesh = {Humans ; *Drinking Water ; Filtration/methods ; *Water Purification/methods ; *Microbiota ; Bacteria/genetics ; Silicon Dioxide/chemistry ; },
abstract = {Slow sand filters (SSF) are widely used in the production of drinking water as a last barrier in the removal of pathogens. This removal mainly depends on the 'Schmutzdecke', a biofilm-like layer on the surface of the sand bed. Most previous studies focused on the total community as revealed by DNA analysis rather than on the active community, which may lead to an incorrect understanding of the SSF ecology. In the current study, we determined and compared the DNA- (total) and RNA-displayed (active) communities in the Schmutzdecke layer from 10 full-scale slow sand filters and further explored the SSF core microbiome in terms of both presence (DNA) and activity (RNA). Discrepancies were observed between the total and the active community, although there was a consistent grouping in the PCoA analysis. The DNA-displayed community may be somewhat inflated, while the RNA-displayed community could reveal low abundance (or rare) but active community members. The overall results imply that both DNA (presence) and RNA (activity) data should be considered to prevent the underestimation of organisms of functional importance but lower abundance. Microbial communities of studied mature Schmutzdecke were shaped by the influent water. Nevertheless, a core microbiome was shared by the mature Schmutzdeckes from independent filters, representing the dominant and consistent microbial community composition in slow sand filters. In the DNA samples, a total of 33 VSC families ('very strict core', with a relative abundance >0.1% and 100% prevalence) were observed across all filters. Among the RNA samples, there were 18 VSC families, including 16 families that overlapped with the DNA VSC families and 2 unique RNA VSC families. The core microbial community structure was influenced by the operational parameters, including the Schmutzdecke age and the sand size, and was less influenced by water flow. In addition, indicator organisms ('biomarkers') for the Schmutzdecke age, which show the longest duration that SSF can maintain a good operation, were observed in our study. The abundant presence of bacteria belonging to bacteriap25 and Caldilineaceae was associated with older Schmutzdeckes, revealing longer periods of stable operation performance of the filter, while the high abundance of bacteria belonging to Bdellovibrionaceae and Bryobacteraceae related to short periods of stable operation performance.},
}
@article {pmid37579703,
year = {2023},
author = {Li, Z and Wang, J and Fan, J and Yue, H and Zhang, X},
title = {Marine toxin domoic acid alters protistan community structure and assembly process in sediments.},
journal = {Marine environmental research},
volume = {191},
number = {},
pages = {106131},
doi = {10.1016/j.marenvres.2023.106131},
pmid = {37579703},
issn = {1879-0291},
mesh = {*Marine Toxins ; Kainic Acid/toxicity ; Eukaryota ; *Microbiota ; },
abstract = {Domoic acid (DA)-producing algal blooms have been the issue of worldwide concerns in recent decades, but there has never been any attempt to investigate the effects of DA on microbial ecology in marine environments. Protists are considered to be key regulators of microbial activity, community structure and evolution, we therefore explore the effect of DA on the ecology of protists via metagenome in this work. The results indicate that trace amounts of DA can act as a stressor to alter alpha and beta diversity of protistan community. Among trophic functional groups, consumers and phototrophs are negative responders of DA, implying DA is potentially capable of functional-level effects in the ocean. Moreover, microecological theory reveals that induction of DA increases the role of deterministic processes in microbial community assembly, thus altering the biotic relationships and successional processes in symbiotic patterns. Finally, we demonstrate that the mechanism by which DA shapes protistan ecological network is by acting on phototrophs, which triggers cascading effects in networks and eventually leading to shifts in ecological succession of protists. Overall, our results present the first perspective regarding the effects of DA on marine microbial ecology, which will supplement timely information on the ecological impacts of DA in the ocean.},
}
@article {pmid37573698,
year = {2023},
author = {Song, Y and Zhang, S and Lu, J and Duan, R and Chen, H and Ma, Y and Si, T and Luo, M},
title = {Reed restoration decreased nutrients in wetlands with dredged sediments: Microbial community assembly and function in rhizosphere.},
journal = {Journal of environmental management},
volume = {344},
number = {},
pages = {118700},
doi = {10.1016/j.jenvman.2023.118700},
pmid = {37573698},
issn = {1095-8630},
mesh = {*Rhizosphere ; Wetlands ; Bacteria ; Archaea ; *Microbiota ; Plants ; Nutrients ; Geologic Sediments/chemistry ; },
abstract = {Using dredged sediments as substrate for aquatic plants is a low-cost and ecological friendly way for in situ aquatic ecological restoration. However, the limited information available about how aquatic plant restoration affects the microbial ecology and nutrients in dredged sediments. In this study, nutrient contents, enzyme activities, and bacterial and archaeal communities in vertical sediment layers were determined in bulk and reed zones of wetlands constructed with dredged sediments in west Lake Taihu for three years. Reed restoration significantly decreased total nitrogen, total phosphorus, and organic carbon contents and increased alkaline phosphatase, urease, and sucrase activities compared to bulk area. Bacterial communities in vertical sediment layers had higher similarity in reed zone in comparison to bulk zone, and many bacterial and archaeal genera were only detected in reed rhizosphere zones. Compared with the bulk zone, the reed restoration area has a higher abundance of phylum Actinobacteriota, Hydrothermarchaeota, and class α-proteobacteria. The assembly process of the bacterial and archaeal communities was primarily shaped by dispersal limitation (67.03% and 32.97%, respectively), and stochastic processes were enhanced in the reed recovery area. Network analysis show that there were more complicated interactions among bacteria and archaea and low-abundance taxa were crucial in maintaining the microbial community stability in rhizosphere of reed zone. PICRUST2 analysis demonstrate that reed restoration promotes metabolic pathways related to C and N cycle in dredged sediments. These data highlight that using dredged sediments as substrates for aquatic plants can transform waste material into a valuable resource, enhancing the benefits to the environment.},
}
@article {pmid37567875,
year = {2023},
author = {Molbert, N and Ghanavi, HR and Johansson, T and Mostadius, M and Hansson, MC},
title = {An evaluation of DNA extraction methods on historical and roadkill mammalian specimen.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13080},
pmid = {37567875},
issn = {2045-2322},
mesh = {Animals ; *Chloroform ; *DNA/genetics ; Phenol ; Phenols ; Mammals/genetics ; Silicon Dioxide ; },
abstract = {Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.},
}
@article {pmid37567306,
year = {2023},
author = {Schroll, M and Liu, L and Einzmann, T and Keppler, F and Grossart, HP},
title = {Methane accumulation and its potential precursor compounds in the oxic surface water layer of two contrasting stratified lakes.},
journal = {The Science of the total environment},
volume = {903},
number = {},
pages = {166205},
doi = {10.1016/j.scitotenv.2023.166205},
pmid = {37567306},
issn = {1879-1026},
abstract = {Methane (CH4) supersaturation in oxygenated waters is a widespread phenomenon despite the traditional perception of strict anoxic methanogenesis. This notion has recently been challenged by successive findings of processes and mechanisms that produce CH4 in oxic environments. While some of the processes contributing to the vertical accumulation of CH4 in the oxygenated upper water layers of freshwater lakes have been identified, temporal variations as well as drivers are still poorly understood. In this study, we investigated the accumulation of CH4 in oxic water layers of two contrasting lakes in Germany: Lake Willersinnweiher (shallow, monomictic, eutrophic) and Lake Stechlin (deep, dimictic, eutrophic) from 2019 to 2020. The dynamics of isotopic values of CH4 and the role of potential precursor compounds of oxic CH4 production were explored. During the study period, persistent strong CH4 supersaturation (relative to air) was observed in the surface waters, mostly concentrated around the thermocline. The magnitude of vertical CH4 accumulation strongly varied over season and was generally more pronounced in shallow Lake Willersinnweiher. In both lakes, increases in CH4 concentrations from the surface to the thermocline mostly coincided with an enrichment in [13]C-CH4 and [2]H-CH4, indicating a complex interaction of multiple processes such as CH4 oxidation, CH4 transport from littoral sediments and oxic CH4 production, sustaining and controlling this CH4 supersaturation. Furthermore, incubation experiments with [13]C- and [2]H-labelled methylated P-, N- and C- compounds clearly showed that methylphosphonate, methylamine and methionine acted as potent precursors of accumulating CH4 and at least partly sustained CH4 supersaturation. This highlights the need to better understand the mechanisms underlying CH4 accumulation by focusing on production and transport pathways of CH4 and its precursor compounds, e.g., produced via phytoplankton. Such knowledge forms the foundation to better predict aquatic CH4 dynamics and its subsequent rates of emission to the atmosphere.},
}
@article {pmid37564072,
year = {2023},
author = {Michoud, G and Kohler, TJ and Ezzat, L and Peter, H and Nattabi, JK and Nalwanga, R and Pramateftaki, P and Styllas, M and Tolosano, M and De Staercke, V and Schön, M and Marasco, R and Daffonchio, D and Bourquin, M and Busi, SB and Battin, TJ},
title = {The dark side of the moon: first insights into the microbiome structure and function of one of the last glacier-fed streams in Africa.},
journal = {Royal Society open science},
volume = {10},
number = {8},
pages = {230329},
pmid = {37564072},
issn = {2054-5703},
abstract = {The glaciers on Africa's 'Mountains of the Moon' (Rwenzori National Park, Uganda) are predicted to disappear within the next decades owing to climate change. Consequently, the glacier-fed streams (GFSs) that drain them will vanish, along with their resident microbial communities. Despite the relevance of microbial communities for performing ecosystem processes in equatorial GFSs, their ecology remains understudied. Here, we show that the benthic microbiome from the Mt. Stanley GFS is distinct at several levels from other GFSs. Specifically, several novel taxa were present, and usually common groups such as Chrysophytes and Polaromonas exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while greater than 80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS, and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.},
}
@article {pmid37563275,
year = {2023},
author = {Epp Schmidt, D and Maul, JE and Yarwood, SA},
title = {Quantitative Amplicon Sequencing Is Necessary to Identify Differential Taxa and Correlated Taxa Where Population Sizes Differ.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2790-2801},
pmid = {37563275},
issn = {1432-184X},
support = {1828910//NSF/ ; },
mesh = {*Bacteria/genetics ; Population Density ; *Microbiota/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {High-throughput, multiplexed-amplicon sequencing has become a core tool for understanding environmental microbiomes. As researchers have widely adopted sequencing, many open-source analysis pipelines have been developed to compare microbiomes using compositional analysis frameworks. However, there is increasing evidence that compositional analyses do not provide the information necessary to accurately interpret many community assembly processes. This is especially true when there are large gradients that drive distinct community assembly processes. Recently, sequencing has been combined with Q-PCR (among other sources of total quantitation) to generate "Quantitative Sequencing" (QSeq) data. QSeq more accurately estimates the true abundance of taxa, is a more reliable basis for inferring correlation, and, ultimately, can be more reliably related to environmental data to infer community assembly processes. In this paper, we use a combination of published data sets, synthesis, and empirical modeling to offer guidance for which contexts QSeq is advantageous. As little as 5% variation in total abundance among experimental groups resulted in more accurate inference by QSeq than compositional methods. Compositional methods for differential abundance and correlation unreliably detected patterns in abundance and covariance when there was greater than 20% variation in total abundance among experimental groups. Whether QSeq performs better for beta diversity analysis depends on the question being asked, and the analytic strategy (e.g., what distance metric is being used); for many questions and methods, QSeq and compositional analysis are equivalent for beta diversity analysis. QSeq is especially useful for taxon-specific analysis; QSeq transformation and analysis should be the default for answering taxon-specific questions of amplicon sequence data. Publicly available bioinformatics pipelines should incorporate support for QSeq transformation and analysis.},
}
@article {pmid37555066,
year = {2023},
author = {Mashamaite, L and Lebre, PH and Varliero, G and Maphosa, S and Ortiz, M and Hogg, ID and Cowan, DA},
title = {Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1203216},
pmid = {37555066},
issn = {1664-302X},
abstract = {INTRODUCTION: The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica.<br><br>METHODS: We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons.<br><br>RESULTS AND DISCUSSION: Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.},
}
@article {pmid37552473,
year = {2023},
author = {Jiang, Z and Liu, S and Zhang, D and Sha, Z},
title = {The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2781-2789},
pmid = {37552473},
issn = {1432-184X},
mesh = {*Nitrates ; Pacific Ocean ; Chlorophyll A ; *Thiosulfates ; Seawater/microbiology ; Sulfur/metabolism ; Nitrogen/metabolism ; Carbon ; Chitin ; Phylogeny ; },
abstract = {To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.},
}
@article {pmid37550791,
year = {2023},
author = {Pitiriga, V and Bakalis, J and Theodoridou, K and Dimitroulia, E and Saroglou, G and Tsakris, A},
title = {Comparison of microbial colonization rates between central venous catheters and peripherally inserted central catheters.},
journal = {Antimicrobial resistance and infection control},
volume = {12},
number = {1},
pages = {74},
pmid = {37550791},
issn = {2047-2994},
mesh = {Humans ; *Central Venous Catheters/adverse effects ; *Catheterization, Central Venous/adverse effects/methods ; Retrospective Studies ; Critical Illness ; *Catheter-Related Infections/prevention &amp; control ; Risk Factors ; *Sepsis ; *Anti-Infective Agents ; },
abstract = {BACKGROUND: Central venous catheters (CVCs) and peripherally inserted central catheters (PICCs), have been widely used as intravascular devices in critically ill patients. However, they might evoke complications, such as catheter colonization that has been considered as predisposing factor for central line-associated bloodstream infections (CLABSIs). Although numerous studies have compared the risk of bloodstream infections between PICCs and CVCs, comparative studies on their colonization rates are limited.<br><br>OBJECTIVES: The episodes of catheter colonization in critically ill patients with CVCs or PICCs were retrospectively analysed during a two-year period in a Greek tertiary care hospital and colonization rates, microbial profiles and antimicrobial susceptibility&#xa0;patterns were compared.<br><br>METHODS: Clinical and laboratory data of consecutive hospitalized critically-ill patients who underwent PICC and CVC placement between May 2017-May 2019 were analysed. All catheters were examined by the semiquantitative culture technique for bacterial pathogens, either as a routine process after catheter removal or after suspicion of infection. Species identification and antimicrobial resistance patterns were determined by the Vitek2 automated system.<br><br>RESULTS: During the survey period a total of 122/1187 (10.28%) catheter colonization cases were identified among CVCs and 19/639 (2.97%) cases among PICCs (p&#x2009;=&#x2009;0.001). The colonization rate was 12.48/1000 catheter-days for the&#xa0;CVC group and 1.71/1000 catheter-days for the&#xa0;PICC group (p&#x2009;<&#x2009;0.001). The colonization rate per 1000 catheter-days due to multidrug-resistant organisms (MDROs) was 3.85 in all study cases, 7.26 (71/122) in the&#xa0;CVC group and 0.63 (7/19) in the&#xa0;PICC group (p&#x2009;<&#x2009;0.001). Within the&#xa0;CVC group, the most common microorganism isolated was MDR Acinetobacter baumannii (n&#x2009;=&#x2009;38, 31.1%) followed by MDR Klebsiella pneumoniae (n&#x2009;=&#x2009;20, 16.4%). In the&#xa0;PICC group, the predominant microorganism isolated was Candida spp. (n&#x2009;=&#x2009;5, 23.8%) followed by MDR K. pneumoniae and MDR A. baumannii in equal numbers (n&#x2009;=&#x2009;3, 14.2%).<br><br>CONCLUSION: PICC lines were associated with significantly lower colonization rates comparing to the&#xa0;CVC&#xa0;ones. In addition, patterns of microbial colonization revealed a trend over the predominance of MDR gram-negatives in CVCs suggesting that PICCs might be a&#xa0;safer alternative for prolonged inpatient intravascular access. Prevention programs directed by local microbial ecology may diminish catheter colonization rates and CLABSIs.},
}
@article {pmid37550373,
year = {2023},
author = {Yu, L and Khachaturyan, M and Matschiner, M and Healey, A and Bauer, D and Cameron, B and Cusson, M and Emmett Duffy, J and Joel Fodrie, F and Gill, D and Grimwood, J and Hori, M and Hovel, K and Hughes, AR and Jahnke, M and Jenkins, J and Keymanesh, K and Kruschel, C and Mamidi, S and Menning, DM and Moksnes, PO and Nakaoka, M and Pennacchio, C and Reiss, K and Rossi, F and Ruesink, JL and Schultz, ST and Talbot, S and Unsworth, R and Ward, DH and Dagan, T and Schmutz, J and Eisen, JA and Stachowicz, JJ and Van de Peer, Y and Olsen, JL and Reusch, TBH},
title = {Author Correction: Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina).},
journal = {Nature plants},
volume = {9},
number = {8},
pages = {1370},
doi = {10.1038/s41477-023-01504-y},
pmid = {37550373},
issn = {2055-0278},
}
@article {pmid37548146,
year = {2023},
author = {Ruiz, J and de Celis, M and Diaz-Colunga, J and Vila, JC and Benitez-Dominguez, B and Vicente, J and Santos, A and Sanchez, A and Belda, I},
title = {Predictability of the community-function landscape in wine yeast ecosystems.},
journal = {Molecular systems biology},
volume = {19},
number = {9},
pages = {e11613},
pmid = {37548146},
issn = {1744-4292},
mesh = {*Saccharomyces cerevisiae/genetics ; *Wine ; Ecosystem ; Phylogeny ; Fermentation ; Yeasts ; },
abstract = {Predictively linking taxonomic composition and quantitative ecosystem functions is a major aspiration in microbial ecology, which must be resolved if we wish to engineer microbial consortia. Here, we have addressed this open question for an ecological function of major biotechnological relevance: alcoholic fermentation in wine yeast communities. By exhaustively phenotyping an extensive collection of naturally occurring wine yeast strains, we find that most ecologically and industrially relevant traits exhibit phylogenetic signal, allowing functional traits in wine yeast communities to be predicted from taxonomy. Furthermore, we demonstrate that the quantitative contributions of individual wine yeast strains to the function of complex communities followed simple quantitative rules. These regularities can be integrated to quantitatively predict the function of newly assembled consortia. Besides addressing theoretical questions in functional ecology, our results and methodologies can provide a blueprint for rationally managing microbial processes of biotechnological relevance.},
}
@article {pmid37547726,
year = {2023},
author = {Gibson, E and Zimmerman, NB},
title = {Urban biogeography of fungal endophytes across San Francisco.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15454},
pmid = {37547726},
issn = {2167-8359},
mesh = {Humans ; Endophytes/genetics ; Cities ; San Francisco ; Hot Temperature ; *Fungi, Unclassified ; Plants/microbiology ; Trees/microbiology ; *Microbiota ; },
abstract = {In natural and agricultural systems, the plant microbiome-the microbial organisms associated with plant tissues and rhizosphere soils-has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue to transition out of rural areas and into cities, understanding the factors that shape environmental microbial communities in urban ecosystems stands to become increasingly important.},
}
@article {pmid37544074,
year = {2023},
author = {Fu, S and Wang, R and Zhang, J and Xu, Z and Yang, X and Yang, Q},
title = {Temporal variability of microbiome in the different plankton hosts revealed distinct environmental persistence of Vibrio parahaemolyticus in shrimp farms.},
journal = {Microbiological research},
volume = {275},
number = {},
pages = {127464},
doi = {10.1016/j.micres.2023.127464},
pmid = {37544074},
issn = {1618-0623},
mesh = {Plankton/genetics ; *Vibrio parahaemolyticus/genetics ; *Chlorella ; Hemolysin Proteins/genetics ; *Microbiota/genetics ; Aquaculture ; },
abstract = {Plankton-bacteria interactions may play essential roles in maintaining the persistence of pathogenic Vibrio spp. However, the actual plankton host of the toxigenic Vibrio parahaemolyticus that harbors thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) remains unclear. To answer this question, we measured the abundance of toxigenic and nontoxigenic Vibrio parahaemolyticus in different types of plankton by most probable number (MPN)-PCR. We next investigated the dynamics of the microbiomes of rearing water, copepods, Chlorella, four predominant diatom genera (Nitzschia, Melosira, Skeletonema and Chaetoceros) and the gut of the shrimp in two recirculated shrimp farming systems from April to September using high-throughput 16 S rRNA amplicon sequencing. The survival of trh-positive and trh-negative V. parahaemolyticus in seawater and different plankton hosts was examined under low temperature and starvation conditions. The results showed that copepods harbored the highest proportion of trh-positive V. parahaemolyticus, followed by diatoms. Chitinous diatoms (CD) harbored a high proportion of Vibrionaceae, of which a high abundance of V. parahaemolyticus was found in summer. In contrast, Vibrio spp. is rarely found in Chlorella and nonchitinous diatoms. Taxon-specific associations were also observed, including a relatively high abundance of Vibrio and Halodesulfovibrio on copepods and covariation of Aeromonas and Bacillus inside the Chlorella. The survival assays showed that, in comparison to trh-negative V. parahaemolyticus, trh-positive V. parahaemolyticus showed better survival in copepods and CD under starvation conditions and maintained high persistence in the above hosts at low temperature. In conclusion, the results herein suggested that chitinous plankton might provide protection for V. parahaemolyticus, especially trh-positive V. parahaemolyticus, and improve their persistence under harsh conditions. Our study provided in-depth insights into the persistence of V. parahaemolyticus in the environment, which would promote targeted disease prevention measures.},
}
@article {pmid37543702,
year = {2023},
author = {Tang, L and O'Dwyer, J and Kimyon, &#xd6; and Manefield, MJ},
title = {Microbial community composition of food waste before anaerobic digestion.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12703},
pmid = {37543702},
issn = {2045-2322},
mesh = {Anaerobiosis ; Food ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; *Microbiota/genetics ; Bacteria/genetics ; Bioreactors/microbiology ; Methane ; Sewage/microbiology ; },
abstract = {Anaerobic digestion is widely used to process and recover value from food waste. Commercial food waste anaerobic digestion facilities seek improvements in process efficiency to enable higher throughput. There is limited information on the composition of microbial communities in food waste prior to digestion, limiting rational exploitation of the catalytic potential of microorganisms in pretreatment processes. To address this knowledge gap, bacterial and fungal communities in food waste samples from a commercial anaerobic digestion facility were characterised over 3 months. The abundance of 16S rRNA bacterial genes was approximately five orders of magnitude higher than the abundance of the fungal intergenic spacer (ITS) sequence, suggesting the numerical dominance of bacteria over fungi in food waste before anaerobic digestion. Evidence for the mass proliferation of bacteria in food waste during storage prior to anaerobic digestion is presented. The composition of the bacterial community shows variation over time, but lineages within the Lactobacillaceae family are consistently dominant. Nitrogen content and pH are correlated to community variation. These findings form a foundation for understanding the microbial ecology of food waste and provide opportunities to further improve the throughput of anaerobic digestion.},
}
@article {pmid37542810,
year = {2023},
author = {De Paepe, J and Garcia Gragera, D and Arnau Jimenez, C and Rabaey, K and Vlaeminck, SE and Gòdia, F},
title = {Continuous cultivation of microalgae yields high nutrient recovery from nitrified urine with limited supplementation.},
journal = {Journal of environmental management},
volume = {345},
number = {},
pages = {118500},
doi = {10.1016/j.jenvman.2023.118500},
pmid = {37542810},
issn = {1095-8630},
mesh = {Humans ; *Microalgae/metabolism ; Calcium/metabolism ; Edetic Acid/metabolism ; Magnesium ; Nutrients ; Photobioreactors ; Phosphorus/metabolism ; Dietary Supplements ; Biomass ; Nitrogen/metabolism ; },
abstract = {Microalgae can play a key role in the bioeconomy, particularly in combination with the valorisation of waste streams as cultivation media. Urine is an example of a widely available nutrient-rich waste stream, and alkaline stabilization and subsequent full nitrification in a bioreactor yields a stable nitrate-rich solution. In this study, such nitrified urine served as a culture medium for the edible microalga Limnospira indica. In batch cultivation, nitrified urine without additional supplements yielded a lower biomass concentration, nutrient uptake and protein content compared to modified Zarrouk medium, as standard medium. To enhance the nitrogen uptake efficiency and biomass production, nitrified urine was supplemented with potentially limiting elements. Limited amounts of phosphorus (36 mg L[-1]), magnesium (7.9 mg L[-1]), calcium (12.2 mg L[-1]), iron (2.0 mg L[-1]) and EDTA (88.5 mg Na2-EDTA.2H2O L[-1]) rendered the nitrified urine matrix as effective as modified Zarrouk medium in terms of biomass production (OD750 of 1.2), nutrient uptake (130 mg N L[-1]) and protein yield (47%) in batch culture. Urine precipitates formed by alkalinisation could in principle supply enough phosphorus, calcium and magnesium, requiring only external addition of iron, EDTA and inorganic carbon. Subsequently, the suitability of supplemented nitrified urine as a culture medium was confirmed in continuous Limnospira cultivation in a CSTR photobioreactor. This qualifies nitrified urine as a valuable and sustainable microalgae growth medium, thereby creating novel nutrient loops on Earth and in Space, i.e., in regenerative life support systems for human deep-space missions.},
}
@article {pmid37542791,
year = {2023},
author = {van den Bergh, SG and Chardon, I and Meima-Franke, M and Costa, OYA and Korthals, GW and de Boer, W and Bodelier, PLE},
title = {The intrinsic methane mitigation potential and associated microbes add product value to compost.},
journal = {Waste management (New York, N.Y.)},
volume = {170},
number = {},
pages = {17-32},
doi = {10.1016/j.wasman.2023.07.027},
pmid = {37542791},
issn = {1879-2456},
abstract = {Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 &amp; ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h[-1] g dw compost[-1] and 25.19 ± 6.75 pmol h[-1] g dw compost[-1], respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.},
}
@article {pmid37542538,
year = {2023},
author = {Niu, J and Chen, D and Shang, C and Xiao, L and Wang, Y and Zeng, W and Zheng, X and Chen, Z and Du, X and Chen, X},
title = {Niche Differentiation of Biofilm Microorganisms in a Full-scale Municipal Drinking Water Distribution System in China and Their Implication for Biofilm Control.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2770-2780},
pmid = {37542538},
issn = {1432-184X},
mesh = {*Drinking Water ; Water Quality ; Bacteria/genetics ; Proteobacteria ; Biofilms ; Archaea/genetics ; *Bacillus ; Water Supply ; Water Microbiology ; },
abstract = {Biofilms on the inner surface of a drinking water distribution system (DWDS) affect water quality and stability. Understanding the niche differentiation of biofilm microbial communities is necessary for the efficient control of DWDS biofilms. However, biofilm studies are difficult to conduct in the actual DWDS because of inaccessibility to the pipes buried underground. Taking the opportunity of infrastructure construction and relevant pipeline replacement in China, biofilms in a DWDS (a water main and its branch pipes) were collected in situ, followed by analysis on the abundances and community structures of bacterial and archaeal using quantitative PCR and high-throughput sequencing, respectively. Results showed that archaea were detected only in the biofilms of the water main, with a range of 9.4×10[3]~1.1×10[5] copies/cm[2]. By contrast, bacteria were detected in the biofilms of branch pipes and the distal part of the water main, with a range of 8.8×10[3]~9.6×10[6] copies/cm[2]. Among the biofilm samples, the archaeal community in the central part of the water main showed the highest richness and diversity. Nitrosopumilus was found to be predominant (86.22%) in the biofilms of the proximal part of the water main. However, Methanobrevibacter (87.15%) predominated in the distal part of the water main. The bacterial community of the water main and branch pipes was primarily composed of Firmicutes and Proteobacteria at the phylum level, respectively. Regardless of archaea or bacteria, only few operational taxonomic units (OTUs) (<0.5% of total OTUs) were shared by all the biofilms, indicating the niche differentiation of biofilm microorganisms. Moreover, the high Mn content in the biofilms of the distal sampling location (D3) in the water main was linked to the predominance of Bacillus. Functional gene prediction revealed that the proportion of infectious disease-related genes was 0.44-0.67% in the tested biofilms. Furthermore, functional genes related to the resistance of the bacterial community to disinfections and antibiotics were detected in all the samples, that is, glutathione metabolism-relating genes (0.14-0.65%) and beta-lactam resistance gene (0.01-0.05%). The results of this study indicate the ubiquity of archaea and bacteria in the biofilms of water main and branch pipes, respectively, and pipe diameters could be a major influencing factor on bacterial community structure. In the water main, the key finding was the predominant existence of archaea, particularly Nitrosopumilus and methanogen. Hence, their routine monitoring and probable influences on water quality in pipelines with large diameter should be given more attention. Besides, since Mn-related Bacillus and suspected pathogenic Enterococcus were detected in the biofilm, supplementation of disinfectant may be a feasible strategy for inhibiting their growth and ensuring water quality. In addition, the monitoring on their abundance variation could help to determine the frequency and methods of pipeline maintenance.},
}
@article {pmid37542537,
year = {2023},
author = {Ren, Z and Ye, S and Li, H and Huang, X and Chen, L and Cao, S and Chen, T},
title = {Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2756-2769},
pmid = {37542537},
issn = {1432-184X},
mesh = {Animals ; *Permafrost ; Tibet ; Soil/chemistry ; *Microbiota ; *Arthropods ; Soil Microbiology ; *Ciliophora/genetics ; },
abstract = {Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.},
}
@article {pmid37541415,
year = {2023},
author = {He, Q and Yan, X and Wang, H and Ji, Y and Li, J and Liu, L and Bi, P and Xu, P and Xu, B and Ma, J},
title = {Towards a better understanding of the anaerobic/oxic/anoxic-aerobic granular sludge process (AOA-AGS) for simultaneous low-strength wastewater treatment and in situ sludge reduction from ambient to winter temperatures.},
journal = {Environmental research},
volume = {236},
number = {Pt 2},
pages = {116822},
doi = {10.1016/j.envres.2023.116822},
pmid = {37541415},
issn = {1096-0953},
abstract = {The new anaerobic/oxic/anoxic-aerobic granular sludge (AOA-AGS) merits the advantages of effective carbon utilization and low-carbon treatment. However, low temperature poses stressing concerns and the resisting mechanism remains much unknown. Herein, an AOA-AGS process was configured for simultaneous nitrification, denitrification and phosphorus removal (SNDPR) with low-strength wastewater from ambient (>15 °C) to winter temperatures (<15 °C). Results showed that simultaneously advanced nutrients removal, and dramatic in situ sludge reduction (Yobs of 0.093 g MLSS/g COD) were gained regardless of seasonally decreasing temperatures. Winter temperatures even amplified Candidatus Competibacter predominating from 20.11% to 34.74%, which laid the core basis for endogenous denitrification, sludge minimization and temperature resistance. A removal model was thus proposed given the observed functional groups, and doubts were also raised for future investigations. This study would aid a better understanding on the microbial ecology and engineering aspects of the new AOA-AGS process treating low-strength wastewater at low temperatures.},
}
@article {pmid37537784,
year = {2023},
author = {Guan, X and Zhao, Z and Jiang, J and Fu, L and Liu, J and Pan, Y and Gao, S and Wang, B and Chen, Z and Wang, X and Sun, H and Jiang, B and Dong, Y and Zhou, Z},
title = {Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient.},
journal = {Environmental microbiology reports},
volume = {15},
number = {6},
pages = {545-556},
pmid = {37537784},
issn = {1758-2229},
support = {2022JH2/101300155//Applied Basic Research Project of Liaoning Province/ ; 2022XTCX0504//Fundamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; 2021RT08//Innovation and Entrepreneurship Program for High-level Talent of Dalian/ ; 2021921071//Liaoning BaiQianWan Talents Program/ ; },
mesh = {*Archaea/genetics ; Salinity ; Prokaryotic Cells ; Seawater ; *Microbiota ; Sodium Chloride ; },
abstract = {Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.},
}
@article {pmid37537681,
year = {2023},
author = {Mendes, LW and Raaijmakers, JM and de Hollander, M and Sepo, E and Gómez Expósito, R and Chiorato, AF and Mendes, R and Tsai, SM and Carrión, VJ},
title = {Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {68},
pmid = {37537681},
issn = {2524-6372},
support = {2014/03217-3, 2015/00251-9, 2020/00469-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 408191/2018-0, 307670/2021-0, 302591/2019-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 88887.185941/2018-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {BACKGROUND: Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.<br><br>RESULTS: Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.<br><br>CONCLUSION: Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.},
}
@article {pmid37535084,
year = {2023},
author = {Pan, Q and Shikano, I and Liu, TX and Felton, GW},
title = {Correction to: Helicoverpa zea-Associated Gut Bacteria as Drivers in Shaping Plant Anti-herbivore Defense in Tomato.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2183},
doi = {10.1007/s00248-023-02281-z},
pmid = {37535084},
issn = {1432-184X},
}
@article {pmid37535083,
year = {2023},
author = {Šaraba, V and Milovanovic, J and Nikodinovic-Runic, J and Budin, C and de Boer, T and Ciric, M},
title = {Brackish Groundwaters Contain Plastic- and Cellulose-Degrading Bacteria.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2747-2755},
pmid = {37535083},
issn = {1432-184X},
mesh = {*Cellulose/metabolism ; Ecosystem ; Plastics ; Bacteria ; *Groundwater ; },
abstract = {The selected brackish groundwater occurrences in the geotectonic regions of Inner Dinarides of western Serbia (Obrenovačka Banja) and Serbian crystalline core (Lomnički Kiseljak and Velika Vrbnica) were sampled for isolation and identification of plastic- and lignocellulose-degrading bacteria, as well as for the assessment of their enzymatic potential. The examined occurrences belong to the cold and warm (subthermal), weakly alkaline, neutral, and weakly acidic groundwater, and their genetic types are HCO3-Na + K and HCO3-Ca, Mg. The most abundant genera identified by next-generation 16S sequencing of cultivated groundwater samples belong to Aeromonas and Exiguobacterium. Of isolates screened on plastic and lignocellulosic substrates, 85.3% demonstrated growth and/or degrading activity on at least one tested substrate, with 27.8% isolates degrading plastic substrate Impranil® DLN-SD (SD), 1.9% plastic substrate bis(2-hydroxyethyl)terephthalate, and 5.6% carboxymethyl cellulose (CMC). Isolates degrading SD that were identified by 16S rDNA sequencing belonged to genera Stenotrophomonas, Flavobacterium, Pantoea, Enterobacter, Pseudomonas, Serratia, Acinetobacter, and Proteus, while isolates degrading CMC belonged to genera Rhizobium and Shewanella. All investigated brackish groundwaters harbor bacteria with potential in degradation of plastics or cellulose. Taking into account that microplastics contamination of groundwater resources is becoming a significant problem, the finding of plastic-degrading bacteria may have potential in bioremediation treatments of polluted groundwater. Subterranean ecosystems, which are largely untapped resources of biotechnologically relevant enzymes, are not traditionally considered the environment of choice for screening for plastic- and cellulose-degrading bacteria and therefore deserve a special attention from this aspect.},
}
@article {pmid37533451,
year = {2023},
author = {Pandey, S and Kim, ES and Cho, JH and Song, M and Doo, H and Kim, S and Keum, GB and Kwak, J and Ryu, S and Choi, Y and Kang, J and Lee, JJ and Kim, HB},
title = {Swine gut microbiome associated with non-digestible carbohydrate utilization.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1231072},
pmid = {37533451},
issn = {2297-1769},
abstract = {Non-digestible carbohydrates are an unavoidable component in a pig's diet, as all plant-based feeds contain different kinds of non-digestible carbohydrates. The major types of non-digestible carbohydrates include non-starch polysaccharides (such as cellulose, pectin, and hemicellulose), resistant starch, and non-digestible oligosaccharides (such as fructo-oligosaccharide and xylo-oligosaccharide). Non-digestible carbohydrates play a significant role in balancing the gut microbial ecology and overall health of the swine by promoting the production of short chain fatty acids. Although non-digestible carbohydrates are rich in energy, swine cannot extract this energy on their own due to the absence of enzymes required for their degradation. Instead, they rely on gut microbes to utilize these carbohydrates for energy production. Despite the importance of non-digestible carbohydrate degradation, limited studies have been conducted on the swine gut microbes involved in this process. While next-generation high-throughput sequencing has aided in understanding the microbial compositions of the swine gut, specific information regarding the bacteria involved in non-digestible carbohydrate degradation remains limited. Therefore, it is crucial to investigate and comprehend the bacteria responsible for the breakdown of non-digestible carbohydrates in the gut. In this mini review, we have discussed the major bacteria involved in the fermentation of different types of non-digestible carbohydrates in the large intestine of swine, shedding light on their potential roles and contributions to swine nutrition and health.},
}
@article {pmid37532947,
year = {2023},
author = {Jabir, T and Jain, A and Vipindas, PV and Krishnan, KP},
title = {Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard).},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2733-2746},
pmid = {37532947},
issn = {1432-184X},
mesh = {*Estuaries ; *Water ; Svalbard ; Nitrogen Fixation/genetics ; Nitrogen ; Stochastic Processes ; },
abstract = {Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3[+]) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.},
}
@article {pmid37531050,
year = {2023},
author = {Zhang, D and Sun, J and Wang, D and Peng, S and Wang, Y and Lin, X and Yang, X and Hua, Q and Wu, P},
title = {Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {41},
pages = {94347-94360},
pmid = {37531050},
issn = {1614-7499},
support = {BK20201110//Natural Science Foundation of Jiangsu Province/ ; 2021BEE02025//Key Research and Development Program of Ningxia/ ; NMKJXM202009//Science and Technology Major Project of Inner Mongolia/ ; },
mesh = {Animals ; Swine ; *Mycobiome ; Manure/microbiology ; Chickens/genetics ; *Composting ; RNA, Ribosomal, 16S ; Soil ; Bacteria/genetics ; *Actinomycetales/genetics ; },
abstract = {Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.},
}
@article {pmid37528183,
year = {2023},
author = {Wang, L and Wang, J and Yuan, J and Tang, Z and Wang, J and Zhang, Y},
title = {Long-Term Organic Fertilization Strengthens the Soil Phosphorus Cycle and Phosphorus Availability by Regulating the pqqC- and phoD-Harboring Bacterial Communities.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2716-2732},
pmid = {37528183},
issn = {1432-184X},
mesh = {*Soil/chemistry ; *Phosphorus/metabolism ; Fertilizers/analysis ; Carbon ; Bacteria/genetics/metabolism ; Soil Microbiology ; Minerals ; Fertilization ; },
abstract = {The pqqC and phoD genes encode pyrroloquinoline quinone synthase and alkaline phosphomonoesterase (ALP), respectively. These genes play a crucial role in regulating the solubilization of inorganic phosphorus (Pi) and the mineralization of organic phosphorus (Po), making them valuable markers for P-mobilizing bacterial. However, there is limited understanding of how the interplay between soil P-mobilizing bacterial communities and abiotic factors influences P transformation and availability in the context of long-term fertilization scenarios. We used real-time polymerase chain reaction and high-throughput sequencing to explore the characteristics of soil P-mobilizing bacterial communities and their relationships with key physicochemical properties and P fractions under long-term fertilization scenarios. In a 38-year fertilization experiment, six fertilization treatments were selected. These treatments were sorted into three groups: the non-P-amended group, including no fertilization and mineral NK fertilizer; the sole mineral-P-amended group, including mineral NP and NPK fertilizer; and the organically amended group, including sole organic fertilizer and organic fertilizer plus mineral NPK fertilizer. The organically amended group significantly increased soil labile P (Ca2-P and enzyme-P) and Olsen-P content and proportion but decreased non-labile P (Ca10-P) proportion compared with the sole mineral-P-amended group, indicating enhanced P availability in the soil. Meanwhile, the organically amended group significantly increased soil ALP activity and pqqC and phoD gene abundances, indicating that organic fertilization promotes the activity and abundance of microorganisms involved in P mobilization processes. Interestingly, the organically amended group dramatically reshaped the community structure of P-mobilizing bacteria and increased the relative abundance of Acidiphilium, Panacagrimonas, Hansschlegelia, and Beijerinckia. These changes had a greater positive impact on ALP activity, labile P, and Olsen-P content compared to the abundance of P-mobilizing genes alone, indicating their importance in driving P mobilization processes. Structural equation modeling indicated that soil organic carbon and Po modulated the relationship between P-mobilizing bacterial communities and labile P and Olsen-P, highlighting the influence of SOC and Po on the functioning of P-mobilizing bacteria and their impact on P availability. Overall, our study demonstrates that organic fertilization has the potential to reshape the structure of P-mobilizing bacterial communities, leading to increased P mobilization and availability in the soil. These findings contribute to our understanding of the mechanisms underlying P cycling in agricultural systems and provide valuable insights for enhancing microbial P mobilization through organic fertilization.},
}
@article {pmid37527741,
year = {2023},
author = {Antonelli, P and Peruzzo, A and Mancin, M and Boscolo Anzoletti, A and Dall'Ara, S and Orsini, M and Bordin, P and Arcangeli, G and Zanolin, B and Barco, L and Losasso, C},
title = {Tetrodotoxin in bivalve mollusks: An integrated study towards the comprehension of the influencing factors of a newly native phenomenon.},
journal = {Chemosphere},
volume = {339},
number = {},
pages = {139682},
doi = {10.1016/j.chemosphere.2023.139682},
pmid = {37527741},
issn = {1879-1298},
mesh = {Animals ; Tetrodotoxin/toxicity ; *Tandem Mass Spectrometry ; Comprehension ; *Bivalvia ; Neurotoxins ; Phytoplankton ; },
abstract = {Tetrodotoxins (TTXs) are potent neurotoxins named after the Tetraodontidae fish family. The ingestion of TTX-contaminated flesh can cause neurotoxic symptoms and can lead to death. In 2017 symptoms the European Food Safety Authority (EFSA) recognized the threat to food safety resulting from TTX exposure via food consumption and, thus, proposed a safety limit of 44 μg/kg of TTX in marine gastropods and bivalves. To date, however, TTXs have not yet been included in the list of biotoxins to be monitored within the European Union, even though, in a few cases, levels of TTX found were higher than the EFSA limit. The origin of TTX production is debated and the roles of both biotic and abiotic factors on TTX-mediated toxic events remain unclear. In order to meet these knowledge requests the present study was aimed to investigate the role of seawater temperature, pH, water conductivity, and oxygen saturation, along with the marine phytoplankton community and the bacterial community of mussels and oysters on the accumulation of TTX and analogues in the bivalves. Abiotic parameters were measured by means of a multi-parametric probe, phytoplankton community was analyzed by optic microscopy while microbial community was described by amplicon metataxonomic sequencing, TTXs concentration in the collected matrices were measured by HILIC-MS/MS. A possible role of seawater pH and temperature, among the investigated abiotic factors, in regulating the occurrence of TTXs was found. Regarding biotic variables, a possible influence of Vibrio, Shewanella and Flavobacteriaceae in the occurrence of TTXs was found. Concurrently, Prorocentrum cordatum cell numbers were correlated to the incidence of TTX in mussels. The results herein collected suggest that environmental variables play a consistent part in the occurrence of TTX in the edible bivalve habitats, and there are also indications of a potential role played by specific bacteria taxa in association with phytoplankton.},
}
@article {pmid37527740,
year = {2023},
author = {Wang, Y and Gao, Y and Lu, X and Gadow, SI and Zhuo, G and Hu, W and Song, Y and Zhen, G},
title = {Bioelectrochemical anaerobic membrane bioreactor enables high methane production from methanolic wastewater: Roles of microbial ecology and microstructural integrity of anaerobic biomass.},
journal = {Chemosphere},
volume = {339},
number = {},
pages = {139676},
doi = {10.1016/j.chemosphere.2023.139676},
pmid = {37527740},
issn = {1879-1298},
mesh = {*Wastewater ; *Methanol ; Sewage/chemistry ; Anaerobiosis ; Biomass ; Methane/metabolism ; Bioreactors ; Waste Disposal, Fluid ; Membranes, Artificial ; },
abstract = {The disintegration of anaerobic sludge and blockage of membrane pores has impeded the practical application of anaerobic membrane bioreactor (AnMBR) in treating methanolic wastewater. In this study, bioelectrochemical system (BES) was integrated into AnMBR to alleviate sludge dispersion and membrane fouling as well as enhance bioconversion of methanol. Bioelectrochemical regulation effect induced by BES enhanced methane production rate from 4.94 ± 0.52 to 5.39 ± 0.37 L/Lreactor/d by accelerating the enrichment of electroactive microorganisms and the agglomeration of anaerobic sludge via the adhesive and chemical bonding force. 16 S rRNA gene high-throughput sequencing demonstrated that bioelectrochemical stimulation had modified the metabolic pathways by regulating the key functional microbial communities. Methanogenesis via the common methylotrophic Methanomethylovorans was partially substituted by the hydrogenotrophic Candidatus_Methanofastidiosum, etc. The metabolic behaviors of methanol are bioelectrochemistry-dependent, and controlling external voltage is thus an effective strategy for ensuring robust electron transfer, low membrane fouling, and long-term process stability.},
}
@article {pmid37525505,
year = {2024},
author = {Effelsberg, N and Kobusch, I and Schollenbruch, H and Linnemann, S and Bang, C and Franke, A and Köck, R and Boelhauve, M and Mellmann, A},
title = {Pilot study on nasal microbiota dynamics and MRSA carriage of a pig cohort housed on straw bedding.},
journal = {Molecular microbiology},
volume = {122},
number = {3},
pages = {403-412},
doi = {10.1111/mmi.15136},
pmid = {37525505},
issn = {1365-2958},
support = {01KI2009A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 01KI2009B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {Animals ; *Methicillin-Resistant Staphylococcus aureus/genetics/isolation &amp; purification ; Swine ; *Staphylococcal Infections/microbiology ; *Microbiota ; *Housing, Animal ; *RNA, Ribosomal, 16S/genetics ; *Carrier State/microbiology ; *Nose/microbiology ; Pilot Projects ; Bedding and Linens/microbiology ; Swine Diseases/microbiology ; },
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) can be transmitted between pigs and humans on farms. Hence, the reduction of MRSA carriage in pigs could decrease the risk of zoonotic transmission. Recently, straw bedding has been found to significantly reduce MRSA carriage in pigs. The mechanisms behind this effect remain unclear but changes in the nasal microbiome may play a role. In this exploratory study, the nasal microbiota of pigs kept on straw was examined using V1/V2 16S rRNA gene sequencing. Nasal swabs were collected from 13 pigs at six different time points during the course of a full fattening cycle resulting in 74 porcine samples. In addition, straw samples were collected at each time point. Eleven out of 13 pigs were MRSA positive at housing-in. We found a strong temporal pattern in the microbial communities. Both microbial diversity and abundance of Staphylococcus species peaked in week 5 after introduction to the straw stable decreased in week 10, when all pigs turned MRSA-negative, and increased again toward the end of the fattening period. These findings show that the introduction of pigs into a new environment has a huge impact on their nasal microbiota, which might lead to unfavorable conditions for MRSA. Moreover, other Staphylococcus species may play a role in eliminating MRSA carriage. We designed a follow-up study including two different husbandry systems to further assess these effects.},
}
@article {pmid37523041,
year = {2024},
author = {Li, S and Young, T and Archer, S and Lee, K and Alfaro, AC},
title = {Gut microbiome resilience of green-lipped mussels, Perna canaliculus, to starvation.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {27},
number = {2},
pages = {571-580},
pmid = {37523041},
issn = {1618-1905},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Perna ; RNA, Ribosomal, 16S/genetics ; *Resilience, Psychological ; Bacteria/genetics ; },
abstract = {Host gut microbiomes play an important role in animal health and resilience to conditions, such as malnutrition and starvation. These host-microbiome relationships are poorly understood in the marine mussel Perna canaliculus, which experiences significant variations in food quantity and quality in coastal areas. Prolonged starvation may be a contributory factor towards incidences of mass mortalities in farmed mussel populations, resulting in highly variable production costs and unreliable market supplies. Here, we examine the gut microbiota of P. canaliculus in response to starvation and subsequent re-feeding using high-throughput amplicon sequencing of the 16S rRNA gene. Mussels showed no change in bacterial species richness when subjected to a 14-day starvation, followed by re-feeding/recovery. However, beta bacteria diversity revealed significant shifts (PERMANOVA p-value < 0.001) in community structure in the starvation group and no differences in the subsequent recovery group (compared to the control group) once they were re-fed, highlighting their recovery capability and resilience. Phylum-level community profiles revealed an elevation in dominance of Proteobacteria (ANCOM-BC p-value <0.001) and Bacteroidota (ANCOM-BC p-value = 0.04) and lower relative abundance of Cyanobacteria (ANCOM-BC p-value = 0.01) in the starvation group compared to control and recovery groups. The most abundant genus-level shifts revealed relative increases of the heterotroph Halioglobus (p-value < 0.05) and lowered abundances of the autotroph Synechococcus CC9902 in the starvation group. Furthermore, a SparCC correlation network identified co-occurrence of a cluster of genera with elevated relative abundance in the starved mussels that were positively correlated with Synechococcus CC9902. The findings from this work provide the first insights into the effect of starvation on the resilience capacity of Perna canaliculus gut microbiota, which is of central importance to understanding the effect of food variation and limitation in farmed mussels.},
}
@article {pmid37520283,
year = {2023},
author = {Wentzien, NM and Fernández-González, AJ and Villadas, PJ and Valverde-Corredor, A and Mercado-Blanco, J and Fernández-López, M},
title = {Thriving beneath olive trees: The influence of organic farming on microbial communities.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {3575-3589},
pmid = {37520283},
issn = {2001-0370},
abstract = {Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 10[6] ± 1.62 × 10[5] (CM) to 4.54 × 10[6] ± 8.07 × 10[5] (OM) copies of the 18 S rRNA gene g[-1] soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.},
}
@article {pmid37516570,
year = {2023},
author = {Parizadeh, M and Arrieta, MC},
title = {The global human gut microbiome: genes, lifestyles, and diet.},
journal = {Trends in molecular medicine},
volume = {29},
number = {10},
pages = {789-801},
doi = {10.1016/j.molmed.2023.07.002},
pmid = {37516570},
issn = {1471-499X},
mesh = {Humans ; *Gastrointestinal Microbiome ; Bacteria ; *Microbiota ; Diet ; Life Style ; },
abstract = {A growing number of human gut microbiome studies consistently describe differences between human populations. Here, we review how factors related to host genetics, ethnicity, lifestyle, and geographic location help explain this variation. Studies from contrasting environmental scenarios point to diet and lifestyle as the most influential. The effect of human migration and displacement demonstrates how the microbiome adapts to newly adopted lifestyles and contributes to the profound biological and health consequences attributed to migration. This information strongly suggests against a universal scale for healthy or dysbiotic gut microbiomes, and prompts for additional microbiome population surveys, particularly from less industrialized nations. Considering these important differences will be critical for designing strategies to diagnose and restore dysbiosis in various human populations.},
}
@article {pmid37515622,
year = {2023},
author = {Mi, JX and Liu, KL and Ding, WL and Zhang, MH and Wang, XF and Shaukat, A and Rehman, MU and Jiao, XL and Huang, SC},
title = {Comparative analysis of the gut microbiota of wild wintering whooper swans (Cygnus Cygnus), captive black swans (Cygnus Atratus), and mute swans (Cygnus Olor) in Sanmenxia Swan National Wetland Park of China.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {41},
pages = {93731-93743},
pmid = {37515622},
issn = {1614-7499},
support = {No. 32202876//National Natural Science Foundation of China/ ; No. 30501374//Special Support Fund for High-level Talents of Henan Agricultural University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Wetlands ; Ecosystem ; RNA, Ribosomal, 16S ; *Anseriformes ; Birds ; Ducks ; China ; },
abstract = {The gastrointestinal microbiota, a complex ecosystem, is involved in the physiological activities of hosts and the development of diseases. Birds occupy a critical ecological niche in the ecosystem, performing a variety of ecological functions and possessing a complex gut microbiota composition. However, the gut microbiota of wild and captive birds has received less attention in the same region. We profiled the fecal gut microbiome of wild wintering whooper swans (Cygnus Cygnus; Cyg group, n = 25), captive black swans (Cygnus Atratus; Atr group, n = 20), and mute swans (Cygnus Olor; Olor group, n = 30) using 16S rRNA gene sequencing to reveal differences in the gut microbial ecology. The results revealed that the three species of swans differed significantly in terms of the alpha and beta diversity of their gut microbiota, as measured by ACE, Chao1, Simpson and Shannon indices, principal coordinates analysis (PCoA) and non-metricmulti-dimensional scaling (NMDS) respectively. Based on the results of the linear discriminant analysis effect size (LEfSe) and random forest analysis, we found that there were substantial differences in the relative abundance of Gottschalkia, Trichococcus, Enterococcus, and Kurthia among the three groups. Furthermore, an advantageous pattern of interactions between microorganisms was shown by the association network analysis. Among these, Gottschalkia had the higher area under curve (AUC), which was 0.939 (CI = 0.879-0.999), indicating that it might be used as a biomarker to distinguish between wild and captive black swans. Additionally, PICRUSt2 predictions indicated significant differences in gut microbiota functions between wild and captive trumpeter swans, with the gut microbiota functions of Cyg group focusing on carbohydrate metabolism, membrane transport, cofactor, and vitamin metabolism pathways, the Atr group on lipid metabolism, and the Olor group on cell motility, amino acid metabolism, and replication and repair pathways. These findings showed that the gut microbiota of wild and captive swans differed, which is beneficial to understand the gut microecology of swans and to improve regional wildlife conservation strategies.},
}
@article {pmid37512939,
year = {2023},
author = {Mourgela, RN and Kioukis, A and Pourjam, M and Lagkouvardos, I},
title = {Large-Scale Integration of Amplicon Data Reveals Massive Diversity within Saprospirales, Mostly Originating from Saline Environments.},
journal = {Microorganisms},
volume = {11},
number = {7},
pages = {},
pmid = {37512939},
issn = {2076-2607},
abstract = {The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of traditional isolation methods, with the inherited limitations of culture-based approaches. This study utilized the extensive information available in public sequence repositories combined with recent analytical tools to evaluate the global evidence-based diversity of the Saprospirales order. Our analysis resulted in 1183 novel molecular families, 15,033 novel molecular genera, and 188 K novel molecular species. Of those, 7 novel families, 464 novel genera, and 1565 species appeared in abundances at ≥0.1%. Saprospirales were detected in various environments, such as saline water, freshwater, soil, various hosts, wastewater treatment plants, and other bioreactors. Overall, saline water was the environment showing the highest prevalence of Saprospirales, with bioreactors and wastewater treatment plants being the environments where they occurred with the highest abundance. Lewinellaceae was the family containing the majority of the most prevalent species detected, while Saprospiraceae was the family with the majority of the most abundant species found. This analysis should prime researchers to further explore, in a more targeted way, the Saprospirales proportion of microbial dark matter.},
}
@article {pmid37512925,
year = {2023},
author = {St-Pierre, B and Perez Palencia, JY and Samuel, RS},
title = {Impact of Early Weaning on Development of the Swine Gut Microbiome.},
journal = {Microorganisms},
volume = {11},
number = {7},
pages = {},
pmid = {37512925},
issn = {2076-2607},
support = {Hatch projects SD00H719-20 and SD00H682-19//South Dakota State University Agricultural Experiment Station / USDA National Institute of Food and Agriculture/ ; },
abstract = {Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.},
}
@article {pmid37512843,
year = {2023},
author = {Cowan, DA and Cary, SC and DiRuggiero, J and Eckardt, F and Ferrari, B and Hopkins, DW and Lebre, PH and Maggs-Kölling, G and Pointing, SB and Ramond, JB and Tribbia, D and Warren-Rhodes, K},
title = {'Follow the Water': Microbial Water Acquisition in Desert Soils.},
journal = {Microorganisms},
volume = {11},
number = {7},
pages = {},
pmid = {37512843},
issn = {2076-2607},
support = {80256//National Research Foundation/ ; },
abstract = {Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.},
}
@article {pmid37511881,
year = {2023},
author = {Walther-Antonio, M and Schulze-Makuch, D},
title = {The Hypothesis of a "Living Pulse" in Cells.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {37511881},
issn = {2075-1729},
abstract = {Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside environment. Here, we propose that the sum of these processes in a microbial cell is equivalent to a pulse in complex organisms and suggest a first approach to measure the "living pulse" in microorganisms. We emphasize that if a "living pulse" can be shown to exist, it would have far-reaching applications, such as for finding life in extreme environments on Earth and in extraterrestrial locations, as well as making sure that life is not present where it should not be, such as during medical procedures and in the food processing industry.},
}
@article {pmid37511821,
year = {2023},
author = {Schulze-Makuch, D and Irwin, LN},
title = {Life Unknown: Preliminary Scheme for a Magnetotrophic Organism.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {37511821},
issn = {2075-1729},
abstract = {No magnetotrophic organism on Earth is known to use magnetic fields as an energy source or the storage of information. However, a broad diversity of life forms is sensitive to magnetic fields and employs them for orientation and navigation, among other purposes. If the magnetic field strength were much larger, such as that on planets around neutron stars or magnetars, metabolic energy could be obtained from these magnetic fields in principle. Here, we introduce three hypothetical models of magnetotrophic organisms that obtain energy via the Lorentz force. Even if an organism uses magnetic fields only as an energy source, but otherwise is relying on biochemistry, this organism would be by definition a magnetotrophic form of life as we do not know it.},
}
@article {pmid37511182,
year = {2023},
author = {Turbant, F and Waeytens, J and Blache, A and Esnouf, E and Raussens, V and Węgrzyn, G and Achouak, W and Wien, F and Arluison, V},
title = {Interactions and Insertion of Escherichia coli Hfq into Outer Membrane Vesicles as Revealed by Infrared and Orientated Circular Dichroism Spectroscopies.},
journal = {International journal of molecular sciences},
volume = {24},
number = {14},
pages = {},
pmid = {37511182},
issn = {1422-0067},
support = {101004806//Trans-National Access (TNA) of Molecular-Scale Biophysics Research Infrastructure (MOSBRI)/ ; 08254//IEA/PICS CNRS/ ; ANR-11-IDEX-0003-02//Investissements d'Avenir &#xbb; program, through the "ADI 2021 Paris Saclay/ ; 2016/21/N/NZ1/02850//National Science Center Poland/ ; 531-D020-D242-23//University of Gdansk/ ; },
mesh = {Escherichia coli/genetics/metabolism ; Circular Dichroism ; *Escherichia coli Proteins/genetics/metabolism ; *RNA, Small Untranslated/genetics ; Host Factor 1 Protein/genetics/metabolism ; RNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; },
abstract = {The possible carrier role of Outer Membrane Vesicles (OMVs) for small regulatory noncoding RNAs (sRNAs) has recently been demonstrated. Nevertheless, to perform their function, these sRNAs usually need a protein cofactor called Hfq. In this work we show, by using a combination of infrared and circular dichroism spectroscopies, that Hfq, after interacting with the inner membrane, can be translocated into the periplasm, and then be exported in OMVs, with the possibility to be bound to sRNAs. Moreover, we provide evidence that Hfq interacts with and is inserted into OMV membranes, suggesting a role for this protein in the release of sRNA outside the vesicle. These findings provide clues to the mechanism of host-bacteria interactions which may not be defined solely by protein-protein and protein-outer membrane contacts, but also by the exchange of RNAs, and in particular sRNAs.},
}
@article {pmid37509218,
year = {2023},
author = {Li, G and Jin, Y and Chen, B and Lin, A and Wang, E and Xu, F and Hu, G and Xiao, C and Liu, H and Hou, X and Zhang, B and Song, J},
title = {Exploring the Relationship between the Gut Mucosal Virome and Colorectal Cancer: Characteristics and Correlations.},
journal = {Cancers},
volume = {15},
number = {14},
pages = {},
pmid = {37509218},
issn = {2072-6694},
support = {Nos. 81873553//National Natural Science Foundation of China/ ; Nos. 81800465//National Natural Science Foundation of China/ ; },
abstract = {The fecal virome has been reported to be associated with CRC. However, little is known about the mucosal virome signature in CRC. This study aimed to determine the viral community within CRC tissues and their contributions to colorectal carcinogenesis. Colonic mucosal biopsies were harvested from patients with CRC (biopsies of both neoplasia and adjacent normal tissue (CRC-A)) and healthy controls (HC). The shot-gun metagenomic sequencing of virus-like particles (VLPs) was performed on the biopsies. Viral community, functional pathways, and their correlations to clinical data were analyzed. Fluorescence in situ hybridizations (FISH) for the localization of viruses in the intestine was performed, as well as quantitative PCR for the detection of Torque teno virus load in human mucosal VLP DNA. A greater number and proportion of core species were found in CRC tissues than in CRC-A and HC tissues. The diversity of the mucosal virome in CRC tissues was significantly increased compared to that in HC and CRC-A tissues. The mucosal virome signature of CRC tissues were significantly different from those of HC and CRC-A tissues at the species level. The abundances of eukaryotic viruses from the Anelloviridae family and its sub-species Torque teno virus (TTV) were significantly higher in CRC patients than in HC. Furthermore, increased levels of TTV in the intestinal lamina propria were found in the CRC group. Multiple viral functions of TTV associated with carcinogenesis were enriched in CRC tissues. We revealed for the first time that the mucosal virobiota signature of CRC is characterized by a higher diversity and more eukaryotic viruses. The enrichment of TTV species in CRC tissues suggests that they may play an oncogenic role in CRC. Targeting eukaryotic viruses in the gut may provide novel strategies for the prevention and treatment of CRC.},
}
@article {pmid37507629,
year = {2024},
author = {Daba, G and Daelemans, R and Berecha, G and Geerinck, MWJ and Verreth, C and Crauwels, S and Lievens, B and Honnay, O},
title = {Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {27},
number = {2},
pages = {525-534},
pmid = {37507629},
issn = {1618-1905},
mesh = {*Coffea/genetics/microbiology ; Ethiopia ; *Basidiomycota/genetics ; Polymorphism, Genetic ; Plant Diseases/microbiology ; },
abstract = {Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.},
}
@article {pmid37507489,
year = {2023},
author = {Daraz, U and Erhunmwunse, AS and Dubeux, JCB and Mackowiak, C and Guerra, VA and Hsu, CM and Ma, J and Li, Y and Yang, X and Liao, HL and Wang, XB},
title = {Soil Bacterial Communities Across Seven Rhizoma Peanut Cultivars (Arachis glabrata Benth.) Respond to Seasonal Variation.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2703-2715},
pmid = {37507489},
issn = {1432-184X},
mesh = {*Soil ; Seasons ; *Arachis/microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Soil Microbiology ; },
abstract = {Soil microorganisms play key roles in soil nutrient transformations and have a notable effect on plant growth and health. Different plant genotypes can shape soil microbial patterns via the secretion of root exudates and volatiles, but it is uncertain how a difference in soil microorganisms induced by crop cultivars will respond to short-term seasonal variations. A field experiment was conducted to assess the changes in soil bacterial communities of seven rhizoma peanut (Arachis glabrata Benth, RP) cultivars across two growing seasons, April (Spring season) and October (Fall season). Soils' bacterial communities were targeted using 16S rRNA gene amplicon sequencing. Bacterial community diversity and taxonomic composition among rhizoma peanut cultivars were significantly affected by seasons, cultivars, and their interactions (p < 0.05). Alpha diversity, as estimated by the OTU richness and Simpson index, was around onefold decrease in October than in April across most of the RP cultivars, while the soils from Arblick and Latitude had around one time higher alpha diversity in both seasons compared with other cultivars. Beta diversity differed significantly in April (R = 0.073, p < 0.01) and October (R = 0.084, p < 0.01) across seven cultivars. Bacterial dominant taxa (at phylum and genus level) were strongly affected by seasons and varied towards more dominant groups that have functional potentials involved in nutrient cycling from April to October. A large shift in water availability induced by season variations in addition to host cultivar's effects can explain the observed patterns in diversity, composition, and co-occurrence of bacterial taxa. Overall, our results demonstrate an overriding effect of short-term seasonal variations on soil bacterial communities associated with different crop cultivars. The findings suggest that season-induced shifts in environmental conditions could exert stronger impacts on soil microorganisms than the finer-scale rhizosphere effect from crop cultivars, and consequently influence largely microbe-mediated soil processes and crop health in agricultural ecosystems.},
}
@article {pmid37507488,
year = {2023},
author = {Gonçalves, OS and Santana, MF},
title = {Uncovering the Secrets of Slow-Growing Bacteria in Tropical Savanna Soil Through Isolation and Genomic Analysis.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2687-2702},
pmid = {37507488},
issn = {1432-184X},
mesh = {*Soil ; RNA, Ribosomal, 16S/genetics/metabolism ; *Grassland ; Bacteria ; Genomics ; Soil Microbiology ; Phylogeny ; },
abstract = {One gram of soil holds ten billion bacteria of thousands of different species, but most remain unknown, and one of the serious issues is intrinsic to slow-growing bacteria. In this study, we aimed to isolate and characterize slow-growing bacteria from Brazilian Cerrado soil. Over a period of 4 weeks, we conducted an incubation process and selected a total of 92 isolates. These isolates, consisting mostly of slow-growing bacteria, have the ability to thrive in low-water conditions and possess features that promote plant growth. To identify the isolated bacteria, we performed 16S rRNA sequencing analysis and found that the slow-growing strains were genetically similar to known bacterial species but also belonged to a novel group of species. The new strains identified were Caballeronia sp., Neobacillus sp., Bradyrhizobium sp., and high GC Gram-positive species. Furthermore, we conducted growth experiments using various culture media and temperature conditions. These experiments revealed an extended lag phase for five strains, indicating their slow growth characteristics. Genomic analysis of these five slow-growing bacteria showed their potential to participate in biogeochemical cycles, metabolize various carbohydrates, encode proteins with a role in promoting plant growth and have biosynthetic potential for secondary metabolites. Taken together, our findings reveal the untapped potential of slow-growing bacteria in tropical savanna soils.},
}
@article {pmid37507453,
year = {2023},
author = {Villela, H and Modolon, F and Schultz, J and Delgadillo-Ordoñez, N and Carvalho, S and Soriano, AU and Peixoto, RS},
title = {Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12273},
pmid = {37507453},
issn = {2045-2322},
mesh = {*Hydrocarbons/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; *Petroleum/metabolism ; Bacteria/genetics ; Alkanes/metabolism ; Biodegradation, Environmental ; },
abstract = {Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.},
}
@article {pmid37507436,
year = {2023},
author = {Melaugh, G and Martinez, VA and Baker, P and Hill, PJ and Howell, PL and Wozniak, DJ and Allen, RJ},
title = {Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {52},
pmid = {37507436},
issn = {2055-5008},
support = {BB/R012415/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI077628/AI/NIAID NIH HHS/United States ; R01 AI134895/AI/NIAID NIH HHS/United States ; R01 AI143916/AI/NIAID NIH HHS/United States ; },
mesh = {*Biofilms ; *Pseudomonas aeruginosa ; Polysaccharides, Bacterial/metabolism ; DNA ; },
abstract = {Pseudomonas aeruginosa forms suspended multicellular aggregates when cultured in liquid media. These aggregates may be important in disease, and/or as a pathway to biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have both been implicated in aggregation, but previous results depend strongly on the experimental conditions. Here we develop a quantitative microscopy-based method for assessing changes in the size distribution of suspended aggregates over time in growing cultures. For exponentially growing cultures of P. aeruginosa PAO1, we find that aggregation is mediated by cell-associated Psl, rather than by either eDNA or secreted Psl. These aggregates arise de novo within the culture via a growth process that involves both collisions and clonal growth, and Psl non-producing cells do not aggregate with producers. In contrast, we find that stationary phase (overnight) cultures contain a different type of multicellular aggregate, in which both eDNA and Psl mediate cohesion. Our findings suggest that the physical and biological properties of multicellular aggregates may be very different in early-stage vs late-stage bacterial cultures.},
}
@article {pmid37505287,
year = {2023},
author = {Feckler, A and Baudy-Groh, P and Friedrichs, L and Gonçalves, S and Lüderwald, S and Risse-Buhl, U and Bundschuh, M},
title = {Diatoms Reduce Decomposition of and Fungal Abundance on Less Recalcitrant Leaf Litter via Negative Priming.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2674-2686},
pmid = {37505287},
issn = {1432-184X},
support = {2017-0507//Vetenskapsr&#xe5;det/ ; },
mesh = {*Diatoms/metabolism ; Fungi/metabolism ; Rivers ; Plant Leaves/microbiology ; Carbon/metabolism ; Ecosystem ; },
abstract = {Heterotrophic microbial decomposers colonize submerged leaf litter in close spatial proximity to periphytic algae that exude labile organic carbon during photosynthesis. These exudates are conjectured to affect microbial decomposers' abundance, resulting in a stimulated (positive priming) or reduced (negative priming) leaf litter decomposition. Yet, the occurrence, direction, and intensity of priming associated with leaf material of differing recalcitrance remains poorly tested. To assess priming, we submerged leaf litter of differing recalcitrance (Alnus glutinosa [alder; less recalcitrant] and Fagus sylvatica [beech; more recalcitrant]) in microcosms and quantified bacterial, fungal, and diatom abundance as well as leaf litter decomposition over 30 days in absence and presence of light. Diatoms did not affect beech decomposition but reduced alder decomposition by 20% and alder-associated fungal abundance by 40% in the treatments including all microbial groups and light, thus showing negative priming. These results suggest that alder-associated heterotrophs acquired energy from diatom exudates rather than from leaf litter. Moreover, it is suggested that these heterotrophs have channeled energy to alternative (reproductive) pathways that may modify energy and nutrient availability for the remaining food web and result in carbon pools protected from decomposition in light-exposed stream sections.},
}
@article {pmid37505057,
year = {2024},
author = {Choudhary, M and Minsavage, GV and Goss, EM and Timilsina, S and Coutinho, TA and Vallad, GE and Paret, ML and Jones, JB},
title = {Whole-Genome-Sequence-Based Classification of Xanthomonas euvesicatoria pv. eucalypti and Computational Analysis of the Type III Secretion System.},
journal = {Phytopathology},
volume = {114},
number = {1},
pages = {47-60},
doi = {10.1094/PHYTO-05-23-0150-R},
pmid = {37505057},
issn = {0031-949X},
mesh = {Type III Secretion Systems ; Phylogeny ; *Eucalyptus ; Plant Diseases/microbiology ; *Xanthomonas ; },
abstract = {Xanthomonas spp. infect a wide range of annual and perennial plants. Bacterial blight in young seedlings of Eucalyptus spp. in Indonesia was originally identified as X. perforans. However, these strains failed to elicit a hypersensitive response (HR) on either tomatoes or peppers. Two of the strains, EPK43 and BCC 972, when infiltrated into tomato and pepper leaves, failed to grow to significant levels in comparison with well-characterized X. euvesicatoria pv. perforans (Xp) strains. Furthermore, spray inoculation of 'Bonny Best' tomato plants with a bacterial suspension of the Eucalyptus strains resulted in no obvious symptoms. We sequenced the whole genomes of eight strains isolated from two Eucalyptus species between 2007 and 2015. The strains had average nucleotide identities (ANIs) of at least 97.8 with Xp and X. euvesicatoria pv. euvesicatoria (Xeu) strains, both of which are causal agents of bacterial spot of tomatoes and peppers. A comparison of the Eucalyptus strains revealed that the ANI values were >99.99% with each other. Core genome phylogeny clustered all Eucalyptus strains with X. euvesicatoria pv. rosa. They formed separate clades, which included X. euvesicatoria pv. alangii, X. euvesicatoria pv. citrumelonis, and X. euvesicatoria pv. alfalfae. Based on ANI, phylogenetic relationships, and pathogenicity, we designated these Eucalyptus strains as X. euvesicatoria pv. eucalypti (Xee). Comparative analysis of sequenced strains provided unique profiles of type III secretion effectors. Core effector XopD, present in all pathogenic Xp and Xeu strains, was absent in the Xee strains. Comparison of the hrp clusters of Xee, Xp, and Xeu genomes revealed that HrpE in Xee strains was very different from that in Xp and Xeu. To determine if it was functional, we deleted the gene and complemented with the Xee hrpE, confirming it was essential for secretion of type III effectors. HrpE has a hypervariable N-terminus in Xanthomonas spp., in which the N-terminus of Xee strains differs significantly from those of Xeu and Xp strains.},
}
@article {pmid37500801,
year = {2023},
author = {Esser, SP and Rahlff, J and Zhao, W and Predl, M and Plewka, J and Sures, K and Wimmer, F and Lee, J and Adam, PS and McGonigle, J and Turzynski, V and Banas, I and Schwank, K and Krupovic, M and Bornemann, TLV and Figueroa-Gonzalez, PA and Jarett, J and Rattei, T and Amano, Y and Blaby, IK and Cheng, JF and Brazelton, WJ and Beisel, CL and Woyke, T and Zhang, Y and Probst, AJ},
title = {A predicted CRISPR-mediated symbiosis between uncultivated archaea.},
journal = {Nature microbiology},
volume = {8},
number = {9},
pages = {1619-1633},
pmid = {37500801},
issn = {2058-5276},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Archaea/genetics/metabolism ; *Symbiosis/genetics ; Genomics ; Plasmids ; DNA/metabolism ; },
abstract = {CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.},
}
@article {pmid37496156,
year = {2022},
author = {Wolfsberger, W and Chhugani, K and Shchubelka, K and Frolova, A and Salyha, Y and Zlenko, O and Arych, M and Dziuba, D and Parkhomenko, A and Smolanka, V and Gümüş, ZH and Sezgin, E and Diaz-Lameiro, A and Toth, VR and Maci, M and Bortz, E and Kondrashov, F and Morton, PM and Łabaj, PP and Romero, V and Hlávka, J and Mangul, S and Oleksyk, TK},
title = {Scientists without borders: lessons from Ukraine.},
journal = {GigaScience},
volume = {12},
number = {},
pages = {},
pmid = {37496156},
issn = {2047-217X},
support = {R33 CA263705/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Ukraine ; *Armed Conflicts ; *Science ; },
abstract = {Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades' worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.},
}
@article {pmid37491575,
year = {2023},
author = {Kim, JM and Yoo, SY and An, JS and Woo, JJ and Cho, YD and Park, HE and Karm, MH},
title = {Effect of a multichannel oral irrigator on periodontal health and the oral microbiome.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12043},
pmid = {37491575},
issn = {2045-2322},
mesh = {Humans ; Administration, Oral ; Dental Plaque Index ; *Microbiota ; *Periodontal Diseases ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Oral biofilms or dental plaques are one of the major etiological factors for diverse oral diseases. We aimed to evaluate the effect of a multichannel oral irrigator (MCOI) on periodontal health in 29 participants randomly divided into two groups: the MCOI group and the control group. To evaluate the effect of the MCOI on periodontal health, the modified Quigley Hein Plaque Index (PI), Mühlemann-Son Sulcus Bleeding Index (SBI), bleeding on probing (BOP), and swelling were evaluated and compared before and after MCOI use for 3 days. Although PI and SBI showed statistically significant increases in the control group, the MCOI group showed no significant changes in either parameter. Moreover, the percentage of BOP was significantly lower in the MCOI group. Saliva samples were analyzed by 16s rRNA amplicon sequencing to investigate changes in the oral microbiome. Sequencing results showed that Porphyromonas spp. were significantly increased in the control group, whereas no significant change was detected in the MCOI group. Using the MCOI, enriched populations and functional pathways were detected in pioneer species comprising non-mutans streptococci. These findings provide evidence of the effectiveness of the MCOI in maintaining periodontal health and a healthy microbial ecology in the oral cavity.},
}
@article {pmid37486583,
year = {2023},
author = {Zaman, R and Antonioli, F and Shah, A and Ullah, A and May, C and Klutsch, JG and Erbilgin, N},
title = {A Pine in Distress: How Infection by Different Pathogenic Fungi Affect Lodgepole Pine Chemical Defenses.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2666-2673},
pmid = {37486583},
issn = {1432-184X},
mesh = {Animals ; *Pinus/microbiology ; *Coleoptera/microbiology ; *Weevils ; Canada ; Terpenes ; },
abstract = {In North America, lodgepole pine is frequently subjected to attacks by various biotic agents that compromise its ability to defend against subsequent attacks by insect herbivores. We investigated whether infections of lodgepole pine by different pathogenic fungal species have varying effects on its defense chemistry. We selected two common pathogens, Atropellis canker, Atropellis piniphila, and western gall rust, Endocronartium harknessii, affecting mature lodgepole pine trees in western Canada. We also included three ophiostomatoid fungi Grosmannia clavigera, Ophiostoma montium, and Leptographium longiclavatum associated with the mountain pine beetle (Dendroctonus ponderosae), because they are commonly used to investigate induced defenses of host trees of bark beetles. We collected phloem samples from lodgepole pines infected with the rust or the canker and healthy lodgepole pines in the same stand. We also inoculated mature lodgepole pines with the three fungal symbionts and collected phloem samples 2 weeks later when the defense chemistry was at its highest level. Different fungal species differentially altered the terpene chemistry of lodgepole pine trees. E. harknessii and the fungal symbionts altered the terpene chemistry in a similar pattern while trees responded to the infection by the A. piniphila differently. Our study highlights the importance of considering specific biotic stress agents in tree susceptibility or resistance to the subsequent attacks by insect herbivores, such as mountain pine beetle.},
}
@article {pmid37485515,
year = {2023},
author = {Němečková, K and Mareš, J and Procházková, L and Culka, A and Košek, F and Wierzchos, J and Nedbalová, L and Dudák, J and Tymlová, V and Žemlička, J and Kust, A and Zima, J and Nováková, E and Jehlička, J},
title = {Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1175066},
pmid = {37485515},
issn = {1664-302X},
abstract = {In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.},
}
@article {pmid37485507,
year = {2023},
author = {Thiele, S and Vader, A and Thomson, S and Saubrekka, K and Petelenz, E and Müller, O and Bratbak, G and Øvreås, L},
title = {Seasonality of the bacterial and archaeal community composition of the Northern Barents Sea.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1213718},
pmid = {37485507},
issn = {1664-302X},
abstract = {The Barents Sea is a transition zone between the Atlantic and the Arctic Ocean. The ecosystem in this region is highly variable, and a seasonal baseline of biological factors is needed to monitor the effects of global warming. In this study, we report the results from the investigations of the bacterial and archaeal community in late winter, spring, summer, and early winter along a transect through the northern Barents Sea into the Arctic Ocean east of Svalbard using 16S rRNA metabarcoding. Winter samples were dominated by members of the SAR11 clade and a community of nitrifiers, namely Cand. Nitrosopumilus and LS-NOB (Nitrospinia), suggest a prevalence of chemoautotrophic metabolisms. During spring and summer, members of the Gammaproteobacteria (mainly members of the SAR92 and OM60(NOR5) clades, Nitrincolaceae) and Bacteroidia (mainly Polaribacter, Formosa, and members of the NS9 marine group), which followed a succession based on their utilization of different phytoplankton-derived carbon sources, prevailed. Our results indicate that Arctic marine bacterial and archaeal communities switch from carbon cycling in spring and summer to nitrogen cycling in winter and provide a seasonal baseline to study the changes in these processes in response to the effects of climate change.},
}
@article {pmid37485503,
year = {2023},
author = {Van Holm, W and Lauwens, K and De Wever, P and Schuermans, A and Zayed, N and Pamuk, F and Saghi, M and Fardim, P and Bernaerts, K and Boon, N and Teughels, W},
title = {Probiotics for oral health: do they deliver what they promise?.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1219692},
pmid = {37485503},
issn = {1664-302X},
abstract = {Probiotics have demonstrated oral health benefits by influencing the microbiome and the host. Although promising, their current use is potentially constrained by several restrictions. One such limiting factor lies in the prevailing preparation of a probiotic product. To commercialize the probiotic, a shelf stable product is achieved by temporarily inactivating the live probiotic through drying or freeze drying. Even though a lyophilized probiotic can be kept dormant for an extended period of time, their viability can be severely compromised, making their designation as probiotics questionable. Additionally, does the application of an inactive probiotic directly into the oral cavity make sense? While the dormancy may allow for survival on its way towards the gut, does it affect their capacity for oral colonisation? To evaluate this, 21 probiotic product for oral health were analysed for the number of viable (probiotic), culturable (CFU) and dead (postbiotic) cells, to verify whether the commercial products indeed contain what they proclaim. After isolating and uniformly lyophilizing three common probiotic species in a simple yet effective lyoprotective medium, the adhesion to saliva covered hydroxyapatite discs of lyophilized probiotics was compared to fresh or reactivated lyophilized probiotics. Unfortunately, many of the examined products failed to contain the claimed amounts of viable cells, but also the strains used were inadequately characterized and lacked clinical evidence for that unknown strain, questioning their label of a 'probiotic'. Additionally, lyophilized probiotics demonstrated low adhesive capacity compared to their counterparts, prompting the question of why fresh or reactivated probiotics are not currently used.},
}
@article {pmid37482337,
year = {2023},
author = {Santás-Miguel, V and Arias-Estévez, M and Rodríguez-Seijo, A and Arenas-Lago, D},
title = {Use of metal nanoparticles in agriculture. A review on the effects on plant germination.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {334},
number = {},
pages = {122222},
doi = {10.1016/j.envpol.2023.122222},
pmid = {37482337},
issn = {1873-6424},
mesh = {*Metal Nanoparticles/toxicity ; Silver/toxicity ; Agriculture/methods ; Soil ; *Nanoparticles ; Nanotechnology ; Germination ; },
abstract = {Agricultural nanotechnology has become a powerful tool to help crops and improve agricultural production in the context of a growing world population. However, its application can have some problems with the development of harvests, especially during germination. This review evaluates nanoparticles with essential (Cu, Fe, Ni and Zn) and non-essential (Ag and Ti) elements on plant germination. In general, the effect of nanoparticles depends on several factors (dose, treatment time, application method, type of nanoparticle and plant). In addition, pH and ionic strength are relevant when applying nanoparticles to the soil. In the case of essential element nanoparticles, Fe nanoparticles show better results in improving nutrient uptake, improving germination, and the possibility of magnetic properties could favor their use in the removal of pollutants. In the case of Cu and Zn nanoparticles, they can be beneficial at low concentrations, while their excess presents toxicity and negatively affects germination. About nanoparticles of non-essential elements, both Ti and Ag nanoparticles can be helpful for nutrient uptake. However, their potential effects depend highly on the crop type, particle size and concentration. Overall, nanotechnology in agriculture is still in its early stages of development, and more research is needed to understand potential environmental and public health impacts.},
}
@article {pmid37482010,
year = {2023},
author = {Pan, Y and Sun, RZ and Wang, Y and Chen, GL and Fu, YY and Yu, HQ},
title = {Carbon source shaped microbial ecology, metabolism and performance in denitrification systems.},
journal = {Water research},
volume = {243},
number = {},
pages = {120330},
doi = {10.1016/j.watres.2023.120330},
pmid = {37482010},
issn = {1879-2448},
mesh = {*Carbon/chemistry ; *Denitrification ; Methanol ; Glycerol ; Bioreactors/microbiology ; Acetates ; Glucose ; Nitrogen/metabolism ; Nitrates/metabolism ; },
abstract = {The limited information on microbial interactions and metabolic patterns in denitrification systems, especially those fed with different carbon sources, has hindered the establishment of ecological linkages between microscale connections and macroscopic reactor performance. In this work, denitrification performance, metabolic patterns, and ecological structure were investigated in parallel well-controlled bioreactors with four representative carbon sources, i.e., methanol, glycerol, acetate, and glucose. After long-term acclimation, significant differences were observed among the four bioreactors in terms of denitrification rates, organic utilization, and heterotrophic bacterial yields. Different carbon sources induced the succession of denitrifying microbiota toward different ecological structures and exhibited distinct metabolic patterns. Methanol-fed reactors showed distinctive microbial carbon utilization pathways and a more intricate microbial interaction network, leading to significant variations in organic utilization and metabolite production compared to other carbon sources. Three keystone taxa belonging to the Verrucomicrobiota phylum, SJA-15 order and the Kineosphaera genus appeared as network hubs in the methanol, glycerol, and acetate-fed systems, playing essential roles in their ecological functions. Several highly connected species were also identified within the glucose-fed system. The close relationship between microbial metabolites, ecological structures, and system performances suggests that this complex network relationship may greatly contribute to the efficient operation of bioreactors.},
}
@article {pmid37482007,
year = {2023},
author = {Wang, M and Wang, X and Zhou, S and Chen, Z and Chen, M and Feng, S and Li, J and Shu, W and Cao, B},
title = {Strong succession in prokaryotic association networks and community assembly mechanisms in an acid mine drainage-impacted riverine ecosystem.},
journal = {Water research},
volume = {243},
number = {},
pages = {120343},
doi = {10.1016/j.watres.2023.120343},
pmid = {37482007},
issn = {1879-2448},
mesh = {*Ecosystem ; Mining ; *Microbiota ; Microbial Consortia ; Fresh Water ; Iron ; },
abstract = {Acid mine drainage (AMD) serves as an ideal model system for investigating microbial ecology, interaction, and assembly mechanism in natural environments. While previous studies have explored the structure and function of microbial communities in AMD, the succession patterns of microbial association networks and underlying assembly mechanisms during natural attenuation processes remain elusive. Here, we investigated prokaryotic microbial diversity and community assembly along an AMD-impacted river, from the extremely acidic, heavily polluted headwaters to the nearly neutral downstream sites. Microbial diversity was increased along the river, and microbial community composition shifted from acidophile-dominated to freshwater taxa-dominated communities. The complexity and relative modularity of the microbial networks were also increased, indicating greater network stability during succession. Deterministic processes, including abiotic selection of pH and high contents of sulfur and iron, governed community assembly in the headwaters. Although the stochasticity ratio was increased downstream, manganese content, microbial negative cohesion, and relative modularity played important roles in shaping microbial community structure. Overall, this study provides valuable insights into the ecological processes that govern microbial community succession in AMD-impacted riverine ecosystems. These findings have important implications for in-situ remediation of AMD contamination.},
}
@article {pmid37480518,
year = {2023},
author = {O'Brien, L and Siboni, N and Seymour, JR and Balzer, M and Mitrovic, S},
title = {Tributary Inflows to a Regulated River Influence Bacterial Communities and Increase Bacterial Carbon Assimilation.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2642-2654},
pmid = {37480518},
issn = {1432-184X},
mesh = {*Rivers/chemistry ; *Carbon ; Ecosystem ; Water ; Bacteria/genetics ; },
abstract = {Inflows from unregulated tributaries change the physical, chemical, and biotic conditions in receiving regulated rivers, impacting microbial community structure and metabolic function. Understanding how tributary inflows affect bacterial carbon production (BCP) is integral to understanding energy transfer in riverine ecosystems. To investigate the role of tributary inflows on bacterial community composition and BCP, a ~90th percentile natural flow event was sampled over 5 days along the Lachlan River and its tributaries within the Murray-Darling Basin of eastern Australia. Increased tributary inflows after rainfall corresponded with a significantly different and more diverse bacterial community in the regulated mainstem. The major contributor to this difference was an increase in relative abundance of bacterial groups with a potential metabolic preference for humic substances (Burkholderiaceae Polynucleobacter, Alcaligenaceae GKS98 freshwater group, Saccharimonadia) and a significant decrease in Spirosomaceae Pseudarcicella, known to metabolise algal exudates. Increases in orthophosphate and river discharge explained 31% of community change, suggesting a combination of resource delivery and microbial community coalescence as major drivers. BCP initially decreased significantly with tributary inflows, but the total load of carbon assimilated by bacteria increased by up to 20 times with flow due to increased water volume. The significant drivers of BCP were dissolved organic carbon, water temperature, and conductivity. Notably, BCP was not correlated with bacterial diversity or community composition. Tributary inflows were shown to alter mainstem bacterial community structure and metabolic function to take advantage of fresh terrestrial dissolved organic material, resulting in substantial changes to riverine carbon assimilation over small times scales.},
}
@article {pmid37480517,
year = {2023},
author = {Aguado-López, D and Bartolomé, C and Lopes, AR and Henriques, D and Segura, SK and Maside, X and Pinto, MA and Higes, M and Martín-Hernández, R},
title = {Frequent Parasitism of Apis mellifera by Trypanosomatids in Geographically Isolated Areas with Restricted Beekeeping Movements.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2655-2665},
pmid = {37480517},
issn = {1432-184X},
support = {project No. SBPLY/19/180501/000334//Consejer&#xed;a de Educaci&#xf3;n, Cultura y Deportes, of the Junta de Castilla - La Mancha (European Regional development Fund)/ ; Grant no. PRE2018-084878, RTA2017-00004-C02-01//Ministerio de Asuntos Econ&#xf3;micos y Transformaci&#xf3;n Digital/ ; program COMPETE 2020-POCI//Programa Operacional para a Competividade e Internacionaliza&#xe7;&#xe3;o/ ; project BeeHappy (POCI-01-0145-FEDER-029871)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/143627/2019//Funda&#xe7;ao para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0007/2021//SusTEC/ ; INCRECYT program//European Social Funds/ ; },
mesh = {Animals ; Bees ; *Beekeeping ; *Trypanosomatina/genetics/parasitology ; Crithidia/genetics/parasitology ; Symbiosis ; Azores ; },
abstract = {Trypanosomatids form a group of high prevalence protozoa that parasitise honey bees, with Lotmaria passim as the predominant species worldwide. However, the knowledge about the ecology of trypanosomatids in isolated areas is limited. The Portuguese archipelagos of Madeira and Azores provide an interesting setting to investigate these parasites because of their geographic isolation, and because they harbour honey bee populations devoid of two major enemies: Varroa destructor and Nosema ceranae. Hence, a total of 661 honey bee colonies from Madeira and the Azores were analysed using different molecular techniques, through which we found a high prevalence of trypanosomatids despite the isolation of these islands. L. passim was the predominant species and, in most colonies, was the only one found, even on islands free of V. destructor and/or N. ceranae with severe restrictions on colony movements to prevent the spread of them. However, islands with V. destructor had a significantly higher prevalence of L. passim and, conversely, islands with N. ceranae did not shown any significant correlation with the trypanosomatid. Crithidia bombi was detected in Madeira and on three islands of the Azores, almost always coincident with L. passim. By contrast, Crithidia mellificae was not detected in any sample. A high-throughput sequencing analysis distinguished two main haplotypes of L. passim, which accounted for 98% of the total sequence reads. This work suggests that L. passim and C. bombi are parasites that have been associated with honey bees predating the spread of V. destructor and N. ceranae.},
}
@article {pmid37479828,
year = {2023},
author = {Ravindhiran, R and Sivarajan, K and Sekar, JN and Murugesan, R and Dhandapani, K},
title = {Listeria monocytogenes an Emerging Pathogen: a Comprehensive Overview on Listeriosis, Virulence Determinants, Detection, and Anti-Listerial Interventions.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2231-2251},
pmid = {37479828},
issn = {1432-184X},
mesh = {Animals ; Humans ; *Listeria monocytogenes/genetics ; *Listeria ; Virulence ; Food Microbiology ; *Listeriosis/diagnosis/epidemiology/microbiology ; Virulence Factors/genetics ; },
abstract = {Listeria monocytogenes, the third most deleterious zoonotic pathogen, is a major causative agent of animal and human listeriosis, an infection related to the consumption of contaminated food products. Even though, this pathogen has been responsible for the outbreaks of foodborne infections in the early 1980s, the major outbreaks have been reported during the past two decades. Listeriosis infection in the host is a rare but life-threatening disease with major public health and economic implications. Extensive reports on listeriosis outbreaks are associated with milk and milk products, meat and meat products, and fresh produce. This bacterium can adapt to any environmental and stress conditions, making it a prime causative agent for major foodborne diseases. The pathogen could survive an antibiotic treatment and persist in the host cell, thereby escaping the standard diagnostic practices. The current review strives to provide concise information on the epidemiology, serotypes, and pathogenesis of the L. monocytogenes to decipher the knowledge on the endurance of the pathogen inside the host and food products as a vehicle for Listeria contaminations. In addition, various detection methods for Listeria species from food samples and frontline regimens of L. monocytogenes treatment have also been discussed.},
}
@article {pmid37479827,
year = {2023},
author = {Hirata, K and Asahi, T and Kataoka, K},
title = {Spatial and Sexual Divergence of Gut Bacterial Communities in Field Cricket Teleogryllus occipitalis (Orthoptera: Gryllidae).},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2627-2641},
pmid = {37479827},
issn = {1432-184X},
mesh = {Animals ; Female ; Male ; *Gastrointestinal Microbiome ; *Gryllidae ; RNA, Ribosomal, 16S/genetics ; *Cricket Sport ; Bacteria/genetics ; },
abstract = {The insect gut is colonized by microbes that confer a myriad of beneficial services to the host, including nutritional support, immune enhancement, and even influence behavior. Insect gut microbes show dynamic changes due to the gut compartments, sex, and seasonal and geographic influences. Crickets are omnivorous hemimetabolous insects that have sex-specific roles, such as males producing chirping sounds for communication and exhibiting fighting behavior. However, limited information is available on their gut bacterial communities, hampering studies on functional compartmentalization of the gut and sex-specific roles of the gut microbiota in omnivorous insects. Here, we report a metagenomic analysis of the gut bacteriome of the field cricket Teleogryllus occipitalis using 16S rRNA V3-V4 amplicon sequencing to identify sex- and compartment-dependent influences on its diversity and function. The structure of the gut microbiota is strongly influenced by their gut compartments rather than sex. The species richness and diversity analyses revealed large difference in the bacterial communities between the gut compartments while minor differences were observed between the sexes. Analysis of relative abundance and predicted functions revealed that nitrogen- and oxygen-dependent metabolism and amino acid turnover were subjected to functional compartmentalization in the gut. Comparisons between the sexes revealed differences in the gut microbiota, reflecting efficiency in energy use, including glycolytic and carbohydrate metabolism, suggesting a possible involvement in egg production in females. This study provides insights into the gut compartment dependent and sex-specific roles of host-gut symbiont interactions in crickets and the industrial production of crickets.},
}
@article {pmid37478594,
year = {2023},
author = {Tang, Y and Wang, C and Holm, PE and Hansen, HCB and Brandt, KK},
title = {Impacts of biochar materials on copper speciation, bioavailability, and toxicity in chromated copper arsenate polluted soil.},
journal = {Journal of hazardous materials},
volume = {459},
number = {},
pages = {132067},
doi = {10.1016/j.jhazmat.2023.132067},
pmid = {37478594},
issn = {1873-3336},
mesh = {Humans ; Copper/toxicity ; *Trace Elements ; Biological Availability ; *Soil Pollutants/metabolism ; Charcoal ; Soil ; Triticum/metabolism ; },
abstract = {Trace element polluted soils pose risks to human and environmental health. Biochar can decrease trace element bioavailability in soils, but their resulting ability to reduce soil toxicity may vary significantly depending on feedstocks used, pyrolysis conditions, and the target pollutants. Chromated copper arsenate (CCA) polluted sites are common, but only very few types of biochar have been tested for these sites. Hence, we tested fourteen well-characterized biochar materials for their ability to bind Cu and reduce toxicity in a CCA polluted soil in a 56-day experiment. Biochar (1%, wt/wt) increased plant (wheat, Triticum aestivum L.) shoot and root growth by 6-58% and 0-73%, reduced soil toxicity to Arthrobacter globiformis by 7-55%, decreased bioavailable Cu (Pseudomonas fluorescens bioreporter) by 5-65%, and decreased free Cu[2+] ion activities by 27-89%. The A. globiformis solid-contact test constituted a sensitive ecotoxicological endpoint and deserves further attention for assessment of soil quality. Oil seed rape straw biochar generally performed better than other tested biochar materials. Biochar performance was positively correlated with its high cation exchange capacity, multiple surface functional groups, and high nitrogen and phosphorus content. Our results pave the way for future selection of feedstocks for creation of modified biochar materials with optimal performance in CCA polluted soil.},
}
@article {pmid37476672,
year = {2023},
author = {Zhang, Y and Wang, R},
title = {The human gut phageome: composition, development, and alterations in disease.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1213625},
pmid = {37476672},
issn = {1664-302X},
abstract = {The human gastrointestinal tract is colonized by a large number of microorganisms, including bacteria, archaea, viruses, and eukaryotes. The bacterial community has been widely confirmed to have a significant impact on human health, while viruses, particularly phages, have received less attention. Phages are viruses that specifically infect bacteria. They are abundant in the biosphere and exist in a symbiotic relationship with their host bacteria. Although the application of high-throughput sequencing and bioinformatics technology has greatly improved our understanding of the genomic diversity, taxonomic composition, and spatio-temporal dynamics of the human gut phageome, there is still a large portion of sequencing data that is uncharacterized. Preliminary studies have predicted that the phages play a crucial role in driving microbial ecology and evolution. Prior to exploring the function of phages, it is necessary to address the obstacles that hinder establishing a comprehensive sequencing database with sufficient biological properties and understanding the impact of phage-bacteria interactions on human health. In this study, we provide an overview of the human gut phageome, including its composition, structure, and development. We also explore the various factors that may influence the phageome based on current research, including age, diet, ethnicity, and geographical location. Additionally, we summarize the relationship between the phageome and human diseases, such as IBD, IBS, obesity, diabetes, and metabolic syndrome.},
}
@article {pmid37474781,
year = {2023},
author = {Yu, L and Khachaturyan, M and Matschiner, M and Healey, A and Bauer, D and Cameron, B and Cusson, M and Emmett Duffy, J and Joel Fodrie, F and Gill, D and Grimwood, J and Hori, M and Hovel, K and Hughes, AR and Jahnke, M and Jenkins, J and Keymanesh, K and Kruschel, C and Mamidi, S and Menning, DM and Moksnes, PO and Nakaoka, M and Pennacchio, C and Reiss, K and Rossi, F and Ruesink, JL and Schultz, ST and Talbot, S and Unsworth, R and Ward, DH and Dagan, T and Schmutz, J and Eisen, JA and Stachowicz, JJ and Van de Peer, Y and Olsen, JL and Reusch, TBH},
title = {Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina).},
journal = {Nature plants},
volume = {9},
number = {8},
pages = {1207-1220},
pmid = {37474781},
issn = {2055-0278},
mesh = {*Ecosystem ; *Zosteraceae/genetics ; Canada ; Phylogeography ; Oceans and Seas ; },
abstract = {Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.},
}
@article {pmid37470815,
year = {2023},
author = {Lee, K and Bogdanova, A and Missaoui, A},
title = {Host Genetic Background Effect on Vertical Seed Transmission of Epichloë Endophyte Strains in Tall Fescue.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2618-2626},
pmid = {37470815},
issn = {1432-184X},
mesh = {Endophytes/genetics ; *Lolium/genetics/microbiology ; *Epichloe/genetics ; Poaceae ; Seeds/microbiology ; *Festuca/microbiology ; },
abstract = {Tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) is a cool-season perennial grass widely grown for forage and turf. Tall fescue lives in association with a fungal endophyte that helps the grass overcome abiotic and biotic stressors. The endophyte is asexual and transmits vertically from the tall fescue plant to the next generation through the seed. Producers of endophyte-infected tall fescue must have endophyte infection in at least 70% of their seed. Therefore, endophyte seed transmission is vital in breeding and seed production. Transfer of endophytes from their native host to different backgrounds of elite tall fescue cultivars can lead to a low seed transmission of the endophyte to the seed. This study screened 23 previously uncharacterized endophyte strains for transmissibility when artificially inoculated into continental and Mediterranean-type host tall fescue. We found no correlation between the rate of successful inoculation and the seed transmission rate of the endophyte in the new host. Nor did the seed transmission rate of the endophyte strains in their native host correlate with the seed transmission rate of the endophyte in the new host. Five strains exhibited seed transmission above 70% in both Mediterranean and Continental host backgrounds and will be characterized further for potential use in cultivar development.},
}
@article {pmid37469593,
year = {2023},
author = {Riedel, T and Bunk, B and Schröttner, P},
title = {Editorial: Characterization of rare and recently first described human pathogenic bacteria.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1212627},
pmid = {37469593},
issn = {2235-2988},
mesh = {Humans ; *Bacteria/genetics ; *Genome, Bacterial ; },
}
@article {pmid37468677,
year = {2023},
author = {Banas, I and Esser, SP and Turzynski, V and Soares, A and Novikova, P and May, P and Moraru, C and Hasenberg, M and Rahlff, J and Wilmes, P and Klingl, A and Probst, AJ},
title = {Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere.},
journal = {The ISME journal},
volume = {17},
number = {10},
pages = {1789-1792},
pmid = {37468677},
issn = {1751-7370},
support = {863664/ERC_/European Research Council/International ; },
mesh = {*Archaea/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Viruses/genetics ; DNA, Viral/genetics ; },
abstract = {Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.},
}
@article {pmid37466247,
year = {2024},
author = {Avasthi, I and Lerner, H and Grings, J and Gräber, C and Schleheck, D and Cölfen, H},
title = {Biodegradable Mineral Plastics.},
journal = {Small methods},
volume = {8},
number = {4},
pages = {e2300575},
doi = {10.1002/smtd.202300575},
pmid = {37466247},
issn = {2366-9608},
support = {//Carl-Zeiss Foundation/ ; },
abstract = {Mineral plastics are a promising class of bio-inspired materials that offer exceptional properties, like self-heal ability, stretchability in the hydrogel state, and high hardness, toughness, transparency, and non-flammability in the dry state along with reversible transformation into the hydrogel by addition of water. This enables easy reshape-ability and recycling like the solubility in mild acids to subsequently form mineral plastics again by base addition. However, current mineral plastics rely on petrochemistry, are hardly biodegradable, and thus persistent in nature. This work presents the next generation of mineral plastics, which are bio-based and biodegradable, making them a promising, new class of polymers for the development of environmentally friendly materials. Physically cross-linked (poly)glutamic-acid (PGlu)-based mineral plastics are synthesized using various alcohol-water mixtures, metal ion ratios and molecular weights. The rheological properties are easily adjusted using these parameters. The general procedure involves addition of equimolar solution of CaCl2 to PGlu in equal volumes followed by addition of iPrOH (iPrOH:H2O = 1:1) under vigorous stirring conditions. The ready biodegradability of PGlu/CaFe mineral plastic is confirmed in this study where the elements N, Ca, and Fe present in it tend to act as additional nutrients, supporting the growth of microorganisms and consequently, promoting the biodegradation process.},
}
@article {pmid37461605,
year = {2023},
author = {Simpson, AC and Sengupta, P and Zhang, F and Hameed, A and Parker, CW and Singh, NK and Miliotis, G and Rekha, PD and Raman, K and Mason, CE and Venkateswaran, K},
title = {Phylogenetic affiliations and genomic characterization of novel bacterial species and their abundance in the International Space Station.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37461605},
issn = {2693-5015},
support = {R01 MH117406/MH/NIMH NIH HHS/United States ; },
abstract = {BACKGROUND: With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS).<br><br>RESULTS: The analysis of their 16S rRNA gene sequences revealed <99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited <93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average ucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, when compared to any known bacterial species, were less than <94% and 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including &#x3b2;-lactone and type III polyketide synthase (T3PKS) clusters.<br><br>CONCLUSIONS: Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10[T] (=NRRL B-65660[T]), Leifsonia virtsii, F6_8S_P_1A[T] (=NRRL B-65661[T]), Leifsonia williamsii, F6_8S_P_1B[T] (=NRRL B- 65662[T] and DSMZ 115932[T]), Paenibacillus vandeheii, F6_3S_P_1C[T](=NRRL B-65663[T] and DSMZ 115940[T]), and Sporosarcina highlanderae F6_3S_P_2 T(=NRRL B-65664[T] and DSMZ 115943[T]). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.},
}
@article {pmid37459919,
year = {2023},
author = {Wang, L and Zhu, L and Liang, C and Huang, X and Liu, Z and Huo, J and Zhang, Y and Zhang, Y and Chen, L and Xu, H and Li, X and Xu, L and Kuang, M and Wong, CC and Yu, J},
title = {Targeting N6-methyladenosine reader YTHDF1 with siRNA boosts antitumor immunity in NASH-HCC by inhibiting EZH2-IL-6 axis.},
journal = {Journal of hepatology},
volume = {79},
number = {5},
pages = {1185-1200},
doi = {10.1016/j.jhep.2023.06.021},
pmid = {37459919},
issn = {1600-0641},
abstract = {BACKGROUND &amp; AIMS: RNA N[6]-methyladenosine (m[6]A) reader protein YTHDF1 has been implicated in cancer; however, its role in hepatocellular carcinoma (HCC), especially in non-alcoholic steatohepatitis-associated HCC (NASH-HCC), remains unknown. Here, we investigated the functional role of YTHDF1 in NASH-HCC and its interplay with the tumor immune microenvironment.<br><br>METHODS: Hepatocyte-specific Ythdf1-overexpressing mice were subjected to a NASH-HCC-inducing diet. Tumor-infiltrating immune cells were profiled with single-cell RNA-sequencing, flow cytometry, and immunostaining. The molecular target of YTHDF1 was elucidated with RNA-sequencing, m[6]A-sequencing, YTHDF1 RNA immunoprecipitation-sequencing, proteomics, and ribosome-profiling. Ythdf1 in NASH-HCC models was targeted by lipid nanoparticle (LNP)-encapsulated small-interfering Ythdf1.<br><br>RESULTS: YTHDF1 is overexpressed in tumor tissues compared to adjacent peri-tumor tissues from patients with NASH-HCC. Liver-specific Ythdf1 overexpression drives tumorigenesis in dietary models of spontaneous NASH-HCC. Single-cell RNA-sequencing and flow cytometry revealed that Ythdf1 induced accumulation of myeloid-derived suppressor cells (MDSCs) and suppressed cytotoxic CD8[+] T-cell function. Mechanistically, Ythdf1 expression in NASH-HCC cells induced the secretion of IL-6, which mediated MDSC recruitment and activation, leading to CD8[+] T-cell dysfunction. EZH2 mRNA was identified as a key YTHDF1 target. YTHDF1 binds to m[6]A-modified EZH2 mRNA and promotes EZH2 translation. EZH2 in turn increased expression and secretion of IL-6. Ythdf1 knockout synergized with anti-PD-1 treatment to suppress tumor growth in NASH-HCC allografts. Furthermore, therapeutic targeting of Ythdf1 using LNP-encapsulated small-interfering RNA significantly increased the efficacy of anti-PD-1 blockade in NASH-HCC allografts.<br><br>CONCLUSIONS: We identified that YTHDF1 promotes NASH-HCC tumorigenesis via EZH2-IL-6 signaling, which recruits and activates MDSCs to cause cytotoxic CD8[+] T-cell dysfunction. YTHDF1 may be a novel therapeutic target to improve responses to anti-PD-1 immunotherapy in NASH-HCC.<br><br>IMPACT AND IMPLICATIONS: YTHDF1, a N[6]-methyladenosine reader, is upregulated in patients with non-alcoholic steatohepatitis (NASH)-associated hepatocellular carcinoma (HCC); however, its role in modulating the tumor immune microenvironment in NASH-HCC remains unclear. Here, we show that Ythdf1 mediates immunosuppression in NASH-HCC and that targeting YTHDF1 in combination with immune checkpoint blockade elicits robust antitumor immune responses. Our findings suggest novel therapeutic targets for potentiating the efficacy of immune checkpoint blockade in NASH-HCC and provide the rationale for developing YTHDF1 inhibitors for the treatment of NASH-HCC.},
}
@article {pmid37459796,
year = {2023},
author = {Sabbe, K and D'Haen, L and Boon, N and Ganigué, R},
title = {Predicting the performance of chain elongating microbiomes through flow cytometric fingerprinting.},
journal = {Water research},
volume = {243},
number = {},
pages = {120323},
doi = {10.1016/j.watres.2023.120323},
pmid = {37459796},
issn = {1879-2448},
mesh = {Fermentation ; *Caproates ; Flow Cytometry ; Bioreactors/microbiology ; *Microbiota ; },
abstract = {As part of the circular bio-economy paradigm shift, waste management and valorisation practices have moved away from sanitation and towards the production of added-value compounds. Recently, the development of mixed culture bioprocess for the conversion of waste(water) to platform chemicals, such as medium chain carboxylic acids, has attracted significant interest. Often, the microbiology of these novel bioprocesses is less diverse and more prone to disturbances, which can lead to process failure. This issue can be tackled by implementing an advanced monitoring strategy based on the microbiology of the process. In this study, flow cytometry was used to monitor the microbiology of lactic acid chain elongation for the production of caproic acid, and assess its performance both qualitatively and quantitatively. Two continuous stirred tank reactors for chain elongation were monitored flow cytometrically for over 336 days. Through community typing, four specific community types could be identified and correlated to both a specific functionality and genotypic diversity. Additionally, the machine-learning algorithms trained in this study demonstrated the ability to predict production rates of, amongst others, caproic acid with high accuracy in the present (R[2] > 0.87) and intermediate accuracy in the near future (R[2] > 0.63). The identification of specific community types and the development of predictive algorithms form the basis of advanced bioprocess monitoring based on flow cytometry, and have the potential to improve bioprocess control and optimization, leading to better product quality and yields.},
}
@article {pmid37458953,
year = {2024},
author = {Vélez-Martínez, GA and Reyes-Ardila, WL and Duque-Zapata, JD and Rugeles-Silva, PA and Muñoz Flórez, JE and López-Álvarez, D},
title = {Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {27},
number = {2},
pages = {377-391},
pmid = {37458953},
issn = {1618-1905},
mesh = {*Ecosystem ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Colombia ; Bacteria/genetics ; Forests ; Fungi/genetics ; Soil Microbiology ; },
abstract = {The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.},
}
@article {pmid37458790,
year = {2023},
author = {Huang, S and Lentendu, G and Fujinuma, J and Shiono, T and Kubota, Y and Mitchell, EAD},
title = {Soil Micro-eukaryotic Diversity Patterns Along Elevation Gradient Are Best Estimated by Increasing the Number of Elevation Steps Rather than Within Elevation Band Replication.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2606-2617},
pmid = {37458790},
issn = {1432-184X},
support = {182531/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Soil ; *Biodiversity ; Soil Microbiology ; Japan ; Nitrogen ; },
abstract = {The development of high-throughput sequencing (HTS) of environmental DNA (eDNA) has stimulated the study of soil microbial diversity patterns and drivers at all scales. However, given the heterogeneity of soils, a challenge is to define effective and efficient sampling protocols that allow sound comparison with other records, especially vegetation. In studies of elevational diversity pattern, a trade-off is choosing between replication within elevation bands vs. sampling more elevation bands. We addressed this question for soil protists along an elevation gradient on Mt. Asahi, Hokkaido, Japan. We compared two sampling approaches: (1) the replicate strategy (five replicates at six elevational bands, total = 30) and (2) the transect strategy (one sample in each of 16 different elevational bands). Despite a nearly twofold lower sampling effort, the transect strategy yielded congruent results compared to the replicate strategy for the estimation of elevational alpha diversity pattern: the regression coefficients between diversity indices and elevation did not differ between the two options. Furthermore, for a given total number of samples, gamma diversity estimated across the entire transect was higher when sampling more elevational bands as compared to replication from fewer elevational bands. Beta diversity (community composition turnover) was lower within a given elevational band than between adjacent bands and increased with elevation distance. In redundancy analyses, soil organic matter-related variable (the first principal component of soil organic matter, water content, total organic carbon, and nitrogen by whom were highly correlated) and elevation best explained elevational beta diversity pattern for both sampling approaches. Taken together, our results suggest that sampling a single plot per elevation band will be sufficient to obtain a good estimate of soil micro-eukaryotic diversity patterns along elevation gradients. This study demonstrated the effectiveness of the transect strategy in estimating diversity patterns along elevation gradients which is instructive for future environmental or even experimental studies. While not advocating for completely replacing replication-based sampling practices, it is important to note that both replicate and transect strategies have their merits and can be employed based on specific research goals and resource limitations.},
}
@article {pmid37458590,
year = {2023},
author = {Masuda, T and Inomura, K and Mareš, J and Kodama, T and Shiozaki, T and Matsui, T and Suzuki, K and Takeda, S and Deutsch, C and Prášil, O and Furuya, K},
title = {Coexistence of Dominant Marine Phytoplankton Sustained by Nutrient Specialization.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0400022},
pmid = {37458590},
issn = {2165-0497},
mesh = {Phytoplankton ; Ecosystem ; Seawater/microbiology ; Nitrates ; *Synechococcus ; Nitrogen ; *Ammonium Compounds ; },
abstract = {Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, but the basis for their coexistence has not been quantitatively demonstrated. Here, we combine in situ microcosm experiments and an ecological model to show that this coexistence can be sustained by specialization in the uptake of distinct nitrogen (N) substrates at low-level concentrations that prevail in subtropical environments. In field incubations, the response of both Prochlorococcus and Synechococcus to nanomolar N amendments demonstrates N limitation of growth in both populations. However, Prochlorococcus showed a higher affinity to ammonium, whereas Synechococcus was more adapted to nitrate uptake. A simple ecological model demonstrates that the differential nutrient preference inferred from field experiments with these genera may sustain their coexistence. It also predicts that as the supply of NO3[-] decreases, as expected under climate warming, the dominant genera should undergo a nonlinear shift from Synechococcus to Prochlorococcus, a pattern that is supported by subtropical field observations. Our study suggests that the evolution of differential nutrient affinities is an important mechanism for sustaining the coexistence of genera and that climate change is likely to shift the relative abundance of the dominant plankton genera in the largest biomes in the ocean. IMPORTANCE Our manuscript addresses the following fundamental question in microbial ecology: how do different plankton using the same essential nutrients coexist? Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, which support a significant amount of marine primary production. The geographical distributions of these two organisms are largely overlapping, but the basis for their coexistence in these biomes remains unclear. In this study, we combined in situ microcosm experiments and an ecosystem model to show that the coexistence of these two organisms can arise from specialization in the uptake of distinct nitrogen substrates; Prochlorococcus prefers ammonium, whereas Synechococcus prefers nitrate when these nutrients exist at low concentrations. Our framework can be used for simulating and predicting the coexistence in the future ocean and may provide hints toward understanding other similar types of coexistence.},
}
@article {pmid37458207,
year = {2023},
author = {Seto, M and Kondoh, M},
title = {Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity.},
journal = {Ecology letters},
volume = {26},
number = {10},
pages = {1714-1725},
doi = {10.1111/ele.14287},
pmid = {37458207},
issn = {1461-0248},
support = {JPMEERF20214103//Environmental Restoration and Conservation Agency/ ; JP19H05641//Japan Society for the Promotion of Science/ ; JP19K06853//Japan Society for the Promotion of Science/ ; JP21H05315//Japan Society for the Promotion of Science/ ; JP22K06390//Japan Society for the Promotion of Science/ ; JP23H04652//Japan Society for the Promotion of Science/ ; },
mesh = {*Ecosystem ; *Symbiosis/physiology ; Thermodynamics ; },
abstract = {Microbial life in low-energy ecosystems relies on individual energy conservation, optimizing energy use in response to interspecific competition and mutualistic interspecific syntrophy. Our study proposes a novel community-level strategy for increasing energy use efficiency. By utilizing an oxidation-reduction (redox) reaction network model that represents microbial redox metabolic interactions, we investigated multiple species-level competition and cooperation within the network. Our results suggest that microbial functional diversity allows for metabolic handoffs, which in turn leads to increased energy use efficiency. Furthermore, the mutualistic division of labour and the resulting complexity of redox pathways actively drive material cycling, further promoting energy exploitation. Our findings reveal the potential of self-organized ecological interactions to develop efficient energy utilization strategies, with important implications for microbial ecosystem functioning and the co-evolution of life and Earth.},
}
@article {pmid37454793,
year = {2023},
author = {Qi, L and Li, R and Wu, Y and Ibeanusi, V and Chen, G},
title = {Spatial distribution and assembly processes of bacterial communities in northern Florida freshwater springs.},
journal = {Environmental research},
volume = {235},
number = {},
pages = {116584},
doi = {10.1016/j.envres.2023.116584},
pmid = {37454793},
issn = {1096-0953},
mesh = {*Ecosystem ; Phylogeny ; Florida ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Fresh Water ; *Microbiota ; },
abstract = {Freshwater microorganisms are an essential component of the global biogeochemical cycle and a significant contributory factor in water quality. Unraveling the mechanisms controlling microbial community spatial distribution is crucial for the assessment of water quality and health of aquatic ecosystems. This research provided a comprehensive analysis of microbial communities in Florida freshwater springs. The 16S rRNA gene sequencing and bioinformatics analyses revealed the bacterial compositional heterogeneity as well as numerous unique ASVs and biomarkers in different springs. Statistical analysis showed both geographic distance and environmental variables contributed to regional bacterial community variation, while nitrate was the dominant environmental stressor that shaped the bacterial communities. The phylogenetic bin-based null model characterized both deterministic and stochastic factors contributing to community assembly in Florida springs, with the majority of bins dominated by ecological drift. Mapping of predicted pathways to the MetaCyc database revealed the inconsistency between microbial taxonomic and functional profiles, implying the functional redundancy pattern. Collectively, our work sheds insights into the microbial spatial distribution, community assembly, and function traits in one of the world's most productive aquifers. Therefore, this work provides a unique view of the health of Florida's artesian springs and offers new perspectives for freshwater quality assessment and sustainable management.},
}
@article {pmid37453005,
year = {2023},
author = {Nagpal, S and Mande, SS},
title = {Environmental insults and compensative responses: when microbiome meets cancer.},
journal = {Discover oncology},
volume = {14},
number = {1},
pages = {130},
pmid = {37453005},
issn = {2730-6011},
support = {PhD Sponsorship//Tata Consultancy Services/ ; },
abstract = {Tumor microenvironment has recently been ascribed a new hallmark-the polymorphic microbiome. Accumulating evidence regarding the tissue specific territories of tumor-microbiome have opened new and interesting avenues. A pertinent question is regarding the functional consequence of the interface between host-microbiome and cancer. Given microbial communities have predominantly been explored through an ecological perspective, it is important that the foundational aspects of ecological stress and the fight to 'survive and thrive' are accounted for tumor-micro(b)environment as well. Building on existing evidence and classical microbial ecology, here we attempt to characterize the ecological stresses and the compensative responses of the microorganisms inside the tumor microenvironment. What insults would microbes experience inside the cancer jungle? How would they respond to these insults? How the interplay of stress and microbial quest for survival would influence the fate of tumor? This work asks these questions and tries to describe this underdiscussed ecological interface of the tumor and its microbiota. It is hoped that a larger scientific thought on the importance of microbial competition sensing vis-à-vis tumor-microenvironment would be stimulated.},
}
@article {pmid37452612,
year = {2024},
author = {Hoque, E and Fritscher, J},
title = {Are anaerobic fungi crucial hidden players of microbiomes in anoxic environment?.},
journal = {Critical reviews in microbiology},
volume = {50},
number = {5},
pages = {540-563},
doi = {10.1080/1040841X.2023.2224425},
pmid = {37452612},
issn = {1549-7828},
mesh = {*Anaerobiosis ; *Microbiota ; Biofilms ; *Environment ; Fossils/microbiology ; *Mucor/classification/genetics/isolation &amp; purification ; *Aquatic Organisms/isolation &amp; purification ; DNA, Fungal/genetics ; Geologic Sediments/microbiology ; Adaptation, Physiological ; Groundwater/microbiology ; },
abstract = {Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research.},
}
@article {pmid37452527,
year = {2023},
author = {Soder-Walz, JM and Wasmund, K and Deobald, D and Vicent, T and Adrian, L and Marco-Urrea, E},
title = {Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses.},
journal = {Environmental microbiology},
volume = {25},
number = {11},
pages = {2604-2620},
doi = {10.1111/1462-2920.16464},
pmid = {37452527},
issn = {1462-2920},
mesh = {*Proteomics ; *Bacteria/genetics ; Genomics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Dehalobacter (Firmicutes) encompass obligate organohalide-respiring bacteria used for bioremediation of groundwater contaminated with halogenated organics. Various aspects of their biochemistry remain unknown, including the identities and interactions of respiratory proteins. Here, we sequenced the genome of Dehalobacter sp. strain 8M and analysed its protein expression. Strain 8M encodes 22 reductive dehalogenase homologous (RdhA) proteins. RdhA D8M_v2_40029 (TmrA) was among the two most abundant proteins during growth with trichloromethane and 1,1,2-trichloroethane. To examine interactions of respiratory proteins, we used blue native gel electrophoresis together with dehalogenation activity tests and mass spectrometry. The highest activities were found in gel slices with the highest abundance of TmrA. Protein distributions across gel lanes provided biochemical evidence that the large and small subunits of the membrane-bound [NiFe] uptake hydrogenase (HupL and HupS) interacted strongly and that HupL/S interacted weakly with RdhA. Moreover, the interaction of RdhB and membrane-bound b-type cytochrome HupC was detected. RdhC proteins, often encoded in rdh operons but without described function, migrated in a protein complex not associated with HupL/S or RdhA. This study provides the first biochemical evidence of respiratory protein interactions in Dehalobacter, discusses implications for the respiratory architecture and advances the molecular comprehension of this unique respiratory chain.},
}
@article {pmid37449414,
year = {2023},
author = {Ni, G and Leung, PM and Daebeler, A and Guo, J and Hu, S and Cook, P and Nicol, GW and Daims, H and Greening, C},
title = {Nitrification in acidic and alkaline environments.},
journal = {Essays in biochemistry},
volume = {67},
number = {4},
pages = {753-768},
pmid = {37449414},
issn = {1744-1358},
mesh = {*Nitrification ; *Ammonia/metabolism ; Ecosystem ; Oxidation-Reduction ; Bacteria/metabolism ; },
abstract = {Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.},
}
@article {pmid37446198,
year = {2023},
author = {Gu, X and Cao, Z and Zhao, L and Seswita-Zilda, D and Zhang, Q and Fu, L and Li, J},
title = {Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions.},
journal = {International journal of molecular sciences},
volume = {24},
number = {13},
pages = {},
pmid = {37446198},
issn = {1422-0067},
support = {RFSOCC2023-2025//Impact and Response of Antarctic Seas to Climate Change/ ; RFSOCC2023-2025//Jiang Li/ ; },
mesh = {Metagenomics ; Bacteria/genetics/metabolism ; *Rhodophyta/genetics ; Metagenome ; *Seaweed ; Polysaccharides/metabolism ; },
abstract = {Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.},
}
@article {pmid37442613,
year = {2023},
author = {Demarquest, G and Lajoie, G},
title = {Bacterial endophytes of sugar maple leaves vary more idiosyncratically than epiphytes across a large geographic area.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {9},
pages = {},
doi = {10.1093/femsec/fiad079},
pmid = {37442613},
issn = {1574-6941},
mesh = {Humans ; *Ecosystem ; Endophytes ; *Acer ; Bacteria/genetics ; Plants ; Plant Leaves/microbiology ; },
abstract = {Bacteria from the leaf surface and the leaf tissue have been attributed with several beneficial properties for their plant host. Though physically connected, the microbial ecology of these compartments has mostly been studied separately such that we lack an integrated understanding of the processes shaping their assembly. We sampled leaf epiphytes and endophytes from the same individuals of sugar maple across the northern portion of its range to evaluate if their community composition was driven by similar processes within and across populations differing in plant traits and overall abiotic environment. Leaf compartment explained most of the variation in community diversity and composition across samples. Leaf epiphytic communities were driven more by host and site characteristics than endophytic communities, whose community composition was more idiosyncratic across samples. Our results suggest a greater importance of priority effects and opportunistic colonization in driving community assembly of leaf endophytes. Understanding the comparative assembly of bacterial communities at the surface and inside plant leaves may be particularly useful for leveraging their respective potential for improving the health of plants in natural and anthropized ecosystems.},
}
@article {pmid37440561,
year = {2023},
author = {Fiedler, S and Schrader, H and Theobalt, N and Hofmann, I and Geiger, T and Arndt, D and Wanke, R and Schwaiger, J and Blutke, A},
title = {Standardized tissue sampling guidelines for histopathological and molecular analyses of rainbow trout (Oncorhynchus mykiss) in ecotoxicological studies.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0288542},
pmid = {37440561},
issn = {1932-6203},
mesh = {Animals ; *Oncorhynchus mykiss ; Ecotoxicology ; Reproducibility of Results ; *Water Pollutants, Chemical/toxicity ; },
abstract = {In ecotoxicology, evaluation of toxicities and no observed effect concentrations (NOEC) of test compounds in experimental fish is commonly based on molecular-, biochemical- and analytical chemistry analyses of organ/tissue samples and the assessment of (histo-) pathological lesions. Standardization of organ/tissue sampling locations, sample numbers, and sample processing contributes to warrant the reproducibility and inter- and intra-study comparability of analysis results. The present article provides the first comprehensive tissue sampling guidelines specifically adapted to rainbow trout (Oncorhynchus mykiss) as a frequently used fish species in ecotoxicological studies. A broad spectrum of ~40 different organs and tissues is covered. Appropriate sampling locations, sample sizes and sample numbers for subsequent routine histopathological evaluation (all organs/tissue) and for molecular analyses (~30 organs/tissues) are described in detail and illustrated with schematic drawings and representative macroscopic and histological images. These field-proven sampling guidelines were developed based on the pertinent literature and practical experience in ecotoxicological fish studies. They are intended to serve as a standard reference for any routine ecotoxicological study using rainbow trout as a test system. A broad application of the featured tissue sampling procedures will help to improve the reproducibility of analyses and to reduce inter- and intra-study variability induced by sampling bias and (normal) inter-sample morphological variation, and will therefore provide a robust basis for reliable characterization of toxicity and NOEC identification of diverse test substances and aquatic pollutants.},
}
@article {pmid37438876,
year = {2023},
author = {Basile, A and Heinken, A and Hertel, J and Smarr, L and Li, W and Treu, L and Valle, G and Campanaro, S and Thiele, I},
title = {Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2226921},
pmid = {37438876},
issn = {1949-0984},
support = {757922/ERC_/European Research Council/International ; RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Microbiota ; Inflammation ; Liver ; Anti-Bacterial Agents ; Escherichia coli ; },
abstract = {We report the first use of constraint-based microbial community modeling on a single individual with episodic inflammation of the gastrointestinal tract, who has a well documented set of colonic inflammatory biomarkers, as well as metagenomically-sequenced fecal time series covering seven dates over 16 months. Between the first two time steps the individual was treated with both steroids and antibiotics. Our methodology enabled us to identify numerous time-correlated microbial species and metabolites. We found that the individual's dynamical microbial ecology in the disease state led to time-varying in silico overproduction, compared to healthy controls, of more than 24 biologically important metabolites, including methane, thiamine, formaldehyde, trimethylamine N-oxide, folic acid, serotonin, histamine, and tryptamine. The microbe-metabolite contribution analysis revealed that some Dialister species changed metabolic pathways according to the inflammation phases. At the first time point, characterized by the highest levels of serum (complex reactive protein) and fecal (calprotectin) inflammation biomarkers, they produced L-serine or formate. The production of the compounds, through a cascade effect, was mediated by the interaction with pathogenic Escherichia coli strains and Desulfovibrio piger. We integrated the microbial community metabolic models of each time point with a male whole-body, organ-resolved model of human metabolism to track the metabolic consequences of dysbiosis at different body sites. The presence of D. piger in the gut microbiome influenced the sulfur metabolism with a domino effect affecting the liver. These results revealed large longitudinal variations in an individual's gut microbiome ecology and metabolite production, potentially impacting other organs in the body. Future simulations with more time points from an individual could permit us to assess how external drivers, such as diet change or medical interventions, drive microbial community dynamics.},
}
@article {pmid37438797,
year = {2023},
author = {Nguyen, LH and Okin, D and Drew, DA and Battista, VM and Jesudasen, SJ and Kuntz, TM and Bhosle, A and Thompson, KN and Reinicke, T and Lo, CH and Woo, JE and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Das Adhikari, U and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, MB and Kwon, DS and Huttenhower, C and Chan, AT and Lai, PS},
title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.},
journal = {Genome medicine},
volume = {15},
number = {1},
pages = {49},
pmid = {37438797},
issn = {1756-994X},
support = {K01 DK120742/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; UL1 TR002541/TR/NCATS NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Microbiota ; Metagenome ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.<br><br>METHODS: We profiled 127 hospitalized patients with COVID-19 (n&#x2009;=&#x2009;79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.<br><br>RESULTS: Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease.<br><br>CONCLUSIONS: Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.},
}
@article {pmid37438590,
year = {2023},
author = {Nava, V and Chandra, S and Aherne, J and Alfonso, MB and Antão-Geraldes, AM and Attermeyer, K and Bao, R and Bartrons, M and Berger, SA and Biernaczyk, M and Bissen, R and Brookes, JD and Brown, D and Cañedo-Argüelles, M and Canle, M and Capelli, C and Carballeira, R and Cereijo, JL and Chawchai, S and Christensen, ST and Christoffersen, KS and de Eyto, E and Delgado, J and Dornan, TN and Doubek, JP and Dusaucy, J and Erina, O and Ersoy, Z and Feuchtmayr, H and Frezzotti, ML and Galafassi, S and Gateuille, D and Gonçalves, V and Grossart, HP and Hamilton, DP and Harris, TD and Kangur, K and Kankılıç, GB and Kessler, R and Kiel, C and Krynak, EM and Leiva-Presa, &#xc0; and Lepori, F and Matias, MG and Matsuzaki, SS and McElarney, Y and Messyasz, B and Mitchell, M and Mlambo, MC and Motitsoe, SN and Nandini, S and Orlandi, V and Owens, C and Özkundakci, D and Pinnow, S and Pociecha, A and Raposeiro, PM and Rõõm, EI and Rotta, F and Salmaso, N and Sarma, SSS and Sartirana, D and Scordo, F and Sibomana, C and Siewert, D and Stepanowska, K and Tavşanoğlu, &#xdc;N and Tereshina, M and Thompson, J and Tolotti, M and Valois, A and Verburg, P and Welsh, B and Wesolek, B and Weyhenmeyer, GA and Wu, N and Zawisza, E and Zink, L and Leoni, B},
title = {Plastic debris in lakes and reservoirs.},
journal = {Nature},
volume = {619},
number = {7969},
pages = {317-322},
pmid = {37438590},
issn = {1476-4687},
mesh = {Ecosystem ; *Lakes/chemistry ; *Plastics/analysis/classification ; *Water Pollution/analysis/statistics &amp; numerical data ; Surveys and Questionnaires ; Urbanization ; *Water Supply ; Human Activities ; },
abstract = {Plastic debris is thought to be widespread in freshwater ecosystems globally[1]. However, a lack of comprehensive and comparable data makes rigorous assessment of its distribution challenging[2,3]. Here we present a standardized cross-national survey that assesses the abundance and type of plastic debris (>250 μm) in freshwater ecosystems. We sample surface waters of 38 lakes and reservoirs, distributed across gradients of geographical position and limnological attributes, with the aim to identify factors associated with an increased observation of plastics. We find plastic debris in all studied lakes and reservoirs, suggesting that these ecosystems play a key role in the plastic-pollution cycle. Our results indicate that two types of lakes are particularly vulnerable to plastic contamination: lakes and reservoirs in densely populated and urbanized areas and large lakes and reservoirs with elevated deposition areas, long water-retention times and high levels of anthropogenic influence. Plastic concentrations vary widely among lakes; in the most polluted, concentrations reach or even exceed those reported in the subtropical oceanic gyres, marine areas collecting large amounts of debris[4]. Our findings highlight the importance of including lakes and reservoirs when addressing plastic pollution, in the context of pollution management and for the continued provision of lake ecosystem services.},
}
@article {pmid37436063,
year = {2023},
author = {Smets, W and Chock, MK and Walsh, CM and Vanderburgh, CQ and Kau, E and Lindow, SE and Fierer, N and Koskella, B},
title = {Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0111123},
pmid = {37436063},
issn = {2150-7511},
mesh = {*Bacteria/genetics ; *Microbiota ; Plants/microbiology ; Plant Leaves/microbiology ; },
abstract = {Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain unclear, with previous studies reporting contradictory results regarding the importance of bacterial dispersal versus host selection. This discrepancy could be driven in part because leaf microbiome studies typically consider the upper and lower leaf surfaces as a single entity despite these habitats possessing considerable anatomical differences. We characterized the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces across 24 plant species. Leaf surface pH and stomatal density were found to shape phyllosphere community composition, and the underside of leaves had lower richness and higher abundances of core community members than upper leaf surfaces. We found fewer endemic bacteria on the upper leaf surfaces, suggesting that dispersal is more important in shaping these communities, with host selection being a more important force in microbiome assembly on lower leaf surfaces. Our study illustrates how changing the scale in which we observe microbial communities can impact our ability to resolve and predict microbial community assembly patterns on leaf surfaces. IMPORTANCE Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves.},
}
@article {pmid37434715,
year = {2023},
author = {Trexler, RV and Van Goethem, MW and Goudeau, D and Nath, N and Malmstrom, RR and Northen, TR and Couradeau, E},
title = {BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1176751},
pmid = {37434715},
issn = {1664-302X},
abstract = {Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.},
}
@article {pmid37433981,
year = {2023},
author = {Gomes, AFF and de Almeida, LG and Cônsoli, FL},
title = {Comparative Genomics of Pesticide-Degrading Enterococcus Symbionts of Spodoptera frugiperda (Lepidoptera: Noctuidae) Leads to the Identification of Two New Species and the Reappraisal of Insect-Associated Enterococcus Species.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2583-2605},
pmid = {37433981},
issn = {1432-184X},
support = {140835/2019-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2010/13714-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2011/50877-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Animals ; Spodoptera/genetics ; *Insecticides ; *Pesticides ; Larva ; Enterococcus/genetics ; Genomics ; DNA ; Zea mays ; },
abstract = {Enterococcus species have been described as core members of the microbial community of Spodoptera frugiperda (Lepidoptera: Noctuidae) and have been previously reported as insecticide degrading agents. This study aimed to investigate the molecular composition of these microbial symbionts of S. frugiperda to better understand their association with the host and their potential for insecticide metabolization. Through phenotypic assays and comparative genomic analyses of several pesticide-degrading Enterococcus isolated from the gut of S. frugiperda larvae, we identified two new species: Enterococcus entomosocium n. sp. and Enterococcus spodopteracolus n. sp. Their identities as new species were confirmed by whole genome alignment, utilizing cut-offs of 95-96% for the average nucleotide identity (ANI) and 70% for the digital DNA: DNA hybridization (dDDH) values. The systematic positioning of these new species within the genus Enterococcus was resolved using genome-based analysis, revealing Enterococcus casseliflavus as a sister group of E. entomosocium n. sp., and Enterococcus mundtii as a sister group of E. spodopteracolus n. sp. Comparative genomic analyses of several isolates of E. entomosocium n. sp. and E. spodopteracolus n. sp. provided a better assessment of the interactions established in the symbiotic association with S. frugiperda and led to the discovery of misidentified new species of Enterococcus associated with insects. Our analyses indicated that the potential of E. entomosocium n. sp. and E. spodopteracolus n. sp. to metabolize different pesticides arises from molecular mechanisms that result in rapid evolution of new phenotypes in response to environmental stressors, in this case, the pesticides their host insect is exposed to.},
}
@article {pmid37433980,
year = {2023},
author = {Candelori, A and Di Giuseppe, G and Villalobo, E and Sjödin, A and Vallesi, A},
title = {Bipolar Biogeographical Distribution of Parafrancisella Bacteria Carried by the Ciliate Euplotes.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3128-3132},
pmid = {37433980},
issn = {1432-184X},
support = {PNRA18_00152//PNRA (Programma Nazionale di Ricerca in Antartide)/ ; },
mesh = {Phylogeny ; *Euplotes/genetics/microbiology ; *Francisella ; Cytoplasm ; Antarctic Regions ; },
abstract = {Parafrancisella adeliensis, a Francisella-like endosymbiont, was found to reside in the cytoplasm of an Antarctic strain of the bipolar ciliate species, Euplotes petzi. To inquire whether Euplotes cells collected from distant Arctic and peri-Antarctic sites host Parafrancisella bacteria, wild-type strains of the congeneric bipolar species, E. nobilii, were screened for Parafrancisella by in situ hybridization and 16S gene amplification and sequencing. Results indicate that all Euplotes strains analyzed contained endosymbiotic bacteria with 16S nucleotide sequences closely similar to the P. adeliensis 16S gene sequence. This finding suggests that Parafrancisella/Euplotes associations are not endemic to Antarctica, but are common in both the Antarctic and Arctic regions.},
}
@article {pmid37432727,
year = {2023},
author = {Wang, J and Shi, K and Jing, Z and Ge, Y},
title = {Metagenomic Evidence for Cobamide Producers Driving Prokaryotic Co-occurrence Associations and Potential Function in Wastewater Treatment Plants.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {29},
pages = {10640-10651},
doi = {10.1021/acs.est.3c02181},
pmid = {37432727},
issn = {1520-5851},
mesh = {*Cobamides ; Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {Cobamides are required by most organisms but are only produced by specific prokaryotic taxa. These commonly shared cofactors play significant roles in shaping the microbial community and ecosystem function. Wastewater treatment plants (WWTPs) are the world's most common biotechnological systems; knowledge about sharing of cobamides among microorganisms is predicted to be important to decipher the complex microbial relationships in these systems. Herein, we explored prokaryotic potential cobamide producers in global WWTP systems based on metagenomic analyses. A set of 8253 metagenome-assembled genomes (MAGs) were recovered and 1276 (15.5%) of them were identified as cobamide producers, which could potentially be used for the practical biological manipulation of WWTP systems. Moreover, 8090 of the total recovered MAGs (98.0%) contained at least one enzyme family dependent on cobamides, indicating the sharing of cobamides among microbial members in WWTP systems. Importantly, our results showed that the relative abundance and number of cobamide producers improved the complexity of microbial co-occurrence networks and most nitrogen, sulfur, and phosphorus cycling gene abundances, indicating the significance of cobamides in microbial ecology and their potential function in WWTP systems. These findings enhance the knowledge of cobamide producers and their functions in WWTP systems, which has important implications for improving the efficiency of microbial wastewater treatment processes.},
}
@article {pmid37432469,
year = {2023},
author = {DiPietro, AG and Bryant, SA and Zanger, MM and Williamson, KE},
title = {Understanding Viral Impacts in Soil Microbial Ecology Through the Persistence and Decay of Infectious Bacteriophages.},
journal = {Current microbiology},
volume = {80},
number = {9},
pages = {276},
pmid = {37432469},
issn = {1432-0991},
mesh = {*Bacteriophages ; Soil Microbiology ; Ecology ; Fresh Water ; Soil ; },
abstract = {Marine bacteriophages have been well characterized in terms of decay rates, population dynamics in relation to their hosts, and their impacts on biogeochemical cycles in the global ocean. Knowledge in soil bacteriophage ecology lags considerably behind, with few studies documenting population dynamics with hosts and even fewer reporting phage decay rates. By using sterile soil or aquatic microcosms inoculated with single bacteriophage isolates, phage decay rates (loss of infectivity over time) were determined, independent of host interactions, for 5 model phage isolates. Decay rates varied by phage from 0.11-2.07% h[-1] in soils to 0.07-0.28% h[-1] in aquatic microcosms. For phages incubated in both soil and aquatic microcosms, the observed decay rate was consistently higher in soil microcosms than in aquatic microcosms by at least a factor of two. However, when decay rates for soil phage isolates in the present study were compared to those reported for marine and freshwater phage isolates from previous studies, the decay constants for soil phages were, on average, 4 times lower than those for aquatic phages. Slower rates of phage decay in soils indicate a lower turnover rate, which may have subsequent and potentially far-reaching impacts on virus-mediated mortality and bacterial activity. The wide range of decay rates observed in the present study and the lack of information on this critical aspect of virus-host dynamics in soil emphasizes the need for continued research in this field.},
}
@article {pmid37431054,
year = {2022},
author = {Seo, H and Lee, S and Park, H and Jo, S and Kim, S and Rahim, MA and Ul-Haq, A and Barman, I and Lee, Y and Seo, A and Kim, M and Jung, IY and Song, HY},
title = {Characteristics and Microbiome Profiling of Korean Gochang Bokbunja Vinegar by the Fermentation Process.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {20},
pages = {},
pmid = {37431054},
issn = {2304-8158},
support = {2021040D288//Gochang Bokbunja vinegar Research Project/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; },
abstract = {As NGS (next-generation sequencing) technology develops, metagenomics-based microbial ecology, that is, microbiome research, has recently led to the science of fermented food. Based on the above technology, a study was conducted to understand the characteristics of vinegar made from bokbunja, a local crop in Gochang-gun, Korea. Physicochemical characteristics of vinegar, organic acid analysis, microbial community analysis, and electronic tongue analysis were explored while fermenting the vinegar for 70 days under eight fermentation conditions according to the concentration of bokbunja liquid (100% or 50%), type of fermenter (porcelain jar or stainless container), and fermentation environment (natural outdoor conditions or temperature/oxygen controlled). As a result, distinct microbial community patterns were found in the stage of acetic acid fermentation and, accordingly, this fermentation of Gochang vinegar is classified into three categories. Vinegar prepared by the traditional method of outdoor fermentation using jars showed characteristics of "Acetobacter (42.1%)/Lactobacillus (56.9%) fusion fermentation". Under conditions where oxygen and temperature were controlled indoors using jars, characteristics of "Komagataeibacter (90.2%) fermentation" were found. "Lactobacillus (92.2%) fermentation" characteristics were discovered under natural outdoor conditions using stainless steel containers. These fermentation pattern differences were related to taxonomic phylogenetic diversity, which was also considered involved in determining organic acid production and taste. These results will be helpful as a scientific basis for understanding the fermentation characteristics of Gochang vinegar and developing high-value-added traditional vinegar products.},
}
@article {pmid37428189,
year = {2023},
author = {Rellegadla, S and Prajapat, G and Jain, S and Agrawal, A},
title = {Microbial communities succession post to polymer flood demonstrate a role in enhanced oil recovery.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {17},
pages = {5531-5544},
pmid = {37428189},
issn = {1432-0614},
support = {IMP/2018/000589//SERB Department of Science and Technology/ ; BT/PR25132/NER/95/1034/2017//Department of Biotechnology, Ministry of Science and Technology, India/ ; 09/1131(0028)/2019-EMR-I//CSIR India/ ; },
abstract = {The role of indigenous microbial communities in residual oil extraction following a recovery process is not well understood. This study investigated the dynamics of resident microbial communities in oil-field simulating sand pack bioreactors after the polymer flooding stage resumed with waterflooding and explored their contribution to the oil extraction process. The microbial community succession was studied through high-throughput sequencing of 16S rRNA genes. The results revealed alternating dominance of minority populations, including Dietzia sps., Acinetobacter sps., Soehngenia sps., and Paracoccus sps., in each bioreactor following the flooding process. Additionally, the post-polymer waterflooding stage led to higher oil recovery, with hydroxyethylcellulose, tragacanth gum, and partially hydrolyzed polyacrylamide polymer-treated bioreactors yielding additional recovery of 4.36%, 5.39%, and 3.90% residual oil in place, respectively. The dominant microbial communities were previously reported to synthesize biosurfactants and emulsifiers, as well as degrade and utilize hydrocarbons, indicating their role in aiding the recovery process. However, the correlation analysis of the most abundant taxa showed that some species were more positively correlated with the oil recovery process, while others acted as competitors for the carbon source. The study also found that higher biomass favored the plugging of high permeability zones in the reservoir, facilitating the dislodging of crude oil in new channels. In conclusion, this study suggests that microbial populations significantly shift upon polymer treatment and contribute synergistically to the oil recovery process depending on the characteristics of the polymers injected. KEY POINTS: • Post-polymer flooded microbial ecology shows unique indigenous microbial consortia. • Injected polymers are observed to act as enrichment substrates by resident communities. • The first study to show successive oil recovery stage post-polymer flood without external influence.},
}
@article {pmid37426976,
year = {2023},
author = {Wang, M and Cernava, T},
title = {Editorial: The phyllosphere microbiome.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1234843},
pmid = {37426976},
issn = {1664-462X},
}
@article {pmid37423403,
year = {2023},
author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Quintanilla-Carvajal, MX and Díaz, LE and Alzate, JF and Junca, H and Rodríguez Orjuela, JA and Villamil Diaz, LM},
title = {Evaluation of dietary single probiotic isolates and probiotic multistrain consortia in growth performance, gut histology, gut microbiota, immune regulation, and infection resistance of Nile tilapia, Oreochromis niloticus, shows superior monostrain performance.},
journal = {Fish &amp; shellfish immunology},
volume = {140},
number = {},
pages = {108928},
doi = {10.1016/j.fsi.2023.108928},
pmid = {37423403},
issn = {1095-9947},
mesh = {Animals ; *Cichlids ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Diet/veterinary ; *Tilapia ; Animal Feed/analysis ; *Fish Diseases ; Dietary Supplements ; },
abstract = {The probiotic potential of a designed bacterial consortia isolated from a competitive exclusion culture originally obtained from the intestinal contents of tilapia juveniles were evaluated on Nile tilapia alevins. The growth performance, intestinal histology, microbiota effects, resistance to Streptococcus agalactiae challenge, and immune response were assessed. In addition, the following treatments were included in a commercial feed: A12+M4+M10 (Lactococcus lactis A12, Priestia megaterium M4, and Priestia sp. M10), M4+M10 (P. megaterium M4, and Priestia sp. M10) and the single bacteria as controls; A12 (L. lactis A12), M4 (P. megaterium M4), M10 (Priestia sp. M10), also a commercial feed without any probiotic addition was included as a control. The results showed that all probiotic treatments improved the growth performance, intestinal histology, and resistance during experimental infection with S. agalactiae in comparison to the control fish. Also, the administration of probiotics resulted in the modulation of genes associated with the innate and adaptive immune systems that were non-dependent on microbial colonization. Surprisingly, L. lactis A12 alone induced benefits in fish compared to the microbial consortia, showing the highest increase in growth rate, survival during experimental infection with S. agalactiae, increased intestinal fold length, and the number of differentially expressed genes. Lastly, we conclude that a competitive exclusion culture is a reliable source of probiotics, and monostrain L. lactis A12 has comparable or even greater probiotic potential than the bacterial consortia.},
}
@article {pmid37422225,
year = {2023},
author = {Villar-dePablo, M and Ascaso, C and Rodríguez-Pérez, E and Urizal, M and Wierzchos, J and Pérez-Ortega, S and de Los Ríos, A},
title = {Innovative approaches to accurately assess the effectiveness of biocide-based treatments to fight biodeterioration of Cultural Heritage monuments.},
journal = {The Science of the total environment},
volume = {897},
number = {},
pages = {165318},
doi = {10.1016/j.scitotenv.2023.165318},
pmid = {37422225},
issn = {1879-1026},
mesh = {*Disinfectants/pharmacology ; *Cyanobacteria ; *Ascomycota ; Microscopy ; },
abstract = {The development of diagnostic methods to accurately assess the effects of treatments on lithobiont colonization remains a challenge for the conservation of Cultural Heritage monuments. In this study, we tested the efficacy of biocide-based treatments on microbial colonization of a dolostone quarry, in the short and long-term, using a dual analytical strategy. We applied a metabarcoding approach to characterize fungal and bacterial communities over time, integrated with microscopy techniques to analyze the interactions of microorganisms with the substrate and evaluate the effectiveness. These communities were dominated by the bacterial phyla Actinobacteriota, Proteobacteria and Cyanobacteria, and the fungal order Verrucariales, which include taxa previously reported as biodeteriogenic agents and observed here associated with biodeterioration processes. Following the treatments, changes over time in the abundance profiles depend on taxa. While Cyanobacteriales, Cytophagales and Verrucariales decreased in abundance, other groups, such as Solirubrobacteriales, Thermomicrobiales and Pleosporales increased. These patterns could be related not only to the specific effects of the biocide on the different taxa, but also to different recolonization abilities of those organisms. The different susceptibility to treatments could be associated with the inherent cellular properties of different taxa, but differences in biocide penetration to endolithic microhabitats could be involved. Our results demonstrate the importance of both removing epilithic colonization and applying biocides to act against endolithic forms. Recolonization processes could also explain some of the taxon-dependent responses, especially in the long-term. Taxa showing resistance, and those benefiting from nutrient accumulation in the form of cellular debris following treatments, may have an advantage in colonizing treated areas, pointing to the need for long-term monitoring of a wide range of taxa. This study highlights the potential utility of combining metabarcoding and microscopy to analyze the effects of treatments and design appropriate strategies to combat biodeterioration and establish preventive conservation protocols.},
}
@article {pmid37419360,
year = {2023},
author = {Martin-Pozas, T and Fernandez-Cortes, A and Cuezva, S and Cañaveras, JC and Benavente, D and Duarte, E and Saiz-Jimenez, C and Sanchez-Moral, S},
title = {New insights into the structure, microbial diversity and ecology of yellow biofilms in a Paleolithic rock art cave (Pindal Cave, Asturias, Spain).},
journal = {The Science of the total environment},
volume = {897},
number = {},
pages = {165218},
doi = {10.1016/j.scitotenv.2023.165218},
pmid = {37419360},
issn = {1879-1026},
mesh = {*Caves/microbiology ; Spain ; *Bacteria ; Ecology ; Biofilms ; },
abstract = {In the absence of sunlight, caves harbor a great diversity of microbial colonies to extensive biofilms with different sizes and colors visible to the naked eye. One of the most widespread and visible types of biofilm are those with yellow hues that can constitute a serious problem for the conservation of cultural heritage in many caves, such as Pindal Cave (Asturias, Spain). This cave, declared a World Heritage Site by UNESCO for its Paleolithic parietal art, shows a high degree of development of yellow biofilms that represents a real threat to the conservation of painted and engraved figures. This study aims to: 1) identify the microbial structures and the most characteristic taxa composing the yellow biofilms, 2) seek the linked microbiome reservoir primarily contributing to their growth; 3) seed light on the driving vectors that contribute to their formation and determine the subsequent proliferation and spatial distribution. To achieve this goal, we used amplicon-based massive sequencing, in combination with other techniques such as microscopy, in situ hybridization and environmental monitoring, to compare the microbial communities of yellow biofilms with those of drip waters, cave sediments and exterior soil. The results revealed microbial structures related to the phylum Actinomycetota and the most characteristic bacteria in yellow biofilms, represented by the genera wb1-P19, Crossiella, Nitrospira, and Arenimonas. Our findings suggest that sediments serve as potential reservoirs and colonization sites for these bacteria that can develop into biofilms under favorable environmental and substrate conditions, with a particular affinity for speleothems and rugged-surfaced rocks found in condensation-prone areas. This study presents an exhaustive study of microbial communities of yellow biofilms in a cave, which could be used as a procedure for the identification of similar biofilms in other caves and to design effective conservation strategies in caves with valuable cultural heritage.},
}
@article {pmid37419243,
year = {2023},
author = {Loyola-Fonseca, SC and Campello, AF and Rodrigues, RCV and Alves, FRF and Brasil, SC and Vilela, CLS and Gonçalves, LS and Provenzano, JC and Siqueira, JF and Rôças, IN},
title = {Disinfection and Shaping of Vertucci Class II Root Canals after Preparation with Two Instrument Systems and Supplementary Ultrasonic Activation of Sodium Hypochlorite.},
journal = {Journal of endodontics},
volume = {49},
number = {9},
pages = {1183-1190},
doi = {10.1016/j.joen.2023.06.017},
pmid = {37419243},
issn = {1878-3554},
mesh = {*Dental Pulp Cavity/diagnostic imaging/microbiology ; *Sodium Hypochlorite/therapeutic use ; X-Ray Microtomography ; Disinfection ; Ultrasonics ; Root Canal Preparation ; },
abstract = {INTRODUCTION: This study compared disinfection and shaping after root canal preparation with either XP-endo Shaper or TruNatomy instrument systems, supplemented by ultrasonic activation of sodium hypochlorite (NaOCl) with either stainless-steel (SS) or nickel-titanium (NiTi) inserts.<br><br>METHODS: Mesial roots from mandibular molars with Vertucci class II configuration were divided into 2 groups (n&#xa0;=&#xa0;24) based on anatomically paired micro-computed tomography (micro-CT) analyses. Pre and postpreparation micro-CT scans were obtained to evaluate the shaping performance. The canals were contaminated with a mixed bacterial culture for 30&#xa0;days and then subjected to preparation with either XP-endo Shaper or TruNatomy instruments using NaOCl irrigation. Supplementary ultrasonic activation of NaOCl was conducted using either an SS (TruNatomy group) or NiTi (XP-endo Shaper group) insert. Bacteriological samples were taken from the canals before preparation (S1), after preparation (S2), and after the supplementary approach (S3). Bacterial reduction was evaluated using a quantitative real-time polymerase chain reaction.<br><br>RESULTS: Preparation with both instrument systems significantly reduced bacterial counts (P&#xa0;<&#xa0;.01). After preparation, 36% (TruNatomy) and 35% (XP-endo Shaper) were negative for bacteria. These values increased to 59% and 65% after ultrasonic activation with the SS and NiTi inserts, respectively. The quantitative data in S2 showed that XP-endo Shaper promoted a significantly higher bacterial reduction than TruNatomy (P&#xa0;<&#xa0;.05). No significant intragroup differences were observed after ultrasonic activation (P&#xa0;>&#xa0;.05), probably because the SS insert promoted a significantly higher S2-to-S3 reduction than the NiTi insert (P&#xa0;<&#xa0;.01). Micro-CT analysis revealed no significant differences in the unprepared areas between the groups (P&#xa0;>&#xa0;.05).<br><br>CONCLUSIONS: The XP-endo Shaper caused a significantly higher bacterial reduction than TruNatomy in Vertucci class II canals. Better antibacterial results after ultrasonic activation were observed for the SS ultrasonic inserts than for the NiTi inserts.},
}
@article {pmid37418833,
year = {2024},
author = {Crump, BC and Bowen, JL},
title = {The Microbial Ecology of Estuarine Ecosystems.},
journal = {Annual review of marine science},
volume = {16},
number = {},
pages = {335-360},
doi = {10.1146/annurev-marine-022123-101845},
pmid = {37418833},
issn = {1941-0611},
mesh = {Animals ; Humans ; *Wetlands ; Estuaries ; Food Chain ; Carbon ; *Microbiota ; },
abstract = {Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.},
}
@article {pmid37417553,
year = {2023},
author = {Jansma, J and Thome, NU and Schwalbe, M and Chatziioannou, AC and Elsayed, SS and van Wezel, GP and van den Abbeele, P and van Hemert, S and El Aidy, S},
title = {Dynamic effects of probiotic formula ecologic®825 on human small intestinal ileostoma microbiota: a network theory approach.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2232506},
pmid = {37417553},
issn = {1949-0984},
mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; *Microbiota ; *Probiotics/pharmacology ; Propionates/pharmacology ; Enterobacteriaceae ; },
abstract = {The gut microbiota plays a pivotal role in health and disease. The use of probiotics as microbiota-targeted therapies is a promising strategy to improve host health. However, the molecular mechanisms involved in such therapies are often not well understood, particularly when targeting the small intestinal microbiota. In this study, we investigated the effects of a probiotic formula (Ecologic®825) on the adult human small intestinal ileostoma microbiota. The results showed that supplementation with the probiotic formula led to a reduction in the growth of pathobionts, such as Enterococcaceae and Enterobacteriaceae, and a decrease in ethanol production. These changes were associated with significant alterations in nutrient utilization and resistance to perturbations. These probiotic mediated alterations which coincided with an initial increase in lactate production and decrease in pH were followed by a sharp increase in the levels of butyrate and propionate. Moreover, the probiotic formula increased the production of multiple N-acyl amino acids in the stoma samples. The study demonstrates the utility of network theory in identifying novel microbiota-targeted therapies and improving existing ones. Overall, the findings provide insights into the dynamic molecular mechanisms underlying probiotic therapies, which can aid in the development of more effective treatments for a range of conditions.},
}
@article {pmid37415044,
year = {2023},
author = {King, NG and Uribe, R and Moore, PJ and Earp, HS and Gouraguine, A and Hinostroza, D and Perez-Matus, A and Smith, K and Smale, DA},
title = {Multiscale Spatial Variability and Stability in the Structure and Diversity of Bacterial Communities Associated with the Kelp Eisenia cokeri in Peru.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2574-2582},
pmid = {37415044},
issn = {1432-184X},
support = {MR/S032827/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Kelp/microbiology ; Ecosystem ; Peru ; Bacteria/genetics ; Biodiversity ; *Microbiota ; },
abstract = {Ecological communities are structured by a range of processes that operate over a range of spatial scales. While our understanding of such biodiversity patterns in macro-communities is well studied, our understanding at the microbial level is still lacking. Bacteria can be free living or associated with host eukaryotes, forming part of a wider "microbiome," which is fundamental for host performance and health. For habitat forming foundation-species, host-bacteria relationships likely play disproportionate roles in mediating processes for the wider ecosystem. Here, we describe host-bacteria communities across multiple spatial scales (i.e., from 10s of m to 100s of km) in the understudied kelp, Eisenia cokeri, in Peru. We found that E. cokeri supports a distinct bacterial community compared to the surrounding seawater, but the structure of these communities varied markedly at the regional (~480 km), site (1-10 km), and individual (10s of m) scale. The marked regional-scale differences we observed may be driven by a range of processes, including temperature, upwelling intensity, or regional connectivity patterns. However, despite this variability, we observed consistency in the form of a persistent core community at the genus level. Here, the genera Arenicella, Blastopirellula, Granulosicoccus, and Litorimonas were found in >80% of samples and comprised ~53% of total sample abundance. These genera have been documented within bacterial communities associated with kelps and other seaweed species from around the world and may be important for host function and wider ecosystem health in general.},
}
@article {pmid37415043,
year = {2023},
author = {Shao, Q and Lin, Z and Xu, Z and Zhu, Z and Zhou, C and Yan, X},
title = {Integrated Biogeography and Assembly Mechanisms of Microeukaryotic Communities in Coastal Waters Near Shellfish Cultivation.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2560-2573},
pmid = {37415043},
issn = {1432-184X},
support = {2022J195//Natural Science Foundation of Ningbo/ ; 2022S116//Public Welfare Science and Technology Project of Ningbo/ ; 2018YFD0900702//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Ecosystem ; Plankton/genetics ; *Diatoms ; China ; *Dinoflagellida/genetics ; *Arthropods ; Shellfish ; },
abstract = {The Lianjiang coast in the East China Sea is a typical subtropical marine ecosystem, and shellfish cultivation occupies almost all of the available tidal flats. Many studies have investigated the effects of shellfish cultivation on benthic organisms and sediments, while the impact of shellfish cultivation on plankton ecosystems is still poorly understood. This study investigated the biogeographical patterns of microeukaryotic communities from Lianjiang coastal waters in four seasons using 18S ribosomal RNA gene amplicon sequencing. Microeukaryotes were mainly comprised of Dinoflagellata, Diatomea, Arthropoda, Ciliophora, Chlorophyta, Protalveolata, Cryptophyceae, and Ochrophyta, and presented significant differences in three habitats (the aquaculture area, confluent area, and offshore area) and four seasons. Similarity percentage analysis revealed that Paracalanus parvus, Heterocapsa rotundata, Bestiolina similis, and five additional key taxa contributed to spatio-temporal differences. Seasonal environmental and spatial factors explained 27.47% of microeukaryotic community variation on average, with 11.11% of the variation shared. Environmental variables, particularly depth, pH, and nitrite concentration, were strongly associated with the microeukaryotic community compositions. The neutral community model further demonstrated that stochastic processes were sufficient in shaping substantial variation in microeukaryotic communities across four seasons, which may reveal the remaining unexplained microeukaryotic community variation. We further divided four seasons into the aquaculture stages and non-aquaculture stages, and speculated that aquaculture activities may increase the dispersal limitation of microeukaryotes in coastal waters, especially for the big bodied-microbes like Arthropoda. The results provide a better understanding of the biogeographical patterns, processes, and mechanisms of microeukaryotic communities near shellfish cultivation.},
}
@article {pmid37408642,
year = {2023},
author = {Kasahara, K and Leygeber, M and Seiffarth, J and Ruzaeva, K and Drepper, T and Nöh, K and Kohlheyer, D},
title = {Enabling oxygen-controlled microfluidic cultures for spatiotemporal microbial single-cell analysis.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1198170},
pmid = {37408642},
issn = {1664-302X},
abstract = {Microfluidic cultivation devices that facilitate O2 control enable unique studies of the complex interplay between environmental O2 availability and microbial physiology at the single-cell level. Therefore, microbial single-cell analysis based on time-lapse microscopy is typically used to resolve microbial behavior at the single-cell level with spatiotemporal resolution. Time-lapse imaging then provides large image-data stacks that can be efficiently analyzed by deep learning analysis techniques, providing new insights into microbiology. This knowledge gain justifies the additional and often laborious microfluidic experiments. Obviously, the integration of on-chip O2 measurement and control during the already complex microfluidic cultivation, and the development of image analysis tools, can be a challenging endeavor. A comprehensive experimental approach to allow spatiotemporal single-cell analysis of living microorganisms under controlled O2 availability is presented here. To this end, a gas-permeable polydimethylsiloxane microfluidic cultivation chip and a low-cost 3D-printed mini-incubator were successfully used to control O2 availability inside microfluidic growth chambers during time-lapse microscopy. Dissolved O2 was monitored by imaging the fluorescence lifetime of the O2-sensitive dye RTDP using FLIM microscopy. The acquired image-data stacks from biological experiments containing phase contrast and fluorescence intensity data were analyzed using in-house developed and open-source image-analysis tools. The resulting oxygen concentration could be dynamically controlled between 0% and 100%. The system was experimentally tested by culturing and analyzing an E. coli strain expressing green fluorescent protein as an indirect intracellular oxygen indicator. The presented system allows for innovative microbiological research on microorganisms and microbial ecology with single-cell resolution.},
}
@article {pmid37406718,
year = {2023},
author = {Lv, T and Wang, D and Hui, J and Cheng, W and Ai, H and Qin, L and Huang, M and Feng, M and Wu, Y},
title = {Effect of return activated sludge diversion ratio on phosphorus removal performance in side-stream enhanced biological phosphorus removal (S2EBPR) process.},
journal = {Environmental research},
volume = {235},
number = {},
pages = {116546},
doi = {10.1016/j.envres.2023.116546},
pmid = {37406718},
issn = {1096-0953},
mesh = {*Sewage ; *Phosphorus ; Bioreactors ; Wastewater ; Carbon ; },
abstract = {In this study, a lab-scale continuous flow side-stream enhanced biological phosphorus (P) removal (S2EBPR) reactor was operated for 247 days treating synthetic wastewater with influent carbon to phosphorus (C/P) ratio of 25.0 g COD/g P and influent PO4[3-]-P of 7.4 ± 0.3 mg P/L. The effect of the return activated sludge (RAS) diversion ratio on S2EBPR reactor was investigated by comparing P removal performance, microbial activity, and community structure. The results showed that the RAS diversion ratio of 8.0%, by yielding a side-stream sludge retention time (SRTSS) of ∼60 h, resulted in the lowest effluent PO4[3-]-P concentration of 0.5 ± 0.3 mg P/L. The results of in situ process profiles and ex situ P release and uptake batch tests under different RAS diversion conditions showed that the more anaerobic P release was obtained in the side-stream reactor, the higher the P removal efficiency and EBPR activity were achieved. The stoichiometric ratios observed in EBPR activity tests indicated a polyphosphate accumulating organisms (PAOs) metabolism mainly dependent on the glycolysis pathway. The results of microbial ecology analysis revealed that the optimized SRTSS would give a competitive advantage to PAOs in the S2EBPR process. By obtaining statistically reliable results, this study would provide guidance for wastewater treatment plants to achieve optimal P removal performance in S2EBPR configuration.},
}
@article {pmid37406090,
year = {2023},
author = {Pollak, S},
title = {Plant DNA in feces as a nutritional crystal ball.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {29},
pages = {e2309172120},
pmid = {37406090},
issn = {1091-6490},
mesh = {*DNA, Plant/analysis ; Feces/chemistry ; },
}
@article {pmid37405949,
year = {2023},
author = {Almeida-Silva, F and Van de Peer, Y},
title = {Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms.},
journal = {Molecular biology and evolution},
volume = {40},
number = {7},
pages = {},
pmid = {37405949},
issn = {1537-1719},
mesh = {Phylogeny ; *Gene Regulatory Networks ; *Magnoliopsida/genetics ; Gene Duplication ; Evolution, Molecular ; Genome, Plant ; Polyploidy ; },
abstract = {Angiosperms have a complex history of whole-genome duplications (WGDs), with varying numbers and ages of WGD events across clades. These WGDs have greatly affected the composition of plant genomes due to the biased retention of genes belonging to certain functional categories following their duplication. In particular, regulatory genes and genes encoding proteins that act in multiprotein complexes have been retained in excess following WGD. Here, we inferred protein-protein interaction (PPI) networks and gene regulatory networks (GRNs) for seven well-characterized angiosperm species and explored the impact of both WGD and small-scale duplications (SSDs) in network topology by analyzing changes in frequency of network motifs. We found that PPI networks are enriched in WGD-derived genes associated with dosage-sensitive intricate systems, and strong selection pressures constrain the divergence of WGD-derived genes at the sequence and PPI levels. WGD-derived genes in network motifs are mostly associated with dosage-sensitive processes, such as regulation of transcription and cell cycle, translation, photosynthesis, and carbon metabolism, whereas SSD-derived genes in motifs are associated with response to biotic and abiotic stress. Recent polyploids have higher motif frequencies than ancient polyploids, whereas WGD-derived network motifs tend to be disrupted on the longer term. Our findings demonstrate that both WGD and SSD have contributed to the evolution of angiosperm GRNs, but in different ways, with WGD events likely having a more significant impact on the short-term evolution of polyploids.},
}
@article {pmid37405460,
year = {2023},
author = {Suzuki, K and Katashima, K and Miki, T and Igarashi, H and Xu, Q and Ohkubo, S and Iwaishi, S and Harada, N},
title = {Bacterial Community Composition Under Paddy Conditions Is More Strongly Affected by the Difference in Soil Type than by Field Management.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2552-2559},
pmid = {37405460},
issn = {1432-184X},
mesh = {*Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Bacteria/genetics ; Agriculture/methods ; },
abstract = {In this study, we aimed to investigate the effects of soil type and field management on bacterial communities in paddy soils, taking into account the differences in soil physicochemical properties. We collected soil samples from 51 paddy fields in six prefectures in Japan. The paddy fields were managed under organic regimes (26 fields), natural-farming regimes (12 fields), or conventional regimes (13 fields). The paddy fields were classified into four soil types: andosol, gray lowland soil, gley soil, and gray upland soil. Soil DNA was extracted from the soil samples collected 2 to 10 weeks after the flooding, and the 16S rRNA gene amplicon sequencing analysis was performed. The bacterial community compositions were dominated by the phylum Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, and Firmicutes in all fields. The difference in soil type had significant effects on α-diversities of the bacterial communities, although the field management had no effect. The soil bacterial communities in the gley soils and gray upland soils individually formed different groups from those in the other soils, while the andosol and gray lowland soils tended to form relatively similar bacterial communities. On the other hand, the effects of the field management were estimated to be smaller than those of soil type. The β-diversity of the bacterial community compositions were significantly correlated with soil pH, total nitrogen content, total carbon content, and divalent iron content. Our results suggest that the soil microbial community in paddy fields may be strongly influenced by soil physiochemical properties derived from differences in soil type.},
}
@article {pmid37404190,
year = {2023},
author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG},
title = {Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {7},
pages = {e0017723},
pmid = {37404190},
issn = {1098-5336},
support = {T32 DK077653-29//HHS | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Bacteriophages/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Fruit ; Host Microbial Interactions ; },
abstract = {Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system. IMPORTANCE Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms is CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate the bacteria and phage populations from a simple marine microbial community, known as "pink berries", found in salt marshes of Falmouth, Massachusetts, as a model of phage-host coevolution. We identify eight novel phages and characterize a case of putative CRISPR-driven phage evolution as well as an instance of HGT between a phage and its host, together suggesting that phages have large evolutionary impacts in a naturally occurring microbial community.},
}
@article {pmid37404136,
year = {2023},
author = {Li, H and Zhou, H and Yang, S and Dai, X},
title = {Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {7},
pages = {e0070123},
pmid = {37404136},
issn = {1098-5336},
mesh = {*Ecosystem ; China ; },
abstract = {Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.},
}
@article {pmid37402057,
year = {2023},
author = {Hkiri, N and Aounallah, F and Fouzai, K and Chouchani, C and Asses, N},
title = {Ability of marine-derived fungi isolated from polluted saline environment for enzymatic hydrocarbon remediation.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {54},
number = {3},
pages = {1983-2000},
pmid = {37402057},
issn = {1678-4405},
mesh = {*Lignin/metabolism ; Laccase/genetics/metabolism ; Peroxidases/metabolism ; Fungi/metabolism ; *Petroleum/metabolism ; Biodegradation, Environmental ; },
abstract = {Marine-derived fungi have attracted much attention due to their ability to present a new biosynthetic diversity. About 50 fungal isolates were obtained from Tunisian Mediterranean seawater and then screened for the presence of lignin-peroxidase (LiP), manganese-dependent peroxidase (MnP), and laccase (Lac) activities. The results obtained from both qualitative and quantitative assays showed that four of marine fungi isolates had a high potential to produce lignin-degrading enzymes. They were characterized taxonomically by a molecular method, based on international spacer (ITS) rDNA sequence analysis, as Chaetomium jodhpurense (MH667651.1), Chaetomium maderasense (MH665977.1), Paraconiothyrium variabile (MH667653.1), and Phoma betae (MH667655.1) which have been reported as producers of ligninolytic enzyme in the literature. The enzymatic activities and culture conditions were optimized using a Fractional Factorial design (2 [7- 4]). Then, fungal strains were incubated with the addition of 1% of crude oil in 50% of seawater for 25 days to evaluate their abilities to simultaneously degrade hydrocarbon compounds and to produce ligninolytic enzymes. The strain P. variabile exhibited the highest crude oil degradation rate (48.3%). Significant production of ligninolytic enzymes was recorded during the degradation process, which reached 2730 U/L for the MnP, 410 U/L for LiP, and 168.5 U/L for Lac. The FTIR and GC-MS analysis confirmed that the isolates rapidly biodegrade crude oil under ecological and economic conditions.},
}
@article {pmid37401933,
year = {2023},
author = {Chen, L and Xin, X and Li, J and Han, C and Xiong, W and Luo, Y and Sun, R and Zhang, J},
title = {Phosphorus Fertilization Boosts Mineral-Associated Soil Organic Carbon Formation Associated with Phagotrophic Protists.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2541-2551},
pmid = {37401933},
issn = {1432-184X},
support = {42177332//National Natural Science Foundation of China/ ; XDA24020104 and XDA28020203//Strategic Priority Research Program of Chinese Academy of Sciences/ ; 2022YFD1500203 and 2022YFD1500401//National Key Research and Development Program of China/ ; 2023325//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; CARS-03-15 and CARS-52//China Agriculture Research System/ ; },
mesh = {*Soil ; *Phosphorus/metabolism ; Carbon/metabolism ; Soil Microbiology ; Minerals/metabolism ; Bacteria/genetics/metabolism ; Fertilizers/analysis ; Fertilization ; },
abstract = {Long-term fertilization affects soil organic C accumulation. A growing body of research has revealed critical roles of bacteria in soil organic C accumulation, particularly through mineral-associated organic C (MAOC) formation. Protists are essential components of soil microbiome, but the relationships between MAOC formation and protists under long-term fertilization remain unclear. Here, we used cropland soil from a long-term fertilization field trial and conducted two microcosm experiments with [13]C-glucose addition to investigate the effects of N and P fertilizations on MAOC formation and the relationships with protists. The results showed that long-term fertilization (especially P fertilization) significantly (P < 0.05) increased [13]C-MAOC content. Compared with P-deficient treatment, P replenishment enriched the number of protists (mainly Amoebozoa and Cercozoa) and bacteria (mainly Acidobacteriota, Bacteroidota, and Gammaproteobacteria), and significantly (P < 0.001) promoted the abundances of bacterial functional genes controlling C, N, P, and S metabolisms. The community composition of phagotrophic protists prominently (P < 0.001) correlated with the bacterial community composition, bacterial functional gene abundance, and [13]C-MAOC content. Co-occurrence networks of phagotrophic protists and bacteria were more connected in soil with the N inoculum added than in soil with the NP inoculum added. P replenishment strengthened bacterial [13]C assimilation (i.e., [13]C-phospholipid fatty acid content), which negatively (P < 0.05) correlated with the number and relative abundance of phagotrophic Cercozoa. Together, these results suggested that P fertilization boosts MAOC formation associated with phagotrophic protists. Our study paves the way for future research to harness the potential of protists to promote belowground C accrual in agroecosystems.},
}
@article {pmid37396621,
year = {2023},
author = {Moens, F and Vandevijver, G and De Blaiser, A and Larsson, A and Spreafico, F and Augustijns, P and Marzorati, M},
title = {The Dynamic Intestinal Absorption Model (Diamod®), an in vitro tool to study the interconnected kinetics of gastrointestinal solubility, supersaturation, precipitation, and intestinal permeation processes of oral drugs.},
journal = {International journal of pharmaceutics: X},
volume = {5},
number = {},
pages = {100177},
pmid = {37396621},
issn = {2590-1567},
abstract = {This study aimed at developing the Diamod® as a dynamic gastrointestinal transfer model with physically interconnected permeation. The Diamod® was validated by studying the impact of the intraluminal dilution of a cyclodextrin-based itraconazole solution and the negative food effect for indinavir sulfate for which clinical data are available demonstrating that the systemic exposure was strongly mediated by interconnected solubility, precipitation, and permeation processes. The Diamod® accurately simulated the impact of water intake on the gastrointestinal behavior of a Sporanox® solution. Water intake significantly decreased the duodenal solute concentrations of itraconazole as compared to no intake of water. Despite this duodenal behavior the amount of permeated itraconazole was not affected by water intake as observed in vivo. Next to this, the Diamod® accurately simulated the negative food effect for indinavir sulfate. Different fasted and fed state experiments demonstrated that this negative food effect was mediated by an increased stomach pH, entrapment of indinavir in colloidal structures and the slower gastric emptying of indinavir under fed state conditions. Therefore, it can be concluded that the Diamod® is a useful in vitro model to mechanistically study the gastrointestinal performance of drugs.},
}
@article {pmid37395875,
year = {2023},
author = {Simon, MP and Schatz, M and Böhm, L and Papp, I and Grossart, HP and Andersen, TJ and Bálint, M and Düring, RA},
title = {Dissent in the sediment? Lake sediments as archives of short- and long-range impact of anthropogenic activities in northeastern Germany.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {36},
pages = {85867-85888},
pmid = {37395875},
issn = {1614-7499},
support = {DFG BA 4843/2-1//Deutsche Forschungsgemeinschaft/ ; K314/2020//Deutsche Forschungsgemeinschaft/ ; K314/2020//Leibniz-Gemeinschaft/ ; },
mesh = {DDT/analysis ; Lakes/analysis ; Anthropogenic Effects ; Dissent and Disputes ; *Water Pollutants, Chemical/analysis ; *Pesticides/analysis ; *Hydrocarbons, Chlorinated/analysis ; Geologic Sediments/chemistry ; Environmental Monitoring/methods ; China ; },
abstract = {The suitability of lake sediment cores to reconstruct past inputs, regional pollution, and usage patterns of pesticides has been shown previously. Until now, no such data exist for lakes in eastern Germany. Therefore, 10 sediment cores (length 1 m) of 10 lakes in eastern Germany, the territory of the former German Democratic Republic (GDR), were collected and cut into 5-10-mm layers. In each layer, concentrations of trace elements (TEs) As, Cd, Cr, Cu, Ni, Pb, S, and Zn, as well as of organochlorine pesticides (OCPs), i.e., dichlorodiphenyltrichloroethane (DDT) and hexachlorocyclohexane (HCH), were analyzed. A miniaturized solid-liquid extraction technique in conjunction with headspace solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) was used for the latter. The progression of TE concentrations over time is uniform. It follows a trans-regional pattern and is indicative of activity and policy making in West Germany before 1990 instead of those in the GDR. Of OCPs, only transformation products of DDT were found. Congener ratios indicate a mainly aerial input. In the lakes' profiles, several regional features and responses to national policies and measures are visible. Dichlorodiphenyldichloroethane (DDD) concentrations reflect the history of DDT use in the GDR. Lake sediments proved to be suitable to archive short- and long-range impacts of anthropogenic activity. Our data can be used to complement and validate other forms of environmental pollution long-term monitoring and to check for the efficiency of pollution countermeasures in the past.},
}
@article {pmid37393557,
year = {2023},
author = {Madrigal-Trejo, D and Sánchez-Pérez, J and Espinosa-Asuar, L and Valdivia-Anistro, JA and Eguiarte, LE and Souza, V},
title = {A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2252-2270},
pmid = {37393557},
issn = {1432-184X},
support = {IG200319//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; 970341//Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACYT)/ ; R20F009//http://dx.doi.org/10.13039/501100020884/ ; },
mesh = {Metagenome ; *Cyanobacteria/genetics ; Archaea/genetics ; *Microbiota ; Bacteroidetes/genetics ; },
abstract = {Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant marginalized environments. These structures are considered highly stable ecosystems. In this study, we evaluate the ecological stability of dome-forming microbial mats in a modern, water-level fluctuating, hypersaline pond located in the Cuatro Ciénegas Basin, Mexico. We conducted metagenomic sampling of the site from 2016 to 2019 and detected 2250 genera of Bacteria and Archaea, with only <20 belonging to the abundant taxa (>1%). The microbial community was dominated by Proteobacteria, Euryarchaeota, Bacteroidetes, Firmicutes, and Cyanobacteria, and was compositionally sensitive to disturbances, leading to high taxonomic replacement even at the phylum level, with a significant increase in Archaea from [Formula: see text]1-4% to [Formula: see text]33% throughout the 2016-2019 study period. Although a core community represented most of the microbial community (>75%), relative abundances shifted significantly between samples, as demonstrated by changes in the abundance of Coleofasciculus from 10.2% in 2017 to 0.05% in 2019. Although functional differences between seasons were subtle, co-occurrence networks suggest differential ecological interactions between the seasons, with the addition of a new module during the rainy season and the potential shift in hub taxa. Functional composition was slightly more similar between samples, but basic processes such as carbohydrate, amino acid, and nucleic acid metabolisms were widely distributed among samples. Major carbon fixation processes included sulfur oxidation, nitrogen fixation, and photosynthesis (both oxygenic and anoxygenic), as well as the Wood-Ljundgahl and Calvin cycles.},
}
@article {pmid37392205,
year = {2023},
author = {Woźniak, M and Tyśkiewicz, R and Siebielec, S and Gałązka, A and Jaroszuk-Ściseł, J},
title = {Metabolic Profiling of Endophytic Bacteria in Relation to Their Potential Application as Components of Multi-Task Biopreparations.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2527-2540},
pmid = {37392205},
issn = {1432-184X},
mesh = {Humans ; *Ecosystem ; *Bacteria ; Endophytes ; Crops, Agricultural ; Stress, Physiological ; },
abstract = {Agricultural crops are exposed to various abiotic and biotic stresses that can constrain crop productivity. Focusing on a limited subset of key groups of organisms has the potential to facilitate the monitoring of the functions of human-managed ecosystems. Endophytic bacteria can enhance plant stress resistance and can help plants to cope with the negative impacts of stress factors through the induction of different mechanisms, influencing plant biochemistry and physiology. In this study, we characterise endophytic bacteria isolated from different plants based on their metabolic activity and ability to synthesise 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD), the activity of hydrolytic exoenzymes, the total phenolic compounds (TPC) and iron-complexing compounds (ICC). Test GEN III MicroPlate indicated that the evaluated endophytes are highly metabolically active, and the best used substrates were amino acids, which may be important in selecting potential carrier components for bacteria in biopreparations. The ACCD activity of strain ES2 (Stenotrophomonas maltophilia) was the highest, whereas that of strain ZR5 (Delftia acidovorans) was the lowest. Overall, the obtained results indicated that ∼91.3% of the isolates were capable of producing at least one of the four hydrolytic enzymes. In addition, most of the tested strains produced ICC and TPC, which play a significant role in reducing stress in plants. The results of this study suggest that the tested endophytic bacterial strains can potentially be used to mitigate climate change-associated stresses in plants and to inhibit plant pathogens.},
}
@article {pmid37392204,
year = {2023},
author = {Berçot, MR and Queiroz, PRM and Grynberg, P and Togawa, R and Martins, &#xc9;S and Rocha, GT and Monnerat, RG},
title = {Distribution and Genetic Diversity of Genes from Brazilian Bacillus thuringiensis Strains Toxic to Agricultural Insect Pests Revealed by Real-Time PCR.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2515-2526},
pmid = {37392204},
issn = {1432-184X},
mesh = {Animals ; *Bacillus thuringiensis/genetics ; Endotoxins/genetics/chemistry ; Real-Time Polymerase Chain Reaction ; Bacillus thuringiensis Toxins ; Brazil ; Bacterial Proteins/genetics/chemistry ; Insecta ; Genetic Variation ; Hemolysin Proteins/genetics/chemistry ; },
abstract = {Bacillus thuringiensis is a Gram-positive aerobic bacterium and the most used biopesticide worldwide. Given the importance of B. thuringiensis strain characterization for the development of new bioinsecticides or transgenic events and the identification and classification of new B. thuringiensis genes and strains to understand its distribution and diversity, this work is aimed at creating a gene identification system based on qPCR reactions utilizing core B. thuringiensis genes cry1, cry2, cry3, cry4, cry5, app6, cry7, cry8, cry9, cry10, cry11, vpb1, vpa2, vip3, cyt1, and cyt2 for the characterization of 257 strains of B. thuringiensis. This system was based on the Invertebrate Bacteria Collection from Embrapa Genetic Resources and Biotechnology and analyzed (a) the degree of correlation between the distribution of these strains and the origin of the substrate from which the strain was isolated and (b) between its distribution and geoclimatic conditions. This study made it possible to observe that the cry1, cry2, and vip3A/B genes occur homogeneously in the Brazilian territory, and some genes are found in specific regions. The biggest reservoir of variability is within B. thuringiensis strains in each region, and it is suggested that both geoclimatic conditions and regional crops interfere with the genetic diversity of the B. thuringiensis strains present in the region, and B. thuringiensis strains can constantly exchange genetic information.},
}
@article {pmid37391884,
year = {2023},
author = {Grosicki, GJ and Pugh, J and Wosinska, L and Quilter, K and Mattimoe, D and Allen, J and Joyce, SA and O'Sullivan, O and Close, GL},
title = {Ultra-Endurance triathlon competition shifts fecal metabolome independent of changes to microbiome composition.},
journal = {Journal of applied physiology (Bethesda, Md. : 1985)},
volume = {135},
number = {3},
pages = {549-558},
doi = {10.1152/japplphysiol.00024.2023},
pmid = {37391884},
issn = {1522-1601},
mesh = {Humans ; Male ; Female ; Physical Endurance/physiology ; *Athletic Performance/physiology ; Swimming/physiology ; *Microbiota ; Metabolome ; },
abstract = {Understanding changes to gut microbiota composition and metabolic output in response to acute exercise may be necessary for understanding the mechanisms mediating the long-term health and performance benefits of exercise. Our primary objective was to characterize acute changes in the fecal microbiome and metabolome following participation in an ultra-endurance (3.9 km swim, 180.2 km bike, 42.2 km run) triathlon. An exploratory aim was to determine associations between athlete-specific factors [race performance (i.e., completion time) and lifetime years of endurance training] with pre-race gut microbiota and metabolite profiles. Stool samples from 12 triathletes (9 males/3 females; 43 ± 14 yr, 23 ± 2 kg/m[2]) were collected ≤48 h before and the first bowel movement following race completion. Intra- and inter-individual diversity of bacterial species and individual bacterial taxa were unaltered following race completion (P > 0.05). However, significant reductions (P < 0.05) in free and secondary bile acids [deoxycholic acid (DCA), 12-keto-lithocholic acid (12-ketoLCA)] and short-chain fatty acids (butyric and pivalic acids), and significant increases (P < 0.05) in long-chain fatty acids (oleic and palmitoleic acids) were observed. Exploratory analyses revealed several associations between pre-race bacterial taxa and fecal metabolites with race performance and lifetime history of endurance training (P < 0.05). These findings suggest that 1) acute ultra-endurance exercise shifts microbial metabolism independent of changes to community composition and 2) athlete performance level and training history relate to resting-state gut microbial ecology.NEW &amp; NOTEWORTHY This is the first study to characterize acute changes in gut microbial ecology and metabolism following an ultra-endurance triathlon. We demonstrate changes in gut microbial community function, but not structure, as well as several associations between gut microbiome and fecal metabolome characteristics with race completion time and lifetime history of endurance training. These data add to a small but growing body of literature seeking to characterize the acute and chronic effects of exercise on the gut microbial ecosystem.},
}
@article {pmid37391045,
year = {2023},
author = {Abele, M and Doll, E and Bayer, FP and Meng, C and Lomp, N and Neuhaus, K and Scherer, S and Kuster, B and Ludwig, C},
title = {Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes.},
journal = {Molecular &amp; cellular proteomics : MCP},
volume = {22},
number = {8},
pages = {100612},
pmid = {37391045},
issn = {1535-9484},
mesh = {*Proteome/analysis ; *Proteomics/methods ; Workflow ; Peptides/chemistry ; Escherichia coli ; },
abstract = {Bacteria are the most abundant and diverse organisms among the kingdoms of life. Due to this excessive variance, finding a unified, comprehensive, and safe workflow for quantitative bacterial proteomics is challenging. In this study, we have systematically evaluated and optimized sample preparation, mass spectrometric data acquisition, and data analysis strategies in bacterial proteomics. We investigated workflow performances on six representative species with highly different physiologic properties to mimic bacterial diversity. The best sample preparation strategy was a cell lysis protocol in 100% trifluoroacetic acid followed by an in-solution digest. Peptides were separated on a 30-min linear microflow liquid chromatography gradient and analyzed in data-independent acquisition mode. Data analysis was performed with DIA-NN using a predicted spectral library. Performance was evaluated according to the number of identified proteins, quantitative precision, throughput, costs, and biological safety. With this rapid workflow, over 40% of all encoded genes were detected per bacterial species. We demonstrated the general applicability of our workflow on a set of 23 taxonomically and physiologically diverse bacterial species. We could confidently identify over 45,000 proteins in the combined dataset, of which 30,000 have not been experimentally validated before. Our work thereby provides a valuable resource for the microbial scientific community. Finally, we grew Escherichia coli and Bacillus cereus in replicates under 12 different cultivation conditions to demonstrate the high-throughput suitability of the workflow. The proteomic workflow we present in this manuscript does not require any specialized equipment or commercial software and can be easily applied by other laboratories to support and accelerate the proteomic exploration of the bacterial kingdom.},
}
@article {pmid37389724,
year = {2024},
author = {Das, S and Roy, R and Paul, P and Chakraborty, P and Chatterjee, S and Malik, M and Sarkar, S and Das Gupta, A and Maiti, D and Tribedi, P},
title = {Piperine, a Plant Alkaloid, Exhibits Efficient Disintegration of the Pre-existing Biofilm of Staphylococcus aureus: a Step Towards Effective Management of Biofilm Threats.},
journal = {Applied biochemistry and biotechnology},
volume = {196},
number = {3},
pages = {1272-1291},
pmid = {37389724},
issn = {1559-0291},
support = {R&amp;D/2020/F2//The Neotia University/ ; },
mesh = {Humans ; Staphylococcus aureus ; Biofilms ; *Alkaloids/pharmacology ; Benzodioxoles/pharmacology ; *Staphylococcal Infections ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Piperidines ; *Polyunsaturated Alkamides ; },
abstract = {Staphylococcus aureus causes a range of chronic infections in humans by exploiting its biofilm machinery and drug-tolerance property. Although several strategies have been proposed to eradicate biofilm-linked issues, here, we have explored whether piperine, a bioactive plant alkaloid, can disintegrate an already existing Staphylococcal biofilm. Towards this direction, the cells of S. aureus were allowed to develop biofilm first followed by treatment with the test concentrations (8 and 16 µg/mL) of piperine. In this connection, several assays such as total protein recovery assay, crystal violet assay, extracellular polymeric substances (EPS) measurement assay, fluorescein diacetate hydrolysis assay, and fluorescence microscopic image analysis confirmed the biofilm-disintegrating property of piperine against S. aureus. Piperine reduced the cellular auto-aggregation by decreasing the cell surface hydrophobicity. On further investigation, we observed that piperine could down regulate the dltA gene expression that might reduce the cell surface hydrophobicity of S. aureus. It was also observed that the piperine-induced accumulation of reactive oxygen species (ROS) could enhance biofilm disintegration by decreasing the cell surface hydrophobicity of the test organism. Together, all the observations suggested that piperine could be used as a potential molecule for the effective management of the pre-existing biofilm of S. aureus.},
}
@article {pmid37387230,
year = {2024},
author = {Falkenberg, R and Sigl, L and Fochler, M},
title = {From 'making lists' to conducting 'well-rounded' studies: Epistemic re-orientations in soil microbial ecology.},
journal = {Social studies of science},
volume = {54},
number = {1},
pages = {78-104},
pmid = {37387230},
issn = {1460-3659},
mesh = {*Soil ; *Soil Microbiology ; },
abstract = {Soil microbial ecology is a relatively young research field that became established around the middle of the 20th century and has grown considerably since then. We analyze two epistemic re-orientations in the field, asking how possibilities for creating do-able problems within current conditions of research governance and researchers' collective sense-making about new, more desirable modes of research were intertwined in these developments. We show that a first re-orientation towards molecular omics studies was comparably straightforward to bring about, because it allowed researchers to gain resources for their work and to build careers-in other words, to create do-able problems. Yet, over time this mode of research developed into a scientific bandwagon from which researchers found it difficult to depart, even as they considered this kind of work as producing mostly descriptive studies rather than exploring interesting and important ecological questions. Researchers currently wish to re-orient their field again, towards a new mode of conducting 'well-rounded' interdisciplinary and ecologically-relevant studies. This re-orientation is, however, not easy to put into practice. In contrast to omics studies, this new mode of research does not easily enable the creation of do-able problems for two reasons. First, it is not as readily 'packaged' and hence more difficult to align with institutional and funding frameworks as well as with demands for productivity and career building. Second, while the first re-orientation was part of a broader exciting bandwagon across the life sciences and promised apparent discoveries, the current re-orientation goes along with a different sense of novelty, exploring complex environmental relations and building an understanding at the intersection of disciplines, instead of pushing a clearly circumscribed frontier. Ultimately, our analysis raises questions about whether current conditions of research governance structurally privilege particular kinds of scientific re-orientation over others.},
}
@article {pmid37387175,
year = {2023},
author = {Grover, S and Markin, A and Anderson, TK and Eulenstein, O},
title = {Phylogenetic diversity statistics for all clades in a phylogeny.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {39 Suppl 1},
pages = {i177-i184},
pmid = {37387175},
issn = {1367-4811},
support = {75N93021C00015/AI/NIAID NIH HHS/United States ; },
mesh = {Phylogeny ; *Biological Evolution ; *Algorithms ; Computer Simulation ; Software ; },
abstract = {The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats.},
}
@article {pmid37383638,
year = {2023},
author = {McAtee, TB and Pinnell, LJ and Powledge, SA and Wolfe, CA and Morley, PS and Richeson, JT},
title = {Effects of respiratory virus vaccination and bovine respiratory disease on the respiratory microbiome of feedlot cattle.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1203498},
pmid = {37383638},
issn = {1664-302X},
abstract = {INTRODUCTION: The objectives of this study were to evaluate the impacts of two modified-live virus (MLV) vaccination protocols and respiratory disease (BRD) occurrence on the microbial community composition of the nasopharynx in feedlot cattle.<br><br>METHODS: The treatment groups included in this randomized controlled trial included: 1) no viral respiratory vaccination (CON), 2) intranasal, trivalent, MLV respiratory vaccine in addition to a parenteral BVDV type I and II vaccine (INT), and 3) parenteral, pentavalent, MLV respiratory vaccination against the same agents (INJ). Calves (n = 525) arrived in 5 truckload blocks and were stratified by body weight, sex, and presence of a pre-existing identification ear-tag. A total of 600 nasal swab samples were selected for DNA extraction and subsequent 16S rRNA gene sequencing to characterize the microbiome of the upper respiratory tract. Nasal swabs collected on d 28 from healthy cattle were used to evaluate the impact of vaccination on upper respiratory tract (URT) microbial communities.<br><br>RESULTS: Firmicutes were less abundant in INT calves (n = 114; P < 0.05) and this difference was attributed to decreased relative abundance (RA) of Mycoplasma spp. (P = 0.04). Mannheimia and Pasteurella had lower RA in INT (P < 0.05). The microbiome in healthy animals on d 28 had increased Proteobacteria (largely Moraxella spp.) and decreased Firmicutes (comprised almost exclusively of Mycoplasma spp.) compared to animals that were treated for or died from BRD (P < 0.05). Cattle that died had a greater RA of Mycoplasma spp. in their respiratory microbiome on d 0 (P < 0.02). Richness was similar on d 0 and 28, but diversity increased for all animals on d 28 (P>0.05).},
}
@article {pmid37383354,
year = {2023},
author = {Kim, S and Kwak, J and Song, M and Cho, J and Kim, ES and Keum, GB and Doo, H and Pandey, S and Cho, JH and Ryu, S and Kim, S and Im, YM and Kim, HB},
title = {Effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and intestinal microbiome in weaned pigs.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1140718},
pmid = {37383354},
issn = {2297-1769},
abstract = {INTRODUCTION: This study was conducted to evaluate the effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and gut microbiome in weaned pigs.<br><br>METHODS: A total of 300 crossbred pigs [(Landrace &#xd7; Yorkshire]&#x2009;&#xd7;&#x2009;Duroc; 8.87&#x2009;&#xb1;&#x2009;0.34&#x2009; kg of average initial body weight [BW]; 4&#x2009; weeks of age) were divided into two dietary treatments (15 pigs/pen, 10 replicates/treatment) using a randomized complete block design (block&#x2009;=&#x2009;BW): control (CON) and the effective microorganism (MEM). The CON was not treated, while the MEM was treated with the mixture of L. casei (1 &#xd7; 10[7]&#x2009;CFU/mL) and S. cerevisiae (1 &#xd7; 10[7]&#x2009;CFU/mL) at 3&#x2009;mL/pig/day for 4&#x2009; weeks via the drinking water supply. Two feces and one blood sample from the randomly selected pigs in each pen were collected on D1 and D28 after weaning. Pigs were individually weighed, and pen feed intakes were recorded to evaluate pig growth performance. For the gut microbiome analysis, 16S rRNA gene hypervariable regions (V5 to V6) were sequenced using the Illumina MiSeq platform, and Quantitative Insight into Microbial Ecology (QIIME) and Microbiome Helper pipeline were used for 16S rRNA gene sequence analysis.<br><br>RESULTS AND DISCUSSION: The daily weight gain and feed efficiency of MEM were significantly higher than those of CON (p&#x2009;<&#x2009;0.001). There were no significant differences in hematological parameters and immune responses between CON and MEM. However, MEM had significantly lower Treponema genus, whereas significantly higher Lactobacillus and Roseburia genera compared to CON. Overall, our data showed that L. casei and S. cerevisiae mixture could promote growth performance through the modulation of gut microbiota in pigs. This study will help to understand the correlation between the growth performance and the gut microbiome.},
}
@article {pmid37382454,
year = {2023},
author = {Liu, W and Cui, X and Wang, X and Shen, C and Ji, L and Zhang, M and Wong, MH and Zhang, J and Shan, S},
title = {Sugarcane mosaic virus reduced bacterial diversity and network complexity in the maize root endosphere.},
journal = {mSystems},
volume = {8},
number = {4},
pages = {e0019823},
pmid = {37382454},
issn = {2379-5077},
mesh = {*Zea mays/genetics ; Soil Microbiology ; *Microbiota/genetics ; Plant Roots/microbiology ; RNA, Ribosomal, 16S ; Endophytes/genetics ; Bacteria/genetics ; },
abstract = {Sugarcane mosaic virus (SCMV) causes mosaic disease in crops such as maize and sugarcane by its vector-an aphid-and is transmitted top-down into the root system. However, understanding of the effects of the aphid-borne virus on root-associated microbes after plant invasion remains limited. The current project investigated maize root-associated (rhizosphere and endosphere) bacterial communities, potential interspecies interaction, and assembly processes in response to SCMV invasion based on 16S rRNA gene amplicon sequencing. SCMV was detected in the roots 9 days after inoculation, and leaf mosaic and chlorosis appeared. The SCMV invasion markedly reduced the α-diversity of endosphere bacteria compared with uninoculated controls (Mock). The connectivity and complexity of the bacterial co-occurrence network in the root endosphere decreased after SCMV invasion, implying that the plant virus may alter root endophyte-microbial interactions. Moreover, a signature that deviates more from stochastic processes was observed in virus-infected plants. Unexpectedly, the rhizosphere bacterial communities were rarely affected by the viral invasion. This study lays the foundation for elucidating the fate of the microbial component of the plant holobiont following aphid-borne virus exposure. IMPORTANCE Biotic (e.g., soil-borne viruses) stress can alter root-associated bacterial communities, essential in maintaining host plant growth and health. However, the regulation of root-associated microorganisms by plant viruses from shoots is still largely unknown. Our results show that plant virus invasion leads to reduced and simpler inter-microbial communication in the maize endosphere. In addition, stochastic processes act on bacterial community assembly in both rhizosphere and endosphere, and bacterial communities in virus-invaded plant endosphere tend to shift toward deterministic processes. Our study highlights the negative effects of plant viruses on root endophytes from the microbial ecology perspective, which may be microbially mediated mechanisms of plant diseases.},
}
@article {pmid37382302,
year = {2023},
author = {Puente-Sánchez, F and Hoetzinger, M and Buck, M and Bertilsson, S},
title = {Exploring environmental intra-species diversity through non-redundant pangenome assemblies.},
journal = {Molecular ecology resources},
volume = {23},
number = {7},
pages = {1724-1736},
doi = {10.1111/1755-0998.13826},
pmid = {37382302},
issn = {1755-0998},
support = {892961//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 2019-02336//Svenska Forskningsr&#xe5;det Formas/ ; 2017-04422//Vetenskapsr&#xe5;det/ ; 2018-05973//Vetenskapsr&#xe5;det/ ; },
mesh = {Phylogeny ; *Bacteria/genetics ; Metagenome ; Algorithms ; *Microbiota ; Metagenomics/methods ; },
abstract = {At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined "species", whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species-level niche adaptation among others) and accessory regions (present only in some, and responsible for intra-species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra-species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.},
}
@article {pmid37379878,
year = {2023},
author = {Abel, SM and Wu, F and Primpke, S and Gerdts, G and Brandt, A},
title = {Journey to the deep: plastic pollution in the hadal of deep-sea trenches.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {333},
number = {},
pages = {122078},
doi = {10.1016/j.envpol.2023.122078},
pmid = {37379878},
issn = {1873-6424},
mesh = {*Plastics/analysis ; *Water Pollutants, Chemical/analysis ; Environmental Pollution/analysis ; Microplastics ; Oceans and Seas ; },
abstract = {The global increase of plastic production, linked with an overall plastic misuse and waste mismanagement, leads to an inevitable increase of plastic debris that ends up in our oceans. One of the major sinks of this pollution is the deep-sea floor, which is hypothesized to accumulate in its deepest points, the hadal trenches. Little is known about the magnitude of pollution in these trenches, given the remoteness of these environments, numerous factors influencing the input and sinking behavior of plastic debris from shallower environments. This study represents to the best of our knowledge the largest survey of (macro)plastic debris sampled at hadal depths, down to 9600 m. Industrial packaging and material assignable to fishing activities were the most common debris items in the Kuril Kamchatka trench, most likely deriving from long-distance transport by the Kuroshio extension current (KE) or from regional marine traffic and fishing activities. The chemical analysis by (Attenuated Total Reflection Fourier transform infrared (ATR-FTIR) spectroscopy revealed that the main polymers detected were polyethylene (PE), polypropylene (PP) and nylon. Plastic waste is reaching the depths of the trench, although some of the items were only partially broken down. This finding suggests that complete breakdown into secondary microplastics (MP) may not always occur at the sea surface or though the water column. Due to increased brittleness, plastic debris may break apart upon reaching the hadal trench floor where plastic degrading factors were thought to be, coming off. The KKT's remote location and high sedimentation rates make it a potential site for high levels of plastic pollution, potentially making it one of the world's most heavily contaminated marine areas and an oceanic plastic deposition zone.},
}
@article {pmid37378294,
year = {2023},
author = {Xie, P and Huang, K and Deng, A and Mo, P and Xiao, F and Wu, F and Xiao, D and Wang, Y},
title = {The diversity and abundance of bacterial and fungal communities in the rhizosphere of Cathaya argyrophylla are affected by soil physicochemical properties.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1111087},
pmid = {37378294},
issn = {1664-302X},
abstract = {Cathaya argyrophylla is an ancient Pinaceae species endemic to China that is listed on the IUCN Red List. Although C. argyrophylla is an ectomycorrhizal plant, the relationship between its rhizospheric soil microbial community and soil properties related to the natural habitat remains unknown. High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences was used to survey the C. argyrophylla soil community at four natural spatially distributed points in Hunan Province, China, and functional profiles were predicted using PICRUSt2 and FUNGuild. The dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, and the dominant genus was Acidothermus. The dominant fungal phyla were Basidiomycota and Ascomycota, while Russula was the dominant genus. Soil properties were the main factors leading to changes in rhizosphere soil bacterial and fungal communities, with nitrogen being the main driver of changes in soil microbial communities. The metabolic capacities of the microbial communities were predicted to identify differences in their functional profiles, including amino acid transport and metabolism, energy production and conversion, and the presence of fungi, including saprotrophs and symbiotrophs. These findings illuminate the soil microbial ecology of C. argyrophylla, and provide a scientific basis for screening rhizosphere microorganisms that are suitable for vegetation restoration and reconstruction for this important threatened species.},
}
@article {pmid37375921,
year = {2023},
author = {Qi, Y and Ma, L and Ghani, MI and Peng, Q and Fan, R and Hu, X and Chen, X},
title = {Effects of Drought Stress Induced by Hypertonic Polyethylene Glycol (PEG-6000) on Passiflora edulis Sims Physiological Properties.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {12},
pages = {},
pmid = {37375921},
issn = {2223-7747},
support = {2021-229, HZJD [2022]001//Guizhou Provincial Science and Technology Program/ ; Guike AA21196003//Science and Technology Base &amp; Talent Project of Guangxi Province/ ; 2021YFD1100303-3//National Key Research and Development Program of China/ ; 2019-04//Guizhou University Cultivation Project/ ; },
abstract = {Passion fruit is known to be sensitive to drought, and in order to study the physiological and biochemical changes that occur in passion fruit seedlings under drought stress, a hypertonic polyethylene glycol (PEG) solution (5%, 10%, 15%, and 20%) was used to simulate drought stress in passion fruit seedlings. We explored the physiological changes in passion fruit seedlings under drought stress induced by PEG to elucidate their response to drought stress and provide a theoretical basis for drought-resistant cultivation of passion fruit seedlings. The results show that drought stress induced by PEG had a significant effect on the growth and physiological indices of passion fruit. Drought stress significantly decreased fresh weight, chlorophyll content, and root vitality. Conversely, the contents of soluble protein (SP), proline (Pro), and malondialdehyde (MDA) increased gradually with the increasing PEG concentration and prolonged stress duration. After nine days, the SP, Pro and MDA contents were higher in passion fruit leaves and roots under 20% PEG treatments compared with the control. Additionally, with the increase in drought time, the activities of antioxidant enzymes such as peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) showed an increasing trend and then a decreasing trend, and they reached the highest value at the sixth day of drought stress. After rehydration, SP, Pro and MDA contents in the leaves and roots of passion fruit seedlings was reduced. Among all the stress treatments, 20% PEG had the most significant effect on passion fruit seedlings. Therefore, our study demonstrated sensitive concentrations of PEG to simulate drought stress on passion fruit and revealed the physiological adaptability of passion fruit to drought stress.},
}
@article {pmid37375077,
year = {2023},
author = {Xu, ZS and Ju, T and Yang, X and Gänzle, M},
title = {A Meta-Analysis of Bacterial Communities in Food Processing Facilities: Driving Forces for Assembly of Core and Accessory Microbiomes across Different Food Commodities.},
journal = {Microorganisms},
volume = {11},
number = {6},
pages = {},
pmid = {37375077},
issn = {2076-2607},
support = {Food Microbiology and Probiotics//Canada Research Chairs/ ; Accelerate Fellowship//Mitacs/ ; },
abstract = {Microbial spoilage is a major cause of food waste. Microbial spoilage is dependent on the contamination of food from the raw materials or from microbial communities residing in food processing facilities, often as bacterial biofilms. However, limited research has been conducted on the persistence of non-pathogenic spoilage communities in food processing facilities, or whether the bacterial communities differ among food commodities and vary with nutrient availability. To address these gaps, this review re-analyzed data from 39 studies from various food facilities processing cheese (n = 8), fresh meat (n = 16), seafood (n = 7), fresh produce (n = 5) and ready-to-eat products (RTE; n = 3). A core surface-associated microbiome was identified across all food commodities, including Pseudomonas, Acinetobacter, Staphylococcus, Psychrobacter, Stenotrophomonas, Serratia and Microbacterium. Commodity-specific communities were additionally present in all food commodities except RTE foods. The nutrient level on food environment surfaces overall tended to impact the composition of the bacterial community, especially when comparing high-nutrient food contact surfaces to floors with an unknown nutrient level. In addition, the compositions of bacterial communities in biofilms residing in high-nutrient surfaces were significantly different from those of low-nutrient surfaces. Collectively, these findings contribute to a better understanding of the microbial ecology of food processing environments, the development of targeted antimicrobial interventions and ultimately the reduction of food waste and food insecurity and the promotion of food sustainability.},
}
@article {pmid37375028,
year = {2023},
author = {Villeneuve, K and Turcotte-Blais, V and Lazar, CS},
title = {Effect of Snowmelt on Groundwater Bacterial Community Composition and Potential Role of Surface Environments as Microbial Seed Bank in Two Distinct Aquifers from the Region of Quebec, Canada.},
journal = {Microorganisms},
volume = {11},
number = {6},
pages = {},
pmid = {37375028},
issn = {2076-2607},
support = {RGPIN-2019-06670//Natural Sciences and Engineering Research Council/ ; Aquatic Environmental Genomics//Canada Research Chairs/ ; },
abstract = {Events of groundwater recharge are associated with changes in the composition of aquifer microbial communities but also abiotic conditions. Modification in the structure of the community can be the result of different environmental condition favoring or hindering certain taxa, or due to the introduction of surface-derived taxa. Yet, in both cases, the local hydrogeochemical settings of the aquifer is likely to affect the amount of variation observed. Therefore, in our study, we used 16S rRNA gene sequencing to assess how microbial communities change in response to snowmelt and the potential connectivity between subsurface and surface microbiomes in two distinct aquifers located in the region of Vaudreuil-Soulanges (Québec, Canada). At both sites, we observed an increase in groundwater level and decrease in temperature following the onset of snow melt in March 2019. Bacterial community composition of each aquifer was significantly different (p < 0.05) between samples collected prior and after groundwater recharge. Furthermore, microbial source tracking results suggested a low contribution of surface environments to the groundwater microbiome except for in the months associated with recharge (March 2019 and April 2019). Overall, despite differences in soil permeability between both sites, the period of snow melt was followed by important changes in the composition of microbial communities from aquifers.},
}
@article {pmid37375009,
year = {2023},
author = {Satari, L and Iglesias, A and Porcar, M},
title = {The Microbiome of Things: Appliances, Machines, and Devices Hosting Artificial Niche-Adapted Microbial Communities.},
journal = {Microorganisms},
volume = {11},
number = {6},
pages = {},
pmid = {37375009},
issn = {2076-2607},
support = {ID101000470//European Union (MICRO4BIOGAS project)/ ; },
abstract = {As it is the case with natural substrates, artificial surfaces of man-made devices are home to a myriad of microbial species. Artificial products are not necessarily characterized by human-associated microbiomes; instead, they can present original microbial populations shaped by specific environmental-often extreme-selection pressures. This review provides a detailed insight into the microbial ecology of a range of artificial devices, machines, and appliances, which we argue are specific microbial niches that do not necessarily fit in the "build environment" microbiome definition. Instead, we propose here the Microbiome of Things (MoT) concept analogous to the Internet of Things (IoT) because we believe it may be useful to shed light on human-made, but not necessarily human-related, unexplored microbial niches.},
}
@article {pmid37374902,
year = {2023},
author = {Heczko, P and Kozień, &#x141; and Strus, M},
title = {Special Issue "An Update on Lactobacillus": Editorial.},
journal = {Microorganisms},
volume = {11},
number = {6},
pages = {},
pmid = {37374902},
issn = {2076-2607},
abstract = {As indicated in the introduction to this Special Issue, as of 2020, the original genus Lactobacillus comprised over 260 recognized species, a figure which is probably much higher now [...].},
}
@article {pmid37369788,
year = {2023},
author = {Fukui, Y and Abe, M and Kobayashi, M},
title = {Effects of Hyphomonas Strains on the Growth of Red Algae Pyropia Species by Attaching Specifically to Their Rhizoids.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2502-2514},
pmid = {37369788},
issn = {1432-184X},
mesh = {*Rhodophyta ; *Seaweed ; Seawater ; Bacteria ; Vitamins ; },
abstract = {Bacteria and marine macroalgae form close associations, while various bacteria affect the morphogenesis and growth of macroalgae. Hyphomonas strains exhibit normal morphogenetic activity in protoplasts of the red alga Pyropia yezoensis (nori). However, the effects of the bacteria on the growth of Pyropia from protoplast cells to regenerated thalli remain unknown. Here, we assessed the growth of P. yezoensis and Pyropia tenera using combined cultures of three Hyphomonas strains (LNM10-16, SCM-2, and LNM-9) and three algal media (artificial seawater with vitamins, artificial seawater, and natural seawater) over 7 weeks. Third week after culture, the three Hyphomonas strains showed almost similar levels of normal growth activity for both Pyropia species. However, at 7 weeks, significant differences were observed among the three Hyphomonas strains in terms of length, length-to-width ratio, and normal morphology of Pyropia thalli. LNM10-16 significantly promoted the thalli length and length-to-width ratios of both Pyropia species in artificial seawater without vitamins and natural seawater, compared with the other two Hyphomonas strains. P. yezoensis cultured in artificial seawater with vitamins showed a much higher demand for LNM10-16 in development of the thalli length than P. tenera. These results may be explained by differences in the growth activities of Hyphomonas strains and the nutrient requirements of Pyropia species. Furthermore, the bacteria were more specifically attached to the rhizoid surfaces of both species. This study is the first to reveal that Hyphomonas strains affect the growth of Pyropia species by attaching to their rhizoids.},
}
@article {pmid37365511,
year = {2023},
author = {Chang, Y and Sun, H and Liu, S and He, Y and Zhao, S and Wang, J and Wang, T and Zhang, J and Gao, J and Yang, Q and Li, M and Zhao, X},
title = {Identification of BBX gene family and its function in the regulation of microtuber formation in yam.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {354},
pmid = {37365511},
issn = {1471-2164},
support = {5101049470215//Postdoctor Initiative Foundation of Henan Normal University/ ; 21A180013//Colleges and Universities in Henan Province Key Scientific Research Project Funding Scheme/ ; CARS-21//Agriculture Research System of China/ ; 224200510011//The Zhongyuan high level talents special support plan-Science and Technology Innovation Leading Talents/ ; 2021YFD1600100//Special National Key Research and Development Plan/ ; 81274019//National Natural Science Foundation of China/ ; 5201049160163//Henan Normal University and Wen County People's Government Jointly Build National Yam Germplasm Resource Garden Project/ ; },
mesh = {*Dioscorea/genetics/metabolism ; Gene Expression Profiling ; Multigene Family ; Photoperiod ; Circadian Rhythm ; Gene Expression Regulation, Plant ; Plant Proteins/metabolism ; },
abstract = {BBX proteins play important roles in all of the major light-regulated developmental processes. However, no systematic analysis of BBX gene family regarding the regulation of photoperiodic microtuber formation has been previously performed in yam. In this study, a systematic analysis on the BBX gene family was conducted in three yam species, with the results, indicating that this gene plays a role in regulating photoperiodic microtuber formation. These analyses included identification the BBX gene family in three yam species, their evolutionary relationships, conserved domains, motifs, gene structure, cis-acting elements, and expressional patterns. Based on these analyses, DoBBX2/DoCOL5 and DoBBX8/DoCOL8 showing the most opposite pattern of expression during microtuber formation were selected as candidate genes for further investigation. Gene expression analysis showed DoBBX2/DoCOL5 and DoBBX8/DoCOL8 were highest expressed in leaves and exhibited photoperiod responsive expression patterns. Besides, the overexpression of DoBBX2/DoCOL5 and DoBBX8/DoCOL8 in potato accelerated tuber formation under short-day (SD) conditions, whereas only the overexpression of DoBBX8/DoCOL8 enhanced the accelerating effect of dark conditions on tuber induction. Tuber number was increased in DoBBX8/DoCOL8 overexpressing plants under dark, as well as in DoBBX2/DoCOL5 overexpressing plants under SD. Overall, the data generated in this study may form the basis of future functional characterizations of BBX genes in yam, especially regarding their regulation of microtuber formation via the photoperiodic response pathway.},
}
@article {pmid37364132,
year = {2023},
author = {Schleyer, G and Kuhlisch, C and Ziv, C and Ben-Dor, S and Malitsky, S and Schatz, D and Vardi, A},
title = {Lipid biomarkers for algal resistance to viral infection in the ocean.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {27},
pages = {e2217121120},
pmid = {37364132},
issn = {1091-6490},
support = {101053543/ERC_/European Research Council/International ; },
mesh = {Humans ; *Viruses ; Phytoplankton/metabolism ; *Haptophyta/metabolism ; *Virus Diseases ; Biomarkers/metabolism ; Oceans and Seas ; Lipids ; },
abstract = {Marine viruses play a key role in regulating phytoplankton populations, greatly affecting the biogeochemical cycling of major nutrients in the ocean. Resistance to viral infection has been reported for various phytoplankton species under laboratory conditions. Nevertheless, the occurrence of resistant cells in natural populations is underexplored due to the lack of sensitive tools to detect these rare phenotypes. Consequently, our current understanding of the ecological importance of resistance and its underlying mechanisms is limited. Here, we sought to identify lipid biomarkers for the resistance of the bloom-forming alga Emiliania huxleyi to its specific virus, E. huxleyi virus (EhV). By applying an untargeted lipidomics approach, we identified a group of glycosphingolipid (GSL) biomarkers that characterize resistant E. huxleyi strains and were thus termed resistance-specific GSLs (resGSLs). Further, we detected these lipid biomarkers in E. huxleyi isolates collected from induced E. huxleyi blooms and in samples collected during an open-ocean E. huxleyi bloom, indicating that resistant cells predominantly occur during the demise phase of the bloom. Last, we show that the GSL composition of E. huxleyi cultures that recover following infection and gain resistance to the virus resembles that of resistant strains. These findings highlight the metabolic plasticity and coevolution of the GSL biosynthetic pathway and underscore its central part in this host-virus arms race.},
}
@article {pmid37362850,
year = {2023},
author = {McDonagh, F and Cormican, M and Morris, D and Burke, L and Singh, NK and Venkateswaran, K and Miliotis, G},
title = {Medical Astro-Microbiology: Current Role and Future Challenges.},
journal = {Journal of the Indian Institute of Science},
volume = {},
number = {},
pages = {1-26},
pmid = {37362850},
issn = {0970-4140},
abstract = {The second and third decades of the twenty-first century are marked by a flourishing of space technology which may soon realise human aspirations of a permanent multiplanetary presence. The prevention, control and management of infection with microbial pathogens is likely to play a key role in how successful human space aspirations will become. This review considers the emerging field of medical astro-microbiology. It examines the current evidence regarding the risk of infection during spaceflight via host susceptibility, alterations to the host's microbiome as well as exposure to other crew members and spacecraft's microbiomes. It also considers the relevance of the hygiene hypothesis in this regard. It then reviews the current evidence related to infection risk associated with microbial adaptability in spaceflight conditions. There is a particular focus on the International Space Station (ISS), as one of the only two crewed objects in low Earth orbit. It discusses the effects of spaceflight related stressors on viruses and the infection risks associated with latent viral reactivation and increased viral shedding during spaceflight. It then examines the effects of the same stressors on bacteria, particularly in relation to changes in virulence and drug resistance. It also considers our current understanding of fungal adaptability in spaceflight. The global public health and environmental risks associated with a possible re-introduction to Earth of invasive species are also briefly discussed. Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars. Overall, this review summarises much of our current understanding of medical astro-microbiology and identifies significant knowledge gaps.},
}
@article {pmid37356531,
year = {2023},
author = {Wang, H and Lin, L and Zhang, L and Han, P and Ju, F},
title = {Microbiome assembly mechanism and functional potential in enhanced biological phosphorus removal system enriched with Tetrasphaera-related polyphosphate accumulating organisms.},
journal = {Environmental research},
volume = {233},
number = {},
pages = {116494},
doi = {10.1016/j.envres.2023.116494},
pmid = {37356531},
issn = {1096-0953},
mesh = {*Phosphorus ; Polyphosphates/metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; *Actinomycetales/genetics/metabolism ; Bacteria/genetics/metabolism ; Bioreactors ; Sewage/microbiology ; },
abstract = {Tetrasphaera-related polyphosphate accumulating organisms (PAOs) are the key functional guilds for enhanced biological phosphorus removal (EBPR) systems. Their biomass enrichment can be enhanced by the nitrification inhibitor allylthiourea (ATU). However, the underlying assembly mechanism and the functional potential of the EBPR microbiome regulated by ATU are unclear. This study investigates the effect of ATU on microbiome assembly and functional potential by closely following the microbiota dynamics in an EBPR system enriched with Tetrasphaera-related PAOs for 288-days before, during and after ATU addition. The results showed that ATU addition increased microbiota structural similarity and compositional convergence, and enhanced determinism in the assembly of EBPR microbiome. During exposure to ATU, Tetrasphaera-related PAOs were governed by homogeneous selection and the dominant species revealed by 16S rRNA gene-based phylogenetic analysis shifted from clade III to clade I. Meanwhile, ATU supply promoted significant enrichment of functional genes involved in phosphate transport (pit) and polyphosphate synthesis and degradation (ppk1 and ppk2), whereas both Nitrosomonas and ammonia monooxygenase-encoding genes (amoA/B/C) assignable to this group of nitrifying bacteria decreased. Moreover, ATU addition relieved the significant abundance correlation between filamentous bacteria Ca. Promineofilum and denitrifying Brevundimonas (FDR-adjusted P < 0.01), damaging their potential synergic or cooperative interactions, thus weakening their competitiveness against Tetrasphaera-related PAOs. Notably, ATU withdrawn created opportunistic conditions for the unexpected explosive growth and predominance of Thiothrix filaments, leading to a serious bulking event. Our study provides new insights into the microbial ecology of Tetrasphaera-related PAOs in EBPR system, which could guide the establishment of an efficient microbiota for EBPR.},
}
@article {pmid37356163,
year = {2023},
author = {Yuan, W and Xu, EG and Li, L and Zhou, A and Peijnenburg, WJGM and Grossart, HP and Liu, W and Yang, Y},
title = {Tracing and trapping micro- and nanoplastics: Untapped mitigation potential of aquatic plants?.},
journal = {Water research},
volume = {242},
number = {},
pages = {120249},
doi = {10.1016/j.watres.2023.120249},
pmid = {37356163},
issn = {1879-2448},
abstract = {Micro- and nanoplastics are emerging concerns due to their environmental ubiquity and currently largely unknown ecological impacts. Leveraging on a recently developed method using europium-doped polystyrene particles (PS-Eu), our present work aimed to accurately trace the uptake and transport of micro- and nanoplastics in aquatic plants and shed insights into the potential of different aquatic plants for trapping and removal of plastics from water environment. Seedlings of Vallisneria denseserrulata Makino (submerged plant), Iris tectorum Maxim (emergent plant), and Eichhornia crassipes Solms (floating plant) were exposed to 100 nm and 2 μm PS-Eu in freshwater (5 μg/mL) or sediments (5 μg/g) for 8 weeks. Fluorescence imaging clearly evidenced that PS-Eu mainly accumulated in the intercellular space and were transported from roots to leaves via the apoplastic path and vascular bundle. Mass spectrum analysis demonstrated that up to 6250 μg/g nanoplastics were trapped in aquatic plants (mainly in roots) with a bioconcentration factor of 306.5, depending on exposure routes and plant species. Owing to their excellent capture capability and high tolerance to plastic exposures, floating plants like E. crassipes are promising for immobilizing and removing fine plastics from the water environment.},
}
@article {pmid37354976,
year = {2023},
author = {Kable, ME and Chin, EL and Huang, L and Stephensen, CB and Lemay, DG},
title = {Association of Estimated Daily Lactose Consumption, Lactase Persistence Genotype (rs4988235), and Gut Microbiota in Healthy Adults in the United States.},
journal = {The Journal of nutrition},
volume = {153},
number = {8},
pages = {2163-2173},
doi = {10.1016/j.tjnut.2023.06.025},
pmid = {37354976},
issn = {1541-6100},
mesh = {Male ; Female ; Humans ; Adult ; United States ; Lactose ; *Lactose Intolerance/genetics ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Dairy Products ; Lactase/genetics ; Genotype ; },
abstract = {BACKGROUND: Lactase persistence (LP) is a heritable trait in which lactose can be digested throughout adulthood. Lactase nonpersistent (LNP) individuals who consume lactose may experience microbial adaptations in response to undigested lactose.<br><br>OBJECTIVES: The objective of the study was to estimate lactose from foods reported in the Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24) and determine the interaction between lactose consumption, LP genotype, and gut microbiome in an observational cross-sectional study of healthy adults in the United States (US).<br><br>METHODS: Average daily lactose consumption was estimated for 279 healthy US adults, genotyped for the lactase gene -13910G>A polymorphism (rs4988235) by matching ASA24-reported foods to foods in the Nutrition Coordinating Center Food and Nutrient Database. Analysis of covariance was used to identify whether the A genotype (LP) influenced lactose and total dairy consumption, with total energy intake and weight as covariates. The 16S rRNA V4/V5 region, amplified from bacterial DNA extracted from each frozen stool sample, was sequenced using Illumina MiSeq (300 bp paired-end) and analyzed using Quantitative Insights Into Microbial Ecology (QIIME)2 (version 2019.10). Differential abundances of bacterial taxa were analyzed using DESeq2 likelihood ratio tests.<br><br>RESULTS: Across a diverse set of ethnicities, LP subjects consumed more lactose than LNP subjects. Lactobacillaceae abundance was highest in LNP subjects who consumed more than 12.46 g/d (upper tercile). Within Caucasians and Hispanics, family Lachnospiraceae was significantly enriched in the gut microbiota of LNP individuals consuming the upper tercile of lactose across both sexes.<br><br>CONCLUSIONS: Elevated lactose consumption in individuals with the LNP genotype is associated with increased abundance of family Lactobacillaceae and Lachnospriaceae, taxa that contain multiple genera capable of utilizing lactose. This trial was registered on clinicaltrials.gov as NCT02367287.},
}
@article {pmid37350274,
year = {2023},
author = {Rupp, ME and Van Schooneveld, TC and Starlin, R and Quick, J and Snyder, GM and Passaretti, CL and Stevens, MP and Cawcutt, K},
title = {Hospital return-to-work practices for healthcare providers infected with severe acute respiratory coronavirus virus 2 (SARS-CoV-2).},
journal = {Infection control and hospital epidemiology},
volume = {44},
number = {12},
pages = {2081-2084},
doi = {10.1017/ice.2023.133},
pmid = {37350274},
issn = {1559-6834},
mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; Return to Work ; Hospitals ; Health Personnel ; },
abstract = {A survey of academic medical-center hospital epidemiologists indicated substantial deviation from Centers for Disease Control and Prevention guidance regarding healthcare providers (HCPs) recovering from coronavirus disease 2019 (COVID-19) returning to work. Many hospitals continue to operate under contingency status and have HCPs return to work earlier than recommended.},
}
@article {pmid37348760,
year = {2023},
author = {Eudy, BJ and Odle, J and Lin, X and Maltecca, C and Walter, KR and McNulty, NP and Fellner, V and Jacobi, SK},
title = {Dietary Prebiotic Oligosaccharides and Arachidonate Alter the Fecal Microbiota and Mucosal Lipid Composition of Suckling Pigs.},
journal = {The Journal of nutrition},
volume = {153},
number = {8},
pages = {2249-2262},
doi = {10.1016/j.tjnut.2023.06.019},
pmid = {37348760},
issn = {1541-6100},
mesh = {Animals ; Swine ; *Prebiotics ; *Microbiota ; Oligosaccharides/pharmacology/analysis ; Feces/microbiology ; Intestinal Mucosa ; Lipids ; },
abstract = {BACKGROUND: Early intestinal development is important to infant vitality, and optimal formula composition can promote gut health.<br><br>OBJECTIVES: The objectives were to evaluate the effects of arachidonate (ARA) and/or prebiotic oligosaccharide (PRE) supplementation in formula on the development of the microbial ecosystem and colonic health parameters.<br><br>METHODS: Newborn piglets were fed 4 formulas containing ARA [0.5 compared with 2.5% of dietary fatty acids (FAs)] and PRE (0 compared with 8 g/L, containing a 1:1 mixture of galactooligosaccharides and polydextrose) in a 2 x 2 factorial design for 22 d. Fecal samples were collected weekly and analyzed for relative microbial abundance. Intestinal samples were collected on day 22 and analyzed for mucosal FAs, pH, and short-chain FAs (SCFAs).<br><br>RESULTS: PRE supplementation significantly increased genera within Bacteroidetes and Firmicutes, including Anaerostipes, Mitsuokella, Prevotella, Clostridium IV, and Bulleidia, and resulted in progressive separation from controls as determined by Principal Coordinates Analysis. Concentrations of SCFA increased from 70.98 to 87.37 mM, with an accompanying reduction in colonic pH. ARA supplementation increased the ARA content of the colonic mucosa from 2.35-5.34% of total FAs. PRE supplementation also altered mucosal FA composition, resulting in increased linoleic acid (11.52-16.33% of total FAs) and ARA (2.35-5.16% of total FAs).<br><br>CONCLUSIONS: Prebiotic supplementation during the first 22 d of life altered the gut microbiota of piglets and increased the abundance of specific bacterial genera. These changes correlated with increased SCFA, which may benefit intestinal development. Although dietary ARA did not alter the microbiota, it increased the ARA content of the colonic mucosa, which may support intestinal development and epithelial repair. Prebiotic supplementation also increased unsaturation of FAs in the colonic mucosa. Although the mechanism requires further investigation, it may be related to altered microbial ecology or biohydrogenation of FA.},
}
@article {pmid37347668,
year = {2023},
author = {Verbeelen, T and Van Houdt, R and Leys, N and Ganigué, R and Mastroleo, F},
title = {RNA extraction protocol from low-biomass bacterial Nitrosomonas europaea and Nitrobacter winogradskyi cultures for whole transcriptome studies.},
journal = {STAR protocols},
volume = {4},
number = {3},
pages = {102358},
pmid = {37347668},
issn = {2666-1667},
mesh = {*Nitrosomonas europaea/genetics ; Nitrosomonas/genetics ; Transcriptome/genetics ; Biomass ; Bacteria/genetics ; RNA ; *Nitrobacter ; },
abstract = {RNA-sequencing for whole transcriptome analysis requires high-quality RNA in adequate amounts, which can be difficult to generate with low-biomass-producing bacteria where sample volume is limited. We present an RNA extraction protocol for low-biomass-producing autotrophic bacteria Nitrosomonas europaea and Nitrobacter winogradskyi cultures. We describe steps for sample collection, lysozyme-based enzymatic lysis, and a commercial silica-column-based RNA extraction. We then detail evaluation of RNA yield and quality for downstream applications such as RNA-Seq. For complete details on the use and execution of this protocol, please refer to Verbeelen et al.[1].},
}
@article {pmid37346753,
year = {2023},
author = {Petrin, S and Wijnands, L and Benincà, E and Mughini-Gras, L and Delfgou-van Asch, EHM and Villa, L and Orsini, M and Losasso, C and Olsen, JE and Barco, L},
title = {Assessing phenotypic virulence of Salmonella enterica across serovars and sources.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1184387},
pmid = {37346753},
issn = {1664-302X},
abstract = {INTRODUCTION: Whole genome sequencing (WGS) is increasingly used for characterizing foodborne pathogens and it has become a standard typing technique for surveillance and research purposes. WGS data can help assessing microbial risks and defining risk mitigating strategies for foodborne pathogens, including Salmonella enterica.<br><br>METHODS: To test the hypothesis that (combinations of) different genes can predict the probability of infection [P(inf)] given exposure to a certain pathogen strain, we determined P(inf) based on invasion potential of 87 S. enterica strains belonging to 15 serovars isolated from animals, foodstuffs and human patients, in an in vitro gastrointestinal tract (GIT) model system. These genomes were sequenced with WGS and screened for genes potentially involved in virulence. A random forest (RF) model was applied to assess whether P(inf) of a strain could be predicted based on the presence/absence of those genes. Moreover, the association between P(inf) and biofilm formation in different experimental conditions was assessed.<br><br>RESULTS AND DISCUSSION: P(inf) values ranged from 6.7E-05 to 5.2E-01, showing variability both among and within serovars. P(inf) values also varied between isolation sources, but no unambiguous pattern was observed in the tested serovars. Interestingly, serovars causing the highest number of human infections did not show better ability to invade cells in the GIT model system, with strains belonging to other serovars displaying even higher infectivity. The RF model did not identify any virulence factor as significant P(inf) predictors. Significant associations of P(inf) with biofilm formation were found in all the different conditions for a limited number of serovars, indicating that the two phenotypes are governed by different mechanisms and that the ability to form biofilm does not correlate with the ability to invade epithelial cells. Other omics techniques therefore seem more promising as alternatives to identify genes associated with P(inf), and different hypotheses, such as gene expression rather than presence/absence, could be tested to explain phenotypic virulence [P(inf)].},
}
@article {pmid37345931,
year = {2023},
author = {Aldeguer-Riquelme, B and Antón, J and Santos, F},
title = {Distribution, abundance, and ecogenomics of the Palauibacterales, a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum.},
journal = {mSystems},
volume = {8},
number = {4},
pages = {e0021523},
pmid = {37345931},
issn = {2379-5077},
mesh = {*Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Metagenome/genetics ; Lakes ; },
abstract = {The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales. This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N2O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales. Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes, as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H2. Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.},
}
@article {pmid37343911,
year = {2023},
author = {Andrade, L and P Ryan, M and P Burke, L and Hynds, P and Weatherill, J and O'Dwyer, J},
title = {Assessing antimicrobial and metal resistance genes in Escherichia coli from domestic groundwater supplies in rural Ireland.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {333},
number = {},
pages = {121970},
doi = {10.1016/j.envpol.2023.121970},
pmid = {37343911},
issn = {1873-6424},
mesh = {Animals ; Cattle ; Humans ; Swine ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Ireland ; *Anti-Infective Agents/pharmacology ; Microbial Sensitivity Tests ; },
abstract = {Natural ecosystems can become significant reservoirs and/or pathways for antimicrobial resistance (AMR) dissemination, with the potential to affect nearby microbiological, animal, and ultimately human communities. This is further accentuated in environments that provide direct human exposure, such as drinking water. To date, however, few studies have investigated AMR dissemination potential and the presence of co-selective stressors (e.g., metals/metalloids) in groundwater environments of human health significance. Accordingly, the present study analysed samples from rural (drinking) groundwater supplies (i.e., private wells) in the Republic of Ireland, where land use is dominated by livestock grazing activities. In total, 48 Escherichia coli isolates tested phenotypically for antimicrobial susceptibility in an earlier study were further subject to whole genome sequencing (WGS) and corresponding water samples were further analysed for trace metal/metalloid concentrations. Eight isolates (i.e., 16.7%) were genotypically resistant to antimicrobials, confirming prior phenotypic results through the identification of ten antimicrobial resistance genes (ARGs); namely: aph(3″)-lb (strA; n=7), aph(6)-Id (strA; n = 6), blaTEM (n = 6), sul2 (n = 6), tetA (n = 4), floR (n = 2), dfrA5 (n = 1), tetB (n = 1), and tetY (n = 1). Additional bioinformatic analysis revealed that all ARGs were plasmid-borne, except for two of the six sul2 genes, and that 31.2% of all tested isolates (n = 15) and 37.5% of resistant ones (n = 3) carried virulence genes. Study results also found no significant relationships between metal concentrations and ARG abundance. Additionally, just one genetic linkage was identified between ARGs and a metal resistance gene (MRG), namely merA, a mercury-resistant gene found on the same plasmid as blaTEM, dfrA5, strA, strB, and sul2 in the only isolate of inferred porcine (as opposed to bovine) origin. Overall, findings suggest that ARG (and MRG) acquisition may be occurring prior to groundwater ingress, and are likely a legacy issue arising from agricultural practices.},
}
@article {pmid37342144,
year = {2023},
author = {Wilberts, L and Rojas-Preciado, N and Jacquemyn, H and Lievens, B},
title = {Fungal strain and crop cultivar affect growth of sweet pepper plants after root inoculation with entomopathogenic fungi.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1196765},
pmid = {37342144},
issn = {1664-462X},
abstract = {As endophytes, entomopathogenic fungi can protect plants against biotic and abiotic stresses and at the same time promote plant growth and plant health. To date, most studies have investigated whether Beauveria bassiana can enhance plant growth and plant health, while only little is known about other entomopathogenic fungi. In this study, we evaluated whether root inoculation of the entomopathogenic fungi Akanthomyces muscarius ARSEF 5128, B. bassiana ARSEF 3097 and Cordyceps fumosorosea ARSEF 3682 can promote plant growth of sweet pepper (Capsicum annuum L.), and whether effects are cultivar-dependent. Plant height, stem diameter, number of leaves, canopy area, and plant weight were assessed four weeks following inoculation in two independent experiments using two cultivars of sweet pepper (cv. 'IDS RZ F1' and cv. 'Maduro'). Results showed that the three entomopathogenic fungi were able to enhance plant growth, particularly canopy area and plant weight. Further, results showed that effects significantly depended on cultivar and fungal strain, with the strongest fungal effects obtained for cv. 'IDS RZ F1', especially when inoculated with C. fumosorosea. We conclude that inoculation of sweet pepper roots with entomopathogenic fungi can stimulate plant growth, but effects depend on fungal strain and crop cultivar.},
}
@article {pmid37339946,
year = {2023},
author = {Ma, L and Liu, KW and Li, Z and Hsiao, YY and Qi, Y and Fu, T and Tang, GD and Zhang, D and Sun, WH and Liu, DK and Li, Y and Chen, GZ and Liu, XD and Liao, XY and Jiang, YT and Yu, X and Hao, Y and Huang, J and Zhao, XW and Ke, S and Chen, YY and Wu, WL and Hsu, JL and Lin, YF and Huang, MD and Li, CY and Huang, L and Wang, ZW and Zhao, X and Zhong, WY and Peng, DH and Ahmad, S and Lan, S and Zhang, JS and Tsai, WC and Van de Peer, Y and Liu, ZJ},
title = {Diploid and tetraploid genomes of Acorus and the evolution of monocots.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3661},
pmid = {37339946},
issn = {2041-1723},
mesh = {*Tetraploidy ; *Acorus ; Phylogeny ; Diploidy ; Genome ; },
abstract = {Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.},
}
@article {pmid37338413,
year = {2023},
author = {Bittleston, LS and Wolock, CJ and Maeda, J and Infante, V and Ané, JM and Pierce, NE and Pringle, A},
title = {Carnivorous Nepenthes Pitchers with Less Acidic Fluid House Nitrogen-Fixing Bacteria.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {7},
pages = {e0081223},
pmid = {37338413},
issn = {1098-5336},
mesh = {Animals ; *Nitrogen-Fixing Bacteria ; RNA, Ribosomal, 16S/genetics ; Insecta ; Bacteria/genetics ; Nitrogen/analysis ; Alkynes ; },
abstract = {Carnivorous pitcher plants are uniquely adapted to nitrogen limitation, using pitfall traps to acquire nutrients from insect prey. Pitcher plants in the genus Sarracenia may also use nitrogen fixed by bacteria inhabiting the aquatic microcosms of their pitchers. Here, we investigated whether species of a convergently evolved pitcher plant genus, Nepenthes, might also use bacterial nitrogen fixation as an alternative strategy for nitrogen capture. First, we constructed predicted metagenomes of pitcher organisms from three species of Singaporean Nepenthes using 16S rRNA sequence data and correlated predicted nifH abundances with metadata. Second, we used gene-specific primers to amplify and quantify the presence or absence of nifH directly from 102 environmental samples and identified potential diazotrophs with significant differential abundance in samples that also had positive nifH PCR tests. Third, we analyzed nifH in eight shotgun metagenomes from four additional Bornean Nepenthes species. Finally, we conducted an acetylene reduction assay using greenhouse-grown Nepenthes pitcher fluids to confirm nitrogen fixation is indeed possible within the pitcher habitat. Results show active acetylene reduction can occur in Nepenthes pitcher fluid. Variation in nifH from wild samples correlates with Nepenthes host species identity and pitcher fluid acidity. Nitrogen-fixing bacteria are associated with more neutral fluid pH, while endogenous Nepenthes digestive enzymes are most active at low fluid pH. We hypothesize Nepenthes species experience a trade-off in nitrogen acquisition; when fluids are acidic, nitrogen is primarily acquired via plant enzymatic degradation of insects, but when fluids are neutral, Nepenthes plants take up more nitrogen via bacterial nitrogen fixation. IMPORTANCE Plants use different strategies to obtain the nutrients that they need to grow. Some plants access their nitrogen directly from the soil, while others rely on microbes to access the nitrogen for them. Carnivorous pitcher plants generally trap and digest insect prey, using plant-derived enzymes to break down insect proteins and generate a large portion of the nitrogen that they subsequently absorb. In this study, we present results suggesting that bacteria living in the fluids formed by Nepenthes pitcher plants can fix nitrogen directly from the atmosphere, providing an alternative pathway for plants to access nitrogen. These nitrogen-fixing bacteria are only likely to be present when pitcher plant fluids are not strongly acidic. Interestingly, the plant's enzymes are known to be more active under strongly acidic conditions. We propose a potential trade-off where pitcher plants sometimes access nitrogen using their own enzymes to digest prey and at other times take advantage of bacterial nitrogen fixation.},
}
@article {pmid37338363,
year = {2023},
author = {Ye, L and Yang, X and Zhang, B and Zhou, J and Tian, H and Zhang, X and Li, X},
title = {Seasonal Succession of Fungal Communities in Native Truffle (Tuber indicum) Ecosystems.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {7},
pages = {e0019523},
pmid = {37338363},
issn = {1098-5336},
mesh = {Ecosystem ; Seasons ; *Mycobiome ; *Ascomycota ; *Mycorrhizae ; Soil ; Soil Microbiology ; },
abstract = {Truffles are a rare underground fungus and one of the most expensive, and sought-after kitchen ingredients in the world. Microbial ecology plays an important role in the annual growth cycle of truffles, but fungal communities in native truffle ecosystems are still largely unknown, especially for Tuber indicum from China. In this study, the spatial and temporal dynamics of soil physicochemical properties and fungal communities were described associated with four T. indicum-producing plots (TPPs) and one non-truffle-producing plot in four successive growing seasons. A total of 160 biological samples were collected, 80 of which were used for the determination of 10 soil physicochemical indices and 80 for Illumina-based analysis of the fungal microbiome. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. Ascomycetes, Basidiomycetes, and Mucormycoides dominated. The core microbiome work on the microecological changes in TPPs, and the identified core members contribute to the seasonal succession of communities. The genus Tuber occupies a central position in healthy TPPs. There was a strong correlation between soil physicochemical properties and fungal communities. The genus Tuber showed a positive correlation with Ca, Mg, and total nitrogen, but a negative correlation with total phosphorus and available potassium. This study describes the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum, and highlights the succession of core communities in truffle plots, which contribute to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China. IMPORTANCE The spatial and temporal dynamics of soil physicochemical properties and fungal communities associated with four Tuber indicum-producing plots and one non truffle producing plot in four different growing seasons are described. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. This study examines the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum and highlights the succession of core communities in truffle plots, which contributes to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China.},
}
@article {pmid37338299,
year = {2023},
author = {Hurst, JH and Kelly, MS},
title = {Leveraging the human microbiota to target bacterial respiratory pathogens: new paths toward an expanded antimicrobial armamentarium.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0085423},
pmid = {37338299},
issn = {2150-7511},
support = {K01 AI173398/AI/NIAID NIH HHS/United States ; },
mesh = {Child ; Humans ; Moraxella catarrhalis/drug effects ; *Anti-Infective Agents ; *Respiratory Tract Infections/drug therapy/microbiology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; },
abstract = {Acute respiratory infections are the most frequent infections across the lifespan and are the leading infectious cause of death among children globally. Bacterial respiratory infections are routinely treated with antibiotics, nearly all of which are derived from microbial natural products. Unfortunately, antibiotic-resistant bacteria are an increasingly frequent cause of respiratory infections, and there are few new antibiotics in development that target these pathogens. In the article by Stubbendieck et al., the authors identified Rothia species that demonstrate in vitro and ex vivo growth inhibition of the respiratory pathobiont Moraxella catarrhalis. The authors present experiments suggesting that this activity is mediated at least in part through the secretion of a novel peptidoglycan endopeptidase that targets the M. catarrhalis cell wall. In this commentary, we discuss these findings in the context of the urgent threat of antimicrobial resistance and highlight the promise of the human respiratory microbiota as a source of novel biotherapeutics.},
}
@article {pmid37336018,
year = {2023},
author = {Liu, H and Wang, Y and Shi, X},
title = {Co-existing antibiotics alter the enantioselective dissipation characteristics of zoxamide and drive combined impact on soil microenvironment.},
journal = {Journal of environmental management},
volume = {344},
number = {},
pages = {118340},
doi = {10.1016/j.jenvman.2023.118340},
pmid = {37336018},
issn = {1095-8630},
mesh = {Anti-Bacterial Agents/pharmacology ; Soil ; Stereoisomerism ; *Oxytetracycline/analysis ; Tetracycline ; Sulfamethoxazole ; Bacteria ; *Soil Pollutants/analysis ; },
abstract = {Co-existence of antibiotics (ABX) in soil may expand the environmental harm of pesticide pollution. Our study investigated the combined effects of five antibiotics chlortetracycline (CTC), oxytetracycline (OTC), tetracycline (TC), sulfamethoxazole (SMX), enrofloxacin (ENR) on enantioselective fate of zoxamide (ZXM) and soil health. The results showed that S-(+)-ZXM preferentially dissipated in soil. ABX prolonged dissipation half-life and reduced enantioselectivity of ZXM. Soil was detected to be more acidic after long-term treatment of ZXM and ABX. Lowest soil available N, P, K were found in ZXM + SMX, ZXM + OTC and ZXM + SMX groups at 80 days, respectively. ABX had demonstrated effective promotion of catalase (S-CAT), urease (S-UE) and negative impact on dehydrogenase (S-DHA), sucrase (S-SC) activities. Bacteria Lysobacter, Sphingomonas and fungus Mortierella were identified as the most dominant genera, which possessed as potential microbial resources for removal of composite pollution from ZXM and ABX. SMX and TC, SMX, ENR, respectively, contributed to the alteration of bacteria and fungi community abundance. Soil acidity, available N and enzyme activity showed stronger correlations with bacteria and fungi compared to other environmental factors. Our findings highlighted the interactions between ZXM and ABX from the perspective of soil microenvironment changes. Moreover, a theoretical basis for the mechanism was actively provided.},
}
@article {pmid37333658,
year = {2023},
author = {Schultz, J and Modolon, F and Peixoto, RS and Rosado, AS},
title = {Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1167718},
pmid = {37333658},
issn = {1664-302X},
abstract = {More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.},
}
@article {pmid37333098,
year = {2023},
author = {Grodner, B and Shi, H and Farchione, O and Vill, AC and Ntekas, I and Diebold, PJ and Zipfel, WR and Brito, IL and Vlaminck, I},
title = {Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37333098},
issn = {2692-8205},
support = {DP2 AI138242/AI/NIAID NIH HHS/United States ; R33 CA235302/CA/NCI NIH HHS/United States ; S10 OD018516/OD/NIH HHS/United States ; },
abstract = {The frequent exchange of mobile genetic elements (MGEs) between bacteria accelerates the spread of functional traits, including antimicrobial resistance, within the human microbiome. Yet, progress in understanding these intricate processes has been hindered by the lack of tools to map the spatial spread of MGEs in complex microbial communities, and to associate MGEs to their bacterial hosts. To overcome this challenge, we present an imaging approach that pairs single molecule DNA Fluorescence In Situ Hybridization (FISH) with multiplexed ribosomal RNA FISH, thereby enabling the simultaneous visualization of both MGEs and host bacterial taxa. We used this methodology to spatially map bacteriophage and antimicrobial resistance (AMR) plasmids in human oral biofilms, and we studied the heterogeneity in their spatial distributions and demonstrated the ability to identify their host taxa. Our data revealed distinct clusters of both AMR plasmids and prophage, coinciding with densely packed regions of host bacteria in the biofilm. These results suggest the existence of specialized niches that maintain MGEs within the community, possibly acting as local hotspots for horizontal gene transfer. The methods introduced here can help advance the study of MGE ecology and address pressing questions regarding antimicrobial resistance and phage therapy.},
}
@article {pmid37331053,
year = {2023},
author = {Araujo, FF and Salvador, GLO and Lupatini, GC and Pereira, APA and Costa, RM and de Aviz, RO and de Alcantara Neto, F and Mendes, LW and Araujo, ASF},
title = {Exploring the diversity and composition of soil microbial communities in different soybean-maize management systems.},
journal = {Microbiological research},
volume = {274},
number = {},
pages = {127435},
doi = {10.1016/j.micres.2023.127435},
pmid = {37331053},
issn = {1618-0623},
mesh = {*Soil/chemistry ; Zea mays/microbiology ; Glycine max ; Soil Microbiology ; *Microbiota ; },
abstract = {Soybean-maize are cultivated in different management systems, such as no-tillage and pastures, which presents potential to add organic residues, and it can potentially impacts the soil microbial community present in these systems. Thus, this study aimed to examine the effects of different soybean-maize management practices on the diversity and composition of soil microbial communities. Specifically, 16 S rRNA amplicon sequencing was used to investigate whether the use of pasture species in a fallowing system influences microbial communities in a soybean-maize rotation system, as compared to conventional tillage and no-tillage systems. The results indicate that the inclusion of the pasture species Urochloa brizantha in soybean-maize management systems leads to distinct responses within the soil microbial community. It was found that different soybean-maize management systems, particularly those with U. brizantha, affected the microbial community, likely due to the management applied to this pasture species. The system with 3 years of fallowing before soybean-maize showed the lowest microbial richness (∼2000 operational taxonomic units) and diversity index (∼6.0). Proteobacteria (∼30%), Acidobacteria (∼15%), and Verrucomicrobia (∼10%) were found to be the most abundant phyla in the soil under tropical native vegetation, while soils under cropland had an increased abundance of Firmicutes (∼30% to ∼50%) and Actinobacteria (∼30% to ∼35%). To summarize, this study identified the impacts of various soybean-maize management practices on the soil microbial community and emphasized the advantages of adding U. brizantha as a fallow species.},
}
@article {pmid37327546,
year = {2023},
author = {Ostermeyer, P and Folens, K and Verbruggen, F and Bonin, L and Hennebel, T and Korneel, R},
title = {A sulfate reducing bioreactor controlled by an electrochemical system enables near-zero chemical treatment of metallurgical wastewater.},
journal = {Water research},
volume = {242},
number = {},
pages = {120215},
doi = {10.1016/j.watres.2023.120215},
pmid = {37327546},
issn = {1879-2448},
mesh = {*Wastewater ; *Sulfates/chemistry ; Sewage/chemistry ; Metals ; Bioreactors ; Waste Disposal, Fluid/methods ; },
abstract = {Metallurgical wastewaters are characterized by a low pH (<4), high concentrations of sulfate (15 gSO4[2-] L[-1]), and metal(loid)s. Current treatment requires the consumption of chemicals such as alkali and high levels of waste sludge generation. In this study, we have shown that combining water electrolysis and sulfate reducing bioreactors enables the in-situ generation of base and H2, eliminating the need for base and electron donor addition, resulting in the near-zero treatment of metallurgical wastewater. By extracting cations from the effluent of the system to the bioreactor, the bioreactor pH could be maintained by the in-situ production of alkali. The current for pH control varied between 112-753 mol electrons per m[3] wastewater or 5-48 A m[-2] electrode area. High concentrations of sulfate in the influent and addition of CO2 increased the current required to maintain a steady bioreactor pH. On the other hand, a high sulfate reduction rate and increased influent pH lowered the current required for pH control. Moreover, the current efficiency varied from 14% to 91% and increased with higher pH and cation (Na[+], NH4[+], K[+], Mg[2+], Ca[2+]) concentrations in the middle compartment of the electrochemical cell. The salinity was lowered from 70-120 mS cm[-1] in the influent to 5-20 mS cm[-1] in the system effluent. The energy consumption of the electrochemical pH control varied between 10 and 100 kWh m[-3] and was affected by the conductivity of the wastewater. Industrial wastewater was treated successfully with an average energy consumption of 39 ± 7 kWh m[-3], removing sulfate from 15 g SO4[2-] L[-1] to 0.5 ± 0.5 g SO4[2-] L[-1] at a reduction rate of 20 ± 1 gSO4[2-] L[-1] d[-1]..Metal(loid)s such as As, Cd, Cu, Pb, Te, Tl, Ni and Zn were removed to levels of 1-50 µg L[-1].},
}
@article {pmid37326636,
year = {2023},
author = {Dos Santos Ribeiro, P and Carvalho, NB and Aburjaile, F and Sousa, T and Veríssimo, G and Gomes, T and Neves, F and Blanco, L and Lima, JA and de Oliveira, D and Jaiswal, AK and Brenig, B and Soares, S and Ramos, R and Matiuzzi, M and Góes-Neto, A and Figueira, CP and Costa, F and Ristow, P and Azevedo, V},
title = {Environmental Biofilms from an Urban Community in Salvador, Brazil, Shelter Previously Uncharacterized Saprophytic Leptospira.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2488-2501},
pmid = {37326636},
issn = {1432-184X},
support = {001//Coordination for the Improvement of Higher Education Personnel (Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior - CAPES)/ ; 423415/2021-2//National Council for Scientific and Technological Development (CNPq) Universal project/ ; 23038.000776/2017-54//INCT IN-TREE/ ; },
mesh = {Animals ; Rats ; *Leptospira/genetics ; *Leptospirosis/microbiology ; Brazil ; Biofilms ; DNA ; },
abstract = {Biofilms are complex microecosystems with valuable ecological roles that can shelter a variety of microorganisms. Spirochetes from the genus Leptospira have been observed to form biofilms in vitro, in rural environments, and in the kidneys of reservoir rats. The genus Leptospira is composed of pathogenic and non-pathogenic species, and the description of new species is ongoing due to the advent of whole genome sequencing. Leptospires have increasingly been isolated from water and soil samples. To investigate the presence of Leptospira in environmental biofilms, we collected three distinct samples of biofilms formed in an urban setting with poor sanitation: Pau da Lima, in Salvador, Bahia, Brazil. All biofilm samples were negative for the presence of pathogenic leptospires via conventional PCR, but cultures containing saprophytic Leptospira were identified. Whole genomes were generated and analyzed for twenty isolates obtained from these biofilms. For species identification, we used digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analysis. The obtained isolates were classified into seven presumptive species from the saprophytic S1 clade. ANI and dDDH analysis suggest that three of those seven species were new. Classical phenotypic tests confirmed the novel isolated bacteria as saprophytic Leptospira. The isolates presented typical morphology and ultrastructure according to scanning electron microscopy and formed biofilms under in vitro conditions. Our data indicate that a diversity of saprophytic Leptospira species survive in the Brazilian poorly sanitized urban environment, in a biofilm lifestyle. We believe our results contribute to a better understanding of Leptospira biology and ecology, considering biofilms as natural environmental reservoirs for leptospires.},
}
@article {pmid37325551,
year = {2023},
author = {Cao, Y and Almeida-Silva, F and Zhang, WP and Ding, YM and Bai, D and Bai, WN and Zhang, BW and Van de Peer, Y and Zhang, DY},
title = {Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae).},
journal = {Molecular biology and evolution},
volume = {40},
number = {6},
pages = {msad121},
doi = {10.1093/molbev/msad121/7175457},
pmid = {37325551},
issn = {1537-1719},
mesh = {Calcium ; *Calcium Carbonate ; Genetic Speciation ; Genomics ; *Juglandaceae ; },
abstract = {When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes, and its only congeneric species, P. strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics, and the driving forces underneath the incipient speciation of the two Platycarya lineages.},
}
@article {pmid37323900,
year = {2023},
author = {Ho, PM and Nazeer, RR and Welch, M},
title = {Therapeutic interventions alter ecological interactions among cystic fibrosis airway microbiota.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1178131},
pmid = {37323900},
issn = {1664-302X},
support = {NC/P001564/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; },
abstract = {The airways of people with cystic fibrosis (CF) often harbor a diverse microbiota and in recent years, much effort has been invested in cataloguing these. In spite of providing a wealth of insight, this cataloguing tells us little about how the organisms interact with one another in the CF airways. However, such relationships can be inferred using the theoretical framework of the Lotka-Volterra (LV) model. In the current work, we use a generalized Lotka-Volterra model to interrogate the nationwide data collected and curated by the UK CF Registry. This longitudinal dataset (covering the period 2008-2020) contains annual depositions that record the presence/absence of microbial taxa in each patient, their medication, and their CF genotype. Specifically, we wanted to identify trends in ecological relationships between the CF microbiota at a nationwide level, and whether these are potentially affected by medication. Our results show that some medications have a distinct influence on the microbial interactome, especially those that potentially influence the "gut-lung axis" or mucus viscosity. In particular, we found that patients treated with a combination of antimicrobial agents (targeting the airway microbiota), digestive enzymes (assisting in the assimilation of dietary fats and carbohydrates), and DNase (to reduce mucus viscosity) displayed a distinctly different airway interactome compared with patients treated separately with these medications.},
}
@article {pmid37323646,
year = {2023},
author = {Rodrigues-Filho, JL and Macêdo, RL and Sarmento, H and Pimenta, VRA and Alonso, C and Teixeira, CR and Pagliosa, PR and Netto, SA and Santos, NCL and Daura-Jorge, FG and Rocha, O and Horta, P and Branco, JO and Sartor, R and Muller, J and Cionek, VM},
title = {From ecological functions to ecosystem services: linking coastal lagoons biodiversity with human well-being.},
journal = {Hydrobiologia},
volume = {850},
number = {12-13},
pages = {2611-2653},
pmid = {37323646},
issn = {0018-8158},
abstract = {In this review we highlight the relevance of biodiversity that inhabit coastal lagoons, emphasizing how species functions foster processes and services associated with this ecosystem. We identified 26 ecosystem services underpinned by ecological functions performed by bacteria and other microbial organisms, zooplankton, polychaetae worms, mollusks, macro-crustaceans, fishes, birds, and aquatic mammals. These groups present high functional redundancy but perform complementary functions that result in distinct ecosystem processes. Because coastal lagoons are located in the interface between freshwater, marine and terrestrial ecosystems, the ecosystem services provided by the biodiversity surpass the lagoon itself and benefit society in a wider spatial and historical context. The species loss in coastal lagoons due to multiple human-driven impacts affects the ecosystem functioning, influencing negatively the provision of all categories of services (i.e., supporting, regulating, provisioning and cultural). Because animals' assemblages have unequal spatial and temporal distribution in coastal lagoons, it is necessary to adopt ecosystem-level management plans to protect habitat heterogeneity and its biodiversity, ensuring the provision of services for human well-being to multi-actors in the coastal zone.},
}
@article {pmid37318372,
year = {2023},
author = {Rani, S and Sørensen, MT and Estellé, J and Noel, SJ and Nørskov, N and Krogh, U and Foldager, L and Højberg, O},
title = {Gastrointestinal Microbial Ecology of Weaned Piglets Fed Diets with Different Levels of Glyphosate.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0061523},
pmid = {37318372},
issn = {2165-0497},
mesh = {Animals ; Swine ; *Dysbiosis ; *Gastrointestinal Tract ; Diet/veterinary ; Stomach ; Cecum ; Acids ; },
abstract = {Glyphosate possesses antimicrobial properties, and the present study investigated potential effects of feed glyphosate on piglet gastrointestinal microbial ecology. Weaned piglets were allocated to four diets (glyphosate contents [mg/kg feed]: 0 mg/kg control [CON; i.e., basal diet with no glyphosate added], 20 mg/kg as Glyphomax commercial herbicide [GM20], and 20 mg/kg [IPA20] and 200 mg/kg [IPA200] as glyphosate isopropylamine [IPA] salt). Piglets were sacrificed after 9 and 35 days of treatment, and stomach, small intestine, cecum, and colon digesta were analyzed for glyphosate, aminomethylphosphonic acid (AMPA), organic acids, pH, dry matter content, and microbiota composition. Digesta glyphosate contents reflected dietary levels (on day 35, 0.17, 16.2, 20.5, and 207.5 mg/kg colon digesta, respectively). Overall, we observed no significant glyphosate-associated effects on digesta pH, dry matter content, and-with few exceptions-organic acid levels. On day 9, only minor gut microbiota changes were observed. On day 35, we observed a significant glyphosate-associated decrease in species richness (CON, 462; IPA200, 417) and in the relative abundance of certain Bacteroidetes genera: CF231 (CON, 3.71%; IPA20, 2.33%; IPA200, 2.07%) and g_0.24 (CON, 3.69%; IPA20, 2.07%; IPA200, 1.75%) in cecum. No significant changes were observed at the phylum level. In the colon, we observed a significant glyphosate-associated increase in the relative abundance of Firmicutes (CON, 57.7%; IPA20, 69.4%; IPA200, 66.1%) and a decrease in Bacteroidetes (CON, 32.6%; IPA20, 23.5%). Significant changes were only observed for few genera, e.g., g_0.24 (CON, 7.12%; IPA20, 4.59%; IPA200, 4.00%). In conclusion, exposing weaned piglets to glyphosate-amended feed did not affect gastrointestinal microbial ecology to a degree that was considered actual dysbiosis, e.g., no potential pathogen bloom was observed. IMPORTANCE Glyphosate residues can be found in feed made from genetically modified glyphosate-resistant crops treated with glyphosate or from conventional crops, desiccated with glyphosate before harvest. If these residues affect the gut microbiota to an extent that is unfavorable to livestock health and productivity, the widespread use of glyphosate on feed crops may need to be reconsidered. Few in vivo studies have been conducted to investigate potential impact of glyphosate on the gut microbial ecology and derived health issues of animals, in particular livestock, when exposed to dietary glyphosate residues. The aim of the present study was therefore to investigate potential effects on the gastrointestinal microbial ecology of newly weaned piglets fed glyphosate-amended diets. Piglets did not develop actual gut dysbiosis when fed diets, containing a commercial herbicide formulation or a glyphosate salt at the maximum residue level, defined by the European Union for common feed crops, or at a 10-fold-higher level.},
}
@article {pmid37318344,
year = {2023},
author = {Diner, RE and Zimmer-Faust, A and Cooksey, E and Allard, S and Kodera, SM and Kunselman, E and Garodia, Y and Verhougstraete, MP and Allen, AE and Griffith, J and Gilbert, JA},
title = {Host and Water Microbiota Are Differentially Linked to Potential Human Pathogen Accumulation in Oysters.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {7},
pages = {e0031823},
pmid = {37318344},
issn = {1098-5336},
support = {K12 GM068524/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; Water ; *Ostreidae/microbiology ; *Vibrio parahaemolyticus ; *Vibrio vulnificus ; *Bivalvia ; Bacteria/genetics ; },
abstract = {Oysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter-feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering human health. While pathogen concentrations in coastal waters are often linked to environmental conditions and runoff events, these do not always correlate with pathogen concentrations in oysters. Additional factors related to the microbial ecology of pathogenic bacteria and their relationship with oyster hosts likely play a role in accumulation but are poorly understood. In this study, we investigated whether microbial communities in water and oysters were linked to accumulation of Vibrio parahaemolyticus, Vibrio vulnificus, or fecal indicator bacteria. Site-specific environmental conditions significantly influenced microbial communities and potential pathogen concentrations in water. Oyster microbial communities, however, exhibited less variability in microbial community diversity and accumulation of target bacteria overall and were less impacted by environmental differences between sites. Instead, changes in specific microbial taxa in oyster and water samples, particularly in oyster digestive glands, were linked to elevated levels of potential pathogens. For example, increased levels of V. parahaemolyticus were associated with higher relative abundances of cyanobacteria, which could represent an environmental vector for Vibrio spp. transport, and with decreased relative abundance of Mycoplasma and other key members of the oyster digestive gland microbiota. These findings suggest that host and microbial factors, in addition to environmental variables, may influence pathogen accumulation in oysters. IMPORTANCE Bacteria in the marine environment cause thousands of human illnesses annually. Bivalves are a popular seafood source and are important in coastal ecology, but their ability to concentrate pathogens from the water can cause human illness, threatening seafood safety and security. To predict and prevent disease, it is critical to understand what causes pathogenic bacteria to accumulate in bivalves. In this study, we examined how environmental factors and host and water microbial communities were linked to potential human pathogen accumulation in oysters. Oyster microbial communities were more stable than water communities, and both contained the highest concentrations of Vibrio parahaemolyticus at sites with warmer temperatures and lower salinities. High oyster V. parahaemolyticus concentrations corresponded with abundant cyanobacteria, a potential vector for transmission, and a decrease in potentially beneficial oyster microbes. Our study suggests that poorly understood factors, including host and water microbiota, likely play a role in pathogen distribution and pathogen transmission.},
}
@article {pmid37317205,
year = {2023},
author = {Maatouk, M and Rolain, JM and Bittar, F},
title = {Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation.},
journal = {Microorganisms},
volume = {11},
number = {5},
pages = {},
pmid = {37317205},
issn = {2076-2607},
support = {M&#xe9;diterran&#xe9;e Infection 10-IAHU-03//Agence Nationale de la Recherche/ ; },
abstract = {Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.},
}
@article {pmid37317127,
year = {2023},
author = {Varliero, G and Lebre, PH and Frey, B and Fountain, AG and Anesio, AM and Cowan, DA},
title = {Glacial Water: A Dynamic Microbial Medium.},
journal = {Microorganisms},
volume = {11},
number = {5},
pages = {},
pmid = {37317127},
issn = {2076-2607},
support = {129227//National Research Foundation/ ; },
abstract = {Microbial communities and nutrient dynamics in glaciers and ice sheets continuously change as the hydrological conditions within and on the ice change. Glaciers and ice sheets can be considered bioreactors as microbiomes transform nutrients that enter these icy systems and alter the meltwater chemistry. Global warming is increasing meltwater discharge, affecting nutrient and cell export, and altering proglacial systems. In this review, we integrate the current understanding of glacial hydrology, microbial activity, and nutrient and carbon dynamics to highlight their interdependence and variability on daily and seasonal time scales, as well as their impact on proglacial environments.},
}
@article {pmid37317116,
year = {2023},
author = {Malajacan, GT and Nacario, MAG and Obusan, MCM and Rivera, WL},
title = {Host-Associated Bacteroides 16S rDNA-Based Markers for Source Tracking of Fecal Pollution in Laguna Lake, Philippines.},
journal = {Microorganisms},
volume = {11},
number = {5},
pages = {},
pmid = {37317116},
issn = {2076-2607},
support = {N/A//Department of Science and Technology/ ; },
abstract = {Sources of fecal contamination in Laguna Lake, Philippines, were identified using a library-independent microbial source tracking method targeting host-associated Bacteroides 16S rDNA-based markers. Water samples from nine lake stations were assessed for the presence of the fecal markers HF183 (human), BoBac (cattle), Pig-2-Bac (swine), and DuckBac (duck) from August 2019 to January 2020. HF183 (average concentration = 1.91 log10 copies/mL) was the most frequently detected, while Pig-2-Bac (average concentration = 2.47 log10 copies/mL) was the most abundant. The detected marker concentrations in different stations corresponded to the land use patterns around the lake. Generally, all marker concentrations were higher during the wet season (August-October), suggesting the effect of rainfall-associated factors on the movement and retention of markers from sources. There was a significant association (ρ = 0.45; p < 0.001) between phosphate and the concentration of HF183, suggesting domestic sewage-derived pollution. The markers had acceptable sensitivity and specificity, i.e., HF183 (S = 0.88; R = 0.99), Pig-2-Bac (S = 1.00; R = 1.00), and DuckBac (S = 0.94; R = 1.00), and therefore may be used for the continuous monitoring of fecal pollution in the lake and in designing interventions to improve the quality of the lake water.},
}
@article {pmid37317051,
year = {2023},
author = {Wang, M and Sun, X and Cao, B and Chiariello, NR and Docherty, KM and Field, CB and Gao, Q and Gutknecht, JLM and Guo, X and He, G and Hungate, BA and Lei, J and Niboyet, A and Le Roux, X and Shi, Z and Shu, W and Yuan, M and Zhou, J and Yang, Y},
title = {Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay.},
journal = {Global change biology},
volume = {29},
number = {18},
pages = {5429-5444},
doi = {10.1111/gcb.16811},
pmid = {37317051},
issn = {1365-2486},
support = {//G. Evelyn Hutchinson postdoctoral fellowship from Yale Institute for Biospheric Studies at Yale University/ ; //The Simons Foundation postdoctoral fellowship in Marine Microbial Ecology/ ; 2019A1515110345//Guangdong Basis and Applied Basic Research Foundation grant/ ; 2021A1515011497//Guangdong Basis and Applied Basic Research Foundation grant/ ; 20223BBG74S02//Key Technology R&amp;D Program of Jiangxi Province/ ; 41825016//National Natural Science Foundation of China/ ; 41877048//National Natural Science Foundation of China/ ; 42007297//National Natural Science Foundation of China/ ; DE-SC0004601//Office of Science and Office of Biological and Environmental Research (DOE-BER) of the U.S. Department of Energy Genomic Science Program/ ; DE-SC0010715//Office of Science and Office of Biological and Environmental Research (DOE-BER) of the U.S. Department of Energy Genomic Science Program/ ; //Office of the Vice President for Research at the University of Oklahoma/ ; 2019FY100700//Science &amp; Technology Fundamental Resources Investigation Program/ ; //The French CNRS/INSU-EC2CO Program (project INTERACT)/ ; //The French Institute of Agriculture, Food and Environment Research (INRAE, ECODIV Department)/ ; //The Morgan Family Foundation/ ; //The Packard Foundation/ ; 2019QZKK0503//The Second Tibetan Plateau Scientific Expedition and Research (STEP) Program/ ; DEB-0092642//US National Science Foundation/ ; DEB-0445324//US National Science Foundation/ ; },
mesh = {*Grassland ; Carbon ; Climate Change ; *Microbiota ; Nitrogen ; },
abstract = {Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere-climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2 . Collectively, we demonstrate that long-term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere-climate feedback in Mediterranean-type water-limited ecosystems, namely how eP induces soil C loss via microbe-plant-soil interplay.},
}
@article {pmid37316492,
year = {2023},
author = {Cuypers, WL and Meysman, P and Weill, FX and Hendriksen, RS and Beyene, G and Wain, J and Nair, S and Chattaway, MA and Perez-Sepulveda, BM and Ceyssens, PJ and de Block, T and Lee, WWY and Pardos de la Gandara, M and Kornschober, C and Moran-Gilad, J and Veldman, KT and Cormican, M and Torpdahl, M and Fields, PI and Černý, T and Hardy, L and Tack, B and Mellor, KC and Thomson, N and Dougan, G and Deborggraeve, S and Jacobs, J and Laukens, K and Van Puyvelde, S},
title = {A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3517},
pmid = {37316492},
issn = {2041-1723},
support = {BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_PC_16093/MRC_/Medical Research Council/United Kingdom ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Ethiopia/epidemiology ; Genomics ; Salmonella/genetics ; },
abstract = {Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.},
}
@article {pmid37314477,
year = {2023},
author = {An, Y and Braga, MP and Garcia, SL and Grudzinska-Sterno, M and Hambäck, PA},
title = {Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2477-2487},
pmid = {37314477},
issn = {1432-184X},
support = {#2019-4980//The Swedish Research Council Vetenskapsr&#xe5;det to PAH/ ; },
mesh = {Animals ; *Coleoptera/microbiology ; Phylogeny ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Insecta ; Bacteria/genetics ; },
abstract = {Gut microbes play important roles for their hosts. Previous studies suggest that host-microbial systems can form long-term associations over evolutionary time and the dynamic changes of the intestinal system may represent major driving forces and contribute to insect dietary diversification and speciation. Our study system includes a set of six closely related leaf beetle species (Galerucella spp.) and our study aims to separate the roles of host phylogeny and ecology in determining the gut microbial community and to identify eventual relationship between host insects and gut bacteria. We collected adult beetles from their respective host plants and quantified their microbial community using 16S rRNA sequencing. The results showed that the gut bacteria community composition was structured by host beetle phylogeny, where more or less host-specific gut bacteria interact with the different Galerucella species. For example, the endosymbiotic bacteria Wolbachia was found almost exclusively in G. nymphaea and G. sagittariae. Diversity indicators also suggested that α- and β-diversities of gut bacteria communities varied among host beetle species. Overall, our results suggest a phylogenetically controlled co-occurrence pattern between the six closely related Galerucella beetles and their gut bacteria, indicating the potential of co-evolutionary processes occurring between hosts and their gut bacterial communities.},
}
@article {pmid37310275,
year = {2023},
author = {Saati-Santamaría, Z},
title = {Global Map of Specialized Metabolites Encoded in Prokaryotic Plasmids.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0152323},
pmid = {37310275},
issn = {2165-0497},
mesh = {Humans ; *Bacteria/genetics ; Secondary Metabolism/genetics ; Plasmids/genetics ; *Multigene Family ; },
abstract = {Plasmids are the main mobile elements responsible for horizontal gene transfer (HGT) in microorganisms. These replicons extend the metabolic spectrum of their host cells by carrying functional genes. However, it is still unknown to what extent plasmids carry biosynthetic gene clusters (BGCs) related to the production of secondary or specialized metabolites (SMs). Here, we analyzed 9,183 microbial plasmids to unveil their potential to produce SMs, finding a large diversity of cryptic BGCs in a few varieties of prokaryotic host taxa. Some of these plasmids harbored 15 or more BGCs, and many others were exclusively dedicated to mobilizing BGCs. We found an occurrence pattern of BGCs within groups of homologous plasmids shared by a common taxon, mainly in host-associated microbes (e.g., Rhizobiales, Enterobacteriaceae members). Our results add to the knowledge of the ecological functions and potential industrial uses of plasmids and shed light on the dynamics and evolution of SMs in prokaryotes. IMPORTANCE Plasmids are mobile DNA elements that can be shared among microbial cells, and they are useful for bringing to fruition some microbial ecological traits. However, it is not known to what extent plasmids harbor genes related to the production of specialized/secondary metabolites (SMs). In microbes, these metabolites are frequently useful for defense purposes, signaling, etc. In addition, these molecules usually have biotechnological and clinical applications. Here, we analyzed the content, dynamics, and evolution of genes related to the production of SMs in >9,000 microbial plasmids. Our results confirm that some plasmids act as a reservoir of SMs. We also found that some families of biosynthetic gene clusters are exclusively present in some groups of plasmids shared among closely related microbes. Host-associated bacteria (e.g., plant and human microbes) harbor the majority of specialized metabolites encoded in plasmids. These results provide new knowledge about microbial ecological traits and might enable the discovery of novel metabolites.},
}
@article {pmid37308155,
year = {2023},
author = {Timmis, K and Verstraete, W and Regina, VR and Hallsworth, JE},
title = {The Pareto principle: To what extent does it apply to resource acquisition in stable microbial communities and thereby steer their geno-/ecotype compositions and interactions between their members?.},
journal = {Environmental microbiology},
volume = {25},
number = {7},
pages = {1221-1231},
doi = {10.1111/1462-2920.16438},
pmid = {37308155},
issn = {1462-2920},
mesh = {*Ecotype ; Genotype ; *Microbiota/genetics ; },
abstract = {The Pareto principle, or 20:80 rule, describes resource distribution in stable communities whereby 20% of community members acquire 80% of a key resource. In this Burning Question, we ask to what extent the Pareto principle applies to the acquisition of limiting resources in stable microbial communities; how it may contribute to our understanding of microbial interactions, microbial community exploration of evolutionary space, and microbial community dysbiosis; and whether it can serve as a benchmark of microbial community stability and functional optimality?},
}
@article {pmid37303746,
year = {2023},
author = {Martinez-Rabert, E and Sloan, WT and Gonzalez-Cabaleiro, R},
title = {Multiscale models driving hypothesis and theory-based research in microbial ecology.},
journal = {Interface focus},
volume = {13},
number = {4},
pages = {20230008},
pmid = {37303746},
issn = {2042-8898},
abstract = {Hypothesis and theory-based studies in microbial ecology have been neglected in favour of those that are descriptive and aim for data-gathering of uncultured microbial species. This tendency limits our capacity to create new mechanistic explanations of microbial community dynamics, hampering the improvement of current environmental biotechnologies. We propose that a multiscale modelling bottom-up approach (piecing together sub-systems to give rise to more complex systems) can be used as a framework to generate mechanistic hypotheses and theories (in-silico bottom-up methodology). To accomplish this, formal comprehension of the mathematical model design is required together with a systematic procedure for the application of the in-silico bottom-up methodology. Ruling out the belief that experimentation before modelling is indispensable, we propose that mathematical modelling can be used as a tool to direct experimentation by validating theoretical principles of microbial ecology. Our goal is to develop methodologies that effectively integrate experimentation and modelling efforts to achieve superior levels of predictive capacity.},
}
@article {pmid37303745,
year = {2023},
author = {Sloan, WT and Gómez-Borraz, TL},
title = {Engineering biology in the face of uncertainty.},
journal = {Interface focus},
volume = {13},
number = {4},
pages = {20230001},
pmid = {37303745},
issn = {2042-8898},
abstract = {Combining engineering and biology surely must be a route to delivering solutions to the world's most pressing problems in depleting resources, energy and the environment. Engineers and biologists have long recognized the power in coupling their disciplines and have evolved a healthy variety of approaches to realizing technologies. Yet recently, there has been a movement to narrow the remit of engineering biology. Its definition as 'the application of engineering principles to the design of biological systems' ought to encompass a broad church. However, the emphasis is firmly on construction '…of novel biological devices and systems from standardized artificial parts' within cells. Thus, engineering biology has become synonymous with synthetic biology, despite the many longstanding technologies that use natural microbial communities. The focus on the nuts and bolts of synthetic organisms may be deflecting attention from the significant challenge of delivering solutions at scale, which cuts across all engineering biology, synthetic and natural. Understanding, let alone controlling, every component of an engineered system is an unrealistic goal. To realize workable solutions in a timely manner we must develop systematic ways of engineering biology in the face of the uncertainties that are inherent in biological systems and that arise through lack of knowledge.},
}
@article {pmid37303743,
year = {2023},
author = {Sierocinski, P and Stilwell, P and Padfield, D and Bayer, F and Buckling, A},
title = {The ecology of scale: impact of volume on coalescence and function in methanogenic communities.},
journal = {Interface focus},
volume = {13},
number = {4},
pages = {20220089},
pmid = {37303743},
issn = {2042-8898},
abstract = {Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities) on community composition and function. Our results show that there is an effect of scale on biogas production. Furthermore, we see a link between community evenness and volume, with smaller scale communities having higher evenness. Despite those differences, the overall patterns of community coalescence are very similar at all scales, with coalescence leading to levels of biogas production comparable with that of the best-performing component community. The increase in biogas with increasing volume plateaus, suggesting there is a volume where productivity stays stable over large volumes. Our findings are reassuring for ecologists studying large ecosystems and industries operating pilot scale facilities, as they support the validity of pilot scale studies in this field.},
}
@article {pmid37302588,
year = {2023},
author = {Rosinger, C and Rousk, J and Bonkowski, M and Rethemeyer, J and Jaeschke, A},
title = {Rewetting the hyper-arid Atacama Desert soil reactivates a carbon-starved microbial decomposer community and also triggers archaeal metabolism.},
journal = {The Science of the total environment},
volume = {892},
number = {},
pages = {164785},
doi = {10.1016/j.scitotenv.2023.164785},
pmid = {37302588},
issn = {1879-1026},
mesh = {*Archaea ; Soil ; Carbon ; Glycerol ; Soil Microbiology ; Bacteria ; *Microbiota ; Fatty Acids ; Phospholipids ; },
abstract = {Extreme environmental conditions make soils of the hyper-arid Atacama Desert one of the most hostile habitats for life on the planet. During the short intervals of moisture availability that occur, it remains unresolved how soil microorganisms physiologically respond to such dramatic environmental changes. Therefore, we simulated a precipitation event - without (H2O) and with (H2O + C) labile carbon (C) supplementation - and investigated the responses in microbial communities (using phospholipid fatty acids (PLFAs) and archaeal glycerol dialkyl glycerol tetraether (GDGTs)) and physiology (by means of respiration, bacterial and fungal growth and C-use efficiency (CUE)) during a five-day incubation. We demonstrated that bacterial and fungal growth does occur in these extreme soils following rewetting, albeit at 100-10,000-fold lower rates compared to previously studied soil systems. C supplementation increased levels of bacterial growth and respiration responses by 5- and 50-fold, respectively, demonstrating a C-limited microbial decomposer community. While the microbial CUE following rewetting was c. 14 %, the addition of labile C during rewetting resulted in a substantial reduction (c. 1.6 %). Consistent with these interpretations, the PLFA composition clearly shifted from saturated towards more unsaturated and branched PLFAs, which could arise from (i) a physiological adaptation of the cell membrane to changing osmotic conditions or (ii) a community composition shift. Significant increases in total PLFA concentrations were solely found with H2O + C addition. Contrary to other recent studies, we found evidence for a metabolically active archaeal community in these hyper-arid soils upon rewetting. We conclude that (i) microorganisms in this extreme soil habitat can be activated and grow within days following rewetting, (ii) available C is the limiting factor for microbial growth and biomass gains, and (iii) that an optimization of tolerating the extreme conditions while maintaining a high CUE comes at the expense of very poor resource-use efficiency during high resource availability.},
}
@article {pmid37302271,
year = {2023},
author = {Sakarika, M and Ganigué, R and Rabaey, K},
title = {Corrigendum to "Methylotrophs: from C1 compounds to food" [Curr Opin Biotechnol 75 (2022) 102685].},
journal = {Current opinion in biotechnology},
volume = {82},
number = {},
pages = {102964},
doi = {10.1016/j.copbio.2023.102964},
pmid = {37302271},
issn = {1879-0429},
}
@article {pmid37301781,
year = {2023},
author = {Zhu, YL and Huang, YJ and Nuerhamanti, N and Bai, XY and Wang, HN and Zhu, XY and Zhang, W},
title = {Composition and Distribution Characteristics of Rhizosphere Bacterial Community of Ammodendron bifolium Growing in Takeermohuer Desert Are Different from Those in Non-rhizosphere.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2461-2476},
pmid = {37301781},
issn = {1432-184X},
support = {32160309//National Science Foundation of China/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
mesh = {*Rhizosphere ; Bacteria ; Proteobacteria ; Acidobacteria ; *Fabaceae ; Soil/chemistry ; Nitrogen ; Soil Microbiology ; },
abstract = {Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing and endangered plant in Takeermohuer Desert, and bacterial community associated with this plant rhizosphere is still unclear. In this study, we studied the composition and diversity of bacterial community from A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using traditional bacterial isolation and high-throughput sequencing approaches, and preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. Results showed that Takeermohuer Desert with high salinity has been an oligotrophic environment, while the rhizosphere exhibited eutrophication resulting from high content SOM (soil organic matter) and SAN (soil alkaline nitrogen) compared with bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phyla level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in eutrophic rhizosphere, and Firmicutes (9.8%) and Chloroflexi (6.9%) relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genus was Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD indexes in rhizosphere were significantly higher than those in bulk soil at the same soil depth, and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in Takeermohuer Desert were Actinobacteria, Acidobacteria, Proteobacteria, and Chlorofexi. Furthermore, the major environmental factors affecting rhizosphere bacterial community were EC (electrical conductivity), SOM, STN (soil total nitrogen), SAN, and SAK (soil available potassium), while bulk soil were distance and C/N (STC/STN). We concluded that A. bifolium rhizosphere bacterial community is different from non-rhizosphere in composition, distribution, and environmental influencing factors, which will have important significances for understanding their ecological functions and maintaining biodiversity.},
}
@article {pmid37300728,
year = {2023},
author = {Wasmund, K and Trueba-Santiso, A and Vicent, T and Adrian, L and Vuilleumier, S and Marco-Urrea, E},
title = {Proteogenomics of the novel Dehalobacterium formicoaceticum strain EZ94 highlights a key role of methyltransferases during anaerobic dichloromethane degradation.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {33},
pages = {80602-80612},
pmid = {37300728},
issn = {1614-7499},
support = {CTM2016-75587-C2-1-R//Agencia Estatal de Investigaci&#xf3;n/ ; PID2019-103989RB-100//Agencia Estatal de Investigaci&#xf3;n/ ; BES-2014-070817//Ministerio de Econom&#xed;a y Competitividad/ ; ANR-17-CE07-0009//Agence Nationale de la Recherche/ ; },
mesh = {Anaerobiosis ; *Proteogenomics ; Methylene Chloride ; Methyltransferases/metabolism ; Biodegradation, Environmental ; Proteome/metabolism ; },
abstract = {Dichloromethane (DCM, methylene chloride) is a toxic, high-volume industrial pollutant of long-standing. Anaerobic biodegradation is crucial for its removal from contaminated environments, yet prevailing mechanisms remain unresolved, especially concerning dehalogenation. In this study, we obtained an assembled genome of a novel DCM-degrading strain, Dehalobacterium formicoaceticum strain EZ94, from a stable DCM-degrading consortium, and we analyzed its proteome during degradation of DCM. A gene cluster recently predicted to play a major role in anaerobic DCM catabolism (the mec cassette) was found. Methyltransferases and other proteins encoded by the mec cassette were among the most abundant proteins produced, suggesting their involvement in DCM catabolism. Reductive dehalogenases were not detected. Genes and corresponding proteins for a complete Wood-Ljungdahl pathway, which could enable further metabolism of DCM carbon, were also found. Unlike for the anaerobic DCM degrader "Ca. F. warabiya," no genes for metabolism of the quaternary amines choline and glycine betaine were identified. This work provides independent and supporting evidence that mec-associated methyltransferases are key to anaerobic DCM metabolism.},
}
@article {pmid37296446,
year = {2023},
author = {Peral-Aranega, E and Saati-Santamaría, Z and Ayuso-Calles, M and Kostovčík, M and Veselská, T and Švec, K and Rivas, R and Kolařik, M and García-Fraile, P},
title = {New insight into the bark beetle ips typographus bacteriome reveals unexplored diversity potentially beneficial to the host.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {53},
pmid = {37296446},
issn = {2524-6372},
support = {19-09072S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; },
abstract = {BACKGROUND: Ips typographus (European spruce bark beetle) is the most destructive pest of spruce forests in Europe. As for other animals, it has been proposed that the microbiome plays important roles in the biology of bark beetles. About the bacteriome, there still are many uncertainties regarding the taxonomical composition, insect-bacteriome interactions, and their potential roles in the beetle ecology. Here, we aim to deep into the ecological functions and taxonomical composition of I. typographus associated bacteria.<br><br>RESULTS: We assessed the metabolic potential of a collection of isolates obtained from different life stages of I. typographus beetles. All strains showed the capacity to hydrolyse one or more complex polysaccharides into simpler molecules, which may provide an additional carbon source to its host. Also, 83.9% of the strains isolated showed antagonistic effect against one or more entomopathogenic fungi, which could assist the beetle in its fight against this pathogenic threat. Using culture-dependent and -independent techniques, we present a taxonomical analysis of the bacteriome associated with the I. typographus beetle during its different life stages. We have observed an evolution of its bacteriome, which is diverse at the larval phase, substantially diminished in pupae, greater in the teneral adult phase, and similar to that of the larval stage in mature adults. Our results suggest that taxa belonging to the Erwiniaceae family, and the Pseudoxanthomonas and Pseudomonas genera, as well as an undescribed genus within the Enterobactereaceae family, are part of the core microbiome and may perform vital roles in maintaining beetle fitness.<br><br>CONCLUSION: Our results indicate that isolates within the bacteriome of I. typographus beetle have the metabolic potential to increase beetle fitness by proving additional and assimilable carbon sources for the beetle, and by antagonizing fungi entomopathogens. Furthermore, we observed that isolates from adult beetles are more likely to have these capacities but those obtained from larvae showed strongest antifungal activity. Our taxonomical analysis showed that Erwinia typographi, Pseudomonas bohemica, and Pseudomonas typographi species along with Pseudoxanthomonas genus, and putative new taxa belonging to the Erwiniaceae and Enterobacterales group are repeatedly present within the bacteriome of I. typographus beetles, indicating that these species might be part of the core microbiome. In addition to Pseudomonas and Erwinia group, Staphylococcus, Acinetobacter, Curtobacterium, Streptomyces, and Bacillus genera seem to also have interesting metabolic capacities but are present in a lower frequency. Future studies involving bacterial-insect interactions or analysing other potential roles would provide more insights into the bacteriome capacity to be beneficial to the beetle.},
}
@article {pmid37296336,
year = {2023},
author = {Yu, T and Nie, J and Zang, H and Zeng, Z and Yang, Y},
title = {Peanut-based Rotation Stabilized Diazotrophic Communities and Increased Subsequent Wheat Yield.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2447-2460},
pmid = {37296336},
issn = {1432-184X},
support = {2016YFD0300205-01//National Key Research and Development Program of China/ ; 31901470//National Natural Science Foundation of China/ ; },
mesh = {*Agriculture/methods ; Arachis ; Triticum ; Soil/chemistry ; *Fabaceae ; Nitrogen/analysis ; },
abstract = {The introduction of legumes into rotations can improve nitrogen use efficiency and crop yield; however, its microbial mechanism involved remains unclear. This study aimed to explore the temporal impact of peanut introduction on microorganisms related to nitrogen metabolism in rotation systems. In this study, the dynamics of diazotrophic communities in two crop seasons and wheat yields of two rotation systems: winter wheat - summer maize (WM) and spring peanut → winter wheat - summer maize (PWM) in the North China Plain were investigated. Our results showed that peanut introduction increased wheat yield and biomass by 11.6% (p < 0.05) and 8.9%, respectively. Lower Chao1 and Shannon indexes of the diazotrophic communities were detected in soils that sampling in June compared with those sampling in September, although no difference was found between WM and PWM. Principal co-ordinates analysis (PCoA) showed that rotation system significantly changed the diazotrophic community structures (PERMANOVA; p < 0.05). Compared with WM, the genera of Azotobacter, Skermanella, Azohydromonas, Rhodomicrobium, Azospirillum, Unclassified_f_Opitutaceae, and Unclassified_f_Rhodospirillaceae were significantly enriched (p < 0.05) in PWM. Furthermore, rotation system and sampling time significantly influenced soil properties, which significantly correlated with the top 15 genera in relative abundance. Partial least squares path modeling (PLS-PM) analysis further showed that the diazotrophic community diversity (alpha- and beta-diversity) and soil properties (pH, SOC and TN) significantly affected wheat yield. In conclusion, legume inclusion has the potential to stabilize diazotrophic community structure at the temporal scales and increase subsequent crop yield.},
}
@article {pmid37294090,
year = {2023},
author = {Upadhyay, V and Suryawanshi, RK and Tasoff, P and McCavitt-Malvido, M and Kumar, RG and Murray, VW and Noecker, C and Bisanz, JE and Hswen, Y and Ha, CWY and Sreekumar, B and Chen, IP and Lynch, SV and Ott, M and Lee, S and Turnbaugh, PJ},
title = {Mild SARS-CoV-2 infection results in long-lasting microbiota instability.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0088923},
pmid = {37294090},
issn = {2150-7511},
support = {K08 HL165106/HL/NHLBI NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; R01 AT011117/AT/NCCIH NIH HHS/United States ; F31 AI164671/AI/NIAID NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; },
mesh = {Animals ; Mice ; Mice, Inbred C57BL ; SARS-CoV-2 ; *COVID-19 ; *Microbiota ; Mammals ; },
abstract = {Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2-positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls. These results were confirmed and extended in the K18-humanized angiotensin-converting enzyme 2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the USA), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila. Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2, it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.},
}
@article {pmid37293832,
year = {2023},
author = {Mortier, C and Quintelier, K and De Craemer, AS and Renson, T and Deroo, L and Dumas, E and Verheugen, E and Coudenys, J and Decruy, T and Lukasik, Z and Van Gassen, S and Saeys, Y and Hoorens, A and Lobatón, T and Van den Bosch, F and Van de Wiele, T and Venken, K and Elewaut, D},
title = {Gut Inflammation in Axial Spondyloarthritis Patients is Characterized by a Marked Type 17 Skewed Mucosal Innate-like T Cell Signature.},
journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)},
volume = {75},
number = {11},
pages = {1969-1982},
doi = {10.1002/art.42627},
pmid = {37293832},
issn = {2326-5205},
mesh = {Humans ; Interleukin-17/metabolism ; Nuclear Receptor Subfamily 1, Group F, Member 3 ; Leukocytes, Mononuclear/metabolism ; Inflammation/metabolism ; *Spondylarthritis/metabolism ; *Spondylitis, Ankylosing ; Mucous Membrane/metabolism ; },
abstract = {OBJECTIVE: Patients with spondyloarthritis (SpA) often present with microscopic signs of gut inflammation, a risk factor for progressive disease. We investigated whether mucosal innate-like T cells are involved in dysregulated interleukin-23 (IL-23)/IL-17 responses in the gut-joint axis in SpA.<br><br>METHODS: Ileal and colonic intraepithelial lymphocytes (IELs), lamina propria lymphocytes (LPLs), and paired peripheral blood mononuclear cells (PBMCs) were isolated from treatment-naive patients with nonradiographic axial SpA with (n&#xa0;=&#xa0;11) and without (n&#xa0;=&#xa0;14) microscopic gut inflammation and healthy controls (n&#xa0;=&#xa0;15) undergoing ileocolonoscopy. The presence of gut inflammation was assessed histopathologically. Immunophenotyping of innate-like T cells and conventional T cells was performed using intracellular flow cytometry. Unsupervised clustering analysis was done by FlowSOM technology. Serum IL-17A levels were measured via Luminex.<br><br>RESULTS: Microscopic gut inflammation in nonradiographic axial SpA was characterized by increased ileal intraepithelial &#x3b3;&#x3b4;-hi T cells, a &#x3b3;&#x3b4;-T cell subset with elevated &#x3b3;&#x3b4;-T cell receptor expression. &#x3b3;&#x3b4;-hi T cells&#xa0;were also increased in PBMCs of patients with nonradiographic axial SpA versus healthy controls and were strongly associated with Ankylosing Spondylitis Disease Activity Score. The abundance of mucosal-associated invariant T cells and invariant natural killer T cells was unaltered. Innate-like T cells in the inflamed gut showed increased ROR&#x3b3;t, IL-17A, and IL-22 levels with loss of T-bet, a signature that was less pronounced in conventional T cells. Presence of gut inflammation was associated with higher serum IL-17A levels. In patients treated with tumor necrosis factor blockade, the proportion of &#x3b3;&#x3b4;-hi cells and ROR&#x3b3;t expression in blood was completely restored.<br><br>CONCLUSION: Intestinal innate-like T cells display marked type 17 skewing in the inflamed gut mucosa of patients with nonradiographic axial SpA. &#x3b3;&#x3b4;-hi T cells are linked to intestinal inflammation and disease activity in SpA.},
}
@article {pmid37291701,
year = {2023},
author = {Suarez, C and Hackl, T and Wilen, BM and Persson, F and Hagelia, P and Jetten, MSM and Dalcin Martins, P},
title = {Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.},
journal = {FEMS microbiology letters},
volume = {370},
number = {},
pages = {},
pmid = {37291701},
issn = {1574-6968},
mesh = {*Metagenome ; *Planctomycetes ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; Manganese ; Iron ; Oxidation-Reduction ; },
abstract = {The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.},
}
@article {pmid37287124,
year = {2023},
author = {Klein-Gordon, JM and Johnson, KB and Loper, JE and Stockwell, VO},
title = {Contribution of Native Plasmids of Pantoea vagans C9-1 to Epiphytic Fitness and Fire Blight Management on Apple and Pear Flowers and Fruits.},
journal = {Phytopathology},
volume = {113},
number = {12},
pages = {2187-2196},
doi = {10.1094/PHYTO-04-23-0144-SA},
pmid = {37287124},
issn = {0031-949X},
mesh = {*Malus/microbiology ; Fruit ; *Pantoea/genetics ; *Pyrus/microbiology ; Plant Diseases/prevention &amp; control/microbiology ; Plasmids ; *Erwinia amylovora/genetics ; Flowers/microbiology ; },
abstract = {Pantoea vagans C9-1 (C9-1) is a biological control bacterium that is applied to apple and pear trees during bloom for suppression of fire blight, caused by Erwinia amylovora. Strain C9-1 has three megaplasmids: pPag1, pPag2, and pPag3. Prior bioinformatic studies predicted these megaplasmids have a role in environmental fitness and/or biocontrol efficacy. Plasmid pPag3 is part of the large Pantoea plasmid (LPP-1) group that is present in all Pantoea spp. and has been hypothesized to contribute to environmental colonization and persistence, while pPag2 is less common. We assessed fitness of C9-1 derivatives cured of pPag2 and/or pPag3 on pear and apple flowers and fruit in experimental orchards. We also assessed the ability of a C9-1 derivative lacking pPag3 to reduce populations of E. amylovora on flowers and disease incidence. Previously, we determined that tolerance to stresses imposed in vitro was compromised in derivatives of C9-1 lacking pPag2 and/or pPag3; however, in this study, the loss of pPag2 and/or pPag3 did not consistently reduce the fitness of C9-1 on flowers in orchards. Over the summer, pPag3 contributed to survival of C9-1 on developing apple and pear fruit in two of five trials, whereas loss of pPag2 did not significantly affect survival of C9-1. We also found that loss of pPag3 did not affect C9-1's ability to reduce E. amylovora populations or fire blight incidence on apple flowers. Our findings partially support prior hypotheses that LPP-1 in Pantoea species contributes to persistence on plant surfaces but questions whether LPP-1 facilitates host colonization.},
}
@article {pmid37286586,
year = {2023},
author = {Leung, H and Xiong, L and Ni, Y and Busch, A and Bauer, M and Press, AT and Panagiotou, G},
title = {Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {35},
pmid = {37286586},
issn = {2055-5008},
mesh = {Mice ; Animals ; Bile Acids and Salts ; Ecosystem ; *Cholestasis/complications/pathology ; *Liver Diseases/complications ; Cytokines ; *Gastrointestinal Microbiome ; },
abstract = {Currently, there is evidence that alteration in the gut ecosystem contributes to the development of liver diseases, however, the complex mechanisms involved are still unclear. We induced cholestasis in mice by bile duct ligation (BDL), mirroring the phenotype of a bile duct obstruction, to understand how gut microbiota alterations caused by an impaired flow of bile acid to the gut contribute to the pathogenesis and progression of liver disease. We performed longitudinal stool, heart, and liver sampling using mice receiving BDL and controls receiving sham operation (ShamOP). Shotgun metagenomics profiling using fecal samples taken before and on day 1, day 3, and day 7 after surgery was performed, and the cytokines and clinical chemistry profiles from heart blood, as well as the liver bile acids profile, were measured. The BDL surgery reshaped the microbiome of mice, resulting in highly distinct characteristics compared to the ShamOP. Our analysis of the microbiome pathways and ECs revealed that BDL reduces the production of hepatoprotective compounds in the gut, such as biotin, spermidine, arginine, and ornithine, which were negatively associated with inflammatory cytokines (IL-6, IL-23, MCP-1). The reduction of the functional potential of the gut microbiota in producing those hepatoprotective compounds is associated with the decrease of beneficial bacteria species from Anaerotruncus, Blautia, Eubacterium, and Lachnoclostridium genera, as well as the increase of disease-associated bacteria e.g., Escherichia coli and Entercoccus faecalis. Our findings advances our knowledge of the gut microbiome-bile acids-liver triangle, which may serve as a potential therapeutic strategy for liver diseases.},
}
@article {pmid37285553,
year = {2023},
author = {McKinlay, JB},
title = {Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding.},
journal = {Annual review of microbiology},
volume = {77},
number = {},
pages = {277-297},
doi = {10.1146/annurev-micro-032521-023815},
pmid = {37285553},
issn = {1545-3251},
mesh = {*Bacteria ; Homeostasis ; },
abstract = {The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding. Despite common claims, diffusion of most intracellular metabolites across a membrane is unlikely. Instead, passive and active transporters are likely involved, possibly purging excess metabolites as part of homeostasis. Re-acquisition of metabolites by a producer limits the opportunities for cross-feeding. However, a competitive recipient can stimulate metabolite externalization and initiate a positive-feedback loop of reciprocal cross-feeding.},
}
@article {pmid37285121,
year = {2023},
author = {Tran, PQ and Bachand, SC and Hotvedt, JC and Kieft, K and McDaniel, EA and McMahon, KD and Anantharaman, K},
title = {Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria.},
journal = {mSystems},
volume = {8},
number = {3},
pages = {e0020123},
pmid = {37285121},
issn = {2379-5077},
support = {Hatch project 1025641//U.S. Department of Agriculture (USDA)/ ; CSP 394//Joint Genome Institute (JGI)/ ; //Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
mesh = {*Hydrogen Sulfide/metabolism ; Cysteine/metabolism ; Ecosystem ; Sulfides/metabolism ; Bacteria/genetics ; Sulfur/metabolism ; Lakes/microbiology ; Oxygen/metabolism ; Genomics ; },
abstract = {The sulfur-containing amino acid cysteine is abundant in the environment, including in freshwater lakes. Biological cysteine degradation can result in hydrogen sulfide (H2S), a toxic and ecologically relevant compound that is a central player in biogeochemical cycling in aquatic environments. Here, we investigated the ecological significance of cysteine in oxic freshwater, using isolated cultures, controlled experiments, and multiomics. We screened bacterial isolates enriched from natural lake water for their ability to produce H2S when provided cysteine. We identified 29 isolates (Bacteroidota, Proteobacteria, and Actinobacteria) that produced H2S. To understand the genomic and genetic basis for cysteine degradation and H2S production, we further characterized three isolates using whole-genome sequencing (using a combination of short-read and long-read sequencing) and tracked cysteine and H2S levels over their growth ranges: Stenotrophomonas maltophilia (Gammaproteobacteria), S. bentonitica (Gammaproteobacteria), and Chryseobacterium piscium (Bacteroidota). Cysteine decreased and H2S increased, and all three genomes had genes involved in cysteine degradation. Finally, to assess the presence of these organisms and genes in the environment, we surveyed a 5-year time series of metagenomic data from the same isolation source (Lake Mendota, Madison, WI, USA) and identified their presence throughout the time series. Overall, our study shows that diverse isolated bacterial strains can use cysteine and produce H2S under oxic conditions, and we show evidence using metagenomic data that this process may occur more broadly in natural freshwater lakes. Future considerations of sulfur cycling and biogeochemistry in oxic environments should account for H2S production from the degradation of organosulfur compounds. IMPORTANCE Hydrogen sulfide (H2S), a naturally occurring gas with both biological and abiotic origins, can be toxic to living organisms. In aquatic environments, H2S production typically originates from anoxic (lacking oxygen) environments, such as sediments, or the bottom layers of thermally stratified lakes. However, the degradation of sulfur-containing amino acids such as cysteine, which all cells and life forms rely on, can be a source of ammonia and H2S in the environment. Unlike other approaches for biological H2S production such as dissimilatory sulfate reduction, cysteine degradation can occur in the presence of oxygen. Yet, little is known about how cysteine degradation influences sulfur availability and cycling in freshwater lakes. In our study, we identified diverse bacteria from a freshwater lake that can produce H2S in the presence of O2. Our study highlights the ecological importance of oxic H2S production in natural ecosystems and necessitates a change in our outlook on sulfur biogeochemistry.},
}
@article {pmid37283549,
year = {2023},
author = {Oba, PM and Carroll, MQ and Sieja, KM and Yang, X and Epp, TY and Warzecha, CM and Varney, JL and Fowler, JW and Coon, CN and Swanson, KS},
title = {Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, metabolite concentrations, and microbiota populations of dogs undergoing transport stress.},
journal = {Journal of animal science},
volume = {101},
number = {},
pages = {},
pmid = {37283549},
issn = {1525-3163},
mesh = {Dogs ; Female ; Male ; Animals ; *Saccharomyces cerevisiae/metabolism ; Fermentation ; Diet/veterinary ; Dietary Supplements/analysis ; Feces/microbiology ; *Microbiota ; Bacteria ; Animal Feed/analysis ; },
abstract = {Previously, a Saccharomyces cerevisiae fermentation product (SCFP) positively altered fecal microbiota, fecal metabolites, and immune cell function of adult dogs. Our objective was to determine the fecal characteristics, microbiota, and metabolites of SCFP-supplemented dogs subjected to transport stress. All procedures were approved by the Four Rivers Kennel IACUC prior to experimentation. Thirty-six adult dogs (18 male, 18 female; age: 7.1 ± 0.77 yr; body weight: 28.97 ± 3.67 kg) were randomly assigned to be controls or receive SCFP supplementation (250 mg/dog/d) (N = 18/group) for 11 wk. At that time, fresh fecal samples were collected before and after transport in a hunting dog trailer with individual kennels. The trailer was driven 40 miles round trip for about 45 min. Fecal microbiota data were evaluated using Quantitative Insights Into Microbial Ecology 2, while all other data were analyzed using the Mixed Models procedure of Statistical Analysis System. Effects of treatment, transport, and treatment × transport were tested, with P < 0.05 being considered significant. Transport stress increased fecal indole concentrations and relative abundances of fecal Actinobacteria, Collinsella, Slackia, Ruminococcus, and Eubacterium. In contrast, relative abundances of fecal Fusobacteria, Streptococcus, and Fusobacterium were reduced by transport. Fecal characteristics, metabolites, and bacterial alpha and beta diversity measures were not affected by diet alone. Several diet × transport interactions were significant, however. Following transport, relative abundance of fecal Turicibacter increased in SCFP-supplemented dogs, but decreased in controls. Following transport, relative abundances of fecal Proteobacteria, Bacteroidetes, Prevotella, and Sutterella increased in controls, but not in SCFP-supplemented dogs. In contrast, relative abundances of fecal Firmicutes, Clostridium, Faecalibacterium, and Allobaculum increased and fecal Parabacteroides and Phascolarctobacterium decreased after transport stress in SCFP-supplemented dogs, but not in controls. Our data demonstrate that both transport stress and SCFP alter fecal microbiota in dogs, with transport being the primary cause for shifts. SCFP supplementation may provide benefits to dogs undergoing transport stress, but more research is necessary to determine proper dosages. More research is also necessary to determine if and how transport stress impacts gastrointestinal microbiota and other indicators of health.},
}
@article {pmid37280438,
year = {2023},
author = {Ndour, PMS and Bargaz, A and Rchiad, Z and Pawlett, M and Clark, IM and Mauchline, TH and Harris, J and Lyamlouli, K},
title = {Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2211-2230},
pmid = {37280438},
issn = {1432-184X},
mesh = {*Soil/chemistry ; *Agricultural Inoculants ; Carbon ; Agriculture/methods ; Soil Microbiology ; },
abstract = {Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.},
}
@article {pmid37280212,
year = {2023},
author = {Weyhenmeyer, GA and Obertegger, U and Rudebeck, H and Jakobsson, E and Jansen, J and Zdorovennova, G and Bansal, S and Block, BD and Carey, CC and Doubek, JP and Dugan, H and Erina, O and Fedorova, I and Fischer, JM and Grinberga, L and Grossart, HP and Kangur, K and Knoll, LB and Laas, A and Lepori, F and Meier, J and Palshin, N and Peternell, M and Pulkkanen, M and Rusak, JA and Sharma, S and Wain, D and Zdorovennov, R},
title = {Author Correction: Towards critical white ice conditions in lakes under global warming.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3283},
doi = {10.1038/s41467-023-39005-3},
pmid = {37280212},
issn = {2041-1723},
}
@article {pmid37280177,
year = {2023},
author = {Gralka, M},
title = {Searching for Principles of Microbial Ecology Across Levels of Biological Organization.},
journal = {Integrative and comparative biology},
volume = {63},
number = {6},
pages = {1520-1531},
pmid = {37280177},
issn = {1557-7023},
mesh = {Animals ; *Ecosystem ; *Microbiota ; Ecology ; },
abstract = {Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex microbial communities, is a major challenge. To what extent are these different levels of organization governed by separate principles, and how can we connect these levels to develop predictive models for the dynamics and function of microbial communities? Here, we will discuss recent advances that point towards principles of microbial communities, rooted in various disciplines from physics, biochemistry, and dynamical systems. By considering the marine carbon cycle as a concrete example, we demonstrate how the integration of levels of biological organization can offer deeper insights into the impact of increasing temperatures, such as those associated with climate change, on ecosystem-scale processes. We argue that by focusing on principles that transcend specific microbiomes, we can pave the way for a comprehensive understanding of microbial community dynamics and the development of predictive models for diverse ecosystems.},
}
@article {pmid37279442,
year = {2023},
author = {Suzzi, AL and Stat, M and Gaston, TF and Huggett, MJ},
title = {Spatial patterns in host-associated and free-living bacterial communities across six temperate estuaries.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {7},
pages = {},
pmid = {37279442},
issn = {1574-6941},
mesh = {Animals ; *Estuaries ; Australia ; Bacteria/genetics ; Seawater/microbiology ; *Microbiota ; },
abstract = {A major goal of microbial ecology is to establish the importance of spatial and environmental factors in driving community variation. Their relative importance likely varies across spatial scales, but focus has primarily been on free-living communities within well-connected aquatic environments rather than less connected island-like habitats such as estuaries, and key host-associated communities within these systems. Here we sampled both free-living (seawater and sediment) and host-associated (estuarine fish hindgut microbiome, Pelates sexlineatus) communities across six temperate Australian estuaries spanning ∼500 km. We find that spatial and environmental factors have different influences on these communities, with seawater demonstrating strong distance-decay relationships (R = -0.69) and significant associations with a range of environmental variables. Distance-decay relationships were weak for sediment communities but became stronger over smaller spatial scales (within estuaries, R = -0.5), potentially reflecting environmental filtering across biogeochemical gradients or stochastic processes within estuary sediments. Finally, P. sexlineatus hindgut microbiome communities displayed weak distance-decay relationships (R = -0.36), and limited variation explained by environmental variables, indicating the significance of host-related factors in driving community variation. Our findings provide important ecological insights into the spatial distributions and driving forces of both free-living and host-associated bacterial patterns across temperate estuarine systems.},
}
@article {pmid37278908,
year = {2023},
author = {Gao, H and Wu, M and Liu, H and Ou, Y and Zhang, T and Duan, X},
title = {Unraveling the Positive Effect of Soil Moisture on the Bioaugmentation of Petroleum-Contaminated Soil Using Bioinformatics.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2436-2446},
pmid = {37278908},
issn = {1432-184X},
mesh = {*Petroleum ; Soil/chemistry ; *Soil Pollutants/analysis ; Soil Microbiology ; Biodegradation, Environmental ; Hydrocarbons/metabolism ; Bacteria/genetics/metabolism ; Computational Biology ; },
abstract = {Petroleum contamination is a severe threat to the soil environment. Previous studies have demonstrated that petroleum degradation efficiency is promoted by enhancing soil moisture content (MC). However, the effects of MC on soil microbial ecological functions during bioremediation remain unclear. Here, we investigated the impacts of 5% and 15% of moisture contents on petroleum degradation, soil microbial structures and functions, and the related genes using high-throughput sequencing and gene function prediction. Results indicated that petroleum biodegradation efficiency was increased by 8.06% in the soils with 15% MC when compared to that with 5% of MC. The complexity and stability of soil microbial community structures with 15% MC were higher than those in the soils with 5% MC when hydrocarbon-degrading bacterial flora (HDBF) were inoculated into the soils. Fifteen percent of moisture content strengthened the interaction of the bacterial community network and reduced the loss of some key bacteria species including Mycobacterium, Sphingomonas, and Gemmatimonas. Some downregulated gene pathways relating to bioaugmentation were enhanced in the soils with 15% MC. The results suggested that the dynamic balances of microbial communities and the metabolic interactions by 15% MC treatment are the driving forces for the enhancement of bioremediation in petroleum-contaminated soil.},
}
@article {pmid37278524,
year = {2023},
author = {Dedrick, S and Warrier, V and Lemon, KP and Momeni, B},
title = {When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities.},
journal = {mSystems},
volume = {8},
number = {3},
pages = {e0075722},
pmid = {37278524},
issn = {2379-5077},
support = {R35 GM141806/GM/NIGMS NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; T32 HL007427/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; Microbial Interactions ; Models, Theoretical ; Models, Biological ; Bacteria ; },
abstract = {To alter microbial community composition for therapeutic purposes, an accurate and reliable modeling framework capable of predicting microbial community outcomes is required. Lotka-Volterra (LV) equations have been utilized to describe a breadth of microbial communities, yet, the conditions in which this modeling framework is successful remain unclear. Here, we propose that a set of simple in vitro experiments-growing each member in cell-free spent medium obtained from other members-can be used as a test to decide whether an LV model is appropriate for describing microbial interactions of interest. We show that for LV to be a good candidate, the ratio of growth rate to carrying capacity of each isolate when grown in the cell-free spent media of other isolates should remain constant. Using an in vitro community of human nasal bacteria as a tractable system, we find that LV can be a good approximation when the environment is low-nutrient (i.e., when growth is limited by the availability of nutrients) and complex (i.e., when multiple resources, rather than a few, determine growth). These findings can help clarify the range of applicability of LV models and reveal when a more complex model may be necessary for predictive modeling of microbial communities. IMPORTANCE Although mathematical modeling can be a powerful tool to draw useful insights in microbial ecology, it is crucial to know when a simplified model adequately represents the interactions of interest. Here, we take advantage of bacterial isolates from the human nasal passages as a tractable model system and conclude that the commonly used Lotka-Volterra model can represent interactions among microbes well when the environment is complex (with many interaction mediators) and low-nutrient. Our work highlights the importance of considering both realism and simplicity when choosing a model to represent microbial interactions.},
}
@article {pmid37278360,
year = {2023},
author = {Zayed, N and Ghesquière, J and Kamarudin, NHN and Bernaerts, K and Boon, N and Braem, A and Van Holm, W and Teughels, W},
title = {Oral Biofilm Cryotherapy as a Novel Ecological Modulation Approach.},
journal = {Journal of dental research},
volume = {102},
number = {9},
pages = {1038-1046},
doi = {10.1177/00220345231172688},
pmid = {37278360},
issn = {1544-0591},
mesh = {*Anti-Infective Agents ; Bacterial Load ; Biofilms ; Cryotherapy ; },
abstract = {Oral cryotherapy is used in dentistry as a safe, simple, and low-cost treatment for a variety of oral lesions. It is well known for its ability to aid in the healing process. However, its effect on oral biofilms is unknown. As a result, the purpose of this study was to assess the effects of cryotherapy on in vitro oral biofilms. In vitro multispecies oral biofilms were grown on the surface of hydroxyapatite discs in symbiotic or dysbiotic states. CryoPen X+ was used to treat the biofilms, whereas untreated biofilms served as control. One set of biofilms was collected for study immediately after cryotherapy, whereas another group was reincubated for 24 h to permit biofilm recovery. Changes in biofilm structure were analyzed with a confocal laser scanning microscope (CLSM) and a scanning electron microscope (SEM), while biofilm ecology and community compositional changes were analyzed with viability DNA extraction and quantitative polymerase chain reaction (v-qPCR) analysis. One cryo-cycle immediately reduced biofilm load by 0.2 to 0.4 log10 Geq/mL, which increased with additional treatment cycles. Although the bacterial load of the treated biofilms recovered to the same level as the control biofilms within 24 h, the CLSM detected structural alterations. Compositional alterations were also detected by SEM, corroborating the v-qPCR findings that showed ≈≤10% incidence of pathogenic species compared to nontreated biofilms that encompassed ≈45% and 13% pathogenic species in dysbiotic and symbiotic biofilms, respectively. Spray cryotherapy showed promising results in a novel conceptual approach to the control of oral biofilms. Acting selectively by targeting oral pathobionts and retaining commensals, spray cryotherapy could modify the ecology of in vitro oral biofilms to become more symbiotic and prevent the evolution of dysbiosis without the use of antiseptics/antimicrobials.},
}
@article {pmid37275175,
year = {2023},
author = {Timmusk, S and Pall, T and Raz, S and Fetsiukh, A and Nevo, E},
title = {The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1141862},
pmid = {37275175},
issn = {1664-302X},
abstract = {Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.},
}
@article {pmid37272971,
year = {2023},
author = {Zhang, Y and Wang, M and Cheng, W and Huang, C and Ren, J and Zhai, H and Niu, L},
title = {Temporal and Spatial Variation Characteristics and Influencing Factors of Bacterial Community in Urban Landscape Lakes.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2424-2435},
pmid = {37272971},
issn = {1432-184X},
support = {51809211//National Natural Science Foundation of China/ ; 20JY045//Shaanxi Provincial Education Department/ ; 2018M633548//China Postdoctoral Science Foundation/ ; },
mesh = {Humans ; *Lakes/microbiology ; Bacteria/genetics ; Proteobacteria ; *Actinobacteria ; Seasons ; China ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Urban landscape lakes are closely related to human activity, but there are limited studies on their bacterial community characteristics and risks to human health. In this study, four different types of urban landscape lakes in Xi'an were selected, and the bacterial community structures in different seasons were analyzed by Illumina Nova high-throughput sequencing technology. Seasonal variations in bacterial communities were analyzed by linear discriminant analysis, STAMP difference analysis, and nonmetric multidimensional scaling. Redundancy analysis was used to investigate the influencing factors. Furthermore, the metabolic functions of bacterial communities were predicted by Tax4Fun. There were clear seasonal differences in the α-diversity of bacteria, with bacterial diversity being higher in winter than in summer in the four urban landscape lakes, and the diversity of different water sources was different; the distributions of Proteobacteria, Actinobacteria, Chloroflexi, and Verrucomicrobia had significant seasonal differences; and the dominant bacteria at the genus level had obvious temporal and spatial differences. Furthermore, a variety of environmental factors had an impact on bacterial communities, and temperature, DO, and nitrogen were the primary factors affecting the seasonal variation in bacteria. There are also significant seasonal differences in the metabolic functions of bacterial communities. These results are helpful for understanding the current status of bacteria in the aquatic environments of such urban landscape lakes.},
}
@article {pmid37272815,
year = {2023},
author = {Tang, K and Tao, L and Wang, Y and Wang, Q and Fu, C and Chen, B and Zhang, Z and Fu, Y},
title = {Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {6},
pages = {e0074723},
pmid = {37272815},
issn = {1098-5336},
mesh = {Animals ; *Gastrointestinal Microbiome ; Seasons ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Endangered Species ; Animals, Wild ; *Galliformes/genetics ; },
abstract = {Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.},
}
@article {pmid37272792,
year = {2023},
author = {Wu, X and Gushgari-Doyle, S and Lui, LM and Hendrickson, AJ and Liu, Y and Jagadamma, S and Nielsen, TN and Justice, NB and Simmons, T and Hess, NJ and Joyner, DC and Hazen, TC and Arkin, AP and Chakraborty, R},
title = {Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {6},
pages = {e0050023},
pmid = {37272792},
issn = {1098-5336},
mesh = {*Bacteria/metabolism ; *Microbiota ; Carbon/metabolism ; Tennessee ; },
abstract = {Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.},
}
@article {pmid37272710,
year = {2023},
author = {Miller, SE and Colman, AS and Waldbauer, JR},
title = {Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities.},
journal = {mSystems},
volume = {8},
number = {3},
pages = {e0123822},
pmid = {37272710},
issn = {2379-5077},
mesh = {*Permafrost/microbiology ; Bacteria/genetics ; Tundra ; Soil/chemistry ; Plants ; Acidobacteria ; *Alphaproteobacteria ; *Betaproteobacteria ; Carbon/metabolism ; },
abstract = {Microbial activity in Arctic soils controls the cycling of significant stores of organic carbon and nutrients. We studied in situ processes in Alaskan soils using original metaproteomic methods in order to relate important heterotrophic functions to microbial taxa and to understand the microbial response to Arctic greening. Major bacterial groups show strong metabolic specialization in organic topsoils. α-/β-/γ-Proteobacteria specialized in the acquisition of small, soluble compounds, whereas Acidobacteria, Actinobacteria, and other detritosphere groups specialized in the degradation of plant-derived polymers. α-/β-/γ-Proteobacteria dominated the expression of transporters for common root exudates and limiting nitrogenous compounds, supporting an ecological model of dependence upon plants for carbon and competition with plants for nitrogen. Detritosphere groups specialized in distinct substrates, with Acidobacteria producing the most enzymes for hemicellulose depolymerization. Acidobacteria was the most active group across the three plant ecotypes sampled-the largely nonvascular, lower biomass intertussock and the largely vascular, higher biomass tussock and shrub. Functional partitioning among bacterial groups was stable between plant ecotypes, but certain functions associated with α-/β-/γ-Proteobacteria were more strongly expressed in higher biomass ecotypes. We show that refined metaproteomic approaches can elucidate soil microbial ecology as well as biogeochemical trajectories of major carbon stocks. IMPORTANCE The Arctic is warming twice as fast as the rest of the planet, and Arctic soils currently store twice as much carbon as the entire atmosphere-two facts that make understanding how Arctic soil microbial communities are responding to climate change particularly urgent. Greening of vegetation cover across the Arctic landscape is one of the most prominent climate-driven shifts in Arctic terrestrial ecology, with potentially profound effects on biogeochemical cycling by the soil microbiome. Here we use metaproteomics to document microbial metabolic functions that drive soil carbon and nutrient cycling processes in an Arctic tundra landscape. We identify functional roles among bacterial taxonomic groups that are largely stable across vegetation types, with certain functions strongly expressed by rhizosphere groups reflecting a community metabolic response to greening.},
}
@article {pmid37270320,
year = {2023},
author = {M Venturini, A and B Gontijo, J and A Mandro, J and Berenguer, E and Peay, KG and M Tsai, S and Bohannan, BJM},
title = {Soil microbes under threat in the Amazon Rainforest.},
journal = {Trends in ecology &amp; evolution},
volume = {38},
number = {8},
pages = {693-696},
doi = {10.1016/j.tree.2023.04.014},
pmid = {37270320},
issn = {1872-8383},
mesh = {*Soil ; *Ecosystem ; Rainforest ; Biodiversity ; Climate Change ; },
abstract = {Soil microorganisms are sensitive indicators of land-use and climate change in the Amazon, revealing shifts in important processes such as greenhouse gas (GHG) production, but they have been overlooked in conservation and management initiatives. Integrating soil biodiversity with other disciplines while expanding sampling efforts and targeted microbial groups is crucially needed.},
}
@article {pmid37268771,
year = {2023},
author = {Listmann, L and Peters, C and Rahlff, J and Esser, SP and Schaum, CE},
title = {Seasonality and Strain Specificity Drive Rapid Co-evolution in an Ostreococcus-Virus System from the Western Baltic Sea.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2414-2423},
pmid = {37268771},
issn = {1432-184X},
support = {CLICCS//Exzellenzcluster Ozean der Zukunft/ ; Start up Prof. Dr. Elisa Schaum//University of Hamburg, Germany/ ; RA3432/1-1//DFG/ ; 730984//Assemble Plus/ ; },
mesh = {*Ecosystem ; Phytoplankton/genetics ; *Chlorophyta ; },
abstract = {Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host's responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus-virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.},
}
@article {pmid37268258,
year = {2023},
author = {Yu, Y and Fu, D and Zhou, H and Su, J and Chen, S and Lv, G},
title = {Potential application of Atractylodes macrocephala Koidz. as a natural drug for bone mass regulation: A review.},
journal = {Journal of ethnopharmacology},
volume = {315},
number = {},
pages = {116718},
doi = {10.1016/j.jep.2023.116718},
pmid = {37268258},
issn = {1872-7573},
mesh = {*Atractylodes ; *Oils, Volatile ; China ; Plant Extracts/pharmacology ; Anti-Inflammatory Agents/pharmacology ; },
abstract = {The root of Atractylodes macrocephala Koidz. (AM) has been used for thousands of years in China, and it's extracts contain various constituents, such as volatile oils, polysaccharides, and lactones, with a myriad of pharmacological effects, including improves the healthy state of the gastrointestinal system and regulating immunity, hormone secretion, anti-inflammatory, antibacterial, antioxidation, anti-aging, and antitumor properties. Recently, researchers have focused on the effect of AM in regulating bone mass; therefore, its potential mechanism of action in regulating bone mass needs to be elucidated.<br><br>AIM OF REVIEW: This study reviewed the known and possible mechanisms of bone mass regulation by AM.<br><br>MATERIALS AND METHODS: Cochrane, Medline via PubMed, Embase, CENTRAL, CINAHL, Web of Science, Chinese biomedical literature database, Chinese Science and Technology Periodical Database, and Wanfang Database were used to search AM root extracts-related studies. The retrieval date was from the establishment of the database to January 1, 2023.<br><br>RESULTS: By summarizing 119 natural active substances that have been isolated from AM root to date, we explored its possible targets and pathways (such as Hedgehog, Wnt/&#x3b2;-catenin, and BMP/Smads pathways etc.) for bone growth and presented our position on possible future research/perspectives in the regulation of bone mass using this plant.<br><br>CONCLUSIONS: AM root extracts (incuding aqueous, ethanol etc.) promotes osteogenesis and inhibits osteoclastogenesis. These functions promote the absorption of nutrients, regulate gastrointestinal motility and intestinal microbial ecology, regulate endocrine function, strengthen bone immunity, and exert anti-inflammatory and antioxidant effects.},
}
@article {pmid37266990,
year = {2023},
author = {Nikolaidis, M and Hesketh, A and Frangou, N and Mossialos, D and Van de Peer, Y and Oliver, SG and Amoutzias, GD},
title = {A panoramic view of the genomic landscape of the genus Streptomyces.},
journal = {Microbial genomics},
volume = {9},
number = {6},
pages = {},
pmid = {37266990},
issn = {2057-5858},
mesh = {*Genomics ; *Streptomyces/genetics/metabolism ; Codon ; Multigene Family ; },
abstract = {We delineate the evolutionary plasticity of the ecologically and biotechnologically important genus Streptomyces, by analysing the genomes of 213 species. Streptomycetes genomes demonstrate high levels of internal homology, whereas the genome of their last common ancestor was already complex. Importantly, we identify the species-specific fingerprint proteins that characterize each species. Even among closely related species, we observed high interspecies variability of chromosomal protein-coding genes, species-level core genes, accessory genes and fingerprints. Notably, secondary metabolite biosynthetic gene clusters (smBGCs), carbohydrate-active enzymes (CAZymes) and protein-coding genes bearing the rare TTA codon demonstrate high intraspecies and interspecies variability, which emphasizes the need for strain-specific genomic mining. Highly conserved genes, such as those specifying genus-level core proteins, tend to occur in the central region of the chromosome, whereas those encoding proteins with evolutionarily volatile species-level fingerprints, smBGCs, CAZymes and TTA-codon-bearing genes are often found towards the ends of the linear chromosome. Thus, the chromosomal arms emerge as the part of the genome that is mainly responsible for rapid adaptation at the species and strain level. Finally, we observed a moderate, but statistically significant, correlation between the total number of CAZymes and three categories of smBGCs (siderophores, e-Polylysin and type III lanthipeptides) that are related to competition among bacteria.},
}
@article {pmid37264467,
year = {2023},
author = {Wainwright, BJ and Millar, T and Bowen, L and Semon, L and Hickman, KJE and Lee, JN and Yeo, ZY and Zahn, G},
title = {The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {47},
pmid = {37264467},
issn = {2524-6372},
support = {IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; },
abstract = {BACKGROUND: Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival.<br><br>CONCLUSION: The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.},
}
@article {pmid37264141,
year = {2023},
author = {Zehnle, H and Laso-Pérez, R and Lipp, J and Riedel, D and Benito Merino, D and Teske, A and Wegener, G},
title = {Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes.},
journal = {Nature microbiology},
volume = {8},
number = {7},
pages = {1199-1212},
pmid = {37264141},
issn = {2058-5276},
mesh = {Archaea ; *Petroleum/metabolism ; *Hydrothermal Vents ; Anaerobiosis ; Alkanes/metabolism ; Sulfates/metabolism ; },
abstract = {Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.},
}
@article {pmid37263428,
year = {2023},
author = {Van Peteghem, L and Matassa, S and Rabaey, K and Sakarika, M},
title = {Microbial protein from recovered nitrogen: Nutritional quality, safety, and feasibility assessment.},
journal = {The Science of the total environment},
volume = {892},
number = {},
pages = {164525},
doi = {10.1016/j.scitotenv.2023.164525},
pmid = {37263428},
issn = {1879-1026},
mesh = {Adult ; Humans ; Nitrogen/metabolism ; Feasibility Studies ; Nutritive Value ; Biomass ; *Metals, Heavy ; Amino Acids ; Lipids ; *Pesticides ; },
abstract = {In contrast to traditional agriculture, microbial protein (MP) production is highly efficient in nitrogen (N) usage and can be employed to valorize a variety of recovered resources, thereby increasing the overall sustainability of food production. The present study aimed to establish the potential of seven recovered N sources originating from different waste streams for MP production using ethanol and acetate as growth substrates. The evaluation was based on specific growth rate, biomass yield, nutritional quality (i.e. macromolecular composition, amino acid (AA) and lipid profile) and food safety (i.e. concentration of heavy metals, polyaromatic hydrocarbons (PAH), pesticides and antibiotics) of the MP. The majority of the recovered N sources did not affect the kinetics and had a minor impact on the biomass yield, compared to their commercial equivalents. The nutritional content of the biomass was similar to soy flour and did not show major variations in AA and lipid profile for the different recovered N sources. Considering the heavy metal content, an average-weighing adult should not consume >53-213 g of the microbial biomass produced on recovered N per day due to its high copper content. A substantial amount of PAH were also found in the biomass. A daily consumption of 20 g/person/day would impose 2.0-2.8 times higher dietary exposure than the mean PAH exposure through nutrition in the EU, indicating a potential concern for human health. On the other hand, the biomass was free of antibiotics, and the traces of pesticides found did not raise any major concern for food applications. Based on the results of this work, no evidence was found to restrict the application of microbial biomass produced on recovered nitrogen as food.},
}
@article {pmid37260833,
year = {2023},
author = {Myers, KS and Ingle, AT and Walters, KA and Fortney, NW and Scarborough, MJ and Donohue, TJ and Noguera, DR},
title = {Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {11},
number = {},
pages = {1197175},
pmid = {37260833},
issn = {2296-4185},
abstract = {The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.},
}
@article {pmid37260392,
year = {2023},
author = {Putman, LI and Schaerer, LG and Wu, R and Kulas, DG and Zolghadr, A and Ong, RG and Shonnard, DR and Techtmann, SM},
title = {Deconstructed Plastic Substrate Preferences of Microbial Populations from the Natural Environment.},
journal = {Microbiology spectrum},
volume = {11},
number = {4},
pages = {e0036223},
pmid = {37260392},
issn = {2165-0497},
mesh = {*Plastics/metabolism ; *Polyethylene/metabolism ; RNA, Ribosomal, 16S/genetics ; Polyethylene Terephthalates/metabolism ; Bacteria ; },
abstract = {Over half of the world's plastic waste is landfilled, where it is estimated to take hundreds of years to degrade. Given the continued use and disposal of plastic products, it is vital that we develop fast and effective ways to utilize plastic waste. Here, we explore the potential of tandem chemical and biological processing to process various plastics quickly and effectively. Four samples of compost or sediment were used to set up enrichment cultures grown on mixtures of compounds, including disodium terephthalate and terephthalic acid (monomers of polyethylene terephthalate), compounds derived from the chemical deconstruction of polycarbonate, and pyrolysis oil derived from high-density polyethylene plastics. Established enrichment communities were also grown on individual substrates to investigate the substrate preferences of different taxa. Biomass harvested from the cultures was characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. These data reveal low-diversity microbial communities structured by differences in culture inoculum, culture substrate source plastic type, and time. Microbial populations from the classes Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Acidobacteriae were significantly enriched when grown on substrates derived from high-density polyethylene and polycarbonate. The metagenomic data contain abundant aromatic and aliphatic hydrocarbon degradation genes relevant to the biodegradation of deconstructed plastic substrates used here. We show that microbial populations from diverse environments are capable of growth on substrates derived from the chemical deconstruction or pyrolysis of multiple plastic types and that paired chemical and biological processing of plastics should be further developed for industrial applications to manage plastic waste. IMPORTANCE The durability and impermeable nature of plastics have made them a popular material for numerous applications, but these same qualities make plastics difficult to dispose of, resulting in massive amounts of accumulated plastic waste in landfills and the natural environment. Since plastic use and disposal are projected to increase in the future, novel methods to effectively break down and dispose of current and future plastic waste are desperately needed. We show that the products of chemical deconstruction or pyrolysis of plastic can successfully sustain the growth of low-diversity microbial communities. These communities were enriched from multiple environmental sources and are capable of degrading complex xenobiotic carbon compounds. This study demonstrates that tandem chemical and biological processing can be used to degrade multiple types of plastics over a relatively short period of time and may be a future avenue for the mitigation of rapidly accumulating plastic waste.},
}
@article {pmid37259890,
year = {2023},
author = {Geisen, S and Lara, E and Mitchell, E},
title = {Contemporary issues, current best practice and ways forward in soil protist ecology.},
journal = {Molecular ecology resources},
volume = {23},
number = {7},
pages = {1477-1487},
doi = {10.1111/1755-0998.13819},
pmid = {37259890},
issn = {1755-0998},
mesh = {*Ecosystem ; *Soil ; Eukaryota/genetics ; Ecology ; Biodiversity ; Bacteria ; },
abstract = {Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non-experts include protists in their still mostly bacterial and/or fungal-focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence-based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non-experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.},
}
@article {pmid37258870,
year = {2023},
author = {Yung, PYM and Tan, SM},
title = {Targeted Enrichment of Low-Abundance and Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH Probes Designed from Next Generation Sequencing Dataset.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {303-315},
pmid = {37258870},
issn = {1940-6029},
mesh = {*High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Methods to obtain high-quality assembled genomic information of rare and unclassified member species in complex microbial communities remain a high priority in microbial ecology. Additionally, the supplementation of three-dimensional spatial information that highlights the morphology and spatial interaction would provide additional insights to its ecological role in the community. Fluorescent in-situ hybridization (FISH) coupling with fluorescence-activated cell sorting (FACS) is a powerful tool that enables the detection, visualization, and separation of low-abundance microbial members in samples containing complex microbial compositions. Here, we have described the workflow from designing the appropriate FISH probes from metagenomics or metatranscriptomics datasets to the preparation and treatment of samples to be used in FISH-FACS procedures.},
}
@article {pmid37257612,
year = {2023},
author = {Cheng, X and Zeng, Z and Liu, X and Li, L and Wang, H and Zhao, R and Bodelier, PLE and Wang, W and Wang, Y and Tuovinen, OH},
title = {Methanotrophs dominate methanogens and act as a methane sink in a subterranean karst cave.},
journal = {The Science of the total environment},
volume = {892},
number = {},
pages = {164562},
doi = {10.1016/j.scitotenv.2023.164562},
pmid = {37257612},
issn = {1879-1026},
mesh = {*Methane ; Caves/microbiology ; Soil Microbiology ; Soil ; *Methylococcaceae ; },
abstract = {Karst caves are potential sinks of atmospheric methane due to microbial consumption. However, knowledge gaps on methanogens (methane producing microorganisms) and their interaction with methane-oxidizing bacteria (MOB) hinder our further understanding about methane dynamics in karst caves. Here we reported methanogenic community composition and their interaction with MOBs in the Heshang Cave to comprehensively understand methane cycling in subsurface biosphere. MOBs in karst cave were dominated by high-affinity MOB, upland soil cluster (USC), with USCγ pmoA gene abundance within the range of 1.34 × 10[4] to 1.8 × 10[7] copies·g[-1] DW. In contrast, methanogens were dominated by Methanoregula and cluster ZC-I. The mcrA numbers were 7.21 × 10[3] to 8.31 × 10[4] copies·g[-1] DW, 1-3 orders of magnitude lower than those of MOB. The inter-domain network analysis indicated that MOBs and methanogens cooperated more in the interior of the cave. Despite of the higher number of methanogenic nodes in the network, MOB dominated the keystone taxa, suggesting a leading functional role of MOB. MOB in caves showed a comparable with or higher potential methane oxidizing rate (PMOR, 0.63 ng CH4·g[-1] DW·h[-1] in sediment versus 11.02 ng CH4·g[-1] DW·h[-1] in weathered rock) than those in soils, whereas methane produced by methanogens was undetected. Collectively, high absolute abundances of MOB, high PMORs, the dominance of methanotrophic keystone taxa in the inter-domain network confirmed the superiority of MOBs over methanogens in the oligotrophic karst cave, mounting new evidence on caves as an important methane sink in terms of the interaction between methanogens and MOBs.},
}
@article {pmid37257501,
year = {2023},
author = {Osorio-Doblado, AM and Feldmann, KP and Lourenco, JM and Stewart, RL and Smith, WB and Tedeschi, LO and Fluharty, FL and Callaway, TR},
title = {Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology.},
journal = {Journal of animal science},
volume = {101},
number = {},
pages = {},
pmid = {37257501},
issn = {1525-3163},
mesh = {Animals ; *Ecosystem ; *Digestion ; Rumen/metabolism ; Ruminants ; Diet/veterinary ; Bacteria/metabolism ; Fermentation ; Animal Feed/analysis ; },
abstract = {The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.},
}
@article {pmid37257378,
year = {2023},
author = {Sun, W and Jing, Z},
title = {Migration of rare and abundant species, assembly mechanisms, and ecological networks of microbiomes in drinking water treatment plants: Effects of different treatment processes.},
journal = {Journal of hazardous materials},
volume = {457},
number = {},
pages = {131726},
doi = {10.1016/j.jhazmat.2023.131726},
pmid = {37257378},
issn = {1873-3336},
mesh = {*Drinking Water ; Charcoal ; *Water Purification/methods ; *Microbiota ; *Ozone ; },
abstract = {Microorganisms play an important role in the degradation of pollutants. However, they also cause problems in drinking water distribution systems, such as pipe corrosion and biofilm growth. The microbial assembly mechanisms and molecular ecological networks associated with different drinking water treatment processes have not yet been clearly analyzed. Therefore, this study investigated the microbiomes of three processes (coal filtration-activated carbon, ozone-activated carbon and UV, and ozone-activated carbon) during different seasons. The results showed that the microbial composition and diversity among the different processes and during different seasons. Water treatment processes had deterministic effects on the microbial assembly process and significantly changed the composition of rare and abundant species, altering the size and modules of molecular ecology networks. Rare species considered as keystone species play important roles in microbial ecology and microbial community construction. Ozone-activated carbon and UV/chlorination decreased the bacterial concentration, increased the deterministic process of microbial assembly, and significantly reduced the size of the network, which is of great significance to microbial control in drinking water. This research broadens our perspectives on the microbial assembly associated with drinking water treatment processes and contributes to ensuring the safe supply of drinking water.},
}
@article {pmid37253619,
year = {2023},
author = {Takahashi, N and Terauchi, Y and Tanaka, T and Yoshimi, A and Yabu, H and Abe, K},
title = {Involvement of ionic interactions in self-assembly and resultant rodlet formation of class I hydrophobin RolA from Aspergillus oryzae.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {87},
number = {8},
pages = {857-864},
doi = {10.1093/bbb/zbad066},
pmid = {37253619},
issn = {1347-6947},
support = {17H03787//Japan Society for the Promotion of Science/ ; },
mesh = {*Fungal Proteins/metabolism ; *Aspergillus oryzae/metabolism ; Polymers/chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; },
abstract = {Hydrophobins are small amphiphilic proteins that are conserved in filamentous fungi. They localized on the conidial surface to make it hydrophobic, which contributes to conidial dispersal in the air, and helps fungi to infect plants and mammals and degrade polymers. Hydrophobins self-assemble and undergo structural transition from the amorphous state to the rodlet (rod-like multimeric structure) state. However, it remains unclear whether the amorphous or rodlet state is biologically functional and what external factors regulate state transition. In this study, we analyzed the self-assembly of hydrophobin RolA of Aspergillus oryzae in detail and identified factors regulating this process. Using atomic force microscopy, we observed RolA rodlet formation over time, and determined "rodlet elongation rate" and "rodlet formation frequency." Changes in these kinetic parameters in response to pH and salt concentration suggest that RolA rodlet formation is regulated by the strength of ionic interactions between RolA molecules.},
}
@article {pmid37249591,
year = {2023},
author = {Wu-Chuang, A and Hartmann, D and Maitre, A and Mateos-Hernández, L and Frantová, H and Urbanová, V and Obregon, D and Cabezas-Cruz, A and Perner, J},
title = {Variation of bacterial community assembly over developmental stages and midgut of Dermanyssus gallinae.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2400-2413},
pmid = {37249591},
issn = {1432-184X},
support = {205/2018//Programa Nacional de Becas de Postgrado en el Exterior "Don Carlos Antonio L&#xf3;pez"/ ; SGCE - RAPPORT N&#xb0; 0300//Collectivit&#xe9; de Corse/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; 22-18424M and 22-12648J//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; },
mesh = {Animals ; Female ; Chickens/parasitology ; *Poultry Diseases/parasitology/prevention &amp; control ; *Mites/microbiology ; Life Cycle Stages ; Bacteria/genetics ; *Mite Infestations/parasitology/prevention &amp; control ; },
abstract = {Bacterial microbiota play an important role in the fitness of arthropods, but the bacterial microflora in the parasitic mite Dermanyssus gallinae is only partially explored; there are gaps in our understanding of the microbiota localization and in our knowledge of microbial community assembly. In this work, we have visualized, quantified the abundance, and determined the diversity of bacterial occupancy, not only across developmental stages of D. gallinae, but also in the midgut of micro-dissected female D. gallinae mites. We explored community assembly and the presence of keystone taxa, as well as predicted metabolic functions in the microbiome of the mite. The diversity of the microbiota and the complexity of co-occurrence networks decreased with the progression of the life cycle. However, several bacterial taxa were present in all samples examined, indicating a core symbiotic consortium of bacteria. The relatively higher bacterial abundance in adult females, specifically in their midguts, implicates a function linked to the biology of D. gallinae mites. If such an association proves to be important, the bacterial microflora qualifies itself as an acaricidal or vaccine target against this troublesome pest.},
}
@article {pmid37247701,
year = {2023},
author = {Garrido-Benavent, I and de Los Ríos, A and Núñez-Zapata, J and Ortiz-Álvarez, R and Schultz, M and Pérez-Ortega, S},
title = {Ocean crossers: A tale of disjunctions and speciation in the dwarf-fruticose Lichina (lichenized Ascomycota).},
journal = {Molecular phylogenetics and evolution},
volume = {185},
number = {},
pages = {107829},
doi = {10.1016/j.ympev.2023.107829},
pmid = {37247701},
issn = {1095-9513},
mesh = {Phylogeny ; *Ascomycota/genetics ; *Lichens/genetics ; Fossils ; Oceans and Seas ; Phylogeography ; },
abstract = {Lichens thrive in rocky coastal areas in temperate and cold regions of both hemispheres. Species of the genus Lichina, which form characteristic black fruiting thalli associated with cyanobacteria, often create distinguishable bands in the intertidal and supralittoral zones. The present study uses a comprehensive specimen dataset and four gene loci to (1) delineate and discuss species boundaries in this genus, (2) assess evolutionary relationships among species, and (3) infer the most likely causes of their current geographic distribution in the Northern and Southern hemispheres. A dated phylogeny describes the time frame in which extant disjunctions of species and populations were established. The results showed that the genus is integrated by four species, with Lichina pygmaea, L. confinis and the newly described L. canariensis from rocky seashores in the Canary Islands, occurring in the Northern Hemisphere, whereas L. intermedia is restricted to the Southern Hemisphere. Lichina intermedia hosted a much higher intraspecific genetic diversity than the other species, with subclades interpreted as species-level lineages by the different species delimitation approaches. However, a conservative taxonomic approach was adopted. This species showed a striking disjunct distribution between Australasia and southern South America. The timing for the observed interspecific and intraspecific divergences and population disjunctions postdated continental plate movements, suggesting that long-distance dispersal across body waters in the two hemispheres played a major role in shaping the current species distributions. Such ocean crossings were, as in L. canariensis, followed by speciation. New substitution rates for the nrITS of the genus Lichina were inferred using a tree spanning the major Ascomycota lineages calibrated using fossils. In conclusion, this work lays the foundation for a better understanding of the evolution through time and space of maritime lichens.},
}
@article {pmid37247028,
year = {2023},
author = {Gao, K and Li, W and Gan, E and Li, J and Jiang, L and Liu, Y},
title = {Impacts of 10 Years of Elevated CO2 and Warming on Soil Fungal Diversity and Network Complexity in a Chinese Paddy Field.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2386-2399},
pmid = {37247028},
issn = {1432-184X},
mesh = {*Ascomycota ; *Basidiomycota ; Carbon Dioxide ; Fungi/genetics ; *Oryza ; Soil/chemistry ; *Soil Microbiology ; China ; },
abstract = {Climatic change conditions (elevated CO2 and warming) have been known to threaten agricultural sustainability and grain yield. Soil fungi play an important role in maintaining agroecosystem functions. However, little is known about the responses of fungal community in paddy field to elevated CO2 and warming. Herein, using internal transcribed spacer (ITS) gene amplicon sequencing and co-occurrence network methods, the responses of soil fungal community to factorial combinations of elevated CO2 (550 ppm), and canopy warming (+2 °C) were explored in an open-air field experiment for 10 years. Elevated CO2 significantly increased the operational taxonomic unit (OTU) richness and Shannon diversity of fungal communities in both rice rhizosphere and bulk soils, whereas the relative abundances of Ascomycota and Basidiomycota were significantly decreased and increased under elevated CO2, respectively. Co-occurrence network analysis showed that elevated CO2, warming, and their combination increased the network complexity and negative correlation of the fungal community in rhizosphere and bulk soils, suggesting that these factors enhanced the competition of microbial species. Warming resulted in a more complex network structure by altering topological roles and increasing the numbers of key fungal nodes. Principal coordinate analysis indicated that rice growth stages rather than elevated CO2 and warming altered soil fungal communities. Specifically, the changes in diversity and network complexity were greater at the heading and ripening stages than at the tillering stage. Furthermore, elevated CO2 and warming significantly increased the relative abundances of pathotrophic fungi and reduced those of symbiotrophic fungi in both rhizosphere and bulk soils. Overall, the results indicate that long-term CO2 exposure and warming enhance the complexity and stability of soil fungal community, potentially threatening crop health and soil functions through adverse effects on fungal community functions.},
}
@article {pmid37242886,
year = {2023},
author = {Mattelin, V and Verfaille, L and Kundu, K and De Wildeman, S and Boon, N},
title = {A New Colorimetric Test for Accurate Determination of Plastic Biodegradation.},
journal = {Polymers},
volume = {15},
number = {10},
pages = {},
pmid = {37242886},
issn = {2073-4360},
support = {HBC.2019.2622//Flemish Agency for Innovation &amp; Enterpreneurship (VLAIO)/ ; },
abstract = {As plastic waste is accumulating in both controlled waste management settings and natural settings, much research is devoted to search for solutions, also in the field of biodegradation. However, determining the biodegradability of plastics in natural environments remains a big challenge due to the often very low biodegradation rates. Many standardised test methods for biodegradation in natural environments exist. These are often based on mineralisation rates in controlled conditions and are thus indirect measurements of biodegradation. It is of interest for both researchers and companies to have tests that are more rapid, easier, and more reliable to screen different ecosystems and/or niches for their plastic biodegradation potential. In this study, the goal is to validate a colorimetric test, based on carbon nanodots, to screen biodegradation of different types of plastics in natural environments. After introducing carbon nanodots into the matrix of the target plastic, a fluorescent signal is released upon plastic biodegradation. The in-house-made carbon nanodots were first confirmed regarding their biocompatibility and chemical and photostability. Subsequently, the effectivity of the developed method was evaluated positively by an enzymatic degradation test with polycaprolactone with Candida antarctica lipase B. Finally, validation experiments were performed with enriched microorganisms and real environmental samples (freshwater and seawater), of which the results were compared with parallel, frequently used biodegradation measures such as O2 and CO2, dissolved organic carbon, growth and pH, to assess the reliability of the test. Our results indicate that this colorimetric test is a good alternative to other methods, but a combination of different methods gives the most information. In conclusion, this colorimetric test is a good fit to screen, in high throughput, the depolymerisation of plastics in natural environments and under different conditions in the lab.},
}
@article {pmid37236880,
year = {2023},
author = {Malard, LA and Guisan, A},
title = {Into the microbial niche.},
journal = {Trends in ecology &amp; evolution},
volume = {38},
number = {10},
pages = {936-945},
doi = {10.1016/j.tree.2023.04.015},
pmid = {37236880},
issn = {1872-8383},
mesh = {*Ecosystem ; *Metagenomics ; },
abstract = {The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.},
}
@article {pmid37236039,
year = {2023},
author = {Anderson, AG and Bedford, MR and Parsons, CM},
title = {Effects of adaptation diet and exogenous enzymes on true metabolizable energy and cecal microbial ecology, short-chain fatty acid profile, and enzyme activity in roosters fed barley and rye diets.},
journal = {Poultry science},
volume = {102},
number = {7},
pages = {102768},
pmid = {37236039},
issn = {1525-3171},
mesh = {Animals ; Male ; *Chickens/physiology ; Dietary Supplements ; *Hordeum ; Secale ; Diet/veterinary ; Fatty Acids, Volatile ; Animal Feed/analysis ; Digestion/physiology ; Animal Nutritional Physiological Phenomena ; },
abstract = {Three experiments evaluated effects of adaptation diet and exogenous β-glucanase and xylanase on TMEn of barley and rye. Single Comb White Leghorn roosters were fed adaptation diets based on corn/soybean meal (SBM), barley/SBM with and without β-glucanase, or rye/corn/SBM with and without xylanase for 4 wk. In Experiments 1 and 2, after the adaptation period, TMEn was determined using a 48 h precision-fed rooster assay for 100% barley or 100% rye diets with or without β-glucanase or xylanase, respectively. Experiment 3 consisted only of feeding adaptation diets for 4 wk. Cecal samples were collected at the end of experiments for microbial ecology, short-chain fatty acid (SCFA) profiles, and enzyme activity analyses. In Experiments 1 and 2, β-glucanase increased (P < 0.05) TMEn of barley, and there was no significant effect of adaptation diet on TMEn values. Total cecal Eubacteria and Ruminococcaceae were decreased (P < 0.05) and Escherichia coli were increased (P < 0.05) at the end of the TMEn assay compared with the end of the adaptation period (with no TMEn assay). There was a large decrease (P < 0.05) for most cecal SCFA at the end of the TMEn assay compared with the end of the adaptation period. Both cecal β-glucanase and xylanase activity were increased for birds fed adaptation diets containing the respective enzyme. In Experiment 3, there were no consistent effects of adaptation diet on cecal microbial profiles or SCFA but cecal β-glucanase activity was increased (P < 0.05) by exogenous β-glucanase for barley and cecal xylanase activity was increased (P < 0.05) by exogenous xylanase for rye. Overall, the results indicated that TMEn of barley was increased by exogenous β-glucanase, adaptation diet did not significantly influence the TMEn response to the dietary enzymes, and cecal fermentation (based on cecal SCFA) was greatly reduced by the TMEn assay. Cecal β-glucanase and xylanase activity, however, were often increased by feeding high barley and high rye diets containing exogenous enzymes.},
}
@article {pmid37235689,
year = {2023},
author = {Esteves, SM and Jadoul, A and Iacono, F and Schloesser, M and Bosman, B and Carnol, M and Druet, T and Cardol, P and Hanikenne, M},
title = {Natural variation of nutrient homeostasis among laboratory and field strains of Chlamydomonas reinhardtii.},
journal = {Journal of experimental botany},
volume = {74},
number = {17},
pages = {5198-5217},
doi = {10.1093/jxb/erad194},
pmid = {37235689},
issn = {1460-2431},
mesh = {*Chlamydomonas reinhardtii/metabolism ; Photosynthesis/physiology ; *Chlamydomonas/metabolism ; Micronutrients/metabolism ; Homeostasis ; },
abstract = {Natural variation among individuals and populations exists in all species, playing key roles in response to environmental stress and adaptation. Micro- and macronutrients have a wide range of functions in photosynthetic organisms, and mineral nutrition thus plays a sizable role in biomass production. To maintain nutrient concentrations inside the cell within physiological limits and prevent the detrimental effects of deficiency or excess, complex homeostatic networks have evolved in photosynthetic cells. The microalga Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic model for studying such mechanisms. In this work, 24 Chlamydomonas strains, comprising field isolates and laboratory strains, were examined for intraspecific differences in nutrient homeostasis. Growth and mineral content were quantified in mixotrophy, as full nutrition control, and compared with autotrophy and nine deficiency conditions for macronutrients (-Ca, -Mg, -N, -P, and -S) and micronutrients (-Cu, -Fe, -Mn, and -Zn). Growth differences among strains were relatively limited. However, similar growth was accompanied by highly divergent mineral accumulation among strains. The expression of nutrient status marker genes and photosynthesis were scored in pairs of contrasting field strains, revealing distinct transcriptional regulation and nutrient requirements. Leveraging this natural variation should enable a better understanding of nutrient homeostasis in Chlamydomonas.},
}
@article {pmid37235378,
year = {2023},
author = {Gomes, TC and Conrado, R and Oliveira, RC and Selari, PJRG and Melo, IS and Araújo, WL and Maria, DA and De Souza, AO},
title = {Effect of Monocerin, a Fungal Secondary Metabolite, on Endothelial Cells.},
journal = {Toxins},
volume = {15},
number = {5},
pages = {},
pmid = {37235378},
issn = {2072-6651},
mesh = {Humans ; Human Umbilical Vein Endothelial Cells ; Cells, Cultured ; *Cellular Senescence ; *Lactones/pharmacology ; Cell Proliferation ; },
abstract = {This study reports the isolation and identification of the endophytic fungus Exserohilum rostratum through molecular and morphological analysis using optical and transmission electron microscopy (TEM), as well as the procurement of its secondary metabolite monocerin, an isocoumarin derivative. Considering the previously observed biological activities of monocerin, this study was performed on human umbilical vein endothelial cells (HUVECs) that are widely used as an in vitro model for several different purposes. Important parameters, such as cell viability, senescence-associated β-galactosidase, cellular proliferation by using 5(6)-carboxyfluorescein diacetate N-succinimidyl ester (CFSE), apoptosis analysis with annexin, cellular morphology through scanning electron microscopy (SEM), and laser confocal analysis were evaluated after exposing the cells to monocerin. After 24 h of exposure to monocerin at 1.25 mM, there was more than 80% of cell viability and a low percentage of cells in the early and late apoptosis and necrosis. Monocerin increased cell proliferation and did not induce cell senescence. Morphological analysis showed cellular integrity. The study demonstrates aspects of the mechanism of action of monocerin on endothelial cell proliferation, suggesting the possibility of its pharmaceutical application, such as in regenerative medicine.},
}
@article {pmid37234538,
year = {2023},
author = {Sarrocco, S and Herrera-Estrella, A and Collinge, DB},
title = {Editorial: Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1203870},
pmid = {37234538},
issn = {1664-302X},
}
@article {pmid37233803,
year = {2023},
author = {Leonhardt, F and Keller, A and Arranz Aveces, C and Ernst, R},
title = {From Alien Species to Alien Communities: Host- and Habitat-Associated Microbiomes in an Alien Amphibian.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2373-2385},
pmid = {37233803},
issn = {1432-184X},
mesh = {Animals ; Introduced Species ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Anura ; },
abstract = {Alien species can host diverse microbial communities. These associated microbiomes may be important in the invasion process and their analysis requires a holistic community-based approach. We analysed the skin and gut microbiome of Eleutherodactylus johnstonei from native range populations in St Lucia and exotic range populations in Guadeloupe, Colombia, and European greenhouses along with their respective environmental microbial reservoir through a 16S metabarcoding approach. We show that amphibian-associated and environmental microbial communities can be considered as meta-communities that interact in the assembly process. High proportions of bacteria can disperse between frogs and environment, while respective abundances are rather determined by niche effects driven by the microbial community source and spatial environmental properties. Environmental transmissions appeared to have higher relevance for skin than for gut microbiome composition and variation. We encourage further experimental studies to assess the implications of turnover in amphibian-associated microbial communities and potentially invasive microbiota in the context of invasion success and impacts. Within this novel framework of "nested invasions," (meta-)community ecology thinking can complement and widen the traditional perspective on biological invasions.},
}
@article {pmid37230351,
year = {2023},
author = {Bossolani, JW and Leite, MFA and Momesso, L and Ten Berge, H and Bloem, J and Kuramae, EE},
title = {Nitrogen input on organic amendments alters the pattern of soil-microbe-plant co-dependence.},
journal = {The Science of the total environment},
volume = {890},
number = {},
pages = {164347},
doi = {10.1016/j.scitotenv.2023.164347},
pmid = {37230351},
issn = {1879-1026},
mesh = {*Soil/chemistry ; *Nitrogen ; Carbon ; Crops, Agricultural ; Triticum ; Soil Microbiology ; Bacteria ; Fertilizers ; },
abstract = {The challenges of nitrogen (N) management in agricultural fields include minimizing N losses while maximizing profitability and soil health. Crop residues can alter N and carbon (C) cycle processes in the soil and modulate the responses of the subsequent crop and soil- microbe-plant interactions. Here, we aim to understand how organic amendments with low and high C/N ratio, combined or not with mineral N may change soil bacterial community and their activity in the soil. Organic amendments with different C/N ratios were combined or not with N fertilization as follows: i) unamended soil (control), ii) grass clover silage (GC; low C/N ratio), and iii) wheat straw (WS; high C/N ratio). The organic amendments modulated the bacterial community assemblage and increased microbial activity. WS amendment had the strongest effects on hot water extractable carbon, microbial biomass N and soil respiration, which were linked with changes in bacterial community composition compared with GC-amended and unamended soil. By contrast, N transformation processes in the soil were more pronounced in GC-amended and unamended soil than in WS-amended soil. These responses were stronger in the presence of mineral N input. WS amendment induced greater N immobilization in the soil, even with mineral N input, impairing crop development. Interestingly, N input in unamended soil altered the co-dependence between the soil and the bacterial community to favor a new co-dependence among the soil, plant and microbial activity. In GC-amended soil, N fertilization shifted the dependence of the crop plant from the bacterial community to soil characteristics. Finally, the combined N input with WS amendment (organic carbon input) placed microbial activity at the center of the interrelationships between the bacterial community, plant, and soil. This emphasizes the crucial importance of microorganisms in the functioning of agroecosystems. To achieve higher yields in crops managed with various organic amendments, it is essential to incorporate mineral N management practices. This becomes particularly crucial when the soil amendments have a high C/N ratio.},
}
@article {pmid37229861,
year = {2023},
author = {Zou, J and Cai, L and Lin, J and Wang, R and Li, J and Jia, M},
title = {Anaerobic fermentation of aerobic granular sludge: Insight into the effect of granule size and sludge structure on hydrolysis and acidification.},
journal = {Journal of environmental management},
volume = {343},
number = {},
pages = {118202},
doi = {10.1016/j.jenvman.2023.118202},
pmid = {37229861},
issn = {1095-8630},
mesh = {Fermentation ; *Sewage/chemistry ; Hydrolysis ; Anaerobiosis ; *Bioreactors ; Bacteria ; Hydrolases ; Fatty Acids, Volatile ; Hydrogen-Ion Concentration ; Waste Disposal, Fluid/methods ; },
abstract = {Aerobic granular sludge (AGS) has different physicochemical properties and microbial communities compared to conventional activated sludge (CAS), which may result in different behaviors during anaerobic fermentation and require further investigation. This study investigated the effect of granule size and sludge structure on the hydrolysis and acidification of AGS. Experimental results show that AGS exhibited significantly higher soluble chemical oxygen demand (SCOD) dissolution and total volatile fatty acids (TVFA) production (330.6-430.3 mg/gVSS and 231.0-312.5 mgCOD/gVSS) compared to conventional activated sludge (CAS) (167.0 mg/gVSS and 133.3 mgCOD/gVSS). This is because AGS (90.6-96.9 mg/gVSS) had higher extracellular polymeric substances (EPS) content than CAS (81.2 mg/gVSS). EPS can not only serve as substrates but also release the trapped hydrolases. Moreover, the relative abundances of hydrolytic/acidogenic bacteria and genes were higher in AGS (0.46%-3.60% and 3.01 × 10[-3]%-4.04 × 10[-3]%) than in CAS (0.30% and 1.23 × 10[-3]%). The optimal granule size for AGS fermentation was found to be 500-1600 μm. The crushing of granule structure promoted the dissolution of small amounts of EPS and the release of some trapped hydrolases, thereby potentially enhancing the enzyme-substrate contacts and bacteria-substrate interactions. Therefore, the highest SCOD dissolution (510.6 mg/gVSS) and TVFA production (352.1 mgCOD/gVSS) from crushed 500-1600 μm AGS were observed. Overall, the findings of this study provide valuable insights into the recovery of organic carbon from AGS via anaerobic fermentation.},
}
@article {pmid37227467,
year = {2023},
author = {S Camargo, T and A Nickele, M and Reis Filho, W and do R C Penteado, S and C de Queiroz, E and G Auer, C},
title = {Correction to: Fungal Community Associated with the Leaf-Cutting Ant Acromyrmex crassispinus (Hymenoptera: Formicidae) Colonies: A Search for Potential Biocontrol Agents.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {3138},
doi = {10.1007/s00248-023-02247-1},
pmid = {37227467},
issn = {1432-184X},
}
@article {pmid37225998,
year = {2023},
author = {Tao, F and Huang, Y and Hungate, BA and Manzoni, S and Frey, SD and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Jiang, L and Lehmann, J and Wang, YP and Houlton, BZ and Ahrens, B and Mishra, U and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y},
title = {Microbial carbon use efficiency promotes global soil carbon storage.},
journal = {Nature},
volume = {618},
number = {7967},
pages = {981-985},
pmid = {37225998},
issn = {1476-4687},
mesh = {*Carbon/analysis/metabolism ; *Carbon Sequestration ; Climate Change ; *Ecosystem ; Plants ; *Soil/chemistry ; *Soil Microbiology ; Datasets as Topic ; Deep Learning ; },
abstract = {Soils store more carbon than other terrestrial ecosystems[1,2]. How soil organic carbon (SOC) forms and persists remains uncertain[1,3], which makes it challenging to understand how it will respond to climatic change[3,4]. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss[5-7]. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways[4,6,8-11], microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes[12,13]. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved[7,14,15]. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.},
}
@article {pmid37225918,
year = {2023},
author = {Elston, KM and Phillips, LE and Leonard, SP and Young, E and Holley, JC and Ahsanullah, T and McReynolds, B and Moran, NA and Barrick, JE},
title = {The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {49},
pmid = {37225918},
issn = {2730-6151},
support = {R35 GM131738/GM/NIGMS NIH HHS/United States ; },
abstract = {Toolkits of plasmids and genetic parts streamline the process of assembling DNA constructs and engineering microbes. Many of these kits were designed with specific industrial or laboratory microbes in mind. For researchers interested in non-model microbial systems, it is often unclear which tools and techniques will function in newly isolated strains. To address this challenge, we designed the Pathfinder toolkit for quickly determining the compatibility of a bacterium with different plasmid components. Pathfinder plasmids combine three different broad-host-range origins of replication with multiple antibiotic resistance cassettes and reporters, so that sets of parts can be rapidly screened through multiplex conjugation. We first tested these plasmids in Escherichia coli, a strain of Sodalis praecaptivus that colonizes insects, and a Rosenbergiella isolate from leafhoppers. Then, we used the Pathfinder plasmids to engineer previously unstudied bacteria from the family Orbaceae that were isolated from several fly species. Engineered Orbaceae strains were able to colonize Drosophila melanogaster and could be visualized in fly guts. Orbaceae are common and abundant in the guts of wild-caught flies but have not been included in laboratory studies of how the Drosophila microbiome affects fly health. Thus, this work provides foundational genetic tools for studying microbial ecology and host-associated microbes, including bacteria that are a key constituent of the gut microbiome of a model insect species.},
}
@article {pmid37225767,
year = {2023},
author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Lacombe, B and Le Roux, X and Perrier, L and Sales-Mabily, L and Laumond, M and Vinyeta, M and Moulin, P and Beurier, G and Rouan, L and Cornet, D and Vasseur, F},
title = {AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {314},
pmid = {37225767},
issn = {2052-4463},
support = {ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Adaptation, Physiological ; *Arabidopsis/genetics ; Biological Evolution ; Databases, Factual ; Plant Leaves ; },
abstract = {Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.},
}
@article {pmid37223788,
year = {2023},
author = {Venbrux, M and Crauwels, S and Rediers, H},
title = {Current and emerging trends in techniques for plant pathogen detection.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1120968},
pmid = {37223788},
issn = {1664-462X},
abstract = {Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.},
}
@article {pmid37222807,
year = {2023},
author = {Broman, E and Abdelgadir, M and Bonaglia, S and Forsberg, SC and Wikström, J and Gunnarsson, JS and Nascimento, FJA and Sjöling, S},
title = {Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2357-2372},
pmid = {37222807},
issn = {1432-184X},
support = {3150-3.1.1-2017//&#xd6;stersj&#xf6;stiftelsen/ ; 2020-0002//Naturv&#xe5;rdsverket/ ; 1.1-1602-0106//Statens geotekniska institut/ ; },
mesh = {Nitrates ; *Ammonium Compounds ; Denitrification ; Nitrogen ; *Microbiota ; Oxidation-Reduction ; },
abstract = {Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.},
}
@article {pmid37222806,
year = {2023},
author = {Korpita, TM and Muths, EL and Watry, MK and McKenzie, VJ},
title = {Captivity, Reintroductions, and the Rewilding of Amphibian-associated Bacterial Communities.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2271-2281},
pmid = {37222806},
issn = {1432-184X},
support = {D19ZO-044//Morris Animal Foundation/ ; 2123583//National Science Foundation/ ; },
mesh = {Humans ; Animals ; *Bufonidae/microbiology ; Larva/microbiology ; Bacteria/genetics ; *Microbiota ; Skin/microbiology ; },
abstract = {Many studies have noted differences in microbes associated with animals reared in captivity compared to their wild counterparts, but few studies have examined how microbes change when animals are reintroduced to the wild after captive rearing. As captive assurance populations and reintroduction programs increase, a better understanding of how microbial symbionts respond during animal translocations is critical. We examined changes in microbes associated with boreal toads (Anaxyrus boreas), a threatened amphibian, after reintroduction to the wild following captive rearing. Previous studies demonstrate that developmental life stage is an important factor in amphibian microbiomes. We collected 16S marker-gene sequencing datasets to investigate: (i) comparisons of the skin, mouth, and fecal bacteria of boreal toads across four developmental life stages in captivity and the wild, (ii) tadpole skin bacteria before and after reintroduction to the wild, and (iii) adult skin bacteria during reintroduction to the wild. We demonstrated that differences occur across skin, fecal, and mouth bacterial communities in captive versus wild boreal toads, and that the degree of difference depends on developmental stage. Skin bacterial communities from captive tadpoles were more similar to their wild counterparts than captive post-metamorphic individuals were to their wild counterparts. When captive-reared tadpoles were introduced to a wild site, their skin bacteria changed rapidly to resemble wild tadpoles. Similarly, the skin bacterial communities of reintroduced adult boreal toads also shifted to resemble those of wild toads. Our results indicate that a clear microbial signature of captivity in amphibians does not persist after release into natural habitat.},
}
@article {pmid37222805,
year = {2023},
author = {Rodríguez, MF and Gomez, AP and Parra-Giraldo, CM and Ceballos-Garzon, A},
title = {Proteomics and Genetic Approaches Elucidate the Circulation of Low Variability Staphylococcus aureus Strains on Colombian Dairy Farms.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2320-2329},
pmid = {37222805},
issn = {1432-184X},
mesh = {Animals ; Cattle ; Humans ; Female ; Staphylococcus aureus/genetics ; Farms ; Colombia/epidemiology ; Proteomics ; *Mastitis, Bovine/epidemiology ; *Staphylococcal Infections/epidemiology/veterinary ; Milk ; },
abstract = {Staphylococcus aureus is one of the most prevalent pathogens causing bovine mastitis in the world, in part because of its ease of adaptation to various hosts and the environment. This study aimed to determine the prevalence of S. aureus in Colombian dairy farms and its relationship with the causal network of subclinical mastitis. From thirteen dairy farms enrolled, 1288 quarter milk samples (QMS) and 330 teat samples were taken from cows with positive (70.1%) and negative California Mastitis Test (CMT). In addition, 126 samples from the milking parlor environment and 40 from workers (nasal) were collected. On each dairy farm, a survey was conducted, and the milking process was monitored on the day of sampling. S. aureus was identified in 176 samples, i.e., 138 QMS, 20 from teats, 8 from the milking parlor environment, and 10 from workers' nasal swabs. Isolates identified as S. aureus underwent proteomics (clustering of mass spectrum) and molecular (tuf, coa, spa Ig, clfA, and eno genes) analysis. Regarding proteomics results, isolates were distributed into three clusters, each with members from all sources and all farms. Concerning molecular analysis, the virulence-related genes clfA and eno were identified in 41.3% and 37.8% of S. aureus isolates, respectively. We provide evidence on the circulation of S. aureus strains with limited variability among animals, humans, and the environment. The parameters with the lowest compliance in the farms which may be implicated in the transmission of S. aureus are the lack of handwashing and abnormal milk handling.},
}
@article {pmid37222804,
year = {2023},
author = {Liu, B and Wang, Y and Zhang, H and Zhou, Y and Zhang, C and Yang, N and Wang, W},
title = {The Variations of Microbial Diversity and Community Structure Along Different Stream Orders in Wuyi Mountains.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2330-2343},
pmid = {37222804},
issn = {1432-184X},
mesh = {*Bacteria/genetics ; Fresh Water/microbiology ; Water/chemistry ; *Microbiota ; Oxygen ; },
abstract = {The surface water is an important habitat for freshwater microorganisms, but there is a lack of understanding of the pattern of microbial diversity and structure in stream continuums of small subtropical forest watersheds. Therefore, this study aimed to understand the variations in microbial diversity and community structure along stream orders (1-5) in the small subtropical forest catchments of the Wuyi Mountains. Using GIS software, 20 streams were chosen and classified into 5 orders. Illumina sequencing was used to analyze the dynamics of microbial communities, along with stream orders and hydro-chemical properties of stream water were also determined. Our results indicated that the bacterial and fungal richness (ACE index) was higher in low-order (1 and 2 orders) streams than in high-order (3, 4, and 5 orders) streams, with the highest value in the order 2 streams (P < 0.05). The water temperature and dissolved oxygen were positively correlated with fungal richness (P < 0.05). The bacterial rare taxa had a significant correlation with the abundance taxa (P < 0.05). The relative abundances of Bacteroidetes, Actinobacteria, and Chytridiomycota microbial phyla were significantly different among different order streams (P < 0.05). Using the neutral community model, we found that the fungal community structure was significantly shaped by hydro-chemical properties, while the bacterial community structure was largely regulated by stochastic processes. Our findings suggest that variations in microbial community structure in subtropical headwaters are largely shaped by the water temperature and dissolved oxygen.},
}
@article {pmid37222803,
year = {2023},
author = {Malesevic, M and Stanisavljevic, N and Matijasevic, D and Curcic, J and Tasic, V and Tasic, S and Kojic, M},
title = {Metagenomic Analysis of Bacterial Community and Isolation of Representative Strains from Vranjska Banja Hot Spring, Serbia.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2344-2356},
pmid = {37222803},
issn = {1432-184X},
support = {451-03-47/2023-01/200042//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; },
mesh = {*Hot Springs/microbiology ; Serbia ; Phylogeny ; Bacteria ; Metagenome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The hot spring Vranjska Banja is the hottest spring on the Balkan Peninsula with a water temperature of 63-95 °C and a pH value of 7.1, in situ. According to the physicochemical analysis, Vranjska Banja hot spring belongs to the bicarbonated and sulfated hyperthermal waters. The structures of microbial community of this geothermal spring are still largely unexplored. In order to determine and monitor the diversity of microbiota of the Vranjska Banja hot spring, a comprehensive culture-independent metagenomic analysis was conducted in parallel with a culture-dependent approach for the first time. Microbial profiling using amplicon sequencing analysis revealed the presence of phylogenetically novel taxa, ranging from species to phyla. Cultivation-based methods resulted in the isolation of 17 strains belonging to the genera Anoxybacillus, Bacillus, Geobacillus, and Hydrogenophillus. Whole-genome sequencing of five representative strains was then performed. The genomic characterization and OrthoANI analysis revealed that the Vranjska Banja hot spring harbors phylogenetically novel species of the genus Anoxybacillus, proving its uniqueness. Moreover, these isolates contain stress response genes that enable them to survive in the harsh conditions of the hot springs. The results of the in silico analysis show that most of the sequenced strains have the potential to produce thermostable enzymes (proteases, lipases, amylases, phytase, chitinase, and glucanase) and various antimicrobial molecules that can be of great importance for industrial, agricultural, and biotechnological applications. Finally, this study provides a basis for further research and understanding of the metabolic potential of these microorganisms.},
}
@article {pmid37221307,
year = {2023},
author = {Djotan, AKG and Matsushita, N and Fukuda, K},
title = {Correction to: Paired root-soil samples and metabarcoding reveal taxon-based colonization strategies in arbuscular mycorrhizal fungi communities in Japanese cedar and cypress stands.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2147-2148},
doi = {10.1007/s00248-023-02246-2},
pmid = {37221307},
issn = {1432-184X},
}
@article {pmid37221014,
year = {2023},
author = {Carr, EC and Barton, Q and Grambo, S and Sullivan, M and Renfro, CM and Kuo, A and Pangilinan, J and Lipzen, A and Keymanesh, K and Savage, E and Barry, K and Grigoriev, IV and Riekhof, WR and Harris, SD},
title = {Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche.},
journal = {G3 (Bethesda, Md.)},
volume = {13},
number = {8},
pages = {},
pmid = {37221014},
issn = {2160-1836},
mesh = {*Melanins ; *Exophiala/genetics ; Fungi ; Ecosystem ; Soil ; },
abstract = {Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primar yeast form. These fungi grow in xeric, nutrient depletes environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community are not well understood. We have isolated 2 novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e. E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin which can potentially provide ultraviolet resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.},
}
@article {pmid37217203,
year = {2023},
author = {Dundore-Arias, JP and Michalska-Smith, M and Millican, M and Kinkel, LL},
title = {More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes.},
journal = {Annual review of phytopathology},
volume = {61},
number = {},
pages = {403-423},
doi = {10.1146/annurev-phyto-021021-041457},
pmid = {37217203},
issn = {1545-2107},
mesh = {*Biological Evolution ; *Microbiota ; Organizations ; Phenotype ; Soil ; },
abstract = {Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.},
}
@article {pmid37216901,
year = {2023},
author = {Cao, Y and Almeida-Silva, F and Zhang, WP and Ding, YM and Bai, D and Bai, WN and Zhang, BW and Van de Peer, Y and Zhang, DY},
title = {Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae).},
journal = {Molecular biology and evolution},
volume = {40},
number = {6},
pages = {},
pmid = {37216901},
issn = {1537-1719},
support = {833522/ERC_/European Research Council/International ; },
mesh = {Asia, Eastern ; Calcium ; *Calcium Carbonate ; Genetic Speciation ; Genomics ; *Juglandaceae/genetics/physiology ; },
abstract = {When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes and its only congeneric species, Platycarya strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole-genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics and the driving forces underneath the incipient speciation of the two Platycarya lineages.},
}
@article {pmid37213502,
year = {2023},
author = {Díaz, M and Monfort-Lanzas, P and Quiroz-Moreno, C and Rivadeneira, E and Castillejo, P and Arnau, V and Díaz, W and Agathos, SN and Sangari, FJ and Jarrín-V, P and Molina, CA},
title = {The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1154815},
pmid = {37213502},
issn = {1664-302X},
abstract = {A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40 years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change.},
}
@article {pmid37212664,
year = {2023},
author = {Wu, SY and Ou, CC and Lee, ML and Hsin, IL and Kang, YT and Jan, MS and Ko, JL},
title = {Polysaccharide of Ganoderma lucidum Ameliorates Cachectic Myopathy Induced by the Combination Cisplatin plus Docetaxel in Mice.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0313022},
pmid = {37212664},
issn = {2165-0497},
mesh = {Mice ; Animals ; Cisplatin/adverse effects ; Cachexia/chemically induced/drug therapy ; Docetaxel/adverse effects ; *Reishi ; Mice, Inbred C57BL ; Muscular Atrophy/chemically induced/drug therapy ; *Muscular Diseases/chemically induced/complications ; *Neoplasms ; Polysaccharides/therapeutic use ; },
abstract = {Cachexia is a lethal muscle-wasting syndrome associated with cancer and chemotherapy use. Mounting evidence suggests a correlation between cachexia and intestinal microbiota, but there is presently no effective treatment for cachexia. Whether the Ganoderma lucidum polysaccharide Liz-H exerts protective effects on cachexia and gut microbiota dysbiosis induced by the combination cisplatin plus docetaxel (cisplatin + docetaxel) was investigated. C57BL/6J mice were intraperitoneally injected with cisplatin + docetaxel, with or without oral administration of Liz-H. Body weight, food consumption, complete blood count, blood biochemistry, and muscle atrophy were measured. Next-generation sequencing was also performed to investigate changes to gut microbial ecology. Liz-H administration alleviated the cisplatin + docetaxel-induced weight loss, muscle atrophy, and neutropenia. Furthermore, upregulation of muscle protein degradation-related genes (MuRF-1 and Atrogin-1) and decline of myogenic factors (MyoD and myogenin) after treatment of cisplatin and docetaxel were prevented by Liz-H. Cisplatin and docetaxel treatment resulted in reducing comparative abundances of Ruminococcaceae and Bacteroides, but Liz-H treatment restored these to normal levels. This study indicates that Liz-H is a good chemoprotective reagent for cisplatin + docetaxel-induced cachexia. IMPORTANCE Cachexia is a multifactorial syndrome driven by metabolic dysregulation, anorexia, systemic inflammation, and insulin resistance. Approximately 80% of patients with advanced cancer have cachexia, and cachexia is the cause of death in 30% of cancer patients. Nutritional supplementation has not been shown to reverse cachexia progression. Thus, developing strategies to prevent and/or reverse cachexia is urgent. Polysaccharide is a major biologically active compound in the fungus Ganoderma lucidum. This study is the first to report that G. lucidum polysaccharides could alleviate chemotherapy-induced cachexia via reducing expression of genes that are known to drive muscle wasting, such as MuRF-1 and Atrogin-1. These results suggest that Liz-H is an effective treatment for cisplatin + docetaxel-induced cachexia.},
}
@article {pmid37211607,
year = {2023},
author = {Liu, Y and Wang, H and Qian, X and Gu, J and Chen, W and Shen, X and Tao, S and Jiao, S and Wei, G},
title = {Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {109},
pmid = {37211607},
issn = {2049-2618},
mesh = {*Glycyrrhiza/chemistry ; Allelopathy ; Glycyrrhizic Acid ; Metagenomics ; Rhizosphere ; },
abstract = {BACKGROUND: Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities under influence of allelochemicals in licorice remains limited. In the present study, the responses and effects of rhizobacterial communities on licorice allelopathy were investigated using a combination of multi-omics sequencing and pot experiments, under allelochemical addition and rhizobacterial inoculation treatments.<br><br>RESULTS: Here, we demonstrated that exogenous glycyrrhizin inhibits licorice development, and reshapes and enriches specific rhizobacteria and corresponding functions related to glycyrrhizin degradation. Moreover, the Novosphingobium genus accounted for a relatively high proportion of the enriched taxa and appeared in metagenomic assembly genomes. We further characterized the different capacities of single and synthetic inoculants to degrade glycyrrhizin and elucidated their distinct potency for alleviating licorice allelopathy. Notably, the single replenished N (Novosphingobium resinovorum) inoculant had the greatest allelopathy alleviation effects in licorice seedlings.<br><br>CONCLUSIONS: Altogether, the findings highlight that exogenous glycyrrhizin simulates the allelopathic autotoxicity effects of licorice, and indigenous single rhizobacteria had greater effects than synthetic inoculants in protecting licorice growth from allelopathy. The results of the present study enhance our understanding of rhizobacterial community dynamics during licorice allelopathy, with potential implications for resolving continuous cropping obstacle in medicinal plant agriculture using rhizobacterial biofertilizers. Video Abstract.},
}
@article {pmid37211183,
year = {2023},
author = {Yokoyama, D and Kikuchi, J},
title = {Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water.},
journal = {Environmental research},
volume = {231},
number = {Pt 3},
pages = {116202},
doi = {10.1016/j.envres.2023.116202},
pmid = {37211183},
issn = {1096-0953},
mesh = {Humans ; *Rivers ; Phylogeny ; Multiomics ; *Microbiota ; Stochastic Processes ; },
abstract = {Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.},
}
@article {pmid37209180,
year = {2023},
author = {Kostešić, E and Mitrović, M and Kajan, K and Marković, T and Hausmann, B and Orlić, S and Pjevac, P},
title = {Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2305-2319},
pmid = {37209180},
issn = {1432-184X},
mesh = {*Hot Springs/microbiology ; Croatia ; *Cyanobacteria/genetics ; Temperature ; *Chloroflexi ; Biofilms ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.},
}
@article {pmid37207751,
year = {2023},
author = {Jin, Z and Shen, M and Wang, L and Wang, C and Gao, M and Yu, G and Chang, Z and Zhang, X},
title = {Antibacterial and immunoregulatory activity of an antimicrobial peptide hepcidin in loach (Misgurnus anguillicaudatus).},
journal = {International journal of biological macromolecules},
volume = {242},
number = {Pt 2},
pages = {124833},
doi = {10.1016/j.ijbiomac.2023.124833},
pmid = {37207751},
issn = {1879-0003},
mesh = {Animals ; Hepcidins/genetics/metabolism ; Antimicrobial Peptides ; Anti-Bacterial Agents/pharmacology ; Saccharomyces cerevisiae/metabolism ; Gene Expression Regulation ; Amino Acid Sequence ; Fish Proteins/chemistry ; Gram-Negative Bacteria/metabolism ; Gram-Positive Bacteria/metabolism ; *Cypriniformes/genetics ; *Bacterial Infections ; Peptides/metabolism ; Bacteria/metabolism ; Amino Acids/metabolism ; },
abstract = {Antimicrobial peptides (AMPs) are members of humoral immunity and particpate in resisting microbial invasion. In this study, an AMP gene hepcidin was obtained from the oriental loach Misgurnus anguillicaudatus and named Ma-Hep. This Ma-Hep encodes a peptide of 90 amino acids, with a predicted active peptide segment (Ma-sHep) of 25 amino acids at C terminus. Stimulation by a bacterial pathogen Aeromonas hydrophila resulted in significant up-regulation of Ma-Hep transcripts in loach midgut, head kidney, and gill. Ma-Hep and Ma-sHep proteins were expressed in Pichia pastoris and their antibacterial activity was examined. Results showed that Ma-sHep possessed stronger antibacterial activity against various Gram-positive and Gram-negative bacteria, compared to Ma-Hep. Scanning electron microscopy showed that Ma-sHep might kill bacteria by destroying bacterial cell membranes. Moreover, we found that Ma-sHep had an inhibitory effect on blood cell apoptosis induced by A. hydrophila and facilitated the bacterial phagocytosis and clearance in loach. Histopathological analysis indicated Ma-sHep could protect liver and gut of loach from bacterial infection. Ma-sHep has high thermal stability and PH stability, which is conducive to further feed addition. Feed supplemented with Ma-sHep expressing yeast improved the intestinal flora of loach by increasing the dominant bacteria and decreasing the harmful bacteria. Feed supplemented with Ma-sHep expressing yeast also regulated the expression of inflammatory related factors in various tissues of loach and reduced the mortality of loach upon bacterial infection. These findings show that the antibacterial peptide Ma-sHep is involved in the antibacterial defense of loach and can be used as a candidate for new antimicrobial agents in aquaculture.},
}
@article {pmid37206339,
year = {2023},
author = {Rasmussen, KL and Stamps, BW and Vanzin, GF and Ulrich, SM and Spear, JR},
title = {Spatial and temporal dynamics at an actively silicifying hydrothermal system.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1172798},
pmid = {37206339},
issn = {1664-302X},
abstract = {Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park (YNP), Wyoming, actively gushing silicon-rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone's outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM, respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation <32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophile Thermocrinis dominates the hydrothermal source biofilm community, and the thermophiles Meiothermus and Leptococcus dominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such as Leptococcus, Chloroflexus, and Chloracidobacterium act as primary producers for the system, supporting heterotrophic growth of taxa such as Raineya, Tepidimonas, and Meiothermus. Community dynamics illustrate large changes yearly driven by abundance shifts of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.},
}
@article {pmid37206314,
year = {2023},
author = {Van de Walle, A and Kim, M and Alam, MK and Wang, X and Wu, D and Dash, SR and Rabaey, K and Kim, J},
title = {Greywater reuse as a key enabler for improving urban wastewater management.},
journal = {Environmental science and ecotechnology},
volume = {16},
number = {},
pages = {100277},
pmid = {37206314},
issn = {2666-4984},
abstract = {Sustainable water management is essential to guaranteeing access to safe water and addressing the challenges posed by climate change, urbanization, and population growth. In a typical household, greywater, which includes everything but toilet waste, constitutes 50-80% of daily wastewater generation and is characterized by low organic strength and high volume. This can be an issue for large urban wastewater treatment plants designed for high-strength operations. Segregation of greywater at the source for decentralized wastewater treatment is therefore necessary for its proper management using separate treatment strategies. Greywater reuse may thus lead to increased resilience and adaptability of local water systems, reduction in transport costs, and achievement of fit-for-purpose reuse. After covering greywater characteristics, we present an overview of existing and upcoming technologies for greywater treatment. Biological treatment technologies, such as nature-based technologies, biofilm technologies, and membrane bioreactors (MBR), conjugate with physicochemical treatment methods, such as membrane filtration, sorption and ion exchange technologies, and ultraviolet (UV) disinfection, may be able to produce treated water within the allowable parameters for reuse. We also provide a novel way to tackle challenges like the demographic variance of greywater quality, lack of a legal framework for greywater management, monitoring and control systems, and the consumer perspective on greywater reuse. Finally, benefits, such as the potential water and energy savings and sustainable future of greywater reuse in an urban context, are discussed.},
}
@article {pmid37204848,
year = {2023},
author = {Rattray, JB and Kramer, PJ and Gurney, J and Thomas, S and Brown, SP},
title = {The dynamic response of quorum sensing to density is robust to signal supplementation and individual signal synthase knockouts.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {5},
pages = {},
pmid = {37204848},
issn = {1465-2080},
support = {R21 AI156817/AI/NIAID NIH HHS/United States ; },
mesh = {*Quorum Sensing/genetics ; *Bacterial Proteins/genetics/metabolism ; Homoserine/metabolism ; Pseudomonas aeruginosa/metabolism ; Dietary Supplements ; },
abstract = {Quorum sensing (QS) is a widespread mechanism of environment sensing and behavioural coordination in bacteria. At its core, QS is based on the production, sensing and response to small signalling molecules. Previous work with Pseudomonas aeruginosa shows that QS can be used to achieve quantitative resolution and deliver a dosed response to the bacteria's density environment, implying a sophisticated mechanism of control. To shed light on how the mechanistic signal components contribute to graded responses to density, we assess the impact of genetic (AHL signal synthase deletion) and/or signal supplementation (exogenous AHL addition) perturbations on lasB reaction-norms to changes in density. Our approach condenses data from 2000 timeseries (over 74 000 individual observations) into a comprehensive view of QS-controlled gene expression across variation in genetic, environmental and signal determinants of lasB expression. We first confirm that deleting either (∆lasI, ∆rhlI) or both (∆lasIrhlI) AHL signal synthase gene attenuates QS response to density. In the ∆rhlI background we show persistent yet attenuated density-dependent lasB expression due to native 3-oxo-C12-HSL signalling. We then test if density-independent quantities of AHL signal (3-oxo-C12-HSL, C4-HSL) added to the WT either flatten or increase responsiveness to density and find that the WT response is robust to all tested concentrations of signal, alone or in combination. We then move to progressively supplementing the genetic knockouts and find that cognate signal supplementation of a single AHL signal (∆lasI +3-oxo-C12-HSL, ∆rhlI +C4HSL) is sufficient to restore the ability to respond in a density-dependent manner to increasing density. We also find that dual signal supplementation of the double AHL synthase knockout restores the ability to produce a graded response to increasing density, despite adding a density-independent amount of signal. Only the addition of high concentrations of both AHLs and PQS can force maximal lasB expression and ablate responsiveness to density. Our results show that density-dependent control of lasB expression is robust to multiple combinations of QS gene deletion and density-independent signal supplementation. Our work develops a modular approach to query the robustness and mechanistic bases of the central environmental sensing phenotype of quorum sensing.},
}
@article {pmid37201636,
year = {2023},
author = {He, Y and Xu, M and Lu, S and Zou, W and Wang, Y and Fakhar-E-Alam Kulyar, M and Iqbal, M and Li, K},
title = {Seaweed polysaccharides treatment alleviates injury of inflammatory responses and gut barrier in LPS-induced mice.},
journal = {Microbial pathogenesis},
volume = {180},
number = {},
pages = {106159},
doi = {10.1016/j.micpath.2023.106159},
pmid = {37201636},
issn = {1096-1208},
mesh = {Mice ; Humans ; Animals ; *Lipopolysaccharides/pharmacology ; Dysbiosis/chemically induced/drug therapy ; RNA, Ribosomal, 16S/genetics ; *Seaweed ; Polysaccharides/pharmacology ; Bacteria ; Vegetables ; },
abstract = {Gastrointestinal (GI) disease is a common digestive tract disease effects health of millions of human globally each year, thus the role of intestinal microflora had been emphasized. Seaweed polysaccharides featured a wide range of pharmacological activities, such as antioxidant activity and pharmacological action, but whether they can alleviate the dysbiosis of gut microbial ecology caused by lipopolysaccharide (LPS) exposure has not been well conducted. In this study, we investigated the effects of different concentration of seaweed polysaccharides on LPS-induced intestinal disorder by using hematoxylin and eosin (H&amp;E) staining and 16S rRNA high-throughput sequencing. Histopathological results indicated that the intestinal structure in the LPS-induced group was damaged. Furthermore, LPS exposure not only reduced the intestinal microbial diversity in mice but also induced considerable transformation in its composition, along with significant increase in pathogenic bacteria (Helicobacter, Citrobacter and Mucispirillum) and decrease in beneficial bacteria (Firmicutes, Lactobacillus, Akkermansia and Parabacteroides). Nonetheless, seaweed polysaccharides administration could recover the gut microbial dysbiosis and the loss of gut microbial diversity induced by LPS exposure. In summary, seaweed polysaccharides were effective against LPS-induced intestinal damage in mice via the modulation of intestinal microecology.},
}
@article {pmid37200211,
year = {2023},
author = {Pascual, J and Lepleux, C and Methner, A and Spröer, C and Bunk, B and Overmann, J},
title = {Arcobacter roscoffensis sp. nov., a marine bacterium isolated from coastal seawater.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.005895},
pmid = {37200211},
issn = {1466-5034},
mesh = {*Fatty Acids/chemistry ; Phospholipids/analysis ; *Arcobacter ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; Seawater/microbiology ; },
abstract = {A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2[T], was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2[T] was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2[T] was closely related to Arcobacter lekithochrous LFT 1.7[T] and Arcobacter caeni RW17-10[T](95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2[T] was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA-DNA hybridization, indicated that strain ARW1-2F2[T] represents a new Arcobacter species. The predominant fatty acids were C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c/C18 : 1 ω6c. The results of a polyphasic analysis supported the description of strain ARW1-2F2[T] as representing a novel species of the genus Arcobacter, for which the name Arcobacter roscoffensis sp. nov. is proposed with the type strain ARW1-2F2[T] (DSM 29169[T]=KCTC 52423[T]).},
}
@article {pmid37199998,
year = {2023},
author = {Getz, EW and Lanclos, VC and Kojima, CY and Cheng, C and Henson, MW and Schön, ME and Ettema, TJG and Faircloth, BC and Thrash, JC},
title = {The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct.},
journal = {mSystems},
volume = {8},
number = {3},
pages = {e0017923},
pmid = {37199998},
issn = {2379-5077},
support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation/ ; OCE-1945279, EF-2125191//National Science Foundation/ ; },
mesh = {*Seawater/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Aquatic Organisms ; Bacteria/genetics ; *Alphaproteobacteria ; },
abstract = {Bacterioplankton of the SAR11 clade are the most abundant marine microorganisms and consist of numerous subclades spanning order-level divergence (Pelagibacterales). The assignment of the earliest diverging subclade V (a.k.a. HIMB59) to the Pelagibacterales is highly controversial, with multiple recent phylogenetic studies placing them completely separate from SAR11. Other than through phylogenomics, subclade V has not received detailed examination due to limited genomes from this group. Here, we assessed the ecogenomic characteristics of subclade V to better understand the role of this group in comparison to the Pelagibacterales. We used a new isolate genome, recently released single-amplified genomes and metagenome-assembled genomes, and previously established SAR11 genomes to perform a comprehensive comparative genomics analysis. We paired this analysis with the recruitment of metagenomes spanning the open ocean, coastal, and brackish systems. Phylogenomics, average amino acid identity, and 16S rRNA gene phylogeny indicate that SAR11 subclade V is synonymous with the ubiquitous AEGEAN-169 clade and support the contention that this group represents a taxonomic family. AEGEAN-169 shared many bulk genome qualities with SAR11, such as streamlining and low GC content, but genomes were generally larger. AEGEAN-169 had overlapping distributions with SAR11 but was metabolically distinct from SAR11 in its potential to transport and utilize a broader range of sugars as well as in the transport of trace metals and thiamin. Thus, regardless of the ultimate phylogenetic placement of AEGEAN-169, these organisms have distinct metabolic capacities that likely allow them to differentiate their niche from canonical SAR11 taxa. IMPORTANCE One goal of marine microbiologists is to uncover the roles various microorganisms are playing in biogeochemical cycles. Success in this endeavor relies on differentiating groups of microbes and circumscribing their relationships. An early-diverging group (subclade V) of the most abundant bacterioplankton, SAR11, has recently been proposed as a separate lineage that does not share a most recent common ancestor. But beyond phylogenetics, little has been done to evaluate how these organisms compare with SAR11. Our work leverages dozens of new genomes to demonstrate the similarities and differences between subclade V and SAR11. In our analysis, we also establish that subclade V is synonymous with a group of bacteria established from 16S rRNA gene sequences, AEGEAN-169. Subclade V/AEGEAN-169 has clear metabolic distinctions from SAR11 and their shared traits point to remarkable convergent evolution if they do not share a most recent common ancestor.},
}
@article {pmid37196970,
year = {2023},
author = {Farrell, ML and Chueiri, A and O'Connor, L and Duane, S and Maguire, M and Miliotis, G and Cormican, M and Hooban, B and Leonard, A and Gaze, WH and Devane, G and Tuohy, A and Burke, LP and Morris, D},
title = {Assessing the impact of recreational water use on carriage of antimicrobial resistant organisms.},
journal = {The Science of the total environment},
volume = {888},
number = {},
pages = {164201},
doi = {10.1016/j.scitotenv.2023.164201},
pmid = {37196970},
issn = {1879-1026},
mesh = {Adult ; Humans ; *Enterobacteriaceae Infections/epidemiology ; Water ; beta-Lactamases ; Carbapenems ; Feces ; *Gammaproteobacteria ; *Anti-Infective Agents ; Anti-Bacterial Agents ; },
abstract = {Understanding the role of exposure to natural recreational waters in the acquisition and transmission of antimicrobial resistance (AMR) is an area of increasing interest. A point prevalence study was carried out in the island of Ireland to determine the prevalence of colonisation with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and carbapenem-resistant Enterobacterales (CRE) in recreational water users (WU) and matched controls. A total of 411 adult participants (199 WU, 212 controls) submitted at least one faecal sample between September 2020 - October 2021. In total, 80 Enterobacterales were isolated from 73 participants. ESBL-PE were detected in 29 (7.1 %) participants (7 WU, 22 controls), and CRE were detected in nine (2.2 %) participants (4 WU, 5 controls). No carbapenemase-producing Enterobacterales (CPE) were detected. WU were significantly less likely to harbour ESBL-PE than controls (risk ratio = 0.34, 95 % CI 0.148 to 0.776, χ[2] 7.37, p = 0.007). This study demonstrates the occurrence of ESBL-PE and CRE in healthy participants in Ireland. Recreational exposure to bathing water in Ireland was associated with a decreased prevalence of colonisation with ESBL-PE and CRE.},
}
@article {pmid37196741,
year = {2023},
author = {Lin, B and Tan, B and Zhang, Q and Li, M and Peng, H and Su, J and He, J and Zhang, Y and Liu, X and Wu, N},
title = {Unraveling the nexus of Cr (VI), aniline, and microbial ecology on aniline-degrading biosystem: Removal efficiency, sludge type, microbial ecology.},
journal = {Bioresource technology},
volume = {382},
number = {},
pages = {129185},
doi = {10.1016/j.biortech.2023.129185},
pmid = {37196741},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Denitrification ; Bioreactors/microbiology ; Nitrification ; Aniline Compounds/metabolism ; Nitrogen/metabolism ; },
abstract = {In order to explore the stress principle of Cr (Ⅵ) on aniline biodegradation system, a control group and experimental groups with the concentration of Cr (Ⅵ) at 2, 5, 8 mg/L were set up. The results demonstrated that Cr (Ⅵ) had minimal effects on the degradation efficiency of aniline but significantly inhibited nitrogen removal function. When Cr (Ⅵ) concentration was below 5 mg/L, the nitrification performance recovered spontaneously, while denitrification performance was severely impaired. Furthermore, the secretion of extracellular polymeric substances (EPS) and its fluorescence substance concentration were strongly inhibited with increasing Cr (Ⅵ) concentration. High-throughput sequencing revealed that the experimental groups were enriched with Leucobacter and Cr (Ⅵ)-reducing bacteria, but the abundance of nitrifiers and denitrifiers was significantly decreased compared to the control group. Overall, the effects of Cr (Ⅵ) stress at different concentrations on nitrogen removal performance were more significant than those on aniline degradation.},
}
@article {pmid37196568,
year = {2023},
author = {Xu, Y and Teng, Y and Wang, X and Ren, W and Zhao, L and Luo, Y and Christie, P and Greening, C},
title = {Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil.},
journal = {Environment international},
volume = {176},
number = {},
pages = {107962},
doi = {10.1016/j.envint.2023.107962},
pmid = {37196568},
issn = {1873-6750},
mesh = {*Polychlorinated Biphenyls/analysis ; *Rhizobium/metabolism ; *Fabaceae/metabolism ; Ecosystem ; *Soil Pollutants/analysis ; Biodegradation, Environmental ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of [13]C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.},
}
@article {pmid37195192,
year = {2023},
author = {Wang, J and Pan, Z and Yu, J and Zhang, Z and Li, YZ},
title = {Global assembly of microbial communities.},
journal = {mSystems},
volume = {8},
number = {3},
pages = {e0128922},
pmid = {37195192},
issn = {2379-5077},
support = {32070030//National Natural Science Foundation of China (NSFC)/ ; 2018YFA0900400, 2018YFA0901704//MOST | National Key Research and Development Program of China (NKPs)/ ; ZR2022QC229//Science Foundation for Youths of Shandong Province/ ; 2022M711918//China Postdoctoral Science Foundation/ ; SDCX-ZG-20220201//Postdoctoral Innovation Project of Shandong Province ()/ ; 32201303//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Bacteria/genetics ; *Microbiota/genetics ; Microbial Interactions ; Genes, Bacterial ; Stochastic Processes ; },
abstract = {Different habitats harbor different microbial communities with elusive assembly mechanisms. This study comprehensively investigated the global assembly mechanisms of microbial communities and effects of community-internal influencing factors using the Earth Microbiome Project (EMP) data set. We found that deterministic and stochastic processes contribute approximately equally to global microbial community assembly, and, specifically, deterministic processes generally play a major role in free-living and plant-associated (but not plant corpus) environments, while stochastic processes are the major contributor in animal-associated environments. In contrast with the assembly of microorganisms, the assembly of functional genes, predicted from PICRUSt, is mainly attributed to deterministic processes in all microbial communities. The sink and source microbial communities are normally assembled using similar mechanisms, and the core microorganisms are specific to different environment types. On a global scale, deterministic processes are positively related to the community alpha diversity, microbial interaction degree and bacterial predatory-specific gene abundance. Our analysis provides a panoramic picture and regularities of global and environment-typical microbial community assemblies. IMPORTANCE With the development of sequencing technologies, the research topic of microbial ecology has evolved from the analysis of community composition to community assembly, including the relative contribution of deterministic and stochastic processes for the formation and maintenance of community diversity. Many studies have reported the microbial assembly mechanisms in various habitats, but the assembly regularities of global microbial communities remain unknown. In this study, we analyzed the EMP data set using a combined pipeline to explore the assembly mechanisms of global microbial communities, microbial sources to construct communities, core microbes in different environment types, and community-internal factors influencing assembly. The results provide a panoramic picture and rules of global and environment-typical microbial community assemblies, which enhances our understandings of the mechanisms globally controlling community diversity and species coexistence.},
}
@article {pmid37193669,
year = {2023},
author = {Delbaere, K and Roegiers, I and Bron, A and Durif, C and Van de Wiele, T and Blanquet-Diot, S and Marinelli, L},
title = {The small intestine: dining table of host-microbiota meetings.},
journal = {FEMS microbiology reviews},
volume = {47},
number = {3},
pages = {},
pmid = {37193669},
issn = {1574-6976},
mesh = {*Intestine, Small/microbiology ; *Microbiota ; Diet ; },
abstract = {Growing evidence suggests the importance of the small intestinal bacteria in the diet-host-microbiota dialogue in various facets of health and disease. Yet, this body site is still poorly explored and its ecology and mechanisms of interaction with the host are just starting to be unraveled. In this review, we describe the current knowledge on the small intestinal ecology, its composition and diversity, and how the intestinal bacteria in homeostatic conditions participate in nutrient digestion and absorption. We illustrate the importance of a controlled bacterial density and of the preservation of absorptive surface for the host's nutritional status. In particular, we discuss these aspects of the small intestinal environment in the framework of two disease conditions, namely small intestinal bacterial overgrowth (SIBO) and short bowel syndrome (SBS). We also detail in vivo, ex vivo, and in vitro models developed to simulate the small intestinal environment, some applied for (diet-)host-bacteria interaction studies. Lastly, we highlight recent technological, medical, and scientific advances applicable to investigate this complex and yet understudied body environment to broaden our knowledge in support of further progress in the medical practice, and to proceed towards the integration of the (small)intestinal bacteria in personalized therapeutic approaches.},
}
@article {pmid37191674,
year = {2023},
author = {Zhao, J and Fan, D and Guo, W and Wu, J and Zhang, X and Zhuang, X and Kong, W},
title = {Precipitation Drives Soil Protist Diversity and Community Structure in Dry Grasslands.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2293-2304},
pmid = {37191674},
issn = {1432-184X},
support = {41771303//NSFC/ ; },
mesh = {*Ecosystem ; Grassland ; Soil/chemistry ; Biomass ; Plants ; *Microbiota ; Soil Microbiology ; },
abstract = {Protists are essential components of soil microbial communities, mediating nutrient cycling and ecosystem functions in terrestrial ecosystems. However, their distribution patterns and driving factors, particularly, the relative importance of climate, plant and soil factors, remain largely unknown. This limits our understanding of soil protist roles in ecosystem functions and their responses to climate change. This is particularly a concern in dryland ecosystems where soil microbiomes are more important for ecosystem functions because plant diversity and growth are heavily constrained by environmental stresses. Here, we explored protist diversity and their driving factors in grassland soils on the Tibetan Plateau, which is a typical dryland region with yearly low temperatures. Soil protist diversity significantly decreased along the gradient of meadow, steppe, and desert. Soil protist diversity positively correlated with precipitation, plant biomass and soil nutrients, but these correlations were changed by grazing. Structural equation and random forest models demonstrated that precipitation dominated soil protist diversity directly and indirectly by influencing plant and soil factors. Soil protist community structure gradually shifted along meadow, steppe and desert, and was driven more by precipitation than by plant and soil factors. Soil protist community compositions were dominated by Cercozoa, Ciliophora and Chlorophyta. In particular, Ciliophora increased but Chlorophyta decreased in relative abundance along the gradient of meadow, steppe and desert. These results demonstrate that precipitation plays more important roles in driving soil protist diversity and community structure than plant and soil factors, suggesting that future precipitation change profoundly alters soil protist community and functions in dry grasslands.},
}
@article {pmid37190986,
year = {2023},
author = {Yang, Y and Suyamud, B and Liang, S and Liang, X and Wan, W and Zhang, W},
title = {Distinct spatiotemporal succession of bacterial generalists and specialists in the lacustrine plastisphere.},
journal = {Environmental microbiology},
volume = {25},
number = {12},
pages = {2746-2760},
doi = {10.1111/1462-2920.16400},
pmid = {37190986},
issn = {1462-2920},
support = {[2020SWG04]//Foundation of the State Key Laboratory of Water Resources and Hydropower Engineering Science (Wuhan University), China/ ; E0291P0101//Funding Project of Sino-Africa Joint Research Center, Chinese Academy of Sciences/ ; 32071614//National Natural Science Foundation of China/ ; 42107147//National Natural Science Foundation of China/ ; Y9519802//the Starting Research Fund and Opening Research Fund from Key Laboratory of Aquatic Botany and Watershed Ecology, Chinese Academy of Sciences/ ; E0520202//the Starting Research Fund and Opening Research Fund from Key Laboratory of Aquatic Botany and Watershed Ecology, Chinese Academy of Sciences/ ; },
mesh = {*Ecosystem ; *Plastics ; Bacteria/genetics ; Stochastic Processes ; },
abstract = {The assembly processes of generalists and specialists and their driving mechanisms during spatiotemporal succession is a central issue in microbial ecology but a poorly researched subject in the plastisphere. We investigated the composition variation, spatiotemporal succession, and assembly processes of bacterial generalists and specialists in the plastisphere, including non-biodegradable (NBMPs) and biodegradable microplastics (BMPs). Although the composition of generalists and specialists on NBMPs differed from that of BMPs, colonization time mainly mediated the composition variation. The relative abundance of generalists and the relative contribution of species replacement were initially increased and then decreased with colonization time, while the specialists initially decreased and then increased. Besides, the richness differences also affected the composition variation of generalists and specialists in the plastisphere, and the generalists were more susceptible to richness differences than corresponding specialists. Furthermore, the assembly of generalists in the plastisphere was dominated by deterministic processes, while stochastic processes dominated the assembly of specialists. The network stability test showed that the community stability of generalists on NBMPs and BMPs was lower than corresponding specialists. Our results suggested that different ecological assembly processes shaped the spatiotemporal succession of bacterial generalists and specialists in the plastisphere, but were less influenced by polymer types.},
}
@article {pmid37188915,
year = {2023},
author = {Moeller, FU and Herbold, CW and Schintlmeister, A and Mooshammer, M and Motti, C and Glasl, B and Kitzinger, K and Behnam, F and Watzka, M and Schweder, T and Albertsen, M and Richter, A and Webster, NS and Wagner, M},
title = {Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta.},
journal = {The ISME journal},
volume = {17},
number = {8},
pages = {1208-1223},
pmid = {37188915},
issn = {1751-7370},
support = {T 1218/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; *Porifera/microbiology ; Taurine ; Ammonia ; Carbon ; Symbiosis ; Phylogeny ; },
abstract = {Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.},
}
@article {pmid37188366,
year = {2023},
author = {Harder, CB and Hesling, E and Botnen, SS and Lorberau, KE and Dima, B and von Bonsdorff-Salminen, T and Niskanen, T and Jarvis, SG and Ouimette, A and Hester, A and Hobbie, EA and Taylor, AFS and Kauserud, H},
title = {Mycena species can be opportunist-generalist plant root invaders.},
journal = {Environmental microbiology},
volume = {25},
number = {10},
pages = {1875-1893},
doi = {10.1111/1462-2920.16398},
pmid = {37188366},
issn = {1462-2920},
mesh = {*Mycorrhizae ; *Agaricales ; Symbiosis ; Plants/microbiology ; Plant Roots/microbiology ; },
abstract = {Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of [13] C/[15] N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published [13] C/[15] N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.},
}
@article {pmid37187536,
year = {2023},
author = {Liao, Q and Ye, Y and Li, Z and Chen, H and Zhuo, L},
title = {Prediction of miRNA-disease associations in microbes based on graph convolutional networks and autoencoders.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1170559},
pmid = {37187536},
issn = {1664-302X},
abstract = {MicroRNAs (miRNAs) are short RNA molecular fragments that regulate gene expression by targeting and inhibiting the expression of specific RNAs. Due to the fact that microRNAs affect many diseases in microbial ecology, it is necessary to predict microRNAs' association with diseases at the microbial level. To this end, we propose a novel model, termed as GCNA-MDA, where dual-autoencoder and graph convolutional network (GCN) are integrated to predict miRNA-disease association. The proposed method leverages autoencoders to extract robust representations of miRNAs and diseases and meantime exploits GCN to capture the topological information of miRNA-disease networks. To alleviate the impact of insufficient information for the original data, the association similarity and feature similarity data are combined to calculate a more complete initial basic vector of nodes. The experimental results on the benchmark datasets demonstrate that compared with the existing representative methods, the proposed method has achieved the superior performance and its precision reaches up to 0.8982. These results demonstrate that the proposed method can serve as a tool for exploring miRNA-disease associations in microbial environments.},
}
@article {pmid37186228,
year = {2023},
author = {Woksepp, H and Camara, F and Bonnedahl, J},
title = {High prevalence of blaCTX-M-15 type extended-spectrum beta-lactamases in Gambian hooded vultures (Necrosyrtes monachus): A threatened species with substantial human interaction.},
journal = {MicrobiologyOpen},
volume = {12},
number = {2},
pages = {e1349},
pmid = {37186228},
issn = {2045-8827},
mesh = {Animals ; Humans ; *Escherichia coli ; *Escherichia coli Infections/microbiology ; Endangered Species ; Gambia ; Colistin ; Prevalence ; beta-Lactamases/genetics ; Anti-Bacterial Agents/pharmacology ; Klebsiella pneumoniae/genetics ; Birds ; Microbial Sensitivity Tests ; },
abstract = {One hundred fecal samples from hooded vultures in the Gambia (Banjul area) were investigated for the presence of bacteria with extended-spectrum cephalosporin- (ESBL/AmpC), carbapenemases, and colistin resistance. No Enterobacteriales carrying carbapenemases or resistance against colistin were detected. Fifty-four ESBL-producing Escherichia coli and five ESBL-producing Klebsiella pneumoniae isolates were identified in 52 of the samples, of which 52 E. coli and 4 K. pneumoniae yielded passed sequencing results. Fifty of the E. coli had ESBL phenotype and genotype harboring blaCTX-M genes, of which 88.5% (n = 46) were the blaCTX-M-15 gene, commonly found on the African continent. Furthermore, the genetic context around blaCTX-M-15 was similar between isolates, being colocalized with ISKpn19. In contrast, cgMLST analysis of the E. coli harboring ESBL genes revealed a genetic distribution over a large fraction of the currently known existing E. coli populations in the Gambia. Hooded vultures in the Gambia thus have a high ESBL E. coli-prevalence (>50%) with low diversity regarding key resistance genes. Furthermore, given the urban presence and frequent interactions between hooded vultures and humans, data from this study implies hooded vultures as potential vectors contributing to the further dissemination of antibiotic-resistance genes.},
}
@article {pmid37185621,
year = {2023},
author = {Li, J and Liu, T and McIlroy, SJ and Tyson, GW and Guo, J},
title = {Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {39},
pmid = {37185621},
issn = {2730-6151},
abstract = {The microbial guild coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an innovative process to achieve energy-efficient nitrogen removal with the beneficial use of methane in biogas or in anaerobically treated wastewater. Here, metagenomics and metatranscriptomics were used to reveal the microbial ecology of two biofilm systems, which incorporate anammox and n-DAMO for high-level nitrogen removal in low-strength domestic sewage and high-strength sidestream wastewater, respectively. We find that different nitrogen loadings (i.e., 0.1 vs. 1.0 kg N/m[3]/d) lead to different combinations of anammox bacteria and anaerobic methanotrophs ("Candidatus Methanoperedens" and "Candidatus Methylomirabilis"), which play primary roles for carbon and nitrogen transformations therein. Despite methane being the only exogenous organic carbon supplied, heterotrophic populations (e.g., Verrucomicrobiota and Bacteroidota) co-exist and actively perform partial denitrification or dissimilatory nitrate reduction to ammonium (DNRA), likely using organic intermediates from the breakdown of methane and biomass as carbon sources. More importantly, two novel genomes belonging to "Ca. Methylomirabilis" are recovered, while one surprisingly expresses nitrate reductases, which we designate as "Ca. Methylomirabilis nitratireducens" representing its inferred capability in performing nitrate-dependent anaerobic methane oxidation. This finding not only suggests a previously neglected possibility of "Ca. Methylomirabilis" bacteria in performing methane-dependent nitrate reduction, and also challenges the previous understanding that the methane-dependent complete denitrification from nitrate to dinitrogen gas is carried out by the consortium of bacteria and archaea.},
}
@article {pmid37184385,
year = {2023},
author = {Sänger, PA and Knüpfer, M and Kegel, M and Spanier, B and Liebler-Tenorio, EM and Fuchs, TM},
title = {Regulation and Functionality of a Holin/Endolysin Pair Involved in Killing of Galleria mellonella and Caenorhabditis elegans by Yersinia enterocolitica.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {6},
pages = {e0003623},
pmid = {37184385},
issn = {1098-5336},
mesh = {Animals ; Humans ; *Yersinia enterocolitica/genetics ; Caenorhabditis elegans/metabolism ; *Moths/microbiology ; *Bacterial Toxins/metabolism ; Insecta ; *Insecticides/metabolism ; Luciferases ; Bacterial Proteins/genetics/metabolism ; },
abstract = {The insecticidal toxin complex (Tc) proteins are produced by several insect-associated bacteria, including Yersinia enterocolitica strain W22703, which oscillates between two distinct pathogenicity phases in invertebrates and humans. The mechanism by which this high-molecular-weight toxin is released into the extracellular surrounding, however, has not been deciphered. In this study, we investigated the regulation and functionality of a phage-related holin/endolysin (HE) cassette located within the insecticidal pathogenicity island Tc-PAIYe of W22703. Using the Galleria mellonella infection model and luciferase reporter fusions, we revealed that quorum sensing contributes to the insecticidal activity of W22703 upon influencing the transcription of tcaR2, which encodes an activator of the tc and HE genes. In contrast, a lack of the Yersinia modulator, YmoA, stimulated HE gene transcription, and mutant W22703 ΔymoA exhibited a stronger toxicity toward insect larvae than did W22703. A luciferase reporter fusion demonstrated transcriptional activation of the HE cassette in vivo, and a significantly larger extracellular amount of subunit TcaA was found in W22703 ΔymoA relative to its ΔHE mutant. Using competitive growth assays, we demonstrated that at least in vitro, the TcaA release upon HE activity is not mediated by cell lysis of a significant part of the population. Oral infection of Caenorhabditis elegans with a HE deletion mutant attenuated the nematocidal activity of the wild type, similar to the case with a mutant lacking a Tc subunit. We conclude that the dual holin/endolysin cassette of yersiniae is a novel example of a phage-related function adapted for the release of a bacterial toxin. IMPORTANCE Members of the genus Yersinia cause gastroenteritis in humans but also exhibit toxicity toward invertebrates. A virulence factor required for this environmental life cycle stage is the multisubunit toxin complex (Tc), which is distinct from the insecticidal toxin of Bacillus thuringiensis and has the potential to be used in pest control. The mechanism by which this high-molecular-weight Tc is secreted from bacterial cells has not been uncovered. Here, we show that a highly conserved phage-related holin/endolysin pair, which is encoded by the genes holY and elyY located between the Tc subunit genes, is essential for the insecticidal activity of Y. enterocolitica and that its activation increases the amount of Tc subunits in the supernatant. Thus, the dual holY-elyY cassette of Y. enterocolitica constitutes a new example for a type 10 secretion system to release bacterial toxins.},
}
@article {pmid37182790,
year = {2023},
author = {Refisch, A and Sen, ZD and Klassert, TE and Busch, A and Besteher, B and Danyeli, LV and Helbing, D and Schulze-Späte, U and Stallmach, A and Bauer, M and Panagiotou, G and Jacobsen, ID and Slevogt, H and Opel, N and Walter, M},
title = {Microbiome and immuno-metabolic dysregulation in patients with major depressive disorder with atypical clinical presentation.},
journal = {Neuropharmacology},
volume = {235},
number = {},
pages = {109568},
doi = {10.1016/j.neuropharm.2023.109568},
pmid = {37182790},
issn = {1873-7064},
mesh = {Humans ; *Depressive Disorder, Major/metabolism ; Brain/metabolism ; *Microbiota ; },
abstract = {Depression is highly prevalent (6% 1-year prevalence) and is the second leading cause of disability worldwide. Available treatment options for depression are far from optimal, with response rates only around 50%. This is most likely related to a heterogeneous clinical presentation of major depression disorder (MDD), suggesting different manifestations of underlying pathophysiological mechanisms. Poorer treatment outcomes to first-line antidepressants were reported in MDD patients endorsing an "atypical" symptom profile that is characterized by preserved reactivity in mood, increased appetite, hypersomnia, a heavy sensation in the limbs, and interpersonal rejection sensitivity. In recent years, evidence has emerged that immunometabolic biological dysregulation is an important underlying pathophysiological mechanism in depression, which maps more consistently to atypical features. In the last few years human microbial residents have emerged as a key influencing variable associated with immunometabolic dysregulations in depression. The microbiome plays a critical role in the training and development of key components of the host's innate and adaptive immune systems, while the immune system orchestrates the maintenance of key features of the host-microbe symbiosis. Moreover, by being a metabolically active ecosystem commensal microbes may have a huge impact on signaling pathways, involved in underlying mechanisms leading to atypical depressive symptoms. In this review, we discuss the interplay between the microbiome and immunometabolic imbalance in the context of atypical depressive symptoms. Although research in this field is in its infancy, targeting biological determinants in more homogeneous clinical presentations of MDD may offer new avenues for the development of novel therapeutic strategies for treatment-resistant depression. This article is part of the Special Issue on "Microbiome &amp; the Brain: Mechanisms &amp; Maladies".},
}
@article {pmid37180236,
year = {2023},
author = {Huang, W and Li, S and Li, S and Laanbroek, HJ and Zhang, Q},
title = {Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1151768},
pmid = {37180236},
issn = {1664-302X},
abstract = {The microbial community plays an important role in the biogeochemical cycles in water aquatic ecosystems, and it is regulated by environmental variables. However, the relationships between microbial keystone taxa and water variables, which play a pivotal role in aquatic ecosystems, has not been clarified in detail. We analyzed the seasonal variation in microbial communities and co-occurrence network in the representative areas taking Lake Dongqian as an example. Both pro- and eukaryotic community compositions were more affected by seasons than by sites, and the prokaryotes were more strongly impacted by seasons than the eukaryotes. Total nitrogen, pH, temperature, chemical oxygen demand, dissolved oxygen and chlorophyll a significantly affected the prokaryotic community, while the eukaryotic community was significantly influenced by total nitrogen, ammonia, pH, temperature and dissolved oxygen. The eukaryotic network was more complex than that of prokaryotes, whereas the number of eukaryotic keystone taxa was less than that of prokaryotes. The prokaryotic keystone taxa belonged mainly to Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes. It is noteworthy that some of the keystone taxa involved in nitrogen cycling are significantly related to total nitrogen, ammonia, temperature and chlorophyll a, including Polaromonas, Albidiferax, SM1A02 and Leptolyngbya so on. And the eukaryotic keystone taxa were found in Ascomycota, Choanoflagellida and Heterophryidae. The mutualistic pattern between pro- and eukaryotes was more evident than the competitive pattern. Therefore, it suggests that keystone taxa could be as bio-indicators of aquatic ecosystems.},
}
@article {pmid37178239,
year = {2023},
author = {Nandni, and Rani, S and Chopra, G and Wati, L},
title = {Deciphering the Potential of Sulphur-Oxidizing Bacteria for Sulphate Production Correlating with pH Change.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2282-2292},
pmid = {37178239},
issn = {1432-184X},
mesh = {*Sulfates ; *Bacteria ; Soil ; Soil Microbiology ; Oxidation-Reduction ; Sulfur ; Hydrogen-Ion Concentration ; },
abstract = {Sulphur, available in the form of sulphate, is one of the essential nutrients that is required by plants. Bacteria capable of oxidizing reduced forms of sulphur to sulphate play an important role in sulphur nutrition for plants. The present study was conducted to isolate, screen, and characterize sulphur-oxidizing bacteria from different soil samples collected from mustard rhizosphere and fly ash mixed soil. A total of 33 sulphur-oxidizing bacterial isolates (HMSOB1-33) were retrieved from soil and further screened for sulphur-oxidizing ability. Maximum solubilization index (3.76), pH reduction (3.93), and sulphate production (173.61 µg/ml) were observed for the isolate HMSOB2 which on the basis of 16S rDNA sequencing was identified as Pantoea dispersa with sequence similarity 98.22%. Four other selected bacterial isolates were identified as Bacillus megaterium, Bacillus tropicus, Bacillus velezensis, and Bacillus cereus. Sulphate solubilization index (SSI) correlated positively (r = 0.91) with sulphate production; however, pH showed negative correlation (r = - 0.82) with SSI as well as sulphate production after 120 h of incubation. These promising bacterial isolates could be further explored as bioinoculant after assessing plant growth traits.},
}
@article {pmid37177981,
year = {2023},
author = {Bier, RL and Mosher, JJ and Kaplan, LA and Kan, J},
title = {Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America.},
journal = {Environmental microbiology},
volume = {25},
number = {10},
pages = {1860-1874},
doi = {10.1111/1462-2920.16396},
pmid = {37177981},
issn = {1462-2920},
mesh = {*Ecosystem ; Bacteria/genetics ; Fresh Water ; Acidobacteria ; *Microbiota ; Central America ; },
abstract = {A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.},
}
@article {pmid37173204,
year = {2023},
author = {Pan, X and Raaijmakers, JM and Carrión, VJ},
title = {Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning.},
journal = {Trends in microbiology},
volume = {31},
number = {9},
pages = {959-971},
doi = {10.1016/j.tim.2023.03.018},
pmid = {37173204},
issn = {1878-4380},
mesh = {Animals ; Humans ; *Ecosystem ; *Bacteroidetes/genetics ; Host Microbial Interactions ; Ecology ; Genome ; Plants ; Soil Microbiology ; },
abstract = {Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.},
}
@article {pmid37173060,
year = {2023},
author = {Krebs, NF and Belfort, MB and Meier, PP and Mennella, JA and O'Connor, DL and Taylor, SN and Raiten, DJ},
title = {Infant factors that impact the ecology of human milk secretion and composition-a report from "Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)" Working Group 3.},
journal = {The American journal of clinical nutrition},
volume = {117 Suppl 1},
number = {Suppl 1},
pages = {S43-S60},
pmid = {37173060},
issn = {1938-3207},
support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; },
mesh = {Female ; Infant ; Infant, Newborn ; Humans ; *Milk, Human ; Lactation/physiology ; *Premature Birth ; Breast Feeding ; Infant Nutritional Physiological Phenomena ; },
abstract = {Infants drive many lactation processes and contribute to the changing composition of human milk through multiple mechanisms. This review addresses the major topics of milk removal; chemosensory ecology for the parent-infant dyad; the infant's inputs into the composition of the human milk microbiome; and the impact of disruptions in gestation on the ecology of fetal and infant phenotypes, milk composition, and lactation. Milk removal, which is essential for adequate infant intake and continued milk synthesis through multiple hormonal and autocrine/paracrine mechanisms, should be effective, efficient, and comfortable for both the lactating parent and the infant. All 3 components should be included in the evaluation of milk removal. Breastmilk "bridges" flavor experiences in utero with postweaning foods, and the flavors become familiar and preferred. Infants can detect flavor changes in human milk resulting from parental lifestyle choices, including recreational drug use, and early experiences with the sensory properties of these recreational drugs impact subsequent behavioral responses. Interactions between the infant's own developing microbiome, that of the milk, and the multiple environmental factors that are drivers-both modifiable and nonmodifiable-in the microbial ecology of human milk are explored. Disruptions in gestation, especially preterm birth and fetal growth restriction or excess, impact the milk composition and lactation processes such as the timing of secretory activation, adequacy of milk volume and milk removal, and duration of lactation. Research gaps are identified in each of these areas. To assure a sustained and robust breastfeeding ecology, these myriad infant inputs must be systematically considered.},
}
@article {pmid37169795,
year = {2023},
author = {Conners, R and León-Quezada, RI and McLaren, M and Bennett, NJ and Daum, B and Rakonjac, J and Gold, VAM},
title = {Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {2724},
pmid = {37169795},
issn = {2041-1723},
support = {BB/R008639/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R000484/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Humans ; Cryoelectron Microscopy ; Ecosystem ; *Bacteriophages/genetics ; *Inovirus/genetics ; Bacteria ; *Virus Diseases ; },
abstract = {Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.},
}
@article {pmid37166501,
year = {2023},
author = {Weber, M and Göpfert, B and von Wezyk, S and Savin-Hoffmeyer, M and Lipski, A},
title = {Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1676-1685},
pmid = {37166501},
issn = {1432-184X},
support = {41.2015.02//Ministry for Environment, Agriculture, Conservation and Consumer Protection of the State of North Rhine-Westphalia/ ; },
mesh = {Animals ; Cattle ; Female ; RNA, Ribosomal, 16S/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Tetracycline ; Cloxacillin ; Drug Resistance, Microbial/genetics ; Cell Count ; Genes, Bacterial ; },
abstract = {The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R[2] = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R[2] = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.},
}
@article {pmid37166500,
year = {2023},
author = {Zeng, Z and Yang, Z and Yang, A and Li, Y and Zhang, H},
title = {Genetic Evidence for Colletotrichum gloeosporioides Transmission Between the Invasive Plant Ageratina adenophora and Co-occurring Neighbor Plants.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2192-2201},
pmid = {37166500},
issn = {1432-184X},
support = {2021Z022//Postgraduate Research and Innovation Foundation of Yunnan University/ ; 2022YFF1302402//National key research and development program of China/ ; },
mesh = {*Ageratina/genetics/microbiology ; Introduced Species ; Ecosystem ; *Colletotrichum/genetics ; },
abstract = {To understand the disease-mediated invasion of exotic plants and the potential risk of disease transmission in local ecosystems, it is necessary to characterize population genetic structure and spatio-temporal dynamics of fungal community associated with both invasive and co-occurring plants. In this study, multiple genes were used to characterize the genetic diversity of 165 strains of Colletotrichum gloeosporioides species complex (CGSC) isolated from healthy leaves and symptomatic leaves of invasive plant Ageratina adenophora, as well as symptomatic leaves of its neighbor plants from eleven geographic sites in China. The data showed that these CGSC strains had a high genetic diversity in each geographic site (all Hd > 0.67 and Pi > 0.01). Haplotype diversity and nucleotide diversity varied greatly in individual gene locus: gs had the highest haplotype diversity (Hd = 0.8972), gapdh had the highest nucleotide diversity (Pi = 0.0705), and ITS had the lowest nucleotide diversity (Pi = 0.0074). Haplotypes were not clustered by geographic site, invasive age, or isolation source. AMOVA revealed that the genetic variation was mainly from within-populations, regardless of geographic or isolation origin. Both AMOVA and neutrality tests indicated these CGSC strains occurred gene exchange among geographic populations but did not experience population expansion along with A. adenophora invasion progress. Our data indicated that A. adenophora primarily accumulated these CGSC fungi in the introduced range, suggesting a high frequency of CGSC transmission between A. adenophora and co-occurring neighbor plants. This study is valuable for understanding the disease-mediated plant invasion and the potential risk of disease transmission driven by exotic plants in local ecosystems.},
}
@article {pmid37163314,
year = {2023},
author = {Cai, P and Zhang, W and Duan, X and Gong, S and Qiu, Z and Zhu 朱, M&#x58a8;},
title = {First Report of Powdery Mildew Caused by Golovinomyces bolayi on Veronica persica in Central China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-04-23-0641-PDN},
pmid = {37163314},
issn = {0191-2917},
abstract = {Veronica persica, Persian speedwell, is a flowering plant belonging to the family Plantaginaceae. Due to its showy flowers, this plant is widely planted in many home gardens, city parks and universities in China. From April to June 2021, signs and symptoms of powdery mildew were found on leaves of V. persica growing on the campus of Henan Normal University, Henan Province, China. Signs initially appeared as thin white colonies and subsequently white powdery masses were abundant on the adaxial and abaxial surfaces of leaves and covered up to 99 % of the leaf area. The infected leaves showed chlorotic, deformed or senescence features. About 150 V. persica plants were monitored and more than 90 % of the plants showed these signs and symptoms. Conidiophores (n = 20) were 108 to 220 × 10 to 13 μm and composed of foot cells, followed by short cells and conidia. Conidia were hyaline, doliiform-subcylindrical shaped, 21 to 37 × 15 to 22 μm, and showed distinct fibrosin bodies. Conidial germ tubes were produced at the perihilar position. No chasmothecia were observed. The observed morphological characteristics were consistent with those of previously documented Golovinomyces bolayi (Braun and Cook 2012). To further confirm the powdery mildew fungus, structures of the pathogen were harvested and total genomic DNA was isolated using the method previously described by Zhu et al. (2019, 2021). Using the primers ITS1/ITS4, the internal transcribed spacer (ITS) region of rDNA was amplified (White et al. 1990) and the amplicon was sequenced. The resulting sequence was deposited into GenBank under Accession No. MZ343575 and was 100 % identical (592/592 bp) to G. bolayi on Kalanchoe blossfeldiana (LC417096) (Braun et al. 2019). The additional phylogenetic analysis clearly illustrated that the identified fungus and G. bolayi were clustered in the same branch (Zhu et al. 2022a; Zhu et al. 2022b). To test pathogenicity, healthy V. persica plants were collected from the campus of Henan Normal University and leaf surfaces of three plants were inoculated by dusting fungal conidia from mildew-infested leaves using pressurized air. Three plants without inoculation served as a control. The spore-treated and non-treated plants were separately placed in two growth chambers (temperature, 18℃; humidity, 60%; light/dark, 16h/8h). Seven- to eight-days post-inoculation, pathogen signs were noticeable on inoculated plants, whereas control plants remained healthy. Similar results were obtained by conducting the pathogenicity assays twice. Therefore, based on the analysis, G. bolayi was identified and confirmed as the causal agent of the powdery mildew. This pathogen has been reported on V. persica in Iran (Golmohammadi et al. 2019). However, to our best knowledge, there is no report concerning the powdery mildew caused by G. bolayi on V. persica in China. Recently, G. bolayi was segregated from species clades of G. orontii complex (Braun et al. 2019). Our record of the molecular characterization of G. bolayi will support the further phylogeny and taxonomy analysis of the G. orontii complex. The sudden outbreak of powdery mildew caused by G. bolayi on V. persica may detract from plant health and ornamental value. The identification and confirmation of this disease expands the understanding of this causal agent and will offer support for future powdery mildew control.},
}
@article {pmid37162342,
year = {2023},
author = {Cruz-Paredes, C and Tájmel, D and Rousk, J},
title = {Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {5},
pages = {e0209022},
pmid = {37162342},
issn = {1098-5336},
mesh = {Temperature ; *Ecosystem ; Soil ; Soil Microbiology ; Climate Change ; Europe ; Carbon ; *Microbiota ; },
abstract = {Temperature is a major determinant of biological process rates, and microorganisms are key regulators of ecosystem carbon (C) dynamics. Temperature controls microbial rates of decomposition, and thus warming can stimulate C loss, creating positive feedback to climate change. If trait distributions that define temperature relationships of microbial communities can adapt to altered temperatures, they could modulate the strength of this feedback, but if this occurs remains unclear. In this study, we sampled soils from a latitudinal climate gradient across Europe. We established the temperature relationships of microbial growth and respiration rates and used these to investigate if and with what strength the community trait distributions for temperature were adapted to their local environment. Additionally, we sequenced bacterial and fungal amplicons to link the variance in community composition to changes in temperature traits. We found that microbial temperature trait distributions varied systematically with climate, suggesting that an increase in mean annual temperature (MAT) of 1°C will result in warm-shifted microbial temperature trait distributions equivalent to an increase in temperature minimum (Tmin) of 0.20°C for bacterial growth, 0.07°C for fungal growth, and 0.10°C for respiration. The temperature traits for bacterial growth were thus more responsive to warming than those for respiration and fungal growth. The microbial community composition also varied with temperature, enabling the interlinkage of taxonomic information with microbial temperature traits. Our work shows that the adaptation of microbial temperature trait distributions to a warming climate will affect the C-climate feedback, emphasizing the need to represent this to capture the microbial feedback to climate change. IMPORTANCE One of the largest uncertainties of global warming is if the microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades of research effort, the strength of this feedback to warming remains unknown. We here present evidence that microbial temperature relationships vary systematically with environmental temperatures along a climate gradient and use this information to forecast how microbial temperature traits will create feedback between the soil C cycle and climate warming. We show that the current use of a universal temperature sensitivity is insufficient to represent the microbial feedback to climate change and provide new estimates to replace this flawed assumption in Earth system models. We also demonstrate that temperature relationships for rates of microbial growth and respiration are differentially affected by warming, with stronger responses to warming for microbial growth (soil C formation) than for respiration (C loss from soil to atmosphere), which will affect the atmosphere-land C balance.},
}
@article {pmid37161621,
year = {2023},
author = {Talukdar, D and Bandopadhyay, P and Ray, Y and Paul, SR and Sarif, J and D'Rozario, R and Lahiri, A and Das, S and Bhowmick, D and Chatterjee, S and Das, B and Ganguly, D},
title = {Association of gut microbial dysbiosis with disease severity, response to therapy and disease outcomes in Indian patients with COVID-19.},
journal = {Gut pathogens},
volume = {15},
number = {1},
pages = {22},
pmid = {37161621},
issn = {1757-4749},
support = {BT/PR38173/MED/97/474/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; MLP-129//Council of Scientific and Industrial Research, India/ ; },
abstract = {BACKGROUND: Severe coronavirus disease 2019 (COVID-19) is associated with systemic hyper-inflammation. An adaptive interaction between gut microbiota and host immune systems is important for intestinal homeostasis and systemic immune regulation. The association of gut microbial composition and functions with COVID-19 disease severity is sparse, especially in India. We analysed faecal microbial diversity and abundances in a cohort of Indian COVID-19 patients to identify key signatures in the gut microbial ecology in patients with severe COVID-19 disease as well as in response to different therapies. The composition of the gut microbiome was characterized using 16Sr RNA gene sequences of genomic DNA extracted from faecal samples of 52 COVID-19 patients. Metabolic pathways across the groups were predicted using PICRUSt2. All statistical analyses were done using Vegan in the R environment. Plasma cytokine abundance at recruitment was measured in a multiplex assay.<br><br>RESULTS: The gut microbiome composition of mild and severe patients was found to be significantly different. Immunomodulatory commensals, viz. Lachnospiraceae family members and Bifidobacteria producing butyrate and short-chain fatty acids (SCFAs), were under represented in patients with severe COVID-19, with an increased abundance of opportunistic pathogens like Eggerthella. The higher abundance of Lachnoclostridium in severe disease was reduced in response to convalescent plasma therapy. Specific microbial genera showed distinctive trends in enriched metabolic pathways, strong correlations with blood plasma cytokine levels, and associative link to disease outcomes.<br><br>CONCLUSION: Our study indicates that, along with SARS-CoV-2, a dysbiotic gut microbial community may also play an important role in COVID-19 severity through modulation of host immune responses.},
}
@article {pmid37158858,
year = {2023},
author = {Bi, S and Lai, H and Guo, D and Yi, H and Li, H and Liu, X and Chen, Q and Chen, J and Zhang, Z and Wei, X and Li, G and Xin, G},
title = {The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {16},
pmid = {37158858},
issn = {2730-7182},
mesh = {Animals ; *Tilapia ; Fisheries ; Fusobacterium ; Fusobacteria ; Firmicutes ; *Microbiota/genetics ; *Verbenaceae ; Water ; },
abstract = {BACKGROUND: Artificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.<br><br>RESULTS: The results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats.&#xa0;In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.<br><br>CONCLUSIONS: This study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.},
}
@article {pmid37156959,
year = {2023},
author = {Banaszkiewicz, S and Tabiś, A and Wałecki, B and Łyżwińska, K and Bystroń, J and Bania, J},
title = {spa Types and Staphylococcal Enterotoxin Production of Staphylococcus aureus Isolated from Wild Boar.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2184-2191},
pmid = {37156959},
issn = {1432-184X},
mesh = {Animals ; Swine ; Humans ; *Staphylococcus aureus/genetics ; Enterotoxins/genetics ; Sus scrofa ; *Staphylococcal Infections/veterinary/epidemiology/microbiology ; },
abstract = {Little is known about the structure of S. aureus population and the enterotoxin gene content in wild boar. In 1025 nasal swabs from wild boars, 121 S. aureus isolates were identified. Staphylococcal enterotoxin (SE) genes were identified in 18 isolates (14.9%). The seb gene was found in 2 S. aureus isolates, sec in 2 isolates, the see and seh genes were found in 4 and 11 isolates, respectively. The production of SEs was evaluated in bacteria grown in microbial broth. Concentration of SEB reached 2.70 µg/ml after 24 h and 4.46 µg/ml at 48 h. SEC was produced at 952.6 ng/ml after 24 h and 7.2 µg/ml at 48 h. SEE reached 124.1 ng/ml after 24 h and 191.6 ng/ml at 48 h of culture. SEH production reached 4.36 µg/ml at 24 h and 5.42 µg/ml at 48 h of culture. Thirty-nine spa types were identified among S. aureus isolates. The most prevalent spa types were t091 and t1181, followed by t4735 and t742, t3380 and t127. Twelve new spa types, i.e., t20572‒t20583 were identified. The wild boar S. aureus population was shown to contain previously identified animal/human-associated spa types and spa types not identified in humans or animals. We also indicate that wildlife animals can be a significant reservoir of see-positive S. aureus.},
}
@article {pmid37155494,
year = {2023},
author = {Gomez-Alvarez, V and Siponen, S and Kauppinen, A and Hokajärvi, AM and Tiwari, A and Sarekoski, A and Miettinen, IT and Torvinen, E and Pitkänen, T},
title = {A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland.},
journal = {Water research},
volume = {229},
number = {},
pages = {119495},
pmid = {37155494},
issn = {1879-2448},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
mesh = {Metagenome ; *Drinking Water/microbiology ; Finland ; Bacteria/metabolism ; *Microbiota/genetics ; Archaea/genetics ; *Disinfectants ; Metagenomics ; },
abstract = {The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.},
}
@article {pmid37154919,
year = {2023},
author = {Pan, Q and Shikano, I and Liu, TX and Felton, GW},
title = {Helicoverpa zea-Associated Gut Bacteria as Drivers in Shaping Plant Anti-herbivore Defense in Tomato.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2173-2182},
pmid = {37154919},
issn = {1432-184X},
mesh = {Humans ; Animals ; *Solanum lycopersicum ; Zea mays ; Plant Defense Against Herbivory ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Moths ; Larva/microbiology ; Bacteria/genetics ; Enterobacteriaceae ; Herbivory ; },
abstract = {Insect-associated bacteria can mediate the intersection of insect and plant immunity. In this study, we aimed to evaluate the effects of single isolates or communities of gut-associated bacteria of Helicoverpa zea larvae on herbivore-induced defenses in tomato. We first identified bacterial isolates from the regurgitant of field-collected H. zea larvae by using a culture-dependent method and 16S rRNA gene sequencing. We identified 11 isolates belonging to the families Enterobacteriaceae, Streptococcaceae, Yersiniaceae, Erwiniaceae, and unclassified Enterobacterales. Seven different bacterial isolates, namely Enterobacteriaceae-1, Lactococcus sp., Klebsiella sp. 1, Klebsiella sp. 3, Enterobacterales, Enterobacteriaceae-2, and Pantoea sp., were selected based on their phylogenetic relationships to test their impacts on insect-induced plant defenses. We found that the laboratory population of H. zea larvae inoculated with individual isolates did not induce plant anti-herbivore defenses, whereas larvae inoculated with a bacterial community (combination of the 7 bacterial isolates) triggered increased polyphenol oxidase (PPO) activity in tomato, leading to retarded larval development. Additionally, field-collected H. zea larvae with an unaltered bacterial community in their gut stimulated higher plant defenses than the larvae with a reduced gut microbial community. In summary, our findings highlight the importance of the gut microbial community in mediating interactions between herbivores and their host plants.},
}
@article {pmid37150906,
year = {2023},
author = {Rasmussen, TS and Mentzel, CMJ and Danielsen, MR and Jakobsen, RR and Zachariassen, LSF and Castro Mejia, JL and Brunse, A and Hansen, LH and Hansen, CHF and Hansen, AK and Nielsen, DS},
title = {Fecal virome transfer improves proliferation of commensal gut Akkermansia muciniphila and unexpectedly enhances the fertility rate in laboratory mice.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2208504},
pmid = {37150906},
issn = {1949-0984},
mesh = {Pregnancy ; Male ; Humans ; Female ; Mice ; Animals ; Infant ; *Gastrointestinal Microbiome ; Virome ; Birth Rate ; Mice, Inbred C57BL ; Verrucomicrobia ; Feces ; Cell Proliferation ; },
abstract = {Probiotics are intended to improve gastrointestinal health when consumed. However, the probiotics marketed today only colonize the densely populated gut to a limited extent. Bacteriophages comprise the majority of viruses in the human gut virome and there are strong indications that they play important roles in shaping the gut microbiome. Here, we investigate the use of fecal virome transplantation (FVT, sterile filtrated feces) as a mean to alter the gut microbiome composition to lead the way for persistent colonization of two types of probiotics: Lacticaseibacillus rhamnosus GG (LGG) representing a well-established probiotic and Akkermansia muciniphila (AKM) representing a putative next-generation probiotic. Male and female C57BL/6NTac mice were cohoused in pairs from 4 weeks of age and received the following treatment by oral gavage at week 5 and 6: AKM+FVT, LGG+FVT, probiotic sham (Pro-sham)+FVT, LGG+Saline, AKM+Saline, and control (Pro-sham+Saline). The FVT donor material originated from mice with high relative abundance of A. muciniphila. All animals were terminated at age 9 weeks. The FVT treatment did not increase the relative abundance of the administered LGG or AKM in the recipient mice. Instead FVT significantly (p < 0.05) increased the abundance of naturally occurring A. muciniphila compared to the control. This highlights the potential of propagating the existing commensal "probiotics" that have already permanently colonized the gut. Being co-housed male and female, a fraction of the female mice became pregnant. Unexpectedly, the FVT treated mice were found to have a significantly (p < 0.05) higher fertility rate independent of probiotic administration. These preliminary observations urge for follow-up studies investigating interactions between the gut microbiome and fertility.},
}
@article {pmid37150044,
year = {2023},
author = {Hu, D and Li, S and Liu, X and Liu, H and Liu, G},
title = {Kinetic model derivation for design, building and operation of solid waste treatment unit based on system dynamics and computer simulation.},
journal = {Waste management (New York, N.Y.)},
volume = {166},
number = {},
pages = {58-69},
doi = {10.1016/j.wasman.2023.04.037},
pmid = {37150044},
issn = {1879-2456},
mesh = {Solid Waste/analysis ; Computer Simulation ; Conservation of Natural Resources ; Models, Theoretical ; Ecosystem ; *Refuse Disposal ; *Waste Management ; },
abstract = {Solid waste disposal is significantly important to maintaining normal operation of both natural and artificial ecosystems. In this study, a kinetic model of solid waste treatment unit (SWTU) was upfront developed based on microbial ecology, system dynamics, cybernetics and digital simulation, which accurately described the relationships and interactions between solid waste decomposition (SWD) processes and biotic/abiotic factors. Then a specific SWTU prototype was designed and built from this kinetic model. A 370-day experiment demonstrated that SWTU maintained normal operation with robust stability and desired dynamic behaviors, and effectively disposed the solid waste. Therefore, this kinetic model was highly valid due to its high structural and behavioral similarity with the prototype. This research could lay a strong theoretical foundation for further closed-loop control as well as optimization of SWTU, and provide scientific guidance to environmental management as well as sustainable development.},
}
@article {pmid37149807,
year = {2023},
author = {Pjevac, P and Bartosik, T and Schneider, S and Eckl-Dorna, J},
title = {Pitfalls in sampling and analyzing low-biomass human nasal microbiome samples.},
journal = {The Journal of allergy and clinical immunology},
volume = {152},
number = {1},
pages = {304},
doi = {10.1016/j.jaci.2023.04.001},
pmid = {37149807},
issn = {1097-6825},
mesh = {Humans ; Biomass ; *Nose ; *Microbiota ; Specimen Handling ; RNA, Ribosomal, 16S ; },
}
@article {pmid37149500,
year = {2023},
author = {Kharshandi, F and Kayang, H},
title = {Antagonistic potential of rhizobacterial isolates against fungal pathogens causing rhizome rot in turmeric.},
journal = {Archives of microbiology},
volume = {205},
number = {6},
pages = {221},
pmid = {37149500},
issn = {1432-072X},
support = {(332490, Ref.No:20/12/2015(ii)EU-V))//University Grants Commission, India/ ; },
mesh = {*Rhizome/microbiology ; *Curcuma/microbiology ; Plant Diseases/prevention &amp; control/microbiology ; Antifungal Agents/pharmacology ; Bacteria ; },
abstract = {The study aims to select potent bacterial antagonists to be used as biocontrol agents against rhizome rot disease in turmeric (Curcuma longa L.). A total of 48 bacterial isolates were isolated from the rhizosphere of turmeric. These isolates were screened for their in vitro antagonism against Fusarium solani FS-01 and Pythium aphanidermatum (ITCC 7908). Production of volatile organic compounds and chitinase activity were also performed. Among the tested isolates, two bacterial isolates (IJ2 and IJ10) showed the highest inhibitory activity against these fungal pathogens. GC/MS analysis of the crude extract produced by Pseudomonas sp. IJ2 and B. subtilis IJ10 was found to contain many bioactive compounds with antifungal and antimicrobial activities. The rhizome treatment with these isolates exhibited the lowest percent disease severity with high biocontrol efficacy against the tested pathogens. These isolates with promising antagonistic potential, therefore, can be used as biocontrol agents against rhizome rot in turmeric.},
}
@article {pmid37149269,
year = {2023},
author = {Li, Y and Kuramae, EE and Nasir, F and Wang, E and Zhang, Z and Li, J and Yao, Z and Tian, L and Sun, Y and Luo, S and Guo, L and Ren, G and Tian, C},
title = {Addition of cellulose degrading bacterial agents promoting keystone fungal-mediated cellulose degradation during aerobic composting: Construction the complex co-degradation system.},
journal = {Bioresource technology},
volume = {381},
number = {},
pages = {129132},
doi = {10.1016/j.biortech.2023.129132},
pmid = {37149269},
issn = {1873-2976},
mesh = {Animals ; Cattle ; *Cellulose/metabolism ; *Composting ; Agriculture ; Soil ; Bacillus subtilis/metabolism ; Manure/microbiology ; },
abstract = {To excavate a complex co-degradation system for decomposing cellulose more efficiently, cellulose-degrading bacteria, including Bacillus subtilis WF-8, Bacillus licheniformis WF-11, Bacillus Cereus WS-1 and Streptomyces Nogalater WF-10 were added during maize straw and cattle manure aerobic composting. Bacillus and Streptomyces successfully colonized, which improve cellulose degrading ability. Continuous colonization of cellulose-degrading bacteria can promote the fungi to produce more precursors for humus and promote the negative correlation with Ascomycota. In the current study, the addition of cellulose-degrading bacteria has resulted in the rapid development of Mycothermus and Remersonia in the phylum Ascomycota as keystone fungal genera which constitute the foundation of the co-degradation system. Network analysis reveals the complex co-degradation system of efficient cellulose bacteria and mature fungi to treat cellulose in the process of straw aerobic composting mainly related to the influence of total carbon (TC) /total nitrogen (TN) and humic acid (HA)/fulvic acid (FA). This research offers a complex co-degradation system more efficiently to decompose cellulose aiming to maintain the long-term sustainability of agriculture.},
}
@article {pmid37148310,
year = {2023},
author = {Burgess, WL and Bishop, CD},
title = {Bacterial Diversity in Egg Capsular Fluid of the Spotted Salamander Ambystoma maculatum Decreases with Embryonic Development.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1789-1798},
pmid = {37148310},
issn = {1432-184X},
support = {RGPIN-2015-05040//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Ambystoma ; Capsules ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; Embryonic Development ; },
abstract = {Egg capsules within egg masses of the spotted salamander Ambystoma maculatum host a symbiosis with the unicellular green alga Oophila amblystomatis. However, this alga is not the only microbe to inhabit those capsules, and the significance of these additional taxa for the symbiosis is unknown. Spatial and temporal patterns of bacterial diversity in egg capsules of A. maculatum have recently begun to be characterized, but patterns of bacterial diversity as a function of embryonic development are unknown. We sampled fluid from individual capsules in egg masses over a large range of host embryonic development in 2019 and 2020. We used 16S rRNA gene amplicon sequencing to examine how diversity and relative abundance of bacteria changed with embryonic development. In general, bacterial diversity decreased as embryos developed; significant differences were observed (depending on the metric) by embryonic development, pond, and year, and there were interaction effects. The function of bacteria in what is thought of as a bipartite symbiosis calls for further research.},
}
@article {pmid37148309,
year = {2023},
author = {Gazulla, CR and Cabello, AM and Sánchez, P and Gasol, JM and Sánchez, O and Ferrera, I},
title = {A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2161-2172},
pmid = {37148309},
issn = {1432-184X},
support = {CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; PID2019-110128RB-I00/AEI/10.13039/501100011033//Agencia Estatal de Investigaci&#xf3;n/ ; },
mesh = {Phylogeny ; Metagenomics ; Bacterial Proteins/genetics ; *Gammaproteobacteria ; *Alphaproteobacteria/genetics ; },
abstract = {Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes.},
}
@article {pmid37146562,
year = {2023},
author = {Todorović, I and Abrouk, D and Kyselková, M and Lavire, C and Rey, M and Raičević, V and Jovičić-Petrović, J and Moënne-Loccoz, Y and Muller, D},
title = {Two novel species isolated from wheat rhizospheres in Serbia: Pseudomonas serbica sp. nov. and Pseudomonas serboccidentalis sp. nov.},
journal = {Systematic and applied microbiology},
volume = {46},
number = {4},
pages = {126425},
doi = {10.1016/j.syapm.2023.126425},
pmid = {37146562},
issn = {1618-0984},
mesh = {*Pseudomonas ; *Triticum/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Serbia ; Rhizosphere ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Bacterial Typing Techniques ; Nucleic Acid Hybridization ; },
abstract = {Pseudomonas strains IT-194P, IT-215P, IT-P366[T] and IT-P374[T] were isolated from the rhizospheres of wheat grown in soils sampled from different fields (some of them known to be disease-suppressive) located near Mionica, Serbia. Phylogenetic analysis of the 16S rRNA genes and of whole genome sequences showed that these strains belong to two potentially new species, one containing strains IT-P366[T] and IT-194P and clustering (whole genome analysis) next to P. umsongensis DSM16611[T], and another species containing strains IT-P374[T] and IT-215P and clustering next to P. koreensis LMG21318[T]. Genome analysis confirmed the proposition of novel species, as ANI was below the threshold of 95% and dDDH below 70% for strains IT-P366[T] (compared with P. umsongensis DSM16611[T]) and IT-P374[T] (compared with P. koreensis LMG21318[T]). Unlike P. umsongensis DSM16611[T], strains of P. serbica can grow on D-mannitol, but not on pectin, D-galacturonic acid, L-galactonic acid lactone and α-hydroxybutyric acid. In contrary to P. koreensis LMG21318[T], strains of P. serboccidentalis can use sucrose, inosine and α-ketoglutaric acid (but not L-histidine) as carbon sources. Altogether, these results indicate the existence of two novel species for which we propose the names Pseudomonas serbica sp. nov., with the type strain IT-P366[T] (=CFBP 9060 [T] = LMG 32732 [T] = EML 1791 [T]) and Pseudomonas serboccidentalis sp. nov., with the type strain IT-P374[T] (=CFBP 9061 [T] = LMG 32734 [T] = EML 1792 [T]). Strains from this study presented a set of phytobeneficial functions modulating plant hormonal balance, plant nutrition and plant protection, suggesting a potential as Plant Growth-Promoting Rhizobacteria (PGPR).},
}
@article {pmid37145936,
year = {2023},
author = {Fiskal, A and Shuster, J and Fischer, S and Joshi, P and Raghunatha Reddy, L and Wulf, SE and Kappler, A and Fischer, H and Herrig, I and Meier, J},
title = {Microbially influenced corrosion and rust tubercle formation on sheet piles in freshwater systems.},
journal = {Environmental microbiology},
volume = {25},
number = {10},
pages = {1796-1815},
doi = {10.1111/1462-2920.16393},
pmid = {37145936},
issn = {1462-2920},
mesh = {*Ferric Compounds ; Corrosion ; RNA, Ribosomal, 16S/genetics ; X-Ray Microtomography ; *Bacteria/genetics ; Minerals ; Fresh Water ; Oxidation-Reduction ; },
abstract = {The extent of how complex natural microbial communities contribute to metal corrosion is still not fully resolved, especially not for freshwater environments. In order to elucidate the key processes, we investigated rust tubercles forming massively on sheet piles along the river Havel (Germany) applying a complementary set of techniques. In-situ microsensor profiling revealed steep gradients of O2 , redox potential and pH within the tubercle. Micro-computed tomography and scanning electron microscopy showed a multi-layered inner structure with chambers and channels and various organisms embedded in the mineral matrix. Using Mössbauer spectroscopy we identified typical corrosion products including electrically conductive iron (Fe) minerals. Determination of bacterial gene copy numbers and sequencing of 16S rRNA and 18S rRNA amplicons supported a densely populated tubercle matrix with a phylogenetically and metabolically diverse microbial community. Based on our results and previous models of physic(electro)chemical reactions, we propose here a comprehensive concept of tubercle formation highlighting the crucial reactions and microorganisms involved (such as phototrophs, fermenting bacteria, dissimilatory sulphate and Fe(III) reducers) in metal corrosion in freshwaters.},
}
@article {pmid37142893,
year = {2023},
author = {Paul, P and Sarkar, S and Dastidar, DG and Shukla, A and Das, S and Chatterjee, S and Chakraborty, P and Tribedi, P},
title = {1, 4-naphthoquinone efficiently facilitates the disintegration of pre-existing biofilm of Staphylococcus aureus through eDNA intercalation.},
journal = {Folia microbiologica},
volume = {68},
number = {6},
pages = {843-854},
pmid = {37142893},
issn = {1874-9356},
mesh = {Humans ; Staphylococcus aureus/genetics ; Ethidium/pharmacology ; *Naphthoquinones/pharmacology ; DNA/pharmacology ; Biofilms ; *Staphylococcal Infections ; },
abstract = {1, 4-naphthoquinone, a plant-based quinone derivative, has gained much attention for its effectiveness against several biofilm-linked diseases. The biofilm inhibitory effect of 1, 4-naphthoquinone against Staphylococcus aureus has already been reported in our previous study. We observed that the extracellular DNA (eDNA) could play an important role in holding the structural integrity of the biofilm. Hence, in this study, efforts have been directed to examine the possible interactions between 1, 4-naphthoquinone and DNA. An in silico analysis indicated that 1, 4-naphthoquinone could interact with DNA through intercalation. To validate the same, UV-Vis spectrophotometric analysis was performed in which a hypochromic shift was observed when the said molecule was titrated with calf-thymus DNA (CT-DNA). Thermal denaturation studies revealed a change of 8℃ in the melting temperature (Tm) of CT-DNA when complexed with 1, 4-naphthoquinone. The isothermal calorimetric titration (ITC) assay revealed a spontaneous intercalation between CT-DNA and 1, 4-naphthoquinone with a binding constant of 0.95 ± 0.12 × 10[8]. Furthermore, DNA was run through an agarose gel electrophoresis with a fixed concentration of ethidium bromide and increasing concentrations of 1, 4-naphthoquinone. The result showed that the intensity of ethidium bromide-stained DNA got reduced concomitantly with the gradual increase of 1, 4-naphthoquinone suggesting its intercalating nature. To gain further confidence, the pre-existing biofilm was challenged with ethidium bromide wherein we observed that it could also show biofilm disintegration. Therefore, the results suggested that 1, 4-naphthoquinone could exhibit disintegration of the pre-existing biofilm of Staphylococcus aureus through eDNA intercalation.},
}
@article {pmid37142736,
year = {2023},
author = {Mukorako, P and St-Pierre, DH and Flamand, N and Biertho, L and Lebel, S and Lemoine, N and Plamondon, J and Roy, MC and Tchernof, A and Varin, TV and Marette, A and Silvestri, C and Di Marzo, V and Richard, D},
title = {Hypoabsorptive surgeries cause limb-dependent changes in the gut endocannabinoidome and microbiome in association with beneficial metabolic effects.},
journal = {International journal of obesity (2005)},
volume = {47},
number = {7},
pages = {630-641},
pmid = {37142736},
issn = {1476-5497},
mesh = {Male ; Rats ; Animals ; Rats, Wistar ; Chromatography, Liquid ; RNA, Ribosomal, 16S ; Tandem Mass Spectrometry ; *Biliopancreatic Diversion/methods ; Duodenum/surgery ; *Gastrointestinal Hormones ; *Gastrointestinal Microbiome ; Gastrectomy ; Tyrosine ; *Obesity, Morbid/surgery ; *Gastric Bypass/methods ; Retrospective Studies ; },
abstract = {OBJECTIVE: To determine whether the metabolic benefits of hypoabsorptive surgeries are associated with changes in the gut endocannabinoidome (eCBome) and microbiome.<br><br>METHODS: Biliopancreatic diversion with duodenal switch (BPD-DS) and single anastomosis duodeno-ileal bypass with sleeve gastrectomy (SADI-S) were performed in diet-induced obese (DIO) male Wistar rats. Control groups fed a high-fat diet (HF) included sham-operated (SHAM HF) and SHAM HF-pair-weighed to BPD-DS (SHAM HF-PW). Body weight, fat mass gain, fecal energy loss, HOMA-IR, and gut-secreted hormone levels were measured. The levels of eCBome lipid mediators and prostaglandins were quantified in different intestinal segments by LC-MS/MS, while expression levels of genes encoding eCBome metabolic enzymes and receptors were determined by RT-qPCR. Metataxonomic (16S rRNA) analysis was performed on residual distal jejunum, proximal jejunum, and ileum contents.<br><br>RESULTS: BPD-DS and SADI-S reduced fat gain and HOMA-IR, while increasing glucagon-like peptide-1 (GLP-1) and peptide tyrosine tyrosine (PYY) levels in HF-fed rats. Both surgeries induced potent limb-dependent alterations in eCBome mediators and in gut microbial ecology. In response to BPD-DS and SADI-S, changes in gut microbiota were significantly correlated with those of eCBome mediators. Principal component analyses revealed connections between PYY, N-oleoylethanolamine (OEA), N-linoleoylethanolamine (LEA), Clostridium, and Enterobacteriaceae_g_2 in the proximal and distal jejunum and in the ileum.<br><br>CONCLUSIONS: BPD-DS and SADI-S caused limb-dependent changes in the gut eCBome and microbiome. The present results indicate that these variables could significantly influence the beneficial metabolic outcome of hypoabsorptive bariatric surgeries.},
}
@article {pmid37138640,
year = {2023},
author = {Sorouri, B and Rodriguez, CI and Gaut, BS and Allison, SD},
title = {Variation in Sphingomonas traits across habitats and phylogenetic clades.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1146165},
pmid = {37138640},
issn = {1664-302X},
abstract = {Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.},
}
@article {pmid37138619,
year = {2023},
author = {Yin, H and Zhao, M and Pan, G and Zhang, H and Yang, R and Sun, J and Yu, Z and Bai, C and Xue, Y},
title = {Effects of Bacillus subtilis or Lentilactobacillus buchneri on aerobic stability, and the microbial community in aerobic exposure of whole plant corn silage.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1177031},
pmid = {37138619},
issn = {1664-302X},
abstract = {This study aimed to evaluate the effects of Bacillus subtilis or Lentilactobacillus buchneri on the fermentation quality, aerobic stability, and bacterial and fungal communities of whole plant corn silage during aerobic exposure. Whole plant corn was harvested at the wax maturity stage, which chopped to a length of approximately 1 cm, and treated with the following: distilled sterile water control, 2.0 × 10[5] CFU/g of Lentilactobacillus buchneri (LB) or 2.0 × 10[5] CFU/g of Bacillus subtilis (BS) for 42 days silage. Then, the samples were exposed to air (23-28[°]C) after opening and sampled at 0, 18 and 60 h, to investigate fermentation quality, bacterial and fungal communities, and aerobic stability. Inoculation with LB or BS increased the pH value, acetic acid, and ammonia nitrogen content of silage (P < 0.05), but it was still far below the threshold of inferior silage, the yield of ethanol was reduced (P < 0.05), and satisfactory fermentation quality was achieved. With the extension of the aerobic exposure time, inoculation with LB or BS prolonged the aerobic stabilization time of silage, attenuated the trend of pH increase during aerobic exposure, and increased the residues of lactic acid and acetic acid. The bacterial and fungal alpha diversity indices gradually declined, and the relative abundance of Basidiomycota and Kazachstania gradually increased. The relative abundance of Weissella and unclassified_f_Enterobacteria was higher and the relative abundance of Kazachstania was lower after inoculation with BS compared to the CK group. According to the correlation analysis, Bacillus and Kazachstania are bacteria and fungi that are more closely related to aerobic spoilage and inoculation with LB or BS could inhibit spoilage. The FUNGuild predictive analysis indicated that the higher relative abundance of fungal parasite-undefined saprotroph in the LB or BS groups at AS2, may account for its good aerobic stability. In conclusion, silage inoculated with LB or BS had better fermentation quality and improved aerobic stability by effectively inhibiting the microorganisms that induce aerobic spoilage.},
}
@article {pmid37133496,
year = {2023},
author = {Donohue, ME and Hert, ZL and Karrick, CE and Rowe, AK and Wright, PC and Randriamanandaza, LJ and Zakamanana, F and Nomenjanahary, ES and Everson, KM and Weisrock, DW},
title = {Lemur Gut Microeukaryotic Community Variation Is Not Associated with Host Phylogeny, Diet, or Habitat.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2149-2160},
pmid = {37133496},
issn = {1432-184X},
mesh = {Animals ; Phylogeny ; *Lemur ; RNA, Ribosomal, 16S/genetics ; Diet/veterinary ; *Microbiota ; },
abstract = {Identifying the major forces driving variation in gut microbiomes enhances our understanding of how and why symbioses between hosts and microbes evolved. Gut prokaryotic community variation is often closely associated with host evolutionary and ecological variables. Whether these same factors drive variation in other microbial taxa occupying the animal gut remains largely untested. Here, we present a one-to-one comparison of gut prokaryotic (16S rRNA metabarcoding) and microeukaryotic (18S rRNA metabarcoding) community patterning among 12 species of wild lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological niche diversity. We found that while lemur gut prokaryotic community diversity and composition vary with host taxonomy, diet, and habitat, gut microeukaryotic communities have no detectable association with any of these factors. We conclude that gut microeukaryotic community composition is largely random, while gut prokaryotic communities are conserved among host species. It is likely that a greater proportion of gut microeukaryotic communities comprise taxa with commensal, transient, and/or parasitic symbioses compared with gut prokaryotes, many of which form long-term relationships with the host and perform important biological functions. Our study highlights the importance of greater specificity in microbiome research; the gut microbiome contains many "omes" (e.g., prokaryome, eukaryome), each comprising different microbial taxa shaped by unique selective pressures.},
}
@article {pmid37133495,
year = {2023},
author = {Saikrishna, K and Talukdar, D and Das, S and Bakshi, S and Chakravarti, P and Jana, P and Karmakar, S and Wig, N and Das, B and Ray, A},
title = {Study on Effects of Probiotics on Gut Microbiome and Clinical Course in Patients with Critical Care Illnesses.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1814-1828},
pmid = {37133495},
issn = {1432-184X},
support = {5/9/1208/2019-Nut, Dt. 16.09.2019//Indian Council of Medical Research/ ; No. BT/PR30159/MED/15/188/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Probiotics/therapeutic use ; Critical Care ; Disease Progression ; },
abstract = {Ventilator-associated pneumonia (VAP) is a nosocomial infection contracted by ventilator patients in which bacteria colonize the upper digestive tract and contaminated secretions are released into the lower airway. This nosocomial infection increases the morbidity and mortality of the patients as well as the cost of treatment. Probiotic formulations have recently been proposed to prevent the colonization of these pathogenic bacteria. In this prospective observational study, we aimed to investigate the effects of probiotics on gut microbiota and their relation to clinical outcomes in mechanically ventilated patients. For this study, 35 patients were recruited (22 probiotic-treated and 13 without probiotic treatment) from a cohort of 169 patients. Patients in the probiotic group were given a dose of 6 capsules of a commercially available probiotic (VSL#3®:112.5 billion CFU/cap) in three divided doses for 10 days. Sampling was carried out after each dose to monitor the temporal change in the gut microbiota composition. To profile the microbiota, we used a 16S rRNA metagenomic approach, and differences among the groups were computed using multivariate statistical analyses. Differences in gut microbial diversity (Bray Curtis and Jaccard distance, p-value > 0.05) between the probiotic-treated group and the control group were not observed. Furthermore, treatment with probiotics resulted in the enrichment of Lactobacillus and Streptococcus in the gut microbiota of the probiotic-treated groups. Our results demonstrated that probiotics might lead to favorable alterations in gut microbiome characteristics. Future studies should focus on the appropriate dosages and frequency of probiotics, which can lead to improved clinical outcomes.},
}
@article {pmid37131715,
year = {2023},
author = {Wu, L and Wang, XW and Tao, Z and Wang, T and Zuo, W and Zeng, Y and Liu, YY and Dai, L},
title = {Data-driven prediction of colonization outcomes for complex microbial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.04.19.537502},
pmid = {37131715},
issn = {2692-8205},
abstract = {Complex microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse physical, biochemical, and ecological processes governing microbial dynamics. Here, we proposed a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validated this approach using synthetic data, finding that machine learning models (including Random Forest and neural ODE) can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conducted colonization experiments for two commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approach can successfully predict the colonization outcomes. Furthermore, we found that while most resident species were predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., the presence of Enterococcus faecalis inhibits the invasion of E. faecium . The presented results suggest that the data-driven approach is a powerful tool to inform the ecology and management of complex microbial communities.},
}
@article {pmid37130890,
year = {2023},
author = {Onyango, LA and Ngonga, FA and Karanja, EN and Kuja, JO and Boga, HI and Cowan, DA and Mwangi, KW and Maghenda, MW and Marinho Lebre, PBN and Kambura, AK},
title = {The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {7156},
pmid = {37130890},
issn = {2045-2322},
mesh = {Kenya ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Forests ; Bacteria/genetics ; Archaea/genetics ; *Microbiota/genetics ; Soil Microbiology ; },
abstract = {Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.},
}
@article {pmid37129484,
year = {2023},
author = {Farr, AD and Pesce, D and Das, SG and Zwart, MP and de Visser, JAGM},
title = {The Fitness of Beta-Lactamase Mutants Depends Nonlinearly on Resistance Level at Sublethal Antibiotic Concentrations.},
journal = {mBio},
volume = {14},
number = {3},
pages = {e0009823},
pmid = {37129484},
issn = {2150-7511},
mesh = {*Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; Cefotaxime/pharmacology ; Drug Resistance, Microbial/genetics ; Selection, Genetic ; Mutation ; },
abstract = {Adaptive evolutionary processes are constrained by the availability of mutations which cause a fitness benefit and together make up the fitness landscape, which maps genotype space onto fitness under specified conditions. Experimentally derived fitness landscapes have demonstrated a predictability to evolution by identifying limited "mutational routes" that evolution by natural selection may take between low and high-fitness genotypes. However, such studies often utilize indirect measures to determine fitness. We estimated the competitive fitness of mutants relative to all single-mutation neighbors to describe the fitness landscape of three mutations in a β-lactamase enzyme. Fitness assays were performed at sublethal concentrations of the antibiotic cefotaxime in a structured and unstructured environment. In the unstructured environment, the antibiotic selected for higher-resistance types-but with an equivalent fitness for a subset of mutants, despite substantial variation in resistance-resulting in a stratified fitness landscape. In contrast, in a structured environment with a low antibiotic concentration, antibiotic-susceptible genotypes had a relative fitness advantage, which was associated with antibiotic-induced filamentation. These results cast doubt that highly resistant genotypes have a unique selective advantage in environments with subinhibitory concentrations of antibiotics and demonstrate that direct fitness measures are required for meaningful predictions of the accessibility of evolutionary routes. IMPORTANCE The evolution of antibiotic-resistant bacterial populations underpins the ongoing antibiotic resistance crisis. We aim to understand how antibiotic-degrading enzymes can evolve to cause increased resistance, how this process is constrained, and whether it can be predictable. To this end, competition experiments were performed with a combinatorially complete set of mutants of a β-lactamase gene subject to subinhibitory concentrations of the antibiotic cefotaxime. While some mutations confer on their hosts high resistance to cefotaxime, in competition these mutations do not always confer a selective advantage. Specifically, high-resistance mutants had equivalent fitnesses despite different resistance levels and even had selective disadvantages under conditions involving spatial structure. Together, our findings suggest that the relationship between resistance level and fitness at subinhibitory concentrations is complex; predicting the evolution of antibiotic resistance requires knowledge of the conditions that select for resistant genotypes and the selective advantage evolved types have over their predecessors.},
}
@article {pmid37127597,
year = {2023},
author = {Mosquera, KD and Nilsson, LKJ and de Oliveira, MR and Rocha, EM and Marinotti, O and Håkansson, S and Tadei, WP and de Souza, AQL and Terenius, O},
title = {Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {156},
pmid = {37127597},
issn = {1756-3305},
support = {348-2012-622//Swedish Research Council/ ; },
mesh = {Animals ; *Anopheles/genetics ; *Malaria ; Brazil ; Mosquito Vectors ; RNA, Ribosomal, 16S ; Larva ; *Microbiota ; Bacteria ; Water ; },
abstract = {BACKGROUND: The neotropical anopheline mosquito Anopheles darlingi is a major malaria vector in the Americas. Studies on mosquito-associated microbiota have shown that symbiotic bacteria play a major role in host biology. Mosquitoes acquire and transmit microorganisms over their life cycle. Specifically, the microbiota of immature forms is largely acquired from their aquatic environment. Therefore, our study aimed to describe the microbial communities associated with An. darlingi immature forms and their breeding sites in the Coari municipality, Brazilian Amazon.<br><br>METHODS: Larvae, pupae, and breeding water were collected in two different geographical locations. Samples were submitted for DNA extraction and high-throughput 16S rRNA gene sequencing was conducted. Microbial ecology analyses were performed to explore and compare the bacterial profiles of An. darlingi and their aquatic habitats.<br><br>RESULTS: We found lower richness and diversity in An. darlingi microbiota than in water samples, which suggests that larvae are colonized by a subset of the bacterial community present in their breeding sites. Moreover, the bacterial community composition of the immature mosquitoes and their breeding water differed according to their collection sites, i.e., the microbiota associated with An. darlingi reflected that in the aquatic habitats where they developed. The three most abundant bacterial classes across the An. darlingi samples were Betaproteobacteria, Clostridia, and Gammaproteobacteria, while across the water samples they were Gammaproteobacteria, Bacilli, and Alphaproteobacteria.<br><br>CONCLUSIONS: Our findings reinforce the current evidence that the environment strongly shapes the composition and diversity of mosquito microbiota. A better understanding of mosquito-microbe interactions will contribute to identifying microbial candidates impacting host fitness and disease transmission.},
}
@article {pmid37127168,
year = {2023},
author = {Liu, YC and Ramiro-Garcia, J and Paulo, LM and Braguglia, CM and Gagliano, MC and O'Flaherty, V},
title = {Psychrophilic and mesophilic anaerobic treatment of synthetic dairy wastewater with long chain fatty acids: Process performances and microbial community dynamics.},
journal = {Bioresource technology},
volume = {380},
number = {},
pages = {129124},
doi = {10.1016/j.biortech.2023.129124},
pmid = {37127168},
issn = {1873-2976},
mesh = {*Wastewater ; Anaerobiosis ; Sewage/microbiology ; Bioreactors/microbiology ; Fatty Acids ; *Microbiota ; Methane ; },
abstract = {Facilitating the anaerobic degradation of long chain fatty acids (LCFA) is the key to unlock the energy potential of lipids-rich wastewater. In this study, the feasibility of psychrophilic anaerobic treatment of LCFA-containing dairy wastewater was assessed and compared to mesophilic anaerobic treatment. The results showed that psychrophilic treatment at 15 ℃ was feasible for LCFA-containing dairy wastewater, with high removal rates of soluble COD (>90%) and LCFA (∼100%). However, efficient long-term treatment required prior acclimation of the biomass to psychrophilic temperatures. The microbial community analysis revealed that putative syntrophic fatty acid bacteria and Methanocorpusculum played a crucial role in LCFA degradation during both mesophilic and psychrophilic treatments. Additionally, a fungal-bacterial biofilm was found to be important during the psychrophilic treatment. Overall, these findings demonstrate the potential of psychrophilic anaerobic treatment for industrial wastewaters and highlight the importance of understanding the microbial communities involved in the process.},
}
@article {pmid37126126,
year = {2023},
author = {Kearns, PJ and Winter, AS and Woodhams, DC and Northup, DE},
title = {The Mycobiome of Bats in the American Southwest Is Structured by Geography, Bat Species, and Behavior.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1565-1574},
pmid = {37126126},
issn = {1432-184X},
support = {P14AC00793//Carlsbad, Caverns National Park (CAVE) Award/ ; P14AC00588//El Malpais National Monument award/ ; P12AC10812//Grand Canyon Parashant National Monument (PARA) Award/ ; TE-EAA-01222014//T and E/ ; 12516000000045//New Mexico Department of Game and Fish/ ; IOS-1845634//National Science Foundation/ ; },
mesh = {Animals ; *Mycobiome ; *Chiroptera/microbiology ; Fungi/genetics ; *Microbiota ; Geography ; },
abstract = {Bats are widespread mammals that play key roles in ecosystems as pollinators and insectivores. However, there is a paucity of information about bat-associated microbes, in particular their fungal communities, despite the important role microbes play in host health and overall host function. The emerging fungal disease, white-nose syndrome, presents a potential challenge to the bat microbiome and understanding healthy bat-associated taxa will provide valuable information about potential microbiome-pathogen interactions. To address this knowledge gap, we collected 174 bat fur/skin swabs from 14 species of bats captured in five locations in New Mexico and Arizona and used high-throughput sequencing of the fungal internal transcribed (ITS) region to characterize bat-associated fungal communities. Our results revealed a highly heterogeneous bat mycobiome that was structured by geography and bat species. Furthermore, our data suggest that bat-associated fungal communities are affected by bat foraging, indicating the bat skin microbiota is dynamic on short time scales. Finally, despite the strong effects of site and species, we found widespread and abundant taxa from several taxonomic groups including the genera Alternaria and Metschnikowia that have the potential to be inhibitory towards fungal and bacterial pathogens.},
}
@article {pmid37125162,
year = {2023},
author = {Miao, Y and Colosimo, F and Mouser, PJ and De Long, S and Hanson Rhoades, A},
title = {Editorial: Emerging microbiological processes and tools that shine in pilot- and field-scale environmental engineering applications.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1194772},
doi = {10.3389/fmicb.2023.1194772},
pmid = {37125162},
issn = {1664-302X},
}
@article {pmid37124757,
year = {2023},
author = {Esquivel-Hernández, DA and Martínez-López, YE and Sánchez-Castañeda, JP and Neri-Rosario, D and Padrón-Manrique, C and Giron-Villalobos, D and Mendoza-Ortíz, C and Resendis-Antonio, O},
title = {A network perspective on the ecology of gut microbiota and progression of type 2 diabetes: Linkages to keystone taxa in a Mexican cohort.},
journal = {Frontiers in endocrinology},
volume = {14},
number = {},
pages = {1128767},
pmid = {37124757},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology ; *Glucose Intolerance/epidemiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Glucose ; },
abstract = {INTRODUCTION: The human gut microbiota (GM) is a dynamic system which ecological interactions among the community members affect the host metabolism. Understanding the principles that rule the bidirectional communication between GM and its host, is one of the most valuable enterprise for uncovering how bacterial ecology influences the clinical variables in the host.<br><br>METHODS: Here, we used SparCC to infer association networks in 16S rRNA gene amplicon data from the GM of a cohort of Mexican patients with type 2 diabetes (T2D) in different stages: NG (normoglycemic), IFG (impaired fasting glucose), IGT (impaired glucose tolerance), IFG + IGT (impaired fasting glucose plus impaired glucose tolerance), T2D and T2D treated (T2D with a 5-year ongoing treatment).<br><br>RESULTS: By exploring the network topology from the different stages of T2D, we observed that, as the disease progress, the networks lose the association between bacteria. It suggests that the microbial community becomes highly sensitive to perturbations in individuals with T2D. With the purpose to identify those genera that guide this transition, we computationally found keystone taxa (driver nodes) and core genera for a Mexican T2D cohort. Altogether, we suggest a set of genera driving the progress of the T2D in a Mexican cohort, among them Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005, Alistipes, Anaerostipes, and Terrisporobacter.<br><br>DISCUSSION: Based on a network approach, this study suggests a set of genera that can serve as a potential biomarker to distinguish the distinct degree of advances in T2D for a Mexican cohort of patients. Beyond limiting our conclusion to one population, we present a computational pipeline to link ecological networks and clinical stages in T2D, and desirable aim to advance in the field of precision medicine.},
}
@article {pmid37120943,
year = {2023},
author = {Gounari, Z and Bonatsou, S and Ferrocino, I and Cocolin, L and Papadopoulou, OS and Panagou, EZ},
title = {Exploring yeast diversity of dry-salted naturally black olives from Greek retail outlets with culture dependent and independent molecular methods.},
journal = {International journal of food microbiology},
volume = {398},
number = {},
pages = {110226},
doi = {10.1016/j.ijfoodmicro.2023.110226},
pmid = {37120943},
issn = {1879-3460},
mesh = {*Sodium Chloride ; *Olea/chemistry ; Staphylococcus aureus ; Greece ; Food Microbiology ; Yeasts/genetics ; Enterobacteriaceae ; Fermentation ; },
abstract = {In the present study, the physicochemical (pH, water activity, moisture content, salt concentration) classical plate counts (total viable counts, yeasts, lactic acid bacteria, Staphylococcus aureus, Pseudomonas spp., Enterobacteriaceae) and amplicon sequencing of naturally black dry-salted olives obtained from different retail outlets of the Greek market were investigated. According to the results, the values of the physicochemical characteristics presented great variability among the samples. Specifically, pH and water activity (aw) values ranged between 4.0 and 5.0, as well as between 0.58 and 0.91, respectively. Moisture content varied between 17.3 and 56.7 % (g Η2Ο/100 g of olive pulp), whereas salt concentration ranged from 5.26 to 9.15 % (g NaCl/100 g of olive pulp). No lactic acid bacteria, S. aureus, Pseudomonas spp. and Enterobacteriaceae were detected. The mycobiota consisted of yeasts that were further characterized and identified by culture-dependent (rep-PCR, ITS-PCR, and RFLP) and amplicon target sequencing (ATS). Pichia membranifaciens, Candida sorbosivorans, Citeromyces nyonsensis, Candida etchelsii, Wickerhamomyces subpelliculosus, Candida apicola, Wickerhamomyces anomalus, Torulaspora delbrueckii and Candida versatilis were the dominant species according to ITS sequencing (culture-dependent), while ATS revealed the dominance of C. etchelsii, Pichia triangularis, P. membranifaciens, and C. versatilis among samples. The results of this study demonstrated considerable variability in quality attributes among the different commercial samples of dry-salted olives, reflecting a lack of standardization in the processing of this commercial style. However, the majority of the samples were characterized by satisfactory microbiological and hygienic quality and complied with the requirements of the trade standard for table olives of the International Olive Council (IOC) for this processing style in terms of salt concentration. In addition, the diversity of yeast species was elucidated for the first time in commercially available products, increasing our knowledge on the microbial ecology of this traditional food. Further investigation into the technological and multifunctional traits of the dominant yeast species may result in better control during dry-salting and enhance the quality and shelf-life of the final product.},
}
@article {pmid37119999,
year = {2023},
author = {Goswami, V and Deepika, S and Diwakar, S and Kothamasi, D},
title = {Arbuscular mycorrhizas amplify the risk of heavy metal transfer to human food chain from fly ash ameliorated agricultural soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {329},
number = {},
pages = {121733},
doi = {10.1016/j.envpol.2023.121733},
pmid = {37119999},
issn = {1873-6424},
mesh = {Humans ; *Mycorrhizae/chemistry ; Soil ; Coal Ash/analysis ; Food Chain ; Lead/analysis ; *Metals, Heavy/analysis ; Agriculture ; Plants ; *Environmental Pollutants/analysis ; *Soil Pollutants/analysis ; Plant Roots/chemistry ; },
abstract = {Soil contaminants threaten global food security by posing threats to food safety through food chain pollution. Fly ash is a potential agent of soil contamination that contains heavy metals and hazardous pollutants. However, being rich in macro- and micronutrients that have direct beneficial effects on plant growth, fly ash has been recommended as a low-cost soil ameliorant in agriculture in countries of the Global South. Arbuscular mycorrhizal fungi (AMF), ubiquitous in agricultural soils, enhance efficiency of plant nutrient uptake from soils but can equally increase uptake of toxic pollutants from fly ash ameliorated soils to edible crop tissues. We investigated AMF-mediated amplification of nutrient and heavy metal uptake from fly ash amended soils to shoots, roots and grains of barley. We used a microcosm-based experiment to analyse the impacts of fly ash amendments to soil in concentrations of 0 (control), 15, 30 or 50% respectively, on root colonization by AMF Rhizophagus irregularis and AMF-mediated transfer of N, P and heavy metals: Ni, Co, Pb and Cr to barley tissues. These concentrations of fly ash are equivalent to 0, 137, 275 and 458 t ha[-1] respectively, in soil. Root AMF colonization correlated negatively with fly ash concentration and was not detected at 50% fly ash amendment. Shoots, roots and grains of mycorrhizal barley grown with 15, 30 and 50% fly ash amendments had significantly higher concentrations of Ni, Co, Pb and Cr compared to the control and their respective non-mycorrhizal counterparts. Presence of heavy metals in barley plants grown with fly ash amended soil and their increased AMF-mediated translocation to edible grains may significantly enhance the volume of heavy metals entering the human food chain. We recommend careful assessment of manipulation of agricultural soils with fly ash as heavy metal accumulation in agricultural soils and human tissues may cause irreversible damage.},
}
@article {pmid37117817,
year = {2023},
author = {Woo, AYM and Aguilar Ramos, MA and Narayan, R and Richards-Corke, KC and Wang, ML and Sandoval-Espinola, WJ and Balskus, EP},
title = {Targeting the human gut microbiome with small-molecule inhibitors.},
journal = {Nature reviews. Chemistry},
volume = {7},
number = {5},
pages = {319-339},
pmid = {37117817},
issn = {2397-3358},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.},
}
@article {pmid37115262,
year = {2023},
author = {Camargo, TS and Nickele, MA and Filho, WR and do Rocio Chiarello Penteado, S and de Queiroz, EC and Auer, CG},
title = {Fungal Community Associated with the Leaf-Cutting Ant Acromyrmex crassispinus (Hymenoptera: Formicidae) Colonies: a Search for Potential Biocontrol Agents.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1281-1291},
pmid = {37115262},
issn = {1432-184X},
mesh = {Humans ; Animals ; *Ants/microbiology ; Fungi ; *Mycobiome ; Biological Control Agents ; *Penicillium ; Brazil ; Symbiosis ; },
abstract = {The leaf-cutting ant Acromyrmex crassispinus is considered an important pest in forest plantations in southern Brazil. This work aimed to study the fungal community associated with A. crassispinus colonies, subjected to treatments with subdoses of granulated baits (sulfluramid), which might reduce the ability of the ants to care for their symbiotic fungus and other fungi (maybe biocontrol fungi) would take over, to prospect for potential biological control agents. Samplings of fungus gardens and dead ants allowed the identification of 195 fungal isolates, distributed in 29 families, 36 genera, and 53 species. The most frequent genera were Trichoderma (49.2%), Penicillium (13.8%), Chaetomium (6.2%), and Fusarium (3.6%). This is the first study that conducted a survey of antagonistic and entomopathogenic fungi to A. crassispinus and its symbiotic fungus, reporting for the first time the occurrence of potential biological control agents. Escovopsis weberi, Fusarium oxysporum, Rhizomucor variabilis, Trichoderma atroviride, Trichoderma harzianum, Trichoderma koningiopsis, and Trichoderma spirale are considered some of the potential biocontrol organisms.},
}
@article {pmid37115261,
year = {2023},
author = {Djotan, AKG and Matsushita, N and Fukuda, K},
title = {Paired Root-Soil Samples and Metabarcoding Reveal Taxon-Based Colonization Strategies in Arbuscular Mycorrhizal Fungi Communities in Japanese Cedar and Cypress Stands.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2133-2146},
pmid = {37115261},
issn = {1432-184X},
mesh = {*Mycorrhizae/genetics ; *Cryptomeria ; *Cupressus ; Plant Roots/microbiology ; Fungi/genetics ; *Glomeromycota/genetics ; Soil ; Soil Microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) in the roots and soil surrounding their hosts are typically independently investigated and little is known of the relationships between the communities of the two compartments. We simultaneously collected root and surrounding soil samples from Cryptomeria japonica (Cj) and Chamaecyparis obtusa (Co) at three environmentally different sites. Based on molecular and morphological analyses, we characterized their associated AMF communities. Cj was more densely colonized than Co and that root colonization intensity was significantly correlated with soil AMF diversity. The communities comprised 15 AMF genera dominated by Glomus and Paraglomus and 1443 operational taxonomic units (OTUs) of which 1067 and 1170 were in roots and soil, respectively. AMF communities were significantly different among sites, and the root AMF communities were significantly different from those of soil at each site. The root and soil AMF communities responded differently to soil pH. At the genus level, Glomus and Acaulospora were abundant in roots while Paraglomus and Redeckera were abundant in soil. Our findings suggest that AMF colonizing roots are protected from environmental stresses in soil. However, the root-soil-abundant taxa have adapted to both environments and represent a model AMF symbiont. This evidence of strategic exploitation of the rhizosphere by AMF supports prior hypotheses and provides insights into community ecology.},
}
@article {pmid37114064,
year = {2023},
author = {Berman, TS and Weinberg, M and Moreno, KR and Czirják, G&#xc1; and Yovel, Y},
title = {In sickness and in health: the dynamics of the fruit bat gut microbiota under a bacterial antigen challenge and its association with the immune response.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1152107},
pmid = {37114064},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Chiroptera/genetics ; RNA, Ribosomal, 16S/genetics ; Haptoglobins ; Bacteria/genetics ; Immunity ; },
abstract = {INTRODUCTION: Interactions between the gut microbiome (GM) and the immune system influence host health and fitness. However, few studies have investigated this link and GM dynamics during disease in wild species. Bats (Mammalia: Chiroptera) have an exceptional ability to cope with intracellular pathogens and a unique GM adapted to powered flight. Yet, the contribution of the GM to bat health, especially immunity, or how it is affected by disease, remains unknown.<br><br>METHODS: Here, we examined the dynamics of the Egyptian fruit bats' (Rousettus aegyptiacus) GM during health and disease. We provoked an inflammatory response in bats using lipopolysaccharides (LPS), an endotoxin of Gram-negative bacteria. We then measured the inflammatory marker haptoglobin, a major acute phase protein in bats, and analyzed the GM (anal swabs) of control and challenged bats using high-throughput 16S rRNA sequencing, before the challenge, 24h and 48h post challenge.<br><br>RESULTS: We revealed that the antigen challenge causes a shift in the composition of the bat GM (e.g., Weissella, Escherichia, Streptococcus). This shift was significantly correlated with haptoglobin concentration, but more strongly with sampling time. Eleven bacterial sequences were correlated with haptoglobin concentration and nine were found to be potential predictors of the strength of the immune response, and implicit of infection severity, notably Weissella and Escherichia. The bat GM showed high resilience, regaining the colony's group GM composition rapidly, as bats resumed foraging and social activities.<br><br>CONCLUSION: Our results demonstrate a tight link between bat immune response and changes in their GM, and emphasize the importance of integrating microbial ecology in ecoimmunological studies of wild species. The resilience of the GM may provide this species with an adaptive advantage to cope with infections and maintain colony health.},
}
@article {pmid37113665,
year = {2023},
author = {Crognale, S and Massimi, A and Sbicego, M and Braguglia, CM and Gallipoli, A and Gazzola, G and Gianico, A and Tonanzi, B and Di Pippo, F and Rossetti, S},
title = {Ecology of food waste chain-elongating microbiome.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {11},
number = {},
pages = {1157243},
pmid = {37113665},
issn = {2296-4185},
abstract = {Microbial chain elongation has emerged as a valuable bioprocess for obtaining marketable products, such as medium chain fatty acids usable in several industrial applications, from organic waste. The understanding of the microbiology and microbial ecology in these systems is crucial to apply these microbiomes in reliable production processes controlling microbial pathways to promote favourable metabolic processes, which will in turn increase product specificity and yields. In this research, the dynamics, cooperation/competition and potentialities of bacterial communities involved in the long-term lactate-based chain elongation process from food waste extract were evaluated under different operating conditions by DNA/RNA amplicon sequencing and functional profile prediction. The feeding strategies and the applied organic loading rates strongly affected the microbial community composition. The use of food waste extract promoted the selection of primary fermenters (i.e., Olsenella, Lactobacillus) responsible for the in situ production of electron donors (i.e., lactate). The discontinuous feeding and the organic loading rate 15 gCOD L[-1] d[-1] selected the best performing microbiome in which microbes coexist and cooperate to complete the chain elongation process. Both at DNA and RNA level, this microbiome was composed by the lactate producer Olsenella, the short chain fatty acids producers Anaerostipes, Clostridium sensu stricto 7, C. sensu stricto 12, Corynebacterium, Erysipelotrichaceae UCG-004, F0332, Leuconostoc, and the chain elongator Caproiciproducens. This microbiome also showed the highest predicted abundance of short-chain acyl-CoA dehydrogenase, the functional enzyme responsible for the chain elongation process. The combined approach herein used allowed to study the microbial ecology of chain elongation process from food waste by identifying the main functional groups, establishing the presence of potential biotic interactions within the microbiomes, and predicting metabolic potentialities. This study provided pivotal indications for the selection of high-performance microbiome involved in caproate production from food waste that can serve as a basis for further improving system performance and engineering the process scale-up.},
}
@article {pmid37112890,
year = {2023},
author = {Turzynski, V and Griesdorn, L and Moraru, C and Soares, AR and Simon, SA and Stach, TL and Rahlff, J and Esser, SP and Probst, AJ},
title = {Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition.},
journal = {Viruses},
volume = {15},
number = {4},
pages = {},
pmid = {37112890},
issn = {1999-4915},
mesh = {Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Biofilms ; *Groundwater ; *Viruses/genetics ; },
abstract = {Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.},
}
@article {pmid37111201,
year = {2023},
author = {Wong, MCS and Zhang, L and Ching, JYL and Mak, JWY and Huang, J and Wang, S and Mok, CKP and Wong, A and Chiu, OL and Fung, YT and Cheong, PK and Tun, HM and Ng, SC and Chan, FKL},
title = {Effects of Gut Microbiome Modulation on Reducing Adverse Health Outcomes among Elderly and Diabetes Patients during the COVID-19 Pandemic: A Randomised, Double-Blind, Placebo-Controlled Trial (IMPACT Study).},
journal = {Nutrients},
volume = {15},
number = {8},
pages = {},
pmid = {37111201},
issn = {2072-6643},
support = {COVID19F07//Food and Health Bureau/ ; },
mesh = {Aged ; Humans ; *COVID-19 ; *Gastrointestinal Microbiome ; Pandemics/prevention &amp; control ; COVID-19 Vaccines ; *Diabetes Mellitus ; Outcome Assessment, Health Care ; Double-Blind Method ; },
abstract = {Gut microbiota is believed to be a major determinant of health outcomes. We hypothesised that a novel oral microbiome formula (SIM01) can reduce the risk of adverse health outcomes in at-risk subjects during the coronavirus disease 2019 (COVID-19) pandemic. In this single-centre, double-blind, randomised, placebo-controlled trial, we recruited subjects aged ≥65 years or with type two diabetes mellitus. Eligible subjects were randomised in a 1:1 ratio to receive three months of SIM01 or placebo (vitamin C) within one week of the first COVID-19 vaccine dose. Both the researchers and participants were blinded to the groups allocated. The rate of adverse health outcomes was significantly lower in the SIM01 group than the placebo at one month (6 [2.9%] vs. 25 [12.6], p < 0.001) and three months (0 vs. 5 [3.1%], p = 0.025). At three months, more subjects who received SIM01 than the placebo reported better sleep quality (53 [41.4%] vs. 22 [19.3%], p < 0.001), improved skin condition (18 [14.1%] vs. 8 [7.0%], p = 0.043), and better mood (27 [21.2%] vs. 13 [11.4%], p = 0.043). Subjects who received SIM01 showed a significant increase in beneficial Bifidobacteria and butyrate-producing bacteria in faecal samples and strengthened the microbial ecology network. SIM01 reduced adverse health outcomes and restored gut dysbiosis in elderly and diabetes patients during the COVID-19 pandemic.},
}
@article {pmid37110442,
year = {2023},
author = {Maimone, G and Azzaro, M and Placenti, F and Paranhos, R and Cabral, AS and Decembrini, F and Zaccone, R and Cosenza, A and Rappazzo, AC and Patti, B and Basilone, G and Cuttitta, A and Ferreri, R and Aronica, S and Ferla, R},
title = {A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea).},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
pmid = {37110442},
issn = {2076-2607},
abstract = {A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm[3]), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm[3]). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.},
}
@article {pmid37110372,
year = {2023},
author = {Zhou, T and Zhao, F and Xu, K},
title = {Information Scale Correction for Varying Length Amplicons Improves Eukaryotic Microbiome Data Integration.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
pmid = {37110372},
issn = {2076-2607},
support = {41930533//National Natural Science Foundation of China/ ; 41976099//National Natural Science Foundation of China/ ; XDB42000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2022206//Youth Innovation Promotion Association CAS/ ; },
abstract = {The integration and reanalysis of big data provide valuable insights into microbiome studies. However, the significant difference in information scale between amplicon data poses a key challenge in data analysis. Therefore, reducing batch effects is crucial to enhance data integration for large-scale molecular ecology data. To achieve this, the information scale correction (ISC) step, involving cutting different length amplicons into the same sub-region, is essential. In this study, we used the Hidden Markov model (HMM) method to extract 11 different 18S rRNA gene v4 region amplicon datasets with 578 samples in total. The length of the amplicons ranged from 344 bp to 720 bp, depending on the primer position. By comparing the information scale correction of amplicons with varying lengths, we explored the extent to which the comparability between samples decreases with increasing amplicon length. Our method was shown to be more sensitive than V-Xtractor, the most popular tool for performing ISC. We found that near-scale amplicons exhibited no significant change after ISC, while larger-scale amplicons exhibited significant changes. After the ISC treatment, the similarity among the data sets improved, especially for long amplicons. Therefore, we recommend adding ISC processing when integrating big data, which is crucial for unlocking the full potential of microbial community studies and advancing our knowledge of microbial ecology.},
}
@article {pmid37110315,
year = {2023},
author = {Lashani, E and Amoozegar, MA and Turner, RJ and Moghimi, H},
title = {Use of Microbial Consortia in Bioremediation of Metalloid Polluted Environments.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
pmid = {37110315},
issn = {2076-2607},
abstract = {Metalloids are released into the environment due to the erosion of the rocks or anthropogenic activities, causing problems for human health in different world regions. Meanwhile, microorganisms with different mechanisms to tolerate and detoxify metalloid contaminants have an essential role in reducing risks. In this review, we first define metalloids and bioremediation methods and examine the ecology and biodiversity of microorganisms in areas contaminated with these metalloids. Then we studied the genes and proteins involved in the tolerance, transport, uptake, and reduction of these metalloids. Most of these studies focused on a single metalloid and co-contamination of multiple pollutants were poorly discussed in the literature. Furthermore, microbial communication within consortia was rarely explored. Finally, we summarized the microbial relationships between microorganisms in consortia and biofilms to remove one or more contaminants. Therefore, this review article contains valuable information about microbial consortia and their mechanisms in the bioremediation of metalloids.},
}
@article {pmid37110258,
year = {2023},
author = {Thomas, P and Knox, OGG and Powell, JR and Sindel, B and Winter, G},
title = {The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised?.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
pmid = {37110258},
issn = {2076-2607},
support = {P2-007//Future Food Systems Cooperative Research Centre (CRC) Ltd., funded under the Australian Commonwealth Government CRC Program/ ; },
abstract = {Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe-plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host-microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment.},
}
@article {pmid37108739,
year = {2023},
author = {Codoñer-Franch, P and Gombert, M and Martínez-Raga, J and Cenit, MC},
title = {Circadian Disruption and Mental Health: The Chronotherapeutic Potential of Microbiome-Based and Dietary Strategies.},
journal = {International journal of molecular sciences},
volume = {24},
number = {8},
pages = {},
pmid = {37108739},
issn = {1422-0067},
support = {CEX2021-001189-S/MCIN/AEI/10.13039/501100011033//A grant by the Spanish Ministry of Science and Innovation (MCIN/AEI)/ ; },
mesh = {Humans ; *Mental Health ; Drug Chronotherapy ; Diet ; Circadian Rhythm/physiology ; *Gastrointestinal Microbiome ; },
abstract = {Mental illness is alarmingly on the rise, and circadian disruptions linked to a modern lifestyle may largely explain this trend. Impaired circadian rhythms are associated with mental disorders. The evening chronotype, which is linked to circadian misalignment, is a risk factor for severe psychiatric symptoms and psychiatric metabolic comorbidities. Resynchronization of circadian rhythms commonly improves psychiatric symptoms. Furthermore, evidence indicates that preventing circadian misalignment may help reduce the risk of psychiatric disorders and the impact of neuro-immuno-metabolic disturbances in psychiatry. The gut microbiota exhibits diurnal rhythmicity, as largely governed by meal timing, which regulates the host's circadian rhythms. Temporal circadian regulation of feeding has emerged as a promising chronotherapeutic strategy to prevent and/or help with the treatment of mental illnesses, largely through the modulation of gut microbiota. Here, we provide an overview of the link between circadian disruption and mental illness. We summarize the connection between gut microbiota and circadian rhythms, supporting the idea that gut microbiota modulation may aid in preventing circadian misalignment and in the resynchronization of disrupted circadian rhythms. We describe diurnal microbiome rhythmicity and its related factors, highlighting the role of meal timing. Lastly, we emphasize the necessity and rationale for further research to develop effective and safe microbiome and dietary strategies based on chrononutrition to combat mental illness.},
}
@article {pmid37106747,
year = {2023},
author = {Ghouili, E and Abid, G and Hogue, R and Jeanne, T and D'Astous-Pagé, J and Sassi, K and Hidri, Y and M'Hamed, HC and Somenahally, A and Xue, Q and Jebara, M and Nefissi Ouertani, R and Riahi, J and de Oliveira, AC and Muhovski, Y},
title = {Date Palm Waste Compost Application Increases Soil Microbial Community Diversity in a Cropping Barley (Hordeum vulgare L.) Field.},
journal = {Biology},
volume = {12},
number = {4},
pages = {},
pmid = {37106747},
issn = {2079-7737},
abstract = {Application of date palm waste compost is quite beneficial in improving soil properties and crop growth. However, the effect of its application on soil microbial communities is less understood. High-throughput sequencing and quantitative real-time PCR (qPCR) were used to evaluate the effect of compost application on the soil microbial composition in a barley field during the tillering, booting and ripening stages. The results showed that compost treatment had the highest bacterial and fungal abundance, and its application significantly altered the richness (Chao1 index) and α-diversity (Shannon index) of fungal and bacterial communities. The dominant bacterial phyla found in the samples were Proteobacteria and Actinobacteria while the dominant fungal orders were Ascomycota and Mortierellomycota. Interestingly, compost enriched the relative abundance of beneficial microorganisms such as Chaetomium, Actinobacteriota, Talaromyces and Mortierella and reduced those of harmful microorganisms such as Alternaria, Aspergillus and Neocosmospora. Functional prediction based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that amplicon sequence variant (ASV) sequences related to energy metabolism, amino acid metabolism and carbohydrate metabolism were associated with compost-treated soil. Based on Fungi Functional Guild (FUNGuild), identified fungi community metabolic functions such as wood saprotroph, pathotroph, symbiotroph and endophyte were associated with compost-treated soil. Overall, compost addition could be considered as a sustainable practice for establishing a healthy soil microbiome and subsequently improving the soil quality and barley crop production.},
}
@article {pmid37103739,
year = {2024},
author = {Balakrishnan, K and Krishnaa, D and Balakrishnan, G and Manickam, M and Abdulkader, AM and Dharumadurai, D},
title = {Association of Bacterial Communities with Psychedelic Mushroom and Soil as Revealed in 16S rRNA Gene Sequencing.},
journal = {Applied biochemistry and biotechnology},
volume = {196},
number = {5},
pages = {2566-2590},
pmid = {37103739},
issn = {1559-0291},
mesh = {*Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Microbiota/drug effects ; Agaricales/genetics ; Psilocybe ; Rhizosphere ; },
abstract = {Microbial communities' resident in the mushroom fruiting body and the soil around it play critical roles in the growth and propagation of the mushroom. Among the microbial communities associated with psychedelic mushrooms and the rhizosphere soil, bacterial communities are considered vital since their presence greatly influences the health of the mushrooms. The present study aimed at finding the microbiota present in the psychedelic mushroom Psilocybe cubensis and the soil the mushroom inhabits. The study was conducted at two different locations in Kodaikanal, Tamil Nadu, India. The composition and structure of microbial communities in the mushroom fruiting body and the soil were deciphered. The genomes of the microbial communities were directly assessed. High-throughput amplicon sequencing revealed distinct microbial diversity in the mushroom and the related soil. The interaction of environmental and anthropogenic factors appeared to have a significant impact on the mushroom and soil microbiome. The most abundant bacterial genera were Ochrobactrum, Stenotrophomonas, Achromobacter, and Brevundimonas. Thus, the study advances the knowledge of the composition of the microbiome and microbial ecology of a psychedelic mushroom, and paves the way for in-depth investigation of the influence of microbiota on the mushroom, with special emphasis on the impact of bacterial communities on mushroom growth. Further studies are required for a deeper understanding of the microbial communities that influence the growth of P. cubensis mushroom.},
}
@article {pmid37103495,
year = {2023},
author = {Towett-Kirui, S and Morrow, JL and Close, S and Royer, JE and Riegler, M},
title = {Bacterial Communities Are Less Diverse in a Strepsipteran Endoparasitoid than in Its Fruit Fly Hosts and Dominated by Wolbachia.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2120-2132},
pmid = {37103495},
issn = {1432-184X},
support = {IC150100026//Australian Research Council (ARC) Industrial Transformation Training Centre (ITTC) Fruit Fly Biosecurity Innovation/ ; },
mesh = {*Wolbachia/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota ; High-Throughput Nucleotide Sequencing ; },
abstract = {Microbiomes play vital roles in insect fitness and health and can be influenced by interactions between insects and their parasites. Many studies investigate the microbiome of free-living insects, whereas microbiomes of endoparasitoids and their interactions with parasitised insects are less explored. Due to their development in the constrained environment within a host, endoparasitoids are expected to have less diverse yet distinct microbiomes. We used high-throughput 16S rRNA gene amplicon sequencing to characterise the bacterial communities of Dipterophagus daci (Strepsiptera) and seven of its tephritid fruit fly host species. Bacterial communities of D. daci were less diverse and contained fewer taxa relative to the bacterial communities of the tephritid hosts. The strepsipteran's microbiome was dominated by Pseudomonadota (formerly Proteobacteria) (> 96%), mainly attributed to the presence of Wolbachia, with few other bacterial community members, indicative of an overall less diverse microbiome in D. daci. In contrast, a dominance of Wolbachia was not found in flies parasitised by early stages of D. daci nor unparasitised flies. Yet, early stages of D. daci parasitisation resulted in structural changes in the bacterial communities of parasitised flies. Furthermore, parasitisation with early stages of D. daci with Wolbachia was associated with a change in the relative abundance of some bacterial taxa relative to parasitisation with early stages of D. daci lacking Wolbachia. Our study is a first comprehensive characterisation of bacterial communities in a Strepsiptera species together with the more diverse bacterial communities of its hosts and reveals effects of concealed stages of parasitisation on host bacterial communities.},
}
@article {pmid37101565,
year = {2023},
author = {Mosquera-Romero, S and Ntagia, E and Rousseau, DPL and Esteve-Núñez, A and Prévoteau, A},
title = {Water treatment and reclamation by implementing electrochemical systems with constructed wetlands.},
journal = {Environmental science and ecotechnology},
volume = {16},
number = {},
pages = {100265},
pmid = {37101565},
issn = {2666-4984},
abstract = {Seasonal or permanent water scarcity in off-grid communities can be alleviated by recycling water in decentralized wastewater treatment systems. Nature-based solutions, such as constructed wetlands (CWs), have become popular solutions for sanitation in remote locations. Although typical CWs can efficiently remove solids and organics to meet water reuse standards, polishing remains necessary for other parameters, such as pathogens, nutrients, and recalcitrant pollutants. Different CW designs and CWs coupled with electrochemical technologies have been proposed to improve treatment efficiency. Electrochemical systems (ECs) have been either implemented within the CW bed (ECin-CW) or as a stage in a sequential treatment (CW + EC). A large body of literature has focused on ECin-CW, and multiple scaled-up systems have recently been successfully implemented, primarily to remove recalcitrant organics. Conversely, only a few reports have explored the opportunity to polish CW effluents in a downstream electrochemical module for the electro-oxidation of micropollutants or electro-disinfection of pathogens to meet more stringent water reuse standards. This paper aims to critically review the opportunities, challenges, and future research directions of the different couplings of CW with EC as a decentralized technology for water treatment and recovery.},
}
@article {pmid37101495,
year = {2023},
author = {Nakato, GV and Wicker, E and Coutinho, TA and Mahuku, G and Studholme, DJ},
title = {Corrigendum to "A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences" [Heliyon 4 (12) (December 2018) Article e01080].},
journal = {Heliyon},
volume = {9},
number = {3},
pages = {e14606},
doi = {10.1016/j.heliyon.2023.e14606},
pmid = {37101495},
issn = {2405-8440},
abstract = {[This corrects the article DOI: 10.1016/j.heliyon.2018.e01080.].},
}
@article {pmid37101136,
year = {2023},
author = {Mosquera, KD and Martínez Villegas, LE and Rocha Fernandes, G and Rocha David, M and Maciel-de-Freitas, R and A Moreira, L and Lorenzo, MG},
title = {Egg-laying by female Aedes aegypti shapes the bacterial communities of breeding sites.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {97},
pmid = {37101136},
issn = {1741-7007},
mesh = {Animals ; Humans ; Female ; *Aedes ; Mosquito Vectors ; Water ; Bacteria/genetics ; Oviposition ; Larva ; },
abstract = {BACKGROUND: Aedes aegypti, the main arboviral mosquito vector, is attracted to human dwellings and makes use of human-generated breeding sites. Past research has shown that bacterial communities associated with such sites undergo compositional shifts as larvae develop and that exposure to different bacteria during larval stages can have an impact on mosquito development and life-history traits. Based on these facts, we hypothesized that female Ae. aegypti shape the bacteria communities of breeding sites during oviposition as a form of niche construction to favor offspring fitness.<br><br>RESULTS: To test this hypothesis, we first verified that gravid females can act as mechanical vectors of bacteria. We then elaborated an experimental scheme to test the impact of oviposition on breeding site microbiota. Five different groups of experimental breeding sites were set up with a sterile aqueous solution of larval food, and subsequently exposed to (1) the environment alone, (2) surface-sterilized eggs, (3) unsterilized eggs, (4) a non-egg laying female, or (5) oviposition by a gravid female. The microbiota of these differently treated sites was assessed by amplicon-oriented DNA sequencing once the larvae from the sites with eggs had completed development and formed pupae. Microbial ecology analyses revealed significant differences between the five treatments in terms of diversity. In particular, between-treatment shifts in abundance profiles were detected, showing that females induce a significant decrease in microbial alpha diversity through oviposition. In addition, indicator species analysis pinpointed bacterial taxa with significant predicting values and fidelity coefficients for the samples in which single females laid eggs. Furthermore, we provide evidence regarding how one of these indicator taxa, Elizabethkingia, exerts a positive effect on the development and fitness of mosquito larvae.<br><br>CONCLUSIONS: Ovipositing females impact the composition of the microbial community associated with a breeding site, promoting certain bacterial taxa over those prevailing in the environment. Among these bacteria, we found known mosquito symbionts and showed that they can improve offspring fitness if present in the water where eggs are laid. We deem this oviposition-mediated bacterial community shaping as a form of niche construction initiated by the gravid female.},
}
@article {pmid37100151,
year = {2023},
author = {Wang, B and Zhu, C and Hu, Y and Zhang, B and Wang, J},
title = {Dynamics of microbial community composition during degradation of silks in burial environment.},
journal = {The Science of the total environment},
volume = {883},
number = {},
pages = {163694},
doi = {10.1016/j.scitotenv.2023.163694},
pmid = {37100151},
issn = {1879-1026},
mesh = {*Soil Microbiology ; Bacteria/metabolism ; Silk ; *Microbiota/genetics ; Soil/chemistry ; Burial ; },
abstract = {The silk residues in the soil formed the unique niche, termed "silksphere." Here, we proposed a hypothesis that silksphere microbiota have great potential as a biomarker for unraveling the degradation of the ancient silk textiles with great archaeological and conservation values. To test our hypothesis, in this study, we monitored the dynamics of microbial community composition during silk degradation via both indoor soil microcosmos model and outdoor environment with amplicon sequencing against 16S and ITS gene. Microbial community divergence was evaluated with Welch two sample t-test, PCoA, negative binomial generalized log-linear model and clustering, etc. Community assembly mechanisms differences between silksphere and bulk soil microbiota were compared with dissimilarity-overlap curve (DOC) model, Neutral model and Null model. A well-established machine learning algorithm, random forest, was also applied to the screening of potential biomarkers of silk degradation. The results illustrated the ecological and microbial variability during the microbial degradation of silk. Vast majority of microbes populating the silksphere microbiota strongly diverged from those in bulk soil. Certain microbial flora can serve as an indicator of silk degradation, which would lead to a novel perspective to perform identification of archaeological silk residues in the field. To sum up, this study provides a new perspective to perform the identification of archaeological silk residue through the dynamics of microbial communities.},
}
@article {pmid37099394,
year = {2023},
author = {McCartney, AL and Hoyles, L},
title = {The role of Klebsiella populations in preterm infants.},
journal = {Biochemical Society transactions},
volume = {51},
number = {2},
pages = {887-896},
pmid = {37099394},
issn = {1470-8752},
mesh = {Infant ; Infant, Newborn ; Humans ; *Infant, Premature ; Retrospective Studies ; Klebsiella ; Feces/microbiology ; *Sepsis/microbiology ; Bacteria ; },
abstract = {The preterm infant microbiota is dominated by Enterobacteriaceae (Escherichia, Klebsiella or Enterobacter spp.), Enterococcus and Staphylococcus spp. Recent work has demonstrated the development of this microbiota is predictable and driven by simple microbe-microbe interactions. Because of their systemic immaturity, including an underdeveloped immune system, preterm infants are susceptible to a range of infections. Numerous retrospective studies have examined the association of the preterm gut microbiota with diseases such as necrotizing enterocolitis (NEC), early-onset sepsis and late-onset sepsis. To date, no single bacterium has been associated with infection in these infants, but a Klebsiella/Enterococcus-dominated faecal microbiota is associated with an increased risk of developing NEC. Staphylococci aid and enterococci inhibit establishment/maintenance of gastrointestinal Klebsiella populations in preterm infants, though the mechanisms underlying these interactions are poorly understood. Klebsiella spp. recovered from healthy and sick preterm infants display similar antimicrobial resistance and virulence profiles, giving no clues as to why some infants develop potentially life-threatening diseases while others do not. The identification of cytotoxin-producing Klebsiella oxytoca sensu lato in the gut microbiota of some preterm infants has led to the suggestion that these bacteria may contribute to NEC in a subset of neonates. This mini review highlights current knowledge on Klebsiella spp. contributing to the preterm gut microbiota and provides insights into areas of research that warrant further attention.},
}
@article {pmid37099156,
year = {2023},
author = {Nguyen, PN and Rehan, SM},
title = {Environmental Effects on Bee Microbiota.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1487-1498},
pmid = {37099156},
issn = {1432-184X},
mesh = {Humans ; Animals ; Bees ; *Ecosystem ; Animals, Wild ; Urbanization ; *Microbiota ; Climate ; Agriculture ; Pollination ; },
abstract = {Anthropogenic activities and increased land use, which include industrialization, agriculture and urbanization, directly affect pollinators by changing habitats and floral availability, and indirectly by influencing their microbial composition and diversity. Bees form vital symbioses with their microbiota, relying on microorganisms to perform physiological functions and aid in immunity. As altered environments and climate threaten bees and their microbiota, characterizing the microbiome and its complex relationships with its host offers insights into understanding bee health. This review summarizes the role of sociality in microbiota establishment, as well as examines if such factors result in increased susceptibility to altered microbiota due to environmental changes. We characterize the role of geographic distribution, temperature, precipitation, floral resources, agriculture, and urbanization on bee microbiota. Bee microbiota are affected by altered surroundings regardless of sociality. Solitary bees that predominantly acquire their microbiota through the environment are particularly sensitive to such effects. However, the microbiota of obligately eusocial bees are also impacted by environmental changes despite typically well conserved and socially inherited microbiota. We provide an overview of the role of microbiota in plant-pollinator relationships and how bee microbiota play a larger role in urban ecology, offering microbial connections between animals, humans, and the environment. Understanding bee microbiota presents opportunities for sustainable land use restoration and aiding in wildlife conservation.},
}
@article {pmid37099155,
year = {2023},
author = {Wang, B and Qi, M and Ma, Y and Zhang, B and Hu, Y},
title = {Microbiome Diversity and Cellulose Decomposition Processes by Microorganisms on the Ancient Wooden Seawall of Qiantang River of Hangzhou, China.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2109-2119},
pmid = {37099155},
issn = {1432-184X},
mesh = {Humans ; *Cellulose/metabolism ; Rivers ; *Microbiota/genetics ; Fungi/genetics ; Bacteria/genetics ; Wood/microbiology ; },
abstract = {Archaeological wood, also known as wooden cultural relics, refers to ancient wood that has been worked by humans. Further insights into the decomposition mechanism of archaeological wood are needed for its preventive conservation. In this study, we assessed the microbiome diversity and cellulose decomposition processes on a 200-year-old ancient wooden seawall - the Qiantang River of Hangzhou, China. We used high-throughput sequencing (HTS) to deduce the metagenomic functions, particularly the cellulose-decomposing pathway of the microbial communities, through bioinformatical approaches. The predominant cellulose-decomposing microorganisms were then verified with traditional isolation, culture, and identification method. The results showed that the excavation of archaeological wood significantly altered the environment, accelerating the deterioration process of the archaeological wood through the carbohydrate metabolism and the xenobiotic biodegradation and metabolism pathways, under the comprehensive metabolism of complex ecosystem formed by bacteria, archaea, fungi, microfauna, plants, and algae. Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria were found to be the predominant source of bacterial cellulose-decomposing enzymes. Accordingly, we suggest relocating the wooden seawall to an indoor environment with controllable conditions to better preserve it. In addition, these results provide further evidence for our viewpoints that HTS techniques, combined with rational bioinformatical data interpretation approaches, can serve as powerful tools for the preventive protection of cultural heritage.},
}
@article {pmid37098915,
year = {2023},
author = {Kim, N and Vargas, P and Fortuna, K and Wagemans, J and Rediers, H},
title = {Draft Genome Sequences of 27 Rhizogenic Agrobacterium Biovar 1 Strains, the Causative Agent of Hairy Root Disease.},
journal = {Microbiology resource announcements},
volume = {12},
number = {5},
pages = {e0012423},
pmid = {37098915},
issn = {2576-098X},
support = {HBC.2017.0816//Agentschap Innoveren en Ondernemen (VLAIO)/ ; C14/19/074//KU Leuven (Katholieke Universiteit Leuven)/ ; C3/19/047//KU Leuven (Katholieke Universiteit Leuven)/ ; },
abstract = {Rhizogenic Agrobacterium biovar 1 strains are important plant pathogens that cause hairy root disease in Cucurbitaceae and Solanaceae crops cultivated under hydroponic conditions. In contrast to tumorigenic agrobacteria, only a few genome sequences of rhizogenic agrobacteria are currently available. Here, we report the draft genome sequences of 27 rhizogenic Agrobacterium strains.},
}
@article {pmid37097879,
year = {2023},
author = {Stewart, CJ},
title = {2022 Fleming Prize Lecture: diet-microbe-host interaction in early life.},
journal = {Journal of medical microbiology},
volume = {72},
number = {4},
pages = {},
doi = {10.1099/jmm.0.001662},
pmid = {37097879},
issn = {1473-5644},
mesh = {Infant ; Female ; Infant, Newborn ; Humans ; Middle Aged ; *Infant, Premature ; Host Microbial Interactions ; Milk, Human ; *Microbiota ; Diet ; },
abstract = {The last decade has witnessed a meteoric rise in research focused on characterizing the human microbiome and identifying associations with disease risk. The advent of sequencing technology has all but eradicated gel-based fingerprinting approaches for studying microbial ecology, while at the same time traditional microbiological culture is undergoing a renaissance. Although multiplexed high-throughput sequencing is relatively new, the discoveries leading to this are nearly 50 years old, coinciding with the inaugural Microbiology Society Fleming Prize lecture. It was an honour to give the 2022 Fleming Prize lecture and this review will cover the topics from that lecture. The focus will be on the bacterial community in early life, beginning with term infants before moving on to infants delivered prematurely. The review will discuss recent work showing how human milk oligosaccharides (HMOs), an abundant but non-nutritious component of breast milk, can modulate infant microbiome and promote the growth of Bifidobacterium spp. This has important connotations for preterm infants at risk of necrotizing enterocolitis, a devastating intestinal disease representing the leading cause of death and long-term morbidity in this population. With appropriate mechanistic studies, it may be possible to harness the power of breast milk bioactive factors and infant gut microbiome to improve short- and long-term health in infants.},
}
@article {pmid37097592,
year = {2023},
author = {Paul, P and Roy, R and Das, S and Sarkar, S and Chatterjee, S and Mallik, M and Shukla, A and Chakraborty, P and Tribedi, P},
title = {The combinatorial applications of 1,4-naphthoquinone and tryptophan inhibit the biofilm formation of Staphylococcus aureus.},
journal = {Folia microbiologica},
volume = {68},
number = {5},
pages = {801-811},
pmid = {37097592},
issn = {1874-9356},
mesh = {Humans ; *Staphylococcus aureus ; Tryptophan/pharmacology ; Extracellular Polymeric Substance Matrix ; Anti-Bacterial Agents/pharmacology ; *Staphylococcal Infections/drug therapy/microbiology ; Biofilms ; Microbial Sensitivity Tests ; },
abstract = {Microorganisms embedded within an extracellular polymeric matrix are known as biofilm. The extensive use of antibiotics to overcome the biofilm-linked challenges has led to the emergence of multidrug-resistant strains. Staphylococcus aureus is one such nosocomial pathogen that is known to cause biofilm-linked infections. Thus, novel strategies have been adopted in this study to inhibit the biofilm formation of S. aureus. Two natural compounds, namely, 1,4-naphthoquinone (a quinone derivative) and tryptophan (aromatic amino acid), have been chosen as they could independently show efficient antibiofilm activity. To enhance the antibiofilm potential, the two compounds were combined and tested against the same organism. Several experiments like crystal violet (CV) assay, protein estimation, extracellular polymeric substance (EPS) extraction, and estimation of metabolic activity confirmed that the combination of the two compounds could significantly inhibit the biofilm formation of S. aureus. To comprehend the underlying mechanism, efforts were further directed to understand whether the two compounds could inhibit biofilm formation by compromising the cell surface hydrophobicity of the bacteria. The results revealed that the cell surface hydrophobicity got reduced by ~ 49% when the compounds were applied together. Thus, the combinations could show enhanced antibiofilm activity by attenuating cell surface hydrophobicity. Further studies revealed that the selected concentrations of the compounds could disintegrate (~ 70%) the pre-existing biofilm of the test bacteria without showing any antimicrobial activity. Hence, the combined application of tryptophan and 1,4-naphthoquinone could be used to inhibit the biofilm threats of S. aureus.},
}
@article {pmid37097162,
year = {2023},
author = {Masasa, M and Kushmaro, A and Nguyen, D and Chernova, H and Shashar, N and Guttman, L},
title = {Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0051423},
pmid = {37097162},
issn = {2165-0497},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; *Sea Urchins/genetics ; Seafood ; Digestion ; Sulfates ; },
abstract = {Dietary influence on the microbiome in algivorous sea urchins such as Tripneustes gratilla elatensis suggests a bacterial contribution to the digestion of fiber-rich seaweed. An ecological insight into the spatial arrangement in the gut bacterial community will improve our knowledge of host-microbe relations concerning the involved taxa, their metabolic repertoire, and the niches of activity. Toward this goal, we investigated the bacterial communities in the esophagus, stomach, and intestine of Ulva-fed sea urchins through 16S rRNA amplicon sequencing, followed by the prediction of their functional genes. We revealed communities with distinct features, especially those in the esophagus and intestine. The esophageal community was less diverse and was poor in food digestive or fermentation genes. In contrast, bacteria that can contribute to the digestion of the dietary Ulva were common in the stomach and intestine and consisted of genes for carbohydrate decomposition, fermentation, synthesis of short-chain fatty acids, and various ways of N and S metabolism. Bacteroidetes and Firmicutes were found as the main phyla in the gut and are presumably also necessary in food digestion. The abundant sulfate-reducing bacteria in the stomach and intestine from the genera Desulfotalea, Desulfitispora, and Defluviitalea may aid in removing the excess sulfate from the decomposition of the algal polysaccharides. Although these sea urchins were fed with Ulva, genes for the degradation of polysaccharides of other algae and plants were present in this sea urchin gut microbiome. We conclude that the succession of microbial communities along the gut obtained supports the hypothesis on bacterial contribution to food digestion. IMPORTANCE Alga grazing by the sea urchin Tripneustes gratilla elatensis is vital for nutrient recycling and constructing new reefs. This research was driven by the need to expand the knowledge of bacteria that may aid this host in alga digestion and their phylogeny, roles, and activity niches. We hypothesized alterations in the bacterial compositional structure along the gut and their association with the potential contribution to food digestion. The current spatial insight into the sea urchin's gut microbiome ecology is novel and reveals how distinct bacterial communities are when distant from each other in this organ. It points to keynote bacteria with genes that may aid the host in the digestion of the complex sulfated polysaccharides in dietary Ulva by removing the released sulfates and fermentation to provide energy. The gut bacteria's genomic arsenal may also help to gain energy from diets of other algae and plants.},
}
@article {pmid37093231,
year = {2023},
author = {Ichige, R and Urabe, J},
title = {Divergence of the Host-Associated Microbiota with the Genetic Distance of Host Individuals Within a Parthenogenetic Daphnia Species.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2097-2108},
pmid = {37093231},
issn = {1432-184X},
support = {JPMJSP2114//Japan Science and Technology Agency/ ; KAKENHI:20H03315//Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research/ ; },
mesh = {Animals ; *Daphnia/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Genotype ; },
abstract = {The taxonomic composition of the microbiota in the gut and epidermis of animals is known to vary among genetically and physiologically different host individuals within the same species. However, it is not clear whether the taxonomic composition diverges with increasing genetic distance of the host individuals. To unveil this uncertainty, we compared the host-associated microbiota among the genotypes within and between genetically distant lineages of parthenogenetic Daphnia cf. pulex across different physiological states, namely, well-fed, starved, and dead. Metagenomic analysis with 16S rRNA showed that, regardless of the host genotypes, diversity of the host-associated microbiota was high when the host individuals were fed food and gradually decreased when they were starved until they died. However, the difference in the host-associated microbiota, that is, β-diversity, was significant among the genotypes within and between the host lineages when they were fed. Although some bacteria in the microbiota, such as Limnohabitans, Rhodococcus, and Aeromicrobium, were found abundantly and commonly in all host genotypes; others, such as those of Holosoporacea, were found only in the genotypes of a specific lineage. Accordingly, the β-diversity tended to increase with increasing genetic distance of the host individuals. These results support an idea that the host-associated microbiota diverged with genetic divergence in the host species and that at least some bacteria are highly dependent on the genetically specific metabolites produced by the host individuals.},
}
@article {pmid37093057,
year = {2023},
author = {Chen, Q and Fan, Y and Zhang, B and Yan, C and Zhang, Q and Ke, Y and Chen, Z and Wang, L and Shi, H and Hu, Y and Huang, Q and Su, J and Xie, C and Zhang, X and Zhou, L and Ren, J and Xu, H},
title = {Capsulized Fecal Microbiota Transplantation Induces Remission in Patients with Ulcerative Colitis by Gut Microbial Colonization and Metabolite Regulation.},
journal = {Microbiology spectrum},
volume = {11},
number = {3},
pages = {e0415222},
pmid = {37093057},
issn = {2165-0497},
mesh = {Humans ; Bacteria ; *Colitis, Ulcerative/therapy/microbiology ; *Communicable Diseases ; Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; },
abstract = {Fecal microbiota transplantation (FMT) can induce clinical remission in ulcerative colitis (UC) patients. Enemas, nasoduodenal tubes, and colonoscopies are the most common routes for FMT administration. However, there is a lack of definitive evidence regarding the effectiveness of capsulized FMT treatment in UC patients. In this study, we administered capsulized FMT to 22 patients with active UC to assess the efficiency of capsulized FMT and determine the specific bacteria and metabolite factors associated with the response to clinical remission. Our results showed that the use of capsulized FMT was successful in the treatment of UC patients. Capsulized FMT induced clinical remission and clinical response in 57.1% (12 of 21) and 76.2% (16 of 21) of UC patients, respectively. Gut bacterial richness was increased after FMT in patients who achieved remission. Patients in remission after FMT exhibited enrichment of Alistipes sp. and Odoribacter splanchnicus, along with increased levels of indolelactic acid. Patients who did not achieve remission exhibited enrichment of Escherichia coli and Klebsiella and increased levels of biosynthesis of 12,13-DiHOME (12,13-dihydroxy-9Z-octadecenoic acid) and lipopolysaccharides. Furthermore, we identified a relationship between specific bacteria and metabolites and the induction of remission in patients. These findings may provide new insights into FMT in UC treatment and provide reference information about therapeutic microbial manipulation of FMT to enhance its effects. (This study has been registered at ClinicalTrails.gov under registration no. NCT03426683). IMPORTANCE Fecal microbiota transplantation has been successfully used in patients. Recently, capsulized FMT was reported to induce a response in patients with UC. However, limited patients were enrolled in such studies, and the functional factors of capsulized FMT have not been reported in the remission of patients with UC. In this study, we prospectively recruited patients with UC to receive capsulized FMT. First, we found that capsulized FMT could induce clinical remission in 57.1% of patients and clinical response in 76.2% after 12 weeks, which was more acceptable. Second, we found a relationship between the decrease of opportunistic pathogen and lipopolysaccharide synthesis in patients in remission after capsulized FMT. We also identified an association between specific bacteria and metabolites and remission induction in patients after capsulized FMT. These findings put forward a possibility for patients to receive FMT at home and provide reference information about therapeutic microbial manipulation of FMT to enhance its effects.},
}
@article {pmid37090461,
year = {2023},
author = {Al-Rshaidat, MMD and Al-Sharif, S and Refaei, AA and Shewaikani, N and Alsayed, AR and Rayyan, YM},
title = {Evaluating the clinical application of the immune cells' ratios and inflammatory markers in the diagnosis of inflammatory bowel disease.},
journal = {Pharmacy practice},
volume = {21},
number = {1},
pages = {2755},
pmid = {37090461},
issn = {1885-642X},
abstract = {OBJECTIVE: Inflammatory Bowel Diseases (IBDs) are chronic inflammatory conditions of the gastrointestinal tract, including Crohn's disease (CD) and ulcerative colitis (UC). Developing methods for effective screening and diagnosis is extremely needed. Accordingly, this study aims to evaluate the potential of immune cells ratios in the diagnosis of IBD.<br><br>METHODS: This case-control study includes data from Jordan University Hospital (JUH) medical records for IBD patients with age- and gender-matched healthy controls.<br><br>RESULTS: This study included 46 participants, of which 56.52% had IBD, 54.35% were males, with insignificant differences in sex, age, and body mass index (BMI) between IBD patients and controls (p>0.05). In the CD group, the variables with the highest sensitivity and specificity (HSS) were neutrophil-to-lymphocyte (NLR) (75%, 80%) and platelet-to-lymphocytes (PLR) (75%, 90%), in UC group; mean corpuscular hemoglobin (MCH) (80%, 80%). In CD group, the combinations giving the HSS were PLR+NLR (76%, 90.9%), C-reactive protein (CRP)+PLR (76%, 90.9%), and CRP+NLR (73.07%, 90%). In UC group, the combinations giving the HSS were erythrocyte sedimentation rate (ESR)+PLR (76.9%, 100%), PLR+MCH (74.07%, 100%), PLR+CRP (71.42%, 100%), and PLR+NLR (71.42%, 100%). Regression analysis identified five different combinations of significance in the diagnosis of CD and UC. Higher Youden's index was used and defined the most beneficial clinical combinations as NLR+PLR and CRP+PLR for CD, whereas ESR+PLR for UC.<br><br>CONCLUSION: Implications to our study include the clinical application of immune cell ratios, inflammatory markers, and their different combinations along with patients' history and physical examination findings for easier, faster, and more cost-effective diagnosis of IBDs.},
}
@article {pmid37088849,
year = {2023},
author = {Mills, TJT and Nelson, TM and Pearson, LA and Neilan, BA},
title = {Hive Transplantation Has Minimal Impact on the Core Gut Microbiome of the Australian Stingless Bee, Tetragonula carbonaria.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2086-2096},
pmid = {37088849},
issn = {1432-184X},
support = {FF0883440//Australian Research Council/ ; },
mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; Australia ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Urticaria ; },
abstract = {Bacteria residing in the guts of pollinating insects play a key role in nutrient acquisition, digestion, and resistance to pests and diseases. Imbalances in microbial flora in response to environmental change and stress can therefore impact insect health and resilience. This study is aimed at defining the core gut microbiome of the Australian native stingless bee, Tetragonula carbonaria, and exploring the impact of colony transplantation on gut health. The gut microbiomes of nine forager bees from natural (log) and manufactured (box) hives were examined via 16S rRNA gene amplicon sequencing. Some differences were observed at the ASV level between the microbiomes of log and box hive bees. However, a core microbiome, dominated by Lactobacillus spp., unclassified Acetobacteraceae spp., and Bombella spp., was maintained. Further, the inferred functional potential of the microbiomes was consistent across all individuals. This study highlights that although hive transplantation has an impact on the overall diversity of stingless bee gut microbiomes, it is unlikely to have a significant negative impact on the overall health and resilience of the colony.},
}
@article {pmid37088357,
year = {2023},
author = {Selhorst, P and Lequime, S and Dudas, G and Proesmans, S and Lutumba, P and Katshongo, F and Ramadan, K and Micalessi, I and Ahuka-Mundeke, S and Vanlerberghe, V and Van Esbroeck, M and Ariën, KK},
title = {Phylogeographic analysis of dengue virus serotype 1 and cosmopolitan serotype 2 in Africa.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {133},
number = {},
pages = {46-52},
doi = {10.1016/j.ijid.2023.04.391},
pmid = {37088357},
issn = {1878-3511},
mesh = {Humans ; *Dengue Virus/genetics ; *Dengue/epidemiology ; Serogroup ; Phylogeny ; Bayes Theorem ; Africa/epidemiology ; Genotype ; Disease Outbreaks ; Fever/epidemiology ; },
abstract = {OBJECTIVES: The origin and spread of dengue virus (DENV) circulating in Africa remain poorly characterized, with African sequences representing <1% of global sequence data.<br><br>METHODS: Whole genome sequencing was performed on serum samples (n&#xa0;=&#xa0;29) from an undifferentiated fever study in 2016 in the Democratic Republic of Congo (DRC), and from febrile travelers returning from Africa. The evolutionary history of the newly acquired African DENV-1 (n&#xa0;=&#xa0;1) and cosmopolitan genotype DENV-2 (n&#xa0;=&#xa0;18) genomes was reconstructed using a phylogeographic, time-scaled Bayesian analysis on a curated DENV panel including all known African sequences.<br><br>RESULTS: A minimum of 10 and eight introductions could be identified into Africa for DENV-1 and cosmopolitan DENV-2, respectively, almost all originating from Asia. Three introductions were previously unknown. The currently circulating virus comprises mainly the recently introduced clades and one long-established African clade. Robust geographical clustering suggests limited spread of DENV after each introduction. Our data identified the DRC as the source of the 2018 Angolan DENV-2 epidemic, and similarly, the 2013 Angolan DENV-1 outbreak as the origin of our DRC study.<br><br>CONCLUSION: Active genomic surveillance of DENV in Africa at the portals of entry might help early outbreak response and limit sero- and genotype spread and human disease burden.},
}
@article {pmid37086855,
year = {2023},
author = {Buivydaitė, &#x17d; and Aryal, L and Corrêa, FB and Chen, T and Langlois, V and Elberg, CL and Netherway, T and Wang, R and Zhao, T and Acharya, B and Emerson, JB and Hillary, L and Khadka, RB and Mason-Jones, K and Sapkota, R and Sutela, S and Trubl, G and White, RA and Winding, A and Carreira, C},
title = {Meeting report: The first soil viral workshop 2022.},
journal = {Virus research},
volume = {331},
number = {},
pages = {199121},
pmid = {37086855},
issn = {1872-7492},
mesh = {Humans ; Ecology ; Food Chain ; Genome, Viral ; *Viruses ; },
abstract = {Soil viral ecology is a growing research field; however, the state of knowledge still lags behind that of aquatic systems. Therefore, to facilitate progress, the first Soil Viral Workshop was held to encourage international scientific discussion and collaboration, suggest guidelines for future research, and establish soil viral research as a concrete research area. The workshop took place at Søminestationen, Denmark, between 15 and 17th of June 2022. The meeting was primarily held in person, but the sessions were also streamed online. The workshop was attended by 23 researchers from ten different countries and from a wide range of subfields and career stages. Eleven talks were presented, followed by discussions revolving around three major topics: viral genomics, virus-host interactions, and viruses in the soil food web. The main take-home messages and suggestions from the discussions are summarized in this report.},
}
@article {pmid37086668,
year = {2023},
author = {Wu, K and Atasoy, M and Zweers, H and Rijnaarts, H and Langenhoff, A and Fernandes, TV},
title = {Impact of wastewater characteristics on the removal of organic micropollutants by Chlorella sorokiniana.},
journal = {Journal of hazardous materials},
volume = {453},
number = {},
pages = {131451},
doi = {10.1016/j.jhazmat.2023.131451},
pmid = {37086668},
issn = {1873-3336},
mesh = {Wastewater ; *Chlorella ; Carbon ; Phosphates ; *Microalgae ; Biomass ; Nitrogen ; },
abstract = {Microalgae-based technologies can be used for the removal of organic micropollutants (OMPs) from different types of wastewater. However, the effect of wastewater characteristics on the removal is still poorly understood. In this study, the removal of sixteen OMPs by Chlorella sorokiniana, cultivated in three types of wastewater (anaerobically digested black water (AnBW), municipal wastewater (MW), and secondary clarified effluent (SCE)), were assessed. During batch operational mode, eleven OMPs were removed from AnBW and MW. When switching from batch to continuous mode (0.8 d HRT), the removal of most OMPs from AnBW and MW decreased, suggesting that a longer retention time enhances the removal of some OMPs. Most OMPs were not removed from SCE since poor nutrient availability limited C. sorokiniana growth. Further correlation analyses between wastewater characteristics, biomass and OMPs removal indicated that the wastewater soluble COD and biomass concentration predominantly affected the removal of OMPs. Lastly, carbon uptake rate had a higher effect on the removal of OMPs than nitrogen and phosphate uptake rate. These data will give an insight on the implementation of microalgae-based technologies for the removal of OMPs in wastewater with varying strengths and nutrient availability.},
}
@article {pmid37084659,
year = {2023},
author = {Zeng, Z and Yue, W and Kined, C and Wang, P and Liu, R and Liu, J and Chen, X},
title = {Bacillus licheniformis reverses the environmental ceftriaxone sodium-induced gut microbial dysbiosis and intestinal inflammation in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {257},
number = {},
pages = {114890},
doi = {10.1016/j.ecoenv.2023.114890},
pmid = {37084659},
issn = {1090-2414},
mesh = {Humans ; Mice ; Animals ; Ceftriaxone/pharmacology ; *Bacillus licheniformis/genetics ; *Gastrointestinal Microbiome ; Dysbiosis/chemically induced ; RNA, Ribosomal, 16S/genetics ; Caco-2 Cells ; Inflammation/drug therapy ; Bacteria/genetics ; Anti-Bacterial Agents/toxicity ; Firmicutes/genetics ; },
abstract = {Antibiotics used as a common clinical treatment have saved many lives. Widespread use of antibiotic therapy has been known to disrupt the balance of pathogenic bacteria, host-associated microorganisms and environment. However, our understanding of Bacillus licheniformis for health benefits and ability to restore the ceftriaxone sodium-induced gut microbial dysbiosis is severely limited. We used Caco-2 cell, H&amp;E (hematoxylin-eosin staining), RT-PCR and 16S rRNA sequencing techniques to investigate the influence of Bacillus licheniformis on gut microbial dysbiosis and inflammation following ceftriaxone sodium treatment. The results showed that treatment of ceftriaxone sodium in 7 days suppressed the expression of Nf-κB pathway mRNA levels, which caused cytoplasmic vacuolization in intestinal tissues, afterward, the administration of Bacillus licheniformis could effectively restore intestinal morphology and inflammation levels. Moreover, the ceftriaxone sodium treatment entirely affected the intestinal microbial ecology, leading to a decrease in microbial abundance. Firmicutes, Proteobacteria, and Epsilonbacteraeota were the most predominant phyla in each of the four groups. Specifically, the MA group (ceftriaxone sodium treatment) resulted in a significant decrease in the relative abundance of 2 bacterial phyla and 20 bacterial genera compared to the administration of Bacillus licheniformis after ceftriaxone sodium treatment. The supplementation of Bacillus licheniformis could increase the growth of Firmicutes and Lactobacillus and encourage the construction of a more mature and stable microbiome. Furthermore, Bacillus licheniformis could restore the intestinal microbiome disorders and inflammation levels following ceftriaxone sodium treatment.},
}
@article {pmid37082712,
year = {2023},
author = {Song, W and Zhang, S and Li, X and Gao, C and Cai, J and Li, Y},
title = {Editorial: Relationship between intestinal microbiome and vasculitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1165730},
pmid = {37082712},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis ; *Vasculitis ; },
}
@article {pmid37082182,
year = {2023},
author = {Zhang, J and Wang, J and Labes, A and Zeng, R},
title = {Editorial: Marine microbial-derived molecules and their potential medical and cosmetic applications, volume II.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1188008},
doi = {10.3389/fmicb.2023.1188008},
pmid = {37082182},
issn = {1664-302X},
}
@article {pmid37081077,
year = {2023},
author = {Zorz, J and Li, C and Chakraborty, A and Gittins, DA and Surcon, T and Morrison, N and Bennett, R and MacDonald, A and Hubert, CRJ},
title = {SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {33},
pmid = {37081077},
issn = {2730-6151},
abstract = {Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson's r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.},
}
@article {pmid37076812,
year = {2023},
author = {De Wolfe, TJ and Wright, ES},
title = {Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {107},
pmid = {37076812},
issn = {1471-2180},
support = {T15 LM007059/LM/NLM NIH HHS/United States ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles.<br><br>RESULTS: Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an&#xa0;increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%).<br><br>CONCLUSIONS: Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.},
}
@article {pmid37075990,
year = {2023},
author = {Svigruha, R and Prikler, B and Farkas, A and Ács, A and Fodor, I and Tapolczai, K and Schmidt, J and Bordós, G and Háhn, J and Harkai, P and Kaszab, E and Szoboszlay, S and Pirger, Z},
title = {Presence, variation, and potential ecological impact of microplastics in the largest shallow lake of Central Europe.},
journal = {The Science of the total environment},
volume = {883},
number = {},
pages = {163537},
doi = {10.1016/j.scitotenv.2023.163537},
pmid = {37075990},
issn = {1879-1026},
mesh = {*Microplastics ; Plastics ; Ecosystem ; Progestins ; Lakes/chemistry ; Polyethylene ; *Water Pollutants, Chemical/analysis ; },
abstract = {The presence of microplastics (MPs) in the global ecosystem has generated a rapidly growing concern worldwide. Although their presence in the marine environment has been well-studied, much less data are available on their abundance in freshwaters. MPs alone and in combination with different chemicals has been shown to cause acute and chronic effects on algae and aquatic invertebrate and vertebrate species at different biological levels. However, the combined ecotoxicological effects of MPs with different chemicals on aquatic organisms are still understudied in many species and the reported data are often controversial. In the present study, we investigated, for the first time, the presence of MPs in Lake Balaton, which is the largest shallow lake of Central Europe and an important summer holiday destination. Moreover, we exposed neonates of the well-established ecotoxicological model organism Daphnia magna to different MPs (polystyrene [3 μm] or polyethylene [≤ 100 μm]) alone and in combination with three progestogen compounds (progesterone, drospirenone, levonorgestrel) at an environmentally relevant concentration (10 ng L[-1]) for 21 days. The presence of 7 polymer types of MPs in the size range of 50-100 μm was detected in Lake Balaton. Similarly to the global trends, polypropylene and polyethylene MPs were the most common types of polymer. The calculated polymer-independent average particle number was 5.5 particles m[-3] (size range: 50 μm - 100 μm) which represents the values detected in other European lakes. Our ecotoxicological experiments confirmed that MPs and progestogens can affect D. magna at the behavioral (body size and reproduction) and biochemical (detoxification-related enzyme activity) levels. The joint effects were negligible. The presence of MPs may lead to reduced fitness in the aquatic biota in freshwaters such as Lake Balaton, however, the potential threat of MPs as vectors for progestogens may be limited.},
}
@article {pmid37071646,
year = {2023},
author = {Poudel, SK and Padmanabhan, R and Dave, H and Guinta, K and Stevens, T and Sanaka, MR and Chahal, P and Sohal, DPS and Khorana, AA and Eng, C},
title = {Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease.},
journal = {PloS one},
volume = {18},
number = {4},
pages = {e0283021},
pmid = {37071646},
issn = {1932-6203},
mesh = {Humans ; Bile ; RNA, Ribosomal, 16S/genetics ; Cholangiopancreatography, Endoscopic Retrograde ; *Pancreatic Neoplasms/genetics/pathology ; *Cholangiocarcinoma/genetics/pathology ; *Bile Duct Neoplasms/pathology ; Bile Ducts, Intrahepatic/pathology ; Pancreatic Ducts/pathology ; },
abstract = {BACKGROUND: The prognostic and pathophysiologic significance of the biliary microbiota in pancreaticobiliary malignancies is little understood. Our goal was to find malignancy-related microbiomic fingerprints in bile samples taken from patients with benign and malignant pancreaticobiliary diseases.<br><br>METHODS: Bile specimens were collected from consenting patients during routine endoscopic retrograde cholangiopancreatography. We used PowerViral RNA/DNA Isolation kit to extract DNA from bile specimens. The Illumina 16S Metagenomic Sequencing Library Preparation guide was used to amplify the bacterial 16S rRNA gene and create libraries. QIIME (Quantitative Insights Into Microbial Ecology), Bioconductor phyloseq, microbiomeSeq, and mixMC packages were used for post-sequencing analysis.<br><br>RESULTS: Of 46 enrolled patients, 32 patients had pancreatic cancers, 6 had cholangiocarcinoma and 1 had gallbladder cancer. Rest of the patients had benign diseases including gallstones, and acute and chronic pancreatitis. We used multivariate approach in mixMC to classify Operational Taxonomic Units (OTUs). Doing this, we found a predominance of genera Dickeya (p = 0.00008), [Eubacterium] hallii group (p = 0.0004), Bacteroides (p = 0.0006), Faecalibacterium (p = 0.006), Escherichia-Shigella (p = 0.008), and Ruminococcus 1 (p = 0.008) in bile samples from pancreaticobiliary cancers as compared to benign diseases. Additionally, bile samples from patients with pancreatic cancer exhibited a predominance of genus Rothia (p = 0.008) as compared to those with cholangiocarcinoma, whereas bile samples from patients with cholangiocarcinoma exhibited a predominance of genera Akkermansia (p = 0.031) and Achromobacter (p = 0.031) as compared to those with pancreatic cancers.<br><br>CONCLUSIONS: Both benign and malignant pancreaticobiliary diseases have distinct microbiomic fingerprints. The relative abundance of OTUs in bile samples varies between patients with benign and malignant pancreaticobiliary diseases, as well as between cholangiocarcinoma and pancreatic cancer. Our data suggest that either these OTUs play a role in carcinogenesis or that benign disease-specific microenvironmental changes differ from cancer-specific microenvironmental changes, resulting to a clear separation of OTU clusters. We need more research to confirm and expand on our findings.},
}
@article {pmid37070710,
year = {2023},
author = {García Mendez, DF and Sanabria, J and Wist, J and Holmes, E},
title = {Effect of Operational Parameters on the Cultivation of the Gut Microbiome in Continuous Bioreactors Inoculated with Feces: A Systematic Review.},
journal = {Journal of agricultural and food chemistry},
volume = {71},
number = {16},
pages = {6213-6225},
pmid = {37070710},
issn = {1520-5118},
mesh = {Humans ; *Gastrointestinal Microbiome ; Feces ; Gastrointestinal Tract ; Bioreactors ; },
abstract = {Since the early 1980s, multiple researchers have contributed to the development of in vitro models of the human gastrointestinal system for the mechanistic interrogation of the gut microbiome ecology. Using a bioreactor for simulating all the features and conditions of the gastrointestinal system is a massive challenge. Some conditions, such as temperature and pH, are readily controlled, but a more challenging feature to simulate is that both may vary in different regions of the gastrointestinal tract. Promising solutions have been developed for simulating other functionalities, such as dialysis capabilities, peristaltic movements, and biofilm growth. This research field is under constant development, and further efforts are needed to drive these models closer to in vivo conditions, thereby increasing their usefulness for studying the gut microbiome impact on human health. Therefore, understanding the influence of key operational parameters is fundamental for the refinement of the current bioreactors and for guiding the development of more complex models. In this review, we performed a systematic search for operational parameters in 229 papers that used continuous bioreactors seeded with human feces. Despite the reporting of operational parameters for the various bioreactor models being variable, as a result of a lack of standardization, the impact of specific operational parameters on gut microbial ecology is discussed, highlighting the advantages and limitations of the current bioreactor systems.},
}
@article {pmid37069235,
year = {2023},
author = {Zhang, Y and Liu, T and Li, MM and Hua, ZS and Evans, P and Qu, Y and Tan, S and Zheng, M and Lu, H and Jiao, JY and Lücker, S and Daims, H and Li, WJ and Guo, J},
title = {Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira.},
journal = {The ISME journal},
volume = {17},
number = {7},
pages = {993-1003},
pmid = {37069235},
issn = {1751-7370},
support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Ammonia/metabolism ; Ecosystem ; *Hot Springs ; Oxidation-Reduction ; Bacteria/genetics/metabolism ; Nitrification ; *Ammonium Compounds/metabolism ; Nitrates/metabolism ; Phylogeny ; Archaea/genetics ; },
abstract = {The recent discovery of Nitrospira species capable of complete ammonia oxidation (comammox) in non-marine natural and engineered ecosystems under mesothermal conditions has changed our understanding of microbial nitrification. However, little is known about the occurrence of comammox bacteria or their ability to survive in moderately thermal and/or hyperthermal habitats. Here, we report the wide distribution of comammox Nitrospira in five terrestrial hot springs at temperatures ranging from 36 to 80°C and provide metagenome-assembled genomes of 11 new comammox strains. Interestingly, the identification of dissimilatory nitrate reduction to ammonium (DNRA) in thermophilic comammox Nitrospira lineages suggests that they have versatile ecological functions as both sinks and sources of ammonia, in contrast to the described mesophilic comammox lineages, which lack the DNRA pathway. Furthermore, the in situ expression of key genes associated with nitrogen metabolism, thermal adaptation, and oxidative stress confirmed their ability to survive in the studied hot springs and their contribution to nitrification in these environments. Additionally, the smaller genome size and higher GC content, less polar and more charged amino acids in usage profiles, and the expression of a large number of heat shock proteins compared to mesophilic comammox strains presumably confer tolerance to thermal stress. These novel insights into the occurrence, metabolic activity, and adaptation of comammox Nitrospira in thermal habitats further expand our understanding of the global distribution of comammox Nitrospira and have significant implications for how these unique microorganisms have evolved thermal tolerance strategies.},
}
@article {pmid37065146,
year = {2023},
author = {Vannier, P and Farrant, GK and Klonowski, A and Gaidos, E and Thorsteinsson, T and Marteinsson, V&#xde;},
title = {Metagenomic analyses of a microbial assemblage in a subglacial lake beneath the Vatnajökull ice cap, Iceland.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1122184},
pmid = {37065146},
issn = {1664-302X},
abstract = {Skaftárkatlar are two subglacial lakes located beneath the Vatnajökull ice cap in Iceland associated with geothermal and volcanic activity. Previous studies of these lakes with ribosomal gene (16S rDNA) tag sequencing revealed a limited diversity of bacteria adapted to cold, dark, and nutrient-poor waters. In this study, we present analyses of metagenomes from the lake which give new insights into its microbial ecology. Analyses of the 16S rDNA genes in the metagenomes confirmed the existence of a low-diversity core microbial assemblage in the lake and insights into the potential metabolisms of the dominant members. Seven taxonomic genera, Sulfuricurvum, Sulfurospirillum, Acetobacterium, Pelobacter/Geobacter, Saccharibacteria, Caldisericum, and an unclassified member of Prolixibacteraceae, comprised more than 98% of the rDNA reads in the library. Functional characterisation of the lake metagenomes revealed complete metabolic pathways for sulphur cycling, nitrogen metabolism, carbon fixation via the reverse Krebs cycle, and acetogenesis. These results show that chemolithoautotrophy constitutes the main metabolism in this subglacial ecosystem. This assemblage and its metabolisms are not reflected in enrichment cultures, demonstrating the importance of in situ investigations of this environment.},
}
@article {pmid37060391,
year = {2023},
author = {Adhikari, NP and Adhikari, S},
title = {First report on the bacterial community composition, diversity, and functions in Ramsar site of Central Himalayas, Nepal.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {5},
pages = {573},
pmid = {37060391},
issn = {1573-2959},
mesh = {RNA, Ribosomal, 16S/genetics ; Nepal ; *Environmental Monitoring ; *Bacteria/genetics ; Wetlands ; Water ; },
abstract = {Wetland bacterial communities are highly sensitive to altered hydrology and the associated change in water physicochemical and biological properties leading to shifts in community composition and diversity, hence affecting the ecological roles. However, relevant studies are lacking in the wetlands of central Himalayas Nepal. Thus, we aimed to explore the variation of bacterial communities, diversity, and ecologic functions in the wet and dry periods of a wetland (designed as Ramsar site, Ramsar no 2257) by using 16S rRNA gene-based Illumina MiSeq sequencing. We reported a pronounced variation in water physicochemical and biological properties (temperature, pH, Chla, DOC, and TN), bacterial diversity, and community composition. Bacterial communities in the dry season harbored significantly higher alpha diversity, while significantly higher richness and abundance were reflected in the wet season. Our results uncovered the effect of nutrients on bacterial abundance, richness, and community composition. Fourteen percent of the total OTUs were shared in two hydrological periods, and the largest portion of unique OTUs (58%) was observed in the dry season. Planctomycetes and Bacteroidetes dominated the wet season exclusive OTUs; meanwhile, Actinobacteria dominated the dry season exclusive OTUs. Bacteria in these wetlands exhibited divergent ecological functions during the dry and wet seasons. By disclosing the variation of water bacterial communities in different hydrologic periods and their relationship with environmental factors, this first-hand work in the Ramsar site of Nepal will develop a baseline dataset for the scientific community that will assist in understanding the wetland's microbial ecology and biogeography.},
}
@article {pmid37056166,
year = {2023},
author = {Lindsay, RJ and Holder, PJ and Talbot, NJ and Gudelj, I},
title = {Metabolic efficiency reshapes the seminal relationship between pathogen growth rate and virulence.},
journal = {Ecology letters},
volume = {26},
number = {6},
pages = {896-907},
pmid = {37056166},
issn = {1461-0248},
support = {BB/T015985/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Virulence ; *Biological Evolution ; },
abstract = {A cornerstone of classical virulence evolution theories is the assumption that pathogen growth rate is positively correlated with virulence, the amount of damage pathogens inflict on their hosts. Such theories are key for incorporating evolutionary principles into sustainable disease management strategies. Yet, empirical evidence raises doubts over this central assumption underpinning classical theories, thus undermining their generality and predictive power. In this paper, we identify a key component missing from current theories which redefines the growth-virulence relationship in a way that is consistent with data. By modifying the activity of a single metabolic gene, we engineered strains of Magnaporthe oryzae with different nutrient acquisition and growth rates. We conducted in planta infection studies and uncovered an unexpected non-monotonic relationship between growth rate and virulence that is jointly shaped by how growth rate and metabolic efficiency interact. This novel mechanistic framework paves the way for a much-needed new suite of virulence evolution theories.},
}
@article {pmid37055390,
year = {2023},
author = {Dudek, NK and Galaz-Montoya, JG and Shi, H and Mayer, M and Danita, C and Celis, AI and Viehboeck, T and Wu, GH and Behr, B and Bulgheresi, S and Huang, KC and Chiu, W and Relman, DA},
title = {Previously uncharacterized rectangular bacterial structures in the dolphin mouth.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {2098},
pmid = {37055390},
issn = {2041-1723},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P41 GM103832/GM/NIGMS NIH HHS/United States ; RM1 GM135102/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; *Neisseriaceae/genetics ; *Bottle-Nosed Dolphin ; Mouth ; Bacterial Structures ; },
abstract = {Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining revealed multiple paired bands within RBSs, suggesting the presence of cells dividing along the longitudinal axis. Cryogenic transmission electron microscopy and tomography showed parallel membrane-bound segments that are likely cells, encapsulated by an S-layer-like periodic surface covering. RBSs displayed unusual pilus-like appendages with bundles of threads splayed at the tips. We present multiple lines of evidence, including genomic DNA sequencing of micromanipulated RBSs, 16S rRNA gene sequencing, and fluorescence in situ hybridization, suggesting that RBSs are bacterial and distinct from the genera Simonsiella and Conchiformibius (family Neisseriaceae), with which they share similar morphology and division patterning. Our findings highlight the diversity of novel microbial forms and lifestyles that await characterization using tools complementary to genomics such as microscopy.},
}
@article {pmid37049481,
year = {2023},
author = {Pham, VT and Steinert, RE and Duysburgh, C and Ghyselinck, J and Marzorati, M and Dekker, PJT},
title = {In Vitro Effect of Enzymes and Human Milk Oligosaccharides on FODMAP Digestion and Fecal Microbiota Composition.},
journal = {Nutrients},
volume = {15},
number = {7},
pages = {},
pmid = {37049481},
issn = {2072-6643},
support = {Company funds//DSM/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome ; Ecosystem ; Milk, Human ; Oligosaccharides ; Fatty Acids, Volatile ; *Gastrointestinal Microbiome ; Digestion ; },
abstract = {Fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) cause intestinal discomfort in patients with irritable bowel syndrome (IBS). An enzyme mix (2500 SU invertase, 2400 GalU α-galactosidase, 10,000 ALU β-galactosidase) optimized for FODMAP digestion, and/or human milk oligosaccharides (HMO) (2'-FL, DFL, and LNnT), were evaluated for effects on microbial community activity and composition in short-term colonic incubations using the fecal microbiota of four patients with IBS-D symptoms under the following test conditions: (i) FODMAP, (ii) pre-digested (with enzyme mix) FODMAP, (iii) FODMAP + HMO, and (iv) pre-digested FODMAP + HMO. Pre-digested FODMAP reduced short-chain fatty acid (SCFA) production versus FODMAP; HMO restored this. A 10-day experiment with the simulator of the human intestinal microbial ecosystem (SHIME[®]), using fecal samples from two patients with IBS-D, further evaluated these findings. FODMAP resulted in decreased microbial diversity versus blank. Pre-digestion with the enzyme mix restored microbial diversity, improved FODMAP digestibility, and reduced gas pressure versus undigested FODMAP; however, SCFA production decreased. HMO restored SCFA production along with an increase in gas pressure and increased abundance of Lachnospiraceae. When used in combination, the FODMAP enzyme mix and HMO may resolve FODMAP-related IBS symptoms while maintaining a healthy gut microbiome via prebiotic activity.},
}
@article {pmid37044393,
year = {2022},
author = {Datta, R and Maity, P and Bhadury, P and Rizvi, AN and Raghunathan, C},
title = {An Updated Checklist of Free-living Marine Nematodes from Coastal India.},
journal = {Zootaxa},
volume = {5196},
number = {2},
pages = {151-196},
doi = {10.11646/zootaxa.5196.2.1},
pmid = {37044393},
issn = {1175-5334},
mesh = {Animals ; Chromadorea ; Ecosystem ; India ; *Nematoda ; Rhabditoidea ; Checklist ; Aquatic Organisms ; },
abstract = {The present study provides an updated species list of free-living marine nematodes reported from coastal India (Coasts and Islands) based on the thorough consultation of literature published from 1956 to 2022. This exercise resulted in a total of 617 valid species belonging to 266 genera, 48 families, 21 superfamilies and 9 orders. Class Chromadorea comprises 487 species represented by 205 genera, while class Enoplea includes 130 species belonging to 61 genera. The most common family was Xyalidae, with 76 species and the least common families having a single species each were represented by Aegialoalaimidae, Rhadinematidae, Aphanolaimidae, Rhabditidae, Pandolaimidae and Rhabdodemaniidae. The checklist provides a robust framework for the distribution and biogeography of free-living marine nematodes from the Indian waters and could be used to relate with marine ecosystems of other countries.},
}
@article {pmid37044259,
year = {2023},
author = {Kim, HS and Keum, HL and Chung, IY and Nattkemper, L and Head, CR and Koh, A and Sul, WJ and Pastar, I and Yosipovitch, G},
title = {Characterization of a Perturbed Skin Microbiome in Prurigo Nodularis and Lichen Simplex Chronicus.},
journal = {The Journal of investigative dermatology},
volume = {143},
number = {10},
pages = {2082-2085.e5},
doi = {10.1016/j.jid.2023.03.1669},
pmid = {37044259},
issn = {1523-1747},
mesh = {Humans ; *Neurodermatitis/diagnosis ; *Prurigo/diagnosis ; Skin ; Diagnosis, Differential ; },
}
@article {pmid37042985,
year = {2023},
author = {Zhang, Y and Xia, X and Wan, L and Han, BP and Liu, H and Jing, H},
title = {Microbial Communities Are Shaped by Different Ecological Processes in Subtropical Reservoirs of Different Trophic States.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2073-2085},
pmid = {37042985},
issn = {1432-184X},
mesh = {*Plankton ; *Microbiota ; Eukaryota ; Seasons ; },
abstract = {Understanding microbial community structure and the underlying control mechanisms are fundamental purposes of aquatic ecology. However, little is known about the seasonality and how trophic conditions regulate plankton community in subtropical reservoirs. In this study, we study the prokaryotic and picoeukaryotic communities and their interactions during wet and dry seasons in two subtropical reservoirs: one at oligotrophic state and another at mesotrophic state. Distinct microbial community compositions (prokaryotes and picoeukaryotes) and seasonal variation pattern were detected in the oligotrophic and mesotrophic reservoirs. The interactions between prokaryotic and picoeukaryotic communities were more prevalent in the oligotrophic reservoir, suggesting enhanced top-down control of small eukaryotic grazers on the prokaryotic communities. On the other hand, the microbial community in the mesotrophic reservoir was more influenced by physico-chemical parameters and showed a stronger seasonal variation, which may be the result of distinct nutrient levels in wet and dry seasons, indicating the importance of bottom-up control. Our study contributes to new understandings of the environmental and biological processes that shape the structure and dynamics of the planktonic microbial communities in reservoirs of different trophic states.},
}
@article {pmid37039841,
year = {2023},
author = {Del Campo, EM and Gasulla, F and Hell, AF and González-Hourcade, M and Casano, LM},
title = {Comparative Transcriptomic and Proteomic Analyses Provide New Insights into the Tolerance to Cyclic Dehydration in a Lichen Phycobiont.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1725-1739},
pmid = {37039841},
issn = {1432-184X},
mesh = {*Transcriptome ; Dehydration ; *Lichens/physiology ; Proteome/metabolism ; Proteomics ; Desiccation ; },
abstract = {Desiccation tolerance (DT) is relatively frequent in non-vascular plants and green algae. However, it is poorly understood how successive dehydration/rehydration (D/R) cycles shape their transcriptomes and proteomes. Here, we report a comprehensive analysis of adjustments on both transcript and protein profiles in response to successive D/R cycles in Coccomyxa simplex (Csol), isolated from the lichen Solorina saccata. A total of 1833 transcripts and 2332 proteins were differentially abundant as a consequence of D/R; however, only 315 of these transcripts/proteins showed similar trends. Variations in both transcriptomes and proteomes along D/R cycles together with functional analyses revealed an extensive decrease in transcript and protein levels during dehydration, most of them involved in gene expression, metabolism, substance transport, signalling and folding catalysis, among other cellular functions. At the same time, a series of protective transcripts/proteins, such as those related to antioxidant defence, polyol metabolism and autophagy, was upregulated during dehydration. Overall, our results show a transient decrease in most cellular functions as a result of drying and a gradual reactivation of specific cell processes to accommodate the hydration status along successive D/R cycles. This study provides new insights into key mechanisms involved in the DT of Csol and probably other dehydration-tolerant microalgae. In addition, functionally characterising the high number of genes/proteins of unknown functions found in this study may lead to the discovery of new DT mechanisms.},
}
@article {pmid37037922,
year = {2023},
author = {Lemke, M and DeSalle, R},
title = {The Role of Microbial Ecology in Restoration Ecology in the Age of Genomics: A Summary of the Microbial Ecology Special Issue.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1136-1141},
pmid = {37037922},
issn = {1432-184X},
mesh = {*Ecology ; *Genomics ; },
}
@article {pmid37037808,
year = {2023},
author = {Song, A and Su, J and Wang, H and Zhang, Z and Zhang, X and Van de Peer, Y and Chen, F and Fang, W and Guan, Z and Zhang, F and Wang, Z and Wang, L and Ding, B and Zhao, S and Ding, L and Liu, Y and Zhou, L and He, J and Jia, D and Zhang, J and Chen, C and Yu, Z and Sun, D and Jiang, J and Chen, S and Chen, F},
title = {Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {2021},
pmid = {37037808},
issn = {2041-1723},
mesh = {*Chrysanthemum/genetics ; Phylogeny ; Plant Breeding ; Gene Expression Profiling ; Flowers/genetics ; Chromosomes ; },
abstract = {Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum is challenging due to its complex genetic background. Here, we report a near-complete assembly and annotation for C. morifolium comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69 Mb). Comparative and evolutionary analyses reveal a whole-genome triplication (WGT) event shared by Chrysanthemum species approximately 6 million years ago (Mya) and the possible lineage-specific polyploidization of C. morifolium approximately 3 Mya. Multilevel evidence suggests that C. morifolium is likely a segmental allopolyploid. Furthermore, a combination of genomics and transcriptomics approaches demonstrate the C. morifolium genome can be used to identify genes underlying key ornamental traits. Phylogenetic analysis of CmCCD4a traces the flower colour breeding history of cultivated chrysanthemum. Genomic resources generated from this study could help to accelerate chrysanthemum genetic improvement.},
}
@article {pmid37032887,
year = {2023},
author = {Prendergast, DM and Slowey, R and Burgess, CM and Murphy, D and Johnston, D and Morris, D and O' Doherty, &#xc1; and Moriarty, J and Gutierrez, M},
title = {Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1118264},
pmid = {37032887},
issn = {1664-302X},
abstract = {BACKGROUND: The Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance genes to other bacterial species present in the same environment. Due to their impact on human health and the paucity of new antibiotics, the World Health Organization (WHO) categorized carbapenem resistant and ESBL-producing as critical. Enterobacterales are ubiquitous and the role of the environment in the transmission of AMR organisms or antimicrobial resistance genes (ARGs) must be examined in tackling AMR in both humans and animals under the one health approach. Animal manure is recognized as an important source of AMR bacteria entering the environment, in which resistant genes can accumulate.<br><br>METHODS: To gain a better understanding of the dissemination of third generation cephalosporin and fluoroquinolone resistance genes between isolates in the environment, we applied whole genome sequencing (WGS) to Enterobacterales (79 E. coli, 1 Enterobacter cloacae, 1 Klebsiella pneumoniae, and 1 Citrobacter gillenii) isolated from farm effluents in Ireland before (n&#x2009;=&#x2009;72) and after (n&#x2009;=&#x2009;10) treatment by integrated constructed wetlands (ICWs). DNA was extracted using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) followed by WGS on a MiSeq platform (Illumina, Eindhoven, Netherlands) using v3 chemistry as 300-cycle paired-end runs. AMR genes and point mutations were identified and compared to the phenotypic results for better understanding of the mechanisms of resistance and resistance transmission.<br><br>RESULTS: A wide variety of cephalosporin and fluoroquinolone resistance genes (mobile genetic elements (MGEs) and chromosomal mutations) were identified among isolates that mostly explained the phenotypic AMR patterns. A total of 31 plasmid replicon types were identified among the 82 isolates, with a subset of them (n&#x2009;=&#x2009;24), identified in E. coli isolates. Five plasmid replicons were confined to the Enterobacter cloacae isolate and two were confined to the Klebsiella pneumoniae isolate. Virulence genes associated with functions including stress, survival, regulation, iron uptake secretion systems, invasion, adherence and toxin production were identified.<br><br>CONCLUSION: Our study showed that antimicrobial resistant organisms (AROs) can persist even following wastewater treatment and could transmit AMR of clinical relevance to the environment and ultimately pose a risk to human or animal health.},
}
@article {pmid37030359,
year = {2023},
author = {Yang, X and Duan, P and Hicks, L and Wang, K and Li, D},
title = {Mechanisms underlying the responses of microbial carbon and nitrogen use efficiencies to nitrogen addition are mediated by topography in a subtropical forest.},
journal = {The Science of the total environment},
volume = {880},
number = {},
pages = {163236},
doi = {10.1016/j.scitotenv.2023.163236},
pmid = {37030359},
issn = {1879-1026},
mesh = {*Nitrogen/analysis ; *Carbon ; Forests ; Biomass ; Soil/chemistry ; Phosphorus ; Soil Microbiology ; },
abstract = {Microbial carbon use efficiency (CUE) and nitrogen use efficiency (NUE) are key parameters determining the fate of C and N in soils. Atmospheric N deposition has been found to heavily impact multiple soil C and N transformations, but we lack understanding of the responses of CUE and NUE to N deposition, and it remains uncertain whether responses may be mediated by topography. Here, a N addition experiment with three treatment levels (0, 50 and 100 kg N ha[-1] yr[-1]) was conducted in the valley and on the slope of a subtropical karst forest. Nitrogen addition increased microbial CUE and NUE at both topographic positions, but the underlying mechanisms differed. In the valley, the increase in CUE was associated with an increase in soil fungal richness:biomass and lower litter C:N, whereas on the slope, the response was linked with a reduced ratio of dissolved soil organic C (DOC) to available phosphorus (AVP) which reduced respiration, and increased root N:P stoichiometry. In the valley, the increase in NUE was explained by stimulated microbial N growth relative to gross N mineralization, which was associated with increased ratios of soil total dissolved N:AVP and fungal richness:biomass. In contrast, on the slope, the increase in NUE was attributed to reduced gross N mineralization, linked to increased DOC:AVP. Overall, our results highlight how topography-driven soil substrate availability and microbial properties can regulate microbial CUE and NUE.},
}
@article {pmid37030231,
year = {2023},
author = {Liu, H and Jiao, Q and Fan, L and Jiang, Y and Alyemeni, MN and Ahmad, P and Chen, Y and Zhu, M and Liu, H and Zhao, Y and Liu, F and Liu, S and Li, G},
title = {Integrated physio-biochemical and transcriptomic analysis revealed mechanism underlying of Si-mediated alleviation to cadmium toxicity in wheat.},
journal = {Journal of hazardous materials},
volume = {452},
number = {},
pages = {131366},
doi = {10.1016/j.jhazmat.2023.131366},
pmid = {37030231},
issn = {1873-3336},
mesh = {*Cadmium/toxicity/metabolism ; Silicon/pharmacology/chemistry ; Triticum/metabolism ; Transcriptome ; Antioxidants/metabolism ; *Soil Pollutants/toxicity/metabolism ; },
abstract = {Cadmium (Cd) contamination has resulted in serious reduction of crop yields. Silicon (Si), as a beneficial element, regulates plant growth to heavy metal toxicity mainly through reducing metal uptake and protecting plants from oxidative injury. However, the molecular mechanism underlying Si-mediated Cd toxicity in wheat has not been well understood. This study aimed to reveal the beneficial role of Si (1 mM) in alleviating Cd-induced toxicity in wheat (Triticum aestivum) seedlings. The results showed that exogenous supply of Si decreased Cd concentration by 67.45% (root) and 70.34% (shoot), and maintained ionic homeostasis through the function of important transporters, such as Lsi, ZIP, Nramp5 and HIPP. Si ameliorated Cd-induced photosynthetic performance inhibition through up-regulating photosynthesis-related genes and light harvesting-related genes. Si minimized Cd-induced oxidative stress by decreasing MDA contents by 46.62% (leaf) and 75.09% (root), and helped re-establish redox homeostasis by regulating antioxidant enzymes activities, AsA-GSH cycle and expression of relevant genes through signal transduction pathway. The results revealed molecular mechanism of Si-mediated wheat tolerance to Cd toxicity. Si fertilizer is suggested to be applied in Cd contaminated soil for food safety production as a beneficial and eco-friendly element.},
}
@article {pmid37026303,
year = {2023},
author = {Pal, S and Vani, G and Donthineni, PR and Basu, S and Arunasri, K},
title = {Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye.},
journal = {Indian journal of ophthalmology},
volume = {71},
number = {4},
pages = {1566-1573},
pmid = {37026303},
issn = {1998-3689},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Dry Eye Syndromes ; *Sjogren's Syndrome/diagnosis/complications ; Tears ; *Microbiota ; Bacteria/genetics ; },
abstract = {PURPOSE: To understand the bacterial microbiome changes associated with Sjogren's syndrome (SS) and non-Sjogren's syndrome (NSS) aqueous-deficient dry eyes compared to healthy eyes.<br><br>METHODS: Bacterial microbiome was generated from the deoxyribonucleic acid of tear film samples in healthy (n = 33), SS (n = 17), and NSS (n = 28) individuals. Sequencing of the V3-V4 region of the 16S rRNA gene was performed on the Illumina HiSeq2500 platform. Quantitative Insights Into Microbial Ecology (QIIME) pipeline was used to assign taxa to sequences. Statistical analysis was performed in R to assess the alpha diversity and beta diversity indices. Significant changes between the healthy, SS, and NSS cohorts were depicted by principal coordinate analysis (PCoA), differential abundance, and network analysis.<br><br>RESULTS: Tear microbiome was generated in healthy, SS, and NSS samples. Phyla Actinobacteria, Firmicutes, and Bacteroidetes showed significant changes in SS and NSS compared to healthy. Genera Lactobacillus and Bacillus were predominantly present in all samples. PCoA and heat map analysis showed distinct clusters for SS and NSS from the healthy cohort. Genera Prevotella, Coriobacteriaceae UCG-003, Enterococcus, Streptomyces, Rhodobacter, Ezakiella, and Microbacterium significantly increased in abundance in SS and NSS compared to a healthy cohort. Bacteria-bacteria interaction in SS, NSS, and healthy cohorts was predicted by CoNet network analysis. This analysis predicted a major hub of interaction for the pro-inflammatory bacterium Prevotella in the SS and NSS cohorts.<br><br>CONCLUSION: The results of the study indicate significant changes in the phyla and genera in SS and NSS compared to healthy. Both discriminative analysis and network analysis indicated a possible association of predominant pro-inflammatory bacteria with SS and NSS.},
}
@article {pmid37024470,
year = {2023},
author = {Young, E and Melaugh, G and Allen, RJ},
title = {Active layer dynamics drives a transition to biofilm fingering.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {17},
pmid = {37024470},
issn = {2055-5008},
support = {682237/ERC_/European Research Council/International ; BB/R012415/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Biofilms/growth &amp; development ; },
abstract = {The emergence of spatial organisation in biofilm growth is one of the most fundamental topics in biofilm biophysics and microbiology. It has long been known that growing biofilms can adopt smooth or rough interface morphologies, depending on the balance between nutrient supply and microbial growth; this 'fingering' transition has been linked with the average width of the 'active layer' of growing cells at the biofilm interface. Here we use long-time individual-based simulations of growing biofilms to investigate in detail the driving factors behind the biofilm-fingering transition. We show that the transition is associated with dynamical changes in the active layer. Fingering happens when gaps form in the active layer, which can cause local parts of the biofilm interface to pin, or become stationary relative to the moving front. Pinning can be transient or permanent, leading to different biofilm morphologies. By constructing a phase diagram for the transition, we show that the controlling factor is the magnitude of the relative fluctuations in the active layer thickness, rather than the active layer thickness per se. Taken together, our work suggests a central role for active layer dynamics in controlling the pinning of the biofilm interface and hence biofilm morphology.},
}
@article {pmid37024159,
year = {2023},
author = {Vikram, S and Ramond, JB and Ortiz, M and Maggs-Kölling, G and Pelser, K and Cowan, DA},
title = {Soil fungal diversity and assembly along a xeric stress gradient in the central Namib Desert.},
journal = {Fungal biology},
volume = {127},
number = {4},
pages = {997-1003},
doi = {10.1016/j.funbio.2023.03.001},
pmid = {37024159},
issn = {1878-6146},
mesh = {*Soil/chemistry ; Bacteria ; Soil Microbiology ; Desert Climate ; *Ascomycota ; },
abstract = {The Namib Desert of south-western Africa is one of the oldest deserts in the world and possesses unique geographical, biological and climatic features. While research through the last decade has generated a comprehensive survey of the prokaryotic communities in Namib Desert soils, little is yet known about the diversity and function of edaphic fungal communities, and even less of their responses to aridity. In this study, we have characterized soil fungal community diversity across the longitudinal xeric gradient across the Namib desert (for convenience, divided into the western fog zone, the central low-rainfall zone and the eastern high-rainfall zone), using internal transcribed sequence (ITS) metabarcoding. Ascomycota, Basidiomycota and Chytridiomycota consistently dominated the Namib Desert edaphic fungal communities and a core mycobiome composed of only 15 taxa, dominated by members of the class Dothideomycetes (Ascomycota), was identified. However, fungal community structures were significantly different in the fog, low-rainfall and high-rainfall zones. Furthermore, Namib Desert gravel plain fungal community assembly was driven by both deterministic and stochastic processes; the latter dominating in the all three xeric zones. We also present data that suggest that the inland limit of fog penetration represents an ecological barrier to fungal dispersal across the Namib Desert.},
}
@article {pmid37020129,
year = {2023},
author = {Berman, TS and Izraeli, Y and Lalzar, M and Mozes-Daube, N and Lepetit, D and Tabic, A and Varaldi, J and Zchori-Fein, E},
title = {RNA Viruses Are Prevalent and Active Tenants of the Predatory Mite Phytoseiulus persimilis (Acari: Phytoseiidae).},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2060-2072},
pmid = {37020129},
issn = {1432-184X},
support = {397/21//Israel Science Foundation/ ; },
mesh = {Humans ; Animals ; *Mites ; Pest Control, Biological ; *RNA Viruses/genetics ; Predatory Behavior ; *Tetranychidae ; },
abstract = {Many arthropod species harbor a diverse range of viruses. While much is known about pathogenic viruses of some economically important insects and arthropods involved in disease transmission, viruses associated with mites have rarely been studied. The main objective of this study was to characterize the virome of Phytoseiulus persimilis (Phytoseiidae), a predatory mite commercially used worldwide for the biological control of the key pest Tetranychus urticae (Tetranichidae). A combination of de novo transcriptome assembly and virion sequencing, revealed that RNA viruses are highly prevalent and active tenants of commercial populations of P. persimilis, comprising on average 9% of the mite's total mRNA. Seventeen RNA viruses dominated the mite's virome (i.e., were highly transcribed) with over half (n = 10) belonging to the order Picornavirales, + ssRNA viruses that infect a large range of hosts, including arthropods. Screening of the 17 dominant virus sequences in P. persimilis and T. urticae revealed that three viruses (two Picornavirales of the families Iflaviridae and Dicistroviridae, and one unclassified Riboviria) are unique to P. persimilis and three others (two unclassified Picornavirales and one unclassified Riboviria) are present in both mite species. Most of the sequences were related to viruses previously documented in economically important arthropods, while others have rarely been documented before in arthropods. These findings demonstrate that P. persimilis, like many other arthropods, harbors a diverse RNA virome, which might affect the mite's physiology and consequently its efficiency as a biological control agent.},
}
@article {pmid37017718,
year = {2023},
author = {Thompson, CC and Tschoeke, D and Coutinho, FH and Leomil, L and Garcia, GD and Otsuki, K and Turcq, BJ and Moreira, LS and Turcq, PFM and Cordeiro, RC and Asp, NE and Thompson, FL},
title = {Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2202-2209},
pmid = {37017718},
issn = {1432-184X},
mesh = {*Microbiota/genetics ; Bacteria ; Metagenome ; Rivers/microbiology ; Lakes/microbiology ; Geologic Sediments/microbiology ; },
abstract = {The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.},
}
@article {pmid37010970,
year = {2023},
author = {May, AK},
title = {Host Microbiome Threats in the Intensive Care Unit.},
journal = {Surgical infections},
volume = {24},
number = {3},
pages = {276-283},
doi = {10.1089/sur.2023.029},
pmid = {37010970},
issn = {1557-8674},
mesh = {Humans ; *Microbiota ; Anti-Bacterial Agents/therapeutic use ; Intensive Care Units ; Dysbiosis/therapy ; },
abstract = {Human microbiota demonstrate diversity and balance that is adaptive for the host and supports maintaining homeostasis. Although acute illness or injury may derange microbiota diversity and the proportion of potentially pathogenic microbes, that derangement may be further exacerbated by commonly deployed intensive care unit (ICU) therapeutic and practices. These include antibiotic administration, delayed luminal nutrition, acid suppression, and vasopressor infusion. Furthermore, the local ICU microbial ecology, regardless of disinfection practices, shapes the patient's microbiota, especially with the acquisition of multi-drug-resistant pathogens. Current approaches to protect a normal microbiome, or restore a deranged one, are part of a multifaceted approach that may include antibiotic stewardship and infection control practices as microbiome-directed therapeutics emerge.},
}
@article {pmid37010558,
year = {2023},
author = {Khatri, S and Chaudhary, P and Shivay, YS and Sharma, S},
title = {Role of Fungi in Imparting General Disease Suppressiveness in Soil from Organic Field.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2047-2059},
pmid = {37010558},
issn = {1432-184X},
support = {fellowship//University Grants Commission/ ; fellowship//University of Queensland - Indian Institute of Technology Delhi Academy of Research/ ; MI02024//IITD-ICAR/ ; MI02535//IITD-TUD/ ; },
mesh = {*Soil ; *Fungi/genetics ; Bacteria ; Agriculture/methods ; Organic Agriculture/methods ; Soil Microbiology ; },
abstract = {Soil microbial communities are key players responsible for imparting suppressive potential to the soil against soil-borne phytopathogens. Fungi have an immense potential to inhibit soil-borne phytopathogens, but the fungal counterpart has been less explored in this context. We assessed the composition of fungal communities in soil under long-term organic and conventional farming practice, and control soil. The disease-suppressive potential of organic field was already established. A comparative analysis of the disease suppressiveness contributed by the fungal component of soil from conventional and organic farms was assessed using dual culture assays. The quantification of biocontrol markers and total fungi was done; the characterization of fungal community was carried out using ITS-based amplicon sequencing. Soil from organic field exhibited higher disease-suppressive potential than that from conventional farming, against the pathogens selected for the study. Higher levels of hydrolytic enzymes such as chitinase and cellulase, and siderophore production were observed in soil from the organic field compared to the conventional field. Differences in community composition were observed under conventional and organic farming, with soil from organic field exhibiting specific enrichment of key biocontrol fungal genera. The fungal alpha diversity was lower in soil from the organic field compared to the conventional field. Our results highlight the role of fungi in contributing to general disease-suppressive ability of the soil against phytopathogens. The identification of fungal taxa specifically associated with organic farming can aid in understanding the mechanism of disease suppression under such a practice, and can be exploited to induce general disease suppressiveness in otherwise conducive soil.},
}
@article {pmid37010433,
year = {2023},
author = {Fortuna, KJ and Holtappels, D and Venneman, J and Baeyen, S and Vallino, M and Verwilt, P and Rediers, H and De Coninck, B and Maes, M and Van Vaerenbergh, J and Lavigne, R and Wagemans, J},
title = {Back to the Roots: Agrobacterium-Specific Phages Show Potential to Disinfect Nutrient Solution from Hydroponic Greenhouses.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {4},
pages = {e0021523},
pmid = {37010433},
issn = {1098-5336},
mesh = {*Bacteriophages/genetics ; Agrobacterium ; Hydroponics ; Hydrogen Peroxide/pharmacology ; Mutation ; },
abstract = {Agrobacterium biovar 1 is a soilborne plant pathogen with the ability to colonize the irrigation system of greenhouses, causing hairy root disease (HRD). Currently, management focuses on using hydrogen peroxide to disinfect the nutrient solution, but due to the emergence of resistant strains, its efficacy and sustainability are questioned. Using a relevant collection of pathogenic Agrobacterium biovar 1 strains, OLIVR1 to 6, six phages specific to this pathogen and belonging to three different genera were isolated from Agrobacterium biovar 1-infected greenhouses. All phages were named OLIVR, referring to their location of isolation, Onze-Lieve-Vrouwe-Waver, and were characterized by whole-genome analysis, confirming their strictly lytic lifestyle. They remained stable under greenhouse-relevant conditions. To assess the efficacy of the phages, their ability to disinfect greenhouse nutrient solution inoculated with agrobacteria was tested. Each of the phages infected their host, but their ability to decrease the bacterial concentration differed. For instance, OLIVR1 reduced the bacterial concentration with 4 log units without phage resistance emerging. While OLIVR4 and OLIVR5 were also infectious in nutrient solution, they did not always decrease the bacterial load below the limit of detection, and phage resistance emerged. Finally, the mutations causing phage resistance by receptor modification were identified. For OLIVR4-resistant Agrobacterium isolates, but not for OLIVR5-resistant isolates, motility decreased. Together, these data show the potential of some of these phages as disinfectant of nutrient solution, and they might be a valuable tool to tackle HRD. IMPORTANCE Hairy root disease, caused by rhizogenic Agrobacterium biovar 1 is a rapidly emerging bacterial disease worldwide. It affects tomatoes, cucumbers, eggplant, and bell pepper, causing high yield losses in hydroponic greenhouses. Recent findings suggest that the current management practices, mainly focusing on UV-C and hydrogen peroxide to disinfect contaminated water, have a questionable efficacy. Hence, we investigate the potential of phages as a biological means of preventing this disease. Using a diverse collection of Agrobacterium biovar 1, we isolated three different phage species that together infect 75% of the collection. Since these phages are strictly lytic, while remaining both stable and infectious under greenhouse-relevant conditions, they might be suitable candidates for biological control.},
}
@article {pmid37009161,
year = {2023},
author = {Cummings, S and Ardor Bellucci, LM and Seabrook, S and Raineault, NA and McPhail, KL and Thurber, AR},
title = {Variations and gradients between methane seep and off-seep microbial communities in a submarine canyon system in the Northeast Pacific.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15119},
pmid = {37009161},
issn = {2167-8359},
mesh = {*Seawater ; Methane/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; *Microbiota/genetics ; },
abstract = {Methane seeps are highly abundant marine habitats that contribute sources of chemosynthetic primary production to marine ecosystems. Seeps also factor into the global budget of methane, a potent greenhouse gas. Because of these factors, methane seeps influence not only local ocean ecology, but also biogeochemical cycles on a greater scale. Methane seeps host specialized microbial communities that vary significantly based on geography, seep gross morphology, biogeochemistry, and a diversity of other ecological factors including cross-domain species interactions. In this study, we collected sediment cores from six seep and non-seep locations from Grays and Quinault Canyons (46-47°N) off Washington State, USA, as well as one non-seep site off the coast of Oregon, USA (45°N) to quantify the scale of seep influence on biodiversity within marine habitats. These samples were profiled using 16S rRNA gene sequencing. Predicted gene functions were generated using the program PICRUSt2, and the community composition and predicted functions were compared among samples. The microbial communities at seeps varied by seep morphology and habitat, whereas the microbial communities at non-seep sites varied by water depth. Microbial community composition and predicted gene function clearly transitioned from on-seep to off-seep in samples collected from transects moving away from seeps, with a clear ecotone and high diversity where methane-fueled habitats transition into the non-seep deep sea. Our work demonstrates the microbial and metabolic sphere of influence that extends outwards from methane seep habitats.},
}
@article {pmid37008301,
year = {2022},
author = {Deyaert, S and Moens, F and Pirovano, W and van den Bogert, B and Klaassens, ES and Marzorati, M and Van de Wiele, T and Kleerebezem, M and Van den Abbeele, P},
title = {Development of a reproducible small intestinal microbiota model and its integration into the SHIME[®]-system, a dynamic in vitro gut model.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1054061},
pmid = {37008301},
issn = {1664-302X},
abstract = {The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its interactions with ingested compounds, primarily due to the inaccessibility of this region in vivo. This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME[®]-technology. Essential parameters were identified and optimized from a screening experiment testing different inoculation strategies, nutritional media, and environmental parameters over an 18-day period. Subjecting a synthetic bacterial consortium to the selected conditions resulted in a stable microbiota that was representative in terms of abundance [8.81 ± 0.12 log (cells/ml)], composition and function. Indeed, the observed community mainly consisted of the genera Streptococcus, Veillonella, Enterococcus, Lactobacillus, and Clostridium (qPCR and 16S rRNA gene targeted Illumina sequencing), while nutrient administration boosted lactate production followed by cross-feeding interactions towards acetate and propionate. Furthermore, similarly as in vivo, bile salts were only partially deconjugated and only marginally converted into secondary bile salts. After confirming reproducibility of the small intestinal microbiota model, it was integrated into the established M-SHIME® where it further increased the compositional relevance of the colonic community. This long-term in vitro model provides a representative simulation of the ileal bacterial community, facilitating research of the ileum microbiota dynamics and activity when, for example, supplemented with microbial or diet components. Furthermore, integration of this present in vitro simulation increases the biological relevance of the current M-SHIME® technology.},
}
@article {pmid37002423,
year = {2023},
author = {Pushpakumara, BLDU and Tandon, K and Willis, A and Verbruggen, H},
title = {The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2032-2046},
pmid = {37002423},
issn = {1432-184X},
support = {DP200101613//Australian Research Council grant/ ; },
mesh = {Animals ; *Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Chlorophyta ; *Microbiota ; Coral Reefs ; },
abstract = {Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.},
}
@article {pmid37001600,
year = {2023},
author = {Gilles, S and Meinzer, M and Landgraf, M and Kolek, F and von Bargen, S and Pack, K and Charalampopoulos, A and Ranpal, S and Luschkova, D and Traidl-Hoffmann, C and Jochner-Oette, S and Damialis, A and Büttner, C},
title = {Betula pendula trees infected by birch idaeovirus and cherry leaf roll virus: Impacts of urbanisation and NO2 levels.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {327},
number = {},
pages = {121526},
doi = {10.1016/j.envpol.2023.121526},
pmid = {37001600},
issn = {1873-6424},
mesh = {Humans ; *Trees ; Betula ; *Nepovirus ; Urbanization ; Nitrogen Dioxide ; Plants ; },
abstract = {Viruses are frequently a microbial biocontaminant of healthy plants. The occurrence of the infection can be also due to environmental stress, like urbanisation, air pollution and increased air temperature, especially under the ongoing climate change. The aim of the present study was to investigate the hypothesis that worsened air quality and fewer green areas may favour the higher frequency of common viral infections, particularly in a common tree in temperate and continental climates, Betula pendula ROTH. We examined 18 trees, during the years 2015-2017, the same always for each year, in the region of Augsburg, Germany. By specific PCR, the frequency of two viruses, Cherry leaf roll virus (CLRV, genus Nepovirus, family Secoviridae), which is frequent in birch trees, and a novel virus tentatively named birch idaeovirus (BIV), which has been only recently described, were determined in pollen samples. The occurrence of the viruses was examined against the variables of urban index, air pollution (O3 and NO2), air temperature, and tree morphometrics (trunk perimeter, tree height, crown height and diameter). Generalized Non-linear models (binomial logit with backward stepwise removal of independent variables) were employed. During the study period, both CLRV and BIV were distributed widely throughout the investigated birch individuals. CLRV seemed to be rather cosmopolitan and was present independent of any abiotic factor. BIV's occurrence was mostly determined by higher values of the urban index and of NO2. Urban birch trees, located next to high-traffic roads with higher NO2 levels, are more likely to be infected by BIV. Increased environmental stress may lead to more plant viral infections. Here we suggest that this is particularly true for urban spaces, near high-traffic roads, where plants may be more stressed, and we recommend taking mitigation measures for controlling negative human interventions.},
}
@article {pmid37001406,
year = {2023},
author = {Vaezzadeh, V and Yi, X and Rais, FR and Bong, CW and Thomes, MW and Lee, CW and Zakaria, MP and Wang, AJ and Zhong, G and Zhang, G},
title = {Corrigendum to "Distribution of black carbon and PAHs in sediments of Peninsular Malaysia" [Mar. Pollut. Bull.172 (2021) 112871].},
journal = {Marine pollution bulletin},
volume = {190},
number = {},
pages = {114797},
doi = {10.1016/j.marpolbul.2023.114797},
pmid = {37001406},
issn = {1879-3363},
}
@article {pmid37001405,
year = {2023},
author = {Kundu, K and Van Landuyt, J and Mattelin, V and Martin, B and Neyts, M and Parmentier, K and Boon, N},
title = {Enhanced removal of warfare agent tri-nitro-toluene by a Methylophaga-dominated microbiome.},
journal = {Marine pollution bulletin},
volume = {190},
number = {},
pages = {114866},
doi = {10.1016/j.marpolbul.2023.114866},
pmid = {37001405},
issn = {1879-3363},
mesh = {*Methanol/metabolism ; *Trinitrotoluene/metabolism ; Bacteria/metabolism ; North Sea ; },
abstract = {Historical exposure of the marine environment to 2,4,6-trinitrotoluene (TNT) happened due to the dumping of left-over munitions. Despite significant research on TNT decontamination, the potential of marine microbiome for TNT degradation remains only little explored. In this study, TNT degradation experiments were conducted with sediment located near the World War I munition dumpsite - Paardenmarkt in the Belgian part of North Sea. A slow removal was observed using TNT as sole source of C and N, which could be enhanced by adding methanol. Degradation was reflected in nitro-reduced metabolites and microbial growth. 16S Illumina sequencing analysis revealed several enriched genera that used TNT as a sole source of C and N - Colwellia, Thalossospira, and Methylophaga. Addition of methanol resulted in increased abundance of Methylophaga, which corresponded to the rapid removal of TNT. Methanol enhanced the degradation by providing additional energy and establishing syntrophic association between methanol-utilizing and TNT-utilizing bacteria.},
}
@article {pmid37000232,
year = {2023},
author = {Stupar, M and Savković, &#x17d; and Popović, S and Simić, GS and Grbić, ML},
title = {Speleomycology of Air in Stopića Cave (Serbia).},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2021-2031},
pmid = {37000232},
issn = {1432-184X},
mesh = {Animals ; Humans ; *Fungi ; Caves/microbiology ; Serbia ; Pandemics ; *COVID-19 ; Seasons ; Air Microbiology ; Environmental Monitoring/methods ; },
abstract = {Fungi can colonize organic matter present in subterranean sites and have a significant role as dwellers in different microniches of cave habitats. In order to analyze the content of airborne fungal propagules in different parts of "Stopića Cave," a touristic site in Serbia, air sampling was carried out in three seasons during 2020, prior to and during the onset of COVID-19 pandemic. Culturable mycobiota was identified using both microscopic techniques and ITS region/BenA gene barcoding, while multivariate analyses were employed to establish the link between fungal taxa and different environmental factors. The maximal measured fungal propagule concentrations were recorded during spring sampling which were based on fungal propagule concentration categories; the cave environment matches the category V. A total of 29 fungal isolates were identified, while Aspergillus, Cladosporium, Fusarium, Lecanicillium, Mucor, and Penicillium were the most diverse genera. According to the trophic mode, most of the isolated fungal species were pathotrophs (75.86%), but when regarding ecological guilds, the most dominant were undefined saprobes and animal pathogens (41.38% for each). Show caves are especially vulnerable to human impacts, and the fungal propagules' concentration within the caves could be good indices for the level of ecological disturbance.},
}
@article {pmid37000231,
year = {2023},
author = {Kurm, V and Visser, J and Schilder, M and Nijhuis, E and Postma, J and Korthals, G},
title = {Soil Suppressiveness Against Pythium ultimum and Rhizoctonia solani in Two Land Management Systems and Eleven Soil Health Treatments.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1709-1724},
pmid = {37000231},
issn = {1432-184X},
support = {KB-33-006//Ministerie van Landbouw, Natuur en Voedselkwaliteit/ ; LWV20042/BO-56-001-061//Ministerie van Landbouw, Natuur en Voedselkwaliteit/ ; },
mesh = {*Soil ; *Pythium ; Conservation of Natural Resources ; Soil Microbiology ; Rhizoctonia ; Plant Diseases/prevention &amp; control/microbiology ; },
abstract = {The soil microbiome is known to be crucial for the control of soil-borne plant diseases. However, there is still little knowledge on how to modify the soil microbiome to induce or increase disease suppressiveness. In the present study, we applied eleven soil health treatments combined with conventional and organic agricultural management in a long-term field experiment. Suppressiveness against Pythium ultimum and Rhizoctonia solani was assessed in bioassays for 2 years. In addition, the microbiome community composition and microbial abundance were determined. We found that while several treatments changed the microbial community composition compared to the control, only a combination treatment of anaerobic soil disinfestation, hair meal, and compost addition resulted in suppressiveness against P. ultimum. Pythium suppressiveness is likely to have been caused by an increased microbial abundance and activity. Moreover, the increased abundance of several bacterial taxa, such as Pseudomonas sp., Chryseobacterium sp., members of the family Chitinophagaceae, and the fungal genus Mortierella sp. and family Trichosporonaceae, was measured. There was no overall difference in suppressiveness between conventional and organic land management. Also, no suppressiveness against R. solani could be detected. Our results indicate that a treatment combining the reduction of microorganisms followed by a recovery phase with high amounts of organic amendments may be more effective in inducing suppressiveness than treatments consisting of only one of these measures.},
}
@article {pmid37000121,
year = {2023},
author = {Lopes, LD and Futrell, SL and Wright, EE and Danalatos, GJ and Castellano, MJ and Vyn, TJ and Archontoulis, SV and Schachtman, DP},
title = {Soil depth and geographic distance modulate bacterial β-diversity in deep soil profiles throughout the U.S. Corn Belt.},
journal = {Molecular ecology},
volume = {32},
number = {13},
pages = {3718-3732},
doi = {10.1111/mec.16945},
pmid = {37000121},
issn = {1365-294X},
mesh = {*Soil ; *Zea mays/genetics ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {Understanding how microbial communities are shaped across spatial dimensions is of fundamental importance in microbial ecology. However, most studies on soil biogeography have focused on the topsoil microbiome, while the factors driving the subsoil microbiome distribution are largely unknown. Here we used 16S rRNA amplicon sequencing to analyse the factors underlying the bacterial β-diversity along vertical (0-240 cm of soil depth) and horizontal spatial dimensions (~500,000 km[2]) in the U.S. Corn Belt. With these data we tested whether the horizontal or vertical spatial variation had stronger impacts on the taxonomic (Bray-Curtis) and phylogenetic (weighted Unifrac) β-diversity. Additionally, we assessed whether the distance-decay (horizontal dimension) was greater in the topsoil (0-30 cm) or subsoil (in each 30 cm layer from 30-240 cm) using Mantel tests. The influence of geographic distance versus edaphic variables on the bacterial communities from the different soil layers was also compared. Results indicated that the phylogenetic β-diversity was impacted more by soil depth, while the taxonomic β-diversity changed more between geographic locations. The distance-decay was lower in the topsoil than in all subsoil layers analysed. Moreover, some subsoil layers were influenced more by geographic distance than any edaphic variable, including pH. Although different factors affected the topsoil and subsoil biogeography, niche-based models explained the community assembly of all soil layers. This comprehensive study contributed to elucidating important aspects of soil bacterial biogeography including the major impact of soil depth on the phylogenetic β-diversity, and the greater influence of geographic distance on subsoil than on topsoil bacterial communities in agroecosystems.},
}
@article {pmid36999338,
year = {2023},
author = {Garbeva, P and Avalos, M and Ulanova, D and van Wezel, GP and Dickschat, JS},
title = {Volatile sensation: The chemical ecology of the earthy odorant geosmin.},
journal = {Environmental microbiology},
volume = {25},
number = {9},
pages = {1565-1574},
doi = {10.1111/1462-2920.16381},
pmid = {36999338},
issn = {1462-2920},
mesh = {*Odorants/analysis ; *Bacteria/genetics/metabolism ; Naphthols/chemistry/metabolism ; Sensation ; },
abstract = {Geosmin may be the most familiar volatile compound, as it lends the earthy smell to soil. The compound is a member of the largest family of natural products, the terpenoids. The broad distribution of geosmin among bacteria in both terrestrial and aquatic environments suggests that this compound has an important ecological function, for example, as a signal (attractant or repellent) or as a protective specialized metabolite against biotic and abiotic stresses. While geosmin is part of our everyday life, scientists still do not understand the exact biological function of this omnipresent natural product. This minireview summarizes the current general observations regarding geosmin in prokaryotes and introduces new insights into its biosynthesis and regulation, as well as its biological roles in terrestrial and aquatic environments.},
}
@article {pmid36998391,
year = {2023},
author = {Rajala, P and Bomberg, M},
title = {Editorial: Geomicrobes: Life in terrestrial deep subsurface, volume II.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1169127},
pmid = {36998391},
issn = {1664-302X},
}
@article {pmid36996916,
year = {2023},
author = {Hidalgo, J and Epelde, L and Anza, M and Becerril, JM and Garbisu, C},
title = {Mycoremediation with Agaricus bisporus and Pleurotus ostreatus growth substrates versus phytoremediation with Festuca rubra and Brassica sp. for the recovery of a Pb and γ-HCH contaminated soil.},
journal = {Chemosphere},
volume = {327},
number = {},
pages = {138538},
doi = {10.1016/j.chemosphere.2023.138538},
pmid = {36996916},
issn = {1879-1298},
mesh = {*Pleurotus ; Soil ; Hexachlorocyclohexane ; *Festuca ; Lead ; Biodegradation, Environmental ; *Brassica ; *Agaricus ; },
abstract = {Mycoremediation with mushroom growth substrates can be used for the recovery of mixed contaminated soils due to the benefits derived from the physicochemical characteristics of the substrates, the activity of extracellular enzymes secreted by the fungi, and the presence of the fungal mycelia. The objective of this work was to assess the potential of Agaricus bisporus and Pleurotus ostreatus growth substrates (inoculated mushroom substrates vs. spent mushroom substrates) for the mycoremediation of soils co-contaminated with lead and lindane (γ-HCH). We compared the efficiency of these mycoremediation strategies with the phytoremediation with Brassica spp. Or Festuca rubra plants, in terms of both reduction in contaminant levels and enhancement of soil health. An enhanced soil health was achieved as a result of the application of mycoremediation treatments, compared to phytoremediation and control (untreated) treatments. The application of P. ostreatus inoculated substrate led to the most significant reduction in γ-HCH concentration (up to 88.9% compared to corresponding controls). In the presence of inoculated mushroom substrate, P. ostreatus fruiting bodies extracted more Pb than Brassica spp. Or F. rubra plants. Mycoremediation with P. ostreatus growth substrates appears a promising strategy for the recovery of the health of soils co-contaminated with Pb and γ-HCH.},
}
@article {pmid36991472,
year = {2023},
author = {Wang, Y and Jiménez, DJ and Zhang, Z and van Elsas, JD},
title = {Functioning of a tripartite lignocellulolytic microbial consortium cultivated under two shaking conditions: a metatranscriptomic study.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {16},
number = {1},
pages = {54},
pmid = {36991472},
issn = {2731-3654},
abstract = {BACKGROUND: In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic lignocellulolytic microbial consortium composed of the bacteria Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1. Here, the gene expression profiles of each strain in this consortium were examined after growth at two shaking speeds (180 and 60 rpm) at three time points (1, 5 and 13 days).<br><br>RESULTS: The results indicated that, at 60&#xa0;rpm, C. freundii so4 switched, to a large extent, from aerobic to flexible&#xa0;(aerobic/microaerophilic/anaerobic) metabolism, resulting in continued slow growth till late stage. In addition, Coniochaeta sp. 2T2.1 tended to occur to a larger extent in the hyphal form, with genes encoding adhesion proteins being highly expressed. Much like at 180&#xa0;rpm, at 60&#xa0;rpm, S. paramultivorum w15 and Coniochaeta sp. 2T2.1 were key players in hemicellulose degradation processes, as evidenced from the respective CAZy-specific transcripts. Coniochaeta sp. 2T2.1 exhibited expression of genes encoding arabinoxylan-degrading enzymes (i.e., of CAZy groups GH10, GH11, CE1, CE5 and GH43), whereas, at 180&#xa0;rpm, some of these genes were suppressed at early stages of growth. Moreover, C. freundii so4 stably expressed genes that were predicted to encode proteins with (1) &#x3b2;-xylosidase/&#x3b2;-glucosidase and (2) peptidoglycan/chitinase activities, (3) stress response- and detoxification-related proteins. Finally, S. paramultivorum w15 showed involvement in vitamin B2 generation in the early stages across the two shaking speeds, while this role was taken over by C. freundii so4 at late stage at 60&#xa0;rpm.<br><br>CONCLUSIONS: We provide evidence that S. paramultivorum w15 is involved in the degradation of mainly hemicellulose and in vitamin B2 production, and C. freundii so4 in the degradation of oligosaccharides or sugar dimers, next to detoxification processes. Coniochaeta sp. 2T2.1 was held to be strongly involved in cellulose and xylan (at early stages), next to lignin modification processes (at later stages). The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite microbial consortium.},
}
@article {pmid36989794,
year = {2023},
author = {Goswami, V and Deepika, S and Chandra, R and Babu, CR and Kothamasi, D},
title = {Arbuscular mycorrhizas accelerate the degradation of colour containing organic pollutants present in distillery spent wash leachates.},
journal = {Journal of hazardous materials},
volume = {452},
number = {},
pages = {131291},
doi = {10.1016/j.jhazmat.2023.131291},
pmid = {36989794},
issn = {1873-3336},
mesh = {*Mycorrhizae ; *Environmental Pollutants ; Color ; Oxides ; Esters ; },
abstract = {Distillery spent wash (DSW) from molasses-based distilleries is being used as a low-cost alternative to chemical fertilizers in countries like India and Brazil. However, using DSW as a fertilizer substitute causes organic pollutant leaching, including melanoidins and caramel colourants that turn bodies of water dark brown. This study investigated the arbuscular mycorrhiza (AM) mediated degradation of organic pollutants in DSW. Mycorrhizal and non-mycorrhizal Sorghum bicolor were grown in microcosms for 16 weeks. The plants were fertilized with either raw DSW or Hoagland solution. Leachates draining from the microcosms after fertilization were collected three times in 30-day intervals. Each 30-day collection was preceded by two fertilizations. A gas chromatography-mass spectrometry comparative analyses of raw DSW with leachates of the third collection from mycorrhizal and non-mycorrhizal microcosms was made. Sixty-five and 42 complex organic compounds were detected in raw DSW and leachate collected from the non-mycorrhizal pots respectively. Only 26 compounds were detected in leachate collected from mycorrhizal pots. Absent from leachate of the mycorrhizal pots were: colour-containing organic compounds diacetone alcohol; 3-amino-2-cyano-6-methyl-6,7-dihydrothieno[2,3-b]pyrazine S-oxide; cyclohexane; 1,2-benzenedicarboxylic acid, butyl 8-methylnonyl ester; 2-pyrrolidinone; and acetic acid, dodecyl ester present in raw DSW. The results indicate that AM fungi can degrade organic pollutants in DSW.},
}
@article {pmid36988842,
year = {2023},
author = {Messaoudi, Y and Smichi, N and Allaf, T and Besombes, C and Allaf, K and Gargouri, M},
title = {Instant Controlled Pressure-Drop (DIC) for Volatile Compound Extraction and Bioethanol Production from Empty Aleppo Pinecones and Eucalyptus Chips: Process Optimization and Statistical Modeling.},
journal = {Applied biochemistry and biotechnology},
volume = {195},
number = {11},
pages = {7086-7109},
pmid = {36988842},
issn = {1559-0291},
mesh = {*Eucalyptus ; *Oils, Volatile/chemistry ; Fermentation ; },
abstract = {Several plant species contain volatile compounds extracted as "essential oils" through different technologies. After essential oil extraction, the residual solid is a lignocellulosic solid waste. This work proposes the instant controlled pressure-drop (DIC) technology to autovaporize volatile compounds and modify the lignocellulosic matrix. Indeed, DIC technology is a thermomechanical process based on short-time/high-temperature and pressure pretreatment. It enhances the saccharification and fermentation process (SSF) for bioethanol production. A 3-variable design of experiments optimized the DIC processing parameters to reach 100% efficiency (EE) of volatile compound extraction using response surface methodology (RSM). Eucalyptus chips presented 50 volatile identified compounds after 7 min of DIC treatment. 1,8-Cineole, β-phellandrene, aromadendrene, eudesmol, and spathulenol are the most important volatile compounds. The empty Aleppo pinecones delivered 32 volatile compounds in 5 min of DIC treatment, the most important of which were caryophyllene, nortricyclene, verbenol, and camphor. After the autovaporization extraction stage, solid fraction residues were hydrolyzed and fermented in the same stirred bioreactor, using SSF strategy for 72 h at 37 °C. The highest bioethanol yields reached 73.9% and 54.82% (g per 100 g DM) from eucalyptus chip and empty Aleppo pinecone, respectively.},
}
@article {pmid36987547,
year = {2023},
author = {Coats, ER and Appel, FJ and Guho, N and Brinkman, CK and Mellin, J},
title = {Interrogating the performance and microbial ecology of an enhanced biological phosphorus removal/post-anoxic denitrification process at bench and pilot scales.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {95},
number = {4},
pages = {e10852},
doi = {10.1002/wer.10852},
pmid = {36987547},
issn = {1554-7531},
support = {2018-67022-27894//National Institute of Food and Agriculture/ ; IDA01720//National Institute of Food and Agriculture/ ; IDA01585//National Institute of Food and Agriculture/ ; CBET-1705728//National Science Foundation/ ; //Sorenson Family Endowment/ ; },
mesh = {*Phosphorus ; *Denitrification ; Bioreactors/microbiology ; Bacteria ; Carbon ; Fatty Acids, Volatile ; Sewage ; },
abstract = {Research focused on interrogating post-anoxic enhanced biological phosphorus removal (EBPR) at bench and pilot scales. Average bench-scale effluent ranged from 0.33 to 1.4 mgP/L, 0.35 to 3.7 mgNH3 -N/L, and 1.1 to 3.9 mgNOx -N/L. Comparatively, the pilot achieved effluent (50th percentile/average) of 0.13/0.2 mgP/L, 9.7/8.2 mgNH3 -N/L, and 0.38/3.3 mgNOx -N/L under dynamic influent and environmental conditions. For EBPR process monitoring, P:C ratio data indicated that 0.2-0.4 molP/molC will result in stable EBPR; relatedly, a target design influent volatile fatty acid (VFA):P ratio would exceed 15 mgCOD/mgP. Post-anoxic EBPR was enriched for Nitrobacter spp. at 1.70%-20.27%, with Parcubacteria also dominating; the former is putatively associated with nitritation and the latter is a putative fermenting heterotrophic organism. Post-anoxic specific denitrification rates (SDNRs) (20°C) ranged from 0.70 to 3.10 mgN/gVSS/h; there was a strong correlation (R[2] = 0.94) between the SDNR and %Parcubacteria for systems operated at a 20-day solids residence time (SRT). These results suggest that carbon substrate potentially generated by this putative fermenter may enhance post-anoxic EBPR. PRACTITIONER POINTS: Post-anoxic EBPR can achieve effluent of <0.2 mgP/L and <12 mgN/L. The P:C and VFA:P ratios can be predictive for EBPR process monitoring. Post-anoxic EBPR was enriched for Nitrobacter spp. over Nitrospira spp. and also for Parcubacteria, which is a putative fermenting heterotrophic organism. Post-anoxic specific denitrification rates (20°C) ranged from 0.70 to 3.10 mgN/gVSS/h. BLASTn analysis of 16S rDNA PAO primer set was shown to be improved to 93.8% for Ca. Accumulibacter phosphatis and 73.2%-94.0% for all potential PAOs.},
}
@article {pmid36985355,
year = {2023},
author = {Masigol, H and Grossart, HP and Taheri, SR and Mostowfizadeh-Ghalamfarsa, R and Pourmoghaddam, MJ and Bouket, AC and Khodaparast, SA},
title = {Utilization of Low Molecular Weight Carbon Sources by Fungi and Saprolegniales: Implications for Their Ecology and Taxonomy.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
pmid = {36985355},
issn = {2076-2607},
support = {GR1540/23-1//Leibniz-Institute of Freshwater Ecology and Inland Fisheries/ ; No.4728//Deputy of Research and Technology of the University of Guilan/ ; },
abstract = {Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.},
}
@article {pmid36985156,
year = {2023},
author = {Nayduch, D and Neupane, S and Pickens, V and Purvis, T and Olds, C},
title = {House Flies Are Underappreciated Yet Important Reservoirs and Vectors of Microbial Threats to Animal and Human Health.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
pmid = {36985156},
issn = {2076-2607},
support = {3020-32000-018-00D//United States Department of Agriculture/ ; },
abstract = {House flies are well recognized as filth-associated organisms and public nuisances. House flies create sanitation issues when they bridge the gap between microbe-rich breeding environments and animal/human habitations. Numerous scientific surveys have demonstrated that house flies harbor bacterial pathogens that pose a threat to humans and animals. More extensive and informative surveys incorporating next-generation sequencing technologies have shown that house fly carriage of pathogens and harmful genetic elements, such as antimicrobial resistance genes, is more widespread and dangerous than previously thought. Further, there is a strong body of research confirming that flies not only harbor but also transmit viable, and presumably infectious, bacterial pathogens. Some pathogens replicate and persist in the fly, permitting prolonged shedding and dissemination. Finally, although the drivers still have yet to be firmly determined, the potential range of dissemination of flies and their associated pathogens can be extensive. Despite this evidence, the house flies' role as reservoirs, disseminators, and true, yet facultative, vectors for pathogens have been greatly underestimated and underappreciated. In this review, we present key studies that bolster the house fly's role both an important player in microbial ecology and population biology and as transmitters of microbial threats to animal and human health.},
}
@article {pmid36983540,
year = {2023},
author = {Veas-Mattheos, K and Almendras, K and Pezoa, M and Muster, C and Orlando, J},
title = {High Andean Steppes of Southern Chile Contain Little-Explored Peltigera Lichen Symbionts.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {3},
pages = {},
pmid = {36983540},
issn = {2309-608X},
support = {FONDECYT 1181510//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ICN2021_002//Millennium Science Initiative/ ; },
abstract = {Peltigera lichens can colonize extreme habitats, such as high-elevation ecosystems, but their biodiversity is still largely unknown in these environments, especially in the southern hemi- sphere. We assessed the genetic diversity of mycobionts and cyanobionts of 60 Peltigera lichens collected in three high Andean steppes of southern Chile using LSU, β-tubulin, COR3 and ITS loci for mycobionts, and SSU and rbcLX loci for cyanobionts. We obtained 240 sequences for the different mycobiont markers and 118 for the cyanobiont markers, including the first report of β-tubulin sequences of P. patagonica through modifying a previously designed primer. Phylogenetic analyses, ITS scrutiny and variability of haplotypes were used to compare the sequences with those previously reported. We found seven mycobiont species and eleven cyanobiont haplotypes, including considerable novel symbionts. This was reflected by ~30% of mycobionts and ~20% of cyanobionts haplotypes that yielded less than 99% BLASTn sequence identity, 15 new sequences of the ITS1-HR, and a putative new Peltigera species associated with 3 Nostoc haplotypes not previously reported. Our results suggest that high Andean steppe ecosystems are habitats of unknown or little-explored lichen species and thus valuable environments to enhance our understanding of global Peltigera biodiversity.},
}
@article {pmid36983467,
year = {2023},
author = {Hkiri, N and Olicón-Hernández, DR and Pozo, C and Chouchani, C and Asses, N and Aranda, E},
title = {Simultaneous Heavy Metal-Polycyclic Aromatic Hydrocarbon Removal by Native Tunisian Fungal Species.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {3},
pages = {},
pmid = {36983467},
issn = {2309-608X},
support = {B-RNM-204-UGR20//Regional Government of Andalusia/ ; 20230427//Instituto Polit&#xe9;cnico Nacional. Mexico/ ; },
abstract = {Multi-contamination by organic pollutants and toxic metals is common in anthropogenic and industrial environments. In this study, the five fungal strains Chaetomium jodhpurense (MH667651.1), Chaetomium maderasense (MH665977.1), Paraconiothyrium variabile (MH667653.1), Emmia lacerata, and Phoma betae (MH667655.1), previously isolated in Tunisia, were investigated for the simultaneous removal and detoxification of phenanthrene (PHE) and benzo[a]anthracene (BAA), as well as heavy metals (HMs) (Cu, Zn, Pb and Ag) in Kirk's media. The removal was analysed using HPLC, ultra-high performance liquid chromatography (UHPLC) coupled to a QToF mass spectrometer, transmission electron microscopy, and toxicology was assessed using phytotoxicity (Lepidium sativum seeds) and Microtox[®] (Allivibrio fisherii) assays. The PHE and BAA degradation rates, in free HMs cultures, reached 78.8% and 70.7%, respectively. However, the addition of HMs considerably affected the BAA degradation rate. The highest degradation rates were associated with the significant production of manganese-peroxidase, lignin peroxidase, and unspecific peroxygenase. The Zn and Cu removal efficacy was considerably higher with live cells than dead cells. Transmission electron microscopy confirmed the involvement of both bioaccumulation and biosorption processes in fungal HM removal. The environmental toxicological assays proved that simultaneous PAH and HM removal was accompanied by detoxification. The metabolites produced during co-treatment were not toxic for plant tissues, and the acute toxicity was reduced. The obtained results indicate that the tested fungi can be applied in the remediation of sites simultaneously contaminated with PAHs and HMs.},
}
@article {pmid36979988,
year = {2023},
author = {Lindner, C and Looijesteijn, E and Dijck, HV and Bovee-Oudenhoven, I and Heerikhuisen, M and Broek, TJVD and Marzorati, M and Triantis, V and Nauta, A},
title = {Infant Fecal Fermentations with Galacto-Oligosaccharides and 2'-Fucosyllactose Show Differential Bifidobacterium longum Stimulation at Subspecies Level.},
journal = {Children (Basel, Switzerland)},
volume = {10},
number = {3},
pages = {},
pmid = {36979988},
issn = {2227-9067},
support = {none//FrieslandCampina (Netherlands)/ ; },
abstract = {The objective of the current study was to evaluate the potential of 2'-FL and GOS, individually and combined, in beneficially modulating the microbial composition of infant and toddler (12-18 months) feces using the micro-Matrix bioreactor. In addition, the impacts of GOS and 2'-FL, individually and combined, on the outgrowth of fecal bifidobacteria at (sub)species level was investigated using the baby M-SHIME[®] model. For young toddlers, significant increases in the genera Bifidobacterium, Veillonella, and Streptococcus, and decreases in Enterobacteriaceae, Clostridium XIVa, and Roseburia were observed in all supplemented fermentations. In addition, GOS, and combinations of GOS and 2'-FL, increased Collinsella and decreased Salmonella, whereas 2'-FL, and combined GOS and 2'-FL, decreased Dorea. Alpha diversity increased significantly in infants with GOS and/or 2'-FL, as well as the relative abundances of the genera Veillonella and Akkermansia with 2'-FL, and Lactobacillus with GOS. Combinations of GOS and 2'-FL significantly stimulated Veillonella, Lactobacillus, Bifidobacterium, and Streptococcus. In all supplemented fermentations, Proteobacteria decreased, with the most profound decreases accomplished by the combination of GOS and 2'-FL. When zooming in on the different (sub)species of Bifidobacterium, GOS and 2'-FL were shown to be complementary in stimulating breast-fed infant-associated subspecies of Bifidobacterium longum in a dose-dependent manner: GOS stimulated Bifidobacterium longum subsp. longum, whereas 2'-FL supported outgrowth of Bifidobacterium longum subsp. infantis.},
}
@article {pmid36978500,
year = {2023},
author = {Peruzzo, A and Vascellari, M and Massaro, A and Mancin, M and Stefani, A and Orsini, M and Danesi, P and Petrin, S and Carminato, A and Santoro, MM and Speranza, R and Losasso, C and Capelli, G},
title = {Giardia duodenalis Colonization Slightly Affects Gut Microbiota and Hematological Parameters in Clinically Healthy Dogs.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {6},
pages = {},
pmid = {36978500},
issn = {2076-2615},
support = {RC-IZSVE 8/2019)//Ministero della Salute/ ; },
abstract = {Giardia duodenalis (Giardia) is a worldwide cause of acute diarrheal disease both in humans and animals. The primary aim of this study was to investigate possible variations in gut microbiota in a population of asymptomatic dogs (n = 31), naturally infected or not by Giardia. Gut microbiota and the hematological, biochemical, and fecal parameters related to intestinal function were investigated. Giardia infection was associated with a significant shift of beta diversity, showing a relevant reduction of Gammaproteobacteria and an increase of Fusobacteria in male-positive dogs if compared with negatives. A significant imbalance of different bacterial taxa, with particular reference to the Erysipelotrichales, Lactobacillales, Clostridiales, and Burkholderiales orders, was observed, with the first two being higher in Giardia-positive dogs. Giardia-positive males displayed significantly higher values of cCRP than negative males as well as positive females, supporting the presence of a pro-inflammatory state. Taken together, these results indicate that the presence of Giardia does not substantially modify the microbial ecology of the intestine nor the hematological markers of disease. Thus treatments against Giardia should be considered with caution in asymptomatic subjects.},
}
@article {pmid36978419,
year = {2023},
author = {Perestrelo, S and Amaro, A and Brouwer, MSM and Clemente, L and Ribeiro Duarte, AS and Kaesbohrer, A and Karpíšková, R and Lopez-Chavarrias, V and Morris, D and Prendergast, D and Pista, A and Silveira, L and Skarżyńska, M and Slowey, R and Veldman, KT and Zając, M and Burgess, C and Alvarez, J},
title = {Building an International One Health Strain Level Database to Characterise the Epidemiology of AMR Threats: ESBL-AmpC Producing E. coli as An Example-Challenges and Perspectives.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
pmid = {36978419},
issn = {2079-6382},
support = {773830//European Union's Horizon 2020/ ; },
abstract = {Antimicrobial resistance (AMR) is one of the top public health threats nowadays. Among the most important AMR pathogens, Escherichia coli resistant to extended spectrum cephalosporins (ESC-EC) is a perfect example of the One Health problem due to its global distribution in animal, human, and environmental sources and its resistant phenotype, derived from the carriage of plasmid-borne extended-spectrum and AmpC β-lactamases, which limits the choice of effective antimicrobial therapies. The epidemiology of ESC-EC infection is complex as a result of the multiple possible sources involved in its transmission, and its study would require databases ideally comprising information from animal (livestock, companion, wildlife), human, and environmental sources. Here, we present the steps taken to assemble a database with phenotypic and genetic information on 10,763 ESC-EC isolates retrieved from multiple sources provided by 13 partners located in eight European countries, in the frame of the DiSCoVeR Joint Research project funded by the One Health European Joint Programme (OH-EJP), along with its strengths and limitations. This database represents a first step to help in the assessment of different geographical and temporal trends and transmission dynamics in animals and humans. The work performed highlights aspects that should be considered in future international efforts, such as the one presented here.},
}
@article {pmid36978279,
year = {2023},
author = {Horsch, CCA and Antunes, PM and Fahey, C and Grandy, AS and Kallenbach, CM},
title = {Trait-based assembly of arbuscular mycorrhizal fungal communities determines soil carbon formation and retention.},
journal = {The New phytologist},
volume = {239},
number = {1},
pages = {311-324},
doi = {10.1111/nph.18914},
pmid = {36978279},
issn = {1469-8137},
mesh = {*Mycorrhizae ; Soil/chemistry ; Carbon ; *Mycobiome ; *Glomeromycota ; *Sorghum ; Phosphorus ; Soil Microbiology ; Plant Roots/microbiology ; },
abstract = {Fungi are crucial for soil organic carbon (SOC) formation, especially for the more persistent mineral-associated organic C (MAOC) pool. Yet, evidence for this often overlooks arbuscular mycorrhizal fungi (AMF) communities and how their composition and traits impact SOC accumulation. We grew sudangrass with AMF communities representing different traits conserved at the family level: competitors, from the Gigasporaceae family; ruderals, from the Glomeraceae family; or both families combined. We labeled sudangrass with [13] C-CO2 to assess AMF contributions to SOC, impacts on SOC priming, and fungal biomass persistence in MAOC. Single-family AMF communities decreased total SOC by 13.8%, likely due to fungal priming. Despite net SOC losses, all AMF communities contributed fungal C to soil but only the Glomeraceae community initially contributed to MAOC. After a month of decomposition, both the Glomeraceae and mixed-family communities contributed to MAOC formation. Plant phosphorus uptake, but not hyphal chemistry, was positively related to AMF soil C and MAOC accumulation. Arbuscular mycorrhizal fungi contribution to MAOC is dependent on the specific traits of the AMF community and related to phosphorus uptake. These findings provide insight into how variations in AMF community composition and traits, and thus processes like environmental filtering of AMF, may impact SOC accumulation.},
}
@article {pmid36975801,
year = {2023},
author = {Carter, KA and Fodor, AA and Balkus, JE and Zhang, A and Serrano, MG and Buck, GA and Engel, SM and Wu, MC and Sun, S},
title = {Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0100322},
pmid = {36975801},
issn = {2379-5077},
support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 MD011504/MD/NIMHD NIH HHS/United States ; T32 AI007140/AI/NIAID NIH HHS/United States ; },
mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; *Premature Birth/genetics ; *Microbiota/genetics ; Vagina/microbiology ; },
abstract = {Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are "flying blind" with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth (<32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus-dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners-dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome's gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.},
}
@article {pmid36973438,
year = {2023},
author = {Xu, Z and Chen, J and Li, Y and Shekarriz, E and Wu, W and Chen, B and Liu, H},
title = {High Microeukaryotic Diversity in the Cold-Seep Sediment.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2003-2020},
pmid = {36973438},
issn = {1432-184X},
support = {SMSEGL20SC02//Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL20SC01//Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; PRG-2020-389//Leverhulme Trust Research Project Grant/ ; GML2019ZD0409//Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 16101917//Research Grants Council of Hong Kong/ ; },
mesh = {Animals ; *Ecosystem ; Geologic Sediments/chemistry ; Methane/chemistry ; Biodiversity ; *Dinoflagellida/genetics ; Phylogeny ; },
abstract = {Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25 cm) from sediment cores. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.},
}
@article {pmid36971795,
year = {2023},
author = {Lemke, M and DeSalle, R},
title = {The Role of Microbial Genomics in Restoration Ecology: An Introduction.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {779-780},
doi = {10.1007/s00248-023-02207-9},
pmid = {36971795},
issn = {1432-184X},
mesh = {*Ecology ; *Genomics ; },
}
@article {pmid36970136,
year = {2023},
author = {Munley, JA and Nagpal, R and Hanson, NC and Mirzaie, A and Laquian, L and Mohr, AM and Efron, PA and Arnaoutakis, DJ and Cooper, MA},
title = {Chronic mesenteric ischemia-induced intestinal dysbiosis resolved after revascularization.},
journal = {Journal of vascular surgery cases and innovative techniques},
volume = {9},
number = {2},
pages = {101084},
pmid = {36970136},
issn = {2468-4287},
abstract = {OBJECTIVE: Chronic mesenteric ischemia (CMI) is a debilitating condition arising from intestinal malperfusion from mesenteric artery stenosis or occlusion. Mesenteric revascularization has been the standard of care but can result in substantial morbidity and mortality. Most of the perioperative morbidity has been secondary to postoperative multiple organ dysfunction, potentially from ischemia-reperfusion injury. The intestinal microbiome is a dense community of microorganisms in the gastrointestinal tract that help regulate pathways ranging from nutritional metabolism to the immune response. We hypothesized that patients with CMI will have microbiome perturbations that contribute to this inflammatory response and could potentially normalize in the postoperative period.<br><br>METHODS: We performed a prospective study of patients with CMI who had undergone mesenteric bypass and/or stenting from 2019 to 2020. Stool samples were collected at three time points: preoperatively at the clinic, perioperatively within 14&#xa0;days after surgery, and postoperatively at the clinic at >30&#xa0;days after revascularization. Stool samples from healthy controls were used for comparison. The microbiome was measured using 16S rRNA sequencing on an Illumina-MiSeq sequence platform and analyzed using the QIIME2 (quantitative insights into microbial ecology 2)-DADA2 bioinformatics pipeline with the Silva database. Beta-diversity was analyzed using a principal coordinates analysis and permutational analysis of variance. Alpha-diversity (microbial richness and evenness) was compared using the nonparametric Mann-Whitney U test. Microbial taxa unique to CMI patients vs controls were identified using linear discriminatory analysis effect size analysis. P&#xa0;< .05 was considered statistically significant.<br><br>RESULTS: Eight patients with CMI had undergone mesenteric revascularization (25% men; average age, 71&#xa0;years). Nine healthy controls were also analyzed (78% men; average age, 55&#xa0;years). Bacterial alpha-diversity (number of operational taxonomic units) was dramatically reduced preoperatively compared with that of the controls (P&#xa0;= .03). However, revascularization partially restored the species richness and evenness in the perioperative and postoperative phases. Beta-diversity was only different between the perioperative and postoperative groups (P&#xa0;= .03). Further analyses revealed increased abundance of Bacteroidetes and Clostridia taxa preoperatively and perioperatively compared with the controls, which was reduced during the postoperative period.<br><br>CONCLUSIONS: The results from the present study have shown that patients with CMI have intestinal dysbiosis that resolves after revascularization. The intestinal dysbiosis is characterized by the loss of alpha-diversity, which is restored perioperatively and maintained postoperatively. This microbiome restoration demonstrates the importance of intestinal perfusion to sustain gut homeostasis and suggests that microbiome modulation could be a possible intervention to ameliorate acute and subacute postoperative outcomes in these patients.},
}
@article {pmid36964230,
year = {2023},
author = {Abdullahi, IN and Juárez-Fernández, G and Höfle, U and Latorre-Fernández, J and Cardona-Cabrera, T and Mínguez-Romero, D and Zarazaga, M and Lozano, C and Torres, C},
title = {Staphylococcus aureus Carriage in the Nasotracheal Cavities of White Stork Nestlings (Ciconia ciconia) in Spain: Genetic Diversity, Resistomes and Virulence Factors.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1993-2002},
pmid = {36964230},
issn = {1432-184X},
support = {Marie Sklodowska-Curie grant agreement N&#xb0; 801586//European Union's H2020 research and innovation programme/ ; PID2019-106158RB-I00//MCIN/ AEI /10.13039/501100011033/ ; SBPLY/19/180501/000325//Regional government of Castilla - La Mancha by the European Union's funds for regional development (FEDER)/ ; },
mesh = {Animals ; Staphylococcus aureus/genetics ; *Methicillin-Resistant Staphylococcus aureus/genetics ; Virulence Factors/genetics ; Clindamycin ; Multilocus Sequence Typing ; Spain/epidemiology ; Ecosystem ; Anti-Bacterial Agents/pharmacology ; Birds ; Genetic Variation ; *Staphylococcal Infections/veterinary/epidemiology ; Microbial Sensitivity Tests ; },
abstract = {The molecular ecology of Staphylococcus aureus in migratory birds (such as white storks) is necessary to understand their relevance in the "One Health" ecosystems. This study determined the nasotracheal carriage rates of S. aureus from white storks in Southern Spain and genetically characterized the within-host diversity. A collection of 67 S. aureus strains, previously obtained from 87 white stork nestlings (52 nasal and 85 tracheal samples) fed by their parents with food foraged in natural and landfill habitats, were tested for their antimicrobial resistance (AMR) phenotypes. Moreover, the AMR genotypes, immune evasion cluster (IEC), virulence genes and the detection of CC398 lineage were studied by PCR. The spa types and multilocus-sequencing-typing (MLST) were also determined by PCR and sequencing. Staphylococcus aureus carriage was found in 31% of storks (36.5%/11.9% in nasal/tracheal samples). All isolates were methicillin-susceptible (MSSA) and 8.8% of them were also susceptible to all tested antibiotics. The AMR phenotype/percentage/genes detected were as follows: penicillin/79.1%/blaZ; erythromycin-clindamycin-inducible/19.1%/ermA, ermT; tetracycline/11.9%/tetK; clindamycin/4.5%/lnuA and ciprofloxacin/4.5%. Twenty-one different spa types, including 2 new ones (t7778-ST15-CC15 and t18009-ST26-CC25), were detected and ascribed to 11 clonal complexes (CCs). MSSA-CC398 (8.2%), MSSA-CC15 (7.1%) and MSSA-ST291 (5.9%) were the most prevalent lineages in storks. Moreover, tst-positive (MSSA-CC22-t223 and MSSA-CC30-t1654), eta-positive (MSSA-CC9-t209) and etb-positive strains (MSSA-CC45-t015) were detected in four storks. The 18.5% of storks harboured distinct MSSA strains (with different lineages and/or AMR genes). Nestlings of storks foraging in landfills (10 CCs) had more diverse S. aureus strains than those of parents foraging in natural habitats (3 CCs). Low level of AMR was demonstrated among S. aureus strains. The predominance of MSSA-CC398 (an emergent clade) and toxigenic MSSA strains in stork nestlings highlight the need for continuous surveillance of S. aureus in wild birds.},
}
@article {pmid36964199,
year = {2023},
author = {Kavagutti, VS and Chiriac, MC and Ghai, R and Salcher, MM and Haber, M},
title = {Isolation of phages infecting the abundant freshwater Actinobacteriota order 'Ca. Nanopelagicales'.},
journal = {The ISME journal},
volume = {17},
number = {6},
pages = {943-946},
pmid = {36964199},
issn = {1751-7370},
mesh = {*Bacteriophages ; Bacteria/genetics ; Gene Transfer, Horizontal ; Metagenome ; Fresh Water/microbiology ; Genome, Viral ; Phylogeny ; },
abstract = {Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.},
}
@article {pmid36963636,
year = {2023},
author = {Campos, EVR and Pereira, ADES and Aleksieienko, I and do Carmo, GC and Gohari, G and Santaella, C and Fraceto, LF and Oliveira, HC},
title = {Encapsulated plant growth regulators and associative microorganisms: Nature-based solutions to mitigate the effects of climate change on plants.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {331},
number = {},
pages = {111688},
doi = {10.1016/j.plantsci.2023.111688},
pmid = {36963636},
issn = {1873-2259},
mesh = {*Plant Growth Regulators/metabolism ; *Climate Change ; Ecosystem ; Ultraviolet Rays ; Plants/metabolism ; },
abstract = {Over the past decades, the atmospheric CO2 concentration and global average temperature have been increasing, and this trend is projected to soon become more severe. This scenario of climate change intensifies abiotic stress factors (such as drought, flooding, salinity, and ultraviolet radiation) that threaten forest and associated ecosystems as well as crop production. These factors can negatively affect plant growth and development with a consequent reduction in plant biomass accumulation and yield, in addition to increasing plant susceptibility to biotic stresses. Recently, biostimulants have become a hotspot as an effective and sustainable alternative to alleviate the negative effects of stresses on plants. However, the majority of biostimulants have poor stability under environmental conditions, which leads to premature degradation, shortening their biological activity. To solve these bottlenecks, micro- and nano-based formulations containing biostimulant molecules and/or microorganisms are gaining attention, as they demonstrate several advantages over their conventional formulations. In this review, we focus on the encapsulation of plant growth regulators and plant associative microorganisms as a strategy to boost their application for plant protection against abiotic stresses. We also address the potential limitations and challenges faced for the implementation of this technology, as well as possibilities regarding future research.},
}
@article {pmid36963187,
year = {2023},
author = {Wang, B and Xiao, L and Xu, A and Mao, W and Wu, Z and Hicks, LC and Jiang, Y and Xu, J},
title = {Silicon fertilization enhances the resistance of tobacco plants to combined Cd and Pb contamination: Physiological and microbial mechanisms.},
journal = {Ecotoxicology and environmental safety},
volume = {255},
number = {},
pages = {114816},
doi = {10.1016/j.ecoenv.2023.114816},
pmid = {36963187},
issn = {1090-2414},
mesh = {Cadmium/analysis ; Silicon/pharmacology ; Nicotiana/metabolism ; Lead/toxicity ; Fertilizers/analysis ; *Metals, Heavy/metabolism ; Soil/chemistry ; Fertilization ; *Soil Pollutants/analysis ; },
abstract = {Remediation of soil contaminated with cadmium (Cd) and lead (Pb) is critical for tobacco production. Silicon (Si) fertilizer can relieve heavy metal stress and promote plant growth, however, it remains unknown whether fertilization with Si can mitigate the effects of Cd and Pb on tobacco growth and alter microbial community composition in polluted soils. Here we assessed the effect of two organic (OSiFA, OSiFB) and one mineral Si fertilizer (MSiF) on Cd and Pb accumulation in tobacco plants, together with responses in plant biomass, physiological parameters and soil bacterial communities in pot experiments. Results showed that Si fertilizer relieved Cd and Pb stress on tobacco, thereby promoting plant growth: Si fertilizer reduced available Cd and Pb in the soil by 37.3 % and 28.6 %, respectively, and decreased Cd and Pb contents in the plant tissue by 42.0-55.5 % and 17.2-25.6 %, resulting in increased plant biomass by 13.0-30.5 %. Fertilization with Si alleviated oxidative damage by decreasing malondialdehyde content and increasing peroxidase and ascorbate peroxidase content. In addition, Si fertilization increased photosynthesis, chlorophyll and carotenoid content. Microbial community structure was also affected by Si fertilization. Proteobacteria and Actinobacteria were the dominant phylum in the Cd and Pb contaminated soils, but Si fertilization reduced the abundance of Actinobacteria. Si fertilization also altered microbial metabolic pathways associated with heavy metal resistance. Together, our results suggest that both organic and mineral Si fertilizers can promote tobacco growth by relieving plant physiological stress and favoring a heavy metal tolerant soil microbial community.},
}
@article {pmid36960281,
year = {2023},
author = {Kapinusova, G and Lopez Marin, MA and Uhlik, O},
title = {Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1089630},
pmid = {36960281},
issn = {1664-302X},
abstract = {In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.},
}
@article {pmid36959175,
year = {2023},
author = {Bjerg, JJ and Lustermans, JJM and Marshall, IPG and Mueller, AJ and Brokjær, S and Thorup, CA and Tataru, P and Schmid, M and Wagner, M and Nielsen, LP and Schramm, A},
title = {Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1614},
pmid = {36959175},
issn = {2041-1723},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Oxidation-Reduction ; *Oxygen ; Geologic Sediments/microbiology ; *Deltaproteobacteria ; Bacteria/genetics ; Sulfides ; },
abstract = {Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.},
}
@article {pmid36958555,
year = {2023},
author = {Zhang, X and Chen, L and Wang, Y and Jiang, P and Hu, Y and Ouyang, S and Wu, H and Lei, P and Kuzyakov, Y and Xiang, W},
title = {Plantations thinning: A meta-analysis of consequences for soil properties and microbial functions.},
journal = {The Science of the total environment},
volume = {877},
number = {},
pages = {162894},
doi = {10.1016/j.scitotenv.2023.162894},
pmid = {36958555},
issn = {1879-1026},
mesh = {*Soil/chemistry ; Ecosystem ; Soil Microbiology ; Forests ; Trees ; Biomass ; Nitrogen/analysis ; *Microbiota ; Carbon/analysis ; },
abstract = {Thinning is a widely-used management practice to reduce tree competition and improve wood production and quality in forest plantations. Thinning affects the soil ecosystem by changing the microclimate and plant growth, as well as litter inputs above and belowground, with all the resulting consequences for microbial communities and functions. Although many case studies have been carried out, a comprehensive understanding of the thinning effects on soil properties and microbial communities and functions in plantations remains to be explored. In this study, a meta-analysis was performed on 533 paired observations based on 90 peer-reviewed articles to evaluate the general responses of soil (mainly 0-20 cm depth) physicochemical properties, microbial biomass and community structure, and enzyme activities to thinning. Results showed that thinning increased soil temperature (13 %), moisture (8.0 %), electric conductivity (13 %), and the contents of total nitrogen (TN, 4.1 %), dissolved organic carbon (DOC, 9.7 %), nitrate N (NO3[-]-N, 27 %) and available phosphorous (22 %). For microbial properties, thinning decreased the fungi to bacteria ratio (F:B, -28 %) and the gram-positive bacteria to gram-negative bacteria ratio (G+:G-, -12 %), while increased microbial biomass C (7.1 %), microbial respiration (13 %), and nutrient-cycle related enzyme activities, including phenol oxidase (14 %), cellobiohydrolase (21 %), urease (10 %), and acid phosphatase (9 %). In particular, moderate thinning (30-60 % intensity) has higher conservation benefits for soil C and nutrients than light and heavy intensity, thus being recommended as the optimal thinning activity. This meta-analysis suggests that thinning consistently altered soil properties, shifted microbial community compositions from K- to-r strategist dominance, and stimulated microbial activities. These results are essential for optimizing plantation thinning management and provide evidence for applying the macro-ecology theory to ecosystem disturbance in soil microbial ecology.},
}
@article {pmid36948064,
year = {2023},
author = {Goswami, P and Bhadury, P},
title = {First record of an Anthropocene marker plastiglomerate in Andaman Island, India.},
journal = {Marine pollution bulletin},
volume = {190},
number = {},
pages = {114802},
doi = {10.1016/j.marpolbul.2023.114802},
pmid = {36948064},
issn = {1879-3363},
mesh = {Ecosystem ; *Environmental Monitoring ; *Environmental Pollutants ; Environmental Pollution ; India ; *Plastics ; Polyethylene ; Waste Products ; },
abstract = {One of the most significant environmental issues confronting our world is plastic trash, which is of particular concern to the marine environment. The sedimentary record of the planet may likely one day contain a horizon of plastic that can be potentially identified as an Anthropocene marker. Here we report the presence of 'plastiglomerate' from coastal habitats located in the Aves Island, Andaman Sea, India. This novel form of plastic pollution forms with the incineration of plastic litter in the environment and then mixing of organic/inorganic composite materials in the molten plastic matrix. The plastic pollutants were collected from the Aves Island beach during marine litter surveys. Micro-Raman (μ-Raman) spectroscopy was used to evaluate and confirm all putative plastic forms. Plastiglomerates were made of a polyethylene (PE) and polyvinyl chloride (PVC) matrix with inclusions of rock and sand. Therefore, our research offers new insight into the intricate process of plastiglomerates formation.},
}
@article {pmid36947551,
year = {2023},
author = {Bourne, ME and Gloder, G and Weldegergis, BT and Slingerland, M and Ceribelli, A and Crauwels, S and Lievens, B and Jacquemyn, H and Dicke, M and Poelman, EH},
title = {Parasitism causes changes in caterpillar odours and associated bacterial communities with consequences for host-location by a hyperparasitoid.},
journal = {PLoS pathogens},
volume = {19},
number = {3},
pages = {e1011262},
pmid = {36947551},
issn = {1553-7374},
mesh = {Animals ; Odorants ; Larva ; *Butterflies/parasitology ; *Wasps/parasitology ; Host-Parasite Interactions ; },
abstract = {Microorganisms living in and on macroorganisms may produce microbial volatile compounds (mVOCs) that characterise organismal odours. The mVOCs might thereby provide a reliable cue to carnivorous enemies in locating their host or prey. Parasitism by parasitoid wasps might alter the microbiome of their caterpillar host, affecting organismal odours and interactions with insects of higher trophic levels such as hyperparasitoids. Hyperparasitoids parasitise larvae or pupae of parasitoids, which are often concealed or inconspicuous. Odours of parasitised caterpillars aid them to locate their host, but the origin of these odours and its relationship to the caterpillar microbiome are unknown. Here, we analysed the odours and microbiome of the large cabbage white caterpillar Pieris brassicae in relation to parasitism by its endoparasitoid Cotesia glomerata. We identified how bacterial presence in and on the caterpillars is correlated with caterpillar odours and tested the attractiveness of parasitised and unparasitised caterpillars to the hyperparasitoid Baryscapus galactopus. We manipulated the presence of the external microbiome and the transient internal microbiome of caterpillars to identify the microbial origin of odours. We found that parasitism by C. glomerata led to the production of five characteristic volatile products and significantly affected the internal and external microbiome of the caterpillar, which were both found to have a significant correlation with caterpillar odours. The preference of the hyperparasitoid was correlated with the presence of the external microbiome. Likely, the changes in external microbiome and body odour after parasitism were driven by the resident internal microbiome of caterpillars, where the bacterium Wolbachia sp. was only present after parasitism. Micro-injection of Wolbachia in unparasitised caterpillars increased hyperparasitoid attraction to the caterpillars compared to untreated caterpillars, while no differences were found compared to parasitised caterpillars. In conclusion, our results indicate that host-parasite interactions can affect multi-trophic interactions and hyperparasitoid olfaction through alterations of the microbiome.},
}
@article {pmid36947169,
year = {2023},
author = {Hammerle, F and Quirós-Guerrero, L and Wolfender, JL and Peintner, U and Siewert, B},
title = {Highlighting the Phototherapeutical Potential of Fungal Pigments in Various Fruiting Body Extracts with Informed Feature-Based Molecular Networking.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1972-1992},
pmid = {36947169},
issn = {1432-184X},
support = {P 31915/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Singlet Oxygen/analysis ; *Antineoplastic Agents ; Plant Extracts ; Fruiting Bodies, Fungal/chemistry ; },
abstract = {Fungal pigments are characterized by a diverse set of chemical backbones, some of which present photosensitizer-like structures. From the genus Cortinarius, for example, several biologically active photosensitizers have been identified leading to the hypothesis that photoactivity might be a more general phenomenon in the kingdom Fungi. This paper aims at testing the hypothesis. Forty-eight fruiting body-forming species producing pigments from all four major biosynthetic pathways (i.e., shikimate-chorismate, acetate-malonate, mevalonate, and nitrogen heterocycles) were selected and submitted to a workflow combining in vitro chemical and biological experiments with state-of-the-art metabolomics. Fungal extracts were profiled by high-resolution mass spectrometry and subsequently explored by spectral organization through feature-based molecular networking (FBMN), including advanced metabolite dereplication techniques. Additionally, the photochemical properties (i.e., light-dependent production of singlet oxygen), the phenolic content, and the (photo)cytotoxic activity of the extracts were studied. Different levels of photoactivity were found in species from all four metabolic groups, indicating that light-dependent effects are common among fungal pigments. In particular, extracts containing pigments from the acetate-malonate pathway, e.g., extracts from Bulgaria inquinans, Daldinia concentrica, and Cortinarius spp., were not only efficient producers of singlet oxygen but also exhibited photocytotoxicity against three different cancer cell lines. This study explores the distribution of photobiological traits in fruiting body forming fungi and highlights new sources for phototherapeutics.},
}
@article {pmid36946113,
year = {2023},
author = {Kauai, F and Mortier, F and Milosavljevic, S and Van de Peer, Y and Bonte, D},
title = {Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1995},
pages = {20222456},
pmid = {36946113},
issn = {1471-2954},
mesh = {Humans ; *Ploidies ; *Diploidy ; Polyploidy ; Chromosomes ; Reproduction ; },
abstract = {Polyploidy, i.e. the occurrence of multiple sets of chromosomes, is regarded as an important phenomenon in plant ecology and evolution, with all flowering plants likely having a polyploid ancestry. Owing to genome shock, minority cytotype exclusion and reduced fertility, polyploids emerging in diploid populations are expected to face significant challenges to successful establishment. Their establishment and persistence are often explained by possible fitness or niche differences that would relieve the competitive pressure with diploid progenitors. Experimental evidence for such advantages is, however, not unambiguous, and considerable niche overlap exists among most polyploid species and their diploid counterparts. Here, we develop a neutral spatially explicit eco-evolutionary model to understand whether neutral processes can explain the eco-evolutionary patterns of polyploids. We present a general mechanism for polyploid establishment by showing that sexually reproducing organisms assemble in space in an iterative manner, reducing frequency-dependent mating disadvantages and overcoming potential reduced fertility issues. Moreover, we construct a mechanistic theoretical framework that allows us to understand the long-term evolution of mixed-ploidy populations and show that our model is remarkably consistent with recent phylogenomic estimates of species extinctions in the Brassicaceae family.},
}
@article {pmid36946107,
year = {2023},
author = {Jones, KR and Hughey, MC and Belden, LK},
title = {Colonization order of bacterial isolates on treefrog embryos impacts microbiome structure in tadpoles.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1995},
pages = {20230308},
pmid = {36946107},
issn = {1471-2954},
mesh = {Animals ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anura/genetics ; Biota ; Bacteria ; },
abstract = {Priority effects, or impacts of colonization order, may have lasting influence on ecological community composition. The embryonic microbiome is subject to stochasticity in colonization order of bacteria. Stochasticity may be especially impactful for embryos developing in bacteria-rich environments, such as the embryos of many amphibians. To determine if priority effects experienced as embryos impacted bacterial community composition in newly hatched tadpoles, we selectively inoculated the embryos of laboratory-raised hourglass treefrogs, Dendropsophus ebraccatus, with bacteria initially isolated from the skin of wild D. ebraccatus adults over 2 days. First, embryos were inoculated with two bacteria in alternating sequences. Next, we evaluated the outcomes of priority effects in an in vitro co-culture assay absent of host factors. We then performed a second embryo experiment, inoculating embryos with one of three bacteria on the first day and a community of five target bacteria on the second. Through 16S rRNA gene amplicon sequencing, we observed relative abundance shifts in tadpole bacteria communities due to priority effects. Our results suggest that the initial bacterial source pools of embryos shape bacterial communities at later life stages; however, the magnitude of those changes is dependent on the host environment and the identity of bacterial colonists.},
}
@article {pmid36945867,
year = {2023},
author = {Snyder, GM and Passaretti, CL and Stevens, MP},
title = {Hospital approaches to universal masking after public health "unmasking" guidance.},
journal = {Infection control and hospital epidemiology},
volume = {44},
number = {5},
pages = {845-846},
doi = {10.1017/ice.2023.9},
pmid = {36945867},
issn = {1559-6834},
mesh = {Humans ; *Public Health ; *Hospitals ; },
}
@article {pmid36944303,
year = {2023},
author = {Trebuch, LM and Sohier, J and Altenburg, S and Oyserman, BO and Pronk, M and Janssen, M and Vet, LEM and Wijffels, RH and Fernandes, TV},
title = {Enhancing phosphorus removal of photogranules by incorporating polyphosphate accumulating organisms.},
journal = {Water research},
volume = {235},
number = {},
pages = {119748},
doi = {10.1016/j.watres.2023.119748},
pmid = {36944303},
issn = {1879-2448},
mesh = {*Polyphosphates ; *Phosphorus ; Bioreactors ; Sewage ; Photobioreactors ; Carbon ; Nitrogen ; },
abstract = {Photogranules are a novel wastewater treatment technology that can utilize the sun's energy to treat water with lower energy input and have great potential for nutrient recovery applications. They have been proven to efficiently remove nitrogen and carbon but show lower conversion rates for phosphorus compared to established treatment systems, such as aerobic granular sludge. In this study, we successfully introduced polyphosphate accumulating organisms (PAOs) to an established photogranular culture. We operated photobioreactors in sequencing batch mode with six cycles per day and alternating anaerobic (dark) and aerobic (light) phases. We were able to increase phosphorus removal/recovery by 6 times from 5.4 to 30 mg/L/d while maintaining similar nitrogen and carbon removal compared to photogranules without PAOs. To maintain PAOs activity, alternating anaerobic feast and aerobic famine conditions were required. In future applications, where aerobic conditions are dependent on in-situ oxygenation via photosynthesis, the process will rely on sunlight availability. Therefore, we investigated the feasibility of the process under diurnal cycles with a 12-h anaerobic phase during nighttime and six short cycles during the 12 h daytime. The 12-h anaerobic phase had no adverse effect on the PAOs and phototrophs. Due to the extension of one anaerobic phase to 12 h the six aerobic phases were shortened by 47% and consequently decreased the light hours per day. This resulted in a decrease of phototrophs, which reduced nitrogen removal and biomass productivity up to 30%. Finally, we discuss and suggest strategies to apply PAO-enriched photogranules at large-scale.},
}
@article {pmid36943084,
year = {2023},
author = {Kop, LFM and Koch, H and Spieck, E and van Alen, T and Cremers, G and Daims, H and Lücker, S},
title = {Complete Genome Sequence of Nitrospina watsonii 347, Isolated from the Black Sea.},
journal = {Microbiology resource announcements},
volume = {12},
number = {4},
pages = {e0007823},
pmid = {36943084},
issn = {2576-098X},
support = {SIAM grant 024.002.002//Dutch Ministry of Education, Culture and Science/ ; VI.Veni.192.086//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; },
abstract = {Here, we present the complete genome sequence of Nitrospina watsonii 347, a nitrite-oxidizing bacterium isolated from the Black Sea at a depth of 100 m. The genome has a length of 3,011,914 bp with 2,895 predicted coding sequences. Its predicted metabolism is similar to that of Nitrospina gracilis with differences in defense against reactive oxygen species.},
}
@article {pmid36943059,
year = {2023},
author = {Durán-Viseras, A and Sánchez-Porro, C and Viver, T and Konstantinidis, KT and Ventosa, A},
title = {Discovery of the Streamlined Haloarchaeon Halorutilus salinus, Comprising a New Order Widespread in Hypersaline Environments across the World.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0119822},
pmid = {36943059},
issn = {2379-5077},
mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; *Euryarchaeota/genetics ; *Halobacteriales/genetics ; },
abstract = {The class Halobacteria is one of the most diverse groups within the Euryarchaeota phylum, whose members are ubiquitously distributed in hypersaline environments, where they often constitute the major population. Here, we report the discovery and isolation of a new halophilic archaeon, strain F3-133[T] exhibiting ≤86.3% 16S rRNA gene identity to any previously cultivated archaeon, and, thus, representing a new order. Analysis of available 16S rRNA gene amplicon and metagenomic data sets showed that the new isolate represents an abundant group in intermediate-to-high salinity ecosystems and is widely distributed across the world. The isolate presents a streamlined genome, which probably accounts for its ecological success in nature and its fastidious growth in culture. The predominant osmoprotection mechanism appears to be the typical salt-in strategy used by other haloarchaea. Furthermore, the genome contains the complete gene set for nucleotide monophosphate degradation pathway through archaeal RuBisCO, being within the first halophilic archaea representatives reported to code this enzyme. Genomic comparisons with previously described representatives of the phylum Euryarchaeota were consistent with the 16S rRNA gene data in supporting that our isolate represents a novel order within the class Halobacteria for which we propose the names Halorutilales ord. nov., Halorutilaceae fam. nov., Halorutilus gen. nov. and Halorutilus salinus sp. nov. IMPORTANCE The discovery of the new halophilic archaeon, Halorutilus salinus, representing a novel order, family, genus, and species within the class Halobacteria and phylum Euryarchaeota clearly enables insights into the microbial dark matter, expanding the current taxonomical knowledge of this group of archaea. The in-depth comparative genomic analysis performed on this new taxon revealed one of the first known examples of an Halobacteria representative coding the archaeal RuBisCO gene and with a streamlined genome, being ecologically successful in nature and explaining its previous non-isolation. Altogether, this research brings light into the understanding of the physiology of the Halobacteria class members, their ecological distribution, and capacity to thrive in hypersaline environments.},
}
@article {pmid36943046,
year = {2023},
author = {Diener, C and Gibbons, SM},
title = {More is Different: Metabolic Modeling of Diverse Microbial Communities.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0127022},
pmid = {36943046},
issn = {2379-5077},
support = {R01 DK133468/DK/NIDDK NIH HHS/United States ; },
mesh = {*Models, Biological ; *Microbial Consortia ; },
abstract = {Microbial consortia drive essential processes, ranging from nitrogen fixation in soils to providing metabolic breakdown products to animal hosts. However, it is challenging to translate the composition of microbial consortia into their emergent functional capacities. Community-scale metabolic models hold the potential to simulate the outputs of complex microbial communities in a given environmental context, but there is currently no consensus for what the fitness function of an entire community should look like in the presence of ecological interactions and whether community-wide growth operates close to a maximum. Transitioning from single-taxon genome-scale metabolic models to multitaxon models implies a growth cone without a well-specified growth rate solution for individual taxa. Here, we argue that dynamic approaches naturally overcome these limitations, but they come at the cost of being computationally expensive. Furthermore, we show how two nondynamic, steady-state approaches approximate dynamic trajectories and pick ecologically relevant solutions from the community growth cone with improved computational scalability.},
}
@article {pmid36941122,
year = {2023},
author = {Logroño, W and Kleinsteuber, S and Kretzschmar, J and Harnisch, F and De Vrieze, J and Nikolausz, M},
title = {The microbiology of Power-to-X applications.},
journal = {FEMS microbiology reviews},
volume = {47},
number = {2},
pages = {},
doi = {10.1093/femsre/fuad013},
pmid = {36941122},
issn = {1574-6976},
mesh = {*Electrolysis ; *Hydrogen/metabolism ; },
abstract = {Power-to-X (P2X) technologies will play a more important role in the conversion of electric power to storable energy carriers, commodity chemicals and even food and feed. Among the different P2X technologies, microbial components form cornerstones of individual process steps. This review comprehensively presents the state-of-the-art of different P2X technologies from a microbiological standpoint. We are focusing on microbial conversions of hydrogen from water electrolysis to methane, other chemicals and proteins. We present the microbial toolbox needed to gain access to these products of interest, assess its current status and research needs, and discuss potential future developments that are needed to turn todays P2X concepts into tomorrow's technologies.},
}
@article {pmid36939866,
year = {2023},
author = {Malard, LA and Bergk-Pinto, B and Layton, R and Vogel, TM and Larose, C and Pearce, DA},
title = {Snow Microorganisms Colonise Arctic Soils Following Snow Melt.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1661-1675},
pmid = {36939866},
issn = {1432-184X},
support = {675546//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 1192//Institut Polaire Fran&#xe7;ais Paul Emile Victor/ ; },
mesh = {*Soil ; *Ecosystem ; Snow ; Arctic Regions ; },
abstract = {Arctic soils are constantly subjected to microbial invasion from either airborne, marine, or animal sources, which may impact local microbial communities and ecosystem functioning. However, in winter, Arctic soils are isolated from outside sources other than snow, which is the sole source of microorganisms. Successful colonisation of soil by snow microorganisms depends on the ability to survive and compete of both, the invading and resident community. Using shallow shotgun metagenome sequencing and amplicon sequencing, this study monitored snow and soil microbial communities throughout snow melt to investigate the colonisation process of Arctic soils. Microbial colonisation likely occurred as all the characteristics of successful colonisation were observed. The colonising microorganisms originating from the snow were already adapted to the local environmental conditions and were subsequently subjected to many similar conditions in the Arctic soil. Furthermore, competition-related genes (e.g. motility and virulence) increased in snow samples as the snow melted. Overall, one hundred potentially successful colonisers were identified in the soil and, thus, demonstrated the deposition and growth of snow microorganisms in soils during melt.},
}
@article {pmid36934908,
year = {2023},
author = {Kalantzis, D and Daskaloudis, I and Lacoere, T and Stasinakis, AS and Lekkas, DF and De Vrieze, J and Fountoulakis, MS},
title = {Granular activated carbon stimulates biogas production in pilot-scale anaerobic digester treating agro-industrial wastewater.},
journal = {Bioresource technology},
volume = {376},
number = {},
pages = {128908},
doi = {10.1016/j.biortech.2023.128908},
pmid = {36934908},
issn = {1873-2976},
mesh = {*Wastewater ; *Charcoal/chemistry ; Waste Disposal, Fluid ; Biofuels ; Anaerobiosis ; Bioreactors ; Methane ; },
abstract = {This work examines the continuous addition (5 g/L) of conductive granular activated carbon (GAC) in an integrated pilot-scale unit containing an anaerobic digester (180 L) and an aerobic submerged membrane bioreactor (1600 L) connected in series for the treatment of agro-industrial wastewater. Biogas production increased by 32 % after the addition of GAC. Methanosaeta was the dominant methanogen in the digester, and its relative abundance increased after the addition of GAC. The final effluent after post-treatment with the aerobic membrane bioreactor had a total solids content <0.01 g/L and a chemical oxygen demand between 120 and 150 mg/L. A simple cost analysis showed that GAC addition is potentially profitable, but alternatives ways of retaining the GAC in the system need to be found. Overall, this study provides useful scientific data for the possible application of GAC in full-scale biogas projects.},
}
@article {pmid36934439,
year = {2023},
author = {Runde, J and Veseli, I and Fogarty, EC and Watson, AR and Clayssen, Q and Yosef, M and Shaiber, A and Verma, R and Quince, C and Gerasimidis, K and Rubin, DT and Eren, AM},
title = {Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn's Disease.},
journal = {Journal of Crohn's &amp; colitis},
volume = {17},
number = {7},
pages = {1103-1113},
doi = {10.1093/ecco-jcc/jjad031},
pmid = {36934439},
issn = {1876-4479},
mesh = {Humans ; *Crohn Disease ; Enteral Nutrition ; Remission Induction ; Bacteria ; *Microbiota ; },
abstract = {BACKGROUND AND AIMS: Exclusive enteral nutrition [EEN] is a dietary intervention to induce clinical remission in children with active luminal Crohn's disease [CD]. While changes in the gut microbial communities have been implicated in achieving this remission, a precise understanding of the role of microbial ecology in the restoration of gut homeostasis is lacking.<br><br>METHODS: Here we reconstructed genomes from the gut metagenomes of 12 paediatric subjects who were sampled before, during and after EEN. We then classified each microbial population into distinct 'phenotypes' or patterns of response based on changes in their relative abundances throughout the therapy on a per-individual basis.<br><br>RESULTS: Our data show that children achieving clinical remission during therapy were enriched with microbial populations that were either suppressed or that demonstrated a transient bloom as a function of EEN. In contrast, this ecosystem-level response was not observed in cases of EEN failure. Further analysis revealed that populations that were suppressed during EEN were significantly more prevalent in healthy children and adults across the globe compared with those that bloomed ephemerally during the therapy.<br><br>CONCLUSIONS: These observations taken together suggest that successful outcomes of EEN are marked by a temporary emergence of microbial populations that are rare in healthy individuals, and a concomitant reduction in microbes that are commonly associated with gut homeostasis. Our work is a first attempt to highlight individual-specific, complex environmental factors that influence microbial response in EEN. This model offers a novel, alternative viewpoint to traditional taxonomic strategies used to characterize associations with health and disease states.},
}
@article {pmid36930295,
year = {2023},
author = {Harsonowati, W and Rahayuningsih, S and Yuniarti, E and Susilowati, DN and Manohara, D and Sipriyadi, and Widyaningsih, S and Akhdiya, A and Suryadi, Y and Tentrem, T},
title = {Bacterial Metal-Scavengers Newly Isolated from Indonesian Gold Mine-Impacted Area: Bacillus altitudinis MIM12 as Novel Tools for Bio-Transformation of Mercury.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1646-1660},
pmid = {36930295},
issn = {1432-184X},
mesh = {*Mercury ; Gold ; Indonesia ; Cadmium ; Lead ; Bacteria/genetics ; Environmental Monitoring ; },
abstract = {Selikat river, located in the north part of Bengkulu Province, Indonesia, has critical environmental and ecological issues of contamination by mercury due to artisanal small-scale gold mining (ASGM) activities. The present study focused on the identification and bioremediation efficiency of the mercury-resistant bacteria (MRB) isolated from ASGM-impacted areas in Lebong Tambang village, Bengkulu Province, and analyzed their merA gene function in transforming Hg[2+] to Hg[0]. Thirty-four MRB isolates were isolated, and four out of the 34 isolates exhibited not only the highest degree of resistance to Hg (up to 200 ppm) but also to cadmium (Cd), chromium (Cr), copper (Cu), and lead (Pb). Further analysis shows that all four selected isolates harbor a merA operon-encoded mercuric ion (Hg[2+]) reductase enzyme, with the Hg bioremediation efficiency varying from 71.60 to 91.30%. Additionally, the bioremediation efficiency for Cd, Cr, Cu, and Pb ranged from 54.36 to 98.37%. Among the 34, two isolates identified as Bacillus altitudinis possess effective and superior multi-metal degrading capacity up to 91.30% for Hg, 98.07% for Cu, and 54.36% for Cr. A pilot-scale study exhibited significant in situ bioremediation of Hg from gold mine tailings of 82.10 and 95.16% at 4- and 8-day intervals, respectively. Interestingly, translated nucleotide blast against bacteria and Bacilli merA sequence databases suggested that B. altitudinis harbor merA gene is the first case among Bacilli with the possibility exhibits a novel mechanism of bioremediation, considering our new finding. This study is the first to report the structural and functional Hg-resistant bacterial diversity of unexplored ASGM-impacted areas, emphasizing their biotechnological potential as novel tools for the biological transformation and adsorption of mercury and other toxic metals.},
}
@article {pmid36928747,
year = {2023},
author = {Zhang, Y and Liu, F and Liang, H and Gao, D},
title = {Correction to: Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline Alkaline Wetland: a Metagenomic Analysis.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {2210},
doi = {10.1007/s00248-023-02205-x},
pmid = {36928747},
issn = {1432-184X},
}
@article {pmid36927871,
year = {2023},
author = {Doulidis, PG and Galler, AI and Hausmann, B and Berry, D and Rodríguez-Rojas, A and Burgener, IA},
title = {Gut microbiome signatures of Yorkshire Terrier enteropathy during disease and remission.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {4337},
pmid = {36927871},
issn = {2045-2322},
support = {898858/MCCC_/Marie Curie/United Kingdom ; },
mesh = {Humans ; Dogs ; Animals ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Microbiota ; Bacteroidetes ; },
abstract = {The role of the gut microbiome in developing Inflammatory Bowel Disease (IBD) in humans and dogs has received attention in recent years. Evidence suggests that IBD is associated with alterations in gut microbial composition, but further research is needed in veterinary medicine. The impact of IBD treatment on the gut microbiome needs to be better understood, especially in a breed-specific form of IBD in Yorkshire Terriers known as Yorkshire Terrier Enteropathy (YTE). This study aimed to investigate the difference in gut microbiome composition between YTE dogs during disease and remission and healthy Yorkshire Terriers. Our results showed a significant increase in specific taxa such as Clostridium sensu stricto 1, Escherichia-Shigella, and Streptococcus, and a decrease in Bacteroides, Prevotella, Alloprevotella, and Phascolarctobacterium in YTE dogs compared to healthy controls. No significant difference was found between the microbiome of dogs in remission and those with active disease, suggesting that the gut microbiome is affected beyond clinical recovery.},
}
@article {pmid36926228,
year = {2023},
author = {Zayed, N and Figueiredo, J and Van Holm, W and Boon, N and Bernaerts, K and Teughels, W},
title = {Mode of killing determines the necrotrophic response of oral bacteria.},
journal = {Journal of oral microbiology},
volume = {15},
number = {1},
pages = {2184930},
pmid = {36926228},
issn = {2000-2297},
abstract = {BACKGROUND: Bacteria respond to changes in their environment, such as nutrient depletion and antimicrobials exposure. Antimicrobials result not only in bacterial death, but also have a hand in determining species abundances and ecology of the oral biofilms. Proximity of dead bacterial cells to living ones is an important environmental change or stress factor. Dead bacteria represent high concentrations of nutrients, such as proteins, lipids, sugars, and nucleic acids. Living bacteria can use these biomasses as a nutrients source, which is termed necrotrophy.<br><br>AIM: This study investigates the effect of exposing living oral bacteria (planktonic and biofilms) to their dead siblings after being killed by heat or hydrogen peroxide.<br><br>RESULTS: Tested bacterial species showed different responses towards the dead cells, depending on the mode of killing, the nutritional value of the culture media, and the the dead cells density. The multispecies oral biofilms showed different responses towards the supplementation of dead cells during biofilm development, while matured biofilms were more resilient.<br><br>CONCLUSION: This study indicates that dead bacteria resulting from antiseptics use may imbalance the nutrient availability in the oral cavity, resulting in overgrowth of opportunistic species, and hence ecological changes in oral communities, or introducing new bacterial phenotypes.},
}
@article {pmid36925466,
year = {2023},
author = {Rachid, CTCC and Balieiro, FC and Peixoto, RS and Fonseca, ES and Jesus, HE and Novotny, EH and Chaer, GM and Santos, FM and Tiedje, JM and Rosado, AS},
title = {Mycobiome structure does not affect field litter decomposition in Eucalyptus and Acacia plantations.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1106422},
pmid = {36925466},
issn = {1664-302X},
abstract = {Mixed tree plantations have been studied because of their potential to improve biomass production, ecosystem diversity, and soil quality. One example is a mixture of Eucalyptus and Acacia trees, which is a promising strategy to improve microbial diversity and nutrient cycling in soil. We examined how a mixture of these species may influence the biochemical attributes and fungal community associated with leaf litter, and the effects on litter decomposition. We studied the litter from pure and mixed plantations, evaluating the effects of plant material and incubation site on the mycobiome and decomposition rate using litterbags incubated in situ. Our central hypothesis was litter fungal community would change according to incubation site, and it would interfere in litter decomposition rate. Both the plant material and the incubation locale significantly affected the litter decomposition. The origin of the litter was the main modulator of the mycobiome, with distinct communities from one plant species to another. The community changed with the incubation time but the incubation site did not influence the mycobiome community. Our data showed that litter and soil did not share the main elements of the community. Contrary to our hypothesis, the microbial community structure and diversity lacked any association with the decomposition rate. The differences in the decomposition pattern are explained basically as a function of the exchange of nitrogen compounds between the litter.},
}
@article {pmid36923055,
year = {2023},
author = {Correa, F and Luise, D and Negrini, C and Ruggeri, R and Bosi, P and Trevisi, P},
title = {Effect of two milk supplements and two ways of administration on growth performance, welfare and fecal microbial ecology of suckling piglets.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1050414},
pmid = {36923055},
issn = {2297-1769},
abstract = {INTRODUCTION: The aim of this study was to evaluate the effect of two MS formulas, DanMilk™ (AB Neo, Denmark) (MS1) and Neopigg[®] RescueMilk (Provimi, Netherlands) (MS2) administered manually and to compare two ways of administration (manual vs automatic) of MS1 on growth performance, health, fecal microbial profile, behavior, and skin lesions of piglets during suckling and post-weaning.<br><br>METHODS: Forty litters (528 piglets) were divided into 4 groups: 1) Control group receiving no MS (CON); 2) MS1 administered automatically (A-MS1); 3) MS1 administered manually (Ma-MS1) 4) MS2 administered manually (Ma-MS2). All groups had access to sow milk and creep feed. On day 5 after birth (d0), litters were equalized (13.2 piglets/litter &#xb1; 0.8 SD), thereafter no cross-fostering was allowed. Piglets were weighed at day 5 after birth (d0), at the end of milk supplementation (d14), at weaning (d21 of the trial, 26 days of age) and ten days post-weaning (d31). Piglet welfare was assessed using behavioral and lesion measures at d4 and d10. Feces were collected at d14 and d21.<br><br>RESULTS AND DISCUSSION: During the suckling period, A-MS1 had lowest mortality (p < 0.05), while Ma-MS1 had lower mortality compared with CON and Ma-MS2 (p < 0.05). Negative social behavior at d4, was more frequent in MS groups (A-MS1, Ma-MS1, Ma-MS2) compared to CON group (p = 0.03). Growth performance and lesion prevalence were not affected by MS provision. During lactation, Ma-MS2 group had a higher percentage of piglets not eating during suckling at d18 compared with Ma-MS1 (p = 0.03). MS1 increased microbial diversity compared with CON at d14 (Chao1, p = 0.02; Shannon, p = 0.03) and compared with CON (Shannon, p < 0.05; InvSimpson, p = 0.01) and Ma-MS2 (Chao1, p < 0.05; Shannon, p = 0.05, InvSimpson p = 0.01) at d21. Groups that received MS1 were characterized by genera producing short-chain fatty acids (SCFAs), i.e., Lachnospiraceae (A-MS1) and Oscillospiraceae (Ma-MS1). MS composition and availability can contribute to reduce piglet's mortality during the suckling phase and can also affect intestinal microbiota by favoring the presence of SCFAs producing bacteria.},
}
@article {pmid36920955,
year = {2023},
author = {Schada von Borzyskowski, L},
title = {Taking Synthetic Biology to the Seas: From Blue Chassis Organisms to Marine Aquaforming.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {24},
number = {13},
pages = {e202200786},
doi = {10.1002/cbic.202200786},
pmid = {36920955},
issn = {1439-7633},
mesh = {*Synthetic Biology ; Oceans and Seas ; *Bacteria/metabolism ; Biotechnology ; Aquatic Organisms/metabolism ; },
abstract = {Oceans cover 71 % of Earth's surface and are home to hundreds of thousands of species, many of which are microbial. Knowledge about marine microbes has strongly increased in the past decades due to global sampling expeditions, and hundreds of detailed studies on marine microbial ecology, physiology, and biogeochemistry. However, the translation of this knowledge into biotechnological applications or synthetic biology approaches using marine microbes has been limited so far. This review highlights key examples of marine bacteria in synthetic biology and metabolic engineering, and outlines possible future work based on the emerging marine chassis organisms Vibrio natriegens and Halomonas bluephagenesis. Furthermore, the valorization of algal polysaccharides by genetically enhanced microbes is presented as an example of the opportunities and challenges associated with blue biotechnology. Finally, new roles for marine synthetic biology in tackling pressing global challenges, including climate change and marine pollution, are discussed.},
}
@article {pmid36917283,
year = {2023},
author = {Anand, U and Pal, T and Yadav, N and Singh, VK and Tripathi, V and Choudhary, KK and Shukla, AK and Sunita, K and Kumar, A and Bontempi, E and Ma, Y and Kolton, M and Singh, AK},
title = {Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1455-1486},
pmid = {36917283},
issn = {1432-184X},
mesh = {*Symbiosis ; *Endophytes/physiology ; Fungi/physiology ; Stress, Physiological ; Plants/microbiology ; Agriculture ; },
abstract = {Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.},
}
@article {pmid36916881,
year = {2023},
author = {Hadjirin, NF and van Tonder, AJ and Blane, B and Lees, JA and Kumar, N and Delappe, N and Brennan, W and McGrath, E and Parkhill, J and Cormican, M and Peacock, SJ and Ludden, C},
title = {Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study.},
journal = {Microbial genomics},
volume = {9},
number = {3},
pages = {},
pmid = {36916881},
issn = {2057-5858},
support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Escherichia coli/genetics ; Ireland/epidemiology ; Retrospective Studies ; *Klebsiella pneumoniae/genetics ; Genomics ; },
abstract = {The spread of carbapenemase-producing Enterobacterales (CPE) is of major public health concern. The transmission dynamics of CPE in hospitals, particularly at the national level, are not well understood. Here, we describe a retrospective nationwide genomic surveillance study of CPE in Ireland between 2012 and 2017. We sequenced 746 national surveillance CPE samples obtained between 2012 and 2017. After clustering the sequences, we used thresholds based on pairwise SNPs, and reported within-host diversity along with epidemiological data to infer recent putative transmissions. All clusters in circulating clones, derived from high-resolution phylogenies, of a species (Klebsiella pneumoniae, Escherichia coli, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter hormaechei and Citrobacter freundii) were individually examined for evidence of transmission. Antimicrobial resistance trends over time were also assessed. We identified 352 putative transmission events in six species including widespread and frequent transmissions in three species. We detected putative outbreaks in 4/6 species with three hospitals experiencing prolonged outbreaks. The bla OXA-48 gene was the main cause of carbapenem resistance in Ireland in almost all species. An expansion in the number of sequence types carrying bla OXA-48 was an additional cause of the increasing prevalence of carbapenemase-producing K. pneumoniae and E. coli.},
}
@article {pmid36916137,
year = {2024},
author = {Elhalis, H and Chin, XH and Chow, Y},
title = {Soybean fermentation: Microbial ecology and starter culture technology.},
journal = {Critical reviews in food science and nutrition},
volume = {64},
number = {21},
pages = {7648-7670},
doi = {10.1080/10408398.2023.2188951},
pmid = {36916137},
issn = {1549-7852},
mesh = {*Fermentation ; *Glycine max ; *Soy Foods/microbiology/analysis ; Food Microbiology ; Fungi/metabolism ; Nutritive Value ; Fermented Foods/microbiology ; Food Handling/methods ; },
abstract = {Fermented soybean products, including Soya sauce, Tempeh, Miso, and Natto have been consumed for decades, mainly in Asian countries. Beans are processed using either solid-state fermentation, submerged fermentation, or a sequential of both methods. Traditional ways are still used to conduct the fermentation processes, which, depending on the fermented products, might take a few days or even years to complete. Diverse microorganisms were detected during fermentation in various processes with Bacillus species or filamentous fungi being the two main dominant functional groups. Microbial activities were essential to increase the bean's digestibility, nutritional value, and sensory quality, as well as lower its antinutritive factors. The scientific understanding of fermentation microbial communities, their enzymes, and their metabolic activities, however, still requires further development. The use of a starter culture is crucial, to control the fermentation process and ensure product consistency. A broad understanding of the spontaneous fermentation ecology, biochemistry, and the current starter culture technology is essential to facilitate further improvement and meet the needs of the current extending and sustainable economy. This review covers what is currently known about these aspects and reveals the limited available information, along with the possible directions for future starter culture design in soybean fermentation.},
}
@article {pmid36915862,
year = {2023},
author = {Freixa, A and Ortiz-Rivero, J and Sabater, S},
title = {Artificial substrata to assess ecological and ecotoxicological responses in river biofilms: Use and recommendations.},
journal = {MethodsX},
volume = {10},
number = {},
pages = {102089},
pmid = {36915862},
issn = {2215-0161},
abstract = {River biofilms are biological consortia of autotrophs and heterotrophs colonizing most solid surfaces in rivers. Biofilm composition and biomass differ according to the environmental conditions, having different characteristics between systems and even between river habitats. Artificial substrata (AS) are an alternative for in situ or laboratory experiments to handle the natural variability of biofilms. However, specific research goals may require decisions on colonization time or type of substrata. Substrata properties (i.e., texture, roughness, hydrophobicity) and the colonization period and site are selective factors of biofilm characteristics. Here we describe the uses of artificial substrata in the assessment of ecological and ecotoxicological responses and propose a decision tree for the best use of artificial substrata in river biofilm studies. We propose departing from the purpose of the study to define the necessity of obtaining a realistic biofilm community, from which it may be defined the colonization time, the colonization site, and the type of artificial substratum. Having a simple or mature biofilm community should guide our decisions on the colonization time and type of substrata to be selected for the best use of AS in biofilm studies. Tests involving contaminants should avoid adsorbing materials while those ecologically oriented may use any AS mimicking those substrata occurring in the streambed.•We review the utilization of different artificial substrata to colonize biofilm in river ecology and ecotoxicology.•We propose a decision tree to guide on selecting the appropriate artificial substrata and colonization site and duration.•Type of artificial substrata (material, size, shape...) and colonization duration are to be decided according to the specific purpose of the study.},
}
@article {pmid36914121,
year = {2023},
author = {Rožman, M and Lekunberri, I and Grgić, I and Borrego, CM and Petrović, M},
title = {Effects of combining flow intermittency and exposure to emerging contaminants on the composition and metabolic response of streambed biofilm bacterial communities.},
journal = {The Science of the total environment},
volume = {877},
number = {},
pages = {162818},
doi = {10.1016/j.scitotenv.2023.162818},
pmid = {36914121},
issn = {1879-1026},
mesh = {*Ecosystem ; *Water Pollutants, Chemical/analysis ; Dissolved Organic Matter ; Bacteria/genetics ; Rivers/chemistry ; Biofilms ; },
abstract = {Freshwater ecosystems are characterised by the co-occurrence of stressors that simultaneously affect the biota. Among these, flow intermittency and chemical pollution severely impair the diversity and functioning of streambed bacterial communities. Using an artificial streams mesocosm facility, this study examined how desiccation and pollution caused by emerging contaminants affect the composition of stream biofilm bacterial communities, their metabolic profiles, and interactions with their environment. Through an integrative analysis of the composition of biofilm communities, characterization of their metabolome and composition of the dissolved organic matter, we found strong genotype-to-phenotype interconnections. The strongest correlation was found between the composition and metabolism of the bacterial community, both of which were influenced by incubation time and desiccation. Unexpectedly, no effect of the emerging contaminants was observed, which was due to the low concentration of the emerging contaminants and the dominant impact of desiccation. However, biofilm bacterial communities modified the chemical composition of their environment under the effect of pollution. Considering the tentatively identified classes of metabolites, we hypothesised that the biofilm response to desiccation was mainly intracellular while the response to chemical pollution was extracellular. The present study demonstrates that metabolite and dissolved organic matter profiling may be effectively integrated with compositional analysis of stream biofilm communities to yield a more complete picture of changes in response to stressors.},
}
@article {pmid36912945,
year = {2023},
author = {Bouchachi, N and Obernosterer, I and Carpaneto Bastos, C and Li, F and Scenna, L and Marie, B and Crispi, O and Catala, P and Ortega-Retuerta, E},
title = {Effects of Phosphorus Limitation on the Bioavailability of DOM Released by Marine Heterotrophic Prokaryotes.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1961-1971},
pmid = {36912945},
issn = {1432-184X},
mesh = {*Dissolved Organic Matter ; Biological Availability ; *Phosphorus/analysis ; Bacteria ; Mediterranean Sea ; },
abstract = {Heterotrophic prokaryotes (HP) contribute largely to dissolved organic matter (DOM) processing in the ocean, but they also release diverse organic substances. The bioavailability of DOM released by HP under varying environmental conditions has not been fully elucidated. In this study, we investigated the bioavailability of DOM released by a single bacterial strain (Sphingopyxis alaskensis) and 2 natural HP communities grown under P-replete and P-limited conditions. The released DOM (HP-DOM) was used as a substrate for natural HP communities at a coastal site in the Northwestern Mediterranean Sea. We followed changes in HP growth, enzymatic activity, diversity, and community composition together with the consumption of HP-DOM fluorescence (FDOM). HP-DOM produced under P-replete and P-limited conditions promoted significant growth in all incubations. No clear differences in HP-DOM lability released under P-repletion and P-limitation were evidenced based on the HP growth, and P-limitation was not demonstrated to decrease HP-DOM lability. However, HP-DOM supported the growth of diverse HP communities, and P-driven differences in HP-DOM quality were selected for different indicator taxa in the degrading communities. The humic-like fluorescence, commonly considered recalcitrant, was consumed during the incubations when this peak was initially dominating the FDOM pool, and this consumption coincided with higher alkaline phosphatase activity. Taken together, our findings emphasize that HP-DOM lability is dependent on both DOM quality, which is shaped by P availability, and the composition of the consumer community.},
}
@article {pmid36912675,
year = {2023},
author = {Oswin, HP and Haddrell, AE and Hughes, C and Otero-Fernandez, M and Thomas, RJ and Reid, JP},
title = {Oxidative Stress Contributes to Bacterial Airborne Loss of Viability.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0334722},
pmid = {36912675},
issn = {2165-0497},
abstract = {While the airborne decay of bacterial viability has been observed for decades, an understanding of the mechanisms driving the decay has remained elusive. The airborne transport of bacteria is often a key step in their life cycle and as such, characterizing the mechanisms driving the airborne decay of bacteria is an essential step toward a more complete understanding of microbial ecology. Using the Controlled Electrodynamic Levitation and Extraction of Bioaerosols onto a Substrate (CELEBS), it was possible to systematically evaluate the impact of different physicochemical and environmental parameters on the survival of Escherichia coli in airborne droplets of Luria Bertani broth. Rather than osmotic stress driving the viability loss, as was initially considered, oxidative stress was found to play a key role. As the droplets evaporate and equilibrate with the surrounding environment, the surface-to-volume ratio increases, which in turn increased the formation of reactive oxygen species in the droplet. These reactive oxygen species appear to play a key role in driving the airborne loss of viability of E. coli. IMPORTANCE The airborne transport of bacteria has a wide range of impacts, from disease transmission to cloud formation. By understanding the factors that influence the airborne stability of bacteria, we can better understand these processes. However, while we have known for several decades that airborne bacteria undergo a gradual loss of viability, we have not previously identified the mechanisms driving this process. In this work, we discovered that oxygen surrounding an airborne droplet facilitates the formation of reactive oxygen species within the droplet, which then gradually damage and kill bacteria within the droplet. This discovery indicates that adaptations to help bacteria deal with oxidative stress may also aid their airborne survival and be essential adaptations for bacterial airborne pathogens. Understanding the adaptations bacteria need to survive in airborne droplets could eventually lead to the development of novel antimicrobials designed to inhibit their airborne survival, helping to prevent the transmission of disease.},
}
@article {pmid36911623,
year = {2023},
author = {Meng, H and Peng, Y and Li, P and Su, J and Jiang, Y and Fu, X},
title = {Global trends in research of high-throughput sequencing technology associated with chronic wounds from 2002 to 2022: A bibliometric and visualized study.},
journal = {Frontiers in surgery},
volume = {10},
number = {},
pages = {1089203},
pmid = {36911623},
issn = {2296-875X},
abstract = {BACKGROUND: Chronic wounds are a complex medical problem. With the difficulty of skin healing, the microbial ecology of chronic wounds is an essential factor affecting wound healing. High-throughput sequencing (HTS) technology is a vital method to reveal the microbiome diversity and population structure of chronic wounds.<br><br>OBJECTIVE: The aim of this paper was to delineate the scientific output characteristics, research trends, hotspots and frontiers of HTS technologies related to chronic wounds globally over the past 20 years.<br><br>METHODS: We searched the Web of Science Core Collection (WoSCC) database for articles published between 2002 and 2022 and their full record information. The Bibliometrix software package was used to analyze bibliometric indicators and VOSviewer visualization analysis results.<br><br>RESULTS: Ultimately, a total of 449 original articles were reviewed, and the results showed that the number of annual publications (Nps) about HTS associated with chronic wounds has steadily increased over the last 20 years. The United States and China produce the most articles and have the highest H-index, while the United States and England have the largest number of citations (Nc) in this field. The University of California, Wound Repair and Regeneration and National Institutes of Health Nih United States were the most published institutions, journals and fund resources, respectively. The global research could be divided into 3 clusters as follows: microbial infection of chronic wounds, the healing process of wounds and microscopic processes, skin repair mechanism stimulated by antimicrobial peptides and oxidative stress. In recent years, "wound healing", "infections", "expression", "inflammation", "chronic wounds", "identification" and "bacteria" "angiogenesis", "biofilms" and "diabetes" were the most frequently used keywords. In addition, research on "prevalence", "gene expression", "inflammation" and "infection" has recently become a hotspot.<br><br>CONCLUSIONS: This paper compares the research hotspots and directions in this field globally from the perspectives of countries, institutions and authors, analyzes the trend of international cooperation, and reveals the future development direction of the field and research hotspots of great scientific research value. Through this paper, we can further explore the value of HTS technology in chronic wounds to better solve the problem of chronic wounds.},
}
@article {pmid36911268,
year = {2023},
author = {Polk, C and Sampson, M and Fairman, RT and DeWitt, ME and Leonard, M and Neelakanta, A and Davidson, L and Roshdy, D and Branner, C and McCurdy, L and Ludden, T and Tapp, H and Passaretti, C},
title = {Evaluation of a health system's implementation of a monkeypox care model under the RE-AIM framework.},
journal = {Therapeutic advances in infectious disease},
volume = {10},
number = {},
pages = {20499361231158463},
pmid = {36911268},
issn = {2049-9361},
abstract = {OBJECTIVE: Emerging infectious diseases challenge healthcare systems to implement new models of care. We aim to evaluate the rapid implementation of a new care model for monkeypox in our health system.<br><br>DESIGN: This is a retrospective case series evaluation under the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) framework of implementation of a testing and care model for monkeypox in a large, integrated health system.<br><br>METHODS: Atrium Health implemented education of providers, testing protocols, and management of potential monkeypox cases using electronic health record (EHR) data capabilities, telehealth, and collaboration between multiple disciplines. The first 4 weeks of care model implementation were evaluated under the RE-AIM framework.<br><br>RESULTS: One hundred fifty-three patients were tested for monkeypox by 117 unique providers at urgent care, emergency departments, and infectious disease clinics in our healthcare system between 18 July 2022 and 14 August 2022. Fifty-eight monkeypox cases were identified, compared with 198 cases in the state during the time period, a disproportionate number compared with the health system service area, and 52 patients were assessed for need for tecovirimat treatment. The number of tests performed and providers sending tests increased during the study period.<br><br>CONCLUSION: Implementation of a dedicated care model leveraging EHR data support, telehealth, and cross-disciplinary collaboration led to more effective identification and management of emerging infectious diseases and is important for public health.<br><br>PLAIN LANGUAGE SUMMARY: Impact of care model implementation on monkeypox New infectious diseases challenge health systems to implement new care practices. Our health system responded to this challenge by implementing a care model for education, testing, and clinical care of monkeypox patients. We analyzed results from implementing the model. We were able to identify a disproportionate number of monkeypox cases compared with the rest of our state by using our model to educate medical providers, encourage testing, and ensure patients had access to best disease care. Implementation of care models for testing and management of new diseases will improve patient care and public health.},
}
@article {pmid36910186,
year = {2023},
author = {Niu, T and Xu, Y and Chen, J and Qin, L and Li, Z and Yang, Y and Liang, J},
title = {Bacterial taxonomic and functional profiles from Bohai Sea to northern Yellow Sea.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1139950},
pmid = {36910186},
issn = {1664-302X},
abstract = {Microbial distribution patterns are the result of a combination of biotic and abiotic factors, which are the core issues in microbial ecology research. To better understand the biogeographic pattern of bacteria in water environments from the Bohai Sea to the northern Yellow Sea, the effects of environmental factors, and spatial distance on the structure of bacterial communities in marine water were investigated using high-throughput sequencing technology based on 16S rRNA genes. The results showed that Proteobacteria, Bacteroidetes, Actinobacteri, Desulfobacterota, and Bdellovibrionota were the dominant phyla in the study area. A clear spatial pattern in the bacterial community was observed, and environmental factors, including salinity, nutrient concentration, carbon content, total phosphorus, dissolved oxygen, and seawater turbidity emerged as the central environmental factors regulating the variation in bacterial communities. In addition, the study provides direct evidence of the existence of dispersal limitation in this strongly connected marine ecological system. Therefore, these results revealed that the variation in bacterial community characteristics was attributed to environmental selection, accompanied by the regulation of stochastic diffusion. The network analysis demonstrated a nonrandom co-occurrence pattern in the microbial communities with distinct spatial distribution characteristics. It is implied that the biogeography patterns of bacterial community may also be associated with the characteristics of co-occurrence characterize among bacterial species. Furthermore, the PICRUSt analysis indicated a clear spatial distribution of functional characteristics in bacterial communities. This functional variation was significantly modulated by the environmental characteristics of seawater but uncoupled from the taxonomic characteristics of bacterial communities (e.g., diversity characteristics, community structure, and co-occurrence relationships). Together, this findings represent a significant advance in linking seawater to the mechanisms underlying bacterial biogeographic patterns and community assembly, co-occurrence patterns, and ecological functions, providing new insights for identifying the microbial ecology as well as the biogeochemical cycle in the marine environment.},
}
@article {pmid36906178,
year = {2023},
author = {Stanhope, J and Weinstein, P},
title = {Exposure to environmental microbiota may modulate gut microbial ecology and the immune system.},
journal = {Mucosal immunology},
volume = {16},
number = {2},
pages = {99-103},
doi = {10.1016/j.mucimm.2023.03.001},
pmid = {36906178},
issn = {1935-3456},
mesh = {*Gastrointestinal Microbiome ; *Microbiota ; Immune System ; },
}
@article {pmid36906027,
year = {2023},
author = {Cahill, N and Hooban, B and Fitzhenry, K and Joyce, A and O'Connor, L and Miliotis, G and McDonagh, F and Burke, L and Chueiri, A and Farrell, ML and Bray, JE and Delappe, N and Brennan, W and Prendergast, D and Gutierrez, M and Burgess, C and Cormican, M and Morris, D},
title = {First reported detection of the mobile colistin resistance genes, mcr-8 and mcr-9, in the Irish environment.},
journal = {The Science of the total environment},
volume = {876},
number = {},
pages = {162649},
doi = {10.1016/j.scitotenv.2023.162649},
pmid = {36906027},
issn = {1879-1026},
mesh = {*Colistin/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Wastewater ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Klebsiella pneumoniae ; Plasmids ; Microbial Sensitivity Tests ; },
abstract = {The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collected were assessed for the presence of antimicrobial resistant bacteria using Brilliance ESBL, Brilliance CRE, mSuperCARBA and McConkey agar containing a ciprofloxacin disc. All water and integrated constructed wetland influent and effluent samples were filtered and enriched in buffered peptone water prior to culture, while wastewater samples were cultured directly. Isolates collected were identified via MALDI-TOF, were tested for susceptibility to 16 antimicrobials, including colistin, and subsequently underwent whole genome sequencing. Overall, eight mcr positive Enterobacterales (one mcr-8 and seven mcr-9) were recovered from six samples (freshwater (n = 2), healthcare facility wastewater (n = 2), wastewater treatment plant influent (n = 1) and integrated constructed wetland influent (piggery farm waste) (n = 1)). While the mcr-8 positive K. pneumoniae displayed resistance to colistin, all seven mcr-9 harbouring Enterobacterales remained susceptible. All isolates demonstrated multi-drug resistance and through whole genome sequencing analysis, were found to harbour a wide variety of antimicrobial resistance genes i.e., 30 ± 4.1 (10-61), including the carbapenemases, blaOXA-48 (n = 2) and blaNDM-1 (n = 1), which were harboured by three of the isolates. The mcr genes were located on IncHI2, IncFIIK and IncI1-like plasmids. The findings of this study highlight potential sources and reservoirs of mcr genes in the environment and illustrate the need for further research to gain a better understanding of the role the environment plays in the persistence and dissemination of antimicrobial resistance.},
}
@article {pmid36905734,
year = {2023},
author = {Ongena, S and de Walle, AV and Mosquera-Romero, S and Driesen, N and Gutierrez, L and Rabaey, K},
title = {Comparison of MBR and MBBR followed by UV or electrochemical disinfection for decentralized greywater treatment.},
journal = {Water research},
volume = {235},
number = {},
pages = {119818},
doi = {10.1016/j.watres.2023.119818},
pmid = {36905734},
issn = {1879-2448},
mesh = {*Waste Disposal, Fluid/methods ; *Escherichia coli ; Disinfection ; Biofilms ; Bioreactors ; Membranes, Artificial ; },
abstract = {Greywater is an attractive source for water reuse at the household or building level, particularly for non-potable applications. Two greywater treatment approaches are membrane bioreactors (MBR) and moving bed biofilm reactors (MBBR), yet, their performance has not been compared so far within their respective treatment flowsheets, including post-disinfection. Two lab-scale treatment trains were operated on synthetic greywater: a) MBR with either polymeric (chlorinated polyethylene, C-PE, 165 days) or ceramic (silicon carbide, SiC, 199 days) membranes coupled with UV disinfection; and b) single-stage (66 days) or two-stage (124 days) MBBR coupled with an electrochemical cell (EC) for in-situ disinfectant generation. Water quality was constantly monitored, and Escherichia coli log removals were assessed through spike tests. Under low-flux operation of the MBR (<8 L·m [-] [2]·h [-] [1]), the SiC membranes delayed the onset of membrane fouling and needed less frequent cleaning compared to C-PE membranes. Both treatment systems met most water quality requirements for unrestricted greywater reuse, at a 10-fold lower reactor volume for the MBR than the MBBR. However, neither the MBR nor the two-staged MBBR allowed adequate nitrogen removal, and the MBBR did not consistently meet effluent chemical oxygen demand and turbidity requirements. Both EC and UV provided non-detectable E. coli concentrations in the effluent. Although the EC provided residual disinfection, scaling and fouling decreased its energetic and disinfection performance over time, making it less efficient than UV disinfection. Several outlines to improve the performance of both treatment trains and disinfection processes are proposed, thus, allowing a fit-for-use approach that leverages the advantages of the respective treatment trains. Results from this investigation will assist in elucidating the most efficient, robust, and low-maintenance technology and configurations for small-scale greywater treatment for reuse.},
}
@article {pmid36901656,
year = {2023},
author = {Song, L},
title = {Toward Understanding Microbial Ecology to Restore a Degraded Ecosystem.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {5},
pages = {},
pmid = {36901656},
issn = {1660-4601},
mesh = {Humans ; *Ecosystem ; *Microbiota ; Fecal Microbiota Transplantation ; },
abstract = {The microbial community plays an important role in maintaining human health, addressing climate change, maintaining environmental quality, etc. High-throughput sequencing leads to the discovery and identification of more microbial community composition and function in diverse ecosystems. Microbiome therapeutics such as fecal microbiota transplantation for human health and bioaugmentation for activated sludge restoration have drawn great attention. However, microbiome therapeutics cannot secure the success of microbiome transplantation. This paper begins with a view on fecal microbiota transplantation and bioaugmentation and is followed by a parallel analysis of these two microbial therapeutic strategies. Accordingly, the microbial ecology mechanisms behind them were discussed. Finally, future research on microbiota transplantation was proposed. Successful application of both microbial therapeutics for human disease and bioremediation for contaminated environments relies on a better understanding of the microbial "entangled bank" and microbial ecology of these environments.},
}
@article {pmid36896143,
year = {2023},
author = {Pous, N and Bañeras, L and Corvini, PF and Liu, SJ and Puig, S},
title = {Direct ammonium oxidation to nitrogen gas (Dirammox) in Alcaligenes strain HO-1: The electrode role.},
journal = {Environmental science and ecotechnology},
volume = {15},
number = {},
pages = {100253},
pmid = {36896143},
issn = {2666-4984},
abstract = {It has been recently suggested that Alcaligenes use a previously unknown pathway to convert ammonium into dinitrogen gas (Dirammox) via hydroxylamine (NH2OH). This fact alone already implies a significant decrease in the aeration requirements for the process, but the process would still be dependent on external aeration. This work studied the potential use of a polarised electrode as an electron acceptor for ammonium oxidation using the recently described Alcaligenes strain HO-1 as a model heterotrophic nitrifier. Results indicated that Alcaligenes strain HO-1 requires aeration for metabolism, a requirement that cannot be replaced for a polarised electrode alone. However, concomitant elimination of succinate and ammonium was observed when operating a previously grown Alcaligenes strain HO-1 culture in the presence of a polarised electrode and without aeration. The usage of a polarised electrode together with aeration did not increase the succinate nor the nitrogen removal rates observed with aeration alone. However, current density generation was observed along a feeding batch test representing an electron share of 3% of the ammonium removed in the presence of aeration and 16% without aeration. Additional tests suggested that hydroxylamine oxidation to dinitrogen gas could have a relevant role in the electron discharge onto the anode. Therefore, the presence of a polarised electrode supported the metabolic functions of Alcaligenes strain HO-1 on the simultaneous oxidation of succinate and ammonium.},
}
@article {pmid36884370,
year = {2023},
author = {Álvarez-Pérez, S and de Vega, C and Vanoirbeek, K and Tsuji, K and Jacquemyn, H and Fukami, T and Michiels, C and Lievens, B},
title = {Phylogenomic analysis of the genus Rosenbergiella and description of Rosenbergiella gaditana sp. nov., Rosenbergiella metrosideri sp. nov., Rosenbergiella epipactidis subsp. epipactidis subsp. nov., Rosenbergiella epipactidis subsp. californiensis subsp. nov., Rosenbergiella epipactidis subsp. japonicus subsp. nov., Rosenbergiella nectarea subsp. nectarea subsp. nov. and Rosenbergiella nectarea subsp. apis subsp. nov., isolated from floral nectar and insects.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {3},
pages = {},
doi = {10.1099/ijsem.0.005777},
pmid = {36884370},
issn = {1466-5034},
mesh = {Bees ; Animals ; *Plant Nectar ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Bacterial Typing Techniques ; Base Composition ; *Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Insecta ; },
abstract = {The genus Rosenbergiella is one of the most frequent bacterial inhabitants of flowers and a usual member of the insect microbiota worldwide. To date, there is only one publicly available Rosenbergiella genome, corresponding to the type strain of Rosenbergiella nectarea (8N4[T]), which precludes a detailed analysis of intra-genus phylogenetic relationships. In this study, we obtained draft genomes of the type strains of the other Rosenbergiella species validly published to date (R. australiborealis, R. collisarenosi and R. epipactidis) and 23 additional isolates of flower and insect origin. Isolate S61[T], retrieved from the nectar of an Antirrhinum sp. flower collected in southern Spain, displayed low average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values when compared with other Rosenbergiella members (≤86.5 and ≤29.8 %, respectively). Similarly, isolate JB07[T], which was obtained from the floral nectar of Metrosideros polymorpha plants in Hawaii (USA) had ≤95.7 % ANI and ≤64.1 % isDDH with other Rosenbergiella isolates. Therefore, our results support the description of two new Rosenbergiella species for which we propose the names Rosenbergiella gaditana sp. nov. (type strain: S61[T]=NCCB 100789[T]=DSM 111181[T]) and Rosenbergiella metrosideri sp. nov. (JB07[T]=NCCB 100888[T]=LMG 32616[T]). Additionally, some R. epipactidis and R. nectarea isolates showed isDDH values<79 % with other conspecific isolates, which suggests that these species include subspecies for which we propose the names Rosenbergiella epipactidis subsp. epipactidis subsp. nov. (S256[T]=CECT 8502[T]=LMG 27956[T]), Rosenbergiella epipactidis subsp. californiensis subsp. nov. (FR72[T]=NCCB 100898[T]=LMG 32786[T]), Rosenbergiella epipactidis subsp. japonicus subsp. nov. (K24[T]=NCCB 100924[T]=LMG 32785[T]), Rosenbergiella nectarea subsp. nectarea subsp. nov. (8N4[T] = DSM 24150[T] = LMG 26121[T]) and Rosenbergiella nectarea subsp. apis subsp. nov. (B1A[T]=NCCB 100810[T]= DSM 111763[T]), respectively. Finally, we present the first phylogenomic analysis of the genus Rosenbergiella and update the formal description of the species R. australiborealis, R. collisarenosi, R. epipactidis and R. nectarea based on new genomic and phenotypic information.},
}
@article {pmid36882570,
year = {2023},
author = {Bourceau, OM and Ferdelman, T and Lavik, G and Mussmann, M and Kuypers, MMM and Marchant, HK},
title = {Simultaneous sulfate and nitrate reduction in coastal sediments.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {17},
pmid = {36882570},
issn = {2730-6151},
abstract = {The oscillating redox conditions that characterize coastal sandy sediments foster microbial communities capable of respiring oxygen and nitrate simultaneously, thereby increasing the potential for organic matter remineralization, nitrogen (N)-loss and emissions of the greenhouse gas nitrous oxide. It is unknown to what extent these conditions also lead to overlaps between dissimilatory nitrate and sulfate respiration. Here, we show that sulfate and nitrate respiration co-occur in the surface sediments of an intertidal sand flat. Furthermore, we found strong correlations between dissimilatory nitrite reduction to ammonium (DNRA) and sulfate reduction rates. Until now, the nitrogen and sulfur cycles were assumed to be mainly linked in marine sediments by the activity of nitrate-reducing sulfide oxidisers. However, transcriptomic analyses revealed that the functional marker gene for DNRA (nrfA) was more associated with microorganisms known to reduce sulfate rather than oxidise sulfide. Our results suggest that when nitrate is supplied to the sediment community upon tidal inundation, part of the sulfate reducing community may switch respiratory strategy to DNRA. Therefore increases in sulfate reduction rate in-situ may result in enhanced DNRA and reduced denitrification rates. Intriguingly, the shift from denitrification to DNRA did not influence the amount of N2O produced by the denitrifying community. Our results imply that microorganisms classically considered as sulfate reducers control the potential for DNRA within coastal sediments when redox conditions oscillate and therefore retain ammonium that would otherwise be removed by denitrification, exacerbating eutrophication.},
}
@article {pmid36881623,
year = {2023},
author = {Rohwer, RR and Hale, RJ and Vander Zanden, MJ and Miller, TR and McMahon, KD},
title = {Species invasions shift microbial phenology in a two-decade freshwater time series.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {11},
pages = {e2211796120},
pmid = {36881623},
issn = {1091-6490},
support = {DBI-2011002//National Science Foundation (NSF)/ ; WIS01516//USDA | National Institute of Food and Agriculture (NIFA)/ ; WIS01789//USDA | National Institute of Food and Agriculture (NIFA)/ ; WIS03004//USDA | National Institute of Food and Agriculture (NIFA)/ ; WIS01912//USDA | National Institute of Food and Agriculture (NIFA)/ ; DEB-9632853//National Science Foundation (NSF)/ ; DEB-0217533//National Science Foundation (NSF)/ ; DEB-0822700//National Science Foundation (NSF)/ ; DEB-1440297//National Science Foundation (NSF)/ ; MCB-9977903//National Science Foundation (NSF)/ ; DEB-0702395//National Science Foundation (NSF)/ ; DEB-1344254//National Science Foundation (NSF)/ ; },
mesh = {Animals ; Time Factors ; *Actinobacteria ; Bacteroidetes ; *Cladocera ; *Dreissena ; Fresh Water ; *Microbiota ; },
abstract = {Invasive species impart abrupt changes on ecosystems, but their impacts on microbial communities are often overlooked. We paired a 20 y freshwater microbial community time series with zooplankton and phytoplankton counts, rich environmental data, and a 6 y cyanotoxin time series. We observed strong microbial phenological patterns that were disrupted by the invasions of spiny water flea (Bythotrephes cederströmii) and zebra mussels (Dreissena polymorpha). First, we detected shifts in Cyanobacteria phenology. After the spiny water flea invasion, Cyanobacteria dominance crept earlier into clearwater; and after the zebra mussel invasion, Cyanobacteria abundance crept even earlier into the diatom-dominated spring. During summer, the spiny water flea invasion sparked a cascade of shifting diversity where zooplankton diversity decreased and Cyanobacteria diversity increased. Second, we detected shifts in cyanotoxin phenology. After the zebra mussel invasion, microcystin increased in early summer and the duration of toxin production increased by over a month. Third, we observed shifts in heterotrophic bacteria phenology. The Bacteroidota phylum and members of the acI Nanopelagicales lineage were differentially more abundant. The proportion of the bacterial community that changed differed by season; spring and clearwater communities changed most following the spiny water flea invasion that lessened clearwater intensity, while summer communities changed least following the zebra mussel invasion despite the shifts in Cyanobacteria diversity and toxicity. A modeling framework identified the invasions as primary drivers of the observed phenological changes. These long-term invasion-mediated shifts in microbial phenology demonstrate the interconnectedness of microbes with the broader food web and their susceptibility to long-term environmental change.},
}
@article {pmid36880579,
year = {2023},
author = {Chen, L and Wang, G and Teng, M and Wang, L and Yang, F and Jin, G and Du, H and Xu, Y},
title = {Non-gene-editing microbiome engineering of spontaneous food fermentation microbiota-Limitation control, design control, and integration.},
journal = {Comprehensive reviews in food science and food safety},
volume = {22},
number = {3},
pages = {1902-1932},
doi = {10.1111/1541-4337.13135},
pmid = {36880579},
issn = {1541-4337},
mesh = {Fermentation ; *Microbiota ; Food ; Food Microbiology ; },
abstract = {Non-gene-editing microbiome engineering (NgeME) is the rational design and control of natural microbial consortia to perform desired functions. Traditional NgeME approaches use selected environmental variables to force natural microbial consortia to perform the desired functions. Spontaneous food fermentation, the oldest kind of traditional NgeME, transforms foods into various fermented products using natural microbial networks. In traditional NgeME, spontaneous food fermentation microbiotas (SFFMs) are typically formed and controlled manually by the establishment of limiting factors in small batches with little mechanization. However, limitation control generally leads to trade-offs between efficiency and the quality of fermentation. Modern NgeME approaches based on synthetic microbial ecology have been developed using designed microbial communities to explore assembly mechanisms and target functional enhancement of SFFMs. This has greatly improved our understanding of microbiota control, but such approaches still have shortcomings compared to traditional NgeME. Here, we comprehensively describe research on mechanisms and control strategies for SFFMs based on traditional and modern NgeME. We discuss the ecological and engineering principles of the two approaches to enhance the understanding of how best to control SFFM. We also review recent applied and theoretical research on modern NgeME and propose an integrated in vitro synthetic microbiota model to bridge gaps between limitation control and design control for SFFM.},
}
@article {pmid36880421,
year = {2023},
author = {Anand, S and Hallsworth, JE and Timmis, J and Verstraete, W and Casadevall, A and Ramos, JL and Sood, U and Kumar, R and Hira, P and Dogra Rawat, C and Kumar, A and Lal, S and Lal, R and Timmis, K},
title = {Weaponising microbes for peace.},
journal = {Microbial biotechnology},
volume = {16},
number = {6},
pages = {1091-1111},
pmid = {36880421},
issn = {1751-7915},
mesh = {Humans ; *Industrial Microbiology ; *Technology ; },
abstract = {There is much human disadvantage and unmet need in the world, including deficits in basic resources and services considered to be human rights, such as drinking water, sanitation and hygiene, healthy nutrition, access to basic healthcare, and a clean environment. Furthermore, there are substantive asymmetries in the distribution of key resources among peoples. These deficits and asymmetries can lead to local and regional crises among peoples competing for limited resources, which, in turn, can become sources of discontent and conflict. Such conflicts have the potential to escalate into regional wars and even lead to global instability. Ergo: in addition to moral and ethical imperatives to level up, to ensure that all peoples have basic resources and services essential for healthy living and to reduce inequalities, all nations have a self-interest to pursue with determination all available avenues to promote peace through reducing sources of conflicts in the world. Microorganisms and pertinent microbial technologies have unique and exceptional abilities to provide, or contribute to the provision of, basic resources and services that are lacking in many parts of the world, and thereby address key deficits that might constitute sources of conflict. However, the deployment of such technologies to this end is seriously underexploited. Here, we highlight some of the key available and emerging technologies that demand greater consideration and exploitation in endeavours to eliminate unnecessary deprivations, enable healthy lives of all and remove preventable grounds for competition over limited resources that can escalate into conflicts in the world. We exhort central actors: microbiologists, funding agencies and philanthropic organisations, politicians worldwide and international governmental and non-governmental organisations, to engage - in full partnership - with all relevant stakeholders, to 'weaponise' microbes and microbial technologies to fight resource deficits and asymmetries, in particular among the most vulnerable populations, and thereby create humanitarian conditions more conducive to harmony and peace.},
}
@article {pmid36875992,
year = {2022},
author = {Tadrent, N and Dedeine, F and Hervé, V},
title = {SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes.},
journal = {F1000Research},
volume = {11},
number = {},
pages = {1522},
pmid = {36875992},
issn = {2046-1402},
mesh = {*Metagenome ; Workflow ; *Software ; Metagenomics/methods ; Computational Biology ; },
abstract = {Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM, GUNC), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Importantly, these additional MAGs showed no significant difference compared to the other ones in terms of completeness, contamination, genome size nor relative abundance. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.},
}
@article {pmid36878770,
year = {2023},
author = {Lyng, M and Kovács, &#xc1;T},
title = {Frenemies of the soil: Bacillus and Pseudomonas interspecies interactions.},
journal = {Trends in microbiology},
volume = {31},
number = {8},
pages = {845-857},
doi = {10.1016/j.tim.2023.02.003},
pmid = {36878770},
issn = {1878-4380},
mesh = {*Pseudomonas/genetics ; *Bacillus/genetics ; Soil ; Soil Microbiology ; Bacteria ; },
abstract = {Bacillus and Pseudomonas ubiquitously occur in natural environments and are two of the most intensively studied bacterial genera in the soil. They are often coisolated from environmental samples, and as a result, several studies have experimentally cocultured bacilli and pseudomonads to obtain emergent properties. Even so, the general interaction between members of these genera is virtually unknown. In the past decade, data on interspecies interactions between natural isolates of Bacillus and Pseudomonas has become more detailed, and now, molecular studies permit mapping of the mechanisms behind their pairwise ecology. This review addresses the current knowledge about microbe-microbe interactions between strains of Bacillus and Pseudomonas and discusses how we can attempt to generalize the interaction on a taxonomic and molecular level.},
}
@article {pmid36877031,
year = {2023},
author = {Barnett, SE and Egan, R and Foster, B and Eloe-Fadrosh, EA and Buckley, DH},
title = {Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing.},
journal = {mBio},
volume = {14},
number = {2},
pages = {e0358422},
pmid = {36877031},
issn = {2150-7511},
mesh = {*Life History Traits ; Soil/chemistry ; Soil Microbiology ; Bacteria/genetics/metabolism ; Carbon/metabolism ; Isotopes/metabolism ; Metagenomics ; },
abstract = {Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.},
}
@article {pmid36876069,
year = {2023},
author = {Ge, W and Ren, Y and Dong, C and Shao, Q and Bai, Y and He, Z and Yao, T and Zhang, Y and Zhu, G and Deshmukh, SK and Han, Y},
title = {New perspective: Symbiotic pattern and assembly mechanism of Cantharellus cibarius-associated bacteria.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1074468},
pmid = {36876069},
issn = {1664-302X},
abstract = {Cantharellus cibarius, an ectomycorrhizal fungus belonging to the Basidiomycetes, has significant medicinal and edible value, economic importance, and ecological benefits. However, C. cibarius remains incapable of artificial cultivation, which is thought to be due to the presence of bacteria. Therefore, much research has focused on the relationship between C. cibarius and bacteria, but rare bacteria are frequently overlooked, and symbiotic pattern and assembly mechanism of the bacterial community associated with C. cibarius remain unknown. In this study, the assembly mechanism and driving factors of both abundant and rare bacterial communities of C. cibarius were revealed by the null model. The symbiotic pattern of the bacterial community was examined using a co-occurrence network. Metabolic functions and phenotypes of the abundant and rare bacteria were compared using METAGENassist2, and the impacts of abiotic variables on the diversity of abundant and rare bacteria were examined using partial least squares path modeling. In the fruiting body and mycosphere of C. cibarius, there was a higher proportion of specialist bacteria compared with generalist bacteria. Dispersal limitation dominated the assembly of abundant and rare bacterial communities in the fruiting body and mycosphere. However, pH, 1-octen-3-ol, and total phosphorus of the fruiting body were the main driving factors of bacterial community assembly in the fruiting body, while available nitrogen and total phosphorus of the soil affected the assembly process of the bacterial community in the mycosphere. Furthermore, bacterial co-occurrence patterns in the mycosphere may be more complex compared with those in the fruiting body. Unlike the specific potential functions of abundant bacteria, rare bacteria may provide supplementary or unique metabolic pathways (such as sulfite oxidizer and sulfur reducer) to enhance the ecological function of C. cibarius. Notably, while volatile organic compounds can reduce mycosphere bacterial diversity, they can increase fruiting body bacterial diversity. Findings from this study further, our understanding of C. cibarius-associated microbial ecology.},
}
@article {pmid36876066,
year = {2023},
author = {Melcher, M and Hodgskiss, LH and Mardini, MA and Schleper, C and Rittmann, SKR},
title = {Analysis of biomass productivity and physiology of Nitrososphaera viennensis grown in continuous culture.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1076342},
pmid = {36876066},
issn = {1664-302X},
abstract = {Microbial ammonia oxidation is the first and usually rate limiting step in nitrification and is therefore an important step in the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) play an important role in nitrification. Here, we report a comprehensive analysis of biomass productivity and the physiological response of Nitrososphaera viennensis to different ammonium and carbon dioxide (CO2) concentrations aiming to understand the interplay between ammonia oxidation and CO2 fixation of N. viennensis. The experiments were performed in closed batch in serum bottles as well as in batch, fed-batch, and continuous culture in bioreactors. A reduced specific growth rate (μ) of N. viennensis was observed in batch systems in bioreactors. By increasing CO2 gassing μ could be increased to rates comparable to that of closed batch systems. Furthermore, at a high dilution rate (D) in continuous culture (≥ 0.7 of μmax) the biomass to ammonium yield (Y(X/NH3)) increased up to 81.7% compared to batch cultures. In continuous culture, biofilm formation at higher D prevented the determination of D crit. Due to changes in Y(X/NH3) and due to biofilm, nitrite concentration becomes an unreliable proxy for the cell number in continuous cultures at D towards μmax. Furthermore, the obscure nature of the archaeal ammonia oxidation prevents an interpretation in the context of Monod kinetics and thus the determination of K S. Our findings indicate that the physiological response of N. viennensis might be regulated with different enzymatic make-ups, according to the ammonium catalysis rate. We reveal novel insights into the physiology of N. viennensis that are important for biomass production and the biomass yield of AOA. Moreover, our study has implications to the field of archaea biology and microbial ecology by showing that bioprocess technology and quantitative analysis can be applied to decipher environmental factors affecting the physiology and productivity of AOA.},
}
@article {pmid36875535,
year = {2022},
author = {Zhang, H and Xing, D and Wu, Y and Jin, R and Liu, D and Deines, P},
title = {Editorial: Microbial ecology and function of the aquatic systems.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1109221},
pmid = {36875535},
issn = {1664-302X},
}
@article {pmid36872509,
year = {2023},
author = {Munley, JA and Kelly, LS and Park, G and Gillies, GS and Pons, EE and Kannan, KB and Whitley, EM and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM},
title = {Multicompartmental traumatic injury induces sex-specific alterations in the gut microbiome.},
journal = {The journal of trauma and acute care surgery},
volume = {95},
number = {1},
pages = {30-38},
pmid = {36872509},
issn = {2163-0763},
support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; T32 GM008721/GM/NIGMS NIH HHS/United States ; },
mesh = {Rats ; Animals ; Male ; Female ; *Gastrointestinal Microbiome ; Rats, Sprague-Dawley ; Occludin ; RNA, Ribosomal, 16S ; Lipopolysaccharides ; },
abstract = {BACKGROUND: Previous preclinical studies have demonstrated an altered gut microbiome after traumatic injury; however, the impact of sex on dysbiosis remains unknown. We hypothesized that the "pathobiome" phenotype induced by multicompartmental injuries and chronic stress is host sex specific with unique microbiome signatures.<br><br>METHODS: Male and proestrus female Sprague-Dawley rats (n = 8/group) aged 9 weeks to 11 weeks were subjected to either multicompartmental injury (PT) (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), PT plus 2 hours daily chronic restraint stress (PT/CS) or naive controls. Fecal microbiome was measured on Days 0 and 2 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity was assessed using Chao1 (number of different unique species) and Shannon (species richness and evenness) indices. Beta-diversity was assessed using principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin and lipopolysaccharide binding protein. Histologic evaluation of ileum and colon tissues was scored for injury by a blinded pathologist. Analyses were performed in GraphPad and R, with significance defined as p < 0.05 between males versus females.<br><br>RESULTS: At baseline, females had significantly elevated alpha-diversity (Chao1, Shannon indices) compared with males (p < 0.05) which was no longer present 2 days postinjury in PT and PT/CS. Beta-diversity also differed significantly between males and females after PT (p = 0.01). At Day 2, the microbial composition in PT/CS females was dominated by Bifidobacterium , whereas PT males demonstrated elevated levels of Roseburia (p < 0.01). The PT/CS males had significantly elevated ileum injury scores compared with females (p = 0.0002). Plasma occludin was higher in PT males compared with females (p = 0.004); plasma lipopolysaccharide binding protein was elevated in PT/CS males (p = 0.03).<br><br>CONCLUSION: Multicompartmental trauma induces significant alterations in microbiome diversity and taxa, but these signatures differ by host sex. These findings suggest that sex is an important biological variable that may influence outcomes after severe trauma and critical illness.},
}
@article {pmid36869137,
year = {2023},
author = {Rifkin, RF and Vikram, S and Alcorta, J and Ramond, JB and Cowan, DA and Jakobsson, M and Schlebusch, CM and Lombard, M},
title = {Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {240},
pmid = {36869137},
issn = {2399-3642},
support = {NGS-371R-18//National Geographic Society/ ; },
mesh = {Humans ; Child ; *Rickettsia felis ; Africa, Southern ; DNA ; South Africa ; DNA, Ancient ; },
abstract = {The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.},
}
@article {pmid36868548,
year = {2023},
author = {Zeng, X and Cao, Y and Wang, L and Wang, M and Wang, Q and Yang, Q},
title = {Viability and transcriptional responses of multidrug resistant E. coli to chromium stress.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {324},
number = {},
pages = {121346},
doi = {10.1016/j.envpol.2023.121346},
pmid = {36868548},
issn = {1873-6424},
mesh = {*Escherichia coli/genetics/metabolism ; *Chromium/toxicity ; Transcriptome ; Reactive Oxygen Species/metabolism ; },
abstract = {The viability of multidrug resistant (MDR) bacteria in environment is critical for the spread of antimicrobial resistance. In this study, two Escherichia coli strains, MDR LM13 and susceptible ATCC25922, were used to elucidate differences in their viability and transcriptional responses to hexavalent chromium (Cr(VI)) stress. The results show that the viability of LM13 was notably higher than that of ATCC25922 under 2-20 mg/L Cr(VI) exposure with bacteriostatic rates of 3.1%-57%, respectively, for LM13 and 0.9%-93.1%, respectively, for ATCC25922. The levels of reactive oxygen species and superoxide dismutase in ATCC25922 were much higher than those in LM13 under Cr(VI) exposure. Additionally, 514 and 765 differentially expressed genes were identified from the transcriptomes of the two strains (log2|FC| > 1, p < 0.05). Among them, 134 up-regulated genes were enriched in LM13 in response to external pressure, but only 48 genes were annotated in ATCC25922. Furthermore, the expression levels of antibiotic resistance genes, insertion sequences, DNA and RNA methyltransferases, and toxin-antitoxin systems were generally higher in LM13 than in ATCC25922. This work shows that MDR LM13 has a stronger viability under Cr(VI) stress, and therefore may promote the dissemination of MDR bacteria in environment.},
}
@article {pmid36866381,
year = {2023},
author = {Lin, J and Yu, D and Pan, R and Cai, J and Liu, J and Zhang, L and Wen, X and Peng, X and Cernava, T and Oufensou, S and Migheli, Q and Chen, X and Zhang, X},
title = {Improved YOLOX-Tiny network for detection of tobacco brown spot disease.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1135105},
pmid = {36866381},
issn = {1664-462X},
abstract = {INTRODUCTION: Tobacco brown spot disease caused by Alternaria fungal species is a major threat to tobacco growth and yield. Thus, accurate and rapid detection of tobacco brown spot disease is vital for disease prevention and chemical pesticide inputs.<br><br>METHODS: Here, we propose an improved YOLOX-Tiny network, named YOLO-Tobacco, for the detection of tobacco brown spot disease under open-field scenarios. Aiming to excavate valuable disease features and enhance the integration of different levels of features, thereby improving the ability to detect dense disease spots at different scales, we introduced hierarchical mixed-scale units (HMUs) in the neck network for information interaction and feature refinement between channels. Furthermore, in order to enhance the detection of small disease spots and the robustness of the network, we also introduced convolutional block attention modules (CBAMs) into the neck network.<br><br>RESULTS: As a result, the YOLO-Tobacco network achieved an average precision (AP) of 80.56% on the test set. The AP was 3.22%, 8.99%, and 12.03% higher than that obtained by the classic lightweight detection networks YOLOX-Tiny network, YOLOv5-S network, and YOLOv4-Tiny network, respectively. In addition, the YOLO-Tobacco network also had a fast detection speed of 69 frames per second (FPS).<br><br>DISCUSSION: Therefore, the YOLO-Tobacco network satisfies both the advantages of high detection accuracy and fast detection speed. It will likely have a positive impact on early monitoring, disease control, and quality assessment in diseased tobacco plants.},
}
@article {pmid36864462,
year = {2023},
author = {Keuschnig, C and Vogel, TM and Barbaro, E and Spolaor, A and Koziol, K and Björkman, MP and Zdanowicz, C and Gallet, JC and Luks, B and Layton, R and Larose, C},
title = {Selection processes of Arctic seasonal glacier snowpack bacterial communities.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {35},
pmid = {36864462},
issn = {2049-2618},
mesh = {Bayes Theorem ; *Ice Cover ; Seasons ; *Bacteria/genetics ; Biodiversity ; },
abstract = {BACKGROUND: Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories.<br><br>METHODS: We sampled snow from 22 glacier sites on 7 glaciers across Svalbard in April during the maximum snow accumulation period and prior to the melt period to evaluate the factors that drive snowpack metataxonomy. These snowpacks were seasonal, accumulating in early winter on bare ice and firn and completely melting out in autumn. Using a Bayesian fitting strategy to evaluate Hubbell's Unified Neutral Theory of Biodiversity at multiple sites, we tested for neutrality and defined immigration rates at different taxonomic levels. Bacterial abundance and diversity were measured and the amount of potential ice-nucleating bacteria was calculated. The chemical composition (anions, cations, organic acids) and particulate impurity load (elemental and organic carbon) of the winter and spring snowpack were also characterized. We used these data in addition to geographical information to assess possible niche-based effects on snow microbial communities using multivariate and variable partitioning analysis.<br><br>RESULTS: While certain taxonomic signals were found to fit the neutral assembly model, clear evidence of niche-based selection was observed at most sites. Inorganic chemistry was not linked directly to diversity, but helped to identify predominant colonization sources and predict microbial abundance, which was tightly linked to sea spray. Organic acids were the most significant predictors of microbial diversity. At low organic acid concentrations, the snow microbial structure represented the seeding community closely, and evolved away from it at higher organic acid concentrations, with concomitant increases in bacterial numbers.<br><br>CONCLUSIONS: These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth. Video Abstract.},
}
@article {pmid36864279,
year = {2023},
author = {Ma, X and Ding, J and Ren, H and Xin, Q and Li, Z and Han, L and Liu, D and Zhuo, Z and Liu, C and Ren, Z},
title = {Distinguishable Influence of the Delivery Mode, Feeding Pattern, and Infant Sex on Dynamic Alterations in the Intestinal Microbiota in the First Year of Life.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1799-1813},
pmid = {36864279},
issn = {1432-184X},
support = {2020T130609//China Postdoctoral Science Foundation/ ; 2020T130109ZX//China Postdoctoral Science Foundation/ ; SBGJ2018004//Henan Provincial Medical Science and Technology Project/ ; 2018YFC2000500//National Key Research and Development Program of China/ ; 182102310404//Henan Province Science and Technology Project/ ; 202102310055//Henan Province Science and Technology Project/ ; 21A320055//Key Scientific Research Projects of Higher Education Institutions in Henan Province/ ; 20A320056//and Key Scientific Research Projects of Higher Education Institutions in Henan Province/ ; },
mesh = {Humans ; Infant ; Male ; Female ; Pregnancy ; *Cesarean Section ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Breast Feeding ; Feces/microbiology ; Bacteroidetes/genetics ; Feeding Behavior ; },
abstract = {The delivery mode, the feeding pattern and infant sex significantly influence the development of the infant gut flora. However, the extent to which these factors contribute to the establishment of the gut microbiota at different stages has rarely been studied. The factors that play a dominant role in determining microbial colonization of the infant gut at specific time points are unknown. The purpose of this study was to assess the different contributions of the delivery mode, the feeding pattern and infant sex to the composition of the infant gut microbiome. Here, 213 fecal samples from 55 infants at five ages (0, 1, 3, 6, and 12 months postpartum) were collected, and the composition of the gut microbiota via 16S rRNA sequencing was analyzed. The results showed that the average relative abundances of four genera, Bifidobacterium, Bacteroides, Parabacteroides, and Phascolarctobacterium, were increased in vaginally delivered infants versus cesarean section-delivered infants, while those of ten genera, such as Salmonella and Enterobacter, were reduced. The relative proportions of Anaerococcus and Peptostreptococcaceae were higher in exclusive breastfeeding than in combined feeding, while those of Coriobacteriaceae, Lachnospiraceae and Erysipelotrichaceae were lower. The average relative abundances of two genera, Alistipes and Anaeroglobus, were increased in male infants compared with female infants, whereas those of the phyla Firmicutes and Proteobacteria were reduced. During the first year of life, the average UniFrac distances revealed that the individual difference in the gut microbial composition in vaginally delivered infants was greater than that in cesarean section-delivered infants (P < 0.001) and that infants who received combined feeding had greater individual microbiota differences than exclusively breastfed infants (P < 0.01). The delivery mode, infant sex, and the feeding pattern were the dominant factors determining colonization of the infant gut microbiota at 0 months, from 1 to 6 months, and at 12 months postpartum, respectively. This study demonstrated for the first time that infant sex accounted for the dominant contribution to infant gut microbial development from 1 to 6 months postpartum. More broadly, this study effectively established the extent to which the delivery mode, the feeding pattern and infant sex contribute to the development of the gut microbiota at various time points during the first year of life.},
}
@article {pmid36861302,
year = {2023},
author = {Lopes, LD and Futrell, SL and Bergmeyer, E and Hao, J and Schachtman, DP},
title = {Root exudate concentrations of indole-3-acetic acid (IAA) and abscisic acid (ABA) affect maize rhizobacterial communities at specific developmental stages.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {3},
pages = {},
doi = {10.1093/femsec/fiad019},
pmid = {36861302},
issn = {1574-6941},
mesh = {*Abscisic Acid ; *Plant Growth Regulators ; Zea mays ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; Bacteria/genetics ; Rhizosphere ; Soil Microbiology ; },
abstract = {Root exudates shape the rhizosphere microbiome, but little is known about the specific compounds in root exudates that are important. Here, we investigated the impacts of the plant-synthesized phytohormones indole-3-acetic acid (IAA) and abscisic acid (ABA) exuded by roots on the maize rhizobacterial communities. To identify maize genotypes that differed in the root exudate concentrations of IAA and ABA, we screened hundreds of inbred lines using a semi-hydroponic system. Twelve genotypes with variable exudate concentrations of IAA and ABA were selected for a replicated field experiment. Bulk soil, rhizosphere, and root endosphere samples were collected at two vegetative and one reproductive maize developmental stage. IAA and ABA concentrations in rhizosphere samples were quantified by liquid chromatography-mass spectrometry. The bacterial communities were analyzed by V4 16S rRNA amplicon sequencing. Results indicated that IAA and ABA concentrations in root exudates significantly affected the rhizobacterial communities at specific developmental stages. ABA impacted the rhizosphere bacterial communities at later developmental stages, whereas IAA affected the rhizobacterial communities at the vegetative stages. This study contributed to our knowledge about the influence that specific root exudate compounds have on the rhizobiome composition, showing that the phytohormones IAA and ABA exuded by roots have a role in the plant-microbiome interactions.},
}
@article {pmid36860022,
year = {2023},
author = {Mandal, A and Ghosh, A and Saha, R and Bhadury, P},
title = {Seasonal variability of modern benthic foraminifera assemblages in a mangrove ecosystem from northeast coastal Bay of Bengal.},
journal = {Marine pollution bulletin},
volume = {188},
number = {},
pages = {114679},
doi = {10.1016/j.marpolbul.2023.114679},
pmid = {36860022},
issn = {1879-3363},
mesh = {Humans ; Bays ; Ecosystem ; *Foraminifera ; Seasons ; *Cyclonic Storms ; },
abstract = {Benthic foraminifera assemblages, nutrient dynamics of surface and porewater from 10 intertidal sites spanning over two years (2019-2020) covering two major estuaries in Sundarbans mangrove were evaluated to understand role of seasonal precipitation and primary production (driven by eddy nutrients) with a focus on standing crop. Benthic foraminifera abundance ranged between 280 individuals/10 cc in pre-monsoon (2019), 415 individuals/10 cc in post-monsoon 2019 and 630 individuals/10 cc in post-monsoon (2020). Standing crop was highest in post-monsoon coinciding with eddy nutrients driven stoichiometry and increase in abundance of large diatom cells. Calcareous and agglutinated foraminifer taxa Ammonia sp.1, Quinqueloculina seminulum, Entzia macrescens and Textularia sp. respectively were frequent. Entzia macrescens was found in dense mangrove vegetation sites; exhibited strong relationship with sediment texture and pore water total organic carbon. One of the major findings is mangroves with pneumatophores improves oxygen availability in sediment and leads to an increase in standing crop.},
}
@article {pmid36859706,
year = {2023},
author = {Pinheiro, Y and Faria da Mota, F and Peixoto, RS and van Elsas, JD and Lins, U and Mazza Rodrigues, JL and Rosado, AS},
title = {A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {230},
pmid = {36859706},
issn = {2399-3642},
support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
mesh = {*Actinobacteria ; Carbon ; *Extreme Environments ; *Bacillaceae ; *Alphaproteobacteria ; },
abstract = {A thermophilic, chemolithoautotrophic, and aerobic microbial consortium (termed carbonitroflex) growing in a nutrient-poor medium and an atmosphere containing N2, O2, CO2, and CO is investigated as a model to expand our understanding of extreme biological systems. Here we show that the consortium is dominated by Carbonactinospora thermoautotrophica (strain StC), followed by Sphaerobacter thermophilus, Chelatococcus spp., and Geobacillus spp. Metagenomic analysis of the consortium reveals a mutual relationship among bacteria, with C. thermoautotrophica StC exhibiting carboxydotrophy and carbon-dioxide storage capacity. C. thermoautotrophica StC, Chelatococcus spp., and S. thermophilus harbor genes encoding CO dehydrogenase and formate oxidase. No pure cultures were obtained under the original growth conditions, indicating that a tightly regulated interactive metabolism might be required for group survival and growth in this extreme oligotrophic system. The breadwinner hypothesis is proposed to explain the metabolic flux model and highlight the vital role of C. thermoautotrophica StC (the sole keystone species and primary carbon producer) in the survival of all consortium members. Our data may contribute to the investigation of complex interactions in extreme environments, exemplifying the interconnections and dependency within microbial communities.},
}
@article {pmid36858219,
year = {2023},
author = {Ouradou, A and Veillette, M and Bélanger Cayouette, A and Corbin, S and Boulanger, C and Dorner, S and Duchaine, C and Bédard, E},
title = {Effect of odor treatment systems on bioaerosol microbial concentration and diversity from wastewater treatment plants.},
journal = {The Science of the total environment},
volume = {874},
number = {},
pages = {162419},
doi = {10.1016/j.scitotenv.2023.162419},
pmid = {36858219},
issn = {1879-1026},
mesh = {Odorants ; *Legionella ; Bacteria ; *Water Purification/methods ; *Air Pollutants ; Water Microbiology ; },
abstract = {Biofiltration, activated carbon and chemical scrubbing are technologies used for odor control in wastewater treatment plants. These systems may also influence the airborne microbial load in treated air. The study objectives were to 1) evaluate the capacity of three odor control system technologies to reduce the airborne concentration of total bacteria, Legionella, L. pneumophila, non-tuberculous mycobacteria (NTM) and Cladosporium in winter and summer seasons and 2) to describe the microbial ecology of the biofiltration system and evaluate its impact on treated air microbial diversity. A reduction of the total bacterial concentration up to 25 times was observed after odor treatment. Quantification by qPCR revealed the presence of Legionella spp. in all air samples ranging between 26 and 1140 GC/m[3], while L. pneumophila was not detected except for three samples below the limit of quantification. A significant increase of up to 25-fold of Legionella spp. was noticed at the outlet of two of the three treatment systems. NTM were ubiquitously detected before air treatment (up to 2500 GC/m[3]) and were significantly reduced by all 3 systems (up to 13-fold). Cladosporium was measured at low concentrations for each system (< 190 GC/m[3]), with 68 % of the air samples below the limit of detection. Biodiversity results revealed that biofiltration system is an active process that adapts to air pollutants over time. Legionella spp. were detected in significant abundance in the air once treated in winter (up to 27 %). Nevertheless, the abundance of protozoan hosts is low and does not explain the multiplication of Legionella spp. The season remains the most influential factor shaping biodiversity. In summer only, air biofiltration caused a significant enrichment of the biodiversity. Although odor control technologies are not designed for bacterial mitigation, findings from this study suggest their potential to reduce the abundance of some genera harboring pathogenic species.},
}
@article {pmid36858028,
year = {2023},
author = {Martins, SJ and Pasche, J and Silva, HAO and Selten, G and Savastano, N and Abreu, LM and Bais, HP and Garrett, KA and Kraisitudomsook, N and Pieterse, CMJ and Cernava, T},
title = {The Use of Synthetic Microbial Communities to Improve Plant Health.},
journal = {Phytopathology},
volume = {113},
number = {8},
pages = {1369-1379},
doi = {10.1094/PHYTO-01-23-0016-IA},
pmid = {36858028},
issn = {0031-949X},
abstract = {Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.},
}
@article {pmid36857007,
year = {2023},
author = {Senabio, JA and de Campos Pereira, F and Pietro-Souza, W and Sousa, TF and Silva, GF and Soares, MA},
title = {Enhanced mercury phytoremediation by Pseudomonodictys pantanalensis sp. nov. A73 and Westerdykella aquatica P71.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {54},
number = {2},
pages = {949-964},
pmid = {36857007},
issn = {1678-4405},
support = {.0568258/2014//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Mato Grosso/ ; },
mesh = {*Mercury/metabolism ; Biodegradation, Environmental ; *Ascomycota/metabolism ; Endophytes ; Plant Growth Regulators/metabolism ; *Soil Pollutants/metabolism ; Plant Roots/microbiology ; },
abstract = {Mercury is a non-essential and toxic metal that induces toxicity in most organisms, but endophytic fungi can develop survival strategies to tolerate and respond to metal contaminants and other environmental stressors. The present study demonstrated the potential of mercury-resistant endophytic fungi in phytoremediation. We examined the functional traits involved in plant growth promotion, phytotoxicity mitigation, and mercury phytoremediation in seven fungi strains. The endophytic isolates synthesized the phytohormone indole-3-acetic acid, secreted siderophores, and solubilized phosphate in vitro. Inoculation of maize (Zea mays) plants with endophytes increased plant growth attributes by up to 76.25%. The endophytic fungi stimulated mercury uptake from the substrate and promoted its accumulation in plant tissues (t test, p < 0.05), preferentially in the roots, which thereby mitigated the impacts of metal phytotoxicity. Westerdykella aquatica P71 and the newly identified species Pseudomonodictys pantanalensis nov. A73 were the isolates that presented the best phytoremediation potential. Assembling and annotation of P. pantanalensis A73 and W. aquatica P71 genomes resulted in genome sizes of 45.7 and 31.8 Mb that encoded 17,774 and 11,240 protein-coding genes, respectively. Some clusters of genes detected were involved in the synthesis of secondary metabolites such as dimethylcoprogen (NRPS) and melanin (T1PKS), which are metal chelators with antioxidant activity; mercury resistance (merA and merR1); oxidative stress (PRX1 and TRX1); and plant growth promotion (trpS and iscU). Therefore, both fungi species are potential tools for the bioremediation of mercury-contaminated soils due to their ability to reduce phytotoxicity and assist phytoremediation.},
}
@article {pmid36855215,
year = {2023},
author = {Hernandez-Becerra, N and Cliffe, L and Xiu, W and Boothman, C and Lloyd, JR and Nixon, SL},
title = {New microbiological insights from the Bowland shale highlight heterogeneity of the hydraulically fractured shale microbiome.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {14},
pmid = {36855215},
issn = {2524-6372},
support = {2018-000061-02EXTF-00218//Mexican National Council for Science and Technology/ ; NE/R013462/1//NERC/ ; },
abstract = {BACKGROUND: Hydraulically fractured shales offer a window into the deep biosphere, where hydraulic fracturing creates new microbial ecosystems kilometers beneath the surface of the Earth. Studying the microbial communities from flowback fluids that are assumed to inhabit these environments provides insights into their ecophysiology, and in particular their ability to survive in these extreme environments as well as their influence on site operation e.g. via problematic biofouling processes and/or biocorrosion. Over the past decade, research on fractured shale microbiology has focused on wells in North America, with a few additional reported studies conducted in China. To extend the knowledge in this area, we characterized the geochemistry and microbial ecology of two exploratory shale gas wells in the Bowland Shale, UK. We then employed a meta-analysis approach to compare geochemical and 16S rRNA gene sequencing data from our study site with previously published research from geographically distinct formations spanning China, Canada and the USA.<br><br>RESULTS: Our findings revealed that fluids recovered from exploratory wells in the Bowland are characterized by moderate salinity and high microbial diversity. The microbial community was dominated by lineages known to degrade hydrocarbons, including members of Shewanellaceae, Marinobacteraceae, Halomonadaceae and Pseudomonadaceae. Moreover, UK fractured shale communities lacked the usually dominant Halanaerobium lineages. From our meta-analysis, we infer that chloride concentrations play a dominant role in controlling microbial community composition. Spatio-temporal trends were also apparent, with different shale formations giving rise to communities of distinct diversity and composition.<br><br>CONCLUSIONS: These findings highlight an unexpected level of compositional heterogeneity across fractured shale formations, which is not only relevant to inform management practices but also provides insight into the ability of diverse microbial consortia to tolerate the extreme conditions characteristic of the engineered deep subsurface.},
}
@article {pmid36851794,
year = {2023},
author = {Dart, E and Fuhrman, JA and Ahlgren, NA},
title = {Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics.},
journal = {Viruses},
volume = {15},
number = {2},
pages = {},
pmid = {36851794},
issn = {1999-4915},
support = {1R01GM120624-01A1/NH/NIH HHS/United States ; },
mesh = {*Bacteriophages/genetics ; Host Specificity ; Metagenome ; Pacific Ocean ; Seasons ; *Synechococcus ; },
abstract = {Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage-host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of monthly viral and cellular fraction metagenomes. Cyanophage communities contained thousands of mostly low-abundance (<2% relative abundance) species with varying temporal dynamics, categorized as seasonally recurring or non-seasonal and occurring persistently, occasionally, or sporadically (detected in ≥85%, 15-85%, or <15% of samples, respectively). Viromes contained mostly seasonal and persistent phages (~40% each), while cellular fraction metagenomes had mostly sporadic species (~50%), reflecting that these sample sets capture different steps of the infection cycle-virions from prior infections or within currently infected cells, respectively. Two groups of seasonal phages correlated to Synechococcus or Prochlorococcus were abundant in spring/summer or fall/winter, respectively. Cyanophages likely have a strong influence on the host community structure, as their communities explained up to 32% of host community variation. These results support how both seasonally recurrent and apparent stochastic processes, likely determined by host availability and different host-range strategies among phages, are critical to phage-host interactions and dynamics, consistent with both the Kill-the-Winner and the Bank models.},
}
@article {pmid36849610,
year = {2023},
author = {Spescha, A and Zwyssig, M and Hess Hermida, M and Moix, A and Bruno, P and Enkerli, J and Campos-Herrera, R and Grabenweger, G and Maurhofer, M},
title = {When Competitors Join Forces: Consortia of Entomopathogenic Microorganisms Increase Killing Speed and Mortality in Leaf- and Root-Feeding Insect Hosts.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1947-1960},
pmid = {36849610},
issn = {1432-184X},
mesh = {Animals ; Reproducibility of Results ; *Pest Control, Biological ; Insecta ; Larva/microbiology ; *Rhabditida/microbiology ; Plant Leaves ; },
abstract = {Combining different biocontrol agents (BCA) is an approach to increase efficacy and reliability of biological control. If several BCA are applied together, they have to be compatible and ideally work together. We studied the interaction of a previously selected BCA consortium of entomopathogenic pseudomonads (Pseudomonas chlororaphis), nematodes (Steinernema feltiae associated with Xenorhabdus bovienii), and fungi (Metarhizium brunneum). We monitored the infection course in a leaf- (Pieris brassicae) and a root-feeding (Diabrotica balteata) pest insect after simultaneous application of the three BCA as well as their interactions inside the larvae in a laboratory setting. The triple combination caused the highest mortality and increased killing speed compared to single applications against both pests. Improved efficacy against P. brassicae was mainly caused by the pseudomonad-nematode combination, whereas the nematode-fungus combination accelerated killing of D. balteata. Co-monitoring of the three BCA and the nematode-associated Xenorhabdus symbionts revealed that the four organisms are able to co-infect the same larva. However, with advancing decay of the cadaver there is increasing competition and cadaver colonization is clearly dominated by the pseudomonads, which are known for their high competitivity in the plant rhizosphere. Altogether, the combination of the three BCA increased killing efficacy against a Coleopteran and a Lepidopteran pest which indicates that this consortium could be applied successfully against a variety of insect pests.},
}
@article {pmid36847986,
year = {2023},
author = {Rawat, J and Kumar, V and Ahlawat, P and Tripathi, LK and Tomar, R and Kumar, R and Dholpuria, S and Gupta, PK},
title = {Current Trends on the Effects of Metal-Based Nanoparticles on Microbial Ecology.},
journal = {Applied biochemistry and biotechnology},
volume = {195},
number = {10},
pages = {6168-6182},
pmid = {36847986},
issn = {1559-0291},
mesh = {Animals ; Ecosystem ; *Metal Nanoparticles/toxicity ; *Nanoparticles ; Soil ; Agriculture ; *Soil Pollutants ; },
abstract = {The growing field of nanotechnology and its many applications have led to the irregular release of nanoparticles (NPs), with unintended effects on the environment and continued contamination of water bodies. Metallic NPs are used more frequently in extreme environmental conditions due to their higher efficiency, which attracts more attention in various applications. Due to improper pre-treatment of biosolids, inefficient wastewater treatment practices, and other unregulated agricultural practices continue to contaminate the environment. In particular, the uncontrolled use of NPs in various industrial applications has led to damage to the microbial flora and caused irreplaceable damage to animals and plants. This study focuses on the effect of different doses, types, and compositions of NP on the ecosystem. The review also mentions the impact of various metallic NPs on microbial ecology, their interactions with microorganisms, ecotoxicity studies, and dosage evaluation of the NPs, mainly focused on the review article. However, further research is still needed to understand the complexity of interactions between NPs and microbes in soil and aquatic ecosystems.},
}
@article {pmid36844628,
year = {2023},
author = {Morales-Rodríguez, M and Paniagua-García, L and Narayanan, J and Zamudio-Meza, H and Moreno-Torres, RV and Cortés-González, CC and Juanico-Lorán, JA and Martínez-Pérez, B and Fernández-Retana, J},
title = {Insulin‑like growth factor axis: A potential nanotherapy target for resistant cervical cancer tumors (Review).},
journal = {Oncology letters},
volume = {25},
number = {3},
pages = {128},
pmid = {36844628},
issn = {1792-1082},
abstract = {Cervical cancer is among the most frequently occurring neoplasms worldwide, and it particularly affects individuals in developing countries. Factors such as the low quality of screening tests, the high incidence of locally advanced cancer stages and the intrinsic resistance of certain tumors are the main causes of failure in the treatment of this neoplasm. Due to advances in the understanding of carcinogenic mechanisms and bioengineering research, advanced biological nanomaterials have been manufactured. The insulin-like growth factor (IGF) system comprises multiple growth factor receptors, including IGF receptor 1. These receptors are activated by binding to their respective growth factor ligands, IGF-1 and IGF-2, and insulin, and play an important role in the development, maintenance, progression, survival and treatment resistance of cervical cancer. In the present review, the role of the IGF system in cervical cancer and three nanotechnological applications that use elements of this system are described, namely Trap decoys, magnetic iron oxide nanoparticles and protein nanotubes. Their use in the treatment of resistant cervical cancer tumors is also discussed.},
}
@article {pmid36841075,
year = {2023},
author = {Parente, E and Zotta, T and Giavalisco, M and Ricciardi, A},
title = {Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments.},
journal = {International journal of food microbiology},
volume = {391-393},
number = {},
pages = {110124},
doi = {10.1016/j.ijfoodmicro.2023.110124},
pmid = {36841075},
issn = {1879-3460},
mesh = {Humans ; Animals ; *Lactobacillaceae/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Bacteria/genetics ; },
abstract = {Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments. We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9 % of the type strain sequences can be unambiguously assigned to species. We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The ecological distribution of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained. We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.},
}
@article {pmid36838501,
year = {2023},
author = {Bai, S and Zhang, J and Qi, X and Zeng, J and Wu, S and Peng, X},
title = {Changes of In Situ Prokaryotic and Eukaryotic Communities in the Upper Sanya River to the Sea over a Nine-Hour Period.},
journal = {Microorganisms},
volume = {11},
number = {2},
pages = {},
pmid = {36838501},
issn = {2076-2607},
abstract = {The transition areas of riverine, estuarine, and marine environments are particularly valuable for the research of microbial ecology, biogeochemical processes, and other physical-chemical studies. Although a large number of microbial-related studies have been conducted within such systems, the vast majority of sampling have been conducted over a large span of time and distance, which may lead to separate batches of samples receiving interference from different factors, thus increasing or decreasing the variability between samples to some extent. In this study, a new in situ filtration system was used to collect membrane samples from six different sampling sites along the Sanya River, from upstream freshwater to the sea, over a nine-hour period. We used high-throughput sequencing of 16S and 18S rRNA genes to analyze the diversity and composition of prokaryotic and eukaryotic communities. The results showed that the structures of these communities varied according to the different sampling sites. The α-diversity of the prokaryotic and eukaryotic communities both decreased gradually along the downstream course. The structural composition of prokaryotic and eukaryotic communities changed continuously with the direction of river flow; for example, the relative abundances of Rhodobacteraceae and Flavobacteriaceae increased with distance downstream, while Sporichthyaceae and Comamonadaceae decreased. Some prokaryotic taxa, such as Phycisphaeraceae and Chromobacteriaceae, were present nearly exclusively in pure freshwater environments, while some additional prokaryotic taxa, including the SAR86 clade, Clade I, AEGEAN-169 marine group, and Actinomarinaceae, were barely present in pure freshwater environments. The eukaryotic communities were mainly composed of the Chlorellales X, Chlamydomonadales X, Sphaeropleales X, Trebouxiophyceae XX, Annelida XX, and Heteroconchia. The prokaryotic and eukaryotic communities were split into abundant, common, and rare communities for NCM analysis, respectively, and the results showed that assembly of the rare community assembly was more impacted by stochastic processes and less restricted by species dispersal than that of abundant and common microbial communities for both prokaryotes and eukaryotes. Overall, this study provides a valuable reference and new perspectives on microbial ecology during the transition from freshwater rivers to estuaries and the sea.},
}
@article {pmid36838461,
year = {2023},
author = {Zhao, RZ and Zhang, WJ and Zhao, ZF and Qiu, XC},
title = {Determinants and Assembly Mechanism of Bacterial Community Structure in Ningxia Section of the Yellow River.},
journal = {Microorganisms},
volume = {11},
number = {2},
pages = {},
pmid = {36838461},
issn = {2076-2607},
support = {NXYLXK2021A03//Ningxia University first-class discipline (water conservancy engineering) construction subsidy project/ ; 2019BFG02014//Key Research and Development Plan (key project) of Ningxia Hui Autonomous Region/ ; 2020AAC03280//Natural Science Foundation of Ningxia Province/ ; },
abstract = {The Yellow River is a valuable resource in the Ningxia Hui Autonomous Region and plays a vital role in local human activities and biodiversity. Bacteria are a crucial component of river ecosystems, but the driving factors and assembly mechanisms of bacterial community structure in this region remain unclear. Herein, we documented the bacterial community composition, determinants, co-occurrence pattern, and assembly mechanism for surface water and sediment. In comparison to sediment, the bacterioplankton community showed significant seasonal variation, as well as less diversity and abundance. The network topology parameters indicated that the sediment bacterial network was more stable than water, but the bacterioplankton network had higher connectivity. In this lotic ecosystem, CODMn, Chl a, and pH affected the structure of the bacterioplankton community, while TP was the primary factor influencing the structure of the sediment bacterial community. The combined results of the neutral community model and the phylogenetic null model indicate that Bacterial communities in both habitats were mainly affected by stochastic processes, with ecological processes dominated by ecological drift for bacterioplankton and dispersal limitation for sediment bacteria. These results provide essential insights into future research on microbial ecology, environmental monitoring, and classified management in the Ningxia section of the Yellow River.},
}
@article {pmid36838363,
year = {2023},
author = {Zwarycz, AS and Whitworth, DE},
title = {Myxobacterial Predation: A Standardised Lawn Predation Assay Highlights Strains with Unusually Efficient Predatory Activity.},
journal = {Microorganisms},
volume = {11},
number = {2},
pages = {},
pmid = {36838363},
issn = {2076-2607},
abstract = {Myxobacteria prey upon a broad range of microorganisms. Lawn assays are commonly used to quantify myxobacterial predation-myxobacterial suspensions are spotted onto prey lawns, and monitored via spot expansion. The diversity in motility behaviours of myxobacterial strains and differing assay protocols in myxobacteriology laboratories led us to develop a highly-specified assay, which was applied to 28 myxobacterial strains preying on seven phytopathogenic prey species. Generally, prey organisms showed no qualitative differences in their susceptibility/resistance to myxobacterial predation. For most myxobacteria, prey did not stimulate, and in ~50% of cases actively hindered colony expansion. Only ~25% of predator/prey strain combinations exhibited greater colony expansion than in the absence of nutrients. The activity of predatory strains against different prey correlated, implying effective predators may have relatively non-specific predation mechanisms (e.g., broad specificity proteases/lipases), but no correlation was observed between predatory activity and phylogeny. Predation on dead (but intact) or lysed prey cells gave greater colony expansion than on live prey. Occasional strains grew substantially faster on dead compared to lysed cells, or vice-versa. Such differences in accessing nutrients from live, dead and lysed cells indicates there are strain-specific differences in the efficiencies/machineries of prey killing and nutrient acquisition, which has important implications for the ecology of myxobacterial predators and their prey.},
}
@article {pmid36838349,
year = {2023},
author = {Pradeep Ram, AS and Sime-Ngando, T},
title = {Differential Effects of Viruses on the Growth Efficiency of Freshwater Bacterioplankton in Eutrophic Relative to Non-Eutrophic Lakes.},
journal = {Microorganisms},
volume = {11},
number = {2},
pages = {},
pmid = {36838349},
issn = {2076-2607},
abstract = {In aquatic environments, the consensus of viral impact on bacterial carbon metabolism with the nutrient environment as an important axis is limited. Henceforth, we explored the viral regulation of carbon-based bacterial growth efficiency (BGE) in a set of freshwater systems from French Massif Central, which were broadly classified based on two trophic statuses: eutrophic and non-eutrophic lakes. Comparative analysis showed that microbial abundances (viruses and bacteria) were 3-fold higher in eutrophic compared with non-eutrophic lakes, and so were bacterial production and viral lytic infection. The observed variability in BGE (10-60%) was explained by the uncoupling between bacterial respiration and production. Viruses through selective lysis of susceptible host communities had an antagonistic impact on BGE in the eutrophic lakes, whereas the release of substrates via viral shunt exerted a synergistic influence on the carbon metabolism of non-targeted host populations in non-eutrophic lakes. The decisive effect of the two individual processes (i.e., lysis and substrate release) on BGE was supported by regressions of bacterial abundance as a function of bacterial production, which is considered as a proxy of top-down processes. The role of viruses through their negative impact via mortality and positive impact via substrate supply can eventually have implications on carbon transfer through bacterioplankton in freshwaters.},
}
@article {pmid36836352,
year = {2023},
author = {Adedayo, AA and Babalola, OO},
title = {Fungi That Promote Plant Growth in the Rhizosphere Boost Crop Growth.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {2},
pages = {},
pmid = {36836352},
issn = {2309-608X},
support = {UID132595//The National Research Foundation of South Africa grant/ ; },
abstract = {The fungi species dwelling in the rhizosphere of crop plants, revealing functions that endeavor sustainability of the plants, are commonly referred to as 'plant-growth-promoting fungi' (PGPF). They are biotic inducers that provide benefits and carry out important functions in agricultural sustainability. The problem encountered in the agricultural system nowadays is how to meet population demand based on crop yield and protection without putting the environment and human and animal health at risk based on crop production. PGPF including Trichoderma spp., Gliocladium virens, Penicillium digitatum, Aspergillus flavus, Actinomucor elegans, Podospora bulbillosa, Arbuscular mycorrhizal fungi, etc., have proven their ecofriendly nature to ameliorate the production of crops by improving the growth of the shoots and roots of crop plants, the germination of seeds, the production of chlorophyll for photosynthesis, and the abundant production of crops. PGPF's potential mode of action is as follows: the mineralization of the major and minor elements required to support plants' growth and productivity. In addition, PGPF produce phytohormones, induced resistance, and defense-related enzymes to inhibit or eradicate the invasion of pathogenic microbes, in other words, to help the plants while encountering stress. This review portrays the potential of PGPF as an effective bioagent to facilitate and promote crop production, plant growth, resistance to disease invasion, and various abiotic stresses.},
}
@article {pmid36836247,
year = {2023},
author = {Wang, J and Qin, S and Fan, R and Peng, Q and Hu, X and Yang, L and Liu, Z and Baccelli, I and Migheli, Q and Berg, G and Chen, X and Cernava, T},
title = {Plant Growth Promotion and Biocontrol of Leaf Blight Caused by Nigrospora sphaerica on Passion Fruit by Endophytic Bacillus subtilis Strain GUCC4.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {2},
pages = {},
pmid = {36836247},
issn = {2309-608X},
support = {2021YFE0107700//National Key research and Development of China/ ; Guike AA21196003//Science and Technology Base &amp; Talent Project of Guangxi Province/ ; 2019-1410;2021-229;HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; KY2021-026//Outstanding Young Scientist Program of Guizhou Province/ ; 2022-36-Z01-KF12//Guangxi Key Laboratory of Rice Genetics and Breeding Opening Research Project/ ; 111 Program; D20023//Guizhou University Cultivation Project 2019-04 and Program for Introducing Talents to Chinese Universities/ ; },
abstract = {Passion fruit (Passiflora edulis Sims) is widely cultivated in tropic and sub-tropic regions for the production of fruit, flowers, cosmetics, and for pharmacological applications. Its high economic, nutritional, and medical values elicit the market demand, and the growing areas are rapidly increasing. Leaf blight caused by Nigrospora sphaerica is a new and emerging disease of passion fruit in Guizhou, in southwest China, where the unique karst mountainous landscape and climate conditions are considered potential areas of expansion for passion fruit production. Bacillus species are the most common biocontrol and plant-growth-promotion bacteria (PGPB) resources in agricultural systems. However, little is known about the endophytic existence of Bacillus spp. in the passion fruit phyllosphere as well as their potential as biocontrol agents and PGPB. In this study, 44 endophytic strains were isolated from 15 healthy passion fruit leaves, obtained from Guangxi province, China. Through purification and molecular identification, 42 of the isolates were ascribed to Bacillus species. Their inhibitory activity against N. sphaerica was tested in vitro. Eleven endophytic Bacillus spp. strains inhibited the pathogen by >65%. All of them produced biocontrol- and plant-growth-promotion-related metabolites, including indole-3-acetic acid (IAA), protease, cellulase, phosphatase, and solubilized phosphate. Furthermore, the plant growth promotion traits of the above 11 endophytic Bacillus strains were tested on passion fruit seedlings. One isolate, coded B. subtilis GUCC4, significantly increased passion fruit stem diameter, plant height, leaf length, leaf surface, fresh weight, and dry weight. In addition, B. subtilis GUCC4 reduced the proline content, which indicated its potential to positively regulate passion fruit biochemical properties and resulted in plant growth promotion effects. Finally, the biocontrol efficiencies of B. subtilis GUCC4 against N. sphaerica were determined in vivo under greenhouse conditions. Similarly to the fungicide mancozeb and to a commercial B. subtilis-based biofungicide, B. subtilis GUCC4 significantly reduced disease severity. These results suggest that B. subtilis GUCC4 has great potential as a biological control agent and as PGPB on passion fruit.},
}
@article {pmid36835503,
year = {2023},
author = {Alsayed, AR and Abed, A and Khader, HA and Al-Shdifat, LMH and Hasoun, L and Al-Rshaidat, MMD and Alkhatib, M and Zihlif, M},
title = {Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
pmid = {36835503},
issn = {1422-0067},
mesh = {Humans ; *Precision Medicine ; Prospective Studies ; Lung/microbiology ; *Microbiota/genetics ; Bacteria/genetics ; },
abstract = {The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.},
}
@article {pmid36834682,
year = {2023},
author = {Deng, Q and Liu, H and Lu, Q and Gangurde, SS and Du, P and Li, H and Li, S and Liu, H and Wang, R and Huang, L and Chen, R and Fan, C and Liang, X and Chen, X and Hong, Y},
title = {Silicon Application for the Modulation of Rhizosphere Soil Bacterial Community Structures and Metabolite Profiles in Peanut under Ralstonia solanacearum Inoculation.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
pmid = {36834682},
issn = {1422-0067},
support = {2020B020219003 and 2022B0202060004//Guangdong Provincial Key Research and Development Program-Modern Seed Industry/ ; CARS-13//China Agriculture Research System of MOF and MARA/ ; 32001442 and 32172051//National Natural Science Foundation of China/ ; 2021M700895//China Postdoctoral Science Foundation/ ; 2020A1515010021 and 2021A1515010811//Guangdong Basic and Applied Basic Research Foundation/ ; 20200503//Guangdong Provincial Department of Science and Technology Project- International Scientific and Technological Cooperation/ ; 2019KJ136-02//Technology Special Fund of Guangdong Province Agriculture and Rural Affairs Department/ ; 202201010281//Guangzhou Basic and Applied Basic Research Foundation/ ; 202104TD//Agricultural Competitive Industry Discipline Team Building Project of Guangdong Academy of Agricultural Sciences/ ; R2020PY-JX004, R2020PY-JG005 and R2021PY-QY003//Special Fund for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Science/ ; 202101//Foundation of Director of Crop Research Institute of Guangdong Academy of Agriculture Sciences/ ; 202201//Open Fund of Guangdong Provincial Key Laboratory of Crop Genetic Improvement/ ; 2021A0505030047//Science and Technology Planning Project of Guangdong Province/ ; 20171BBF60036//Jiangxi Provincial Key R&amp;D Program Project/ ; },
mesh = {*Arachis/genetics ; *Ralstonia solanacearum/metabolism ; Silicon/metabolism ; Soil/chemistry ; Rhizosphere ; Bacteria/metabolism ; Plant Diseases/microbiology ; },
abstract = {Silicon (Si) has been shown to promote peanut growth and yield, but whether Si can enhance the resistance against peanut bacterial wilt (PBW) caused by Ralstonia solanacearum, identified as a soil-borne pathogen, is still unclear. A question regarding whether Si enhances the resistance of PBW is still unclear. Here, an in vitro R. solanacearum inoculation experiment was conducted to study the effects of Si application on the disease severity and phenotype of peanuts, as well as the microbial ecology of the rhizosphere. Results revealed that Si treatment significantly reduced the disease rate, with a decrement PBW severity of 37.50% as compared to non-Si treatment. The soil available Si (ASi) significantly increased by 13.62-44.87%, and catalase activity improved by 3.01-3.10%, which displayed obvious discrimination between non-Si and Si treatments. Furthermore, the rhizosphere soil bacterial community structures and metabolite profiles dramatically changed under Si treatment. Three significantly changed bacterial taxa were observed, which showed significant abundance under Si treatment, whereas the genus Ralstonia genus was significantly suppressed by Si. Similarly, nine differential metabolites were identified to involve into unsaturated fatty acids via a biosynthesis pathway. Significant correlations were also displayed between soil physiochemical properties and enzymes, the bacterial community, and the differential metabolites by pairwise comparisons. Overall, this study reports that Si application mediated the evolution of soil physicochemical properties, the bacterial community, and metabolite profiles in the soil rhizosphere, which significantly affects the colonization of the Ralstonia genus and provides a new theoretical basis for Si application in PBW prevention.},
}
@article {pmid36834619,
year = {2023},
author = {Cruz-Rubio, JM and Riva, A and Cybulska, J and Zdunek, A and Berry, D and Loeppert, R and Viernstein, H and Praznik, W and Maghuly, F},
title = {Neutral and Pectic Heteropolysaccharides Isolated from Opuntia joconostle Mucilage: Composition, Molecular Dimensions and Prebiotic Potential.},
journal = {International journal of molecular sciences},
volume = {24},
number = {4},
pages = {},
pmid = {36834619},
issn = {1422-0067},
support = {Scholarship 440539//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {*Opuntia/chemistry ; Prebiotics ; Plant Breeding ; Polysaccharides/chemistry ; Galactans ; },
abstract = {Opuntia joconostle is a semi-wild cactus cultivated for its fruit. However, the cladodes are often discarded, wasting the potentially useful mucilage in them. The mucilage is composed primarily of heteropolysaccharides, characterized by their molar mass distribution, monosaccharide composition, structural features (by vibrational spectroscopy, FT IR, and atomic force microscopy, AFM), and fermentability by known saccharolytic commensal members of the gut microbiota. After fractionation with ion exchange chromatography, four polysaccharides were found: one neutral (composed mainly of galactose, arabinose, and xylose) and three acidic, with a galacturonic acid content from 10 to 35%mol. Their average molar masses ranged from 1.8 × 10[5] to 2.8 × 10[5] g·mol[-1]. Distinct structural features such as galactan, arabinan, xylan, and galacturonan motifs were present in the FT IR spectra. The intra- and intermolecular interactions of the polysaccharides, and their effect on the aggregation behavior, were shown by AFM. The composition and structural features of these polysaccharides were reflected in their prebiotic potential. Lactobacilli and Bifidobacteria were not able to utilize them, whereas members of Bacteroidetes showed utilization capacity. The obtained data suggest a high economic potential for this Opuntia species, with potential uses such as animal feed in arid areas, precise prebiotic, and symbiotic formulations, or as the carbon skeleton source in a green refinery. Our methodology can be used to evaluate the saccharides as the phenotype of interest, helping to guide the breeding strategy.},
}
@article {pmid36826588,
year = {2023},
author = {Morris, N and Alldred, M and Zarnoch, C and Alter, SE},
title = {Estuarine Sediment Microbiomes from a Chronosequence of Restored Urban Salt Marshes.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {916-930},
pmid = {36826588},
issn = {1432-184X},
mesh = {*Wetlands ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Geologic Sediments/microbiology ; *Microbiota ; Bacteria ; Nitrogen/metabolism ; Carbon/metabolism ; },
abstract = {Salt marshes play an important role in the global nutrient cycle. The sediments in these systems harbor diverse and complex bacterial communities possessing metabolic capacities that provide ecosystem services such as nutrient cycling and removal. On the East Coast of the USA, salt marshes have been experiencing degradation due to anthropogenic stressors. Salt marsh islands within Jamaica Bay, New York City (USA), are surrounded by a large highly urbanized watershed and have declined in area. Restoration efforts have been enacted to reduce further loss, but little is known about how microbial communities develop following restoration activities, or how processes such as nitrogen cycling are impacted. Sediment samples were collected at two sampling depths from five salt marsh islands to characterize the bacterial communities found in marsh sediment including a post-restoration chronosequence of 3-12 years. We used 16s rRNA amplicon sequencing to define alpha and beta diversity, taxonomic composition, and predicted metabolic profile of each sediment sample. We found significant differences in alpha diversity between sampling depths, and significant differences in beta diversity, taxonomic composition, and predicted metabolic capacity among the five sampling locations. The youngest restored site and the degraded natural sampling site exhibited the most distinct communities among the five sites. Our findings suggest that while the salt marsh islands are located in close proximity to each other, they harbor distinct bacterial communities that can be correlated with post-restoration age, marsh health, and other environmental factors such as availability of organic carbon. IMPORTANCE: Salt marshes play a critical role in the global nutrient cycle due to sediment bacteria and their metabolic capacities. Many East Coast salt marshes have experienced significant degradation over recent decades, thought largely to be due to anthropogenic stressors such as nitrogen loading, urban development, and sea-level rise. Salt marsh islands in Jamaica Bay (Queens/Brooklyn NY) are exposed to high water column nitrogen due to wastewater effluent. Several receding marsh islands have been subjected to restoration efforts to mitigate this loss. Little is known about the effect marsh restoration has on bacterial communities, their metabolic capacity, or how they develop post-restoration. Here, we describe the bacterial communities found in marsh islands including a post-restoration chronosequence of 3-12 years and one degraded marsh island that remains unrestored. We found distinct communities at marsh sites, despite their geographic proximity. Differences in diversity and community composition were consistent with changes in organic carbon availability that occur during marsh development, and may result in differences in ecosystem function among sites.},
}
@article {pmid36826587,
year = {2023},
author = {Lemke, M and DeSalle, R},
title = {The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {781-795},
pmid = {36826587},
issn = {1432-184X},
mesh = {*Ecology ; Genomics ; *Microbiota ; Genome, Bacterial ; },
abstract = {Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.},
}
@article {pmid36825884,
year = {2023},
author = {Thiele, S and Vader, A and Øvreås, L},
title = {The mystery of the ice cold rose-Microbiome of an Arctic winter frost flower.},
journal = {MicrobiologyOpen},
volume = {12},
number = {1},
pages = {e1345},
pmid = {36825884},
issn = {2045-8827},
mesh = {RNA, Ribosomal, 16S/genetics ; Arctic Regions ; *Bacteria ; *Microbiota ; Archaea/genetics ; Flowers ; Ice Cover/microbiology ; },
abstract = {Under very cold conditions, delicate ice-crystal structures called frost flowers emerge on the surface of newly formed sea ice. These understudied, ephemeral structures include saline brine, organic material, inorganic nutrients, and bacterial and archaeal communities in their brine channels. Hitherto, only a few frost flowers have been studied during spring and these have been reported to be dominated by Rhizobia or members of the SAR11 clade. Here we report on the microbiome of frost flowers sampled during the winter and polar night in the Barents Sea. There was a distinct difference in community profile between the extracted DNA and RNA, but both were dominated by members of the SAR11 clade (78% relative abundance and 41.5% relative activity). The data further suggested the abundance and activity of Cand. Nitrosopumilus, Nitrospinia, and Nitrosomonas. Combined with the inference of marker genes based on the 16S rRNA gene data, this indicates that sulfur and nitrogen cycling are likely the major metabolism in these ephemeral structures.},
}
@article {pmid36825091,
year = {2023},
author = {Bogdan, DF and Baricz, AI and Chiciudean, I and Bulzu, PA and Cristea, A and Năstase-Bucur, R and Levei, EA and Cadar, O and Sitar, C and Banciu, HL and Moldovan, OT},
title = {Diversity, distribution and organic substrates preferences of microbial communities of a low anthropic activity cave in North-Western Romania.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {962452},
pmid = {36825091},
issn = {1664-302X},
abstract = {INTRODUCTION: Karst caves are characterized by relatively constant temperature, lack of light, high humidity, and low nutrients availability. The diversity and functionality of the microorganisms dwelling in caves micro-habitats are yet underexplored. Therefore, in-depth investigations of these ecosystems aid in enlarging our understanding of the microbial interactions and microbially driven biogeochemical cycles. Here, we aimed at evaluating the diversity, abundance, distribution, and organic substrate preferences of microbial communities from Peștera cu Apă din Valea Leșului (Leșu Cave) located in the Apuseni Mountains (North-Western Romania).<br><br>MATERIALS AND METHODS: To achieve this goal, we employed 16S rRNA gene amplicon sequencing and community-level physiological profiling (CLPP) paralleled by the assessment of environmental parameters of cave sediments and water.<br><br>RESULTS AND DISCUSSION: Pseudomonadota (synonym Proteobacteria) was the most prevalent phylum detected across all samples whereas the abundance detected at order level varied among sites and between water and sediment samples. Despite the general similarity at the phylum-level in Le&#x219;u Cave across the sampled area, the results obtained in this study suggest that specific sites drive bacterial community at the order-level, perhaps sustaining the enrichment of unique bacterial populations due to microenvironmental conditions. For most of the dominant orders the distribution pattern showed a positive correlation with C-sources such as putrescine, &#x3b3;-amino butyric acid, and D-malic acid, while particular cases were positively correlated with polymers (Tween 40, Tween 80 and &#x3b1;-cyclodextrin), carbohydrates (&#x3b1;-D-lactose, i-erythritol, D-mannitol) and most of the carboxylic and ketonic acids. Physicochemical analysis reveals that sediments are geochemically distinct, with increased concentration of Ca, Fe, Al, Mg, Na and K, whereas water showed low nitrate concentration. Our PCA indicated the clustering of different dominant orders with Mg, As, P, Fe, and Cr. This information serves as a starting point for further studies in elucidating the links between the taxonomic and functional diversity of subterranean microbial communities.},
}
@article {pmid36823577,
year = {2023},
author = {Shao, K and Zhang, L and Ba, T and Chao, J and Gao, G},
title = {Bacterial community composition of the sediment in Sayram Lake, an alpine lake in the arid northwest of China.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {47},
pmid = {36823577},
issn = {1471-2180},
mesh = {*Lakes/microbiology ; Geologic Sediments/microbiology ; Bacteria/genetics ; *Microbiota ; China ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Sediment bacterial communities play a critical role in biogeochemical cycling in alpine lake ecosystems. However, little is known about the sediment microbial communities in these lakes. In this study, the bacterial community composition (BCC) and their relationships with environmental factors of the sediment in Sayram Lake, the largest alpine and cold-water inland lake, China was analyzed using Illumina MiSeq sequencing. In total, we obtained 618,271 high quality sequences. The results showed that the bacterial communities with 30 phyla and 546 genera, were spread out among the 5 furface sediment samples, respectively. The communities were dominated by Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, Actinobacteria, Verrucomicrobia and Bacteroidetes, accounting for 48.15 ± 8.10%, 11.23 ± 3.10%, 8.42 ± 2.15%, 8.37 ± 2.26%, 7.40 ± 3.05%, 5.62 ± 1.25%, 4.18 ± 2.12% and 2.24 ± 1.10% of the total reads, respectively. At the genus level, the communities were dominated by Aquabacterium, Pseudomonas, Woeseia, MND1, Ignavibacterium and Truepera, accounting for 7.89% ± 8.24%, 2.32% ± 1.05%, 2.14% ± 0.94%, 2% ± 1.22%, 0.94% ± 0.14% and 0.80% ± 0.14% of the total reads, respectively. Statistical analyses showed the similarity of the sediment bacterial communities at our field sites was considerably low, far below 35%, and total organic carbon (TOC) was the dominant environmental factor affecting the spatial changes of BCC in the sediment. Thus, this study greatly improving our understanding of the microbial ecology of alpine lake in the arid and semi-arid ecosystems today so seriously threatened.},
}
@article {pmid36822952,
year = {2023},
author = {Pilosof, S},
title = {Conceptualizing microbe-plasmid communities as complex adaptive systems.},
journal = {Trends in microbiology},
volume = {31},
number = {7},
pages = {672-680},
doi = {10.1016/j.tim.2023.01.007},
pmid = {36822952},
issn = {1878-4380},
mesh = {*Ecology ; *Microbiota ; Plasmids/genetics ; Microbial Interactions ; },
abstract = {Plasmids shape microbial communities' diversity, structure, and function. Nevertheless, we lack a mechanistic understanding of how community structure and dynamics emerge from local microbe-plasmid interactions and coevolution. Addressing this gap is challenging because multiple processes operate simultaneously at multiple levels of organization. For example, immunity operates between a plasmid and a cell, but incompatibility mechanisms regulate coexistence between plasmids. Conceptualizing microbe-plasmid communities as complex adaptive systems is a promising approach to overcoming these challenges. I illustrate how agent-based evolutionary modeling, extended by network analysis, can be used to quantify the relative importance of local processes governing community dynamics. These theoretical developments can advance our understanding of plasmid ecology and evolution, especially when combined with empirical data.},
}
@article {pmid36821051,
year = {2023},
author = {Karnachuk, OV and Panova, IA and Rusanov, II and Schetinina, L and Lepokurova, OY and Domrocheva, EV and Kadnikov, VV and Avakyan, MR and Lukina, AP and Glukhova, LB and Pimenov, NV and Ravin, NV},
title = {Coexistence of Psychrophilic, Mesophilic, and Thermophilic Sulfate-Reducing Bacteria in a Deep Subsurface Aquifer Associated with Coal-Bed Methane Production.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1934-1946},
pmid = {36821051},
issn = {1432-184X},
support = {21-14-00114//Russian Science Foundation/ ; 22-14-00178//Russian Science Foundation/ ; },
mesh = {Bacteria ; Coal/microbiology ; RNA, Ribosomal, 16S/genetics ; *Desulfovibrio/genetics ; Water ; Methane ; *Groundwater ; Sulfates ; },
abstract = {The microbial community of subsurface environments remains understudied due to limited access to deep strata and aquifers. Coal-bed methane (CBM) production is associated with a large number of wells pumping water out of coal seams. CBM wells provide access to deep biotopes associated with coal-bed water. Temperature is one of the key constraints for the distribution and activity of subsurface microorganisms, including sulfate-reducing prokaryotes (SRP). The 16S rRNA gene amplicon sequencing coupled with in situ sulfate reduction rate (SRR) measurements with a radioactive tracer and cultivation at various temperatures revealed that the SRP community of the coal bed water of the Kuzbass coal basin is characterized by an overlapping mesophilic-psychrophilic boundary. The genus Desulfovibrio comprised a significant share of the SRP community. The D. psychrotolerans strain 1203, which has a growth optimum below 20 °C, dominated the cultivated SRP. SRR in coal bed water varied from 0.154 ± 0.07 to 2.04 ± 0.048 nmol S cm[-3] day[-1]. Despite the ambient water temperature of ~ 10-20 °C, an active thermophilic SRP community occurred in the fracture water, which reduced sulfate with the rate of 0.159 ± 0.023 to 0.198 ± 0.007 nmol S cm[-3] day[-1] at 55 °C. A novel moderately thermophilic "Desulforudis audaxviator"-clade SRP has been isolated in pure culture from the coal-bed water.},
}
@article {pmid36820832,
year = {2023},
author = {Rosas-Salazar, C and Kimura, KS and Shilts, MH and Strickland, BA and Freeman, MH and Wessinger, BC and Gupta, V and Brown, HM and Boone, HH and Rajagopala, SV and Turner, JH and Das, SR},
title = {Upper respiratory tract microbiota dynamics following COVID-19 in adults.},
journal = {Microbial genomics},
volume = {9},
number = {2},
pages = {},
pmid = {36820832},
issn = {2057-5858},
support = {R21 AI154016/AI/NIAID NIH HHS/United States ; R21 AI149262/AI/NIAID NIH HHS/United States ; R21 AI142321/AI/NIAID NIH HHS/United States ; R01 HL146401/HL/NHLBI NIH HHS/United States ; K23 HL148638/HL/NHLBI NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; P30 EY008126/EY/NEI NIH HHS/United States ; G20 RR030956/RR/NCRR NIH HHS/United States ; },
mesh = {Humans ; Adult ; Middle Aged ; *COVID-19 ; SARS-CoV-2 ; *Microbiota ; Respiratory System ; },
abstract = {To date, little is known about the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, on the upper respiratory tract (URT) microbiota over time. To fill this knowledge gap, we used 16S ribosomal RNA gene sequencing to characterize the URT microbiota in 48 adults, including (1) 24 participants with mild-to-moderate COVID-19 who had serial mid-turbinate swabs collected up to 21 days after enrolment and (2) 24 asymptomatic, uninfected controls who had mid-turbinate swabs collected at enrolment only. To compare the URT microbiota between groups in a comprehensive manner, different types of statistical analyses that are frequently employed in microbial ecology were used, including ⍺-diversity, β-diversity and differential abundance analyses. Final statistical models included age, sex and the presence of at least one comorbidity as covariates. The median age of all participants was 34.00 (interquartile range=28.75-46.50) years. In comparison to samples from controls, those from participants with COVID-19 had a lower observed species index at day 21 (linear regression coefficient=-13.30; 95 % CI=-21.72 to -4.88; q=0.02). In addition, the Jaccard index was significantly different between samples from participants with COVID-19 and those from controls at all study time points (PERMANOVA q<0.05 for all comparisons). The abundance of three amplicon sequence variants (ASVs) (one Corynebacterium ASV, Frederiksenia canicola, and one Lactobacillus ASV) were decreased in samples from participants with COVID-19 at all seven study time points, whereas the abundance of one ASV (from the family Neisseriaceae) was increased in samples from participants with COVID-19 at five (71.43 %) of the seven study time points. Our results suggest that mild-to-moderate COVID-19 can lead to alterations of the URT microbiota that persist for several weeks after the initial infection.},
}
@article {pmid36819055,
year = {2023},
author = {Ugwuanyi, IR and Fogel, ML and Bowden, R and Steele, A and De Natale, G and Troise, C and Somma, R and Piochi, M and Mormone, A and Glamoclija, M},
title = {Comparative metagenomics at Solfatara and Pisciarelli hydrothermal systems in Italy reveal that ecological differences across substrates are not ubiquitous.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1066406},
pmid = {36819055},
issn = {1664-302X},
abstract = {INTRODUCTION: Continental hydrothermal systems (CHSs) are geochemically complex, and they support microbial communities that vary across substrates. However, our understanding of these variations across the complete range of substrates in CHS is limited because many previous studies have focused predominantly on aqueous settings.<br><br>METHODS: Here we used metagenomes in the context of their environmental geochemistry to investigate the ecology of different substrates (i.e., water, mud and fumarolic deposits) from Solfatara and Pisciarelli.<br><br>RESULTS AND DISCUSSION: Results indicate that both locations are lithologically similar with distinct fluid geochemistry. In particular, all substrates from Solfatara have similar chemistry whereas Pisciarelli substrates have varying chemistry; with water and mud from bubbling pools exhibiting high SO4 [2-] and NH4 [+] concentrations. Species alpha diversity was found to be different between locations but not across substrates, and pH was shown to be the most important driver of both diversity and microbial community composition. Based on cluster analysis, microbial community structure differed significantly between Pisciarelli substrates but not between Solfatara substrates. Pisciarelli mud pools, were dominated by (hyper)thermophilic archaea, and on average, bacteria dominated Pisciarelli fumarolic deposits and all investigated Solfatara environments. Carbon fixation and sulfur oxidation were the most important metabolic pathways fueled by volcanic outgassing at both locations. Together, results demonstrate that ecological differences across substrates are not a widespread phenomenon but specific to the system. Therefore, this study demonstrates the importance of analyzing different substrates of a CHS to understand the full range of microbial ecology to avoid biased ecological assessments.},
}
@article {pmid36818730,
year = {2023},
author = {Noordijk, B and Nijland, R and Carrion, VJ and Raaijmakers, JM and de Ridder, D and de Lannoy, C},
title = {baseLess: lightweight detection of sequences in raw MinION data.},
journal = {Bioinformatics advances},
volume = {3},
number = {1},
pages = {vbad017},
pmid = {36818730},
issn = {2635-0041},
abstract = {SUMMARY: With its candybar form factor and low initial investment cost, the MinION brought affordable portable nucleic acid analysis within reach. However, translating the electrical signal it outputs into a sequence of bases still requires mid-tier computer hardware, which remains a caveat when aiming for deployment of many devices at once or usage in remote areas. For applications focusing on detection of a target sequence, such as infectious disease monitoring or species identification, the computational cost of analysis may be reduced by directly detecting the target sequence in the electrical signal instead. Here, we present baseLess, a computational tool that enables such target-detection-only analysis. BaseLess makes use of an array of small neural networks, each of which efficiently detects a fixed-size subsequence of the target sequence directly from the electrical signal. We show that baseLess can accurately determine the identity of reads between three closely related fish species and can classify sequences in mixtures of 20 bacterial species, on an inexpensive single-board computer.<br><br>baseLess and all code used in data preparation and validation are available on Github at https://github.com/cvdelannoy/baseLess, under an MIT license. Used validation data and scripts can be found at https://doi.org/10.4121/20261392, under an MIT license.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.},
}
@article {pmid36817258,
year = {2022},
author = {Castro, AE and De Ungria, MCA},
title = {Methods used in microbial forensics and epidemiological investigations for stronger health systems.},
journal = {Forensic sciences research},
volume = {7},
number = {4},
pages = {650-661},
pmid = {36817258},
issn = {2471-1411},
abstract = {This review discusses microbial forensics as an emerging science that finds application in protecting human health. It is important to distinguish naturally acquired infections from those caused by the intentional release of microorganisms to the environment. This information is crucial in formulating procedures against the spread of infectious diseases and prosecuting persons who may be involved in acts of biocrime, bioterrorism, or biowarfare. A comparison between epidemiological investigations and microbial forensic investigations is provided. In addition, a discussion on how microbial forensics strengthens health systems is included in this review. Microbial forensic investigations and epidemiologic examinations employ similar concepts and involve identifying and characterising the microbe of interest. Both fields require formulating an appropriate case definition, determining a pathogen's mode of transmission, and identifying the source(s) of infection. However, the two subdisciplines differ in their objectives. An epidemiological investigation aims to identify the pathogen's source to prevent the spread of the disease. Microbial forensics focuses on source-tracking to facilitate the prosecution of persons responsible for the spread of a pathogen. Both fields use molecular techniques in analysing and comparing DNA, gene products, and biomolecules to identify and characterise the microorganisms of interest. We included case studies to show methods used in microbial forensic investigations, a brief discussion of the public significance of microbial forensic systems, and a roadmap for establishing a system at a national level. This system is expected to strengthen a country's capacity to respond to public health emergencies. Several factors must be considered in establishing national microbial forensic systems. First is the inherent ubiquity, diversity, and adaptability of microorganisms that warrants the use of robust and accurate molecular typing systems. Second, the availability of facilities and scientists who have been trained in epidemiology, molecular biology, bioinformatics, and data analytics. Human resources and infrastructure are critical requirements because formulating strategies and allocating resources in times of infectious disease outbreaks must be data-driven. Establishing and maintaining a national microbial forensic system to strengthen capacities in conducting forensic and epidemiological investigations should be prioritised by all countries, accompanied by a national policy that sets the legislative framework and provides for the system's financial requirements.},
}
@article {pmid36815773,
year = {2023},
author = {Nestor, E and Toledano, G and Friedman, J},
title = {Interactions between Culturable Bacteria Are Predicted by Individual Species' Growth.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0083622},
pmid = {36815773},
issn = {2379-5077},
mesh = {*Bacteria/genetics ; Microbial Consortia ; Microbial Interactions ; *Microbiota/genetics ; },
abstract = {Predicting interspecies interactions is a key challenge in microbial ecology given that interactions shape the composition and functioning of microbial communities. However, predicting microbial interactions is challenging because they can vary considerably depending on species' metabolic capabilities and environmental conditions. Here, we employ machine learning models to predict pairwise interactions between culturable bacteria based on their phylogeny, monoculture growth capabilities, and interactions with other species. We trained our models on one of the largest available pairwise interactions data set containing over 7,500 interactions between 20 species from two taxonomic groups that were cocultured in 40 different carbon environments. Our models accurately predicted both the sign (accuracy of 88%) and the strength of effects (R[2] of 0.87) species had on each other's growth. Encouragingly, predictions with comparable accuracy could be made even when not relying on information about interactions with other species, which are often hard to measure. However, species' monoculture growth was essential to the model, as predictions based solely on species' phylogeny and inferred metabolic capabilities were significantly less accurate. These results bring us one step closer to a predictive understanding of microbial communities, which is essential for engineering beneficial microbial consortia. IMPORTANCE In order to understand the function and structure of microbial communities, one must know all pairwise interactions that occur between the different species within the community, as these interactions shape the community's structure and functioning. However, measuring all pairwise interactions can be an extremely difficult task especially when dealing with big complex communities. Because of that, predicting interspecies interactions is a key challenge in microbial ecology. Here, we use machine learning models in order to accurately predict the type and strength of interactions. We trained our models on one of the largest available pairwise interactions data set, containing over 7,500 interactions between 20 different species that were cocultured in 40 different environments. Our results show that, in general, accurate predictions can be made, and that the ability of each species to grow on its own in the given environment contributes the most to predictions. Being able to predict microbial interactions would put us one step closer to predicting the functionality of microbial communities and to rationally microbiome engineering.},
}
@article {pmid36814573,
year = {2023},
author = {Cheng, X and Xiang, X and Yun, Y and Wang, W and Wang, H and Bodelier, PLE},
title = {Archaea and their interactions with bacteria in a karst ecosystem.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1068595},
pmid = {36814573},
issn = {1664-302X},
abstract = {Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 [+] availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca[2+], and NO2 [-]. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.},
}
@article {pmid36813568,
year = {2023},
author = {Gonzalez-Garcia, L and Guevara-Barrientos, D and Lozano-Arce, D and Gil, J and Díaz-Riaño, J and Duarte, E and Andrade, G and Bojacá, JC and Hoyos-Sanchez, MC and Chavarro, C and Guayazan, N and Chica, LA and Buitrago Acosta, MC and Bautista, E and Trujillo, M and Duitama, J},
title = {New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads.},
journal = {Life science alliance},
volume = {6},
number = {5},
pages = {},
pmid = {36813568},
issn = {2575-1077},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Algorithms ; Sequence Analysis, DNA/methods ; Genome ; Software ; },
abstract = {Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. We present new algorithms for assembling long DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers selected by a hash function derived from the k-mer distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from haploid and diploid samples of different species. Our algorithms showed competitive accuracy and computational efficiency, compared with other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.},
}
@article {pmid36813189,
year = {2023},
author = {Zhu, X and Guo, Z and Wang, N and Liu, J and Zuo, Y and Li, K and Song, C and Song, Y and Gong, C and Xu, X and Yuan, F and Zhang, L},
title = {Environmental stress stimulates microbial activities as indicated by cyclopropane fatty acid enhancement.},
journal = {The Science of the total environment},
volume = {873},
number = {},
pages = {162338},
doi = {10.1016/j.scitotenv.2023.162338},
pmid = {36813189},
issn = {1879-1026},
mesh = {*Fatty Acids ; *Soil Microbiology ; Soil/chemistry ; Wetlands ; China ; },
abstract = {Soil microbial responses to environmental stress remain a critical question in microbial ecology. The content of cyclopropane fatty acid (CFA) in cytomembrane has been widely used to evaluate environmental stress on microorganisms. Here, we used CFA to investigate the ecological suitability of microbial communities and found a stimulating impact of CFA on microbial activities during wetland reclamation in Sanjiang Plain, Northeastern China. The seasonality of environmental stress resulted in the fluctuation of CFA content in the soil, which suppressed microbial activities due to nutrient loss upon wetland reclamation. After land conversion, the aggravation of temperature stress to microbes increased the CFA content by 5 % (autumn) to 163 % (winter), which led to the suppression of microbial activities by 7 %-47 %. By contrast, the warmer soil temperature and permeability decreased the CFA content by 3 % to 41 % and consequently aggravated the microbial reduction by 15 %-72 % in spring and summer. Complex microbial communities of 1300 CFA-produced species were identified using a sequencing approach, suggesting that soil nutrients dominated the differentiation in these microbial community structures. Further analysis with structural equation modeling highlighted the important function of CFA content to environmental stress and the stimulating influence of CFA induced by environmental stress on microbial activities. Our study shows the biological mechanisms of seasonal CFA content for microbial adaption to environmental stress under wetland reclamation. It advances our knowledge of microbial physiology affecting soil element cycling caused by anthropogenic activities.},
}
@article {pmid36811710,
year = {2023},
author = {Akter, S and Wos-Oxley, ML and Catalano, SR and Hassan, MM and Li, X and Qin, JG and Oxley, AP},
title = {Host Species and Environment Shape the Gut Microbiota of Cohabiting Marine Bivalves.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1755-1772},
pmid = {36811710},
issn = {1432-184X},
support = {2014/027//Fisheries Research and Development Corporation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Mytilus/microbiology ; Bacteria/genetics ; *Crassostrea/microbiology ; },
abstract = {Pacific oysters (Crassostrea gigas) and Mediterranean mussels (Mytilus galloprovincialis) are commercially important marine bivalves that frequently coexist and have overlapping feeding ecologies. Like other invertebrates, their gut microbiota is thought to play an important role in supporting their health and nutrition. Yet, little is known regarding the role of the host and environment in driving these communities. Here, bacterial assemblages were surveyed from seawater and gut aspirates of farmed C. gigas and co-occurring wild M. galloprovincialis in summer and winter using Illumina 16S rRNA gene sequencing. Unlike seawater, which was dominated by Pseudomonadata, bivalve samples largely consisted of Mycoplasmatota (Mollicutes) and accounted for >50% of the total OTU abundance. Despite large numbers of common (core) bacterial taxa, bivalve-specific species (OTUs) were also evident and predominantly associated with Mycoplasmataceae (notably Mycoplasma). An increase in diversity (though with varied taxonomic evenness) was observed in winter for both bivalves and was associated with changes in the abundance of core and bivalve-specific taxa, including several representing host-associated and environmental (free-living or particle-diet associated) organisms. Our findings highlight the contribution of the environment and the host in defining the composition of the gut microbiota in cohabiting, intergeneric bivalve populations.},
}
@article {pmid36810880,
year = {2023},
author = {Varliero, G and Lebre, PH and Stevens, MI and Czechowski, P and Makhalanyane, T and Cowan, DA},
title = {The use of different 16S rRNA gene variable regions in biogeographical studies.},
journal = {Environmental microbiology reports},
volume = {15},
number = {3},
pages = {216-228},
pmid = {36810880},
issn = {1758-2229},
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Genes, rRNA ; Sequence Analysis, DNA ; *Bacteria/genetics ; },
abstract = {16S rRNA gene amplicon sequencing is routinely used in environmental surveys to identify microbial diversity and composition of the samples of interest. The dominant sequencing technology of the past decade (Illumina) is based on the sequencing of 16S rRNA hypervariable regions. Online sequence data repositories, which represent an invaluable resource for investigating microbial distributional patterns across spatial, environmental or temporal scales, contain amplicon datasets from diverse 16S rRNA gene variable regions. However, the utility of these sequence datasets is potentially reduced by the use of different 16S rRNA gene amplified regions. By comparing 10 Antarctic soil samples sequenced for five different 16S rRNA amplicons, we explore whether sequence data derived from diverse 16S rRNA variable regions can be validly used as a resource for biogeographical studies. Patterns of shared and unique taxa differed among samples as a result of variable taxonomic resolutions of the assessed 16S rRNA variable regions. However, our analyses also suggest that the use of multi-primer datasets for biogeographical studies of the domain Bacteria is a valid approach to explore bacterial biogeographical patterns due to the preservation of bacterial taxonomic and diversity patterns across different variable region datasets. We deem composite datasets useful for biogeographical studies.},
}
@article {pmid36810610,
year = {2023},
author = {Muro, T and Hikida, H and Fujii, T and Kiuchi, T and Katsuma, S},
title = {Two Complete Genomes of Male-Killing Wolbachia Infecting Ostrinia Moth Species Illuminate Their Evolutionary Dynamics and Association with Hosts.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1740-1754},
pmid = {36810610},
issn = {1432-184X},
support = {17H06431//Japan Society for the Promotion of Science/ ; 22H00366//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; Male ; *Moths/genetics ; *Wolbachia/genetics ; Phylogeny ; Sex Ratio ; Genomics ; },
abstract = {Wolbachia is an extremely widespread intracellular symbiont which causes reproductive manipulation on various arthropod hosts. Male progenies are killed in Wolbachia-infected lineages of the Japanese Ostrinia moth population. While the mechanism of male killing and the evolutionary interaction between host and symbiont are significant concerns for this system, the absence of Wolbachia genomic information has limited approaches to these issues. We determined the complete genome sequences of wFur and wSca, the male-killing Wolbachia of Ostrinia furnacalis and Ostrinia scapulalis. The two genomes shared an extremely high degree of homology, with over 95% of the predicted protein sequences being identical. A comparison of these two genomes revealed nearly minimal genome evolution, with a strong emphasis on the frequent genome rearrangements and the rapid evolution of ankyrin repeat-containing proteins. Additionally, we determined the mitochondrial genomes of both species' infected lineages and performed phylogenetic analyses to deduce the evolutionary dynamics of Wolbachia infection in the Ostrinia clade. According to the inferred phylogenetic relationship, two possible scenarios were proposed: (1) Wolbachia infection was established in the Ostrinia clade prior to the speciation of related species such as O. furnacalis and O. scapulalis, or (2) Wolbachia infection in these species was introgressively transferred from a currently unidentified relative. Simultaneously, the relatively high homology of mitochondrial genomes suggested recent Wolbachia introgression between infected Ostrinia species. The findings of this study collectively shed light on the host-symbiont interaction from an evolutionary standpoint.},
}
@article {pmid36810576,
year = {2023},
author = {Klawonn, I and Van den Wyngaert, S and Iversen, MH and Walles, TJW and Flintrop, CM and Cisternas-Novoa, C and Nejstgaard, JC and Kagami, M and Grossart, HP},
title = {Fungal parasitism on diatoms alters formation and bio-physical properties of sinking aggregates.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {206},
pmid = {36810576},
issn = {2399-3642},
support = {3332/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Diatoms ; Phytoplankton ; Food Chain ; Bacteria ; Fresh Water/microbiology ; },
abstract = {Phytoplankton forms the base of aquatic food webs and element cycling in diverse aquatic systems. The fate of phytoplankton-derived organic matter, however, often remains unresolved as it is controlled by complex, interlinked remineralization and sedimentation processes. We here investigate a rarely considered control mechanism on sinking organic matter fluxes: fungal parasites infecting phytoplankton. We demonstrate that bacterial colonization is promoted 3.5-fold on fungal-infected phytoplankton cells in comparison to non-infected cells in a cultured model pathosystem (diatom Synedra, fungal microparasite Zygophlyctis, and co-growing bacteria), and even ≥17-fold in field-sampled populations (Planktothrix, Synedra, and Fragilaria). Additional data obtained using the Synedra-Zygophlyctis model system reveals that fungal infections reduce the formation of aggregates. Moreover, carbon respiration is 2-fold higher and settling velocities are 11-48% lower for similar-sized fungal-infected vs. non-infected aggregates. Our data imply that parasites can effectively control the fate of phytoplankton-derived organic matter on a single-cell to single-aggregate scale, potentially enhancing remineralization and reducing sedimentation in freshwater and coastal systems.},
}
@article {pmid36809975,
year = {2023},
author = {Bovio-Winkler, P and Guerrero, LD and Erijman, L and Oyarzúa, P and Suárez-Ojeda, ME and Cabezas, A and Etchebehere, C},
title = {Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {45},
pmid = {36809975},
issn = {1471-2180},
mesh = {*Sewage ; *Chloroflexi/genetics/metabolism ; Ecosystem ; In Situ Hybridization, Fluorescence ; Anaerobic Ammonia Oxidation ; Bioreactors ; Anaerobiosis ; Nitrogen/metabolism ; Oxidation-Reduction ; },
abstract = {BACKGROUND: The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor.<br><br>RESULTS: Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus 'Ca. Villigracilis'. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization.<br><br>CONCLUSION: Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.},
}
@article {pmid36809072,
year = {2023},
author = {Yuan, S and Friman, VP and Balcazar, JL and Zheng, X and Ye, M and Sun, M and Hu, F},
title = {Viral and Bacterial Communities Collaborate through Complementary Assembly Processes in Soil to Survive Organochlorine Contamination.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {3},
pages = {e0181022},
pmid = {36809072},
issn = {1098-5336},
mesh = {Soil ; Bacteria ; *Microbiota ; Soil Microbiology ; *Viruses ; *Pesticides/metabolism ; *Hydrocarbons, Chlorinated/metabolism ; },
abstract = {The ecological drivers that direct the assembly of viral and host bacterial communities are largely unknown, even though viral-encoded accessory genes help host bacteria survive in polluted environments. To understand the ecological mechanism(s) of viruses and hosts synergistically surviving under organochlorine pesticide (OCP) stress, we investigated the community assembly processes of viruses and bacteria at the taxon and functional gene levels in clean and OCP-contaminated soils in China using a combination of metagenomics/viromics and bioinformatics approaches. We observed a decreased richness of bacterial taxa and functional genes but an increased richness of viral taxa and auxiliary metabolic genes (AMGs) in OCP-contaminated soils (from 0 to 2,617.6 mg · kg[-1]). In OCP-contaminated soils, the assembly of bacterial taxa and genes was dominated by a deterministic process, of which the relative significance was 93.0% and 88.7%, respectively. In contrast, the assembly of viral taxa and AMGs was driven by a stochastic process, which contributed 83.1% and 69.2%, respectively. The virus-host prediction analysis, which indicated Siphoviridae was linked to 75.0% of bacterial phyla, and the higher migration rate of viral taxa and AMGs in OCP-contaminated soil suggested that viruses show promise for the dissemination of functional genes among bacterial communities. Taken together, the results of this study indicated that the stochastic assembly processes of viral taxa and AMGs facilitated bacterial resistance to OCP stress in soils. Moreover, our findings provide a novel avenue for understanding the synergistic interactions between viruses and bacteria from the perspective of microbial ecology, highlighting the significance of viruses in mediating bioremediation of contaminated soils. IMPORTANCE The interaction between viral communities and microbial hosts has been studied extensively, and the viral community affects host community metabolic function through AMGs. Microbial community assembly is the process by which species colonize and interact to establish and maintain communities. This is the first study that aimed to understand the assembly process of bacterial and viral communities under OCP stress. The findings of this study provide information about microbial community responses to OCP stress and reveal the collaborative interactions between viral and bacterial communities to resist pollutant stress. Thereby, we highlight the importance of viruses in soil bioremediation from the perspective of community assembly.},
}
@article {pmid36808010,
year = {2023},
author = {Khodse, VB and Amberkar, U and Khandeparker, R and Ramaiah, N},
title = {Variability of biochemical compounds in surface sediments along the eastern margin of the Arabian Sea.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {3},
pages = {414},
pmid = {36808010},
issn = {1573-2959},
mesh = {*Galactose ; *Mannose ; Arabinose ; Ribose ; Fucose ; Rhamnose ; Environmental Monitoring ; Hexoses ; Glucose ; Uronic Acids ; Geologic Sediments/analysis ; },
abstract = {Different fractions of organic matter in surface sediments from three transects along the eastern margin of the Arabian Sea (AS) were quantified to determine the sources of organic matter, and also to study its impact on microbial community structure. From the extensive analyses of different biochemical parameters, it was evident that the distribution of total carbohydrate (TCHO), total neutral carbohydrate (TNCHO), proteins, lipids, and uronic acids (URA) concentrations and yield (% TCHO-C/TOC) are affected by organic matter (OM) sources and microbial degradation of sedimentary OM. Monosaccharide compositions from surface sediment was quantified to assess the sources and diagenetic fate of carbohydrates, suggesting that the deoxysugars (rhamnose plus fucose) had significant inverse relationship (r = 0.928, n = 13, p < 0.001) with hexoses (mannose plus galactose plus glucose) and positive relationship (r = 0.828, n = 13, p < 0.001) with pentoses (ribose plus arabinose plus xylose). This shows that marine microorganisms are the source of carbohydrates and there is no influence of terrestrial OM along the eastern margin of AS. During the degradation of algal material, the hexoses seem to be preferentially used by heterotrophic organisms in this region. Arabinose plus galactose (glucose free wt %) values between 28 and 64 wt% indicate that OM was derived from phytoplankton, zooplankton, and non-woody tissues. In the principal component analysis, rhamnose, fucose, and ribose form one cluster of positive loadings while glucose, galactose, and mannose form another cluster of negative loadings which suggest that during OM sinking process, hexoses were removed resulting in increase in bacterial biomass and microbial sugars. Results indicate sediment OM to be derived from marine microbial source along the eastern margin of AS.},
}
@article {pmid36806012,
year = {2023},
author = {Janakiev, T and Milošević, &#x110; and Petrović, M and Miljković, J and Stanković, N and Zdravković, DS and Dimkić, I},
title = {Chironomus riparius Larval Gut Bacteriobiota and Its Potential in Microplastic Degradation.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1909-1922},
pmid = {36806012},
issn = {1432-184X},
support = {451-03-68/2022-14/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 101072777//Integrated Cross-Sectoral Solutions to Micro- and Nanoplastic Pollution in Soil and Groundwater Ecosystem - Plastic Underground HORIZON - MSCA - 2021- DN (2022-2026)/ ; },
mesh = {Animals ; *Microplastics ; Plastics ; Nylons ; Larva ; Ecosystem ; *Chironomidae ; Polyvinyl Chloride ; Bacteria ; Polyethylenes ; },
abstract = {Chironomus riparius are sediment-dwelling invertebrates in freshwater ecosystems and are used as indicators of environmental pollution. Their habitat is threatened by high levels of contaminants such as microplastics and organic matter. A promising strategy for the eco-friendly degradation of pollutants is the use of bacteria and their enzymatic activity. The aim of this study was to characterize for the first time bacteriobiota associated with the gut of C. riparius larvae from nature and laboratory samples, to compare it with sediment and food as potential sources of gut microbiota, and to assess its ability to degrade cellulose, proteins, and three different types of microplastics (polyethylene, polyvinyl chloride, and polyamide). The metabarcoding approach highlighted Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota as most abundant in both gut samples. Culturable microbiota analysis revealed Metabacillus idriensis, Peribacillus simplex, Neobacillus cucumis, Bacillus thuringiensis/toyonensis, and Fictibacillus phosphorivorans as five common species for nature and laboratory samples. Two P. simplex and one P. frigoritolerans isolates showed the ability for intensive growth on polyethylene, polyvinyl chloride, and polyamide. Both cellulolytic and proteolytic activity was observed for Paenibacillus xylanexedens and P. amylolyticus isolates. The characterized strains are promising candidates for the development of environmentally friendly strategies to degrade organic pollution and microplastics in freshwater ecosystems.},
}
@article {pmid36805785,
year = {2023},
author = {Capri, FC and Prazzi, E and Casamento, G and Gambino, D and Cassata, G and Alduina, R},
title = {Correlation Between Microbial Community and Hatching Failure in Loggerhead Sea Turtle Caretta caretta.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1923-1933},
pmid = {36805785},
issn = {1432-184X},
mesh = {Animals ; *Turtles ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Ecology ; Bacteria/genetics ; },
abstract = {Microbial communities provide essential information about host ecology and could be helpful as a tool to improve species conservation efforts. However, microbes can also infect and compromise the host development process and viability. Caretta caretta is the most widespread marine turtle species in the Mediterranean basin and is the only species of sea turtle nesting along the Italian coasts. Little is known about the microbiota composition of the nest of sea turtles and its correlation with hatching failures. In this study, the microbial composition of two nests of C. caretta featuring different rates of hatching success from a nesting beach in Lampedusa (Italy) was analyzed and compared. The bacterial community was determined using culture-dependent methods and next-generation sequencing based on 16S rRNA gene metabarcoding analysis. Our results showed five dominant bacterial phyla (Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, and Firmicutes) and indicated different bacterial families (Pseudomonadaceae and Brucellaceae) as likely causes of hatching failures. Besides, our findings demonstrated the nests' active role in modulating the sand's bacterial communities. This study suggests microbiological analysis could be a valuable tool in monitoring nests to take preventive actions and reduce hatching failures.},
}
@article {pmid36805022,
year = {2023},
author = {Kodera, SM and Sharma, A and Martino, C and Dsouza, M and Grippo, M and Lutz, HL and Knight, R and Gilbert, JA and Negri, C and Allard, SM},
title = {Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {10},
pmid = {36805022},
issn = {2524-6372},
abstract = {BACKGROUND: Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention.<br><br>RESULTS: Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality.<br><br>CONCLUSIONS: This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.},
}
@article {pmid36803622,
year = {2023},
author = {Ceron-Chafla, P and de Vrieze, J and Rabaey, K and van Lier, JB and Lindeboom, REF},
title = {Steering the product spectrum in high-pressure anaerobic processes: CO2 partial pressure as a novel tool in biorefinery concepts.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {16},
number = {1},
pages = {27},
pmid = {36803622},
issn = {2731-3654},
support = {676070//Horizon 2020 Framework Programme/ ; },
abstract = {BACKGROUND: Elevated CO2 partial pressure (pCO2) has been proposed as a potential steering parameter for selective carboxylate production in mixed culture fermentation. It is anticipated that intermediate product spectrum and production rates, as well as changes in the microbial community, are (in)directly influenced by elevated pCO2. However, it remains unclear how pCO2 interacts with other operational conditions, namely substrate specificity, substrate-to-biomass (S/X) ratio and the presence of an additional electron donor, and what effect pCO2 has on the exact composition of fermentation products. Here, we investigated possible steering effects of elevated pCO2 combined with (1) mixed substrate (glycerol/glucose) provision; (2) subsequent increments in substrate concentration to increase the S/X ratio; and (3) formate as an additional electron donor.<br><br>RESULTS: Metabolite predominance, e.g., propionate vs. butyrate/acetate, and cell density, depended on interaction effects between pCO2-S/X ratio and pCO2-formate. Individual substrate consumption rates were negatively impacted by the interaction effect between pCO2-S/X ratio and were not re-established after lowering the S/X ratio and adding formate. The product spectrum was influenced by the microbial community composition, which in turn, was modified by substrate type and the interaction effect between pCO2-formate. High propionate and butyrate levels strongly correlated with Negativicutes and Clostridia predominance, respectively. After subsequent pressurized fermentation phases, the interaction effect between pCO2-formate enabled a shift from propionate towards succinate production when mixed substrate was provided.<br><br>CONCLUSIONS: Overall, interaction effects between elevated pCO2, substrate specificity, high S/X ratio and availability of reducing equivalents from formate, rather than an isolated pCO2 effect, modified the proportionality of propionate, butyrate and acetate in pressurized mixed substrate fermentations at the expense of reduced consumption rates and increased lag-phases. The interaction effect between elevated pCO2 and formate was beneficial for succinate production and biomass growth with a glycerol/glucose mixture as the substrate. The positive effect may be attributed to the availability of extra reducing equivalents, likely enhanced carbon fixating activity and hindered propionate conversion due to increased concentration of undissociated carboxylic acids.},
}
@article {pmid36802019,
year = {2023},
author = {Ortiz-Rivero, J and Garrido-Benavent, I and Heiðmarsson, S and de Los Ríos, A},
title = {Moss and Liverwort Covers Structure Soil Bacterial and Fungal Communities Differently in the Icelandic Highlands.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1893-1908},
pmid = {36802019},
issn = {1432-184X},
mesh = {*Hepatophyta ; Iceland ; Soil ; *Mycobiome ; *Bryophyta ; Bacteria/genetics ; *Microbiota ; Soil Microbiology ; },
abstract = {Cryptogamic covers extend over vast polar tundra regions and their main components, e.g., bryophytes and lichens, are frequently the first visible colonizers of deglaciated areas. To understand their role in polar soil development, we analyzed how cryptogamic covers dominated by different bryophyte lineages (mosses and liverworts) influence the diversity and composition of edaphic bacterial and fungal communities as well as the abiotic attributes of underlying soils in the southern part of the Highlands of Iceland. For comparison, the same traits were examined in soils devoid of bryophyte covers. We measured an increase in soil C, N, and organic matter contents coupled with a lower pH in association with bryophyte cover establishment. However, liverwort covers showed noticeably higher C and N contents than moss covers. Significant changes in diversity and composition of bacterial and fungal communities were revealed between (a) bare and bryophyte-covered soils, (b) bryophyte covers and the underlying soils, and (c) moss and liverworts covers. These differences were more obvious for fungi than bacteria, and involved different lineages of saprotrophic and symbiotic fungi, which suggests a certain specificity of microbial taxa to particular bryophyte groups. In addition, differences observed in the spatial structure of the two bryophyte covers may be also responsible for the detected differences in microbial community diversity and composition. Altogether, our findings indicate that soil microbial communities and abiotic attributes are ultimately affected by the composition of the most conspicuous elements of cryptogamic covers in polar regions, which is of great value to predict the biotic responses of these ecosystems to future climate change.},
}
@article {pmid36801973,
year = {2023},
author = {Morgan-Lang, C and Hallam, SJ},
title = {A Guide to Gene-Centric Analysis Using TreeSAPP.},
journal = {Current protocols},
volume = {3},
number = {2},
pages = {e671},
doi = {10.1002/cpz1.671},
pmid = {36801973},
issn = {2691-1299},
support = {//Natural Sciences and Engineering Research Council/ ; //Genome Canada/ ; //Genome British Columbia/ ; //the Digital Research Alliance of Canada/ ; //the G. Unger Vetlesen and Ambrose Monell Foundations/ ; //the U.S. Department of Energy (DOE) Joint Genome Institute (JGI)/ ; //and the Facilities Integrating Collaborations for User Science (FICUS)/ ; },
mesh = {*Software ; Phylogeny ; *Algorithms ; Metagenomics/methods ; Sequence Alignment ; },
abstract = {Gene-centric analysis is commonly used to chart the structure, function, and activity of microbial communities in natural and engineered environments. A common approach is to create custom ad hoc reference marker gene sets, but these come with the typical disadvantages of inaccuracy and limited utility beyond assigning query sequences taxonomic labels. The Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software package standardizes analysis of phylogenetic and functional marker genes and improves predictive performance using a classification algorithm that leverages information-rich reference packages consisting of a multiple sequence alignment, a profile hidden Markov model, taxonomic lineage information, and a phylogenetic tree. Here, we provide a set of protocols that link the various analysis modules in TreeSAPP into a coherent process that both informs and directs the user experience. This workflow, initiated from a collection of candidate reference sequences, progresses through construction and refinement of a reference package to marker identification and normalized relative abundance calculations for homologous sequences in metagenomic and metatranscriptomic datasets. The alpha subunit of methyl-coenzyme M reductase (McrA) involved in biological methane cycling is presented as a use case given its dual role as a phylogenetic and functional marker gene driving an ecologically relevant process. These protocols fill several gaps in prior TreeSAPP documentation and provide best practices for reference package construction and refinement, including manual curation steps from trusted sources in support of reproducible gene-centric analysis. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Creating reference packages Support Protocol 1: Installing TreeSAPP Support Protocol 2: Annotating traits within a phylogenetic context Basic Protocol 2: Updating reference packages Basic Protocol 3: Calculating relative abundance of genes in metagenomic and metatranscriptomic datasets.},
}
@article {pmid36801035,
year = {2023},
author = {Law, CKY and Kundu, K and Bonin, L and Peñacoba-Antona, L and Bolea-Fernandez, E and Vanhaecke, F and Rabaey, K and Esteve-Núñez, A and De Gusseme, B and Boon, N},
title = {Electrochemically assisted production of biogenic palladium nanoparticles for the catalytic removal of micropollutants in wastewater treatment plants effluent.},
journal = {Journal of environmental sciences (China)},
volume = {128},
number = {},
pages = {203-212},
doi = {10.1016/j.jes.2022.08.018},
pmid = {36801035},
issn = {1001-0742},
mesh = {Wastewater ; Palladium/chemistry ; *Metal Nanoparticles ; *Water Purification ; *Water Pollutants, Chemical/metabolism ; },
abstract = {Biogenic palladium nanoparticles (bio-Pd NPs) are used for the reductive transformation and/or dehalogenation of persistent micropollutants. In this work, H2 (electron donor) was produced in situ by an electrochemical cell, permitting steered production of differently sized bio-Pd NPs. The catalytic activity was first assessed by the degradation of methyl orange. The NPs showing the highest catalytic activity were selected for the removal of micropollutants from secondary treated municipal wastewater. The synthesis at different H2 flow rates (0.310 L/hr or 0.646 L/hr) influenced the bio-Pd NPs size. The NPs produced over 6 hr at a low H2 flow rate had a larger size (D50 = 39.0 nm) than those produced in 3 hr at a high H2 flow rate (D50 = 23.2 nm). Removal of 92.1% and 44.3% of methyl orange was obtained after 30 min for the NPs with sizes of 39.0 nm and 23.2 nm, respectively. Bio-Pd NPs of 39.0 nm were used to treat micropollutants present in secondary treated municipal wastewater at concentrations ranging from µg/L to ng/L. Effective removal of 8 compounds was observed: ibuprofen (69.5%) < sulfamethoxazole (80.6%) < naproxen (81.4%) < furosemide (89.7%) < citalopram (91.7%) < diclofenac (91.9%) < atorvastatin (> 94.3%) < lorazepam (97.2%). Removal of fluorinated antibiotics occurred at > 90% efficiency. Overall, these data indicate that the size, and thus the catalytic activity of the NPs can be steered and that the removal of challenging micropollutants at environmentally relevant concentrations can be achieved through the use of bio-Pd NPs.},
}
@article {pmid36799977,
year = {2023},
author = {Zhao, H and Yang, S and Qin, X and Huang, J and Huang, H and Li, W and Jiang, G and Tang, J and Dong, K and Li, N},
title = {Disentangling the Ecological Processes and Driving Forces Shaping the Seasonal Pattern of Halobacteriovorax Communities in a Subtropical Estuary.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1881-1892},
pmid = {36799977},
issn = {1432-184X},
mesh = {*Ecosystem ; Seasons ; *Estuaries ; Phylogeny ; Proteobacteria ; },
abstract = {Halobacteriovorax are predatory bacteria that have a significant ecological role in marine environments. However, understanding of dynamics of populations, driving forces, and community composition of Halobacteriovorax groups in natural marine environments is still limited. Here, we used high-throughput sequencing to study the underlying mechanisms governing the diversity and assembly of the Halobacteriovorax community at spatiotemporal scales in a subtropical estuary. Phylogenetic analysis showed that 10 of 15 known Halobacteriovorax clusters were found in the studied estuary. Halobacteriovorax α-diversity and β-diversity exhibited significant seasonal variation. Variation partitioning analysis showed that the effect of nutrients was greater than that of other measured water properties on Halobacteriovorax community distribution. The results of Spearman's and Mantel's tests indicated that the trophic pollutants dissolved inorganic phosphorus (DIP) and NH4[+]-N in the estuary were the key factors that significantly affected Halobacteriovorax species and community diversity. In addition, this work indicated that the biological stoichiometry (especially N/P) of nutrients exerted a significant influence on the Halobacteriovorax community. Furthermore, we found that both deterministic and stochastic processes contributed to the turnover of Halobacteriovorax communities, and environmental filtering dominated the assembly of estuarine Halobacteriovorax communities. Overall, we provide new insights into the mechanisms in the generation and maintenance of the Halobacteriovorax community in marine environments.},
}
@article {pmid36799146,
year = {2023},
author = {Gsell, AS and Biere, A and de Boer, W and de Bruijn, I and Eichhorn, G and Frenken, T and Geisen, S and van der Jeugd, H and Mason-Jones, K and Meisner, A and Thakur, MP and van Donk, E and Zwart, MP and Van de Waal, DB},
title = {Environmental refuges from disease in host-parasite interactions under global change.},
journal = {Ecology},
volume = {104},
number = {4},
pages = {e4001},
doi = {10.1002/ecy.4001},
pmid = {36799146},
issn = {1939-9170},
mesh = {Animals ; *Host-Parasite Interactions/physiology ; *Parasites ; Temperature ; Acclimatization ; Adaptation, Physiological ; Climate Change ; },
abstract = {The physiological performance of organisms depends on their environmental context, resulting in performance-response curves along environmental gradients. Parasite performance-response curves are generally expected to be broader than those of their hosts due to shorter generation times and hence faster adaptation. However, certain environmental conditions may limit parasite performance more than that of the host, thereby providing an environmental refuge from disease. Thermal disease refuges have been extensively studied in response to climate warming, but other environmental factors may also provide environmental disease refuges which, in turn, respond to global change. Here, we (1) showcase laboratory and natural examples of refuges from parasites along various environmental gradients, and (2) provide hypotheses on how global environmental change may affect these refuges. We strive to synthesize knowledge on potential environmental disease refuges along different environmental gradients including salinity and nutrients, in both natural and food-production systems. Although scaling up from single host-parasite relationships along one environmental gradient to their interaction outcome in the full complexity of natural environments remains difficult, integrating host and parasite performance-response can serve to formulate testable hypotheses about the variability in parasitism outcomes and the occurrence of environmental disease refuges under current and future environmental conditions.},
}
@article {pmid36796331,
year = {2023},
author = {Sanchez, A and Bajic, D and Diaz-Colunga, J and Skwara, A and Vila, JCC and Kuehn, S},
title = {The community-function landscape of microbial consortia.},
journal = {Cell systems},
volume = {14},
number = {2},
pages = {122-134},
doi = {10.1016/j.cels.2022.12.011},
pmid = {36796331},
issn = {2405-4720},
mesh = {*Microbial Consortia/genetics ; *Microbiota/genetics ; Ecology ; },
abstract = {Quantitatively linking the composition and function of microbial communities is a major aspiration of microbial ecology. Microbial community functions emerge from a complex web of molecular interactions between cells, which give rise to population-level interactions among strains and species. Incorporating this complexity into predictive models is highly challenging. Inspired by a similar problem in genetics of predicting quantitative phenotypes from genotypes, an ecological community-function (or structure-function) landscape could be defined that maps community composition and function. In this piece, we present an overview of our current understanding of these community landscapes, their uses, limitations, and open questions. We argue that exploiting the parallels between both landscapes could bring powerful predictive methodologies from evolution and genetics into ecology, providing a boost to our ability to engineer and optimize microbial consortia.},
}
@article {pmid36792869,
year = {2023},
author = {Tai, JB and Ferrell, MJ and Yan, J and Waters, CM},
title = {New Insights into Vibrio cholerae Biofilms from Molecular Biophysics to Microbial Ecology.},
journal = {Advances in experimental medicine and biology},
volume = {1404},
number = {},
pages = {17-39},
pmid = {36792869},
issn = {0065-2598},
support = {DP2 GM146253/GM/NIGMS NIH HHS/United States ; R01 AI158433/AI/NIAID NIH HHS/United States ; R35 GM139537/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Vibrio cholerae ; *Cholera/epidemiology/microbiology ; Pandemics ; *COVID-19 ; Biofilms ; },
abstract = {With the discovery that 48% of cholera infections in rural Bangladesh villages could be prevented by simple filtration of unpurified waters and the detection of Vibrio cholerae aggregates in stools from cholera patients it was realized V. cholerae biofilms had a central function in cholera pathogenesis. We are currently in the seventh cholera pandemic, caused by O1 serotypes of the El Tor biotypes strains, which initiated in 1961. It is estimated that V. cholerae annually causes millions of infections and over 100,000 deaths. Given the continued emergence of cholera in areas that lack access to clean water, such as Haiti after the 2010 earthquake or the ongoing Yemen civil war, increasing our understanding of cholera disease remains a worldwide public health priority. The surveillance and treatment of cholera is also affected as the world is impacted by the COVID-19 pandemic, raising significant concerns in Africa. In addition to the importance of biofilm formation in its life cycle, V. cholerae has become a key model system for understanding bacterial signal transduction networks that regulate biofilm formation and discovering fundamental principles about bacterial surface attachment and biofilm maturation. This chapter will highlight recent insights into V. cholerae biofilms including their structure, ecological role in environmental survival and infection, regulatory systems that control them, and biomechanical insights into the nature of V. cholerae biofilms.},
}
@article {pmid36790500,
year = {2023},
author = {Elsherbini, J and Corzett, C and Ravaglioli, C and Tamburello, L and Polz, M and Bulleri, F},
title = {Epilithic Bacterial Assemblages on Subtidal Rocky Reefs: Variation Among Alternative Habitats at Ambient and Enhanced Nutrient Levels.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1552-1564},
pmid = {36790500},
issn = {1432-184X},
mesh = {Animals ; *Ecosystem ; *Forests ; Nutrients ; Sea Urchins ; Coral Reefs ; },
abstract = {Temperate rocky reefs often support mosaics of alternative habitats such as macroalgal forests, algal turfs and sea urchin barrens. Although the composition of epilithic microbial biofilms (EMBs) is recognized as a major determinant of macroalgal recruitment, their role in regulating the stability of alternative habitats on temperate rocky reefs remains unexplored. On shallow rocky reefs of the Island of Capraia (NW Mediterranean), we compared EMB structure among canopy stands formed by the fucoid Ericaria brachycarpa, algal turfs, and urchin barrens under ambient versus experimentally enhanced nutrient levels. The three habitats shared a core microbial community consisting of 21.6 and 25.3% of total ASVs under ambient and enhanced nutrient conditions, respectively. Although Gammaproteobacteria, Alphaproteobacteria and Flavobacteriia were the most abundant classes across habitats, multivariate analyses at the ASV level showed marked differences in EMB composition among habitats. Enhancing nutrient level had no significant effect on EMBs, although it increased their similarity between macroalgal canopy and turf habitats. At both ambient and enriched nutrient levels, ASVs mostly belonging to Proteobacteria and Bacteroidetes were more abundant in EMBs from macroalgal canopies than barrens. In contrast, ASVs belonging to the phylum of Proteobacteria and, in particular, to the families of Rhodobacteraceae and Flavobacteriaceae at ambient nutrient levels and of Rhodobacteraceae and Bacteriovoracaceae at enhanced nutrient levels were more abundant in turf than canopy habitats. Our results show that primary surfaces from alternative habitats that form mosaics on shallow rocky reefs in oligotrophic areas host distinct microbial communities that are, to some extent, resistant to moderate nutrient enhancement. Understanding the role of EMBs in generating reinforcing feedback under different nutrient loading regimes appears crucial to advance our understanding of the mechanisms underpinning the stability of habitats alternative to macroalgal forests as well as their role in regulating reverse shifts.},
}
@article {pmid36788337,
year = {2023},
author = {Bayer, N and Hausmann, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G},
title = {Correction: Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.},
journal = {Leukemia},
volume = {37},
number = {3},
pages = {724},
doi = {10.1038/s41375-023-01839-7},
pmid = {36788337},
issn = {1476-5551},
}
@article {pmid36786580,
year = {2023},
author = {Gittins, DA and Bhatnagar, S and Hubert, CRJ},
title = {Environmental Selection and Biogeography Shape the Microbiome of Subsurface Petroleum Reservoirs.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0088422},
pmid = {36786580},
issn = {2379-5077},
mesh = {*Petroleum/metabolism ; RNA, Ribosomal, 16S/genetics ; Oil and Gas Fields ; *Microbiota/genetics ; Carbon ; },
abstract = {Petroleum reservoirs within the deep biosphere are extreme environments inhabited by diverse microbial communities and represent biogeochemical hot spots in the subsurface. Despite the ecological and industrial importance of oil reservoir microbiomes, systematic study of core microbial taxa and their associated genomic attributes spanning different environmental conditions is limited. Here, we compile and compare 343 16S rRNA gene amplicon libraries and 25 shotgun metagenomic libraries from oil reservoirs in different parts of the world to test for the presence of core taxa and functions. These oil reservoir libraries do not share any core taxa at the species, genus, family, or order levels, and Gammaproteobacteria was the only taxonomic class detected in all samples. Instead, taxonomic composition varies among reservoirs with different physicochemical characteristics and with geographic distance highlighting environmental selection and biogeography in these deep biosphere habitats. Gene-centric metagenomic analysis reveals a functional core of metabolic pathways including carbon acquisition and energy-yielding strategies consistent with biogeochemical cycling in other subsurface environments. Genes for anaerobic hydrocarbon degradation are observed in a subset of the samples and are therefore not considered to represent core functions in oil reservoirs despite hydrocarbons representing an abundant source of carbon in these deep biosphere settings. Overall, this work reveals common and divergent features of oil reservoir microbiomes that are shaped by and responsive to environmental factors, highlighting controls on subsurface microbial community assembly. IMPORTANCE This comprehensive analysis showcases how environmental selection and geographic distance influence the microbiome of subsurface petroleum reservoirs. We reveal substantial differences in the taxonomy of the inhabiting microbes but shared metabolic function between reservoirs with different in situ temperatures and between reservoirs separated by large distances. The study helps understand and advance the field of deep biosphere science by providing an ecological framework and footing for geologists, chemists, and microbiologists studying these habitats to elucidate major controls on deep biosphere microbial ecology.},
}
@article {pmid36786571,
year = {2023},
author = {Ji, M and Fan, X and Cornell, CR and Zhang, Y and Yuan, MM and Tian, Z and Sun, K and Gao, R and Liu, Y and Zhou, J},
title = {Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming.},
journal = {mBio},
volume = {14},
number = {2},
pages = {e0300922},
pmid = {36786571},
issn = {2150-7511},
mesh = {Soil/chemistry ; Biodiversity ; Temperature ; Tundra ; *Microbiota/physiology ; Climate Change ; *Viruses/metabolism ; Soil Microbiology ; Carbon/metabolism ; },
abstract = {The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.},
}
@article {pmid36786067,
year = {2023},
author = {Caroli, AP and Mansoldo, FRP and Cardoso, VS and Lage, CLS and Carmo, FL and Supuran, CT and Beatriz Vermelho, A},
title = {Are patents important indicators of innovation for Chagas disease treatment?.},
journal = {Expert opinion on therapeutic patents},
volume = {33},
number = {3},
pages = {193-209},
doi = {10.1080/13543776.2023.2176219},
pmid = {36786067},
issn = {1744-7674},
mesh = {Humans ; *Trypanosoma cruzi ; Patents as Topic ; *Chagas Disease/drug therapy/epidemiology/parasitology ; Drug Delivery Systems ; *Trypanocidal Agents/pharmacology/therapeutic use ; },
abstract = {INTRODUCTION: Chagas disease is a neglected, endemic disease in 21 countries, spreading to non-endemic countries too. Like other neglected diseases affecting primarily low- and middle-income countries, low investment and the absence of new chemical entities from the industry occurred. Increased knowledge about the parasite, drug targets, and vector control has been observed, but this was not translated into new drugs. The partnerships of pharmaceutical companies with academies and consolidated networks to increment the new drugs and treatment research in Chagas disease are shown. The current review analyzes in detail the patents dealing with compounds candidates for new drugs and treatment. The patent search was performed using Orbit Intelligence® software in the 2001-2021 period.<br><br>AREAS COVERED: The author focused specifically on patents for the treatment, the new candidates disclosed in the patents, and the barriers to innovation.<br><br>EXPERT OPINION: Patents in Chagas disease have been increasing in the last years, although they do not bring new compounds to an effective treatment.},
}
@article {pmid36781140,
year = {2023},
author = {Vos, M and Hering, D and Gessner, MO and Leese, F and Schäfer, RB and Tollrian, R and Boenigk, J and Haase, P and Meckenstock, R and Baikova, D and Bayat, H and Beermann, A and Beisser, D and Beszteri, B and Birk, S and Boden, L and Brauer, V and Brauns, M and Buchner, D and Burfeid-Castellanos, A and David, G and Deep, A and Doliwa, A and Dunthorn, M and Enß, J and Escobar-Sierra, C and Feld, CK and Fohrer, N and Grabner, D and Hadziomerovic, U and Jähnig, SC and Jochmann, M and Khaliq, S and Kiesel, J and Kuppels, A and Lampert, KP and Le, TTY and Lorenz, AW and Madariaga, GM and Meyer, B and Pantel, JH and Pimentel, IM and Mayombo, NS and Nguyen, HH and Peters, K and Pfeifer, SM and Prati, S and Probst, AJ and Reiner, D and Rolauffs, P and Schlenker, A and Schmidt, TC and Shah, M and Sieber, G and Stach, TL and Tielke, AK and Vermiert, AM and Weiss, M and Weitere, M and Sures, B},
title = {The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release.},
journal = {The Science of the total environment},
volume = {872},
number = {},
pages = {162196},
doi = {10.1016/j.scitotenv.2023.162196},
pmid = {36781140},
issn = {1879-1026},
mesh = {*Ecosystem ; *Rivers ; },
abstract = {Our capacity to predict trajectories of ecosystem degradation and recovery is limited, especially when impairments are caused by multiple stressors. Recovery may be fast or slow and either complete or partial, sometimes result in novel ecosystem states or even fail completely. Here, we introduce the Asymmetric Response Concept (ARC) that provides a basis for exploring and predicting the pace and magnitude of ecological responses to, and release from, multiple stressors. The ARC holds that three key mechanisms govern population, community and ecosystem trajectories. Stress tolerance is the main mechanism determining responses to increasing stressor intensity, whereas dispersal and biotic interactions predominantly govern responses to the release from stressors. The shifting importance of these mechanisms creates asymmetries between the ecological trajectories that follow increasing and decreasing stressor intensities. This recognition helps to understand multiple stressor impacts and to predict which measures will restore communities that are resistant to restoration.},
}
@article {pmid36775167,
year = {2023},
author = {Archer, SDJ and Lee, KC and Caruso, T and Alcami, A and Araya, JG and Cary, SC and Cowan, DA and Etchebehere, C and Gantsetseg, B and Gomez-Silva, B and Hartery, S and Hogg, ID and Kansour, MK and Lawrence, T and Lee, CK and Lee, PKH and Leopold, M and Leung, MHY and Maki, T and McKay, CP and Al Mailem, DM and Ramond, JB and Rastrojo, A and Šantl-Temkiv, T and Sun, HJ and Tong, X and Vandenbrink, B and Warren-Rhodes, KA and Pointing, SB},
title = {Contribution of soil bacteria to the atmosphere across biomes.},
journal = {The Science of the total environment},
volume = {871},
number = {},
pages = {162137},
doi = {10.1016/j.scitotenv.2023.162137},
pmid = {36775167},
issn = {1879-1026},
mesh = {*Ecosystem ; Soil ; Bacteria ; Atmosphere ; *Microbiota ; Temperature ; Soil Microbiology ; },
abstract = {The dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivity.},
}
@article {pmid36775144,
year = {2023},
author = {Liu, L and Zhu, L and Yan, R and Yang, Y and Adams, JM and Liu, J},
title = {Abundant bacterial subcommunity is structured by a stochastic process in an agricultural system with P fertilizer inputs.},
journal = {The Science of the total environment},
volume = {871},
number = {},
pages = {162178},
doi = {10.1016/j.scitotenv.2023.162178},
pmid = {36775144},
issn = {1879-1026},
mesh = {*Ecosystem ; *Fertilizers ; Soil Microbiology ; Soil ; Bacteria ; Stochastic Processes ; },
abstract = {Soil microorganisms play an important role in agroecosystems and are related to ecosystem functioning. Nevertheless, little is understood about their community assembly and the major factors regulating stochastic and deterministic processes, particularly with respect to the comparison of abundant and rare bacterial subcommunities in agricultural systems. Here, we investigated the assembly of abundant and rare bacterial subcommunities in fields with different crops (maize and wheat) and phosphorus (P) fertilizer input at three different growth stages on the Loess Plateau. The high-throughput sequencing dataset was assessed using null and neutral community models. We found that abundant bacteria was governed by the stochastic process of homogenizing dispersal, but rare bacterial subcommunity was predominant by deterministic processes in maize and wheat fields due to broader niche breadths of abundant species. Soil nitrogen (N) and P also determined the assembly of abundant and rare soil subcommunities. The relative abundance and composition of the abundant and rare bacterial subcommunities were also influenced by soil nutrients (soil available P (AP) and NO3[-]-N) and agricultural practices (P fertilization and crop cultivation). In addition, the abundant bacterial community was more susceptible to P fertilizer input than that of the rare bacteria, and a higher relative abundance of abundant bacteria was observed in the P70 treatment both in maize and wheat soils. The microbial co-occurrence network analysis indicated that the maize field and low nutrient treatment exhibited stronger associations and that the abundant bacteria showed fewer interconnections. This study provides new insights toward understanding the mechanisms for the assembly of abundant and rare bacterial taxa in dryland cropping systems, enhancing our understanding of ecosystem diversity theory in microbial ecology.},
}
@article {pmid36773920,
year = {2023},
author = {Pico-Tomàs, A and Mejías-Molina, C and Zammit, I and Rusiñol, M and Bofill-Mas, S and Borrego, CM and Corominas, L},
title = {Surveillance of SARS-CoV-2 in sewage from buildings housing residents with different vulnerability levels.},
journal = {The Science of the total environment},
volume = {872},
number = {},
pages = {162116},
pmid = {36773920},
issn = {1879-1026},
mesh = {Aged ; Humans ; *Sewage ; Wastewater ; SARS-CoV-2 ; Housing ; *COVID-19/epidemiology ; },
abstract = {During the last three years, various restrictions have been set up to limit the transmission of the Coronavirus Disease (COVID-19). While these rules apply at a large scale (e.g., country-wide level) human-to-human transmission of the virus that causes COVID-19, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), occurs at a small scale. Different preventive policies and testing protocols were implemented in buildings where COVID-19 poses a threat (e.g., elderly residences) or constitutes a disruptive force (e.g., schools). In this study, we sampled sewage from different buildings (a school, a university campus, a university residence, and an elderly residence) that host residents of different levels of vulnerability. Our main goal was to assess the agreement between the SARS-CoV-2 concentration in wastewater and the policies applied in these buildings. All buildings were sampled using passive samplers while 24 h composite samples were also collected from the elderly residence. Results showed that passive samplers performed comparably well to composite samples while being cost-effective to keep track of COVID-19 prevalence. In the elderly residence, the comparison of sampling protocols (passive vs. active) combined with the strict clinical testing allowed us to compare the sensitivities of the two methods. Active sampling was more sensitive than passive sampling, as the former was able to detect a COVID-19 prevalence of 0.4 %, compared to a prevalence of 2.2 % for passive sampling. The number of COVID-19-positive individuals was tracked clinically in all the monitored buildings. More frequent detection of SARS-CoV-2 in wastewater was observed in residential buildings than in non-residential buildings using passive samplers. In all buildings, sewage surveillance can be used to complement COVID-19 clinical testing regimes, as the detection of SARS-CoV-2 in wastewater remained positive even when no COVID-19-positive individuals were reported. Passive sampling is useful for building managers to adapt their COVID-19 mitigation policies.},
}
@article {pmid36773636,
year = {2023},
author = {Honeyman, AS and Merl, T and Spear, JR and Koren, K},
title = {Optode-based chemical imaging of laboratory burned soil reveals millimeter-scale heterogeneous biogeochemical responses.},
journal = {Environmental research},
volume = {224},
number = {},
pages = {115469},
doi = {10.1016/j.envres.2023.115469},
pmid = {36773636},
issn = {1096-0953},
mesh = {*Soil/chemistry ; *Bacteria/metabolism ; Archaea/genetics ; Water ; RNA/metabolism ; Soil Microbiology ; },
abstract = {Soil spatial responses to fire are unclear. Using optical chemical sensing with planar 'optodes', pH and dissolved O2 concentration were tracked spatially with a resolution of 360 μm per pixel for 72 h after burning soil in the laboratory with a butane torch (∼1300 °C) and then sprinkling water to simulate a postfire moisture event. Imaging data from planar optodes correlated with microbial activity (quantified via RNA transcripts). Post-fire and post-wetting, soil pH increased throughout the entire ∼13 cm × 17 cm × 20 cm rectangular cuboid of sandy loam soil. Dissolved O2 concentrations were not impacted until the application of water postfire. pH and dissolved O2 both negatively correlated (p < 0.05) with relative transcript expression for galactose metabolism, the degradation of aromatic compounds, sulfur metabolism, and narH. Additionally, dissolved O2 negatively correlated (p < 0.05) with the relative activity of carbon fixation pathways in Bacteria and Archaea, amoA/amoB, narG, nirK, and nosZ. nifH was not detected in any samples. Only amoB and amoC correlated with depth in soil (p < 0.05). Results demonstrate that postfire soils are spatially complex on a mm scale and that using optode-based chemical imaging as a chemical navigator for RNA transcript sampling is effective.},
}
@article {pmid36771744,
year = {2023},
author = {Vasilchenko, AV and Poshvina, DV and Semenov, MV and Timofeev, VN and Iashnikov, AV and Stepanov, AA and Pervushina, AN and Vasilchenko, AS},
title = {Triazoles and Strobilurin Mixture Affects Soil Microbial Community and Incidences of Wheat Diseases.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
pmid = {36771744},
issn = {2223-7747},
support = {075-15-2021-1345 unique identifier RF----193021X0012//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Pesticides are widely used in agriculture as a pest control strategy. Despite the benefits of pesticides on crop yields, the persistence of chemical residues in soil has an unintended impact on non-targeted microorganisms. In the present study, we evaluated the potential adverse effects of a mixture of fungicides (difenoconazole, epoxiconazole, and kresoxim-methyl) on soil fungal and bacterial communities, as well as the manifestation of wheat diseases. In the fungicide-treated soil, the Shannon indices of both fungal and bacterial communities decreased, whereas the Chao1 indices did not differ compared to the control soil. Among bacterial taxa, the relative abundances of Arthrobacter and Sphingomonas increased in fungicide-treated soil due to their ability to utilize fungicides and other toxic compounds. Rhizopus and plant-beneficial Chaetomium were the dominant fungal genera, with their prevalence increasing by 2-4 times in the fungicide-treated soil. The genus Fusarium, which includes phytopathogenic species, which are notably responsible for root rot, was the most abundant taxon in each of the two conditions but its relative abundance was two times lower in fungicide-treated soils, consistent with a lower level of disease incidence in plants. The prediction of metabolic pathways revealed that the soil bacterial community had a high potential for degrading various pollutants, and the soil fungal community was in a state of recovery after the application of quinone outside inhibitor (QoI) fungicides. Fungicide-treated soil was characterized by an increase in soil microbial carbon, compared with the control soil. Collectively, the obtained results suggest that the application of difenoconazole, epoxiconazole, and kresoxim-methyl is an effective approach for pest control that does not pose a hazard for the soil ecosystem in the short term. However, it is necessary to carry out additional sampling to take into account the spatio-temporal impact of this fungicide mixture on the functional properties of the soil.},
}
@article {pmid36766201,
year = {2023},
author = {Mudoor Sooresh, M and Willing, BP and Bourrie, BCT},
title = {Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
pmid = {36766201},
issn = {2304-8158},
support = {202102309//Alberta Innovates/ ; ALLRP-556600-20//Natural Sciences and Engineering Research Council/ ; },
abstract = {Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.},
}
@article {pmid36765824,
year = {2023},
author = {Pandey, H and Tang, DWT and Wong, SH and Lal, D},
title = {Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities.},
journal = {Cancers},
volume = {15},
number = {3},
pages = {},
pmid = {36765824},
issn = {2072-6694},
support = {021337-00001//NTU Start Up Grant and Wang Lee Wah Memorial Fund/ ; },
abstract = {Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths worldwide. While CRC is thought to be an interplay between genetic and environmental factors, several lines of evidence suggest the involvement of gut microbiota in promoting inflammation and tumor progression. Gut microbiota refer to the ~40 trillion microorganisms that inhabit the human gut. Advances in next-generation sequencing technologies and metagenomics have provided new insights into the gut microbial ecology and have helped in linking gut microbiota to CRC. Many studies carried out in humans and animal models have emphasized the role of certain gut bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, in the onset and progression of CRC. Metagenomic studies have opened up new avenues for the application of gut microbiota in the diagnosis, prevention, and treatment of CRC. This review article summarizes the role of gut microbiota in CRC development and its use as a biomarker to predict the disease and its potential therapeutic applications.},
}
@article {pmid36765150,
year = {2023},
author = {Xu, G and Zhao, X and Zhao, S and Rogers, MJ and He, J},
title = {Salinity determines performance, functional populations, and microbial ecology in consortia attenuating organohalide pollutants.},
journal = {The ISME journal},
volume = {17},
number = {5},
pages = {660-670},
pmid = {36765150},
issn = {1751-7370},
mesh = {*Chloroflexi/genetics ; *Environmental Pollutants ; Salinity ; *Polychlorinated Biphenyls/analysis/chemistry ; Biodegradation, Environmental ; *Microbiota ; Physical Functional Performance ; },
abstract = {Organohalide pollutants are prevalent in coastal regions due to extensive intervention by anthropogenic activities, threatening public health and ecosystems. Gradients in salinity are a natural feature of coasts, but their impacts on the environmental fate of organohalides and the underlying microbial communities remain poorly understood. Here we report the effects of salinity on microbial reductive dechlorination of tetrachloroethene (PCE) and polychlorinated biphenyls (PCBs) in consortia derived from distinct environments (freshwater and marine sediments). Marine-derived microcosms exhibited higher halotolerance during PCE and PCB dechlorination, and a halotolerant dechlorinating culture was enriched from these microcosms. The organohalide-respiring bacteria (OHRB) responsible for PCE and PCB dechlorination in marine microcosms shifted from Dehalococcoides to Dehalobium when salinity increased. Broadly, lower microbial diversity, simpler co-occurrence networks, and more deterministic microbial community assemblages were observed under higher salinity. Separately, we observed that inhibition of dechlorination by high salinity could be attributed to suppressed viability of Dehalococcoides rather than reduced provision of substrates by syntrophic microorganisms. Additionally, the high activity of PCE dechlorinating reductive dehalogenases (RDases) in in vitro tests under high salinity suggests that high salinity likely disrupted cellular components other than RDases in Dehalococcoides. Genomic analyses indicated that the capability of Dehalobium to perform dehalogenation under high salinity was likely owing to the presence of genes associated with halotolerance in its genomes. Collectively, these mechanistic and ecological insights contribute to understanding the fate and bioremediation of organohalide pollutants in environments with changing salinity.},
}
@article {pmid36764950,
year = {2023},
author = {Kim, C and Staver, LW and Chen, X and Bulseco, A and Cornwell, JC and Malkin, SY},
title = {Microbial Community Succession Along a Chronosequence in Constructed Salt Marsh Soils.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {931-950},
pmid = {36764950},
issn = {1432-184X},
mesh = {*Wetlands ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Methane ; },
abstract = {In this study, we examined the succession of soil microbial communities across a chronosequence of newly constructed salt marshes constructed primarily of fine-grained dredge material, using 16S rRNA amplicon sequences. Alpha diversity in the subsurface horizons was initially low and increased to reference levels within 3 years of marsh construction, while alpha diversity in the newly accumulating organic matter-rich surface soils was initially high and remained unchanged. Microbial community succession was fastest in the surface horizon (~ 24 years to reference equivalency) and became progressively slower with depth in the subsurface horizons (~ 30-67 years). Random forest linear regression analysis was used to identify important taxa driving the trajectories toward reference conditions. In the parent material, putative sulfate-reducers (Desulfobacterota), methanogens (Crenarchaeota, especially Methanosaeta), and fermenters (Chloroflexi and Clostridia) increased over time, suggesting an enrichment of these metabolisms over time, similar to natural marshes. Concurrently in the surface soils, the relative abundances of putative methane-, methyl-, and sulfide oxidizers, especially among Gammaproteobacteria, increased over time, suggesting the co-development of sulfide and methane removal metabolisms in marsh soils. Finally, we observed that the surface soil communities at one of the marshes did not follow the trajectory of the others, exhibiting a greater relative abundance of anaerobic taxa. Uniquely in this dataset, this marsh was developing signs of excessive inundation stress in terms of vegetation coverage and soil geochemistry. Therefore, we suggest that soil microbial community structure may be effective bioindicators of salt marsh inundation and are worthy of further targeted investigation.},
}
@article {pmid36763113,
year = {2023},
author = {Mason, ARG and Cavagnaro, TR and Guerin, GR and Lowe, AJ},
title = {Soil Bacterial Assemblage Across a Production Landscape: Agriculture Increases Diversity While Revegetation Recovers Community Composition.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1098-1112},
pmid = {36763113},
issn = {1432-184X},
mesh = {*Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Agriculture ; Bacteria/genetics ; Plants ; Soil Microbiology ; },
abstract = {Aboveground ecological impacts associated with agricultural land use change are evident as natural plant communities are replaced with managed production systems. These impacts have been extensively studied, unlike those belowground, which remain poorly understood. Soil bacteria are good candidates to monitor belowground ecological dynamics due to their prevalence within the soil system and ability to survive under harsh and changing conditions. Here, we use soil physicochemical assessment and 16S rRNA gene sequencing to investigate the soil physical and bacterial assemblage changes across a mixed-use agricultural landscape. We assess soil from remnant vegetation (Eucalyptus mallee), new and old vineyards, old pasture, and recently revegetated areas. Elevated concentrations of nitrogen (NO3[-]) and plant-available (Colwell) phosphorus were identified in the managed vineyard systems, highlighting the impact of agricultural inputs on soil nutrition. Alpha diversity comparison revealed a significant difference between the remnant mallee vegetation and the vineyard systems, with vineyards supporting highest bacterial diversity. Bacterial community composition of recently revegetated areas was similar to remnant vegetation systems, suggesting that bacterial communities can respond quickly to aboveground changes, and that actions taken to restore native plant communities may also act to recover natural microbial communities, with implications for soil and plant health. Findings here suggest that agriculture may disrupt the correlation between above- and belowground diversities by altering the natural processes that otherwise govern this relationship (e.g. disturbance, plant production, diversity of inputs), leading to the promotion of belowground microbial diversity in agricultural systems.},
}
@article {pmid36758734,
year = {2023},
author = {Wu, X and Chen, S and Yan, Q and Yu, F and Shao, H and Zheng, X and Zhang, X},
title = {Gpr35 shapes gut microbial ecology to modulate hepatic steatosis.},
journal = {Pharmacological research},
volume = {189},
number = {},
pages = {106690},
doi = {10.1016/j.phrs.2023.106690},
pmid = {36758734},
issn = {1096-1186},
mesh = {Mice ; Animals ; *Gastrointestinal Microbiome/genetics ; *Fatty Liver/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Obesity/metabolism ; Diet, High-Fat ; Mice, Inbred C57BL ; Liver/metabolism ; },
abstract = {The gut microbiome is closely shaped by host genetic and dietary factors to regulate metabolic health and disease. However, the signaling mechanisms underlying such interactions have been largely unclear. Here we identify G protein-coupled receptor 35 (Gpr35) as a regulator of gut microbial ecology and the susceptibility to obesity and hepatic steatosis in mice. Both global and intestinal epithelia specific ablation of Gpr35 aggravated high-fat diet (HFD)-induced metabolic disturbance and hepatic steatosis in mice. Gpr35 deficiency induced a remarkable loss of goblet cells and an extensive remodeling of the gut microbiome, featuring enrichment of the Bacteroides and Ruminococcus genera. Antibiotics treatment and co-housing alleviated the metabolic disturbance markers in Gpr35 deficient mice. Spatiotemporal profiling and mono-colonization screening revealed that Ruminococcus gnavus synergized with HFD to promote hepatic steatosis possibly via tryptophan and phenylalanine pathway metabolites. Our results provide mechanistic insights into a genetic-diet-microbe interplay that dictates susceptibility to metabolic disorder.},
}
@article {pmid36758644,
year = {2023},
author = {Xie, Y and Jia, M and De Wilde, F and Daeninck, K and De Clippeleir, H and Verstraete, W and Vlaeminck, SE},
title = {Feasibility of packed-bed trickling filters for partial nitritation/anammox: Effects of carrier material, bottom ventilation openings, hydraulic loading rate and free ammonia.},
journal = {Bioresource technology},
volume = {373},
number = {},
pages = {128713},
doi = {10.1016/j.biortech.2023.128713},
pmid = {36758644},
issn = {1873-2976},
mesh = {*Ammonia ; Anaerobic Ammonia Oxidation ; Feasibility Studies ; Bioreactors ; Nitrogen ; Oxidation-Reduction ; *Ammonium Compounds ; },
abstract = {This study pioneers the feasibility of cost-effective partial nitritation/anammox (PN/A) in packed-bed trickling filters (TFs). Three parallel TFs tested different carrier materials, the presence or absence of bottom ventilation openings, hydraulic loading rates (HLR, 0.4-2.2 m[3] m[-2] h[-1]), and free ammonia (FA) levels on synthetic medium. The inexpensive Argex expanded clay was recommended due to the similar nitrogen removal rates as commercially used plastics. Top-only ventilation at an optimum HLR of 1.8 m[3] m[-2] h[-1] could remove approximately 60% of the total nitrogen load (i.e., 300 mg N L[-1] d[-1], 30 °C) and achieve relatively low NO3[-]-N accumulation (13%). Likely FA levels of around 1.3-3.2 mg N L[-1] suppressed nitratation. Most of the total nitrogen removal took place in the upper third of the reactor, where anammox activity was highest. Provided further optimizations, the results demonstrated TFs are suitable for low-energy shortcut nitrogen removal.},
}
@article {pmid36758435,
year = {2023},
author = {Liu, J and Xu, G and Zhao, S and Chen, C and Rogers, MJ and He, J},
title = {Mechanistic and microbial ecological insights into the impacts of micro- and nano- plastics on microbial reductive dehalogenation of organohalide pollutants.},
journal = {Journal of hazardous materials},
volume = {448},
number = {},
pages = {130895},
doi = {10.1016/j.jhazmat.2023.130895},
pmid = {36758435},
issn = {1873-3336},
mesh = {*Environmental Pollutants ; Microplastics/toxicity ; Plastics ; Ecosystem ; Biodegradation, Environmental ; },
abstract = {Micro- and nano-plastics are prevalent in diverse ecosystems, but their impacts on biotransformation of organohalide pollutants and underpinning microbial communities remain poorly understood. Here we investigated the influence of micro- and nano-plastics on microbial reductive dehalogenation at strain and community levels. Generally, microplastics including polyethylene (PE), polystyrene (PS), polylactic acid (PLA), and a weathered microplastic mixture increased dehalogenation rate by 10 - 217% in both the Dehalococcoides isolate and enrichment culture, whereas the effects of polyvinyl chloride (PVC) and a defined microplastic mixture depended on their concentrations and cultures. Contrarily, nano-PS (80 nm) consistently inhibited dehalogenation due to increased production of reactive oxygen species. Nevertheless, the enrichment culture showed higher tolerance to nano-PS inhibition, implying crucial roles of non-dehalogenating populations in ameliorating nanoplastic inhibition. The variation in dehalogenation activity was linked to altered organohalide-respiring bacteria (OHRB) growth and reductive dehalogenase (RDase) gene transcription. Moreover, microplastics changed the community structure and benefited the enrichment of OHRB, favoring the proliferation of Dehalogenimonas. More broadly, the assembly of microbial communities on plastic biofilms was more deterministic than that in the planktonic cells, with more complex co-occurrence networks in the former. Collectively, these findings contribute to better understanding the fate of organohalides in changing environments with increasing plastic pollution.},
}
@article {pmid36757423,
year = {2023},
author = {Moreno, IJ and Brahamsha, B and Donia, MS and Palenik, B},
title = {Diverse Microbial Hot Spring Mat Communities at Black Canyon of the Colorado River.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1534-1551},
pmid = {36757423},
issn = {1432-184X},
mesh = {Humans ; *Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; Colorado ; Rivers ; Biodiversity ; *Cyanobacteria/genetics ; *Microbiota/genetics ; Phylogeny ; },
abstract = {The thermophilic microbial mat communities at hot springs in the Black Canyon of the Colorado River, thought to harbor the protistan human pathogen Naegleria fowleri, were surveyed using both culture-independent and -dependent methods to further understand the ecology of these hot spring microbiomes. Originating from Lake Mead source water, seven spring sites were sampled, varying in temperature from 25 to 55 °C. Amplicon-based high-throughput sequencing of twelve samples using 16S rRNA primers (hypervariable V4 region) revealed that most mats are dominated by cyanobacterial taxa, some but not all similar to those dominating the mats at other studied hot spring systems. 18S rRNA amplicon sequencing (V9 region) demonstrated a diverse community of protists and other eukaryotes including a highly abundant amoebal sequence related to Echinamoeba thermarum. Additional taxonomic and diversity metric analyses using near full-length 16S and 18S rRNA gene sequencing allowed a higher sequence-based resolution of the community. The mat sequence data suggest a major diversification of the cyanobacterial orders Leptolyngbyales, as well as microdiversity among several cyanobacterial taxa. Cyanobacterial isolates included some representatives of ecologically abundant taxa. A Spearman correlation analysis of short-read amplicon sequencing data supported the co-occurrences of populations of cyanobacteria, chloroflexi, and bacteroidetes providing evidence of common microbial co-occurrences across the Black Canyon hot springs.},
}
@article {pmid36755119,
year = {2023},
author = {Fairén, AG and Rodríguez, N and Sánchez-García, L and Rojas, P and Uceda, ER and Carrizo, D and Amils, R and Sanz, JL},
title = {Ecological successions throughout the desiccation of Tirez lagoon (Spain) as an astrobiological time-analog for wet-to-dry transitions on Mars.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {1423},
pmid = {36755119},
issn = {2045-2322},
support = {818602/ERC_/European Research Council/International ; },
mesh = {*Extraterrestrial Environment ; Desiccation ; Spain ; *Mars ; Water ; },
abstract = {Tirez was a small and seasonal endorheic athalassohaline lagoon that was located in central Spain. In recent years, the lagoon has totally dried out, offering for the first time the opportunity to analyze its desiccation process as a "time-analog" to similar events occurred in paleolakes with varying salinity during the wet-to-dry transition on early Mars. On the martian cratered highlands, an early period of water ponding within enclosed basins evolved to a complete desiccation of the lakes, leading to deposition of evaporitic sequences during the Noachian and into the Late Hesperian. As Tirez also underwent a process of desiccation, here we describe (i) the microbial ecology of Tirez when the lagoon was still active 20 years ago, with prokaryotes adapted to extreme saline conditions; (ii) the composition of the microbial community in the dried lake sediments today, in many case groups that thrive in sediments of extreme environments; and (iii) the molecular and isotopic analysis of the lipid biomarkers that can be recovered from the sediments today. We discuss the implications of these results to better understanding the ecology of possible Martian microbial communities during the wet-to-dry transition at the end of the Hesperian, and how they may inform about research strategies to search for possible biomarkers in Mars after all the water was lost.},
}
@article {pmid36754866,
year = {2023},
author = {Martiarena, MJS and Deveau, A and Montoya, QV and Flórez, LV and Rodrigues, A},
title = {The Hyphosphere of Leaf-Cutting Ant Cultivars Is Enriched with Helper Bacteria.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1773-1788},
pmid = {36754866},
issn = {1432-184X},
mesh = {Animals ; *Ants/microbiology ; Bacteria ; Hyphae ; *Actinobacteria ; Cellulose ; Symbiosis ; },
abstract = {Bacteria can live in a variety of interkingdom communities playing key ecological roles. The microbiome of leaf-cutting attine ant colonies are a remarkable example of such communities, as they support ants' metabolic processes and the maintenance of ant-fungus gardens. Studies on this topic have explored the bacterial community of the whole fungus garden, without discerning bacterial groups associated with the nutrient storage structures (gongylidia) of ant fungal cultivars. Here we studied bacteria isolated from the surface of gongylidia in the cultivars of Atta sexdens and Acromyrmex coronatus, to assess whether the bacterial community influences the biology of the fungus. A total of 10 bacterial strains were isolated from gongylidia (Bacillus sp., Lysinibacillus sp., Niallia sp., Staphylococcus sp., Paenibacillus sp., Pantoea sp., Staphylococcus sp., and one Actinobacteria). Some bacterial isolates increased gongylidia production and fungal biomass while others had inhibitory effects. Eight bacterial strains were confirmed to form biofilm-like structures on the fungal cultivar hyphae. They also showed auxiliary metabolic functions useful for the development of the fungal garden such as phosphate solubilization, siderophore production, cellulose and chitin degradation, and antifungal activity against antagonists of the fungal cultivar. Bacteria-bacteria interaction assays revealed heterogeneous behaviors including synergism and competition, which might contribute to regulate the community structure inside the garden. Our results suggest that bacteria and the ant fungal cultivar interact directly, across a continuum of positive and negative interactions within the community. These complex relationships could ultimately contribute to the stability of the ant-fungus mutualism.},
}
@article {pmid36752910,
year = {2023},
author = {Campos, MA and Zhang, Q and Acuña, JJ and Rilling, JI and Ruiz, T and Carrazana, E and Reyno, C and Hollenback, A and Gray, K and Jaisi, DP and Ogram, A and Bai, J and Zhang, L and Xiao, R and Elias, M and Sadowsky, MJ and Hu, J and Jorquera, MA},
title = {Structure and Functional Properties of Bacterial Communities in Surface Sediments of the Recently Declared Nutrient-Saturated Lake Villarrica in Southern Chile.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1513-1533},
pmid = {36752910},
issn = {1432-184X},
support = {NSFC19001//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; REDES190079//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; },
mesh = {Humans ; *Lakes/microbiology ; Chile ; *Bacteria/genetics ; Proteobacteria/genetics ; Genes, Bacterial ; Bacteroidetes/genetics ; Geologic Sediments/microbiology ; },
abstract = {Lake Villarrica, one of Chile's main freshwater water bodies, was recently declared a nutrient-saturated lake due to increased phosphorus (P) and nitrogen (N) levels. Although a decontamination plan based on environmental parameters is being established, it does not consider microbial parameters. Here, we conducted high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR) analyses to reveal the structure and functional properties of bacterial communities in surface sediments collected from sites with contrasting anthropogenic pressures in Lake Villarrica. Alpha diversity revealed an elevated bacterial richness and diversity in the more anthropogenized sediments. The phylum Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria dominated the community. The principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed significant differences in bacterial communities of sampling sites. Predicted functional analysis showed that N cycling functions (e.g., nitrification and denitrification) were significant. The microbial co-occurrence networks analysis suggested Chitinophagaceae, Caldilineaceae, Planctomycetaceae, and Phycisphaerae families as keystone taxa. Bacterial functional genes related to P (phoC, phoD, and phoX) and N (nifH and nosZ) cycling were detected in all samples by qPCR. In addition, an RDA related to N and P cycling revealed that physicochemical properties and functional genes were positively correlated with several nitrite-oxidizing, ammonia-oxidizing, and N-fixing bacterial genera. Finally, denitrifying gene (nosZ) was the most significant factor influencing the topological characteristics of co-occurrence networks and bacterial interactions. Our results represent one of a few approaches to elucidate the structure and role of bacterial communities in Chilean lake sediments, which might be helpful in conservation and decontamination plans.},
}
@article {pmid36752639,
year = {2023},
author = {Mukherjee, S and Bhadury, P and Mitra, S and Naha, S and Saha, B and Dutta, S and Basu, S},
title = {Hypervirulent Klebsiella pneumoniae Causing Neonatal Bloodstream Infections: Emergence of NDM-1-Producing Hypervirulent ST11-K2 and ST15-K54 Strains Possessing pLVPK-Associated Markers.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0412122},
pmid = {36752639},
issn = {2165-0497},
abstract = {Klebsiella pneumoniae is a major cause of neonatal sepsis. Hypervirulent Klebsiella pneumoniae (hvKP) that cause invasive infections and/or carbapenem-resistant hvKP (CR-hvKP) limit therapeutic options. Such strains causing neonatal sepsis have rarely been studied. Characterization of neonatal septicemic hvKP/CR-hvKP strains in terms of resistance and virulence was carried out. Antibiotic susceptibility, molecular characterization, evaluation of clonality, in vitro virulence, and transmissibility of carbapenemase genes were evaluated. Whole-genome sequencing (WGS) and mouse lethality assays were performed on strains harboring pLVPK-associated markers. About one-fourth (26%, 28/107) of the studied strains, leading to mortality in 39% (11/28) of the infected neonates, were categorized as hvKP. hvKP-K2 was the prevalent pathotype (64.2%, 18/28), but K54 and K57 were also identified. Most strains were clonally diverse belonging to 12 sequence types, of which ST14 was most common. Majority of hvKPs possessed virulence determinants, strong biofilm-forming, and high serum resistance ability. Nine hvKPs were carbapenem-resistant, harboring blaNDM-1/blaNDM-5 on conjugative plasmids of different replicon types. Two NDM-1-producing high-risk clones, ST11 and ST15, had pLVPK-associated markers (rmpA, rmpA2, iroBCDEN, iucABCDiutA, and peg-344), of which one co-transferred the markers along with blaNDM-1. The 2 strains revealed high inter-genomic resemblance with the other hvKP reference genomes, and were lethal in mouse model. To the best of our knowledge, this study is the first to report on the NDM-1-producing hvKP ST11-K2 and ST15-K54 strains causing fatal neonatal sepsis. The presence of pLVPK-associated markers and blaNDM-1 in high-risk clones, and the co-transmission of these genes via conjugation calls for surveillance of these strains. IMPORTANCE Klebsiella pneumoniae is a leading cause of sepsis in newborns and adults. Among the 2 major pathotypes of K. pneumoniae, classical (cKP) and hypervirulent (hvKP), hvKP causes community-acquired severe fatal invasive infections in even healthy individuals, as it possesses several virulence factors. The lack of comprehensive studies on neonatal septicemic hvKPs prompted this work. Nearly 26% diverse hvKP strains were recovered possessing several resistance and virulence determinants. The majority of them exhibited strong biofilm-forming and high serum resistance ability. Nine of these strains were also carbapenem (last-resort antibiotic)-resistant, of which 2 high-risk clones (ST11-K2 and ST15-K54) harbored markers (pLVPK) noted for their virulence, and were lethal in the mouse model. Genome-level characterization of the high-risk clones showed resemblance with the other hvKP reference genomes. The presence of transmissible carbapenem-resistant gene, blaNDM, along with pLVPK-markers calls for vigilance, as most clinical microbiology laboratories do not test for them.},
}
@article {pmid36752053,
year = {2023},
author = {Táncsics, A and Banerjee, S and Soares, A and Bedics, A and Kriszt, B},
title = {Combined Omics Approach Reveals Key Differences between Aerobic and Microaerobic Xylene-Degrading Enrichment Bacterial Communities: Rhodoferax─A Hitherto Unknown Player Emerges from the Microbial Dark Matter.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {7},
pages = {2846-2855},
doi = {10.1021/acs.est.2c09283},
pmid = {36752053},
issn = {1520-5851},
mesh = {Xylenes/analysis/metabolism ; Phylogeny ; *Hydrocarbons, Aromatic/metabolism ; Bacteria/genetics ; *Dioxygenases/genetics/metabolism ; Biodegradation, Environmental ; },
abstract = {Among monoaromatic hydrocarbons, xylenes, especially the ortho and para isomers, are the least biodegradable compounds in oxygen-limited subsurface environments. Although much knowledge has been gained regarding the anaerobic degradation of xylene isomers in the past 2 decades, the diversity of those bacteria which are able to degrade them under microaerobic conditions is still unknown. To overcome this limitation, aerobic and microaerobic xylene-degrading enrichment cultures were established using groundwater taken from a xylene-contaminated site, and the associated bacterial communities were investigated using a polyphasic approach. Our results show that the xylene-degrading bacterial communities were distinctly different between aerobic and microaerobic enrichment conditions. Although members of the genus Pseudomonas were the most dominant in both types of enrichments, the Rhodoferax and Azovibrio lineages were only abundant under microaerobic conditions, while Sphingobium entirely replaced them under aerobic conditions. Analysis of a metagenome-assembled genome of a Rhodoferax-related bacterium revealed aromatic hydrocarbon-degrading ability by identifying two catechol 2,3-dioxygenases in the genome. Moreover, phylogenetic analysis indicated that both enzymes belonged to a newly defined subfamily of type I.2 extradiol dioxygenases (EDOs). Aerobic and microaerobic xylene-degradation experiments were conducted on strains Sphingobium sp. AS12 and Pseudomonas sp. MAP12, isolated from the aerobic and microaerobic enrichments, respectively. The obtained results, together with the whole-genome sequence data of the strains, confirmed the observation that members of the genus Sphingobium are excellent aromatic hydrocarbon degraders but effective only under clear aerobic conditions. Overall, it was concluded that the observed differences between the bacterial communities of aerobic and microaerobic xylene-degrading enrichments were driven primarily by (i) the method of aromatic ring activation (monooxygenation vs dioxygenation), (ii) the type of EDO enzymes, and (iii) the ability of degraders to respire utilizing nitrate.},
}
@article {pmid36750476,
year = {2023},
author = {Nicolosi, G and Gonzalez-Pimentel, JL and Piano, E and Isaia, M and Miller, AZ},
title = {First Insights into the Bacterial Diversity of Mount Etna Volcanic Caves.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1632-1645},
pmid = {36750476},
issn = {1432-184X},
support = {PID2019-108672RJ-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RYC2019-026885-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PTDC/CTA-AMB/0608/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECIND/01147/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PIE_20214AT021//Consejo Superior de Investigaciones Cient&#xed;ficas/ ; },
mesh = {*Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Biodiversity ; *Microbiota ; Phylogeny ; },
abstract = {While microbial communities in limestone caves across the world are relatively understood, knowledge of the microbial composition in lava tubes is lagging behind. These caves are found in volcanic regions worldwide and are typically lined with multicolored microbial mats on their walls and ceilings. The Mount Etna (Sicily, S-Italy) represents one of the most active volcanos in the world. Due to its outstanding biodiversity and geological features, it was declared Natural Heritage of Humanity by the UNESCO in 2013. Despite the presence of more than 200 basaltic lava tubes, the microbial diversity of these hypogean systems has never been investigated so far. Here, we investigated bacterial communities in four lava tubes of Mount Etna volcano. Field emission scanning electron microscopy (FESEM) was carried out for the morphological characterization and detection of microbial features. We documented an abundant presence of microbial cells with different morphotypes including rod-shaped, filamentous, and coccoidal cells with surface appendages, resembling actinobacteria reported in other lava tubes across the world. Based on 16S rRNA gene analysis, the colored microbial mats collected were mostly composed of bacteria belonging to the phyla Actinomycetota, Pseudomonadota, Acidobacteriota, Chloroflexota, and Cyanobacteria. At the genus level, the analysis revealed a dominance of the genus Crossiella, which is actively involved in biomineralization processes, followed by Pseudomonas, Bacillus, Chujaibacter, and Sphingomonas. The presence of these taxa is associated with the carbon, nitrogen, and ammonia cycles, and some are possibly related to the anthropic disturbance of these caves. This study provides the first insight into the microbial diversity of the Etna volcano lava tubes, and expands on previous research on microbiology of volcanic caves across the world.},
}
@article {pmid36749701,
year = {2023},
author = {Girolamini, L and Pascale, MR and Salaris, S and Mazzotta, M and Orsini, M and Grottola, A and Zini, N and Cristino, S},
title = {Corrigendum: Legionella bononiensis sp. nov., isolated from a hotel water distribution system in northern Italy.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.005710},
pmid = {36749701},
issn = {1466-5034},
}
@article {pmid36749697,
year = {2023},
author = {Pradel, N and Fardeau, ML and Bunk, B and Spröer, C and Boedeker, C and Wolf, J and Neumann-Schaal, M and Pester, M and Spring, S},
title = {Aminithiophilus ramosus gen. nov., sp. nov., a sulphur-reducing bacterium isolated from a pyrite-forming enrichment culture, and taxonomic revision of the family Synergistaceae.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.005691},
pmid = {36749697},
issn = {1466-5034},
mesh = {*Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Sequence Analysis, DNA ; *Bacteria/genetics ; Sewage/microbiology ; Sulfides ; Phospholipids/chemistry ; },
abstract = {A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2[T] could be affiliated with the phylum Synergistota. Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with Aminiphilus circumscriptus ILE-2[T] (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a Methanospirillum species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C15 : 0. Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus, represented by the type strain J.5.4.2-T.3.5.2[T] (=DSM 107166[T]=NBRC 114655[T]) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus. In addition, we suggest reclassifying certain members of the Synergistaceae into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiaceae fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.},
}
@article {pmid36748549,
year = {2023},
author = {Soares, A and Edwards, A and An, D and Bagnoud, A and Bradley, J and Barnhart, E and Bomberg, M and Budwill, K and Caffrey, SM and Fields, M and Gralnick, J and Kadnikov, V and Momper, L and Osburn, M and Mu, A and Moreau, JW and Moser, D and Purkamo, L and Rassner, SM and Sheik, CS and Sherwood Lollar, B and Toner, BM and Voordouw, G and Wouters, K and Mitchell, AC},
title = {A global perspective on bacterial diversity in the terrestrial deep subsurface.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {1},
pages = {},
pmid = {36748549},
issn = {1465-2080},
mesh = {Water Microbiology ; Bacteria/genetics ; *Microbiota/genetics ; Biomass ; Metagenomics ; *Gammaproteobacteria ; RNA, Ribosomal, 16S ; },
abstract = {While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.},
}
@article {pmid36747985,
year = {2023},
author = {Green, GBH and DePaola, A and Linville, JG and Morrow, CD and Bej, AK},
title = {High-throughput amplicon sequencing datasets of coastal sediments from three locations of the Gulf of Mexico, USA.},
journal = {Data in brief},
volume = {47},
number = {},
pages = {108895},
pmid = {36747985},
issn = {2352-3409},
support = {P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; },
abstract = {We present high-throughput amplicon sequence (HTS) datasets of the purified microbial metacommunity DNA of coastal surface sediments from Portersville Bay (PVB) (n = 3), Bayou La Batre (BLB) (n = 3), and Mobile Bay (MOB) (n = 3) of the U.S. Gulf of Mexico (U.S. Gulf Coast). The PVB samples were collected from the oyster aquaculture Shellevator™ system; the BLB samples were from locations on the shoreline adjacent to wild oysters attached to rocks and likely polluted from sewage and possibly chemical contamination from boats, shipyards, and seafood processing facilities; and MOB samples were adjacent to aquaculture oysters in bottom cages. The amplicons of the V4 hypervariable segment of the 16S rRNA gene from each sample were sequenced on an Illumina MiSeq to generate these HTS datasets. The raw sequences were quality-checked, demultiplexed into FASTQ files, denoised using DADA2, and subsampled. Then, the FASTA formatted sequences were assigned the taxonomic ids to amplicon sequence variants (ASVs) against the silva-138-99-nb-classifier using the Quantitative Insights Into Microbial Ecology (QIIME2 v2022.2). The applicability of the HTS datasets was confirmed by microbial taxa analysis at the phylum level using the "qiime taxa collapse" command. All HTS datasets are available through the BioSample Submission Portal under the BioProject ID PRJNA876773 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA876773).},
}
@article {pmid36746236,
year = {2023},
author = {Zhang, L and Hu, C and Zhang, Z and Liu, R and Liu, G and Xue, D and Wang, Z and Wu, C and Wu, X and She, J and Shi, F},
title = {Association between prior appendectomy and the risk and course of Crohn's disease: A systematic review and meta-analysis.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {47},
number = {3},
pages = {102090},
doi = {10.1016/j.clinre.2023.102090},
pmid = {36746236},
issn = {2210-741X},
mesh = {Humans ; *Crohn Disease ; Appendectomy ; Cohort Studies ; *Appendix ; Case-Control Studies ; },
abstract = {BACKGROUND AND AIMS: The appendix has an important immune function in both health and disease, and appendectomy may influence microbial ecology and immune function. This meta-analysis aims to assess the association between appendectomy and the risk and course of Crohn's disease (CD).<br><br>METHODS: PubMed, EMBASE, and the Cochrane Library were used to identify all studies published until June 2022. Data from studies evaluating the association between appendectomy and CD were reviewed.<br><br>RESULTS: A total of 28 studies were included in the final analysis, comprising 22 case-control and 6 cohort studies. A positive relationship between prior appendectomy and the risk of developing CD was observed in both case-control studies (odds ratio [OR]: 1.59, 95% confidence interval [CI]: 1.22-2.08) and cohort studies (relative risk [RR]: 2.28, 95% CI: 1.66-3.14). The elevated risk of CD persisted 5 years post-appendectomy (RR&#xa0;=&#xa0;1.24, 95% CI: 1.12-1.36). The risk of developing CD was similarly elevated regardless of the presence (RR&#xa0;=&#xa0;1.64, 95% CI: 1.17-2.31) or absence (RR&#xa0;=&#xa0;2.77, 95% CI: 1.84-4.16) of appendicitis in patients. Moreover, significant differences were found in the proportion of terminal ileum lesions (OR&#xa0;=&#xa0;1.63; 95% CI: 1.38-1.93) and colon lesions (OR&#xa0;=&#xa0;0.70; 95% CI: 0.5-0.84) between CD patients with appendectomy and those without appendectomy.<br><br>CONCLUSIONS: The risk of developing CD following an appendectomy is significant and persists 5 years postoperatively. Moreover, the elevated risk of CD may mainly occur in the terminal ileum.},
}
@article {pmid36744882,
year = {2023},
author = {Liu, X and Lyu, L and Li, J and Sen, B and Bai, M and Stajich, JE and Collier, JL and Wang, G},
title = {Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0424722},
pmid = {36744882},
issn = {2165-0497},
abstract = {Labyrinthulomycetes are a group of ubiquitous and diverse unicellular Stramenopiles and have long been known for their vital role in ocean carbon cycling. However, their ecological function from the perspective of organic matter degradation remains poorly understood. This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains, namely, Botryochytrium sp. strain S-28 and Oblongichytrium sp. strain S-429, and provides molecular analysis of their ecological functions using comparative genomics and a biochemical assay. Our results suggest that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems because of the significant differences in gene function among different genera. Certain strains could degrade wheat bran independently by secreting cellulase. The key glycoside hydrolase families (GH1, GH5, and GH9) related to cellulase and the functional domains of carbohydrate-active enzymes (CAZymes) were more enriched in their genomes. This group can actively participate in marine biochemical cycles as decomposers. In contrast, other strains that could not produce cellulase may thrive as "leftover scavengers" and act as a source of nutrients to the higher-trophic-level plankton. In addition, our findings emphasize the dual roles of endoglucanase, acting as both exo- and endoglucanases, in the process of cellulose degradation. Using genomic, biochemical, and phylogenetic analyses, our study provides a broader insight into the nutritional patterns and ecological functions of Labyrinthulomycetes. IMPORTANCE Unicellular heterotrophic eukaryotes are an important component of marine ecosystems. However, their ecological functions and modes of nutrition remain largely unknown. Our current understanding of marine microbial ecology is incomplete without integrating these heterotrophic microeukaryotes into the food web models. This study focuses on the unicellular fungus-like protists Labyrinthulomycetes and provides two high-quality genomes of cellulase-producing Labyrinthulomycetes. Our study uncovers the basis of their cellulase production by deciphering the results of genomic, biochemical, and phylogenetic analyses. This study instigates a further investigation of the molecular mechanism of organic matter utilization by Labyrinthulomycetes in the world's oceans.},
}
@article {pmid36744088,
year = {2023},
author = {Wang, D and Tang, G and Yu, J and Li, Y and Wang, Y and Chen, L and Lei, X and Cao, Y and Yao, J},
title = {Litter size influences rumen microbiota and fermentation efficiency, thus determining host early growth in goats.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1098813},
pmid = {36744088},
issn = {1664-302X},
abstract = {INTRODUCTION: Multiple litters are accompanied by low birth weight, low survival rates, and growth rates in goats during early life. Regulating rumen microbiota structure can indirectly or directly affect host metabolism and animal growth. However, the relationship between high litter size and rumen microbiome, rumen fermentation, and growth performance in goat kids is unclear.<br><br>METHODS: In the present study, thirty 6-month-old, female goats were investigated, of which 10 goats were randomly chosen from single, twin and triplet goats respectively, and their birth weight was recorded. From birth, all goats were subjected to the same feed and management practices. Individual weaning and youth body weight were measured, and the rumen fluid samples were collected to characterize the bacterial communities and to determine the ruminal volatile fatty acids (VFA), free amino acids (AA), and free fatty acids (FA) concentration of those young goats.<br><br>RESULTS AND DISCUSSION: Compared with the single and twin goats, triplet goats have lower weaning and youth body weight and average daily gain (ADG). Ruminal propionate, butyrate, and total VFA were decreased in triplet goats. Meanwhile, ruminal AA, such as branched chain amino acids (BCAA), essential amino acids (EAA), unsaturated fatty acids (UFA), and monounsaturated fatty acids (MUFA) were decreased, while saturated fatty acids (SFA) and odd and branched chain fatty acids (OBCFA) were increased in triplet goats. Our results also revealed that litter size significantly affected the rumen bacterial communities, and triplet goats had a lower the Firmicutes: Bacteroidota ratio, the abundance of Firmicutes phylum, Rikenellaceae family, and Rikenellaceae RC9 gut group, and had a higher proportion of Prevotellaceae family, and several genera of Prevotellaceae, such as Prevotella, and unclassified f Prevotellaceae. Furthermore, Spearman's correlation network analysis showed that the changes in the rumen bacteria were associated with changes in rumen metabolites. In conclusion, this study revealed that high litter size could bring disturbances to the microbial communities and decrease the rumen fermentation efficiency and growth performance, which can be utilized to better understand variation in microbial ecology that will improve growth performance in triplet goats.},
}
@article {pmid36741554,
year = {2022},
author = {Lombard, L and van Doorn, R and Groenewald, JZ and Tessema, T and Kuramae, EE and Etolo, DW and Raaijmakers, JM and Crous, PW},
title = {Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia.},
journal = {Fungal systematics and evolution},
volume = {10},
number = {},
pages = {177-215},
pmid = {36741554},
issn = {2589-3831},
abstract = {Sorghum production is seriously threatened by the root parasitic weeds (RPWs) Striga hermonthica and Striga asiatica in sub-Saharan Africa. Research has shown that Striga control depends on eliminating its seed reserves in soil. Several species of the genus Fusarium (Nectriaceae, Hypocreales), which have been isolated from diseased Striga plants have proven to be highly pathogenic to all developmental stages of these RPWs. In the present study 439 isolates of Fusarium spp. were found associated with soils from Sorghum growing fields, Sorghum rhizosphere, or as endophytes with Sorghum roots and seeds, or as endophytes of Striga stems and seeds. Based on multi-locus phylogenies of combinations of CaM, tef1, rpb1 and rpb2 alignments, and morphological characteristics, 42 species were identified, including three species that are newly described, namely F. extenuatum and F. tangerinum from Sorghum soils, and F. pentaseptatum from seed of Striga hermonthica. Using a previously published AFLP-derived marker that is specific to detect isolates of F. oxysporum f.sp. strigae, an effective soil-borne biocontrol agent against Striga, we also detected the gene in several other Fusarium species. As these isolates were all associated with the Striga/Sorghum pathosystem, the possibility of horizontal gene transfer among these fusaria will be of interest to further investigate in future. Citation: Lombard L, van Doorn R, Groenewald JZ, Tessema T, Kuramae EE, Etolo DW, Raaijmakers JM, Crous PW (2022). Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia. Fungal Systematics and Evolution 10: 177-215. doi: 10.3114/fuse.2022.10.08.},
}
@article {pmid36739987,
year = {2023},
author = {Liu, Q and Zhu, J and Wang, L and Wang, X and Huang, Z and Zhao, F and Zou, J and Liu, Y and Ma, J},
title = {Interpreting the degradation mechanism of triclosan in microbial fuel cell by combining analysis microbiome community and degradation pathway.},
journal = {Chemosphere},
volume = {321},
number = {},
pages = {137983},
doi = {10.1016/j.chemosphere.2023.137983},
pmid = {36739987},
issn = {1879-1298},
mesh = {*Triclosan/metabolism ; *Bioelectric Energy Sources ; Biodegradation, Environmental ; Bacteria/metabolism ; *Microbiota ; },
abstract = {Microbes play a dominant role for the transformation of organic contaminants in the environment, while a significant gap exists in understanding the degradation mechanism and the function of different species. Herein, the possible bio-degradation of triclosan in microbial fuel cell was explored, with the investigation of degradation kinetics, microbial community, and possible degradation products. 5 mg/L of triclosan could be degraded within 3 days, and an intermediate degradation product (2,4-dichlorophen) could be further degraded in system. 32 kinds of dominant bacteria (relative intensity >0.5%) were identified in the biofilm, and 10 possible degradation products were identified. By analyzing the possible involved bioreactions (including decarboxylation, dehalogenation, dioxygenation, hydrolysis, hydroxylation, and ring-cleavage) of the dominant bacteria and possible degradation pathway of triclosan based on the identified products, biodegradation mechanism and function of the bacteria involved in the degradation of triclosan was clarified simultaneously. This study provides useful information for further interpreting the degradation mechanism of organic pollutants in mixed flora by combining analysis microbiome community and degradation pathway.},
}
@article {pmid36739716,
year = {2023},
author = {Doni, L and Oliveri, C and Lasa, A and Di Cesare, A and Petrin, S and Martinez-Urtaza, J and Coman, F and Richardson, A and Vezzulli, L},
title = {Large-scale impact of the 2016 Marine Heatwave on the plankton-associated microbial communities of the Great Barrier Reef (Australia).},
journal = {Marine pollution bulletin},
volume = {188},
number = {},
pages = {114685},
doi = {10.1016/j.marpolbul.2023.114685},
pmid = {36739716},
issn = {1879-3363},
mesh = {Animals ; Ecosystem ; Coral Reefs ; Plankton ; RNA, Ribosomal, 16S ; *Anthozoa ; Australia ; Bacteria/genetics ; *Microbiota ; },
abstract = {The Great Barrier Reef (GBR) is the world's largest coral ecosystem and is threatened by climate change. This study investigated the impact of the 2016 Marine Heatwave (MHW) on plankton associated microbial communities along a ∼800 km transect in the GBR. 16S rRNA gene metabarcoding of archived plankton samples collected from November 2014 to August 2016 in this region showed a significant increase in Planctomycetes and bacteria belonging to the genus Vibrio and Synechococcus during and after the heatwave. Notably, Droplet Digital PCR and targeted metagenomic analysis applied on samples collected four months after the MHW event revealed the presence of several potential pathogenic Vibrio species previously associated with diseases in aquatic animals. Overall, the 2016 MHW significantly impacted the surface picoplankton community and fostered the spread of potentially pathogenic bacteria across the GBR providing an additional threat for marine biodiversity in this area.},
}
@article {pmid36737902,
year = {2023},
author = {Cabezas-Terán, K and Grootaert, C and Ortiz, J and Donoso, S and Ruales, J and Van Bockstaele, F and Van Camp, J and Van de Wiele, T},
title = {In vitro bioaccessibility and uptake of β-carotene from encapsulated carotenoids from mango by-products in a coupled gastrointestinal digestion/Caco-2 cell model.},
journal = {Food research international (Ottawa, Ont.)},
volume = {164},
number = {},
pages = {112301},
doi = {10.1016/j.foodres.2022.112301},
pmid = {36737902},
issn = {1873-7145},
mesh = {Animals ; Humans ; *beta Carotene/metabolism ; Carotenoids/metabolism ; Caco-2 Cells ; *Mangifera/metabolism ; Provitamins ; Inulin ; Birds/metabolism ; Digestion ; },
abstract = {β-carotene is a carotenoid with provitamin A activity and other health benefits, which needs to become bioavailable upon oral intake to exert its biological activity. A better understanding of its behaviour and stability in the gastrointestinal tract and means to increase its bioavailability are highly needed. Using an in vitro gastrointestinal digestion method coupled to an intestinal cell model, we explored the stability, gastrointestinal bioaccessibility and cellular uptake of β-carotene from microparticles containing carotenoid extracts derived from mango by-products. Three types of microparticles were tested: one with the carotenoid extract as such, one with added inulin and one with added fructooligosaccharides. Overall, β-carotene was relatively stable during the in vitro digestion, as total recoveries were above 68 %. Prebiotics in the encapsulating material, especially inulin, enhanced the bioaccessibility of β-carotene almost 2-fold compared to microparticles without prebiotics. Likewise, β-carotene bioaccessibility increased proportionally with bile salt concentrations during digestion. Yet, a bile salts level above 10 mM did not contribute markedly to β-carotene bioaccessibility of prebiotic containing microparticles. Cellular uptake experiments with non-filtered gastrointestinal digests yielded higher absolute levels of β-carotene taken up in the epithelial cells as compared to uptake assays with filtered digests. However, the proportional uptake of β-carotene was higher for filtered digests (24 - 31 %) than for non-filtered digests (2 - 8 %). Matrix-dependent carotenoid uptake was only visible in the unfiltered medium, thereby pointing to possible other cellular transport mechanisms of non-micellarized carotenoids, besides the concentration effect. Regardless of a filtration step, inulin-amended microparticles consistently resulted in a higher β-carotene uptake than regular microparticles or FOS-amended microparticles. In conclusion, encapsulation of carotenoid extracts from mango by-products displayed chemical stability and release of a bioaccessible β-carotene fraction upon gastrointestinal digestion. This indicates the potential of the microparticles to be incorporated into functional foods with provitamin A activity.},
}
@article {pmid36737826,
year = {2023},
author = {Forgie, AJ and Pepin, DM and Ju, T and Tollenaar, S and Sergi, CM and Gruenheid, S and Willing, BP},
title = {Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {21},
pmid = {36737826},
issn = {2049-2618},
mesh = {Humans ; Animals ; Mice ; *Vitamin B 12/pharmacology ; *Citrobacter rodentium ; Host Microbial Interactions ; Colon ; Dietary Supplements ; },
abstract = {BACKGROUND: Vitamin B12 supplements typically contain doses that far exceed the recommended daily amount, and high exposures are generally considered safe. Competitive and syntrophic interactions for B12 exist between microbes in the gut. Yet, to what extent excessive levels contribute to the activities of the gut microbiota remains unclear. The objective of this study was to evaluate the effect of B12 on microbial ecology using a B12 supplemented mouse model with Citrobacter rodentium, a mouse-specific pathogen. Mice were fed a standard chow diet and received either water or water supplemented with B12 (cyanocobalamin: ~120 μg/day), which equates to approximately 25 mg in humans. Infection severity was determined by body weight, pathogen load, and histopathologic scoring. Host biomarkers of inflammation were assessed in the colon before and after the pathogen challenge.<br><br>RESULTS: Cyanocobalamin supplementation enhanced pathogen colonization at day 1 (P < 0.05) and day 3 (P < 0.01) postinfection. The impact of B12 on gut microbial communities, although minor, was distinct and attributed to the changes in the Lachnospiraceae populations and reduced alpha diversity. Cyanocobalamin treatment disrupted the activity of the low-abundance community members of the gut microbiota. It enhanced the amount of interleukin-12 p40 subunit protein (IL12/23p40; P < 0.001) and interleukin-17a (IL-17A; P < 0.05) in the colon of na&#xef;ve mice. This immune phenotype was microbe dependent, and the response varied based on the baseline microbiota. The cecal metatranscriptome revealed that excessive cyanocobalamin decreased the expression of glucose utilizing genes by C. rodentium, a metabolic attribute previously associated with pathogen virulence.<br><br>CONCLUSIONS: Oral vitamin B12 supplementation promoted C. rodentium colonization in mice by altering the activities of the Lachnospiraceae populations in the gut. A lower abundance of select Lachnospiraceae species correlated to higher p40 subunit levels, while the detection of Parasutterella exacerbated inflammatory markers in the colon of na&#xef;ve mice. The B12-induced change in gut ecology enhanced the ability of C. rodentium colonization by impacting key microbe-host interactions that help with pathogen exclusion. This research provides insight into how B12 impacts the gut microbiota and highlights potential consequences of disrupting microbial B12 competition/sharing through over-supplementation. Video Abstract.},
}
@article {pmid36736839,
year = {2023},
author = {Zhao, L and Dou, Q and Chen, S and Wang, Y and Yang, Q and Chen, W and Zhang, H and Du, Y and Xie, M},
title = {Adsorption abilities and mechanisms of Lactobacillus on various nanoplastics.},
journal = {Chemosphere},
volume = {320},
number = {},
pages = {138038},
doi = {10.1016/j.chemosphere.2023.138038},
pmid = {36736839},
issn = {1879-1298},
mesh = {Humans ; *Microplastics/chemistry ; Lactobacillus ; Adsorption ; Polypropylenes/chemistry ; Polyethylene/chemistry ; *Water Pollutants, Chemical/analysis ; Plastics/chemistry ; },
abstract = {As a new type of pollutants, nanoplastics (NPs), which are easily ingested by humans from food wraps, salt, drinking water, have been widely detected in various water environments, and are a threat to human health. It is therefore urgent to develop an efficient method to remove NPs from the diet or relief its harm. In the present study, the possibility of a well-known human probiotic, lactic acid bacteria (LAB), was evaluated to remove NPs from food as an absorbent. The results indicated that LAB from infant feces could efficiently absorb three types NPs, i.e. polypropylene (PP), polyethylene (PE), and polyvinyl chloride (PVC) with the adsorption rates of PP > PE > PVC (PP 78.57%, PE 71.59%, PVC 66.57%) and the Nile red-stained NPs being aggregated on the surfaces of Lactobacillus cells. The smaller the particle size, the stronger the ability of NP adsorption on the cell surface. The hydrophobicity of NPs and bacterial cells affected the adsorption process. The measurement of adsorption rates of different cell components indicated that the overall adsorption effect of cell was better than that of individual cell component. The results of molecular dynamics analysis revealed that adsorption was mainly caused by electrostatic interactions, van der Waals forces, and hydrogen bonds. The hydrophobic interaction was also involved in adsorption process. Overall, this research may provide new information for developing new strategies for NPs removal in intestinal environment.},
}
@article {pmid36735066,
year = {2023},
author = {Modenutti, B and Martyniuk, N and Bastidas Navarro, M and Balseiro, E},
title = {Glacial Influence Affects Modularity in Bacterial Community Structure in Three Deep Andean North-Patagonian Lakes.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1869-1880},
pmid = {36735066},
issn = {1432-184X},
mesh = {*Lakes/microbiology ; *Bacteria/genetics ; Ice Cover/microbiology ; Argentina ; },
abstract = {We analyze the bacteria community composition and the ecological processes structuring these communities in three deep lakes that receive meltwater from the glaciers of Mount Tronador (North-Patagonia, Argentina). Lakes differ in their glacial connectivity and in their turbidity due to glacial particles. Lake Ventisquero Negro is a recently formed proglacial lake and it is still in contact with the glacier. Lakes Mascardi and Frías lost their glacial connectivity during the Pleistocene-Holocene transition. Total dissolved solid concentration has a significant contribution to the environmental gradient determining the segregation of the three lakes. The newly formed lake Ventisquero Negro conformed a particular bacterial community that seemed to be more related to the microorganisms coming from glacier melting than to the other lakes of the basin. The net relatedness index (NRI) showed that the bacterial community of lake Ventisquero Negro is determined by environmental filtering, while in the other lakes, species interaction would be a more important driver. The co-occurrence network analysis showed an increase in modularity and in the number of modules when comparing Lake Ventisquero Negro with the two large glacier-fed lakes suggesting an increase in heterogeneity. At the same time, the presence of modules with phototrophic bacteria (Cyanobium strains) in lakes Frías and Mascardi would reflect the increase of this functional photosynthetic association. Overall, our results showed that the reduction in ice masses in Patagonia will affect downstream large deep Piedmont lakes losing the glacial influence in their bacterial communities.},
}
@article {pmid36735065,
year = {2023},
author = {Graham, EB and Knelman, JE},
title = {Implications of Soil Microbial Community Assembly for Ecosystem Restoration: Patterns, Process, and Potential.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {809-819},
pmid = {36735065},
issn = {1432-184X},
mesh = {*Ecosystem ; Soil/chemistry ; Ecology ; Soil Microbiology ; *Microbiota ; },
abstract = {While it is now widely accepted that microorganisms provide essential functions in restoration ecology, the nature of relationships between microbial community assembly and ecosystem recovery remains unclear. There has been a longstanding challenge to decipher whether microorganisms facilitate or simply follow ecosystem recovery, and evidence for each is mixed at best. We propose that understanding microbial community assembly processes is critical to understanding the role of microorganisms during ecosystem restoration and thus optimizing management strategies. We examine how the connection between environment, community structure, and function is fundamentally underpinned by the processes governing community assembly of these microbial communities. We review important factors to consider in evaluating microbial community structure in the context of ecosystem recovery as revealed in studies of microbial succession: (1) variation in community assembly processes, (2) linkages to ecosystem function, and (3) measurable microbial community attributes. We seek to empower restoration ecology with microbial assembly and successional understandings that can generate actionable insights and vital contexts for ecosystem restoration efforts.},
}
@article {pmid36735064,
year = {2023},
author = {Tessler, M and Cunningham, SW and Ingala, MR and Warring, SD and Brugler, MR},
title = {An Environmental DNA Primer for Microbial and Restoration Ecology.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {796-808},
pmid = {36735064},
issn = {1432-184X},
mesh = {*DNA, Environmental/genetics ; DNA Primers ; DNA Barcoding, Taxonomic/methods ; Ecology ; DNA/genetics ; Environmental Monitoring ; Biodiversity ; },
abstract = {Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.},
}
@article {pmid36734313,
year = {2023},
author = {Hassan, MM and van Vliet, AHM and Higgins, O and Burke, LP and Chueiri, A and O'Connor, L and Morris, D and Smith, TJ and La Ragione, RM},
title = {Rapid culture-independent loop-mediated isothermal amplification detection of antimicrobial resistance markers from environmental water samples.},
journal = {Microbial biotechnology},
volume = {16},
number = {5},
pages = {977-989},
pmid = {36734313},
issn = {1751-7915},
mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Nucleic Acid Amplification Techniques/methods ; Escherichia coli ; Water ; Sensitivity and Specificity ; *Escherichia coli Proteins ; },
abstract = {Environmental water is considered one of the main vehicles for the transmission of antimicrobial resistance (AMR), posing an increasing threat to humans and animals health. Continuous efforts are being made to eliminate AMR; however, the detection of AMR pathogens from water samples often requires at least one culture step, which is time-consuming and can limit sensitivity. In this study, we employed comparative genomics to identify the prevalence of AMR genes within among: Escherichia coli, Klebsiella, Salmonella enterica and Acinetobacter, using publicly available genomes. The mcr-1, blaKPC (KPC-1 to KPC-4 alleles), blaOXA-48, blaOXA-23 and blaVIM (VIM-1 and VIM-2 alleles) genes are of great medical and veterinary significance, thus were selected as targets for the development of isothermal loop-mediated amplification (LAMP) detection assays. We also developed a rapid and sensitive sample preparation method for an integrated culture-independent LAMP-based detection from water samples. The developed assays successfully detected the five AMR gene markers from pond water within 1 h and were 100% sensitive and specific with a detection limit of 0.0625 μg/mL and 10 cfu/mL for genomic DNA and spiked bacterial cells, respectively. The integrated detection can be easily implemented in resource-limited areas to enhance One Health AMR surveillances and improve diagnostics.},
}
@article {pmid36728429,
year = {2023},
author = {Graffius, S and Garzón, JFG and Zehl, M and Pjevac, P and Kirkegaard, R and Flieder, M and Loy, A and Rattei, T and Ostrovsky, A and Zotchev, SB},
title = {Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris.},
journal = {Microbiology spectrum},
volume = {11},
number = {2},
pages = {e0435322},
pmid = {36728429},
issn = {2165-0497},
abstract = {Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two Streptomyces isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. IMPORTANCE A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge Spongilla lacustris to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.},
}
@article {pmid36725750,
year = {2023},
author = {Tessler, M and David, FJ and Cunningham, SW and Herstoff, EM},
title = {Rewilding in Miniature: Suburban Meadows Can Improve Soil Microbial Biodiversity and Soil Health.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1077-1086},
pmid = {36725750},
issn = {1432-184X},
mesh = {Humans ; *Soil/chemistry ; *Grassland ; Soil Microbiology ; Biodiversity ; Ecosystem ; Bacteria/genetics ; },
abstract = {Lawns are a ubiquitous, human-made environment created for human enjoyment, leisure, and aesthetics. While net positive for carbon storage, lawns can have negative environmental impacts. Lawns require frequent mowing, which produces high levels of CO2 pollution and kills off native plants. Lawn fertilizing creates its own environmental pollution. One (presumed) ecologically-friendly alternative to lawns is restoration, or rewilding, of these spaces as meadows, which need less maintenance (e.g., infrequent mowing). However, little work has compared lawns against small-scale meadows for biodiversity outside of pollinator studies. Here, we tested the hypotheses that compared to lawns, meadows have (1) unique and higher levels of soil microbial biodiversity and (2) different soil physical and chemical characteristics. We conducted bacterial (16S) and fungal (ITS2) metabarcoding, and found that both bacteria and fungi are indeed more diverse in meadows (significantly so for bacteria). Species composition between meadows and lawns was significantly different for both types of microbes, including higher levels of mycorrhizal fungi in meadows. We also found that chemistry (e.g., potassium and metrics relating to pH) differed significantly between lawns and meadows and was more optimal for plant growth in the meadows. We believe these differences are caused by the different organisms dwelling in these habitats. In summary, these findings point to notable-positive-shifts in microbial and chemical compositions within meadows, further indicating that meadow restoration benefits biodiversity and soil health.},
}
@article {pmid36725749,
year = {2023},
author = {Sullivan, TJ and Roberts, H and Bultman, TL},
title = {Genetic Covariation Between the Vertically Transmitted Endophyte Epichloë canadensis and Its Host Canada Wildrye.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1686-1695},
pmid = {36725749},
issn = {1432-184X},
mesh = {Endophytes/genetics ; Symbiosis ; *Epichloe/genetics ; Poaceae/microbiology ; *Elymus/genetics/microbiology ; },
abstract = {Symbiotic mutualisms are thought to be stabilized by correlations between the interacting genotypes which may be strengthened via vertical transmission and/or reduced genetic variability within each species. Vertical transmission, however, may weaken interactions over time as the endosymbionts would acquire mutations that could not be purged. Additionally, temporal variation in a conditional mutualism could create genetic variation and increased variation in the interaction outcome. In this study, we assessed genetic variation in both members of a symbiosis, the endosymbiotic fungal endophyte Epichloë canadensis and its grass host Canada wildrye (Elymus canadensis). Both species exhibited comparable levels of diversity, mostly within populations rather than between. There were significant differences between populations, although not in the same pattern for the two species, and the differences were not correlated with geographic distance for either species. Interindividual genetic distance matrices for the two species were significantly correlated, although all combinations of discriminant analysis of principle components (DAPC) defined multilocus genotype groups were found suggesting that strict genotype matching is not necessary. Variation in interaction outcome is common in grass/endophyte interactions, and our results suggest that the accumulation of mutations overtime combined with temporal variation in selection pressures increasing genetic variation in the symbiosis may be the cause.},
}
@article {pmid36725211,
year = {2023},
author = {Hernández-Gómez, O and Hua, J},
title = {From the organismal to biosphere levels: environmental impacts on the amphibian microbiota.},
journal = {FEMS microbiology reviews},
volume = {47},
number = {1},
pages = {},
doi = {10.1093/femsre/fuad002},
pmid = {36725211},
issn = {1574-6976},
mesh = {Animals ; *Ecosystem ; *Microbiota ; Amphibians ; Phylogeny ; },
abstract = {This review summarizes the role of environmental factors on amphibian microbiotas at the organismal, population, community, ecosystem, and biosphere levels. At the organismal-level, tissue source, disease status, and experimental manipulations were the strongest predictors of variation in amphibian microbiotas. At the population-level, habitat quality, disease status, and ancestry were commonly documented as drivers of microbiota turnover. At the community-level, studies focused on how species' niche influence microbiota structure and function. At the ecosystem-level, abiotic and biotic reservoirs were important contributors to microbiota structure. At the biosphere-level, databases, sample banks, and seminatural experiments were commonly used to describe microbiota assembly mechanisms among temperate and tropical amphibians. Collectively, our review demonstrates that environmental factors can influence microbiotas through diverse mechanisms at all biological scales. Importantly, while environmental mechanisms occurring at each of the different scales can interact to shape microbiotas, the past 10 years of research have mostly been characterized by targeted approaches at individual scales. Looking forward, efforts considering how environmental factors at multiple organizational levels interact to shape microbiota diversity and function are paramount. Generating opportunities for meaningful cross-disciplinary interactions and supporting infrastructure for research that spans biological scales are imperative to addressing this gap.},
}
@article {pmid36723682,
year = {2023},
author = {Bulannga, RB and Schmidt, S},
title = {Two Predators, One Prey - the Interaction Between Bacteriophage, Bacterivorous Ciliates, and Escherichia coli.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1620-1631},
pmid = {36723682},
issn = {1432-184X},
support = {132700//NRF/ ; },
mesh = {*Bacteriophages ; Escherichia coli ; *Ciliophora ; *Tetrahymena ; *Paramecium ; Bacteria ; },
abstract = {Bacterivorous ciliates and lytic bacteriophages are two major predators in aquatic environments, competing for the same type of prey. This study investigated the possible interaction of these different microorganisms and their influence on the activity of each other. Therefore, two bacterivorous ciliates, Paramecium sp. RB1 and Tetrahymena sp. RB2, were used as representative ciliates; a T4-like Escherichia coli targeting lytic bacteriophage as a model virus; and E. coli ATCC 25922 as a susceptible bacterial host and prey. The growth of the two ciliates with E. coli ATCC 25922 as prey was affected by the presence of phage particles. The grazing activity of the two ciliates resulted in more than a 99% reduction of the phage titer and bacterial cell numbers. However, viable phage particles were recovered from individual washed cells of the two ciliates after membrane filtration. Therefore, ciliates such as Paramecium sp. RB1 and Tetrahymena sp. RB2 can remove bacteriophages present in natural and artificial waters by ingesting the viral particles and eliminating bacterial host cells required for viral replication. The ingestion of phage particles may marginally contribute to the nutrient supply of the ciliates. However, the interaction of phage particles with ciliate cells may contribute to the transmission of bacteriophages in aquatic environments.},
}
@article {pmid36723077,
year = {2023},
author = {Lennon, JT and Frost, SDW and Nguyen, NK and Peralta, AL and Place, AR and Treseder, KK},
title = {Microbiology and Climate Change: a Transdisciplinary Imperative.},
journal = {mBio},
volume = {14},
number = {1},
pages = {e0333522},
pmid = {36723077},
issn = {2150-7511},
mesh = {*Climate Change ; *Policy ; Technology ; },
abstract = {Climate change is a complex problem involving nonlinearities and feedback that operate across scales. No single discipline or way of thinking can effectively address the climate crisis. Teams of natural scientists, social scientists, engineers, economists, and policymakers must work together to understand, predict, and mitigate the rapidly accelerating impacts of climate change. Transdisciplinary approaches are urgently needed to address the role that microorganisms play in climate change. Here, we demonstrate with case studies how diverse teams and perspectives provide climate-change insight related to the range expansion of emerging fungal pathogens, technological solutions for harmful cyanobacterial blooms, and the prediction of disease-causing microorganisms and their vector populations using massive networks of monitoring stations. To serve as valuable members of a transdisciplinary climate research team, microbiologists must reach beyond the boundaries of their immediate areas of scientific expertise and engage in efforts to build open-minded teams aimed at scalable technologies and adoptable policies.},
}
@article {pmid36722970,
year = {2023},
author = {Melnik, AV and Callewaert, C and Dorrestein, K and Broadhead, R and Minich, JJ and Ernst, M and Humphrey, G and Ackermann, G and Gathercole, R and Aksenov, AA and Knight, R and Dorrestein, PC},
title = {The Molecular Effect of Wearing Silver-Threaded Clothing on the Human Skin.},
journal = {mSystems},
volume = {8},
number = {1},
pages = {e0092222},
pmid = {36722970},
issn = {2379-5077},
support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; R01 GM107550/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Female ; Silver/analysis ; Clothing ; Skin/chemistry ; Textiles ; *Microbiota ; Bacteria/genetics ; *Propionibacteriaceae ; },
abstract = {With growing awareness that what we put in and on our bodies affects our health and wellbeing, little is still known about the impact of textiles on the human skin. Athletic wear often uses silver threading to improve hygiene, but little is known about its effect on the body's largest organ. In this study, we investigated the impact of such clothing on the skin's chemistry and microbiome. Samples were collected from different body sites of a dozen volunteers over the course of 12 weeks. The changes induced by the antibacterial clothing were specific for individuals, but more so defined by gender and body site. Unexpectedly, the microbial biomass on skin increased in the majority of the volunteers when wearing silver-threaded T-shirts. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. Both effects were mainly observed for women. The hallmark of the induced changes was an increase in the abundance of various monounsaturated fatty acids (MUFAs), especially in the upper back. Several microbe-metabolite associations were uncovered, including Cutibacterium, detected in the upper back area, which was correlated with the distribution of MUFAs, and Anaerococcus spp. found in the underarms, which were associated with a series of different bile acids. Overall, these findings point to a notable impact of the silver-threaded material on the skin microbiome and chemistry. We observed that relatively subtle changes in the microbiome result in pronounced shifts in molecular composition. IMPORTANCE The impact of silver-threaded material on human skin chemistry and microbiome is largely unknown. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. The major change was an increase in the abundance of various monounsaturated fatty acids that were also correlated with Cutibacterium. Additionally, Anaerococcus spp., found in the underarms, were associated with different bile acids in the armpit samples. Overall, the impact of the silver-threaded clothing was gender and body site specific.},
}
@article {pmid36721064,
year = {2023},
author = {van Kasteren, S and Rozen, DE},
title = {Using click chemistry to study microbial ecology and evolution.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {9},
pmid = {36721064},
issn = {2730-6151},
abstract = {Technological advances have largely driven the revolution in our understanding of the structure and function of microbial communities. Culturing, long the primary tool to probe microbial life, was supplanted by sequencing and other -omics approaches, which allowed detailed quantitative insights into species composition, metabolic potential, transcriptional activity, secretory responses and more. Although the ability to characterize "who's there" has never been easier or cheaper, it remains technically challenging and expensive to understand what the diverse species and strains that comprise microbial communities are doing in situ, and how these behaviors change through time. Our aim in this brief review is to introduce a developing toolkit based on click chemistry that can accelerate and reduce the expense of functional analyses of the ecology and evolution of microbial communities. After first outlining the history of technological development in this field, we will discuss key applications to date using diverse labels, including BONCAT, and then end with a selective (biased) view of areas where click-chemistry and BONCAT-based approaches stand to have a significant impact on our understanding of microbial communities.},
}
@article {pmid36720878,
year = {2023},
author = {Vincent, F and Gralka, M and Schleyer, G and Schatz, D and Cabrera-Brufau, M and Kuhlisch, C and Sichert, A and Vidal-Melgosa, S and Mayers, K and Barak-Gavish, N and Flores, JM and Masdeu-Navarro, M and Egge, JK and Larsen, A and Hehemann, JH and Marrasé, C and Simó, R and Cordero, OX and Vardi, A},
title = {Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {510},
pmid = {36720878},
issn = {2041-1723},
mesh = {Humans ; *Eukaryota ; Eukaryotic Cells ; Bacteria ; Carbon ; *Virus Diseases ; },
abstract = {Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global elemental cycling. Upon demise of the bloom, organic carbon is partly respired and partly transferred to either higher trophic levels, bacterial biomass production or sinking. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains largely unquantified. Here, we characterize the interplay between viral infection and the composition of a bloom-associated microbiome and consequently the evolving biogeochemical landscape, by conducting a large-scale mesocosm experiment where we monitor seven induced coccolithophore blooms. The blooms show different degrees of viral infection and reveal that only high levels of viral infection are followed by significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, upon viral infection the biomass of eukaryotic heterotrophs (thraustochytrids) rivals that of bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection causes a 2-4 fold increase in per-cell rates of extracellular carbon release in the form of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.},
}
@article {pmid36719456,
year = {2023},
author = {Lin, Z and Zheng, X and Chen, J},
title = {Deciphering pH-dependent microbial taxa and functional gene co-occurrence in the coral Galaxea fascicularis.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1856-1868},
pmid = {36719456},
issn = {1432-184X},
mesh = {Animals ; *Anthozoa/microbiology ; Seawater/microbiology ; Hydrogen-Ion Concentration ; Bacteria/genetics ; *Microbiota/genetics ; Carbon ; Coral Reefs ; },
abstract = {How the coral microbiome responds to oceanic pH changes due to anthropogenic climate change, including ocean acidification and deliberate artificial alkalization, remains an open question. Here, we applied a 16S profile and GeoChip approach to microbial taxonomic and gene functional landscapes in the coral Galaxea fascicularis under three pH levels (7.85, 8.15, and 8.45) and tested the influence of pH changes on the cell growth of several coral-associated strains and bacterial populations. Statistical analysis of GeoChip-based data suggested that both ocean acidification and alkalization destabilized functional cores related to aromatic degradation, carbon degradation, carbon fixation, stress response, and antibiotic biosynthesis in the microbiome, which are related to holobiont carbon cycling and health. The taxonomic analysis revealed that bacterial species richness was not significantly different among the three pH treatments, but the community compositions were significantly distinct. Acute seawater alkalization leads to an increase in pathogens as well as a stronger taxonomic shift than acidification, which is worth considering when using artificial ocean alkalization to protect coral ecosystems from ocean acidification. In addition, our co-occurrence network analysis reflected microbial community and functional shifts in response to pH change cues, which will further help to understand the functional ecological role of the microbiome in coral resilience.},
}
@article {pmid36717392,
year = {2023},
author = {Pavlova, ON and Tupikin, AE and Chernitsyna, SM and Bukin, YS and Lomakina, AV and Pogodaeva, TV and Nikonova, AA and Bukin, SV and Zemskaya, TI and Kabilov, MR},
title = {Description and Genomic Analysis of the First Facultatively Lithoautotrophic, Thermophilic Bacteria of the Genus Thermaerobacter Isolated from Low-temperature Sediments of Lake Baikal.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1604-1619},
pmid = {36717392},
issn = {1432-184X},
support = {0279-2021-0006//Ministry of Science and Higher Education of the Russian Federation/ ; 22-14-00084//Russian Science Foundation/ ; },
mesh = {Temperature ; *Lakes/analysis ; Sequence Analysis, DNA ; *Bacteria, Aerobic/genetics ; Genomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics/analysis ; Bacterial Typing Techniques ; },
abstract = {Members of the genus Thermaerobacter belong to the phylum Firmicutes and all isolates characterised to date are strictly aerobic and thermophilic. They were isolated from a mud sample of the Challenger Deep in the Mariana Trench, hydrothermal vents, and silt compost. A novel thermophilic, facultatively lithoautotrophic bacteria of the genus Thermaerobacter, strain PB12/4term (=VKM B-3151[T]), with a metabolism that is uncharacteristic of the type species, was isolated from low-temperature surface sediments near the Posolsk Bank methane seep, Lake Baikal, Russia. The new strain grows with molecular hydrogen as electron donor, elemental sulfur, and thiosulfate as electron acceptors, and CO2/[Formula: see text] as carbon source. The genome of strain PB12/4term consists of one chromosome with a total length of 2.820.915 bp and the G+C content of the genomic DNA was 72.2%. The phylogenomic reconstruction based on 120 conserved bacterial single-copy proteins revealed that strain PB12/4term belongs to the genus Thermaerobacter within in the class Thermaerobacteria, phylum Firmicutes_E. The strain PB12/4term is closely related to Thermaerobacter subterraneus DSM 13965 (ANI=95.08%, AF=0.91) and Thermaerobacter marianensis DSM 12885 (ANI=84.98%, AF=0.77). Genomic and experimental data confirm the ability of the Thermaerobacter PB12/4term pure culture to facultatively lithotrophic growth, which is provided by the presence of [NiFe]hydrogenase enzymes that are absent in T. marianensis DSM 12885 and T. subterraneus DSM 13965. The data obtained on the physiological and biochemical differences of strain PB12/4term provide a deeper insight into the species diversity and functional activity of the genus Thermaerobacter.},
}
@article {pmid36717391,
year = {2023},
author = {Ma, W and Lin, L and Peng, Q},
title = {Origin, Selection, and Succession of Coastal Intertidal Zone-Derived Bacterial Communities Associated with the Degradation of Various Lignocellulose Substrates.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1589-1603},
pmid = {36717391},
issn = {1432-184X},
support = {91951116//National Natural Science Foundation of China/ ; 2019YFA0606704//Key Technologies Research and Development Program of Anhui Province/ ; },
mesh = {*Lignin/metabolism ; Ecosystem ; Bacteria/metabolism ; Microbial Consortia ; *Oryza/metabolism ; },
abstract = {Terrestrial microbial consortia were reported to play fundamental roles in the global carbon cycle and renewable energy production through the breakdown of complex organic carbon. However, we have a poor understanding of how biotic/abiotic factors combine to influence consortia assembly and lignocellulose degradation in aquatic ecosystems. In this study, we used 96 in situ lignocellulose enriched, coastal intertidal zone-derived bacterial consortia as the initial inoculating consortia and developed 384 cultured consortia under different lignocellulose substrates (aspen, pine, rice straw, and purified Norway spruce lignin) with gradients of salinity and temperature. As coastal consortia, salinity was the strongest driver for assembly, followed by Norway spruce lignin, temperature, and aspen. Moreover, a conceptual model was proposed to demonstrate different succession dynamics between consortia under herbaceous and woody lignocelluloses. The succession of consortium under Norway spruce lignin is greatly related with abiotic factors, while its substrate degradation is mostly correlated with biotic factors. A discrepant pattern was observed in the consortium under rice straw. Finally, we developed four groups of versatile, yet specific consortia. Our study not only reveals that coastal intertidal wetlands are important natural resources to enrich lignocellulolytic degrading consortia but also provides insights into the succession and ecological function of coastal consortium.},
}
@article {pmid36716515,
year = {2023},
author = {Pateraki, C and Magdalinou, E and Skliros, D and Flemetakis, E and Rabaey, K and Koutinas, A},
title = {Transcriptional regulation in key metabolic pathways of Actinobacillus succinogenes in the presence of electricity.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {151},
number = {},
pages = {108376},
doi = {10.1016/j.bioelechem.2023.108376},
pmid = {36716515},
issn = {1878-562X},
mesh = {Fermentation ; *Actinobacillus/genetics/metabolism ; Metabolic Networks and Pathways ; Electricity ; },
abstract = {The potential of renewable energy application via direct electrode interaction for the production of bio-based chemicals is a promising technology. The utilization of extracellular energy in pure culture fermentations aims in intracellular redox balance regulation in order to improve fermentation efficiency. This work evaluates the impact of a bioelectrochemical system in succinic acid fermentation and the metabolic response of Actinobacillus succinogenes. The metabolic pathway regulation of A. succinogenes was evaluated via RNA expression of the key enzymes that participate in TCA cycle, pyruvate metabolism and oxidative phosphorylation. The genes that were significantly overexpressed in BES compared to non-BES were phosphoenolpyruvate carboxykinase (0.4-fold change), inorganic pyrophosphatase (2.3-fold change) and hydrogenase (2.2-fold change) and the genes that were significantly underexpressed were fumarase (-0.94-fold change), pyruvate kinase (-6.9-fold change), all subunits of fumarate reductase (-2.1 to -1.17-fold change), cytochromes I and II (-1.25 and -1.02-fold change, respectively) and two C4-carboxylic acid transporters.},
}
@article {pmid36713329,
year = {2022},
author = {Gusareva, ES and Gaultier, NE and Uchida, A and Premkrishnan, BNV and Heinle, CE and Phung, WJ and Wong, A and Lau, KJX and Yap, ZH and Koh, Y and Ang, PN and Putra, A and Panicker, D and Lee, JGH and Neves, LC and Drautz-Moses, DI and Schuster, SC},
title = {Short-range contributions of local sources to ambient air.},
journal = {PNAS nexus},
volume = {1},
number = {2},
pages = {pgac043},
pmid = {36713329},
issn = {2752-6542},
abstract = {Recent developments in aerobiology have enabled the investigation of airborne biomass with high temporal and taxonomic resolution. In this study, we assess the contributions of local sources to ambient air within a 160,000 m[2] tropical avian park (AP). We sequenced and analyzed 120 air samples from seven locations situated 160 to 400 m apart, representing distinct microhabitats. Each microhabitat contained a characteristic air microbiome, defined by the abundance and richness of its airborne microbial community members, supported by both, PCoA and Random Forest analysis. Each outdoor microhabitat contained 1% to 18.6% location-specific taxa, while a core microbiome of 27.1% of the total taxa was shared. To identify and assess local sources, we compared the AP dataset with a DVE reference dataset from a location 2 km away, collected during a year-round sampling campaign. Intersection of data from the two sites demonstrated 61.6% of airborne species originated from local sources of the AP, 34.5% from ambient air background, and only 3.9% of species were specific to the DVE reference site. In-depth taxonomic analysis demonstrated association of bacteria-dominated air microbiomes with indoor spaces, while fungi-dominated airborne microbial biomass was predominant in outdoor settings with ample vegetation. The approach presented here demonstrates an ability to identify local source contributions against an ambient air background, despite the prevailing mixing of air masses caused by atmospheric turbulences.},
}
@article {pmid36713171,
year = {2022},
author = {Zhang, X and Wang, Y and Xu, Y and Babalola, BJ and Xiang, S and Ma, J and Su, Y and Fan, Y},
title = {Stochastic processes dominate community assembly of ectomycorrhizal fungi associated with Picea crassifolia in the Helan Mountains, China.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1061819},
pmid = {36713171},
issn = {1664-302X},
abstract = {INTRODUCTION: Understanding the underlying mechanisms of microbial community assembly is a fundamental topic in microbial ecology. As an integral part of soil organisms, ectomycorrhizal (EM) fungi play vital roles in ecosystems. Picea crassifolia is an important pine species in the Helan Mountains in Inner Mongolia, China, with high ecological and economic values. However, studies of EM fungal diversity and mechanisms underlying community assembly on this pine species are limited.<br><br>METHODS: In this study, we investigated EM fungal communities associated with P. crassifolia from 45 root samples across three sites in the Helan Mountains using Illumina Miseq sequencing of the fungal rDNA ITS2 region.<br><br>RESULTS: A total of 166 EM fungal OTUs belonging to 24 lineages were identified, of which Sebacina and Tomentella-Thelephora were the most dominant lineages. Ordination analysis revealed that EM fungal communities were significantly different among the three sites. Site/fungus preference analysis showed that some abundant EM fungal OTUs preferred specific sites. Ecological process analysis implied that dispersal limitation and ecological drift in stochastic processes dominantly determined the community assembly of EM fungi.<br><br>DISCUSSION: Our study indicates that P. crassifolia harbors a high EM fungal diversity and highlights the important role of the stochastic process in driving community assembly of mutualistic fungi associated with a single plant species in a semi-arid forest in northwest China.},
}
@article {pmid36713170,
year = {2022},
author = {Lin, J and Li, G and Sun, L and Wang, S and Meng, X and Sun, L and Yuan, L and Xu, L},
title = {Varieties and ensiling: Impact on chemical composition, fermentation quality and bacterial community of alfalfa.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1091491},
pmid = {36713170},
issn = {1664-302X},
abstract = {INTRODUCTION: Six species of alfalfa commonly found in northern China were collected in the present study.<br><br>METHODS: The chemical composition and epiphytic microbial communities during the ensiling were analyzed; and their effects on fermentation quality and silage bacterial communities were assessed. The effects of physicochemical characteristics of alfalfa on the bacterial community were also investigated in terms of nutritional sources of microbial growth and reproduction.<br><br>RESULTS AND DISCUSSION: The results showed that the chemical composition was significantly different in various alfalfa varieties, yet, the dominant genera attached to each variety of alfalfa was similar, except for pantoea (p<0.05). After ensiling, both the fermentation quality and microbial community changed obviously (p<0.05). Specifically, ZM2 had lower pH and ammonia nitrogen (NH3-N) content but higher LA content than other varieties of alfalfa silage. Beneficial bacteria such as Lentilactobacillus and Lactiplantibacillus were predominant in ZM2, which accounted for the higher fermentation quality. Significant correlations between the chemical composition of silage, fermentation quality and bacterial communities composition were observed. Moreover, variations in bacteria community structure during the fermentation of alfalfa were mainly influenced by water-soluble carbohydrates (36.79%) and dry matter (21.77%).<br><br>CONCLUSION: In conclusion, this study revealed the influence of chemical composition on microbial community and fermentation quality, laying the groundwork for future studies on high-quality silage.},
}
@article {pmid36709487,
year = {2023},
author = {Stahl, LM and Olson, JB},
title = {Investigating the interactive effects of temperature, pH, and salinity on Naegleria fowleri persistence.},
journal = {The Journal of eukaryotic microbiology},
volume = {70},
number = {3},
pages = {e12964},
doi = {10.1111/jeu.12964},
pmid = {36709487},
issn = {1550-7408},
mesh = {Humans ; *Naegleria fowleri ; Temperature ; Salinity ; Sodium Chloride ; *Amebiasis ; Water ; Hydrogen-Ion Concentration ; *Central Nervous System Protozoal Infections ; },
abstract = {Naegleria fowleri causes primary amoebic meningoencephalitis, a deadly infection that occurs when free-living amoebae enter the nose via freshwater and travel to the brain. N. fowleri naturally thrives in freshwater and soil and is thought to be associated with elevated water temperatures. While environmental and laboratory studies have sought to identify what environmental factors influence its presence, many questions remain. This study investigated the interactive effects of temperature, pH, and salinity on N. fowleri in deionized and environmental waters. Three temperatures (15, 25, 35°C), pH values (6.5, 7.5, 8.5), and salinity concentrations (0.5%, 1.5%, 2.5% NaCl) were used to evaluate the growth of N. fowleri via ATP luminescent assays. Results indicated N. fowleri grew best at 25°C, and multiple interactive effects occurred between abiotic factors. Interactions varied slightly by water type but were largely driven by temperature and salinity. Lower temperature increased N. fowleri persistence at higher salinity levels, while low salinity (0.5% NaCl) supported N. fowleri growth at all temperatures. This research provided an experimental approach to assess interactive effects influencing the persistence of N. fowleri. As climate change impacts water temperatures and conditions, understanding the microbial ecology of N. fowleri will be needed minimize pathogen exposure.},
}
@article {pmid36709366,
year = {2023},
author = {Song, W and Qin, Z and Hu, X and Han, H and Li, A and Zhou, X and Li, Y and Li, R},
title = {Using Bayesian networks with Tabu-search algorithm to explore risk factors for hyperhomocysteinemia.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {1610},
pmid = {36709366},
issn = {2045-2322},
mesh = {Humans ; *Hyperhomocysteinemia ; Bayes Theorem ; Risk Factors ; Smoking ; Algorithms ; Homocysteine ; },
abstract = {Hyperhomocysteinemia (HHcy) is a condition closely associated with cardiovascular and cerebrovascular diseases. Detecting its risk factors and taking some relevant interventions still represent the top priority to lower its prevalence. Yet, in discussing risk factors, Logistic regression model is usually adopted but accompanied by some defects. In this study, a Tabu Search-based BNs was first constructed for HHcy and its risk factors, and the conditional probability between nodes was calculated using Maximum Likelihood Estimation. Besides, we tried to compare its performance with Hill Climbing-based BNs and Logistic regression model in risk factor detection and discuss its prospect in clinical practice. Our study found that Age, sex, α1-microgloblobumin to creatinine ratio, fasting plasma glucose, diet and systolic blood pressure represent direct risk factors for HHcy, and smoking, glycosylated hemoglobin and BMI constitute indirect risk factors for HHcy. Besides, the performance of Tabu Search-based BNs is better than Hill Climbing-based BNs. Accordingly, BNs with Tabu Search algorithm could be a supplement for Logistic regression, allowing for exploring the complex network relationship and the overall linkage between HHcy and its risk factors. Besides, Bayesian reasoning allows for risk prediction of HHcy, which is more reasonable in clinical practice and thus should be promoted.},
}
@article {pmid36708393,
year = {2023},
author = {Kļaviņa, D and Lione, G and Kenigsvalde, K and Pellicciaro, M and Muižnieks, I and Silbauma, L and Jansons, J and Gaitnieks, T and Gonthier, P},
title = {Host-associated Intraspecific Phenotypic Variation in the Saprobic Fungus Phlebiopsis gigantea.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1847-1855},
pmid = {36708393},
issn = {1432-184X},
support = {1.1.1.1/20/A/095//European Regional Development Fund/ ; 5-5.9.1_007q_101_21_79//JSC Latvian State Forests/ ; },
mesh = {Fungi ; *Polyporales ; *Pinus sylvestris/microbiology ; *Abies ; Biological Variation, Population ; *Picea/microbiology ; },
abstract = {Whether intraspecific phenotypic variation in saprobic fungi may be driven by the host of origin has received little attention. We addressed this issue by testing hypotheses using the model system Phlebiopsis gigantea, a wood destroying fungus associated with Picea abies and Pinus sylvestris, among others, and widely employed in practical forestry as a biological control agent. By examining approximately 60 sympatric P. gigantea isolates from both P. abies and P. sylvestris, we showed that the former grew in vitro significantly (P < 0.05) slower than the latter (average 5.56 mm/day vs. 6.84) while producing 1.8-fold significantly higher number of mitospores. An overall significant trade-off between these two phenotypic traits was detected, in particular for isolates originating from P. abies. Comparative inoculation experiments of a subsample of isolates and the assessment of mycelial growth in logs of both hosts allowed to reject the hypothesis that isolates are equally fit in terms of growth rate in wood of both hosts regardless of the host of origin. Tree models revealed that the growth rate of isolates was associated not only with the wood species in which the isolates were inoculated (P < 0.001), P. sylvestris being more rapidly colonized than P. abies, but also with the host of origin of isolates (P < 0.001). Results showed that P. gigantea isolates originating from different hosts differ phenotypically in terms of some key phenotypic traits demonstrating that a host-driven intraspecific phenotypic variation may occur in saprobic fungi.},
}
@article {pmid36708392,
year = {2023},
author = {Figueiredo, MA and da Silva, TH and Pinto, OHB and Leite, MGP and de Oliveira, FS and Messias, MCTB and Rosa, LH and Câmara, PEAS and Lopes, FAC and Kozovits, AR},
title = {Metabarcoding of Soil Fungal Communities in Rupestrian Grassland Areas Preserved and Degraded by Mining: Implications for Restoration.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1045-1055},
pmid = {36708392},
issn = {1432-184X},
mesh = {*Mycobiome ; Grassland ; Soil ; Ecosystem ; Biodiversity ; Fungi/genetics ; Soil Microbiology ; },
abstract = {Rupestrian grasslands are vegetation complexes of the Cerrado biome (Brazilian savanna), exhibiting simultaneously great biodiversity and important open-pit mining areas. There is a strong demand for the conservation of remaining areas and restoration of degraded. This study evaluated, using next-generation sequencing, the diversity and ecological aspects of soil fungal communities in ferruginous rupestrian grassland areas preserved and degraded by bauxite mining in Brazil. In the preserved and degraded area, respectively, 565 and 478 amplicon sequence variants (ASVs) were detected. Basidiomycota and Ascomycota comprised nearly 72% of the DNA, but Ascomycota showed greater abundance than Basidiomycota in the degraded area (64% and 10%, respectively). In the preserved area, taxa of different hierarchical levels (Agaromycetes, Agaricales, Mortierelaceae, and Mortierella) associated with symbiosis and decomposition were predominant. However, taxa that colonize environments under extreme conditions and pathogens (Dothideomycetes, Pleoporales, Pleosporaceae, and Curvularia) prevailed in the degraded area. The degradation reduced the diversity, and modified the composition of taxa and predominant ecological functions in the community. The lack of fungi that facilitate plant establishment and development in the degraded area suggests the importance of seeking the restoration of this community to ensure the success of the ecological restoration of the environment. The topsoil of preserved area can be a source of inocula of several groups of fungi important for the restoration process but which occur in low abundance or are absent in the degraded area.},
}
@article {pmid36707764,
year = {2023},
author = {Pantoja-Feliciano, IG and Karl, JP and Perisin, M and Doherty, LA and McClung, HL and Armstrong, NJ and Renberg, R and Racicot, K and Branck, T and Arcidiacono, S and Soares, JW},
title = {In vitro gut microbiome response to carbohydrate supplementation is acutely affected by a sudden change in diet.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {32},
pmid = {36707764},
issn = {1471-2180},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Diet ; Feces/microbiology ; Carbohydrates ; Starch/metabolism ; Dietary Supplements ; },
abstract = {BACKGROUND: Interactions between diet, stress and the gut microbiome are of interest as a means to modulate health and performance. Here, in vitro fermentation was used to explore the effects of a sudden change in diet, 21 days sole sustenance on the Meal, Ready-to-Eat (MRE) U.S. military combat ration, on inter-species competition and functional potential of the human gut microbiota. Human fecal samples collected before and after MRE intervention or consuming a habitual diet (HAB) were introduced to nutrient-rich media supplemented with starch for in vitro fermentation under ascending colon conditions. 16S rRNA amplicon and Whole-metagenome sequencing (WMS) were used to measure community composition and functional potential. Specific statistical analyses were implemented to detect changes in relative abundance from taxa, genes and pathways.<br><br>RESULTS: Differential changes in relative abundance of 11 taxa, Dorea, Lachnospira, Bacteroides fragilis, Akkermansia muciniphila, Bifidobacterium adolescentis, Betaproteobacteria, Enterobacteriaceae, Bacteroides egerthii, Ruminococcus bromii, Prevotella, and Slackia, and nine Carbohydrate-Active Enzymes, specifically GH13_14, over the 24&#xa0;h fermentation were observed as a function of the diet intervention and correlated to specific taxa of interest.<br><br>CONCLUSIONS: These findings suggest that consuming MRE for 21&#xa0;days acutely effects changes in gut microbiota structure in response to carbohydrate but may induce alterations in metabolic capacity. Additionally, these findings demonstrate the potential of starch as a candidate supplemental strategy to functionally modulate specific gut commensals during stress-induced states.},
}
@article {pmid36706488,
year = {2023},
author = {Veloso, S and Amouroux, D and Lanceleur, L and Cagnon, C and Monperrus, M and Deborde, J and Laureau, CC and Duran, R},
title = {Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments.},
journal = {Journal of hazardous materials},
volume = {448},
number = {},
pages = {130858},
doi = {10.1016/j.jhazmat.2023.130858},
pmid = {36706488},
issn = {1873-3336},
mesh = {*Geologic Sediments/chemistry ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Rivers/microbiology ; Metals/toxicity ; Estuaries ; Pharmaceutical Preparations ; },
abstract = {The fluctuation of environmental conditions drives the structure of microbial communities in estuaries, highly dynamic ecosystems. Microorganisms inhabiting estuarine sediments play a key role in ecosystem functioning. They are well adapted to the changing conditions, also threatened by the presence of pollutants. In order to determine the environmental characteristics driving the organization of the microbial assemblages, we conducted a seasonal survey along the Adour Estuary (Bay of Biscay, France) using 16S rRNA gene Illumina sequencing. Microbial diversity data were combined with a set of chemical analyses targeting metals and pharmaceuticals. Microbial communities were largely dominated by Proteobacteria (41 %) and Bacteroidota (32 %), showing a strong organization according to season, with an important shift in winter. The composition of microbial communities showed spatial distribution according to three main areas (upstream, middle, and downstream estuary) revealing the influence of the Adour River. Further analyses indicated that the microbial community was influenced by biogeochemical parameters (Corg/Norg and δ[13]C) and micropollutants, including metals (As, Cu, Mn, Sn, Ti, and Zn) and pharmaceuticals (norfloxacin, oxolinic acid and trimethoprim). Network analysis revealed specific modules, organized around keystone taxa, linked to a pollutant type, providing information of paramount importance to understand the microbial ecology in estuarine ecosystems.},
}
@article {pmid36705425,
year = {2023},
author = {Birzle, C and Schrader, H and Blutke, A and Ferling, H and Scholz-Göppel, K and Wanke, R and Schwaiger, J},
title = {Detection of Diclofenac-Induced Alterations in Rainbow Trout (Oncorhynchus mykiss) Using Quantitative Stereological Methods.},
journal = {Environmental toxicology and chemistry},
volume = {42},
number = {4},
pages = {859-872},
doi = {10.1002/etc.5573},
pmid = {36705425},
issn = {1552-8618},
support = {76e0100000123//Bavarian State Ministry for the Environment and Health (STMUV), Munich/ ; },
mesh = {Male ; Animals ; Diclofenac/toxicity ; *Oncorhynchus mykiss ; Reproducibility of Results ; Anti-Inflammatory Agents, Non-Steroidal/toxicity ; Kidney ; *Water Pollutants, Chemical/analysis ; Gills ; },
abstract = {In 2013, the nonsteroidal anti-inflammatory drug diclofenac (DCF) was included in the watch list for emerging pollutants under the European Union Water Framework Directive. Frequently, monitoring data revealed DCF concentrations in surface waters exceeding the proposed environmental quality standards of 0.04 µg L[-1] and 0.126 µg L[-1] . In recent literature, the possible effects of DCF on fish are discussed controversially. To contribute to a realistic risk assessment of DCF, a 28-day exposure experiment was carried on rainbow trout (Oncorhynchus mykiss). To warrant reliability of data, experiments were conducted considering the Criteria for Reporting and Evaluating Ecotoxicity Data. The test concentrations of DCF used (0.1, 0.5, 1, 5, 25, and 100 µg L[-1]) also included environmentally relevant concentrations. The lowest-observed-effect concentration (LOEC) for a significant decrease in the plasma concentrations of the DCF biomarker prostaglandin E2 was 0.5 µg L[-1] (male fish). For objective evaluation of relevant histomorphological parameters of gills and trunk kidneys, unbiased quantitative stereological methods were applied. In the gills, significant increases in the thickness of the secondary lamella and in the true harmonic mean of barrier thickness in secondary lamellae were present at DCF concentrations of 25 µg L[-1] and 100 µg L[-1] . In the trunk kidneys, the absolute and relative volumes of nephrons were significantly decreased, paralleled by a significant increase of the volume of the interstitial renal tissue. With regard to quantitative histomorphological alterations in the trunk kidney, the observed LOEC was 0.5 µg L[-1] . The quantitative histomorphological analyses that were conducted allow identification and objective quantification of even subtle but significant morphological effects and thus provide an important contribution for the comparability of study results for the determination of no-observed-effect concentrations (NOEC). Environ Toxicol Chem 2023;42:859-872. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.},
}
@article {pmid36702929,
year = {2023},
author = {Li, T and Wang, X and Wang, X and Huang, J and Shen, L},
title = {Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1829-1846},
pmid = {36702929},
issn = {1432-184X},
support = {KZ201810028047//Beijing Natural Science Fund-Beijing Municipal Education Commission jointly funded key projects/ ; 41271495//National Natural Science Foundation of China/ ; },
mesh = {*Nitrification ; Ammonia ; Oxidation-Reduction ; Soil Microbiology ; Archaea/genetics ; *Microbiota ; Nitrogen ; Soil/chemistry ; Phylogeny ; },
abstract = {The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4[+] content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.},
}
@article {pmid36701921,
year = {2023},
author = {Onyango, SO and Beerens, K and Li, Q and Van Camp, J and Desmet, T and Van de Wiele, T},
title = {Glycosidic linkage of rare and new-to-nature disaccharides reshapes gut microbiota in vitro.},
journal = {Food chemistry},
volume = {411},
number = {},
pages = {135440},
doi = {10.1016/j.foodchem.2023.135440},
pmid = {36701921},
issn = {1873-7072},
mesh = {*Trehalose ; *Gastrointestinal Microbiome ; Glycosides ; RNA, Ribosomal, 16S ; Disaccharides/pharmacology ; Bacteria/genetics ; Glucosides ; },
abstract = {The impact of glycosidic linkage of seven rare and new-to-nature disaccharides on gut bacteria was assessed in vitro. The community shift of the inocula from four donors in response to 1 % (w/v) disaccharide supplementation was captured by sequencing the 16S rRNA gene. A significant loss of bacterial alpha diversity, short lag time, low pH, and high total short-chain fatty acid displayed a faster fermentation of trehalose(Glc-α1,1α-Glc) and fibrulose(fructan, DP2-10). Bacteroides reduced in relative abundance under disaccharide supplementation suggesting a loss in complex carbohydrates metabolizing capacity. Fibrulose and l-arabinose glucoside(Glc-α1,3-l-Ara) significantly stimulated bifidobacteria but was suppressed with trehalose, ribose glucoside(Glc-α1,2-Rib), and 4'-epitrehalose(Glc-α1,1α-Gal) supplementation. Albeit insignificant, bifidobacteria increased with 4'-epikojibiose(Glc-α1,2-Gal), nigerose(Glc-α1,3-Glc), and kojibiose(Glc-α1,2-Glc). Prior conditioning of inoculum in kojibiose medium profoundly induced bifidobacteria by 44 % and 55 % upon reinoculation into kojibiose and fibrulose-supplemented media respectively. This study has demonstrated the importance of the disaccharide structure-function relationship in driving the gut bacterial community.},
}
@article {pmid36700533,
year = {2023},
author = {Palau, J and Trueba-Santiso, A and Yu, R and Mortan, SH and Shouakar-Stash, O and Freedman, DL and Wasmund, K and Hunkeler, D and Marco-Urrea, E and Rosell, M},
title = {Dual C-Br Isotope Fractionation Indicates Distinct Reductive Dehalogenation Mechanisms of 1,2-Dibromoethane in Dehalococcoides- and Dehalogenimonas-Containing Cultures.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {5},
pages = {1949-1958},
pmid = {36700533},
issn = {1520-5851},
mesh = {Carbon Isotopes/analysis/metabolism ; *Dehalococcoides/metabolism ; *Ethylene Dibromide ; Organic Chemicals ; Biodegradation, Environmental ; Chemical Fractionation ; },
abstract = {Brominated organic compounds such as 1,2-dibromoethane (1,2-DBA) are highly toxic groundwater contaminants. Multi-element compound-specific isotope analysis bears the potential to elucidate the biodegradation pathways of 1,2-DBA in the environment, which is crucial information to assess its fate in contaminated sites. This study investigates for the first time dual C-Br isotope fractionation during in vivo biodegradation of 1,2-DBA by two anaerobic enrichment cultures containing organohalide-respiring bacteria (i.e., either Dehalococcoides or Dehalogenimonas). Different εbulk[C] values (-1.8 ± 0.2 and -19.2 ± 3.5‰, respectively) were obtained, whereas their respective εbulk[Br] values were lower and similar to each other (-1.22 ± 0.08 and -1.2 ± 0.5‰), leading to distinctly different trends (ΛC-Br = Δδ[13]C/Δδ[81]Br ≈ εbulk[C]/εbulk[Br]) in a dual C-Br isotope plot (1.4 ± 0.2 and 12 ± 4, respectively). These results suggest the occurrence of different underlying reaction mechanisms during enzymatic 1,2-DBA transformation, that is, concerted dihaloelimination and nucleophilic substitution (SN2-reaction). The strongly pathway-dependent ΛC-Br values illustrate the potential of this approach to elucidate the reaction mechanism of 1,2-DBA in the field and to select appropriate εbulk[C] values for quantification of biodegradation. The results of this study provide valuable information for future biodegradation studies of 1,2-DBA in contaminated sites.},
}
@article {pmid36700061,
year = {2023},
author = {Sathiananthamoorthy, S and Florman, K and Richard, D and Cheng, KK and Torri, V and McCaig, F and Harber, M and Rohn, JL},
title = {Application of Various Techniques to Gain Insights Into the Complex Urinary Tract Microbial Communities of Renal Transplant Recipients.},
journal = {Transplantation direct},
volume = {9},
number = {2},
pages = {e1418},
pmid = {36700061},
issn = {2373-8731},
abstract = {UNLABELLED: Urinary tract infections (UTIs) are prevalent in renal transplant (RTX) recipients and associated with worse outcomes. Early detection by sensitive diagnostic tests and appropriate treatment strategies in this cohort is therefore crucial, but evidence has shown that current methods may miss genuine infections. Research has shed light on the urinary tract microbial ecology of healthy individuals and nontransplant patients with UTI, but information on the RTx cohort is scant. We conducted a cross-sectional study to (i) compare the gold standard diagnostic culture with alternative techniques and (ii) characterize RTx patient urinary microbial communities.<br><br>METHODS: Midstream urine specimens were collected from 51 RTx patients attending a renal transplant clinic and 27 asymptomatic controls. Urinary microscopy, dipstick, and routine culture were performed. To improve sensitivity of microbial detection, we cultured the urinary cell sediment and performed 16S rRNA gene sequencing on urine. Uroplakin-positive urothelial cells shed in urine were analyzed by immunofluorescence staining for any bacterial association.<br><br>RESULTS: Sediment culture and 16S rRNA sequencing confirmed detection deficiencies of diagnostic culture and revealed differences in the urobiomes of RTx patients and controls. Specifically, Gardnerella, Escherichia, and Lactobacillus were most abundant in patients, whereas Lactobacillus, Streptococcus, and Gardnerella were most abundant in controls. The application of both culture and sequencing provided a more nuanced view of the urinary microbial communities.<br><br>CONCLUSIONS: This study provides insight into the potential problems of diagnostic culture within RTx patients and sheds light on their urinary microbial inhabitants. Further work may identify key microbial signatures and facilitate the development of better tools for UTI detection within this cohort, which could allow targeted intervention before an infection leads to serious consequences. http://links.lww.com/TXD/A479.},
}
@article {pmid36699726,
year = {2022},
author = {Shen, Y and Yu, F and Qiu, L and Gao, M and Xu, P and Zhang, L and Liao, X and Wang, M and Hu, X and Sun, Y and Pan, Y},
title = {Ecological influence by colonization of fluoride-resistant Streptococcus mutans in oral biofilm.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1106392},
pmid = {36699726},
issn = {2235-2988},
mesh = {Humans ; *Streptococcus mutans ; Fluorides/pharmacology ; In Situ Hybridization, Fluorescence ; *Dental Caries ; RNA, Ribosomal, 16S/genetics ; Biofilms ; },
abstract = {BACKGROUND: Dental caries is one of the oldest and most common infections in humans. Improved oral hygiene practices and the presence of fluoride in dentifrices and mouth rinses have greatly reduced the prevalence of dental caries. However, increased fluoride resistance in microbial communities is concerning. Here, we studied the effect of fluoride-resistant Streptococcus mutans (S. mutans) on oral microbial ecology and compare it with wild-type S. mutans in vitro.<br><br>METHODS: Biofilm was evaluated for its polysaccharide content, scanning electron microscopy (SEM) imaging, acid-producing ability, and related lactic dehydrogenase (LDH), arginine deiminase (ADS), and urease enzymatic activity determination. Fluorescence in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (qRT-PCR) were used to evaluate the S. mutans ratio within the biofilm. It was followed by 16S rRNA sequencing to define the oral microbial community.<br><br>RESULTS: Fluoride-resistant S. mutans produced increased polysaccharides in presence of NaF (P < 0.05). The enzymatic activities related to both acid and base generation were less affected by the fluoride. In presence of 275 ppm NaF, the pH in the fluoride-resistant strain sample was lower than the wild type. We observed that with the biofilm development and accumulative fluoride concentration, the fluoride-resistant strain had positive relationships with other bacteria within the oral microbial community, which enhanced its colonization and survival. Compared to the wild type, fluoride-resistant strain significantly increased the diversity and difference of oral microbial community at the initial stage of biofilm formation (4 and 24 h) and at a low fluoride environment (0 and 275 ppm NaF) (P < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that fluoride-resistant strain enhanced the metabolic pathways and glucose transfer.<br><br>CONCLUSIONS: Fluoride-resistant S. mutans affected the microecological balance of oral biofilm and its cariogenic properties in vitro, indicating its negative impact on fluoride's caries prevention effect.},
}
@article {pmid36699674,
year = {2022},
author = {Siddiqui, JA and Fan, R and Naz, H and Bamisile, BS and Hafeez, M and Ghani, MI and Wei, Y and Xu, Y and Chen, X},
title = {Insights into insecticide-resistance mechanisms in invasive species: Challenges and control strategies.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {1112278},
pmid = {36699674},
issn = {1664-042X},
abstract = {Threatening the global community is a wide variety of potential threats, most notably invasive pest species. Invasive pest species are non-native organisms that humans have either accidentally or intentionally spread to new regions. One of the most effective and first lines of control strategies for controlling pests is the application of insecticides. These toxic chemicals are employed to get rid of pests, but they pose great risks to people, animals, and plants. Pesticides are heavily used in managing invasive pests in the current era. Due to the overuse of synthetic chemicals, numerous invasive species have already developed resistance. The resistance development is the main reason for the failure to manage the invasive species. Developing pesticide resistance management techniques necessitates a thorough understanding of the mechanisms through which insects acquire insecticide resistance. Insects use a variety of behavioral, biochemical, physiological, genetic, and metabolic methods to deal with toxic chemicals, which can lead to resistance through continuous overexpression of detoxifying enzymes. An overabundance of enzymes causes metabolic resistance, detoxifying pesticides and rendering them ineffective against pests. A key factor in the development of metabolic resistance is the amplification of certain metabolic enzymes, specifically esterases, Glutathione S-transferase, Cytochromes p450 monooxygenase, and hydrolyses. Additionally, insect guts offer unique habitats for microbial colonization, and gut bacteria may serve their hosts a variety of useful services. Most importantly, the detoxification of insecticides leads to resistance development. The complete knowledge of invasive pest species and their mechanisms of resistance development could be very helpful in coping with the challenges and effectively developing effective strategies for the control of invasive species. Integrated Pest Management is particularly effective at lowering the risk of chemical and environmental contaminants and the resulting health issues, and it may also offer the most effective ways to control insect pests.},
}
@article {pmid36698845,
year = {2022},
author = {Song, W and Liu, Y and Qiu, L and Qing, J and Li, A and Zhao, Y and Li, Y and Li, R and Zhou, X},
title = {Machine learning-based warning model for chronic kidney disease in individuals over 40 years old in underprivileged areas, Shanxi Province.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {930541},
pmid = {36698845},
issn = {2296-858X},
abstract = {INTRODUCTION: Chronic kidney disease (CKD) is a progressive disease with high incidence but early imperceptible symptoms. Since China's rural areas are subject to inadequate medical check-ups and single disease screening programme, it could easily translate into end-stage renal failure. This study aimed to construct an early warning model for CKD tailored to impoverished areas by employing machine learning (ML) algorithms with easily accessible parameters from ten rural areas in Shanxi Province, thereby, promoting a forward shift of treatment time and improving patients' quality of life.<br><br>METHODS: From April to November 2019, CKD opportunistic screening was carried out in 10 rural areas in Shanxi Province. First, general information, physical examination data, blood and urine specimens were collected from 13,550 subjects. Afterward, feature selection of explanatory variables was performed using LASSO regression, and target datasets were balanced using the SMOTE (synthetic minority over-sampling technique) algorithm, i.e., albuminuria-to-creatinine ratio (ACR) and &#x3b1;1-microglobulin-to-creatinine ratio (MCR). Next, Bagging, Random Forest (RF) and eXtreme Gradient Boosting (XGBoost) were employed for classification of ACR outcomes and MCR outcomes, respectively.<br><br>RESULTS: 12,330 rural residents were included in this study, with 20 explanatory variables. The cases with increased ACR and increased MCR represented 1,587 (12.8%) and 1,456 (11.8%), respectively. After conducting LASSO, 14 and 15 explanatory variables remained in these two datasets, respectively. Bagging, RF, and XGBoost performed well in classification, with the AUC reaching 0.74, 0.87, 0.87, 0.89 for ACR outcomes and 0.75, 0.88, 0.89, 0.90 for MCR outcomes. The five variables contributing most to the classification of ACR outcomes and MCR outcomes constituted SBP, TG, TC, and Hcy, DBP and age, TG, SBP, Hcy and FPG, respectively. Overall, the machine learning algorithms could emerge as a warning model for CKD.<br><br>CONCLUSION: ML algorithms in conjunction with rural accessible indexes boast good performance in classification, which allows for an early warning model for CKD. This model could help achieve large-scale population screening for CKD in poverty-stricken areas and should be promoted to improve the quality of life and reduce the mortality rate.},
}
@article {pmid37938751,
year = {2022},
author = {Jia, X and Dini-Andreote, F and Salles, JF},
title = {Unravelling the interplay of ecological processes structuring the bacterial rare biosphere.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {96},
pmid = {37938751},
issn = {2730-6151},
abstract = {Most ecological communities harbor many rare species (i.e., the rare biosphere), however, relatively little is known about how distinct ecological processes structure their existence. Here, we used spatiotemporal data on soil bacterial communities along a natural ecosystem gradient to model the relative influences of assembly processes structuring the rare and common biospheres. We found a greater influence of homogeneous selection (i.e., imposed by spatiotemporally constant variables) mediating the assembly of the rare biosphere, whereas the common biosphere was mostly governed by variable selection (i.e., imposed by spatial and/or temporal fluctuating variables). By partitioning the different types of rarity, we found homogeneous selection to explain the prevalence of permanently rare taxa, thus suggesting their persistence at low abundances to be restrained by physiological traits. Conversely, the dynamics of conditionally rare taxa were mostly structured by variable selection, which aligns with the ability of these taxa to switch between rarity and commonness as responses to environmental spatiotemporal variations. Taken together, our study contributes to the establishment of a link between conceptual and empirical developments in the ecology of the soil microbial rare biosphere. Besides, this study provides a framework to better understand, model, and predict the existence and dynamics of microbial rare biospheres across divergent systems and scales.},
}
@article {pmid37938754,
year = {2022},
author = {Díaz Rodríguez, CA and Díaz-García, L and Bunk, B and Spröer, C and Herrera, K and Tarazona, NA and Rodriguez-R, LM and Overmann, J and Jiménez, DJ},
title = {Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {89},
pmid = {37938754},
issn = {2730-6151},
abstract = {The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.},
}
@article {pmid37938693,
year = {2022},
author = {Zauner, S and Vogel, M and Polzin, J and Yuen, B and Mußmann, M and El-Hacen, EM and Petersen, JM},
title = {Microbial communities in developmental stages of lucinid bivalves.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {56},
pmid = {37938693},
issn = {2730-6151},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 31010/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Bivalves from the family Lucinidae host sulfur-oxidizing bacterial symbionts, which are housed inside specialized gill epithelial cells and are assumed to be acquired from the environment. However, little is known about the Lucinidae life cycle and symbiont acquisition in the wild. Some lucinid species broadcast their gametes into the surrounding water column, however, a few have been found to externally brood their offspring by the forming gelatinous egg masses. So far, symbiont transmission has only been investigated in one species that reproduces via broadcast spawning. Here, we show that the lucinid Loripes orbiculatus from the West African coast forms egg masses and these are dominated by diverse members of the Alphaproteobacteria, Clostridia, and Gammaproteobacteria. The microbial communities of the egg masses were distinct from those in the environments surrounding lucinids, indicating that larvae may shape their associated microbiomes. The gill symbiont of the adults was undetectable in the developmental stages, supporting horizontal transmission of the symbiont with environmental symbiont acquisition after hatching from the egg masses. These results demonstrate that L. orbiculatus acquires symbionts from the environment independent of the host's reproductive strategy (brooding or broadcast spawning) and reveal previously unknown associations with microbes during lucinid early development.},
}
@article {pmid37938753,
year = {2022},
author = {Alcolombri, U and Pioli, R and Stocker, R and Berry, D},
title = {Single-cell stable isotope probing in microbial ecology.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {55},
pmid = {37938753},
issn = {2730-6151},
support = {P 27831/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.},
}
@article {pmid37938683,
year = {2022},
author = {Marasco, R and Fusi, M and Ramond, JB and Van Goethem, MW and Seferji, K and Maggs-Kölling, G and Cowan, DA and Daffonchio, D},
title = {The plant rhizosheath-root niche is an edaphic "mini-oasis" in hyperarid deserts with enhanced microbial competition.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {47},
pmid = {37938683},
issn = {2730-6151},
abstract = {Plants have evolved unique morphological and developmental adaptations to cope with the abiotic stresses imposed by (hyper)arid environments. Such adaptations include the formation of rhizosheath-root system in which mutualistic plant-soil microbiome associations are established: the plant provides a nutrient-rich and shielded environment to microorganisms, which in return improve plant-fitness through plant growth promoting services. We hypothesized that the rhizosheath-root systems represent refuge niches and resource islands for the desert edaphic microbial communities. As a corollary, we posited that microorganisms compete intensively to colonize such "oasis" and only those beneficial microorganisms improving host fitness are preferentially selected by plant. Our results show that the belowground rhizosheath-root micro-environment is largely more hospitable than the surrounding gravel plain soil with higher nutrient and humidity contents, and cooler temperatures. By combining metabarcoding and shotgun metagenomics, we demonstrated that edaphic microbial biomass and community stability increased from the non-vegetated soils to the rhizosheath-root system. Concomitantly, non-vegetated soil communities favored autotrophy lifestyle while those associated with the plant niches were mainly heterotrophs and enriched in microbial plant growth promoting capacities. An intense inter-taxon microbial competition is involved in the colonization and homeostasis of the rhizosheath zone, as documented by significant enrichment of antibiotic resistance genes and CRISPR-Cas motifs. Altogether, our results demonstrate that rhizosheath-root systems are "edaphic mini-oases" and microbial diversity hotspots in hyperarid deserts. However, to colonize such refuge niches, the desert soil microorganisms compete intensively and are therefore prepared to outcompete potential rivals.},
}
@article {pmid37938286,
year = {2022},
author = {Yeh, YC and Fuhrman, JA},
title = {Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {36},
pmid = {37938286},
issn = {2730-6151},
support = {1737409//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 3779//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 549943//Simons Foundation/ ; },
abstract = {Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005-2018), using SSU rRNA gene sequencing from two size fractions (0.2-1 and 1-80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46-93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships.},
}
@article {pmid37938248,
year = {2022},
author = {Song, J and Beule, L and Jongmans-Hochschulz, E and Wichels, A and Gerdts, G},
title = {The travelling particles: community dynamics of biofilms on microplastics transferred along a salinity gradient.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {35},
pmid = {37938248},
issn = {2730-6151},
support = {03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
abstract = {Microplastics (MP), as novel substrata for microbial colonization within aquatic ecosystems, are a matter of growing concern due to their potential to propagate foreign or invasive species across different environments. MP are known to harbour a diversity of microorganisms, yet little is understood of the dynamics of their biofilms and their capacity to successfully displace these microorganisms across different aquatic ecosystems typically marked by steep salinity gradients. To address this, we performed an in situ sequential incubation experiment to simulate MP transport from riverine to coastal seawaters using synthetic (high-density polyethylene, HDPE and tyre wear, TW) and natural (Wood) substrata. Bacterial communities on incubated particles were compared to each other as well as to those in surrounding waters, and their dynamics along the gradient investigated. All communities differed significantly from each other in their overall structure along the salinity gradient and were shaped by different ecological processes. While HDPE communities were governed by environmental selection, those on TW and Wood were dominated by stochastic events of dispersal and drift. Upon transfer into coastal seawaters, an almost complete turnover was observed among HDPE and TW communities. While synthetic particles displaced a minor proportion of communities across the salinity gradient, some of these comprised putatively pathogenic and resistant taxa. Our findings present an extensive assessment of MP biofilms and their dynamics upon displacement across different aquatic systems, presenting new insights into the role of MP as transport vectors.},
}
@article {pmid37938679,
year = {2022},
author = {Junkins, EN and McWhirter, JB and McCall, LI and Stevenson, BS},
title = {Environmental structure impacts microbial composition and secondary metabolism.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {15},
pmid = {37938679},
issn = {2730-6151},
support = {80NSSC19K0479//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19K0479//National Aeronautics and Space Administration (NASA)/ ; },
abstract = {Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.},
}
@article {pmid37938685,
year = {2022},
author = {Jiang, G and Zhang, Y and Gan, G and Li, W and Wan, W and Jiang, Y and Yang, T and Zhang, Y and Xu, Y and Wang, Y and Shen, Q and Wei, Z and Dini-Andreote, F},
title = {Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {10},
pmid = {37938685},
issn = {2730-6151},
abstract = {The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.},
}
@article {pmid38089065,
year = {2022},
author = {Berkhout, M and Zoetendal, E and Plugge, C and Belzer, C},
title = {Use of synthetic communities to study microbial ecology of the gut.},
journal = {Microbiome research reports},
volume = {1},
number = {1},
pages = {4},
pmid = {38089065},
issn = {2771-5965},
abstract = {The application of in vitro synthetic microbial communities is an excellent approach to model the ecological interactions between microbes in the human gastrointestinal tract. Although DNA-based studies have provided a wealth of information, they do not consider the ecological properties of the human gut microbiota. Ecological interactions between gut microbes of interest can be studied by applying synthetic communities. This review describes the considerations that should be taken into account when constructing a synthetic community by discussing example research questions that can be answered by using a synthetic microbial community, the choice of microbial species, the growth conditions, possible reactor setups, and the parameters to analyze.},
}
@article {pmid37091220,
year = {2022},
author = {Obase, K},
title = {Morphological characteristics of ectomycorrhizas formed by in vitro synthesis between conifer seedlings and Tuber mycelial strains of the Puberulum clade isolated in Japan.},
journal = {Mycoscience},
volume = {63},
number = {1},
pages = {39-44},
pmid = {37091220},
issn = {1340-3540},
abstract = {Seedlings of Pinus densiflora and Abies sachalinensis were inoculated with Tuber mycelial strains of the Puberulum clade in vitro to examine the morphological characteristics of their ectomycorrhizas. Axenically germinated seedlings were inoculated with the mycelia of five taxa from the Puberulum clade and grown in glass jars for 4 mo in an illuminated incubator. The seedlings were successfully colonized by the inoculated Tuber strains, as confirmed by the nuclear ribosomal internal transcribed spacer barcoding of the synthesized ectomycorrhizas. The ectomycorrhizas were characterized by a pale yellow to brown color, short needle-shaped cystidia, and net-like hyphal arrangement, and epidermoid cells on the mantle surface; notably, these features are similar to the ectomycorrhizas of various Puberulum clade members. As the ectomycorrhizas of different Tuber species are indistinguishable by morphological characters, molecular techniques are necessary to identify ectomycorrhizas formed by Tuber species within the Puberulum clade.},
}
@article {pmid37744128,
year = {2021},
author = {Otto, EC and Held, BW and Gould, TJ and Blanchette, RA},
title = {Fungal Diversity in Multiple Post-harvest Aged Red Pine Stumps and Their Potential Influence on Heterobasidion Root Rot in Managed Stands Across Minnesota.},
journal = {Frontiers in fungal biology},
volume = {2},
number = {},
pages = {782181},
pmid = {37744128},
issn = {2673-6128},
abstract = {Thinning operations that occur in managed red pine (Pinus resinosa) stands, create tree stumps that can serve as a habitat for fungi, especially Heterobasidion irregulare, the cause of a serious root disease. Different fungi can colonize stumps early and the community of fungi can change over time as initial fungal species become replaced. Samples were collected from both the native and non-native range of red pine from stumps that were cut at different time periods. Stumps that were harvested at 0-1, 2-3, 5-6, and 10-12 years before sampling were used to provide data on the diversity of fungi that colonize tree stumps and how these communities can change over time as well as how they influence colonization of H. irregulare. Traditional culturing methods and Illumina MiSeq sequencing were used to identify the fungi in the samples. Of particular interest was Phlebiopsis gigantea, which can colonize cut stumps and prevent H. irregulare from becoming established. Overall, P. gigantea was the most abundant fungus isolated and sequenced via Illumina MiSeq. Results show that Phlebiopsis gigantea was isolated from 90% of all stumps sampled for sites harvested within 3 years of sampling in the native range of red pine compared to 33% in the non-native range. For Illumina MiSeq, 5,940 total amplicon sequence variants (ASVs) were detected. P. gigantea represented 14% of the total reads and composed 19% of the reads in the native range and 8% in non-native range of red pine. Furthermore, P. gigantea represented 38% of the reads for stumps that were harvested within 3 years of sampling in the native range of red pine compared to 14% in the non-native range. These results help demonstrate that a higher amount of P. gigantea is present in the native range of red pine and could be acting as a native biological control agent. Additional fungi, including Resinicium bicolor, Hypochnicium cremicolor, Leptographium spp., and others identified at different cutting times are also discussed. Finally, different diversity indices revealed similar, but slightly higher diversity for southern sites via Shannon and Simpson Diversity indices. Beta diversity demonstrated a similar species composition in stumps harvested at different times with these stumps being grouped together based on harvesting years.},
}
@article {pmid36765158,
year = {2021},
author = {Nuccio, EE and Nguyen, NH and Nunes da Rocha, U and Mayali, X and Bougoure, J and Weber, PK and Brodie, E and Firestone, M and Pett-Ridge, J},
title = {Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {72},
pmid = {36765158},
issn = {2730-6151},
support = {SCW1711//DOE | SC | Biological and Environmental Research (BER)/ ; DE-SC0010570//DOE | SC | Biological and Environmental Research (BER)/ ; DE-SC0016247//DOE | SC | Biological and Environmental Research (BER)/ ; DE-SC0020163//DOE | SC | Biological and Environmental Research (BER)/ ; SCW1421//DOE | SC | Biological and Environmental Research (BER)/ ; SCW1589//DOE | SC | Biological and Environmental Research (BER)/ ; SCW1678//DOE | SC | Biological and Environmental Research (BER)/ ; },
abstract = {Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis ("community RNA-Seq") and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in [13]CO2-labeled microcosms amended with [15]N-root litter to identify the preferences of rhizosphere organisms for root exudates ([13]C) versus decaying root biomass ([15]N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group's more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.},
}
@article {pmid37693795,
year = {2021},
author = {Crous, PW and Osieck, ER and Jurjević, &#x17d; and Boers, J and van Iperen, AL and Starink-Willemse, M and Dima, B and Balashov, S and Bulgakov, TS and Johnston, PR and Morozova, OV and Pinruan, U and Sommai, S and Alvarado, P and Decock, CA and Lebel, T and McMullan-Fisher, S and Moreno, G and Shivas, RG and Zhao, L and Abdollahzadeh, J and Abrinbana, M and Ageev, DV and Akhmetova, G and Alexandrova, AV and Altés, A and Amaral, AGG and Angelini, C and Antonín, V and Arenas, F and Asselman, P and Badali, F and Baghela, A and Bañares, A and Barreto, RW and Baseia, IG and Bellanger, JM and Berraf-Tebbal, A and Biketova, AY and Bukharova, NV and Burgess, TI and Cabero, J and Câmara, MPS and Cano-Lira, JF and Ceryngier, P and Chávez, R and Cowan, DA and de Lima, AF and Oliveira, RL and Denman, S and Dang, QN and Dovana, F and Duarte, IG and Eichmeier, A and Erhard, A and Esteve-Raventós, F and Fellin, A and Ferisin, G and Ferreira, RJ and Ferrer, A and Finy, P and Gaya, E and Geering, ADW and Gil-Durán, C and Glässnerová, K and Glushakova, AM and Gramaje, D and Guard, FE and Guarnizo, AL and Haelewaters, D and Halling, RE and Hill, R and Hirooka, Y and Hubka, V and Iliushin, VA and Ivanova, DD and Ivanushkina, NE and Jangsantear, P and Justo, A and Kachalkin, AV and Kato, S and Khamsuntorn, P and Kirtsideli, IY and Knapp, DG and Kochkina, GA and Koukol, O and Kovács, GM and Kruse, J and Kumar, TKA and Kušan, I and Læssøe, T and Larsson, E and Lebeuf, R and Levicán, G and Loizides, M and Marinho, P and Luangsa-Ard, JJ and Lukina, EG and Magaña-Dueñas, V and Maggs-Kölling, G and Malysheva, EF and Malysheva, VF and Martín, B and Martín, MP and Matočec, N and McTaggart, AR and Mehrabi-Koushki, M and Mešić, A and Miller, AN and Mironova, P and Moreau, PA and Morte, A and Müller, K and Nagy, LG and Nanu, S and Navarro-Ródenas, A and Nel, WJ and Nguyen, TH and Nóbrega, TF and Noordeloos, ME and Olariaga, I and Overton, BE and Ozerskaya, SM and Palani, P and Pancorbo, F and Papp, V and Pawłowska, J and Pham, TQ and Phosri, C and Popov, ES and Portugal, A and Pošta, A and Reschke, K and Reul, M and Ricci, GM and Rodríguez, A and Romanowski, J and Ruchikachorn, N and Saar, I and Safi, A and Sakolrak, B and Salzmann, F and Sandoval-Denis, M and Sangwichein, E and Sanhueza, L and Sato, T and Sastoque, A and Senn-Irlet, B and Shibata, A and Siepe, K and Somrithipol, S and Spetik, M and Sridhar, P and Stchigel, AM and Stuskova, K and Suwannasai, N and Tan, YP and Thangavel, R and Tiago, I and Tiwari, S and Tkalčec, Z and Tomashevskaya, MA and Tonegawa, C and Tran, HX and Tran, NT and Trovão, J and Trubitsyn, VE and Van Wyk, J and Vieira, WAS and Vila, J and Visagie, CM and Vizzini, A and Volobuev, SV and Vu, DT and Wangsawat, N and Yaguchi, T and Ercole, E and Ferreira, BW and de Souza, AP and Vieira, BS and Groenewald, JZ},
title = {Fungal Planet description sheets: 1284-1382.},
journal = {Persoonia},
volume = {47},
number = {},
pages = {178-374},
pmid = {37693795},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antartica, Cladosporium austrolitorale from coastal sea sand. Australia, Austroboletus yourkae on soil, Crepidotus innuopurpureus on dead wood, Curvularia stenotaphri from roots and leaves of Stenotaphrum secundatum and Thecaphora stajsicii from capsules of Oxalis radicosa. Belgium, Paraxerochrysium coryli (incl. Paraxerochrysium gen. nov.) from Corylus avellana. Brazil, Calvatia nordestina on soil, Didymella tabebuiicola from leaf spots on Tabebuia aurea, Fusarium subflagellisporum from hypertrophied floral and vegetative branches of Mangifera indica and Microdochium maculosum from living leaves of Digitaria insularis. Canada, Cuphophyllus bondii from a grassland. Croatia, Mollisia inferiseptata from a rotten Laurus nobilis trunk. Cyprus, Amanita exilis on calcareous soil. Czech Republic, Cytospora hippophaicola from wood of symptomatic Vaccinium corymbosum. Denmark, Lasiosphaeria deviata on pieces of wood and herbaceous debris. Dominican Republic, Calocybella goethei among grass on a lawn. France (Corsica), Inocybe corsica on wet ground. France (French Guiana), Trechispora patawaensis on decayed branch of unknown angiosperm tree and Trechispora subregularis on decayed log of unknown angiosperm tree. Germany, Paramicrothecium sambuci (incl. Paramicrothecium gen. nov.) on dead stems of Sambucus nigra. India, Aureobasidium microtermitis from the gut of a Microtermes sp. termite, Laccaria diospyricola on soil and Phylloporia tamilnadensis on branches of Catunaregam spinosa. Iran, Pythium serotinoosporum from soil under Prunus dulcis. Italy, Pluteus brunneovenosus on twigs of broadleaved trees on the ground. Japan, Heterophoma rehmanniae on leaves of Rehmannia glutinosa f. hueichingensis. Kazakhstan, Murispora kazachstanica from healthy roots of Triticum aestivum. Namibia, Caespitomonium euphorbiae (incl. Caespitomonium gen. nov.) from stems of an Euphorbia sp. Netherlands, Alfaria junci, Myrmecridium junci, Myrmecridium juncicola, Myrmecridium juncigenum, Ophioceras junci, Paradinemasporium junci (incl. Paradinemasporium gen. nov.), Phialoseptomonium junci, Sporidesmiella juncicola, Xenopyricularia junci and Zaanenomyces quadripartis (incl. Zaanenomyces gen. nov.), from dead culms of Juncus effusus, Cylindromonium everniae and Rhodoveronaea everniae from Evernia prunastri, Cyphellophora sambuci and Myrmecridium sambuci from Sambucus nigra, Kiflimonium junci, Sarocladium junci, Zaanenomyces moderatricis-academiae and Zaanenomyces versatilis from dead culms of Juncus inflexus, Microcera physciae from Physcia tenella, Myrmecridium dactylidis from dead culms of Dactylis glomerata, Neochalara spiraeae and Sporidesmium spiraeae from leaves of Spiraea japonica, Neofabraea salicina from Salix sp., Paradissoconium narthecii (incl. Paradissoconium gen. nov.) from dead leaves of Narthecium ossifragum, Polyscytalum vaccinii from Vaccinium myrtillus, Pseudosoloacrosporiella cryptomeriae (incl. Pseudosoloacrosporiella gen. nov.) from leaves of Cryptomeria japonica, Ramularia pararhabdospora from Plantago lanceolata, Sporidesmiella pini from needles of Pinus sylvestris and Xenoacrodontium juglandis (incl. Xenoacrodontium gen. nov. and Xenoacrodontiaceae fam. nov.) from Juglans regia. New Zealand, Cryptometrion metrosideri from twigs of Metrosideros sp., Coccomyces pycnophyllocladi from dead leaves of Phyllocladus alpinus, Hypoderma aliforme from fallen leaves Fuscopora solandri and Hypoderma subiculatum from dead leaves Phormium tenax. Norway, Neodevriesia kalakoutskii from permafrost and Variabilispora viridis from driftwood of Picea abies. Portugal, Entomortierella hereditatis from a biofilm covering a deteriorated limestone wall. Russia, Colpoma junipericola from needles of Juniperus sabina, Entoloma cinnamomeum on soil in grasslands, Entoloma verae on soil in grasslands, Hyphodermella pallidostraminea on a dry dead branch of Actinidia sp., Lepiota sayanensis on litter in a mixed forest, Papiliotrema horticola from Malus communis, Paramacroventuria ribis (incl. Paramacroventuria gen. nov.) from leaves of Ribes aureum and Paramyrothecium lathyri from leaves of Lathyrus tuberosus. South Africa, Harzia combreti from leaf litter of Combretum collinum ssp. sulvense, Penicillium xyleborini from Xyleborinus saxesenii, Phaeoisaria dalbergiae from bark of Dalbergia armata, Protocreopsis euphorbiae from leaf litter of Euphorbia ingens and Roigiella syzygii from twigs of Syzygium chordatum. Spain, Genea zamorana on sandy soil, Gymnopus nigrescens on Scleropodium touretii, Hesperomyces parexochomi on Parexochomus quadriplagiatus, Paraphoma variabilis from dung, Phaeococcomyces kinklidomatophilus from a blackened metal railing of an industrial warehouse and Tuber suaveolens in soil under Quercus faginea. Svalbard and Jan Mayen, Inocybe nivea associated with Salix polaris. Thailand, Biscogniauxia whalleyi on corticated wood. UK, Parasitella quercicola from Quercus robur. USA, Aspergillus arizonicus from indoor air in a hospital, Caeliomyces tampanus (incl. Caeliomyces gen. nov.) from office dust, Cippumomyces mortalis (incl. Cippumomyces gen. nov.) from a tombstone, Cylindrium desperesense from air in a store, Tetracoccosporium pseudoaerium from air sample in house, Toxicocladosporium glendoranum from air in a brick room, Toxicocladosporium losalamitosense from air in a classroom, Valsonectria portsmouthensis from air in men's locker room and Varicosporellopsis americana from sludge in a water reservoir. Vietnam, Entoloma kovalenkoi on rotten wood, Fusarium chuoi inside seed of Musa itinerans, Micropsalliota albofelina on soil in tropical evergreen mixed forests and Phytophthora docyniae from soil and roots of Docynia indica. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Jurjević Ž, et al. 2021. Fungal Planet description sheets: 1284-1382. Persoonia 47: 178-374. https://doi.org/10.3767/persoonia.2021.47.06.},
}
@article {pmid37744139,
year = {2021},
author = {Yoshimi, A and Hagiwara, D and Ono, M and Fukuma, Y and Midorikawa, Y and Furukawa, K and Fujioka, T and Mizutani, O and Sato, N and Miyazawa, K and Maruyama, JI and Marui, J and Yamagata, Y and Nakajima, T and Tanaka, C and Abe, K},
title = {Downregulation of the ypdA Gene Encoding an Intermediate of His-Asp Phosphorelay Signaling in Aspergillus nidulans Induces the Same Cellular Effects as the Phenylpyrrole Fungicide Fludioxonil.},
journal = {Frontiers in fungal biology},
volume = {2},
number = {},
pages = {675459},
pmid = {37744139},
issn = {2673-6128},
abstract = {Many eukaryotic histidine-to-aspartate (His-Asp) phosphorelay systems consist of three types of signal transducers: a His-kinase (HK), a response regulator (RR), and a histidine-containing phosphotransfer intermediate (HPt). In general, the HPt acts as an intermediate between the HK and the RR and is indispensable for inducing appropriate responses to environmental stresses. In a previous study, we attempted but were unable to obtain deletion mutants of the ypdA gene in order to characterize its function in the filamentous fungus Aspergillus nidulans. In the present study, we constructed the CypdA strain in which ypdA expression is conditionally regulated by the A. nidulans alcA promoter. We constructed CypdA strains with RR gene disruptions (CypdA-sskAΔ, CypdA-srrAΔ, and CypdA-sskAΔsrrAΔ). Suppression of YpdA induced by ypdA downregulation activated the downstream HogA mitogen-activated protein kinase cascade. YpdA suppression caused severe growth defects and abnormal hyphae, with features such as enhanced septation, a decrease in number of nuclei, nuclear fragmentation, and hypertrophy of vacuoles, both regulated in an SskA-dependent manner. Fludioxonil treatment caused the same cellular responses as ypdA suppression. The growth-inhibitory effects of fludioxonil and the lethality caused by ypdA downregulation may be caused by the same or similar mechanisms and to be dependent on both the SskA and SrrA pathways.},
}
@article {pmid37938641,
year = {2021},
author = {Röttjers, L and Vandeputte, D and Raes, J and Faust, K},
title = {Null-model-based network comparison reveals core associations.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {36},
pmid = {37938641},
issn = {2730-6151},
support = {STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Microbial network construction and analysis is an important tool in microbial ecology. Such networks are often constructed from statistically inferred associations and may not represent ecological interactions. Hence, microbial association networks are error prone and do not necessarily reflect true community structure. We have developed anuran, a toolbox for investigation of noisy networks with null models. Such models allow researchers to generate data under the null hypothesis that all associations are random, supporting identification of nonrandom patterns in groups of association networks. This toolbox compares multiple networks to identify conserved subsets (core association networks, CANs) and other network properties that are shared across all networks. We apply anuran to a time series of fecal samples from 20 women to demonstrate the existence of CANs in a subset of the sampled individuals. Moreover, we use data from the Global Sponge Project to demonstrate that orders of sponges have a larger CAN than expected at random. In conclusion, this toolbox is a resource for investigators wanting to compare microbial networks across conditions, time series, gradients, or hosts.},
}
@article {pmid37938227,
year = {2021},
author = {Reitmeier, S and Hitch, TCA and Treichel, N and Fikas, N and Hausmann, B and Ramer-Tait, AE and Neuhaus, K and Berry, D and Haller, D and Lagkouvardos, I and Clavel, T},
title = {Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {31},
pmid = {37938227},
issn = {2730-6151},
abstract = {16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.},
}
@article {pmid37938246,
year = {2021},
author = {Hill, JE and Raaijmakers, JM and Smidt, H},
title = {Editorial.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {10},
doi = {10.1038/s43705-021-00013-3},
pmid = {37938246},
issn = {2730-6151},
}
@article {pmid37089255,
year = {2021},
author = {Obase, K and Yamanaka, S and Kinoshita, A and Tamai, Y and Yamanaka, T},
title = {Phylogenetic placements and cultural characteristics of Tuber species isolated from ectomycorrhizas.},
journal = {Mycoscience},
volume = {62},
number = {2},
pages = {124-131},
pmid = {37089255},
issn = {1340-3540},
abstract = {Pure cultures of Tuber were isolated from ectomycorrhizal root tips in Abies sachalinensis plantations in Hokkaido, Japan. Their phylogenetic relationships as well as vegetative hyphal characteristics on culture media were reported. Phylogenetic analysis based on the internal transcribed spacer within ribosomal DNA settled well-supported eight lineages within Puberulum, Latisporum, and Maculatum clades in Tuber. Three and one lineages were grouped with undescribed species of Puberulum clade in Japan and that of the Latisporum group in China, respectively. Two lineages were closely associated to but distinct from an undescribed species of Puberulum clade in Japan. One lineage did not group with any sequences in the International Nucleotide Sequence Database (INSD), proposing a new taxon in the Latisporum group. One lineage was grouped with T. foetidum in Maculatum clade. All strains in each lineage displayed yellowish white, thin, filamentous colonies on Melin-Norkrans agar medium. Various differences in morphological characteristics of hyphae on pure cultures of various strains were noted, but they were frequently uncommon among strains of the same taxa. Isolation from ectomycorrhizal root tips can be among the effective ways to acquire pure cultures of Tuber strains.},
}
@article {pmid37333959,
year = {2020},
author = {Zeibich, L and Guhl, J and Drake, HL},
title = {Impact of water content and dietary organic carbon richness on gut bacteria in the earthworm Lumbricus terrestris.},
journal = {FEMS microbes},
volume = {1},
number = {1},
pages = {xtaa002},
pmid = {37333959},
issn = {2633-6685},
abstract = {Many higher and lower animal gut ecosystems have complex resident microbial communities. In contrast, ingested soil is the primary source of the gut microbial diversity of earthworms, invertebrates of fundamental importance to the terrestrial biosphere. Earthworms also harbor a few endemic bacteria including Tenericutes-affiliated Candidatus Lumbricincola of unknown function. Gut microbes are subject to nutrient fluctuations due to dilution effects during gut passage, the nutrient richness of the anoxic gut, and dietary organic carbon, factors that could alter their activity/detection. This study's objective was to assess the potential impact of these factors on the occurrence and activity of ingested and endemic bacteria in gut content of Lumbricus terrestris. Fermentation product profiles of anoxic undiluted and diluted gut content treatments were similar, suggesting that experimental increase in water content and nutrient dilution had marginal impact on fermentation. However, 16S ribosomal Ribonucleic Acid (16S rRNA) sequence abundances indicated that stimulated bacterial taxa were not identical in undiluted and diluted treatments, with dominate potentially functionally redundant phylotypes being affiliated to the Firmicutes, Fusobacteria and Proteobacteria. Although the earthworm-associated Tenericutes were not stimulated in these treatments, the occurrence of three Tenericutes-affiliated phylotypes varied with the organic carbon richness of the earthworm diet, with two phylotypes being associated with high organic carbon richness. 16S rRNA sequence abundances indicated that other dominant gut taxa also varied with dietary organic carbon richness. These findings illustrate that functionally redundant ingested bacteria and earthworm-associated Tenericutes might be influenced by nutrient fluctuations in the gut and organic carbon richness of the earthworm diet.},
}
@article {pmid37128070,
year = {2020},
author = {Vandeweyer, D and Lievens, B and Van Campenhout, L},
title = {Identification of bacterial endospores and targeted detection of foodborne viruses in industrially reared insects for food.},
journal = {Nature food},
volume = {1},
number = {8},
pages = {511-516},
pmid = {37128070},
issn = {2662-1355},
support = {141129//Agentschap Innoveren en Ondernemen (Flanders Innovation &amp; Entrepreneurship)/ ; PDM/18/159//KU Leuven (Katholieke Universiteit Leuven)/ ; },
abstract = {With edible insects being increasingly produced, food safety authorities have called for the determination of microbiological challenges posed to human health. Here, we find that the bacterial endospore fraction in industrially reared mealworm and cricket samples is largely comprised of Bacillus cereus group members that can pose insect or human health risks. Hepatitis A virus, hepatitis E virus and norovirus genogroup II were not detected in the sample collection, indicating a low food safety risk from these viral pathogens.},
}
@article {pmid36697862,
year = {2023},
author = {Kennedy, KM and de Goffau, MC and Perez-Muñoz, ME and Arrieta, MC and Bäckhed, F and Bork, P and Braun, T and Bushman, FD and Dore, J and de Vos, WM and Earl, AM and Eisen, JA and Elovitz, MA and Ganal-Vonarburg, SC and Gänzle, MG and Garrett, WS and Hall, LJ and Hornef, MW and Huttenhower, C and Konnikova, L and Lebeer, S and Macpherson, AJ and Massey, RC and McHardy, AC and Koren, O and Lawley, TD and Ley, RE and O'Mahony, L and O'Toole, PW and Pamer, EG and Parkhill, J and Raes, J and Rattei, T and Salonen, A and Segal, E and Segata, N and Shanahan, F and Sloboda, DM and Smith, GCS and Sokol, H and Spector, TD and Surette, MG and Tannock, GW and Walker, AW and Yassour, M and Walter, J},
title = {Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.},
journal = {Nature},
volume = {613},
number = {7945},
pages = {639-649},
pmid = {36697862},
issn = {1476-4687},
support = {BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 HD102318/HD/NICHD NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; R01 CA219871/CA/NCI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 100974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; R01 AI139240/AI/NIAID NIH HHS/United States ; MR/K021133/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 NR014784/NR/NINR NIH HHS/United States ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI120489/AI/NIAID NIH HHS/United States ; R01 HD098867/HD/NICHD NIH HHS/United States ; R33 HL137063/HL/NHLBI NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Female ; Humans ; Pregnancy ; Amniotic Fluid/immunology/microbiology ; *Biomass ; Mammals ; *Microbiota/genetics ; Placenta/immunology/microbiology ; *Fetus/immunology/microbiology ; *DNA Contamination ; Reproducibility of Results ; },
abstract = {Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.},
}
@article {pmid36697746,
year = {2023},
author = {Yan, Y and Lin, T and Xie, W and Zhang, D and Jiang, Z and Han, Q and Zhu, X and Zhang, H},
title = {Contrasting Mechanisms Determine the Microeukaryotic and Syndiniales Community Assembly in a Eutrophic bay.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1575-1588},
pmid = {36697746},
issn = {1432-184X},
support = {42076158//National Natural Science Foundation of China/ ; 42076156//National Natural Science Foundation of China/ ; LY22D060002//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFC3101702//National Key Research and Development Program of China/ ; SJLY2020005//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; SOEDZZ2202//Project of State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography/ ; },
mesh = {Ecosystem ; Bays ; *Dinoflagellida/genetics ; *Diatoms/genetics ; RNA, Ribosomal, 18S/genetics ; Seasons ; },
abstract = {Syndiniales is a diverse parasitic group, increasingly gaining attention owing to its high taxonomic diversity in marine ecosystems and inhibitory effects on the dinoflagellate blooms. However, their seasonal dynamics, host interactions, and mechanisms of community assembly are largely unknown, particularly in eutrophic waters. Here, using 18S rRNA gene amplicon sequencing, we intended to elucidate the interactions between Syndiniales and microeukaryotes, as well as community assembly processes in a eutrophic bay. The results showed that Syndiniales group II was dominating throughout the year, with substantially higher abundance in the winter and spring, whereas Syndiniales group I was more abundant in the summer and autumn. Temperature and Dinoflagellata were the most important abiotic and biotic factors driving variations of the Syndiniales community, respectively. The assembly processes of microeukaryotes and Syndiniales were completely different, with the former being controlled by a balance between homogeneous selection and drift and the latter being solely governed by drift. Network analysis revealed that Syndiniales group II had the largest number of interactions with microeukaryotes, and they primarily associated with Dinoflagellata in the winter, while interactions with Chlorophyta and Bacillariophyta increased dramatically in summer and autumn. These findings provide significant insights in understanding the interactions and assembly processes of Syndiniales throughout the year, which is critical in revealing the roles of single-celled parasites in driving protist dynamics in eutrophic waters.},
}
@article {pmid36697704,
year = {2023},
author = {Jentzsch, L and Grossart, HP and Plewe, S and Schulze-Makuch, D and Goldhammer, T},
title = {Response of cyanobacterial mats to ambient phosphate fluctuations: phosphorus cycling, polyphosphate accumulation and stoichiometric flexibility.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {6},
pmid = {36697704},
issn = {2730-6151},
abstract = {Cyanobacterial mats inhabit a variety of aquatic habitats, including the most extreme environments on Earth. They can thrive in a wide range of phosphorus (P) levels and are thus important players for ecosystem primary production and P cycling at the sediment-water interface. Polyphosphate (polyP), the major microbial P storage molecule, is assigned a critical role in compensating for phosphate fluctuations in planktonic cyanobacteria, but little is known about potentially analogous mechanisms of mat-forming cyanobacteria. To investigate acclimation strategies of cyanobacterial mats to fluctuating phosphate concentrations, laboratory batch experiments were conducted, in which the cosmopolitan mat-forming, marine cyanobacterium Sodalinema stali was exposed to low dissolved P concentrations, followed by a P pulse. Our results show that the cyanobacteria dynamically adjusted cellular P content to ambient phosphate concentrations and that they had accumulated polyP during periods of high phosphate availability, which was subsequently recycled to sustain growth during phosphate scarcity. However, following the depletion of dispensable cellular P sources, including polyP, we observed a reallocation of P contained in DNA into polyP, accompanied by increasing alkaline phosphatase activity. This suggests a change of the metabolic focus from growth towards maintenance and the attempt to acquire organic P, which would be naturally contained in the sediment. P overplus uptake following a simulated P pulse further suggests that Sodalinema-dominated mats exhibit elaborated mechanisms to cope with severe P fluctuations to overcome unfavourable environmental conditions, and potentially modulate critical P fluxes in the aquatic cycle.},
}
@article {pmid36696803,
year = {2023},
author = {Huang, X and Chen, Q and Fan, Y and Yang, R and Gong, G and Yan, C and Song, Y and Zhang, B and Xi, S and Huang, Y and Xu, H},
title = {Fructooligosaccharides attenuate non-alcoholic fatty liver disease by remodeling gut microbiota and association with lipid metabolism.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {159},
number = {},
pages = {114300},
doi = {10.1016/j.biopha.2023.114300},
pmid = {36696803},
issn = {1950-6007},
mesh = {Mice ; Animals ; *Non-alcoholic Fatty Liver Disease/metabolism ; Lipid Metabolism ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Liver ; Diet, High-Fat/adverse effects ; Choline/metabolism/pharmacology/therapeutic use ; Methionine/metabolism ; },
abstract = {BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a common liver disease highly associated with metabolic diseases and gut dysbiosis. Several clinical trials have confirmed that fructooligosaccharides (FOSs) are a viable alternative treatment for NAFLD. However, the mechanisms underlying the activities of FOSs remain unclear.<br><br>METHODS: In this study, the effects of FOSs were investigated with the use of two C57BL/6&#xa0;J mouse models of NAFLD induced by a high-fat, high-cholesterol (HFHC) diet and a methionine- and choline-deficient (MCD) diet, respectively. The measured metabolic parameters included body, fat, and liver weights; and blood glucose, glucose tolerance, and serum levels of glutamate transaminase, aspartate transaminase, and triglycerides. Liver tissues were collected for histological analysis. In addition, 16&#xa0;S rRNA sequencing was conducted to investigate the effects of FOSs on the composition of the gut microbiota of mice in the HFHC and MCD groups and treated with FOSs.<br><br>RESULTS: FOS treatment attenuated severe metabolic changes and hepatic steatosis caused by the HFHC and MCD diets. In addition, FOSs remodeled the structure of gut microbiota in mice fed the HFHC and MCD diets, as demonstrated by increased abundances of Bacteroidetes (phylum level), Klebsiella variicola, Lactobacillus gasseri, and Clostridium perfringens (species level); and decreased abundances of Verrucomicrobia (phylum level) and the Fissicatena group (genus level). Moreover, the expression levels of genes associated with lipid metabolism and inflammation (i.e., ACC1, PPAR&#x3b3;, CD36, MTTP, APOC3, IL-6, and IL-1&#x3b2;) were down-regulated after FOS treatment.<br><br>CONCLUSION: FOSs alleviated the pathological phenotype of NAFLD via remodeling of the gut microbiota composition and decreasing hepatic lipid metabolism, suggesting that FOSs as functional dietary supplements can potentially reduce the risk of NAFLD.},
}
@article {pmid36695828,
year = {2023},
author = {Hilderbrand, RH and Bambakidis, T and Crump, BC},
title = {The Roles of Microbes in Stream Restorations.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {853-861},
pmid = {36695828},
issn = {1432-184X},
mesh = {Animals ; *Ecosystem ; Rivers ; Fishes ; Biomass ; *Microbiota ; Biofilms ; },
abstract = {The goods and services provided by riverine systems are critical to humanity, and our reliance increases with our growing population and demands. As our activities expand, these systems continue to degrade throughout the world even as we try to restore them, and many efforts have not met expectations. One way to increase restoration effectiveness could be to explicitly design restorations to promote microbial communities, which are responsible for much of the organic matter breakdown, nutrient removal or transformation, pollutant removal, and biomass production in river ecosystems. In this paper, we discuss several design concepts that purposefully create conditions for these various microbial goods and services, and allow microbes to act as ecological restoration engineers. Focusing on microbial diversity and function could improve restoration effectiveness and overall ecosystem resilience to the stressors that caused the need for the restoration. Advances in next-generation sequencing now allow the use of microbial 'omics techniques (e.g., metagenomics, metatranscriptomics) to assess stream ecological conditions in similar fashion to fish and benthic macroinvertebrates. Using representative microbial communities from stream sediments, biofilms, and the water column may greatly advance assessment capabilities. Microbes can assess restorations and ecosystem function where animals may not currently be present, and thus may serve as diagnostics for the suitability of animal reintroductions. Emerging applications such as ecological metatranscriptomics may further advance our understanding of the roles of specific restoration designs towards ecological services as well as assess restoration effectiveness.},
}
@article {pmid36695592,
year = {2023},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Site Specialization of Human Oral Veillonella Species.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0404222},
pmid = {36695592},
issn = {2165-0497},
support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Veillonella/genetics ; Mouth/microbiology ; Tongue/microbiology ; Palatine Tonsil ; *Microbiota ; },
abstract = {Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns of Veillonella species across the oral cavity is fundamental to understanding their oral ecology. In this study, we used a combination of pangenomic analysis and oral metagenomic information to clarify Veillonella taxonomy and to test the site specialist hypothesis for the Veillonella genus, which contends that most oral bacterial species are adapted to live at specific oral sites. Using isolate genome sequences combined with shotgun metagenomic sequence data, we showed that Veillonella species have clear, differential site specificity: Veillonella parvula showed strong preference for supra- and subgingival plaque, while closely related V. dispar, as well as more distantly related V. atypica, preferred the tongue dorsum, tonsils, throat, and hard palate. In addition, the provisionally named Veillonella sp. Human Microbial Taxon 780 showed strong site specificity for keratinized gingiva. Using comparative genomic analysis, we identified genes associated with thiamine biosynthesis and the reductive pentose phosphate cycle that may enable Veillonella species to occupy their respective habitats. IMPORTANCE Understanding the microbial ecology of the mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that different Veillonella species have clear ecological preferences in the oral cavity of healthy humans, validating the site specialist hypothesis. Furthermore, the gene pool of different Veillonella species was found to be reflective of their ecology, illuminating the potential role of vitamins and carbohydrates in determining Veillonella distribution patterns and interspecies interactions.},
}
@article {pmid36694586,
year = {2022},
author = {Thirumala, M and Sai Krishna, E and Sindhu Priya, P and Vishnuvardhan Reddy, S},
title = {Characterization of a novel Fluoride resistant bacterial isolate and its capability of Fluoride bioremediation.},
journal = {AIMS microbiology},
volume = {8},
number = {4},
pages = {470-483},
pmid = {36694586},
issn = {2471-1888},
abstract = {A Gram positive rod shaped bacterium designated as isolate H1 with Fluoride resistance up to 4 g/L sodium fluoride (NaF) in LB (Luria-Bertani) agar was isolated from a ground water sample of Narketpally area, Nalgonda district, Telangana, India. The colonies of isolate H1 were off white in color. Growth patterns of isolate H1 were observed at two different concentrations, 100 and 250 ppm, of NaF and also without NaF in the medium. In cases where NaF was present in the media, the lag phases of the growth curves were extended when compared to the absence of NaF. Optimum pH required for the organism's growth was 8. Isolate H1 required a temperature of 37 °C with 150 rpm and 2% NaCl for its optimal growth in the medium without NaF. Meanwhile, isolate H1 could thrive in a diverse pH range, i.e., pH 5-10, and at an NaCl concentration of up to 11% in the medium with NaF. Based on morphological, biochemical and molecular characterization, isolate H1 was identified as belonging to the genus Bacillus. It showed 98.47% 16S rDNA gene sequence similarity with Bacillus australimaris NH71_1[T]. Isolate H1 showed high fluoride removals of 22.5% and 38.2% with 100 and 250 mg/L of NaF in the LB broth when incubated at pH 8 and a temperature of 37 °C with 150 rpm for 3 day. Hence, this organism could be a promising isolate to apply for defluoridation of ground water in fluoride contaminthe ated areas.},
}
@article {pmid36694253,
year = {2023},
author = {Uiterwijk, M and Vojta, L and Šprem, N and Beck, A and Jurković, D and Kik, M and Duscher, GG and Hodžić, A and Reljić, S and Sprong, H and Beck, R},
title = {Diversity of Hepatozoon species in wild mammals and ticks in Europe.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {27},
pmid = {36694253},
issn = {1756-3305},
mesh = {Dogs ; Animals ; *Wolves ; *Coccidiosis/epidemiology/veterinary/parasitology ; *Eucoccidiida/genetics ; *Ixodes/parasitology ; *Ixodidae/parasitology ; Foxes/parasitology ; Europe/epidemiology ; Rodentia ; *Mustelidae ; Animals, Domestic ; },
abstract = {BACKGROUND: Hepatozoon spp. are tick-borne parasites causing subclinical to clinical disease in wild and domestic animals. Aim of this study was to determine Hepatozoon prevalence and species distribution among wild mammals and ticks in Europe.<br><br>METHODS: Samples of wild mammals and ticks, originating from Austria, Bosnia and Herzegovina, Croatia, Belgium and the Netherlands, were tested with PCR to amplify a&#x2009;~&#x2009;670-bp fragment of the small subunit ribosomal RNA gene.<br><br>RESULTS: Of the 2801 mammal samples that were used for this study, 370 (13.2%) tested positive. Hepatozoon canis was detected in samples of 178 animals (3 Artiodactyla, 173 Carnivora, 1 Eulipotyphia, 1 Lagomorpha), H. martis in 125 (3 Artiodactyla, 122 Carnivora), H. sciuri in 13 (all Rodentia), Hepatozoon sp. in 47 (among which Hepatozoon sp. Vole isolate, all Rodentia) and H. ayorgbor in 4 (all Rodentia). Regarding origin, 2.9% (6/208) tested positive from Austria, 2.8% (1/36) from Bosnia and Herzegovina, 14.6% (173/1186) from Croatia and 13.9% (190/1371) from Belgium/the Netherlands. Of the 754 ticks collected, 0.0% (0/35) Hyalomma sp., 16.0% (4/25) Dermacentor spp., 0.0% (0/23) Haemaphysalis spp., 5.3% (24/50) Ixodes and 1.4% (3/221) Rhipicephalus spp. tested positive for Hepatozoon (4.2%; 32/754), most often H. canis (n&#x2009;=&#x2009;22).<br><br>CONCLUSIONS: Hepatozoon canis is most present in mammals (especially in Carnivora such as gray wolves and golden jackals) and ticks, followed by H. martis, which was found merely in stone martens and pine martens. None of the rodent-associated Hepatozoon spp. were detected in the ticks, suggesting the possible implication of other arthropod species or non-vectorial routes in the transmission cycle of the hemoprotozoans in rodents. Our findings of H. canis in ticks other than R. sanguineus add to the observation that other ticks are also involved in the life cycle of Hepatozoon. Now that presence of Hepatozoon has been demonstrated in red foxes, gray wolves, mustelids and rodents from the Netherlands and/or Belgium, veterinary clinicians should be aware of the possibility of spill-over to domestic animals, such as dogs.},
}
@article {pmid36694053,
year = {2023},
author = {Arroyo, MC and Laurie, I and Rotsaert, C and Marzorati, M and Risso, D and Karnik, K},
title = {Age-Dependent Prebiotic Effects of Soluble Corn Fiber in M-SHIME[®] Gut Microbial Ecosystems.},
journal = {Plant foods for human nutrition (Dordrecht, Netherlands)},
volume = {78},
number = {1},
pages = {213-220},
pmid = {36694053},
issn = {1573-9104},
support = {PO 4500037596//Tate &amp; Lyle PLC/ ; },
mesh = {Humans ; Prebiotics/analysis ; Zea mays ; *Gastrointestinal Microbiome ; Lipopolysaccharides/pharmacology ; Caco-2 Cells ; Fatty Acids, Volatile/metabolism ; *Microbiota ; },
abstract = {Soluble corn fiber (SCF) has demonstrated prebiotic effects in clinical studies. Using an in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME[®]) model, the effects of SCF treatment on colonic microbiota composition and metabolic activity and on host-microbiome interactions were evaluated using fecal samples from healthy donors of different ages (baby [≤ 2 years], n = 4; adult [18-45 years], n = 2; elderly [70 years], n = 1). During the 3-week treatment period, M-SHIME[®] systems were supplemented with SCF daily (baby, 1.5, 3, or 4.5 g/d; adult, 3 or 8.5 g/d; and elderly, 8.5 g/d). M-SHIME[®] supernatants were evaluated for their effect on the intestinal epithelial cell barrier and inflammatory responses in lipopolysaccharide. (LPS)-stimulated cells. Additionally, short-chain fatty acid (SCFA) production and microbial community composition were assessed. In the baby and adult models, M-SHIME[®] supernatants from SCF treated vessels protected Caco-2 membrane integrity from LPS-induced damage. SCF treatment resulted in the expansion of Bacteroidetes, Firmicutes, and Bifidobacterial, as well as increased SCFA production in all age groups. SCF tended to have the greatest effect on propionate production. These findings demonstrate the prebiotic potential of SCF in babies, adults, and the elderly and provide insight into the mechanisms behind the observed prebiotic effects.},
}
@article {pmid36687598,
year = {2022},
author = {Midani, FS and David, LA},
title = {Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {910390},
pmid = {36687598},
issn = {1664-302X},
support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; },
abstract = {Cross feeding between microbes is ubiquitous, but its impact on the diversity and productivity of microbial communities is incompletely understood. A reductionist approach using simple microbial communities has the potential to detect cross feeding interactions and their impact on ecosystem properties. However, quantifying abundance of more than two microbes in a community in a high throughput fashion requires rapid, inexpensive assays. Here, we show that multicolor flow cytometry combined with a machine learning-based classifier can rapidly quantify species abundances in simple, synthetic microbial communities. Our approach measures community structure over time and detects the exchange of metabolites in a four-member community of fluorescent Bacteroides species. Notably, we quantified species abundances in co-cultures and detected evidence of cooperation in polysaccharide processing and competition for monosaccharide utilization. We also observed that co-culturing on simple sugars, but not complex sugars, reduced microbial productivity, although less productive communities maintained higher community diversity. In summary, our multicolor flow cytometric approach presents an economical, tractable model system for microbial ecology using well-studied human bacteria. It can be extended to include additional species, evaluate more complex environments, and assay response of communities to a variety of disturbances.},
}
@article {pmid36684671,
year = {2023},
author = {Huang, F and Zhu, C and Huang, M and Song, X and Peng, A},
title = {The root enrichment of bacteria is consistent across different stress-resistant plant species.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14683},
pmid = {36684671},
issn = {2167-8359},
mesh = {*Microbiota ; Soil Microbiology ; Phylogeny ; Plant Roots/microbiology ; Plants ; *Burkholderia ; },
abstract = {Bacteria, inhabiting around and in plant roots, confer many beneficial traits to promote plant growth and health. The secretion of root exudates modulates the nutritional state of the rhizosphere and root area, further selecting specific bacteria taxa and shaping the bacteria communities. Many studies of the rhizosphere effects have demonstrated that selection by the plant rhizosphere consistently enriches a set of bacteria taxa, and this is conserved across different plant species. Root selection effects are considered to be stronger than the rhizosphere selection effects, yet studies are limited. Here, we focus on the root selection effects across a group of 11 stress-resistant plant species. We found that the root selection consistently reduced the alpha diversity (represented by total number of observed species, Shannon's diversity, and phylogenetic diversity) and altered the structure and composition of bacteria communities. Furthermore, root selection tended to enrich for clusters of bacteria genera including Pantoea, Akkermansia, Blautia, Acinetobacter, Burkholderia-Paraburkholderia, Novosphingobium, Massilia, Pseudomonas, Chryseobacterium, and Stenotrophomonas. Our study offers some basic knowledge for understanding the microbial ecology of the plant root, and suggests that several bacteria genera are of interest for future studies.},
}
@article {pmid36683960,
year = {2023},
author = {Li, Y and Deng, X and Zhang, N and Shen, Z and Li, R and Shen, Q and Salles, JF},
title = {Rhizosphere suppression hinders antibiotic resistance gene (ARG) spread under bacterial invasion.},
journal = {One health (Amsterdam, Netherlands)},
volume = {16},
number = {},
pages = {100481},
pmid = {36683960},
issn = {2352-7714},
abstract = {The rhizosphere is an extremely important component of the "one health" scenario by linking the soil microbiome and plants, in which the potential enrichment of antibiotic resistance genes (ARGs) might ultimately flow into the human food chain. Despite the increased occurrence of soil-borne diseases, which can lead to increased use of pesticides and antibiotic-producing biocontrol agents, the understanding of the dynamics of ARG spread in the rhizosphere is largely overlooked. Here, tomato seedlings grown in soils conducive and suppressive to the pathogen Ralstonia solanacearum were selected as a model to investigate ARG spread in the rhizosphere with and without pathogen invasion. Metagenomics data revealed that R. solanacearum invasion increased the density of ARGs and mobile genetic elements (MGEs). Although we found ARGs originating from human pathogenic bacteria in both soils, the enrichment was alleviated in the suppressive soil. In summary, the suppressive soil hindered ARG spread through pathogen suppression and had a lower number of taxa carrying antibiotic resistance.},
}
@article {pmid36683707,
year = {2022},
author = {Chen, Q and Fan, Y and Zhang, B and Yan, C and Chen, Z and Wang, L and Hu, Y and Huang, Q and Su, J and Ren, J and Xu, H},
title = {Specific fungi associated with response to capsulized fecal microbiota transplantation in patients with active ulcerative colitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1086885},
pmid = {36683707},
issn = {2235-2988},
mesh = {Humans ; *Colitis, Ulcerative/therapy ; *Fecal Microbiota Transplantation/adverse effects ; Feces/microbiology ; Fungi/genetics ; Remission Induction ; Treatment Outcome ; },
abstract = {OBJECTIVE: Fecal microbiota transplantation (FMT) is a novel microbial treatment for patients with ulcerative colitis (UC). In this study, we performed a clinical trial of capsulized FMT in UC patients to determine the association between the gut fungal community and capsulized FMT outcomes.<br><br>DESIGN: This study recruited patients with active UC (N = 22) and healthy individuals (donor, N = 9) according to the criteria. The patients received capsulized FMT three times a week. Patient stool samples were collected before (week 0) and after FMT follow-up visits at weeks 1, 4, and 12. Fungal communities were analysed using shotgun metagenomic sequencing.<br><br>RESULTS: According to metagenomic analysis, fungal community evenness index was greater in samples collected from patients, and the overall fungal community was clustered among the samples collected from donors. The dominant fungi in fecal samples collected from donors and patients were Ascomycota and Basidiomycota. However, capsulized FMT ameliorated microbial fungal diversity and altered fungal composition, based on metagenomic analysis of fecal samples collected before and during follow-up visits after capsulized FMT. Fungal diversity decreased in samples collected from patients who achieved remission after capsulized FMT, similar to samples collected from donors. Patients achieving remission after capsulized FMT had specific enrichment of Kazachstania naganishii, Pyricularia grisea, Lachancea thermotolerans, and Schizosaccharomyces pombe compared with patients who did not achieve remission. In addition, the relative abundance of P. grisea was higher in remission fecal samples during the follow-up visit. Meanwhile, decreased levels of pathobionts, such as Candida and Debaryomyces hansenii, were associated with remission in patients receiving capsulized FMT.<br><br>CONCLUSION: In the metagenomic analysis of fecal samples from donors and patients with UC receiving capsulized FMT, shifts in gut fungal diversity and composition were associated with capsulized FMT and validated in patients with active UC. We also identified the specific fungi associated with the induction of remission. ClinicalTrails.gov (NCT03426683).},
}
@article {pmid36683444,
year = {2023},
author = {Gegenbauer, C and Bellaire, A and Schintlmeister, A and Schmid, MC and Kubicek, M and Voglmayr, H and Zotz, G and Richter, A and Mayer, VE},
title = {Exo- and endophytic fungi enable rapid transfer of nutrients from ant waste to orchid tissue.},
journal = {The New phytologist},
volume = {238},
number = {5},
pages = {2210-2223},
pmid = {36683444},
issn = {1469-8137},
mesh = {Animals ; *Ants ; Nitrogen/metabolism ; Fungi/metabolism ; *Ascomycota/metabolism ; *Orchidaceae ; *Hypocreales ; Nutrients ; },
abstract = {The epiphytic orchid Caularthron bilamellatum sacrifices its water storage tissue for nutrients from the waste of ants lodging inside its hollow pseudobulb. Here, we investigate whether fungi are involved in the rapid translocation of nutrients. Uptake was analysed with a [15] N labelling experiment, subsequent isotope ratio mass spectrometry (IRMS) and secondary ion mass spectrometry (ToF-SIMS and NanoSIMS). We encountered two hyphae types: a thick melanized type assigned to 'black fungi' (Chaetothyriales, Cladosporiales, and Mycosphaerellales) in ant waste, and a thin endophytic type belonging to Hypocreales. In few cell layers, both hyphae types co-occurred. [15] N accumulation in both hyphae types was conspicuous, while for translocation to the vessels only Hypocreales were involved. There is evidence that the occurrence of the two hyphae types results in a synergism in terms of nutrient uptake. Our study provides the first evidence that a pseudobulb (=stem)-born endophytic network of Hypocreales is involved in the rapid translocation of nitrogen from insect-derived waste to the vegetative and reproductive tissue of the host orchid. For C. bilamellatum that has no contact with the soil, ant waste in the hollow pseudobulbs serves as equivalent to soil in terms of nutrient sources.},
}
@article {pmid36683151,
year = {2023},
author = {Vallier, M and Suwandi, A and Ehrhardt, K and Belheouane, M and Berry, D and Čepić, A and Galeev, A and Johnsen, JM and Grassl, GA and Baines, JF},
title = {Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2164448},
pmid = {36683151},
issn = {1949-0984},
mesh = {Humans ; Mice ; Animals ; Morganella ; *Blood Group Antigens ; RNA, Ribosomal, 16S ; *Gastrointestinal Microbiome ; Genotype ; },
abstract = {Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel "pathometagenomic" approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.},
}
@article {pmid36681674,
year = {2023},
author = {Van Holm, W and Carvalho, R and Delanghe, L and Eilers, T and Zayed, N and Mermans, F and Bernaerts, K and Boon, N and Claes, I and Lebeer, S and Teughels, W},
title = {Antimicrobial potential of known and novel probiotics on in vitro periodontitis biofilms.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {3},
pmid = {36681674},
issn = {2055-5008},
support = {G091218N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G091218N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G091218N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; HBC.2020.2873//Agentschap Innoveren en Ondernemen (Flanders Innovation &amp; Entrepreneurship)/ ; Lacto-Be 26850//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Lacto-Be 26850//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Humans ; *Periodontitis/drug therapy ; Lactobacillus/physiology ; Biofilms ; *Anti-Infective Agents/pharmacology ; *Probiotics/pharmacology ; },
abstract = {Several oral diseases are characterized by a shift within the oral microbiome towards a pathogenic, dysbiotic composition. Broad-spectrum antimicrobials are often part of patient care. However, because of the rising antibiotic resistance, alternatives are increasingly desirable. Alternatively, supplying beneficial species through probiotics is increasingly showing favorable results. Unfortunately, these probiotics are rarely evaluated comparatively. In this study, the in vitro effects of three known and three novel Lactobacillus strains, together with four novel Streptococcus salivarius strains were comparatively evaluated for antagonistic effects on proximal agar growth, antimicrobial properties of probiotic supernatant and the probiotic's effects on in vitro periodontal biofilms. Strain-specific effects were observed as differences in efficacy between genera and differences within genera. While some of the Lactobacillus candidates were able to reduce the periodontal pathobiont A. actinomycetemcomitans, the S. salivarius strains were not. However, the S. salivarius strains were more effective against periodontal pathobionts P. intermedia, P. gingivalis, and F. nucleatum. Vexingly, most of the Lactobacillus strains also negatively affected the prevalence of commensal species within the biofilms, while this was lower for S. salivarius strains. Both within lactobacilli and streptococci, some strains showed significantly more inhibition of the pathobionts, indicating the importance of proper strain selection. Additionally, some species showed reductions in non-target species, which can result in unexpected and unexplored effects on the whole microbiome.},
}
@article {pmid36677477,
year = {2023},
author = {Neidhöfer, C and Sib, E and Benhsain, AH and Mutschnik-Raab, C and Schwabe, A and Wollkopf, A and Wetzig, N and Sieber, MA and Thiele, R and Döhla, M and Engelhart, S and Mutters, NT and Parčina, M},
title = {Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
pmid = {36677477},
issn = {2076-2607},
abstract = {Indoor spaces exhibit microbial compositions that are distinctly dissimilar from one another and from outdoor spaces. Unique in this regard, and a topic that has only recently come into focus, is the microbiome of hospitals. While the benefits of knowing exactly which microorganisms propagate how and where in hospitals are undoubtedly beneficial for preventing hospital-acquired infections, there are, to date, no standardized procedures on how to best study the hospital microbiome. Our study aimed to investigate the microbiome of hospital sanitary facilities, outlining the extent to which hospital microbiome analyses differ according to sample-preparation protocol. For this purpose, fifty samples were collected from two separate hospitals-from three wards and one hospital laboratory-using two different storage media from which DNA was extracted using two different extraction kits and sequenced with two different primer pairs (V1-V2 and V3-V4). There were no observable differences between the sample-preservation media, small differences in detected taxa between the DNA extraction kits (mainly concerning Propionibacteriaceae), and large differences in detected taxa between the two primer pairs V1-V2 and V3-V4. This analysis also showed that microbial occurrences and compositions can vary greatly from toilets to sinks to showers and across wards and hospitals. In surgical wards, patient toilets appeared to be characterized by lower species richness and diversity than staff toilets. Which sampling sites are the best for which assessments should be analyzed in more depth. The fact that the sample processing methods we investigated (apart from the choice of primers) seem to have changed the results only slightly suggests that comparing hospital microbiome studies is a realistic option. The observed differences in species richness and diversity between patient and staff toilets should be further investigated, as these, if confirmed, could be a result of excreted antimicrobials.},
}
@article {pmid36677425,
year = {2023},
author = {Shedleur-Bourguignon, F and Duchemin, T and P Thériault, W and Longpré, J and Thibodeau, A and Hocine, MN and Fravalo, P},
title = {Distinct Microbiotas Are Associated with Different Production Lines in the Cutting Room of a Swine Slaughterhouse.},
journal = {Microorganisms},
volume = {11},
number = {1},
pages = {},
pmid = {36677425},
issn = {2076-2607},
support = {RDCPJ 520873-17//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {The microorganisms found on fresh, raw meat cuts at a slaughterhouse can influence the meat's safety and spoilage patterns along further stages of processing. However, little is known about the general microbial ecology of the production environment of slaughterhouses. We used 16s rRNA sequencing and diversity analysis to characterize the microbiota heterogeneity on conveyor belt surfaces in the cutting room of a swine slaughterhouse from different production lines (each associated with a particular piece/cut of meat). Variation of the microbiota over a period of time (six visits) was also evaluated. Significant differences of alpha and beta diversity were found between the different visits and between the different production lines. Bacterial genera indicative of each visit and production line were also identified. We then created random forest models that, based on the microbiota of each sample, allowed us to predict with 94% accuracy to which visit a sample belonged and to predict with 88% accuracy from which production line it was taken. Our results suggest a possible influence of meat cut on processing surface microbiotas, which could lead to better prevention, surveillance, and control of microbial contamination of meat during processing.},
}
@article {pmid36671807,
year = {2023},
author = {Kropochev, AI and Lashin, SA and Matushkin, YG and Klimenko, AI},
title = {Trait-Based Method of Quantitative Assessment of Ecological Functional Groups in the Human Intestinal Microbiome.},
journal = {Biology},
volume = {12},
number = {1},
pages = {},
pmid = {36671807},
issn = {2079-7737},
support = {No. &#x41c;&#x41a;-3363.2022.1.4.//Russian presidential grant for support of young scientists/ ; },
abstract = {We propose the trait-based method for quantifying the activity of functional groups in the human gut microbiome based on metatranscriptomic data. It allows one to assess structural changes in the microbial community comprised of the following functional groups: butyrate-producers, acetogens, sulfate-reducers, and mucin-decomposing bacteria. It is another way to perform a functional analysis of metatranscriptomic data by focusing on the ecological level of the community under study. To develop the method, we used published data obtained in a carefully controlled environment and from a synthetic microbial community, where the problem of ambiguity between functionality and taxonomy is absent. The developed method was validated using RNA-seq data and sequencing data of the 16S rRNA amplicon on a simplified community. Consequently, the successful verification provides prospects for the application of this method for analyzing natural communities of the human intestinal microbiota.},
}
@article {pmid36662284,
year = {2023},
author = {He, T and Zhang, X and Du, J and Gilliam, FS and Yang, S and Tian, M and Zhang, C and Zhou, Y},
title = {Arbuscular Mycorrhizal Fungi Shift Soil Bacterial Community Composition and Reduce Soil Ammonia Volatilization and Nitrous Oxide Emissions.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {951-964},
pmid = {36662284},
issn = {1432-184X},
support = {No. 182300410013//Natural Science Foundation of Henan Province of China/ ; No. 30500712//Science and Technology Innovation Fund of Henan Agricultural University/ ; No. 2018YFD0200605//National Key Research and Development Program of China/ ; },
mesh = {*Soil ; Nitrous Oxide ; Ammonia/analysis ; *Mycorrhizae/chemistry ; Volatilization ; Nitrogen ; Fertilizers/analysis ; Agriculture ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) establish mutualistic relationships with the majority of terrestrial plants, increasing plant uptake of soil nitrogen (N) in exchange for photosynthates. And may influence soil ammonia (NH3) volatilization and nitrous oxide (N2O) emissions directly by improving plant N uptake, and/or indirectly by modifying soil bacterial community composition for the soil C availability increasing. However, the effects of AMF on soil NH3 volatilization and N2O emissions and their underlying mechanisms remain unclear. We carried out two independent experiments using contrasting methods, one with a compartmental box device (in 2016) and the other with growth pot experiment (in 2020) to examine functional relationships between AMF and soil NH3 volatilization and N2O emissions under varying N input. The presence of AMF significantly reduced soil NH3 volatilization and N2O emissions while enhancing plant biomass and plant N acquisition, and reducing soil NH4[+] and NO3[-], even with high N input. The presence of AMF also significantly reduced the relative abundance within the bacterial orders Sphingomonadales and Rhizobiales. Sphingomonadales correlated significantly and positively with soil NH3 volatilization in 2016 and N2O emissions, whereas Rhizobiales correlated positively with soil N2O emissions. High N input significantly increased soil NH3 volatilization and N2O emissions with increasing relative abundance of Sphingomonadales and Rhizobiales. These findings demonstrate the contribution of AMF in regulating NH3 and N2O emission by improving plant N uptake and altering soil bacterial communities. They also suggest that altering the rhizosphere microbiome might offer additional potential for restoration of N-enriched agroecosystems.},
}
@article {pmid36656658,
year = {2023},
author = {Zhang, S and Van Haesebroeck, J and Yang, Q and Defoirdt, T},
title = {Indole-3-acetic acid increases the survival of brine shrimp challenged with vibrios belonging to the Harveyi clade.},
journal = {Journal of fish diseases},
volume = {46},
number = {5},
pages = {477-486},
doi = {10.1111/jfd.13759},
pmid = {36656658},
issn = {1365-2761},
support = {//Bijzonder Onderzoeksfonds UGent/ ; //China Scholarship Council/ ; //Scientific Research Fund of Flanders/ ; },
mesh = {Animals ; *Artemia/microbiology ; *Indoleacetic Acids/pharmacology ; Larva ; *Vibrio parahaemolyticus/drug effects/physiology ; },
abstract = {Vibrios belonging to the Harveyi clade (including closely related species such as Vibrio campbellii, Vibrio harveyi and Vibrio parahaemolyticus) are important pathogens of aquatic organisms. In this study, we investigated the use of indole-3-acetic acid to control disease caused by Harveyi clade vibrios. Indole-3-acetic acid, which can be produced by various seaweeds and microalgae, was added to the rearing water of brine shrimp larvae challenged with 12 different Harveyi clade Vibrio strains. Indole-3-acetic acid significantly decreased the virulence of 10 of the strains without any effect on their growth. The latter is important as it will minimize the selective pressure for resistance development. The survival rate of brine shrimp larvae increased from 1.2-fold to 4.8-fold upon treatment with 400 μM indole-3-acetic acid. Additionally, indole-3-acetic acid significantly decreased the swimming motility in 10 of the strains and biofilm formation in eight of the strains. The mRNA levels of the pirA and pirB toxin genes were decreased to 46% and 42% by indole-3-acetic acid in the AHPND-causing strain V. parahaemolyticus M0904. Hence, our data demonstrate that indole-3-acetic acid has the potential to be an effective virulence inhibitor to control infections in aquaculture.},
}
@article {pmid36654062,
year = {2022},
author = {Song, W and Qiu, L and Qing, J and Zhi, W and Zha, Z and Hu, X and Qin, Z and Gong, H and Li, Y},
title = {Using Bayesian network model with MMHC algorithm to detect risk factors for stroke.},
journal = {Mathematical biosciences and engineering : MBE},
volume = {19},
number = {12},
pages = {13660-13674},
doi = {10.3934/mbe.2022637},
pmid = {36654062},
issn = {1551-0018},
mesh = {Humans ; Bayes Theorem ; *Algorithms ; *Stroke/epidemiology ; Risk Factors ; Logistic Models ; },
abstract = {Stroke is a major chronic non-communicable disease with high incidence, high mortality, and high recurrence. To comprehensively digest its risk factors and take some relevant measures to lower its prevalence is of great significance. This study aimed to employ Bayesian Network (BN) model with Max-Min Hill-Climbing (MMHC) algorithm to explore the risk factors for stroke. From April 2019 to November 2019, Shanxi Provincial People's Hospital conducted opportunistic screening for stroke in ten rural areas in Shanxi Province. First, we employed propensity score matching (PSM) for class balancing for stroke. Afterwards, we used Chi-square testing and Logistic regression model to conduct a preliminary analysis of risk factors for stroke. Statistically significant variables were incorporated into BN model construction. BN structure learning was achieved using MMHC algorithm, and its parameter learning was achieved with Maximum Likelihood Estimation. After PSM, 748 non-stroke cases and 748 stroke cases were included in this study. BN was built with 10 nodes and 12 directed edges. The results suggested that age, fasting plasma glucose, systolic blood pressure, and family history of stroke constitute direct risk factors for stroke, whereas sex, educational levels, high density lipoprotein cholesterol, diastolic blood pressure, and urinary albumin-to-creatinine ratio represent indirect risk factors for stroke. BN model with MMHC algorithm not only allows for a complicated network relationship between risk factors and stroke, but also could achieve stroke risk prediction through Bayesian reasoning, outshining traditional Logistic regression model. This study suggests that BN model boasts great prospects in risk factor detection for stroke.},
}
@article {pmid36652878,
year = {2023},
author = {Lin, Q and De Vrieze, J and Li, L and Fang, X and Li, X},
title = {Interconnected versus unconnected microorganisms: Does it matter in anaerobic digestion functioning.},
journal = {Journal of environmental management},
volume = {331},
number = {},
pages = {117307},
doi = {10.1016/j.jenvman.2023.117307},
pmid = {36652878},
issn = {1095-8630},
mesh = {Animals ; Swine ; Anaerobiosis ; Phylogeny ; *Manure ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Methane ; Bioreactors ; Biofuels ; },
abstract = {Microorganisms in anaerobic digestion (AD) are essential for wastes/pollutants treatment and energy recovery. Due to microbial enormous diversity, developing effective perspectives to understand microbial roles therein is urgent. This study conducted AD of swine manure, used an ensemble-based network analysis to distinguish interconnected, unconnected, copresence (positively interconnected) and mutual-exclusion (negatively interconnected) microorganisms within microbial communities, and explored their importance towards AD performances, using amplicon sequencing of 16S rRNA and 16S rRNA gene. Our analyses revealed greater importance of interconnected than unconnected microorganisms towards CH4 production and AD multifunctionality, which was attributed to higher niche breadth, deterministic community assembly, community stability and phylogenetic conservatism. The diversity was higher in unconnected than interconnected microorganisms, but was not linked to AD performances. Compared to copresence microorganisms, mutual-exclusion microorganisms showed greater and equal importance towards CH4 production and AD multifunctionality, which was attributed to their roles in stabilizing microbial communities. The increased feedstock biodegradability, by replacing part of manure with fructose or apple waste, hardly affected the relative importance of interconnected versus unconnected microorganisms towards CH4 production or AD multifunctionality. Our findings develop a new framework to understand microbial roles, and have important implications in targeted manipulation of critical microorganisms in waste-treatment systems.},
}
@article {pmid36651641,
year = {2023},
author = {Daebeler, A and Güell-Bujons, Q and Mooshammer, M and Zechmeister, T and Herbold, CW and Richter, A and Wagner, M and Daims, H},
title = {Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline-alkaline lakes.},
journal = {Environmental microbiology},
volume = {25},
number = {5},
pages = {1055-1067},
pmid = {36651641},
issn = {1462-2920},
support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Lakes ; *Nitrites ; Nitrates ; Ammonia ; Nitrification ; Bacteria/genetics ; Archaea/genetics ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Nitrite-oxidizing bacteria (NOB) catalyse the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.},
}
@article {pmid36648219,
year = {2023},
author = {Jiang, C and Zeng, H},
title = {Unique Habitat of Karst Tiankengs Changes the Taxonomy and Potential Metabolism of Soil Microbial Communities.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0231622},
pmid = {36648219},
issn = {2165-0497},
mesh = {Humans ; *Ecosystem ; Soil/chemistry ; Soil Microbiology ; Biodiversity ; *Microbiota ; Bacteria/genetics ; },
abstract = {Microbial communities in karst ecosystems have been extensively studied. However, in a class of deep-lying habitats with unique climates (karst tiankeng), the structure and ecological functions of microorganisms receive little attention, which is essential for understanding the biogeochemistry of karst tiankeng. Herein, microorganisms from inside (ITK) and outside (OTK) karst tiankengs were analyzed by high-throughput sequencing and multivariate statistical analysis. The results showed that the structure and function of soil bacterial communities inside and outside karst tiankengs were significantly different. The ITK microbial communities presented significantly higher Shannon diversity due to the abundant nutrients in karst tiankeng soil. Random molecular ecological network analysis revealed that the ITK network was simpler and more vulnerable and may be susceptible to environmental changes. More positive links within the network indicate that microorganisms adapt to the karst tiankeng through synergies. The keystones in karst tiankeng were mainly involved in the decomposition of soil organic matter and carbon/nitrogen cycles. Although soil total phosphorus and available potassium regulate microbial community structure variation, dispersal limitation is the predominant ecological process within the microbial community in karst tiankeng. In addition, the functional profiles of the microbial communities reveal that some human diseases (such as infectious diseases) exist in OTK. Collectively, these findings have enhanced our understanding of microbial interactions, ecological functions, and community composition processes in karst tiankeng ecosystems. IMPORTANCE Constrained by the trapped terrain, a unique ecosystem has formed in karst tiankeng. Soil microorganisms are essential for the formation and maintenance of ecosystems, but soil microbial ecology research in karst tiankeng is still lacking. In this study, representative habitats inside and outside karst tiankeng were selected to study the taxonomy and potential metabolism of soil microbial communities. The results show that the unique habitat of karst tiankeng reshapes the composition, structure, and function of soil microbial communities. Our results contribute to enhancing our understanding of sustainable recovery strategies in fragile ecosystems and understanding the biodiversity value of karst tiankeng under climate change.},
}
@article {pmid36646914,
year = {2023},
author = {Gruppuso, L and Receveur, JP and Fenoglio, S and Bona, F and Benbow, ME},
title = {Hidden Decomposers: the Role of Bacteria and Fungi in Recently Intermittent Alpine Streams Heterotrophic Pathways.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1499-1512},
pmid = {36646914},
issn = {1432-184X},
mesh = {*Rivers/microbiology ; Biodegradation, Environmental ; *Fungi/genetics/metabolism ; Bacteria/genetics/metabolism ; Plant Leaves/microbiology ; Ecosystem ; },
abstract = {The frequency of flow intermittency and drying events in Alpine rivers is expected to increase due to climate change. These events can have significant consequences for stream ecological communities, though the effects of reduced flow conditions on microbial communities of decomposing allochthonous leaf material require additional research. In this study, we investigated the bacterial and fungal communities associated with the decomposition of two common species of leaf litter, chestnut (Castanea sativa), and oak (Quercus robur). A sampling of experimentally placed leaf bags occurred over six collection dates (up to 126 days after placement) at seven stream sites in the Western Italian Alps with historically different flow conditions. Leaf-associated bacterial and fungal communities were identified using amplicon-based, high-throughput sequencing. Chestnut and oak leaf material harbored distinct bacterial and fungal communities, with a number of taxonomic groups differing in abundance, though bacterial community structure converged later in decomposition. Historical flow conditions (intermittent vs perennial rivers) and observed conditions (normal flow, low flow, ongoing drying event) had weaker effects on bacterial and fungal communities compared to leaf type and collection date (i.e., length of decomposition). Our findings highlight the importance of leaf characteristics (e.g., C:N ratios, recalcitrance) to the in-stream conditioning of leaf litter and a need for additional investigations of drying events in Alpine streams. This study provides new information on the microbial role in leaf litter decomposition with expected flow changes associated with a global change scenario.},
}
@article {pmid36646913,
year = {2023},
author = {Maucourt, F and Cébron, A and Budzinski, H and Le Menach, K and Peluhet, L and Czarnes, S and Melayah, D and Chapulliot, D and Vallon, L and Plassart, G and Hugoni, M and Fraissinet-Tachet, L},
title = {Prokaryotic, Microeukaryotic, and Fungal Composition in a Long-Term Polychlorinated Biphenyl-Contaminated Brownfield.},
journal = {Microbial ecology},
volume = {86},
number = {3},
pages = {1696-1708},
pmid = {36646913},
issn = {1432-184X},
mesh = {*Polychlorinated Biphenyls/analysis/chemistry/metabolism ; *Soil Pollutants/analysis ; Biodegradation, Environmental ; Soil Microbiology ; Bacteria/genetics/metabolism ; Soil/chemistry ; },
abstract = {Polychlorinated biphenyls (PCBs) are recognized as persistent organic pollutants and accumulate in organisms, soils, waters, and sediments, causing major health and ecological perturbations. Literature reported PCB bio-transformation by fungi and bacteria in vitro, but data about the in situ impact of those compounds on microbial communities remained scarce while being useful to guide biotransformation assays. The present work investigated for the first time microbial diversity from the three-domains-of-life in a long-term contaminated brownfield (a former factory land). Soil samples were ranked according to their PCB concentrations, and a significant increase in abundance was shown according to increased concentrations. Microbial communities structure showed a segregation from the least to the most PCB-polluted samples. Among the identified microorganisms, Bacteria belonging to Gammaproteobacteria class, as well as Fungi affiliated to Saccharomycetes class or Pleurotaceae family, including some species known to transform some PCBs were abundantly retrieved in the highly polluted soil samples.},
}
@article {pmid36645380,
year = {2023},
author = {Mynard, P and Algar, AC and Lancaster, LT and Bocedi, G and Fahri, F and Gubry-Rangin, C and Lupiyaningdyah, P and Nangoy, M and Osborne, OG and Papadopulos, AST and Sudiana, IM and Juliandi, B and Travis, JMJ and Herrera-Alsina, L},
title = {Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models.},
journal = {Systematic biology},
volume = {72},
number = {1},
pages = {106-119},
pmid = {36645380},
issn = {1076-836X},
mesh = {Phylogeny ; Phenotype ; *Genetic Speciation ; },
abstract = {Understanding the origins of diversity and the factors that drive some clades to be more diverse than others are important issues in evolutionary biology. Sophisticated SSE (state-dependent speciation and extinction) models provide insights into the association between diversification rates and the evolution of a trait. The empirical data used in SSE models and other methods is normally imperfect, yet little is known about how this can affect these models. Here, we evaluate the impact of common phylogenetic issues on inferences drawn from SSE models. Using simulated phylogenetic trees and trait information, we fitted SSE models to determine the effects of sampling fraction (phylogenetic tree completeness) and sampling fraction mis-specification on model selection and parameter estimation (speciation, extinction, and transition rates) under two sampling regimes (random and taxonomically biased). As expected, we found that both model selection and parameter estimate accuracies are reduced at lower sampling fractions (i.e., low tree completeness). Furthermore, when sampling of the tree is imbalanced across sub-clades and tree completeness is ≤ 60%, rates of false positives increase and parameter estimates are less accurate, compared to when sampling is random. Thus, when applying SSE methods to empirical datasets, there are increased risks of false inferences of trait dependent diversification when some sub-clades are heavily under-sampled. Mis-specifying the sampling fraction severely affected the accuracy of parameter estimates: parameter values were over-estimated when the sampling fraction was specified as lower than its true value, and under-estimated when the sampling fraction was specified as higher than its true value. Our results suggest that it is better to cautiously under-estimate sampling efforts, as false positives increased when the sampling fraction was over-estimated. We encourage SSE studies where the sampling fraction can be reasonably estimated and provide recommended best practices for SSE modeling. [Trait dependent diversification; SSE models; phylogenetic tree completeness; sampling fraction.].},
}
@article {pmid36644938,
year = {2023},
author = {van Neerbos, FAC and Dewitte, P and Wäckers, F and Wenseleers, T and Jacquemyn, H and Lievens, B},
title = {Bacterial volatiles elicit differential olfactory responses in insect species from the same and different trophic levels.},
journal = {Insect science},
volume = {30},
number = {5},
pages = {1464-1480},
doi = {10.1111/1744-7917.13176},
pmid = {36644938},
issn = {1744-7917},
abstract = {Insect communities consist of species from several trophic levels that have to forage for suitable resources among and within larger patches of nonresources. To locate their resources, insects use diverse stimuli, including olfactory, visual, acoustic, tactile and gustatory cues. While most research has focused on cues derived from plants and other insects, there is mounting evidence that insects also respond to volatile organic compounds (VOCs) emitted by microorganisms. However, to date little is known about how the olfactory response of insects within and across different trophic levels is affected by bacterial VOCs. In this study, we used Y-tube bioassays and chemical analysis of VOCs to assess how VOCs emitted by bacteria affect the olfactory response of insects of the same and different trophic levels. Experiments were performed using two aphid species (Amphorophora idaei Börner and Myzus persicae var. nicotianae Blackman), three primary parasitoid species (Aphidius colemani Viereck, A. ervi Haliday, and A. matricariae Viereck), and two hyperparasitoid species (Asaphes suspensus Nees and Dendrocerus aphidum Rondani). Olfactory responses were evaluated for three bacterial strains (Bacillus pumilus ST18.16/133, Curtobacterium sp. ST18.16/085, and Staphylococcus saprophyticus ST18.16/160) that were isolated from the habitat of the insects. Results revealed that insects from all trophic levels responded to bacterial volatiles, but olfactory responses varied between and within trophic levels. All bacteria produced the same set of volatile compounds, but often in different relative concentrations. For 11 of these volatiles we found contrasting correlations between their concentration and the behavior of the primary parasitoids and hyperparasitoids. Furthermore, olfactometer experiments on three of these compounds confirmed the contrasting olfactory responses of primary parasitoids and hyperparasitoids. The potential of these findings for the development of novel semiochemical-based strategies to improve biological aphid control has been discussed.},
}
@article {pmid36644338,
year = {2022},
author = {Romano, F and Symiakaki, K and Pitta, P},
title = {Sex in the wild: repeated observations of planktonic ciliate conjugation from field samples.},
journal = {Journal of plankton research},
volume = {44},
number = {2},
pages = {333-336},
pmid = {36644338},
issn = {0142-7873},
abstract = {Ciliate conjugation is considered a rare event to encounter in the field and it is mostly reported from cultures. In this work, we describe a synchronized conjugation event of planktonic ciliates that was discovered twice; in September 2019, at two different locations in the Cretan Sea, Eastern Mediterranean, and in October 2020. In 2019, first, at 2 m depth of the coastal station POSEIDON-HCB, in samples fixed with acid Lugol and formaldehyde, we found 340 and 200 mating pairs L[-1]of different ciliate species, respectively; and second, at the Heraklion port, we found 220 mating pairs L[-1] of Strombidinopsis sp. and 1960 mating pairs L[-1] of Strombidium sp. At the Heraklion port visited again in 2020, we found 800 mating pairs L[-1] of Strombidinopsis sp. and 200 mating pairs L[-1] of Strombidium sp. Since detailed descriptions of conjugation in pelagic oligotrich ciliates are missing, our observations indicate that ciliate conjugation could be a frequent and periodic phenomenon, under specific conditions.},
}
@article {pmid36643595,
year = {2023},
author = {Villa, F and Wu, YL and Zerboni, A and Cappitelli, F},
title = {Corrigendum: In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface.},
journal = {Bioscience},
volume = {73},
number = {1},
pages = {69},
doi = {10.1093/biosci/biac109},
pmid = {36643595},
issn = {0006-3568},
abstract = {[This corrects the article DOI: 10.1093/biosci/biac091.].},
}
@article {pmid36640506,
year = {2023},
author = {Lamprea Pineda, PA and Demeestere, K and Toledo, M and Boon, N and Van Langenhove, H and Walgraeve, C},
title = {Long-term biofiltration of gaseous N,N-dimethylformamide: Operational performance and microbial diversity analysis at different conditions.},
journal = {Journal of hazardous materials},
volume = {447},
number = {},
pages = {130767},
doi = {10.1016/j.jhazmat.2023.130767},
pmid = {36640506},
issn = {1873-3336},
mesh = {*Gases/analysis ; Dimethylformamide ; *Air Pollutants/analysis ; Temperature ; Filtration/methods ; Biodegradation, Environmental ; },
abstract = {N,N-Dimethylformamide (DMF) is an organic solvent produced in large quantities worldwide. It is considered as a hazardous air pollutant and its emission should be controlled. However, only a limited number of studies have been performed on the removal of gaseous DMF by biological technologies. In this paper, we evaluate the removal of DMF under mesophilic and thermophilic conditions in a lab-scale biofilter for 472 days. The results show that, at ambient temperature, the biofilter achieved an average removal efficiency (RE) of 99.7 ± 0.3 % at Inlet Loads (ILs) up to 297 ± 52 g DFM m[-3] h[-1] (Empty Bed Residence Time (EBRTs) of 10.7 s). However, a decrease in EBRT (6.4 s) led to an unstable outlet concentration and, thus, to a drop in the biofilter performance (average RE: 90 ± 9 %). Moreover, an increase in temperature up to 65 °C led to a gradual decrease in RE (till 91 ± 7 %). Microbial analysis indicates that once the microorganisms encountered DMF, Rhizobiaceae dominated followed by Alcaligenaceae. Afterwards, a strong decrease in Rhizobiaceae was observed at every increase in temperature, and at 65 °C, the taxa were more heterogeneous. Overall, our experimental results indicate that biofiltration is a promising technique to remove DMF from waste gas streams.},
}
@article {pmid36639537,
year = {2023},
author = {Osvatic, JT and Yuen, B and Kunert, M and Wilkins, L and Hausmann, B and Girguis, P and Lundin, K and Taylor, J and Jospin, G and Petersen, JM},
title = {Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis.},
journal = {The ISME journal},
volume = {17},
number = {3},
pages = {453-466},
pmid = {36639537},
issn = {1751-7370},
mesh = {Phylogeny ; *Symbiosis/genetics ; Adaptation, Physiological ; Biological Evolution ; Bacteria/genetics ; Water ; *Hydrothermal Vents ; },
abstract = {Chemosynthetic symbioses between bacteria and invertebrates occur worldwide from coastal sediments to the deep sea. Most host groups are restricted to either shallow or deep waters. In contrast, Lucinidae, the most species-rich family of chemosymbiotic invertebrates, has both shallow- and deep-sea representatives. Multiple lucinid species have independently colonized the deep sea, which provides a unique framework for understanding the role microbial symbionts play in evolutionary transitions between shallow and deep waters. Lucinids acquire their symbionts from their surroundings during early development, which may allow them to flexibly acquire symbionts that are adapted to local environments. Via metagenomic analyses of museum and other samples collected over decades, we investigated the biodiversity and metabolic capabilities of the symbionts of 22 mostly deep-water lucinid species. We aimed to test the theory that the symbiont played a role in adaptation to life in deep-sea habitats. We identified 16 symbiont species, mostly within the previously described genus Ca. Thiodiazotropha. Most genomic functions were shared by both shallow-water and deep-sea Ca. Thiodiazotropha, though nitrogen fixation was exclusive to shallow-water species. We discovered multiple cases of symbiont switching near deep-sea hydrothermal vents and cold seeps, where distantly related hosts convergently acquired novel symbionts from a different bacterial order. Finally, analyses of selection revealed consistently stronger purifying selection on symbiont genomes in two extreme habitats - hydrothermal vents and an oxygen-minimum zone. Our findings reveal that shifts in symbiont metabolic capability and, in some cases, acquisition of a novel symbiont accompanied adaptation of lucinids to challenging deep-sea habitats.},
}
@article {pmid36635570,
year = {2023},
author = {Strachan, CR and Yu, XA and Neubauer, V and Mueller, AJ and Wagner, M and Zebeli, Q and Selberherr, E and Polz, MF},
title = {Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome.},
journal = {Nature microbiology},
volume = {8},
number = {2},
pages = {309-320},
pmid = {36635570},
issn = {2058-5276},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Female ; Cattle ; Animals ; *Rumen/metabolism ; *Microbiota/genetics ; Genome ; Acetates/metabolism ; },
abstract = {The activities of different microbes in the cow rumen have been shown to modulate the host's ability to utilize plant biomass, while the host-rumen interface has received little attention. As datasets collected worldwide have pointed to Campylobacteraceae as particularly abundant members of the rumen epithelial microbiome, we targeted this group in a subset of seven cows with meta- and isolate genome analysis. We show that the dominant Campylobacteraceae lineage has recently speciated into two populations that were structured by genome-wide selective sweeps followed by population-specific gene import and recombination. These processes led to differences in gene expression and enzyme domain composition that correspond to the ability to utilize acetate, the main carbon source for the host, at the cost of inhibition by propionate. This trade-off in competitive ability further manifests itself in differential dynamics of the two populations in vivo. By exploring population-level adaptations that otherwise remain cryptic in culture-independent analyses, our results highlight how recent evolutionary dynamics can shape key functional roles in the rumen microbiome.},
}
@article {pmid36635489,
year = {2023},
author = {Wang, J and Raza, W and Jiang, G and Yi, Z and Fields, B and Greenrod, S and Friman, VP and Jousset, A and Shen, Q and Wei, Z},
title = {Bacterial volatile organic compounds attenuate pathogen virulence via evolutionary trade-offs.},
journal = {The ISME journal},
volume = {17},
number = {3},
pages = {443-452},
pmid = {36635489},
issn = {1751-7370},
support = {BB/T010606/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Volatile Organic Compounds/pharmacology ; Virulence/genetics ; *Bacillus ; Adaptation, Physiological ; Soil ; *Ralstonia solanacearum/genetics ; Plant Diseases/microbiology ; },
abstract = {Volatile organic compounds (VOCs) produced by soil bacteria have been shown to exert plant pathogen biocontrol potential owing to their strong antimicrobial activity. While the impact of VOCs on soil microbial ecology is well established, their effect on plant pathogen evolution is yet poorly understood. Here we experimentally investigated how plant-pathogenic Ralstonia solanacearum bacterium adapts to VOC-mixture produced by a biocontrol Bacillus amyloliquefaciens T-5 bacterium and how these adaptations might affect its virulence. We found that VOC selection led to a clear increase in VOC-tolerance, which was accompanied with cross-tolerance to several antibiotics commonly produced by soil bacteria. The increasing VOC-tolerance led to trade-offs with R. solanacearum virulence, resulting in almost complete loss of pathogenicity in planta. At the genetic level, these phenotypic changes were associated with parallel mutations in genes encoding lipopolysaccharide O-antigen (wecA) and type-4 pilus biosynthesis (pilM), which both have been linked with outer membrane permeability to antimicrobials and plant pathogen virulence. Reverse genetic engineering revealed that both mutations were important, with pilM having a relatively larger negative effect on the virulence, while wecA having a relatively larger effect on increased antimicrobial tolerance. Together, our results suggest that microbial VOCs are important drivers of bacterial evolution and could potentially be used in biocontrol to select for less virulent pathogens via evolutionary trade-offs.},
}
@article {pmid36631688,
year = {2023},
author = {Rasmussen, TS and Koefoed, AK and Deng, L and Muhammed, MK and Rousseau, GM and Kot, W and Sprotte, S and Neve, H and Franz, CMAP and Hansen, AK and Vogensen, FK and Moineau, S and Nielsen, DS},
title = {CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice.},
journal = {The ISME journal},
volume = {17},
number = {3},
pages = {432-442},
pmid = {36631688},
issn = {1751-7370},
support = {//CIHR/Canada ; },
mesh = {Animals ; Mice ; *Bacteriophages/genetics ; CRISPR-Cas Systems ; Bacteria/genetics ; Base Sequence ; Plasmids ; },
abstract = {Many bacteria and archaea harbor the adaptive CRISPR-Cas system, which stores small nucleotide fragments from previous invasions of nucleic acids via viruses or plasmids. This molecular archive blocks further invaders carrying identical or similar nucleotide sequences. However, few of these systems have been confirmed experimentally to be active in gut bacteria. Here, we demonstrate experimentally that the type I-C CRISPR-Cas system of the prevalent gut bacterium Eggerthella lenta can specifically target and cleave foreign DNA in vitro by using a plasmid transformation assay. We also show that the CRISPR-Cas system acquires new immunities (spacers) from the genome of a virulent E. lenta phage using traditional phage assays in vitro but also in vivo using gnotobiotic (GB) mice. Both high phage titer and an increased number of spacer acquisition events were observed when E. lenta was exposed to a low multiplicity of infection in vitro, and three phage genes were found to contain protospacer hotspots. Fewer new spacer acquisitions were detected in vivo than in vitro. Longitudinal analysis of phage-bacteria interactions showed sustained coexistence in the gut of GB mice, with phage abundance being approximately one log higher than the bacteria. Our findings show that while the type I-C CRISPR-Cas system is active in vitro and in vivo, a highly virulent phage in vitro was still able to co-exist with its bacterial host in vivo. Taken altogether, our results suggest that the CRISPR-Cas defense system of E. lenta provides only partial immunity in the gut.},
}
@article {pmid36631293,
year = {2023},
author = {Mason, AR and Taylor, LS and DeBruyn, JM},
title = {Microbial ecology of vertebrate decomposition in terrestrial ecosystems.},
journal = {FEMS microbiology ecology},
volume = {99},
number = {2},
pages = {},
doi = {10.1093/femsec/fiad006},
pmid = {36631293},
issn = {1574-6941},
mesh = {Animals ; Humans ; *Ecosystem ; Vertebrates/metabolism ; Ecology ; Soil Microbiology ; Soil ; *Microbiota ; Mammals ; },
abstract = {Vertebrate decomposition results in an ephemeral disturbance of the surrounding environment. Microbial decomposers are recognized as key players in the breakdown of complex organic compounds, controlling carbon and nutrient fate in the ecosystem and potentially serving as indicators of time since death for forensic applications. As a result, there has been increasing attention on documenting the microbial communities associated with vertebrate decomposition, or the 'necrobiome'. These necrobiome studies differ in the vertebrate species, microhabitats (e.g. skin vs. soil), and geographic locations studied, but many are narrowly focused on the forensic application of microbial data, missing the larger opportunity to understand the ecology of these communities. To further our understanding of microbial dynamics during vertebrate decomposition and identify knowledge gaps, there is a need to assess the current works from an ecological systems perspective. In this review, we examine recent work pertaining to microbial community dynamics and succession during vertebrate (human and other mammals) decomposition in terrestrial ecosystems, through the lens of a microbial succession ecological framework. From this perspective, we describe three major microbial microhabitats (internal, external, and soil) in terms of their unique successional trajectories and identify three major knowledge gaps that remain to be addressed.},
}
@article {pmid36629441,
year = {2023},
author = {Šigutová, H and Šigut, M and Pyszko, P and Kostovčík, M and Kolařík, M and Drozd, P},
title = {Seasonal Shifts in Bacterial and Fungal Microbiomes of Leaves and Associated Leaf-Mining Larvae Reveal Persistence of Core Taxa Regardless of Diet.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0316022},
pmid = {36629441},
issn = {2165-0497},
mesh = {Animals ; *Mycobiome ; Larva ; Seasons ; Bacteria/genetics ; Diet ; },
abstract = {Microorganisms are key mediators of interactions between insect herbivores and their host plants. Despite a substantial interest in studying various aspects of these interactions, temporal variations in microbiomes of woody plants and their consumers remain understudied. In this study, we investigated shifts in the microbiomes of leaf-mining larvae (Insecta: Lepidoptera) and their host trees over one growing season in a deciduous temperate forest. We used 16S and ITS2 rRNA gene metabarcoding to profile the bacterial and fungal microbiomes of leaves and larvae. We found pronounced shifts in the leaf and larval microbiota composition and richness as the season progressed, and bacteria and fungi showed consistent patterns. The quantitative similarity between leaf and larval microbiota was very low for bacteria (~9%) and decreased throughout the season, whereas fungal similarity increased and was relatively high (~27%). In both leaves and larvae, seasonality, along with host taxonomy, was the most important factor shaping microbial communities. We identified frequently occurring microbial taxa with significant seasonal trends, including those more prevalent in larvae (Streptococcus, Candida sake, Debaryomyces prosopidis, and Neoascochyta europaea), more prevalent in leaves (Erwinia, Seimatosporium quercinum, Curvibasidium cygneicollum, Curtobacterium, Ceramothyrium carniolicum, and Mycosphaerelloides madeirae), and frequent in both leaves and larvae (bacterial strain P3OB-42, Methylobacterium/Methylorubrum, Bacillus, Acinetobacter, Cutibacterium, and Botrytis cinerea). Our results highlight the importance of considering seasonality when studying the interactions between plants, herbivorous insects, and their respective microbiomes, and illustrate a range of microbial taxa persistent in larvae, regardless of their occurrence in the diet. IMPORTANCE Leaf miners are endophagous insect herbivores that feed on plant tissues and develop and live enclosed between the epidermis layers of a single leaf for their entire life cycle. Such close association is a precondition for the evolution of more intimate host-microbe relationships than those found in free-feeding herbivores. Simultaneous comparison of bacterial and fungal microbiomes of leaves and their tightly linked consumers over time represents an interesting study system that could fundamentally contribute to the ongoing debate on the microbial residence of insect gut. Furthermore, leaf miners are ideal model organisms for interpreting the ecological and evolutionary roles of microbiota in host plant specialization. In this study, the larvae harbored specific microbial communities consisting of core microbiome members. Observed patterns suggest that microbes, especially bacteria, may play more important roles in the caterpillar holobiont than generally presumed.},
}
@article {pmid36629429,
year = {2023},
author = {Dragone, NB and Whittaker, K and Lord, OM and Burke, EA and Dufel, H and Hite, E and Miller, F and Page, G and Slayback, D and Fierer, N},
title = {The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga.},
journal = {mBio},
volume = {14},
number = {1},
pages = {e0331322},
pmid = {36629429},
issn = {2150-7511},
mesh = {Tonga ; *Cyanobacteria/metabolism ; Volcanic Eruptions/analysis ; Sulfur/metabolism ; },
abstract = {The island of Hunga Tonga Hunga Ha'apai (HTHH) in the Kingdom of Tonga was formed by Surtseyan eruptions and persisted for 7 years before being obliterated by a massive volcanic eruption on 15 January 2022. Before it was destroyed, HTHH was an unparalleled natural laboratory to study primary succession on a newly formed landmass. We characterized the microbial communities found on the surface sediments of HTHH using a combination of quantitative PCR, marker gene sequencing, and shotgun metagenomic analyses. Contrary to expectations, photosynthetic cyanobacteria were not detected in these sediments, even though they are typically dominant in the earliest stages of primary succession in other terrestrial environments. Instead, our results suggest that the early sediment communities were composed of a diverse array of bacterial taxa, including trace gas oxidizers, anoxygenic photosynthesizers, and chemolithotrophs capable of metabolizing inorganic sulfur, with these bacteria likely sourced from nearby active geothermal environments. While the destruction of HTHH makes it impossible to revisit the site to conduct in situ metabolic measurements or observe how the microbial communities might have continued to change over time, our results do suggest that the early microbial colonizers have unique origins and metabolic capabilities. IMPORTANCE The volcanic island of Hunga Tonga Hunga Ha'apai in the Kingdom of Tonga represents a very rare example of new island formation and thus a unique opportunity to study how organisms colonize a new landmass. We found that the island was colonized by diverse microbial communities shortly after its formation in 2015, with these microbes likely originating from nearby geothermal environments. Primary succession in this system was distinct from that typically observed in other terrestrial environments, with the early microbial colonizers relying on unique metabolic strategies to survive on the surface of this newly formed island, including the capacity to generate energy via sulfur and trace gas metabolism.},
}
@article {pmid36623784,
year = {2023},
author = {Anedda, E and Farrell, ML and Morris, D and Burgess, CM},
title = {Evaluating the impact of heavy metals on antimicrobial resistance in the primary food production environment: A scoping review.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {320},
number = {},
pages = {121035},
doi = {10.1016/j.envpol.2023.121035},
pmid = {36623784},
issn = {1873-6424},
mesh = {*Anti-Bacterial Agents/toxicity/analysis ; Manure/analysis ; Drug Resistance, Bacterial/genetics ; *Metals, Heavy/toxicity/analysis ; Copper/analysis ; Genes, Bacterial ; Soil ; },
abstract = {Heavy metals are naturally occurring environmental compounds, which can influence antimicrobial resistance (AMR) dissemination. However, there is limited information on how heavy metals may act as a selective pressure on AMR in the primary food production environment. This review aims to examine the literature on this topic in order to identify knowledge gaps. A total of 73 studies, which met pre-established criteria, were included. These investigations were undertaken between 2008 and 2021, with a significant increase in the last three years. The majority of studies included were undertaken in China. Soil, water and manure were the most common samples analysed, and the sampling locations varied from areas with a natural presence of heavy metals, areas intentionally amended with heavy metals or manure, to areas close to industrial activity or mines. Fifty-four per cent of the investigations focused on the analysis of four or more heavy metals, and copper and zinc were the metals most frequently analysed (n = 59, n = 49, respectively). The findings of this review highlight a link between heavy metals and AMR in the primary food production environment. Heavy metals impacted the abundance and dissemination of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs), with MGEs also observed as playing a key role in the spread of ARGs and metal resistance genes (MRGs). Harmonization of methodologies used in future studies would increase the opportunity for comparison between studies. Further research is also required to broaden the availability of data at a global level.},
}
@article {pmid36621691,
year = {2023},
author = {Cui, H and Xu, R and Yu, Z and Meng, F},
title = {Phylogenetic group-based assembly and co-occurrence pattern of the microbial community in full-scale wastewater treatment plants during the Chinese spring festival.},
journal = {Chemosphere},
volume = {316},
number = {},
pages = {137775},
doi = {10.1016/j.chemosphere.2023.137775},
pmid = {36621691},
issn = {1879-1298},
mesh = {Sewage ; Phylogeny ; Holidays ; Bioreactors ; *Microbiota ; *Gammaproteobacteria ; *Water Purification ; },
abstract = {The quality and quantity of domestic sewage discharge vary significantly during the Chinese Spring Festival due to the huge population shift. The dynamics of microbial community traits during the Spring Festival, particularly the phylogenetic group-based assembly and co-occurrence patterns, are however little understood. Here, influent and activated sludge samples from 2 full-scale wastewater treatment plants were collected bi-daily throughout a 20-day Spring Festival period and subjected to high-throughput Illumina-MiSeq sequencing. The findings revealed that the microbial communities in the activated sludge displayed a comparatively stable pattern, and that the influent communities experienced significant temporal fluctuations in terms of diversity and composition. The characterization by "Infer Community Assembly Mechanisms by Phylogenetic-bin based null model" demonstrated that for Competibacter glycogen-accumulating organisms, the assembly mechanism shifted from deterministic process (HoS = 69.5%) before the Spring Festival to stochastic process (DR = 65.9%) after the Spring Festival. The network analysis revealed that the network structure of sludge communities was more stable before the Spring Festival than that after the Spring Festival. Additionally, sludge communities had no keystone species in common with the influent before the Spring Festival, while the sludge and influent communities shared two keystone taxa after the Spring Festival (Sebaldella and Candidatus Competibacter). This study would deepen our understanding of the microbial ecology in biological wastewater treatment systems, which also aids in managing wastewater treatment plants.},
}
@article {pmid36615993,
year = {2022},
author = {Mosquera-Romero, S and Anaya-Garzon, J and Garcia-Timermans, C and Van Dorpe, J and Hoorens, A and Commenges-Bernole, N and Verbeken, K and Rabaey, K and Varia, J},
title = {Combined Gold Recovery and Nanoparticle Synthesis in Microbial Systems Using Fractional Factorial Design.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {13},
number = {1},
pages = {},
pmid = {36615993},
issn = {2079-4991},
abstract = {Green synthesis of gold nanoparticles (AuNPs) using microorganisms has been generally studied aiming for high-yield production and morphologies appropriated for various applications, such as bioremediation, (bio)sensors, and (bio)catalysis. Numerous approaches showed the individual effect of factors influencing the synthesis of AuNPs with limited analysis of the governing factors enhancing the production and desired quality of the precipitates. This study proposes a fractional-factorial design to investigate the simultaneous influence of seven environmental factors (cell concentration, temperature, anoxic/oxic conditions, pH, gold concentration, electron donor type, and bacterial species) on the recovery yield and synthesis of targeted AuNPs. Various sizes and morphologies of the AuNPs were obtained by varying the environmental factors studied. The factors with significant effects (i.e., 0.2 mM Au and pH 5) were selected according to statistical analysis for optimal removal of 88.2 ± 3.5% of gold and with the production of valuable 50 nm AuNPs, which are known for their enhanced sensitivity. Implications of the cytochrome-C on the bacterial mechanisms and the provision of electron donors via an electrochemical system are further discussed. This study helps develop gold recovery and nanoparticle synthesis methods, focusing on the determining factor(s) for efficient, low-cost, green synthesis of valuable materials.},
}
@article {pmid36611775,
year = {2022},
author = {Imperatore, R and Fronte, B and Scicchitano, D and Orso, G and Marchese, M and Mero, S and Licitra, R and Coccia, E and Candela, M and Paolucci, M},
title = {Dietary Supplementation with a Blend of Hydrolyzable and Condensed Tannins Ameliorates Diet-Induced Intestinal Inflammation in Zebrafish (Danio rerio).},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {1},
pages = {},
pmid = {36611775},
issn = {2076-2615},
abstract = {The current study evaluated the effects of hydrolyzable and condensed tannins from chestnut and quebracho wood, respectively (TSP, Silvafeed[®]), on zebrafish with intestinal inflammation induced by a plant-based diet (basal diet). Four experimental diets were prepared as follows: the basal diet + 0 TSP, the basal diet + TSP at 0.9 g/kg of feed, the basal diet + TSP at 1.7 g/kg of feed, and the basal diet + TSP at 3.4 g/kg of feed. Eighty-four zebrafish (Danio rerio) were fed for 12 days with the experimental diets. In zebrafish fed the basal diet, intestine integrity appeared to be altered, with damaged intestinal villi, high immunoexpression of tumor necrosis factor-α (TNFα) and cyclooxygenase 2 (COX2), and high expression of the cox2, interleukin 1 (il-1b), interleukin 8 (cxcl8-l1), and tnfα genes. The tannin treatment partially restored intestinal morphology and downregulated the expression of cytokines. The best activity was detected with 1.7 and 3.4 g/kg of feed. In the guts of all groups, Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes were the most represented phyla. The most represented genera were Plesiomonas and Sphingomonas, belonging to the Proteobacteria phylum; Cetobacterium, belonging to the Fusobacteria phylum; and Lactobacillus, belonging to the Firmicutes phylum. No significant differences were detected among groups, except for a slight decrease in the Fusobacteria phylum and slight increases in the Shewanella and Bacteroides genera with TSP. In conclusion, these results suggest that tannins can improve the zebrafish intestinal inflammation caused by a terrestrial-plant-based diet in a dose-dependent manner.},
}
@article {pmid36610634,
year = {2023},
author = {Li, C and Liu, C and Liu, J and Feng, C},
title = {Insight into the temporal dynamics of microbial succession and ecology mechanisms in biological activated carbon tanks.},
journal = {The Science of the total environment},
volume = {866},
number = {},
pages = {161366},
doi = {10.1016/j.scitotenv.2022.161366},
pmid = {36610634},
issn = {1879-1026},
mesh = {*Charcoal/chemistry ; *Microbiota ; Microbial Consortia ; Biodiversity ; China ; },
abstract = {Biological activated carbon (BAC) has long been applied in China to guarantee water quality and to achieve drinking water regulations. However, a knowledge gap remains regarding the temporal dynamics of microbial communities, particularly microbe-based assembly and co-occurrence patterns. Accordingly, this study investigated the evolution of BAC microbial communities using a pilot-scale system and examined by multivariate ecological combined with high-throughput Illumina sequencing and statistical methods. The results showed that BAC microbial diversity reached its peak in 2 years and declined thereafter. Microbial communities composition was accompanied by significant temporal evolution in the BAC biofilm. Deterministic processes gained in importance along with time, especially homogeneous selection which contributed 59.09 %-75.63 % to the community assembly in 8-yr, 9-yr, and 10-yr BAC. According to co-occurrence network analysis, microbial networks have more unstable structures over time, as evidenced by higher modularity, heightened connectivity, and fewer keystones. Moreover, the interaction between microbial taxa tended to have a higher proportion of competitive relationships during the operation of the BAC tank, ranging from 13.51 % to 76.35 %. Based on these dynamic ecological processes, microbial community succession in BAC biofilm might undergo four phases: community establishment (Years 0-2); community stability (Years 2-5); community quasi-degradation (Years 5-8); community degradation (Years 8-10). The performance of BAC was greatly influenced by community development, and contaminant removal gradually decreased as community succession proceeded. These results add to our knowledge of microbial ecology and provide the basis for further research into microbial communities' regulation strategies in BAC tanks.},
}
@article {pmid36602317,
year = {2023},
author = {An, XL and Xu, JX and Xu, MR and Zhao, CX and Li, H and Zhu, YG and Su, JQ},
title = {Dynamics of Microbial Community and Potential Microbial Pollutants in Shopping Malls.},
journal = {mSystems},
volume = {8},
number = {1},
pages = {e0057622},
pmid = {36602317},
issn = {2379-5077},
mesh = {Humans ; *Environmental Pollutants ; *Microbiota/genetics ; Soil ; Public Health ; Built Environment ; },
abstract = {Shopping malls offer various niches for microbial populations, potentially serving as sources and reservoirs for the spread of microorganisms of public health concern. However, knowledge about the microbiome and the distribution of human pathogens in malls is largely unknown. Here, we examine the microbial community dynamics and genotypes of potential pathogens from floor and escalator surfaces in shopping malls and adjacent road dusts and greenbelt soils. The distribution pattern of microbial communities is driven primarily by habitats and seasons. A significant enrichment of human-associated microbiota in the indoor environment indicates that human interactions with surfaces might be another strong driver for mall microbiomes. Neutral community models suggest that the microbial community assembly is strongly driven by stochastic processes. Distinct performances of microbial taxonomic signatures for environmental classifications indicate the consistent differences of microbial communities of different seasons/habitats and the strong anthropogenic effect on homogenizing microbial communities of shopping malls. Indoor environments harbored higher concentrations of human pathogens than outdoor samples, also carrying a high proportion of antimicrobial resistance-associated multidrug efflux genes and virulence genes. These findings enhanced the understanding of the microbiome in the built environment and the interactions between humans and the built environment, providing a basis for tracking biothreats and communicable diseases and developing sophisticated early warning systems. IMPORTANCE Shopping malls are distinct microbial environments which can facilitate a constant transmission of microorganisms of public health concern between humans and the built environment or between human and human. Despite extensive investigation of the natural environmental microbiome, no comprehensive profile of microbial ecology has been reported in malls. Characterizing microbial distribution, potential pathogens, and antimicrobial resistance will enhance our understanding of how these microbial communities are formed, maintained, and transferred and help establish a baseline for biosurveillance of potential public health threats in malls.},
}
@article {pmid36596939,
year = {2023},
author = {Lemberger, U and Pjevac, P and Hausmann, B and Berry, D and Moser, D and Jahrreis, V and Özsoy, M and Shariat, SF and Veser, J},
title = {The microbiome of kidney stones and urine of patients with nephrolithiasis.},
journal = {Urolithiasis},
volume = {51},
number = {1},
pages = {27},
pmid = {36596939},
issn = {2194-7236},
mesh = {Humans ; *Metabolic Syndrome ; RNA, Ribosomal, 16S/genetics ; *Kidney Calculi/diagnosis ; *Nephrolithiasis/urine ; *Microbiota ; Bacteria ; },
abstract = {The incidence of nephrolithiasis is rising worldwide. Although it is a multifactorial disease, lifestyle plays a major role in its etiology. Another considerable factor could be an aberrant microbiome. In our observational single-center study, we aimed to investigate the composition of bacteria in kidney stones and urine focusing on patients with features of metabolic syndrome. Catheterized urine and kidney stones were collected prospectively from 100 consecutive patients undergoing endoscopic nephrolithotomy between 2020 and 2021 at our clinic. Microbiome composition was analyzed via 16S rRNA gene amplicon sequencing. Detection of bacteria was successful in 24% of the analyzed kidney stones. These patients had a prolonged length of stay compared to patients without verifiable bacteria in their stones (2.9 vs 1.5 days). Patients with features of metabolic syndrome were characterized by kidney stones colonized with classical gastrointestinal bacteria and displayed a significant enrichment of Enterococcaceae and Enterobacteriaceae. Stones of patients without features of metabolic syndrome characterized by Ureaplasma and Staphylococcaceae. Patients with bacteria in their kidney stones exhibit a longer length of stay, possibly due to more complex care. Patients presenting with features of metabolic syndrome displayed a distinct stone microbiome compared to metabolically fit patients. Understanding the role of bacteria in stone formation could enable targeted therapy, prevention of post-operative complications and new therapeutic strategies.},
}
@article {pmid36592956,
year = {2023},
author = {Martiniuk, JT and Hamilton, J and Dodsworth, T and Measday, V},
title = {Grape-associated fungal community patterns persist from berry to wine on a fine geographical scale.},
journal = {FEMS yeast research},
volume = {23},
number = {},
pages = {},
pmid = {36592956},
issn = {1567-1364},
mesh = {*Vitis/microbiology ; *Wine/microbiology ; *Mycobiome ; Fruit ; Geography ; Fermentation ; },
abstract = {Wine grape fungal community composition is influenced by abiotic factors including geography and vintage. Compositional differences may correlate with different wine metabolite composition and sensory profiles, suggesting a microbial role in the shaping of a wine's terroir, or regional character. While grape and wine-associated fungal community composition has been studied extensively at a regional and sub-regional scale, it has not been explored in detail on fine geographical scales over multiple harvests. Over two years, we examined the fungal communities on Vitis Vinifera cv. Pinot noir grape berry surfaces, in crushed grapes, and in lab spontaneous fermentations from three vineyards within a < 1 km radius in Canada's Okanagan Valley wine region. We also evaluated the effect of winery environment exposure on fungal community composition by sampling grapes crushed and fermented in the winery at commercial scale. Spatiotemporal community structure was evident among grape berry surface, crushed grape and fermentation samples, with each vineyard exhibiting a distinct fungal community signature. Crushed grape fungal populations were richer in fermentative yeast species compared to grape berry surface fungal populations. Our study suggests that, as on a regional level, fungal populations may contribute to fine-scale -terroir,' with significant implications for single-vineyard wines.},
}
@article {pmid36592918,
year = {2023},
author = {Burke, LP and Chique, C and Fitzhenry, K and Chueiri, A and O'Connor, L and Hooban, B and Cahill, N and Brosnan, E and Olaore, L and Sullivan, E and Reilly, L and Morris, D and Hynds, P and O'Dwyer, J},
title = {Characterization of Shiga toxin-producing Escherichia coli presence, serogroups and risk factors from private groundwater sources in western Ireland.},
journal = {The Science of the total environment},
volume = {866},
number = {},
pages = {161302},
doi = {10.1016/j.scitotenv.2022.161302},
pmid = {36592918},
issn = {1879-1026},
mesh = {Animals ; Sheep ; *Shiga-Toxigenic Escherichia coli ; Serogroup ; Ireland/epidemiology ; *Escherichia coli Proteins/genetics ; Risk Factors ; Feces ; },
abstract = {Over recent years, Ireland has reported the highest crude incidence rates of Shiga toxin-producing Escherichia coli (STEC) enteritis in Europe. Unregulated private groundwater sources have emerged as an important potential transmission route for STEC, with up to 750,000 Irish residents reliant on these sources for domestic waters. This study aimed to investigate the prevalence and serogroup profile of STEC contamination from domestic private wells in western Ireland. Fifty-two groundwater sources were analysed during two sampling campaigns in the autumn (September/October) of 2019 (n = 21) and 2021 (n = 31). Untreated groundwater samples (30 L) were collected and analysed using the "CapE" (capture, amplify, extract) method. Extracted DNA was tested using multiplex real-time PCR for Shiga toxin stx1 and/or stx2 and eae genes. STEC positive DNA samples were tested for clinically relevant serogroups by real-time PCR. Data relating to 27 potential groundwater contamination risk factors were geospatially linked to each well and assessed for association with E. coli, stx1 and/or stx2 and eae presence/absence. Overall, 20/52 wells (38.4 %) were positive for E. coli (median concentration 8.5 MPN/100 mL as assessed by Colilert-18 method). Stx1 and/or stx2 was detected in 10/52 (19.2 %) wells overall and 8/20 E. coli positive wells, equating to a STEC to "generic" E. coli detection ratio of 40 %. Six of these wells (30 %) were also positive for eae. One or more serogroup-specific gene targets were identified in all but one stx1 and/or stx2 positive sample, with O145 (n = 6), O157 (n = 5) and O103 (n = 4) most prevalent. STEC presence was significantly associated with decreasing well depth (U = -2.243; p = 0.024) and increasing 30-day mean antecedent rainfall (U = 2.126; p = 0.034). Serogroup O104 was associated with increased sheep density (U = 2.089; p = 0.044) and detection of stx1 and/or stx2 + eae with increased septic tank density (U = 2.246 p = 0.023). Findings indicate high detection rates of clinically relevant STEC in E. coli contaminated groundwater sources in Ireland.},
}
@article {pmid36590596,
year = {2022},
author = {Hu, X and Fan, R and Song, W and Qing, J and Yan, X and Li, Y and Duan, Q and Li, Y},
title = {Landscape of intestinal microbiota in patients with IgA nephropathy, IgA vasculitis and Kawasaki disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {1061629},
pmid = {36590596},
issn = {2235-2988},
mesh = {Humans ; *Glomerulonephritis, IGA ; *Mucocutaneous Lymph Node Syndrome/complications/diagnosis ; *Gastrointestinal Microbiome ; *IgA Vasculitis ; *Vasculitis/diagnosis/genetics ; Immunoglobulin A ; },
abstract = {OBJECTIVE: To explore the common differential flora of IgAN, Kawasaki disease and IgA vasculitis by screening and analyzing the differential intestinal flora between the three disease groups of IgAN, Kawasaki disease and IgA vasculitis and their healthy controls.<br><br>METHODS: Papers on 16srRNA sequencing-related intestinal flora of IgAN, Kawasaki disease and IgA vasculitis were searched in databases, the literature was systematically collated and analysed, the original data was download from the relevant databases, and then the operational taxonomic unit and species classification analysis were performed. Besides, Alpha diversity analysis and Beta diversity analysis were performed to screen for IgAN, Kawasaki disease and I1gA vasculitis groups and finally compare the common intestinal differential flora among the three groups.<br><br>RESULTS: Among the common differential flora screened, Lachnospiracea_incertae_sedis was lower in both the IgAN and Kawasaki disease groups than in the respective healthy controls; Coprococcus was low in the IgAN group but high in the IgA vasculitis group. Fusicatenibacter was lower in both the Kawasaki disease and IgA vasculitis groups than in their respective healthy controls, and Intestinibacter was low in the Kawasaki disease group, but its expression was high in the IgA vasculitis group.<br><br>CONCLUSION: The dysbiosis of the intestinal flora in the three groups of patients with IgAN, Kawasaki disease and IgA vasculitis, its effect on the immunity of the organism and its role in the development of each disease group remain unclear, and the presence of their common differential flora may further provide new ideas for the association of the pathogenesis of the three diseases.},
}
@article {pmid36590430,
year = {2022},
author = {Krohn, C and Khudur, L and Dias, DA and van den Akker, B and Rees, CA and Crosbie, ND and Surapaneni, A and O'Carroll, DM and Stuetz, RM and Batstone, DJ and Ball, AS},
title = {The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1079136},
pmid = {36590430},
issn = {1664-302X},
abstract = {The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.},
}
@article {pmid36587901,
year = {2023},
author = {Lietaer, L and Pascottini, OB and Lacoere, T and Kerckhof, FM and Martens, A and Van de Wiele, T and Opsomer, G},
title = {Studying the pre-implantation uterine microbiota in cattle using transabdominal laparoscopic low-volume lavage: Aiming for zero-contamination.},
journal = {Journal of microbiological methods},
volume = {205},
number = {},
pages = {106664},
doi = {10.1016/j.mimet.2022.106664},
pmid = {36587901},
issn = {1872-8359},
mesh = {Pregnancy ; Cattle ; Animals ; Female ; *Therapeutic Irrigation ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Microbiota/genetics ; DNA/genetics ; Bacteria/genetics ; DNA, Bacterial/genetics ; },
abstract = {Recent studies have suggested that bacteria associated with the female reproductive tract - the uterine microbiota - may be important for reproductive health and pregnancy success. Therefore, uterine microbiome research gained much interest in the last few years. However, it is challenging to study late postpartum uterine samples, since they hold a low microbial biomass. Next-generation sequencing techniques are very sensitive for microbial identification, but they cannot make a distinction between actual microbiota and contaminant bacteria or their DNA. Our aim was to test a new method to sample the bovine uterine lumen in vivo, while minimizing the risk of cross-contamination. In order to evaluate this method, we performed a descriptive assessment of the microbial composition of the obtained samples. Transabdominal, laparoscopic sampling of the uterine lumen was conducted in five Holstein-Friesian cows. Uterine fluid from the uterine horns was collected by low-volume lavage. DNA from the samples was extracted using two different DNA extraction methods, and negative controls (sampling blank controls and DNA extraction blank controls) were included. Bacteria were identified using 16S rRNA gene amplicon sequencing. In this proof-of-concept study, no evidence for authentically present uterine microbiota could be found. During laparoscopic sampling, some practical challenges were encountered, and the reliability of low-volume-lavage for the collection of a low microbial biomass could be questioned. By comparing two DNA extraction methods, a significant contamination background could be noticed originating from the DNA extraction kits.},
}
@article {pmid36586465,
year = {2023},
author = {McDonagh, F and Singh, NK and Venkateswaran, K and Lonappan, AM and Hallahan, B and Tuohy, A and Burke, L and Kovarova, A and Miliotis, G},
title = {First complete genome of a multidrug-resistant strain of the novel human pathogen Kalamiella piersonii (GABEKP28) identified in human saliva.},
journal = {Journal of global antimicrobial resistance},
volume = {32},
number = {},
pages = {31-34},
doi = {10.1016/j.jgar.2022.12.003},
pmid = {36586465},
issn = {2213-7173},
mesh = {Humans ; *Saliva ; *Genome, Bacterial ; Whole Genome Sequencing ; Plasmids/genetics ; Virulence ; Virulence Factors/genetics ; },
abstract = {OBJECTIVES: Kalamiella piersonii is a newly identified bacterial species, first isolated from surfaces of the International Space Station (ISS). It also appears as a novel human pathogen reported to be implicated in bacteremia and kidney stone disease. Here, we report the first complete genome of a multidrug-resistant strain of K. piersonii (GABEKP28), isolated from the saliva of a patient with treatment-resistant schizophrenia (TRS), to determine the mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and virulence factors (VFs) harboured by such a strain of this novel species.<br><br>METHODS: Whole-genome sequencing was performed using DNABSEQ (PE150) and Nanopore MinION platforms. Hybrid assembly was conducted using Unicycler v0.5.0. Genome assembly quality was verified using QUAST v5.0.2. The assembly was annotated using PROKKA v1.14.5. ARGs and VFs were identified using Abricate v1.0.0.<br><br>RESULTS: K. piersonii strain GABEKP28 was classified as multidrug-resistant while also carrying plasmidic genetic determinants associated with a hypervirulent phenotype. The complete genome size is 3 881 479 bp and has a guanine-cytosine content of 57.76% while it encodes for 3 525 chromosome coding sequences. The strain was also identified to carry three plasmids of 513 647 bp, 261 771 bp, and 106 029 bp, respectively.<br><br>CONCLUSIONS: K.piersonii GABEKP28 is the first complete genome of this species to be submitted to GenBank and only the second to be sequenced from a human host. The whole-genome sequencing data with multiple plasmids, ARGs, and VFs will aid in understanding the pathogenicity, evolution, and phylogeny of this novel opportunistic pathogen.},
}
@article {pmid36585490,
year = {2023},
author = {Zhao, J and Wang, Z and Li, C and Shi, T and Liang, Y and Jiao, N and Zhang, Y},
title = {Significant Differences in Planktonic Virus Communities Between "Cellular Fraction" (0.22 ~ 3.0 µm) and "Viral Fraction" (&lt; 0.22 μm) in the Ocean.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {825-842},
pmid = {36585490},
issn = {1432-184X},
support = {41876174//National Natural Science Foundation of China/ ; },
mesh = {Plankton/genetics ; *Viruses/genetics ; *Bacteriophages ; Seawater ; Genome, Viral ; Oceans and Seas ; Metagenome ; Metagenomics ; },
abstract = {Compared to free-living viruses (< 0.22 m) in the ocean, planktonic viruses in the "cellular fraction" (0.22 ~ 3.0 μm) are now far less well understood, and the differences between them remain largely unexplored. Here, we revealed that even in the same seawater samples, the "cellular fraction" comprised significantly distinct virus communities from the free virioplankton, with only 13.87% overlap in viral contigs at the species level. Compared to the viral genomes deposited in NCBI RefSeq database, 99% of the assembled viral genomes in the "cellular fraction" represented novel genera. Notably, the assembled (near-) complete viral genomes within the "cellular fraction" were significantly larger than that in the "viral fraction," and the "cellular fraction" contained three times more species of giant viruses or jumbo phages with genomes > 200 kb than the "viral fraction." The longest complete genomes of jumbo phage (~ 252 kb) and giant virus (~ 716 kb) were both detected only in the "cellular fraction." Moreover, a relatively higher proportion of proviruses were predicted within the "cellular fraction" than "viral fraction." Besides the substantial divergence in viral community structure, the different fractions also contained their unique viral auxiliary metabolic genes; e.g., those potentially participating in inorganic carbon fixation in deep sea were detected only in the "cellular-fraction" viromes. In addition, there was a considerable divergence in the community structure of both "cellular fraction" and "viral fraction" viromes between the surface and deep-sea habitats, suggesting that they might have similar environmental adaptation properties. The findings deepen our understanding of the complexity of viral community structure and function in the ocean.},
}
@article {pmid36585489,
year = {2023},
author = {Zhang, Y and Liu, F and Liang, H and Gao, D},
title = {Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline-Alkaline Wetland: a Metagenomic Analysis.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {985-996},
pmid = {36585489},
issn = {1432-184X},
support = {31470543//National Natural Science Foundation of China/ ; },
mesh = {*Greenhouse Gases ; Wetlands ; Freezing ; Carbon Dioxide ; Nitrous Oxide ; Carbon ; Methane/analysis ; Soil ; },
abstract = {Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61-80.71 mg/(m[2]‧h), the average CH4 flux decreased from 10.72 to 1.96-3.94 mg/(m[2]‧h), and the average N2O flux decreased from 56.17 to - 27.14 to - 20.70 μg/(m[2]‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.},
}
@article {pmid36584949,
year = {2023},
author = {Fraser, MW and Martin, BC and Wong, HL and Burns, BP and Kendrick, GA},
title = {Sulfide intrusion in a habitat forming seagrass can be predicted from relative abundance of sulfur cycling genes in sediments.},
journal = {The Science of the total environment},
volume = {864},
number = {},
pages = {161144},
doi = {10.1016/j.scitotenv.2022.161144},
pmid = {36584949},
issn = {1879-1026},
mesh = {*Geologic Sediments ; Ecosystem ; Sulfides ; Sulfur ; Australia ; *Microbiota ; },
abstract = {Sulfide intrusion from sediments is an increasingly recognized contributor to seagrass declines globally, yet the relationship between sediment microorganisms and sulfide intrusion has received little attention. Here, we use metagenomic sequencing and stable isotope ([34]S) analysis to examine this relationship in Cockburn Sound, Australia, a seagrass-dominated embayment with a gradient of sulfide stress and seagrass declines. There was a significant positive relationship between sulfide intrusion into seagrasses and sulfate reduction genes in sediment microbial communities, which was greatest at sites with long term seagrass declines. This is the first demonstration of a significant link between sulfur cycling genes present in seagrass sediments and sulfide intrusion in a habitat-forming seagrass that is experiencing long-term shoot density decline. Given that microorganisms respond rapidly to environmental change, the quantitative links established in this study can be used as a potential management tool to enable the prediction of sulfide stress on large habitat forming seagrasses; a global issue expected to worsen with climate change.},
}
@article {pmid36584719,
year = {2023},
author = {Andrzejak, T and Raje, H and LaFleur, G and Willis, J and Boopathy, R},
title = {Water quality and antibiotic resistance in the recreational waters.},
journal = {Bioresource technology},
volume = {370},
number = {},
pages = {128546},
doi = {10.1016/j.biortech.2022.128546},
pmid = {36584719},
issn = {1873-2976},
mesh = {*Water Quality ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The overuse and improper disposal of antibiotics results in antibiotic resistance. This raises concern over the presence of antibiotic resistant bacteria (ARB) in waterways and pose health risks of antibiotic resistant infections to water recreationists. The purpose of this study was to monitor water quality, microbial ecology, and antibiotic resistance in water and biofilm on submerged plastics at two public boat launches in southeastern Louisiana. Water and biofilm samples were collected once a month, in triplicate, from two public boat launches in Louisiana, USA for a year. Water quality metrics included nitrate, ammonia, sulfate, phosphate, and organic carbon. Water samples were tested for total and fecal coliform abundance and the presence of ARB. Out of 131 bacterial isolates studied from these two sites, 86% of them tested positive for antibiotic resistance with multi-drug resistance. Antibiotic resistance genes (ARGs) for sulfonamide (sul2), bacitracin (bacA) and ampicillin (ampA) were identified in bacterial isolates from water and biofilm samples at both sites. Molecular genetic diversity analysis identified distinct taxonomic diversity differences in biofilm bacteria compared to the planktonic bacteria in the surrounding water. Biofilm samples showed increased diversity at the phylum, genus, and species levels.},
}
@article {pmid36583056,
year = {2022},
author = {Doster, E and Pinnell, LJ and Noyes, NR and Parker, JK and Anderson, CA and Booker, CW and Hannon, SJ and McAllister, TA and Gow, SP and Belk, KE and Morley, PS},
title = {Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {970358},
pmid = {36583056},
issn = {1664-302X},
abstract = {INTRODUCTION: Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle.<br><br>METHODS: This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics.<br><br>RESULTS: Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively).<br><br>DISCUSSION: Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.},
}
@article {pmid36583045,
year = {2022},
author = {Puig, S and Bañeras, L and Heijne, AT and Paquete, CM},
title = {Editorial: Latest breakthroughs in microbial electrochemistry research.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1100272},
doi = {10.3389/fmicb.2022.1100272},
pmid = {36583045},
issn = {1664-302X},
}
@article {pmid36579161,
year = {2022},
author = {Metcalf, CJE and Tepekule, B and Bruijning, M and Koskella, B},
title = {Hosts, microbiomes, and the evolution of critical windows.},
journal = {Evolution letters},
volume = {6},
number = {6},
pages = {412-425},
pmid = {36579161},
issn = {2056-3744},
abstract = {The absence of microbial exposure early in life leaves individuals vulnerable to immune overreaction later in life, manifesting as immunopathology, autoimmunity, or allergies. A key factor is thought to be a "critical window" during which the host's immune system can "learn" tolerance, and beyond which learning is no longer possible. Animal models indicate that many mechanisms have evolved to enable critical windows, and that their time limits are distinct and consistent. Such a variety of mechanisms, and precision in their manifestation suggest the outcome of strong evolutionary selection. To strengthen our understanding of critical windows, we explore their underlying evolutionary ecology using models encompassing demographic and epidemiological transitions, identifying the length of the critical window that would maximize fitness in different environments. We characterize how direct effects of microbes on host mortality, but also indirect effects via microbial ecology, will drive the optimal length of the critical window. We find that indirect effects such as magnitude of transmission, duration of infection, rates of reinfection, vertical transmission, host demography, and seasonality in transmission all have the effect of redistributing the timing and/or likelihood of encounters with microbial taxa across age, and thus increasing or decreasing the optimal length of the critical window. Declining microbial population abundance and diversity are predicted to result in increases in immune dysfunction later in life. We also make predictions for the length of the critical window across different taxa and environments. Overall, our modeling efforts demonstrate how critical windows will be impacted over evolution as a function of both host-microbiome/pathogen interactions and dispersal, raising central questions about potential mismatches between these evolved systems and the current loss of microbial diversity and/or increases in infectious disease.},
}
@article {pmid36578577,
year = {2022},
author = {Hsu, PL and Di, HJ and Cameron, K and Podolyan, A and Chau, H and Luo, J and Miller, B and Carrick, S and Johnstone, P and Ferguson, S and Wei, W and Shen, J and Zhang, L and Liu, H and Zhao, T and Wei, W and Ding, W and Pan, H and Liu, Y and Li, B},
title = {Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1048735},
pmid = {36578577},
issn = {1664-302X},
abstract = {The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha[-1]) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil.},
}
@article {pmid36578575,
year = {2022},
author = {Coutinho, TA and Jacques, MA and Jones, J},
title = {Editorial: Emergence and re-emergence of plant diseases caused by Xanthomonas species.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1081601},
pmid = {36578575},
issn = {1664-302X},
}
@article {pmid36578568,
year = {2022},
author = {Dirren-Pitsch, G and Bühler, D and Salcher, MM and Bassin, B and Le Moigne, A and Schuler, M and Pernthaler, J and Posch, T},
title = {FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1070232},
pmid = {36578568},
issn = {1664-302X},
abstract = {Planktonic ciliate species form multiple trophic guilds and are central components of freshwater food webs. Progress in molecular analytical tools has opened new insight into ciliate assemblages. However, high and variable 18S rDNA copy numbers, typical for ciliates, make reliable quantification by amplicon sequencing extremely difficult. For an exact determination of abundances, the classical morphology-based quantitative protargol staining is still the method of choice. Morphotype analyses, however, are time consuming and need specific taxonomic expertise. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) may represent a promising tool for the analysis of planktonic ciliates by combining molecular identification with microscopic quantification. We tested the applicability of CARD-FISH using nine cultured ciliate species. Eight species- and three genus-specific oligonucleotide probes were designed based on their 18S rRNA genes. The CARD-FISH protocol was adapted and the specificity of probes was established. We subsequently examined the precision of quantitation by CARD-FISH on single cultures and mock assemblages. Successful tests on lake water samples proved that planktonic ciliates could be identified and quantified in field samples by CARD-FISH. Double hybridizations allowed studying interspecific predator prey interactions between two ciliate species. In summary, we demonstrate that CARD-FISH with species-specific probes can facilitate studies on the population dynamics of closely related, small sized or cryptic species at high sampling frequencies.},
}
@article {pmid36578531,
year = {2023},
author = {Lasa, AV and Guevara, M&#xc1; and Villadas, PJ and Fernández-González, AJ and Cervera, MT and Fernández-López, M},
title = {Bacteriome dataset from the rhizosphere of trees in a Pinus pinaster and Pinus halepensis dominated forest subjected to drought conditions.},
journal = {Data in brief},
volume = {46},
number = {},
pages = {108805},
pmid = {36578531},
issn = {2352-3409},
abstract = {The Mediterranean basin is drastically affected by intense and frequent droughts, which jeopardize the diversity and survival of its forest, for example, Pinus pinaster forests. The dynamics of the bacterial communities inhabiting the rhizosphere of Pinus pinaster and other plants from a pine dominated forest under contrasting hydric conditions was monitored. The forest was located in Sierra de Oria (southeast Spain), and it was mainly composed by P. pinaster, P. halepensis, woody shrub species and herbaceous plants. 18 trees visually belonging to P. pinaster located along the perimeter and across the forest were selected for the analysis. All the trees were separated at least 50 m each other. Although all of them belonged to P. pinaster morphologically according to visual identification, the genotyping of the roots confirmed that they corresponded to P. pinaster, P. halepensis, and other plant species different from genus Pinus, although in the last case it was not possible to identify the plant species. At a distance less than 50 cm from the trunk, the litter and topsoil were removed, and the soil closely attached to non-suberified roots (rhizosphere soil) was collected (depth of 5-25 cm). Sampling was carried out in two seasons with contrasting temperature and rainfall patterns: on July 18, 2017 (summer) and April 24, 2018 (spring). After rhizosphere soil DNA and RNA extraction (and cDNA synthesis), a metabarcoding approach was followed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene and its derived transcripts by Illumina MiSeq platform. Sequencing reads were bioinformatically processed; specifically, they were filtered, trimmed, clustered into ASV (Amplicon Sequence Variants), and taxonomically identified. As a result, a total of 1,123,209 and 1,089,359 quality sequences were obtained from DNA and RNA-derived libraries, which resulted in 5,241 and 5,231 ASVs, respectively. Total communities (DNA) were mainly dominated by phyla Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Bacteroidetes in summer and spring, while potentially active populations (RNA libraries) were rich in Proteobacteria, Acidobacteria, Candidate division WPS-1, Actinobacteria and Verrucomicrobia both in summer and spring. On the other hand, DNA libraries were mainly dominated by genera Sphingomonas and acidobacterial groups Gp4 and Gp6, while potentially active bacteria (RNA) were rich in acidobacterial Gp3, Gp4, Gp6 and Phenylobacterium, although their relative abundance depended on the considered season. This dataset can provide valuable information about bacterial candidates which could be used as bioindicators of drought conditions. In addition to shifts in the bacterial relative abundance due to seasonal changes, the ratio RNA-based cDNA:DNA could be calculated as proxy of the potential activity of bacterial taxa. Moreover, these data could aid in developing bioformulations based on microorganisms which could be resistant to desiccation and involved in the drought resistance mechanisms of the host plant.},
}
@article {pmid36577993,
year = {2022},
author = {Qi, Q and Wang, L and Gebremedhin, MA and Li, S and Wang, X and Shen, J and Zhu, Y and Andegiorgish, AK and Cheng, Y and Shi, L and Zhou, J and Yang, Y and Kang, Y and Yang, W and Zhu, Z and Zeng, L},
title = {The impact of early-life antibiotics and probiotics on gut microbial ecology and infant health outcomes: a Pregnancy and Birth Cohort in Northwest China (PBCC) study protocol.},
journal = {BMC pediatrics},
volume = {22},
number = {1},
pages = {738},
pmid = {36577993},
issn = {1471-2431},
support = {81872633//National Natural Science Foundation of China/ ; 2017YFC0907200//National Key Research and Development Program of China/ ; 2017YFC0907201//National Key Research and Development Program of China/ ; 2020JM-077//Natural Science Basic Research Plan of the Shaanxi Province/ ; 202006280219//China Scholarship Council/ ; },
mesh = {Infant ; Infant, Newborn ; Humans ; Female ; Pregnancy ; Child, Preschool ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome ; Infant Health ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Birth Cohort ; Cohort Studies ; *Probiotics/therapeutic use ; },
abstract = {BACKGROUND: Unreasonable use of antibiotics and probiotics can alter the gut ecology, leading to antibiotic resistance and suboptimal health outcomes during early life. Our study aims are to clarify the association among antibiotic and probiotic exposure in early life, the microecology of the gut microbiota, and the development of antibiotic resistance; to investigate the long-term impact of antibiotics and probiotics on the health outcomes of infants and young children; and to provide a theoretical basis for the rational use of antibiotics and probiotics from a life course perspective.<br><br>METHODS: The study is a prospective, longitudinal birth cohort study conducted in Shaanxi Province, China from 2018 to 2024. A total of 3,000 eligible mother-child pairs will be enrolled from rural, suburban, and urban areas. The recruitment of the participants begins at pregnancy, and the newborns will be followed up for 2&#xa0;years at successive timepoints: within 3&#xa0;days after birth, 42&#xa0;days after birth, and at 3, 6, 12, 18, and 24&#xa0;months of age. Sociodemographic data, environmental exposures, dietary patterns, psychological conditions, and medical and drug histories are collected. Cognitive and behavioural development among infants and young children and questionnaires on antibiotic knowledge and behaviour among caregivers will be collected at 12 and 24&#xa0;months of age. The faecal samples are collected and analysed by 16S rRNA high-throughput sequencing and quantitative PCR (qPCR) for antibiotic resistance genes.<br><br>DISCUSSION: The findings will inform antibiotic and probiotic use for pregnant women and infants and contribute to establishing rational use strategies of antibiotics and probiotics for paediatricians, health practitioners, and drug administration policy-makers.<br><br>TRIAL REGISTRATION: The study was registered on the Chinese Clinical Trial Registry (ChiCTR) platform, http://www.chictr.org.cn (Record ID: ChiCTR2100047531, June 20, 2021).},
}
@article {pmid36576521,
year = {2023},
author = {Westreich, LR and Westreich, ST and Tobin, PC},
title = {Bacterial and Fungal Symbionts in Pollen Provisions of a Native Solitary Bee in Urban and Rural Environments.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1416-1427},
pmid = {36576521},
issn = {1432-184X},
support = {1012774//USDA-NIFA McIntire Stennis Cooperative Forestry Program/ ; },
mesh = {Bees ; Animals ; *Bacteria/genetics ; Seasons ; *Pollen ; Washington ; },
abstract = {Among insects, symbionts such as bacteria and fungi can be linked to their physiology and immature development, and in some cases are part of a defense system against parasites and diseases. Current bacterial and fungal symbiont associations in solitary bees are understudied, especially in the Pacific Northwest region of the USA. We collected pollen provisions from the native spring-foraging solitary bee, Osmia lignaria Say, across two distinct foraging periods over 2 years at 22 sites along an urban-to-rural gradient in western Washington. We then used next-generation sequencing to identify bacterial and fungi within pollen provisions and assessed the effect of their richness and diversity on O. lignaria larval development success and adult emergence. We detected a significantly positive relationship between bacterial diversity in pollen with O. lignaria larval developmental success, and higher bacterial richness and diversity during the later foraging period. Fungal generic richness and diversity decreased with increasing plant richness. Although neither was associated with O. lignaria developmental success, we did detect Ascosphaera spp. known to be pathogenic to O. lignaria and other bee species. Neither bacterial or fungal richness or diversity was affected by site type when classified as urban or rural. This study provides new information on bacterial and fungal symbionts present in pollen provisions of a native solitary bee when foraging across urban and rural areas of the Pacific Northwest.},
}
@article {pmid36575570,
year = {2023},
author = {Zhou, J and Song, W and Tu, Q},
title = {To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities.},
journal = {Briefings in bioinformatics},
volume = {24},
number = {1},
pages = {},
doi = {10.1093/bib/bbac594},
pmid = {36575570},
issn = {1477-4054},
support = {ZR2020YQ21//National Natural Science Foundation of China/ ; 2019YFA0606700//National Key Research and Development Program of China/ ; },
mesh = {*Metagenome ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; },
abstract = {High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.},
}
@article {pmid36575453,
year = {2022},
author = {Barone, M and Garelli, S and Rampelli, S and Agostini, A and Matysik, S and D'Amico, F and Krautbauer, S and Mazza, R and Salituro, N and Fanelli, F and Iozzo, P and Sanz, Y and Candela, M and Brigidi, P and Pagotto, U and Turroni, S},
title = {Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior.},
journal = {BMC medicine},
volume = {20},
number = {1},
pages = {500},
pmid = {36575453},
issn = {1741-7015},
support = {613979//Seventh Framework Programme/ ; 245009//Seventh Framework Programme/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Obesity/genetics ; Diet ; Feeding Behavior/physiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Obesity and related co-morbidities represent a major health challenge nowadays, with a rapidly increasing incidence worldwide. The gut microbiome has recently emerged as a key modifier of human health that can affect the development and progression of obesity, largely due to its involvement in the regulation of food intake and metabolism. However, there are still few studies that have in-depth explored the functionality of the human gut microbiome in obesity and even fewer that have examined its relationship to eating behaviors.<br><br>METHODS: In an attempt to advance our knowledge of the gut-microbiome-brain axis in the obese phenotype, we thoroughly characterized the gut microbiome signatures of obesity in a well-phenotyped Italian female cohort from the NeuroFAST and MyNewGut EU FP7 projects. Fecal samples were collected from 63 overweight/obese and 37 normal-weight women and analyzed via a multi-omics approach combining 16S rRNA amplicon sequencing, metagenomics, metatranscriptomics, and lipidomics. Associations with anthropometric, clinical, biochemical, and nutritional data were then sought, with particular attention to cognitive and behavioral domains of eating.<br><br>RESULTS: We identified four compositional clusters of the gut microbiome in our cohort that, although not distinctly associated with weight status, correlated differently with eating habits and behaviors. These clusters also differed in functional features, i.e., transcriptional activity and fecal metabolites. In particular, obese women with uncontrolled eating behavior were mostly characterized by low-diversity microbial steady states, with few and poorly interconnected species (e.g., Ruminococcus torques and Bifidobacterium spp.), which exhibited low transcriptional activity, especially of genes involved in secondary bile acid biosynthesis and neuroendocrine signaling (i.e., production of neurotransmitters, indoles and ligands for cannabinoid receptors). Consistently, high amounts of primary bile acids as well as sterols were found in their feces.<br><br>CONCLUSIONS: By finding peculiar gut microbiome profiles associated with eating patterns, we laid the foundation for elucidating gut-brain axis communication in the obese phenotype. Subject to confirmation of the hypotheses herein generated, our work could help guide the design of microbiome-based precision interventions, aimed at rewiring microbial networks to support a healthy diet-microbiome-gut-brain axis, thus counteracting obesity and related complications.},
}
@article {pmid36574886,
year = {2023},
author = {Lee, M and Yoo, K and Kim, H and Song, KG and Kim, D and Tiedje, JM and Lee, PH and Park, J},
title = {Metatranscriptional characterization of metabolic dynamics in anaerobic membrane bioreactor producing methane from low-strength wastewater.},
journal = {Bioresource technology},
volume = {370},
number = {},
pages = {128532},
doi = {10.1016/j.biortech.2022.128532},
pmid = {36574886},
issn = {1873-2976},
mesh = {*Wastewater ; Waste Disposal, Fluid/methods ; Anaerobiosis ; Methane/metabolism ; Bioreactors/microbiology ; *Euryarchaeota/metabolism ; Membranes, Artificial ; },
abstract = {An anaerobic membrane bioreactor (AnMBR) with media is an emerging carbon-neutral biotechnology for low-strength wastewater (LSWW) treatment and methane recovery. Understanding metabolic dynamics among methanogens and syntrophic bacteria is important in optimizing the design and operation of AnMBR. However, little is known about it, especially in media-attached microbial communities. This study explored metabolic dynamics to compare media-attached and suspended conditions. Accordingly, metagenomes and metatranscriptomes from AnMBRs with polymeric media and fed with different influent concentrations (350 and 700 mg-COD/L) were analyzed. Metabolic dynamics were profoundly influenced by the different growth habitats and influent conditions, although the applied influent concentrations are within the range of typical LSWW. Metabolic dynamics prediction results suggest that media-attached-growth habitats may have provided a more favorable microenvironment for methanogens to grow and produce methane, especially under low influent conditions. These findings provide significant implications for optimizing floating media design and operation of AnMBR-producing methane from LSWW.},
}
@article {pmid36574041,
year = {2023},
author = {Lozano, IL and González-Olalla, JM and Medina-Sánchez, JM},
title = {New Insights for the Renewed Phytoplankton-Bacteria Coupling Concept: the Role of the Trophic Web.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {810-824},
pmid = {36574041},
issn = {1432-184X},
support = {B-RNM-310-UGR20//Consejer&#xed;a de Transformaci&#xf3;n Econ&#xf3;mica, Industria, Conocimiento y Universidades/ ; PID2020-118872RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; LifeWatch-2019-10-UGR-01//FEDER Funds/ ; },
mesh = {*Phytoplankton/metabolism ; *Ecosystem ; Bacteria/metabolism ; Carbon/metabolism ; },
abstract = {It is widely accepted that in many aquatic ecosystems bacterioplankton is dependent on and regulated by organic carbon supplied by phytoplankton, leading to coupled algae-bacteria relationship. In this study, an in-depth analysis of this relationship has been carried out by combining two approaches: (i) a correlation analyses between heterotrophic bacterial production (BP) vs. primary production (PP) or algal excretion of organic carbon (EOC), (ii) the balance between bacterial carbon demands (BCD) and the supply of C as EOC, measured as BCD:EOC ratio. During the study period (2013-2016), the algae-bacteria relationship was constantly changing from a coupling in 2013, uncoupling in 2014 and 2015, and an incipient return to coupling (in 2016). Our results show that top-down control (bacterivory) by algal mixotrophy acts as a decoupling force since it provides a fresh C source different to algal EOC to satisfy bacterial carbon demands. Notably, a relationship between the BCD:EOC ratio and the ecosystem metabolic balance (Primary production (PP): respiration (R)) was found, suggesting that PP:R may be a good predictor of the algae-bacteria coupling. This analysis, including the comparison between basal and potential ecosystem metabolic balance, can be a tool to improve knowledge on the interaction between both biotics compartments, which the traditional analyses on coupling may not capture.},
}
@article {pmid36571608,
year = {2023},
author = {la Rosa, GM and García-Oliva, F and Ovando-Vázquez, C and Celis-García, LB and López-Reyes, L and López-Lozano, NE},
title = {Amino Acids in the Root Exudates of Agave lechuguilla Torr. Favor the Recruitment and Enzymatic Activity of Nutrient-Improvement Rhizobacteria.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1176-1188},
pmid = {36571608},
issn = {1432-184X},
support = {Basic Science 254406//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {*Agave ; Amino Acids ; Plant Roots/microbiology ; Bacteria ; Rhizosphere ; *Alphaproteobacteria ; *Microbiota ; Plants/microbiology ; Exudates and Transudates ; Nutrients ; Arginine ; Phosphorus ; Soil Microbiology ; },
abstract = {Agave lechuguilla is a widely distributed plant in arid ecosystems. It has been suggested that its microbiome is partially responsible for its great adaptability to the oligotrophic environments of the Chihuahuan Desert. To lead the recruitment of beneficial rhizobacteria, the root exudates are essential; however, the amino acids contained within these compounds had been largely overlooked. Thus, we investigated how the variations of amino acids in the rhizosphere at different growth stages of A. lechuguilla affect the rhizobacterial community composition, its functions, and activity of the beneficial bacteria. In this regard, it was found that arginine and tyrosine were related to the composition of the rhizobacterial community associated to A. lechuguilla, where the most abundant genera were from the phylum Proteobacteria and Bacteroidetes. Moreover, Firmicutes was largely represented by Bacillus in the phosphorus-mineralizing bacteria community, which may indicate its great distribution and versatility in the harsh environments of the Chihuahuan Desert. In contrast, we found a high proportion of Unknown taxa of nitrogen-fixing bacteria, reflecting the enormous diversity in the rhizosphere of these types of plants that remains to be explored. This work also reports the influence of micronutrients and the amino acids methionine and arginine over the increased activity of the nitrogen-fixing and phosphorus-mineralizing bacteria in the rhizosphere of lechuguillas. In addition, the results highlight the multiple beneficial functions present in the microbiome that could help the host to tolerate arid conditions and improve nutrient availability.},
}
@article {pmid36569156,
year = {2022},
author = {Meller, S and Al Khatri, MSA and Alhammadi, HK and Álvarez, G and Alvergnat, G and Alves, LC and Callewaert, C and Caraguel, CGB and Carancci, P and Chaber, AL and Charalambous, M and Desquilbet, L and Ebbers, H and Ebbers, J and Grandjean, D and Guest, C and Guyot, H and Hielm-Björkman, A and Hopkins, A and Kreienbrock, L and Logan, JG and Lorenzo, H and Maia, RCC and Mancilla-Tapia, JM and Mardones, FO and Mutesa, L and Nsanzimana, S and Otto, CM and Salgado-Caxito, M and de Los Santos, F and da Silva, JES and Schalke, E and Schoneberg, C and Soares, AF and Twele, F and Vidal-Martínez, VM and Zapata, A and Zimin-Veselkoff, N and Volk, HA},
title = {Expert considerations and consensus for using dogs to detect human SARS-CoV-2-infections.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {1015620},
pmid = {36569156},
issn = {2296-858X},
}
@article {pmid36565551,
year = {2023},
author = {Li, Q and Stautemas, J and Omondi Onyango, S and De Mey, M and Duchi, D and Tuenter, E and Hermans, N and Calders, P and Van de Wiele, T},
title = {Human gut microbiota stratified by (+)-catechin metabolism dynamics reveals colon region-dependent metabolic profile.},
journal = {Food chemistry},
volume = {408},
number = {},
pages = {135203},
doi = {10.1016/j.foodchem.2022.135203},
pmid = {36565551},
issn = {1873-7072},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Catechin/metabolism ; Colon/microbiology ; *Microbiota ; Bacteria/genetics/metabolism ; Metabolome ; },
abstract = {Catechins have proven to have several health benefits, yet a huge interindividual variability occurs. The metabolic potency of the colonic microbiota towards catechin is a key determinant of this variability. Microbiota from two donors - previously characterized as a fast and a slow converter- were incubated with (+)-catechin in vitro. The robustness of in vitro metabolic profiles was verified by well-fitted human trials. The colon region-dependent and donor-dependent patterns were reflected in both metabolic features and colonic microbiota composition. Upstream and downstream metabolites were mainly detected in the proximal and distal colons, respectively, and were considered important explanatory variables for microbiota clustering in the corresponding colon regions. Higher abundances of two catechin-metabolizing bacteria, Eggerthella and Flavonifractor were found in the distal colon compared to the proximal colon and in slow converter than fast converter. Additionally, these two bacteria were enriched in treatment samples compared to sham treatment samples.},
}
@article {pmid36564013,
year = {2023},
author = {Kreth, J and Merritt, J},
title = {Illuminating the oral microbiome and its host interactions: tools and approaches for molecular ecological studies.},
journal = {FEMS microbiology reviews},
volume = {47},
number = {1},
pages = {},
pmid = {36564013},
issn = {1574-6976},
support = {R01 DE022083/DE/NIDCR NIH HHS/United States ; R01 DE029492/DE/NIDCR NIH HHS/United States ; R21 DE029612/DE/NIDCR NIH HHS/United States ; R35 DE028252/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; Biofilms ; },
abstract = {A more comprehensive understanding of oral diseases like caries and periodontitis is dependent on an intimate understanding of the microbial ecological processes that are responsible for disease development. With this review, we provide a comprehensive overview of relevant molecular ecology techniques that have played critical roles in the current understanding of human oral biofilm development, interspecies interactions, and microbiome biogeography. The primary focus is on relevant technologies and examples available in the oral microbiology literature. However, most, if not all, of the described technologies should be readily adaptable for studies of microbiomes from other mucosal sites in the body. Therefore, this review is intended to serve as a reference guide used by microbiome researchers as they inevitably transition into molecular mechanistic studies of the many significant phenotypes observed clinically.},
}
@article {pmid36563760,
year = {2023},
author = {Xie, L and Li, W and Pang, X and Liu, Q and Yin, C},
title = {Soil properties and root traits are important factors driving rhizosphere soil bacterial and fungal community variations in alpine Rhododendron nitidulum shrub ecosystems along an altitudinal gradient.},
journal = {The Science of the total environment},
volume = {864},
number = {},
pages = {161048},
doi = {10.1016/j.scitotenv.2022.161048},
pmid = {36563760},
issn = {1879-1026},
mesh = {*Mycobiome ; Rhizosphere ; Soil/chemistry ; *Rhododendron ; Soil Microbiology ; Fungi ; Bacteria ; *Microbiota ; },
abstract = {Both soil properties and plant root traits are pivotal factors affecting microbial communities. However, there is still limited information about their importance in shaping rhizosphere soil microbial communities, particularly in less-studied alpine shrub ecosystems. To investigate the effects of altitude (3300, 3600, 3900, and 4200 m) on the diversity and composition of rhizosphere soil bacterial and fungal communities, as well as the factors shaping rhizosphere soil microbial communities, we conducted this study in alpine Rhododendron nitidulum shrub ecosystems from the Zheduo mountain of the eastern Tibetan Plateau. Results demonstrated that bacterial community diversity and richness decreased to the lowest value at 3600 m and then increased at higher altitudes compared with 3300 m; whereas fungal richness at 3300 m was much lower than at other altitudes, and was closely related to soil properties and root traits. The composition of rhizosphere soil bacterial and fungal communities at the low altitude (3300 m) was different from that at high altitudes. Permutational multivariate analysis of variance and redundancy analysis indicated that soil properties (soil water content, pH, NO3[-]-N, and available phosphorus) and root traits (surface area, and maximum depth) were the major factors explaining the variations of rhizosphere soil bacterial and fungal communities. Specific bacterial and fungal taxa along altitudes were identified. The bacterial taxa Planctomycetota was dominant at 3300 and 3600 m with low soil nutrient availability and high root surface area, whereas the fungal taxa Mortierellomycota was abundant at 3900 and 4200 m with high soil nutrient availability and low root surface area. These results suggested that different soil microbes can respond differently to altitude. This study provides a novel insight into factors driving rhizosphere soil bacterial and fungal community variations, which could improve our understanding of microbial ecology in alpine R. nitidulum shrub ecosystems along altitude.},
}
@article {pmid36562630,
year = {2023},
author = {Larrouy, JL and Dhami, MK and Jones, EE and Ridgway, HJ},
title = {Physiological stage drives fungal community dynamics and diversity in Leptospermum scoparium (mānuka) flowers.},
journal = {Environmental microbiology},
volume = {25},
number = {3},
pages = {766-771},
doi = {10.1111/1462-2920.16324},
pmid = {36562630},
issn = {1462-2920},
mesh = {Leptospermum ; *Mycobiome ; Flowers/microbiology ; Plant Nectar ; *Microbiota ; Pollination ; },
abstract = {Flowers are an important niche for microbes, and microbes in turn influence plant fitness. As flower morphology and biology change rapidly over time, dynamic niches for microbes are formed and lost. Floral physiology at each life stage can therefore influence arrival, persistence and loss of microbial species; however, this remains little understood despite its potential consequences for host reproductive success. Through internal transcribed spacer 1 (ITS1) community profiling, we characterized the effect of transitioning through five floral stages of mānuka (Leptospermum scoparium), from immature bud to spent flower, and subsequent allocation to seed, on the flower-inhabiting fungal community. We found nectar-consuming yeasts from Aureobasidium and Vishniacozyma genera and functionally diverse filamentous fungi from the Cladosporium genus dominated the anthosphere. The candidate core microbiota persisted across this dynamic niche despite high microbial turnover, as observed in shifts in community composition and diversity as flowers matured and senesced. The results demonstrated that floral stages are strong drivers of anthosphere fungal community assembly and dynamics. This study represents the first detailed exploration of fungi through floral development, building on fundamental knowledge in microbial ecology of healthy flowers.},
}
@article {pmid36560818,
year = {2022},
author = {Budzyńska, D and Zwart, MP and Hasiów-Jaroszewska, B},
title = {Defective RNA Particles of Plant Viruses-Origin, Structure and Role in Pathogenesis.},
journal = {Viruses},
volume = {14},
number = {12},
pages = {},
pmid = {36560818},
issn = {1999-4915},
mesh = {Animals ; Humans ; RNA, Viral/genetics ; *Plant Viruses/genetics ; *RNA Viruses/genetics ; RNA, Satellite ; Virus Replication ; Defective Viruses/genetics ; },
abstract = {The genomes of RNA viruses may be monopartite or multipartite, and sub-genomic particles such as defective RNAs (D RNAs) or satellite RNAs (satRNAs) can be associated with some of them. D RNAs are small, deletion mutants of a virus that have lost essential functions for independent replication, encapsidation and/or movement. D RNAs are common elements associated with human and animal viruses, and they have been described for numerous plant viruses so far. Over 30 years of studies on D RNAs allow for some general conclusions to be drawn. First, the essential condition for D RNA formation is prolonged passaging of the virus at a high cellular multiplicity of infection (MOI) in one host. Second, recombination plays crucial roles in D RNA formation. Moreover, during virus propagation, D RNAs evolve, and the composition of the particle depends on, e.g., host plant, virus isolate or number of passages. Defective RNAs are often engaged in transient interactions with full-length viruses-they can modulate accumulation, infection dynamics and virulence, and are widely used, i.e., as a tool for research on cis-acting elements crucial for viral replication. Nevertheless, many questions regarding the generation and role of D RNAs in pathogenesis remain open. In this review, we summarise the knowledge about D RNAs of plant viruses obtained so far.},
}
@article {pmid36557627,
year = {2022},
author = {Tao, L and Chai, J and Liu, H and Huang, W and Zou, Y and Wu, M and Peng, B and Wang, Q and Tang, K},
title = {Characterization and Dynamics of the Gut Microbiota in Rice Fishes at Different Developmental Stages in Rice-Fish Coculture Systems.},
journal = {Microorganisms},
volume = {10},
number = {12},
pages = {},
pmid = {36557627},
issn = {2076-2607},
support = {2022NSFSC1711//Natural Science Foundation of Sichuan Province, China/ ; 341965//Starting Research Funding from Sichuan Normal University/ ; SYJS2021030//Experimental Technology Funding from Sichuan Normal University/ ; },
abstract = {The rice-fish system (RFS), a traditional coculture farming model, was selected as a "globally important agricultural heritage system." Host-associated microbiota play important roles in development, metabolism, physiology, and immune function. However, studies on the gut microbiota of aquatic animals in the RFS are scarce, especially the lack of baseline knowledge of the dynamics of gut microbial communities in rice fish during different developmental stages. In this study, we characterized the microbial composition, community structure, and functions of several sympatric aquatic animals (common carp (Cyprinus carpio), crucian carp (Carassius carassius), and black-spotted frogs (Pelophylax nigromaculatus)), and the environment (water) in the RFS using 16S rRNA gene sequencing. Moreover, we investigated stage-specific signatures in the gut microbiota of common carp throughout the three developmental stages (juvenile, sub-adult, and adult). Our results indicated that the Fusobacteriota, Proteobacteria, and Firmicutes were dominant gut microbial phyla in rice fish. The differences in gut microbial compositions and community structure between the three aquatic species were observed. Although no significant differences in alpha diversity were observed across the three developmental stages, the microbial composition and community structure varied with development in common carp in the RFS, with an increase in the relative abundance of Firmicutes in sub-adults and a shift in the functional features of the community. This study sheds light on the gut microbiota of aquatic animals in the RFS. It deepens our understanding of the dynamics of gut microflora during common carp development, which may help improve aquaculture strategies in the RFS.},
}
@article {pmid36557593,
year = {2022},
author = {Delgadillo-Ordoñez, N and Raimundo, I and Barno, AR and Osman, EO and Villela, H and Bennett-Smith, M and Voolstra, CR and Benzoni, F and Peixoto, RS},
title = {Red Sea Atlas of Coral-Associated Bacteria Highlights Common Microbiome Members and Their Distribution across Environmental Gradients-A Systematic Review.},
journal = {Microorganisms},
volume = {10},
number = {12},
pages = {},
pmid = {36557593},
issn = {2076-2607},
support = {BAS/1/1095-01-01 and FCC/1/1973-51-01//King Abdullah University of Science and Technology/ ; },
abstract = {The Red Sea is a suitable model for studying coral reefs under climate change due to its strong environmental gradient that provides a window into future global warming scenarios. For instance, corals in the southern Red Sea thrive at temperatures predicted to occur at the end of the century in other biogeographic regions. Corals in the Red Sea thrive under contrasting thermal and environmental regimes along their latitudinal gradient. Because microbial communities associated with corals contribute to host physiology, we conducted a systematic review of the known diversity of Red Sea coral-associated bacteria, considering geographic location and host species. Our assessment comprises 54 studies of 67 coral host species employing cultivation-dependent and cultivation-independent techniques. Most studies have been conducted in the central and northern Red Sea, while the southern and western regions remain largely unexplored. Our data also show that, despite the high diversity of corals in the Red Sea, the most studied corals were Pocillopora verrucosa, Dipsastraea spp., Pleuractis granulosa, and Stylophora pistillata. Microbial diversity was dominated by bacteria from the class Gammaproteobacteria, while the most frequently occurring bacterial families included Rhodobacteraceae and Vibrionaceae. We also identified bacterial families exclusively associated with each of the studied coral orders: Scleractinia (n = 125), Alcyonacea (n = 7), and Capitata (n = 2). This review encompasses 20 years of research in the Red Sea, providing a baseline compendium for coral-associated bacterial diversity.},
}
@article {pmid36554499,
year = {2022},
author = {Dania, MI and Faraji, B and Wachira, J},
title = {Micronutrient Biosynthesis Potential of Spontaneous Grain Fermentation Microbiomes.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {24},
pages = {},
pmid = {36554499},
issn = {1660-4601},
support = {U54 MD013376/MD/NIMHD NIH HHS/United States ; UL1 GM118973/GM/NIGMS NIH HHS/United States ; 5UL1GM118973/GM/NIGMS NIH HHS/United States ; 5U54MD013376/NH/NIH HHS/United States ; },
mesh = {Humans ; Fermentation ; Micronutrients/metabolism ; Phylogeny ; Bacteria ; *Microbiota ; Edible Grain ; *Trace Elements/metabolism ; },
abstract = {Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics. The purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analyses were conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) were generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipelines with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were differences in the relative abundances of the dominant taxa of bacteria that are involved in the spontaneous fermentation of millet namely Lactobacillaceae, Burkholderiaceae, Streptococcaceae, Leuconostocaceae, and Acetobacteraceae. Clostridiaceae was the dominant family in one dataset. The incidence of Lactobacillaceae and Bifidobacteriaceae suggest the probiotic characteristics of fermented millet. The datasets were collected with fermentations that were mediated by autochthonous microorganisms and the presence of some potential pathogens such as Enterobacteriaceae, Clostridiaceae, Aeromonadaceae, Microbacteiaceae, Pseudomonadaceae, and Neisseriaceae which suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as essential amino acids and vitamins, suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.},
}
@article {pmid36549925,
year = {2023},
author = {Hodžić, A and Alić, A},
title = {Hepatozoon silvestris: an emerging feline vector-borne pathogen in Europe?.},
journal = {Trends in parasitology},
volume = {39},
number = {3},
pages = {163-166},
doi = {10.1016/j.pt.2022.12.001},
pmid = {36549925},
issn = {1471-5007},
mesh = {Cats ; Animals ; *Eucoccidiida/genetics ; *Coccidiosis/epidemiology/veterinary/parasitology ; Europe/epidemiology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Hepatozoon silvestris (Adeleorina: Hepatozoidae) is a recently described agent of feline hepatozoonosis. Although possibly emerging in Europe, this apicomplexan parasite is still largely unknown. Here, we provide insight into our current knowledge of the parasite's distribution, biology, and pathogenesis of the associated disease.},
}
@article {pmid36549441,
year = {2023},
author = {Bilbija, B and Spitzweg, C and Papoušek, I and Fritz, U and Földvári, G and Mullett, M and Ihlow, F and Sprong, H and Civáňová Křížová, K and Anisimov, N and Belova, OA and Bonnet, SI and Bychkova, E and Czułowska, A and Duscher, GG and Fonville, M and Kahl, O and Karbowiak, G and Kholodilov, IS and Kiewra, D and Krčmar, S and Kumisbek, G and Livanova, N and Majláth, I and Manfredi, MT and Mihalca, AD and Miró, G and Moutailler, S and Nebogatkin, IV and Tomanović, S and Vatansever, Z and Yakovich, M and Zanzani, S and Široký, P},
title = {Dermacentor reticulatus - a tick on its way from glacial refugia to a panmictic Eurasian population.},
journal = {International journal for parasitology},
volume = {53},
number = {2},
pages = {91-101},
doi = {10.1016/j.ijpara.2022.11.002},
pmid = {36549441},
issn = {1879-0135},
mesh = {Dogs ; Animals ; *Dermacentor/genetics ; Phylogeny ; Bayes Theorem ; Refugium ; *Rhipicephalus sanguineus ; },
abstract = {The ornate dog tick (Dermacentor reticulatus) shows a recently expanding geographic distribution. Knowledge on its intraspecific variability, population structure, rate of genetic diversity and divergence, including its evolution and geographic distribution, is crucial to understand its dispersal capacity. All such information would help to evaluate the potential risk of future spread of associated pathogens of medical and veterinary concern. A set of 865 D. reticulatus ticks was collected from 65 localities across 21 countries, from Portugal in the west to Kazakhstan and southern Russia in the east. Cluster analyses of 16 microsatellite loci were combined with nuclear (ITS2, 18S) and mitochondrial (12S, 16S, COI) sequence data to uncover the ticks' population structures and geographical patterns. Approximate Bayesian computation was applied to model evolutionary relationships among the found clusters. Low variability and a weak phylogenetic signal showing an east-west cline were detected both for mitochondrial and nuclear sequence markers. Microsatellite analyses revealed three genetic clusters, where the eastern and western cluster gradient was supplemented by a third, northern cluster. Alternative scenarios could explain such a tripartite population structure by independent formation of clusters in separate refugia, limited gene flow connected with isolation by distance causing a "bipolar pattern", and the northern cluster deriving from admixture between the eastern and western populations. The best supported demographic scenario of this tick species indicates that the northern cluster derived from admixture between the eastern and western populations 441 (median) to 224 (mode) generations ago, suggesting a possible link with the end of the Little Ice Age in Europe.},
}
@article {pmid36548240,
year = {2022},
author = {Lee, JR and Terauds, A and Carwardine, J and Shaw, JD and Fuller, RA and Possingham, HP and Chown, SL and Convey, P and Gilbert, N and Hughes, KA and McIvor, E and Robinson, SA and Ropert-Coudert, Y and Bergstrom, DM and Biersma, EM and Christian, C and Cowan, DA and Frenot, Y and Jenouvrier, S and Kelley, L and Lee, MJ and Lynch, HJ and Njåstad, B and Quesada, A and Roura, RM and Shaw, EA and Stanwell-Smith, D and Tsujimoto, M and Wall, DH and Wilmotte, A and Chadès, I},
title = {Threat management priorities for conserving Antarctic biodiversity.},
journal = {PLoS biology},
volume = {20},
number = {12},
pages = {e3001921},
pmid = {36548240},
issn = {1545-7885},
mesh = {Animals ; Humans ; *Conservation of Natural Resources ; Antarctic Regions ; Biodiversity ; Introduced Species ; *Spheniscidae ; Climate Change ; Ecosystem ; },
abstract = {Antarctic terrestrial biodiversity faces multiple threats, from invasive species to climate change. Yet no large-scale assessments of threat management strategies exist. Applying a structured participatory approach, we demonstrate that existing conservation efforts are insufficient in a changing world, estimating that 65% (at best 37%, at worst 97%) of native terrestrial taxa and land-associated seabirds are likely to decline by 2100 under current trajectories. Emperor penguins are identified as the most vulnerable taxon, followed by other seabirds and dry soil nematodes. We find that implementing 10 key threat management strategies in parallel, at an estimated present-day equivalent annual cost of US$23 million, could benefit up to 84% of Antarctic taxa. Climate change is identified as the most pervasive threat to Antarctic biodiversity and influencing global policy to effectively limit climate change is the most beneficial conservation strategy. However, minimising impacts of human activities and improved planning and management of new infrastructure projects are cost-effective and will help to minimise regional threats. Simultaneous global and regional efforts are critical to secure Antarctic biodiversity for future generations.},
}
@article {pmid36545206,
year = {2022},
author = {Molina, V and Lavergne, C and Eissler, Y and Junier, P},
title = {Editorial: Microbial ecology and ecosystems from a Southern perspective.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1098400},
pmid = {36545206},
issn = {1664-302X},
}
@article {pmid36542127,
year = {2023},
author = {Davis, TS and Stewart, JE and Clark, C and Van Buiten, C},
title = {Nutritional Profile and Ecological Interactions of Yeast Symbionts Associated with North American Spruce Beetle (Dendroctonus rufipennis).},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1268-1280},
pmid = {36542127},
issn = {1432-184X},
support = {2046109//Division of Integrative Organismal Systems/ ; },
mesh = {Animals ; *Coleoptera/microbiology ; *Phenylethyl Alcohol ; Yeasts ; Symbiosis ; *Ophiostomatales ; *Picea ; North America ; },
abstract = {To better understand functional ecology of bark beetle-microbial symbioses, we characterized yeast associates of North American spruce beetle (Dendroctous rufipennis Kirby) across populations. Seven yeast species were detected; Wickerhamomyces canadensis (Wickerham) Kurtzman et al. (Sachharomycetales: Saccharomycetaceae) was the most common (74% of isolates) and found in all populations. Isolates of W. canadensis were subsequently tested for competitive interactions with symbiotic (Leptographium abietinum, = Grosmannia abietina) and pathogenic (Beauvaria bassiana) filamentous fungi, and isolates were nutritionally profiled (protein and P content). Exposure to yeast headspace emissions had isolate-dependent effects on colony growth of symbiotic and pathogenic fungi; most isolates of W. canadensis slightly inhibited growth rates of symbiotic (L. abietinum, mean effect: - 4%) and entomopathogenic (B. bassiana, mean effect: - 6%) fungi. However, overall variation was high (range: - 35.4 to + 88.6%) and some yeasts enhanced growth of filamentous fungi whereas others were consistently inhibitory. The volatile 2-phenylethanol was produced by W. canadensis and synthetic 2-phenylethanol reduced growth rates of both L. abietinum and B. bassiana by 36% on average. Mean protein and P content of Wickerhamomyces canadensis cultures were 0.8% and 7.2%, respectively, but isolates varied in nutritional content and protein content was similar to that of host tree phloem. We conclude that W. canadensis is a primary yeast symbiont of D. rufipennis in the Rocky Mountains and emits volatiles that can affect growth of associated microbes. Wickerhamomyces canadensis isolates vary substantially in limiting nutrients (protein and P), but concentrations are less than reported for the symbiotic filamentous fungus L. abietinum.},
}
@article {pmid36542126,
year = {2023},
author = {Wicaksono, WA and Buko, A and Kusstatscher, P and Cernava, T and Sinkkonen, A and Laitinen, OH and Virtanen, SM and Hyöty, H and Berg, G},
title = {Impact of Cultivation and Origin on the Fruit Microbiome of Apples and Blueberries and Implications for the Exposome.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {973-984},
pmid = {36542126},
issn = {1432-184X},
support = {874864//Horizon 2020 Framework Programme/ ; },
mesh = {Humans ; Fruit/microbiology ; *Malus ; *Blueberry Plants/chemistry ; *Exposome ; *Microbiota ; },
abstract = {Vegetables and fruits are a crucial part of the planetary health diet, directly affecting human health and the gut microbiome. The objective of our study was to understand the variability of the fruit (apple and blueberry) microbiome in the frame of the exposome concept. The study covered two fruit-bearing woody species, apple and blueberry, two countries of origin (Austria and Finland), and two fruit production methods (naturally grown and horticultural). Microbial abundance, diversity, and community structures were significantly different for apples and blueberries and strongly influenced by the growing system (naturally grown or horticultural) and country of origin (Austria or Finland). Our results indicated that bacterial communities are more responsive towards these factors than fungal communities. We found that fruits grown in the wild and within home gardens generally carry a higher microbial diversity, while commercial horticulture homogenized the microbiome independent of the country of origin. This can be explained by horticultural management, including pesticide use and post-harvest treatments. Specific taxonomic indicators were identified for each group, i.e., for horticultural apples: Pseudomonas, Ralstonia, and Stenotrophomonas. Interestingly, Ralstonia was also found to be enriched in horticultural blueberries in comparison to such that were home and wildly grown. Our study showed that the origin of fruits can strongly influence the diversity and composition of their microbiome, which means that we are exposed to different microorganisms by eating fruits from different origins. Thus, the fruit microbiome needs to be considered an important but relatively unexplored external exposomic factor.},
}
@article {pmid36539202,
year = {2023},
author = {Almeida-Silva, F and Zhao, T and Ullrich, KK and Schranz, ME and Van de Peer, Y},
title = {syntenet: an R/Bioconductor package for the inference and analysis of synteny networks.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {1},
pages = {},
pmid = {36539202},
issn = {1367-4811},
support = {833522//European Research Council/International ; 833522//European Union's Horizon 2020 Research and Innovation Program/ ; },
mesh = {Synteny ; Phylogeny ; *Software ; *Genome ; },
abstract = {SUMMARY: Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny analyses. Here, we present syntenet, an R package to infer and analyze synteny networks from whole-genome protein sequence data. The package offers a simple and complete framework, including data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Graphical functions are also available to create publication-ready plots. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate.<br><br>syntenet is available on Bioconductor (https://bioconductor.org/packages/syntenet), and the source code is available on a GitHub repository (https://github.com/almeidasilvaf/syntenet).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid36538089,
year = {2023},
author = {Moukarzel, R and Ridgway, HJ and Waller, L and Guerin-Laguette, A and Cripps-Guazzone, N and Jones, EE},
title = {Soil Arbuscular Mycorrhizal Fungal Communities Differentially Affect Growth and Nutrient Uptake by Grapevine Rootstocks.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1035-1049},
pmid = {36538089},
issn = {1432-184X},
support = {Strategic Science Investment Fund//New Zealand Institute for Plant and Food Research Limited/ ; Project P/471778/08//New Zealand Institute for Plant and Food Research Limited/ ; },
mesh = {*Mycorrhizae ; Ecosystem ; Soil ; *Mycobiome ; Crops, Agricultural ; Nutrients ; Soil Microbiology ; Plant Roots/microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) deliver potentially significant services in sustainable agricultural ecosystems, yet we still lack evidence showing how AMF abundance and/or community composition can benefit crops. In this study, we manipulated AMF communities in grapevine rootstock and measured plant growth and physiological responses. Glasshouse experiments were set up to determine the interaction between rootstock variety and different AMF communities, using AMF communities originating under their own (i.e., "home") soil and other rootstocks' (i.e., "away") soil. The results revealed that specific AMF communities had differential effects on grapevine rootstock growth and nutrient uptake. It was demonstrated that a rootstock generally performed better in the presence of its own AMF community. This study also showed that AMF spore diversity and the relative abundance of certain species is an important factor as, when present in equal abundance, competition between species was indicated to occur, resulting in a reduction in the positive growth outcomes. Moreover, there was a significant difference between the communities with some AMF communities increasing plant growth and nutrient uptake compared with others. The outcomes also demonstrated that some AMF communities indirectly influenced the chlorophyll content in grapevine leaves through the increase of specific nutrients such as K, Mn, and Zn. The findings also indicated that some AMF species may deliver particular benefits to grapevine plants. This work has provided an improved understanding of community level AMF-grapevine interaction and delivered an increased knowledge of the ecosystem services they provide which will benefit the wine growers and the viticulture industry.},
}
@article {pmid36537799,
year = {2023},
author = {Tyc, O and Kulkarni, P and Ossowicki, A and Tracanna, V and Medema, MH and van Baarlen, P and van IJcken, WFJ and Verhoeven, KJF and Garbeva, P},
title = {Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis.},
journal = {mSystems},
volume = {8},
number = {1},
pages = {e0057422},
pmid = {36537799},
issn = {2379-5077},
mesh = {*Soil ; Metabolome ; Symbiosis ; *Comamonadaceae ; },
abstract = {Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-μm filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that in soil there are bacteria that can pass through a 0.1-μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1-μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.},
}
@article {pmid36534053,
year = {2023},
author = {Amaneesh, C and Anna Balan, S and Silpa, PS and Kim, JW and Greeshma, K and Aswathi Mohan, A and Robert Antony, A and Grossart, HP and Kim, HS and Ramanan, R},
title = {Gross Negligence: Impacts of Microplastics and Plastic Leachates on Phytoplankton Community and Ecosystem Dynamics.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {1},
pages = {5-24},
doi = {10.1021/acs.est.2c05817},
pmid = {36534053},
issn = {1520-5851},
mesh = {Animals ; Humans ; *Ecosystem ; *Plastics/analysis ; Microplastics/toxicity ; Phytoplankton ; Aquatic Organisms ; },
abstract = {Plastic debris is an established environmental menace affecting aquatic systems globally. Recently, microplastics (MP) and plastic leachates (PL) have been detected in vital human organs, the vascular system, and in vitro animal studies positing severe health hazards. MP and PL have been found in every conceivable aquatic ecosystem─from open oceans and deep sea floors to supposedly pristine glacier lakes and snow covered mountain catchment sites. Many studies have documented the MP and PL impacts on a variety of aquatic organisms, whereby some exclusively focus on aquatic microorganisms. Yet, the specific MP and PL impacts on primary producers have not been systematically analyzed. Therefore, this review focuses on the threats posed by MP, PL, and associated chemicals on phytoplankton, their comprehensive impacts at organismal, community, and ecosystem scales, and their endogenous amelioration. Studies on MP- and PL-impacted individual phytoplankton species reveal the production of reactive oxygen species, lipid peroxidation, physical damage of thylakoids, and other physiological and metabolic changes, followed by homo- and heteroaggregations, ultimately eventuating in decreased photosynthesis and primary productivity. Likewise, analyses of the microbial community in the plastisphere show a radically different profile compared to the surrounding planktonic diversity. The plastisphere also enriches multidrug-resistant bacteria, cyanotoxins, and pollutants, accelerating microbial succession, changing the microbiome, and thus, affecting phytoplankton diversity and evolution. These impacts on cellular and community scales manifest in changed ecosystem dynamics with widespread bottom-up and top-down effects on aquatic biodiversity and food web interactions. These adverse effects─through altered nutrient cycling─have "knock-on" impacts on biogeochemical cycles and greenhouse gases. Consequently, these impacts affect provisioning and regulating ecosystem services. Our citation network analyses (CNA) further demonstrate dire effects of MP and PL on all trophic levels, thereby unsettling ecosystem stability and services. CNA points to several emerging nodes indicating combined toxicity of MP, PL, and their associated hazards on phytoplankton. Taken together, our study shows that ecotoxicity of plastic particles and their leachates have placed primary producers and some aquatic ecosystems in peril.},
}
@article {pmid36533929,
year = {2023},
author = {Rojas, CA and Holekamp, KE and Viladomat Jasso, M and Souza, V and Eisen, JA and Theis, KR},
title = {Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study.},
journal = {mSystems},
volume = {8},
number = {1},
pages = {e0096522},
pmid = {36533929},
issn = {2379-5077},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Hyaenidae/genetics ; RNA, Ribosomal, 16S/genetics ; *Carnivora/genetics ; Metagenomics ; },
abstract = {The gut microbiome provides vital functions for mammalian hosts, yet research on its variability and function across adult life spans and multiple generations is limited in large mammalian carnivores. Here, we used 16S rRNA gene and metagenomic high-throughput sequencing to profile the bacterial taxonomic composition, genomic diversity, and metabolic function of fecal samples collected from 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya, over a 23-year period spanning three generations. The metagenomic data came from four of these hyenas and spanned two 2-year periods. With these data, we determined the extent to which host factors predicted variation in the gut microbiome and identified the core microbes present in the guts of hyenas. We also investigated novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition varied temporally, but despite this, a core set of 14 bacterial genera were identified. The strongest predictors of the microbiome were host identity and age, suggesting that hyenas possess individualized microbiomes and that these may change with age during adulthood. The gut microbiome functional profiles of the four adult hyenas were also individual specific and were associated with prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyenas' guts; some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species-level matches to genomes in existing reference databases. IMPORTANCE There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host's life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores, and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores, but over 80% of MAGs were novel and from species not previously represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of nonmodel wild hosts, using multiple sequencing methods and computational approaches and at distinct scales of analysis.},
}
@article {pmid36533921,
year = {2023},
author = {Graf, F and Zehentner, B and Fellner, L and Scherer, S and Neuhaus, K},
title = {Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0235122},
pmid = {36533921},
issn = {2165-0497},
mesh = {*Escherichia coli O157/genetics/metabolism ; *Escherichia coli Proteins/genetics ; Base Sequence ; Genes, Overlapping ; Ribosome Profiling ; },
abstract = {The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel overlapping open reading frames in Escherichia coli O157:H7 EDL933 (EHEC). Indeed, the overlapping candidate genes are equipped with typical structural elements required for transcription and translation, i.e., promoters, transcription start sites, as well as terminators, all of which were experimentally verified. Translationally arrested mutants, unable to produce the overlapping encoded protein, were found to have a growth disadvantage when grown competitively against the wild type. Thus, the phenotypes found imply biological functionality of the genes at the level of proteins produced. The addition of 3 more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes emphasizes the underestimated coding capacity of bacterial genomes. IMPORTANCE The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated, since such genes are not allowed in genome annotations. However, ribosome profiling catches mRNA in the moment of being template for protein production. Using this technique and subsequent experiments, we verified 3 novel overlapping genes encoded in antisense of known genes. This adds more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes.},
}
@article {pmid36533904,
year = {2023},
author = {Timmis, K and Berry, D and Bonfante, P and Coleman, M and Cunliffe, M and Danchin, A and Galperin, M and Huang, W and Lopez, P and Stewart, F and Wood, T},
title = {Juan Luis Ramos: An exceptional Editor of Environmental Microbiology.},
journal = {Environmental microbiology},
volume = {25},
number = {3},
pages = {595-596},
doi = {10.1111/1462-2920.16315},
pmid = {36533904},
issn = {1462-2920},
}
@article {pmid36530964,
year = {2022},
author = {Inomura, K and Deutsch, C and Jahn, O and Dutkiewicz, S and Follows, MJ},
title = {Global patterns in marine organic matter stoichiometry driven by phytoplankton ecophysiology.},
journal = {Nature geoscience},
volume = {15},
number = {12},
pages = {1034-1040},
pmid = {36530964},
issn = {1752-0894},
abstract = {The proportion of major elements in marine organic matter links cellular processes to global nutrient, oxygen and carbon cycles. Differences in the C:N:P ratios of organic matter have been observed between ocean biomes, but these patterns have yet to be quantified from the underlying small-scale physiological and ecological processes. Here we use an ecosystem model that includes adaptive resource allocation within and between ecologically distinct plankton size classes to attribute the causes of global patterns in the C:N:P ratios. We find that patterns of N:C variation are largely driven by common physiological adjustment strategies across all phytoplankton, while patterns of N:P are driven by ecological selection for taxonomic groups with different phosphorus storage capacities. Although N:C varies widely due to cellular adjustment to light and nutrients, its latitudinal gradient is modest because of depth-dependent trade-offs between nutrient and light availability. Strong latitudinal variation in N:P reflects an ecological balance favouring small plankton with lower P storage capacity in the subtropics, and larger eukaryotes with a higher cellular P storage capacity in nutrient-rich high latitudes. A weaker N:P difference between southern and northern hemispheres, and between the Atlantic and Pacific oceans, reflects differences in phosphate available for cellular storage. Despite simulating only two phytoplankton size classes, the emergent global variability of elemental ratios resembles that of all measured species, suggesting that the range of growth conditions and ecological selection sustain the observed diversity of stoichiometry among phytoplankton.},
}
@article {pmid36530180,
year = {2023},
author = {Messadi, N and Mechmeche, M and Setti, K and Tizemmour, Z and Hamdi, M and Kachouri, F},
title = {Optimization of Extraction Parameters and Characterization of Tunisian Date Extract: A Scientific Approach Toward Their Utilization.},
journal = {Sugar tech : an international journal of sugar crops &amp; related industries},
volume = {25},
number = {2},
pages = {460-472},
pmid = {36530180},
issn = {0972-1525},
abstract = {UNLABELLED: The response surface methodology (RSM) was used in order to select the extraction conditions of extract from Kentichi date powder; a by-product of the date-processing process. Powder/solvent ratio, extraction temperature, and extraction time all had an impact on sugar yield, and these model factors have quadratic effects influencing sugar yield. Optimal extraction was obtained with 300 g/L powder/solvent ratio, 32.7 °C extraction temperature, and 2.1 h extraction time. Under these conditions, Kentichi date powder's (KDP) sugar yield was 77.1%, which was close to the predicted value of the model (80.50%). The results of Kentichi date powder extract (KDPE) showed that the total sugar content is 160.09 g/L. However, the protein content is 10.31 g/L with a majority of the essential amino acids (essentially glutamic acid (28.39 mg/L) and aspartic acid (9.65 mg/L)). The determination of antioxidant activity of KDPE showed a high activity (DPPH IC50 = 4.8 mg/mL, ABTS IC50 = 3 mg/mL, FRAP = 4.70 μmol AAE/mL and, TAA = 18.04 μmol Fe(II)/mL). The results show also that the freeze-drying technique has a lot of potential for producing powder from KDPE with many desirable properties. The findings indicate that KDPE with a high nutritional value could be used as a component for the formulation of functional foods.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12355-022-01223-2.},
}
@article {pmid36529834,
year = {2023},
author = {Kormas, K and Nikouli, E and Kousteni, V and Damalas, D},
title = {Midgut Bacterial Microbiota of 12 Fish Species from a Marine Protected Area in the Aegean Sea (Greece).},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1405-1415},
pmid = {36529834},
issn = {1432-184X},
mesh = {Animals ; Greece ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Fishes ; },
abstract = {Fish microbiome science is progressing fast, but it is biased toward farmed or laboratory fish species against natural fish populations, which remain considerably underinvestigated. We analyzed the midgut bacterial microbiota of 45 specimens of 12 fish species collected from the Gyaros Island marine protected area (Aegean Sea, Greece). The species belong to seven taxonomic families and are either herbivores or omnivores. Mucosa midgut bacterial diversity was assessed by amplicon metabarcoding of the 16S rRNA V3-V4 gene region. A total of 854 operational taxonomic units (OTUs) were identified. In each fish species, between 2 and 18 OTUs dominated with cumulative relative abundance ≥ 70%. Most of the dominating bacterial taxa have been reported to occur both in wild and farmed fish populations. The midgut bacterial communities were different among the 12 fish species, except for Pagrus pagrus and Pagellus erythrinus, which belong to the Sparidae family. No differentiation of the midgut bacterial microbiota was found based on feeding habits, i.e., omnivorous vs. carnivorous. Comparing wild and farmed P. pagrus midgut bacterial microbiota revealed considerable variation between them. Our results expand the gut microbiota of wild fish and support the host species effect as the more likely factor shaping intestinal bacterial microbiota.},
}
@article {pmid36528730,
year = {2023},
author = {Bizic, M and Brad, T and Ionescu, D and Barbu-Tudoran, L and Zoccarato, L and Aerts, JW and Contarini, PE and Gros, O and Volland, JM and Popa, R and Ody, J and Vellone, D and Flot, JF and Tighe, S and Sarbu, SM},
title = {Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species.},
journal = {The ISME journal},
volume = {17},
number = {3},
pages = {340-353},
pmid = {36528730},
issn = {1751-7370},
mesh = {*Caves/chemistry ; Sulfur/metabolism ; *Epsilonproteobacteria/metabolism ; Romania ; Phylogeny ; },
abstract = {Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O2 (~7%). The cave's surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3[-] as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.},
}
@article {pmid36528203,
year = {2023},
author = {Jaiswal, S and Singh, DK and Shukla, P},
title = {Degradation effectiveness of hexachlorohexane (ϒ-HCH) by bacterial isolate Bacillus cereus SJPS-2, its gene annotation for bioremediation and comparison with Pseudomonas putida KT2440.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {318},
number = {},
pages = {120867},
doi = {10.1016/j.envpol.2022.120867},
pmid = {36528203},
issn = {1873-6424},
mesh = {*Hexachlorocyclohexane/metabolism ; Biodegradation, Environmental ; *Pseudomonas putida/genetics ; Bacillus cereus/genetics ; Molecular Sequence Annotation ; },
abstract = {The contamination of Hexachlorohexane (Lindane) in soil and water has toxic effects due to its persistent nature. In our study, an indigenous HCH (gamma isomer) degrading bacterium viz Bacillus cereus SJPS-2 was isolated from Yamuna river water using enrichment culture method. The growth curve indicated that Bacillus cereus SJPS-2 was able to degrade ϒ-HCH effectively with 80.98% degradation. Further, process was improved by using immobilization using alginate beads which showed enhanced degradation (89.34%). Interestingly, in presence of fructose, the ϒ-HCH degradation was up to 79.24% with exponential growth curve whereas the degradation was only 5.61% in presence of glucose revealing diauxic growth curve. Furthermore, The FTIR results confirmed the potential lindane degradation capability of Bacillus cereus SJPS-2 and the bonds were recorded at wavelengths viz. 2900-2500 cm-[1], 3300-2800 cm-[1] and 785-540 cm-[1]. Similarity, the GC studies also reconfirmed the degradation potential with retention time (RT) of ethyl acetate and lindane was 2.12 and 11.0 respectively. Further, we studied the metabolic pathway involved for lindane utilization in Bacillus cereus using KEGG-KASS and functional gene annotation through Rapid Annotation using Subsystems Technology (RAST) resulted in the annotation of the lin genes (lin A, lin B, lin C, lin X, lin D, lin E) and respective encoding enzymes. The comparative ϒ-HCH degradation potential of B. cereus and P. putida KT2440 was also evaluated. The island viewer showed the different colors on circular genome indicate the coordinates of genomic islands resulted with some common genomic islands (GEIs) between both bacteria indicating the possibility of horizontal gene transfer at contaminated site or natural environment. These genomic islands (GEIs) contribute in the rearrangement genetic material or to evolve bacteria in stress conditions, as a result the metabolic pathways evolve by formation of catabolic genes. This study establishes the potential of Bacillus cereus SJPS-2 for effectual ϒ-HCH degradation.},
}
@article {pmid36524228,
year = {2022},
author = {Othieno, J and Njagi, O and Masika, S and Apamaku, M and Tenge, E and Mwasa, B and Kimondo, P and Gardner, E and Von Dobschuetz, S and Muriira, J and Adul, B and Mwongela, L and Hambe, HA and Nyariki, T and Fasina, FO},
title = {Knowledge, attitudes, and practices on camel respiratory diseases and conditions in Garissa and Isiolo, Kenya.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {1022146},
pmid = {36524228},
issn = {2297-1769},
abstract = {BACKGROUND: Livestock farmers' attitudes, practices, and behaviors are major factors in infection prevention and control of animal diseases. Kenya has the fourth largest global camel population, and the industry has grown over the last two decades, transforming beyond the traditional camel-keeping areas to include peri-urban camel trade and value chain growth. The dromedary camel is resilient, and it is a preferred species in the arid and semi-arid areas (ASALs) of Kenya. However, it still faces many health and production challenges; to identify infection drivers and risky behaviors for camel respiratory illnesses and conditions in Kenya, we conducted a knowledge, attitudes, and practices (KAP) survey.<br><br>METHOD: Using a set of tools (questionnaires, key informant interviews, and focus group discussions), we interviewed camel owners, herders, agro-veterinary outlets, and other relevant value chain stakeholders in Garissa and Isiolo counties (n = 85). Data were analyzed using descriptive and analytic statistics.<br><br>RESULTS: Most camel owners/herders are male and most are relatively uneducated (85.5%). The camels were used primarily for milk and meat production, income generation, and transport. Larger herd sizes (>30 camels) and owner/herder's lack of formal education are risk factors for owner-reported respiratory illnesses in camels. Major clinical signs of respiratory conditions were coughing (85.7%), nasal discharge (59.7%), and fever (23.4%). Diseases, lack of feeds, theft, and marketing challenges are the major constraints to camel production in Kenya. Owners-herders use drugs indiscriminately and this may contribute to antimicrobial resistance challenges.<br><br>CONCLUSION: Practitioners in the camel value chain want more commitment from the government and animal health officials on support services and access to veterinary services. Watering points, grazing areas, and marketing points are the primary areas for congregating camels and have a significant potential for disease spread. Kenya camels have a massive capacity for rural and ASALs' livelihoods transformation but the identified health challenges, and other issues must be addressed. Further studies on the Kenyan camels' respiratory microbial ecology are important to understand microbial risks and reduce the burden of zoonotic infections. Intensification of risk communication and community engagement, and messaging targeted at behavior change interventions should be directed at camel value chain actors.},
}
@article {pmid36523823,
year = {2022},
author = {Bernasconi, R and Lund, MA and Blanchette, ML},
title = {Non-charismatic waterbodies and ecosystem disservices: Mine pit lakes are underrepresented in the literature.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1063594},
pmid = {36523823},
issn = {1664-302X},
abstract = {Pit lakes are one of the greatest legacies of open-cut mining. Despite the potential hazards of these lakes, they represent newly formed ecosystems with great scientific and ecological potential. Although thousands of pit lakes occur on every inhabited continent, with more being created, the microbial ecology of pit lakes is relatively under-researched. We evaluated the current state of microbial research in pit lakes by performing a Web of Science search and creating a literature database. Study lakes were categorized according to location and water quality (pH and conductivity) which is a key community and environmental concern. Research technology employed in the study was also categorized. We compared research effort in lakes, rivers, and streams which are the more "charismatic" inland aquatic ecosystems. Pit lake publications on microbes from 1987 to 2022 (n = 128) were underrepresented in the literature relative to rivers and streams (n = 321) and natural lakes (n = 948). Of the 128 pit lake publications, 28 were within the field of geochemistry using indirect measures of microbial activity. Most pit lake microbial research was conducted in a few acidic lakes in Germany due to social pressure for remediation and government initiative. Relatively few studies have capitalized on emerging technology. Pit lake microbial research likely lags other more charismatic ecosystems given that they are viewed as performing "ecosystem disservices," but this is socially complex and requires further research. Improving understanding of microbial dynamics in pit lakes will allow scientists to deliver safer pit lakes to communities.},
}
@article {pmid36523636,
year = {2022},
author = {Morales, C and Rojas, G and Rebolledo, C and Rojas-Herrera, M and Arias-Carrasco, R and Cuadros-Orellana, S and Maracaja-Coutinho, V and Saavedra, K and Leal, P and Lanas, F and Salazar, LA and Saavedra, N},
title = {Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {943609},
pmid = {36523636},
issn = {2235-2988},
mesh = {Adult ; Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Microbiota ; Cholesterol ; },
abstract = {INTRODUCTION: In recent years, several studies have evidenced the importance of the microbiome to host physiology as metabolism regulator, along with its potential role in triggering various diseases. In this study, we analyzed the gut microbiota in hypercholesterolemic (cases) and normocholesterolemic (controls) individuals to identify characteristic microbial signature for each condition.<br><br>METHODS: Stool samples were obtained from 57 adult volunteers (27 hypercholesterolemic and 30 controls). The taxonomic profiling of microbial communities was performed using high-throughput sequencing of 16S rRNA V3-V4 amplicons, followed by data analysis using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and linear discriminant analysis (LDA) effect size (LEfSe).<br><br>RESULTS: Significant differences were observed in weight, height, body mass index (BMI) and serum levels of triglycerides, total cholesterol and low-density lipoprotein cholesterol (LDL-C) between the groups (p<0.05). LEfSe showed differentially abundant prokaryotic taxa (&#x3b1;=0.05, LDA score > 2.0) in the group of hypercholesterolemic individuals (Methanosphaera, Rothia, Chromatiales, Clostridiales, Bacillaceae and Coriobacteriaceae) and controls (Faecalibacterium, Victivallis and Selenomonas) at various taxonomic levels. In addition, through the application of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2), the predominance of pathways related to biosynthesis in hypercholesterolemic patients was established, compared to controls in which degradation pathways were predominant. Finally, in the analysis of co-occurrence networks, it was possible to identify associations between the microorganisms present in both studied groups.<br><br>CONCLUSION: Our results point out to unique microbial signatures, which likely play a role on the cholesterol metabolism in the studied population.},
}
@article {pmid36523515,
year = {2022},
author = {Thongthaisong, P and Kasada, M and Grossart, HP and Wollrab, S},
title = {Critical role of parasite-mediated energy pathway on community response to nutrient enrichment.},
journal = {Ecology and evolution},
volume = {12},
number = {12},
pages = {e9622},
pmid = {36523515},
issn = {2045-7758},
abstract = {Parasites form an integral part of food webs, however, they are often ignored in classic food web theory or limited to the investigation of trophic transmission pathways. Specifically, direct consumption of parasites by nonhost predators is rarely considered, while it can contribute substantially to energy flow in food webs. In aquatic systems, chytrids constitute a major group of fungal parasites whose free-living infective stages (zoospores) form a highly nutritional food source to zooplankton. Thereby, the consumption of zoospores can create an energy pathway from otherwise inedible phytoplankton to zooplankton ("mycoloop"). This parasite-mediated energy pathway might be of special importance during phytoplankton blooms dominated by inedible or toxic primary producers like cyanobacteria, which are on the rise with eutrophication and global warming. We theoretically investigated community dynamics and energy transfer in a food web consisting of an edible nonhost and an inedible host phytoplankton species, a parasitic fungus, and a zooplankton species grazing on edible phytoplankton and fungi. Food web dynamics were investigated along a nutrient gradient contrasting nonadaptive zooplankton species representative for filter feeders like cladocerans and zooplankton with the ability to actively adapt their feeding preferences like many copepod species. Overall, the importance of the mycoloop for zooplankton increases with nutrient availability. This increase is smooth for nonadaptive consumers. For adaptive consumers, we observe an abrupt shift from an almost exclusive preference for edible phytoplankton at low nutrient levels to a strong preference for parasitic fungi at high nutrient levels. The model predicts that parasitic fungi could contribute up to 50% of the zooplankton diet in nutrient-rich environments, which agrees with empirical observations on zooplankton gut content from eutrophic systems during blooms of inedible diatoms or cyanobacteria. Our findings highlight the role of parasite-mediated energy pathways for predictions of energy flow and community composition under current and future environmental change.},
}
@article {pmid36523400,
year = {2022},
author = {Upadhyay, V and Suryawanshi, R and Tasoff, P and McCavitt-Malvido, M and Kumar, GR and Murray, VW and Noecker, C and Bisanz, JE and Hswen, Y and Ha, C and Sreekumar, B and Chen, IP and Lynch, SV and Ott, M and Lee, S and Turnbaugh, PJ},
title = {Mild SARS-CoV-2 infection results in long-lasting microbiota instability.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2022.12.07.519508},
pmid = {36523400},
issn = {2692-8205},
support = {T32 AI060537/AI/NIAID NIH HHS/United States ; },
abstract = {UNLABELLED: Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2 positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls, as long as 154 days after their positive test. These results were confirmed and extended in the K18-hACE2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila . Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology.<br><br>IMPORTANCE: Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2 it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.},
}
@article {pmid36521745,
year = {2023},
author = {Araujo, ASF and Jia, X and Miranda, ARL and Pereira, APA and Melo, VMM and Rocha, SMB and Costa, RM and Saraiva, TCDS and Mendes, LW and Salles, JF},
title = {Changes in the bacterial rare biosphere after permanent application of composted tannery sludge in a tropical soil.},
journal = {Chemosphere},
volume = {313},
number = {},
pages = {137487},
doi = {10.1016/j.chemosphere.2022.137487},
pmid = {36521745},
issn = {1879-1298},
mesh = {*Soil/chemistry ; Sewage/chemistry ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; RNA, Ribosomal, 16S ; },
abstract = {Composted tannery sludge (CTS) promotes shifts in soil chemical properties, affecting microbial communities. Although the effect of CTS application on the bacterial community has been studied, it is unclear whether this impact discriminates between the dominant and rare species. This present study investigated how the dominant and rare bacterial communities respond over time to different concentrations of CTS application (0, 2.5, 5, 10, and 20 tons/ha) for 180 days. The richness of operational taxonomic units (OTU) was 30-fold higher in the rare than in the dominant biosphere. While some phyla shifted their relative abundance differently in the dominant and rare biosphere, some genera increased their relative abundance under higher CTS concentrations, such as Nocardioides (∼100%), Rubrobacter (∼300%), and Nordella (∼400%). Undominated processes largely governed the dominant biosphere (76.97%), followed by homogeneous (12.51%) and variable (8.03%) selection, and to a lesser extent, the dispersal limitation (2.48%). The rare biosphere was driven by the CTS application as evidenced by the exclusively homogeneous selection (100%). This study showed that the rare biosphere was more sensitive to changes in soil chemical parameters due to CTS application, which evidences the importance explore this portion of the bacterial community for its biotechnological use in contaminated soils.},
}
@article {pmid36520668,
year = {2022},
author = {Ibberson, CB and Barraza, JP and Holmes, AL and Cao, P and Whiteley, M},
title = {Precise spatial structure impacts antimicrobial susceptibility of S. aureus in polymicrobial wound infections.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {51},
pages = {e2212340119},
pmid = {36520668},
issn = {1091-6490},
support = {K22 AI155927/AI/NIAID NIH HHS/United States ; R01 GM116547/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Mice ; Animals ; Staphylococcus aureus ; *Methicillin-Resistant Staphylococcus aureus ; Pseudomonas aeruginosa ; *Wound Infection/drug therapy ; *Staphylococcal Infections/drug therapy ; Anti-Bacterial Agents/pharmacology ; *Coinfection ; *Pseudomonas Infections/drug therapy ; Biofilms ; },
abstract = {A hallmark of microbial ecology is that interactions between members of a community shape community function. This includes microbial communities in human infections, such as chronic wounds, where interactions can result in more severe diseases. Staphylococcus aureus is the most common organism isolated from human chronic wound infections and has been shown to have both cooperative and competitive interactions with Pseudomonas aeruginosa. Still, despite considerable study, most interactions between these microbes have been characterized using in vitro well-mixed systems, which do not recapitulate the infection environment. Here, we characterized interactions between S. aureus and P. aeruginosa in chronic murine wounds, focusing on the role that both macro- and micro-scale spatial structures play in disease. We discovered that S. aureus and P. aeruginosa coexist at high cell densities in murine wounds. High-resolution imaging revealed that these microbes establish a patchy distribution, only occupying 5 to 25% of the wound volume. Using a quantitative framework, we identified a precise spatial structure at both the macro (mm)- and micro (µm)-scales, which was largely mediated by P. aeruginosa production of the antimicrobial 2-heptyl-4-hydroxyquinoline N-oxide, while the antimicrobial pyocyanin had no impact. Finally, we discovered that this precise spatial structure enhances S. aureus tolerance to aminoglycoside antibiotics but not vancomycin. Our results provide mechanistic insights into the biogeography of S. aureus and P. aeruginosa coinfected wounds and implicate spatial structure as a key determinant of antimicrobial tolerance in wound infections.},
}
@article {pmid36520387,
year = {2023},
author = {Melayah, D and Bontemps, Z and Bruto, M and Nguyen, A and Oger, P and Hugoni, M},
title = {Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2605},
number = {},
pages = {17-35},
pmid = {36520387},
issn = {1940-6029},
mesh = {*Ecosystem ; *Archaea/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Biodiversity ; },
abstract = {High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.},
}
@article {pmid36520176,
year = {2023},
author = {Martínez-Yáñez, MG and Silva-Ortega, CO and Hernández-Aranda, VA and Vallejo-Pérez, MR and Alcalá-Briseño, R and Vega-Manriquez, DX and Aguilar-Benítez, G and Jarquin-Gálvez, R and Lara-Ávila, JP},
title = {Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {959-972},
pmid = {36520176},
issn = {1432-184X},
support = {236066//CONACYT-SEP/ ; 806623//CONACYT/ ; },
mesh = {*Solanum lycopersicum ; *Composting ; Soil/chemistry ; Bacteria ; *Microbiota ; Nitrogen ; Soil Microbiology ; },
abstract = {Mature composts and their water-based extracts, known as aerated compost teas (ACTs), are biofertilizers that share bioactive effects like soil restoration and plant health promotion, widely used for sustainable agriculture. Bioactive effects of compost and ACTs could be associated with their physicochemical and biological characteristics, like carbon/nitrogen (C/N) ratio and microbiota structure respectively. In our study, we elaborated ACTs using mature homemade compost, wheat bran, and grass clippings, following the C/N ratio criteria. Irrigation of tomato plantlets with ACT whose C/N ratio was close to the expected C/N ratio for mature compost evidenced plant growth promotion. Exploring the bacterial microbiota of elaborated ACTs and origin compost revealed significant structural differences, including phyla involved in N mineralization and free-living N-fixing bacteria. Therefore, ACTs harbor diverse bacterial microbiota involved in the N cycle, which would enrich plant and soil bacterial communities at the taxonomic and functional levels. Furthermore, ACTs are considered a part of agroecological and circular economy approaches.},
}
@article {pmid36519160,
year = {2022},
author = {Frąc, M and Hannula, ES and Bełka, M and Salles, JF and Jedryczka, M},
title = {Soil mycobiome in sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1033824},
pmid = {36519160},
issn = {1664-302X},
abstract = {The soil microbiome contributes to several ecosystem processes. It plays a key role in sustainable agriculture, horticulture and forestry. In contrast to the vast number of studies focusing on soil bacteria, the amount of research concerning soil fungal communities is limited. This is despite the fact that fungi play a crucial role in the cycling of matter and energy on Earth. Fungi constitute a significant part of the pathobiome of plants. Moreover, many of them are indispensable to plant health. This group includes mycorrhizal fungi, superparasites of pathogens, and generalists; they stabilize the soil mycobiome and play a key role in biogeochemical cycles. Several fungal species also contribute to soil bioremediation through their uptake of high amounts of contaminants from the environment. Moreover, fungal mycelia stretch below the ground like blood vessels in the human body, transferring water and nutrients to and from various plants. Recent advances in high-throughput sequencing combined with bioinformatic tools have facilitated detailed studies of the soil mycobiome. This review discusses the beneficial effects of soil mycobiomes and their interactions with other microbes and hosts in both healthy and unhealthy ecosystems. It may be argued that studying the soil mycobiome in such a fashion is an essential step in promoting sustainable and regenerative agriculture.},
}
@article {pmid36518175,
year = {2022},
author = {Tang, Q and Huang, J and Zhang, S and Qin, H and Dong, Y and Wang, C and Li, D and Zhou, R},
title = {Characterizing the correlation between species/strain-specific starter with community assembly and metabolic regulation in Xiaoqu Pei.},
journal = {Current research in microbial sciences},
volume = {3},
number = {},
pages = {100170},
pmid = {36518175},
issn = {2666-5174},
abstract = {Studying the correlation between microbiome metabolism and flavor of fermented foods has garnered significant attention recently. Understanding the contribution of metabolic regulation and environmental stress to microecosystems is essential for exploring the mechanisms of action of traditional fermented foods. Here, the interaction between microbial communities was investigated using a Xiaoqu fermentation system, processed as "simulative microecosystems," in which starters were composed of Rhizopus-specific species/strains, Meyerozyma guilliermondii, and Bacillus licheniformis. The differences between community succession and metabolites were also explored. The results indicated that Rhizopus species/strain specificity affected starch hydrolyzation, resulting in a remarkable difference in the type and content of organic acids. This further suggested that the differences in nutrient abundance and organic acids influenced the colonization of microorganisms in the fermentation system, thereby influencing the succession of their communities. The fungi in the community predominantly originated from starters, whereas the bacteria were derived from both the environment and starter. Environmentally colonized microbes were the major contributors to the co-occurrence network and were strongly correlated with network. Regional characteristics of fermented foods were closely related to environmental microbes. These results contribute to the understanding of microbial assembly and flavor metabolism in fermented foods and provide strategies for quality regulation.},
}
@article {pmid36516408,
year = {2023},
author = {Kasanke, CP and Zhao, Q and Alfaro, T and Walter, CA and Hobbie, SE and Cheeke, TE and Hofmockel, KS},
title = {Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands.},
journal = {Molecular ecology},
volume = {32},
number = {5},
pages = {1133-1148},
doi = {10.1111/mec.16823},
pmid = {36516408},
issn = {1365-294X},
support = {NSF-DEB-1042132//National Science Foundation/ ; NSF-DEB-1234162//National Science Foundation/ ; NSF-DEB-1556418//National Science Foundation/ ; NSF-DEB-1831944//National Science Foundation/ ; },
mesh = {*Mycorrhizae ; Ecosystem ; Grassland ; Soil Microbiology ; Soil/chemistry ; Plants/microbiology ; North America ; Plant Roots/microbiology ; Fungi/genetics ; },
abstract = {Nutrient exchange forms the basis of the ancient symbiotic relationship that occurs between most land plants and arbuscular mycorrhizal (AM) fungi. Plants provide carbon (C) to AM fungi and fungi provide the plant with nutrients such as nitrogen (N) and phosphorous (P). Nutrient addition can alter this symbiotic coupling in key ways, such as reducing AM fungal root colonization and changing the AM fungal community composition. However, environmental parameters that differentiate ecosystems and drive plant distribution patterns (e.g., pH, moisture), are also known to impact AM fungal communities. Identifying the relative contribution of environmental factors impacting AM fungal distribution patterns is important for predicting biogeochemical cycling patterns and plant-microbe relationships across ecosystems. To evaluate the relative impacts of local environmental conditions and long-term nutrient addition on AM fungal abundance and composition across grasslands, we studied experimental plots amended for 10 years with N, P, or N and P fertilizer in different grassland ecosystem types, including tallgrass prairie, montane, shortgrass prairie, and desert grasslands. Contrary to our hypothesis, we found ecosystem type, not nutrient treatment, was the main driver of AM fungal root colonization, diversity, and community composition, even when accounting for site-specific nutrient limitations. We identified several important environmental drivers of grassland ecosystem AM fungal distribution patterns, including aridity, mean annual temperature, root moisture, and soil pH. This work provides empirical evidence for niche partitioning strategies of AM fungal functional guilds and emphasizes the importance of long-term, large scale research projects to provide ecologically relevant context to nutrient addition studies.},
}
@article {pmid36516248,
year = {2022},
author = {Diaz-Tang, G and Meneses, EM and Patel, K and Mirkin, S and García-Diéguez, L and Pajon, C and Barraza, I and Patel, V and Ghali, H and Tracey, AP and Blanar, CA and Lopatkin, AJ and Smith, RP},
title = {Growth productivity as a determinant of the inoculum effect for bactericidal antibiotics.},
journal = {Science advances},
volume = {8},
number = {50},
pages = {eadd0924},
pmid = {36516248},
issn = {2375-2548},
support = {R15 AI159902/AI/NIAID NIH HHS/United States ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Bacteria ; },
abstract = {Understanding the mechanisms by which populations of bacteria resist antibiotics has implications in evolution, microbial ecology, and public health. The inoculum effect (IE), where antibiotic efficacy declines as the density of a bacterial population increases, has been observed for multiple bacterial species and antibiotics. Several mechanisms to account for IE have been proposed, but most lack experimental evidence or cannot explain IE for multiple antibiotics. We show that growth productivity, the combined effect of growth and metabolism, can account for IE for multiple bactericidal antibiotics and bacterial species. Guided by flux balance analysis and whole-genome modeling, we show that the carbon source supplied in the growth medium determines growth productivity. If growth productivity is sufficiently high, IE is eliminated. Our results may lead to approaches to reduce IE in the clinic, help standardize the analysis of antibiotics, and further our understanding of how bacteria evolve resistance.},
}
@article {pmid36516075,
year = {2023},
author = {Hu, A and Meng, F and Tanentzap, AJ and Jang, KS and Wang, J},
title = {Dark Matter Enhances Interactions within Both Microbes and Dissolved Organic Matter under Global Change.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {1},
pages = {761-769},
doi = {10.1021/acs.est.2c05052},
pmid = {36516075},
issn = {1520-5851},
mesh = {*Ecosystem ; *Dissolved Organic Matter ; Bacteria/metabolism ; Climate ; China ; },
abstract = {There are vast but uncharacterized microbial taxa and chemical metabolites (that is, dark matter) across the Earth's ecosystems. A lack of knowledge about dark matter hinders a complete understanding of microbial ecology and biogeochemical cycles. Here, we examine sediment bacteria and dissolved organic matter (DOM) in 300 microcosms along experimental global change gradients in subtropical and subarctic climate zones of China and Norway, respectively. We develop an indicator to quantify the importance of dark matter by comparing co-occurrence network patterns with and without dark matter in bacterial or DOM assemblages. In both climate zones, dark matter constitutes approximately 30-56% of bacterial taxa and DOM metabolites and changes connectivity within bacterial and DOM assemblages by between -15.5 and +61.8%. Dark matter is generally more important for changing network connectivity within DOM assemblages than those of microbes, especially in the subtropical zone. However, the importance of dark matter along global change gradients is strongly correlated between bacteria and DOM and consistently increased toward higher primary productivity because of increasing temperatures and nutrient enrichment. Our findings highlight the importance of microbial and chemical dark matter for changing biogeochemical interactions under global change.},
}
@article {pmid36511762,
year = {2023},
author = {Leite, MFA and Liu, B and Gómez Cardozo, E and Silva, HRE and Luz, RL and Muchavisoy, KHM and Moraes, FHR and Rousseau, GX and Kowalchuk, G and Gehring, C and Kuramae, EE},
title = {Microbiome resilience of Amazonian forests: Agroforest divergence to bacteria and secondary forest succession convergence to fungi.},
journal = {Global change biology},
volume = {29},
number = {5},
pages = {1314-1327},
pmid = {36511762},
issn = {1365-2486},
support = {A080/2013//Brazilian Council of Higher Education/ ; },
mesh = {*Ecosystem ; Forests ; Soil ; *Microbiota ; Fungi ; Bacteria ; Soil Microbiology ; },
abstract = {An alarming and increasing deforestation rate threatens Amazon tropical ecosystems and subsequent degradation due to frequent fires. Agroforestry systems (AFS) may offer a sustainable alternative, reportedly mimicking the plant-soil interactions of the natural mature forest (MF). However, the role of microbial community in tropical AFS remains largely unknown. This knowledge is crucial for evaluating the sustainability of AFS and practices given the key role of microbes in the aboveground-belowground interactions. The current study, by comparing different AFS and successions of secondary and MFs, showed that AFS fostered distinct groups of bacterial community, diverging from the MFs, likely a result of management practices while secondary forests converged to the same soil microbiome found in the MF, by favoring the same groups of fungi. Model simulations reveal that AFS would require profound changes in aboveground biomass and in soil factors to reach the same microbiome found in MFs. In summary, AFS practices did not result in ecosystems mimicking natural forest plant-soil interactions but rather reshaped the ecosystem to a completely different relation between aboveground biomass, soil abiotic properties, and the soil microbiome.},
}
@article {pmid36511717,
year = {2023},
author = {Chen, Y and Lyu, Y and Zhang, J and Li, Q and Lyu, L and Zhou, Y and Kong, J and Zeng, X and Zhang, S and Li, J},
title = {Riddles of Lost City: Chemotrophic Prokaryotes Drives Carbon, Sulfur, and Nitrogen Cycling at an Extinct Cold Seep, South China Sea.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0333822},
pmid = {36511717},
issn = {2165-0497},
mesh = {*Geologic Sediments/microbiology ; *Ecosystem ; Carbon/metabolism ; Methane/metabolism ; Archaea/metabolism ; Bacteria/genetics/metabolism ; Hydrocarbons/metabolism ; Proteobacteria/metabolism ; Sulfur/metabolism ; Nitrogen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Deep-sea cold seeps are one of the most productive ecosystems that sustained by hydrocarbons carried by the fluid. Once the seep fluid ceases, the thriving autotrophic communities die out, terming as the extinct seep. But heterotrophic fauna can still survive even for thousands of years. The critical role of prokaryotes in active seeps are well defined, but their functions in extinct seeps are poorly understood to date. Here, we clarified the diversity, taxonomic specificity, interspecies correlation, and metabolic profiles of sediment prokaryotes at an extinct seep site of Haima cold seep, South China Sea. Alpha diversity of archaea significantly increased, while that of bacteria remained unchanged in extinct seep compared to active seep. However, archaea composition did not differ significantly at extinct seep from active or nonseep sites based on weighted-unifrac dissimilarity, while bacteria composition exhibited significant difference. Distribution of archaea and bacteria showed clear specificity to extinct seeps, indicating the unique life strategies here. Prokaryotes might live chemolithoautotrophically on cycling of inorganic carbon, sulfur, and nitrogen, or chemoorganotrophically on recycling of hydrocarbons. Notably, many of the extinct seep specific species and networked keystone lineages are classified as Proteobacteria. Regarding the functional diversity and metabolic flexibility of this clade, Proteobacteria is supposed to integrate the geochemical cycles and play a critical role in energy and resource supplement for microbiome in extinct seep. Collectively, our findings shed lights on the microbial ecology and functional diversity in extinct seeps, providing new understanding of biogeochemical cycling after fluid cessation. IMPORTANCE This research paper uncovered the potential mechanisms for microbiota mediated geochemical cycling in extinct cold seep, advancing our understanding in deep sea microbiology ecology.},
}
@article {pmid36511696,
year = {2023},
author = {Higgins, O and Chueiri, A and O'Connor, L and Lahiff, S and Burke, L and Morris, D and Pfeifer, NM and Santamarina, BG and Berens, C and Menge, C and Caniça, M and Manageiro, V and Kisand, V and Hassan, MM and Gardner, B and van Vliet, AHM and La Ragione, RM and Gonzalez-Zorn, B and Smith, TJ},
title = {Portable Differential Detection of CTX-M ESBL Gene Variants, blaCTX-M-1 and blaCTX-M-15, from Escherichia coli Isolates and Animal Fecal Samples Using Loop-Primer Endonuclease Cleavage Loop-Mediated Isothermal Amplification.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0331622},
pmid = {36511696},
issn = {2165-0497},
mesh = {Humans ; Animals ; Swine ; *Escherichia coli ; *Escherichia coli Infections/diagnosis/veterinary/epidemiology ; beta-Lactamases/genetics ; Anti-Bacterial Agents ; Enterobacteriaceae/genetics ; DNA ; },
abstract = {Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by Enterobacteriaceae confer resistance to clinically relevant third-generation cephalosporins. CTX-M group 1 variants, CTX-M-1 and CTX-M-15, are the leading ESBL-producing Enterobacteriaceae associated with animal and human infection, respectively, and are an increasing antimicrobial resistance (AMR) global health concern. The blaCTX-M-1 and blaCTX-M-15 genes encoding these variants have an approximate nucleotide sequence similarity of 98.7%, making effective differential diagnostic monitoring difficult. Loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) enables rapid real-time multiplex pathogen detection with single-base specificity and portable on-site testing. We have developed an internally controlled multiplex CTX-M-1/15 LEC-LAMP assay for the differential detection of blaCTX-M-1 and blaCTX-M-15. Assay analytical specificity was established using a panel of human, animal, and environmental Escherichia coli isolates positive for blaCTX-M-1 (n = 18), blaCTX-M-15 (n = 35), and other closely related blaCTX-Ms (n = 38) from Ireland, Germany, and Portugal, with analytical sensitivity determined using probit regression analysis. Animal fecal sample testing using the CTX-M-1/15 LEC-LAMP assay in combination with a rapid DNA extraction protocol was carried out on porcine fecal samples previously confirmed to be PCR-positive for E. coli blaCTX-M. Portable instrumentation was used to further analyze each fecal sample and demonstrate the on-site testing capabilities of the LEC-LAMP assay with the rapid DNA extraction protocol. The CTX-M-1/15 LEC-LAMP assay demonstrated complete analytical specificity for the differential detection of both variants with sensitive low-level detection of 8.5 and 9.8 copies per reaction for blaCTX-M-1 and blaCTX-M-15, respectively, and E. coli blaCTX-M-1 was identified in all blaCTX-M positive porcine fecal samples tested. IMPORTANCE CTX-M ESBL-producing E. coli is an increasing AMR public health issue with the transmission between animals and humans via zoonotic pathogens now a major area of interest. Accurate and timely identification of ESBL-expressing E. coli CTX-M variants is essential for disease monitoring, targeted antibiotic treatment and infection control. This study details the first report of portable diagnostics technology for the rapid differential detection of CTX-M AMR markers blaCTX-M-1 and blaCTX-M-15, facilitating improved identification and surveillance of these closely related variants. Further application of this portable internally controlled multiplex CTX-M-1/15 LEC-LAMP assay will provide new information on the transmission and prevalence of these CTX-M ESBL alleles. Furthermore, this transferable diagnostic technology can be applied to other new and emerging relevant AMR markers of interest providing more efficient and specific portable pathogen detection for improved epidemiological surveillance.},
}
@article {pmid36511682,
year = {2023},
author = {Teng, W and Liao, B and Chen, M and Shu, W},
title = {Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0214522},
pmid = {36511682},
issn = {2165-0497},
mesh = {Phylogeny ; Base Composition ; *Bacteria/genetics ; Mutation ; *Genomics ; Evolution, Molecular ; },
abstract = {Bacterial evolution is characterized by strong purifying selection as well as rapid adaptive evolution in changing environments. In this context, the genomic GC content (genomic GC) varies greatly but presents some level of phylogenetic stability, making it challenging to explain based on current hypotheses. To illuminate the evolutionary mechanisms of the genomic GC, we analyzed the base composition and functional inventory of 11,083 representative genomes. A phylogenetically constrained bimodal distribution of the genomic GC, which mainly originated from parallel divergences in the early evolution, was demonstrated. Such variation of the genomic GC can be well explained by DNA replication and repair (DRR), in which multiple pathways correlate with the genomic GC. Furthermore, the biased conservation of various stress-related genes, especially the DRR-related ones, implies distinct adaptive processes in the ancestral lineages of high- or low-GC clades which are likely induced by major environmental changes. Our findings support that the mutational biases resulting from these legacies of ancient adaptation have changed the course of adaptive evolution and generated great variation in the genomic GC. This highlights the importance of indirect effects of natural selection, which indicates a new model for bacterial evolution. IMPORTANCE GC content has been shown to be an important factor in microbial ecology and evolution, and the genomic GC of bacteria can be characterized by great intergenomic heterogeneity, high intragenomic homogeneity, and strong phylogenetic inertia, as well as being associated with the environment. Current hypotheses concerning direct selection or mutational biases cannot well explain these features simultaneously. Our findings of the genomic GC showing that ancient adaptations have transformed the DRR system and that the resulting mutational biases further contributed to a bimodal distribution of it offer a more reasonable scenario for the mechanism. This would imply that, when thinking about the evolution of life, diverse processes of adaptation exist, and combined effects of natural selection should be considered.},
}
@article {pmid36510309,
year = {2022},
author = {Boekhorst, J and Venlet, N and Procházková, N and Hansen, ML and Lieberoth, CB and Bahl, MI and Lauritzen, L and Pedersen, O and Licht, TR and Kleerebezem, M and Roager, HM},
title = {Stool energy density is positively correlated to intestinal transit time and related to microbial enterotypes.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {223},
pmid = {36510309},
issn = {2049-2618},
mesh = {Adult ; Humans ; Feces/microbiology ; *Gastrointestinal Microbiome ; Bacteroides ; Prevotella ; *Microbiota ; },
abstract = {BACKGROUND: It has been hypothesised that the gut microbiota causally affects obesity via its capacity to extract energy from the diet. Yet, evidence elucidating the role of particular human microbial community structures and determinants of microbiota-dependent energy harvest is lacking.<br><br>RESULTS: Here, we investigated whether energy extraction from the diet in 85 overweight adults, estimated by dry stool energy density, was associated with intestinal transit time and variations in microbial community diversity and overall structure stratified as enterotypes. We hypothesised that a slower intestinal transit would allow for more energy extraction. However, opposite of what we expected, the stool energy density was positively associated with intestinal transit time. Stratifications into enterotypes showed that individuals with a Bacteroides enterotype (B-type) had significantly lower stool energy density, shorter intestinal transit times, and lower alpha-diversity compared to individuals with a Ruminococcaceae enterotype (R-type). The Prevotella (P-type) individuals appeared in between the B- and R-type. The differences in stool energy density between enterotypes were not explained by differences in habitual diet, intake of dietary fibre or faecal bacterial cell counts. However, the R-type individuals showed higher urinary and faecal levels of microbial-derived proteolytic metabolites compared to the B-type, suggesting increased colonic proteolysis in the R-type individuals. This could imply a less effective colonic energy extraction in the R-type individuals compared to the B-type individuals. Notably, the R-type had significantly lower body weight compared to the B-type.<br><br>CONCLUSIONS: Our findings suggest that gut microbial energy harvest is diversified among individuals by intestinal transit time and associated gut microbiome ecosystem variations. A better understanding of these associations could support the development of personalised nutrition and improved weight-loss strategies. Video Abstract.},
}
@article {pmid36509943,
year = {2023},
author = {Li, W and Ma, ZS},
title = {The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1428-1437},
pmid = {36509943},
issn = {1432-184X},
mesh = {Animals ; Humans ; SARS-CoV-2/genetics ; *COVID-19 ; *Chiroptera ; *Microbiota/genetics ; Bacteria/genetics ; Respiratory System ; },
abstract = {The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae, a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies.},
}
@article {pmid36506396,
year = {2022},
author = {Daba, G and Berecha, G and Lievens, B and Hundera, K and Helsen, K and Honnay, O},
title = {Contrasting coffee leaf rust epidemics between forest coffee and semi-forest coffee agroforestry systems in SW-Ethiopia.},
journal = {Heliyon},
volume = {8},
number = {12},
pages = {e11892},
pmid = {36506396},
issn = {2405-8440},
abstract = {Ethiopian Arabica coffee is produced in different agroforestry systems which differ in forest management intensity. In forest coffee systems (FC), coffee shrubs grow naturally in the understory of Afromontane forests with little human intervention, whereas in semi-forest coffee systems (SFC) thinning of the canopy and removal of the understory is applied. Coffee leaf rust (CLR) disease is a growing concern for coffee agroforestry, but to what extent infection pressure is affected by management intensity is poorly known. Here we assessed CLR infection through time across FC and SFC systems in SW-Ethiopia. CLR infection was significantly higher for SFC, with a gradual reduction of this difference during the beginning of dry season (November) through main rainy season of (July). Our findings also demonstrated that CLR infections were significantly lower in the FC system as compared to SFC system in both years 2015/16 and 2020/21. The higher CLR infection was partly explained by lower crown cover and higher human impact. We expect that reduced wind speed and droplet penetration under closed canopies and reduced human-facilitated spore dispersal are the dominating mechanisms behind lower CLR infection in FC systems, yet lower coffee density in FC may also play a role. Overall, our results indicate that although higher management intensity still generally results in higher total yields per hectare, proportionally larger losses due to CLR infection can be expected. Therefore, introducing more coffee genetic diversity, screening resistant coffee varieties and increasing canopy cover in the SFC will mitigate the CLR disease pressure and guarantee the sustainability of higher yields of the system in the future. Also, lower yields in the FC will be rewarded through providing price premiums so that farmers instantly get a higher price for their lower yield, guaranteeing livelihoods.},
}
@article {pmid36504693,
year = {2022},
author = {Amano, C and Zhao, Z and Sintes, E and Reinthaler, T and Stefanschitz, J and Kisadur, M and Utsumi, M and Herndl, GJ},
title = {Limited carbon cycling due to high-pressure effects on the deep-sea microbiome.},
journal = {Nature geoscience},
volume = {15},
number = {12},
pages = {1041-1047},
pmid = {36504693},
issn = {1752-0894},
support = {I 486/FWF_/Austrian Science Fund FWF/Austria ; P 28781/FWF_/Austrian Science Fund FWF/Austria ; P 35587/FWF_/Austrian Science Fund FWF/Austria ; Z 194/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Deep-sea microbial communities are exposed to high-pressure conditions, which has a variable impact on prokaryotes depending on whether they are piezophilic (that is, pressure-loving), piezotolerant or piezosensitive. While it has been suggested that elevated pressures lead to higher community-level metabolic rates, the response of these deep-sea microbial communities to the high-pressure conditions of the deep sea is poorly understood. Based on microbial activity measurements in the major oceanic basins using an in situ microbial incubator, we show that the bulk heterotrophic activity of prokaryotic communities becomes increasingly inhibited at higher hydrostatic pressure. At 4,000 m depth, the bulk heterotrophic prokaryotic activity under in situ hydrostatic pressure was about one-third of that measured in the same community at atmospheric pressure conditions. In the bathypelagic zone-between 1,000 and 4,000 m depth-~85% of the prokaryotic community was piezotolerant and ~5% of the prokaryotic community was piezophilic. Despite piezosensitive-like prokaryotes comprising only ~10% (mainly members of Bacteroidetes, Alteromonas) of the deep-sea prokaryotic community, the more than 100-fold metabolic activity increase of these piezosensitive prokaryotes upon depressurization leads to high apparent bulk metabolic activity. Overall, the heterotrophic prokaryotic activity in the deep sea is likely to be substantially lower than hitherto assumed, with major impacts on the oceanic carbon cycling.},
}
@article {pmid36503688,
year = {2022},
author = {Delgado-Baquerizo, M and Hu, HW and Maestre, FT and Guerra, CA and Eisenhauer, N and Eldridge, DJ and Zhu, YG and Chen, QL and Trivedi, P and Du, S and Makhalanyane, TP and Verma, JP and Gozalo, B and Ochoa, V and Asensio, S and Wang, L and Zaady, E and Illán, JG and Siebe, C and Grebenc, T and Zhou, X and Liu, YR and Bamigboye, AR and Blanco-Pastor, JL and Duran, J and Rodríguez, A and Mamet, S and Alfaro, F and Abades, S and Teixido, AL and Peñaloza-Bojacá, GF and Molina-Montenegro, MA and Torres-Díaz, C and Perez, C and Gallardo, A and García-Velázquez, L and Hayes, PE and Neuhauser, S and He, JZ},
title = {The global distribution and environmental drivers of the soil antibiotic resistome.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {219},
pmid = {36503688},
issn = {2049-2618},
support = {CLIMIFUN//Horizon 2020/ ; MUSGONET LRA17\1193//British Ecological Society/ ; DP210100332//Australian Research Council/ ; DP210100332//Australian Research Council/ ; },
mesh = {Humans ; *Soil ; *Anti-Bacterial Agents/pharmacology ; Ecology ; Phenotype ; },
abstract = {BACKGROUND: Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth's largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs.<br><br>RESULTS: We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs.<br><br>CONCLUSIONS: Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome. Video Abstract.},
}
@article {pmid36503639,
year = {2023},
author = {Hodžić, A and Dheilly, NM and Cabezas-Cruz, A and Berry, D},
title = {The helminth holobiont: a multidimensional host-parasite-microbiota interaction.},
journal = {Trends in parasitology},
volume = {39},
number = {2},
pages = {91-100},
doi = {10.1016/j.pt.2022.11.012},
pmid = {36503639},
issn = {1471-5007},
mesh = {Animals ; Humans ; *Parasites ; *Helminths/genetics ; *Microbiota ; *Helminthiasis/parasitology ; *Gastrointestinal Microbiome ; },
abstract = {Gastrointestinal helminths have developed multiple mechanisms by which they manipulate the host microbiome to make a favorable environment for their long-term survival. While the impact of helminth infections on vertebrate host immunity and its gut microbiota is relatively well studied, little is known about the structure and functioning of microbial populations supported by metazoan parasites. Here we argue that an integrated understanding of the helminth-associated microbiome and its role in the host disease pathogenesis may facilitate the discovery of specific microbial and/or genetic patterns critical for parasite biology and subsequently pave the way for the development of alternative control strategies against parasites and parasitic disease.},
}
@article {pmid36502425,
year = {2023},
author = {Ye, F and Sun, Z and Moore, SS and Wu, J and Hong, Y and Wang, Y},
title = {Discrepant Effects of Flooding on Assembly Processes of Abundant and Rare Communities in Riparian Soils.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1164-1175},
pmid = {36502425},
issn = {1432-184X},
support = {51908145//National Natural Science Foundation of China/ ; 41977153//National Natural Science Foundation of China/ ; 2022A1515010828//Natural Science Foundation of Guangdong Province/ ; },
mesh = {*Ecosystem ; Soil ; Soil Microbiology ; Bacteria/genetics ; Archaea ; *Microbiota ; Carbon ; },
abstract = {Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon-nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations.},
}
@article {pmid36500505,
year = {2022},
author = {Ben Rejeb, I and Charfi, I and Baraketi, S and Hached, H and Gargouri, M},
title = {Bread Surplus: A Cumulative Waste or a Staple Material for High-Value Products?.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {23},
pages = {},
pmid = {36500505},
issn = {1420-3049},
mesh = {*Refuse Disposal ; Bread/analysis ; Recycling/methods ; Food Handling ; Waste Disposal Facilities ; Waste Products/analysis ; },
abstract = {Food waste has been widely valorized in the past years in order to develop eco-friendly materials. Among others, bread waste is currently of increasing interest, as it is considered a huge global issue with serious environmental impacts and significant economic losses that have become even greater in the post-pandemic years due to an increase in cereal prices, which has led to higher production costs and bread prices. Owing to its richness in polysaccharides, bread waste has been previously studied for its physico-chemical characteristics and its numerous biotechnological applications. The present review highlights the re-use of bread waste and its valorization as a valuable resource by making value-added products through numerous technological processes to increase efficiency at all stages. Many research studies reporting several transformation methods of surplus bread into ethanol, lactic acid, succinic acid, biohydrogen, hydroxymethylfurfural, proteins and pigments, glucose-fructose syrup, aroma compounds, and enzymes are widely discussed. The wide variety of suggested applications for recycling bread waste provides significant insights into the role of technology development in potentially maximizing resource recovery and consequently contributing to environmental performance by reducing the amount of bread waste in landfills.},
}
@article {pmid36500302,
year = {2022},
author = {Kuttithodi, AM and Nikhitha, D and Jacob, J and Narayanankutty, A and Mathews, M and Olatunji, OJ and Rajagopal, R and Alfarhan, A and Barcelo, D},
title = {Antioxidant, Antimicrobial, Cytotoxicity, and Larvicidal Activities of Selected Synthetic Bis-Chalcones.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {23},
pages = {},
pmid = {36500302},
issn = {1420-3049},
mesh = {Animals ; Antioxidants/pharmacology/chemistry ; Microbial Sensitivity Tests ; *Chalcones/pharmacology ; Anthocyanins ; Plant Extracts/chemistry ; *Anti-Infective Agents/pharmacology ; Anti-Bacterial Agents/pharmacology/chemistry ; Escherichia coli ; },
abstract = {Plants are known to have numerous phytochemicals and other secondary metabolites with numerous pharmacological and biological properties. Among the various compounds, polyphenols, flavonoids, anthocyanins, alkaloids, and terpenoids are the predominant ones that have been explored for their biological potential. Among these, chalcones and bis-chalcones are less explored for their biological potential under in vitro experiments, cell culture models, and animal studies. In the present study, we evaluated six synthetic bis-chalcones that were different in terms of their aromatic cores, functional group substitution, and position of substitutions. The results indicated a strong antioxidant property in terms of DPPH and ABTS radical-scavenging potentials and ferric-reducing properties. In addition, compounds 1, 2, and 4 exhibited strong antibacterial activities against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Salmonella enteritidis. The disc diffusion assay values were indicative of the antibacterial properties of these compounds. Overall, the study indicated the antioxidant and antimicrobial properties of the compounds. Our preliminary studies point to the potential of this class of compounds for further in vivo investigation.},
}
@article {pmid36495359,
year = {2023},
author = {Liu, W and Qiu, K and Xie, Y and Huang, Y and Wang, R and Li, H and Meng, W and He, Y and Li, Y and Li, H and Zhao, P and Yang, Y},
title = {High-Throughput Absolute Quantification Sequencing Reveals that a Combination of Leguminous Shrubs Is Effective in Driving Soil Bacterial Diversity During the Process of Desertification Reversal.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1145-1163},
pmid = {36495359},
issn = {1432-184X},
support = {2019BEB04011//Ningxia Key Research and Development Project/ ; [2019] 160//Ningxia High-Level Talent Innovation Program/ ; 42001095//National Natural Science Foundation of China/ ; 2020AAC03273//Ningxia Natural Science Foundation/ ; },
mesh = {*Ecosystem ; Soil/chemistry ; *Fabaceae ; RNA, Ribosomal, 16S/genetics ; Carbon/analysis ; Conservation of Natural Resources ; Bacteria/genetics ; China ; Phosphorus/analysis ; Potassium/analysis ; Soil Microbiology ; },
abstract = {Desertification leads to the extreme fragility of ecosystems and seriously threatens ecosystem functioning in desert areas. The planting of xerophytes, especially leguminous shrubs, is an effective and common means to reverse desertification. Soil microorganisms play a crucial role in nutrient cycling and energy flow in ecosystems. However, the effects of introducing leguminous shrubs on soil microbial diversity and the relevant mechanisms are not clear. Here, we employed the high-throughput absolute quantification 16S rRNA sequencing method to analyze the diversity of soil bacteria in sand-fixing areas of mixed shrublands with three combinations of shrubs, i.e., C. korshinskii × Corethrodendron scoparium (CaKCoS), C. korshinskii × Calligonum mongolicum (CaKCaM), and C. scoparium × C. mongolicum (CoSCaM), in the south of the Mu Us Sandy Land, China. This area suffered from moving dunes 20 years ago, but after introducing these shrubs to fix the dunes, the ecosystem was restored. Additionally, the effects of soil physicochemical properties on soil bacterial composition and diversity were analyzed with redundancy analysis (RDA) and structural equation modeling (SEM). It was found that the Shannon index of soil bacteria in CaKCoS was significantly higher than that in CaKCaM and CoSCaM, and the abundance of the dominant phyla, including Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Thaumarchaeota, Armatimonadetes, candidate_division_WPS-1, and Nitrospirae, increased significantly in CaKCoS and CaKCaM compared to that in CoSCaM. RDA showed that the majority of soil properties, such as total nitrogen (TN), available potassium (AK), N:P ratio, soil moisture (SM), and available phosphorus (AP), were important soil environmental factors affecting the abundance of the dominant phyla, and RDA1 and RDA2 accounted for 56.66% and 2.35% of the total variation, respectively. SEM showed that the soil bacterial α-diversity was positively affected by the soil organic carbon (SOC), N:P ratio, and total phosphorus (TP). Moreover, CaKCoS had higher SM, total carbon (TC), total potassium (TK), and AP than CaKCaM and CoSCaM. Collectively, these results highlight a conceptual framework in which the combination of leguminous shrubs can effectively drive soil bacterial diversity by improving soil physicochemical properties and maintaining ecosystem functioning during desertification reversal.},
}
@article {pmid36482478,
year = {2022},
author = {Hodžić, A and Alić, A and Spahić, A and Harl, J and Beck, R},
title = {Genetic diversity of Echinococcus granulosus sensu lato from animals and humans in Bosnia and Herzegovina.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {457},
pmid = {36482478},
issn = {1756-3305},
mesh = {Humans ; Sheep ; Cattle ; Animals ; Swine ; *Echinococcus granulosus ; *Echinococcus/genetics ; *Echinococcosis/veterinary ; Genotype ; Genetic Variation ; *Cysts ; },
abstract = {BACKGROUND: Cystic echinococcosis (CE) is recognized as one of the most prevalent zoonotic diseases in Bosnia and Herzegovina. However, no systemic investigation of the genetic diversity of Echinococcus granulosus sensu lato circulating among animals and humans in the country has been performed to date.<br><br>METHODS: In this preliminary study, we analysed one cyst each from 36 sheep, 27 cattle, 27 pigs, 11 wild boars and 16 human patients for amplification and partial sequencing of the adenosine triphosphate 6 (atp6) and cytochrome c oxidase 1 (cox1) genes. The host species, fertility rate and organ cyst location were recorded for each subject involved in the study.<br><br>RESULTS: Overall, the atp6 gene was successfully amplified and sequenced from 110 samples, while 96 of the PCRs for cox1 were positive. Three zoonotic genotypes of E. granulosus sensu stricto (G1 and G3) and Echinococcus canadensis (G7) were identified in our isolates based on analyses of the atp6 gene. These genotypes were represented by 11 different genetic variants (haplotypes), six of which were identified for the first time in the present study.<br><br>CONCLUSIONS: This study demonstrates, for the first time, that CE in Bosnia and Herzegovina is predominantly caused by E. granulosus sensu stricto and E. canadensis clusters, which exhibited a lower genetic diversity compared to isolates from other European countries. Further molecular studies employing other mitochondrial and nuclear genes are required to better understand the transmission cycles of E. granulosus sensu stricto among intermediate and definitive hosts in the country.},
}
@article {pmid36480164,
year = {2023},
author = {Engelberts, JP and Robbins, SJ and Herbold, CW and Moeller, FU and Jehmlich, N and Laffy, PW and Wagner, M and Webster, NS},
title = {Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta.},
journal = {Environmental microbiology},
volume = {25},
number = {3},
pages = {646-660},
pmid = {36480164},
issn = {1462-2920},
support = {294343/ERC_/European Research Council/International ; },
mesh = {Animals ; *Porifera/microbiology ; Phylogeny ; Archaea/metabolism ; *Microbiota ; Symbiosis/physiology ; },
abstract = {Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe-host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host-microbe interactions and provide a basis for in-depth physiological experiments.},
}
@article {pmid36480133,
year = {2023},
author = {Eck, M and Schwab, ST and Nelson, TF and Wurst, K and Iberl, S and Schleheck, D and Link, C and Battagliarin, G and Mecking, S},
title = {Biodegradable High-Density Polyethylene-like Material.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {62},
number = {6},
pages = {e202213438},
pmid = {36480133},
issn = {1521-3773},
mesh = {*Polyethylene ; Biodegradation, Environmental ; *Polyesters/chemistry ; Hydrolysis ; },
abstract = {We report a novel polyester material generated from readily available biobased 1,18-octadecanedicarboxylic acid and ethylene glycol possesses a polyethylene-like solid-state structure and also tensile properties similar to high density polyethylene (HDPE). Despite its crystallinity, high melting point (Tm =96 °C) and hydrophobic nature, polyester-2,18 is subject to rapid and complete hydrolytic degradation in in vitro assays with isolated naturally occurring enzymes. Under industrial composting conditions (ISO standard 14855-1) the material is biodegraded with mineralization above 95 % within two months. Reference studies with polyester-18,18 (Tm =99 °C) reveal a strong impact of the nature of the diol repeating unit on degradation rates, possibly related to the density of ester groups in the amorphous phase. Depolymerization by methanolysis indicates suitability for closed-loop recycling.},
}
@article {pmid36479626,
year = {2022},
author = {Geerinck, MWJ and Van Hee, S and Gloder, G and Crauwels, S and Colazza, S and Jacquemyn, H and Cusumano, A and Lievens, B},
title = {Diversity and composition of the microbiome associated with eggs of the Southern green stinkbug, Nezara viridula (Hemiptera: Pentatomidae).},
journal = {MicrobiologyOpen},
volume = {11},
number = {6},
pages = {e1337},
pmid = {36479626},
issn = {2045-8827},
mesh = {Animals ; *Hemiptera ; Belgium ; Italy ; *Microbiota ; },
abstract = {Although microbial communities of insects from larval to adult stage have been increasingly investigated in recent years, little is still known about the diversity and composition of egg-associated microbiomes. In this study, we used high-throughput amplicon sequencing and quantitative PCR to get a better understanding of the microbiome of insect eggs and how they are established using the Southern green stinkbug Nezara viridula (L.) (Hemiptera: Pentatomidae) as a study object. First, to determine the bacterial community composition, egg masses from two natural populations in Belgium and Italy were examined. Subsequently, microbial community establishment was assessed by studying stinkbug eggs of different ages obtained from laboratory strains (unlaid eggs collected from the ovaries, eggs less than 24 h old, and eggs collected 4 days after oviposition). Both the external and internal egg-associated microbiomes were analyzed by investigating egg washes and surface-sterilized washed eggs, respectively. Eggs from the ovaries were completely devoid of bacteria, indicating that egg-associated bacteria were deposited on the eggs during or after oviposition. The bacterial diversity of deposited eggs was very low, with on average 6.1 zero-radius operational taxonomic units (zOTUs) in the external microbiome and 1.2 zOTUs in internal samples of egg masses collected from the field. Bacterial community composition and density did not change significantly over time, suggesting limited bacterial growth. A Pantoea-like symbiont previously found in the midgut of N. viridula was found in every sample and generally occurred at high relative and absolute densities, especially in the internal egg samples. Additionally, some eggs harbored a Sodalis symbiont, which has previously been found in the abdomen of several insects, but so far not in N. viridula populations. We conclude that the egg-associated bacterial microbiome of N. viridula is species-poor and dominated by a few symbionts, particularly the species-specific obligate Pantoea-like symbiont.},
}
@article {pmid36478428,
year = {2022},
author = {Lee, JS and Lee, SM and Son, HS and Yoon, YN and Shin, JE and Sul, WJ and Yu, DA and Choe, YB and Lee, YW},
title = {Analysis of the Microbiome of the Ear Canal in Normal Individuals and Patients with Chronic Otitis Externa.},
journal = {Annals of dermatology},
volume = {34},
number = {6},
pages = {461-471},
pmid = {36478428},
issn = {2005-3894},
support = {//Konkuk University/Korea ; },
abstract = {BACKGROUND: Recently, microbiome research has been actively conducted for various skin areas. However, no study has yet compared the microbiome of bacteria and fungi in the ear canal of healthy individuals and patients with chronic otitis externa in Korea.<br><br>OBJECTIVE: This study aimed to investigate the difference in the distribution of fungal and bacterial microbial communities in ear canal samples of healthy individuals and patients with chronic otitis externa.<br><br>METHODS: In 24 patients with bilateral chronic otitis externa and 24 healthy controls, cotton swabs were used to obtain samples from the bilateral ear canal. To characterize the fungal and bacterial communities, we sequenced and analyzed the 16S rRNA V4-V5 and ITS1 regions using Quantitative Insights into Microbial Ecology 2, respectively.<br><br>RESULTS: The alpha diversity analysis for bacteria and fungi confirmed that both richness and evenness decreased in the patient group. The beta diversity analysis for bacteria confirmed that these parameters differed between the control and patient groups. The beta diversity analysis for fungi showed no difference between the groups.<br><br>CONCLUSION: We observed different skin microbiomes in the patients with chronic otitis externa compared with those in the healthy individuals.},
}
@article {pmid36478022,
year = {2023},
author = {Watson, M and May, G and Bushley, KE},
title = {Sources of Fungal Symbionts in the Microbiome of a Mobile Insect Host, Spodoptera frugiperda.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {900-913},
pmid = {36478022},
issn = {1432-184X},
support = {Natural History Award//Bell Museum of Natural History, University of Minnesota/ ; },
mesh = {Animals ; Spodoptera/microbiology ; *Insecta ; Plants ; Larva ; *Microbiota ; },
abstract = {The sources of fungal symbionts of insects are not well understood, yet the acquisition and assembly of fungal communities in mobile insect hosts have important implications for the ecology of migratory insects and their plant hosts. To determine potential sources of fungi associated with the fall armyworm (Spodoptera frugiperda), we characterized the fungal communities associated with four different ecological compartments (insects, infested leaves, uninfested leaves, and soil) and estimated the contributions of each of these potential sources to the insect's fungal microbiome. Results show that insect fungal community composition was distinct from and more varied than the composition of fungal communities in the environment of those insects (plants and soil). Among the sources evaluated, on average we found a surprisingly large apparent contribution from other congeneric S. frugiperda insect larvae (ca. 25%) compared to the contribution from soil or plant sources (< 5%). However, a large proportion of the insect microbiome could not be attributed to the sampled sources and was instead attributed to unknown sources (ca. 50%). Surprisingly, we found little evidence for exchange of fungal taxa, with the exception of a Fusarium oxysporum and a Cladosporium sp. OTU, between larvae and the infested leaves on which they fed. Together, our results suggest that mobile insects such as S. frugiperda obtain their fungal symbionts from a variety of sources, not limited to plants and soil, but including conspecific insects and other unsampled environmental sources, and that transmission among insects may play an important role in acquisition of fungal symbionts.},
}
@article {pmid36475832,
year = {2023},
author = {Jens, JN and Breiner, DJ and Neve, RL and Fiebig, MM and Phelan, VV},
title = {MBRA-2: a Modified Chemostat System to Culture Biofilms.},
journal = {Microbiology spectrum},
volume = {11},
number = {1},
pages = {e0292822},
pmid = {36475832},
issn = {2165-0497},
support = {R35 GM128690/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Biofilms ; Culture Media ; *Microbiota ; Bioreactors ; Pseudomonas aeruginosa ; Plankton ; },
abstract = {Culture-dependent approaches for investigating microbial ecology aim to model the nutrient content of specific environments by simplifying the system for high-resolution molecular analysis. These in vitro systems are enticing due to their increased throughput compared to animal models, flexibility in modulating nutrient content and community composition, scaling of culture volume to isolate biological molecules, and control of environmental parameters, such as temperature, humidity, and nutrient flow. However, different devices are used to investigate homogenous, planktonic microbial communities and heterogeneous biofilms. Here, we present the minibioreactor array 2 (MBRA-2) with media rails, a benchtop multireactor system derived from the MBRA system that enables researchers to use the same system to grow planktonic and biofilm cultures. We simplified flow through the system and reduced contamination, leakage, and time required for array assembly by designing and implementing a reusable media rail to replace the branched tubing traditionally used to convey media through chemostat arrays. Additionally, we altered the structure of the six-bioreactor strip to incorporate a removable lid to provide easy access to the bioreactor wells, enabling biofilm recovery and thorough cleaning for reuse. Using Pseudomonas aeruginosa, a model biofilm-producing organism, we show that the technical improvements of the MBRA-2 for biofilms growth does not disrupt the function of the bioreactor array. IMPORTANCE The MBRA-2 with media rails provides an accessible system for investigators to culture heterogenous, suspended biofilms under constant flow.},
}
@article {pmid36475750,
year = {2023},
author = {Wollein Waldetoft, K and Sundius, S and Kuske, R and Brown, SP},
title = {Defining the Benefits of Antibiotic Resistance in Commensals and the Scope for Resistance Optimization.},
journal = {mBio},
volume = {14},
number = {1},
pages = {e0134922},
pmid = {36475750},
issn = {2150-7511},
support = {R01 DE020100/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Bacteria ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Symbiosis ; *Microbiota ; Drug Resistance, Bacterial ; },
abstract = {Antibiotic resistance is a major medical and public health challenge, characterized by global increases in the prevalence of resistant strains. The conventional view is that all antibiotic resistance is problematic, even when not in pathogens. Resistance in commensal bacteria poses risks, as resistant organisms can provide a reservoir of resistance genes that can be horizontally transferred to pathogens or may themselves cause opportunistic infections in the future. While these risks are real, we propose that commensal resistance can also generate benefits during antibiotic treatment of human infection, by promoting continued ecological suppression of pathogens. To define and illustrate this alternative conceptual perspective, we use a two-species mathematical model to identify the necessary and sufficient ecological conditions for beneficial resistance. We show that the benefits are limited to species (or strain) interactions where commensals suppress pathogen growth and are maximized when commensals compete with, rather than prey on or otherwise exploit pathogens. By identifying benefits of commensal resistance, we propose that rather than strictly minimizing all resistance, resistance management may be better viewed as an optimization problem. We discuss implications in two applied contexts: bystander (nontarget) selection within commensal microbiomes and pathogen treatment given polymicrobial infections. IMPORTANCE Antibiotic resistance is commonly viewed as universally costly, regardless of which bacterial cells express resistance. Here, we derive an opposing logic, where resistance in commensal bacteria can lead to reductions in pathogen density and improved outcomes on both the patient and public health scales. We use a mathematical model of commensal-pathogen interactions to define the necessary and sufficient conditions for beneficial resistance, highlighting the importance of reciprocal ecological inhibition to maximize the benefits of resistance. More broadly, we argue that determining the benefits as well as the costs of resistances in human microbiomes can transform resistance management from a minimization to an optimization problem. We discuss applied contexts and close with a review of key resistance optimization dimensions, including the magnitude, spectrum, and mechanism of resistance.},
}
@article {pmid36472419,
year = {2022},
author = {Coker, J and Zhalnina, K and Marotz, C and Thiruppathy, D and Tjuanta, M and D'Elia, G and Hailu, R and Mahosky, T and Rowan, M and Northen, TR and Zengler, K},
title = {A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology.},
journal = {mSystems},
volume = {7},
number = {6},
pages = {e0095122},
pmid = {36472419},
issn = {2379-5077},
support = {T32 GM007198/GM/NIGMS NIH HHS/United States ; },
mesh = {*Soil ; Reproducibility of Results ; Soil Microbiology ; Plant Roots ; *Microbiota ; Plants/microbiology ; },
abstract = {Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.},
}
@article {pmid36471016,
year = {2023},
author = {Wang, YJ and He, XH and Meng, LL and Zou, YN and Wu, QS},
title = {Extraradical Mycorrhizal Hyphae Promote Soil Carbon Sequestration through Difficultly Extractable Glomalin-Related Soil Protein in Response to Soil Water Stress.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1023-1034},
pmid = {36471016},
issn = {1432-184X},
support = {32272643//National Natural Science Foundation of China/ ; 31372017//National Natural Science Foundation of China/ ; T201604//Plan in Scientific and Technological Innovation Team of Outstanding Young Scientists, Hubei Provincial Department of Education, China/ ; },
mesh = {*Mycorrhizae ; Soil/chemistry ; Hyphae ; Carbon Sequestration ; Carbon/metabolism ; Dehydration/metabolism ; Fungal Proteins/metabolism ; Glycoproteins/metabolism ; },
abstract = {Soil water stress (WS) affects the decomposition of soil organic carbon (SOC) and carbon (C) emissions. Glomalin, released by arbuscular mycorrhizal fungi into soil that has been defined as glomalin-related soil protein (GRSP), is an important pool of SOC, with hydrophobic characteristics. We hypothesized that mycorrhizal fungi have a positive effect on SOC pools under soil WS for C sequestration in GRSP secreted by extraradical mycorrhizal hyphae. A microsystem was used to establish a root chamber (co-existence of roots and extraradical mycorrhizal hyphae) and a hyphal chamber (the presence of extraradical mycorrhizal hyphae) to study changes in plant growth, leaf water potential, soil aggregate stability, SOC, GRSP, C concentrations in GRSP (CGRSP), and the contribution of CGRSP to SOC after inoculating Rhizophagus intraradices with trifoliate orange (Poncirus trifoliata) in the root chamber under adequate water (AW) and WS. Inoculation with R. intraradices alleviated negative effects on leaf water potential and plant growth after 7 weeks of WS. Soil WS decreased SOC and mean weight diameter (MWD), while AMF inoculation led to an increase in SOC and MWD in both chambers, with the most prominent increase in the hyphal chamber under WS. The C concentration in easily extractable GRSP (EE-GRSP) and difficultly extractable GRSP (DE-GRSP) was 7.32 - 12.57 and 24.90 - 32.60 mg C/g GRSP, respectively. WS reduced CGRSP, while AMF mitigated the reduction. Extraradical mycorrhizal hyphae increased GRSP production and CGRSP, along with a more prominent increase in DE-GRSP under WS than under AW. Extraradical mycorrhizal hyphae increased the contribution of CDE-GRSP to SOC only under WS. CEE-GRSP and CDE-GRSP were significantly positively correlated with SOC and MWD. It is concluded that extraradical mycorrhizal hyphae prominently promoted C sequestration of recalcitrant DE-GRSP under soil WS, thus contributing more organic C accumulation and preservation in aggregates and soil C pool.},
}
@article {pmid36468868,
year = {2023},
author = {Zeng, L and Walker, AR and Burne, RA and Taylor, ZA},
title = {Glucose Phosphotransferase System Modulates Pyruvate Metabolism, Bacterial Fitness, and Microbial Ecology in Oral Streptococci.},
journal = {Journal of bacteriology},
volume = {205},
number = {1},
pages = {e0035222},
pmid = {36468868},
issn = {1098-5530},
support = {R01 DE012236/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Hydrogen Peroxide/metabolism ; Glucose/metabolism ; *Dental Caries ; Streptococcus mutans/genetics ; Lactic Acid/metabolism ; Acids/metabolism ; Pyruvates/metabolism ; Biofilms ; },
abstract = {Spontaneous mutants with defects in the primary glucose phosphotransferase permease (manLMNO) of Streptococcus sanguinis SK36 showed enhanced fitness at low pH. Transcriptomics and metabolomics with a manL deletion mutant (SK36/manL) revealed redirection of pyruvate to production of acetate and formate, rather than lactate. These observations were consistent with measurements of decreased lactic acid accumulation and increased excretion of acetate, formate, pyruvate, and H2O2. Genes showing increased expression in SK36/manL included those encoding carbohydrate transporters, extracellular glycosidases, intracellular polysaccharide metabolism, and arginine deiminase and pathways for metabolism of acetoin, ethanolamine, ascorbate, and formate, along with genes required for membrane biosynthesis and adhesion. Streptococcus mutans UA159 persisted much better in biofilm cocultures with SK36/manL than with SK36, an effect that was further enhanced by culturing the biofilms anaerobically but dampened by adding arginine to the medium. We posited that the enhanced persistence of S. mutans with SK36/manL was in part due to excess excretion of pyruvate by the latter, as addition of pyruvate to S. mutans-S. sanguinis cocultures increased the proportions of UA159 in the biofilms. Reducing the buffer capacity or increasing the concentration of glucose benefited UA159 when cocultured with SK36, but not with SK36/manL, likely due to the altered metabolism and enhanced acid tolerance of the mutant. When manL was deleted in S. mutans or Streptococcus gordonii, the mutants presented altered fitness characteristics. Our study demonstrated that phosphotransferase system (PTS)-dependent modulation of central metabolism can profoundly affect streptococcal fitness and metabolic interactions, revealing another dimension in commensal-pathogen relationships influencing dental caries development. IMPORTANCE Dental caries is underpinned by a dysbiotic microbiome and increased acid production. As beneficial bacteria that can antagonize oral pathobionts, oral streptococci such as S. sanguinis and S. gordonii can ferment many carbohydrates, despite their relative sensitivity to low pH. We characterized the molecular basis for why mutants of glucose transporter ManLMNO of S. sanguinis showed enhanced production of hydrogen peroxide and ammonia and improved persistence under acidic conditions. A metabolic shift involving more than 300 genes required for carbohydrate transport, energy production, and envelope biogenesis was observed. Significantly, manL mutants engineered in three different oral streptococci displayed altered capacities for acid production and interspecies antagonism, highlighting the potential for targeting the glucose-PTS to modulate the pathogenicity of oral biofilms.},
}
@article {pmid36468853,
year = {2022},
author = {Zhang, B and Zhao, C and Zhang, X and Li, X and Zhang, Y and Liu, X and Yin, J and Li, X and Wang, J and Wang, S},
title = {An Elemental Diet Enriched in Amino Acids Alters the Gut Microbial Community and Prevents Colonic Mucus Degradation in Mice with Colitis.},
journal = {mSystems},
volume = {7},
number = {6},
pages = {e0088322},
pmid = {36468853},
issn = {2379-5077},
mesh = {Mice ; Humans ; Animals ; Amino Acids/adverse effects ; Expectorants/adverse effects ; *Colitis/chemically induced ; *Microbiota ; Bacteria ; Mucus/metabolism ; },
abstract = {The role of dietary amino acids or intact proteins in the progression of colitis remains controversial, and the mechanism involving gut microbes is unclear. Here, we investigated the effects of an elemental diet (ED) enriched in amino acids and a polymeric diet enriched in intact protein on the pathogenesis of dextran sulfate sodium (DSS)-induced colitis in mice. Our results showed that the ED induced remission of colitis in mice. Notably, ED treatment reduced the abundance of the mucolytic bacteria Akkermansia and Bacteroides, which was attributed to decreased colonic protein fermentation. Consistently, the activities of mucolytic enzymes were decreased, leading to protection against mucus layer degradation and microbial invasion. Fecal microbiota transplantation from ED-fed mice reshaped microbial ecology and alleviated intestinal inflammation in recipient mice. The ED failed to induce remission of colitis in pseudogermfree mice. Together, our results demonstrate the critical role of the gut microbiota in the prevention of colitis by an ED. IMPORTANCE The prevalence of inflammatory bowel disease is rapidly increasing and has become a global burden. Several specific amino acids have been shown to benefit mucosal healing and colitis remission. However, the role of amino acids or intact proteins in diets and enteral nutrition formulas is controversial, and the mechanisms involving gut microbes remain unclear. In this study, we investigated the effects of an elemental diet (ED) enriched in amino acids and a polymeric diet enriched in intact protein on the pathogenesis of colitis in mice. The underlying mechanisms were explored by utilizing fecal microbiota transplantation and pseudogermfree mice. ED treatment reduced the abundance of mucolytic bacteria, thereby protecting the mucus layer from microbial invasion and degradation. For the first time, we convincingly demonstrated the critical role of gut microbiota in the effects of the ED. This study may provide new insights into the gut microbiota-diet interaction and its role in human health.},
}
@article {pmid36466646,
year = {2022},
author = {Twing, KI and Ward, LM and Kane, ZK and Sanders, A and Price, RE and Pendleton, HL and Giovannelli, D and Brazelton, WJ and McGlynn, SE},
title = {Microbial ecology of a shallow alkaline hydrothermal vent: Strýtan Hydrothermal Field, Eyjafördur, northern Iceland.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {960335},
pmid = {36466646},
issn = {1664-302X},
abstract = {Strýtan Hydrothermal Field (SHF) is a submarine system located in Eyjafördur in northern Iceland composed of two main vents: Big Strýtan and Arnarnesstrýtan. The vents are shallow, ranging from 16 to 70 m water depth, and vent high pH (up to 10.2), moderate temperature (T max ∼70°C), anoxic, fresh fluids elevated in dissolved silica, with slightly elevated concentrations of hydrogen and methane. In contrast to other alkaline hydrothermal vents, SHF is unique because it is hosted in basalt and therefore the high pH is not created by serpentinization. While previous studies have assessed the geology and geochemistry of this site, the microbial diversity of SHF has not been explored in detail. Here we present a microbial diversity survey of the actively venting fluids and chimneys from Big Strýtan and Arnarnesstrýtan, using 16S rRNA gene amplicon sequencing. Community members from the vent fluids are mostly aerobic heterotrophic bacteria; however, within the chimneys oxic, low oxygen, and anoxic habitats could be distinguished, where taxa putatively capable of acetogenesis, sulfur-cycling, and hydrogen metabolism were observed. Very few archaea were observed in the samples. The inhabitants of SHF are more similar to terrestrial hot spring samples than other marine sites. It has been hypothesized that life on Earth (and elsewhere in the solar system) could have originated in an alkaline hydrothermal system, however all other studied alkaline submarine hydrothermal systems to date are fueled by serpentinization. SHF adds to our understandings of hydrothermal vents in relationship to microbial diversity, evolution, and possibly the origin of life.},
}
@article {pmid36465136,
year = {2022},
author = {Simmonds, EG and Adjei, KP and Andersen, CW and Hetle Aspheim, JC and Battistin, C and Bulso, N and Christensen, HM and Cretois, B and Cubero, R and Davidovich, IA and Dickel, L and Dunn, B and Dunn-Sigouin, E and Dyrstad, K and Einum, S and Giglio, D and Gjerløw, H and Godefroidt, A and González-Gil, R and Gonzalo Cogno, S and Große, F and Halloran, P and Jensen, MF and Kennedy, JJ and Langsæther, PE and Laverick, JH and Lederberger, D and Li, C and Mandeville, EG and Mandeville, C and Moe, E and Navarro Schröder, T and Nunan, D and Sicacha-Parada, J and Simpson, MR and Skarstein, ES and Spensberger, C and Stevens, R and Subramanian, AC and Svendsen, L and Theisen, OM and Watret, C and O'Hara, RB},
title = {Insights into the quantification and reporting of model-related uncertainty across different disciplines.},
journal = {iScience},
volume = {25},
number = {12},
pages = {105512},
pmid = {36465136},
issn = {2589-0042},
abstract = {Quantifying uncertainty associated with our models is the only way we can express how much we know about any phenomenon. Incomplete consideration of model-based uncertainties can lead to overstated conclusions with real-world impacts in diverse spheres, including conservation, epidemiology, climate science, and policy. Despite these potentially damaging consequences, we still know little about how different fields quantify and report uncertainty. We introduce the "sources of uncertainty" framework, using it to conduct a systematic audit of model-related uncertainty quantification from seven scientific fields, spanning the biological, physical, and political sciences. Our interdisciplinary audit shows no field fully considers all possible sources of uncertainty, but each has its own best practices alongside shared outstanding challenges. We make ten easy-to-implement recommendations to improve the consistency, completeness, and clarity of reporting on model-related uncertainty. These recommendations serve as a guide to best practices across scientific fields and expand our toolbox for high-quality research.},
}
@article {pmid36463738,
year = {2023},
author = {Li, J and Yu, S and Liu, Q and Wang, D and Yang, L and Wang, J and Zuo, R},
title = {Screening of hazardous groundwater pollutants responsible for microbial ecological consequences by integrated nontargeted analysis and high-throughput sequencing technologies.},
journal = {Journal of hazardous materials},
volume = {445},
number = {},
pages = {130516},
doi = {10.1016/j.jhazmat.2022.130516},
pmid = {36463738},
issn = {1873-3336},
mesh = {*Environmental Pollutants/analysis ; *Groundwater/chemistry ; *Microbiota ; Beijing ; High-Throughput Nucleotide Sequencing ; *Water Pollutants, Chemical/toxicity/analysis ; Environmental Monitoring ; },
abstract = {Organic contaminants, especially hydrophobic organic contaminants (HOCs), pose potential ecological threats even at environmental concentrations. Characterization of HOC profiles and identification of key environmental stressors are vital but still challenging in groundwater quality management. In this study, a strategy for identifying the key environmental stressors among HOCs in groundwater based on integrated chemical monitoring technologies and microbial ecology analysis methods was proposed and applied to typical groundwater samples. Specifically, the characteristics of HOCs were systematically analyzed based on nontargeted and targeted approaches, and microbial community assembly and specific biomarker analysis were combined to determine the major ecological processes and key environmental stressors. The results showed that a total of 234 HOCs were detected in groundwater collected from Tongzhou, Beijing; among them, phthalate esters (PAEs) were screened out as key environmental stressors, considering that they made relatively higher microbial ecology contributions. Furthermore, their influences on the structure and function of the groundwater microbial community were evaluated by adopting high-throughput sequencing and bioinformatics analysis technologies. These findings confirmed PAEs as vital determinants driving microbial assembly, shifting community structure, and regulating community function in groundwater; in addition, the findings validated the feasibility and suitability of the proposed strategy.},
}
@article {pmid36460563,
year = {2023},
author = {Sutherland, WJ and Bennett, C and Brotherton, PNM and Butterworth, HM and Clout, MN and Côté, IM and Dinsdale, J and Esmail, N and Fleishman, E and Gaston, KJ and Herbert-Read, JE and Hughes, A and Kaartokallio, H and Le Roux, X and Lickorish, FA and Matcham, W and Noor, N and Palardy, JE and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Pretty, J and Scobey, R and Spalding, MD and Tonneijck, FH and Tubbs, N and Watson, JEM and Wentworth, JE and Wilson, JD and Thornton, A},
title = {A global biological conservation horizon scan of issues for 2023.},
journal = {Trends in ecology &amp; evolution},
volume = {38},
number = {1},
pages = {96-107},
doi = {10.1016/j.tree.2022.10.005},
pmid = {36460563},
issn = {1872-8383},
mesh = {*Ecosystem ; *Conservation of Natural Resources ; Biodiversity ; Forecasting ; Fisheries ; },
abstract = {We present the results of our 14th horizon scan of issues we expect to influence biological conservation in the future. From an initial set of 102 topics, our global panel of 30 scientists and practitioners identified 15 issues we consider most urgent for societies worldwide to address. Issues are novel within biological conservation or represent a substantial positive or negative step change at global or regional scales. Issues such as submerged artificial light fisheries and accelerating upper ocean currents could have profound negative impacts on marine or coastal ecosystems. We also identified potentially positive technological advances, including energy production and storage, improved fertilisation methods, and expansion of biodegradable materials. If effectively managed, these technologies could realise future benefits for biological diversity.},
}
@article {pmid36460187,
year = {2023},
author = {Liu, X and Zhang, J and Si, J and Li, P and Gao, H and Li, W and Chen, Y},
title = {What happens to gut microorganisms and potential repair mechanisms when meet heavy metal(loid)s.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {317},
number = {},
pages = {120780},
doi = {10.1016/j.envpol.2022.120780},
pmid = {36460187},
issn = {1873-6424},
mesh = {Humans ; *Metals, Heavy/toxicity/analysis ; *Arsenic/analysis ; Chromium ; Cadmium ; *Metalloids ; Risk Assessment ; *Soil Pollutants/analysis ; Environmental Monitoring ; China ; Soil ; },
abstract = {Heavy metal (loid) pollution is a significant threat to human health, as the intake of heavy metal (loid)s can cause disturbances in intestinal microbial ecology and metabolic disorders, leading to intestinal and systemic diseases. Therefore, it is important to understand the effects of heavy metal (loid)s on intestinal microorganisms and the necessary approaches to restore them after damage. This review provides a summary of the effects of common toxic elements, such as lead (Pb), cadmium (Cd), chromium (Cr), and metalloid arsenic (As), on the microbial community and structure, metabolic pathways and metabolites, and intestinal morphology and structure. The effects of heavy metal (loid)s on metabolism are focused on energy, nitrogen, and short-chain fatty acid metabolism. We also discussed the main solutions for recovery of intestinal microorganisms from the effects of heavy metal (loid)s, namely the supplementation of probiotics, recombinant bacteria with metal resistance, and the non-toxic transformation of heavy metal (loid) ions by their own intestinal flora. This article provides insight into the toxic effects of heavy metals and As on gut microorganisms and hosts and provides additional therapeutic options to mitigate the damage caused by these toxic elements.},
}
@article {pmid36460149,
year = {2023},
author = {Araujo, ASF and Miranda, ARL and Pereira, APA and de Melo, WJ and Melo, VMM and Ventura, SH and Brito Junior, ES and de Medeiros, EV and Araujo, FF and Mendes, LW},
title = {Microbial communities in the rhizosphere of maize and cowpea respond differently to chromium contamination.},
journal = {Chemosphere},
volume = {313},
number = {},
pages = {137417},
doi = {10.1016/j.chemosphere.2022.137417},
pmid = {36460149},
issn = {1879-1298},
mesh = {Chromium/analysis ; Rhizosphere ; Zea mays ; *Vigna ; Soil Microbiology ; Bacteria ; *Microbiota ; Soil ; Firmicutes ; *Soil Pollutants/analysis ; },
abstract = {Chromium (Cr) contamination can affect microorganisms in the soil, but the response of the microbial community in the rhizosphere of plants grown in Cr-contaminated soils is poorly understood. Therefore, this study assessed the microbial community, by amplicon sequencing, in the rhizosphere of maize and cowpea growing in uncontaminated (∼6.0 mg kg[-1] Cr) and Cr-contaminated soils (∼250 mg kg[-1] Cr). Comparing Cr-contaminated and uncontaminated soils, the microbial community in the maize rhizosphere clustered separately, while the microbial community in the cowpea rhizosphere did not present clear clustering. The microbial richness ranged from ∼5000 (rhizosphere in Cr-contaminated soil) to ∼8000 OTUs (in uncontaminated soil). In the comparison of specific bacterial groups in the rhizosphere of maize, Firmicutes were enriched in Cr-contaminated soil, including Bacilli, Bacillales, and Paenibacillus. Cowpea rhizosphere showed a higher abundance of six microbial groups in Cr-contaminated soil, highlighting Rhizobiales, Pedomicrobium, and Gemmatimonadetes. The microbial community in both rhizospheres presented a similar proportion of specialists comparing uncontaminated (2.2 and 3.4% in the rhizosphere of maize and cowpea, respectively) and Cr-contaminated soils (1.8 and 3.2% in the rhizosphere of maize and cowpea, respectively). This study showed that each plant species drove differently the microbial community in the rhizosphere, with an important effect of Cr-contamination on the microbial community assembly.},
}
@article {pmid36455460,
year = {2023},
author = {Rothman, JA and Saghir, A and Chung, SA and Boyajian, N and Dinh, T and Kim, J and Oval, J and Sharavanan, V and York, C and Zimmer-Faust, AG and Langlois, K and Steele, JA and Griffith, JF and Whiteson, KL},
title = {Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes.},
journal = {Water research},
volume = {229},
number = {},
pages = {119421},
doi = {10.1016/j.watres.2022.119421},
pmid = {36455460},
issn = {1879-2448},
mesh = {Humans ; *Wastewater ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Sewage/microbiology ; Bacteria/genetics ; RNA ; Genes, Bacterial ; },
abstract = {Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs (as measured through PERMANOVA, P < 0.001) and that the relative abundance of many individual AMR genes/variants increased over time (as measured with MaAsLin2, Padj < 0.05). Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.},
}
@article {pmid36452921,
year = {2022},
author = {Xu, H and Wu, N and Na, N and Sun, L and Zhao, Y and Ding, H and Fang, Y and Wang, T and Xue, Y and Zhong, J},
title = {Fermentation weight loss, fermentation quality, and bacterial community of ensiling of sweet sorghum with lactic acid bacteria at different silo densities.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1013913},
pmid = {36452921},
issn = {1664-302X},
abstract = {Sweet sorghum is an important forage in arid and semi-arid climatic regions. This study aimed to reveal the fermentation weight loss (FWL), fermentation quality, and bacterial community of ensiling of sweet sorghum with lactic acid bacteria LAB; (Lactiplantibacillus plantarum and Lentilactobacillus buchneri) at different silo densities. For this study, sweet sorghum was harvested at the first spikelet of inflorescence stage and ensiled without or with LAB (CK or L) in polyethylene laboratory-scale silos (diameter, 20 cm; height, 30 cm) at densities of 650 (CK_650 and L_650), 700 (CK_700 and L_700), and 750 kg/m[3] (CK_750 and L_750), respectively. The FWL, fermentation quality, microbial counts, and bacterial community of the silage were assessed after 100 days of ensiling. L_750 had a lower FWL than CK_650, _700, and _750 after 100 days of ensiling (P < 0.005), and the FWL was affected by silo density and inoculating LAB (P < 0.005). All silages had low pH (<4.0) and ammonia nitrogen content (<50 g/kg total nitrogen) and did not contain propionic and butyric acids; moreover, inoculating LAB increased lactic and acetic acids (P < 0.005). Bacterial communities in inoculated and uninoculated silages were clustered together, respectively, and clearly separated from each other. The total abundance of Lactiplantibacillus and Lentilactobacillus in fresh forage was <1%. Lactiplantibacillus had the highest abundance in all silages (from 71.39 to 93.27%), followed by Lentilactobacillus (from 3.59 to 27.63%). Inoculating LAB increased the abundance of Lentilactobacillus in each silo density (P < 0.005) and decreased Lactiplantibacillus in the silage in densities of 700 and 750 kg/m[3] (P < 0.005); moreover, increasing silo density decreased Lactiplantibacillus abundance and increased Lentilactobacillus abundance in inoculated silages (P < 0.005). Overall, sweet sorghum silage showed satisfactory fermentation quality, with a density of no <650 kg/m[3], and inoculating LAB improved fermentation quality and reduced FWL. Lactiplantibacillus and Lentilactobacillus presented as minor taxa in fresh sweet sorghum and dominated the bacterial community of all silages. Inoculating LAB was the main factor affecting the bacterial community of sweet sorghum silage. Moreover, inoculating LAB and increasing silo density can contribute to the decreasing Lactiplantibacillus abundance and increasing Lentilactobacillus abundance.},
}
@article {pmid36451971,
year = {2022},
author = {Villa, F and Wu, YL and Zerboni, A and Cappitelli, F},
title = {In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface.},
journal = {Bioscience},
volume = {72},
number = {12},
pages = {1156-1175},
pmid = {36451971},
issn = {0006-3568},
abstract = {Pigment-based color is one of the most important phenotypic traits of biofilms at the mineral-air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral-air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities' structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.},
}
@article {pmid36449026,
year = {2023},
author = {Badger Hanson, E and Docherty, KM},
title = {Mini-review: Current and Future Perspectives on Microbially Focused Restoration Strategies in Tallgrass Prairies.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1087-1097},
pmid = {36449026},
issn = {1432-184X},
support = {Graduate College//Western Michigan University/ ; Doctoral Fellowship//Western Michigan University/ ; Graduate Student Research Grant//Western Michigan University/ ; },
mesh = {*Ecosystem ; *Grassland ; Soil Microbiology ; Soil ; Carbon/metabolism ; },
abstract = {Ecosystem restoration is a critical conservation strategy, especially for increasing resilience and resistance to climate change. Current restoration efforts that convert reclaimed agricultural land to native tallgrass prairies typically focus on aboveground communities, but it can take decades to restore soil microbial biodiversity and function using these strategies, if they recover at all. This incomplete restoration can have detrimental impacts on longer-term restoration goals, such as supporting late-successional plant species and facilitating soil carbon sequestration. Soil microorganisms are key components in determining the fate of organic material that enters the soil. They mediate decomposition rates and contribute to plant-microbe-soil interactions, produce microbial biomass, necromass, and metabolic products, and physically protect soil carbon through aggregation. Interactions with plants and controls over soil carbon vary widely depending on the specific microbial taxa present, their physiology, their functional capabilities, and their responses to environmental stressors. Thus, the ability for new restorations, prairie conservation corridors, and prairies planted in marginal lands to act as carbon sinks and help balance greenhouse gas emissions can depend on the success of microbial restoration. Next-generation sequencing approaches can support novel methods for evaluating existing restoration practices and developing microbially focused management strategies. This review summarizes the growing body of literature describing microbially focused tallgrass prairie restoration and considers when and how integrating next-generation sequencing approaches into management efforts can be beneficial. We provide a roadmap for future restoration efforts where microbial ecologists, restoration ecologists, and land managers can work together to meet their goals to promote climate-ready restored ecosystems.},
}
@article {pmid36445401,
year = {2023},
author = {Bates, KA and Friesen, J and Loyau, A and Butler, H and Vredenburg, VT and Laufer, J and Chatzinotas, A and Schmeller, DS},
title = {Environmental and Anthropogenic Factors Shape the Skin Bacterial Communities of a Semi-Arid Amphibian Species.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1393-1404},
pmid = {36445401},
issn = {1432-184X},
support = {ANR-15-MASC-0001-P3//Belmont Forum/ ; Junior Research Fellowship//St. Hilda's College, University of Oxford/ ; },
mesh = {Animals ; Anthropogenic Effects ; *Chytridiomycota ; Bufonidae ; Skin/microbiology ; Bacteria/genetics ; *Ranavirus ; },
abstract = {The amphibian skin microbiome is important in maintaining host health, but is vulnerable to perturbation from changes in biotic and abiotic conditions. Anthropogenic habitat disturbance and emerging infectious diseases are both potential disrupters of the skin microbiome, in addition to being major drivers of amphibian decline globally. We investigated how host environment (hydrology, habitat disturbance), pathogen presence, and host biology (life stage) impact the skin microbiome of wild Dhofar toads (Duttaphrynus dhufarensis) in Oman. We detected ranavirus (but not Batrachochytrium dendrobatidis) across all sampling sites, constituting the first report of this pathogen in Oman, with reduced prevalence in disturbed sites. We show that skin microbiome beta diversity is driven by host life stage, water source, and habitat disturbance, but not ranavirus infection. Finally, although trends in bacterial diversity and differential abundance were evident in disturbed versus undisturbed sites, bacterial co-occurrence patterns determined through network analyses revealed high site specificity. Our results therefore provide support for amphibian skin microbiome diversity and taxa abundance being associated with habitat disturbance, with bacterial co-occurrence (and likely broader aspects of microbial community ecology) being largely site specific.},
}
@article {pmid36445161,
year = {2022},
author = {Sylvain, F&#xc9; and Leroux, N and Normandeau, &#xc9; and Holland, A and Bouslama, S and Mercier, PL and Luis Val, A and Derome, N},
title = {Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont.},
journal = {Microbiology spectrum},
volume = {10},
number = {6},
pages = {e0206422},
pmid = {36445161},
issn = {2165-0497},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Gills/chemistry/microbiology ; Fishes/genetics/microbiology ; *Microbiota/physiology ; Water ; Genomics ; Bacteria/genetics ; },
abstract = {Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.},
}
@article {pmid36445112,
year = {2022},
author = {Sánchez-Navarro, R and Nuhamunada, M and Mohite, OS and Wasmund, K and Albertsen, M and Gram, L and Nielsen, PH and Weber, T and Singleton, CM},
title = {Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem.},
journal = {mSystems},
volume = {7},
number = {6},
pages = {e0063222},
pmid = {36445112},
issn = {2379-5077},
mesh = {*Metagenome/genetics ; Sewage ; Multigene Family/genetics ; *Microbiota/genetics ; Genome, Bacterial/genetics ; },
abstract = {Microorganisms produce a wide variety of secondary/specialized metabolites (SMs), the majority of which are yet to be discovered. These natural products play multiple roles in microbiomes and are important for microbial competition, communication, and success in the environment. SMs have been our major source of antibiotics and are used in a range of biotechnological applications. In silico mining for biosynthetic gene clusters (BGCs) encoding the production of SMs is commonly used to assess the genetic potential of organisms. However, as BGCs span tens to over 200 kb, identifying complete BGCs requires genome data that has minimal assembly gaps within the BGCs, a prerequisite that was previously only met by individually sequenced genomes. Here, we assess the performance of the currently available genome mining platform antiSMASH on 1,080 high-quality metagenome-assembled bacterial genomes (HQ MAGs) previously produced from wastewater treatment plants (WWTPs) using a combination of long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies. More than 4,200 different BGCs were identified, with 88% of these being complete. Sequence similarity clustering of the BGCs implies that the majority of this biosynthetic potential likely encodes novel compounds, and few BGCs are shared between genera. We identify BGCs in abundant and functionally relevant genera in WWTPs, suggesting a role of secondary metabolism in this ecosystem. We find that the assembly of HQ MAGs using long-read sequencing is vital to explore the genetic potential for SM production among the uncultured members of microbial communities. IMPORTANCE Cataloguing secondary metabolite (SM) potential using genome mining of metagenomic data has become the method of choice in bioprospecting for novel compounds. However, accurate biosynthetic gene cluster (BGC) detection requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until very recently with new long-read technologies. Here, we determined the biosynthetic potential of activated sludge (AS), the microbial community used in resource recovery and wastewater treatment, by mining high-quality metagenome-assembled genomes generated from long-read data. We found over 4,000 BGCs, including BGCs in abundant process-critical bacteria, with no similarity to the BGCs of characterized products. We show how long-read MAGs are required to confidently assemble complete BGCs, and we determined that the AS BGCs from different studies have very little overlap, suggesting that AS is a rich source of biosynthetic potential and new bioactive compounds.},
}
@article {pmid36444830,
year = {2022},
author = {Russo, V and Ancora, M and Gatta, V and Orsini, M and Prencipe, G and Peserico, A and Colosimo, A and El Khatib, M and Mauro, A and Di Berardino, C and Scialabba, S and Tiboni, GM and Marcacci, M and Cammà, C and Barboni, B},
title = {Profiling of mitochondrial heteroplasmy in single human oocytes by next-generation sequencing.},
journal = {Molecular reproduction and development},
volume = {89},
number = {12},
pages = {646-654},
doi = {10.1002/mrd.23655},
pmid = {36444830},
issn = {1098-2795},
mesh = {Humans ; *Heteroplasmy ; *Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Oocytes/metabolism ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Mitochondrial DNA (mtDNA) plays a crucial role in the development of a competent oocyte. Indeed, mtDNA alterations may predispose to chromosome nondisjunction, resulting in infertility due to a reduced vitality and quality of oocytes and embryos. In this methods paper, the multiple displacement amplification approach was applied in combination with next-generation sequencing (NGS) to amplify and sequence, in single-end, the entire mtDNA of single human oocytes to directly construct genomic NGS libraries, and subsequently, to highlight and quantify the mutations they presented. The bioinformatic workflow was carried out with a specific ad hoc developed in-house software. This approach proved to be sensitive and specific, also highlighting the mutations present in heteroplasmy, showing deletion, insertion or substitution mutations in the genes involved in the respiratory chain, even if the found variants were benign or of uncertain meaning. The analysis of mtDNA mutations in the oocyte could provide a better understanding of specific genetic abnormalities and of their possible effect on oocyte developmental competence. This study shows how this approach, based on a massive parallel sequencing of clonally amplified DNA molecules, allows to sequence the entire mitochondrial genome of single oocytes in a short time and with a single analytical run and to verify mtDNA mutations.},
}
@article {pmid36443470,
year = {2022},
author = {Jang, H and Koh, H and Gu, W and Kang, B},
title = {Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {20465},
pmid = {36443470},
issn = {2045-2322},
mesh = {Humans ; Cloud Computing ; *Microbiota ; *Gastrointestinal Microbiome ; Mouth ; Skin ; },
abstract = {Pairing (or blocking) is a design technique that is widely used in comparative microbiome studies to efficiently control for the effects of potential confounders (e.g., genetic, environmental, or behavioral factors). Some typical paired (block) designs for human microbiome studies are repeated measures designs that profile each subject's microbiome twice (or more than twice) (1) for pre and post treatments to see the effects of a treatment on microbiome, or (2) for different organs of the body (e.g., gut, mouth, skin) to see the disparity in microbiome between (or across) body sites. Researchers have developed a sheer number of web-based tools for user-friendly microbiome data processing and analytics, though there is no web-based tool currently available for such paired microbiome studies. In this paper, we thus introduce an integrative web-based tool, named MiPair, for design-based comparative analysis with paired microbiome data. MiPair is a user-friendly web cloud service that is built with step-by-step data processing and analytic procedures for comparative analysis between (or across) groups or between baseline and other groups. MiPair employs parametric and non-parametric tests for complete or incomplete block designs to perform comparative analyses with respect to microbial ecology (alpha- and beta-diversity) and taxonomy (e.g., phylum, class, order, family, genus, species). We demonstrate its usage through an example clinical trial on the effects of antibiotics on gut microbiome. MiPair is an open-source software that can be run on our web server (http://mipair.micloud.kr) or on user's computer (https://github.com/yj7599/mipairgit).},
}
@article {pmid36442715,
year = {2023},
author = {Islam, T and Albracht-Schulte, K and Ramalingam, L and Schlabritz-Lutsevich, N and Park, OH and Zabet-Moghaddam, M and Kalupahana, NS and Moustaid-Moussa, N},
title = {Anti-inflammatory mechanisms of polyphenols in adipose tissue: role of gut microbiota, intestinal barrier integrity and zinc homeostasis.},
journal = {The Journal of nutritional biochemistry},
volume = {115},
number = {},
pages = {109242},
doi = {10.1016/j.jnutbio.2022.109242},
pmid = {36442715},
issn = {1873-4847},
mesh = {Humans ; *Gastrointestinal Microbiome ; Polyphenols/pharmacology ; Lipopolysaccharides/pharmacology ; Anthocyanins/pharmacology ; Obesity/microbiology ; Inflammation/drug therapy ; Anti-Inflammatory Agents/pharmacology ; Homeostasis ; Zinc/pharmacology ; Dysbiosis/microbiology ; },
abstract = {Obesity is associated with an imbalance of micro-and macro-nutrients, gut dysbiosis, and a "leaky" gut phenomenon. Polyphenols, such as curcumin, resveratrol, and anthocyanins may alleviate the systemic effects of obesity, potentially by improving gut microbiota, intestinal barrier integrity (IBI), and zinc homeostasis. The essential micronutrient zinc plays a crucial role in the regulation of enzymatic processes, including inflammation, maintenance of the microbial ecology, and intestinal barrier integrity. In this review, we focus on IBI- which prevents intestinal lipopolysaccharide (LPS) leakage - as a critical player in polyphenol-mediated protective effects against obesity-associated white adipose tissue (WAT) inflammation. This occurs through mechanisms that block the movement of the bacterial endotoxin LPS across the gut barrier. Available research suggests that polyphenols reduce WAT and systemic inflammation via crosstalk with inflammatory NF-κB, the mammalian target of rapamycin (mTOR) signaling and zinc homeostasis.},
}
@article {pmid36442312,
year = {2023},
author = {Zhong, X and Yu, S and Xu, H},
title = {Colonization dynamics in body-size spectrum of protozoan periphytons for marine bioassessment using two modified sampling systems.},
journal = {Marine pollution bulletin},
volume = {186},
number = {},
pages = {114382},
doi = {10.1016/j.marpolbul.2022.114382},
pmid = {36442312},
issn = {1879-3363},
mesh = {Ecosystem ; Biodiversity ; *Periphyton ; Environmental Monitoring/methods ; *Ciliophora ; China ; },
abstract = {The body-size spectrum of microperiphytons has been proved to be a powerful tool for bioassessment. To explore colonization dynamics in body-size spectrum of periphytic protozoa in two modified sampling systems of both glass slide (mGS) and polyurethane foam unit (mPFU), a 28-day colonization survey was conducted in coastal waters of the Yellow Sea, China. A total of 7 body-size ranks were identified from 62 species, with 7 ranks (60 species) in the mGS and 6 ranks (37 species) in the mPFU system. The stable pattern with similar body-size spectra was found earlier in the mGS system than mPFU system during the colonization period. Both the trajectory and bootstrapped average analyses revealed that the colonization dynamics were significantly different in the body-size spectrum between the two methods. Based on our data, it suggests that the mGS system might be a better choice than the mPFU system for bioassessment in marine ecosystems.},
}
@article {pmid36441249,
year = {2023},
author = {Scherer, BP and Mast, A},
title = {Red Mangrove Propagule Bacterial Communities Vary With Geographic, But Not Genetic Distance.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1010-1022},
pmid = {36441249},
issn = {1432-184X},
mesh = {Humans ; *Rhizophoraceae/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Florida ; },
abstract = {Bacterial communities associated with plant propagules remain understudied, despite the opportunities that propagules represent as dispersal vectors for bacteria to new sites. These communities may be the product of a combination of environmental influence and inheritance from parent to offspring. The relative role of these mechanisms could have significant implications for our understanding of plant-microbe interactions. We studied the correlates of microbiome community similarities across an invasion front of red mangroves (Rhizophora mangle L.) in Florida, where the species is expanding northward. We collected georeferenced propagule samples from 110 individuals of red mangroves across 11 populations in Florida and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. We found no core community of bacterial amplicon sequence variants (ASVs) across the Florida range of red mangroves, though there were some ASVs shared among individuals within most populations. Populations differed significantly as measured by Bray-Curtis dissimilarity, but not Unifrac distance. We generated data from 6 microsatellite loci from 60 individuals across 9 of the 11 populations. Geographic distance was correlated with beta diversity, but genetic distance was not. We conclude that red mangrove propagule bacterial communities are likely influenced more by local environmental acquisition than by inheritance.},
}
@article {pmid36440485,
year = {2022},
author = {Alsayed, AR and Al-Dulaimi, A and Alkhatib, M and Al Maqbali, M and Al-Najjar, MAA and Al-Rshaidat, MMD},
title = {A comprehensive clinical guide for Pneumocystis jirovecii pneumonia: a missing therapeutic target in HIV-uninfected patients.},
journal = {Expert review of respiratory medicine},
volume = {16},
number = {11-12},
pages = {1167-1190},
doi = {10.1080/17476348.2022.2152332},
pmid = {36440485},
issn = {1747-6356},
mesh = {Humans ; *Pneumonia, Pneumocystis/complications/diagnosis/drug therapy ; *COVID-19/complications ; *Pneumocystis carinii ; Immunocompromised Host ; *HIV Infections/complications ; },
abstract = {INTRODUCTION: Pneumocystis jirovecii is an opportunistic, human-specific fungus that causes Pneumocystis pneumonia (PCP). PCP symptoms are nonspecific. A patient with P. jirovecii and another lung infection faces a diagnostic challenge. It may be difficult to determine which of these agents is responsible for the clinical symptoms, preventing effective treatment. Diagnostic and treatment efforts have been made more difficult by the rising frequency with which coronavirus 2019 (COVID-19) and PCP co-occur.<br><br>AREAS COVERED: Herein, we provide a comprehensive review of clinical and pharmacological recommendations along with a literature review of PCP in immunocompromised patients focusing on HIV-uninfected patients.<br><br>EXPERT OPINION: PCP may be masked by identifying co-existing pathogens that are not necessarily responsible for the observed infection. Patients with severe form COVID-19 should be examined for underlying immunodeficiency, and co-infections must be considered as co-infection with P. jirovecii may worsen COVID-19's severity and fatality. PCP should be investigated in patients with PCP risk factors who come with pneumonia and suggestive radiographic symptoms but have not previously received PCP prophylaxis. PCP prophylaxis should be explored in individuals with various conditions that impair the immune system, depending on their PCP risk.},
}
@article {pmid36439796,
year = {2022},
author = {Bandini, F and Vaccari, F and Soldano, M and Piccinini, S and Misci, C and Bellotti, G and Taskin, E and Cocconcelli, PS and Puglisi, E},
title = {Rigid bioplastics shape the microbial communities involved in the treatment of the organic fraction of municipal solid waste.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1035561},
pmid = {36439796},
issn = {1664-302X},
abstract = {While bioplastics are gaining wide interest in replacing conventional plastics, it is necessary to understand whether the treatment of the organic fraction of municipal solid waste (OFMSW) as an end-of-life option is compatible with their biodegradation and their possible role in shaping the microbial communities involved in the processes. In the present work, we assessed the microbiological impact of rigid polylactic acid (PLA) and starch-based bioplastics (SBB) spoons on the thermophilic anaerobic digestion and the aerobic composting of OFMSW under real plant conditions. In order to thoroughly evaluate the effect of PLA and SBB on the bacterial, archaeal, and fungal communities during the process, high-throughput sequencing (HTS) technology was carried out. The results suggest that bioplastics shape the communities' structure, especially in the aerobic phase. Distinctive bacterial and fungal sequences were found for SBB compared to the positive control, which showed a more limited diversity. Mucor racemosus was especially abundant in composts from bioplastics' treatment, whereas Penicillium roqueforti was found only in compost from PLA and Thermomyces lanuginosus in that from SBB. This work shed a light on the microbial communities involved in the OFMSW treatment with and without the presence of bioplastics, using a new approach to evaluate this end-of-life option.},
}
@article {pmid36436634,
year = {2023},
author = {Sakarika, M and Regueira, A and Rabaey, K and Ganigué, R},
title = {Thermophilic caproic acid production from grass juice by sugar-based chain elongation.},
journal = {The Science of the total environment},
volume = {860},
number = {},
pages = {160501},
doi = {10.1016/j.scitotenv.2022.160501},
pmid = {36436634},
issn = {1879-1026},
mesh = {*Caproates ; Fermentation ; *Bioreactors ; Sugars ; Carbohydrates ; Carboxylic Acids ; Glucose ; },
abstract = {Medium chain carboxylic acids (MCCA) such as caproic acid have a plethora of applications, ranging from food additives to bioplastics. MCCA can be produced via microbial chain elongation using waste and side-streams as substrates, a process that can be more sustainable than conventional production routes. Most chain elongation studies have focused on mesophilic conditions, with only two recent studies hinting at the possibility of thermophilic chain elongation, but a systematic study of its mechanisms is lacking. Here, we investigated thermophilic chain elongation from grass juice, to understand the effect of key operational parameters (pH, temperature, substrate) on the process performance and to establish the key microbial genera and their role in the system. The genus Caproiciproducens was identified as responsible for thermophilic chain elongation, and caproic acid production was most favorable at pH 6.0 and 50 °C among the conditions tested, reaching an average concentration of 3.4 g/L. Batch experiments showed that the substrate for caproic acid production were glucose and xylose, while lactic acid led to the production of only butyric acid. Fed-batch experiments showed that substrate availability and the presence of caproic acid in the system play a major role in shaping the profile of thermophilic chain elongation. The increase of the total sugar concentration by glucose addition (without changing the organic load) during continuous operation led to a microbial community dominated (75 %) by Caproiciproducens and increased by 76 % the final average caproic acid concentration to 6.0 g/L (13 gCOD/L) which represented 32 % (g/g) of the total carboxylic acids. The highest concentration achieved was 7.2 g/L (day 197) which is the highest concentration reported under thermophilic conditions thus far. The results of this work pave the way to the potential development of thermophilic systems for upgrading various underexplored abundant and cheap sugar-rich side-streams to caproic acid.},
}
@article {pmid36436244,
year = {2023},
author = {Sun, W and Qian, X and Wang, X and Gu, J},
title = {Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion.},
journal = {Journal of environmental management},
volume = {326},
number = {Pt B},
pages = {116864},
doi = {10.1016/j.jenvman.2022.116864},
pmid = {36436244},
issn = {1095-8630},
mesh = {Cattle ; Animals ; *Manure/analysis ; *Anti-Bacterial Agents/pharmacology/metabolism ; Enrofloxacin/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; },
abstract = {Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.},
}
@article {pmid36434466,
year = {2023},
author = {Hietaranta, E and Juottonen, H and Kytöviita, MM},
title = {Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems.},
journal = {Oecologia},
volume = {201},
number = {1},
pages = {59-72},
pmid = {36434466},
issn = {1432-1939},
mesh = {Bees ; Animals ; *Pollination ; Insecta ; Plants ; Pollen ; *Microbiota ; Flowers ; },
abstract = {Basic knowledge on dispersal of microbes in pollinator networks is essential for plant, insect, and microbial ecology. Thorough understanding of the ecological consequences of honeybee farming on these complex plant-pollinator-microbe interactions is a prerequisite for sustainable honeybee keeping. Most research on plant-pollinator-microbe interactions have focused on temperate agricultural systems. Therefore, information on a wild plant that is a seasonal bottleneck for pollinators in cold climate such as Salix phylicifolia is of specific importance. We investigated how floral visitation by insects influences the community structure of bacteria and fungi in Salix phylicifolia inflorescences under natural conditions. Insect visitors were experimentally excluded with net bags. We analyzed the microbiome and measured pollen removal in open and bagged inflorescences in sites where honeybees were foraging and in sites without honeybees. Site and plant individual explained most of the variation in floral microbial communities. Insect visitation and honeybees had a smaller but significant effect on the community composition of microbes. Honeybees had a specific effect on the inflorescence microbiome and, e.g., increased the relative abundance of operational taxonomic units (OTUs) from the bacterial order Lactobacillales. Site had a significant effect on the amount of pollen removed from inflorescences but this was not due to honeybees. Insect visitors increased bacterial and especially fungal OTU richness in the inflorescences. Pollinator visits explained 38% variation in fungal richness, but only 10% in bacterial richness. Our work shows that honeybee farming affects the floral microbiome in a wild plant in rural boreal ecosystems.},
}
@article {pmid36434303,
year = {2023},
author = {Querejeta, M and Hervé, V and Perdereau, E and Marchal, L and Herniou, EA and Boyer, S and Giron, D},
title = {Changes in Bacterial Community Structure Across the Different Life Stages of Black Soldier Fly (Hermetia illucens).},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1254-1267},
pmid = {36434303},
issn = {1432-184X},
support = {EX004527//Conseil R&#xe9;gional du Centre-Val de Loire/ ; EX011185//European Regional Development Fund/ ; AYUD/2021/58607//Fundaci&#xf3;n para el Fomento en Asturias de la Investigaci&#xf3;n Cient&#xed;fica Aplicada y la Tecnolog&#xed;a/ ; },
mesh = {Animals ; *Diptera/microbiology ; Larva/microbiology ; Digestion ; Pupa ; *Microbiota ; Bacteria/genetics ; },
abstract = {The digestive capacity of organic compounds by the black soldier fly (BSF, Hermetia illucens, Diptera: Stratiomyidae, Linnaeus, 1758) is known to rely on complex larva-microbiota interactions. Although insect development is known to be a driver of changes of bacterial communities, the fluctuations along BSF life cycle in terms of composition and diversity of bacterial communities are still unknown. In this work, we used a metabarcoding approach to explore the differences in bacterial diversity along all four BSF developmental stages: eggs, larvae, pupae, and adult. We detected not only significant differences in bacterial community composition and species richness along the development of BSF, but also nine prevalent amplicon single variants (ASVs) forming the core microbiota. Out of the 2010 ASVs identified, 160 were significantly more abundant in one of the life stages. Moreover, using PICRUSt2, we inferred 27 potential metabolic pathways differentially used among the BSF life cycle. This distribution of metabolic pathways was congruent with the bacterial taxonomic distribution among life stages, demonstrating that the functional requirements of each phase of development are drivers of bacterial composition and diversity. This study provides a better understanding of the different metabolic processes occurring during BSF development and their links to changes in bacterial taxa. This information has important implications for improving bio-waste processing in such an economically important insect species.},
}
@article {pmid36432829,
year = {2022},
author = {May-Mutul, CG and López-Garrido, MA and O'Connor-Sánchez, A and Peña-Ramírez, YJ and Labrín-Sotomayor, NY and Estrada-Medina, H and Ferrer, MM},
title = {Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {22},
pages = {},
pmid = {36432829},
issn = {2223-7747},
support = {CB 2017-2018 A1S30471//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Honors-thesis-grants 31490//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Honors-thesis-grants 31430//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
abstract = {During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.},
}
@article {pmid36431270,
year = {2022},
author = {Cheng, T and Zhi, H and Liu, Y and Zhang, S and Song, Z and Li, Y},
title = {Dual Anti-Glomerular Basement Membrane and Anti-Neutrophil Cytoplasmic Antibodies-Positive Rapidly Progressive Glomerulonephritis with Rheumatoid Arthritis and Sjogren's Syndrome: A Case Report and Literature Review.},
journal = {Journal of clinical medicine},
volume = {11},
number = {22},
pages = {},
pmid = {36431270},
issn = {2077-0383},
support = {82170716//National Natural Science Foundation of China/ ; },
abstract = {Rapidly progressive glomerulonephritis (RPGN) is a life-threatening disease characterized by rapid progressive deterioration of renal function and extensive formation of crescents. Some antibodies tend to be positive, such as a perinuclear anti-neutrophil cytoplasmic antibody (p-ANCA) and anti-glomerular basement membrane (anti-GBM) antibodies, in most patients with the disease. However, cases of double positivity for the above antibodies are considered to be rare. In addition, both rheumatoid arthritis (RA) and Sjogren's syndrome (SS) are deemed to be independent immune disorders that can cause renal impairment. Nevertheless, the association between RPGN and these two diseases has not been elucidated in previous studies. Here, we provide a case of RPGN with the concurrence of RA and SS characterized by double positivity in anti-GBM antibodies and p-ANCA. After aggressive treatment with cyclophosphamide, glucocorticoids, and plasma exchange, the patient improved significantly. Despite the malignant event of arteriovenous fistula rupture and bleeding during treatment, the patient survived with renal function recovery for the rest of the follow-up period.},
}
@article {pmid36431177,
year = {2022},
author = {Zhi, W and Yuan, X and Song, W and Jin, G and Li, Y},
title = {Fecal Microbiota Transplantation May Represent a Good Approach for Patients with Focal Segmental Glomerulosclerosis: A Brief Report.},
journal = {Journal of clinical medicine},
volume = {11},
number = {22},
pages = {},
pmid = {36431177},
issn = {2077-0383},
support = {82170716//National Natural Science Foundation of China, Gut microbiota promotes IgAN through CASP-1/IL-1&#x3b2;-driven increased intestinal permeability/ ; },
abstract = {This is the first report of fecal microbiota transplantation (FMT) in patients with chronic kidney disease. The patient was subjected to focal segmental glomerulosclerosis (FSGS), with onset in April 2021. The main manifestation featured abnormal renal function and no proteinuria at the level of nephrotic syndrome. In May 2021, she showed biopsy-proven FSGS and was treated with glucocorticoid. However, after glucocorticoid reduction, the patient's serum creatinine increased again, so she adjusted the dosage and continued use until now. In April 2022, the patient was prescribed the FMT capsules. After FMT, the renal function remained stable, urinary protein decreased, reaching the clinical standard of complete remission, and there was no recurrence after glucocorticoid reduction. Furthermore, the patient showed significantly decreased hyperlipidemia, triglyceride (TG) and cholesterol (CHO) after FMT. During FMT, the level of cytokines fluctuated slightly, but returned to the pre-transplantation level after three months. From this, we conclude that FMT is a potential adjuvant therapy for FSGS, and patients can benefit from improving renal function and dyslipidemia.},
}
@article {pmid36430059,
year = {2022},
author = {Savadova-Ratkus, K and Mazur-Marzec, H and Karosienė, J and Sivonen, K and Suurnäkki, S and Kasperovičienė, J and Paškauskas, R and Koreivienė, J},
title = {Cyanobacteria and Their Metabolites in Mono- and Polidominant Shallow Eutrophic Temperate Lakes.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {22},
pages = {},
pmid = {36430059},
issn = {1660-4601},
mesh = {*Lakes ; Ecosystem ; *Cyanobacteria ; Biota ; Biomass ; },
abstract = {Monodominant (one species dominates) or polidominant (multiple species dominate) cyanobacterial blooms are pronounced in productive freshwater ecosystems and pose a potential threat to the biota due to the synthesis of toxins. Seasonal changes in cyanobacteria species and cyanometabolites composition were studied in two shallow temperate eutrophic lakes. Data on cyanobacteria biomass and diversity of dominant species in the lakes were combined with chemical and molecular analyses of fifteen potentially toxin-producing cyanobacteria species (248 isolates from the lakes). Anatoxin-a, saxitoxin, microcystins and other non-ribosomal peptides formed the diverse profiles in monodominant (Planktothrix agardhii) and polidominant (Aphanizomenon gracile, Limnothrix spp. and Planktolyngbya limnetica) lakes. However, the harmfulness of the blooms depended on the ability of the dominant species to synthesize cyanometabolites. It was confirmed that P. agardhii produced a greater amount and diverse range of MCs and other NRPs. In the polidominant lake, isolates of the co-dominant A. gracile, L. planctonica and P. limnetica synthesized no or only small amounts of cyanometabolites. In general, the profile of cyanometabolites was greater in cyanobacteria isolates than in environmental samples, indicating a high potential for toxic cyanobacteria bloom.},
}
@article {pmid36427812,
year = {2023},
author = {Ramsperger, AFRM and Bergamaschi, E and Panizzolo, M and Fenoglio, I and Barbero, F and Peters, R and Undas, A and Purker, S and Giese, B and Lalyer, CR and Tamargo, A and Moreno-Arribas, MV and Grossart, HP and Kühnel, D and Dietrich, J and Paulsen, F and Afanou, AK and Zienolddiny-Narui, S and Eriksen Hammer, S and Kringlen Ervik, T and Graff, P and Brinchmann, BC and Nordby, KC and Wallin, H and Nassi, M and Benetti, F and Zanella, M and Brehm, J and Kress, H and Löder, MGJ and Laforsch, C},
title = {Nano- and microplastics: a comprehensive review on their exposure routes, translocation, and fate in humans.},
journal = {NanoImpact},
volume = {29},
number = {},
pages = {100441},
doi = {10.1016/j.impact.2022.100441},
pmid = {36427812},
issn = {2452-0748},
mesh = {Humans ; *Microplastics/metabolism ; *Plastics/metabolism ; Ecosystem ; Gastrointestinal Tract/metabolism ; Respiratory System/metabolism ; },
abstract = {Contamination of the environment with nano-and microplastic particles (NMPs) and its putative adverse effects on organisms, ecosystems, and human health is gaining increasing scientific and public attention. Various studies show that NMPs occur abundantly within the environment, leading to a high likelihood of human exposure to NMPs. Here, different exposure scenarios can occur. The most notable exposure routes of NMPs into the human body are via the airways and gastrointestinal tract (GIT) through inhalation or ingestion, but also via the skin due to the use of personal care products (PCPs) containing NMPs. Once NMPs have entered the human body, it is possible that they are translocated from the exposed organ to other body compartments. In our review article, we combine the current knowledge on the (1) exposure routes of NMPs to humans with the basic understanding of the potential (2) translocation mechanisms into human tissues and, consequently, their (3) fate within the human body. Regarding the (1) exposure routes, we reviewed the current knowledge on the occurrence of NMPs in food, beverages, personal care products and the air (focusing on indoors and workplaces) and found that the studies suggest an abundant presence of MPs within the exposure scenarios. The overall abundance of MPs in exposure matrices relevant to humans highlights the importance of understanding whether NMPs have the potential for tissue translocation. Therefore, we describe the current knowledge on the potential (2) translocation pathways of NMPs from the skin, GIT and respiratory systems to other body compartments. Here, particular attention was paid to how likely NMPs can translocate from the primary exposed organs to secondary organs due to naturally occurring defence mechanisms against tissue translocation. Based on the current understanding, we conclude that a dermal translocation of NMPs is rather unlikely. In contrast, small MPs and NPs can generally translocate from the GIT and respiratory system to other tissues. Thus, we reviewed the existing literature on the (3) fate of NMPs within the human body. Based on the current knowledge of the contamination of human exposure routes and the potential translocation mechanisms, we critically discuss the size of the detected particles reported in the fate studies. In some cases, the particles detected in human tissue samples exceed the size of a particle to overcome biological barriers allowing particle translocation into tissues. Therefore, we emphasize the importance of critically reading and discussing the presented results of NMP in human tissue samples.},
}
@article {pmid36424853,
year = {2023},
author = {Chang, J and Duong, TA and Schoeman, C and Ma, X and Roodt, D and Barker, N and Li, Z and Van de Peer, Y and Mizrachi, E},
title = {The genome of the king protea, Protea cynaroides.},
journal = {The Plant journal : for cell and molecular biology},
volume = {113},
number = {2},
pages = {262-276},
pmid = {36424853},
issn = {1365-313X},
support = {833522/ERC_/European Research Council/International ; },
mesh = {*Proteaceae/genetics ; Ecosystem ; Genomics ; South Africa ; Soil ; },
abstract = {The king protea (Protea cynaroides), an early-diverging eudicot, is the most iconic species from the Megadiverse Cape Floristic Region, and the national flower of South Africa. Perhaps best known for its iconic flower head, Protea is a key genus for the South African horticulture industry and cut-flower market. Ecologically, the genus and the family Proteaceae are important models for radiation and adaptation, particularly to soils with limited phosphorus bio-availability. Here, we present a high-quality chromosome-scale assembly of the P. cynaroides genome as the first representative of the fynbos biome. We reveal an ancestral whole-genome duplication event that occurred in the Proteaceae around the late Cretaceous that preceded the divergence of all crown groups within the family and its extant diversity in all Southern continents. The relatively stable genome structure of P. cynaroides is invaluable for comparative studies and for unveiling paleopolyploidy in other groups, such as the distantly related sister group Ranunculales. Comparative genomics in sequenced genomes of the Proteales shows loss of key arbuscular mycorrhizal symbiosis genes likely ancestral to the family, and possibly the order. The P. cynaroides genome empowers new research in plant diversification, horticulture and adaptation, particularly to nutrient-poor soils.},
}
@article {pmid36423548,
year = {2023},
author = {Wu, D and Zhao, J and Su, Y and Yang, M and Dolfing, J and Graham, DW and Yang, K and Xie, B},
title = {Explaining the resistomes in a megacity's water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria.},
journal = {Water research},
volume = {228},
number = {Pt A},
pages = {119359},
doi = {10.1016/j.watres.2022.119359},
pmid = {36423548},
issn = {1879-2448},
support = {MR/P028195/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Drinking Water ; China ; Water Supply ; Bacteria/genetics ; Anti-Bacterial Agents ; },
abstract = {Antibiotic resistance genes (ARGs) in drinking water sources suggest the possible presence of resistant microorganisms that jeopardize human health. However, explanations for the presence of specific ARGs in situ are largely unknown, especially how their prevalence is affected by local microbial ecology, taxa assembly and community-wide gene transfer. Here, we characterized resistomes and bacterial communities in the Taipu River catchment, which feeds a key drinking water reservoir to a global megacity, Shanghai. Overall, ARG abundances decreased significantly as the river flowed downstream towards the reservoir (P < 0.01), whereas the waterborne bacteria assembled deterministically (|βNRI| > 2.0) as a function of temperature and dissolved oxygen conditions with the assembly-dominant taxa (e.g. Ilumatobacteraceae and Cyanobiaceae) defining local resistomes (P < 0.01, Cohen's D = 4.22). Bacterial hosts of intragenomic ARGs stayed at the same level across the catchment (60 ∼ 70 genome copies per million reads). Among them, the putative resistant pathogens (e.g. Burkholderiaceae) carried mixtures of ARGs that exhibited high transmission probability (transfer counts = 126, P < 0.001), especially with the microbial assembly-dominant taxa. These putative resistant pathogens had densities ranging form 3.0 to 4.0 × 10[6] cell/L, which was more pronouncedly affected by resistome and microbial assembly structures than environmental factors (SEM, std-coeff β = 0.62 vs. 0.12). This work shows that microbial assembly and resistant pathogens play predominant roles in prevelance and dissemination of resistomes in receiving water, which deserves greater attention in devisng control strategies for reducing in-situ ARGs and resistant strains in a catchment.},
}
@article {pmid36423338,
year = {2022},
author = {Abera, S and Shimels, M and Tessema, T and Raaijmakers, JM and Dini-Andreote, F},
title = {Back to the roots: defining the core microbiome of Sorghum bicolor in agricultural field soils from the centre of origin.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {12},
pages = {},
doi = {10.1093/femsec/fiac136},
pmid = {36423338},
issn = {1574-6941},
mesh = {Humans ; *Sorghum ; Soil ; Plant Roots ; *Microbiota/genetics ; Rhizosphere ; Edible Grain ; },
abstract = {Sorghum is a major staple crop in sub-Saharan Africa with yields severely impacted by biotic and abiotic factors. Here, we analysed the taxonomic diversity and biogeographical distribution of bacterial taxa of 48 agricultural fields along a transect of approximately 2000 km across the Ethiopian sorghum belt, the centre of origin of sorghum. The ultimate goal is to identify-yet-unexplored-beneficial plant-microbe associations. Based on bulk soil bacterial communities and DArT-SNP analyses of 59 sorghum accessions, we selected three microbiologically distinct field soils and 12 sorghum genotypes, including commercial varieties, wild relatives, and farmer-preferred landraces. The results showed a core rhizosphere microbiome of 2125 amplicon sequence variants (ASVs), belonging to eight bacterial families consistently found across the three soil types and the 12 sorghum genotypes. Integration of the rhizosphere bacterial community analysis with DArT-SNP sorghum genotyping revealed the association of differentially abundant ASVs with sorghum genotypic traits, including the distinct recruitment of Pseudomonadaceae by the stay-green, drought-tolerant, and wild sorghum genotypes. Collectively, these results provide new insights into the core and accessory bacterial taxa in the sorghum rhizosphere in the centre of origin, setting a baseline for targeted isolation and functional characterization of putative beneficial rhizobacteria.},
}
@article {pmid36422381,
year = {2022},
author = {Cantillo-González, A and Anguita, J and Rojas, C and Vargas, IT},
title = {Winogradsky Bioelectrochemical System as a Novel Strategy to Enrich Electrochemically Active Microorganisms from Arsenic-Rich Sediments.},
journal = {Micromachines},
volume = {13},
number = {11},
pages = {},
pmid = {36422381},
issn = {2072-666X},
support = {FONDECYT 1201134//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDAP 15110020//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; },
abstract = {Bioelectrochemical systems (BESs) have been extensively studied for treatment and remediation. However, BESs have the potential to be used for the enrichment of microorganisms that could replace their natural electron donor or acceptor for an electrode. In this study, Winogradsky BES columns with As-rich sediments extracted from an Andean watershed were used as a strategy to enrich lithotrophic electrochemically active microorganisms (EAMs) on electrodes (i.e., cathodes). After 15 months, Winogradsky BESs registered power densities up to 650 μWcm[-2]. Scanning electron microscopy and linear sweep voltammetry confirmed microbial growth and electrochemical activity on cathodes. Pyrosequencing evidenced differences in bacterial composition between sediments from the field and cathodic biofilms. Six EAMs from genera Herbaspirillum, Ancylobacter, Rhodococcus, Methylobacterium, Sphingomonas, and Pseudomonas were isolated from cathodes using a lithoautotrophic As oxidizers culture medium. These results suggest that the tested Winogradsky BES columns result in an enrichment of electrochemically active As-oxidizing microorganisms. A bioelectrochemical boost of centenarian enrichment approaches, such as the Winogradsky column, represents a promising strategy for prospecting new EAMs linked with the biogeochemical cycles of different metals and metalloids.},
}
@article {pmid36421212,
year = {2022},
author = {Stoll, ML and Wang, J and Kau, CH and Pierce, MK and Morrow, CD and Geurs, NC},
title = {Pro-Inflammatory Oral Microbiota in Juvenile Spondyloarthritis: A Pilot Study.},
journal = {Children (Basel, Switzerland)},
volume = {9},
number = {11},
pages = {},
pmid = {36421212},
issn = {2227-9067},
support = {P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; P30Ar050948/NH/NIH HHS/United States ; UL1TR000165/NH/NIH HHS/United States ; },
abstract = {The role of the microbiota in the pathogenesis of arthritis is gaining increasing attention. While multiple studies have queried the intestinal microbiota, very few have analyzed the contents of the oral microbiota. In this pilot study, we obtained salivary and sub-gingival specimens from a cohort of six healthy controls and five children with well-controlled spondyloarthritis (SpA) and performed 16S sequencing on bacteria obtained from both habitats. The Quantitative Insight into Microbial Ecology tool suite was used to generate operational taxonomic units, Phyloseq was used for diversity analyses, and DeSeq2 was used to compare abundances while adjusting for multiple comparisons. A repeat specimen was obtained from one subject during a flare. Clustering based upon diagnosis was observed from both habitats, with decreased alpha diversity seen within the plaque obtained from the patients vs. controls. Among the differentially abundant taxa were statistically significantly increased plaque Fusobacterium and salivary Rothia mucilaginosa among the patients compared to the controls. Additionally, the abundance of plaque Fusobacterium increased in one patient at the time of a flare. Our data suggest that the oral cavity may harbor bacteria involved in the pathogenesis of spondyloarthritis; additional studies are warranted.},
}
@article {pmid36419905,
year = {2023},
author = {Zhang, X and Arbour, T and Zhang, D and Wei, S and Rabaey, K},
title = {Microbial electrosynthesis of acetate from CO2 under hypersaline conditions.},
journal = {Environmental science and ecotechnology},
volume = {13},
number = {},
pages = {100211},
pmid = {36419905},
issn = {2666-4984},
abstract = {Microbial electrosynthesis (MES) enables the bioproduction of multicarbon compounds from CO2 using electricity as the driver. Although high salinity can improve the energetic performance of bioelectrochemical systems, acetogenic processes under elevated salinity are poorly known. Here MES under 35-60 g L[-1] salinity was evaluated. Acetate production in two-chamber MES systems at 35 g L[-1] salinity (seawater composition) gradually decreased within 60 days, both under -1.2 V cathode potential (vs. Ag/AgCl) and -1.56 A m[-2] reductive current. Carbonate precipitation on cathodes (mostly CaCO3) likely declined the production through inhibiting CO2 supply, the direct electrode contact for acetogens and H2 production. Upon decreasing Ca[2+] and Mg[2+] levels in three-chamber reactors, acetate was stably produced over 137 days along with a low cathode apparent resistance at 1.9 ± 0.6 mΩ m[2] and an average production rate at 3.80 ± 0.21 g m[-2] d[-1]. Increasing the salinity step-wise from 35 to 60 g L[-1] gave the most efficient acetate production at 40 g L[-1] salinity with average rates of acetate production and CO2 consumption at 4.56 ± 3.09 and 7.02 ± 4.75 g m[-2] d[-1], respectively. The instantaneous coulombic efficiency for VFA averaged 55.1 ± 31.4%. Acetate production dropped at higher salinity likely due to the inhibited CO2 dissolution and acetogenic metabolism. Acetobacterium up to 78% was enriched on cathodes as the main acetogen at 35 g L[-1]. Under high-salinity selection, 96.5% Acetobacterium dominated on the cathode along with 34.0% Sphaerochaeta in catholyte. This research provides a first proof of concept that MES starting from CO2 reduction can be achieved at elevated salinity.},
}
@article {pmid36419170,
year = {2022},
author = {Chang, J and Tian, L and Leite, MFA and Sun, Y and Shi, S and Xu, S and Wang, J and Chen, H and Chen, D and Zhang, J and Tian, C and Kuramae, EE},
title = {Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {196},
pmid = {36419170},
issn = {2049-2618},
mesh = {*Oryza/microbiology ; Nitrogen ; Carbon ; Manganese ; Iron ; Bacteria/genetics ; Soil ; },
abstract = {BACKGROUND: The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome.<br><br>RESULTS: Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots.<br><br>CONCLUSION: We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera. Video Abstract.},
}
@article {pmid36415023,
year = {2022},
author = {Baumgartner, M and Zirnbauer, R and Schlager, S and Mertens, D and Gasche, N and Sladek, B and Herbold, C and Bochkareva, O and Emelianenko, V and Vogelsang, H and Lang, M and Klotz, A and Moik, B and Makristathis, A and Berry, D and Dabsch, S and Khare, V and Gasche, C},
title = {Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2143218},
pmid = {36415023},
issn = {1949-0984},
mesh = {Humans ; *Enteropathogenic Escherichia coli/genetics ; *Colitis, Ulcerative ; *Escherichia coli Infections ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases ; },
abstract = {With increasing urbanization and industrialization, the prevalence of inflammatory bowel diseases (IBDs) has steadily been rising over the past two decades. IBD involves flares of gastrointestinal (GI) inflammation accompanied by microbiota perturbations. However, microbial mechanisms that trigger such flares remain elusive. Here, we analyzed the association of the emerging pathogen atypical enteropathogenic E. coli (aEPEC) with IBD disease activity. The presence of diarrheagenic E. coli was assessed in stool samples from 630 IBD patients and 234 age- and sex-matched controls without GI symptoms. Microbiota was analyzed with 16S ribosomal RNA gene amplicon sequencing, and 57 clinical aEPEC isolates were subjected to whole-genome sequencing and in vitro pathogenicity experiments including biofilm formation, epithelial barrier function and the ability to induce pro-inflammatory signaling. The presence of aEPEC correlated with laboratory, clinical and endoscopic disease activity in ulcerative colitis (UC), as well as microbiota dysbiosis. In vitro, aEPEC strains induce epithelial p21-activated kinases, disrupt the epithelial barrier and display potent biofilm formation. The effector proteins espV and espG2 distinguish aEPEC cultured from UC and Crohn's disease patients, respectively. EspV-positive aEPEC harbor more virulence factors and have a higher pro-inflammatory potential, which is counteracted by 5-ASA. aEPEC may tip a fragile immune-microbiota homeostasis and thereby contribute to flares in UC. aEPEC isolates from UC patients display properties to disrupt the epithelial barrier and to induce pro-inflammatory signaling in vitro.},
}
@article {pmid36413896,
year = {2023},
author = {Mijnendonckx, K and Rogiers, T and Giménez Del Rey, FJ and Merroun, ML and Williamson, A and Ali, MM and Charlier, D and Leys, N and Boon, N and Van Houdt, R},
title = {PrsQ2, a small periplasmic protein involved in increased uranium resistance in the bacterium Cupriavidus metallidurans.},
journal = {Journal of hazardous materials},
volume = {444},
number = {Pt A},
pages = {130410},
doi = {10.1016/j.jhazmat.2022.130410},
pmid = {36413896},
issn = {1873-3336},
mesh = {*Uranium/toxicity ; *Cupriavidus/genetics ; Uranyl Nitrate ; Acclimatization ; },
abstract = {Uranium contamination is a widespread problem caused by natural and anthropogenic activities. Although microorganisms thrive in uranium-contaminated environments, little is known about the actual molecular mechanisms mediating uranium resistance. Here, we investigated the resistance mechanisms driving the adaptation of Cupriavidus metallidurans NA4 to toxic uranium concentrations. We selected a spontaneous mutant able to grow in the presence of 1 mM uranyl nitrate compared to 250 µM for the parental strain. The increased uranium resistance was acquired via the formation of periplasmic uranium-phosphate precipitates facilitated by the increased expression of a genus-specific small periplasmic protein, PrsQ2, regulated as non-cognate target of the CzcS2-CzcR2 two-component system. This study shows that bacteria can adapt to toxic uranium concentrations and explicates the complete genetic circuit behind the adaptation.},
}
@article {pmid36413834,
year = {2023},
author = {Páez-Watson, T and van Loosdrecht, MCM and Wahl, SA},
title = {Predicting the impact of temperature on metabolic fluxes using resource allocation modelling: Application to polyphosphate accumulating organisms.},
journal = {Water research},
volume = {228},
number = {Pt A},
pages = {119365},
doi = {10.1016/j.watres.2022.119365},
pmid = {36413834},
issn = {1879-2448},
mesh = {Temperature ; *Polyphosphates ; *Resource Allocation ; Biomass ; Sewage ; },
abstract = {The understanding of microbial communities and the biological regulation of its members is crucial for implementation of novel technologies using microbial ecology. One poorly understood metabolic principle of microbial communities is resource allocation and biosynthesis. Resource allocation theory in polyphosphate accumulating organisms (PAOs) is limited as a result of their slow imposed growth rate (typical sludge retention times of at least 4 days) and limitations to quantify changes in biomass components over a 6 hours cycle (less than 10% of their growth). As a result, there is no direct evidence supporting that biosynthesis is an exclusive aerobic process in PAOs that alternate continuously between anaerobic and aerobic phases. Here, we apply resource allocation metabolic flux analysis to study the optimal phenotype of PAOs over a temperature range of 4 °C to 20 °C. The model applied in this research allowed to identify optimal metabolic strategies in a core metabolic model with limited constraints based on biological principles. The addition of a constraint limiting biomass synthesis to be an exclusive aerobic process changed the metabolic behaviour and improved the predictability of the model over the studied temperature range by closing the gap between prediction and experimental findings. The results validate the assumption of limited anaerobic biosynthesis in PAOs, specifically "Candidatus Accumulibacter" related species. Interestingly, the predicted growth yield was lower, suggesting that there are mechanistic barriers for anaerobic growth not yet understood nor reflected in the current models of PAOs. Moreover, we identified strategies of resource allocation applied by PAOs at different temperatures as a result of the decreased catalytic efficiencies of their biochemical reactions. Understanding resource allocation is paramount in the study of PAOs and their currently unknown complex metabolic regulation, and metabolic modelling based on biological first principles provides a useful tool to develop a mechanistic understanding.},
}
@article {pmid36410318,
year = {2023},
author = {Kelly, LC and Rivett, DW and Pakostova, E and Creer, S and Cotterell, T and Johnson, DB},
title = {Mineralogy affects prokaryotic community composition in an acidic metal mine.},
journal = {Microbiological research},
volume = {266},
number = {},
pages = {127257},
doi = {10.1016/j.micres.2022.127257},
pmid = {36410318},
issn = {1618-0623},
mesh = {*Archaea ; Acids/metabolism ; Bacteria ; *Microbiota ; Sulfides/metabolism ; Minerals/metabolism ; },
abstract = {The microbial ecology of acidic mine and sulfide cave ecosystems is well characterised with respect to aquatic communities, typically revealing low taxonomic complexity and dominance by a relatively limited number of cosmopolitan acidophilic bacterial and archaeal taxa. Whilst pH, temperature, and geochemistry are recognised drivers of diversity in these ecosystems, the specific question of a possible influence of substratum mineralogy on microbial community composition remains unanswered. Here we address this void, using 81 subterranean mineral samples from a low temperature abandoned, acidic, sulfide ore mine system at Mynydd Parys (Parys Mountain in English), Wales, UK. Four primary and 15 secondary minerals were identified via x-ray diffraction, each sample containing a maximum of five and an average of two minerals. The mineralogy of primary (e.g. pyrite and quartz) and secondary (e.g. melanterite and pisanite) minerals was significantly correlated with prokaryotic community structure at multiple taxonomic levels, implying that the mineralosphere effect reported in less extreme terrestrial environments is also implicated in driving prokaryotic community composition in extremely acidic, base metal-bearing sulfide mineralisation at Mynydd Parys. Twenty phyla were identified, nine of which were abundant (mean relative abundance >1%). While taxa characteristic of acidic mines were detected, for example Leptospirillum (phylum Nitrospirae), Acidithiobacillus (phylum Proteobacteria), Sulfobacillus (phylum Firmicutes) and Ferroplasma (phylum Euryarchaeota), their abundance in individual samples was highly variable. Indeed, in the majority of the 81 samples investigated the abundance of these and other typical acidic mine taxa was low, with 25% of samples devoid of sequences from recognised acidic mine taxa. Most notable amongst the bacterial taxa not previously reported in such environments were the recently cultivated Muribaculaceae family (phylum Bacteroidetes), which often dominated Mynydd Parys samples regardless of their mineralogical content. Our results pose further questions regarding the mechanisms by which taxa not previously reported in such extreme environments appear to survive in Mynydd Parys, opening up research pathways for exploring the biodiversity drivers underlying microbial community composition and function in extremely acidic mine environments.},
}
@article {pmid36409329,
year = {2023},
author = {Changey, F and Aissaoui, G and Plain, C and Ranger, J and Legout, A and Zeller, B and Epron, D and Lerch, TZ},
title = {Prolonged Effect of Forest Soil Compaction on Methanogen and Methanotroph Seasonal Dynamics.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1447-1452},
pmid = {36409329},
issn = {1432-184X},
support = {12-60-C0057//ADEME- REACTIF program/ ; },
mesh = {*Soil ; Seasons ; Bacteria/genetics ; Oxidation-Reduction ; *Euryarchaeota ; Forests ; Methane ; Soil Microbiology ; },
abstract = {Methane (CH4) oxidation by methanotrophic bacteria in forest soils is the largest biological sink for this greenhouse gas on earth. However, the compaction of forest soils by logging traffic has previously been shown to reduce the potential rate of CH4 uptake. This change could be due to not only a decrease of methanotrophs but also an increase in methanogen activity. In this study, we investigated whether the decrease in CH4 uptake by forest soils, subjected to compaction by heavy machinery 7 years earlier, can be explained by quantitative and qualitative changes in methanogenic and methanotrophic communities. We measured the functional gene abundance and polymorphism of CH4 microbial oxidizers (pmoA) and producers (mcrA) at different depths and during different seasons. Our results revealed that the soil compaction effect on the abundance of both genes depended on season and soil depth, contrary to the effect on gene polymorphism. Bacterial pmoA abundance was significantly lower in the compacted soil than in the controls across all seasons, except in winter in the 0-10 cm depth interval and in summer in the 10-20 cm depth interval. In contrast, archaeal mcrA abundance was higher in compacted than control soil in winter and autumn in the two soil depths investigated. This study shows the usefulness of using pmoA and mcrA genes simultaneously in order to better understand the spatial and temporal variations of soil CH4 fluxes and the potential effect of physical disturbances.},
}
@article {pmid36407791,
year = {2022},
author = {Rawat, D and Sharma, U and Poria, P and Finlan, A and Parker, B and Sharma, RS and Mishra, V},
title = {Iron-dependent mutualism between Chlorella sorokiniana and Ralstonia pickettii forms the basis for a sustainable bioremediation system.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {83},
pmid = {36407791},
issn = {2730-6151},
support = {2021_BPS_0039//British Phycological Society (BPS)/ ; 345775672//Newton Fund/ ; },
abstract = {Phototrophic communities of autotrophic microalgae and heterotrophic bacteria perform complex tasks of nutrient acquisition and tackling environmental stress but remain underexplored as a basis for the bioremediation of emerging pollutants. In industrial monoculture designs, poor iron uptake by microalgae limits their productivity and biotechnological efficacy. Iron supplementation is expensive and ineffective because iron remains insoluble in an aqueous medium and is biologically unavailable. However, microalgae develop complex interkingdom associations with siderophore-producing bacteria that help solubilize iron and increase its bioavailability. Using dye degradation as a model, we combined environmental isolations and synthetic ecology as a workflow to design a simplified microbial community based on iron and carbon exchange. We established a mutualism between the previously non-associated alga Chlorella sorokiniana and siderophore-producing bacterium Ralstonia pickettii. Siderophore-mediated increase in iron bioavailability alleviated Fe stress for algae and increased the reductive iron uptake mechanism and bioremediation potential. In exchange, C. sorokiniana produced galactose, glucose, and mannose as major extracellular monosaccharides, supporting bacterial growth. We propose that extracellular iron reduction by ferrireductase is crucial for azoreductase-mediated dye degradation in microalgae. These results demonstrate that iron bioavailability, often overlooked in cultivation, governs microalgal growth, enzymatic processes, and bioremediation potential. Our results suggest that phototrophic communities with an active association for iron and carbon exchange have the potential to overcome challenges associated with micronutrient availability, while scaling up bioremediation designs.},
}
@article {pmid36406446,
year = {2022},
author = {Guo, R and Ma, X and Zhang, J and Liu, C and Thu, CA and Win, TN and Aung, NL and Win, HS and Naing, S and Li, H and Zhou, F and Wang, P},
title = {Microbial community structures and important taxa across oxygen gradients in the Andaman Sea and eastern Bay of Bengal epipelagic waters.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1041521},
pmid = {36406446},
issn = {1664-302X},
abstract = {In oceanic oxygen minimum zones (OMZs), the abundances of aerobic organisms significantly decrease and energy shifts from higher trophic levels to microorganisms, while the microbial communities become critical drivers of marine biogeochemical cycling activities. However, little is known of the microbial ecology of the Andaman Sea and eastern Bay of Bengal (BoB) OMZs. In the present study, a total of 131 samples which from the Andaman Sea and eastern BoB epipelagic waters were analyzed. The microbial community distribution patterns across oxygen gradients, including oxygenic zones (OZs, dissolved oxygen [DO] ≥ 2 mg/L), oxygen limited zones (OLZs, 0.7 mg/L < DO < 2 mg/L), and OMZs (DO ≤ 0.7 mg/L), were investigated. Mantel tests and Spearman's correlation analysis revealed that DO was the most important driver of microbial community structures among several environmental factors. Microbial diversity, richness, and evenness were highest in the OLZs and lowest in the OZs. The microbial community compositions of OZ and OMZ waters were significantly different. Random forest analysis revealed 24 bioindicator taxa that differentiated OZ, OLZ, and OMZ water communities. These bioindicator taxa included Burkholderiaceae, HOC36, SAR11 Clade IV, Thioglobaceae, Nitrospinaceae, SAR86, and UBA10353. Further, co-occurrence network analysis revealed that SAR202, AEGEAN-169, UBA10353, SAR406, and Rhodobacteraceae were keystone taxa among the entire interaction network of the microbial communities. Functional prediction further indicated that the relative abundances of microbial populations involved in nitrogen and sulfur cycling were higher in OMZs. Several microbial taxa, including the Thioglobaceae, Nitrospinaceae, SAR202, SAR406, WPS-2, UBA10353, and Woeseiaceae, may be involved in nitrogen and/or sulfur cycling, while also contributing to oxygen consumption in these waters. This study consequently provides new insights into the microbial community structures and potentially important taxa that contribute to oxygen consumption in the Andaman Sea and eastern BoB OMZ.},
}
@article {pmid36401317,
year = {2022},
author = {Nata'ala, MK and Avila Santos, AP and Coelho Kasmanas, J and Bartholomäus, A and Saraiva, JP and Godinho Silva, S and Keller-Costa, T and Costa, R and Gomes, NCM and Ponce de Leon Ferreira de Carvalho, AC and Stadler, PF and Sipoli Sanches, D and Nunes da Rocha, U},
title = {MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {57},
pmid = {36401317},
issn = {2524-6372},
support = {VH-NG-1248 Micro 'Big Data'//Hemlholtz Association/ ; 460129525//Deutsche Forschungsgemeinschaft/ ; 91759074//Petroleum Trust Development Fund, Nigeria/ ; 91759074//Deutscher Akademischer Austauschdienst/ ; },
abstract = {BACKGROUND: Metagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. However, data mining and interpretation can be challenging due to mis-annotated and misleading metadata entries. In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. To this end, we have manually curated the associated metadata of several thousands of microbial metagenomes currently deposited at SRA and MG-RAST.<br><br>RESULTS: In total, 125 terms were curated according to 17 different classes (e.g., biome, material, oceanic zone, geographic feature&#xa0;and oceanographic phenomena). Other standardized features include sample attributes (e.g., salinity, depth), sample location (e.g., latitude, longitude), and sequencing features (e.g., sequencing platform, sequence count). MarineMetagenomeDB version 1.0 contains 11,449 marine metagenomes from SRA and MG-RAST distributed across all oceans and several seas. Most samples were sequenced using Illumina sequencing technology (84.33%). More than 55% of the samples were collected from the Pacific and the Atlantic Oceans. About 40% of the samples had their biomes assigned as 'ocean'. The 'Quick Search' and 'Advanced Search' tabs allow users to use different filters to select samples of interest dynamically in the web app. The interactive map allows the visualization of samples based on their location on the world map. The web app is also equipped with a novel download tool (on both Windows and Linux operating systems), that allows easy download of raw sequence data of selected samples from their respective repositories. As a use case, we demonstrated how to use the&#xa0;MarineMetagenomeDB web app to select estuarine metagenomes for&#xa0;potential large-scale microbial biogeography studies.<br><br>CONCLUSION: The MarineMetagenomeDB is a powerful resource for non-bioinformaticians to find marine metagenome samples with curated metadata and stimulate meta-studies involving marine microbiomes. Our user-friendly web app is publicly available at https://webapp.ufz.de/marmdb/ .},
}
@article {pmid36400616,
year = {2023},
author = {Secchi, G and Amalfitano, N and Carafa, I and Franciosi, E and Gallo, L and Schiavon, S and Sturaro, E and Tagliapietra, F and Bittante, G},
title = {Milk metagenomics and cheese-making properties as affected by indoor farming and summer highland grazing.},
journal = {Journal of dairy science},
volume = {106},
number = {1},
pages = {96-116},
doi = {10.3168/jds.2022-22449},
pmid = {36400616},
issn = {1525-3198},
mesh = {Female ; Humans ; Cattle ; Animals ; *Cheese/analysis ; Milk ; Farms ; Metagenomics ; Agriculture ; },
abstract = {The study of the complex relationships between milk metagenomics and milk composition and cheese-making efficiency as affected by indoor farming and summer highland grazing was the aim of the present work. The experimental design considered monthly sampling (over 5 mo) of the milk produced by 12 Brown Swiss cows divided into 2 groups: the first remained on a lowland indoor farm from June to October, and the second was moved to highland pastures in July and then returned to the lowland farm in September. The resulting 60 milk samples (2 kg each) were used to analyze milk composition, milk coagulation, curd firming, and syneresis processes, and to make individual model cheeses to measure cheese yields and nutrient recoveries in the cheese. After DNA extraction and Illumina Miseq sequencing, milk microbiota amplicons were also processed by means of an open-source pipeline called Quantitative Insights Into Microbial Ecology (Qiime2, version 2018.2; https://qiime2.org). Out of a total of 44 taxa analyzed, 13 bacterial taxa were considered important for the dairy industry (lactic acid bacteria, LAB, 5 taxa; and spoilage bacteria, 4) and for human (other probiotics, 2) and animal health (pathogenic bacteria, 2). The results revealed the transhumant group of cows transferred to summer highland pastures showed an increase in almost all the LAB taxa, bifidobacteria, and propionibacteria, and a reduction in spoilage taxa. All the metagenomic changes disappeared when the transhumant cows were moved back to the permanent indoor farm. The relationships between 17 microbial traits and 30 compositional and technological milk traits were investigated through analysis of correlation and latent explanatory factor analysis. Eight latent factors were identified, explaining 75.3% of the total variance, 2 of which were mainly based on microbial traits: pro-dairy bacteria (14% of total variance, improving during summer pasturing) and pathogenic bacteria (6.0% of total variance). Some bacterial traits contributed to other compositional-technological latent factors (gelation, udder health, and caseins).},
}
@article {pmid36399842,
year = {2022},
author = {Li, Y and Ling, J and Xue, J and Huang, J and Zhou, X and Wang, F and Hou, W and Zhao, J and Xu, Y},
title = {Acute stress of the typical disinfectant glutaraldehyde-didecyldimethylammonium bromide (GD) on sludge microecology in livestock wastewater treatment plants: Effect and its mechanisms.},
journal = {Water research},
volume = {227},
number = {},
pages = {119342},
doi = {10.1016/j.watres.2022.119342},
pmid = {36399842},
issn = {1879-2448},
mesh = {Swine ; Animals ; Sewage ; *Disinfectants/pharmacology ; Glutaral/pharmacology ; Livestock ; *African Swine Fever ; Reactive Oxygen Species ; *COVID-19 ; *Water Purification ; Nitrogen ; },
abstract = {Glutaraldehyde and didecyldimethylammonium bromide (GD) is a disinfectant widely used to prevent African swine fever (ASF) in livestock farms. However, the effect of residual GD on the activated sludge microbial ecology of receiving wastewater treatment plants (WWTPs) remains largely unknown. In this study, seven simulated systems were established to research the effects of GD on WWTPs and reveal the underlying mechanisms of microecological responses to GD at different concentrations. Both the nitrogen and carbon removal rates decreased with increasing GD concentrations, and nitrogen metabolism was inhibited more obviously, but the inhibition weakened with increasing stress duration. Microorganisms activated their SoxRS systems to promote ATP synthesis and electron transfer to support the hydrolysis and efflux of GD by producing a small number of ROS when exposed to GD at less than 1 mg/L. The overproduction of ROS led to a decrease of antioxidant and nitrogen removal enzyme activities, and upregulation of the porin gene increased the risk of GD entering the intracellular space upon exposure to GD at concentrations higher than 1 mg/L. Some denitrifiers survived via resistance and their basic capabilities of sugar metabolism and nitrogen assimilation. Notably, low concentrations of disinfectants could promote vertical and horizontal transfer of multiple resistance genes, especially aminoglycosides, among microorganisms, which might increase not only the adaptation capability of denitrifiers but also the risk to ecological systems. Therefore, the risks of disinfectants targeting ASF on ecology and health as well as the effects of disinfectant residuals from the COVID-19 epidemic should receive more attention.},
}
@article {pmid36399746,
year = {2022},
author = {Sinclair, P and Brackley, CA and Carballo-Pacheco, M and Allen, RJ},
title = {Model for Quorum-Sensing Mediated Stochastic Biofilm Nucleation.},
journal = {Physical review letters},
volume = {129},
number = {19},
pages = {198102},
doi = {10.1103/PhysRevLett.129.198102},
pmid = {36399746},
issn = {1079-7114},
mesh = {*Quorum Sensing ; *Biofilms ; Bacteria ; },
abstract = {Surface-attached bacterial biofilms cause disease and industrial biofouling, as well as being widespread in the natural environment. Density-dependent quorum sensing is one of the mechanisms implicated in biofilm initiation. Here we present and analyze a model for quorum-sensing triggered biofilm initiation. In our model, individual, planktonic bacteria adhere to a surface, proliferate, and undergo a collective transition to a biofilm phenotype. This model predicts a stochastic transition between a loosely attached, finite layer of bacteria near the surface and a growing biofilm. The transition is governed by two key parameters: the collective transition density relative to the carrying capacity and the immigration rate relative to the detachment rate. Biofilm initiation is complex, but our model suggests that stochastic nucleation phenomena may be relevant.},
}
@article {pmid36399658,
year = {2022},
author = {Simmer, RA and Schnoor, JL},
title = {Phytoremediation, Bioaugmentation, and the Plant Microbiome.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {23},
pages = {16602-16610},
pmid = {36399658},
issn = {1520-5851},
support = {P30 ES005605/ES/NIEHS NIH HHS/United States ; },
mesh = {Biodegradation, Environmental ; *Soil Pollutants/metabolism ; Plants/metabolism ; Soil ; *Microbiota ; },
abstract = {Understanding plant biology and related microbial ecology as a means to phytoremediate soil and groundwater contamination has broadened and advanced the field of environmental engineering and science over the past 30 years. Using plants to transform and degrade xenobiotic organic pollutants delivers new methods for environmental restoration. Manipulations of the plant microbiome through bioaugmentation, endophytes, adding various growth factors, genetic modification, and/or selecting the microbial community via insertion of probiotics or phages for gene transfer are future areas of research to further expand this green, cost-effective, aesthetically pleasing technology─phytoremediation.},
}
@article {pmid36399496,
year = {2023},
author = {Terlouw, BR and Blin, K and Navarro-Muñoz, JC and Avalon, NE and Chevrette, MG and Egbert, S and Lee, S and Meijer, D and Recchia, MJJ and Reitz, ZL and van Santen, JA and Selem-Mojica, N and Tørring, T and Zaroubi, L and Alanjary, M and Aleti, G and Aguilar, C and Al-Salihi, SAA and Augustijn, HE and Avelar-Rivas, JA and Avitia-Domínguez, LA and Barona-Gómez, F and Bernaldo-Agüero, J and Bielinski, VA and Biermann, F and Booth, TJ and Carrion Bravo, VJ and Castelo-Branco, R and Chagas, FO and Cruz-Morales, P and Du, C and Duncan, KR and Gavriilidou, A and Gayrard, D and Gutiérrez-García, K and Haslinger, K and Helfrich, EJN and van der Hooft, JJJ and Jati, AP and Kalkreuter, E and Kalyvas, N and Kang, KB and Kautsar, S and Kim, W and Kunjapur, AM and Li, YX and Lin, GM and Loureiro, C and Louwen, JJR and Louwen, NLL and Lund, G and Parra, J and Philmus, B and Pourmohsenin, B and Pronk, LJU and Rego, A and Rex, DAB and Robinson, S and Rosas-Becerra, LR and Roxborough, ET and Schorn, MA and Scobie, DJ and Singh, KS and Sokolova, N and Tang, X and Udwary, D and Vigneshwari, A and Vind, K and Vromans, SPJM and Waschulin, V and Williams, SE and Winter, JM and Witte, TE and Xie, H and Yang, D and Yu, J and Zdouc, M and Zhong, Z and Collemare, J and Linington, RG and Weber, T and Medema, MH},
title = {MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D603-D610},
pmid = {36399496},
issn = {1362-4962},
support = {F32 AT011475/AT/NCCIH NIH HHS/United States ; R01 AI155694/AI/NIAID NIH HHS/United States ; U24 AT010811/AT/NCCIH NIH HHS/United States ; },
mesh = {*Genomics ; *Genome ; Multigene Family ; Biosynthetic Pathways/genetics ; },
abstract = {With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.},
}
@article {pmid36399337,
year = {2023},
author = {Janssen, K and Krasenbrink, J and Strangfeld, S and Kroheck, S and Josten, M and Engeser, M and Bierbaum, G},
title = {Elucidation of the Bridging Pattern of the Lantibiotic Pseudomycoicidin.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {24},
number = {2},
pages = {e202200540},
pmid = {36399337},
issn = {1439-7633},
mesh = {*Bacteriocins/chemistry ; *Methicillin-Resistant Staphylococcus aureus ; Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology/chemistry ; Sulfides ; Disulfides ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {Lantibiotics are post-translationally modified antibiotic peptides with lanthionine thioether bridges that represent potential alternatives to conventional antibiotics. The lantibiotic pseudomycoicidin is produced by Bacillus pseudomycoides DSM 12442 and is effective against many Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. While prior work demonstrated that pseudomycoicidin possesses one disulfide bridge and four thioether bridges, the ring topology has so far remained unclear. Here, we analyzed several pseudomycoicidin analogues that are affected in ring formation via MALDI-TOF-MS and tandem mass spectrometry with regard to their dehydration and fragmentation patterns, respectively. As a result, we propose a bridging pattern involving Thr8 and Cys13, Thr10 and Cys16, Ser18 and Cys21, and Ser20 and Cys26, thus, forming two double ring systems. Additionally, we localized the disulfide bridge to connect Cys3 and Cys7 and, therefore, fully elucidated the bridging pattern of pseudomycoicidin.},
}
@article {pmid36396943,
year = {2022},
author = {Minich, JJ and Härer, A and Vechinski, J and Frable, BW and Skelton, ZR and Kunselman, E and Shane, MA and Perry, DS and Gonzalez, A and McDonald, D and Knight, R and Michael, TP and Allen, EE},
title = {Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6978},
pmid = {36396943},
issn = {2041-1723},
support = {T32 GM139790/GM/NIGMS NIH HHS/United States ; P01 ES021921/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; Biomass ; *Fishes ; Ecology ; *Microbiota ; Gills ; Vertebrates ; Mammals ; },
abstract = {Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, representing ~25% of local marine fish diversity. We compare alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces. We show that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes. Patterns of phylosymbiosis are observed across the gill, skin and hindgut. In a quantitative synthesis of vertebrate hindguts (569 species), we also show that mammals have the highest gamma diversity when controlling for host species number while fishes have the highest percent of unique microbial taxa. The composite dataset will be useful to vertebrate microbiota researchers and fish biologists interested in microbial ecology, with applications in aquaculture and fisheries management.},
}
@article {pmid36388928,
year = {2022},
author = {Plunder, S and Burkard, M and Lauer, UM and Venturelli, S and Marongiu, L},
title = {Determination of phage load and administration time in simulated occurrences of antibacterial treatments.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {1040457},
pmid = {36388928},
issn = {2296-858X},
abstract = {The use of phages as antibacterials is becoming more and more common in Western countries. However, a successful phage-derived antibacterial treatment needs to account for additional features such as the loss of infective virions and the multiplication of the hosts. The parameters critical inoculation size (V F) and failure threshold time (T F) have been introduced to assure that the viral dose (V ϕ) and administration time (T ϕ) would lead to the extinction of the targeted bacteria. The problem with the definition of V F and T F is that they are non-linear equations with two unknowns; thus, obtaining their explicit values is cumbersome and not unique. The current study used machine learning to determine V F and T F for an effective antibacterial treatment. Within these ranges, a Pareto optimal solution of a multi-criterial optimization problem (MCOP) provided a pair of V ϕ and T ϕ to facilitate the user's work. The algorithm was tested on a series of in silico microbial consortia that described the outgrowth of a species at high cell density by another species initially present at low concentration. The results demonstrated that the MCOP-derived pairs of V ϕ and T ϕ could effectively wipe out the bacterial target within the context of the simulation. The present study also introduced the concept of mediated phage therapy, where targeting booster bacteria might decrease the virulence of a pathogen immune to phagial infection and highlighted the importance of microbial competition in attaining a successful antibacterial treatment. In summary, the present work developed a novel method for investigating phage/bacteria interactions that can help increase the effectiveness of the application of phages as antibacterials and ease the work of microbiologists.},
}
@article {pmid36386706,
year = {2022},
author = {Zhao, M and Zhang, H and Pan, G and Yin, H and Sun, J and Yu, Z and Bai, C and Xue, Y},
title = {Effect of exogenous microorganisms on the fermentation quality, nitrate degradation and bacterial community of sorghum-sudangrass silage.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1052837},
pmid = {36386706},
issn = {1664-302X},
abstract = {This study aims to investigate the effects of adding Lactobacillus buchneri (LB), Lactobacillus brevis (LBR) and Bacillus subtilis (BS) on the fermentation quality, nitrate degradation and bacterial community of sorghum-sudangrass silage. The results showed that the addition of LB significantly increased the pH and acetic acid content (p < 0.05), but high-quality silage was obtained. The addition of LBR and BS improved the fermentation quality of sorghum-sudangrass silage. The use of additives reduced the nitrate content in sorghum-sudangrass silage. The LB group increased the release of N2O at 3-7 days of ensiling (p < 0.05), and LBR and BS increased the release of N2O at 1-40 days of ensiling (p < 0.05). On the first day of ensiling, all silages were dominated by Weisslla, over 3 days of ensiling all silages were dominated by Lactobacillus. Acinetobacter, Serratia, Aquabacterium, and unclassified_f_enterobacteriaceae showed significant negative correlations with nitrate degradation during sorghum-sudangrass ensiling (p < 0.05). The BS and LBR groups increased the metabolic abundance of denitrification, dissimilatory nitrate reduction, and assimilatory nitrate reduction (p < 0.05). Overall, the additive ensures the fermentation quality of sorghum-sudangrass silage and promotes the degradation of nitrate by altering the bacterial community.},
}
@article {pmid36386657,
year = {2022},
author = {Liu, J and Wang, X and Liu, J and Liu, X and Zhang, XH and Liu, J},
title = {Comparison of assembly process and co-occurrence pattern between planktonic and benthic microbial communities in the Bohai Sea.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1003623},
pmid = {36386657},
issn = {1664-302X},
abstract = {Unraveling the mechanisms structuring microbial community is a central goal in microbial ecology, but a detailed understanding of how community assembly processes relate to living habitats is still lacking. Here, via 16S rRNA gene amplicon sequencing, we investigated the assembly process of microbial communities in different habitats [water verse sediment, free-living (FL) verse particle-associated (PA)] and their impacts on the inter-taxa association patterns in the coastal Bohai Sea, China. The results showed clear differences in the composition and diversity of microbial communities among habitats, with greater dissimilarities between water column and sediment than between FL and PA communities. The microbial community assembly was dominated by dispersal limitation, ecological drift, and homogeneous selection, but their relative importance varied in different habitats. The planktonic communities were mainly shaped by dispersal limitation and ecological drift, whereas homogeneous selection played a more important role in structuring the benthic communities. Furthermore, the assembly mechanisms differed between FL and PA communities, especially in the bottom water with a greater effect of ecological drift and dispersal limitation on the FL and PA fractions, respectively. Linking assembly process to co-occurrence pattern showed that the relative contribution of deterministic processes (mainly homogeneous selection) increased under closer co-occurrence relationships. By contrast, stochastic processes exerted a higher effect when there were less inter-taxa connections. Overall, our findings demonstrate contrasting ecological processes underpinning microbial community distribution in different habitats including different lifestyles, which indicate complex microbial dynamic patterns in coastal systems with high anthropogenic perturbations.},
}
@article {pmid36386638,
year = {2022},
author = {Djeni, TN and Keisam, S and Kouame, KH and Assohoun-Djeni, CN and Ake, FDM and Amoikon, LST and Tuikhar, N and Labala, RK and Dje, MK and Jeyaram, K},
title = {Dynamics of microbial populations and metabolites of fermenting saps throughout tapping process of ron and oil palm trees in Côte d'Ivoire.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {954917},
pmid = {36386638},
issn = {1664-302X},
abstract = {Palm wine fermentation is a complex microbial process that evolves with tapping times. The dynamics in microbiota and metabolites throughout palm wine tapping days is still not established, which are critical for the distinctive characteristics of palm wine taste and quality, and thus the mastery of the daily quality fluctuation during tapping. We analyzed the changes in microbial community structure by amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region, and metabolite profile changes using mass spectrometry in palm wine collected over 25-30 days tapping of ron (Borassus aethiopum) and oil palms (Elaeis guineensis) from Côte d'Ivoire. The stage-wise collected palm wine samples showed distinct changes in microbial diversity and pH, supporting microbial community dynamics during palm wine tapping. Results highlighted the dominance of Saccharomyces cerevisiae in early stages and the emergence of non-Saccharomyces yeasts, particularly Hanseniaspora spp. in the later stages of oil palm wine tapping, vice versa in the case of ron palm wine tapping, with a unique presence of Saccharomycodes in the later stages (15-30 days). Fructophilic lactic acid bacteria (FLAB), mainly Fructobacillus and Leuconostoc, encountered in both types of palm wine tapping showed a decline at later stages of oil palm wine tapping. In this type of palm wine, acetic acid bacteria with genera Acetobacter and Glucanoacetobacter, by surpassing Lactobacillus in the last stage become dominant, whereas Lactobacillus remained dominant in ron palm wine throughout tapping days. The decline in the relative abundance of gevotroline and essential amino acids during the later stages of palm wine tapping (15-25 days) supports the difference in the health benefits of the palm wine obtained from different days of tapping, indicating that early stages of tapping is more nutritional and healthy than the later stages. The microbial dynamics may be a potential indicator of metabolite changes during palm sap fermentation, thus contributing to establish particular features of palm wines in different stages of tapping. This understanding of microbial ecology and chemical composition changes during palm wine tapping can be used as biomarkers to assess palm wine's quality and help to design an optimum starter culture.},
}
@article {pmid36385637,
year = {2023},
author = {Natalini, JG and Singh, S and Segal, LN},
title = {The dynamic lung microbiome in health and disease.},
journal = {Nature reviews. Microbiology},
volume = {21},
number = {4},
pages = {222-235},
pmid = {36385637},
issn = {1740-1534},
support = {R37 CA244775/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Lung/microbiology ; *Microbiota ; Bacteria ; },
abstract = {New methods and technologies within the field of lung biology are beginning to shed new light into the microbial world of the respiratory tract. Long considered to be a sterile environment, it is now clear that the human lungs are frequently exposed to live microbes and their by-products. The nature of the lung microbiome is quite distinct from other microbial communities inhabiting our bodies such as those in the gut. Notably, the microbiome of the lung exhibits a low biomass and is dominated by dynamic fluxes of microbial immigration and clearance, resulting in a bacterial burden and microbiome composition that is fluid in nature rather than fixed. As our understanding of the microbial ecology of the lung improves, it is becoming increasingly apparent that certain disease states can disrupt the microbial-host interface and ultimately affect disease pathogenesis. In this Review, we provide an overview of lower airway microbial dynamics in health and disease and discuss future work that is required to uncover novel therapeutic targets to improve lung health.},
}
@article {pmid36384808,
year = {2022},
author = {Park, J and Davis, K and Lajoie, G and Parfrey, LW},
title = {Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {55},
pmid = {36384808},
issn = {2524-6372},
support = {2021-03160//NSERC Discovery/ ; },
abstract = {BACKGROUND: Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the microbiome is highly diverse and variable in space and time. Identifying core taxa is one way forward but there are many methods and thresholds in use. This study leverages a large dataset of microbial communities associated with the widespread brown macroalga, Fucus distichus, across sites and years on one island in British Columbia, Canada. We compare three different methodological approaches to identify core taxa at the amplicon sequence variant (ASV) level from this dataset: (1) frequency analysis of taxa on F. distichus performed over the whole dataset, (2) indicator species analysis (IndVal) over the whole dataset that identifies frequent taxa that are enriched on F. distichus in comparison to the local environment, and (3) a two-step IndVal method that identifies taxa that are consistently enriched on F. distichus across sites and time points. We then investigated a F. distichus time-series dataset to see if those core taxa are seasonally consistent on another remote island in British Columbia, Canada. We then evaluate host-specificity of the identified F. distichus core ASVs using comparative data from 32 other macroalgal species sampled at one of the sites.<br><br>RESULTS: We show that a handful of core ASVs are consistently identified by both frequency analysis and IndVal approaches with alternative definitions, although no ASVs were always present on F. distichus and IndVal identified a diverse array of F. distichus indicator taxa across sites on Calvert Island in multiple years. Frequency analysis captured a broader suit of taxa, while IndVal was better at identifying host-specific microbes. Finally, two-step IndVal identified hundreds of indicator ASVs for particular sites/timepoints but only 12 that were indicators in a majority (>&#x2009;6 out of 11) of sites/timepoints. Ten of these ASVs were also indicators on Quadra Island, 250&#xa0;km away. Many F. distichus-core ASVs are generally found on multiple macroalgal species, while a few ASVs are highly specific to F. distichus.<br><br>CONCLUSIONS: Different methodological approaches with variable set thresholds influence core identification, but a handful of core taxa are apparently identifiable as they are widespread and temporally associated with F. distichus and enriched in comparison to the environment. Moreover, we show that many of these core ASVs of F. distichus are found on multiple macroalgal hosts, indicating that most occupy a macroalgal generalist niche rather than forming highly specialized associations with F. distichus. Further studies should test whether macroalgal generalists or specialists are more likely to engage in biologically important exchanges with host.},
}
@article {pmid36383236,
year = {2023},
author = {Peralta-Maraver, I and Rutere, C and Horn, MA and Reche, I and Behrends, V and Reiss, J and Robertson, AL},
title = {Correction to: Intermediate levels of predation and nutrient enrichment enhance the activity of ibuprofen degrading bacteria.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1442},
doi = {10.1007/s00248-022-02145-y},
pmid = {36383236},
issn = {1432-184X},
}
@article {pmid36378688,
year = {2022},
author = {Bermúdez-Méndez, E and Bronsvoort, KF and Zwart, MP and van de Water, S and Cárdenas-Rey, I and Vloet, RPM and Koenraadt, CJM and Pijlman, GP and Kortekaas, J and Wichgers Schreur, PJ},
title = {Incomplete bunyavirus particles can cooperatively support virus infection and spread.},
journal = {PLoS biology},
volume = {20},
number = {11},
pages = {e3001870},
pmid = {36378688},
issn = {1545-7885},
mesh = {Animals ; Humans ; *Rift Valley fever virus/genetics ; *Orthobunyavirus ; *Rift Valley Fever/genetics/metabolism ; *Virus Diseases ; Virion/metabolism ; *Culicidae ; *Arboviruses ; Mammals ; },
abstract = {Bunyaviruses lack a specific mechanism to ensure the incorporation of a complete set of genome segments into each virion, explaining the generation of incomplete virus particles lacking one or more genome segments. Such incomplete virus particles, which may represent the majority of particles produced, are generally considered to interfere with virus infection and spread. Using the three-segmented arthropod-borne Rift Valley fever virus as a model bunyavirus, we here show that two distinct incomplete virus particle populations unable to spread autonomously are able to efficiently complement each other in both mammalian and insect cells following co-infection. We further show that complementing incomplete virus particles can co-infect mosquitoes, resulting in the reconstitution of infectious virus that is able to disseminate to the mosquito salivary glands. Computational models of infection dynamics predict that incomplete virus particles can positively impact virus spread over a wide range of conditions, with the strongest effect at intermediate multiplicities of infection. Our findings suggest that incomplete particles may play a significant role in within-host spread and between-host transmission, reminiscent of the infection cycle of multipartite viruses.},
}
@article {pmid36378579,
year = {2023},
author = {Matassa, S and Boeckx, P and Boere, J and Erisman, JW and Guo, M and Manzo, R and Meerburg, F and Papirio, S and Pikaar, I and Rabaey, K and Rousseau, D and Schnoor, J and Smith, P and Smolders, E and Wuertz, S and Verstraete, W},
title = {How can we possibly resolve the planet's nitrogen dilemma?.},
journal = {Microbial biotechnology},
volume = {16},
number = {1},
pages = {15-27},
pmid = {36378579},
issn = {1751-7915},
mesh = {Animals ; *Nitrogen/analysis ; *Fertilizers/analysis ; Planets ; Soil ; Fossil Fuels ; Agriculture ; },
abstract = {Nitrogen is the most crucial element in the production of nutritious feeds and foods. The production of reactive nitrogen by means of fossil fuel has thus far been able to guarantee the protein supply for the world population. Yet, the production and massive use of fertilizer nitrogen constitute a major threat in terms of environmental health and sustainability. It is crucial to promote consumer acceptance and awareness towards proteins produced by highly effective microorganisms, and their potential to replace proteins obtained with poor nitrogen efficiencies from plants and animals. The fact that reactive fertilizer nitrogen, produced by the Haber Bosch process, consumes a significant amount of fossil fuel worldwide is of concern. Moreover, recently, the prices of fossil fuels have increased the cost of reactive nitrogen by a factor of 3 to 5 times, while international policies are fostering the transition towards a more sustainable agro-ecology by reducing mineral fertilizers inputs and increasing organic farming. The combination of these pressures and challenges opens opportunities to use the reactive nitrogen nutrient more carefully. Time has come to effectively recover used nitrogen from secondary resources and to upgrade it to a legal status of fertilizer. Organic nitrogen is a slow-release fertilizer, it has a factor of 2.5 or higher economic value per unit nitrogen as fertilizer and thus adequate technologies to produce it, for instance by implementing photobiological processes, are promising. Finally, it appears wise to start the integration in our overall feed and food supply chains of the exceptional potential of biological nitrogen fixation. Nitrogen produced by the nitrogenase enzyme, either in the soil or in novel biotechnology reactor systems, deserves to have a 'renaissance' in the context of planetary governance in general and the increasing number of people who desire to be fed in a sustainable way in particular.},
}
@article {pmid36374338,
year = {2023},
author = {Yan, Y and Xie, Y and Zhang, J and Li, R and Ali, A and Cai, Z and Huang, X and Liu, L},
title = {Effects of Reductive Soil Disinfestation Combined with Liquid-Readily Decomposable Compounds and Solid Plant Residues on the Bacterial Community and Functional Composition.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1132-1144},
pmid = {36374338},
issn = {1432-184X},
support = {32160748//National Natural Science Foundation of China/ ; },
mesh = {*Soil/chemistry ; Bacteria/genetics ; *Microbiota ; Soil Microbiology ; },
abstract = {Reductive soil disinfestation (RSD) incorporated with sole plant residues or liquid-readily decomposable compounds is an effective management strategy to improve soil health. However, the synthetic effects of RSD incorporated with liquid-readily decomposable compounds and solid plant residues on soil ecosystem services remain unclear. Field experiments were carried out to investigate the effects of untreated soil (CK), RSD incorporated with sawdust (SA), molasses (MO), and their combinations (SA + MO) on the bacterial community and functional composition. The results showed that RSD treatments significantly altered soil bacterial community structure compared to CK treatment. The bacterial community structure and composition in MO and SA + MO treatments were clustered compared to SA treatment. This was mainly attributed to the readily decomposable carbon sources in molasses having a stronger driving force to reshape the soil microbial community during the RSD process. Furthermore, the functional compositions, such as the disinfestation efficiency of F. oxysporum (96.4 - 99.1%), abundances of nitrogen functional genes, soil metabolic activity, and functional diversity, were significantly increased in all of the RSD treatments. The highest disinfestation efficiency and abundances of denitrification (nirS and nrfA) and nitrogen fixation (nifH) genes were observed in SA + MO treatment. Specifically, SA + MO treatment enriched more abundant beneficial genera, e.g., Oxobacter, Paenibacillus, Cohnella, Rummeliibacillus, and Streptomyces, which were significantly and positively linked to disinfestation efficiency, soil metabolic activity, and denitrification processes. Our results indicated that combining RSD practices with liquid-readily decomposable compounds and solid plant residues could effectively improve soil microbial community and functional composition.},
}
@article {pmid36374046,
year = {2022},
author = {Agarwal, V and Inomura, K and Mouw, CB},
title = {Quantitative Analysis of the Trade-Offs of Colony Formation for Trichodesmium.},
journal = {Microbiology spectrum},
volume = {10},
number = {6},
pages = {e0202522},
pmid = {36374046},
issn = {2165-0497},
mesh = {*Trichodesmium/metabolism ; Nitrogen Fixation ; Nitrogen Cycle ; Nitrogen/metabolism ; Carbon/metabolism ; },
abstract = {There is considerable debate about the benefits and trade-offs for colony formation in a major marine nitrogen fixer, Trichodesmium. To quantitatively analyze the trade-offs, we developed a metabolic model based on carbon fluxes to compare the performance of Trichodesmium colonies and free trichomes under different scenarios. Despite reported reductions in carbon fixation and nitrogen fixation rates for colonies relative to free trichomes, we found that model colonies can outperform individual cells in several cases. The formation of colonies can be advantageous when respiration rates account for a high proportion of the carbon fixation rate. Negative external influence on vital rates, such as mortality due to predation or micronutrient limitations, can also create a net benefit for colony formation relative to individual cells. In contrast, free trichomes also outcompete colonies in many scenarios, such as when respiration rates are equal for both colonies and individual cells or when there is a net positive external influence on rate processes (i.e., optimal environmental conditions regarding light and temperature or high nutrient availability). For both colonies and free trichomes, an increase in carbon fixation relative to nitrogen fixation rates would increase their relative competitiveness. These findings suggest that the formation of colonies in Trichodesmium might be linked to specific environmental and ecological circumstances. Our results provide a road map for empirical studies and models to evaluate the conditions under which colony formation in marine phytoplankton can be sustained in the natural environment. IMPORTANCE Trichodesmium is a marine filamentous cyanobacterium that fixes nitrogen and is an important contributor to the global nitrogen cycle. In the natural environment, Trichodesmium can exist as individual cells (trichomes) or as colonies (puffs and tufts). In this paper, we try to answer a longstanding question in marine microbial ecology: how does colony formation benefit the survival of Trichodesmium? To answer this question, we developed a carbon flux model that utilizes existing published rates to evaluate whether and when colony formation can be sustained. Enhanced respiration rates, influential external factors such as environmental conditions and ecological interactions, and variable carbon and nitrogen fixation rates can all create scenarios for colony formation to be a viable strategy. Our results show that colony formation is an ecologically beneficial strategy under specific conditions, enabling Trichodesmium to be a globally significant organism.},
}
@article {pmid36373138,
year = {2022},
author = {Hillary, LS and Adriaenssens, EM and Jones, DL and McDonald, JE},
title = {RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels.},
journal = {ISME communications},
volume = {2},
number = {},
pages = {34},
pmid = {36373138},
issn = {2730-6151},
support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {The distribution and diversity of RNA viruses in soil ecosystems are largely unknown, despite their significant impact on public health, ecosystem functions, and food security. Here, we characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3462 viral contigs in RNA viromes from purified virus-like-particles in five soil-types and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited minimal similarity in viral community composition, but with >10-fold more viral contigs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses predicted soil RNA viral communities are formed from viruses of bacteria, plants, fungi, vertebrates and invertebrates, with only 12% of viral contigs belonging to the bacteria-infecting Leviviricetes class. 11% of viral contigs were found to be most closely related to members of the Ourmiavirus genus, suggesting that members of this clade of plant viruses may be far more widely distributed and diverse than previously thought. These results contrast with soil DNA viromes which are typically dominated by bacteriophages. RNA viral communities, therefore, have the potential to exert influence on inter-kingdom interactions across terrestrial biomes.},
}
@article {pmid36372840,
year = {2023},
author = {Ye, G and Chen, J and Yang, P and Hu, HW and He, ZY and Wang, D and Cao, D and Zhang, W and Wu, B and Wu, Y and Wei, X and Lin, Y},
title = {Non-native Plant Species Invasion Increases the Importance of Deterministic Processes in Fungal Community Assembly in a Coastal Wetland.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1120-1131},
pmid = {36372840},
issn = {1432-184X},
support = {42077041//National Natural Science Foundation of China/ ; 2021J011038//Natural Science Foundation of Fujian Province/ ; },
mesh = {*Wetlands ; *Mycobiome ; Introduced Species ; Plants ; Poaceae/physiology ; Soil/chemistry ; Fungi/genetics ; Soil Microbiology ; China ; },
abstract = {Fungal communities are essential to the maintenance of soil multifunctionality. Plant invasion represents a growing challenge for the conservation of soil biodiversity across the globe, but the impact of non-native species invasion on fungal diversity, community structure, and assembly processes remains largely unknown. Here, we examined the diversity, community composition, functional guilds, and assembly process of fungi at three soil depths underneath a native species, three non-native species, and a bare tidal flat from a coastal wetland. Plant species was more important than soil depth in regulating the diversity, community structure, and functional groups of fungi. Non-native species, especially Spartina alterniflora, increased fungal diversity, altered fungal community structure, and increased the relative abundance of saprotrophic and pathogenic fungi in coastal wetland soils. Stochastic processes played a predominant role in driving fungal community assembly, explaining more than 70% of the relative contributions. However, compared to a native species, non-native species, especially S. alterniflora, reduced the relative influence of stochastic processes in fungal community assembly. Collectively, our results provide novel evidence that non-native species can increase fungal diversity, the relative abundance of saprotrophic and pathogenic fungi, and deterministic processes in the assembly of fungi in coastal wetlands, which can expand our knowledge of the dynamics of fungal communities in subtropical coastal wetlands.},
}
@article {pmid36370453,
year = {2022},
author = {Alfradique Monteiro, D and Fazolato, CSB and Martins, LF and Tavora Coelho da Costa Rachid, C},
title = {The bacteriome of the halophyte Atriplex nummularia (old man saltbush) in salt-affected soils - an ecological model.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {12},
pages = {},
doi = {10.1093/femsec/fiac135},
pmid = {36370453},
issn = {1574-6941},
mesh = {Humans ; Male ; *Atriplex/genetics ; Salt-Tolerant Plants/microbiology ; Soil ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride ; Bacteria/genetics ; Plant Roots/microbiology ; Soil Microbiology ; },
abstract = {Halophytes, plants capable of growing under saline conditions, are an important source of bacteria with biotechnological potential for plant growth under extreme conditions. In this study, we evaluated the halophyte Atriplex nummularia bacteriome assemblage from three different salinized sites in northeastern Brazil with different edaphoclimatic characteristics, understanding the participation of the plant in the assembly of its microbiome. We sampled 30 specimens, from which the leaves, roots, and rhizospheric soil were subjected to 16S rRNA gene sequencing, bringing forth patterns of alpha and beta diversity, taxonomical composition, co-occurrence network, and the core microbiome of each compartment. Overall, this species harbors a very restricted set of endophytic microbes, and communities showed an increasing gradient of complexity (soil > root > leaf), reflecting a change in the main selective pressure being active over the microbial community. Although the leaf bacteriome was influenced basically by host factors, the soil community was modulated by the environment, and the root bacteriome was structured by both factors. These results help us understand how plant-microbe interactions occur in saline environments. As these plants shelter microbes that potentially alleviate abiotic stresses, we discuss how culture-independent methods could contribute to the prospection of plant growth promoting bacteria in plants.},
}
@article {pmid36369598,
year = {2023},
author = {Havenga, M and Halleen, F and Baloyi, A and Bester, M and Linde, CC and Mostert, L},
title = {Predominant Clonal Reproduction with Infrequent Genetic Recombination of Phaeoacremonium minimum in Western Cape Vineyards.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {887-899},
pmid = {36369598},
issn = {1432-184X},
mesh = {*Genetics, Population ; Farms ; Genotype ; *Reproduction ; Recombination, Genetic ; Genetic Variation ; Microsatellite Repeats ; },
abstract = {Phaeoacremonium minimum is an important esca and Petri disease pathogen that causes dieback of grapevines in South Africa. Little is known regarding the reproductive strategy of the pathogen. Sexual reproduction could lead to a better adaptation of the pathogen to disease management strategies by combining alleles through recombination. The study aimed to investigate the genetic diversity and recombination potential of eight populations in the Western Cape, from six commercial vineyards and two nursery rootstock mother blocks. This was achieved by developing and applying nine polymorphic microsatellites and mating-type-specific markers. Thirty-seven genotypes were identified from 295 isolates. Populations were characterised by the same dominant genotype (MLG20 occurring 65.43%), low genotypic diversity (H) and high numbers of clones (81.36% of dataset). However, genotypes from the same sampling sites were not closely related based on a minimum spanning network and had high molecular variation within populations (94%), suggesting that multiple introductions of different genotypes occurred over time. Significant linkage disequilibrium among loci (r̅d) further indicated a dominant asexual cycle, even though perithecia have been observed in these four populations. The two rootstock mother blocks had unique genotypes and genotypes shared with the vineyard populations. Propagation material obtained from infected rootstock mother blocks could lead to the spread of more genotypes to newly established vineyards. Based on our results, it is important to determine the health status of rootstock mother blocks. Management strategies must focus on reducing aerial inoculum to prevent repeated infections and further spread of P. minimum genotypes.},
}
@article {pmid36368693,
year = {2022},
author = {Poppeliers, SWM and Hefting, M and Dorrepaal, E and Weedon, JT},
title = {Functional microbial ecology in arctic soils: the need for a year-round perspective.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {12},
pages = {},
pmid = {36368693},
issn = {1574-6941},
mesh = {*Soil ; Arctic Regions ; Climate Change ; Carbon Cycle ; *Microbiota ; },
abstract = {The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.},
}
@article {pmid36368382,
year = {2023},
author = {Monahan, C and Morris, D and Nag, R and Cummins, E},
title = {Risk ranking of macrolide antibiotics - Release levels, resistance formation potential and ecological risk.},
journal = {The Science of the total environment},
volume = {859},
number = {Pt 2},
pages = {160022},
doi = {10.1016/j.scitotenv.2022.160022},
pmid = {36368382},
issn = {1879-1026},
mesh = {Humans ; *Anti-Bacterial Agents/toxicity ; *Macrolides/toxicity ; Azithromycin/toxicity ; Clarithromycin ; Erythromycin ; },
abstract = {Antibiotic resistance (AR) development in natural water bodies is a significant source of concern. Macrolide antibiotics in particular have been identified as pollutants of concern for AR development throughout the literature, as well as by state and international authorities. This study utilises a probabilistic model to examine the risk of AR development arising from human-use macrolide residues, utilising administration rates from Ireland as a case study. Stages modelled included level of administration, excretion, degradation in wastewater, removal in wastewater treatment, assuming conventional activated sludge (CAS) treatment, and dilution. Release estimates per day, as well as risk quotient values for antibiotic resistance development and ecological impact, are generated for erythromycin, clarithromycin, and azithromycin. In the modelled scenario in which conventional activated sludge treatment is utilised in wastewater treatment, this model ranks risk of resistance development for each antibiotic in the order clarithromycin > azithromycin > erythromycin, with mean risk quotient values of 0.50, 0.34 and 0.12, respectively. A membrane bioreactor scenario was also modelled, which reduced risk quotient values for all three macrolides by at least 50 %. Risk of ecological impact for each antibiotic was also examined, by comparing environmental concentrations predicted to safety limits based on toxicity data for cyanobacteria and other organisms from the literature, with azithromycin being identified as the macrolide of highest risk. This study compares and quantifies the risk of resistance development and ecological impact for a high-risk antibiotic group in the Irish context, and demonstrates the potential for risk reduction achieved by adoption of alternative (e.g. membrane bioreactor) technology.},
}
@article {pmid36368371,
year = {2023},
author = {Kumar, A and Ajay, A and Dasgupta, B and Bhadury, P and Sanyal, P},
title = {Deciphering the nitrate sources and processes in the Ganga river using dual isotopes of nitrate and Bayesian mixing model.},
journal = {Environmental research},
volume = {216},
number = {Pt 4},
pages = {114744},
doi = {10.1016/j.envres.2022.114744},
pmid = {36368371},
issn = {1096-0953},
mesh = {*Rivers ; Nitrates/analysis ; Environmental Monitoring ; Bayes Theorem ; *Water Pollutants, Chemical/analysis ; Nitrogen Isotopes/analysis ; Fertilizers/analysis ; China ; },
abstract = {The dual isotopes of dissolved NO3- (n = 43) has been used to delineate the nitrate sources and N-cycling processes in the Ganga river. The proportional contribution of nitrate from different sources has been estimated using the Bayesian mixing model. The seasonal NO3- concentration in the lower stretch of the river Ganga varied between 4.1 and 64.1 μM with higher concentration during monsoon and post-monsoon season and lower concentration during the pre-monsoon and winter season. The temporal variation in the isotopic values ranged between +0.0 and +9.6‰ for δ[15]NNO3- and -1.2 to +11.0‰ for δ[18]ONO3-. The spatial NO3- concentration during the post-monsoon season varied between 23.2 and 57.7 μM, with higher values from the middle and lower values from the lower stretch of the river Ganga. The isotopic ratio during the post-monsoon season varied between -1.0 and +11.3‰ for δ[15]NNO3- and -4.6 to +5.2‰ for δ[18]ONO3-. The temporal dataset from the lower stretch of the river Ganga showed the dominance of nitrate derived from the nitrification of soil organic matter (SOM) (average ∼53.4%). The nitrate contribution from synthetic fertilizers was observed to be higher during the post-monsoon season (34.7 ± 23.4%) compared to that in the monsoon (25.5 ± 19.5%) and pre-monsoon (22.2 ± 19.6%) season. No significant seasonal variations were observed in the nitrate input from manure/sewage (∼13.9%). Spatial samples collected during the post-monsoon season showed higher contribution of synthetic fertilizer in the lower stretch (34.6 ± 22.7%) compared to the middle stretch (21.1 ± 18.2%), which indicates greater influence of the agricultural activity in the lower stretch. The dual isotope study of dissolved NO3- established that the nitrate in the Ganga river water is mostly derived from the nitrification of incoming organic compounds and is subsequently removed via assimilatory nitrate uptake. The study also emphasises significant nitrification and assimilatory nitrate removal processes operating in the mixing zone of the Ganga river and Hooghly estuary.},
}
@article {pmid36365043,
year = {2022},
author = {Han, H and Saed, YA and Song, W and Wang, M and Li, Y},
title = {Prevalence of Non-SARS-CoV-2 Respiratory Pathogens and Co-Infection with SARS-CoV-2 in the Early Stage of COVID-19 Epidemic.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {36365043},
issn = {2076-0817},
abstract = {BACKGROUND: This study aims to reflect the prevalence of non-SARS-CoV-2 respiratory pathogens and co-infection with SARS-CoV-2 in the early stage of the COVID-19 epidemic, considering SARS-CoV-2 broke out during influenza season and its symptoms resemble those of influenza.<br><br>METHODS: A total of 685 nucleic acid samples of respiratory pathogens were collected from 1 November 2019 to 20 January 2020 and were detected by the 13 Respiratory Pathogen Multiplex Detection Kit and Novel Coronavirus (2019-nCoV) Nucleic Acid Diagnostic Kit.<br><br>RESULTS: In Wuhan, human rhinovirus was the most frequent infectious pathogen in November (31.5%) and human respiratory syncytial virus appeared the most in December and January (37.1%, 8.6%, respectively). Detection of SARS-CoV-2 first appeared from January 1 to January 10. Generally, 115 patients of 616 patients (18.7%) from Wuhan were infected with SARS-CoV-2, and only two children were co-infected with other respiratory pathogens. In Taiyuan, influenza A virus was detected most frequently in December and January (30.3%, 12%, respectively) without infection of SARS-CoV-2.<br><br>CONCLUSIONS: Some cases diagnosed with influenza before routine nucleic acid testing of SARS-CoV-2 were attributed to COVID-19. Co-infection between SARS-CoV-2 and other non-SARS-CoV-2 respiratory pathogens existed in the early stage of COVID-19 epidemic.},
}
@article {pmid36364003,
year = {2022},
author = {Jivkova, D and Sathiyanarayanan, G and Harir, M and Hertkorn, N and Schmitt-Kopplin, P and Sanhaji, G and Fochesato, S and Berthomieu, C and Heyraud, A and Achouak, W and Santaella, C and Heulin, T},
title = {Production and Characterization of a Novel Exopolysaccharide from Ramlibacter tataouinensis.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {21},
pages = {},
pmid = {36364003},
issn = {1420-3049},
mesh = {Humans ; Gas Chromatography-Mass Spectrometry ; *Comamonadaceae ; Rhamnose ; *Cysts ; Polysaccharides, Bacterial/chemistry ; },
abstract = {The current study examines the desiccation-resistant Ramlibacter tataouinensis TTB310[T] as a model organism for the production of novel exopolysaccharides and their structural features. This bacterium is able to produce dividing forms of cysts which synthesize cell-bound exopolysaccharide. Initial experiments were conducted on the enrichment of cyst biomass for exopolysaccharide production under batch-fed conditions in a pilot-scale bioreactor, with lactate as the source of carbon and energy. The optimized medium produced significant quantities of exopolysaccharide in a single growth phase, since the production of exopolysaccharide took place during the division of the cysts. The exopolysaccharide layer was extracted from the cysts using a modified trichloroacetic acid method. The biochemical characterization of purified exopolysaccharide was performed by gas chromatography, ultrahigh-resolution mass spectrometry, nuclear magnetic resonance, and Fourier-transform infrared spectrometry. The repeating unit of exopolysaccharide was a decasaccharide consisting of ribose, glucose, rhamnose, galactose, mannose, and glucuronic acid with the ratio 3:2:2:1:1:1, and additional substituents such as acetyl, succinyl, and methyl moieties were also observed as a part of the exopolysaccharide structure. This study contributes to a fundamental understanding of the novel structural features of exopolysaccharide from a dividing form of cysts, and, further, results can be used to study its rheological properties for various industrial applications.},
}
@article {pmid36363794,
year = {2022},
author = {Zaitseva, S and Badmaev, N and Kozyreva, L and Dambaev, V and Barkhutova, D},
title = {Microbial Community in the Permafrost Thaw Gradient in the South of the Vitim Plateau (Buryatia, Russia).},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
pmid = {36363794},
issn = {2076-2607},
support = {19-29-05250//Russian Foundation for Basic Research/ ; },
abstract = {Soil microbial communities play key roles in biogeochemical cycles and greenhouse gas formation during the decomposition of the released organic matter in the thawing permafrost. The aim of our research was to assess the taxonomic prokaryotic diversity in soil-ecological niches of the Darkhituy-Khaimisan transect during the initial period of soil thawing. We investigated changes in the microbial communities present in the active layer of four sites representing distinct habitats (larch forest, birch forest, meadow steppe and thermokarst lake). We explore the relationship between the biogeochemical differences among habitats and the active layer microbial community via a spatial (across habitats, and with depth through the active layer) community survey using high-throughput Illumina sequencing. Microbial communities showed significant differences between active and frozen layers and across ecosystem types, including a high relative abundance of Alphaproteobacteria, Firmicutes, Crenarchaeota, Bacteroidota and Gemmatimonadota in the active layer and a high relative abundance of Actinobacteriota and Desulfobacterota in the frozen layer. Soil pH, temperature and moisture were the most significant parameters underlying the variations in the microbial community composition. CCA suggested that the differing environmental conditions between the four soil habitats had strong influences on microbial distribution and diversity and further explained the variability of soil microbial community structures.},
}
@article {pmid36363713,
year = {2022},
author = {Hurtado-McCormick, V and Trevathan-Tackett, SM and Bowen, JL and Connolly, RM and Duarte, CM and Macreadie, PI},
title = {Pathways for Understanding Blue Carbon Microbiomes with Amplicon Sequencing.},
journal = {Microorganisms},
volume = {10},
number = {11},
pages = {},
pmid = {36363713},
issn = {2076-2607},
support = {DP200100575//Australian Research Council/ ; DE210101029//Australian Research Council/ ; DEB2203322//National Science Foundation/ ; },
abstract = {The capacity of Blue Carbon Ecosystems to act as carbon sinks is strongly influenced by the metabolism of soil-associated microbes, which ultimately determine how much carbon is accumulated or returned to the atmosphere. The rapid evolution of sequencing technologies has facilitated the generation of tremendous amounts of data on what taxa comprise belowground microbial assemblages, largely available as isolated datasets, offering an opportunity for synthesis research that informs progress on understanding Blue Carbon microbiomes. We identified questions that can be addressed with a synthesis approach, including the high variability across datasets, space, and time due to differing sampling techniques, ecosystem or vegetation specificity, and the relationship between microbiome community and edaphic properties, particularly soil carbon. To address these questions, we collated 34 16S rRNA amplicon sequencing datasets, including bulk soil or rhizosphere from seagrass, mangroves, and saltmarshes within publicly available repositories. We identified technical and theoretical challenges that precluded a synthesis of multiple studies with currently available data, and opportunities for addressing the knowledge gaps within Blue Carbon microbial ecology going forward. Here, we provide a standardisation toolbox that supports enacting tasks for the acquisition, management, and integration of Blue Carbon-associated sequencing data and metadata to potentially elucidate novel mechanisms behind Blue Carbon dynamics.},
}
@article {pmid36360970,
year = {2022},
author = {Sousa, V and Spratt, D and Davrandi, M and Mardas, N and Beltrán, V and Donos, N},
title = {Oral Microcosm Biofilms Grown under Conditions Progressing from Peri-Implant Health, Peri-Implant Mucositis, and Peri-Implantitis.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {21},
pages = {},
pmid = {36360970},
issn = {1660-4601},
support = {/DH_/Department of Health/United Kingdom ; },
mesh = {Humans ; *Peri-Implantitis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Mucositis ; Biofilms ; *Microbiota/genetics ; Bacteria/genetics ; },
abstract = {Peri-implantitis is a disease influenced by dysbiotic microbial communities that play a role in the short- and long-term outcomes of its clinical treatment. The ecological triggers that establish the progression from peri-implant mucositis to peri-implantitis remain unknown. This investigation describes the development of a novel in vitro microcosm biofilm model. Biofilms were grown over 30 days over machined titanium discs in a constant depth film fermentor (CDFF), which was inoculated (I) with pooled human saliva. Following longitudinal biofilm sampling across peri-implant health (PH), peri-implant mucositis (PM), and peri-implantitis (PI) conditions, the characterisation of the biofilms was performed. The biofilm analyses included imaging by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM), selective and non-selective culture media of viable biofilms, and 16S rRNA gene amplification and sequencing. Bacterial qualitative shifts were observed by CLSM and SEM across conditions, which were defined by characteristic phenotypes. A total of 9 phyla, 83 genera, and 156 species were identified throughout the experiment. The phyla Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria showed the highest prevalence in PI conditions. This novel in vitro microcosm model provides a high-throughput alternative for growing microcosm biofilms resembling an in vitro progression from PH-PM-PI conditions.},
}
@article {pmid36358990,
year = {2022},
author = {Scott, E and De Paepe, K and Van de Wiele, T},
title = {Postbiotics and Their Health Modulatory Biomolecules.},
journal = {Biomolecules},
volume = {12},
number = {11},
pages = {},
pmid = {36358990},
issn = {2218-273X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics ; Fatty Acids, Volatile ; Vitamins ; Inflammation ; },
abstract = {Postbiotics are a new category of biotics that have the potential to confer health benefits but, unlike probiotics, do not require living cells to induce health effects and thus are not subject to the food safety requirements that apply to live microorganisms. Postbiotics are defined as a "preparation of inanimate microorganisms and/or their components that confers a health benefit on the host". Postbiotic components include short-chain fatty acids, exopolysaccharides, vitamins, teichoic acids, bacteriocins, enzymes and peptides in a non-purified inactivated cell preparation. While research into postbiotics is in its infancy, there is increasing evidence that postbiotics have the potential to modulate human health. Specifically, a number of postbiotics have been shown to improve gut health by strengthening the gut barrier, reducing inflammation and promoting antimicrobial activity against gut pathogens. Additionally, research is being conducted into the potential application of postbiotics to other areas of the body, including the skin, vagina and oral cavity. The purpose of this review is to set out the current research on postbiotics, demonstrate how postbiotics are currently used in commercial products and identify a number of knowledge gaps where further research is needed to identify the potential for future applications of postbiotics.},
}
@article {pmid36358119,
year = {2022},
author = {Calatayud, M and Duysburgh, C and Van den Abbeele, P and Franckenstein, D and Kuchina-Koch, A and Marzorati, M},
title = {Long-Term Lactulose Administration Improves Dysbiosis Induced by Antibiotic and C. difficile in the PathoGut[TM] SHIME Model.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {36358119},
issn = {2079-6382},
abstract = {Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and an important nosocomial infection with different severity degrees. Disruption of the gut microbiota by broad-spectrum antibiotics creates a proper environment for C. difficile colonization, proliferation, and clinical disease onset. Restoration of the gut microbial ecosystem through prebiotic interventions can constitute an effective complementary treatment of CDI. Using an adapted simulator of the human gut microbial ecosystem, the PathoGut[TM] SHIME, the effect of different long-term and repeated dose lactulose treatments was tested on C. difficile germination and growth in antibiotic-induced dysbiotic gut microbiota environments. The results showed that lactulose reduced the growth of viable C. difficile cells following clindamycin treatment, shifted the antibiotic-induced dysbiotic microbial community, and stimulated the production of health-promoting metabolites (especially butyrate). Recovery of the gut microenvironment by long-term lactulose administration following CDI was also linked to lactate production, decrease in pH and modulation of bile salt metabolism. At a structural level, lactulose showed a significant bifidogenic potential and restored key commensal members of the gut ecosystem such as Lactobacillaceae, Veillonellaceae and Lachnospiraceae. These results support further human intervention studies aiming to validate the in vitro beneficial effects of lactulose on gut microbiome recovery during antibiotic exposure and CDI.},
}
@article {pmid36356812,
year = {2023},
author = {Kim, M and Cui, F},
title = {Identification of bacterial communities in conventional wastewater treatment sludge to inform inoculation of the anammox process.},
journal = {Chemosphere},
volume = {311},
number = {Pt 2},
pages = {137167},
doi = {10.1016/j.chemosphere.2022.137167},
pmid = {36356812},
issn = {1879-1298},
mesh = {*Wastewater ; Sewage/microbiology ; Denitrification ; Anaerobic Ammonia Oxidation ; Bioreactors/microbiology ; Oxidation-Reduction ; Anaerobiosis ; Bacteria/genetics ; Nitrogen ; *Water Purification ; },
abstract = {This study uses 16 S rRNA gene pyrosequencing for the identification of a vast number of wastewater bacterial communities to investigate the evolution of bacterial communities in the Anammox process. Four lab-scale Anammox reactors inoculated with different conventional wastewater treatment sludge (activated sludge, livestock wastewater treatment sludge, denitrification sludge, and anaerobic digestion sludge) were operated under identical operating conditions for more than 400 days. The phylum Planctomycetes was present in all seeds of conventional sludge with a relative abundance of 1-3%. In particular, the known Anammox bacteria Candidatus Brocadia was found in the seed of the denitrification sludge. The reactor inoculated with denitrification sludge demonstrated the most effective nitrogen removal of ∼80% with successful cultivation of Anammox bacteria. This study found that the performance of the Anammox process is related to the presence of Nitrospira genus (nitrite-oxidizing bacteria) and that symbiotic association with other functional groups can lead to nitrogen removal. The outcomes of this study can provide vital insight into the study of microbial ecology for the cultivation of Anammox bacteria.},
}
@article {pmid36355167,
year = {2022},
author = {Yoon, KH and Indong, RA and Lee, JI},
title = {Making "Sense" of Ecology from a Genetic Perspective: Caenorhabditis elegans, Microbes and Behavior.},
journal = {Metabolites},
volume = {12},
number = {11},
pages = {},
pmid = {36355167},
issn = {2218-1989},
support = {2021R1A2C101178312//National Research Foundation of Korea/ ; 2019R1C1C1008708//National Research Foundation of Korea/ ; },
abstract = {Our knowledge of animal and behavior in the natural ecology is based on over a century's worth of valuable field studies. In this post-genome era, however, we recognize that genes are the underpinning of ecological interactions between two organisms. Understanding how genes contribute to animal ecology, which is essentially the intersection of two genomes, is a tremendous challenge. The bacterivorous nematode Caenorhabditis elegans, one of the most well-known genetic animal model experimental systems, experiences a complex microbial world in its natural habitat, providing us with a window into the interplay of genes and molecules that result in an animal-microbial ecology. In this review, we will discuss C. elegans natural ecology, how the worm uses its sensory system to detect the microbes and metabolites that it encounters, and then discuss some of the fascinating ecological dances, including behaviors, that have evolved between the nematode and the microbes in its environment.},
}
@article {pmid36354324,
year = {2022},
author = {Saati-Santamaría, Z and Baroncelli, R and Rivas, R and García-Fraile, P},
title = {Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution.},
journal = {Microbiology spectrum},
volume = {10},
number = {6},
pages = {e0237022},
pmid = {36354324},
issn = {2165-0497},
mesh = {Animals ; *Ecosystem ; Phylogeny ; *Pseudomonas/genetics ; Genomics ; Adaptation, Physiological/genetics ; },
abstract = {Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.},
}
@article {pmid36352414,
year = {2022},
author = {Pitiriga, V and Bakalis, J and Theodoridou, K and Kanellopoulos, P and Saroglou, G and Tsakris, A},
title = {Lower risk of bloodstream infections for peripherally inserted central catheters compared to central venous catheters in critically ill patients.},
journal = {Antimicrobial resistance and infection control},
volume = {11},
number = {1},
pages = {137},
pmid = {36352414},
issn = {2047-2994},
mesh = {Adult ; Humans ; *Central Venous Catheters/adverse effects ; *Catheter-Related Infections/epidemiology/etiology ; *Catheterization, Central Venous/adverse effects ; Retrospective Studies ; Critical Illness ; Risk Factors ; *Sepsis/epidemiology ; },
abstract = {BACKGROUND: Peripherally inserted central venous catheters (PICCs) serve as an alternative to short-term central venous catheters (CVCs) for providing intravenous access in hospitalized patients. Although a number of studies suggest that PICCs are associated with a lower risk of central line-associated bloodstream infections (CLABSIs) than CVCs, recent data concerning specific patient groups support the contrary. In this regard, we are comparing CVC- and PICC-related CLABSI rates developed in a selected group of critically ill inpatients and evaluating the CLABSI microbiological distribution.<br><br>METHODS: The study was conducted at a tertiary care hospital in Greece between May 2017 and May 2019. We performed a two-year retrospective analysis of the data collected from medical records of consecutive adult patients who underwent PICC or CVC placement.<br><br>RESULTS: A total of 1187 CVCs placed for 9774 catheter-days and 639 PICCs placed for 11,110 catheter-days, were reported and analyzed during the study period. Among CVCs, a total of 59 (4.9%) CLABSIs were identified, while among PICCs, 18 (2.8%) cases presented CLABSI (p&#x2009;=&#x2009;0.029). The CLABSI incidence rate per 1,000 catheter-days was 6.03 for CVC group and 1.62 for PICC group (p&#x2009;<&#x2009;0.001). The CLABSI rate due to multidrug-resistant organisms (MDROs) among the two groups was 3.17 in CVC group and 0.36 in PICC group (p&#x2009;<&#x2009;0.001). Within CLABSI-CVC group, the most common microorganism detected was MDR Acinetobacter baumannii (27.1%) followed by MDR Klebsiella pneumoniae (22%). In CLABSI-PICC group, the predominant microorganism was Candida spp. (33.3%) followed by non-MDR gram-negative pathogens (22.2%).<br><br>CONCLUSIONS: PICC lines were associated with significantly lower CLABSI rates comparing to CVC although they were in place longer than CVC lines. Given their longer time to the development of infection, PICCs may be a safer alternative for prolonged inpatient IV access. The high prevalence of CLABSI-MDROs depicts the local microbial ecology, emphasizing the need of&#xa0;public health awareness.},
}
@article {pmid36352137,
year = {2023},
author = {Graber, LC and Ramalho, MO and Powell, S and Moreau, CS},
title = {Identifying the Role of Elevation, Geography, and Species Identity in Structuring Turtle Ant (Cephalotes Latreille, 1802) Bacterial Communities.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1240-1253},
pmid = {36352137},
issn = {1432-184X},
support = {DEB 1442256//National Science Foundation/ ; DEB 1900357//National Science Foundation/ ; },
mesh = {Animals ; *Ants/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Geography ; *Microbiota ; Bacteria/genetics ; },
abstract = {Bacterial communities in animals are often necessary for hosts to survive, particularly for hosts with nutrient-limited diets. The composition, abundance, and richness of these bacterial communities may be shaped by host identity and external ecological factors. The turtle ants (genus Cephalotes) are predominantly herbivorous and known to rely on bacterial communities to enrich their diet. Cephalotes have a broad Neotropical distribution, with high diversity in the South American Cerrado, a geologically and biologically diverse savanna. Using 16S rRNA amplicon sequencing, we examined the bacterial communities of forty-one Cephalotes samples of sixteen different species collected from multiple locations across two sites in the Cerrado (MG, Brazil) and compared the bacterial communities according to elevation, locality, species, and species group, defined by host phylogeny. Beta diversity of bacterial communities differed with respect to all categories but particularly strongly when compared by geographic location, species, and species group. Differences seen in species and species groups can be partially explained by the high abundance of Mesorhizobium in Cephalotes pusillus and Cephalotes depressus species groups, when compared to other clades via the Analysis of Composition of Microbiome (ANCOM). Though the Cephalotes bacterial community is highly conserved, results from this study indicate that multiple external factors can affect and change bacterial community composition and abundance.},
}
@article {pmid36350347,
year = {2023},
author = {Ayilara, MS and Adeleke, BS and Babalola, OO},
title = {Correction to: Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1454},
doi = {10.1007/s00248-022-02141-2},
pmid = {36350347},
issn = {1432-184X},
}
@article {pmid36350260,
year = {2022},
author = {Collin, B and Auffan, M and Doelsch, E and Proux, O and Kieffer, I and Ortet, P and Santaella, C},
title = {Bacterial Metabolites and Particle Size Determine Cerium Oxide Nanomaterial Biotransformation.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {23},
pages = {16838-16847},
doi = {10.1021/acs.est.2c05280},
pmid = {36350260},
issn = {1520-5851},
mesh = {Particle Size ; *Cerium/chemistry ; Soil/chemistry ; *Metal Nanoparticles/chemistry ; Bacteria ; *Nanostructures ; },
abstract = {Soil is a major receptor of manufactured nanomaterials (NMs) following unintentional releases or intentional uses. Ceria NMs have been shown to undergo biotransformation in plant and soil organisms with a partial Ce(IV) reduction into Ce(III), but the influence of environmentally widespread soil bacteria is poorly understood. We used high-energy resolution fluorescence-detected X-ray absorption spectroscopy (HERFD-XAS) with an unprecedented detection limit to assess Ce speciation in a model soil bacterium (Pseudomonas brassicacearum) exposed to CeO2 NMs of different sizes and shapes. The findings revealed that the CeO2 NM's size drives the biotransformation process. No biotransformation was observed for the 31 nm CeO2 NMs, contrary to 7 and 4 nm CeO2 NMs, with a Ce reduction of 64 ± 14% and 70 ± 15%, respectively. This major reduction appeared quickly, from the early exponential bacterial growth phase. Environmentally relevant organic acid metabolites secreted by Pseudomonas, especially in the rhizosphere, were investigated. The 2-keto-gluconic and citric acid metabolites alone were able to induce a significant reduction in 4 nm CeO2 NMs. The high biotransformation measured for <7 nm NMs would affect the fate of Ce in the soil and biota.},
}
@article {pmid36349406,
year = {2023},
author = {Chen, H and Fang, Y and Zwaenepoel, A and Huang, S and Van de Peer, Y and Li, Z},
title = {Revisiting ancient polyploidy in leptosporangiate ferns.},
journal = {The New phytologist},
volume = {237},
number = {4},
pages = {1405-1417},
pmid = {36349406},
issn = {1469-8137},
support = {833522//European Research Council/International ; },
mesh = {*Ferns/genetics ; Phylogeny ; Gene Duplication ; Genome Size ; Polyploidy ; Evolution, Molecular ; Genome, Plant ; },
abstract = {Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building KS -age distributions and applying substitution rate corrections and by conducting statistical gene tree-species tree reconciliation analyses. Our integrative analyses not only identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree-species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often-overlooked issues.},
}
@article {pmid36346444,
year = {2023},
author = {Palmer, B and Lawson, D and Lipson, DA},
title = {Years After a Fire, Biocrust Microbial Communities are Similar to Unburned Communities in a Coastal Grassland.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1028-1044},
pmid = {36346444},
issn = {1432-184X},
mesh = {Ecosystem ; Grassland ; *Microbiota ; *Fires ; Bacteria/genetics ; Chlorophyll ; Soil ; },
abstract = {Microbial communities are integral for ecosystem processes and their taxonomic composition and function may be altered by a disturbance such as fire. Biocrusts are composed of macroscopic and microscopic organisms and are important for a variety of ecosystem functions, such as nutrient cycling and erosion control. We sought to understand if biocrust community composition and function were altered 1 year after a prescribed fire and 6 years after a wildfire in a coastal California grassland on San Clemente Island. We used shotgun metagenomic sequencing and measurements of chlorophyll content, exopolysaccharide production related to soil stability, and nitrogen fixation. There were no differences in the community composition between unburned samples and the samples burned in the prescribed fire and wildfire. Chlorophyll content differed between the prescribed fire and the controls; however, there were no measured differences in exopolysaccharide production, and nitrogen fixation. However, the wildfire and their respective unburned samples had different functions based on the gene annotations. We compiled one Actinobacteria metagenome-assembled genome from the shotgun sequences which had genes for oxidative and heat stress tolerance. These results suggest that the biocrust community can reach a community composition and function similar to the unburned biocrusts within a year after a prescribed burn and 6 years after a wildfire. However, legacy effects of the wildfire may present themselves in the differences between functional gene sequences. Due to their ability to match the undisturbed community composition and function within years and without intervention, future restoration work should consider the biocrusts in their restoration plans as they may provide valuable ecosystem functions after a disturbance.},
}
@article {pmid36345526,
year = {2022},
author = {DeWitt, ME and Polk, C and Williamson, J and Shetty, AK and Passaretti, CL and McNeil, CJ and Fairman, RT and Sampson, MM and Dalton, C and Sanders, JW},
title = {Global monkeypox case hospitalisation rates: A rapid systematic review and meta-analysis.},
journal = {EClinicalMedicine},
volume = {54},
number = {},
pages = {101710},
pmid = {36345526},
issn = {2589-5370},
abstract = {BACKGROUND: Estimates of the case hospitalization rate and case fatality rate when hospital care is available for monkeypox (MPX) infections have not been well defined. This rapid systematic review and meta-analysis aimed to estimate the case hospitalisation rate and case fatality rate where hospital care is available.<br><br>METHODS: We systematically searched PubMed, Embase, the Lancet Preprints, and MedRxiv for studies published between Jan 1, 1950 and Aug 2, 2022. We included documents which contained both the number of cases and associated hospitalisations of MPX infections. From eligible studies we extracted the country, the year of the study, the study design type, the clade of MPX, the participant characteristics, transmission type, any treatments used, number of cases (including suspected, probable, or laboratory confirmed diagnosis), number of hospitalizations, hospitalized patient outcomes, and case definition. Case hospitalization rate (CHR) was defined as the proportion of cases that were admitted to hospital care while case fatality rate (CFR) was defined as the proportion of cases that died. CHR and CFR were analysed in a fully Bayesian meta-analytic framework using random effects models, including sub-group analysis with heterogeneity assessed using I[2].<br><br>FINDINGS: Of the 259 unique documents identified, 19 studies were eligible for inclusion. Included studies represented 7553 reported cases among which there were 555 hospitalizations. Of the 7540 cases for which outcomes were available, there were 15 recorded deaths. The median age of cases was 35 years (interquartile range 28-38, n&#xa0;=&#xa0;2010) and primarily male (7339/7489, 98%) in studies where age or sex were available. Combined CHR was estimated to be 14.1% (95% credible interval, 7.5-25.0, I[2] 97.4%), with a high degree of heterogeneity. Further analysis by outbreak period indicates CHRs of 49.8% (28.2-74.0, I[2] 81.4%), 21.7% (7.2-52.1, I[2] 57.7%), and 5.8% (3.2-9.4, I[2] 92.4%) during the pre-2017, 2017-2021, and 2022 outbreaks, respectively, again with high levels of heterogeneity. CFR was estimated to be 0.03% (0.0-0.44, I[2] 99.9%), with evidence of large heterogeneity between the studies.<br><br>INTERPRETATION: There is limited data for MPX hospitalization rates in countries where MPX has been traditionally non-endemic until the current outbreak. Due to substantial heterogeneity, caution is needed when interpreting these findings. Health care organizations should be cognizant of the potential increase in healthcare utilization. Rapid identification of infection and use of appropriate therapies such as antivirals play a role reducing the CHR and associated CFR.<br><br>FUNDING: None.},
}
@article {pmid36345334,
year = {2022},
author = {Verbeelen, T and Van Houdt, R and Leys, N and Ganigué, R and Mastroleo, F},
title = {Optimization of RNA extraction for bacterial whole transcriptome studies of low-biomass samples.},
journal = {iScience},
volume = {25},
number = {11},
pages = {105311},
pmid = {36345334},
issn = {2589-0042},
abstract = {We developed a procedure for extracting maximal amounts of high-quality RNA from low-biomass producing (autotrophic) bacteria for experiments where sample volume is limited. Large amounts of high-quality RNA for downstream analyses cannot be obtained using larger quantities of culture volume. The performance of standard commercial silica-column based kit protocols and these procedures amended by ultrasonication or enzymatic lysis were assessed. The ammonium-oxidizing Nitrosomonas europaea and nitrite-oxidizing Nitrobacter winogradskyi were used as model organisms for optimization of the RNA isolation protocol. Enzymatic lysis through lysozyme digestion generated high-quality, high-yield RNA samples. Subsequent RNA-seq analysis resulted in qualitative data for both strains. The RNA extraction procedure is suitable for experiments with volume and/or biomass limitations, e.g., as encountered during space flight experiments. Furthermore, it will also result in higher RNA yields for whole transcriptome experiments where sample volume and/or biomass was increased to compensate the low-biomass characteristic of autotrophs.},
}
@article {pmid36344828,
year = {2023},
author = {Bringhurst, B and Allert, M and Greenwold, M and Kellner, K and Seal, JN},
title = {Environments and Hosts Structure the Bacterial Microbiomes of Fungus-Gardening Ants and their Symbiotic Fungus Gardens.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1374-1392},
pmid = {36344828},
issn = {1432-184X},
support = {IOS-1552822//Directorate for Biological Sciences/ ; DEB-1354629//Directorate for Biological Sciences/ ; },
mesh = {Animals ; Gardens ; Gardening ; *Ants/microbiology ; Fungi/genetics ; Symbiosis/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Phylogeny ; },
abstract = {The fungus gardening-ant system is considered a complex, multi-tiered symbiosis, as it is composed of ants, their fungus, and microorganisms associated with either ants or fungus. We examine the bacterial microbiome of Trachymyrmex septentrionalis and Mycetomoellerius turrifex ants and their symbiotic fungus gardens, using 16S rRNA Illumina sequencing, over a region spanning approximately 350 km (east and central Texas). Typically, microorganisms can be acquired from a parent colony (vertical transmission) or from the environment (horizontal transmission). Because the symbiosis is characterized by co-dispersal of the ants and fungus, elements of both ant and fungus garden microbiome could be characterized by vertical transmission. The goals of this study were to explore how both the ant and fungus garden bacterial microbiome are acquired. The main findings were that different mechanisms appear to explain the structure the microbiomes of ants and their symbiotic fungus gardens. Ant associated microbiomes had a strong host ant signature, which could be indicative of vertical inheritance of the ant associated bacterial microbiome or an unknown mechanism of active uptake or screening. On the other hand, the bacterial microbiome of the fungus garden was more complex in that some bacterial taxa appear to be structured by the ant host species, whereas others by fungal lineage or the environment (geographic region). Thus bacteria in fungus gardens appear to be acquired both horizontally and vertically.},
}
@article {pmid36342171,
year = {2022},
author = {Jin, H and Li, X and Wang, H and Cápiro, NL and Li, X and Löffler, FE and Yan, J and Yang, Y},
title = {Anaerobic Biohydrogenation of Isoprene by Acetobacterium wieringae Strain Y.},
journal = {mBio},
volume = {13},
number = {6},
pages = {e0208622},
pmid = {36342171},
issn = {2150-7511},
mesh = {*Acetobacterium/genetics/metabolism ; Anaerobiosis ; Proteomics ; Oxidoreductases/metabolism ; },
abstract = {Isoprene is a ubiquitously distributed, biogenic, and climate-active organic compound. Microbial isoprene degradation in oxic environments is fairly well understood; however, studies exploring anaerobic isoprene metabolism remain scarce, with no isolates for study available. Here, we obtained an acetogenic isolate, designated Acetobacterium wieringae strain Y, which hydrogenated isoprene to a mixture of methyl-1-butenes at an overall rate of 288.8 ± 20.9 μM day[-1] with concomitant acetate production at a rate of 478.4 ± 5.6 μM day[-1]. Physiological characterization demonstrated that isoprene was not utilized in a respiratory process; rather, isoprene promoted acetogenesis kinetically. Bioinformatic analysis and proteomics experiments revealed the expression of candidate ene-reductases responsible for isoprene biohydrogenation. Notably, the addition of isoprene to strain Y cultures stimulated the expression of proteins associated with the Wood-Ljungdahl pathway, indicating unresolved impacts of isoprene on carbon cycling and microbial ecology in anoxic environments (e.g., promoting CO2 plus H2 reductive acetogenesis while inhibiting methanogenesis). Our new findings advance understanding of microbial transformation of isoprene under anoxic conditions and suggest that anoxic environments are isoprene sinks. IMPORTANCE Isoprene is the most abundant, biologically generated, volatile organic compound on Earth, with estimated emissions in the same magnitude as methane. Nonetheless, a comprehensive knowledge of isoprene turnover in the environment is lacking, impacting global isoprene flux models and our understanding of the environmental fate and longevity of isoprene. A critical knowledge gap that has remained largely unexplored until recently is the microbiology and associated molecular mechanisms involved in the anaerobic biotransformation of isoprene. By integrating culture-dependent approaches with omics techniques, we isolated an acetogen, Acetobacterium wieringae strain Y, capable of anaerobic biohydrogenation of isoprene. We obtained the complete genome of strain Y, and proteomic experiments identified candidate ene-reductases for catalyzing the asymmetric reduction of the electronically activated carbon-carbon double bond of isoprene. We also demonstrated that isoprene biohydrogenation stimulates the expression of Wood-Ljungdahl pathway enzymes. This study emphasizes the ecological roles of specialized Acetobacterium on the natural cycling of isoprene in anoxic environments and the potential effects of isoprene biohydrogenation on acetogens and methanogens, which have implications for global climate change and bioenergy production.},
}
@article {pmid36338036,
year = {2022},
author = {Kraemer, SA and Barbosa da Costa, N and Oliva, A and Huot, Y and Walsh, DA},
title = {A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {995418},
pmid = {36338036},
issn = {1664-302X},
abstract = {Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome - the diversity of ARGs - under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.},
}
@article {pmid36334202,
year = {2023},
author = {Tian, L and Wang, L and Zhang, X and Huang, X and Wang, F and Zhu, S and Li, X and Guan, Y},
title = {Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {9},
pages = {24284-24298},
pmid = {36334202},
issn = {1614-7499},
support = {21-1-4-sf-11-nsh//science and technology program for public wellbeing of qingdao/ ; },
mesh = {*Denitrification ; Bioreactors/microbiology ; Seasons ; Multiomics ; Proteomics ; *Microbiota ; Biofilms ; Nitrogen ; },
abstract = {The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.},
}
@article {pmid36334118,
year = {2023},
author = {Stouvenakers, G and Massart, S and Jijakli, MH},
title = {First Study Case of Microbial Biocontrol Agents Isolated from Aquaponics Through the Mining of High-Throughput Sequencing Data to Control Pythium aphanidermatum on Lettuce.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1107-1119},
pmid = {36334118},
issn = {1432-184X},
mesh = {Animals ; *Fungicides, Industrial ; *Pythium ; Lactuca ; Pest Control, Biological ; Plant Diseases/prevention &amp; control/microbiology ; Water ; High-Throughput Nucleotide Sequencing ; },
abstract = {Aquaponics is defined as a sustainable and integrated system that combines fish aquaculture and hydroponic plant production in the same recirculated water loop. A recent study using high-throughput sequencing (HTS) technologies highlighted that microbial communities from an aquaponic system could control one of the most problematic pathogens in soilless lettuce culture, namely, Pythium aphanidermatum. Therefore, this study aims at isolating the microorganisms responsible for this biocontrol action. Based on the most promising genera identified by HTS, an innovative strategy for isolating and testing original biocontrol agents from aquaponic water was designed to control P. aphanidermatum. Eighty-two bacterial strains and 18 fungal strains were isolated, identified by Sanger sequencing, and screened in vivo to control damping-off of lettuce seeds caused by P. aphanidermatum. Out of these 100 isolates, the eight most efficacious ones were selected and further tested individually to control root rot disease caused by the same pathogen at a later stage of lettuce growth. Strains SHb30 (Sphingobium xenophagum), G2 (Aspergillus flavus), and Chito13 (Mycolicibacterium fortuitum) decreased seed damping-off at a better rate than a propamocarb fungicide and a Pseudomonas chlororaphis registered biocontrol agent did. In root rot bioassays, lettuce mortality was prevented by applying strains G2 and Chito13, which were at least as efficacious as the fungicide or biopesticide controls. Lettuce disease symptoms and mortality were eradicated by strain SHb30 in the first bioassay, but not in the second one. These results show that aquaponic systems are promising sources of original biocontrol agents, and that HTS-guided strategies could represent interesting approaches to identify new biocontrol agents.},
}
@article {pmid36333944,
year = {2022},
author = {Zhang, S and Yang, Q and Defoirdt, T},
title = {Indole analogues decreasing the virulence of Vibrio campbellii towards brine shrimp larvae.},
journal = {Microbial biotechnology},
volume = {15},
number = {12},
pages = {2917-2928},
pmid = {36333944},
issn = {1751-7915},
support = {//China Scholarship Council/ ; 1500219N//Scientific Research Fund of Flanders/ ; //Special Research Fund of Ghent University/ ; },
mesh = {Animals ; *Artemia/microbiology ; Larva/microbiology ; *Vibrio ; },
abstract = {Indole signalling has been proposed as a potential target for the development of novel virulence inhibitors to control bacterial infections. However, the major structural features of indole analogues that govern antivirulence activity remain unexplored. Therefore, we investigated the impact of 26 indole analogues on indole-regulated virulence phenotypes in Vibrio campbellii and on the virulence of the bacterium in a gnotobiotic brine shrimp model. The results demonstrated that 10 indole analogues significantly increased the fluorescence of indole reporter strain Vibrio cholerae S9149, 21 of them decreased the swimming motility of V. campbellii, and 13 of them significantly decreased the biofilm formation of V. campbellii. Further, we found that 1-methylindole, indene, 2,3-benzofuran, thianaphthene, indole-3-acetonitrile, methyl indole-3-carboxylate, 3-methylindole, and indole-2-carboxaldehyde exhibited a significant protective effect on brine shrimp larvae against V. campbellii infection, resulting in survival rates of challenged brine shrimp above 80%. The highest survival of shrimp larvae (98%) was obtained with indole-3-acetonitrile, even at a relatively low concentration of 20 μM. Importantly, the indole analogues did not affect bacterial growth, both in vitro and in vivo. These results indicate the potential of indole analogues in applications aiming at the protection of shrimp from vibriosis.},
}
@article {pmid36333915,
year = {2023},
author = {Berry, O and Briand, E and Bagot, A and Chaigné, M and Meslet-Cladière, L and Wang, J and Grovel, O and Jansen, JJ and Ruiz, N and du Pont, TR and Pouchus, YF and Hess, P and Bertrand, S},
title = {Deciphering interactions between the marine dinoflagellate Prorocentrum lima and the fungus Aspergillus pseudoglaucus.},
journal = {Environmental microbiology},
volume = {25},
number = {2},
pages = {250-267},
pmid = {36333915},
issn = {1462-2920},
mesh = {Marine Toxins ; *Dinoflagellida/metabolism ; Aspergillus ; Chromatography, High Pressure Liquid/methods ; *Microalgae/metabolism ; },
abstract = {The comprehension of microbial interactions is one of the key challenges in marine microbial ecology. This study focused on exploring chemical interactions between the toxic dinoflagellate Prorocentrum lima and a filamentous fungal species, Aspergillus pseudoglaucus, which has been isolated from the microalgal culture. Such interspecies interactions are expected to occur even though they were rarely studied. Here, a co-culture system was designed in a dedicated microscale marine-like condition. This system allowed to explore microalgal-fungal physical and metabolic interactions in presence and absence of the bacterial consortium. Microscopic observation showed an unusual physical contact between the fungal mycelium and dinoflagellate cells. To delineate specialized metabolome alterations during microalgal-fungal co-culture metabolomes were monitored by high-performance liquid chromatography coupled to high-resolution mass spectrometry. In-depth multivariate statistical analysis using dedicated approaches highlighted (1) the metabolic alterations associated with microalgal-fungal co-culture, and (2) the impact of associated bacteria in microalgal metabolome response to fungal interaction. Unfortunately, only a very low number of highlighted features were fully characterized. However, an up-regulation of the dinoflagellate toxins okadaic acid and dinophysistoxin 1 was observed during co-culture in supernatants. Such results highlight the importance to consider microalgal-fungal interactions in the study of parameters regulating toxin production.},
}
@article {pmid36333353,
year = {2022},
author = {Barret, M and Gandois, L and Thalasso, F and Martinez Cruz, K and Sepulveda Jauregui, A and Lavergne, C and Teisserenc, R and Aguilar, P and Gerardo Nieto, O and Etchebehere, C and Martins Dellagnezze, B and Bovio Winkler, P and Fochesatto, GJ and Tananaev, N and Svenning, MM and Seppey, C and Tveit, A and Chamy, R and Astorga España, MS and Mansilla, A and Van de Putte, A and Sweetlove, M and Murray, AE and Cabrol, L},
title = {A combined microbial and biogeochemical dataset from high-latitude ecosystems with respect to methane cycle.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {674},
pmid = {36333353},
issn = {2052-4463},
mesh = {Carbon Dioxide/analysis ; *Greenhouse Gases ; Methane/analysis ; *Microbiota ; Soil ; Wetlands ; },
abstract = {High latitudes are experiencing intense ecosystem changes with climate warming. The underlying methane (CH4) cycling dynamics remain unresolved, despite its crucial climatic feedback. Atmospheric CH4 emissions are heterogeneous, resulting from local geochemical drivers, global climatic factors, and microbial production/consumption balance. Holistic studies are mandatory to capture CH4 cycling complexity. Here, we report a large set of integrated microbial and biogeochemical data from 387 samples, using a concerted sampling strategy and experimental protocols. The study followed international standards to ensure inter-comparisons of data amongst three high-latitude regions: Alaska, Siberia, and Patagonia. The dataset encompasses different representative environmental features (e.g. lake, wetland, tundra, forest soil) of these high-latitude sites and their respective heterogeneity (e.g. characteristic microtopographic patterns). The data included physicochemical parameters, greenhouse gas concentrations and emissions, organic matter characterization, trace elements and nutrients, isotopes, microbial quantification and composition. This dataset addresses the need for a robust physicochemical framework to conduct and contextualize future research on the interactions between climate change, biogeochemical cycles and microbial communities at high-latitudes.},
}
@article {pmid36332310,
year = {2023},
author = {Daille, LK and Aguirre, J and Anguita, J and Galarce, C and Caro-Lara, L and Armijo, F and Vargas, IT and Pizarro, G and Walczak, M and De la Iglesia, R},
title = {When material science meets microbial ecology: Bacterial community selection on stainless steels in natural seawater.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {221},
number = {},
pages = {112955},
doi = {10.1016/j.colsurfb.2022.112955},
pmid = {36332310},
issn = {1873-4367},
mesh = {Humans ; *Steel ; *Stainless Steel ; Materials Science ; Corrosion ; Seawater/microbiology ; Biofilms ; Bacteria ; Oxides ; },
abstract = {The passive film depends on the alloy's composition and the exposure conditions. How the surface composition affects the selection of microbial biofilms though, has not been fully elucidated or incorporated into the analysis of corrosive biofilms. The degradation of stainless steel (SS) exposed to natural seawater was studied to understand how the oxide layer composition of SS could affect the selection and variability of the bacterial community. To accomplish this goal, austenitic and superferritic SS grades were exposed to natural seawater on the central coast of Chile. The deterioration of steel and qualitative description of biofilm formation was monitored at different exposure periods. Biofilms were evaluated based on massive sequencing analysis of the bacterial community and subsequent ecological studies. The results revealed that variability of the calculated corrosion rate correlated with the similarity of the bacterial community within samples from each SS and its corrosion inferred capacity. The associated bacterial families showed a higher representation in SSs with a more significant increase in the Fe/Cr ratio over the exposure time. These findings revealed that iron content in the oxide layer represents a key feature of the surface composition for selecting bacterial assemblages in marine environments.},
}
@article {pmid36332298,
year = {2022},
author = {Lin, Q and De Vrieze, J and Fang, X and Li, L and Li, X},
title = {Microbial life strategy with high rRNA operon copy number facilitates the energy and nutrient flux in anaerobic digestion.},
journal = {Water research},
volume = {226},
number = {},
pages = {119307},
doi = {10.1016/j.watres.2022.119307},
pmid = {36332298},
issn = {1879-2448},
mesh = {Swine ; Animals ; *rRNA Operon ; RNA, Ribosomal, 16S/genetics ; *Manure ; Anaerobiosis ; DNA Copy Number Variations ; Nutrients ; Bioreactors ; Methane ; },
abstract = {Microbial life strategy, reflected by rRNA operon (rrn) copy number, determines microbial ecological roles. However, the relationship between microbial life strategy and the energy and nutrient flux in anaerobic digestion (AD) remains elusive. This study investigated microbial rrn copy number and expression ratio using amplicon sequencing of 16S rRNA gene and 16S rRNA, and monitored CH4 daily production to approximate the status of energy and nutrient flux in semi-continuous AD. A significantly positive correlation between the mean rrn copy number of microbial communities in digestate and CH4 daily production was detected in the control treatment fed swine manure. The reduced feedstock complexity, by replacing parts of swine manure with fructose or apple waste, weakened the correlation. When feedstock complexity was increased again, the correlation was strengthened again. Similar results were detected in mean rrn expression ratio of microbial communities. The responses of mean rrn copy number and expression ratio of communities to feedstock addition differed between the reduced feedstock complexity and the control treatment, as well as between in digestate and in straw. Our findings reveal a novel relationship between microbial community life strategy and the energy and nutrient flux, and the roles of feedstock characteristics therein in AD.},
}
@article {pmid36331579,
year = {2023},
author = {Cortés-Pérez, S and Ferrera-Cerrato, R and Rodríguez-Zaragoza, S and Alarcón, A},
title = {Short-Term Evaluation of the Spatial Distribution of Trophic Groups of Amoebae in the Rhizosphere of Zea mays Inoculated with Rhizophagus intraradices.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {997-1009},
pmid = {36331579},
issn = {1432-184X},
mesh = {Plant Roots/microbiology ; Zea mays/microbiology ; Rhizosphere ; Ecosystem ; *Amoeba ; *Mycorrhizae ; Seedlings ; Bacteria ; Soil ; },
abstract = {Primary production in terrestrial ecosystems is sustained by plants, microbiota, and fungi, which are the major organic matter providers in the root zone, setting in motion the soil food webs. Predators like soil amoebae voraciously feed on bacteria, fungi, and microbial eukaryotes releasing the nutrients sequestered in their biomass. Early food web setting up is crucial for seedling nutrition and its further development after establishment. Mycorrhizal fungi are more than phosphorus providers, and we wonder what their role is in structuring the predators' trophic groups in the root zone. We evaluated the effect of Rhizophagus intraradices inoculated in Zea mays (mycorrhizosphere), on the structuration of amoebae trophic groups along vertical and horizontal (3, 6, and 9 cm) soil distribution when compared to un-inoculated plants, after 20 days in microcosms. Amoebae species richness was highest in non-mycorrhizal seedlings in the root zone at 6- to 9-cm depth, and 3 cm away from plants. More bacterial species are needed when plants are devoid of mycorrhiza, and their influence is constrained 3 cm away from roots. Higher diversity of trophic groups was recorded at mycorrhizal seedlings and at the compartment influenced by the mycelium at 6- to 9-cm depth. The highest bacterivorous diversity, higher number of rare species and protozoa-eating amoebae, and the absence of fungivorous group recorded at the mycorrhizosphere of Z. mays, indicate that the community was very different from the non-mycorrhizal plants. We conclude that the arbuscular mycorrhizal fungus exerts significant changes on the community of trophic groups of amoebae.},
}
@article {pmid36331034,
year = {2022},
author = {Schrad, N and Pensky, J and Gorski, G and Beganskas, S and Fisher, AT and Saltikov, C},
title = {Soil characteristics and redox properties of infiltrating water are determinants of microbial communities at managed aquifer recharge sites.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {12},
pages = {},
doi = {10.1093/femsec/fiac130},
pmid = {36331034},
issn = {1574-6941},
mesh = {Soil/chemistry ; *Groundwater/chemistry ; *Microbiota ; Carbon/analysis ; Oxidation-Reduction ; Soil Microbiology ; },
abstract = {In this study, we conducted a meta-analysis of soil microbial communities at three, pilot-scale field sites simulating shallow infiltration for managed aquifer recharge (MAR). We evaluated shifts in microbial communities after infiltration across site location, through different soils, with and without carbon-rich amendments added to test plots. Our meta-analysis aims to enable more effective MAR basin design by identifying potentially important interactions between soil physical-geochemical parameters and microbial communities across several geographically separate MAR basins. We hypothesized infiltration and carbon amendments would lead to common changes in subsurface microbial communities at multiple field sites but instead found distinct differences. Sites with coarser (mainly sandy) soil had large changes in diversity and taxa abundance, while sites with finer soils had fewer significant changes in genera, despite having the greatest increase in nitrogen cycling. Below test plots amended with a carbon-rich permeable reactive barrier, we observed more nitrate removal and a decrease in genera capable of nitrification. Multivariate statistics determined that the soil texture (a proxy for numerous soil characteristics) was the main determinant of whether the microbial community composition changed because of infiltration. These results suggest that microbial communities in sandy soil with carbon-rich amendments are most impacted by infiltration. Soil composition is a critical parameter that links between microbial communities and nutrient cycling during infiltration and could influence the citing and operation of MAR to benefit water quality and supply.},
}
@article {pmid36330300,
year = {2022},
author = {Klein, M and Stewart, JD and Porter, SS and Weedon, JT and Kiers, ET},
title = {Evolution of manipulative microbial behaviors in the rhizosphere.},
journal = {Evolutionary applications},
volume = {15},
number = {10},
pages = {1521-1536},
pmid = {36330300},
issn = {1752-4571},
abstract = {The rhizosphere has been called "one of the most complex ecosystems on earth" because it is a hotspot for interactions among millions of microbial cells. Many of these are microbes are also participating in a dynamic interplay with host plant tissues, signaling pathways, and metabolites. Historically, breeders have employed a plant-centric perspective when trying to harness the potential of microbiome-derived benefits to improve productivity and resilience of economically important plants. This is potentially problematic because: (i) the evolution of the microbes themselves is often ignored, and (ii) it assumes that the fitness of interacting plants and microbes is strictly aligned. In contrast, a microbe-centric perspective recognizes that putatively beneficial microbes are still under selection to increase their own fitness, even if there are costs to the host. This can lead to the evolution of sophisticated, potentially subtle, ways for microbes to manipulate the phenotype of their hosts, as well as other microbes in the rhizosphere. We illustrate this idea with a review of cases where rhizosphere microbes have been demonstrated to directly manipulate host root growth, architecture and exudation, host nutrient uptake systems, and host immunity and defense. We also discuss indirect effects, whereby fitness outcomes for the plant are a consequence of ecological interactions between rhizosphere microbes. If these consequences are positive for the plant, they can potentially be misconstrued as traits that have evolved to promote host growth, even if they are a result of selection for unrelated functions. The ubiquity of both direct microbial manipulation of hosts and context-dependent, variable indirect effects leads us to argue that an evolutionary perspective on rhizosphere microbial ecology will become increasingly important as we continue to engineer microbial communities for crop production.},
}
@article {pmid36329848,
year = {2022},
author = {Xu, H and Xue, Y and Na, N and Wu, N and Zhao, Y and Sun, L and Qili, M and Wang, T and Zhong, J},
title = {Fermentation quality, bacterial community, and aerobic stability of ensiling Leymus chinensis with lactic acid bacteria or/and water after long-term storage.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {959018},
pmid = {36329848},
issn = {1664-302X},
abstract = {Leymus chinensis is a major forage resource for herbivores on typical steppe and meadow steppes in Northern China. This study aimed to reveal the fermentation quality, bacterial community, and aerobic stability of L. chinensis silage treated with lactic acid bacteria or/and water after long-term storage. Leymus chinensis was harvested at the heading stage and ensiled with lactic acid bacteria [LAB, 2.00 ml/kg fresh weight (FW) of LAB, L], water (100 ml/kg FW of distilled water, W), or a combination of both [2.00 ml/kg fresh weight (FW) of LAB and 100 ml/kg FW of distilled water, LW] in polyethylene laboratory-scale silos (diameter, 20 cm; height, 30 cm) at a density of 650 kg/m[3]. As a control silage (CK), untreated L. chinensis silage was also assessed. The samples were taken at 0 day of opening after 300 days of ensiling (CK_0d, L_0d, W_0d, and LW_0d) and at 10 days of opening (CK_10d, L_10d, W_10d, and LW_10d). The fermentation quality, microbial counts, bacterial community, and aerobic stability of the silage were assessed. The CK_0d contained higher pH and aerobic bacteria count, and lower LA and BC concentrations than L_0d, W_0d, and LW_0d (p < 0.05), and the LAB and yeasts were only detected in CK at 0 day of opening. Lactobacillus had the most abundance among bacterial genera in all silages at 0 day of opening. Just CK had 2°C above the ambient temperature during aerobic exposure (at 224 h). During aerobic exposure, the pH and microbial counts in CK increased (p < 0.05), and Lactobacillus in L and LW had decreasing abundance (p < 0.05). The CK_10d had higher pH and microbial counts, and lower lactic acid and buffering capacity than L_10d, W_10d, and LW_10d (p < 0.05). At 10 days of opening, the coliforms and yeasts were just detected in CK, and Lactobacillus also had the most abundance among bacterial genera in all silages at 10 days of opening. Overall, inoculating LAB and adding water improved the fermentation quality and the aerobic exposure of L. chinensis silage after long-term storage. The activities of coliforms and yeasts during aerobic exposure contributed to the aerobic deterioration of L. chinensis silage without any treating. Lactobacillus dominated the bacterial communities of all silage at 0 and 10 days of opening. During aerobic exposure, the abundance of Lactobacillus reduced in L. chinensis silage treated with LAB or water.},
}
@article {pmid36329282,
year = {2023},
author = {Fang, FZ and Chen, SL and Gui, HY and Li, ZJ and Zhang, XF},
title = {Long-Read Sequencing Analysis Revealed the Impact of Forest Conversion on Soil Fungal Diversity in Limu Mountain, Hainan.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {872-886},
pmid = {36329282},
issn = {1432-184X},
mesh = {Animals ; *Ecosystem ; *Soil/chemistry ; Fungi/genetics ; Soil Microbiology ; Forests ; },
abstract = {Soil fungi are essential to soil microorganisms that play an important role in the ecosystem's soil carbon cycle and mineral nutrient transformation. Understanding the structural characteristics and diversity of soil fungal communities helps understand the health of forest ecosystems. The transition from tropical rainforest to artificial forest greatly impacts the composition and diversity of fungal communities. Hainan Limushan tropical rainforest National Park has a large area of artificial forests. Ecologists have conducted in-depth studies on the succession of animals and plants to regenerate tropical rainforests. There are few reports on the diversity of soil fungi and its influencing factors in the succession of tropical rainforests in Limu Mountain. In this study, 44 soil samples from five different stands were collected in the tropical rainforest of Limushan, Hainan. High-throughput sequencing of rDNA in its region was used to analyze fungal communities and study their α and β diversity. Analysis of variance and multiple regression models was used to analyze soil variables and fungal functional groups to determine the effects of interaction between fungi and environmental factors. A total of 273,996 reads and 1290 operational taxonomic units (OTUs) were obtained, belonging to 418 species, 325 genera, 159 families, eight phyla, 30 classes, and 73 orders. The results showed that the composition of soil fungal communities in the five stands was similar, with ascomycetes accounting for 70.5% and basidiomycetes accounting for 14.7%. α and β diversity analysis showed that soil fungi in Limushan tropical rainforest had high abundance and diversity. Multiple regression analysis between soil variables and functional groups showed that organic matter, TN, TP, TK, and AK were excellent predictors for soil fungi. TP was the strongest predictor in all functional groups except soil saprotroph. Organic matter and total nitrogen were the strongest predictors of soil rot. The transformation from tropical rainforest to artificial forest in Limushan did not change the soil fungal community structure, but the richness and diversity of soil fungi changed. The forest transformation did not lead to decreased soil fungal abundance and diversity. Different vegetation types and soil properties affect the diversity of soil fungal communities. We found that Caribbean pine plantations can improve soil fungal diversity, while long-term Eucalyptus spp. plantations may reduce soil fungal diversity.},
}
@article {pmid36329197,
year = {2022},
author = {van Spanning, RJM and Guan, Q and Melkonian, C and Gallant, J and Polerecky, L and Flot, JF and Brandt, BW and Braster, M and Iturbe Espinoza, P and Aerts, JW and Meima-Franke, MM and Piersma, SR and Bunduc, CM and Ummels, R and Pain, A and Fleming, EJ and van der Wel, NN and Gherman, VD and Sarbu, SM and Bodelier, PLE and Bitter, W},
title = {Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem.},
journal = {Nature microbiology},
volume = {7},
number = {12},
pages = {2089-2100},
pmid = {36329197},
issn = {2058-5276},
mesh = {*Ecosystem ; Proteomics ; Phylogeny ; Methane/metabolism ; *Mycobacterium/genetics ; },
abstract = {So far, only members of the bacterial phyla Proteobacteria and Verrucomicrobia are known to grow methanotrophically under aerobic conditions. Here we report that this metabolic trait is also observed within the Actinobacteria. We enriched and cultivated a methanotrophic Mycobacterium from an extremely acidic biofilm growing on a cave wall at a gaseous chemocline interface between volcanic gases and the Earth's atmosphere. This Mycobacterium, for which we propose the name Candidatus Mycobacterium methanotrophicum, is closely related to well-known obligate pathogens such as M. tuberculosis and M. leprae. Genomic and proteomic analyses revealed that Candidatus M. methanotrophicum expresses a full suite of enzymes required for aerobic growth on methane, including a soluble methane monooxygenase that catalyses the hydroxylation of methane to methanol and enzymes involved in formaldehyde fixation via the ribulose monophosphate pathway. Growth experiments combined with stable isotope probing using [13]C-labelled methane confirmed that Candidatus M. methanotrophicum can grow on methane as a sole carbon and energy source. A broader survey based on 16S metabarcoding suggests that species closely related to Candidatus M. methanotrophicum may be abundant in low-pH, high-methane environments.},
}
@article {pmid36329192,
year = {2022},
author = {Slack, E and Diard, M},
title = {Resistance is futile? Mucosal immune mechanisms in the context of microbial ecology and evolution.},
journal = {Mucosal immunology},
volume = {15},
number = {6},
pages = {1188-1198},
pmid = {36329192},
issn = {1935-3456},
mesh = {Animals ; Humans ; Immunoglobulin A, Secretory ; Mucous Membrane ; *Gastrointestinal Microbiome ; Bacteria ; *Vaccines ; Inflammation ; Intestinal Mucosa ; Mammals ; },
abstract = {In the beginning it was simple: we injected a protein antigen and studied the immune responses against the purified protein. This elegant toolbox uncovered thousands of mechanisms via which immune cells are activated. However, when we consider immune responses against real infectious threats, this elegant simplification misses half of the story: the infectious agents are typically evolving orders-of-magnitude faster than we are. Nowhere is this more pronounced than in the mammalian large intestine. A bacterium representing only 0.1% of the human gut microbiota will have a population size of 10[9] clones, each actively replicating. Moreover, the evolutionary pressure from other microbes is at least as profound as direct effects of the immune system. Therefore, to really understand intestinal immune mechanisms, we need to understand both the host response and how rapid microbial evolution alters the apparent outcome of the response. In this review we use the examples of intestinal inflammation and secretory immunoglobulin A (SIgA) to highlight what is already known (Fig. 1). Further, we will explore how these interactions can inform immunotherapy and prophylaxis. This has major implications for how we design effective mucosal vaccines against increasingly drug-resistant bacterial pathogens Fig. 1 THE IMMUNE RESPONSE SHAPES THE FITNESS LANDSCAPE IN THE GASTRO-INTESTINAL TRACT.: The red arrows depict possible evolutionary paths of a novel colonizer along adaptive peaks in the intestinal fitness landscapes that change with the status of the host immune system. The flat surfaces represent the non-null fitness baselines (values x or y) at which a bacterium can establish at minimum carrying capacity. a In the healthy gut, metabolic competence, resistance to aggressions by competitors and predators, swift adaptation to rapid fluctuations as well as surviving acidic pH and the flow of the intestinal content, represent potent selective pressures and as many opportunities for bacteria to increase fitness by phenotypic or genetic variations. b When pathogens trigger acute inflammation, bacteria must adapt to iron starvation, killing by immune cells and antimicrobial peptides, and oxidative stress, while new metabolic opportunities emerge. c When high-affinity SIgA are produced against a bacterium, e.g., after oral vaccination, escape of SIgA by altering or losing surface epitopes becomes crucial for maximum fitness. However, escaping polyvalent SIgA responses after vaccination with "evolutionary trap" vaccines leads to evolutionary trade-offs: A fitness maximum is reached in the vaccinated host gut that represents a major disadvantage for transmission into naïve hosts (fitness diminished below x) (d).},
}
@article {pmid36328255,
year = {2023},
author = {Abdullah Al, M and Wang, W and Jin, L and Chen, H and Xue, Y and Jeppesen, E and Majaneva, M and Xu, H and Yang, J},
title = {Planktonic ciliate community driven by environmental variables and cyanobacterial blooms: A 9-year study in two subtropical reservoirs.},
journal = {The Science of the total environment},
volume = {858},
number = {Pt 2},
pages = {159866},
doi = {10.1016/j.scitotenv.2022.159866},
pmid = {36328255},
issn = {1879-1026},
mesh = {*Ciliophora/classification/physiology ; *Cyanobacteria/physiology ; *Ecosystem ; Eutrophication ; Lakes/microbiology/parasitology ; Phylogeny ; Plankton/classification/physiology ; Biodiversity ; Population Dynamics ; },
abstract = {It is well-established that environmental variability and cyanobacterial blooms have major effects on the assembly and functioning of bacterial communities in both marine and freshwater habitats. It remains unclear, however, how the ciliate community responds to such changes over the long-term, particularly in subtropical lake and reservoir ecosystems. We analysed 9-year planktonic ciliate data series from the surface water of two subtropical reservoirs to elucidate the role of cyanobacterial bloom and environmental variabilities on the ciliate temporal dynamics. We identified five distinct periods of cyanobacterial succession in both reservoirs. Using multiple time-scale analyses, we found that the interannual variability of ciliate communities was more strongly related to cyanobacterial blooms than to other environmental variables or to seasonality. Moreover, the percentage of species turnover across cyanobacterial bloom and non-bloom periods increased significantly with time over the 9-year period. Phylogenetic analyses further indicated that 84 %-86 % of ciliate community turnover was governed by stochastic dispersal limitation or undominated processes, suggesting that the ciliate communities in subtropical reservoirs were mainly controlled by neutral processes. However, short-term blooms increased the selection pressure and drove 30 %-53 % of the ciliate community turnover. We found that the ciliate community composition was influenced by environmental conditions with nutrients, cyanobacterial biomass and microzooplankton having direct and/or indirect significant effects on the ciliate taxonomic or functional community dynamics. Our results provide new insights into the long-term temporal dynamics of planktonic ciliate communities under cyanobacterial bloom disturbance.},
}
@article {pmid36327936,
year = {2022},
author = {Wong, YY and Lee, CW and Chai, SCY and Lim, JH and Bong, CW and Sim, EUH and Narayanan, K and Hii, YS and Wang, AJ},
title = {Distribution of faecal indicator bacteria in tropical waters of Peninsular Malaysia and their decay rates in tropical seawater.},
journal = {Marine pollution bulletin},
volume = {185},
number = {Pt A},
pages = {114297},
doi = {10.1016/j.marpolbul.2022.114297},
pmid = {36327936},
issn = {1879-3363},
mesh = {*Escherichia coli/physiology ; Malaysia ; *Seawater/microbiology ; Feces/microbiology ; Bacteria ; Water Microbiology ; },
abstract = {We investigated the appropriateness of faecal indicator bacteria in tropical waters. We compared total coliform (undetectable to 7.2 × 10[5] cfu 100 mL[-1]), faecal coliform (undetectable to 6.1 × 10[5] cfu 100 mL[-1]) and enterococci (undetectable to 3.1 × 10[4] cfu 100 mL[-1]) distribution in Peninsular Malaysia. Faecal indicator bacteria was highest in freshwater, and lowest in seawater (q > 4.18, p < 0.01). We also measured the decay rates of Escherichia coli and Enterococcus faecium in microcosms. In seawater, average decay rate for E. coli was 0.084 ± 0.029 h[-1], and higher than E. faecium (0.048 ± 0.024 h[-1]) (t = 2.527, p < 0.05). Grazing accounted for 54 % of both E. coli and E. faecium decay. E. coli decayed in the <0.02 μm seawater fraction (0.023 ± 0.012 h[-1]) but E. faecium sometimes grew. Seawater warming further uncoupled the response from both E. coli and E. faecium as E. faecium grew and E. coli decayed with warming. Our results suggested that the prevalence of faecal indicator bacteria in tropical waters was not due to faecal pollution alone, and this will have serious implications towards the use of these faecal indicator bacteria.},
}
@article {pmid36327839,
year = {2023},
author = {Moreira, VA and Cravo-Laureau, C and de Carvalho, ACB and Baldy, A and Bidone, ED and Sabadini-Santos, E and Duran, R},
title = {Microbial indicators along a metallic contamination gradient in tropical coastal sediments.},
journal = {Journal of hazardous materials},
volume = {443},
number = {Pt B},
pages = {130244},
doi = {10.1016/j.jhazmat.2022.130244},
pmid = {36327839},
issn = {1873-3336},
mesh = {Geologic Sediments ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Brazil ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; *Metals, Heavy/analysis ; },
abstract = {The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.},
}
@article {pmid36326874,
year = {2023},
author = {Chen, T and Zhao, M and Tang, X and Wang, W and Zhang, M and Tang, J and Wang, W and Wei, W and Ma, B and Zou, Y and Zhang, N and Mi, J and Wang, Y and Liao, X and Wu, Y},
title = {Serious Risk of Tigecycline Resistance in Escherichia coli Isolated from Swine Manure.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {947-958},
pmid = {36326874},
issn = {1432-184X},
mesh = {Humans ; Swine ; Animals ; Tigecycline/pharmacology ; *Escherichia coli/genetics ; *Manure/microbiology ; Doxycycline ; Anti-Bacterial Agents/pharmacology ; Tetracycline ; Microbial Sensitivity Tests ; },
abstract = {The emergence of the plasmid-mediated tigecycline resistance gene tetX family in pig farms has attracted worldwide attention. The use of tetracycline antibiotics in pig farms has a facilitating effect on the prevalence of the tetX family, but the relationship among its presence, expression, and resistance phenotype in resistant bacteria is unknown. In this study, the presence and expression characteristics of tetracycline resistance genes (TRGs) in 89 strains of doxycycline-resistant E. coli (DRE) isolated from pig manure samples from 20 pig farms under low concentrations of doxycycline stress (2 μg/mL) were analyzed. The detection rate of tetO was 96.63%, which is higher than those of other TRGs, such as tetA (94.38%), tetX (76.40%), tetB (73.03%), and tet(X4) (69.66%). At least three TRG types were present in DRE strains, which thus showed extensive resistance to tetracycline antibiotics, and 37% of these strains were resistant to tigecycline. In the presence of a low concentration of doxycycline, tetA played an important role, and the expression and existence ratio of TRGs indicated low expression of TRGs. Furthermore, the doxycycline resistance of DRE was jointly determined by the total absolute abundance of TRGs, and the absolute abundance of tetX and tet(X4) was significantly positively associated with tigecycline resistance in DRE (P < 0.05). Overall, DRE isolated from swine manure is an important reservoir of the tetX family, which suggests that DRE in swine manure has a high risk of tigecycline resistance, poses a potential threat to human health, and should be of public concern.},
}
@article {pmid36326287,
year = {2022},
author = {Bandekar, M and Abdolahpur Monikh, F and Kekäläinen, J and Tahvanainen, T and Kortet, R and Zhang, P and Guo, Z and Akkanen, J and Leskinen, JTT and Gomez-Gonzalez, MA and Krishna Darbha, G and Grossart, HP and Valsami-Jones, E and Kukkonen, JVK},
title = {Submicron Plastic Adsorption by Peat, Accumulation in Sphagnum Mosses and Influence on Bacterial Communities in Peatland Ecosystems.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {22},
pages = {15661-15671},
pmid = {36326287},
issn = {1520-5851},
mesh = {*Sphagnopsida/chemistry/microbiology ; Soil/chemistry ; Adsorption ; Plastics ; Bacteria ; *Microbiota ; },
abstract = {The smallest fraction of plastic pollution, submicron plastics (SMPs <1 μm) are expected to be ubiquitous in the environment. No information is available about SMPs in peatlands, which have a key role in sequestering carbon in terrestrial ecosystems. It is unknown how these plastic particles might behave and interact with (micro)organisms in these ecosystems. Here, we show that the chemical composition of polystyrene (PS) and poly(vinyl chloride) (PVC)-SMPs influenced their adsorption to peat. Consequently, this influenced the accumualtion of SMPs by Sphagnum moss and the composition and diversity of the microbial communities in peatland. Natural organic matter (NOM), which adsorbs from the surrounding water to the surface of SMPs, decreased the adsorption of the particles to peat and their accumulation by Sphagnum moss. However, the presence of NOM on SMPs significantly altered the bacterial community structure compared to SMPs without NOM. Our findings show that peatland ecosystems can potentially adsorb plastic particles. This can not only impact mosses themselves but also change the local microbial communities.},
}
@article {pmid36324386,
year = {2022},
author = {Li, Y and Xin, X and Song, W and Zhang, X and Chen, S and Wang, Q and Li, A and Li, Y},
title = {VHL syndrome without clear family history: A rare case report and literature review of Chinese patients.},
journal = {Frontiers in neurology},
volume = {13},
number = {},
pages = {951054},
pmid = {36324386},
issn = {1664-2295},
abstract = {OBJECTIVE: To analyze the clinical manifestations and imaging features of a hospitalized patient with intermittent headache who was finally diagnosed with von Hippel-Lindau (VHL) syndrome and to perform whole-exon gene detection to improve the understanding of the diagnosis and treatment strategies of the disease.<br><br>METHODS: A case of suspected VHL syndrome in Shanxi Provincial People's Hospital was analyzed. Proband DNA was also extracted for whole exome sequencing and screened for causative mutation sites, which were validated by Sanger sequencing. The literature about VHL gene mutations in Chinese patients in the past 10 years were also reviewed.<br><br>RESULTS: There is a heterozygous mutation site c.499C > G on the VHL gene on the short arm of chromosome 3 of the patient, which is a missense mutation. The mutation results in the substitution of arginine with glycine at amino acid 167 of the encoded protein, which may be primarily responsible for the disease in the patient with VHL syndrome. However, the mutation did not occur in other family members.<br><br>CONCLUSION: Early recognition and treatment of VHL syndrome can be available with genetic testing technology. Strengthening the understanding of this complex genetic disease and improving the diagnostic rate of VHL syndrome are helpful for the precise treatment of patients with this disease, which may help prolong the survival time of patients to a certain extent and improve their quality of life.},
}
@article {pmid36323973,
year = {2023},
author = {Ma, Y and Li, P and Zhong, H and He, M and Wang, B and Mou, X and Wu, L},
title = {The Ecological Differentiation of Particle-Attached and Free-Living Bacterial Communities in a Seasonal Flooding Lake-the Poyang Lake.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {795-809},
pmid = {36323973},
issn = {1432-184X},
support = {31660027//National Natural Science Foundation of China/ ; 31971470//National Natural Science Foundation of China/ ; 31560143//National Natural Science Foundation of China/ ; 2017ZX07301002-05//Collaborative Innovation Center for Water Treatment Technology and Materials/ ; 20202BAB203025//Natural Science Foundation of Jiangxi Province/ ; 20192ACB20021//Natural Science Foundation of Jiangxi Province/ ; },
mesh = {*Lakes/microbiology ; Seasons ; *Bacteria/genetics/metabolism ; Bacteroidetes ; China ; Water/metabolism ; },
abstract = {Particle-attached (PA) and free-living (FL) bacterial communities play essential roles in the biogeochemical cycling of essential nutrients in aquatic environments. However, little is known about the factors that drive the differentiation of bacterial lifestyles, especially in flooding lake systems. Here we assessed the compositional and functional similarities between the FL and PA bacterial fractions in a typical flooding lake-the Poyang Lake (PYL) of China. The results revealed that PA communities had significantly different compositions and functions from FL communities in every hydrological period, and the diversity of both PA and FL communities was affected mainly by the water regime rather than bacterial lifestyles. PA communities were more diverse and enriched with Proteobacteria and Bacteroidetes, while FL communities had more Actinobacteria. There was a higher abundance of photosynthetic and nitrogen-cycling bacterial groups in PA communities, but a higher abundance of members involved in hydrocarbon degradation, aromatic hydrocarbon degradation, and methylotrophy in FL communities. Water properties (e.g., temperature, pH, total phosphorus) significantly regulated the lifestyle variations of PA and FL bacteria in PYL. Collectively, our results have demonstrated a clear ecological differentiation of PA and FL bacterial communities in flooding lakes, suggesting that the connectivity between FL and PA bacterial fractions is water property-related rather than water regime-related.},
}
@article {pmid36322177,
year = {2023},
author = {Stupar, M and Savković, &#x17d; and Breka, K and Stamenković, S and Krizmanić, I and Vukojević, J and Grbić, ML},
title = {A Variety of Fungal Species on the Green Frogs' Skin (Pelophylax esculentus complex) in South Banat.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {859-871},
pmid = {36322177},
issn = {1432-184X},
mesh = {Animals ; Rana esculenta ; *Rana clamitans ; Ranidae/microbiology ; Anura ; Skin/microbiology ; },
abstract = {In the last several decades, amphibian populations have been declining worldwide. Many factors have been linked to global amphibian decline, including habitat destruction, pollution, introduced species, global environmental changes, and emerging infectious diseases. Recent studies of amphibian skin infections were mainly focused on the presence of chytridiomycosis, neglecting other members of the frogs' skin communities. The diversity pattern of fungal dwellers on the skin of green frogs (Pelophylax esculentus complex) was investigated. A total of 100 adults were sampled from three localities in South Banat (northern Serbia) over three consecutive years and detected fungal dwellers were identified using light microscopy and ITS and BenA gene sequencing. Structures belonging to fungi and fungus-like organisms including a variety of spores and different mycelia types were documented in the biofilm formed on amphibian skin, and are classified into 10 groups. In total, 42 fungal isolates were identified to species, section, or genus level. The difference in mycobiota composition between sampling points (localities and green frog taxa) was documented. The highest number of fungal structures and isolates was recorded on the hybrid taxon P. esculentus and locality Stevanove ravnice. Parental species showed a markedly lower diversity than the hybrid taxon and were more similar in diversity patterns and were placed in the same homogenous group. The locality Stevanove ravnice exhibited more pronounced differences in diversity pattern than the other two localities and was placed in a distinct and separate homogenous group. Among the fungal isolates, the highest isolation frequency was documented for Alternaria alternata, Aspergillus sp. sect. Nigri, Epicoccum nigrum, Fusarium proliferatum, and Trichoderma atroviride. Among the documented species, dematiaceous fungi, causative agents of chromomycosis in amphibians, were also recorded in this research with high isolation frequency. Also, some rare fungal species such as Quambalaria cyanescens and Pseudoteniolina globosa are documented for the first time in this research as microbial inhabitants of amphibian skin.},
}
@article {pmid36321898,
year = {2022},
author = {Spencer-Williams, I and Balangoda, A and Dabundo, R and Elliott, E and Haig, SJ},
title = {Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams.},
journal = {Microbiology spectrum},
volume = {10},
number = {6},
pages = {e0215822},
pmid = {36321898},
issn = {2165-0497},
mesh = {*Rivers/microbiology ; Lead/chemistry ; Phosphates ; *Drinking Water ; Corrosion ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Many cities across the nation are plagued by lead contamination in drinking water. As such, many drinking water utilities have undertaken lead service line (LSL) replacement to prevent further lead contamination. However, given the urgency of lead mitigation, and the socioeconomic challenges associated with LSL replacement, cities have used phosphate-based corrosion inhibitors (i.e., orthophosphate) alongside LSL replacement. While necessary to ensure public health protection from lead contamination, the addition of orthophosphate into an aging and leaking drinking water system may increase the concentration of phosphate leaching into urban streams characterized by century-old failing water infrastructure. Such increases in phosphate availability may cascade into nutrient and microbial community composition shifts. The purpose of this study was to determine how this occurs and to understand whether full-scale distribution system orthophosphate addition impacts the microbial ecology of urban streams. Through monthly collection of water samples from five urban streams before and after orthophosphate addition, significant changes in microbial community composition (16S rRNA amplicon sequencing) and in the relative abundance of typical freshwater taxa were observed. In addition, key microbial phosphorus and nitrogen metabolism genes (e.g., two component regulatory systems) were predicted to change via BugBase. No significant differences in the absolute abundances of total bacteria, Cyanobacteria, and "Candidatus Accumulibacter" were observed. Overall, the findings from this study provide further evidence that urban streams are compromised by unintentional hydrologic connections with drinking water infrastructure. Moreover, our results suggest that infiltration of phosphate-based corrosion inhibitors can impact urban streams and have important, as-yet-overlooked impacts on urban stream microbial communities. IMPORTANCE Elevated lead levels in drinking water supplies are a public health risk. As such, it is imperative for cities to urgently address lead contamination from aging drinking water supplies by way of lead service line replacements and corrosion control methods. However, when applying corrosion control methods, it is also important to consider the chemical and microbiological effects that can occur in natural settings, given that our water infrastructure is aging and more prone to leaks and breaks. Here, we examine the impacts on the microbial ecology of five urban stream systems before and after full-scale distribution system orthophosphate addition. Overall, the results suggest that infiltration of corrosion inhibitors may impact microbial communities; however, future work should be done to ascertain the true impact to protect both public and environmental health.},
}
@article {pmid36320358,
year = {2022},
author = {Simões, ACP and Fernandes, RP and Barreto, MS and Marques da Costa, GB and de Godoy, MG and Freire, DMG and Pereira, N},
title = {Growth of Methylobacterium organophilum in Methanol for the Simultaneous Production of Single-Cell Protein and Metabolites of Interest.},
journal = {Food technology and biotechnology},
volume = {60},
number = {3},
pages = {338-349},
pmid = {36320358},
issn = {1330-9862},
abstract = {RESEARCH BACKGROUND: This study aims to monitor the growth of the methylotrophic bacteria Methylobacterium organophilum in a culture medium with methanol as a carbon source and to verify the production of unicellular proteins and other biomolecules, such as carotenoids, exopolysaccharides and polyhydroxyalkanoates, making them more attractive as animal feed.<br><br>EXPERIMENTAL APPROACH: Bacterial growth was studied in shake flasks using different carbon/nitrogen (C:N) ratios to determine their best ratio for achieving the highest volumetric productivity of cells and substrate consumption rate. This optimal parameter was further used in a fed-batch operating bioreactor system to define the kinetic profile of cell growth. Methanol consumption was measured by HPLC analysis and the extracted pigments were analyzed by liquid chromatography/mass spectrometry. Chemical composition and rheological properties of the produced exopolysaccharides were also determined.<br><br>RESULTS AND CONCLUSIONS: The best experimental parameters were verified using an initial methanol concentration of 7 g/L in the culture medium. The same initial substrate concentration was used in the fed-batch operation and after 60 h of cultivation 5 g/L of biomass were obtained. The accumulation of carotenoids associated with cell growth was monitored, reaching a concentration of 1.6 mg/L at the end of the process. These pigments were then analyzed and characterized as a set of xanthophylls (oxidized carotenoids). In addition, two other product types were identified during the fed-batch operation: exopolysaccharides, which reached a concentration of 8.9 g/L at the end of the cultivation, and an intracellular granular structure that was detected by transmission electron microscopy (TEM), suggesting the accumulation of polyhydroxyalkanoate (PHA), most likely polyhydroxybutyrate.<br><br>Methylobacterium organophilum demonstrated a unique ability to produce compounds of commercial interest. The distinct metabolic diversity of this bacterium makes room for its use in biorefineries.},
}
@article {pmid36319743,
year = {2023},
author = {Ayilara, MS and Adeleke, BS and Babalola, OO},
title = {Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1113-1135},
pmid = {36319743},
issn = {1432-184X},
support = {123634//National Research Foundation/ ; 132595//National Research Foundation/ ; },
mesh = {*Glycine max/microbiology ; Bioprospecting ; Bacteria/genetics/metabolism ; Agriculture ; *Microbiota ; Soil ; Crops, Agricultural ; Soil Microbiology ; },
abstract = {This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.},
}
@article {pmid36318280,
year = {2023},
author = {Hill, AJ and Grisnik, M and Walker, DM},
title = {Bacterial Skin Assemblages of Sympatric Salamanders Are Primarily Shaped by Host Genus.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1364-1373},
pmid = {36318280},
issn = {1432-184X},
mesh = {Animals ; *Urodela/microbiology ; RNA, Ribosomal, 16S/genetics ; *Skin/microbiology ; Animals, Wild ; Bacteria/genetics ; },
abstract = {Bacterial assemblages on the skins of amphibians are known to influence pathogen resistance and other important physiological functions in the host. Host-specific factors and the environment play significant roles in structuring skin assemblages. This study used high-throughput 16S rRNA sequencing and multivariate analyses to examine differences in skin-bacterial assemblages from 246 salamanders belonging to three genera in the lungless family Plethodontidae along multiple spatial gradients. Composition and α- and β-diversity of bacterial assemblages were defined, indicator species were identified for each host group, and the relative influences of host- versus environment-specific ecological factors were evaluated. At the broadest spatial scale, host genus, host species, and sampling site were predictive of skin assemblage structure, but host genus and species were more influential after controlling for the marginal effects of site, as well as nestedness of site. Furthermore, assemblage similarity within each host genus did not change with increasing geographic distance. At the smallest spatial scale, site-specific climate analyses revealed different relationships to climatic variables for each of the three genera, and these relationships were determined by host ecomode. Variation in bacterial assemblages of terrestrial hosts correlated with landscape-level climatic variability, and this pattern decayed with increasing water dependence of the host. Results from this study highlight host-specific considerations for researchers studying wildlife diseases in co-occurring, yet ecologically divergent, species.},
}
@article {pmid36317499,
year = {2022},
author = {Bachimanchi, H and Midtvedt, B and Midtvedt, D and Selander, E and Volpe, G},
title = {Microplankton life histories revealed by holographic microscopy and deep learning.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36317499},
issn = {2050-084X},
support = {677511/ERC_/European Research Council/International ; },
mesh = {Animals ; *Phytoplankton ; *Deep Learning ; Microscopy ; Zooplankton ; Oceans and Seas ; Seawater ; },
abstract = {The marine microbial food web plays a central role in the global carbon cycle. However, our mechanistic understanding of the ocean is biased toward its larger constituents, while rates and biomass fluxes in the microbial food web are mainly inferred from indirect measurements and ensemble averages. Yet, resolution at the level of the individual microplankton is required to advance our understanding of the microbial food web. Here, we demonstrate that, by combining holographic microscopy with deep learning, we can follow microplanktons throughout their lifespan, continuously measuring their three-dimensional position and dry mass. The deep-learning algorithms circumvent the computationally intensive processing of holographic data and allow rapid measurements over extended time periods. This permits us to reliably estimate growth rates, both in terms of dry mass increase and cell divisions, as well as to measure trophic interactions between species such as predation events. The individual resolution provides information about selectivity, individual feeding rates, and handling times for individual microplanktons. The method is particularly useful to detail the rates and routes of organic matter transfer in micro-zooplankton, the most important and least known group of primary consumers in the oceans. Studying individual interactions in idealized small systems provides insights that help us understand microbial food webs and ultimately larger-scale processes. We exemplify this by detailed descriptions of micro-zooplankton feeding events, cell divisions, and long-term monitoring of single cells from division to division.},
}
@article {pmid36316374,
year = {2022},
author = {Noiset, P and Cabirol, N and Rojas-Oropeza, M and Warrit, N and Nkoba, K and Vereecken, NJ},
title = {Honey compositional convergence and the parallel domestication of social bees.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {18280},
pmid = {36316374},
issn = {2045-2322},
support = {T.0255.20//Fonds De La Recherche Scientifique - FNRS/ ; },
mesh = {Bees ; Animals ; *Honey/analysis ; Domestication ; Magnetic Resonance Spectroscopy ; Thailand ; Mexico ; },
abstract = {Honey collection evolved from simple honey hunting to the parallel and independent domestication of different species of bees in various parts of the world. In this study, we investigate the extent to which the composition of Apis and stingless bee honeys has been a driver in the selection of different bee species for domestication in Mesoamerica (Mexico) and Asia (Thailand) using a sampling design that combines peak honey profiling by H1 NMR spectroscopy with the collection of honeys from domesticated and undomesticated bee species. Our results show that, independently of the region of the world considered, domesticated stingless bees produce honey whose compositional profiles differ from those of the non-domesticated species and exhibit more similarities towards honeys produced by the domesticated Apis species. Our results provide evidence for the first time that the search for natural sweeteners in the environment by our ancestors led to the parallel and independent domestication of social bees producing honeys with similar compositional profiles.},
}
@article {pmid36314760,
year = {2022},
author = {Florent, P and Cauchie, HM and Herold, M and Ogorzaly, L},
title = {Bacteriophages pass through candle-shaped porous ceramic filters: Application for the collection of viruses in soil water.},
journal = {MicrobiologyOpen},
volume = {11},
number = {5},
pages = {e1314},
pmid = {36314760},
issn = {2045-8827},
mesh = {*Bacteriophages/genetics ; Soil ; Porosity ; Water ; *Viruses ; Ceramics ; },
abstract = {Despite the ubiquity of viruses in soils, their diversity in soil water has not been explored, mainly due to the difficulty of collecting them. In hydrology, soil water is usually collected using porous candles. This study proposes using these porous candles as a new tool for sampling viruses in soil water to analyze their passage through the ceramic part of the candles. The recovery of the viruses was determined after filtration under laboratory conditions using three model bacteriophages (MS2, ΦX174, and Φ6) and Escherichia coli, at neutral and acidic pH. Then, a field experiment was carried out where soil water filtration and viral identification by metagenomic shotgun were performed. At neutral pH, all bacteriophages tested successfully passed through the porous candles during the filtration process, with reductions of 0.02 log, 0.16 log, and 0.55 log for MS2 ΦX174 and Φ6, respectively. At pH 4.4, the passage of MS2 was not affected while ΦX174 underwent a slight reduction in recovery, probably caused by adsorption onto the filter material. Regarding the application of the porous candles in the field, the results obtained allowed the successful recovery of viruses, exposing porous candles as a new method suitable for the collection of viruses from soil water in the context of the study of viral communities.},
}
@article {pmid36314757,
year = {2022},
author = {Brauer, A and Bengtsson, MM},
title = {DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes.},
journal = {MicrobiologyOpen},
volume = {11},
number = {5},
pages = {e1323},
pmid = {36314757},
issn = {2045-8827},
mesh = {*Eukaryota/genetics ; Archaea/genetics ; Bacteria/genetics ; *Microbiota/genetics ; DNA/genetics ; },
abstract = {DNA extraction and preservation bias is a recurring topic in DNA sequencing-based microbial ecology. The different methodologies can lead to distinct outcomes, which has been demonstrated especially in studies investigating prokaryotic community composition. Eukaryotic microbes are ubiquitous, diverse, and increasingly a subject of investigation in addition to bacteria and archaea. However, little is known about how the choice of DNA preservation and extraction methodology impacts perceived eukaryotic community composition. In this study, we compared the effect of two DNA preservation methods and six DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass (Zostera marina) leaves from the Baltic Sea. We found that, whereas both DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than for prokaryotes. In particular, soft-bodied and hard-shelled eukaryotes like nematodes and diatoms, respectively, were differentially abundant depending on the extraction method. We conclude that careful consideration of DNA preservation and extraction methodology is crucial to achieving representative community profiles of eukaryotes in marine biofilms and likely all other habitats containing diverse eukaryotic microbial communities.},
}
@article {pmid36314752,
year = {2022},
author = {Orsini, M and Ianni, A and Zinzula, L},
title = {Brucella ceti and Brucella pinnipedialis genome characterization unveils genetic features that highlight their zoonotic potential.},
journal = {MicrobiologyOpen},
volume = {11},
number = {5},
pages = {e1329},
pmid = {36314752},
issn = {2045-8827},
mesh = {Animals ; Humans ; *Brucella/genetics ; *Brucellosis/microbiology ; *Caniformia/microbiology ; Cetacea/microbiology ; },
abstract = {The Gram-negative bacteria Brucella ceti and Brucella pinnipedialis circulate in marine environments primarily infecting marine mammals, where they cause an often-fatal disease named brucellosis. The increase of brucellosis among several species of cetaceans and pinnipeds, together with the report of sporadic human infections, raises concerns about the zoonotic potential of these pathogens on a large scale and may pose a threat to coastal communities worldwide. Therefore, the characterization of the B. ceti and B. pinnipedialis genetic features is a priority to better understand the pathological factors that may impact global health. Moreover, an in-depth functional analysis of the B. ceti and B. pinnipedialis genome in the context of virulence and pathogenesis was not undertaken so far. Within this picture, here we present the comparative whole-genome characterization of all B. ceti and B. pinnipedialis genomes available in public resources, uncovering a collection of genetic tools possessed by these aquatic bacterial species compared to their zoonotic terrestrial relatives. We show that B. ceti and B. pinnipedialis genomes display a wide host-range infection capability and a polyphyletic phylogeny within the genus, showing a genomic structure that fits the canonical definition of closeness. Functional genome annotation led to identifying genes related to several pathways involved in mechanisms of infection, others conferring pan-susceptibility to antimicrobials and a set of virulence genes that highlight the similarity of B. ceti and B. pinnipedialis genotypes to those of Brucella spp. displaying human-infecting phenotypes.},
}
@article {pmid36312987,
year = {2022},
author = {Ma, K and Tu, Q},
title = {Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1011269},
pmid = {36312987},
issn = {1664-302X},
abstract = {Revealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biological communities. Similar approaches have been recently extended to the field of microbial ecology. However, the profiling of highly diverse biological communities (e.g., microbial communities) is severely influenced by random sampling issues, leading to undersampled community profiles and overestimated β-diversity, which may further affect stochasticity inference in community assembly. By implementing simulated datasets, this study demonstrate that microbial stochasticity inference is also affected due to random sampling issues associated with microbial profiling. The effects on microbial stochasticity inference for the whole community and the abundant subcommunities were different using different randomization methods in generating null communities. The stochasticity of rare subcommunities, however, was persistently overestimated irrespective of which randomization method was used. Comparatively, the stochastic ratio approach was more sensitive to random sampling issues, whereas the Raup-Crick metric was more affected by randomization methods. As more studies begin to focus on the mechanisms governing abundant and rare subcommunities, we urge cautions be taken for microbial stochasticity inference based on β-diversity, especially for rare subcommunities. Randomization methods to generate null communities shall also be carefully selected. When necessary, the cutoff used for judging the relative importance of deterministic vs. stochastic processes shall be redefined.},
}
@article {pmid36312976,
year = {2022},
author = {Quagliariello, A and Ramiro, RS and Couce, A and Martino, ME},
title = {Editorial: Integrating multi-scale approaches for predicting microbiome ecology and evolution.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1045045},
pmid = {36312976},
issn = {1664-302X},
}
@article {pmid36309426,
year = {2023},
author = {Jääskeläinen, E and Säde, E and Rönkkö, T and Hultman, J and Johansson, P and Riekkola, ML and Björkroth, J},
title = {Marination increased tyramine levels in rainbow trout fillet strips packaged under modified atmosphere.},
journal = {Food microbiology},
volume = {109},
number = {},
pages = {104099},
doi = {10.1016/j.fm.2022.104099},
pmid = {36309426},
issn = {1095-9998},
mesh = {Animals ; *Oncorhynchus mykiss ; Tyramine ; Meat/microbiology ; Atmosphere ; },
abstract = {Marinades are increasingly used to manufacture raw fish products. In corresponding meats, marinating is known to have a major effect on the composition of the microbiome, but the effect of marinating on fish is not known as well. This knowledge gap prompted our study of the microbial ecology and amine formation in marinated and unmarinated modified atmosphere commercially packaged rainbow trout fillet strips. According to our findings, marination increased the maximum concentrations (7-8 log CFU/g) of psychrotrophic bacteria by one logarithmic unit and led to 5 times higher average tyramine concentrations than the corresponding unmarinated product. Instead, trimethylamine concentrations were 30 times higher in the unmarinated product than those in the marinated one. According to the 16 S rRNA sequence analyses, lactic acid bacteria (LAB) predominated in the marinated strips one day after the use-by date, whereas in the unmarinated strips Fusobacteriaceae and LAB were the dominating taxa. Based on the culture-dependent analysis, Latilactobacillus fuchuensis was the prevailing LAB in both products. Since the subset of L. fuchuensis strains tested was able to produce tyramine in vitro, we hypothesise that the use of the acidic marinade activated the production of tyrosine-decarboxylating enzymes in L. fuchuensis and led to the increased tyramine concentrations.},
}
@article {pmid36307735,
year = {2023},
author = {Hladnik, M and Unković, N and Janakiev, T and Grbić, ML and Arbeiter, AB and Stanković, S and Janaćković, P and Gavrilović, M and Rančić, D and Bandelj, D and Dimkić, I},
title = {An Insight into an Olive Scab on the "Istrska Belica" Variety: Host-Pathogen Interactions and Phyllosphere Mycobiome.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1343-1363},
pmid = {36307735},
issn = {1432-184X},
support = {451-03-68/2022-14/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; P1-0386//Javna Agencija za Raziskovalno Dejavnost RS/ ; SLO-SRB-2018/19-OAN//Bilateral scientific - research cooperation between SRB and RS/ ; },
mesh = {*Olea/microbiology ; *Mycobiome ; *Ascomycota ; *Basidiomycota ; Host-Pathogen Interactions ; },
abstract = {The olive tree is one of the most important agricultural plants, affected by several pests and diseases that cause a severe decline in health status leading to crop losses. Olive leaf spot disease caused by the fungus Venturia oleaginea can result in complete tree defoliation and consequently lower yield. The aim of the study was to obtain new knowledge related to plant-pathogen interaction, reveal mechanisms of plant defense against the pathogen, and characterize fungal phyllosphere communities on infected and symptomless leaves that could contribute to the development of new plant breeding strategies and identification of novel biocontrol agents. The highly susceptible olive variety "Istrska Belica"' was selected for a detailed evaluation. Microscopy analyses led to the observation of raphides in the mesophyll and parenchyma cells of infected leaves and gave new insight into the complex V. oleaginea pathogenesis. Culturable and total phyllosphere mycobiota, obtained via metabarcoding approach, highlighted Didymella, Aureobasidium, Cladosporium, and Alternaria species as overlapping between infected and symptomless leaves. Only Venturia and Erythrobasidium in infected and Cladosporium in symptomless samples with higher abundance showed statistically significant differences. Based on the ecological role of identified taxa, it can be suggested that Cladosporium species might have potential antagonistic effects on V. oleaginea.},
}
@article {pmid36306091,
year = {2023},
author = {Jameson, E and Taubert, M and Angel, R and Coyotzi, S and Chen, Y and Eyice, &#xd6; and Schäfer, H and Murrell, JC and Neufeld, JD and Dumont, MG},
title = {DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2555},
number = {},
pages = {261-282},
pmid = {36306091},
issn = {1940-6029},
mesh = {RNA, Ribosomal, 16S/genetics/chemistry ; Carbon Isotopes/chemistry ; Isotope Labeling/methods ; *DNA/chemistry ; *Proteins/chemistry ; Biomarkers ; RNA, Messenger ; },
abstract = {Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of [13]C, [18]O, or [15]N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.},
}
@article {pmid36305941,
year = {2023},
author = {Costas-Selas, C and Martínez-García, S and Logares, R and Hernández-Ruiz, M and Teira, E},
title = {Role of Bacterial Community Composition as a Driver of the Small-Sized Phytoplankton Community Structure in a Productive Coastal System.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {777-794},
pmid = {36305941},
issn = {1432-184X},
support = {EM2013/023//Xunta de Galicia/ ; ED481A-2019/290//Xunta de Galicia/ ; ED431I 2020/03//Xunta de Galicia/ ; CTM2017-83362-R//Ministerio de Econom&#xed;a y Competitividad/ ; PID2019-110011RB-C33)//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {Humans ; *Phytoplankton ; *Plankton ; Bacteria ; Seasons ; Eukaryota ; },
abstract = {We present here the first detailed description of the seasonal patterns in bacterial community composition (BCC) in shelf waters off the Ría de Vigo (Spain), based on monthly samplings during 2 years. Moreover, we studied the relationship between bacterial and small-sized eukaryotic community composition to identify potential biotic interactions among components of these two communities. Bacterial operational taxonomic unit (OTU) richness and diversity systematically peaked in autumn-winter, likely related to low resource availability during this period. BCC showed seasonal and vertical patterns, with Rhodobacteraceae and Flavobacteriaceae families dominating in surface waters, and SAR11 clade dominating at the base of the photic zone (30 m depth). BCC variability was significantly explained by environmental variables (e.g., temperature of water, solar radiation, or dissolved organic matter). Interestingly, a strong and significant correlation was found between BCC and small-sized eukaryotic community composition (ECC), which suggests that biotic interactions may play a major role as structuring factors of the microbial plankton in this productive area. In addition, co-occurrence network analyses revealed strong and significant, mostly positive, associations between bacteria and small-sized phytoplankton. Positive associations likely result from mutualistic relationships (e.g., between Dinophyceae and Rhodobacteraceae), while some negative correlations suggest antagonistic interactions (e.g., between Pseudo-nitzchia sp. and SAR11). These results support the key role of biotic interactions as structuring factors of the small-sized eukaryotic community, mostly driven by positive associations between small-sized phytoplankton and bacteria.},
}
@article {pmid36304282,
year = {2022},
author = {Saenz, C and Nigro, E and Gunalan, V and Arumugam, M},
title = {MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration.},
journal = {Frontiers in bioinformatics},
volume = {2},
number = {},
pages = {846922},
pmid = {36304282},
issn = {2673-7647},
abstract = {Omics technologies have revolutionized microbiome research allowing the characterization of complex microbial communities in different biomes without requiring their cultivation. As a consequence, there has been a great increase in the generation of omics data from metagenomes and metatranscriptomes. However, pre-processing and analysis of these data have been limited by the availability of computational resources, bioinformatics expertise and standardized computational workflows to obtain consistent results that are comparable across different studies. Here, we introduce MIntO (Microbiome Integrated meta-Omics), a highly versatile pipeline that integrates metagenomic and metatranscriptomic data in a scalable way. The distinctive feature of this pipeline is the computation of gene expression profile through integrating metagenomic and metatranscriptomic data taking into account the community turnover and gene expression variations to disentangle the mechanisms that shape the metatranscriptome across time and between conditions. The modular design of MIntO enables users to run the pipeline using three available modes based on the input data and the experimental design, including de novo assembly leading to metagenome-assembled genomes. The integrated pipeline will be relevant to provide unique biochemical insights into microbial ecology by linking functions to retrieved genomes and to examine gene expression variation. Functional characterization of community members will be crucial to increase our knowledge of the microbiome's contribution to human health and environment. MIntO v1.0.1 is available at https://github.com/arumugamlab/MIntO.},
}
@article {pmid36304272,
year = {2022},
author = {Karaoz, U and Brodie, EL},
title = {microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes.},
journal = {Frontiers in bioinformatics},
volume = {2},
number = {},
pages = {918853},
pmid = {36304272},
issn = {2673-7647},
abstract = {Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.},
}
@article {pmid36303775,
year = {2021},
author = {Hu, B and Canon, S and Eloe-Fadrosh, EA and Anubhav, and Babinski, M and Corilo, Y and Davenport, K and Duncan, WD and Fagnan, K and Flynn, M and Foster, B and Hays, D and Huntemann, M and Jackson, EKP and Kelliher, J and Li, PE and Lo, CC and Mans, D and McCue, LA and Mouncey, N and Mungall, CJ and Piehowski, PD and Purvine, SO and Smith, M and Varghese, NJ and Winston, D and Xu, Y and Chain, PSG},
title = {Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.},
journal = {Frontiers in bioinformatics},
volume = {1},
number = {},
pages = {826370},
pmid = {36303775},
issn = {2673-7647},
abstract = {The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.},
}
@article {pmid36303759,
year = {2021},
author = {Giulia, A and Anna, S and Antonia, B and Dario, P and Maurizio, C},
title = {Extending Association Rule Mining to Microbiome Pattern Analysis: Tools and Guidelines to Support Real Applications.},
journal = {Frontiers in bioinformatics},
volume = {1},
number = {},
pages = {794547},
pmid = {36303759},
issn = {2673-7647},
abstract = {Boosted by the exponential growth of microbiome-based studies, analyzing microbiome patterns is now a hot-topic, finding different fields of application. In particular, the use of machine learning techniques is increasing in microbiome studies, providing deep insights into microbial community composition. In this context, in order to investigate microbial patterns from 16S rRNA metabarcoding data, we explored the effectiveness of Association Rule Mining (ARM) technique, a supervised-machine learning procedure, to extract patterns (in this work, intended as groups of species or taxa) from microbiome data. ARM can generate huge amounts of data, making spurious information removal and visualizing results challenging. Our work sheds light on the strengths and weaknesses of pattern mining strategy into the study of microbial patterns, in particular from 16S rRNA microbiome datasets, applying ARM on real case studies and providing guidelines for future usage. Our results highlighted issues related to the type of input and the use of metadata in microbial pattern extraction, identifying the key steps that must be considered to apply ARM consciously on 16S rRNA microbiome data. To promote the use of ARM and the visualization of microbiome patterns, specifically, we developed microFIM (microbial Frequent Itemset Mining), a versatile Python tool that facilitates the use of ARM integrating common microbiome outputs, such as taxa tables. microFIM implements interest measures to remove spurious information and merges the results of ARM analysis with the common microbiome outputs, providing similar microbiome strategies that help scientists to integrate ARM in microbiome applications. With this work, we aimed at creating a bridge between microbial ecology researchers and ARM technique, making researchers aware about the strength and weaknesses of association rule mining approach.},
}
@article {pmid36303234,
year = {2022},
author = {Yin, G and Chen, F and Chen, G and Yang, X and Huang, Q and Chen, L and Chen, M and Zhang, W and Ou, M and Cao, M and Lin, H and Chen, M and Xu, H and Ren, J and Chen, Y and Chen, Z},
title = {Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals.},
journal = {Journal of ovarian research},
volume = {15},
number = {1},
pages = {117},
pmid = {36303234},
issn = {1757-2215},
support = {81200619//National Natural Science Foundation of China/ ; 81900541//National Natural Science Foundation of China/ ; A2020390//Medical Scientific Research Foundation of Guangdong Province of China/ ; 210715106900958//Guangdong Provincial Science and Technology Special Fund/ ; },
mesh = {Humans ; Female ; *Polycystic Ovary Syndrome ; *Mycobiome ; Overweight/complications ; RNA, Ribosomal, 16S ; Metabolome ; Bacteria/genetics ; },
abstract = {To characterize the gut bacteriome, mycobiome and serum metabolome profiles in polycystic ovary syndrome (PCOS) patients with normal/overweight individuals and evaluate a potential microbiota-related diagnostic method development for PCOS, 16S rRNA and ITS2 gene sequencing using 88 fecal samples and 87 metabolome analysis from serum samples are conducted and PCOS classifiers based on multiomics markers are constructed. There are significant bacterial, fungal community and metabolite differences among PCOS patients and healthy volunteers with normal/overweight individuals. Healthy individuals with overweight/obesity display less abnormal metabolism than PCOS patients and uniquely higher abundance of the fungal genus Mortierella. Nine bacterial genera, 4 predicted pathways, 11 fungal genera and top 30 metabolites are screened out which distinguish PCOS from healthy controls, with AUCs of 0.84, 0.64, 0.85 and 1, respectively. The metabolite-derived model is more accurate than the microbe-based model in discriminating normal BMI PCOS (PCOS-LB) from normal BMI healthy (Healthy-LB), PCOS-HB from Healthy-HB. Featured bacteria, fungi, predicted pathways and serum metabolites display higher associations with free androgen index (FAI) in the cooccurrence network. In conclusion, our data reveal that hyperandrogenemia plays a central role in the dysbiosis of intestinal microecology and the change in metabolic status in patients with PCOS and that its effect exceeds the role of BMI. Healthy women with high BMI showed unique microbiota and metabolic features.The priority of predictive models in discriminating PCOS from healthy status in this study were serum metabolites, fungal taxa and bacterial taxa.},
}
@article {pmid36303146,
year = {2022},
author = {Xu, X and Dodd, AN},
title = {Is there crosstalk between circadian clocks in plants and the rhizomicrobiome?.},
journal = {BMC biology},
volume = {20},
number = {1},
pages = {241},
pmid = {36303146},
issn = {1741-7007},
support = {BBS/E/J/000PR9788/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Rhizosphere ; *Circadian Clocks ; Circadian Rhythm ; Soil Microbiology ; *Microbiota ; Plants/microbiology ; *Arabidopsis ; Soil ; },
abstract = {Circadian clocks occur across the kingdoms of life, including some fungi and bacteria present in the root-associated soil known as the rhizosphere. Recent work from Amy Newman and colleagues, published in BMC Biology, has discovered that the circadian clock in Arabidopsis plants affects the rhythmicity of rhizosphere microbial communities This brings into play the exciting question of whether there is a bidirectional rhythmic interaction between plants and their rhizomicrobiome. Here, we discuss how the findings of Newman et al. suggest that soil microbiomes can have both self-sustained and plant-imposed rhythmicity, and the challenges of plant-microbiome circadian clock research.},
}
@article {pmid36301703,
year = {2022},
author = {Xiang, L and Harindintwali, JD and Wang, F and Redmile-Gordon, M and Chang, SX and Fu, Y and He, C and Muhoza, B and Brahushi, F and Bolan, N and Jiang, X and Ok, YS and Rinklebe, J and Schaeffer, A and Zhu, YG and Tiedje, JM and Xing, B},
title = {Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {23},
pages = {16546-16566},
pmid = {36301703},
issn = {1520-5851},
mesh = {Humans ; Soil/chemistry ; *Soil Pollutants/analysis ; *Environmental Pollutants ; Ecosystem ; Biodegradation, Environmental ; Plants ; Bacteria ; },
abstract = {The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.},
}
@article {pmid36301451,
year = {2022},
author = {Woo, C and Bhuiyan, MIU and Kim, D and Kumari, P and Lee, SK and Park, JY and Dong, K and Lee, K and Yamamoto, N},
title = {DNA metabarcoding-based study on bacteria and fungi associated with house dust mites (Dermatophagoides spp.) in settled house dust.},
journal = {Experimental &amp; applied acarology},
volume = {88},
number = {3-4},
pages = {329-347},
pmid = {36301451},
issn = {1572-9702},
mesh = {Animals ; Humans ; *Pyroglyphidae ; *Dust ; DNA Barcoding, Taxonomic ; Ecosystem ; RNA, Ribosomal, 16S ; Bacteria/genetics ; },
abstract = {House dust mites (HDMs) including Dermatophagoides spp. are an important cause of respiratory allergies. However, their relationship with microorganisms in house dust has not been fully elucidated. Here, we characterized bacteria and fungi associated with HDMs in house dust samples collected in 107 homes in Korea by using DNA barcode sequencing of bacterial 16S rRNA gene, fungal internal transcribed spacer 2 (ITS2) region, and arthropod cytochrome c oxidase I (COI) gene. Our inter-kingdom co-occurrence network analysis and/or indicator species analysis identified that HDMs were positively related with a xerophilic fungus Wallemia, mycoparasitic fungi such as Cystobasidium, and some human skin-related bacterial and fungal genera, and they were negatively related with the hygrophilous fungus Cephalotrichum. Overall, our study has succeeded in adding novel insights into HDM-related bacteria and fungi in the house dust ecosystem, and in confirming the historically recognized fact that HDMs are associated with xerophilic fungi such as Wallemia. Understanding the microbial ecology in house dust is thought to be important for elucidating the etiology of human diseases including allergies, and our study revealed baseline information of house dust ecology in relation to HDMs. The findings could be useful from a perspective of human health.},
}
@article {pmid36300970,
year = {2022},
author = {Deng, Y and Mauri, M and Vallet, M and Staudinger, M and Allen, RJ and Pohnert, G},
title = {Dynamic Diatom-Bacteria Consortia in Synthetic Plankton Communities.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {22},
pages = {e0161922},
pmid = {36300970},
issn = {1098-5336},
mesh = {*Diatoms ; Plankton ; Phytoplankton ; *Flavobacteriaceae ; Ecosystem ; *Microalgae/microbiology ; },
abstract = {Microalgae that form phytoplankton live and die in a complex microbial consortium in which they co-exist with bacteria and other microorganisms. The dynamics of species succession in the plankton depends on the interplay of these partners. Bacteria utilize substrates produced by the phototrophic algae, while algal growth can be supported by bacterial exudates. Bacteria might also use chemical mediators with algicidal properties to attack algae. To elucidate whether specific bacteria play universal or context-specific roles in the interaction with phytoplankton, we investigated the effect of cocultured bacteria on the growth of 8 microalgae. An interaction matrix revealed that the function of a given bacterium is highly dependent on the cocultured partner. We observed no universally algicidal or universally growth-promoting bacteria. The activity of bacteria can even change during the aging of an algal culture from inhibitory to stimulatory or vice versa. We further established a synthetic phytoplankton/bacteria community with the centric diatom, Coscinodiscus radiatus, and 4 phylogenetically distinctive bacterial isolates, Mameliella sp., Roseovarius sp., Croceibacter sp., and Marinobacter sp. Supported by a Lotka-Volterra model, we show that interactions within the consortium are specific and that the sum of the pairwise interactions can explain algal and bacterial growth in the community. No synergistic effects between bacteria in the presence of the diatom was observed. Our survey documents highly species-specific interactions that are dependent on algal fitness, bacterial metabolism, and community composition. This species specificity may underly the high complexity of the multi-species plankton communities observed in nature. IMPORTANCE The marine food web is fueled by phototrophic phytoplankton. These algae are central primary producers responsible for the fixation of ca. 40% of the global CO2. Phytoplankton always co-occur with a diverse bacterial community in nature. This diversity suggests the existence of ecological niches for the associated bacteria. We show that the interaction between algae and bacteria is highly species-specific. Furthermore, both, the fitness stage of the algae and the community composition are relevant in determining the effect of bacteria on algal growth. We conclude that bacteria should not be sorted into algicidal or growth supporting categories; instead, a context-specific function of the bacteria in the plankton must be considered. This functional diversity of single players within a consortium may underly the observed diversity in the plankton.},
}
@article {pmid36296484,
year = {2022},
author = {Gao, J and Wang, M and Huang, W and You, Y and Zhan, J},
title = {Indigenous Saccharomyces cerevisiae Could Better Adapt to the Physicochemical Conditions and Natural Microbial Ecology of Prince Grape Must Compared with Commercial Saccharomyces cerevisiae FX10.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {20},
pages = {},
pmid = {36296484},
issn = {1420-3049},
support = {201905410610663//Screening, Identification and Development of Wild Saccharomyces cerevisiae/ ; },
mesh = {Saccharomyces cerevisiae ; *Vitis/chemistry ; Glycerol ; *Wine/analysis ; Fermentation ; },
abstract = {Indigenous Saccharomyces cerevisiae, as a new and useful tool, can be used in fermentation to enhance the aroma characteristic qualities of the wine-production region. In this study, we used indigenous S. cerevisiae L59 and commercial S. cerevisiae FX10 to ferment Prince (a new hybrid variety from Lion Winery) wine, detected the basic physicochemical parameters and the dynamic changes of fungal communities during fermentation, and analyzed the correlations between fungal communities and volatile compounds. The results showed that the indigenous S. cerevisiae L59 could quickly adapt to the specific physicochemical conditions and microbial ecology of the grape must, showing a strong potential for winemaking. Compared with commercial S. cerevisiae FX10, the wine fermented by indigenous S. cerevisiae L59 contained more glycerol and less organic acids, contributing to a rounder taste. The results of volatile compounds indicated that the indigenous S. cerevisiae L59 had a positive effect on adding rosy, honey, pineapple and other sweet aroma characteristics to the wine. Overall, the study we performed showed that selection of indigenous S. cerevisiae from the wine-producing region as a starter for wine fermentation is conducive to improving the aroma profile of wine and preserving the aroma of the grape variety.},
}
@article {pmid36296348,
year = {2022},
author = {Lorenzi, AS and Bonatelli, ML and Chia, MA and Peressim, L and Quecine, MC},
title = {Opposite Sides of Pantoea agglomerans and Its Associated Commercial Outlook.},
journal = {Microorganisms},
volume = {10},
number = {10},
pages = {},
pmid = {36296348},
issn = {2076-2607},
abstract = {Multifaceted microorganisms such as the bacterium Pantoea colonize a wide range of habitats and can exhibit both beneficial and harmful behaviors, which provide new insights into microbial ecology. In the agricultural context, several strains of Pantoea spp. can promote plant growth through direct or indirect mechanisms. Members of this genus contribute to plant growth mainly by increasing the supply of nitrogen, solubilizing ammonia and inorganic phosphate, and producing phytohormones (e.g., auxins). Several other studies have shown the potential of strains of Pantoea spp. to induce systemic resistance and protection against pests and pathogenic microorganisms in cultivated plants. Strains of the species Pantoea agglomerans deserve attention as a pest and phytopathogen control agent. Several of them also possess a biotechnological potential for therapeutic purposes (e.g., immunomodulators) and are implicated in human infections. Thus, the differentiation between the harmful and beneficial strains of P. agglomerans is mandatory to apply this bacterium safely as a biofertilizer or biocontroller. This review specifically evaluates the potential of the strain-associated features of P. agglomerans for bioprospecting and agricultural applications through its biological versatility as well as clarifying its potential animal and human health risks from a genomic point of view.},
}
@article {pmid36296237,
year = {2022},
author = {Trego, A and Keating, C and Nzeteu, C and Graham, A and O'Flaherty, V and Ijaz, UZ},
title = {Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data.},
journal = {Microorganisms},
volume = {10},
number = {10},
pages = {},
pmid = {36296237},
issn = {2076-2607},
support = {NE/L011956/1//Natural Environment Research Council/ ; EP/P029329/1//Engineering and Physical Sciences Research Council/ ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; TC/2014/0016//Enterprise Ireland/ ; 14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 16/RC/3889/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.},
}
@article {pmid36296177,
year = {2022},
author = {Leite, MFA and van den Broek, SWEB and Kuramae, EE},
title = {Current Challenges and Pitfalls in Soil Metagenomics.},
journal = {Microorganisms},
volume = {10},
number = {10},
pages = {},
pmid = {36296177},
issn = {2076-2607},
abstract = {Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.},
}
@article {pmid36292810,
year = {2022},
author = {Ghosh, S and Namin, SM and Jung, C},
title = {Differential Bacterial Community of Bee Bread and Bee Pollen Revealed by 16s rRNA High-Throughput Sequencing.},
journal = {Insects},
volume = {13},
number = {10},
pages = {},
pmid = {36292810},
issn = {2075-4450},
support = {NRF- 2018R1A6A1A03024862//National Research Foundation of Korea/ ; 20211362A00-2123-BD01//Korean forest service/ ; },
abstract = {We investigated the bacterial community of bee bread and bee pollen samples using an approach through 16 s rRNA high-throughput sequencing. The results revealed a higher bacterial diversity in bee bread than in bee pollen as depicted in taxonomic profiling, as well as diversity indices such as the Shannon diversity index (3.7 to 4.8 for bee bread and 1.1 to 1.7 for bee pollen samples) and Simpson’s index (>0.9 for bee bread and 0.4−0.5 for bee pollen). Principal component analysis showed a distinct difference in bacterial communities. The higher bacterial diversity in the bee bread than bee pollen could presumably be due to factors such as storage period, processing of food, fermentation, and high sugar environment. However, no effect of the feed (rapeseed or oak pollen patties or even natural inflow) was indicated on the bacterial composition of bee bread, presumably because of the lack of restriction of foraged pollen inflow in the hive. The diverse bacterial profile of the bee bread could contribute to the nutritional provisioning as well as enhance the detoxification process; however, a thorough investigation of the functional role of individual bacteria genera remains a task for future studies.},
}
@article {pmid36286524,
year = {2022},
author = {Akob, DM and Sutton, JM and Bushman, TJ and Baesman, SM and Klein, E and Shrestha, Y and Andrews, R and Fierst, JL and Kolton, M and Gushgari-Doyle, S and Oremland, RS and Freeman, JL},
title = {Acetylenotrophic and Diazotrophic Bradyrhizobium sp. Strain I71 from TCE-Contaminated Soils.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {22},
pages = {e0121922},
pmid = {36286524},
issn = {1098-5336},
mesh = {*Bradyrhizobium ; *Trichloroethylene/metabolism ; Nitrogen Fixation/genetics ; Soil/chemistry ; Acetylene/metabolism ; Phylogeny ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {Acetylene (C2H2) is a molecule rarely found in nature, with very few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs; however, we hypothesize there may yet be unrecognized diversity of acetylenotrophs in nature. This study expands the known diversity of acetylenotrophs by isolating the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils. Strain I71 is a member of the class Alphaproteobacteria and exhibits acetylenotrophic and diazotrophic activities, the only two enzymatic reactions known to transform acetylene. This unique capability in the isolated strain may increase the genus' economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants. Computational analyses indicate that the Bradyrhizobium sp. strain I71 genome contains 522 unique genes compared to close relatives. Moreover, applying a novel hidden Markov model of known acetylene hydratase (AH) enzymes identified a putative AH enzyme. Protein annotation with I-TASSER software predicted the AH from the microbe Syntrophotalea acetylenica as the closest structural and functional analog. Furthermore, the putative AH was flanked by horizontal gene transfer (HGT) elements, like that of AH in anaerobic acetylenotrophs, suggesting an unknown source of acetylene or acetylenic substrate in the environment that is selecting for the presence of AH. IMPORTANCE The isolation of Bradyrhizobium strain I71 expands the distribution of acetylene-consuming microbes to include a group of economically important microorganisms. Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. Additionally, acetylene-consuming microbes have been shown to work in tandem with other microbes to degrade soil contaminants. Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium. These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues.},
}
@article {pmid36286523,
year = {2022},
author = {Van Peteghem, L and Sakarika, M and Matassa, S and Rabaey, K},
title = {The Role of Microorganisms and Carbon-to-Nitrogen Ratios for Microbial Protein Production from Bioethanol.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {22},
pages = {e0118822},
pmid = {36286523},
issn = {1098-5336},
mesh = {Humans ; *Nitrogen ; *Carbon ; Biomass ; Ethanol/metabolism ; Yeasts/metabolism ; Fermentation ; Biofuels ; },
abstract = {With industrial agriculture increasingly challenging our ecological limits, alternative food production routes such as microbial protein (MP) production are receiving renewed interest. Among the multiple substrates so far evaluated for MP production, renewable bioethanol (EtOH) is still underexplored. Therefore, the present study investigated the cultivation of five microorganisms (2 bacteria, 3 yeasts) under carbon (C), nitrogen (N), and dual C-N-limiting conditions (molar C/N ratios of 5, 60, and 20, respectively) to evaluate the production (specific growth rate, protein and biomass yield, production cost) as well as the nutritional characteristics (protein and carbohydrate content, amino acid [AA] profile) of MP production from bioethanol. Under C-limiting conditions, all the selected microorganisms showed a favorable AA profile for human nutrition (average AA score of 1.5 or higher), with a negative correlation between protein content and growth rate. Maximal biomass yields were achieved under conditions where no extracellular acetate was produced. Cyberlindnera saturnus and Wickerhamomyces anomalus displayed remarkably high biomass yields (0.40 to 0.82 g cell dry weight [CDW]/g EtOHconsumed), which was reflected in the lowest estimated biomass production costs when cultivated with a C/N ratio of 20. Finally, when the production cost was evaluated on a protein basis, Corynebacterium glutamicum grown under C-limiting conditions showed the most promising economic outlook. IMPORTANCE The global protein demand is rapidly increasing at rates that cannot be sustained, with projections showing 78% increased global protein needs by 2050 (361 compared to 202 million tonprotein/year in 2017). In the absence of dedicated mitigation strategies, the environmental effects of our current food production system (relying on agriculture) are expected to surpass the planetary boundaries-the safe operating space for humanity-by 2050. Here, we illustrate the potential of bioethanol-renewable ethanol produced from side streams-as a main resource for the production of microbial protein, a radically different food production strategy in comparison to traditional agriculture, with the potential to be more sustainable. This study unravels the kinetic, productive, and nutritional potential for microbial protein production from bioethanol using the bacteria Methylorubrum extorquens and Corynebacterium glutamicum and the yeasts Wickerhamomyces anomalus, Cyberlindnera saturnus, and Metschnikowia pulcherrima, setting the scene for microbial protein production from renewable ethanol.},
}
@article {pmid36282736,
year = {2022},
author = {Sarkar, A and Prescott, SM and Dutra, S and Yoo, JY and Gordon, J and Shaffer, E and McSkimming, D and Groer, ME},
title = {Relationships of the very low birth weight infant microbiome with neurodevelopment at 2 and 4 years of age.},
journal = {Developmental psychobiology},
volume = {64},
number = {7},
pages = {e22317},
pmid = {36282736},
issn = {1098-2302},
support = {R01 HD086805/HD/NICHD NIH HHS/United States ; R01 NR015446/NR/NINR NIH HHS/United States ; R21 NR013094/NR/NINR NIH HHS/United States ; },
mesh = {Infant, Newborn ; Infant ; Adult ; Humans ; Child, Preschool ; *Infant, Very Low Birth Weight ; Intensive Care Units, Neonatal ; Gestational Age ; Birth Weight ; *Microbiota ; Anti-Bacterial Agents ; },
abstract = {Very low birth weight (VLBW) infants (<1500 g) are at risk for poor neurodevelopmental outcomes depending on gestational age (GA), birth weight (BW), and morbidity in early life. The contribution of the gut microbiome is not well understood. Stool samples were collected weekly in the neonatal intensive care unit (NICU) from 24 VLBW infants for 6 weeks after admission and then again at 2 and 4 years of age. The Battelle Development Inventory-2 Screening Test (BDI-2 ST) was administered at 2- and 4-year time points. VLBW infants had dysbiotic microbiota in the NICU that progressed for most to an adult-type microbiota by 4 years of age. The BDI-2 ST results at age of 2 years triggered referral for further testing in 14 toddlers (70%), and by 4 years of age only seven of these 14 continued to require referral. Both NICU infant stool diversity and particular microbial amplicon sequence variants were associated with BDI-2 ST subscales, particularly for cognition, adaptive, and communication subscales, when controlled for GA, BW, and antibiotic exposure. Network analysis of the NICU infant stool microbial ecology showed differences in children needing neurodevelopmental referral. The results of this preliminary study indicate that the neonatal gut microbiome plays a role in early cognitive and behavioral neurodevelopment.},
}
@article {pmid36282286,
year = {2023},
author = {Ortiz, WE and Carlos-Shanley, C and Huertas, M},
title = {Impact of Sublethal Concentrations of Nitrite on Goldfish (Carassius auratus) Microbiomes.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1331-1342},
pmid = {36282286},
issn = {1432-184X},
mesh = {Animals ; *Goldfish ; *Nitrites ; Aquaculture ; Gills/microbiology ; Water ; },
abstract = {Elevated concentrations of nitrite are toxic to fish and can cause a myriad of well documented issues. However, the effects of sublethal concentrations of nitrite on fish health, and specifically, fish tissue microbiomes have not been studied. To test the effects of nitrite exposure, goldfish were exposed to sublethal concentrations of nitrite, 0.0 mM, 0.1 mM, and 1.0 mM, for 2 months. The bacteria in the nose, skin, gills, and water were then extracted and sequenced to identify changes to the microbial composition. The water microbiome was not significantly changed by the added nitrite; however, each of the tissue microbiomes was changed by at least one of the treatments. The skin and gill microbiomes were significantly different between the control and 1.0 mM treatment and the nose microbiome showed significant changes between the control and both the 0.1 mM and 1.0 mM treatments. Thus, sublethal concentrations of nitrite in the environment caused a shift in the fish tissue microbiomes independently of the water microbiome. These changes could lead to an increased chance of infection, disrupt organ systems, and raise the mortality rate of fish. In systems with high nitrite concentrations, like intensive aquaculture setups or polluted areas, the effects of nitrite on the microbiomes could negatively affect fish populations.},
}
@article {pmid36280326,
year = {2022},
author = {Narendrakumar, L and Ray, A},
title = {Respiratory tract microbiome and pneumonia.},
journal = {Progress in molecular biology and translational science},
volume = {192},
number = {1},
pages = {97-124},
doi = {10.1016/bs.pmbts.2022.07.002},
pmid = {36280326},
issn = {1878-0814},
mesh = {Humans ; *Microbiota ; Dysbiosis ; *Pneumonia ; *Respiratory Tract Infections/microbiology ; Lung ; },
abstract = {The respiratory system, like the gut, harbors a vast variety of microorganisms which include bacteria, viruses and fungi. The advent of next generation sequencing and multi-omic approaches has revealed the diversity and functional significances of microorganisms in the respiratory health. It has been identified that there has been a co-evolution of indigenous respiratory microbiota and the human immune system. However, an immune response is usually generated when the homeostasis of the microbiota is disturbed. The respiratory microbiome has been identified to be important in shaping the respiratory immunity. Gut microbiota and oral microbiota are also known to be pivotal in shaping the immune system of the respiratory tract and influence its microbial dynamics. Proteobacteria, Firmicutes, and Bacteroidetes have been identified to be predominant in the respiratory system. While, Streptococcus, Prevotella, Fusobacteria, and Veillonella forms the major part, potential pathogens, such as Haemophilus and Neisseria, also form a small fraction of the healthy lung microbiome. Dysbiosis of respiratory microbiome can lead to increased colonization of opportunistic pathogens that can lead to respiratory infections such as pneumonia. This chapter describes the microbial diversity of respiratory system and the role of respiratory microbiome during respiratory infections like pneumonia. The chapter also discusses few strategies that have been proved effective in preventing pneumonia.},
}
@article {pmid36275752,
year = {2022},
author = {Xin, X and Wang, Q and Qing, J and Song, W and Gui, Y and Li, X and Li, Y},
title = {Th17 cells in primary Sjögren's syndrome negatively correlate with increased Roseburia and Coprococcus.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {974648},
pmid = {36275752},
issn = {1664-3224},
mesh = {Humans ; *Th17 Cells ; RNA, Ribosomal, 16S/genetics ; *Sjogren's Syndrome ; Galactose ; Peptidoglycan ; Bacteria/genetics ; Inflammation/complications ; Pyrimidines ; Amino Acids ; Glyoxylates ; Glucuronates ; Pentoses ; Butyrates ; },
abstract = {BACKGROUND: Dysbiosis of the gut microbiota is closely related to chronic systemic inflammation and autoimmunity, playing an essential role in the pathogenesis of primary Sjögren's syndrome (pSS). Abnormalities in the proportions of blood T lymphocyte subtype, that is Th17/Treg, were detected in pSS patients. We aimed to determine the associations between gut microbiota and Th17/Treg in pSS.<br><br>METHOD: 98 pSS patients and 105 healthy controls (NC) were enrolled between Dec 1, 2018, and Aug 31, 2019. The baseline information and clinical parameters on pSS patients and healthy controls were collected. 16S rRNA sequencing was performed to characterize the gut microbiome and identify gut microbes that are differentially abundant between patients and healthy controls. Lastly, associations between relative abundances of specific bacterial taxa in the gut and clinical outcome parameters were evaluated.<br><br>RESULTS: Patients with pSS show decreased gut microbial diversity and richness, decreased abundance of butyrate producing bacteria, such as Roseburia and Coprococcus, and increased abundance of other taxa, such as Eubacterium rectale and Roseburia inulinivorans. These bacteria are enriched with functions related to glycolytic and lipogenic, energy, substance, galactose, pentose metabolism pathways and glucuronate interconversions, decreased with functions related to peptidoglycan biosynthesis, pyrimidine metabolism pathways. An integrative analysis identified pSS-related specific bacterial taxa in the gut, for which the abundance of Eubacterium rectale is negatively correlated with Th17/Treg. Furthermore, the pathways of biosynthesis of secondary metabolites, biosynthesis of amino acids, peptidoglycan biosynthesis and pyrimidine, galactose, pentose, microbial metabolism in diverse environments, glyoxylate and dicarboxylate metabolism are associated with Treg or Th17/Treg.<br><br>CONCLUSIONS: Primary Sj&#xf6;gren's syndrome could lead to decreased gut microbial diversity and richness of intestinal flora in patients. The proportions of Th17 and Treg cells induced by microbiota were predictive pSS manifestations and accounted for the pSS severity.},
}
@article {pmid36274442,
year = {2022},
author = {Tims, S and Marsaux, C and Pinto, A and Daly, A and Karall, D and Kuhn, M and Santra, S and Roeselers, G and Knol, J and MacDonald, A and Scholl-Bürgi, S},
title = {Altered gut microbiome diversity and function in patients with propionic acidemia.},
journal = {Molecular genetics and metabolism},
volume = {137},
number = {3},
pages = {308-322},
doi = {10.1016/j.ymgme.2022.09.012},
pmid = {36274442},
issn = {1096-7206},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Propionic Acidemia ; Propionates ; Feces/microbiology ; Butyrates ; },
abstract = {Propionic acidemia (PA) is an inherited metabolic disorder of propionate metabolism, where the gut microbiota may play a role in pathophysiology and therefore, represent a relevant therapeutic target. Little is known about the gut microbiota composition and activity in patients with PA. Although clinical practice varies between metabolic treatment centers, management of PA requires combined dietary and pharmaceutical treatments, both known to affect the gut microbiota. This study aimed to characterize the gut microbiota and its metabolites in fecal samples of patients with PA compared with healthy controls from the same household. Eight patients (aged 3-14y) and 8 controls (4-31y) were recruited from Center 1 (UK) and 7 patients (11-33y) and 6 controls (15-54y) from Center 2 (Austria). Stool samples were collected 4 times over 3 months, alongside data on dietary intakes and medication usage. Several microbial taxa differed between patients with PA and controls, particularly for Center 1, e.g., Proteobacteria levels were increased, whereas butyrate-producing genera, such as Roseburia and Faecalibacterium, were decreased. Most measured microbial metabolites were lower in patients with PA, and butyrate was particularly depleted in patients from Center 1. Furthermore, microbiota profile of these patients showed the lowest compositional and functional diversity, and lowest stability over 3 months. As the first study to map the gut microbiota of patients with PA, this work represents an important step forward for developing new therapeutic strategies to further improve PA clinical status. New dietary strategies should consider microbial propionate production as well as butyrate production and microbiota stability.},
}
@article {pmid36270682,
year = {2022},
author = {Ahrodia, T and Das, S and Bakshi, S and Das, B},
title = {Structure, functions, and diversity of the healthy human microbiome.},
journal = {Progress in molecular biology and translational science},
volume = {191},
number = {1},
pages = {53-82},
doi = {10.1016/bs.pmbts.2022.07.003},
pmid = {36270682},
issn = {1878-0814},
mesh = {Humans ; *Microbiota ; Bacteria/genetics ; Metagenome ; *Gastrointestinal Microbiome ; Archaea ; },
abstract = {Taxonomic composition and functional potency of microbes associated with different parts of the human body have largely been explored by culture-independent metagenome sequencing. The diverse microbiota living throughout the human body is made up of thousands of microbial taxa from all three domains of life: Archaea, Bacteria, and Eukarya. Microbial load and functional potency in different body sites are well distinct and have minimal resemblance at higher taxonomic levels between the two habitats. The highest microbial load, diversity, and functional potency including biosynthesis of essential nutrients, chemical modifications of dietary components, and sources of immunomodulatory molecules, are found in the gut microbiome. However, the inter-individual diversity and dynamics of the human microbiome in a given body habitat vary greatly over time. Both environmental factors and host genetics contribute significantly to shaping microbial community structure and its stability. A basic understanding of native microbial compositions and their functional potency and stability in different parts of healthy humans living across geography will help us to identify disease-specific microbiota and develop potential microbiome-based therapeutics. Here, we updated our current understanding of the diversity, dynamics, and functional potency of microbiomes associated with different parts of the human body.},
}
@article {pmid36270678,
year = {2022},
author = {Purohit, A and Alam, MJ and Kandiyal, B and Shalimar, and Das, B and Banerjee, SK},
title = {Gut microbiome and non-alcoholic fatty liver disease.},
journal = {Progress in molecular biology and translational science},
volume = {191},
number = {1},
pages = {187-206},
doi = {10.1016/bs.pmbts.2022.07.004},
pmid = {36270678},
issn = {1878-0814},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Non-alcoholic Fatty Liver Disease/therapy/complications/microbiology ; Prebiotics ; Dysbiosis ; Fecal Microbiota Transplantation ; *Probiotics/therapeutic use ; },
abstract = {The human gastrointestinal tract (GIT) contains a dynamic and diverse collection of bacteria, archaea, and fungi termed the "gut microbiome." The gut microbiome has a major impact on the host during homeostasis and disease. The connection between both the host and the microbiome is complex, although its manipulation may assist prevent or treating a multitude of morbidities. These microorganisms play a critical role in the host's energy metabolism and homeostasis. According to new research, the microbes in the gastrointestinal tract play a substantial role in host health, and alterations in its composition and function might lead to the emergence of metabolic disorders like non-alcoholic fatty liver disease (NAFLD). The resilience of the GIT microbial ecology and its tolerance to perturbation are robust but not ideal. Several factors may disrupt the GIT microbiome's homeostasis leading to dysbiosis, characterized by an imbalanced equilibrium and perturbations in gut homeostasis. Irritable bowel disease (IBD), malnutrition, and metabolic disorders, such as NAFLD, have been associated with the dysbiotic gut microbiome. Recent evidence suggests that utilizing medications, prebiotics, probiotics, and fecal microbiota transplantation (FMT) to manipulate the microbiome could be a viable method for treating NAFLD.},
}
@article {pmid36270674,
year = {2022},
author = {Das, B},
title = {An introduction to human microbiome.},
journal = {Progress in molecular biology and translational science},
volume = {191},
number = {1},
pages = {1-28},
doi = {10.1016/bs.pmbts.2022.06.026},
pmid = {36270674},
issn = {1878-0814},
mesh = {Humans ; *Microbiota ; Dysbiosis ; Bacteria ; Archaea ; Host Microbial Interactions ; },
abstract = {The microbiome is an assemblage of a complex community of microbes (bacteria, archaea, fungi, algae, protists, and viruses) and their biomolecules occupying a well-defined habitat in or on a living or non-living object. All the environmentally exposed surfaces of the human body are colonized with trillions of microbes from all three major domains of life, including bacteria, archea, and microscopic eukarya. However, the richness, abundance, and functional potency of microbial taxa living in different parts of the human body are distinct. The Presence of common microbial taxa in different body habitats is also very rare. With the recent development of next generation sequencing technologies, it has been established that the indigenous microbial community in the human body and their functional attributes within a given body habitat vary over time, between ethnic groups and health status of the host. Perturbation of homeostasis in community structures or functions due to any extrinsic factors can alter mutualistic host-microbe interactions and may lead to disease. In addition, the dysbiotic state of the microbiome can also affect the efficacy of therapeutics, prolong treatment duration and lead to undesired treatment outcomes. In this chapter, structure, functions, diversity and dynamics of human microbiome in health and diseases, factors that alter microbial composition, interactions between microbial taxa and xenobiotics, and therapeutic efficacy of drugs in dysbiotic conditions are highlighted.},
}
@article {pmid36270377,
year = {2023},
author = {Evariste, L and Mouchet, F and Pinelli, E and Flahaut, E and Gauthier, L and Barret, M},
title = {Gut microbiota impairment following graphene oxide exposure is associated to physiological alterations in Xenopus laevis tadpoles.},
journal = {The Science of the total environment},
volume = {857},
number = {Pt 2},
pages = {159515},
doi = {10.1016/j.scitotenv.2022.159515},
pmid = {36270377},
issn = {1879-1026},
mesh = {Animals ; *Gastrointestinal Microbiome ; Larva ; *Graphite/toxicity ; Xenopus laevis ; *Microbiota ; Bacteria/genetics ; },
abstract = {Graphene-based nanomaterials such as graphene oxide (GO) possess unique properties triggering high expectations for the development of technological applications. Thus, GO is likely to be released in aquatic ecosystems. It is essential to evaluate its ecotoxicological potential to ensure a safe use of these nanomaterials. In amphibians, previous studies highlighted X. laevis tadpole growth inhibitions together with metabolic disturbances and genotoxic effects following GO exposure. As GO is known to exert bactericidal effects whereas the gut microbiota constitutes a compartment involved in host homeostasis regulation, it is important to determine if this microbial compartment constitutes a toxicological pathway involved in known GO-induced host physiological impairments. This study investigates the potential link between gut microbial communities and host physiological alterations. For this purpose, X. laevis tadpoles were exposed during 12 days to GO. Growth rate was monitored every 2 days and genotoxicity was assessed through enumeration of micronucleated erythrocytes. Genomic DNA was also extracted from the whole intestine to quantify gut bacteria and to analyze the community composition. GO exposure led to a dose dependent growth inhibition and genotoxic effects were detected following exposure to low doses. A transient decrease of the total bacteria was noticed with a persistent shift in the gut microbiota structure in exposed animals. Genotoxic effects were associated to gut microbiota remodeling characterized by an increase of the relative abundance of Bacteroides fragilis. The growth inhibitory effects would be associated to a shift in the Firmicutes/Bacteroidetes ratio while metagenome inference suggested changes in metabolic pathways and upregulation of detoxification processes. This work indicates that the gut microbiota compartment is a biological compartment of interest as it is integrative of host physiological alterations and should be considered for ecotoxicological studies as structural or functional impairments could lead to later life host fitness loss.},
}
@article {pmid36270363,
year = {2023},
author = {Regueira, A and Turunen, R and Vuoristo, KS and Carballa, M and Lema, JM and Uusitalo, J and Mauricio-Iglesias, M},
title = {Model-aided targeted volatile fatty acid production from food waste using a defined co-culture microbial community.},
journal = {The Science of the total environment},
volume = {857},
number = {Pt 2},
pages = {159521},
doi = {10.1016/j.scitotenv.2022.159521},
pmid = {36270363},
issn = {1879-1026},
mesh = {Food ; Caproates ; Coculture Techniques ; *Refuse Disposal ; Fatty Acids, Volatile ; Butyrates ; *Microbiota ; Carbon ; Bioreactors ; Fermentation ; Hydrogen-Ion Concentration ; },
abstract = {The production of volatile fatty acids (VFA) is gaining momentum due to their central role in the emerging carboxylate platform. Particularly, the production of the longest VFA (from butyrate to caproate) is desired due to their increased economic value and easier downstream processing. While the use of undefined microbial cultures is usually preferred with organic waste streams, the use of defined microbial co-culture processes could tackle some of their drawbacks such as poor control over the process outcome, which often leads to low selectivity for the desired products. However, the extensive experimentation needed to design a co-culture system hinders the use of this technology. In this work, a workflow based on the combined use of mathematical models and wet experimentation is proposed to accelerate the design of novel bioprocesses. In particular, a co-culture consisting of Pediococcus pentosaceus and Megaphaera cerevisiae is used to target the production of high-value odd- and even‑carbon VFA. An unstructured kinetic model was developed, calibrated and used to design experiments with the goal of increasing the selectivity for the desired VFA, which were experimentally validated. In the case of even‑carbon VFA, the experimental validation showed an increase of 38 % in caproate yield and, in the case of enhanced odd‑carbon VFA experiments, the yield of butyrate and caproate diminished by 62 % and 94 %, respectively, while propionate became one of the main end products and valerate yield value increased from 0.007 to 0.085 gvalearte per gconsumed sugar. The workflow followed in this work proved to be a sound tool for bioprocess design due to its capacity to explore and design new experiments in silico in a fast way and ability to quickly adapt to new scenarios.},
}
@article {pmid36267243,
year = {2022},
author = {Huang, W and Zhu, L and Song, W and Zhang, M and Teng, L and Wu, M},
title = {Crosstalk between the Gut and Brain in Ischemic Stroke: Mechanistic Insights and Therapeutic Options.},
journal = {Mediators of inflammation},
volume = {2022},
number = {},
pages = {6508046},
pmid = {36267243},
issn = {1466-1861},
mesh = {Humans ; Prebiotics ; *Ischemic Stroke ; Fecal Microbiota Transplantation ; *Probiotics/therapeutic use ; Brain/metabolism ; *Stroke/therapy/metabolism ; },
abstract = {There has been a significant amount of interest in the past two decades in the study of the evolution of the gut microbiota, its internal and external impacts on the gut, and risk factors for cerebrovascular disorders such as cerebral ischemic stroke. The network of bidirectional communication between gut microorganisms and their host is known as the microbiota-gut-brain axis (MGBA). There is mounting evidence that maintaining gut microbiota homeostasis can frequently enhance the effectiveness of ischemic stroke treatment by modulating immune, metabolic, and inflammatory responses through MGBA. To effectively monitor and cure ischemic stroke, restoring a healthy microbial ecology in the gut may be a critical therapeutic focus. This review highlights mechanistic insights on the MGBA in disease pathophysiology. This review summarizes the role of MGBA signaling in the development of stroke risk factors such as aging, hypertension, obesity, diabetes, and atherosclerosis, as well as changes in the microbiota in experimental or clinical populations. In addition, this review also examines dietary changes, the administration of probiotics and prebiotics, and fecal microbiota transplantation as treatment options for ischemic stroke as potential health benefits. It will become more apparent how the MGBA affects human health and disease with continuing advancements in this emerging field of biomedical sciences.},
}
@article {pmid36267180,
year = {2022},
author = {Wang, M and Tu, Q},
title = {Effective data filtering is prerequisite for robust microbial association network construction.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {1016947},
pmid = {36267180},
issn = {1664-302X},
abstract = {Microorganisms do not exist as individual population in the environment. Rather, they form complex assemblages that perform essential ecosystem functions and maintain ecosystem stability. Besides the diversity and composition of microbial communities, deciphering their potential interactions in the form of association networks has attracted many microbiologists and ecologists. Much effort has been made toward the methodological development for constructing microbial association networks. However, microbial profiles suffer dramatically from zero values, which hamper accurate association network construction. In this study, we investigated the effects of zero-value issues associated with microbial association network construction. Using the TARA Oceans microbial profile as an example, different zero-value-treatment approaches were comparatively investigated using different correlation methods. The results suggested dramatic variations of correlation coefficient values for differently treated microbial profiles. Most specifically, correlation coefficients among less frequent microbial taxa were more affected, whichever method was used. Negative correlation coefficients were more problematic and sensitive to network construction, as many of them were inferred from low-overlapped microbial taxa. Consequently, microbial association networks were greatly differed. Among various approaches, we recommend sequential calculation of correlation coefficients for microbial taxa pairs by excluding paired zero values. Filling missing values with pseudo-values is not recommended. As microbial association network analyses have become a widely used technique in the field of microbial ecology and environmental science, we urge cautions be made to critically consider the zero-value issues in microbial data.},
}
@article {pmid36266277,
year = {2022},
author = {Sauvaitre, T and Van Landuyt, J and Durif, C and Roussel, C and Sivignon, A and Chalancon, S and Uriot, O and Van Herreweghen, F and Van de Wiele, T and Etienne-Mesmin, L and Blanquet-Diot, S},
title = {Role of mucus-bacteria interactions in Enterotoxigenic Escherichia coli (ETEC) H10407 virulence and interplay with human microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {8},
number = {1},
pages = {86},
pmid = {36266277},
issn = {2055-5008},
mesh = {Humans ; *Enterotoxigenic Escherichia coli/physiology ; Interleukin-8/genetics ; Virulence ; Diarrhea ; Caco-2 Cells ; *Escherichia coli Infections/microbiology ; Travel ; *Microbiota ; Bacteria ; Mucus ; Mucins ; },
abstract = {The intestinal mucus layer has a dual role in human health constituting a well-known microbial niche that supports gut microbiota maintenance but also acting as a physical barrier against enteric pathogens. Enterotoxigenic Escherichia coli (ETEC), the major agent responsible for traveler's diarrhea, is able to bind and degrade intestinal mucins, representing an important but understudied virulent trait of the pathogen. Using a set of complementary in vitro approaches simulating the human digestive environment, this study aimed to describe how the mucus microenvironment could shape different aspects of the human ETEC strain H10407 pathophysiology, namely its survival, adhesion, virulence gene expression, interleukin-8 induction and interactions with human fecal microbiota. Using the TNO gastrointestinal model (TIM-1) simulating the physicochemical conditions of the human upper gastrointestinal (GI) tract, we reported that mucus secretion and physical surface sustained ETEC survival, probably by helping it to face GI stresses. When integrating the host part in Caco2/HT29-MTX co-culture model, we demonstrated that mucus secreting-cells favored ETEC adhesion and virulence gene expression, but did not impede ETEC Interleukin-8 (IL-8) induction. Furthermore, we proved that mucosal surface did not favor ETEC colonization in a complex gut microbial background simulated in batch fecal experiments. However, the mucus-specific microbiota was widely modified upon the ETEC challenge suggesting its role in the pathogen infectious cycle. Using multi-targeted in vitro approaches, this study supports the major role played by mucus in ETEC pathophysiology, opening avenues in the design of new treatment strategies.},
}
@article {pmid36265143,
year = {2023},
author = {Zhu 朱墨, M and Duan, X and Cai, P and Qiu, Z and Li 李正男, Z},
title = {Genome Sequence Resource of Trichothecium roseum (ZM-Tr2021), the Causal Agent of Postharvest Pink Rot.},
journal = {Plant disease},
volume = {107},
number = {1},
pages = {205-209},
doi = {10.1094/PDIS-03-22-0655-A},
pmid = {36265143},
issn = {0191-2917},
mesh = {*Hypocreales ; *Ascomycota/genetics ; },
}
@article {pmid36262799,
year = {2022},
author = {Faust, V and van Alen, TA and Op den Camp, HJM and Vlaeminck, SE and Ganigué, R and Boon, N and Udert, KM},
title = {Ammonia oxidation by novel "Candidatus Nitrosacidococcus urinae" is sensitive to process disturbances at low pH and to iron limitation at neutral pH.},
journal = {Water research X},
volume = {17},
number = {},
pages = {100157},
pmid = {36262799},
issn = {2589-9147},
abstract = {Acid-tolerant ammonia-oxidizing bacteria (AOB) can open the door to new applications, such as partial nitritation at low pH. However, they can also be problematic because chemical nitrite oxidation occurs at low pH, leading to the release of harmful nitrogen oxide gases. In this publication, the role of acid-tolerant AOB in urine treatment was explored. On the one hand, the technical feasibility of ammonia oxidation under acidic conditions for source-separated urine with total nitrogen concentrations up to 3.5 g-N L[-1] was investigated. On the other hand, the abundance and growth of acid-tolerant AOB at more neutral pH was explored. Under acidic conditions (pH of 5), ammonia oxidation rates of 500 mg-N L[-1] d[-1] and 10 g-N g-VSS[-1] d[-1] were observed, despite high concentrations of 15 mg-N L[-1] of the AOB-inhibiting compound nitrous acid and low concentration of 0.04 mg-N L[-1] of the substrate ammonia. However, ammonia oxidation under acidic conditions was very sensitive to process disturbances. Even short periods of less than 12 h without oxygen or without influent resulted in a complete cessation of ammonia oxidation with a recovery time of up to two months, which is a problem for low maintenance applications such as decentralized treatment. Furthermore, undesirable nitrogen losses of about 10% were observed. Under acidic conditions, a novel AOB strain was enriched with a relative abundance of up to 80%, for which the name "Candidatus (Ca.) Nitrosacidococcus urinae" is proposed. While Nitrosacidococcus members were present only to a small extent (0.004%) in urine nitrification reactors operated at pH values between 5.8 and 7, acid-tolerant AOB were always enriched during long periods without influent, resulting in an uncontrolled drop in pH to as low as 2.5. Long-term experiments at different pH values showed that the activity of "Ca. Nitrosacidococcus urinae" decreased strongly at a pH of 7, where they were also outcompeted by the acid-sensitive AOB Nitrosomonas halophila. The experiment results showed that the decreased activity of "Ca. Nitrosacidococcus urinae" correlated with the limited availability of dissolved iron at neutral pH.},
}
@article {pmid36261994,
year = {2022},
author = {De La Fuente, MJ and De la Iglesia, R and Farias, L and Glasner, B and Torres-Rojas, F and Muñoz, D and Daims, H and Lukumbuzya, M and Vargas, IT},
title = {Enhanced nitrogen and carbon removal in natural seawater by electrochemical enrichment in a bioelectrochemical reactor.},
journal = {Journal of environmental management},
volume = {323},
number = {},
pages = {116294},
doi = {10.1016/j.jenvman.2022.116294},
pmid = {36261994},
issn = {1095-8630},
mesh = {Nitrogen/chemistry ; Denitrification ; Nitrification ; Wastewater ; Carbon ; Nitrates ; Bioreactors ; RNA, Ribosomal, 16S ; Nitrites ; *Graphite ; In Situ Hybridization, Fluorescence ; *Ammonium Compounds ; Seawater ; },
abstract = {Municipal and industrial wastewater discharges in coastal and marine environments are of major concern due to their high carbon and nitrogen loads and the resulted phenomenon of eutrophication. Bioelectrochemical reactors (BERs) for simultaneous nitrogen and carbon removal have gained attention owing to their cost efficiency and versatility, as well as the possibility of electrochemical enrich specific groups. This study presented a scalable two-chamber BERs using graphite granules as electrode material. BERs were inoculated and operated for 37 days using natural seawater with high concentrations of ammonium and acetate. The BERs demonstrated a maximum current density of 0.9 A m[-3] and removal rates of 7.5 mg NH4[+]-N L[-1] d[-1] and 99.5 mg L[-1] d[-1] for total organic carbon (TOC). Removals observed for NH4[+]-N and TOC were 96.2% and 68.7%, respectively. The results of nutrient removal (i.e., ammonium, nitrate, nitrite and TOC) and microbial characterization (i.e., next-generation sequencing of the 16S rRNA gene and fluorescence in situ hybridization) showed that BERs operated with a poised cathode at -260 mV (vs. Ag/AgCl) significantly enriched nitrifying microorganisms in the anode and denitrifying microorganisms and planctomycetes in the cathode. Interestingly, the electrochemical enrichment did not increase the total number of microorganisms in the formed biofilms but controlled their composition. Thus, this work shows the first successful attempt to electrochemically enrich marine nitrifying and denitrifying microorganisms and presents a technique to accelerate the start-up process of BERs to remove dissolved inorganic nitrogen and total organic carbon from seawater.},
}
@article {pmid36259773,
year = {2022},
author = {Eliades, SJ and Colston, TJ and Siler, CD},
title = {Gut microbial ecology of Philippine gekkonids: ecoevolutionary effects on microbiome compositions.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {12},
pages = {},
pmid = {36259773},
issn = {1574-6941},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Philippines ; *Microbiota/genetics ; Symbiosis ; },
abstract = {Given the rapidly changing landscapes of habitats across the globe, a sound understanding of host-associated microbial communities and the ecoevolutionary forces that shape them is needed to assess general organismal adaptability. Knowledge of the symbiotic endogenous microbiomes of most reptilian species worldwide remains limited. We sampled gut microbiomes of geckos spanning nine species and four genera in the Philippines to (i) provide baseline data on gut microbiota in these host species, (ii) test for significant associations between host phylogenetic relationships and observed microbial assemblages, potentially indicative of phylosymbiosis, and (iii) identify correlations between multiple ecoevolutionary factors (e.g. species identity, habitat tendencies, range extents, and maximum body sizes) and gut microbiomes in Philippine gekkonids. We recovered no significant association between interspecific host genetic distances and observed gut microbiomes, providing limited evidence for phylosymbiosis in this group. Philippine gekkonid microbiomes were associated most heavily with host species identity, though marked variation among conspecifics at distinct sampling sites indicates that host locality influences gut microbiomes as well. Interestingly, individuals grouped as widespread and microendemic regardless of host species identity displayed significant differences in alpha and beta diversity metrics examined, likely driven by differences in rare OTU presence between groups. These results provide much needed insight in host-associated microbiomes in wild reptiles and the ecoevolutionary forces that structure such communities.},
}
@article {pmid36259715,
year = {2022},
author = {Conacher, CG and Naidoo-Blassoples, RK and Rossouw, D and Bauer, FF},
title = {A Transcriptomic Analysis of Higher-Order Ecological Interactions in a Eukaryotic Model Microbial Ecosystem.},
journal = {mSphere},
volume = {7},
number = {6},
pages = {e0043622},
pmid = {36259715},
issn = {2379-5042},
mesh = {*Saccharomyces cerevisiae/genetics/metabolism ; *Wine ; Ecosystem ; Transcriptome ; Gene Expression Profiling ; },
abstract = {Nonlinear ecological interactions within microbial ecosystems and their contribution to ecosystem functioning remain largely unexplored. Higher-order interactions, or interactions in systems comprised of more than two members that cannot be explained by cumulative pairwise interactions, are particularly understudied, especially in eukaryotic microorganisms. The wine fermentation ecosystem presents an ideal model to study yeast ecosystem establishment and functioning. Some pairwise ecological interactions between wine yeast species have been characterized, but very little is known about how more complex, multispecies systems function. Here, we evaluated nonlinear ecosystem properties by determining the transcriptomic response of Saccharomyces cerevisiae to pairwise versus tri-species culture. The transcriptome revealed that genes expressed during pairwise coculture were enriched in the tri-species data set but also that just under half of the data set comprised unique genes attributed to a higher-order response. Through interactive protein-association network visualizations, a holistic cell-wide view of the gene expression data was generated, which highlighted known stress response and metabolic adaptation mechanisms which were specifically activated during tri-species growth. Further, extracellular metabolite data corroborated that the observed differences were a result of a biotic stress response. This provides exciting new evidence showing the presence of higher-order interactions within a model microbial ecosystem. IMPORTANCE Higher-order interactions are one of the major blind spots in our understanding of microbial ecosystems. These systems remain largely unpredictable and are characterized by nonlinear dynamics, in particular when the system is comprised of more than two entities. By evaluating the transcriptomic response of S. cerevisiae to an increase in culture complexity from a single species to two- and three-species systems, we were able to confirm the presence of a unique response in the more complex setting that could not be explained by the responses observed at the pairwise level. This is the first data set that provides molecular targets for further analysis to explain unpredictable ecosystem dynamics in yeast.},
}
@article {pmid36258041,
year = {2023},
author = {Wang, J and Shi, X and Tan, Y and Wang, L and Zhang, G},
title = {Elevated O3 Exerts Stronger Effects than Elevated CO2 on the Functional Guilds of Fungi, but Collectively Increase the Structural Complexity of Fungi in a Paddy Soil.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1096-1106},
pmid = {36258041},
issn = {1432-184X},
support = {42077209//National Natural Science Foundation of China/ ; 32071631//National Natural Science Foundation of China/ ; 41907022//National Natural Science Foundation of China/ ; 31901165//National Natural Science Foundation of China/ ; 2020J01186//Natural Science Foundation of Fujian Province/ ; 2020J01138//Natural Science Foundation of Fujian Province/ ; },
mesh = {*Soil ; Carbon Dioxide ; Biomass ; Fungi/genetics ; Carbon ; Soil Microbiology ; *Ozone/pharmacology ; },
abstract = {Global climate change is characterized by altered global atmospheric composition, including elevated CO2 and O3, with important consequences on soil fungal communities. However, the function and community composition of soil fungi in response to elevated CO2 together with elevated O3 in paddy soils remain largely unknown. Here we used twelve open-top chamber facilities (OTCs) to evaluate the interactive effect of CO2 (+ 200 ppm) and O3 (+ 40 ppb) on the diversity, gene abundance, community structure, and functional composition of soil fungi during the growing seasons of two rice cultivars (Japonica, Wuyujing 3 vs. Nangeng 5055) in a Chinese paddy soil. Elevated CO2 and O3 showed no individual or combined effect on the gene abundance or relative abundance of soil fungi, but increased structural complexity of soil fungal communities, indicating that elevated CO2 and/or O3 promoted the competition of species-species interactions. When averaged both cultivars, elevated CO2 showed no individual effect on the diversity or abundance of functional guilds of soil fungi. By contrast, elevated O3 significantly reduced the relative abundance and diversity of symbiotrophic fungi by an average of 47.2% and 39.1%, respectively. Notably, elevated O3 exerts stronger effects on the functional processes of fungal communities than elevated CO2. The structural equation model revealed that elevated CO2 and/or O3 indirectly affected the functional composition of soil fungi through community structure and diversity of soil fungi. Root C/N and soil environmental parameters were identified as the top direct predictors for the community structure of soil fungi. Furthermore, significant correlations were identified between saprotrophic fungi and root biomass, symbiotrophic fungi and root carbon, the pathotroph-symbiotroph and soil pH, as well as pathotroph-saprotroph-symbiotroph and soil microbial biomass carbon. These results suggest that climatic factors substantially affected the functional processes of soil fungal, and threatened soil function and food production, highlighting the detrimental impacts of high O3 on the function composition of soil biota.},
}
@article {pmid36257429,
year = {2023},
author = {Chen, H and Liu, K and Yang, E and Chen, J and Gu, Y and Wu, S and Yang, M and Wang, H and Wang, D and Li, H},
title = {A critical review on microbial ecology in the novel biological nitrogen removal process: Dynamic balance of complex functional microbes for nitrogen removal.},
journal = {The Science of the total environment},
volume = {857},
number = {Pt 2},
pages = {159462},
doi = {10.1016/j.scitotenv.2022.159462},
pmid = {36257429},
issn = {1879-1026},
mesh = {*Nitrogen ; *Denitrification ; Acyl-Butyrolactones ; Quorum Sensing ; Bacteria ; },
abstract = {The novel biological nitrogen removal process has been extensively studied for its high nitrogen removal efficiency, energy efficiency, and greenness. A successful novel biological nitrogen removal process has a stable microecological equilibrium and benign interactions between the various functional bacteria. However, changes in the external environment can easily disrupt the dynamic balance of the microecology and affect the activity of functional bacteria in the novel biological nitrogen removal process. Therefore, this review focuses on the microecology in existing the novel biological nitrogen removal process, including the growth characteristics of functional microorganisms and their interactions, together with the effects of different influencing factors on the evolution of microbial communities. This provides ideas for achieving a stable dynamic balance of the microecology in a novel biological nitrogen removal process. Furthermore, to investigate deeply the mechanisms of microbial interactions in novel biological nitrogen removal process, this review also focuses on the influence of quorum sensing (QS) systems on nitrogen removal microbes, regulated by which bacteria secrete acyl homoserine lactones (AHLs) as signaling molecules to regulate microbial ecology in the novel biological nitrogen removal process. However, the mechanisms of action of AHLs on the regulation of functional bacteria have not been fully determined and the composition of QS system circuits requires further investigation. Meanwhile, it is necessary to further apply molecular analysis techniques and the theory of systems ecology in the future to enhance the exploration of microbial species and ecological niches, providing a deeper scientific basis for the development of a novel biological nitrogen removal process.},
}
@article {pmid36257158,
year = {2022},
author = {Yang, Y and Lu, Z and Azari, M and Kartal, B and Du, H and Cai, M and Herbold, CW and Ding, X and Denecke, M and Li, X and Li, M and Gu, JD},
title = {Discovery of a new genus of anaerobic ammonium oxidizing bacteria with a mechanism for oxygen tolerance.},
journal = {Water research},
volume = {226},
number = {},
pages = {119165},
doi = {10.1016/j.watres.2022.119165},
pmid = {36257158},
issn = {1879-2448},
mesh = {*Ammonium Compounds/metabolism ; Anaerobiosis ; Catalase ; Nitrates/metabolism ; Oxygen/metabolism ; Bacteria, Anaerobic/genetics/metabolism ; Oxidation-Reduction ; Bacteria/metabolism ; },
abstract = {In the past 20 years, there has been a major stride in understanding the core mechanism of anaerobic ammonium-oxidizing (anammox) bacteria, but there are still several discussion points on their survival strategies. Here, we discovered a new genus of anammox bacteria in a full-scale wastewater-treating biofilm system, tentatively named "Candidatus Loosdrechtia aerotolerans". Next to genes of all core anammox metabolisms, it encoded and transcribed genes involved in the dissimilatory nitrate reduction to ammonium (DNRA), which coupled to oxidation of small organic acids, could be used to replenish ammonium and sustain their metabolism. Surprisingly, it uniquely harbored a new ferredoxin-dependent nitrate reductase, which has not yet been found in any other anammox genome and might confer a selective advantage to it in nitrate assimilation. Similar to many other microorganisms, superoxide dismutase and catalase related to oxidative stress resistance were encoded and transcribed by "Ca. Loosdrechtia aerotolerans". Interestingly, bilirubin oxidase (BOD), likely involved in oxygen resistance of anammox bacteria under fluctuating oxygen concentrations, was identified in "Ca. Loosdrechtia aerotolerans" and four Ca. Brocadia genomes, and its activity was demonstrated using purified heterologously expressed proteins. A following survey of oxygen-active proteins in anammox bacteria revealed the presence of other previously undetected oxygen defense systems. The novel cbb3-type cytochrome c oxidase and bifunctional catalase-peroxidase may confer a selective advantage to Ca. Kuenenia and Ca. Scalindua that face frequent changes in oxygen concentrations. The discovery of this new genus significantly broadens our understanding of the ecophysiology of anammox bacteria. Furthermore, the diverse oxygen tolerance strategies employed by distinct anammox bacteria advance our understanding of their niche adaptability and provide valuable insight for the operation of anammox-based wastewater treatment systems.},
}
@article {pmid36255374,
year = {2022},
author = {Castillo, DJ and Dithugoe, CD and Bezuidt, OK and Makhalanyane, TP},
title = {Microbial ecology of the Southern Ocean.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {11},
pages = {},
doi = {10.1093/femsec/fiac123},
pmid = {36255374},
issn = {1574-6941},
mesh = {*Ecosystem ; Seawater/microbiology ; Phytoplankton ; Carbon Cycle ; *Microbiota ; Oceans and Seas ; },
abstract = {The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.},
}
@article {pmid36252671,
year = {2023},
author = {Wang, Z and Li, K and Shen, X and Yan, F and Zhao, X and Xin, Y and Ji, L and Xiang, Q and Xu, X and Li, D and Ran, J and Xu, X and Chen, Q},
title = {Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China.},
journal = {The Science of the total environment},
volume = {857},
number = {Pt 2},
pages = {159439},
doi = {10.1016/j.scitotenv.2022.159439},
pmid = {36252671},
issn = {1879-1026},
mesh = {*Methane ; *Wetlands ; Nitrogen ; Anaerobiosis ; Soil ; Rivers ; Oxidation-Reduction ; },
abstract = {Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH4). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO3[-]), sulfate (SO4[2-]), and nitrous oxide (N2O) flux, among them, soil N substances (TN, NO3[-], N2O) have essential regulatory roles in the AOM process, while NO3[-] and N2O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH4 sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH4 biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.},
}
@article {pmid36252516,
year = {2022},
author = {Calatayud, M and Xiong, C and Selma-Royo, M and van de Wiele, T},
title = {Arsenolipids reduce butyrate levels and influence human gut microbiota in a donor-dependent way.},
journal = {Ecotoxicology and environmental safety},
volume = {246},
number = {},
pages = {114175},
doi = {10.1016/j.ecoenv.2022.114175},
pmid = {36252516},
issn = {1090-2414},
support = {I 2412/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Butyrates/pharmacology ; *Arsenic/toxicity ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; },
abstract = {Arsenolipids are organic arsenic species with variable toxicity. Accurate assessment of the risks derived from arsenic-contaminated seafood intake requires studying the interplay between arsenolipids and the human gut microbiota. This research used the in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME) to assess the effect of defined chemical standards of arsenolipids (AsFA 362 and AsHC 332) on a simulated healthy human gut microbiota (n = 4). Microbial-derived metabolites were quantified by gas chromatography and microbiota structure was characterized by 16S rRNA gene sequencing. A specific reduction in butyrate production (control=5.28 ± 0.3 mM; AsFAs=4.56 ± 0.4 mM; AsHC 332=4.4 ± 0.6 mM, n = 4 donors), concomitant with a reduction in the abundance of Lachnospiraceae UCG-004 group and the Faecalibacterium genus was observed, albeit in a donor-dependent manner. Furthermore, an increase in Escherichia/Shigella, Proteobacteria and Fusobacterium abundance was observed after arsenolipid treatments, depending on individual microbiota background. These alterations in microbial functionality and microbial community structure suggest a detrimental effect of arsenolipids intake towards the commensal gut microbiome, and consequently, on human health.},
}
@article {pmid36251278,
year = {2022},
author = {Ross, DE and Lipus, D and Gulliver, D},
title = {Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms.},
journal = {Environmental microbiology},
volume = {24},
number = {12},
pages = {5984-5997},
doi = {10.1111/1462-2920.16251},
pmid = {36251278},
issn = {1462-2920},
mesh = {*Methanomicrobiales/metabolism ; *Metagenomics ; Metagenome ; Hydrocarbons/metabolism ; Methane/metabolism ; Bacteria ; },
abstract = {Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes (MAGs) to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin (AppB). Our analyses resulted in the recovery of over 40 MAGs from 8 coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. The data presented herein provides novel insights into AppB coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.},
}
@article {pmid36246995,
year = {2022},
author = {Mörkl, S and Oberascher, A and Tatschl, JM and Lackner, S and Bastiaanssen, TFS and Butler, MI and Moser, M and Frühwirth, M and Mangge, H and Cryan, JF and Dinan, TG and Holasek, SJ},
title = {Cardiac vagal activity is associated with gut-microbiome patterns in women-An exploratory pilot study.},
journal = {Dialogues in clinical neuroscience},
volume = {24},
number = {1},
pages = {1-9},
pmid = {36246995},
issn = {1958-5969},
mesh = {Female ; *Gastrointestinal Microbiome/physiology ; Humans ; Interleukin-6 ; *Microbiota ; Pilot Projects ; },
abstract = {INTRODUCTION: A functional reciprocity between the gut microbiome and vagal nerve activity has been suggested, however, human studies addressing this phenomenon are limited.<br><br>METHODS: Twenty-four-hour cardiac vagal activity (CVA) was assessed from 73 female participants (aged 24.5&#x2009;&#xb1;&#x2009;4.3&#x2009;years). Additionally, stool samples were subjected to 16SrRNA gene analysis (V1-V2). Quantitative Insights Into Microbial Ecology (QIIME) was used to analyse microbiome data. Additionally, inflammatory parameters (such as CRP and IL-6) were derived from serum samples.<br><br>RESULTS: Daytime CVA correlated significantly with gut microbiota diversity (r sp&#x2009;=&#x2009;0.254, p&#x2009;=&#x2009;0.030), CRP (r sp&#x2009;=&#x2009;-0.348, p&#x2009;=&#x2009;0.003), and IL-6 (r sp&#x2009;=&#x2009;-0.320, p&#x2009;=&#x2009;0.006). When the group was divided at the median of 24&#x2009;h CVA (Mdn = 1.322), the following features were more abundant in the high CVA group: Clostridia (Linear discriminant analysis effect size (LDA)&#x2009;=&#x2009;4.195, p&#x2009;=&#x2009;0.029), Clostridiales (LDA = 4.195, p&#x2009;=&#x2009;0.029), Lachnospira (LDA = 3.489, p&#x2009;=&#x2009;0.004), Ruminococcaceae (LDA = 4.073, p&#x2009;=&#x2009;0.010), Faecalibacterium (LDA = 3.982, p&#x2009;=&#x2009;0.042), Lactobacillales (LDA = 3.317, p&#x2009;=&#x2009;0.029), Bacilli (LDA = 3.294, p&#x2009;=&#x2009;0.0350), Streptococcaceae (LDA = 3.353, p&#x2009;=&#x2009;0.006), Streptococcus (LDA = 3.332, p&#x2009;=&#x2009;0.011). Based on Dirichlet multinomial mixtures two enterotypes could be detected, which differed significantly in CVA, age, BMI, CRP, IL-6, and diversity.<br><br>CONCLUSIONS: As an indicator of gut-brain communication, gut microbiome analysis could be extended by measurements of CVA to enhance our understanding of signalling via microbiota-gut-brain-axis and its alterations through psychobiotics.},
}
@article {pmid36243459,
year = {2022},
author = {Pinnell, LJ and Morley, PS},
title = {The Microbial Ecology of Liver Abscesses in Cattle.},
journal = {The Veterinary clinics of North America. Food animal practice},
volume = {38},
number = {3},
pages = {367-381},
doi = {10.1016/j.cvfa.2022.08.004},
pmid = {36243459},
issn = {1558-4240},
mesh = {Animals ; Bacteroidetes/genetics ; Cattle ; *Cattle Diseases ; Humans ; *Liver Abscess/veterinary ; *Microbiota/genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Emerging evidence regarding the microbiome of liver abscesses (LAs) and the gastrointestinal tract of cattle suggests that a reexamination of the etiopathogenesis of LAs is warranted. Microbiome studies using 16S rRNA gene sequencing have demonstrated that LAs are highly polymicrobial, and hundreds of bacterial taxa are typically found in these lesions at slaughter. Fusobacteria and Bacteroidetes are equally dominant phyla within LAs, followed by Proteobacteria. The gut-liver axis (ie, bidirectional crosstalk between the gut and liver) is linked with a variety of liver diseases in humans, and investigation of host-microbiome interactions in cattle may lead to improved methods of prevention.},
}
@article {pmid36242623,
year = {2023},
author = {Li, W and Li, X and Wang, W and Zhang, S and Cui, J and Peng, Y and Zhao, Y},
title = {Impact of Sulfoxaflor Exposure on Bacterial Community and Developmental Performance of the Predatory Ladybeetle Propylea japonica.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1226-1239},
pmid = {36242623},
issn = {1432-184X},
mesh = {Animals ; *Insecticides/pharmacology ; Ecosystem ; *Coleoptera ; Larva ; Bacteria/genetics ; },
abstract = {Insects maintain a vast number of symbiotic bacteria, and these symbionts play key roles in the hosts' life processes. Propylea japonica (Coleoptera: Coccinellidae) is an abundant and widespread ladybeetle in agricultural fields in Asia. Both larvae and adults of P. japonica are likely to be exposed to insecticide residue in the field during their predatory activity. Sulfoxaflor is a highly powerful insecticide that has strong efficacy in controlling sap-sucking pests. To date, there have been several studies on the acute and long-term toxicity of sulfoxaflor to insects, but few studies have reported the impact of sulfoxaflor on the predators' micro-ecosystems. This study was to determine the impact of sulfoxaflor on the symbiotic bacteria and developmental performance of P. japonica. In the present study, two concentrations (1 mg/L and 5 mg/L) and two exposure periods (1 day and 5 days) were set for P. japonica under sulfoxaflor exposure. The survival rate, developmental duration, pupation rate, emergence rate, and body weight of P. japonica were examined. Moreover, the bacterial community of P. japonica was investigated by high-throughput 16S ribosomal RNA gene sequencing. Our results indicated that bacterial community of P. japonica was mainly composed of Staphylococcus, Pantoea, Acinetobacter, Rhodococcus, and Ralstonia at the genus level. The bacterial community of P. japonica in 1 mg/L and 5 mg/L sulfoxaflor groups was significantly altered on day 1, compared with that in control group. The results also showed that the larval duration was significantly prolonged but the pupal duration was significantly shortened in both sulfoxaflor groups. Meanwhile, the pupation and emergence rate was not significantly changed, but the body weights of adults were significantly decreased in both sulfoxaflor groups. Our study will provide a new perspective for evaluating the safety of pesticides to beneficial arthropods.},
}
@article {pmid36239777,
year = {2023},
author = {Tian, C and Lv, Y and Yang, Z and Zhang, R and Zhu, Z and Ma, H and Li, J and Zhang, Y},
title = {Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {933-946},
pmid = {36239777},
issn = {1432-184X},
support = {41676177//National Natural Science Foundation of China/ ; 41921006//National Natural Science Foundation of China/ ; 41676175//National Natural Science Foundation of China/ ; 41676188//National Natural Science Foundation of China/ ; SL2020MS022//Oceanic Interdisciplinary Program of Shanghai Jiao Tong University/ ; 21TQ1400201//Shanghai Pilot Program for Basic Research of Shanghai Jiao Tong University/ ; },
mesh = {*Soil/chemistry ; Svalbard ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Ice Cover/microbiology ; Soil Microbiology ; },
abstract = {Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.},
}
@article {pmid36239764,
year = {2022},
author = {Nissen, L and Aniballi, C and Casciano, F and Elmi, A and Ventrella, D and Zannoni, A and Gianotti, A and Bacci, ML},
title = {Maternal amoxicillin affects piglets colon microbiota: microbial ecology and metabolomics in a gut model.},
journal = {Applied microbiology and biotechnology},
volume = {106},
number = {22},
pages = {7595-7614},
pmid = {36239764},
issn = {1432-0614},
mesh = {Animals ; Swine ; Female ; *Gastrointestinal Microbiome ; Amoxicillin/pharmacology ; Colon ; *Microbiota ; Metabolomics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The first weeks of life represent a crucial stage for microbial colonization of the piglets' gastrointestinal tract. Newborns' microbiota is unstable and easily subject to changes under stimuli or insults. Nonetheless, the administration of antibiotics to the sow is still considered as common practice in intensive farming for pathological conditions in the postpartum. Therefore, transfer of antibiotic residues through milk may occurs, affecting the piglets' colon microbiota. In this study, we aimed to extend the knowledge on antibiotic transfer through milk, employing an in vitro dedicated piglet colon model (MICODE-Multi Unit In vitro Colon Model). The authors' focus was set on the shifts of the piglets' microbiota composition microbiomics (16S r-DNA MiSeq and qPCR-quantitative polymerase chain reaction) and on the production of microbial metabolites (SPME GC/MS-solid phase micro-extraction gas chromatography/mass spectrometry) in response to milk with different concentrations of amoxicillin. The results showed an effective influence of amoxicillin in piglets' microbiota and metabolites production; however, without altering the overall biodiversity. The scenario is that of a limitation of pathogens and opportunistic taxa, e.g., Staphylococcaceae and Enterobacteriaceae, but also a limitation of commensal dominant Lactobacillaceae, a reduction in commensal Ruminococcaceae and a depletion in beneficial Bifidobactericeae. Lastly, an incremental growth of resistant species, such as Enterococcaceae or Clostridiaceae, was observed. To the authors' knowledge, this study is the first evaluating the impact of antibiotic residues towards the piglets' colon microbiota in an in vitro model, opening the way to include such approach in a pipeline of experiments where a reduced number of animals for testing is employed. KEY POINTS: • Piglet colon model to study antibiotic transfer through milk. • MICODE resulted a robust and versatile in vitro gut model. • Towards the "3Rs" Principles to replace, reduce and refine the use of animals used for scientific purposes (Directive 2010/63/UE).},
}
@article {pmid36238597,
year = {2022},
author = {Sinclair, P and Longyear, J and Reynolds, K and Finnie, AA and Brackley, CA and Carballo-Pacheco, M and Allen, RJ},
title = {A computational model for microbial colonization of an antifouling surface.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {920014},
pmid = {36238597},
issn = {1664-302X},
abstract = {Biofouling of marine surfaces such as ship hulls is a major industrial problem. Antifouling (AF) paints delay the onset of biofouling by releasing biocidal chemicals. We present a computational model for microbial colonization of a biocide-releasing AF surface. Our model accounts for random arrival from the ocean of microorganisms with different biocide resistance levels, biocide-dependent proliferation or killing, and a transition to a biofilm state. Our computer simulations support a picture in which biocide-resistant microorganisms initially form a loosely attached layer that eventually transitions to a growing biofilm. Once the growing biofilm is established, immigrating microorganisms are shielded from the biocide, allowing more biocide-susceptible strains to proliferate. In our model, colonization of the AF surface is highly stochastic. The waiting time before the biofilm establishes is exponentially distributed, suggesting a Poisson process. The waiting time depends exponentially on both the concentration of biocide at the surface and the rate of arrival of resistant microorganisms from the ocean. Taken together our results suggest that biofouling of AF surfaces may be intrinsically stochastic and hence unpredictable, but immigration of more biocide-resistant species, as well as the biological transition to biofilm physiology, may be important factors controlling the time to biofilm establishment.},
}
@article {pmid36229976,
year = {2022},
author = {De Spiegeleer, A and Wynendaele, E and Descamps, A and Debunne, N and Braeckman, BP and De Mey, M and Coudenys, J and Crombez, L and Verbeke, F and Janssens, Y and Janky, R and Goossens, E and Vlaeminck, C and Duchi, D and Andries, V and Dumas, E and Petrovic, M and Van de Wiele, T and Knappe, D and Hoffmann, R and Mouly, V and Bigot, A and Vereecke, L and Van Immerseel, F and Van Den Noortgate, N and De Spiegeleer, B and Elewaut, D},
title = {The bacterial quorum sensing peptide iAM373 is a novel inducer of sarcopenia.},
journal = {Clinical and translational medicine},
volume = {12},
number = {10},
pages = {e1053},
pmid = {36229976},
issn = {2001-1326},
support = {P40 OD010440/OD/NIH HHS/United States ; },
mesh = {Bacteria ; Humans ; Oligopeptides ; Peptides ; *Quorum Sensing ; *Sarcopenia ; },
}
@article {pmid36224329,
year = {2022},
author = {Bayer, N and Hausmann, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G},
title = {Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.},
journal = {Leukemia},
volume = {36},
number = {11},
pages = {2705-2714},
pmid = {36224329},
issn = {1476-5551},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Graft vs Host Disease/etiology ; *Gastrointestinal Microbiome ; Immunity ; },
abstract = {The composition of the gut microbiome influences the clinical course after allogeneic hematopoietic stem cell transplantation (HSCT), but little is known about the relevance of skin microorganisms. In a single-center, observational study, we recruited a cohort of 50 patients before undergoing conditioning treatment and took both stool and skin samples up to one year after HSCT. We could confirm intestinal dysbiosis following HSCT and report that the skin microbiome is likewise perturbed in HSCT-recipients. Overall bacterial colonization of the skin was decreased after conditioning. Particularly patients that developed acute skin graft-versus-host disease (aGVHD) presented with an overabundance of Staphylococcus spp. In addition, a loss in alpha diversity was indicative of aGVHD development already before disease onset and correlated with disease severity. Further, co-localization of CD45[+] leukocytes and staphylococci was observed in the skin of aGVHD patients even before disease development and paralleled with upregulated genes required for antigen-presentation in mononuclear phagocytes. Overall, our data reveal disturbances of the skin microbiome as well as cutaneous immune response in HSCT recipients with changes associated with cutaneous aGVHD.},
}
@article {pmid36224114,
year = {2023},
author = {Rohrbach, S and Gkoutselis, G and Hink, L and Weig, AR and Obst, M and Diekmann, A and Ho, A and Rambold, G and Horn, MA},
title = {Microplastic polymer properties as deterministic factors driving terrestrial plastisphere microbiome assembly and succession in the field.},
journal = {Environmental microbiology},
volume = {25},
number = {12},
pages = {2681-2697},
doi = {10.1111/1462-2920.16234},
pmid = {36224114},
issn = {1462-2920},
support = {SFB1357-391977956//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Plastics ; Microplastics ; Polymers ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Soil ; },
abstract = {Environmental microplastic (MP) is ubiquitous in aquatic and terrestrial ecosystems providing artificial habitats for microbes. Mechanisms of MP colonization, MP polymer impacts, and effects on soil microbiomes are largely unknown in terrestrial systems. Therefore, we experimentally tested the hypothesis that MP polymer type is an important deterministic factor affecting MP community assembly by incubating common MP polymer types in situ in landfill soil for 14 months. 16S rRNA gene amplicon sequencing indicated that MP polymers have specific impacts on plastisphere microbiomes, which are subsets of the soil microbiome. Chloroflexota, Gammaproteobacteria, certain Nitrososphaerota, and Nanoarchaeota explained differences among MP polymers and time points. Plastisphere microbial community composition derived from different MP diverged over time and was enriched in potential pathogens. PICRUSt predictions of pathway abundances and quantitative PCR of functional marker genes indicated that MP polymers exerted an ambivalent effect on genetic potentials of biogeochemical cycles. Overall, the data indicate that (i) polymer type as deterministic factor rather than stochastic factors drives plastisphere community assembly, (ii) MP impacts greenhouse gas metabolism, xenobiotic degradation and pathogen distribution, and (iii) MP serves as an ideal model system for studying fundamental questions in microbial ecology such as community assembly mechanisms in terrestrial environments.},
}
@article {pmid36216061,
year = {2023},
author = {Sabba, F and Farmer, M and Jia, Z and Di Capua, F and Dunlap, P and Barnard, J and Qin, CD and Kozak, JA and Wells, G and Downing, L},
title = {Impact of operational strategies on a sidestream enhanced biological phosphorus removal (S2EBPR) reactor in a carbon limited wastewater plant.},
journal = {The Science of the total environment},
volume = {857},
number = {Pt 1},
pages = {159280},
doi = {10.1016/j.scitotenv.2022.159280},
pmid = {36216061},
issn = {1879-1026},
mesh = {*Wastewater ; *Phosphorus ; Carbon ; Bioreactors ; Sewage ; },
abstract = {Water resource recovery facilities are faced with stringent effluent phosphorus limits to reduce nutrient pollution. Enhanced biological phosphorus removal (EBPR) is the most common biological route to remove phosphorus; however, many facilities struggle to achieve consistent performance due to limited carbon availability in the influent wastewater. A promising process to improve carbon availability is through return activated sludge (RAS) fermentation via sidestream EBPR (S2EBPR). In this study, a full-scale S2EBPR pilot was operated with a sidestream plus carbon configuration (SSRC) at a carbon-limited facility. A model based on the pilot test was developed and calibrated in the SUMO platform and used to explore routes for improving orthophosphate (OP) effluent compliance. Modeling results showed that RAS diversion by itself was not sufficient to drive OP removal to permit limits of 1 mg L[-1], therefore, other strategies were evaluated. Supplemental carbon addition of MicroC® at 1.90 L min[-1] and controlling the phosphorus concentration below 3.5 mgP L[-1] in the primary effluent (PE) proved to be valid supplemental strategies to achieve OP removal below 1 mg L[-1] most of the time. In particular, the proposed supplemental carbon flow rate would result in an improvement of the rbCOD:P ratio from 17:1 to 26:1. The synergistic approach of RAS diversion and supplemental carbon addition increased the polyphosphate accumulating organisms (PAO) population while minimizing the supplemental carbon needed to achieve consistent phosphorus removal. Overall, this pilot and modeling study shows that joint strategies, including RAS diversion, carbon addition and PE control, can be effective to achieve optimal control of OP effluent.},
}
@article {pmid36215761,
year = {2022},
author = {Uroosa, and Kazmi, SSUH and Warren, A and Zhong, X and Xu, H},
title = {Effects of nitrofurazone on ecosystem function in marine environments: A case study on microbial fauna.},
journal = {Marine pollution bulletin},
volume = {184},
number = {},
pages = {114216},
doi = {10.1016/j.marpolbul.2022.114216},
pmid = {36215761},
issn = {1879-3363},
mesh = {*Ecosystem ; Nitrofurazone/toxicity ; Environmental Monitoring ; *Ciliophora ; Anti-Bacterial Agents ; },
abstract = {To evaluate the effects of nitrofurazone on functional processes in marine ecosystems, periphytic protozoan communities were exposed to different concentrations of the antibiotic for a 10-day duration. Species trait distributions in the tested communities were observed during exposure to five concentrations of nitrofurazone. A fuzzy coding system with seven traits and seventeen categories was used to summarize the changes in functional patterns of the test organisms. Nitrofurazone had a significant influence on the function process of the periphytic ciliate communities. Bacterivores with flattened bodies were sensitive to the toxicant whereas sessile and cylindrical raptors showed a high tolerance to nitrofurazone, invariably dominating communities exposed to high concentrations. Bootstrapped-average analysis demonstrated a significant change in functional patterns at highest nitrofurazone concentrations (8 mg l[-1]). Based on these findings, it is suggested that nitrofurazone may negatively influence ecosystem function in marine environments.},
}
@article {pmid36215464,
year = {2022},
author = {Chevrette, MG and Thomas, CS and Hurley, A and Rosario-Meléndez, N and Sankaran, K and Tu, Y and Hall, A and Magesh, S and Handelsman, J},
title = {Microbiome composition modulates secondary metabolism in a multispecies bacterial community.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {42},
pages = {e2212930119},
pmid = {36215464},
issn = {1091-6490},
support = {T32 GM135066/GM/NIGMS NIH HHS/United States ; S10 RR029531/RR/NCRR NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents ; Benzamides ; Humans ; *Microbiota ; Secondary Metabolism ; *Siderophores/genetics/metabolism ; },
abstract = {Bacterial secondary metabolites are a major source of antibiotics and other bioactive compounds. In microbial communities, these molecules can mediate interspecies interactions and responses to environmental change. Despite the importance of secondary metabolites in human health and microbial ecology, little is known about their roles and regulation in the context of multispecies communities. In a simplified model of the rhizosphere composed of Bacillus cereus, Flavobacterium johnsoniae, and Pseudomonas koreensis, we show that the dynamics of secondary metabolism depend on community species composition and interspecies interactions. Comparative metatranscriptomics and metametabolomics reveal that the abundance of transcripts of biosynthetic gene clusters (BGCs) and metabolomic molecular features differ between monocultures or dual cultures and a tripartite community. In both two- and three-member cocultures, P. koreensis modified expression of BGCs for zwittermicin, petrobactin, and other secondary metabolites in B. cereus and F. johnsoniae, whereas the BGC transcriptional response to the community in P. koreensis itself was minimal. Pairwise and tripartite cocultures with P. koreensis displayed unique molecular features that appear to be derivatives of lokisin, suggesting metabolic handoffs between species. Deleting the BGC for koreenceine, another P. koreensis metabolite, altered transcript and metabolite profiles across the community, including substantial up-regulation of the petrobactin and bacillibactin BGCs in B. cereus, suggesting that koreenceine represses siderophore production. Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.},
}
@article {pmid36214570,
year = {2022},
author = {Utter, DR and Cavanaugh, CM and Borisy, GG},
title = {Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations.},
journal = {mBio},
volume = {13},
number = {6},
pages = {e0241422},
pmid = {36214570},
issn = {2150-7511},
support = {R01 DE030136/DE/NIDCR NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {Two major viewpoints have been put forward for how microbial populations change, differing in whether adaptation is driven principally by gene-centric or genome-centric processes. Longitudinal sampling at microbially relevant timescales, i.e., days to weeks, is critical for distinguishing these mechanisms. Because of its significance for both microbial ecology and human health and its accessibility and high level of curation, we used the oral microbiota to study bacterial intrapopulation genome dynamics. Metagenomes were generated by shotgun sequencing of total community DNA from the healthy tongues of 17 volunteers at four to seven time points obtained over intervals of days to weeks. We obtained 390 high-quality metagenome-assembled genomes (MAGs) defining population genomes from 55 genera. The vast majority of genes in each MAG were tightly linked over the 2-week sampling window, indicating that the majority of the population's genomes were temporally stable at the MAG level. MAG-defined populations were composed of up to 5 strains, as determined by single-nucleotide-variant frequencies. Although most were stable over time, individual strains carrying over 100 distinct genes that rose from low abundance to dominance in a population over a period of days were detected. These results indicate a genome-wide as opposed to a gene-level process of population change. We infer that genome-wide selection of ecotypes is the dominant mode of adaptation in the oral populations over short timescales. IMPORTANCE The oral microbiome represents a microbial community of critical relevance to human health. Recent studies have documented the diversity and dynamics of different bacteria to reveal a rich, stable ecosystem characterized by strain-level dynamics. However, bacterial populations and their genomes are neither monolithic nor static; their genomes are constantly evolving to lose, gain, or alter their functional potential. To better understand how microbial genomes change in complex communities, we used culture-independent approaches to reconstruct the genomes (MAGs) for bacterial populations that approximated different species, in 17 healthy donors' mouths over a 2-week window. Our results underscored the importance of strain-level dynamics, which agrees with and expands on the conclusions of previous research. Altogether, these observations reveal patterns of genomic dynamics among strains of oral bacteria occurring over a matter of days.},
}
@article {pmid36213689,
year = {2022},
author = {He, KJ and Zhang, YF and Liang, LY and Cheng, XS and Gong, G and Ouyang, XM and Lin, Y and Guleng, B},
title = {ncRNAs-mediated high expression of TICRR promotes tumor cell proliferation and migration and is correlated with poor prognosis and tumor immune infiltration of hepatocellular carcinoma.},
journal = {Molecular therapy. Nucleic acids},
volume = {30},
number = {},
pages = {80-94},
pmid = {36213689},
issn = {2162-2531},
abstract = {TICRR is a regulatory factor of DNA replication with ToPBP1 interaction. At present, the underlying function and mechanisms of TICRR remain unclear in LIHC. Our objective was to assess the function and prognosis of TICRR in LIHC. We conducted a differential expression analysis, GO/KEGG, and GSEA enrichment analysis of TICRR in LIHC. We also carried out the gene frequency and SCNA of TICRR. We found that TICRR could serve as an independent prognostic marker in LIHC by univariate and multivariate analysis. In addition, we observed that TICRR was related to immune infiltration, and TICRR had positive correlation with PD1/PD-L1 and CTLA-4 in LIHC. The hsa-miR-126-3p/IPO9-AS1 may be the candidate ncRNAs to regulate the expression of TICRR. The high rate of SCNV of TICRR might have critical effect on the function of CTL cells in LIHC. We further demonstrate through a series of experiments that TICRR facilitated the proliferation and metastasis of liver cancer cells in vitro. Altogether, TICRR might be a potential biomarker and therapeutic target in LIHC.},
}
@article {pmid36213308,
year = {2022},
author = {Vinyard, JR and Faciola, AP},
title = {Unraveling the pros and cons of various in vitro methodologies for ruminant nutrition: a review.},
journal = {Translational animal science},
volume = {6},
number = {4},
pages = {txac130},
pmid = {36213308},
issn = {2573-2102},
abstract = {To decrease the time and cost of experiments as well as the use of animals in nutrition research, in vitro methodologies have become more commonplace in the field of ruminant nutrition. Therefore, the objectives of this review are 1) to describe the development of different in vitro methodologies, 2) to discuss the application, utilization, and advantages of in vitro methodologies, 3) to discuss shortcomings of in vitro methodologies, and 4) to describe the potential developments that may be able to improve in vitro methods. Having been used for decades, some in vitro methodologies such as pure, batch, and continuous cultures have been very well documented and utilized to investigate a wide array of different aspects of nutrition, including the effects of different dietary compositions, individual fermentation end products, and impacts on the microbiome of the rumen. However, both batch and pure cultures can result in a build-up of end products that may inhibit fermentation, as they culture ruminal contents or defined strains of bacteria, respectfully. Continuous culture; however, allows for the removal of end products but, similar to pure and batch cultures, is applicable only to ruminal fermentation and cannot provide information regarding intestinal digestion and bioavailability. This information for in vitro can only be provided using an assay designed for total tract digestibility, which is the three-step procedure (TSP). The TSP may be improved by coupling it with cell culture to investigate the absorption of nutrients in both the ruminal and intestinal phases of the methodology; however, the TSP needs further development to investigate all nutrients and the methodologies available for cell culture are still relatively new to ruminant nutrition. Therefore, while in vitro methodologies provide useful data in the field of ruminant nutrition without the continuous use of animals, there is still much work to be done to improve the methodologies to further apply them.},
}
@article {pmid36208750,
year = {2023},
author = {Gros, M and Mas-Pla, J and Sànchez-Melsió, A and Čelić, M and Castaño, M and Rodríguez-Mozaz, S and Borrego, CM and Balcázar, JL and Petrović, M},
title = {Antibiotics, antibiotic resistance and associated risk in natural springs from an agroecosystem environment.},
journal = {The Science of the total environment},
volume = {857},
number = {Pt 1},
pages = {159202},
doi = {10.1016/j.scitotenv.2022.159202},
pmid = {36208750},
issn = {1879-1026},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/analysis ; Escherichia coli/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Tetracyclines/analysis ; *Natural Springs ; Sulfonamides ; Water ; China ; },
abstract = {This study investigates the occurrence, transport, and risks associated to antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic resistant Escherichia coli (AR-E. coli) in eleven natural springs in an agroecosystem environment with intense livestock production, where groundwater nitrate concentration usually sets above 50 mg L[-1]. Out of 23 multiple-class antibiotics monitored, tetracycline and sulfonamide residues were the most ubiquitous, and they were detected at concentrations ranging from ng L[-1] to μg L[-1]. Five ARGs were monitored, conferring resistance to the antibiotic classes of major use in livestock production. Thus, genes conferring resistance to sulfonamides (sul1 and sul2) and tetracyclines (tetW) as well as a gene proxy for anthropogenic pollution (intI1) were present in most springs. sul1 was the most abundant, with absolute concentrations ranging from 4 × 10[2] to 5.6 × 10[6] gene copies L[-1] water. AR-E. coli showing resistance to sulfonamides and tetracyclines was also detected, with a prevalence up to approximately 40 % in some sites but with poor correlations with the concentration of antibiotic residues and ARGs. The occurrence of antibiotics, ARGs and AR-E. coli was characterized by large seasonal variations which were mostly associated to both hydrological factors and reactive transport processes. Finally, a risk assessment approach pointed out towards low risk for both the groundwater environment and human health, when spring water is used for direct human consumption, associated with the occurrence of antibiotics, ARGs and AR-E. coli. However, long-term effects cannot be neglected, and proper actions must be taken to preserve groundwater quality.},
}
@article {pmid36207335,
year = {2022},
author = {Tao, J and Wang, W and Weissman, JL and Zhang, Y and Chen, S and Zhu, Y and Zhang, C and Hou, S},
title = {Size-fractionated microbiome observed during an eight-month long sampling in Jiaozhou Bay and the Yellow Sea.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {605},
pmid = {36207335},
issn = {2052-4463},
support = {Nos. 42141003//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Bays/microbiology ; China ; Genome, Microbial ; Metagenome ; *Microbiota ; Oceans and Seas ; },
abstract = {Jiaozhou Bay is a typical semi-enclosed bay with a temperate climate imposed by strong anthropogenic influence. To investigate microbial biodiversity and ecosystem services in this highly dynamic coastal environment, we conducted a monthly microbial survey spanning eight months at two stations in the bay and the open Yellow Sea starting in April 2015. This report provides a comprehensive inventory of amplicon sequences and environmental microbial genomes from this survey. In total, 2,543 amplicon sequence variants were obtained with monthly relative abundance profiles in three size fractions (>2.7 μm, 2.7-0.7 μm, and 0.7-0.22 μm). Shotgun metagenomes yielded 915 high-quality metagenome-assembled genomes with ≥50% completeness and ≤5% contamination. These environmental genomes comprise 27 bacterial and 5 archaeal phyla. We expect this comprehensive dataset will facilitate a better understanding of coastal microbial ecology.},
}
@article {pmid36206900,
year = {2023},
author = {Sauter, D and Steuer, A and Wasmund, K and Hausmann, B and Szewzyk, U and Sperlich, A and Gnirss, R and Cooper, M and Wintgens, T},
title = {Microbial communities and processes in biofilters for post-treatment of ozonated wastewater treatment plant effluent.},
journal = {The Science of the total environment},
volume = {856},
number = {Pt 2},
pages = {159265},
doi = {10.1016/j.scitotenv.2022.159265},
pmid = {36206900},
issn = {1879-1026},
mesh = {Filtration/methods ; RNA, Ribosomal, 16S ; *Water Purification/methods ; Charcoal ; *Microbiota ; Coal ; *Water Pollutants, Chemical ; },
abstract = {Ozonation is an established solution for organic micropollutant (OMP) abatement in tertiary wastewater treatment. Biofiltration is the most common process for the biological post-treatment step, which is generally required to remove undesired oxidation products from the reaction of ozone with water matrix compounds. This study comparatively investigates the effect of filter media on the removal of organic contaminants and on biofilm properties for biologically activated carbon (BAC) and anthracite biofilters. Biofilms were analysed in two pilot-scale filters that have been operated for >50,000 bed volumes as post-treatment for ozonated wastewater treatment plant effluent. In parallel, the removal performance of bulk organics and OMP, including differentiation of adsorption and biotransformation through sodium azide inhibition, were carried out in bench-scale filter columns filled with material from the pilot filters. The use of BAC instead of anthracite resulted in an improved removal of organic bulk parameters, dissolved oxygen, and OMP. The OMP removal observed in the BAC filter but not in the anthracite filter was based on adsorption for most of the investigated compounds. For valsartan, however, biotransformation was found to be the dominant pathway, indicating that conditions for biotransformation of certain OMP are better on BAC than on anthracite. Adenosine triphosphate analyses in the media-attached biofilms of the pilot filters showed that biomass concentrations in the BAC filter were significantly higher than in the anthracite filter. The microbial communities (16S rRNA gene sequencing) appeared to be similar with respect to the types of organisms occurring on both filter materials. Alpha diversity also exhibited little variation between filter media. Beta diversity analysis, however, revealed that filter media and bed depth substantially influenced the biofilm composition. In practice, the impact of filter media on biofilm properties and biotransformation processes should be considered for the design of biofilters.},
}
@article {pmid36205738,
year = {2023},
author = {Quero, GM and Piredda, R and Basili, M and Maricchiolo, G and Mirto, S and Manini, E and Seyfarth, AM and Candela, M and Luna, GM},
title = {Host-associated and Environmental Microbiomes in an Open-Sea Mediterranean Gilthead Sea Bream Fish Farm.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1319-1330},
pmid = {36205738},
issn = {1432-184X},
mesh = {Animals ; *Sea Bream ; Fisheries ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Aquaculture ; },
abstract = {Gilthead seabream is among the most important farmed fish species in the Mediterranean Sea. Several approaches are currently applied to assure a lower impact of diseases and higher productivity, including the exploration of the fish microbiome and its manipulation as a sustainable alternative to improve aquaculture practices. Here, using 16S rRNA gene high-throughput sequencing, we explored the microbiome of farmed seabream to assess similarities and differences among microbial assemblages associated to different tissues and compare them with those in the surrounding environment. Seabream had distinct associated microbiomes according to the tissue and compared to the marine environment. The gut hosted the most diverse microbiome; different sets of dominant ASVs characterized the environmental and fish samples. The similarity between fish and environmental microbiomes was higher in seawater than sediment (up to 7.8 times), and the highest similarity (3.9%) was observed between gill and seawater, suggesting that gills are more closely interacting with the environment. We finally analyzed the potential connections occurring among microbiomes. These connections were relatively low among the host's tissues and, in particular, between the gut and the others fish-related microbiomes; other tissues, including skin and gills, were found to be the most connected microbiomes. Our results suggest that, in mariculture, seabream microbiomes reflect only partially those in their surrounding environment and that the host is the primary driver shaping the seabream microbiome. These data provide a step forward to understand the role of the microbiome in farmed fish and farming environments, useful to enhance disease control, fish health, and environmental sustainability.},
}
@article {pmid36205737,
year = {2023},
author = {Feng, SW and Lu, JL and Liang, JL and Wu, ZH and Yi, X and Wen, P and Li, FL and Liao, B and Jia, P and Shu, WS and Li, JT},
title = {Functional Guilds, Community Assembly, and Co-occurrence Patterns of Fungi in Metalliferous Mine Tailings Ponds in Mainland China.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {843-858},
pmid = {36205737},
issn = {1432-184X},
support = {42077117//National Natural Science Foundation of China/ ; 42177009//National Natural Science Foundation of China/ ; 41622106//National Natural Science Foundation of China/ ; 2019B110207001//Key-Area Research and Development Program of Guangdong Province/ ; 2021B1515120039//Guangdong Basic and Applied Basic Research Foundation/ ; 2020A1515010937//Natural Science Foundation of Guangdong Province of China/ ; },
mesh = {*Ponds ; *Soil Microbiology ; China ; Soil ; Fungi/genetics ; },
abstract = {Metalliferous mine tailings ponds are generally characterized by low levels of nutrient elements, sustained acidic conditions, and high contents of toxic metals. They represent one kind of extreme environments that are believed to resemble the Earth's early environmental conditions. There is increasing evidence that the diversity of fungi inhabiting mine tailings ponds is much higher than previously thought. However, little is known about functional guilds, community assembly, and co-occurrence patterns of fungi in such habitats. As a first attempt to address this critical knowledge gap, we employed high-throughput sequencing to characterize fungal communities in 33 mine tailings ponds distributed across 18 provinces of mainland China. A total of 5842 fungal phylotypes were identified, with saprotrophic fungi being the major functional guild. The predictors of fungal diversity in whole community and sub-communities differed considerably. Community assembly of the whole fungal community and individual functional guilds were primarily governed by stochastic processes. Total soil nitrogen and total phosphorus mediated the balance between stochastic and deterministic processes of the fungal community assembly. Co-occurrence network analysis uncovered a high modularity of the whole fungal community. The observed main modules largely consisted of saprotrophic fungi as well as various phylotypes that could not be assigned to known functional guilds. The richness of core fungal phylotypes, occupying vital positions in co-occurrence network, was positively correlated with edaphic properties such as soil enzyme activity. This indicates the important roles of core fungal phylotypes in soil organic matter decomposition and nutrient cycling. These findings improve our understanding of fungal ecology of extreme environments.},
}
@article {pmid36204622,
year = {2022},
author = {Banerjee, S and Bedics, A and Tóth, E and Kriszt, B and Soares, AR and Bóka, K and Táncsics, A},
title = {Isolation of Pseudomonas aromaticivorans sp. nov from a hydrocarbon-contaminated groundwater capable of degrading benzene-, toluene-, m- and p-xylene under microaerobic conditions.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {929128},
pmid = {36204622},
issn = {1664-302X},
abstract = {Members of the genus Pseudomonas are known to be widespread in hydrocarbon contaminated environments because of their remarkable ability to degrade a variety of petroleum hydrocarbons, including BTEX (benzene, toluene, ethylbenzene and xylene) compounds. During an enrichment investigation which aimed to study microaerobic xylene degradation in a legacy petroleum hydrocarbon-contaminated groundwater, a novel Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated as MAP12[T] was isolated. It was capable of degrading benzene, toluene, meta- and para- xylene effectively under both aerobic and microaerobic conditions. The 16S rRNA gene sequence analysis revealed that strain MAP12[T] belongs to the genus Pseudomonas, with the highest 16S rRNA gene similarity to Pseudomonas linyingensis LYBRD3-7 [T] (98.42%), followed by Pseudomonas sagittaria JCM 18195 [T] (98.29%) and Pseudomonas alcaliphila JCM 10630 [T] (98.08%). Phylogenomic tree constructed using a concatenated alignment of 92 core genes indicated that strain MAP12[T] is distinct from any known Pseudomonas species. The draft genome sequence of strain MAP12[T] is 4.36 Mb long, and the G+C content of MAP12[T] genome is 65.8%. Orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) analyses confirmed that strain MAP12[T] is distinctly separated from its closest neighbors (OrthoANI < 89 %; dDDH < 36%). Though several members of the genus Pseudomonas are well known for their aerobic BTEX degradation capability, this is the first report of a novel Pseudomonas species capable of degrading xylene under microaerobic conditions. By applying genome-resolved metagenomics, we were able to partially reconstruct the genome of strain MAP12 [T] from metagenomics sequence data and showed that strain MAP12 [T] was an abundant member of the xylene-degrading bacterial community under microaerobic conditions. Strain MAP12[T] contains ubiquinone 9 (Q9) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine as major polar lipids. The major cellular fatty acids of strain MAP12[T] are summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c). The results of this polyphasic study support that strain MAP12[T] represents a novel species of the genus Pseudomonas, hence the name of Pseudomonas aromaticivorans sp. nov. is proposed for this strain considering its aromatic hydrocarbon degradation capability. The type strain is MAP12[T] (=LMG 32466, =NCAIM B.02668).},
}
@article {pmid36204070,
year = {2022},
author = {Zhang, H and Ma, Y and Shao, J and Di, R and Zhu, F and Yang, Z and Sun, J and Zhang, X and Zheng, C},
title = {Changes in soil bacterial community and functions by substituting chemical fertilizer with biogas slurry in an apple orchard.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {1013184},
pmid = {36204070},
issn = {1664-462X},
abstract = {Growing concerns about the negative environmental effects of excessive chemical fertilizer input in fruit production have resulted in many attempts looking for adequate substitution. Biogas slurry as a representative organic fertilizer has the potential to replace chemical fertilizer for improvement of sustainability. However, it is still poorly known how biogas slurry applications may affect the composition of soil microbiome. Here, we investigated different substitution rates of chemical fertilizer with biogas slurry treatment (the control with no fertilizer and biogas slurry, CK; 100% chemical fertilizer, CF; biogas slurry replacing 50% of chemical fertilizer, CBS; and biogas slurry replacing 100% of chemical fertilizer, BS) in an apple orchard. Soil bacterial community and functional structure among treatments were determined using Illumina sequencing technology coupled with Functional Annotation of Prokaryotic Taxonomy (FAPROTAX) analysis. Leaf nutrient contents, apple fruit and soil parameters were used to assess plant and soil quality. Results showed that most of fruit parameters and soil properties were significantly varied in the four treatments. CBS treatment increased the contents of soil organic matter, alkali nitrogen and available potassium average by 49.8%, 40.7% and 27.9%, respectively. Treatments with biogas slurry application increased the single fruit weight, fresh weight, and dry weight of apple fruit average by 15.6%, 18.8% and 17.8, respectively. Soil bacterial community dominance and composition were significantly influenced by substituting of chemical fertilizer with biogas slurry. Biogas slurry application enhanced the relative abundance of some beneficial taxa (e.g. Acidobacteria Gp5 and Gp7, Parasegetibacter) and functional groups related to carbon and nitrogen cycling such as chemoheterotrophy, cellulolysis, and nitrogen fixation. Soil available phosphorus and potassium, pH and electrical conductivity were identified having a high potential for regulating soil bacterial specific taxa and functional groups. This study showed that the proper ratio application (50%: 50%) of biogas slurry with chemical fertilizer could regulate soil bacterial composition and functional structure via changes in soil nutrients. The variations of bacterial community could potentially take significant ecological roles in maintaining apple plant growth, soil fertility and functionality.},
}
@article {pmid36203239,
year = {2023},
author = {Munley, JA and Kelly, LS and Pons, EE and Kannan, KB and Coldwell, PS and Whitley, EM and Gillies, GS and Efron, PA and Nagpal, R and Mohr, AM},
title = {Multicompartmental traumatic injury and the microbiome: Shift to a pathobiome.},
journal = {The journal of trauma and acute care surgery},
volume = {94},
number = {1},
pages = {15-22},
pmid = {36203239},
issn = {2163-0763},
support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; T32 GM008721/GM/NIGMS NIH HHS/United States ; },
mesh = {Rats ; Animals ; Male ; Rats, Sprague-Dawley ; Critical Illness ; Occludin ; RNA, Ribosomal, 16S ; *Multiple Trauma ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Previous animal models have demonstrated altered gut microbiome after mild traumatic injury; however, the impact of injury severity and critical illness is unknown. We hypothesized that a rodent model of severe multicompartmental injuries and chronic stress would demonstrate microbiome alterations toward a "pathobiome" characterized by an overabundance of pathogenic organisms, which would persist 1 week after injury.<br><br>METHODS: Male Sprague-Dawley rats (n = 8 per group) were subjected to either multiple injuries (PT) (lung contusion, hemorrhagic shock, cecectomy, and bifemoral pseudofractures), PT plus daily chronic restraint stress for 2 hours (PT/CS), or naive controls. Fecal microbiome was measured on days 0, 3, and 7 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology 2 bioinformatics analysis. Microbial &#x3b1; diversity was assessed using Chao1 and Shannon indices, and &#x3b2; diversity with principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin; ileum and descending colon tissues were reviewed for injury. Analyses were performed in GraphPad (GraphPad Software, La Jolla, CA) and R (R Foundation for Statistical Computing, Vienna, Austria), with significance defined as p < 0.05.<br><br>RESULTS: There were significant alterations in &#x3b2; diversity at day 3 and between all groups. By day 3, both PT and PT/CS demonstrated significantly depleted bacterial diversity (Chao1) (p = 0.01 and p = 0.001, respectively) versus naive, which persisted up to day 7 in PT/CS only (p = 0.001). Anaerostipes and Rothia dominated PT and Lactobacillus bloomed in PT/CS cohorts by day 7. Plasma occludin was significantly elevated in PT/CS compared with naive (p = 0.04), and descending colon of both PT and PT/CS showed significantly higher injury compared with naive (p = 0.005, p = 0.006).<br><br>CONCLUSIONS: Multiple injuries with and without chronic stress induces significant alterations in microbiome diversity and composition within 3 days; these changes are more prominent and persist for 1 week postinjury with stress. This rapid and persistent transition to a "pathobiome" phenotype represents a critical phenomenon that may influence outcomes after severe trauma and critical illness.},
}
@article {pmid36202959,
year = {2022},
author = {Guerrero-Latorre, L and Collado, N and Abasolo, N and Anzaldi, G and Bofill-Mas, S and Bosch, A and Bosch, L and Busquets, S and Caimari, A and Canela, N and Carcereny, A and Chacón, C and Ciruela, P and Corbella, I and Domingo, X and Escoté, X and Espiñeira, Y and Forés, E and Gandullo-Sarró, I and Garcia-Pedemonte, D and Girones, R and Guix, S and Hundesa, A and Itarte, M and Mariné-Casadó, R and Martínez, A and Martínez-Puchol, S and Mas-Capdevila, A and Mejías-Molina, C and Rafa, MMI and Munné, A and Pintó, RM and Pueyo-Ros, J and Robusté-Cartró, J and Rusiñol, M and Sanfeliu, R and Teichenné, J and Torrell, H and Corominas, L and Borrego, CM},
title = {The Catalan Surveillance Network of SARS-CoV-2 in Sewage: design, implementation, and performance.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {16704},
pmid = {36202959},
issn = {2045-2322},
mesh = {*COVID-19/epidemiology ; Humans ; Pandemics ; RNA, Viral ; *SARS-CoV-2 ; Sewage ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; },
abstract = {Wastewater-based epidemiology has shown to be an efficient tool to track the circulation of SARS-CoV-2 in communities assisted by wastewater treatment plants (WWTPs). The challenge comes when this approach is employed to help Health authorities in their decision-making. Here, we describe the roadmap for the design and deployment of SARSAIGUA, the Catalan Surveillance Network of SARS-CoV-2 in Sewage. The network monitors, weekly or biweekly, 56 WWTPs evenly distributed across the territory and serving 6 M inhabitants (80% of the Catalan population). Each week, samples from 45 WWTPs are collected, analyzed, results reported to Health authorities, and finally published within less than 72 h in an online dashboard (https://sarsaigua.icra.cat). After 20 months of monitoring (July 20-March 22), the standardized viral load (gene copies/day) in all the WWTPs monitored fairly matched the cumulative number of COVID-19 cases along the successive pandemic waves, showing a good fit with the diagnosed cases in the served municipalities (Spearman Rho = 0.69). Here we describe the roadmap of the design and deployment of SARSAIGUA while providing several open-access tools for the management and visualization of the surveillance data.},
}
@article {pmid36202936,
year = {2022},
author = {Fournier, E and Denis, S and Dominicis, A and Van de Wiele, T and Alric, M and Mercier-Bonin, M and Etienne-Mesmin, L and Blanquet-Diot, S},
title = {A child is not an adult: development of a new in vitro model of the toddler colon.},
journal = {Applied microbiology and biotechnology},
volume = {106},
number = {21},
pages = {7315-7336},
pmid = {36202936},
issn = {1432-0614},
mesh = {Adult ; Infant ; Humans ; Child, Preschool ; Child ; *Propionates ; Colon ; Fatty Acids, Volatile ; Feces ; *Microbiota ; Butyrates ; Methane ; },
abstract = {Early life is a critical period where gut ecosystem and functions are being established with significant impact on health. For regulatory, technical, and cost reasons, in vitro gut models can be used as a relevant alternative to in vivo assays. An exhaustive literature review was conducted to adapt the Mucosal Artificial Colon (M-ARCOL) to specific physicochemical (pH, transit time, and nutritional composition of ileal effluents) and microbial parameters from toddlers in the age range of 6 months-3 years, resulting in the Tm-ARCOL. In vitro fermentations were performed to validate this newly developed colonic model compared to in vivo toddler data. Results were also compared to those obtained with the classical adult configuration. Fecal samples from 5 toddlers and 4 adults were used to inoculate bioreactors, and continuous fermentations were performed for 8 days. Gut microbiota structure (lumen and mucus-associated microbiota) and functions (gas and short-chain fatty acids) were monitored. Clearly distinct microbial signatures were obtained between the two in vitro conditions, with lower α-diversity indices and higher abundances of infant-related microbial populations (e.g., Bifidobacteriaceae, Enterobacteriaceae) in toddler versus adult conditions. In accordance with in vivo data, methane was found only in adult bioreactors, while higher percentage of acetate but lower proportions of propionate and butyrate was measured in toddlers compared to adults. This new in vitro model will provide a powerful platform for gut microbiome mechanistic studies in a pediatric context, both in nutritional- (e.g., nutrients, probiotics, prebiotics) and health-related (e.g., drugs, enteric pathogens) studies. KEY POINTS: • Development of a novel in vitro colonic model recapitulating the toddler environment. • Specific toddler versus adult digestive conditions are preserved in vitro. • The new model provides a powerful platform for microbiome mechanistic studies.},
}
@article {pmid36202391,
year = {2023},
author = {Haskell-Ramsay, CF and Dodd, FL and Smith, D and Cuthbertson, L and Nelson, A and Lodge, JK and Jackson, PA},
title = {Mixed Tree Nuts, Cognition, and Gut Microbiota: A 4-Week, Placebo-Controlled, Randomized Crossover Trial in Healthy Nonelderly Adults.},
journal = {The Journal of nutrition},
volume = {152},
number = {12},
pages = {2778-2788},
pmid = {36202391},
issn = {1541-6100},
mesh = {Humans ; Aged ; *Gastrointestinal Microbiome ; Cross-Over Studies ; Cognition ; *Cognitive Dysfunction ; Bacteria/genetics ; },
abstract = {BACKGROUND: Beneficial effects of nut supplementation on cognitive function have previously been demonstrated in young and older adults. Alterations to gut microbiota have also been shown following tree nut consumption. However, no data exists on the effects of nuts on cognition and intestinal microbial communities assessed within the same study.<br><br>OBJECTIVES: The study aimed to examine the effects of daily consumption of tree nuts for 4 wk on cognitive function (primary outcome), mood, metabolomics, and gut microbial species (secondary outcomes) in healthy, nonelderly adults.<br><br>METHODS: This randomized, placebo-controlled, double-blind, counterbalanced crossover study assessed the effects of 4 wk of supplementation with 30&#xa0;g/d mixed tree nuts versus placebo on cognition and mood in 79 healthy adults aged 18-49 y. Metabolic responses, gut bacterial community structure, and the potential for these to impact cognition were explored using a multi-omic approach. Bacterial community analysis was conducted in Quantitative Insights Into Microbial Ecology 2 (QIIME2).<br><br>RESULTS: Mixed model analysis indicated that nut consumption led to significant improvements to accuracy (placebo M&#xa0;=&#xa0;92.2%&#xa0;compared with NUTS M&#xa0;=&#xa0;94.5%; P&#xa0;=&#xa0;0.019) and speed of response (placebo M&#xa0;=&#xa0;788&#xa0;ms compared with NUTS M&#xa0;=&#xa0;757&#xa0;ms; P&#xa0;=&#xa0;0.004) on a picture recognition task. No significant changes to bacterial community &#x3b1; or &#x3b2; diversity were observed when comparing nut consumption to the placebo arm. However, an unclassified Lachnospiraceae amplicon sequence variant (ASV) was significantly enriched in participants when supplemented with nuts (P&#xa0;=&#xa0;0.015). No correlations were observed between the changes to picture recognition and the changes to the unclassified Lachnospiraceae ASV. There were no significant changes to the urinary metabolome.<br><br>CONCLUSIONS: These findings indicate a positive effect of nut on cognition following only 4 wk of consumption in a healthy nonelderly sample, as well as upregulation of a microbial taxa associated with gut health. The effects appear to be independent of one another, but further exploration is required in those experiencing cognitive decline and/or gut dysbiosis.},
}
@article {pmid36198042,
year = {2022},
author = {Yan, C and Kwek, E and Ding, HF and He, Z and Ma, KY and Zhu, H and Chen, ZY},
title = {Dietary Oxidized Cholesterol Aggravates Chemically Induced Murine Colon Inflammation and Alters Gut Microbial Ecology.},
journal = {Journal of agricultural and food chemistry},
volume = {70},
number = {41},
pages = {13289-13301},
doi = {10.1021/acs.jafc.2c05001},
pmid = {36198042},
issn = {1520-5118},
mesh = {Mice ; Humans ; Animals ; *Gastrointestinal Microbiome ; Dextran Sulfate/adverse effects ; Cholesterol, Dietary ; Mice, Inbred C57BL ; *Colitis/chemically induced/microbiology ; Colon/microbiology ; Fatty Acids, Volatile/pharmacology ; Inflammation ; Disease Models, Animal ; },
abstract = {Western diet with a higher intake of fat and cholesterol has been claimed as an intestinal inflammation trigger. Human diet contains both cholesterol and oxidized cholesterol. Oxidized cholesterol has been claimed to be associated with various inflammation diseases, but its effects on colitis and gut microbiome remain largely unknown. The present study was the first time to investigate the effect of the oxidized cholesterol on gut microbiota and dextran sodium sulfate-induced colitis using mice as a model. The results showed that oxidized cholesterol promoted colitis by exacerbating bleeding, body weight decrease, colon shortening, gut barrier damage, oxidative stress, and gut inflammation, whereas non-oxidized cholesterol had no effect. Meanwhile, oxidized cholesterol could adversely modulate the gut microbiota by increasing the relative abundance of pro-inflammatory bacteria (including Escherichia-Shigella and Bacteroides) and decreasing that of beneficial bacteria (Lachnospiraceae_NK4A136_group and Odoribacter). In addition, oxidized cholesterol significantly reduced the production of fecal short-chain fatty acids in colitis mice. It was concluded that oxidized cholesterol was a potential dietary factor of gut dysbiosis.},
}
@article {pmid36197502,
year = {2023},
author = {Pin Viso, ND and Rizzo, PF and Young, BJ and Gabioud, E and Bres, P and Riera, NI and Merino, L and Farber, MD and Crespo, DC},
title = {The Use of Raw Poultry Waste as Soil Amendment Under Field Conditions Caused a Loss of Bacterial Genetic Diversity Together with an Increment of Eutrophic Risk and Phytotoxic Effects.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1082-1095},
pmid = {36197502},
issn = {1432-184X},
support = {PIUNAHUR5-04//UNaHur/ ; },
mesh = {Animals ; *Soil/chemistry ; *Poultry ; Manure ; Fertilizers ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Genetic Variation ; },
abstract = {Poultry waste has been used as fertilizer to avoid soil degradation caused by the long-term application of chemical fertilizer. However, few studies have evaluated field conditions where livestock wastes have been used for extended periods of time. In this study, physicochemical parameters, metabarcoding of the 16S rRNA gene, and ecotoxicity indexes were used for the characterization of chicken manure and poultry litter to examine the effect of their application to agricultural soils for 10 years. Poultry wastes showed high concentrations of nutrients and increased electrical conductivity leading to phytotoxic effects on seeds. The bacterial communities were dominated by typical members of the gastrointestinal tract, noting the presence of pathogenic bacteria. Soils subjected to poultry manure applications showed statistically higher values of total and extractable phosphorous, increasing the risk of eutrophication. Moreover, while the soil bacterial community remained dominated by the ones related to the biogeochemical cycles of nutrients and plant growth promotion, losses of alpha diversity were observed on treated soils. Altogether, our work would contribute to understand the effects of common local agricultural practices and support the adoption of the waste treatment process in compliance with environmental sustainability guidelines.},
}
@article {pmid36196151,
year = {2022},
author = {Zhang, YW and Cao, MM and Li, YJ and Lu, PP and Dai, GC and Zhang, M and Wang, H and Rui, YF},
title = {Fecal microbiota transplantation ameliorates bone loss in mice with ovariectomy-induced osteoporosis via modulating gut microbiota and metabolic function.},
journal = {Journal of orthopaedic translation},
volume = {37},
number = {},
pages = {46-60},
pmid = {36196151},
issn = {2214-031X},
abstract = {BACKGROUND: Osteoporosis (OP) is a systemic metabolic bone disease characterized by decreased bone mass and destruction of bone microstructure, which tends to result in enhanced bone fragility and related fractures. The postmenopausal osteoporosis (PMOP) has a relatively high proportion, and numerous studies reveal that estrogen-deficiency is related to the imbalance of gut microbiota (GM), impaired intestinal mucosal barrier function and enhanced inflammatory reactivity. However, the underlying mechanisms remain unclear and the existing interventions are also scarce.<br><br>METHODS: In this study, we established a mouse model induced by ovariectomy (OVX) and conducted fecal microbiota transplantation (FMT) by gavage every day for 8 weeks. Subsequently, the bone mass and microarchitecture of mice were evaluated by the micro computed tomography (Micro-CT). The intestinal permeability, pro-osteoclastogenic cytokines expression, osteogenic and osteoclastic activities were detected by the immunohistological analysis, histological examination, enzyme-linked immunosorbent assay (ELISA) and western blot analysis accordingly. Additionally, the composition and abundance of GM were assessed by 16S rRNA sequencing and the fecal short chain fatty acids (SCFAs) level was measured by metabolomics.<br><br>RESULTS: Our results demonstrated that FMT inhibited the excessive osteoclastogenesis and prevented the OVX-induced bone loss. Specifically, compared with the OVX group, FMT enhanced the expressions of tight junction proteins (zonula occludens protein 1 (ZO-1) and Occludin) and suppressed the release of pro-osteoclastogenic cytokines (tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) and interleukin-1&#x3b2; (IL-1&#x3b2;)). Furthermore, FMT also optimized the composition and abundance of GM, and increased the fecal SCFAs level (mainly acetic acid and propionic acid).<br><br>CONCLUSIONS: Collectively, based on GM-bone axis, FMT prevented the OVX-induced bone loss by correcting the imbalance of GM, improving the SCFAs level, optimizing the intestinal permeability and suppressing the release of pro-osteoclastogenic cytokines, which may be an alternative option to serve as a promising candidate for the prevention and treatment of PMOP in the future.<br><br>This study indicates the ingenious involvement of GM-bone axis in PMOP and the role of FMT in reshaping the status of GM and ameliorating the bone loss in OVX-induced mice. FMT might serve as a promising candidate for the prevention and treatment of PMOP in the future.},
}
@article {pmid36196117,
year = {2022},
author = {Dong, H and Huang, L and Zhao, L and Zeng, Q and Liu, X and Sheng, Y and Shi, L and Wu, G and Jiang, H and Li, F and Zhang, L and Guo, D and Li, G and Hou, W and Chen, H},
title = {A critical review of mineral-microbe interaction and co-evolution: mechanisms and applications.},
journal = {National science review},
volume = {9},
number = {10},
pages = {nwac128},
pmid = {36196117},
issn = {2053-714X},
abstract = {Mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation and precipitation of minerals through their activity, resulting in either genetically controlled or metabolism-induced biomineralization. Through these interactions, minerals and microbes co-evolve through Earth history. Mineral-microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral-microbe interactions for the benefit of humankind.},
}
@article {pmid36194291,
year = {2023},
author = {Lomelí-Ortega, CO and Barajas-Sandoval, DR and Martínez-Villalobos, JM and Jaramillo, CR and Chávez, EM and Gómez-Gil, B and Balcázar, JL and Quiroz-Guzmán, E},
title = {A Broad-Host-Range Phage Cocktail Selectively and Effectively Eliminates Vibrio Species from Shrimp Aquaculture Environment.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1443-1446},
pmid = {36194291},
issn = {1432-184X},
support = {Aquaculture program//Centro de Investigaciones Biol&#xf3;gicas del Noroeste/ ; },
mesh = {Animals ; *Bacteriophages ; *Vibrio ; *Penaeidae/microbiology ; Aquaculture ; },
abstract = {The protective effects of a phage cocktail composed of vB_Vc_SrVc2 and vB_Vc_SrVc9 were tested in Pacific white shrimp (Litopenaeus vannamei) postlarvae, which were originally isolated from diseased shrimps and selected due to their broad-host-range properties against several pathogenic Vibsrio species. We used culture-dependent and culture-independent approaches to explore its effect on bacterial communities associated with shrimp postlarvae. Both methods revealed that the levels of Vibrio species were significantly reduced after phage cocktail administration. Phage-treated shrimp also exhibisuppted lesser damage and higher lipid accumulation in B cells of the hepatopancreas, as revealed by histopathological examination. Taken together, this study provides clear evidence that phage therapy can selectively and effectively reduce Vibrio species, thereby providing an environmentally safe alternative to the prophylactic use of antibiotics in shrimp aquaculture.},
}
@article {pmid36194136,
year = {2022},
author = {Fang, Y and Stanford, K and Yang, X},
title = {Lactic Acid Resistance and Population Structure of Escherichia coli from Meat Processing Environment.},
journal = {Microbiology spectrum},
volume = {10},
number = {5},
pages = {e0135222},
pmid = {36194136},
issn = {2165-0497},
mesh = {Cattle ; Animals ; Escherichia coli ; Lactic Acid ; Phylogeny ; Meat ; Anti-Bacterial Agents/pharmacology ; Food Handling ; *Anti-Infective Agents/pharmacology ; *Disinfectants/pharmacology ; Sugar Acids/analysis/pharmacology ; Colony Count, Microbial ; Food Microbiology ; Food Contamination/analysis ; },
abstract = {To explore the effect of beef processing on Escherichia coli populations in relation to lactic acid resistance, this study investigated the links among acid response, phylogenetic structure, genome diversity, and genotypes associated with acid resistance of meat plant E. coli. Generic E. coli isolates (n = 700) were from carcasses, fabrication equipment, and beef products. Acid treatment was carried out in Luria-Bertani broth containing 5.5% lactic acid (pH 2.9). Log reductions of E. coli ranged from <0.5 to >5 log CFU/mL (median: 1.37 log). No difference in lactic acid resistance was observed between E. coli populations recovered before and after a processing step or antimicrobial interventions. E. coli from the preintervention carcasses were slightly more resistant than E. coli isolated from equipment, differing by <0.5 log unit. Acid-resistant E. coli (log reduction <1, n = 45) had a higher prevalence of genes related to energy metabolism (ydj, xap, ato) and oxidative stress (fec, ymjC) than the less resistant E. coli (log reduction >1, n = 133). The ydj and ato operons were abundant in E. coli from preintervention carcasses. In contrast, fec genes were abundant in E. coli from equipment surfaces. The preintervention E. coli contained phylogroups A and B1 in relatively equal proportions. Phylogroup B1 predominated (95%) in the population from equipment. Of note, E. coli collected after sanitation shared either the antigens of O8 or H21. Additionally, genome diversity decreased after chilling and equipment sanitation. Overall, beef processing did not select for E. coli resistant to lactic acid but shaped the population structure. IMPORTANCE Antimicrobial interventions have significantly reduced the microbial loads on carcasses/meat products; however, the wide use of chemical and physical biocides has raised concerns over their potential for selecting resistant populations in the beef processing environment. Phenotyping of acid resistance and whole-genome analysis described in this study demonstrated beef processing practices led to differences in acid resistance, genotype, and population structure between carcass- and equipment-associated E. coli but did not select for the acid-resistant population. Results indicate that genes coding for the metabolism of long-chain sugar acids (ydj) and short-chain fatty acids (ato) were more prevalent in carcass-associated than equipment-associated E. coli. These results suggest E. coli from carcasses and equipment surfaces have been exposed to different selective pressures. The findings improve our understanding of the microbial ecology of E. coli in food processing environments and in general.},
}
@article {pmid36192537,
year = {2022},
author = {Zaremba, M and Dakineviciene, D and Golovinas, E and Zagorskaitė, E and Stankunas, E and Lopatina, A and Sorek, R and Manakova, E and Ruksenaite, A and Silanskas, A and Asmontas, S and Grybauskas, A and Tylenyte, U and Jurgelaitis, E and Grigaitis, R and Timinskas, K and Venclovas, &#x10c; and Siksnys, V},
title = {Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD[+] depletion.},
journal = {Nature microbiology},
volume = {7},
number = {11},
pages = {1857-1869},
pmid = {36192537},
issn = {2058-5276},
mesh = {*NAD/genetics/metabolism ; Prokaryotic Cells/metabolism ; Argonaute Proteins/genetics ; DNA/metabolism ; *Bacteriophages/genetics/metabolism ; Interspersed Repetitive Sequences ; },
abstract = {Argonaute (Ago) proteins are found in all three domains of life. The so-called long Agos are composed of four major domains (N, PAZ, MID and PIWI) and contribute to RNA silencing in eukaryotes (eAgos) or defence against invading mobile genetic elements in prokaryotes (pAgos). The majority (~60%) of pAgos identified bioinformatically are shorter (comprising only MID and PIWI domains) and are typically associated with Sir2, Mrr or TIR domain-containing proteins. The cellular function and mechanism of short pAgos remain enigmatic. Here we show that Geobacter sulfurreducens short pAgo and the NAD[+]-bound Sir2 protein form a stable heterodimeric complex. The GsSir2/Ago complex presumably recognizes invading plasmid or phage DNA and activates the Sir2 subunit, which triggers endogenous NAD[+] depletion and cell death, and prevents the propagation of invading DNA. We reconstituted NAD[+] depletion activity in vitro and showed that activated GsSir2/Ago complex functions as a NADase that hydrolyses NAD[+] to ADPR. Thus, short Sir2-associated pAgos provide defence against phages and plasmids, underscoring the diversity of mechanisms of prokaryotic Agos.},
}
@article {pmid36192536,
year = {2022},
author = {Garb, J and Lopatina, A and Bernheim, A and Zaremba, M and Siksnys, V and Melamed, S and Leavitt, A and Millman, A and Amitai, G and Sorek, R},
title = {Multiple phage resistance systems inhibit infection via SIR2-dependent NAD[+] depletion.},
journal = {Nature microbiology},
volume = {7},
number = {11},
pages = {1849-1856},
pmid = {36192536},
issn = {2058-5276},
mesh = {*NAD/metabolism ; Silent Information Regulator Proteins, Saccharomyces cerevisiae/genetics/metabolism ; Sirtuin 2/genetics ; *Bacteriophages/genetics/metabolism ; NAD+ Nucleosidase ; },
abstract = {Defence-associated sirtuins (DSRs) comprise a family of proteins that defend bacteria from phage infection via an unknown mechanism. These proteins are common in bacteria and harbour an N-terminal sirtuin (SIR2) domain. In this study we report that DSR proteins degrade nicotinamide adenine dinucleotide (NAD[+]) during infection, depleting the cell of this essential molecule and aborting phage propagation. Our data show that one of these proteins, DSR2, directly identifies phage tail tube proteins and then becomes an active NADase in Bacillus subtilis. Using a phage mating methodology that promotes genetic exchange between pairs of DSR2-sensitive and DSR2-resistant phages, we further show that some phages express anti-DSR2 proteins that bind and repress DSR2. Finally, we demonstrate that the SIR2 domain serves as an effector NADase in a diverse set of phage defence systems outside the DSR family. Our results establish the general role of SIR2 domains in bacterial immunity against phages.},
}
@article {pmid36190138,
year = {2022},
author = {Weissman, JL and Peras, M and Barnum, TP and Fuhrman, JA},
title = {Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.},
journal = {mSystems},
volume = {7},
number = {5},
pages = {e0074522},
pmid = {36190138},
issn = {2379-5077},
mesh = {Humans ; *Metagenome/genetics ; Benchmarking ; Codon Usage ; *Microbiota/genetics ; },
abstract = {Trait inference from mixed-species assemblages is a central problem in microbial ecology. Frequently, sequencing information from an environment is available, but phenotypic measurements from individual community members are not. With the increasing availability of molecular data for microbial communities, bioinformatic approaches that map metagenome to (meta)phenotype are needed. Recently, we developed a tool, gRodon, that enables the prediction of the maximum growth rate of an organism from genomic data on the basis of codon usage patterns. Our work and that of other groups suggest that such predictors can be applied to mixed-species communities in order to derive estimates of the average community-wide maximum growth rate. Here, we present an improved maximum growth rate predictor designed for metagenomes that corrects a persistent GC bias in the original gRodon model for metagenomic prediction. We benchmark this predictor with simulated metagenomic data sets to show that it has superior performance on mixed-species communities relative to earlier models. We go on to provide guidance on data preprocessing and show that calling genes from assembled contigs rather than directly from reads dramatically improves performance. Finally, we apply our predictor to large-scale metagenomic data sets from marine and human microbiomes to illustrate how community-wide growth prediction can be a powerful approach for hypothesis generation. Altogether, we provide an updated tool with clear guidelines for users about the uses and pitfalls of metagenomic prediction of the average community-wide maximal growth rate. IMPORTANCE Microbes dominate nearly every known habitat, and therefore tools to survey the structure and function of natural microbial communities are much needed. Metagenomics, in which the DNA content of an entire community of organisms is sequenced all at once, allows us to probe the genetic diversity contained in a habitat. Yet, mapping metagenomic information to the actual traits of community members is a difficult and largely unsolved problem. Here, we present and validate a tool that allows users to predict the average maximum growth rate of a microbial community directly from metagenomic data. Maximum growth rate is a fundamental characteristic of microbial species that can give us a great deal of insight into their ecological role, and by applying our community-level predictor to large-scale metagenomic data sets from marine and human-associated microbiomes, we show how community-wide growth prediction can be a powerful approach for hypothesis generation.},
}
@article {pmid36189957,
year = {2022},
author = {Hunter, BT and Flury, JD and Cocioba, SS and Cope-Arguello, ML and Helms, JM and García, KH and Dominguez, G and Taniguchi, DA and Becket, E},
title = {Engineering an incubation environment that mimics in situ conditions for in vitro coastal microbiome studies.},
journal = {BioTechniques},
volume = {73},
number = {4},
pages = {183-191},
pmid = {36189957},
issn = {1940-9818},
support = {R15 ES033027/ES/NIEHS NIH HHS/United States ; R25 GM066341/GM/NIGMS NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; Temperature ; },
abstract = {Coastal environments are dynamic and can vary widely on short- or long-term scales depending on location and weather. Incubation equipment that reflects these changes through programmable gradient light and temperature cycles would permit more precise in vitro coastal microbiome studies. Here we present an open-source incubation environment that mimics in situ conditions for in vitro coastal microbiome studies using a modified shaking water bath that has fully customizable temperature and light gradients that can also mimic real-time field conditions. We compared coastal microbial community profiles incubated in situ and in our build mimicking field conditions over 48 h. Analyses of congruence indicated significant overlap (p > 0.2) between microbial communities incubated in situ and in vitro at each time point.},
}
@article {pmid36189437,
year = {2022},
author = {Moussa, DG and Sharma, AK and Mansour, TA and Witthuhn, B and Perdigão, J and Rudney, JD and Aparicio, C and Gomez, A},
title = {Functional signatures of ex-vivo dental caries onset.},
journal = {Journal of oral microbiology},
volume = {14},
number = {1},
pages = {2123624},
pmid = {36189437},
issn = {2000-2297},
support = {R01 DE026117/DE/NIDCR NIH HHS/United States ; R90 DE023058/DE/NIDCR NIH HHS/United States ; },
abstract = {BACKGROUND: The etiology of dental caries remains poorly understood. With the advent of next-generation sequencing, a number of studies have focused on the microbial ecology of the disease. However, taxonomic associations with caries have not been consistent. Researchers have also pursued function-centric studies of the caries microbial communities aiming to identify consistently conserved functional pathways. A major question is whether changes in microbiome are a cause or a consequence of the disease. Thus, there is a critical need to define conserved functional signatures at the onset of dental caries.<br><br>METHODS: Since it is unethical to induce carious lesions clinically, we developed an innovative longitudinal ex-vivo model integrated with the advanced non-invasive multiphoton second harmonic generation bioimaging to spot the very early signs of dental caries, combined with 16S rRNA short amplicon sequencing and liquid chromatography-mass spectrometry-based targeted metabolomics.<br><br>FINDINGS: For the first time, we induced longitudinally monitored caries lesions validated with the scanning electron microscope. Consequently, we spotted the caries onset and, associated with it, distinguished five differentiating metabolites - Lactate, Pyruvate, Dihydroxyacetone phosphate, Glyceraldehyde 3-phosphate (upregulated) and Fumarate (downregulated). Those metabolites co-occurred with certain bacterial taxa; Streptococcus, Veillonella, Actinomyces, Porphyromonas, Fusobacterium, and Granulicatella, regardless of the abundance of other taxa.<br><br>INTERPRETATION: These findings are crucial for understanding the etiology and dynamics of dental caries, and devising targeted interventions to prevent disease progression.},
}
@article {pmid36188424,
year = {2022},
author = {Geldenhuys, J and Redelinghuys, MJ and Lombaard, HA and Ehlers, MM and Cowan, D and Kock, MM},
title = {Diversity of the gut, vaginal and oral microbiome among pregnant women in South Africa with and without pre-eclampsia.},
journal = {Frontiers in global women's health},
volume = {3},
number = {},
pages = {810673},
pmid = {36188424},
issn = {2673-5059},
abstract = {BACKGROUND: Changes in microbial communities are a known characteristic of various inflammatory diseases and have been linked to adverse pregnancy outcomes, such as preterm birth. However, there is a paucity of information regarding the taxonomic composition and/or diversity of microbial communities in pre-eclampsia. The aim of this study was to determine the diversity of the gut, vaginal and oral microbiome in a cohort of South African pregnant women with and without pre-eclampsia. The diversity of the gut, vaginal and oral microbiome was determined by targeted next generation sequencing (NGS) of the V3 and V4 region of the 16S rRNA gene on the Illumina MiSeq platform.<br><br>RESULTS: In this study population, pre-eclampsia was associated with a significantly higher alpha diversity (P = 0.0472; indicated by the Shannon index) in the vaginal microbiome accompanied with a significant reduction in Lactobacillus spp. (P = 0.0275), compared to normotensive pregnant women. Lactobacillus iners was identified as the predominant species of the vaginal microbiome in both cohorts. High inter-individual variation in alpha diversity was observed in the gut and oral microbiome in both cohorts. Although differences in the relative abundance of bacteria at all phylogenetic levels were observed, overall microbial composition of the gut, oral and vaginal microbiome was not significantly different in the pre-eclampsia cohort compared to the normotensive cohort.<br><br>CONCLUSION: Collectively, a reduction of Lactobacillus spp., and predominance of L. iners in pregnant women with pre-eclampsia could suggest an unstable vaginal microbiome that might predispose pregnant women to develop pre-eclampsia. The lack of significant structural changes in the gut, oral and vaginal microbiome does not suggest that the characterized communities play a role in pre-eclampsia, but could indicate a characteristic unique to the study population. The current study provided novel information on the diversity of the gut, oral and vaginal microbiome among pregnant women in South Africa with and without pre-eclampsia. The current study provides a baseline for further investigations on the potential role of microbial communities in pre-eclampsia.},
}
@article {pmid36187988,
year = {2022},
author = {Zufiaurre, A and Felip, M and Camarero, L and Sala-Faig, M and Juhanson, J and Bonilla-Rosso, G and Hallin, S and Catalan, J},
title = {Bacterioplankton seasonality in deep high-mountain lakes.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {935378},
pmid = {36187988},
issn = {1664-302X},
abstract = {Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes.},
}
@article {pmid36187961,
year = {2022},
author = {Yang, X and Yu, X and He, Q and Deng, T and Guan, X and Lian, Y and Xu, K and Shu, L and Wang, C and Yan, Q and Yang, Y and Wu, B and He, Z},
title = {Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {956860},
pmid = {36187961},
issn = {1664-302X},
abstract = {Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.},
}
@article {pmid36187958,
year = {2022},
author = {Li, Y and Zhang, Y and Xue, S},
title = {pH mediated assemblage of carbon, nitrogen, and sulfur related microbial communities in petroleum reservoirs.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {952285},
pmid = {36187958},
issn = {1664-302X},
abstract = {Microorganisms are the core drivers of biogeochemistry processes in petroleum reservoirs and have been widely used to enhance petroleum recovery. However, systematic information about the microbial communities related to the C-N-S cycle in petroleum reservoirs under different pH conditions remains poorly understood. In this study, 16S rRNA gene data from 133 petroleum samples were collected, and 756 C-N-S related genera were detected. The Chao1 richness and Shannon diversity indices for the C-N-S-related microbial communities showed significant differences among different pH conditions and at the lowest levels in acidic conditions with pH values of 4.5-6.5. In addition, pH was the most important factor influencing the C-N-S related microbial communities and contributed to 17.95% of the variation in the methanogenesis community. A total of 55 functional genera were influenced by pH, which accounted for 42.08% of the C-N-S related genera. Among them, the genera Pseudomonas and Arcobacter were the highest and were concentrated in acidic conditions with pH values of 4.5-6.5. In parallel, 56 predicted C-N-S related genes were examined, and pH affected 16 of these genes, including putative chitinase, mcrA, mtrB, cysH, narGHIVYZ, nirK, nirB, nifA, sat, aprAB, and dsrAB. Furthermore, the co-occurrence networks of the C-N-S related microbial communities distinctly varied among the different pH conditions. The acidic environment exhibited the lowest complex network with the lowest keystone taxa number, and Escherichia-Shigella was the only keystone group that existed in all three networks. In summary, this study strengthened our knowledge regarding the C-N-S related microbial communities in petroleum reservoirs under different pH conditions, which is of great significance for understanding the microbial ecology and geochemical cycle of petroleum reservoirs.},
}
@article {pmid36185017,
year = {2022},
author = {Zhang, Y and Xue, S and Chang, X and Li, Y and Yue, X},
title = {Nutrients Changed the Assembly Processes of Profuse and Rare Microbial Communities in Coals.},
journal = {Polish journal of microbiology},
volume = {71},
number = {3},
pages = {359-370},
pmid = {36185017},
issn = {2544-4646},
mesh = {*Coal ; Firmicutes/genetics ; Methane ; *Microbiota ; Nutrients ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Nutrient stimulation is considered effective for improving biogenic coalbed methane production potential. However, our knowledge of the microbial assembly process for profuse and rare microbial communities in coals under nutrient stimulation is still limited. This study collected 16S rRNA gene data from 59 microbial communities in coals for a meta-analysis. Among these communities, 116 genera were identified as profuse taxa, and the remaining 1,637 genera were identified as rare taxa. Nutrient stimulation increased the Chao1 richness of profuse and rare genera and changed the compositions of profuse and rare genera based on nonmetric multidimensional scaling with Bray-Curtis dissimilarities. In addition, many profuse and rare genera belonging to Proteobacteria and Acidobacteria were reduced, whereas those belonging to Euryarchaeota and Firmicutes were increased under nutrient stimulation. Concomitantly, the microbial co-occurrence relationship network was also altered by nutrient addition, and many rare genera mainly belonging to Firmicutes, Bacteroides, and Euryarchaeota also comprised the key microorganisms. In addition, the compositions of most of the profuse and rare genera in communities were driven by stochastic processes, and nutrient stimulation increased the relative contribution of dispersal limitation for both profuse and rare microbial community assemblages and that of variable selection for rare microbial community assemblages. In summary, this study strengthened our knowledge regarding the mechanistic responses of coal microbial diversity and community composition to nutrient stimulation, which are of great importance for understanding the microbial ecology of coals and the sustainability of methane production stimulated by nutrients.},
}
@article {pmid36182151,
year = {2023},
author = {Wang, C and Yao, Z and Zhan, P and Yi, X and Chen, J and Xiong, J},
title = {Significant tipping points of sediment microeukaryotes forewarn increasing antibiotic pollution.},
journal = {Journal of environmental sciences (China)},
volume = {124},
number = {},
pages = {429-439},
doi = {10.1016/j.jes.2021.10.031},
pmid = {36182151},
issn = {1001-0742},
mesh = {*Ammonium Compounds ; *Anti-Bacterial Agents ; Environmental Biomarkers ; Phosphates ; Tetracyclines ; Wastewater ; },
abstract = {Antibiotic pollution imposes urgent threats to public health and microbial-mediated ecological processes. Existing studies have primarily focused on bacterial responses to antibiotic pollution, but they ignored the microeukaryotic counterpart, though microeukaryotes are functionally important (e.g., predators and saprophytes) in microbial ecology. Herein, we explored how the assembly of sediment microeukaryotes was affected by increasing antibiotic pollution at the inlet (control) and across the outlet sites along a shrimp wastewater discharge channel. The structures of sediment microeukaryotic community were substantially altered by the increasing nutrient and antibiotic pollutions, which were primarily controlled by the direct effects of phosphate and ammonium (-0.645 and 0.507, respectively). In addition, tetracyclines exerted a large effect (0.209), including direct effect (0.326) and indirect effect (-0.117), on the microeukaryotic assembly. On the contrary, the fungal subcommunity was relatively resistant to antibiotic pollution. Segmented analysis depicted nonlinear responses of microeukaryotic genera to the antibiotic pollution gradient, as supported by the significant tipping points. We screened 30 antibiotic concentration-discriminatory taxa of microeukaryotes, which can quantitatively and accurately predict (98.7% accuracy) the in-situ antibiotic concentration. Sediment microeukaryotic (except fungal) community is sensitive to antibiotic pollution, and the identified bioindicators could be used for antibiotic pollution diagnosis.},
}
@article {pmid36181942,
year = {2022},
author = {Shen, Z and Xie, G and Zhang, Y and Yu, B and Shao, K and Gao, G and Tang, X},
title = {Similar assembly mechanisms but distinct co-occurrence patterns of free-living vs. particle-attached bacterial communities across different habitats and seasons in shallow, eutrophic Lake Taihu.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {314},
number = {},
pages = {120305},
doi = {10.1016/j.envpol.2022.120305},
pmid = {36181942},
issn = {1873-6424},
mesh = {*Lakes/microbiology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; Seasons ; Bacteria/genetics ; Phosphorus ; Nitrogen ; Methane ; Carbon ; },
abstract = {Eutrophication due to nitrogen and phosphorus input is an increasing problem in lake ecosystems. Free-living (FL) and particle-attached (PA) bacterial communities play a primary role in mediating biogeochemical processes in these lakes and in responding to eutrophication. However, knowledge of factors governing function, assembly mechanisms, and co-occurrence patterns of these communities remain poorly understood and are key challenges in microbial ecology. To address this knowledge gap, we collected 96 samples from Lake Taihu across four seasons and investigated the bacterial community using 16S rRNA gene sequencing. Our results demonstrate that the α-diversity, β-diversity, community composition, and functional composition of FL and PA bacterial communities exhibited differing spatiotemporal dynamics. FL and PA bacterial communities displayed similar distance-decay relationships across seasons. Deterministic processes (i.e., environmental filtering and species interaction) were the primary factors shaping community assembly in both FL and PA bacteria. Similar environmental factors shaped bacterial community structure while different environmental factors drove bacterial functional composition. Habitat filtering influenced enrichment of bacteria within specific functional groups. Among them, the FL bacterial community appeared to play a critical role in methane-utilization, whereas the PA bacteria contributed more to biogeochemical cycling of carbon. FL and PA bacterial communities exhibited distinct co-occurrence pattern across different seasons. In the FL network, Methylotenera and Methylophilaceae were identified as keystone taxa, while Burkholderiaceae and the hgcI clade were keystone taxa in the PA network. The PA bacterial community appeared to possess greater stability in the face of environmental change than did FL counterparts. These results broaden our knowledge of the driving factors, co-occurrence patterns, and assembly processes in FL and PA bacterial communities in eutrophic ecosystems and provide improved insight into the underlying mechanisms responsible for these results.},
}
@article {pmid36180800,
year = {2023},
author = {Uroosa, and Kazmi, SSUH and Rahman, MS and Xu, H},
title = {Can functional units of periphytic protozoan communities be used to evaluate the effects of harmful algal blooms on ecological quality in marine ecosystems?.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {6},
pages = {16408-16417},
pmid = {36180800},
issn = {1614-7499},
mesh = {*Ecosystem ; Harmful Algal Bloom ; *Dinoflagellida ; },
abstract = {Based on biological traits, the ecological quality status under the pressure of two harmful algal bloom (HAB) species was evaluated using functional units (FUs) of periphytic protozoan communities. Five treatments with different concentrations of Alexandrium tamarense and Gymnodinium catenatum, i.e., 10[0], 10[2], 10[3], 10[4], and 10[5] cells ml[-1], were used. A total of 20 FUs were identified from 25 test protozoan species. Among these FUs, vagile algivores with large sizes showed a decreasing trend (i.e., in diversity and abundance) with increasing concentrations of algae, while vagile bacterivores and non-selectives with small sizes dominated at concentrations of 10[4] cells ml[-1] of both algal species. Ellipse tests on pair-wise functional distinctness indices revealed a significant departure of test protozoan communities from an expected functional distinctness breadth when algal concentrations exceeded 10[4] cells ml[-1]. Based on these findings, it was concluded that FUs of periphytic protozoa may be a useful tool for evaluating the effects of HABs on ecological quality status in marine ecosystems.},
}
@article {pmid36180621,
year = {2023},
author = {Signorini, M and Midolo, G and Cesco, S and Mimmo, T and Borruso, L},
title = {A Matter of Metals: Copper but Not Cadmium Affects the Microbial Alpha-Diversity of Soils and Sediments - a Meta-analysis.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1071-1081},
pmid = {36180621},
issn = {1432-184X},
support = {TN200V//Libera Universit&#xe0; di Bolzano/ ; },
mesh = {Copper/analysis ; Cadmium ; Soil ; *Soil Pollutants/analysis ; Soil Microbiology ; *Metals, Heavy/analysis ; Bacteria/genetics ; },
abstract = {Heavy metal (HM) accumulation in soil affects plants and soil fauna, yet the effect on microbial alpha-diversity remains unclear, mainly due to the absence of dedicated research synthesis (e.g. meta-analysis). Here, we report the first meta-analysis of the response of soil microbial alpha-diversity to the experimental addition of cadmium (Cd) and copper (Cu). We considered studies conducted between 2013 and 2022 using DNA metabarcoding of bacterial and fungal communities to overcome limitations of other cultivation- and electrophoresis-based techniques. Fungi were discarded due to the limited study number (i.e. 6 studies). Bacterial studies resulted in 66 independent experiments reported in 32 primary papers from four continents. We found a negative dose-dependent response for Cu but not for Cd for bacterial alpha-diversity in the environments, only for Cu additions exceeding 29.6 mg kg[-1] (first loss of - 0.06% at 30 mg kg[-1]). The maximal loss of bacterial alpha-diversity registered was 13.89% at 3837 mg kg[-1]. Our results first highlight that bacterial communities behave differently to soil pollution depending on the metal. Secondly, our study suggests that even extreme doses of Cu do not cause a dramatic loss in alpha-diversity, highlighting how the behaviour of bacterial communities diverges from soil macro-organisms.},
}
@article {pmid36179845,
year = {2023},
author = {Dziurzynski, M and Gorecki, A and Pawlowska, J and Istel, L and Decewicz, P and Golec, P and Styczynski, M and Poszytek, K and Rokowska, A and Gorniak, D and Dziewit, L},
title = {Revealing the diversity of bacteria and fungi in the active layer of permafrost at Spitsbergen island (Arctic) - Combining classical microbiology and metabarcoding for ecological and bioprospecting exploration.},
journal = {The Science of the total environment},
volume = {856},
number = {Pt 2},
pages = {159072},
doi = {10.1016/j.scitotenv.2022.159072},
pmid = {36179845},
issn = {1879-1026},
mesh = {*Bioprospecting ; Soil Microbiology ; *Permafrost ; Ecosystem ; Biodiversity ; Svalbard ; Bacteria/genetics ; Soil ; Fungi/genetics ; Arctic Regions ; },
abstract = {Arctic soils are constantly subjected to extreme environmental conditions such as low humidity, strong winds, high salinity, freeze-thaw cycles, UV exposition, and low nutrient availability, therefore, they have developed unique microbial ecosystems. These environments provide excellent opportunities to study microbial ecology and evolution within pristine (i.e. with limited anthropogenic influence) regions since the High Arctic is still considered one of the wildest and least explored environments on the planet. This environment is also of interest for the screening and recovery of unique microbial strains suitable for various biotechnological applications. In this study, a combination of culture-depended and culture-independent approaches was used to determine the cultivation bias in studies of the diversity of cold-active microorganisms. Cultivation bias is a reduction in recovered diversity, introduced when applying a classical culturing technique. Six different soil types, collected in the vicinity of the Polish Polar Station Hornsund (Spitsbergen, Norway), were tested. It was revealed that the used media allowed recovery of only 6.37 % of bacterial and 20 % of fungal genera when compared with a culture-independent approach. Moreover, it was shown that a combination of R2A and Marine Broth media recovered as much as 93.6 % of all cultivable bacterial genera detected in this study. Based on these results, a novel protocol for genome-guided bioprospecting, combining a culture-dependent approach, metabarcoding, next-generation sequencing, and genomic data reuse was developed. With this methodology, 14 psychrotolerant, multi-metal-resistant strains, including the highly promising Rhodococcus spp., were obtained. These strains, besides increased metal tolerance, have a petroleum hydrocarbon utilization capacity, and thus may be good candidates for future bioremediation technologies, also suited to permanently cold regions.},
}
@article {pmid36179842,
year = {2023},
author = {Romans-Casas, M and Perona-Vico, E and Dessì, P and Bañeras, L and Balaguer, MD and Puig, S},
title = {Boosting ethanol production rates from carbon dioxide in MES cells under optimal solventogenic conditions.},
journal = {The Science of the total environment},
volume = {856},
number = {Pt 1},
pages = {159124},
doi = {10.1016/j.scitotenv.2022.159124},
pmid = {36179842},
issn = {1879-1026},
mesh = {*Carbon Dioxide ; *Ethanol ; Biofuels ; Electricity ; Acetic Acid ; Electrodes ; },
abstract = {Microbial Electrosynthesis (MES) has been widely applied for acetic acid (HA) production from CO2 and electricity. Ethanol (EtOH) has a higher market value than HA, and wide application in industry and as a biofuel. However, it has only been obtained sporadically and at low concentrations, probably due to sub-optimal operating conditions. This study aimed at enhancing EtOH productivity in MES cells by jointly optimising key operation parameters, including pH, H2 and CO2 partial pressure (pH2 and pCO2), and HA concentration, to promote solventogenesis. Two H-type cells were operated in fed-batch mode at -0.8 V vs. SHE with CO2 as the sole carbon source. A mixed culture, enriched with Clostridium ljungdahlii was used as the biocatalyst. The combination of low pH (<4.5) and pCO2 (<0.3 atm), along with high HA concentration (about 6 g L[-1]) and pH2 (>3 atm), were mandatory conditions for maintaining an efficient solventogenic culture, dominated by Clostridium sp., capable of high-rate EtOH production. The maximum EtOH production rate was 10.95 g m[-2] d[-1], and a concentration of 5.28 g L[-1] was achieved. Up to 30 % of the electrons and 15.2 % of the carbon provided were directed towards EtOH production, and 28.1 kWh were required for the synthesis of 1 kg of EtOH from CO2. These results highlight that strict conditions are required for a continuous, reliable, EtOH production in MES cells. Future investigation should focus on improving cell configuration to achieve EtOH production at higher current densities while minimizing the electric energy input.},
}
@article {pmid36178538,
year = {2023},
author = {Ishigami, K and Jang, S and Itoh, H and Kikuchi, Y},
title = {Obligate Gut Symbiotic Association with Caballeronia in the Mulberry Seed Bug Paradieuches dissimilis (Lygaeoidea: Rhyparochromidae).},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1307-1318},
pmid = {36178538},
issn = {1432-184X},
support = {21F21090//Japan Society for the Promotion of Science/ ; 20H03303//Ministry of Education, Culture, Sports, Science and Technology (MEXT) KAKENHI/ ; },
mesh = {Humans ; Animals ; Adult ; *Morus ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Heteroptera/genetics/microbiology ; *Burkholderiaceae ; Insecta ; Bacteria ; },
abstract = {Many insects possess symbiotic bacteria in their bodies, and microbial symbionts play pivotal metabolic roles for their hosts. Members of the heteropteran superfamilies Coreoidea and Lygaeoidea stinkbugs harbor symbionts of the genus Caballeronia in their intestinal tracts. Compared with symbiotic associations in Coreoidea, those in Lygaeoidea insects are still less understood. Here, we investigated a symbiotic relationship involving the mulberry seed bug Paradieuches dissimilis (Lygaeoidea: Rhyparochromidae) using histological observations, cultivation of the symbiont, 16S rRNA gene amplicon sequencing, and infection testing of cultured symbionts. Histological observations and cultivation revealed that P. dissimilis harbors Caballeronia symbionts in the crypts of its posterior midgut. 16S rRNA gene amplicon sequencing of field-collected P. dissimilis confirmed that the genus Caballeronia is dominant in the midgut of natural populations of P. dissimilis. In addition, PCR diagnostics showed that the eggs were free of symbiotic bacteria, and hatchlings horizontally acquired the symbionts from ambient soil. Infection and rearing experiments revealed that symbiont-free aposymbiotic individuals had abnormal body color, small body size, and, strikingly, a low survival rate, wherein no individuals reached adulthood, indicating an obligate cooperative mutualism between the mulberry seed bug and Caballeronia symbionts.},
}
@article {pmid36175476,
year = {2022},
author = {Gan, L and Zheng, J and Xu, WH and Lin, J and Liu, J and Zhang, Y and Wu, Z and Lv, Z and Jia, Y and Guo, Q and Chen, S and Liu, C and Defoirdt, T and Qin, Q and Liu, Y},
title = {Deciphering the virulent Vibrio harveyi causing spoilage in muscle of aquatic crustacean Litopenaeus vannamei.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {16296},
pmid = {36175476},
issn = {2045-2322},
mesh = {Animals ; Humans ; Lithium ; Muscle Fibers, Skeletal ; *Penaeidae ; Seafood ; *Vibrio ; *Vibrio cholerae ; },
abstract = {The muscle of aquatic crustaceans is perishable and susceptible to environmental contamination. Vibrio harveyi is a widely occurring pathogen in aquatic animals. Here, bath treatment with a virulent V. harveyi strain (which was added directly in the rearing water to imitate environmental contamination) isolated from the muscle of the whiteleg shrimp, Litopenaeus vannamei, caused the muscle of Li. vannamei to display a whitish-opaque appearance due to microscopic changes including muscle lysis, muscle fiber damage and microbial colonization. When administered orally by incorporating this isolate in feed (which is an imitation of infection via natural route), rather than direct invasion followed by colonization in the muscle, this isolate indirectly stimulated severe muscle necrosis in Li. vannamei via steering the enrichment of two important (human) pathogens, V. cholerae and V. vulnificus, and one environmental bacterium Pseudomonas oleovorans, based on the meta-taxonomic analyses. In addition to the scientifically proven viral diseases, our research proved that bacterial agents are also capable of causing muscle spoilage in crustaceans via changing the microbial composition, and that the crustaceans might be exploited as the wide-spectrum sensitive bio-detector to indicate the extent of microbial contamination.},
}
@article {pmid36173731,
year = {2022},
author = {Girolamini, L and Pascale, MR and Salaris, S and Mazzotta, M and Orsini, M and Grottola, A and Zini, N and Cristino, S},
title = {Legionella bononiensis sp. nov., isolated from a hotel water distribution system in northern Italy.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.005512},
pmid = {36173731},
issn = {1466-5034},
mesh = {Agar ; Bacterial Typing Techniques ; Base Composition ; Catalase/genetics ; Charcoal ; Ciprofloxacin ; Cycloheximide ; Cysteine/genetics ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Gelatinases/genetics ; Glycine/genetics ; Hippurates ; *Legionella ; Nucleotides ; Phylogeny ; Polymyxin B/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Vancomycin ; Water ; },
abstract = {Legionella-like isolates, strains 27fs60, 30fs61 and 30cs62[T], were isolated from a hotel water distribution system in the Emilia-Romagna region, Italy. Isolates were Gram- and Ziehl Neelsen-stain-negative, rod-shaped, with transitory flagella presence and able to grow at 32-37 °C (with an optimum at 32 °C) on buffered charcoal-yeast extract agar with l-cysteine, glycine-vancomycin-polymyxin B-cycloheximide agar and Wadowsky-Yee medium agar. The strains showed positive reactions for oxidase, hippurate and gelatinase and a weakly positive reaction for catalase. Based on the EUCAST cut-off, strain 30cs62[T] was resistant to ciprofloxacin (5 mg l[-1]). The mip and rpoB gene sequences of the three strains showed close matches to those of Legionella quateirensis ATCC 49507[T] with similarity values of 98.2 and 94.5 %, respectively. Whole genome sequencing of the three strains was performed, resulting in G+C contents of 39.0, 39.1 and 39.0 mol%, respectively. The identity percentage measured by average nucleotide identity between the three strains and their respective closest strains were: 91.32 % L. quateirensis NCTC 12376[T], 91.45 % L. quateirensis ATCC 49507[T] and 91.45 % L. quateirensis ATCC 49507[T], respectively. The digital DNA-DNA hybridization analysis demonstrated how the isolates were separated from the most related phylogenetic Legionella species (L. quateirensis ATCC 49507[T], ≤40.10 % DNA-DNA relatedness). The concatenated phylogenetic tree based on 16S rRNA, mip, rpoB and rnpB genes, shows a close relationship with L. quateirensis ATCC 49507[T]. The results obtained confirm the status of an independent species. The name proposed for this species is Legionella bononiensis sp. nov. with 30cs62[T] (=ATCC TSD-262[T]=DSM 112526[T]) as the type strain.},
}
@article {pmid36173132,
year = {2022},
author = {Izcue, J and Palacios-García, I and Rojas Traverso, F and Koller, M and Parada, FJ},
title = {Perspectives on Inequity and Health Disparities in Chile and Their Relationship to Microbial Ecology.},
journal = {mSystems},
volume = {7},
number = {5},
pages = {e0149621},
pmid = {36173132},
issn = {2379-5077},
mesh = {Humans ; Chile/epidemiology ; *COVID-19/epidemiology ; Income ; *Pandemics ; },
abstract = {Among countries in the Organisation for Economic Cooperation and Development (OECD), Chile stands out as having important inequalities in income distribution, dietary quality, access to urban green spaces, and health outcomes. People in lower socioeconomic groups consistently show higher rates of noncommunicable chronic diseases and are being hit the hardest by the COVID-19 pandemic. These chronic conditions are increasingly considered to be shaped, or affected by, the human gut microbiome. Moreover, inequity as an overarching concept might also be associated with microbial patterns and if so, this may represent a novel pathway through which to address health and other disparities. Focusing on the case of Chile, our goal is to contribute to a critical discussion and motivate researchers and policymakers to consider the role of the microbiome in social equity in future endeavors.},
}
@article {pmid36172557,
year = {2022},
author = {Li, J and Yu, X and Shan, Q and Shi, Z and Li, J and Zhao, X and Chang, C and Yu, J},
title = {Integrated volatile metabolomic and transcriptomic analysis provides insights into the regulation of floral scents between two contrasting varieties of Lonicera japonica.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {989036},
pmid = {36172557},
issn = {1664-462X},
abstract = {Lonicera japonica Thunb., belonging to the Caprifoliaceae family, is an important traditional Chinese medicinal plant. The L. japonica flower (LJF) is widely used in medicine, cosmetics, drinks, and food due to its medicinal and sweet-smelling properties. Considerable efforts have been devoted to investigating the pharmacological activities of LJF; however, the regulatory mechanism of the floral scents remains unknown. We previously selected and bred an elite variety of L. japonica var. chinensis Thunb. called 'Yujin2', which has a strong aroma and is used in functional drinks and cosmetics. In order to reveal the regulatory mechanism of the floral scents of LJF, volatile metabolomic and transcriptomic analyses of the LJF at the silver flowering stage of 'Yujin2' (strong aroma) and 'Fengjin1' (bland odor) were performed. Our results revealed that a total of 153 metabolites and 9,523 genes were differentially regulated in LJF between 'Yujin2' and 'Fengjin1'. The integrated analysis of omics data indicated that the biosynthetic pathways of terpenoids (i.e., monoterpenoids, including geraniol and alpha-terpineol; sesquiterpenoids, including farnesol, farnesal, and alpha-farnesene; triterpenoid squalene), tryptophan and its derivatives (methyl anthranilate), and fatty acid derivatives, were major contributors to the stronger aroma of 'Yujin2' compared to 'Fengjin1'. Moreover, several genes involved in the terpenoid biosynthetic pathway were characterized using quantitative real-time PCR. These results provide insights into the metabolic mechanisms and molecular basis of floral scents in LJF, enabling future screening of genes related to the floral scent regulation, such as alpha-terpineol synthase, geranylgeranyl diphosphate synthase, farnesyl pyrophosphate synthase, anthranilate synthase, as well as transcription factors such as MYB, WRKY, and LFY. The knowledge from this study will facilitate the breeding of quality-improved and more fragrant variety of L. japonica for ornamental purpose and functional beverages and cosmetics.},
}
@article {pmid36171563,
year = {2022},
author = {Junghare, M and Frey, J and Naji, KM and Spiteller, D and Vaaje-Kolstad, G and Schink, B},
title = {Isophthalate:coenzyme A ligase initiates anaerobic degradation of xenobiotic isophthalate.},
journal = {BMC microbiology},
volume = {22},
number = {1},
pages = {227},
pmid = {36171563},
issn = {1471-2180},
mesh = {Acetyl Coenzyme A/metabolism ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Anaerobiosis ; Base Composition ; Benzoates/metabolism ; Carbon ; Carcinogens ; Coenzyme A/metabolism ; Coenzyme A Ligases ; *Diphosphates ; *Environmental Pollutants ; Escherichia coli/metabolism ; Glutarates ; Hydroxybenzoates ; Mutagens ; Oxygen ; Phenylacetates/metabolism ; Phthalic Acids ; Phylogeny ; Plastics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Sulfur ; Xenobiotics ; },
abstract = {BACKGROUND: Environmental contamination from synthetic plastics and their additives is a widespread problem. Phthalate esters are a class of refractory synthetic organic compounds which are widely used in plastics, coatings, and for several industrial applications such as packaging, pharmaceuticals, and/or paints. They are released into the environment during production, use and disposal, and some of them are potential mutagens and carcinogens. Isophthalate (1,3-benzenedicarboxylic acid) is a synthetic chemical that is globally produced at a million-ton scale for industrial applications and is considered a priority pollutant. Here we describe the biochemical characterization of an enzyme involved in anaerobic degradation of isophthalate by the syntrophically fermenting bacterium Syntrophorhabdus aromaticivorans strain UI that activate isophthalate to isophthalyl-CoA followed by its decarboxylation to benzoyl-CoA.<br><br>RESULTS: Isophthalate:Coenzyme A ligase (IPCL, AMP-forming) that activates isophthalate to isophthalyl-CoA was heterologously expressed in E. coli (49.6&#x2009;kDa) for biochemical characterization. IPCL is homologous to phenylacetate-CoA ligase that belongs to the family of ligases that form carbon-sulfur bonds. In the presence of coenzyme A, Mg[2+] and ATP, IPCL converts isophthalate to isophthalyl-CoA, AMP and pyrophosphate (PPi). The enzyme was specifically induced after anaerobic growth of S. aromaticivorans in a medium containing isophthalate as the sole carbon source. Therefore, IPCL exhibited high substrate specificity and affinity towards isophthalate. Only substrates that are structurally related to isophthalate, such as glutarate and 3-hydroxybenzoate, could be partially converted to the respective coenzyme A esters. Notably, no activity could be measured with substrates such as phthalate, terephthalate&#xa0;and benzoate. Acetyl-CoA or succinyl-CoA did not serve as CoA donors. The enzyme has a theoretical pI of 6.8 and exhibited optimal activity between&#xa0;pH 7.0 to 7.5. The optimal temperature was between 25&#x2009;&#xb0;C and 37&#x2009;&#xb0;C. Denaturation temperature (Tm) of IPCL was found to be at about&#xa0;63&#x2009;&#xb0;C. The apparent KM values for isophthalate, CoA, and ATP were 409&#x2009;&#x3bc;M, 642&#x2009;&#x3bc;M, and 3580&#x2009;&#x3bc;M, respectively. Although S. aromaticivorans is a strictly anaerobic bacterium, the enzyme was found to be&#xa0;oxygen-insensitive and catalysed isophthalyl-CoA formation under both anoxic and oxic conditions.<br><br>CONCLUSION: We have successfully cloned&#xa0;the ipcl gene, expressed and characterized the corresponding IPCL&#xa0;enzyme, which plays a key role in isophthalate activation that initiates its activation and&#xa0;further degradation by S. aromaticivorans. Its biochemical characterization represents an important step in the elucidation of the complete degradation pathway of isophthalate.},
}
@article {pmid36170274,
year = {2022},
author = {Mohammed, A and Hu, J and Murugesan, R and Cheng, HW},
title = {Effects of a synbiotic as an antibiotic alternative on behavior, production performance, cecal microbial ecology, and jejunal histomorphology of broiler chickens under heat stress.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0274179},
pmid = {36170274},
issn = {1932-6203},
mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Diet/veterinary ; Dietary Supplements ; Escherichia coli ; *Escherichia coli Infections ; *Heat Stress Disorders ; Heat-Shock Response ; Male ; *Synbiotics ; },
abstract = {The aim of this study was to examine if synbiotics present similar efficiency to a common antibiotic used in poultry production under heat stress (HS) conditions. Two hundred and forty-one-day-old male Ross 708 broiler chicks were distributed among 3 treatments with 8 pens per treatment of 80 birds each for a 42-day trial. From day 15, birds were heat stressed (32°C for 9 h daily, HS) and fed the basal diet (CONT), the basal diet mixed with an antibiotic (Bactiracin Methylene Disalicylate) (0.05 g/kg of feed, BMD) or a synbiotic (0.5 g/kg of feed, SYN). The treatment effects on bird behavior, production performance, jejunal histomorphology, and cecal microbial ecology were examined. Behavioral observation was recorded by using instantaneous scan sampling technique. Production parameters were measured on day 14, 28, and 42. Cecal microbial populations of Escherichia coli and Lactobacilli and jejunal histomorphological parameters were measured at day 42. The results showed that, SYN birds exhibited more feeding and preening but less drinking and panting behaviors compared with both BMD and CONT birds (P < 0.05). The SYN birds also had higher body weight (BW) at both day 28 and 42 compared to CONT birds (P < 0.05). At the end of the experiment, the counts of Escherichia coli of SYN birds were at the similar levels of BMD but were lower than that of CONT birds (P < 0.05); while there were no treatment effects on the populations of Lactobacilli (P > 0.05). In addition, SYN birds had greater villus height compared with both CONT and BMD birds (P < 0.05). These findings suggest that the dietary synbiotic supplement has significant performance and welfare benefits, with the potential to be used as an alternative to antibiotics for poultry meat production, especially during hot seasons.},
}
@article {pmid36167684,
year = {2022},
author = {Seong, HJ and Roux, S and Hwang, CY and Sul, WJ},
title = {Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {157},
pmid = {36167684},
issn = {2049-2618},
mesh = {*Bacteriophages/genetics ; DNA ; DNA Methylation/genetics ; Metagenome/genetics ; Metagenomics ; Methyltransferases/genetics ; *Microbiota/genetics ; },
abstract = {BACKGROUND: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life.<br><br>RESULTS: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.<br><br>CONCLUSIONS: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.},
}
@article {pmid36166154,
year = {2023},
author = {Duarte, IO and Hissa, DC and Quintela, BCSF and Rabelo, MC and Oliveira, FADS and Lima, NCB and Melo, VMM},
title = {Genomic Analysis of Surfactant-Producing Bacillus vallismortis TIM68: First Glimpse at Species Pangenome and Prediction of New Plipastatin-Like Lipopeptide.},
journal = {Applied biochemistry and biotechnology},
volume = {195},
number = {2},
pages = {753-771},
pmid = {36166154},
issn = {1559-0291},
support = {312462/2017-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {*Lipopeptides/pharmacology ; Surface-Active Agents/pharmacology/chemistry ; *Bacillus/genetics ; Genomics ; },
abstract = {Surfactants are applied in several industrial processes when the modification of interface activity and the stability of colloidal systems are required. Lipopeptides are a class of microbial biosurfactants produced by species of the Bacillus genus. The present study aimed at assembling and analyzing the genome of a new Bacillus vallismortis strain, TIM68, that was shown to produce surfactant lipopeptides. The draft genome was also screened for common virulence factors and antibiotics resistance genes to investigate the strain biosafety. Comparative genomics analyses, i.e., synteny, average nucleotide identity (ANI), and pangenome, were also carried out using strain TIM68 and publicly available B. vallismortis complete and partial genomes. Three peptide synthetase operons were found in TIM68 genome, and they were surfactin A, mojavensin, and a novel plipastatin-like lipopeptide named vallisin. No virulence factors that render pathogenicity to the strain have been identified, but a region of prophage, that may contain unknown pathogenic factors, has been predicted. The pangenome of the species was characterized as closed, with 57% of genes integrating the core genome. The results obtained here on the genetic potential of TIM68 strain should contribute to its exploration in biotechnological applications.},
}
@article {pmid36166070,
year = {2023},
author = {Alcantara, DMC and Ikeda, P and Souza, CS and de Mello, VVC and Torres, JM and Lourenço, EC and Bassini-Silva, R and Herrera, HM and Machado, RZ and Barros-Battesti, DM and Graciolli, G and André, MR},
title = {Multilayer Networks Assisting to Untangle Direct and Indirect Pathogen Transmission in Bats.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1292-1306},
pmid = {36166070},
issn = {1432-184X},
support = {2018/02753-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/14124-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 59/300.187/2016//Funda&#xe7;&#xe3;o de Apoio ao Desenvolvimento do Ensino, Ci&#xea;ncia e Tecnologia do Estado de Mato Grosso do Sul/ ; 302420/2017-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303802/2021-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 308768/2017-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; E-26/202.158/2015//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; RED-00253-16//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; },
mesh = {Animals ; *Chiroptera/microbiology ; Brazil ; *Mites ; },
abstract = {The importance of species that connect the different types of interactions is becoming increasingly recognized, and this role may be related to specific attributes of these species. Multilayer networks have two or more layers, which represent different types of interactions, for example, between different parasites and hosts that are nonetheless connected. The understanding of the ecological relationship between bats, ectoparasites, and vector-borne bacteria could shed some light on the complex transmission cycles of these pathogens. In this study, we investigated a multilayer network in Brazil formed by interactions between bat-bacteria, bat-ectoparasite, and ectoparasite-bacteria, and asked how these interactions overlap considering different groups and transmission modes. The multilayer network was composed of 31 nodes (12 bat species, 14 ectoparasite species, and five bacteria genera) and 334 links, distributed over three layers. The multilayer network has low modularity and shows a core-periphery organization, that is, composed of a few generalist species with many interactions and many specialist species participating in few interactions in the multilayer network. The three layers were needed to accurately describe the multilayer structure, while aggregation leads to loss of information. Our findings also demonstrated that the multilayer network is influenced by a specific set of species that can easily be connected to the behavior, life cycle, and type of existing interactions of these species. Four bat species (Artibeus lituratus, A. planirostris, Phyllostomus discolor, and Platyrrhinus lineatus), one ectoparasite species (Steatonyssus) and three bacteria genera (Ehrlichia, hemotropic Mycoplasma and Neorickettsia) are the most important species for the multilayer network structure. Finally, our study brings an ecological perspective under a multilayer network approach on the interactions between bats, ectoparasites, and pathogens. By using a multilayer approach (different types of interactions), it was possible to better understand these different ecological interactions and how they affect each other, advancing our knowledge on the role of bats and ectoparasites as potential pathogen vectors and reservoirs, as well as the modes of transmission of these pathogens.},
}
@article {pmid36164984,
year = {2022},
author = {Li, HB and Xu, ML and Xu, XD and Tang, YY and Jiang, HL and Li, L and Xia, WJ and Cui, N and Bai, J and Dai, ZM and Han, B and Li, Y and Peng, B and Dong, YY and Aryal, S and Manandhar, I and Eladawi, MA and Shukla, R and Kang, YM and Joe, B and Yang, T},
title = {Faecalibacterium prausnitzii Attenuates CKD via Butyrate-Renal GPR43 Axis.},
journal = {Circulation research},
volume = {131},
number = {9},
pages = {e120-e134},
pmid = {36164984},
issn = {1524-4571},
support = {R01 HL143082/HL/NHLBI NIH HHS/United States ; R21 AG079357/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; Butyrates/pharmacology/therapeutic use ; Disease Models, Animal ; *Faecalibacterium prausnitzii ; Inflammation ; Kidney/physiology ; Receptors, G-Protein-Coupled/genetics ; *Renal Insufficiency, Chronic ; },
abstract = {BACKGROUND: Despite available clinical management strategies, chronic kidney disease (CKD) is associated with severe morbidity and mortality worldwide, which beckons new solutions. Host-microbial interactions with a depletion of Faecalibacterium prausnitzii in CKD are reported. However, the mechanisms about if and how F prausnitzii can be used as a probiotic to treat CKD remains unknown.<br><br>METHODS: We evaluated the microbial compositions in 2 independent CKD populations for any potential probiotic. Next, we investigated if supplementation of such probiotic in a mouse CKD model can restore gut-renal homeostasis as monitored by its effects on suppression on renal inflammation, improvement in gut permeability and renal function. Last, we investigated the molecular mechanisms underlying the probiotic-induced beneficial outcomes.<br><br>RESULTS: We observed significant depletion of Faecalibacterium in the patients with CKD in both Western (n=283) and Eastern populations (n=75). Supplementation of F prausnitzii to CKD mice reduced renal dysfunction, renal inflammation, and lowered the serum levels of various uremic toxins. These are coupled with improved gut microbial ecology and intestinal integrity. Moreover, we demonstrated that the beneficial effects in kidney induced by F prausnitzii-derived butyrate were through the GPR (G protein-coupled receptor)-43.<br><br>CONCLUSIONS: Using a mouse CKD model, we uncovered a novel beneficial role of F prausnitzii in the restoration of renal function in CKD, which is, at least in part, attributed to the butyrate-mediated GPR-43 signaling in the kidney. Our study provides the necessary foundation to harness the therapeutic potential of F prausnitzii for ameliorating CKD.},
}
@article {pmid36163700,
year = {2023},
author = {Orsi, WD},
title = {Quantitative microbial ecology: Future challenges and opportunities.},
journal = {Environmental microbiology},
volume = {25},
number = {1},
pages = {91-96},
doi = {10.1111/1462-2920.16204},
pmid = {36163700},
issn = {1462-2920},
mesh = {*Ecology ; *Ecosystem ; },
}
@article {pmid36161873,
year = {2024},
author = {Orner, KD and Deleu, E and Rabaey, K and Nelson, KL},
title = {Accelerating urea hydrolysis in fresh urine by modifying operating conditions of a sequencing batch reactor.},
journal = {Environmental technology},
volume = {45},
number = {5},
pages = {845-853},
doi = {10.1080/09593330.2022.2129456},
pmid = {36161873},
issn = {1479-487X},
mesh = {*Urea ; Hydrolysis ; *Urease ; Soil ; Nitrogen/analysis ; Bioreactors ; },
abstract = {A number of existing and emerging technologies can recover nitrogen from urine. A preliminary step in many nitrogen recovery processes is hydrolyzing urea to ammonium, a biologically-mediated process that can take days to weeks without intervention. The ability to achieve urea hydrolysis quickly and reliably would increase the feasibility of decentralized nitrogen recovery, especially where space and treatment time are constrained. The goal of this research was to determine whether urea hydrolysis could be accelerated by providing an inoculum containing microorganisms likely to have urease activity (feces or soil), providing a carrier to support attached growth (plastic carriers, granular activated carbon, or no carrier), and modifying the hydraulic retention time (HRT; 1.3, 2, and 4 days) and feeding frequency (Δt = 4, 24 h). Inoculated reactors achieved significantly more urea hydrolysis, and reactors inoculated with soil were able to sustain higher urea hydrolysis rates over time than those inoculated with feces. The mean zero-order rate constants (mM/hr) for reactors with a soil inoculum (15.1) were about three times higher than that of reactors with an inoculum of feces (4.9). A reactor with GAC and an inoculum of soil fed daily with fresh urine achieved greater than 90% hydrolysis with an HRT of 2 days; results suggest the HRT could be reduced to 16 h without reducing performance. No significant benefit was provided by increasing the frequency of feedings for the same HRT, likely because urease enzymes were saturated and operating at maximum hydrolysis rates during most of the reaction period.},
}
@article {pmid36161499,
year = {2023},
author = {Alonso-Reyes, DG and Galván, FS and Irazoqui, JM and Amadio, A and Tschoeke, D and Thompson, F and Albarracín, VH and Farias, ME},
title = {Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {914-932},
pmid = {36161499},
issn = {1432-184X},
support = {2019-03216//PICT RAICES/ ; G603//PIUNT/ ; },
mesh = {*Altitude ; *Cyanobacteria/genetics/metabolism ; Photosynthesis ; Light ; Lakes/microbiology ; },
abstract = {Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin-Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood-Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.},
}
@article {pmid36160194,
year = {2022},
author = {Guajardo-Leiva, S and Alarcón, J and Gutzwiller, F and Gallardo-Cerda, J and Acuña-Rodríguez, IS and Molina-Montenegro, M and Crandall, KA and Pérez-Losada, M and Castro-Nallar, E},
title = {Source and acquisition of rhizosphere microbes in Antarctic vascular plants.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {916210},
pmid = {36160194},
issn = {1664-302X},
abstract = {Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.},
}
@article {pmid36159733,
year = {2022},
author = {Van de Walle, A and Torfs, E and Gaublomme, D and Rabaey, K},
title = {In silico assessment of household level closed water cycles: Towards extreme decentralization.},
journal = {Environmental science and ecotechnology},
volume = {10},
number = {},
pages = {100148},
pmid = {36159733},
issn = {2666-4984},
abstract = {Water management in most of the developed world is currently practiced in a highly centralized manner, leading to major infrastructure and energy costs to transport water. To decrease the impacts of water scarcity and climate change, the decentralization of water can increase local robustness. In extremis, decentralization can involve building or house level water supply and treatment. Here, we constructed a MATLAB/Simulink model for two decentralized water management configurations at the household level, assuming the socio-environmental setting of Flanders, Belgium. Independence from the potable water grid and sewer system was pursued through rainwater harvesting, reuse of wastewater streams fit-for-purpose, and discharge via infiltration. The mass balance for water was calculated over the system boundaries showing high potential for independence from the grid with a reasonable treatment train and storage options. Next, the risk of contaminant accumulation within the circular system was assessed, showing a key limitation on decentralized system performance necessitating a system purge. Up to 59% of system rainwater usage was due to the replacement of this purge. Employing treatment units with high (95%) contaminant rejection efficiencies eliminated contaminant accumulation issues. The raw model output was quantitatively assessed by constructing four newly proposed key performance indicators (KPIs), quantifying system independence, circularity, drought tolerance and local water body recharge, which allowed for facilitated system comparison and communication to stakeholders. A sensitivity analysis was performed in which the effect of input parameter variability and uncertainty on system performance was quantified. The sensitivity analysis showed the importance of water recovery and contaminant removal efficiencies of the applied treatment technologies on system performance when contaminant accumulation in the system forms an issue. In systems not severely affected by pollutant accumulation, parameters such as inhabitant number and roof surface had the largest effect. As a whole, this work shows the potential of extreme decentralization of water systems and addresses the obstacle towards implementation formed by the accumulation of contaminants due to system circularity. Additionally, this study provides a framework for operational and technological decision support of decentralized household-scale water systems and, by extension, for future water policy-making.},
}
@article {pmid36158753,
year = {2022},
author = {Ostermeyer, P and Van Landuyt, J and Bonin, L and Folens, K and Williamson, A and Hennebel, T and Rabaey, K},
title = {High rate production of concentrated sulfides from metal bearing wastewater in an expanded bed hydrogenotrophic sulfate reducing bioreactor.},
journal = {Environmental science and ecotechnology},
volume = {11},
number = {},
pages = {100173},
pmid = {36158753},
issn = {2666-4984},
abstract = {Metallurgical wastewaters contain high concentrations of sulfate, up to 15 g L[-1]. Sulfate-reducing bioreactors are employed to treat these wastewaters, reducing sulfates to sulfides which subsequently co-precipitate metals. Sulfate loading and reduction rates are typically restricted by the total H2S concentration. Sulfide stripping, sulfide precipitation and dilution are the main strategies employed to minimize inhibition by H2S, but can be adversely compromised by suboptimal sulfate reduction, clogging and additional energy costs. Here, metallurgical wastewater was treated for over 250 days using two hydrogenotrophic granular activated carbon expanded bed bioreactors without additional removal of sulfides. H2S toxicity was minimized by operating at pH 8 ± 0.15, resulting in an average sulfate removal of 7.08 ± 0.08 g L[-1], sulfide concentrations of 2.1 ± 0.2 g L[-1] and peaks up to 2.3 ± 0.2 g L[-1]. A sulfate reduction rate of 20.6 ± 0.9 g L[-1] d[-1] was achieved, with maxima up to 27.2 g L[-1] d[-1], which is among the highest reported considering a literature review of 39 studies. The rates reported here are 6-8 times higher than those reported for other reactors without active sulfide removal and the only reported for expanded bed sulfate-reducing bioreactors using H2. By increasing the influent sulfate concentration and maintaining high sulfide concentrations, sulfate reducers were promoted while fermenters and methanogens were suppressed. Industrial wastewater containing 4.4 g L[-1] sulfate, 0.036 g L[-1] nitrate and various metals (As, Fe, Tl, Zn, Ni, Sb, Co and Cd) was successfully treated with all metal(loid)s, nitrates and sulfates removed below discharge limits.},
}
@article {pmid36154441,
year = {2022},
author = {Zhang, S and Yang, Q and Defoirdt, T},
title = {Halogenated Indoles Decrease the Virulence of Vibrio campbellii in a Gnotobiotic Brine Shrimp Model.},
journal = {Microbiology spectrum},
volume = {10},
number = {5},
pages = {e0268922},
pmid = {36154441},
issn = {2165-0497},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Artemia/microbiology ; Germ-Free Life ; Indoles/pharmacology ; Peptide Hydrolases/pharmacology ; *Vibrio ; Virulence/genetics ; Virulence Factors/genetics ; },
abstract = {Indole signaling is viewed as a potential target for antivirulence therapy against antibiotic-resistant pathogens because of its link with the production of virulence factors. This study examined the antimicrobial and antivirulence properties of 44 indoles toward Vibrio campbellii. Based on the results, 17 halogenated indole analogues were selected, as they significantly improved the survival of brine shrimp larvae challenged with V. campbellii. Specifically, 6-bromoindole, 7-bromoindole, 4-fluoroindole, 5-iodoindole, and 7-iodoindole showed a high protective effect, improving the survival of brine shrimp to over 80% even at a low concentration of 10 μM. To explore the impact of selected indole analogues on bacterial virulence phenotypes, swimming motility, biofilm formation, protease activity, and hemolytic activity of V. campbellii were determined. The results showed that all of the 17 selected indole analogues decreased swimming motility at both 10 μM and 100 μM. Most of the indole analogues decreased biofilm formation at a concentration of 100 μM. In contrast, only a slightly decreased protease activity and no effect on hemolytic activity were observed at both concentrations. To our knowledge, this is the first study of the structure-activity relation of halogenated indole analogues with respect to virulence inhibition of a pathogenic bacterium in an in vivo host model system, and the results demonstrate the potential of these compounds in applications aiming at the protection of shrimp from vibriosis, a major disease in aquaculture. IMPORTANCE Bacterial diseases are a major problem in the aquaculture industry. In order to counter this problem, farmers have been using antibiotics, and this has led to the evolution and spread of antibiotic resistance. In order for the aquaculture industry to further grow in a sustainable way, novel and sustainable methods to control diseases are needed. We previously reported that indole signaling is a valid target for the development of novel therapies to control disease caused by Vibrio campbellii and related bacteria, which are among the major bacterial pathogens in aquaculture. In the present study, we identified indole analogues that are more potent in protecting brine shrimp (a model organism for shrimp) from V. campbellii. To our knowledge, this is the first study of the structure-activity relation of halogenated indole analogues with respect to virulence inhibition of a pathogenic bacterium in an in vivo host model system.},
}
@article {pmid36153325,
year = {2022},
author = {Zhu, H and Xu, L and Luan, G and Zhan, T and Kang, Z and Li, C and Lu, X and Zhang, X and Zhu, Z and Zhang, Y and Li, Y},
title = {A miniaturized bionic ocean-battery mimicking the structure of marine microbial ecosystems.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {5608},
pmid = {36153325},
issn = {2041-1723},
mesh = {*Bioelectric Energy Sources ; Bionics ; Hydrogels ; *Microbiota ; Oceans and Seas ; },
abstract = {Marine microbial ecosystems can be viewed as a huge ocean-battery charged by solar energy. It provides a model for fabricating bio-solar cell, a bioelectrochemical system that converts light into electricity. Here, we fabricate a bio-solar cell consisting of a four-species microbial community by mimicking the ecological structure of marine microbial ecosystems. We demonstrate such ecological structure consisting of primary producer, primary degrader, and ultimate consumers is essential for achieving high power density and stability. Furthermore, the four-species microbial community is assembled into a spatial-temporally compacted cell using conductive hydrogel as a sediment-like anaerobic matrix, forming a miniaturized bionic ocean-battery. This battery directly converts light into electricity with a maximum power of 380 μW and stably operates for over one month. Reproducing the photoelectric conversion function of marine microbial ecosystems in this bionic battery overcomes the sluggish and network-like electron transfer, showing the biotechnological potential of synthetic microbial ecology.},
}
@article {pmid36152855,
year = {2023},
author = {Zhang, X and Shen, M and Wang, C and Gao, M and Wang, L and Jin, Z and Xia, X},
title = {Impact of aluminum exposure on oxidative stress, intestinal changes and immune responses in red swamp crayfish (Procambarus clarkii).},
journal = {The Science of the total environment},
volume = {855},
number = {},
pages = {158902},
doi = {10.1016/j.scitotenv.2022.158902},
pmid = {36152855},
issn = {1879-1026},
mesh = {Animals ; *Astacoidea ; *Aluminum/toxicity ; Hemocytes ; Oxidative Stress ; Immunity ; },
abstract = {Aluminum (Al) is an abundant metal that has been classified as a threatening pollutant due to indiscriminate use and anthropogenic activities. This study aimed to evaluate the impacts of Al on crayfish (Procambarus clarkii), including biochemical change, histological alteration, gut microbial community diversification, and immune changes. The bioaccumulation of Al was detected in the hemolymph and intestine of crayfish after Al exposure at different time points. Results showed that Al exposure significantly induced oxidative stress and caused pathohistological changes on intestinal barrier structures in crayfish. It was found that the intestinal microbiota was affected by retained Al and the intestinal community diversity was changed after Al treated in the crayfish. Furthermore, Al exposure affected the immunity in crayfish, by altering the expression of a set of immune-related genes, as well as reducing the phenoloxidase and lysozyme activities. Moreover, Al exposure promoted hemocytes apoptosis and impaired hemophagocytic capacity against Vibro parahamolyticus, resulting in higher mortality of crayfish upon bacterial infection. Taken these results together, we conclude that excessive Al exposure caused adverse effects on multiple biological processes of crayfish and Al pollution is a potential threat to crayfish culture.},
}
@article {pmid36152034,
year = {2023},
author = {Weingarten, EA and Jackson, CR},
title = {Microbial Composition of Freshwater Marsh Sediment Responds more Strongly to Microcosm Seawater Addition than Simulated Nitrate or Phosphate Eutrophication.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1060-1070},
pmid = {36152034},
issn = {1432-184X},
mesh = {*Wetlands ; *Nitrates ; Phosphates ; Fresh Water ; Seawater ; Eutrophication ; },
abstract = {As sea level rise impacts coastal wetlands, saltmarsh will overtake coastal freshwater marsh in many areas, but changes in the sediment microbiome in response to saltwater intrusion are difficult to predict. Coastal freshwater marsh sediment was exposed to ambient, brackish, and saline conditions as well as to elevated nitrate and phosphate to model the combined stresses of saltwater intrusion and coastal eutrophication. Initially, sediment prokaryotic composition was similar to prior studies of freshwater marsh but diverged over time, reflecting the magnitude of increase in saltwater. There was no observed effect of nutrient amendment, potentially ranking seawater intrusion as a higher-importance compositional driver. Although the previously described loss of methanogenic populations and promotion of sulfate reducers in response to saltwater exposure was observed, taxonomic distribution was not similar to typical meso-polyhaline wetlands. Without colonization by marine taxa, such a community may be short-lived naturally, ultimately equilibrating with more common saltmarsh species. However, the recapitulation of salinity concentration by freshwater sediment microbial composition demonstrates the overwhelming nature of saltwater intrusion relative to other drivers like eutrophication.},
}
@article {pmid36151709,
year = {2022},
author = {Prosser, JI},
title = {How and why in microbial ecology: An appeal for scientific aims, questions, hypotheses and theories.},
journal = {Environmental microbiology},
volume = {24},
number = {11},
pages = {4973-4980},
doi = {10.1111/1462-2920.16221},
pmid = {36151709},
issn = {1462-2920},
mesh = {*Ecology ; *Environmental Microbiology ; },
abstract = {This article precedes a series of articles on the important questions, hypotheses and theories in microbial ecology. It considers why, as scientists, we ask questions and propose hypotheses and what makes them important, good or significant. Emphasis is placed on 'scientific' questions, the need for scientific aims and on possible reasons for, and inadequacy of aim-less studies and question free studies. Current global issues surrounding the climate crisis, pandemics and antibiotic resistance focus attention on science and scientists. They exemplify the urgent need for greater understanding of the interactions between microbes and their biological and physicochemical environments, that is, of microbial ecology. They also provide examples of reaction against science and scientists and highlight why we must be clear regarding what defines (good) science, its power and limitations, and ensure that this is communicated to stakeholders and the general public.},
}
@article {pmid36151339,
year = {2023},
author = {Zhou, X and Lee, J and Yun, J and Kim, J and Yang, Y and Kang, H},
title = {Distinct Nitrification Rates and Nitrifiers in Needleleaf and Evergreen Broadleaf Forest Soils.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1050-1059},
pmid = {36151339},
issn = {1432-184X},
mesh = {*Soil/chemistry ; *Nitrification ; Ecosystem ; Ammonia ; Phylogeny ; Oxidation-Reduction ; Soil Microbiology ; Archaea ; Forests ; },
abstract = {Research on niche specialization in the microbial communities of ammonia oxidizers is important for assessing the consequences of vegetation shift on nitrogen (N) cycling. In this study, soils were sampled from three tree stands (needleleaf, mixed, and evergreen broadleaf) from the Hannam experimental forest in South Korea in spring (May 2019), summer (August 2019), autumn (November 2019), and winter (January 2020). Quantitative polymerase chain reaction (qPCR) and high-throughput sequencing were used to measure the abundance and community structure of various nitrifiers: ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) as well as complete ammonia oxidizers (comammox). Nitrification rates and total ammonia oxidizer abundance were significantly higher in needleleaf forest soil than those in other forest stands, and they were lowest in evergreen broadleaf forest soil. Comammox clade B was most abundant in needleleaf and evergreen broadleaf forest soils, while AOA were significantly more abundant in mixed forest soil. The abundances of comammox clade B and AOA were negatively correlated with dissolved organic carbon. Phylogenetic analysis showed that NT-alpha and NS-gamma-2.3.2 were the most abundant AOA lineages in all the samples. The seasonal of AOA, AOB, and comammox varied with the sites, suggesting the need to examine the combinations of environmental factors when considering the effects of seasonal changes in the environment. Overall, the results suggest that potential vegetation shifts in forest ecosystems might affect nitrification activities by regulating the abundance and community structure of ammonia oxidizers.},
}
@article {pmid36150718,
year = {2022},
author = {Kritzberg, E and Bååth, E},
title = {Seasonal variation in temperature sensitivity of bacterial growth in a temperate soil and lake.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {10},
pages = {},
pmid = {36150718},
issn = {1574-6941},
mesh = {Bacteria/metabolism ; *Lakes ; Seasons ; *Soil ; Temperature ; Water/metabolism ; },
abstract = {Faster bacterial biomass turnover is expected in water compared to soil, which would result in more rapid community adaption to changing environmental conditions, including temperature. Bacterial community adaptation for growth is therefore predicted to have larger seasonal amplitudes in lakes than in soil. To test this prediction, we compared the seasonal variation in temperature adaptation of bacterial community growth in a soil and lake in Southern Sweden (Tin situ 0-20°C, mean 10°C) during 1.5 years, based on monthly samplings including two winters and summers. An indicator of community adaptation, minimum temperature for growth (Tmin), was calculated from bacterial growth measurements (Leu incorporation) using the Ratkowsky model. The seasonal variation in Tmin (sinusoidal function, R2 = 0.71) was most pronounced for the lake bacterial community, with an amplitude for Tmin of 3.0°C (-4.5 to -10.5°C) compared to 0.6°C (-7 to -8°C) for the soil. Thus, Tmin in water increased by 0.32°C/degree change of Tin situ. Similar differences were also found when comparing four lakes and soils in the winter and summer (amplitudes 2.9°C and 0.9°C for lakes and soils, respectively). Thus, seasonal variation in temperature adaptation has to be taken into account in lakes, while for soils a constant Tmin can be used.},
}
@article {pmid36150364,
year = {2022},
author = {Mitrović, M and Kostešić, E and Marković, T and Selak, L and Hausmann, B and Pjevac, P and Orlić, S},
title = {Microbial community composition and hydrochemistry of underexplored geothermal waters in Croatia.},
journal = {Systematic and applied microbiology},
volume = {45},
number = {6},
pages = {126359},
doi = {10.1016/j.syapm.2022.126359},
pmid = {36150364},
issn = {1618-0984},
mesh = {RNA, Ribosomal, 16S/genetics ; Ammonia/metabolism ; Croatia ; Phylogeny ; *Hot Springs/microbiology ; Archaea ; *Microbiota/genetics ; Bacteria/genetics ; },
abstract = {In Croatia, a variety of geothermal springs with a wide temperature range and varied hydrochemical conditions exist, and they may harbor different niches for the distribution of microbial communities. In this study, 19 different sites, mainly located in central and eastern Croatia, were selected for primary characterization of spring hydrochemistry and microbial community composition. Using 16S rRNA gene amplicon sequencing, it was found that the bacterial communities that dominated most geothermal waters were related to Proteobacteria and Campylobacteria, while most archaeal sequences were related to Crenarchaeota. At the genus level, the prokaryotic community was highly site-specific and was often dominated by a single genus, including sites dominated by Hydrogenophilus, Sulfuricurvum, Sulfurovum, Thiofaba and Nitrospira, while the most abundant archaeal genera were affiliated to the ammonia-oxidizing archaea, Candidatus Nitrosotenuis and Candidatus Nitrososphaera. Whereas the microbial communities were overall highly location-specific, temperature, pH, ammonia, nitrate, total nitrogen, sulfate and hydrogen sulfide, as well as dissolved organic and inorganic carbon, were the abiotic factors that significantly affected microbial community composition. Furthermore, an aquifer-type effect was observed in the community composition, but there was no pronounced seasonal variability for geothermal spring communities (i.e. the community structure was mainly stable during the three seasons sampled). These results surprisingly pointed to stable and geographically unique microbial communities that were adapted to different geothermal water environments throughout Croatia. Knowing which microbial communities are present in these extreme habitats is essential for future research. They will allow us to explore further the microbial metabolisms prevailing at these geothermal sites that have high potential for biotechnological uses, as well as the establishment of the links between microbial community structure and the physicochemical environment of geothermal waters.},
}
@article {pmid36145836,
year = {2022},
author = {Vidal, C and González, F and Santander, C and Pérez, R and Gallardo, V and Santos, C and Aponte, H and Ruiz, A and Cornejo, P},
title = {Management of Rhizosphere Microbiota and Plant Production under Drought Stress: A Comprehensive Review.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {18},
pages = {},
pmid = {36145836},
issn = {2223-7747},
support = {ANID/FONDECYT/1210964//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANID/FONDAP/15130015//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; InES19-FRO19001//Ministry of Education/ ; FONDECYT1210964//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANID/FONDAP/15130015//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; InES19.FRO19001//Ministry of Education/ ; },
abstract = {Drought generates a complex scenario worldwide in which agriculture should urgently be reframed from an integrative point of view. It includes the search for new water resources and the use of tolerant crops and genotypes, improved irrigation systems, and other less explored alternatives that are very important, such as biotechnological tools that may increase the water use efficiency. Currently, a large body of evidence highlights the role of specific strains in the main microbial rhizosphere groups (arbuscular mycorrhizal fungi, yeasts, and bacteria) on increasing the drought tolerance of their host plants through diverse plant growth-promoting (PGP) characteristics. With this background, it is possible to suggest that the joint use of distinct PGP microbes could produce positive interactions or additive beneficial effects on their host plants if their co-inoculation does not generate antagonistic responses. To date, such effects have only been partially analyzed by using single omics tools, such as genomics, metabolomics, or proteomics. However, there is a gap of information in the use of multi-omics approaches to detect interactions between PGP and host plants. This approach must be the next scale-jump in the study of the interaction of soil-plant-microorganism. In this review, we analyzed the constraints posed by drought in the framework of an increasing global demand for plant production, integrating the important role played by the rhizosphere biota as a PGP agent. Using multi-omics approaches to understand in depth the processes that occur in plants in the presence of microorganisms can allow us to modulate their combined use and drive it to increase crop yields, improving production processes to attend the growing global demand for food.},
}
@article {pmid36145178,
year = {2022},
author = {Overbeeke, A and Lang, M and Hausmann, B and Watzka, M and Nikolov, G and Schwarz, J and Kohl, G and De Paepe, K and Eislmayr, K and Decker, T and Richter, A and Berry, D},
title = {Impaired Mucosal Homeostasis in Short-Term Fiber Deprivation Is Due to Reduced Mucus Production Rather Than Overgrowth of Mucus-Degrading Bacteria.},
journal = {Nutrients},
volume = {14},
number = {18},
pages = {},
pmid = {36145178},
issn = {2072-6643},
support = {741623/ERC_/European Research Council/International ; P27831-B28//FWF Austrian Science Fund/ ; LS18-053//Vienna Science and Technology Fund/ ; MAINTAIN DOC 69//FWF Austrian Science Fund/ ; },
mesh = {Bacteria ; Butyrates/metabolism ; *Dietary Fiber/metabolism ; Homeostasis ; Intestinal Mucosa/metabolism ; *Mucus/metabolism ; },
abstract = {The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis. Seven days of fiber-deficiency affected intestinal anatomy and physiology, seen by reduced intestinal length and loss of the colonic crypt-structure. Moreover, the mucus layer was diminished, muc2 expression decreased, and impaired mucus secretion was detected by stable isotope probing. Quantitative microbiome profiling of the gut microbiota showed a diet-induced reduction in bacterial load and decreased diversity across the intestinal tract, including taxa with fiber-degrading and butyrate-producing capabilities. Most importantly, there was little change in the absolute abundance of known mucus-degrading bacteria, although, due to the general loss of taxa, relative abundance would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, suggesting erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders.},
}
@article {pmid36144291,
year = {2022},
author = {Kuzyk, SB and Ma, X and Yurkov, V},
title = {Seasonal Dynamics of Lake Winnipeg's Microbial Communities Reveal Aerobic Anoxygenic Phototrophic Populations Coincide with Sunlight Availability.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
pmid = {36144291},
issn = {2076-2607},
support = {5492-2018//Natural Sciences and Engineering Research Council/ ; },
abstract = {In this first comprehensive study of Lake Winnipeg's microbial communities, limnetic and littoral euphotic zones were examined during each season from 2016 through 2020. Classical cultivation and modern high-throughput sequencing techniques provided quantification and identification of key phototrophic populations, including aerobic anoxygenic phototrophs (AAP). Annual dynamics found total heterotrophs reached 4.23 × 10[6] CFU/g in littoral sands, and 7.69 × 10[4] CFU/mL in summer littoral waters on oligotrophic media, higher counts than for copiotrophic compositions. Limnetic numbers inversely dipped to 4.34 × 10[3] CFU/mL midsummer. Cultured AAP did not follow heterotrophic trends, instead peaking during the spring in both littoral and limnetic waters as 19.1 and 4.7% of total copiotrophs, or 3.9 and 4.9% of oligotrophs, decreasing till autumn each year. Complementary observations came from environmental 16S V4 rRNA gene analysis, as AAP made up 1.49 and 1.02% of the littoral and limnetic sequenced communities in the spring, declining with seasonal progression. Spatial and temporal fluctuations of microbes compared to environmental factors exposed photosynthetic populations to independently and regularly fluctuate in the ecosystem. Oxygenic phototrophic numbers expectantly matched the midsummer peak of Chl a and b, oxygenic photosynthesis related carbon fixation, and water temperature. Independently, AAP particularly colonized spring littoral areas more than limnetic, and directly corresponded to habitat conditions that specifically promoted growth: the requirement of light and organic material.},
}
@article {pmid36143410,
year = {2022},
author = {Johnston-Monje, D and Gutiérrez, JP and Becerra Lopez-Lavalle, LA},
title = {Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants.},
journal = {Life (Basel, Switzerland)},
volume = {12},
number = {9},
pages = {},
pmid = {36143410},
issn = {2075-1729},
abstract = {A plant's health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant-microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.},
}
@article {pmid36139115,
year = {2022},
author = {Qing, J and Zheng, F and Zhi, H and Yaigoub, H and Tirichen, H and Li, Y and Zhao, J and Qiang, Y and Li, Y},
title = {Identification of Unique Genetic Biomarkers of Various Subtypes of Glomerulonephritis Using Machine Learning and Deep Learning.},
journal = {Biomolecules},
volume = {12},
number = {9},
pages = {},
pmid = {36139115},
issn = {2218-273X},
mesh = {Biomarkers/analysis ; *Deep Learning ; *Glomerulonephritis/genetics/metabolism ; Humans ; Kidney Glomerulus/chemistry/metabolism/pathology ; Macrophages/metabolism ; },
abstract = {(1) Objective: Identification of potential genetic biomarkers for various glomerulonephritis (GN) subtypes and discovering the molecular mechanisms of GN. (2) Methods: four microarray datasets of GN were downloaded from Gene Expression Omnibus (GEO) database and merged to obtain the gene expression profiles of eight GN subtypes. Then, differentially expressed immune-related genes (DIRGs) were identified to explore the molecular mechanisms of GN, and single-sample gene set enrichment analysis (ssGSEA) was performed to discover the abnormal inflammation in GN. In addition, a nomogram model was generated using the R package "glmnet", and the calibration curve was plotted to evaluate the predictive power of the nomogram model. Finally, deep learning (DL) based on a multilayer perceptron (MLP) network was performed to explore the characteristic genes for GN. (3) Results: we screened out 274 common up-regulated or down-regulated DIRGs in the glomeruli and tubulointerstitium. These DIRGs are mainly involved in T-cell differentiation, the RAS signaling pathway, and the MAPK signaling pathway. ssGSEA indicates that there is a significant increase in DC (dendritic cells) and macrophages, and a significant decrease in neutrophils and NKT cells in glomeruli, while monocytes and NK cells are increased in tubulointerstitium. A nomogram model was constructed to predict GN based on 7 DIRGs, and 20 DIRGs of each subtype of GN in glomeruli and tubulointerstitium were selected as characteristic genes. (4) Conclusions: this study reveals that the DIRGs are closely related to the pathogenesis of GN and could serve as genetic biomarkers in GN. DL further identified the characteristic genes that are essential to define the pathogenesis of GN and develop targeted therapies for eight GN subtypes.},
}
@article {pmid36138209,
year = {2023},
author = {Liu, Q and Zhang, H and Huang, X},
title = {Strong Linkage Between Symbiotic Bacterial Community and Host Age and Morph in a Hemipteran Social Insect.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1213-1225},
pmid = {36138209},
issn = {1432-184X},
support = {31970446//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Female ; Biological Evolution ; *Aphids/microbiology ; Insecta ; Symbiosis/physiology ; *Buchnera/genetics ; },
abstract = {The relationships between symbionts and insects are complex, and symbionts usually have diverse ecological and evolutionary effects on their hosts. The phloem sap-sucking aphids are good models to study the interactions between insects and symbiotic microorganisms. Although aphids usually exhibit remarkable life cycle complexity, most previous studies on symbiotic diversity sampled only apterous viviparous adult females or very few morphs. In this study, high-throughput 16S rDNA amplicon sequencing was used to assess the symbiotic bacterial communities of eleven morphs or developmental stages of the social aphid Pseudoregma bambucicola. We found there were significant differences in bacterial composition in response to different morphs and developmental stages, and for the first time, we revealed male aphids hosted very different symbiotic composition featured with low abundance of dominant symbionts but high diversity of total symbionts. The relative abundance of Pectobacterium showed relatively stable across different types of samples, while that of Wolbachia fluctuated greatly, indicating the former may have a consistent function in this species and the latter may provide specific function for certain morphs or developmental stages. Our study presents new evidence of complexity of symbiotic associations and indicates strong linkage between symbiotic bacterial community and host age and morph.},
}
@article {pmid36138151,
year = {2022},
author = {Simpson, RC and Shanahan, ER and Batten, M and Reijers, ILM and Read, M and Silva, IP and Versluis, JM and Ribeiro, R and Angelatos, AS and Tan, J and Adhikari, C and Menzies, AM and Saw, RPM and Gonzalez, M and Shannon, KF and Spillane, AJ and Velickovic, R and Lazar, AJ and Damania, AV and Mishra, AK and Chelvanambi, M and Banerjee, A and Ajami, NJ and Wargo, JA and Macia, L and Holmes, AJ and Wilmott, JS and Blank, CU and Scolyer, RA and Long, GV},
title = {Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome.},
journal = {Nature medicine},
volume = {28},
number = {11},
pages = {2344-2352},
pmid = {36138151},
issn = {1546-170X},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Prospective Studies ; Immunotherapy/adverse effects ; *Melanoma/therapy ; Diet ; },
abstract = {The gut microbiota shapes the response to immune checkpoint inhibitors (ICIs) in cancer, however dietary and geographic influences have not been well-studied in prospective trials. To address this, we prospectively profiled baseline gut (fecal) microbiota signatures and dietary patterns of 103 trial patients from Australia and the Netherlands treated with neoadjuvant ICIs for high risk resectable metastatic melanoma and performed an integrated analysis with data from 115 patients with melanoma treated with ICIs in the United States. We observed geographically distinct microbial signatures of response and immune-related adverse events (irAEs). Overall, response rates were higher in Ruminococcaceae-dominated microbiomes than in Bacteroidaceae-dominated microbiomes. Poor response was associated with lower fiber and omega 3 fatty acid consumption and elevated levels of C-reactive protein in the peripheral circulation at baseline. Together, these data provide insight into the relevance of native gut microbiota signatures, dietary intake and systemic inflammation in shaping the response to and toxicity from ICIs, prompting the need for further studies in this area.},
}
@article {pmid36135386,
year = {2022},
author = {Mason, AR and McKee-Zech, HS and Hoeland, KM and Davis, MC and Campagna, SR and Steadman, DW and DeBruyn, JM},
title = {Body Mass Index (BMI) Impacts Soil Chemical and Microbial Response to Human Decomposition.},
journal = {mSphere},
volume = {7},
number = {5},
pages = {e0032522},
pmid = {36135386},
issn = {2379-5042},
support = {I01 BX000180/BX/BLRD VA/United States ; },
mesh = {Humans ; *Soil/chemistry ; *Soil Microbiology ; Body Mass Index ; Bacteria ; Cadaver ; },
abstract = {Microorganisms are key decomposers of vertebrate mortalities, breaking down body tissues and impacting decomposition progress. During human decomposition, both extrinsic environmental factors and intrinsic cadaver-related factors have the potential to impact microbial decomposers either directly or indirectly via altered physical or chemical conditions. While extrinsic factors (e.g., temperature, humidity) explain some variation in microbial response during human decomposition in terrestrial settings, recent work has noted that even under the same environmental conditions, individuals can have different decomposition patterns, highlighting the potential for intrinsic factors to impact microbial decomposers. The goal of this study was to investigate the effects of several intrinsic factors (age, sex, diseases at time of death, and body mass index [BMI]) on chemical and microbial changes in decomposition-impacted soils. In a field study conducted at the University of Tennessee Anthropology Research Facility, soils were collected from the decomposition-impacted area surrounding 19 deceased human individuals through the end of active decomposition. Soil physicochemical parameters were measured, and microbial (bacterial and fungal) communities were assessed via amplicon sequencing. BMI was shown to explain some variation in soil pH and microbial response to human decomposition. Hierarchical linear mixed (HLM) effects models revealed that BMI category significantly explained variation in pH response within decomposition-impacted soils over time (HLM F = 9.647; P < 0.001). Additionally, the relative abundance of soil Saccharomycetes in decomposition soils under underweight donors displayed little to no changes (mean maximum change in relative abundance, +6.6%), while all other BMI categories displayed an increased relative abundance of these organisms over time (normal, +50.6%; overweight, +64.4%; and obese, +64.6%) (HLM F = 3.441; P = 0.11). Together, these results reveal intrinsic factors influencing decomposition patterns, especially within the soil environment, and suggest BMI is an important factor for controlling decomposition processes. IMPORTANCE This work begins to address questions about interindividual variation in vertebrate decomposition attributed to intrinsic factors, that is, properties of the carcass or cadaver itself. Most research on factors affecting decomposition has focused on the extrinsic environment, such as temperature or humidity. While these extrinsic factors do explain some variation in decomposition patterns, interindividual variability is still observed. Understanding how intrinsic factors influence microbial decomposers will help reveal the ecological impacts of decomposition. This work also has forensic applications, as soil chemical and biological changes have been suggested as indicators of postmortem interval. We reveal factors that explain variation in the decomposition environment that should be considered in these estimates. This is particularly important as we consider the implications of variations in human populations due to diet, age, BMI, disease, toxicological loading, etc. on forensic investigations dealing with decomposing remains.},
}
@article {pmid36133177,
year = {2022},
author = {Villegas-Plazas, M and Villamil, L and Martínez-Silva, MA and González-Jiménez, T and Salazar, M and Güiza, L and Mendoza, M and Junca, H},
title = {Microbiome composition and autochthonous probiotics from contrasting probiosis/dysbiosis states in cobia (Rachycentron canadum) fish epitheliocystis.},
journal = {Access microbiology},
volume = {4},
number = {8},
pages = {acmi000405},
pmid = {36133177},
issn = {2516-8290},
abstract = {Microbiome components and bacterial isolates related to healthy and epitheliocystis states in aquaculture cycles of cobia fish were studied. We detected well-defined 16S rRNA amplicon gene sequence variants showing differential abundance in healthy or diseased cycles. Isolation trials were performed, and experimental tests were used to determine probiotic potential of the bacterial strains obtained from water, tissues or live food used in this aquaculture model. The taxonomic affiliation of these strains was cross-compared against microbiome components, finding that some of them had close or identical affiliation to the abundant types found in healthy cycles. Strains belonging to the groups already identified as predominant by culture-independent means were screened as potential probiotics based on desirable activities such as antagonism and antibiosis against marine pathogenic bacteria, quorum quenching, bile acid resistance, antibiotic sensitivity and enzymatic activities for improved nutrient digestion. We have also found that in the tracking of microbiome composition across different developmental stages of cobia, healthy cycles exhibited a consistent high relative abundance of a Mesobacillus sp., while in the diseased cycle the emergence of a Vibrio sp. was observed. Our study suggests that epithelocystis in cobia is associated with a displacement of a symbiotic microbiome community linked to the increase frequency of Vibrio species.},
}
@article {pmid36133174,
year = {2022},
author = {Beirne, C and McCann, E and McDowell, A and Miliotis, G},
title = {Genetic determinants of antimicrobial resistance in three multi-drug resistant strains of Cutibacterium acnes isolated from patients with acne: a predictive in silico study.},
journal = {Access microbiology},
volume = {4},
number = {8},
pages = {acmi000404},
pmid = {36133174},
issn = {2516-8290},
abstract = {OBJECTIVES: Using available whole genome data, the objective of this in silico study was to identify genetic mechanisms that could explain the antimicrobial resistance profile of three multi-drug resistant (MDR) strains (CA17, CA51, CA39) of the skin bacterium Cutibacterium acnes previously recovered from patients with acne. In particular, we were interested in detecting novel genetic determinants associated with resistance to fluoroquinolone and macrolide antibiotics that could then be confirmed experimentally.<br><br>METHODS: A range of open source bioinformatics tools were used to 'mine' genetic determinants of antimicrobial resistance and plasmid borne contigs, and to characterise the phylogenetic diversity of the MDR strains.<br><br>RESULTS: As probable mechanisms of resistance to fluoroquinolones, we identified a previously described resistance associated allelic variant of the gyrA gene with a 'deleterious' S101L mutation in type IA1 strains CA51 (ST1) and CA39 (ST1), as well as a novel E761R 'deleterious' mutation in the type II strain CA17 (ST153). A distinct genomic sequence of the efflux protein YfmO which is potentially associated with resistance to MLSB antibiotics was also present in CA17; homologues in CA51, CA39, and other strains of Cutibacterium acnes , were also found but differed in amino acid content. Strikingly, in CA17 we also identified a circular 2.7&#x2009;kb non-conjugative plasmid (designated pCA17) that closely resembled a 4.8&#x2009;kb plasmid (pYU39) from the MDR Salmonella enterica strain YU39.<br><br>CONCLUSIONS: This study has provided a detailed explanation of potential genetic determinants for MDR in the Cutibacterium acnes strains CA17, CA39 and CA51. Further laboratory investigations will be required to validate these in silico results, especially in relation to pCA17.},
}
@article {pmid36132223,
year = {2022},
author = {Yanez-Montalvo, A and Aguila, B and Gómez-Acata, ES and Guerrero-Jacinto, M and Oseguera, LA and Falcón, LI and Alcocer, J},
title = {Shifts in water column microbial composition associated to lakes with different trophic conditions: "Lagunas de Montebello" National Park, Chiapas, México.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13999},
pmid = {36132223},
issn = {2167-8359},
mesh = {*Lakes/analysis ; Ecosystem ; Chlorophyll A ; Mexico ; RNA, Ribosomal, 16S/genetics ; Parks, Recreational ; *Cyanobacteria/genetics ; },
abstract = {Eutrophication is a global problem causing the reduction of water quality and the loss of ecosystem goods and services. The lakes of the "Lagunas de Montebello" National Park (LMNP), Chiapas, Mexico, not only represent unique and beautiful natural scenic sites in southern Mexico but are also a national protected area and RAMSAR site. Unfortunately, some of these lakes started showing eutrophication signs since 2003. Anthropogenic activities (e.g., land-use change from forested to agricultural and urban development) are leading to water quality and trophic state alterations of the lakes of the LMNP. This study shows the results of a coupled limnological characterization and high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene to analyze the microbial composition of the water column in a set of oligotrophic and eutrophic lakes. Chlorophyll a (Chl-a) was the main environmental parameter correlated with the trophic conditions of the lakes. Although the microbial diversity was similar, the microbial composition changed significantly from oligo to eutrophic lakes. Proteobacteria, Firmicutes, and Cyanobacteria were the main components of oligotrophic lakes, and Cyanobacteria, Proteobacteria, and Bacteroidetes of eutrophic lakes. While Acinetobacter (Proteobacteria) and Cyanobium (a unicellular cyanobacterium) dominated in oligotrophic lakes, the filamentous, bloom-forming, and toxin-producing cyanobacteria Planktothrix was the dominant genus in eutrophic lakes. High-throughput sequencing allowed the detection of changes in the composition of the microbial component in oligotrophic lakes, suggesting a shift towards eutrophication, highlighting the relevance of sensitive monitoring protocols of these ecosystems to implement remediation programs for eutrophicated lakes and conservation strategies for those yet pristine.},
}
@article {pmid36130296,
year = {2022},
author = {Kerr, BJ and Trachsel, JM and Bearson, BL and Loving, CL and Bearson, SMD and Byrne, KA and Pearce, SC and Ramirez, SM and Gabler, NK and Schweer, WP and Helm, ET and De Mille, CM},
title = {Evaluation of digestively resistant or soluble fibers, short- and medium-chain fatty acids, trace minerals, and antibiotics in nonchallenged nursery pigs on performance, digestibility, and intestinal integrity.},
journal = {Journal of animal science},
volume = {100},
number = {11},
pages = {},
pmid = {36130296},
issn = {1525-3163},
mesh = {Swine ; Animals ; *Animal Nutritional Physiological Phenomena ; Animal Feed/analysis ; Digestion ; *Trace Elements/pharmacology ; Anti-Bacterial Agents/pharmacology ; Diet/veterinary ; Zea mays ; Fatty Acids, Volatile/pharmacology ; Starch/pharmacology ; Butyrates/pharmacology ; },
abstract = {Three experiments (EXP) were conducted to determine the effect of feed additives on performance, intestinal integrity, gastrointestinal volatile fatty acids (VFA), and energy and nutrient digestion in nonchallenged nursery pigs. In EXP 1, 480 pigs (6.36-kg body weight, BW) were placed into 96 pens with 5 pigs/pen, and allotted to 1 of 10 dietary treatments: 1) negative control containing no feed additive (NC), 2) NC + 44 mg chlortetracycline and 38.5 mg tiamulin/kg diet (CTsb), 3) NC + 5% resistant potato starch (RSpo), 4) NC + 5% soluble corn fiber (SCF), 5) NC + 5% sugar beet pulp (SBP), 6) NC + 0.30% fatty acid mix (FAM), 7) NC + 0.10% phytogenic blend of essential oils and flavoring compounds (PHY), 8) NC + 50 mg Cu and 1,600 mg zinc oxide/kg diet (CuZn), 9) NC + 5% resistant corn starch (RScn), and 10) NC + 0.05% β-glucan (BG) for 28 d. There was no impact of dietary treatment on BW gain or feed intake (P ≥ 0.22). Pigs fed diets containing SCF, CTsb, and RSpo resulted in microbial community differences compared to pigs fed the NC (P < 0.05). In EXP 2, 48 barrows (12.8 kg BW) were selected at the end of EXP 1 and fed the same dietary treatments they had previously received: 1) NC, 2) NC + 5% RScn, 3) NC + 5% SCF, and 4) NC + FAM for 8 d. There was no effect of feeding diets containing RScn, SCF, or FAM on in vivo intestinal permeability (P ≤ 0.21). Ileal or colon pH, concentrations of VFA did not differ due to dietary treatment (P ≥ 0.36), but pigs fed diets containing FAM resulted in a greater butyric acid concentration in the cecum compared to pigs fed the NC (P ≤ 0.05). In EXP 3, 156 pigs (6.11 kg BW) were placed into 52 pens with 3 pigs/pen and allotted to 1 of 4 dietary treatments arranged in a factorial manner: 1) NC, 2) NC + 5% RSpo, 3) NC + 0.30% FAM, and 4) NC + 5% RSpo + 0.30% FAM for 24 d. Feeding pigs diets containing RSpo did not affect BW gain (P = 0.91) while pigs fed diets containing FAM grew improved BW gain (P = 0.09). Colonic butyric acid concentrations were greater in pigs fed diets containing RSpo (P = 0.03), while pigs fed diets containing FAM exhibited reduced total VFA concentrations (P = 0.11). The results indicate that supplementing diets with digestively resistant but fermentable fibers, short- and medium-chain fatty acids, or antibiotics do not have a consistent effect, positive or negative, on markers of intestinal integrity or barrier function, intestinal VFA patterns, ATTD of energy and nutrients, or on pig performance.},
}
@article {pmid36128567,
year = {2022},
author = {El Amrani, B},
title = {Aspects of the rhizospheric microbiota and their interactions with the soil ecosystem.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {26},
number = {5},
pages = {442-448},
doi = {10.18699/VJGB-22-54},
pmid = {36128567},
issn = {2500-0462},
abstract = {Soil microbial communities play a key role in the evolution of the rhizosphere. In addition, proper exploration of these microbial resources represents a promising strategy that guarantees the health and sustainability of all ecosystems connected to the ground. Under the inf luence of environmental conditions, microbial communities can change compositions in terms of abundance and diversity. Beyond the descriptive level, the current orientation of microbial ecology is to link these structures to the functioning of ecosystems; specif ically, to understand the effect of environmental factors on the functional structure of microbial communities in ecosystems. This review focuses on the main interactions between the indigenous soil microf lora and the major constituents of the rhizosphere to understand, on the one hand, how microbial biodiversity can improve plant growth and maintain homeostasis of the rhizospheric ecosystem, on the other hand, how the maintenance and enrichment of plant biodiversity can contribute to the conservation of soil microbial diversity; knowing that these microorganisms are also controlled by the abiotic properties of the soil. Overall, understanding the dynamics of the rhizosphere microbiome is essential for developing innovative strategies in the f ield of protecting and maintaining the proper functioning of the soil ecosystem.},
}
@article {pmid36128049,
year = {2022},
author = {Külekci, B and Schwarz, S and Brait, N and Perkmann-Nagele, N and Jaksch, P and Hoetzenecker, K and Puchhammer-Stöckl, E and Goerzer, I},
title = {Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation.},
journal = {Virus evolution},
volume = {8},
number = {2},
pages = {veac076},
pmid = {36128049},
issn = {2057-1577},
support = {P 31503/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Mixed human cytomegalovirus (HCMV) strain infections are frequent in lung transplant recipients (LTRs). To date, the influence of the donor (D) and recipient (R) HCMV serostatus on intra-host HCMV strain composition and viral population dynamics after transplantation is only poorly understood. Here, we investigated ten pre-transplant lungs from HCMV-seropositive donors and 163 sequential HCMV-DNA-positive plasma and bronchoalveolar lavage samples from fifty LTRs with multiviremic episodes post-transplantation. The study cohort included D+R+ (38 per cent), D+R- (36 per cent), and D-R+ (26 per cent) patients. All samples were subjected to quantitative genotyping by short amplicon deep sequencing, and twenty-four of them were additionally PacBio long-read sequenced for genotype linkages. We find that D+R+ patients show a significantly elevated intra-host strain diversity compared to D+R- and D-R+ patients (P = 0.0089). Both D+ patient groups display significantly higher viral population dynamics than D- patients (P = 0.0061). Five out of ten pre-transplant donor lungs were HCMV DNA positive, whereof three multiple HCMV strains were detected, indicating that multi-strain transmission via lung transplantation is likely. Using long reads, we show that intra-host haplotypes can share distinctly linked genotypes, which limits overall intra-host diversity in mixed infections. Together, our findings demonstrate donor-derived strains as the main source of increased HCMV strain diversity and dynamics post-transplantation. These results foster strategies to mitigate the potential transmission of the donor strain reservoir to the allograft, such as ex vivo delivery of HCMV-selective immunotoxins prior to transplantation to reduce latent HCMV.},
}
@article {pmid36126627,
year = {2022},
author = {Xu, G and He, J},
title = {Resilience of organohalide-detoxifying microbial community to oxygen stress in sewage sludge.},
journal = {Water research},
volume = {224},
number = {},
pages = {119055},
doi = {10.1016/j.watres.2022.119055},
pmid = {36126627},
issn = {1879-2448},
mesh = {Bacteria/chemistry ; Biodegradation, Environmental ; *Chloroflexi/genetics ; *Environmental Pollutants ; Halogenated Diphenyl Ethers ; Humans ; *Microbiota ; Oxygen ; Sewage ; *Tetrachloroethylene ; },
abstract = {Organohalide pollutants are prevalent in the environment, causing harms to wildlife and human. Organohalide-respiring bacteria (OHRB) could detoxify these pollutants in anaerobic environments, but the most competent OHRB (i.e., Dehalococcoides) is susceptible to oxygen. This study reports exceptional resistance and resilience of sewage sludge microbial communities to oxygen stress for attenuation of structurally distinct organohalide pollutants, including tetrachloroethene, tetrabromobisphenol A, and polybrominated diphenyl ethers. The dehalogenation rate constant of these organohalide pollutants in oxygen-exposed sludge microcosms was maintained as 74-120% as that in the control without oxygen exposure. Subsequent top-down experiments clarified that sludge flocs and non-OHRB contributed to alleviating oxygen stress on OHRB. In the dehalogenating microcosms, multiple OHRB (Dehahlococcoides, Dehalogenimonas, and Sulfurospirillum) harboring distinct reductive dehalogenase genes (pceA, pteA, tceA, vcrA, and bdeA) collaborated to detoxify organohalide pollutants but responded differentially to oxygen stress. Comprehensive microbial community analyses (taxonomy, diversity, and structure) demonstrated certain resilience of the sludge-derived dehalogenating microbial communities to oxygen stress. Additionally, microbial co-occurrence networks were intensified by oxygen stress in most microcosms, as a possible stress mitigation strategy. Altogether the mechanistic and ecological findings in this study contribute to remediation of organohalide-contaminated sites encountering oxygen disturbance.},
}
@article {pmid36123806,
year = {2022},
author = {Zhang, Y and Yang, X and Van de Peer, Y and Chen, J and Marchal, K and Shi, T},
title = {Evolution of isoform-level gene expression patterns across tissues during lotus species divergence.},
journal = {The Plant journal : for cell and molecular biology},
volume = {112},
number = {3},
pages = {830-846},
pmid = {36123806},
issn = {1365-313X},
support = {833522/ERC_/European Research Council/International ; },
mesh = {*Lotus/genetics ; Gene Duplication ; Genes, Duplicate ; Protein Isoforms/genetics ; *Arabidopsis/genetics ; *Nelumbo/genetics ; Gene Expression ; Evolution, Molecular ; },
abstract = {Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contributions of the two key mechanisms to the evolution of gene function are largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea and Nelumbo nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms of local, small-scale duplicates, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection pressure for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contributed to the diversity of gene function during the evolution of lotus.},
}
@article {pmid36123554,
year = {2023},
author = {Xu, MP and Zhi, RC and Jian, JN and Feng, YZ and Han, XH and Zhang, W},
title = {Changes in Soil Organic C Fractions and C Pool Stability Are Mediated by C-Degrading Enzymes in Litter Decomposition of Robinia pseudoacacia Plantations.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1189-1199},
pmid = {36123554},
issn = {1432-184X},
mesh = {*Soil/chemistry ; Ecosystem ; *Robinia ; Carbon/metabolism ; Lignin/metabolism ; Cellulose/metabolism ; Hydrolases/metabolism ; Soil Microbiology ; Oxidoreductases ; Forests ; China ; },
abstract = {Litter decomposition is the main source of soil organic carbon (SOC) pool, regarding as an important part of terrestrial ecosystem C dynamics. The turnover of SOC is mainly regulated by extracellular enzymes secreted by microorganisms. However, the response mechanism of soil C-degrading enzymes and SOC in litter decomposition remains unclear. To clarify how SOC fraction dynamics respond to C-degrading enzymes in litter decomposition, we used field experiments to collect leaf litter and SOC fractions from the underlying layer in Robinia pseudoacacia plantations on the Loess Plateau. Our results showed that SOC, easily oxidizable organic C, dissolved organic C, and microbial biomass C increased significantly during the decomposition process. Litter decomposition significantly decreased soil hydrolase activity, but slightly increased oxidase activity. Correlation analysis results showed that SOC fractions were significantly positively correlated with the litter mass, lignin, soil moisture, and oxidase activity, but significantly negatively correlated with cellulose content and soil pH. Partial least squares path models revealed that soil C-degrading enzymes can directly or indirectly affect the changes of soil C fractions. The most direct factors affecting the SOC fractions of topsoil during litter decomposition were litter lignin and cellulose degradation, soil pH, and C-degrading enzymes. Furthermore, regression analysis showed that the decrease of SOC stability in litter decomposition was closely related to the decrease of soil hydrolase to oxidase ratio. These results highlighted that litter degradation-induced changes in C-degrading enzyme activity significantly affected SOC fractions. Furthermore, the distribution of soil hydrolases and oxidases affected the stability of SOC during litter decomposition. These findings provided a theoretical framework for a more comprehensive understanding of C turnover and stabilization mechanisms between plant and soil.},
}
@article {pmid36123442,
year = {2022},
author = {Hedlund, BP and Chuvochina, M and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, IC and Venter, SN and Whitman, WB},
title = {SeqCode: a nomenclatural code for prokaryotes described from sequence data.},
journal = {Nature microbiology},
volume = {7},
number = {10},
pages = {1702-1708},
pmid = {36123442},
issn = {2058-5276},
mesh = {*Metagenome ; *Prokaryotic Cells ; },
abstract = {Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.},
}
@article {pmid36122204,
year = {2022},
author = {Peng, R and Xu, Y and Tian, S and Unver, T and Liu, Z and Zhou, Z and Cai, X and Wang, K and Wei, Y and Liu, Y and Wang, H and Hu, G and Zhang, Z and Grover, CE and Hou, Y and Wang, Y and Li, P and Wang, T and Lu, Q and Wang, Y and Conover, JL and Ghazal, H and Wang, Q and Zhang, B and Van Montagu, M and Van de Peer, Y and Wendel, JF and Liu, F},
title = {Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {39},
pages = {e2208496119},
pmid = {36122204},
issn = {1091-6490},
mesh = {Cotton Fiber ; *Evolution, Molecular ; Genetic Variation/genetics ; *Genome, Plant/genetics ; *Gossypium/classification/genetics ; Isomerases/genetics/metabolism ; Tetraploidy ; },
abstract = {Allotetraploid cotton (Gossypium) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD)6, Ge] and Gossypium stephensii [(AD)7, Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)1, Ghp]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs, Ge, and domesticated G. hirsutum. We describe genomic structural variation that arose during Gossypium evolution and describe its correlates-including phenotypic differentiation, genetic isolation, and genetic convergence-that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.},
}
@article {pmid36118848,
year = {2022},
author = {Rabapane, KJ and Ijoma, GN and Matambo, TS},
title = {Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {946449},
pmid = {36118848},
issn = {1664-8021},
abstract = {Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.},
}
@article {pmid36113308,
year = {2022},
author = {Alves, KJ and Pylro, VS and Nakayama, CR and Vital, VG and Taketani, RG and Santos, DG and Rodrigues, JLM and Tsai, SM and Andreote, FD},
title = {Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change.},
journal = {Microbiological research},
volume = {265},
number = {},
pages = {127178},
doi = {10.1016/j.micres.2022.127178},
pmid = {36113308},
issn = {1618-0623},
mesh = {Archaea ; Bacteria ; Brazil ; *Euryarchaeota/genetics ; *Greenhouse Gases/analysis/metabolism ; Methane ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Amazonian forest conversion into agricultural and livestock areas is considered one of the activities that contribute most to the emission of greenhouse gases, including methane. Biogenic methane production is mainly performed by methanogenic Archaea, which underscores the importance of understanding the drivers shaping microbial communities involved in the methane cycling and changes in methane metabolism. Here, we aimed to investigate the composition and structure of bacterial and archaeal communities in tropical soils in response to land-use changes, emphasizing the methanogenic communities. We collected soil samples from primary forest, pasture, and secondary forest of the Amazonian region and used a strategy based on the enrichment of the methanogenic community with three different methanogenic substrates followed by measurements of methane emission, quantification of mcrA gene copies by qPCR, and total 16 S rRNA gene sequencing (metataxonomics). We observed variations in the structure of bacterial and archaeal communities of soils under different uses. The richness of methanogenic communities was higher in pasture than forest soils and this richness remained during the incubation period, and as a consequence, the enrichment induced earlier methane emission in pastures-derived samples. Furthermore, pastures enrichments exhibited methanogenic archaea networks more complex than primary and secondary forests. In conclusion, pastures harbor a richer and more responsive methanogenic community than forest samples, suggesting that conversion of forest areas to pasture may boost methane emission.},
}
@article {pmid36112603,
year = {2022},
author = {Miller, JC and Satheesh Babu, AK and Petersen, C and Wankhade, UD and Robeson, MS and Putich, MN and Mueller, JE and O'Farrell, AS and Cho, JM and Chintapalli, SV and Jalili, T and Symons, JD and Anandh Babu, PV},
title = {Gut Microbes Are Associated with the Vascular Beneficial Effects of Dietary Strawberry on Metabolic Syndrome-Induced Vascular Inflammation.},
journal = {Molecular nutrition &amp; food research},
volume = {66},
number = {22},
pages = {e2200112},
pmid = {36112603},
issn = {1613-4133},
support = {R03 AG052848/AG/NIA NIH HHS/United States ; R01 AT010247/AT/NCCIH NIH HHS/United States ; R01 HL141540/HL/NHLBI NIH HHS/United States ; P30 DK020579/DK/NIDDK NIH HHS/United States ; R03AGO52848/HL/NHLBI NIH HHS/United States ; },
mesh = {Male ; Mice ; Animals ; *Fragaria/chemistry ; *Metabolic Syndrome/etiology/drug therapy ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Inflammation ; },
abstract = {SCOPE: Metabolic syndrome (MetS) alters the gut microbial ecology and increases the risk of cardiovascular disease. This study investigates whether strawberry consumption reduces vascular complications in an animal model of MetS and identifies whether this effect is associated with changes in the composition of gut microbes.<br><br>METHODS AND RESULTS: Seven-week-old male mice consume diets with 10% (C) or 60% kcal from fat (high-fat diet fed mice; HF) for 12 weeks and subgroups are fed a 2.35% freeze-dried strawberry supplemented diet (C+SB or HF+SB). This nutritional dose is equivalent to &#x2248;160 g of strawberry. After 12 weeks treatment, vascular inflammation is enhanced in HF versus C mice as shown by an increased monocyte binding to vasculature, elevated serum chemokines, and increased mRNA expression of inflammatory molecules. However, strawberry supplementation suppresses vascular inflammation in HF+SB versus HF mice. Metabolic variables, blood pressure, and indices of vascular function were similar among the groups. Further, the abundance of opportunistic microbe is decreased in HF+SB. Importantly, circulating chemokines are positively associated with opportunistic microbes and negatively associated with the commensal microbes (Bifidobacterium and Facalibaculum).<br><br>CONCLUSION: Dietary strawberry decreases the abundance of opportunistic microbe and this is associated with a decrease in vascular inflammation resulting from MetS.},
}
@article {pmid36112501,
year = {2023},
author = {Abdel-Rahman, LIH and Morgan, XC},
title = {Searching for a Consensus Among Inflammatory Bowel Disease Studies: A Systematic Meta-Analysis.},
journal = {Inflammatory bowel diseases},
volume = {29},
number = {1},
pages = {125-139},
pmid = {36112501},
issn = {1536-4844},
mesh = {Humans ; *Colitis, Ulcerative/pathology ; Consensus ; *Inflammatory Bowel Diseases ; *Crohn Disease/pathology ; Feces ; },
abstract = {BACKGROUND: Numerous studies have examined the gut microbial ecology of patients with Crohn's disease (CD) and ulcerative colitis, but inflammatory bowel disease-associated taxa and ecological effect sizes are not consistent between studies.<br><br>METHODS: We systematically searched PubMed and Google Scholar and performed a meta-analysis of 13 studies to analyze how variables such as sample type (stool, biopsy, and lavage) affect results in inflammatory bowel disease gut microbiome studies, using uniform bioinformatic methods for all primary data.<br><br>RESULTS: Reduced alpha diversity was a consistent feature of both CD and ulcerative colitis but was more pronounced in CD. Disease contributed significantly variation in beta diversity in most studies, but effect size varied, and the effect of sample type was greater than the effect of disease. Fusobacterium was the genus most consistently associated with CD, but disease-associated genera were mostly inconsistent between studies. Stool studies had lower heterogeneity than biopsy studies, especially for CD.<br><br>CONCLUSIONS: Our results indicate that sample type variation is an important contributor to study variability that should be carefully considered during study design, and stool is likely superior to biopsy for CD studies due to its lower heterogeneity.},
}
@article {pmid36112189,
year = {2023},
author = {Peralta-Maraver, I and Rutere, C and Horn, MA and Reche, I and Behrends, V and Reiss, J and Robertson, AL},
title = {Intermediate Levels of Predation and Nutrient Enrichment Enhance the Activity of Ibuprofen-Degrading Bacteria.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1438-1441},
pmid = {36112189},
issn = {1432-184X},
support = {641939//Horizon 2020 Framework Programme/ ; },
mesh = {Animals ; *Ecosystem ; *Food Chain ; Ibuprofen/metabolism ; Predatory Behavior ; Bacteria/metabolism ; },
abstract = {Water is the most indispensable natural resource; yet, organic pollution of freshwater sources is widespread. In recent years, there has been increasing concern over the vast array of emerging organic contaminants (EOCs) in the effluent of wastewater treatment plants (WWTPs). Several of these EOCs are degraded within the pore space of riverbeds by active microbial consortia. However, the mechanisms behind this ecosystem service are largely unknown. Here, we report how phosphate concentration and predator-prey interactions drive the capacity of bacteria to process a model EOC (ibuprofen). The presence of phosphate had a significant positive effect on the population growth rate of an ibuprofen-degrading strain. Thus, when phosphate was present, ibuprofen removal efficiency increased. Moreover, low and medium levels of predation, by a ciliated protozoan, stimulated bacterial population growth. This unimodal effect of predation was lost under high phosphate concentration, resulting in the flattening of the relationships between predator density and population growth of ibuprofen degraders. Our results suggest that moderate nutrient and predation levels promote the growth rate of bacterial degraders and, consequently, the self-purifying capability of the system. These findings enhance our understanding of the mechanisms by which riverbed communities drive the processing of EOCs.},
}
@article {pmid36111808,
year = {2022},
author = {Marzorati, M and Bubeck, S and Bayne, T and Krishnan, K and Giusto, M},
title = {Effects of combined prebiotic, probiotic, IgG and amino acid supplementation on the gut microbiome of patients with inflammatory bowel disease.},
journal = {Future microbiology},
volume = {17},
number = {},
pages = {1307-1324},
doi = {10.2217/fmb-2022-0066},
pmid = {36111808},
issn = {1746-0921},
mesh = {Amino Acids ; Caco-2 Cells ; Dietary Supplements ; Fatty Acids, Volatile/pharmacology ; Flavonoids ; *Gastrointestinal Microbiome ; Humans ; Immunoglobulin G ; *Inflammatory Bowel Diseases/drug therapy ; Interleukin-10 ; Interleukin-6 ; Prebiotics ; *Probiotics/pharmacology ; },
abstract = {Background: The effects of the Total Gut Restoration (TGR) system supplementation on the gut microbiome were evaluated. Materials &amp; methods: A mucosal in vitro simulation of the human gastrointestinal tract (M-SHIME[®]) system was inoculated with fecal samples from patients with inflammatory bowel disease. Chambers were supplemented for 5 days with the TGR system (five probiotic Bacillus strains, prebiotic mixture, immunoglobulin concentrate, amino acids and prebiotic flavonoids). Results: Compared with unsupplemented controls, supplementation was associated with a significant increase in short-chain fatty acid production, and changes to the microbiome were observed. Supernatants from supplemented chambers improved intestinal barrier function, increased IL-6 and IL-10 production and decreased MCP1 production versus control in Caco-2/THP1 coculture. Conclusion: Daily TGR supplementation facilitated changes to the gut microbiome of patients with inflammatory bowel disease.},
}
@article {pmid36110415,
year = {2022},
author = {Song, W and Gong, H and Wang, Q and Zhang, L and Qiu, L and Hu, X and Han, H and Li, Y and Li, R and Li, Y},
title = {Using Bayesian networks with Max-Min Hill-Climbing algorithm to detect factors related to multimorbidity.},
journal = {Frontiers in cardiovascular medicine},
volume = {9},
number = {},
pages = {984883},
pmid = {36110415},
issn = {2297-055X},
abstract = {OBJECTIVES: Multimorbidity (MMD) is a medical condition that is linked with high prevalence and closely related to many adverse health outcomes and expensive medical costs. The present study aimed to construct Bayesian networks (BNs) with Max-Min Hill-Climbing algorithm (MMHC) algorithm to explore the network relationship between MMD and its related factors. We also aimed to compare the performance of BNs with traditional multivariate logistic regression model.<br><br>METHODS: The data was downloaded from the Online Open Database of CHARLS 2018, a population-based longitudinal survey. In this study, we included 10 variables from data on demographic background, health status and functioning, and lifestyle. Missing value imputation was first performed using Random Forest. Afterward, the variables were included into logistic regression model construction and BNs model construction. The structural learning of BNs was achieved using MMHC algorithm and the parameter learning was conducted using maximum likelihood estimation.<br><br>RESULTS: Among 19,752 individuals (9,313 men and 10,439 women) aged 64.73 &#xb1; 10.32 years, there are 9,129 ones without MMD (46.2%) and 10,623 ones with MMD (53.8%). Logistic regression model suggests that physical activity, sex, age, sleep duration, nap, smoking, and alcohol consumption are associated with MMD (P < 0.05). BNs, by establishing a complicated network relationship, reveals that age, sleep duration, and physical activity have a direct connection with MMD. It also shows that education levels are indirectly connected to MMD through sleep duration and residence is indirectly linked to MMD through sleep duration.<br><br>CONCLUSION: BNs could graphically reveal the complex network relationship between MMD and its related factors, outperforming traditional logistic regression model. Besides, BNs allows for risk reasoning for MMD through Bayesian reasoning, which is more consistent with clinical practice and thus holds some application prospects.},
}
@article {pmid36108399,
year = {2022},
author = {Sun, H and Xia, J and Wu, B and Ren, H and Zhang, X and Ye, L},
title = {Aerobic starvation treatment of activated sludge enhances the degradation efficiency of refractory organic compounds.},
journal = {Water research},
volume = {224},
number = {},
pages = {119069},
doi = {10.1016/j.watres.2022.119069},
pmid = {36108399},
issn = {1879-2448},
mesh = {Benzhydryl Compounds ; Bioreactors/microbiology ; Fluorocarbons ; Gabapentin ; Humans ; Phenols ; RNA, Ribosomal, 16S/genetics ; *Sewage/chemistry ; *Wastewater ; },
abstract = {Many refractory organic compounds (ROCs) in wastewater are toxic to human and aquatic organisms. Here, we reported an aerobic starvation approach to improve the degradation efficiencies of ROCs in activated sludge systems. The highest degradation rates of bisphenol AF (BPAF) (11.4 mg/g VSS · h) and gabapentin (GBP) (8.9 mg/g VSS · h) were achieved on the second day of the starvation process. While, the degradation rate of bisphenol A (BPA) on the 43rd day reached the maximum value of 0.8 mg/g VSS ·h, which was significantly higher than that of the seeding sludge (0.01 mg/g VSS · h). To investigate the mechanisms of this finding, we applied magnetic-nanoparticle mediated isolation, 16S rRNA gene sequencing, metagenomic sequencing and metatranscriptomic sequencing to analyze the microbial community structures and functions during the starvation process. The results showed that the increase of the BPA degradation ability was caused by the increase of the relative abundance of BPA degrading bacteria (Sphingomonas, Achromobacter, etc.), while, the enhancement of BPAF and GBP degradation was attributed to the increase of the expression of ROC degrading genes. Overall, these results improve our understanding of the microbial ecology of starved activated sludge and provide useful information for the future development of ROC removal technologies.},
}
@article {pmid36106503,
year = {2023},
author = {Law, CKY and Bolea-Fernandez, E and Liu, T and Bonin, L and Wallaert, E and Verbeken, K and De Gusseme, B and Vanhaecke, F and Boon, N},
title = {The influence of H2 partial pressure on biogenic palladium nanoparticle production assessed by single-cell ICP-mass spectrometry.},
journal = {Microbial biotechnology},
volume = {16},
number = {5},
pages = {901-914},
pmid = {36106503},
issn = {1751-7915},
mesh = {*Metal Nanoparticles ; Palladium ; Partial Pressure ; Mass Spectrometry/methods ; Spectrum Analysis ; },
abstract = {The production of biogenic palladium nanoparticles (bio-Pd NPs) is widely studied due to their high catalytic activity, which depends on the size of nanoparticles (NPs). Smaller NPs (here defined as <100 nm) are more efficient due to their higher surface/volume ratio. In this work, inductively coupled plasma-mass spectrometry (ICP-MS), flow cytometry (FCM) and transmission electron microscopy (TEM) were combined to obtain insight into the formation of these bio-Pd NPs. The precipitation of bio-Pd NPs was evaluated on a cell-per-cell basis using single-cell ICP-MS (SC-ICP-MS) combined with TEM images to assess how homogenously the particles were distributed over the cells. The results provided by SC-ICP-MS were consistent with those provided by "bulk" ICP-MS analysis and FCM. It was observed that heterogeneity in the distribution of palladium over an entire cell population is strongly dependent on the Pd[2+] concentration, biomass and partial H2 pressure. The latter three parameters affected the particle size, ranging from 15.6 to 560 nm, and exerted a significant impact on the production of the bio-Pd NPs. The TEM combined with SC-ICP-MS revealed that the mass distribution for bacteria with high Pd content (144 fg Pd cell[-1]) indicated the presence of a large number of very small NPs (D50 = 15.6 nm). These results were obtained at high cell density (1 × 10[5] ± 3 × 10[4] cells μl[-1]) and H2 partial pressure (180 ml H2). In contrast, very large particles (D50 = 560 nm) were observed at low cell density (3 × 10[4] ± 10 × 10[2] cells μl[-1]) and H2 partial pressure (10-100 ml H2). The influence of the H2 partial pressure on the nanoparticle size and the possibility of size-tuned nanoparticles are presented.},
}
@article {pmid36106339,
year = {2022},
author = {Van Wyk, JC and Sewell, BT and Danson, MJ and Tsekoa, TL and Sayed, MF and Cowan, DA},
title = {Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase.},
journal = {Current research in structural biology},
volume = {4},
number = {},
pages = {256-270},
pmid = {36106339},
issn = {2665-928X},
abstract = {Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4-7.6 kJ/mol increase in the activation energy of thermal inactivation at 63 °C. High resolution X-ray crystal structures (1.15-1.80 Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising.},
}
@article {pmid36102128,
year = {2023},
author = {Sampson, MM and Polk, CM and Fairman, RT and DeWitt, ME and Leonard, MK and Davidson, L and McCurdy, L and Passaretti, CL},
title = {Monkeypox testing delays: The need for drastic expansion of education and testing for monkeypox virus.},
journal = {Infection control and hospital epidemiology},
volume = {44},
number = {2},
pages = {348-349},
doi = {10.1017/ice.2022.237},
pmid = {36102128},
issn = {1559-6834},
mesh = {Humans ; *Monkeypox virus ; *Mpox (monkeypox) ; Educational Status ; },
}
@article {pmid36100598,
year = {2022},
author = {Metz, S and Huber, P and Mateus-Barros, E and Junger, PC and de Melo, M and Bagatini, IL and Izaguirre, I and Câmara Dos Reis, M and Llames, ME and Accattatis, V and Quiroga, MV and Devercelli, M and Schiaffino, MR and Niño-García, JP and Bastidas Navarro, M and Modenutti, B and Vieira, H and Saraceno, M and Sabio Y García, CA and Pereira, E and González-Revello, A and Piccini, C and Unrein, F and Alonso, C and Sarmento, H},
title = {A georeferenced rRNA amplicon database of aquatic microbiomes from South America.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {565},
pmid = {36100598},
issn = {2052-4463},
mesh = {Bacteria/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; South America ; Water Microbiology ; },
abstract = {The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.},
}
@article {pmid36100325,
year = {2022},
author = {Xu, Q and Vandenkoornhuyse, P and Li, L and Guo, J and Zhu, C and Guo, S and Ling, N and Shen, Q},
title = {Microbial generalists and specialists differently contribute to the community diversity in farmland soils.},
journal = {Journal of advanced research},
volume = {40},
number = {},
pages = {17-27},
pmid = {36100325},
issn = {2090-1224},
mesh = {Bacteria ; *Ecosystem ; Farms ; *Soil ; Soil Microbiology ; },
abstract = {INTRODUCTION: Microbial generalists and specialists are thought to have distinct impacts on community dynamics, while there have been limited efforts to estimate their contribution to microbial diversity.<br><br>OBJECTIVES: We aimed to resolve this research gap in microbial ecology to strengthen our understanding of the biogeography of microbial diversity, with implications for global-scale biodiversity mapping.<br><br>METHODS: Herein, we identified the ecological characteristics of microbial generalists and specialists across over 3,000 farmland soil samples from eleven countries that encompassed seven climate types.<br><br>RESULTS: Considering the distinct distributions of generalists and specialists in degree of connexions, betweenness and as key species in network topology, both generalists and specialists contributed to species interactions, though through different modalities. A stronger signature of deterministic processes in specialists indicated their lower tolerance to environment fluctuations. Generalists, in contrast, were more characterized by stochastic processes with higher diversification and transition rates that suggested more important roles in maintaining community stability when exposed to environmental disturbances. The relationship between latitude and diversity combining with distance-decay effects showed that generalists dampened microbial biogeographical patterns, with contrasting impacts by specialists.<br><br>CONCLUSION: By demonstrating the ecological characteristics of microbial generalists and specialists, this study deepens our understanding of microbial diversity and highlights the need to impart systematic distinctions among different categories of species when modelling and predicting the fate of ecosystems in the face of global climate change, rather than assuming that species are functionally equivalent.},
}
@article {pmid36098749,
year = {2023},
author = {Angelella, G and Nalam, V and Nachappa, P and White, J and Kaplan, I},
title = {Correction to: Endosymbionts Differentially Alter Exploratory Probing Behavior of a Nonpersistent Plant Virus Vector.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1453},
doi = {10.1007/s00248-022-02107-4},
pmid = {36098749},
issn = {1432-184X},
}
@article {pmid36094300,
year = {2022},
author = {Brugiroux, S and Berry, D and Ring, D and Barnich, N and Daims, H and Stecher, B},
title = {Specific Localization and Quantification of the Oligo-Mouse-Microbiota (OMM[12]) by Fluorescence In Situ Hybridization (FISH).},
journal = {Current protocols},
volume = {2},
number = {9},
pages = {e548},
doi = {10.1002/cpz1.548},
pmid = {36094300},
issn = {2691-1299},
mesh = {Animals ; In Situ Hybridization, Fluorescence/methods ; Mice ; *Microbiota ; Oligonucleotide Probes ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The oligo-mouse-microbiota (OMM[12]) is a widely used syncom that colonizes gnotobiotic mice in a stable manner. It provides several fundamental functions to its murine host, including colonization resistance against enteric pathogens. Here, we designed and validated specific fluorescence in situ hybridization (FISH) probes to detect and quantify OMM[12] strains on intestinal tissue cross sections. 16S rRNA-specific probes were designed, and specificity was validated on fixed pure cultures. A hybridization protocol was optimized for sensitive detection of the individual bacterial cells in cryosections. Using this method, we showed that the intestinal mucosal niche of Akkermansia muciniphila can be influenced by global gut microbial community context. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Localization and quantification of OMM[12] single strains in mouse cecum cross section Support Protocol: Establishment of specific FISH probe set for OMM[12] syncom.},
}
@article {pmid36087683,
year = {2022},
author = {Yaigoub, H and Fath, N and Tirichen, H and Wu, C and Li, R and Li, Y},
title = {Bidirectional crosstalk between dysbiotic gut microbiota and systemic lupus erythematosus: What is new in therapeutic approaches?.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {244},
number = {},
pages = {109109},
doi = {10.1016/j.clim.2022.109109},
pmid = {36087683},
issn = {1521-7035},
mesh = {*Autoimmune Diseases ; Autoimmunity ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Lupus Erythematosus, Systemic ; *Microbiota ; },
abstract = {Systemic lupus erythematosus is an autoimmune disease characterized by chronic inflammation and multiple organs damage. Its pathogenesis is complex and involves multiple factors including gut microbiota. Accumulating evidence indicates the interaction of microbial communities with the host immune system to maintain a state of homeostasis. Imbalances within the gut microbial composition and function may contribute to the development of many autoimmune diseases including SLE. In this review, we aim to highlight the dysregulation of commensal bacteria and their metabolites in the gastrointestinal tract and the resulting autoimmune responses in lupus and to decrypt the cross-link between the altered gut microbiota and the immune system in the SLE condition. We also provide new insights into targeting gut microbiota as a promising therapeutic approach to treat and manage SLE.},
}
@article {pmid36084824,
year = {2022},
author = {Van Winckel, T and Ngo, N and Sturm, B and Al-Omari, A and Wett, B and Bott, C and Vlaeminck, SE and De Clippeleir, H},
title = {Enhancing bioflocculation in high-rate activated sludge improves effluent quality yet increases sensitivity to surface overflow rate.},
journal = {Chemosphere},
volume = {308},
number = {Pt 2},
pages = {136294},
doi = {10.1016/j.chemosphere.2022.136294},
pmid = {36084824},
issn = {1879-1298},
mesh = {Flocculation ; *Sewage ; *Waste Disposal, Fluid/methods ; },
abstract = {High-rate activated sludge (HRAS) relies on good bioflocculation and subsequent solid-liquid separation to maximize the capture of organics. However, full-scale applications often suffer from poor and unpredictable effluent suspended solids (ESS). While the biological aspects of bioflocculation are thoroughly investigated, the effects of fines (settling velocity < 0.6 m[3]/m[2]/h), shear and surface overflow rate (SOR) are unclear. This work tackled the impact of fines, shear, and SOR on the ESS in absence of settleable influent solids. This was assessed on a full-scale HRAS step-feed (SF) and pilot-scale HRAS contact-stabilization (CS) configuration using batch settling tests, controlled clarifier experiments, and continuous operation of reactors. Fines contributed up to 25% of the ESS in the full-scale SF configuration. ESS decreased up to 30 mg TSS/L when bioflocculation was enhanced with the CS configuration. The feast-famine regime applied in CS promoted the production of high-quality extracellular polymeric substances (EPS). However, this resulted in a narrow and unfavorable settling velocity distribution, with 50% ± 5% of the sludge mass settling between 0.6 and 1.5 m[3]/m[2]/h, thus increasing sensitivity towards SOR changes. A low shear environment (20 s[-1]) before the clarifier for at least one min was enough to ensure the best possible settling velocity distribution, regardless of prior shear conditions. Overall, this paper provides a more complete view on the drivers of ESS in HRAS systems, creating the foundation for the design of effective HRAS clarifiers. Tangible recommendations are given on how to manage fines and establish the optimal settling velocity of the sludge.},
}
@article {pmid36083443,
year = {2022},
author = {Fournier, GP and Parsons, CW and Cutts, EM and Tamre, E},
title = {Standard Candles for Dating Microbial Lineages.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2569},
number = {},
pages = {41-74},
pmid = {36083443},
issn = {1940-6029},
mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Eukaryotic Cells ; Evolution, Molecular ; *Fossils ; Phylogeny ; Plants/genetics ; },
abstract = {Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.},
}
@article {pmid36081452,
year = {2022},
author = {Duan, Q and Tian, L and Feng, J and Ping, X and Li, L and Yaigoub, H and Li, R and Li, Y},
title = {Trametenolic Acid Ameliorates the Progression of Diabetic Nephropathy in db/db Mice via Nrf2/HO-1 and NF-κB-Mediated Pathways.},
journal = {Journal of immunology research},
volume = {2022},
number = {},
pages = {6151847},
pmid = {36081452},
issn = {2314-7156},
mesh = {Albumins/metabolism ; Animals ; Antioxidants/metabolism ; Body Weight ; *Diabetes Mellitus ; *Diabetic Nephropathies/drug therapy ; Glutathione/metabolism ; Heme Oxygenase-1/metabolism ; Interleukin-6/metabolism ; Mice ; NF-E2-Related Factor 2/metabolism ; NF-kappa B/metabolism ; Oxidative Stress ; Superoxide Dismutase/metabolism ; *Triterpenes/therapeutic use ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Diabetic nephropathy (DN) is a fatal complication of diabetes and the main cause of end-stage renal disease. Due to the suboptimal effects of current treatments, there is an urgent need to develop new therapeutic strategies for DN. Trametenolic acid (TA), a lanostane-type tetracyclic triterpenoid, is one of the main active ingredients extracted from the natural product Inonotus obliquus. Our study was aimed at clarifying the potential protective effects of TA on DN and its underlying mechanism. In this research, C57BLKS/db (db/db) mice were used as the spontaneous DN model, and TA (10 mg/kg/d) was intraperitoneally injected for 4 consecutive weeks. Ratio of right kidney weight/body weight was calculated, and the contents of serum creatinine (Scr), blood urea nitrogen (BUN), and urine albumin were detected. The activities of superoxide dismutase (SOD) and catalase (CAT) and the contents of reductive glutathione (GSH) and malondialdehyde (MDA) were measured. The histopathological changes of renal tissues were observed by hematoxylin and eosin (HE), periodic acid-Schiff (PAS), and Masson staining. The protein expressions of nuclear factor erythroid 2-related factor 2 (Nrf2), heme oxygenase-1 (HO-1), NAD(P)H:quinone oxidoreductase-1 (NQO-1), nuclear factor kappa B (NF-κB), proinflammation cytokine tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β), Nephrin, and Podocin were detected by western blot assay. Immunohistochemistry was utilized to detect expressions of collagen III (COL-III) and fibronectin (FN). Our results showed that TA administration significantly reduced the ratio of right kidney weight/body weight, BUN, Scr, and urine albumin levels and alleviated the histopathological changes of DN mice. Moreover, TA administration remarkably increased GSH content and SOD and CAT activities and decreased MDA content. Western blot assay demonstrated that TA activated Nrf2 signaling and increased the expression of downstream antioxidant enzymes HO-1 and NQO-1. Further studies illustrated that NF-κB signaling was inhibited, and downstream proinflammation cytokine expressions of TNF-α, IL-6, and IL-1β were also downregulated. In addition, we also found that TA administration significantly increased the expression of nephrin and podocin proteins and reduced the protein expression of COL-III and FN. These findings suggested that TA exhibited a renoprotective effect by ameliorating oxidative stress and inflammation via Nrf2/HO-1 and NF-κB signaling pathways.},
}
@article {pmid36078654,
year = {2022},
author = {Zou, J and Yang, J and He, H and Wang, X and Mei, R and Cai, L and Li, J},
title = {Effect of Seed Sludge Type on Aerobic Granulation, Pollutant Removal and Microbial Community in a Sequencing Batch Reactor Treating Real Textile Wastewater.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {17},
pages = {},
pmid = {36078654},
issn = {1660-4601},
mesh = {Aerobiosis ; Bioreactors/microbiology ; *Environmental Pollutants ; *Microbiota ; Nitrogen ; Sewage/microbiology ; Textiles ; Waste Disposal, Fluid/methods ; Wastewater ; },
abstract = {The aerobic granulation, pollutant removal, and microbial community in real textile wastewater (TWW) treatment were compared using conventional activated sludge (CAS) and preformed aerobic granular sludge (AGS) in synthetic wastewater as seed in two reactors, reactor-1 (R1) and reactor-2 (R2), respectively. The results showed that complete granulation was achieved in R1 (sludge volume index at 5 min (SVI5) and 30 min (SVI30): 19.4 mL/g; granule size: 210 μm) within 65 days, while it only required 28 days in R2 (SVI5 and SVI30: 27.3 mL/g; granule size: 496 μm). The removal of COD, NH4[+]-N and TN in R1 (49.8%, 98.8%, and 41.6%) and R2 (53.6%, 96.9%, and 40.8%) were comparable in 100% real TWW treatment, but stable performance was achieved much faster in R2. The real TWW had an inhibitory effect on heterotrophic bacteria activity, but it had no inhibition on ammonia-oxidizing bacteria activity. AGS with a larger particle size had a higher microbial tolerance to real TWW. Furthermore, filamentous Thiothrix in the AGS in R2 disappeared when treating real TWW, leading to the improvement of sludge settleability. Thus, seeding preformed AGS is suggested as a rapid start-up method for a robust AGS system in treating real TWW.},
}
@article {pmid36077481,
year = {2022},
author = {Villalba, LA and Kasada, M and Zoccarato, L and Wollrab, S and Grossart, HP},
title = {Differing Escape Responses of the Marine Bacterium Marinobacter adhaerens in the Presence of Planktonic vs. Surface-Associated Protist Grazers.},
journal = {International journal of molecular sciences},
volume = {23},
number = {17},
pages = {},
pmid = {36077481},
issn = {1422-0067},
support = {not asigned yet//Leibniz Association/ ; },
mesh = {Bacteria ; Ecosystem ; Humans ; Marinobacter ; *Plankton ; *Stramenopiles ; Water ; },
abstract = {Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers. We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time. In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment. In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population. Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion. This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events.},
}
@article {pmid36076760,
year = {2022},
author = {Mutalub, YB and Abdulwahab, M and Mohammed, A and Yahkub, AM and Al-Mhanna, SB and Yusof, W and Tang, SP and Rasool, AHG and Mokhtar, SS},
title = {Gut Microbiota Modulation as a Novel Therapeutic Strategy in Cardiometabolic Diseases.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {17},
pages = {},
pmid = {36076760},
issn = {2304-8158},
support = {1001/PPSP/8012346//Universiti Sains Malaysia/ ; },
abstract = {The human gut harbors microbial ecology that is in a symbiotic relationship with its host and has a vital function in keeping host homeostasis. Inimical alterations in the composition of gut microbiota, known as gut dysbiosis, have been associated with cardiometabolic diseases. Studies have revealed the variation in gut microbiota composition in healthy individuals as compared to the composition of those with cardiometabolic diseases. Perturbation of host-microbial interaction attenuates physiological processes and may incite several cardiometabolic disease pathways. This imbalance contributes to cardiometabolic diseases via metabolism-independent and metabolite-dependent pathways. The aim of this review was to elucidate studies that have demonstrated the complex relationship between the intestinal microbiota as well as their metabolites and the development/progression of cardiometabolic diseases. Furthermore, we systematically itemized the potential therapeutic approaches for cardiometabolic diseases that target gut microbiota and/or their metabolites by following the pathophysiological pathways of disease development. These approaches include the use of diet, prebiotics, and probiotics. With the exposition of the link between gut microbiota and cardiometabolic diseases, the human gut microbiota therefore becomes a potential therapeutic target in the development of novel cardiometabolic agents.},
}
@article {pmid36076344,
year = {2023},
author = {Xu, H and Qian, Y and Jia, S and Shi, Z and Zhong, Q},
title = {Comparative analysis of subgingival microbiota in patients with mild, moderate, and severe chronic periodontitis.},
journal = {Oral diseases},
volume = {29},
number = {7},
pages = {2865-2877},
doi = {10.1111/odi.14373},
pmid = {36076344},
issn = {1601-0825},
support = {20184Y0244//Shanghai Municipal Health and Family Planning Commission/ ; },
mesh = {Humans ; *Chronic Periodontitis/therapy ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Gingival Crevicular Fluid ; *Microbiota/genetics ; },
abstract = {In this study, we explored the suspected pathogens of chronic periodontitis at different stages of occurrence and development. We collected 100 gingival crevicular fluid samples, 27, 27, and 26 from patients with mild, moderate, and severe chronic periodontitis, respectively, and 20 from healthy individuals. Pathogens were detected using a 16S rRNA metagenomic approach. Quantitative Insights in Microbial Ecology, Mothur, and other software were used to analyze the original data, draw relative abundance histograms and heat maps, and calculate flora abundance and diversity indexes. We identified 429 operational taxonomic units, covering 13 phyla, 20 classes, 32 orders, 66 families, and 123 genera from the four groups of samples. Each group showed microbial diversity, and the number of new species of bacterial flora in the gingival crevicular fluid samples gradually increased from the healthy to the severe chronic periodontitis group. There was a significant difference in the relative abundance of the core flora at the phylum, class, order, family, and genus classification levels. Our data indicated a certain correlation between the changes in the subgingival microbial structure and the occurrence and development of chronic periodontitis, which might be able to provide a reference for the diagnosis, treatment and prevention of chronic periodontitis.},
}
@article {pmid36075785,
year = {2023},
author = {Martín-Rodríguez, AJ},
title = {Respiration-induced biofilm formation as a driver for bacterial niche colonization.},
journal = {Trends in microbiology},
volume = {31},
number = {2},
pages = {120-134},
doi = {10.1016/j.tim.2022.08.007},
pmid = {36075785},
issn = {1878-4380},
mesh = {*Biofilms ; Oxidation-Reduction ; *Bacteria/metabolism ; Oxygen/metabolism ; Respiration ; },
abstract = {Depending on their physiology and metabolism, bacteria can carry out diverse redox processes for energy acquisition, which facilitates adaptation to environmental or host-associated niches. Of these processes, respiration, using oxygen or alternative terminal electron acceptors, is energetically the most favorable in heterotrophic bacteria. The biofilm lifestyle, a coordinated multicellular behavior, is ubiquitous in bacteria and is regulated by a variety of intrinsic and extrinsic cues. Respiration of distinct electron acceptors has been shown to induce biofilm formation or dispersal. The notion of biofilm formation regulation by electron acceptor availability and respiration has often been considered species-specific. However, recent evidence suggests that this phenomenon can be strain-specific, even in strains sharing the same functional respiratory pathways, thereby implying subtle regulatory mechanisms. On this basis, I argue that induction of biofilm formation by sensing and respiration of electron acceptors might direct subgroups of redox-specialized strains to occupy certain niches. A palette of respiration and electron-transfer-mediated microbial social interactions within biofilms may broaden ecological opportunities. The strain specificity of this phenomenon represents an important opportunity to identify key molecular mechanisms and their ecophysiological significance, which in turn may lay the ground for applications in areas ranging from biotechnology to the prevention of antimicrobial resistance.},
}
@article {pmid36075698,
year = {2022},
author = {Van Holm, W and Verspecht, T and Carvalho, R and Bernaerts, K and Boon, N and Zayed, N and Teughels, W},
title = {Glycerol strengthens probiotic effect of Limosilactobacillus reuteri in oral biofilms: A synergistic synbiotic approach.},
journal = {Molecular oral microbiology},
volume = {37},
number = {6},
pages = {266-275},
doi = {10.1111/omi.12386},
pmid = {36075698},
issn = {2041-1014},
mesh = {Humans ; *Limosilactobacillus reuteri/metabolism ; Glycerol/pharmacology/metabolism ; *Synbiotics ; *Probiotics/pharmacology ; Biofilms ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; },
abstract = {Both in vitro and in vivo studies have shown that the probiotic Limosilactobacillus reuteri can improve oral health. Limosilactobacillus reuteri species are known to produce the antimicrobial "reuterin" from glycerol. In order to further increase its antimicrobial activity, this study evaluated the effect of the combined use of glycerol and Limosilactobacillus reuteri (ATCC PTA 5289) in view of using a synergistic synbiotic over a probiotic. An antagonistic agar growth and a multispecies biofilm model showed that the antimicrobial potential of the probiotic was significantly enhanced against periodontal pathobionts and anaerobic commensals when supplemented with glycerol. Synbiotic biofilms also showed a significant reduction in inflammatory expression of human oral keratinocytes (HOK-18A), but only when the keratinocytes were preincubated with the probiotic. Probiotic preincubation of keratinocytes or probiotic and synbiotic treatment of biofilms alone was insufficient to significantly reduce inflammatory expression. Overall, this study shows that combining glycerol with the probiotic L. reuteri into a synergistic synbiotic can greatly improve the effectiveness of the latter.},
}
@article {pmid36073497,
year = {2022},
author = {Lammers, A and Nazipi, S and Zweers, H and Bilde, T and Schramm, A and Garbeva, P and Lalk, M},
title = {Antimicrobial volatiles emitted by members of the nest microbiome of social spiders.},
journal = {FEMS microbiology letters},
volume = {369},
number = {1},
pages = {},
doi = {10.1093/femsle/fnac088},
pmid = {36073497},
issn = {1574-6968},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Antifungal Agents/pharmacology ; *Microbiota ; *Spiders ; *Streptomyces ; },
abstract = {Microbes produce and respond to a range of structurally and functionally diverse volatiles. Many microbial volatiles have antimicrobial properties. Since volatiles can diffuse through complex 3D systems like spider nests, they are promising pathogen protection for social arthropods. Here, we analyzed the volatilomes of five nest microbiome members of the Namibian, social spider Stegodyphus dumicola, namely the bacteria Massilia sp. IC2-278, Massilia sp. IC2-477, Sphingomonas sp. IC-11, Streptomyces sp. IC-207, and the fungus Aureobasidium sp. CE_32, and tested their antimicrobial activity against two putative spider pathogens, namely Bacillus thuringiensis and Purpureocillium lilacinum. Most nest microbiome members released volatilomes with antibacterial and/or antifungal activities under in vitro conditions. The analysis of their volatilomes using GC/Q-TOF revealed that they include numerous antimicrobial volatiles. We tested the antimicrobial activity of five pure volatile compounds found in the volatilomes and revealed that all of them were antibacterial and/or antifungal. We could not identify the same antimicrobial volatiles as in a previous in situ study, but our results indicate that social spider-associated microorganisms as a source of antimicrobial volatiles are important for pathogen inhibition. Additionally, we showed the influence of the volatilomes on the antibiotic sensitivity of B. thuringiensis offering novel approaches to counter antibiotic resistance.},
}
@article {pmid36073311,
year = {2022},
author = {McLean, AR and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Site-tropism of streptococci in the oral microbiome.},
journal = {Molecular oral microbiology},
volume = {37},
number = {6},
pages = {229-243},
pmid = {36073311},
issn = {2041-1014},
support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE027958/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Streptococcus/genetics ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; Mouth/microbiology ; Tropism ; Phylogeny ; },
abstract = {A detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat type within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here, we assess whether individual species within this genus are specialists using publicly available genomic sequence data that provide species-level resolution. We chose a set of high-quality representative genomes for human oral Streptococcus species. Onto these genomes, we mapped shotgun metagenomic sequencing reads from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every abundant Streptococcus species in the healthy human oral cavity showed strong site-tropism and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. Substantial overlap between the core genes of these three species suggests that site-specialization is determined by subtle differences in genomic content.},
}
@article {pmid36069784,
year = {2022},
author = {Hahn, MW and Pitt, A and Schmidt, J and Koll, U and Wolf, J and Whitman, WB and Bodelier, PLE and Neumann-Schaal, M},
title = {Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.005513},
pmid = {36069784},
issn = {1466-5034},
mesh = {*Alcaligenaceae/genetics ; Animals ; Bacteria/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Gastropoda ; Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {We present two strains affiliated with the GKS98 cluster. This phylogenetically defined cluster is representing abundant, mainly uncultured freshwater bacteria, which were observed by many cultivation-independent studies on the diversity of bacteria in various freshwater lakes and streams. Bacteria affiliated with the GKS98 cluster were detected by cultivation-independent methods in freshwater systems located in Europe, Asia, Africa and the Americas. The two strains, LF4-65[T] (=CCUG 56422[T]=DSM 107630[T]) and MWH-P2sevCIIIb[T] (=CCUG 56420[T]=DSM 107629[T]), are aerobic chemoorganotrophs, both with genome sizes of 3.2 Mbp and G+C values of 52.4 and 51.0 mol%, respectively. Phylogenomic analyses based on concatenated amino acid sequences of 120 proteins suggest an affiliation of the two strains with the family Alcaligenaceae and revealed Orrella amnicola and Orrella marina (= Algicoccus marinus) as being the closest related, previously described species. However, the calculated phylogenomic trees clearly suggest that the current genus Orrella represents a polyphyletic taxon. Based on the branching order in the phylogenomic trees, as well as the revealed phylogenetic distances and chemotaxonomic traits, we propose to establish the new genus Zwartia gen. nov. and the new species Z. hollandica sp. nov. to harbour strain LF4-65[T] and the new genus Jezberella gen. nov. and the new species J. montanilacus sp. nov. to harbour strain MWH-P2sevCIIIb[T]. Furthermore, we propose the reclassification of the species Orrella amnicola in the new genus Sheuella gen. nov. The new genera Zwartia, Jezberella and Sheuella together represent taxonomically the GKS98 cluster.},
}
@article {pmid36069437,
year = {2022},
author = {Eddie, BJ and Bird, LJ and Pelikan, C and Mussmann, M and Martínez-Pérez, C and Pinamang, P and Malanoski, AP and Glaven, SM},
title = {Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales.},
journal = {mSphere},
volume = {7},
number = {5},
pages = {e0022322},
pmid = {36069437},
issn = {2379-5042},
support = {P 31010/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Carbon Dioxide/metabolism ; *Chromatiaceae ; Sulfur ; Iron/metabolism ; Cytochromes ; Oxidoreductases ; Heme ; },
abstract = {Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.},
}
@article {pmid36068360,
year = {2023},
author = {Xie, Z and Xu, G and Miao, F and Kong, H and Hu, M and Wang, Y},
title = {Predator Presence Alters Intestinal Microbiota in Mussel.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {1200-1212},
pmid = {36068360},
issn = {1432-184X},
support = {31872587//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Mytilus ; *Brachyura ; Biodiversity ; },
abstract = {Intestinal microbes are essential participants in host vital activities. The composition of the microbiota is closely related to the environmental factors. Predator presence may impact on intestinal microbiota of prey. In the present study, stone crab Charybdis japonica was used as potential predator, an external stress on mussel Mytilus coruscus, to investigate the intestinal microbiota alteration in M. coruscus. We set up two forms of predator presence including free crab and trapped crab, with a blank treatment without crab. The composition of intestinal microbiota in mussels among different treatments showed significant differences by 16S rRNA techniques. The biodiversity increased with trapped crab presence, but decreased with free crab presence. Neisseria, the most abundant genus, fell with the presence of crabs. Besides, the Arcobacter, a kind of pathogenic bacteria, increased with free crab presence. Regarding PICRUTs analysis, Environmental Information Processing, Genetic Information Processing and Metabolism showed differences in crab presence treatments compared with the blank, with a bit higher in the presence of free crab than trapped crab. In conclusion, trapped crab effects activated the metabolism and immunity of the intestinal flora, but free crabs made mussels more susceptible to disease and mortality, corresponding to the decreased biodiversity and the increased Arcobacter in their intestine.},
}
@article {pmid36067300,
year = {2022},
author = {Saunders, JK and McIlvin, MR and Dupont, CL and Kaul, D and Moran, DM and Horner, T and Laperriere, SM and Webb, EA and Bosak, T and Santoro, AE and Saito, MA},
title = {Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {37},
pages = {e2200014119},
pmid = {36067300},
issn = {1091-6490},
support = {R01 GM135709/GM/NIGMS NIH HHS/United States ; },
mesh = {Archaea/classification/enzymology ; *Archaeal Proteins/analysis ; Bacteria/classification/enzymology ; *Bacterial Proteins/analysis ; Biodiversity ; *Microbiota ; *Nitrification ; Nitrite Reductases/metabolism ; Pacific Ocean ; Proteomics/methods ; *Seawater/microbiology ; },
abstract = {Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.},
}
@article {pmid36067150,
year = {2022},
author = {Wilberts, L and Vuts, J and Caulfield, JC and Thomas, G and Birkett, MA and Herrera-Malaver, B and Verstrepen, KJ and Sobhy, IS and Jacquemyn, H and Lievens, B},
title = {Impact of endophytic colonization by entomopathogenic fungi on the behavior and life history of the tobacco peach aphid Myzus persicae var. nicotianae.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0273791},
pmid = {36067150},
issn = {1932-6203},
mesh = {Animals ; *Aphids/physiology ; *Beauveria/physiology ; *Capsicum ; Insecta ; Nicotiana ; },
abstract = {Entomopathogenic fungi can adopt an endophytic lifestyle and provide protection against insect herbivores and plant pathogens. So far, most studies have focused on Beauveria bassiana to increase plant resistance against abiotic and biotic stresses, while only little is known for other entomopathogenic fungi. In this study, we investigated whether root inoculation of sweet pepper (Capsicum annuum L.) by the entomopathogenic fungi Akanthomyces muscarius ARSEF 5128 and B. bassiana ARSEF 3097 can improve resistance against the tobacco peach aphid Myzus persicae var. nicotianae. First, dual-choice experiments were performed to test the hypothesis that the fungi deter aphids via modifying plant volatile profiles. Next, we tested the hypothesis that endophytic colonization negatively affects aphid life history traits, such as fecundity, development and mortality rate. Aphids were significantly attracted to the odor of plants inoculated with A. muscarius over non-inoculated plants. Plants inoculated with A. muscarius emitted significantly higher amounts of β-pinene than non-inoculated plants, and significantly higher amounts of indole than B. bassiana-inoculated and non-inoculated plants. Inoculation with the fungal strains also caused significantly higher emission of terpinolene. Further, both aphid longevity and fecundity were significantly reduced by 18% and 10%, respectively, when feeding on plants inoculated with A. muscarius, although intrinsic rate of population increase did not differ between inoculated and non-inoculated plants. Sweet pepper plants inoculated with B. bassiana ARSEF 3097 did not elicit a significant behavioral response nor affected the investigated life history traits. We conclude that endophytic colonization by entomopathogenic fungi has the potential to alter olfactory behavior and performance of M. persicae var. nicotianae, but effects are small and depend on the fungal strain used.},
}
@article {pmid36065063,
year = {2022},
author = {Nottingham, AT and Scott, JJ and Saltonstall, K and Broders, K and Montero-Sanchez, M and Püspök, J and Bååth, E and Meir, P},
title = {Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt.},
journal = {Nature microbiology},
volume = {7},
number = {10},
pages = {1650-1660},
pmid = {36065063},
issn = {2058-5276},
mesh = {Carbon ; Carbon Dioxide/metabolism ; Respiration ; *Soil ; *Soil Microbiology ; },
abstract = {Perturbation of soil microbial communities by rising temperatures could have important consequences for biodiversity and future climate, particularly in tropical forests where high biological diversity coincides with a vast store of soil carbon. We carried out a 2-year in situ soil warming experiment in a tropical forest in Panama and found large changes in the soil microbial community and its growth sensitivity, which did not fully explain observed large increases in CO2 emission. Microbial diversity, especially of bacteria, declined markedly with 3 to 8 °C warming, demonstrating a breakdown in the positive temperature-diversity relationship observed elsewhere. The microbial community composition shifted with warming, with many taxa no longer detected and others enriched, including thermophilic taxa. This community shift resulted in community adaptation of growth to warmer temperatures, which we used to predict changes in soil CO2 emissions. However, the in situ CO2 emissions exceeded our model predictions threefold, potentially driven by abiotic acceleration of enzymatic activity. Our results suggest that warming of tropical forests will have rapid, detrimental consequences both for soil microbial biodiversity and future climate.},
}
@article {pmid36064650,
year = {2022},
author = {Morillo-Lopez, V and Sjaarda, A and Islam, I and Borisy, GG and Mark Welch, JL},
title = {Corncob structures in dental plaque reveal microhabitat taxon specificity.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {145},
pmid = {36064650},
issn = {2049-2618},
support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE027958/DE/NIDCR NIH HHS/United States ; },
mesh = {Bacteria/genetics ; Biofilms ; *Dental Plaque ; Humans ; In Situ Hybridization, Fluorescence/methods ; Mouth/microbiology ; Streptococcus ; *Zea mays ; },
abstract = {BACKGROUND: The human mouth is a natural laboratory for studying how bacterial communities differ across habitats. Different bacteria colonize different surfaces in the mouth-teeth, tongue dorsum, and keratinized and non-keratinized epithelia-despite the short physical distance between these habitats and their connection through saliva. We sought to determine whether more tightly defined microhabitats might have more tightly defined sets of resident bacteria. A microhabitat may be characterized, for example, as the space adjacent to a particular species of bacterium. Corncob structures of dental plaque, consisting of coccoid bacteria bound to filaments of Corynebacterium cells, present an opportunity to analyze the community structure of one such well-defined microhabitat within a complex natural biofilm. Here, we investigate by fluorescence in situ hybridization and spectral imaging the composition of the cocci decorating the filaments.<br><br>RESULTS: The range of taxa observed in corncobs was limited to a small subset of the taxa present in dental plaque. Among four major groups of dental plaque streptococci, two were the major constituents of corncobs, including one that was the most abundant Streptococcus species in corncobs despite being relatively rare in dental plaque overall. Images showed both Streptococcus types in corncobs in all individual donors, suggesting that the taxa have different ecological roles or that mechanisms exist for stabilizing the persistence of functionally redundant taxa in the population. Direct taxon-taxon interactions were observed not only between the Streptococcus cells and the central corncob filament but also between Streptococcus cells and the limited subset of other plaque bacteria detected in the corncobs, indicating species ensembles involving these taxa as well.<br><br>CONCLUSIONS: The spatial organization we observed in corncobs suggests that each of the microbial participants can interact with multiple, albeit limited, potential partners, a feature that may encourage the long-term stability of the community. Additionally, our results suggest the general principle that a precisely defined microhabitat will be inhabited by a small and well-defined set of microbial taxa. Thus, our results are important for understanding the structure and organizing principles of natural biofilms and lay the groundwork for future work to modulate and control biofilms for human health. Video Abstract.},
}
@article {pmid36063938,
year = {2023},
author = {Navarrete, AA and Aburto, F and González-Rocha, G and Guzmán, CM and Schmidt, R and Scow, K},
title = {Anthropogenic degradation alter surface soil biogeochemical pools and microbial communities in an Andean temperate forest.},
journal = {The Science of the total environment},
volume = {854},
number = {},
pages = {158508},
doi = {10.1016/j.scitotenv.2022.158508},
pmid = {36063938},
issn = {1879-1026},
mesh = {Soil/chemistry ; Forests ; Bacteria ; *Ascomycota ; *Microbiota ; Soil Microbiology ; },
abstract = {Soil microbial communities regulate a myriad of critical biogeochemical functions in forest ecosystems. Anthropogenic disturbances in natural forests could drive major shifts in plant and microbial communities resulting in substantial biogeochemical alterations. We evaluated the effect of anthropogenic disturbances in the soils of Andean temperate forests with different levels of degradation: i) mature forest (MF), ii) secondary forest (SF), iii) degraded forest (DF), and iv) deforested site converted into a prairie (DP). We quantified total soil carbon, nitrogen and phosphorous (TC, TN, and TP), and available nutrient stocks. The soil microbial community structure (i.e., composition, diversity, and abundance) was assessed under each condition from amplicon sequence variants (ASVs) obtained via NGS-Illumina sequencing and subsequent microbiome analysis. There were no significant differences in TC, TN, and TP across the forested states (MF, SF, DF). The deforested site condition presented significantly higher soil TC, TN, and TP and the lowest C:N, C:P, and N:P ratios. The DP soil microbiome was significantly more diverse in bacteria (D' = 0.47 ± 0.04); and fungi (H' = 5.11 ± 0.33). The bacterial microbiome was dominated by Proteobacteria (45.35 ± 0.89 %), Acidobacteria (20.73 ± 1.48 %), Actinobacteria (12.59 ± 0.34 %), and Bacteroidetes (7.32 ± 0.36 %) phyla in all sites. The soil fungal community was dominated by the phyla Ascomycota (42.11 ± 0.95 %), Mortierellomycota (28.74 ± 2.25 %), Basidiomycota (24.61 ± 0.52), and Mucoromycota (2.06 ± 0.43 %). Yet, there were significant differences at the genus level across conditions. Forest to prairie conversion facilitated the introduction of exotic bacterial and fungal taxa associated with agricultural activities and livestock grazing (∼50 % of DP core microbiome composed of unique ASVs). For example, the ammonia-oxidizing bacteria community emerged as a dominant group in the DP soils, along with a reduction in the ectomycorrhizal fungi community. The surface soil microbial community was surprisingly resistant to forest degradation and did not show a clear succession along the degradation gradient, but it was strongly altered after deforestation.},
}
@article {pmid36063436,
year = {2022},
author = {Li, Y and Bletsa, M and Zisi, Z and Boonen, I and Gryseels, S and Kafetzopoulou, L and Webster, JP and Catalano, S and Pybus, OG and Van de Perre, F and Li, H and Li, Y and Li, Y and Abramov, A and Lymberakis, P and Lemey, P and Lequime, S},
title = {Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History.},
journal = {Molecular biology and evolution},
volume = {39},
number = {10},
pages = {},
pmid = {36063436},
issn = {1537-1719},
mesh = {Animals ; Evolution, Molecular ; Genome, Viral ; Humans ; *Pestivirus/genetics ; Phylogeny ; Shrews/genetics ; *Viruses/genetics ; *Zika Virus/genetics ; *Zika Virus Infection ; },
abstract = {As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.},
}
@article {pmid36061686,
year = {2022},
author = {Liu, B and Chen, J and Li, Y},
title = {Keystone Microorganisms Regulate the Methanogenic Potential in Coals with Different Coal Ranks.},
journal = {ACS omega},
volume = {7},
number = {34},
pages = {29901-29908},
pmid = {36061686},
issn = {2470-1343},
abstract = {Microorganisms are the core drivers of coal biogeochemistry and are closely related to the formation of coalbed methane. However, it remains poorly understood about the network relationship and stability of microbial communities in coals with different ranks. In this study, a high-throughput sequencing data set was analyzed to understand the microbial co-occurrence network in coals with different ranks including anthracite, medium-volatile bituminous, and high-volatile bituminous. The results showed similar topological properties for the microbial networks among coals with different ranks, but a great difference was found in the microbial composition in different large modules among coals with different ranks, and these three networks had three, four, and four large modules with seven, nine, and nine phyla, respectively. Among these networks, a total of 46 keystone taxa were identified in large modules, and these keystone taxa were different in coals with different ranks. Bacteria dominated the keystone taxa in the microbial network, and these bacterial keystone taxa mainly belonged to phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Besides, the removal of the key microbial data could reduce the community stability of microbial communities in bituminous coals. A partial least-squares path model further showed that these bacterial keystone taxa indirectly affected methanogenic potential by maintaining the microbial community stability and bacterial diversity. In summary, these results showed that keystone taxa played an important role in determining the community diversity, maintaining the microbial community stability, and controlling the methanogenic potential, which is of great significance for understanding the microbial ecology and the geochemical cycle of coal seams.},
}
@article {pmid36061525,
year = {2022},
author = {von Hoermann, C and Weithmann, S and Sikorski, J and Nevo, O and Szpila, K and Grzywacz, A and Grunwald, JE and Reckel, F and Overmann, J and Steiger, S and Ayasse, M},
title = {Linking bacteria, volatiles and insects on carrion: the role of temporal and spatial factors regulating inter-kingdom communication via volatiles.},
journal = {Royal Society open science},
volume = {9},
number = {8},
pages = {220555},
pmid = {36061525},
issn = {2054-5703},
abstract = {Multi-kingdom community complexity and the chemically mediated dynamics between bacteria and insects have recently received increased attention in carrion research. However, the strength of these inter-kingdom interactions and the factors that regulate them are poorly studied. We used 75 piglet cadavers across three forest regions to survey the relationship between three actors (epinecrotic bacteria, volatile organic compounds (VOCs) and flies) during the first 4 days of decomposition and the factors that regulate this interdependence. The results showed a dynamic bacterial change during decomposition (temperature-time index) and across the forest management gradient, but not between regions. Similarly, VOC emission was dynamic across a temperature-time index and the forest management gradient but did not differ between regions. However, fly occurrence was dynamic across both space and time. The strong interdependence between the three actors was mainly regulated by the temperature-time index and the study regions, thereby revealing regulation at temporal and spatial scales. Additionally, the actor interdependence was stable across a gradient of forest management intensity. By combining different actors of decomposition, we have expanded our knowledge of the holistic mechanisms regulating carrion community dynamics and inter-kingdom interactions, an important precondition for better describing food web dynamics and entire ecosystem functions.},
}
@article {pmid36061322,
year = {2022},
author = {Jones, PA and Frischer, D and Mueller, S and Le, T and Schwanes, A and Govindaraju, A and Shalvarjian, K and Leducq, JB and Marx, CJ and Martinez-Gomez, NC and Lee, JA},
title = {Methylothon: a Versatile Course-Based High School Research Experience in Microbiology and Bioinformatics with Pink Bacteria.},
journal = {Journal of microbiology &amp; biology education},
volume = {23},
number = {2},
pages = {},
pmid = {36061322},
issn = {1935-7877},
support = {T32 GM132022/GM/NIGMS NIH HHS/United States ; },
abstract = {Methylothon is an inquiry-based high school learning module in microbial ecology, molecular biology, and bioinformatics that centers around pink-pigmented plant-associated methylotrophic bacteria. Here, we present an overview of the module's learning goals, describe course resources (available for public use at http://methylothon.com), and relate lessons learned from adapting Methylothon for remote learning during the pandemic in spring of 2021. This curriculum description is intended not only for instructors but also for microbial ecology researchers with an interest in conducting K-12 outreach. The original in-person version of the module allows students to isolate their own strains of methylotrophic bacteria from plants they sample from the environment, to identify these using PCR, sequencing, and phylogenetic analysis, and to contribute their strains to original research in a university lab. The adapted version strengthens the focus on bioinformatics and increases its flexibility and accessibility by making the lab portion optional and adopting free web-based tools. Student feedback and graded assignments from spring 2021 revealed that the lesson was especially effective at introducing the concepts of BLAST and phylogenetic trees and that students valued and felt inspired by the opportunity to conduct hands-on work and to participate in community science.},
}
@article {pmid36059518,
year = {2022},
author = {Qing, J and Hu, X and Li, C and Song, W and Tirichen, H and Yaigoub, H and Li, Y},
title = {Fucose as a potential therapeutic molecule against the immune-mediated inflammation in IgA nepharopathy: An unrevealed link.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {929138},
pmid = {36059518},
issn = {1664-3224},
mesh = {Fucose ; *Gene Expression Profiling ; *Glomerulonephritis, IGA/drug therapy/genetics/metabolism ; Humans ; Immunoglobulin A/genetics ; Inflammation/genetics ; },
abstract = {BACKGROUND: IgA nephropathy (IgAN) is an autoimmune disease that affects people of any age and is an important cause of end-stage renal disease. However, the pathogenesis and pathophysiology of IgAN is not clear. This article aimed to explore the immune-mediated inflammation and genetic mechanisms in IgAN.<br><br>METHODS: The transcriptome sequencing data of IgAN glomeruli in the Gene Expression Omnibus database were downloaded.&#xa0;Single-sample gene set enrichment analysis was used to estimate the immune microenvironment of the merged microarray data and GSE141295. IgAN samples were divided into two clusters by cluster analysis. "limma" and "DEseq2" package in R were used to identify differentially expressed genes (DEGs). The weighted gene co-expression network analysis (WGCNA) was used to identify the co-expression modules related to inflammation in IgAN. R software package "clusterProfiler" was used for enrichment analysis, whereas Short Time-Series Expression Miner (STEM) analysis was used to identify the trend of gene expression. Machine-learn (ML) was performed using the shiny app. Finally, Drug Signatures Database (DSigDB) was used to identify potential molecules for treating IgAN.<br><br>RESULTS: The infiltration of macrophages in IgAN glomeruli was increased, whereas CD4+ T cells, especially inducedregulatory T cells (iTregs) were decreased. A total of 1,104 common DEGs were identified from the merged data and GSE141295. Brown module was identified to have the highest inflammatory correlation with IgAN using WGCNA, and 15 hub genes were screened from this module. Among these 15 hub genes, 14 increased with the severity of IgAN inflammation based on STEM analysis. Neural network (nnet) is considered as the best model to predict the severity of IgAN. Fucose identified from DSigDB has a potential biological activity to treat IgAN.<br><br>CONCLUSION: The increase of macrophages and the decrease of iTregs in glomeruli represent the immune-mediated inflammation of IgAN, and fucose may be a potential therapeutic molecule against IgAN because it affects genes involved in the severe inflammation of IgAN.},
}
@article {pmid36056428,
year = {2022},
author = {Ma, X and Wang, T and Shi, Z and Chiariello, NR and Docherty, K and Field, CB and Gutknecht, J and Gao, Q and Gu, Y and Guo, X and Hungate, BA and Lei, J and Niboyet, A and Le Roux, X and Yuan, M and Yuan, T and Zhou, J and Yang, Y},
title = {Correction: Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {144},
pmid = {36056428},
issn = {2049-2618},
}
@article {pmid36056039,
year = {2022},
author = {Arandia-Gorostidi, N and Berthelot, H and Calabrese, F and Stryhanyuk, H and Klawonn, I and Iversen, M and Nahar, N and Grossart, HP and Ploug, H and Musat, N},
title = {Efficient carbon and nitrogen transfer from marine diatom aggregates to colonizing bacterial groups.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {14949},
pmid = {36056039},
issn = {2045-2322},
mesh = {Bacteria/metabolism ; Biomass ; Carbon/metabolism ; *Diatoms/metabolism ; Nitrogen/metabolism ; },
abstract = {Bacterial degradation of sinking diatom aggregates is key for the availability of organic matter in the deep-ocean. Yet, little is known about the impact of aggregate colonization by different bacterial taxa on organic carbon and nutrient cycling within aggregates. Here, we tracked the carbon (C) and nitrogen (N) transfer from the diatom Leptocylindrus danicus to different environmental bacterial groups using a combination of [13]C and [15]N isotope incubation (incubated for 72 h), CARD-FISH and nanoSIMS single-cell analysis. Pseudoalteromonas bacterial group was the first colonizing diatom-aggregates, succeeded by the Alteromonas group. Within aggregates, diatom-attached bacteria were considerably more enriched in [13]C and [15]N than non-attached bacteria. Isotopic mass balance budget indicates that both groups showed comparable levels of diatom C in their biomass, accounting for 19 ± 7% and 15 ± 11%, respectively. In contrast to C, bacteria of the Alteromonas groups showed significantly higher levels of N derived from diatoms (77 ± 28%) than Pseudoalteromonas (47 ± 17%), suggesting a competitive advantage for Alteromonas in the N-limiting environments of the deep-sea. Our results imply that bacterial succession within diatom aggregates may largely impact taxa-specific C and N uptake, which may have important consequences for the quantity and quality of organic matter exported to the deep ocean.},
}
@article {pmid36054689,
year = {2022},
author = {Calvo-Martin, E and Teira, E and Álvarez-Salgado, XA and Rocha, C and Jiang, S and Justel-Díez, M and Ibánhez, JSP},
title = {On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries.},
journal = {Environmental microbiology},
volume = {24},
number = {12},
pages = {5859-5881},
pmid = {36054689},
issn = {1462-2920},
mesh = {*Estuaries ; RNA, Ribosomal, 16S/genetics ; Archaea/genetics ; *Groundwater ; Oxygen ; },
abstract = {Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.},
}
@article {pmid36054683,
year = {2023},
author = {Fan, L and Chen, J and Pan, L and Xin, X and Geng, B and Yang, L and Wang, Q and Ma, W and Lou, Y and Bian, J and Cui, X and Li, J and Wang, L and Chen, Z and Wang, W and Cui, C and Li, S and Gao, Q and Song, Q and Deng, Y and Fan, J and Yu, J and Zhang, H and Li, Y and Cai, J},
title = {Alterations of Gut Microbiome, Metabolome, and Lipidome in Takayasu Arteritis.},
journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)},
volume = {75},
number = {2},
pages = {266-278},
doi = {10.1002/art.42331},
pmid = {36054683},
issn = {2326-5205},
mesh = {Humans ; *Takayasu Arteritis/drug therapy ; *Gastrointestinal Microbiome/genetics ; Lipidomics ; Inflammation ; Metabolome ; *Behcet Syndrome ; *Cardiovascular Diseases ; },
abstract = {OBJECTIVE: Mounting evidence has linked microbiome and metabolome to systemic autoimmunity and cardiovascular diseases (CVDs). Takayasu arteritis (TAK) is a rare disease that shares features of immune-related inflammatory diseases and CVDs, about which there is relatively limited information. This study was undertaken to characterize gut microbial dysbiosis and its crosstalk with phenotypes in TAK.<br><br>METHODS: To address the discriminatory signatures, we performed shotgun sequencing of fecal metagenome across a discovery cohort (n&#xa0;=&#xa0;97) and an independent validation cohort (n&#xa0;=&#xa0;75) including TAK patients, healthy controls, and controls with Beh&#xe7;et's disease (BD). Interrogation of untargeted metabolomics and lipidomics profiling of plasma and fecal samples were also used to refine features mediating associations between microorganisms and TAK phenotypes.<br><br>RESULTS: A combined model of bacterial species, including unclassified Escherichia, Veillonella parvula, Streptococcus parasanguinis, Dorea formicigenerans, Bifidobacterium adolescentis, Lachnospiraceae bacterium 7 1 58FAA, Escherichia coli, Streptococcus salivarius, Klebsiella pneumoniae, Bifidobacterium longum, and Lachnospiraceae Bacterium 5 1 63FAA, distinguished TAK patients from controls with areas under the curve (AUCs) of 87.8%, 85.9%, 81.1%, and 71.1% in training, test, and validation sets including healthy or BD controls, respectively. Diagnostic species were directly or indirectly (via metabolites or lipids) correlated with TAK phenotypes of vascular involvement, inflammation, discharge medication, and prognosis. External validation against publicly metagenomic studies (n&#xa0;=&#xa0;184) on hypertension, atrial fibrillation, and healthy controls, confirmed the diagnostic accuracy of the model for TAK.<br><br>CONCLUSION: This study first identifies the discriminatory gut microbes in TAK. Dysbiotic microbes are also linked to TAK phenotypes directly or indirectly via metabolic and lipid modules. Further explorations of the microbiome-metagenome interface in TAK subtype prediction and pathogenesis are suggested.},
}
@article {pmid36053304,
year = {2023},
author = {Trumhová, K and Klimešová, V and Pichrtová, M},
title = {Seasonal Dynamics of Zygnema (Zygnematophyceae) Mats from the Austrian Alps.},
journal = {Microbial ecology},
volume = {86},
number = {2},
pages = {763-776},
pmid = {36053304},
issn = {1432-184X},
support = {980518//Univerzita Karlova v Praze/ ; 204069//Univerzita Karlova v Praze/ ; },
mesh = {Seasons ; *Ecosystem ; Phylogeny ; Austria ; *Streptophyta ; Water ; },
abstract = {Filamentous green algae of the genus Zygnema are an essential part of hydro-terrestrial ecosystems. Despite several studies on their resistance to natural stresses, little is known about the composition of their assemblages and the changes they undergo over time. Two sites at altitudes above 2200 m a.s.l. in the Austrian Alps were selected for a 2-year observation period and sampled five times. Molecular phylogenetic analysis of the 152 isolated strains of Zygnema sp. was performed based on the rbcL and trnG sequences. Seven genotypes were found at these sites during the samplings, but their proportion varied throughout the seasons. The site with a more stable water regime also had a more stable representation of genotypes, in contrast to the site with fluctuating water availability. The mats formed resistant pre-akinetes at the end of the season with reduced photosynthetic activity. Contrary to expectations, the mats were not exposed to extremely cold temperatures in winter due to snow cover. Some genotypes have been previously observed at this site, indicating that the population composition is stable. This work highlights the importance of resistant pre-akinetes in surviving winter conditions, the ability of algae to re-establish mats, and the need to address the hidden diversity of the genus Zygnema.},
}
@article {pmid36050462,
year = {2022},
author = {Fang, Y and Qin, X and Liao, Q and Du, R and Luo, X and Zhou, Q and Li, Z and Chen, H and Jin, W and Yuan, Y and Sun, P and Zhang, R and Zhang, J and Wang, L and Cheng, S and Yang, X and Yan, Y and Zhang, X and Zhang, Z and Bai, S and Van de Peer, Y and Lucas, WJ and Huang, S and Yan, J},
title = {The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences.},
journal = {Nature plants},
volume = {8},
number = {9},
pages = {1024-1037},
pmid = {36050462},
issn = {2055-0278},
support = {833522//European Research Council/International ; },
mesh = {*Adiantum/genetics ; *Ferns/genetics ; Genome, Plant ; Phylogeny ; },
abstract = {Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. Here we report a chromosome-level genome assembly of Adiantum capillus-veneris L., a model homosporous fern. This fern genome comprises 30 pseudochromosomes with a size of 4.8-gigabase and a contig N50 length of 16.22 Mb. Gene co-expression network analysis uncovered that homospore development in ferns has relatively high genetic similarities with that of the pollen in seed plants. Analysing fern defence response expands understanding of evolution and diversity in endogenous bioactive jasmonates in plants. Moreover, comparing fern genomes with those of other land plants reveals changes in gene families important for the evolutionary novelties within the euphyllophyte clade. These results lay a foundation for studies on fern genome evolution and function, as well as the origin and evolution of euphyllophytes.},
}
@article {pmid36049255,
year = {2022},
author = {Whitman, WB and Chuvochina, M and Hedlund, BP and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, I and Venter, SN},
title = {Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type.},
journal = {Systematic and applied microbiology},
volume = {45},
number = {5},
pages = {126305},
pmid = {36049255},
issn = {1618-0984},
support = {P20 GM103440/GM/NIGMS NIH HHS/United States ; },
mesh = {*Archaea/genetics ; *Bacteria/genetics ; Base Sequence ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.},
}
@article {pmid36048618,
year = {2022},
author = {Li, G and Wu, C and Wang, D and Srinivasan, V and Kaeli, DR and Dy, JG and Gu, AZ},
title = {Machine Learning-Based Determination of Sampling Depth for Complex Environmental Systems: Case Study with Single-Cell Raman Spectroscopy Data in EBPR Systems.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {18},
pages = {13473-13484},
doi = {10.1021/acs.est.1c08768},
pmid = {36048618},
issn = {1520-5851},
mesh = {*Biological Products ; Humans ; Machine Learning ; *Phosphorus/chemistry ; Polyphosphates ; Sewage ; Spectrum Analysis, Raman ; },
abstract = {Rapid progress in various advanced analytical methods, such as single-cell technologies, enable unprecedented and deeper understanding of microbial ecology beyond the resolution of conventional approaches. A major application challenge exists in the determination of sufficient sample size without sufficient prior knowledge of the community complexity and, the need to balance between statistical power and limited time or resources. This hinders the desired standardization and wider application of these technologies. Here, we proposed, tested and validated a computational sampling size assessment protocol taking advantage of a metric, named kernel divergence. This metric has two advantages: First, it directly compares data set-wise distributional differences with no requirements on human intervention or prior knowledge-based preclassification. Second, minimal assumptions in distribution and sample space are made in data processing to enhance its application domain. This enables test-verified appropriate handling of data sets with both linear and nonlinear relationships. The model was then validated in a case study with Single-cell Raman Spectroscopy (SCRS) phenotyping data sets from eight different enhanced biological phosphorus removal (EBPR) activated sludge communities located across North America. The model allows the determination of sufficient sampling size for any targeted or customized information capture capacity or resolution level. Promised by its flexibility and minimal restriction of input data types, the proposed method is expected to be a standardized approach for sampling size optimization, enabling more comparable and reproducible experiments and analysis on complex environmental samples. Finally, these advantages enable the extension of the capability to other single-cell technologies or environmental applications with data sets exhibiting continuous features.},
}
@article {pmid36048179,
year = {2023},
author = {Cook, K and Taylor, AD and Sharma, J and Taylor, DL},
title = {Inter-annual Persistence of Canopy Fungi Driven by Abundance Despite High Spatial Turnover.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {261-270},
pmid = {36048179},
issn = {1432-184X},
support = {DEB-1355155//National Science Foundation/ ; },
mesh = {*Ecosystem ; Fungi ; Trees/microbiology ; Rainforest ; *Mycobiome ; Soil Microbiology ; Biodiversity ; },
abstract = {While it is now well established that fungal community composition varies spatially at a variety of scales, temporal turnover of fungi is less well understood. Here we studied inter-annual community compositional changes of fungi in a rainforest tree canopy environment. We tracked fungal community shifts over 3 years in three substrate types (live bryophytes, dead bryophytes, and host tree bark) and compared these changes to amounts of community turnover seen at small spatial scales in the same system. The effect of substrate type on fungal community composition was stronger than that of sampling year, which was very small but significant. Although levels of temporal turnover varied among substrates, with greater turnover in live bryophytes than other substrates, the amount of turnover from year to year was comparable to what is seen at spatial distances between 5 and 9 cm for the same substrate. Stability of communities was largely driven by a few fungi with high relative abundances. A majority of fungal occurrences were at low relative abundances (≤ 0.1%). These fungi tended to be short lived and persisted to following years ≤ 50% of the time, depending on substrate. Their presence and persistence are likely impacted by stochastic processes like dispersal limitation and disturbance. Most samples contained only one or a few fungi at high relative abundance (≥ 10%) that persisted half or more of the time. These more abundant and persistent fungi are expected to have sustained functional interactions within the canopy ecosystem.},
}
@article {pmid36047700,
year = {2022},
author = {Versluis, DM and Schoemaker, R and Looijesteijn, E and Muysken, D and Jeurink, PV and Paques, M and Geurts, JMW and Merks, RMH},
title = {A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota.},
journal = {mSystems},
volume = {7},
number = {5},
pages = {e0044622},
pmid = {36047700},
issn = {2379-5077},
mesh = {Infant ; Humans ; Infant, Newborn ; *Gastrointestinal Microbiome ; Anaerobiosis ; Lactose/metabolism ; Bifidobacterium ; *Microbiota ; Bacteria ; Enterobacteriaceae ; },
abstract = {The human intestinal microbiota starts to form immediately after birth and is important for the health of the host. During the first days, facultatively anaerobic bacterial species generally dominate, such as Enterobacteriaceae. These are succeeded by strictly anaerobic species, particularly Bifidobacterium species. An early transition to Bifidobacterium species is associated with health benefits; for example, Bifidobacterium species repress growth of pathogenic competitors and modulate the immune response. Succession to Bifidobacterium is thought to be due to consumption of intracolonic oxygen present in newborns by facultative anaerobes, including Enterobacteriaceae. To study if oxygen depletion suffices for the transition to Bifidobacterium species, here we introduced a multiscale mathematical model that considers metabolism, spatial bacterial population dynamics, and cross-feeding. Using publicly available metabolic network data from the AGORA collection, the model simulates ab initio the competition of strictly and facultatively anaerobic species in a gut-like environment under the influence of lactose and oxygen. The model predicts that individual differences in intracolonic oxygen in newborn infants can explain the observed individual variation in succession to anaerobic species, in particular Bifidobacterium species. Bifidobacterium species became dominant in the model by their use of the bifid shunt, which allows Bifidobacterium to switch to suboptimal yield metabolism with fast growth at high lactose concentrations, as predicted here using flux balance analysis. The computational model thus allows us to test the internal plausibility of hypotheses for bacterial colonization and succession in the infant colon. IMPORTANCE The composition of the infant microbiota has a great impact on infant health, but its controlling factors are still incompletely understood. The frequently dominant anaerobic Bifidobacterium species benefit health, e.g., they can keep harmful competitors under control and modulate the intestinal immune response. Controlling factors could include nutritional composition and intestinal mucus composition, as well as environmental factors, such as antibiotics. We introduce a modeling framework of a metabolically realistic intestinal microbial ecology in which hypothetical scenarios can be tested and compared. We present simulations that suggest that greater levels of intraintestinal oxygenation more strongly delay the dominance of Bifidobacterium species, explaining the observed variety of microbial composition and demonstrating the use of the model for hypothesis generation. The framework allowed us to test a variety of controlling factors, including intestinal mixing and transit time. Future versions will also include detailed modeling of oligosaccharide and mucin metabolism.},
}
@article {pmid36044056,
year = {2023},
author = {Li, W and Xie, L and Zhao, C and Hu, X and Yin, C},
title = {Nitrogen Fertilization Increases Soil Microbial Biomass and Alters Microbial Composition Especially Under Low Soil Water Availability.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {536-548},
pmid = {36044056},
issn = {1432-184X},
mesh = {*Soil/chemistry ; Biomass ; *Carbon/chemistry ; Nitrogen/analysis ; Water ; Soil Microbiology ; Fertilization ; },
abstract = {Soil microbial biomass and composition are affected by resource supply and water availability. However, the response of soil microbial communities to nitrogen fertilization under different water availability conditions is unclear. Therefore, this study conducted a 6-year pot experiment comprising five watering regimes (40%, 50%, 60%, 80%, and 100% of field capacity (FC)) and three nitrogen fertilization levels (NH4NO3 solution; 0 [N0], 20 [N1], and 40 [N2] g N m[-2] year[-1]) to investigate soil microbial biomass, composition, and properties. The results indicated that soil microbial biomass and composition were more strongly affected by nitrogen fertilization compared with water regime. Nitrogen fertilization increased soil microbial biomass and altered soil microbial community composition, especially under low soil water availability. Soil microbial biomass was positively linearly associated with soil water regimes under N0, whereas it responded polynomially to soil water regimes under N1 and N2. The maximal soil microbial biomass was observed at FC80 for N1 and FC60 for N2. Furthermore, the biomass of soil microbial groups with high nitrogen and carbon acquisition ability as well as the enzyme activities of carbon and nitrogen cycling (β-1,4-glucosidase and β-1,4-N-acetyl-glucosaminidase, respectively) were stimulated by nitrogen fertilization. Soil microbial biomass was affected directly by nitrogen fertilization and indirectly by nitrogen and water regimes, via altering soil pH, dissolved inorganic nitrogen (NH4[+]-N and NO3[-]-N) concentration, and soil organic carbon concentration. This study provides new insights into the effect of interaction between soil nitrogen and water availabilities on soil microbial biomass, composition, and its underlying mechanism.},
}
@article {pmid36041615,
year = {2022},
author = {Leistenschneider, C and Le Bohec, C and Eisen, O and Houstin, A and Neff, S and Primpke, S and Zitterbart, DP and Burkhardt-Holm, P and Gerdts, G},
title = {No evidence of microplastic ingestion in emperor penguin chicks (Aptenodytes forsteri) from the Atka Bay colony (Dronning Maud Land, Antarctica).},
journal = {The Science of the total environment},
volume = {851},
number = {Pt 2},
pages = {158314},
doi = {10.1016/j.scitotenv.2022.158314},
pmid = {36041615},
issn = {1879-1026},
mesh = {Animals ; Humans ; *Spheniscidae ; Microplastics ; Antarctic Regions ; Plastics ; Ecosystem ; Bays ; Eating ; },
abstract = {Microplastic (<5 mm; MP) pollution has been an emerging threat for marine ecosystems around the globe with increasing evidence that even the world's most remote areas, including Antarctica, are no longer unaffected. Few studies however, have examined MP in Antarctic biota, and especially those from Antarctic regions with low human activity, meaning little is known about the extent to which biota are affected. The aim of this study was to investigate, for the first time, the occurrence of MP in the emperor penguin (Aptenodytes forsteri), the only penguin species breeding around Antarctica during the austral winter, and an endemic apex predator in the Southern Ocean. To assess MP ingestion, the gizzards of 41 emperor penguin chicks from Atka Bay colony (Dronning Maud Land, Antarctica), were dissected and analyzed for MP >500 μm using Attenuated Total Reflection Fourier-transform Infrared (ATR-FTIR) spectroscopy. A total of 85 putative particles, mostly in the shape of fibers (65.9 %), were sorted. However, none of the particles were identified as MP applying state-of-the-art methodology. Sorted fibers were further evidenced to originate from contamination during sample processing and analyses. We find that MP concentrations in the local food web of the Weddell Sea and Dronning Maud Land coastal and marginal sea-ice regions; the feeding grounds to chick-rearing emperor penguin adults, are currently at such low levels that no detectable biomagnification is occurring via trophic transfer. Being in contrast to MP studies on other Antarctic and sub-Antarctic penguin species, our comparative discussion including these studies, highlights the importance for standardized procedures for sampling, sample processing and analyses to obtain comparable results. We further discuss other stomach contents and their potential role for MP detection, as well as providing a baseline for the long-term monitoring of MP in apex predator species from this region.},
}
@article {pmid36040152,
year = {2022},
author = {He, J and Shen, X and Zhang, N and Sun, C and Shao, Y},
title = {Smartphones as an Ecological Niche of Microorganisms: Microbial Activities, Assembly, and Opportunistic Pathogens.},
journal = {Microbiology spectrum},
volume = {10},
number = {5},
pages = {e0150822},
pmid = {36040152},
issn = {2165-0497},
mesh = {Humans ; RNA, Ribosomal, 16S ; Smartphone ; Phylogeny ; Pandemics ; *COVID-19 ; *Microbiota ; Bacteria/genetics ; Adenosine Triphosphate ; },
abstract = {Smartphone usage and contact frequency are unprecedentedly high in this era, and they affect humans mentally and physically. However, the characteristics of the microorganisms associated with smartphones and smartphone hygiene habits remain unclear. In this study, using various culture-independent techniques, including high-throughput sequencing, real-time quantitative PCR (RT-qPCR), the ATP bioluminescence system, and electron microscopy, we investigated the structure, assembly, quantity, and dynamic metabolic activity of the bacterial community on smartphone surfaces and the user's dominant and nondominant hands. We found that smartphone microbiotas are more similar to the nondominant hand microbiotas than the dominant hand microbiotas and show significantly decreased phylogenetic diversity and stronger deterministic processes than the hand microbiota. Significant interindividual microbiota differences were observed, contributing to an average owner identification accuracy of 70.6% using smartphone microbiota. Furthermore, it is estimated that approximately 1.75 × 10[6] bacteria (2.24 × 10[4]/cm[2]) exist on the touchscreen of a single smartphone, and microbial activities remain stable for at least 48 h. Scanning electron microscopy detected large fragments harboring microorganisms, suggesting that smartphone microbiotas live on the secreta or other substances, e.g., human cell debris and food debris. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. Taken together, our results demonstrate that smartphone surfaces not only are a reservoir of microbes but also provide an ecological niche in which microbiotas, particularly opportunistic pathogens, can survive, be active, and even grow. IMPORTANCE Currently, people spend an average of 4.2 h per day on their smartphones. Due to the COVID-19 pandemic, this figure may still be increasing. The high frequency of smartphone usage may allow microbes, particularly pathogens, to attach to-and even survive on-phone surfaces, potentially causing adverse effects on humans. We employed various culture-independent techniques in this study to evaluate the microbiological features and hygiene of smartphones, including community assembly, bacterial load, and activity. Our data showed that deterministic processes drive smartphone microbiota assembly and that approximately 1.75 × 10[6] bacteria exist on a single smartphone touchscreen, with activities being stable for at least 48 h. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. This work expands our understanding of the microbial ecology of smartphone surfaces and might facilitate the development of electronic device cleaning/hygiene guidelines to support public health.},
}
@article {pmid36037277,
year = {2022},
author = {Carregosa, D and Pinto, C and Ávila-Gálvez, M&#xc1; and Bastos, P and Berry, D and Santos, CN},
title = {A look beyond dietary (poly)phenols: The low molecular weight phenolic metabolites and their concentrations in human circulation.},
journal = {Comprehensive reviews in food science and food safety},
volume = {21},
number = {5},
pages = {3931-3962},
doi = {10.1111/1541-4337.13006},
pmid = {36037277},
issn = {1541-4337},
mesh = {*Diet ; Flavonoids/metabolism ; Fruit ; Humans ; Molecular Weight ; *Phenols ; },
abstract = {A large number of epidemiological studies have shown that consumption of fruits, vegetables, and beverages rich in (poly)phenols promote numerous health benefits from cardiovascular to neurological diseases. Evidence on (poly)phenols has been applied mainly to flavonoids, yet the role of phenolic acids has been largely overlooked. Such phenolics present in food combine with those resulting from gut microbiota catabolism of flavonoids and chlorogenic acids and those produced by endogenous pathways, resulting in large concentrations of low molecular weight phenolic metabolites in human circulation. Independently of the origin, in human intervention studies using diets rich in (poly)phenols, a total of 137 low molecular weight phenolic metabolites have been detected and quantified in human circulation with largely unknown biological function. In this review, we will pinpoint two main aspects of the low molecular weight phenolic metabolites: (i) the microbiota responsible for their generation, and (ii) the analysis (quali- and quantitative) in human circulation and their respective pharmacokinetics. In doing so, we aim to drive scientific advances regarding the ubiquitous roles of low molecular weight phenolic metabolites using physiologically relevant concentrations and under (patho)physiologically relevant conditions in humans.},
}
@article {pmid36034889,
year = {2022},
author = {He, KJ and Dong, JH and Ouyang, XM and Huo, YN and Cheng, XS and Lin, Y and Li, Y and Gong, G and Liu, J and Ren, JL and Guleng, B},
title = {Glycerol monolaurate ameliorates DSS-induced acute colitis by inhibiting infiltration of Th17, neutrophils, macrophages and altering the gut microbiota.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {911315},
pmid = {36034889},
issn = {2296-861X},
abstract = {BACKGROUND AND AIMS: Inflammatory bowel disease (IBD) places a heavy medical burden on countries and families due to repeated and prolonged attacks, and the incidence and prevalence of IBD are increasing worldwide. Therefore, finding an effective treatment is a matter of great urgency. Glycerol monolaurate (GML), which has a twelve-carbon chain, is a compound naturally found in human breast milk. Some studies have shown that GML has antibacterial and anti-inflammatory effects. However, the specific mechanism of action remains unclear.<br><br>METHODS: Acute colitis was established in mice using 3% DSS, and glycerol monolaurate (500 mg&#xb7;kg-[1]) was administered for two weeks. QPCR and western blotting were performed to examine the inflammatory status. Mice described were subjected to flow cytometry analysis for immune cell activation.<br><br>RESULTS: GML treated alleviated macroscopic symptoms such as shortened colons, increased spleen weight, and caused weight loss in mice with DSS-induced colitis. In addition, GML decreased the expression of pro-inflammatory factors (NF-&#x3b1;, IL-1&#x3b2; and IL-1&#x3b1;) and increased the expression of anti-inflammatory factors (IL-10 and TGF-&#x3b2;). GML inhibited the activation of the MAPK and NF-&#x3ba;B signalling pathways, improved tissue damage, and increased the expression of intestinal tight junction proteins. In addition, LPMCs extracted from intestinal tissue via flow cytometry showed that GML treatment led to a decrease of Th17 cells, Neutrophils and Macrophages. 16S rDNA sequencing showed that GML increased the abundance of commensal bacterium such as Akkermansia and Lactobacillus murinus.<br><br>CONCLUSIONS: We showed that oral administration of GML ameliorated DSS-induced colitis by inhibiting infiltration of Th17 cells, Neutrophils, and Macrophages, protecting the intestinal mucosal barrier and altered the abundance of commensal bacterium. This study provides new insights into the biological function and therapeutic potential of GML in the treatment of IBD.},
}
@article {pmid36030743,
year = {2022},
author = {Chen, W and Wei, J and Su, Z and Wu, L and Liu, M and Huang, X and Yao, P and Wen, D},
title = {Deterministic mechanisms drive bacterial communities assembly in industrial wastewater treatment system.},
journal = {Environment international},
volume = {168},
number = {},
pages = {107486},
doi = {10.1016/j.envint.2022.107486},
pmid = {36030743},
issn = {1873-6750},
mesh = {Wastewater ; Sewage/chemistry ; Bacteria ; *Microbiota ; *Water Purification ; },
abstract = {Microbial communities are responsible for biological treatment of many industrial wastewater, but our knowledge of their diversity, assembly patterns, and function is still poor. Here, we analyzed the bacterial communities of wastewater and activated sludge samples taken from 11 full-scale industrial wastewater treatment plants (IWWTPs) characterized by the same process design but different wastewater types and WWTP compartments. We found significantly different diversity and compositions of bacterial assemblages among distinct wastewater types and IWWTPs compartments. IWWTPs bacterial communities exhibited a clear species abundance distribution. The dispersal-driven process was weak in shaping IWWTP communities. Meanwhile, environmental and operating conditions were important factors in regulating the structure of the activated sludge community and pollutants removal, indicating that bacterial community was largely driven by deterministic mechanisms. The core microbial community in IWWTPs was different from that in municipal wastewater treatment plants (MWWTPs), and many taxa (e.g. the genus Citreitalea) rarely were detected before, indicating IWWTPs harbored unique core bacterial communities. Furthermore, we found that bacterial community compositions were strongly linked to activated sludge function. These findings are important to both microbial ecologists and environmental engineers, who may optimize the operation strategies jointly for maintaining biodiversity, which in turn may promote a more stable performance of the IWWTP. Overall, our study enhances the mechanistic understanding of the IWWTP microbial community diversity, assembly patterns, and function, and provides important implications for microbial ecology and wastewater treatment processes.},
}
@article {pmid36030426,
year = {2022},
author = {Barman, D and Dkhar, MS},
title = {Characterization and purification of esterase from Cellulomonas fimi DB19 isolated from Zanthoxylum armatum with its possible role in diesel biodegradation.},
journal = {Archives of microbiology},
volume = {204},
number = {9},
pages = {580},
pmid = {36030426},
issn = {1432-072X},
mesh = {Azo Compounds ; Cellulomonas ; Enzyme Stability ; *Esterases ; Hydrogen Peroxide ; Hydrogen-Ion Concentration ; Temperature ; *Zanthoxylum ; },
abstract = {Endophytic bacteria inhabit all or part of their life cycle within the tissues of healthy plants, without causing any apparent symptoms of disease. They are treasure trove of several hydrolytic enzymes with distinct characteristics. Esterase is one of such enzymes and this study aims to characterize esterase produced by endophytic actinobacteria Cellulomonas fimi DB19 isolated from Zanthoxylum armatum with its capacity to degrade diesel oil. The enzyme was purified with purification fold 8.22 and specific activity 124.72 U/mg with 16.43% recovery. The purified enzyme showed a single protein band on SDS-PAGE having molecular mass of approximately 39 kDa. The Km and Vmax value for p-nitrophenyl acetate were 2.23 mM and 22.04 U/mL, respectively. The enzyme was stable in the pH range 6-9 with its optimal activity at pH 8.0. The enzyme was stable at 40 °C and retained more than 80% activity after incubation for two h. The enzyme activity was positively influenced in the presence of Na[+], Ba[2+], Ca[2+], and negatively by Mn[2+], and Mg[2+]. The EDTA and PMSF inhibited the enzyme activity and retained its activity in the presence of SDS, H2O2, β-mercaptoethanol, and organic solvents. Application of the isolate in degradation of diesel showed that its growth and degradation capacity enhanced in media supplemented with 0.2-4% of diesel oil with maximum at 3% of diesel oil. Furthermore, esterase activity was greater in media containing diesel than control which is suggesting the plausible role of esterase produced by Cellulomonas fimi DB19 in the degradation of diesel oil.},
}
@article {pmid36029817,
year = {2022},
author = {Wang, P and Cao, J and Mao, L and Zhu, L and Zhang, Y and Zhang, L and Jiang, H and Zheng, Y and Liu, X},
title = {Effect of H3PO4-modified biochar on the fate of atrazine and remediation of bacterial community in atrazine-contaminated soil.},
journal = {The Science of the total environment},
volume = {851},
number = {Pt 2},
pages = {158278},
doi = {10.1016/j.scitotenv.2022.158278},
pmid = {36029817},
issn = {1879-1026},
mesh = {*Atrazine/analysis ; *Soil Pollutants/analysis ; Adsorption ; Charcoal/chemistry ; Soil/chemistry ; Bacteria ; *Pesticides ; Phosphorus ; *Environmental Restoration and Remediation ; },
abstract = {The application of chemically modified biochar is a promising strategy for the remediation of contaminated (e.g., pesticides) soil. In this study, H3PO4 was used to modify peanut shell to improve the remediation performance of biochar. Surface area (980.19 m[2]/g), pore volume (0.12 cm[3]/g), and the functional groups (OH, CO, and phosphorus-containing groups) on the biochar were increased by H3PO4 treatment. The sorption experimental data were well fitted by Freundlich model, while the sorption affinity (Kf) of H3PO4 modified biochar (PBC) for atrazine was 128 times greater than that of the untreated biochar (BC) in the aquatic systems. The Kf values of PBC-amended soil to atrazine were increased by 13.57 times than that of single soil. The strong sorption of PBC on atrazine delayed the degradation of atrazine in soil, and the residual percentage of atrazine in soil and soil-PBC mixture were 4.90% and 71.44% at the end of 60-day incubation, with the degradation half-life increased from 13.3 to 121.6 d. The analysis of high-throughput sequencing results showed that atrazine reduced the diversity of soil microbial community, but the abundance of microorganisms with degradation function increased and became dominant species. The addition of PBC in soil accelerated the microbial remediation of atrazine stress, which may promote the soil nitrogen cycle. Therefore, amendment of atrazine contaminated soil with PBC can reduce the environmental risk of atrazine and benefit the soil microbial ecology.},
}
@article {pmid36028909,
year = {2022},
author = {Somerville, V and Schowing, T and Chabas, H and Schmidt, RS and von Ah, U and Bruggmann, R and Engel, P},
title = {Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {137},
pmid = {36028909},
issn = {2049-2618},
mesh = {Bacteria ; *Bacteriophages ; *Cheese ; Genome, Bacterial ; Metagenome ; },
abstract = {BACKGROUND: Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments.<br><br>RESULTS: We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles.<br><br>CONCLUSIONS: Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry. Video Abstract.},
}
@article {pmid36016781,
year = {2022},
author = {Zhimo, VY and Kumar, A and Biasi, A and Abdelfattah, A and Sharma, VK and Salim, S and Feygenberg, O and Bartuv, R and Freilich, S and Whitehead, SR and Wisniewski, M and Droby, S},
title = {Assembly and dynamics of the apple carposphere microbiome during fruit development and storage.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {928888},
pmid = {36016781},
issn = {1664-302X},
abstract = {Microbial communities associated with fruit can contribute to quality and pathogen resistance, but little is known about their assembly and dynamics during fruit development and storage. Three apple cultivars growing under the same environmental conditions were utilized to examine the apple carposphere microbiome composition and structure at different developmental stages and storage. There was a significant effect (Adonis, p ≤ 0.001) of fruit genotype and its developmental stages and storage times on the fruit surface microbial assemblage and a strong temporal microbial community succession was detected (Mantel test: R ≤ 0.5, p = 0.001) in both bacterial and fungal communities. A set of 15 bacterial and 35 fungal core successional taxa and members exhibiting differential abundances at different fruit stages were identified. For the first time, we show the existence of underlying universal dynamics in the assembly of fruit-associated microbiomes. We also provide evidence of strong microbial cross-domain associations and uncover potential microbe-microbe correlations in the apple carposphere. Together our findings shed light on how the fruit carposphere assemble and change over time, and provide new insights into fruit microbial ecology.},
}
@article {pmid36014090,
year = {2022},
author = {Schultz, J and Parise, MTD and Parise, D and Medeiros, LG and Sousa, TJ and Kato, RB and Uetanabaro, APT and Araújo, F and Ramos, RTJ and de Castro Soares, S and Brenig, B and de Carvalho Azevedo, VA and Góes-Neto, A and Rosado, AS},
title = {Unraveling the Genomic Potential of the Thermophilic Bacterium Anoxybacillus flavithermus from an Antarctic Geothermal Environment.},
journal = {Microorganisms},
volume = {10},
number = {8},
pages = {},
pmid = {36014090},
issn = {2076-2607},
support = {Baseline Grant//King Abdullah University of Science and Technology/ ; },
abstract = {Antarctica is a mosaic of extremes. It harbors active polar volcanoes, such as Deception Island, a marine stratovolcano having notable temperature gradients over very short distances, with the temperature reaching up to 100 °C near the fumaroles and subzero temperatures being noted in the glaciers. From the sediments of Deception Island, we isolated representatives of the genus Anoxybacillus, a widely spread genus that is mainly encountered in thermophilic environments. However, the phylogeny of this genus and its adaptive mechanisms in the geothermal sites of cold environments remain unknown. To the best of our knowledge, this is the first study to unravel the genomic features and provide insights into the phylogenomics and metabolic potential of members of the genus Anoxybacillus inhabiting the Antarctic thermophilic ecosystem. Here, we report the genome sequencing data of seven A. flavithermus strains isolated from two geothermal sites on Deception Island, Antarctic Peninsula. Their genomes were approximately 3.0 Mb in size, had a G + C ratio of 42%, and were predicted to encode 3500 proteins on average. We observed that the strains were phylogenomically closest to each other (Average Nucleotide Identity (ANI) > 98%) and to A. flavithermus (ANI 95%). In silico genomic analysis revealed 15 resistance and metabolic islands, as well as genes related to genome stabilization, DNA repair systems against UV radiation threats, temperature adaptation, heat- and cold-shock proteins (Csps), and resistance to alkaline conditions. Remarkably, glycosyl hydrolase enzyme-encoding genes, secondary metabolites, and prophage sequences were predicted, revealing metabolic and cellular capabilities for potential biotechnological applications.},
}
@article {pmid36014036,
year = {2022},
author = {Thiele, S and Storesund, JE and Fernández-Méndez, M and Assmy, P and Øvreås, L},
title = {A Winter-to-Summer Transition of Bacterial and Archaeal Communities in Arctic Sea Ice.},
journal = {Microorganisms},
volume = {10},
number = {8},
pages = {},
pmid = {36014036},
issn = {2076-2607},
support = {U17 CE002015/CE/NCIPC CDC HHS/United States ; },
abstract = {The Arctic is warming 2-3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community.},
}
@article {pmid36014023,
year = {2022},
author = {Ouwerkerk, JP and Tytgat, HLP and Elzinga, J and Koehorst, J and Van den Abbeele, P and Henrissat, B and Gueimonde, M and Cani, PD and Van de Wiele, T and Belzer, C and de Vos, WM},
title = {Comparative Genomics and Physiology of Akkermansia muciniphila Isolates from Human Intestine Reveal Specialized Mucosal Adaptation.},
journal = {Microorganisms},
volume = {10},
number = {8},
pages = {},
pmid = {36014023},
issn = {2076-2607},
support = {BOF12-GOA-008//Ghent University/ ; Advanced Grand 250172 - Microbes Inside/ERC_/European Research Council/International ; Spinoza Award Willem M. de Vos/NWO_/Dutch Research Council/Netherlands ; SIAM Gravity Grant 024.002.002/NWO_/Dutch Research Council/Netherlands ; FRFS-WELBIO: WELBIO-CR-2022A-02//Fund for Scientific Research/ ; },
abstract = {Akkermansia muciniphila is a champion of mucin degradation in the human gastrointestinal tract. Here, we report the isolation of six novel strains from healthy human donors and their genomic, proteomic and physiological characterization in comparison to the type-strains A. muciniphila MucT and A. glycaniphila PytT. Complete genome sequencing revealed that, despite their large genomic similarity (>97.6%), the novel isolates clustered into two distinct subspecies of A. muciniphila: Amuc1, which includes the type-strain MucT, and AmucU, a cluster of unassigned strains that have not yet been well characterized. CRISPR analysis showed all strains to be unique and confirmed that single healthy subjects can carry more than one A. muciniphila strain. Mucin degradation pathways were strongly conserved amongst all isolates, illustrating the exemplary niche adaptation of A. muciniphila to the mucin interface. This was confirmed by analysis of the predicted glycoside hydrolase profiles and supported by comparing the proteomes of A. muciniphila strain H2, belonging to the AmucU cluster, to MucT and A. glycaniphila PytT (including 610 and 727 proteins, respectively). While some intrinsic resistance was observed among the A. muciniphila straind, none of these seem to pose strain-specific risks in terms of their antibiotic resistance patterns nor a significant risk for the horizontal transfer of antibiotic resistance determinants, opening the way to apply the type-strain MucT or these new A. muciniphila strains as next generation beneficial microbes.},
}
@article {pmid36009876,
year = {2022},
author = {Nakatani, H and Yamada, N and Hashimoto, N and Okazaki, F and Arakawa, T and Tamaru, Y and Hori, K},
title = {Perturbation by Antimicrobial Bacteria of the Epidermal Bacterial Flora of Rainbow Trout in Flow-Through Aquaculture.},
journal = {Biology},
volume = {11},
number = {8},
pages = {},
pmid = {36009876},
issn = {2079-7737},
support = {JPMJMI18CF//Japan Science and Technology Agency/ ; JP 20H02539//Japan Society for the Promotion of Science/ ; },
abstract = {The bacterial flora of the epidermal mucus of fish is closely associated with the host's health and susceptibility to pathogenic infections. In this study, we analyzed the epidermal mucus bacteria of rainbow trout (Oncorhynchus mykiss) reared in flow-through aquaculture under environmental perturbations. Over ~2 years, the bacteria present in the skin mucus and water were analyzed based on the 16S rDNA sequences. The composition of the mucus bacterial community showed significant monthly fluctuations, with frequent changes in the dominant bacterial species. Analysis of the beta- and alpha-diversity of the mucus bacterial flora showed the fluctuations of the composition of the flora were caused by the genera Pseudomonas, Yersinia, and Flavobacterium, and some species of Pseudomonas and Yersinia in the mucus were identified as antimicrobial bacteria. Examination of the antimicrobial bacteria in the lab aquarium showed that the natural presence of antimicrobial bacteria in the mucus and water, or the purposeful addition of them to the rearing water, caused a transition in the mucus bacteria community composition. These results demonstrate that specific antimicrobial bacteria in the water or in epidermal mucus comprise one of the causes of changes in fish epidermal mucus microflora.},
}
@article {pmid36008420,
year = {2022},
author = {Weyhenmeyer, GA and Obertegger, U and Rudebeck, H and Jakobsson, E and Jansen, J and Zdorovennova, G and Bansal, S and Block, BD and Carey, CC and Doubek, JP and Dugan, H and Erina, O and Fedorova, I and Fischer, JM and Grinberga, L and Grossart, HP and Kangur, K and Knoll, LB and Laas, A and Lepori, F and Meier, J and Palshin, N and Peternell, M and Pulkkanen, M and Rusak, JA and Sharma, S and Wain, D and Zdorovennov, R},
title = {Towards critical white ice conditions in lakes under global warming.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {4974},
pmid = {36008420},
issn = {2041-1723},
mesh = {Global Warming ; Humans ; *Ice ; Ice Cover ; *Lakes ; Seasons ; Temperature ; },
abstract = {The quality of lake ice is of uppermost importance for ice safety and under-ice ecology, but its temporal and spatial variability is largely unknown. Here we conducted a coordinated lake ice quality sampling campaign across the Northern Hemisphere during one of the warmest winters since 1880 and show that lake ice during 2020/2021 commonly consisted of unstable white ice, at times contributing up to 100% to the total ice thickness. We observed that white ice increased over the winter season, becoming thickest and constituting the largest proportion of the ice layer towards the end of the ice cover season when fatal winter drownings occur most often and light limits the growth and reproduction of primary producers. We attribute the dominance of white ice before ice-off to air temperatures varying around the freezing point, a condition which occurs more frequently during warmer winters. Thus, under continued global warming, the prevalence of white ice is likely to substantially increase during the critical period before ice-off, for which we adjusted commonly used equations for human ice safety and light transmittance through ice.},
}
@article {pmid36005399,
year = {2022},
author = {Pacheco, AR and Pauvert, C and Kishore, D and Segrè, D},
title = {Toward FAIR Representations of Microbial Interactions.},
journal = {mSystems},
volume = {7},
number = {5},
pages = {e0065922},
pmid = {36005399},
issn = {2379-5077},
support = {R21 CA260382/CA/NCI NIH HHS/United States ; UH2 AG064704/AG/NIA NIH HHS/United States ; R21CA260382//NIH, National Cancer Institute/ ; UH2AG064704//HHS | NIH | National Institute on Aging (NIA)/ ; },
mesh = {*Microbial Interactions ; *Microbiota ; },
abstract = {Despite an ever-growing number of data sets that catalog and characterize interactions between microbes in different environments and conditions, many of these data are neither easily accessible nor intercompatible. These limitations present a major challenge to microbiome research by hindering the streamlined drawing of inferences across studies. Here, we propose guiding principles to make microbial interaction data more findable, accessible, interoperable, and reusable (FAIR). We outline specific use cases for interaction data that span the diverse space of microbiome research, and discuss the untapped potential for new insights that can be fulfilled through broader integration of microbial interaction data. These include, among others, the design of intercompatible synthetic communities for environmental, industrial, or medical applications, and the inference of novel interactions from disparate studies. Lastly, we envision potential trajectories for the deployment of FAIR microbial interaction data based on existing resources, reporting standards, and current momentum within the community.},
}
@article {pmid36005392,
year = {2022},
author = {Richter, I and Radosa, S and Cseresnyés, Z and Ferling, I and Büttner, H and Niehs, SP and Gerst, R and Scherlach, K and Figge, MT and Hillmann, F and Hertweck, C},
title = {Toxin-Producing Endosymbionts Shield Pathogenic Fungus against Micropredators.},
journal = {mBio},
volume = {13},
number = {5},
pages = {e0144022},
pmid = {36005392},
issn = {2150-7511},
support = {P40 OD010440/OD/NIH HHS/United States ; },
mesh = {Animals ; *Burkholderia/metabolism ; *Antimitotic Agents/metabolism ; Macrolides ; Symbiosis ; *Oryza/microbiology ; *Toxins, Biological ; Seedlings ; Soil ; },
abstract = {The fungus Rhizopus microsporus harbors a bacterial endosymbiont (Mycetohabitans rhizoxinica) for the production of the antimitotic toxin rhizoxin. Although rhizoxin is the causative agent of rice seedling blight, the toxinogenic bacterial-fungal alliance is, not restricted to the plant disease. It has been detected in numerous environmental isolates from geographically distinct sites covering all five continents, thus raising questions regarding the ecological role of rhizoxin beyond rice seedling blight. Here, we show that rhizoxin serves the fungal host in fending off protozoan and metazoan predators. Fluorescence microscopy and coculture experiments with the fungivorous amoeba Protostelium aurantium revealed that ingestion of R. microsporus spores is toxic to P. aurantium. This amoebicidal effect is caused by the dominant bacterial rhizoxin congener rhizoxin S2, which is also lethal toward the model nematode Caenorhabditis elegans. By combining stereomicroscopy, automated image analysis, and quantification of nematode movement, we show that the fungivorous nematode Aphelenchus avenae actively feeds on R. microsporus that is lacking endosymbionts, whereas worms coincubated with symbiotic R. microsporus are significantly less lively. This study uncovers an unexpected ecological role of rhizoxin as shield against micropredators. This finding suggests that predators may function as an evolutionary driving force to maintain toxin-producing endosymbionts in nonpathogenic fungi. IMPORTANCE The soil community is a complex system characterized by predator-prey interactions. Fungi have developed effective strategies to defend themselves against predators. Understanding these strategies is of critical importance for ecology, medicine, and biotechnology. In this study, we shed light on the defense mechanisms of the phytopathogenic Rhizopus-Mycetohabitans symbiosis that has spread worldwide. We report an unexpected role of rhizoxin, a secondary metabolite produced by the bacterium M. rhizoxinica residing within the hyphae of R. microsporus. We show that this bacterial secondary metabolite is utilized by the fungal host to successfully fend off fungivorous protozoan and metazoan predators and thus identified a fundamentally new function of this infamous cytotoxic compound. This endosymbiont-dependent predator defense illustrates an unusual strategy employed by fungi that has broader implications, since it may serve as a model for understanding how animal predation acts as an evolutionary driving force to maintain endosymbionts in nonpathogenic fungi.},
}
@article {pmid36002667,
year = {2023},
author = {Lopes, RB and Faria, M and Souza, DA and Sosa-Gómez, DR},
title = {Potential Impact of Chemical Fungicides on the Efficacy of Metarhizium rileyi and the Occurrence of Pandora gammae on Caterpillars in Soybean Crops.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {647-657},
pmid = {36002667},
issn = {1432-184X},
support = {20.19.02.007.00.00//Embrapa Recursos Gen&#xe9;ticos e Biotecnologia/ ; PQ 309070/2020-1//National Council for Scientific and Technological Development (CNPq - BR)/ ; },
mesh = {Animals ; Glycine max ; *Moths ; *Metarhizium ; Larva/microbiology ; Crops, Agricultural ; *Fungicides, Industrial/pharmacology ; },
abstract = {Entomopathogenic fungi may play a crucial role in the regulation of caterpillar populations in soybean crops, either through natural occurrences or applied as mycopesticides. In the present work, we reported the naturally occurring entomopathogenic fungus Pandora gammae attacking the caterpillar Chrysodeixis includens, with infection rates in field trials ran in two consecutive years in the 10-35% range. As many chemicals are potentially harmful to entomopathogenic fungi, this work aimed to investigate the potential impact of two chemical fungicides (azoxystrobin + benzovindiflupyr and trifloxistrobina + prothioconazole) used to control soybean rust (Phakopsora pachyrhizi) on the natural occurrence of P. gammae and Metarhizium rileyi, as well as the efficacy of the latter fungus applied as different formulations against the soybean caterpillars Anticarsia gemmatalis and C. includens. Under laboratory conditions, fungicides used at field-recommended rates had a considerable negative impact on the germinability of M. riley on the medium surface, and all tested formulations did not protect conidia from damage by these chemicals. This harmful effect also impacted host infectivity, as the larval mortality owing to this fungus was reduced by 30-40% compared to that of the fungicide-free treatments. In field trials conducted in two subsequent years, unformulated and formulated M. rileyi conidia applied to soybean plants produced primary infection sites in caterpillar populations after a single spray. Spraying unformulated or formulated M. rileyi conidia following fungicide application on plants did not affect host infection rates over time. Moreover, the use of M. rileyi-based formulations or chemical fungicide did not interfere with the natural infection rates by P. gammae on its host, C. includens. Although a higher degree of exposure to non-selective fungicides can negatively affect fungal entomopathogens, a single foliar application of fungicides may be harmless to both M. rileyi and P. gammae in soybean fields. Additionally, this work showed that naturally occurring wasps and tachnids also play an important role in the regulation of A. gemmatalis and, notably, C. includens, with parasitism rates above 40-50% in some cases.},
}
@article {pmid36001047,
year = {2023},
author = {Shaffer, M and Thurimella, K and Sterrett, JD and Lozupone, CA},
title = {SCNIC: Sparse correlation network investigation for compositional data.},
journal = {Molecular ecology resources},
volume = {23},
number = {1},
pages = {312-325},
pmid = {36001047},
issn = {1755-0998},
support = {T15 LM009451/LM/NLM NIH HHS/United States ; 4 T15 LM009451-10//U.S. National Library of Medicine/ ; //National Science Foundation/ ; },
mesh = {*Software ; Algorithms ; *Microbiota ; },
abstract = {Microbiome studies are often limited by a lack of statistical power due to small sample sizes and a large number of features. This problem is exacerbated in correlative studies of multi-omic datasets. Statistical power can be increased by finding and summarizing modules of correlated observations, which is one dimensionality reduction method. Additionally, modules provide biological insight as correlated groups of microbes can have relationships among themselves. To address these challenges, we developed SCNIC: Sparse Cooccurrence Network Investigation for compositional data. SCNIC is open-source software that can generate correlation networks and detect and summarize modules of highly correlated features. Modules can be formed using either the Louvain Modularity Maximization (LMM) algorithm or a Shared Minimum Distance algorithm (SMD) that we newly describe here and relate to LMM using simulated data. We applied SCNIC to two published datasets and we achieved increased statistical power and identified microbes that not only differed across groups, but also correlated strongly with each other, suggesting shared environmental drivers or cooperative relationships among them. SCNIC provides an easy way to generate correlation networks, identify modules of correlated features and summarize them for downstream statistical analysis. Although SCNIC was designed considering properties of microbiome data, such as compositionality and sparsity, it can be applied to a variety of data types including metabolomics data and used to integrate multiple data types. SCNIC allows for the identification of functional microbial relationships at scale while increasing statistical power through feature reduction.},
}
@article {pmid35998537,
year = {2022},
author = {Qin, Z and Zhao, Z and Xia, L and Ohore, OE},
title = {Unraveling the ecological mechanisms of bacterial succession in epiphytic biofilms on Vallisneria natans and Hydrilla verticillata during bioremediation of phenanthrene and pyrene polluted wetland.},
journal = {Journal of environmental management},
volume = {321},
number = {},
pages = {115986},
doi = {10.1016/j.jenvman.2022.115986},
pmid = {35998537},
issn = {1095-8630},
mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Biofilms ; Ecosystem ; *Hydrocharitaceae ; *Phenanthrenes ; *Polycyclic Aromatic Hydrocarbons ; Pyrenes ; Wetlands ; },
abstract = {In wetland ecosystem, the microbial succession in epiphytic biofilms of submerged macrophytes remains to be fully elucidated, especially submerged macrophytes used to remediate organic pollutants contaminated sediment. Herein, 16 S rRNA gene sequencing was used to investigate the bacterial dynamics and ecological processes in the biofilms of two typical submerged macrophytes (Vallisneria natans and Hydrilla verticillata) settled in sediment polluted by polycyclic aromatic hydrocarbons (PAHs) at two growth periods. The results presented that the variations of bacterial community in the biofilms were influenced by attached surfaces (explanation ratio: 17.30%), incubation time (32.30%) and environmental factors (39.10%). Bacterial community assembly was mainly driven by dispersal limitation which triggered more positive co-occurrence associations in microbial networks, maintaining ecological stability in the process of bioremediation of PAHs. Additionally, the functional redundancy strength of bacterial community was more affected by attached surface than incubation time. The structural equation model illustrated that community assembly drove β-diversity and explained a part of ecological functions. Environmental factors, community assembly, and β-diversity jointly affected microbial networks. Overall, our study offers new insights into the microbial ecology in biofilms attached on the submerged macrophytes settled in PAH-polluted sediment, providing important information for deeply understanding submerged macrophyte-biofilm complex and promoting sustainable phytoremediation in shallow lacustrine and marshy ecosystems.},
}
@article {pmid35997797,
year = {2023},
author = {Javal, M and Terblanche, JS and Benoit, L and Conlong, DE and Lloyd, JR and Smit, C and Chapuis, MP},
title = {Does Host Plant Drive Variation in Microbial Gut Communities in a Recently Shifted Pest?.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {636-646},
pmid = {35997797},
issn = {1432-184X},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Microbiota ; Larva/microbiology ; *Coleoptera/microbiology ; Bacteria/genetics ; Plants ; },
abstract = {Biotic interactions can modulate the responses of organisms to environmental stresses, including diet changes. Gut microbes have substantial effects on diverse ecological and evolutionary traits of their hosts, and microbial communities can be highly dynamic within and between individuals in space and time. Modulations of the gut microbiome composition and their potential role in the success of a species to maintain itself in a new environment have been poorly studied to date. Here we examine this question in a large wood-boring beetle Cacosceles newmannii (Cerambycidae), that was recently found thriving on a newly colonized host plant. Using 16S metabarcoding, we assessed the gut bacterial community composition of larvae collected in an infested field and in "common garden" conditions, fed under laboratory-controlled conditions on four either suspected or known hosts (sugarcane, tea tree, wattle, and eucalyptus). We analysed microbiome variation (i.e. diversity and differentiation), measured fitness-related larval growth, and studied host plant lignin and cellulose contents, since their degradation is especially challenging for wood-boring insects. We show that sugarcane seems to be a much more favourable host for larval growth. Bacterial diversity level was the highest in field-collected larvae, whereas lab-reared larvae fed on sugarcane showed a relatively low level of diversity but very specific bacterial variants. Bacterial communities were mainly dominated by Proteobacteria, but were significantly different between sugarcane-fed lab-reared larvae and any other hosts or field-collected larvae. We identified changes in the gut microbiome associated with different hosts over a short time frame, which support the hypothesis of a role of the microbiome in host switches.},
}
@article {pmid35997493,
year = {2022},
author = {Floudas, D and Gentile, L and Andersson, E and Kanellopoulos, SG and Tunlid, A and Persson, P and Olsson, U},
title = {X-Ray Scattering Reveals Two Mechanisms of Cellulose Microfibril Degradation by Filamentous Fungi.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {17},
pages = {e0099522},
pmid = {35997493},
issn = {1098-5336},
mesh = {*Agaricales/metabolism ; *Basidiomycota/metabolism ; Cellulose/metabolism ; Fungi/metabolism ; Lignin/metabolism ; Microfibrils/metabolism ; Wood/microbiology ; X-Rays ; },
abstract = {Mushroom-forming fungi (Agaricomycetes) employ enzymatic and nonenzymatic cellulose degradation mechanisms, the latter presumably relying on Fenton-generated radicals. The effects of the two mechanisms on the cellulose microfibrils structure remain poorly understood. We examined cellulose degradation caused by litter decomposers and wood decomposers, including brown-rot and white-rot fungi and one fungus with uncertain wood decay type, by combining small- and wide-angle X-ray scattering. We also examined the effects of commercial enzymes and Fenton-generated radicals on cellulose using the same method. We detected two main degradation or modification mechanisms. The first characterized the mechanism used by most fungi and resembled enzymatic cellulose degradation, causing simultaneous microfibril thinning and decreased crystalline cellulose. The second mechanism was detected in one brown-rot fungus and one litter decomposer and was characterized by patchy amorphogenesis of crystalline cellulose without substantial thinning of the fibers. This pattern did not resemble the effect of Fenton-generated radicals, suggesting a more complex mechanism is involved in the destruction of cellulose crystallinity by fungi. Furthermore, our results showed a mismatch between decay classifications and cellulose degradation patterns and that even within litter decomposers two degradation mechanisms were found, suggesting higher functional diversity under current ecological classifications of fungi. IMPORTANCE Cellulose degradation by fungi plays a fundamental role in terrestrial carbon cycling, but the mechanisms by which fungi cope with the crystallinity of cellulose are not fully understood. We used X-ray scattering to analyze how fungi, a commercial enzyme mix, and a Fenton reaction-generated radical alter the crystalline structure of cellulose. Our data revealed two mechanisms involved in crystalline cellulose degradation by fungi: one that results in the thinning of the cellulose fibers, resembling the enzymatic degradation of cellulose, and one that involves amorphogenesis of crystalline cellulose by yet-unknown pathways, resulting in a patchy-like degradation pattern. These results pave the way to a deeper understanding of cellulose degradation and the development of novel ways to utilize crystalline cellulose.},
}
@article {pmid35997077,
year = {2022},
author = {Cho, GY and Whang, KS},
title = {Aquibacillus saliphilus sp. nov., a moderately halophilic bacterium isolated from a grey saltern.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {8},
pages = {},
doi = {10.1099/ijsem.0.005496},
pmid = {35997077},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Fatty Acids/chemistry ; Phospholipids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; },
abstract = {A novel moderately halophilic bacterium, designated strain KHM2[T], was isolated from the sediment of a grey solar saltern located on Sinui Island, Shinan, Republic of Korea. Cells were rod-shaped, endospore-forming, Gram-stain-positive, motile and facultative anaerobic. Strain KHM2[T] performed anaerobic respiration using nitrates and did not produce glucose acids, indicating the absence of fermentation. Strain KHM2[T] grew at 10-45 °C (optimum, 37 °C), pH 6.0-10.0 (optimum, pH 8.0) and with 1.0-20.0 % (w/v) NaCl (optimum, 10.0%). Based on 16S rRNA gene sequence similarity and chemotaxonomic properties, strain KHM2[T] was assigned to the genus Aquibacillus, with high 16S rRNA gene sequence similarity to Aquibacillus halophilus B6B[T] (98.2%) and less than 96.8 % similarity to the other recognized members of the genus Aquibacillus. The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and one unidentified phospholipid (PL). Major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The average nucleotide identity and digital DNA-DNA hybridization values of strain KHM2[T] with A. halophilus B6B[T] were 77.6 and 22.0 %, respectively. Based on the results of polyphasic analysis, strain KHM2[T] is proposed to represent a bacterial species within the genus Aquibacillus with the name Aquibacillus saliphilus sp. nov. The type strain is KHM2[T] (=KACC 19068[T]=NBRC 112577[T]).},
}
@article {pmid35996183,
year = {2022},
author = {Cowan, DA and Lebre, PH and Amon, C and Becker, RW and Boga, HI and Boulangé, A and Chiyaka, TL and Coetzee, T and de Jager, PC and Dikinya, O and Eckardt, F and Greve, M and Harris, MA and Hopkins, DW and Houngnandan, HB and Houngnandan, P and Jordaan, K and Kaimoyo, E and Kambura, AK and Kamgan-Nkuekam, G and Makhalanyane, TP and Maggs-Kölling, G and Marais, E and Mondlane, H and Nghalipo, E and Olivier, BW and Ortiz, M and Pertierra, LR and Ramond, JB and Seely, M and Sithole-Niang, I and Valverde, A and Varliero, G and Vikram, S and Wall, DH and Zeze, A},
title = {Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {131},
pmid = {35996183},
issn = {2049-2618},
mesh = {Biodiversity ; Desert Climate ; Ecosystem ; *Microbiota/genetics ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {BACKGROUND: Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents.<br><br>RESULTS: The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation.<br><br>CONCLUSION: This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.},
}
@article {pmid35995772,
year = {2022},
author = {Nyongesa, S and Weber, PM and Bernet, &#xc8; and Pulido, F and Nieves, C and Nieckarz, M and Delaby, M and Viehboeck, T and Krause, N and Rivera-Millot, A and Nakamura, A and Vischer, NOE and vanNieuwenhze, M and Brun, YV and Cava, F and Bulgheresi, S and Veyrier, FJ},
title = {Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {4853},
pmid = {35995772},
issn = {2041-1723},
mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; *Cell Division ; Cell Wall/metabolism ; Mammals/microbiology ; *Neisseriaceae/cytology ; Peptidoglycan/metabolism ; },
abstract = {Rod-shaped bacteria typically elongate and divide by transverse fission. However, several bacterial species can form rod-shaped cells that divide longitudinally. Here, we study the evolution of cell shape and division mode within the family Neisseriaceae, which includes Gram-negative coccoid and rod-shaped species. In particular, bacteria of the genera Alysiella, Simonsiella and Conchiformibius, which can be found in the oral cavity of mammals, are multicellular and divide longitudinally. We use comparative genomics and ultrastructural microscopy to infer that longitudinal division within Neisseriaceae evolved from a rod-shaped ancestor. In multicellular longitudinally-dividing species, neighbouring cells within multicellular filaments are attached by their lateral peptidoglycan. In these bacteria, peptidoglycan insertion does not appear concentric, i.e. from the cell periphery to its centre, but as a medial sheet guillotining each cell. Finally, we identify genes and alleles associated with multicellularity and longitudinal division, including the acquisition of amidase-encoding gene amiC2, and amino acid changes in proteins including MreB and FtsA. Introduction of amiC2 and allelic substitution of mreB in a rod-shaped species that divides by transverse fission results in shorter cells with longer septa. Our work sheds light on the evolution of multicellularity and longitudinal division in bacteria, and suggests that members of the Neisseriaceae family may be good models to study these processes due to their morphological plasticity and genetic tractability.},
}
@article {pmid35993706,
year = {2022},
author = {Kojima, CY and Getz, EW and Thrash, JC},
title = {RRAP: RPKM Recruitment Analysis Pipeline.},
journal = {Microbiology resource announcements},
volume = {11},
number = {9},
pages = {e0064422},
pmid = {35993706},
issn = {2576-098X},
support = {OCE-1747681//National Science Foundation (NSF)/ ; OCE-1945279//National Science Foundation (NSF)/ ; Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; },
abstract = {A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automates this process using Bowtie2 and SAMtools.},
}
@article {pmid35992701,
year = {2022},
author = {Nimonkar, YS and Godambe, T and Kulkarni, A and Patel, T and Paul, D and Paul, D and Rale, V and Prakash, O},
title = {Oligotrophy vs. copiotrophy in an alkaline and saline habitat of Lonar Lake.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {939984},
pmid = {35992701},
issn = {1664-302X},
abstract = {We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic microbes from the sediment were enumerated by the three-tube most probable number (MPN) method using an array of nutrient-rich and oligotrophic (≈10-20 mg carbon L[-1]) media offering simulated natural conditions of pH and salinity. A total of 50 strains from 15 different genera and 30 different species were isolated from the highest positive dilutions of MPN to identify the taxa of oligotrophs and copiotrophic microorganisms dominating in Lonar Lake. We did not get any true oligotrophs due to their adaptation to higher carbon levels during the isolation procedure. On the contrary, several true copiotrophs, which could not adapt and survive on a low-carbon medium, were isolated. It is also observed that changes in medium composition and nutrient level altered the selection of organisms from the same sample. Our data indicate that copiotrophic microorganisms dominate the eutrophic Lonar Lake, which is also supported by the past metagenomics studies from the same site. We also reported that quick depletion of carbon from oligotrophic medium worked as a limiting factor, inducing cell death after 2-3 generations and preventing the development of visible colonies on plates and sufficient optical density in liquid medium. Therefore, a long-term supply of low levels of carbon, followed by isolation on enriched media, can serve as a good strategy in isolation of novel taxa of microorganism, with industrial or environmental importance.},
}
@article {pmid35992662,
year = {2022},
author = {Tang, X and Yangjing, G and Zhuoma, G and Guo, X and Cao, P and Yi, B and Wang, W and Ji, D and Pasquali, M and Baccelli, I and Migheli, Q and Chen, X and Cernava, T},
title = {Biological characterization and in vitro fungicide screenings of a new causal agent of wheat Fusarium head blight in Tibet, China.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {941734},
pmid = {35992662},
issn = {1664-302X},
abstract = {Wheat (Triticum aestivum L.) is an important cereal crop, widely grown throughout the temperate zones, and also suitable for cultivation at higher elevations. Fusarium head blight (FHB) is a highly destructive disease of wheat throughout the globe. In July 2020, serious wheat FHB symptoms were observed in open fields located in Linzhi City, southeast of Tibet, China. The causal agent was identified as Fusarium avenaceum (Fr.) Sacc. by amplification and sequencing of the internal transcribed spacer (ITS) region, translation elongation factor 1-alpha (EF-1α) gene, and RNA polymerase II subunit (RPB-2) gene, as well as by morphological characterization. Koch's postulates were confirmed by a pathogenicity test on healthy spikes, including re-isolation and identification. To our knowledge, this is the first report of F. avenaceum causing FHB on wheat in Tibet, China. Moreover, to determine pathogen characteristics that may be useful for future disease management, the utilization of different carbon and nitrogen resources, temperature, light, and ultraviolet (UV) irradiation on mycelium growth and conidia germination were studied. Soluble starch and peptone were the best carbon, and nitrogen source for the pathogen respectively. The optimal temperatures for the pathogen's mycelium growth and conidia germination were 15-20°C, matching the average temperature during the growing season in Linzhi (Tibet). Meanwhile, alternating 8-h light and 16-h dark was shown to be conducive to mycelia growth, and complete darkness facilitated conidia germination. In addition, UV Irradiation of 48 MJ/cm[2], approximately 100 times of the local condition, did not inhibit the germination of conidia. Furthermore, in vitro screening of effective fungicides was conducted. Among the seven tested pesticides, carbendazim showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 2.1 mg/L. Propiconazole also showed sufficient inhibitory effects against F. avenaceum, with an EC50 value of 2.6 mg/L. The study provides insights into the newly identified causal agent of wheat FHB in Tibet, China, as well as first pathogen characteristics and promising candidate substances for its management.},
}
@article {pmid35987172,
year = {2022},
author = {Silva, DFD and Moreira, JV and Sousa, LIS and Santana, MC and Mota, JCA and Queiroz, ADS and Nascimento, &#xcd;VD and Silva, AMM and Araújo, ASF and Melo, VMM and Medeiros, &#xc9;V and Cardoso, EJBN and Pereira, APA},
title = {Arbuscular mycorrhizal fungi community in soils under desertification and restoration in the Brazilian semiarid.},
journal = {Microbiological research},
volume = {264},
number = {},
pages = {127161},
doi = {10.1016/j.micres.2022.127161},
pmid = {35987172},
issn = {1618-0623},
mesh = {Brazil ; Conservation of Natural Resources ; Fungi ; *Glomeromycota ; Humans ; *Mycorrhizae ; Plant Roots/microbiology ; Soil/chemistry ; Soil Microbiology ; Spores, Fungal ; },
abstract = {Soil desertification has a significant social, economic, and environmental impact worldwide. Mycorrhizal diversity remains poorly understood in semiarid regions impacted by desertification, especially in Brazilian drylands. More importantly, positive impacts of grazing exclusion on mycorrhizal communities are still incipient. Here, we hypothesized that overgrazing changes the structure of Arbuscular Mycorrhizal Fungi (AMF) community compared to native areas and, grazing exclusion is effective to restore the AMF community. Thus, we analyzed the status of AMF community in soils under desertification (overgrazing) and restoration (twenty-years of grazing exclusion) in the Brazilian semiarid. AMF-spores were extracted via humid decantation methodology, morphologically classified, and alpha diversity metrics were calculated. Soil samples were chemically, and physically characterized and multivariate statistical analyses were applied to verify the impact of soil degradation and restoration on AMF-community. Briefly, native, and restored areas presented higher contents of organic matter, phosphorus, microbial carbon, and β-glucosidase activity. However, degraded soil showed higher Al[3+], Na[+,] and bulk soil density values. The abundance of AMF spores was higher in restored soil, followed by degraded and native vegetation, and Shannon's diversity index was significantly higher in restored soils, followed by native vegetation. AMF-spores were classified into four families (Gigasporaceae > Acaulosporaceae > Glomeraceae > Ambisporaceae). Ambisporaceae was closed correlated with degraded soil, mainly with Al[3+], Na[+], and bulk soil density properties. On the other hand, Acaulosporaceae and Glomeraceae were positively correlated with native vegetation and restored soil, respectively, thereby improving Shannon index, richness, enzyme activity, and soil respiration. Thus, grazing exclusion, in long term, can be a good strategy to restore AMF-diversity in soils in the Brazilian semiarid.},
}
@article {pmid35987022,
year = {2022},
author = {Mian, G and Belfiore, N and Musetti, R and Tomasi, D and Cantone, P and Lovat, L and Lupinelli, S and Iacumin, L and Celotti, E and Golinelli, F},
title = {Effect of a triacontanol-rich biostimulant on the ripening dynamic and wine must technological parameters in Vitis vinifera cv. 'Ribolla Gialla'.},
journal = {Plant physiology and biochemistry : PPB},
volume = {188},
number = {},
pages = {60-69},
doi = {10.1016/j.plaphy.2022.07.032},
pmid = {35987022},
issn = {1873-2690},
mesh = {Crops, Agricultural ; Fatty Alcohols ; Fruit/metabolism ; *Vitis/metabolism ; *Wine/analysis ; },
abstract = {Biostimulants are organic compounds which can influence the biochemical activity of the whole plant. Lately, great attention has been focused on the possibility of using these stimulants in the viticulture sector. Due to this, the aim of this work was to investigate the foliar application of a biostimulant made by Fabaceae tissue, rich in amino acids and peptides along with the high presence of natural triacontanol (C30H62O) (>6 mg kg[-1]), previously reported in many crops as chemicals able to stimulate different yield components, the technological composition of musts still having an effect on some of the microbial population of different fruits/crops. Hence, this research was conducted during the growing seasons 2020 and 2021 in a commercial vineyard of the 'Ribolla Gialla' grapevine (Vitis vinifera, L.), in the Friuli Venezia Giulia Region (North-Eastern Italy), in order to understand the effect on this woody perennial crop not yet investigated. After a two-year-study, a physiological response occurred, as ripening and veraision were brought forward in the treated plants as well as the harvest time, having higher enological parameters (sugars, total titrable acidity and citric acid content) than the non-treated at every stage. Thus, grapes in the treated plants reached a full technological maturity earlier than the non-treated, in both study years. There was a positive effect on must microbial ecology important for winemaking, hence, the biostimulant have promoted the growth of the microbial community on berry skin translating into what found in the must.},
}
@article {pmid35982656,
year = {2022},
author = {Rothman, JA and Saghir, A and Chung, SA and Boyajian, N and Dinh, T and Kim, J and Oval, J and Sharavanan, V and York, C and Zimmer-Faust, AG and Langlois, K and Steele, JA and Griffith, JF and Whiteson, KL},
title = {Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {35982656},
issn = {2692-8205},
support = {P30 CA062203/CA/NCI NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; S10 OD021718/OD/NIH HHS/United States ; S10 RR025496/RR/NCRR NIH HHS/United States ; },
abstract = {Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically-important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs and that the relative abundance of many individual AMR genes/variants increased over time and may be connected to antibiotic use during the COVID-19 pandemic. Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.},
}
@article {pmid35980043,
year = {2022},
author = {Belk, AD and Frazier, AN and Fuerniss, LK and Delmore, R and Belk, K and Borlee, B and Geornaras, I and Martin, JN and Metcalf, JL},
title = {A Pilot Study: the Development of a Facility-Associated Microbiome and Its Association with the Presence of Listeria Spp. in One Small Meat Processing Facility.},
journal = {Microbiology spectrum},
volume = {10},
number = {5},
pages = {e0204522},
pmid = {35980043},
issn = {2165-0497},
mesh = {Humans ; *Listeria/genetics ; Pilot Projects ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Meat ; *Microbiota/genetics ; Food Contamination/analysis ; },
abstract = {Microbial communities which persist in food processing facilities may have a detrimental impact on food safety and spoilage. In meat processing, Listeria monocytogenes is an organism of concern due to its ability to cause significant human illnesses and persist in refrigerated environments. The microbial ecology of Listeria spp. in small meat processing facilities has not been well characterized. Therefore, we collected samples from a newly constructed meat processing facility as an opportunity to investigate several research objectives: (i) to determine whether a stable, consistent microbiome develops in a small meat processing facility during the first 18 months of operation, (ii) to evaluate the environmental factors that drive microbial community formation, and (iii) to elucidate the relationship between microbial communities and the presence of Listeria species. We evaluated microbiomes using 16S rRNA gene sequencing and Listeria presence using quantitative PCR. We demonstrated that microbial communities differentiate by the functional room type, which is representative of several environmental differences such as temperature, sources of microbes, and activity. Temperature was an especially important factor; in rooms with low temperatures, communities were dominated by psychotrophs, especially Pseudomonas, while warmer rooms supported greater diversity. A stable core community formed in facility drains, indicating that mechanisms which cause persistence are present in the communities. The overall presence of Listeria in the facility was low but could be tied to specific organisms within a room, and the species of Listeria could be stratified by room function. IMPORTANCE This study provides critical knowledge to improve meat safety and quality from small meat processing facilities. Principally, it demonstrates the importance of facility design and room condition to the development of important microbial communities; temperature, sanitation regimen, and physical barriers all influence the ability of microorganisms to join the stable core community. It also demonstrates a relationship between the microbial community and Listeria presence in the facility, showing the importance of managing facility sanitation plans for not only pathogens, but also the general facility microbiome.},
}
@article {pmid35979497,
year = {2022},
author = {Monteiro, GGTN and Barros, DJ and Gabriel, GVM and Venturini, AM and Veloso, TGR and Vazquez, GH and Oliveira, LC and Neu, V and Bodelier, PLE and Mansano, CFM and Tsai, SM and Navarrete, AA},
title = {Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {913453},
pmid = {35979497},
issn = {1664-302X},
abstract = {Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2 [-]), which can be further oxidized to nitrate (NO3 [-]). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2 [-] and NO3 [-], with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4 [+]) and NO3 [-]-and NO2 [-]-dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils.},
}
@article {pmid35978986,
year = {2022},
author = {Crous, PW and Sandoval-Denis, M and Costa, MM and Groenewald, JZ and van Iperen, AL and Starink-Willemse, M and Hernández-Restrepo, M and Kandemir, H and Ulaszewski, B and de Boer, W and Abdel-Azeem, AM and Abdollahzadeh, J and Akulov, A and Bakhshi, M and Bezerra, JDP and Bhunjun, CS and Câmara, MPS and Chaverri, P and Vieira, WAS and Decock, CA and Gaya, E and Gené, J and Guarro, J and Gramaje, D and Grube, M and Gupta, VK and Guarnaccia, V and Hill, R and Hirooka, Y and Hyde, KD and Jayawardena, RS and Jeewon, R and Jurjević, &#x17d; and Korsten, L and Lamprecht, SC and Lombard, L and Maharachchikumbura, SSN and Polizzi, G and Rajeshkumar, KC and Salgado-Salazar, C and Shang, QJ and Shivas, RG and Summerbell, RC and Sun, GY and Swart, WJ and Tan, YP and Vizzini, A and Xia, JW and Zare, R and González, CD and Iturriaga, T and Savary, O and Coton, M and Coton, E and Jany, JL and Liu, C and Zeng, ZQ and Zhuang, WY and Yu, ZH and Thines, M},
title = {Fusarium and allied fusarioid taxa (FUSA). 1.},
journal = {Fungal systematics and evolution},
volume = {9},
number = {},
pages = {161-200},
pmid = {35978986},
issn = {2589-3831},
abstract = {Seven Fusarium species complexes are treated, namely F. aywerte species complex (FASC) (two species), F. buharicum species complex (FBSC) (five species), F. burgessii species complex (FBURSC) (three species), F. camptoceras species complex (FCAMSC) (three species), F. chlamydosporum species complex (FCSC) (eight species), F. citricola species complex (FCCSC) (five species) and the F. concolor species complex (FCOSC) (four species). New species include Fusicolla elongata from soil (Zimbabwe), and Neocosmospora geoasparagicola from soil associated with Asparagus officinalis (Netherlands). New combinations include Neocosmospora akasia, N. awan, N. drepaniformis, N. duplosperma, N. geoasparagicola, N. mekan, N. papillata, N. variasi and N. warna. Newly validated taxa include Longinectria gen. nov., L. lagenoides, L. verticilliforme, Fusicolla gigas and Fusicolla guangxiensis. Furthermore, Fusarium rosicola is reduced to synonymy under N. brevis. Finally, the genome assemblies of Fusarium secorum (CBS 175.32), Microcera coccophila (CBS 310.34), Rectifusarium robinianum (CBS 430.91), Rugonectria rugulosa (CBS 126565), and Thelonectria blattea (CBS 952.68) are also announced here. Citation: Crous PW, Sandoval-Denis M, Costa MM, Groenewald JZ, van Iperen AL, Starink-Willemse M, Hernández-Restrepo M, Kandemir H, Ulaszewski B, de Boer W, Abdel-Azeem AM, Abdollahzadeh J, Akulov A, Bakhshi M, Bezerra JDP, Bhunjun CS, Câmara MPS, Chaverri P, Vieira WAS, Decock CA, Gaya E, Gené J, Guarro J, Gramaje D, Grube M, Gupta VK, Guarnaccia V, Hill R, Hirooka Y, Hyde KD, Jayawardena RS, Jeewon R, Jurjević Ž, Korsten L, Lamprecht SC, Lombard L, Maharachchikumbura SSN, Polizzi G, Rajeshkumar KC, Salgado-Salazar C, Shang Q-J, Shivas RG, Summerbell RC, Sun GY, Swart WJ, Tan YP, Vizzini A, Xia JW, Zare R, González CD, Iturriaga T, Savary O, Coton M, Coton E, Jany J-L, Liu C, Zeng Z-Q, Zhuang W-Y, Yu Z-H, Thines M (2022). Fusarium and allied fusarioid taxa (FUSA). 1. Fungal Systematics and Evolution 9: 161-200. doi: 10.3114/fuse.2022.09.08.},
}
@article {pmid35978183,
year = {2023},
author = {Tong, CY and Derek, CJC},
title = {Novel Extrapolymeric Substances Biocoating on Polyvinylidene Fluoride Membrane for Enhanced Attached Growth of Navicula incerta.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {549-562},
pmid = {35978183},
issn = {1432-184X},
support = {RUI/8014065//Universiti Sains Malaysia/ ; },
mesh = {*Biofilms ; Polyvinyls/metabolism ; Extracellular Polymeric Substance Matrix ; Polysaccharides/metabolism ; *Microalgae/metabolism ; },
abstract = {Cell adhesion is always the first step in biofilm development. With the emergence of attached cultivation systems, this study aims to promote a cost-effective approach for sustainable cultivation of microalgae, Navicula incerta, by pre-coating the main substrates, commercial polyvinylidene fluoride (PVDF) membranes with its own washed algal cells and self-produced soluble extracellular polymeric substances (EPS) for strengthened biofilm development. The effects of pH value (6 to 9), cell suspension volume (10 to 30 mL), and EPS volume (10 to 50 mL) were statistically optimized by means of response surface methodology toolkit. Model outputs revealed good agreement with cell adhesion data variation less than 1% at optimized pre-coating conditions (7.20 pH, 30 mL cell suspension volume, and 50 mL EPS volume). Throughout long-term biofilm cultivation, results demonstrated that EPS pre-coating substantially improved the attached microalgae density by as high as 271% than pristine PVDF due to rougher surface and the presence of sticky exopolymer particles. Nutrients absorbed via the available EPS coating from the bulk medium made the immobilized cells to release less polysaccharides on an average of 30% less than uncoated PVDF. This work suggests that adhesive polymer binders derived from organic sources can be effectively integrated into the development of high-performance novel materials as biocoating for immobilized microalgae cultivation.},
}
@article {pmid35977570,
year = {2022},
author = {Read-Daily, B and Ben Maamar, S and Sabba, F and Green, S and Nerenberg, R},
title = {Effect of nitrous oxide (N2O) on the structure and function of nitrogen-oxide reducing microbial communities.},
journal = {Chemosphere},
volume = {307},
number = {Pt 3},
pages = {135819},
doi = {10.1016/j.chemosphere.2022.135819},
pmid = {35977570},
issn = {1879-1298},
mesh = {Bacteria/genetics/metabolism ; Denitrification ; *Greenhouse Gases/analysis ; *Microbiota ; Nitrates/chemistry ; Nitrites/metabolism ; Nitrogen/analysis ; Nitrogen Dioxide/analysis ; Nitrous Oxide/analysis ; Sewage/chemistry ; },
abstract = {Nitrous oxide (N2O) is a potent greenhouse gas that can be produced by nitrifying and denitrifying bacteria. Yet the effects of N2O on microbial communities is not well understood. We used batch tests to explore the effects of N2O on mixed denitrifying communities. Batch tests were carried out with acetate as the electron donor and with the following electron acceptors: nitrate (NO3[-]), nitrite (NO2[-]), N2O, NO3[-] + N2O, and NO2[-] + N2O. Activated sludge from a municipal wastewater treatment plant was used as the inoculum. The bacteria grew readily with N2O as the sole acceptor. When N2O was provided along with NO3[-] or NO2[-], it was used concurrently and resulted in higher growth rates than the same acceptors without added N2O. The microbial communities resulting from N2O addition were significantly different at the genus level from those with just NO3[-] or NO2[-]. Tests with N2O as the sole added acceptor revealed a reduced diversity. Analysis of inferred gene content using PICRUSt2 indicated a greater abundance of genera with a complete denitrification pathway when growing on N2O or NO2[-], relative to all other tests. This suggests that specific N2O reduction rates are high, and that N2O alone selects for a low-diversity, fully denitrifying community. When N2O is present with NO2[-] or NO3[-], the microbial communities were more diverse and did not select exclusively for full denitrifiers. N2O alone appears to select for a "generalist" community with full denitrification pathways and lower diversity. In terms of denitrification genes, the combination of acceptors with N2O appeared to increase the number of microbes carrying nirK, while fully denitrifying bacteria appear more likely to carry nirS. Lastly, all the taxa in NO2[-] and N2O samples were predicted to harbor nosZ. This suggests the potential for reduced N2O emissions in denitrifying systems.},
}
@article {pmid35977400,
year = {2022},
author = {IJdema, F and De Smet, J and Crauwels, S and Lievens, B and Van Campenhout, L},
title = {Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {9},
pages = {},
pmid = {35977400},
issn = {1574-6941},
mesh = {Animals ; Bacteria/genetics ; *Diptera/microbiology ; Genes, rRNA ; Larva/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors 'Study', 'Age' and 'Feed' (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.},
}
@article {pmid35975997,
year = {2022},
author = {Lensink, MJ and Li, Y and Lequime, S},
title = {Aquatic Flaviviruses.},
journal = {Journal of virology},
volume = {96},
number = {17},
pages = {e0043922},
pmid = {35975997},
issn = {1098-5514},
mesh = {Animals ; Aquaculture ; *Aquatic Organisms/isolation &amp; purification/virology ; Biological Evolution ; Fishes/virology ; *Flavivirus/isolation &amp; purification ; *Flavivirus Infections/virology ; Humans ; },
abstract = {Flaviviruses are positive-sense single-stranded RNA viruses, including some well-known human pathogens such as Zika, dengue, and yellow fever viruses, which are primarily associated with mosquito and tick vectors. The vast majority of flavivirus research has focused on terrestrial environments; however, recent findings indicate that a range of flaviviruses are also present in aquatic environments, both marine and freshwater. These flaviviruses are found in various hosts, including fish, crustaceans, molluscs, and echinoderms. Although the effects of aquatic flaviviruses on the hosts they infect are not all known, some have been detected in farmed species and may have detrimental effects on the aquaculture industry. Exploration of the evolutionary history through the discovery of the Wenzhou shark flavivirus in both a shark and crab host is of particular interest since the potential dual-host nature of this virus may indicate that the invertebrate-vertebrate relationship seen in other flaviviruses may have a more profound evolutionary root than previously expected. Potential endogenous viral elements and the range of novel aquatic flaviviruses discovered thus shed light on virus origins and evolutionary history and may indicate that, like terrestrial life, the origins of flaviviruses may lie in aquatic environments.},
}
@article {pmid35971012,
year = {2023},
author = {Giongo, A and Dos Anjos Borges, LG and Simão, TLL and Eizirik, E and Utz, LRP},
title = {Structure and Dynamics of Periphyton in a Neotropical Freshwater Lake, with Emphasis on Ciliates and Their Relationships with Bacterial Taxa.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {187-199},
pmid = {35971012},
issn = {1432-184X},
support = {476310/2011-3//CNPq/ ; 001//Capes/ ; },
mesh = {Lakes ; Ecosystem ; *Periphyton ; *Ciliophora/genetics ; *Oligohymenophorea/genetics ; },
abstract = {Periphyton communities in freshwater systems play an essential role in biogeochemical processes, but knowledge of their structure and dynamics lags far behind other environments. We used eDNA metabarcoding of 16S and 18S rRNA markers to investigate the formation and establishment of a periphytic community, in addition to a morphology-based approach for peritrich ciliate determinations, its most abundant group. We sampled two nearby sites within a large Neotropical lake at four time points, aiming to assess whether periphyton establishment can be replicated on this local scale. Producers and denitrifiers were abundant in the community, illustrating the relevant role of biofilms in freshwater nutrient recycling. Among microeukaryotes, peritrich ciliates dominated the community, with genera Epistylis and Vorticella being the most abundant and showing a clear succession at both sites. Other ciliates were morphologically identified and, in some cases, their occurrence was strongly related to bacterial abundance. The structure of both prokaryotic and eukaryotic components of periphyton was not different, while the turnover dynamics differed between the two sites, in spite of their adjacent locations and similar abiotic properties. This indicates that the establishment of these communities can vary even on a local scale within a lake ecosystem.},
}
@article {pmid35969955,
year = {2022},
author = {Yin, W and Zhang, B and Zhang, H and Zhang, D and Leiviskä, T},
title = {Vertically co-distributed vanadium and microplastics drive distinct microbial community composition and assembly in soil.},
journal = {Journal of hazardous materials},
volume = {440},
number = {},
pages = {129700},
doi = {10.1016/j.jhazmat.2022.129700},
pmid = {35969955},
issn = {1873-3336},
mesh = {*Microbiota ; Microplastics ; Plastics ; *Soil/chemistry ; Soil Microbiology ; Vanadium ; },
abstract = {Vanadium (V) and microplastics in soils draw increasing attention considering their significant threats to ecosystems. However, little is known about the vertical co-distribution of V and microplastics in soil profile and their combined effects on microbial community dynamics and assembly. This study investigated the spatial distribution of V and microplastics in the soils at a V smelting site and the associated microbial community characteristics along the vertical gradient. Both V and microplastics were found in the 50 cm soil profile with average concentrations of 203.5 ± 314.4 mg/kg and 165.1 ± 124.8 item/kg, respectively. Topsoil (0-20 cm) and subsoil (20-50 cm) displayed distinct microbial community compositions. Metal-tolerant (e.g., Spirochaeta, Rubellimicrobium) and organic-degrading (e.g., Bradyrhizobium, Pseudolabrys) taxa as biomarkers were more abundant in the topsoil layer. V and microplastics directly affected the microbial structure in the topsoil and had indirect influences in the subsoil, with direct impacts from organic matter. In topsoil, deterministic processes were more prevalent for community assembly, whereas stochastic processes governed the subsoil. The interspecific relationship was closer in topsoil with greater network complexity and higher modularity. These findings promote the understanding of distinct heterogeneity of microbial communities jointly driven by V and microplastics in soil environment.},
}
@article {pmid35968126,
year = {2022},
author = {Naqqash, T and Malik, KA and Imran, A and Hameed, S and Shahid, M and Hanif, MK and Majeed, A and Iqbal, MJ and Qaisrani, MM and van Elsas, JD},
title = {Inoculation With Azospirillum spp. Acts as the Liming Source for Improving Growth and Nitrogen Use Efficiency of Potato.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {929114},
pmid = {35968126},
issn = {1664-462X},
abstract = {Nitrogen (N) is one of the limiting factors for plant growth, and it is mainly supplied exogenously by fertilizer application. It is well documented that diazotrophic rhizobacteria improve plant growth by fixing atmospheric N in the soil. The present study investigates the nitrogen-fixing potential of two Azospirillum spp. strains using the [15]N isotope-dilution method. The two diazotrophic strains (TN03 and TN09) native to the rhizosphere of potato belong to the genus Azospirillum (16S rRNA gene accession numbers LN833443 and LN833448, respectively). Both strains were able to grow on an N-free medium with N-fixation potential (138-143 nmol mg[-1] protein h[-1]) and contained the nifH gene. Strain TN03 showed highest indole acetic acid (IAA) production (30.43 μg/mL), while TN09 showed highest phosphate solubilization activity (249.38 μg/mL) while both diazotrophs showed the production of organic acids. A [15]N dilution experiment was conducted with different fertilizer inputs to evaluate the N-fixing potential of both diazotrophs in pots. The results showed that plant growth parameters and N contents increased significantly by the inoculations. Moreover, reduced [15]N enrichment was found compared to uninoculated controls that received similar N fertilizer levels. This validates the occurrence of N-fixation through isotopic dilution. Strain TN09 showed higher N-fixing potential than TN03 and the uninoculated controls. Inoculation with either strain also showed a remarkable increase in plant growth under field conditions. Thus, there were remarkable increases in N use efficiency, N uptake and N utilization levels. Confocal laser scanning and transmission electron microscopy showed that TN03 is an ectophyte, i.e., present outside root cells or within the grooves of root hairs, while TN09 is an endophyte, i.e., present within root cells, forming a strong association withroot it. This study confirms that diazotrophic Azospirillum spp. added to potato systems can improve plant growth and N use efficiency, opening avenues for improvement of potato crop growth with reduced input of N fertilizer.},
}
@article {pmid35966858,
year = {2022},
author = {Song, W and Zhou, X and Duan, Q and Wang, Q and Li, Y and Li, A and Zhou, W and Sun, L and Qiu, L and Li, R and Li, Y},
title = {Using random forest algorithm for glomerular and tubular injury diagnosis.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {911737},
pmid = {35966858},
issn = {2296-858X},
abstract = {OBJECTIVES: Chronic kidney disease (CKD) is a common chronic condition with high incidence and insidious onset. Glomerular injury (GI) and tubular injury (TI) represent early manifestations of CKD and could indicate the risk of its development. In this study, we aimed to classify GI and TI using three machine learning algorithms to promote their early diagnosis and slow the progression of CKD.<br><br>METHODS: Demographic information, physical examination, blood, and morning urine samples were first collected from 13,550 subjects in 10 counties in Shanxi province for classification of GI and TI. Besides, LASSO regression was employed for feature selection of explanatory variables, and the SMOTE (synthetic minority over-sampling technique) algorithm was used to balance target datasets, i.e., GI and TI. Afterward, Random Forest (RF), Naive Bayes (NB), and logistic regression (LR) were constructed to achieve classification of GI and TI, respectively.<br><br>RESULTS: A total of 12,330 participants enrolled in this study, with 20 explanatory variables. The number of patients with GI, and TI were 1,587 (12.8%) and 1,456 (11.8%), respectively. After feature selection by LASSO, 14 and 15 explanatory variables remained in these two datasets. Besides, after SMOTE, the number of patients and normal ones were 6,165, 6,165 for GI, and 6,165, 6,164 for TI, respectively. RF outperformed NB and LR in terms of accuracy (78.14, 80.49%), sensitivity (82.00, 84.60%), specificity (74.29, 76.09%), and AUC (0.868, 0.885) for both GI and TI; the four variables contributing most to the classification of GI and TI represented SBP, DBP, sex, age and age, SBP, FPG, and GHb, respectively.<br><br>CONCLUSION: RF boasts good performance in classifying GI and TI, which allows for early auxiliary diagnosis of GI and TI, thus facilitating to help alleviate the progression of CKD, and enjoying great prospects in clinical practice.},
}
@article {pmid35966660,
year = {2022},
author = {Young, E and Allen, RJ},
title = {Lineage dynamics in growing biofilms: Spatial patterns of standing vs. de novo diversity.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {915095},
pmid = {35966660},
issn = {1664-302X},
support = {682237/ERC_/European Research Council/International ; },
abstract = {Microbial biofilms show high phenotypic and genetic diversity, yet the mechanisms underlying diversity generation and maintenance remain unclear. Here, we investigate how spatial patterns of growth activity within a biofilm lead to spatial patterns of genetic diversity. Using individual-based computer simulations, we show that the active layer of growing cells at the biofilm interface controls the distribution of lineages within the biofilm, and therefore the patterns of standing and de novo diversity. Comparing biofilms of equal size, those with a thick active layer retain more standing diversity, while de novo diversity is more evenly distributed within the biofilm. In contrast, equal-sized biofilms with a thin active layer retain less standing diversity, and their de novo diversity is concentrated at the top of the biofilm, and in fewer lineages. In the context of antimicrobial resistance, biofilms with a thin active layer may be more prone to generate lineages with multiple resistance mutations, and to seed new resistant biofilms via sloughing of resistant cells from the upper layers. Our study reveals fundamental "baseline" mechanisms underlying the patterning of diversity within biofilms.},
}
@article {pmid35965269,
year = {2023},
author = {Lima, LFO and Alker, AT and Papudeshi, B and Morris, MM and Edwards, RA and de Putron, SJ and Dinsdale, EA},
title = {Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {392-407},
pmid = {35965269},
issn = {1432-184X},
mesh = {Animals ; *Anthozoa/microbiology ; Ecosystem ; Metagenome ; Coral Reefs ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Seawater/microbiology ; },
abstract = {The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.},
}
@article {pmid35962889,
year = {2022},
author = {Oliveira, MET and Paulino, GVB and Dos Santos Júnior, ED and da Silva Oliveira, FA and Melo, VMM and Ursulino, JS and de Aquino, TM and Shetty, AK and Landell, MF and Gitaí, DLG},
title = {Multi-omic Analysis of the Gut Microbiome in Rats with Lithium-Pilocarpine-Induced Temporal Lobe Epilepsy.},
journal = {Molecular neurobiology},
volume = {59},
number = {10},
pages = {6429-6446},
pmid = {35962889},
issn = {1559-1182},
support = {311553/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313769/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 312889/2021-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 315895/2021-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; *Epilepsy/metabolism ; *Epilepsy, Temporal Lobe/metabolism ; *Gastrointestinal Microbiome ; Lithium ; Pilocarpine ; Rats ; },
abstract = {Evidence supports that the gut microbiota and bacteria-dependent metabolites influence the maintenance of epileptic brain activity. However, the alterations in the gut microbiota between epileptic versus healthy individuals are poorly understood. We used a multi-omic approach to evaluate the changes in the composition of gut metagenome as well in the fecal metabolomic profile in rats before and after being submitted to status epilepticus (SE)-induced temporal lobe epilepsy (TLE). The 16S ribosomal RNA (rRNA) sequencing of fecal samples coupled to bioinformatic analysis revealed taxonomic, compositional, and functional shifts in epileptic rats. The species richness (Chao1 index) was significantly lower in the post-TLE group, and the β-diversity analysis revealed clustering separated from the pre-TLE group. The taxonomic abundance analysis showed a significant increase of phylum Desulfobacterota and a decrease of Patescibacteria in the post-TLE group. The DESEq2 and LEfSe analysis resulted in 18 genera significantly enriched between post-TLE and pre-TLE groups at the genus level. We observed that epileptic rats present a peculiar metabolic phenotype, including a lower concentration of D-glucose and L-lactic acid and a higher concentration of L-glutamic acid and glycine. The microbiota-host metabolic correlation analysis showed that the genera differentially abundant in post-TLE rats are associated with the altered metabolites, especially the proinflammatory Desulfovibrio and Marvinbryantia, which were enriched in epileptic animals and positively correlated with these excitatory neurotransmitters and carbohydrate metabolites. Therefore, our data revealed a correlation between dysbacteriosis in epileptic animals and fecal metabolites that are known to be relevant for maintaining epileptic brain activity by enhancing chronic inflammation, an excitatory-inhibitory imbalance, and/or a metabolic disturbance. These data are promising and suggest that targeting the gut microbiota could provide a novel avenue for preventing and treating acquired epilepsy. However, the causal relationship between these microbial/metabolite components and the SRS occurrence still needs further exploration.},
}
@article {pmid35962839,
year = {2023},
author = {Gadoin, E and Desnues, C and d'Orbcastel, ER and Bouvier, T and Auguet, JC and Dagorn, L and Moroh, JL and Adingra, A and Bettarel, Y},
title = {Fishing for the Microbiome of Tropical Tuna.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {742-755},
pmid = {35962839},
issn = {1432-184X},
mesh = {Animals ; *Tuna/microbiology ; Hunting ; Histamine ; Bacteria/genetics ; *Microbiota ; },
abstract = {Although tunas represent a significant part of the global fish economy and a major nutritional resource worldwide, their microbiome still remains poorly documented. Here, we conducted an analysis of the taxonomic composition of the bacterial communities inhabiting the gut, skin, and liver of two most consumed tropical tuna species (skipjack and yellowfin), from individuals caught in the Atlantic and Indian oceans. We hypothesized that each organ harbors a specific microbial assemblage whose composition might vary according to different biotic (sex, species) and/or abiotic (environmental) factors. Our results revealed that the composition of the tuna microbiome was totally independent of fish sex, regardless of the species and ocean considered. Instead, the main determinants of observed diversity were (i) tuna species for the gut and (ii) sampling site for the skin mucus layer and (iii) a combination of both parameters for the liver. Interestingly, 4.5% of all amplicon sequence variants (ASV) were shared by the three organs, highlighting the presence of a core-microbiota whose most abundant representatives belonged to the genera Mycoplasma, Cutibacterium, and Photobacterium. Our study also revealed the presence of a unique and diversified bacterial assemblage within the tuna liver, comprising a substantial proportion of potential histamine-producing bacteria, well known for their pathogenicity and their contribution to fish poisoning cases. These results indicate that this organ is an unexplored microbial niche whose role in the health of both the host and consumers remains to be elucidated.},
}
@article {pmid35962280,
year = {2023},
author = {Bizarria, R and de Castro Pietrobon, T and Rodrigues, A},
title = {Uncovering the Yeast Communities in Fungus-Growing Ant Colonies.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {624-635},
pmid = {35962280},
issn = {1432-184X},
support = {2019/03746-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/24412-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 305269/2018-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 142396/2019-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {*Fungi ; Yeasts/genetics ; Ecology ; *Ascomycota ; Gardening ; Gardens ; Symbiosis ; Phylogeny ; },
abstract = {Yeast-insect interactions are compelling models to study the evolution, ecology, and diversification of yeasts. Fungus-growing (attine) ants are prominent insects in the Neotropics that evolved an ancient fungiculture of basidiomycete fungi over 55-65 million years, supplying an environment for a hidden yeast diversity. Here we assessed the yeast diversity in the attine ant environment by thoroughly sampling fungus gardens across four out of five ant fungiculture systems: Acromyrmex coronatus and Mycetomoellerius tucumanus standing for leaf-cutting and higher-attine fungicultures, respectively; Apterostigma sp., Mycetophylax sp., and Mycocepurus goeldii as ants from the lower-attine fungiculture. Among the fungus gardens of all fungus-growing ants examined, we found taxonomically unique and diverse microbial yeast communities across the different fungicultures. Ascomycete yeasts were the core taxa in fungus garden samples, with Saccharomycetales as the most frequent order. The genera Aureobasidium, Candida, Papiliotrema, Starmerella, and Sugiyamaella had the highest incidence in fungus gardens. Despite the expected similarity within the same fungiculture system, colonies of the same ant species differed in community structure. Among Saccharomycotina yeasts, few were distinguishable as killer yeasts, with a classical inhibition pattern for the killer phenotype, differing from earlier observations in this environment, which should be further investigated. Yeast mycobiome in fungus gardens is distinct between colonies of the same fungiculture and each ant colony harbors a distinguished and unique yeast community. Fungus gardens of attine ants are emergent environments to study the diversity and ecology of yeasts associated with insects.},
}
@article {pmid35960845,
year = {2022},
author = {Amend, AS and Swift, SOI and Darcy, JL and Belcaid, M and Nelson, CE and Buchanan, J and Cetraro, N and Fraiola, KMS and Frank, K and Kajihara, K and McDermot, TG and McFall-Ngai, M and Medeiros, M and Mora, C and Nakayama, KK and Nguyen, NH and Rollins, RL and Sadowski, P and Sparagon, W and Téfit, MA and Yew, JY and Yogi, D and Hynson, NA},
title = {A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {33},
pages = {e2204146119},
pmid = {35960845},
issn = {1091-6490},
support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bacteria ; *Ecosystem ; *Microbiota ; *Plants/microbiology ; },
abstract = {Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts' microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.},
}
@article {pmid35960594,
year = {2022},
author = {Koistinen, VM and Hedberg, M and Shi, L and Johansson, A and Savolainen, O and Lehtonen, M and Aura, AM and Hanhineva, K and Landberg, R},
title = {Metabolite Pattern Derived from Lactiplantibacillus plantarum-Fermented Rye Foods and In Vitro Gut Fermentation Synergistically Inhibits Bacterial Growth.},
journal = {Molecular nutrition &amp; food research},
volume = {66},
number = {21},
pages = {e2101096},
pmid = {35960594},
issn = {1613-4133},
mesh = {Humans ; Secale/chemistry ; Bread/analysis/microbiology ; Fermentation ; Triticum/chemistry ; *Fermented Foods ; Lactobacillaceae ; *Lactobacillales ; Food Microbiology ; },
abstract = {SCOPE: Fermentation improves many food characteristics using microbes, such as lactic acid bacteria (LAB). Recent studies suggest fermentation may also enhance the health properties, but mechanistic evidence is lacking. The study aims to identify a metabolite pattern reproducibly produced during sourdough and in vitro colonic fermentation of various whole-grain rye products and how it affects the growth of bacterial species of potential importance to health and disease.<br><br>METHODS AND RESULTS: The study uses Lactiplantibacillus plantarum DSMZ 13890 strain, previously shown to favor rye as its substrate. Using LC-MS metabolomics, the study finds seven microbial metabolites commonly produced during the fermentations, including dihydroferulic acid, dihydrocaffeic acid, and five amino acid metabolites, and stronger inhibition is achieved when exposing the bacteria to a mixture of the metabolites in vitro compared to individual compound exposures.<br><br>CONCLUSION: The study suggests that metabolites produced by LAB may synergistically modulate the local microbial ecology, such as in the gut. This could provide new hypotheses on how fermented foods influence human health via diet-microbiota interactions.},
}
@article {pmid35959366,
year = {2022},
author = {Lopez, LR and Ahn, JH and Alves, T and Arthur, JC},
title = {Microenvironmental Factors that Shape Bacterial Metabolites in Inflammatory Bowel Disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {934619},
pmid = {35959366},
issn = {2235-2988},
support = {P40 OD010995/OD/NIH HHS/United States ; R01 DK124617/DK/NIDDK NIH HHS/United States ; R21 AI159786/AI/NIAID NIH HHS/United States ; },
mesh = {Bacteria ; Dysbiosis/microbiology ; Enterobacteriaceae ; Fibrosis ; *Gastrointestinal Microbiome ; Humans ; Inflammation/microbiology ; *Inflammatory Bowel Diseases/microbiology ; },
abstract = {Inflammatory bowel disease (IBD) is a significant global health problem that involves chronic intestinal inflammation and can involve severe comorbidities, including intestinal fibrosis and inflammation-associated colorectal cancer (CRC). Disease-associated alterations to the intestinal microbiota often include fecal enrichment of Enterobacteriaceae, which are strongly implicated in IBD development. This dysbiosis of intestinal flora accompanies changes in microbial metabolites, shaping host:microbe interactions and disease risk. While there have been numerous studies linking specific bacterial taxa with IBD development, our understanding of microbial function in the context of IBD is limited. Several classes of microbial metabolites have been directly implicated in IBD disease progression, including bacterial siderophores and genotoxins. Yet, our microbiota still harbors thousands of uncharacterized microbial products. In-depth discovery and characterization of disease-associated microbial metabolites is necessary to target these products in IBD treatment strategies. Towards improving our understanding of microbiota metabolites in IBD, it is important to recognize how host relevant factors influence microbiota function. For example, changes in host inflammation status, metal availability, interbacterial community structure, and xenobiotics all play an important role in shaping gut microbial ecology. In this minireview, we outline how each of these factors influences gut microbial function, with a specific focus on IBD-associated Enterobacteriaceae metabolites. Importantly, we discuss how altering the intestinal microenvironment could improve the treatment of intestinal inflammation and associated disorders, like intestinal fibrosis and CRC.},
}
@article {pmid35954765,
year = {2022},
author = {Kuczewski, E and Henaff, L and Regard, A and Argaud, L and Lukaszewicz, AC and Rimmelé, T and Cassier, P and Fredenucci, I and Loeffert-Frémiot, S and Khanafer, N and Vanhems, P},
title = {Bacterial Cross-Transmission between Inanimate Surfaces and Patients in Intensive Care Units under Real-World Conditions: A Repeated Cross-Sectional Study.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {15},
pages = {},
pmid = {35954765},
issn = {1660-4601},
mesh = {*Acinetobacter baumannii ; Bacteria ; *Cross Infection/epidemiology/microbiology ; Cross-Sectional Studies ; Humans ; Intensive Care Units ; },
abstract = {Background/Objectives: Contaminated surfaces play an important role in the nosocomial infection of patients in intensive care units (ICUs). This study, conducted in two ICUs at Edouard Herriot Hospital (Lyon, France), aimed to describe rooms' microbial ecology and explore the potential link between environmental contamination and patients' colonization and/or infection. Methods: Environmental samples were realized once monthly from January 2020 to December 2021 on surfaces close to the patient (bedrails, bedside table, and dedicated stethoscope) and healthcare workers' high-touch surfaces, which were distant from the patient (computer, worktop/nurse cart, washbasin, and hydro-alcoholic solution/soap dispenser). Environmental bacteria were compared to the cultures of the patients hospitalized in the sampled room over a period of ± 10 days from the environmental sampling. Results: Overall, 137 samples were collected: 90.7% of the samples close to patients, and 87.9% of the distant ones were positives. Overall, 223 bacteria were isolated, mainly: Enterococcus faecalis (15.7%), Pantoea agglomerans (8.1%), Enterobacter cloacae/asburiae (6.3%), Bacillus cereus and other Bacillus spp (6.3%), Enterococcusfaecium (5.8%), Stenotrophomonas maltophilia (5.4%), and Acinetobacter baumannii (4.9%). Throughout the study, 142 patients were included, of which, n = 67 (47.2%) were infected or colonized by at least one bacterium. In fourteen cases, the same bacterial species were found both in environment and patient samples, with the suspicion of a cross-contamination between the patient-environment (n = 10) and environment-patient (n = 4). Conclusions: In this work, we found a high level of bacterial contamination on ICU rooms' surfaces and described several cases of potential cross-contamination between environment and patients in real-world conditions.},
}
@article {pmid35953677,
year = {2023},
author = {Grisnik, M and Grinath, JB and Munafo, JP and Walker, DM},
title = {Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {713-726},
pmid = {35953677},
issn = {1432-184X},
support = {1016031//National Institute of Food and Agriculture/ ; 32801-00803//Tennessee Wildlife Resources Agency/ ; },
mesh = {Animals ; *Chiroptera/microbiology ; Nose/microbiology ; Antifungal Agents ; Skin/microbiology ; Bacteria/genetics ; },
abstract = {Understanding how host-associated microbial assemblages respond to pathogen invasion has implications for host health. Until recently, most investigations have focused on understanding the taxonomic composition of these assemblages. However, recent studies have suggested that microbial assemblage taxonomic composition is decoupled from its function, with assemblages being taxonomically varied but functionally constrained. The objective of this investigation was to understand how the Tri-colored bat, Perimyotis subflavus cutaneous microbial assemblage responds to fungal pathogen invasion within a functional context. We hypothesized that at a broad scale (e.g., KEGG pathways), there will be no difference in the functional assemblages between the white nose pathogen, Pseudogymnoascus destructans, positive and negative bats; and this pattern will be driven by the functional redundancy of bacterial taxa. At finer scales (e.g., gene models), we postulate differences in function attributed to interactions between bacteria and P. destructans, resulting in the production of antifungal metabolites. To test this, we used a combination of shotgun metagenomic and amplicon sequencing to characterize the bat cutaneous microbial assemblage in the presence/absence of P. destructans. Results showed that while there was a shift in taxonomic assemblage composition between P. destructans positive and negative bats, there was little overall difference in microbial function. Functional redundancy across bacterial taxa was clear at a broad-scale; however, both redundancy and variation in bacterial capability related to defense against pathogens was evident at finer scales. While functionality of the microbial assemblage was largely conserved in relation to P. destructans, the roles of particular functional pathways in resistance to fungal pathogens require further attention.},
}
@article {pmid35948833,
year = {2023},
author = {Díaz-Pérez, SP and Solis, CS and López-Bucio, JS and Valdez Alarcón, JJ and Villegas, J and Reyes-De la Cruz, H and Campos-Garcia, J},
title = {Pathogenesis in Pseudomonas aeruginosa PAO1 Biofilm-Associated Is Dependent on the Pyoverdine and Pyocyanin Siderophores by Quorum Sensing Modulation.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {727-741},
pmid = {35948833},
issn = {1432-184X},
support = {256119//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 2.14//Universidad Michoacana de San Nicol&#xe1;s de Hidalgo/ ; },
mesh = {Humans ; Animals ; *Quorum Sensing ; *Siderophores ; Pseudomonas aeruginosa/genetics ; Pyocyanine ; Biofilms ; Virulence Factors/genetics ; Phenazines ; Bacterial Proteins/genetics ; },
abstract = {Pseudomonas aeruginosa is an opportunistic pathogenic bacterium for humans, animals, and plants, through producing different molecular factors such as biofilm, siderophores, and other virulence factors which favor bacterial establishment and infection in the host. In P. aeruginosa PAO1, the production of these factors is regulated by the bacterial quorum sensing (QS) mechanisms. From them, siderophores are involved in iron acquisition, transport, and homeostasis. They are also considered some of the main virulence factors in P. aeruginosa; however, detailed mechanisms to induce bacterial pathogenesis are poorly understood. In this work, through reverse genetics, we evaluated the function of bacterial pathogenesis in the pvd cluster genes, which are required for synthesizing the siderophore pyoverdine (PVD). Single pvdI, pvdJ, pvdL, and double mutant strains were analyzed, and contrary to expected, the pvdL and pvdI mutations increased the concentration of PVD and other phenazines, such as pyocyanin (PYO) and phenazine-1-carboxylic acid (PCA) and also an increased biofilm production and morphology depending on the autoinducer 2-alkyl-4-quinolone (PQS) and the QS molecules acyl-homoserine lactones. Consequently, in the in vivo pathogenicity model of Caenorhabditis elegans, the mutations in pvdI, pvdJ, and pvdL increased the survival of the worms exposed to supernatants or biofilms of the bacterial cultures. However, the double mutant pvdI/pvdJ increased its toxicity in agreeing with the biofilm production, PVD, PYO, and PCA. The findings indicate that the mutations in pvd genes encode non-ribosomal peptide synthetases impacted the biofilm's structure, but suppressively also of the phenazines, confirming that the siderophores contribute to the bacterial establishment and pathogenicity of P. aeruginosa PAO1.},
}
@article {pmid35948832,
year = {2023},
author = {Ali, A and Elrys, AS and Liu, L and Xia, Q and Wang, B and Li, Y and Dan, X and Iqbal, M and Zhao, J and Huang, X and Cai, Z},
title = {Deciphering the Synergies of Reductive Soil Disinfestation Combined with Biochar and Antagonistic Microbial Inoculation in Cucumber Fusarium Wilt Suppression Through Rhizosphere Microbiota Structure.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {980-997},
pmid = {35948832},
issn = {1432-184X},
support = {42090060//National Natural Science Foundation of China/ ; U21A20226//National Natural Science Foundation of China/ ; 2021 M691622//Postdoctoral Research Foundation of China/ ; },
mesh = {*Fusarium ; *Cucumis sativus ; Soil/chemistry ; Carbon ; Rhizosphere ; *Microbiota ; Bacteria ; *Bacillus ; Soil Microbiology ; Plant Diseases/prevention &amp; control/microbiology ; },
abstract = {Application of reductive soil disinfestation (RSD), biochar, and antagonistic microbes have become increasingly popular strategies in a microbiome-based approach to control soil-borne diseases. The combined effect of these remediation methods on the suppression of cucumber Fusarium wilt associated with microbiota reconstruction, however, is still unknown. In this study, we applied RSD treatment together with biochar and microbial application of Trichoderma and Bacillus spp. in Fusarium-diseased cucumbers to investigate their effects on wilt suppression, soil chemical changes, microbial abundances, and the rhizosphere communities. The results showed that initial RSD treatment followed by biochar amendment (RSD-BC) and combined applications of microbial inoculation and biochar (RSD-SQR-T37-BC) decreased nitrate concentration and raised soil pH, soil organic carbon (SOC), and ammonium in the treated soils. Under RSD, the applications of Bacillus (RSD-SQR), Trichoderma (RSD-T37), and biochar (RSD-BC) suppressed wilt incidence by 26.8%, 37.5%, and 32.5%, respectively, compared to non-RSD treatments. Moreover, RSD-SQR-T37-BC and RSD-T37 caused greater suppressiveness of Fusarium wilt and F. oxysporum by 57.0 and 33.5%, respectively. Rhizosphere beta diversity and alpha diversity revealed a difference between RSD-treated and non-RSD microbial groups. The significant increase in the abundance, richness, and diversity of bacteria, and the decrease in the abundance and diversity of fungi under RSD-induced treatments attributed to the general suppression. Identified bacterial (Bacillus, Pseudoxanthomonas, Flavobacterium, Flavisolibacter, and Arthrobacter) and fungal (Trichoderma, Chaetomium, Cladosporium, Psathyrella, and Westerdykella) genera were likely the potential antagonists of specific disease suppression for their significant increase of abundances under RSD-treated soils and high relative importance in linear models. This study infers that the RSD treatment induces potential synergies with biochar amendment and microbial applications, resulting in enhanced general-to-specific suppression mechanisms by changing the microbial community composition in the cucumber rhizosphere.},
}
@article {pmid35948105,
year = {2022},
author = {Han, T and Wang, K and Rushimisha, IE and Ye, H and Sun, Y and Zhao, L and Weng, L and Li, Y and Li, X},
title = {Influence of biocurrent self-generated by indigenous microorganisms on soil quality.},
journal = {Chemosphere},
volume = {307},
number = {Pt 3},
pages = {135864},
doi = {10.1016/j.chemosphere.2022.135864},
pmid = {35948105},
issn = {1879-1298},
mesh = {Nitrogen ; Phosphorus ; Potassium ; *Soil/chemistry ; *Soil Microbiology ; Water ; },
abstract = {The redox process driven by anaerobic respiration is a link between matter conversion and energy exchange in soil biogeochemistry. Microbial extracellular electron transfer forming biocurrents is a force in element cycling and community living in soil. However, the effect of indigenous microorganisms generating biocurrents on soil quality is unclear. We found that soil biocurrent showed little adverse influence on soil pH, cation exchange capacity, and available nitrogen, phosphorus and potassium and deblocked sequestered organic matter (29%). In addition, the bioelectric field derived from biocurrent obviously forced the migration of mineral elements, which was a supplement to the theory of water-salt transport, providing a new perspective on element transport. Moreover, the soil biocurrent directly regulated the availability of Ca and Fe (increase of 7-fold), indicating that electron transfer plays an important role in weathering and mineralization and thus pedogenesis. From a microbial ecology point of view, the soil bacterial richness and diversity were perfectly restored to their original state when the biocurrent stopped; including bacterial functions; although a temporary enrichment of certain species was observed. The above results provide new insights into the interactions between electron transfer and soil quality and confirm the safety of soil bioelectrochemical technology.},
}
@article {pmid35944516,
year = {2023},
author = {Goldman, AD and Kaçar, B},
title = {Very early evolution from the perspective of microbial ecology.},
journal = {Environmental microbiology},
volume = {25},
number = {1},
pages = {5-10},
doi = {10.1111/1462-2920.16144},
pmid = {35944516},
issn = {1462-2920},
mesh = {*Evolution, Molecular ; Genome ; Ecology ; Gene Transfer, Horizontal ; *Microbiota ; Phylogeny ; Biological Evolution ; },
abstract = {The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.},
}
@article {pmid35943262,
year = {2022},
author = {Laanbroek, HJ and Cassman, NA and Keijzer, RM and Kuramae, EE},
title = {The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {17},
pages = {e0078322},
pmid = {35943262},
issn = {1098-5336},
mesh = {Bacteria/genetics ; Bioreactors/microbiology ; Carbon ; Grassland ; *Microbiota ; Nitrification ; Nitrites ; Nitrobacter/genetics ; Nitrogen ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Soil ; },
abstract = {Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacter winogradskyi create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that the assembly of a community of heterotrophic microorganisms around N. winogradskyi depends on the ecosystem from which the heterotrophs are picked. To test this hypothesis, pure cultures of N. winogradskyi were grown in continuously nitrite-fed bioreactors in a mineral medium free of added organic carbon that had been inoculated with diluted sewage sludge or with a suspension from a grassland soil. Samples for chemical and 16S rRNA gene amplicon analyses were taken after each volume change in the bioreactor. At the end of the enrichment runs, samples for shotgun metagenomics were also collected. Already after two volume changes, the transformations in community structure became less dynamic. The enrichment of heterotrophs from both sewage and soil was highly stochastic and yielded different dominant genera in most of the enrichment runs that were independent of the origin of the inoculum. Hence, the hypothesis had to be refuted. Notwithstanding the large variation in taxonomic community structure among the enrichments, the functional compositions of the communities were statistically not different between soil- and sludge-based enrichments. IMPORTANCE In the process of aerobic nitrification, nitrite-oxidizing bacteria together with ammonia-oxidizing microorganisms convert mineral nitrogen from its most reduced appearance, i.e., ammonium, into its most oxidized form, i.e., nitrate. Because the form of mineral nitrogen has large environmental implications, nitrite-oxidizing bacteria such as Nitrobacter winogradskyi play a central role in the global biogeochemical nitrogen cycle. In addition to this central role, the autotrophic nitrite-oxidizing bacteria also play a fundamental role in the global carbon cycle. They form the basis of heterotrophic food webs, in which the assimilated carbon is recycled. Little is known about the heterotrophic microorganisms that participate in these food webs, let alone their assembly in different ecosystems. This study showed that the assembly of microbial food webs by N. winogradskyi was a highly stochastic process and independent of the origin of the heterotrophic microorganisms, but the functional characteristics of the different food webs were similar.},
}
@article {pmid35942165,
year = {2022},
author = {Abid, L and Smiri, M and Federici, E and Lievens, B and Manai, M and Yan, Y and Sadfi-Zouaoui, N},
title = {Diversity of rhizospheric and endophytic bacteria isolated from dried fruit of Ficus carica.},
journal = {Saudi journal of biological sciences},
volume = {29},
number = {9},
pages = {103398},
pmid = {35942165},
issn = {1319-562X},
abstract = {There is currently an increasing demand for the characterization of endophytic bacteria isolated from different parts of plants (rhizosphere, roots, fruit, leaf) in order to improve the organic agriculture practices. The current research was performed to identify both rhizospheric bacteria isolated from the rhizosphere of Ficus carica in three different sites in the north of Tunisia and endophytic bacteria isolated from dried figs. We then characterized them for a diversity of plant growth-promoting (PGP) activities. A collection of 120 isolates from rhizospheric soil and 9 isolates from dried figs was obtained and purified. 16SrDNA gene amplification of rhizospheric bacteria revealed significant diversity and allowed for the assigning of the isolates to 6 phyla: Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Representative strains of the collection (90 strains) were tested for numerous PGP activities and resistance to abiotic stresses. The most common PGP trait for all bacteria from the three regions was siderophore production (62%), followed by cellulase (38%), then protease activity (37%), then by lipases activity (17%) and lastly by solubilization of phosphates (9%). Twenty -three strains that showed most PGP traits were selected, 8 strains presented 12 or more, and 15 strains displayed between 7 and 11 of 17 PGP activities. The majority of the isolates manifested a possible adaptation to abiotic stress and unfavorable environments. PCR-DGGE analysis of soil rhizosphere of the three sites allowed also for the acquisition of a Cluster analysis of rhizospheric bacterial communities. Our current study identified and characterized for the first time in Tunisia rhizospheric and endophytic bacteria from dried fruit of Ficus carica.},
}
@article {pmid35941249,
year = {2023},
author = {de La Harpe, M and Gütlin, A and Chiang, C and Dietemann, V and Dainat, B},
title = {Influence of Honey bee Nutritive Jelly Type and Dilution on its Bactericidal Effect on Melissococcus plutonius, the Etiological Agent of European Foulbrood.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {617-623},
pmid = {35941249},
issn = {1432-184X},
mesh = {Bees ; Animals ; Larva/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Enterococcaceae ; Bacteria ; },
abstract = {To defend themselves against pathogenic microorganisms, honey bees resort to social immunity mechanisms, such as the secretion of antibiotic compounds in the jelly they feed to their larvae. Whereas the bactericidal activity of jelly fed to queen larvae is well studied, little is known about the bioactivity of compositionally different jelly fed to worker larvae. However, the numerous worker larvae are likely to drive the spread of the microorganism and influence its virulence and pathogenesis. Diluted jelly or extracts are mostly used for jelly bioactivity tests, which may bias the evaluation of the pathogen's resistance and virulence. Here, we compared the bactericidal effect of pure and diluted jellies destined for queen and worker larvae on Melissococcus plutonius, the etiological agent of the European foulbrood (EFB) disease of honey bees, and on a secondary invader bacteria, Enterococcus faecalis. We tested three strains of M. plutonius with varying virulence to investigate the association between resistance to antibacterial compounds and virulence. The resistance of the bacteria varied but was not strictly correlated with their virulence and was lower in pure than in diluted jelly. Resistance differed according to whether the jelly was destined for queen or worker larvae, with some strains being more resistant to queen jelly and others to worker jelly. Our results provide a biologically realistic assessment of host defenses via nutritive jelly and contribute to a better understanding of the ecology of M. plutonius and of secondary invaders bacteria in the honey bee colony environment, thus shedding light on the selective forces affecting their virulence and on their role in EFB pathogenesis.},
}
@article {pmid35940746,
year = {2022},
author = {Xian, S and Zhong, H and Yi, B and Liu, X and Shen, G and Li, M and Zhang, Z and Luo, Q and Li, S and Zhou, M and Xu, F and Chen, A},
title = {Identification of pellicle formation related microorganisms in traditional Sichuan paocai through metagenomic sequence and the effects of Baijiu/Salt on pellicle and volatile components.},
journal = {Food research international (Ottawa, Ont.)},
volume = {159},
number = {},
pages = {111130},
doi = {10.1016/j.foodres.2022.111130},
pmid = {35940746},
issn = {1873-7145},
mesh = {Fermentation ; *Lactobacillus/metabolism ; Metagenome ; Metagenomics ; Pichia ; *Saccharomycetales ; },
abstract = {The occurrence of pellicle on the surface of paocai brine is a common undesirable phenomenon during the multi-rounds of paocai fermentation, which is mainly caused by the growth of microorganisms related to pellicle formation. But the detailed information on these microorganisms and volatile components produced by them, as well as the changes of the microorganisms during the process of paocai recovery, are still rare in the literature. Therefore, the purpose of this study was (1) to analyze the pellicle formation related microorganisms by comparing the differential microorganisms in initial brine and the brine when pellicle occurred through metagenomic sequencing technology, (2) to explore the changes of microorganisms in the fermentation system after addition Baijiu and/or salt, and (3) to further detect the VOCs in paocai samples by gas chromatography-mass spectrometry (GC-MS). The relationship between VOCs and the selected marker microorganisms was also determined. The results showed that the diversity of fungi was increased when pellicle formed, the pellicle formation related microorganisms mainly belonged to six genus, including Kazachstania, Lactobacillus, Pichia, Candida, Lachancea, and Saccharomyces. Apart from the unknown function and basic life activities of microorganisms, the metabolic activities of these pellicle formation related microorganisms were mainly carbohydrate transport and metabolism, and amino acid transport and metabolism. The growth of pellicle formation related microorganisms could be inhibited by adding Baijiu (1.5% v/v), but the addition of salt (7% salt (w/v) did not promote this inhibitory effect. Through PCA analysis, it was found that the VOCs of paocai were significantly affected by adding Baijiu and Baijiu and salt. The undesirable smell at the beginning of pellicle formation may be related to Propanoic acid, hexyl ester, 1,3-Dimethyl-1-cyclohexene, Oxime-, methoxy-phenyl- and Phenylethyl Alcohol.},
}
@article {pmid35940271,
year = {2022},
author = {Selak, L and Marković, T and Pjevac, P and Orlić, S},
title = {Microbial marker for seawater intrusion in a coastal Mediterranean shallow Lake, Lake Vrana, Croatia.},
journal = {The Science of the total environment},
volume = {849},
number = {},
pages = {157859},
doi = {10.1016/j.scitotenv.2022.157859},
pmid = {35940271},
issn = {1879-1026},
mesh = {Croatia ; *Ecosystem ; *Lakes ; RNA, Ribosomal, 16S ; Salinity ; Seawater ; Sulfates ; Sulfur ; Water ; },
abstract = {Climate change-induced rising sea levels and prolonged dry periods impose a global threat to the freshwater scarcity on the coastline: salinization. Lake Vrana is the largest surface freshwater resource in mid-Dalmatia, while the local springs are heavily used in agriculture. The karstified carbonate ridge that separates this shallow lake from the Adriatic Sea enables seawater intrusion if the lakes' precipitation-evaporation balance is disturbed. In this study, the impact of anthropogenic activities and drought exuberated salinization on microbial communities was tracked in Lake Vrana and its inlets, using 16S rRNA gene sequencing. The lack of precipitation and high water temperatures in summer months introduced an imbalance in the water regime of the lake, allowing for seawater intrusion, mainly via the karst conduit Jugovir. The determined microbial community spatial differences in the lake itself and the main drainage canals were driven by salinity, drought, and nutrient loading. Particle-associated and free-living microorganisms both strongly responded to the ecosystem perturbations, and their co-occurrence was driven by the salinization event. Notably, a bloom of halotolerant taxa, predominant the sulfur-oxidizing genus Sulfurovum, emerged with increased salinity and sulfate concentrations, having the potential to be used as an indicator for salinization of shallow coastal lakes. Following summer salinization, lake water column homogenization took from a couple of weeks up to a few months, while the entire system displayed increased salinity despite increased precipitation. This study represents a valuable contribution to understanding the impact of the Freshwater Salinization Syndrome on Mediterranean lakes' microbial communities and the ecosystem resilience.},
}
@article {pmid35940233,
year = {2022},
author = {Fox, A and Widmer, F and Lüscher, A},
title = {Soil microbial community structures are shaped by agricultural systems revealing little temporal variation.},
journal = {Environmental research},
volume = {214},
number = {Pt 3},
pages = {113915},
pmid = {35940233},
issn = {1096-0953},
mesh = {Agriculture ; Bacteria ; Fungi ; *Microbiota ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {Many studies in soil microbial ecology are undertaken with a single sampling event, with the influence of temporal progression rarely being considered. Under field conditions, soil samples were taken from different agricultural systems; a sown grassland to maize rotation (MC), an intensively managed permanent grassland (INT), as well as extensively managed permanent grasslands with high (EXT_HP), low to sufficient (EXT_LP) and deficient available P (EXT_DP), six times throughout the 2017 growing season. Thus, this study aimed to determine if any differences in soil microbiome structures between both sharply contrasting (MC - INT - EXT), slightly differing (EXT_HP - EXT_DP) and quite similar (EXT_HP - EXT_LP and EXT_LP - EXT_DP) agricultural systems persist through changing growth conditions within the growing season. For both fungal and bacterial community structure, the influence of agricultural system (CV = 0.256, P < 0.001 and CV = 0.145, P < 0.01, respectively) was much greater than that of temporal progression (√CV = 0.065 and 0.042, respectively, both P < 0.001). Importantly, nearly all agricultural systems persistently harbored significantly distinct fungal community structures across each of the six sampling events (all at least P < 0.05). There were not as many pairwise differences in bacterial community structure between the agricultural systems, but some did persist (MC and EXT_HP ∼ EXT_DP, all P < 0.001). Additionally, persistent indicator fungal OTUs (IndVal >0.7, P ≤ 0.05) associated to each agricultural system (except EXT_LP) were found in each of the six sampling events. These results highlight the temporal stability of pairwise differences in soil microbiome structures between established agricultural systems through changing plant growth conditions, even between those with a comparable management regime. This is a highly relevant finding in informing the sampling strategy of studies in soil microbial ecology as well as for designing efficient soil biodiversity monitoring systems.},
}
@article {pmid35938717,
year = {2022},
author = {Okazaki, Y and Nakano, SI and Toyoda, A and Tamaki, H},
title = {Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes.},
journal = {mSystems},
volume = {7},
number = {4},
pages = {e0043322},
pmid = {35938717},
issn = {2379-5077},
mesh = {*Lakes/microbiology ; Ecosystem ; Nucleotides ; Metagenome ; Bacteria/genetics ; *Bacteriophages/genetics ; },
abstract = {Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, a MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution metagenomic exploration of microdiversity by combining spatiotemporal (2 depths × 12 months) sampling from a pelagic freshwater system, high-quality MAG reconstruction using long- and short-read metagenomic sequences, and profiling of single nucleotide variants (SNVs) and structural variants (SVs) through mapping of short and long reads to the MAGs, respectively. We reconstructed 575 MAGs, including 29 circular assemblies, providing high-quality reference genomes of freshwater bacterioplankton. Read mapping against these MAGs identified 100 to 101,781 SNVs/Mb and 0 to 305 insertions, 0 to 467 deletions, 0 to 41 duplications, and 0 to 6 inversions for each MAG. Nonsynonymous SNVs were accumulated in genes potentially involved in cell surface structural modification to evade phage recognition. Most (80.2%) deletions overlapped with a gene coding region, and genes of prokaryotic defense systems were most frequently (>8% of the genes) overlapped with a deletion. Some such deletions exhibited a monthly shift in their allele frequency, suggesting a rapid turnover of genotypes in response to phage predation. MAGs with extremely low microdiversity were either rare or opportunistic bloomers, suggesting that population persistency is key to their genomic diversification. The results concluded that prokaryotic genomic diversification is driven primarily by viral load and constrained by a population bottleneck. IMPORTANCE Identifying intraspecies genomic diversity (microdiversity) is crucial to understanding microbial ecology and evolution. However, microdiversity among environmental assemblages is not well investigated, because most microbes are difficult to culture. In this study, we performed cultivation-independent exploration of bacterial genomic microdiversity in a lake ecosystem using a combination of short- and long-read metagenomic analyses. The results revealed the broad spectrum of genomic microdiversity among the diverse bacterial species in the ecosystem, which has been overlooked by conventional approaches. Our ecosystem-wide exploration further allowed comparative analysis among the genomes and genes and revealed factors behind microbial genomic diversification, namely, that diversification is driven primarily by resistance against viral infection and constrained by the population size.},
}
@article {pmid35937361,
year = {2022},
author = {Cardini, U and Marín-Guirao, L and Montilla, LM and Marzocchi, U and Chiavarini, S and Rimauro, J and Quero, GM and Petersen, JM and Procaccini, G},
title = {Nested interactions between chemosynthetic lucinid bivalves and seagrass promote ecosystem functioning in contaminated sediments.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {918675},
pmid = {35937361},
issn = {1664-462X},
abstract = {In seagrass sediments, lucinid bivalves and their chemoautotrophic bacterial symbionts consume H2S, relying indirectly on the plant productivity for the presence of the reduced chemical. Additionally, the role of lucinid bivalves in N provisioning to the plant (through N2 fixation by the symbionts) was hypothesized. Thus, lucinids may contribute to sediment detoxification and plant fitness. Seagrasses are subject to ever-increasing human pressure in coastal environments. Here, disentangling nested interactions between chemosynthetic lucinid bivalves and seagrass exposed to pollution may help to understand seagrass ecosystem dynamics and to develop successful seagrass restoration programs that consider the roles of animal-microbe symbioses. We evaluated the capacity of lucinid bivalves (Loripes orbiculatus) to promote nutrient cycling and seagrass (Cymodocea nodosa) growth during a 6-week mesocosm experiment. A fully crossed design was used to test for the effect of sediment contamination (metals, nutrients, and hydrocarbons) on plant and bivalve (alone or interacting) fitness, assessed by mortality, growth, and photosynthetic efficiency, and for the effect of their nested interaction on sediment biogeochemistry. Plants performed better in the contaminated sediment, where a larger pool of dissolved nitrogen combined with the presence of other trace elements allowed for an improved photosynthetic efficiency. In fact, pore water nitrogen accumulated during the experiment in the controls, while it was consumed in the contaminated sediment. This trend was accentuated when lucinids were present. Concurrently, the interaction between clams and plants benefitted both organisms and promoted plant growth irrespective of the sediment type. In particular, the interaction with lucinid clams resulted in higher aboveground biomass of C. nodosa in terms of leaf growth, leaf surface, and leaf biomass. Our results consolidate the notion that nested interactions involving animal-microbe associations promote ecosystem functioning, and potentially help designing unconventional seagrass restoration strategies that exploit chemosynthetic symbioses.},
}
@article {pmid35937348,
year = {2022},
author = {Zhu, M and Liu, Y and Cai, P and Duan, X and Sang, S and Qiu, Z},
title = {Jasmonic acid pretreatment improves salt tolerance of wheat by regulating hormones biosynthesis and antioxidant capacity.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {968477},
pmid = {35937348},
issn = {1664-462X},
abstract = {Salt stress is a severe environmental factor that detrimentally affects wheat growth and production worldwide. Previous studies illustrate that exogenous jasmonic acid (JA) significantly improved salt tolerance in plants. However, little is known about the underlying molecular mechanisms of JA induced physiochemical changes in wheat seedlings under salt stress conditions. In this study, biophysiochemical and transcriptome analysis was conducted to explore the mechanisms of exogenous JA induced salt tolerance in wheat. Exogenous JA increased salt tolerance of wheat seedlings by alleviating membrane lipid oxidation, improving root morphology, enhancing the contents of ABA, JA and SA and increasing relative water content. In the RNA-seq profiles, we identified a total of 54,263 unigenes and 1,407 unigenes showed differentially expressed patterns in JA pretreated wheat seedlings exposed to salt stress comparing to those with salt stress alone. Subsequently, gene ontology (GO) and KEGG pathway enrichment analysis characterized that DEGs involved in linoleic acid metabolism and plant hormone signal transduction pathways were up-regulated predominantly in JA pretreated wheat seedlings exposed to salt stress. We noticed that genes that involved in antioxidative defense system and that encoding transcription factors were mainly up- or down-regulated. Moreover, SOD, POD, CAT and APX activities were increased in JA pretreated wheat seedlings exposed to salt stress, which is in accordance with the transcript profiles of the relevant genes. Taken together, our results demonstrate that the genes and enzymes involved in physiological and biochemical processes of antioxidant system, plant hormones and transcriptional regulation contributed to JA-mediated enhancement of salt tolerance in wheat. These findings will facilitate the elucidation of the potential molecular mechanisms associated with JA-dependent amelioration of salt stress in wheat and lay theoretical foundations for future studies concerning the improvement of plant tolerance to abiotic environmental stresses.},
}
@article {pmid35935241,
year = {2022},
author = {Bergmann, GE and Leveau, JHJ},
title = {A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {877519},
pmid = {35935241},
issn = {1664-302X},
abstract = {Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.},
}
@article {pmid35933499,
year = {2022},
author = {Ray, AE and Zaugg, J and Benaud, N and Chelliah, DS and Bay, S and Wong, HL and Leung, PM and Ji, M and Terauds, A and Montgomery, K and Greening, C and Cowan, DA and Kong, W and Williams, TJ and Hugenholtz, P and Ferrari, BC},
title = {Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts.},
journal = {The ISME journal},
volume = {16},
number = {11},
pages = {2547-2560},
pmid = {35933499},
issn = {1751-7370},
support = {FT170100341//Department of Education and Training | Australian Research Council (ARC)/ ; APP5191146//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Carbon Cycle ; *Hydrogenase/genetics ; Ribulose-Bisphosphate Carboxylase ; Soil/chemistry ; Soil Microbiology ; Verrucomicrobia ; },
abstract = {Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly (p < 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic diversity within RuBisCO form IE (rbcL1E), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.},
}
@article {pmid35933411,
year = {2022},
author = {Zhang, H and Wang, M and Wang, H and Chen, H and Cao, L and Zhong, Z and Lian, C and Zhou, L and Li, C},
title = {Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {480},
pmid = {35933411},
issn = {2052-4463},
support = {42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Archaea/genetics ; Bacteria/genetics ; *Genome, Microbial ; Geologic Sediments/microbiology ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Cold seep microbial communities are fascinating ecosystems on Earth which provide unique models for understanding the living strategies in deep-sea distinct environments. In this study, 23 metagenomes were generated from samples collected in the Site-F cold seep field in South China Sea, including the sea water closely above the invertebrate communities, the cold seep fluids, the fluids under the invertebrate communities and the sediment column around the seep vent. By binning tools, we retrieved a total of 768 metagenome assembled genome (MAGs) that were estimated to be >60% complete. Of the MAGs, 61 were estimated to be >90% complete, while an additional 105 were >80% complete. Phylogenomic analysis revealed 597 bacterial and 171 archaeal MAGs, of which nearly all were distantly related to known cultivated isolates. In the 768 MAGs, the abundant Bacteria in phylum level included Proteobacteria, Desulfobacterota, Bacteroidota, Patescibacteria and Chloroflexota, while the abundant Archaea included Asgardarchaeota, Thermoplasmatota, and Thermoproteota. These results provide a dataset available for further interrogation of deep-sea microbial ecology.},
}
@article {pmid35933162,
year = {2022},
author = {Kumar, S and Kumar, V and Ambika, AAA and Nag, D and Kumar, V and Darnal, S and Thakur, V and Patial, V and Singh, D},
title = {Microbial pigments: Learning from Himalayan perspective to industrial applications.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {49},
number = {5},
pages = {},
pmid = {35933162},
issn = {1476-5535},
abstract = {Pigments are an essential part of life on earth, ranging from microbes to plants and humans. The physiological and environmental cues induce microbes to produce a broad spectrum of pigments, giving them adaptation and survival advantages. Microbial pigments are of great interest due to their natural origin, diverse biological activities, and wide applications in the food, pharmaceutical, cosmetics, and textile industries. Despite noticeable research on pigment-producing microbes, commercial successes are scarce, primarily from higher, remote, and inaccessible Himalayan niches. Therefore, substantial bioprospection integrated with advanced biotechnological strategies is required to commercialize microbial pigments successfully. The current review elaborates on pigment-producing microbes from a Himalayan perspective, offering tremendous opportunities for industrial applications. Additionally, it illustrates the ecological significance of microbial pigments and emphasizes the current status and prospects of microbial pigments production above the test tube scale.},
}
@article {pmid35932316,
year = {2023},
author = {Pedrolo, AM and Matteoli, FP and Soares, CRFS and Arisi, ACM},
title = {Comparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {563-574},
pmid = {35932316},
issn = {1432-184X},
mesh = {*Herbaspirillum/genetics/metabolism ; Nitrogen Fixation/genetics ; Phylogeny ; Genomics ; },
abstract = {The genus Herbaspirillum gained the spotlight due to the several reports of diazotrophic strains and promising results in plant-growth field assays. However, as diversity exploration of Herbaspirillum species gained momentum, it became clearer that the plant beneficial lifestyle was not the only form of ecological interaction in this genus, due to reports of phytopathogenesis and nosocomial infections. Here we performed a deep search across all publicly available Herbaspirillum genomes. Using a robust core genome phylogeny, we have found that all described species are well delineated, being the only exception H. aquaticum and H. huttiense clade. We also uncovered that the nif genes are only highly prevalent in H. rubrisubalbicans; however, irrespective to the species, all nif genes share the same gene arrangement with high protein identity, and are present in only two main types, in inverted strands. By means of a NifHDKENB phylogenetic tree, we have further revealed that the Herbaspirillum nif sequences may have been acquired from the same last common ancestor belonging to the Nitrosomonadales order.},
}
@article {pmid35931774,
year = {2023},
author = {Gómez-Molina, E and Sánchez, S and Puig-Pey, M and García-Barreda, S},
title = {Intraspecific Competition Results in Reduced Evenness of Tuber melanosporum Mating-Type Abundance from the Nursery Stage.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {253-260},
pmid = {35931774},
issn = {1432-184X},
support = {Collaboration agreement for the operation of CIET//Diputaci&#xf3;n de Huesca/ ; },
mesh = {*Ascomycota/genetics ; *Mycorrhizae ; Reproduction ; Seedlings/microbiology ; *Quercus/microbiology ; },
abstract = {The highly prized black truffle is a fungus mostly harvested in orchards planted with mycorrhizal seedlings. It is an obligatory outcrossing fungus with a single MAT locus containing two alternative mating-type idiomorphs. In the orchards, at the mycorrhizal level, these mating types are frequently spatially segregated. Some studies found that this segregation was pronounced from the nursery stage, whereas others did not find such a marked segregation. Besides, information on the host tree species and nursery conditions used in Spain, one of the main truffle-producing countries, are very scarce. In this study, we investigated the temporal dynamics of mating types in nursery seedlings of Quercus ilex and Quercus faginea, as well as the influence of cultural conditions in the nursery. Our results indicated that at the plant level, there was a trend for one of the mating types to dominate over the other from the first to the second year in the nursery, in both host species and both nursery conditions tested. However, this segregation process was not so sharp as previously reported. Our results support the hypothesis that intraspecific competition results in reduced evenness of mating-type abundance from the nursery stage, although almost all seedlings maintained both mating types and, at the seedling batch scale, the occurrence of both mating types was roughly balanced.},
}
@article {pmid35930073,
year = {2023},
author = {Morales-Poole, JR and de Vega, C and Tsuji, K and Jacquemyn, H and Junker, RR and Herrera, CM and Michiels, C and Lievens, B and Álvarez-Pérez, S},
title = {Sugar Concentration, Nitrogen Availability, and Phylogenetic Factors Determine the Ability of Acinetobacter spp. and Rosenbergiella spp. to Grow in Floral Nectar.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {377-391},
pmid = {35930073},
issn = {1432-184X},
support = {742964//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; RYC2018-023847-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; DFG//Deutsche Forschungsgemeinschaft/ ; JU2856/2-2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Bees ; Animals ; *Plant Nectar/analysis/chemistry/physiology ; Phylogeny ; *Sugars/analysis ; Carbohydrates/analysis ; Flowers/microbiology ; Glucose ; Sucrose/analysis ; Fructose/analysis ; Enterobacteriaceae/genetics ; },
abstract = {The floral nectar of angiosperms harbors a variety of microorganisms that depend predominantly on animal visitors for their dispersal. Although some members of the genus Acinetobacter and all currently known species of Rosenbergiella are thought to be adapted to thrive in nectar, there is limited information about the response of these bacteria to variation in the chemical characteristics of floral nectar. We investigated the growth performance of a diverse collection of Acinetobacter (n = 43) and Rosenbergiella (n = 45) isolates obtained from floral nectar and the digestive tract of flower-visiting bees in a set of 12 artificial nectars differing in sugar content (15% w/v or 50% w/v), nitrogen content (3.48/1.67 ppm or 348/167 ppm of total nitrogen/amino nitrogen), and sugar composition (only sucrose, 1/3 sucrose + 1/3 glucose + 1/3 fructose, or 1/2 glucose + 1/2 fructose). Growth was only observed in four of the 12 artificial nectars. Those containing elevated sugar concentration (50% w/v) and low nitrogen content (3.48/1.67 ppm) were limiting for bacterial growth. Furthermore, phylogenetic analyses revealed that the ability of the bacteria to grow in different types of nectar is highly conserved between closely related isolates and genotypes, but this conservatism rapidly vanishes deeper in phylogeny. Overall, these results demonstrate that the ability of Acinetobacter spp. and Rosenbergiella spp. to grow in floral nectar largely depends on nectar chemistry and bacterial phylogeny.},
}
@article {pmid35929359,
year = {2022},
author = {Mandal, S and Kundu, S and Uddin, MR and Das, P and Paul, P and Roy, P and Tribedi, P and Sahoo, P},
title = {Identification of a novel quinoline-based UV-protective pigment from a psychrotrophic Arctic bacterium.},
journal = {Journal of applied microbiology},
volume = {133},
number = {5},
pages = {3059-3068},
doi = {10.1111/jam.15760},
pmid = {35929359},
issn = {1365-2672},
mesh = {RNA, Ribosomal, 16S/genetics ; Sodium Chloride ; Methanol ; Acetone ; Bacteria/genetics ; *Anti-Infective Agents ; *Quinolines/pharmacology ; Soil ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Arctic Regions ; Bacterial Typing Techniques ; },
abstract = {AIMS: Psychrotrophs are extremophilic microorganisms that grow optimally in low temperature having many unique bioactive molecules of biotechnological applications. In this study, we characterized a pigment from an arctic bacterium with protective activity towards UV exposure.<br><br>METHODS AND RESULTS: The present research reports isolation and characterization of a psychrotrophic bacteria, RSAP2, from the soil sample of NyAlesund (78&#xb0;56"N, 11&#xb0;54"E), Svalbard, Norway. The strain showed closest 16S rRNA gene sequence similarity (99.9%) with Kocuria indica NIO-1021. RSAP2 is a Gram-positive, coccoid aerobe which produces a yellow pigment. The optimal parameters for pigment production while grown in LB medium were 3% (w/v) NaCl and 4&#x2009;days of incubation of the culture at 20&#xb0;C and pH&#xa0;9 with shaking (180&#x2009;rpm). The pigment was extracted in methanol and acetone (2:1) and further purified through column chromatography. It was characterized by mass spectrometry, UV-visible, fluorescence, IR, [1] H NMR, [13] C NMR spectroscopy and CHNS/O analysis. The pigment has a molecular weight of about 258 daltons and the molecular formula was determined as C15 H18 N2 O2 and is a quinoline derivative. We show that the pigment can protect Escherichia coli against UV-mediated mutagenesis. We further demonstrate that the pigment displays a significant antimicrobial effect and in sublethal concentrations it impairs biofilm formation ability of the model organism Staphylococcus aureus.<br><br>CONCLUSIONS: The pigment of a psychrotrophic Arctic bacterium, most likely a strain of K. indica, was purified and its chemical structure was determined. The quinoline-based pigment has the ability to protect live cells from UV induced damage.<br><br>Analysis and characterization of this newly isolated quinoline-based pigment is a potential candidate for future application in skin care products.},
}
@article {pmid35927589,
year = {2023},
author = {Zhu, W and Zhu, M and Liu, X and Xia, J and Yin, H and Li, X},
title = {Different Responses of Bacteria and Microeukaryote to Assembly Processes and Co-occurrence Pattern in the Coastal Upwelling.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {174-186},
pmid = {35927589},
issn = {1432-184X},
support = {42076108//the National Natural Science Foundation of China/ ; 42161144006 or 3511/21//the National Natural Science Foundation of China/ ; 2021RC169//the Natural Science Foundation of Hainan Province/ ; ZDYF2020177//the Hainan Provincial Key Research and Development Program/ ; KYQD(ZR)1805//the Foundation of Hainan University/ ; },
mesh = {*Bacteria/genetics ; *Microbiota ; Phylogeny ; Eukaryota ; },
abstract = {Upwelling may generate unique hydrological and environmental heterogeneity, leading to enhanced diffusion to reshape microbial communities. However, it remains largely unknown how different microbial taxa respond to highly complex and dynamic upwelling systems. In the present study, geographic patterns and co-occurrence network of different microbial communities in response to upwelling were examined. Our results showed that coastal upwelling shaped prokaryotic and eukaryotic microbial community and decreased their diversity. In addition, bacteria and microeukaryote had similar biogeographical patterns with distinct assembly mechanisms. The impact of stochastic processes on bacteria was significantly stronger compared with microeukaryote in upwelling. Lower network complexity but more frequent interaction was found in upwelling microbial co-occurrence. However, the upwelling environment increased the robustness and modularity of bacterial network, while eukaryotic network was just the opposite. Co-occurrence networks of bacteria and microeukaryote showed significant distance-decay patterns, while the bacterial network had a stronger spatial variation. Temperature and salinity were the strongest environmental factors affecting microbial coexistence, whereas the topological characteristics of bacterial and eukaryotic networks had different responses to the upwelling environment. These findings expanded our understanding of biogeographic patterns of microbial community and ecological network and the underlying mechanisms of different microbial taxa in upwelling.},
}
@article {pmid35927588,
year = {2023},
author = {He, D and Guo, Z and Shen, W and Ren, L and Sun, D and Yao, Q and Zhu, H},
title = {Fungal Communities Are More Sensitive to the Simulated Environmental Changes than Bacterial Communities in a Subtropical Forest: the Single and Interactive Effects of Nitrogen Addition and Precipitation Seasonality Change.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {521-535},
pmid = {35927588},
issn = {1432-184X},
mesh = {Ecosystem ; *Mycobiome ; Nitrogen/analysis ; Forests ; Bacteria/genetics ; *Microbiota ; Soil/chemistry ; China ; Soil Microbiology ; Fungi/genetics ; },
abstract = {Increased nitrogen deposition (N factor) and changes in precipitation patterns (W factor) can greatly impact soil microbial communities in tropical/subtropical forests. Although knowledge about the effects of a single factor on soil microbial communities is growing rapidly, little is understood about the interactive effects of these two environmental change factors. In this study, we investigated the responses of soil bacterial and fungal communities to the short-term simulated environmental changes (nitrogen addition, precipitation seasonality change, and their combination) in a subtropical forest in South China. The interaction between N and W factors was detected significant for affecting some soil physicochemical properties (such as pH, soil water, and NO3[-] contents). Fungi were more susceptible to treatment than bacteria in a variety of community traits (alpha, beta diversity, and network topological features). The N and W factors act antagonistically to affect fungal alpha diversity, and the interaction effect was detected significant for the dry season. The topological features of the meta-community (containing both bacteria and fungi) network overrode the alpha and beta diversity of bacterial or fungal communities in explaining the variation of soil enzyme activities. The associations between Ascomycota fungi and Gammaproteobacteria or Alphaproteobacteria might be important in mediating the inter-kingdom interactions. In summary, our results suggested that fungal communities were more sensitive to N and W factors (and their interaction) than bacterial communities, and the treatments' effects were more prominent in the dry season, which may have great consequences in soil processes and ecosystem functions in subtropical forests.},
}
@article {pmid35925231,
year = {2023},
author = {Chinta, YD and Araki, H},
title = {Cover Crop Amendments and Lettuce Plant Growth Stages Alter Rhizobacterial Properties and Roles in Plant Performance.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {446-459},
pmid = {35925231},
issn = {1432-184X},
support = {18H02310//japan society for the promotion of science/ ; },
mesh = {*Lactuca/genetics/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; *Soil/chemistry ; Bacteria/genetics ; Plant Development ; Soil Microbiology ; Rhizosphere ; Plant Roots/microbiology ; },
abstract = {Lettuce plants respond differently to cover crop amendments by altering their biomass and nitrogen uptake (Nup) at different plant growth stages. Nonetheless, plant-microbe interactions involved in the alterations are scarcely studied. This study elucidated how the properties of the soil microbial community inhabiting the rhizosphere associated with lettuce (Lactuca sativa L. var. crispa "Red fire") change during plant growth stages. Lettuce plants were cultivated in control soil and soil with rye, hairy vetch (HV), and rye plus HV (rye + HV) cover crop amendments. Rhizosphere soil samples were collected at the mid-growth and mature stages of plant development. DNA was extracted from the soil, and the 16S rRNA region was amplified using polymerase chain reaction to analyze bacterial genes and community structures and functions. Cover crop amendments and plant growth stages increased or decreased the relative abundances of bacterial taxa at the genus level. Plant maturity decreased 16S rRNA gene expression and the number of bacterial operational taxonomic units in all treatments. The unique, core, and shared taxa with low relative abundances may be associated with improved lettuce Nup and lettuce shoot and root biomass at each plant growth stage under different cover crop amendments based on multivariate analysis between plant indicators and bacterial genera groups. This study revealed the importance of bacterial groups with low relative abundance in plant-microbe interactions; such bacteria may promote the cover crop application for high lettuce productivity.},
}
@article {pmid35925016,
year = {2022},
author = {Cheng, X and Wang, H and Zeng, Z and Li, L and Zhao, R and Bodelier, PLE and Wang, Y and Liu, X and Su, C and Liu, S},
title = {Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves.},
journal = {Environmental microbiology reports},
volume = {14},
number = {6},
pages = {886-896},
doi = {10.1111/1758-2229.13112},
pmid = {35925016},
issn = {1758-2229},
mesh = {*Methylococcaceae ; Ecosystem ; Soil Microbiology ; Soil ; Methane ; Oxidation-Reduction ; },
abstract = {Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane-oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption, we collected weathered rocks and sediments from three different caves in southwestern China. We determined the potential methane oxidization rates in the range of 1.25 ± 0.08 to 1.87 ± 0.41 ng CH4 g[-1] DW h[-1] , which are comparable to those reported in forest and grassland soils. Results showed that alkaline oligotrophic caves harbour high numbers of atmMOB, particularly upland soil cluster (USC), which significantly correlated with temperature, CH4 and CO2 concentrations. The absolute abundance of USCγ was higher than that of USCα. USCγ-OPS (open patch soil) and USCγ-SS (subsurface soil) dominated in most samples, whereas USCα-BFS (boreal forest soil) only predominated in the sediments near cave entrances, indicating niche differentiation of atmMOB in caves. Overwhelming dominance of homogenous selection in community assembly resulted in convergence of atmMOB communities. Collectively, our results demonstrated the niche differentiation of USC in subsurface alkaline caves and their non-negligible methane-oxidizing potential, providing brand-new knowledge about atmMOB ecology in subsurface biosphere.},
}
@article {pmid35924847,
year = {2022},
author = {Gude, S and Pherribo, GJ and Taga, ME},
title = {A Salvaging Strategy Enables Stable Metabolite Provisioning among Free-Living Bacteria.},
journal = {mSystems},
volume = {7},
number = {4},
pages = {e0028822},
pmid = {35924847},
issn = {2379-5077},
support = {R01 GM114535/GM/NIGMS NIH HHS/United States ; R35 GM139633/GM/NIGMS NIH HHS/United States ; },
mesh = {*Vitamin B 12 ; *Cobamides ; Bacteria/metabolism ; Escherichia coli/metabolism ; Vitamins/metabolism ; },
abstract = {All organisms rely on complex metabolites such as amino acids, nucleotides, and cofactors for essential metabolic processes. Some microbes synthesize these fundamental ingredients of life de novo, while others rely on uptake to fulfill their metabolic needs. Although certain metabolic processes are inherently "leaky," the mechanisms enabling stable metabolite provisioning among microbes in the absence of a host remain largely unclear. In particular, how can metabolite provisioning among free-living bacteria be maintained under the evolutionary pressure to economize resources? Salvaging, the process of "recycling and reusing," can be a metabolically efficient route to obtain access to required resources. Here, we show experimentally how precursor salvaging in engineered Escherichia coli populations can lead to stable, long-term metabolite provisioning. We find that salvaged cobamides (vitamin B12 and related enzyme cofactors) are readily made available to nonproducing population members, yet salvagers are strongly protected from overexploitation. We also describe a previously unnoted benefit of precursor salvaging, namely, the removal of the nonfunctional, proliferation-inhibiting precursor. As long as compatible precursors are present, any microbe possessing the terminal steps of a biosynthetic process can, in principle, forgo de novo biosynthesis in favor of salvaging. Consequently, precursor salvaging likely represents a potent, yet overlooked, alternative to de novo biosynthesis for the acquisition and provisioning of metabolites in free-living bacterial populations. IMPORTANCE Recycling gives new life to old things. Bacteria have the ability to recycle and reuse complex molecules they encounter in their environment to fulfill their basic metabolic needs in a resource-efficient way. By studying the salvaging (recycling and reusing) of vitamin B12 precursors, we found that metabolite salvaging can benefit others and provide stability to a bacterial community at the same time. Salvagers of vitamin B12 precursors freely share the result of their labor yet cannot be outcompeted by freeloaders, likely because salvagers retain preferential access to the salvaging products. Thus, salvaging may represent an effective, yet overlooked, mechanism of acquiring and provisioning nutrients in microbial populations.},
}
@article {pmid35920032,
year = {2022},
author = {Heinz, J and Doellinger, J and Maus, D and Schneider, A and Lasch, P and Grossart, HP and Schulze-Makuch, D},
title = {Perchlorate-specific proteomic stress responses of Debaryomyces hansenii could enable microbial survival in Martian brines.},
journal = {Environmental microbiology},
volume = {24},
number = {11},
pages = {5051-5065},
doi = {10.1111/1462-2920.16152},
pmid = {35920032},
issn = {1462-2920},
mesh = {Perchlorates/metabolism ; Extraterrestrial Environment ; *Debaryomyces ; Proteomics ; *Mars ; },
abstract = {If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganisms on the cellular level. Here, we present the first proteomic investigation on the perchlorate-specific stress responses of the halotolerant yeast Debaryomyces hansenii and compare these to generally known salt stress adaptations. We found that the responses to NaCl and NaClO4 -induced stresses share many common metabolic features, for example, signalling pathways, elevated energy metabolism, or osmolyte biosynthesis. Nevertheless, several new perchlorate-specific stress responses could be identified, such as protein glycosylation and cell wall remodulations, presumably in order to stabilize protein structures and the cell envelope. These stress responses would also be relevant for putative life on Mars, which-given the environmental conditions-likely developed chaotropic defence strategies such as stabilized confirmations of biomacromolecules or the formation of cell clusters.},
}
@article {pmid35918440,
year = {2023},
author = {Wu, Q and Ji, M and Yu, S and Li, J and Wu, X and Ju, X and Liu, B and Zhang, X},
title = {Distinct Denitrifying Phenotypes of Predominant Bacteria Modulate Nitrous Oxide Metabolism in Two Typical Cropland Soils.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {509-520},
pmid = {35918440},
issn = {1432-184X},
support = {31971526//National Natural Science Foundation of China/ ; 31861133018//National Natural Science Foundation of China/ ; XDB40020204//Chinese Academy of Sciences/ ; 2017YFD0200102//Key Technologies Research and Development Program/ ; },
mesh = {*Soil ; *Nitrous Oxide ; Denitrification ; Soil Microbiology ; Bacteria/genetics ; Carbon ; Nitrogen ; Crops, Agricultural ; },
abstract = {Denitrifying nitrous oxide (N2O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N2O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different supplements of nitrate and glucose to simulate the varying nitrogen and carbon conditions. The results show that N2O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of nitrogen and carbon. The abundance of most denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N2O production (nirS and nirK) to the gene responsible for N2O reduction (nosZ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities, with a higher abundance of N2O-generating bacteria in BF and a higher abundance of N2O-reducing bacteria in FF. High accumulation of N2O was verified by the bacterial isolates of Rhodanobacter predominated in BF due to a lack of N2O reduction capacity. The dominance of Castellaniella and others in FF led to a rapid reduction in N2O and thus less N2O accumulation, as demonstrated when the corresponding isolate was inoculated into the studied soils. Therefore, the different phenotypes of N2O metabolism of the distinct denitrifiers predominantly colonized the two soils, causing differing N2O accumulation. This knowledge would help to develop a strategy for mitigating N2O emissions in agricultural soils by regulating the phenotypes of N2O metabolism.},
}
@article {pmid35918056,
year = {2023},
author = {Santos Correa, S and Schultz, J and Lauersen, KJ and Soares Rosado, A},
title = {Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways.},
journal = {Journal of advanced research},
volume = {47},
number = {},
pages = {75-92},
pmid = {35918056},
issn = {2090-1224},
mesh = {*Photosynthesis ; *Carbon Dioxide/metabolism ; Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Carbon Cycle ; Plants/metabolism ; },
abstract = {BACKGROUND: Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin-Benson-Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms.<br><br>AIM OF REVIEW: In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field.<br><br>Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging "omics" data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.},
}
@article {pmid35916938,
year = {2023},
author = {Tang, Y and Wang, S and Jin, X and Zhou, D and Lin, Q and Liu, Z and Zhang, X and Dumont, HJ},
title = {Extensive Carbon Contribution of Inundated Terrestrial Plants to Zooplankton Biomass in a Eutrophic Lake.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {163-173},
pmid = {35916938},
issn = {1432-184X},
support = {32071566//National Natural Science Foundation of China/ ; 2022A1515011074//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Humans ; Animals ; *Zooplankton ; Carbon/metabolism ; Lakes ; Ecosystem ; Biomass ; Food Chain ; Phytoplankton/metabolism ; *Cyanobacteria/metabolism ; },
abstract = {Organic carbon derived from terrestrial plants contributes to aquatic consumers, e.g., zooplankton in lakes. The degree of the contribution depends on the availability of terrestrial organic carbon in lake organic pool and the transfer efficiency of the carbon. Terrestrial organic carbon is poor-quality food for zooplankton with a mismatch of nutrition content and was incorporated to zooplankton with much lower efficiency than phytoplankton. Contributions of terrestrial carbon to zooplankton generally decrease with an increase in phytoplankton production, indicating a preferential incorporation of phytoplankton in previous investigations. However, in eutrophic lakes, the dominating cyanobacteria were of poor quality and incorporated to consumers inefficiently too. In that case, zooplankton in eutrophic wetlands, where cyanobacteria dominate the phytoplankton production and massive terrestrial plants are inundated, may not preferentially incorporate poor food-quality phytoplankton resource to their biomass. Therefore, we hypothesize that carbon contributions of terrestrial vegetation to zooplankton and to lake particulate organic pool should be similar in such aquatic ecosystems. We tested this hypothesis by sampling zooplankton and carbon sources in Ming Lake (Jinan University Campus, southern China) which was overgrown by terrestrial plants after drying and re-flooded. After 60 days of observations at weekly (or biweekly) intervals, applying stable carbon ([13]C), nitrogen ([15] N), and hydrogen ([2]H) isotopic analysis and a stable isotope mixing model, we estimated the occurrence of extensive carbon contribution (≥ 50%) of flooded terrestrial plants to cladocerans and copepods. Contribution of inundated terrestrial plants to cladocerans was similar to that to lake particulate organic pool. Thus, our study quantified the role of terrestrial carbon in eutrophic wetlands, enhancing our understanding of cross-ecosystem interactions in food webs with an emphasis on the resource quality.},
}
@article {pmid35916937,
year = {2023},
author = {Pellegrinetti, TA and Cotta, SR and Sarmento, H and Costa, JS and Delbaje, E and Montes, CR and Camargo, PB and Barbiero, L and Rezende-Filho, AT and Fiore, MF},
title = {Bacterial Communities Along Environmental Gradients in Tropical Soda Lakes.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {892-903},
pmid = {35916937},
issn = {1432-184X},
support = {2016/14227-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {*Lakes/chemistry/microbiology ; Brazil ; Eutrophication ; *Cyanobacteria/growth &amp; development/isolation &amp; purification ; Metagenomics ; },
abstract = {Soda lake environments are known to be variable and can have distinct differences according to geographical location. In this study, we investigated the effects of different environmental conditions of six adjacent soda lakes in the Pantanal biome (Mato Grosso do Sul state, Brazil) on bacterial communities and their functioning using a metagenomic approach combined with flow cytometry and chemical analyses. Ordination analysis using flow cytometry and water chemistry data from two sampling periods (wet and dry) clustered soda lakes into three different profiles: eutrophic turbid (ET), oligotrophic turbid (OT), and clear vegetated oligotrophic (CVO). Analysis of bacterial community composition and functioning corroborated this ordination; the exception was one ET lake, which was similar to one OT lake during the wet season, indicating drastic shifts between seasons. Microbial abundance and diversity increased during the dry period, along with a considerable number of limnological variables, all indicative of a strong effect of the precipitation-evaporation balance in these systems. Cyanobacteria were associated with high electric conductivity, pH, and nutrient availability, whereas Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were correlated with landscape morphology variability (surface water, surface perimeter, and lake volume) and with lower salinity and pH levels. Stress response metabolism was enhanced in OT and ET lakes and underrepresented in CVO lakes. The microbiome dataset of this study can serve as a baseline for restoring impacted soda lakes. Altogether, the results of this study demonstrate the sensitivity of tropical soda lakes to climate change, as slight changes in hydrological regimes might produce drastic shifts in community diversity.},
}
@article {pmid35915645,
year = {2022},
author = {Mitiku, G and Rybka, D and Klein-Gunnewiek, P and Tessema, T and Raaijmakers, JM and Etalo, DW},
title = {Molecular detection and quantification of the Striga seedbank in agricultural soils.},
journal = {Weed research},
volume = {62},
number = {3},
pages = {181-191},
pmid = {35915645},
issn = {0043-1737},
abstract = {Striga hermonthica (Del.) Benth is a devastating parasitic weed in Sub-Saharan Africa (SSA) and its soil seedbank is the major factor contributing to its prevalence and persistence. To date, there is a little information on the Striga seedbank density in agricultural fields in SSA due to the lack of reliable detection and quantification methods. We developed a high-throughput method that combines density- and size-based separation techniques with quantitative polymerase chain reaction (qPCR)-based detection of Striga seeds in soil. The method was optimised and validated by introducing increasing numbers of Striga seeds in two physicochemically different Striga-free agricultural soils. The results showed that as little as one seed of S. hermonthica per 150 g of soil could be detected. This technique was subsequently tested on soil samples of 48 sorghum fields from different agro-ecological zones in Ethiopia to map the geospatial distribution of the Striga seedbank along a trajectory of more than 1500 km. Considerable variation in Striga seed densities was observed. Striga seeds were detectable in 75% of the field soils with densities up to 86 seeds per 150 g of soil. The Striga seed density in soil and the number of emerged Striga plants in the field showed a non-linear relationship. In conclusion, the method developed allows for accurate mapping of the Striga seedbank in physicochemically diverse SSA field soils and can be used to assess the impact of management strategies on Striga seedbank dynamics.},
}
@article {pmid35914169,
year = {2022},
author = {Gwak, JH and Awala, SI and Nguyen, NL and Yu, WJ and Yang, HY and von Bergen, M and Jehmlich, N and Kits, KD and Loy, A and Dunfield, PF and Dahl, C and Hyun, JH and Rhee, SK},
title = {Sulfur and methane oxidation by a single microorganism.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {32},
pages = {e2114799119},
pmid = {35914169},
issn = {1091-6490},
mesh = {*Bacteria/metabolism ; *Methane/metabolism ; Oxidation-Reduction ; Proteomics ; *Sulfur/metabolism ; Thiosulfates/metabolism ; },
abstract = {Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic-anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, 'Methylovirgula thiovorans' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox-rDsr pathway and the S4I system. Strain HY1 employed the Calvin-Benson-Bassham cycle for CO2 fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic-anoxic interface environments.},
}
@article {pmid35913610,
year = {2023},
author = {Cusumano, A and Bella, P and Peri, E and Rostás, M and Guarino, S and Lievens, B and Colazza, S},
title = {Nectar-Inhabiting Bacteria Affect Olfactory Responses of an Insect Parasitoid by Altering Nectar Odors.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {364-376},
pmid = {35913610},
issn = {1432-184X},
support = {FFR_D13-2018/2021//Universit&#xe0; degli Studi di Palermo/ ; },
mesh = {Animals ; *Plant Nectar ; *Odorants ; Insecta ; Flowers ; Bacteria ; Pollination ; },
abstract = {Floral nectar is ubiquitously colonized by a variety of microorganisms among which yeasts and bacteria are the most common. Microorganisms inhabiting floral nectar can alter several nectar traits, including nectar odor by producing microbial volatile organic compounds (mVOCs). Evidence showing that mVOCs can affect the foraging behavior of insect pollinators is increasing in the literature, whereas the role of mVOCs in altering the foraging behavior of third-trophic level organisms such as insect parasitoids is largely overlooked. Parasitoids are frequent visitors of flowers and are well known to feed on nectar. In this study, we isolated bacteria inhabiting floral nectar of buckwheat, Fagopyrum esculentum (Polygonales: Polygonaceae), to test the hypothesis that nectar bacteria affect the foraging behavior of the egg parasitoid Trissolcus basalis (Hymenoptera: Scelionidae) via changes in odors of nectar. In behavioral assays, we found that T. basalis wasps are attracted toward nectar fermented by 4 out of the 14 bacterial strains isolated, which belong to Staphylococcus epidermidis, Terrabacillus saccharophilus (both Firmicutes), Pantoea sp. (Proteobacteria), and Curtobacterium sp. (Actinobacteria). Results of chemical investigations revealed significant differences in the volatile blend composition of nectars fermented by the bacterial isolates. Our results indicate that nectar-inhabiting bacteria play an important role in the interactions between flowering plants and foraging parasitoids. These results are also relevant from an applied perspective as flowering resources, such as buckwheat, are largely used in agriculture to promote conservation biological control of insect pests.},
}
@article {pmid35913161,
year = {2022},
author = {Lesniak, NA and Tomkovich, S and Henry, A and Taylor, A and Colovas, J and Bishop, L and McBride, K and Schloss, PD},
title = {Diluted Fecal Community Transplant Restores Clostridioides difficile Colonization Resistance to Antibiotic-Perturbed Murine Communities.},
journal = {mBio},
volume = {13},
number = {4},
pages = {e0136422},
pmid = {35913161},
issn = {2150-7511},
support = {U19 AI090871/AI/NIAID NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Cefoperazone/pharmacology ; Clindamycin/pharmacology/therapeutic use ; Clostridioides ; *Clostridioides difficile ; *Clostridium Infections/microbiology/prevention &amp; control ; Disease Susceptibility ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Streptomycin/pharmacology/therapeutic use ; },
abstract = {Fecal communities transplanted into individuals can eliminate recurrent Clostridioides difficile infection (CDI) with high efficacy. However, this treatment is only used once CDI becomes resistant to antibiotics or has recurred multiple times. We sought to investigate whether a fecal community transplant (FCT) pretreatment could be used to prevent CDI altogether. We treated male C57BL/6 mice with either clindamycin, cefoperazone, or streptomycin and then inoculated them with the microbial community from untreated mice before challenge with C. difficile. We measured colonization and sequenced the V4 region of the 16S rRNA gene to understand the dynamics of the murine fecal community in response to the FCT and C. difficile challenge. Clindamycin-treated mice became colonized with C. difficile but cleared it naturally and did not benefit from the FCT. Cefoperazone-treated mice became colonized by C. difficile, but the FCT enabled clearance of C. difficile. In streptomycin-treated mice, the FCT was able to prevent C. difficile from colonizing. We then diluted the FCT and repeated the experiments. Cefoperazone-treated mice no longer cleared C. difficile. However, streptomycin-treated mice colonized with 1:10[2] dilutions resisted C. difficile colonization. Streptomycin-treated mice that received an FCT diluted 1:10[3] became colonized with C. difficile but later cleared the infection. In streptomycin-treated mice, inhibition of C. difficile was associated with increased relative abundance of a group of bacteria related to Porphyromonadaceae and Lachnospiraceae. These data demonstrate that C. difficile colonization resistance can be restored to a susceptible community with an FCT as long as it complements the missing populations. IMPORTANCE Antibiotic use, ubiquitous with the health care environment, is a major risk factor for Clostridioides difficile infection (CDI), the most common nosocomial infection. When C. difficile becomes resistant to antibiotics, a fecal microbiota transplant from a healthy individual can effectively restore the gut bacterial community and eliminate the infection. While this relationship between the gut bacteria and CDI is well established, there are no therapies to treat a perturbed gut community to prevent CDI. This study explored the potential of restoring colonization resistance to antibiotic-induced susceptible gut communities. We described the effect that gut bacterial community variation has on the effectiveness of a fecal community transplant for inhibiting CDI. These data demonstrated that communities susceptible to CDI can be supplemented with fecal communities but that the effectiveness depended on the structure of the community following the perturbation. Thus, a reduced bacterial community may be able to recover colonization resistance in patients treated with antibiotics.},
}
@article {pmid35909604,
year = {2022},
author = {Jepsen, T and Jensen, B and Jørgensen, NOG},
title = {Volatiles produced by Streptomyces spp. delay rot in apples caused by Colletotrichum acutatum.},
journal = {Current research in microbial sciences},
volume = {3},
number = {},
pages = {100121},
pmid = {35909604},
issn = {2666-5174},
abstract = {Volatile organic compounds (VOCs) produced by microorganisms may prevent postharvest rot in fruits. Here, it was examined if VOCs from different species of Streptomyces can control infection in apples caused by the fungal pathogen Colletotrichum acutatum. Incubation of C. acutatum-infected apples in semi-closed boxes with actively growing strains of three Streptomyces (S. coelicolor, S. diastatochromogenes and Streptomyces strain 2R) showed that VOCs reduced rot areas of the apples by 45-66% after 8 days and 39-57% after 10 days, relative to infected apples incubated without Streptomyces. No differences in inhibition among the three strains were seen. In contrast, a mutant strain of Streptomyces that lacks major genes involved in biosynthesis of secondary metabolites, did not reduce development of rot in the apples. Furthermore, Streptomyces VOCs reduced radial hyphal growth of C. acutatum on agar. Several of the VOCs produced by three Streptomyces strains have previously shown fungicidal properties. Although the specific VOCs being active in inhibition of C. acutatum remain to be determined, VOCs may have a great potential as biofumigants to minimize postharvest diseases in fruits.},
}
@article {pmid35903477,
year = {2022},
author = {Olmo, R and Wetzels, SU and Armanhi, JSL and Arruda, P and Berg, G and Cernava, T and Cotter, PD and Araujo, SC and de Souza, RSC and Ferrocino, I and Frisvad, JC and Georgalaki, M and Hansen, HH and Kazou, M and Kiran, GS and Kostic, T and Krauss-Etschmann, S and Kriaa, A and Lange, L and Maguin, E and Mitter, B and Nielsen, MO and Olivares, M and Quijada, NM and Romaní-Pérez, M and Sanz, Y and Schloter, M and Schmitt-Kopplin, P and Seaton, SC and Selvin, J and Sessitsch, A and Wang, M and Zwirzitz, B and Selberherr, E and Wagner, M},
title = {Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems - A Selection of Case Studies.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {834622},
pmid = {35903477},
issn = {1664-302X},
abstract = {Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.},
}
@article {pmid35902889,
year = {2022},
author = {Ma, X and Wang, T and Shi, Z and Chiariello, NR and Docherty, K and Field, CB and Gutknecht, J and Gao, Q and Gu, Y and Guo, X and Hungate, BA and Lei, J and Niboyet, A and Le Roux, X and Yuan, M and Yuan, T and Zhou, J and Yang, Y},
title = {Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {112},
pmid = {35902889},
issn = {2049-2618},
mesh = {Carbon ; Ecosystem ; *Microbiota/genetics ; Nitrogen/metabolism ; *Soil ; Soil Microbiology ; },
abstract = {BACKGROUND: Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m[-2] year[-1] of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century.<br><br>RESULTS: Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition.<br><br>CONCLUSIONS: We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. Video Abstract.},
}
@article {pmid35896536,
year = {2022},
author = {Lin, C and Peñaranda, JSD and Dendooven, J and Detavernier, C and Schaubroeck, D and Boon, N and Baets, R and Le Thomas, N},
title = {UV photonic integrated circuits for far-field structured illumination autofluorescence microscopy.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {4360},
pmid = {35896536},
issn = {2041-1723},
mesh = {Light ; *Lighting ; *Microscopy/methods ; Photons ; },
abstract = {Ultra-violet (UV) light has still a limited scope in optical microscopy despite its potential advantages over visible light in terms of optical resolution and of interaction with a wide variety of biological molecules. The main challenge is to control in a robust, compact and cost-effective way UV light beams at the level of a single optical spatial mode and concomitantly to minimize the light propagation loss. To tackle this challenge, we present here photonic integrated circuits made of aluminum oxide thin layers that are compatible with both UV light and high-volume manufacturing. These photonic circuits designed at a wavelength of 360 nm enable super-resolved structured illumination microscopy with conventional wide-field microscopes and without modifying the usual protocol for handling the object to be imaged. As a biological application, we show that our UV photonic chips enable to image the autofluorescence of yeast cells and reveal features unresolved with standard wide-field microscopy.},
}
@article {pmid35893569,
year = {2022},
author = {Mugani, R and Khalloufi, FE and Redouane, EM and Haida, M and Zerrifi, SEA and Campos, A and Kasada, M and Woodhouse, J and Grossart, HP and Vasconcelos, V and Oudra, B},
title = {Bacterioplankton Associated with Toxic Cyanobacteria Promote Pisum sativum (Pea) Growth and Nutritional Value through Positive Interactions.},
journal = {Microorganisms},
volume = {10},
number = {8},
pages = {},
pmid = {35893569},
issn = {2076-2607},
support = {823860//European Commission/ ; },
abstract = {Research on Plant Growth-Promoting Bacteria (PGPB) has focused much more on rhizospheric bacteria. However, PGPB associated with toxic cyanobacterial bloom (TCB) could enter the rhizosphere through irrigation water, helping plants such as Pisum sativum L. (pea) overcome oxidative stress induced by microcystin (MC) and improve plant growth and nutritional value. This study aimed to isolate bacteria associated with toxic cyanobacteria, test PGPB properties, and inoculate them as a consortium to pea seedlings irrigated with MC to investigate their role in plant protection as well as in improving growth and nutritional value. Two bacterioplankton isolates and one rhizosphere isolate were isolated and purified on a mineral salt medium supplemented with 1000 μg/L MC and identified via their 16S rRNA gene. The mixed strains were inoculated to pea seedlings in pots irrigated with 0, 50, and 100 μg/L MC. We measured the morphological and physiological parameters of pea plants at maturity and evaluated the efficiency of the plant’s enzymatic and non-enzymatic antioxidant responses to assess the role and contribution of PGPB. Both bacterioplankton isolates were identified as Starkeya sp., and the rhizobacterium was identified as Brevundimonas aurantiaca. MC addition significantly (p < 0.05) reduced all the growth parameters of the pea, i.e., total chlorophyll content, leaf quantum yield, stomatal conductance, carotenoids, and polyphenol contents, in an MC concentration-dependent manner, while bacterial presence positively affected all the measured parameters. In the MC treatment, the levels of the pea’s antioxidant traits, including SOD, CAT, POD, PPO, GST, and ascorbic acid, were increased in the sterile pots. In contrast, these levels were reduced with double and triple PGPB addition. Additionally, nutritional values such as sugars, proteins, and minerals (Ca and K) in pea fruits were reduced under MC exposure but increased with PGPB addition. Overall, in the presence of MC, PGPB seem to positively interact with pea plants and thus may constitute a natural alternative for soil fertilization when irrigated with cyanotoxin-contaminated water, increasing the yield and nutritional value of crops.},
}
@article {pmid35892285,
year = {2023},
author = {von Gastrow, L and Michel, E and Legrand, J and Amelot, R and Segond, D and Guezenec, S and Rué, O and Chable, V and Goldringer, I and Dousset, X and Serpolay-Bessoni, E and Taupier-Letage, B and Vindras-Fouillet, C and Onno, B and Valence, F and Sicard, D},
title = {Microbial community dispersal from wheat grains to sourdoughs: A contribution of participatory research.},
journal = {Molecular ecology},
volume = {32},
number = {10},
pages = {2413-2427},
doi = {10.1111/mec.16630},
pmid = {35892285},
issn = {1365-294X},
mesh = {Humans ; *Triticum/microbiology ; Community-Based Participatory Research ; Fermentation ; Food Microbiology ; *Microbiota/genetics ; Bacteria/genetics ; Yeasts/genetics ; Bread/analysis/microbiology ; },
abstract = {Understanding microbial dispersal is critical to understand the dynamics and evolution of microbial communities. However, microbial dispersal is difficult to study because of uncertainty about their vectors of migration. This applies to both microbial communities in natural and human-associated environments. Here, we studied microbial dispersal along the sourdoughs bread-making chain using a participatory research approach. Sourdough is a naturally fermented mixture of flour and water. It hosts a community of bacteria and yeasts whose origins are only partially known. We analysed the potential of wheat grains and flour to serve as an inoculum for sourdough microbial communities using 16S rDNA and ITS1 metabarcoding. First, in an experiment involving farmers, a miller and bakers, we followed the microbiota from grains to newly initiated and propagated sourdoughs. Second, we compared the microbiota of 46 sourdough samples collected everywhere in France, and of the flour used for their back-slopping. The core microbiota detected on the seeds, in the flour and in the sourdough was composed mainly of microbes known to be associated with plants and not living in sourdoughs. No sourdough yeast species were detected on grains and flours. Sourdough lactic acid bacteria were rarely found in flour. When they were, they did not have the same amplicon sequence variant (ASV) as found in the corresponding sourdough. However, the low sequencing depth for bacteria in flour did not allow us to draw definitive conclusion. Thus, our results showed that sourdough yeasts did not come from flour, and suggest that neither do sourdough LAB.},
}
@article {pmid35890046,
year = {2022},
author = {Orsini, M and Petrin, S and Corrò, M and Baggio, G and Spagnolo, E and Losasso, C},
title = {Anthroponotic-Based Transfer of Staphylococcus to Dog: A Case Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {7},
pages = {},
pmid = {35890046},
issn = {2076-0817},
support = {RC IZSVE 16/18//Ministero della Salute/ ; },
abstract = {Although usually harmless, Staphylococcus spp. can cause nosocomial and community-onset skin and soft tissue infections in both humans and animals; thus, it is considered a significant burden for healthcare systems worldwide. Companion animals have been identified as potential reservoirs of pathogenic Staphylococcus with specific reference to Methicillin Resistant Staphylococcus aureus (MRSA). In this study, we investigated the circulation and the genetic relationships of a collection of Staphylococcus spp. isolates in a family composed of four adults (a mother, father, grandmother, and grandfather), one child, and a dog, which were sampled over three years. The routes of transmission among humans and between humans and the dog werelyzed. The results displayed the circulation of many Staphylococcus lineages, belonging to different species and sequence types (ST) and being related to both human and pet origins. However, among the observed host-switch events, one of them clearly underpinnthroponotic route from a human to a dog. This suggests that companion animals can potentially have a role as a carrier of Staphylococcus, thus posing a serious concern about MRSA spreading within human and animal microbial communities.},
}
@article {pmid35889095,
year = {2022},
author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Junca, H and Sidjabat, HE and Cano-Lozano, JA and Villamil Díaz, LM},
title = {Competitive Exclusion Bacterial Culture Derived from the Gut Microbiome of Nile Tilapia (Oreochromis niloticus) as a Resource to Efficiently Recover Probiotic Strains: Taxonomic, Genomic, and Functional Proof of Concept.},
journal = {Microorganisms},
volume = {10},
number = {7},
pages = {},
pmid = {35889095},
issn = {2076-2607},
support = {ING181-2016//Universidad de La Sabana/ ; INGPHD-6-2017//Universidad de La Sabana/ ; INGPHD-9-2019//Universidad de La Sabana/ ; 808-2018-contract CT 329-2019//MINCIENCIAS- Patrimonio Aut&#xf3;nomo Fondo Nacional de Financiamiento para la Ciencia, la Tecnolog&#xed;a y la Innovaci&#xf3;n Francisco Jos&#xe9; de Caldas/ ; 727-2015, contract CT 122-2017//MINCIENCIAS/ ; },
abstract = {This study aims to mine a previously developed continuous-flow competitive exclusion culture (CFCEC) originating from the Tilapia gut microbiome as a rational and efficient autochthonous probiotic strain recovery source. Three isolated strains were tested on their adaptability to host gastrointestinal conditions, their antibacterial activities against aquaculture bacterial pathogens, and their antibiotic susceptibility patterns. Their genomes were fully sequenced, assembled, annotated, and relevant functions inferred, such as those related to pinpointed probiotic activities and phylogenomic comparative analyses to the closer reported strains/species relatives. The strains are possible candidates of novel genus/species taxa inside Lactococcus spp. and Priestia spp. (previously known as Bacillus spp.) These results were consistent with reports on strains inside these phyla exhibiting probiotic features, and the strains we found are expanding their known diversity. Furthermore, their pangenomes showed that these bacteria have indeed a set of so far uncharacterized genes that may play a role in the antagonism to competing strains or specific symbiotic adaptations to the fish host. In conclusion, CFCEC proved to effectively allow the enrichment and further pure culture isolation of strains with probiotic potential.},
}
@article {pmid35886559,
year = {2022},
author = {Shen, W and Long, Y and Qiu, Z and Gao, N and Masuda, Y and Itoh, H and Ohba, H and Shiratori, Y and Rajasekar, A and Senoo, K},
title = {Investigation of Rice Yields and Critical N Losses from Paddy Soil under Different N Fertilization Rates with Iron Application.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {14},
pages = {},
pmid = {35886559},
issn = {1660-4601},
mesh = {Agriculture ; Fertilization ; Fertilizers/analysis ; Iron ; Nitrogen/analysis ; Nitrous Oxide/analysis ; *Oryza/chemistry ; Powders ; *Soil/chemistry ; Urea ; },
abstract = {The application of iron powder stimulated the growth of iron-reducing bacteria as a respiratory substrate and enhanced their nitrogen (N)-fixing activity in flooded paddy soils. High N fertilization (urea) in the flooded paddy soils has caused adverse environmental impacts such as ammonia (NH3) volatilization, nitrous oxide (N2O) emissions, and nitrate (NO3[-]) leaching. This study aims to investigate the effects of N fertilization rates in combination with an iron amendment on rice yields and N losses from flooded paddy fields. We performed a 2-year field plot experiment with traditional rice-wheat rotation in China's Yangtze River Delta. The investigation consisted of seven treatments, including 100%, 80%, 60%, and 0% of the conventional N (urea and commercial organic manure) fertilization rate, and 80%, 60%, and 0% of the conventional N with the iron powder (≥99% purity) amendment. The rice yields decreased with a reduction in the conventional N fertilization rate, whereas they were comparable after the iron application under the 80% and 60% conventional N rate. The critical N losses, including NH3 volatilization, N2O emissions, and NO3[-] and NH4[+] leaching, generally decreased with a reduction in the conventional N fertilization rate. These N losses were significantly greater after the iron amendment compared with the non-amended treatments under the 80% and 60% conventional N fertilization rate in the first rice-growing season. However, it was comparable between the iron-amended and the non-amended treatments in the second season. Furthermore, NO3[-] leaching was the most significant N loss throughout the two rice seasons, followed by NH3 volatilization. The iron amendment significantly increased soil Fe[2+] content compared with the non-amended treatments irrespective of N fertilization, suggesting the reduction of amended iron by iron-reducing bacteria and their simultaneous N fixation. A combination of the iron application with 60-80% of the conventional N fertilization rate could maintain rice yields similar to the conventional N fertilization rate while reducing the critical N losses in the flooded paddy field tested in this study. Our study leads to the establishment of novel and practical rice cultivation, which is a step towards the development of green agriculture.},
}
@article {pmid35884216,
year = {2022},
author = {Duysburgh, C and Van den Abbeele, P and Franckenstein, D and Westphal, M and Kuchinka-Koch, A and Marzorati, M},
title = {Co-Administration of Lactulose Crystals with Amoxicillin Followed by Prolonged Lactulose Treatment Promotes Recovery of the Human Gut Microbiome In Vitro.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {7},
pages = {},
pmid = {35884216},
issn = {2079-6382},
abstract = {The validated SHIME model was used to assess the effect of repeated administration of two different lactulose dosages (5 g/d and 10 g/d) on the human gut microbiome during and following amoxicillin-clavulanic acid treatment. First, antibiotic treatment strongly decreased Bifidobacteriaceae levels from 54.4% to 0.6% and from 23.8% to 2.3% in the simulated proximal and distal colon, respectively, coinciding with a marked reduction in butyrate concentrations. Treatment with lactulose enhanced acetate and lactate levels during antibiotic treatment, likely through lactulose fermentation by Lachnospiraceae and Lactobacillaceae. One week after cessation of antibiotic treatment, Bifidobacteriaceae levels re-increased to 20.4% and 7.6% in the proximal and distal colon of the 5 g lactulose/d co-administered unit, as compared with 1.0% and 2.2% in the antibiotic-treated unit, and were even further stimulated upon extension of lactulose administration. Marked butyrogenic effects were observed upon prolonged lactulose supplementation, suggesting the establishment of cross-feeding interactions between Bifidobacteriaceae and butyrate producers. Furthermore, a limited Enterobacteriaceae outgrowth following antibiotic treatment was observed upon dosing with 10 g lactulose/d, indicating inhibition of pathogenic colonization by lactulose following antibiotic therapy. Overall, lactulose seems to be an interesting candidate for limiting the detrimental effects of amoxicillin-clavulanic acid on the human gut microbiome, though further studies are warranted to confirm these findings.},
}
@article {pmid35883112,
year = {2022},
author = {Romo Bechara, N and Wasserberg, G and Raymann, K},
title = {Microbial ecology of sand fly breeding sites: aging and larval conditioning alter the bacterial community composition of rearing substrates.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {265},
pmid = {35883112},
issn = {1756-3305},
support = {R01 AI123327/AI/NIAID NIH HHS/United States ; R01AI123327//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Animals ; Bacteria/genetics ; Breeding ; Female ; Larva ; Mosquito Vectors ; *Phlebotomus/genetics ; *Psychodidae/genetics ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Sand flies vector several human pathogens, including Leishmania species, which cause leishmaniases. A leishmaniasis vaccine does not yet exist, so the most common prevention strategies involve personal protection and insecticide spraying. However, insecticides can impact non-target organisms and are becoming less effective because of the evolution of resistance. An alternative control strategy is the attract-and-kill approach, where the vector is lured to a lethal trap, ideally located in oviposition sites that will attract gravid females. Oviposition traps containing attractive microbes have proven successful for the control of some mosquito populations but have not been developed for sand flies. Gravid female sand flies lay their eggs in decomposing organic matter on which the larvae feed and develop. Studies have demonstrated that gravid females are particularly attracted to larval conditioned (containing eggs and larvae) and aged rearing substrates. An isolate-based study has provided some evidence that bacteria play a role in the attraction of sand flies to conditioned substrates. However, the overall bacterial community structure of conditioned and aged substrates and how they change over time has not been investigated.<br><br>METHODS: The goal of this study was to characterize the bacterial communities of rearing and oviposition substrates that have been shown to vary in attractiveness to gravid sand flies in previous behavioral studies. Using 16S rRNA amplicon sequencing we determined the bacterial composition in fresh, aged, and larval-conditioned substrates at four time points representing the main life-cycle stages of developing sand flies. We compared the diversity, presence, and abundance of taxa across substrate types and time points in order to identify how aging and larval-conditioning impact bacterial community structure.<br><br>RESULTS: We found that the bacterial communities significantly change within and between substrates over time. We also identified bacteria that might be responsible for attraction to conditioned and aged substrates, which could be potential candidates for the development of attract-and-kill strategies for sand flies.<br><br>CONCLUSION: This study demonstrated that both aging and larval conditioning induce shifts in the bacterial communities of sand fly oviposition and rearing substrates, which may explain the previously observed preference of gravid female sand flies to substrates containing second/third-instar larvae (conditioned) and substrates aged the same amount of time without larvae (aged).},
}
@article {pmid35882347,
year = {2022},
author = {Aziz, A and Rameez, H and Sengar, A and Sharma, D and Farooqi, IH and Basheer, F},
title = {Biogas production and nutrients removal from slaughterhouse wastewater using integrated anaerobic and aerobic granular intermittent SBRs - Bioreactors stability and microbial dynamics.},
journal = {The Science of the total environment},
volume = {848},
number = {},
pages = {157575},
doi = {10.1016/j.scitotenv.2022.157575},
pmid = {35882347},
issn = {1879-1026},
mesh = {Abattoirs ; Ammonia ; Anaerobiosis ; Bacteria ; Biofuels ; Bioreactors ; Carbon ; *Environmental Pollutants ; Nitrites ; Nutrients ; Waste Disposal, Fluid/methods ; *Wastewater/microbiology ; },
abstract = {Slaughterhouse wastewater (SWW) was effectively treated in sequential anaerobic and aerobic granular intermittent sequencing batch reactors (ASBR+ISBR) for 665 days at different HRTs (48 h, 32 h, 24 h, and 12 h). The ASBR was stable at each HRT but performed relatively well at 12 h (OLR - 7.8-9.8 kg COD/m[3]-d) in terms of pollutants removal and biogas production than previously conducted research. The average biogas production was about 17.3 L/day having 70-76 % of CH4 which could subsidize around 52 % of electricity demand while saving 103 US dollars/day if installed at full scale. In the case of post aerobic granular ISBR, carbon and nutrients removal (N&amp;P) was achieved by enriching granules (1.7-2.2 mm) at low DO (0.5-0.8 mg/L) via the nitrite pathway. The ISBR was also well stable at 12 h HRT (average OLR of 2.1 kg COD/m[3]-d) and met the effluent discharge guidelines recommended by the Central Pollution Control Board of India. During steady-state conditions (12 h HRT), the average removal efficiencies for COD, TSS, O&amp;G, TN, and PO4-P were 98.8 %, 96.4 %, 98.7 %, 93.4 %, and 86.6 % respectively from combined ASBR and ISBR. The microbial analysis confirmed Euryarchaeota, Proteobacteria, Firmicutes, Chloroflexi, Bacteroidetes, Planctomycetes, and Synergistetes as the dominant phyla in ASBR. Methanosaeta (21.56 %) and Methanosarcina (6.48 %) were the prevailing methanogens for CH4 production. The leading phyla observed in ISBR were Bacteroidetes, Proteobacteria, Firmicutes, Armatimonadetes, Verrucomicrobia, Chloroflexi, and Planctomycetes. Heterotrophic AOB (Thauera, Xanthomonadaceae, Pseudomonas, Sphingomonadaceae, and Rhodococcus) were mainly detected in the system for ammonia oxidation besides common autotrophic AOB. Similarly, a known PAO (Accumulibacter) was not identified but other PAO (Rhodocyclaceae, Dechloromonas, Pseudomonas, Flavobacteriaceae, and Sphingobacteriaceae) were prevalent inside aerobic granular ISBR that contributed to both carbon and nutrients removal. The results obtained would help implement the investigated reactor configurations at the pilot and full scale for SWW treatment.},
}
@article {pmid35882195,
year = {2022},
author = {Lyng, M and Kovács, &#xc1;T},
title = {Microbial ecology: Metabolic heterogeneity and the division of labor in multicellular structures.},
journal = {Current biology : CB},
volume = {32},
number = {14},
pages = {R771-R774},
doi = {10.1016/j.cub.2022.06.008},
pmid = {35882195},
issn = {1879-0445},
abstract = {Many bacterial species are capable of differentiating to create phenotypic heterogeneity. Using the aggregate-forming marine bacterium Vibrio splendidus, a new study reveals how this organism differentiates to form spherical structures with a motile, carbon-storing core and a non-motile shell.},
}
@article {pmid35881247,
year = {2023},
author = {King, NG and Smale, DA and Thorpe, JM and McKeown, NJ and Andrews, AJ and Browne, R and Malham, SK},
title = {Core Community Persistence Despite Dynamic Spatiotemporal Responses in the Associated Bacterial Communities of Farmed Pacific Oysters.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {154-162},
pmid = {35881247},
issn = {1432-184X},
support = {MR/S032827/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Crassostrea/microbiology ; Temperature ; Bacteria/genetics ; Seasons ; Seawater/microbiology ; },
abstract = {A breakdown in host-bacteria relationships has been associated with the progression of a number of marine diseases and subsequent mortality events. For the Pacific oyster, Crassostrea gigas, summer mortality syndrome (SMS) is one of the biggest constraints to the growth of the sector and is set to expand into temperate systems as ocean temperatures rise. Currently, a lack of understanding of natural spatiotemporal dynamics of the host-bacteria relationship limits our ability to develop microbially based monitoring approaches. Here, we characterised the associated bacterial community of C. gigas, at two Irish oyster farms, unaffected by SMS, over the course of a year. We found C. gigas harboured spatiotemporally variable bacterial communities that were distinct from bacterioplankton in surrounding seawater. Whilst the majority of bacteria-oyster associations were transient and highly variable, we observed clear patterns of stability in the form of a small core consisting of six persistent amplicon sequence variants (ASVs). This core made up a disproportionately large contribution to sample abundance (34 ± 0.14%), despite representing only 0.034% of species richness across the study, and has been associated with healthy oysters in other systems. Overall, our study demonstrates the consistent features of oyster bacterial communities across spatial and temporal scales and provides an ecologically meaningful baseline to track environmental change.},
}
@article {pmid35880896,
year = {2022},
author = {Sun, Y and Shi, J and Wang, X and Ding, C and Wang, J},
title = {Deciphering the Mechanisms Shaping the Plastisphere Microbiota in Soil.},
journal = {mSystems},
volume = {7},
number = {4},
pages = {e0035222},
pmid = {35880896},
issn = {2379-5077},
mesh = {*Microplastics ; Plastics ; Soil ; Soil Microbiology ; Polyesters ; *Microbiota/genetics ; Polyethylene ; },
abstract = {The gradual accumulation of microplastics has aroused increasing concern for the unique niche, termed "plastisphere." As research so far has focused on their characteristics in aquatic ecosystems, our understanding of the colonization and assembly of the attached bacterial communities on microplastics in soil ecosystems remains poor. Here, we aimed to characterize the plastisphere microbiomes of two types of microplastics (polylactic acid [PLA] and polyethylene [PE]) differing in their biodegradability in two different soils. After incubation for 60 days, considerably lower alpha diversity of bacterial community was observed on the microplastic surfaces, and prominent divergences occurred in the microbial community compositions between the plastisphere and the bulk soil. The temperature, rather than polymer type, significantly induced the differences between the plastisphere communities. The rRNA gene operon (rrn) copy numbers were significantly higher in the PLA plastisphere, suggesting potential degradation. The co-occurrence network analysis showed that the PE plastisphere exhibited greater network complexity and stronger stability than those in the PLA plastisphere. The stochasticity ratio indicated the remarkable importance of stochastic process on community assembly in PE and PLA plastispheres, while the null model analysis showed the nonnegligible roles of deterministic processes in shaping the plastisphere communities. Higher contributions of homogenous selection in the PLA plastisphere were observed in comparison with the PE plastisphere, which could probably be attributed to the selective pressure induced by microplastic degradation. Our findings enhance our mechanistic understanding of the diversity patterns and assembly processes of plastisphere in soil environments and have important implications for microbial ecology and microplastic risk assessment. IMPORTANCE The increasing pervasive microplastic pollution is creating a new environmental compartment, termed plastisphere. Even though there was conclusive information characterizing the plastisphere, the underlying mechanisms shaping the bacterial communities in the plastisphere in the soil remain unclear. Therefore, we incubated two types of microplastics (PE and PLA) in two different soils and explored the differences between plastisphere and bulk soil communities. Additionally, the co-occurrence network and the assembly processes of plastisphere were subjected to further analysis. Our results highlight the importance of selective recruitment of microplastics and contribute to the understanding of the diversity patterns and assembly processes of plastisphere in soil environments.},
}
@article {pmid35880097,
year = {2022},
author = {Strik, DPBTB and Ganigué, R and Angenent, LT},
title = {Editorial: Microbial Chain Elongation- Close the Carbon Loop by Connecting-Communities.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {10},
number = {},
pages = {894490},
pmid = {35880097},
issn = {2296-4185},
}
@article {pmid35878855,
year = {2022},
author = {Camacho-Sanchez, M and Camacho, M and Redondo-Gómez, S and Mateos-Naranjo, E},
title = {Bacterial assemblage in Mediterranean salt marshes: Disentangling the relative importance of seasonality, zonation and halophytes.},
journal = {The Science of the total environment},
volume = {846},
number = {},
pages = {157514},
doi = {10.1016/j.scitotenv.2022.157514},
pmid = {35878855},
issn = {1879-1026},
mesh = {Bacteria ; *Chenopodiaceae ; Phylogeny ; Rhizosphere ; *Salt-Tolerant Plants/microbiology ; Soil ; Soil Microbiology ; Wetlands ; },
abstract = {Salt marshes gather a high diversity of prokaryotes across their environmental gradients. Most of this diversity and the factors determining their community assemblage are unknown. We massively sequenced a portion of the 16S gene to characterize the diversity of prokaryotes in soils from a salt marsh in Río Piedras, Southern Spain. We sampled in the four seasons, and in five plots dominated by a different halophyte (Spartina maritima, S. densiflora, Salicornia ramosissima, Arthrocaulon macrostachyum and Atriplex portulacoides) growing under different environmental conditions and representing different stages in the marsh ecological succession. Soil was sampled in their rhizosphere and adjacent bulk soil. We report the effects of different factors explaining prokaryotic beta diversity in the marsh: zonation (50 %), seasonality (14 %), and halophyte rhizosphere (7 %). Proteobacteria and Bacteroidota were the most abundant phyla. Firmicutes had a peak in winter and Desulfobacterota with other bacteria involved in sulfur cycling were abundant in the low marsh plots from S. maritima. Alpha diversity was highest in spring and decreased in winter. We detected a marked phylogenetic turnover between seasons and in rhizospheric soil respect to adjacent bulk soil for most pairwise comparisons. The effect of halophyte on its rhizosphere was species-specific, being S. maritima the species with more differentiated taxa between rhizosphere versus surrounding bulk soil. Our work highlights how the complex interaction between marsh zonation, seasonality and rhizosphere, onsets processes structuring bacterial community assemblage in salt marsh soils.},
}
@article {pmid35876854,
year = {2023},
author = {Perliński, P and Mudryk, ZJ and Zdanowicz, M and Kubera, &#x141;},
title = {Abundance of Live and Dead Bacteriopsammon Inhabiting Sandy Ecosystems of Recreational Marine Beaches of the Southern Baltic Sea.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {350-363},
pmid = {35876854},
issn = {1432-184X},
mesh = {*Sand ; *Ecosystem ; Bathing Beaches ; Seawater ; Bacteria ; Environmental Monitoring ; },
abstract = {The study was carried out on four non-tidal sandy marine beaches located on the Polish part of the southern Baltic Sea coast. We applied a LIVE/DEAD™ BacLight™ Bacterial Viability Kit (Invitrogen™) method to determine the abundance of live and dead bacteriopsammon. Live psammon bacteria cells constituted 31-53% of the total number of bacteria inhabiting sand of the studied beaches. Abundance of live and dead psammon bacteria generally differed along the horizontal profile in all beaches. The maximum density of bacteria was noted in the dune and the middle part of the beach (dry zones) and the minimum in wet zones, i.e., under seawater surface and at the swash zone. Generally along the vertical profile, the highest numbers of two studied bacterial groups were noted in the surface sand layer, while with increasing sediment depth their numbers significantly decreased. The abundance of live and dead bacteria showed a distinct seasonal variation.},
}
@article {pmid35873980,
year = {2022},
author = {Gouka, L and Vogels, C and Hansen, LH and Raaijmakers, JM and Cordovez, V},
title = {Genetic, Phenotypic and Metabolic Diversity of Yeasts From Wheat Flag Leaves.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {908628},
pmid = {35873980},
issn = {1664-462X},
abstract = {The phyllosphere, the aboveground part of a plant, is a harsh environment with diverse abiotic and biotic stresses, including oscillating nutrient availability and temperature as well as exposure to UV radiation. Microbial colonization of this dynamic environment requires specific adaptive traits, including tolerance to fluctuating temperatures, the production of secondary metabolites and pigments to successfully compete with other microorganisms and to withstand abiotic stresses. Here, we isolated 175 yeasts, comprising 15 different genera, from the wheat flag leaf and characterized a selection of these for various adaptive traits such as substrate utilization, tolerance to different temperatures, biofilm formation, and antagonism toward the fungal leaf pathogen Fusarium graminearum. Collectively our results revealed that the wheat flag leaf is a rich resource of taxonomically and phenotypically diverse yeast genera that exhibit various traits that can contribute to survival in the harsh phyllosphere environment.},
}
@article {pmid35872283,
year = {2022},
author = {Macêdo, WV and Poulsen, JS and Zaiat, M and Nielsen, JL},
title = {Proteogenomics identification of TBBPA degraders in anaerobic bioreactor.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {310},
number = {},
pages = {119786},
doi = {10.1016/j.envpol.2022.119786},
pmid = {35872283},
issn = {1873-6424},
mesh = {Anaerobiosis ; Biodegradation, Environmental ; Bioreactors ; Ecosystem ; Isotopes ; *Polybrominated Biphenyls ; *Proteogenomics ; },
abstract = {Tetrabromobisphenol A (TBBPA) is the most used flame retardant worldwide and has become a threat to aquatic ecosystems. Previous research into the degradation of this micropollutant in anaerobic bioreactors has suggested several identities of putative TBBPA degraders. However, the organisms actively degrading TBBPA under in situ conditions have so far not been identified. Protein-stable isotope probing (protein-SIP) has become a cutting-edge technique in microbial ecology for enabling the link between identity and function under in situ conditions. Therefore, it was hypothesized that combining protein-based stable isotope probing with metagenomics could be used to identify and provide genomic insight into the TBBPA-degrading organisms. The identified [13]C-labelled peptides were found to belong to organisms affiliated to Phytobacter, Clostridium, Sporolactobacillus, and Klebsilla genera. The functional classification of identified labelled peptides revealed that TBBPA is not only transformed by cometabolic reactions, but also assimilated into the biomass. By application of the proteogenomics with labelled micropollutants (protein-SIP) and metagenome-assembled genomes, it was possible to extend the current perspective of the diversity of TBBPA degraders in wastewater and predict putative TBBPA degradation pathways. The study provides a link to the active TBBPA degraders and which organisms to favor for optimized biodegradation.},
}
@article {pmid35870225,
year = {2022},
author = {Collinge, DB and Jensen, B and Jørgensen, HJ},
title = {Fungal endophytes in plants and their relationship to plant disease.},
journal = {Current opinion in microbiology},
volume = {69},
number = {},
pages = {102177},
doi = {10.1016/j.mib.2022.102177},
pmid = {35870225},
issn = {1879-0364},
mesh = {*Endophytes/genetics ; *Fungi/genetics/metabolism ; Plant Diseases ; Plant Growth Regulators/metabolism ; Plants/microbiology ; },
abstract = {The enigmatic endophytic fungi are beginning to reveal their secrets. Like pathogens, they can manipulate the host for their own benefit to create their own optimal habitat. Some endophytic manipulations induce resistance or otherwise outcompete pathogens and can thus be exploited for biological control. Like pathogens and other symbionts, endophytes produce effector proteins and other molecules, ranging from specialised metabolites, phytohormones and microRNAs, to manipulate their hosts and other microorganisms they meet. There is a continuum from endophyte to pathogen: some organisms can infest or cause disease in some hosts, but not in others. Molecular genetics approaches coupled with functional characterisation have demonstrated their worth for understanding the biological phenomena underlying endophytic fungal interactions.},
}
@article {pmid35869999,
year = {2023},
author = {Pant, A and Maiti, TK and Mahajan, D and Das, B},
title = {Human Gut Microbiota and Drug Metabolism.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {97-111},
pmid = {35869999},
issn = {1432-184X},
support = {DST/INSPIRE/04/2020/001246//Department of Science and Technology, Government of India/ ; THSTI Intramural//Department of Biotechnology, Government of India/ ; 2021//Department of Biotechnology, Government of India/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Microbiota/physiology ; Xenobiotics/metabolism/pharmacology ; },
abstract = {The efficacy of drugs widely varies in individuals, and the gut microbiota plays an important role in this variability. The commensal microbiota living in the human gut encodes several enzymes that chemically modify systemic and orally administered drugs, and such modifications can lead to activation, inactivation, toxification, altered stability, poor bioavailability, and rapid excretion. Our knowledge of the role of the human gut microbiome in therapeutic outcomes continues to evolve. Recent studies suggest the existence of complex interactions between microbial functions and therapeutic drugs across the human body. Therapeutic drugs or xenobiotics can influence the composition of the gut microbiome and the microbial encoded functions. Both these deviations can alter the chemical transformations of the drugs and hence treatment outcomes. In this review, we provide an overview of (i) the genetic ecology of microbially encoded functions linked with xenobiotic degradation; (ii) the effect of drugs on the composition and function of the gut microbiome; and (iii) the importance of the gut microbiota in drug metabolism.},
}
@article {pmid35869965,
year = {2022},
author = {West, JR and Whitman, T},
title = {Disturbance by soil mixing decreases microbial richness and supports homogenizing community assembly processes.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {9},
pages = {},
pmid = {35869965},
issn = {1574-6941},
mesh = {Bacteria ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Soil ; *Soil Microbiology ; },
abstract = {The spatial heterogeneity of soil's microhabitats warrants the study of ecological patterns and community assembly processes in the context of physical disturbance that disrupts the inherent spatial isolation of soil microhabitats and microbial communities. By mixing soil at various frequencies in a 16-week lab incubation, we explored the effects of physical disturbance on soil bacterial richness, community composition, and community assembly processes. We hypothesized that well-mixed soil would harbor a less rich microbial community, with community assembly marked by homogenizing dispersal and homogeneous selection. Using 16S rRNA gene sequencing, we inferred community assembly processes, estimated richness and differential abundance, and calculated compositional dissimilarity. Findings supported our hypotheses, with > 20% decrease in soil bacterial richness in well-mixed soil. Soil mixing caused communities to diverge from unmixed controls (Bray-Curtis dissimilarity; 0.75 vs. 0.25), while reducing within-group heterogeneity. Our results imply that the vast diversity observed in soil may be supported by spatial heterogeneity and isolation of microbial communities, and also provide insight into the effects of physical disturbance and community coalescence events. By isolating and better understanding the effects of spatial heterogeneity and disconnectivity on soil microbial communities, we can better extrapolate how anthropogenic disturbances may affect broad soil functions.},
}
@article {pmid35869541,
year = {2022},
author = {Palomo, A and Azevedo, D and Touceda-Suárez, M and Domingo-Félez, C and Mutlu, AG and Dechesne, A and Wang, Y and Zhang, T and Smets, BF},
title = {Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {39},
pmid = {35869541},
issn = {2524-6372},
support = {REA 607492//FP7 People: Marie-Curie Actions/ ; REA 607492//FP7 People: Marie-Curie Actions/ ; Expa-N 13391//Villlum Fonden/ ; Expa-N 13391//Villlum Fonden/ ; },
abstract = {Obtaining efficient autotrophic ammonia removal (aka partial nitritation-anammox, or PNA) requires a balanced microbiome with abundant aerobic and anaerobic ammonia oxidizing bacteria and scarce nitrite oxidizing bacteria. Here, we analyzed the microbiome of an efficient PNA process that was obtained by sequential feeding and periodic aeration. The genomes of the dominant community members were inferred from metagenomes obtained over a 6 month period. Three Brocadia spp. genomes and three Nitrosomonas spp. genomes dominated the autotrophic community; no NOB genomes were retrieved. Two of the Brocadia spp. genomes lacked the genomic potential for nitrite reduction. A diverse set of heterotrophic genomes was retrieved, each with genomic potential for only a fraction of the denitrification pathway. A mutual dependency in amino acid and vitamin synthesis was noted between autotrophic and heterotrophic community members. Our analysis suggests a highly-reticulated nitrogen cycle in the examined PNA microbiome with nitric oxide exchange between the heterotrophs and the anammox guild.},
}
@article {pmid35867140,
year = {2023},
author = {López-Hernández, J and García-Cárdenas, E and López-Bucio, JS and Jiménez-Vázquez, KR and de la Cruz, HR and Ferrera-Rodríguez, O and Santos-Rodríguez, DL and Ortiz-Castro, R and López-Bucio, J},
title = {Screening of Phosphate Solubilization Identifies Six Pseudomonas Species with Contrasting Phytostimulation Properties in Arabidopsis Seedlings.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {431-445},
pmid = {35867140},
issn = {1432-184X},
support = {A1-S-34768//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {*Arabidopsis/genetics/metabolism ; Pseudomonas/genetics ; Seedlings ; Phosphates/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Plant Roots/microbiology ; Indoleacetic Acids/metabolism ; Bacteria/genetics ; },
abstract = {The interaction of plants with bacteria and the long-term success of their adaptation to challenging environments depend upon critical traits that include nutrient solubilization, remodeling of root architecture, and modulation of host hormonal status. To examine whether bacterial promotion of phosphate solubilization, root branching and the host auxin response may account for plant growth, we isolated and characterized ten bacterial strains based on their high capability to solubilize calcium phosphate. All strains could be grouped into six Pseudomonas species, namely P. brassicae, P. baetica, P. laurylsulfatiphila, P. chlororaphis, P. lurida, and P. extremorientalis via 16S rRNA molecular analyses. A Solibacillus isronensis strain was also identified, which remained neutral when interacting with Arabidopsis roots, and thus could be used as inoculation control. The interaction of Arabidopsis seedlings with bacterial streaks from pure cultures in vitro indicated that their phytostimulation properties largely differ, since P. brassicae and P. laurylsulfatiphila strongly increased shoot and root biomass, whereas the other species did not. Most bacterial isolates, except P. chlororaphis promoted lateral root formation, and P. lurida and P. chlororaphis strongly enhanced expression of the auxin-inducible gene construct DR5:GUS in roots, but the most bioactive probiotic bacterium P. brassicae could not enhance the auxin response. Inoculation with P. brassicae and P. lurida improved shoot and root growth in medium supplemented with calcium phosphate as the sole Pi source. Collectively, our data indicate the differential responses of Arabidopsis seedlings to inoculation with several Pseudomonas species and highlight the potential of P. brassicae to manage phosphate nutrition and plant growth in a more eco-friendly manner.},
}
@article {pmid35867139,
year = {2023},
author = {Birnbaum, C and Wood, J and Lilleskov, E and Lamit, LJ and Shannon, J and Brewer, M and Grover, S},
title = {Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {875-891},
pmid = {35867139},
issn = {1432-184X},
support = {DEB-1 146 149//National Science Foundation/ ; ID 1445//U.S. Department of Energy/ ; SLaM/2020/118//Australian Centre for International Agricultural Research/ ; },
mesh = {Australia ; Carbon/metabolism ; *Ecosystem ; Manganese ; *Microbiota ; Nitrogen/analysis ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Peatland ecosystems cover only 3% of the world's land area; however, they store one-third of the global soil carbon (C). Microbial communities are the main drivers of C decomposition in peatlands, yet we have limited knowledge of their structure and function. While the microbial communities in the Northern Hemisphere peatlands are well documented, we have limited understanding of microbial community composition and function in the Southern Hemisphere peatlands, especially in Australia. We investigated the vertical stratification of prokaryote and fungal communities from Wellington Plains peatland in the Australian Alps. Within the peatland complex, bog peat was sampled from the intact peatland and dried peat from the degraded peatland along a vertical soil depth gradient (i.e., acrotelm, mesotelm, and catotelm). We analyzed the prokaryote and fungal community structure, predicted functional profiles of prokaryotes using PICRUSt, and assigned soil fungal guilds using FUNGuild. We found that the structure and function of prokaryotes were vertically stratified in the intact bog. Soil carbon, manganese, nitrogen, lead, and sodium content best explained the prokaryote composition. Prokaryote richness was significantly higher in the intact bog acrotelm compared to degraded bog acrotelm. Fungal composition remained similar across the soil depth gradient; however, there was a considerable increase in saprotroph abundance and decrease in endophyte abundance along the vertical soil depth gradient. The abundance of saprotrophs and plant pathogens was two-fold higher in the degraded bog acrotelm. Soil manganese and nitrogen content, electrical conductivity, and water table level (cm) best explained the fungal composition. Our results demonstrate that both fungal and prokaryote communities are shaped by soil abiotic factors and that peatland degradation reduces microbial richness and alters microbial functions. Thus, current and future changes to the environmental conditions in these peatlands may lead to altered microbial community structures and associated functions which may have implications for broader ecosystem function changes in peatlands.},
}
@article {pmid35867138,
year = {2023},
author = {Mathur, V and Ulanova, D},
title = {Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {25-48},
pmid = {35867138},
issn = {1432-184X},
support = {ECR/2017/001466//SERB (Ministry of S&amp;T, Govt. of India)/ ; Four dimensions Kuroshio Marine Science (4D-KMS) Project//Ministry of Education, Culture, Sports, Science and Technology, Japan/ ; },
mesh = {*Ecosystem ; *Plants/metabolism ; Adaptation, Physiological ; Symbiosis ; Environmental Pollution ; },
abstract = {Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.},
}
@article {pmid35866234,
year = {2022},
author = {Mahmud, MR and Akter, S and Tamanna, SK and Mazumder, L and Esti, IZ and Banerjee, S and Akter, S and Hasan, MR and Acharjee, M and Hossain, MS and Pirttilä, AM},
title = {Impact of gut microbiome on skin health: gut-skin axis observed through the lenses of therapeutics and skin diseases.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2096995},
pmid = {35866234},
issn = {1949-0984},
mesh = {Dysbiosis/therapy ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Prebiotics ; *Probiotics/therapeutic use ; Skin ; *Skin Diseases/therapy ; },
abstract = {The human intestine hosts diverse microbial communities that play a significant role in maintaining gut-skin homeostasis. When the relationship between gut microbiome and the immune system is impaired, subsequent effects can be triggered on the skin, potentially promoting the development of skin diseases. The mechanisms through which the gut microbiome affects skin health are still unclear. Enhancing our understanding on the connection between skin and gut microbiome is needed to find novel ways to treat human skin disorders. In this review, we systematically evaluate current data regarding microbial ecology of healthy skin and gut, diet, pre- and probiotics, and antibiotics, on gut microbiome and their effects on skin health. We discuss potential mechanisms of the gut-skin axis and the link between the gut and skin-associated diseases, such as psoriasis, atopic dermatitis, acne vulgaris, rosacea, alopecia areata, and hidradenitis suppurativa. This review will increase our understanding of the impacts of gut microbiome on skin conditions to aid in finding new medications for skin-associated diseases.},
}
@article {pmid35864173,
year = {2023},
author = {Tian, C and Pang, J and Bu, C and Wu, S and Bai, H and Li, Y and Guo, Q and Siddique, KHM},
title = {The Microbiomes in Lichen and Moss Biocrust Contribute Differently to Carbon and Nitrogen Cycles in Arid Ecosystems.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {497-508},
pmid = {35864173},
issn = {1432-184X},
support = {2016YFE0203400//National Key Research and Development Program of China/ ; 2017YFC0504703//National Key Research and Development Program of China/ ; 41971131//National Natural Scientific Foundation of China/ ; },
mesh = {Ecosystem ; *Lichens ; Carbon ; Nitrates ; Soil/chemistry ; *Bryophyta ; Nitrogen Fixation ; *Microbiota ; Soil Microbiology ; Nitrogen/chemistry ; },
abstract = {Biological soil crusts (biocrusts) are distributed in arid and semiarid regions across the globe. Microorganisms are an essential component in biocrusts. They add and accelerate critical biochemical processes. However, little is known about the functional genes and metabolic processes of microbiomes in lichen and moss biocrust. This study used shotgun metagenomic sequencing to compare the microbiomes of lichen-dominated and moss-dominated biocrust and reveal the microbial genes and metabolic pathways involved in carbon and nitrogen cycling. The results showed that Actinobacteria, Bacteroidetes, and Acidobacteria were more abundant in moss biocrust than lichen biocrust, while Proteobacteria and Cyanobacteria were more abundant in lichen biocrust than moss biocrust. The relative abundance of carbohydrate-active enzymes and enzymes associated with carbon and nitrogen metabolism differed significantly between microbiomes of the two biocrust types. However, in the microbial communities of both biocrust types, respiration pathways dominated over carbon fixation pathways. The genes encoding carbon monoxide dehydrogenase were more abundant than those encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) involved in carbon fixation. Similarly, metabolic N-pathway diversity was dominated by nitrogen reduction, followed by denitrification, with nitrogen fixation the lowest proportion. Gene diversity involved in N cycling differed between the microbiomes of the two biocrust types. Assimilatory nitrate reduction genes had higher relative abundance in lichen biocrust, whereas dissimilatory nitrate reduction genes had higher relative abundance in moss biocrust. As dissolved organic carbon and soil organic carbon are considered the main drivers of the community structure in the microbiome of biocrust, these results indicate that biocrust type has a pivotal role in microbial diversity and related biogeochemical cycling.},
}
@article {pmid35863929,
year = {2022},
author = {Ouamba, AJK and Gagnon, M and LaPointe, G and Chouinard, PY and Roy, D},
title = {Graduate Student Literature Review: Farm management practices: Potential microbial sources that determine the microbiota of raw bovine milk.},
journal = {Journal of dairy science},
volume = {105},
number = {9},
pages = {7276-7287},
doi = {10.3168/jds.2021-21758},
pmid = {35863929},
issn = {1525-3198},
mesh = {Animals ; Bacteria ; Cattle ; *Dairying/methods ; Farms ; Female ; Humans ; Lactation ; *Microbiota ; Milk/microbiology ; Students ; },
abstract = {Environmental and herd-associated factors such as geographical location, climatic conditions, forage types, bedding, soil, animal genetics, herd size, housing, lactation stage, and udder health are exploited by farmers to dictate specific management strategies that ensure dairy operation profitability and enhance the sustainability of milk production. Along with milking routines, milking systems, and storage conditions, these farming practices greatly influence the microbiota of raw milk, as evidenced by several recent studies. During the past few years, the increased interest in high-throughput sequencing technologies combined with culture-dependent methods to investigate dairy microbial ecology has improved our understanding of raw milk community dynamics throughout storage and processing. However, knowledge is still lacking on the niche-specific communities in the farm environment, and on the factors that determine bacteria transfer to the raw milk. This review summarizes findings from the past 2 decades regarding the effects of farm management practices on the diversity of bacterial species that determine the microbiological quality of raw cow milk.},
}
@article {pmid35862964,
year = {2022},
author = {Zhang, Q and Zou, X and Wu, S and Wu, N and Chen, X and Zhou, W},
title = {Effects of Pyroligneous Acid on Diversity and Dynamics of Antibiotic Resistance Genes in Alfalfa Silage.},
journal = {Microbiology spectrum},
volume = {10},
number = {4},
pages = {e0155422},
pmid = {35862964},
issn = {2165-0497},
mesh = {Ammonia ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Fermentation ; Humans ; Lactobacillus/genetics ; *Medicago sativa/chemistry/microbiology ; *Silage/analysis/microbiology ; Terpenes ; Tetracyclines ; },
abstract = {Antibiotic resistance genes (ARGs) are recognized as contaminants due to their potential risk for human and environment. The aim of the present study is to investigate the effects of pyroligneous acid (PA), a waste of biochar production, on fermentation characteristics, diversity, and dynamics of ARGs during ensiling of alfalfa using metagenomic analysis. The results indicated that PA decreased (P < 0.05) dry matter loss, pH value, gas production, coliform bacteria count, protease activity, and nonprotein-N, ammonia-N, and butyric acid contents and increased (P < 0.05) lactic acid content during ensiling. During fermentation, Bacteria, Firmicutes, and Lactobacillus were the most abundant at kingdom, phylum, and genus levels, respectively. Pyroligneous acid reduced the relative abundance of Bacteria and Firmicutes and increased that of Lactobacillus. The detected ARGs belonged to 36 drug classes, including mainly macrolides, tetracycline, lincosamides, and phenicol. These types of ARGs decreased during fermentation and were further reduced by PA. These types of ARGs were positively correlated (P < 0.05) with fermentation parameters like pH value and ammonia-N content and with bacterial communities. At the genus level, the top several drug classes, including macrolide, tetracycline, lincosamide, phenicol, oxazolidinone, streptogramin, pleuromutilin, and glycopeptide, were positively correlated with Staphylococcus, Streptococcus, Listeria, Bacillus, Klebsiella, Clostridium, and Enterobacter, the potential hosts of ARGs. Overall, ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community composition. Ensiling could be a feasible way to mitigate ARGs in forages. The addition of PA could not only improve fermentation quality but also reduce ARG pollution of alfalfa silage. IMPORTANCE Antibiotic resistance genes (ARGs) are considered environmental pollutants posing a potential human health risk. Silage is an important and traditional feed, mainly for ruminants. ARGs in silages might influence the diversity and distribution of ARGs in animal intestinal and feces and then the manure and the manured soil. However, the diversity and dynamics of ARGs in silage during fermentation are still unknown. We ensiled alfalfa, one of the most widely used forages, with or without pyroligneous acid (PA), which was proved to have the ability to reduce ARGs in soils. The results showed that ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community. The majority of ARGs in alfalfa silage reduced during fermentation. The addition of PA could improve silage quality and reduce ARG pollution in alfalfa silage. This study can provide useful information for understanding and controlling ARG pollution in animal production.},
}
@article {pmid35862940,
year = {2022},
author = {Molina-Santiago, C and Pearson, JR and Berlanga-Clavero, MV and Pérez-Lorente, AI and de Vicente, A and Romero, D},
title = {A Noninvasive Method for Time-Lapse Imaging of Microbial Interactions and Colony Dynamics.},
journal = {Microbiology spectrum},
volume = {10},
number = {4},
pages = {e0093922},
pmid = {35862940},
issn = {2165-0497},
mesh = {Bacteria ; Biofilms ; *Microbial Interactions ; *Microbiota ; Time-Lapse Imaging ; },
abstract = {Complex interactions between microbial populations can greatly affect the overall properties of a microbial community, sometimes leading to cooperation and mutually beneficial coexistence, or competition and the death or displacement of organisms or subpopulations. Interactions between different biofilm populations are highly relevant in diverse scientific areas, from antimicrobial resistance to microbial ecology. The utilization of modern microscopic techniques has provided a new and interesting insight into how bacteria interact at the cellular level to form and maintain microbial biofilms. However, our ability to follow complex intraspecies and interspecies interactions in vivo at the microscopic level has remained somewhat limited. Here, we detailed BacLive, a novel noninvasive method for tracking bacterial growth and biofilm dynamics using high-resolution fluorescence microscopy and an associated ImageJ processing macro (https://github.com/BacLive) for easier data handling and image analysis. Finally, we provided examples of how BacLive can be used in the analysis of complex bacterial communities. IMPORTANCE Communication and interactions between single cells are continuously defining the structure and composition of microbial communities temporally and spatially. Methods routinely used to study these communities at the cellular level rely on sample manipulation which makes microscopic time-lapse experiments impossible. BacLive was conceived as a method for the noninvasive study of the formation and development of bacterial communities, such as biofilms, and the formation dynamics of specialized subpopulations in time-lapse experiments at a colony level. In addition, we developed a tool to simplify the processing and analysis of the data generated by this method.},
}
@article {pmid35862824,
year = {2022},
author = {Schultz, J and Modolon, F and Rosado, AS and Voolstra, CR and Sweet, M and Peixoto, RS},
title = {Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter.},
journal = {mSystems},
volume = {7},
number = {4},
pages = {e0036722},
pmid = {35862824},
issn = {2379-5077},
mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; *Microbiota/genetics ; Metagenome ; Biotechnology ; },
abstract = {The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.},
}
@article {pmid35862808,
year = {2022},
author = {Dove, NC and Carrell, AA and Engle, NL and Klingeman, DM and Rodriguez, M and Wahl, T and Tschaplinski, TJ and Muchero, W and Schadt, CW and Cregger, MA},
title = {Relationships between Sphaerulina musiva Infection and the Populus Microbiome and Metabolome.},
journal = {mSystems},
volume = {7},
number = {4},
pages = {e0012022},
pmid = {35862808},
issn = {2379-5077},
mesh = {*Populus/genetics ; *Ascomycota/genetics ; *Microbiota/genetics ; Trees/microbiology ; Metabolome ; },
abstract = {Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.},
}
@article {pmid35862804,
year = {2022},
author = {Green, EA and Klassen, JL},
title = {Trachymyrmex septentrionalis Ant Microbiome Assembly Is Unique to Individual Colonies and Castes.},
journal = {mSphere},
volume = {7},
number = {4},
pages = {e0098921},
pmid = {35862804},
issn = {2379-5042},
mesh = {Animals ; Female ; Male ; *Ants/microbiology ; Fungi ; Larva ; *Microbiota ; United States ; },
abstract = {Within social insect colonies, microbiomes often differ between castes due to their different functional roles and between colony locations. Trachymyrmex septentrionalis fungus-growing ants form colonies throughout the eastern United States and northern Mexico that include workers, female and male alates (unmated reproductive castes), larvae, and pupae. How T. septentrionalis microbiomes vary across this geographic range and between castes is unknown. Our sampling of individual ants from colonies across the eastern United States revealed a conserved T. septentrionalis worker ant microbiome and revealed that worker ant microbiomes are more conserved within colonies than between them. A deeper sampling of individual ants from two colonies that included all available castes (pupae, larvae, workers, and female and male alates), from both before and after adaptation to controlled laboratory conditions, revealed that ant microbiomes from each colony, caste, and rearing condition were typically conserved within but not between each sampling category. Tenericute bacterial symbionts were especially abundant in these ant microbiomes and varied widely in abundance between sampling categories. This study demonstrates how individual insect colonies primarily drive the composition of their microbiomes and shows that these microbiomes are further modified by developmental differences between insect castes and the different environmental conditions experienced by each colony. IMPORTANCE This study investigates microbiome assembly in the fungus-growing ant Trachymyrmex septentrionalis, showing how colony, caste, and lab adaptation influence the microbiome and revealing unique patterns of mollicute symbiont abundance. We find that ant microbiomes differ strongly between colonies but less so within colonies. Microbiomes of different castes and following lab adaptation also differ in a colony-specific manner. This study advances our understanding of the nature of individuality in social insect microbiomes and cautions against the common practice of only sampling a limited number of populations to understand microbiome diversity and function.},
}
@article {pmid35862792,
year = {2022},
author = {Wale, N},
title = {mSphere of Influence: There's More to (a Pathogen's) Life than Growing Fast.},
journal = {mSphere},
volume = {7},
number = {4},
pages = {e0027722},
pmid = {35862792},
issn = {2379-5042},
mesh = {*Virulence ; },
abstract = {Nina Wale works in the field of infectious disease evolution and ecology. In this mSphere of Influence article, she reflects on how the paper by Roller and Schmidt, "The physiology and ecological implications of efficient growth" (B. R. Roller and T. M. Schmidt, ISME J 9:1481-1487, 2015, https://doi.org/10.1038/ismej.2014.235) broadened her thinking about how microbes acquire and allocate resources and, in so doing, set her research on pathogen virulence evolution in a new direction.},
}
@article {pmid35862730,
year = {2022},
author = {Smith, DJ and Kharbush, JJ and Kersten, RD and Dick, GJ},
title = {Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {14},
pages = {e0180321},
pmid = {35862730},
issn = {1098-5336},
mesh = {Acidobacteria/metabolism ; Amino Acids/metabolism ; Carbon/metabolism ; *Cyanobacteria/genetics ; Ecosystem ; Hydrogen Peroxide/metabolism ; Lakes/microbiology ; *Microcystis/genetics/metabolism ; Nitrogen/metabolism ; Phytoplankton/metabolism ; Vitamin B 12/metabolism ; },
abstract = {Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H2O2. Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide.},
}
@article {pmid35859070,
year = {2023},
author = {Ienes-Lima, J and Prichula, J and Abadie, M and Borges-Martins, M and Frazzon, APG},
title = {First Report of Culturable Skin Bacteria in Melanophryniscus admirabilis (Admirable Redbelly Toad).},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {756-761},
pmid = {35859070},
issn = {1432-184X},
support = {#305495/2018-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico do Brasil/ ; #309769/2020-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; PROAP//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Animals ; *Chytridiomycota ; Bufonidae ; Forests ; Bacteria ; Skin/microbiology ; },
abstract = {Melanophryniscus admirabilis is a small toad, critically endangered with a microendemic distribution in the Atlantic Forest in southern Brazil. The amphibian skin microbiome is considered one of the first lines of defense against pathogenic infections, such as Batrachochytrium dendrobatidis (Bd). The knowledge of skin amphibian microbiomes is important to numerous fields, including species conservation, detection, and quantification of environmental changes and stressors. In the present study, we investigated, for the first time, cultivable bacteria in the skin of wild M. admirabilis, and detected Bd fungus by nested polymerase chain reaction (PCR) technique. Skin swab samples were collected from 15 wild M. admirabilis, and the isolation of bacteria was performed by means of different culture strategies. A total of 62 bacterial isolates being Bacillus (n = 22; 34.48%), Citrobacter (n = 10; 16.13%), and Serratia (n = 12; 19.35%) were more frequently isolated genera. Interestingly, all skin samples tested were Bd negative. Some bacterial genera identified in our study might be acting in a synergic relationship and protecting them against the Bd fungus. In addition, these bacteria may play an essential role in maintaining this species in an environment modulated by anthropic actions. This first report of skin cultivable bacteria from M. admirabilis natural population improves our knowledge of skin amphibian microbiomes, contributing to a better understanding of their ecology and how this species has survived in an environment modulated by anthropic action.},
}
@article {pmid35859069,
year = {2023},
author = {Alvarenga, DO and Elmdam, IV and Timm, AB and Rousk, K},
title = {Chemical Stimulation of Heterocyte Differentiation by the Feather Moss Hylocomium splendens: a Potential New Step in Plant-Cyanobacteria Symbioses.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {419-430},
pmid = {35859069},
issn = {1432-184X},
support = {7027-00011B//Danmarks Frie Forskningsfond/ ; },
mesh = {Ecosystem ; Stimulation, Chemical ; Nitrogen Fixation/physiology ; *Bryophyta/physiology ; *Bryopsida/metabolism/microbiology ; *Cyanobacteria/metabolism ; Nitrogenase/metabolism ; Plant Extracts ; },
abstract = {Cyanobacteria associated with mosses play a key role in the nitrogen (N) cycle in unpolluted ecosystems. Mosses have been found to release molecules that induce morphophysiological changes in epiphytic cyanobionts. Nevertheless, the extent of moss influence on these microorganisms remains unknown. To evaluate how mosses or their metabolites influence N2 fixation rates by cyanobacteria, we assessed the nitrogenase activity, heterocyte frequency and biomass of a cyanobacterial strain isolated from the feather moss Hylocomium splendens and a non-symbiotic strain when they were either growing by themselves, together with H. splendens or exposed to H. splendens water, acetone, ethanol, or isopropanol extracts. The same cyanobacterial strains were added to another moss (Taxiphyllum barbieri) and a liverwort (Monosolenium tenerum) to assess if these bryophytes affect N2 fixation differently. Although no significant increases in nitrogenase activity by the cyanobacteria were observed when in contact with H. splendens shoots, both the symbiotic and non-symbiotic cyanobacteria increased nitrogenase activity as well as heterocyte frequency significantly upon exposure to H. splendens ethanol extracts. Contact with T. barbieri shoots, on the other hand, did lead to increases in nitrogenase activity, indicating low host-specificity to cyanobacterial activity. These findings suggest that H. splendens produces heterocyte-differentiating factors (HDFs) that are capable of stimulating cyanobacterial N2 fixation regardless of symbiotic competency. Based on previous knowledge about the chemical ecology and dynamics of moss-cyanobacteria interactions, we speculate that HDF expression by the host takes place in a hypothetical new step occurring after plant colonization and the repression of hormogonia.},
}
@article {pmid35858363,
year = {2022},
author = {Miller, SD},
title = {Boat encounter with the 2019 Java bioluminescent milky sea: Views from on-deck confirm satellite detection.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {29},
pages = {e2207612119},
pmid = {35858363},
issn = {1091-6490},
mesh = {*Bacteria ; Indonesia ; Luminescence ; Oceans and Seas ; *Satellite Imagery ; *Seawater/microbiology ; *Ships ; },
abstract = {"Milky seas" are massive swaths of uniformly and steadily glowing ocean seen at night. The phenomenon is thought to be caused by luminous bacteria, but details of milky sea composition, structure, cause, and implications in nature remain largely uncertain. Between late July and early September 2019, specialized low-light satellite sensors detected a possible bioluminescent milky sea south of Java, Indonesia, spanning >100,000 km[2]. Upon learning of these findings, crew members of the yacht Ganesha reached out to confirm and share details of their personal encounter with this same event. Here, we document Ganesha's experience as recalled by the crew, compare their course to satellite data, and assess their photography of this milky sea.},
}
@article {pmid35857039,
year = {2023},
author = {Matsumura, E and Morinaga, K and Fukuda, K},
title = {Host Specificity and Seasonal Variation in the Colonization of Tubakia sensu lato Associated with Evergreen Oak Species in Eastern Japan.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {240-252},
pmid = {35857039},
issn = {1432-184X},
support = {JP16H06737//Japan Society for the Promotion of Science/ ; },
mesh = {*Quercus/microbiology ; Seasons ; Host Specificity ; Japan ; *Ascomycota ; Endophytes ; },
abstract = {Foliar fungal endophytes are ubiquitous and hyperdiverse, and tend to be host-specific among dominant forest tree species. The fungal genus Tubakia sensu lato is comprised of foliar pathogens and endophytes that exhibit host preference for Quercus and other Fagaceae species. To clarify interspecific differences in ecological characteristics among Tubakia species, we examined the endophyte communities of seven evergreen Quercus spp. at three sites in eastern Japan during summer and winter. Host tree species was the most significant factor affecting endophyte community composition. Tubakia species found at the study sites were divided into five specialists and three generalists according to their relative abundance in each host species and their host ranges. Specialists were dominant on their own host in summer, and their abundance declined in winter. To test the hypothesis that generalists are more widely adapted to their environment than specialists, we compared their spore germination rates at different temperatures. Spores of generalist Tubakia species were more tolerant of colder temperatures than were spores of specialist Tubakia species, supporting our hypothesis. Seasonal and site variations among Tubakia species were also consistent with our hypothesis. Host identity and ecology were significantly associated with endophyte community structure.},
}
@article {pmid35856685,
year = {2022},
author = {Forchielli, E and Sher, D and Segrè, D},
title = {Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies.},
journal = {mSystems},
volume = {7},
number = {4},
pages = {e0007022},
pmid = {35856685},
issn = {2379-5077},
mesh = {*Seawater/chemistry ; Phylogeny ; Oceans and Seas ; Bacteria/genetics ; *Microbiota/genetics ; Phytoplankton/genetics ; Carbon/metabolism ; },
abstract = {Microbial communities, through their metabolism, drive carbon cycling in marine environments. These complex communities are composed of many different microorganisms including heterotrophic bacteria, each with its own nutritional needs and metabolic capabilities. Yet, models of ecosystem processes typically treat heterotrophic bacteria as a "black box," which does not resolve metabolic heterogeneity nor address ecologically important processes such as the successive modification of different types of organic matter. Here we directly address the heterogeneity of metabolism by characterizing the carbon source utilization preferences of 63 heterotrophic bacteria representative of several major marine clades. By systematically growing these bacteria on 10 media containing specific subsets of carbon sources found in marine biomass, we obtained a phenotypic fingerprint that we used to explore the relationship between metabolic preferences and phylogenetic or genomic features. At the class level, these bacteria display broadly conserved patterns of preference for different carbon sources. Despite these broad taxonomic trends, growth profiles correlate poorly with phylogenetic distance or genome-wide gene content. However, metabolic preferences are strongly predicted by a handful of key enzymes that preferentially belong to a few enriched metabolic pathways, such as those involved in glyoxylate metabolism and biofilm formation. We find that enriched pathways point to enzymes directly involved in the metabolism of the corresponding carbon source and suggest potential associations between metabolic preferences and other ecologically relevant traits. The availability of systematic phenotypes across multiple synthetic media constitutes a valuable resource for future quantitative modeling efforts and systematic studies of interspecies interactions. IMPORTANCE Half of the Earth's annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter released from phytoplankton. Here, we characterize the diversity of metabolic preferences across many representative heterotrophs by systematically growing them on different fractions of dissolved organic carbon. Our analysis suggests that different clades of bacteria have substantially distinct preferences for specific carbon sources, in a way that cannot be simply mapped onto phylogeny. These preferences are associated with the presence of specific genes and pathways, reflecting an association between metabolic capabilities and ecological lifestyles. In addition to helping understand the importance of heterotrophs under different conditions, the phenotypic fingerprint we obtained can help build higher resolution quantitative models of global microbial activity and biogeochemical cycles in the oceans.},
}
@article {pmid35856563,
year = {2022},
author = {Lesniak, NA and Schubert, AM and Flynn, KJ and Leslie, JL and Sinani, H and Bergin, IL and Young, VB and Schloss, PD},
title = {The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity.},
journal = {mBio},
volume = {13},
number = {4},
pages = {e0118322},
pmid = {35856563},
issn = {2150-7511},
support = {T32 AI007528/AI/NIAID NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; U2C DK110768/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteria/genetics ; Bile Acids and Salts ; *Clostridioides difficile ; *Clostridium Infections/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Mice ; },
abstract = {The severity of Clostridioides difficile infections (CDI) has increased over the last few decades. Patient age, white blood cell count, and creatinine levels as well as C. difficile ribotype and toxin genes have been associated with disease severity. However, it is unclear whether specific members of the gut microbiota are associated with variations in disease severity. The gut microbiota is known to interact with C. difficile during infection. Perturbations to the gut microbiota are necessary for C. difficile to colonize the gut. The gut microbiota can inhibit C. difficile colonization through bile acid metabolism, nutrient consumption, and bacteriocin production. Here, we sought to demonstrate that members of the gut bacterial communities can also contribute to disease severity. We derived diverse gut communities by colonizing germfree mice with different human fecal communities. The mice were then infected with a single C. difficile ribotype 027 clinical isolate, which resulted in moribundity and histopathologic differences. The variation in severity was associated with the human fecal community that the mice received. Generally, bacterial populations with pathogenic potential, such as Enterococcus, Helicobacter, and Klebsiella, were associated with more-severe outcomes. Bacterial groups associated with fiber degradation and bile acid metabolism, such as Anaerotignum, Blautia, Lactonifactor, and Monoglobus, were associated with less-severe outcomes. These data indicate that, in addition to the host and C. difficile subtype, populations of gut bacteria can influence CDI disease severity. IMPORTANCE Clostridioides difficile colonization can be asymptomatic or develop into an infection ranging in severity from mild diarrhea to toxic megacolon, sepsis, and death. Models that predict severity and guide treatment decisions are based on clinical factors and C. difficile characteristics. Although the gut microbiome plays a role in protecting against CDI, its effect on CDI disease severity is unclear and has not been incorporated into disease severity models. We demonstrated that variation in the microbiome of mice colonized with human feces yielded a range of disease outcomes. These results revealed groups of bacteria associated with both severe and mild C. difficile infection outcomes. Gut bacterial community data from patients with CDI could improve our ability to identify patients at risk of developing more severe disease and improve interventions that target C. difficile and the gut bacteria to reduce host damage.},
}
@article {pmid35852610,
year = {2022},
author = {Kankonkar, HT and Khandeparker, RS},
title = {Microplastics a Novel Substratum for Polyhydroxyalkanoate (PHA)-Producing Bacteria in Aquatic Environments.},
journal = {Current microbiology},
volume = {79},
number = {9},
pages = {258},
pmid = {35852610},
issn = {1432-0991},
mesh = {*Bacillus/genetics/metabolism ; Bacteria/genetics/metabolism ; Carbon/metabolism ; Microplastics ; Plastics/metabolism ; *Polyhydroxyalkanoates ; },
abstract = {Polyhydroxyalkanoates (PHA) being biological polymers have attracted great attention. PHA have similar properties to that of synthetic plastic and are biodegradable. To discourage plastic pollution in the environment alternative solutions to the plastic pollution has to be readily available. High cost in production of PHA limits the production of these polymers at industrial scale. Bacteria are screened for PHA from diverse niches to meet the current requirements of cheap PHA production at industrial level. The microbial biofilm formed on the surface of microplastic could be a potential source in providing bacteria of economic importance. This paper is an attempt to search microplastic niche for potential PHA producers. PHA production variation was observed with different parameters such as type of carbon source, nitrogen source concentration and also time of incubation. Bacillus sp. CM27 showed maximum PHA yield up to 32.1% among other isolates at 48 h with 2% glucose as carbon source. Optimization of media leads to increase in PHA yield (37.69%) of CDW in Bacillus sp. CM27. Amino acid sequence of Bacillus sp.CM27 showed the presence of PhaC box with sequence, G-Y-C-M-G-G having cysteine in the middle of the box. The extracted polymer was confirmed by FTIR spectroscopy.},
}
@article {pmid35849862,
year = {2022},
author = {Vaezzadeh, V and Thomes, MW and Kunisue, T and Tue, NM and Zhang, G and Zakaria, MP and Affendi, YA and Yap, FC and Chew, LL and Teoh, HW and Lee, CW and Bong, CW},
title = {Corrigendum to "Examination of barnacles' potential to be used as bioindicators of persistent organic pollutants in coastal ecosystem: A Malaysia case study" [Chemosphere 263 (2021) 128272].},
journal = {Chemosphere},
volume = {307},
number = {Pt 1},
pages = {135742},
doi = {10.1016/j.chemosphere.2022.135742},
pmid = {35849862},
issn = {1879-1298},
}
@article {pmid35845424,
year = {2022},
author = {Hessler, T and Harrison, STL and Huddy, RJ},
title = {Integrated Kinetic Modelling and Microbial Profiling Provide Insights Into Biological Sulfate-Reducing Reactor Design and Operation.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {10},
number = {},
pages = {897094},
pmid = {35845424},
issn = {2296-4185},
abstract = {Biological sulfate reduction (BSR) is an attractive approach for the bioremediation of sulfate-rich wastewater streams. Many sulfate-reducing microorganisms (SRM), which facilitate this process, have been well-studied in pure culture. However, the role of individual members of microbial communities within BSR bioreactors remains understudied. In this study we investigated the performance of two up-flow anaerobic packed bed reactors (UAPBRs) supplemented primarily with acetate and with lactate, respectively, during a hydraulic retention time (HRT) study set up to remediate sulfate-rich synthetic wastewater over the course of 1,000 + days. Plug-flow hydrodynamics led to a continuum of changing volumetric sulfate reduction rates (VSRRs), available electron donors, degrees of biomass retention and compositions of microbial communities throughout these reactors. Microbial communities throughout the successive zones of the reactors were resolved using 16S rRNA gene amplicon sequencing which allowed the association of features of performance with discrete microorganisms. The acetate UAPBR achieved a maximum VSRR of 23.2 mg.L[-1]. h[-1] at a one-day HRT and a maximum sulfate conversion of the 1 g/L sulfate of 96% at a four-day HRT. The sulfate reduction reactions in this reactor could be described with a reaction order of 2.9, an important observation for optimisation and future scale-up. The lactate UAPBR achieved a 96% sulfate conversion at one-day HRT, corresponding with a VSRR of 40.1 mg.L[-1]. h[-1]. Lactate was supplied in this reactor at relatively low concentrations necessitating the subsequent use of propionate and acetate, by-products of lactate fermentation with acetate also a by-product of incomplete lactate oxidation, to achieve competitive performance. The consumption of these electron donors could be associated with specific SRM localised within biofilms of discrete zones. The sulfate reduction rates in the lactate UAPBR could be modelled as first-order reactions, indicating effective rates were conferred by these propionate- and acetate-oxidising SRM. Our results demonstrate how acetate, a low-cost substrate, can be used effectively despite low associated SRM growth rates, and that lactate, a more expensive substrate, can be used sparingly to achieve high VSRR and sulfate conversions. We further identified the preferred environment of additional microorganisms to inform how these microorganisms could be enriched or diminished in BSR reactors.},
}
@article {pmid35844603,
year = {2022},
author = {Zhang, Q and Chen, Q and Yan, C and Niu, C and Zhou, J and Liu, J and Song, Y and Zhou, F and Fan, Y and Ren, J and Xu, H and Zhang, B},
title = {The Absence of STING Ameliorates Non-Alcoholic Fatty Liver Disease and Reforms Gut Bacterial Community.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {931176},
pmid = {35844603},
issn = {1664-3224},
mesh = {Animals ; Bacteria ; CD8-Positive T-Lymphocytes/metabolism ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Inflammation ; Mice ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/etiology/metabolism ; },
abstract = {Non-alcoholic fatty liver disease (NAFLD) is one of the primary causes of cirrhosis and a major risk factor for hepatocellular carcinoma and liver-related death. It has been correlated with changes in the gut microbiota, which promote its development by regulating insulin resistance, bile acid and choline metabolism, and inflammation. Recent studies suggested a controversial role of the stimulator of interferon genes (STING) in the development of NAFLD. Here, we showed that as an immune regulator, STING aggravates the progression of NAFLD in diet-induced mice and correlated it with the changes in hepatic lipid metabolism and gut microbiota diversity. After feeding wild-type (WT) and STING deletion mice with a normal control diet (NCD) or a high-fat diet (HFD), the STING deletion mice showed decreased lipid accumulation and liver inflammation compared with WT mice fed the same diet. In addition, STING specifically produced this hepatoprotective effect by inhibiting the activation of CD8[+] T cells. The gut microbiota analysis revealed significant differences in intestinal bacteria between STING deletion mice and WT mice under the same diet and environmental conditions; moreover, differential bacterial genera were associated with altered metabolic phenotypes and involved in related metabolic pathways. Overall, our findings reveal the important regulatory role that STING plays in the progression of NAFLD. In addition, the change in intestinal microbiota diversity may be the contributing factor.},
}
@article {pmid35842525,
year = {2023},
author = {Kou, Y and Li, C and Tu, B and Li, J and Li, X},
title = {The Responses of Ammonia-Oxidizing Microorganisms to Different Environmental Factors Determine Their Elevational Distribution and Assembly Patterns.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {485-496},
pmid = {35842525},
issn = {1432-184X},
support = {32171550//the National Natural Science Foundation of China/ ; 31870473//the National Natural Science Foundation of China/ ; XDA20020401//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2021371//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2019QZKK0600//the Second Tibetan Plateau Scientic Expedition and Research Program/ ; Sino BON//China Biodiversity Observation Networks/ ; },
mesh = {*Bacteria/genetics ; Ammonia ; Soil Microbiology ; Oxidation-Reduction ; Archaea/genetics ; Soil ; Nitrification ; *Betaproteobacteria ; Phylogeny ; },
abstract = {The assembly mechanisms shaping the elevational patterns of diversity and community structure in ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are not well understood. We investigated the diversities, co-occurrence network patterns, key drivers, and potential activities of AOA and AOB communities along a large altitudinal gradient. The α-diversity of the AOA communities exhibited a monotonically decreasing pattern with increasing elevation, whereas a sinusoidal pattern was observed for the AOB communities. The mean annual temperature was the single factor that most strongly influenced the α-diversity of the AOA communities; however, the interactions of plant richness, soil conductivity, and total nitrogen made comparable contributions to the α-diversity of the AOB communities. Moreover, the β-diversities of the AOA and AOB communities were divided into two distinct clusters by elevation, i.e., low- (1800-2600 m) and high-altitude (2800-4100 m) sections. These patterns were attributed mainly to the soil pH, followed by variations in plant richness along the altitudinal gradient. In addition, the AOB communities were more important to the soil nitrification potential in the low-altitude section, whereas the AOA communities contributed more to the soil nitrification potential in the high-altitude section. Overall, this study revealed the key factors shaping the elevational patterns of ammonia-oxidizing communities and might predict the consequences of changes in ammonia-oxidizing communities.},
}
@article {pmid35842340,
year = {2022},
author = {Gouka, L and Raaijmakers, JM and Cordovez, V},
title = {Ecology and functional potential of phyllosphere yeasts.},
journal = {Trends in plant science},
volume = {27},
number = {11},
pages = {1109-1123},
doi = {10.1016/j.tplants.2022.06.007},
pmid = {35842340},
issn = {1878-4372},
mesh = {Bacteria ; *Ecology ; Fungi ; Plant Leaves ; Plants/microbiology ; *Yeasts/genetics ; },
abstract = {The phyllosphere (i.e., the aerial parts of plants) harbors a rich microbial life, including bacteria, fungi, viruses, and yeasts. Current knowledge of yeasts stems primarily from industrial and medical research on Saccharomyces cerevisiae and Candida albicans, both of which can be found on plant tissues. For most other yeasts found in the phyllosphere, little is known about their ecology and functions. Here, we explore the diversity, dynamics, interactions, and genomics of yeasts associated with plant leaves and how tools and approaches developed for model yeasts can be adopted to disentangle the ecology and natural functions of phyllosphere yeasts. A first genomic survey exemplifies that we have only scratched the surface of the largely unexplored functional potential of phyllosphere yeasts.},
}
@article {pmid35840683,
year = {2023},
author = {Hubert, J and Nesvorna, M and Bostlova, M and Sopko, B and Green, SJ and Phillips, TW},
title = {The Effect of Residual Pesticide Application on Microbiomes of the Storage Mite Tyrophagus putrescentiae.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1527-1540},
pmid = {35840683},
issn = {1432-184X},
support = {21-337-J//Kansas State Research and Extension/ ; LTAUSA19012//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; },
mesh = {Animals ; *Acaridae/microbiology ; *Pesticides/pharmacology ; *Pesticide Residues/pharmacology ; *Microbiota ; *Mites/microbiology ; *Bacillus/genetics ; *Bartonella ; *Pyrethrins/pharmacology ; },
abstract = {Arthropods can host well-developed microbial communities, and such microbes can degrade pesticides and confer tolerance to most types of pests. Two cultures of the stored-product mite Tyrophagus putrescentiae, one with a symbiotic microbiome containing Wolbachia and the other without Wolbachia, were compared on pesticide residue (organophosphate: pirimiphos-methyl and pyrethroid: deltamethrin, deltamethrin + piperonyl butoxide)-containing diets. The microbiomes from mite bodies, mite feces and debris from the spent mite diet were analyzed using barcode sequencing. Pesticide tolerance was different among mite cultures and organophosphate and pyrethroid pesticides. The pesticide residues influenced the microbiome composition in both cultures but without any remarkable trend for mite cultures with and without Wolbachia. The most influenced bacterial taxa were Bartonella-like and Bacillus for both cultures and Wolbachia for the culture containing this symbiont. However, there was no direct evidence of any effect of Wolbachia on pesticide tolerance. The high pesticide concentration residues in diets reduced Wolbachia, Bartonella-like and Bacillus in mites of the symbiotic culture. This effect was low for Bartonella-like and Bacillus in the asymbiotic microbiome culture. The results showed that the microbiomes of mites are affected by pesticide residues in the diets, but the effect is not systemic. No actual detoxification effect by the microbiome was observed for the tested pesticides.},
}
@article {pmid35840682,
year = {2023},
author = {Williams, A and Birt, HWG and Raghavendra, A and Dennis, PG},
title = {Cropping System Diversification Influences Soil Microbial Diversity in Subtropical Dryland Farming Systems.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1473-1484},
pmid = {35840682},
issn = {1432-184X},
mesh = {*Soil ; *Carbon ; Soil Microbiology ; Phylogeny ; Agriculture/methods ; Nitrogen ; },
abstract = {Conventional dryland cropping systems are characterised by low crop diversity and frequent fallows. This has significant impacts on soil microbes that underpin soil function. Diversifying crop rotations can potentially counter these effects; however, limited data exists on the impacts of diversified crop rotations on soil microbes in drylands. Using phylogenetic marker gene sequencing, we characterised soil microbial diversity in conventional and diversified dryland crop rotations in subtropical Australia. This included winter and summer dominant rotations. Conventional systems were cereal-dominant with a crop-fallow rotation. Diversified systems included greater crop diversity, double crops, cover crops, and a multi-year ley pasture. In summer rotations with increased crop diversity and cover crops, bacterial and fungal richness increased, and distinct communities were formed compared to fallow land. Often, these community shifts were associated with greater soil organic carbon (SOC) and nitrogen. All winter rotations had distinct fungal communities and ley pasture resulted in greater fungal diversity compared to other rotations. No effects of the winter rotations were evident on bacterial communities. Our results show that diversification of dryland crop rotations leads to significant shifts in soil microbial communities in both winter and summer cropping systems. Both summer and winter rotations incorporating cover crops and ley pasture had greater soil respiration and nitrogen, indicating increases in soil fertility. These rotations may offer an alternative to conventional crop-fallow rotations to counter ongoing declines in soil health.},
}
@article {pmid35839698,
year = {2022},
author = {Babaahmadifooladia, M and da Silva Junior, EC and Van de Wiele, T and Du Laing, G and Jacxsens, L},
title = {Probabilistic chronic dietary exposure assessment adjusted for bioaccessible fraction to metals by consumption of seaweed and derived foods.},
journal = {Food chemistry},
volume = {395},
number = {},
pages = {133588},
doi = {10.1016/j.foodchem.2022.133588},
pmid = {35839698},
issn = {1873-7072},
mesh = {Cadmium ; Dietary Exposure ; Lead ; *Mercury ; *Metals, Heavy/analysis ; Risk Assessment ; *Seaweed ; Vegetables ; },
abstract = {The chronic exposure to heavy elements, i.e. Ni, As, Cd, Hg and Pb the evaluation of toxicological risk through intake of raw or seaweed based foods for Belgian consumers is presented in this study. The bioaccessible fraction, obtained for different metals, were used to refine the exposure values to avoid overestimation in the reported exposures. The decrease in the exposure values was higher for As with average bioaccessible fraction of 56.8% followed by Pb, Cd, Ni and Hg. The pure seaweeds show more approximation or exceeding of toxicological limits compared to the composite foodstuffs. For all elements (except Hg), toxicological limits are approached at the maximum exposure situation due to consumption of certain seaweed-based foods. Further, the study demonstrates that the introduction of innovative foods on an emerging market may result in potential health issues due to the shift in consumption patterns as the increased consumption of seaweed and their derivatives in Europe.},
}
@article {pmid35838347,
year = {2022},
author = {Rijkers, R and Rousk, J and Aerts, R and Sigurdsson, BD and Weedon, JT},
title = {Optimal growth temperature of Arctic soil bacterial communities increases under experimental warming.},
journal = {Global change biology},
volume = {28},
number = {20},
pages = {6050-6064},
pmid = {35838347},
issn = {1365-2486},
mesh = {Arctic Regions ; Bacteria/genetics ; *Carbon/chemistry ; Climate Change ; *Soil/chemistry ; Soil Microbiology ; Temperature ; },
abstract = {Future climate warming in the Arctic will likely increase the vulnerability of soil carbon stocks to microbial decomposition. However, it remains uncertain to what extent decomposition rates will change in a warmer Arctic, because extended soil warming could induce temperature adaptation of bacterial communities. Here we show that experimental warming induces shifts in the temperature-growth relationships of bacterial communities, which is driven by community turnover and is common across a diverse set of 8 (sub) Arctic soils. The optimal growth temperature (Topt) of the soil bacterial communities increased 0.27 ± 0.039 (SE) and 0.07 ± 0.028°C per °C of warming over a 0-30°C gradient, depending on the sampling moment. We identify a potential role for substrate depletion and time-lag effects as drivers of temperature adaption in soil bacterial communities, which possibly explain discrepancies between earlier incubation and field studies. The changes in Topt were accompanied by species-level shifts in bacterial community composition, which were mostly soil specific. Despite the clear physiological responses to warming, there was no evidence for a common set of temperature-responsive bacterial amplicon sequence variants. This implies that community composition data without accompanying physiological measurements may have limited utility for the identification of (potential) temperature adaption of soil bacterial communities in the Arctic. Since bacterial communities in Arctic soils are likely to adapt to increasing soil temperature under future climate change, this adaptation to higher temperature should be implemented in soil organic carbon modeling for accurate predictions of the dynamics of Arctic soil carbon stocks.},
}
@article {pmid35836424,
year = {2022},
author = {Muster, C and Leiva, D and Morales, C and Grafe, M and Schloter, M and Carú, M and Orlando, J},
title = {Peltigera frigida Lichens and Their Substrates Reduce the Influence of Forest Cover Change on Phosphate Solubilizing Bacteria.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {843490},
pmid = {35836424},
issn = {1664-302X},
abstract = {Phosphorus (P) is one of the most critical macronutrients in forest ecosystems. More than 70 years ago, some Chilean Patagonian temperate forests suffered wildfires and the subsequent afforestation with foreign tree species such as pines. Since soil P turnover is interlinked with the tree cover, this could influence soil P content and bioavailability. Next to soil microorganisms, which are key players in P transformation processes, a vital component of Patagonian temperate forest are lichens, which represent microbial hotspots for bacterial diversity. In the present study, we explored the impact of forest cover on the abundance of phosphate solubilizing bacteria (PSB) from three microenvironments of the forest floor: Peltigera frigida lichen thallus, their underlying substrates, and the forest soil without lichen cover. We expected that the abundance of PSB in the forest soil would be strongly affected by the tree cover composition since the aboveground vegetation influences the edaphic properties; but, as P. frigida has a specific bacterial community, lichens would mitigate this impact. Our study includes five sites representing a gradient in tree cover types, from a mature forest dominated by the native species Nothofagus pumilio, to native second-growth forests with a gradual increase in the presence of Pinus contorta in the last sites. In each site, we measured edaphic parameters, P fractions, and the bacterial potential to solubilize phosphate by quantifying five specific marker genes by qPCR. The results show higher soluble P, labile mineral P, and organic matter in the soils of the sites with a higher abundance of P. contorta, while most of the molecular markers were less abundant in the soils of these sites. Contrarily, the abundance of the molecular markers in lichens and substrates was less affected by the tree cover type. Therefore, the bacterial potential to solubilize phosphate is more affected by the edaphic factors and tree cover type in soils than in substrates and thalli of P. frigida lichens. Altogether, these results indicate that the microenvironments of lichens and their substrates could act as an environmental buffer reducing the influence of forest cover composition on bacteria involved in P turnover.},
}
@article {pmid35835965,
year = {2023},
author = {Larsen, S and Albanese, D and Stegen, J and Franceschi, P and Coller, E and Zanzotti, R and Ioriatti, C and Stefani, E and Pindo, M and Cestaro, A and Donati, C},
title = {Distinct and Temporally Stable Assembly Mechanisms Shape Bacterial and Fungal Communities in Vineyard Soils.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {337-349},
pmid = {35835965},
issn = {1432-184X},
mesh = {*Mycobiome ; Soil Microbiology ; Soil ; Fungi/genetics ; *Microbiota ; Bacteria/genetics ; },
abstract = {Microbial communities in agricultural soils are fundamental for plant growth and in vineyard ecosystems contribute to defining regional wine quality. Managing soil microbes towards beneficial outcomes requires knowledge of how community assembly processes vary across taxonomic groups, spatial scales, and through time. However, our understanding of microbial assembly remains limited. To quantify the contributions of stochastic and deterministic processes to bacterial and fungal assembly across spatial scales and through time, we used 16 s rRNA gene and ITS sequencing in the soil of an emblematic wine-growing region of Italy.Combining null- and neutral-modelling, we found that assembly processes were consistent through time, but bacteria and fungi were governed by different processes. At the within-vineyard scale, deterministic selection and homogenising dispersal dominated bacterial assembly, while neither selection nor dispersal had clear influence over fungal assembly. At the among-vineyard scale, the influence of dispersal limitation increased for both taxonomic groups, but its contribution was much larger for fungal communities. These null-model-based inferences were supported by neutral modelling, which estimated a dispersal rate almost two orders-of-magnitude lower for fungi than bacteria.This indicates that while stochastic processes are important for fungal assembly, bacteria were more influenced by deterministic selection imposed by the biotic and/or abiotic environment. Managing microbes in vineyard soils could thus benefit from strategies that account for dispersal limitation of fungi and the importance of environmental conditions for bacteria. Our results are consistent with theoretical expectations whereby larger individual size and smaller populations can lead to higher levels of stochasticity.},
}
@article {pmid35834007,
year = {2022},
author = {Mańkowska, K and Marchelek-Myśliwiec, M and Kochan, P and Kosik-Bogacka, D and Konopka, T and Grygorcewicz, B and Roszkowska, P and Cecerska-Heryć, E and Siennicka, A and Konopka, J and Dołęgowska, B},
title = {Microbiota in sports.},
journal = {Archives of microbiology},
volume = {204},
number = {8},
pages = {485},
pmid = {35834007},
issn = {1432-072X},
mesh = {Bacteria/genetics ; Bifidobacterium ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Lactobacillus ; *Microbiota ; *Probiotics ; },
abstract = {The influence of microbiota on the human body is currently the subject of many studies. The composition of bacteria colonizing the gastrointestinal tract varies depending on genetic make-up, lifestyle, use of antibiotics or the presence of diseases. The diet is also important in the species diversity of the microbiota. This study is an analysis of the relationships between physical activity, diet, and the microbiota of the gastrointestinal tract in athletes. This review shows the differences in the microbial composition in various sports disciplines, the influence of probiotics on the microbiome, the consequence of which may be achieved even better sports results. Physical activity increases the number of bacteria, mainly of the Clostridiales order and the genus: Lactobacillus, Prevotella, Bacteroides, and Veillonella, and their number varies depending on the sports discipline. These bacteria are present in athletes in sports that require a high VO2 max. The players' diet also influences the composition of the microbiota. A diet rich in dietary fiber increases the amount of Lactobacillus or Bifidobacterium bacteria, probiotic microorganisms, which indicates the need to supplement the diet with probiotic preparations. It is impossible to suggest an unambiguous answer to how the microbiota of the gastrointestinal tract changes in athletes and requires further analyzes.},
}
@article {pmid35831642,
year = {2023},
author = {Kluting, K and Strid, Y and Six, D and Rosling, A},
title = {Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {224-239},
pmid = {35831642},
issn = {1432-184X},
support = {2014-458//Svenska Forskningsr&#xe5;det Formas/ ; SSWF 17-1-Chdre//Stiftelsen Stina Werners Fond/ ; },
mesh = {Animals ; *Pinus sylvestris ; *Mycobiome ; *Wildfires ; Phloem ; *Weevils ; *Coleoptera/microbiology ; *Pinus/microbiology ; Fungi/genetics ; Trees ; },
abstract = {Forest fire is known to positively affect bark beetle populations by providing fire-damaged trees with impaired defenses for infestation. Tomicus piniperda, the common pine shoot beetle, breeds and lays eggs under the bark of stressed pine trees and is considered a serious forest pest within its native range. Wood-colonizing fungi have been hypothesized to improve substrate quality and detoxify tree defensive chemistry to indirectly facilitate tree colonization by beetles. While some bark beetle species form symbiotic associations with fungi and actively vector their partners when colonizing new trees, T. piniperda does not have mycangia or body hairs for specific vectoring of fungi. To explore the T. piniperda-associated fungal community for signs of specific association, we used ITS metabarcoding to separately characterize fungal communities associated with surface and gut of male and female beetles. We also characterized the temporal changes in fungal community and nutrient status of pine phloem with and without beetle galleries. Sampling was performed 2 years after a natural forest fire and included both burnt and unburnt sites. In our study system, we find that forest fire significantly impacts the fungal community composition associated with T. piniperda and that fire may also indirectly change nutrient availability in phloem to beetle galleries. We conclude that T. piniperda can vector fungi to newly colonized trees but the absence of positive effects on substrate quality and minimal effects of sex indicate that vectoring of associated fungal communities is not a strategy associated with the T. piniperda life cycle.},
}
@article {pmid35822810,
year = {2022},
author = {Senn, S and Pangell, K and Bowerman, AL},
title = {Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia.},
journal = {Biotech (Basel (Switzerland))},
volume = {11},
number = {1},
pages = {},
pmid = {35822810},
issn = {2673-6284},
abstract = {The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10[-5]), Bradyhizobium (p = 1 × 10[-8]), and Paenibacillus (p = 1.46 × 10[-6]). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10[-3]) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.},
}
@article {pmid35822787,
year = {2022},
author = {Khoo, C and Duysburgh, C and Marzorati, M and Van den Abbeele, P and Zhang, D},
title = {A Freeze-Dried Cranberry Powder Consistently Enhances SCFA Production and Lowers Abundance of Opportunistic Pathogens In Vitro.},
journal = {Biotech (Basel (Switzerland))},
volume = {11},
number = {2},
pages = {},
pmid = {35822787},
issn = {2673-6284},
abstract = {The American cranberry, Vaccinium macrocarpon, contains fibers and (poly)phenols that could exert health-promoting effects through modulation of gut microbiota. This study aimed to investigate how a freeze-dried whole cranberry powder (FCP) modulated metabolite production and microbial composition using both a 48-h incubation strategy and a long-term human gut simulator study with the M-SHIME (Mucosal Simulator of the Human Intestinal Microbial Ecosystem). FCP was repeatedly administered over three weeks. The studies included five and three study subjects, respectively. In both models, FCP significantly increased levels of health-related short-chain fatty acids (SCFA: acetate, propionate and butyrate), while decreased levels of branched-chain fatty acids (markers of proteolytic fermentation). Interestingly, FCP consistently increased luminal Bacteroidetes abundances in the proximal colon of the M-SHIME (+17.5 ± 9.3%) at the expense of Proteobacteria (-10.2 ± 1.5%). At family level, this was due to the stimulation of Bacteroidaceae and Prevotellaceae and a decrease of Pseudomonodaceae and Enterobacteriaceae. Despite of interpersonal differences, FCP also increased the abundance of families of known butyrate producers. Overall, FCP displayed an interesting prebiotic potential in vitro given its selective utilization by host microorganisms and potential health-related effects on inhibition of pathogens and selective stimulation of beneficial metabolites.},
}
@article {pmid35821127,
year = {2023},
author = {Roy, J and Reichel, R and Brüggemann, N and Rillig, MC},
title = {Functional, not Taxonomic, Composition of Soil Fungi Reestablishes to Pre-mining Initial State After 52 Years of Recultivation.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {213-223},
pmid = {35821127},
issn = {1432-184X},
mesh = {Agriculture ; *Ecosystem ; *Fungi/classification/genetics/metabolism ; Plants/microbiology ; Soil/chemistry ; *Soil Microbiology ; *Environmental Restoration and Remediation ; Introns/genetics ; Mining ; Biodiversity ; },
abstract = {Open-cast mining leads to the loss of naturally developed soils and their ecosystem functions and services. Soil restoration after mining aims to restore the agricultural productivity in which the functions of the fungal community play a crucial role. Whether fungi reach a comparable functional state as in the soil before mining within half a century of recultivation is still unanswered. Here, we characterised the soil fungal community using ITS amplicon Illumina sequencing across a 52-year chronosequence of agricultural recultivation after open-cast mining in northern Europe. Both taxonomic and functional community composition showed profound shifts over time, which could be attributed to the changes in nutrient status, especially phosphorus availability. However, taxonomic composition did not reach the pre-mining state, whereas functional composition did. Importantly, we identified a positive development of arbuscular mycorrhizal root fungal symbionts after the initial three years of alfalfa cultivation, followed by a decline after conversion to conventional farming, with arbuscular mycorrhizal fungi being replaced by soil saprobes. We conclude that appropriate agricultural management can steer the fungal community to its functional pre-mining state despite stochasticity in the reestablishment of soil fungal communities. Nonetheless, conventional agricultural management results in the loss of plant symbionts, favouring non-symbiotic fungi.},
}
@article {pmid35819480,
year = {2023},
author = {Alberoni, D and Di Gioia, D and Baffoni, L},
title = {Alterations in the Microbiota of Caged Honeybees in the Presence of Nosema ceranae Infection and Related Changes in Functionality.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {601-616},
pmid = {35819480},
issn = {1432-184X},
mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; *Nosema ; Bacteria/genetics ; *Neisseriaceae ; },
abstract = {Several studies have outlined that changes in the honeybee gut microbial composition may impair important metabolic functions supporting the honeybees' life. Gut dysbiosis may be caused by diseases like Nosema ceranae or by other anthropic, environmental or experimental stressors. The present work contributes to increasing knowledge on the dynamics of the gut microbiome acquisition in caged honeybees, an experimental condition frequently adopted by researchers, with or without infection with N. ceranae, and fed with a bacterial mixture to control N. ceranae development. Changes of the gut microbiota were elucidated comparing microbial profile of caged and open-field reared honeybees. The absolute abundance of the major gut microbial taxa was studied with both NGS and qPCR approaches, whereas changes in the functionality were based on RAST annotations and manually curated. In general, all caged honeybees showed important changes in the gut microbiota, with [Formula: see text]-proteobacteria (Frischella, Gilliamella and Snodgrassella) lacking in all caged experimental groups. Caged honeybees infected with N. ceranae showed also a strong colonization of environmental taxa like Citrobacter, Cosenzaea and Morganella, as well as possibly pathogenic bacteria such as Serratia. The colonization of Serratia did not occur in presence of the bacterial mixture. The functionality prediction revealed that environmental bacteria or the supplemented bacterial mixture increased the metabolic potential of the honeybee gut microbiome compared to field and caged controls.},
}
@article {pmid35818766,
year = {2022},
author = {Sánchez-Suárez, J and Díaz, L and Junca, H and Garcia-Bonilla, E and Villamil, L},
title = {Microbiome composition of the marine sponge Cliona varians at the neotropical southern Caribbean Sea displays a predominant core of Rhizobiales and Nitrosopumilaceae.},
journal = {Journal of applied microbiology},
volume = {133},
number = {3},
pages = {2027-2038},
doi = {10.1111/jam.15714},
pmid = {35818766},
issn = {1365-2672},
support = {80740-168-2019//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n (Minciencias)/ ; ING-175-2016//Universidad de La Sabana/ ; },
mesh = {Animals ; Archaea ; Caribbean Region ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; *Porifera/microbiology ; Seawater/microbiology ; },
abstract = {AIMS: This work aims to characterize the microbial diversity of the encrusting sponge Cliona varians, a pore-forming and coral reef bioeroding marine sponge of emerging spread related to ocean acidification.<br><br>METHODS AND RESULTS: We analysed the microbiome composition by 16S V4 amplicon next-generation sequencing in a community of the bioeroding coral reef encrusting/excavating marine sponge Cliona varians thriving at the Southern Caribbean Sea. About 87.21% and 6.76% of the sequences retrieved were assigned to the domain Bacteria and Archaea. The most predominant operational taxonomic units were classified as members of the order Rhizobiales and family Nitrosopumilaceae, representing members of not yet characterized genera. Features found strictly conserved in the strain/genomic representatives reported in those microbial taxa are nitrogen fixation and transformation.<br><br>CONCLUSION: Our results suggest, in accordance with recent results, that these microbiome members and associated functions could be contributing to the biological fitness of the sponge to be able to colonize and bioerode in environments with low access and scarce availability of nitrogen sources.<br><br>Coral reefs bioresources such as sponge holobionts are intriguing and complex ecosystem units. This study contributes to the knowledge of how C. varians microbiota is composed or shaped, which is crucial to understand its ecological functions.},
}
@article {pmid35818006,
year = {2022},
author = {Mesa, V},
title = {Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2512},
number = {},
pages = {181-197},
doi = {10.1007/978-1-0716-2429-6_11},
pmid = {35818006},
issn = {1940-6029},
mesh = {Bacteria/genetics ; *Metagenomics ; Plant Roots/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; },
abstract = {The diversity of microbes associated with plant roots is in the order of tens of thousands of species. It is estimated that only 0.1-1.0% of the living bacteria present in soils can be cultured under standard conditions. The microbial marker-gene sequence data and the next-generation sequencing technologies have enabled systemic studies of root-associated microbiomes. Molecular techniques can be used to generate comprehensive taxonomic profiles of the microorganisms present in roots. The aim of this chapter is to provide a standard method for the obtention of rhizosphere and endosphere fractions, and a generic workflow of the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software to analysis of 16S rRNA marker-gene.},
}
@article {pmid35817179,
year = {2022},
author = {Liu, Y and Xi, Y and Xie, T and Liu, H and Su, Z and Huang, Y and Xu, W and Wang, D and Zhang, C and Li, X},
title = {Enhanced removal of diclofenac via coupling Pd catalytic and microbial processes in a H2-based membrane biofilm reactor: Performance, mechanism and biofilm microbial ecology.},
journal = {Chemosphere},
volume = {307},
number = {Pt 1},
pages = {135597},
doi = {10.1016/j.chemosphere.2022.135597},
pmid = {35817179},
issn = {1879-1298},
mesh = {Biofilms ; *Bioreactors ; Catalysis ; *Diclofenac ; Humans ; Membranes ; },
abstract = {Diclofenac (DCF) is a most widely used anti-inflammatory drug, which has attracted worldwide attention given its low biodegradability and ecological damage, especially toxic effects on mammals including humans. In this study, a H2-based membrane biofilm reactor (H2-MBfR) was constructed with well-dispersed Pd nanoparticles generated in situ. The Pd-MBfR was applied for catalytic reductive dechlorination of DCF. In batch tests, DCF concentration had significantly effect on the rate and extent DCF removal, and NO3[-] had negative impact on DCF reductive dechlorination. Over 67% removal of 0.5 mg/L DCF and 99% removal of 10 mg/L NO3[-]-N were achieved in 90 min, and the highest removal of 97% was obtained at 0.5 mg/L DCF in the absence of NO3[-]. Over 78 days of continuous operation, the highest steady-state removal flux of DCF was 0.0097 g/m[2]/d. LC-MS analysis indicated that the major product was 2-anilinephenylacetic acid (APA). Dechlorination was the main removal process of DCF mainly owing to the catalytic reduction by PdNPs, microbial reduction, and the synergistic reduction of microbial and PdNPs catalysis using direct delivery of H2. Moreover, DCF reductive Dechlorination shifted the microbial community in the biofilms and Sporomusa was responsible for DCF degradation. In summary, this work expands a remarkable feasibility of sustainable catalytic removal of DCF.},
}
@article {pmid35817167,
year = {2022},
author = {Khan, MA and Singh, D and Arif, A and Sodhi, KK and Singh, DK and Islam, SN and Ahmad, A and Akhtar, K and Siddique, HR},
title = {Protective effect of green synthesized Selenium Nanoparticles against Doxorubicin induced multiple adverse effects in Swiss albino mice.},
journal = {Life sciences},
volume = {305},
number = {},
pages = {120792},
doi = {10.1016/j.lfs.2022.120792},
pmid = {35817167},
issn = {1879-0631},
mesh = {Animals ; Antibiotics, Antineoplastic/therapeutic use ; Antioxidants/metabolism ; Cardiotoxicity/etiology ; Chromatography, Liquid ; Doxorubicin/toxicity ; Humans ; Mice ; *Nanoparticles ; Proto-Oncogene Proteins c-bcl-2 ; Reactive Oxygen Species ; *Selenium/pharmacology ; Tandem Mass Spectrometry ; },
abstract = {AIMS: Doxorubicin (DOX) is a widely used drug against multiple cancers. However, its clinical Use is often restricted due to multiple adverse effects. Recently, Selenium Nanoparticles (SeNPs) are gaining attention due to their low toxicity and higher biocompatibility, making them attractive nanoparticles (NPs) in medical and pharmaceutical sciences. Therefore, the current study aimed to assess if our biosynthesized SeNP from the endophytic fungus Fusarium oxysporum conjugated with DOX could alleviate the DOX-induced adverse effects.<br><br>MAIN METHODS: For this purpose, we investigated various genotoxic, biochemical, histopathological, and immunohistochemical parameters and finally analyzed the metabolite profile by LC-MS/MS.<br><br>KEY FINDINGS: We observed that DOX causes an increase in reactive oxygen and nitrogen species (ROS, RNS), 8-OHdG, and malondialdehyde (MDA), decreases antioxidant defense systems and reduces BCL-2 expression in cardiac tissue. In addition, a significant increase in DNA damage and alteration in the cytoarchitecture of the liver, kidney, and heart tissues was observed by Comet Tail Length and histopathological studies, respectively. Interestingly, the DOX-SeNP conjugate reduced ROS/RNS, 8-OHdG, and MDA levels in the liver, kidney, and heart tissues. It also restored the antioxidant enzymes and cytoarchitectures of the examined tissues, reduced genotoxicity, and increased the BCL-2 levels. Finally, metabolic profiling showed that DOX reduced the number of cardioprotective metabolites, which DOX-SeNP restored.<br><br>SIGNIFICANCE: Collectively, the present results describe the protective effect of DOX-conjugated SeNP against DOX-induced toxicities. In conclusion, DOX-SeNP conjugate might be better for treating patients receiving DOX alone. However, it warrants further thorough investigation.},
}
@article {pmid35811862,
year = {2022},
author = {Li, Y and Liu, B and Chen, J and Yue, X},
title = {Carbon-Nitrogen-Sulfur-Related Microbial Taxa and Genes Maintained the Stability of Microbial Communities in Coals.},
journal = {ACS omega},
volume = {7},
number = {26},
pages = {22671-22681},
pmid = {35811862},
issn = {2470-1343},
abstract = {Coal microbes are the predominant form of life in the subsurface ecosystem, which play a vital role in biogeochemical cycles. However, the systematic information about carbon-nitrogen-sulfur (C-N-S)-related microbial communities in coal seams is limited. In this study, 16S rRNA gene data from a total of 93 microbial communities in coals were collected for meta-analysis. The results showed that 718 functional genera were related to the C-N-S cycle, wherein N2 fixation, denitrification, and C degradation groups dominated in relative abundance, Chao1 richness, Shannon diversity, and niche width. Genus Pseudomonas having the most C-N-S-related functions showed the highest relative abundance, and genus Herbaspirillum with a higher abundance participated in C degradation, CH4 oxidation, N2 fixation, ammoxidation, and denitrification. Such Herbaspirillum was a core genus in the co-occurrence network of microbial prokaryotes and showed higher levels in weight degree, betweenness centrality, and eigenvector centrality. In addition, most of the methanogens could fix N2 and dominated in the N2 fixation groups. Among them, genera Methanoculleus and Methanosaeta showed higher levels in the betweenness centrality index. In addition, the genus Clostridium was linked to the methanogenesis co-occurrence network module. In parallel, the S reduction gene was present in the highest total relative abundance of genes, followed by the C degradation and the denitrification genes, and S genes (especially cys genes) were the main genes linked to the co-occurrence network of the C-N-S-related genes. In summary, this study strengthened our knowledge regarding the C-N-S-related coal microbial communities, which is of great significance in understanding the microbial ecology and geochemical cycle of coals.},
}
@article {pmid35809121,
year = {2023},
author = {Carvalho, MJ and S Oliveira, AL and Santos Pedrosa, S and Pintado, M and Pinto-Ribeiro, I and Madureira, AR},
title = {Skin Microbiota and the Cosmetic Industry.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {86-96},
pmid = {35809121},
issn = {1432-184X},
support = {027578//Fundo Europeu de Desenvolvimento Regional (FEDER)/ ; 01-0247//Programa Operacional Competitividade e Internacionaliza&#xe7;&#xe3;o (POCI)/ ; UID/Multi/50016/2019//Fundo Regional para a Ci&#xea;ncia e Tecnologia/ ; },
mesh = {Humans ; *Cosmetics/pharmacology ; Homeostasis ; *Microbiota/drug effects ; *Skin/microbiology ; *Host Microbial Interactions/drug effects ; Industry/standards/trends ; },
abstract = {Skin harbors an important microbial ecosystem - the skin microbiota that is in homeostasis with its host and is beneficial for human health. Cosmetic products have the potential to interfere with this microbial community; therefore their impact should be assessed. The aim of this review is to highlight the importance of skin microbiota in the cosmetic industry. Several studies determined that cosmetic ingredients have the potential to disrupt the skin microbiota equilibrium leading to the development of skin diseases and dysregulation of immune response. These studies led their investigation by using different methodologies and models, concluding that methods must be chosen according to the aim of the study, the skin site to be evaluated, and the target population of the cosmetics. Overall, it is crucial to test the impact of cosmetics in the skin microbiota and to stablish standard procedures, as well as specific criteria that allow to classify a cosmetic product as skin microbiota friendly.},
}
@article {pmid35804731,
year = {2022},
author = {Clodoveo, ML and Muraglia, M and Crupi, P and Hbaieb, RH and De Santis, S and Desantis, A and Corbo, F},
title = {The Tower of Babel of Pharma-Food Study on Extra Virgin Olive Oil Polyphenols.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {13},
pages = {},
pmid = {35804731},
issn = {2304-8158},
abstract = {Much research has been conducted to reveal the functional properties of extra virgin olive oil polyphenols on human health once EVOO is consumed regularly as part of a balanced diet, as in the Mediterranean lifestyle. Despite the huge variety of research conducted, only one effect of EVOO polyphenols has been formally approved by EFSA as a health claim. This is probably because EFSA's scientific opinion is entrusted to scientific expertise about food and medical sciences, which adopt very different investigative methods and experimental languages, generating a gap in the scientific communication that is essential for the enhancement of the potentially useful effects of EVOO polyphenols on health. Through the model of the Tower of Babel, we propose a challenge for science communication, capable of disrupting the barriers between different scientific areas and building bridges through transparent data analysis from the different investigative methodologies at each stage of health benefits assessment. The goal of this work is the strategic, distinctive, and cost-effective integration of interdisciplinary experiences and technologies into a highly harmonious workflow, organized to build a factual understanding that translates, because of trade, into health benefits for buyers, promoting EVOOs as having certified health benefits, not just as condiments.},
}
@article {pmid35802409,
year = {2022},
author = {Edwards, A and Soares, A and Debbonaire, A and Edwards Rassner, SM},
title = {Before you go: a packing list for portable DNA sequencing of microbiomes and metagenomes.},
journal = {Microbiology (Reading, England)},
volume = {168},
number = {7},
pages = {},
doi = {10.1099/mic.0.001220},
pmid = {35802409},
issn = {1465-2080},
mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; },
}
@article {pmid35802173,
year = {2023},
author = {Rocha, FP and Ronque, MUV and Lyra, ML and Bacci, M and Oliveira, PS},
title = {Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants : Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {699-712},
pmid = {35802173},
issn = {1432-184X},
support = {Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 2017/26162-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/04824-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2014/23141-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/16645-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 163546/2020-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441036/2016-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 307541/2018-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 306115/2013-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 302219/2017-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303730/2021-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; *Ants ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Brazil ; Bacteria/genetics ; },
abstract = {Ants have long been known for their associations with other taxa, including macroscopic fungi and symbiotic bacteria. Recently, many ant species have had the composition and function of their bacterial communities investigated. Due to its behavioral and ecological diversity, the subfamily Ponerinae deserves more attention regarding its associated microbiota. Here, we used the V4 region of the 16S rRNA gene to characterize the bacterial communities of Odontomachus chelifer (ground-nesting) and Odontomachus hastatus (arboreal), two ponerine trap-jaw species commonly found in the Brazilian savanna ("Cerrado") and Atlantic rainforest. We investigated habitat effects (O. chelifer in the Cerrado and the Atlantic rainforest) and species-specific effects (both species in the Atlantic rainforest) on the bacterial communities' structure (composition and abundance) in two different body parts: cuticle and gaster. Bacterial communities differed in all populations studied. Cuticular communities were more diverse, while gaster communities presented variants common to other ants, including Wolbachia and Candidatus Tokpelaia hoelldoblerii. Odontomachus chelifer populations presented different communities in both body parts, highlighting the influence of habitat type. In the Atlantic rainforest, the outcome depended on the body part targeted. Cuticular communities were similar between species, reinforcing the habitat effect on bacterial communities, which are mainly composed of environmentally acquired taxa. Gaster communities, however, differed between the two Odontomachus species, suggesting species-specific effects and selective filters. Unclassified Firmicutes and uncultured Rhizobiales variants are the main components accounting for the observed differences. Our study indicates that both host species and habitat act synergistically, but to different degrees, to shape the bacterial communities in these Odontomachus species.},
}
@article {pmid35802172,
year = {2023},
author = {Mejia, MP and Rojas, CA and Curd, E and Renshaw, MA and Edalati, K and Shih, B and Vincent, N and Lin, M and Nguyen, PH and Wayne, R and Jessup, K and Parker, SS},
title = {Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {998-1012},
pmid = {35802172},
issn = {1432-184X},
support = {CA-16-376437//Office of the President, University of California/ ; 443952-SR-69085//La Kretz and Stunt Ranch Reserve Grant/ ; },
mesh = {Soil/chemistry ; *Volatile Organic Compounds/metabolism ; *Soil Pollutants/analysis ; *Metals, Heavy/metabolism ; Bacteria ; *Microbiota ; *Petroleum ; *Environmental Pollutants ; Cobalt/metabolism ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; Biodegradation, Environmental ; },
abstract = {Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.},
}
@article {pmid35802014,
year = {2022},
author = {Zhu, M and Duan, X and Cai, P and Chai, J and Ji, J and Li, Y},
title = {First report of Podosphaera fusca Causing Powdery Mildew on Coreopsis lanceolata in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-12-20-2630-PDN},
pmid = {35802014},
issn = {0191-2917},
abstract = {Coreopsis lanceolata, known as lance-leaf coreopsis, is a perennial plant with high ornamental value. It is widely grown in many public parks and home gardens in China due to its showy flowers. From May to June 2020, typical powdery mildew-signs and symptoms were seen on leaves of C. lanceolata cultivated in the east campus of Henan Normal University, Henan Province, China. Abundant white powder-like masses in spot- or coalesced-lesions were on ad- and abaxial surfaces of plant leaves and covered up to 50 % of the leaf area. The infected leaves were deformed and eventually prematurely senescent. Approximately 80 % of observed C. lanceolata plants showed these signs and symptoms. Unbranched conidiophores (n = 25) were 90 to 200 × 12 to 20 μm and showed a foot cell, followed by 1 to 3 short cells and conidia. Ellipsoid-ovoid shaped conidia (n = 30) were 22 to 36 × 15 to 23 μm, with a length/width ratio of 1.4 to 2.4. No chasmothecia were detected. The powdery mildew fungus was initially identified as Podosphaera fusca based on the morphological characteristics. Total genomic DNA of the pathogen was extracted and the rDNA internal transcribed spacer (ITS) region was amplified and sequenced using the primers ITS1/ITS4 (White et al. 1990; Zhu et al. 2019). The obtained sequence was deposited into GenBank under Accession No. MT899186 and was 100 % identical to P. fusca (JX546297) from Herba eupatorii (Ding et al. 2013). To perform pathogenicity assays, leaf surface of three healthy plants was inoculated with fungal conidia according to a previously described method (Zhu et al. 2021). As a control, three non-inoculated plants were used. The control and inoculated plants were placed separately in two growth chambers (light/dark, 16 h/8 h; humidity, 65 %; temperature, 20 ℃). Fourteen- to sixteen-days post inoculation, powdery mildew signs were noticed on inoculated plants, whereas control remained asymptomatic. Similar results were found by performing two repeated pathogenicity assays. Therefore, based on the morphological and molecular analysis, the pathogen was identified and confirmed as P. fusca. This fungus has been reported on C. lanceolata in Korea (Park et al. 2010) and Italy (Garibaldi et al. 2007). This is, to the best of our knowledge, the first report of P. fusca on C. lanceolata in China. The sudden occurrence of this powdery mildew disease on C. lanceolata may adversely affect the health of valuable ornamentals in China. The precise identification of the causal agent of this powdery mildew of C. lanceolata is a preliminary step in developing effective disease management strategies.},
}
@article {pmid35799308,
year = {2023},
author = {Holderman, NR and Ferrer-González, FX and Glushka, J and Moran, MA and Edison, AS},
title = {Dissolved organic metabolite extraction from high-salt media.},
journal = {NMR in biomedicine},
volume = {36},
number = {4},
pages = {e4797},
doi = {10.1002/nbm.4797},
pmid = {35799308},
issn = {1099-1492},
support = {S10 OD021623/OD/NIH HHS/United States ; },
mesh = {*Seawater/chemistry/microbiology ; *Phytoplankton/metabolism ; Bacteria/metabolism ; Organic Chemicals/metabolism ; Water/metabolism ; },
abstract = {We describe considerations and strategies for developing a nuclear magnetic resonance (NMR) sample preparation method to extract low molecular weight metabolites from high-salt spent media in a model coculture system of phytoplankton and marine bacteria. Phytoplankton perform half the carbon fixation and oxygen generation on Earth. A substantial fraction of fixed carbon becomes part of a metabolite pool of small molecules known as dissolved organic matter (DOM), which are taken up by marine bacteria proximate to phytoplankton. There is an urgent need to elucidate these metabolic exchanges due to widespread anthropogenic transformations on the chemical, phenotypic, and species composition of seawater. These changes are increasing water temperature and the amount of CO2 absorbed by the ocean at energetic costs to marine microorganisms. Little is known about the metabolite-mediated, structured interactions occurring between phytoplankton and associated marine bacteria, in part because of challenges in studying high-salt solutions on various analytical platforms. NMR analysis is problematic due to the high-salt content of both natural seawater and culture media for marine microbes. High-salt concentration degrades the performance of the radio frequency coil, reduces the efficiency of some pulse sequences, limits signal-to-noise, and prolongs experimental time. The method described herein can reproducibly extract low molecular weight DOM from small-volume, high-salt cultures. It is a promising tool for elucidating metabolic flux between marine microorganisms and facilitates genetic screens of mutant microorganisms.},
}
@article {pmid35795698,
year = {2022},
author = {Salerno, B and Cornaggia, M and Sabatino, R and Di Cesare, A and Furlan, M and Barco, L and Orsini, M and Cordioli, B and Mantovani, C and Bano, L and Losasso, C},
title = {Calves as Main Reservoir of Antibiotic Resistance Genes in Dairy Farms.},
journal = {Frontiers in public health},
volume = {10},
number = {},
pages = {918658},
pmid = {35795698},
issn = {2296-2565},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Cattle ; Drug Resistance, Microbial/genetics ; Farms ; *Genes, Bacterial ; Penicillins/pharmacology ; },
abstract = {A side effect of antibiotic usage is the emergence and dissemination of antibiotic resistance genes (ARGs) within microbial communities. The spread of ARGs among pathogens has emerged as a public health concern. While the distribution of ARGs is documented on a global level, their routes of transmission have not been clarified yet; for example, it is not clear whether and to what extent the emergence of ARGs originates in farms, following the selective pressure exerted by antibiotic usage in animal husbandry, and if they can spread into the environment. Here we address this cutting edge issue by combining data regarding antimicrobial usage and quantitative data from selected ARGs (blaTEM, blaCTXM, ermB, vanA, qnrS, tetA, sul2, and mcr-1) encoding for resistance to penicillins, macrolides-lincosamides-streptogramins, glycopeptides, quinolones, tetracyclines, sulfonamides, and colistin at the farm level. Results suggest that dairy farms could be considered a hotspot of ARGs, comprising those classified as the highest risk for human health and that a correlation existed between the usage of penicillins and blaTEM abundances, meaning that, although the antibiotic administration is not exclusive, it remains a certain cause of the ARGs' selection and spread in farms. Furthermore, this study identified the role of calves as the main source of ARGs spread in dairy farms, claiming the need for targeted actions in this productive category to decrease the load of ARGs along the production chain.},
}
@article {pmid35788867,
year = {2023},
author = {Kim, SB and Lyou, ES and Kim, MS and Lee, TK},
title = {Bacterial Resuscitation from Starvation-Induced Dormancy Results in Phenotypic Diversity Coupled with Translational Activity Depending on Carbon Substrate Availability.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {325-336},
pmid = {35788867},
issn = {1432-184X},
support = {2020R1C1C1006249//National Research Foundation of Korea/ ; },
mesh = {Animals ; Cattle ; *Carbon/metabolism ; Phenotype ; *Bacteria/genetics/metabolism ; Adaptation, Physiological ; },
abstract = {Dormancy is a survival strategy of stressed bacteria inhabiting a various environment. Frequent dormant-active transitions owing to environmental changes play an important role in functional redundancy. However, a proper understanding of the phenotypic changes in bacteria during these transitions remains to be clarified. In this study, orthogonal approaches, such as electron microscopy, flow cytometry, and Raman spectroscopy, which can evaluate phenotypic heterogeneity at the single-cell level, were used to observe morphological and molecular phenotypic changes in resuscitated cells, and RNA sequencing (RNASeq) was used to determine the genetic characteristics associated with phenotypes. Within 12 h of the resuscitation process, morphological (cell size and shape) and physiological (growth and viability) characteristics as well as molecular phenotypes (cellular components) were found to be recovered to the extent that they were similar to those in active cells. The recovery rate and detailed phenotypic properties of the resuscitated cells differed significantly depending on the type or concentration of carbon sources. RNASeq analysis revealed that genes related to translation were significantly upregulated under all resuscitation conditions. The simpler the carbon source (e.g., glucose), the higher the expression of genes involved in cellular repair, and the more complex the carbon source (e.g., beef extract), the higher the expression of genes associated with increased energy production associated with cellular aerobic respiration. This study of phenotypic plasticity of resuscitated cells provides fundamental insight into understanding the adaptive fine-tuning of the microbiome in response to environmental changes and the functional redundancy resulting from phenotype heterogeneity.},
}
@article {pmid35788422,
year = {2023},
author = {Baubin, C and Ran, N and Siebner, H and Gillor, O},
title = {Divergence of Biocrust Active Bacterial Communities in the Negev Desert During a Hydration-Desiccation Cycle.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {474-484},
pmid = {35788422},
issn = {1432-184X},
support = {993/11//Israeli Science Academy/ ; },
mesh = {*Ecosystem ; Desiccation ; Desert Climate ; *Cyanobacteria/physiology ; Chlorophyll ; Soil ; Soil Microbiology ; },
abstract = {Rain events in arid environments are highly unpredictable and intersperse extended periods of drought. Therefore, tracking changes in desert soil bacterial communities during rain events, in the field, was seldom attempted. Here, we assessed rain-mediated dynamics of active bacterial communities in the Negev Desert biological soil crust (biocrust). Biocrust samples were collected during, and after a medium rainfall and dry soil was used as a control; we evaluated the changes in active bacterial composition, potential function, potential photosynthetic activity, and extracellular polysaccharide (EPS) production. We hypothesized that rain would activate the biocrust phototrophs (mainly Cyanobacteria), while desiccation would inhibit their activity. In contrast, the biocrust Actinobacteria would decline during rewetting and revive with desiccation. Our results showed that hydration increased chlorophyll content and EPS production. As expected, biocrust rewetting activated Cyanobacteria, which replaced the former dominant Actinobacteria, boosting potential autotrophic functions. However, desiccation of the biocrust did not immediately change the bacterial composition or potential function and was followed by a delayed decrease in chlorophyll and EPS levels. This dramatic shift in the community upon rewetting led to modifications in ecosystem services. We propose that following a rain event, the response of the active bacterial community lagged behind the biocrust water content due to the production of EPS which delayed desiccation and temporarily sustained the biocrust community activity.},
}
@article {pmid35785246,
year = {2022},
author = {Jiang, X and Wang, L},
title = {Grassland-based ruminant farming systems in China: Potential, challenges and a way forward.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {10},
number = {},
pages = {243-248},
pmid = {35785246},
issn = {2405-6383},
abstract = {With an increasing demand for high-quality, eco-friendly food products and growing concerns over ecological conservation, the development of ecology-based alternatives for ruminant production in China is urgently needed. This review discusses the capabilities for integrating grassland grazing into existing livestock farming systems to meet the contemporary human needs for high-quality foods and ecologically stable environments. Additionally, this review provides a critical analysis of the challenges and future directions associated with grassland-based ruminant farming systems. Integrating nutritional manipulation with grazing manipulation is critical for improving the productivity of grassland-based ecosystems and natural ecological functions. Biodiversity is the primary determinant of grassland ecosystem functions, while the composition and function of rumen microbiomes determine ruminant production performance. Future studies should focus on the following aspects: 1) how livestock grazing regulates grassland biodiversity and the mechanisms of grassland biodiversity maintenance, offering an important scientific basis for guiding grazing manipulation practices, including grazing intensity, livestock types, and grazing management practices; to 2) characterize the microbial ecology within the rumen of grazing ruminants to offer clarified instruction for the nutritional manipulation of grazing ruminants. Our recommendation includes creating a transdisciplinary system that integrates ecology, animal nutrition, and animal behavior to develop grassland-based ruminant farming systems sustainably, thereby achieving high-quality animal production and environmentally sustainable goals.},
}
@article {pmid35783424,
year = {2022},
author = {O'Brien, J and McParland, EL and Bramucci, AR and Ostrowski, M and Siboni, N and Ingleton, T and Brown, MV and Levine, NM and Laverock, B and Petrou, K and Seymour, J},
title = {The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {894026},
pmid = {35783424},
issn = {1664-302X},
abstract = {The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2-2 μm and >2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.},
}
@article {pmid35783390,
year = {2022},
author = {Sanchez-Cid, C and Keuschnig, C and Torzewski, K and Stachnik, &#x141; and Kępski, D and Luks, B and Nawrot, A and Niedzielski, P and Vogel, TM and Larose, C},
title = {Environmental and Anthropogenic Factors Shape the Snow Microbiome and Antibiotic Resistome.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {918622},
pmid = {35783390},
issn = {1664-302X},
abstract = {Winter tourism can generate environmental pollution and affect microbial ecology in mountain ecosystems. This could stimulate the development of antibiotic resistance in snow and its dissemination through the atmosphere and through snow melting. Despite these potential impacts, the effect of winter tourism on the snow antibiotic resistome remains to be elucidated. In this study, snow samples subjected to different levels of anthropogenic activities and surrounding forest were obtained from the Sudety Mountains in Poland to evaluate the impact of winter tourism on snow bacteria using a metagenomic approach. Bacterial community composition was determined by the sequencing of the V3-V4 hypervariable region of the 16S rRNA gene and the composition of the antibiotic resistome was explored by metagenomic sequencing. Whereas environmental factors were the main drivers of bacterial community and antibiotic resistome composition in snow, winter tourism affected resistome composition in sites with similar environmental conditions. Several antibiotic resistance genes (ARGs) showed a higher abundance in sites subjected to human activities. This is the first study to show that anthropogenic activities may influence the antibiotic resistome in alpine snow. Our results highlight the need to survey antibiotic resistance development in anthropogenically polluted sites.},
}
@article {pmid35780192,
year = {2023},
author = {Borsanelli, AC and Athayde, FRF and Saraiva, JR and Riggio, MP and Dutra, IS},
title = {Dysbiosis and Predicted Functions of the Dental Biofilm of Dairy Goats with Periodontitis.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {687-698},
pmid = {35780192},
issn = {1432-184X},
support = {4-299//United States Agency for International Development/ ; },
mesh = {Animals ; Dysbiosis/veterinary ; *Periodontitis/veterinary/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; Biofilms ; },
abstract = {Periodontitis is a polymicrobial biofilm-induced inflammatory disease associated with a dysbiotic microbial community and severely affects the health and welfare of animals. However, little is known regarding the dental microbiota associated with this disease in goats. In this study, we used high-throughput sequencing, network analysis, and predicted functions to investigate the microbiota of clinically healthy goats and those with periodontitis and identify possible pathogens and proteins associated with the disease. Dental microbiomes of goats with periodontitis were richer, and network analyses showed that the number of negative interactions was higher in the networks of animals with periodontitis. Based on the interrelationships, Porphyromonas, Fusobacterium, and Prevotella were suggested to play an important role in the dental microbiota associated with goat periodontitis. Protein families linked to translation, cytoplasmatic translation, and rRNA processing were more abundant in the dental microbiota of goats with periodontitis. In conclusion, the dental biofilm microbiota associated with goat periodontitis seems to be dysbiotic and has significant antagonistic interactions, which discriminate healthy animals from diseased animals and highlight the importance of key bacteria. Thus, these novel findings contribute to the evolution of knowledge regarding the etiopathogenesis of goat periodontitis and possibly to the development of periodontitis control measures.},
}
@article {pmid35778570,
year = {2022},
author = {Lee, HJ and Whang, KS},
title = {Roseomonas rosulenta sp. nov., isolated from rice paddy soil.},
journal = {Archives of microbiology},
volume = {204},
number = {7},
pages = {445},
pmid = {35778570},
issn = {1432-072X},
mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; *Methylobacteriaceae ; *Oryza/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; },
abstract = {Three bacterial isolates, Gram-stain-negative, non-motile, coccobacilli-shaped bacteria, strains OP-27[T], OP-5 and OP-30, were isolated from rice paddy soil. Phylogenetic analyses based on 16S rRNA gene sequences revealed that three isolates belonged to the genus Roseomonas, showing the highest sequence similarities to Roseomonas sediminicola FW-3[T] (98.1%) and Roseomonas lacus TH-G33[T] (98.0%). The genome size of strain OP-27[T] was 5.2 Mb in a single contig with DNA G+C content of 71.2%. The genome included 5164 predicted protein-coding genes, as well as 48 tRNA, 4 rRNA and 4 mRNA genes. The average nucleotide identity value between strain OP-27[T] and type strains of related species of the genus Roseomonas were 81.1-83.1%, and the digital DNA-DNA hybridization values of strain OP-27[T] and the related strains were 24.6-26.8%, respectively. The DNA-DNA hybridization values between strains OP-27[T], OP-5 and OP-30 were 84-100% and its closest relative, Roseomonas sediminicola KACC 16616[T] was 21.1%. The major fatty acids were C18:1 ω7c, C18:1 2-OH and C16:0 and predominant quinone was Q-10. Based on its distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, the three strains are considered to represent novel species of the genus Roseomonas, for which the name Roseomonas rosulenta sp. nov. is proposed. The type strain is OP-27[T] (=KACC 21501[T]= NBRC 114497[T]).},
}
@article {pmid35777363,
year = {2022},
author = {Schwartzman, JA and Ebrahimi, A and Chadwick, G and Sato, Y and Roller, BRK and Orphan, VJ and Cordero, OX},
title = {Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles.},
journal = {Current biology : CB},
volume = {32},
number = {14},
pages = {3059-3069.e7},
pmid = {35777363},
issn = {1879-0445},
support = {R25 GM067110/GM/NIGMS NIH HHS/United States ; },
mesh = {*Alginates/metabolism ; Animals ; Carbon ; Humans ; *Life Cycle Stages ; },
abstract = {Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static "shell" surrounding a motile, carbon-storing "core." Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbon-storing cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.},
}
@article {pmid35776963,
year = {2022},
author = {Viitamäki, S and Pessi, IS and Virkkala, AM and Niittynen, P and Kemppinen, J and Eronen-Rasimus, E and Luoto, M and Hultman, J},
title = {The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {8},
pages = {},
pmid = {35776963},
issn = {1574-6941},
mesh = {Arctic Regions ; Bacteria/genetics ; Carbon/analysis ; Finland ; *Microbiota ; Plants ; *Soil/chemistry ; Soil Microbiology ; Tundra ; },
abstract = {Due to climate change, increased microbial activity in high-latitude soils may lead to higher greenhouse gas (GHG) emissions. However, microbial GHG production and consumption mechanisms in tundra soils are not thoroughly understood. To investigate how the diversity and functional potential of bacterial and archaeal communities vary across vegetation types and soil layers, we analyzed 116 soil metatranscriptomes from 73 sites in the Finnish sub-Arctic. Meadow soils were characterized by higher pH and lower soil organic matter (SOM) and carbon/nitrogen ratio. By contrast, dwarf shrub-dominated ecosystems had higher SOM and lower pH. Although Actinobacteria, Acidobacteria, Alphaproteobacteria and Planctomycetes were dominant in all communities, there were significant differences at the genus level between vegetation types; plant polymer-degrading groups were more active in shrub-dominated soils than in meadows. Given that climate-change scenarios predict the expansion of shrubs at high latitudes, our results indicate that tundra soil microbial communities harbor potential decomposers of increased plant litter, which may affect the rate of carbon turnover in tundra soils. Additionally, transcripts of methanotrophs were detected in the mineral layer of all soils, which may moderate methane fluxes. This study provides new insights into possible shifts in tundra microbial diversity and activity due to climate change.},
}
@article {pmid35775832,
year = {2022},
author = {Muurinen, J and Muziasari, WI and Hultman, J and Pärnänen, K and Narita, V and Lyra, C and Fadlillah, LN and Rizki, LP and Nurmi, W and Tiedje, JM and Dwiprahasto, I and Hadi, P and Virta, MPJ},
title = {Antibiotic Resistomes and Microbiomes in the Surface Water along the Code River in Indonesia Reflect Drainage Basin Anthropogenic Activities.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {21},
pages = {14994-15006},
pmid = {35775832},
issn = {1520-5851},
mesh = {Humans ; *Rivers/microbiology ; Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; Genes, Bacterial ; Water ; Indonesia ; Anthropogenic Effects ; *Microbiota ; Bacteria/genetics ; },
abstract = {Water and sanitation are important factors in the emergence of antimicrobial resistance in low- and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and effluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and MGEs and 16S rRNA gene amplicon sequencing to analyze the bacterial communities. The community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs, which correlated with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs were no longer detectable in marine waters at the ocean entrance. Our work provides information on the impact of different influents on river health as well as sheds light on how land use contributes to the river resistome and microbiome.},
}
@article {pmid35771243,
year = {2022},
author = {Bai, X and Dinkla, IJT and Muyzer, G},
title = {Microbial ecology of biofiltration used for producing safe drinking water.},
journal = {Applied microbiology and biotechnology},
volume = {106},
number = {13-16},
pages = {4813-4829},
pmid = {35771243},
issn = {1432-0614},
support = {17840//NWO-TTW/ ; },
mesh = {Charcoal ; *Drinking Water ; Filtration ; Organic Chemicals ; Sand ; *Water Pollutants, Chemical ; *Water Purification ; },
abstract = {Biofiltration is a water purification technology playing a pivotal role in producing safe drinking water. This technology attracts many interests worldwide due to its advantages, such as no addition of chemicals, a low energy input, and a high removal efficiency of organic compounds, undesirable taste and odours, and pathogens. The current review describes the microbial ecology of three biofiltration processes that are routinely used in drinking water treatment plants, i.e. (i) rapid sand filtration (RSF), (ii) granular activated carbon filtration (GACF), and (iii) slow sand filtration (SSF). We summarised and compared the characteristics, removal performance, and corresponding (newly revealed) mechanisms of the three biofiltration processes. Specifically, the microbial ecology of the different biofilter processes and the role of microbial communities in removing nutrients, organic compounds, and pathogens were reviewed. Finally, we highlight the limitations and challenges in the study of biofiltration in drinking water production, and propose future perspectives for obtaining a comprehensive understanding of the microbial ecology of biofiltration, which is needed to promote and optimise its further application. KEY POINTS: • Biofilters are composed of complex microbiomes, primarily shaped by water quality. • Conventional biofilters contribute to address safety challenges in drinking water. • Studies may underestimate the active/functional role of microbiomes in biofilters.},
}
@article {pmid35770362,
year = {2022},
author = {Sridhar, B and Wilhelm, RC and Debenport, SJ and Fahey, TJ and Buckley, DH and Goodale, CL},
title = {Microbial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soils.},
journal = {Global change biology},
volume = {28},
number = {18},
pages = {5399-5415},
doi = {10.1111/gcb.16321},
pmid = {35770362},
issn = {1365-2486},
mesh = {Bacteria/metabolism ; Carbon/metabolism ; Forests ; Fungi/metabolism ; *Microbiota ; *Mycorrhizae/metabolism ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Microbial community structure and function regularly covary with soil pH, yet effects of these interactions on soil carbon are rarely tested experimentally within natural ecosystems. We investigated the enduring (25 year) impacts of liming on microbial community structure and decomposition at an acidic northern hardwood forest, where experimental liming increased pH one unit and surprisingly doubled the organic carbon stocks of the forest floor. We show that this increase in carbon storage corresponded with restructuring of the bacterial and fungal communities that drive decomposition. In the Oe horizon, liming reduced the activities of five extracellular enzymes that mediate decomposition, while the Oa horizon showed an especially large (64%) reduction in the activity of a sixth, peroxidase, which is an oxidative enzyme central to lignocellulose degradation. Decreased enzyme activities corresponded with loss of microbial taxa important for lignocellulose decay, including large reductions in the dominant ectomycorrhizal genera Russula and Cenococcum, saprotrophic and wood decaying fungi, and Actinobacteria (Thermomonosporaceae). These results demonstrate the importance of pH as a dominant regulator of microbial community structure and illustrate how changes to this structure can produce large, otherwise unexpected increases in carbon storage in forest soils.},
}
@article {pmid35770167,
year = {2022},
author = {Girolamini, L and Pascale, MR and Mazzotta, M and Spiteri, S and Marino, F and Salaris, S and Grottola, A and Orsini, M and Cristino, S},
title = {Combining Traditional and Molecular Techniques Supports the Discovery of a Novel Legionella Species During Environmental Surveillance in a Healthcare Facility.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {900936},
pmid = {35770167},
issn = {1664-302X},
abstract = {Legionella surveillance plays a significant role not only to prevent the risk of infection but also to study the ecology of isolates, their characteristics, and how their prevalence changes in the environment. The difficulty in Legionella isolation, identification, and typing results in a low notification rate; therefore, human infection is still underestimated. In addition, during Legionella surveillance, the special attention given to Legionella pneumophila leads to an underestimation of the prevalence and risk of infection for other species. This study describes the workflow performed during environmental Legionella surveillance that resulted in the isolation of two strains, named 8cVS16 and 9fVS26, associated with the genus Legionella. Traditional and novel approaches such as standard culture technique, MALDI-TOF MS, gene sequencing, and whole-genome sequencing (WGS) analysis were combined to demonstrate that isolates belong to a novel species. The strain characteristics, the differences between macrophage infectivity potential (mip), RNA polymerase β subunit (rpoB), and reference gene sequences, the average nucleotide identity (ANI) of 90.4%, and the DNA-DNA digital hybridization (dDDH) analysis of 43% demonstrate that these isolates belong to a new Legionella species. The finding suggests that, during the culture technique, special attention should be paid to the characteristics of the isolates that are less associated with the Legionella genus in order to investigate the differences found using more sensitive methods. The characterization of the two newly discovered isolates based on morphological, biochemical, and microscopic characteristics is currently underway and will be described in another future study.},
}
@article {pmid35770161,
year = {2022},
author = {Pan, Y and Li, G and Su, L and Zheng, P and Wang, Y and Shen, Z and Chen, Z and Han, Q and Gong, J},
title = {Seagrass Colonization Alters Diversity, Abundance, Taxonomic, and Functional Community Structure of Benthic Microbial Eukaryotes.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {901741},
pmid = {35770161},
issn = {1664-302X},
abstract = {Seagrass form high productive ecosystems in coastal environments. However, the effects of these coastal plants on the structure and function of the belowground eukaryotic microbiome remain elusive. In this study, we characterized the community of microbial eukaryotes (microeukaryotes) in both vegetated and unvegetated sediments using 18S rRNA gene amplicon sequencing and quantitative PCR. Analysis of sequencing data showed that the eelgrass (Zostera marina) colonization decreased the alpha diversity indices of benthic microeukaryotes. Apicomplexa represented an average of 83% of reads across all samples, with a higher proportion at the vegetated sites. The taxonomic community structure was significantly different between these two types of sediments, for which the concentration of NH 4 + in sediment porewater and salinity could account. Phylogenetic analyses of long 18S rRNA genes (around 1,030 bp) indicated these apicomplexan parasites are closely related to gregarine Lecudina polymorpha. Determination of 18S rRNA gene abundances provided evidence that the eelgrass markedly promoted the biomass of the gregarine and all microeukaryotes in the seagrass-colonized sediments and confirmed that the gregarine was hosted by a polychaete species. Significantly higher gene abundances of heterotrophs and mixotrophs were found at the vegetated sites, which could be explained by the finer sediments and short supply of dissolved inorganic nitrogen, respectively. The pigmented protists were more abundant in 18S rRNA gene copies at the lower and higher pH levels than at the intermediate. Nevertheless, the fractions of heterotrophs and phototrophs in the community were significantly related to porewater N:P ratio. These results indicate that seagrass colonization significantly induces an increase in overall biomass and a decrease in diversity of benthic microeukaryotes, making them more heterotrophic. This study also highlights that the hotspot of eukaryotic parasites could be linked with the high productivity of a natural ecosystem.},
}
@article {pmid35769467,
year = {2022},
author = {Qing, J and Li, C and Hu, X and Song, W and Tirichen, H and Yaigoub, H and Li, Y},
title = {Differentiation of T Helper 17 Cells May Mediate the Abnormal Humoral Immunity in IgA Nephropathy and Inflammatory Bowel Disease Based on Shared Genetic Effects.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {916934},
pmid = {35769467},
issn = {1664-3224},
mesh = {Biomarkers/metabolism ; Cell Differentiation/immunology ; *Glomerulonephritis, IGA/immunology ; Humans ; Immunity, Humoral ; *Inflammatory Bowel Diseases/genetics/immunology ; *MicroRNAs/genetics ; *Th17 Cells/cytology/immunology ; },
abstract = {BACKGROUND: IgA nephropathy (IgAN) is the most frequent glomerulonephritis in inflammatory bowel disease (IBD). However, the inter-relational mechanisms between them are still unclear. This study aimed to explore the shared gene effects and potential immune mechanisms in IgAN and IBD.<br><br>METHODS: The microarray data of IgAN and IBD in the Gene Expression Omnibus (GEO) database were downloaded. The differential expression analysis was used to identify the shared differentially expressed genes (SDEGs). Besides, the shared transcription factors (TFs) and microRNAs (miRNAs) in IgAN and IBD were screened using humanTFDB, HMDD, ENCODE, JASPAR, and ChEA databases. Moreover, weighted gene co-expression network analysis (WGCNA) was used to identify the shared immune-related genes (SIRGs) related to IgAN and IBD, and R software package org.hs.eg.db (Version3.1.0) were used to identify common immune pathways in IgAN and IBD.<br><br>RESULTS: In this study, 64 SDEGs and 28 SIRGs were identified, and the area under the receiver operating characteristic curve (ROC) of 64 SDEGs was calculated and two genes (MVP, PDXK) with high area under the curve (AUC) in both IgAN and IBD were screened out as potential diagnostic biomarkers. We then screened 3 shared TFs (SRY, MEF2D and SREBF1) and 3 miRNAs (hsa-miR-146, hsa-miR-21 and hsa-miR-320), and further found that the immune pathways of 64SDEGs, 28SIRGs and 3miRNAs were mainly including B cell receptor signaling pathway, Fc&#x3b3;R-mediated phagocytosis, IL-17 signaling pathway, toll-like receptor signaling pathway, TNF signaling pathway, TRP channels, T cell receptor signaling pathway, Th17 cell differentiation, and cytokine-cytokine receptor interaction.<br><br>CONCLUSION: Our work revealed the differentiation of Th17 cells may mediate the abnormal humoral immunity in IgAN and IBD patients and identified novel gene candidates that could be used as biomarkers or potential therapeutic targets.},
}
@article {pmid35768458,
year = {2022},
author = {Catania, T and Li, Y and Winzer, T and Harvey, D and Meade, F and Caridi, A and Leech, A and Larson, TR and Ning, Z and Chang, J and Van de Peer, Y and Graham, IA},
title = {Author Correction: A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3755},
doi = {10.1038/s41467-022-31568-x},
pmid = {35768458},
issn = {2041-1723},
}
@article {pmid35768269,
year = {2022},
author = {Yin, H and Huang, J and Hu, M},
title = {Moderate-Intensity Exercise Improves Endothelial Function by Altering Gut Microbiome Composition in Rats Fed a High-Fat Diet.},
journal = {Journal of Nippon Medical School = Nippon Ika Daigaku zasshi},
volume = {89},
number = {3},
pages = {316-327},
doi = {10.1272/jnms.JNMS.2022_89-307},
pmid = {35768269},
issn = {1347-3409},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; Endothelium/metabolism ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; Obesity/etiology/metabolism/therapy ; RNA, Ribosomal, 16S/genetics ; Rats ; Vascular Endothelial Growth Factor A ; },
abstract = {BACKGROUND: Obesity changes gut microbial ecology and is related to endothelial dysfunction. Although the correlation between gut microbial ecology and endothelial dysfunction has been studied in obese persons, the underlying mechanisms by which exercise enhances endothelial function in this group remain unclear. This study investigated whether exercise improves endothelial function and alters gut microbiome composition in rats fed a high-fat diet (HFD).<br><br>METHODS: Obesity was induced by an HFD for 11 weeks. Whole-body composition and endothelium-dependent relaxation of mesenteric arteries were measured. Blood biochemical tests were performed, and gut microbiomes were characterized by 16S rRNA gene sequencing on an Illumina HiSeq platform.<br><br>RESULTS: Exercise training for 8 weeks improved body composition in HFD-fed rats. Furthermore, compared with the untrained/HFD group, aerobic exercise significantly increased acetylcholine-induced, endothelium-dependent relaxation in mesenteric arteries (P < 0.05) and circulating vascular endothelial growth factor levels (P < 0.01) and decreased circulating C-reactive protein levels (P < 0.05). In addition, exercise and HFD resulted in alterations in the composition of the gut microbiome; exercise reduced the relative abundance of Clostridiales and Romboutsia. Moreover, 12 species of bacteria, including Romboutsia, were significantly associated with parameters of endothelial function in the overall sample.<br><br>CONCLUSIONS: These results suggest that aerobic exercise enhances endothelial function in HFD-fed rats by altering the composition of the gut microbiota. These findings provide new insights on the application of physical exercise for improving endothelial function in obese persons.},
}
@article {pmid35764676,
year = {2022},
author = {Van den Wyngaert, S and Ganzert, L and Seto, K and Rojas-Jimenez, K and Agha, R and Berger, SA and Woodhouse, J and Padisak, J and Wurzbacher, C and Kagami, M and Grossart, HP},
title = {Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits.},
journal = {The ISME journal},
volume = {16},
number = {9},
pages = {2242-2254},
pmid = {35764676},
issn = {1751-7370},
support = {WY175/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; AG 284/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WU 890/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GR1540/30-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Chytridiomycota/genetics ; *Diatoms/genetics/microbiology ; Fungi/genetics ; Lakes/microbiology ; *Parasites ; Phytoplankton/microbiology ; },
abstract = {Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.},
}
@article {pmid35762794,
year = {2022},
author = {Roguet, A and Newton, RJ and Eren, AM and McLellan, SL},
title = {Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure.},
journal = {mSystems},
volume = {7},
number = {4},
pages = {e0011822},
pmid = {35762794},
issn = {2379-5077},
support = {R01 AI091829/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Anti-Bacterial Agents ; Bacteria/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; United States ; *Wastewater ; },
abstract = {Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.},
}
@article {pmid35761925,
year = {2022},
author = {Modin, O and Fuad, N and Abadikhah, M and I'Ons, D and Ossiansson, E and Gustavsson, DJI and Edefell, E and Suarez, C and Persson, F and Wilén, BM},
title = {A relationship between phages and organic carbon in wastewater treatment plant effluents.},
journal = {Water research X},
volume = {16},
number = {},
pages = {100146},
pmid = {35761925},
issn = {2589-9147},
abstract = {With stringent effluent requirements and the implementation of new processes for micropollutant removal, it is increasingly important for wastewater treatment plants (WWTPs) to understand the factors affecting effluent quality. Phages (viruses infecting prokaryotes) are abundant in the biological treatment processes. They can contribute to organic carbon in the treated effluent both because they are organic in nature and occur in the effluent and because they cause lysis of microorganisms. Today very little is known about the effects of phages on effluent quality. The goal of this study was, therefore, to determine the relationship between phages and organic carbon in WWTP effluents. We also examined the diversity, taxonomy, and host-association of DNA phages using metagenomics. Effluent samples were collected from four WWTPs treating municipal wastewater. Significant differences in both organic carbon and virus-like particle concentrations were observed between the plants and there was a linear relationship between the two parameters. The phage communities were diverse with many members being taxonomically unclassified. Putative hosts were dominated by bacteria known to be abundant in activated sludge systems such as Comamonadaceae. The composition of phages differed between the WWTPs, suggesting that local conditions shape the communities. Overall, our findings suggest that the abundance and composition of phages are related to effluent quality. Thus, there is a need for further research clarifying the association between phage dynamics and WWTP function.},
}
@article {pmid35761577,
year = {2022},
author = {Kothe, CI and Mohellibi, N and Renault, P},
title = {Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {157},
number = {},
pages = {111265},
doi = {10.1016/j.foodres.2022.111265},
pmid = {35761577},
issn = {1873-7145},
mesh = {Animals ; Biodiversity ; Brazil ; *Cheese/analysis ; Food Microbiology ; *Lactobacillales/genetics ; *Lactococcus lactis/genetics ; Metagenomics ; Streptococcus thermophilus/genetics ; Yeasts ; },
abstract = {Brazilian artisanal cheeses date from the first Portuguese settlers and evolved via local factors, resulting in unique products that are now part of the patrimony and identity of different Brazilian regions. In this study, we combined several culture-independent approaches, including 16S/ITS metagenetics, assembly- and deep profiling-metagenomics to characterize the originality of the microbiota of five varieties of Brazilian artisanal cheeses from the South and Southeast regions of Brazil. Their core microbiota contained mainly lactic acid bacteria (LAB), of which Lactococcus lactis subsp. lactis was the most frequent, followed by Streptococcus thermophilus in the South region. Moreover, several samples from the Southeast region contained, as dominant LAB, two other food Streptococci belonging to a new species of the salivarius group and S. infantarius. Rinds of samples from the Southeast region were dominated by the halotolerant bacterium Corynebacterium variabile, and the yeasts Diutina catenulata, followed by Debaryomyces hansenii and Kodamaea ohmeri. Rinds from the South region contained mainly LAB due to their short ripening time, and the predominant yeast was D. hansenii. Phylogenomic analysis based on L. lactis metagenome-assembled genomes (MAGs) showed that most Brazilian strains are closely related and form a different clade from those whose genomes are available at this time, indicating that they belong to a specific group. Lastly, functional analysis showed that S. infantarius acquired a ∼ 26 kb DNA fragment from S. thermophilus starter strains that carry the LacSZ system, allowing fast lactose assimilation, an adaptation advantage for growth in milk. Finally, our study identified several areas of concern, such as the presence of somatic cell DNA and high levels of antibiotic resistance genes in several cheese microbiota, suggesting that milk from diseased animals may still be used occasionally. Overall, the data from this study highlight the potential value of the traditional and artisanal cheese production network in Brazil, and provide a metagenomic-based scheme to help manage this resource safely.},
}
@article {pmid35761554,
year = {2022},
author = {Sequino, G and Valentino, V and Villani, F and De Filippis, F},
title = {Omics-based monitoring of microbial dynamics across the food chain for the improvement of food safety and quality.},
journal = {Food research international (Ottawa, Ont.)},
volume = {157},
number = {},
pages = {111242},
doi = {10.1016/j.foodres.2022.111242},
pmid = {35761554},
issn = {1873-7145},
mesh = {*Food Chain ; Food Safety ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; },
abstract = {The diffusion of high-throughput sequencing has dramatically changed the study of food microbial ecology. Amplicon-based description of the microbial community may be routinary implemented in the food industry to understand how the processing parameters and the raw material quality may affect the microbial community of the final product, as well as how the community changes during the shelf-life. In addition, application of shotgun metagenomics may represent an invaluable resource to understand the functional potential of the microbial community, identifying the presence of spoilage-associated activities or genes related to pathogenesis. Finally, retrieving Metagenome-Assembled Genomes (MAGs) of relevant species may be useful for strain-tracking along the food chain and in case of food poisoning outbreaks. This review gives an overview of the possible applications of sequencing-based approaches in the study of food microbial ecology, highlighting limitations that still prevent the spreading of these techniques to the food industry.},
}
@article {pmid35761415,
year = {2022},
author = {Liu, Y and Yang, M and Tang, L and Wang, F and Huang, S and Liu, S and Lei, Y and Wang, S and Xie, Z and Wang, W and Zhao, X and Tang, B and Yang, S},
title = {TLR4 regulates RORγt[+] regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {98},
pmid = {35761415},
issn = {2049-2618},
mesh = {*Akkermansia ; Animals ; *Colitis/immunology ; Colon ; Dextran Sulfate/adverse effects ; Inflammation ; Mice ; Mice, Inbred C57BL ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; *T-Lymphocytes, Regulatory/immunology ; *Toll-Like Receptor 4/genetics ; },
abstract = {BACKGROUND: Well-balanced interactions between gut microbiota and the immune system are essential to prevent chronic intestinal inflammation, as observed in inflammatory bowel diseases (IBD). Toll-like receptor 4 (TLR4) functions as a sensor mediating the crosstalk between the intestinal commensal microbiome and host immunity, but the influence of TLR4 on the shaping of intestinal microbiota and immune responses during colon inflammation remains poorly characterized. We investigated whether the different susceptibilities to colitis between wild-type (WT) and TLR4[-/-] mice were gut microbiota-dependent and aimed to identify the potential immunity modulation mechanism.<br><br>METHODS: We performed antibiotic depletion of the microbiota, cohousing experiments, and faecal microbiota transplantation (FMT) in WT and TLR4[-/-] mice to assess the influence of TLR4 on intestinal microbial ecology. 16S rRNA sequencing was performed to dissect microbial discrepancies, and dysbiosis-associated immune perturbation was investigated by flow cytometry. Akkermansia muciniphila (A. muciniphila)-mediated immune modulation was confirmed through the T-cell transfer colitis model and bone marrow chimaera construction.<br><br>RESULTS: TLR4[-/-] mice experienced enhanced susceptibility to DSS-induced colitis. 16S rRNA sequencing showed notable discrepancy in the gut microbiota between WT and TLR4[-/-] mice. In particular, A. muciniphila contributed most to distinguishing the two groups. The T-cell transfer colitis model and bone marrow transplantation (BMT) consistently demonstrated that A. muciniphila ameliorated colitis by upregulating ROR&#x3b3;t[+] Treg cell-mediated immune responses. Mucosal biopsies from human manifested parallel outcomes with colon tissue from WT mice, as evidenced by the positive correlation between TLR4 expression and intestinal A. muciniphila colonization during homeostasis.<br><br>CONCLUSIONS: Our results demonstrate a novel protective role of TLR4 against intestinal inflammation, wherein it can modulate A. muciniphila-associated immune responses. These findings provide a new perspective on host-commensal symbiosis, which may be beneficial for developing potential therapeutic strategies. Video abstract.},
}
@article {pmid35760840,
year = {2022},
author = {Piel, D and Bruto, M and Labreuche, Y and Blanquart, F and Goudenège, D and Barcia-Cruz, R and Chenivesse, S and Le Panse, S and James, A and Dubert, J and Petton, B and Lieberman, E and Wegner, KM and Hussain, FA and Kauffman, KM and Polz, MF and Bikard, D and Gandon, S and Rocha, EPC and Le Roux, F},
title = {Phage-host coevolution in natural populations.},
journal = {Nature microbiology},
volume = {7},
number = {7},
pages = {1075-1086},
pmid = {35760840},
issn = {2058-5276},
mesh = {*Bacteriophages/genetics ; Host Specificity ; },
abstract = {Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting co-occurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.},
}
@article {pmid35754723,
year = {2022},
author = {Waring, B and Gee, A and Liang, G and Adkins, S},
title = {A quantitative analysis of microbial community structure-function relationships in plant litter decay.},
journal = {iScience},
volume = {25},
number = {7},
pages = {104523},
pmid = {35754723},
issn = {2589-0042},
abstract = {Soil microbes play a central role in ecosystem element cycling. Yet a central question in microbial ecology remains unanswered: to what extent does the taxonomic composition of soil microbial communities mediate biogeochemical process rates? In this quantitative review, we explore the mechanisms that lead to variation in the strength of microbial community structure-function relationships over space and time. To evaluate these mechanisms, we conduct a meta-analysis of studies that have monitored the decomposition of sterilized plant litter inoculated with different microbial assemblages. We find that the influence of microbial community composition on litter decay is pervasive and strong, rivalling in magnitude the influence of litter chemistry on decomposition. However, no single environmental or experimental attribute was correlated with variation in the inoculum effect. These results emphasize the need to better understand ecological dynamics within microbial communities, particularly emergent features such as cross-feeding networks, to improve predictions of soil biogeochemical function.},
}
@article {pmid35753302,
year = {2022},
author = {Zhang, K and Hu, J and Yang, S and Xu, W and Wang, Z and Zhuang, P and Grossart, HP and Luo, Z},
title = {Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1.},
journal = {Journal of hazardous materials},
volume = {437},
number = {},
pages = {129406},
doi = {10.1016/j.jhazmat.2022.129406},
pmid = {35753302},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; Carbon/metabolism ; Cladosporium ; Esterases/metabolism ; Fungi/metabolism ; Lipase ; *Polyesters/chemistry ; *Polyurethanes/chemistry ; Soil Microbiology ; },
abstract = {Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80% of Impranil PU after 3 days of incubation at 28 ℃ by breaking the carbonyl groups (1732 cm[-1]) and C-N-H bonds (1532 cm[-1] and 1247 cm[-1]) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation" was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.},
}
@article {pmid35752808,
year = {2022},
author = {Wang, Q and Chen, Y and Yang, Q and Zhao, J and Feng, L and Wang, M},
title = {SR5AL serves as a key regulatory gene in lycopene biosynthesis by Blakeslea trispora.},
journal = {Microbial cell factories},
volume = {21},
number = {1},
pages = {126},
pmid = {35752808},
issn = {1475-2859},
support = {21A180014//Key Scientific Research Project of Colleges and Universities in Henan Province/ ; 212102110322//Science and Technology Department of Henan Province/ ; },
mesh = {Genes, Regulator ; Lycopene/metabolism ; *Mucorales/genetics/metabolism ; Oxidoreductases/metabolism ; },
abstract = {BACKGROUND: Trisporic acids are considered to be key regulators of carotenoid biosynthesis and sexual reproduction in zygomycetes, but the mechanisms underlying this regulation have not been fully elucidated.<br><br>RESULTS: In this study, the relationships between trisporic acids and lycopene synthesis were investigated in Blakeslea trispora. The lycopene concentration in single fermentation by the (-) strain with the addition of 24&#xa0;&#x3bc;g/L trisporic acids was slightly higher than that observed in mated fermentation. After transcriptomic analysis, a steroid 5&#x3b1;-reductase-like gene, known as SR5AL in B. trispora, was first reported. 5&#x3b1;-Reductase inhibitors reduced lycopene biosynthesis and downregulated the expression of sex determination and carotenoid biosynthesis genes. Overexpression of the SR5AL gene upregulated these genes, regardless of whether trisporic acids were added.<br><br>CONCLUSION: These findings indicated that the SR5AL gene is a key gene associated with the response to trisporic acids.},
}
@article {pmid35752802,
year = {2022},
author = {Darcy, JL and Amend, AS and Swift, SOI and Sommers, PS and Lozupone, CA},
title = {specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {34},
pmid = {35752802},
issn = {2524-6372},
support = {5 T15 LM009451-12/NH/NIH HHS/United States ; 1255972//National Science Foundation/ ; },
abstract = {BACKGROUND: Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.<br><br>RESULTS: We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.<br><br>CONCLUSIONS: specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.},
}
@article {pmid35752717,
year = {2022},
author = {Leung, PM and Daebeler, A and Chiri, E and Hanchapola, I and Gillett, DL and Schittenhelm, RB and Daims, H and Greening, C},
title = {A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen.},
journal = {The ISME journal},
volume = {16},
number = {9},
pages = {2213-2219},
pmid = {35752717},
issn = {1751-7370},
support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Ammonia/metabolism ; Bacteria ; *Hydrogen/metabolism ; Nitrification ; *Nitrites/metabolism ; Oxidation-Reduction ; Proteomics ; },
abstract = {Chemolithoautotrophic nitrite-oxidising bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidiser Nitrospira moscoviensis oxidises hydrogen (H2) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [Km(app) = 32 nM]. Atmospheric H2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Thermodynamic modelling revealed that H2 oxidation theoretically generates higher power yield than nitrite oxidation at low substrate concentrations and significantly contributes to growth at elevated nitrite concentrations. Collectively, this study suggests atmospheric H2 oxidation enhances the growth and survival of NOB amid variability of nitrite supply, extends the phenomenon of atmospheric H2 oxidation to an eighth phylum (Nitrospirota), and reveals unexpected new links between the global hydrogen and nitrogen cycles. Long classified as obligate nitrite oxidisers, our findings suggest H2 may primarily support growth and survival of certain NOB in natural environments.},
}
@article {pmid35751580,
year = {2022},
author = {Akritidou, T and Smet, C and Akkermans, S and Tonti, M and Williams, J and Van de Wiele, T and Van Impe, JFM},
title = {A protocol for the cultivation and monitoring of ileal gut microbiota surrogates.},
journal = {Journal of applied microbiology},
volume = {133},
number = {3},
pages = {1919-1939},
doi = {10.1111/jam.15684},
pmid = {35751580},
issn = {1365-2672},
support = {1224620N//Fonds Wetenschappelijk Onderzoek/ ; G062519N//Fonds Wetenschappelijk Onderzoek/ ; C24/18/046//KU Leuven/ ; },
mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome ; Ileum/microbiology ; Intestine, Small ; *Microbiota ; },
abstract = {AIMS: This research aimed to develop and validate a cultivation and monitoring protocol that is suitable for a surrogate microbial community that accounts for the gut microbiota of the ileum of the small intestine.<br><br>METHODS AND RESULTS: Five bacterial species have been selected as representatives of the ileal gut microbiota and a general anaerobic medium (MS-BHI, as minimally supplemented brain heart infusion) has been constructed and validated against BCCM/LGM recommended and commercial media. Moreover, appropriate selective/differential media have been investigated for monitoring each ileal gut microbiota surrogate. Results showed that MS-BHI was highly efficient in displaying individual and collective behaviour of the ileal gut microbiota species, when compared with other types of media. Likewise, the selective/differential media managed to identify and describe the behaviour of their targeted species.<br><br>CONCLUSIONS: MS-BHI renders a highly efficient, inexpensive and easy-to-prepare cultivation and enumeration alternative for the surrogate ileal microbiota species. Additionally, the selective/differential media can identify and quantify the bacteria of the surrogate ileal microbial community.<br><br>The selected gut microbiota species can represent an in vitro ileal community, forming the basis for future studies on small intestinal microbiota. MS-BHI and the proposed monitoring protocol can be used as a standard for gut microbiota studies that utilize conventional microbiological techniques.},
}
@article {pmid35751418,
year = {2022},
author = {Jeon, JS and Rybka, D and Carreno-Quintero, N and De Vos, R and Raaijmakers, JM and Etalo, DW},
title = {Metabolic signatures of rhizobacteria-induced plant growth promotion.},
journal = {Plant, cell &amp; environment},
volume = {45},
number = {10},
pages = {3086-3099},
doi = {10.1111/pce.14385},
pmid = {35751418},
issn = {1365-3040},
mesh = {*Arabidopsis/genetics ; Flavonoids/metabolism ; Herbivory ; Plant Development ; Plant Roots/microbiology ; Plant Shoots ; },
abstract = {Various root-colonizing bacterial species can promote plant growth and trigger systemic resistance against aboveground leaf pathogens and herbivore insects. To date, the underlying metabolic signatures of these rhizobacteria-induced plant phenotypes are poorly understood. To identify core metabolic pathways that are targeted by growth-promoting rhizobacteria, we used combinations of three plant species and three rhizobacterial species and interrogated plant shoot chemistry by untargeted metabolomics. A substantial part (50%-64%) of the metabolites detected in plant shoot tissue was differentially affected by the rhizobacteria. Among others, the phenylpropanoid pathway was targeted by the rhizobacteria in each of the three plant species. Differential regulation of the various branches of the phenylpropanoid pathways showed an association with either plant growth promotion or growth reduction. Overall, suppression of flavonoid biosynthesis was associated with growth promotion, while growth reduction showed elevated levels of flavonoids. Subsequent assays with 12 Arabidopsis flavonoid biosynthetic mutants revealed that the proanthocyanidin branch plays an essential role in rhizobacteria-mediated growth promotion. Our study also showed that a number of pharmaceutically and nutritionally relevant metabolites in the plant shoot were significantly increased by rhizobacterial treatment, providing new avenues to use rhizobacteria to tilt plant metabolism towards the biosynthesis of valuable natural plant products.},
}
@article {pmid35750182,
year = {2022},
author = {Mishra, S and Wang, W and Xia, S and Lin, L and Yang, X},
title = {Spatial pattern of functional genes abundance reveals the importance of PhoD gene harboring bacterial community for maintaining plant growth in the tropical forest of Southwestern China.},
journal = {The Science of the total environment},
volume = {842},
number = {},
pages = {156863},
doi = {10.1016/j.scitotenv.2022.156863},
pmid = {35750182},
issn = {1879-1026},
mesh = {Bacteria/genetics ; China ; Ecosystem ; Forests ; Humans ; *Microbiota ; Phosphorus/analysis ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {The concept of microbial functional genes has added a new dimension to microbial ecology research by improving the model of microbial community-ecosystem functions relationship. However, our knowledge vis-à-vis fine-scale spatial distribution pattern of functional genes and their probable impact on plant community in the hyper-diverse tropical forest ecosystem is very limited. Here, we investigated the spatial pattern of functional genes abundance (NirK, AOA, AOB, and PhoD), identified key influencing factors, and distinguished the key functional group supporting the plant community in a tropical rainforest located in Xishuangbanna. In total, 200 soil samples and vegetation data of ~4800 individuals of plants across a 1 ha study area were collected. Our results detected higher spatial variability with a maximum magnitude of abundance for PhoD gene (4.53 × 10[7] copies) followed by NirK (2.71 × 10[6] copies), AOA (1.97 × 10[6] copies), and AOB (7.38 × 10[4] copies). A strong spatial dependence was observed for PhoD and NirK over the distance of 17 and 18 m, respectively. Interestingly, the N:P stoichiometry played a critical role in structuring the spatial pattern of the most abundant PhoD gene. The significant positive and negative relationship of PhoD with N:P ratio and available phosphorus, respectively, indicated that the P-limiting environment was a driving factor for recruitment of PhoD gene community. The structural equation modeling ascertained the direct positive impact of PhoD on plant biomass and high demand of available P by plants suggesting that the organic phosphorus mineralization process is essential to maintain plant productivity by re-establishing the availability of the most limiting P nutrient. Our preliminary study improves our understanding of how microbial functional genes-environment associations could be used for monitoring soil health and its overall impact on ecosystem multifunctionality. Finally, we intend to conduct the study at a large spatial scale for achieving a holistic view.},
}
@article {pmid35749983,
year = {2022},
author = {Chavez-Rico, VS and Bodelier, PLE and van Eekert, M and Sechi, V and Veeken, A and Buisman, C},
title = {Producing organic amendments: Physicochemical changes in biowaste used in anaerobic digestion, composting, and fermentation.},
journal = {Waste management (New York, N.Y.)},
volume = {149},
number = {},
pages = {177-185},
doi = {10.1016/j.wasman.2022.06.005},
pmid = {35749983},
issn = {1879-2456},
mesh = {Anaerobiosis ; Carbon ; *Composting/methods ; Fermentation ; Soil/chemistry ; },
abstract = {Organic amendments (OAs) produced via composting, anaerobic digestion, or lactic acid fermentation, can be used to replenish soil carbon. Not all OAs production technologies preserve C and nutrients in the same way. In this study, we compared the influence of these technologies (i.e., treatments) on C and nutrient preservation and OAs chemical composition after production. We produced compost, digestate, and lactic-acid fermentation product using the same biowaste-resembling model substrate using three reactors under laboratory conditions. We compared the chemical conversions and end-products using mass balances over C, N, and P. Overall results show that losses are minimal under reducing production conditions. Fermentation and digestion conserved 99% and 64% of C; and 93% and 100% of N, respectively. While compost conservation of nutrients was limited to 25% of C and 38% of N. Digestate had the highest concentrations of C, N, and P in the water-soluble phase, enabling their accessibility for soil microbes. Concentrations in the fermentation product were one order of magnitude lower but still higher than in compost. The treatments also influence the final availability of C, N, and P, which could potentially improve the fertilising and soil-improving properties of produced OAs. Our results show that under reducing conditions, losses of C, N, and P can be decreased while increasing OAs applications in terms of sources for soil-microbial development.},
}
@article {pmid35749381,
year = {2022},
author = {Favila, N and Madrigal-Trejo, D and Legorreta, D and Sánchez-Pérez, J and Espinosa-Asuar, L and Eguiarte, LE and Souza, V},
title = {MicNet toolbox: Visualizing and unraveling a microbial network.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0259756},
pmid = {35749381},
issn = {1932-6203},
mesh = {Cluster Analysis ; Computational Biology/methods ; Microbial Consortia ; *Microbiota ; *Software ; },
abstract = {Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code's functions with ease.},
}
@article {pmid35746816,
year = {2022},
author = {Aguirre Sourrouille, Z and Schwarzer, S and Lequime, S and Oksanen, HM and Quax, TEF},
title = {The Viral Susceptibility of the Haloferax Species.},
journal = {Viruses},
volume = {14},
number = {6},
pages = {},
pmid = {35746816},
issn = {1999-4915},
mesh = {Archaea ; DNA Viruses ; Genomics ; *Haloferax/genetics ; Host Specificity ; },
abstract = {Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus-host model systems. Euryarchaea belonging to the genus Haloferax are interesting models, as a reliable genetic system and versatile microscopy methods are available. However, only one virus infecting the Haloferax species is currently available. In this study, we tested ~100 haloarchaeal virus isolates for their infectivity on 14 Haloferax strains. From this, we identified 10 virus isolates in total capable of infecting Haloferax strains, which represented myovirus or siphovirus morphotypes. Surprisingly, the only susceptible strain of all 14 tested was Haloferax gibbonsii LR2-5, which serves as an auspicious host for all of these 10 viruses. By applying comparative genomics, we shed light on factors determining the host range of haloarchaeal viruses on Haloferax. We anticipate our study to be a starting point in the study of haloarchaeal virus-host interactions.},
}
@article {pmid35745275,
year = {2022},
author = {Natividad, JM and Marsaux, B and Rodenas, CLG and Rytz, A and Vandevijver, G and Marzorati, M and Van den Abbeele, P and Calatayud, M and Rochat, F},
title = {Human Milk Oligosaccharides and Lactose Differentially Affect Infant Gut Microbiota and Intestinal Barrier In Vitro.},
journal = {Nutrients},
volume = {14},
number = {12},
pages = {},
pmid = {35745275},
issn = {2072-6643},
support = {NA//Nestl&#xe9; Research, Soci&#xe9;t&#xe9; des Produits Nestl&#xe9;/ ; 812969//European Union's Horizon 2020 research and innovation program/ ; },
mesh = {Caco-2 Cells ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Lactose/metabolism/pharmacology ; *Milk, Human/metabolism ; Oligosaccharides/metabolism ; },
abstract = {BACKGROUND: The infant gut microbiota establishes during a critical window of opportunity when metabolic and immune functions are highly susceptible to environmental changes, such as diet. Human milk oligosaccharides (HMOs) for instance are suggested to be beneficial for infant health and gut microbiota. Infant formulas supplemented with the HMOs 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT) reduce infant morbidity and medication use and promote beneficial bacteria in the infant gut ecosystem. To further improve infant formula and achieve closer proximity to human milk composition, more complex HMO mixtures could be added. However, we currently lack knowledge about their effects on infants' gut ecosystems.<br><br>METHOD: We assessed the effect of lactose, 2'-FL, 2'-FL + LNnT, and a mixture of six HMOs (HMO6: consisting of 2'-FL, LNnT, difucosyllactose, lacto-N-tetraose, 3'- and 6'-sialyllactose) on infant gut microbiota and intestinal barrier integrity using a combination of in vitro models to mimic the microbial ecosystem (baby M-SHIME[&#xae;]) and the intestinal epithelium (Caco-2/HT29-MTX co-culture).<br><br>RESULTS: All the tested products had bifidogenic potential and increased SCFA levels; however, only the HMOs' fermented media protected against inflammatory intestinal barrier disruption. 2'-FL/LNnT and HMO6 promoted the highest diversification of OTUs within the Bifidobactericeae family, whereas beneficial butyrate-producers were specifically enriched by HMO6.<br><br>CONCLUSION: These results suggest that increased complexity in HMO mixture composition may benefit the infant gut ecosystem, promoting different bifidobacterial communities and protecting the gut barrier against pro-inflammatory imbalances.},
}
@article {pmid35744740,
year = {2022},
author = {Kozień, &#x141; and Gallienne, E and Martin, O and Front, S and Strus, M and Heczko, P},
title = {PDIA, an Iminosugar Compound with a Wide Biofilm Inhibitory Spectrum Covering Both Gram-Positive and Gram-Negative Human Bacterial Pathogens.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
pmid = {35744740},
issn = {2076-2607},
support = {2018/31/B/NZ6/02443//National Science Center/ ; N N401 547040//National Science Center/ ; },
abstract = {Many difficult-to-treat human infections related to catheters and other indwelling devices are caused by bacteria residing in biofilms. One of the key properties of microorganisms residing in a biofilm is decreased susceptibility towards antimicrobial agents. Therefore, many different approaches have been researched to destroy or inhibit biofilm production by bacteria. Different iminosugars (IS) were reported to inhibit biofilm formation in S. mutans, S. aureus, and P. aeruginosa. The aim of this study was to look for a spectrum of the activity in one of these IS. The iminosugar PDIA beta-1-C-propyl-1,4-dideoxy-1,4-imino-L-arabinitol was tested in vitro at the same concentration against 30 different strains of the most important Gram-negative and Gram-positive human pathogens looking for their biofilm production and viability at different time intervals. It appeared that PDIA inhibited biofilm production of Enterobacter spp., P. aeruginosa, Enterococcus spp. and S. aureus in 8 h, and Klebsiella spp., Acinetobacter spp. and S.epidermidis in 24 h. PDIA caused no growth inhibition of the tested bacteria at a concentration of 0.9 mM. Our results indicate a broad-spectrum biofilm inhibitory activity of PDIA. which may be the basis for future application studies that will help in control of the associated device and biofilm-related infections caused by a wide spectrum of the causative agents.},
}
@article {pmid35744736,
year = {2022},
author = {Shi, Z and Kong, Q and Li, X and Xu, W and Mao, C and Wang, Y and Song, W and Huang, J},
title = {The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
pmid = {35744736},
issn = {2076-2607},
support = {2018YFD0900701//the National Key Research and Development Program of China/ ; 31801984, 32030015//National Natural Science Foundation of China/ ; 2019333//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; },
abstract = {DNA based sequencing technology has revolutionized the field of microbial ecology and environmental studies. However, biases can be introduced at all experimental steps and, thus, affect the interpretation of microbial community. So far, previous studies on the biases introduced from the key steps of DNA extraction and primer sets mainly focused on the bacterial communities in soil or sediment samples, while little is known about the effect on the eukaryotic microbial communities. Here, we studied the effects of three different DNA extraction kits on both prokaryotic and micro-eukaryotic communities by 16S and 18S rRNA gene amplicon sequencing, and further disentangled the influence of primer choice on the micro-eukaryotic communities. Our results showed that the FastDNA SPIN Kit for Soil and DNeasy PowerSoil Kit produced much higher DNA yield with good reproducibility, and observed more eukaryotic OTUs compared to the MinkaGene DNA extraction kit, but all three kits exhibited comparable ability in recovering bacterial alpha diversity. Of the two primer sets, both targeting the V4 region of the 18S rRNA gene, the TAR primer set detected higher number of unique OTUs than the EK primer set, while the EK primer set resulted in longer amplicons and better reproducibility between replicates. Based on our findings, we recommend using the DNeasy PowerSoil Kit with the EK primer set to capture the abundant micro-eukaryotic taxa from freshwater sediment samples. If a more complete picture of the eukaryotic microbial community is desired, the TAR primer set in combination with the FastDNA SPIN Kit is more efficient in this study.},
}
@article {pmid35744686,
year = {2022},
author = {Hossain, KS and Amarasena, S and Mayengbam, S},
title = {B Vitamins and Their Roles in Gut Health.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
pmid = {35744686},
issn = {2076-2607},
support = {Funding no. 20210719//Memorial University of Newfoundland/ ; },
abstract = {B vitamins act as coenzymes in a myriad of cellular reactions. These include energy production, methyl donor generation, neurotransmitter synthesis, and immune functions. Due to the ubiquitous roles of these vitamins, their deficiencies significantly affect the host's metabolism. Recently, novel roles of B vitamins in the homeostasis of gut microbial ecology and intestinal health continue to be unravelled. This review focuses on the functional roles and biosynthesis of B vitamins and how these vitamins influence the growth and proliferation of the gut microbiota. We have identified the gut bacteria that can produce vitamins, and their biosynthetic mechanisms are presented. The effects of B vitamin deficiencies on intestinal morphology, inflammation, and its effects on intestinal disorders are also discussed.},
}
@article {pmid35744611,
year = {2022},
author = {Costa, OYA and de Hollander, M and Kuramae, EE and Bodelier, PLE},
title = {PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
pmid = {35744611},
issn = {2076-2607},
abstract = {The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets.},
}
@article {pmid35741397,
year = {2022},
author = {Micci, A and Zhang, Q and Chang, X and Kingsley, K and Park, L and Chiaranunt, P and Strickland, R and Velazquez, F and Lindert, S and Elmore, M and Vines, PL and Crane, S and Irizarry, I and Kowalski, KP and Johnston-Monje, D and White, JF},
title = {Histochemical Evidence for Nitrogen-Transfer Endosymbiosis in Non-Photosynthetic Cells of Leaves and Inflorescence Bracts of Angiosperms.},
journal = {Biology},
volume = {11},
number = {6},
pages = {},
pmid = {35741397},
issn = {2079-7737},
abstract = {We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. Through histochemical analysis, we detected hormones (including ethylene and nitric oxide), superoxide, and nitrogenous chemicals (including nitric oxide and nitrate) around bacteria within plant cells. Bacteria were observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. Most notably, bacteria showing nitrate formation based on histochemical staining were present in glandular trichomes of some dicots (e.g., Humulus lupulus and Cannabis sativa). Glandular trichome chemistry is hypothesized to function to scavenge oxygen around bacteria and reduce oxidative damage to intracellular bacterial cells. Experiments to assess the differential absorption of isotopic nitrogen into plants suggest the assimilation of nitrogen into actively growing tissues of plants, where bacteria are most active and carbohydrates are more available. The leaf and bract cell endosymbiosis types outlined in this paper have not been previously reported and may be important in facilitating plant growth, development, oxidative stress resistance, and nutrient absorption into plants. It is unknown whether leaf and bract cell endosymbioses are significant in increasing the nitrogen content of plants. From the experiments that we conducted, it is impossible to know whether plant trichomes evolved specifically as organs for nitrogen fixation or if, instead, trichomes are structures in which bacteria easily colonize and where some casual nitrogen transfer may occur between bacteria and plant cells. It is likely that the endosymbioses seen in leaves and bracts are less efficient than those of root nodules of legumes in similar plants. However, the presence of endosymbioses that yield nitrate in plants could confer a reduced need for soil nitrogen and constitute increased nitrogen-use efficiency, even if the actual amount of nitrogen transferred to plant cells is small. More research is needed to evaluate the importance of nitrogen transfer within leaf and bract cells of plants.},
}
@article {pmid35739682,
year = {2022},
author = {Wang, C and Wang, L and Ok, YS and Tsang, DCW and Hou, D},
title = {Soil plastisphere: Exploration methods, influencing factors, and ecological insights.},
journal = {Journal of hazardous materials},
volume = {430},
number = {},
pages = {128503},
doi = {10.1016/j.jhazmat.2022.128503},
pmid = {35739682},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; Ecosystem ; Microplastics ; *Plastics ; *Soil/chemistry ; },
abstract = {Microplastic (MP), an emerging contaminant, is globally prevalent and poses potential environmental threats and ecological risks to both aquatic and terrestrial ecosystems. When MPs enter into natural environments, they may serve as artificial substrates for microbial colonization and plastisphere formation, providing new ecological niches for microorganisms. Recent studies of the plastisphere have focused on aquatic ecosystems. However, our understanding of the soil plastisphere e.g. its formation process, microbial ecology, co-transport of organic pollutants and heavy metals, and effects on biogeochemical processes is still very limited. This review summarizes latest methods used to explore the soil plastisphere, assesses the factors influencing the microbial ecology of the soil plastisphere, and sheds light on potential ecological risks caused by the soil plastisphere. The formation and succession of soil plastisphere communities can be driven by MP characteristics and soil environmental factors. The soil plastisphere may affect a series of ecological processes, especially the co-transport of environmental contaminants, biodegradation of MPs, and soil carbon cycling. We aim to narrow the knowledge gap between the soil and aquatic plastisphere, and provide valuable guidance for future research on the soil plastisphere in MP-contaminated soils.},
}
@article {pmid35739580,
year = {2022},
author = {Dey, S and Rout, AK and Behera, BK and Ghosh, K},
title = {Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {32},
pmid = {35739580},
issn = {2524-6372},
abstract = {It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.},
}
@article {pmid35739325,
year = {2023},
author = {Legeay, J and Hijri, M},
title = {A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {75-85},
pmid = {35739325},
issn = {1432-184X},
mesh = {*Soil ; *Microbiota ; Geography ; Soil Microbiology ; },
abstract = {In the last decade, various large-scale projects describing soil microbial diversity across large geographical gradients have been undertaken. However, many questions remain unanswered about the best ways to conduct these studies. In this review, we present an overview of the experience gathered during these projects, and of the challenges that future projects will face, such as standardization of protocols and results, considering the temporal variation of microbiomes, and the legal constraints limiting such studies. We also present the arguments for and against the exhaustive description of soil microbiomes. Finally, we look at future developments of soil microbiome studies, notably emphasizing the important role of cultivation techniques.},
}
@article {pmid35738377,
year = {2022},
author = {Merino, N and Jackson, TR and Campbell, JH and Kersting, AB and Sackett, J and Fisher, JC and Bruckner, JC and Zavarin, M and Hamilton-Brehm, SD and Moser, DP},
title = {Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow.},
journal = {The Science of the total environment},
volume = {842},
number = {},
pages = {156768},
doi = {10.1016/j.scitotenv.2022.156768},
pmid = {35738377},
issn = {1879-1026},
mesh = {Geology ; *Groundwater/chemistry ; Hydrology ; *Microbiota ; Nevada ; },
abstract = {Subsurface microbial community distribution patterns are influenced by biogeochemical and groundwater fluxes and may inform hydraulic connections along groundwater-flow paths. This study examined the regional-scale microbial community of the Death Valley Regional Flow System and evaluated whether subsurface communities can be used to identify groundwater-flow paths between recharge and discharge areas. Samples were collected from 36 sites in three groundwater basins: Pahute Mesa-Oasis Valley (PMOV), Ash Meadows (AM), and Alkali Flat-Furnace Creek Ranch (AFFCR). Microbial diversity within and between communities varied by location, and communities were separated into two overall groups that affiliated with the AM and PMOV/AFFCR basins. Network analysis revealed patterns between clusters of common microbes that represented groundwaters with similar geochemical conditions and largely corroborated hydraulic connections between recharge and discharge areas. Null model analyses identified deterministic and stochastic ecological processes contributing to microbial community assemblages. Most communities were more different than expected and governed by dispersal limitation, geochemical differences, or undominating processes. However, certain communities from sites located within or near the Nevada National Security Site were more similar than expected and dominated by homogeneous dispersal or selection. Overall, the (dis)similarities between the microbial communities of DVRFS recharge and discharge areas supported previously documented hydraulic connections between: (1) Spring Mountains and Ash Meadows; (2) Frenchman and Yucca Flat and Amargosa Desert; and (3) Amargosa Desert and Death Valley. However, only a portion of the flow path between Pahute Mesa and Oasis Valley could be supported by microbial community analyses, likely due to well-associated artifacts in samples from the two Oasis Valley sites. This study demonstrates the utility of combining microbial data with hydrologic, geologic, and water-chemistry information to comprehensively characterize groundwater systems, highlighting both strengths and limitations of this approach.},
}
@article {pmid35730934,
year = {2022},
author = {Morris, MM and Kimbrel, JA and Geng, H and Tran-Gyamfi, MB and Yu, ET and Sale, KL and Lane, TW and Mayali, X},
title = {Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina.},
journal = {mSphere},
volume = {7},
number = {4},
pages = {e0023122},
pmid = {35730934},
issn = {2379-5042},
mesh = {*Biofuels ; Biomass ; Metagenome ; *Microbiota ; Symbiosis ; },
abstract = {Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function of the algal microbiome that coinhabits these ecosystems. Here, we describe the assembly mechanisms, taxonomic structure, and metabolic potential of bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated with algal cultures that were either free of bacteria or coincubated with one of two different strains of alga-associated bacteria and were sampled across five time points taken over multiple harvesting rounds of a 40-day experiment. Using quantitative analyses of metagenome-assembled genomes (MAGs), we tracked bacterial community compositional abundance and taxon-specific functional capacity involved in algal-bacterial interactions. One of the inoculated bacteria (Alteromonas sp.) persisted and dispersed across mesocosms, whereas the other inoculated strain (Phaeobacter gallaeciensis) disappeared by day 17 while a taxonomically similar but functionally distinct Phaeobacter strain became established. The inoculated strains were less abundant than 6 numerically dominant newly recruited taxa with functional capacities for mutualistic or saprophytic lifestyles, suggesting a generalist approach to persistence. This includes a highly abundant unclassified Rhodobacteraceae species that fluctuated between 25% and 77% of the total community. Overall, we did not find evidence for priority effects exerted by the distinct inoculum conditions; all mesocosms converged with similar microbial community compositions by the end of the experiment. Instead, we infer that the 15 total populations were retained due to host selection, as they showed high metabolic potential for algal-bacterial interactions such as recycling alga-produced carbon and nitrogen and production of vitamins and secondary metabolites associated with algal growth and senescence, including B vitamins, tropodithietic acid, and roseobacticides. IMPORTANCE Bacteria proliferate in nutrient-rich aquatic environments, including engineered algal biofuel systems, where they remineralize photosynthates, exchange secondary metabolites with algae, and can influence system output of biomass or oil. Despite this, knowledge on the microbial ecology of algal cultivation systems is lacking, and the subject is worthy of investigation. Here, we used metagenomics to characterize the metabolic capacities of the predominant bacteria associated with the biofuel-relevant microalga Microchloropsis salina and to predict testable metabolic interactions between algae and manipulated communities of bacteria. We identified a previously undescribed and uncultivated organism that dominated the community. Collectively, the microbial community may interact with the alga in cultivation via exchange of secondary metabolites which could affect algal success, which we demonstrate as a possible outcome from controlled experiments with metabolically analogous isolates. These findings address the scalability of lab-based algal-bacterial interactions through to cultivation systems and more broadly provide a framework for empirical testing of genome-based metabolic predictions.},
}
@article {pmid35729185,
year = {2022},
author = {Beterams, A and Calatayud Arroyo, M and De Paepe, K and De Craemer, AS and Elewaut, D and Venken, K and Van de Wiele, T},
title = {In vitro triple coculture with gut microbiota from spondyloarthritis patients is characterized by inter-individual differences in inflammatory responses.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10475},
pmid = {35729185},
issn = {2045-2322},
mesh = {Coculture Techniques ; *Gastrointestinal Microbiome ; Humans ; Individuality ; Phylogeny ; *Spondylarthritis ; },
abstract = {Spondyloarthritis is a group of chronic inflammatory diseases that primarily affects axial or peripheral joints and is frequently associated with inflammation at non-articular sites. The disease is multifactorial, involving genetics, immunity and environmental factors, including the gut microbiota. In vivo, microbiome contributions are difficult to assess due to the multifactorial disease complexity. In a proof-of-concept approach, we therefore used a triple coculture model of immune-like, goblet and epithelial cells to investigate whether we could detect a differential impact from spondyloarthritis- vs. healthy-derived gut microbiota on host cell response. Despite their phylogenetic resemblance, flow cytometry-based phenotypic clustering revealed human-derived gut microbiota from healthy origin to cluster together and apart from spondyloarthritis donors. At host level, mucus production was higher upon exposure to healthy microbiota. Pro-inflammatory cytokine responses displayed more inter-individual variability in spondyloarthritis than in healthy donors. Interestingly, the high dominance in the initial sample of one patient of Prevotella, a genus previously linked to spondyloarthritis, resulted in the most differential host response upon 16 h host-microbe coincubation. While future research should further focus on inter-individual variability by using gut microbiota from a large cohort of patients, this study underscores the importance of the gut microbiota during the SpA disease course.},
}
@article {pmid35726107,
year = {2022},
author = {Khuntia, HK and Paliwal, A and Kumar, DR and Chanakya, HN},
title = {Review on solid-state anaerobic digestion of lignocellulosic biomass and organic solid waste.},
journal = {Environmental monitoring and assessment},
volume = {194},
number = {7},
pages = {514},
pmid = {35726107},
issn = {1573-2959},
mesh = {Anaerobiosis ; Biofuels/analysis ; Biomass ; Bioreactors ; Environmental Monitoring ; Lignin ; Methane ; *Refuse Disposal/methods ; *Solid Waste/analysis ; },
abstract = {Sustainable management of organic solid wastes especially the municipal solid waste (MSW) is essential for the realization of various sustainable development goals (SDGs). Resource recovery centric waste processing technologies generate valorizable products to meet the operations and maintenance (O&amp;M) costs while reducing the GHG emissions. Solid-state anaerobic digestion (SSAD) of organic solid wastes is a biomethanation process performed at a relatively higher total solids (TS) loading in the range of 10-45%. SSAD overcomes various limitations posed by conventional anaerobic slurry digesters such as higher degradable matter per unit volume of the bioreactor resulting in a smaller footprint, low freshwater consumption, low wastewater generation, simple upstream and downstream processes, relatively lower operation, and maintenance costs. This review elucidates the recent developments and critical assessment of different aspects of SSAD, such as bioreactor design, operational strategy, process performances, mass balance, microbial ecology, applications, and mathematical models. A critical assessment revealed that the operating scale of SSAD varies between 1000 and 100,000 ts/year at organic loading rate (OLR) of 2-15 g volatile solids (VS)/L·day. The SSAD experiences process failures due to the formation of volatile fatty acids (VFAs), biogas pockets and clogging of the digestate outlet. Acclimatization of microbes accelerates the startup phase, steady-state performances, and the enrichment of syntrophic microbes with 10-50 times greater population of cellulolytic and xylanolytic microbes in thermophilic SSAD over mesophilic SSAD. Experimental limitations in the accurate determination of rate constants and the oversimplification of biochemical reactions result in an inaccurate prediction by the models.},
}
@article {pmid35724776,
year = {2022},
author = {Chang, J and van Veen, JA and Tian, C and Kuramae, EE},
title = {A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production.},
journal = {The Science of the total environment},
volume = {842},
number = {},
pages = {156706},
doi = {10.1016/j.scitotenv.2022.156706},
pmid = {35724776},
issn = {1879-1026},
mesh = {Crop Production ; Crops, Agricultural/microbiology ; Domestication ; Edible Grain ; *Microbiota ; *Mycorrhizae ; *Oryza/microbiology ; Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; },
abstract = {The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.},
}
@article {pmid35722352,
year = {2022},
author = {Paddock, KJ and Finke, DL and Kim, KS and Sappington, TW and Hibbard, BE},
title = {Patterns of Microbiome Composition Vary Across Spatial Scales in a Specialist Insect.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {898744},
pmid = {35722352},
issn = {1664-302X},
abstract = {Microbial communities associated with animals vary based on both intrinsic and extrinsic factors. Of many possible determinants affecting microbiome composition, host phylogeny, host diet, and local environment are the most important. How these factors interact across spatial scales is not well understood. Here, we seek to identify the main influences on microbiome composition in a specialist insect, the western corn rootworm (WCR; Diabrotica virgifera virgifera), by analyzing the bacterial communities of adults collected from their obligate host plant, corn (Zea mays), across several geographic locations and comparing the patterns in communities to its congeneric species, the northern corn rootworm (NCR; Diabrotica barberi). We found that bacterial communities of WCR and NCR shared a portion of their bacterial communities even when collected from disparate locations. However, within each species, the location of collection significantly influenced the composition of their microbiome. Correlations of geographic distance between sites with WCR bacterial community composition revealed different patterns at different spatial scales. Community similarity decreased with increased geographic distance at smaller spatial scales (~25 km between the nearest sites). At broad spatial scales (>200 km), community composition was not correlated with distances between sites, but instead reflected the historical invasion path of WCR across the United States. These results suggest bacterial communities are structured directly by dispersal dynamics at small, regional spatial scales, while landscape-level genetic or environmental differences may drive community composition across broad spatial scales in this specialist insect.},
}
@article {pmid35722289,
year = {2022},
author = {Rocha, ADL and Ferrari, RG and Pereira, WE and de Lima, LA and Givisiez, PEN and Moreno-Switt, AI and Toro, M and Delgado-Suárez, EJ and Meng, J and de Oliveira, CJB},
title = {Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {802625},
pmid = {35722289},
issn = {1664-302X},
support = {U01 FD001418/FD/FDA HHS/United States ; },
abstract = {The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.},
}
@article {pmid35722279,
year = {2022},
author = {Egenriether, S and Sanford, R and Yang, WH and Kent, AD},
title = {Nitrogen Cycling Microbial Diversity and Operational Taxonomic Unit Clustering: When to Prioritize Accuracy Over Speed.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {730340},
pmid = {35722279},
issn = {1664-302X},
abstract = {BACKGROUND: Assessments of the soil microbiome provide valuable insight to ecosystem function due to the integral role microorganisms play in biogeochemical cycling of carbon and nutrients. For example, treatment effects on nitrogen cycling functional groups are often presented alongside one another to demonstrate how agricultural management practices affect various nitrogen cycling processes. However, the functional groups commonly evaluated in nitrogen cycling microbiome studies range from phylogenetically narrow (e.g., N-fixation, nitrification) to broad [e.g., denitrification, dissimilatory nitrate reduction to ammonium (DNRA)]. The bioinformatics methods used in such studies were developed for 16S rRNA gene sequence data, and how these tools perform across functional genes of different phylogenetic diversity has not been established. For example, an OTU clustering method that can accurately characterize sequences harboring comparatively little diversity may not accurately resolve the diversity within a gene comprised of a large number of clades. This study uses two nitrogen cycling genes, nifH, a gene which segregates into only three distinct clades, and nrfA, a gene which is comprised of at least eighteen clades, to investigate differences which may arise when using heuristic OTU clustering (abundance-based greedy clustering, AGC) vs. true hierarchical OTU clustering (Matthews Correlation Coefficient optimizing algorithm, Opti-MCC). Detection of treatment differences for each gene were evaluated to demonstrate how conclusions drawn from a given dataset may differ depending on clustering method used.<br><br>RESULTS: The heuristic and hierarchical methods performed comparably for the more conserved gene, nifH. The hierarchical method outperformed the heuristic method for the more diverse gene, nrfA; this included both the ability to detect treatment differences using PERMANOVA, as well as higher resolution in taxonomic classification. The difference in performance between the two methods may be traced to the AGC method's preferential assignment of sequences to the most abundant OTUs: when analysis was limited to only the largest 100 OTUs, results from the AGC-assembled OTU table more closely resembled those of the Opti-MCC OTU table. Additionally, both AGC and Opti-MCC OTU tables detected comparable treatment differences using the rank-based ANOSIM test. This demonstrates that treatment differences were preserved using both clustering methods but were structured differently within the OTU tables produced using each method.<br><br>CONCLUSION: For questions which can be answered using tests agnostic to clustering method (e.g., ANOSIM), or for genes of relatively low phylogenetic diversity (e.g., nifH), most upstream processing methods should lead to similar conclusions from downstream analyses. For studies involving more diverse genes, however, care should be exercised to choose methods that ensure accurate clustering for all genes. This will mitigate the risk of introducing Type II errors by allowing for detection of comparable treatment differences for all genes assessed, rather than disproportionately detecting treatment differences in only low-diversity genes.},
}
@article {pmid35720594,
year = {2022},
author = {Kong, Z and Liu, H},
title = {Modification of Rhizosphere Microbial Communities: A Possible Mechanism of Plant Growth Promoting Rhizobacteria Enhancing Plant Growth and Fitness.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {920813},
pmid = {35720594},
issn = {1664-462X},
abstract = {Plant beneficial bacteria, defined as plant growth-promoting rhizobacteria (PGPR), play a crucial role in plants' growth, stress tolerance and disease prevention. In association with the rhizosphere of plants, PGPR facilitate plant growth and development either directly or indirectly through multiple mechanisms, including increasing available mineral nutrients, moderating phytohormone levels and acting as biocontrol agents of phytopathogens. It is generally accepted that the effectiveness of PGPR inoculants is associated with their ability to colonize, survive and persist, as well as the complex network of interactions in the rhizosphere. Despite the promising plant growth promotion results commonly reported and mostly attributed to phytohormones or other organic compounds produced by PGPR inoculants, little information is available on the potential mechanisms underlying such positive effects via modifying rhizosphere microbial community and soil functionality. In this review, we overviewed the effects of PGPR inoculants on rhizosphere microbial ecology and soil function, hypothesizing that PGPR may indirectly promote plant growth and health via modifying the composition and functioning of rhizosphere microbial community, and highlighting the further directions for investigating the role of PGPR in rhizosphere from an ecological perspective.},
}
@article {pmid35717339,
year = {2022},
author = {Grote, M},
title = {Microbes before microbiology: Christian Gottfried Ehrenberg and Berlin's infusoria.},
journal = {Endeavour},
volume = {46},
number = {1-2},
pages = {100815},
doi = {10.1016/j.endeavour.2022.100815},
pmid = {35717339},
issn = {1873-1929},
mesh = {*Bacteria ; Berlin ; Christianity ; *Historiography ; },
abstract = {Naturalist Christian Gottfried Ehrenberg pioneered research on living and fossil infusoria (including protists and bacteria) since the 1830s by collecting samples from all over the world, thus describing numerous microbes and discussing their effects for the planet and for humankind. This article introduces Ehrenberg as a natural historian of microbes and situates his work in the nineteenth century life sciences with respect to debates about cell theory, evolution, and concepts of disease. I argue that in spite of occurring before these major conceptual innovations of the life sciences, Ehrenberg's work on the diversity of microbes found in earth or air is more exciting than historiography has made it appear so far, especially in light of today's ecological microbiology.},
}
@article {pmid35714745,
year = {2022},
author = {DeVilbiss, SE and Steele, MK and Brown, BL and Badgley, BD},
title = {Stream bacterial diversity peaks at intermediate freshwater salinity and varies by salt type.},
journal = {The Science of the total environment},
volume = {840},
number = {},
pages = {156690},
doi = {10.1016/j.scitotenv.2022.156690},
pmid = {35714745},
issn = {1879-1026},
mesh = {Bacteria ; Chlorides/chemistry ; Fresh Water/chemistry ; *Rivers/chemistry ; *Salinity ; Salts ; Sodium Chloride ; },
abstract = {Anthropogenic freshwater salinization is an emerging and widespread water quality stressor that increases salt concentrations of freshwater, where specific upland land-uses produce distinct ionic profiles. In-situ studies find salinization in disturbed landscapes is correlated with declines in stream bacterial diversity, but cannot isolate the effects of salinization from multiple co-occurring stressors. By manipulating salt concentration and type in controlled microcosm studies, we identified direct and complex effects of freshwater salinization on bacterial diversity in the absence of other stressors common in field studies using chloride salts. Changes in both salt concentration and cation produced distinct bacterial communities. Bacterial richness, or the total number of amplicon sequence variants (ASVs) detected, increased at conductivities as low as 350 μS cm[-1], which is opposite the observations from field studies. Richness remained elevated at conductivities as high as 1500 μS cm[-1] in communities exposed to a mixture of Ca, Mg, and K chloride salts, but decreased in communities exposed to NaCl, revealing a classic subsidy-stress response. Exposure to different chloride salts at the same conductivity resulted in distinct bacterial community structure, further supporting that salt type modulates responses of bacterial communities to freshwater salinization. Community variability peaked at 125-350 μS cm[-1] and was more similar at lower and upper conductivities suggesting possible shifts in deterministic vs. stochastic assembly mechanisms across freshwater salinity gradients. Based on these results, we hypothesize that modest freshwater salinization (125-350 μS cm[-1]) lessens hypo-osmotic stress, reducing the importance of salinity as an environmental filter at intermediate freshwater ranges but effects of higher salinities at the upper freshwater range differ based on salt type. Our results also support previous findings that ~300 μS cm[-1] is a biological effect concentration and effective salt management strategies may need to consider variable effects of different salt types associated with land-use.},
}
@article {pmid35714546,
year = {2022},
author = {Kazmi, SSUH and Uroosa, and Warren, A and Zhong, X and Xu, H},
title = {Corrigendum to "Insights into the ecotoxicity of nitrofurazone in marine ecosystems based on body-size spectra of periphytic ciliates" [Mar. Pollut. Bull. 174 (2022) 113217 1-8].},
journal = {Marine pollution bulletin},
volume = {181},
number = {},
pages = {113841},
doi = {10.1016/j.marpolbul.2022.113841},
pmid = {35714546},
issn = {1879-3363},
}
@article {pmid35713683,
year = {2023},
author = {Lau, NS and Ting, SY and Sam, KK and M, J and Wong, SC and Wu, X and Waiho, K and Fazhan, H and Shu-Chien, AC},
title = {Correction to: Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {589},
doi = {10.1007/s00248-022-02059-9},
pmid = {35713683},
issn = {1432-184X},
}
@article {pmid35713682,
year = {2023},
author = {Sandy, M and Bui, TI and Abá, KS and Ruiz, N and Paszalek, J and Connor, EW and Hawkes, CV},
title = {Plant Host Traits Mediated by Foliar Fungal Symbionts and Secondary Metabolites.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {408-418},
pmid = {35713682},
issn = {1432-184X},
support = {2017-67013-29207//National Institute of Food and Agriculture/ ; HATCH accesssion no 1018688//National Institute of Food and Agriculture/ ; },
mesh = {*Endophytes/physiology ; Plants ; Phenotype ; Biomass ; Plant Physiological Phenomena ; *Panicum/microbiology ; Fungi/genetics ; },
abstract = {Fungal symbionts living inside plant leaves ("endophytes") can vary from beneficial to parasitic, but the mechanisms by which the fungi affect the plant host phenotype remain poorly understood. Chemical interactions are likely the proximal mechanism of interaction between foliar endophytes and the plant, as individual fungal strains are often exploited for their diverse secondary metabolite production. Here, we go beyond single strains to examine commonalities in how 16 fungal endophytes shift plant phenotypic traits such as growth and physiology, and how those relate to plant metabolomics profiles. We inoculated individual fungi on switchgrass, Panicum virgatum L. This created a limited range of plant growth and physiology (2-370% of fungus-free controls on average), but effects of most fungi overlapped, indicating functional similarities in unstressed conditions. Overall plant metabolomics profiles included almost 2000 metabolites, which were broadly correlated with plant traits across all the fungal treatments. Terpenoid-rich samples were associated with larger, more physiologically active plants and phenolic-rich samples were associated with smaller, less active plants. Only 47 metabolites were enriched in plants inoculated with fungi relative to fungus-free controls, and of these, Lasso regression identified 12 metabolites that explained from 14 to 43% of plant trait variation. Fungal long-chain fatty acids and sterol precursors were positively associated with plant photosynthesis, conductance, and shoot biomass, but negatively associated with survival. The phytohormone gibberellin, in contrast, was negatively associated with plant physiology and biomass. These results can inform ongoing efforts to develop metabolites as crop management tools, either by direct application or via breeding, by identifying how associations with more beneficial components of the microbiome may be affected.},
}
@article {pmid35712047,
year = {2022},
author = {Guseva, K and Darcy, S and Simon, E and Alteio, LV and Montesinos-Navarro, A and Kaiser, C},
title = {From diversity to complexity: Microbial networks in soils.},
journal = {Soil biology &amp; biochemistry},
volume = {169},
number = {},
pages = {108604},
pmid = {35712047},
issn = {0038-0717},
abstract = {Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial communities. However, this approach is unfortunately often used to draw conclusions which are far beyond the scientific evidence it can provide, which has damaged its reputation for soil microbial analysis. In this Perspectives Paper, we would like to sharpen the view for the real potential of microbial co-occurrence analysis in soils, and at the same time raise awareness regarding its limitations and the many ways how it can be misused or misinterpreted.},
}
@article {pmid35711777,
year = {2022},
author = {Jiang, Y and Luo, J and Huang, D and Liu, Y and Li, DD},
title = {Machine Learning Advances in Microbiology: A Review of Methods and Applications.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {925454},
pmid = {35711777},
issn = {1664-302X},
abstract = {Microorganisms play an important role in natural material and elemental cycles. Many common and general biology research techniques rely on microorganisms. Machine learning has been gradually integrated with multiple fields of study. Machine learning, including deep learning, aims to use mathematical insights to optimize variational functions to aid microbiology using various types of available data to help humans organize and apply collective knowledge of various research objects in a systematic and scaled manner. Classification and prediction have become the main achievements in the development of microbial community research in the direction of computational biology. This review summarizes the application and development of machine learning and deep learning in the field of microbiology and shows and compares the advantages and disadvantages of different algorithm tools in four fields: microbiome and taxonomy, microbial ecology, pathogen and epidemiology, and drug discovery.},
}
@article {pmid35711776,
year = {2022},
author = {You, J and Zhang, H and Zhu, H and Xue, Y and Cai, Y and Zhang, G},
title = {Microbial Community, Fermentation Quality, and in vitro Degradability of Ensiling Caragana With Lactic Acid Bacteria and Rice Bran.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {804429},
pmid = {35711776},
issn = {1664-302X},
abstract = {This study aimed to assess the effects of microbial inoculants and growth stage on fermentation quality, microbial community, and in vitro degradability of Caragana silage from different varieties. Caragana intermedia (CI) and Caragana korshinskii (CK) harvested at the budding (BU) and blooming (BL) stages were used as raw materials to prepare silage, respectively. The silages at each growth stage were treated for ensiling alone (control), with 5% rice bran (RB), a combination of RB with commercial Lactobacillus plantarum (RB + LP), and a combination of RB with a selected strain Lactobacillus plantarum L694 (RB + L694). The results showed that the crude protein (CP) content of CI was higher than that of CK, and delay in harvest resulted in greater CP content in Caragana at BL stage. After 60 days of fermentation, the concentrations of lactic acid (LA) in the RB + L694 treatments were higher than those in control treatments (p < 0.05), while the pH, concentrations of NH3-N, neutral detergent fiber with the addition of α-amylase (aNDF) were lower than those in control treatments (p < 0.05). RB + L694 treatments could decrease acid detergent fiber (ADF) content except in CIBL. In CK silages, adding RB + L694 could reduce bacterial diversity and richness (p < 0.05). Compared with the control, RB + L694 treatment contained higher Lactobacillus and Enterobacter (p < 0.05). In vitro NDF and DM degradability (IVNDFD and IVDMD) was mostly affected by growth period, and additive RB + l694 treatment had higher IVDMD and lower IVNDFD than other treatments (p < 0.05). Consequently, the varieties, growth stages, and additives could influence the fermentation process, while the blooming stage should be selected in both Caragana. Furthermore, the results showed that RB and L. plantarum could exert a positive effect on fermentation quality of Caragana silage by shifting bacterial community composition, and RB + L694 treatments outperformed other additives.},
}
@article {pmid35711751,
year = {2022},
author = {Bannon, C and Rapp, I and Bertrand, EM},
title = {Community Interaction Co-limitation: Nutrient Limitation in a Marine Microbial Community Context.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {846890},
pmid = {35711751},
issn = {1664-302X},
abstract = {The simultaneous limitation of productivity by two or more nutrients, commonly referred to as nutrient co-limitation, affects microbial communities throughout the marine environment and is of profound importance because of its impacts on various biogeochemical cycles. Multiple types of co-limitation have been described, enabling distinctions based on the hypothesized mechanisms of co-limitation at a biochemical level. These definitions usually pertain to individuals and do not explicitly, or even implicitly, consider complex ecological dynamics found within a microbial community. However, limiting and co-limiting nutrients can be produced in situ by a subset of microbial community members, suggesting that interactions within communities can underpin co-limitation. To address this, we propose a new category of nutrient co-limitation, community interaction co-limitation (CIC). During CIC, one part of the community is limited by one nutrient, which results in the insufficient production or transformation of a biologically produced nutrient that is required by another part of the community, often primary producers. Using cobalamin (vitamin B12) and nitrogen fixation as our models, we outline three different ways CIC can arise based on current literature and discuss CIC's role in biogeochemical cycles. Accounting for the inherent and complex roles microbial community interactions play in generating this type of co-limitation requires an expanded toolset - beyond the traditional approaches used to identify and study other types of co-limitation. We propose incorporating processes and theories well-known in microbial ecology and evolution to provide meaningful insight into the controls of community-based feedback loops and mechanisms that give rise to CIC in the environment. Finally, we highlight the data gaps that limit our understanding of CIC mechanisms and suggest methods to overcome these and further identify causes and consequences of CIC. By providing this framework for understanding and identifying CIC, we enable systematic examination of the impacts this co-limitation can have on current and future marine biogeochemical processes.},
}
@article {pmid35710629,
year = {2022},
author = {Oyserman, BO and Flores, SS and Griffioen, T and Pan, X and van der Wijk, E and Pronk, L and Lokhorst, W and Nurfikari, A and Paulson, JN and Movassagh, M and Stopnisek, N and Kupczok, A and Cordovez, V and Carrión, VJ and Ligterink, W and Snoek, BL and Medema, MH and Raaijmakers, JM},
title = {Disentangling the genetic basis of rhizosphere microbiome assembly in tomato.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3228},
pmid = {35710629},
issn = {2041-1723},
support = {U01 GM110706/GM/NIGMS NIH HHS/United States ; },
mesh = {Iron/metabolism ; *Solanum lycopersicum/metabolism ; *Microbiota/genetics ; Plant Breeding ; Plants/metabolism ; Rhizosphere ; },
abstract = {Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.},
}
@article {pmid35710200,
year = {2022},
author = {Antosiak, A and Šulčius, S and Malec, P and Tokodi, N and Łobodzińska, A and Dziga, D},
title = {Cyanophage infections reduce photosynthetic activity and expression of CO2 fixation genes in the freshwater bloom-forming cyanobacterium Aphanizomenon flos-aquae.},
journal = {Harmful algae},
volume = {116},
number = {},
pages = {102215},
doi = {10.1016/j.hal.2022.102215},
pmid = {35710200},
issn = {1878-1470},
mesh = {Aphanizomenon ; Carbon ; *Carbon Dioxide ; *Cyanobacteria ; DNA Replication ; DNA, Viral ; Ecosystem ; Fresh Water ; Photosynthesis ; Virus Replication ; },
abstract = {Cyanobacteria play a significant role in ecosystem functioning as photosynthetic and CO2 fixing microorganisms. Whether and to what extent cyanophages alter these carbon and energy cycles in their cyanobacterial hosts is still poorly understood. In this study, we investigated changes in photosynthetic activity (PSII), expression of genes associated with the light phase of photosynthesis (psbA, petA, ndhK) and carbon metabolism (rbcL, zwf) as well as intracellular ATP and NADHP concentrations in freshwater bloom-forming filamentous cyanobacterium Aphanizomenon flos-aquae infected by cyanophage vB_AphaS-CL131. We found that PSII activity and expression level of rbcL genes, indicating potential for CO2 fixation, had decreased in response to cyanophage adsorption and DNA injection. During the period of viral DNA replication and assembly, PSII performance and gene expression remained at this decreased level and did not change significantly, indicating lack of transcriptional shutdown by the cyanophage. Combined, these observations suggest that although there is little to no interference between cyanophage DNA replication, host transcription and cellular metabolism, A. flos-aquae underwent a physiological state-shift toward lower efficiency of carbon and energy cycling. This further suggest potential cascading effect for co-occurring non-infected members of the microbial community.},
}
@article {pmid35706139,
year = {2022},
author = {Purkamo, L and Ó Dochartaigh, B and MacDonald, A and Cousins, C},
title = {Following the flow-Microbial ecology in surface- and groundwaters in the glacial forefield of a rapidly retreating glacier in Iceland.},
journal = {Environmental microbiology},
volume = {24},
number = {12},
pages = {5840-5858},
pmid = {35706139},
issn = {1462-2920},
mesh = {Ice Cover/microbiology ; Iceland ; Rivers ; *Microbiota ; *Groundwater ; },
abstract = {The retreat of glaciers in response to climate change has major impacts on the hydrology and ecosystems of glacier forefield catchments. Microbes are key players in ecosystem functionality, supporting the supply of ecosystem services that glacier systems provide. The interaction between surface and groundwaters in glacier forefields has only recently gained much attention, and how these interactions influence the microbiology is still unclear. Here, we identify the microbial communities in groundwater from shallow (<15 m deep) boreholes in a glacial forefield floodplain ('sandur') aquifer at different distances from the rapidly retreating Virkisjökull glacier, Iceland, and with varying hydraulic connectivity with the glacial meltwater river that flows over the sandur. Groundwater communities are shown to differ from those in nearby glacial and non-glacial surface water communities. Groundwater-meltwater interactions and groundwater flow dynamics affect the microbial community structure, leading to different microbial communities at different sampling points in the glacier forefield. Groundwater communities differ from those in nearby glacial and non-glacial surface waters. Functional potential for microbial nitrogen and methane cycling was detected, although the functional gene copy numbers of specific groups were low.},
}
@article {pmid35705745,
year = {2023},
author = {Song, L and Wang, Y and Zhang, R and Yang, S},
title = {Microbial Mediation of Carbon, Nitrogen, and Sulfur Cycles During Solid Waste Decomposition.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {311-324},
pmid = {35705745},
issn = {1432-184X},
support = {52000016//National Natural Science Foundation of China/ ; 51578642//National Natural Science Foundation of China/ ; },
mesh = {*Solid Waste/analysis ; Nitrogen/analysis ; Carbon ; RNA, Ribosomal, 16S/genetics ; Carbon Dioxide ; Bacteria/genetics ; Archaea/genetics ; *Microbiota ; Sulfur ; Waste Disposal Facilities ; },
abstract = {Landfills are a unique "terrestrial ecosystem" and serve as a significant carbon sink. Microorganisms convert biodegradable substances in municipal solid waste (MSW) to CH4, CO2, and microbial biomass, consisting of the carbon cycling in landfills. Microbial-mediated N and S cycles are also the important biogeochemical process during MSW decomposition, resulting in N2O and H2S emission, respectively. Meanwhile, microbial-mediated N and S cycles affect carbon cycling. How microbial community structure and function respond to C, N, and S cycling during solid waste decomposition, however, are not well-characterized. Here, we show the response of bacterial and archaeal community structure and functions to C, N, and S cycling during solid waste decomposition in a long-term (265 days) operation laboratory-scale bioreactor through 16S rRNA-based pyrosequencing and metagenomics analysis. Bacterial and archaeal community composition varied during solid waste decomposition. Aerobic respiration was the main pathway for CO2 emission, while anaerobic C fixation was the main pathway in carbon fixation. Methanogenesis and denitrification increased during solid waste decomposition, suggesting increasing CH4 and N2O emission. In contract, fermentation decreased along solid waste decomposition. Interestingly, Clostridiales were abundant and showed potential for several pathways in C, N, and S cycling. Archaea were involved in many pathways of C and N cycles. There is a shift between bacteria and archaea involvement in N2 fixation along solid waste decomposition that bacteria Clostridiales and Bacteroidales were initially dominant and then Methanosarcinales increased and became dominant in methanogenic phase. These results provide extensive microbial mediation of C, N, and S cycling profiles during solid waste decomposition.},
}
@article {pmid35705744,
year = {2023},
author = {García-Sánchez, JC and Arredondo-Centeno, J and Segovia-Ramírez, MG and Tenorio Olvera, AM and Parra-Olea, G and Vredenburg, VT and Rovito, SM},
title = {Factors Influencing Bacterial and Fungal Skin Communities of Montane Salamanders of Central Mexico.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {670-686},
pmid = {35705744},
issn = {1432-184X},
support = {221614//Conacyt/ ; 2015-01-721//Conacyt/ ; 1633948//National Science Foundation/ ; },
mesh = {Animals ; *Urodela/microbiology ; *Mycobiome ; Mexico ; Phylogeny ; Amphibians/microbiology ; Bacteria/genetics ; Skin/microbiology ; },
abstract = {Host microbial communities are increasingly seen as an important component of host health. In amphibians, the first land vertebrates that are threatened by a fungal skin disease globally, our understanding of the factors influencing the microbiome of amphibian skin remains incomplete because recent studies have focused almost exclusively on bacteria, and little information exists on fungal communities associated with wild amphibian species. In this study, we describe the effects of host phylogeny, climate, geographic distance, and infection with a fungal pathogen on the composition and structure of bacterial and fungal communities in seven tropical salamander species that occur in the Trans-Mexican Volcanic Belt of Central Mexico. We find that host phylogenetic relatedness is correlated with bacterial community composition while a composite climatic variable of temperature seasonality and precipitation is significantly associated with fungal community composition. We also estimated co-occurrence networks for bacterial and fungal taxa and found differences in the degree of connectivity and the distribution of negative associations between the two networks. Our results suggest that different factors may be responsible for structuring the bacterial and fungal communities of amphibian skin and that the inclusion of fungi in future studies could shed light on important functional interactions within the microbiome.},
}
@article {pmid35703548,
year = {2022},
author = {Honeyman, AS and Fegel, TS and Peel, HF and Masters, NA and Vuono, DC and Kleiber, W and Rhoades, CC and Spear, JR},
title = {Statistical Learning and Uncommon Soil Microbiota Explain Biogeochemical Responses after Wildfire.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {13},
pages = {e0034322},
pmid = {35703548},
issn = {1098-5336},
mesh = {*Fires ; *Microbiota ; Soil ; Water Quality ; *Wildfires ; },
abstract = {Wildfires are a perennial event globally, and the biogeochemical underpinnings of soil responses at relevant spatial and temporal scales are unclear. Soil biogeochemical processes regulate plant growth and nutrient losses that affect water quality, yet the response of soil after variable intensity fire is difficult to explain and predict. To address this issue, we examined two wildfires in Colorado, United States, across the first and second postfire years and leveraged statistical learning (SL) to predict and explain biogeochemical responses. We found that SL predicts biogeochemical responses in soil after wildfire with surprising accuracy. Of the 13 biogeochemical analytes analyzed in this study, 9 are best explained with a hybrid microbiome + biogeochemical SL model. Biogeochemical-only models best explain 3 features, and 1 feature is explained equally well with the hybrid and biogeochemical-only models. In some cases, microbiome-only SL models are also effective (such as predicting NH4[+]). Whenever a microbiome component is employed, selected features always involve uncommon soil microbiota (i.e., the "rare biosphere" [existing at <1% mean relative abundance]). Here, we demonstrate that SL paired with DNA sequence and biogeochemical data predicts environmental features in postfire soils, although this approach could likely be applied to any biogeochemical system. IMPORTANCE Soil biogeochemical processes are critical to plant growth and water quality and are substantially disturbed by wildfire. However, soil responses to fire are difficult to predict. To address this issue, we developed a large environmental data set that tracks postfire changes in soil and used statistical learning (SL) to build models that exploit complex data to make predictions about biogeochemical responses. Here, we show that SL depends upon uncommon microbiota in soil (the "rare biosphere") to make surprisingly accurate predictions about soil biogeochemical responses to wildfire. Using SL to explain variation in a natively chaotic environmental system is mechanism independent. Likely, the approach that we describe for combining SL with microbiome and biogeochemical parameters has practical applications across a range of issues in the environmental sciences where predicting responses would be useful.},
}
@article {pmid35701635,
year = {2023},
author = {Vignale, FA and Bernal Rey, D and Pardo, AM and Almasqué, FJ and Ibarra, JG and Fernández Do Porto, D and Turjanski, AG and López, NI and Helman, RJM and Raiger Iustman, LJ},
title = {Spatial and Seasonal Variations in the Bacterial Community of an Anthropogenic Impacted Urban Stream.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {862-874},
pmid = {35701635},
issn = {1432-184X},
support = {PUE2016 22920160100064CO//conicet/ ; 20020170200338BA//Secretar&#xed;a de Ciencia y T&#xe9;cnica, Universidad de Buenos Aires/ ; 20020170100310BA//Secretar&#xed;a de Ciencia y T&#xe9;cnica, Universidad de Buenos Aires/ ; },
mesh = {Humans ; *Rivers/microbiology ; Seasons ; RNA, Ribosomal, 16S/genetics ; *Anthropogenic Effects ; Bacteria/genetics ; },
abstract = {Environmental changes and human activities can alter the structure and diversity of aquatic microbial communities. In this work, we analyzed the bacterial community dynamics of an urban stream to understand how these factors affect the composition of river microbial communities. Samples were taken from a stream situated in Buenos Aires, Argentina, which flows through residential, peri-urban horticultural, and industrial areas. For sampling, two stations were selected: one influenced by a series of industrial waste treatment plants and horticultural farms (PL), and the other influenced by residential areas (R). Microbial communities were analyzed by sequence analysis of 16S rRNA gene amplicons along an annual cycle. PL samples showed high nutrient content compared with R samples. The diversity and richness of the R site were more affected by seasonality than those of the PL site. At the amplicon sequence variants level, beta diversity analysis showed a differentiation between cool-season (fall and winter) and warm-season (spring and summer) samples, as well as between PL and R sites. This demonstrated that there is spatial and temporal heterogeneity in the composition of the bacterial community, which should be considered if a bioremediation strategy is applied. The taxonomic composition analysis also revealed a differential seasonal cycle of phototrophs and chemoheterotrophs between the sampling sites, as well as different taxa associated with each sampling site. This analysis, combined with a comparative analysis of global rivers, allowed us to determine the genera Arcobacter, Simplicispira, Vogesella, and Sphingomonas as potential bioindicators of anthropogenic disturbance.},
}
@article {pmid35700773,
year = {2022},
author = {Chen, H and Pan, Y and Zhou, Q and Liang, C and Wong, CC and Zhou, Y and Huang, D and Liu, W and Zhai, J and Gou, H and Su, H and Zhang, X and Xu, H and Wang, Y and Kang, W and Kei Wu, WK and Yu, J},
title = {METTL3 Inhibits Antitumor Immunity by Targeting m[6]A-BHLHE41-CXCL1/CXCR2 Axis to Promote Colorectal Cancer.},
journal = {Gastroenterology},
volume = {163},
number = {4},
pages = {891-907},
doi = {10.1053/j.gastro.2022.06.024},
pmid = {35700773},
issn = {1528-0012},
mesh = {Animals ; Basic Helix-Loop-Helix Transcription Factors ; *CD8-Positive T-Lymphocytes/metabolism ; Cell Line, Tumor ; Chemokine CXCL1 ; *Colorectal Neoplasms/pathology ; Cytokines/metabolism ; Humans ; Methyltransferases/genetics/metabolism ; Mice ; Mice, Knockout ; Phenylurea Compounds ; Receptors, Interleukin-8B/genetics/metabolism ; Triazoles ; RNA, Guide, CRISPR-Cas Systems ; },
abstract = {BACKGROUND &amp; AIMS: N[6]-Methyladenosine (m[6]A) is the most prevalent RNA modification and recognized as an important epitranscriptomic mechanism in colorectal cancer (CRC). We aimed to exploit whether and how tumor-intrinsic m[6]A modification driven by methyltransferase like 3 (METTL3) can dictate the immune landscape of CRC.<br><br>METHODS: Mettl3 knockout mice, CD34[+] humanized mice, and different syngeneic mice models were used. Immune cell composition and cytokine level were analyzed by flow cytometry and Cytokine 23-Plex immunoassay, respectively. M[6]A sequencing and RNA sequencing were performed to identify downstream targets and pathways of METTL3. Human CRC specimens (n&#xa0;= 176) were used to evaluate correlation between METTL3 expression and myeloid-derived suppressor cell (MDSC) infiltration.<br><br>RESULTS: We demonstrated that silencing of METTL3 in CRC cells reduced MDSC accumulation to sustain activation and proliferation of CD4[+] and CD8[+] T cells, and eventually suppressed CRC in Apc[Min/+]Mettl3[+/-] mice, CD34[+] humanized mice, and syngeneic mice models. Mechanistically, METTL3 activated the m[6]A-BHLHE41-CXCL1 axis by analysis of m[6]A sequencing, RNA sequencing, and cytokine arrays. METTL3 promoted BHLHE41 expression in an m[6]A-dependent manner, which subsequently induced CXCL1 transcription to enhance MDSC migration in&#xa0;vitro. However, the effect was negligible on BHLHE41 depletion, CXCL1 protein or CXCR2 inhibitor SB265610 administration, inferring that METTL3 promotes MDSC migration via BHLHE41-CXCL1/CXCR2. Consistently, depletion of MDSCs by anti-Gr1 antibody or SB265610 blocked the tumor-promoting effect of METTL3 in&#xa0;vivo. Importantly, targeting METTL3 by METTL3-single guide RNA or specific inhibitor potentiated the effect of anti-programmed cell death protein 1 (anti-PD1) treatment.<br><br>CONCLUSIONS: Our study identifies METTL3 as a potential therapeutic target for CRC immunotherapy whose inhibition reverses immune suppression through the m[6]A-BHLHE41-CXCL1 axis. METTL3 inhibition plus anti-PD1 treatment shows promising antitumor efficacy against CRC.},
}
@article {pmid35700135,
year = {2022},
author = {Deng, Z and Hou, K and Valencak, TG and Luo, XM and Liu, J and Wang, H},
title = {AI-2/LuxS Quorum Sensing System Promotes Biofilm Formation of Lactobacillus rhamnosus GG and Enhances the Resistance to Enterotoxigenic Escherichia coli in Germ-Free Zebrafish.},
journal = {Microbiology spectrum},
volume = {10},
number = {4},
pages = {e0061022},
pmid = {35700135},
issn = {2165-0497},
mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Biofilms ; Carbon-Sulfur Lyases/genetics/metabolism ; *Enterotoxigenic Escherichia coli/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Inflammation ; *Lacticaseibacillus rhamnosus/metabolism ; Quorum Sensing ; Zebrafish/metabolism ; },
abstract = {The LuxS enzyme plays a key role in both quorum sensing (QS) and the regulation of bacterial growth. It catalyzes the production of autoinducer-2 (AI-2) signaling molecule, which is a component of the methyl cycle and methionine metabolism. This study aimed at investigating the differences between the Lactobacillus rhamnosus GG (LGG) wild-type strain (WT) and its luxS mutant (ΔluxS) during biofilm formation and when resisting to inflammation caused by Enterotoxigenic Escherichia coli (ETEC) in germ-free zebrafish. Our results suggest that in the absence of luxS when LGG was knocked out, biofilm formation, extracellular polysaccharide secretion and adhesion were all compromised. Addition of synthetic AI-2 indeed rescued, at least partially, the deficiencies observed in the mutant strain. The colonizing and immunomodulatory function in WT versus ΔluxS mutants were further studied in a germ-free zebrafish model. The concentration of AI-2 signaling molecules decreased sharply in zebrafish infected with the ΔluxS. At the same time, compared with the ΔluxS, the wild-type strain could colonize the germ-free zebrafish more effectively. Our transcriptome results suggest that genes involved in immunity, signal transduction, and cell adhesion were downregulated in zebrafish infected with ΔluxS and WT. In the WT, the immune system of germ-free zebrafish was activated more effectively through the MAPK and NF-κB pathway, and its ability to fight the infection against ETEC was increased. Together, our results demonstrate that the AI-2/LuxS system plays an important role in biofilm formation to improve LGG and alleviate inflammation caused by ETEC in germ-free zebrafish. IMPORTANCE Lactobacillus rhamnosus GG is a widely used probiotic to improve host intestinal health, promote growth, reduce diarrhea, and modulate immunity. In recent years, the bacterial quorum sensing system has attracted much attention; however, there has not been much research on the effect of the LuxS/AI-2 quorum sensing system of Lactobacillus on bacteriostasis, microbial ecology balance, and immune regulation in intestine. In this study, we used germ-free zebrafish as an animal model to compare the differences between wild-type and luxS mutant strains. We showed how AI-2/LuxS QS affects the release of AI-2 and how QS regulates the colonization, EPS synthesis and biofilm formation of LGG. This study provides an idea for the targeted regulation of animal intestinal health with probiotics by controlling bacteria quorum sensing system.},
}
@article {pmid35697795,
year = {2022},
author = {Wu, L and Zhang, Y and Guo, X and Ning, D and Zhou, X and Feng, J and Yuan, MM and Liu, S and Guo, J and Gao, Z and Ma, J and Kuang, J and Jian, S and Han, S and Yang, Z and Ouyang, Y and Fu, Y and Xiao, N and Liu, X and Wu, L and Zhou, A and Yang, Y and Tiedje, JM and Zhou, J},
title = {Reduction of microbial diversity in grassland soil is driven by long-term climate warming.},
journal = {Nature microbiology},
volume = {7},
number = {7},
pages = {1054-1062},
pmid = {35697795},
issn = {2058-5276},
mesh = {Bacteria ; Biodiversity ; Ecosystem ; *Grassland ; *Soil ; Soil Microbiology ; },
abstract = {Anthropogenic climate change threatens ecosystem functioning. Soil biodiversity is essential for maintaining the health of terrestrial systems, but how climate change affects the richness and abundance of soil microbial communities remains unresolved. We examined the effects of warming, altered precipitation and annual biomass removal on grassland soil bacterial, fungal and protistan communities over 7 years to determine how these representative climate changes impact microbial biodiversity and ecosystem functioning. We show that experimental warming and the concomitant reductions in soil moisture play a predominant role in shaping microbial biodiversity by decreasing the richness of bacteria (9.6%), fungi (14.5%) and protists (7.5%). Our results also show positive associations between microbial biodiversity and ecosystem functional processes, such as gross primary productivity and microbial biomass. We conclude that the detrimental effects of biodiversity loss might be more severe in a warmer world.},
}
@article {pmid35697683,
year = {2022},
author = {Paredes, GF and Viehboeck, T and Markert, S and Mausz, MA and Sato, Y and Liebeke, M and König, L and Bulgheresi, S},
title = {Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9725},
pmid = {35697683},
issn = {2045-2322},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P28743-B22/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; Chromadorea ; *Chromatiaceae ; Hypoxia ; *Nematoda/microbiology ; Oxygen/metabolism ; Sand ; Sulfides ; Sulfur/metabolism ; },
abstract = {Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also highly expressed when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worm's Toll-like innate immunity pathway and several immune effectors (e.g., bactericidal/permeability-increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires the oxidative phosphorylation and reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.},
}
@article {pmid35697586,
year = {2022},
author = {Ayeni, KI and Berry, D and Wisgrill, L and Warth, B and Ezekiel, CN},
title = {Early-life chemical exposome and gut microbiome development: African research perspectives within a global environmental health context.},
journal = {Trends in microbiology},
volume = {30},
number = {11},
pages = {1084-1100},
doi = {10.1016/j.tim.2022.05.008},
pmid = {35697586},
issn = {1878-4380},
mesh = {Adult ; Dysbiosis/chemically induced ; Environmental Health ; *Exposome ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; *Metals, Heavy ; *Mycotoxins ; *Pesticide Residues ; Xenobiotics ; },
abstract = {The gut microbiome of neonates, infants, and toddlers (NITs) is very dynamic, and only begins to stabilize towards the third year of life. Within this period, exposure to xenobiotics may perturb the gut environment, thereby driving or contributing to microbial dysbiosis, which may negatively impact health into adulthood. Despite exposure of NITs globally, but especially in Africa, to copious amounts and types of xenobiotics - such as mycotoxins, pesticide residues, and heavy metals - little is known about their influence on the early-life microbiome or their effects on acute or long-term health. Within the African context, the influence of fermented foods, herbal mixtures, and the delivery environment on the early-life microbiome are often neglected, despite being potentially important factors that influence the microbiome. Consequently, data on in-depth understanding of the microbiome-exposome interactions is lacking in African cohorts. Collecting and evaluating such data is important because exposome-induced gut dysbiosis could potentially favor disease progression.},
}
@article {pmid35696896,
year = {2022},
author = {Kazmi, SSUH and Uroosa, and Xu, H and Xuexi, T},
title = {Corrigendum to "An approach to determining the nitrofurazone-induced toxic dynamics for ecotoxicity assessment using protozoan periphytons in marine ecosystems" [Mar. Pollut. Bull. 175 (2022) 113329 1-7].},
journal = {Marine pollution bulletin},
volume = {180},
number = {},
pages = {113836},
doi = {10.1016/j.marpolbul.2022.113836},
pmid = {35696896},
issn = {1879-3363},
}
@article {pmid35695510,
year = {2022},
author = {Maciá-Vicente, JG and Bai, B and Qi, R and Ploch, S and Breider, F and Thines, M},
title = {Nutrient Availability Does Not Affect Community Assembly in Root-Associated Fungi but Determines Fungal Effects on Plant Growth.},
journal = {mSystems},
volume = {7},
number = {3},
pages = {e0030422},
pmid = {35695510},
issn = {2379-5077},
mesh = {Plant Roots ; Symbiosis ; *Arabidopsis ; *Mycorrhizae/physiology ; Plants ; *Microbiota ; Nutrients ; },
abstract = {Nonmycorrhizal root-colonizing fungi are key determinants of plant growth, driving processes ranging from pathogenesis to stress alleviation. Evidence suggests that they might also facilitate host access to soil nutrients in a mycorrhiza-like manner, but the extent of their direct contribution to plant nutrition is unknown. To study how widespread such capacity is across root-colonizing fungi, we surveyed soils in nutrient-limiting habitats using plant baits to look for fungal community changes in response to nutrient conditions. We established a fungal culture collection and used Arabidopsis thaliana inoculation bioassays to assess the ability of fungi to facilitate host's growth in the presence of organic nutrients unavailable to plants. Plant baits captured a representation of fungal communities extant in natural habitats and showed that nutrient limitation has little influence on community assembly. Arabidopsis thaliana inoculated with 31 phylogenetically diverse fungi exhibited a consistent fungus-driven growth promotion when supplied with organic nutrients compared to untreated plants. However, direct phosphorus measurement and RNA-seq data did not support enhanced nutrient uptake but rather that growth effects may result from changes in the plant's immune response to colonization. The widespread and consistent host responses to fungal colonization suggest that distinct, locally adapted nonmycorrhizal fungi affect plant performance across habitats. IMPORTANCE Recent studies have shown that root-associated fungi that do not engage in classical mycorrhizal associations can facilitate the hosts' access to nutrients in a mycorrhiza-like manner. However, the generality of this capacity remains to be tested. Root-associated fungi are frequently deemed major determinants of plant diversity and performance, but in the vast majority of cases their ecological roles in nature remain unknown. Assessing how these plant symbionts affect plant productivity, diversity, and fitness is important to understanding how plant communities function. Recent years have seen important advances in the understanding of the main drivers of the diversity and structure of plant microbiomes, but a major challenge is still linking community properties with function. This study contributes to the understanding of the cryptic function of root-associated fungi by testing their ability to participate in a specific process: nutrient acquisition by plants.},
}
@article {pmid35694162,
year = {2022},
author = {Karl, CM and Vidakovic, A and Pjevac, P and Hausmann, B and Schleining, G and Ley, JP and Berry, D and Hans, J and Wendelin, M and König, J and Somoza, V and Lieder, B},
title = {Individual Sweet Taste Perception Influences Salivary Characteristics After Orosensory Stimulation With Sucrose and Noncaloric Sweeteners.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {831726},
pmid = {35694162},
issn = {2296-861X},
abstract = {Emerging evidence points to a major role of salivary flow and viscoelastic properties in taste perception and mouthfeel. It has been proposed that sweet-tasting compounds influence salivary characteristics. However, whether perceived differences in the sensory properties of structurally diverse sweet-tasting compounds contribute to salivary flow and saliva viscoelasticity as part of mouthfeel and overall sweet taste perception remains to be clarified. In this study, we hypothesized that the sensory diversity of sweeteners would differentially change salivary characteristics in response to oral sweet taste stimulation. Therefore, we investigated salivary flow and saliva viscoelasticity from 21 healthy test subjects after orosensory stimulation with sucrose, rebaudioside M (RebM), sucralose, and neohesperidin dihydrochalcone (NHDC) in a crossover design and considered the basal level of selected influencing factors, including the basal oral microbiome. All test compounds enhanced the salivary flow rate by up to 1.51 ± 0.12 g/min for RebM compared to 1.10 ± 0.09 g/min for water within the 1st min after stimulation. The increase in flow rate was moderately correlated with the individually perceived sweet taste (r = 0.3, p < 0.01) but did not differ between the test compounds. The complex viscosity of saliva was not affected by the test compounds, but the analysis of covariance showed that it was associated (p < 0.05) with mucin 5B (Muc5B) concentration. The oral microbiome was of typical composition and diversity but was strongly individual-dependent (permutational analysis of variance (PERMANOVA): R [2] = 0.76, p < 0.001) and was not associated with changes in salivary characteristics. In conclusion, this study indicates an impact of individual sweet taste impressions on the flow rate without measurable changes in the complex viscosity of saliva, which may contribute to the overall taste perception and mouthfeel of sweet-tasting compounds.},
}
@article {pmid35691180,
year = {2022},
author = {Kazmi, SSUH and Uroosa, and Xu, H and Warren, A},
title = {Corrigendum to "A community-based approach to analyzing the ecotoxicity of nitrofurazone using periphytic protozoa" [Mar. Pollut. Bull. 175 (2022) 113165 1-6].},
journal = {Marine pollution bulletin},
volume = {180},
number = {},
pages = {113837},
doi = {10.1016/j.marpolbul.2022.113837},
pmid = {35691180},
issn = {1879-3363},
}
@article {pmid35689685,
year = {2023},
author = {Mills, JG and Selway, CA and Thomas, T and Weyrich, LS and Lowe, AJ},
title = {Schoolyard Biodiversity Determines Short-Term Recovery of Disturbed Skin Microbiota in Children.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {658-669},
pmid = {35689685},
issn = {1432-184X},
mesh = {Humans ; Child ; *Microbiota ; Biodiversity ; Forests ; Skin ; },
abstract = {Creating biodiverse urban habitat has been proposed, with growing empirical support, as an intervention for increasing human microbial diversity and reducing associated diseases. However, ecological understanding of urban biodiversity interventions on human skin microbiota remains limited. Here, we experimentally test the hypotheses that disturbed skin microbiota recover better in outdoor schoolyard environments and that greater biodiversity provides a greater response. Repeating the experiment three times, we disturbed skin microbiota of fifty-seven healthy 10-to-11-year-old students with a skin swab (i.e., cleaning), then exposed them to one school environment-either a 'classroom' (n = 20), 'sports field' (n = 14), or biodiverse 'forest' (n = 23)-for 45 min. Another skin swab followed the exposure to compare 'before' and 'after' microbial communities. After 45 min, the disturbance immediately followed by outdoor exposure, especially the 'forest', had an enriching and diversifying effect on skin microbiota, while 'classroom' exposure homogenised inter-personal variability. Each effect compounded over consecutive days indicating longer-term exposure outcomes. The experimental disturbance also reduced the core skin microbiota, and only outdoor environments were able to replenish lost species richness to core membership (n species > 50% prevalent). Overall, we find that environmental setting, especially including biodiversity, is important in human microbiota recovery periods and that the outdoors provide resilience to skin communities. This work also has implications for the inclusion of short periods of outside or forest exposure in school scheduling. Future investigations of the health impacts of permanent urban biodiversity interventions are needed.},
}
@article {pmid35687346,
year = {2023},
author = {Morata, A and Arroyo, T and Bañuelos, MA and Blanco, P and Briones, A and Cantoral, JM and Castrillo, D and Cordero-Bueso, G and Del Fresno, JM and Escott, C and Escribano-Viana, R and Fernández-González, M and Ferrer, S and García, M and González, C and Gutiérrez, AR and Loira, I and Malfeito-Ferreira, M and Martínez, A and Pardo, I and Ramírez, M and Ruiz-Muñoz, M and Santamaría, P and Suárez-Lepe, JA and Vilela, A and Capozzi, V},
title = {Wine yeast selection in the Iberian Peninsula: Saccharomyces and non-Saccharomyces as drivers of innovation in Spanish and Portuguese wine industries.},
journal = {Critical reviews in food science and nutrition},
volume = {63},
number = {31},
pages = {10899-10927},
doi = {10.1080/10408398.2022.2083574},
pmid = {35687346},
issn = {1549-7852},
mesh = {Saccharomyces cerevisiae ; *Wine/analysis ; Portugal ; Fermentation ; Biotechnology ; *Vitis ; },
abstract = {Yeast selection for the wine industry in Spain started in 1950 for the understanding of the microbial ecology, and for the selection of optimal strains to improve the performance of alcoholic fermentation and the overall wine quality. This process has been strongly developed over the last 30 years, firstly on Saccharomyces cerevisiae, and, lately, with intense activity on non-Saccharomyces. Several thousand yeast strains have been isolated, identified and tested to select those with better performance and/or specific technological properties. The present review proposes a global survey of this massive ex-situ preservation of eukaryotic microorganisms, a reservoir of biotechnological solutions for the wine sector, overviewing relevant screenings that led to the selection of strains from 12 genera and 22 species of oenological significance. In the first part, the attention goes to the selection programmes related to relevant wine-producing areas (i.e. Douro, Extremadura, Galicia, La Mancha and Uclés, Ribera del Duero, Rioja, Sherry area, and Valencia). In the second part, the focus shifted on specific non-Saccharomyces genera/species selected from different Spanish and Portuguese regions, exploited to enhance particular attributes of the wines. A fil rouge of the dissertation is the design of tailored biotechnological solutions for wines typical of given geographic areas.},
}
@article {pmid35685924,
year = {2022},
author = {Barcoto, MO and Rodrigues, A},
title = {Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {812143},
pmid = {35685924},
issn = {1664-302X},
abstract = {Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.},
}
@article {pmid35681050,
year = {2022},
author = {Andreu-Sánchez, S and Aubert, G and Ripoll-Cladellas, A and Henkelman, S and Zhernakova, DV and Sinha, T and Kurilshikov, A and Cenit, MC and Jan Bonder, M and Franke, L and Wijmenga, C and Fu, J and van der Wijst, MGP and Melé, M and Lansdorp, P and Zhernakova, A},
title = {Genetic, parental and lifestyle factors influence telomere length.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {565},
pmid = {35681050},
issn = {2399-3642},
mesh = {*Aging/genetics ; Epigenesis, Genetic ; Female ; Humans ; Life Style ; Parents ; Pregnancy ; *Telomere/genetics ; },
abstract = {The average length of telomere repeats (TL) declines with age and is considered to be a marker of biological ageing. Here, we measured TL in six blood cell types from 1046 individuals using the clinically validated Flow-FISH method. We identified remarkable cell-type-specific variations in TL. Host genetics, environmental, parental and intrinsic factors such as sex, parental age, and smoking are associated to variations in TL. By analysing the genome-wide methylation patterns, we identified that the association of maternal, but not paternal, age to TL is mediated by epigenetics. Single-cell RNA-sequencing data for 62 participants revealed differential gene expression in T-cells. Genes negatively associated with TL were enriched for pathways related to translation and nonsense-mediated decay. Altogether, this study addresses cell-type-specific differences in telomere biology and its relation to cell-type-specific gene expression and highlights how perinatal factors play a role in determining TL, on top of genetics and lifestyle.},
}
@article {pmid35680917,
year = {2022},
author = {Willson, AM and Trugman, AT and Powers, JS and Smith-Martin, CM and Medvigy, D},
title = {Climate and hydraulic traits interact to set thresholds for liana viability.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3332},
pmid = {35680917},
issn = {2041-1723},
mesh = {*Ecosystem ; Forests ; Plants ; Trees ; *Tropical Climate ; },
abstract = {Lianas, or woody vines, and trees dominate the canopy of tropical forests and comprise the majority of tropical aboveground carbon storage. These growth forms respond differently to contemporary variation in climate and resource availability, but their responses to future climate change are poorly understood because there are very few predictive ecosystem models representing lianas. We compile a database of liana functional traits (846 species) and use it to parameterize a mechanistic model of liana-tree competition. The substantial difference between liana and tree hydraulic conductivity represents a critical source of inter-growth form variation. Here, we show that lianas are many times more sensitive to drying atmospheric conditions than trees as a result of this trait difference. Further, we use our competition model and projections of tropical hydroclimate based on Representative Concentration Pathway 4.5 to show that lianas are more susceptible to reaching a hydraulic threshold for viability by 2100.},
}
@article {pmid35680131,
year = {2022},
author = {Kim, HJ and Kim, JH and Han, SA and Kim, W},
title = {Compositional Alterations of the Nasal Microbiome and Staphylococcus aureus-Characterized Dysbiosis in the Nasal Mucosa of Patients With Allergic Rhinitis.},
journal = {Clinical and experimental otorhinolaryngology},
volume = {15},
number = {4},
pages = {335-345},
pmid = {35680131},
issn = {1976-8710},
support = {//National Research Foundation of Korea/ ; 2016R1D1A1B01- 014116//Ministry of Education/ ; 2019M3C9A6091945//Ministry of Education/ ; HI20C0546//Ministry of Health &amp; Welfare of the Republic of Korea/ ; },
abstract = {OBJECTIVES: Host-microbial commensalism can shape the innate immune response in the nasal mucosa, and the microbial characteristics of nasal mucus directly impact the mechanisms of the initial allergic responses in the nasal epithelium. We sought to determine alterations of the microbial composition in the nasal mucus of patients with allergic rhinitis (AR) and to elucidate the interplay between dysbiosis of the nasal microbiome and allergic inflammation.<br><br>METHODS: In total, 364,923 high-quality bacterial 16S ribosomal RNA-encoding gene sequence reads from 104 middle turbinate mucosa samples from healthy participants and patients with AR were obtained and analyzed using the Quantitative Insights into Microbial Ecology pipeline.<br><br>RESULTS: We analyzed the microbiota in samples of nasal mucus from patients with AR (n=42) and clinically healthy participants (n=30). The Proteobacteria (Ralstonia genus) and Actinobacteria (Propionibacterium genus) phyla were predominant in the nasal mucus of healthy subjects, whereas the Firmicutes (Staphylococcus genus) phylum was significantly abundant in the nasal mucus of patients with AR. In particular, the Ralstonia genus was significantly dominant in the clinically healthy subjects. Additional pyrosequencing data from 32 subjects (healthy participants: n=15, AR patients: n=17) revealed a greater abundance of Staphylococcus epidermidis, Corynebacterium accolens, and Nocardia coeliaca, accounting for 41.55% of mapped sequences in the nasal mucus of healthy participants. Dysbiosis of the nasal microbiome was more pronounced in patients with AR, and Staphylococcus aureus exhibited the greatest abundance (37.69%) in their nasal mucus, in association with a positive response to house dust mites and patients' age and height.<br><br>CONCLUSION: This study revealed alterations in the nasal microbiome in the nasal mucus of patients with AR at the levels of microbial genera and species. S. aureus-dominant dysbiosis was distinctive in the nasal mucus of patients with AR, suggesting a role of host-microbial commensalism in allergic inflammation.},
}
@article {pmid35679938,
year = {2022},
author = {Wu, K and Tizzani, R and Zweers, H and Rijnaarts, H and Langenhoff, A and Fernandes, TV},
title = {Removal processes of individual and a mixture of organic micropollutants in the presence of Scenedesmus obliquus.},
journal = {The Science of the total environment},
volume = {838},
number = {Pt 4},
pages = {156526},
doi = {10.1016/j.scitotenv.2022.156526},
pmid = {35679938},
issn = {1879-1026},
mesh = {Carbamazepine ; *Chlorophyceae ; Clarithromycin ; Diclofenac ; Metoprolol ; *Microalgae ; *Scenedesmus ; Wastewater ; *Water Pollutants, Chemical/analysis ; },
abstract = {Organic micropollutants (OMPs) need to be removed from wastewater as they can negatively affect aquatic organisms. It has been demonstrated that microalgae-based technologies are efficient in removing OMPs from wastewater. In this study, the removal processes and kinetics of six persistent OMPs (diclofenac, clarithromycin, benzotriazole, metoprolol, carbamazepine and mecoprop) were studied during cultivation of Scenedesmus obliquus in batch mode. These OMPs were added as individual compounds and in a mixture. Short experiments (8 days) were performed to avoid masking of OMP removal processes by light and nutrient limitation. The results show that diclofenac, clarithromycin, and benzotriazole were mainly removed by photodegradation (diclofenac), biodegradation (benzotriazole), or a combination of these two processes (clarithromycin). Peroxidase was involved in intracellular and extracellular biodegradation when benzotriazole was present as individual compound. Carbamazepine, metoprolol and mecoprop showed no biodegradation or photodegradation, and neglectable removal (<5%) by bioadsorption and bioaccumulation. Using an OMP mixture had an adverse effect on the photodegradation of clarithromycin and diclofenac, with reduced first-order kinetic constants compared to the individual compounds. Benzotriazole biodegradation was inhibited by the presence of the OMP mixture. This indicates that the presence of OMPs inhibits the photodegradation and biodegradation of some individual OMPs. These results will improve our understanding of removal processes of individual and mixtures of OMPs by microalgae-based technologies for wastewater treatment.},
}
@article {pmid35677244,
year = {2022},
author = {Ahmad, M and Imtiaz, M and Shoib Nawaz, M and Mubeen, F and Imran, A},
title = {What Did We Learn From Current Progress in Heat Stress Tolerance in Plants? Can Microbes Be a Solution?.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {794782},
pmid = {35677244},
issn = {1664-462X},
abstract = {Temperature is a significant parameter in agriculture since it controls seed germination and plant growth. Global warming has resulted in an irregular rise in temperature posing a serious threat to the agricultural production around the world. A slight increase in temperature acts as stress and exert an overall negative impact on different developmental stages including plant phenology, development, cellular activities, gene expression, anatomical features, the functional and structural orientation of leaves, twigs, roots, and shoots. These impacts ultimately decrease the biomass, affect reproductive process, decrease flowering and fruiting and significant yield losses. Plants have inherent mechanisms to cope with different stressors including heat which may vary depending upon the type of plant species, duration and degree of the heat stress. Plants initially adapt avoidance and then tolerance strategies to combat heat stress. The tolerance pathway involves ion transporter, osmoprotectants, antioxidants, heat shock protein which help the plants to survive under heat stress. To develop heat-tolerant plants using above-mentioned strategies requires a lot of time, expertise, and resources. On contrary, plant growth-promoting rhizobacteria (PGPRs) is a cost-effective, time-saving, and user-friendly approach to support and enhance agricultural production under a range of environmental conditions including stresses. PGPR produce and regulate various phytohormones, enzymes, and metabolites that help plant to maintain growth under heat stress. They form biofilm, decrease abscisic acid, stimulate root development, enhance heat shock proteins, deamination of ACC enzyme, and nutrient availability especially nitrogen and phosphorous. Despite extensive work done on plant heat stress tolerance in general, very few comprehensive reviews are available on the subject especially the role of microbes for plant heat tolerance. This article reviews the current studies on the retaliation, adaptation, and tolerance to heat stress at the cellular, organellar, and whole plant levels, explains different approaches, and sheds light on how microbes can help to induce heat stress tolerance in plants.},
}
@article {pmid35677075,
year = {2022},
author = {Lai, P and Nguyen, L and Okin, D and Drew, D and Battista, V and Jesudasen, S and Kuntz, T and Bhosle, A and Thompson, K and Reinicke, T and Lo, CH and Woo, J and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Adhikari, UD and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, M and Kwon, D and Huttenhower, C and Chan, A},
title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {35677075},
issn = {2693-5015},
support = {K01 DK120742/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; UL1 TR002541/TR/NCATS NIH HHS/United States ; },
abstract = {The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. We profiled 127 hospitalized patients with COVID-19 (n=79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. 48 species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID", suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with predicting whether stool was obtained from patients with severe vs. moderate COVID-19. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to validate these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.},
}
@article {pmid35676296,
year = {2022},
author = {Suarez, C and Sedlacek, CJ and Gustavsson, DJI and Eiler, A and Modin, O and Hermansson, M and Persson, F},
title = {Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.},
journal = {NPJ biofilms and microbiomes},
volume = {8},
number = {1},
pages = {47},
pmid = {35676296},
issn = {2055-5008},
mesh = {Anaerobic Ammonia Oxidation ; Bacteria/genetics ; Biofilms ; Bioreactors/microbiology ; *Microbiota ; *Nitrites ; },
abstract = {The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.},
}
@article {pmid35675172,
year = {2022},
author = {Jammer, A and Akhtar, SS and Amby, DB and Pandey, C and Mekureyaw, MF and Bak, F and Roth, PM and Roitsch, T},
title = {Enzyme activity profiling for physiological phenotyping within functional phenomics: plant growth and stress responses.},
journal = {Journal of experimental botany},
volume = {73},
number = {15},
pages = {5170-5198},
doi = {10.1093/jxb/erac215},
pmid = {35675172},
issn = {1460-2431},
support = {//Ministry of Education, Youth and Sports of Czech/ ; //NordForsk/ ; //Innovation Fund Denmark/ ; //Novo Nordisk Fonden/ ; },
mesh = {Crops, Agricultural/genetics ; *Phenomics ; Phenotype ; *Plant Breeding ; Plant Development/genetics ; Stress, Physiological/genetics ; },
abstract = {High-throughput profiling of key enzyme activities of carbon, nitrogen, and antioxidant metabolism is emerging as a valuable approach to integrate cell physiological phenotyping into a holistic functional phenomics approach. However, the analyses of the large datasets generated by this method represent a bottleneck, often keeping researchers from exploiting the full potential of their studies. We address these limitations through the exemplary application of a set of data evaluation and visualization tools within a case study. This includes the introduction of multivariate statistical analyses that can easily be implemented in similar studies, allowing researchers to extract more valuable information to identify enzymatic biosignatures. Through a literature meta-analysis, we demonstrate how enzyme activity profiling has already provided functional information on the mechanisms regulating plant development and response mechanisms to abiotic stress and pathogen attack. The high robustness of the distinct enzymatic biosignatures observed during developmental processes and under stress conditions underpins the enormous potential of enzyme activity profiling for future applications in both basic and applied research. Enzyme activity profiling will complement molecular -omics approaches to contribute to the mechanistic understanding required to narrow the genotype-to-phenotype knowledge gap and to identify predictive biomarkers for plant breeding to develop climate-resilient crops.},
}
@article {pmid35672295,
year = {2022},
author = {Catania, T and Li, Y and Winzer, T and Harvey, D and Meade, F and Caridi, A and Leech, A and Larson, TR and Ning, Z and Chang, J and Van de Peer, Y and Graham, IA},
title = {A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3150},
pmid = {35672295},
issn = {2041-1723},
support = {BB/K018809/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Alkaloids/metabolism ; *Benzylisoquinolines/metabolism ; Gene Fusion ; *Morphinans/metabolism ; *Papaver/genetics/metabolism ; Plant Proteins/genetics/metabolism ; },
abstract = {The STORR gene fusion event is considered essential for the evolution of the promorphinan/morphinan subclass of benzylisoquinoline alkaloids (BIAs) in opium poppy as the resulting bi-modular protein performs the isomerization of (S)- to (R)-reticuline essential for their biosynthesis. Here, we show that of the 12 Papaver species analysed those containing the STORR gene fusion also contain promorphinans/morphinans with one important exception. P. californicum encodes a functionally conserved STORR but does not produce promorphinans/morphinans. We also show that the gene fusion event occurred only once, between 16.8-24.1 million years ago before the separation of P. californicum from other Clade 2 Papaver species. The most abundant BIA in P. californicum is (R)-glaucine, a member of the aporphine subclass of BIAs, raising the possibility that STORR, once evolved, contributes to the biosynthesis of more than just the promorphinan/morphinan subclass of BIAs in the Papaveraceae.},
}
@article {pmid35669957,
year = {2022},
author = {Adedayo, AA and Babalola, OO and Prigent-Combaret, C and Cruz, C and Stefan, M and Kutu, F and Glick, BR},
title = {The application of plant growth-promoting rhizobacteria in Solanum lycopersicum production in the agricultural system: a review.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13405},
pmid = {35669957},
issn = {2167-8359},
mesh = {Humans ; Animals ; *Solanum lycopersicum ; Agriculture ; Plant Development ; Plants/microbiology ; Bacteria ; Soil/chemistry ; *Alphaproteobacteria ; },
abstract = {Food safety is a significant challenge worldwide, from plantation to cultivation, especially for perishable products such as tomatoes. New eco-friendly strategies are needed, and beneficial microorganisms might be a sustainable solution. This study demonstrates bacteria activity in the tomato plant rhizosphere. Further, it investigates the rhizobacteria's structure, function, and diversity in soil. Rhizobacteria that promote the growth and development of tomato plants are referred to as plant growth-promoting bacteria (PGPR). They form a series of associations with plants and other organisms in the soil through a mutualistic relationship where both parties benefit from living together. It implies the antagonistic activities of the rhizobacteria to deter pathogens from invading tomato plants through their roots. Some PGPR are regarded as biological control agents that hinder the development of spoilage organisms and can act as an alternative for agricultural chemicals that may be detrimental to the health of humans, animals, and some of the beneficial microbes in the rhizosphere soil. These bacteria also help tomato plants acquire essential nutrients like potassium (K), magnesium (Mg), phosphorus (P), and nitrogen (N). Some rhizobacteria may offer a solution to low tomato production and help tackle food insecurity and farming problems. In this review, an overview of soil-inhabiting rhizobacteria focused on improving the sustainable production of Solanum lycopersicum.},
}
@article {pmid35669004,
year = {2022},
author = {Green, GBH and Williams, MB and Chehade, SB and Morrow, CD and Watts, SA and Bej, AK},
title = {High-throughput amplicon sequencing datasets of the metacommunity DNA of the gut microbiota of Zebrafish Danio rerio fed diets with differential quantities of protein and fat contents.},
journal = {Data in brief},
volume = {42},
number = {},
pages = {108313},
pmid = {35669004},
issn = {2352-3409},
support = {P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; },
abstract = {In this paper, we present high-throughput amplicon sequence (HTS) datasets of the gut microbiota of male and female Zebrafish Danio rerio fed diets consisting of sub-optimal and above-optimal quantities of proteins and fats. The HTS datasets were generated using an Illumina MiSeq targeting the V4 hypervariable segment of the 16S rRNA gene. The raw sequence reads were quality checked, demultiplexed into FASTQ files, denoised using DADA2 (q2-dada2 denoise-paired), and subsampled. Taxonomic ids were then assigned to amplicon sequence variants (ASVs) against the silva-138-99-nb-classifier for taxonomic output using the Quantitative Insights Into Microbial Ecology (QIIME2 v2021.4). The resultant taxa list was generated at the phylum level to confirm the applicability of the HTS dataset using the "qiime taxa collapse" command. These HTS datasets of the metagenome can be accessed through the BioSample Submission Portal (https://www.ncbi.nlm.nih.gov/bioproject/) under the BioProject IDs PRJNA772302 and PRJNA772305.},
}
@article {pmid35668112,
year = {2022},
author = {Berlanga-Clavero, MV and Molina-Santiago, C and Caraballo-Rodríguez, AM and Petras, D and Díaz-Martínez, L and Pérez-García, A and de Vicente, A and Carrión, VJ and Dorrestein, PC and Romero, D},
title = {Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon.},
journal = {Nature microbiology},
volume = {7},
number = {7},
pages = {1001-1015},
pmid = {35668112},
issn = {2058-5276},
support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; },
mesh = {*Bacillus subtilis/metabolism ; *Cucurbitaceae/microbiology ; Extracellular Polymeric Substance Matrix ; Lipid Droplets ; Seeds/microbiology ; },
abstract = {Beneficial microorganisms are used to stimulate the germination of seeds; however, their growth-promoting mechanisms remain largely unexplored. Bacillus subtilis is commonly found in association with different plant organs, providing protection against pathogens or stimulating plant growth. We report that application of B. subtilis to melon seeds results in genetic and physiological responses in seeds that alter the metabolic and developmental status in 5-d and 1-month-old plants upon germination. We analysed mutants in different components of the extracellular matrix of B. subtilis biofilms in interaction with seeds and found cooperation in bacterial colonization of seed storage tissues and growth promotion. Combining confocal microscopy with fluorogenic probes, we found that two specific components of the extracellular matrix, amyloid protein TasA and fengycin, differentially increased the concentrations of reactive oxygen species inside seeds. Further, using electron and fluorescence microscopy and metabolomics, we showed that both TasA and fengycin targeted the oil bodies in the seed endosperm, resulting in specific changes in lipid metabolism and accumulation of glutathione-related molecules. In turn, this results in two different plant growth developmental programmes: TasA and fengycin stimulate the development of radicles, and fengycin alone stimulate the growth of adult plants and resistance in the phylloplane to the fungus Botrytis cinerea. Understanding mechanisms of bacterial growth promotion will enable the design of bespoke growth promotion strains.},
}
@article {pmid35667433,
year = {2022},
author = {Van Le, A and Straub, D and Planer-Friedrich, B and Hug, SJ and Kleindienst, S and Kappler, A},
title = {Microbial communities contribute to the elimination of As, Fe, Mn, and NH4[+] from groundwater in household sand filters.},
journal = {The Science of the total environment},
volume = {838},
number = {Pt 4},
pages = {156496},
doi = {10.1016/j.scitotenv.2022.156496},
pmid = {35667433},
issn = {1879-1026},
mesh = {*Ammonium Compounds ; *Arsenic ; Ferrous Compounds ; *Groundwater/microbiology ; Manganese ; *Microbiota ; Oxidation-Reduction ; },
abstract = {Household sand filters (SFs) are widely applied to remove iron (Fe), manganese (Mn), arsenic (As), and ammonium (NH4[+]) from groundwater in the Red River delta, Vietnam. Processes in the filters probably include a combination of biotic and abiotic reactions. However, there is limited information on the microbial communities treating varied groundwater compositions and on whether biological oxidation of Fe(II), Mn(II), As(III), and NH4[+] contributes to the overall performance of SFs. We therefore analyzed the removal efficiencies, as well as the microbial communities and their potential activities, of SFs fed by groundwater with varying compositions from low (3.3 μg L[-1]) to high (600 μg L[-1]) As concentrations. The results revealed that Fe(II)-, Mn(II)-, NH4[+]-, and NO2[-]-oxidizing microorganisms were prevalent and contributed to the performance of SFs. Additionally, groundwater composition was responsible for the differences among the present microbial communities. We found i) microaerophilic Fe(II) oxidation by Sideroxydans in all SFs, with the highest abundance in SFs fed by low-As and high-Fe groundwater, ii) Hyphomicropbiaceae as the main Mn(II)-oxidizers in all SFs, iii) As sequestration on formed Fe and Mn (oxyhydr)oxide minerals, iv) nitrification by ammonium-oxidizing archaea (AOA) followed by nitrite-oxidizing bacteria (NOB), and v) unexpectedly, the presence of a substantial amount of methane monooxygenase genes (pmoA), suggesting microbial methane oxidation taking place in SFs. Overall, our study revealed diverse microbial communities in SFs used for purifying arsenic-contaminated groundwater, and our data indicate an important contribution of microbial activities to the key functional processes in SFs.},
}
@article {pmid35666722,
year = {2022},
author = {Boezen, D and Ali, G and Wang, M and Wang, X and van der Werf, W and Vlak, JM and Zwart, MP},
title = {Empirical estimates of the mutation rate for an alphabaculovirus.},
journal = {PLoS genetics},
volume = {18},
number = {6},
pages = {e1009806},
pmid = {35666722},
issn = {1553-7404},
mesh = {Animals ; Mutation ; Mutation Rate ; *Nucleopolyhedroviruses/genetics ; Spodoptera ; },
abstract = {Mutation rates are of key importance for understanding evolutionary processes and predicting their outcomes. Empirical mutation rate estimates are available for a number of RNA viruses, but few are available for DNA viruses, which tend to have larger genomes. Whilst some viruses have very high mutation rates, lower mutation rates are expected for viruses with large genomes to ensure genome integrity. Alphabaculoviruses are insect viruses with large genomes and often have high levels of polymorphism, suggesting high mutation rates despite evidence of proofreading activity by the replication machinery. Here, we report an empirical estimate of the mutation rate per base per strand copying (s/n/r) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV). To avoid biases due to selection, we analyzed mutations that occurred in a stable, non-functional genomic insert after five serial passages in Spodoptera exigua larvae. Our results highlight that viral demography and the stringency of mutation calling affect mutation rate estimates, and that using a population genetic simulation model to make inferences can mitigate the impact of these processes on estimates of mutation rate. We estimated a mutation rate of μ = 1×10-7 s/n/r when applying the most stringent criteria for mutation calling, and estimates of up to μ = 5×10-7 s/n/r when relaxing these criteria. The rates at which different classes of mutations accumulate provide good evidence for neutrality of mutations occurring within the inserted region. We therefore present a robust approach for mutation rate estimation for viruses with stable genomes, and strong evidence of a much lower alphabaculovirus mutation rate than supposed based on the high levels of polymorphism observed.},
}
@article {pmid35665438,
year = {2022},
author = {Sun, J and Li, S and Fan, C and Cui, K and Tan, H and Qiao, L and Lu, L},
title = {N-Acetylglucosamine Promotes Tomato Plant Growth by Shaping the Community Structure and Metabolism of the Rhizosphere Microbiome.},
journal = {Microbiology spectrum},
volume = {10},
number = {3},
pages = {e0035822},
pmid = {35665438},
issn = {2165-0497},
mesh = {Acetylglucosamine ; Chitin ; *Solanum lycopersicum/microbiology ; *Microbiota/physiology ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Communication between plants and microorganisms is vital because it influences their growth, development, defense, propagation, and metabolism in achieving maximal fitness. N-acetylglucosamine (N-GlcNAc), the building block of bacterial and fungal cell walls, was first reported to promote tomato plant growth via stimulation of microorganisms typically known to dominate the tomato root rhizosphere, such as members of Proteobacteria and Actinobacteria. Using KEGG pathway analysis of the rhizosphere microbial operational taxonomic units, the streptomycin biosynthesis pathway was enriched in the presence of N-GlcNAc. The biosynthesis of 3-hydroxy-2-butanone (acetoin) and 2,3-butanediol, two foremost types of plant growth promotion-related volatile organic compounds, were activated in both Bacillus subtilis and Streptomyces thermocarboxydus strains when they were cocultured with N-GlcNAc. In addition, the application of N-GlcNAc increased indole-3-acetic acid production in a dose-dependent manner in strains of Bacillus cereus, Proteus mirabilis, Pseudomonas putida, and S. thermocarboxydus that were isolated from an N-GlcNAc-treated tomato rhizosphere. Overall, this study found that N-GlcNAc could function as microbial signaling molecules to shape the community structure and metabolism of the rhizosphere microbiome, thereby regulating plant growth and development and preventing plant disease through complementary plant-microbe interactions. IMPORTANCE While the benefits of using plant growth-promoting rhizobacteria (PGPRs) to enhance crop production have been recognized and studied extensively under laboratory conditions, the success of their application in the field varies immensely. More fundamentally explicit processes of positive, plant-PGPRs interactions are needed. The utilization of organic amendments, such as chitin and its derivatives, is one of the most economical and practical options for improving soil and substrate quality as well as plant growth and resilience. In this study, we observed that the chitin monomer N-GlcNAc, a key microbial signaling molecule produced through interactions between chitin, soil microbes, and the plants, positively shaped the community structure and metabolism of the rhizosphere microbiome of tomatoes. Our findings also provide a new direction for enhancing the benefits and stability of PGPRs in the field.},
}
@article {pmid35662397,
year = {2022},
author = {Yu, Y and van der Zwaag, M and Wedman, JJ and Permentier, H and Plomp, N and Jia, X and Kanon, B and Eggens-Meijer, E and Buist, G and Harmsen, H and Kok, J and Salles, JF and Wertheim, B and Hayflick, SJ and Strauss, E and Grzeschik, NA and Schepers, H and Sibon, OCM},
title = {Coenzyme A precursors flow from mother to zygote and from microbiome to host.},
journal = {Molecular cell},
volume = {82},
number = {14},
pages = {2650-2665.e12},
doi = {10.1016/j.molcel.2022.05.006},
pmid = {35662397},
issn = {1097-4164},
mesh = {Animals ; *Coenzyme A/genetics/metabolism ; Drosophila/metabolism ; Female ; Humans ; *Microbiota ; Mothers ; Phosphotransferases (Alcohol Group Acceptor)/metabolism ; Zygote/metabolism ; },
abstract = {Coenzyme A (CoA) is essential for metabolism and protein acetylation. Current knowledge holds that each cell obtains CoA exclusively through biosynthesis via the canonical five-step pathway, starting with pantothenate uptake. However, recent studies have suggested the presence of additional CoA-generating mechanisms, indicating a more complex system for CoA homeostasis. Here, we uncovered pathways for CoA generation through inter-organismal flows of CoA precursors. Using traceable compounds and fruit flies with a genetic block in CoA biosynthesis, we demonstrate that progeny survive embryonal and early larval development by obtaining CoA precursors from maternal sources. Later in life, the microbiome can provide the essential CoA building blocks to the host, enabling continuation of normal development. A flow of stable, long-lasting CoA precursors between living organisms is revealed. This indicates the presence of complex strategies to maintain CoA homeostasis.},
}
@article {pmid35661942,
year = {2022},
author = {Schmid, K and Reis-Filho, JA and Loiola, M and Harvey, ES and de Kikuchi, RKP and Giarrizzo, T},
title = {Habitat-specific fish fauna responses to different management regimes in the largest coral reef complex in the South Atlantic.},
journal = {Marine environmental research},
volume = {178},
number = {},
pages = {105661},
doi = {10.1016/j.marenvres.2022.105661},
pmid = {35661942},
issn = {1879-0291},
mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; *Coral Reefs ; Ecosystem ; Fishes ; *Sharks ; },
abstract = {While marine protected areas (MPAs) are increasing worldwide, it is still needed to assess the effectiveness of those already consolidated. Methods and ecological assessments to understanding integrated and habitat-specific management regimes are still scarce and insufficient for policy implications and biodiversity conservation. Through Baited Remote Underwater Video (BRUV), we used fish assemblages as proxy of ecological and managerial status in two reef habitat types along three protection levels at Abrolhos Bank - the largest and most biodiverse coral reef complex of the South Atlantic. We found completely distinct responses in the fish fauna between the top (shallow) and bottom (deep) habitats of the unique "chapeirões" pinnacle reef formations. In the most protected zone (no-take), higher richness and abundance of commercial fish and more diverse trophic structure was observed. Particularly, large (sharks and groupers) and small carnivores (snappers) were more abundant and distributed more homogeneously over both reef habitats in the strictly enforced no-take zone. Abundance of these top-predators decreased from the low enforcement no-take zone to the multiple use area, where they were often absent while their typical preys (primary and secondary consumers) were thriving, notably in the top habitats. These outcomes highlight the importance to focus investigations not selectively on a single habitat type or depth zone in order to properly assess MPA effectiveness. Consequently, the monitoring and protection of fish species supported by marine spatial planning may benefit from an improved understanding of ecological functioning provided by MPA performance.},
}
@article {pmid35660593,
year = {2022},
author = {Pensky, J and Fisher, AT and Gorski, G and Schrad, N and Dailey, H and Beganskas, S and Saltikov, C},
title = {Enhanced cycling of nitrogen and metals during rapid infiltration: Implications for managed recharge.},
journal = {The Science of the total environment},
volume = {838},
number = {Pt 4},
pages = {156439},
doi = {10.1016/j.scitotenv.2022.156439},
pmid = {35660593},
issn = {1879-1026},
mesh = {Carbon ; *Groundwater ; Humans ; Metals ; Nitrates/analysis ; Nitrogen ; Soil ; *Water Pollutants, Chemical/metabolism ; },
abstract = {We present results from a series of plot-scale field experiments to quantify physical infiltration dynamics and the influence of adding a carbon-rich, permeable reactive barrier (PRB) for the cycling of nitrogen and associated trace metals during rapid infiltration for managed aquifer recharge (MAR). Recent studies suggest that adding a bio-available carbon source to soils can enhance denitrification rates and associated N load reduction during moderate-to-rapid infiltration (≤1 m/day). We examined the potential for N removal during faster infiltration (>1 m/day), through coarse and carbon-poor soils, and how adding a carbon-rich PRB (wood chips) affects subsurface redox conditions and trace metal mobilization. During rapid infiltration, plots amended with a carbon-rich PRB generally demonstrated modest increases in subsurface loads of dissolved organic carbon, nitrite, manganese and iron, decreases in loads of nitrate and ammonium, and variable changes in arsenic. These trends differed considerably from those seen during infiltration through native soil without a carbon-rich PRB. Use of a carbon-rich soil amendment increased the fraction of dissolved N species that was removed at equivalent inflowing N loads. There is evidence that N removal took place primarily via denitrification. Shifts in microbial ecology following infiltration in all of the plots included increases in the relative abundances of microbes in the families Comamonadaceae, Pseudomonadaceae, Methylophilaceae, Rhodocyclaceae and Sphingomonadaceae, all of which contain genera capable of carrying out denitrification. These results, in combination with studies that have tested other soil types, flow rates, and system scales, show how water quality can be improved during infiltration for managed recharge, even during rapid infiltration, with a carbon-rich soil amendment.},
}
@article {pmid35659305,
year = {2022},
author = {Chiriac, MC and Bulzu, PA and Andrei, AS and Okazaki, Y and Nakano, SI and Haber, M and Kavagutti, VS and Layoun, P and Ghai, R and Salcher, MM},
title = {Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {84},
pmid = {35659305},
issn = {2049-2618},
mesh = {Animals ; Bacteria ; In Situ Hybridization, Fluorescence ; Lakes/microbiology ; *Metagenome/genetics ; *Metagenomics ; Phylogeny ; },
abstract = {BACKGROUND: The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters; however, their diversity, abundance, and role in surface freshwaters is largely unexplored. Here, we attempt to close these knowledge gaps by deep metagenomic sequencing of 119 samples of 17 different freshwater lakes located in Europe and Asia. Moreover, we applied Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) for a first visualization of distinct CPR lineages in freshwater samples.<br><br>RESULTS: A total of 174 dereplicated metagenome-assembled genomes (MAGs) of diverse CPR lineages were recovered from the investigated lakes, with a higher prevalence from hypolimnion samples (162 MAGs). They have reduced genomes (median size 1 Mbp) and were generally found in low abundances (0.02-14.36 coverage/Gb) and with estimated slow replication rates. The analysis of genomic traits and CARD-FISH results showed that the radiation is an eclectic group in terms of metabolic capabilities and potential lifestyles, ranging from what appear to be free-living lineages to host- or particle-associated groups. Although some complexes of the electron transport chain were present in the CPR MAGs, together with ion-pumping rhodopsins and heliorhodopsins, we believe that they most probably adopt a fermentative metabolism. Terminal oxidases might function in O2 scavenging, while heliorhodopsins could be involved in mitigation against oxidative stress.<br><br>CONCLUSIONS: A high diversity of CPR MAGs was recovered, and distinct CPR lineages did not seem to be limited to lakes with specific trophic states. Their reduced metabolic capacities resemble the ones described for genomes in groundwater and animal-associated samples, apart from Gracilibacteria that possesses more complete metabolic pathways. Even though this radiation is mostly host-associated, we also observed organisms from different clades (ABY1, Paceibacteria, Saccharimonadia) that appear to be unattached to any other organisms or were associated with 'lake snow' particles (ABY1, Gracilibacteria), suggesting a broad range of potential life-strategies in this phylum. Video Abstract.},
}
@article {pmid35657425,
year = {2023},
author = {Meena, M and Yadav, G and Sonigra, P and Nagda, A and Mehta, T and Swapnil, P and Harish, and Marwal, A and Kumar, S},
title = {Multifarious Responses of Forest Soil Microbial Community Toward Climate Change.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {49-74},
pmid = {35657425},
issn = {1432-184X},
mesh = {*Ecosystem ; Climate Change ; Soil/chemistry ; Forests ; *Microbiota ; Nitrogen/analysis ; Soil Microbiology ; Carbon ; },
abstract = {Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.},
}
@article {pmid35655857,
year = {2022},
author = {Wang, Y and Tian, L and Sun, L and Zhou, W and Zhi, W and Qing, J and Abdi Saed, Y and Dong, L and Zhang, X and Li, Y},
title = {Gut Microbes in Immunoglobulin A Nephropathy and Their Potential Therapeutic Applications.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {823267},
pmid = {35655857},
issn = {2296-858X},
abstract = {Microbial ecosystem consists of a complex community of bacterial interactions and its host microenvironment (tissue, cell, metabolite). Because the interaction between gut microbiota and host involves many diseases and seriously affects human health, the study of the interaction mechanism between gut microbiota and host has attracted great attention. The gut microbiome is made up of 100 trillion bacteria that have both beneficial and adverse effects on human health. The development of IgA Nephropathy results in changes in the intestinal microbial ecosystem that affect host physiology and health. Similarly, changes in intestinal microbiota also affect the development of IgA Nephropathy. Thus, the gut microbiome represents a novel therapeutic target for improving the outcome of IgA Nephropathy, including hematuria symptoms and disease progression. In this review, we summarize the effect of intestinal microbiota on IgA Nephropathy in recent years and it has been clarified that the intestinal microbiota has a great influence on the pathogenesis and treatment of IgA Nephropathy.},
}
@article {pmid35655089,
year = {2022},
author = {Morelli, G and Patuzzi, I and Losasso, C and Ricci, A and Contiero, B and Andrighetto, I and Ricci, R},
title = {Characterization of intestinal microbiota in normal weight and overweight Border Collie and Labrador Retriever dogs.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9199},
pmid = {35655089},
issn = {2045-2322},
mesh = {Animals ; Bacteria/genetics ; Dogs ; Feces/microbiology ; Firmicutes/genetics ; *Gastrointestinal Microbiome/genetics ; Mice ; Obesity/microbiology ; Overweight/veterinary ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Obesity in dogs is an emerging issue that affects canine health and well-being. Its development is ascribed to several factors, including genetic predisposition and dietary management, and recent evidence suggests that intestinal microbiota may be involved as well. Previous works have shown obesity to be linked to significant changes in gut microbiota composition in humans and mice, but only limited information is available on the role played by canine gut microbiota. The aim of this exploratory study was to investigate whether composition of canine faecal microbiota may be influenced by overweight condition and breed. All the enrolled companion dogs were young adults, intact, healthy, and fed commercial extruded pet food; none had received antibiotics, probiotics or immunosuppressant drugs in the previous six months. Labrador Retriever (LR) and Border Collie (BC) were chosen as reference breeds and Body Condition Score (BCS) on a 9-point scale as reference method for evaluating body fat. The faecal microbial communities of 15 lean (BCS 4-5/9; 7 LRs and 8 BCs) and 14 overweight (BCS > 5/9; 8 LRs and 6 BCs) family dogs were analysed using 16S rRNA gene sequencing. Moreover, for each dog, the daily intake of energy (kcal/d) and dietary macronutrients (g/d) were calculated according to an accurate feeding history collection. Firmicutes and Bacteroidetes resulted the predominant phyla (51.5 ± 10.0% and 33.4 ± 8.5%, respectively) in all dogs. Bioinformatic and statistical analysis revealed that no bacterial taxon differed significantly based on body condition, except for genus Allisonella (p < 0.05); BC gut microbiota was richer (p < 0.05) in bacteria belonging to phyla Actinobacteria (family Coriobacteriaceae in particular) and Firmicutes (Allobaculum and Roseburia genera). No remarkable differences were recorded either for diversity indices (i.e., alpha diversity, p > 0.10) or for divergence within the sample set (i.e., beta diversity, p > 0.05). PERMANOVA tests performed on single factors demonstrated the tendency of dietary protein to influence the recruited dogs' microbiota beta-diversity at amplicon sequence variant level (p = 0.08). In conclusion, the faecal microbiota of dogs involved in this exploratory study showed no major variations based on body condition. However, our findings suggested that certain bacterial taxa previously acknowledged in obesity-related studies may be detected in dissimilar amounts depending on canine breed.},
}
@article {pmid35655088,
year = {2022},
author = {de la Fuente Cantó, C and Diouf, MN and Ndour, PMS and Debieu, M and Grondin, A and Passot, S and Champion, A and Barrachina, C and Pratlong, M and Gantet, P and Assigbetsé, K and Kane, N and Cubry, P and Diedhiou, AG and Heulin, T and Achouak, W and Vigouroux, Y and Cournac, L and Laplaze, L},
title = {Genetic control of rhizosheath formation in pearl millet.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9205},
pmid = {35655088},
issn = {2045-2322},
mesh = {Genome-Wide Association Study ; *Pennisetum/genetics ; Quantitative Trait Loci ; Rhizosphere ; Soil/chemistry ; },
abstract = {The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub-Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.},
}
@article {pmid35654854,
year = {2023},
author = {Monroy, S and Larrañaga, A and Martínez, A and Pérez, J and Molinero, J and Basaguren, A and Pozo, J},
title = {Temperature Sensitivity of Microbial Litter Decomposition in Freshwaters: Role of Leaf Litter Quality and Environmental Characteristics.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {839-852},
pmid = {35654854},
issn = {1432-184X},
support = {CGL2010-22129-C04-01//Ministry of Science and Innovation of the Spanish Government/ ; BES-2012-060743//Spanish Ministry of Economy and Competitiveness/ ; DOKBERRI 2018 I//UPV/EHU/ ; },
mesh = {Temperature ; *Ecosystem ; Biomass ; Plant Leaves/microbiology ; *Alnus/microbiology ; Fresh Water ; },
abstract = {Ongoing global warming is expected to alter temperature-dependent processes. Nevertheless, how co-occurring local drivers will influence temperature sensitivity of plant litter decomposition in lotic ecosystems remains uncertain. Here, we examined the temperature sensitivity of microbial-mediated decomposition, microbial respiration, fungal biomass and leaf nutrients of two plant species varying in litter quality. We also assessed whether the type of microbial community and stream water characteristics influence such responses to temperature. We incubated alder (Alnus glutinosa) and eucalypt (Eucalyptus globulus) litter discs in three streams differing in autumn-winter water temperature (range 4.6-8.9 °C). Simultaneously, in laboratory microcosms, litter discs microbially conditioned in these streams were incubated at 5, 10 and 15 °C with water from the conditioning stream and with a water control from an additional stream. Both in the field and in the laboratory, higher temperatures enhanced litter decomposition rates, except for eucalypt in the field. Leaf quality modified the response of decomposition to temperature in the field, with eucalypt leaf litter showing a lower increase, whereas it did not in the laboratory. The origin of microbial community only affected the decomposition rates in the laboratory, but it did not modify the response to temperature. Water quality only defined the phosphorus content of the leaf litter or the fungal biomass, but it did not modify the response to temperature. Our results suggest that the acceleration in decomposition by global warming will be shaped by local factors, mainly by leaf litter quality, in headwater streams.},
}
@article {pmid35652980,
year = {2022},
author = {Behairi, S and Baha, N and Barakat, M and Ortet, P and Achouak, W and Heulin, T and Kaci, Y},
title = {Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {2},
pages = {18},
pmid = {35652980},
issn = {1433-4909},
support = {14MDU907//French-Algerian Hubert Curien Partnership Program (PHC) TASSILI/ ; },
mesh = {Algeria ; Bacteria ; *Microbiota ; *Rhizosphere ; Salt-Tolerant Plants/microbiology ; Sodium Chloride ; Soil ; Soil Microbiology ; },
abstract = {Hypersaline ecosystems host a particular microbiota, which can be specifically recruited by halophytes. In order to broaden our knowledge of hypersaline ecosystems, an in natura study was conducted on the microbiota associated with the halophyte Halocnemum strobilaceum from alkaline-saline arid soil in Algeria. We collected and identified a total of 414 strains isolated from root tissues (RT), root-adhering soil (RAS), non-adhering rhizospheric soil (NARS) and bulk soil (BS) using different NaCl concentrations. Our data showed that halophilic and halotolerant bacterial isolates in BS and the rhizosphere belonged to 32 genera distributed in Proteobacteria (49%), Firmicutes (36%), Actinobacteria (14%) and Bacteroidetes (1%). Bacterial population size and species diversity were greatly increased in the rhizosphere (factor 100). The reservoir of diversity in BS was dominated by the genera Bacillus and Halomonas. Bacillus/Halomonas ratio decreased with the proximity to the roots from 2.2 in BS to 0.3 at the root surface. Salt screening of the strains showed that species belonging to nine genera were able to grow up to 5.1 M NaCl. Thus, we found that H. strobilaceum exerted a strong effect on the diversity of the recruited microbiota with an affinity strongly attributed to the genus Halomonas.},
}
@article {pmid35652935,
year = {2022},
author = {Lürling, M and Mucci, M and Douglas, GB},
title = {Response to "Risk of Collapse in Water Quality in the Guandu River (Rio de Janeiro, Brazil)" by Bacha et al., Published Online 23 August 2021, Microbial Ecology, 10.1007/s00248-021-01,839-z.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {14-19},
pmid = {35652935},
issn = {1432-184X},
mesh = {Brazil ; Environmental Monitoring ; *Rivers ; *Water Pollutants, Chemical/analysis ; Water Quality ; },
}
@article {pmid35652664,
year = {2022},
author = {Smercina, DN and Kim, YM and Lipton, MS and Velickovic, D and Hofmockel, KS},
title = {Bulk and Spatially Resolved Extracellular Metabolome of Free-Living Nitrogen Fixation.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {12},
pages = {e0050522},
pmid = {35652664},
issn = {1098-5336},
mesh = {Bacteria/metabolism ; *Ecosystem ; Metabolome ; Nitrogen/metabolism ; *Nitrogen Fixation ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Soil nitrogen (N) transformations constrain terrestrial net primary productivity and are driven by the activity of soil microorganisms. Free-living N fixation (FLNF) is an important soil N transformation and key N input to terrestrial systems, but the forms of N contributed to soil by FLNF are poorly understood. To address this knowledge gap, a focus on microorganisms and microbial scale processes is needed that links N-fixing bacteria and their contributed N sources to FLNF process rates. However, studying the activity of soil microorganisms in situ poses inherent challenges, including differences in sampling scale between microorganism and process rates, which can be addressed with culture-based studies and an emphasis on microbial-scale measurements. Culture conditions can differ significantly from soil conditions, so it also important that such studies include multiple culture conditions like liquid and solid media as proxies for soil environments like soil pore water and soil aggregate surfaces. Here we characterized extracellular N-containing metabolites produced by two common, diazotrophic soil bacteria in liquid and solid media, with or without N, across two sampling scales (bulk via GC-MS and spatially resolved via MALDI mass spec imaging). We found extracellular production of inorganic and organic N during FLNF, indicating terrestrial N contributions from FLNF occur in multiple forms not only as ammonium as previously thought. Extracellular metabolite profiles differed between liquid and solid media supporting previous work indicating environmental structure influences microbial function. Metabolite profiles also differed between sampling scales underscoring the need to quantify microbial scale conditions to accurately interpret microbial function. IMPORTANCE Free-living nitrogen-fixing bacteria contribute significantly to terrestrial nitrogen availability; however, the forms of nitrogen contributed by this process are poorly understood. This is in part because of inherent challenges to studying soil microorganisms in situ, such as vast differences in scale between microorganism and ecosystem and complexities of the soil system (e.g., opacity, chemical complexity). Thus, upscaling important ecosystem processes driven by soil microorganisms, like free-living nitrogen fixation, requires microbial-scale measurements in controlled systems. Our work generated bulk and spatially resolved measurements of nitrogen released during free-living nitrogen fixation under two contrasting growth conditions analogous to soil pores and aggregates. This work allowed us to determine that diverse forms of nitrogen are likely contributed to terrestrial systems by free-living nitrogen bacteria. We also demonstrated that microbial habitat (e.g., liquid versus solid media) alters microbial activity and that measurement of microbial activity is altered by sampling scale (e.g., bulk versus spatially resolved) highlighting the critical importance of quantifying microbial-scale processes to upscaling of ecosystem function.},
}
@article {pmid35651031,
year = {2022},
author = {Huang, R and Shen, L and Yu, H and Jiang, J and Qin, Y and Liu, Y and Zhang, J and Song, Y},
title = {Evaluation of rain-shelter cultivation mode effects on microbial diversity during Cabernet Sauvignon (Vitis vinifera L.) maturation in Jingyang, Shaanxi, China.},
journal = {Food research international (Ottawa, Ont.)},
volume = {156},
number = {},
pages = {111165},
doi = {10.1016/j.foodres.2022.111165},
pmid = {35651031},
issn = {1873-7145},
mesh = {Bacteria/classification ; China ; Fruit/chemistry/microbiology ; Fungi/classification ; *Microbiota ; *Rain ; *Vitis/chemistry/microbiology ; *Wine/analysis/microbiology ; },
abstract = {Rainfall particularly under continental climates with monsoonal tendency impacts the vineyard microbial niches during grapevine growth. With microbial community shifts, vine traits (grape flavor and yield) cultivated/protected under rain-shelter may ultimately be altered. Such cultivation may influence microflora dynamics via meteorological parameter variations, however this is unclear yet. Here, we used Cabernet Sauvignon, a prevalent red cultivar among wine growing regions, to evaluate the effects of the rain-shelter cultivation on the microorganism diversity. We found that average air temperature under rain-shelter conditions was 2-3 °C higher than the non-covered group, while air humidity the maximum reduction was 5.79% (p < 0.05). After grape setting stage, similar trends were observed on soil temperature (increased) and humidity (lowered) under the treatments (p < 0.05). UV and precipitation of rain-shelter treatment were less by a total of 72% and 96%, respectively (p < 0.05). The rain-shelter management presented lower fungal and bacterial OTUs. The fungal alpha diversity on leaves and branches under rain-shelter was lower (p < 0.05) than the control as the grape ripeness, with Ascomycota, Mycosphaerella and Cladosporium as the principal fungi. Our results revealed that the fungal microbiota patterns were differentiated by the cultivations from setting stage to the entire véraison and then tended to be similar at harvesting. Only branch fungal patterns were observed asymmetrically at all stages. Meanwhile, bacterial diversity and distribution varied on colonization locations where Proteobacteria and Actinobacteria were the primary bacteria phyla. Bacterial community structures overlapped at harvest, while the differences were observed between two cultivations at other stages, excluding grape berry. The rain-shelter cultivation reduced the abundance of Alternaria and Colletotrichum that may adversely affect grapevine health. Multivariate statistical analysis suggested that the effect of vineyard microclimate on microbiota distribution and succession were influenced by cultivation modes and grapevine developmental stages. This research provides evidence to address the dynamics of microbial ecology from vineyard to grape under rain-shelter cultivation, and its benefits as a sustainable vineyard management.},
}
@article {pmid35650293,
year = {2023},
author = {Ren, Z and Ma, K and Jia, X and Wang, Q and Zhang, C and Li, X},
title = {Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {904-915},
pmid = {35650293},
issn = {1432-184X},
mesh = {*Lakes/microbiology ; *Metagenomics ; Water ; Rivers ; Nitrogen ; Sulfates ; },
abstract = {Thermokarst lakes have long been recognized as biogeochemical hotspots, especially as sources of greenhouse gases. On the Qinghai-Tibet Plateau, thermokarst lakes are experiencing extensive changes due to faster warming. For a deep understanding of internal lake biogeochemical processes, we applied metagenomic analyses to investigate the microbial diversity and their biogeochemical roles in sediment and water of thermokarst lakes in the Yellow River Source Area (YRSA). Sediment microbial communities (SMCs) had lower species and gene richness than water microbial communities (WMCs). Bacteria were the most abundant component in both SMCs and WMCs with significantly different abundant genera. The functional analyses showed that both SMCs and WMCs had low potential in methanogenesis but strong in aerobic respiration, nitrogen assimilation, exopolyphosphatase, glycerophosphodiester phosphodiesterases, and polyphosphate kinase. Moreover, SMCs were enriched in genes involved in anaerobic carbon fixation, aerobic carbon fixation, fermentation, most nitrogen metabolism pathways, dissimilatory sulfate reduction, sulfide oxidation, polysulfide reduction, 2-phosphonopropionate transporter, and phosphate regulation. WMCs were enriched in genes involved in assimilatory sulfate reduction, sulfur mineralization, phosphonoacetate hydrolase, and phosphonate transport. Functional potentials suggest the differences of greenhouse gas emission, nutrient cycling, and living strategies between SMCs and WMCs. This study provides insight into the main biogeochemical processes and their properties in thermokarst lakes in YRSA, improving our understanding of the roles and fates of these lakes in a warming world.},
}
@article {pmid35648155,
year = {2023},
author = {Ma, M and Chen, X and Li, S and Luo, J and Han, R and Xu, L},
title = {Composition and Diversity of Gut Bacterial Community in Different Life Stages of a Leaf Beetle Gastrolina depressa.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {590-600},
pmid = {35648155},
issn = {1432-184X},
mesh = {Animals ; *Coleoptera ; *Gastrointestinal Microbiome ; Larva/microbiology ; Bacteria/genetics ; Life Cycle Stages ; },
abstract = {Insect gut bacteria have a significant impact on host biology, which has a favorable or negative impact on insect fitness. The walnut leaf beetle (Gastrolina depressa) is a notorious pest in China, causing severe damage to Juglandaceae trees including Juglans regia and Pterocarya rhoifolia. To date, however, we know surprisingly little about the gut microbiota of G. depressa. This study used a high-throughput sequencing platform to investigate the gut bacterial community of G. depressa throughout its life cycle, including the 1st, 2nd, and 3rd instar larvae, as well as male, female, and pre-pregnant female adults. Our results showed that the diversity of the gut bacterial community in larvae was generally higher than that in adults, and young larvae (1st and 2nd larvae) possessed the most diversified and abundant community. Principal coordinate analysis results showed that the gut microbiota of adults cluster together, which is independent of the 1st and 2nd instar larvae. The main phyla were Proteobacteria and Firmicutes in the microbial community of G. depressa, while the dominant genera were Enterobacter, Rosenbergiella, Erwinia, Pseudomonas, and Lactococcus. The gut bacteria of G. depressa were mostly enriched in metabolic pathways (carbohydrate metabolism and amino acid metabolism) as revealed by functional prediction. This study contributes to a better knowledge of G. depressa's gut microbiota and its potential interactions with the host insect, facilitating the development of a microbial-based pest management strategy.},
}
@article {pmid35648154,
year = {2023},
author = {Doniger, T and Kerfahi, D and Wachtel, C and Marais, E and Maggs-Kölling, G and Sherman, C and Adams, JM and Steinberger, Y},
title = {Plant Gender Affects Soil Fungal Microbiota Associated with Welwitschia mirabilis, an Unusual Desert Gymnosperm.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {200-212},
pmid = {35648154},
issn = {1432-184X},
mesh = {*Mycobiome ; Cycadopsida ; *Mirabilis ; Soil/chemistry ; Plants/microbiology ; *Ascomycota ; Soil Microbiology ; },
abstract = {In a recent study, we found a distinct soil bacterial community associated with male and female plants of the desert gymnosperm Welwitschia mirabilis. In this subsequent study, we also found that the soil fungal community associated with Welwitschia differs between male and female plants, and between unvegetated areas and the soil under plants. Site location, pH, and soil moisture also had an important influence on the composition of the fungal community. A number of Ascomycota and Chytrid species were found to be distinct indicators of male and female plants, respectively, but there was no overall difference at the phylum level or in terms of diversity. The unvegetated areas between plants also differed in terms of several Ascomycota OTUs. Network connectivity of the fungal communities was found to be higher under both male and female Welwitschia plants than in unvegetated control areas. As with the bacterial community, it is unclear what processes produce the gender-distinct fungal community, and also the more general plant-associated community, and also what the effects on the biology of the plants are. One possibility behind the gender-related difference in fungal community is that there are differences in the production of pollen or nectar between the two plant genders, affecting the below-ground soil community.},
}
@article {pmid35647000,
year = {2022},
author = {Zhi, W and Song, W and Abdi Saed, Y and Wang, Y and Li, Y},
title = {Fecal Capsule as a Therapeutic Strategy in IgA Nephropathy: A Brief Report.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {914250},
pmid = {35647000},
issn = {2296-858X},
abstract = {In this brief report, we reported an IgA nephropathy (IgAN) patient who presented in November 2020 with an acute exacerbation with massive proteinuria and diarrhea. He had the earliest onset in 2018 when his IgAN was diagnosed by renal biopsy. He has been treated with active ACEI/ARB drugs for more than 90 days, intermittent steroid therapy, combined with anti-infective therapy. Although his acute symptoms resolved with each episode, he became increasingly severe as the interval between episodes shortened. Accordingly, the immunosuppressive drugs were administered under the KDIGO guidelines and related guidelines. However, the patient and his family refused this treatment. We pondered over the possible pathogenesis of IgAN, and after a full discussion with the patient and his family, FMT was administered to him after obtaining his informed consent. During the FMT procedure, one healthy volunteer (the doctor himself) also took the FMT capsules. In the end, the patient's urine protein dropped significantly and even turned negative after treatment. Neither the patient nor the healthy volunteer experienced any serious adverse effects during the use of the capsules and the subsequent 6-month follow-up period. We also used metagenomic sequencing to analyze the intestinal flora of patients before and after treatment, and a gradual increase stood out in the abundance of the patient's intestinal flora after drug administration.},
}
@article {pmid35646730,
year = {2022},
author = {Yang, I and Claussen, H and Arthur, RA and Hertzberg, VS and Geurs, N and Corwin, EJ and Dunlop, AL},
title = {Subgingival Microbiome in Pregnancy and a Potential Relationship to Early Term Birth.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {873683},
pmid = {35646730},
issn = {2235-2988},
support = {K01 NR016971/NR/NINR NIH HHS/United States ; R01 NR014800/NR/NINR NIH HHS/United States ; },
mesh = {Female ; Humans ; Infant, Newborn ; *Microbiota ; *Periodontal Diseases ; Porphyromonas gingivalis/genetics ; Pregnancy ; *Premature Birth ; RNA, Ribosomal, 16S/genetics ; Term Birth ; },
abstract = {BACKGROUND: Periodontal disease in pregnancy is considered a risk factor for adverse birth outcomes. Periodontal disease has a microbial etiology, however, the current state of knowledge about the subgingival microbiome in pregnancy is not well understood.<br><br>OBJECTIVE: To characterize the structure and diversity of the subgingival microbiome in early and late pregnancy and explore relationships between the subgingival microbiome and preterm birth among pregnant Black women.<br><br>METHODS: This longitudinal descriptive study used 16S rRNA sequencing to profile the subgingival microbiome of 59 Black women and describe microbial ecology using alpha and beta diversity metrics. We also compared microbiome features across early (8-14 weeks) and late (24-30 weeks) gestation overall and according to gestational age at birth outcomes (spontaneous preterm, spontaneous early term, full term).<br><br>RESULTS: In this sample of Black pregnant women, the top twenty bacterial taxa represented in the subgingival microbiome included a spectrum representative of various stages of biofilm progression leading to periodontal disease, including known periopathogens Porphyromonas gingivalis and Tannerella forsythia. Other organisms associated with periodontal disease reflected in the subgingival microbiome included several Prevotella spp., and Campylobacter spp. Measures of alpha or beta diversity did not distinguish the subgingival microbiome of women according to early/late gestation or full term/spontaneous preterm birth; however, alpha diversity differences in late pregnancy between women who spontaneously delivered early term and women who delivered full term were identified. Several taxa were also identified as being differentially abundant according to early/late gestation, and full term/spontaneous early term births.<br><br>CONCLUSIONS: Although the composition of the subgingival microbiome is shifted toward complexes associated with periodontal disease, the diversity of the microbiome remains stable throughout pregnancy. Several taxa were identified as being associated with spontaneous early term birth. Two, in particular, are promising targets of further investigation. Depletion of the oral commensal Lautropia mirabilis in early pregnancy and elevated levels of Prevotella melaninogenica in late pregnancy were both associated with spontaneous early term birth.},
}
@article {pmid35644105,
year = {2022},
author = {Bossaert, S and Kocijan, T and Winne, V and Schlich, J and Herrera-Malaver, B and Verstrepen, KJ and Van Opstaele, F and De Rouck, G and Crauwels, S and Lievens, B},
title = {Beer ethanol and iso-α-acid level affect microbial community establishment and beer chemistry throughout wood maturation of beer.},
journal = {International journal of food microbiology},
volume = {374},
number = {},
pages = {109724},
doi = {10.1016/j.ijfoodmicro.2022.109724},
pmid = {35644105},
issn = {1879-3460},
mesh = {*Beer/microbiology ; Ethanol ; Fermentation ; *Microbiota ; Saccharomyces cerevisiae ; Wood ; },
abstract = {Sour beers produced by barrel-aging of conventionally fermented beers are becoming increasingly popular. However, as the intricate interactions between the wood, the microbes and the beer are still unclear, wood maturation often leads to inconsistent end products with undesired sensory properties. Previous research on industrial barrel-aging of beer suggests that beer parameters like the ethanol content and bitterness play an important role in the microbial community composition and beer chemistry, but their exact impact still remains to be investigated. In this study, an experimentally tractable lab-scale system based on an in-vitro community of four key bacteria (Acetobacter malorum, Gluconobacter oxydans, Lactobacillus brevis and Pediococcus damnosus) and four key yeasts (Brettanomyces bruxellensis, Candida friedrichii, Pichia membranifaciens and Saccharomyces cerevisiae) that are consistently associated with barrel-aging of beer, was used to test the hypotheses that beer ethanol and bitterness impact microbial community composition and beer chemistry. Experiments were performed using different levels of ethanol (5.2 v/v%, 8 v/v% and 11 v/v%) and bitterness (13 ppm, 35 ppm and 170 ppm iso-α-acids), and beers were matured for 60 days. Samples were taken after 0, 10, 20, 30 and 60 days to monitor population densities and beer chemistry. Results revealed that all treatments and the maturation time significantly affected the microbial community composition and beer chemistry. More specifically, the ethanol treatments obstructed growth of L. brevis and G. oxydans and delayed fungal growth. The iso-α-acid treatments hindered growth of L. brevis and stimulated growth of P. membranifaciens, while the other strains remained unaffected. Beer chemistry was found to be affected by higher ethanol levels, which led to an increased extraction of wood-derived compounds. Furthermore, the distinct microbial communities also induced changes in the chemical composition of the beer samples, leading to concentration differences in beer- and wood-derived compounds like 4-ethyl guaiacol, 4-ethyl phenol, cis-oak lactone, vanillin, furfural and 5-hydroxymethyl furfural. Altogether, our results indicate that wood-aging of beer is affected by biotic and abiotic parameters, influencing the quality of the final product. Additionally, this work provides a new, cost-effective approach to study the production of barrel-aged beers based on a simplified microbial community model.},
}
@article {pmid35644095,
year = {2022},
author = {Cao, Y and Zhao, J and Wang, Q and Bai, S and Yang, Q and Wei, Y and Wang, R},
title = {Industrial aerobic composting and the addition of microbial agents largely reduce the risks of heavy metal and ARG transfer through livestock manure.},
journal = {Ecotoxicology and environmental safety},
volume = {239},
number = {},
pages = {113694},
doi = {10.1016/j.ecoenv.2022.113694},
pmid = {35644095},
issn = {1090-2414},
mesh = {Animals ; Anti-Bacterial Agents ; *Composting/methods ; Genes, Bacterial ; Livestock ; Manure/microbiology ; *Metals, Heavy/toxicity ; },
abstract = {Composting is an effective and necessary modality in the recycling of agricultural wastes such as livestock manure, furfural, and straw. However, the risks of heavy metals (HMs) and antibiotic resistance genes (ARGs) during industrial-scale composting process have not been adequately assessed, especially with the addition of bacterial agents. In this study, changes in HMs toxicity, ARGs propagation and microbial community structure during industrial-scale aerobic composting of livestock manure were firstly investigated with various substrates addition. Moreover, the effect of the addition of bacterial agents (Bacillus strains) was evaluated. The results showed that industrial aerobic composting process could immobilize various HMs with different extents and significantly reduce the levels of ARGs such as intl1 and oqxB genes. The addition of Bacillus strains could further reduce the levels of most detected ARGs and the bioavailability of Cu and Cr, and the relative abundance of ereA and tetA was undetectable in some materials. After composting, the main bacterial community structures were similar among different substrates irrespective of bacterial agents and indicated that the composting process was the main driver for their change. This study provides a scientific reference for the safe reuse of livestock manure.},
}
@article {pmid35643931,
year = {2022},
author = {Ueckermann, V and Lebre, P and Geldenhuys, J and Hoosien, E and Cowan, D and van Rensburg, LJ and Ehlers, M},
title = {The lung microbiome in HIV-positive patients with active pulmonary tuberculosis.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {8975},
pmid = {35643931},
issn = {2045-2322},
mesh = {*Coinfection/complications ; *HIV Infections/complications ; *HIV Seropositivity/complications ; Humans ; Lung ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Tuberculosis, Pulmonary/microbiology ; },
abstract = {Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIV-positive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.},
}
@article {pmid35643312,
year = {2022},
author = {Chen, X and Chen, J and Yu, X and Sanganyado, E and Wang, L and Li, P and Liu, W},
title = {Effects of norfloxacin, copper, and their interactions on microbial communities in estuarine sediment.},
journal = {Environmental research},
volume = {212},
number = {Pt D},
pages = {113506},
doi = {10.1016/j.envres.2022.113506},
pmid = {35643312},
issn = {1096-0953},
mesh = {Bacteria ; *Copper/toxicity ; Estuaries ; Geologic Sediments ; *Microbiota ; Norfloxacin ; },
abstract = {The discharge of antibiotics and metals in estuaries is of great concern since they threaten microbial communities that are critical for maintaining ecosystem function. To understand single and combined effects of norfloxacin (0-20 μg g[-1]) and copper (40 μg g[-1]) on microbial ecology in estuaries, we evaluated changes in bacteria population, inhibition rates, and microbial composition in estuarine sediments over a 28-day period. Bacteria population significantly decreased following single and combined exposure to norfloxacin and copper throughout the incubation period, except on Day 28 in treatments exposed to copper, 20 μg g[-1] norfloxacin, or both. These three treatment groups had lower Shannon diversity and Simpson's indices on Day 28 than other treatments and the controls suggesting recovery in bacteria population did not correspond with recovery in richness and evenness. Furthermore, functional predictions revealed that the effect of time and contaminants were significantly different on some microbial community functions on Day 28, especially the combination of Cu and high concentration NFX, including aerobic chemoheterotrophy, methanol oxidation and methylotrophy. Thus, norfloxacin and copper had significant adverse effects on microbial communities in estuarine sediments; however, the combined effects were variable and depended on exposure duration and antibiotic concentration.},
}
@article {pmid35643062,
year = {2022},
author = {Reinl, KL and Harris, TD and Elfferich, I and Coker, A and Zhan, Q and De Senerpont Domis, LN and Morales-Williams, AM and Bhattacharya, R and Grossart, HP and North, RL and Sweetman, JN},
title = {The role of organic nutrients in structuring freshwater phytoplankton communities in a rapidly changing world.},
journal = {Water research},
volume = {219},
number = {},
pages = {118573},
doi = {10.1016/j.watres.2022.118573},
pmid = {35643062},
issn = {1879-2448},
mesh = {*Eutrophication ; Fresh Water ; Lakes ; Nitrogen ; Nutrients ; Phosphorus ; *Phytoplankton/physiology ; },
abstract = {Carbon, nitrogen, and phosphorus are critical macroelements in freshwater systems. Historically, researchers and managers have focused on inorganic forms, based on the premise that the organic pool was not available for direct uptake by phytoplankton. We now know that phytoplankton can tap the organic nutrient pool through a number of mechanisms including direct uptake, enzymatic hydrolysis, mixotrophy, and through symbiotic relationships with microbial communities. In this review, we explore these mechanisms considering current and projected future anthropogenically-driven changes to freshwater systems. In particular, we focus on how naturally- and anthropogenically- derived organic nutrients can influence phytoplankton community structure. We also synthesize knowledge gaps regarding phytoplankton physiology and the potential challenges of nutrient management in an organically dynamic and anthropogenically modified world. Our review provides a basis for exploring these topics and suggests several avenues for future work on the relation between organic nutrients and eutrophication and their ecological implications in freshwater systems.},
}
@article {pmid35643037,
year = {2022},
author = {Arora, K and Carafa, I and Fava, F and Tuohy, KM and Nikoloudaki, O and Gobbetti, M and Cagno, RD},
title = {Sourdough performances of the golden cereal Tritordeum: Dynamics of microbial ecology, biochemical and nutritional features.},
journal = {International journal of food microbiology},
volume = {374},
number = {},
pages = {109725},
doi = {10.1016/j.ijfoodmicro.2022.109725},
pmid = {35643037},
issn = {1879-3460},
mesh = {Bread/microbiology ; *Edible Grain/microbiology ; Fermentation ; Flour/microbiology ; Food Microbiology ; Lactobacillaceae ; *Lactobacillales ; Saccharomyces cerevisiae ; Weissella ; },
abstract = {The novel cereal 'Tritordeum' was employed in sourdough fermentation for bread making using a traditional backslopping procedure over 10 days. Culture-dependent and culture-independent approaches were used to characterize microbial ecology during sourdough preparation and propagation. Sourdough reached the highest microbial diversity after three days of propagation. Microbial diversity decreased as sourdough reached maturity (day 5). Microbiota dominance shifted from Weissella to Lactiplantibacillus genera after 5 days of propagation. Lactic acid bacteria (LAB) showed a constant increase throughout the propagations starting from 3.9 ± 0.24 log CFU g[-1] on day 0 up to 8.0 ± 0.39 log CFU g[-1] on day 5. Weissella confusa/cibaria and Weissella paramesenteroides were the most prevalent LAB species until day 5 of propagation, while Lactiplantibacillus plantarum was the most prevalent thereafter. Yeasts were present in low cell density (2.0 ± 0.11 log CFU g[-1]) until the fourth backslopping (day 4) and then gradually increased until day 10 (5.0 ± 0.29 log CFU g[-1]), with Saccharomyces cerevisiae being the most prevalent and dominant species. Lactic and acetic acid concentrations increased throughout Tritordeum sourdough propagations, indicative of a proportional decrease of fermentation quotient (lactic acid/acetic acid) from 13.54 ± 1.29 to 4.08 ± 0.15. Utilization of glucose, fructose and sucrose was observed, followed a progressive increase in mannitol concentrations beginning from day 4. The nutritional potential (total phenol content, antioxidant activity, dietary fiber content and total free amino acids) remained elevated during sourdough propagations. Antinutritional factors (phytic acid and raffinose) were reduced to minimal concentrations by day 10. Finally, texture analysis of Tritordeum sourdough bread was demonstrated to have better cohesiveness, resilience and firmness compared to baker's yeast bread, confirming its potential to improve functionality and use in sourdough biotechnology.},
}
@article {pmid35642946,
year = {2022},
author = {Ginnan, NA and De Anda, NI and Campos Freitas Vieira, F and Rolshausen, PE and Roper, MC},
title = {Microbial Turnover and Dispersal Events Occur in Synchrony with Plant Phenology in the Perennial Evergreen Tree Crop Citrus sinensis.},
journal = {mBio},
volume = {13},
number = {3},
pages = {e0034322},
pmid = {35642946},
issn = {2150-7511},
mesh = {Aged ; Bacteria/genetics ; *Citrus sinensis ; Humans ; *Microbiota ; Phylogeny ; Plants ; },
abstract = {Emerging research indicates that plant-associated microbes can alter plant developmental timing. However, it is unclear if host phenology affects microbial community assembly. Microbiome studies in annual or deciduous perennial plants face challenges in separating effects of tissue age from phenological driven effects on the microbiome. In contrast, evergreen perennial trees, like Citrus sinensis, retain leaves for years, allowing for uniform sampling of similarly aged leaves from the same developmental cohort. This aids in separating phenological effects on the microbiome from impacts due to annual leaf maturation/senescence. Here, we used this system to test the hypothesis that host phenology acts as a driver of microbiome composition. Citrus sinensis leaves and roots were sampled during seven phenological stages. Using amplicon-based sequencing, followed by diversity, phylogenetic, differential abundance, and network analyses, we examined changes in bacterial and fungal communities. Host phenological stage is the main determinant of microbiome composition, particularly within the foliar bacteriome. Microbial enrichment/depletion patterns suggest that microbial turnover and dispersal were driving these shifts. Moreover, a subset of community shifts were phylogenetically conserved across bacterial clades, suggesting that inherited traits contribute to microbe-microbe and/or plant-microbe interactions during specific phenophases. Plant phenology influences microbial community composition. These findings enhance understanding of microbiome assembly and identify microbes that potentially influence plant development and reproduction. IMPORTANCE Research at the forefront of plant microbiome studies indicates that plant-associated microbes can alter the timing of plant development (phenology). However, it is unclear if host phenological stage affects microbial community assembly. Microbiome studies in annual or deciduous perennial plants can face difficulty in separating effects of tissue age from phenological driven effects on the microbiome. Evergreen perennial plants, like sweet orange, maintain mature leaves for multiple years, allowing for uniform sampling of similarly aged tissue across host reproductive stages. Using this system, multiyear sampling, and high-throughput sequencing, we identified plant phenology as a major driver of microbiome composition, particularly within the leaf-associated bacterial communities. Distinct changes in microbial patterns suggest that microbial turnover and dispersal are mechanisms driving these community shifts. Additionally, closely related bacteria have similar abundance patterns across plant stages, indicating that inherited microbial traits may influence how bacteria respond to host developmental changes. Overall, this study illustrates that plant phenology does indeed govern microbiome seasonal shifts and identifies microbial candidates that may affect plant reproduction and development.},
}
@article {pmid35641581,
year = {2023},
author = {Hu, S and He, R and Zeng, J and Zhao, D and Wang, S and He, F and Yu, Z and Wu, QL},
title = {Lower Compositional Variation and Higher Network Complexity of Rhizosphere Bacterial Community in Constructed Wetland Compared to Natural Wetland.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {965-979},
pmid = {35641581},
issn = {1432-184X},
support = {2021NIGLAS-CJH01//Project of Young Scientist Group of NIGLAS/ ; QYZDJ-SSW-DQC030//Key Research Program of Frontier Science, CAS/ ; U2040201//National Natural Science Foundation of China/ ; 32022050//National Natural Science Foundation of China/ ; 31730013//National Natural Science Foundation of China/ ; 31971478//National Natural Science Foundation of China/ ; 32171563//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Wetlands ; Rhizosphere ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria ; *Microbiota ; Soil Microbiology ; },
abstract = {Macrophyte rhizosphere microbes, as crucial components of the wetland ecosystem, play an important role in maintaining the function and stability of natural and constructed wetlands. Distinct environmental conditions and management practices between natural and constructed wetlands would affect macrophytes rhizosphere microbial communities and their associated functions. Nevertheless, the understanding of the diversity, composition, and co-occurrence patterns of the rhizosphere bacterial communities in natural and constructed wetlands remains unclear. Here, we used 16S rRNA gene high-throughput sequencing to characterize the bacterial community of the rhizosphere and bulk sediments of macrophyte Phragmites australis in representative natural and constructed wetlands. We observed higher alpha diversity of the bacterial community in the constructed wetland than that of the natural wetland. Additionally, the similarity of bacterial community composition between rhizosphere and bulk sediments in the constructed wetland was increased compared to that of the natural wetland. We also found that plants recruit specific taxa with adaptive functions in the rhizosphere of different wetland types. Rhizosphere samples of the natural wetland significantly enriched the functional bacterial groups that mainly related to nutrient cycling and plant-growth-promoting, while those of the constructed wetland-enriched bacterial taxa with potentials for biodegradation. Co-occurrence network analysis showed that the interactions among rhizosphere bacterial taxa in the constructed wetland were more complex than those of the natural wetland. This study broadens our understanding of the distinct selection processes of the macrophytes rhizosphere-associated microbes and the co-occurrence network patterns in different wetland types. Furthermore, our findings emphasize the importance of plant-microbe interactions in wetlands and further suggest P. australis rhizosphere enriched diverse functional bacteria that might enhance the wetland performance through biodegradation, nutrient cycling, and supporting plant growth.},
}
@article {pmid35640890,
year = {2022},
author = {Sadiq, FA and Hansen, MF and Burmølle, M and Heyndrickx, M and Flint, S and Lu, W and Chen, W and Zhang, H},
title = {Trans-kingdom interactions in mixed biofilm communities.},
journal = {FEMS microbiology reviews},
volume = {46},
number = {5},
pages = {},
doi = {10.1093/femsre/fuac024},
pmid = {35640890},
issn = {1574-6976},
mesh = {*Archaea/physiology ; Bacteria/metabolism ; *Biofilms ; Ecosystem ; Plants ; Quorum Sensing ; },
abstract = {The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life, which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonize a surface develop architecturally complex surface-adhered communities, which we refer to as biofilms. They are embedded in polymeric structural scaffolds and serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed coexistence of microorganisms from all domains of life, including Bacteria, Archaea, and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.},
}
@article {pmid35640512,
year = {2022},
author = {Piras, F and Nakhla, G and Murgolo, S and De Ceglie, C and Mascolo, G and Bell, K and Jeanne, T and Mele, G and Santoro, D},
title = {Optimal integration of vacuum UV with granular biofiltration for advanced wastewater treatment: Impact of process sequence on CECs removal and microbial ecology.},
journal = {Water research},
volume = {220},
number = {},
pages = {118638},
doi = {10.1016/j.watres.2022.118638},
pmid = {35640512},
issn = {1879-2448},
mesh = {Charcoal/chemistry ; Oxidation-Reduction ; Ultraviolet Rays ; Vacuum ; Wastewater/chemistry ; *Water Pollutants, Chemical/chemistry ; *Water Purification ; *Zeolites ; },
abstract = {This study explored process synergies attainable by integrating a vacuum ultraviolet-based advanced oxidation process with biofiltration. A comparison using granular activated carbon or granular zeolite as filtration media were examined in context of advanced wastewater treatment for potable reuse. Six biofiltration columns, three with granular activated carbon and three with granular zeolite, were operated in parallel and batch-fed daily with nitrified secondary effluent. After achieving a pseudo-steady state through the filter columns, vacuum ultraviolet treatment was applied as pre-treatment or as post-treatment, at two different applied energies (i.e., VUV-E1=1 kWh/m[3] and VUV-E10=10 kWh/m[3]). Once granular activated carbon had transitioned to biologically activated carbon, as determined based on soluble chemical oxygen demand removal, adsorption was still observed as the main mechanism for contaminants of emerging concern and nitrate removal. Vacuum ultraviolet pre-treatment markedly improved contaminants of emerging concern removal through the integrated system, achieving 40% at VUV-E1 and 90% at VUV-E10. When applied as post-treatment to zeolite column effluents, VUV-E1 and VUV-E10 further increased contaminants of emerging concern removal by 20% and 90%, respectively. In the zeolite system, vacuum ultraviolet pre-treatment also increased soluble chemical oxygen demand removal efficiency, indicating that higher energy vacuum ultraviolet increased biodegradability. Total prokaryotes were two-fold more abundant in biologically activated carbon than in zeolite, with vacuum ultraviolet pretreatment markedly affecting microbial diversity, both in terms of richness and composition. Media type only marginally affected microbial richness in the biofilters but showed a marked impact on structural composition. No clear relationship between compositional structure and depth was observed.},
}
@article {pmid35638872,
year = {2022},
author = {Jonassen, KR and Ormåsen, I and Duffner, C and Hvidsten, TR and Bakken, LR and Vick, SHW},
title = {A Dual Enrichment Strategy Provides Soil- and Digestate-Competent Nitrous Oxide-Respiring Bacteria for Mitigating Climate Forcing in Agriculture.},
journal = {mBio},
volume = {13},
number = {3},
pages = {e0078822},
pmid = {35638872},
issn = {2150-7511},
mesh = {Agriculture ; Bacteria/genetics/metabolism ; Denitrification ; Fertilizers/analysis ; *Nitrous Oxide/metabolism ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {Manipulating soil metabolism through heavy inoculation with microbes is feasible if organic wastes can be utilized as the substrate for growth and vector as a fertilizer. This, however, requires organisms active in both digestate and soil (generalists). Here, we present a dual enrichment strategy to enrich and isolate such generalists among N2O-respiring bacteria (NRB) in soil and digestates, to be used as an inoculum for strengthening the N2O-reduction capacity of soils. The enrichment strategy utilizes sequential batch enrichment cultures alternating between sterilized digestate and soil as substrates, with each batch initiated with limited O2 and unlimited N2O. The cultures were monitored for gas kinetics and community composition. As predicted by a Lotka-Volterra competition model, cluster analysis identified generalist operational taxonomic units (OTUs) which became dominant, digestate/soil-specialists which did not, and a majority that were gradually diluted out. We isolated several NRBs circumscribed by generalist OTUs. Their denitrification genes and phenotypes predicted a variable capacity to act as N2O-sinks, while all genomes predicted broad catabolic capacity. The latter contrasts with previous attempts to enrich NRB by anaerobic incubation of unsterilized digestate only, which selected for organisms with a catabolic capacity limited to fermentation products. The two isolates with the most promising characteristics as N2O sinks were a Pseudomonas sp. with a full-fledged denitrification-pathway and a Cloacibacterium sp. carrying only N2O reductase (clade II), and soil experiments confirmed their capacity to reduce N2O-emissions from soil. The successful enrichment of NRB with broad catabolic spectra suggests that the concept of dual enrichment should also be applicable for enrichment of generalists with traits other than N2O reduction. IMPORTANCE N2O emissions from farmed soils are a major source of climate forcing. Here, denitrifying bacteria act as both source and sink for N2O, determined by regulatory traits or the absence of genes coding for the enzymes producing or reducing N2O. One approach to reducing emissions is to amend large numbers of N2O-reducing bacteria (NRB) to soil. This was shown to be feasible by growing NRB to high densities in organic wastes and then applying them as fertilizers. The effect on N2O emissions, however, was transient because the isolated NRBs were unsuited to soil. Here, we have developed an enrichment strategy selecting for organisms with generalist lifestyles, tolerant of rapid environmental changes. This was used to isolate robust NRBs that grow both in digestate and when amended to soils. This strategy opens an avenue for obtaining not just robust NRBs to reduce N2O emissions, but any organism destined for application to complex environments.},
}
@article {pmid35638840,
year = {2022},
author = {Zhang, S and Xia, X and Wang, J and Li, X and Xin, Y and Bao, J and Han, L and Qin, W and Yang, Z},
title = {Biogeographic Patterns and Elevational Differentiation of Sedimentary Bacterial Communities across River Systems in China.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {12},
pages = {e0059722},
pmid = {35638840},
issn = {1098-5336},
mesh = {Bacteria/genetics ; Biodiversity ; China ; *Ecosystem ; *Rivers/microbiology ; },
abstract = {Bacterial biodiversity is tightly correlated with ecological functions of natural systems, and bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning. However, the biogeographic pattern and elevational differentiation of sedimentary bacterial diversity have rarely been studied in cross-river systems at a continental scale. This study analyzed the biogeographic patterns and elevational differentiations of the entire, abundant, and rare bacterial (sub)communities as well as the underlying mechanisms across nine rivers that span distinct geographic regions and large elevational gradients in China. We found that bacterial rare and abundant subcommunities shared similar biogeographic patterns and both demonstrated strong distance-decay relationships, despite their distinct community compositions. However, both null model and variation partitioning analysis results showed that while environmental selection governed rare subcommunity assemblies (contribution: 51.9%), dispersal limitation (62.7%) controlled the assembly of abundant subcommunities. The disparity was associated with the broader threshold width of abundant taxa to water temperature and pH variations than rare taxa. Elevation-induced bacterial composition variations were more evident than latitude-induced ones. Some specific operational taxonomic units (OTUs), representing 16.4% of the total sequences, much preferentially and even exclusively lived in high-elevation or low-elevation habitats and demonstrated some adaptations to local conditions. Greater positive: negative link ratios in bacterial co-occurrence networks of low elevations than high elevations (P < 0.05) partly resulted from their harboring higher organic carbon: nitrogen ratios. Together, this study draws a biogeographic picture of sedimentary bacterial communities in a continental-scale riverine system and highlights the importance of incorporating elevation-associated patterns of microbial diversity into riverine microbial ecology studies. IMPORTANCE Bacterial diversity is tightly correlated with the nutrient cycling of river systems. However, previous studies on bacterial diversity are mainly constrained to one single river system, although microbial biogeography and its drivers exhibit strong spatial scale dependence. Moreover, elevational differentiations of bacterial communities across river systems have also rarely been studied. Bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning, and they share similar biogeographic patterns in some environments but not in others. Therefore, we explored the biogeography of the entire, abundant, and rare (sub)communities in nine rivers that cover a wide space range and large elevational gradient in China. Our results revealed that bacterial rare and abundant subcommunities shared similar biogeographic patterns but their assembly mechanisms were much different in these rivers. Moreover, bacterial communities showed evident differentiations between high elevations and low elevations. These findings will facilitate a better understanding of bacterial diversity features in river systems.},
}
@article {pmid35633375,
year = {2023},
author = {Araujo, ASF and de Araujo Pereira, AP and Melo, VMM and de Medeiros, EV and Mendes, LW},
title = {Environmental DNA Sequencing to Monitor Restoration Practices on Soil Bacterial and Archaeal Communities in Soils Under Desertification in the Brazilian Semiarid.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1072-1076},
pmid = {35633375},
issn = {1432-184X},
mesh = {Humans ; *Archaea/genetics ; Soil/chemistry ; *DNA, Environmental ; Conservation of Natural Resources ; Brazil ; Soil Microbiology ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Soils from Brazilian semiarid regions are highly vulnerable to desertification due to their geology, climate, human actions, and intensive land use that contribute to desertification. Therefore, areas under desertification have increased in the Brazilian semiarid region and it has negatively changed the soil bacterial and archaeal communities and their functionality. On the other hand, although restoration strategies are expensive and there are few soils restoration programs, some practices have been applied to restore these soils under desertification. For instance, conservationist practices and grazing exclusion have been strategically implemented, and they created a new altered soil condition for soil microbial communities, boosting soil microbial diversity. Here, we discuss the potential of these restoration strategies to recover the richness and diversity of soil bacterial and archaeal communities that were described through environmental DNA (eDNA) sequencing of soil samples. eDNA sequencing results show that areas where restoration strategies have been applied in regions under desertification in the Brazilian semiarid have increased species richness, diversity, and structure of the bacterial and archaeal community. In addition, network connectivity and functionality of the soil microorganisms have been improved over time. Altogether, we show that management strategies for soil restoration have positive effects on soil microbial communities and these effects can be monitored using the eDNA sequencing approach.},
}
@article {pmid35633186,
year = {2022},
author = {Ravegnini, G and Fosso, B and Ricci, R and Gorini, F and Turroni, S and Serrano, C and Pilco-Janeta, DF and Zhang, Q and Zanotti, F and De Robertis, M and Nannini, M and Pantaleo, MA and Hrelia, P and Angelini, S},
title = {Analysis of microbiome in gastrointestinal stromal tumors: Looking for different players in tumorigenesis and novel therapeutic options.},
journal = {Cancer science},
volume = {113},
number = {8},
pages = {2590-2599},
pmid = {35633186},
issn = {1349-7006},
support = {//FG and FZ were supported by the Fondazione Cassa di Risparmio di Bologna (CARISBO)/ ; },
mesh = {Cell Transformation, Neoplastic ; *Gastrointestinal Neoplasms/genetics ; *Gastrointestinal Stromal Tumors/genetics/pathology ; Humans ; *Microbiota ; Mutation ; Proto-Oncogene Proteins c-kit/genetics ; },
abstract = {Preclinical forms of gastrointestinal stromal tumor (GIST), small asymptomatic lesions, called microGIST, are detected in approximately 30% of the general population. Gastrointestinal stromal tumor driver mutation can be already detected in microGISTs, even if they do not progress into malignant cancer; these mutations are necessary, but insufficient events to foster tumor progression. Here we profiled the tissue microbiota of 60 gastrointestinal specimens in three different patient cohorts-micro, low-risk, and high-risk or metastatic GIST-exploring the compositional structure, predicted function, and microbial networks, with the aim of providing a complete overview of microbial ecology in GIST and its preclinical form. Comparing microGISTs and GISTs, both weighted and unweighted UniFrac and Bray-Curtis dissimilarities showed significant community-level separation between them and a pronounced difference in Proteobacteria, Firmicutes, and Bacteroidota was observed. Through the LEfSe tool, potential microbial biomarkers associated with a specific type of lesion were identified. In particular, GIST samples were significantly enriched in the phylum Proteobacteria compared to microGISTs. Several pathways involved in sugar metabolism were also highlighted in GISTs; this was expected as cancer usually displays high aerobic glycolysis in place of oxidative phosphorylation and rise of glucose flux to promote anabolic request. Our results highlight that specific differences do exist in the tissue microbiome community between GIST and benign lesions and that microbiome restructuration can drive the carcinogenesis process.},
}
@article {pmid35631287,
year = {2022},
author = {Sauvaitre, T and Van Herreweghen, F and Delbaere, K and Durif, C and Van Landuyt, J and Fadhlaoui, K and Huille, S and Chaucheyras-Durand, F and Etienne-Mesmin, L and Blanquet-Diot, S and Van de Wiele, T},
title = {Lentils and Yeast Fibers: A New Strategy to Mitigate Enterotoxigenic Escherichia coli (ETEC) Strain H10407 Virulence?.},
journal = {Nutrients},
volume = {14},
number = {10},
pages = {},
pmid = {35631287},
issn = {2072-6643},
mesh = {Caco-2 Cells ; Diarrhea ; Dietary Fiber/pharmacology ; *Enterotoxigenic Escherichia coli ; *Escherichia coli Infections/prevention &amp; control ; Humans ; *Lens Plant ; Plant Extracts ; Saccharomyces cerevisiae ; Travel ; Virulence ; },
abstract = {Dietary fibers exhibit well-known beneficial effects on human health, but their anti-infectious properties against enteric pathogens have been poorly investigated. Enterotoxigenic Escherichia coli (ETEC) is a major food-borne pathogen that causes acute traveler's diarrhea. Its virulence traits mainly rely on adhesion to an epithelial surface, mucus degradation, and the secretion of two enterotoxins associated with intestinal inflammation. With the increasing burden of antibiotic resistance worldwide, there is an imperious need to develop novel alternative strategies to control ETEC infections. This study aimed to investigate, using complementary in vitro approaches, the inhibitory potential of two dietary-fiber-containing products (a lentil extract and yeast cell walls) against the human ETEC reference strain H10407. We showed that the lentil extract decreased toxin production in a dose-dependent manner, reduced pro-inflammatory interleukin-8 production, and modulated mucus-related gene induction in ETEC-infected mucus-secreting intestinal cells. We also report that the yeast product reduced ETEC adhesion to mucin and Caco-2/HT29-MTX cells. Both fiber-containing products strengthened intestinal barrier function and modulated toxin-related gene expression. In a complex human gut microbial background, both products did not elicit a significant effect on ETEC colonization. These pioneering data demonstrate the promising role of dietary fibers in controlling different stages of the ETEC infection process.},
}
@article {pmid35630477,
year = {2022},
author = {Johnson, MS and Burns, BP and Herdean, A and Angeloski, A and Ralph, P and Morris, T and Kindler, G and Wong, HL and Kuzhiumparambil, U and Sedger, LM and Larkum, AWD},
title = {A Cyanobacteria Enriched Layer of Shark Bay Stromatolites Reveals a New Acaryochloris Strain Living in Near Infrared Light.},
journal = {Microorganisms},
volume = {10},
number = {5},
pages = {},
pmid = {35630477},
issn = {2076-2607},
abstract = {The genus Acaryochloris is unique among phototrophic organisms due to the dominance of chlorophyll d in its photosynthetic reaction centres and light-harvesting proteins. This allows Acaryochloris to capture light energy for photosynthesis over an extended spectrum of up to ~760 nm in the near infra-red (NIR) spectrum. Acaryochloris sp. has been reported in a variety of ecological niches, ranging from polar to tropical shallow aquatic sites. Here, we report a new Acarychloris strain isolated from an NIR-enriched stratified microbial layer 4-6 mm under the surface of stromatolite mats located in the Hamelin Pool of Shark Bay, Western Australia. Pigment analysis by spectrometry/fluorometry, flow cytometry and spectral confocal microscopy identifies unique patterns in pigment content that likely reflect niche adaption. For example, unlike the original A. marina species (type strain MBIC11017), this new strain, Acarychloris LARK001, shows little change in the chlorophyll d/a ratio in response to changes in light wavelength, displays a different Fv/Fm response and lacks detectable levels of phycocyanin. Indeed, 16S rRNA analysis supports the identity of the A. marina LARK001 strain as close to but distinct from from the A. marina HICR111A strain first isolated from Heron Island and previously found on the Great Barrier Reef under coral rubble on the reef flat. Taken together, A. marina LARK001 is a new cyanobacterial strain adapted to the stromatolite mats in Shark Bay.},
}
@article {pmid35630422,
year = {2022},
author = {Scoma, A and Khor, WC and Coma, M and Heyer, R and Props, R and Bouts, T and Benndorf, D and Li, D and Zhang, H and Rabaey, K},
title = {Lignocellulose Fermentation Products Generated by Giant Panda Gut Microbiomes Depend Ultimately on pH Rather than Portion of Bamboo: A Preliminary Study.},
journal = {Microorganisms},
volume = {10},
number = {5},
pages = {},
pmid = {35630422},
issn = {2076-2607},
abstract = {Giant pandas feed almost exclusively on bamboo but miss lignocellulose-degrading genes. Their gut microbiome may contribute to their nutrition; however, the limited access to pandas makes experimentation difficult. In vitro incubation of dung samples is used to infer gut microbiome activity. In pandas, such tests indicated that green leaves are largely fermented to ethanol at neutral pH and yellow pith to lactate at acidic pH. Pandas may feed on either green leaves or yellow pith within the same day, and it is unclear how pH, dung sample, fermentation products and supplied bamboo relate to one another. Additionally, the gut microbiome contribution to solid bamboo digestion must be appropriately assessed. Here, gut microbiomes derived from dung samples with mixed colors were used to ferment green leaves, also by artificially adjusting the initial pH. Gut microbiomes digestion of solid lignocellulose accounted for 30-40% of the detected final fermentation products. At pH 6.5, mixed-color dung samples had the same fermentation profile as green dung samples (mainly alcohols), while adjusting the initial pH to 4.5 resulted in the profile of yellow dung samples (mainly lactate). Metaproteomics confirmed that gut microbiomes attacked hemicellulose, and that the panda's alpha amylase was the predominant enzyme (up to 75%).},
}
@article {pmid35630387,
year = {2022},
author = {Smercina, D and Zambare, N and Hofmockel, K and Sadler, N and Bredeweg, EL and Nicora, C and Markillie, LM and Aufrecht, J},
title = {Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics.},
journal = {Microorganisms},
volume = {10},
number = {5},
pages = {},
pmid = {35630387},
issn = {2076-2607},
abstract = {The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates-parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.},
}
@article {pmid35628778,
year = {2022},
author = {Tao, S and Zhang, Y and Tian, C and Duplessis, S and Zhang, N},
title = {Elevated Ozone Concentration and Nitrogen Addition Increase Poplar Rust Severity by Shifting the Phyllosphere Microbial Community.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {5},
pages = {},
pmid = {35628778},
issn = {2309-608X},
support = {2021ZY02//Fundamental Research Funds for the Central Universities/ ; 2021M690418//China Postdoctoral Science Foundation/ ; },
abstract = {Tropospheric ozone and nitrogen deposition are two major environmental pollutants. A great deal of research has focused on the negative impacts of elevated O3 and the complementary effect of soil N addition on the physiological properties of trees. However, it has been overlooked how elevated O3 and N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host-pathogen-environment interplay. Here, we examined the effects of elevated O3 and soil N addition on poplar leaf rust [Melampsora larici-populina] severity of two susceptible hybrid poplars [clone '107': Populus euramericana cv. '74/76'; clone '546': P. deltoides Í P. cathayana] in Free-Air-Controlled-Environment plots, in addition, the link between Mlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone '107' significantly increased under elevated O3 or N addition only; however, the negative impact of elevated O3 could be significantly mitigated when accompanied by N addition, likewise, this trade-off was reflected in its phyllosphere microbial α-diversity responding to elevated O3 and N addition. However, rust severity of clone '546' did not differ significantly in the cases of elevated O3 and N addition. Mlp infection altered microbial community composition and increased its sensitivity to elevated O3, as determined by the markedly different abundance of taxa. Elevated O3 and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings suggest that poplars require a changing phyllosphere microbial associations to optimize plant immunity in response to environmental changes.},
}
@article {pmid35624481,
year = {2022},
author = {Tian, Z and Pu, H and Cai, D and Luo, G and Zhao, L and Li, K and Zou, J and Zhao, X and Yu, M and Wu, Y and Yang, T and Guo, P and Hu, X},
title = {Characterization of the bacterial microbiota in different gut and oral compartments of splendid japalure (Japalura sensu lato).},
journal = {BMC veterinary research},
volume = {18},
number = {1},
pages = {205},
pmid = {35624481},
issn = {1746-6148},
support = {2019QD09//Doctor Launch Project of Yibin University/ ; 2019QD10//Doctor Launch Project of Yibin University/ ; XDA 20050201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2019QZKK05010105//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; },
mesh = {Animals ; Bacteria/genetics ; Bacteroidetes/genetics ; Feces/microbiology ; Firmicutes/genetics ; *Lizards ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Gut and oral microbes form complex communities and play key roles in co-evolution with their hosts. However, little is understood about the bacterial community in lizards.<br><br>RESULTS: In this study, we investigated the gut and oral bacterial communities in Japalura sensu lato from Sichuan Province, China, using 16S rRNA gene sequencing. Results showed that Bacteroidota (36.5%) and Firmicutes (32.8%) were the main phyla in the gut, while Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota were the dominant phyla in the oral cavity. 16&#xa0;S rRNA sequencing analysis of fecal samples showed that: (1) Bacteroidota was the most abundant in Japalura sensu lato, which was different from the bacterial community of insectivorous animals; (2) Bacteroidota, Firmicutes, Actinobacteriota, Fusobacteriota, and Cyanobacteria were the most abundant phylum in Japalura sensu lato. (3) Proteobacteria was the dominant phylum in Japalura sensu lato and other domestic insectivorous lizards (Shinisaurus crocodilurus, Phrynocephalus vlangalii, and Takydromus septentrionalis); (4) Comparing with the bacterial community of Shinisaurus crocodilurus, Phrynocephalus vlangalii, Takydromus septentrionalis, Liolaemus parvus, L. ruibali, and Phymaturus williamsi, Desulfobacterota was uniquely present in the gut of Japalura sensu lato. 16&#xa0;S rRNA sequencing of oral samples showed that Chloroflexi and Deinococcota phyla were enriched in the oral cavity, which may have a significant influence on living in extreme environments.<br><br>CONCLUSIONS: Thus, based on 16&#xa0;S rRNA sequencing analysis of the community composition of the gut and oral microbiomes, this study firstly represents a foundation for understanding the gut and oral microbial ecology of Japalura sensu lato, and constitutes a detail account of the diversity of the microbiota inhabiting the gut and oral cavity of Japalura sensu lato. Further researches will continue to reveal how gut and oral microbial communities may be impacting the ecology and evolution of lizards.},
}
@article {pmid35624343,
year = {2023},
author = {Vázquez, V and León, P and Gordillo, FJL and Jiménez, C and Concepción, I and Mackenzie, K and Bresnan, E and Segovia, M},
title = {High-CO2 Levels Rather than Acidification Restrict Emiliania huxleyi Growth and Performance.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {127-143},
pmid = {35624343},
issn = {1432-184X},
support = {FC14-RNM-27//Universidad de M&#xe1;laga/ ; },
mesh = {*Seawater ; *Haptophyta/physiology ; Carbon Dioxide/metabolism ; Hydrogen-Ion Concentration ; Photosynthesis ; },
abstract = {The coccolithophore Emiliania huxleyi shows a variety of responses to ocean acidification (OA) and to high-CO2 concentrations, but there is still controversy on differentiating between these two factors when using different strains and culture methods. A heavily calcified type A strain isolated from the Norwegian Sea was selected and batch cultured in order to understand whether acclimation to OA was mediated mainly by CO2 or H[+], and how it impacted cell growth performance, calcification, and physiological stress management. Emiliania huxleyi responded differently to each acidification method. CO2-enriched aeration (1200 µatm, pH 7.62) induced a negative effect on the cells when compared to acidification caused by decreasing pH alone (pH 7.60). The growth rates of the coccolithophore were more negatively affected by high pCO2 than by low pH without CO2 enrichment with respect to the control (400 µatm, pH 8.1). High CO2 also affected cell viability and promoted the accumulation of reactive oxygen species (ROS), which was not observed under low pH. This suggests a possible metabolic imbalance induced by high CO2 alone. In contrast, the affinity for carbon uptake was negatively affected by both low pH and high CO2. Photochemistry was only marginally affected by either acidification method when analysed by PAM fluorometry. The POC and PIC cellular quotas and the PIC:POC ratio shifted along the different phases of the cultures; consequently, calcification did not follow the same pattern observed in cell stress and growth performance. Specifically, acidification by HCl addition caused a higher proportion of severely deformed coccoliths, than CO2 enrichment. These results highlight the capacity of CO2 rather than acidification itself to generate metabolic stress, not reducing calcification.},
}
@article {pmid35622094,
year = {2023},
author = {Zhang, Z and Zhao, H and Mou, S and Nair, S and Zhao, J and Jiao, N and Zhang, Y},
title = {Phage Infection Benefits Marine Diatom Phaeodactylum tricornutum by Regulating the Associated Bacterial Community.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {144-153},
pmid = {35622094},
issn = {1432-184X},
support = {2020YFA0608304//National Key Research and Development Programs of China/ ; },
mesh = {*Diatoms/physiology ; *Bacteriophages ; Bacteria ; Aquatic Organisms ; },
abstract = {The interaction between marine phyto- and bacterioplankton is regulated by multiple environmental and biological factors. Among them, phages as the major regulators of bacterial mortality are considered to have important impacts on algae-associated bacteria and algae-bacteria relationship. However, little is currently known about the actual impact of phages from this perspective. Here, we revealed that phage infection improved the maximum quantum efficiency of photosystem II of Phaeodactylum tricornutum by regulating the associated bacterial community. Specifically, phage infection weakened bacterial abundance and eliminated their negative effects on the diatom. Unexpectedly, the structure of the bacterial community co-cultured with the diatom was not significantly affected, likely because the shaping effect of the diatom on the bacterial community structure can far outcompete or mask the impact of phage infection. Our results established a link between algae, bacteria, and phages, suggesting that phage infection benefits the diatom by regulating the associated bacterial community.},
}
@article {pmid35620054,
year = {2022},
author = {Yaigoub, H and Tirichen, H and Xin, X and Shi, S and Wu, C and Li, R and Li, Y},
title = {Isolation of Viable Single Cells With High Yield and Purity Using a Small Amount of Human Kidney Tissue Biopsy.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {822275},
pmid = {35620054},
issn = {2296-634X},
abstract = {Objective: Establishment of an efficient method of preparing human kidney single cell suspension, using a very small amount of tissue puncture. Methods: Samples of human kidney tissue puncture were cut into pieces, and then 80 μL of the digestive enzyme were added to each punctured tissue to induce enzymatic digestion. The enzyme combination is composed of collagenases, DNase and hyaluronidase and the sample was incubated 20 min at 37°C. The obtained cell suspension was filtered through a 70 μm cell strainer, centrifuged at 300 g for 5 min and the supernatant was removed, then the pellet was resuspended in 3 ml of DMEM (Dulbecco's Modified Eagle's Medium). Cell suspension was sorted and purified by flow sorting to remove dead cells and obtain a cell suspension with higher viability rate. Results: We found that 1) diverse single cells of human kidney can be obtained by the digestive enzyme, as observed under the light microscope, with different sizes, normal cell morphology and good dispersion. 2) (2-3) × 10[6] single cells can be extracted from one fresh punctured kidney tissue of about 10 mg, with a cell viability rate of more than 80%. Conclusion: In this work we generated a comprehensive and high-resolution single-cell method, which is simple and efficient for preparing single cell suspension from a minimal amount of human kidney tissue. This method can facilitate the study of renal cell biology and the pathogenesis of kidney diseases.},
}
@article {pmid35618944,
year = {2023},
author = {Lau, NS and Ting, SY and Sam, KK and M, J and Wong, SC and Wu, X and Waiho, K and Fazhan, H and Shu-Chien, AC},
title = {Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {575-588},
pmid = {35618944},
issn = {1432-184X},
mesh = {Animals ; *Brachyura ; *Gastrointestinal Microbiome ; Fatty Acids, Unsaturated/metabolism ; Diet ; Lipid Metabolism ; },
abstract = {Although numerous studies in aquatic organisms have linked lipid metabolism with intestinal bacterial structure, the possibility of the gut microbiota participating in the biosynthesis of beneficial long-chain polyunsaturated fatty acid (LC-PUFA) remains vague. We profiled the gut microbiota of the mud crab Scylla olivacea fed with either a LC-PUFA rich (FO) or a LC-PUFA-poor but C18-PUFA substrate-rich (LOCO) diet. Additionally, a diet with a similar profile as LOCO but with the inclusion of an antibiotic, oxolinic acid (LOCOAB), was also used to further demarcate the possibility of LC-PUFA biosynthesis in gut microbiota. Compared to diet FO treatment, crabs fed diet LOCO contained a higher proportion of Proteobacteria, notably two known taxonomy groups with PUFA biosynthesis capacity, Vibrio and Shewanella. Annotation of metagenomic datasets also revealed enrichment in the KEGG pathway of unsaturated fatty acid biosynthesis and polyketide synthase-like system sequences with this diet. Intriguingly, diet LOCOAB impeded the presence of Vibrio and Shewanella and with it, the function of unsaturated fatty acid biosynthesis. However, there was an increase in the function of short-chain fatty acid production, accompanied by a shift towards the abundance of phyla Bacteroidota and Spirochaetota. Collectively, these results exemplified bacterial communities and their corresponding PUFA biosynthesis pathways in the microbiota of an aquatic crustacean species.},
}
@article {pmid35617903,
year = {2022},
author = {Xiong, C and Calatayud, M and van de Wiele, T and Francesconi, K},
title = {Gut microbiota metabolize arsenolipids in a donor dependent way.},
journal = {Ecotoxicology and environmental safety},
volume = {239},
number = {},
pages = {113662},
doi = {10.1016/j.ecoenv.2022.113662},
pmid = {35617903},
issn = {1090-2414},
mesh = {*Arsenic/analysis ; *Arsenicals/chemistry ; Chromatography, High Pressure Liquid/methods ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; },
abstract = {Understanding the interplay between the gut microbiome and arsenolipids can help us manage the potential health risk of consuming seafood, but little is known about the bioconversion fate of arsenolipids in the gastrointestinal tract. We use an in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME) to mimic the digestive tract of four healthy donors during exposure to two arsenolipids (an arsenic fatty acid AsFA 362 or an arsenic hydrocarbon AsHC 332). The metabolites were analyzed by HPLC-mass spectrometry. The human gut bacteria accumulated arsenolipids in a donor-dependent way, with higher retention of AsHC 332. Colonic microbiota partly transformed both arsenolipids to their thioxo analogs, while AsFA 362 was additionally transformed into arsenic-containing fatty esters, arsenic-containing fatty alcohols, and arsenic-containing sterols. There was no significant difference in water-soluble arsenicals between arsenolipid treatments. The study shows that arsenolipids can be quickly biotransformed into several lipid-soluble arsenicals of unknown toxicity, which cannot be excluded when considering potential implications on human health.},
}
@article {pmid35615500,
year = {2022},
author = {Laber, CP and Pontiller, B and Bunse, C and Osbeck, CMG and Pérez-Martínez, C and Di Leo, D and Lundin, D and Legrand, C and Pinhassi, J and Farnelid, H},
title = {Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {828459},
pmid = {35615500},
issn = {1664-302X},
abstract = {The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3-V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 × 10[4] cells ml[-1]. This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord.},
}
@article {pmid35610383,
year = {2023},
author = {Pierangeli, GMF and Domingues, MR and Choueri, RB and Hanisch, WS and Gregoracci, GB and Benassi, RF},
title = {Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {297-310},
pmid = {35610383},
issn = {1432-184X},
mesh = {*Archaea/genetics ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Water Quality ; },
abstract = {Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.},
}
@article {pmid35610382,
year = {2023},
author = {Dhar, K and Panneerselvan, L and Subashchandrabose, SR and Venkateswarlu, K and Megharaj, M},
title = {Anaerobic Degradation of Naphthalene and Pyrene by Sulfate-Reducing Cultures Enriched from Former Manufactured Gas Plant Soil.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {271-281},
pmid = {35610382},
issn = {1432-184X},
support = {RTP scholarship//University of Newcastle/ ; },
mesh = {Anaerobiosis ; *Sulfates/metabolism ; Naphthalenes/metabolism ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Pyrenes ; Biodegradation, Environmental ; },
abstract = {Biodegradation of polycyclic aromatic hydrocarbons (PAHs) under completely anaerobic sulfate-reducing conditions is an energetically challenging process. To date, anaerobic degradations of only two-ringed naphthalene and three-ringed phenanthrene by sediment-free and enriched sulfate-reducing bacteria have been reported. In this study, sulfate-reducing enrichment cultures capable of degrading naphthalene and four-ringed PAH, pyrene, were enriched from a contaminated former gas plant site soil. Bacterial community composition analysis revealed that a naphthalene-degrading enrichment culture, MMNap, was dominated (84.90%) by a Gram-positive endospore-forming member of the genus Desulfotomaculum with minor contribution (8.60%) from a member of Clostridium. The pyrene-degrading enrichment, MMPyr, was dominated (97.40%) by a species of Desulfotomaculum. The sequences representing the Desulfotomaculum phylotypes shared 98.80% similarity to each other. After 150 days of incubation, MMNap degraded 195 µM naphthalene with simultaneous reduction of sulfate and accumulation of sulfide. Similarly, MMPyr degraded 114 µM pyrene during 180 days of incubation with nearly stochiometric sulfate consumption and sulfide accumulation. In both cases, the addition of sulfate reduction inhibitor, molybdate (20 mM), resulted in complete cessation of the substrate utilization and sulfate reduction that clearly indicated the major role of the sulfate-reducing Desulfotomaculum in biodegradation of the two PAHs. This study is the first report on anaerobic pyrene degradation by a matrix-free, strictly anaerobic, and sulfate-reducing enrichment culture.},
}
@article {pmid35609949,
year = {2022},
author = {De Wit, G and Svet, L and Lories, B and Steenackers, HP},
title = {Microbial Interspecies Interactions and Their Impact on the Emergence and Spread of Antimicrobial Resistance.},
journal = {Annual review of microbiology},
volume = {76},
number = {},
pages = {179-192},
doi = {10.1146/annurev-micro-041320-031627},
pmid = {35609949},
issn = {1545-3251},
mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Bacterial ; Microbial Interactions ; },
abstract = {Bacteria are social organisms that commonly live in dense communities surrounded by a multitude of other species. The competitive and cooperative interactions between these species not only shape the bacterial communities but also influence their susceptibility to antimicrobials. While several studies have shown that mixed-species communities are more tolerant toward antimicrobials than their monospecies counterparts, only limited empirical data are currently available on how interspecies interactions influence resistance development. We here propose a theoretic framework outlining the potential impact of interspecies social behavior on different aspects of resistance development. We identify factors by which interspecies interactions might influence resistance evolution and distinguish between their effect on (a) the emergence of a resistant mutant and (b) the spread of this resistance throughout the population. Our analysis indicates that considering the social life of bacteria is imperative to the rational design of more effective antibiotic treatment strategies with a minimal hazard for resistance development.},
}
@article {pmid35608637,
year = {2023},
author = {Perini, L and Gostinčar, C and Likar, M and Frisvad, JC and Kostanjšek, R and Nicholes, M and Williamson, C and Anesio, AM and Zalar, P and Gunde-Cimerman, N},
title = {Interactions of Fungi and Algae from the Greenland Ice Sheet.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {282-296},
pmid = {35608637},
issn = {1432-184X},
support = {675546//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; NE/M021025/1//Natural Environment Research Council/ ; 856416//H2020 European Research Council/ ; P1-0170//Javna Agencija za Raziskovalno Dejavnost RS/ ; P1-0198//Javna Agencija za Raziskovalno Dejavnost RS/ ; J4-2549//Javna Agencija za Raziskovalno Dejavnost RS/ ; DNRF137//Danmarks Grundforskningsfond/ ; 2871//Agilent Foundation/ ; },
mesh = {*Ice Cover/microbiology ; Greenland ; Benzocycloheptenes ; *Streptophyta ; Fungi ; },
abstract = {Heavily pigmented glacier ice algae Ancylonema nordenskiöldii and Ancylonema alaskanum (Zygnematophyceae, Streptophyta) reduce the bare ice albedo of the Greenland Ice Sheet, amplifying melt from the largest cryospheric contributor to eustatic sea-level rise. Little information is available about glacier ice algae interactions with other microbial communities within the surface ice environment, including fungi, which may be important for sustaining algal bloom development. To address this substantial knowledge gap and investigate the nature of algal-fungal interactions, an ex situ co-cultivation experiment with two species of fungi, recently isolated from the surface of the Greenland Ice Sheet (here proposed new species Penicillium anthracinoglaciei Perini, Frisvad and Zalar, Mycobank (MB 835602), and Articulospora sp.), and the mixed microbial community dominated by glacier ice algae was performed. The utilization of the dark pigment purpurogallin carboxylic acid-6-O-β-D-glucopyranoside (C18H18O12) by the two fungi was also evaluated in a separate experiment. P. anthracinoglaciei was capable of utilizing and converting the pigment to purpurogallin carboxylic acid, possibly using the sugar moiety as a nutrient source. Furthermore, after 3 weeks of incubation in the presence of P. anthracinoglaciei, a significantly slower decline in the maximum quantum efficiency (Fv/Fm, inverse proxy of algal stress) in glacier ice algae, compared to other treatments, was evident, suggesting a positive relationship between these species. Articulospora sp. did uptake the glycosylated purpurogallin, but did not seem to be involved in its conversion to aglycone derivative. At the end of the incubation experiments and, in conjunction with increased algal mortality, we detected a substantially increasing presence of the zoosporic fungi Chytridiomycota suggesting an important role for them as decomposers or parasites of glacier ice algae.},
}
@article {pmid35607968,
year = {2022},
author = {Semler, AC and Fortney, JL and Fulweiler, RW and Dekas, AE},
title = {Cold Seeps on the Passive Northern U.S. Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {11},
pages = {e0046822},
pmid = {35607968},
issn = {1098-5336},
mesh = {*Archaea/metabolism ; Geologic Sediments/microbiology ; Methane/metabolism ; Methanosarcinales/genetics ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/microbiology ; },
abstract = {Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Atlantic Margin (USAM). We sampled in and around four USAM seeps and combined pore water geochemistry measurements with amplicon sequencing of 16S rRNA and mcrA (DNA and RNA) to investigate the microbial communities present, their assembly processes, and how they compare to communities at previously studied sites. We found that the USAM seeps contained communities consistent with the canonical seep microbiome at the class and order levels but differed markedly at the sequence variant level, especially within the anaerobic methanotrophic (ANME) archaea. The ANME populations were highly uneven, with just a few dominant mcrA sequence variants at each seep. Interestingly, the USAM seeps did not form a distinct phylogenetic cluster when compared with other previously described seeps around the world. Consistent with this, we found only a very weak (though statistically significant) distance-decay trend in seep community similarity across a global data set. Ecological assembly indices suggest that the USAM seep communities were assembled primarily deterministically, in contrast to the surrounding nonseep sediments, where stochastic processes dominated. Together, our results suggest that the primary driver of seep microbial community composition is local geochemistry-specifically methane, sulfide, nitrate, acetate, and ammonium concentrations-rather than the geologic context, the composition of nearby seeps, or random events of dispersal. IMPORTANCE Cold seeps are now known to be widespread features of passive continental margins, including the northern U.S. Atlantic Margin (USAM). Methane seepage is expected to intensify at these relatively shallow seeps as bottom waters warm and underlying methane hydrates dissociate. While methanotrophic microbial communities might reduce or prevent methane release, microbial communities on passive margins have rarely been characterized. In this study, we investigated the Bacteria and Archaea at four cold seeps on the northern USAM and found that despite being colocated on the same continental slope, the communities significantly differ by site at the sequence variant level, particularly methane-cycling community members. Differentiation by site was not observed in similarly spaced background sediments, raising interesting questions about the dispersal pathways of cold seep microorganisms. Understanding the genetic makeup of these discrete seafloor ecosystems and how their microbial communities develop will be increasingly important as the climate changes.},
}
@article {pmid35604764,
year = {2022},
author = {Benítez-Páez, A and Hartstra, AV and Nieuwdorp, M and Sanz, Y},
title = {Species- and strain-level assessment using rrn long-amplicons suggests donor's influence on gut microbial transference via fecal transplants in metabolic syndrome subjects.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2078621},
pmid = {35604764},
issn = {1949-0984},
mesh = {Bacteria/genetics ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; *Metabolic Syndrome/microbiology/physiopathology/therapy ; Nucleotides ; },
abstract = {Fecal microbiota transplantation (FMT) is currently used for treating Clostridium difficile infection and explored for other clinical applications in experimental trials. However, the effectiveness of this therapy could vary, and partly depend on the donor's bacterial species engraftment, whose evaluation is challenging because there are no cost-effective strategies for accurately tracking the microbe transference. In this regard, the precise identification of bacterial species inhabiting the human gut is essential to define their role in human health unambiguously. We used Nanopore-based device to sequence bacterial rrn operons (16S-ITS-23S) and to reveal species-level abundance changes in the human gut microbiota of a FMT trial. By assessing the donor and recipient microbiota before and after FMT, we further evaluated whether this molecular approach reveals strain-level genetic variation to demonstrate microbe transfer and engraftment. Strict control over sequencing data quality and major microbiota covariates was critical for accurately estimating the changes in gut microbial species abundance in the recipients after FMT. We detected strain-level variation via single-nucleotide variants (SNVs) at rrn regions in a species-specific manner. We showed that it was possible to explore successfully the donor-bacterial strain (e.g., Parabacteroides merdae) engraftment in recipients of the FMT by assessing the nucleotide frequencies at rrn-associated SNVs. Our findings indicate that the engraftment of donors' microbiota is to some extent correlated with the improvement of metabolic health in recipients and that parameters such as the baseline gut microbiota configuration, sex, and age of donors should be considered to ensure the success of FMT in humans. The study was prospectively registered at the Dutch Trial registry - NTR4488 (https://www.trialregister.nl/trial/4488).},
}
@article {pmid35604433,
year = {2023},
author = {Fang, J and Jiang, W and Meng, S and He, W and Wang, G and Guo, E and Yan, Y},
title = {Polychaete Bioturbation Alters the Taxonomic Structure, Co-occurrence Network, and Functional Groups of Bacterial Communities in the Intertidal Flat.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {112-126},
pmid = {35604433},
issn = {1432-184X},
support = {41876185//National Natural Science Foundation of China/ ; 2020TD50//Central Public-interest Scientific Institution Basal Research Fund/ ; ZR2020QC046//Shandong Province Natural Science Foundation/ ; 2018YFJH0703//Key Projects of Science and Technology Innovation of Shandong Province/ ; },
mesh = {Humans ; Animals ; Bacteria/genetics ; *Polychaeta ; *Environmental Restoration and Remediation ; *Microbiota ; Bacteroidetes ; Geologic Sediments/microbiology ; },
abstract = {Polychaetes are important benthic macrofauna that lives in sediments, usually in intertidal flats with high organic content and high sulfide. It has been suggested that polychaete bioturbation could perform environmental remediation. During the process, the microbial community plays important roles. Here, we used high-throughput sequencing technology to study the bioturbation effects on the bacterial community in the polychaete (Perinereis aibuhitensis) burrows at different tidal positions in intertidal flat. The results showed that the bacterial communities were dramatically influenced by the polychaete bioturbation. The ACE, Chao, and Shannon indices of the polychaete burrows increased in summer. Dominant phyla in the polychaete burrows were Proteobacteria, Campilobacterota, Desulfobacterota, Chloroflexi, and Bacteroidota, and the dominant bacterial families were Sulfurvaceae, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, Desulfobulbaceae, and Sulfurimonadaceae. Results of linear discriminant analysis effect size (LEfSe) showed that groups that include organic matter degraders, such as Bacteroidota, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, and groups that include sulfur oxidizers, such as Campilobacterota, Sulfurovaceae, Rhodobacteraceae, Desulfobulbaceae, and Sulfurimonadaceae, were significantly increased due to the polychaete bioturbation. The polychaete bioturbation reduced the complexity of the bacterial co-occurrence network while increased its modularity and homogeneity. The polychaete bioturbation also changed the functional groups, which significantly enhanced in functional groups of aerobic nitrite oxidation, nitration, dark thiosulfate oxidation, dark sulfur oxidation, and dark sulfite oxidation, while nitrogen respiration and nitrate respiration decreased. These results provide insight into the impact of bacterial communities under the intertidal polychaete bioturbation.},
}
@article {pmid35604432,
year = {2023},
author = {Salazar, B and Ortiz, A and Keswani, C and Minkina, T and Mandzhieva, S and Pratap Singh, S and Rekadwad, B and Borriss, R and Jain, A and Singh, HB and Sansinenea, E},
title = {Bacillus spp. as Bio-factories for Antifungal Secondary Metabolites: Innovation Beyond Whole Organism Formulations.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {1-24},
pmid = {35604432},
issn = {1432-184X},
support = {LabNOTs-21-01AB//Ministry of Science and Higher Education of the Russian Federationt/ ; },
mesh = {Humans ; Agriculture/methods/trends ; *Antifungal Agents/metabolism ; *Bacillus/genetics/metabolism ; Fungicides, Industrial/metabolism ; *Plant Diseases/prevention &amp; control/microbiology ; *Industrial Microbiology ; Crops, Agricultural/microbiology ; *Pest Control, Biological/methods/trends ; Multigene Family/genetics ; },
abstract = {Several fungi act as parasites for crops causing huge annual crop losses at both pre- and post-harvest stages. For years, chemical fungicides were the solution; however, their wide use has caused environmental contamination and human health problems. For this reason, the use of biofungicides has been in practice as a green solution against fungal phytopathogens. In the context of a more sustainable agriculture, microbial biofungicides have the largest share among the commercial biocontrol products that are available in the market. Precisely, the genus Bacillus has been largely studied for the management of plant pathogenic fungi because they offer a chemically diverse arsenal of antifungal secondary metabolites, which have spawned a heightened industrial engrossment of it as a biopesticide. In this sense, it is indispensable to know the wide arsenal that Bacillus genus has to apply these products for sustainable agriculture. Having this idea in our minds, in this review, secondary metabolites from Bacillus having antifungal activity are chemically and structurally described giving details of their action against several phytopathogens. Knowing the current status of Bacillus secreted antifungals is the base for the goal to apply these in agriculture and it is addressed in depth in the second part of this review.},
}
@article {pmid35602031,
year = {2022},
author = {Schultz, J and Argentino, ICV and Kallies, R and Nunes da Rocha, U and Rosado, AS},
title = {Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {885557},
pmid = {35602031},
issn = {1664-302X},
abstract = {Extreme temperature gradients in polar volcanoes are capable of selecting different types of extremophiles. Deception Island is a marine stratovolcano located in maritime Antarctica. The volcano has pronounced temperature gradients over very short distances, from as high as 100°C in the fumaroles to subzero next to the glaciers. These characteristics make Deception a promising source of a variety of bioproducts for use in different biotechnological areas. In this study, we isolated thermophilic bacteria from sediments in fumaroles at two geothermal sites on Deception Island with temperatures between 50 and 100°C, to evaluate the potential capacity of these bacteria to degrade petroleum hydrocarbons and produce biosurfactants under thermophilic conditions. We isolated 126 thermophilic bacterial strains and identified them molecularly as members of genera Geobacillus, Anoxybacillus, and Brevibacillus (all in phylum Firmicutes). Seventy-six strains grew in a culture medium supplemented with crude oil as the only carbon source, and 30 of them showed particularly good results for oil degradation. Of 50 strains tested for biosurfactant production, 13 showed good results, with an emulsification index of 50% or higher of a petroleum hydrocarbon source (crude oil and diesel), emulsification stability at 100°C, and positive results in drop-collapse, oil spreading, and hemolytic activity tests. Four of these isolates showed great capability of degrade crude oil: FB2_38 (Geobacillus), FB3_54 (Geobacillus), FB4_88 (Anoxybacillus), and WB1_122 (Geobacillus). Genomic analysis of the oil-degrading and biosurfactant-producer strain FB4_88 identified it as Anoxybacillus flavithermus, with a high genetic and functional diversity potential for biotechnological applications. These initial culturomic and genomic data suggest that thermophilic bacteria from this Antarctic volcano have potential applications in the petroleum industry, for bioremediation in extreme environments and for microbial enhanced oil recovery (MEOR) in reservoirs. In addition, recovery of small-subunit rRNA from metagenomes of Deception Island showed that Firmicutes is not among the dominant phyla, indicating that these low-abundance microorganisms may be important for hydrocarbon degradation and biosurfactant production in the Deception Island volcanic sediments.},
}
@article {pmid35601228,
year = {2022},
author = {Okeke, ES and Olovo, CV and Nkwoemeka, NE and Okoye, CO and Nwankwo, CEI and Onu, CJ},
title = {Microbial ecology and evolution is key to pandemics: using the coronavirus model to mitigate future public health challenges.},
journal = {Heliyon},
volume = {8},
number = {5},
pages = {e09449},
pmid = {35601228},
issn = {2405-8440},
abstract = {Pandemics are global challenges that lead to total disruption of human activities. From the inception of human existence, all pandemics have resulted in loss of human lives. The coronavirus disease caused by SAR-CoV-2 began in China and is now at the global scale with an increase in mortality and morbidity. Numerous anthropogenic activities have been implicated in the emergence and severity of pandemics, including COVID-19. These activities cause changes in microbial ecology, leading to evolution due to mutation and recombination. This review hypothesized that an understanding of these anthropogenic activities would explain the dynamics of pandemics. The recent coronavirus model was used to study issues leading to microbial evolution, towards preventing future pandemics. Our review highlighted anthropogenic activities, including deforestation, mining activities, waste treatment, burning of fossil fuel, as well as international travels as drivers of microbial evolution leading to pandemics. Furthermore, human-animal interaction has also been implicated in pandemic incidents. Our study recommends substantial control of such anthropogenic activities as having been highlighted as ways to reduce the frequency of mutation, reduce pathogenic reservoirs, and the emergence of infectious diseases.},
}
@article {pmid35598673,
year = {2022},
author = {Abel, SM and Primpke, S and Wu, F and Brandt, A and Gerdts, G},
title = {Human footprints at hadal depths: interlayer and intralayer comparison of sediment cores from the Kuril Kamchatka trench.},
journal = {The Science of the total environment},
volume = {838},
number = {Pt 2},
pages = {156035},
doi = {10.1016/j.scitotenv.2022.156035},
pmid = {35598673},
issn = {1879-1026},
mesh = {Ecosystem ; Environmental Pollution ; Humans ; *Microplastics ; Pacific Ocean ; *Plastics ; },
abstract = {Microplastic (MP) pollution affects almost all ecosystems on Earth. Given the increasing plastic production worldwide and the durability of these polymers, concerns arise about the fate of this material in the environment. A candidate to consider as a depositional final sink of MP is the sea floor and its deepest representatives, hadal trenches, as ultimate sinks. In this study, 13 sediment samples were collected with a multiple-corer at depths between 5740 and 9450 m from the Kuril Kamchatka trench (KKT), in the Northwest (NW) Pacific Ocean. These samples were analysed for MP presence in the upper sediment layer, by slicing the first 5 cm of sediment cores into 1 cm horizontal layers. These were compared against each other and between the sampling areas, in order to achieve a detailed picture of the depositional system of the trench and small-scale perturbations such as bioturbation. The analyses revealed the presence of 215 to 1596 MP particles per kg [-1] sediment (dry weight), with a polymer composition represented by 14 polymer types and the prevalence of particles smaller than 25 μm. A heterogeneous microplastic distribution through the sediment column and different microplastic concentration and polymer types among sampling stations located in different areas of the trench reflects the dynamics of this environment and the numerous forces that drive the deposition processes and the in situ recast of this pollutant at the trench floor.},
}
@article {pmid35598661,
year = {2022},
author = {Müller, V and Chavez-Capilla, T and Feldmann, J and Mestrot, A},
title = {Increasing temperature and flooding enhance arsenic release and biotransformations in Swiss soils.},
journal = {The Science of the total environment},
volume = {838},
number = {Pt 1},
pages = {156049},
doi = {10.1016/j.scitotenv.2022.156049},
pmid = {35598661},
issn = {1879-1026},
mesh = {*Arsenic/analysis ; Biotransformation ; Soil ; *Soil Pollutants/analysis ; Switzerland ; Temperature ; },
abstract = {Reductive dissolution is one of the main causes for arsenic (As) mobilisation in flooded soils while biomethylation and biovolatilisation are two microbial mechanisms that greatly influence the mobility and toxicity of As. Climate change results in more extreme weather events such as flooding and higher temperatures, potentially leading to an increase in As release and biotransformations. Here, we investigated the effects of flooding and temperature on As release, biomethylation and biovolatilisation from As-rich soils with different pH and source of As (one acidic and anthropogenic (Salanfe) and one neutral and geogenic (Liesberg)). Flooded soils incubated at 23 °C for two weeks showed a ~ 3-fold (Liesberg site) and ~ 7-fold (Salanfe site) increase in the total As concentration of soil solution compared to those incubated at 18 °C. Methyl- and thio-As species were found in the acidic soil and soil solution. High temperatures enhanced thiolation and methylation although inorganic As was predominant. We also show that volatile As fluxes increased more than 4-fold between treatments, from 18 ± 5 ng/kg/d at 18 °C to 75 ± 6 ng/kg/d at 23 °C from Salanfe soil. Our results suggest that high As soils with acidic pH can become an important source of As to the surrounding environment according to realistic climatic scenarios, and that biovolatilisation is very sensitive to increases in temperature. This study provides new data and further justifies further investigations into climate-induced changes on As release and speciation and its links to important factors such as microbial ecology and sulfate or iron biogeochemistry. SYNOPSIS: In the studied Swiss soils, elevated temperature increases arsenic mobility through volatilisation and methylation.},
}
@article {pmid35597889,
year = {2022},
author = {Ghuneim, LJ and Raghuvanshi, R and Neugebauer, KA and Guzior, DV and Christian, MH and Schena, B and Feiner, JM and Castillo-Bahena, A and Mielke, J and McClelland, M and Conrad, D and Klapper, I and Zhang, T and Quinn, RA},
title = {Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection.},
journal = {The ISME journal},
volume = {16},
number = {9},
pages = {2065-2075},
pmid = {35597889},
issn = {1751-7370},
support = {R01 AI145925/AI/NIAID NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Coinfection/drug therapy ; *Cystic Fibrosis/drug therapy/microbiology ; Humans ; Metagenome ; Sputum/microbiology ; },
abstract = {Antibiotics are our primary approach to treating complex infections, yet we have a poor understanding of how these drugs affect microbial communities. To better understand antimicrobial effects on host-associated microbial communities we treated cultured sputum microbiomes from people with cystic fibrosis (pwCF, n = 24) with 11 different antibiotics, supported by theoretical and mathematical modeling-based predictions in a mucus-plugged bronchiole microcosm. Treatment outcomes we identified in vitro that were predicted in silico were: 1) community death, 2) community resistance, 3) pathogen killing, and 4) fermenter killing. However, two outcomes that were not predicted when antibiotics were applied were 5) community profile shifts with little change in total bacterial load (TBL), and 6) increases in TBL. The latter outcome was observed in 17.8% of samples with a TBL increase of greater than 20% and 6.8% of samples with an increase greater than 40%, demonstrating significant increases in community carrying capacity in the presence of an antibiotic. An iteration of the mathematical model showed that TBL increase was due to antibiotic-mediated release of pH-dependent inhibition of pathogens by anaerobe fermentation. These dynamics were verified in vitro when killing of fermenters resulted in a higher community carrying capacity compared to a no antibiotic control. Metagenomic sequencing of sputum samples during antibiotic therapy revealed similar dynamics in clinical samples. This study shows that the complex microbial ecology dictates the outcomes of antibiotic therapy against a polymicrobial infection.},
}
@article {pmid35596751,
year = {2023},
author = {Yu, X and Zhang, Y and Shen, M and Dong, S and Zhang, F and Gao, Q and He, P and Shen, G and Yang, J and Wang, Z and Bo, G},
title = {Soil Conditioner Affects Tobacco Rhizosphere Soil Microecology.},
journal = {Microbial ecology},
volume = {86},
number = {1},
pages = {460-473},
pmid = {35596751},
issn = {1432-184X},
support = {027Y2021-011//Hubei tobacco company/ ; 201903//Qingdao (Shandong Province) Tobacco Company/ ; 6651117005, 6651121004//Qingdao Agricultural University/ ; },
mesh = {*Soil/chemistry ; *Fertilizers/analysis ; Nicotiana ; Rhizosphere ; Soil Microbiology ; },
abstract = {Reasonable fertilization management can increase nutrient content and enzyme activity in rhizosphere soil, and even increase soil microbial richness. However, different fertilizers could raise distinct influences on the soil properties, including soil environmental factors (physicochemical properties and enzymatic activities) and microbial community. Here, the effects of two soil amendments (microbial fertilizer and woody peat) on environmental factors and microbial community structure in tobacco rhizosphere soil were evaluated, with the correlations between microbes and environmental factors explored. As the results, microbial fertilizer could effectively alleviate soil acidification, increase available potassium and organic matter contents in soil, and was also beneficial to increase nitrate reductase activity in rhizosphere soil. Fertilizers cause changes in the abundance of certain microbes in the soil. Besides, it was shown that the candidate phyla Gal15, Acidobacterota, Latescibacterota, Mortierellommycota, Basidiomycota, and Rozellomycota in tobacco rhizosphere soil had significant correlation with soil environmental factors. Through the functional analysis of these populations, it can be deduced that the changes in the abundance of certain microorganisms may be an important reason for the differences in environmental factors. All these indicated that the differences of environmental factors in different treatments are closely related to the abundance of some special soil microorganisms. Studying the life activities of these microbes would provide good guidance for exploring the interaction among crops, soil, and microorganisms and improving crop yields.},
}
@article {pmid35596750,
year = {2023},
author = {Arnolds, KL and Yamada, E and Neff, CP and Schneider, JM and Palmer, BE and Lozupone, CA},
title = {Disruption of Genes Encoding Putative Zwitterionic Capsular Polysaccharides of Diverse Intestinal Bacteroides Reduces the Induction of Host Anti-Inflammatory Factors.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1620-1629},
pmid = {35596750},
issn = {1432-184X},
support = {R01 DK104047/DK/NIDDK NIH HHS/United States ; T32 AI007405/AI/NIAID NIH HHS/United States ; T32 AI007405/NH/NIH HHS/United States ; },
mesh = {Humans ; *Interleukin-10/genetics ; *Leukocytes, Mononuclear ; Polysaccharides, Bacterial ; Bacteroides fragilis/genetics ; Anti-Inflammatory Agents ; Bacteria ; },
abstract = {Bacterial zwitterionic capsular polysaccharides (ZPS), such as polysaccharide A (PSA) of the intestinal commensal Bacteroides fragilis, have been shown to modulate T cells, including inducing anti-inflammatory IL-10-secreting T regulatory cells (Tregs). We previously used a genomic screen to identify diverse host-associated bacteria with the predicted genetic capacity to produce ZPSs related to PSA of B. fragilis and hypothesized that genetic disruption (KO) of a key functional gene within these operons would reduce the anti-inflammatory activity of these bacteria. We found that ZPS-KO bacteria in two common gut commensals, Bacteroides uniformis and Bacteroides cellulosilyticus, had a reduced ability to induce Tregs and IL-10 in stimulations of human peripheral blood mononuclear cells (PBMCs). Additionally, we found that macrophage stimulated with either wildtype B. fragilis or B. uniformis produced significantly more IL-10 than KOs, indicating a potentially novel function of ZPS of shifting the cytokine response in macrophages to a more anti-inflammatory state. These findings support the hypothesis that these related ZPS may represent a shared strategy to modulate host immune responses.},
}
@article {pmid35595468,
year = {2022},
author = {Rotoni, C and Leite, MFA and Pijl, A and Kuramae, EE},
title = {Rhizosphere microbiome response to host genetic variability: a trade-off between bacterial and fungal community assembly.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {6},
pages = {},
doi = {10.1093/femsec/fiac061},
pmid = {35595468},
issn = {1574-6941},
mesh = {Bacteria/genetics ; Fungi ; *Microbiota/genetics ; *Mycobiome/genetics ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil Microbiology ; },
abstract = {Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced roots in five commercial cultivars: Barolo, Chic, Chic 45, Chic Cream and Haydar. We observed strong rhizosphere selection for the bacterial community but weaker selection for the fungal community. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. By contrast, rhizosphere fungal selection was not significantly linked to plant genetic dissimilarity. Each chrysanthemum cultivar selected unique bacterial and fungal genera in the rhizosphere. We also observed a trade-off in the rhizosphere selection of bacteria and fungi in which the cultivar with the strongest selection of fungal communities showed the weakest bacterial selection. Finally, bacterial and fungal family taxonomic groups consistently selected by all cultivars were identified (bacteria Chitinophagaceae, Beijerinckiaceae and Acidobacteriaceae, and fungi Pseudeurotiaceae and Chrysozymaceae). Taken together, our findings suggest that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by the genetic dissimilarity between cultivars.},
}
@article {pmid35590462,
year = {2022},
author = {Blakney, AJC and Bainard, LD and St-Arnaud, M and Hijri, M},
title = {Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when they experience drought.},
journal = {Environmental microbiology},
volume = {24},
number = {8},
pages = {3529-3548},
doi = {10.1111/1462-2920.16046},
pmid = {35590462},
issn = {1462-2920},
mesh = {Bacteria/genetics ; *Brassica napus ; Droughts ; Feedback ; Plant Roots/microbiology ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {Soil history operates through time to influence the structure and biodiversity of soil bacterial communities. Examining how different soil histories endure will help clarify the rules of bacterial community assembly. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae species. We hypothesized that the previously established soil histories would continue to structure the subsequent Brassicaceae bacterial root and rhizosphere communities. We used a MiSeq 16S rRNA metabarcoding strategy to determine the impact of different soil histories on the structure and biodiversity of the bacterial root and rhizosphere communities from the five different Brassicaceae host plants. We found that the Brassicaceae hosts were consistently significant factors in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed similar bacterial communities, regardless of different soil histories. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how soil history is involved in the structure and biodiversity of bacterial communities through time is a limitation in microbial ecology and is required for employing microbiome technologies in improving agricultural systems.},
}
@article {pmid35589992,
year = {2023},
author = {King, NG and Moore, PJ and Thorpe, JM and Smale, DA},
title = {Consistency and Variation in the Kelp Microbiota: Patterns of Bacterial Community Structure Across Spatial Scales.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1265-1275},
pmid = {35589992},
issn = {1432-184X},
support = {MR/S032827/1/MRC_/Medical Research Council/United Kingdom ; MR/S032827/1//UKRI/ ; NE/S011692/1//Natural Environment Research Council/ ; },
mesh = {Humans ; *Kelp/microbiology ; Ecosystem ; *Laminaria/microbiology ; Forests ; Bacteria/genetics ; *Microbiota ; },
abstract = {Kelp species are distributed along ~ 25% of the world's coastlines and the forests they form represent some of the world's most productive and diverse ecosystems. Like other marine habitat-formers, the associated microbial community is fundamental for host and, in turn, wider ecosystem functioning. Given there are thousands of bacteria-host associations, determining which relationships are important remains a major challenge. We characterised the associated bacteria of two habitat-forming kelp species, Laminaria hyperborea and Saccharina latissima, from eight sites across a range of spatial scales (10 s of metres to 100 s of km) in the northeast Atlantic. We found no difference in diversity or community structure between the two kelps, but there was evidence of regional structuring (across 100 s km) and considerable variation between individuals (10 s of metres). Within sites, individuals shared few amplicon sequence variants (ASVs) and supported a very small proportion of diversity found across the wider study area. However, consistent characteristics between individuals were observed with individual host communities containing a small conserved "core" (8-11 ASVs comprising 25 and 32% of sample abundances for L. hyperborea and S. latissima, respectively). At a coarser taxonomic resolution, communities were dominated by four classes (Planctomycetes, Gammaproteobacteria, Alphaproteobacteria and Bacteroidia) that made up ~ 84% of sample abundances. Remaining taxa (47 classes) made up very little contribution to overall abundance but the majority of taxonomic diversity. Overall, our study demonstrates the consistent features of kelp bacterial communities across large spatial scales and environmental gradients and provides an ecologically meaningful baseline to track environmental change.},
}
@article {pmid35587374,
year = {2022},
author = {Kohl, KD and Dieppa-Colón, E and Goyco-Blas, J and Peralta-Martínez, K and Scafidi, L and Shah, S and Zawacki, E and Barts, N and Ahn, Y and Hedayati, S and Secor, SM and Rowe, MP},
title = {Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies.},
journal = {Integrative and comparative biology},
volume = {62},
number = {2},
pages = {237-251},
doi = {10.1093/icb/icac045},
pmid = {35587374},
issn = {1557-7023},
support = {IOS-1942587//National Science Foundation/ ; },
mesh = {Animals ; Chitin ; Dipodomys ; *Gastrointestinal Microbiome ; Herbivory ; *Microbiota ; Peromyscus ; Rodentia ; },
abstract = {The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus); and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genus Ruminococcus and highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarily Bacillus and Enterococcus), with some capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology.},
}
@article {pmid35586862,
year = {2022},
author = {Raglin, SS and Kent, AD and Ngumbi, EN},
title = {Herbivory Protection via Volatile Organic Compounds Is Influenced by Maize Genotype, Not Bacillus altitudinis-Enriched Bacterial Communities.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {826635},
pmid = {35586862},
issn = {1664-302X},
abstract = {Belowground, plants interact with beneficial soil microbes such as plant growth-promoting rhizobacteria (PGPR). PGPR are rhizosphere bacteria that colonize roots and elicit beneficial effects in plants such as improved plant growth, pathogen resistance, abiotic stress tolerance, and herbivore protection. Treatment of plants with PGPR has been shown to trigger the emission of volatile organic compounds (VOCs). Volatile emissions can also be triggered by herbivory, termed herbivore-induced plant volatiles (HIPV), with important ramifications for chemical-mediated plant and insect interactions. Much of our current understanding of PGPR and herbivore-induced volatiles is based on studies using one plant genotype, yet domestication and modern breeding has led to the development of diverse germplasm with altered phenotypes and chemistry. In this study, we investigated if volatile emissions triggered by PGPR colonization and herbivory varies by maize genotype and microbial community assemblages. Six maize genotypes representing three decades of crop breeding and two heterotic groups were used, with four microbiome treatments: live or sterilized soil, with or without a Bacillus inoculant. Soil sterilization was used to delay microbiome establishment, resulting in low-diversity treatments. At planting, maize seeds were inoculated with PGPR Bacillus altitudinis AP-283 and grown under greenhouse conditions. Four weeks post planting, plants were subjected to feeding by third instar Helicoverpa zea (Lepidoptera: Noctuidae) larvae. Volatiles were collected using solid phase microextraction and analyzed with gas chromatography-mass spectrometry. Illumina NovaSeq 16S rRNA amplicon sequencing was carried out to characterize the rhizosphere microbiome. Maize genotype significantly influenced total volatile emissions, and relative abundance of volatile classes. We did not document a strong influence of microbe treatment on plant VOC emissions. However, inoculating plants with PGPR improved plant growth under sterile conditions. Taken together, our results suggest that genotypic variation is the dominant driver in HIPV composition and individual HIPV abundances, and any bacterial-mediated benefit is genotype and HIPV-specific. Therefore, understanding the interplay of these factors is necessary to fully harness microbially-mediated benefits and improve agricultural sustainability.},
}
@article {pmid35584587,
year = {2022},
author = {Kuroda, K and Narihiro, T and Shinshima, F and Yoshida, M and Yamaguchi, H and Kurashita, H and Nakahara, N and Nobu, MK and Noguchi, TQP and Yamauchi, M and Yamada, M},
title = {High-rate cotreatment of purified terephthalate and dimethyl terephthalate manufacturing wastewater by a mesophilic upflow anaerobic sludge blanket reactor and the microbial ecology relevant to aromatic compound degradation.},
journal = {Water research},
volume = {219},
number = {},
pages = {118581},
doi = {10.1016/j.watres.2022.118581},
pmid = {35584587},
issn = {1879-2448},
mesh = {Anaerobiosis ; Benzoates ; Bioreactors ; Phthalic Acids ; RNA, Ribosomal, 16S/genetics ; *Sewage ; Waste Disposal, Fluid ; *Wastewater ; },
abstract = {Polyethylene terephthalate (PET) is produced worldwide, mainly as material for plastic drink bottles. PET is produced by polymerization of purified terephthalate (PTA) or dimethyl terephthalate (DMT) with ethylene glycol. During the synthetic manufacturing processes of PTA and DMT, high organic loading wastewater is produced, which is typically treated separately by anaerobic wastewater treatment technologies. Given the high demand for PET, manufacturing plants are expanding globally, which will result in an increase in the amounts of PTA and DMT wastewater in need of treatment. In terms of effective treatment, the cotreatment of PTA and DMT wastewater has several advantages, including lower area and energy requirements. In this study, we examined the performance of an upflow anaerobic sludge blanket (UASB) reactor in cotreating PTA and DMT wastewater with high organic loading, evaluating its removal characteristics after 518 days of continuous operation. In addition, we performed a microbiome analysis of the UASB granular sludge to uncover the microbial interactions and metabolic functions within the reactor. By continuous operation, we achieved an organic removal rate of 6.6 kg m[-3] day[-1]. In addition, we confirmed that aromatic compounds in the complex wastewater from the PTA and DMT manufacturing processes are biodegradable in the following order: benzoate > orthophthalate > terephthalate > isophthalate > p-toluic acid. 16S rRNA gene-based network analysis shows that anaerobic Woesearchaeales belonging to phylum Nanoarchaeota has a positive correlation with Methanoregula, Candidatus Methanofastidiosum, and Methanosarcina, suggesting a symbiotic relationship with methanogens in granular sludge. Shotgun metagenomic analysis revealed that terephthalate, isophthalate/orthophthalate, and benzoate were degraded by different members of Pelotomaculaceae and Syntrophorhabdaceae. According to the genomic information, we propose two new possible routes for orthophthalate degradation by the Syntrophorhabdaceae organism.},
}
@article {pmid35583791,
year = {2022},
author = {Pavan, S and Prabhu, AN and Prasad Gorthi, S and Das, B and Mutreja, A and Shetty, V and Ramamurthy, T and Ballal, M},
title = {Exploring the multifactorial aspects of Gut Microbiome in Parkinson's Disease.},
journal = {Folia microbiologica},
volume = {67},
number = {5},
pages = {693-706},
pmid = {35583791},
issn = {1874-9356},
mesh = {Antiparkinson Agents ; Brain ; *Gastrointestinal Microbiome/physiology ; Humans ; *Parkinson Disease/therapy ; alpha-Synuclein/metabolism ; },
abstract = {Advanced research in health science has broadened our view in approaching and understanding the pathophysiology of diseases and has also revolutionised diagnosis and treatment. Ever since the establishment of Braak's hypothesis in the propagation of alpha-synuclein from the distant olfactory and enteric nervous system towards the brain in Parkinson's Disease (PD), studies have explored and revealed the involvement of altered gut microbiota in PD. This review recapitulates the gut microbiome associated with PD severity, duration, motor and non-motor symptoms, and antiparkinsonian treatment from recent literature. Gut microbial signatures in PD are potential predictors of the disease and are speculated to be used in early diagnosis and treatment. In brief, the review also emphasises on implications of the prebiotic, probiotic, faecal microbiota transplantation, and dietary interventions as alternative treatments in modulating the disease symptoms in PD.},
}
@article {pmid35583685,
year = {2023},
author = {Wu, MH and Li, T and Zhang, GS and Wu, FS and Chen, T and Zhang, BL and Wu, XK and Liu, GX and Zhang, KC and Zhang, W},
title = {Seasonal Variation of Hypolithic Microbiomes in the Gobi Desert : Seasonal Variation of Hypolithic Microbiomes in the Gobi Desert.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1382-1395},
pmid = {35583685},
issn = {1432-184X},
support = {31870479//National Natural Science Foundation of China/ ; 2019YFE0121100//National Key R&amp;D Program of China/ ; 20YF3WA007//Scientific Project of Gansu Province, China/ ; 20JR5RA548//Scientific Project of Gansu Province, China/ ; },
mesh = {Seasons ; Desert Climate ; *Cyanobacteria/genetics ; Temperature ; *Microbiota ; Soil Microbiology ; },
abstract = {Understanding how microbial communities adapt to environmental stresses is critical for interpreting ecological patterns and microbial diversity. In the case of the Gobi Desert, little is known on the environmental factors that explain hypolithic colonization under quartz stones. By analyzing nine hypolithic communities across an arid gradient and the effects of the season of the year in the Hexi Corridor of this desert, we found a significant decrease in hypolithic colonization rates (from 47.24 to 15.73%) with the increasing drought gradient and found two distinct communities in Hot and Cold samples, which survived or proliferated after a hot or a cold period. While Cold communities showed a greater species diversity and a predominance of Cyanobacteria, Hot communities showed a predominance of members of the Proteobacteria and the Firmicutes. In comparison, Cold communities also possessed stronger functions in the photosynthesis and carbon metabolism. Based on the findings of this study, we proposed that the hypolithic communities of the Hexi Corridor of the Gobi Desert might follow a seasonal developmental cycle in which temperature play an important role. Thus after a critical thermal threshold is crossed, heterotrophic microorganisms predominate in the hot period, while Cyanobacteria predominate in the cold period.},
}
@article {pmid35581504,
year = {2023},
author = {Wan, L and Caruso, G and Cao, X and Song, C and Maimone, G and Rappazzo, AC and Laganà, P and Zhou, Y},
title = {Microbial Response to Coastal-Offshore Gradients in Taiwan Straits: Community Metabolism and Total Prokaryotic Abundance as Potential Proxies.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1253-1264},
pmid = {35581504},
issn = {1432-184X},
support = {2016YFE0202100.//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {*Ecosystem ; Taiwan ; *Estuaries ; Rivers ; China ; Environmental Monitoring ; Carbon ; },
abstract = {Located between the South and the East China Sea, the Taiwan Straits (TWS) are a marine shelf-channel area, with unique hydrological and geomorphological features affected by rivers inflow and with recent algal blooms with red tide events. This study aimed at assessing microbial distribution and function and their modulation in response to environmental gradients. Surface (0.5 m) water samples from 16 stations along five north to south transects were collected; total prokaryotic abundance by epifluorescence microscope and carbon substrate utilization patterns by Biolog Ecoplates were estimated. Spatially, a patchy microbial distribution was found, with the highest microbial metabolic levels and prokaryotic abundance in the TWS area between Minjiang River estuary and Pingtan Island, and progressive decreases towards offshore stations. Complex carbon sources and carbohydrates were preferentially metabolized. This study provides a snapshot of the microbial abundance and activity in TWS as a model site of aquatic ecosystems impacted from land inputs; obtained data highlights that microbial metabolism is more sensitive than abundance to environmental changes.},
}
@article {pmid35581020,
year = {2022},
author = {Xie, J and Li, Q and Haesebrouck, F and Van Hoecke, L and Vandenbroucke, RE},
title = {The tremendous biomedical potential of bacterial extracellular vesicles.},
journal = {Trends in biotechnology},
volume = {40},
number = {10},
pages = {1173-1194},
doi = {10.1016/j.tibtech.2022.03.005},
pmid = {35581020},
issn = {1879-3096},
mesh = {Bacteria ; *Cancer Vaccines ; *Extracellular Vesicles ; Host Microbial Interactions ; Lipids ; },
abstract = {Bacterial extracellular vesicles (bEVs) are nano-sized, lipid membrane-delimited particles filled with bacteria-derived components. They have important roles in the physiology and pathogenesis of bacteria, and in bacteria-bacteria and bacteria-host interactions. Interestingly, recent advances in biotechnology have made it possible to engineer the bEV surface and decorate it with diverse biomolecules and nanoparticles (NPs). bEVs have been the focus of significant interest in a range of biomedical fields and are being evaluated as vaccines, cancer immunotherapy agents, and drug delivery vehicles. However, significant hurdles in terms of their safety, efficacy, and mass production need to be addressed to enable their full clinical potential. Here, we review recent advances and remaining obstacles regarding the use of bEVs in different biomedical applications and discuss paths toward clinical translation.},
}
@article {pmid35577973,
year = {2022},
author = {Mangola, SM and Lund, JR and Schnorr, SL and Crittenden, AN},
title = {Ethical microbiome research with Indigenous communities.},
journal = {Nature microbiology},
volume = {7},
number = {6},
pages = {749-756},
pmid = {35577973},
issn = {2058-5276},
support = {RM1 HG009042/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; },
abstract = {Human-microbiome interactions have been associated with evolutionary, cultural and environmental processes. With clinical applications of microbiome research now feasible, it is crucial that the science conducted, particularly among Indigenous communities, adheres to principles of inclusion. This necessitates a transdisciplinary dialogue to decide how biological samples are collected and who benefits from the research and any derived products. As a group of scholars working at the interface of biological and social science, we offer a candid discussion of the lessons learned from our own research and introduce one approach to carry out ethical microbiome research with Indigenous communities.},
}
@article {pmid35576038,
year = {2022},
author = {Kuzikova, I and Andronov, E and Zaytseva, T and Metelkova, L and Zhakovskaya, Z and Medvedeva, N},
title = {A microcosm approach for evaluating the microbial nonylphenol and butyltin biodegradation and bacterial community shifts in co-contaminated bottom sediments from the Gulf of Finland, the Baltic Sea.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {46},
pages = {69849-69860},
pmid = {35576038},
issn = {1614-7499},
mesh = {*Alphaproteobacteria/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; Ecosystem ; Finland ; Geologic Sediments/chemistry ; Phenols ; *Water Pollutants, Chemical/analysis ; },
abstract = {Pollution of aquatic ecosystems with nonylphenol (NP) and butyltins (BuTs) is of great concern due to their effects on endocrine activity, toxicity to aquatic organisms, and extended persistence in sediments. The impact of contamination with NP and/or BuTs on the microbial community structure in marine sediments was investigated using microcosms and high-throughput sequencing. Sediment microcosms with NP (300 mg/kg) and/or BuTs (95 mg/kg) were constructed. Complete removal of monobutyltin (MBT) occurred in the microcosms after 240 days of incubation, while a residual NP rate was 40%. The content of toxic tributyltin (TBT) and dibutyltin (DBT) in the sediments did not change notably. Co-contamination of the sediments with NP and BuTs did not affect the processes of their degradation. The pollutants in the microcosms could have been biodegraded by autochthonous microorganisms. Significantly different and less diverse bacterial communities were observed in the contaminated sediments compared to non-contaminated control. Firmicutes and Gammaproteobacteria dominated in the NP treatment, Actinobacteria and Alphaproteobacteria in the BuT treatment, and Gammaproteobacteria, Alphaproteobacteria, Firmicutes, and Acidobacteria in the NP-BuT mixture treatment. The prevalence of microorganisms from the bacterial genera Halothiobacillus, Geothrix, Methanosarcina, Dyella, Parvibaculum, Pseudomonas, Proteiniclasticum, and bacteria affiliated with the order Rhizobiales may indicate their role in biodegradation of NP and BuTs in the co-contaminated sediments. This study can provide some new insights towards NP and BuT biodegradation and microbial ecology in NP-BuT co-contaminated environment.},
}
@article {pmid35575806,
year = {2023},
author = {Patil, JS and Sathish, K},
title = {Responses of Phytoplankton Benthic Propagules to Macronutrient Enrichment and Varying Light Intensities: Elucidation from Monsoon-Influenced Mandovi and Zuari Riverine System : Responses of Phytoplankton Benthic Propagules to Macronutrient Enrichment and Varying Light Intensities: Elucidation from Monsoon-Influenced Mandovi and Zuari Riverine System.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1367-1381},
pmid = {35575806},
issn = {1432-184X},
support = {//science and engineering research board/ ; },
mesh = {*Phytoplankton ; Nitrates ; Seawater ; Rivers ; Fresh Water ; *Diatoms ; India ; Seasons ; Environmental Monitoring/methods ; Estuaries ; },
abstract = {The ecological importance of phytoplankton-benthic-propagules (PBP) from coastal sediments, except tropical monsoon-influenced rivers and estuaries, is well documented. PBP in such systems is often transported from upstream (near freshwater) to downstream (estuary) through freshwater discharges during monsoon and thereby experiences higher salinities (>30 PSU) and nutrients with varying light conditions due to reducing discharges during the monsoon-break/withdrawal-phase. However, the PBP responses (germination and subsequent growth) to such changes are unknown and are examined here at ~35 PSU salinity. For the study, macronutrients (nitrate, phosphate, silicate, and nitrate+phosphate+silicate) and light intensities were considered to assess the response of PBP representing estuarine, brackish, and near freshwater locations of monsoon-influenced Mandovi and Zuari rivers (Goa, India). Diatoms dominated the viable PBP community, but the maximum growth and sustained photosynthetic activity were observed when all macronutrients were supplied than individually. Here, variable fluorescence technique utility in PBP resurrection (detection of viability and responses) was also explored. The PBP growth was similar for macronutrients but increased with light intensity indicating a longer growth response during monsoon. For PBP (germination and photosynthetic activity), light intensities drive the rate of improvement/development, whereas the nutrients are essential for maintaining vegetative growth upon germination in the region. The PBP dominance of common planktonic species (Skeletonema and Thalassiosira) along the river also signifies the role of seawater intrusion (up to upstream locations) in distribution. Skeletonema and Thalassiosira, which contribute significantly to the total community, are light-sensitive with a similar response and cause single species blooms during monsoon and non-monsoon, respectively, depending on the species' tolerance to salinity.},
}
@article {pmid35575486,
year = {2022},
author = {Peruzzo, A and Losasso, C and Di Castri, A and Drigo, I and Bano, L and Orsini, M},
title = {Genome Sequence of Campylobacter Strain 19-13652, Isolated from Breeding Pheasants.},
journal = {Microbiology resource announcements},
volume = {11},
number = {6},
pages = {e0118421},
pmid = {35575486},
issn = {2576-098X},
support = {IZS VE 03/18 RC//Ministero della Salute (Ministry of Health, Italy)/ ; },
abstract = {We report the whole-genome sequence of a Campylobacter strain that was isolated from breeding pheasants presenting "bulgy eyes" in Italy. Traditional molecular typing methods did not return any reliable result. Whole-genome sequencing and sequence comparison with known genomes did not meet the criteria for assignment to an existing species.},
}
@article {pmid35573175,
year = {2022},
author = {Ghosh, A and Saha, R and Bhadury, P},
title = {Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13169},
pmid = {35573175},
issn = {2167-8359},
mesh = {*Water ; Wetlands ; *Microbiota/genetics ; Metagenome/genetics ; Bacteria/genetics ; Firmicutes/genetics ; },
abstract = {Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.},
}
@article {pmid35572632,
year = {2022},
author = {Aponte, H and Galindo-Castañeda, T and Yáñez, C and Hartmann, M and Rojas, C},
title = {Microbial Community-Level Physiological Profiles and Genetic Prokaryotic Structure of Burned Soils Under Mediterranean Sclerophyll Forests in Central Chile.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {824813},
pmid = {35572632},
issn = {1664-302X},
abstract = {Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou's evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO3 [-] was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.},
}
@article {pmid35569711,
year = {2022},
author = {Matassa, S and Pelagalli, V and Papirio, S and Zamalloa, C and Verstraete, W and Esposito, G and Pirozzi, F},
title = {Direct nitrogen stripping and upcycling from anaerobic digestate during conversion of cheese whey into single cell protein.},
journal = {Bioresource technology},
volume = {358},
number = {},
pages = {127308},
doi = {10.1016/j.biortech.2022.127308},
pmid = {35569711},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Cheese ; Dietary Proteins ; *Nitrogen/analysis ; Whey/chemistry ; Whey Proteins ; },
abstract = {The environmental impact of the dairy industry is heavily influenced by the overproduction of nitrogen- and carbon-rich effluents. The present study proposes an innovative process to recover waste contaminated nitrogen from anaerobic digestate while treating excess cheese whey (CW) and producing high-quality, clean single cell protein (SCP). By relying on direct aeration stripping techniques, employing an airflow subsequently used in the aerobic cheese whey fermentation step, the investigated process was able to strip 41-80% of the total ammonium nitrogen (N-NH4[+]) from liquid digestate. The stripped ammonia gas (NH3) was completely recovered as N-NH4[+] in the acidic CW, and further upcycled into SCP having a total protein content of 74.7% and a balanced amino acids profile. A preliminary techno-economic analysis revealed the potential to directly recover and upcycle nitrogen into SCP at costs (4.3-6.3 €·kgN[-1]) and energetic inputs (90-132 MJ·kgN[-1]) matching those of conventional feed and nitrogen management processes.},
}
@article {pmid35569666,
year = {2022},
author = {Li, K and Bi, Q and Liu, X and Wang, H and Sun, C and Zhu, Y and Lin, X},
title = {Unveiling the role of dissolved organic matter on phosphorus sorption and availability in a 5-year manure amended paddy soil.},
journal = {The Science of the total environment},
volume = {838},
number = {Pt 1},
pages = {155892},
doi = {10.1016/j.scitotenv.2022.155892},
pmid = {35569666},
issn = {1879-1026},
mesh = {Animals ; Dissolved Organic Matter ; Fertilizers/analysis ; *Manure/analysis ; Phosphorus/analysis ; *Soil/chemistry ; Swine ; },
abstract = {Dissolved organic matter (DOM) is an active component of organic manure that is widely used in agroecosystems to increase nutrient availability and consequently enhance crop yields. However, the ways in which soil DOM characteristics are influenced by organic manure and how it contributes to crop yield and soil P availability remains unclear. Here, we conducted a 5-year field experiment and demonstrated that partial replacement of chemical P fertilizer with swine manure could maintain high rice yield and soil available P levels and increase P fertilizer use efficiency (PUE) in comparison to chemical fertilization, even when the total P input was reduced. This suggests that organic manure application can significantly mobilize soil P and increase P availability. Structural equation modeling analysis indicated that the soil pH and humification degree of DOM, rather than DOM content, directly decreased maximum P adsorption capacity. The combined results of the optical spectroscopy and ultrahigh-resolution mass spectroscopy obtained from the laboratory validation experiment based on the DOM-removed soil demonstrated that manure-derived DOM competing with P for adsorption was one of the main reasons for the increase in soil P availability and that the effective DOM components were N-containing lignins, tannins, and condensed polycyclic aromatics with higher O/C and lower H/C ratios. Overall, our results provide solid evidence that soil DOM characteristics are influenced by manure application and facilitate soil P availability, which could help guide the sustainable P management and manure application in agroecosystems.},
}
@article {pmid35569105,
year = {2022},
author = {Deng, X and Zhang, N and Li, Y and Zhu, C and Qu, B and Liu, H and Li, R and Bai, Y and Shen, Q and Falcao Salles, J},
title = {Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities.},
journal = {The New phytologist},
volume = {235},
number = {4},
pages = {1558-1574},
doi = {10.1111/nph.18221},
pmid = {35569105},
issn = {1469-8137},
mesh = {Bacteria/genetics ; Fertilizers ; Plant Diseases/microbiology ; *Ralstonia solanacearum ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Stimulating the development of soil suppressiveness against certain pathogens represents a sustainable solution toward reducing pesticide use in agriculture. However, understanding the dynamics of suppressiveness and the mechanisms leading to pathogen control remain largely elusive. Here, we investigated the mechanisms used by the rhizosphere microbiome induces bacterial wilt disease suppression in a long-term field experiment where continuous application of bio-organic fertilizers (BFs) triggered disease suppressiveness when compared to chemical fertilizer application. We further demonstrated in a glasshouse experiment that the suppressiveness of the rhizosphere bacterial communities was triggered mainly by changes in community composition rather than only by the abundance of the introduced biocontrol strain. Metagenomics approaches revealed that members of the families Sphingomonadaceae and Xanthomonadaceae with the ability to produce secondary metabolites were enriched in the BF plant rhizosphere but only upon pathogen invasion. We experimentally validated this observation by inoculating bacterial isolates belonging to the families Sphingomonadaceae and Xanthomonadaceae into conducive soil, which led to a significant reduction in pathogen abundance and increase in nonribosomal peptide synthetase gene abundance. We conclude that priming of the soil microbiome with BF amendment fostered reactive bacterial communities in the rhizosphere of tomato plants in response to biotic disturbance.},
}
@article {pmid35567250,
year = {2022},
author = {Dranseikienė, D and Balčiūnaitė-Murzienė, G and Karosienė, J and Morudov, D and Juodžiukynienė, N and Hudz, N and Gerbutavičienė, RJ and Savickienė, N},
title = {Cyano-Phycocyanin: Mechanisms of Action on Human Skin and Future Perspectives in Medicine.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
pmid = {35567250},
issn = {2223-7747},
abstract = {Cyano-phycocyanin is one of the active pigments of the blue-green algae and is usually isolated from the filamentous cyanobacteria Arthrospira platensis Gomont (Spirulina). Due to its multiple physiological functions and non-toxicity, cyano-phycocyanin may be a potential substance for the topical treatment of various skin diseases. Considering that the conventional medicine faces drug resistance, insufficient efficacy and side effects, the plant origin compounds can act as an alternative option. Thus, the aim of this paper was to review the wound healing, antimicrobial, antioxidative, anti-inflammatory, antimelanogenic and anticancer properties and mechanisms of cyano-phycocyanin topical activities on human skin. Moreover, possible applications and biotechnological requirements for pharmaceutical forms of cyano-phycocyanin for the treatment of various skin diseases are discussed in this review.},
}
@article {pmid35567212,
year = {2022},
author = {Li, Y and Wang, C and Ge, L and Hu, C and Wu, G and Sun, Y and Song, L and Wu, X and Pan, A and Xu, Q and Shi, J and Liang, J and Li, P},
title = {Environmental Behaviors of Bacillus thuringiensis (Bt) Insecticidal Proteins and Their Effects on Microbial Ecology.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
pmid = {35567212},
issn = {2223-7747},
abstract = {Bt proteins are crystal proteins produced by Bacillus thuringiensis (Bt) in the early stage of spore formation that exhibit highly specific insecticidal activities. The application of Bt proteins primarily includes Bt transgenic plants and Bt biopesticides. Transgenic crops with insect resistance (via Bt)/herbicide tolerance comprise the largest global area of agricultural planting. After artificial modification, Bt insecticidal proteins expressed from Bt can be released into soils through root exudates, pollen, and plant residues. In addition, the construction of Bt recombinant engineered strains through genetic engineering has become a major focus of Bt biopesticides, and the expressed Bt proteins will also remain in soil environments. Bt proteins expressed and released by Bt transgenic plants and Bt recombinant strains are structurally and functionally quite different from Bt prototoxins naturally expressed by B. thuringiensis in soils. The former can thus be regarded as an environmentally exogenous substance with insecticidal toxicity that may have potential ecological risks. Consequently, biosafety evaluations must be conducted before field tests and production of Bt plants or recombinant strains. This review summarizes the adsorption, retention, and degradation behavior of Bt insecticidal proteins in soils, in addition to their impacts on soil physical and chemical properties along with soil microbial diversity. The review provides a scientific framework for evaluating the environmental biosafety of Bt transgenic plants, Bt transgenic microorganisms, and their expression products. In addition, prospective research targets, research methods, and evaluation methods are highlighted based on current research of Bt proteins.},
}
@article {pmid35562794,
year = {2022},
author = {Deehan, EC and Zhang, Z and Riva, A and Armet, AM and Perez-Muñoz, ME and Nguyen, NK and Krysa, JA and Seethaler, B and Zhao, YY and Cole, J and Li, F and Hausmann, B and Spittler, A and Nazare, JA and Delzenne, NM and Curtis, JM and Wismer, WV and Proctor, SD and Bakal, JA and Bischoff, SC and Knights, D and Field, CJ and Berry, D and Prado, CM and Walter, J},
title = {Elucidating the role of the gut microbiota in the physiological effects of dietary fiber.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {77},
pmid = {35562794},
issn = {2049-2618},
support = {RN-298871-372173//CIHR/Canada ; },
mesh = {Adult ; Bacteria ; Bile Acids and Salts/analysis ; Biomarkers/analysis ; Dietary Fiber ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/physiology ; Humans ; Leukocyte L1 Antigen Complex/analysis/pharmacology ; Male ; Obesity/microbiology ; },
abstract = {BACKGROUND: Dietary fiber is an integral part of a healthy diet, but questions remain about the mechanisms that underlie effects and the causal contributions of the gut microbiota. Here, we performed a 6-week exploratory trial in adults with excess weight (BMI: 25-35 kg/m[2]) to compare the effects of a high-dose (females: 25 g/day; males: 35 g/day) supplement of fermentable corn bran arabinoxylan (AX; n = 15) with that of microbiota-non-accessible microcrystalline cellulose (MCC; n = 16). Obesity-related surrogate endpoints and biomarkers of host-microbiome interactions implicated in the pathophysiology of obesity (trimethylamine N-oxide, gut hormones, cytokines, and measures of intestinal barrier integrity) were assessed. We then determined whether clinical outcomes could be predicted by fecal microbiota features or mechanistic biomarkers.<br><br>RESULTS: AX enhanced satiety after a meal and decreased homeostatic model assessment of insulin resistance (HOMA-IR), while MCC reduced tumor necrosis factor-&#x3b1; and fecal calprotectin. Machine learning models determined that effects on satiety could be predicted by fecal bacterial taxa that utilized AX, as identified by bioorthogonal non-canonical amino acid tagging. Reductions in HOMA-IR and calprotectin were associated with shifts in fecal bile acids, but correlations were negative, suggesting that the benefits of fiber may not be mediated by their effects on bile acid pools. Biomarkers of host-microbiome interactions often linked to bacterial metabolites derived from fiber fermentation (short-chain fatty acids) were not affected by AX supplementation when compared to non-accessible MCC.<br><br>CONCLUSION: This study demonstrates the efficacy of purified dietary fibers when used as supplements and suggests that satietogenic effects of AX may be linked to bacterial taxa that ferment the fiber or utilize breakdown products. Other effects are likely microbiome independent. The findings provide a basis for fiber-type specific therapeutic applications and their personalization.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov, NCT02322112 , registered on July 3, 2015. Video Abstract.},
}
@article {pmid35562600,
year = {2023},
author = {Greene, LK and McKenney, EA and Gasper, W and Wrampelmeier, C and Hayer, S and Ehmke, EE and Clayton, JB},
title = {Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1608-1619},
pmid = {35562600},
issn = {1432-184X},
support = {PRFB 1906416//Directorate for Biological Sciences/ ; },
mesh = {Animals ; *Lemur ; Retrospective Studies ; *Lemuridae ; *Microbiota ; *Strepsirhini ; },
abstract = {Most studies of wildlife gut microbiotas understandably rely on feces to approximate consortia along the gastrointestinal tract. We therefore compared microbiome structure and predicted metagenomic function in stomach, small intestinal, cecal, and colonic samples from 52 lemurs harvested during routine necropsies. The lemurs represent seven genera (Cheirogaleus, Daubentonia, Varecia, Hapalemur, Eulemur, Lemur, Propithecus) characterized by diverse feeding ecologies and gut morphologies. In particular, the hosts variably depend on fibrous foodstuffs and show correlative morphological complexity in their large intestines. Across host lineages, microbiome diversity, variability, membership, and function differed between the upper and lower gut, reflecting regional tradeoffs in available nutrients. These patterns related minimally to total gut length but were modulated by fermentation capacity (i.e., the ratio of small to large intestinal length). Irrespective of feeding strategy, host genera with limited fermentation capacity harbored more homogenized microbiome diversity along the gut, whereas those with expanded fermentation capacity harbored cecal and colonic microbiomes with greater diversity and abundant fermentative Ruminococcaceae taxa. While highlighting the value of curated sample repositories for retrospective comparisons, our results confirm that the need to survive on fibrous foods, either routinely or in hypervariable environments, can shape the morphological and microbial features of the lower gut.},
}
@article {pmid35562021,
year = {2022},
author = {Mariën, Q and Ulčar, B and Verleyen, J and Vanthuyne, B and Ganigué, R},
title = {High-rate conversion of lactic acid-rich streams to caproic acid in a fermentative granular system.},
journal = {Bioresource technology},
volume = {355},
number = {},
pages = {127250},
doi = {10.1016/j.biortech.2022.127250},
pmid = {35562021},
issn = {1873-2976},
mesh = {Acetic Acid ; *Bioreactors ; Caproates ; Carbohydrates ; Glucose ; *Lactic Acid ; Rivers ; Sewage/chemistry ; },
abstract = {Lactic acid-driven chain elongation enables upgrading low-value organic streams into caproic acid. Recently, volumetric production rates over 0.5 g L[-1] h[-1]have been reported for carbohydrate-rich streams in expanded granular sludge bed (EGSB) reactors. However, many target streams contain mixtures of carbohydrates and lactic acid, and little is known about their impact on product profile and microbial ecology, or the importance of carbohydrates as substrate to achieve high rates. This manuscript investigated varying glucose-to-lactate ratios and observed that decreasing glucose-content eliminated odd-chain by-products, while glucose omission required acetic acid addition to support lactic acid conversion. Decreasing the glucose-content fed resulted in decreasing amounts of granular biomass, with the disappearance of granules when no glucose was fed. Lowering the HRT to 0.3 days while feeding only lactic and acetic acid likely triggered re-granulation, enabling the highest lactic acid-driven caproic acid production rates reported thus far at 16.4 ± 1.7 g L[-1] d[-1].},
}
@article {pmid35556154,
year = {2023},
author = {Billet, L and Pesce, S and Martin-Laurent, F and Devers-Lamrani, M},
title = {Experimental Evidence for Manure-Borne Bacteria Invasion in Soil During a Coalescent Event: Influence of the Antibiotic Sulfamethazine.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1463-1472},
pmid = {35556154},
issn = {1432-184X},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Sulfamethazine ; Manure/microbiology ; Soil ; Soil Microbiology ; Bacteria/genetics ; },
abstract = {The fertilization of agricultural soil by organic amendment that may contain antibiotics, like manure, can transfer bacterial pathogens and antibiotic-resistant bacteria to soil communities. However, the invasion by manure-borne bacteria in amended soil remains poorly understood. We hypothesized that this kind of process is both influenced by the soil properties (and those of its microbial communities) and by the presence of contaminants such as antibiotics used in veterinary care. To test that, we performed a microcosm experiment in which four different soils were amended or not with manure at an agronomical dose and exposed or not to the antibiotic sulfamethazine (SMZ). After 1 month of incubation, the diversity, structure, and composition of bacterial communities of the soils were assessed by 16S rDNA sequencing. The invasion of manure-borne bacteria was still perceptible 1 month after the soil amendment. The results obtained with the soil already amended in situ with manure 6 months prior to the experiment suggest that some of the bacterial invaders were established in the community over the long term. Even if differences were observed between soils, the invasion was mainly attributable to some of the most abundant OTUs of manure (mainly Firmicutes). SMZ exposure had a limited influence on soil microorganisms but our results suggest that this kind of contaminant can enhance the invasion ability of some manure-borne invaders.},
}
@article {pmid35552795,
year = {2023},
author = {Newcombe, G and Marlin, M and Barge, E and Heitmann, S and Ridout, M and Busby, PE},
title = {Plant Seeds Commonly Host Bacillus spp., Potential Antagonists of Phytopathogens.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1356-1366},
pmid = {35552795},
issn = {1432-184X},
support = {1314095//National Science Foundation/ ; 16.67//National Science Foundation/ ; },
mesh = {Humans ; *Bacillus ; Seeds/microbiology ; Fungi ; Bacteria ; Plants ; *Ascomycota ; },
abstract = {In agriculture, horticulture and plantation forestry, Bacillus species are the most commonly applied antagonists and biopesticides, targeting plant pathogens and insect pests, respectively. Bacillus isolates are also used as bacterial plant biostimulants, or BPBs. Such useful isolates of Bacillus are typically sourced from soil. Here, we show that Bacillus - and other antagonistic microbes - can be sourced from a broad range of plant seeds. We found that culturable Bacillus isolates are common in the seeds of 98 plant species representing 39 families (i.e., 87% of the commonly cultured bacteria belonged to Bacillales). We also found that 83% of the commonly cultured fungi from the seeds of the 98 plant species belonged to just three orders of fungi-Pleosporales, Hypocreales and Eurotiales-that are also associated with antagonism. Furthermore, we confirmed antagonism potential in agaro with seed isolates of Bacillus from Pinus monticola as a representative case. Eight isolates each of seed Bacillus, seed fungi, and foliar fungi, all from P. monticola, were paired in a total of 384 possible pair-wise interactions (with seed and foliar fungi as the targets). Seed Bacillus spp. were the strongest antagonists of the seed and foliar fungi, with a mean interaction strength 2.8 times greater than seed fungi (all either Eurotiales or Hypocreales) and 3.2 times greater than needle fungi. Overall, our study demonstrates that seeds host a taxonomically narrow group of culturable, antagonistic bacteria and fungi.},
}
@article {pmid35552794,
year = {2023},
author = {Chauvet, M and Monjot, A and Moné, A and Lepère, C},
title = {Single Cell Analysis Reveals a New Microsporidia-Host Association in a Freshwater Lake.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1630-1633},
pmid = {35552794},
issn = {1432-184X},
mesh = {*Microsporidia/physiology ; Lakes/parasitology ; Ecosystem ; Food Chain ; Single-Cell Analysis ; },
abstract = {Microsporidia are a large group of obligate intracellular eukaryotic parasites. Recent studies suggest that their diversity can be huge in freshwater lake ecosystems especially in the < 150-µm size fraction. However, little is known about their hosts and therefore their impact on the trophic food web functioning. In this study, single cell analysis and fluorescence microscopy were used to detect new host-parasite association within rotifer communities in lake Aydat (France). Our analysis showed the existence of a potential new species belonging to the Crispospora genus able of infecting the rotifer Kellicottia with a high prevalence (42.5%) suggesting that Microsporidia could have a great impact on the rotifer populations' regulation in lakes.},
}
@article {pmid35550672,
year = {2022},
author = {Samara, J and Moossavi, S and Alshaikh, B and Ortega, VA and Pettersen, VK and Ferdous, T and Hoops, SL and Soraisham, A and Vayalumkal, J and Dersch-Mills, D and Gerber, JS and Mukhopadhyay, S and Puopolo, K and Tompkins, TA and Knights, D and Walter, J and Amin, H and Arrieta, MC},
title = {Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants.},
journal = {Cell host &amp; microbe},
volume = {30},
number = {5},
pages = {696-711.e5},
doi = {10.1016/j.chom.2022.04.005},
pmid = {35550672},
issn = {1934-6069},
mesh = {Bifidobacterium ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Extremely Premature ; Infant, Newborn ; Inflammation ; *Probiotics ; },
abstract = {Probiotics are increasingly administered to premature infants to prevent necrotizing enterocolitis and neonatal sepsis. However, their effects on gut microbiome assembly and immunity are poorly understood. Using a randomized intervention trial in extremely premature infants, we tested the effects of a probiotic product containing four strains of Bifidobacterium species autochthonous to the infant gut and one Lacticaseibacillus strain on the compositional and functional trajectory of microbiome. Daily administration of the mixture accelerated the transition into a mature, term-like microbiome with higher stability and species interconnectivity. Besides infant age, Bifidobacterium strains and stool metabolites were the best predictors of microbiome maturation, and structural equation modeling confirmed probiotics as a major determinant for the trajectory of microbiome assembly. Bifidobacterium-driven microbiome maturation was also linked to an anti-inflammatory intestinal immune milieu. This demonstrates that Bifidobacterium strains are ecosystem engineers that lead to an acceleration of microbiome maturation and immunological consequences in extremely premature infants.},
}
@article {pmid35550507,
year = {2022},
author = {Jamnik, T and Flasch, M and Braun, D and Fareed, Y and Wasinger, D and Seki, D and Berry, D and Berger, A and Wisgrill, L and Warth, B},
title = {Next-generation biomonitoring of the early-life chemical exposome in neonatal and infant development.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {2653},
pmid = {35550507},
issn = {2041-1723},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Biological Monitoring ; Child ; Child Development ; *Exposome ; Female ; Humans ; Infant ; Infant, Newborn ; Tandem Mass Spectrometry/methods ; Xenobiotics/toxicity ; },
abstract = {Exposure to synthetic and natural chemicals is a major environmental risk factor in the etiology of many chronic diseases. Investigating complex co-exposures is necessary for a holistic assessment in exposome-wide association studies. In this work, a sensitive liquid chromatography-tandem mass spectrometry approach was developed and validated. The assay enables the analysis of more than 80 highly-diverse xenobiotics in urine, serum/plasma, and breast milk; with detection limits generally in the pg-ng mL[-1] range. In plasma of extremely-premature infants, 27 xenobiotics are identified; including contamination with plasticizers, perfluorinated alkylated substances and parabens. In breast milk samples collected longitudinally over the first 211 days post-partum, 29 analytes are detected, including pyrrolizidine- and tropane alkaloids which have not been identified in this matrix before. A preliminary estimation of daily toxicant intake via breast milk is conducted. In conclusion, we observe significant early-life co-exposure to multiple toxicants, and demonstrate the method's applicability for large-scale exposomics-type cohort studies.},
}
@article {pmid35549250,
year = {2022},
author = {Xu, G and Ng, HL and Chen, C and Zhao, S and He, J},
title = {Efficient and Complete Detoxification of Polybrominated Diphenyl Ethers in Sediments Achieved by Bioaugmentation with Dehalococcoides and Microbial Ecological Insights.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {12},
pages = {8008-8019},
doi = {10.1021/acs.est.2c00914},
pmid = {35549250},
issn = {1520-5851},
mesh = {Biodegradation, Environmental ; Dehalococcoides ; *Environmental Pollutants ; Geologic Sediments/chemistry ; Halogenated Diphenyl Ethers ; *Tetrachloroethylene ; *Water Pollutants, Chemical ; },
abstract = {Polybrominated diphenyl ethers (PBDEs) are prevalent environmental pollutants, but bioremediation of PBDEs remains to be reported. Here we report accelerated remediation of a penta-BDE mixture in sediments by bioaugmentation with Dehalococcoides mccartyi strains CG1 and TZ50. Bioaugmentation with different amounts of each Dehalococcoides strain enhanced debromination of penta-BDEs compared with the controls. The sediment microcosm spiked with 6.8 × 10[6] cells/mL strain CG1 showed the highest penta-BDEs removal (89.9 ± 7.3%) to diphenyl ether within 60 days. Interestingly, co-contaminant tetrachloroethene (PCE) improved bioaugmentation performance, resulting in faster and more extensive penta-BDEs debromination using less bioinoculants, which was also completely dechlorinated to ethene by introducing D. mccartyi strain 11a. The better bioaugmentation performance in sediments with PCE could be attributed to the boosted growth of the augmented Dehalococcoides and capability of the PCE-induced reductive dehalogenases to debrominate penta-BDEs. Finally, ecological analyses showed that bioaugmentation resulted in more deterministic microbial communities, where the augmented Dehalococcoides established linkages with indigenous microorganisms but without causing obvious alterations of the overall community diversity and structure. Collectively, this study demonstrates that bioaugmentation with Dehalococcoides is a feasible strategy to completely remove PBDEs in sediments.},
}
@article {pmid35547145,
year = {2022},
author = {McElhinney, JMWR and Catacutan, MK and Mawart, A and Hasan, A and Dias, J},
title = {Interfacing Machine Learning and Microbial Omics: A Promising Means to Address Environmental Challenges.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {851450},
pmid = {35547145},
issn = {1664-302X},
abstract = {Microbial communities are ubiquitous and carry an exceptionally broad metabolic capability. Upon environmental perturbation, microbes are also amongst the first natural responsive elements with perturbation-specific cues and markers. These communities are thereby uniquely positioned to inform on the status of environmental conditions. The advent of microbial omics has led to an unprecedented volume of complex microbiological data sets. Importantly, these data sets are rich in biological information with potential for predictive environmental classification and forecasting. However, the patterns in this information are often hidden amongst the inherent complexity of the data. There has been a continued rise in the development and adoption of machine learning (ML) and deep learning architectures for solving research challenges of this sort. Indeed, the interface between molecular microbial ecology and artificial intelligence (AI) appears to show considerable potential for significantly advancing environmental monitoring and management practices through their application. Here, we provide a primer for ML, highlight the notion of retaining biological sample information for supervised ML, discuss workflow considerations, and review the state of the art of the exciting, yet nascent, interdisciplinary field of ML-driven microbial ecology. Current limitations in this sphere of research are also addressed to frame a forward-looking perspective toward the realization of what we anticipate will become a pivotal toolkit for addressing environmental monitoring and management challenges in the years ahead.},
}
@article {pmid35543735,
year = {2023},
author = {Merlin, BL and Moraes, GJ and Cônsoli, FL},
title = {The Microbiota of a Mite Prey-Predator System on Different Host Plants Are Characterized by Dysbiosis and Potential Functional Redundancy.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1590-1607},
pmid = {35543735},
issn = {1432-184X},
support = {2018/24768-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/12004-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Animals ; Female ; *Dysbiosis ; RNA, Ribosomal, 16S/genetics ; Reproduction ; Life Cycle Stages ; Predatory Behavior/physiology ; *Tetranychidae/physiology ; Pest Control, Biological ; },
abstract = {Microbiota has diverse roles in the life cycles of their hosts, affecting their growth, development, behavior, and reproduction. Changes in physiological conditions of the host can also impact the assemblage of host-associated microorganisms. However, little is known of the effects of host plant-prey-predatory mite interactions on mite microbiota. We compared the microbial communities of eggs and adult females of the two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), and of adult females of the predatory mite Neoseiulus californicus (McGregor) (Acari: Phytoseiidae) on four different host plants (cotton, maize, pinto bean, and tomato) by metabarcoding sequencing of the V3-V4 region of the 16S ribosomal RNA gene (16S rRNA), using the Illumina MiSeq platform. Only the egg microbiota of T. urticae was affected by the host plant. The microbiota of the predatory mite N. californicus was very different from that of its prey, and the predator microbiota was unaffected by the different host plant-prey systems tested. Only the microbiota of the eggs of T. urticae carried Serratia as a high fidelity-biomarker, but their low abundance in T. urticae adult females suggests that the association between Serratia and T. urticae is accidental. Biomarker bacteria were also detected in the microbiota of adult females of T. urticae and N. californicus, with different biomarkers in each host plant species. The microbiota associated with eggs and adult females of T. urticae and adult females of N. californicus differed in their functional potential contributions to the host mite.},
}
@article {pmid35538057,
year = {2022},
author = {Patrono, LV and Vrancken, B and Budt, M and Düx, A and Lequime, S and Boral, S and Gilbert, MTP and Gogarten, JF and Hoffmann, L and Horst, D and Merkel, K and Morens, D and Prepoint, B and Schlotterbeck, J and Schuenemann, VJ and Suchard, MA and Taubenberger, JK and Tenkhoff, L and Urban, C and Widulin, N and Winter, E and Worobey, M and Schnalke, T and Wolff, T and Lemey, P and Calvignac-Spencer, S},
title = {Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {2314},
pmid = {35538057},
issn = {2041-1723},
support = {R01 HG006139/HG/NHGRI NIH HHS/United States ; 206298/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Genome, Viral/genetics ; Genomics ; Humans ; *Influenza A Virus, H1N1 Subtype/genetics ; *Influenza A virus/genetics ; *Influenza, Human/epidemiology/genetics ; },
abstract = {The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of local transmission and long-distance dispersal events. Comparison of genomes before and during the pandemic peak shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, local molecular clock modeling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of origination through an intrasubtype reassortment.},
}
@article {pmid35537512,
year = {2022},
author = {Cui, G and Liu, Z and Xu, W and Gao, Y and Yang, S and Grossart, HP and Li, M and Luo, Z},
title = {Metagenomic exploration of antibiotic resistance genes and their hosts in aquaculture waters of the semi-closed Dongshan Bay (China).},
journal = {The Science of the total environment},
volume = {838},
number = {Pt 1},
pages = {155784},
doi = {10.1016/j.scitotenv.2022.155784},
pmid = {35537512},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology ; Aquaculture ; Bays ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Metagenome ; beta-Lactamases/genetics ; },
abstract = {In marine environments, increasing occurrence and numbers of microbial Antibiotic Resistance Gene (ARG) subtypes, especially of new beta-lactamases, have received lots of attention in recent years. Updated databases with novel developed tools provide new opportunities to obtain more comprehensive ARG profiles as well as ARG-carrying hosts. Yet, ARGs in human-associated marine aquaculture environments, e.g. in China, remains largely unknown. Using metagenomic data, we revealed high numbers of Multi-drug Resistance, beta-lactamase and aminoglycoside genes throughout the year. Thereby, Alpha- and Gamma-proteobacteria were assigned to the majority of beta-lactamase-carrying hosts. From Metagenome-assembled genomes, three blaF-like beta-lactamases (91.7-94.7% identity with beta-lactamase from Mycobacterium fortuitum (blaF)) were exclusively observed in an unclassified Mycobacterium genus. Notably, other new beta-lactamases, VMB-1-like (n = 3) (58.5-67.4% identity to Vibrio metallo-beta-lactamase 1 (VMB-1)), were found in Gammaproteobacteria. Additionally, 175 Multi-drug Resistant Organisms possessed at least 3 ARG subtypes, and seven of the potentially pathogenic genera (n = 17) were assigned to Gammaproteobacteria. These results, together with high-risk ARGs (e.g. tetM, dfrA14 and dfrA17), provide hosts and new beta-lactamases of ARGs in Chinese coastal aquaculture.},
}
@article {pmid35537509,
year = {2022},
author = {Xu, N and Zhang, Z and Shen, Y and Zhang, Q and Liu, Z and Yu, Y and Wang, Y and Lei, C and Ke, M and Qiu, D and Lu, T and Chen, Y and Xiong, J and Qian, H},
title = {Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets.},
journal = {The Science of the total environment},
volume = {837},
number = {},
pages = {155807},
doi = {10.1016/j.scitotenv.2022.155807},
pmid = {35537509},
issn = {1879-1026},
mesh = {Algorithms ; *Artificial Intelligence ; High-Throughput Nucleotide Sequencing ; Machine Learning ; *Neural Networks, Computer ; Support Vector Machine ; },
abstract = {The development of machine learning and deep learning provided solutions for predicting microbiota response on environmental change based on microbial high-throughput sequencing. However, there were few studies specifically clarifying the performance and practical of two types of binary classification models to find a better algorithm for the microbiota data analysis. Here, for the first time, we evaluated the performance, accuracy and running time of the binary classification models built by three machine learning methods - random forest (RF), support vector machine (SVM), logistic regression (LR), and one deep learning method - back propagation neural network (BPNN). The built models were based on the microbiota datasets that removed low-quality variables and solved the class imbalance problem. Additionally, we optimized the models by tuning. Our study demonstrated that dataset pre-processing was a necessary process for model construction. Among these 4 binary classification models, BPNN and RF were the most suitable methods for constructing microbiota binary classification models. Using these 4 models to predict multiple microbial datasets, BPNN showed the highest accuracy and the most robust performance, while the RF method was ranked second. We also constructed the optimal models by adjusting the epochs of BPNN and the n_estimators of RF for six times. The evaluation related to performances of models provided a road map for the application of artificial intelligence to assess microbial ecology.},
}
@article {pmid35534014,
year = {2022},
author = {Knapp, BD and Huang, KC},
title = {The Effects of Temperature on Cellular Physiology.},
journal = {Annual review of biophysics},
volume = {51},
number = {},
pages = {499-526},
doi = {10.1146/annurev-biophys-112221-074832},
pmid = {35534014},
issn = {1936-1238},
support = {RM1 GM135102/GM/NIGMS NIH HHS/United States ; },
mesh = {Cell Physiological Phenomena ; *Ecosystem ; *Global Warming ; Humans ; Temperature ; },
abstract = {Temperature impacts biological systems across all length and timescales. Cells and the enzymes that comprise them respond to temperature fluctuations on short timescales, and temperature can affect protein folding, the molecular composition of cells, and volume expansion. Entire ecosystems exhibit temperature-dependent behaviors, and global warming threatens to disrupt thermal homeostasis in microbes that are important for human and planetary health. Intriguingly, the growth rate of most species follows the Arrhenius law of equilibrium thermodynamics, with an activation energy similar to that of individual enzymes but with maximal growth rates and over temperature ranges that are species specific. In this review, we discuss how the temperature dependence of critical cellular processes, such as the central dogma and membrane fluidity, contributes to the temperature dependence of growth. We conclude with a discussion of adaptation to temperature shifts and the effects of temperature on evolution and on the properties of microbial ecosystems.},
}
@article {pmid35533832,
year = {2022},
author = {Lu, S and Zhang, W and Li, X and Xian, J and Hu, Y and Zhou, Y},
title = {Skin bacterial richness and diversity in intensive care unit patients with severe pneumonia.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {121},
number = {},
pages = {75-84},
doi = {10.1016/j.ijid.2022.05.006},
pmid = {35533832},
issn = {1878-3511},
mesh = {Bacteria/genetics ; Humans ; Intensive Care Units ; *Microbiota ; *Pneumonia/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {OBJECTIVES: Patients with severe pneumonia admitted to the intensive care unit (ICU) have a high risk of mortality, and the microbiome is likely to affect the outcome of such patients. However, the composition of the skin microbiota of ICU patients with severe pneumonia remains unclear. In this study, on the basis of 16S ribosomal ribonucleic acid sequencing, we explored the difference in skin bacterial richness and diversity between the ICU patient group (PG) with severe pneumonia and the healthy control group (CG).<br><br>METHODS: The diversity index and taxonomic distribution of skin bacteria were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME) bioinformatics pipeline. Blood, endotracheal aspirate, and bronchoalveolar lavage fluid samples were collected from the same PG subjects for culture.<br><br>RESULTS: Compared with the CG, the diversity of skin bacteria in the PG decreased significantly. Staphylococcus, Acinetobacter, Stenotrophomonas, Enterococcus, Halomonas, and Brevibacillus were differentially abundant in the PG, and most of these bacteria were also identified in the cultures of upper respiratory tract samples of the same PG.<br><br>CONCLUSION: We provide evidence that healthcare-associated infection in ICU patients with severe pneumonia is strongly associated with skin microbiota, which necessitates the prevention and control of skin bacterial pathogens for these patients.},
}
@article {pmid35532036,
year = {2023},
author = {Van Bonn, W and Oliaro, FJ and Pinnell, LJ},
title = {Ultraviolet light alters experimental aquarium water microbial communities.},
journal = {Zoo biology},
volume = {42},
number = {1},
pages = {133-141},
doi = {10.1002/zoo.21701},
pmid = {35532036},
issn = {1098-2361},
mesh = {Animals ; *Water ; Ultraviolet Rays ; Carbon Dioxide ; Animals, Zoo ; Bacteria ; *Microbiota ; },
abstract = {The effect of ultraviolet (UV) light exposure, alone and in combination with CO2 exposure, on the water microbial community composition was tested in replicate experimental aquaria using source water from an established Amazon-themed exhibit housing mixed species of fishes. Total bacterial abundance, α-diversity metrics, and β-diversity metrics were determined 3 weeks and 1 week before, and weekly during 8 weeks of continuous treatment. The UV treatment significantly lowered the overall bacterial abundance while CO2 treatment had no effect. However, the UV exposure effect was variable across phyla. Some phyla were decreased while others were increased, including some of potential clinical significance. At the genus level, there were no significant differences in the relative abundance of Mycobacteria between treatments and an increase in the relative abundance of Aeromonas spp. with UV light treatment. Further work is needed to determine if the observed effects are dose-dependent or if different exposure doses produce different results.},
}
@article {pmid35531295,
year = {2022},
author = {Na, N and Qili, M and Wu, N and Sun, L and Xu, H and Zhao, Y and Wei, X and Xue, Y and Tao, Y},
title = {Bacterial Community and Fermentation Quality of Ensiling Alfalfa With Commercial Lactic Acid Bacterial Additives.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {836899},
pmid = {35531295},
issn = {1664-302X},
abstract = {The aim of this study was to determine the effects of six common commercial lactic acid bacteria (LAB) additives [A1, Lactobacillus plantarum, L. buchneri, and Enterococcus faecalis; A2, L. plantarum and L. casei; A3, L. plantarum and L. buchneri; A4, L. plantarum, L. buchneri, L. casei, and Pediococcus acidilactici; A5, L. plantarum (producing feruloyl esterase); and A6, L. buchneri, P. acidilactici, β-glucanase, and xylanase] on the bacterial community and fermentation quality of alfalfa silage. Alfalfa was harvested at the squaring stage, wilted in the field for 24 h, and ensiled without any additives (Control) or with A1, A2, A3, A4, A5, or A6. Microbial counts, bacterial community, fermentation parameters, and nutritional composition were determined after ensiling for 90 days. The total abundance of LAB genera on alfalfa pre-ensiling was 0.38% in bacterial community. The abundances of Lactobacillus, Enterococcus, and Pediococcus in the Control silage were 42.18, 40.18, and 8.09% of abundance, respectively. The abundances of Lactobacillus in A1-, A2-, A3-, A4-, and A5-treatments were 89.32, 92.93, 92.87, 81.12, and 80.44%, respectively. The abundances of Pediococcus and Lactobacillus in A6-treatment were 70.14 and 24.86%, respectively. Compared with Control silage, LAB-treated silage had lower pH and less ammonia nitrogen and water-soluble carbohydrates concentrations (p < 0.05). Further, the A5- and A6-treatments contained lower neutral detergent fiber, acid detergent fiber, and hemicellulose than other treatments (p < 0.05). Overall, LAB genera were presented as minor taxa in alfalfa pre-ensiling and as dominant taxa in alfalfa silage. Adding LAB additives improved the fermentation quality and altered the bacterial community of alfalfa silage. The main bacterial genera in Control silage were Lactobacillus, Enterococcus, and Pediococcus. Lactobacillus dominated the bacterial communities of A1-, A2-, A3-, A4-, and A5-treatments, while Pediococcus and Lactobacillus were dominant bacterial genera in A6-treatment. Inoculating A5 and A6 degraded the fiber in alfalfa silage. It is necessary to ensile alfalfa with LAB inoculants.},
}
@article {pmid35529946,
year = {2022},
author = {Franzino, T and Boubakri, H and Cernava, T and Abrouk, D and Achouak, W and Reverchon, S and Nasser, W and Haichar, FEZ},
title = {Implications of carbon catabolite repression for plant-microbe interactions.},
journal = {Plant communications},
volume = {3},
number = {2},
pages = {100272},
pmid = {35529946},
issn = {2590-3462},
mesh = {Bacteria/metabolism ; Carbon/metabolism ; *Catabolite Repression/genetics ; Fungi/metabolism ; },
abstract = {Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.},
}
@article {pmid35528619,
year = {2022},
author = {Qing, JB and Song, WZ and Li, CQ and Li, YF},
title = {The Diagnostic and Predictive Significance of Immune-Related Genes and Immune Characteristics in the Occurrence and Progression of IgA Nephropathy.},
journal = {Journal of immunology research},
volume = {2022},
number = {},
pages = {9284204},
pmid = {35528619},
issn = {2314-7156},
mesh = {Female ; *Glomerulonephritis, IGA/diagnosis/genetics ; Humans ; Inflammation/pathology ; Kidney Glomerulus/pathology ; Macrophages/pathology ; Male ; RNA, Messenger/genetics ; },
abstract = {OBJECTIVE: To investigate the potential diagnostic and predictive significance of immune-related genes in IgA nephropathy (IgAN) and discover the abnormal glomerular inflammation in IgAN.<br><br>METHODS: GSE116626 was used as a training set to identify different immune-related genes (DIRGs) and establish machine learning models for the diagnosis of IgAN; then, a nomogram model was generated based on GSE116626, and GSE115857 was used as a test set to evaluate its clinical value. Short Time-Series Expression Miner (STEM) analysis was also performed to explore the changing trend of DIRGs with the progression of IgAN lesions. GSE141344 was used with DIRGs to establish the ceRNA network associated with IgAN progression. Finally, ssGSEA analysis was performed on the GSE141295 dataset to discover the abnormal inflammation in IgAN.<br><br>RESULTS: Machine learning (ML) performed excellently in diagnosing IgAN using six DIRGs. A nomogram model was constructed to predict IgAN based on the six DIRGs. Three trends related to IgAN lesions were identified using STEM analysis. A ceRNA network associated with IgAN progression which contained 8 miRNAs, 14 lncRNAs, and 3 mRNAs was established. A higher macrophage ratio and lower CD4+ T cell ratio in IgAN compared to controls were observed, and the correlation between macrophages and monocytes in the glomeruli of IgAN patients was inverse compared to controls.<br><br>CONCLUSION: This study reveals the diagnostic and predictive significance of DIRGs in IgAN and finds that the imbalance between macrophages and CD4+ immune cells may be an important pathomechanism of IgAN. These results provide potential directions for the treatment and prevention of IgAN.},
}
@article {pmid35526797,
year = {2022},
author = {Zhang, X and Jin, Z and Shen, M and Chang, Z and Yu, G and Wang, L and Xia, X},
title = {Accumulation of polyethylene microplastics induces oxidative stress, microbiome dysbiosis and immunoregulation in crayfish.},
journal = {Fish &amp; shellfish immunology},
volume = {125},
number = {},
pages = {276-284},
doi = {10.1016/j.fsi.2022.05.005},
pmid = {35526797},
issn = {1095-9947},
mesh = {Animals ; Astacoidea/genetics ; Dysbiosis ; Hydrogen Peroxide/metabolism ; *Microbiota ; Microplastics ; Oxidative Stress ; Plastics ; Polyethylene ; *Water Pollutants, Chemical/toxicity ; },
abstract = {Microplastics have become a worldwide pollutant, widely discovered in soil, air and aquatic environment. Microplastics have been found in habitats where crayfish (Procambarus clarkii) cultivated, but the impact of microplastics on crayfish remains unclear. In this study, after 21-day dietary exposure, polyethylene (PE) particles were found to accumulate in intestine, hepatopancreas, gills and hemolymph of crayfish. Furthermore, PE particles can still be detected in these tissues after a 7-day depuration in clean water. PE retained in these tissues caused oxidative stress responses, as indicated by the change of oxidative-stress-related index, such as the increase of H2O2 level and SOD activity. PE exposure also caused hemocytic encapsulation in crayfish hepatopancreas and increase of mucus secretion in intestine. Moreover, PE exposure affected the microbiota balance in crayfish, by reducing the total microbiota abundance and altering the proportions of many bacterial families. Interestingly, results showed that PE exposure led to of lower numbers of hemocytes and declination of phenoloxidase activity. Finally, PE exposure induced the expression of immune-related genes, including transcription factors and antimicrobial peptides. Taken these together, we conclude that PE microplastics exert considerable toxic effects on crayfish and are a potential threat to crayfish aquaculture and consumption. This study provides basic toxicological data toward quantifying and illuminating the impact of PE microplastics on freshwater animals.},
}
@article {pmid35525854,
year = {2023},
author = {da Silva, JL and Mendes, LW and Rocha, SMB and Antunes, JEL and Oliveira, LMS and Melo, VMM and Oliveira, FAS and Pereira, APA and Costa, GDN and da Silva, VB and Gomes, RLF and de Alcantara Neto, F and Lopes, ACA and Araujo, ASF},
title = {Domestication of Lima Bean (Phaseolus lunatus) Changes the Microbial Communities in the Rhizosphere.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1423-1433},
pmid = {35525854},
issn = {1432-184X},
mesh = {*Phaseolus/genetics/microbiology ; Plant Roots/microbiology ; Rhizosphere ; Domestication ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Proteobacteria/genetics ; Plants ; Acidobacteria/genetics ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Plants modulate the soil microbiota and select a specific microbial community in the rhizosphere. However, plant domestication reduces genetic diversity, changes plant physiology, and could have an impact on the associated microbiome assembly. Here, we used 16S rRNA gene sequencing to assess the microbial community in the bulk soil and rhizosphere of wild, semi-domesticated, and domesticated genotypes of lima bean (Phaseolus lunatus), to investigate the effect of plant domestication on microbial community assembly. In general, rhizosphere communities were more diverse than bulk soil, but no differences were found among genotypes. Our results showed that the microbial community's structure was different from wild and semi-domesticated as compared to domesticated genotypes. The community similarity decreased 57.67% from wild to domesticated genotypes. In general, the most abundant phyla were Actinobacteria (21.9%), Proteobacteria (20.7%), Acidobacteria (14%), and Firmicutes (9.7%). Comparing the different genotypes, the analysis showed that Firmicutes (Bacillus) was abundant in the rhizosphere of the wild genotypes, while Acidobacteria dominated semi-domesticated plants, and Proteobacteria (including rhizobia) was enriched in domesticated P. lunatus rhizosphere. The domestication process also affected the microbial community network, in which the complexity of connections decreased from wild to domesticated genotypes in the rhizosphere. Together, our work showed that the domestication of P. lunatus shaped rhizosphere microbial communities from taxonomic to a functional level, changing the abundance of specific microbial groups and decreasing the complexity of interactions among them.},
}
@article {pmid35525510,
year = {2022},
author = {Zhang, Z and Wang, Y and Chen, B and Lei, C and Yu, Y and Xu, N and Zhang, Q and Wang, T and Gao, W and Lu, T and Gillings, M and Qian, H},
title = {Xenobiotic pollution affects transcription of antibiotic resistance and virulence factors in aquatic microcosms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {306},
number = {},
pages = {119396},
doi = {10.1016/j.envpol.2022.119396},
pmid = {35525510},
issn = {1873-6424},
mesh = {Anti-Bacterial Agents/toxicity ; Ciprofloxacin ; Drug Resistance, Microbial/genetics ; Ecosystem ; Genes, Bacterial ; Humans ; *Virulence Factors/genetics ; *Xenobiotics/toxicity ; },
abstract = {Antibiotic resistance genes (ARGs) and virulence factors (VFs) are critical threats to human health. Their abundance in aquatic ecosystems is maintained and enhanced via selection driven by environmental xenobiotics. However, their activity and expression in these environments under xenobiotic stress remains unknown. Here ARG and VF expression profiles were examined in aquatic microcosms under ciprofloxacin, glyphosate and sertraline hydrochloride treatment. Ciprofloxacin increased total expression of ARGs, particularly multidrug resistance genes. Total expression of ARGs and VFs decreased significantly under glyphosate and sertraline treatments. However, in opportunistic human pathogens, these agents increased expression of both ARGs and VFs. Xenobiotic pollutants, such as the compounds we tested here, have the potential to disrupt microbial ecology, promote resistance, and increase risk to human health. This study systematically evaluated the effects of environmental xenobiotics on transcription of ARGs and VFs, both of which have direct relevance to human health. Transcription of such genes has been overlooked in previous studies.},
}
@article {pmid35524818,
year = {2023},
author = {Palacios, OA and Espinoza-Hicks, JC and Camacho-Dávila, AA and López, BR and de-Bashan, LE},
title = {Differences in Exudates Between Strains of Chlorella sorokiniana Affect the Interaction with the Microalga Growth-Promoting Bacteria Azospirillum brasilense : Differences in Exudates Between Strains of Chlorella sorokiniana Affect the Interaction with the Microalga Growth-Promoting Bacteria Azospirillum brasilense.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1412-1422},
pmid = {35524818},
issn = {1432-184X},
support = {284562//CONACYT/ ; },
mesh = {*Chlorella ; *Azospirillum brasilense ; *Microalgae ; Symbiosis ; Exudates and Transudates ; },
abstract = {The microalga Chlorella sorokiniana and the microalgae growth-promoting bacteria (MGPB) Azospirillum brasilense have a mutualistic interaction that can begin within the first hours of co-incubation; however, the metabolites participating in this initial interaction are not yet identified. Nuclear magnetic resonance (NMR) was used in the present study to characterize the metabolites exuded by two strains of C. sorokiniana (UTEX 2714 and UTEX 2805) and A. brasilense Cd when grown together in an oligotrophic medium. Lactate and myo-inositol were identified as carbon metabolites exuded by the two strains of C. sorokiniana; however, only the UTEX 2714 strain exuded glycerol as the main carbon compound. In turn, A. brasilense exuded uracil when grown on the exudates of either microalga, and both microalga strains were able to utilize uracil as a nitrogen source. Interestingly, although the total carbohydrate content was higher in exudates from C. sorokiniana UTEX 2805 than from C. sorokiniana UTEX 2714, the growth of A. brasilense was greater in the exudates from the UTEX 2714 strain. These results highlight the fact that in the exuded carbon compounds differ between strains of the same species of microalgae and suggest that the type, rather than the quantity, of carbon source is more important for sustaining the growth of the partner bacteria.},
}
@article {pmid35522265,
year = {2023},
author = {Sun, Y and Shi, X and He, LY and Xing, Y and Guo, QF and Xiu, ZL and Dong, YS},
title = {Biosynthetic Profile in the Co-culture of Aspergillus sydowii and Bacillus subtilis to Produce Novel Benzoic Derivatives.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1288-1299},
pmid = {35522265},
issn = {1432-184X},
support = {2019-ZD-0143//Natural Science Foundation of Liaoning Province/ ; 202110401131YY//Science and Technology Development Program of Jilin Province of China/ ; },
mesh = {*Bacillus subtilis/genetics ; Coculture Techniques ; *Ecosystem ; Benzoic Acid ; },
abstract = {Microbial co-culture simulates the natural ecosystem through the combination of artificial microbes. This approach has been widely applied in the study of activating silent genes to reveal novel secondary metabolites. However, there are still challenges in determining the biosynthetic pathways. In this study, the effects of microbial co-culture on the morphology of the microbes were verified by the morphological observation. Subsequently, through the strategy combining substrate feeding, stable isotope labeling, and gene expression analysis, the biosynthetic pathways of five benzoic acid derivatives N1-N4 and N7 were demonstrated: the secondary metabolite 10-deoxygerfelin of A. sydowii acted as an inducer to induce B. subtilis to produce benzoic acid, which was further converted into 3-OH-benzoic acid by A. sydowii. Subsequently, A. sydowii used 3-OH-benzoic acid as the substrate to synthesize the new compound N2, and then N1, N3, N4, and N7 were biosynthesized upon the upregulation of hydrolase, hydroxylase, and acyltransferase during co-culture. The plate zone analysis suggested that the biosynthesis of the newly induced compounds N1-N4 was mainly attributed to A. sydowii, and both A. sydowii and B. subtilis were indispensable for the biosynthesis of N7. This study provides an important basis for a better understanding of the interactions among microorganisms, providing new ideas for studying the biosynthetic pathways of the newly induced secondary metabolites in co-culture.},
}
@article {pmid35513592,
year = {2023},
author = {Haag, KL and Caesar, L and da Silveira Regueira-Neto, M and de Sousa, DR and Montenegro Marcelino, V and de Queiroz Balbino, V and Torres Carvalho, A},
title = {Temporal Changes in Gut Microbiota Composition and Pollen Diet Associated with Colony Weakness of a Stingless Bee.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1514-1526},
pmid = {35513592},
issn = {1432-184X},
support = {PQG 19/2551-0001860-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul/ ; Associa&#xe7;&#xe3;o ABELHA #400597/2018-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; PQ #302121/2017-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; Diet ; Bacteria/genetics ; Pollen ; Pollination ; },
abstract = {Compared to honeybees and bumblebees, the effect of diet on the gut microbiome of Neotropical corbiculate bees such as Melipona spp. is largely unknown. These bees have been managed for centuries, but recently an annual disease is affecting M. quadrifasciata, an endangered species kept exclusively by management in Southern Brazil. Here we report the results of a longitudinal metabarcoding study involving the period of M. quadrifasciata colony weakness, designed to monitor the gut microbiota and diet changes preceding an outbreak. We found increasing amounts of bacteria associated to the gut of forager bees 2 months before the first symptoms have been recorded. Simultaneously, forager bees showed decreasing body weight. The accelerated growth of gut-associated bacteria was uneven among taxa, with Bifidobacteriaceae dominating, and Lactobacillaceae decreasing in relative abundance within the bacterial community. Dominant fungi such as Candida and Starmerella also decreased in numbers, and the stingless bee obligate symbiont Zygosaccharomyces showed the lowest relative abundance during the outbreak period. Such changes were associated with pronounced diet shifts, i.e., the rise of Eucalyptus spp. pollen amount in forager bees' guts. Furthermore, there was a negative correlation between the amount of Eucalyptus pollen in diets and the abundance of some bacterial taxa in the gut-associated microbiota. We conclude that diet and subsequent interactions with the gut microbiome are key environmental components of the annual disease and propose the use of diet supplementation as means to sustain the activity of stingless bee keeping as well as native bee pollination services.},
}
@article {pmid35513142,
year = {2022},
author = {Bulgarelli, RG and Leite, MFA and de Hollander, M and Mazzafera, P and Andrade, SAL and Kuramae, EE},
title = {Eucalypt species drive rhizosphere bacterial and fungal community assembly but soil phosphorus availability rearranges the microbiome.},
journal = {The Science of the total environment},
volume = {836},
number = {},
pages = {155667},
doi = {10.1016/j.scitotenv.2022.155667},
pmid = {35513142},
issn = {1879-1026},
mesh = {Bacteria ; Fungi ; *Microbiota/physiology ; *Mycobiome ; Phosphorus ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Soil phosphorus (P) availability may limit plant growth and alter root-soil interactions and rhizosphere microbial community composition. The composition of the rhizosphere microbial community can also be shaped by plant genotype. In this study, we examined the rhizosphere microbial communities of young plants of 24 species of eucalypts (22 Eucalyptus and two Corymbia species) under low or sufficient soil P availability. The taxonomic diversity of the rhizosphere bacterial and fungal communities was assessed by 16S and 18S rRNA gene amplicon sequencing. The taxonomic modifications in response to low P availability were evaluated by principal component analysis, and co-inertia analysis was performed to identify associations between bacterial and fungal community structures and parameters related to plant growth and nutritional status under low and sufficient soil P availability. The sequencing results showed that while both soil P availability and eucalypt species influenced the microbial community assembly, eucalypt species was the stronger determinant. However, when the plants are subjected to low P-availability, the rhizosphere selection became strongest. In response to low P, the bacterial and fungal communities in the rhizosphere of some species showed significant changes, whereas in others remained relatively constant under low and sufficient P. Co-inertia analyses revealed a significant co-dependence between plant nutrient contents and bacterial and fungal community composition only under sufficient P. By contrast, under low P, bacterial community composition was related to plant biomass production. In conclusion, our study shows that eucalypt species identity was the main factor modulating rhizosphere microbial community composition; significant shifts due to P availability were observed only for some eucalypt species.},
}
@article {pmid35507445,
year = {2022},
author = {Bloxham, B and Lee, H and Gore, J},
title = {Diauxic lags explain unexpected coexistence in multi-resource environments.},
journal = {Molecular systems biology},
volume = {18},
number = {5},
pages = {e10630},
pmid = {35507445},
issn = {1744-4292},
support = {R01 GM102311/GM/NIGMS NIH HHS/United States ; },
mesh = {*Adaptation, Physiological ; *Ecosystem ; Models, Biological ; },
abstract = {How the coexistence of species is affected by the presence of multiple resources is a major question in microbial ecology. We experimentally demonstrate that differences in diauxic lags, which occur as species deplete their own environments and adapt their metabolisms, allow slow-growing microbes to stably coexist with faster-growing species in multi-resource environments despite being excluded in single-resource environments. In our focal example, an Acinetobacter species (Aci2) competitively excludes Pseudomonas aurantiaca (Pa) on alanine and on glutamate. However, they coexist on the combination of both resources. Experiments reveal that Aci2 grows faster but Pa has shorter diauxic lags. We establish a tradeoff between Aci2's fast growth and Pa's short lags as their mechanism for coexistence. We model this tradeoff to accurately predict how environmental changes affect community composition. We extend our work by surveying a large set of competitions and observe coexistence nearly four times as frequently when the slow-grower is the fast-switcher. Our work illustrates a simple mechanism, based entirely on supplied-resource growth dynamics, for the emergence of multi-resource coexistence.},
}
@article {pmid35507048,
year = {2023},
author = {McLain, NK and Gomez, MY and Gachomo, EW},
title = {Acetaminophen Levels Found in Recycled Wastewater Alter Soil Microbial Community Structure and Functional Diversity.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1448-1462},
pmid = {35507048},
issn = {1432-184X},
support = {1018746//National Institute of Food and Agriculture, Multistate Research Fund ,/ ; },
mesh = {*Wastewater ; Soil/chemistry ; Acetaminophen/metabolism ; Agricultural Irrigation/methods ; Bacteria/genetics ; Crops, Agricultural ; *Microbiota ; Carboxylic Acids/metabolism ; Soil Microbiology ; },
abstract = {The practice of using recycled wastewater (RWW) has been successfully adopted to address the growing demand for clean water. However, chemicals of emerging concern (CECs) including pharmaceutical products remain in the RWW even after additional cleaning. When RWW is used to irrigate crops or landscapes, these chemicals can enter these and adjacent environments. Unfortunately, the overall composition and concentrations of CECs found in different RWW sources vary, and even the same source can vary over time. Therefore, we selected one compound that is found frequently and in high concentrations in many RWW sources, acetaminophen (APAP), to use for our study. Using greenhouse grown eggplants treated with APAP concentrations within the ranges found in RWW effluents, we investigated the short-term impacts of APAP on the soil bacterial population under agricultural settings. Using Illumina sequencing-based approaches, we showed that APAP has the potential to cause shifts in the microbial community most likely by positively selecting for bacteria that are capable of metabolizing the breakdown products of APAP such as glycosides and carboxylic acids. Community-level physiological profiles of carbon metabolism were evaluated using Biolog EcoPlate as a proxy for community functions. The Biolog plates indicated that the metabolism of amines, amino acids, carbohydrates, carboxylic acids, and polymers was significantly higher in the presence of APAP. Abundance of microorganisms of importance to plant health and productivity was altered by APAP. Our results indicate that the soil microbial community and functions could be altered by APAP at concentrations found in RWW. Our findings contribute to the knowledge base needed to guide policies regulating RWW reuse in agriculture and also highlight the need to further investigate the effects of CECs found in RWW on soil microbiomes.},
}
@article {pmid35504465,
year = {2022},
author = {Li, H and Miller, T and Lu, J and Goel, R},
title = {Nitrogen fixation contribution to nitrogen cycling during cyanobacterial blooms in Utah Lake.},
journal = {Chemosphere},
volume = {302},
number = {},
pages = {134784},
pmid = {35504465},
issn = {1879-1298},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
mesh = {*Cyanobacteria/genetics/metabolism ; Ecosystem ; Eutrophication ; *Lakes/microbiology ; Nitrates ; Nitrogen/analysis ; Nitrogen Fixation ; Utah ; },
abstract = {Nitrogen (N) cycling is an essential process in lake systems and N-fixation is an important component of it. Recent studies have also found that nitrate reduction through heterotrophic denitrification in lake systems did not prevent harmful cyanobacterial blooms, but instead, may have favored the dominance of N2-fixing cyanobacteria. The overall objective of this study was to estimate nitrogen fixation rates and the expressions of associated nitrogenase (nif gene) functional gene at several sites at different occasions in freshwater Utah Lake. For comparison purposes, one time sampling was also conducted in the brackish Farmington Bay of Great Salt Lake (GSL). The microbial ecology of the top 20-cm of surface water was investigated to assess the dominant cyanobacterial communities and N-related metabolisms. Our study revealed that Dolichospermum and Nodularia were potential N2-fixers for Utah Lake and brackish Farmington Bay, respectively. The in situ N2-fixation rates were 0-0.73 nmol N hr[-1]L[-1] for Utah Lake and 0-0.85 nmol N hr[-1]L[-1] for Farmington Bay, and these rates positively correlated with the abundance and expressions of the nif gene. In addition, nitrate reduction was measured in sediment (0.002-0.094 mg N VSS[-1] hr[-1]). Significantly positive correlations were found among amoA, nirS and nirK abundance (R = 0.56-0.87, p < 0.05, Spearman) in both lakes. An exception was the lower nirK gene abundance detected at one site in Farmington Bay where high ammonium retentions were also detected. Based on a mass balance approach, we concluded that the amount of inorganic N loss through denitrification still exceeded the N input by N2-fixation, much like in most lakes, rivers, and marine ecosystems. This indicates that N cycling processes such as denitrification mediated by heterotrophic bacteria contributes to N-export from the lakes resulting in N limitations.},
}
@article {pmid35504213,
year = {2022},
author = {Lee, M and Liang, G and Holland, SI and O'Farrell, C and Osborne, K and Manefield, MJ},
title = {Dehalobium species implicated in 2,3,7,8-tetrachlorodibenzo-p-dioxin dechlorination in the contaminated sediments of Sydney Harbour Estuary.},
journal = {Marine pollution bulletin},
volume = {179},
number = {},
pages = {113690},
doi = {10.1016/j.marpolbul.2022.113690},
pmid = {35504213},
issn = {1879-3363},
mesh = {Bays ; *Benzofurans/analysis ; Dibenzofurans, Polychlorinated/analysis ; *Dioxins/analysis ; Estuaries ; *Polychlorinated Dibenzodioxins/analysis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Polychlorinated dibenzo-p-dioxins and furans (PCDD/F) are some of the most environmentally recalcitrant and toxic compounds. They occur naturally and as by-products of anthropogenic activity. Sydney Harbour Estuary (Sydney, Australia), is heavily contaminated with PCDD/F. Analysis of sediment cores revealed that the contamination source area in Homebush Bay continues to have one of the highest levels of PCDD/F contamination in the world (5207 pg WHO-TEQ g[-1]) with >50% of the toxicity attributed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), the most toxic PCDD/F congener. Comparison of congener profiles at the contamination source area with surrounding bays and historical data provided evidence for the attenuation of 2,3,7,8-TCDD and other congeners at the source area. This finding was supported by the detection of di-, mono- and unchlorinated dibenzo-p-dioxin. Microbial community analysis of sediments by 16S rRNA amplicon sequencing revealed an abundance of lineages from the class Dehalococcoidia (up to 15% of the community), including the genus Dehalobium (up to 0.5%). Anaerobic seawater enrichment cultures using perchloroethene as more biologically available growth substrate enriched the Dehalobium population by more than six-fold. The enrichment culture then proved capable of reductively dechlorinating 2,3,7,8-TCDD to 2,3,7-TriCDD and octachlorodibenzo-p-dibenzodioxin (OCDD) to hepta and hexa congeners. This work is the first to show microbial reductive dehalogenation of 2,3,7,8-TCDD with a bacterium from outside the Dehalococcoides genus, and one of only a few that demonstrates PCDD/F dechlorination in a marine environment.},
}
@article {pmid35503575,
year = {2023},
author = {Dick, JM and Tan, J},
title = {Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1338-1355},
pmid = {35503575},
issn = {1432-184X},
mesh = {RNA, Ribosomal, 16S/genetics ; *Proteome ; *Microbiota/genetics ; Metagenome ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.},
}
@article {pmid35502577,
year = {2022},
author = {Laveilhé, A and Fochesato, S and Lalaouna, D and Heulin, T and Achouak, W},
title = {Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues.},
journal = {Microbial biotechnology},
volume = {15},
number = {7},
pages = {2083-2096},
pmid = {35502577},
issn = {1751-7915},
mesh = {*Alphaproteobacteria ; Bacteria/genetics ; Fungi ; Iron ; Plant Diseases/microbiology/prevention &amp; control ; Rhizosphere ; *Soil Microbiology ; },
abstract = {Pseudomonads play crucial roles in plant growth promotion and control of plant diseases. However, under natural conditions, other microorganisms competing for the same nutrient resources in the rhizosphere may exert negative control over their phytobeneficial characteristics. We assessed the expression of phytobeneficial genes involved in biocontrol, biostimulation and iron regulation such as, phlD, hcnA, acdS, and iron-small regulatory RNAs prrF1 and prrF2 in Pseudomonas brassicacearum co-cultivated with three phytopathogenic fungi, and two rhizobacteria in the presence or absence of Brassica napus, and in relation to iron availability. We found that the antifungal activity of P. brassicacearum depends mostly on the production of DAPG and not on HCN whose production is suppressed by fungi. We have also shown that the two-competing bacterial strains modulate the plant growth promotion activity of P. brassicacearum by modifying the expression of phlD, hcnA and acdS according to iron availability. Overall, it allows us to better understand the complexity of the multiple molecular dialogues that take place underground between microorganisms and between plants and its rhizosphere microbiota and to show that synergy in favour of phytobeneficial gene expression may exist between different bacterial species.},
}
@article {pmid35502341,
year = {2022},
author = {Qing, J and Song, W and Tian, L and Samuel, SB and Li, Y},
title = {Potential Small Molecules for Therapy of Lupus Nephritis Based on Genetic Effect and Immune Infiltration.},
journal = {BioMed research international},
volume = {2022},
number = {},
pages = {2259164},
pmid = {35502341},
issn = {2314-6141},
mesh = {Computational Biology ; Female ; Gene Expression ; Genes, Regulator ; Humans ; *Lupus Erythematosus, Systemic/genetics ; *Lupus Nephritis/drug therapy/genetics ; Male ; Membrane Proteins/genetics ; RNA-Binding Proteins/genetics ; },
abstract = {Lupus nephritis (LN) is the most common and significant complication of systemic lupus erythematosus (SLE) due to its poor prognosis and mortality rates in SLE patients. There is a critical need for new drugs as the pathogenesis of LN remains to be elucidated and immunosuppressive therapy comes with many deficiencies. In this study, 23 hub genes (IFI6, PLSCR1, XAF1, IFI16, IFI44, MX1, IFI44L, IFIT3, IFIT2, IFI27, DDX58, EIF2AK2, IFITM1, RTP4, IFITM3, TRIM22, PARP12, IFIH1, OAS1, HERC6, RSAD2, DDX60, and MX2) were identified through bioinformatics and network analysis and are closely related to interferon production and function. Interestingly, immune cell infiltration analysis and correlation analysis demonstrate a positive correlation between the expression of 23 hub genes and monocyte infiltration in glomeruli and M2 macrophage infiltration in the tubulointerstitium of LN patients. Additionally, the CTD database, DsigDB database, and DREIMT database were used to explore the bridging role of genes in chemicals and LN as well as the potential influence of these chemicals on immune cells. After comparison and discussion, six small molecules (Acetohexamide, Suloctidil, Terfenadine, Prochlorperazine, Mefloquine, and Triprolidine) were selected for their potential ability in treating lupus nephritis.},
}
@article {pmid35501499,
year = {2023},
author = {Liu, Y and Zhang, B and Zhang, Y and Shen, Y and Cheng, C and Yuan, W and Guo, P},
title = {Organic Matter Decomposition in River Ecosystems: Microbial Interactions Influenced by Total Nitrogen and Temperature in River Water.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1236-1252},
pmid = {35501499},
issn = {1432-184X},
support = {2018ZX07111005//the National Science and Technology Major Project of the Ministry of Science and Technology of China/ ; 20200801071GH//the Science and Technology Development Program of Jilin Province/ ; },
mesh = {*Ecosystem ; *Rivers/microbiology ; Nitrogen ; Temperature ; Bacteria/genetics ; Microbial Interactions ; Water ; },
abstract = {Microbes contribute to the organic matter decomposition (OMD) in river ecosystems. This study considers two aspects of OMD in river ecosystems which have not been examined in scientific studies previously, and these are the microbial interactions in OMD and the influence of environmental factors on microbial interactions. Cotton strip (CS), as a substitute for organic matter, was introduced to Luanhe River Basin in China. The results of CS assay, microbial sequencing, and redundancy analysis (RDA) showed that CS selectively enriched bacterial and fungal groups related to cellulose decomposition, achieving cotton strip decomposition (CSD). Bacterial phylum Proteobacteria and fungal phyla Rozellomycota and Ascomycota were the dominant groups associated with CSD. Network analysis and Mantel test results indicated that bacteria and fungi on CS cooperatively formed an interaction network to achieve the CSD. In the network, modules 2 and 4 were significantly positively associated with CSD, which were considered as the key modules in this study. The key modules were mainly composed of phyla Proteobacteria and Ascomycota, indicating that microbes in key modules were the effective decomposers of CS. Although keystone taxa were not directly associated with CSD, they may regulate the genera in key modules to achieve the CSD, since some keystone taxa were linked with the microbial genera associated with CSD in the key modules. Total nitrogen (TN) and temperature in water were the dominant environmental factors positively influenced CSD. The key modules 2 and 4 were positively influenced by water temperature and TN in water, respectively, and two keystone taxa were positively associated with TN. This profoundly revealed that water temperature and TN influenced the OMD through acting on the keystone taxa and key modules in microbial interactions. The research findings help us to understand the microbial interactions influenced by environmental factors in OMD in river ecosystems.},
}
@article {pmid35501031,
year = {2022},
author = {Gómez-Muñoz, B and Efthymiou, A and Dubey, M and Sølve, J and Nicolaisen, M and Jensen, DF and Nybroe, O and Larsen, J},
title = {Cellulose amendment promotes P solubilization by Penicillium aculeatum in non-sterilized soil.},
journal = {Fungal biology},
volume = {126},
number = {5},
pages = {356-365},
doi = {10.1016/j.funbio.2022.03.003},
pmid = {35501031},
issn = {1878-6146},
mesh = {Cellulose ; Sewage ; *Soil ; Soil Microbiology ; Sterilization ; *Talaromyces ; },
abstract = {Successful application of microbial biofertilizers, such as phosphorus (P) solubilizing fungi to agroecosystems, is constrained from the lack of knowledge about their ecology; for example in terms of how they respond to an external input of carbon (C) to get established in the soil. In two soil incubation experiments we examined the performance of the P solubilizing fungus Penicillium aculeatum in non-sterile and semi-sterile (γ-irradiated) soil with different C and P sources. Results from the first experiment with C sources showed that starch and cellulose generally improved P solubilization by P. aculeatum measured as water extractable P (Pwep), though only significantly in non-sterile soil. This coincided with an increased population density of P. aculeatum measured with a hygromycin B resistant strain of this fungus. Soil respiration used to measure soil microbial activity was overall much higher in treatments with C compounds than without C in both non-sterile and semi-sterile soil. However, soil respiration was highest with cellulose in semi-sterile soil, especially in combination with P. aculeatum. Hence, for the second experiment with P sources (tricalcium phosphate (TCP) and sewage sludge ash) cellulose was used as a C source for P. aculeatum growth in all treatments. Main results showed that P. aculeatum in combination with cellulose soil amendment increased soil Pwep independent of soil sterilization and P source treatments. Soil resin P (Pres) and microbial P (Pmic), which represents stocks of potentially plant available P, were also affected from P. aculeatum inoculation. Increased soil Pres from TCP and sewage sludge ash was observed with P. aculeatum independent of soil type. On the other hand soil Pmic was higher after P. aculeatum inoculation only in semi-sterile soil. Population density of P. aculeatum measured with qPCR was maintained or increased in non-sterile and semi-sterile soil, respectively, compared to the original inoculum load of P. aculeatum. In conclusion, our results underline the importance of C source addition for P. aculeatum if used as a biofertilizer. For this, cellulose seems to be a promising option promoting P. aculeatum growth and P solubilization also in non-sterilized soil.},
}
@article {pmid35499645,
year = {2023},
author = {Anderson, KE and Ricigliano, VA and Copeland, DC and Mott, BM and Maes, P},
title = {Social Interaction is Unnecessary for Hindgut Microbiome Transmission in Honey Bees: The Effect of Diet and Social Exposure on Tissue-Specific Microbiome Assembly.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1498-1513},
pmid = {35499645},
issn = {1432-184X},
support = {2022-21000-021-00D//Agricultural Research Service/ ; },
mesh = {Bees ; Animals ; Social Interaction ; *Microbiota ; *Gastrointestinal Microbiome ; Bacteria/genetics ; Diet ; },
abstract = {Honey bees are a model for host-microbial interactions with experimental designs evolving towards conventionalized worker bees. Research on gut microbiome transmission and assembly has examined only a fraction of factors associated with the colony and hive environment. Here, we studied the effects of diet and social isolation on tissue-specific bacterial and fungal colonization of the midgut and two key hindgut regions. We found that both treatment factors significantly influenced early hindgut colonization explaining similar proportions of microbiome variation. In agreement with previous work, social interaction with older workers was unnecessary for core hindgut bacterial transmission. Exposure to natural eclosion and fresh stored pollen resulted in gut bacterial communities that were taxonomically and structurally equivalent to those produced in the natural colony setting. Stressed diets of no pollen or autoclaved pollen in social isolation resulted in decreased fungal abundance and bacterial diversity, and atypical microbiome structure and tissue-specific variation of functionally important core bacteria. Without exposure to the active hive environment, the abundance and strain diversity of keystone ileum species Gilliamella apicola was markedly reduced. These changes were associated with significantly larger ileum microbiotas suggesting that extended exposure to the active hive environment plays an antibiotic role in hindgut microbiome establishment. We conclude that core hindgut microbiome transmission is facultative horizontal with 5 of 6 core hindgut species readily acquired from the built hive structure and natural diet. Our findings contribute novel insights into factors influencing assembly and maintenance of honey bee gut microbiota and facilitate future experimental designs.},
}
@article {pmid35499337,
year = {2022},
author = {Stapelfeldt, HRD and Barnes, SJ and Henson, MW and Thrash, JC},
title = {Draft Genome Sequence of the Marine Flavobacteriaceae sp. Strain LSUCC0859.},
journal = {Microbiology resource announcements},
volume = {11},
number = {5},
pages = {e0018622},
pmid = {35499337},
issn = {2576-098X},
support = {LEQSF[2014-2017]-RDA-06//Louisiana Board of Regents (Board of Regents)/ ; Gulf Research Program Early Career Research Fellowship//National Academies of Sciences, Engineering, and Medicine (NASEM)/ ; Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; },
abstract = {A new marine Flavobacteriaceae sp. strain, LSUCC0859, was isolated off the coast of Louisiana with artificial seawater via high-throughput dilution-to-extinction (DTE) cultivation. The 2,168,862-bp genome sequence provides opportunities to investigate the biology of a poorly understood lineage within the Bacteroidetes.},
}
@article {pmid35499326,
year = {2022},
author = {Rahlff, J and Bornemann, TLV and Lopatina, A and Severinov, K and Probst, AJ},
title = {Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {10},
pages = {e0031522},
pmid = {35499326},
issn = {1098-5336},
mesh = {Antarctic Regions ; *Bacteriophages/genetics ; Ecosystem ; Metagenomics ; Prophages/genetics ; },
abstract = {Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples, especially from polar regions, yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating, or prophages) across the Antarctic continent can be tracked via their genetic signatures, aiding our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria, including Ralstonia spp. We reconstructed the complete genome of a temperate phage with nearly complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which were detected in seawater from the Western Antarctic Peninsula at a distance of 5,338 km from the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp., disperse over long distances despite the harsh conditions of the Antarctic continent. Given that 14 phages associated with two R. pickettii draft genomes isolated from space equipment were identified, we conclude that Ralstonia phages are ideal mobile genetic elements to track dispersal and contamination in ecosystems relevant for astrobiology. IMPORTANCE Host-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to the presence of these bacteria carrying genome-integrated prophages on space-related equipment and the potential for dispersal of host-associated phages demonstrated here, our work has implications for planetary protection, a discipline in astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.},
}
@article {pmid35496989,
year = {2022},
author = {Di Martino, P},
title = {Antimicrobial agents and microbial ecology.},
journal = {AIMS microbiology},
volume = {8},
number = {1},
pages = {1-4},
pmid = {35496989},
issn = {2471-1888},
abstract = {Antimicrobials are therapeutic substances used to prevent or treat infections. Disinfectants are antimicrobial agents applied to non-living surfaces. Every year, several thousand tonnes of antimicrobials and their by-products are released into the environment and in particular into the aquatic environment. This type of xenobiotic has ecological consequences in the natural environment but also in technological environments such as wastewater treatment plants and methane fermentation sewage sludge treatment plants. The constant exposure of microbial communities not only to high concentrations but also to sub-inhibitory concentrations of antibiotics is a key element in the development of antibiotic resistance in aquatic environments and in soils. The future of antimicrobials lies in the development of biosourced or bioinspired molecules. The observation and deciphering of interactions between living organisms is the key to this development.},
}
@article {pmid35495730,
year = {2022},
author = {Nagar, S and Talwar, C and Motelica-Heino, M and Richnow, HH and Shakarad, M and Lal, R and Negi, RK},
title = {Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {848010},
pmid = {35495730},
issn = {1664-302X},
abstract = {Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.},
}
@article {pmid35495644,
year = {2022},
author = {Rangel, F and Enes, P and Gasco, L and Gai, F and Hausmann, B and Berry, D and Oliva-Teles, A and Serra, CR and Pereira, FC},
title = {Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {831034},
pmid = {35495644},
issn = {1664-302X},
support = {ZK 57/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {The aquaculture industry is one of the fastest-growing sectors in animal food production. However, farming of carnivorous fish strongly relies on the use of wild fish-based meals, a practice that is environmentally and economically unsustainable. Insect-based diets constitute a strong candidate for fishmeal substitution, due to their high nutritional value and low environmental footprint. Nevertheless, data on the impact of insect meal (IM) on the gut microbiome of farmed fish are so far inconclusive, and very scarce in what concerns modulation of microbial-mediated functions. Here we use high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR to evaluate the impact of different IMs on the composition and chitinolytic potential of the European sea bass gut digesta- and mucosa-associated communities. Our results show that insect-based diets of distinct origins differently impact the gut microbiota of the European sea bass (Dicentrarchus labrax). We detected clear modulatory effects of IM on the gut microbiota, which were more pronounced in the digesta, where communities differed considerably among the diets tested. Major community shifts were associated with the use of black soldier fly larvae (Hermetia illucens, HM) and pupal exuviae (HEM) feeds and were characterized by an increase in the relative abundance of the Firmicutes families Bacillaceae, Enterococcaceae, and Lachnospiraceae and the Actinobacteria family Actinomycetaceae, which all include taxa considered beneficial for fish health. Modulation of the digesta community by HEM was characterized by a sharp increase in Paenibacillus and a decrease of several Gammaproteobacteria and Bacteroidota members. In turn, a mealworm larvae-based diet (Tenebrio molitor, TM) had only a modest impact on microbiota composition. Further, using quantitative PCR, we demonstrate that shifts induced by HEM were accompanied by an increase in copy number of chitinase ChiA-encoding genes, predominantly originating from Paenibacillus species with effective chitinolytic activity. Our study reveals an HEM-driven increase in chitin-degrading taxa and associated chitinolytic activity, uncovering potential benefits of adopting exuviae-supplemented diets, a waste product of insect rearing, as a functional ingredient.},
}
@article {pmid35494622,
year = {2022},
author = {Guéneau, V and Plateau-Gonthier, J and Arnaud, L and Piard, JC and Castex, M and Briandet, R},
title = {Positive biofilms to guide surface microbial ecology in livestock buildings.},
journal = {Biofilm},
volume = {4},
number = {},
pages = {100075},
pmid = {35494622},
issn = {2590-2075},
abstract = {The increase in human consumption of animal proteins implies changes in the management of meat production. This is followed by increasingly restrictive regulations on antimicrobial products such as chemical biocides and antibiotics, used in particular to control pathogens that can spread zoonotic diseases. Aligned with the One Health concept, alternative biological solutions are under development and are starting to be used in animal production. Beneficial bacteria able to form positive biofilms and guide surface microbial ecology to limit microbial pathogen settlement are promising tools that could complement existing biosecurity practices to maintain the hygiene of livestock buildings. Although the benefits of positive biofilms have already been documented, the associated fundamental mechanisms and the rationale of the microbial composition of these new products are still sparce. This review provides an overview of the envisioned modes of action of positive biofilms used on livestock building surfaces and the resulting criteria for the selection of the appropriate microorganisms for this specific application. Limits and advantages of this biosecurity approach are discussed as well as the impact of such practices along the food chain, from farm to fork.},
}
@article {pmid35493735,
year = {2022},
author = {Kumar, D and Sharma, SR and Adegoke, A and Kennedy, A and Tuten, HC and Li, AY and Karim, S},
title = {Recently Evolved Francisella-Like Endosymbiont Outcompetes an Ancient and Evolutionarily Associated Coxiella-Like Endosymbiont in the Lone Star Tick (Amblyomma americanum) Linked to the Alpha-Gal Syndrome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {787209},
pmid = {35493735},
issn = {2235-2988},
support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; },
mesh = {Amblyomma ; Animals ; Bacteria ; Coxiella ; *Food Hypersensitivity ; *Francisella/genetics ; Humans ; *Ticks/microbiology ; United States ; },
abstract = {BACKGROUND: Ticks are hematophagous arthropods that transmit various bacterial, viral, and protozoan pathogens of public health significance. The lone star tick (Amblyomma americanum) is an aggressive human-biting tick that transmits bacterial and viral pathogens, and its bites are suspected of eliciting the alpha-gal syndrome, a newly emerged delayed hypersensitivity following consumption of red meat in the United States. While ongoing studies have attempted to investigate the contribution of different tick-inherent factors to the induction of alpha-gal syndrome, an otherwise understudied aspect is the contribution of the tick microbiome and specifically obligate endosymbionts to the establishment of the alpha-gal syndrome in humans.<br><br>MATERIALS AND METHODS: Here we utilized a high-throughput metagenomic sequencing approach to cataloging the entire microbial communities residing within different developmental stages and tissues of unfed and blood-fed ticks from laboratory-maintained ticks and three new geographical locations in the United States. The Quantitative Insights Into Microbial Ecology (QIIME2) pipeline was used to perform data analysis and taxonomic classification. Moreover, using a SparCC (Sparse Correlations for Compositional data) network construction model, we investigated potential interactions between members of the microbial communities from laboratory-maintained and field-collected ticks.<br><br>RESULTS: Overall, Francisellaceae was the most dominant bacteria identified in the microbiome of both laboratory-raised and field-collected Am. americanum across all tissues and developmental stages. Likewise, microbial diversity was seen to be significantly higher in field-collected ticks compared with laboratory-maintained ticks as seen with a higher number of both Operational Taxonomic Units and measures of species richness. Several potential positive and negative correlations were identified from our network analysis. We observed a strong positive correlation between Francisellaceae, Rickettsiaceae, and Midichloriaceae in both developmental stages and tissues from laboratory-maintained ticks, whereas ovarian tissues had a strong positive correlation of bacteria in the family Xanthobacteraceae and Rhizobiaceae. A negative interaction was observed between Coxiellaceae and Francisellaceae in Illinois, and all the bacteria detected from ticks from Delaware were negatively correlated.<br><br>CONCLUSION: This study is the first to catalog the microbiome of Am. americanum throughout its developmental stages and different tissue niches and report the potential replacement of Coxiellaceae by Francisellaceae across developmental stages and tissues tested except in ovarian tissues. These unique and significant findings advance our knowledge and open a new avenue of research to further understand the role of tick microbiome in tick-borne diseases and develop a holistic strategy to control alpha-gal syndrome.},
}
@article {pmid35491817,
year = {2022},
author = {Zhang, M and Whiteley, M and Lewin, GR},
title = {Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective.},
journal = {mBio},
volume = {13},
number = {3},
pages = {e0023522},
pmid = {35491817},
issn = {2150-7511},
support = {F32 DE027281/DE/NIDCR NIH HHS/United States ; K99 DE031018/DE/NIDCR NIH HHS/United States ; R01 DE020100/DE/NIDCR NIH HHS/United States ; R01 DE023193/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; Microbial Interactions ; *Microbiota ; Models, Biological ; Mouth ; *Periodontitis ; },
abstract = {The oral microbiota is enormously diverse, with over 700 microbial species identified across individuals that play a vital role in the health of our mouth and our overall well-being. In addition, as oral diseases such as caries (cavities) and periodontitis (gum disease) are mediated through interspecies microbial interactions, this community serves as an important model system to study the complexity and dynamics of polymicrobial interactions. Here, we review historical and recent progress in our understanding of the oral microbiome, highlighting how oral microbiome research has significantly contributed to our understanding of microbial communities, with broad implications in polymicrobial diseases and across microbial community ecology. Further, we explore innovations and challenges associated with analyzing polymicrobial systems and suggest future directions of study. Finally, we provide a conceptual framework to systematically study microbial interactions within complex communities, not limited to the oral microbiota.},
}
@article {pmid35486140,
year = {2023},
author = {Rajarajan, A and Wolinska, J and Walser, JC and Dennis, SR and Spaak, P},
title = {Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1578-1589},
pmid = {35486140},
issn = {1432-184X},
support = {310030 L 166628//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; WO 1587/6-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Daphnia/genetics/microbiology ; *Bacteria/genetics ; Genotype ; Lakes ; },
abstract = {Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.},
}
@article {pmid35486139,
year = {2022},
author = {Bacha, L and de Rezende, CE and Cosenza, C and Ottoni, A and Thompson, C and Thompson, F},
title = {Letter to Microbial Ecology.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {11-13},
pmid = {35486139},
issn = {1432-184X},
mesh = {*Ecology ; },
}
@article {pmid35484416,
year = {2023},
author = {Câmara, PEAS and Bones, FLV and Lopes, FAC and Oliveira, FS and Barreto, CC and Knop Henriques, D and Campos, LP and Carvalho-Silva, M and Convey, P and Rosa, LH},
title = {DNA Metabarcoding Reveals Cryptic Diversity in Forest Soils on the Isolated Brazilian Trindade Island, South Atlantic.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1056-1071},
pmid = {35484416},
issn = {1432-184X},
mesh = {Animals ; Humans ; Child, Preschool ; *DNA Barcoding, Taxonomic ; *Soil ; Brazil ; Eukaryota ; Forests ; Biodiversity ; Bacteria ; Archaea ; Fungi ; Plants ; },
abstract = {Located 1140 km from the South American coastline in the South Atlantic Ocean and with an age of 4 million years, Trindade Island is the most recent volcanic component of Brazilian territory. Its original native vegetation has been severely damaged by human influence, in particular through the introduction of exotic grazing animals such as goats. However, since the complete eradication of goats and other feral animals in the late 1990s, the island's vegetation has been recovering, and even some endemic species that had been considered extinct have been rediscovered. In this study, we set out to characterize the contemporary cryptic diversity in soils of the recovering native forest of Trindade Island using metabarcoding by high throughput sequencing (HTS). The sequence diversity obtained was dominated by microorganisms, including three domains (Bacteria, Archaea, and Eukarya) and five kingdoms (Fungi, Metazoa, Protozoa, Chromista, and Viridiplantae). Bacteria were represented by 20 phyla and 116 taxa, with Archaea by only one taxon. Fungi were represented by seven phyla and 250 taxa, Viridiplantae by five phyla and six taxa, Protozoa by five phyla and six taxa, Metazoa by three phyla and four taxa and Chromista by two phyla and two taxa. Even after the considerable anthropogenic impacts and devastation of the island's natural forest, our sequence data reveal the presence of a rich and complex diversity of microorganisms, invertebrates, and plants and provide important baseline biodiversity information that will contribute to ecological restoration efforts on the island.},
}
@article {pmid35482603,
year = {2022},
author = {Carrizo, D and Vignale, FA and Sánchez-García, L and Farías, ME},
title = {Ecological variability based on lipid biomarkers in astrobiologically interesting wetlands from the Argentinian central Andes.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {5},
pages = {},
doi = {10.1093/femsec/fiac049},
pmid = {35482603},
issn = {1574-6941},
support = {MDM-2017-0737//INTA/ ; MDM-2017-0737//CSIC/ ; 2015/3825//Fund for Scientific and Technological Research/ ; },
mesh = {Archaea/genetics/metabolism ; Biomarkers/metabolism ; Carbon/metabolism ; *Cyanobacteria/metabolism ; Geologic Sediments/microbiology ; Lipids ; Sulfates/metabolism ; *Wetlands ; },
abstract = {Andean wetlands hold extremophilic communities adapted to live in harsh conditions. Here, we investigated the microbial ecology of three high-altitude hypersaline ponds from La Puna region (Argentina) showing an increasing extent of desiccation by analyzing their lipid sedimentary record. We recreated the microbial community structure and the carbon metabolisms in each lacustrine system based on the molecular distribution of lipid biomarkers and their compound-specific carbon and hydrogen isotopic signatures. We detected lipid compounds considered to be biomarkers of cyanobacteria, sulfate-reducing bacteria, purple sulfur bacteria, and archaea in the three Andean ponds, as well as diatoms in the intermediate salinity system. The relative abundance of purple sulfur and sulfate-reducing bacteria decreased with salinity, whereas cyanobacteria and archaea decreased their relative abundance in the mid-saline pond to increase it again and became both prevailing at the highest salinity. Carbon fixation in the three ponds was driven by a combination of the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle, and the reductive acetyl-CoA pathway. This work is the first to describe molecular and isotopic lipid fingerprints in wetlands from the central Andean Puna, and serves as a basis for further biogeochemical studies in the area.},
}
@article {pmid35482107,
year = {2023},
author = {Alemany, I and Pérez-Cembranos, A and Pérez-Mellado, V and Castro, JA and Picornell, A and Ramon, C and Jurado-Rivera, JA},
title = {Faecal Microbiota Divergence in Allopatric Populations of Podarcis lilfordi and P. pityusensis, Two Lizard Species Endemic to the Balearic Islands.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1564-1577},
pmid = {35482107},
issn = {1432-184X},
support = {CGL2015-68139-C2-1-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; FPI-CAIB 2017//Conselleria d'Educaci&#xf3;, Investigaci&#xf3;, Cultura i Esport/ ; },
mesh = {Animals ; *Lizards/microbiology ; Spain ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Feces ; },
abstract = {Gut microbial communities provide essential functions to their hosts and are known to influence both their ecology and evolution. However, our knowledge of these complex associations is still very limited in reptiles. Here we report the 16S rRNA gene faecal microbiota profiles of two lizard species endemic to the Balearic archipelago (Podarcis lilfordi and P. pityusensis), encompassing their allopatric range of distribution through a noninvasive sampling, as an alternative to previous studies that implied killing specimens of these IUCN endangered and near-threatened species, respectively. Both lizard species showed a faecal microbiome composition consistent with their omnivorous trophic ecology, with a high representation of cellulolytic bacteria taxa. We also identified species-specific core microbiota signatures and retrieved lizard species, islet ascription, and seasonality as the main factors in explaining bacterial community composition. The different Balearic Podarcis populations are characterised by harbouring a high proportion of unique bacterial taxa, thus reinforcing their view as unique and divergent evolutionary entities.},
}
@article {pmid35479639,
year = {2022},
author = {Xing, L and Zhi, Q and Hu, X and Liu, L and Xu, H and Zhou, T and Yin, H and Yi, Z and Li, J},
title = {Influence of Association Network Properties and Ecological Assembly of the Foliar Fugal Community on Crop Quality.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {783923},
pmid = {35479639},
issn = {1664-302X},
abstract = {Revealing community assembly and their impacts on ecosystem service is a core issue in microbial ecology. However, what ecological factors play dominant roles in phyllosphere fungal community assembly and how they link to crop quality are largely unknown. Here, we applied internal transcriptional spacer high-throughput sequencing to investigate foliar fungal community assembly across three cultivars of a Solanaceae crop (tobacco) and two planting regions with different climatic conditions. Network analyses were used to reveal the pattern in foliar fungal co-occurrence, and phylogenetic null model analysis was used to elucidate the ecological assembly of foliar fungal communities. We found that the sensory quality of crop leaves and the composition of foliar fungal community varied significantly across planting regions and cultivars. In Guangcun (GC), a region with relatively high humidity and low precipitation, there was a higher diversity and more unique fungal species than the region of Wuzhishan (WZS). Further, we found that the association network of foliar fungal communities in GC was more complex than that in WZS, and the network properties were closely related to the sensory quality of crop. Finally, the results of the phylogenetic analyses show that the stochastic processes played important roles in the foliar fungal community assembly, and their relative importance was significantly correlated with the sensory quality of crop leaves, which implies that ecological assembly processes could affect crop quality. Taken together, our results highlight that climatic conditions, and plant cultivars play key roles in the assembly of foliar fungal communities and crop quality, which enhances our understanding of the connections between the phyllosphere microbiome and ecosystem services, especially in agricultural production.},
}
@article {pmid35478286,
year = {2022},
author = {Clough, SE and Jousset, A and Elphinstone, JG and Friman, VP},
title = {Combining in vitro and in vivo screening to identify efficient Pseudomonas biocontrol strains against the phytopathogenic bacterium Ralstonia solanacearum.},
journal = {MicrobiologyOpen},
volume = {11},
number = {2},
pages = {e1283},
pmid = {35478286},
issn = {2045-8827},
mesh = {Anti-Bacterial Agents/pharmacology ; Antibiosis ; *Solanum lycopersicum/microbiology ; Plant Diseases/microbiology/prevention &amp; control ; Pseudomonas/genetics ; *Ralstonia solanacearum ; },
abstract = {Although plant pathogens are traditionally controlled using synthetic agrochemicals, the availability of commercial bactericides is still limited. One potential control strategy could be the use of plant growth-promoting bacteria (PGPB) to suppress pathogens via resource competition or the production of antimicrobial compounds. This study aimed to conduct in vitro and in vivo screening of eight Pseudomonas strains against Ralstonia solanacearum (the causative agent of bacterial wilt) and to investigate underlying mechanisms of potential pathogen suppression. We found that inhibitory effects were Pseudomonas strain-specific, with strain CHA0 showing the highest pathogen suppression. Genomic screening identified 2,4-diacetylphloroglucinol, pyoluteorin, and orfamides A and B secondary metabolite clusters in the genomes of the most inhibitory strains, which were investigated further. Although all these compounds suppressed R. solanacearum growth, only orfamide A was produced in the growth media based on mass spectrometry. Moreover, orfamide variants extracted from Pseudomonas cultures showed high pathogen suppression. Using the "Micro-Tom" tomato cultivar, it was found that CHA0 could reduce bacterial wilt disease incidence with one of the two tested pathogen strains. Together, these findings suggest that a better understanding of Pseudomonas-Ralstonia interactions in the rhizosphere is required to successfully translate in vitro findings into agricultural applications.},
}
@article {pmid35476456,
year = {2022},
author = {Alvarado, V and Hsu, SC and Wu, Z and Zhuang, H and Lee, PH and Guest, JS},
title = {Roadmap from Microbial Communities to Individuality Modeling for Anaerobic Digestion of Sewage Sludge.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {10},
pages = {6596-6607},
doi = {10.1021/acs.est.1c05258},
pmid = {35476456},
issn = {1520-5851},
mesh = {Acetates ; Anaerobiosis ; Bioreactors/microbiology ; Hydrogen ; Methane ; *Microbiota ; *Sewage/chemistry ; },
abstract = {Biological models describing anaerobic digestion (AD) of sewage sludge have been widely applied to test various control and operation strategies. Anaerobic digestion model 1 (ADM1) provides a generic platform that includes the main processes of AD, excluding homoacetogenesis and the microbial structure. Homoacetogenic bacteria have been identified as important competitors for hydrogen consumption and acetate production. Although recent advances in meta-omics techniques have improved our characterization of AD microbial communities, conventional models treat functional groups as homogeneous and overlook the physiology and behavior of microbial individuality, limiting insights into mechanisms governing process performance. A novel microbial individuality model (MIM) that integrates kinetics, energetics, and agent-based modeling to describe a microbiome's behavior as heterogenic populations, including homoacetogenesis, was developed. The MIM was validated with two datasets from previous studies through daily biogas production, methane content, compound concentrations, and microbial relative abundance changes. The MIM identified the emergence of Methanosaeta at low concentrations of acetate. Moreover, this simulation supports experimental studies confirming that the overlooked homoacetogenesis is an important hydrogen sink in AD. Validated MIMs are expected to provide insights into syntrophic and competitive interactions among microbiomes in AD systems while testing different operational parameters in a virtual environment. The MIM offers a methodological framework to other biological treatment systems and their microbial community dynamics.},
}
@article {pmid35476217,
year = {2022},
author = {Xu, Z and Li, Z and Ren, F and Gao, R and Wang, Z and Zhang, J and Zhao, T and Ma, X and Pu, X and Xin, T and Rombauts, S and Sun, W and Van de Peer, Y and Chen, S and Song, J},
title = {The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales.},
journal = {The Plant journal : for cell and molecular biology},
volume = {111},
number = {1},
pages = {217-230},
pmid = {35476217},
issn = {1365-313X},
support = {833522/ERC_/European Research Council/International ; },
mesh = {*Alkaloids/genetics/metabolism ; *Benzylisoquinolines/metabolism ; *Corydalis/genetics/metabolism ; Evolution, Molecular ; *Papaveraceae/genetics/metabolism ; Phylogeny ; Ranunculales ; },
abstract = {Species belonging to the order Ranunculales have attracted much attention because of their phylogenetic position as a sister group to all other eudicot lineages and their ability to produce unique yet diverse benzylisoquinoline alkaloids (BIAs). The Papaveraceae family in Ranunculales is often used as a model system for studying BIA biosynthesis. Here, we report the chromosome-level genome assembly of Corydalis tomentella, a species of Fumarioideae, one of the two subfamilies of Papaveraceae. Based on comparisons of sequenced Ranunculalean species, we present clear evidence of a shared whole-genome duplication (WGD) event that has occurred before the divergence of Ranunculales but after its divergence from other eudicot lineages. The C. tomentella genome enabled us to integrate isotopic labeling and comparative genomics to reconstruct the BIA biosynthetic pathway for both sanguinarine biosynthesis shared by papaveraceous species and the cavidine biosynthesis that is specific to Corydalis. Also, our comparative analysis revealed that gene duplications, especially tandem gene duplications, underlie the diversification of BIA biosynthetic pathways in Ranunculales. In particular, tandemly duplicated berberine bridge enzyme-like genes appear to be involved in cavidine biosynthesis. In conclusion, our study of the C. tomentella genome provides important insights into the occurrence of WGDs during the early evolution of eudicots, as well as into the evolution of BIA biosynthesis in Ranunculales.},
}
@article {pmid35474408,
year = {2022},
author = {Znidersic, E and Watson, DM},
title = {Acoustic restoration: Using soundscapes to benchmark and fast-track recovery of ecological communities.},
journal = {Ecology letters},
volume = {25},
number = {7},
pages = {1597-1603},
pmid = {35474408},
issn = {1461-0248},
support = {//Charles Sturt University/ ; },
mesh = {*Acoustics ; Animals ; *Benchmarking ; Biota ; Ecosystem ; },
abstract = {We introduce a new approach-acoustic restoration-focusing on the applied utility of soundscapes for restoration, recognising the rich ecological and social values they encapsulate. Broadcasting soundscapes in disturbed areas can accelerate recolonisation of animals and the microbes and propagules they carry; long duration recordings are also ideal sources of data for benchmarking restoration initiatives and evocative engagement tools.},
}
@article {pmid35473973,
year = {2022},
author = {S R, S and H P, S and Prakash, I and Khan, M and H N, PK and Om, H and Basavaraj, K and Murthy, PS},
title = {Microbial ecology and functional coffee fermentation dynamics with Pichia kudriavzevii.},
journal = {Food microbiology},
volume = {105},
number = {},
pages = {104012},
doi = {10.1016/j.fm.2022.104012},
pmid = {35473973},
issn = {1095-9998},
mesh = {*Coffee/chemistry ; Fermentation ; Flavoring Agents/metabolism ; *Pichia/metabolism ; Sugars ; },
abstract = {Specialty coffee can be developed by the application of explicit microorganisms or starters to obtain desired fermentation. In the present study, natural fermentation (NF) of Arabica coffee was carried out spontaneously, the other set was inoculated with Pichia kudriavzevii (Y) starter culture (isolated, identified and mass cultured). The effect of microbial fermentation, metagenomics, production of functional metabolites, volatiles and their sensorial aspects were studied. The bioprocess illustrated cohesive interface of coffee nutrients and microbial communities like Mycobacterium, Acinetobacter, Gordonia, etc., in NF, Lactobacillus and Leuconostoc were prevailing in Y. The Pichia and Rhodotorula dominated in both the groups. The bioactivity of bacteria and fungi induced complex changes in physicochemical features like pH (4.2-5.2), Brix° (9.5-3.0), and metabolic transition in sugar (3.0-0.7%), alcohol (1.4-2.7%), organic acids modulating flavour precursors and organoleptics in the final brew. In the roasted bean, Y exhibited higher sugar (42%), protein (25%), polyphenol (3.5%), CGA (2.5%), caffeine (17.2%), and trigonelline (2.8%) than NF. The volatile profile exhibited increased flavour molecules like furans, ketones, and pyrazines in Y, besides lactone complexes. The organoleptics in Y were highlighted with honey, malt and berry notes. P. kudriavzevii coffee fermentation could be beneficial in specialty coffee production and enhancement of distinct characteristic flavours.},
}
@article {pmid35473303,
year = {2022},
author = {Seki, D and Schauberger, C and Hausmann, B and Berger, A and Wisgrill, L and Berry, D},
title = {Individuality of the Extremely Premature Infant Gut Microbiota Is Driven by Ecological Drift.},
journal = {mSystems},
volume = {7},
number = {3},
pages = {e0016322},
pmid = {35473303},
issn = {2379-5077},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Infant, Newborn ; Infant ; Female ; Humans ; *Gastrointestinal Microbiome/genetics ; Infant, Extremely Premature ; RNA, Ribosomal, 16S/genetics ; Individuality ; Feces ; },
abstract = {The initial contact between humans and their colonizing gut microbiota after birth is thought to have expansive and long-lasting consequences for physiology and health. Premature infants are at high risk of suffering from lifelong impairments, due in part to aberrant development of gut microbiota that can contribute to early-life infections and inflammation. Despite their importance to health, the ecological assembly and succession processes governing gut microbiome composition in premature infants remained incompletely understood. Here, we quantified these ecological processes in a spatiotemporally resolved 16S rRNA gene amplicon sequencing data set of 60 extremely premature neonates using an established mathematical framework. We found that gut colonization during the first months of life is predominantly stochastic, whereby interindividual diversification of microbiota is driven by ecological drift. Dispersal limitations are initially small but have increasing influence at later stages of succession. Furthermore, we find similar trends in a cohort of 32 healthy term-born infants. These results suggest that the uniqueness of individual gut microbiota of extremely premature infants is largely due to stochastic assembly. IMPORTANCE Our knowledge concerning the initial gut microbiome assembly in human neonates is limited, and scientific progression in this interdisciplinary field is hindered due to the individuality in composition of gut microbiota. Our study addresses the ecological processes that result in the observed individuality of microbes in the gastrointestinal tract between extremely premature and term-born infants. We find that initial assembly is mainly driven by neutral ecological processes. Interestingly, while this progression is predominantly random, limitations to the dispersal of microbiota between infants become increasingly important with age and are concomitant features of gut microbiome stability. This indicates that while we cannot predict gut microbiota assembly due to its random nature, we can expect the establishment of certain ecological features that are highly relevant for neonatal health.},
}
@article {pmid35468931,
year = {2022},
author = {Jangid, A and Fukuda, S and Suzuki, Y and Taylor, TD and Ohno, H and Prakash, T},
title = {Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {6748},
pmid = {35468931},
issn = {2045-2322},
mesh = {Animals ; Cellulose/pharmacology ; Diet ; Dietary Fiber/pharmacology ; Edible Grain ; Lactobacillus/genetics ; *Metagenome ; Metagenomics ; Mice ; *Prebiotics ; },
abstract = {In the present study, we elucidated the effect of grain-based (GB) diet containing both soluble and insoluble fibers and purified ingredients-based (PIB) diet containing only insoluble fiber, namely cellulose on mice gut microbiome using whole shotgun based metagenomic sequencing. Although the fiber content in both diet types is the same (5%) the presence of soluble fiber only in the GB diet differentiates it from the PIB diet. The taxonomic analysis of sequenced reads reveals a significantly higher enrichment of probiotic Lactobacilli in the GB group as compared to the PIB group. Further, the enhancement of energy expensive cellular processes namely, cell cycle control, cell division, chromosome partitioning, and transcription is observed in the GB group which could be due to the metabolization of the soluble fiber for faster energy production. In contrast, a higher abundance of cellulolytic bacterial community namely, the members of family Lachnospiraceae and Ruminococcaceae and the metabolism functions are found in the PIB group. The PIB group shows a significant increase in host-derived oligosaccharide metabolism functions indicating that they might first target the host-derived oligosaccharides and self-stored glycogen in addition to utilising the available cellulose. In addition to the beneficial microbial community variations, both the groups also exhibited an increased abundance of opportunistic pathobionts which could be due to an overall low amount of fiber in the diet. Furthermore, backtracing analysis identified probiotic members of Lactobacillus, viz., L. crispatus ST1, L. fermentum CECT 5716, L. gasseri ATCC 33323, L. johnsonii NCC 533 and L. reuteri 100-23 in the GB group, while Bilophila wadsworthia 3_1_6, Desulfovibrio piger ATCC 29098, Clostridium symbiosum WAL-14163, and Ruminococcaceae bacterium D16 in the PIB group. These data suggest that Lactobacilli, a probiotic community of microorganisms, are the predominant functional contributors in the gut of GB diet-fed mice, whereas pathobionts too coexisted with commensals in the gut microbiome of the PIB group. Thus at 5% fiber, GB modifies the gut microbial ecology more effectively than PIB and the inclusion of soluble fiber in the GB diet may be one of the primary factors responsible for this impact.},
}
@article {pmid35464965,
year = {2022},
author = {Petrin, S and Mancin, M and Losasso, C and Deotto, S and Olsen, JE and Barco, L},
title = {Effect of pH and Salinity on the Ability of Salmonella Serotypes to Form Biofilm.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {821679},
pmid = {35464965},
issn = {1664-302X},
abstract = {Salmonella is a major cause of food-borne infections in Europe, and the majority of human infections are caused by only a few serotypes, among them are Salmonella enterica subsp. enterica serotype Enteritidis (hereafter Salmonella Enteritidis), Salmonella Typhimurium, and the monophasic variant of S. Typhimurium. The reason for this is not fully understood, but could include virulence factors as well as increased ability to transfer via the external environment. Formation of biofilm is considered an adaptation strategy used by bacteria to overcome environmental stresses. In order to assess the capability of different Salmonella serotypes to produce biofilm and establish whether this is affected by pH and salinity, 88 Salmonella isolates collected from animal, food, and human sources and belonging to 15 serotypes, including those most frequently responsible for human infections, were tested. Strains were grown in tryptic soy broth (TSB), TSB with 4% NaCl pH 4.5, TSB with 10% NaCl pH 4.5, TSB with 4% NaCl pH 7, or TSB with 10% NaCl pH 7, and biofilm production was assessed after 24 h at 37°C using crystal violet staining. A linear mixed effect model was applied to compare results from the different experimental conditions. Among the tested serotypes, S. Dublin showed the greatest ability to form biofilm even at pH 4.5, which inhibited biofilm production in the other tested serotypes. Salmonella Senftenberg and the monophasic variant of S. Typhimurium showed the highest biofilm production in TSB with 10% NaCl pH 7. In general, pH had a high influence on the ability to form biofilm, and most of the tested strains were not able to produce biofilm at pH 4.5. In contrast, salinity only had a limited influence on biofilm production. In general, serotypes causing the highest number of human infections showed a limited ability to produce biofilm in the tested conditions, indicating that biofilm formation is not a crucial factor in the success of these clones.},
}
@article {pmid35464964,
year = {2022},
author = {Haber, M and Roth Rosenberg, D and Lalzar, M and Burgsdorf, I and Saurav, K and Lionheart, R and Lehahn, Y and Aharonovich, D and Gómez-Consarnau, L and Sher, D and Krom, MD and Steindler, L},
title = {Spatiotemporal Variation of Microbial Communities in the Ultra-Oligotrophic Eastern Mediterranean Sea.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {867694},
pmid = {35464964},
issn = {1664-302X},
abstract = {Marine microbial communities vary seasonally and spatially, but these two factors are rarely addressed together. In this study, the temporal and spatial patterns of the bacterial and archaeal community were studied along a coast-to-offshore transect in the Eastern Mediterranean Sea (EMS) over six cruises, in three seasons of 2 consecutive years. Amplicon sequencing of 16S rRNA genes and transcripts was performed to determine presence and activity, respectively. The ultra-oligotrophic status of the Southeastern Mediterranean Sea was reflected in the microbial community composition dominated by oligotrophic bacterial groups such as SAR11, even at the most coastal station sampled, throughout the year. Seasons significantly affected the microbial communities, explaining more than half of the observed variability. However, the same few taxa dominated the community over the 2-year sampling period, varying only in their degree of dominance. While there was no overall effect of station location on the microbial community, the most coastal site (16 km offshore) differed significantly in community structure and activity from the three further offshore stations in early winter and summer. Our data on the microbial community compositions and their seasonality support previous notions that the EMS behaves like an oceanic gyre.},
}
@article {pmid35464924,
year = {2022},
author = {Wetherington, MT and Nagy, K and Dér, L and Noorlag, J and Galajda, P and Keymer, JE},
title = {Variance in Landscape Connectivity Shifts Microbial Population Scaling.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {831790},
pmid = {35464924},
issn = {1664-302X},
abstract = {Understanding mechanisms shaping distributions and interactions of soil microbes is essential for determining their impact on large scale ecosystem services, such as carbon sequestration, climate regulation, waste decomposition, and nutrient cycling. As the functional unit of soil ecosystems, we focus our attention on the spatial structure of soil macroaggregates. Emulating this complex physico-chemical environment as a patchy habitat landscape we investigate on-chip the effect of changing the connectivity features of this landscape as Escherichia coli forms a metapopulation. We analyze the distributions of E. coli occupancy using Taylor's law, an empirical law in ecology which asserts that the fluctuations in populations is a power law function of the mean. We provide experimental evidence that bacterial metapopulations in patchy habitat landscapes on microchips follow this law. Furthermore, we find that increased variance of patch-corridor connectivity leads to a qualitative transition in the fluctuation scaling. We discuss these results in the context of the spatial ecology of microbes in soil.},
}
@article {pmid35464923,
year = {2022},
author = {Riemann, L and Rahav, E and Passow, U and Grossart, HP and de Beer, D and Klawonn, I and Eichner, M and Benavides, M and Bar-Zeev, E},
title = {Planktonic Aggregates as Hotspots for Heterotrophic Diazotrophy: The Plot Thickens.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {875050},
pmid = {35464923},
issn = {1664-302X},
abstract = {Biological dinitrogen (N2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N2 fixation by NCDs and propose a conceptual framework for aggregate-associated N2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.},
}
@article {pmid35462258,
year = {2022},
author = {Garrido-Baserba, M and Barnosell, I and Molinos-Senante, M and Sedlak, DL and Rabaey, K and Schraa, O and Verdaguer, M and Rosso, D and Poch, M},
title = {The third route: A techno-economic evaluation of extreme water and wastewater decentralization.},
journal = {Water research},
volume = {218},
number = {},
pages = {118408},
doi = {10.1016/j.watres.2022.118408},
pmid = {35462258},
issn = {1879-2448},
mesh = {*Drinking Water ; Humans ; Politics ; Sewage ; *Wastewater ; Water Supply ; },
abstract = {Water systems need to become more locally robust and sustainable in view of increased population demands and supply uncertainties. Decentralized treatment is often assumed to have the potential to improve the technical, environmental, and economic performance of current technologies. The techno-economic feasibility of implementing independent building-scale decentralized systems combining rainwater harvesting, potable water production, and wastewater treatment and recycling was assessed for six main types of buildings ranging from single-family dwellings to high-rise buildings. Five different treatment layouts were evaluated under five different climatic conditions for each type of building. The layouts considered varying levels of source separation (i.e., black, grey, yellow, brown, and combined wastewater) using the corresponding toilet types (vacuum, urine-diverting, and conventional) and the appropriate pipes and pumping requirements. Our results indicate that the proposed layouts could satisfy 100% of the water demand for the three smallest buildings in all but the aridest climate conditions. For the three larger buildings, rainwater would offset annual water needs by approximately 74 to 100%. A comprehensive economic analysis considering CapEx and OpEx indicated that the cost of installing on-site water harvesting and recycling systems would increase the overall construction cost of multi-family buildings by around 6% and single-family dwellings by about 12%, with relatively low space requirements. For buildings or combined water systems with more than 300 people, the estimated total price of on-site water provision (including harvesting, treatment, recycling, and monitoring) ranged from $1.5/m[3] to $2.7/m,[3] which is considerably less than the typical tariffs collected by utilities in the United States and Western Europe. Where buildings can avoid the need to connect to centralized supplies for potable water and sewage disposal, water costs could be even lower. Urine-diversion has the potential to yield the least expensive solution but is the least well developed and had higher uncertainty in the cost analysis. More mature layouts (e.g., membrane bioreactors) exhibited less cost uncertainty and were economically competitive. Our analysis indicates that existing technologies can be used to create economically viable systems that greatly reduce demands on centralized utilities and, under some conditions, eliminate the need for centralized water supply or sewage collection.},
}
@article {pmid35460373,
year = {2023},
author = {Balbuena, S and Castelli, L and Zunino, P and Antúnez, K},
title = {Effect of Chronic Exposure to Sublethal Doses of Imidacloprid and Nosema ceranae on Immunity, Gut Microbiota, and Survival of Africanized Honey Bees.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1485-1497},
pmid = {35460373},
issn = {1432-184X},
support = {ANII-FCE_1_2017_1_135810//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; POS_NAC_2018_1_151557//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; For Women in Science//Fondation L'Or&#xe9;al/ ; },
mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; Neonicotinoids/toxicity ; *Pesticides/pharmacology ; *Nosema/physiology ; },
abstract = {Large-scale honey bee colony losses reported around the world have been associated with intoxication with pesticides, as with the presence of pests and pathogens. Among pesticides, neonicotinoid insecticides are the biggest threat. Due to their extensive use, they can be found in all agricultural environments, including soil, water, and air, are persistent in the environment, and are highly toxic for honey bees. In addition, infection by different pests and pathogens can act synergistically, weakening bees. In this study, we investigated the effects of chronic exposure to sublethal doses of imidacloprid alone or combined with the microsporidia Nosema ceranae on the immune response, deformed wing virus infection (DWV), gut microbiota, and survival of Africanized honey bees. We found that imidacloprid affected the expression of some genes associated with immunity generating an altered physiological state, although it did not favor DWV or N. ceranae infection. The pesticide alone did not affect honey bee gut microbiota, as previously suggested, but when administered to N. ceranae infected bees, it generated significant changes. Finally, both stress factors caused high mortality rates. Those results illustrate the negative impact of imidacloprid alone or combined with N. ceranae on Africanized honey bees and are useful to understand colony losses in Latin America.},
}
@article {pmid35460372,
year = {2023},
author = {Mascuch, SJ and Demko, A and Viulu, S and Ginigini, J and Soapi, K and Jensen, P and Kubanek, J},
title = {Antibiotic Activity Altered by Competitive Interactions Between Two Coral Reef-Associated Bacteria.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1226-1235},
pmid = {35460372},
issn = {1432-184X},
support = {U19 TW007401/TW/FIC NIH HHS/United States ; U19 TW007401/TW/FIC NIH HHS/United States ; },
mesh = {Animals ; Humans ; Coral Reefs ; Anti-Bacterial Agents/pharmacology ; *Anthozoa/microbiology ; *Streptomyces ; Diketopiperazines ; },
abstract = {Microbes produce natural products that mediate interactions with each other and with their environments, representing a potential source of antibiotics for human use. The biosynthesis of some antibiotics whose constitutive production otherwise remains low has been shown to be induced by competing microbes. Competition among macroorganism hosts may further influence the metabolic outputs of members of their microbiomes, especially near host surfaces where hosts and microbial symbionts come into close contact. At multiple field sites in Fiji, we collected matched samples of corals and algae that were freestanding or in physical contact with each other, cultivated bacteria from their surfaces, and explored growth-inhibitory activities of these bacteria against marine and human pathogens. In the course of the investigation, an interaction was discovered between two coral-associated actinomycetes in which an Agrococcus sp. interfered with the antibiotic output of a Streptomyces sp. Several diketopiperazines identified from the antibiotic-producing bacterium could not, on their own, account for the antibiotic activity indicating that other, as yet unidentified molecule(s) or molecular blends, possibly including diketopiperazines, are likely involved. This observation highlights the complex molecular dynamics at play among microbiome constituents. The mechanisms through which microbial interactions impact the biological activities of specialized metabolites deserve further attention considering the ecological and commercial importance of bacterial natural products.},
}
@article {pmid35460285,
year = {2022},
author = {Bartha, L and Mandáková, T and Kovařík, A and Bulzu, PA and Rodde, N and Mahelka, V and Lysak, MA and Fustier, MA and Šafář, J and Cápal, P and Keresztes, L and Banciu, HL},
title = {Intact ribosomal DNA arrays of Potentilla origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer.},
journal = {The New phytologist},
volume = {235},
number = {3},
pages = {1246-1259},
doi = {10.1111/nph.18171},
pmid = {35460285},
issn = {1469-8137},
mesh = {DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; In Situ Hybridization, Fluorescence ; *Liliaceae ; Phylogeny ; *Potentilla/genetics ; },
abstract = {During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support this hypothesis by carrying out genomic, molecular, and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host, albeit much less efficiently than the native counterpart. This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer.},
}
@article {pmid35458219,
year = {2022},
author = {Franck, M and de Toro-Martín, J and V Varin, T and Garneau, V and Pilon, G and Roy, D and Couture, P and Couillard, C and Marette, A and Vohl, MC},
title = {Gut Microbial Signatures of Distinct Trimethylamine N-Oxide Response to Raspberry Consumption.},
journal = {Nutrients},
volume = {14},
number = {8},
pages = {},
pmid = {35458219},
issn = {2072-6643},
support = {MRT-168045//CIHR/ ; not applicable//WA Red Raspberry Commission (WRRC)/ ; },
mesh = {Bacteria ; *Gastrointestinal Microbiome ; Humans ; Methylamines ; *Rubus/metabolism ; },
abstract = {The aim of this exploratory study was to evaluate the gut microbial signatures of distinct trimethylamine N-oxide (TMAO) responses following raspberry consumption. Investigations were carried out in 24 subjects at risk of developing metabolic syndrome who received 280 g/day of frozen raspberries for 8 weeks. Blood and stool samples were collected at weeks 0 and 8. Inter-individual variability in plasma TMAO levels was analyzed, 7 subjects were excluded due to noninformative signals and 17 subjects were kept for analysis and further stratified according to their TMAO response. Whole-metagenome shotgun sequencing analysis was used to determine the impact of raspberry consumption on gut microbial composition. Before the intervention, the relative abundance of Actinobacteriota was significantly higher in participants whose TMAO levels increased after the intervention (p = 0.03). The delta TMAO (absolute differences of baseline and week 8 levels) was positively associated with the abundance of gut bacteria such as Bilophila wadsworthia (p = 0.02; r[2] = 0.37), from the genus Granulicatella (p = 0.03; r[2] = 0.48) or the Erysipelotrichia class (p = 0.03; r[2] = 0.45). Changes in the gut microbial ecology induced by raspberry consumption over an 8-week period presumably impacted quaternary amines-utilizing activity and thus plasma TMAO levels.},
}
@article {pmid35456812,
year = {2022},
author = {Van den Abbeele, P and Ghyselinck, J and Marzorati, M and Koch, AM and Lambert, W and Michiels, J and Chalvon-Demersay, T},
title = {The Effect of Amino Acids on Production of SCFA and bCFA by Members of the Porcine Colonic Microbiota.},
journal = {Microorganisms},
volume = {10},
number = {4},
pages = {},
pmid = {35456812},
issn = {2076-2607},
abstract = {Functional amino acids supplementation to farm animals is considered to not only be beneficial by regulating intestinal barrier, oxidative stress, and immunity, but potentially also by impacting the gut microbiota. The impact of amino acids on a piglet-derived colonic microbiota was evaluated using a 48-h in vitro batch incubation strategy. The combination of 16S rRNA gene profiling with flow cytometry demonstrated that specific microbial taxa were involved in the fermentation of each of the amino acids resulting in the production of specific metabolites. Branched chain amino acids (leucine, isoleucine, valine) strongly increased branched-chain fatty acids (+23.0 mM) and valerate levels (+3.0 mM), coincided with a marked increase of Peptostreptococcaceae. Further, glutamine and glutamate specifically stimulated acetate (~20 mM) and butyrate (~10 mM) production, relating to a stimulation of a range of families containing known butyrate-producing species (Ruminococcaceae, Oscillospiraceae, and Christensenellaceae). Finally, while tryptophan was only fermented to a minor extent, arginine and lysine specifically increased propionate levels (~2 mM), likely produced by Muribaculaceae members. Overall, amino acids were thus shown to be selectively utilized by microbes originating from the porcine colonic microbiota, resulting in the production of health-related short-chain fatty acids, thus confirming the prebiotic potential of specific functional amino acids.},
}
@article {pmid35456724,
year = {2022},
author = {Guo, Z and Bao, Y and Liu, J},
title = {Environmental Difference and Spatial Distance Affect the Fidelity of Variation Source of Microbial Community Structure in Air-Dried Soils.},
journal = {Microorganisms},
volume = {10},
number = {4},
pages = {},
pmid = {35456724},
issn = {2076-2607},
abstract = {Air-dried soil archives are important for microbial ecology research, although the process of air-drying preservation inevitably destroys the original microbial information in soils. Only upon fully understanding the limitations of air-dried soil can it play a greater role. The value of air-dried soil depends on the fidelity of microbial community structure information in the air-dried soil relative to that in fresh soil. To evaluate this, high-throughput sequencing was applied to investigate the microbial community of fresh soils and 227 days air-dried archives from typical farmland under a large spatial scale, and PERMANOVA was used to analyze the explanation proportion (EP) of the spatial factor on the microbial community structure in any paired-fresh or air-dried soils. The results show that for any paired soils, the value of EP ranged from 42.4% to 97.9% (p < 0.001). Importantly, taking fresh soil as a reference, the value of EP declined in air-dried soils (effect size r = 0.79, p < 0.001). Furthermore, the standardized difference in EP between fresh and air-dried soil (NDEP) was used to characterize the fidelity of variance source of microbial community structure in air-dried soils, and correlation tests showed that NDEP was negatively correlated with spatial distance (r = −0.21, p < 0.01) and with environmental difference (r = −0.37, p < 0.001). Further analyses show that larger NDEP was observed at a spatial distance <25 km or an environmental difference <0.58. Variance partitioning analysis showed that 28.0% of the variation in NDEP could be explained, with environmental difference constituting 14.0% and the interaction between the environmental difference and spatial distance constituting the remaining 14.0%. Soil texture was the most important factor for predicting NDEP, followed by soil pH and annual average temperature. This study not only emphasizes the possible decline in EP when using air-dried soils to reveal microbial community patterns, but also implies that air-dried soil is more suitable for addressing scientific questions under a large spatial scale or environmental differences.},
}
@article {pmid35454671,
year = {2022},
author = {Li, Q and Li, L and Li, Q and Wang, J and Nie, S and Xie, M},
title = {Influence of Natural Polysaccharides on Intestinal Microbiota in Inflammatory Bowel Diseases: An Overview.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {8},
pages = {},
pmid = {35454671},
issn = {2304-8158},
support = {20212BCD42016//Key Laboratory of Bioactive Polysaccharides Program of Jiangxi Province/ ; 20212AAF01005//Key Technology Project in Jiangxi Province/ ; 20212BAB215036//Natural Science Foundation of Jiangxi Province/ ; },
abstract = {The incidence of inflammatory bowel disease (IBD) has increased in recent years. Considering the potential side effects of conventional drugs, safe and efficient treatment methods for IBD are required urgently. Natural polysaccharides (NPs) have attracted considerable attention as potential therapeutic agents for IBD owing to their high efficiency, low toxicity, and wide range of biological activities. Intestinal microbiota and their fermentative products, mainly short-chain fatty acids (SCFAs), are thought to mediate the effect of NPs in IBDs. This review explores the beneficial effects of NPs on IBD, with a special focus on the role of intestinal microbes. Intestinal microbiota exert alleviation effects via various mechanisms, such as increasing the intestinal immunity, anti-inflammatory activities, and intestinal barrier protection via microbiota-dependent and microbiota-independent strategies. The aim of this paper was to document evidence of NP-intestinal microbiota-associated IBD prevention, which would be helpful for guidance in the treatment and management of IBD.},
}
@article {pmid35453798,
year = {2022},
author = {Malfertheiner, L and Martínez-Pérez, C and Zhao, Z and Herndl, GJ and Baltar, F},
title = {Phylogeny and Metabolic Potential of the Candidate Phylum SAR324.},
journal = {Biology},
volume = {11},
number = {4},
pages = {},
pmid = {35453798},
issn = {2079-7737},
abstract = {The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former Deltaproteobacteria cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin-Benson-Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats.},
}
@article {pmid35453791,
year = {2022},
author = {Liu, Z and Wang, J and Meng, D and Li, L and Liu, X and Gu, Y and Yan, Q and Jiang, C and Yin, H},
title = {The Self-Organization of Marine Microbial Networks under Evolutionary and Ecological Processes: Observations and Modeling.},
journal = {Biology},
volume = {11},
number = {4},
pages = {},
pmid = {35453791},
issn = {2079-7737},
support = {41877345//National Nature Science Foundation of China/ ; 91851206//National Nature Science Foundation of China/ ; QYZDBSSW-DQC043//Key Research Program of Frontier Sciences of the Chinese Academy of Sciences/ ; },
abstract = {Evolutionary and ecological processes are primary drivers of ecological network constrictions. However, the ways that these processes underpin self-organization and modularity in networks are poorly understood. Here, we performed network analyses to explore the evolutionary and ecological effects on global marine microbial co-occurrence networks across multiple network levels, including those of nodes, motifs, modules and whole networks. We found that both direct and indirect species interactions were evolutionarily and ecologically constrained across at least four network levels. Compared to ecological processes, evolutionary processes generally showed stronger long-lasting effects on indirect interactions and dominated the network assembly of particle-associated communities in spatially homogeneous environments. Regarding the large network path distance, the contributions of either processes to species interactions generally decrease and almost disappear when network path distance is larger than six. Accordingly, we developed a novel mathematical model based on scale-free networks by considering the joint effects of evolutionary and ecological processes. We simulated the self-organization of microbial co-occurrence networks and found that long-lasting effects increased network stability via decreasing link gain or loss. Overall, these results revealed that evolutionary and ecological processes played key roles in the self-organization and modularization of microbial co-occurrence networks.},
}
@article {pmid35449401,
year = {2022},
author = {Li, MH and Liu, KW and Li, Z and Lu, HC and Ye, QL and Zhang, D and Wang, JY and Li, YF and Zhong, ZM and Liu, X and Yu, X and Liu, DK and Tu, XD and Liu, B and Hao, Y and Liao, XY and Jiang, YT and Sun, WH and Chen, J and Chen, YQ and Ai, Y and Zhai, JW and Wu, SS and Zhou, Z and Hsiao, YY and Wu, WL and Chen, YY and Lin, YF and Hsu, JL and Li, CY and Wang, ZW and Zhao, X and Zhong, WY and Ma, XK and Ma, L and Huang, J and Chen, GZ and Huang, MZ and Huang, L and Peng, DH and Luo, YB and Zou, SQ and Chen, SP and Lan, S and Tsai, WC and Van de Peer, Y and Liu, ZJ},
title = {Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy.},
journal = {Nature plants},
volume = {8},
number = {4},
pages = {373-388},
pmid = {35449401},
issn = {2055-0278},
mesh = {*Mycorrhizae/genetics ; *Orchidaceae/genetics/metabolism/microbiology ; Symbiosis ; Trehalase/metabolism ; Trehalose/metabolism ; },
abstract = {To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.},
}
@article {pmid35448576,
year = {2022},
author = {Rojas, EC and Jensen, B and Jørgensen, HJL and Latz, MAC and Esteban, P and Collinge, DB},
title = {The Fungal Endophyte Penicillium olsonii ML37 Reduces Fusarium Head Blight by Local Induced Resistance in Wheat Spikes.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {4},
pages = {},
pmid = {35448576},
issn = {2309-608X},
abstract = {The fungal endophyte Penicillium olsonii ML37 is a biocontrol agent of Fusarium head blight in wheat (caused by Fusarium graminearum), which has shown a limited direct inhibition of fungal growth in vitro. We used RNA-seq and LC-MS/MS analyses to elucidate metabolic interactions of the three-way system Penicillium-wheat-Fusarium in greenhouse experiments. We demonstrated that P. olsonii ML37 colonises wheat spikes and transiently activates plant defence mechanisms, as pretreated spikes show a faster and stronger expression of the defence metabolism during the first 24 h after pathogen inoculation. This effect was transient and the expression of the same genes was lower in the pathogen-infected spikes than in those infected by P. olsonii alone. This response to the endophyte includes the transcriptional activation of several WRKY transcription factors. This early activation is associated with a reduction in FHB symptoms and significantly lower levels of the F. graminearum metabolites 15-acetyl-DON and culmorin. An increase in the Penicillium-associated metabolite asperphanamate confirms colonisation by the endophyte. Our results suggest that the mode of action used by P. olsonii ML37 is via a local defence activation in wheat spikes, and that this fungus has potential as a novel biological alternative in wheat disease control.},
}
@article {pmid35447706,
year = {2022},
author = {Jeske, JT and Gallert, C},
title = {Microbiome Analysis via OTU and ASV-Based Pipelines-A Comparative Interpretation of Ecological Data in WWTP Systems.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {9},
number = {4},
pages = {},
pmid = {35447706},
issn = {2306-5354},
support = {02WCL1469A-J//German Federal Ministry of Education and Research/ ; },
abstract = {Linking community composition and ecosystem function via the cultivation-independent analysis of marker genes, e.g., the 16S rRNA gene, is a staple of microbial ecology and dependent disciplines. The certainty of results, independent of the bioinformatic handling, is imperative for any advances made within the field. In this work, thermophilic anaerobic co-digestion experimental data, together with primary and waste-activated sludge prokaryotic community data, were analyzed with two pipelines that apply different principles when dealing with technical, sequencing, and PCR biases. One pipeline (VSEARCH) employs clustering methods, generating individual operational taxonomic units (OTUs), while the other (DADA2) is based on sequencing error correction algorithms and generates exact amplicon sequence variants (ASVs). The outcomes of both pipelines were compared within the framework of ecological-driven data analysis. Both pipelines provided comparable results that would generally allow for the same interpretations. Yet, the two approaches also delivered community compositions that differed between 6.75% and 10.81% between pipelines. Inconsistencies were also observed linked to biologically driven variability in the samples, which affected the two pipelines differently. These pipeline-dependent differences in taxonomic assignment could lead to different conclusions and interfere with any downstream analysis made for such mis- or not-identified species, e.g., network analysis or predictions of their respective ecosystem service.},
}
@article {pmid35447252,
year = {2022},
author = {Kelly, MR and Whitworth, P and Jamieson, A and Burgess, JG},
title = {Bacterial colonisation of plastic in the Rockall Trough, North-East Atlantic: An improved understanding of the deep-sea plastisphere.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {305},
number = {},
pages = {119314},
doi = {10.1016/j.envpol.2022.119314},
pmid = {35447252},
issn = {1873-6424},
mesh = {Bacteria/genetics ; Environmental Pollution ; *Microbiota/genetics ; *Plastics ; RNA, Ribosomal, 16S ; },
abstract = {Plastic pollution has now been found within multiple ecosystems across the globe. Characterisation of microbial assemblages associated with marine plastic, or the so-called 'plastisphere', has focused predominantly on plastic in the epipelagic zone. Whether this community includes taxa that are consistently enriched on plastic compared to surrounding non plastic surfaces is unresolved, as are the ecological implications. The deep sea is likely a final sink for most of the plastic entering the ocean, yet there is limited information on microbial colonisation of plastic at depth. The aim of this study was to investigate deep-sea microbial communities associated with polystyrene (PS) and polyurethane (PU) with Bath stone used as a control. The substrates (n = 15) were deployed in the Rockall Trough (Atlantic), and recovered 420 days later from a depth of 1796 m. To characterise the bacterial communities, 16S rRNA genes were sequenced using the Illumina MiSeq platform. A dominant core microbiome (taxa shared across all substrates) comprised 8% of total ASVs (amplicon sequence variant) and accounted for 92% of the total community reads. This suggests that many commonly reported members of the plastisphere are simply opportunistic which freely colonise any hard surface. Transiently associated species consisted of approximately 7% of the total community. Thirty genera were enriched on plastic (P < 0.05), representing 1% of the total community. The discovery of novel deep-sea enriched taxa included Aurantivirga, Algivirga, IheB3-7, Spirosoma, HTCC5015, Ekhidna and Calorithrix on PS and Candidatus Obscuribacter, Haloferula, Marine Methylotrophic Group 3, Aliivibrio, Tibeticola and Dethiosulfatarculus on PU. This small fraction of the microbiome include taxa with unique metabolic abilities and show how bacterial communities can be shaped by plastic pollution at depth. This study outlines a novel approach in categorising the plastisphere to elucidate the ecological implications of enriched taxa that show an affinity for colonising plastic.},
}
@article {pmid35446625,
year = {2022},
author = {Li, S and Abdulkadir, N and Schattenberg, F and Nunes da Rocha, U and Grimm, V and Müller, S and Liu, Z},
title = {Stabilizing microbial communities by looped mass transfer.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {17},
pages = {e2117814119},
pmid = {35446625},
issn = {1091-6490},
mesh = {Biotechnology ; Ecology ; *Microbiota ; },
abstract = {Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates μ′. Subsets of cells that did not show net growth μ′SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.},
}
@article {pmid35443156,
year = {2022},
author = {Özçam, M and Oh, JH and Tocmo, R and Acharya, D and Zhang, S and Astmann, TJ and Heggen, M and Ruiz-Ramírez, S and Li, F and Cheng, CC and Vivas, E and Rey, FE and Claesen, J and Bugni, TS and Walter, J and van Pijkeren, JP},
title = {A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by cell-wall acetylation.},
journal = {Cell host &amp; microbe},
volume = {30},
number = {6},
pages = {824-835.e6},
doi = {10.1016/j.chom.2022.03.033},
pmid = {35443156},
issn = {1934-6069},
mesh = {Acetylation ; Animals ; Gastrointestinal Tract/metabolism ; Germ-Free Life ; Mammals/genetics ; Mice ; *Multigene Family ; *Polyketide Synthases/genetics/metabolism ; },
abstract = {The mammalian microbiome encodes numerous secondary metabolite biosynthetic gene clusters; yet, their role in microbe-microbe interactions is unclear. Here, we characterized two polyketide synthase gene clusters (fun and pks) in the gut symbiont Limosilactobacillus reuteri. The pks, but not the fun, cluster encodes antimicrobial activity. Forty-one of 51 L. reuteri strains tested are sensitive to Pks products; this finding was independent of strains' host origin. Sensitivity to Pks was also established in intraspecies competition experiments in gnotobiotic mice. Comparative genome analyses between Pks-resistant and -sensitive strains identified an acyltransferase gene (act) unique to Pks-resistant strains. Subsequent cell-wall analysis of wild-type and act mutant strains showed that Act acetylates cell-wall components, providing resistance to Pks-mediated killing. Additionally, pks mutants lost their competitive advantage, while act mutants lost their Pks resistance in in vivo competition assays. These findings provide insight into how closely related gut symbionts can compete and co-exist in the gastrointestinal tract.},
}
@article {pmid35442877,
year = {2022},
author = {Khanal, M and Timilsina, S and Bhatta, BP and Bophela, K and Coutinho, T and Cochran, K and Malla, S},
title = {Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {4},
pages = {},
doi = {10.1099/ijsem.0.005311},
pmid = {35442877},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Genes, Bacterial ; *Onions/microbiology ; Phylogeny ; Pseudomonas ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {A Gram-stain-negative, aerobic and non-spore-forming bacterial strain, designated 20TX0172[T], was isolated from a rotting onion bulb in Texas, USA. The results of phylogenetic analysis based on the 16S rRNA sequence indicated that the novel strain represented a member of the genus Pseudomonas and had the greatest sequence similarities with Pseudomonas kilonensis 520-20[T] (99.3 %), Pseudomonas corrugata CFBP 2431[T] (99.2 %), and Pseudomonas viciae 11K1[T] (99.2 %) but the 16S rRNA phylogenetic tree displayed a monophyletic clade with Pseudomonas mediterranea CFBP 5447[T]. In the phylogenetic trees based on sequences of four housekeeping genes (gap1, gltA, gyrB and rpoD), the novel strain formed a separate branch, indicating that the strain was distinct phylogenetically from known species of the genus Pseudomonas. The genome-sequence-derived average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel isolate and P. mediterranea DSM 16733[T] were 86.7 and 32.7 %, respectively. These values were below the accepted species cutoff threshold of 96 % ANI and 70 % dDDH, affirming that the strain represented a novel species. The genome size of the novel species was 5.98 Mbp with a DNA G+C content of 60.8 mol%. On the basis of phenotypic and genotypic characteristics, strain 20TX0172[T] represents a novel species of the genus Pseudomonas. The name Pseudomonas uvaldensis sp. nov. is proposed. The type strain is 20TX0172[T] (=NCIMB 15426[T]=CIP 112022[T]).},
}
@article {pmid35439561,
year = {2022},
author = {Fernando Herrera Adarme, O and Eduardo Lobo Baêta, B and Cardoso Torres, M and Camilo Otalora Tapiero, F and Vinicius Alves Gurgel, L and de Queiroz Silva, S and Francisco de Aquino, S},
title = {Biogas production by anaerobic co-digestion of sugarcane biorefinery byproducts: Comparative analyses of performance and microbial community in novel single-and two-stage systems.},
journal = {Bioresource technology},
volume = {354},
number = {},
pages = {127185},
doi = {10.1016/j.biortech.2022.127185},
pmid = {35439561},
issn = {1873-2976},
mesh = {Anaerobiosis ; Biofuels ; Bioreactors ; Cellulose ; Digestion ; Edible Grain ; Methane ; *Microbiota ; *Saccharum ; Sewage/chemistry ; },
abstract = {Anaerobic co-digestion (AcD) of sugarcane biorefinery byproducts (hemicelluloses hydrolysate (HH), vinasse, yeast extract and sugarcane bagasse fly ashes was evaluated using new anaerobic reactors fed with organic loading rates (OLR) from 0.9 to 10.8 gCODL[-1]d[-1]. The best results were obtained in a two-stage system when the OLR was 5.65 gCODL[-1]d[-1], leading to a total chemical oxygen demand (COD) removal of 87.6 % and methane yield of 243NmLCH4gCODr[-1]. Microbial community analyses of sludge from both systems (one and two-stages) revealed structural changes and relationship among the main genus found (Clostridium (62.8%), Bacteroides(11.3 %), Desulfovibrio (19.1 %), Lactobacillus(67.7 %), Lactococcus (22.5%), Longilinea (78%), Methanosaeta (19.2 %) and Syntrophus (18.9 %)) with processes performance, kinetic and hydrodynamic parameters. Moreover, biomass granulation was observed in the novel structured anaerobic reactor operated at single stage due to sugarcane bagasse fly ash addition.},
}
@article {pmid35438534,
year = {2022},
author = {Tiedje, JM and Bruns, MA and Casadevall, A and Criddle, CS and Eloe-Fadrosh, E and Karl, DM and Nguyen, NK and Zhou, J},
title = {Microbes and Climate Change: a Research Prospectus for the Future.},
journal = {mBio},
volume = {13},
number = {3},
pages = {e0080022},
pmid = {35438534},
issn = {2150-7511},
mesh = {Animals ; Carbon Dioxide ; *Climate Change ; Ecosystem ; *Greenhouse Gases ; Methane ; Nitrous Oxide ; },
abstract = {Climate change is the most serious challenge facing humanity. Microbes produce and consume three major greenhouse gases-carbon dioxide, methane, and nitrous oxide-and some microbes cause human, animal, and plant diseases that can be exacerbated by climate change. Hence, microbial research is needed to help ameliorate the warming trajectory and cascading effects resulting from heat, drought, and severe storms. We present a brief summary of what is known about microbial responses to climate change in three major ecosystems: terrestrial, ocean, and urban. We also offer suggestions for new research directions to reduce microbial greenhouse gases and mitigate the pathogenic impacts of microbes. These include performing more controlled studies on the climate impact on microbial processes, system interdependencies, and responses to human interventions, using microbes and their carbon and nitrogen transformations for useful stable products, improving microbial process data for climate models, and taking the One Health approach to study microbes and climate change.},
}
@article {pmid35437690,
year = {2023},
author = {Li, H and Li, Z and Tang, Q and Li, R and Lu, L},
title = {Local-Scale Damming Impact on the Planktonic Bacterial and Eukaryotic Assemblages in the upper Yangtze River.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1323-1337},
pmid = {35437690},
issn = {1432-184X},
support = {51861125204//National Natural Science Foundation of China/ ; 52039006//National Natural Science Foundation of China/ ; cstc2020jscx-msxmX0121//Chongqing Science and Technology Commission/ ; cstc2020jcyj-jqX0010//Chongqing Science and Technology Commission/ ; },
mesh = {*Ecosystem ; *Eukaryota ; Plankton ; Rivers/microbiology ; Bacteria/genetics ; },
abstract = {Dam construction and impoundment cause discontinuities in the natural biophysical gradients in rivers. These discontinuities may alter distinctive habitats and different microbial community assembly mechanisms upstream and downstream of dams, which reflect the potential impacts of damming on riverine aquatic ecosystems. In this study, we investigated the planktonic microbial assemblages of three large dams in the upper Yangtze River by using high-throughput sequencing. The results revealed that the alpha diversity indexes increased downstream of the dams. In addition, more eukaryotic ASVs solely occurred downstream of the dams, which indicated that a large proportion of eukaryotes appeared downstream of the dams. The nonmetric multidimensional scaling analysis indicated that there was no obvious geographic clustering of the planktonic microbial assemblages among the different locations or among the different dams. However, the dam barriers changed dam-related variables (maximum dam height and water level) and local environmental variables (water temperature, DOC, etc.) that could possibly affect the assembly of the planktonic microbial communities that are closest to the dams. A co-occurrence network analysis demonstrated that the keystone taxa of the planktonic bacteria and eukaryotes decreased downstream of the dams. In particular, the keystone taxa of the eukaryotes disappeared downstream of the dams. The robustness analysis indicated that the natural connectivity of the microbial networks decreased more rapidly upstream of the dams, and the downstream eukaryotic network was more stable. In conclusion, damming has a greater impact on planktonic eukaryotes than on bacteria in near-dam areas, and planktonic microbial assemblages were more susceptible to the environmental changes. Our study provides a better understanding of the ecological effects of river damming.},
}
@article {pmid35433514,
year = {2022},
author = {Franklin, S and Aitken, SL and Shi, Y and Sahasrabhojane, PV and Robinson, S and Peterson, CB and Daver, N and Ajami, NA and Kontoyiannis, DP and Shelburne, SA and Galloway-Peña, J},
title = {Oral and Stool Microbiome Coalescence and Its Association With Antibiotic Exposure in Acute Leukemia Patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {848580},
pmid = {35433514},
issn = {2235-2988},
support = {K01 AI143881/AI/NIAID NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA096520/CA/NCI NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Leukemia, Myeloid, Acute/complications/drug therapy ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Failure to maintain segregation of oral and gut microbial communities has been linked to several diseases. We sought to characterize oral-fecal microbiome community coalescence, ectopic extension of oral bacteria, clinical variables contributing to this phenomenon, and associated infectious consequences by analyzing the 16S rRNA V4 sequences of longitudinal fecal (n=551) and oral (n=737) samples from 97 patients with acute myeloid leukemia (AML) receiving induction chemotherapy (IC). Clustering observed in permutation based multivariate analysis of variance (PERMANOVA) of Bray-Curtis dissimilarity and PCoA plot of UniFrac distances between intra-patient longitudinal oral-stool sample pairs suggested potential oral-stool microbial community coalescence. Bray-Curtis dissimilarities and UniFrac distances were used to create an objective definition of microbial community coalescence. We determined that only 23 of the 92 patients exhibited oral-stool community coalescence. This was validated through a linear mixed model which determined that patients who experienced coalescence had an increased proportion of shared to unique OTUs between their oral-stool sample pairs over time compared to non-coalesced patients. Evaluation of longitudinal microbial characteristics revealed that patients who experienced coalescence had increased stool abundance of Streptococcus and Stenotrophomonas compared to non-coalesced patients. When treated as a time-varying covariate, each additional day of linezolid (HR 1.15, 95% CI 1.06 - 1.24, P <0.001), meropenem (HR 1.13, 95% CI 1.05 - 1.21, P = 0.001), metronidazole (HR 1.13, 95% CI 1.05 - 1.21, P = 0.001), and cefepime (HR 1.10, 95% CI 1.01 - 1.18, P = 0.021) increased the hazard of oral-stool microbial community coalescence. Levofloxacin receipt was associated with a lower risk of microbiome community coalescence (HR 0.75, 95% CI 0.61 - 0.93, P = 0.009). By the time of neutrophil recovery, the relative abundance of Bacteroidia (P<0.001), Fusobacteria (P=0.012), and Clostridia (P=0.013) in the stool were significantly lower in patients with oral-gut community coalescence. Exhibiting oral-stool community coalescence was associated with the occurrence of infections prior to neutrophil recovery (P=0.002), as well as infections during the 90 days post neutrophil recovery (P=0.027). This work elucidates specific antimicrobial effects on microbial ecology and furthers the understanding of oral/intestinal microbial biogeography and its implications for adverse clinical outcomes.},
}
@article {pmid35432228,
year = {2022},
author = {Cerbin, S and Pérez, G and Rybak, M and Wejnerowski, &#x141; and Konowalczyk, A and Helmsing, N and Naus-Wiezer, S and Meima-Franke, M and Pytlak, &#x141; and Raaijmakers, C and Nowak, W and Bodelier, PLE},
title = {Methane-Derived Carbon as a Driver for Cyanobacterial Growth.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {837198},
pmid = {35432228},
issn = {1664-302X},
abstract = {Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH4 oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO2) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ[13]C values in cyanobacterial blooms (the lowest detected value -59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO2 released by MOB. On the other hand, [13]C-CH4 labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.},
}
@article {pmid35428940,
year = {2022},
author = {Ganorkar, R and Jadeja, NB and Shanware, A and Ingle, AB},
title = {Characterisation of novel microbial strains Proteus mirabilis and Bordetella avium for heavy metal bioremediation and dye degradation.},
journal = {Archives of microbiology},
volume = {204},
number = {5},
pages = {262},
pmid = {35428940},
issn = {1432-072X},
mesh = {Azo Compounds ; Biodegradation, Environmental ; *Bordetella avium ; *Metals, Heavy/analysis ; Phylogeny ; Proteus mirabilis/genetics ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; Tungsten ; },
abstract = {The entitled study focuses on exploring the microbial diversity and its applicability in the remediation of metal contaminated soil using microbes, which is a reliable and cost effective technique. Tungsten enriched soil of Kuhi-Agargaon-Khobna region (Nagpur, India) were analysed by XRF method to detect heavy metals. The traditional microbiological techniques were used to isolate tungsten tolerant microbes. Applicability of these microbes in bioremediation and Azo dye degradation was mainly studied. The two novel bacterial strains, Proteus mirabilis (RS2K) and Bordetella avium (RS3K), were isolated and identified to show the tolerance to tungsten, using 16S rDNA and phylogenetic analysis. These novel strains have also shown the tolerance to other metallic salts viz., (sodium) tungsten, tungstic acid, ammonium metaparatungstate, mercuric chloride, cobalt chloride and azo dye. These microbes were found to accumulate tungsten intracellularly as confirmed through ICP-MS and SEM-EDS analyses. Microbes exhibited well-equipped cellular mechanisms for metal tolerance to survive in heavy metal-laden ecology. Current study contains substantial potential in bioleaching of heavy metals and green mining along with Nano bioremediation for heavy metal pollution.},
}
@article {pmid35427643,
year = {2022},
author = {Steinbauer, P and Monje, FJ and Kothgassner, O and Goreis, A and Eva, C and Wildner, B and Schned, H and Deindl, P and Seki, D and Berger, A and Olischar, M and Giordano, V},
title = {The consequences of neonatal pain, stress and opiate administration in animal models: An extensive meta-analysis concerning neuronal cell death, motor and behavioral outcomes.},
journal = {Neuroscience and biobehavioral reviews},
volume = {137},
number = {},
pages = {104661},
doi = {10.1016/j.neubiorev.2022.104661},
pmid = {35427643},
issn = {1873-7528},
mesh = {*Analgesics, Opioid/administration &amp; dosage ; Animals ; Animals, Newborn ; Anxiety ; *Cell Death ; Depression ; Movement ; *Neurons/cytology ; *Pain ; },
abstract = {This systematic review and meta-analysis aimed to investigate the association of neonatal exposure to pain, stress, opiate administration alone, as well as opiate administration prior to a painful procedure on neuronal cell death, motor, and behavioral outcomes in rodents. In total, 36 studies investigating the effect of pain (n = 18), stress (n = 15), opiate administration (n = 13), as well as opiate administration prior to a painful event (n = 7) in rodents were included in our meta-analysis. The results showed a large effect of pain (g = 1.37, 95% CI 1.00-1.74, p < .001) on neuronal cell death. Moreover, higher number of neonatal pain events were significantly associated with increased neuronal cell death, increased anxiety (b = -1.18, SE = 0.43, p = .006), and depressant-like behavior (b = 1.74, SE = 0.51, p = .027) in rodents. Both opiates and pain had no impact on motor function (g = 0.26, 95% CI 0.18-0.70, p = .248).},
}
@article {pmid35426077,
year = {2023},
author = {Oliveira, NC and Rodrigues, PAP and Cônsoli, FL},
title = {Host-Adapted Strains of Spodoptera frugiperda Hold and Share a Core Microbial Community Across the Western Hemisphere.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1552-1563},
pmid = {35426077},
issn = {1432-184X},
support = {2011/50877-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/24377-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 462140-2014/8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 403851/2013-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; Spodoptera ; *Zea mays ; Larva ; *Gastrointestinal Microbiome ; Colombia ; },
abstract = {The fall armyworm Spodoptera frugiperda is an important polyphagous agricultural pest in the Western Hemisphere and currently invasive to countries of the Eastern Hemisphere. This species has two host-adapted strains named "rice" and "corn" strains. Our goal was to identify the occurrence of core members in the gut bacterial community of fall armyworm larvae from distinct geographical distribution and/or host strain. We used next-generation sequencing to identify the microbial communities of S. frugiperda from corn fields in Brazil, Colombia, Mexico, Panama, Paraguay, and Peru, and rice fields from Panama. The larval gut microbiota of S. frugiperda larvae did not differ between the host strains nor was it affected by the geographical distribution of the populations investigated. Our findings provide additional support for Enterococcus and Pseudomonas as core members of the bacterial community associated with the larval gut of S. frugiperda, regardless of the site of collection or strain. Further investigations are required for a deeper understanding of the nature of this relationship.},
}
@article {pmid35420423,
year = {2022},
author = {Li, Q and Van Herreweghen, F and Onyango, SO and De Mey, M and Van de Wiele, T},
title = {In Vitro Microbial Metabolism of (+)-Catechin Reveals Fast and Slow Converters with Individual-Specific Microbial and Metabolite Markers.},
journal = {Journal of agricultural and food chemistry},
volume = {70},
number = {34},
pages = {10405-10416},
doi = {10.1021/acs.jafc.2c00551},
pmid = {35420423},
issn = {1520-5118},
mesh = {*Catechin/metabolism ; Fatty Acids, Volatile ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; },
abstract = {The bioavailability of catechin highly relies on gut microbiota which may determine its metabolic profile, resulting in different health outcomes. Here, we investigated in vitro (+)-catechin metabolism by human microbial communities. There were substantial interindividual differences in the metabolic profiles of (+)-catechin, with 5-(3',4'-dihydroxyphenyl)-γ-valerolactone being the major contributor. Furthermore, the microbial metabolic rate of catechin enabled stratification of 12 participants (fast, medium, and slow converters), despite the interference from the strong intrinsic interindividual variability in fecal microbiota. Correlations were established between this stratified population and microbiota features, such as ecosystem diversity. Additionally, fast converters had significantly higher prevalences of amplicon sequence variants (ASVs) with potential capacity of C-ring cleavage (ASV233_Eggerthella and ASV402_Eubacterium), B-ring dihydroxylation (ASV402_Eubacterium), and short-chain fatty acid (SCFA)-producing ASVs. In conclusion, metabolic-capability-based stratification allows us to uncover differences in microbial composition between fast and slow converters, which could help to elucidate interindividual variabilities in the health benefits of catechins.},
}
@article {pmid35420314,
year = {2023},
author = {Fan, X and Chen, H and Yan, G and Ye, M and Yin, C and Li, T and Wakelin, SA and Liang, Y},
title = {Niche Differentiation Among Canonical Nitrifiers and N2O Reducers Is Linked to Varying Effects of Nitrification Inhibitors DCD and DMPP in Two Arable Soils.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1434-1447},
pmid = {35420314},
issn = {1432-184X},
support = {2017YFD0200707//National Key Research and Development Programs of China/ ; 42007083//National Natural Science Foundation of China/ ; 2020M671736//China Postdoctoral Science Foundation/ ; },
mesh = {*Soil/chemistry ; Nitrification ; Dimethylphenylpiperazinium Iodide/pharmacology ; Phosphates ; Ammonia ; Soil Microbiology ; Archaea ; Bacteria ; *Betaproteobacteria ; Oxidation-Reduction ; },
abstract = {The efficacy of nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) varies with soil types. Understanding the microbial mechanisms for this variation may lead to better modelling of NI efficacy and therefore on-farm adoption. This study addressed the response patterns of mineral nitrogen, nitrous oxide (N2O) emission, abundances of N-cycling functional guilds and soil microbiota characteristics, in relation to urea application with or without DCD or DMPP in two arable soils (an alkaline and an acid soil). The inhibition of nitrification rate and N2O emission by NI application occurred by suppressing ammonia-oxidizing bacteria (AOB) abundances and increasing the abundances of nosZI-N2O reducers; however, abundances of ammonia-oxidizing archaea (AOA) were also stimulated with NIs-added in these two arable soils. DMPP generally had stronger inhibition efficiency than DCD, and both NIs' addition decreased Nitrobacter, while increased Nitrospira abundance only in alkaline soil. N2O emissions were positively correlated with AOB and negatively correlated with nosZI in both soils and AOA only in acid soil. Moreover, N2O emissions were also positively correlated with nirK-type denitrifiers in alkaline soil, and clade A comammox in acid soil. Amendment with DCD or DMPP altered soil microbiota community structure, but had minor effect on community composition. These results highlight a crucial role of the niche differentiation among canonical ammonia oxidizers (AOA/AOB), Nitrobacter and Nitrospira, as well as nosZI- and nosZII-N2O reducers in determining the varying efficacies of DCD and DMPP in different arable soils.},
}
@article {pmid35419656,
year = {2023},
author = {Xu, F and Zhu, L and Wang, J and Xue, Y and Liu, K and Zhang, F and Zhang, T},
title = {Nonpoint Source Pollution (NPSP) Induces Structural and Functional Variation in the Fungal Community of Sediments in the Jialing River, China.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1308-1322},
pmid = {35419656},
issn = {1432-184X},
support = {19E061//Science Research Program of China West Normal University/ ; CJZDZYJ47//Environmental Protection Research Program of the Yangtze River/ ; 41907132//National Science Foundation of China/ ; },
mesh = {Humans ; Rivers/microbiology ; *Mycobiome ; *Non-Point Source Pollution ; Ecosystem ; Geologic Sediments/microbiology ; China ; *Basidiomycota/genetics ; *Ascomycota/genetics ; },
abstract = {Nonpoint source pollution (NPSP) from human production and life activities causes severe destruction in river basin environments. In this study, three types of sediment samples (A, NPSP tributary samples; B, non-NPSP mainstream samples; C, NPSP mainstream samples) were collected at the estuary of the NPSP tributaries of the Jialing River. High-throughput sequencing of the fungal-specific internal transcribed spacer (ITS) gene region was used to identify fungal taxa. The impact of NPSP on the aquatic environment of the Jialing River was revealed by analysing the community structure, community diversity, and functions of sediment fungi. The results showed that the dominant phylum of sediment fungi was Rozellomycota, followed by Ascomycota and Basidiomycota (relative abundance > 5%). NPSP caused a significant increase in the relative abundances of Exosporium, Phialosimplex, Candida, Inocybe, Tausonia, and Slooffia, and caused a significant decrease in the relative abundances of Cercospora, Cladosporium, Dokmaia, Setophaeosphaeria, Paraphoma, Neosetophoma, Periconia, Plectosphaerella, Claviceps, Botrytis, and Papiliotrema. These fungal communities therefore have a certain indicator role. In addition, NPSP caused significant changes in the physicochemical properties of Jialing River sediments, such as pH and available nitrogen (AN), which significantly increased the species richness of fungi and caused significant changes in the fungal community β-diversity (P < 0.05). pH, total phosphorus (TP), and AN were the main environmental factors affecting fungal communities in sediments of Jialing River. The functions of sediment fungi mainly involved three types of nutrient metabolism (symbiotrophic, pathotrophic, and saprotrophic) and 75 metabolic circulation pathways. NPSP significantly improved the pentose phosphate pathway, pentose phosphate pathway, and fatty acid beta-oxidation V metabolic circulation pathway functions (P < 0.05) and inhibited the chitin degradation to ethanol, super pathway of heme biosynthesis from glycine, and adenine and adenosine salvage III metabolic circulation pathway functions (P < 0.05). Hence, NPSP causes changes in the community structure and functions of sediment fungi in Jialing River and has adversely affected for the stability of the Jialing River Basin ecosystem.},
}
@article {pmid35416682,
year = {2022},
author = {Wu, J and Jiang, X and Yang, Q and Zhang, Y and Wang, C and Huang, R},
title = {Inhibition of Streptococcus mutans Biofilm Formation by the Joint Action of Oxyresveratrol and Lactobacillus casei.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {9},
pages = {e0243621},
pmid = {35416682},
issn = {1098-5336},
mesh = {Biofilms ; *Dental Caries ; *Dental Plaque ; Glucans ; Humans ; *Lacticaseibacillus casei ; Plant Extracts ; Polyphenols/pharmacology ; Stilbenes ; Streptococcus mutans/genetics ; Water/pharmacology ; },
abstract = {Microbial dysbiosis in dental plaque contributes to the occurrence of dental caries, to which Streptococcus mutans is a major contributor. Lactobacillus casei can be used as probiotic therapy to treat caries by replacing S. mutans within the dental plaque. However, the effects of probiotic treatment are not always stable. Oxyresveratrol (ORV), a plant-derived polyphenol, displays opposite effects in that it inhibits cariogenic and promotes commensal bacteria. Thus, the objectives of this study are to investigate the effects of ORV on bacterial proportions in S. mutans-L. casei biofilm and to elucidate how ORV weakens the competitiveness of S. mutans. Quantitative real-time PCR confirms a decreased S. mutans-L. casei ratio in dual-species biofilm by action of ORV. The culture supernatant of L. casei after being incubated with ORV (ORVLC) is prepared to explore the joint action of ORV and L. casei. ORVLC displays the strongest anti-biofilm effect against S. mutans when compared with the effects of L. casei supernatant or ORV alone. As a result of this treatment, both exopolysaccharides and bacteria contents in the biofilm are greatly reduced. The biofilm is transformed from water-insoluble glucan-dominant to water-soluble glucan-dominant by ORVLC through the modulation of the glycometabolism-related genes of S. mutans. As for the interactions between ORV and L. casei, ORV promotes L. casei to produce acetic acid, which provides L. casei with a competitive advantage against S. mutans. Taken together, ORV may be very suitable as an adjuvant medicine for probiotic therapy in the control of dental caries. IMPORTANCE The homeostatic imbalance in dental plaque associated with a sharp increase in the number of cariogenic bacteria such as Streptococcus mutans is critical for the occurrence and development of caries. Probiotic therapy can restore ecological balance by replacing cariogenic pathogens with probiotics. The current study innovatively finds that oxyresveratrol, a natural polyphenol, can provide probiotic Lactobacillus casei with competitive dominance in its dual-species biofilm with S. mutans. The joint action of oxyresveratrol and L. casei strongly inhibits the biofilm formation of S. mutans. Additionally, oxyresveratrol promotes L. casei to produce acetic acid, which facilitates L. casei to compete with S. mutans. Through the effects of these two mechanisms, oxyresveratrol leads to a significantly decreased S. mutans-L. casei ratio in their dual-species biofilm. Thus, oxyresveratrol is speculated to be an ideal medicine for the prevention and treatment of caries by regulating oral flora balance.},
}
@article {pmid35415771,
year = {2023},
author = {Graça, D and Fernandes, I and Cássio, F and Pascoal, C},
title = {Eco-physiological Responses of Aquatic Fungi to Three Global Change Stressors Highlight the Importance of Intraspecific Trait Variability.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1215-1225},
pmid = {35415771},
issn = {1432-184X},
support = {PTDC/CTA-AMB/31245/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/140761/2018//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04050/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Phylogeny ; *Mitosporic Fungi/physiology ; Rivers/microbiology ; Fresh Water ; Phenotype ; Plant Leaves/microbiology ; Fungi/genetics ; Ecosystem ; },
abstract = {Anthropogenic change at a global scale is affecting life on Earth with impacts on freshwaters. Aquatic hyphomycetes are fungi that drive organic matter decomposition in freshwaters and mediate energy transfer to higher trophic levels. Intraspecific trait variability affects ecological processes and can account for species adaptations to environmental change. To ascertain how aquatic hyphomycetes respond to global change related stressors, we selected 20 strains (7 species), based on their co-occurrence in streams and phylogenetic relatedness. We measured fungal growth rates at different temperatures (7 levels), nutrient concentrations (6 levels) and medium moisture (6 levels). Our results indicate that all stressors affected fungal growth, and responses to nutrient enrichment and moisture were strain specific. Fungal responses to the stressors were not explained by their phylogenetic relatedness. In the absence of stressors, interspecific diversity best explained the variance in fungal traits, while the increase in the stress gradient increased the importance of intraspecific diversity.},
}
@article {pmid35414897,
year = {2022},
author = {Suleiman, M and Pennekamp, F and Choffat, Y and Petchey, OL},
title = {Contrasting resistance and resilience to light variation of the coupled oxic and anoxic components of an experimental microbial ecosystem.},
journal = {Ecology and evolution},
volume = {12},
number = {4},
pages = {e8793},
pmid = {35414897},
issn = {2045-7758},
abstract = {Understanding how microbial communities of aquatic ecosystems respond to environmental change remains a critical challenge in microbial ecology. In this study, we used light-dependent oxic-anoxic micro-ecosystems to understand how the functioning and diversity of aerobic and anaerobic lake analog communities are affected by a pulse light deprivation. Continuous measurements of oxygen concentration were made and a time series of full-length 16S rRNA sequencing was used to quantify changes in alpha- and beta diversity. In the upper oxic layer, oxygen concentration decreased significantly under light reduction, but showed resilience in daily mean, minimum, and maximum after light conditions were restored to control level. Only the amplitude of diurnal fluctuations in oxygen concentrations did not recover fully, and instead tended to remain lower in treated ecosystems. Alpha diversity of the upper oxic layer communities showed a delayed increase after light conditions were restored, and was not resilient in the longer term. In contrast, alpha diversity of the anoxic lower layer communities increased during the light reduction, but was resilient in the longer term. Community composition changed significantly during light reduction, and showed resilience in the oxic layer and lack of resilience in the anoxic layer. Alpha diversity and the amplitude of daily oxygen fluctuations within and among treatments were strongly correlated, suggesting that higher diversity could lead to less variable oxygen concentrations, or vice versa. Our experiment showed that light deprivation induces multifaceted responses of community function (oxygen respiration) and structure, hence focusing on a single stability component could potentially be misleading.},
}
@article {pmid35412096,
year = {2022},
author = {Passarini, MRZ and Ottoni, JR and Costa, PEDS and Hissa, DC and Falcão, RM and Melo, VMM and Balbino, VQ and Mendonça, LAR and Lima, MGS and Coutinho, HDM and Verde, LCL},
title = {Fungal community diversity of heavy metal contaminated soils revealed by metagenomics.},
journal = {Archives of microbiology},
volume = {204},
number = {5},
pages = {255},
pmid = {35412096},
issn = {1432-072X},
support = {DCR-0024-01438.01.00/12//funcap/ ; },
mesh = {Biodegradation, Environmental ; Metagenomics ; *Metals, Heavy/metabolism ; *Mycobiome ; Soil ; Soil Microbiology ; *Soil Pollutants/metabolism ; },
abstract = {The inappropriate disposal of toxic compounds generated by industrial activity has been impacting the environment considerably. Microbial communities inhabiting contaminated sites may represent interesting ecological alternatives for the decontamination of environments. The present work aimed to investigate the fungal diversity and its functionality contained in stream sediments with industrial waste contaminated with heavy metals by using metagenomic approach. A total of 12 fungal orders were retrieved from datasets and, at phylum level, Ascomycota was the most abundant, followed by Basidiomycota, Chytridiomycota and Blastocladiomycota. Higher abundance of sequences was encountered within the less contaminated site, while the lower abundance was found in the sample with the higher contamination with lead. Gene sequences related to DNA repair and heavy metals biosorption processes were found in the four samples analyzed. The genera Aspergillus and Chaetomium, and Saccharomycetales order were highly present within all samples, showing their potential to be used for bioremediation studies. The present work demonstrated the importance of using the metagenomic approach to understand the dynamics and the possible metabolic pathways associated with fungal communities related to environmental samples containing heavy metals, as well as evidenced the importance of improving culturomics techniques for isolating strains with potential application in bioremediation processes of environments contaminated with heavy metals.},
}
@article {pmid35411306,
year = {2022},
author = {Bibbal, D and Ruiz, P and Sapountzis, P and Mazuy-Cruchaudet, C and Loukiadis, E and Auvray, F and Forano, E and Brugère, H},
title = {Persistent Circulation of Enterohemorrhagic Escherichia coli (EHEC) O157:H7 in Cattle Farms: Characterization of Enterohemorrhagic Escherichia coli O157:H7 Strains and Fecal Microbial Communities of Bovine Shedders and Non-shedders.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {852475},
pmid = {35411306},
issn = {2297-1769},
abstract = {Cattle are carriers, without clinical manifestations, of enterohemorrhagic Escherichia coli (EHEC) O157:H7 responsible for life-threatening infections in humans. A better identification of factors playing a role in maintaining persistence of such strains in cattle is required to develop more effective control measures. Hence, we conducted a study to identify farms with a persistent circulation of EHEC O157:H7. The EHEC O157:H7 herd status of 13 farms, which had previously provided bovine EHEC O157:H7 carriers at slaughter was investigated. Two farms were still housing positive young bulls, and this was true over a 1-year period. Only one fecal sample could be considered from a supershedder, and 60% of the carriers shed concentrations below 10 MPN/g. Moreover, EHEC O157:H7 represented minor subpopulations of E. coli. PFGE analysis of the EHEC O157:H7 strains showed that persistent circulation was due either to the persistence of a few predominant strains or to the repeated exposure of cattle to various strains. Finally, we compared fecal microbial communities of shedders (S) (n = 24) and non-shedders (NS) (n = 28), including 43 young bulls and nine cows, from one farm. Regarding alpha diversity, no significant difference between S vs. NS young bulls (n = 43) was observed. At the genus level, we identified 10 amplicon sequence variant (ASV) indicators of the S or NS groups. The bacterial indicators of S belonged to the family XIII UCG-001, Slackia, and Campylobacter genera, and Ruminococcaceae NK4A21A, Lachnospiraceae-UGC-010, and Lachnospiraceae-GCA-900066575 groups. The NS group indicator ASVs were affiliated to Pirellulaceae-1088-a5 gut group, Anaerovibrio, Victivallis, and Sellimonas genera. In conclusion, the characteristics enhancing the persistence of some predominant strains observed here should be explored further, and studies focused on mechanisms of competition among E. coli strains are also needed.},
}
@article {pmid35406804,
year = {2022},
author = {Chidambaram, SB and Rathipriya, AG and Mahalakshmi, AM and Sharma, S and Hediyal, TA and Ray, B and Sunanda, T and Rungratanawanich, W and Kashyap, RS and Qoronfleh, MW and Essa, MM and Song, BJ and Monaghan, TM},
title = {The Influence of Gut Dysbiosis in the Pathogenesis and Management of Ischemic Stroke.},
journal = {Cells},
volume = {11},
number = {7},
pages = {},
pmid = {35406804},
issn = {2073-4409},
mesh = {Dysbiosis/complications ; Fatty Acids, Volatile ; *Gastrointestinal Microbiome/physiology ; Humans ; *Ischemic Stroke ; *Stroke/etiology/therapy ; },
abstract = {Recent research on the gut microbiome has revealed the influence of gut microbiota (GM) on ischemic stroke pathogenesis and treatment outcomes. Alterations in the diversity, abundance, and functions of the gut microbiome, termed gut dysbiosis, results in dysregulated gut-brain signaling, which induces intestinal barrier changes, endotoxemia, systemic inflammation, and infection, affecting post-stroke outcomes. Gut-brain interactions are bidirectional, and the signals from the gut to the brain are mediated by microbially derived metabolites, such as trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFAs); bacterial components, such as lipopolysaccharide (LPS); immune cells, such as T helper cells; and bacterial translocation via hormonal, immune, and neural pathways. Ischemic stroke affects gut microbial composition via neural and hypothalamic-pituitary-adrenal (HPA) pathways, which can contribute to post-stroke outcomes. Experimental and clinical studies have demonstrated that the restoration of the gut microbiome usually improves stroke treatment outcomes by regulating metabolic, immune, and inflammatory responses via the gut-brain axis (GBA). Therefore, restoring healthy microbial ecology in the gut may be a key therapeutic target for the effective management and treatment of ischemic stroke.},
}
@article {pmid35404785,
year = {2022},
author = {Ho, PY and Good, BH and Huang, KC},
title = {Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35404785},
issn = {2050-084X},
support = {F32 GM143859/GM/NIGMS NIH HHS/United States ; RM1 GM135102/GM/NIGMS NIH HHS/United States ; R01 AI147023/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Microbiota ; *Models, Biological ; },
abstract = {Across diverse microbiotas, species abundances vary in time with distinctive statistical behaviors that appear to generalize across hosts, but the origins and implications of these patterns remain unclear. Here, we show that many of these macroecological patterns can be quantitatively recapitulated by a simple class of consumer-resource models, in which the metabolic capabilities of different species are randomly drawn from a common statistical distribution. Our model parametrizes the consumer-resource properties of a community using only a small number of global parameters, including the total number of resources, typical resource fluctuations over time, and the average overlap in resource-consumption profiles across species. We show that variation in these macroscopic parameters strongly affects the time series statistics generated by the model, and we identify specific sets of global parameters that can recapitulate macroecological patterns across wide-ranging microbiotas, including the human gut, saliva, and vagina, as well as mouse gut and rice, without needing to specify microscopic details of resource consumption. These findings suggest that resource competition may be a dominant driver of community dynamics. Our work unifies numerous time series patterns under a simple model, and provides an accessible framework to infer macroscopic parameters of effective resource competition from longitudinal studies of microbial communities.},
}
@article {pmid35403892,
year = {2023},
author = {Marozzi, G and Benucci, GMN and Turchetti, B and Massaccesi, L and Baciarelli Falini, L and Bonito, G and Buzzini, P and Agnelli, A and Donnini, D and Albertini, E},
title = {Correction to: Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {522},
doi = {10.1007/s00248-022-02010-y},
pmid = {35403892},
issn = {1432-184X},
}
@article {pmid35403856,
year = {2022},
author = {Yang, S and Li, L and Peng, X and Zhang, R and Song, L},
title = {Eukaryotic community composition and dynamics during solid waste decomposition.},
journal = {Applied microbiology and biotechnology},
volume = {106},
number = {8},
pages = {3307-3317},
pmid = {35403856},
issn = {1432-0614},
mesh = {Archaea/genetics ; Bioreactors ; Eukaryota ; *Euryarchaeota/genetics ; Methane ; *Refuse Disposal ; Solid Waste/analysis ; Waste Disposal Facilities ; },
abstract = {Consortia of microbial community are involved in organic waste decomposition in municipal solid waste (MSW) landfill via competition, syntropy, and predation. Bacterial and archaeal community structure and function have been extensively studied in this process, whereas the eukaryotic community structure and function are largely unidentified. This gap stands for one of the fundamental researches of microbial ecology, that is, "what is the importance of variation in eukaryotic community structure and function to solid waste decomposition? The main idea of this work is to characterize changes in eukaryotic community composition and the associated driver during solid waste decomposition. Using high throughput sequencing targeting 18S rRNA genes, community composition and dynamics of eukaryotic during solid wasted decomposition were studied, as well as the differences with solid waste and leachate physiochemical parameters. Concomitant to the expected changes in physiochemical factors, eukaryotic community composition and diversity changed along solid waste decomposition indicated by aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) and the structure was shaped by the nutrients (BOD5, total phosphorus, and nitrate) in leachate. Ascomycota, the predominant eukaryote, showed significant (p < 0.05) different structure among AP, ACP, and MP in phylum, genera, and species levels. Abundant Freshwater Opisthokonta was present in MP, suggesting a methane carbon cycling via grazing methane oxidation microorganism. Amoebozoa, Alveolata, Rhizaria, and Stramenopiles showed successional pattern during solid waste decomposition, indicating a short food chain establishment. Characterization on eukaryotic community composition and dynamics during solid waste decomposition are crucial for understanding of microbial consortia ecological function on solid waste decomposition and are also helpful for MSW management.Key points• Abundant Ascomycota significantly differed at AP, ACP, and MP.• Eukaryotic succession indicated a short food chain establishment.• Entire eukaryotic community structure was associated to nutrients in leachate.},
}
@article {pmid35402312,
year = {2022},
author = {Nardos, R and Leung, ET and Dahl, EM and Davin, S and Asquith, M and Gregory, WT and Karstens, L},
title = {Network-Based Differences in the Vaginal and Bladder Microbial Communities Between Women With and Without Urgency Urinary Incontinence.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {759156},
pmid = {35402312},
issn = {2235-2988},
support = {K01 DK116706/DK/NIDDK NIH HHS/United States ; T15 LM007088/LM/NLM NIH HHS/United States ; K12 HD043488/HD/NICHD NIH HHS/United States ; },
mesh = {Bacteria/genetics ; Female ; Humans ; Lactobacillus/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Urinary Bladder/microbiology ; *Urinary Incontinence/microbiology ; Vagina/microbiology ; },
abstract = {BACKGROUND: Little is known about the relationship of proximal urogenital microbiomes in the bladder and the vagina and how this contributes to bladder health. In this study, we use a microbial ecology and network framework to understand the dynamics of interactions/co-occurrences of bacteria in the bladder and vagina in women with and without urgency urinary incontinence (UUI).<br><br>METHODS: We collected vaginal swabs and catheterized urine specimens from 20 women with UUI (cases) and 30 women without UUI (controls). We sequenced the V4 region of the bacterial 16S rRNA gene and evaluated using alpha and beta diversity metrics. We used microbial network analysis to detect interactions in the microbiome and the betweenness centrality measure to identify central bacteria in the microbial network. Bacteria exhibiting maximum betweenness centrality are considered central to the microbe-wide networks and likely maintain the overall microbial network structure.<br><br>RESULTS: There were no significant differences in the vaginal or bladder microbiomes between cases and controls using alpha and beta diversity. Silhouette metric analysis identified two distinct microbiome clusters in both the bladder and vagina. One cluster was dominated by Lactobacillus genus while the other was more diverse. Network-based analyses demonstrated that vaginal and bladder microbial networks were different between cases and controls. In the vagina, there were similar numbers of genera and subgroup clusters in each network for cases and controls. However, cases tend to have more unique bacterial co-occurrences. While Bacteroides and Lactobacillus were the central bacteria with the highest betweenness centrality in controls, Aerococcus had the highest centrality in cases and correlated with bacteria commonly associated with bacterial vaginosis. In the bladder, cases have less than half as many network clusters compared to controls. Lactobacillus was the central bacteria in both groups but associated with several known uropathogens in cases. The number of shared bacterial genera between the bladder and the vagina differed between cases and controls, with cases having larger overlap (43%) compared to controls (29%).<br><br>CONCLUSION: Our study shows overlaps in microbial communities of bladder and vagina, with higher overlap in cases. We also identified differences in the bacteria that are central to the overall community structure.},
}
@article {pmid35396623,
year = {2023},
author = {Koide, RT},
title = {On Holobionts, Holospecies, and Holoniches: the Role of Microbial Symbioses in Ecology and Evolution.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1143-1149},
pmid = {35396623},
issn = {1432-184X},
mesh = {Phylogeny ; *Symbiosis ; *Adaptation, Physiological ; Eukaryota ; Biological Evolution ; },
abstract = {My goal in writing this is to increase awareness of the roles played by microbial symbionts in eukaryote ecology and evolution. Most eukaryotes host one or more species of symbiotic microorganisms, including prokaryotes and fungi. Many of these have profound impacts on the biology of their hosts. For example, microbial symbionts may expand the niches of their hosts, cause rapid adaptation of the host to the environment and re-adaptation to novel conditions via symbiont swapping, facilitate speciation, and fundamentally alter our concept of the species. In some cases, microbial symbionts and multicellular eukaryote hosts have a mutual dependency, which has obvious conservation implications. Hopefully, this contribution will stimulate a reevaluation of important ecological and evolutionary concepts including niche, adaptation, the species, speciation, and conservation of multicellular eukaryotes.},
}
@article {pmid35395701,
year = {2023},
author = {van der Loos, LM and D'hondt, S and Engelen, AH and Pavia, H and Toth, GB and Willems, A and Weinberger, F and De Clerck, O and Steinhagen, S},
title = {Salinity and host drive Ulva-associated bacterial communities across the Atlantic-Baltic Sea gradient.},
journal = {Molecular ecology},
volume = {32},
number = {23},
pages = {6260-6277},
doi = {10.1111/mec.16462},
pmid = {35395701},
issn = {1365-294X},
support = {UIDB/04326/2020//Portugese nation fund from Foundation for Science and Technology/ ; 3F020119//Fonds Wetenschappelijk Onderzoek/ ; 2020-03119//Formas national research program for food/ ; FWO project I001621N//European Marine Biological Resource Centre Belgium/ ; },
mesh = {Humans ; *Ulva/genetics ; Salinity ; Bacteria/genetics ; Baltic States ; Seawater/microbiology ; },
abstract = {The green seaweed Ulva is a model system to study seaweed-bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. We characterized the bacterial communities of 15 Ulva sensu lato species along 2,000 km of coastline in a total of 481 samples. Our results demonstrate that the Ulva-associated bacterial composition was strongly structured by both salinity and host species (together explaining between 34% and 91% of the variation in the abundance of the different bacterial genera). The largest shift in the bacterial consortia coincided with the horohalinicum (5-8 PSU, known as the transition zone from freshwater to marine conditions). Low-salinity communities especially contained high relative abundances of Luteolibacter, Cyanobium, Pirellula, Lacihabitans and an uncultured Spirosomaceae, whereas high-salinity communities were predominantly enriched in Litorimonas, Leucothrix, Sulfurovum, Algibacter and Dokdonia. We identified a small taxonomic core community (consisting of Paracoccus, Sulfitobacter and an uncultured Rhodobacteraceae), which together contributed to 14% of the reads per sample, on average. Additional core taxa followed a gradient model, as more core taxa were shared between neighbouring salinity ranges than between ranges at opposite ends of the Atlantic-Baltic Sea gradient. Our results contradict earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host's adaptation across the environmental gradient.},
}
@article {pmid35394422,
year = {2022},
author = {Meyer, BH and Adam, PS and Wagstaff, BA and Kolyfetis, GE and Probst, AJ and Albers, SV and Dorfmueller, HC},
title = {Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35394422},
issn = {2050-084X},
support = {109357/Z/15/Z//The Wellcome Trust and Royal Society Grant/ ; /WT_/Wellcome Trust/United Kingdom ; 105606/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Archaea/genetics ; Disaccharides ; *Eukaryota ; Phylogeny ; Polysaccharides ; },
abstract = {Protein N-glycosylation is a post-translational modification found in organisms of all domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in Eukaryotes, although the enzyme catalyzing this reaction remains unknown. Here, we report the identification of a thermostable archaeal β-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed its function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed similarities of Agl24 to the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which are catalyzing the same or a similar reaction, respectively. Phylogenetic analysis of Alg14/13 homologs indicates that they are ancient in Eukaryotes, either as a lateral transfer or inherited through eukaryogenesis.},
}
@article {pmid35389344,
year = {2022},
author = {Villanueva, EMF and Lim, PK and Lim, JJJ and Lim, SC and Lau, PY and Koh, KTS and Tan, E and Kairon, RS and See, WA and Liao, JX and Hee, KM and Vijay, V and Maitra, I and Boon, CJ and Fo, K and Wang, YT and Jaya, R and Hew, LA and Lim, YY and Lee, WQ and Lee, ZQ and Foo, H and Dos Santos, AL and Mutwil, M},
title = {Protist.guru: A Comparative Transcriptomics Database for Protists.},
journal = {Journal of molecular biology},
volume = {434},
number = {11},
pages = {167502},
doi = {10.1016/j.jmb.2022.167502},
pmid = {35389344},
issn = {1089-8638},
mesh = {*Databases, Genetic ; *Eukaryota/genetics ; Gene Expression Profiling ; Sequence Analysis, DNA ; *Transcriptome/genetics ; },
abstract = {During the last few decades, the study of microbial ecology has been enabled by molecular and genomic data. DNA sequencing has revealed the surprising extent of microbial diversity and how microbial processes run global ecosystems. However, significant gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still largely neglected. To address this gap, we used gene expression data from 17 protist species to create protist.guru: an online database equipped with tools for identifying co-expressed genes, gene families, and co-expression clusters enriched for specific biological functions. Here, we show how our database can be used to reveal genes involved in essential pathways, such as the synthesis of secondary carotenoids in Haematococcus lacustris. We expect protist.guru to serve as a valuable resource for protistologists, as well as a catalyst for discoveries and new insights into the biological processes of microbial eukaryotes. AVAILABILITY: The database and co-expression networks are freely available from http://protist.guru/. The expression matrices and sample annotations are found in the supplementary data.},
}
@article {pmid35389249,
year = {2022},
author = {Ramond, JB and Jordaan, K and Díez, B and Heinzelmann, SM and Cowan, DA},
title = {Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {86},
number = {2},
pages = {e0010921},
pmid = {35389249},
issn = {1098-5557},
mesh = {*Ecosystem ; *Microbiota ; Nitrification ; Nitrogen ; Nitrogen Cycle ; Plants ; Soil ; Soil Microbiology ; },
abstract = {Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.},
}
@article {pmid35389085,
year = {2023},
author = {Steinigeweg, C and Alkassab, AT and Erler, S and Beims, H and Wirtz, IP and Richter, D and Pistorius, J},
title = {Impact of a Microbial Pest Control Product Containing Bacillus thuringiensis on Brood Development and Gut Microbiota of Apis mellifera Worker Honey Bees.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1300-1307},
pmid = {35389085},
issn = {1432-184X},
mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; *Bacillus thuringiensis ; Lactobacillus ; Bifidobacterium ; },
abstract = {To avoid potential adverse side effects of chemical plant protection products, microbial pest control products (MPCP) are commonly applied as biological alternatives. This study aimed to evaluate the biosafety of a MPCP with the active organism Bacillus thuringiensis ssp. aizawai (strain: ABTS-1857). An in-hive feeding experiment was performed under field-realistic conditions to examine the effect of B. thuringiensis (B. t.) on brood development and the bacterial abundance of the core gut microbiome (Bifidobacterium asteroids, Gilliamella apicola, the group of Lactobacillus and Snodgrasella alvi) in Apis mellifera worker bees. We detected a higher brood termination rate and a non-successful development into worker bees of treated colonies compared to those of the controls. For the gut microbiome, all tested core members showed a significantly lower normalized abundance in bees of the treated colonies than in those of the controls; thus, a general response of the gut microbiome may be assumed. Consequently, colony exposure to B. t. strain ABTS-1857 had a negative effect on brood development under field-realistic conditions and caused dysbiosis of the gut microbiome. Further studies with B. t.-based products, after field-realistic application in bee attractive crops, are needed to evaluate the potential risk of these MPCPs on honey bees.},
}
@article {pmid35388893,
year = {2022},
author = {Águila, B and Yanez-Montalvo, A and Mercado-Juárez, RA and Montejano, GA and Becerra-Absalón, I and Falcón, LI},
title = {Microbialites show a distinct cyanobacterial phylogenetic structure and functional redundancy in Bacalar lagoon and Cenote Azul sinkhole, Yucatan Peninsula, Mexico.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {5},
pages = {},
doi = {10.1093/femsec/fiac039},
pmid = {35388893},
issn = {1574-6941},
support = {IN207220//UNAM/ ; //Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {*Cyanobacteria/genetics ; Metagenomics ; Mexico ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Cyanobacterial components of microbialites from two geographically close systems, the Bacalar lagoon (BL) and the Cenote Azul sinkhole (CA) in Quintana Roo, Mexico, were characterized. BL and CA systems were studied along a longitudinal gradient (north to south) and a depth gradient (5-30 m), respectively. Microscopic observations, 16S rRNA amplicon sequencing, and shotgun metagenomics were used to characterize Cyanobacteria. Both systems showed similar metabolic/functional profiles but harbored completely different cyanobacterial taxa. BL was dominated by Nostocales, including a population of previously undescribed Chakia sp., while CA was dominated by an unknown taxon of Chroococcales, comprising 70% of relative abundance through all depths. Interestingly, cyanobacterial assemblages in microbialites exhibited phylogenetic overdispersion in most of the BL sites, while CA sites exhibited phylogenetic clustering, these differences were attributed to depth/light conditions and possibly different times of geological formation for BL and CA systems.},
}
@article {pmid35388110,
year = {2022},
author = {Zhang, S and Yang, Q and Fu, S and Janssen, CR and Eggermont, M and Defoirdt, T},
title = {Indole decreases the virulence of the bivalve model pathogens Vibrio tasmaniensis LGP32 and Vibrio crassostreae J2-9.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {5749},
pmid = {35388110},
issn = {2045-2322},
mesh = {Animals ; *Bivalvia ; Indoles ; *Vibrio/genetics ; Virulence/genetics ; },
abstract = {Indole signaling plays an important role in bacterial pathogenesis. In this study, the impact of indole on biofilm formation, swimming and swarming motility were explored in Vibrio tasmaniensis LGP32 and Vibrio crassostreae J2-9, two model pathogens of bivalves. The results showed that indole decreased swimming and swarming motility in both strains, and decreased biofilm formation in V. crassostreae J2-9. Furthermore, indole affected a large number of genes at RNA level, including genes related to metabolism, ABC transporters, flagellar assembly, chemotaxis, and response regulators. Finally, the bacterial virulence towards mussel larvae was decreased by pretreatment with indole in both V. tasmaniensis LGP32 and V. crassostreae J2-9. After 5 days, the survival rate of mussel larvae increased 2.4-fold and 2.8-fold in mussel larvae challenged with V. tasmaniensis LGP32 pretreated with 200 µM and 500 µM indole, respectively. The survival rate of mussel larvae increased 1.5-fold and 1.9-fold in mussel larvae challenged with V. crassostreae J2-9 pretreated with 200 µM and 500 µM indole, respectively. These data indicate that indole has a significant impact on the virulence of V. tasmaniensis LGP32 and V. crassostreae J2-9, and indole signaling could be a promising target for antivirulence therapy.},
}
@article {pmid35388078,
year = {2022},
author = {Wahl, A and Huptas, C and Neuhaus, K},
title = {Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {5765},
pmid = {35388078},
issn = {2045-2322},
mesh = {Bacteria/genetics ; *Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing ; RNA ; RNA, Messenger/genetics ; *RNA, Ribosomal/genetics ; Sequence Analysis, RNA/methods ; },
abstract = {Current methods of high-throughput RNA sequencing of prokaryotes, including transcriptome analysis or ribosomal profiling, need deep sequencing to achieve sufficient numbers of effective reads (e.g., mapping to mRNA) in order to also find weakly expressed genetic elements. The fraction of high-quality reads mapping to coding RNAs (i.e., mRNA) is mainly influenced by the large content of rRNA and, to a lesser extent, tRNA in total RNA. Thus, depletion of rRNA increases coverage and thus sequencing costs. RiboZero, a depletion kit based on probe hybridisation and rRNA-removal was found to be most efficient in the past, but it was discontinued in 2018. To facilitate comparability with previous experiments and to help choose adequate replacements, we compare three commercially available rRNA depletion kits also based on hybridization and magnetic beads, i.e., riboPOOLs, RiboMinus and MICROBExpress, with the former RiboZero. Additionally, we constructed biotinylated probes for magnetic bead capture and rRNA depletion in this study. Based on E. coli, we found similar efficiencies in rRNA depletion for riboPOOLs and the self-made depletion method; both comparable to the former RiboZero, followed by RiboMinus, succeeded by MICROBExpress. Further, our in-house protocol allows customized species-specific rRNA or even tRNA depletion or depletion of other RNA targets. Both, the self-made biotinylated probes and riboPOOLs, were most successful in reducing the rRNA content and thereby increasing sequencing depth concerning mRNA reads. Additionally, the number of reads matching to weakly expressed genes are increased. In conclusion, the self-made specific biotinylated probes and riboPOOLs are an adequate replacement for the former RiboZero. Both are very efficient in depleting rRNAs, increasing mRNA reads and thus sequencing efficiency.},
}
@article {pmid35388041,
year = {2022},
author = {Dwużnik-Szarek, D and Mierzejewska, EJ and Kiewra, D and Czułowska, A and Robak, A and Bajer, A},
title = {Update on prevalence of Babesia canis and Rickettsia spp. in adult and juvenile Dermacentor reticulatus ticks in the area of Poland (2016-2018).},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {5755},
pmid = {35388041},
issn = {2045-2322},
mesh = {Animals ; *Babesia/genetics ; *Dermacentor/microbiology ; *Dog Diseases/epidemiology ; Dogs ; Nymph ; Poland/epidemiology ; Prevalence ; *Rhipicephalus sanguineus ; *Rickettsia/genetics ; },
abstract = {Ornate dog tick, Dermacentor reticulatus is an important vector of Babesia canis, and Rickettsia spp. and other pathogens of veterinary and public health interest. The current study is the first to investigate the long-term changes in prevalence of these pathogens in expanding tick populations in Central Europe. Molecular techniques (PCR, sequencing) were applied for the detection of pathogen DNA in adult (n = 2497) and juvenile ticks (1096 larvae and 410 nymphs). DNA of Rickettsia spp. was identified in 35% of adults and 12.6% of juvenile ticks. DNA of B. canis was detected in 3% of adult ticks and only in ticks from the Eastern region (regional prevalence 6%). As previously, no B. canis-positive ticks were found in Western Poland, including ticks from Wrocław area (n = 298). DNA of B. canis was identified in 0.33% of juvenile ticks (in 3 pools of larvae and 2 nymphs) from the Eastern region. In the current study we confirmed high occurrence of R. raoultii in adults ticks from all four zones and relatively high prevalence of B. canis in the Eastern population of D. reticulatus, corresponding well with high incidence of canine babesiosis in this area of Poland. Finally, we confirmed R. raoultii and B. canis infection in all life stages of D. reticulatus ticks.},
}
@article {pmid35385973,
year = {2023},
author = {Alba, C and Sansano-Maestre, J and Cid Vázquez, MD and Martínez-Herrero, MDC and Garijo-Toledo, MM and Azami-Conesa, I and Moraleda Fernández, V and Gómez-Muñoz, MT and Rodríguez, JM},
title = {Captive Breeding and Trichomonas gallinae Alter the Oral Microbiome of Bonelli's Eagle Chicks.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1541-1551},
pmid = {35385973},
issn = {1432-184X},
support = {Grant PR26/16-20328//Santander-UCM/ ; LIFE12 NAT/ES/000701-Integral recovery of Bonelli's eagle population in Spain//LIFE programme/ ; ACIF/2013/055//Conselleria d'Educaci&#xf3;, Investigaci&#xf3;, Cultura i Esport/ ; },
mesh = {Animals ; Humans ; *Trichomonas ; *Eagles ; Europe ; },
abstract = {Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt to describe the oral microbiome of Bonelli's eagle nestlings and evaluate the influence of several factors, such as captivity breeding, Trichomonas gallinae infection, and the presence of lesions at the oropharynx. The core oral microbiome of Bonelli's eagle is composed of Firmicutes, Bacteroidota, Fusobacteria and Proteobacteria as the most abundant phyla, and Megamonas and Bacteroides as the most abundant genera. None of the factors analysed showed a significant influence on alfa diversity, but beta diversity was affected for some of them. Captivity breeding exerted a high influence on the composition of the oral microbiome, with significant differences in the four most abundant phyla, with a relative increase of Proteobacteria and a decrease of the other three phyla in comparison with chicks bred at nest. Some genera were more abundant in captivity bred chicks, such as Escherichia-Shigella, Enterococcus, Lactobacillus, Corynebacterium, Clostridium and Staphylococcus, while Bacteroides, Oceanivirga, Peptostreptococcus, Gemella, Veillonella, Mycoplasma, Suttonella, Alloscardovia, Varibaculum and Campylobacter were more abundant in nest raised chicks. T. gallinae infection slightly influenced the composition of the microbiome, but chicks displaying trichomonosis lesions had a higher relative abundance of Bacteroides and Gemella, being the last one an opportunistic pathogen of abscess complications in humans. Raptor's microbiomes are scarcely studied. This is the first study on the factors that influence the oral microbiome of Bonelli's eagle.},
}
@article {pmid35384214,
year = {2022},
author = {Régimbeau, A and Budinich, M and Larhlimi, A and Pierella Karlusich, JJ and Aumont, O and Memery, L and Bowler, C and Eveillard, D},
title = {Contribution of genome-scale metabolic modelling to niche theory.},
journal = {Ecology letters},
volume = {25},
number = {6},
pages = {1352-1364},
pmid = {35384214},
issn = {1461-0248},
support = {//Fonds Fran&#xe7;ais pour l'Environnement Mondial/ ; 80 PRIME//Centre National de la Recherche Scientifique/ ; ANR-10-LABX-54//MEMO LIFE/ ; ANR-19-CE20-0020//BrownCut/ ; ANR-11-IDEX-0001-02//Universit&#xe9; de Recherche Paris Sciences et Lettres/ ; 835067//H2020 Environment/ ; 862923//H2020 Environment/ ; ANR-10-INBS-09-08//OCEANOMICS/ ; ANR-10-INBS-09-08//FRANCE GENOMIQUE/ ; },
mesh = {*Ecosystem ; Phenotype ; },
abstract = {Standard niche modelling is based on probabilistic inference from organismal occurrence data but does not benefit yet from genome-scale descriptions of these organisms. This study overcomes this shortcoming by proposing a new conceptual niche that resumes the whole metabolic capabilities of an organism. The so-called metabolic niche resumes well-known traits such as nutrient needs and their dependencies for survival. Despite the computational challenge, its implementation allows the detection of traits and the formal comparison of niches of different organisms, emphasising that the presence-absence of functional genes is not enough to approximate the phenotype. Further statistical exploration of an organism's niche sheds light on genes essential for the metabolic niche and their role in understanding various biological experiments, such as transcriptomics, paving the way for incorporating better genome-scale description in ecological studies.},
}
@article {pmid35379841,
year = {2022},
author = {Saeed, M and Rais, M and Akram, A and Williams, MR and Kellner, KF and Hashsham, SA and Davis, DR},
title = {Development and validation of an eDNA protocol for monitoring endemic Asian spiny frogs in the Himalayan region of Pakistan.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {5624},
pmid = {35379841},
issn = {2045-2322},
mesh = {Altitude ; Animals ; DNA, Environmental/*analysis/genetics ; Ecosystem ; Models, Biological ; Pakistan ; Ranidae/genetics/*physiology ; Species Specificity ; },
abstract = {Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both A. hazarensis and N. vicina than for visual encounter surveys. Detection probability using eDNA was greater for both species, particularly for A. hazarensis. The top-ranked detection model for visual encounter surveys included effects of both year and temperature on both species, and the top-ranked occupancy model included effects of elevation and year. The top-ranked detection model for eDNA data was the null model, and the top-ranked occupancy model included effects of elevation, year, and wetland type. To our knowledge, this is the first time an eDNA survey has been used to monitor amphibian species in the Himalayan region.},
}
@article {pmid35378966,
year = {2022},
author = {Liu, X and Lu, S and Shao, Y and Zhang, D and Tu, J and Chen, J},
title = {Disorders of gut microbiota in children with Tetralogy of Fallot.},
journal = {Translational pediatrics},
volume = {11},
number = {3},
pages = {385-395},
pmid = {35378966},
issn = {2224-4344},
abstract = {BACKGROUND: Gut microbiota plays an important role in cardiovascular health and disease, including congenital heart disease (CHD). Tetralogy of Fallot (TOF) is the most common form of cyanotic CHD characterized by systemic chronic hypoxia and sustained pressure overload of the right ventricle. It is well-known that hypoxia and pressure overload can affect gut microbiota. However, the effects of TOF on the gut microbiota remain little understood. This study explored the profile of the gut microbiota in children with unrepaired TOF.<br><br>METHODS: A total of 12 pediatric patients diagnosed with TOF and 9 healthy age- and gender-matched children were enrolled in this study. Fecal samples were collected from every participant and subjected to 16S rDNA gene sequencing. The raw sequencing data were processed using the Quantitative Insights Into Microbial Ecology pipeline.<br><br>RESULTS: A comparison of the gut microbiota revealed that pediatric patients with TOF had developed dysbiosis as reflected by the altered taxonomic composition and impaired functional profile. A total of 14 indicative bacterial genera were identified as differential biomarkers capable of distinguishing between healthy children and TOF patients. Furthermore, functional annotations revealed that the gut microbiota in TOF patients was characterized by increased levels of inflammatory, oxidative, and immune responses, and decreased activities of adaptation, synthesis, and metabolism.<br><br>CONCLUSIONS: Pediatric patients with unrepaired TOF have intestinal dysbacteriosis that is characterized by altered taxonomic composition and impaired functional profile. These findings suggested that the interplay between gut microbiota and the host may be dysregulated in patients with TOF.},
}
@article {pmid35378620,
year = {2023},
author = {Kerfahi, D and Harvey, BP and Kim, H and Yang, Y and Adams, JM and Hall-Spencer, JM},
title = {Whole community and functional gene changes of biofilms on marine plastic debris in response to ocean acidification.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1202-1214},
pmid = {35378620},
issn = {1432-184X},
mesh = {Humans ; *Seawater ; Plastics ; Hydrogen-Ion Concentration ; Ocean Acidification ; Carbon Dioxide ; Biofilms ; *Diatoms/genetics ; },
abstract = {Plastics are accumulating in the world's oceans, while ocean waters are becoming acidified by increased CO2. We compared metagenome of biofilms on tethered plastic bottles in subtidal waters off Japan naturally enriched in CO2, compared to normal ambient CO2 levels. Extending from an earlier amplicon study of bacteria, we used metagenomics to provide direct insights into changes in the full range of functional genes and the entire taxonomic tree of life in the context of the changing plastisphere. We found changes in the taxonomic community composition of all branches of life. This included a large increase in diatom relative abundance across the treatments but a decrease in diatom diversity. Network complexity among families decreased with acidification, showing overall simplification of biofilm integration. With acidification, there was decreased prevalence of genes associated with cell-cell interactions and antibiotic resistance, decreased detoxification genes, and increased stress tolerance genes. There were few nutrient cycling gene changes, suggesting that the role of plastisphere biofilms in nutrient processes within an acidified ocean may not change greatly. Our results suggest that as ocean CO2 increases, the plastisphere will undergo broad-ranging changes in both functional and taxonomic composition, especially the ecologically important diatom group, with possible wider implications for ocean ecology.},
}
@article {pmid35377164,
year = {2022},
author = {Gorski, L and Cooley, MB and Oryang, D and Carychao, D and Nguyen, K and Luo, Y and Weinstein, L and Brown, E and Allard, M and Mandrell, RE and Chen, Y},
title = {Prevalence and Clonal Diversity of over 1,200 Listeria monocytogenes Isolates Collected from Public Access Waters near Produce Production Areas on the Central California Coast during 2011 to 2016.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {8},
pages = {e0035722},
pmid = {35377164},
issn = {1098-5336},
mesh = {Humans ; *Listeria monocytogenes ; *Listeriosis/epidemiology ; Multilocus Sequence Typing ; Prevalence ; Virulence Factors/genetics ; },
abstract = {A 5-year survey of public access surface waters in an agricultural region of the Central California Coast was done to assess the prevalence of the foodborne pathogen Listeria monocytogenes. In nature, L. monocytogenes lives as a saprophyte in soil and water, which are reservoirs for contamination of preharvest produce. Moore swabs were deployed biweekly in lakes, ponds, streams, and rivers during 2011 to 2016. L. monocytogenes was recovered in 1,224 of 2,922 samples, resulting in 41.9% prevalence. Multiple subtypes were isolated from 97 samples, resulting in 1,323 L. monocytogenes isolates. Prevalence was higher in winter and spring and after rain events in some waterways. Over 84% of the isolates were serotype 4b. Whole-genome sequencing was done on 1,248 isolates, and in silico multilocus sequence typing revealed 74 different sequence types (STs) and 39 clonal complexes (CCs). The clones most isolated, CC639, CC183, and CC1, made up 27%, 19%, and 13%, respectively, of the sequenced isolates. Other types were CC663, CC6, CC842, CC4, CC2, CC5, and CC217. All sequenced isolates contained intact copies of core L. monocytogenes virulence genes, and pathogenicity islands LIPI-3 and LIPI-4 were identified in 73% and 63%, respectively, of the sequenced isolates. The virulence factor internalin A was predicted to be intact in all but four isolates, while genes important for sanitizer and heavy metal resistance were found in <5% of the isolates. These waters are not used for crop irrigation directly, but they are available to wildlife and can flood fields during heavy rains. IMPORTANCE Listeria monocytogenes serotype 4b and 1/2a strains are implicated in most listeriosis, and hypervirulent listeriosis stems from strains containing pathogenicity islands LIPI-3 and LIPI-4. The waters and sediments in the Central California Coast agricultural region contain widespread and diverse L. monocytogenes populations, and all the isolates contain intact virulence genes. Emerging clones CC183 and CC639 were the most abundant clones, and major clones CC1, CC4, and CC6 were well represented. CC183 was responsible for three produce-related outbreaks in the last 7 years. Most of the isolates in the survey differ from those of lesser virulence that are often isolated from foods and food processing plants because they contain genes encoding an intact virulence factor, internalin A, and most did not contain genes for sanitizer and heavy metal resistance. This isolate collection is important for understanding L. monocytogenes populations in agricultural and natural regions.},
}
@article {pmid35372103,
year = {2022},
author = {Halaweish, HF and Boatman, S and Staley, C},
title = {Encapsulated Fecal Microbiota Transplantation: Development, Efficacy, and Clinical Application.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {826114},
pmid = {35372103},
issn = {2235-2988},
mesh = {*Clostridioides difficile ; *Clostridium Infections/therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; },
abstract = {Fecal microbiota transplantation (FMT) has been established as a highly restorative therapeutic approach for treating recurrent Clostridioides difficile infection (rCDI). Recently, the use of capsule-based fecal microbiota transplantation (cFMT) has been shown to be a clinically effective approach to restore intestinal microbiota composition. This convenient, oral delivery provides an easy route of administration and a newfound flexibility for clinicians and patients. In this review, we discuss the development of cFMT, paying particular attention to lyophilized cFMT products. We review the available published clinical studies comparing cFMT with lower endoscopic FMT (eFMT) or placebo. We further discuss the pharmacokinetics of FMT, which should be understood in a framework of microbial ecology that considers the complex and dynamic interactions of gut microbiota with host factors and other microorganisms. Promisingly, the results of multiple trials investigating cFMT vs. eFMT in rCDI show cFMT to be as effective as eFMT at preventing rCDI. However, its efficacy in non-rCDI conditions, including obesity and metabolic syndrome, inflammatory bowel disease, HIV, and neurologic conditions, is less clear and more research is needed in these areas. Standardization of formulation, dose, and timing of administration to ensure optimal microbiota engraftment and clinical response is also a challenge to be addressed. Overall, cFMT is a practical method for fecal microbiota transplantation, with similar efficacy to eFMT in the resolution of rCDI, that holds therapeutic potential in a variety of other diseases.},
}
@article {pmid35370685,
year = {2022},
author = {Spisni, E and Turroni, S and Alvisi, P and Spigarelli, R and Azzinnari, D and Ayala, D and Imbesi, V and Valerii, MC},
title = {Nutraceuticals in the Modulation of the Intestinal Microbiota: Current Status and Future Directions.},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {841782},
pmid = {35370685},
issn = {1663-9812},
abstract = {Pharmaceutical interest in the human intestinal microbiota has increased considerably, because of the increasing number of studies linking the human intestinal microbial ecology to an increasing number of non-communicable diseases. Many efforts at modulating the gut microbiota have been made using probiotics, prebiotics and recently postbiotics. However, there are other, still little-explored opportunities from a pharmaceutical point of view, which appear promising to obtain modifications of the microbiota structure and functions. This review summarizes all in vitro, in vivo and clinical studies demonstrating the possibility to positively modulate the intestinal microbiota by using probiotics, prebiotics, postbiotics, essential oils, fungus and officinal plants. For the future, clinical studies investigating the ability to impact the intestinal microbiota especially by using fungus, officinal and aromatic plants or their extracts are required. This knowledge could lead to effective microbiome modulations that might support the pharmacological therapy of most non-communicable diseases in a near future.},
}
@article {pmid35370677,
year = {2022},
author = {Liu, L and Lu, Y and Xu, C and Chen, H and Wang, X and Wang, Y and Cai, B and Li, B and Verstrepen, L and Ghyselinck, J and Marzorati, M and Yao, Q},
title = {The Modulation of Chaihu Shugan Formula on Microbiota Composition in the Simulator of the Human Intestinal Microbial Ecosystem Technology Platform and its Influence on Gut Barrier and Intestinal Immunity in Caco-2/THP1-Blue™ Cell Co-Culture Model.},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {820543},
pmid = {35370677},
issn = {1663-9812},
abstract = {The traditional Chinese medicine (TCM)-Chaihu Shugan Formula (CSF), consisting of several Chinese botanical drugs like Bupleurum, is derived from the ancient Chinese pharmacopeia. It has been used for more than thousands of years in various suboptimal health statuses and diseases induced by chronic stress based on empirical therapy. Recent studies confirm the role of CSF in the development of many diseases, including depression, stress-induced hepatic injury and tumors. However, little has been known about the mechanisms behind the health effects of CSF. Here, we investigate the influence of CSF on the modulation of the simulated colonic microbiota of five healthy donors, gut barrier integrity, and intestinal immunity by combining the simulator of the human intestinal microbial ecosystem (SHIME[®]) technology platform with co-culture of intestinal and immune cells. This approach revealed that CSF stimulated the production of SCFA (acetate, propionate and butyrate) across donors while significantly lowering the production of branched SCFA (bSCFA). In terms of community composition, CSF stimulated a broad spectrum of health-related Bifidobacterium species, which are potent acetate and lactate producers. At the same time, it lowered the abundance of opportunistic pathogenic Escherichia coli. Later, we explore the effect of colonic fermentation of CSF on the gut barrier and intestinal immunity in the Caco-2/THP1-blue™ cell co-culture model. Based on the study using SHIME technology platform, CSF showed protective effects on inflammation-induced intestinal epithelial barrier disruption in all donors. Also, the treatment of CSF showed pronounced anti-inflammatory properties by strongly inducing anti-inflammatory cytokines IL-6 and IL-10 and reducing pro-inflammatory cytokine TNF-α. These findings demonstrate a significant modulatory effect of CSF on intestinal gut microbiota. CSF-microbial fermentation products improved the gut barrier and controlled intestinal inflammation.},
}
@article {pmid35367883,
year = {2022},
author = {Zhu, M and Duan, X and Zeng, Q and Liu, Y and Qiu, Z},
title = {He-Ne laser irradiation ameliorates cadmium toxicity in wheat by modulating cadmium accumulation, nutrient uptake and antioxidant defense system.},
journal = {Ecotoxicology and environmental safety},
volume = {236},
number = {},
pages = {113477},
doi = {10.1016/j.ecoenv.2022.113477},
pmid = {35367883},
issn = {1090-2414},
mesh = {*Antioxidants/metabolism ; *Cadmium/metabolism/toxicity ; Chlorophyll/metabolism ; Glutathione/metabolism ; Glutathione Reductase/metabolism ; Hydrogen Peroxide/metabolism ; Lasers ; Nutrients ; Oxidative Stress ; Plant Breeding ; Seedlings/metabolism ; Superoxide Dismutase/metabolism ; Triticum/metabolism ; },
abstract = {Cadmium (Cd) is one of the most hazardous heavy metals that negatively affect the growth and yield of wheat. He-Ne laser irradiation is known to ameliorate cadmium (Cd) stress in wheat. However, the underlying mechanism of He-Ne laser irradiation on protecting wheat against Cd stress is not well recognized. In present study, Cd-treated wheat showed significant reduction in growth, root morphology and total chlorophyll content, but notably increase of Cd accumulation in both roots and shoots. However, He-Ne laser irradiation dramatically reduced concentrations of malondialdehyde (MDA) and hydrogen peroxide (H2O2), and increased total chlorophyll content and activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) in roots of wheat plants under Cd stress. Further, He-Ne laser irradiation significantly upregulated the transcripts of TaGR (glutathione reductase) and TaGST (glutathione-S-transferase) genes along with the increased activities of GR and GST and glutathione (GSH) concentration in roots of wheat seedlings under Cd stress. In addition, He-Ne laser irradiation enhanced the uptake of mineral elements (N, P, Mg, Fe, Zn and Cu), and significantly decreased Cd uptake and transport mainly through down-regulating the expressions of Cd transport genes (TaHMA2 and TaHMA3) in roots of wheat seedlings under Cd stress. Overall, these findings suggested that He-Ne laser irradiation alleviated the adverse effects of Cd on wheat growth by enhancing antioxidant defense system, improving mineral nutrient status, and decreasing the Cd uptake and transport. This study provides new insights into the roles of He-Ne laser irradiation in the amelioration of Cd stress in wheat and indicates the potential application of this irradiation in crop breeding and growth under Cd stress conditions.},
}
@article {pmid35367386,
year = {2022},
author = {de Lapena, SAB and Terra-Garcia, M and Ward, RADC and Rossoni, RD and Melo, VMM and Junqueira, JC},
title = {Enhancing effect of chitosan on methylene blue-mediated photodynamic therapy against C. albicans: A study in planktonic growth, biofilms, and persister cells.},
journal = {Photodiagnosis and photodynamic therapy},
volume = {38},
number = {},
pages = {102837},
doi = {10.1016/j.pdpdt.2022.102837},
pmid = {35367386},
issn = {1873-1597},
mesh = {Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Biofilms ; Candida ; Candida albicans ; *Chitosan/pharmacology ; Fluconazole/pharmacology ; Methylene Blue/pharmacology ; *Photochemotherapy/methods ; Photosensitizing Agents/pharmacology ; Plankton ; },
abstract = {Chitosan (CS) is a natural polymer extracted from the exoskeleton of crustaceans. Due to its cationic structure, CS has been studied as a possible enhancer of antimicrobial photodynamic therapy (aPDT). The objective was to evaluate the association of CS with methylene blue (MB)-mediated aPDT on Candida albicans, investigating its effects on planktonic growth, biofilms, and cells persistent to fluconazole. The ability of CS to interfere with MB absorption by Candida cells was also evaluated. For the assays, planktonic cells of C. albicans were cultivated for 24 h, and the biofilms were formed for 48 h. For the induction of persister cells, C. albicans was cultivated with high concentration of fluconazole for 48 h. Treatments were performed with MB, CS or MB+CS, followed by irradiation with LED (660 nm). As results, aPDT with MB (300 µm) reduced the planktonic cells by 1.6 log10 CFU, while the MB+CS association led to a reduction of 4.8 log10 CFU. For aPDT in biofilms, there was a microbial reduction of 2.9 log10 CFU for the treatment with MB (600 µm) and 5.3 log10 CFU for MB+CS. In relation to persister cells, the fungal reductions were 0.4 log10 CFU for MB and 1.5 log10 CFU for MB+CS. In the absorption assays, the penetration of MB into Candida cells was increased in the presence of CS. It was concluded that CS enhanced the antimicrobial activity of aPDT in planktonic growth, biofilms, and persister cells of C. albicans, probably by facilitating the penetration of MB into fungal cells.},
}
@article {pmid35366684,
year = {2023},
author = {Bashir, A and Ahmad, T and Farooq, S and Lone, WI and Manzoor, MM and Nalli, Y and Sultan, P and Chaubey, A and Ali, A and Riyaz-Ul-Hassan, S},
title = {A Secondary Metabolite of Cercospora sp., Associated with Rosa damascena Mill., Inhibits Proliferation, Biofilm Production, Ergosterol Synthesis and Other Virulence Factors in Candida albicans.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1276-1287},
pmid = {35366684},
issn = {1432-184X},
mesh = {*Candida albicans/metabolism ; Virulence Factors/metabolism ; *Rosa/metabolism ; Cercospora/metabolism ; Molecular Docking Simulation ; Phylogeny ; Biofilms ; Ergosterol/metabolism ; Cell Proliferation ; Antifungal Agents/pharmacology/metabolism ; Microbial Sensitivity Tests ; },
abstract = {Here we describe the antimicrobial potential of secondary metabolites, fulvic acid (F.A.) and anhydrofulvic acid (AFA), produced by RDE147, an endophyte of Rosa damascena Mill. The endophyte was identified as Cercospora piaropi by ITS and β-tubulin-based phylogenetic analyses, while chemoprofiling of the endophyte by column chromatography and spectroscopy yielded two pure compounds, F.A. and AFA. The compounds demonstrated different antimicrobial profiles, with AFA suppressing the growth of C. albicans at 7.3 µg ml[-1] IC50. Further studies revealed that AFA strongly restricted the biofilm production and hyphae formation in C. albicans by down-regulating several biofilm and morphogenesis-related genes. The time-kill assays confirmed the fungicidal activity of AFA against C. albicans, killing 83.6% of the pathogen cells in 24 h at the MIC concentration, and the post-antibiotic effect (PAE) experiments established the suppression of C. albicans growth for extended time periods. The compound acted synergistically with amphotericin B and nystatin and reduced ergosterol biosynthesis by the pathogen, confirmed by ergosterol estimation and comparative expression profiling of selected genes and molecular docking of AFA with C. albicans squalene epoxidase. AFA also suppressed the expression of several other virulence genes of the fungal pathogen. The study determines the anti-C. albicans potential of AFA and its impact on the biology of the pathogen. It also indicates that Cercospora species may yield potential bioactive molecules, especially fulvic acid derivatives. However, it is imperative to conduct in vivo studies to explore this molecule's therapeutic potential further.},
}
@article {pmid35366074,
year = {2023},
author = {Li, W and Zhou, Z and Li, H and Wang, S and Ren, L and Hu, J and Liu, Q and Wu, C and Tang, C and Hu, F and Zeng, L and Zhao, R and Tao, M and Zhang, C and Qin, Q and Liu, S},
title = {Successional Changes of Microbial Communities and Host-Microbiota Interactions Contribute to Dietary Adaptation in Allodiploid Hybrid Fish.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1190-1201},
pmid = {35366074},
issn = {1432-184X},
support = {NT2021008//the Laboratory of Lingnan Modern Agriculture Project/ ; 21B0053//the Research Foundation of Education Bureau of Hunan Province/ ; U19A2040//National Natural Science Foundation of China/ ; 31730098//National Natural Science Foundation of China/ ; 31802287//National Natural Science Foundation of China/ ; CARS-45//Earmarked Fund for China Agriculture Research System/ ; },
mesh = {Animals ; *Microbiota ; Fishes/microbiology ; Diet/veterinary ; *Gastrointestinal Microbiome ; Bacteria/genetics ; },
abstract = {Host-microbiota interactions play critical roles in host development, immunity, metabolism, and behavior. However, information regarding host-microbiota interactions is limited in fishes due to their complex living environment. In the present study, an allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) was used to investigate the successional changes of the microbial communities and host-microbiota interactions during herbivorous and carnivorous dietary adaptations. The growth level was not significantly different in any developmental stage between the two diet groups of fish. The diversity and composition of the dominant microbial communities showed similar successional patterns in the early developmental stages, but significantly changed during the two dietary adaptations. A large number of bacterial communities coexisted in all developmental stages, whereas the abundance of some genera associated with metabolism, including Acinetobacter, Gemmobacter, Microbacterium, Vibrio, and Aeromonas, was higher in either diet groups of fish. Moreover, the abundance of phylum Firmicutes, Actinobacteria, and Chloroflexi was positively correlated with the host growth level. In addition, Spearman's correlation analysis revealed that the differentially expressed homologous genes in the intestine associated with cell growth, immunity, and metabolism were related to the dominant gut microbiota. Our results present evidence that host genetics-gut microbiota interactions contribute to dietary adaptation in hybrid fish, which also provides basic data for understanding the diversity of dietary adaptations and evolution in fish.},
}
@article {pmid35365572,
year = {2023},
author = {Effenberger, M and Widjaja, AA and Grabherr, F and Schaefer, B and Grander, C and Mayr, L and Schwaerzler, J and Enrich, B and Moser, P and Fink, J and Pedrini, A and Jaschke, N and Kirchmair, A and Pfister, A and Hausmann, B and Bale, R and Putzer, D and Zoller, H and Schafer, S and Pjevac, P and Trajanoski, Z and Oberhuber, G and Adolph, T and Cook, S and Tilg, H},
title = {Interleukin-11 drives human and mouse alcohol-related liver disease.},
journal = {Gut},
volume = {72},
number = {1},
pages = {168-179},
doi = {10.1136/gutjnl-2021-326076},
pmid = {35365572},
issn = {1468-3288},
support = {MC_U120085815/MRC_/Medical Research Council/United Kingdom ; P 29379/FWF_/Austrian Science Fund FWF/Austria ; P 33070/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Humans ; Mice ; Animals ; Interleukin-11/metabolism ; *Liver Diseases, Alcoholic/metabolism ; Liver/metabolism ; *Hepatitis, Alcoholic/metabolism ; Ethanol/toxicity/metabolism ; Hepatocytes/metabolism ; Inflammation/metabolism ; Liver Cirrhosis/pathology ; Mice, Inbred C57BL ; },
abstract = {OBJECTIVE: Alcoholic hepatitis (AH) reflects acute exacerbation of alcoholic liver disease (ALD) and is a growing healthcare burden worldwide. Interleukin-11 (IL-11) is a profibrotic, proinflammatory cytokine with increasingly recognised toxicities in parenchymal and epithelial cells. We explored IL-11 serum levels and their prognostic value in patients suffering from AH and cirrhosis of various aetiology and experimental ALD.<br><br>DESIGN: IL-11 serum concentration and tissue expression was determined in a cohort comprising 50 patients with AH, 110 patients with cirrhosis and 19 healthy volunteers. Findings were replicated in an independent patient cohort (n=186). Primary human hepatocytes exposed to ethanol were studied in vitro. Ethanol-fed wildtype mice were treated with a neutralising murine IL-11 receptor-antibody (anti-IL11RA) and examined for severity signs and markers of ALD.<br><br>RESULTS: IL-11 serum concentration and hepatic expression increased with severity of liver disease, mostly pronounced in AH. In a multivariate Cox-regression, a serum level above 6.4 pg/mL was a model of end-stage liver disease independent risk factor for transplant-free survival in patients with compensated and decompensated cirrhosis. In mice, severity of alcohol-induced liver inflammation correlated with enhanced hepatic IL-11 and IL11RA expression. In vitro and in vivo, anti-IL11RA reduced pathogenic signalling pathways (extracellular signal-regulated kinases, c-Jun N-terminal kinase, NADPH oxidase 4) and protected hepatocytes and murine livers from ethanol-induced inflammation and injury.<br><br>CONCLUSION: Pathogenic IL-11 signalling in hepatocytes plays a crucial role in the pathogenesis of ALD and could serve as an independent prognostic factor for transplant-free survival. Blocking IL-11 signalling might be a therapeutic option in human ALD, particularly AH.},
}
@article {pmid35364696,
year = {2023},
author = {Liu, N and Hu, H and Ma, W and Deng, Y and Dimitrov, D and Wang, Q and Shrestha, N and Su, X and Feng, K and Liu, Y and Hao, B and Zhang, X and Feng, X and Wang, Z},
title = {Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {1013-1027},
pmid = {35364696},
issn = {1432-184X},
support = {2017YFA0605101//national key research development program of china/ ; XDB31000000//the Strategic Priority Research Program of Chinese Academy of Sciences/ ; 32125026//the National Natural Science Foundation of China/ ; 31988102//the National Natural Science Foundation of China/ ; LESP201702//the Youth Fund of Ministry of Education Laboratory for Earth Surface Processes of Peking University/ ; },
mesh = {*Grassland ; *Soil/chemistry ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Fungi/genetics ; Bacteria/genetics ; Archaea/genetics ; },
abstract = {Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.},
}
@article {pmid35363772,
year = {2022},
author = {Zaoli, S and Grilli, J},
title = {The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial communities.},
journal = {PLoS computational biology},
volume = {18},
number = {4},
pages = {e1010043},
pmid = {35363772},
issn = {1553-7358},
mesh = {Benchmarking ; Biodiversity ; *Conservation of Natural Resources ; Logistic Models ; *Microbiota ; },
abstract = {The large taxonomic variability of microbial community composition is a consequence of the combination of environmental variability, mediated through ecological interactions, and stochasticity. Most of the analysis aiming to infer the biological factors determining this difference in community structure start by quantifying how much communities are similar in their composition, trough beta-diversity metrics. The central role that these metrics play in microbial ecology does not parallel with a quantitative understanding of their relationships and statistical properties. In particular, we lack a framework that reproduces the empirical statistical properties of beta-diversity metrics. Here we take a macroecological approach and introduce a model to reproduce the statistical properties of community similarity. The model is based on the statistical properties of individual communities and on a single tunable parameter, the correlation of species' carrying capacities across communities, which sets the difference of two communities. The model reproduces quantitatively the empirical values of several commonly-used beta-diversity metrics, as well as the relationships between them. In particular, this modeling framework naturally reproduces the negative correlation between overlap and dissimilarity, which has been observed in both empirical and experimental communities and previously related to the existence of universal features of community dynamics. In this framework, such correlation naturally emerges due to the effect of random sampling.},
}
@article {pmid35362197,
year = {2022},
author = {Lal, R and Singh, BK and Sar, P and Phale, P},
title = {The assessment of microbial ecology: a special emphasis on the Indian scenario.},
journal = {Environmental microbiology reports},
volume = {14},
number = {3},
pages = {325-329},
doi = {10.1111/1758-2229.13067},
pmid = {35362197},
issn = {1758-2229},
mesh = {Ecology ; *Microbiota ; },
}
@article {pmid35361906,
year = {2022},
author = {Zhang, C and Merana, GR and Harris-Tryon, T and Scharschmidt, TC},
title = {Skin immunity: dissecting the complex biology of our body's outer barrier.},
journal = {Mucosal immunology},
volume = {15},
number = {4},
pages = {551-561},
pmid = {35361906},
issn = {1935-3456},
support = {K08 AR076459/AR/NIAMS NIH HHS/United States ; DP2 AI144968/AI/NIAID NIH HHS/United States ; },
mesh = {Biology ; Immunity, Innate ; *Mucous Membrane ; *Symbiosis ; },
abstract = {Our skin contributes critically to health via its role as a barrier tissue, carefully regulating passage of key substrates while also providing defense against exogenous threats. Immunological processes are integral to almost every skin function and paramount to our ability to live symbiotically with skin commensal microbes and other environmental stimuli. While many parallels can be drawn to immunobiology at other mucosal sites, skin immunity demonstrates unique features that relate to its distinct topography, chemical composition and microbial ecology. Here we provide an overview of skin as an immune organ, with reference to the broader context of mucosal immunology. We review paradigms of innate as well as adaptive immune function and highlight how skin-specific structures such as hair follicles and sebaceous glands interact and contribute to these processes. Finally, we highlight for the mucosal immunology community a few emerging areas of interest for the skin immunity field moving forward.},
}
@article {pmid35361625,
year = {2022},
author = {Lee, TJ and Liu, YC and Liu, WA and Lin, YF and Lee, HH and Ke, HM and Huang, JP and Lu, MJ and Hsieh, CL and Chung, KF and Liti, G and Tsai, IJ},
title = {Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages.},
journal = {Genome research},
volume = {32},
number = {5},
pages = {864-877},
pmid = {35361625},
issn = {1549-5469},
mesh = {Asia ; *Biodiversity ; Humans ; Phylogeny ; *Saccharomyces cerevisiae/genetics ; Taiwan ; Whole Genome Sequencing ; },
abstract = {The ecology and genetic diversity of the model yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace, where the most divergent natural lineage was discovered. Here, we extensively sampled the broadleaf forests across this continental island to probe the ancestral species' diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages that diverged from Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Three lineages are endemic to Taiwan and six are widespread in Asia, making this region a focal biodiversity hotspot. Both ancient and recent admixture events were detected between the natural lineages, and a genetic ancestry component associated with isolates from fruits was detected in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We identified different selection patterns shaping the coding sequences of natural lineages and found fewer gene family expansion and contractions that contrast with domesticated lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.},
}
@article {pmid35360922,
year = {2022},
author = {Kaiser, T and Jahansouz, C and Staley, C},
title = {Network-based approaches for the investigation of microbial community structure and function using metagenomics-based data.},
journal = {Future microbiology},
volume = {17},
number = {},
pages = {621-631},
doi = {10.2217/fmb-2021-0219},
pmid = {35360922},
issn = {1746-0921},
mesh = {Host Microbial Interactions ; *Metagenomics/methods ; *Microbiota ; },
abstract = {Network-based approaches offer a powerful framework to evaluate microbial community organization and function as it relates to a variety of environmental processes. Emerging studies are exploring network theory as a method for data integration that is likely to be critical for the integration of 'omics' data using systems biology approaches. Intricacies of network theory and methodological and computational complexities in network construction, however, impede the use of these tools for translational science. We provide a perspective on the methods of network construction, interpretation and emerging uses for these techniques in understanding host-microbiota interactions.},
}
@article {pmid35359714,
year = {2022},
author = {Rogiers, T and Van Houdt, R and Williamson, A and Leys, N and Boon, N and Mijnendonckx, K},
title = {Molecular Mechanisms Underlying Bacterial Uranium Resistance.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {822197},
pmid = {35359714},
issn = {1664-302X},
abstract = {Environmental uranium pollution due to industries producing naturally occurring radioactive material or nuclear accidents and releases is a global concern. Uranium is hazardous for ecosystems as well as for humans when accumulated through the food chain, through contaminated groundwater and potable water sources, or through inhalation. In particular, uranium pollution pressures microbial communities, which are essential for healthy ecosystems. In turn, microorganisms can influence the mobility and toxicity of uranium through processes like biosorption, bioreduction, biomineralization, and bioaccumulation. These processes were characterized by studying the interaction of different bacteria with uranium. However, most studies unraveling the underlying molecular mechanisms originate from the last decade. Molecular mechanisms help to understand how bacteria interact with radionuclides in the environment. Furthermore, knowledge on these underlying mechanisms could be exploited to improve bioremediation technologies. Here, we review the current knowledge on bacterial uranium resistance and how this could be used for bioremediation applications.},
}
@article {pmid35358890,
year = {2022},
author = {Gui, Y and Sun, Z and Kazmi, SSUH and Rahman, MS and Xu, H},
title = {Insights for monitoring surveys into influence of tidal events on protozoan periphyton fauna along the tidelines of Yellow Sea, Northern China.},
journal = {Marine pollution bulletin},
volume = {178},
number = {},
pages = {113586},
doi = {10.1016/j.marpolbul.2022.113586},
pmid = {35358890},
issn = {1879-3363},
mesh = {Biodiversity ; *Ciliophora ; Ecosystem ; Environmental Monitoring ; *Periphyton ; Surveys and Questionnaires ; },
abstract = {To explore the influence of tidal events on protozoan periphyton fauna along tidelines, a 1-month baseline survey for bioassessment was conducted in an intertidal zone of the Yellow Sea, Northern China. A total of 27 protozoans species were identified among five sampling sites along five tidelines (sites A-E). The periphytic protozoans showed a significant variation in species distribution and community pattern along five tidelines. Species richness decreased from the high tideline (site A) and reached the minimum value at the middle tideline (site C), followed by an increase up to the low tideline (site E). Individual abundances peaked at site C and leveled off at the other four tidelines. Species richness, evenness, and diversity showed low value at site C compared with those at the other four sites. These findings suggest that periphytic protozoan fauna was shaped by tidal events along the tidelines of marine ecosystems.},
}
@article {pmid35358518,
year = {2022},
author = {Shahbaz, M and Bengtson, P and Mertes, JR and Kulessa, B and Kljun, N},
title = {Spatial heterogeneity of soil carbon exchanges and their drivers in a boreal forest.},
journal = {The Science of the total environment},
volume = {831},
number = {},
pages = {154876},
doi = {10.1016/j.scitotenv.2022.154876},
pmid = {35358518},
issn = {1879-1026},
mesh = {Carbon ; Carbon Dioxide/analysis ; Forests ; Methane ; *Soil ; *Taiga ; },
abstract = {Boreal forests have a large impact on the global greenhouse gas balance and their soils constitute an important carbon (C) reservoir. Mature boreal forests are typically a net CO2 sink, but there are also examples of boreal forests that are persistent CO2 sources. The reasons remain often unknown, presumably due to a lack of understanding of how biotic and abiotic drivers interact to determine the microbial respiration of soil organic matter (SOM). This study aimed at identifying the main drivers of microbial SOM respiration and CO2 and CH4 soil chamber-fluxes within dry and wet sampling areas at the mature boreal forest of Norunda, Sweden, a persistent net CO2 source. The spatial heterogeneity of the drivers was assessed with a geostatistical approach combined with stepwise multiple regression. We found that heterotrophic soil respiration increased with SOM content and nitrogen (N) availability, while the SOM reactivity, i.e., SOM specific respiration, was determined by soil moisture and N availability. The latter suggests that microbial activity was N rather than C limited and that microbial N mining might be driving old-SOM decomposition, which was observed through a positive correlation between soil respiration and its δ[13]C values. SOM specific heterotrophic respiration was lower in wet than in dry areas, while no such dependencies were found for chamber-based soil CO2 fluxes, implying that oxygen depletion resulted in lower SOM reactivity. The chamber-based soil CH4 flux differed significantly between the wet and dry areas. In the wet area, we observed net CH4 emission that was positively related to soil moisture and NH4[+]-N content. Taken together, our findings suggest that N availability has a strong regulatory effect on soil CO2 and CH4 emissions at Norunda, and that microbial decomposition of old-SOM to release bioavailable N might be partly responsible for the net CO2 emission at the site.},
}
@article {pmid35357520,
year = {2023},
author = {Castillo-Esparza, JF and Mora-Velasco, KA and Rosas-Saito, GH and Rodríguez-Haas, B and Sánchez-Rangel, D and Ibarra-Juárez, LA and Ortiz-Castro, R},
title = {Microorganisms Associated with the Ambrosial Beetle Xyleborus affinis with Plant Growth-Promotion Activity in Arabidopsis Seedlings and Antifungal Activity Against Phytopathogenic Fungus Fusarium sp. INECOL_BM-06.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1396-1411},
pmid = {35357520},
issn = {1432-184X},
support = {PDCPN-2015-882//CONACYT/ ; FORDECYT-PRONACES 292399//CONACYT/ ; },
mesh = {Animals ; *Fusarium ; Antifungal Agents/metabolism ; Seedlings/microbiology ; *Coleoptera ; *Arabidopsis/microbiology ; *Weevils/microbiology ; Insecta ; Plant Diseases/microbiology ; },
abstract = {Plants interact with a great diversity of microorganisms or insects throughout their life cycle in the environment. Plant and insect interactions are common; besides, a great variety of microorganisms associated with insects can induce pathogenic damage in the host, as mutualist phytopathogenic fungus. However, there are other microorganisms present in the insect-fungal association, whose biological/ecological activities and functions during plant interaction are unknown. In the present work evaluated, the role of microorganisms associated with Xyleborus affinis, an important beetle species within the Xyleborini tribe, is characterized by attacking many plant species, some of which are of agricultural and forestry importance. We isolated six strains of microorganisms associated with X. affinis shown as plant growth-promoting activity and altered the root system architecture independent of auxin-signaling pathway in Arabidopsis seedlings and antifungal activity against the phytopathogenic fungus Fusarium sp. INECOL_BM-06. In addition, evaluating the tripartite interaction plant-microorganism-fungus, interestingly, we found that microorganisms can induce protection against the phytopathogenic fungus Fusarium sp. INECOL_BM-06 involving the jasmonic acid-signaling pathway and independent of salicylic acid-signaling pathway. Our results showed the important role of this microorganisms during the plant- and insect-microorganism interactions, and the biological potential use of these microorganisms as novel agents of biological control in the crops of agricultural and forestry is important.},
}
@article {pmid35357187,
year = {2022},
author = {Holohan, BC and Duarte, MS and Szabo-Corbacho, MA and Cavaleiro, AJ and Salvador, AF and Pereira, MA and Ziels, RM and Frijters, CTMJ and Pacheco-Ruiz, S and Carballa, M and Sousa, DZ and Stams, AJM and O'Flaherty, V and van Lier, JB and Alves, MM},
title = {Principles, Advances, and Perspectives of Anaerobic Digestion of Lipids.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {8},
pages = {4749-4775},
doi = {10.1021/acs.est.1c08722},
pmid = {35357187},
issn = {1520-5851},
mesh = {Anaerobiosis ; Bioreactors ; Lipids ; Methane/metabolism ; *Sewage ; *Waste Disposal, Fluid ; Wastewater ; },
abstract = {Several problems associated with the presence of lipids in wastewater treatment plants are usually overcome by removing them ahead of the biological treatment. However, because of their high energy content, waste lipids are interesting yet challenging pollutants in anaerobic wastewater treatment and codigestion processes. The maximal amount of waste lipids that can be sustainably accommodated, and effectively converted to methane in anaerobic reactors, is limited by several problems including adsorption, sludge flotation, washout, and inhibition. These difficulties can be circumvented by appropriate feeding, mixing, and solids separation strategies, provided by suitable reactor technology and operation. In recent years, membrane bioreactors and flotation-based bioreactors have been developed to treat lipid-rich wastewater. In parallel, the increasing knowledge on the diversity of complex microbial communities in anaerobic sludge, and on interspecies microbial interactions, contributed to extend the knowledge and to understand more precisely the limits and constraints influencing the anaerobic biodegradation of lipids in anaerobic reactors. This critical review discusses the most important principles underpinning the degradation process and recent key discoveries and outlines the current knowledge coupling fundamental and applied aspects. A critical assessment of knowledge gaps in the field is also presented by integrating sectorial perspectives of academic researchers and of prominent developers of anaerobic technology.},
}
@article {pmid35355087,
year = {2023},
author = {Zhang, W and Wan, W and Liu, X and Yang, Y and Liu, M},
title = {Stronger Geographic Limitations Shape a Rapid Turnover and Potentially Highly Connected Network of Core Bacteria on Microplastics.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1179-1189},
pmid = {35355087},
issn = {1432-184X},
support = {32071614//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microplastics ; Plastics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Soil ; Water ; *Microbiota ; },
abstract = {Core microbiota is shared microbial taxa within the same habitat, which is important for understanding the stable and consistent components of the complex microbial assembly. However, information on the microplastic core bacteria from the river ecosystems is poor. Here, we investigated the composition and function of microplastic core bacteria from the Three Gorges Reservoir area along the approximate 662 km of the Yangtze River via full-length 16S rRNA gene sequencing, compared with those in water, sediment, and soil. The results showed that the spatial turnover of bacterial communities in four habitats supported deterministic processes dominated by niche differentiation, which shaped their core bacteria. The composition and function of microplastic core bacteria were significantly different from those in the other three habitats. Rhodobacteraceae was the main component of microplastic core bacteria, while the main component of core bacteria in water, sediment, and soil were Burkholderiaceae (21.90%), Burkholderiaceae (5.01%), Nitrosomonadaceae (4.61%), respectively. Furthermore, microplastic core bacteria had stronger geographic limitations along the Yangtze River in the Three Gorges Reservoir area. Stronger geographic limitations shaped the rapid community turnover and a potentially more connected network for the microplastic core bacteria than water, sediment, and soil. More importantly, microplastic core bacteria had strong potential functions of drug resistance and could cause risks to ecosystems and human health. Microplastic core bacteria were mainly influenced by sediment core bacteria, although the bacteria colonizing on microplastics could be from all the contact environments and original sources. These findings provide important insights into the composition, function, and association of microplastic core bacteria with their surrounding environment.},
}
@article {pmid35355086,
year = {2023},
author = {Li, S and Peng, H and Shi, X and Gu, Q and Shen, Z and Wang, M},
title = {Significant Effects of Associated Microorganisms on the Community of Photosynthetic Picoeukaryotes.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1164-1178},
pmid = {35355086},
issn = {1432-184X},
support = {31800388//National Natural Science Foundation of China/ ; 32071573//National Natural Science Foundation of China/ ; },
mesh = {*Chlorophyta ; RNA, Ribosomal, 16S/genetics ; *Diatoms ; Photosynthesis ; *Stramenopiles/genetics ; Bacteria/genetics ; },
abstract = {Photosynthetic picoeukaryotes (PPEs) form associations with other microorganisms. However, whether and how the associated microbes affect PPE communities remain unknown. We used flow cytometric cell sorting combined with parallel high-throughput sequencing of the 18S and 16S rRNA genes to simultaneously investigate PPEs and their associated microbial communities in the Yangtze-connected Lake Dongting. The lake harbors a great diversity of PPEs. PPE communities exhibited significant temporal rather than spatial variations. Two distinct PPE taxa affiliated with Discostella nipponica and Poterioochromonas malhamensis were dominant during winter/spring and summer, respectively. Parallel high-throughput sequencing revealed a great diversity of associated bacteria and non-pigmented eukaryotes (NPEs) in PPEs sorts. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria among the associated bacteria and fungi among the associated NPEs were dominant. PPEs were more apparently associated with bacteria than with NPEs. The co-occurrence network of PPEs and associated microbes formed five major modules, which exhibited distinct temporal patterns, being specific to a certain period. Variations in PPEs communities were significantly correlated with both environmental factors and associated microbial communities. In variation partitioning analysis, the associated bacteria explained the greatest variations in PPE communities, and associated bacteria and NPEs co-explained a large portion of environmental effects on PPE communities. Our results highlight the significance of associated microbes in shaping PPE communities.},
}
@article {pmid35353006,
year = {2022},
author = {Emmons, AL and Mundorff, AZ and Hoeland, KM and Davoren, J and Keenan, SW and Carter, DO and Campagna, SR and DeBruyn, JM},
title = {Postmortem Skeletal Microbial Community Composition and Function in Buried Human Remains.},
journal = {mSystems},
volume = {7},
number = {2},
pages = {e0004122},
pmid = {35353006},
issn = {2379-5077},
mesh = {Humans ; *Body Remains ; RNA, Ribosomal, 16S/analysis ; *Microbiota/genetics ; DNA ; Soil ; },
abstract = {Bones and teeth can provide a lasting resource to identify human remains following decomposition. Bone can support dynamic communities of micro- and macroscopic scavengers and incidental taxa, which influence the preservation of bone over time. Previously we identified key microbial taxa associated with survivability of DNA in bones of surface-decomposed human remains, observing high intra- and interindividual variation. Here we characterized the postmortem bone microbiome of skeletal remains in a multi-individual burial to better understand subsurface bone colonization and preservation. To understand microbial community origins and assembly, 16S rRNA amplicon sequences from 256 bone and 27 soil samples were compared to bone from individuals who decomposed on the ground surface, and human gut sequences from the American Gut Project. Untargeted metabolomics was applied to a subset of 41 bone samples from buried remains to examine potential microbe-metabolite interactions and infer differences related to community functionality. Results show that postmortem bone microbial communities are distinct from those of the oxic surface soils and the human gut. Microbial communities from surface-deposited bone and shallow buried bone were more similar to those from soils, while bones recovered from saturated areas deeper in the grave showed increased similarity with human gut samples with higher representation of anaerobic taxa, suggesting that the depositional environment affected the established bone microbiome. Correlations between metabolites and microbes indicate that phosphate solubilization is likely an important mechanism of microbially mediated skeletal degradation. This research expands our knowledge of microbial bone colonizers, including colonizers important in a burial environment. IMPORTANCE Understanding the microbes that colonize and degrade bone has important implications for preservation of skeletal elements and identification of unknown human remains. Current research on the postmortem bone microbiome is limited and largely focuses on archaeological or marine contexts. Our research expands our understanding of bone microbiomes in buried remains by characterizing the taxonomic and metabolic diversity of microbes that are colonizing bone after a 4-year postmortem burial interval and examines the potential impact of microbial colonization on human skeletal DNA preservation. Our results indicate that the postmortem bone microbiome is distinct from the human gut and soil. Evidence from combined metabolomic and amplicon sequencing analysis suggests that Pseudomonas and phosphate solubilization likely play a role in skeletal degradation. This work provides important insight into the types and activities of microbes controlling the preservation of buried skeletal remains.},
}
@article {pmid35352861,
year = {2022},
author = {Rousk, J and C Brangarí, A},
title = {Do the respiration pulses induced by drying-rewetting matter for the soil-atmosphere carbon balance?.},
journal = {Global change biology},
volume = {28},
number = {11},
pages = {3486-3488},
pmid = {35352861},
issn = {1365-2486},
mesh = {Atmosphere ; Carbon ; Climate Change ; *Ecosystem ; Respiration ; *Soil ; Soil Microbiology ; },
abstract = {We show that the explosive microbial and biogeochemical dynamics triggered by rewetting dry soil in laboratory experiments also has relevance in intact ecosystems. This highlights an opportunity to use predictions derived from laboratory studies to provide targets in ecosystem-scale biogeochemical studies.},
}
@article {pmid35352237,
year = {2022},
author = {Vissenaekens, H and Grootaert, C and Raes, K and De Munck, J and Smagghe, G and Boon, N and Van Camp, J},
title = {Quercetin Mitigates Endothelial Activation in a Novel Intestinal-Endothelial-Monocyte/Macrophage Coculture Setup.},
journal = {Inflammation},
volume = {45},
number = {4},
pages = {1600-1611},
pmid = {35352237},
issn = {1573-2576},
support = {1S18417N//FWO-Vlaanderen/ ; },
mesh = {*Atherosclerosis/drug therapy/metabolism ; Cell Adhesion ; Coculture Techniques ; Endothelial Cells/metabolism ; Endothelium, Vascular/metabolism ; Humans ; Intercellular Adhesion Molecule-1/metabolism ; Lipopolysaccharides/metabolism/pharmacology ; Macrophages/metabolism ; Monocytes/metabolism ; *Quercetin/pharmacology ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Atherosclerosis initiation is associated with a pro-inflammatory state of the endothelium. Quercetin is a flavonoid abundantly present in plant-based foods, with a possible impact on cardiovascular health. In this study, the effects of quercetin on lipopolysaccharide (LPS)-mediated endothelial inflammation and monocyte adhesion and migration, which are initial steps of the atherogenic process, are studied. Novel in vitro multicellular models simulating the intestinal-endothelial-monocytes/macrophages axis allowed to combine relevant intestinal flavonoid absorption, metabolism and efflux, and the consequent bioactivity towards peripheral endothelial cells. In this triple coculture, quercetin exposure decreased monocyte adhesion to and macrophage migration through an LPS-stressed endothelium, and this was associated with significantly lower levels of soluble vascular cell adhesion molecule-1 (sVCAM-1). Furthermore, quercetin decreased the pro-inflammatory cell environment upon LPS-induced endothelial activation, in terms of tumor necrosis factor- α (TNF-α), interleukin-6 (IL-6), interleukin-8 (IL-8), and sVCAM-1 expression. These findings highlight a mode-of-action by which quercetin may positively impact the initial states of atherosclerosis under more physiologically relevant conditions in terms of quercetin concentrations, metabolites, and intercellular crosstalk.},
}
@article {pmid35350577,
year = {2022},
author = {Song, H and Xiao, K and Chen, Z and Long, Q},
title = {Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {841112},
pmid = {35350577},
issn = {2296-858X},
abstract = {PURPOSE: To analyze the conjunctival sac microbial communities in patients with Sjögren's syndrome-associated dry eyes (SSDE) and non-Sjögren's syndrome-associated dry eyes (NSSDE), compared with normal controls (NC).<br><br>METHODS: Conjunctival sac swab samples from 23 eyes of SSDE, 36 eyes of NSSDE, and 39 eyes of NC were collected. The V3-V4 region of the 16S ribosomal RNA (rRNA) gene high-throughput sequencing was performed on an Illumina MiSeq platform and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Alpha diversity was employed to analyze microbiome diversity through Chao1 and Shannon indexes. Beta diversity was demonstrated by the principal coordinates analysis (PCoA) and Partial Least Squares Discrimination Analysis (PLS-DA). The relative abundance was bioinformatically analyzed at the phylum and genus levels.<br><br>RESULTS: The alpha diversity was lower in patients with dry eye disease (Shannon index: NC vs. SSDE: P = 0.020, NC vs. NSSDE: P = 0.029). The beta diversity showed divergent microbiome composition in different groups (NC vs. SSDE: P = 0.001, NC vs. NSSDE: P = 0.001, NSSDE vs. SSDE: P = 0.005). The top 5 abundant phyla were Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Cyanobacteria in all three groups. The top five abundant genera included Acinetobacter, Staphylococcus, Bacillus, Corynebacterium, and Clostridium_sensu_stricto_1. The relative microbiome abundance was different between groups. The Firmicutes/Bacteroidetes (F/B) ratio was 6.42, 7.31, and 9.71 in the NC, NSSDE, and SSDE groups, respectively (NC vs. SSDE: P = 0.038, NC vs. NSSDE: P = 0.991, SSDE vs. NSSDE: P = 0.048).<br><br>CONCLUSION: The diversity of conjunctival sac microbiome in patients with NSSDE and SSDE was diminished compared with NC. The main microbiome at the phylum and genus level were similar between groups, but the relative abundance had variations. The Firmicutes/Bacteroidetes ratio was higher in the SSDE group.},
}
@article {pmid35348389,
year = {2022},
author = {Jiménez, RR and Carfagno, A and Linhoff, L and Gratwicke, B and Woodhams, DC and Chafran, LS and Bletz, MC and Bishop, B and Muletz-Wolz, CR},
title = {Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {8},
pages = {e0181821},
pmid = {35348389},
issn = {1098-5336},
mesh = {Animals ; Bacteria/genetics ; *Chytridiomycota/genetics ; *Mycoses/microbiology/veterinary ; RNA, Ribosomal, 16S/genetics ; Urodela/microbiology ; },
abstract = {Mucosal defenses are crucial in animals for protection against pathogens and predators. Host defense peptides (antimicrobial peptides, AMPs) as well as skin-associated microbes are key components of mucosal immunity, particularly in amphibians. We integrate microbiology, molecular biology, network-thinking, and proteomics to understand how host and microbially derived products on amphibian skin (referred to as the mucosome) serve as pathogen defenses. We studied defense mechanisms against chytrid pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), in four salamander species with different Batrachochytrium susceptibilities. Bd infection was quantified using qPCR, mucosome function (i.e., ability to kill Bd or Bsal zoospores in vitro), skin bacterial communities using 16S rRNA gene amplicon sequencing, and the role of Bd-inhibitory bacteria in microbial networks across all species. We explored the presence of candidate-AMPs in eastern newts and red-backed salamanders. Eastern newts had the highest Bd prevalence and mucosome function, while red-back salamanders had the lowest Bd prevalence and mucosome function, and two-lined salamanders and seal salamanders were intermediates. Salamanders with highest Bd infection intensity showed greater mucosome function. Bd infection prevalence significantly decreased as putative Bd-inhibitory bacterial richness and relative abundance increased on hosts. In co-occurrence networks, some putative Bd-inhibitory bacteria were found as hub-taxa, with red-backs having the highest proportion of protective hubs and positive associations related to putative Bd-inhibitory hub bacteria. We found more AMP candidates on salamanders with lower Bd susceptibility. These findings suggest that salamanders possess distinct innate mechanisms that affect chytrid fungi. IMPORTANCE How host mucosal defenses interact, and influence disease outcome is critical in understanding host defenses against pathogens. A more detailed understanding is needed of the interactions between the host and the functioning of its mucosal defenses in pathogen defense. This study investigates the variability of chytrid susceptibility in salamanders and the innate defenses each species possesses to mediate pathogens, thus advancing the knowledge toward a deeper understanding of the microbial ecology of skin-associated bacteria and contributing to the development of bioaugmentation strategies to mediate pathogen infection and disease. This study improves the understanding of complex immune defense mechanisms in salamanders and highlights the potential role of the mucosome to reduce the probability of Bd disease development and that putative protective bacteria may reduce likelihood of Bd infecting skin.},
}
@article {pmid35347426,
year = {2022},
author = {Dyczko, D and Kiewra, D and Kolanek, A and Błażej, P},
title = {The influence of local environmental factors in southwestern Poland on the abundance of Ixodes ricinus and prevalence of infection with Borrelia burgdorferi s.l. and B. miyamotoi.},
journal = {Parasitology research},
volume = {121},
number = {6},
pages = {1575-1585},
pmid = {35347426},
issn = {1432-1955},
mesh = {Animals ; *Borrelia/genetics ; *Borrelia burgdorferi/genetics ; Female ; *Ixodes/microbiology ; *Lyme Disease/epidemiology/microbiology ; Male ; Poland/epidemiology ; Prevalence ; },
abstract = {Ticks are important ectoparasites and vectors of pathogens that cause disease in humans and animals. The natural habitat of Ixodes ricinus ticks is forests, which are convenient habitats to search for hosts, including reservoir hosts, and therefore can be an important habitat source of tick-borne pathogens. The aim of the study was to assess the usefulness of detailed forest habitat-type maps to estimate the tick-borne risk at a local scale (Lower Silesia, SW Poland). For the purposes of estimating tick abundance, we used the land cover maps available from the Forest Data Bank. For I. ricinus collection, nine sites located in three forest habitat types were chosen: broadleaf forest, mixed broadleaf and coniferous forest and coniferous forest. Ticks were collected once a month from April to June 2018 and 2019 using the standard flagging method. At each of the nine sites, ticks were collected in four plots, of 100 m[2] each. Tick abundance was analysed using general linear mixed models (GLMM). A total of 2196 (10.1/100 m[2]) ticks were collected, including 2093 Ixodes ricinus (95.3%; 9.6/100 m[2]), 46 Dermacentor reticulatus (2.1%; 0.2/100 m[2]) and 57 Haemaphysalis concinna (2.6%; 0.3/100 m[2]). Among the collected I. ricinus were 589 larvae (28.1%; 2.7/100 m[2]), 1261 nymphs (60.3%; 5.8/100 m[2]), 128 females (6.1%; 0.6/100 m[2]) and 115 males (5.5%; 0.5/100 m[2]). We found a highly significant effect of forest habitat type on the density of ticks for broadleaf forest (coefficient = 1.87267, p-value = 2.79e - 07). Additionally, a significant influence of air temperature and relative humidity on the abundance of ticks was observed. During spring, the peak activity of I. ricinus was recorded in May and June. For DNA amplification of Borrelia burgdorferi s.l., a nested PCR method was used. Out of 494 I. ricinus, 83 (16.8%) were positive for Borrelia spp. The RFLP method showed the occurrence of five species including four belonging to the B. burgdorferi s.l. complex: B. afzelii (30.1%), B. garinii (38.6%), B. valaisiana (2.4%) and B. lusitaniae (18.1%). Furthermore, B. miyamotoi (9.6%), a species belonging to bacteria that cause relapsing fever as well as co-infection of B. miyamotoi/B.lusitaniae (1.2%) were found. The differences in the infection level of Borrelia spp. between broadleaf forest and mixed broadleaf and coniferous forest were statistically significant.},
}
@article {pmid35347370,
year = {2023},
author = {Vipindas, PV and Venkatachalam, S and Jabir, T and Yang, EJ and Cho, KH and Jung, J and Lee, Y and Krishnan, KP},
title = {Water Mass Controlled Vertical Stratification of Bacterial and Archaeal Communities in the Western Arctic Ocean During Summer Sea-Ice Melting.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1150-1163},
pmid = {35347370},
issn = {1432-184X},
mesh = {*Archaea/genetics ; *Water ; Bacteria/genetics ; Seawater/microbiology ; Chlorophyll ; Oceans and Seas ; Arctic Regions ; },
abstract = {The environmental variations and their interactions with the biosphere are vital in the Arctic Ocean during the summer sea-ice melting period in the current scenario of climate change. Hence, we analysed the vertical distribution of bacterial and archaeal communities in the western Arctic Ocean from sea surface melt-ponds to deep water up to a 3040 m depth. The distribution of microbial communities showed a clear stratification with significant differences among different water depths, and the water masses in the Arctic Ocean - surface mixed layer, Atlantic water mass and deep Arctic water - appeared as a major factor explaining their distribution in the water column. A total of 34 bacterial phyla were detected in the seawater and 10 bacterial phyla in melt-ponds. Proteobacteria was the dominant phyla in the seawater irrespective of depth, whereas Bacteroidota was the dominant phyla in the melt-ponds. A fast expectation-maximization microbial source tracking analysis revealed that only limited dispersion of the bacterial community was possible across the stratified water column. The surface water mass contributed 21% of the microbial community to the deep chlorophyll maximum (DCM), while the DCM waters contributed only 3% of the microbial communities to the deeper water masses. Atlantic water mass contributed 37% to the microbial community of the deep Arctic water. Oligotrophic heterotrophic bacteria were dominant in the melt-ponds and surface waters, whereas chemoautotrophic and mixotrophic bacterial and archaeal communities were abundant in deeper waters. Chlorophyll and ammonium were the major environmental factors that determined the surface microbial communities, whereas inorganic nutrient concentrations controlled the deep-water communities.},
}
@article {pmid35347228,
year = {2022},
author = {Zoccarato, L and Sher, D and Miki, T and Segrè, D and Grossart, HP},
title = {A comparative whole-genome approach identifies bacterial traits for marine microbial interactions.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {276},
pmid = {35347228},
issn = {2399-3642},
support = {RGB 0020/2016//Human Frontier Science Program (HFSP)/ ; },
mesh = {*Bacteria/metabolism ; Ecology ; Microbial Interactions ; *Microbiota/genetics ; Phytoplankton/genetics ; },
abstract = {Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.},
}
@article {pmid35346496,
year = {2022},
author = {Dittoe, DK and Olson, EG and Ricke, SC},
title = {Impact of the gastrointestinal microbiome and fermentation metabolites on broiler performance.},
journal = {Poultry science},
volume = {101},
number = {5},
pages = {101786},
pmid = {35346496},
issn = {1525-3171},
mesh = {Animal Feed/analysis ; Animals ; Chickens ; Diet/veterinary ; Fermentation ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism ; *Microbiota ; },
abstract = {Optimal broiler performance is dependent on several factors such as bird genetics, environment management, and nutrition. The gastrointestinal tract microbial ecology and metabolic activities have long been considered factors contributing to broiler performance responses. However, until recently, it was difficult to define the impact of the gastrointestinal microorganisms on the broiler host. With advances in microbiome sequencing technology, there has been a rapid increase in data generated using both experimental and commercial broiler operations. As the gastrointestinal microbiome data becomes more in-depth, opportunities to link microbiota composition to broiler performance metrics such as broiler growth rate and feed conversion efficiency have emerged. In parallel, with the increased understanding of the microbiota, there has been a shift to modulate the microbiome in order to alter metabolic patterns such as fermentation products. In this review, fermentation pathways and metabolites and the relationship with the microbiome will be discussed. Additionally, this review will connect these patterns and interpretations with current broiler performance data and the potential future directions these relationships could take the broiler industry.},
}
@article {pmid35346495,
year = {2022},
author = {Ricke, SC and Dittoe, DK and Olson, EG},
title = {Microbiome applications for laying hen performance and egg production.},
journal = {Poultry science},
volume = {101},
number = {5},
pages = {101784},
pmid = {35346495},
issn = {1525-3171},
mesh = {Animals ; *Chickens ; Female ; Housing, Animal ; *Microbiota ; Reproduction ; },
abstract = {Management of laying hens has undergone considerable changes in the commercial egg industry. Shifting commercial production from cage-based systems to cage-free has impacted the housing environment and created issues not previously encountered. Sources of microorganisms that become established in the early stages of layer chick development may originate from the hen and depend on the microbial ecology of the reproductive tract. Development of the layer hen GIT microbiota appears to occur in stages as the bird matures. Several factors can impact the development of the layer hen GIT, including pathogens, environment, and feed additives such as antibiotics. In this review, the current status of the laying hen GIT microbial consortia and factors that impact the development and function of these respective microbial populations will be discussed, as well as future research directions.},
}
@article {pmid35346494,
year = {2022},
author = {Olson, EG and Dittoe, DK and Jendza, JA and Stock, DA and Ricke, SC},
title = {Application of microbial analyses to feeds and potential implications for poultry nutrition.},
journal = {Poultry science},
volume = {101},
number = {5},
pages = {101789},
pmid = {35346494},
issn = {1525-3171},
mesh = {Animal Feed/analysis ; Animals ; Chickens ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; *Microbiota ; Poultry ; },
abstract = {Poultry nutrition and feed manufacturing are interrelated for a variety of reasons. Diet formulation is essential for optimizing bird growth and feed conversion, but compositional differences and the presence of certain feed additives can alter the gastrointestinal microbial composition and functionality. Not only does dietary composition and digestibility influence poultry performance, but specific physical characteristics such as feed particle size and thermal treatments can impact the avian gastrointestinal tract (GIT) microbiota. Poultry feeds also have a characteristic microbial ecology consisting of pathogenic and nonpathogenic microorganisms. Some feed-borne pathogens such as Salmonella are well studied and linked with the colonization of birds consuming the feed. However, much less is known about the nonpathogenic feed microbiome and what impact that might have on the bird's GIT. This review discusses the potential interaction between poultry feed and the GIT microbiome, microbial ecology of feed, application of microbiome analyses to feed, and approaches for communicating these complex data sets to the poultry industry.},
}
@article {pmid35346493,
year = {2022},
author = {Ricke, SC and Dittoe, DK and Brown, JA and Thompson, DR},
title = {Practical opportunities for microbiome analyses and bioinformatics in poultry processing.},
journal = {Poultry science},
volume = {101},
number = {5},
pages = {101787},
pmid = {35346493},
issn = {1525-3171},
mesh = {Animals ; Chickens/genetics/microbiology ; Computational Biology ; Food Microbiology ; *Microbiota ; *Poultry/microbiology ; },
abstract = {Poultry processing is undergoing changes both in operations as well as microbial methodologies. Traditionally, microbial data has been gathered through a series of culturing methods using liquid media and plating for isolation and enumeration. Both foodborne pathogens and nonpathogenic bacterial populations are estimated to assess food safety risks as well as the potential for spoilage. Bacterial loads from carcasses are important for estimating processing control and the effectiveness of antimicrobial applications. However, these culture-based approaches may only provide part of the microbial ecology landscape associated with chicken carcasses and the subsequent changes that occur in these populations during processing. Newer molecular-based approaches, such as 16S sequencing of the microbiota, offer a means to retrieve a more comprehensive microbial compositional profile. However, such approaches also result in large data sets which must be analyzed and interpreted. As more data is generated, this will require not only bioinformatic programs to process the data but appropriate educational forums to present the processed data to a broad audience.},
}
@article {pmid35343797,
year = {2022},
author = {Busby, TJ and Miller, CR and Moran, NA and Van Leuven, JT},
title = {Global Composition of the Bacteriophage Community in Honey Bees.},
journal = {mSystems},
volume = {7},
number = {2},
pages = {e0119521},
pmid = {35343797},
issn = {2379-5077},
support = {P20 GM104420/GM/NIGMS NIH HHS/United States ; },
mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics ; Bacteria/genetics ; *Microbiota ; Plants ; },
abstract = {The microbial communities in animal digestive systems are critical for host development and health. They stimulate the immune system during development, synthesize important chemical compounds like hormones, aid in digestion, competitively exclude pathogens, etc. Compared to the bacterial and fungal components of the microbiome, we know little about the temporal and spatial dynamics of bacteriophage communities in animal digestive systems. Recently, the bacteriophages of the honey bee gut were characterized in two European bee populations. Most of the bacteriophages described in these two reports were novel, harbored many metabolic genes in their genomes, and had a community structure that suggests coevolution with their bacterial hosts. To describe the conservation of bacteriophages in bees and begin to understand their role in the bee microbiome, we sequenced the virome of Apis mellifera from Austin, TX, and compared bacteriophage compositions among three locations around the world. We found that most bacteriophages from Austin are novel, sharing no sequence similarity with anything in public repositories. However, many bacteriophages are shared among the three bee viromes, indicating specialization of bacteriophages in the bee gut. Our study, along with the two previous bee virome studies, shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacteriophages that primarily infect four of the dominant bacterial phylotypes in the bee gut. IMPORTANCE Viruses that infect bacteria (bacteriophages) are abundant in the microbial communities that live on and in plants and animals. However, our knowledge of the structure, dynamics, and function of these viral communities lags far behind our knowledge of their bacterial hosts. We sequenced the first bacteriophage community of honey bees from the United States and compared the U.S. honey bee bacteriophage community to those of samples from Europe. Our work is an important characterization of an economically critical insect species and shows how bacteriophage communities can contain highly conserved individuals and be highly variable in composition across a wide geographic range.},
}
@article {pmid35343791,
year = {2022},
author = {Zhu, YX and Chang, YW and Wen, T and Yang, R and Wang, YC and Wang, XY and Lu, MX and Du, YZ},
title = {Species Identity Dominates over Environment in Driving Bacterial Community Assembly in Wild Invasive Leaf Miners.},
journal = {Microbiology spectrum},
volume = {10},
number = {2},
pages = {e0026622},
pmid = {35343791},
issn = {2165-0497},
mesh = {Animals ; *Bacteria/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; },
abstract = {The microbiota of invasive animal species may be pivotal to their adaptation and spread, yet the processes driving the assembly and potential sources of host-microbiota remain poorly understood. Here, we characterized microbiota of four Liriomyza leaf miner fly species totaling 310 individuals across 43 geographical populations in China and assessed whether the microbiota of the wild leaf miner was acquired from the soil microbiota or the host plant microbiota, using high-throughput 16S rRNA sequencing. Bacterial communities differed significantly among four leaf miner species but did not mirror host phylogeny. Microbiota diversity in the native L. chinensis was significantly higher than in three invasive leaf miners (i.e., L. trifolii, L. huidobrensis, and L. sativae), yet the microbial community of the invasive species exhibited a more connected and complex network structure. Structural equation models revealed that host species identity was more important than environmental factors (e.g., geography, climate, or plants) in shaping microbiota composition. Using neutral and null model analyses, we found that deterministic processes like variable selection played a primary role in driving microbial community assembly, with some influence by stochastic processes like drift. The relative degree of these processes governing microbiota was likely correlated with host species but independent of either geographical or climatic factors. Finally, source tracking analysis showed that leaf miners might acquire microbes from their host plant rather than the soil. Our results provide a robust assessment of the ecological processes governing bacterial community assembly and potential sources of microbes in invasive leaf miners. IMPORTANCE The invasion of foreign species, including leaf miners, is a major threat to world biota. Host-associated microbiota may facilitate host adaption and expansion in a variety of ways. Thus, understanding the processes that drive leaf miner microbiota assembly is imperative for better management of invasive species. However, how microbial communities assemble during the leaf miner invasions and how predictable the processes remain unexplored. This work quantitatively deciphers the relative importance of deterministic process and stochastic process in governing the assembly of four leaf miner microbiotas and identifies potential sources of leaf miner-colonizing microbes from the soil-plant-leaf miner continuum. Our study provides new insights into the mechanisms underlying the drive of leaf miner microbiota assembly.},
}
@article {pmid35340445,
year = {2022},
author = {Parks, ST and Taylor, C},
title = {Development of a Remote, Course-Based Undergraduate Experience to Facilitate In Silico Study of Microbial Metabolic Pathways.},
journal = {Journal of microbiology &amp; biology education},
volume = {23},
number = {1},
pages = {},
pmid = {35340445},
issn = {1935-7877},
abstract = {Course-based undergraduate research experiences (CUREs) often occur in a physical lab space, but they can also be offered remotely while maintaining course expectations and providing opportunity for authentic student engagement in research. Using a novel framework, remote Microbial Ecology CURE students used microbes isolated via antimicrobial-challenged Winogradsky columns to investigate phylogeny and metabolism through a hypothesis-driven meta-analysis (MA). Students used 16S rRNA and key metabolic enzymes to compare phylogeny; enzymes were modeled and evaluated for putative conserved domains, culminating in primer design and analysis. Using in silico tools facilitated student development of bioinformatics skills. The MA was subdivided into discrete sections in order to (i) provide a timeline for students to remain on schedule throughout a remote-learning lab experience, (ii) encourage feedback throughout the project, and (iii) facilitate student understanding of the experimental design. MA deliverables were designed to be specific figures with individual titles, legends, and analyses to enable their feedback for subsequent presentations. The six key formative deliverables included a word cloud (used to develop the works cited list and hypothesis), a 16S rRNA phylogenetic tree, an annotated metabolic pathway and three-dimensional model of the key metabolic enzyme, a phylogenetic tree based on the key metabolic enzyme, design and analysis of a primer set for the key metabolic enzyme, and a summative poster and graphical abstract. The MA project yielded poster presentations at virtual conferences, lab presentations, and written reports. Using the hypothesis-based MA model encouraged an authentic research experience, enabling students to develop, discuss, and progress in meaningful experiments.},
}
@article {pmid35338380,
year = {2023},
author = {Yuan, B and Guo, M and Wu, W and Zhou, X and Li, M and Xie, S},
title = {Spatial and Seasonal Patterns of Sediment Bacterial Communities in Large River Cascade Reservoirs: Drivers, Assembly Processes, and Co-occurrence Relationship.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {586-603},
pmid = {35338380},
issn = {1432-184X},
support = {91747206//national natural science foundation of china/ ; 42107493//National Natural Science Foundation of China/ ; },
mesh = {*Rivers/microbiology ; *Ecosystem ; Seasons ; Bacteria ; Fresh Water ; China ; },
abstract = {Sediment bacteria play an irreplaceable role in promoting the function and biogeochemical cycle of the freshwater ecosystem; however, little is known about their biogeographical patterns and community assembly mechanisms in large river suffering from cascade development. Here, we investigated the spatiotemporal distribution patterns of bacterial communities employing next-generation sequencing analysis and multivariate statistical analyses from the Lancang River cascade reservoirs during summer and winter. We found that sediment bacterial composition has a significant seasonal turnover due to the modification of cascade reservoirs operation mode, and the spatial consistency of biogeographical models (including distance-decay relationship and covariation of community composition with geographical distance) also has subtle changes. The linear regression between the dissimilarity of bacterial communities in sediments, geographical and environmental distance showed that the synergistic effects of geographical and environmental factors explained the influence on bacterial communities. Furthermore, the environmental difference explained little variations (19.40%) in community structure, implying the homogeneity of environmental conditions across the cascade reservoirs of Lancang River. From the quantification of the ecological process, the homogeneous selection was recognized as the dominating factor of bacterial community assembly. The co-occurrence topological network analyses showed that the key genera were more important than the most connected genera. In general, the assembly of bacterial communities in sediment of cascade reservoirs was mediated by both deterministic and stochastic processes and is always dominated by homogeneous selection with the seasonal switching, but the effects of dispersal limitation and ecological drift cannot be ignored.},
}
@article {pmid35337832,
year = {2022},
author = {Venturini, AM and Dias, NMS and Gontijo, JB and Yoshiura, CA and Paula, FS and Meyer, KM and Nakamura, FM and da França, AG and Borges, CD and Barlow, J and Berenguer, E and Nüsslein, K and Rodrigues, JLM and Bohannan, BJM and Tsai, SM},
title = {Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon.},
journal = {Environmental research},
volume = {212},
number = {Pt A},
pages = {113139},
doi = {10.1016/j.envres.2022.113139},
pmid = {35337832},
issn = {1096-0953},
mesh = {Climate ; Forests ; *Methane/analysis ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.},
}
@article {pmid35335680,
year = {2022},
author = {Morris, CE and Ramirez, N and Berge, O and Lacroix, C and Monteil, C and Chandeysson, C and Guilbaud, C and Blischke, A and Sigurbjörnsdóttir, MA and Vilhelmsson, O&#xde;},
title = {Pseudomonas syringae on Plants in Iceland Has Likely Evolved for Several Million Years Outside the Reach of Processes That Mix This Bacterial Complex across Earth's Temperate Zones.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
pmid = {35335680},
issn = {2076-0817},
abstract = {Here we report, for the first time, the occurrence of the bacteria from the species complex Pseudomonas syringae in Iceland. We isolated this bacterium from 35 of the 38 samples of angiosperms, moss, ferns and leaf litter collected across the island from five habitat categories (boreal heath, forest, subalpine and glacial scrub, grazed pasture, lava field). The culturable populations of P. syringae on these plants varied in size across 6 orders of magnitude, were as dense as 10[7] cfu g[-1] and were composed of strains in phylogroups 1, 2, 4, 6, 7, 10 and 13. P. syringae densities were significantly greatest on monocots compared to those on dicots and mosses and were about two orders of magnitude greater in grazed pastures compared to all other habitats. The phylogenetic diversity of 609 strains of P. syringae from Iceland was compared to that of 933 reference strains of P. syringae from crops and environmental reservoirs collected from 27 other countries based on a 343 bp sequence of the citrate synthase (cts) housekeeping gene. Whereas there were examples of identical cts sequences across multiple countries and continents among the reference strains indicating mixing among these countries and continents, the Icelandic strains grouped into monophyletic lineages that were unique compared to all of the reference strains. Based on estimates of the time of divergence of the Icelandic genetic lineages of P. syringae, the geological, botanical and land use history of Iceland, and atmospheric circulation patterns, we propose scenarios whereby it would be feasible for P. syringae to have evolved outside the reach of processes that tend to mix this bacterial complex across the planet elsewhere.},
}
@article {pmid35335670,
year = {2022},
author = {Chitlapilly Dass, S and Wang, R},
title = {Biofilm through the Looking Glass: A Microbial Food Safety Perspective.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
pmid = {35335670},
issn = {2076-0817},
support = {USDA-NIFA 2020-67017-30776.//United States Department of Agriculture/ ; },
abstract = {Food-processing facilities harbor a wide diversity of microorganisms that persist and interact in multispecies biofilms, which could provide an ecological niche for pathogens to better colonize and gain tolerance against sanitization. Biofilm formation by foodborne pathogens is a serious threat to food safety and public health. Biofilms are formed in an environment through synergistic interactions within the microbial community through mutual adaptive response to their long-term coexistence. Mixed-species biofilms are more tolerant to sanitizers than single-species biofilms or their planktonic equivalents. Hence, there is a need to explore how multispecies biofilms help in protecting the foodborne pathogen from common sanitizers and disseminate biofilm cells from hotspots and contaminate food products. This knowledge will help in designing microbial interventions to mitigate foodborne pathogens in the processing environment. As the global need for safe, high-quality, and nutritious food increases, it is vital to study foodborne pathogen behavior and engineer new interventions that safeguard food from contamination with pathogens. This review focuses on the potential food safety issues associated with biofilms in the food-processing environment.},
}
@article {pmid35333990,
year = {2022},
author = {Sugiyama, N and Uehara, O and Morikawa, T and Paudel, D and Ebata, K and Hiraki, D and Harada, F and Yoshida, K and Kato, S and Nagasawa, T and Miura, H and Abiko, Y and Furuichi, Y},
title = {Gut flora alterations due to lipopolysaccharide derived from Porphyromonas gingivalis.},
journal = {Odontology},
volume = {110},
number = {4},
pages = {673-681},
pmid = {35333990},
issn = {1618-1255},
support = {20H03867//Grant-in-Aid for Scientific Research (B)/ ; },
mesh = {Animals ; Dysbiosis ; *Gastrointestinal Microbiome ; Interleukin-6 ; Lipopolysaccharides/pharmacology ; Mice ; Mice, Inbred C57BL ; *Porphyromonas gingivalis ; RNA, Ribosomal, 16S ; Tumor Necrosis Factor-alpha ; },
abstract = {Gut dysbiosis induces 'leaky gut,' a condition associated with diabetes, NASH, and various auto-immune diseases. Porphyromonas gingivalis is a periodontopathic bacterium which causes periodontal tissue breakdown, and often enters the systemic blood flow. Oral administration of P. gingivalis induced gut dysbiosis in mice model, but no systemic administration of P. gingivalis has been reported thus far. In the present study, we investigated the effect of P. gingivalis-derived lipopolysaccharide (Pg-LPS) on the intestinal flora of our established mouse model. Eight-week-old C57BL/6J mice were intraperitoneally administered Pg-LPS. Three months later, DNA was extracted from stool, and RNA from the small and large intestines. After euthanizing the mice, pathological sections of the intestinal tract were prepared and stained with hematoxylin and eosin (H&amp;E). Tumor necrosis factor alpha (TNF-α), interleukin (IL)-1β, and IL-6 expression levels were evaluated using quantitative PCR. 16S rRNA gene PCR amplicon analysis data were acquired using NGS. Microbial diversity and composition were analyzed using Quantitative Insights into Microbial Ecology 2. Furthermore, alterations in microbial function were performed by PICRUSt2. No significant inflammatory changes were observed in the H&amp;E. No significant differences in the mRNA levels of IL-1β, IL-6, and TNF-α were observed between the groups. Pg-LPS administration decreased the abundance of Allobacterium in the gut. A predictive metagenomic analysis by PICRUSt2 and STAMP showed that 47 pathways increased and 17 pathways decreased after Pg-LPS administration. Systemic application of periodontal pathogens may cause changes in the intestinal flora which may affect the physiological functions of the intestinal tract.},
}
@article {pmid35333950,
year = {2023},
author = {Angra, V and Sehgal, R and Gupta, R},
title = {Trends in PHA Production by Microbially Diverse and Functionally Distinct Communities.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {572-585},
pmid = {35333950},
issn = {1432-184X},
support = {09/237(0168)/2018-EMR-I//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/ ; },
mesh = {Biopolymers ; *Polyhydroxyalkanoates ; Plastics ; Plants ; *Petroleum ; },
abstract = {Along with the wide applications of conventional plastics, they have a large number of disadvantages like their non-biodegradable nature, dependency on fossil fuels and the release of large amounts of toxic materials in the environment. Therefore, to resolve these problems, a number of bioplastics are studied, out of which polyhydroxyalkanoates are considered as the best alternatives. Polyhydroxyalkanoates (PHAs) are produced by microorganisms as intracellular granules during stressful conditions. Though a wide range of organisms can naturally produce PHAs, only a few of them can be used for commercial production. Therefore, more diverse organisms that accumulate a considerable amount of PHAs and also reduce the production cost need to be exploited. Transgenic plants, recombinant bacteria, algae and extremophiles are some diverse organisms that produce a high amount of PHAs at a low cost. So, if potential organisms are used for PHA production, bioplastics will be able to completely replace petroleum-based polymers. Therefore, our review mainly focuses on production of PHAs using potential organisms so that amount of PHAs produced is high and cost-effective which would further help in the commercialization of PHAs.},
}
@article {pmid35332832,
year = {2022},
author = {Crits-Christoph, A and Hallowell, HA and Koutouvalis, K and Suez, J},
title = {Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2055944},
pmid = {35332832},
issn = {1949-0984},
support = {DP5 OD029603/OD/NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota/genetics ; },
abstract = {A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.},
}
@article {pmid35332366,
year = {2023},
author = {Xiang, X and Wang, H and Man, B and Xu, Y and Gong, L and Tian, W and Yang, H},
title = {Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {557-571},
pmid = {35332366},
issn = {1432-184X},
support = {41572325//National Natural Science Foundation of China/ ; CUGQY1922//Fundamental Research Funds for the Central Universities, China University of Geosciences (Wuhan)/ ; 2021F10//Open Research Fund of Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, China/ ; },
mesh = {*Archaea ; *Ecosystem ; Geologic Sediments/chemistry ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Soil ; China ; DNA, Archaeal/genetics ; Phylogeny ; },
abstract = {Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 10[5] to 10[7] copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.},
}
@article {pmid35331758,
year = {2022},
author = {Fang, W and Lin, M and Shi, J and Liang, Z and Tu, X and He, Z and Qiu, R and Wang, S},
title = {Organic carbon and eukaryotic predation synergistically change resistance and resilience of aquatic microbial communities.},
journal = {The Science of the total environment},
volume = {830},
number = {},
pages = {154386},
doi = {10.1016/j.scitotenv.2022.154386},
pmid = {35331758},
issn = {1879-1026},
mesh = {Animals ; *Carbon ; Eukaryota ; *Microbiota ; Predatory Behavior ; Rivers ; Water ; },
abstract = {With rapid global urbanization, anthropogenic activities alter aquatic biota in urban rivers through inputs of dissolved organic carbon (DOC) and nutrients. Microorganisms-mediated global element cycles provide functions in maintaining microbial ecology stability. The DOC (bottom-up control) and microbial predation (top-down control) may synergistically drive the competition and evolution of aquatic microbial communities, as well as their resistance and resilience, for which experimental evidences remain scarce. In this study, laboratory sediment-water column experiments were employed to mimic the organic carbon-driven water blackening and odorization process in urban rivers and to elucidate the impact of DOC on microbial ecology stability. Results showed that low (25-75 mg/L) and high DOC (100-150 mg/L) changed the aquatic microbial community assemblies in different patterns: (1) the low DOC enriched K-selection microorganisms (e.g., C39, Tolumonas and CR08G) with low biomass and low resilience, as well as high resistance to perturbations in changing microbial community assemblies; (2) the high DOC was associated with r-selection microorganisms (e.g., PSB-M-3 and Clostridium) with high biomass and improved resilience, together with low resistance detrimental to microbial ecology stability. Overall, this study provided new insight into the impact of DOC on aquatic microbial community stability, which may help guide sustainable urban river management.},
}
@article {pmid35330304,
year = {2022},
author = {Fatemi, S and Haelewaters, D and Urbina, H and Brown, S and Houston, ML and Aime, MC},
title = {Sporobolomyces lactucae sp. nov. (Pucciniomycotina, Microbotryomycetes, Sporidiobolales): An Abundant Component of Romaine Lettuce Phylloplanes.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {3},
pages = {},
pmid = {35330304},
issn = {2309-608X},
support = {8072-42000-077-00D//Agricultural Research Service/ ; 1010662//National Institute of Food and Agriculture/ ; },
abstract = {Shifts in food microbiomes may impact the establishment of human pathogens, such as virulent lineages of Escherichia coli, and thus are important to investigate. Foods that are often consumed raw, such as lettuce, are particularly susceptible to such outbreaks. We have previously found that an undescribed Sporobolomyces yeast is an abundant component of the mycobiome of commercial romaine lettuce (Lactuca sativa). Here, we formally describe this species as Sporobolomyces lactucae sp. nov. (Pucciniomycotina, Microbotryomycetes, and Sporidiobolales). We isolated multiple strains of this yeast from commercial romaine lettuce purchased from supermarkets in Illinois and Indiana; additional isolates were obtained from various plant phylloplanes in California. S. lactucae is a red-pigmented species that is similar in appearance to other members of the genus Sporobolomyces. However, it can be differentiated by its ability to assimilate glucuronate and D-glucosamine. Gene genealogical concordance supports S. lactucae as a new species. The phylogenetic reconstruction of a four-locus dataset, comprising the internal transcribed spacer and large ribosomal subunit D1/D2 domain of the ribosomal RNA gene, translation elongation factor 1-α, and cytochrome B, places S. lactucae as a sister to the S. roseus clade. Sporobolomyces lactucae is one of the most common fungi in the lettuce microbiome.},
}
@article {pmid35322937,
year = {2022},
author = {Timmis, K and Ramos, JL and Verstraete, W},
title = {Microbial biotechnology to assure national security of supplies of essential resources: energy, food and water, medical reagents, waste disposal and a circular economy.},
journal = {Microbial biotechnology},
volume = {15},
number = {4},
pages = {1021-1025},
pmid = {35322937},
issn = {1751-7915},
mesh = {Biotechnology ; Food ; Indicators and Reagents ; *Refuse Disposal ; Security Measures ; *Waste Management ; Wastewater ; Water ; },
abstract = {The core responsibility of governments is the security of their citizens, and this means inter alia protecting their safety, nutrition and health. Microbiology and microbial biotechnology have key roles to play in improving supply security of essential resources. In this paper, we discuss the urgent need to fully and immediately exploit existing microbial biotechnologies to maximize supply security of energy, food and medical supplies, and of waste management, and to invest in new research specifically targetting supply security of essential resources.},
}
@article {pmid35320603,
year = {2022},
author = {Kohler, TJ and Fodelianakis, S and Michoud, G and Ezzat, L and Bourquin, M and Peter, H and Busi, SB and Pramateftaki, P and Deluigi, N and Styllas, M and Tolosano, M and de Staercke, V and Schön, M and Brandani, J and Marasco, R and Daffonchio, D and Wilmes, P and Battin, TJ},
title = {Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.},
journal = {Global change biology},
volume = {28},
number = {12},
pages = {3846-3859},
pmid = {35320603},
issn = {1365-2486},
mesh = {Bacteria/genetics ; Climate Change ; Ecosystem ; *Ice Cover/microbiology ; *Microbiota ; Phylogeny ; Water ; },
abstract = {The shrinking of glaciers is among the most iconic consequences of climate change. Despite this, the downstream consequences for ecosystem processes and related microbiome structure and function remain poorly understood. Here, using a space-for-time substitution approach across 101 glacier-fed streams (GFSs) from six major regions worldwide, we investigated how glacier shrinkage is likely to impact the organic matter (OM) decomposition rates of benthic biofilms. To do this, we measured the activities of five common extracellular enzymes and estimated decomposition rates by using enzyme allocation equations based on stoichiometry. We found decomposition rates to average 0.0129 (% d[-1]), and that decreases in glacier influence (estimated by percent glacier catchment coverage, turbidity, and a glacier index) accelerates decomposition rates. To explore mechanisms behind these relationships, we further compared decomposition rates with biofilm and stream water characteristics. We found that chlorophyll-a, temperature, and stream water N:P together explained 61% of the variability in decomposition. Algal biomass, which is also increasing with glacier shrinkage, showed a particularly strong relationship with decomposition, likely indicating their importance in contributing labile organic compounds to these carbon-poor habitats. We also found high relative abundances of chytrid fungi in GFS sediments, which putatively parasitize these algae, promoting decomposition through a fungal shunt. Exploring the biofilm microbiome, we then sought to identify bacterial phylogenetic clades significantly associated with decomposition, and found numerous positively (e.g., Saprospiraceae) and negatively (e.g., Nitrospira) related clades. Lastly, using metagenomics, we found evidence of different bacterial classes possessing different proportions of EEA-encoding genes, potentially informing some of the microbial associations with decomposition rates. Our results, therefore, present new mechanistic insights into OM decomposition in GFSs by demonstrating that an algal-based "green food web" is likely to increase in importance in the future and will promote important biogeochemical shifts in these streams as glaciers vanish.},
}
@article {pmid35316575,
year = {2022},
author = {Timmis, K and Verstraete, W},
title = {Multiple intertwined crises facing humanity necessitate a European Environmental Research Organization.},
journal = {Microbial biotechnology},
volume = {15},
number = {4},
pages = {1031-1034},
pmid = {35316575},
issn = {1751-7915},
abstract = {The planet is experiencing all manner of environmental crises, and crises that have their origins in the environment, including global warming, pollution of the air, soil, marine systems and freshwater, loss of habitats and species extinctions, transmission of deadly animal infections to humans, the spread of antimicrobial resistance, to name just a few. Planetary boundaries are being successively breached. Devising and implementing optimal solution and mitigation strategies urgently requires the best possible scientific brains to be harnessed and focused on environmental crises. It is imperative to establish authoritative leadership and the intellectual and organisational framework for this: a European Environmental Research Organisation, modelled on the European Molecular Biology Organisation (EMBO) and Laboratory (EMBL), whose mission is to carry out pioneering research on environmental crisis‐relevant topics, communicate its findings and recommendations to governments, their agencies, the general public, business and other stakeholders, and create outstanding research leaders to populate the best institutions worldwide – a global network of top scientists working together to understand the causes and nature of crises and to devise effective solutions.},
}
@article {pmid35316402,
year = {2022},
author = {Tiwari, N and Bansal, M and Santhiya, D and Sharma, JG},
title = {Insights into microbial diversity on plastisphere by multi-omics.},
journal = {Archives of microbiology},
volume = {204},
number = {4},
pages = {216},
pmid = {35316402},
issn = {1432-072X},
mesh = {Biodegradation, Environmental ; *Ecosystem ; High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Plastics ; },
abstract = {Plastic pollution is a major concern in marine environment as it takes many years to degrade and is one of the greatest threats to marine life. Plastic surface, referred to as plastisphere, provides habitat for growth and proliferation of various microorganisms. The discovery of these microbes is necessary to identify significant genes, enzymes and bioactive compounds that could help in bioremediation and other commercial applications. Conventional culture techniques have been successful in identifying few microbes from these habitats, leaving majority of them yet to be explored. As such, to recognize the vivid genetic diversity of microbes residing in plastisphere, their structure and corresponding ecological roles within the ecosystem, an emerging technique, called metagenomics has been explored. The technique is expected to provide hitherto unknown information on microbes from the plastisphere. Metagenomics along with next generation sequencing provides comprehensive knowledge on microbes residing in plastisphere that identifies novel microbes for plastic bioremediation, bioactive compounds and other potential benefits. The following review summarizes the efficiency of metagenomics and next generation sequencing technology over conventionally used methods for culturing microbes. It attempts to illustrate the workflow mechanism of metagenomics to elucidate diverse microbial profiles. Further, importance of integrated multi-omics techniques has been highlighted in discovering microbial ecology residing on plastisphere for wider applications.},
}
@article {pmid35316343,
year = {2023},
author = {Dallas, JW and Warne, RW},
title = {Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation.},
journal = {Microbial ecology},
volume = {85},
number = {3},
pages = {820-838},
pmid = {35316343},
issn = {1432-184X},
mesh = {Animals ; *Microbiota ; Biodiversity ; Diet ; Bacteria/genetics ; Skin/microbiology ; },
abstract = {During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.},
}
@article {pmid35316342,
year = {2023},
author = {Zhao, X and Fan, X and Gong, Z and Gao, X and Wang, Y and Ni, B},
title = {The Toxic Effects of Cu and CuO Nanoparticles on Euplotes aediculatus.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {544-556},
pmid = {35316342},
issn = {1432-184X},
support = {31672249//national natural science foundation of china/ ; },
mesh = {*Euplotes ; *Metal Nanoparticles/toxicity ; *Nanoparticles ; Copper ; Oxidative Stress ; },
abstract = {The single-celled eukaryote Euplotes aediculatus was chosen to test and compare the toxic effects of Cu and CuO nanoparticles (NPs). The antioxidant enzymatic activity, morphological changes, and functional groups on the membrane were determined using spectrophotometry, microscopy, and Fourier transform infrared spectroscopy after NPs treatment. The toxicity of the NPs to cells was dose-dependent, and the 24 h-LC50 values of the CuNPs and CuONPs were 0.46 µg/L and 1.24 × 10[3] µg/L, respectively. These NPs increased the activities of superoxide dismutase, glutathione peroxidase, and catalase and destroyed the cell structure; moreover, the CuNPs were more toxic than the CuONPs. In addition to the higher enzymatic activity, CuNPs also caused nucleoli disappearance, chromatin condensation, and mitochondrial and pellicle damage. The oxidization of the functional groups of the membrane (PO2 - , C-O-C, and δ(COH) of carbohydrates) also confirmed the severe damage caused by CuNPs. Our study showed that oxidative stress and organelle destruction played important roles in the toxic effects of these NPs on this protozoan. Compared with other aquatic organisms, E. aediculatus can be considered a potential indicator at the preliminary stage of environmental pollution.},
}
@article {pmid35316093,
year = {2022},
author = {Kherfi-Nacer, A and Yan, Z and Bouherama, A and Schmitz, L and Amrane, SO and Franken, C and Schneijderberg, M and Cheng, X and Amrani, S and Geurts, R and Bisseling, T},
title = {High Salt Levels Reduced Dissimilarities in Root-Associated Microbiomes of Two Barley Genotypes.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {35},
number = {7},
pages = {592-603},
doi = {10.1094/MPMI-12-21-0294-FI},
pmid = {35316093},
issn = {0894-0282},
mesh = {Bacteria/genetics ; Genotype ; *Hordeum/genetics/metabolism ; *Microbiota ; Plant Roots/microbiology ; Salt Tolerance ; Soil ; },
abstract = {Plants harbor in and at their roots bacterial microbiomes that contribute to their health and fitness. The microbiome composition is controlled by the environment and plant genotype. Previously, it was shown that the plant genotype-dependent dissimilarity of root microbiome composition of different species becomes smaller under drought stress. However, it remains unknown whether this reduced plant genotype-dependent effect is a specific response to drought stress or a more generic response to abiotic stress. To test this, we studied the effect of salt stress on two distinct barley (Hordeum vulgare L.) genotypes: the reference cultivar Golden Promise and the Algerian landrace AB. As inoculum, we used soil from salinized and degraded farmland on which barley was cultivated. Controlled laboratory experiments showed that plants inoculated with this soil displayed growth stimulation under high salt stress (200 mM) in a plant genotype-independent manner, whereas the landrace AB also showed significant growth stimulation at low salt concentrations. Subsequent analysis of the root microbiomes revealed a reduced dissimilarity of the bacterial communities of the two barley genotypes in response to high salt, especially in the endophytic compartment. High salt level did not reduce α-diversity (richness) in the endophytic compartment of both plant genotypes but was associated with an increased number of shared strains that respond positively to high salt. Among these, Pseudomonas spp. were most abundant. These findings suggest that the plant genotype-dependent microbiome composition is altered generically by abiotic stress.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
}
@article {pmid35314061,
year = {2022},
author = {Girardi, NS and Sosa, AL and Etcheverry, MG and Passone, MA},
title = {In vitro characterization bioassays of the nematophagous fungus Purpureocillium lilacinum: Evaluation on growth, extracellular enzymes, mycotoxins and survival in the surrounding agroecosystem of tomato.},
journal = {Fungal biology},
volume = {126},
number = {4},
pages = {300-307},
doi = {10.1016/j.funbio.2022.02.001},
pmid = {35314061},
issn = {1878-6146},
mesh = {Animals ; Biological Assay ; Dehydration ; *Hypocreales ; *Solanum lycopersicum ; *Mycotoxins ; *Nematoda ; },
abstract = {The effects of water stress and temperature on in vitro growth and enzymatic activity of Purpureocillium lilacinum (Sordariomycetes, Hypocreales, Ophiocordycipitaceae) isolates with demonstrated capacity to control Nacobbus aberrans (Secernentea, Tylenchida, Pratylenchidae) were evaluated in this study. Also, saprophytic and endophytic colonization in tomato plants were determined. P. lilacinum was able to grow under the evaluated levels of osmotic and matric stress, but the increase in water stress caused reductions in radial growth rates. Moreover, the fungal isolates produced chitinases, proteases, and leucinostatins under inductive conditions. The nematophagous fungi were able to develop saprophytically (10[4] CFU g[-1] of soil). Meanwhile, only P. lilacinum SR38 demonstrated endophytic capacity. The results suggest that P. lilacinum can be effectively applied as biocontrol agents of phytoparasitic nematodes in tomatoes under variable agroecological conditions.},
}
@article {pmid35313934,
year = {2022},
author = {Merino, I and de la Fuente, A and Domínguez-Gil, M and Eiros, JM and Tedim, AP and Bermejo-Martín, JF},
title = {Digital PCR applications for the diagnosis and management of infection in critical care medicine.},
journal = {Critical care (London, England)},
volume = {26},
number = {1},
pages = {63},
pmid = {35313934},
issn = {1466-609X},
support = {PI19/00590//Instituto de Salud Carlos III/ ; CD18/00123//Instituto de Salud Carlos III/ ; CM18/00157//Instituto de Salud Carlos III/ ; FI20/00278//Instituto de Salud Carlos III/ ; APT//European Society of Clinical Microbiology and Infectious Diseases/ ; },
mesh = {*COVID-19/diagnosis ; Critical Care ; Humans ; Real-Time Polymerase Chain Reaction/methods ; Reproducibility of Results ; },
abstract = {Infection (either community acquired or nosocomial) is a major cause of morbidity and mortality in critical care medicine. Sepsis is present in up to 30% of all ICU patients. A large fraction of sepsis cases is driven by severe community acquired pneumonia (sCAP), which incidence has dramatically increased during COVID-19 pandemics. A frequent complication of ICU patients is ventilator associated pneumonia (VAP), which affects 10-25% of all ventilated patients, and bloodstream infections (BSIs), affecting about 10% of patients. Management of these severe infections poses several challenges, including early diagnosis, severity stratification, prognosis assessment or treatment guidance. Digital PCR (dPCR) is a next-generation PCR method that offers a number of technical advantages to face these challenges: it is less affected than real time PCR by the presence of PCR inhibitors leading to higher sensitivity. In addition, dPCR offers high reproducibility, and provides absolute quantification without the need for a standard curve. In this article we reviewed the existing evidence on the applications of dPCR to the management of infection in critical care medicine. We included thirty-two articles involving critically ill patients. Twenty-three articles focused on the amplification of microbial genes: (1) four articles approached bacterial identification in blood or plasma; (2) one article used dPCR for fungal identification in blood; (3) another article focused on bacterial and fungal identification in other clinical samples; (4) three articles used dPCR for viral identification; (5) twelve articles quantified microbial burden by dPCR to assess severity, prognosis and treatment guidance; (6) two articles used dPCR to determine microbial ecology in ICU patients. The remaining nine articles used dPCR to profile host responses to infection, two of them for severity stratification in sepsis, four focused to improve diagnosis of this disease, one for detecting sCAP, one for detecting VAP, and finally one aimed to predict progression of COVID-19. This review evidences the potential of dPCR as a useful tool that could contribute to improve the detection and clinical management of infection in critical care medicine.},
}
@article {pmid35312808,
year = {2023},
author = {Caballero, JRI and Lalande, BM and Hanna, JW and Klopfenstein, NB and Kim, MS and Stewart, JE},
title = {Genomic Comparisons of Two Armillaria Species with Different Ecological Behaviors and Their Associated Soil Microbial Communities.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {708-729},
pmid = {35312808},
issn = {1432-184X},
mesh = {*Armillaria/genetics ; Soil ; Trees ; Forests ; *Tracheophyta ; *Pinus ; Genomics ; },
abstract = {Armillaria species show considerable variation in ecological roles and virulence, from mycorrhizae and saprophytes to important root pathogens of trees and horticultural crops. We studied two Armillaria species that can be found in coniferous forests of northwestern USA and southwestern Canada. Armillaria altimontana not only is considered as a weak, opportunistic pathogen of coniferous trees, but it also appears to exhibit in situ biological control against A. solidipes, formerly North American A. ostoyae, which is considered a virulent pathogen of coniferous trees. Here, we describe their genome assemblies and present a functional annotation of the predicted genes and proteins for the two Armillaria species that exhibit contrasting ecological roles. In addition, the soil microbial communities were examined in association with the two Armillaria species within a 45-year-old plantation of western white pine (Pinus monticola) in northern Idaho, USA, where A. altimontana was associated with improved tree growth and survival, while A. solidipes was associated with reduced growth and survival. The results from this study reveal a high similarity between the genomes of the beneficial/non-pathogenic A. altimontana and pathogenic A. solidipes; however, many relatively small differences in gene content were identified that could contribute to differences in ecological lifestyles and interactions with woody hosts and soil microbial communities.},
}
@article {pmid35312065,
year = {2022},
author = {Ceron-Chafla, P and García-Timermans, C and de Vrieze, J and Ganigué, R and Boon, N and Rabaey, K and van Lier, JB and Lindeboom, REF},
title = {Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure.},
journal = {Biotechnology and bioengineering},
volume = {119},
number = {7},
pages = {1792-1807},
pmid = {35312065},
issn = {1097-0290},
mesh = {Fermentation ; Geologic Sediments ; Hydrostatic Pressure ; *Microbiota ; Temperature ; },
abstract = {Fermentation at elevated hydrostatic pressure is a novel strategy targeting product selectivity. However, the role of inoculum history and cross-resistance, that is, acquired tolerance from incubation under distinctive environmental stress, remains unclear in high-pressure operation. In our here presented work, we studied fermentation and microbial community responses of halotolerant marine sediment inoculum (MSI) and anaerobic digester inoculum (ADI), pre-incubated in serum bottles at different temperatures and subsequently exposed to mild hydrostatic pressure (MHP; < 10 MPa) in stainless steel reactors. Results showed that MHP effects on microbial growth, activity, and community structure were strongly temperature-dependent. At moderate temperature (20°C), biomass yield and fermentation were not limited by MHP; suggesting a cross-resistance effect from incubation temperature and halotolerance. Low temperatures (10°C) and MHP imposed kinetic and bioenergetic limitations, constraining growth and product formation. Fermentation remained favorable in MSI at 28°C and ADI at 37°C, despite reduced biomass yield resulting from maintenance and decay proportionally increasing with temperature. Microbial community structure was modified by temperature during the enrichment, and slight differences observed after MHP-exposure did not compromise functionality. Results showed that the relation incubation temperature-halotolerance proved to be a modifier of microbial responses to MHP and could be potentially exploited in fermentations to modulate product/biomass ratio.},
}
@article {pmid35311515,
year = {2022},
author = {Linney, MD and Eppley, JM and Romano, AE and Luo, E and DeLong, EF and Karl, DM},
title = {Microbial Sources of Exocellular DNA in the Ocean.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {7},
pages = {e0209321},
pmid = {35311515},
issn = {1098-5336},
mesh = {*Alphaproteobacteria/genetics ; Bacteria/genetics ; DNA ; *Prochlorococcus/genetics ; Seawater/microbiology ; *Viruses/genetics ; Water ; },
abstract = {Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 μm). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism. IMPORTANCE With advances in metagenomic sequencing, the microbial composition of diverse environmental systems has been investigated, providing new perspectives on potential ecological dynamics and dimensions for experimental investigations. Here, we characterized exocellular free DNA via metagenomics, using a newly developed method that separates free DNA from cells, viruses, and vesicles, and facilitated the independent characterization of each fraction. The fate of this free DNA has both ecological consequences as a nutrient (N and P) source and potential evolutionary consequences as a source of genetic transformation. Here, we document different microbial sources of free DNA at the surface (0 to 200 m) versus depths of 250 to 1,000 m, suggesting that distinct free DNA production mechanisms may be present throughout the oligotrophic water column. Examining microbial processes through the lens of exocellular DNA provides insights into the production of labile dissolved organic matter (i.e., free DNA) at the surface (likely by viral lysis) and processes that influence the fate of sinking, surface-derived organic matter.},
}
@article {pmid35309262,
year = {2022},
author = {Amit, and Jamwal, R and Kumari, S and Kelly, S and Cannavan, A and Singh, DK},
title = {Assessment of geographical origin of virgin coconut oil using inductively coupled plasma mass spectrometry along with multivariate chemometrics.},
journal = {Current research in food science},
volume = {5},
number = {},
pages = {545-552},
pmid = {35309262},
issn = {2665-9271},
abstract = {Recently, Virgin coconut oil (VCO) has emerged as one of the most favorable edible oils because of its application in cooking, frying as well as additive used in food, pharmaceuticals, and cosmetic goods. These qualities have established VCO in high consumer demand and there is a great need of establishing a reliable method for the identification of its geographical origin. Through this present study, for the first time, it has been established that Inductively Coupled Plasma-Mass-Spectrometry (ICP-MS) combined with multivariate chemometrics can be used for the identification of the geographical origin of the VCO samples of various provinces. Principal Component Analysis (PCA), and Linear Discriminant Analysis (LDA) were able to differentiate and classify the VCO samples of different geographical origins. Further, calibration models (Principal Component Regression and Partial Least Square Regression) were developed on the calibration dataset of the elemental concentration obtained from the ICP-MS analysis. An external dataset was used to develop the prediction model to predict the geographical origin of an unknown sample. Both PCR and PLS-R models were successfully able to predict the geographical origin with a high R[2] value (0.999) and low RMSEP value 0.074 and 0.075% v/v of prediction respectively. In conclusion, ICP-MS combined with regression modelling can be used as an excellent tool for the identification of the geographical origin of the VCO samples of various provinces. This whole technique is the most suitable as it has high sensitivity as well as provides easy multi-metal analysis for a single sample of edible oil.},
}
@article {pmid35306576,
year = {2023},
author = {Hanashiro, FTT and De Meester, L and Vanhamel, M and Mukherjee, S and Gianuca, AT and Verbeek, L and van den Berg, E and Souffreau, C},
title = {Bacterioplankton Assembly Along a Eutrophication Gradient Is Mainly Structured by Environmental Filtering, Including Indirect Effects of Phytoplankton Composition.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {400-410},
pmid = {35306576},
issn = {1432-184X},
support = {PF/2010/07//KU Leuven Research Fund Excellence Center/ ; 245968/2012-1//Science Without Borders/ ; },
mesh = {Animals ; *Phytoplankton ; *Ecosystem ; Aquatic Organisms ; Eutrophication ; Zooplankton ; Lakes/microbiology ; },
abstract = {Biotic interactions are suggested to be key factors structuring bacterioplankton community assembly but are rarely included in metacommunity studies. Eutrophication of ponds and lakes provides a useful opportunity to evaluate how bacterioplankton assembly is affected by specific environmental conditions, especially also by biotic interactions with other trophic levels such as phytoplankton and zooplankton. Here, we evaluated the importance of deterministic and stochastic processes on bacterioplankton community assembly in 35 shallow ponds along a eutrophication gradient in Belgium and assessed the direct and indirect effects of phytoplankton and zooplankton community variation on bacterioplankton assembly through a path analysis and network analysis. Environmental filtering by abiotic factors (suspended matter concentration and pH) explained the largest part of the bacterioplankton community variation. Phytoplankton community structure affected bacterioplankton structure through its effect on variation in chlorophyll-a and suspended matter concentration. Bacterioplankton communities were also spatially structured through pH. Overall, our results indicate that environmental variation is a key component driving bacterioplankton assembly along a eutrophication gradient and that indirect biotic interactions can also be important in explaining bacterioplankton community composition. Furthermore, eutrophication led to divergence in community structure and more eutrophic ponds had a higher diversity of bacteria.},
}
@article {pmid35305980,
year = {2022},
author = {Kim, SJ and Kang, S and Xu, H and Bhaskar, P and Chenoli, S},
title = {Special issue: AFoPS on climate and life in poles.},
journal = {Environmental research},
volume = {211},
number = {},
pages = {113125},
doi = {10.1016/j.envres.2022.113125},
pmid = {35305980},
issn = {1096-0953},
mesh = {*Climate ; *Climate Change ; },
}
@article {pmid35302890,
year = {2022},
author = {Koldaeva, A and Tsai, HF and Shen, AQ and Pigolotti, S},
title = {Population genetics in microchannels.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {12},
pages = {e2120821119},
pmid = {35302890},
issn = {1091-6490},
mesh = {*Escherichia coli/genetics ; *Genetics, Population ; Soil ; },
abstract = {SignificanceMany microbial populations proliferate in small channels. In such environments, reproducing cells organize in parallel lanes. Reproducing cells shift these lanes, potentially expelling other cells from the channel. In this paper, we combine theory and experiments to understand how these dynamics affects the diversity of a microbial population. We theoretically predict that genetic diversity is quickly lost along lanes of cells. Our experiments confirm that a population of proliferating Escherichia coli in a microchannel organizes into lanes of genetically identical cells within a few generations. Our findings elucidate the effect of lane formation on populations evolution, with potential applications ranging from microbial ecology in soil to dynamics of epithelial tissues in higher organisms.},
}
@article {pmid35300488,
year = {2022},
author = {Frey, B and Varliero, G and Qi, W and Stierli, B and Walthert, L and Brunner, I},
title = {Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {828977},
pmid = {35300488},
issn = {1664-302X},
abstract = {Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5-10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the "dark matter" of the soil.},
}
@article {pmid35298685,
year = {2023},
author = {Zhang, Z and Han, P and Zheng, Y and Jiao, S and Dong, H and Liang, X and Gao, D and Niu, Y and Yin, G and Liu, M and Hou, L},
title = {Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {383-399},
pmid = {35298685},
issn = {1432-184X},
support = {41725002//China National Funds for Distinguished Young Scientists/ ; },
mesh = {*Soil ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Wetlands ; Bacteria ; China ; },
abstract = {Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats.},
}
@article {pmid35295290,
year = {2022},
author = {Zioutis, C and Seki, D and Bauchinger, F and Herbold, C and Berger, A and Wisgrill, L and Berry, D},
title = {Ecological Processes Shaping Microbiomes of Extremely Low Birthweight Infants.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {812136},
pmid = {35295290},
issn = {1664-302X},
support = {P 27831/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {The human microbiome has been implicated in affecting health outcomes in premature infants, but the ecological processes governing early life microbiome assembly remain poorly understood. Here, we investigated microbial community assembly and dynamics in extremely low birth weight infants (ELBWI) over the first 2 weeks of life. We profiled the gut, oral cavity and skin microbiomes over time using 16S rRNA gene amplicon sequencing and evaluated the ecological forces shaping these microbiomes. Though microbiomes at all three body sites were characterized by compositional instability over time and had low body-site specificity (PERMANOVA, r [2] = 0.09, p = 0.001), they could nonetheless be clustered into four discrete community states. Despite the volatility of these communities, deterministic assembly processes were detectable in this period of initial microbial colonization. To further explore these deterministic dynamics, we developed a probabilistic approach in which we modeled microbiome state transitions in each ELBWI as a Markov process, or a "memoryless" shift, from one community state to another. This analysis revealed that microbiomes from different body sites had distinctive dynamics as well as characteristic equilibrium frequencies. Time-resolved microbiome sampling of premature infants may help to refine and inform clinical practices. Additionally, this work provides an analysis framework for microbial community dynamics based on Markov modeling that can facilitate new insights, not only into neonatal microbiomes but also other human-associated or environmental microbiomes.},
}
@article {pmid35294588,
year = {2022},
author = {Guarin, TC and Li, L and Pagilla, KR},
title = {Microbial community characterization in advanced water reclamation for potable reuse.},
journal = {Applied microbiology and biotechnology},
volume = {106},
number = {7},
pages = {2763-2773},
pmid = {35294588},
issn = {1432-0614},
mesh = {Bacteria/genetics ; *Drinking Water/microbiology ; *Microbiota ; *Ozone ; RNA, Ribosomal, 16S/genetics ; *Water Purification ; },
abstract = {This study investigated the microbial community structure and composition across two treatment steps used in advanced water reclamation for potable reuse applications, namely Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF) and Ozone-Biological Activated Carbon filtration (O3/BAC). The study examined the richness, variations, and similarities of the microorganisms involved at each treatment step to better understand the role of ecology and the dynamics on unit process performance and the microbial community developed within it. The bacterial microbiomes at each treatment step were independently characterized using 16S metagenomic sequencing. Combining both treatment steps, a total of 3801 species were detected. From the total species detected, 38% and 98% were identified at CFCGMF and O3/BAC, respectively. The most abundant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes in both treatment steps. The identified species were classified based on their preferences to free-living style (59%) vs attached-living style (22%) showing a relatively low richness in the BAC media, but higher diversities. At the taxonomic class level, Betaproteobacteria was the predominant in both system processes. Additionally, a list of eight genera were identified as potential bacterial pathogens present in both process effluents. They are Aeromonas, Clostridium, Enterobacter, Escherichia, Flavobacterium, Legionella, Mycobacterium, and Pseudomonas. CFCGMF effluent yielded less pathogenic bacteria than both the ozone and BAC filter effluent from the O3/BAC process unit; their relative abundance accounted for about 2% and 8% for CFCGMF and O3/BAC, respectively. Detailed studies to characterize the microbial communities are crucial in interpreting the mechanisms and synergies between processes performance and microorganisms by identifying the needs and best practices to ensure public health protection. Key points • Microbial communities of two treatment processes are characterized using 16S rRNA sequencing. • Organisms that can tolerate ozone and form biofilms define microbial community in subsequent biofilters. • In relatively low abundances, potential pathogenic bacteria are detected in the treated water.},
}
@article {pmid35292274,
year = {2022},
author = {Chai, G and Wang, D and Shan, J and Jiang, C and Yang, Z and Liu, E and Meng, H and Wang, H and Wang, Z and Qin, L and Xi, J and Ma, Y and Li, H and Qian, Y and Li, J and Lin, Y},
title = {Accumulation of high-molecular-weight polycyclic aromatic hydrocarbon impacted the performance and microbial ecology of bioretention systems.},
journal = {Chemosphere},
volume = {298},
number = {},
pages = {134314},
doi = {10.1016/j.chemosphere.2022.134314},
pmid = {35292274},
issn = {1879-1298},
mesh = {Biological Oxygen Demand Analysis ; *Environmental Pollutants ; Nitrogen/analysis ; *Polycyclic Aromatic Hydrocarbons/analysis ; Soil ; *Soil Pollutants ; },
abstract = {Bioretention has been considered as an effective management practice for urban stormwater in the removal of pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the accumulation of high-molecular-weight (HMW) PAHs in bioretention systems and their potential impact on the pollutants removal performance and microbial ecology are still not fully understood. In this study, comparisons of treatment effectiveness, enzyme activity and microbial community in bioretention systems with different types of media amendments were carried out at different spiking levels of pyrene (PYR). The results showed that the removal efficiencies of chemical oxygen demand (COD) and total nitrogen in the bioretention systems were negatively impacted by the PYR levels. The relative activities of soil dehydrogenase and urease were increasingly inhibited by the elevated PYR level, indicating the declining microbial activity regarding organic matter decomposition. The spiking of PYR negatively affected microbial diversity, and distinct time- and influent-dependent changes in microbial communities were observed. The relative abundance of PAH-degrading microorganisms increased in PYR-spiked systems, while the abundance of nitrifiers decreased. The addition of media amendments was beneficial for the enrichment of microorganisms that are more resistant to PYR-related stress, therefore elevating the COD concentration removal rate by ∼50%. This study gives new insight into the multifaceted impacts of HMW PAH accumulation on microbial fingerprinting and enzyme activities, which may provide guidance on better stormwater management practices via bioretention in terms of improved system longevity and performance.},
}
@article {pmid35290040,
year = {2022},
author = {Patzner, MS and Kainz, N and Lundin, E and Barczok, M and Smith, C and Herndon, E and Kinsman-Costello, L and Fischer, S and Straub, D and Kleindienst, S and Kappler, A and Bryce, C},
title = {Seasonal Fluctuations in Iron Cycling in Thawing Permafrost Peatlands.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {7},
pages = {4620-4631},
pmid = {35290040},
issn = {1520-5851},
mesh = {Ferric Compounds/metabolism ; Iron/metabolism ; Oxidation-Reduction ; *Permafrost ; Seasons ; Soil ; },
abstract = {In permafrost peatlands, up to 20% of total organic carbon (OC) is bound to reactive iron (Fe) minerals in the active layer overlying intact permafrost, potentially protecting OC from microbial degradation and transformation into greenhouse gases (GHG) such as CO2 and CH4. During the summer, shifts in runoff and soil moisture influence redox conditions and therefore the balance of Fe oxidation and reduction. Whether reactive iron minerals could act as a stable sink for carbon or whether they are continuously dissolved and reprecipitated during redox shifts remains unknown. We deployed bags of synthetic ferrihydrite (FH)-coated sand in the active layer along a permafrost thaw gradient in Stordalen mire (Abisko, Sweden) over the summer (June to September) to capture changes in redox conditions and quantify the formation and dissolution of reactive Fe(III) (oxyhydr)oxides. We found that the bags accumulated Fe(III) under constant oxic conditions in areas overlying intact permafrost over the full summer season. In contrast, in fully thawed areas, conditions were continuously anoxic, and by late summer, 50.4 ± 12.8% of the original Fe(III) (oxyhydr)oxides were lost via dissolution. Periodic redox shifts (from 0 to +300 mV) were observed over the summer season in the partially thawed areas. This resulted in the dissolution and loss of 47.2 ± 20.3% of initial Fe(III) (oxyhydr)oxides when conditions are wetter and more reduced, and new formation of Fe(III) minerals (33.7 ± 8.6% gain in comparison to initial Fe) in the late summer under more dry and oxic conditions, which also led to the sequestration of Fe-bound organic carbon. Our data suggest that there is seasonal turnover of iron minerals in partially thawed permafrost peatlands, but that a fraction of the Fe pool remains stable even under continuously anoxic conditions.},
}
@article {pmid35287817,
year = {2022},
author = {Mota-Gutierrez, J and Lis, L and Lasagabaster, A and Nafarrate, I and Ferrocino, I and Cocolin, L and Rantsiou, K},
title = {Campylobacter spp. prevalence and mitigation strategies in the broiler production chain.},
journal = {Food microbiology},
volume = {104},
number = {},
pages = {103998},
doi = {10.1016/j.fm.2022.103998},
pmid = {35287817},
issn = {1095-9998},
mesh = {Abattoirs ; Animals ; *Campylobacter ; *Chickens/microbiology ; Meat/microbiology ; Prevalence ; },
abstract = {This study aims to discuss the microbial ecology of the broiler gut environment, Campylobacter prevalence across the broiler production chain with a follow-up focus on a possible mitigation strategy, based on the use of bacteriophages. Scientific literature published from the last two decades was reviewed and data were collected to establish the ranges of Campylobacter loads from different samples. Results showed that the pathogen load in the sample is likely to increase from the different stages of the production chain. Contamination of water and feed represents the most notable source of contamination during the primary production, while cross-contamination of broiler carcasses, skin, and meat occurs during the slaughter, dressing, and processing via machinery, work surfaces, water, and air partially due to the leaking of contaminated feces from visceral rupture. Knowledge gaps were identified and included: a lack of studies detecting Campylobacter in broilers in most of the European countries over the last decade and a low number of studies determining the bacterial load in crates used to transport broilers to the slaughterhouse. Determining the prevalence of Campylobacter in the broiler industry will enable us to set critical control points to produce broiler flocks and meat products with a low risk of Campylobacter contamination.},
}
@article {pmid35286940,
year = {2022},
author = {Safi, LSL and Tang, KW and Carnegie, RB},
title = {Investigating the epibiotic peritrich Zoothamnium intermedium Precht, 1935: Seasonality and distribution of its relationships with copepods in Chesapeake Bay (USA).},
journal = {European journal of protistology},
volume = {84},
number = {},
pages = {125880},
doi = {10.1016/j.ejop.2022.125880},
pmid = {35286940},
issn = {1618-0429},
mesh = {Animals ; Bays ; *Ciliophora ; *Copepoda ; *Oligohymenophorea ; Plankton ; Water ; },
abstract = {Zoothamnium intermedium is an obligate epibiont ciliate and has been found in a diverse array of hosts and environments. Different studies have reported conflicting distribution patterns and host preferences, even though studies in Chesapeake Bay have suggested that the ciliate has a strong host specificity for two calanoid copepod species. We examined the life cycle, host preferences, and ecological conditions conducive to Z. intermedium presence on copepods in Chesapeake Bay, the largest estuary in North America. The York River tributary was sampled biweekly from fall 2014 through summer 2015 for plankton, peritrichs and bacteria in the water column. Bacterial abundance in the water column peaked in fall and late spring, coinciding with increased abundance and species richness of non-epibiont peritrichs. Among the plankton, only the calanoid copepods Acartia tonsa and Centropages hamatus were colonized by Z. intermedium. The peritrich epibiont displayed higher colonization rates on C. hamatus even when A. tonsa was far more abundant. Multivariate correlation analysis of infestation prevalence on A. tonsa showed a strong correlation with dissolved oxygen, salinity and water temperature. Such correlations, along with differences in host species biology, might be driving the seasonality of this epibiotic relationship.},
}
@article {pmid35286131,
year = {2022},
author = {Huang, K and Sun, X and Zou, Y and Li, H and Xu, P and Zhang, W and Zhang, Y and Li, H and Sun, H and Wang, W and Pang, M and Luo, J},
title = {Comparison of the Endophytic Bacterial Microbiota of Asymptomatic and Symptomatic Ginger Rhizomes During the Activation of Adventitious Bud Development.},
journal = {Plant disease},
volume = {106},
number = {9},
pages = {2470-2479},
doi = {10.1094/PDIS-09-21-2069-RE},
pmid = {35286131},
issn = {0191-2917},
mesh = {Bacteria/genetics ; *Zingiber officinale/chemistry/genetics/microbiology ; *Microbiota ; Plant Extracts ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Bacterial infections are the cause of rhizome rot in ginger (Zingiber officinale). Key members of the endophytic microbial community in ginger rhizomes have not been identified, and their impact on the decay of rhizomes during the activation of adventitious bud development has not been investigated. High-throughput, 16S rRNA amplicon sequencing and inoculation experiments were used to analyze the microbial diversity, community structure and composition, and pathogenicity of isolated bacteria. Our results indicated that the composition of the endophytic microbiota underwent a shift during the progression of rhizome rot disease. Enterobacteriaceae, Lachnospiraceae, and the bacterial genera Clostridium, Bacteroides, Acrobacter, Dysgonomonas, Anaerosinus, Pectobacterium, and Lactococcus were relatively abundant in the bacterial community of rhizomes exhibiting bacterial decay symptoms but were also present in asymptomatic rhizomes. The presence of Enterobacteriaceae and Pseudomonadaceae were positively correlated (ρ = 0.83) at the beginning of the sampling period in the symptomatic group, while a positive correlation (ρ = 0.89) was only observed after 20 days in the asymptomatic group. These data indicate that the co-occurrence of Enterobacteriaceae and Pseudomonadaceae may be associated with the development of ginger rot. Bacterial taxa isolated from ginger rhizomes, such as Enterobacter cloacae, E. hormaechei, and Pseudomonas putida, induced obvious rot symptoms when they were inoculated on ginger rhizomes. Notably, antibiotic-producing bacterial taxa in the Streptococcaceae and Flavobacteriaceae were also relatively abundant in rhizomes with rot and appeared to be linked to the onset of rhizome rot disease. Our results provide important information on the establishment and management of disease in ginger rhizomes.},
}
@article {pmid35285907,
year = {2022},
author = {Nunes, I and Hansen, V and Bak, F and Bonnichsen, L and Su, J and Hao, X and Raymond, NS and Nicolaisen, MH and Jensen, LS and Nybroe, O},
title = {Succession of the wheat seed-associated microbiome as affected by soil fertility level and introduction of Penicillium and Bacillus inoculants in the field.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {3},
pages = {},
pmid = {35285907},
issn = {1574-6941},
mesh = {*Bacillus/genetics/metabolism ; Fertilizers/analysis ; *Microbiota ; *Penicillium/metabolism ; Phosphorus/metabolism ; Seeds ; Soil ; Soil Microbiology ; Triticum/microbiology ; },
abstract = {During germination, the seed releases nutrient-rich exudates into the spermosphere, thereby fostering competition between resident microorganisms. However, insight into the composition and temporal dynamics of seed-associated bacterial communities under field conditions is currently lacking. This field study determined the temporal changes from 11 to 31 days after sowing in the composition of seed-associated bacterial communities of winter wheat as affected by long-term soil fertilization history, and by introduction of the plant growth-promoting microbial inoculants Penicillium bilaiae and Bacillus simplex. The temporal dynamics were the most important factor affecting the composition of the seed-associated communities. An increase in the relative abundance of genes involved in organic nitrogen metabolism (ureC and gdhA), and in ammonium oxidation (amoA), suggested increased mineralization of plant-derived nitrogen compounds over time. Dynamics of the phosphorus cycling genes ppt, ppx and cphy indicated inorganic phosphorus and polyphosphate cycling, as well as phytate hydrolysis by the seed-associated bacteria early after germination. Later, an increase in genes for utilization of organic phosphorus sources (phoD, phoX and phnK) indicated phosphorus limitation. The results indicate that community temporal dynamics are partly driven by changed availability of major nutrients, and reveal no functional consequences of the added inoculants during seed germination.},
}
@article {pmid35285696,
year = {2022},
author = {Song, W and Liu, J and Qin, W and Huang, J and Yu, X and Xu, M and Stahl, D and Jiao, N and Zhou, J and Tu, Q},
title = {Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean.},
journal = {mBio},
volume = {13},
number = {2},
pages = {e0383221},
pmid = {35285696},
issn = {2150-7511},
support = {2019YFA0606700//National Key Research and Development Program of China/ ; 2020YFA0607600//National Key Research and Development Program of China/ ; 2017YFA0604300//National Key Research and Development Program of China/ ; 31971446//National Natural Science Foundation of China (NSFC)/ ; 92051110//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Metagenome ; *Microbiota ; *Nitrogen ; Nitrogen Cycle ; Oceans and Seas ; },
abstract = {Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on "who is doing what, where, and how?", this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory-determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly. IMPORTANCE A critical question in microbial ecology is how the complex microbial communities are formed in natural ecosystems with the existence of thousands different species, thereby performing essential ecosystem functions and maintaining ecosystem stability. Previous studies disentangling the community assembly mechanisms mainly focus on microbial taxa, ignoring the functional traits they carry. By anchoring microbial functional traits and their carrying taxonomic groups involved in nitrogen cycling processes, this study demonstrated an important mechanism associated with the complex microbial community assembly. Evidence shows that the environment selects functional traits rather than taxonomic groups, and functional redundancy underlies stochastic taxonomic community assembly. This study is expected to provide valuable mechanistic insights into the complex microbial community assembly in both natural and artificial ecosystems.},
}
@article {pmid35284961,
year = {2023},
author = {Almeida, EL and Ribiere, C and Frei, W and Kenny, D and Coffey, MF and O'Toole, PW},
title = {Geographical and Seasonal Analysis of the Honeybee Microbiome.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {765-778},
pmid = {35284961},
issn = {1432-184X},
support = {12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Bees ; Animals ; Seasons ; *Microbiota ; Larva ; Bacteria ; Ireland ; },
abstract = {We previously showed that colonies of thriving and non-thriving honeybees co-located in a single geographically isolated apiary harboured strikingly different microbiomes when sampled at a single time point in the honey season. Here, we profiled the microbiome in returning forager bees from 10 to 12 hives in each of 6 apiaries across the southern half of Ireland, at early, middle, and late time points in the 2019 honey production season. Despite the wide range of geographical locations and forage available, apiary site was not the strongest determinant of the honeybee microbiome. However, there was clear clustering of the honeybee microbiome by time point across all apiaries, independent of which apiary was sampled. The clustering of microbiome by time was weaker although still significant in three of the apiaries, which may be connected to their geographic location and other external factors. The potential forage effect was strongest at the second timepoint (June-July) when the apiaries also displayed greatest difference in microbiome diversity. We identified bacteria in the forager bee microbiome that correlated with hive health as measured by counts of larvae, bees, and honey production. These findings support the hypothesis that the global honeybee microbiome and its constituent species support thriving hives.},
}
@article {pmid35282279,
year = {2022},
author = {Amillano-Cisneros, JM and Hernández-Rosas, PT and Gomez-Gil, B and Navarrete-Ramírez, P and Ríos-Durán, MG and Martínez-Chávez, CC and Johnston-Monje, D and Martínez-Palacios, CA and Raggi, L},
title = {Loss of gut microbial diversity in the cultured, agastric fish, Mexican pike silverside (Chirostoma estor: Atherinopsidae).},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13052},
pmid = {35282279},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Esocidae/genetics ; RNA, Ribosomal, 16S/genetics ; Fishes/genetics ; Bacteria/genetics ; },
abstract = {Teleost fish are the most diverse group of extant vertebrates and have varied digestive anatomical structures and strategies, suggesting they also possess an array of different host-microbiota interactions. Differences in fish gut microbiota have been shown to affect host development, the process of gut colonization, and the outcomes of gene-environment or immune system-microbiota interactions. There is generally a lack of studies on the digestive mechanisms and microbiota of agastric short-intestine fish however, meaning that we do not understand how changes in gut microbial diversity might influence the health of these types of fish. To help fill these gaps in knowledge, we decided to study the Mexican pike silverside (Chirostoma estor) which has a simplified alimentary canal (agastric, short-intestine, 0.7 gut relative length) to observe the diversity and metabolic potential of its intestinal microbiota. We characterized gut microbial populations using high-throughput sequencing of the V3 region in bacterial 16S rRNA genes while searching for population shifts resulting associated with fish development in different environments and cultivation methods. Microbiota samples were taken from the digesta, anterior and posterior intestine (the three different intestinal components) of fish that grew wild in a lake, that were cultivated in indoor tanks, or that were raised in outdoor ponds. Gut microbial diversity was significantly higher in wild fish than in cultivated fish, suggesting a loss of diversity when fish are raised in controlled environments. The most abundant phyla observed in these experiments were Firmicutes and Proteobacteria, particularly of the genera Mycoplasma, Staphylococcus, Spiroplasma, and Aeromonas. Of the 14,161 OTUs observed in this experiment, 133 were found in all groups, and 17 of these, belonging to Acinetobacter, Aeromonas, Pseudomonas, and Spiroplasma genera, were found in all samples suggesting the existence of a core C. estor microbiome. Functional metagenomic prediction of bacterial ecological functions using PICRUSt2 suggested that different intestinal components select for functionally distinct microbial populations with variation in pathways related to the metabolism of amino acids, vitamins, cofactors, and energy. Our results provide, for the first time, information on the bacterial populations present in an agastric, short-gut teleost with commercial potential and show that controlled cultivation of this fish reduces the diversity of its intestinal microbiota.},
}
@article {pmid35281910,
year = {2022},
author = {Zou, C and Chen, Y and Li, H and Li, W and Wei, J and Li, Z and Wang, X and Chen, T and Huang, H},
title = {Engineered Bacteria EcN-MT Alleviate Liver Injury in Cadmium-Exposed Mice via its Probiotics Characteristics and Expressing of Metallothionein.},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {857869},
pmid = {35281910},
issn = {1663-9812},
abstract = {Cadmium (Cd) exposure is a widespread problem in many parts of the world, but effective means to treat Cd exposure is still lacking. Hence, an engineered strain expressing metallothionein (MT) named Escherichia coli Nissle 1917 (EcN)-MT was constructed, and its potential in the treatment of Cd exposure was evaluated. The in vitro studies showed that metallothionein expressed by EcN-MT could significantly bind Cd. Further, the in vivo results indicated that EcN-MT strain could reduce 26.3% Cd in the liver and increase 24.7% Cd in the feces, which greatly decreased malondialdehyde (MDA) levels and increased catalase (CAT), glutathione (GSH), and superoxide dismutase (SOD) levels in liver, and reduced the expression of toll-like receptor4 (TLR4), nuclear factor-κB (NF-κB), the myeloid differentiation factor 88 (Myd88) andincreased B-cell lymphoma 2 (Bcl-2)/Bcl-2-Associated X (Bax). Moreover, high throughput sequencing results indicated that EcN-MT strain greatly enhanced the beneficial bacteria of Ruminococcaceae, Lactobacillaceae, Akkermansia, Muribaculaceae, Lachnospiraceae, Dubosiella and restored the disturbed microbial ecology to the normal level. Therefore, the high Cd binding capacity of the expressed metallothionein, together with the beneficial characteristics of the host bacteria EcN, makes EcN-MT a sound reagent for the treatment of subchronic Cd exposure-induced liver injury.},
}
@article {pmid35279466,
year = {2022},
author = {Huang, YM and Jakus, N and Straub, D and Konstantinidis, KT and Blackwell, N and Kappler, A and Kleindienst, S},
title = {'Candidatus ferrigenium straubiae' sp. nov., 'Candidatus ferrigenium bremense' sp. nov., 'Candidatus ferrigenium altingense' sp. nov., are autotrophic Fe(II)-oxidizing bacteria of the family Gallionellaceae.},
journal = {Systematic and applied microbiology},
volume = {45},
number = {3},
pages = {126306},
doi = {10.1016/j.syapm.2022.126306},
pmid = {35279466},
issn = {1618-0984},
mesh = {Bacteria/genetics ; Carbon Cycle ; Ecosystem ; Ferrous Compounds/metabolism ; *Gallionellaceae/genetics/metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Iron(II) [Fe(II)] oxidation coupled to denitrification is recognized as an environmentally important process in many ecosystems. However, the Fe(II)-oxidizing bacteria (FeOB) dominating autotrophic nitrate-reducing Fe(II)-oxidizing enrichment cultures, affiliated with the family Gallionellaceae, remain poorly taxonomically defined due to lack of representative isolates. We describe the taxonomic classification of three novel FeOB based on metagenome-assembled genomes (MAGs) acquired from the autotrophic nitrate-reducing enrichment cultures KS, BP and AG. Phylogenetic analysis of nearly full-length 16S rRNA gene sequences demonstrated that these three FeOB were most closely affiliated to the genera Ferrigenium, Sideroxydans and Gallionella, with up to 96.5%, 95.4% and 96.2% 16S rRNA gene sequence identities to representative isolates of these genera, respectively. In addition, average amino acid identities (AAI) of the genomes compared to the most closely related genera revealed highest AAI with Ferrigenium kumadai An22 (76.35-76.74%), suggesting that the three FeOB are members of this genus. Phylogenetic analysis of conserved functional genes further supported that these FeOB represent three novel species of the genus Ferrigenium. Moreover, the three novel FeOB likely have characteristic features, performing partial denitrification coupled to Fe(II) oxidation and carbon fixation. Scanning electron microscopy of the enrichment cultures showed slightly curved rod-shaped cells, ranging from 0.2-0.7 μm in width and 0.5-2.3 μm in length. Based on the phylogenetic, genomic and physiological characteristics, we propose that these FeOB represent three novel species, 'Candidatus Ferrigenium straubiae' sp. nov., 'Candidatus Ferrigenium bremense' sp. nov. and 'Candidatus Ferrigenium altingense' sp. nov. that might have unique metabolic features among the genus Ferrigenium.},
}
@article {pmid35278970,
year = {2022},
author = {Yao, X and Liu, Y and Liu, X and Qiao, Z and Sun, S and Li, X and Wang, J and Zhang, F and Jiang, X},
title = {Effects of thifluzamide on soil fungal microbial ecology.},
journal = {Journal of hazardous materials},
volume = {431},
number = {},
pages = {128626},
doi = {10.1016/j.jhazmat.2022.128626},
pmid = {35278970},
issn = {1873-3336},
mesh = {Anilides ; Fungi ; *Mycobiome ; *Soil/chemistry ; Soil Microbiology ; Thiazoles ; },
abstract = {Thifluzamide, a succinate dehydrogenase inhibitor fungicide, has been used extensively for many diseases control and has the risk of accumulation in soil ecology. In order to study the ecotoxicity of thifluzamide to soil fungal communities, typical corn field soils in north (Tai'an) and south (Guoyang) China were treated with thifluzamide (0, 0.1, 1.0 and 10.0 mg/kg) and incubated for 60 days. Thifluzamide exposure promoted soil basal respiration, and significantly reduced the number of soil culturable fungi and the abundance of soil fungi (RT-qPCR) in middle and late treatment period (15, 30, 60 days). Illumina Mi-Seq sequencing revealed that thifluzamide could reduce fungal alpha diversity (Sobs, Shannon, Simpson indexes) and change fungal community structure. FUN Guild analysis showed that the relative abundance of Undefined Saprotroph increased after the thifluzamide treatment, whereas that of Plant Pathogen decreased, and we concluded that exposure to thifluzamide could change the function of soil fungi. This study evaluated the soil ecological risk caused by thifluzamide's release into soil, providing a basis for its rational application.},
}
@article {pmid35278563,
year = {2022},
author = {Hooban, B and Fitzhenry, K and O'Connor, L and Miliotis, G and Joyce, A and Chueiri, A and Farrell, ML and DeLappe, N and Tuohy, A and Cormican, M and Morris, D},
title = {A Longitudinal Survey of Antibiotic-Resistant Enterobacterales in the Irish Environment, 2019-2020.},
journal = {The Science of the total environment},
volume = {828},
number = {},
pages = {154488},
doi = {10.1016/j.scitotenv.2022.154488},
pmid = {35278563},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; *Escherichia coli/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Sewage ; Water ; beta-Lactamases/genetics ; },
abstract = {The natural environment represents a complex reservoir of antibiotic-resistant bacteria as a consequence of different wastewater discharges including anthropogenic and agricultural. Therefore, the aim of this study was to examine sewage and waters across Ireland for the presence of antibiotic-resistant Enterobacterales. Samples were collected from the West, East and South of Ireland. Two periods of sampling took place between July 2019 and November 2020, during which 118 water (30 L) and 36 sewage samples (200 mL) were collected. Waters were filtered using the CapE method, followed by enrichment and culturing. Sewage samples were directly cultured on selective agars. Isolates were identified by MALDI-TOF and antibiotic susceptibility testing was performed in accordance with EUCAST criteria. Selected isolates were examined for blaCTX-M, blaVIM, blaIMP, blaOXA-48, blaNDM, and blaKPC by real time PCR and whole genome sequencing (n = 146). A total of 419 Enterobacterales (348 water, 71 sewage) were isolated from all samples. Hospital sewage isolates displayed the highest percentage resistance to many beta-lactam and aminoglycoside antibiotics. Extended-spectrum beta-lactamase-producers were identified in 78% of water and 50% of sewage samples. One or more carbapenemase-producing Enterobacterales were identified at 23 individual sampling sites (18 water, 5 sewage). This included the detection of blaOXA-48 (n = 18), blaNDM (n = 14), blaKPC (n = 4) and blaOXA-484 (n = 1). All NDM-producing isolates harbored the ble-MBL bleomycin resistance gene. Commonly detected sequence types included Klebsiella ST323, ST17, and ST405 as well as E. coli ST131, ST38 and ST10. Core genome MLST comparisons detected identical E. coli isolates from wastewater treatment plant (WWTP) influent and nursing home sewage, and the surrounding waters. Similarly, one Klebsiella pneumoniae isolated from WWTP influent and the surrounding estuarine water were identical. These results highlight the need for regular monitoring of the aquatic environment for the presence of antibiotic-resistant organisms to adequately inform public health policies.},
}
@article {pmid35276108,
year = {2022},
author = {Wu, Y and Liu, X and Dong, Q and Xiao, M and Li, B and Topalović, O and Tao, Q and Tang, X and Huang, R and Chen, G and Li, H and Chen, Y and Feng, Y and Wang, C},
title = {Remediation of petroleum hydrocarbons-contaminated soil: Analysis based on Chinese patents.},
journal = {Chemosphere},
volume = {297},
number = {},
pages = {134173},
doi = {10.1016/j.chemosphere.2022.134173},
pmid = {35276108},
issn = {1879-1298},
mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; China ; Hydrocarbons/metabolism ; *Petroleum/analysis ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {Increasing soil petroleum hydrocarbons (PHs) pollution have caused world-wide concerns. The removal of PHs from soils mainly involves physical, chemical, biological processes and their combinations. To date, most reviews in this field based on research articles, but limited papers focused on the integration of remediation technologies from the perspective of patents. In this study, 20-years Chinese patents related to the remediation of soil PHs were comprehensively analyzed. It showed an increasing number of patent applications and the patents' quantity were positively correlated with Chinese GDP over the years, suggesting the more the economy developed the more environmental problems and corresponding solutions emerged. In addition, chemical technologies were mostly used in a combination to achieve faster and better effects, while the physical technologies were often used alone due to high costs. In all PHs remediation techniques, bacteria-based bioremediation was the most used from 2000 to 2019. Bacillus spp. and Pseudomonas spp. were the most used bacteria for PHs treatment because these taxa were widely harboring functions such as biosurfactant production and hydrocarbon degradation. The future research on joint technologies combining microbial and physicochemical ones for better remediation effect and application are highly encouraged.},
}
@article {pmid35275230,
year = {2023},
author = {Pereira, A and Soares, MC and Santos, T and Poças, A and Pérez-Losada, M and Apprill, A and Sikkel, PC and Xavier, R},
title = {Reef Location and Client Diversity Influence the Skin Microbiome of the Caribbean Cleaner Goby Elacatinus evelynae.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {372-382},
pmid = {35275230},
issn = {1432-184X},
support = {OCE-2023420//National Science Foundation/ ; OCE-2022955//National Science Foundation/ ; OCE-1536794//National Science Foundation/ ; PTDC/BIA-MIC/27995/2017 POCI-01-0145- FEDER-027995//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/00359/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2020.00854.CEECIND//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Animals ; RNA, Ribosomal, 16S ; *Perciformes ; Fishes/microbiology ; Coral Reefs ; *Microbiota ; Caribbean Region ; Bacteria ; },
abstract = {Fish-associated microorganisms are known to be affected by the environment and other external factors, such as microbial transfer between interacting partners. One of the most iconic mutualistic interactions on coral reefs is the cleaning interactions between cleaner fishes and their clients, during which direct physical contact occurs. Here, we characterized the skin bacteria of the Caribbean cleaner sharknose goby, Elacatinus evelynae, in four coral reefs of the US Virgin Islands using sequencing of the V4 region of the 16S rRNA gene. We specifically tested the relationship between gobies' level of interaction with clients and skin microbiota diversity and composition. Our results showed differences in microbial alpha- and beta-diversity in the skin of gobies from different reef habitats and high inter-individual variation in microbiota diversity and structure. Overall, the results showed that fish-to-fish direct contact and specifically, access to a diverse clientele, influences the bacterial diversity and structure of cleaner gobies' skin. Because of their frequent contact with clients, and therefore, high potential for microbial exchange, cleaner fish may serve as models in future studies aiming to understand the role of social microbial transfer in reef fish communities.},
}
@article {pmid35273366,
year = {2022},
author = {Mongelli, V and Lequime, S and Kousathanas, A and Gausson, V and Blanc, H and Nigg, J and Quintana-Murci, L and Elena, SF and Saleh, MC},
title = {Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster.},
journal = {Nature ecology &amp; evolution},
volume = {6},
number = {5},
pages = {565-578},
pmid = {35273366},
issn = {2397-334X},
support = {615220/ERC_/European Research Council/International ; },
mesh = {Animals ; Antiviral Agents/metabolism ; Dicistroviridae ; *Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Immunity, Innate ; *RNA Viruses/metabolism ; },
abstract = {Host-pathogen interactions impose recurrent selective pressures that lead to constant adaptation and counter-adaptation in both competing species. Here, we sought to study this evolutionary arms-race and assessed the impact of the innate immune system on viral population diversity and evolution, using Drosophila melanogaster as model host and its natural pathogen Drosophila C virus (DCV). We isogenized eight fly genotypes generating animals defective for RNAi, Imd and Toll innate immune pathways as well as pathogen-sensing and gut renewal pathways. Wild-type or mutant flies were then orally infected with DCV and the virus was serially passaged ten times via reinfection in naive flies. Viral population diversity was studied after each viral passage by high-throughput sequencing and infection phenotypes were assessed at the beginning and at the end of the evolution experiment. We found that the absence of any of the various immune pathways studied increased viral genetic diversity while attenuating virulence. Strikingly, these effects were observed in a range of host factors described as having mainly antiviral or antibacterial functions. Together, our results indicate that the innate immune system as a whole and not specific antiviral defence pathways in isolation, generally constrains viral diversity and evolution.},
}
@article {pmid35270157,
year = {2022},
author = {Madriz-Ordeñana, K and Pazarlar, S and Jørgensen, HJL and Nielsen, TK and Zhang, Y and Nielsen, KL and Hansen, LH and Thordal-Christensen, H},
title = {The Bacillus cereus Strain EC9 Primes the Plant Immune System for Superior Biocontrol of Fusarium oxysporum.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {5},
pages = {},
pmid = {35270157},
issn = {2223-7747},
support = {34009-16-1068//Green Development and Demonstration Programme (GUDP) of the Ministry of Environment and Food of Denmark/ ; },
abstract = {Antibiosis is a key feature widely exploited to develop biofungicides based on the ability of biological control agents (BCAs) to produce fungitoxic compounds. A less recognised attribute of plant-associated beneficial microorganisms is their ability to stimulate the plant immune system, which may provide long-term, systemic self-protection against different types of pathogens. By using conventional antifungal in vitro screening coupled with in planta assays, we found antifungal and non-antifungal Bacillus strains that protected the ornamental plant Kalanchoe against the soil-borne pathogen Fusarium oxysporum in experimental and commercial production settings. Further examination of one antifungal and one non-antifungal strain indicated that high protection efficacy in planta did not correlate with antifungal activity in vitro. Whole-genome sequencing showed that the non-antifungal strain EC9 lacked the biosynthetic gene clusters associated with typical antimicrobial compounds. Instead, this bacterium triggers the expression of marker genes for the jasmonic and salicylic acid defence pathways, but only after pathogen challenge, indicating that this strain may protect Kalanchoe plants by priming immunity. We suggest that the stimulation of the plant immune system is a promising mode of action of BCAs for the development of novel biological crop protection products.},
}
@article {pmid35268714,
year = {2022},
author = {Lee Díaz, AS and Rizaludin, MS and Zweers, H and Raaijmakers, JM and Garbeva, P},
title = {Exploring the Volatiles Released from Roots of Wild and Domesticated Tomato Plants under Insect Attack.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {5},
pages = {},
pmid = {35268714},
issn = {1420-3049},
support = {765290//European Commission/ ; 024.004.14/NWO_/Dutch Research Council/Netherlands ; },
mesh = {Animals ; Herbivory ; *Solanum lycopersicum/genetics ; *Solanum ; Spodoptera ; *Volatile Organic Compounds ; },
abstract = {Plants produce volatile organic compounds that are important in communication and defense. While studies have largely focused on volatiles emitted from aboveground plant parts upon exposure to biotic or abiotic stresses, volatile emissions from roots upon aboveground stress are less studied. Here, we investigated if tomato plants under insect herbivore attack exhibited a different root volatilome than non-stressed plants, and whether this was influenced by the plant's genetic background. To this end, we analyzed one domesticated and one wild tomato species, i.e., Solanum lycopersicum cv Moneymaker and Solanum pimpinellifolium, respectively, exposed to leaf herbivory by the insect Spodoptera exigua. Root volatiles were trapped with two sorbent materials, HiSorb and PDMS, at 24 h after exposure to insect stress. Our results revealed that differences in root volatilome were species-, stress-, and material-dependent. Upon leaf herbivory, the domesticated and wild tomato species showed different root volatile profiles. The wild species presented the largest change in root volatile compounds with an overall reduction in monoterpene emission under stress. Similarly, the domesticated species presented a slight reduction in monoterpene emission and an increased production of fatty-acid-derived volatiles under stress. Volatile profiles differed between the two sorbent materials, and both were required to obtain a more comprehensive characterization of the root volatilome. Collectively, these results provide a strong basis to further unravel the impact of herbivory stress on systemic volatile emissions.},
}
@article {pmid36398283,
year = {2021},
author = {Jeganathan, P and Holmes, SP},
title = {A Statistical Perspective on the Challenges in Molecular Microbial Biology.},
journal = {Journal of agricultural, biological, and environmental statistics},
volume = {26},
number = {2},
pages = {131-160},
pmid = {36398283},
issn = {1085-7117},
support = {R01 AI112401/AI/NIAID NIH HHS/United States ; },
abstract = {High throughput sequencing (HTS)-based technology enables identifying and quantifying non-culturable microbial organisms in all environments. Microbial sequences have enhanced our understanding of the human microbiome, the soil and plant environment, and the marine environment. All molecular microbial data pose statistical challenges due to contamination sequences from reagents, batch effects, unequal sampling, and undetected taxa. Technical biases and heteroscedasticity have the strongest effects, but different strains across subjects and environments also make direct differential abundance testing unwieldy. We provide an introduction to a few statistical tools that can overcome some of these difficulties and demonstrate those tools on an example. We show how standard statistical methods, such as simple hierarchical mixture and topic models, can facilitate inferences on latent microbial communities. We also review some nonparametric Bayesian approaches that combine visualization and uncertainty quantification. The intersection of molecular microbial biology and statistics is an exciting new venue. Finally, we list some of the important open problems that would benefit from more careful statistical method development.},
}
@article {pmid35935893,
year = {2021},
author = {Crous, PW and Cowan, DA and Maggs-Kölling, G and Yilmaz, N and Thangavel, R and Wingfield, MJ and Noordeloos, ME and Dima, B and Brandrud, TE and Jansen, GM and Morozova, OV and Vila, J and Shivas, RG and Tan, YP and Bishop-Hurley, S and Lacey, E and Marney, TS and Larsson, E and Le Floch, G and Lombard, L and Nodet, P and Hubka, V and Alvarado, P and Berraf-Tebbal, A and Reyes, JD and Delgado, G and Eichmeier, A and Jordal, JB and Kachalkin, AV and Kubátová, A and Maciá-Vicente, JG and Malysheva, EF and Papp, V and Rajeshkumar, KC and Sharma, A and Spetik, M and Szabóová, D and Tomashevskaya, MA and Abad, JA and Abad, ZG and Alexandrova, AV and Anand, G and Arenas, F and Ashtekar, N and Balashov, S and Bañares, &#xc1; and Baroncelli, R and Bera, I and Biketova, AY and Blomquist, CL and Boekhout, T and Boertmann, D and Bulyonkova, TM and Burgess, TI and Carnegie, AJ and Cobo-Diaz, JF and Corriol, G and Cunnington, JH and da Cruz, MO and Damm, U and Davoodian, N and de A Santiago, ALCM and Dearnaley, J and de Freitas, LWS and Dhileepan, K and Dimitrov, R and Di Piazza, S and Fatima, S and Fuljer, F and Galera, H and Ghosh, A and Giraldo, A and Glushakova, AM and Gorczak, M and Gouliamova, DE and Gramaje, D and Groenewald, M and Gunsch, CK and Gutiérrez, A and Holdom, D and Houbraken, J and Ismailov, AB and Istel, &#x141; and Iturriaga, T and Jeppson, M and Jurjević, &#x17d; and Kalinina, LB and Kapitonov, VI and Kautmanová, I and Khalid, AN and Kiran, M and Kiss, L and Kovács, &#xc1; and Kurose, D and Kušan, I and Lad, S and Læssøe, T and Lee, HB and Luangsa-Ard, JJ and Lynch, M and Mahamedi, AE and Malysheva, VF and Mateos, A and Matočec, N and Mešić, A and Miller, AN and Mongkolsamrit, S and Moreno, G and Morte, A and Mostowfizadeh-Ghalamfarsa, R and Naseer, A and Navarro-Ródenas, A and Nguyen, TTT and Noisripoom, W and Ntandu, JE and Nuytinck, J and Ostrý, V and Pankratov, TA and Pawłowska, J and Pecenka, J and Pham, THG and Polhorský, A and Pošta, A and Raudabaugh, DB and Reschke, K and Rodríguez, A and Romero, M and Rooney-Latham, S and Roux, J and Sandoval-Denis, M and Smith, MT and Steinrucken, TV and Svetasheva, TY and Tkalčec, Z and van der Linde, EJ and V D Vegte, M and Vauras, J and Verbeken, A and Visagie, CM and Vitelli, JS and Volobuev, SV and Weill, A and Wrzosek, M and Zmitrovich, IV and Zvyagina, EA and Groenewald, JZ},
title = {Fungal Planet description sheets: 1182-1283.},
journal = {Persoonia},
volume = {46},
number = {},
pages = {313-528},
pmid = {35935893},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indooroopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves of Stipagrostis sp., Nothophaeotheca mirabibensis (incl. Nothophaeotheca gen. nov.) on persistent inflorescence remains of Blepharis obmitrata, Paramyrothecium salvadorae on twigs of Salvadora persica, Preussia procaviicola on dung of Procavia sp., Sordaria equicola on zebra dung, Volutella salvadorae on stems of Salvadora persica. Netherlands, Entoloma ammophilum on sandy soil, Entoloma pseudocruentatum on nutrient poor (acid) soil, Entoloma pudens on plant debris, amongst grasses. New Zealand, Amorocoelophoma neoregeliae from leaf spots of Neoregelia sp., Aquilomyces metrosideri and Septoriella callistemonis from stem discolouration and leaf spots of Metrosideros sp., Cadophora neoregeliae from leaf spots of Neoregelia sp., Flexuomyces asteliae (incl. Flexuomyces gen. nov.) and Mollisia asteliae from leaf spots of Astelia chathamica, Ophioceras freycinetiae from leaf spots of Freycinetia banksii, Phaeosphaeria caricis-sectae from leaf spots of Carex secta. Norway, Cuphophyllus flavipesoides on soil in semi-natural grassland, Entoloma coracis on soil in calcareous Pinus and Tilia forests, Entoloma cyaneolilacinum on soil semi-natural grasslands, Inocybe norvegica on gravelly soil. Pakistan, Butyriboletus parachinarensis on soil in association with Quercus baloot. Poland, Hyalodendriella bialowiezensis on debris beneath fallen bark of Norway spruce Picea abies. Russia, Bolbitius sibiricus on à moss covered rotting trunk of Populus tremula, Crepidotus wasseri on debris of Populus tremula, Entoloma isborscanum on soil on calcareous grasslands, Entoloma subcoracis on soil in subalpine grasslands, Hydropus lecythiocystis on rotted wood of Betula pendula, Meruliopsis faginea on fallen dead branches of Fagus orientalis, Metschnikowia taurica from fruits of Ziziphus jujube, Suillus praetermissus on soil, Teunia lichenophila as endophyte from Cladonia rangiferina. Slovakia, Hygrocybe fulgens on mowed grassland, Pleuroflammula pannonica from corticated branches of Quercus sp. South Africa, Acrodontium burrowsianum on leaves of unidentified Poaceae, Castanediella senegaliae on dead pods of Senegalia ataxacantha, Cladophialophora behniae on leaves of Behnia sp., Colletotrichum cliviigenum on leaves of Clivia sp., Diatrype dalbergiae on bark of Dalbergia armata, Falcocladium heteropyxidicola on leaves of Heteropyxis canescens, Lapidomyces aloidendricola as epiphyte on brown stem of Aloidendron dichotomum, Lasionectria sansevieriae and Phaeosphaeriopsis sansevieriae on leaves of Sansevieria hyacinthoides, Lylea dalbergiae on Diatrype dalbergiae on bark of Dalbergia armata, Neochaetothyrina syzygii (incl. Neochaetothyrina gen. nov.) on leaves of Syzygium chordatum, Nothophaeomoniella ekebergiae (incl. Nothophaeomoniella gen. nov.) on leaves of Ekebergia pterophylla, Paracymostachys euphorbiae (incl. Paracymostachys gen. nov.) on leaf litter of Euphorbia ingens, Paramycosphaerella pterocarpi on leaves of Pterocarpus angolensis, Paramycosphaerella syzygii on leaf litter of Syzygium chordatum, Parateichospora phoenicicola (incl. Parateichospora gen. nov.) on leaves of Phoenix reclinata, Seiridium syzygii on twigs of Syzygium chordatum, Setophoma syzygii on leaves of Syzygium sp., Starmerella xylocopis from larval feed of an Afrotropical bee Xylocopa caffra, Teratosphaeria combreti on leaf litter of Combretum kraussii, Teratosphaericola leucadendri on leaves of Leucadendron sp., Toxicocladosporium pterocarpi on pods of Pterocarpus angolensis. Spain, Cortinarius bonachei with Quercus ilex in calcareus soils, Cortinarius brunneovolvatus under Quercus ilex subsp. ballota in calcareous soil, Extremopsis radicicola (incl. Extremopsis gen. nov.) from root-associated soil in a wet heathland, Russula quintanensis on acidic soils, Tubaria vulcanica on volcanic lapilii material, Tuber zambonelliae in calcareus soil. Sweden, Elaphomyces borealis on soil under Pinus sylvestris and Betula pubescens. Tanzania, Curvularia tanzanica on inflorescence of Cyperus aromaticus. Thailand, Simplicillium niveum on Ophiocordyceps camponoti-leonardi on underside of unidentified dicotyledonous leaf. USA, Calonectria californiensis on leaves of Umbellularia californica, Exophiala spartinae from surface sterilised roots of Spartina alterniflora, Neophaeococcomyces oklahomaensis from outside wall of alcohol distillery. Vietnam, Fistulinella aurantioflava on soil. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Cowan DA, Maggs-Kölling, et al. 2021. Fungal Planet description sheets: 1182-1283. Persoonia 46: 313-528. https://doi.org/10.3767/persoonia.2021.46.11.},
}
@article {pmid35707452,
year = {2021},
author = {Werbin, ZR and Hackos, B and Lopez-Nava, J and Dietze, MC and Bhatnagar, JM},
title = {The National Ecological Observatory Network's soil metagenomes: assembly and basic analysis.},
journal = {F1000Research},
volume = {10},
number = {},
pages = {299},
pmid = {35707452},
issn = {2046-1402},
mesh = {Computational Biology/methods ; *Metagenome ; Metagenomics/methods ; Neon ; *Soil ; },
abstract = {The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON's shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.},
}
@article {pmid36590333,
year = {2021},
author = {Koshy-Chenthittayil, S and Mendes, P and Laubenbacher, R},
title = {Optimization of Agent-Based Models Through Coarse-Graining: A Case Study in Microbial Ecology.},
journal = {Letters in biomathematics},
volume = {8},
number = {1},
pages = {167-178},
pmid = {36590333},
issn = {2373-7867},
support = {R01 AI135128/AI/NIAID NIH HHS/United States ; R01 GM127909/GM/NIGMS NIH HHS/United States ; U01 EB024501/EB/NIBIB NIH HHS/United States ; },
abstract = {Optimization and control are important objectives across biology and biomedicine, and mathematical models are a key enabling technology. This paper reports a computational study of model-based multi-objective optimization in the setting of microbial ecology, using agent-based models. This modeling framework is well-suited to the field, but is not amenable to standard control-theoretic approaches. Furthermore, due to computational complexity, simulation-based optimization approaches are often challenging to implement. This paper presents the results of an approach that combines control-dependent coarse-graining with Pareto optimization, applied to two models of multi-species bacterial biofilms. It shows that this approach can be successful for models whose computational complexity prevents effective simulation-based optimization.},
}
@article {pmid36131874,
year = {2021},
author = {Legin, AA and Schintlmeister, A and Sommerfeld, NS and Eckhard, M and Theiner, S and Reipert, S and Strohhofer, D and Jakupec, MA and Galanski, MS and Wagner, M and Keppler, BK},
title = {Nano-scale imaging of dual stable isotope labeled oxaliplatin in human colon cancer cells reveals the nucleolus as a putative node for therapeutic effect.},
journal = {Nanoscale advances},
volume = {3},
number = {1},
pages = {249-262},
pmid = {36131874},
issn = {2516-0230},
abstract = {Oxaliplatin shows a superior clinical activity in colorectal cancer compared to cisplatin. Nevertheless, the knowledge about its cellular distribution and the mechanisms responsible for the different range of oxaliplatin-responsive tumors is far from complete. In this study, we combined highly sensitive element specific and isotope selective imaging by nanometer-scale secondary ion mass spectrometry (NanoSIMS) with transmission electron microscopy to investigate the subcellular accumulation of oxaliplatin in three human colon cancer cell lines (SW480, HCT116 wt, HCT116 OxR). Oxaliplatin bearing dual stable isotope labeled moieties, i.e. [2]H-labeled diaminocyclohexane (DACH) and [13]C-labeled oxalate, were applied for comparative analysis of the subcellular distribution patterns of the central metal and the ligands. In all the investigated cell lines, oxaliplatin was found to have a pronounced tendency for cytoplasmic aggregation in single membrane bound organelles, presumably related to various stages of the endocytic pathway. Moreover, nuclear structures, heterochromatin and in particular nucleoli, were affected by platinum-drug exposure. In order to explore the consequences of oxaliplatin resistance, subcellular drug distribution patterns were investigated in a pair of isogenic malignant cell lines with distinct levels of drug sensitivity (HCT116 wt and HCT116 OxR, the latter with acquired resistance to oxaliplatin). The subcellular platinum distribution was found to be similar in both cell lines, with only slightly higher accumulation in the sensitive HCT116 wt cells which is inconsistent with the resistance factor of more than 20-fold. Instead, the isotopic analysis revealed a disproportionally high accumulation of the oxalate ligand in the resistant cell line.},
}
@article {pmid35846090,
year = {2021},
author = {Ludwig, H and Hausmann, B and Schreder, M and Pönisch, W and Zojer, N and Knop, S and Gunsilius, E and Egle, A and Petzer, A and Einsele, H and Hajek, R and Weisel, K and Krenosz, KJ and Lang, A and Lechner, D and Greil, R and Berry, D},
title = {Reduced alpha diversity of the oral microbiome correlates with short progression-free survival in patients with relapsed/refractory multiple myeloma treated with ixazomib-based therapy (AGMT MM 1, phase II trial).},
journal = {EJHaem},
volume = {2},
number = {1},
pages = {99-103},
pmid = {35846090},
issn = {2688-6146},
abstract = {Alterations in the human microbiome have been linked to several malignant diseases. Here, we investigated the oral microbiome of 79 patients with relapsed/refractory multiple myeloma (MM) treated with ixazomib-thalidomide-dexamethasone. Increased alpha diversity (Shannon index) at the phylum level was associated with longer progression-free survival (PFS) (10.2 vs 8.5 months, P = .04), particularly in patients with very long (>75% quartile) PFS . Additionally, alpha diversity was lower in patients with progressive disease (P < .05). These findings suggest an interrelationship between the oral microbiome and outcome in patients with MM and encourage a novel direction for diagnostic and/or therapeutic strategies.},
}
@article {pmid36157708,
year = {2020},
author = {Wang, M and Cernava, T},
title = {Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity.},
journal = {Environmental science and ecotechnology},
volume = {4},
number = {},
pages = {100061},
pmid = {36157708},
issn = {2666-4984},
abstract = {Recent studies have shown that various agrochemicals can substantially affect microbial communities; especially those that are associated with cultivated plants. Under certain circumstances, up to 50% of the naturally occurring microorganisms can be negatively affected by common agricultural practices such as seed coating with fungicide-based matrices. Nevertheless, the off-target effects of commonly applied agrochemicals are still understudied in terms of their interferences with microbial communities. At the same time, agrochemical inputs are steadily increasing due to the intensification of agriculture and the increasing pathogen pressure that is currently observed worldwide. In this article, we briefly reflect on the current knowledge related to pesticide interference with microbial communities and discuss negative implications for the plant holobiont as well as such that are spanning beyond local system borders. Cumulative effects of pesticide inputs that cause alterations in microbial functioning likely have unforeseen implications on geochemical cycles that should be addressed with a high priority in ongoing research. A holistic assessment of such implications will allow us to objectively select the most suitable means for food production under the scenario of a growing global population and aggravating climatic conditions. We present three hypothetical solutions that might facilitate a more sustainable and less damaging application of pesticides in the future.},
}
@article {pmid36159604,
year = {2020},
author = {Uria, N and Fiset, E and Pellitero, MA and Muñoz, FX and Rabaey, K and Campo, FJD},
title = {Immobilisation of electrochemically active bacteria on screen-printed electrodes for rapid in situ toxicity biosensing.},
journal = {Environmental science and ecotechnology},
volume = {3},
number = {},
pages = {100053},
pmid = {36159604},
issn = {2666-4984},
abstract = {Microbial biosensors can be an excellent alternative to classical methods for toxicity monitoring, which are time-consuming and not sensitive enough. However, bacteria typically connect to electrodes through biofilm formation, leading to problems due to lack of uniformity or long device production times. A suitable immobilisation technique can overcome these challenges. Still, they may respond more slowly than biofilm-based electrodes because bacteria gradually adapt to electron transfer during biofilm formation. In this study, we propose a controlled and reproducible way to fabricate bacteria-modified electrodes. The method consists of an immobilisation step using a cellulose matrix, followed by an electrode polarization in the presence of ferricyanide and glucose. Our process is short, reproducible and led us to obtain ready-to-use electrodes featuring a high-current response. An excellent shelf-life of the immobilised electrochemically active bacteria was demonstrated for up to one year. After an initial 50% activity loss in the first month, no further declines have been observed over the following 11 months. We implemented our bacteria-modified electrodes to fabricate a lateral flow platform for toxicity monitoring using formaldehyde (3%). Its addition led to a 59% current decrease approximately 20 min after the toxic input. The methods presented here offer the ability to develop a high sensitivity, easy to produce, and long shelf life bacteria-based toxicity detectors.},
}
@article {pmid36204422,
year = {2020},
author = {Li, G and Cortez, MH and Dushoff, J and Weitz, JS},
title = {When to be temperate: on the fitness benefits of lysis vs. lysogeny.},
journal = {Virus evolution},
volume = {6},
number = {2},
pages = {veaa042},
pmid = {36204422},
issn = {2057-1577},
abstract = {Bacterial viruses, that is 'bacteriophage' or 'phage', can infect and lyse their bacterial hosts, releasing new viral progeny. In addition to the lytic pathway, certain bacteriophage (i.e. 'temperate' bacteriophage) can also initiate lysogeny, a latent mode of infection in which the viral genome is integrated into and replicated with the bacterial chromosome. Subsequently, the integrated viral genome, that is the 'prophage', can induce and restart the lytic pathway. Here, we explore the relationship among infection mode, ecological context, and viral fitness, in essence asking: when should viruses be temperate? To do so, we use network loop analysis to quantify fitness in terms of network paths through the life history of an infectious pathogen that start and end with infected cells. This analysis reveals that temperate strategies, particularly those with direct benefits to cellular fitness, should be favored at low host abundances. This finding applies to a spectrum of mechanistic models of phage-bacteria dynamics spanning both explicit and implicit representations of intra-cellular infection dynamics. However, the same analysis reveals that temperate strategies, in and of themselves, do not provide an advantage when infection imposes a cost to cellular fitness. Hence, we use evolutionary invasion analysis to explore when temperate phage can invade microbial communities with circulating lytic phage. We find that lytic phage can drive down niche competition amongst microbial cells, facilitating the subsequent invasion of latent strategies that increase cellular resistance and/or immunity to infection by lytic viruses-notably this finding holds even when the prophage comes at a direct fitness cost to cellular reproduction. Altogether, our analysis identifies broad ecological conditions that favor latency and provide a principled framework for exploring the impacts of ecological context on both the short- and long-term benefits of being temperate.},
}
@article {pmid36159602,
year = {2020},
author = {De Vrieze, J},
title = {The next frontier of the anaerobic digestion microbiome: From ecology to process control.},
journal = {Environmental science and ecotechnology},
volume = {3},
number = {},
pages = {100032},
pmid = {36159602},
issn = {2666-4984},
abstract = {The anaerobic digestion process has been one of the key processes for renewable energy recovery from organic waste streams for over a century. The anaerobic digestion microbiome is, through the continuous development of novel techniques, evolving from a black box to a well-defined consortium, but we are not there yet. In this perspective, I provide my view on the current status and challenges of the anaerobic digestion microbiome, as well as the opportunities and solutions to exploit it. I consider identification and fingerprinting of the anaerobic digestion microbiome as complementary tools to monitor the anaerobic digestion microbiome. However, data availability, method-inherent biases and correct taxa identification hamper the accuracy and reproducibility of anaerobic digestion microbiome characterization. Standardisation of microbiome research in anaerobic digestion and other engineered systems will be essential in the coming decades, for which I proposed some targeted solutions. These will bring anaerobic digestion from a single-purpose energy-recovery technology to a versatile process for integrated resource recovery. It is my opinion that the exploitation of the microbiome will be a driver of innovation, and that it has a key role to play in the bio-based economy of the decades to come.},
}
@article {pmid36160374,
year = {2020},
author = {Wang, X and Aulenta, F and Puig, S and Esteve-Núñez, A and He, Y and Mu, Y and Rabaey, K},
title = {Microbial electrochemistry for bioremediation.},
journal = {Environmental science and ecotechnology},
volume = {1},
number = {},
pages = {100013},
pmid = {36160374},
issn = {2666-4984},
abstract = {Lack of suitable electron donors or acceptors is in many cases the key reason for pollutants to persist in the environment. Externally supplementation of electron donors or acceptors is often difficult to control and/or involves chemical additions with limited lifespan, residue formation or other adverse side effects. Microbial electrochemistry has evolved very fast in the past years - this field relates to the study of electrochemical interactions between microorganisms and solid-state electron donors or acceptors. Current can be supplied in such so-called bioelectrochemical systems (BESs) at low voltage to provide or extract electrons in a very precise manner. A plethora of metabolisms can be linked to electrical current now, from metals reductions to denitrification and dechlorination. In this perspective, we provide an overview of the emerging applications of BES and derived technologies towards the bioremediation field and outline how this approach can be game changing.},
}
@article {pmid35531503,
year = {2019},
author = {Yan, Y and Du, Z and Zhang, L and Feng, L and Sun, D and Dang, Y and Holmes, DE and Smith, JA},
title = {Identification of parameters needed for optimal anaerobic co-digestion of chicken manure and corn stover.},
journal = {RSC advances},
volume = {9},
number = {51},
pages = {29609-29618},
pmid = {35531503},
issn = {2046-2069},
abstract = {While studies have shown that anaerobic co-digestion of chicken manure (CM) and corn stover (CS) is an efficient method to treat these agricultural wastes, the microbial ecology of these systems and optimal parameters for the digestion process are yet to be determined. In this study, the effects of different initial substrate concentrations and CS : CM mixture ratios on co-digestion and microbial community structure were evaluated. Results demonstrated that both the highest cumulative methane yields and methane production rates were obtained from reactors with a CS : CM ratio of 1 : 1 during hemi-solid-state anaerobic digestion (HSS-AD). Cumulative methane yields and methane production rates were 24.8% and 42% lower in solid-state anaerobic digestion (SS-AD) reactors using the same CS : CM ratios. Analysis of microbial community structures revealed that cellulolytic bacteria and a diversity of syntrophic microorganisms capable of direct interspecies electron transfer (DIET) and hydrogen interspecies transfer (HIT) were enriched in the best-performing reactors. Methanosarcina species also dominated during HSS-AD, and their presence was positively correlated with methane production in the reactors.},
}
@article {pmid36659680,
year = {2019},
author = {Zheng, BX and Zhao, Y and Bi, QF and Zhou, GW and Wang, HJ and Hao, XL and Ding, K},
title = {How to disentangle microbially functional complexity: an insight from the network analysis of C, N, P and S cycling genes.},
journal = {Science bulletin},
volume = {64},
number = {16},
pages = {1129-1131},
doi = {10.1016/j.scib.2019.06.011},
pmid = {36659680},
issn = {2095-9281},
}
@article {pmid35557833,
year = {2018},
author = {Zhang, R and Wang, L and Chen, P and Pu, Y},
title = {Shifts in microbial community structure and diversity in a novel waterfall biofilm reactor combined with MBBR under light and dark conditions.},
journal = {RSC advances},
volume = {8},
number = {65},
pages = {37462-37471},
pmid = {35557833},
issn = {2046-2069},
abstract = {In this study, a novel, low-cost, easy-maintenance and effective waterfall aeration biofilm reactor (WFBR) was designed to treat wastewater with MBBR. The chemical oxygen demand (COD), nitrogen removal efficiency, and the microbial community structure in this novel system were evaluated for 70 days under light and dark conditions. The COD and ammonium nitrogen (NH3-N) removal efficiency remained at approximately 90% and 100% respectively after 25 days, even if the influent substrate concentration and illumination condition changes. High-throughput sequencing was used to investigate the composition and function of the microbial community in different fillers in the treatment system. Dark padding, illuminate carrier and fabric play the good performance in nitrogen nitrification, denitrification and fixation respectively. The major classes present were Betaproteobacteria (30.2% on average), Cytophagia (19.8%), Gammaproteobacteria (11.7%), Alphaproteobacteria (11.2%), Sphingobacteriia (5.1%), Flavobacteriia (2.6%), Deltaproteobacteria (2.4%), Verrucomicrobiae (0.7%), Chloroplast (0.6%) and Clostridia (0.5%). These results could provide important guidance for the improvement of MBBR or other tradition wastewater treatment process, and could also enrich our theoretical understanding of microbial ecology.},
}
@article {pmid35539271,
year = {2018},
author = {Zhang, H and Zhao, Z and Chen, S and Wang, Y and Feng, J and Jia, J and Kang, P and Li, S},
title = {Geographical patterns of denitrifying bacterial communities associated with different urban lakes.},
journal = {RSC advances},
volume = {8},
number = {31},
pages = {17079-17090},
pmid = {35539271},
issn = {2046-2069},
abstract = {The geographical variation of denitrifying bacterial communities and water quality parameters in urban lakes distributed across nine provinces in China were determined. The Illumina sequencing data of the denitrifying encoding gene nirS was examined in the samples collected from nine localities (pairwise geographical distance: 200-2600 km). The results showed that fundamental differences in water quality were observed among different urban lakes. The highest nitrate (2.02 mg L[-1]) and total nitrogen (3.82 mg L[-1]) concentrations were observed in Pingzhuang (P < 0.01). The algal cell concentration ranged from 1.29 × 10[8] to 3.0 × 10[9] cell per L. The sequencing data generated a total of 421058 high quality nirS gene reads that resulted in 6369 OTUs (97% cutoff), with Proteobacteria and Firmicutes being the dominant taxa. A co-occurrence network analysis indicated that the top five genera identified as keystone taxa were Dechlorospirillum sp., Alicycliphilus sp., Dechloromonas sp., Pseudogulbenkiania sp., and Paracoccus sp. A redundancy analysis (RDA) further revealed that distinct denitrifying bacterial communities inhabited the different urban lakes, and influenced by urban lake water ammonia nitrogen, manganese and algal cell concentrations. A variance partitioning analysis (VPA) also showed that geographic location was more important than water quality factors in structuring the denitrifying bacterial communities. Together, these results provide new insight into understanding of denitrifying bacterial communities associated with geographically distributed urban lakes on a larger scale, and these results also expand our exploration of aquatic microbial ecology in freshwater bodies.},
}
@article {pmid35919909,
year = {2014},
author = {Legin, AA and Schintlmeister, A and Jakupec, MA and Galanski, MS and Lichtscheidl, I and Wagner, M and Keppler, BK},
title = {NanoSIMS combined with fluorescence microscopy as a tool for subcellular imaging of isotopically labeled platinum-based anticancer drugs.},
journal = {Chemical science},
volume = {5},
number = {8},
pages = {3135-3143},
pmid = {35919909},
issn = {2041-6520},
abstract = {Multi-elemental, isotope selective nano-scale secondary ion mass spectrometry (NanoSIMS) combined with confocal laser-scanning microscopy was used to characterize the subcellular distribution of [15]N-labeled cisplatin in human colon cancer cells. These analyses indicated predominant cisplatin colocalisation with sulfur-rich structures in both the nucleus and cytoplasm. Furthermore, colocalisation of platinum with phosphorus-rich chromatin regions was observed, which is consistent with its binding affinity to DNA as the generally accepted crucial target of the drug. Application of [15]N-labeled cisplatin and subsequent measurement of the nitrogen isotopic composition and determination of the relative intensities of platinum and nitrogen associated secondary ion signals in different cellular compartments with NanoSIMS suggested partial dissociation of Pt-N bonds during the accumulation process, in particular within nucleoli at elevated cisplatin concentrations. This finding raises the question as to whether the observed intracellular dissociation of the drug has implications for the mechanism of action of cisplatin. Within the cytoplasm, platinum mainly accumulated in acidic organelles, as demonstrated by a direct combination of specific fluorescent staining, confocal laser scanning microscopy and NanoSIMS. Different processing of platinum drugs in acidic organelles might be relevant for their detoxification, as well as for their mode of action.},
}
@article {pmid35266794,
year = {2022},
author = {Monsees, I and Turzynski, V and Esser, SP and Soares, A and Timmermann, LI and Weidenbach, K and Banas, J and Kloster, M and Beszteri, B and Schmitz, RA and Probst, AJ},
title = {Erratum for Monsees et al., "Label-Free Raman Microspectroscopy for Identifying Prokaryotic Virocells".},
journal = {mSystems},
volume = {7},
number = {2},
pages = {e0016222},
doi = {10.1128/msystems.00162-22},
pmid = {35266794},
issn = {2379-5077},
}
@article {pmid35266047,
year = {2022},
author = {Proenca, AM and Oliveira, MM and Neves, PFR and Giongo, A and de Oliveira, RR and Ott, CT and Marconatto, L and de Barros Neto, HMC and Ketzer, JMM and Medina-Silva, R},
title = {Genomic, biochemical, and phylogenetic evaluation of bacteria isolated from deep-sea sediment harboring methane hydrates.},
journal = {Archives of microbiology},
volume = {204},
number = {4},
pages = {205},
pmid = {35266047},
issn = {1432-072X},
mesh = {*Bacteria ; Genomics ; Geologic Sediments/microbiology ; *Methane/metabolism ; Phylogeny ; },
abstract = {Over half of the organic carbon on Earth's surface is trapped in marine sediment as methane hydrates. Ocean warming causes hydrate dissociation and methane leakage to the water column, rendering the characterization of microbes from hydrate depositions a pressing matter. Through genomic, phylogenetic, and biochemical assays, we characterize the first microorganisms isolated from the Rio Grande Cone (Brazil), reservoir responsible for massive methane releases to the water column. From sediment harboring rich benthic communities, we obtained 43 strains of Brevibacillus sp., Paenibacillus sp. and groups of Bacillus sp. Methane-enriched samples yielded strains of the Pseudomonas fluorescens complex, exhibiting fluorescent siderophore production and broad multi-carbon catabolism. Genomic characterization of a novel Pseudomonas sp. strain indicated 32 genes not identified in the closest related type-species, including proteins involved with mercury resistance. Our results provide phylogenetic and genomic insights on the first bacterial isolates retrieved from a poorly explored region of the South Atlantic Ocean.},
}
@article {pmid35265531,
year = {2022},
author = {Yang, S and Lyu, X and Zhang, J and Shui, Y and Yang, R and Xu, X},
title = {The Application of Small Molecules to the Control of Typical Species Associated With Oral Infectious Diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {816386},
pmid = {35265531},
issn = {2235-2988},
mesh = {*Communicable Diseases ; *Dental Caries/prevention &amp; control ; Dysbiosis ; Humans ; *Microbiota ; Virulence ; },
abstract = {Oral microbial dysbiosis is the major causative factor for common oral infectious diseases including dental caries and periodontal diseases. Interventions that can lessen the microbial virulence and reconstitute microbial ecology have drawn increasing attention in the development of novel therapeutics for oral diseases. Antimicrobial small molecules are a series of natural or synthetic bioactive compounds that have shown inhibitory effect on oral microbiota associated with oral infectious diseases. Novel small molecules, which can either selectively inhibit keystone microbes that drive dysbiosis of oral microbiota or inhibit the key virulence of the microbial community without necessarily killing the microbes, are promising for the ecological management of oral diseases. Here we discussed the research progress in the development of antimicrobial small molecules and delivery systems, with a particular focus on their antimicrobial activity against typical species associated with oral infectious diseases and the underlying mechanisms.},
}
@article {pmid35264931,
year = {2022},
author = {Muedra, V and Rodilla, V and Llansola, M and Agustí, A and Pla, C and Canto, A and Hernández-Rabaza, V},
title = {Potential Neuroprotective Role of Sugammadex: A Clinical Study on Cognitive Function Assessment in an Enhanced Recovery After Cardiac Surgery Approach and an Experimental Study.},
journal = {Frontiers in cellular neuroscience},
volume = {16},
number = {},
pages = {789796},
pmid = {35264931},
issn = {1662-5102},
abstract = {BACKGROUND: Postoperative cognitive dysfunction affects the quality of recovery, particularly affecting the elderly, and poses a burden on the health system. We hypothesize that the use of sugammadex (SG) could optimize the quality of postoperative cognitive function and overall recovery through a neuroprotective effect.<br><br>METHODS: A pilot observational study on patients undergoing cardiac surgery with enhanced recovery after cardiac surgery (ERACS) approach, was designed to compare SG-treated (n = 14) vs. neostigmine (NG)-treated (n = 7) patients. The Postoperative Quality Recovery Scale (PQRS) was used at different times to evaluate cognitive function and overall recovery of the patients. An online survey among anesthesiologists on SG use was also performed. Additionally, an animal model study was designed to explore the effects of SG on the hippocampus.<br><br>RESULTS: Sugammadex (SG) was associated with favorable postoperative recovery in cognitive domains particularly 30 days after surgery in patients undergoing aortic valve replacement by cardiopulmonary bypass and the ERACS approach; however, it failed to demonstrate a short-term decrease in length of intensive care unit (ICU) and hospital stay. The survey information indicated a positive appreciation of SG recovery properties. SG reverts postoperative memory deficit and induces the expression of anti-inflammatory microglial markers.<br><br>CONCLUSION: The results show a postoperative cognitive improvement by SG treatment in patients undergoing aortic valve replacement procedure by the ERACS approach. Additionally, experimental data from an animal model of mild surgery confirm the cognitive effect of SG and suggest a potential effect over glia cells as an underlying mechanism.},
}
@article {pmid35264088,
year = {2022},
author = {Rana, D and Salave, S and Perla, A and Nadkarni, A and Kolhe, S and Jindal, AB and Mandoli, A and Dwivedi, P and Benival, D},
title = {Bugs as Drugs: Understanding the Linkage between Gut Microbiota and Cancer Treatment.},
journal = {Current drug targets},
volume = {23},
number = {9},
pages = {869-888},
doi = {10.2174/1389450123666220309101345},
pmid = {35264088},
issn = {1873-5592},
mesh = {Carcinogenesis ; Diet ; Dysbiosis/therapy ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; },
abstract = {The commensal microbiota is known to regulate host physiology. Dysbiosis or compromised resilience in the microbial ecology is related to the impending risk of cancer. A potential link between cancer and microbiota is indicated by a lot of evidence. The current review explores in detail the various links leading to and /or facilitating oncogenesis, providing sound reasoning or a basis for its utilization as potential therapeutic targets. The present review emphasizes the existing knowledge of the microbiome in cancer and further elaborates on the factors, like genetic modifications, effects of dietary components, and environmental agents, that are considered to assess the direct and indirect effect of microbes in the process of oncogenesis and on the host's health. Strategies modulating the microbiome and novel biotherapeutics are also discussed. Pharmacomicrobiomics is one such niche accounting for the interplay between the microbiome, xenobiotic, and host responses, which is also looked upon. The literature search strategy for this review was conducted by following the methodology of the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA). The method includes the collection of data from different search engines, like PubMed, ScienceDirect, SciFinder, etc., to get coverage of relevant literature for accumulating appropriate information regarding microbiome, cancer, and their linkages. These considerations are made to expand the existing literature on the role of gut microbiota in the host's health, the interaction between host and microbiota, and the reciprocal relationship between the microbiome and modified neoplastic cells. Potential therapeutic implications of cancer microbiomes that are yet unexplored and have rich therapeutic dividends improving human health are discussed in detail in this review.},
}
@article {pmid35261753,
year = {2022},
author = {Stelzer, JAA and Mesman, JP and Gsell, AS and de Senerpont Domis, LN and Visser, PM and Adrian, R and Ibelings, BW},
title = {Phytoplankton responses to repeated pulse perturbations imposed on a trend of increasing eutrophication.},
journal = {Ecology and evolution},
volume = {12},
number = {3},
pages = {e8675},
pmid = {35261753},
issn = {2045-7758},
abstract = {While eutrophication remains one of the main pressures acting on freshwater ecosystems, the prevalence of anthropogenic and nature-induced stochastic pulse perturbations is predicted to increase due to climate change. Despite all our knowledge on the effects of eutrophication and stochastic events operating in isolation, we know little about how eutrophication may affect the response and recovery of aquatic ecosystems to pulse perturbations. There are multiple ways in which eutrophication and pulse perturbations may interact to induce potentially synergic changes in the system, for instance, by increasing the amount of nutrients released after a pulse perturbation. Here, we performed a controlled press and pulse perturbation experiment using mesocosms filled with natural lake water to address how eutrophication modulates the phytoplankton response to sequential mortality pulse perturbations; and what is the combined effect of press and pulse perturbations on the resistance and resilience of the phytoplankton community. Our experiment showed that eutrophication increased the absolute scale of the chlorophyll-a response to pulse perturbations but did not change the proportion of the response relative to its pre-event condition (resistance). Moreover, the capacity of the community to recover from pulse perturbations was significantly affected by the cumulative effect of sequential pulse perturbations but not by eutrophication itself. By the end of the experiment, some mesocosms could not recover from pulse perturbations, irrespective of the trophic state induced by the press perturbation. While not resisting or recovering any less from pulse perturbations, phytoplankton communities from eutrophying systems showed chlorophyll-a levels much higher than non-eutrophying ones. This implies that the higher absolute response to stochastic pulse perturbations in a eutrophying system may increase the already significant risks for water quality (e.g., algal blooms in drinking water supplies), even if the relative scale of the response to pulse perturbations between eutrophying and non-eutrophying systems remains the same.},
}
@article {pmid35261041,
year = {2022},
author = {Lousada, MB and Lachnit, T and Edelkamp, J and Paus, R and Bosch, TCG},
title = {Hydra and the hair follicle - An unconventional comparative biology approach to exploring the human holobiont.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {44},
number = {5},
pages = {e2100233},
doi = {10.1002/bies.202100233},
pmid = {35261041},
issn = {1521-1878},
mesh = {Animals ; Biology ; Hair Follicle ; Humans ; *Hydra/physiology ; Microbial Interactions ; *Microbiota/physiology ; },
abstract = {The microbiome of human hair follicles (HFs) has emerged as an important player in different HF and skin pathologies, yet awaits in-depth exploration. This raises questions regarding the tightly linked interactions between host environment, nutrient dependency of host-associated microbes, microbial metabolism, microbe-microbe interactions and host immunity. The use of simple model systems facilitates addressing generally important questions and testing overarching, therapeutically relevant principles that likely transcend obvious interspecies differences. Here, we evaluate the potential of the freshwater polyp Hydra, to dissect fundamental principles of microbiome regulation by the host, that is the human HF. In particular, we focus on therapeutically targetable host-microbiome interactions, such as nutrient dependency, microbial interactions and host defence. Offering a new lens into the study of HF - microbiota interactions, we argue that general principles of how Hydra manages its microbiota can inform the development of novel, microbiome-targeting therapeutic interventions in human skin disease.},
}
@article {pmid35260198,
year = {2022},
author = {Xie, Y and Sun, H and Xue, M and Liu, J},
title = {Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake.},
journal = {Animal microbiome},
volume = {4},
number = {1},
pages = {19},
pmid = {35260198},
issn = {2524-4671},
support = {31872380//National Natural Science Foundation of China/ ; CARS-36//Agriculture Research System of China/ ; },
abstract = {BACKGROUND: Rumen microbial composition and functions have vital roles in feed digestion and fermentation and are linked to feed efficiency in cattle. This study selected Holstein cows, which are high in both milk protein content and milk yield, to analyse the relationship between the rumen microbiota and residual feed intake (RFI). Eighteen multiparous lactating cows were divided into low RFI (LRFI, high efficiency, n = 9) and high RFI (HRFI, low efficiency, n = 9) groups to investigate the differences in microbial composition and functions.<br><br>RESULTS: The relative abundances of butyrate producers, including the Clostridium, Butyrivibrio, Eubacterium and Blautia genera, were higher in HRFI cows than in LRFI cows (P&#x2009;<&#x2009;0.05). Four carbohydrate metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate pathway, fructose and mannose metabolism, and butanoate metabolism) and one energy metabolism pathway (methane metabolism), were more abundant in HRFI animals (P&#x2009;<&#x2009;0.05). Quorum sensing and DNA replication pathways were more abundant in HRFI cows. For CAZyme profiles, 14 out of 19 genes encoding carbohydrates-deconstructing enzymes were more abundant in HRFI cows (P&#x2009;<&#x2009;0.05). Seven Lachnospiraceae species associated with carbohydrate metabolism and quorum sensing may contribute to the difference in feed efficiency. Moreover, the LRFI cows had lower abundances of Methanosphaera (P&#x2009;<&#x2009;0.01), Methanobrevibacter ruminantium (P&#x2009;=&#x2009;0.09) and methanogenesis functions (P&#x2009;=&#x2009;0.04).<br><br>CONCLUSIONS: The rumen microbiota of low-efficiency cows has stronger abilities to degrade carbohydrates and produce methane, and quorum sensing pathways could also be associated with differences in feed efficiency. This study provides a deeper understanding of the microbial ecology of dairy cows with different feed efficiencies and highlights the possibility of modulating the rumen microbiome or microbial functions to improve the feed efficiency of dairy cows.},
}
@article {pmid35256948,
year = {2022},
author = {Little, M and Dutta, M and Li, H and Matson, A and Shi, X and Mascarinas, G and Molla, B and Weigel, K and Gu, H and Mani, S and Cui, JY},
title = {Understanding the physiological functions of the host xenobiotic-sensing nuclear receptors PXR and CAR on the gut microbiome using genetically modified mice.},
journal = {Acta pharmaceutica Sinica. B},
volume = {12},
number = {2},
pages = {801-820},
pmid = {35256948},
issn = {2211-3835},
support = {P50 HD103524/HD/NICHD NIH HHS/United States ; R01 ES031098/ES/NIEHS NIH HHS/United States ; R01 ES030197/ES/NIEHS NIH HHS/United States ; R01 GM111381/GM/NIGMS NIH HHS/United States ; P30 ES007033/ES/NIEHS NIH HHS/United States ; R25 ES025503/ES/NIEHS NIH HHS/United States ; R01 CA222469/CA/NCI NIH HHS/United States ; R01 GM057001/GM/NIGMS NIH HHS/United States ; R01 ES025708/ES/NIEHS NIH HHS/United States ; P01 HL029019/HL/NHLBI NIH HHS/United States ; },
abstract = {Pharmacological activation of the xenobiotic-sensing nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) is well-known to increase drug metabolism and reduce inflammation. Little is known regarding their physiological functions on the gut microbiome. In this study, we discovered bivalent hormetic functions of PXR/CAR modulating the richness of the gut microbiome using genetically engineered mice. The absence of PXR or CAR increased microbial richness, and absence of both receptors synergistically increased microbial richness. PXR and CAR deficiency increased the pro-inflammatory bacteria Helicobacteraceae and Helicobacter. Deficiency in both PXR and CAR increased the relative abundance of Lactobacillus, which has bile salt hydrolase activity, corresponding to decreased primary taurine-conjugated bile acids (BAs) in feces, which may lead to higher internal burden of taurine and unconjugated BAs, both of which are linked to inflammation, oxidative stress, and cytotoxicity. The basal effect of PXR/CAR on the gut microbiome was distinct from pharmacological and toxicological activation of these receptors. Common PXR/CAR-targeted bacteria were identified, the majority of which were suppressed by these receptors. hPXR-TG mice had a distinct microbial profile as compared to wild-type mice. This study is the first to unveil the basal functions of PXR and CAR on the gut microbiome.},
}
@article {pmid35254501,
year = {2023},
author = {Wang, T and Kuang, B and Ni, Z and Guo, B and Li, Y and Zhu, G},
title = {Stimulating Anaerobic Degradation of Butyrate via Syntrophomonas wolfei and Geobacter sulfurreducens: Characteristics and Mechanism.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {535-543},
pmid = {35254501},
issn = {1432-184X},
support = {52070176//the National Natural Science Foundation of China/ ; 21876167//the National Natural Science Foundation of China/ ; 51678553//the National Natural Science Foundation of China/ ; },
mesh = {Anaerobiosis ; Electron Transport ; *Geobacter ; Butyric Acid ; },
abstract = {Anaerobic digestion (AD) has been widely applied for the degradation of organic wastewater due to its advantages of high-load operation and energy recovery. However, some challenges, such as low treatment capacity and instability caused by the accumulation of volatile fatty acids, limit its further application. Here, S. wolfei and G. sulfurreducens were initially co-cultured in the anaerobic anode of bio-electrochemical system for degrading butyric acid. Butyrate degradation characteristics in different conditions were quantitatively described. Moreover, G. sulfurreducens simultaneously strengthened the consumption of H2 and acetic acid via direct interspecies electron transfer, thereby strengthening the degradation of butyric acid via a co-metabolic process. During butyrate degradation, the co-culture of S. wolfei and G. sulfurreducens showed more advantages than that of S. wolfei and methanogens. This present study provides a new perspective of butyrate metabolism, which was independent of methanogens in an AD process.},
}
@article {pmid35254236,
year = {2022},
author = {Tomasch, J and Ringel, V and Wang, H and Freese, HM and Bartling, P and Brinkmann, H and Vollmers, J and Jarek, M and Wagner-Döbler, I and Petersen, J},
title = {Fatal affairs - conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales.},
journal = {Microbial genomics},
volume = {8},
number = {3},
pages = {},
pmid = {35254236},
issn = {2057-5858},
mesh = {*Dinoflagellida/genetics ; Plasmids/genetics ; Replicon ; Rhodobacteraceae ; *Roseobacter/genetics ; },
abstract = {The roseobacter group of marine bacteria is characterized by a mosaic distribution of ecologically important phenotypes. These are often encoded on mobile extrachromosomal replicons. So far, conjugation had only been experimentally proven between the two model organisms Phaeobacter inhibens and Dinoroseobacter shibae. Here, we show that two large natural RepABC-type plasmids from D. shibae can be transferred into representatives of all known major Rhodobacterales lineages. Complete genome sequencing of the newly established Phaeobacter inhibens transconjugants confirmed their genomic integrity. The conjugated plasmids were stably maintained as single copy number replicons in the genuine as well as the new host. Co-cultivation of Phaeobacter inhibens and the transconjugants with the dinoflagellate Prorocentrum minimum demonstrated that Phaeobacter inhibens is a probiotic strain that improves the yield and stability of the dinoflagellate culture. The transconjugant carrying the 191 kb plasmid, but not the 126 kb sister plasmid, killed the dinoflagellate in co-culture.},
}
@article {pmid35250945,
year = {2022},
author = {Bai, C and Pan, G and Leng, R and Ni, W and Yang, J and Sun, J and Yu, Z and Liu, Z and Xue, Y},
title = {Effect of Ensiling Density and Storage Temperature on Fermentation Quality, Bacterial Community, and Nitrate Concentration of Sorghum-Sudangrass Silage.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {828320},
pmid = {35250945},
issn = {1664-302X},
abstract = {This study aimed to evaluate the fermentation quality, bacterial community, and nitrate content of sorghum-sudangrass silage with two ensiling densities [550 kg fresh weight (FW)/m[3] (low density, LD) and 650 kg FW/m[3] (high density, HD)] stored at two temperatures [10°C (low temperature, LT) and 25°C (normal temperature, NT)] for 60 days. The fermentation parameters, microbial counts, bacterial community, nutritional composition, and nitrate and nitrite levels were assessed. The pH and ammonia nitrogen (N) in all silages were below 4.0 and 80 g/kg total N, respectively. Compared with LT treatments, NT treatments had lower pH and lactic acid (LA) bacteria and yeasts counts and contained higher LA and LA/acetic acid (LA/AA) (p < 0.05). The LT-LD contained more ammonia-N than LT-HD (p < 0.05) and had higher nitrate and lower nitrate degradation than other treatments (p < 0.05). Lactobacillus was the most dominant genus with all treatments (57.2-66.9%). The LA, LA/AA, and abundances of Pantoea, Pseudomonas, and Enterobacter in the silage negatively correlated with nitrate concentration and positively correlated with nitrate degradation (p < 0.05). Moreover, pH and ammonia-N were positively correlated with nitrate concentration and negatively correlated with nitrate degradation (p < 0.05). Overall, all silage had satisfactory fermentation quality, and the silage with HD and NT had better fermentation quality and higher nitrate degradation. The bacterial communities in all silages were dominated by Lactobacillus. The nitrate degradation during the fermentation process might be related to the fermentation quality and the activity of Pantoea, Pseudomonas, and Enterobacter in silage.},
}
@article {pmid35248630,
year = {2022},
author = {Obieze, CC and Wani, GA and Shah, MA and Reshi, ZA and Comeau, AM and Khasa, DP},
title = {Anthropogenic activities and geographic locations regulate microbial diversity, community assembly and species sorting in Canadian and Indian freshwater lakes.},
journal = {The Science of the total environment},
volume = {826},
number = {},
pages = {154292},
doi = {10.1016/j.scitotenv.2022.154292},
pmid = {35248630},
issn = {1879-1026},
mesh = {Anthropogenic Effects ; Bacteria ; Canada ; Humans ; *Lakes/chemistry ; *Microbiota ; },
abstract = {Freshwater lakes are important reservoirs and sources of drinking water globally. However, the microbiota, which supports the functionality of these ecosystems is threatened by the influx of nutrients, heavy metals and other toxic chemical substances from anthropogenic activities. The influence of these factors on the diversity, assembly mechanisms and co-occurrence patterns of bacterial communities in freshwater lakes is not clearly understood. Hence, samples were collected from six different impacted lakes in Canada and India and examined by 454-pyrosequencing technology. The trophic status of these lakes was determined using specific chemical parameters. Our results revealed that bacterial diversity and community composition was altered by both the lake water chemistry and geographic distance. Anthropogenic activities pervasively influenced species distribution. Dispersal limitation (32.3%), homogenous selection (31.8%) and drift (20%) accounted for the largest proportions of the bacterial community assembly mechanisms. Homogenous selection increased in lakes with higher nutrient concentration, while stochasticity reduced. Community functional profiles revealed that deterministic processes dominated the assembly mechanisms of phylotypes with higher potential for biodegradation, while stochasticity dominated the assembly of phylotypes with potential for antimicrobial resistance. Bacteroidota (44%) and Proteobacteria (34%) were the most abundant phyla. Co-occurrence network analysis revealed that complexity increased in more impacted lakes, while competition and the nature of anthropogenic activity contributed to species sorting. Overall, this study demonstrates that bacterial community changes in freshwater lakes are linked to anthropogenic activities, with corresponding consequences on the distribution of phylotypes of environmental and human health interest.},
}
@article {pmid35248491,
year = {2022},
author = {Barragán-Fonseca, KY and Nurfikari, A and van de Zande, EM and Wantulla, M and van Loon, JJA and de Boer, W and Dicke, M},
title = {Insect frass and exuviae to promote plant growth and health.},
journal = {Trends in plant science},
volume = {27},
number = {7},
pages = {646-654},
doi = {10.1016/j.tplants.2022.01.007},
pmid = {35248491},
issn = {1878-4372},
mesh = {Animals ; *Insecta ; *Plant Development ; Plants ; Soil ; Soil Microbiology ; },
abstract = {Beneficial soil microorganisms can contribute to biocontrol of plant pests and diseases, induce systemic resistance (ISR) against attackers, and enhance crop yield. Using organic soil amendments has been suggested to stimulate the abundance and/or activity of beneficial indigenous microbes in the soil. Residual streams from insect farming (frass and exuviae) contain chitin and other compounds that may stimulate beneficial soil microbes that have ISR and biocontrol activity. Additionally, changes in plant phenotype that are induced by beneficial microorganisms may directly influence plant-pollinator interactions, thus affecting plant reproduction. We explore the potential of insect residual streams derived from the production of insects as food and feed to promote plant growth and health, as well as their potential benefits for sustainable agriculture.},
}
@article {pmid35247805,
year = {2022},
author = {Song, S and Gui, Y and Rahman, MS and Xu, H},
title = {Use of protozoan periphytons for evaluating of environmental heterogeneity in intertidal zones of marine ecosystems.},
journal = {Marine pollution bulletin},
volume = {177},
number = {},
pages = {113498},
doi = {10.1016/j.marpolbul.2022.113498},
pmid = {35247805},
issn = {1879-3363},
mesh = {Biodiversity ; *Ciliophora ; Ecosystem ; Environmental Monitoring ; *Periphyton ; },
abstract = {As an important biological indicator, multivariate dispersion in homogeneity of an observed community is a useful parameter for bioassessment of environmental heterogeneity. To identify the influence of tidal events on homogeneity of protozoan periphyton fauna from the highest tideline to the lowest, a 1-month baseline survey was carried out along five tidelines (sites A-E) in an intertidal zone of the Yellow Sea, northern China. There was a significant influence of tidal events on the homogeneity in both compositional and community structure among five tidelines. The β-diversity measures generally decreased from the highest tideline to the lowest. The biodiversity indices of the protozoans dropped sharply from the highest to the middle tidelines, followed by an increase until to the lowest tideline. These findings suggest that the homogeneity of protozoan periphyton in both species composition and relative abundance was significantly shaped by the environmental heterogeneity in intertidal zones of marine ecosystems.},
}
@article {pmid35246698,
year = {2023},
author = {Fuster, M and Billard, H and Bronner, G and Sime-Ngando, T and Colombet, J},
title = {Occurrence and Seasonal Dynamics of ALNs in Freshwater Lakes Are Influenced by Their Biological Environment.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {523-534},
pmid = {35246698},
issn = {1432-184X},
mesh = {*Lakes ; *Ecosystem ; Seasons ; Prokaryotic Cells ; },
abstract = {Aster-like nanoparticles (ALNs) are femtoentities, recently discovered in different aquatic environments, whose intrinsic nature and ecological features remain to be determined. In this study, we investigate the in situ temporal dynamics of ALNs during 1 year in 3 different lakes, in relation to the physico-chemical and biological environment. ALN abundances in investigated lakes showed a marked seasonal dynamic (from no detectable to 4.28 ± 0.75 × 10[6] ALNs mL[-1]), with characteristic peaks in spring. We recorded a correlation between ALNs and some prokaryotic phyla suggesting a broad and non-specific relationship. From their seasonal dynamics and potential link with prokaryotes, we conclude that ALNs represent an important ecological actor in the functioning of aquatic ecosystems.},
}
@article {pmid35243218,
year = {2022},
author = {Liu, X and Le Roux, X and Salles, JF},
title = {The legacy of microbial inoculants in agroecosystems and potential for tackling climate change challenges.},
journal = {iScience},
volume = {25},
number = {3},
pages = {103821},
pmid = {35243218},
issn = {2589-0042},
abstract = {Microbial inoculations contribute to reducing agricultural systems' environmental footprint by supporting sustainable production and regulating climate change. However, the indirect and cascading effects of microbial inoculants through the reshaping of soil microbiome are largely overlooked. By discussing the underlying mechanisms of plant- and soil-based microbial inoculants, we suggest that a key challenge in microbial inoculation is to understand their legacy on indigenous microbial communities and the corresponding impacts on agroecosystem functions and services relevant to climate change. We explain how these legacy effects on the soil microbiome can be understood by building on the mechanisms driving microbial invasions and placing inoculation into the context of ecological succession and community assembly. Overall, we advocate that generalizing field trials to systematically test inoculants' effectiveness and developing knowledge anchored in the scientific field of biological/microbial invasion are two essential requirements for applying microbial inoculants in agricultural ecosystems to tackle climate change challenges.},
}
@article {pmid35242754,
year = {2021},
author = {Kuchenbuch, A and Frank, R and Ramos, JV and Jahnke, HG and Harnisch, F},
title = {Electrochemical Microwell Plate to Study Electroactive Microorganisms in Parallel and Real-Time.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {9},
number = {},
pages = {821734},
pmid = {35242754},
issn = {2296-4185},
abstract = {Microbial resource mining of electroactive microorganism (EAM) is currently methodically hampered due to unavailable electrochemical screening tools. Here, we introduce an electrochemical microwell plate (ec-MP) composed of a 96 electrochemical deepwell plate and a recently developed 96-channel multipotentiostat. Using the ec-MP we investigated the electrochemical and metabolic properties of the EAM models Shewanella oneidensis and Geobacter sulfurreducens with acetate and lactate as electron donor combined with an individual genetic analysis of each well. Electrochemical cultivation of pure cultures achieved maximum current densities (j max) and coulombic efficiencies (CE) that were well in line with literature data. The co-cultivation of S. oneidensis and G. sulfurreducens led to an increased current density of j max of 88.57 ± 14.04 µA cm[-2] (lactate) and j max of 99.36 ± 19.12 µA cm[-2] (lactate and acetate). Further, a decreased time period of reaching j max and biphasic current production was revealed and the microbial electrochemical performance could be linked to the shift in the relative abundance.},
}
@article {pmid35242286,
year = {2022},
author = {Blakeley-Ruiz, JA and Kleiner, M},
title = {Considerations for constructing a protein sequence database for metaproteomics.},
journal = {Computational and structural biotechnology journal},
volume = {20},
number = {},
pages = {937-952},
pmid = {35242286},
issn = {2001-0370},
support = {R35 GM138362/GM/NIGMS NIH HHS/United States ; T32 DK007737/DK/NIDDK NIH HHS/United States ; },
abstract = {Mass spectrometry-based metaproteomics has emerged as a prominent technique for interrogating the functions of specific organisms in microbial communities, in addition to total community function. Identifying proteins by mass spectrometry requires matching mass spectra of fragmented peptide ions to a database of protein sequences corresponding to the proteins in the sample. This sequence database determines which protein sequences can be identified from the measurement, and as such the taxonomic and functional information that can be inferred from a metaproteomics measurement. Thus, the construction of the protein sequence database directly impacts the outcome of any metaproteomics study. Several factors, such as source of sequence information and database curation, need to be considered during database construction to maximize accurate protein identifications traceable to the species of origin. In this review, we provide an overview of existing strategies for database construction and the relevant studies that have sought to test and validate these strategies. Based on this review of the literature and our experience we provide a decision tree and best practices for choosing and implementing database construction strategies.},
}
@article {pmid35241676,
year = {2022},
author = {Lapidot, Y and Reshef, L and Maya, M and Cohen, D and Gophna, U and Muhsen, K},
title = {Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children.},
journal = {NPJ biofilms and microbiomes},
volume = {8},
number = {1},
pages = {10},
pmid = {35241676},
issn = {2055-5008},
mesh = {Child ; *Crowding ; Family Characteristics ; Humans ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The development of the gut microbiome occurs mainly during the first years of life; however, little is known on the role of environmental and socioeconomic exposures, particularly within the household, in shaping the microbial ecology through childhood. We characterized differences in the gut microbiome of school-age healthy children, in association with socioeconomic disparities and household crowding. Stool samples were analyzed from 176 Israeli Arab children aged six to nine years from three villages of different socioeconomic status (SES). Sociodemographic data were collected through interviews with the mothers. We used 16 S rRNA gene sequencing to characterize the gut microbiome, including an inferred analysis of metabolic pathways. Differential analysis was performed using the analysis of the composition of microbiomes (ANCOM), with adjustment for covariates. An analysis of inferred metagenome functions was performed implementing PICRUSt2. Gut microbiome composition differed across the villages, with the largest difference attributed to socioeconomic disparities, with household crowding index being a significant explanatory variable. Living in a low SES village and high household crowding were associated with increased bacterial richness and compositional differences, including an over-representation of Prevotella copri and depleted Bifidobacterium. Secondary bile acid synthesis, d-glutamine and d-glutamate metabolism and Biotin metabolism were decreased in the lower SES village. In summary, residential SES is a strong determinant of the gut microbiome in healthy school-age children, mediated by household crowding and characterized by increased bacterial richness and substantial taxonomic and metabolic differences. Further research is necessary to explore possible implications of SES-related microbiome differences on children's health and development.},
}
@article {pmid35241064,
year = {2022},
author = {Uehara, O and Abiko, Y and Nagasawa, T and Morikawa, T and Hiraki, D and Harada, F and Kawano, Y and Toraya, S and Matsuoka, H and Paudel, D and Shimizu, S and Yoshida, K and Asaka, M and Furuichi, Y and Miura, H},
title = {Alterations in the oral microbiome of individuals with a healthy oral environment following COVID-19 vaccination.},
journal = {BMC oral health},
volume = {22},
number = {1},
pages = {50},
pmid = {35241064},
issn = {1472-6831},
support = {21-6-14//the 8020 Promotion Foundation/ ; 21-6-14//the 8020 Promotion Foundation/ ; 21-6-14//the 8020 Promotion Foundation/ ; 21-6-14//the 8020 Promotion Foundation/ ; },
mesh = {*COVID-19/prevention &amp; control ; COVID-19 Vaccines ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2 ; Vaccination ; Vaccines, Synthetic ; mRNA Vaccines ; },
abstract = {BACKGROUND: Several reports suggest that the microbiome of the digestive system affects vaccine efficacy and that the severity of coronavirus disease (COVID-19) is associated with decreased diversity of the oral and/or intestinal microbiome. The present study examined the effects of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccine on the oral microbiome.<br><br>METHODS: Forty healthy Japanese oral healthcare personnel were recruited, and unstimulated saliva was collected before vaccination, after the 1st vaccination, and after the 2nd vaccination. Genomic DNA was extracted from saliva samples, and PCR amplicons of the 16S rRNA gene were analyzed using next-generation sequencing. Microbial diversity and composition were analyzed using Quantitative Insights into Microbial Ecology 2. In addition, alterations in microbial function were assessed using PICRUSt2.<br><br>RESULTS: SARS-CoV-2 mRNA vaccination significantly increased oral bacterial diversity and significantly decreased the proportion of the genus Bacteroides.<br><br>CONCLUSIONS: The SARS-CoV-2 mRNA vaccine alters the oral microbiome; accordingly, vaccination might have beneficial effects on oral health.},
}
@article {pmid35237932,
year = {2022},
author = {Kumar, M and Sodhi, KK and Singh, DK},
title = {Draft genome of Serratia sp. R1 gives an insight into the antibiotic resistant genes against multiple antibiotics.},
journal = {Molecular biology reports},
volume = {49},
number = {6},
pages = {4479-4484},
pmid = {35237932},
issn = {1573-4978},
support = {NASF/CA-6030/2017-18//Indian Agricultural Research Institute/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; Cephalosporins/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Infant, Newborn ; Macrolides/pharmacology ; *Metals, Heavy ; Serratia/genetics ; },
abstract = {BACKGROUND: Serratia is a pathogenic bacterium, commonly associated with neonatal intensive care units, and harbors antibiotic-resistant genes against multiple antibiotics e.g., resistance against penams, aminoglycosides, tetracyclines, cephalosporins, and macrolides. In the long-term contaminated habitat, the bacterial communities carry both antibiotic and metal resistance genes. This draft genome sequencing aimed to explore the alarming level of ARGs in the environment, additionally heavy metal-resistant genes were also explored in the draft genome.<br><br>METHODS: Whole-genome sequencing was used to investigate ARGs in Serratia sp. R1. The bacteria were sequenced using Illumina Nova seq sequencer and subjected to genome annotation. The bacterial genome was explored for antibiotic- and metal-resistant genes.<br><br>RESULTS: Sequencing resulted in 8.4&#xa0;Mb genome and a total of 4411 functional genes were characterized in the draft genome. Genes resistant to Beta-lactams, cephalosporins, macrolides, fluoroquinolones, and tetracycline are present in the draft genome. Multiple metal-resistant genes are also present in the sequenced genome.<br><br>CONCLUSION: The genes and proteins providing heavy metal and antibiotic resistance may be used in the bioremediation of environmental antibiotic residues to prevent the spread of antibiotic resistance. The current study can help us to adopt suitable mitigation measures against the multidrug-resistant Serratia.},
}
@article {pmid35237850,
year = {2023},
author = {Giorgio, M and Niccolò, BGM and Benedetta, T and Luisa, M and Leonardo, BF and Gregory, B and Pietro, B and Alberto, A and Domizia, D and Emidio, A},
title = {Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {508-521},
pmid = {35237850},
issn = {1432-184X},
support = {1946445//National Science Foundation/ ; },
mesh = {*Microbiota ; *Ascomycota/chemistry ; Soil ; *Rhizobiaceae ; },
abstract = {Fungi belonging to the genus Tuber produce edible ascocarps known as truffles. Tuber magnatum Picco may be the most appreciated truffle species given its peculiar aroma. While its life cycle is not yet fully elucidated, some studies demonstrated an active role of microorganisms. The main goal of this study was to determine how the T. magnatum microbiome varies across space and time. To address this, we characterized microbial communities associated with T. magnatum through high-throughput amplicon sequencing of internal transcribed spacer (ITS) and 16S rDNAs in three productive natural sites in Italy across 2 years. At each site, four truffles were sampled as well as the soil underneath and at 40, 100, and 200 cm from the harvesting points, to assess for microbial variation between substrates, years, and sites. A statistically significant site-related effect on microbial communities was identified, whereas only the prokaryotic community was significantly affected by the distance of soil from the truffle. Significant differences between sampling years were also found, demonstrating a possible relation among rainfall precipitation and Firmicutes and Actinobacteria. Thirty-six bacterial OTUs in truffles and 11 bacterial OTUs in soils beneath truffles were identified as indicator taxa. As shown for other truffle species, the dominance of Bradyrhizobium, Rhizobium, and Ensifer spp. within the truffle fruiting body suggests an evolutionary adaptation of this microorganism to the genus Tuber. The present work offers novel and relevant insights into the microbial ecology of T. magnatum ecosystems and fruiting bodies. The function and role of these bacteria in the truffle microbiome and life cycle are in need of further investigation.},
}
@article {pmid35236879,
year = {2022},
author = {de Albuquerque, TM and Mendes, LW and Rocha, SMB and Antunes, JEL and Oliveira, LMS and Melo, VMM and Oliveira, FAS and Pereira, APA and da Silva, VB and Gomes, RLF and de Alcantara Neto, F and Lopes, ACA and de Moura Rocha, M and Araujo, ASF},
title = {Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {3472},
pmid = {35236879},
issn = {2045-2322},
mesh = {Bacteria/genetics ; Genotype ; Plant Breeding ; Plant Roots/microbiology ; Plants/genetics ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; *Vigna/genetics/microbiology ; },
abstract = {Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome.},
}
@article {pmid35234997,
year = {2023},
author = {Ribeiro, B and Padua, A and Oliveira, BFR and Puccinelli, G and da Costa Fernandes, F and Laport, MS and Klautau, M},
title = {Uncovering the Microbial Diversity of Two Exotic Calcareous Sponges.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {737-746},
pmid = {35234997},
issn = {1432-184X},
mesh = {Animals ; Ecology ; *Microbiota ; Nitrogen Cycle ; Calcium Carbonate ; *Porifera ; Phylogeny ; },
abstract = {Sponges-associated microorganisms play important roles in their health and ecology; consequently, they may be crucial in the successful adaptation of exotic species to novel environments. However, few studies have focused on the microbial diversity of exotic sponges, especially those with calcium carbonate spicules (class Calcarea). Therefore, this is the first in situ characterization of the microbiota of the exotic calcareous sponges Sycettusa hastifera and Paraleucilla magna. Our results suggest that S. hastifera has a more stable microbiota than P. magna, as there were no differences in its beta diversity among sampling sites. Conversely, P. magna showed significant differences in its microbial communities, perhaps related to its adhesion to artificial substrate and/or shellfish mariculture activities. Each sponge species presented a single dominant proteobacterial OTU potentially active in the nitrogen cycle, which could help sponge detoxification, especially in polluted areas where exotic species usually establish. Our results show the importance of assessing the microbial diversity to unveil host-microorganism relationships and suggest that these associated nitrogen-cycling microorganisms could favor the success of exotic sponges in new environments.},
}
@article {pmid35234496,
year = {2022},
author = {Smets, W and Spada, LM and Gandolfi, I and Wuyts, K and Legein, M and Muyshondt, B and Samson, R and Franzetti, A and Lebeer, S},
title = {Bacterial Succession and Community Dynamics of the Emerging Leaf Phyllosphere in Spring.},
journal = {Microbiology spectrum},
volume = {10},
number = {2},
pages = {e0242021},
pmid = {35234496},
issn = {2165-0497},
mesh = {Bacteria ; *Biodiversity ; Humans ; *Microbiota ; Plant Leaves/microbiology ; Plants ; Trees/microbiology ; },
abstract = {Every year, deciduous trees shed their leaves, and when new leaves emerge next spring, they establish a characteristic bacterial leaf community. In this exploratory study, we assessed the bacterial phyllosphere (aboveground plant surfaces) of eight London plane trees (Platanus × acerifolia) in Antwerp and Milan by sampling weekly during leaf emergence and expansion. We sampled the surfaces of different tree compartments: leaves, leaf buds, branches, and trunk, for up to 6 weeks. Phyllosphere community composition was most strongly determined by tree compartment. Only the communities on the emerging leaves showed changing dynamics over time. The rate of change in the leaf phyllosphere composition, expressed as the beta dissimilarity between consecutive time points, was very high following leaf emergence, with decreasing speed over time, indicating that these communities stabilize over time. We also identified cooccurring groups of bacteria associated with potential stages of ecological succession on the leaves and accordingly named them general cluster, early cluster, middle cluster, and late cluster. Taxa of the general cluster were not only more abundant than the others on leaves, but they were also widespread on other tree compartments. The late cluster was most pronounced in trees surrounded by trafficked urban land use. This study mainly generates hypotheses on the ecological succession on the emerging leaves of deciduous trees in urban environments and contributes to understanding the development of the tree leaf phyllosphere in spring. IMPORTANCE Improving our understanding of phyllosphere ecology is key in successfully applying bacterial biological agents or modulating the leaf microbiome in order to achieve valuable ecosystem services, such as plant protection, plant growth, air purification, and developing a healthy human immune system. Modulation of the phyllosphere microbiome in the field works only with variable success. To improve the impact of our applications in the field, a better understanding of the ecological principles governing phyllosphere dynamics is required. This exploratory study demonstrates how the combination of different analyses of a chronosequence of bacterial communities can provide new ecological insights. With a limited number of sampled trees, we demonstrated different indications of ecological succession of bacterial communities in the leaves and observed a potential impact of intensely trafficked land use becoming apparent in the leaf bacterial communities approximately 3 weeks after leaf emergence, consisting of a separate stage in community development.},
}
@article {pmid35232471,
year = {2022},
author = {France, MT and Fu, L and Rutt, L and Yang, H and Humphrys, MS and Narina, S and Gajer, PM and Ma, B and Forney, LJ and Ravel, J},
title = {Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {66},
pmid = {35232471},
issn = {1474-760X},
support = {UH2 AI083264/AI/NIAID NIH HHS/United States ; R01 NR015495/NR/NINR NIH HHS/United States ; },
mesh = {Bacteria/genetics ; Female ; Humans ; Lactobacillus/genetics ; *Microbiota/genetics ; Mucins ; RNA, Ribosomal, 16S/genetics ; *Vagina/microbiology ; },
abstract = {BACKGROUND: Vaginal bacterial communities dominated by Lactobacillus species are associated with a reduced risk of various adverse health outcomes. However, somewhat unexpectedly, many healthy women have microbiota that are not dominated by lactobacilli. To determine the factors that drive vaginal community composition we characterized the genetic composition and transcriptional activities of vaginal microbiota in healthy women.<br><br>RESULTS: We demonstrate that the abundance of a species is not always indicative of its transcriptional activity and that impending changes in community composition can be predicted from metatranscriptomic data. Functional comparisons highlight differences in the metabolic activities of these communities, notably in their degradation of host produced mucin but not glycogen. Degradation of mucin by communities not dominated by Lactobacillus may play a role in their association with adverse health outcomes. Finally, we show that the transcriptional activities of L. crispatus, L. iners, and Gardnerella vaginalis vary with the taxonomic composition of the communities in which they reside. Notably, L. iners and G. vaginalis both demonstrate lower expression of their cholesterol-dependent cytolysins when co-resident with Lactobacillus spp. and higher expression when co-resident with other facultative and obligate anaerobes. The pathogenic potential of these species may depend on the communities in which they reside and thus could be modulated by interventional strategies.<br><br>CONCLUSIONS: Our results provide insight to the functional ecology of the vaginal microbiota, demonstrate the diagnostic potential of metatranscriptomic data, and reveal strategies for the management of these ecosystems.},
}
@article {pmid35229646,
year = {2022},
author = {Wang, X and Teng, Y and Ren, W and Li, Y and Yang, T and Chen, Y and Zhao, L and Zhang, H and Kuramae, EE},
title = {Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality.},
journal = {mSystems},
volume = {7},
number = {2},
pages = {e0104721},
pmid = {35229646},
issn = {2379-5077},
mesh = {*Soil/chemistry ; Bacteria ; *Microbiota ; Iron ; Nitrogen ; },
abstract = {Soil microbiota plays fundamental roles in maintaining ecosystem functions and services, including biogeochemical processes and plant productivity. Despite the ubiquity of soil microorganisms from the topsoil to deeper layers, their vertical distribution and contribution to element cycling in subsoils remain poorly understood. Here, nine soil profiles (0 to 135 cm) were collected at the local scale (within 300 km) from two canonical paddy soil types (Fe-accumuli and Hapli stagnic anthrosols), representing redoximorphic and oxidative soil types, respectively. Variations with depth in edaphic characteristics and soil bacterial and diazotrophic community assemblies and their associations with element cycling were explored. The results revealed that nitrogen and iron status were the most distinguishing edaphic characteristics of the two soil types throughout the soil profile. The acidic Fe-accumuli stagnic anthrosols were characterized by lower concentrations of free iron oxides and total iron in topsoil and ammonia in deeper layers compared with the Hapli stagnic anthrosols. The bacterial and diazotrophic community assemblies were mainly shaped by soil depth, followed by soil type. Random forest analysis revealed that nitrogen and iron cycling were strongly correlated in Fe-accumuli stagnic anthrosol, whereas in Hapli soil, available sulfur was the most important variable predicting both nitrogen and iron cycling. The distinctive biogeochemical processes could be explained by the differences in enrichment of microbial taxa between the two soil types. The main discriminant clades were the iron-oxidizing denitrifier Rhodanobacter, Actinobacteria, and diazotrophic taxa (iron-reducing Geobacter, Nitrospirillum, and Burkholderia) in Fe-accumuli stagnic anthrosol and the sulfur-reducing diazotroph Desulfobacca in Hapli stagnic anthrosol. IMPORTANCE Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes. This study provides a novel perspective on the vertical distribution of bacterial and diazotrophic communities in two hydragric anthrosols. Microbiome analysis revealed divergent biogeochemical processes in the two paddy soil types, with a dominance of nitrogen-iron cycling processes in Fe-accumuli stagnic anthrosol and sulfur-nitrogen-iron coupling in Hapli stagnic anthrosol. This study advances our understanding of the multiple significant roles played by soil microorganisms, especially diazotrophs, in biogeochemical element cycles, which have important ecological and biogeochemical ramifications.},
}
@article {pmid35229433,
year = {2022},
author = {Yang, S and Poorter, L and Kuramae, EE and Sass-Klaassen, U and Leite, MFA and Costa, OYA and Kowalchuk, GA and Cornelissen, JHC and van Hal, J and Goudzwaard, L and Hefting, MM and van Logtestijn, RSP and Sterck, FJ},
title = {Stem traits, compartments and tree species affect fungal communities on decaying wood.},
journal = {Environmental microbiology},
volume = {24},
number = {8},
pages = {3625-3639},
pmid = {35229433},
issn = {1462-2920},
mesh = {Biodiversity ; Forests ; Fungi/genetics ; *Mycobiome/genetics ; *Trees/microbiology ; Wood/microbiology ; },
abstract = {Dead wood quantity and quality is important for forest biodiversity, by determining wood-inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer- and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long-term carbon dynamics of dead trees.},
}
@article {pmid35229200,
year = {2023},
author = {Sapkota, R and Jørgensen, LN and Boeglin, L and Nicolaisen, M},
title = {Fungal Communities of Spring Barley from Seedling Emergence to Harvest During a Severe Puccinia hordei Epidemic.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {617-627},
pmid = {35229200},
issn = {1432-184X},
support = {6111-00065B//Danmarks Frie Forskningsfond/ ; },
mesh = {*Mycobiome ; *Hordeum ; Fungi ; Seedlings ; Seasons ; *Ascomycota ; Soil Microbiology ; },
abstract = {All plant tissues from leaves, stems, and roots are hosting a wide diversity of fungal species. Our understanding of the assembly of this diversity of fungi during the plant growth cycle is limited. Here, we characterized the mycobiome of three spring barley cultivars grown in Zealand, Denmark, at weekly intervals during a growth season from seedling emergence to senescence and seed maturity. A notable proportion of members of the fungal communities were shared among different plant organs, but community dynamics were tissue-specific. A severe attack of Puccinia hordei occurring during the vegetative stage had profound effects on the mycobiome, and P. hordei biomass displaced that of other taxa. Plant tissue type was the most important factor determining the mycobiome, but also plant age was contributing significantly. Using a random forest model, we found that specific members of the mycobiome were responding differently to plant age, for instance, Olpidium and Articulospora in roots, Dioszegia and Sporobolomyces in leaves, Pyrenophora in stems, and Epicoccum in heads. A co-occurrence network analysis revealed complex interactions among fungal OTUs, and network connectivity was changing as per plant growth stage and plant tissue type. This study contributes to the understanding of assembly of fungal communities in cereals by providing a detailed description of fungal communities associated with barley. This knowledge will be vital for microbiome assisted plant health management and our study will serve as an important baseline for future efforts to harness microbiota in cereal health.},
}
@article {pmid35228910,
year = {2022},
author = {Eisenhofer, R and D'Agnese, E and Taggart, D and Carver, S and Penrose, B},
title = {Microbial biogeography of the wombat gastrointestinal tract.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12982},
pmid = {35228910},
issn = {2167-8359},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Tract ; Feces/chemistry ; *Marsupialia ; Colon ; },
abstract = {Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region-the putative site of primary plant fermentation in wombats-are distinct from the distal colon, and that faecal samples may have limitations in capturing the diversity of these communities. While faeces are still a valuable and effective means of characterising the distal colon microbiota, future work seeking to better understand how GI microbiota impact the energy economy of wombats (and potentially other hindgut-fermenting mammals) may need to take gut biogeography into account.},
}
@article {pmid35227678,
year = {2022},
author = {Chu, Y and Zhao, Z and Cai, L and Zhang, G},
title = {Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis.},
journal = {Environmental research},
volume = {210},
number = {},
pages = {112901},
doi = {10.1016/j.envres.2022.112901},
pmid = {35227678},
issn = {1096-0953},
mesh = {Ecosystem ; Geologic Sediments ; *Metagenome ; Metagenomics ; Phylogeny ; *Viruses/genetics ; },
abstract = {As the most numerous biological entities on Earth, viruses affect the microbial dynamics, metabolism and biogeochemical cycles in the aquatic ecosystems. Viral diversity and functions in ocean have been relatively well studied, but our understanding of viruses in mariculture systems is limited. To fill this knowledge gap, we studied viral diversity and potential biogeochemical impacts of sediments from four different prawn-mariculture ecosystems (mono-culture of prawn and poly-culture of prawn with jellyfish, sea cucumber, and clam) using a metagenomic approach with prior virus-like particles (VLPs) separation. We found that the order Caudovirales was the predominant viral category and accounted for the most volume (78.39% of classified viruses). Sediment viruses were verified to have a high diversity by using the construct phylogenetic tree of terL gene, with three potential novel clades being identified. Meanwhile, compared with viruses inhabiting other ecosystems based on gene-sharing network, our results revealed that mariculture sediments harbored considerable unexplored viral diversity and that maricultural species were potentially important drivers of the viral community structure. Notably, viral auxiliary metabolic genes were identified and suggested that viruses influence carbon and sulfur cycling, as well as cofactors/vitamins and amino acid metabolism, which indirectly participate in biogeochemical cycling. Overall, our findings revealed the genomic diversity and ecological function of viral communities in prawn mariculture sediments, and suggested the role of viruses in microbial ecology and biogeochemistry.},
}
@article {pmid35222324,
year = {2022},
author = {Marois, C and Girard, C and Klanten, Y and Vincent, WF and Culley, AI and Antoniades, D},
title = {Local Habitat Filtering Shapes Microbial Community Structure in Four Closely Spaced Lakes in the High Arctic.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {779505},
pmid = {35222324},
issn = {1664-302X},
abstract = {Arctic lakes are experiencing increasingly shorter periods of ice cover due to accelerated warming at northern high latitudes. Given the control of ice cover thickness and duration over many limnological processes, these changes will have pervasive effects. However, due to their remote and extreme locations even first-order data on lake ecology is lacking for many ecosystems. The aim of this study was to characterize and compare the microbial communities of four closely spaced lakes in Stuckberry Valley (northern Ellesmere Island, Canadian Arctic Archipelago), in the coastal margin zone of the Last Ice Area, that differed in their physicochemical, morphological and catchment characteristics. We performed high-throughput amplicon sequencing of the V4 16S rRNA gene to provide inter- and intra-lake comparisons. Two deep (>25 m) and mostly oxygenated lakes showed highly similar community assemblages that were distinct from those of two shallower lakes (<10 m) with anoxic bottom waters. Proteobacteria, Verrucomicrobia, and Planctomycetes were the major phyla present in the four water bodies. One deep lake contained elevated proportions of Cyanobacteria and Thaumarchaeota that distinguished it from the others, while the shallow lakes had abundant communities of predatory bacteria, as well as microbes in their bottom waters that contribute to sulfur and methane cycles. Despite their proximity, our data suggest that local habitat filtering is the primary determinant of microbial diversity in these systems. This study provides the first detailed examination of the microbial assemblages of the Stuckberry lakes system, resulting in new insights into the microbial ecology of the High Arctic.},
}
@article {pmid35218016,
year = {2022},
author = {Kajihara, KT and Egan, CP and Swift, SOI and Wall, CB and Muir, CD and Hynson, NA},
title = {Core arbuscular mycorrhizal fungi are predicted by their high abundance-occupancy relationship while host-specific taxa are rare and geographically structured.},
journal = {The New phytologist},
volume = {234},
number = {4},
pages = {1464-1476},
doi = {10.1111/nph.18058},
pmid = {35218016},
issn = {1469-8137},
mesh = {Forests ; Fungi ; *Mycobiome ; *Mycorrhizae ; Plant Roots/microbiology ; Soil ; Soil Microbiology ; },
abstract = {Habitat restoration may depend on the recovery of plant microbial symbionts such as arbuscular mycorrhizal (AM) fungi, but this requires a better understanding of the rules that govern their community assembly. We examined the interactions of soil and host-associated AM fungal communities between remnant and restored patches of subtropical montane forests. While AM fungal richness did not differ between habitat types, community membership did and was influenced by geography, habitat and host. These differences were largely driven by rare host-specific AM fungi that displayed near-complete turnover between forest types, while core AM fungal taxa were highly abundant and ubiquitous. The bipartite networks in the remnant forest were more specialized and hosts more specific than in the restored forest. Host-associated AM fungal communities nested within soil communities in both habitats, but only significantly so in the restored forest. Our results provide evidence that restored and remnant forests harbour the same core fungal symbionts, while rare host-specific taxa differ, and that geography, host identity and taxonomic resolution strongly affect the observed distribution patterns of these fungi. We suggest that host-specific interactions with AM fungi, as well as spatial processes, should be explicitly considered to effectively re-establish target host and symbiont communities.},
}
@article {pmid35217776,
year = {2022},
author = {Singleton, CM and Petriglieri, F and Wasmund, K and Nierychlo, M and Kondrotaite, Z and Petersen, JF and Peces, M and Dueholm, MS and Wagner, M and Nielsen, PH},
title = {The novel genus, 'Candidatus Phosphoribacter', previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide.},
journal = {The ISME journal},
volume = {16},
number = {6},
pages = {1605-1616},
pmid = {35217776},
issn = {1751-7370},
support = {16578//Villum Fonden (Villum Foundation)/ ; },
mesh = {*Actinomycetales/genetics/metabolism ; Bioreactors ; Phosphorus/metabolism ; Polyphosphates/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Sewage/microbiology ; Wastewater ; *Water Purification ; },
abstract = {The bacterial genus Tetrasphaera encompasses abundant polyphosphate accumulating organisms (PAOs) that are responsible for enhanced biological phosphorus removal (EBPR) in wastewater treatment plants. Recent analyses of genomes from pure cultures revealed that 16S rRNA genes cannot resolve the lineage, and that Tetrasphaera spp. are from several different genera within the Dermatophilaceae. Here, we examine 14 recently recovered high-quality metagenome-assembled genomes from wastewater treatment plants containing full-length 16S rRNA genes identified as Tetrasphaera, 11 of which belong to the uncultured Tetrasphaera clade 3. We find that this clade represents two distinct genera, named here Ca. Phosphoribacter and Ca. Lutibacillus, and reveal that the widely used model organism Tetrasphaera elongata is less relevant for physiological predictions of this uncultured group. Ca. Phosphoribacter incorporates species diversity unresolved at the 16S rRNA gene level, with the two most abundant and often co-occurring species encoding identical V1-V3 16S rRNA gene amplicon sequence variants but different metabolic capabilities, and possibly, niches. Both Ca. P. hodrii and Ca. P. baldrii were visualised using fluorescence in situ hybridisation (FISH), and PAO capabilities were confirmed with FISH-Raman microspectroscopy and phosphate cycling experiments. Ca. Phosphoribacter represents the most abundant former Tetrasphaera lineage and PAO in EPBR systems in Denmark and globally.},
}
@article {pmid35215763,
year = {2022},
author = {Farooq, T and Hussain, MD and Shakeel, MT and Tariqjaveed, M and Aslam, MN and Naqvi, SAH and Amjad, R and Tang, Y and She, X and He, Z},
title = {Deploying Viruses against Phytobacteria: Potential Use of Phage Cocktails as a Multifaceted Approach to Combat Resistant Bacterial Plant Pathogens.},
journal = {Viruses},
volume = {14},
number = {2},
pages = {},
pmid = {35215763},
issn = {1999-4915},
mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*virology ; Bacteriophages/*physiology ; Biological Control Agents/*pharmacology ; Disease Resistance ; Host-Pathogen Interactions ; *Phage Therapy ; Plant Diseases/microbiology/*prevention &amp; control ; Plants/immunology/*microbiology ; },
abstract = {Plants in nature are under the persistent intimidation of severe microbial diseases, threatening a sustainable food production system. Plant-bacterial pathogens are a major concern in the contemporary era, resulting in reduced plant growth and productivity. Plant antibiotics and chemical-based bactericides have been extensively used to evade plant bacterial diseases. To counteract this pressure, bacteria have evolved an array of resistance mechanisms, including innate and adaptive immune systems. The emergence of resistant bacteria and detrimental consequences of antimicrobial compounds on the environment and human health, accentuates the development of an alternative disease evacuation strategy. The phage cocktail therapy is a multidimensional approach effectively employed for the biocontrol of diverse resistant bacterial infections without affecting the fauna and flora. Phages engage a diverse set of counter defense strategies to undermine wide-ranging anti-phage defense mechanisms of bacterial pathogens. Microbial ecology, evolution, and dynamics of the interactions between phage and plant-bacterial pathogens lead to the engineering of robust phage cocktail therapeutics for the mitigation of devastating phytobacterial diseases. In this review, we highlight the concrete and fundamental determinants in the development and application of phage cocktails and their underlying mechanism, combating resistant plant-bacterial pathogens. Additionally, we provide recent advances in the use of phage cocktail therapy against phytobacteria for the biocontrol of devastating plant diseases.},
}
@article {pmid35215209,
year = {2022},
author = {Sueiro, RA and Leiro, JM and Blanco-Abad, V and Raaijmakers, J and de Bruijn, I and Dirks, RPH and Lamas, J},
title = {Plant- and Bacteria-Derived Compounds with Anti-Philasterides dicentrarchi Activity.},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {2},
pages = {},
pmid = {35215209},
issn = {2076-0817},
support = {ParaFishControl 634429//European Commission/ ; AGL2017-83577-R//Ministry of Economy, Industry and Competitiveness/ ; ED431C2017/31//Xunta de Galicia/ ; },
abstract = {Philasterides dicentrarchi is a scuticociliate that causes high mortalities in farmed fish. Although vaccination is an effective method to prevent scuticociliatosis caused by the homologous serotype, a universal vaccine has not been developed yet. Many compounds have been shown to be toxic to this ciliate species; moreover, most of them are toxic to aquatic life and cannot be used to prevent the disease. We have evaluated the toxicity to P. dicentrarchi of several compounds of natural origin to be used to reduce parasite levels in the seawater. Ciliates were exposed to several compound concentrations, and the mortality was determined at several incubation times. Tomatine, plumbagin and 2',4'-dihydroxychalcone displayed the highest anticiliate activity, with a dose-dependent response. The effects of these compounds on the EPC cell line were also evaluated, finding that 2',4'-dihydroxychalcone displayed the lowest toxicity to fish cells. At 7.54 μM, 2',4'-dihydroxychalcone inhibited 50% parasite growth but only killed about 10% of EPC cells after 24 h incubation. Finally, we evaluated the toxicity of Pseudomonas H6 surfactant (PS) to P. dicentrarchi, finding that PS was toxic to the ciliate but showed lower toxicity to EPC cells. At a concentration of 7.8 μg/mL (LC50 for the ciliate after 3 h incubation), PS killed 14.9% of EPC cells. We conclude that 2',4'-dihydroxychalcone, and PS could be used to reduce parasite levels in seawater, thus decreasing the risk of scuticociliatosis infection in cultured fish.},
}
@article {pmid35208741,
year = {2022},
author = {Šimunović, K and Stefanic, P and Klančnik, A and Erega, A and Mandic Mulec, I and Smole Možina, S},
title = {Bacillus subtilis PS-216 Antagonistic Activities against Campylobacter jejuni NCTC 11168 Are Modulated by Temperature, Oxygen, and Growth Medium.},
journal = {Microorganisms},
volume = {10},
number = {2},
pages = {},
pmid = {35208741},
issn = {2076-2607},
support = {J4-7637//Slovenian Research Agency/ ; J4-2542//Slovenian Research Agency/ ; P4-0116//Slovenian Research Agency/ ; },
abstract = {As the incidence of Campylobacter jejuni and campylobacteriosis grows, so does the need for a better understanding and control of this pathogen. We studied the interactions of C. jejuni NCTC 11168 and a potential probiotic, Bacillus subtilis PS-216, in cocultures at different starting ratios and temperatures (20 °C, 37 °C, 42 °C), under different atmospheres (aerobic, microaerobic), and in different growth media (Mueller-Hinton, chicken litter medium, chicken intestinal-content medium). Under microaerobic conditions, B. subtilis effectively inhibited the growth of C. jejuni at 42 °C (log reduction, 4.19), even when C. jejuni counts surpassed B. subtilis by 1000-fold in the starting inoculum. This inhibition was weaker at 37 °C (log reduction, 1.63), while no impact on CFUs was noted at 20 °C, which is a temperature nonpermissive of C. jejuni growth. Under aerobic conditions, B. subtilis supported C. jejuni survival. B. subtilis PS-216 inhibited the growth of C. jejuni in sterile chicken litter (4.07 log reduction) and in sterile intestinal content (2.26 log reduction). In nonsterile intestinal content, B. subtilis PS-216 was able to grow, to a lesser extent, compared to Mueller-Hinton media, still showing potential as a chicken probiotic that could be integrated into the chicken intestinal microbiota. This study showed the strong influence of environmental parameters on the variability of C. jejuni and B. subtilis interactions. Furthermore, B. subtilis PS-216 antagonism was strongest against C. jejuni NCTC 11168 under conditions that might represent conditions in the chicken environment (42 °C, microaerobic atmosphere, chicken litter medium).},
}
@article {pmid35202888,
year = {2022},
author = {Yu, J and Ma, X and Wang, L and Dong, N and Wang, K and You, Q and Xu, Y and Wang, C and Dong, Z and Shi, Z and Dai, S and Bai, L and Song, CP},
title = {Arabidopsis CAP1 mediates ammonium-regulated root hair growth by influencing vesicle trafficking and the cytoskeletal arrangement in root hair cells.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {49},
number = {10},
pages = {986-989},
doi = {10.1016/j.jgg.2022.02.005},
pmid = {35202888},
issn = {1673-8527},
mesh = {*Arabidopsis/genetics ; *Ammonium Compounds ; *Arabidopsis Proteins/genetics ; Plant Roots/genetics ; },
}
@article {pmid35198897,
year = {2022},
author = {Kreitmeier, M and Ardern, Z and Abele, M and Ludwig, C and Scherer, S and Neuhaus, K},
title = {Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection.},
journal = {iScience},
volume = {25},
number = {2},
pages = {103844},
pmid = {35198897},
issn = {2589-0042},
abstract = {The existence of overlapping genes (OLGs) with significant coding overlaps revolutionizes our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the pathogenic Gram-negative bacterium Pseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here, designated olg1 and olg2, are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes.},
}
@article {pmid35197480,
year = {2022},
author = {Xia, L and Miao, Y and Cao, A and Liu, Y and Liu, Z and Sun, X and Xue, Y and Xu, Z and Xun, W and Shen, Q and Zhang, N and Zhang, R},
title = {Biosynthetic gene cluster profiling predicts the positive association between antagonism and phylogeny in Bacillus.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {1023},
pmid = {35197480},
issn = {2041-1723},
mesh = {Anti-Bacterial Agents/pharmacology ; *Bacillus/genetics ; Biosynthetic Pathways/genetics ; Multigene Family ; Phylogeny ; },
abstract = {Understanding the driving forces and intrinsic mechanisms of microbial competition is a fundamental question in microbial ecology. Despite the well-established negative correlation between exploitation competition and phylogenetic distance, the process of interference competition that is exemplified by antagonism remains controversial. Here, we studied the genus Bacillus, a commonly recognized producer of multifarious antibiotics, to explore the role of phylogenetic patterns of biosynthetic gene clusters (BGCs) in mediating the relationship between antagonism and phylogeny. Comparative genomic analysis revealed a positive association between BGC distance and phylogenetic distance. Antagonistic tests demonstrated that the inhibition phenotype positively correlated with both phylogenetic and predicted BGC distance, especially for antagonistic strains possessing abundant BGCs. Mutant-based verification showed that the antagonism was dependent on the BGCs that specifically harbored by the antagonistic strain. These findings highlight that BGC-phylogeny coherence regulates the positive correlation between congeneric antagonism and phylogenetic distance, which deepens our understanding of the driving force and intrinsic mechanism of microbial interactions.},
}
@article {pmid35196931,
year = {2022},
author = {Rosier, BT and Takahashi, N and Zaura, E and Krom, BP and MartÍnez-Espinosa, RM and van Breda, SGJ and Marsh, PD and Mira, A},
title = {The Importance of Nitrate Reduction for Oral Health.},
journal = {Journal of dental research},
volume = {101},
number = {8},
pages = {887-897},
doi = {10.1177/00220345221080982},
pmid = {35196931},
issn = {1544-0591},
mesh = {Bacteria ; *Dental Caries/prevention &amp; control ; *Halitosis ; Humans ; Nitrates ; Nitric Oxide ; Nitrites ; Oral Health ; *Periodontal Diseases/prevention &amp; control ; Saliva/microbiology ; },
abstract = {Salivary glands concentrate plasma nitrate into saliva, leading to high nitrate concentrations that can reach the millimolar range after a nitrate-rich vegetable meal. Whereas human cells cannot reduce nitrate to nitrite effectively, certain oral bacteria can. This leads to an increase in systemic nitrite that can improve conditions such as hypertension and diabetes through nitric oxide availability. Apart from systemic benefits, it has been proposed that microbial nitrate reduction can also promote oral health. In this review, we discuss evidence associating dietary nitrate with oral health. Oral bacteria can reduce nitrite to nitric oxide, a free radical with antimicrobial properties capable of inhibiting sensitive species such as anaerobes involved in periodontal diseases. Nitrate has also been shown to increase resilience against salivary acidification in vivo and in vitro, thus preventing caries development. One potential mechanism is proton consumption during denitrification and/or bacterial reduction of nitrite to ammonium. Additionally, lactic acid (organic acid involved in oral acidification) and hydrogen sulfide (volatile compound involved in halitosis) can act as electron donors for these processes. The nitrate-reducing bacteria Rothia and Neisseria are consistently found at higher levels in individuals free of oral disease (vs. individuals with caries, periodontitis, and/or halitosis) and increase when nitrate is consumed in clinical studies. Preliminary in vitro and clinical evidence show that bacteria normally associated with disease, such as Veillonella (caries) and Prevotella (periodontal diseases and halitosis), decrease in the presence of nitrate. We propose nitrate as an ecologic factor stimulating eubiosis (i.e., an increase in health-associated species and functions). Finally, we discuss the preventive and therapeutic potential, as well as safety issues, related to the use of nitrate. In vivo evidence is limited; therefore, robust clinical studies are required to confirm the potential benefits of nitrate reduction on oral health.},
}
@article {pmid35196816,
year = {2022},
author = {Ogundero, A and Vignola, M and Connelly, S and Sloan, WT},
title = {Validating Flow Cytometry as a Method for Quantifying Bdellovibrio Predatory Bacteria and Its Prey for Microbial Ecology.},
journal = {Microbiology spectrum},
volume = {10},
number = {1},
pages = {e0103321},
pmid = {35196816},
issn = {2165-0497},
mesh = {Bdellovibrio bacteriovorus/*physiology ; Biofilms ; Flow Cytometry/*methods ; Pseudomonas/*metabolism ; },
abstract = {Bdellovibrio bacteriovorus is a predatory, Gram-negative bacteria that feeds on many pathogenic bacteria and has been investigated as a possible solution for mitigating biofilms in different fields. The application depends on more fundamental ecological studies into the dynamics between Bdellovibrio and their prey. To do so requires an accurate, reliable, and, preferably rapid, way of enumerating the cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated in the enumeration of Bdellovibrio. In this study, we developed a protocol to measure the number of Bdellovibrio in samples of various densities using FCM and compared the results with those of other methods: optical density (OD), PFU assay (PFU), and quantitative PCR (qPCR). We observed a strong correlation between values obtained using FCM and PFU (ρ = 0.923) and FCM and qPCR (ρ = 0.987). Compared to optical density there was a much weaker correlation (ρ = 0.784), which was to be expected given the well-documented uncertainty in converting optical density (OD) to cell numbers. The FCM protocol was further validated by demonstrating its ability to distinguish and count mixed populations of Bdellovibrio and the prey Pseudomonas. Thus, the accuracy of FCM as well as its speed and reproducibility make it a suitable alternative for measuring Bdellovibrio cell numbers, especially where many samples are required to capture the dynamics of predator-prey interactions. IMPORTANCE The rise of antibiotic resistance and the unwanted growth of bacteria is a universally growing problem. Predatory bacteria can be used as a biological alternative to antibiotics because they grow by feeding on other bacteria. To apply this effectively requires further study and a deeper understanding of the forces that drive a prey population to elimination. Initially, such studies require more reliable methods to count these cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated for predatory bacteria. This study develops a protocol to count the predatory bacteria Bdellovibrio bacteriovorus and its Pseudomonas prey using FCM and compare the results with those of other methods, demonstrating its ability for studies into B. bacteriovorus predation dynamics. This could lead to the use of B. bacteriovorus for killing bacterial biofilms in fields, such as drinking water and agriculture.},
}
@article {pmid35196810,
year = {2022},
author = {Rodrigues, C and Hauser, K and Cahill, N and Ligowska-Marzęta, M and Centorotola, G and Cornacchia, A and Garcia Fierro, R and Haenni, M and Nielsen, EM and Piveteau, P and Barbier, E and Morris, D and Pomilio, F and Brisse, S},
title = {High Prevalence of Klebsiella pneumoniae in European Food Products: a Multicentric Study Comparing Culture and Molecular Detection Methods.},
journal = {Microbiology spectrum},
volume = {10},
number = {1},
pages = {e0237621},
pmid = {35196810},
issn = {2165-0497},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Chickens ; Drug Resistance, Multiple, Bacterial ; Europe/epidemiology ; Food Contamination/analysis/*statistics &amp; numerical data ; Foodborne Diseases/microbiology ; Genetic Variation ; Genotype ; Humans ; Klebsiella Infections/epidemiology/microbiology ; Klebsiella pneumoniae/classification/drug effects/genetics/*isolation &amp; purification ; Meat/microbiology ; Microbial Sensitivity Tests ; Phylogeny ; Prevalence ; Salads/microbiology ; beta-Lactamases/genetics/metabolism ; },
abstract = {The Klebsiella pneumoniae species complex (KpSC) is a leading cause of multidrug-resistant human infections. To better understand the potential contribution of food as a vehicle of KpSC, we conducted a multicentric study to define an optimal culture method for its recovery from food matrices and to characterize food isolates phenotypically and genotypically. Chicken meat (n = 160) and salad (n = 145) samples were collected in five European countries and screened for the presence of KpSC using culture-based and zur-khe intergenic region (ZKIR) quantitative PCR (qPCR) methods. Enrichment using buffered peptone water followed by streaking on Simmons citrate agar with inositol (44°C for 48 h) was defined as the most suitable selective culture method for KpSC recovery. A high prevalence of KpSC was found in chicken meat (60% and 52% by ZKIR qPCR and the culture approach, respectively) and salad (30% and 21%, respectively) samples. Genomic analyses revealed high genetic diversity with the dominance of phylogroups Kp1 (91%) and Kp3 (6%). A total of 82% of isolates presented a natural antimicrobial susceptibility phenotype and genotype, with only four CTX-M-15-producing isolates detected. Notably, identical genotypes were found across samples-same food type and same country (15 cases), different food types and same country (1), and same food type and two countries (1)-suggesting high rates of transmission of KpSC within the food sector. Our study provides a novel isolation strategy for KpSC from food matrices and reinforces the view of food as a potential source of KpSC colonization in humans. IMPORTANCE Bacteria of the Klebsiella pneumoniae species complex (KpSC) are ubiquitous, and K. pneumoniae is a leading cause of antibiotic-resistant infections in humans. Despite the urgent public health threat represented by K. pneumoniae, there is a lack of knowledge of the contribution of food sources to colonization and subsequent infection in humans. This is partly due to the absence of standardized methods for characterizing the presence of KpSC in food matrices. Our multicentric study provides and implements a novel isolation strategy for KpSC from food matrices and shows that KpSC members are highly prevalent in salads and chicken meat, reinforcing the view of food as a potential source of KpSC colonization in humans. Despite the large genetic diversity and the low levels of resistance detected, the occurrence of identical genotypes across samples suggests high rates of transmission of KpSC within the food sector, which need to be further explored to define possible control strategies.},
}
@article {pmid35195737,
year = {2023},
author = {Zhao, H and Brearley, FQ and Huang, L and Tang, J and Xu, Q and Li, X and Huang, Y and Zou, S and Chen, X and Hou, W and Pan, L and Dong, K and Jiang, G and Li, N},
title = {Abundant and Rare Taxa of Planktonic Fungal Community Exhibit Distinct Assembly Patterns Along Coastal Eutrophication Gradient.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {495-507},
pmid = {35195737},
issn = {1432-184X},
support = {41966005//National Natural Science Foundation of China/ ; U20A2087//National Natural Science Foundation of China/ ; 2018GXNSFDA281006//Natural Science Foundation of Guangxi Province/ ; 2017GXNSFBA198009//Natural Science Foundation of Guangxi Province/ ; 6020303891251//the "One Hundred Talents" Project of Guangxi/ ; MED202014//the Open Research Fund Program of Key Laboratory of Marine Ecosystem Dynamics, MNR/ ; 2017YJ23003//Foundation of Guangxi Academy of Sciences/ ; 2021KY0391//Basic scientific research capacity improvement project of young and middle-aged teachers in colleges and universities, Guangxi/ ; AD20238059//Research on quantitative remote sensing technology for tropical vegetation and International Joint Laboratory of Ecological &amp; Remote Sensing/ ; },
mesh = {Plankton ; *Mycobiome ; Eutrophication ; *Microbiota ; Nitrogen ; },
abstract = {Revealing planktonic fungal ecology under coastal eutrophication is crucial to our understanding of microbial community shift in marine pollution background. We investigated the diversity, putative interspecies interactions, assembly processes and environmental responses of abundant and rare planktonic fungal communities along a eutrophication gradient present in the Beibu Gulf. The results showed that Dothideomycetes and Agaricomycetes were the predominant classes of abundant and rare fungi, respectively. We found that eutrophication significantly altered the planktonic fungal communities and affected the abundant taxa more than the rare taxa. The abundant and rare taxa were keystone members in the co-occurrence networks, and their interaction was enhanced with increasing nutrient concentrations. Stochastic processes dominated the community assembly of both abundant and rare planktonic fungi across the eutrophication gradient. Heterogeneous selection affected abundant taxa more than rare taxa, whereas homogenizing dispersal had a greater influence on rare taxa. Influences of environmental factors involving selection processes were detected, we found that abundant fungi were mainly influenced by carbon compounds, whereas rare taxa were simultaneously affected by carbon, nitrogen and phosphorus compounds in the Beibu Gulf. Overall, these findings highlight the distinct ecological adaptations of abundant and rare fungal communities to marine eutrophication.},
}
@article {pmid35195736,
year = {2023},
author = {Rangamaran, VR and Sankara Subramanian, SH and Balachandran, KRS and Gopal, D},
title = {Vertical Microbial Profiling of Arabian Sea Oxygen Minimal Zone Reveals Complex Bacterial Communities and Distinct Functional Implications.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {357-371},
pmid = {35195736},
issn = {1432-184X},
mesh = {*Seawater/microbiology ; *Oxygen/metabolism ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria ; Water/metabolism ; Nitrogen/metabolism ; },
abstract = {Arabian Sea harbours one of the largest oxygen minimal zones (OMZs) among the global oceans wherein biogeochemical cycles are regulated through dominant and complex microbial processes. The present study investigated the bacterial communities at various depths of the Arabian Sea OMZ using high-throughput sequencing of the v3-v4 hyper variable region of 16S rRNA gene. A total of 10 samples which included water samples from 8 different depths and 2 sediment samples were analyzed in this study. About 2.7 million sequences were obtained from all the samples. The sequence analysis revealed high bacterial diversity at deep waters and sediment samples and comparatively less species richness at the core OMZ depths. Number of OTUs ranged from 114 to 14441.Taxonomic assignments of the obtained OTUs showed dominant presence of Proteobacteria, Bacteriodetes, and Chloroflexi across all the samples. The identified OTUs were further affiliated to the phyla Marinimicrobia, Colwellia, Nitrospina, Tepidicaulis, Shewanella, Pseudoalteromonas, Woeseia at various depths along the water column. Correlation with abiotic factors suggested distinct variation in bacterial community composition with change in depth and dissolved oxygen (DO) levels. Predictive functional annotation based on bacterial phylotypes suggested presence of active nitrogen, sulphur, carbon, and methane metabolic cycles along the vertical transect of the studied region. Presence of nitrogen reduction bacterial group below the core OMZ depths may potentially provide insight into the expansion of OMZ region in Arabian Sea. Functional profiling further revealed presence of genes related to xenobiotic degradation in the water and sediment samples indicating a potential hotspot for bio-prospection.},
}
@article {pmid35194659,
year = {2023},
author = {Chen, J and Deng, Y and Yu, X and Wu, G and Gao, Y and Ren, A},
title = {Epichloë Endophyte Infection Changes the Root Endosphere Microbial Community Composition of Leymus Chinensis Under Both Potted and Field Growth Conditions.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {604-616},
pmid = {35194659},
issn = {1432-184X},
support = {31971425//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Endophytes ; *Epichloe ; Poaceae/microbiology ; *Microbiota ; Bacteria ; Rhizosphere ; Plants/microbiology ; Soil ; Plant Roots/microbiology ; Soil Microbiology ; },
abstract = {Epichloë endophytes can not only affect the growth and resistance of the host plant but also change the biotic and abiotic properties of the soil where the host is situated. Here, we used endophyte-infected (EI) and endophyte-free (EF) Leymus chinensis as plant materials, to study the microbial diversity and composition in the host root endosphere and rhizosphere soil under both pot and field conditions. The results showed that endophyte infection did not affect the diversity of either bacteria or fungi in the root zone. There were significant differences in both bacterial and fungal communities between the root endosphere and the rhizosphere, and between the field and the pot, while endophytes only affected root endosphere microbial communities. The bacterial families affected by endophyte infection changed from 29.07% under field conditions to 40% under pot conditions. In contrast, the fungal families affected by endophyte infection were maintained at nearly 50% under both field and pot conditions. That is to say, bacterial communities in the root endosphere were more strongly affected by environmental conditions, and in comparison, the fungal communities were more strongly affected by species specificity. Endophytes significantly affected the fungal community composition of the host root endosphere in both potted and field plants, only the effect was more obvious in potted plants. Endophyte infection increased the abundance of three fungal families (Thelebolaceae, Herpotrichiellaceae and Trimorphomycetaceae) under both field and potted conditions. In potted plants, endophytes also altered the dominant fungi from pathogenic Pleosporales to saprophytic Chaetomiaceae. Endophyte infection increased the relative abundance of arbuscular mycorrhizal fungi and saprophytic fungi, especially under potted conditions.Overall, endophytes significantly affected the fungal community composition of the host root endosphere in both potted and field plants. Endophytes had a greater impact on root endosphere microorganisms than the rhizosphere, a greater impact on fungal communities than bacteria, and a greater impact on root endosphere microorganisms under potted conditions than at field sites.},
}
@article {pmid35192040,
year = {2023},
author = {Detcharoen, M and Nilsai, A},
title = {Low Endosymbiont Incidence in Drosophila Species Across Peninsula Thailand.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {730-736},
pmid = {35192040},
issn = {1432-184X},
support = {SCI6404008S//Faculty of Science, Prince of Songkla University/ ; },
mesh = {Animals ; Male ; Drosophila ; Incidence ; Thailand ; Symbiosis ; Bacteroidetes ; *Wolbachia ; *Spiroplasma ; *Rickettsia ; },
abstract = {Arthropods are known to harbor several endosymbionts, such as Cardinium, Rickettsia, Spiroplasma, and Wolbachia. Wolbachia, for example, are the most widespread known endosymbionts in the world, which are found in about half of all arthropod species. To increase their transmission, these endosymbionts must manipulate their hosts in several ways such as cytoplasmic incompatibility and male killing. In tropical regions, endosymbiont diversity has not been studied exhaustively. Here, we checked four endosymbionts, including Cardinium, Rickettsia, Spiroplasma, and Wolbachia, in eleven Drosophila species found in Thai Peninsula. The Wolbachia strain wRi-like was found in all populations of Drosophila ananassae and Drosophila simulans. Furthermore, we found two new strains, wMalA and wMalB, in two populations of Drosophila malerkotliana. Besides Wolbachia, we did not find any of the above endosymbionts in all fly species. This work reveals the hidden diversity of endosymbionts in Drosophila and is the first exhaustive study on Drosophila in the region.},
}
@article {pmid35190857,
year = {2023},
author = {Elmi, F and Etemadifar, Z and Emtiazi, G},
title = {Biosynthesis of Calcite Nanocrystal by a Novel Polyextremophile Bhargavaea cecembensis-Related Strain Isolated from Sandy Soil.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {698-707},
pmid = {35190857},
issn = {1432-184X},
mesh = {*Sand ; Soil ; Calcium Carbonate/chemistry ; Urease ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Nanoparticles ; Chemical Precipitation ; },
abstract = {Urease-producing bacteria are abundant in soils, which can precipitate calcium carbonate nanocrystals by enzymatic hydrolysis of urea in the presence of calcium ions. This process is known as microbially induced calcium carbonate precipitation (MICP), and it has received much attention in recent years as an eco-friendly technology. Therefore, the purpose of the present study was to isolate local extremophile bacterial strains capable of producing calcium carbonate. Among a total of 44 isolated urease-producing strains from sandy soils, one strain with a high level of urease activity (8.16 U/ml) and production of a large amount of calcium carbonate (410 mg/100 ml) was selected for further investigation. 16S rRNA gene sequencing showed that this strain had 99.66% sequence identity to Bhargavaea cecembensis. The SEM-EDX and XRD analyses indicated that irregular vaterite and aggregated nanocalcite were the dominant polymorphs produced by this strain. The size of these nanocalcite crystals ranged between 25 and 42 nm. The selected strain showed high levels of tolerance to different conditions of temperature, pH, and salinity. This strain grows at high temperatures up to 50 °C, alkaline pH (9-11), and high concentrations of NaCl (20-25% w/v). Flow cytometry analysis demonstrated 96% cell viability of the isolated strain after desiccation stress. Bhargavaea was first reported in 2009 as a new genus, and it belongs to the Firmicutes. So far, there has been no report on its MICP potential. The present study is the first one to report nanocrystal calcium carbonate precipitation in polyextremophile Bhargavaea cecembensis, which makes it a suitable candidate for bio-cementation under extreme circumstances.},
}
@article {pmid35188073,
year = {2022},
author = {Ou, Y and Belzer, C and Smidt, H and de Weerth, C},
title = {Development of the gut microbiota in healthy children in the first ten years of life: associations with internalizing and externalizing behavior.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2038853},
pmid = {35188073},
issn = {1949-0984},
mesh = {Bifidobacterium/genetics ; Child ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Longitudinal Studies ; *Microbiota ; Prevotella ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Increasing evidence indicates that psychopathological disorders are associated with the gut microbiota. However, data are largely lacking from long-term longitudinal birth cohorts, especially those comprising low-risk healthy individuals. Therefore, this study aims to describe gut microbiota development in healthy children from birth till age 10 years, as well as to investigate potential associations with internalizing and externalizing behavior.<br><br>RESULTS: Fecal microbial composition of participants in an ongoing longitudinal study (N =&#xa0;193) was analyzed at 1, 3 and 4 months, and 6 and 10 years of age by 16S ribosomal RNA gene sequencing. Based on these data, three clusters were identified in infancy, two of which were predominated by Bifidobacterium. In childhood, four clusters were observed, two of which increased in prevalence with age. One of the childhood clusters, similar to an enterotype, was highly enriched in genus-level taxon Prevotella_9. Breastfeeding had marked associations with microbiota composition up till age 10, implying an extended role in shaping gut microbial ecology. Microbial clusters were not associated with behavior. However, Prevotella_9 in childhood was positively related to mother-reported externalizing behavior at age 10; this was validated in child reports.<br><br>CONCLUSIONS: This study validated previous findings on Bifidobacterium-enriched and -depleted clusters in infancy. Importantly, it also mapped continued development of gut microbiota in middle childhood. Novel associations between gut microbial composition in the first 10 years of life (especially Prevotella_9), and externalizing behavior at age 10 were found. Replications in other cohorts, as well as follow-up assessments, will help determine the significance of these findings.},
}
@article {pmid35185949,
year = {2021},
author = {Matiz-Ceron, L and Reyes, A and Anzola, J},
title = {Taxonomical Evaluation of Plant Chloroplastic Markers by Bayesian Classifier.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {782663},
pmid = {35185949},
issn = {1664-462X},
abstract = {DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.},
}
@article {pmid35185839,
year = {2022},
author = {Sikorski, J and Baumgartner, V and Birkhofer, K and Boeddinghaus, RS and Bunk, B and Fischer, M and Fösel, BU and Friedrich, MW and Göker, M and Hölzel, N and Huang, S and Huber, KJ and Kandeler, E and Klaus, VH and Kleinebecker, T and Marhan, S and von Mering, C and Oelmann, Y and Prati, D and Regan, KM and Richter-Heitmann, T and Rodrigues, JFM and Schmitt, B and Schöning, I and Schrumpf, M and Schurig, E and Solly, EF and Wolters, V and Overmann, J},
title = {The Evolution of Ecological Diversity in Acidobacteria.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {715637},
pmid = {35185839},
issn = {1664-302X},
abstract = {Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success.},
}
@article {pmid35185836,
year = {2021},
author = {Unzueta-Martínez, A and Welch, H and Bowen, JL},
title = {Determining the Composition of Resident and Transient Members of the Oyster Microbiome.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {828692},
pmid = {35185836},
issn = {1664-302X},
abstract = {To better understand how complex microbial communities become assembled on eukaryotic hosts, it is essential to disentangle the balance between stochastic and deterministic processes that drive their assembly. Deterministic processes can create consistent patterns of microbiome membership that result in persistent resident communities, while stochastic processes can result in random fluctuation of microbiome members that are transient with regard to their association to the host. We sampled oyster reefs from six different populations across the east coast of the United States. At each site we collected gill tissues for microbial community analysis and additionally collected and shipped live oysters to Northeastern University where they were held in a common garden experiment. We then examined the microbiome shifts in gill tissues weekly for 6 weeks using 16S rRNA gene amplicon sequencing. We found a strong population-specific signal in the microbial community composition of field-sampled oysters. Surprisingly, the oysters sampled during the common garden experiment maintained compositionally distinct gill-associated microbial communities that reflected their wild population of origin, even after rearing them in a common garden for several weeks. This indicates that oyster gill-associated microbiota are predominantly composed of resident microbes specific to host population, rather than being a reflection of their immediate biotic and abiotic surroundings. However, certain bacterial taxa tended to appear more frequently on individuals from different populations than on individuals from the same population, indicating that there is a small portion of the gill microbiome that is transient and is readily exchanged with the environmental pool of microbes. Regardless, the majority of gill-associated microbes were resident members that were specific to each oyster population, suggesting that there are strong deterministic factors that govern a large portion of the gill microbiome. A small portion of the microbial communities, however, was transient and moved among oyster populations, indicating that stochastic assembly also contributes to the oyster gill microbiome. Our results are relevant to the oyster aquaculture industry and oyster conservation efforts because resident members of the oyster microbiome may represent microbes that are important to oyster health and some of these key members vary depending on oyster population.},
}
@article {pmid35181861,
year = {2022},
author = {Hu, X and Peng, K and Chen, Y and Chen, X and Liu, S and Zhao, Y and Wu, Y and Xu, Z},
title = {Effect of g-C3N4 on biodiversity and structure of bacterial community in sediment of Xiangjiang River under tetracycline pressure.},
journal = {Ecotoxicology (London, England)},
volume = {31},
number = {3},
pages = {503-515},
doi = {10.1007/s10646-022-02525-7},
pmid = {35181861},
issn = {1573-3017},
support = {19A509//Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province/ ; 201801//Key Projects of National Forestry and Grassland Bureau/ ; 31971462//National Aerospace Science Foundation of China/ ; 2021JJ31138//Natural Science Foundation of Hunan Province/ ; },
mesh = {Anti-Bacterial Agents/toxicity ; *Bacteria ; Biodiversity ; Geologic Sediments/chemistry ; *Rivers/chemistry ; Tetracyclines ; },
abstract = {Photocatalysts have been widely prepared and used in wastewater treatment. Although the influence of photocatalyst application on survival and activity of organisms has been examined, its impact on composition and diversity of microbial community is not fully understood. In this study, the impact of photocatalyst g-C3N4 (Graphitic carbon nitride) on microbial communities in riverbed sediments polluted by antibiotic tetracycline (TC) was investigated. The sediment samples collected from the Xiangjiang River of China were exposed to different concentrations of TC, g-C3N4 and TC/g-C3N4 and the bacterial community were analyzed by Illumina sequencing. The results showed that the dominant bacterial phyla were Acidobacteriota, Proteobacteria, Actinobacteriota, and Chloroflexi in the study site. When compared to the control treatments, the application of TC, g-C3N4 and TC/g-C3N4 exhibited distinguishable effects on bacterial community structure in sediments. The presence of TC had greater influence on bacterial composition, while g-C3N4 and TC/g-C3N4 had less influence on bacteria. The diversity and richness of microorganisms in sediment increased under g-C3N4 application and reached the highest values when g-C3N4 was 75 mg/kg. The photocatalyst g-C3N4 restored bacterial community diversity affected by TC, reduced the TC residues in aquatic environment, and eliminated the side effects of TC application in sediments. Our study indicated that g-C3N4 was an environmentally friendly photocatalyst with lightly negative effects on microbial community in riverbed sediments, and could be used for effective remediation of TC-contaminated environments.},
}
@article {pmid35181077,
year = {2022},
author = {Xie, Z and Bai, Y and Chen, G and Dong, W and Peng, Y and Xu, W and Sun, Y and Zeng, X and Liu, Z},
title = {Immunomodulatory activity of polysaccharides from the mycelium of Aspergillus cristatus, isolated from Fuzhuan brick tea, associated with the regulation of intestinal barrier function and gut microbiota.},
journal = {Food research international (Ottawa, Ont.)},
volume = {152},
number = {},
pages = {110901},
doi = {10.1016/j.foodres.2021.110901},
pmid = {35181077},
issn = {1873-7145},
mesh = {Animals ; Aspergillus ; *Gastrointestinal Microbiome ; Immunity ; Mice ; Mycelium/metabolism ; Polysaccharides/pharmacology ; Tea/metabolism ; },
abstract = {Aspergillus cristatus is the dominant fungus involved in the fermentation of Fuzhuan brick tea (FBT). The intracellular polysaccharides (IPSs) from A. cristatus (MK346334, NCBI), isolated from FBT, exhibited immunomodulatory activity in vitro while the effects in vivo on immune system and gut microbiota remain unclear. In this study, IPSs and the purified fraction (IPSs-2) from IPSs were prepared and their immunomodulatory activities were investigated with cyclophosphamide (Cy)-induced immunosuppressive mice. As results, IPSs strengthened the immune function, manifesting in the improvement of body weight, daily intake, immune organ indices, cytokines and immunoglobulin. Meanwhile, IPSs attenuated Cy-induced intestinal barrier injury and promoted the expression of tight junction proteins and mucin, reinforcing the intestinal barrier function. Moreover, IPSs not only promoted the production of short-chain fatty acids and the expression of G protein-coupled receptor (GPR), but also balanced dysbiosis of gut microbiota through elevating the growth of beneficial bacteria while reducing pathobionts to maintain the homeostasis of the microbial ecology. These results suggested that IPSs exerted immunomodulatory activity linking with the restoration of intestinal barrier function and regulation of gut microbiota, which contributes to the development of novel probiotics and effective immunomodulators for strengthening host immunity and gut health.},
}
@article {pmid35181074,
year = {2022},
author = {Young Kim, S and Ban, GH and Won Hong, Y and Ji Jang, M and Ae Kim, S},
title = {Microbiome shifts in sprouts (alfalfa, radish, and rapeseed) during production from seed to sprout using 16S rRNA microbiome sequencing.},
journal = {Food research international (Ottawa, Ont.)},
volume = {152},
number = {},
pages = {110896},
doi = {10.1016/j.foodres.2021.110896},
pmid = {35181074},
issn = {1873-7145},
mesh = {*Brassica napus ; Colony Count, Microbial ; Food Microbiology ; Humans ; Medicago sativa ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Raphanus ; Seeds ; },
abstract = {Sprouts harbor high levels of bacteria and have been implicated in massive outbreaks of foodborne illnesses. The elucidation of microbial profiles in sprouts is important; however, little is known about the changes in the microbial composition during production. The present study aimed to define the microbial ecology of sprouts during the stages of production using 16S rRNA metagenome sequencing and culture-dependent methods. Samples of three types of sprouts (alfalfa, radish, and rapeseed) were collected from each stage of production (seed, soaking, germination 1 (Germ 1), germination 2 (Germ 2), sprouting, unwashed, and washed sprouts; n = 105) and subjected to microbiome analyses as well as quantitative and qualitative analyses. Aerobic plate count (APC) and coliforms levels significantly increased within one day (Germ 1) by 3.9-4.4 and 4.2-5.2 log CFU/g, respectively, and levels up to 8.0-9.0 and 6.9-9.0 log CFU/g, respectively, were recorded at the final stage. During production, the microbial communities in alfalfa sprouts simplified into Enterobacteriaceae (80.97-99.29%), whereas the radish and rapeseed sprouts were dominated by microbial communities belonging to two families, the Enterobacteriaceae (radish: 32-43.4%, rapeseed: 24.11-38.39%) and Pseudomonadaceae (radish: 30.53-46.45%, rapeseed: 41.51-57.34%). This suggests that the sprout manufacturing conditions could promote the growth of particular bacterium. Alpha diversity analysis revealed a diverse bacterial community structure in the seeds; however, the diversity sharply declined until Germ 1 and recovered during the production steps thereafter. Beta diversity results suggested that the pattern of microbial composition, and the major shifts in composition, differed by seed type. Significant changes in the bacterial community were observed during the soaking (alfalfa), Germ 1 (radish), and Germ 2 (rapeseed) stages. The present study is the first fundamental report to investigate microbial changes by during the various stages of the sprouting process. The results highlight the potential risk of sprouts regarding foodborne illness and facilitate the determination of effective intervention points during sprout production.},
}
@article {pmid35179631,
year = {2023},
author = {Mitbavkar, S and D'souza, S},
title = {Seasonal Dynamics of Photosynthetic Picoeukaryotes in a Monsoon-Influenced Tropical Bay: a Flow Cytometric and Chemotaxonomic Approach.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {341-356},
pmid = {35179631},
issn = {1432-184X},
mesh = {Seasons ; Flow Cytometry ; *Bays ; *Phytoplankton ; Photosynthesis ; Biomass ; },
abstract = {The composition and ecology of photosynthetic picoeukaryotes (PPE) are essential for understanding microbial food web functioning. We hypothesize that the simultaneous use of flow cytometry (FCM) and high-performance liquid chromatography (HPLC) tools will aid in discerning the dominant PPE groups contributing to abundance and biomass under prevailing environmental conditions. The PPE seasonal community abundance and pigment biomass were investigated from a southwest monsoon-influenced tropical bay from June 2015 to May 2016. A size-fractionated (<3 µm) approach using FCM and HPLC revealed five and six PPE groups, respectively. Picocryptophytes dominated the PPE biomass under varied environmental conditions, whereas picodiatoms contributed substantially, being abundant under turbulent, low-temperature, nutrient (NO3[-], SiO4[4-])-enriched conditions. The picochlorophytes dominated the community numerically. The relatively higher abundance and biomass of picoprasinophytes and a positive correlation with NO3[-] and NH4[+] imply proliferation under higher nutrient concentrations. The least contributors to biomass were dinoflagellates and picoprymnesiophytes. The relatively larger cell size of picocryptophytes and picodiatoms resulted in higher cumulative biomass, signifying their role in the microbial food web. Our study proposes incorporation of additional indicator pigments in algorithms used to estimate coastal picophytoplankton contribution to total phytoplankton biomass to avoid discrepancies.},
}
@article {pmid35179276,
year = {2022},
author = {Yemmen, C and Gargouri, M},
title = {Potential hazards associated with the consumption of Scombridae fish: Infection and toxicity from raw material and processing.},
journal = {Journal of applied microbiology},
volume = {132},
number = {6},
pages = {4077-4096},
doi = {10.1111/jam.15499},
pmid = {35179276},
issn = {1365-2672},
mesh = {Animals ; Fishes ; *Food Contamination/analysis ; *Metals, Heavy/toxicity ; Seafood ; Tuna/microbiology ; },
abstract = {Scombridae fish (tuna, bonito and mackerel) have significant ecological and economic values. They are very appreciated by consumers worldwide for their high-quality flesh and for their high nutritional value. However, consumption of Scombridae fish is potentially hazardous. Indeed, several cases of infections and toxicity linked to the consumption of Scombridae fish as raw, or processed food products have been reported worldwide. In this review, we presented the most common health risks associated with Scombridae fish consumption. Diseases associated with the consumption of these fish are generally infectious or toxic and are caused by biological hazards, such as bacteria, viruses, parasites or chemicals hazards that enter the body through contaminated fish (polycyclic aromatic hydrocarbons, histamine) or by physical contaminants, such as heavy metals. The risks of contamination exist throughout the food chain, from primary production to the preparation of products for consumption.},
}
@article {pmid35176463,
year = {2022},
author = {Van Peteghem, L and Sakarika, M and Matassa, S and Pikaar, I and Ganigué, R and Rabaey, K},
title = {Towards new carbon-neutral food systems: Combining carbon capture and utilization with microbial protein production.},
journal = {Bioresource technology},
volume = {349},
number = {},
pages = {126853},
doi = {10.1016/j.biortech.2022.126853},
pmid = {35176463},
issn = {1873-2976},
mesh = {*Carbon ; Carbon Dioxide ; *Carbon Footprint ; },
abstract = {Alternative protein sources such as microbial protein (MP) are currently considered to alleviate the burden that food production exerts on the environment. Even though MP production is highly efficient in land and nutrient utilization, their carbon footprint should be improved. Here we propose the use of CCU as a driver for heterotrophic MP production. By comparing different MP production routes starting from liquid substrates derived from CO2 (i.e., formate, acetate, methanol, and ethanol) and their respective metabolic pathways, the potential of this concept as a carbon-neutral food or feed production process was estimated. Acetate and ethanol appear to be the most beneficial substrates for the integrated CCU-to-MP process in terms of electricity demand (acetate: 25 - 54 kWh/kgproduct, ethanol: 28 - 56 kWh/kgproduct). Moreover, recycling CO2 enables a carbon-negative protein production process by 2030 (considering the projected CO2 emissions from electricity in the EU: 0.096 kgCO2-eq/kWh) for formate, acetate, and ethanol (-1.1 up to 13 kgCO2-eq/kgproduct).},
}
@article {pmid35176304,
year = {2022},
author = {Li, JL and Duan, L and Wu, Y and Ahmad, M and Yin, LZ and Luo, XQ and Wang, X and Fang, BZ and Li, SH and Huang, LN and Wu, JX and Mou, XZ and Wang, P and Li, WJ},
title = {Unraveling microbe-mediated degradation of lignin and lignin-derived aromatic fragments in the Pearl River Estuary sediments.},
journal = {Chemosphere},
volume = {296},
number = {},
pages = {133995},
doi = {10.1016/j.chemosphere.2022.133995},
pmid = {35176304},
issn = {1879-1298},
mesh = {Archaea/genetics ; Bacteria/genetics ; Carbon/analysis ; China ; *Estuaries ; Geologic Sediments/microbiology ; Lignin ; *Rivers/microbiology ; },
abstract = {Estuaries are one of the most crucial areas for the transformation and burial of terrestrial organic carbon (TerrOC), playing an important role in the global carbon cycle. While the transformation and degradation of TerrOC are mainly driven by microorganisms, the specific taxa and degradation processes involved remain largely unknown in estuaries. We collected surface sediments from 14 stations along the longitudinal section of the Pearl River Estuary (PRE), P. R. China. By combining analytical chemistry, metagenomics, and bioinformatics methods, we analyzed composition, source and degradation pathways of lignin/lignin-derived aromatic fragments and their potential decomposers in these samples. A diversity of bacterial and archaeal taxa, mostly those from Proteobacteria (Deltaproteobacteria, Gammaproteobacteria etc.), including some lineages (e.g., Nitrospria, Polyangia, Tectomicrobia_uc) not previously implicated in lignin degradation, were identified as potential polymeric lignin or its aromatic fragments degraders. The abundance of lignin degradation pathways genes exhibited distinct spatial distribution patterns with the area adjacent to the outlet of Modaomen as a potential degradation hot zone and the Syringyl lignin fragments, 3,4-PDOG, and 4,5-PDOG pathways as the primary potential lignin aromatic fragments degradation processes. Notably, the abundance of ferulic acid metabolic pathway genes exhibited significant correlations with degree of lignin oxidation and demethylation/demethoxylization and vegetation source. Additionally, the abundance of 2,3-PDOG degradation pathways genes also showed a positive significant correlation with degree of lignin oxidation. Our study provides a meaningful insight into the microbial ecology of TerrOC degradation in the estuary.},
}
@article {pmid35173689,
year = {2021},
author = {Monteiro, MR and Marshall, AJ and Hawes, I and Lee, CK and McDonald, IR and Cary, SC},
title = {Geochemically Defined Space-for-Time Transects Successfully Capture Microbial Dynamics Along Lacustrine Chronosequences in a Polar Desert.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {783767},
pmid = {35173689},
issn = {1664-302X},
abstract = {The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems typically studied. The McMurdo Dry Valleys (MDV) of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change scenarios. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We identified microbial taxa that are consistently responsive to changes in wetness in the soils and reliably associated with long-term dry or wet edaphic conditions. Comparisons between transects defined at static (open-basin) and dynamic (closed-basin) lakes highlighted the capacity for geochemically defined space-for-time gradients to identify lasting deterministic impacts of historical changes in water presence on the structure and diversity of extant microbial communities. We highlight the potential for geochemically defined space-for-time transects to resolve legacy impacts of environmental change when used in conjunction with static and dynamic scenarios, and to inform future environmental scenarios through changes in the microbial community structure, composition, and diversity.},
}
@article {pmid35172890,
year = {2022},
author = {Zhou, Z and Tran, PQ and Breister, AM and Liu, Y and Kieft, K and Cowley, ES and Karaoz, U and Anantharaman, K},
title = {METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {33},
pmid = {35172890},
issn = {2049-2618},
support = {T15 LM007359/LM/NLM NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; },
mesh = {*Genome, Microbial ; Humans ; Lakes ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; },
abstract = {BACKGROUND: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling.<br><br>RESULTS: We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric "MW-score" (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~&#x2009;3 h with 40 CPU threads to process ~&#x2009;100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~&#x2009;45 min, while it takes ~&#x2009;5 h to complete hmmsearch for ~&#x2009;3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut.<br><br>CONCLUSION: METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3&#xa0;at https://github.com/AnantharamanLab/METABOLIC . Video abstract.},
}
@article {pmid35171088,
year = {2022},
author = {Lee, HJ and Whang, KS},
title = {Roseomonas rubea sp. nov., isolated from rice paddy soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {2},
pages = {},
doi = {10.1099/ijsem.0.005251},
pmid = {35171088},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Methylobacteriaceae/classification/isolation &amp; purification ; *Oryza ; Phospholipids/chemistry ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Ubiquinone/analogs &amp; derivatives/chemistry ; },
abstract = {Three pale-red-pigmented, Gram-stain-negative, coccobacilli-shaped, motile and strictly aerobic bacteria, strains MO17[T], MO41 and NPKOSM1, were isolated from rice paddy soil. Colonies were circular with entire edges, convex and pale red. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains MO17[T], MO41 and NPKOSM1 belonged to the genus Roseomonas and were closely related to Roseomonas sediminicola FW-3[T] (98.2 %), Roseomonas oryzicola YC6724[T] (98.0 %), Roseomonas soli 5N26[T] (98.0 %), Roseomonas eburnea BUT-5[T] (97.8 %), Roseomonas alkaliterrae YIM 78007[T] (97.7 %), Roseomonas lacus TH-G33[T] (97.6 %) and Roseomonas terrae DS-48[T] (96.8 %). The DNA-DNA hybridization values between strains MO17[T], MO41 and NPKOSM1 were 84-92 %, and the values between the three strains and their close phylogenetic relatives were also below 70 %. The major cellular fatty acids were C18 : 1 ω7c, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2OH). The predominant respiratory quinone was identified as Q-10. The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and two unknown phospholipids. Based on their distinctive phenotypic, phylogenetic and chemotaxonomic characteristics, the three strains are considered to represent novel species of the genus Roseomonas for which the name Roseomonas rubea sp. nov. is proposed. The type strain is MO17[T] (=KACC 19933[T]=NBRC 114495[T]).},
}
@article {pmid35171049,
year = {2022},
author = {Yu, T and Cheng, L and Liu, Q and Wang, S and Zhou, Y and Zhong, H and Tang, M and Nian, H and Lian, T},
title = {Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence.},
journal = {Microbiology spectrum},
volume = {10},
number = {1},
pages = {e0201121},
pmid = {35171049},
issn = {2165-0497},
mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Glycine max/growth &amp; development/*microbiology ; },
abstract = {Waterlogging causes a significant reduction in soil oxygen levels, which in turn negatively affects soil nutrient use efficiency and crop yields. Rhizosphere microbes can help plants to better use nutrients and thus better adapt to this stress, while it is not clear how the plant-associated microbes respond to waterlogging stress. There are also few reports on whether this response is influenced by different sequencing methods and by different soils. In this study, using partial 16S rRNA sequencing targeting the V4 region and two full-length 16S rRNA sequencing approaches targeting the V1 to V9 regions, the effects of waterlogging on soybean rhizosphere bacterial structure in two types of soil were examined. Our results showed that, compared with the partial 16S sequencing, full-length sequencing, both LoopSeq and Pacific Bioscience (PacBio) 16S sequencing, had a higher resolution. On both types of soil, all the sequencing methods showed that waterlogging significantly affected the bacterial community structure of the soybean rhizosphere and increased the relative abundance of Geobacter. Furthermore, modular analysis of the cooccurrence network showed that waterlogging increased the relative abundance of some microorganisms related to nitrogen cycling when using V4 sequencing and increased the microorganisms related to phosphorus cycling when using LoopSeq and PacBio 16S sequencing methods. Core microorganism analysis further revealed that the enriched members of different species might play a central role in maintaining the stability of bacterial community structure and ecological functions. Together, our study explored the role of microorganisms enriched at the rhizosphere under waterlogging in assisting soybeans to resist stress. Furthermore, compared to partial and PacBio 16S sequencing, LoopSeq offers improved accuracy and reduced sequencing prices, respectively, and enables accurate species-level and strain identification from complex environmental microbiome samples. IMPORTANCE Soybeans are important oil-bearing crops, and waterlogging has caused substantial decreases in soybean production all over the world. The microbes associated with the host have shown the ability to promote plant growth, nutrient absorption, and abiotic resistance. High-throughput sequencing of partial 16S rRNA is the most commonly used method to analyze the microbial community. However, partial sequencing cannot provide correct classification information below the genus level, which greatly limits our research on microbial ecology. In this study, the effects of waterlogging on soybean rhizosphere microbial structure in two soil types were explored using partial 16S rRNA and full-length 16S gene sequencing by LoopSeq and Pacific Bioscience (PacBio). The results showed that full-length sequencing had higher classification resolution than partial sequencing. Three sequencing methods all indicated that rhizosphere bacterial community structure was significantly impacted by waterlogging, and the relative abundance of Geobacter was increased in the rhizosphere in both soil types after suffering waterlogging. Moreover, the core microorganisms obtained by different sequencing methods all contain species related to nitrogen cycling. Together, our study not only explored the role of microorganisms enriched at the rhizosphere level under waterlogging in assisting soybean to resist stress but also showed that LoopSeq sequencing is a less expensive and more convenient method for full-length sequencing by comparing different sequencing methods.},
}
@article {pmid35166563,
year = {2022},
author = {Pudlo, NA and Urs, K and Crawford, R and Pirani, A and Atherly, T and Jimenez, R and Terrapon, N and Henrissat, B and Peterson, D and Ziemer, C and Snitkin, E and Martens, EC},
title = {Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria.},
journal = {mSystems},
volume = {7},
number = {1},
pages = {e0094721},
pmid = {35166563},
issn = {2379-5077},
support = {K01 DK084214/DK/NIDDK NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 DK118024/DK/NIDDK NIH HHS/United States ; R01 DK125445/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Polysaccharides/chemistry ; Bacteria/metabolism ; Dietary Carbohydrates/metabolism ; *Microbiota ; Dietary Fiber/metabolism ; Genomics ; Mucins/metabolism ; },
abstract = {Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central for defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/Bacteroides xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multilocus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors. IMPORTANCE Nonharmful bacteria are the primary microbial symbionts that inhabit the human gastrointestinal tract. These bacteria play many beneficial roles and in some cases can modify disease states, making it important to understand which nutrients sustain specific lineages. This knowledge will in turn lead to strategies to intentionally manipulate the gut microbial ecosystem. We designed a scalable, high-throughput platform for measuring the ability of gut bacteria to utilize polysaccharides, of which many are derived from dietary fiber sources that can be manipulated easily. Our results provide paths to expand phenotypic surveys of more diverse gut bacteria to understand their functions and also to leverage dietary fibers to alter the physiology of the gut microbial community.},
}
@article {pmid35166561,
year = {2022},
author = {Monsees, I and Turzynski, V and Esser, SP and Soares, A and Timmermann, LI and Weidenbach, K and Banas, J and Kloster, M and Beszteri, B and Schmitz, RA and Probst, AJ},
title = {Label-Free Raman Microspectroscopy for Identifying Prokaryotic Virocells.},
journal = {mSystems},
volume = {7},
number = {1},
pages = {e0150521},
pmid = {35166561},
issn = {2379-5077},
mesh = {*Prokaryotic Cells ; Anti-Bacterial Agents ; Ecosystem ; Gram-Negative Bacteria ; Archaea ; *Bacteriophages ; Bacillus subtilis ; },
abstract = {Raman microspectroscopy has been used to thoroughly assess growth dynamics and heterogeneity of prokaryotic cells, yet little is known about how the chemistry of individual cells changes during infection with virulent viruses, resulting in so-called virocells. Here, we investigate biochemical changes of bacterial and archaeal cells of three different species in laboratory cultures before and after addition of their respective viruses using single-cell Raman microspectroscopy. By applying multivariate statistics, we identified significant differences in the spectra of single cells with/without addition of virulent dsRNA phage (phi6) for Pseudomonas syringae. A general ratio of wavenumbers that contributed the greatest differences in the recorded spectra was defined as an indicator for virocells. Based on reference spectra, this difference is likely attributable to an increase in nucleic acid versus protein ratio of virocells. This method also proved successful for identification of Bacillus subtilis cells infected with the double-stranded DNA (dsDNA) phage phi29, displaying a decrease in respective ratio, but failed for archaeal virocells (Methanosarcina mazei with the dsDNA methanosarcina spherical virus) due to autofluorescence. Multivariate and univariate analyses suggest that Raman spectral data of infected cells can also be used to explore the complex biology behind viral infections of bacteria. Using this method, we confirmed the previously described two-stage infection of P. syringae's phi6 and that infection of B. subtilis with phi29 results in a stress response within single cells. We conclude that Raman microspectroscopy is a promising tool for chemical identification of Gram-positive and Gram-negative virocells undergoing infection with virulent DNA or RNA viruses. IMPORTANCE Viruses are highly diverse biological entities shaping many ecosystems across Earth. However, understanding the infection of individual microbial cells and the related biochemical changes remains limited. Using Raman microspectroscopy in conjunction with univariate and multivariate statistics, we established a marker for identification of infected Gram-positive and Gram-negative bacteria. This nondestructive, label-free analytical method at single-cell resolution paves the way for future studies geared towards analyzing virus-host systems of prokaryotes to further understand the complex chemistry and function of virocells.},
}
@article {pmid35159609,
year = {2022},
author = {Tsigkrimani, M and Panagiotarea, K and Paramithiotis, S and Bosnea, L and Pappa, E and Drosinos, EH and Skandamis, PN and Mataragas, M},
title = {Microbial Ecology of Sheep Milk, Artisanal Feta, and Kefalograviera Cheeses. Part II: Technological, Safety, and Probiotic Attributes of Lactic Acid Bacteria Isolates.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
pmid = {35159609},
issn = {2304-8158},
support = {T1EDK-02087//European Union and Greek national funds/ ; },
abstract = {The aim of the present study was to examine 189 LAB strains belonging to the species Enterococcus faecium, E. faecalis, Lactococcus lactis, Pediococcus pentosaceus, Leuconostoc mesenteroides, Lactiplantibacillus pentosus, Latilactobacillus curvatus, Lp. plantarum, Levilactobacillus brevis, and Weissella paramesenteroides isolated form sheep milk, Feta and Kefalograviera cheeses at different ripening stages, for their technological compatibility with dairy products manufacturing, their activities that may compromise safety of the dairy products as well as their capacity to survive in the human gastrointestinal tract. For that purpose, milk acidification and coagulation capacity, caseinolytic, lipolytic, hemolytic, gelatinolytic, and bile salt hydrolase activity, production of exopolysaccharides, antimicrobial compounds, and biogenic amines, as well as acid and bile salt tolerance and antibiotic susceptibility were examined. The faster acidifying strains were Lc. lactis DRD 2658 and P. pentosaceus DRD 2657 that reduced the pH value of skim milk, within 6 h to 5.97 and 5.92, respectively. Strains able to perform weak caseinolysis were detected in all species assessed. On the contrary, lipolytic activity, production of exopolysaccharides, amino acid decarboxylation, hemolytic, gelatinase, and bile salt hydrolase activity were not detected. Variable susceptibility to the antibiotics examined was detected among LAB strains. However, in the majority of the cases, resistance was evident. None of the strains assessed, managed to survive to exposure at pH value 1. On the contrary, 25.9 and 88.9% of the strains survived after exposure at pH values 2 and 3, respectively; the reduction of the population was larger in the first case. The strains survived well after exposure to bile salts. The strain-dependent character of the properties examined was verified. Many strains, belonging to different species, have presented very interesting properties; however, further examination is needed before their potential use as starter or adjunct cultures.},
}
@article {pmid35157872,
year = {2022},
author = {Sperlea, T and Schenk, JP and Dreßler, H and Beisser, D and Hattab, G and Boenigk, J and Heider, D},
title = {The relationship between land cover and microbial community composition in European lakes.},
journal = {The Science of the total environment},
volume = {825},
number = {},
pages = {153732},
doi = {10.1016/j.scitotenv.2022.153732},
pmid = {35157872},
issn = {1879-1026},
mesh = {Environmental Biomarkers ; *Lakes ; *Microbiota ; Water Quality ; },
abstract = {Microbes are essential for element cycling and ecosystem functioning. However, many questions central to understanding the role of microbes in ecology are still open. Here, we analyze the relationship between lake microbiomes and the lakes' land cover. By applying machine learning methods, we quantify the covariance between land cover categories and the microbial community composition recorded in the largest amplicon sequencing dataset of European lakes available to date. Our results show that the aggregation of environmental features or microbial taxa before analysis can obscure ecologically relevant patterns. We observe a comparatively high covariation of the lakes' microbial community with herbaceous and open spaces surrounding the lake; nevertheless, the microbial covariation with land cover categories is generally lower than the covariation with physico-chemical parameters. Combining land cover and physico-chemical bioindicators identified from the same amplicon sequencing dataset, we develop analytical data structures that facilitate insights into the ecology of the lake microbiome. Among these, a list of the environmental parameters sorted by the number of microbial bioindicators we have identified for them points towards apparent environmental drivers of the lake microbial community composition, such as the altitude, conductivity, and area covered herbaceous vegetation surrounding the lake. Furthermore, the response map, a similarity matrix calculated from the Jaccard similarity of the environmental parameters' lists of bioindicators, allows us to study the ecosystem's structure from the standpoint of the microbiome. More specifically, we identify multiple clusters of highly similar and possibly functionally linked ecological parameters, including one that highlights the importance of the calcium-bicarbonate equilibrium for lake ecology. Taken together, we demonstrate the use of machine learning approaches in studying the interplay between microbial diversity and environmental factors and introduce novel approaches to integrate environmental molecular diversity into monitoring and water quality assessments.},
}
@article {pmid35157108,
year = {2023},
author = {Mo, S and He, S and Sang, Y and Li, J and Kashif, M and Zhang, Z and Su, G and Jiang, C},
title = {Integration of Microbial Transformation Mechanism of Polyphosphate Accumulation and Sulfur Cycle in Subtropical Marine Mangrove Ecosystems with Spartina alterniflora Invasion.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {478-494},
pmid = {35157108},
issn = {1432-184X},
support = {31760437//National Natural Science Foundation of China/ ; GUIKEZY21195021//Funding Project of Chinese Central Government Guiding to the Guangxi Local Science and Technology Development/ ; 2019GXNSFFA245011//Natural Science Fund for Distinguished Young Scholars of Guangxi Zhuang Autonomous Region of China/ ; AD20297142//China-ASEAN International Innovative Center for Health Industry of Traditional Chinese Medicine/ ; 2022KA02//Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University/ ; YCBZ2021012//Innovation Project of Guangxi Graduate Education/ ; YCSW2021064//Innovation Project of Guangxi Graduate Education/ ; },
mesh = {*Wetlands ; Polyphosphates/analysis/metabolism ; Phylogeny ; Introduced Species ; Nitrogen/metabolism ; Phosphorus/metabolism ; Poaceae ; *Microbiota ; Sulfur/metabolism ; Sulfates/metabolism ; China ; },
abstract = {Excessive phosphorus can lead to eutrophication in marine and coastal ecosystems. Sulfur metabolism-associated microorganisms stimulate biological phosphorous removal. However, the integrating co-biotransformation mechanism of phosphorus and sulfur in subtropical marine mangrove ecosystems with Spartina alterniflora invasion is poorly understood. In this study, an ecological model of the coupling biotransformation of sulfur and phosphorus is constructed using metagenomic analysis and quantitative polymerase chain reaction strategies. Phylogenetic analysis profiling, a distinctive microbiome with high frequencies of Gammaproteobacteria and Deltaproteobacteria, appears to be an adaptive characteristic of microbial structures in subtropical mangrove ecosystems. Functional analysis reveals that the levels of sulfate reduction, sulfur oxidation, and poly-phosphate (Poly-P) aggregation decrease with increasing depth. However, at depths of 25-50 cm in the mangrove ecosystems with S. alterniflora invasion, the abundance of sulfate reduction genes, sulfur oxidation genes, and polyphosphate kinase (ppk) significantly increased. A strong positive correlation was found among ppk, sulfate reduction, sulfur oxidation, and sulfur metabolizing microorganisms, and the content of sulfide was significantly and positively correlated with the abundance of ppk. Further microbial identification suggested that Desulfobacterales, Anaerolineales, and Chromatiales potentially drove the coupling biotransformation of phosphorus and sulfur cycling. In particular, Desulfobacterales exhibited dominance in the microbial community structure. Our findings provided insights into the simultaneous co-biotransformation of phosphorus and sulfur bioconversions in subtropical marine mangrove ecosystems with S. alterniflora invasion.},
}
@article {pmid35154025,
year = {2021},
author = {DeWolf, EI and Calder, WJ and Harrison, JG and Randolph, GD and Noren, BE and Weinig, C},
title = {Aquatic Macrophytes Are Associated With Variation in Biogeochemistry and Bacterial Assemblages of Mountain Lakes.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {777084},
pmid = {35154025},
issn = {1664-302X},
abstract = {In aquatic systems, microbes likely play critical roles in biogeochemical cycling and ecosystem processes, but much remains to be learned regarding microbial biogeography and ecology. The microbial ecology of mountain lakes is particularly understudied. We hypothesized that microbial distribution among lakes is shaped, in part, by aquatic plant communities and the biogeochemistry of the lake. Specifically, we investigated the associations of yellow water lilies (Nuphar polysepala) with the biogeochemistry and microbial assemblages within mountain lakes at two scales: within a single lake and among lakes within a mountain range. We first compared the biogeochemistry of lakes without water lilies to those colonized to varying degrees by water lilies. Lakes with >10% of the surface occupied by water lilies had lower pH and higher dissolved organic carbon than those without water lilies and had a different microbial composition. Notably, cyanobacteria were negatively associated with water lily presence, a result consistent with the past observation that macrophytes outcompete phytoplankton and can suppress cyanobacterial and algal blooms. To examine the influence of macrophytes on microbial distribution within a lake, we characterized microbial assemblages present on abaxial and adaxial water lily leaf surfaces and in the water column. Microbial diversity and composition varied among all three habitats, with the highest diversity of microbes observed on the adaxial side of leaves. Overall, this study suggests that water lilies influence the biogeochemistry and microbiology of mountains lakes.},
}
@article {pmid35151004,
year = {2022},
author = {Mekureyaw, MF and Pandey, C and Hennessy, RC and Nicolaisen, MH and Liu, F and Nybroe, O and Roitsch, T},
title = {The cytokinin-producing plant beneficial bacterium Pseudomonas fluorescens G20-18 primes tomato (Solanum lycopersicum) for enhanced drought stress responses.},
journal = {Journal of plant physiology},
volume = {270},
number = {},
pages = {153629},
doi = {10.1016/j.jplph.2022.153629},
pmid = {35151004},
issn = {1618-1328},
abstract = {Plant growth-promoting rhizobacteria (PGPR) are known for exerting beneficial effects on plant growth and tolerance to plant pathogens. However, their specific role in mediating protection against abiotic stress remains underexplored. The aim of this study was to characterise the ability of the cytokinin-producing beneficial bacterium Pseudomonas fluorescens G20-18 to enhance tomato growth and boost tolerance to drought stress. Tomato seedlings were root inoculated and their growth and physiological and molecular responses assessed under well-watered conditions and also in response to progressive drought stress and a subsequent recovery period. Root inoculation with G20-18 had a significant positive impact on tomato growth. Furthermore, G20-18 inoculated and drought-stressed plants showed higher leaf chlorophyll and abscisic acid (ABA) content and stomatal closure than non-inoculated controls. Root inoculation also increased the activity of different carbohydrate metabolism enzymes, which are important for root and leaf growth and development in drought stressed plants. A significant increase in the activity of different antioxidant enzymes and total antioxidant capacity correlated with elevated levels of relevant secondary metabolites, such as phenolics, anthocyanins and flavonoids. RNA sequencing revealed distinct qualitative and quantitative differences in gene regulation in response to G20-18. Notably, the number of genes differentially regulated in response to G20-18 was approximately sevenfold higher during drought stress, indicating that root inoculation with the bacteria primed the plants for a much stronger transcriptionally regulated systemic drought stress response. The regulated genes are related to phenylalanine metabolism and other key processes linked to plant growth, development and drought stress resilience. A role of the ability of G20-18 to produce the plant hormone cytokinin for interaction with tomato was established by the cytokinin-deficient biosynthesis mutants CNT1 and CNT2. In comparison with G20-18, the inoculation of plants with CNT1 resulted in a reduced number of differentially regulated genes. The relative change was most prominent under well-watered conditions with a 85 % reduction, corresponding to 462 genes. However, under drought conditions the absolute number of differentially regulated genes was reduced by even 2219 in response to the CNT1 mutant. The relevance of the ability of G20-18 to produce cytokinins for interaction with plants was also evident from differences in growth and specific cell and ecophysiological parameters in response to CNT1 and CNT2. These findings provide novel insights about G20-18's ability to improve drought stress responses and the role of interkingdom signalling by bacterial-derived cytokinins, and contribute to enhance the robustness of the practical application of these microorganisms to improve crop resilience in agricultural production.},
}
@article {pmid35150249,
year = {2022},
author = {Qi, Y and Ossowicki, A and Yergeau, &#xc9; and Vigani, G and Geissen, V and Garbeva, P},
title = {Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth, and microbial communities.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {2},
pages = {},
doi = {10.1093/femsec/fiac017},
pmid = {35150249},
issn = {1574-6941},
mesh = {Agriculture ; *Ascomycota ; *Microbiota ; Plastics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Plastic mulch film residues have been accumulating in agricultural soils for decades, but so far, little is known about its consequences on soil microbial communities and functions. Here, we tested the effects of plastic residues of low-density polyethylene and biodegradable mulch films on soil suppressiveness and microbial community composition. We investigated how plastic residues in a Fusarium culmorum suppressive soil affect the level of disease suppressiveness, plant biomass, nutrient status, and microbial communities in rhizosphere using a controlled pot experiment. The addition of 1% plastic residues to the suppressive soil did not affect the level of suppression and the disease symptoms index. However, we did find that plant biomasses decreased, and that plant nutrient status changed in the presence of plastic residues. No significant changes in bacterial and fungal rhizosphere communities were observed. Nonetheless, bacterial and fungal communities closely attached to the plastisphere were very different from the rhizosphere communities with overrepresentation of potential plant pathogens. The plastisphere revealed a high abundance of specific bacterial phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) and fungal genera (Rhizoctonia and Arthrobotrys). Our work revealed new insights and raises emerging questions for further studies on the impact of microplastics on the agroecosystems.},
}
@article {pmid35149704,
year = {2022},
author = {Ling, N and Wang, T and Kuzyakov, Y},
title = {Rhizosphere bacteriome structure and functions.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {836},
pmid = {35149704},
issn = {2041-1723},
mesh = {Antitoxins ; Bacteria/*classification/genetics ; *Bacterial Physiological Phenomena ; Bacteroidetes ; Biodiversity ; Microbiota/genetics ; Proteobacteria ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil ; *Soil Microbiology ; },
abstract = {Microbial composition and functions in the rhizosphere-an important microbial hotspot-are among the most fascinating yet elusive topics in microbial ecology. We used 557 pairs of published 16S rDNA amplicon sequences from the bulk soils and rhizosphere in different ecosystems around the world to generalize bacterial characteristics with respect to community diversity, composition, and functions. The rhizosphere selects microorganisms from bulk soil to function as a seed bank, reducing microbial diversity. The rhizosphere is enriched in Bacteroidetes, Proteobacteria, and other copiotrophs. Highly modular but unstable bacterial networks in the rhizosphere (common for r-strategists) reflect the interactions and adaptations of microorganisms to dynamic conditions. Dormancy strategies in the rhizosphere are dominated by toxin-antitoxin systems, while sporulation is common in bulk soils. Functional predictions showed that genes involved in organic compound conversion, nitrogen fixation, and denitrification were strongly enriched in the rhizosphere (11-182%), while genes involved in nitrification were strongly depleted.},
}
@article {pmid35148097,
year = {2022},
author = {Kundu, K and Melsbach, A and Heckel, B and Schneidemann, S and Kanapathi, D and Marozava, S and Merl-Pham, J and Elsner, M},
title = {Linking Increased Isotope Fractionation at Low Concentrations to Enzyme Activity Regulation: 4-Cl Phenol Degradation by Arthrobacter chlorophenolicus A6.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {5},
pages = {3021-3032},
pmid = {35148097},
issn = {1520-5851},
mesh = {*Arthrobacter ; *Atrazine ; Biodegradation, Environmental ; Carbon Isotopes/metabolism ; Chemical Fractionation ; Isotopes ; Micrococcaceae ; Phenol ; },
abstract = {Slow microbial degradation of organic trace chemicals ("micropollutants") has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease in isotope fractionation of atrazine revealed a transition from rate-limiting enzyme turnover to membrane permeation as a bottleneck when concentrations fell below the Monod constant of microbial growth. With degradation of the pollutant 4-chlorophenol (4-CP) by Arthrobacter chlorophenolicus A6, this study targeted a bacterium which adapts its enzyme activity to concentrations. Unlike with atrazine degradation, isotope fractionation of 4-CP increased at lower concentrations, from ε(C) = -1.0 ± 0.5‰ in chemostats (D = 0.090 h[-1], 88 mg L[-1]) and ε(C) = -2.1 ± 0.5‰ in batch (c0 = 220 mg L[-1]) to ε(C) = -4.1 ± 0.2‰ in chemostats at 90 μg L[-1]. Surprisingly, fatty acid composition indicated increased cell wall permeability at high concentrations, while proteomics revealed that catabolic enzymes (CphCI and CphCII) were differentially expressed at D = 0.090 h[-1]. These observations support regulation on the enzyme activity level─through either a metabolic shift between catabolic pathways or decreased enzymatic turnover at low concentrations─and, hence, reveal an alternative end-member scenario for bacterial adaptation at low concentrations. Including more degrader strains into this multidisciplinary analytical approach offers the perspective to build a knowledge base on bottlenecks of bioremediation at low concentrations that considers bacterial adaptation.},
}
@article {pmid35146791,
year = {2022},
author = {Mozzachiodi, S and Bai, FY and Baldrian, P and Bell, G and Boundy-Mills, K and Buzzini, P and Čadež, N and Cubillos, FA and Dashko, S and Dimitrov, R and Fisher, KJ and Gibson, B and Gouliamova, D and Greig, D and Heistinger, L and Hittinger, CT and Jecmenica, M and Koufopanou, V and Landry, CR and Mašínová, T and Naumova, ES and Opulente, D and Peña, JJ and Petrovič, U and Tsai, IJ and Turchetti, B and Villarreal, P and Yurkov, A and Liti, G and Boynton, P},
title = {Yeasts from temperate forests.},
journal = {Yeast (Chichester, England)},
volume = {39},
number = {1-2},
pages = {4-24},
doi = {10.1002/yea.3699},
pmid = {35146791},
issn = {1097-0061},
mesh = {Biodiversity ; *Ecosystem ; Forests ; *Trees ; Yeasts/genetics ; },
abstract = {Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here, we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.},
}
@article {pmid35146390,
year = {2022},
author = {Kodera, SM and Das, P and Gilbert, JA and Lutz, HL},
title = {Conceptual strategies for characterizing interactions in microbial communities.},
journal = {iScience},
volume = {25},
number = {2},
pages = {103775},
pmid = {35146390},
issn = {2589-0042},
abstract = {Understanding the sets of inter- and intraspecies interactions in microbial communities is a fundamental goal of microbial ecology. However, the study and quantification of microbial interactions pose several challenges owing to their complexity, dynamic nature, and the sheer number of unique interactions within a typical community. To overcome such challenges, microbial ecologists must rely on various approaches to distill the system of study to a functional and conceptualizable level, allowing for a practical understanding of microbial interactions in both simplified and complex systems. This review broadly addresses the role of several conceptual approaches available for the microbial ecologist's arsenal, examines specific tools used to accomplish such approaches, and describes how the assumptions, expectations, and philosophies underlying these tools change across scales of complexity.},
}
@article {pmid35145031,
year = {2022},
author = {Karita, Y and Limmer, DT and Hallatschek, O},
title = {Scale-dependent tipping points of bacterial colonization resistance.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {7},
pages = {},
pmid = {35145031},
issn = {1091-6490},
support = {R01 GM115851/GM/NIGMS NIH HHS/United States ; S10 OD023532/OD/NIH HHS/United States ; },
mesh = {Acetobacter/drug effects/*physiology ; Anti-Bacterial Agents/pharmacology ; Bacteriological Techniques ; Drug Resistance, Bacterial ; *Lab-On-A-Chip Devices ; Tetracycline/pharmacology ; },
abstract = {Bacteria are efficient colonizers of a wide range of secluded microhabitats, such as soil pores, skin follicles, or intestinal crypts. How the structural diversity of these habitats modulates microbial self-organization remains poorly understood, in part because of the difficulty to precisely manipulate the physical structure of microbial environments. Using a microfluidic device to grow bacteria in crypt-like incubation chambers of systematically varied lengths, we show that small variations in the physical structure of the microhabitat can drastically alter bacterial colonization success and resistance against invaders. Small crypts are uncolonizable; intermediately sized crypts can stably support dilute populations, while beyond a second critical length scale, populations phase separate into a dilute region and a jammed region. The jammed state is characterized by extreme colonization resistance, even if the resident strain is suppressed by an antibiotic. Combined with a flexible biophysical model, we demonstrate that colonization resistance and associated priority effects can be explained by a crowding-induced phase transition, which results from a competition between proliferation and density-dependent cell leakage. The emerging sensitivity to scale underscores the need to control for scale in microbial ecology experiments. Systematic flow-adjustable length-scale variations may serve as a promising strategy to elucidate further scale-sensitive tipping points and to rationally modulate the stability and resilience of microbial colonizers.},
}
@article {pmid35145022,
year = {2022},
author = {Lambert, BS and Groussman, RD and Schatz, MJ and Coesel, SN and Durham, BP and Alverson, AJ and White, AE and Armbrust, EV},
title = {The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {7},
pages = {},
pmid = {35145022},
issn = {1091-6490},
mesh = {Eukaryota/genetics/*physiology ; *Food Chain ; Gene Expression Profiling ; *Machine Learning ; *Models, Biological ; Oceans and Seas ; Plankton/genetics/*physiology ; },
abstract = {Intricate networks of single-celled eukaryotes (protists) dominate carbon flow in the ocean. Their growth, demise, and interactions with other microorganisms drive the fluxes of biogeochemical elements through marine ecosystems. Mixotrophic protists are capable of both photosynthesis and ingestion of prey and are dominant components of open-ocean planktonic communities. Yet the role of mixotrophs in elemental cycling is obscured by their capacity to act as primary producers or heterotrophic consumers depending on factors that remain largely uncharacterized. Here, we develop and apply a machine learning model that predicts the in situ trophic mode of aquatic protists based on their patterns of gene expression. This approach leverages a public collection of protist transcriptomes as a training set to identify a subset of gene families whose transcriptional profiles predict trophic mode. We applied our model to nearly 100 metatranscriptomes obtained during two oceanographic cruises in the North Pacific and found community-level and population-specific evidence that abundant open-ocean mixotrophic populations shift their predominant mode of nutrient and carbon acquisition in response to natural gradients in nutrient supply and sea surface temperature. Metatranscriptomic data from ship-board incubation experiments revealed that abundant mixotrophic prymnesiophytes from the oligotrophic North Pacific subtropical gyre rapidly remodeled their transcriptome to enhance photosynthesis when supplied with limiting nutrients. Coupling this approach with experiments designed to reveal the mechanisms driving mixotroph physiology provides an avenue toward understanding the ecology of mixotrophy in the natural environment.},
}
@article {pmid35142544,
year = {2022},
author = {Girolamini, L and Salaris, S and Orsini, M and Pascale, MR and Mazzotta, M and Grottola, A and Cristino, S},
title = {Draft Genome Sequence of Legionella Species Isolated from Drinking Water in an Italian Industry.},
journal = {Microbiology resource announcements},
volume = {11},
number = {2},
pages = {e0115221},
pmid = {35142544},
issn = {2576-098X},
abstract = {We report the draft genome sequences of an environmental Legionella strain isolated from an industrial water distribution system in Italy. Macrophage infectivity potentiator (mip) and β-subunit of RNA polymerase (rpoB) genes were used to perform the species identification. Whole-genome sequencing (WGS) and average nucleotide identity (ANI) identified the isolate as belonging to a presumptive novel Legionella species, with a genome length of 3,281,851 bp.},
}
@article {pmid35140699,
year = {2021},
author = {Taketani, RG and Dini-Andreote, F and Beier, S and Fernandez, C},
title = {Editorial: Advancements in the Understanding of Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {820697},
pmid = {35140699},
issn = {1664-302X},
}
@article {pmid35139898,
year = {2022},
author = {Qu, J and Cai, Z and Duan, X and Zhang, H and Cheng, H and Han, S and Yu, K and Jiang, Z and Zhang, Y and Liu, Y and Bai, F and Liu, Y and Liu, L and Yang, L},
title = {Pseudomonas aeruginosa modulates alginate biosynthesis and type VI secretion system in two critically ill COVID-19 patients.},
journal = {Cell &amp; bioscience},
volume = {12},
number = {1},
pages = {14},
pmid = {35139898},
issn = {2045-3701},
support = {2020B1515020003//Guangdong Natural Science Foundation for Distinguished Young Scholar/ ; JCYJ20190809144005609//Science and Technology Program of Shenzhen/ ; 2020A1515010586//Guangdong Basic and Applied Basic Research Foundation/ ; 2020B1111170014//Guangdong Province Science and Technology Project/ ; ZDSYS20200811144002008//Shenzhen Innovation Committee of Science and Technology/ ; KQTD20200909113758004//Shenzhen Science and Technology Program/ ; },
abstract = {BACKGROUND: COVID-19 pneumonia has caused huge impact on the health of infected patients and associated with high morbidity and mortality. Shift in the lung microbial ecology upon such viral infection often worsens the disease and increases host susceptibility to superinfections. Bacterial superinfection contributes to the aggravation of COVID-19 and poses a great challenge to clinical treatments. An in-depth investigation on superinfecting bacteria in COVID-19 patients might facilitate understanding of lung microenvironment post virus infections and superinfection mechanism.<br><br>RESULTS: We analyzed the adaptation of two pairs of P. aeruginosa strains with the same MLST type isolated from two critical COVID-19 patients by combining sequencing analysis and phenotypic assays. Both P. aeruginosa strains were found to turn on alginate biosynthesis and attenuate type VI secretion system (T6SS) during short-term colonization in the COVID-19 patients, which results in excessive biofilm formation and virulence reduction-two distinct markers for chronic infections. The macrophage cytotoxicity test and intracellular reactive oxygen species measurement confirmed that the adapted P. aeruginosa strains reduced their virulence towards host cells and are better to escape from host immune clearance than their ancestors.<br><br>CONCLUSION: Our study suggests that SARS-CoV-2 infection can create a lung environment that allow rapid adaptive evolution of bacterial pathogens with genetic traits suitable for chronic infections.},
}
@article {pmid35138931,
year = {2022},
author = {Bjorndahl, P and Bielawski, JP and Liu, L and Zhou, W and Gu, H},
title = {Novel Application of Survival Models for Predicting Microbial Community Transitions with Variable Selection for Environmental DNA.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {6},
pages = {e0214621},
pmid = {35138931},
issn = {1098-5336},
mesh = {*Cyanobacteria/genetics ; *DNA, Environmental ; Harmful Algal Bloom ; *Microbiota ; Seasons ; },
abstract = {Survival analysis is a prolific statistical tool in medicine for inferring risk and time to disease-related events. However, it is underutilized in microbiome research to predict microbial community-mediated events, partly due to the sparsity and high-dimensional nature of the data. We advance the application of Cox proportional hazards (Cox PH) survival models to environmental DNA (eDNA) data with feature selection suitable for filtering irrelevant and redundant taxonomic variables. Selection methods are compared in terms of false positives, sensitivity, and survival estimation accuracy in simulation and in a real data setting to forecast harmful cyanobacterial blooms. A novel extension of a method for selecting microbial biomarkers with survival data (SuRFCox) reliably outperforms other methods. We determine that Cox PH models with SuRFCox-selected predictors are more robust to varied signal, noise, and data correlation structure. SuRFCox also yields the most accurate and consistent prediction of blooms according to cross-validated testing by year over eight different bloom seasons. Identification of common biomarkers among validated survival forecasts over changing conditions has clear biological significance. Survival models with such biomarkers inform risk assessment and provide insight into the causes of critical community transitions. IMPORTANCE In this paper, we report on a novel approach of selecting microorganisms for model-based prediction of the time to critical microbially modulated events (e.g., harmful algal blooms, clinical outcomes, community shifts, etc.). Our novel method for identifying biomarkers from large, dynamic communities of microbes has broad utility to environmental and ecological impact risk assessment and public health. Results will also promote theoretical and practical advancements relevant to the biology of specific organisms. To address the unique challenge posed by diverse environmental conditions and sparse microbes, we developed a novel method of selecting predictors for modeling time-to-event data. Competing methods for selecting predictors are rigorously compared to determine which is the most accurate and generalizable. Model forecasts are applied to show suitable predictors can precisely quantify the risk over time of biological events like harmful cyanobacterial blooms.},
}
@article {pmid35138927,
year = {2022},
author = {Perry, EK and Newman, DK},
title = {Prevalence and Correlates of Phenazine Resistance in Culturable Bacteria from a Dryland Wheat Field.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {6},
pages = {e0232021},
pmid = {35138927},
issn = {1098-5336},
support = {R01 AI127850/AI/NIAID NIH HHS/United States ; 1R01AI127850-01A1//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Bacteria/metabolism ; *Phenazines/metabolism ; Prevalence ; *Triticum/microbiology ; },
abstract = {Phenazines are a class of bacterially produced redox-active natural antibiotics that have demonstrated potential as a sustainable alternative to traditional pesticides for the biocontrol of fungal crop diseases. However, the prevalence of bacterial resistance to agriculturally relevant phenazines is poorly understood, limiting both the understanding of how these molecules might shape rhizosphere bacterial communities and the ability to perform a risk assessment for off-target effects. Here, we describe profiles of susceptibility to the antifungal agent phenazine-1-carboxylic acid (PCA) across more than 100 bacterial strains isolated from a wheat field where PCA producers are indigenous and abundant. We found that Gram-positive bacteria are typically more sensitive to PCA than Gram-negative bacteria, and there was significant variability in susceptibility both within and across phyla. Phenazine-resistant strains were more likely to be isolated from the wheat rhizosphere, where PCA producers were also more abundant, compared to bulk soil. Furthermore, PCA toxicity was pH-dependent for most susceptible strains and broadly correlated with PCA reduction rates, suggesting that uptake and redox-cycling were important determinants of phenazine toxicity. Our results shed light on which classes of bacteria are most likely to be susceptible to phenazine toxicity in acidic or neutral soils. In addition, the taxonomic and phenotypic diversity of our strain collection represents a valuable resource for future studies on the role of natural antibiotics in shaping wheat rhizosphere communities. IMPORTANCE Microbial communities contribute to crop health in important ways. For example, phenazine metabolites are a class of redox-active molecules made by diverse soil bacteria that underpin the biocontrol of diseases of wheat and other crops. Their physiological functions are nuanced. In some contexts, they are toxic. In others, they are beneficial. While much is known about phenazine production and the effect of phenazines on producing strains, our ability to predict how phenazines might shape the composition of environmental microbial communities is poorly constrained. In addition, phenazine prevalence in the rhizosphere has been predicted to increase in arid soils as the climate changes, providing an impetus for further study. As a step toward gaining a predictive understanding of phenazine-linked microbial ecology, we document the effects of phenazines on diverse bacteria that were coisolated from a wheat rhizosphere and identify conditions and phenotypes that correlate with how a strain will respond to phenazines.},
}
@article {pmid35138381,
year = {2022},
author = {Smakman, F and Hall, AR},
title = {Exposure to lysed bacteria can promote or inhibit growth of neighboring live bacteria depending on local abiotic conditions.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {2},
pages = {},
pmid = {35138381},
issn = {1574-6941},
mesh = {*Bacteria/genetics ; *Escherichia coli ; Nutrients ; },
abstract = {Microbial death is extremely common in nature, yet the ecological role of dead bacteria is unclear. Dead cells are assumed to provide nutrients to surrounding microbes, but may also affect them in other ways. We found that adding lysate prepared from dead bacteria to cultures of Escherichia coli in nutrient-rich conditions suppressed their final population density. This is in stark contrast with the notion that the primary role of dead cells is nutritional, although we also observed this type of effect when we added dead bacteria to cultures that were not supplied with other nutrients. We only observed the growth-suppressive effect of our dead-bacteria treatment after they had undergone significant lysis, suggesting a key role for cellular contents released during lysis. Transcriptomic analysis indicated changes in gene expression in response to dead cells in growing populations, particularly in genes involved in motility. This was supported by experiments with genetic knockouts and copy-number manipulation. Because lysis is commonplace in natural and clinical settings, the growth-suppressive effect of dead cells we describe here may be a widespread and previously unrecognized constraint on bacterial population growth.},
}
@article {pmid35137064,
year = {2022},
author = {Šantl-Temkiv, T and Amato, P and Casamayor, EO and Lee, PKH and Pointing, SB},
title = {Microbial ecology of the atmosphere.},
journal = {FEMS microbiology reviews},
volume = {46},
number = {4},
pages = {},
pmid = {35137064},
issn = {1574-6976},
mesh = {*Atmosphere/chemistry ; Metagenomics ; *Microbiota ; },
abstract = {The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.},
}
@article {pmid35137050,
year = {2022},
author = {Kim, B and Westerhuis, JA and Smilde, AK and Floková, K and Suleiman, AKA and Kuramae, EE and Bouwmeester, HJ and Zancarini, A},
title = {Effect of strigolactones on recruitment of the rice root-associated microbiome.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {2},
pages = {},
pmid = {35137050},
issn = {1574-6941},
mesh = {Lactones/analysis/chemistry/pharmacology ; *Microbiota ; *Mycorrhizae ; *Oryza ; Plant Roots/chemistry ; Rhizosphere ; Symbiosis ; },
abstract = {Strigolactones are endogenous plant hormones regulating plant development and are exuded into the rhizosphere when plants experience nutrient deficiency. There, they promote the mutualistic association of plants with arbuscular mycorrhizal fungi that help the plant with the uptake of nutrients from the soil. This shows that plants actively establish-through the exudation of strigolactones-mutualistic interactions with microbes to overcome inadequate nutrition. The signaling function of strigolactones could possibly extend to other microbial partners, but the effect of strigolactones on the global root and rhizosphere microbiome remains poorly understood. Therefore, we analyzed the bacterial and fungal microbial communities of 16 rice genotypes differing in their root strigolactone exudation. Using multivariate analyses, distinctive differences in the microbiome composition were uncovered depending on strigolactone exudation. Moreover, the results of regression modeling showed that structural differences in the exuded strigolactones affected different sets of microbes. In particular, orobanchol was linked to the relative abundance of Burkholderia-Caballeronia-Paraburkholderia and Acidobacteria that potentially solubilize phosphate, while 4-deoxyorobanchol was associated with the genera Dyella and Umbelopsis. With this research, we provide new insight into the role of strigolactones in the interplay between plants and microbes in the rhizosphere.},
}
@article {pmid35135844,
year = {2022},
author = {Sanz, Y and Olivares, M},
title = {Tiny contributors to severe obesity inside the gut.},
journal = {Gut},
volume = {71},
number = {12},
pages = {2376-2378},
pmid = {35135844},
issn = {1468-3288},
mesh = {Humans ; *Obesity, Morbid/complications ; Prebiotics ; Obesity/complications ; },
}
@article {pmid35134909,
year = {2022},
author = {Foster-Nyarko, E and Pallen, MJ},
title = {The microbial ecology of Escherichia coli in the vertebrate gut.},
journal = {FEMS microbiology reviews},
volume = {46},
number = {3},
pages = {},
pmid = {35134909},
issn = {1574-6976},
mesh = {Animals ; Bacteria ; *Escherichia coli ; *Escherichia coli Infections/microbiology ; Symbiosis ; Vertebrates ; },
abstract = {Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.},
}
@article {pmid35134450,
year = {2022},
author = {Weis, S and Jacksch, S and Welkerling, M and Schmidt, MS and Egert, M},
title = {Do it yourself! - Initial experiences with self-synthesized CsTFA for RNA-SIP analyses.},
journal = {Journal of microbiological methods},
volume = {194},
number = {},
pages = {106432},
doi = {10.1016/j.mimet.2022.106432},
pmid = {35134450},
issn = {1872-8359},
mesh = {Carbon Isotopes/chemistry ; Centrifugation, Density Gradient/methods ; Centrifugation, Isopycnic/methods ; Isotope Labeling/methods ; *Isotopes ; *RNA, Bacterial/genetics ; Trifluoroacetic Acid ; },
abstract = {Cesium trifluoroacetate (CsTFA) is a gradient medium for isopycnic centrifugation in RNA-based Stable Isotope Probing (RNA-SIP), an important means to link the structure and function of microbial communities. We report a protocol to easily synthesize CsTFA from cesium carbonate (Cs2CO3) and trifluoroacetic acid (TFA) and show that self-synthesized CsTFA performs similarly to commercial CsTFA in the separation of isotopically labelled and unlabelled bacterial RNA.},
}
@article {pmid35134272,
year = {2022},
author = {Dar, MA and Xie, R and Pandit, RS and Danso, B and Dong, C and Sun, J},
title = {Exploring the region-wise diversity and functions of symbiotic bacteria in the gut system of wood-feeding termite, Coptotermes formosanus, toward the degradation of cellulose, hemicellulose, and organic dyes.},
journal = {Insect science},
volume = {29},
number = {5},
pages = {1414-1432},
doi = {10.1111/1744-7917.13012},
pmid = {35134272},
issn = {1744-7917},
mesh = {Animals ; Bacteria ; Cellulose/metabolism ; Coloring Agents/metabolism ; *Isoptera/microbiology ; Polysaccharides ; Symbiosis ; Wood/metabolism ; Xylans/metabolism ; },
abstract = {The wood-feeding termite Coptotermes formosanus represents a unique and impressive system for lignocellulose degradation. The highly efficient digestion of lignocellulose is achieved through symbiosis with gut symbionts like bacteria. Despite extensive research during the last three decades, diversity of bacterial symbionts residing in individual gut regions of the termite and their associated functions is still lacking. To this end, cellulose, xylan, and dye-decolorization bacteria residing in foregut, midgut, and hindgut regions of C. formosanus were enlisted by using enrichment and culture-dependent molecular methods. A total of 87 bacterial strains were successfully isolated from different gut regions of C. formosanus which belonged to 27 different species of 10 genera, majorly affiliated with Proteobacteria (80%) and Firmicutes (18.3%). Among the gut regions, 37.9% of the total bacterial isolates were observed in the hindgut that demonstrated predominance of cellulolytic bacteria (47.6%). The majority of the xylanolytic and dye-decolorization bacteria (50%) were obtained from the foregut and midgut, respectively. Actinobacteria represented by Dietza sp. was observed in the hindgut only. Based on species richness, the highest diversity was observed in midgut and hindgut regions each of which harbored seven unique bacterial species. The members of Enterobacter, Klebsiella, and Pseudomonas were common among the gut regions. The lignocellulolytic activities of the selected potential bacteria signpost their assistance to the host for lignocellulose digestion. The overall results indicate that C. formosanus harbors diverse communities of lignocellulolytic bacteria in different regions of the gut system. These observations will significantly advance our understanding of the termite-bacteria symbiosis and their microbial ecology uniquely existed in different gut regions of C. formosanus, which may further shed a light on its potential values at termite-modeled biotechnology.},
}
@article {pmid35133186,
year = {2022},
author = {Pan, H and Gao, H and Peng, Z and Chen, B and Chen, S and Liu, Y and Gu, J and Wei, X and Chen, W and Wei, G and Jiao, S},
title = {Aridity Threshold Induces Abrupt Change of Soil Abundant and Rare Bacterial Biogeography in Dryland Ecosystems.},
journal = {mSystems},
volume = {7},
number = {1},
pages = {e0130921},
pmid = {35133186},
issn = {2379-5077},
mesh = {*Soil ; Phylogeny ; Soil Microbiology ; Bacteria ; *Microbiota ; },
abstract = {Aridity, which is increasing worldwide due to climate change, affects the biodiversity and functions of dryland ecosystems. Whether aridification leads to gradual (or abrupt) and systemic (or specific) changes in the biogeography of abundant and rare microbial species is largely unknown. Here, we investigated stress-adaptive changes (aridity-driven, ranging from 0.65 to 0.94) and biogeographic patterns of abundant and rare bacterial communities in different habitats, including agricultural field, forest, wetland, grassland, and desert, in desert oasis transition zones in northern China. We observed abrupt changes at the breakpoint of aridity values (0.92), characterized by diversity (α-diversity and β-diversity), species coexistence, community assembly processes, and phylogenetic niche conservatism. Specifically, when aridity was <0.92, increasing aridity led to more deterministic assembly and species coexistences for the abundant subcommunity, whereas the reverse was observed for the rare subcommunity. The phylogenetic niche conservatism for both subcommunities increased slowly with aridity. When aridity was >0.92, the systemic responses of abundant and rare taxa changed dramatically in a consistent direction, such that both subcommunities rapidly tended to have a more deterministic assembly, species coexistence, and stronger phylogenetic niche conservatism with increasing aridity. In addition, the change rates of abundant taxa were higher than those of rare taxa, indicating the more sensitive responses of abundant taxa along aridity variation. This finding has important implications for understanding the impact of aridity on the structure and function of abundant and rare soil taxa and how diversity maintenance is associated with soil microbiota responding to global change. The abrupt threshold of soil bacteria found can be used for buffering and for building effective adaptation and mitigation measures aimed at maintaining the capacity of drylands for basic ecosystem functioning. IMPORTANCE Aridity, which is increasing worldwide due to climate change, affects the biodiversity and functions of dryland ecosystems. We provided the first statistical evidence for abrupt changes of species coexistence, ecological processes, and niche conservation of abundant and rare soil bacteria triggered by diversity to abrupt increases in aridity. The abrupt threshold of soil bacterial community response to aridity is spatially heterogeneous at the local scale and should be specified according to local conditions for buffering and for building effective adaptation and mitigation measures aimed at maintaining the capacity of drylands for basic ecosystem functioning.},
}
@article {pmid35131944,
year = {2022},
author = {Drautz-Moses, DI and Luhung, I and Gusareva, ES and Kee, C and Gaultier, NE and Premkrishnan, BNV and Lee, CF and Leong, ST and Park, C and Yap, ZH and Heinle, CE and Lau, KJX and Purbojati, RW and Lim, SBY and Lim, YH and Kutmutia, SK and Aung, NW and Oliveira, EL and Ng, SG and Dacanay, J and Ang, PN and Spence, S and Phung, WJ and Wong, A and Kennedy, RJ and Kalsi, N and Sasi, SP and Chandrasekaran, L and Uchida, A and Junqueira, ACM and Kim, HL and Hankers, R and Feuerle, T and Corsmeier, U and Schuster, SC},
title = {Vertical stratification of the air microbiome in the lower troposphere.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {7},
pages = {},
pmid = {35131944},
issn = {1091-6490},
mesh = {Aerosols ; *Air Microbiology ; Altitude ; Atmosphere ; Bacteria/*classification/*isolation &amp; purification ; Humans ; },
abstract = {The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising a meteorological tower and a research aircraft, we conducted synchronized measurements of meteorological parameters and airborne biomass (n = 480) in the vertical air column up to 3,500 m. The taxonomic analysis of metagenomic data revealed differing patterns of airborne microbial community composition with respect to time of day and height above ground. The temporal and spatial resolution of our study demonstrated that the diel cycle of airborne microorganisms is a ground-based phenomenon that is entirely absent at heights >1,000 m. In an integrated analysis combining meteorological and biological data, we demonstrate that atmospheric turbulence, identified by potential temperature and high-frequency three-component wind measurements, is the key driver of bioaerosol dynamics in the lower troposphere. Multivariate regression analysis shows that at least 50% of identified airborne microbial taxa (n = ∼10,000) are associated with either ground or height, allowing for an understanding of dispersal patterns of microbial taxa in the vertical air column. Due to the interconnectedness of atmospheric turbulence and temperature, the dynamics of microbial dispersal are likely to be impacted by rising global temperatures, thereby also affecting ecosystems on the planetary surface.},
}
@article {pmid35131464,
year = {2022},
author = {Blansaer, N and Alloul, A and Verstraete, W and Vlaeminck, SE and Smets, BF},
title = {Aggregation of purple bacteria in an upflow photobioreactor to facilitate solid/liquid separation: Impact of organic loading rate, hydraulic retention time and water composition.},
journal = {Bioresource technology},
volume = {348},
number = {},
pages = {126806},
doi = {10.1016/j.biortech.2022.126806},
pmid = {35131464},
issn = {1873-2976},
mesh = {Biological Oxygen Demand Analysis ; Bioreactors ; *Photobioreactors/microbiology ; *Proteobacteria ; Sewage/chemistry ; Waste Disposal, Fluid/methods ; Wastewater/chemistry ; Water ; },
abstract = {Purple non-sulfur bacteria (PNSB) form an interesting group of microbes for resource recovery from wastewater. Solid/liquid separation is key for biomass and value-added products recovery, yet insights into PNSB aggregation are thus far limited. This study explored the effects of organic loading rate (OLR), hydraulic retention time (HRT) and water composition on the aggregation of Rhodobacter capsulatus in an anaerobic upflow photobioreactor. Between 2.0 and 14.6 gCOD/(L.d), the optimal OLR for aggregation was 6.1 gCOD/(L.d), resulting in a sedimentation flux of 5.9 kgTSS/(m[2].h). With HRT tested between 0.04 and 1.00 d, disaggregation occurred at the relatively long HRT (1 d), possibly due to accumulation of thus far unidentified heat-labile metabolites. Chemical oxygen demand (COD) to nitrogen ratios (6-35 gCOD/gN) and the nitrogen source (ammonium vs. glutamate) also impacted aggregation, highlighting the importance of the type of wastewater and its pre-treatment. These novel insights to improve purple biomass separation pave the way for cost-efficient PNSB applications.},
}
@article {pmid35130833,
year = {2022},
author = {Baruzzo, G and Patuzzi, I and Di Camillo, B},
title = {Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results.},
journal = {BMC bioinformatics},
volume = {22},
number = {Suppl 15},
pages = {618},
pmid = {35130833},
issn = {1471-2105},
support = {PROACTIVE 2017 - C92F17003530005//Department of Information Engineering, University of Padova/ ; },
mesh = {*Bacteria/genetics ; *Data Analysis ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: 16S rRNA-gene sequencing is a valuable approach to characterize the taxonomic content of the whole bacterial population inhabiting a metabolic and spatial niche, providing an important opportunity to study bacteria and their role in many health and environmental mechanisms. The analysis of data produced by amplicon sequencing, however, brings very specific methodological issues that need to be properly addressed to obtain reliable biological conclusions. Among these, 16S count data tend to be very sparse, with many null values reflecting species that are present but got unobserved due to the multiplexing constraints. However, current data workflows do not consider a step in which the information about unobserved species is recovered.<br><br>RESULTS: In this work, we evaluate for the first time the effects of introducing in the 16S data workflow a new preprocessing step, zero-imputation, to recover this lost information. Due to the lack of published zero-imputation methods specifically designed for 16S count data, we considered a set of zero-imputation strategies available for other frameworks, and benchmarked them using in silico 16S count data reflecting different experimental designs. Additionally, we assessed the effect of combining zero-imputation and normalization, i.e. the only preprocessing step in current 16S workflow. Overall, we benchmarked 35 16S preprocessing pipelines assessing their ability to handle data sparsity, identify species presence/absence, recovery sample proportional abundance distributions, and improve typical downstream analyses such as computation of alpha and beta diversity indices and differential abundance analysis.<br><br>CONCLUSIONS: The results clearly show that 16S data analysis greatly benefits from a properly-performed zero-imputation step, despite the choice of the right zero-imputation method having a pivotal role. In addition, we identify a set of best-performing pipelines that could be a valuable indication for data analysts.},
}
@article {pmid35130830,
year = {2022},
author = {Dreier, M and Meola, M and Berthoud, H and Shani, N and Wechsler, D and Junier, P},
title = {High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota.},
journal = {BMC microbiology},
volume = {22},
number = {1},
pages = {48},
pmid = {35130830},
issn = {1471-2180},
mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Cheese/*microbiology ; Computational Biology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; High-Throughput Screening Assays/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Next-generation sequencing (NGS) methods and especially 16S rRNA gene amplicon sequencing have become indispensable tools in microbial ecology. While they have opened up new possibilities for studying microbial communities, they also have one drawback, namely providing only relative abundances and thus compositional data. Quantitative PCR (qPCR) has been used for years for the quantification of bacteria. However, this method requires the development of specific primers and has a low throughput. The constraint of low throughput has recently been overcome by the development of high-throughput qPCR (HT-qPCR), which allows for the simultaneous detection of the most prevalent bacteria in moderately complex systems, such as cheese and other fermented dairy foods. In the present study, the performance of the two approaches, NGS and HT-qPCR, was compared by analyzing the same DNA samples from 21 Raclette du Valais protected designation of origin (PDO) cheeses. Based on the results obtained, the differences, accuracy, and usefulness of the two approaches were studied in detail.<br><br>RESULTS: The results obtained using NGS (non-targeted) and HT-qPCR (targeted) show considerable agreement in determining the microbial composition of the cheese DNA samples studied, albeit the fundamentally different nature of these two approaches. A few inconsistencies in species detection were observed, particularly for less abundant ones. The detailed comparison of the results for 15 bacterial species/groups measured by both methods revealed a considerable bias for certain bacterial species in the measurements of the amplicon sequencing approach. We identified as probable origin to this PCR bias due to primer mismatches, variations in the number of copies for the 16S rRNA gene, and bias introduced in the bioinformatics analysis.<br><br>CONCLUSION: As the normalized microbial composition results of NGS and HT-qPCR agreed for most of the 21 cheese samples analyzed, both methods can be considered as complementary and reliable for studying the microbial composition of cheese. Their combined application proved to be very helpful in identifying potential biases and overcoming methodological limitations in the quantitative analysis of the cheese microbiota.},
}
@article {pmid35129649,
year = {2023},
author = {Doane, MP and Johnson, CJ and Johri, S and Kerr, EN and Morris, MM and Desantiago, R and Turnlund, AC and Goodman, A and Mora, M and Lima, LFO and Nosal, AP and Dinsdale, EA},
title = {The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {747-764},
pmid = {35129649},
issn = {1432-184X},
support = {1330800//National Science Foundation/ ; 1323809//National Science Foundation/ ; },
mesh = {Animals ; *Sharks ; Epidermis ; *Microbiota ; },
abstract = {The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray-Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray-Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.},
}
@article {pmid35128002,
year = {2022},
author = {Costa, DPD and Araujo, ASF and Pereira, APA and Mendes, LW and França, RFD and Silva, TDGED and Oliveira, JB and Araujo, JS and Duda, GP and Menezes, RSC and Medeiros, EV},
title = {Dataset for effects of the transition from dry forest to pasture on diversity and structure of bacterial communities in Northeastern Brazil.},
journal = {Data in brief},
volume = {41},
number = {},
pages = {107842},
pmid = {35128002},
issn = {2352-3409},
abstract = {The data included in this article supplement the research article titled "Forest-to-pasture conversion modifies the soil bacterial community in Brazilian dry forest Caatinga (manuscript ID: STOTEN-D-21-19067R1)". This data article included the analysis of 18 chemical variables in 36 composite samples (included 4 replicates) of soils from the Microregion of Garanhuns (Northeast Brazil) and also partial 16S rRNA gene sequences from genomic DNA extracted from 27 of these samples (included 3 best quality replicates) for paired-end sequencing (up to 2 × 300 bp) in Illumina MiSeq platform (NCBI - BioProject accession: PRJNA753707). Soils were collected in August 2018 in a tropical subhumid region from the Brazilian Caatinga, along with 27 composite samples from the aboveground part of pastures to determine nutritional quality based on leaf N content. The analysis of variance (ANOVA) and post-hoc tests of environmental data and the main alpha-diversity indices based on linear mixed models (LMM) were represented in the tables. In this case, the collection region (C1 - Brejão, C2 - Garanhuns, and C3 - São João) was the random-effect variable and adjacent habitats formed by a forest (FO) and two pastures (PA and PB succeeded by this forest) composed the fixed-effect variable (land cover), both nested within C. In addition, a table with similarity percentages breakdown (SIMPER) was also shown, a procedure to assess the average percent contribution of individual phyla and bacterial classes. The figures showed the details of the study location, sampling procedure, vegetation status through the Normalized Difference Vegetation Index (NDVI), in addition to the general abundance and composition of the main bacterial phyla.},
}
@article {pmid35126404,
year = {2021},
author = {Li, H and Wang, N and Ding, J and Liu, Y and Ding, X and Wei, Y and Li, J and Ding, GC},
title = {Spatial Distribution of the Pepper Blight (Phytophthora capsici) Suppressive Microbiome in the Rhizosphere.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {748542},
pmid = {35126404},
issn = {1664-462X},
abstract = {The properties of plant rhizosphere are dynamic and heterogeneous, serving as different habitat filters for or against certain microorganisms. Herein, we studied the spatial distribution of bacterial communities in the rhizosphere of pepper plants treated with a disease-suppressive or non-suppressive soil. The bacterial richness was significantly (p < 0.05) higher in plants treated with the disease-suppressive soil than in those treated with the non-suppressive soil. Bacterial richness and evenness greatly differed between root parts, with decrease from the upper taproot to the upper fibrous root, the lower taproot, and the lower fibrous root. As expected, the bacterial community in the rhizosphere differed between suppressive and non-suppressive soil. However, the spatial variation (36%) of the bacterial community in the rhizosphere was much greater than that explained by soils (10%). Taxa such as subgroups of Acidobacteria, Nitrosospira, and Nitrospira were known to be selectively enriched in the upper taproot. In vitro Bacillus antagonists against Phytophthora capsici were also preferentially colonized in the taproot, while the genera such as Clostridium, Rhizobium, Azotobacter, Hydrogenophaga, and Magnetospirillum were enriched in the lower taproot or fibrous root. In conclusion, the spatial distribution of bacterial taxa and antagonists in the rhizosphere of pepper sheds light on our understanding of microbial ecology in the rhizosphere.},
}
@article {pmid35125827,
year = {2022},
author = {Hillestad, EMR and van der Meeren, A and Nagaraja, BH and Bjørsvik, BR and Haleem, N and Benitez-Paez, A and Sanz, Y and Hausken, T and Lied, GA and Lundervold, A and Berentsen, B},
title = {Gut bless you: The microbiota-gut-brain axis in irritable bowel syndrome.},
journal = {World journal of gastroenterology},
volume = {28},
number = {4},
pages = {412-431},
pmid = {35125827},
issn = {2219-2840},
mesh = {Brain-Gut Axis ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; *Irritable Bowel Syndrome/therapy ; *Microbiota ; },
abstract = {Irritable bowel syndrome (IBS) is a common clinical label for medically unexplained gastrointestinal symptoms, recently described as a disturbance of the microbiota-gut-brain axis. Despite decades of research, the pathophysiology of this highly heterogeneous disorder remains elusive. However, a dramatic change in the understanding of the underlying pathophysiological mechanisms surfaced when the importance of gut microbiota protruded the scientific picture. Are we getting any closer to understanding IBS' etiology, or are we drowning in unspecific, conflicting data because we possess limited tools to unravel the cluster of secrets our gut microbiota is concealing? In this comprehensive review we are discussing some of the major important features of IBS and their interaction with gut microbiota, clinical microbiota-altering treatment such as the low FODMAP diet and fecal microbiota transplantation, neuroimaging and methods in microbiota analyses, and current and future challenges with big data analysis in IBS.},
}
@article {pmid35124727,
year = {2023},
author = {Tanunchai, B and Ji, L and Schroeter, SA and Wahdan, SFM and Hossen, S and Delelegn, Y and Buscot, F and Lehnert, AS and Alves, EG and Hilke, I and Gleixner, G and Schulze, ED and Noll, M and Purahong, W},
title = {FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {411-428},
pmid = {35124727},
issn = {1432-184X},
mesh = {*Trees/microbiology ; Fungi ; *Mycobiome ; Plant Leaves/microbiology ; },
abstract = {Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and Fun[Fun] databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.},
}
@article {pmid35118509,
year = {2023},
author = {Zhou, J and Kong, Y and Wu, M and Shu, F and Wang, H and Ma, S and Li, Y and Jeppesen, E},
title = {Effects of Nitrogen Input on Community Structure of the Denitrifying Bacteria with Nitrous Oxide Reductase Gene (nosZ I): a Long-Term Pond Experiment.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {454-464},
pmid = {35118509},
issn = {1432-184X},
mesh = {*Ponds ; *Ecosystem ; Nitrogen ; Denitrification ; Bacteria/genetics ; Nitrous Oxide ; Soil Microbiology ; },
abstract = {Excessive nitrogen (N) input is an important factor influencing aquatic ecosystems and has received increasing public attention in the past decades. It remains unclear how N input affects the denitrifying bacterial communities that play a key role in regulating N cycles in various ecosystems. To test our hypothesis-that the abundance and biodiversity of denitrifying bacterial communities decrease with increasing N-we compared the abundance and composition of denitrifying bacteria having nitrous oxide reductase gene (nosZ I) from sediments (0-20 cm) in five experimental ponds with different nitrogen fertilization treatment (TN10, TN20, TN30, TN40, TN50) using quantitative PCR and pyrosequencing techniques. We found that (1) N addition significantly decreased nosZ I gene abundance, (2) the Invsimpson and Shannon indices (reflecting biodiversity) first increased significantly along with the increasing N loading in TN10-TN40 followed by a decrease in TN50, (3) the beta diversity of the nosZ I denitrifier was clustered into three groups along the TN concentration levels: Cluster I (TN50), Cluster II (TN40), and Cluster III (TN10-TN30), (4) the proportions of Alphaproteobacteria and Betaproteobacteria in the high-N treatment (TN50) were significantly lower than in the lower N treatments (TN10-TN30). (5) The TN concentration was the most important factor driving the alteration of denitrifying bacteria assemblages. Our findings shed new light on the response of denitrification-related bacteria to long-term N loading at pond scale and on the response of denitrifying microorganisms to N pollution.},
}
@article {pmid35114951,
year = {2022},
author = {Bi, S and Lai, H and Guo, D and Liu, X and Wang, G and Chen, X and Liu, S and Yi, H and Su, Y and Li, G},
title = {Spatio-temporal variation of bacterioplankton community structure in the Pearl River: impacts of artificial fishery habitat and physicochemical factors.},
journal = {BMC ecology and evolution},
volume = {22},
number = {1},
pages = {10},
pmid = {35114951},
issn = {2730-7182},
mesh = {Aquatic Organisms ; *Cyanobacteria/genetics ; Ecosystem ; Fisheries ; Follow-Up Studies ; RNA, Ribosomal, 16S/genetics ; *Rivers/chemistry ; Water ; },
abstract = {BACKGROUND: Artificial fishery habitat has been widely used in fishery resource protection and water habitat restoration. Although the bacterioplankton plays an important ecological role in fisheries ecosystems, the effect of artificial fishery habitat on bacterioplankton is not clear. In this study, high-throughput sequencing based on the 16S rRNA gene was carried out to study the characteristics of bacterioplankton community structure in artificial fishery habitat and to determine the principal environmental factors that shaped the composition, structure and function of bacterioplankton communities in an unfed aquaculture system.<br><br>RESULTS: The results indicated that the most dominant phyla were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria), Actinobacteria, Cyanobacteria, and Bacteroidetes, which accounted for 28.61%, 28.37%, 19.79%, and 10.25% of the total abundance, respectively. The factors that cause the differences in bacterioplankton community were mainly manifested in three aspects, including the diversity of the community, the role of artificial fishery habitat, and the change of environmental factors. The alpha diversity analysis showed that the diversity and richness index of the bacterioplankton communities were the highest in summer, which indicated that the seasonal variation characteristics had a great influence on it. The CCA analysis identified that the dissolved oxygen, temperature, and ammonium salt were the dominant environmental factors in an unfed aquaculture system. The LEfSe analysis founded 37 indicator species in artificial structure areas (AS group), only 9 kinds existing in the control areas of the open-water group (CW group). Meanwhile, the KEGG function prediction analysis showed that the genes which were related to metabolism in group AS were significantly enhanced.<br><br>CONCLUSIONS: This study can provide reference value for the effect of artificial habitat on bacterioplankton community and provide fundamental information for the follow-up study of ecological benefits of artificial fishery habitat. It may be contributed to apply artificial fishery habitat in more rivers.},
}
@article {pmid35114015,
year = {2022},
author = {Angulo, V and Beriot, N and Garcia-Hernandez, E and Li, E and Masteling, R and Lau, JA},
title = {Plant-microbe eco-evolutionary dynamics in a changing world.},
journal = {The New phytologist},
volume = {234},
number = {6},
pages = {1919-1928},
doi = {10.1111/nph.18015},
pmid = {35114015},
issn = {1469-8137},
mesh = {*Biological Evolution ; *Microbiota ; Plants ; },
abstract = {Both plants and their associated microbiomes can respond strongly to anthropogenic environmental changes. These responses can be both ecological (e.g. a global change affecting plant demography or microbial community composition) and evolutionary (e.g. a global change altering natural selection on plant or microbial populations). As a result, global changes can catalyse eco-evolutionary feedbacks. Here, we take a plant-focused perspective to discuss how microbes mediate plant ecological responses to global change and how these ecological effects can influence plant evolutionary response to global change. We argue that the strong and functionally important relationships between plants and their associated microbes are particularly likely to result in eco-evolutionary feedbacks when perturbed by global changes and discuss how improved understanding of plant-microbe eco-evolutionary dynamics could inform conservation or even agriculture.},
}
@article {pmid35113183,
year = {2023},
author = {Dong, X and Lan, H and Huang, L and Zhang, H and Lin, X and Weng, S and Peng, Y and Lin, J and Wang, JH and Peng, J and Yang, Y},
title = {Metagenomic Views of Microbial Communities in Sand Sediments Associated with Coral Reefs.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {465-477},
pmid = {35113183},
issn = {1432-184X},
mesh = {Animals ; Coral Reefs ; Ecosystem ; Sand ; Metagenomics ; Bacteria/genetics ; *Microbiota ; Proteobacteria ; *Anthozoa/microbiology ; },
abstract = {Reef sediments, the home for microbes with high abundances, provide an important source of carbonates and nutrients for the growth and maintenance of coral reefs. However, there is a lack of systematic research on the composition of microbial community in sediments of different geographic sites and their potential effect on nutrient recycling and health of the coral reef ecosystem. In combination of biogeochemical measurements with gene- and genome-centric metagenomics, we assessed microbial community compositions and functional diversity, as well as profiles of antibiotic resistance genes in surface sediments of 16 coral reef sites at different depths from the Xisha islands in the South China Sea. Reef sediment microbiomes are diverse and novel at lower taxonomic ranks, dominated by Proteobacteria and Planctomycetota. Most reef sediment bacteria potentially participate in biogeochemical cycling via oxidizing various organic and inorganic compounds as energy sources. High abundances of Proteobacteria (mostly Rhizobiales and Woeseiales) are metabolically flexible and contain rhodopsin genes. Various classes of antibiotic resistance genes, hosted by diverse bacterial lineages, were identified to confer resistance to multidrug, aminoglycoside, and other antibiotics. Overall, our findings expanded the understanding of reef sediment microbial ecology and provided insights for their link to the coral reef ecosystem health.},
}
@article {pmid35112152,
year = {2023},
author = {LeBlanc, N},
title = {Green Manures Alter Taxonomic and Functional Characteristics of Soil Bacterial Communities.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {684-697},
pmid = {35112152},
issn = {1432-184X},
support = {2038-22000-016-000-D//USDA-ARS/ ; 2038-22430-003-000-D//USDA-ARS/ ; },
mesh = {*Soil ; Manure ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria ; Plants ; Soil Microbiology ; },
abstract = {Incorporation of plant biomass into soil as green manures can reduce soilborne diseases and improve crop and soil health in agricultural ecosystems. Soil microbial communities can mediate beneficial effects of these amendments, but their response to different types of green manures is poorly understood. This study tested the effect of green manures from broccoli, marigold, and sudangrass on taxonomic and functional characteristics of soil bacterial communities. Green manures were amended to field soil and maintained in microcosms artificially infested with the soilborne plant pathogen Verticillium dahliae. Lettuce seedlings were transplanted into green manure amended and fallow soil and maintained under growth chamber conditions for 12 weeks. Bacterial communities in bulk and rhizosphere soils were characterized using nanopore sequencing of 16S rRNA and shotgun metagenome libraries. Under microcosm conditions, all green manures reduced the abundance of the soilborne plant pathogen V. dahliae and altered the taxonomic composition of bacterial communities. Twelve weeks following amendment, green manures had differential effects on lettuce yield as well as the taxonomic diversity and composition of soil bacterial communities. In addition, multiple green manures increased the abundance of bacterial functional traits in rhizosphere soil related to iron and polysaccharide acquisition and decreased the abundance of functional traits related to bacterial protein secretion systems. This study demonstrates green manures alter the taxonomic composition and functional traits in soil bacterial communities suggesting these changes may impact beneficial effects of green manures on plant and soil health.},
}
@article {pmid35112151,
year = {2023},
author = {Mishra, A and Singh, L and Singh, D},
title = {Unboxing the black box-one step forward to understand the soil microbiome: A systematic review.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {669-683},
pmid = {35112151},
issn = {1432-184X},
mesh = {*Ecosystem ; Soil/chemistry ; Soil Microbiology ; Biodiversity ; *Microbiota ; Climate Change ; },
abstract = {Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.},
}
@article {pmid35108090,
year = {2022},
author = {Choi, O and Cho, J and Kang, B and Lee, Y and Kim, J},
title = {Negatively Regulated Aerobactin and Desferrioxamine E by Fur in Pantoea ananatis Are Required for Full Siderophore Production and Antibacterial Activity, but Not for Virulence.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {6},
pages = {e0240521},
pmid = {35108090},
issn = {1098-5336},
mesh = {Anti-Bacterial Agents/metabolism/pharmacology ; Humans ; Hydroxamic Acids ; Lactams ; *Pantoea/genetics/metabolism ; *Siderophores/metabolism ; Virulence ; },
abstract = {Pantoea ananatis is an emerging plant pathogen that causes disease in economically important crops such as rice, corn, onion, melon, and pineapple, and it also infects humans and insects. In this study, we identified biosynthetic gene clusters of aerobactin and desferrioxamine E (DFO-E) siderophores by using the complete genome of P. ananatis PA13 isolated from rice sheath rot. P. ananatis PA13 exhibited the strongest antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (Enterobacterales). Mutants of aerobactin or DFO-E maintained antibacterial activity against E. amylovora and Y. enterocolitica, as well as in a siderophore activity assay. However, double aerobactin and DFO-E gene deletion mutants completely lost siderophore and antibacterial activity. These results reveal that both siderophore biosynthetic gene clusters are essential for siderophore production and antibacterial activity in P. ananatis PA13. A ferric uptake regulator protein (Fur) mutant exhibited a significant increase in siderophore production, and a Fur-overexpressing strain completely lost antibacterial activity. Expression of the iucA, dfoJ, and foxA genes was significantly increased in the Δfur mutant background, and expression of these genes returned to wild-type levels after fur compensation. These results indicate that Fur negatively regulates aerobactin and DFO-E siderophores. However, siderophore production was not required for P. ananatis virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment. This study is the first to report the regulation and functional characteristics of siderophore biosynthetic genes in P. ananatis. IMPORTANCE Pantoea ananatis is a bacterium that causes diseases in several economically important crops, as well as in insects and humans. This bacterium has been studied extensively as a potentially dangerous pathogen due to its saprophytic ability. Recently, the types, biosynthetic gene clusters, and origin of the siderophores in the Pantoea genus were determined by using genome comparative analyses. However, few genetic studies have investigated the characteristics and functions of siderophores in P. ananatis. The results of this study revealed that the production of aerobactin and desferrioxamine E in the rice pathogen P. ananatis PA13 is negatively regulated by Fur and that these siderophores are essential for antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (Enterobacterales). However, siderophore production was not required for P. ananatis virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment.},
}
@article {pmid35107341,
year = {2022},
author = {Sovacool, KL and Westcott, SL and Mumphrey, MB and Dotson, GA and Schloss, PD},
title = {OptiFit: an Improved Method for Fitting Amplicon Sequences to Existing OTUs.},
journal = {mSphere},
volume = {7},
number = {1},
pages = {e0091621},
pmid = {35107341},
issn = {2379-5042},
support = {R01 CA215574/CA/NCI NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; T32 GM070449/GM/NIGMS NIH HHS/United States ; T32 CA140044/CA/NCI NIH HHS/United States ; },
mesh = {Cluster Analysis ; *Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Assigning amplicon sequences to operational taxonomic units (OTUs) is an important step in characterizing microbial communities across large data sets. A notable difference between de novo clustering and database-dependent reference clustering methods is that OTU assignments from de novo methods may change when new sequences are added. However, one may wish to incorporate new samples to previously clustered data sets without clustering all sequences again, such as when comparing across data sets or deploying machine learning models. Existing reference-based methods produce consistent OTUs but only consider the similarity of each query sequence to a single reference sequence in an OTU, resulting in assignments that are worse than those generated by de novo methods. To provide an efficient method to fit sequences to existing OTUs, we developed the OptiFit algorithm. Inspired by the de novo OptiClust algorithm, OptiFit considers the similarity of all pairs of reference and query sequences to produce OTUs of the best possible quality. We tested OptiFit using four data sets with two strategies: (i) clustering to a reference database and (ii) splitting the data set into a reference and query set, clustering the references using OptiClust, and then clustering the queries to the references. The result is an improved implementation of reference-based clustering. OptiFit produces OTUs of a quality similar to that of OptiClust at faster speeds when using the split data set strategy. OptiFit provides a suitable option for users requiring consistent OTU assignments at the same quality as afforded by de novo clustering methods. IMPORTANCE Advancements in DNA sequencing technology have allowed researchers to affordably generate millions of sequence reads from microorganisms in diverse environments. Efficient and robust software tools are needed to assign microbial sequences into taxonomic groups for characterization and comparison of communities. The OptiClust algorithm produces high-quality groups by comparing sequences to each other, but the assignments can change when new sequences are added to a data set, making it difficult to compare different studies. Other approaches assign sequences to groups by comparing them to sequences in a reference database to produce consistent assignments, but the quality of the groups produced is reduced compared to that with OptiClust. We developed OptiFit, a new reference-based algorithm that produces consistent yet high-quality assignments like OptiClust. OptiFit allows researchers to compare microbial communities across different studies or add new data to existing studies without sacrificing the quality of the group assignments.},
}
@article {pmid35107340,
year = {2022},
author = {Baumann, KBL and Thoma, R and Callbeck, CM and Niederdorfer, R and Schubert, CJ and Müller, B and Lever, MA and Bürgmann, H},
title = {Microbial Nitrogen Transformation Potential in Sediments of Two Contrasting Lakes Is Spatially Structured but Seasonally Stable.},
journal = {mSphere},
volume = {7},
number = {1},
pages = {e0101321},
pmid = {35107340},
issn = {2379-5042},
mesh = {Eutrophication ; *Lakes/microbiology ; *Microbiota ; Nitrates/analysis ; Nitrogen ; },
abstract = {The nitrogen (N) cycle is of global importance, as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbially mediated processes, few studies have investigated the microbial communities involved. In an integrated biogeochemical and microbiological study on a eutrophic and oligotrophic lake, we estimated N removal rates from pore water concentration gradients in sediments. Simultaneously, the abundance of different microbial N transformation genes was investigated using metagenomics on a seasonal and spatial scale. We observed that contrasting nutrient concentrations in sediments were associated with distinct microbial community compositions and significant differences in abundances of various N transformation genes. For both characteristics, we observed a more pronounced spatial than seasonal variability within each lake. The eutrophic Lake Baldegg showed a higher denitrification potential with higher nosZ gene (N2O reductase) abundances and higher nirS:nirK (nitrite reductase) ratios, indicating a greater capacity for complete denitrification. Correspondingly, this lake had a higher N removal efficiency. The oligotrophic Lake Sarnen, in contrast, had a higher potential for nitrification. Specifically, it harbored a high abundance of Nitrospira, including some with the potential for comammox. Our results demonstrate that knowledge of the genomic N transformation potential is important for interpreting N process rates and understanding how the lacustrine sedimentary N cycle responds to variations in trophic conditions. IMPORTANCE Anthropogenic nitrogen (N) inputs can lead to eutrophication in surface waters, especially in N-limited coastal ecosystems. Lakes effectively remove reactive N by transforming it to N2 through microbial denitrification or anammox. The rates and distributions of these microbial processes are affected by factors such as the amount and quality of settling organic material and nitrate concentrations. However, the microbial communities mediating these N transformation processes in freshwater lake sediments remain largely unknown. We provide the first seasonally and spatially resolved metagenomic analysis of the N cycle in sediments of two lakes with different trophic states. We show that lakes with different trophic states select for distinct communities of N-cycling microorganisms with contrasting functional potentials for N transformation.},
}
@article {pmid35106901,
year = {2022},
author = {Herms, CH and Hennessy, RC and Bak, F and Dresbøll, DB and Nicolaisen, MH},
title = {Back to our roots: exploring the role of root morphology as a mediator of beneficial plant-microbe interactions.},
journal = {Environmental microbiology},
volume = {24},
number = {8},
pages = {3264-3272},
pmid = {35106901},
issn = {1462-2920},
mesh = {*Microbiota ; Plant Roots/microbiology ; Plants/microbiology ; Rhizosphere ; *Soil Microbiology ; },
abstract = {Plant breeding for belowground traits that have a positive impact on the rhizosphere microbiome is a promising strategy to sustainably improve crop yields. Root architecture and morphology are understudied plant breeding targets despite their potential to significantly shape microbial community structure and function in the rhizosphere. In this review, we explore the relationship between various root architectural and morphological traits and rhizosphere interactions, focusing on the potential of root diameter to impact the rhizosphere microbiome structure and function while discussing the potential biological and ecological mechanisms underpinning this process. In addition, we propose three future research avenues to drive this research area in an effort to unravel the effect of belowground traits on rhizosphere microbiology. This knowledge will pave the way for new plant breeding strategies that can be exploited for sustainable and high-yielding crop cultivars.},
}
@article {pmid35106579,
year = {2022},
author = {Weinroth, MD and Belk, AD and Dean, C and Noyes, N and Dittoe, DK and Rothrock, MJ and Ricke, SC and Myer, PR and Henniger, MT and Ramírez, GA and Oakley, BB and Summers, KL and Miles, AM and Ault-Seay, TB and Yu, Z and Metcalf, JL and Wells, JE},
title = {Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies.},
journal = {Journal of animal science},
volume = {100},
number = {2},
pages = {},
pmid = {35106579},
issn = {1525-3163},
mesh = {Animals ; Genes, rRNA ; High-Throughput Nucleotide Sequencing/veterinary ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/veterinary ; },
abstract = {Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics-in addition to the traditional considerations when conducting an animal science study-makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise when planning an animal microbiome study from design through analysis. This review includes an overview of 16S rRNA gene sequencing, its advantages, and its limitations; experimental design considerations such as study design, sample size, sample pooling, and sample locations; wet lab considerations such as field handing, microbial cell lysis, low biomass samples, library preparation, and sequencing controls; and computational considerations such as identification of contamination, accounting for uneven sequencing depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In addition to general considerations, we highlight some special considerations by species and sample type.},
}
@article {pmid35106548,
year = {2022},
author = {Nerva, L and Garcia, JF and Favaretto, F and Giudice, G and Moffa, L and Sandrini, M and Cantu, D and Zanzotto, A and Gardiman, M and Velasco, R and Gambino, G and Chitarra, W},
title = {The hidden world within plants: metatranscriptomics unveils the complexity of wood microbiomes.},
journal = {Journal of experimental botany},
volume = {73},
number = {8},
pages = {2682-2697},
doi = {10.1093/jxb/erac032},
pmid = {35106548},
issn = {1460-2431},
support = {C94E19000770008//Italian Ministry for Agriculture and Forestry/ ; },
mesh = {Bacteria/genetics ; *Endophytes ; *Microbiota ; Plants ; Wood ; },
abstract = {The importance of plants as complex entities influenced by genomes of the associated microorganisms is now seen as a new source of variability for a more sustainable agriculture, also in the light of ongoing climate change. For this reason, we investigated through metatranscriptomics whether the taxa profile and behaviour of microbial communities associated with the wood of 20-year-old grapevine plants are influenced by the health status of the host. We report for the first time a metatranscriptome from a complex tissue in a real environment, highlighting that this approach is able to define the microbial community better than referenced transcriptomic approaches. In parallel, the use of total RNA enabled the identification of bacterial taxa in healthy samples that, once isolated from the original wood tissue, displayed potential biocontrol activities against a wood-degrading fungal taxon. Furthermore, we revealed an unprecedented high number of new viral entities (~120 new viral species among 180 identified) associated with a single and limited environment and with potential impact on the whole holobiont. Taken together, our results suggest a complex multitrophic interaction in which the viral community also plays a crucial role in raising new ecological questions for the exploitation of microbial-assisted sustainable agriculture.},
}
@article {pmid35102425,
year = {2023},
author = {McBride, SG and Osburn, ED and Lucas, JM and Simpson, JS and Brown, T and Barrett, JE and Strickland, MS},
title = {Volatile and Dissolved Organic Carbon Sources Have Distinct Effects on Microbial Activity, Nitrogen Content, and Bacterial Communities in Soil.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {659-668},
pmid = {35102425},
issn = {1432-184X},
support = {1023307//National Institute of Food and Agriculture/ ; 1556753//Directorate for Biological Sciences/ ; },
mesh = {*Soil/chemistry ; Dissolved Organic Matter ; Nitrogen/analysis ; Carbon ; Soil Microbiology ; Bacteria ; Proteobacteria ; *Microbiota ; Water ; },
abstract = {Variation in microbial use of soil carbon compounds is a major driver of biogeochemical processes and microbial community composition. Available carbon substrates in soil include both low molecular weight-dissolved organic carbon (LMW-DOC) and volatile organic compounds (VOCs). To compare the effects of LMW-DOC and VOCs on soil chemistry and microbial communities under different moisture regimes, we performed a microcosm experiment with five levels of soil water content (ranging from 25 to 70% water-holding capacity) and five levels of carbon amendment: a no carbon control, two dissolved compounds (glucose and oxalate), and two volatile compounds (methanol and α-pinene). Microbial activity was measured throughout as soil respiration; at the end of the experiment, we measured extractable soil organic carbon and total extractable nitrogen and characterized prokaryotic communities using amplicon sequencing. All C amendments increased microbial activity, and all except oxalate decreased total extractable nitrogen. Likewise, individual phyla responded to specific C amendments-e.g., Proteobacteria increased under addition of glucose, and both VOCs. Further, we observed an interaction between moisture and C amendment, where both VOC treatments had higher microbial activity than LMW-DOC treatments and controls at low moisture. Across moisture and C treatments, we identified that Chloroflexi, Nitrospirae, Proteobacteria, and Verrucomicrobia were strong predictors of microbial activity, while Actinobacteria, Bacteroidetes, and Thaumarcheota strongly predicted soil extractable nitrogen. These results indicate that the type of labile C source available to soil prokaryotes can influence both microbial diversity and ecosystem function and that VOCs may drive microbial functions and composition under low moisture conditions.},
}
@article {pmid35102262,
year = {2022},
author = {Bretzke, K and Preusser, F and Jasim, S and Miller, C and Preston, G and Raith, K and Underdown, SJ and Parton, A and Parker, AG},
title = {Multiple phases of human occupation in Southeast Arabia between 210,000 and 120,000 years ago.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {1600},
pmid = {35102262},
issn = {2045-2322},
abstract = {Changing climatic conditions are thought to be a major control of human presence in Arabia during the Paleolithic. Whilst the Pleistocene archaeological record shows that periods of increased monsoon rainfall attracted human occupation and led to increased population densities, the impact of arid conditions on human populations in Arabia remains largely speculative. Here, we present data from Jebel Faya in Southeast (SE) Arabia, which document four periods of human occupation between c. 210,000 and 120,000 years ago. The Jebel Faya record indicates that human occupation of SE Arabia was more regular and not exclusively linked to major humid periods. Our data show that brief phases of increased rainfall additionally enabled human settlement in the Faya region. These results imply that the mosaic environments in SE Arabia have likely formed a population refugia at the end of the Middle and the beginning of the Late Pleistocene.},
}
@article {pmid35098423,
year = {2022},
author = {Ben Rejeb, I and Khemir, H and Messaoudi, Y and Miled, N and Gargouri, M},
title = {Optimization of Enzymatic Degreasing of Sheep Leather for an Efficient Approach and Leather Quality Improvement Using Fractional Experimental Design.},
journal = {Applied biochemistry and biotechnology},
volume = {194},
number = {5},
pages = {2251-2268},
pmid = {35098423},
issn = {1559-0291},
mesh = {Animals ; Hydrolysis ; Lipase ; *Quality Improvement ; *Research Design ; Sheep ; Skin/chemistry ; },
abstract = {Leather industry is making significant contributions to economic development. However, it is notably leading to a serious environmental pollution. Recently, the enzyme technology developments offer new opportunities for enzymatic application in leather making. In the present investigation, microbial lipases were studied and used in degreasing process of sheep leathers. In order to optimize degreasing efficiency, a fractional experimental design with four parameters (enzyme source, processing stage, lipase amount, and degreasing duration) was used. Lipases A from Aspergillus niger, F from Rhizopus oryzae, R from Penicillium roqueforti, and AY from Candida rugosa were selected for leather degreasing. Enzymatic treatment of sheep skin was carried out during two stages of beamhouse operations: deliming-bating and pickling. Obtained results showed that enzymatic degreasing efficiency is higher than those obtained with the conventional process. Lipase F from Rhizopus oryzae demonstrated the most interesting hydrolysis with yields of 58.3% and 37.2% for delimed and pickled skins, respectively. An enzymatic degreasing process on pickled leather using 0.125% (w/v) of lipase F during 3.5 h is the most promising for an industrial application with a 76.03 of degreasing efficiency. Results of the physico-mechanical tests of leathers having undergone enzymatic treatment complied with industry requirement. The enzymatic treatment may be carried out in the same conditions as employed in leather manufacturing process. Results suggested that the enzymatic degreasing improves the leather quality and reduces the use of chemical compounds and surfactant.},
}
@article {pmid35098330,
year = {2023},
author = {Shen, LD and Geng, CY and Ren, BJ and Jin, JH and Huang, HC and Liu, X and Yang, WT and Yang, YL and Liu, JQ and Tian, MH},
title = {Detection and Quantification of Candidatus Methanoperedens-Like Archaea in Freshwater Wetland Soils.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {441-453},
pmid = {35098330},
issn = {1432-184X},
support = {41977037//National Natural Science Foundation of China/ ; BK20190092//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {*Archaea/genetics ; *Wetlands ; Nitrates ; Soil ; Phylogeny ; Oxidation-Reduction ; Fresh Water ; Methane ; Water ; Iron ; Anaerobiosis ; },
abstract = {Candidatus Methanoperedens-like archaea, which can use multiple electron acceptors (nitrate, iron, manganese, and sulfate) for anaerobic methane oxidation, could play an important role in reducing methane emissions from freshwater wetlands. Currently, very little is known about the distribution and community composition of Methanoperedens-like archaea in freshwater wetlands, particularly based on their alpha subunit of methyl-coenzyme M reductase (mcrA) genes. Here, the community composition, diversity, and abundance of Methanoperedens-like archaea were investigated in a freshwater wetland through high-throughput sequencing and quantitative PCR on their mcrA genes. A large number of Methanoperedens-like mcrA gene sequences (119,250) were recovered, and a total of 31 operational taxonomic units (OTUs) were generated based on 95% sequence similarity cut-off. The majority of Methanoperedens-like sequences can be grouped into three distinct clusters that were closely associated with the known Methanoperedens species which can couple anaerobic methane oxidation to nitrate or iron reduction. The community composition of Methanoperedens-like archaea differed significantly among different sampling sites, and their mcrA gene abundance was 1.49 × 10[6] ~ 4.62 × 10[6] copies g[-1] dry soil in the examined wetland. In addition, the community composition of Methanoperedens-like archaea was significantly affected by the soil water content, and the archaeal abundance was significantly positively correlated with the water content. Our results suggest that the mcrA gene is a good biomarker for detection and quantification of Methanoperedens-like archaea, and provide new insights into the distribution and environmental regulation of these archaea in freshwater wetlands.},
}
@article {pmid35095807,
year = {2021},
author = {Anagnostopoulos, DA and Tsaltas, D},
title = {Current Status, Recent Advances, and Main Challenges on Table Olive Fermentation: The Present Meets the Future.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {797295},
pmid = {35095807},
issn = {1664-302X},
abstract = {Table olives are among the most well-known fermented foods, being a vital part of the Mediterranean pyramid diet. They constitute a noteworthy economic factor for the producing countries since both their production and consumption are exponentially increasing year by year, worldwide. Despite its significance, olive's processing is still craft based, not changed since antiquity, leading to the production of an unstable final product with potential risk concerns, especially related to deterioration. However, based on industrial needs and market demands for reproducible, safe, and healthy products, the modernization of olive fermentation processing is the most important challenge of the current decade. In this sense, the reduction of sodium content and more importantly the use of suitable starter cultures, exhibiting both technological and potential probiotic features, to drive the process may extremely contribute to this need. Prior, to achieve in this effort, the full understanding of table olive microbial ecology during fermentation, including an in-depth determination of microbiota presence and/or dominance and its functionality (genes responsible for metabolite production) that shape the sensorial characteristics of the final product, is a pre-requisite. The advent of meta-omics technology could provide a thorough study of this complex ecosystem, opening in parallel new insights in the field, such as the concept of microbial terroir. Herein, we provide an updated overview in the field of olive fermentation, pointing out some important challenges/perspectives that could be the key to the olive sector's advancement and modernization.},
}
@article {pmid35094098,
year = {2023},
author = {Song, H and Lee, K and Hwang, I and Yang, E and Ha, J and Kim, W and Park, S and Cho, H and Choe, JC and Lee, SI and Jablonski, P},
title = {Dynamics of Bacterial Communities on Eggshells and on Nest Materials During Incubation in the Oriental Tit (Parus minor).},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {429-440},
pmid = {35094098},
issn = {1432-184X},
support = {3344-20180017//National Research Foundation of Korea/ ; 2-2019-1273-001-3//National Research Foundation of Korea/ ; 2021010026//Daegu Gyeongbuk Institute of Science and Technology/ ; 5253-20180100//the BK21 Korea/ ; 21A20131212006//the BK21 Korea/ ; },
mesh = {Animals ; *Egg Shell/microbiology ; Phylogeny ; *Bacteria ; Birds/microbiology ; Skin ; },
abstract = {Eggshell bacterial communities may affect hatching success and nestling's condition. Nest materials are in direct contact with the eggshells, but the relationships with the eggshell microbiome during incubation have not been fully elucidated. Here, we characterize eggshell and nest material bacterial communities and their changes during incubation in the Oriental Tit (Parus minor). Bacterial communities on the nest material were relatively stable and remained distinct from the eggshell communities and had higher diversity and greater phylogenetic clustering than the eggshell communities from the same nest, resulting in lower phylogenetic turnover rate of nest material microbiome during incubation than expected by chance. While the species diversity of both communities did not change during incubation, we found significantly greater changes in the structure of bacterial communities on the eggshell than on the nest material. However, eggshell microbiome remained distinct from nest material microbiome, suggesting independent dynamics of the two microbiomes during incubation. We detected an increase in the relative abundance of several bacterial taxa on the eggshell that likely come from the bird's skin, feathers, cloaca/intestine, or uropygial secretion which suggests some exchange of bacteria between the incubating bird and the eggshell. Furthermore, incubation appeared to promote the abundance of antibiotic producing taxa on the eggshell, which may hypothetically inhibit growth of many bacteria including pathogenic ones. Our results suggest that the future studies should focus on simultaneous monitoring of absolute abundance as well as relative abundance in communities on eggshells, nest materials, and the incubating bird's body.},
}
@article {pmid35094062,
year = {2022},
author = {Berg, JS and Ahmerkamp, S and Pjevac, P and Hausmann, B and Milucka, J and Kuypers, MMM},
title = {How low can they go? Aerobic respiration by microorganisms under apparent anoxia.},
journal = {FEMS microbiology reviews},
volume = {46},
number = {3},
pages = {},
pmid = {35094062},
issn = {1574-6976},
mesh = {*Ecosystem ; Humans ; Hypoxia ; *Oxygen/metabolism ; Respiration ; },
abstract = {Oxygen (O2) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O2 down to nanomolar concentrations. The respiration of O2 at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O2 sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O2 at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here, we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.},
}
@article {pmid35093783,
year = {2022},
author = {Zhong, X and Yu, S and Xu, H and Kim, S},
title = {Can tidal events influence analysis on colonization dynamics in body-size spectrum of periphytic ciliates for marine bioassessment?.},
journal = {Marine pollution bulletin},
volume = {175},
number = {},
pages = {113342},
doi = {10.1016/j.marpolbul.2022.113342},
pmid = {35093783},
issn = {1879-3363},
mesh = {Body Size ; *Ciliophora ; Cluster Analysis ; *Ecosystem ; Environmental Monitoring/methods ; },
abstract = {The tidal influence on body-size spectrum of the protozoan periphytons was explored by using the conventional slide system (CS) and the polyurethane foam enveloped slide system (PFES) in coastal waters during a 1-month study. During the colonization process, clear temporal patterns of the body-size spectrum were observed using the two sampling methods. In terms of relative species number and frequency of occurrence, the rank S4 represented a more stable temporal variability in the PFES system than the CS system during the colonization. Additionally, the small forms (e.g., S1, S2, and S3) were more abundant in the PFES system. The clustering and bootstrapped average analyses demonstrated differences in body-size spectrum of protozoans between the two sampling systems. Our results imply that the body-size spectrum of protozoan periphytons may be impacted by tidal events during colonization process in marine waters.},
}
@article {pmid35092770,
year = {2022},
author = {Baril, X and Durand, AA and Srei, N and Lamothe, S and Provost, C and Martineau, C and Dunfield, K and Constant, P},
title = {The biological sink of atmospheric H2 is more sensitive to spatial variation of microbial diversity than N2O and CO2 emissions in a winter cover crop field trial.},
journal = {The Science of the total environment},
volume = {821},
number = {},
pages = {153420},
doi = {10.1016/j.scitotenv.2022.153420},
pmid = {35092770},
issn = {1879-1026},
mesh = {*Carbon Dioxide/analysis ; *Microbiota ; Nitrous Oxide/analysis ; RNA, Ribosomal, 16S ; Seasons ; Soil ; },
abstract = {The integration of winter cover crop (WCC) in culture rotations promotes multiple ecosystem services, but concomitant microbial diversity and functioning responses in soil have received less attention. A field trial was established to test the hypothesis that enhanced crop diversity with the integration of WCC in a conventional maize-soy rotation promotes microbial diversity and the biological sink of H2 in soil, while reducing N2O emissions to the atmosphere. Vicia villosa (hairy vetch), Avena sativa (oat), and Raphanus sativus (Daikon radish) were cultivated alone or in combinations and flux measurements were performed throughout two subsequent growing seasons. Soil acted as a net sink for H2 and as a net source for CO2 and N2O. CO2 flux was the most sensitive to WCC whereas a significant spatial variation was observed for H2 flux with soil uptake rates observed in the most productive area two-fold greater than the baseline level. Sequencing and quantification of taxonomic and functional genes were integrated to explain variation in trace gas fluxes with compositional changes in soil microbial communities. Fungal communities were the most sensitive to WCC, but neither community abundance nor beta diversity were found to be indicative of fluxes. The alpha diversity of taxonomic and functional genes, expressed as the number of effective species, was integrated into composite variables extracted from multivariate analyses. Only the composite variable computed with the inverse Simpson's index displayed a reproducible pattern throughout both growing seasons, with functional genes and bacterial 16S rRNA gene defining the two most contrasting gradients. The composite variable was decoupled from WCC treatment and explained 19-20% spatial variation of H2 fluxes. The coupling of composite alpha diversity metrics derived from multiple genes with soil processes warrants further investigations to implement novel indicators of soil health in response to changing management practices at the local scale.},
}
@article {pmid35091250,
year = {2022},
author = {Sharma, N and Kumari, R and Thakur, M and Rai, AK and Singh, SP},
title = {Molecular dissemination of emerging antibiotic, biocide, and metal co-resistomes in the Himalayan hot springs.},
journal = {Journal of environmental management},
volume = {307},
number = {},
pages = {114569},
doi = {10.1016/j.jenvman.2022.114569},
pmid = {35091250},
issn = {1095-8630},
mesh = {Anti-Bacterial Agents ; *Disinfectants ; *Hot Springs ; Humans ; Metagenomics ; *Metals, Heavy ; },
abstract = {Growing resistance among microbial communities against antimicrobial compounds, especially antibiotics, is a significant threat to living beings. With increasing antibiotic resistance in human pathogens, it is necessary to examine the habitats having community interests. In the present study, a metagenomic approach has been employed to understand the causes, dissemination, and effects of antibiotic, metal, and biocide resistomes on the microbial ecology of three hot springs, Borong, Lingdem, and Yumthang, located at different altitudes of the Sikkim Himalaya. The taxonomic assessment of these hot springs depicted the predominance of mesophilic organisms, mainly belonging to the phylum Proteobacteria. The enriched microbial metabolism assosiated with energy, cellular processes, adaptation to diverse environments, and defence were deciphered in the metagenomes. The genes representing resistance to semisynthetic antibiotics, e.g., aminoglycosides, fluoroquinolones, fosfomycin, vancomycin, trimethoprim, tetracycline, streptomycin, beta-lactams, multidrug resistance, and biocides such as triclosan, hydrogen peroxide, acriflavin, were abundantly present. Various genes attributing resistance to copper, arsenic, iron, and mercury in metal resistome were detected. Relative abundance, correlation, and genome mapping of metagenome-assembled genomes indicated the co-evolution of antibiotic and metal resistance in predicted novel species belonging to Vogesella, Thiobacillus, and Tepidimona genera. The metagenomic findings were further validated with isolation of microbial cultures, exhibiting resistance against antibiotics and heavy metals, from the hot spring water samples. The study furthers our understanding about the molecular basis of co-resistomes in the ceological niches and their possible impact on the environment.},
}
@article {pmid35090934,
year = {2022},
author = {Amaral, RR and Braga, T and Siqueira, JF and Rôças, IN and da Costa Rachid, CTC and Oliveira, AGG and de Souza Côrtes, MI and Love, RM},
title = {Root Canal Microbiome Associated With Asymptomatic Apical Periodontitis as Determined by High-Throughput Sequencing.},
journal = {Journal of endodontics},
volume = {48},
number = {4},
pages = {487-495},
doi = {10.1016/j.joen.2022.01.012},
pmid = {35090934},
issn = {1878-3554},
mesh = {Dental Pulp Cavity/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; *Periapical Periodontitis/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {INTRODUCTION: Advanced DNA sequencing technology allows more detailed analysis and description of the endodontic microbiome. This study used the MiSeq high-throughput sequencing platform (Illumina, San Diego, CA) to describe the endodontic microbiome of teeth with primary asymptomatic apical periodontitis with no sinus tract.<br><br>METHODS: Root canal samples from 25 patients were prepared for DNA sequencing analysis. Bacterial diversity of the microbiome was identified and compared between cases and according to the size of the related apical periodontitis lesions. Statistical analyses of the operational taxonomic unit distribution was performed using principal component analysis with the Bray-Curtis distance and a principal coordinate analysis, 2-way permutational multivariate analysis of variance. The chi-square or Fisher exact test was used to evaluate the prevalence of different operational taxonomic units related to small and large apical periodontitis lesions.<br><br>RESULTS: Although there was a very high bacterial diversity in the microbiome of teeth with asymptomatic apical periodontitis, 4 phyla dominated the microbiome: Firmicutes (27%), Bacteroidetes (21%), Proteobacteria (21%), and Actinobacteria (12%). There was high variability in species composition between root canal samples with no common species pattern for the cases. Large lesions showed a higher number of species but did not significantly differ from small lesions in bacterial diversity indexes. Bacteroidaceae [G-1] bacterium HMT 272, a previously uncultivated but still unnamed and uncharacterized taxon, was the most prevalent and abundant phylotype.<br><br>CONCLUSIONS: High-throughput sequencing technology confirmed the complexity of the endodontic microbiome and revealed that microbial heterogeneity is a feature between cases. This indicates that various microbial combinations of the endodontic microbiome are able to illicit periapical inflammatory diseases.},
}
@article {pmid35089393,
year = {2023},
author = {Deng, J and Zhou, W and Dai, L and Yuan, Q and Zhou, L and Qi, L and Yu, D},
title = {The Effects of Shrub Removal on Soil Microbial Communities in Primary Forest, Secondary Forest and Plantation Forest on Changbai Mountain.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {642-658},
pmid = {35089393},
issn = {1432-184X},
mesh = {*Soil ; Forests ; Betula ; *Microbiota ; Bacteria ; China ; },
abstract = {Shrub removal is a common management method in forest ecosystems, but comparatively little is known regarding the effects of shrub removal on soil microbial communities among primary forest, secondary forest, and plantation forests in temperate forests, which limits our accurate assessment of sustainable management of understory vegetation removal. Given this, we used a long-term operation experiment across a contrasting mixed broadleaved-Pinus koraiensis forest, Betula platyphylla forest, and Larix gmelinii plantation forest to explore the variations of soil properties and microbial community after 5 years of shrub removal on Changbai Mountain, as well as the contribution of the soil properties and understory plant diversity to the soil microbial community. The results demonstrated that shrub removal could significantly alter soil SWC and TN, TP, and AP contents of the L. gmelinii, as well as N/P of B. platyphylla. Moreover, shrub removal also clearly improved soil bacterial Pielou_e index and Simpson index of mixed broadleaved-P. koraiensis and soil bacterial Simpson index of L. gmelinii, and decreased soil fungal Pielou_e index and Shannon index of L. gmelinii and soil bacterial Pielou_e index and soil fungal Shannon index of B. platyphylla. Identically, shrub removal notably altered the soil bacterial community composition. Soil characteristics and understory plant diversity accounted for 48.02% and 26.88%, and 45.88% and 27.57% of the variance in the bacterial and fungal community composition, respectively. This study aimed to provide an important scientific basis for the restoration and sustainable management of temperate forests in the Changbai Mountain region.},
}
@article {pmid35085485,
year = {2022},
author = {Gowda, K and Ping, D and Mani, M and Kuehn, S},
title = {Genomic structure predicts metabolite dynamics in microbial communities.},
journal = {Cell},
volume = {185},
number = {3},
pages = {530-546.e25},
doi = {10.1016/j.cell.2021.12.036},
pmid = {35085485},
issn = {1097-4172},
mesh = {Biomass ; Denitrification ; Genome ; *Genomics ; *Metabolomics ; Microbiota/*genetics ; Models, Biological ; Nitrates/metabolism ; Nitrites/metabolism ; Phenotype ; Regression Analysis ; Reproducibility of Results ; },
abstract = {The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here, we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community metabolite dynamics, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.},
}
@article {pmid35083529,
year = {2023},
author = {Tian, Q and Jiang, Q and Huang, L and Li, D and Lin, Q and Tang, Z and Liu, F},
title = {Vertical Distribution of Soil Bacterial Communities in Different Forest Types Along an Elevation Gradient.},
journal = {Microbial ecology},
volume = {85},
number = {2},
pages = {628-641},
pmid = {35083529},
issn = {1432-184X},
support = {31700462//national natural science foundation of china/ ; 31870465//national natural science foundation of china/ ; 2020338//youth innovation promotion association of the chinese academy of sciences/ ; },
mesh = {*Soil ; Soil Microbiology ; Forests ; Bacteria ; *Chloroflexi ; },
abstract = {Microorganisms inhabit the entire soil profile and play important roles in nutrient cycling and soil formation. Recent studies have found that soil bacterial diversity and composition differ significantly among soil layers. However, little is known about the vertical variation in soil bacterial communities and how it may change along an elevation gradient. In this study, we collected soil samples from 5 forest types along an elevation gradient in Taibai Mountain to characterize the bacterial communities and their vertical patterns and variations across soil profiles. The richness and Shannon index of soil bacterial communities decreased from surface soils to deep soils in three forest types, and were comparable among soil layers in the other two forests at the medium elevation. The composition of soil bacterial communities differed significantly between soil layers in all forest types, and was primarily affected by soil C availability. Oligotrophic members of the bacterial taxa, such as Chloroflexi, Gemmatimonadetes, Nitrospirae, and AD3, were more abundant in the deep layers. The assembly of soil bacterial communities within each soil profile was mainly governed by deterministic processes based on environmental heterogeneity. The vertical variations in soil bacterial communities differed among forest types, and the soil bacterial communities in the Betula albo-sinensis forest at the medium elevation had the lowest vertical variation. The vertical variation was negatively correlated with mean annual precipitation (MAP), weighted rock content, and weighted sand particle content in soils, among which MAP had the highest explanatory power. These results indicated that the vertical mobilization of microbes with preferential and matrix flows likely enhanced bacterial homogeneity. Overall, our results suggest that the vertical variations in soil bacterial communities differ along the elevation gradient and potentially affect soil biological processes across soil profiles.},
}
@article {pmid35082431,
year = {2022},
author = {Dede, B and Hansen, CT and Neuholz, R and Schnetger, B and Kleint, C and Walker, S and Bach, W and Amann, R and Meyerdierks, A},
title = {Niche differentiation of sulfur-oxidizing bacteria (SUP05) in submarine hydrothermal plumes.},
journal = {The ISME journal},
volume = {16},
number = {6},
pages = {1479-1490},
pmid = {35082431},
issn = {1751-7370},
support = {03G0253//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
mesh = {Bacteria ; *Hydrothermal Vents/microbiology ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/microbiology ; Sulfur/metabolism ; },
abstract = {Hydrothermal plumes transport reduced chemical species and metals into the open ocean. Despite their considerable spatial scale and impact on biogeochemical cycles, niche differentiation of abundant microbial clades is poorly understood. Here, we analyzed the microbial ecology of two bathy- (Brothers volcano; BrV-cone and northwest caldera; NWC) and a mesopelagic (Macauley volcano; McV) plumes on the Kermadec intra-oceanic arc in the South Pacific Ocean. The microbial community structure, determined by a combination of 16S rRNA gene, fluorescence in situ hybridization and metagenome analysis, was similar to the communities observed in other sulfur-rich plumes. This includes a dominance of the vent characteristic SUP05 clade (up to 22% in McV and 51% in BrV). In each of the three plumes analyzed, the community was dominated by a different yet uncultivated chemoautotrophic SUP05 species, here, provisionally named, Candidatus Thioglobus vadi (McV), Candidatus Thioglobus vulcanius (BrV-cone) and Candidatus Thioglobus plumae (BrV-NWC). Statistical analyses, genomic potential and mRNA expression profiles suggested a SUP05 niche partitioning based on sulfide and iron concentration as well as water depth. A fourth SUP05 species was present at low frequency throughout investigated plume samples and may be capable of heterotrophic or mixotrophic growth. Taken together, we propose that small variations in environmental parameters and depth drive SUP05 niche partitioning in hydrothermal plumes.},
}
@article {pmid35081826,
year = {2022},
author = {Morou-Bermúdez, E and Torres-Colón, JE and Bermúdez, NS and Patel, RP and Joshipura, KJ},
title = {Pathways Linking Oral Bacteria, Nitric Oxide Metabolism, and Health.},
journal = {Journal of dental research},
volume = {101},
number = {6},
pages = {623-631},
pmid = {35081826},
issn = {1544-0591},
support = {R01 DE028195/DE/NIDCR NIH HHS/United States ; },
mesh = {*Ammonium Compounds ; Bacteria/metabolism ; *Cardiovascular Diseases ; Humans ; *Microbiota ; Nitrates/metabolism ; Nitric Oxide/metabolism ; Nitrites/metabolism ; },
abstract = {Nitrate-reducing oral bacteria have gained a lot of interest due to their involvement in nitric oxide (NO) synthesis and its important cardiometabolic outcomes. Consortia of nitrate-metabolizing oral bacteria associated with cardiometabolic health and cognitive function have been recently identified. Longitudinal studies and clinical trials have shown that chronic mouthwash use is associated with increased blood pressure and increased risk for prediabetes/diabetes and hypertension. Concurrently, recent studies are beginning to shed some light on the complexity of nitrate reduction pathways of oral bacteria, such as dissimilatory nitrate reduction to ammonium (DNRA), which converts nitrite into ammonium, and denitrification, which converts nitrite to NO, nitrous oxide, and dinitrogen. These pathways can affect the composition and metabolism of the oral microbiome; consequently, salivary nitrate and nitrite metabolism have been proposed as targets for probiotics and oral health. These pathways could also affect systemic NO levels because NO generated through denitrification can be oxidized back to nitrite in the saliva, thus facilitating flux along the NO3[-]-NO2[-]-NO pathway, while DNRA converts nitrite to ammonium, leading to reduced NO. It is, therefore, important to understand which pathway predominates under different oral environmental conditions, since the clinical consequences could be different for oral and systemic health. Recent studies show that oral hygiene measures such as tongue cleaning and dietary nitrate are likely to favor denitrifying bacteria such as Neisseria, which are linked with better cardiometabolic health. A vast body of literature demonstrates that redox potential, carbon-to-nitrate ratio, and nitrate-to-nitrite ratio are key environmental drivers of the competing denitrification and DNRA pathways in various natural and artificial ecosystems. Based on this information, a novel behavioral and microbial model for nitric oxide metabolism and health is proposed, which links lifestyle factors with oral and systemic health through NO metabolism.},
}
@article {pmid35078415,
year = {2022},
author = {Duthoo, E and De Reu, K and Leroy, F and Weckx, S and Heyndrickx, M and Rasschaert, G},
title = {To culture or not to culture: careful assessment of metabarcoding data is necessary when evaluating the microbiota of a modified-atmosphere-packaged vegetarian meat alternative throughout its shelf-life period.},
journal = {BMC microbiology},
volume = {22},
number = {1},
pages = {34},
pmid = {35078415},
issn = {1471-2180},
mesh = {Atmosphere ; Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; DNA Barcoding, Taxonomic/*methods/*standards/statistics &amp; numerical data ; Food Microbiology/*methods/standards ; Food Packaging/methods/standards ; Food Storage/methods/*standards/statistics &amp; numerical data ; Meat Products/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Refrigeration ; *Vegetarians ; },
abstract = {BACKGROUND: As the increased consumption of ready-to-eat meat alternatives is a fairly recent trend, little is known about the composition and dynamics of the microbiota present on such products. Such information is nonetheless valuable in view of spoilage and food safety prevention. Even though refrigeration and modified-atmosphere-packaging (MAP) can extend the shelf-life period, microbial spoilage can still occur in these products. In the present study, the microbiota of a vegetarian alternative to poultry-based charcuterie was investigated during storage, contrasting the use of a culture-dependent method to a culture-independent metagenetic method.<br><br>RESULTS: The former revealed that lactic acid bacteria (LAB) were the most abundant microbial group, specifically at the end of the shelf-life period, whereby Latilactobacillus sakei was the most abundant species. Metabarcoding analysis, in contrast, revealed that DNA of Xanthomonas was most prominently present, which likely was an artifact due to the presence of xanthan gum as an ingredient, followed by Streptococcus and Weissella.<br><br>CONCLUSIONS: Taken together, these results indicated that Lb. sakei was likely the most prominent specific spoilage organisms (SSO) and, additionally, that the use of metagenetic analysis needs to be interpreted with care in this specific type of product. In order to improve the performance of metagenetics in food samples with a high DNA matrix but a low bacterial DNA load, selective depletion techniques for matrix DNA could be explored.},
}
@article {pmid35077695,
year = {2022},
author = {Glass, NL and Rico-Ramírez, AM},
title = {Microbial ecology: Fungal foes and friends.},
journal = {Current biology : CB},
volume = {32},
number = {2},
pages = {R84-R86},
doi = {10.1016/j.cub.2021.12.030},
pmid = {35077695},
issn = {1879-0445},
mesh = {Bacteria ; Friends ; *Fungi ; Humans ; Phenazines ; Soil ; *Soil Microbiology ; },
abstract = {A tripartite interaction between soil fungi, soil bacteria that produce phenazines that are toxic to the fungi, and a second bacterium that sequesters and detoxifies phenazines illustrates the complexity of antagonistic and mutualistic bacterial-fungal interactions.},
}
@article {pmid35076268,
year = {2022},
author = {Perez-Lamarque, B and Krehenwinkel, H and Gillespie, RG and Morlon, H},
title = {Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota.},
journal = {mSystems},
volume = {7},
number = {1},
pages = {e0110421},
pmid = {35076268},
issn = {2379-5077},
mesh = {Animals ; Phylogeny ; Hawaii ; *Spiders ; *Microbiota ; Infectious Disease Transmission, Vertical ; },
abstract = {The degree of similarity between the microbiotas of host species often mirrors the phylogenetic proximity of the hosts. This pattern, referred to as phylosymbiosis, is widespread in animals and plants. While phylosymbiosis was initially interpreted as the signal of symbiotic transmission and coevolution between microbes and their hosts, it is now recognized that similar patterns can emerge even if the microbes are environmentally acquired. Distinguishing between these two scenarios, however, remains challenging. We recently developed HOME (host-microbiota evolution), a cophylogenetic model designed to detect vertically transmitted microbes and host switches from amplicon sequencing data. Here, we applied HOME to the microbiotas of Hawaiian spiders of the genus Ariamnes, which experienced a recent radiation on the archipelago. We demonstrate that although Hawaiian Ariamnes spiders display a significant phylosymbiosis, there is little evidence of microbial vertical transmission. Next, we performed simulations to validate the absence of transmitted microbes in Ariamnes spiders. We show that this is not due to a lack of detection power because of the low number of segregating sites or an effect of phylogenetically driven or geographically driven host switches. Ariamnes spiders and their associated microbes therefore provide an example of a pattern of phylosymbiosis likely emerging from processes other than vertical transmission. IMPORTANCE How host-associated microbiotas assemble and evolve is one of the outstanding questions of microbial ecology. Studies aiming at answering this question have repeatedly found a pattern of "phylosymbiosis," that is, a phylogenetic signal in the composition of host-associated microbiotas. While phylosymbiosis was often interpreted as evidence for vertical transmission and host-microbiota coevolution, simulations have now shown that it can emerge from other processes, including host filtering of environmentally acquired microbes. However, distinguishing the processes driving phylosymbiosis in nature remains challenging. We recently developed a cophylogenetic method that can detect vertical transmission. Here, we applied this method to the microbiotas of recently diverged spiders from the Hawaiian archipelago, which display a clear phylosymbiosis pattern. We found that none of the bacterial operational taxonomic units is vertically transmitted. We show with simulations that this result is not due to methodological artifacts. Thus, we provide a striking empirical example of phylosymbiosis emerging from processes other than vertical transmission.},
}
@article {pmid35074976,
year = {2022},
author = {Roy, P and Sarma, A and Kataki, AC and Rai, AK and Chattopadhyay, I},
title = {Salivary microbial dysbiosis may predict lung adenocarcinoma: A pilot study.},
journal = {Indian journal of pathology &amp; microbiology},
volume = {65},
number = {1},
pages = {123-128},
doi = {10.4103/IJPM.IJPM_1111_20},
pmid = {35074976},
issn = {0974-5130},
mesh = {Adenocarcinoma of Lung/*diagnosis/etiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Biomarkers, Tumor/analysis ; DNA, Bacterial/*genetics ; Dysbiosis/etiology/*microbiology ; Female ; Humans ; India ; Male ; Microbiota/genetics ; Middle Aged ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; },
abstract = {BACKGROUND: Adenocarcinoma is a more common type of Non-small cell lung cancer (NSCLC). Lung cancer showed a statistically significant increment in the Kamrup Urban district of Assam, Tripura, Sikkim, and Manipur of India. The goal of our pilot study is to identify non-invasive microbial biomarkers to detect lung adenocarcinoma (LAC).<br><br>MATERIAL AND METHODS: DNA extraction from saliva samples of five LAC patients and five healthy controls was performed by Qiagen DNeasy blood and tissue kit using Lysozyme (3mg/ml) treatment. 16S rRNA genes of distinct regions (V3-V4) were amplified from saliva DNA by PCR. Paired-end sequencing targeting the V3-V4 region of the 16S rRNA gene has been performed on the Illumina MiSeq platform. Raw sequences were analyzed using the QIIME(Quantitative Insights Into Microbial Ecology) software package.<br><br>RESULTS: Our preliminary results showed that Rothia mucilaginosa, Veillonella dispar, Prevotella melaninogenica, Prevotella pallens, Prevotella copri, Haemophilus parainfluenzae, Neisseria bacilliformis and Aggregatibacter segnis were significantly elevated in saliva of LAC which may serve as potential non-invasive biomarkers for LAC detection. Functional prediction analysis showed that bacterial genes involved in glycosyltransferase, peptidases, amino sugar, and nucleotide sugar metabolism, starch and sucrose metabolism were significantly enriched in LAC.<br><br>CONCLUSION: These salivary bacteria may contribute to the development of LAC by increasing expression of glycosyltransferase and peptidases. However to understand their role in pathobiology, studies are required to perform in large cohort.},
}
@article {pmid35074363,
year = {2022},
author = {Fu, S and Wang, Q and Wang, R and Zhang, Y and Lan, R and He, F and Yang, Q},
title = {Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment.},
journal = {The Science of the total environment},
volume = {820},
number = {},
pages = {153286},
doi = {10.1016/j.scitotenv.2022.153286},
pmid = {35074363},
issn = {1879-1026},
mesh = {*Anti-Bacterial Agents/pharmacology ; Aquaculture ; *Drug Resistance, Bacterial/genetics ; Enterobacter/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Providencia/genetics ; RNA, Ribosomal, 16S ; Shewanella/genetics ; *Vibrio parahaemolyticus/genetics ; },
abstract = {Very little is known about how microbiome interactions shape the horizontal transfer of antibiotic resistance genes in aquacultural environment. To this end, we first conducted 16S rRNA gene amplicon sequencing to monitor the dynamics of bacterial community compositions in one shrimp farm from 2019 to 2020. Next, co-occurrence analysis was then conducted to reveal the interactions network between Vibrio spp. and other species. Subsequently, 21 V. parahaemolyticus isolates and 15 related bacterial species were selected for whole-genome sequencing (WGS). The 16S rDNA amplicon sequencing results identified a remarkable increase of Vibrio and Providencia in September-2019 and a significant rise of Enterobacter and Shewanella in Septtember-2020. Co-occurrence analysis revealed that Vibrio spp. positively interacted with the above species, leading to the sequencing of their isolates to further understand the sharing of the resistant genomic islands (GIs). Subsequent pan-genomic analysis of V. parahaemolyticus genomes identified 278 horizontally transferred genes in 10 GIs, most of which were associated with antibiotic resistance, virulence, and fitness of metabolism. Most of the GIs have also been identified in Providencia, and Enterobacter, suggesting that exchange of genetic traits might occur in V. parahaemolyticus and other cooperative species in a specific niche. No genetic exchange was found between the species with negative relationships. The knowledge generated from this study would greatly improve our capacity to predict and mitigate the emergence of new resistant population and provide practical guidance on the microbial management during the aquacultural activities.},
}
@article {pmid35074352,
year = {2022},
author = {Carcereny, A and Garcia-Pedemonte, D and Martínez-Velázquez, A and Quer, J and Garcia-Cehic, D and Gregori, J and Antón, A and Andrés, C and Pumarola, T and Chacón-Villanueva, C and Borrego, CM and Bosch, A and Guix, S and Pintó, RM},
title = {Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach.},
journal = {Environmental research},
volume = {208},
number = {},
pages = {112720},
pmid = {35074352},
issn = {1096-0953},
mesh = {*COVID-19/epidemiology ; Humans ; *SARS-CoV-2/genetics ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; },
abstract = {Wastewater based epidemiology (WBE) offers an overview of the SARS-CoV-2 variants circulating among the population thereby serving as a proper surveillance method. The variant of concern (VOC) Alpha was first identified in September 2020 in the United Kingdom, and rapidly became dominant across Europe. Our objective was to elucidate the Alpha VOC outcompetition rate and identify mutations in the spike glycoprotein (S) gene, indicative of the circulation of the Alpha VOC and/or other variants in the population through wastewater analysis. In the period covered by this study (November 2020-April 2021), forteen wastewater treatment plants (WWTPs) were weekly sampled. The total number of SARS-CoV-2 genome copies per L (GC/L) was determined with a Real-Time qPCR, targeting the N gene. Surveillance of the Alpha VOC circulation was ascertained using a duplex RT-qPCR, targeting and discriminating the S gene. Our results showed that in a period of 6 weeks the Alpha VOC was present in all the studied WWTPs, and became dominant in 11 weeks on average. The outcompetition rates of the Alpha VOC were estimated, and their relationship with different parameters statistically analyzed. The rapid spread of the Alpha VOC was influenced by its initial input and by the previous circulation of SARS-COV-2 in the population. This latter point could be explained by its higher transmissibility, particularly advantadgeous when a certain degree of herd immunity exists. Moreover, the presence of signature mutations of SARS-COV-2 variants were established by deep-sequencing of the complete S gene. The circulation of the Alpha VOC in the area under study was confirmed, and additionally two combinations of mutations in the S glycoprotein (T73A and D253N, and S477N and A522S) that could affect antibody binding were identified.},
}
@article {pmid35073313,
year = {2022},
author = {Bogdanowski, A and Banitz, T and Muhsal, LK and Kost, C and Frank, K},
title = {McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems.},
journal = {PLoS computational biology},
volume = {18},
number = {1},
pages = {e1009777},
pmid = {35073313},
issn = {1553-7358},
mesh = {Computational Biology/*methods ; *Microbiota ; Software ; *User-Computer Interface ; },
abstract = {Individual-based modeling is widely applied to investigate the ecological mechanisms driving microbial community dynamics. In such models, the population or community dynamics emerge from the behavior and interplay of individual entities, which are simulated according to a predefined set of rules. If the rules that govern the behavior of individuals are based on generic and mechanistically sound principles, the models are referred to as next-generation individual-based models. These models perform particularly well in recapitulating actual ecological dynamics. However, implementation of such models is time-consuming and requires proficiency in programming or in using specific software, which likely hinders a broader application of this powerful method. Here we present McComedy, a modeling tool designed to facilitate the development of next-generation individual-based models of microbial consumer-resource systems. This tool allows flexibly combining pre-implemented building blocks that represent physical and biological processes. The ability of McComedy to capture the essential dynamics of microbial consumer-resource systems is demonstrated by reproducing and furthermore adding to the results of two distinct studies from the literature. With this article, we provide a versatile tool for developing next-generation individual-based models that can foster understanding of microbial ecology in both research and education.},
}
@article {pmid35071939,
year = {2021},
author = {Harder, CB and Persson, S and Christensen, J and Ljubic, A and Nielsen, EM and Hoorfar, J},
title = {Molecular diagnostics of Salmonella and Campylobacter in human/animal fecal samples remain feasible after long-term sample storage without specific requirements.},
journal = {AIMS microbiology},
volume = {7},
number = {4},
pages = {399-414},
pmid = {35071939},
issn = {2471-1888},
abstract = {Rapid advances in the development of sequencing technologies, numbers of commercial providers and diminishing costs have made DNA-based identification and diagnostics increasingly accessible to doctors and laboratories, eliminating the need for local investments in expensive technology and training or hiring of skilled technicians. However, reliable and comparable molecular analyses of bacteria in stool samples are dependent on storage and workflow conditions that do not introduce post-sampling bias, the most important factor being the need to keep the DNA at a stable detectable level. For that reason, there may remain other prohibitively costly requirements for cooling or freezing equipment or special chemical additives. This study investigates the diagnostic detectability of Salmonella and Campylobacter DNA in human, pig and chicken stool samples, stored at different temperatures and with different preservation methods. Stool samples were spiked with 10[6] CFU/mL of both Salmonella and Campylobacter strains stored at -20 °C, 5 °C and 20 °C (Room temperature, RT) and treated with either RNAlater, EDTA or Silica/ethanol. DNA was extracted at 9 different time points within 30 days and quantified by Qubit (total DNA) and qPCR (Salmonella and Campylobacter DNA). We found no statistically significant differences among the different preservation methods, and DNA from both species was easily detected at all time points and at all temperatures, both with and without preservation. This suggests that infections by these bacteria can be diagnosed and possibly also analysed in further detail simply by taking a stool sample in any suitable sealed container that can be transported to laboratory analysis without special storage or preservation requirements. We briefly discuss how this finding can benefit infection control in both developed and developing countries.},
}
@article {pmid35071053,
year = {2021},
author = {Rozas, M and Brillet, F and Callewaert, C and Paetzold, B},
title = {MinION™ Nanopore Sequencing of Skin Microbiome 16S and 16S-23S rRNA Gene Amplicons.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {806476},
pmid = {35071053},
issn = {2235-2988},
mesh = {Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; *Nanopore Sequencing ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; },
abstract = {Human skin microbiome dysbiosis can have clinical consequences. Characterizing taxonomic composition of bacterial communities associated with skin disorders is important for dermatological advancement in both diagnosis and novel treatments. This study aims to analyze and improve the accuracy of taxonomic classification of skin bacteria with MinION™ nanopore sequencing using a defined skin mock community and a skin microbiome sample. We compared the Oxford Nanopore Technologies recommended procedures and concluded that their protocols highly bias the relative abundance of certain skin microbiome genera, most notably a large overrepresentation of Staphylococcus and underrepresentation of Cutibacterium and Corynebacterium. We demonstrated that changes in the amplification protocols improved the accuracy of the taxonomic classification for these three main skin bacterial genera. This study shows that MinION™ nanopore could be an efficient technology for full-length 16S rRNA sequencing; however, the analytical advantage is strongly influenced by the methodologies. The suggested alternatives in the sample processing improved characterization of a complex skin microbiome community using MinION™ nanopore sequencing.},
}
@article {pmid35069532,
year = {2021},
author = {Petit, J and de Bruijn, I and Goldman, MRG and van den Brink, E and Pellikaan, WF and Forlenza, M and Wiegertjes, GF},
title = {β-Glucan-Induced Immuno-Modulation: A Role for the Intestinal Microbiota and Short-Chain Fatty Acids in Common Carp.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {761820},
pmid = {35069532},
issn = {1664-3224},
mesh = {*Animal Feed ; Animals ; *Carps/immunology/microbiology ; Fatty Acids, Volatile/*immunology ; *Gastrointestinal Microbiome/drug effects/immunology ; Immunomodulation/*drug effects ; beta-Glucans/*pharmacology ; },
abstract = {Dietary supplementation of fish with β-glucans has been commonly associated with immunomodulation and generally accepted as beneficial for fish health. However, to date the exact mechanisms of immunomodulation by β-glucan supplementation in fish have remained elusive. In mammals, a clear relation between high-fibre diets, such as those including β-glucans, and diet-induced immunomodulation via intestinal microbiota and associated metabolites has been observed. In this study, first we describe by 16S rRNA sequencing the active naive microbiota of common carp intestine. Based on the abundance of the genus Bacteroides, well known for their capacity to degrade and ferment carbohydrates, we hypothesize that common carp intestinal microbiota could ferment dietary β-glucans. Indeed, two different β-glucan preparations (curdlan and MacroGard[®]) were both fermented in vitro, albeit with distinct fermentation dynamics and distinct production of short-chain fatty acids (SCFA). Second, we describe the potential immunomodulatory effects of the three dominant SCFAs (acetate, butyrate, and propionate) on head kidney leukocytes, showing effects on both nitric oxide production and expression of several cytokines (il-1b, il-6, tnfα, and il-10) in vitro. Interestingly, we also observed a regulation of expression of several gpr40L genes, which were recently described as putative SCFA receptors. Third, we describe how a single in vivo oral gavage of carp with MacroGard[®] modulated simultaneously, the expression of several pro-inflammatory genes (il-1b, il-6, tnfα), type I IFN-associated genes (tlr3.1, mx3), and three specific gpr40L genes. The in vivo observations provide indirect support to our in vitro data and the possible role of SCFAs in β-glucan-induced immunomodulation. We discuss how β-glucan-induced immunomodulatory effects can be explained, at least in part, by fermentation of MacroGard[®] by specific bacteria, part of the naive microbiota of common carp intestine, and how a subsequent production of SFCAs could possibly explain immunomodulation by β-glucan via SCFA receptors present on leukocytes.},
}
@article {pmid35069467,
year = {2021},
author = {Rodríguez-Gijón, A and Nuy, JK and Mehrshad, M and Buck, M and Schulz, F and Woyke, T and Garcia, SL},
title = {A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {761869},
pmid = {35069467},
issn = {1664-302X},
abstract = {Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.},
}
@article {pmid35067749,
year = {2022},
author = {Zhang, L and Lai, JL and Zhang, Y and Luo, XG and Li, ZG},
title = {Correction to: Degradation of Uranium-Contaminated Decontamination Film by UV Irradiation and Microbial Biodegradation.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {451},
doi = {10.1007/s00248-022-01966-1},
pmid = {35067749},
issn = {1432-184X},
}
@article {pmid35066616,
year = {2023},
author = {Sartori, DR and Miñán, AG and Gonzalez, MC and Fernández Lorenzo de Mele, MA},
title = {Different Impact of Suspended Al2O3 Nanoparticles on Microbial Communities: Formation of 2D-Networks (Without Humic Acids) or 3D-Colonies (With Humic Acids).},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {137-145},
pmid = {35066616},
issn = {1432-184X},
support = {2016-1424//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 2019-0631//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 2015-1266//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 11/X900//Universidad Nacional de La Plata/ ; 11/I221//Universidad Nacional de La Plata/ ; PUE 22920170100100CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; 0601//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; },
mesh = {Humic Substances/analysis ; *Zinc Oxide/chemistry ; *Nanoparticles ; Ions ; *Microbiota ; },
abstract = {The use of metal-based and, particularly, Al2O3 nanoparticles (Al2O3-NP) for diverse purposes is exponentially growing. However, the growth of such promissory market is not accompanied by a parallel extensive investigation related to the impact of this pollution on groundwater and biological systems. Pseudomonas species, ubiquitous, environmentally critical microbes, frequently respond to stress conditions with diverse strategies that generally include extracellular polymeric substances (EPS) formation. The aim of this study is to report that changes in the aqueous environment, particularly, the addition of Al2O3-NP without and with humic acids, induce different adaptive strategies of Pseudomonas aeruginosa early biofilms. To this purpose, early biofilms were incubated in diluted culture media without (control) and with Al2O3-NP, and with humic acids (HA-control, HA-Al2O3-NP) for 24 h. 3D colonies with EPS strings and isolated bacteria in their surroundings were detected in the control biofilms. Unlikely, an unusual adaptive behaviour was developed in the presence of Al2O3-NP. Bacteria opt to disassemble the 3D arrangements and to implement a 2D network promoting morphological and size changes of bacterial cells (small coccoid shapes). Remarkably, this strategy allows their temporarily non-EPS-depending survival without decreasing the number of cells. This behaviour was not observed with ZnO-NP, HA-Al2O3-NP, or HA-ZnO-NP. Physicochemical analysis revealed that HA were adsorbed on Al2O3-NP and promoted the Al(III) ions complexation. This supports the hypothesis that the reduction of toxicity of Al ions and the 3D colony formation in the presence of HA-Al2O3-NP is promoted by the complexation of the metal ions with HA components.},
}
@article {pmid35066615,
year = {2023},
author = {Offret, C and Gauthier, O and Despréaux, G and Bidault, A and Corporeau, C and Miner, P and Petton, B and Pernet, F and Fabioux, C and Paillard, C and Le Blay, G},
title = {Microbiota of the Digestive Glands and Extrapallial Fluids of Clams Evolve Differently Over Time Depending on the Intertidal Position.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {288-297},
pmid = {35066615},
issn = {1432-184X},
support = {ANR-17-EURE-0015//Agence Nationale de la Recherche/ ; 678589//Horizon 2020/ ; 2017-Strat&#xe9;gie d'Attractivit&#xe9; Durable//R&#xe9;gion Bretagne/ ; },
mesh = {Animals ; *Bivalvia/microbiology ; *Microbiota ; },
abstract = {The Manila clam (Ruditapes philippinarum) is the second most exploited bivalve in the world but remains threatened by diseases and global changes. Their associated microbiota play a key role in their fitness and acclimation capacities. This study aimed at better understanding the behavior of clam digestive glands and extrapallial fluids microbiota at small, but contrasting spatial and temporal scales. Results showed that environmental variations impacted clam microbiota differently according to the considered tissue. Each clam tissue presented its own microbiota and showed different dynamics according to the intertidal position and sampling period. Extrapallial fluids microbiota was modified more rapidly than digestive glands microbiota, for clams placed on the upper and lower intertidal position, respectively. Clam tissues could be considered as different microhabitats for bacteria as they presented different responses to small-scale temporal and spatial variabilities in natural conditions. These differences underlined a more stringent environmental filter capacity of the digestive glands.},
}
@article {pmid35066415,
year = {2022},
author = {Kazmi, SSUH and Uroosa, and Xu, H and Xuexi, T},
title = {An approach to determining the nitrofurazone-induced toxic dynamics for ecotoxicity assessment using protozoan periphytons in marine ecosystems.},
journal = {Marine pollution bulletin},
volume = {175},
number = {},
pages = {113329},
doi = {10.1016/j.marpolbul.2022.113329},
pmid = {35066415},
issn = {1879-3363},
mesh = {Ecosystem ; Multivariate Analysis ; *Nitrofurazone/toxicity ; *Periphyton ; },
abstract = {With several observable responses and sensitivity of protozoans to nitrofurazone (NFZ), the toxic effects of NFZ on protozoans can be an early warning signal of NFZ contamination in the aquatic environment. To evaluate the toxic dynamics induced by NFZ, protozoan samples were collected using microscopy glass slides and exposed to the five concentrations of NFZ: 0, 1, 2, 4, and 8 mg ml[-1]. Substantial differences in the species composition and toxic-dynamics patterns were observed among all concentrations. Briefly, periphytic euplotids and pleurostomatids were the most prevalent at each concentration level, while dysteriids were less dominant among all treatments. Multivariate analysis revealed significant (P < 0.05) differences in the taxonomic patterns of the test organisms among the five treatments. Furthermore, significant deviation of protozoan communities from the expected taxonomic breadth was observed to occur in a dose-dependent manner. Based on these findings, it is suggested that protozoan periphytons could be used as bioindicators to assess the ecotoxicity of NFZ in the marine environment.},
}
@article {pmid35065823,
year = {2022},
author = {Scherer-Lorenzen, M and Gessner, MO and Beisner, BE and Messier, C and Paquette, A and Petermann, JS and Soininen, J and Nock, CA},
title = {Pathways for cross-boundary effects of biodiversity on ecosystem functioning.},
journal = {Trends in ecology &amp; evolution},
volume = {37},
number = {5},
pages = {454-467},
doi = {10.1016/j.tree.2021.12.009},
pmid = {35065823},
issn = {1872-8383},
mesh = {*Biodiversity ; *Ecosystem ; },
abstract = {The biodiversity-ecosystem functioning concept asserts that processes in ecosystems are markedly influenced by species richness and other facets of biodiversity. However, biodiversity-ecosystem functioning studies have been largely restricted to single ecosystems, ignoring the importance of functional links - such as the exchange of matter, energy, and organisms - between coupled ecosystems. Here we present a basic concept and outline three pathways of cross-boundary biodiversity effects on ecosystem processes and propose an agenda to assess such effects, focusing on terrestrial-aquatic linkages to illustrate the case. This cross-boundary perspective of biodiversity-ecosystem functioning relationships presents a promising frontier for biodiversity and ecosystem science with repercussions for the conservation, restoration, and management of biodiversity and ecosystems from local to landscape scales.},
}
@article {pmid35065228,
year = {2022},
author = {Paquete, CM and Rosenbaum, MA and Bañeras, L and Rotaru, AE and Puig, S},
title = {Let's chat: Communication between electroactive microorganisms.},
journal = {Bioresource technology},
volume = {347},
number = {},
pages = {126705},
doi = {10.1016/j.biortech.2022.126705},
pmid = {35065228},
issn = {1873-2976},
support = {864669/ERC_/European Research Council/International ; },
mesh = {*Bioelectric Energy Sources ; Biofilms ; Communication ; Electrodes ; Electrons ; },
abstract = {Electroactive microorganisms can exchange electrons with other cells or conductive interfaces in their extracellular environment. This property opens the way to a broad range of practical biotechnological applications, from manufacturing sustainable chemicals via electrosynthesis, to bioenergy, bioelectronics or improved, low-energy demanding wastewater treatments. Besides, electroactive microorganisms play key roles in environmental bioremediation, significantly impacting process efficiencies. This review highlights our present knowledge on microbial interactions promoting the communication between electroactive microorganisms in a biofilm on an electrode in bioelectrochemical systems (BES). Furthermore, the immediate knowledge gaps that must be closed to develop novel technologies will also be acknowledged.},
}
@article {pmid35064809,
year = {2023},
author = {Tan, Y and Wang, J and He, Y and Yu, X and Chen, S and Penttinen, P and Liu, S and Yang, Y and Zhao, K and Zou, L},
title = {Organic Fertilizers Shape Soil Microbial Communities and Increase Soil Amino Acid Metabolites Content in a Blueberry Orchard.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {232-246},
pmid = {35064809},
issn = {1432-184X},
support = {KLSFGAGP2020.003//Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda/ ; 2020YJ0338//Department of Science and Technology of Sichuan Province/ ; 2020ZHCG0044//Department of Science and Technology of Sichuan Province/ ; 21GJHZ0113//Department of Science and Technology of Sichuan Province/ ; },
mesh = {Animals ; Cattle ; Soil/chemistry ; Fertilizers/analysis ; *Blueberry Plants/metabolism ; Nitrogen/metabolism ; *Microbiota ; Bacteria ; *Ascomycota/metabolism ; Soil Microbiology ; },
abstract = {The decline in soil nutrients is becoming a major concern of soil degradation. The possibility of using organic waste as a soil additive to increase nutrients and essential components is significant in soil quality protection and waste management. The aim of this study was to investigate the effects of composted spent mushroom substrate (MS), giant panda feces (PF), and cattle manure (CM) as organic fertilizers in soil microbial communities and metabolites in blueberry orchard in China, which were measured by using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomics. Altogether, 45.66% of the bacterial operational taxonomic units (OTUs) and 9.08% of the fungal OTUs were detected in all treatments. Principal coordinates analysis demonstrated that the bacterial and fungal communities in MS and PF treatments were similar, whereas the communities in the not-organic fertilized control (CK) were significantly different from those in the organic fertilizer treatments. Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant bacterial phyla, and Basidiomycota, Ascomycota, and Mortierellomycota the dominant fungal phyla. Redundancy analysis indicated that pH and available potassium were the main factors determining the composition of microbial communities. The fungal genera Postia, Cephalotrichum, and Thermomyces increased in organic fertilizer treatments, and likely promoted the degradation of organic fertilizers into low molecular-weight metabolites (e.g., amino acids). PCA and PLS-DA models showed that the metabolites in CK were different from those in the other three treatments, and those in CM were clearly different from those in MS and PF. Co-occurrence network analysis showed that several taxa correlated positively with amino acid contents. The results of this study provide new insights into organic waste reutilization and new directions for further studies.},
}
@article {pmid35064808,
year = {2023},
author = {Cicala, F and Cisterna-Céliz, JA and Paolinelli, M and Moore, JD and Sevigny, J and Rocha-Olivares, A},
title = {The Role of Diversity in Mediating Microbiota Structural and Functional Differences in Two Sympatric Species of Abalone Under Stressed Withering Syndrome Conditions.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {277-287},
pmid = {35064808},
issn = {1432-184X},
support = {2011-CO1-163322//sagarpa-conacyt/ ; CN-14-14//uc mexus-conacyt/ ; Fund for Scientific Research//cicese/ ; Technological Development FID-2012-01//cicese/ ; },
mesh = {Animals ; Sympatry ; *Gastropoda/microbiology ; *Microbiota ; Proteobacteria/genetics ; *Gastrointestinal Microbiome ; },
abstract = {Withering syndrome (WS) is a gastro-intestinal (GI) infectious disease likely affecting all abalone species worldwide. Structural and functional changes in abalone GI microbiotas under WS-stressed conditions remain poorly investigated. It is unclear if interspecific microbiota differences, such as the presence of certain microbes, their abundance, and functional capabilities, may be involved in the occurrence of this disease. Bacterial microbiotas of healthy Haliotis fulgens and Haliotis corrugata are mainly composed by Tenericutes, Proteobacteria, Fusobacteria, and Spirochaetes. We previously reported species-specific structural and functional profiles of those communities and suggested that they are of consequence to the different susceptibility of each species to WS. Here, we address this question by comparing the structure and function of healthy and dysbiotic microbiota through 454 pyrosequencing and PICRUSt 2, respectively. Our findings suggest that the extent to which WS-stressed conditions may explain structural and functional differences in GI microbiota is contingent on the microbiota diversity itself. Indeed, microbiota differences between stressed and healthy abalone were marginal in the more complex bacterial communities of H. corrugata, in which no significant structural or functional changes were detected. Conversely, significant structural changes were observed in the less complex bacterial microbiota of H. fulgens. Moreover, structural alterations led to a significant downregulation of some metabolic activities conducted by GI bacteria. Accordingly, results suggest that gastro-intestinal bacterial diversity appears to be related with both the health of abalone and the etiology of WS.},
}
@article {pmid35064419,
year = {2022},
author = {Berrios, L},
title = {The genus Caulobacter and its role in plant microbiomes.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {38},
number = {3},
pages = {43},
pmid = {35064419},
issn = {1573-0972},
support = {2109481//National Science Foundation/ ; },
mesh = {Arabidopsis/microbiology ; Biomass ; Caulobacter/*classification/*physiology ; Citrullus/microbiology ; *Host Microbial Interactions ; *Microbiota ; *Plant Growth Regulators ; Plants/*microbiology ; Zea mays/microbiology ; },
abstract = {Recent omics approaches have revealed the prevalent microbial taxa that constitute the microbiome of various plant species. Across global scales and environmental conditions, strains belonging to the bacterial genus Caulobacter have consistently been found in association with various plant species. Aligned with agroecological relevance and biotechnological advances, many scientific communications have demonstrated that several Caulobacter strains (spanning several Caulobacter species) harbor the potential to enhance plant biomass for various plant species ranging from Arabidopsis to Citrullus and Zea mays. In the past several years, co-occurrence data have driven mechanistically resolved communications about select Caulobacter-plant interactions. Given the long-standing history of Caulobacter as a model organism for cell cycle regulation, genetic studies, and the prevalence of Caulobacter species in various plant microbiomes, the genus Caulobacter offers researchers a unique opportunity to leverage for investigating plant-microbe interactions and realizing targeted biotechnological applications. In this review, recent developments regarding Caulobacter-plant interactions are presented in terms of model utility for future biotechnological investigations.},
}
@article {pmid35061792,
year = {2022},
author = {Guo, Z and Lv, L and Liu, D and He, X and Wang, W and Feng, Y and Islam, MS and Wang, Q and Chen, W and Liu, Z and Wu, S and Abied, A},
title = {A global meta-analysis of animal manure application and soil microbial ecology based on random control treatments.},
journal = {PloS one},
volume = {17},
number = {1},
pages = {e0262139},
pmid = {35061792},
issn = {1932-6203},
mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Betaproteobacteria/genetics/isolation &amp; purification ; Biomass ; Databases, Factual ; Fungi/genetics/isolation &amp; purification ; Manure/*analysis/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; RNA, Ribosomal, 18S/genetics/metabolism ; *Soil Microbiology ; },
abstract = {The processes involved in soil domestication have altered the soil microbial ecology. We examined the question of whether animal manure application affects the soil microbial ecology of farmlands. The effects of global animal manure application on soil microorganisms were subjected to a meta-analysis based on randomized controlled treatments. A total of 2303 studies conducted in the last 30 years were incorporated into the analysis, and an additional 45 soil samples were collected and sequenced to obtain 16S rRNA and 18S rRNA data. The results revealed that manure application increased soil microbial biomass. Manure application alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) and inhibited and reduced fungal diversity (M-Z: -1.15 and M-I: -1.03). Inorganic fertilizer replaced cattle and swine manure and provided nutrients to soil microorganisms. The soil samples of the experimental base were analyzed, and the relative abundances of bacteria and fungi were altered compared with no manure application. Manure increased bacterial diversity and reduced fungal diversity. Mrakia frigida and Betaproteobacteriales, which inhibit other microorganisms, increased significantly in the domesticated soil. Moreover, farm sewage treatments resulted in a bottleneck in the manure recovery rate that should be the focus of future research. Our results suggest that the potential risks of restructuring the microbial ecology of cultivated land must be considered.},
}
@article {pmid35061090,
year = {2023},
author = {Yang, Y and Hu, L and Li, X and Wang, J and Jin, G},
title = {Nitrogen Fixation and Diazotrophic Community in Plastic-Eating Mealworms Tenebrio molitor L.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {264-276},
pmid = {35061090},
issn = {1432-184X},
mesh = {Animals ; *Tenebrio/metabolism/microbiology ; Plastics ; Polystyrenes/metabolism ; Nitrogen Fixation ; Biodegradation, Environmental ; Larva/microbiology ; Carbon/metabolism ; Nitrogen/metabolism ; },
abstract = {Mealworms, the larvae of a coleopteran insect Tenebrio molitor L., are capable of eating, living on, and degrading non-hydrolyzable vinyl plastics as sole diet. However, vinyl plastics are carbon-rich but nitrogen-deficient. It remains puzzling how plastic-eating mealworms overcome the nutritional obstacle of nitrogen limitation. Here, we provide the evidence for nitrogen fixation activity within plastic-eating mealworms. Acetylene reduction assays illustrate that the nitrogen-fixing activity ranges from 12.3 ± 0.7 to 32.9 ± 9.3 nmol ethylene·h[-1]·gut[-1] and the corresponding fixed nitrogen equivalents of protein are estimated as 8.6 to 23.0 µg per day per mealworm. Nature nitrogen isotopic analyses of plastic-eating mealworms provide further evidence for the assimilation of fixed nitrogen as a new nitrogen source. Eliminating the gut microbial microbiota with antibiotics impairs the mealworm's ability to fix nitrogen from the atmosphere, indicating the contribution of gut microbiota to nitrogen fixation. By using the traditional culture-dependent technique, PCR and RT-PCR of nifH gene, nitrogen-fixing bacteria diversity within the gut was detected, and the genus Klebsiella was demonstrated to be an important nitrogen-fixing symbiont. These findings first build the relationship between plastic degradation (carbon metabolism) and nitrogen fixation (nitrogen metabolism) within mealworms. Combined with previously reported plastic-degrading capability and nitrogen-fixing activity, mealworms may be potential candidates for up-recycling of plastic waste to produce protein sources.},
}
@article {pmid35059821,
year = {2023},
author = {Mancini, E and Sabatelli, S and Hu, Y and Frasca, S and Di Giulio, A and Audisio, P and Brown, CD and Russell, JA and Trizzino, M},
title = {Uncovering Active Bacterial Symbionts in Three Species of Pollen-feeding Beetles (Nitidulidae: Meligethinae).},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {335-339},
pmid = {35059821},
issn = {1432-184X},
support = {1442144//national science foundation/ ; RP120172B8C07DF1//sapienza universit&#xe0; di roma/ ; CAL/2016//universit&#xe0; degli studi roma tre/ ; },
mesh = {Animals ; *Coleoptera ; RNA, Ribosomal, 16S/genetics ; Insecta ; Pollen ; Plants ; },
abstract = {Microbial symbionts enable many phytophagous insects to specialize on plant-based diets through a range of metabolic services. Pollen comprises one-plant tissue consumed by such herbivores. While rich in lipids and proteins, its nutrient content is often imbalanced and difficult-to-access due to a digestibly recalcitrant cell wall. Pollen quality can be further degraded by harmful allelochemicals. To identify microbes that may aid in palynivory, we performed cDNA-based 16S rRNA metabarcoding on three related pollen beetles (Nitidulidae: Meligethinae) exhibiting different dietary breadths: Brassicogethes aeneus, B. matronalis, and Meligethes atratus. Nine bacterial symbionts (i.e., 97% OTUs) exhibited high metabolic activity during active feeding. Subsequent PCR surveys revealed varying prevalence of those from three Rickettsialles genera-Lariskella, Rickettsia, and Wolbachia-within beetle populations. Our findings lay the groundwork for future studies on the influence of phylogeny and diet on palynivorous insect microbiomes, and roles of symbionts in the use of challenging diets.},
}
@article {pmid35059602,
year = {2022},
author = {Weber, PM and Paredes, GF and Viehboeck, T and Pende, N and Volland, JM and Gros, O and VanNieuwenhze, M and Ott, J and Bulgheresi, S},
title = {FtsZ-mediated fission of a cuboid bacterial symbiont.},
journal = {iScience},
volume = {25},
number = {1},
pages = {103552},
pmid = {35059602},
issn = {2589-0042},
support = {P 31594/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Less than a handful of cuboid and squared cells have been described in nature, which makes them a rarity. Here, we show how Candidatus Thiosymbion cuboideus, a cube-like gammaproteobacterium, reproduces on the surface of marine free-living nematodes. Immunostaining of symbiont cells with an anti-fimbriae antibody revealed that they are host-polarized, as these appendages exclusively localized at the host-proximal (animal-attached) pole. Moreover, by applying a fluorescently labeled metabolic probe to track new cell wall insertion in vivo, we observed that the host-attached pole started septation before the distal one. Similarly, Ca. T. cuboideus cells immunostained with an anti-FtsZ antibody revealed a proximal-to-distal localization pattern of this tubulin homolog. Although FtsZ has been shown to arrange into squares in synthetically remodeled cuboid cells, here we show that FtsZ may also mediate the division of naturally occurring ones. This implies that, even in natural settings, membrane roundness is not required for FtsZ function.},
}
@article {pmid35059423,
year = {2021},
author = {van der Goot, E and Vink, SN and van Vliet, D and van Spronsen, FJ and Falcao Salles, J and van der Zee, EA},
title = {Gut-Microbiome Composition in Response to Phenylketonuria Depends on Dietary Phenylalanine in BTBR Pah[enu2] Mice.},
journal = {Frontiers in nutrition},
volume = {8},
number = {},
pages = {735366},
pmid = {35059423},
issn = {2296-861X},
abstract = {Phenylketonuria (PKU) is a metabolic disorder caused by a hepatic enzyme deficiency causing high blood and brain levels of the amino acid Phenylalanine (Phe), leading to severe cognitive and psychological deficits that can be prevented, but not completely, by dietary treatment. The behavioral outcome of PKU could be affected by the gut-microbiome-brain axis, as diet is one of the major drivers of the gut microbiome composition. Gut-microbiome alterations have been reported in treated patients with PKU, although the question remains whether this is due to PKU, the dietary treatment, or their interaction. We, therefore, examined the effects of dietary Phe restriction on gut-microbiome composition and relationships with behavioral outcome in mice. Male and female BTBR Pah[enu2] mice received either a control diet (normal protein, "high" Phe), liberalized Phe-restricted (33% natural protein restriction), or severe Phe-restricted (75% natural protein restriction) diet with protein substitutes for 10 weeks (n = 14 per group). Their behavioral performance was examined in an open field test, novel and spatial object location tests, and a balance beam. Fecal samples were collected and sequenced for the bacterial 16S ribosomal RNA (rRNA) region. Results indicated that PKU on a high Phe diet reduced Shannon diversity significantly and altered the microbiome composition compared with wild-type animals. Phe-restriction prevented this loss in Shannon diversity but changed community composition even more than the high-Phe diet, depending on the severity of the restriction. Moreover, on a taxonomic level, we observed the highest number of differentially abundant genera in animals that received 75% Phe-restriction. Based on correlation analyses with differentially abundant taxa, the families Entereococacceae, Erysipelotrichaceae, Porphyromonadaceae, and the genus Alloprevotella showed interesting relationships with either plasma Phe levels and/or object memory. According to our results, these bacterial taxa could be good candidates to start examining the microbial metabolic potential and probiotic properties in the context of PKU. We conclude that PKU leads to an altered gut microbiome composition in mice, which is least severe on a liberalized Phe-restricted diet. This may suggest that the current Phe-restricted diet for PKU patients could be optimized by taking dietary effects on the microbiome into account.},
}
@article {pmid35059329,
year = {2021},
author = {Zuppi, M and Hendrickson, HL and O'Sullivan, JM and Vatanen, T},
title = {Phages in the Gut Ecosystem.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {822562},
pmid = {35059329},
issn = {2235-2988},
mesh = {Bacteria ; *Bacteriophages ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Viruses ; },
abstract = {Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the most abundant biological entities on earth found in every explored environment, from the deep sea to the Sahara Desert. Phages are abundant within the human biome and are gaining increasing recognition as potential modulators of the gut ecosystem. For example, they have been connected to gastrointestinal diseases and the treatment efficacy of Fecal Microbiota Transplant. The ability of phages to modulate the human gut microbiome has been attributed to the predation of bacteria or the promotion of bacterial survival by the transfer of genes that enhance bacterial fitness upon infection. In addition, phages have been shown to interact with the human immune system with variable outcomes. Despite the increasing evidence supporting the importance of phages in the gut ecosystem, the extent of their influence on the shape of the gut ecosystem is yet to be fully understood. Here, we discuss evidence for phage modulation of the gut microbiome, postulating that phages are pivotal contributors to the gut ecosystem dynamics. We therefore propose novel research questions to further elucidate the role(s) that they have within the human ecosystem and its impact on our health and well-being.},
}
@article {pmid35058901,
year = {2021},
author = {Gruet, C and Muller, D and Moënne-Loccoz, Y},
title = {Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {782135},
pmid = {35058901},
issn = {1664-302X},
abstract = {Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.},
}
@article {pmid35058082,
year = {2022},
author = {Cunillera-Montcusí, D and Beklioğlu, M and Cañedo-Argüelles, M and Jeppesen, E and Ptacnik, R and Amorim, CA and Arnott, SE and Berger, SA and Brucet, S and Dugan, HA and Gerhard, M and Horváth, Z and Langenheder, S and Nejstgaard, JC and Reinikainen, M and Striebel, M and Urrutia-Cordero, P and Vad, CF and Zadereev, E and Matias, M},
title = {Freshwater salinisation: a research agenda for a saltier world.},
journal = {Trends in ecology &amp; evolution},
volume = {37},
number = {5},
pages = {440-453},
doi = {10.1016/j.tree.2021.12.005},
pmid = {35058082},
issn = {1872-8383},
mesh = {Biodiversity ; Biological Evolution ; Climate Change ; *Ecosystem ; *Fresh Water ; Humans ; },
abstract = {The widespread salinisation of freshwater ecosystems poses a major threat to the biodiversity, functioning, and services that they provide. Human activities promote freshwater salinisation through multiple drivers (e.g., agriculture, resource extraction, urbanisation) that are amplified by climate change. Due to its complexity, we are still far from fully understanding the ecological and evolutionary consequences of freshwater salinisation. Here, we assess current research gaps and present a research agenda to guide future studies. We identified different gaps in taxonomic groups, levels of biological organisation, and geographic regions. We suggest focusing on global- and landscape-scale processes, functional approaches, genetic and molecular levels, and eco-evolutionary dynamics as key future avenues to predict the consequences of freshwater salinisation for ecosystems and human societies.},
}
@article {pmid35056609,
year = {2022},
author = {Tsigkrimani, M and Bakogianni, M and Paramithiotis, S and Bosnea, L and Pappa, E and Drosinos, EH and Skandamis, PN and Mataragas, M},
title = {Microbial Ecology of Artisanal Feta and Kefalograviera Cheeses, Part I: Bacterial Community and Its Functional Characteristics with Focus on Lactic Acid Bacteria as Determined by Culture-Dependent Methods and Phenotype Microarrays.},
journal = {Microorganisms},
volume = {10},
number = {1},
pages = {},
pmid = {35056609},
issn = {2076-2607},
support = {T1EDK-02087//European Union and Greek national funds/ ; },
abstract = {Artisanal cheesemaking is still performed using practices and conditions derived from tradition. Feta and Kefalograviera cheeses are very popular in Greece and have met worldwide commercial success. However, there is a lack of knowledge regarding their lactic acid microecosystem composition and species dynamics during ripening. Thus, the aim of the present study was to assess the microecosystem as well as the autochthonous lactic acid microbiota during the ripening of artisanal Feta and Kefalograviera cheeses. For that purpose, raw sheep's milk intended for cheesemaking, as well as Feta and Kefalograviera cheeses during early and late ripening were analyzed, and the lactic acid microbiota was identified using the classical phenotypic approach, clustering with PCR-RAPD and identification with sequencing of the 16S-rRNA gene, as well as with the Biolog GEN III microplates. In addition, the functional properties of the bacterial community were evaluated using the Biolog EcoPlates, which consists of 31 different carbon sources. In general, concordance between the techniques used was achieved. The most frequently isolated species from raw sheep's milk were Enteroroccus faecium, Lactiplantibacillus plantarum and Pediococcus pentosaceus. The microecosystem of Feta cheese in the early ripening stage was dominated by Lp. plantarum and E. faecium, whereas, in late ripening, the microecosystem was dominated by Weissella paramesenteroides. The microecosystem of Kefalograviera cheese in the early ripening stage was dominated by Levilactobacillus brevis and E. faecium, and in late ripening by W. paramesenteroides and E. faecium. Finally, Carbohydrates was the main carbon source category that metabolized by all microbial communities, but the extent of their utilization was varied. Kefalograviera samples, especially at early ripening, demonstrated higher metabolic activity compared to Feta cheese. However, dominating species within microbial communities of the cheese samples were not significantly different.},
}
@article {pmid35052986,
year = {2022},
author = {Lammers, A and Lalk, M and Garbeva, P},
title = {Air Ambulance: Antimicrobial Power of Bacterial Volatiles.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
pmid = {35052986},
issn = {2079-6382},
support = {398967434 - SFB/TRR261//Deutsche Forschungsgemeinschaft/ ; W10/2018//Wissenschaftsgemeinschaft Gottfried Wilhelm Leibniz e. V. via Leibniz WissenschaftsCampus - ComBioCat/ ; NNF16OC0021110//Novo Nordisk Foundation/ ; },
abstract = {We are currently facing an antimicrobial resistance crisis, which means that a lot of bacterial pathogens have developed resistance to common antibiotics. Hence, novel and innovative solutions are urgently needed to combat resistant human pathogens. A new source of antimicrobial compounds could be bacterial volatiles. Volatiles are ubiquitous produced, chemically divers and playing essential roles in intra- and interspecies interactions like communication and antimicrobial defense. In the last years, an increasing number of studies showed bioactivities of bacterial volatiles, including antibacterial, antifungal and anti-oomycete activities, indicating bacterial volatiles as an exciting source for novel antimicrobial compounds. In this review we introduce the chemical diversity of bacterial volatiles, their antimicrobial activities and methods for testing this activity. Concluding, we discuss the possibility of using antimicrobial volatiles to antagonize the antimicrobial resistance crisis.},
}
@article {pmid35051349,
year = {2022},
author = {Aranda-Díaz, A and Ng, KM and Thomsen, T and Real-Ramírez, I and Dahan, D and Dittmar, S and Gonzalez, CG and Chavez, T and Vasquez, KS and Nguyen, TH and Yu, FB and Higginbottom, SK and Neff, NF and Elias, JE and Sonnenburg, JL and Huang, KC},
title = {Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota.},
journal = {Cell host &amp; microbe},
volume = {30},
number = {2},
pages = {260-272.e5},
pmid = {35051349},
issn = {1934-6069},
support = {R01 DK085025/DK/NIDDK NIH HHS/United States ; RM1 GM135102/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bacteria ; Bacteroides ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Microbiota ; },
abstract = {Efforts to probe the role of the gut microbiota in disease would benefit from a system in which patient-derived bacterial communities can be studied at scale. We addressed this by validating a strategy to propagate phylogenetically complex, diverse, stable, and highly reproducible stool-derived communities in vitro. We generated hundreds of in vitro communities cultured from diverse stool samples in various media; certain media generally preserved inoculum composition, and inocula from different subjects yielded source-specific community compositions. Upon colonization of germ-free mice, community composition was maintained, and the host proteome resembled the host from which the community was derived. Treatment with ciprofloxacin in vivo increased susceptibility to Salmonella invasion in vitro, and the in vitro response to ciprofloxacin was predictive of compositional changes observed in vivo, including the resilience and sensitivity of each Bacteroides species. These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.},
}
@article {pmid35049116,
year = {2022},
author = {Quiroga, MV and Valverde, A and Mataloni, G and Casa, V and Stegen, JC and Cowan, D},
title = {The ecological assembly of bacterial communities in Antarctic wetlands varies across levels of phylogenetic resolution.},
journal = {Environmental microbiology},
volume = {24},
number = {8},
pages = {3486-3499},
pmid = {35049116},
issn = {1462-2920},
mesh = {Antarctic Regions ; Bacteria/genetics ; *Ecosystem ; Phylogeny ; *Wetlands ; },
abstract = {As functional traits are conserved at different phylogenetic depths, the ability to detect community assembly processes can be conditional on the phylogenetic resolution; yet most previous work quantifying their influence has focused on a single level of phylogenetic resolution. Here, we have studied the ecological assembly of bacterial communities from an Antarctic wetland complex, applying null models across different levels of phylogenetic resolution (i.e. clustering ASVs into OTUs with decreasing sequence identity thresholds). We found that the relative influence of the community assembly processes varies with phylogenetic resolution. More specifically, selection processes seem to impose stronger influence at finer (100% sequence similarity ASV) than at coarser (99%-97% sequence similarity OTUs) resolution. We identified environmental features related with the ecological processes and propose a conceptual model for the bacterial community assembly in this Antarctic ecosystem. Briefly, eco-evolutionary processes appear to be leading to different but very closely related ASVs in lotic, lentic and terrestrial environments. In all, this study shows that assessing community assembly processes at different phylogenetic resolutions is key to improve our understanding of microbial ecology. More importantly, a failure to detect selection processes at coarser phylogenetic resolution does not imply the absence of such processes at finer resolutions.},
}
@article {pmid35048168,
year = {2023},
author = {Boscaro, V and Manassero, V and Keeling, PJ and Vannini, C},
title = {Single-cell Microbiomics Unveils Distribution and Patterns of Microbial Symbioses in the Natural Environment.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {307-316},
pmid = {35048168},
issn = {1432-184X},
mesh = {Humans ; Phylogeny ; *Ciliophora/microbiology ; Bacteria/genetics ; Environment ; Symbiosis ; Rickettsiales ; *Euplotes/microbiology ; *Burkholderiaceae ; },
abstract = {Protist-bacteria associations are extremely common. Among them, those involving ciliates of the genus Euplotes are emerging as models for symbioses between prokaryotes and eukaryotes, and a great deal of information is available from cultured representatives of this system. Even so, as for most known microbial symbioses, data on natural populations is lacking, and their ecology remains largely unexplored; how well lab cultures represent actual diversity is untested. Here, we describe a survey on natural populations of Euplotes based on a single-cell microbiomic approach, focusing on taxa that include known endosymbionts of this ciliate. The results reveal an unexpected variability in symbiotic communities, with individual hosts of the same population harboring different sets of bacterial endosymbionts. Co-occurring Euplotes individuals of the same population can even have different essential symbionts, Polynucleobacter and "Candidatus Protistobacter," which might suggest that replacement events could be more frequent in nature than previously hypothesized. Accessory symbionts are even more variable: some showed a strong affinity for one host species, some for a sampling site, and two ("Candidatus Cyrtobacter" and "Candidatus Anadelfobacter") displayed an unusual pattern of competitive exclusion. These data represent the first insight into the prevalence and patterns of bacterial symbionts in natural populations of free-living protists.},
}
@article {pmid35044804,
year = {2022},
author = {Chen, MY and Alexiev, A and McKenzie, VJ},
title = {Bacterial Biofilm Thickness and Fungal Inhibitory Bacterial Richness Both Prevent Establishment of the Amphibian Fungal Pathogen Batrachochytrium dendrobatidis.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {5},
pages = {e0160421},
pmid = {35044804},
issn = {1098-5336},
mesh = {Amphibians/genetics/microbiology ; Animals ; Bacteria ; Batrachochytrium ; Biofilms ; *Chytridiomycota/genetics ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; },
abstract = {Host-associated microbial biofilms can provide protection against pathogen establishment. In many host-microbe symbioses (including, but not limited to humans, plants, insects, and amphibians), there is a correlation between host-associated microbial diversity and pathogen infection risk. Diversity may prevent infection by pathogens through sampling effects and niche complementarity, but an alternative hypothesis may be that microbial biomass is confounded with diversity and that host-associated biofilms are deterring pathogen establishment through space preemption. In this study, we use the amphibian system as a model for host-microbe-pathogen interactions to ask two questions: (i) is bacterial richness confounded with biofilm thickness or cell density, and (ii) to what extent do biofilm thickness, cell density, and bacterial richness each deter the establishment of the amphibian fungal pathogen Batrachochytrium dendrobatidis? To answer these questions, we built a custom biofilm microcosm that mimics the host-environment interface by allowing nutrients to diffuse out of a fine-pore biofilm scaffolding. This created a competitive environment in which bacteria and the fungal pathogen compete for colonization space. We then challenged bacterial biofilms ranging in community richness, biofilm thickness, bacterial cell density, and B. dendrobatidis (also known as Bd)-inhibitory metabolite production with live B. dendrobatidis zoospores to determine how B. dendrobatidis establishment success on membranes varies. We found that biofilm thickness and B. dendrobatidis-inhibitory isolate richness work in complement to reduce B. dendrobatidis establishment success. This work underscores that physical aspects of biofilm communities can play a large role in pathogen inhibition, and in many studies, these traits are not studied. IMPORTANCE Our finding highlights the fact that diversity, as measured through 16S rRNA gene sequencing, may obscure the true mechanisms behind microbe-mediated pathogen defense and that physical space occupation by biofilm-forming symbionts may significantly contribute to pathogen protection. These findings have implications across a wide range of host-microbe systems since 16S rRNA gene sequencing is a standard tool used across many microbial systems. Further, our results are potentially relevant to many host-pathogen systems since host-associated bacterial biofilms are ubiquitous.},
}
@article {pmid35043221,
year = {2023},
author = {Kanisan, DP and Quek, ZBR and Oh, RM and Afiq-Rosli, L and Lee, JN and Huang, D and Wainwright, BJ},
title = {Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {37-48},
pmid = {35043221},
issn = {1432-184X},
mesh = {Animals ; *Anthozoa/microbiology ; Malaysia ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Coral Reefs ; },
abstract = {Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.},
}
@article {pmid35043220,
year = {2023},
author = {Song, B and Li, Y and Yang, L and Shi, H and Li, L and Bai, W and Zhao, Y},
title = {Soil Acidification Under Long-Term N Addition Decreases the Diversity of Soil Bacteria and Fungi and Changes Their Community Composition in a Semiarid Grassland.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {221-231},
pmid = {35043220},
issn = {1432-184X},
support = {31800403//National Natural Science Foundation of China/ ; 41977009//National Natural Science Foundation of China/ ; 41977039//National Natural Science Foundation of China/ ; ZR2020QD115//Natural Science Foundation of Shandong Province/ ; },
mesh = {*Soil/chemistry ; Grassland ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; Fungi/genetics ; Hydrogen-Ion Concentration ; },
abstract = {Soil microorganisms play key roles in terrestrial biogeochemical cycles and ecosystem functions. However, few studies address how long-term nitrogen (N) addition gradients impact soil bacterial and fungal diversity and community composition simultaneously. Here, we investigated soil bacterial and fungal diversity and community composition based on a long-term (17 years) N addition gradient experiment (six levels: 0, 2, 4, 8, 16, 32 gN m[-2] year[-1]) in temperate grassland, using the high-throughput Illumina MiSeq sequencing. Results showed that both soil bacterial and fungal alpha diversity responded nonlinearly to the N input gradient and reduced drastically when the N addition rate reached 32 g N m[-2] year[-1]. The relative abundance of soil bacterial phyla Proteobacteria increased and Acidobacteria decreased significantly with increasing N level. In addition, the relative abundance of bacterial functional groups associated with aerobic ammonia oxidation, aerobic nitrite oxidation, nitrification, respiration of sulfate and sulfur compounds, and chitinolysis significantly decreased under the highest N addition treatment. For soil fungi, the relative abundance of Ascomycota increased linearly along the N enrichment gradient. These results suggest that changes in soil microbial community composition under elevated N do not always support the copiotrophic-oligotrophic hypothesis, and some certain functional bacteria would not simply be controlled by soil nutrients. Further analysis illustrated that reduced soil pH under N addition was the main factor driving variations in soil microbial diversity and community structure in this grassland. Our findings highlight the consistently nonlinear responses of soil bacterial and fungal diversity to increasing N input and the significant effects of soil acidification on soil microbial communities, which can be helpful for the prediction of underground ecosystem processes in light of future rising N deposition.},
}
@article {pmid35042853,
year = {2022},
author = {Kauffman, KM and Chang, WK and Brown, JM and Hussain, FA and Yang, J and Polz, MF and Kelly, L},
title = {Resolving the structure of phage-bacteria interactions in the context of natural diversity.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {372},
pmid = {35042853},
issn = {2041-1723},
mesh = {Bacteria/*genetics/*virology ; Bacteriophages/*genetics ; *Genetic Variation ; Genome, Viral ; Host Specificity ; Models, Biological ; Nucleotides/metabolism ; Phylogeny ; Recombinases/metabolism ; Recombination, Genetic/genetics ; Sequence Analysis, DNA ; Vibrio/virology ; },
abstract = {Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse-with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.},
}
@article {pmid35042205,
year = {2022},
author = {Taylor, D and Verdon, N and Lomax, P and Allen, RJ and Titmuss, S},
title = {Tracking the stochastic growth of bacterial populations in microfluidic droplets.},
journal = {Physical biology},
volume = {19},
number = {2},
pages = {026003},
pmid = {35042205},
issn = {1478-3975},
support = {682237/ERC_/European Research Council/International ; },
mesh = {*Bacteria ; *Microfluidics/methods ; },
abstract = {Bacterial growth in microfluidic droplets is relevant in biotechnology, in microbial ecology, and in understanding stochastic population dynamics in small populations. However, it has proved challenging to automate measurement of absolute bacterial numbers within droplets, forcing the use of proxy measures for population size. Here we present a microfluidic device and imaging protocol that allows high-resolution imaging of thousands of droplets, such that individual bacteria stay in the focal plane and can be counted automatically. Using this approach, we track the stochastic growth of hundreds of replicateEscherichia colipopulations within droplets. We find that, for early times, the statistics of the growth trajectories obey the predictions of the Bellman-Harris model, in which there is no inheritance of division time. Our approach should allow further testing of models for stochastic growth dynamics, as well as contributing to broader applications of droplet-based bacterial culture.},
}
@article {pmid35041070,
year = {2023},
author = {Runge, P and Ventura, F and Kemen, E and Stam, R},
title = {Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {168-183},
pmid = {35041070},
issn = {1432-184X},
support = {STA1547/2//german science foundation/ ; ERC-2018-COG 820124/ERC_/European Research Council/International ; ERC-2018-COG 820124/ERC_/European Research Council/International ; },
mesh = {*Solanum lycopersicum ; Dysbiosis ; Peru ; *Microbiota ; Plant Leaves/microbiology ; Plants/microbiology ; *Solanum ; },
abstract = {Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.},
}
@article {pmid35040702,
year = {2022},
author = {Dragone, NB and Henley, JB and Holland-Moritz, H and Diaz, M and Hogg, ID and Lyons, WB and Wall, DH and Adams, BJ and Fierer, N},
title = {Elevational Constraints on the Composition and Genomic Attributes of Microbial Communities in Antarctic Soils.},
journal = {mSystems},
volume = {7},
number = {1},
pages = {e0133021},
pmid = {35040702},
issn = {2379-5077},
mesh = {*Soil/chemistry ; Antarctic Regions ; Soil Microbiology ; Bacteria ; Archaea ; *Microbiota ; Metagenomics/methods ; },
abstract = {The inland soils found on the Antarctic continent represent one of the more challenging environments for microbial life on Earth. Nevertheless, Antarctic soils harbor unique bacterial and archaeal (prokaryotic) communities able to cope with extremely cold and dry conditions. These communities are not homogeneous, and the taxonomic composition and functional capabilities (genomic attributes) of these communities across environmental gradients remain largely undetermined. We analyzed the prokaryotic communities in soil samples collected from across the Shackleton Glacier region of Antarctica by coupling quantitative PCR, marker gene amplicon sequencing, and shotgun metagenomic sequencing. We found that elevation was the dominant factor explaining differences in the structures of the soil prokaryotic communities, with the drier and saltier soils found at higher elevations harboring less diverse communities and unique assemblages of cooccurring taxa. The higher-elevation soil communities also had lower maximum potential growth rates (as inferred from metagenome-based estimates of codon usage bias) and an overrepresentation of genes associated with trace gas metabolism. Together, these results highlight the utility of assessing community shifts across pronounced environmental gradients to improve our understanding of the microbial diversity found in Antarctic soils and the strategies used by soil microbes to persist at the limits of habitability. IMPORTANCE Antarctic soils represent an ideal system to study how environmental properties shape the taxonomic and functional diversity of microbial communities given the relatively low diversity of Antarctic soil microbial communities and the pronounced environmental gradients that occur across soils located in reasonable proximity to one another. Moreover, the challenging environmental conditions typical of most Antarctic soils present an opportunity to investigate the traits that allow soil microbes to persist in some of the most inhospitable habitats on Earth. We used cultivation-independent methods to study the bacterial and archaeal communities found in soil samples collected from across the Shackleton Glacier region of the Transantarctic Mountains. We show that those environmental characteristics associated with elevation have the greatest impact on the structure of these microbial communities, with the colder, drier, and saltier soils found at higher elevations sustaining less diverse communities that were distinct from those in more hospitable soils with respect to their composition, genomic attributes, and overall life-history strategies. Notably, the harsher conditions found in higher-elevation soils likely select for taxa with lower maximum potential growth rates and an increased reliance on trace gas metabolism to support growth.},
}
@article {pmid35040699,
year = {2022},
author = {David, MM and Tataru, C and Pope, Q and Baker, LJ and English, MK and Epstein, HE and Hammer, A and Kent, M and Sieler, MJ and Mueller, RS and Sharpton, TJ and Tomas, F and Vega Thurber, R and Fern, XZ},
title = {Revealing General Patterns of Microbiomes That Transcend Systems: Potential and Challenges of Deep Transfer Learning.},
journal = {mSystems},
volume = {7},
number = {1},
pages = {e0105821},
pmid = {35040699},
issn = {2379-5077},
mesh = {*Microbiota/physiology ; Machine Learning ; },
abstract = {A growing body of research has established that the microbiome can mediate the dynamics and functional capacities of diverse biological systems. Yet, we understand little about what governs the response of these microbial communities to host or environmental changes. Most efforts to model microbiomes focus on defining the relationships between the microbiome, host, and environmental features within a specified study system and therefore fail to capture those that may be evident across multiple systems. In parallel with these developments in microbiome research, computer scientists have developed a variety of machine learning tools that can identify subtle, but informative, patterns from complex data. Here, we recommend using deep transfer learning to resolve microbiome patterns that transcend study systems. By leveraging diverse public data sets in an unsupervised way, such models can learn contextual relationships between features and build on those patterns to perform subsequent tasks (e.g., classification) within specific biological contexts.},
}
@article {pmid35039906,
year = {2023},
author = {Liu, H and Lin, G and Gao, D and Chen, H and He, M and Lu, J},
title = {Geographic Scale Influences the Interactivities Between Determinism and Stochasticity in the Assembly of Sedimentary Microbial Communities on the South China Sea Shelf.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {121-136},
pmid = {35039906},
issn = {1432-184X},
support = {91858208//National Natural Science Foundation of China/ ; 311020005//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 2019M663209//China Postdoctoral Science Foundation/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Carbon ; China ; },
abstract = {Determinism and stochasticity in microbial community composition decisions have attracted wide attention. However, there is no consensus on their interrelationships and relative importance, and the mechanism controlling the interaction between the two ecological processes remains to be revealed. The interaction of the two ecological processes on the continental shelf of the South China Sea was studied by performing 16S rRNA gene amplicon sequencing on 90 sediments at multiple depths in five sites. Three nearshore sites have higher microbial diversity than those two close to the shelf margin. Different microbial composition was observed between sites and microbial composition of nearshore sites was positively correlated with total nitrogen, total sulfur, total organic carbon, and dissolved oxygen, while that of offshore was positively correlated with total carbon, salinity, and photosynthetically active radiation. The null model test showed that the community composition among layers of the same site and between nearby sites was mainly dominated by the homogeneous selection, while that between distant sites was mainly affected by dispersal limitation, which indicates that geographic scale influences the interactivities of determinism and stochasticity. Our research indicates that the balance of these two ecological processes along the geographic scale is mainly determined by the dispersal ability of microbes and environmental heterogeneity between areas. The study provides new insights into how deterministic and stochastic processes shape microbial community composition on the continental shelf.},
}
@article {pmid35039905,
year = {2023},
author = {Silva-Sanzana, C and Gangas, MV and Zavala, D and Blanco-Herrera, F},
title = {A Recipe for Success: Three Key Strategies Used by Aphids and Pseudomonas syringae to Colonize the Phyllosphere.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {1-8},
pmid = {35039905},
issn = {1432-184X},
support = {1210320//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 3200902//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; PIA/BASAL FB0002//ANID/ ; Programa Iniciativa Cient&#xed;fica Milenio - ICN17_022//ANID/ ; 2021/21211568//ANID/Doctorado Nacional/ ; },
mesh = {Animals ; *Pseudomonas syringae/genetics ; *Aphids ; Phylogeny ; Plants/metabolism ; Plant Diseases ; Bacterial Proteins/genetics ; },
abstract = {Aphids and Pseudomonas syringae are a permanent challenge for agriculture, causing severe losses to the crop industry worldwide. Despite the obvious phylogenetic distance between them, both have become predominant colonizers of the plant kingdom. In this study, we reviewed three key steps of spread and colonization that aphids and P. syringae have mastered to successfully colonize the phyllosphere. These steps involve (i) plant-to-plant movement for locating new nutritional sources, (ii) disruption and modification of the apoplast to facilitate nutrient acquisition, and (iii) suppression of host defenses through effector proteins. In addition, we will provide insights about the direct interaction between aphids and P. syringae and how this yet underrated phenomenon could bring new ecological implications for both organisms beyond their pathogenicity.},
}
@article {pmid35037090,
year = {2023},
author = {Tang, G and Xu, L and Wang, X and Zhang, J},
title = {Effects of Leaf Morphological and Chemical Properties on the Population Sizes of Epiphytes.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {157-167},
pmid = {35037090},
issn = {1432-184X},
mesh = {Population Density ; *Plant Leaves/microbiology ; *Carbohydrates/analysis ; Medicago sativa ; Zea mays ; Sugars/analysis ; },
abstract = {To explore the main factors affecting the distribution of microbes on leaf surfaces, the relationship between population sizes of epiphytes and the morphological structure and main physical and chemical properties of leaves from stylo (Stylosanthes guianensis), alfalfa (Medicago sativa), maize (Zea mays), and cocksfoot (Dactylis glomerata) were investigated. The research results showed that the contents of soluble sugar and total phenolics on the leaf surfaces were positively correlated with those in the leaf tissues (P < 0.001). The leaves with high wax content had better moisture retention capacity. The content of soluble sugar on the leaf surfaces was positively correlated with population sizes of lactic acid bacteria (LAB), aerobic bacteria, yeasts, and molds (P < 0.001). Likewise, a positive correlation was found between the content of inorganic phosphorus on the leaf surfaces and population sizes of LAB and aerobic bacteria. The total amount of wax on leaf surfaces was negatively related to population sizes of microbes, especially aerobic bacteria (P < 0.01) and molds (P < 0.001). On the contrary, the presence of trichomes provides a shelter for epiphytes and was positively correlated with population sizes of epiphytes at different degrees of significance. In conclusion, population sizes of epiphytes on the leaf surfaces were not only affected by chemical properties, but also by morphological traits of leaves.},
}
@article {pmid35034142,
year = {2023},
author = {Tran, HT and Nguyen, HM and Nguyen, TM and Chang, C and Huang, WL and Huang, CL and Chiang, TY},
title = {Microbial Communities Along 2,3,7,8-tetrachlorodibenzodioxin Concentration Gradient in Soils Polluted with Agent Orange Based on Metagenomic Analyses.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {197-208},
pmid = {35034142},
issn = {1432-184X},
support = {105-2622-B-006 -008 -CC2//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Agent Orange ; Soil ; *Polychlorinated Dibenzodioxins/analysis ; *Dioxins ; Bacteria/genetics ; *Microbiota ; Acidobacteria/genetics ; Firmicutes ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The 2,3,7,8-tetrachlorodibenzodioxin (TCDD), a contaminant in Agent Orange released during the US-Vietnam War, led to a severe environmental crisis. Approximately, 50 years have passed since the end of this war, and vegetation has gradually recovered from the pollution. Soil bacterial communities were investigated by 16S metagenomics in habitats with different vegetation physiognomies in Central Vietnam, namely, forests (S0), barren land (S1), grassland (S2), and developing woods (S3). Vegetation complexity was negatively associated with TCDD concentrations, revealing the reasoning behind the utilization of vegetation physiognomy as an indicator for ecological succession along the gradient of pollutants. Stark changes in bacterial composition were detected between S0 and S1, with an increase in Firmicutes and a decrease in Acidobacteria and Bacteroidetes. Notably, dioxin digesters Arthrobacter, Rhodococcus, Comamonadaceae, and Bacialles were detected in highly contaminated soil (S1). Along the TCDD gradients, following the dioxin decay from S1 to S2, the abundance of Firmicutes and Actinobacteria decreased, while that of Acidobacteria increased; slight changes occurred at the phylum level from S2 to S3. Although metagenomics analyses disclosed a trend toward bacterial communities before contamination with vegetation recovery, non-metric multidimensional scaling analysis unveiled a new trajectory deviating from the native state. Recovery of the bacterial community may have been hindered, as indicated by lower bacterial diversity in S3 compared to S0 due to a significant loss of bacterial taxa and recruitment of fewer colonizers. The results indicate that dioxins significantly altered the soil microbiomes into a state of disorder with a deviating trajectory in restoration.},
}
@article {pmid35034141,
year = {2023},
author = {Lin, Y and Ye, G and Hu, HW and Yang, P and Wan, S and Feng, M and He, ZY and He, JZ},
title = {Plant Species-Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {209-220},
pmid = {35034141},
issn = {1432-184X},
support = {41930756//National Natural Science Foundation of China/ ; 42077041//National Natural Science Foundation of China/ ; 2021J011038//Natural Science Foundation of Fujian Province/ ; },
mesh = {*Wetlands ; *Nitrification ; Oxidation-Reduction ; Bacteria ; Ammonia ; Soil/chemistry ; Poaceae ; },
abstract = {Plant species play a crucial role in mediating the activity and community structure of soil microbiomes through differential inputs of litter and rhizosphere exudates, but we have a poor understanding of how plant species influence comammox Nitrospira, a newly discovered ammonia oxidizer with pivotal functionality. Here, we investigate the abundance, diversity, and community structure of comammox Nitrospira underneath five plant species and a bare tidal flat at three soil depths in a subtropical estuarine wetland. Plant species played a critical role in driving the distribution of individual clades of comammox Nitrospira, explaining 59.3% of the variation of community structure. Clade A.1 was widely detected in all samples, while clades A.2.1, A.2.2, A.3 and B showed plant species-dependent distribution patterns. Compared with the native species Cyperus malaccensis, the invasion of Spartina alterniflora increased the network complexity and changed the community structure of comammox Nitrospira, while the invasive effects from Kandelia obovata and Phragmites australis were relatively weak. Soil depths significantly influenced the community structure of comammox Nitrospira, but the effect was much weaker than that from plant species. Altogether, our results highlight the previously unrecognized critical role of plant species in driving the distribution of comammox Nitrospira in a subtropical estuarine wetland.},
}
@article {pmid35033929,
year = {2022},
author = {Sakarika, M and Ganigué, R and Rabaey, K},
title = {Methylotrophs: from C1 compounds to food.},
journal = {Current opinion in biotechnology},
volume = {75},
number = {},
pages = {102685},
doi = {10.1016/j.copbio.2022.102685},
pmid = {35033929},
issn = {1879-0429},
mesh = {Amino Acids/metabolism ; Bacteria/metabolism ; Carbon/metabolism ; Humans ; *Metabolic Engineering ; Methane/metabolism ; *Methanol/metabolism ; },
abstract = {Microbial protein (MP) is back on the table after decades of slumbering interest. One-carbon (C1) substrates are attractive for MP production due to their efficient production from CO2 and renewable electricity, linking carbon capture to food while circumventing agriculture. Here we compared all reported combinations of C1 (formate/methanol/methane) and microorganisms (bacteria/yeasts) in terms of engineering and biomass quality parameters, focusing on the amino acid match with human requirements. This meta-analysis based on >100 studies suggests that methanol is the most promising C1, and methanol-grown microorganisms seem most nutritional with bacteria and yeasts having different merits. More sustainable MP could be produced if metabolic engineering tools yielding microorganisms with more efficient C1 assimilation pathways and steered amino acid profiles are deployed.},
}
@article {pmid35033479,
year = {2022},
author = {Acquier, M and De Précigout, V and Delmas, Y and Dubois, V and M'Zali, F and Zabala, A and De-La-Faille, R and Rubin, S and Cazanave, C and Puges, M and Combe, C and Kaminski, H},
title = {[Diagnosis and treatment of catheter-related bloodstream infection in hemodialysis: 10 years later].},
journal = {Nephrologie &amp; therapeutique},
volume = {18},
number = {2},
pages = {80-88},
doi = {10.1016/j.nephro.2021.08.010},
pmid = {35033479},
issn = {1872-9177},
mesh = {Anti-Bacterial Agents/therapeutic use ; *Bacteremia/diagnosis/drug therapy/epidemiology ; *Catheter-Related Infections/diagnosis/drug therapy/epidemiology ; *Catheterization, Central Venous/adverse effects ; *Central Venous Catheters/adverse effects ; Humans ; *Methicillin-Resistant Staphylococcus aureus ; Renal Dialysis/adverse effects ; },
abstract = {Patients in hemodialysis on central venous catheter as vascular access are at risk of infections. Catheter-related bloodstream infection is one of the most serious catheter-complications in hemodialysis patients. Its clinical and microbiological diagnosis is challenging. The implementation of empiric antibiotic therapy is based on old recommendations proposing the combination of a molecule targeting methicillin-resistant Staphylococcus aureus and a betalactamin active on P. aeruginosa, and also adapting this probabilistic treatment by carrying out a microbiological register on a local scale, which is rarely done. In our hemodialysis center at Bordeaux University Hospital, an analysis of the microorganisms causing all catheter-related bloodstream infection over the period 2018-2020 enabled us to propose, in agreement with the infectious disease specialists, an adapted probabilistic antibiotic therapy protocol. This approach allowed us to observe a low incidence of meticillinoresistance of Staphylococcus. For catheters inserted more than 6 months ago, we observed no Staphylococcus, no multi-resistant Pseudomonas, and only 2% of Enterobacteria resistant to cephalosporins. A frequent updating of the microbiological epidemiology of catheter-related bloodstream infection, in partnership with the infectious diseases team in each hemodialysis center, allowing an adaptation of the probabilistic antibiotic therapy, and seems to have a good feasibility. This strategy might favor the preservation of microbial ecology on an individual and collective scale in maintenance hemodialysis patients.},
}
@article {pmid35031403,
year = {2022},
author = {Wang, W and Wang, H and Cheng, X and Wu, M and Song, Y and Liu, X and Loni, PC and Tuovinen, OH},
title = {Different responses of bacteria and fungi to environmental variables and corresponding community assembly in Sb-contaminated soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {298},
number = {},
pages = {118812},
doi = {10.1016/j.envpol.2022.118812},
pmid = {35031403},
issn = {1873-6424},
mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Fungi ; RNA, Ribosomal, 16S ; Soil ; *Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {Bacterial communities in antimony (Sb) polluted soils have been well addressed, whereas the important players fungal communities are far less studied to date. Here, we report different responses of bacterial and fungal communities to Sb contamination and the ecological processes controlling their community assembly. Soil samples in the Xikuangshan mining area were collected and subjected to high through-put sequencing of 16S rRNA and ITS1 to investigate bacterial and fungal communities, respectively, along an Sb gradient. Sb speciation in the soil samples and other physicochemical parameters were analyzed as well. Bacterial communities were dominated by Deltaproteobacteria in the soil with highest Sb concentration, whereas Chloroflexi were dominant in the soil with lowest Sb concentration. Fungal communities in high-Sb soils were predominated by unclassified Fungi, whilst Leotiomycetes were dominant in low-Sb soil samples. Multivariate analysis indicated that Sb, pH and soil texture were the main drivers to strongly impact microbial communities. We further identified Sb-resistant microbial groups via correlation analysis. In total, 18 bacterial amplicon sequence variants (ASVs) were found to potentially involve in biogeochemical cycles such as Sb oxidation, sulfur oxidation or nitrate reduction, whereas 12 fungal ASVs were singled out for potential heavy metal resistance and plant growth promotion. Community assembly analysis revealed that variable selection contributed 100% to bacterial community assembly under acidic or high Sb concentration conditions, whereas homogeneous selection dominated fungal community assembly with a contribution over 78.9%. The community assembly of Sb-resistant microorganisms was mainly controlled by stochastic process. The results offer new insights into microbial ecology in Sb-contaminated soils, especially on the different responses of microbial communities under identical environmental stress and the different ecological processes underlining bacterial and fungal community assembly.},
}
@article {pmid35030221,
year = {2022},
author = {Lim, K and Rolston, M and Barnum, S and Wademan, C and Leverenz, H},
title = {A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms.},
journal = {PloS one},
volume = {17},
number = {1},
pages = {e0262425},
pmid = {35030221},
issn = {1932-6203},
mesh = {Bacteria/genetics ; Bathroom Equipment/*microbiology ; Biomineralization/genetics ; California/epidemiology ; DNA, Bacterial/genetics ; Drainage, Sanitary/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Toilet Facilities ; },
abstract = {In this study, we examined the total bacterial community associated with ureolytic biomineralization from urine drainage systems. Biomineral samples were obtained from 11 California Department of Transportation public restrooms fitted with waterless, low-flow, or conventional urinals in 2019. Following high throughput 16S rRNA Illumina sequences processed using the DADA2 pipeline, the microbial diversity assessment of 169 biomineral and urine samples resulted in 3,869 reference sequences aggregated as 598 operational taxonomic units (OTUs). Using PERMANOVA testing, we found strong, significant differences between biomineral samples grouped by intrasystem sampling location and urinal type. Biomineral microbial community profiles and alpha diversities differed significantly when controlling for sampling season. Observational statistics revealed that biomineral samples obtained from waterless urinals contained the largest ureC/16S gene copy ratios and were the least diverse urinal type in terms of Shannon indices. Waterless urinal biomineral samples were largely dominated by the Bacilli class (86.1%) compared to low-flow (41.3%) and conventional samples (20.5%), and had the fewest genera that account for less than 2.5% relative abundance per OTU. Our findings are useful for future microbial ecology studies of urine source-separation technologies, as we have established a comparative basis using a large sample size and study area.},
}
@article {pmid35028982,
year = {2022},
author = {Bizic, M and Ionescu, D and Karnatak, R and Musseau, CL and Onandia, G and Berger, SA and Nejstgaard, JC and Lischeid, G and Gessner, MO and Wollrab, S and Grossart, HP},
title = {Land-use type temporarily affects active pond community structure but not gene expression patterns.},
journal = {Molecular ecology},
volume = {31},
number = {6},
pages = {1716-1734},
doi = {10.1111/mec.16348},
pmid = {35028982},
issn = {1365-294X},
mesh = {Agriculture/methods ; Archaea/genetics ; Biodiversity ; *Ecosystem ; *Ponds ; },
abstract = {Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics to understand the responses of active bacterial, archaeal and eukaryotic communities to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel environmental DNA study that suggests the homogenization of biodiversity across KH, conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced for eukaryotes than for bacteria. In contrast, gene expression patterns did not differ between months or across land-use types, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results indicate that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This potential needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes.},
}
@article {pmid35028709,
year = {2023},
author = {Guzzon, R and Bertoldi, D and Roman, T and Zanzotti, R and Franciosi, E},
title = {Spatial and Seasonal Structure of Bacterial Communities Within Alpine Vineyards: Trentino as a Case Study.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {108-120},
pmid = {35028709},
issn = {1432-184X},
mesh = {Humans ; Farms ; Seasons ; *Vitis/microbiology ; Bacteria ; *Microbiota ; },
abstract = {Bacteria have a fundamental role in determining the fitness of grapevine, the composition of grapes and the features of wines but at present, little information is available. In this work, the bacteria colonizing the different portions of grapevine (bark, leaves and grapes) were explored in the vineyards of the Alpine region of Trentino, considering the impact of different environmental and agronomical variables. The vineyards included in the work were selected based on their different geographical positions (altitude) and grapevine training systems in order to explore the whole variability of the grapevine ecosystem. Moreover, the surface amount of copper was measured on grapes and leaves during the vegetative growth. Bacterial analysis, performed using plate counts and Illumina MiSeq, revealed an increase in the concentration of grape bacteria proportional to the progress of the ripening stage. Conversely, the peak of bacterial concentration onto leaf and bark samples occurred in August, probably due to the more favourable environmental conditions. In bark samples, the bacterial microbiota reached the 7 log CFU/cm[2], while 6 log UFC/g were measured in grape samples. A remarkable biodiversity was observed, with 13 phyla, 35 classes, 55 orders, 78 families and 95 genera of bacteria present. The presence of some taxa (Alphaproteobacteria, Desulfovibrionaceae, Clostriadiales, Oscillospira, Lachnospiraceae and Bacteroidales) was ubiquitous in all vineyards, but differences in terms of relative abundance were observed according to the vegetative stage, altitude of the vineyard and training system. Bacteria having oenological implication (Lactobacillus, Pediococcus and Oenococcus) were detected in grape samples collected in August, in low abundance. The data revealed a complex bacterial ecosystem inside the vineyard that, while maintaining common traits, evolves according to environmental and agronomical inputs. This study contributes to define the role of bacteria in the complex balance established in each vineyard between human actions and agricultural environment, known as terroir.},
}
@article {pmid35026246,
year = {2022},
author = {Gregson, BH and Bani, A and Steinfield, L and Holt, D and Whitby, C},
title = {Anaerobes and methanogens dominate the microbial communities in water harvesting ponds used by Kenyan rural smallholder farmers.},
journal = {The Science of the total environment},
volume = {819},
number = {},
pages = {153040},
doi = {10.1016/j.scitotenv.2022.153040},
pmid = {35026246},
issn = {1879-1026},
mesh = {Farmers ; Humans ; Kenya ; *Microbiota ; *Ponds/microbiology ; Water Microbiology ; Water Quality ; },
abstract = {Many rural smallholder farmers in Kenya use water-harvesting ponds, to collect rainwater, as sustainable sources of water for domestic and agricultural purposes. There is currently limited information regarding the microbial ecology in these ponds. Here, we used High Throughput Sequencing (HTS) to characterize the microorganisms present (including potential pathogens and indicator species) alongside ion chromatography to measure water chemistry (anion and cation concentration). Fluoride and magnesium concentration were the strongest predictor variables of the microbial community. Obligately or facultatively anaerobic bacterial genera (e.g. Spirochaeta and Opitutus) were abundant within the bacterial community, whilst Woesearchaeota and methanogens dominated the archaeal community. This suggests the water in the ponds is hypoxic or anoxic, and if used for irrigation, may potentially impact crop yield and viability. In addition, the opportunistic pathogen non-tuberculous mycobacteria (NTM), Mycobacterium fortuitum was found, comprising >1% of the bacterial community, suggesting a potential human health risk. Here we suggest low-cost changes to pond management, to improve or ameliorate pond anoxia and remove pathogens to benefit the livelihoods and welfare of these farms. This study also shows the applicability of HTS to broadly screen the microbial communities, assess water quality, and identify potentially pathogenic groups.},
}
@article {pmid35025628,
year = {2022},
author = {Cowan, DA and Ferrari, BC and McKay, CP},
title = {Out of Thin Air? Astrobiology and Atmospheric Chemotrophy.},
journal = {Astrobiology},
volume = {22},
number = {2},
pages = {225-232},
pmid = {35025628},
issn = {1557-8070},
mesh = {Carbon Monoxide ; Earth, Planet ; *Exobiology ; Extraterrestrial Environment ; Hydrogen ; *Mars ; Planets ; },
abstract = {The emerging understanding of microbial trace gas chemotrophy as a metabolic strategy to support energy and carbon acquisition for microbial survival and growth has significant implications in the search for past, and even extant, life beyond Earth. The use of trace gases, including hydrogen and carbon monoxide as substrates for microbial oxidation, potentially offers a viable strategy with which to support life on planetary bodies that possess a suitable atmospheric composition, such as Mars and Titan. Here, we discuss the current state of knowledge of this process and explore its potential in the field of astrobiological exploration.},
}
@article {pmid35025047,
year = {2022},
author = {Pan, C and Feng, Q and Li, Y and Li, Y and Liu, L and Yu, X and Ren, S},
title = {Rare soil bacteria are more responsive in desertification restoration than abundant bacteria.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {22},
pages = {33323-33334},
pmid = {35025047},
issn = {1614-7499},
support = {41773086//National Natural Science Foundation of China/ ; 42042024//National Natural Science Foundation of China/ ; 31400392//National Natural Science Foundation of China/ ; 31670477//National Natural Science Foundation of China/ ; 18JR2RA026//Gansu Science and Technology Department/ ; },
mesh = {Bacteria ; China ; Conservation of Natural Resources ; *Ecosystem ; *Soil ; Soil Microbiology ; },
abstract = {Soil microbes play key roles in ecosystem functions, especially in the recovery of ecosystems from disturbance, and exploring community assembly under changing environments has long been a central theme in microbial ecology. The response of abundant and rare bacteria in desertified land to restoration is still unclear. Here, we investigated the effects of vegetation restoration on the assemblage patterns of abundant and rare bacteria in soil across the four sandy lands (Hulunbeir, Horqin, Otindag, and Mu Us) in northern China. Our results revealed that abundant bacteria maintained a relatively stable state under restoration, whereas rare taxa were more responsive, indicating the higher resilience of the rare community to change. Our network analysis also showed that restoration promoted destabilizing properties in rare, but not in abundant, bacterial co-occurrence networks in soil. Environmental selection played a key role in abundant and rare community assembly under restoration. Of the two, the rare subcommunity was mainly affected by environmental filtering. The variations in the abundant and rare communities at the sampling sites under restoration were controlled mainly by plant species richness, and stronger effects were observed in the rare taxa. Overall, these results provide new insight into the mechanisms controlling bacterial community assembly in response to vegetation restoration.},
}
@article {pmid35024965,
year = {2022},
author = {Gao, C and Yang, X and Zhao, C and Li, C and Wang, S and Zhang, X and Xue, B and Cao, Z and Zhou, H and Yang, Y and Shen, Z and Yu, P and Wang, J and Li, L and Niu, Z and Qiu, Z},
title = {Characterization of a novel Vibrio parahaemolyticus host-phage pair and antibacterial effect against the host.},
journal = {Archives of virology},
volume = {167},
number = {2},
pages = {531-544},
pmid = {35024965},
issn = {1432-8798},
support = {2018YFD0800104//National Key R&amp;D Program of China/ ; AWS18J004//Special Fund of China/ ; 2019-JCJQ-JJ-163//Special Fund of China/ ; 17JCZDJC39100//Natural Science Foundation of Tianjin City/ ; 19JCYBJC23800//Natural Science Foundation of Tianjin City/ ; 51808468//National Natural Science Foundation of China/ ; },
mesh = {Anti-Bacterial Agents/pharmacology ; *Bacteriophages/genetics ; Genome, Viral ; Humans ; Myoviridae/genetics ; *Vibrio parahaemolyticus/genetics ; },
abstract = {Vibrio parahaemolyticus is a widely recognized pathogen that has caused numerous outbreaks and is prevalent in the marine environment. In this study, we investigated the characteristics of the novel V. parahaemolyticus strain BTXS2 and its associated phage, VB_VpP_BT-1011, isolated from the Bohai Coast (Tianjin, China). Strain BTXS2 is a short coryneform bacterium with a terminal flagellum and is able to utilize and metabolize a wide variety of organic matter because of its unique carbon source utilization and enzyme activity. It grows well in medium between pH 5.0 and 9.0 and salinities of simulated freshwater, estuary water, and seawater (NaCl 0.5%-3%). Multiple antibiotic resistance genes and virulence genes that endanger human health were found in the BTXS2 genome. Phage VB_VpP_BT-1011, which infects BTXS2, is a 40,065-bp double-stranded DNA virus of the family Myoviridae with a latent time of 30 min and burst size of 24 PFU/cell. Like its host, the phage tolerates a broad range of environmental conditions (salinity, 0-3% NaCl; pH 5.0-9.0; temperature, 4-37°C). A host range test showed that the phage only infected and inhibited isolate BTXS2. In summary, we investigated a novel V. parahaemolyticus host-phage pair and the antibacterial effect of the phage on V. parahaemolyticus, providing insights into marine microbial ecology and risks.},
}
@article {pmid35022702,
year = {2022},
author = {Djemiel, C and Maron, PA and Terrat, S and Dequiedt, S and Cottin, A and Ranjard, L},
title = {Inferring microbiota functions from taxonomic genes: a review.},
journal = {GigaScience},
volume = {11},
number = {1},
pages = {},
pmid = {35022702},
issn = {2047-217X},
mesh = {*Ecosystem ; Fungi/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; Soil ; Soil Microbiology ; },
abstract = {Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading to the big data era and improving our ability to link microbial diversity with microbial functions. Recent advances in bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding data and using taxonomic gene information. This cheaper approach in every aspect serves as an alternative to shotgun sequencing. Although these tools are increasingly used by ecologists, an objective evaluation of their modularity, portability, and robustness is lacking. Here, we reviewed 100 scientific papers on functional inference and ecological trait assignment to rank the advantages, specificities, and drawbacks of these tools, using a scientific benchmarking. To date, inference tools have been mainly devoted to bacterial functions, and ecological trait assignment tools, to fungal functions. A major limitation is the lack of reference genomes-compared with the human microbiota-especially for complex ecosystems such as soils. Finally, we explore applied research prospects. These tools are promising and already provide relevant information on ecosystem functioning, but standardized indicators and corresponding repositories are still lacking that would enable them to be used for operational diagnosis.},
}
@article {pmid35020220,
year = {2022},
author = {Sahu, PK and Tilgam, J and Mishra, S and Hamid, S and Gupta, A and K, J and Verma, SK and Kharwar, RN},
title = {Surface sterilization for isolation of endophytes: Ensuring what (not) to grow.},
journal = {Journal of basic microbiology},
volume = {62},
number = {6},
pages = {647-668},
doi = {10.1002/jobm.202100462},
pmid = {35020220},
issn = {1521-4028},
mesh = {Endophytes ; *Plants, Medicinal ; Prospective Studies ; Sterilization ; *Taxus ; },
abstract = {Endophytic microbiota opens a magnificent arena of metabolites that served as a potential source of medicines for treating a variety of ailments and having prospective uses in agriculture, food, cosmetics, and many more. There are umpteen reports of endophytes improving the growth and tolerance of plants. In addition, endophytes from lifesaving drug-producing plants such as Taxus, Nothapodytes, Catharanthus, and so forth have the ability to produce host mimicking compounds. To harness these benefits, it is imperative to isolate the true endophytes, not the surface microflora. The foremost step in endophyte isolation is the removal of epiphytic microbes from plant tissues, called as surface sterilization. The success of surface sterilization decides "what to grow" (the endophytes) and "what not to grow" (the epiphytes). It is very crucial to use an appropriate sterilant solution, concentration, and exposure time to ensure thorough surface disinfection with minimal damage to the endophytic diversity. Commonly used surface sterilants include sodium hypochlorite (2%-10%), ethanol (70%-90%), mercuric chloride (0.1%), formaldehyde (40%), and so forth. In addition, the efficiency could further be improved by pretreatment with surfactants such as Triton X-100, Tween 80, and Tween 20. This review comprehensively deals with the various sterilants and sterilization methods for the isolation of endophytic microbes. In addition, the mechanisms and rationale behind using specific surface sterilants have also been elaborated at length.},
}
@article {pmid35019779,
year = {2022},
author = {Yin, Y and Yuan, Y and Zhang, X and Huhe, and Cheng, Y and Borjigin, S},
title = {Comparison of the Responses of Soil Fungal Community to Straw, Inorganic Fertilizer, and Compost in a Farmland in the Loess Plateau.},
journal = {Microbiology spectrum},
volume = {10},
number = {1},
pages = {e0223021},
pmid = {35019779},
issn = {2165-0497},
mesh = {China ; Composting ; Ecosystem ; Fertilizers/*analysis ; Fungi/classification/genetics/*isolation &amp; purification/metabolism ; *Mycobiome ; Plant Stems/metabolism/microbiology ; Soil/chemistry ; Soil Microbiology ; },
abstract = {The Loess Plateau is located in the arid and semi-arid regions in northern China. The ecosystem is particularly sensitive to natural and anthropogenic disturbances. Fungi can produce extracellular enzymes, decompose a variety of organic matter, and regulate carbon and nutrient balance. We studied the changes of soil fungal community compositions in response to straw, inorganic fertilizer, and compost in a typical farmland in the Loess Plateau. Our results demonstrated that the addition of straw significantly reduces the Shannon index of the fungal community, in addition, the participation of straw significantly affects the composition of the fungal community. Functional prediction based on FUNGuild showed that straw significantly reduced the relative abundance of saprotrophs, pathotrophs, symbiotrophs, lichenized, ectomycorrhizal, and plant pathogens. Although fertilization practices destroyed the co-occurrence pattern among the fungal species, the addition of straw alleviated this affect. No significant effect of straw, compost, and inorganic fertilizers on the co-occurrence pattern among species in the soil fungal community was observed. Compared with compost and inorganic fertilizer, the addition of straw shaped the community composition by changing the relative abundance of fungal functional taxa. Thus, in the fragile Loess Plateau environment, over-fertilizing or non-order-fertilizing may destroy the co-occurrence pattern of the fungal communities and Loess Plateau ecosystem. IMPORTANCE Determining the response of soil fungi in sensitive ecosystems to external environmental disturbances is an important, yet little-known, topic in microbial ecology. In this study, we evaluated the impact of traditional fertilization management practices on the composition, co-occurrence pattern, and functional groups of fungal communities in loessial soil. Our results show that in the fragile Loess Plateau environment, fertilizer management changed the composition of the fungal community and disrupted the co-occurrence pattern between fungi. The application of straw alleviates the destroying of the co-occurrence pattern. The current research emphasizes the necessity of rational fertilization of farmland in loessial soil.},
}
@article {pmid35019678,
year = {2022},
author = {Kong, J and Wang, L and Lin, C and Kuang, F and Zhou, X and Laws, EA and Sun, P and Huang, H and Huang, B},
title = {Contrasting Community Assembly Mechanisms Underlie Similar Biogeographic Patterns of Surface Microbiota in the Tropical North Pacific Ocean.},
journal = {Microbiology spectrum},
volume = {10},
number = {1},
pages = {e0079821},
pmid = {35019678},
issn = {2165-0497},
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Ecosystem ; Eukaryota/classification/genetics/isolation &amp; purification ; *Microbiota ; Pacific Ocean ; Phylogeny ; Seawater/*microbiology/parasitology ; },
abstract = {Marine microbiota are critical components of global biogeochemical cycles. However, the biogeographic patterns and ecological processes that structure them remain poorly understood, especially in the oligotrophic ocean. In this study, we used high-throughput sequencing of 16S and 18S rRNA genes to investigate the distribution patterns of bacterial and microeukaryotic communities and their assembly mechanisms in the surface waters of the tropical North Pacific Ocean. The fact that both the bacterial and the microeukaryotic communities showed similar distribution patterns (i.e., similar distance-decay patterns) and were clustered according to their geographic origin (i.e., the western tropical North Pacific and central tropical North Pacific) suggested that there was a significant biogeographic pattern of microbiota in the North Pacific Ocean. Indices of alpha diversity such as species richness, phylogenetic diversity, and the Shannon diversity index also differed significantly between regions. The correlations were generally similar between spatial and environmental variables and the alpha and beta diversities of bacteria and microeukaryotes across the entire region. The relative importance of ecological processes differed between bacteria and microeukaryotes: ecological drift was the principal mechanism that accounted for the structure of bacterial communities; heterogeneous selection, dispersal limitation, and ecological drift collectively explained much of the turnover of the microeukaryote communities. IMPORTANCE Bacteria and microeukaryotes are extremely diverse groups in the ocean, where they regulate elemental cycling and energy flow. Studies of marine microbial ecology have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology. However, the spatial distribution of marine bacteria and microeukaryotes and the nature of the assembly mechanisms that determine their distribution patterns in oligotrophic marine waters are poorly understood. In this study, we used high-throughput sequencing methods to identify the distribution patterns and ecological processes of bacteria and microeukaryotes in an oligotrophic, tropical ocean. Our study showed that contrasting community assembly mechanisms underlaid similar biogeographic patterns of surface bacterial and microeukaryotic communities in the tropical North Pacific Ocean.},
}
@article {pmid35018483,
year = {2023},
author = {Zhang, W and Qi, T and Yao, L and Wang, W and Yu, F and Yan, Y and Salama, ES and Su, S and Bai, M},
title = {Influence of Environmental Factors on Salivary Microbiota and Their Metabolic Pathway: Next-Generation Sequencing Approach.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {317-329},
pmid = {35018483},
issn = {1432-184X},
support = {31500412//National Natural Science Foundation of China/ ; 20JR5RA327//National Natural Science Foundation of Gansu Province, China/ ; 21JR1RA152//National Natural Science Foundation of Gansu Province, China/ ; 2018-4-66//Lanzhou science and technology plan project/ ; },
mesh = {Humans ; Bacteria/genetics ; *Periodontitis/microbiology ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The current study aimed to investigate the effect of periodontitis and long-term heavy metal (HM) exposure on the salivary microbiome. The patients were divided into four groups as Wu Wei control (WWC) group involved healthy individuals, Wu Wei periodontitis (WWP) patients having periodontitis, Jing Chang with metal pollution periodontally healthy individuals (JCP), and Kuang periodontitis (KP). The most abundant bacteria identified at the phylum level in the WWC group were Bacteroides, Firmicutes, and Fusobacteria. Firmicutes were observed in a significantly higher proportion in the KP group than in the WWC, WWP, and JCP. At the genus level, the WWC has major dominating bacterial genera (such as Leptotrichia, Neisseria, and Fusobacterium) which were similar to WWP and KP group. The significant difference (p < 0.05) was found in alpha diversity while in beta diversity, the significant (p = 0.005) results were found among the four groups. The correlation of oral microbiota revealed that HMs present in the soil (Cr, Ni, and Cu) are associated with the growth of Capnocytophaga, Selenomonas, Aggregatibacter, and Campylobacter. The bacterial functions in the KP group were higher in translation and nucleotide metabolism than in the WWP group. This demonstrated that long-term exposure to HMs can influence the salivary microbiota which can alter the functioning, and diversity of bacteria.},
}
@article {pmid35016024,
year = {2022},
author = {Cáliz, J and Subirats, J and Triadó-Margarit, X and Borrego, CM and Casamayor, EO},
title = {Global dispersal and potential sources of antibiotic resistance genes in atmospheric remote depositions.},
journal = {Environment international},
volume = {160},
number = {},
pages = {107077},
doi = {10.1016/j.envint.2022.107077},
pmid = {35016024},
issn = {1873-6750},
mesh = {*Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Antibiotic resistance has become a major Global Health concern and a better understanding on the global spread mechanisms of antibiotic resistant bacteria (ARB) and intercontinental ARB exchange is needed. We measured atmospheric depositions of antibiotic resistance genes (ARGs) by quantitative (q)PCR in rain/snow collected fortnightly along 4 y. at a remote high mountain LTER (Long-Term Ecological Research) site located above the atmospheric boundary layer (free troposphere). Bacterial composition was characterized by 16S rRNA gene sequencing, and air mass provenances were determined by modelled back trajectories and rain/snow chemical composition. We hypothesize that the free troposphere may act as permanent reservoir and vector for ARB and ARGs global dispersal. We aimed to i) determine whether ARGs are long-range intercontinental and persistently dispersed through aerosols, ii) assess ARGs long-term atmospheric deposition dynamics in a remote high mountain area, and iii) unveil potential diffuse ARGs pollution sources. We showed that the ARGs sul1 (resistance to sulfonamides), tetO (resistance to tetracyclines), and intI1 (a proxy for horizontal gene transfer and anthropogenic pollution) were long-range and persistently dispersed in free troposphere aerosols. Major depositions of tetracyclines resistance matched with intensification of African dust outbreaks. Potential ARB mostly traced their origin back into agricultural soils. Our study unveils that air masses pathways are shaping ARGs intercontinental dispersal and global spread of antibiotic resistances, with potential predictability for interannual variability and remote deposition rates. Because climate regulates aerosolization and long-range air masses movement patterns, we call for a more careful evaluation of the connections between land use, climate change and ARB long-range intercontinental dispersal.},
}
@article {pmid35014098,
year = {2022},
author = {Olesen, AK and Pinilla-Redondo, R and Hansen, MF and Russel, J and Dechesne, A and Smets, BF and Madsen, JS and Nesme, J and Sørensen, SJ},
title = {IncHI1A plasmids potentially facilitate horizontal flow of antibiotic resistance genes to pathogens in microbial communities of urban residential sewage.},
journal = {Molecular ecology},
volume = {31},
number = {5},
pages = {1595-1608},
doi = {10.1111/mec.16346},
pmid = {35014098},
issn = {1365-294X},
mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal/genetics ; *Microbiota ; Plasmids/genetics ; *Sewage/microbiology ; },
abstract = {Horizontal gene transfer via plasmids is important for the dissemination of antibiotic resistance genes among medically relevant pathogens. Specifically, the transfer of IncHI1A plasmids is believed to facilitate the spread of antibiotic resistance genes, such as carbapenemases, within the clinically important family Enterobacteriaceae. The microbial community of urban wastewater treatment plants has been shown to be highly permissive towards conjugal transfer of IncP1 plasmids. Here, we tracked the transfer of the P1 plasmid pB10 and the clinically relevant HI1A plasmid R27 in the microbial communities present in urban residential sewage entering full-scale wastewater treatment plants. We found that both plasmids readily transferred to these communities and that strains in the sewage were able to further disseminate them. Furthermore, R27 has a broad potential host range, but a low host divergence. Interestingly, although the majority of R27 transfer events were to members of Enterobacteriaceae, we found a subset of transfer events to other families, even other phyla. This indicates that HI1A plasmids facilitate horizontal gene transfer both within Enterobacteriaceae, but also across families of, in particular, Gammaproteobacteria, such as Moraxellaceae, Pseudomonadaceae and Shewanellaceae. pB10 displayed a similar potential host range to R27. In contrast to R27, pB10 had a high host divergence. By culture enrichment of the transconjugant communities, we show that sewage strains of Enterobacteriaceae and Aeromonadaceae can stably maintain R27 and pB10, respectively. Our results suggest that dissemination in the urban residual water system of HI1A plasmids may result in an accelerated acquisition of antibiotic resistance genes among pathogens.},
}
@article {pmid35013291,
year = {2022},
author = {Martínez-Pérez, C and Greening, C and Bay, SK and Lappan, RJ and Zhao, Z and De Corte, D and Hulbe, C and Ohneiser, C and Stevens, C and Thomson, B and Stepanauskas, R and González, JM and Logares, R and Herndl, GJ and Morales, SE and Baltar, F},
title = {Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {117},
pmid = {35013291},
issn = {2041-1723},
mesh = {Antarctic Regions ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Carbon Cycle/genetics ; Geologic Sediments/microbiology ; Ice Cover/*microbiology ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; },
abstract = {Throughout coastal Antarctica, ice shelves separate oceanic waters from sunlight by hundreds of meters of ice. Historical studies have detected activity of nitrifying microorganisms in oceanic cavities below permanent ice shelves. However, little is known about the microbial composition and pathways that mediate these activities. In this study, we profiled the microbial communities beneath the Ross Ice Shelf using a multi-omics approach. Overall, beneath-shelf microorganisms are of comparable abundance and diversity, though distinct composition, relative to those in the open meso- and bathypelagic ocean. Production of new organic carbon is likely driven by aerobic lithoautotrophic archaea and bacteria that can use ammonium, nitrite, and sulfur compounds as electron donors. Also enriched were aerobic organoheterotrophic bacteria capable of degrading complex organic carbon substrates, likely derived from in situ fixed carbon and potentially refractory organic matter laterally advected by the below-shelf waters. Altogether, these findings uncover a taxonomically distinct microbial community potentially adapted to a highly oligotrophic marine environment and suggest that ocean cavity waters are primarily chemosynthetically-driven systems.},
}
@article {pmid35011305,
year = {2021},
author = {Li, Q and Van Herreweghen, F and De Mey, M and Goeminne, G and Van de Wiele, T},
title = {The Donor-Dependent and Colon-Region-Dependent Metabolism of (+)-Catechin by Colonic Microbiota in the Simulator of the Human Intestinal Microbial Ecosystem.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {1},
pages = {},
pmid = {35011305},
issn = {1420-3049},
support = {201806820010//China Scholarship Council/ ; BOF18/CHN/064//Ghent University Preference Program/ ; BOF17/GOA/032//Ghent University Special Research Fund/ ; },
mesh = {Adult ; Biological Variation, Population ; Catechin/*metabolism ; Chromatography, High Pressure Liquid ; *Colon ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*metabolism/*microbiology ; Male ; Metabolic Networks and Pathways ; Metabolome ; Metabolomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {The intestinal absorption of dietary catechins is quite low, resulting in most of them being metabolized by gut microbiota in the colon. It has been hypothesized that microbiota-derived metabolites may be partly responsible for the association between catechin consumption and beneficial cardiometabolic effects. Given the profound differences in gut microbiota composition and microbial load between individuals and across different colon regions, this study examined how microbial (+)-catechin metabolite profiles differ between colon regions and individuals. Batch exploration of the interindividual variability in (+)-catechin microbial metabolism resulted in a stratification based on metabolic efficiency: from the 12 tested donor microbiota, we identified a fast- and a slow-converting microbiota that was subsequently inoculated to SHIME, a dynamic model of the human gut. Monitoring of microbial (+)-catechin metabolites from proximal and distal colon compartments with UHPLC-MS and UPLC-IMS-Q-TOF-MS revealed profound donor-dependent and colon-region-dependent metabolite profiles with 5-(3',4'-dihydroxyphenyl)-γ-valerolactone being the largest contributor to differences between the fast- and slow-converting microbiota and the distal colon being a more important region for (+)-catechin metabolism than the proximal colon. Our findings may contribute to further understanding the role of the gut microbiota as a determinant of interindividual variation in pharmacokinetics upon (+)-catechin ingestion.},
}
@article {pmid35011218,
year = {2022},
author = {Naghizadeh, M and Klaver, L and Schönherz, AA and Rani, S and Dalgaard, TS and Engberg, RM},
title = {Impact of Dietary Sodium Butyrate and Salinomycin on Performance and Intestinal Microbiota in a Broiler Gut Leakage Model.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {1},
pages = {},
pmid = {35011218},
issn = {2076-2615},
support = {000//Poultry Production Levy Fund/ ; },
abstract = {Unfavorable alterations of the commensal gut microbiota and dysbacteriosis is a major health problem in the poultry industry. Understanding how dietary intervention alters the microbial ecology of broiler chickens is important for prevention strategies. A trial was conducted with 672 Ross 308 day-old male broilers fed a basic diet (no additives, control) or the basic diet supplemented with 500 mg/kg encapsulated butyrate or 68 mg/kg salinomycin. Enteric challenge was induced by inclusion of 50 g/kg rye in a grower diet and oral gavage of a 10 times overdose of a vaccine against coccidiosis. Compared to control and butyrate-supplemented birds, salinomycin supplementation alleviated growth depression. Compared to butyrate and non-supplemented control, salinomycin increased potentially beneficial Ruminococcaceae and reduced potentially pathogenic Enterobacteriaceae and counts of Lactobacillus salivarius and Clostridium perfringens. Further, salinomycin supplementation was accompanied by a pH decrease and succinic acid increase in ceca, while coated butyrate (0.5 g/kg) showed no or limited effects. Salinomycin alleviated growth depression and maintained intestinal homeostasis in the challenged broilers, while butyrate in the tested concentration showed limited effects. Thus, further investigations are required to identify optimal dietary inclusion rates for butyrate used as alternative to ionophore coccidiostats in broiler production.},
}
@article {pmid35010187,
year = {2021},
author = {Jiang, L and Xian, S and Liu, X and Shen, G and Zhang, Z and Hou, X and Chen, A},
title = {Metagenomic Study on Chinese Homemade Paocai: The Effects of Raw Materials and Fermentation Periods on the Microbial Ecology and Volatile Components.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
pmid = {35010187},
issn = {2304-8158},
support = {No. 2017YFC0505106-3//Research and Development of Utilization Technology of characteristic Biological Resources in Ar-id Valley of Southwest China/ ; },
abstract = {"Chinese paocai" is typically made by fermenting red radish or cabbage with aged brine (6-8 w/w). This study aimed to reveal the effects of paocai raw materials on fermentation microorganisms by metagenomics sequencing technology, and on volatile organic compounds (VOCs) by gas chromatography-mass spectroscopy, using red radish or cabbage fermented for six rounds with aged brine. The results showed that in the same fermentation period, the microbial diversity in cabbage was higher than that in red radish. Secundilactobacillus paracollinoides and Furfurilactobacillus siliginis were the characteristic bacteria in red radish paocai, whereas 15 species of characteristic microbes were found in cabbage. Thirteen kinds of VOCs were different between the two raw materials and the correlation between the microorganisms and VOCs showed that cabbage paocai had stronger correlations than radish paocai for the most significant relationship between 4-isopropylbenzyl alcohol, α-cadinol, terpinolene and isobutyl phenylacetate. The results of this study provide a theoretical basis for understanding the microbiota and their relation to the characteristic flavors of the fermented paocai.},
}
@article {pmid35003029,
year = {2021},
author = {Wang, Z and Solanki, MK and Yu, ZX and Anas, M and Dong, DF and Xing, YX and Malviya, MK and Pang, F and Li, YR},
title = {Genome Characteristics Reveal the Biocontrol Potential of Actinobacteria Isolated From Sugarcane Rhizosphere.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {797889},
pmid = {35003029},
issn = {1664-302X},
abstract = {To understand the beneficial interaction of sugarcane rhizosphere actinobacteria in promoting plant growth and managing plant diseases, this study investigated the potential role of sugarcane rhizospheric actinobacteria in promoting plant growth and antagonizing plant pathogens. We isolated 58 actinobacteria from the sugarcane rhizosphere, conducted plant growth-promoting (PGP) characteristics research, and tested the pathogenic fungi in vitro. Results showed that BTU6 (Streptomyces griseorubiginosus), the most representative strain, regulates plant defense enzyme activity and significantly enhances sugarcane smut resistance by regulating stress resistance-related enzyme (substances (POD, PAL, PPO, TP) in sugarcane) activity in sugarcane. The genomic evaluation indicated that BTU6 has the ability to biosynthesize chitinase, β-1,3-glucanase, and various secondary metabolites and plays an essential role in the growth of sugarcane plants under biotic stress. Potential mechanisms of the strain in improving the disease resistance of sugarcane plants and its potential in biodegrading exogenous chemicals were also revealed. This study showed the importance of sugarcane rhizosphere actinobacteria in microbial ecology and plant growth promotion.},
}
@article {pmid34997964,
year = {2022},
author = {Li, L and Chen, X and Fang, D and Dong, S and Guo, X and Li, N and Campos-Dominguez, L and Wang, W and Liu, Y and Lang, X and Peng, Y and Tian, D and Thomas, DC and Mu, W and Liu, M and Wu, C and Yang, T and Zhang, S and Yang, L and Yang, J and Liu, ZJ and Zhang, L and Zhang, X and Chen, F and Jiao, Y and Guo, Y and Hughes, M and Wang, W and Liu, X and Zhong, C and Li, A and Sahu, SK and Yang, H and Wu, E and Sharbrough, J and Lisby, M and Liu, X and Xu, X and Soltis, DE and Van de Peer, Y and Kidner, C and Zhang, S and Liu, H},
title = {Genomes shed light on the evolution of Begonia, a mega-diverse genus.},
journal = {The New phytologist},
volume = {234},
number = {1},
pages = {295-310},
pmid = {34997964},
issn = {1469-8137},
support = {833522/ERC_/European Research Council/International ; },
mesh = {*Begoniaceae/genetics ; Evolution, Molecular ; Genome ; Phylogeny ; Synteny/genetics ; },
abstract = {Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with c. 2000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana and B. peltatifolia), and whole genome shotgun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22 059-23 444 protein-coding genes. Synteny analysis revealed a lineage-specific whole-genome duplication (WGD) that occurred just before the diversification of Begonia. Functional enrichment of gene families retained after WGD highlights the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade.},
}
@article {pmid34997311,
year = {2023},
author = {Balacco, JR and Vaidya, BP and Hagmann, DF and Goodey, NM and Krumins, JA},
title = {Mycorrhizal Infection Can Ameliorate Abiotic Factors in Urban Soils.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {100-107},
pmid = {34997311},
issn = {1432-184X},
support = {CBET#1603741//national science foundation/ ; },
mesh = {*Mycorrhizae/chemistry ; Soil ; *Metals, Heavy/analysis ; Plants/microbiology ; Biomass ; Plant Roots/microbiology ; *Soil Pollutants/analysis ; },
abstract = {Once abandoned, urban and post-industrial lands can undergo a re-greening, the natural regeneration and succession that leads to surprisingly healthy plant communities, but this process is dependent upon microbial activity and the health of the parent soil. This study aimed to evaluate the effects of arbuscular mycorrhizal fungi (AMF) in facilitating plant production in post-industrial soils. In so doing, we helped to resolve the mechanism through which AMF ameliorate environmental stress in terrestrial plants. An experiment was established in which rye grass (Lolium perenne) was grown in two heavy metal-contaminated soils from an urban brownfield in New Jersey, USA, and one non-contaminated control soil. One set of the treatments received an AMF inoculum (four species in a commercial mix: Glomus intraradices, G. mosseae, G. etunicatum and G. aggregatum) and the other did not. Upon harvest, dried plant biomass, root/shoot ratio, AMF colonization, and extracellular soil phosphatase activity, a proxy for soil microbial functioning, were all measured. Plant biomass increased across all treatments inoculated with AMF, with a significantly higher average shoot and root mass compared to non-inoculated treatments. AMF colonization of the roots in contaminated soil was significantly higher than colonization in control soil, and the root/shoot ratio of plants in contaminated soils was also higher when colonized by AMF. Mycorrhizal infection may help plants to overcome the production limits of post-industrial soils as is seen here with increased infection and growth. The application of this mechanistic understanding to remediation and restoration strategies will improve soil health and plant production in urban environments.},
}
@article {pmid34997310,
year = {2023},
author = {Decker, LE and San Juan, PA and Warren, ML and Duckworth, CE and Gao, C and Fukami, T},
title = {Higher Variability in Fungi Compared to Bacteria in the Foraging Honey Bee Gut.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {330-334},
pmid = {34997310},
issn = {1432-184X},
support = {1737758//Division of Environmental Biology/ ; },
mesh = {Bees ; Animals ; *Gastrointestinal Tract/microbiology ; Bacteria ; *Microbiota ; Stomach ; Fungi ; },
abstract = {Along with bacteria, fungi can represent a significant component of animal- and plant-associated microbial communities. However, we have only begun to describe these fungi, much less examine their effects on most animals and plants. Bacteria associated with the honey bee, Apis mellifera, have been well characterized across different regions of the gut. The mid- and hindgut of foraging bees house a deterministic set of core species that affect host health, whereas the crop, or the honey stomach, harbors a more diverse set of bacteria that is highly variable in composition among individual bees. Whether this contrast between the two regions of the gut also applies to fungi remains unclear despite their potential influence on host health. In honey bees caught foraging at four sites across the San Francisco Peninsula of California, we found that fungi were less distinct in species composition between the crop and the mid- and hindgut than bacteria. Unlike bacteria, fungi varied substantially in species composition throughout the honey bee gut, and much of this variation could be predicted by the location where we collected the bees. These observations suggest that fungi may be transient passengers and unimportant as gut symbionts. However, our findings also indicate that honey bees could be vectors of infectious plant diseases as many of the fungi we found in the honey bee gut are recognized as plant pathogens.},
}
@article {pmid34997309,
year = {2023},
author = {Li, T and Cai, Y and Ma, Q},
title = {Microbial Diversity on the Surface of Historical Monuments in Lingyan Temple, Jinan, China.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {76-86},
pmid = {34997309},
issn = {1432-184X},
support = {2019M662390//Postdoctoral Research Foundation of China/ ; ZR2020QC045//Natural Science Foundation of Shandong Province/ ; 18ZDA221//Major Program of National Fund of Philosophy and Social Science of China (CN)/ ; },
mesh = {*Cyanobacteria/genetics ; Biofilms ; *Microbiota ; China ; },
abstract = {Lingyan Temple is an important part of the World Heritage Mixed Property on Mount Taishan, in which numerous cultural heritage monuments, including exquisite painted arhat statues and inscriptions, display the ancient Chinese Buddhist culture. However, these monuments are suffering aesthetic and structural damage due to rich biofilms. In this study, the microbial communities colonized on historical monuments in different microenvironments were characterized through a combination of culture-dependent techniques and high-throughput sequencing. Microbial diversity was significantly different among the historical sites with different microenvironments. For example, Actinobacteria and Ascomycota were the core phyla in the indoor samples, while they were less abundant in the outdoor samples, and phototrophic microorganisms including Cyanobacteria and green algae were only dominant in the samples near springs. The results suggested that environmental factors such as water and airborne microorganisms may be the main causes influencing microbial distribution. Most of the identified dominant species were common on the historical monuments and could contribute to biodeterioration. This analysis of microbiota will provide further information on the biodeterioration processes and preservation strategies of cultural heritage monuments in Lingyan Temple.},
}
@article {pmid34997308,
year = {2023},
author = {Shi, L and Xia, P and Lin, T and Li, G and Wang, T and Du, X},
title = {Temporal Succession of Bacterial Community Structure, Co-occurrence Patterns, and Community Assembly Process in Epiphytic Biofilms of Submerged Plants in a Plateau Lake.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {87-99},
pmid = {34997308},
issn = {1432-184X},
support = {41867056//National Nature Science Foundation of China/ ; 2021470//Guizhou Science and Technology Department/ ; U1812401//Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province/ ; },
mesh = {*Lakes/microbiology ; Biofilms ; *Microbiota ; Seasons ; },
abstract = {In shallow macrophytic lakes, epiphytic biofilms are formed on the surface of submerged plant stems and leaves because of algae and bacterial accumulation. Epiphytic biofilms significantly impact the health of the host vegetation and the biogeochemical cycling of lake elements. However, community diversity, species interactions, and community assembly mechanisms in epiphytic bacterial communities (EBCs) of plants during different growth periods are not well understood. We investigated the successional dynamics, co-occurrence patterns, and community assembly processes of epiphytic biofilm bacterial communities of submerged plants, Najas marina and Potamogeton lucens, from July to November 2020. The results showed a significant seasonal variation in EBC diversity and richness. Community diversity and richness increased from July to November, and the temperature was the most important driving factor for predicting seasonal changes in EBC community structure. Co-occurrence network analysis revealed that the average degree and graph density of the network increased from July to November, indicating that the complexity of the EBC network increased. The bacterial community co-occurrence network was limited by temperature, pH, and transparency. The phylogeny-based null model analysis showed that deterministic processes dominated the microbial community assembly in different periods, increasing their contribution. In addition, we found that as the dominance of deterministic processes increased, the microbial co-occurrence links increased, and the potential interrelationships between species became stronger. Thus, the findings provide insights into the seasonal variability of EBC assemblage and co-occurrence patterns in lacustrine ecosystems.},
}
@article {pmid34994948,
year = {2022},
author = {Bist, P and Choudhary, S},
title = {Impact of Heavy Metal Toxicity on the Gut Microbiota and Its Relationship with Metabolites and Future Probiotics Strategy: a Review.},
journal = {Biological trace element research},
volume = {200},
number = {12},
pages = {5328-5350},
pmid = {34994948},
issn = {1559-0720},
mesh = {Dysbiosis/chemically induced ; *Environmental Pollutants ; *Gastrointestinal Microbiome ; Heavy Metal Poisoning ; Humans ; *Metals, Heavy/toxicity ; *Probiotics/therapeutic use ; },
abstract = {The gut microbiota has a vital role in the maintenance of intestinal homeostasis. Several studies have revealed that environmental exposure to pollutants such as heavy metals may contribute to the progression of extensive list of diseases which may further lead to perturbations in the gut leading to dysbiosis. This manuscript critically reviews the alterations in the gut microbiota composition and function upon exposure to various toxic heavy metals prevalent in the environment. The disturbance in gut microbial ecology also affects the microbial metabolic profile which may alter the speciation state and bioavailability heavy metals thus affecting metal uptake-absorption/detoxification mechanisms associated to heavy metal metabolism. The toxic effects of various heavy metals either in single or in multimetallic combination and the gut microbiota associated host health and disease condition need a comprehensive assessment with important consideration for therapeutic and protective strategies against the damage to gut microbiota.},
}
@article {pmid34990848,
year = {2022},
author = {Kim, M and Sung, J and Chia, N},
title = {Resource-allocation constraint governs structure and function of microbial communities in metabolic modeling.},
journal = {Metabolic engineering},
volume = {70},
number = {},
pages = {12-22},
doi = {10.1016/j.ymben.2021.12.011},
pmid = {34990848},
issn = {1096-7184},
mesh = {*Microbiota ; },
abstract = {Predictive modeling tools for assessing microbial communities are important for realizing transformative capabilities of microbiomes in agriculture, ecology, and medicine. Constraint-based community-scale metabolic modeling is unique in its potential for making mechanistic predictions regarding both the structure and function of microbial communities. However, accessing this potential requires an understanding of key physicochemical constraints, which are typically considered on a per-species basis. What is needed is a means of incorporating global constraints relevant to microbial ecology into community models. Resource-allocation constraint, which describes how limited resources should be distributed to different cellular processes, sets limits on the efficiency of metabolic and ecological processes. In this study, we investigate the implications of resource-allocation constraints in community-scale metabolic modeling through a simple mechanism-agnostic implementation of resource-allocation constraints directly at the flux level. By systematically performing single-, two-, and multi-species growth simulations, we show that resource-allocation constraints are indispensable for predicting the structure and function of microbial communities. Our findings call for a scalable workflow for implementing a mechanistic version of resource-allocation constraints to ultimately harness the full potential of community-scale metabolic modeling tools.},
}
@article {pmid34990484,
year = {2022},
author = {Gestuveo, RJ and Parry, R and Dickson, LB and Lequime, S and Sreenu, VB and Arnold, MJ and Khromykh, AA and Schnettler, E and Lambrechts, L and Varjak, M and Kohl, A},
title = {Mutational analysis of Aedes aegypti Dicer 2 provides insights into the biogenesis of antiviral exogenous small interfering RNAs.},
journal = {PLoS pathogens},
volume = {18},
number = {1},
pages = {e1010202},
pmid = {34990484},
issn = {1553-7374},
support = {/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Aedes/genetics/*immunology/*virology ; Alphavirus Infections/*immunology ; Animals ; DNA Mutational Analysis ; Mosquito Vectors/virology ; RNA, Small Interfering/immunology ; RNA, Viral/immunology ; Ribonuclease III/genetics/*immunology ; Semliki forest virus ; },
abstract = {The exogenous small interfering RNA (exo-siRNA) pathway is a key antiviral mechanism in the Aedes aegypti mosquito, a widely distributed vector of human-pathogenic arboviruses. This pathway is induced by virus-derived double-stranded RNAs (dsRNA) that are cleaved by the ribonuclease Dicer 2 (Dcr2) into predominantly 21 nucleotide (nt) virus-derived small interfering RNAs (vsiRNAs). These vsiRNAs are used by the effector protein Argonaute 2 within the RNA-induced silencing complex to cleave target viral RNA. Dcr2 contains several domains crucial for its activities, including helicase and RNase III domains. In Drosophila melanogaster Dcr2, the helicase domain has been associated with binding to dsRNA with blunt-ended termini and a processive siRNA production mechanism, while the platform-PAZ domains bind dsRNA with 3' overhangs and subsequent distributive siRNA production. Here we analyzed the contributions of the helicase and RNase III domains in Ae. aegypti Dcr2 to antiviral activity and to the exo-siRNA pathway. Conserved amino acids in the helicase and RNase III domains were identified to investigate Dcr2 antiviral activity in an Ae. aegypti-derived Dcr2 knockout cell line by reporter assays and infection with mosquito-borne Semliki Forest virus (Togaviridae, Alphavirus). Functionally relevant amino acids were found to be conserved in haplotype Dcr2 sequences from field-derived Ae. aegypti across different continents. The helicase and RNase III domains were critical for silencing activity and 21 nt vsiRNA production, with RNase III domain activity alone determined to be insufficient for antiviral activity. Analysis of 21 nt vsiRNA sequences (produced by functional Dcr2) to assess the distribution and phasing along the viral genome revealed diverse yet highly consistent vsiRNA pools, with predominantly short or long sequence overlaps including 19 nt overlaps (the latter representing most likely true Dcr2 cleavage products). Combined with the importance of the Dcr2 helicase domain, this suggests that the majority of 21 nt vsiRNAs originate by processive cleavage. This study sheds new light on Ae. aegypti Dcr2 functions and properties in this important arbovirus vector species.},
}
@article {pmid34989745,
year = {2022},
author = {Hua, Q and Han, Y and Zhao, H and Zhang, H and Yan, B and Pei, S and He, X and Li, Y and Meng, X and Chen, L and Zhong, F and Li, D},
title = {Punicalagin alleviates renal injury via the gut-kidney axis in high-fat diet-induced diabetic mice.},
journal = {Food &amp; function},
volume = {13},
number = {2},
pages = {867-879},
doi = {10.1039/d1fo03343c},
pmid = {34989745},
issn = {2042-650X},
mesh = {Animals ; Diabetes Mellitus, Experimental/*complications ; Diabetic Nephropathies/*drug therapy ; *Diet, High-Fat ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Hydrolyzable Tannins/*pharmacology ; Inflammation/metabolism ; Kidney/*metabolism ; Mice ; Mice, Inbred C57BL ; Pomegranate/chemistry ; },
abstract = {Diabetic renal injury was associated with dysbiosis of the gut microbiota and intestinal barrier. Punicalagin (PU) from pomegranates potentially impacts the microbial ecosystem, intestinal barrier, and renal function. Therefore, we hypothesized that PU may improve diabetic renal injury by modulating the gut-kidney axis. The present study evaluated the effect of PU on the gut-kidney axis and kidney function in a diabetic renal injury mouse model induced by a high-fat diet (HFD). Mice were fed a HFD without PU or with at doses of 50 and 100 mg kg[-1] d[-1] for 8 weeks. Targeted metabolomics by GC-MS and 16S rRNA sequencing were implemented to determine short-chain fatty acids (SCFAs) and microbes. Further RNA sequencing analyses were performed to determine which differentially expressed genes were changed by PU. Compared with the DM model group, PU supplementation improved diabetic renal injury, ameliorated kidney architecture and function, and reshaped gut microbial ecology. Additionally, PU reversed HFD-induced gut barrier dysfunction, promoted cecal SCFA concentrations and inhibited serum lipopolysaccharide (LPS) and diamine oxidase (DAO) levels. Moreover, correlation analysis found that cecal SCFAs were significantly negatively correlated with inflammation-related genes in the kidney. The present results indicated that PU, a promising bioactive polyphenol, successfully improved diabetic renal injury, most likely through the gut-kidney axis.},
}
@article {pmid34988711,
year = {2022},
author = {Liu, Q and Lai, Z and Wang, C and Ni, J and Gao, Y},
title = {Seasonal variation significantly affected bacterioplankton and eukaryoplankton community composition in Xijiang River, China.},
journal = {Environmental monitoring and assessment},
volume = {194},
number = {2},
pages = {55},
pmid = {34988711},
issn = {1573-2959},
support = {NA//Fund of Survey and Evaluation of the Fishery Environmental Capacity in the Important River Waters of Guangxi/ ; 2018YFD0900802//Key Technologies Research and Development Program/ ; 2021SJ-TD1//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 2019A1515011589//Guangdong Basic and Applied Basic Research Foundation/ ; },
mesh = {Aquatic Organisms ; China ; *Ecosystem ; Environmental Monitoring ; Plankton ; RNA, Ribosomal, 16S ; *Rivers ; Seasons ; },
abstract = {Both bacterioplankton and eukaryoplankton communities play important roles in the geochemical cycles and energy flows of river ecosystems. However, whether a seasonal change in bacterioplankton and eukaryoplankton communities is synchronous remains unclear. To test the synchronicity and analyze how physical and chemical environmental factors affect these communities, we compared bacterioplankton and eukaryoplankton communities in surface water samples between March (dry season) and June (rainfall season) considering water environmental factors. Our results showed that there was no significant difference in operational taxonomic unit number, Shannon index, and Chao1 index in bacterioplankton and eukaryoplankton communities between March and June. However, principal component analysis showed that the communities were significantly different between the sampling times and sampling sites. Water temperature (WT), oxidation-reduction potential (ORP), water transparency (SD), NO3-N, and NH3 significantly influenced bacterioplankton communities, and WT, SD, ORP, and NH4-N significantly influenced eukaryoplankton communities in the river. These results implied that compared with the sampling sites, sampling times more significantly affected the bacterioplankton and eukaryoplankton river communities by influencing WT, ORP, SD, and nitrogen forms.},
}
@article {pmid34988622,
year = {2022},
author = {Liberti, A and Natarajan, O and Atkinson, CGF and Dishaw, LJ},
title = {Secreted immunoglobulin domain effector molecules of invertebrates and management of gut microbial ecology.},
journal = {Immunogenetics},
volume = {74},
number = {1},
pages = {99-109},
pmid = {34988622},
issn = {1432-1211},
mesh = {Animals ; Drosophila melanogaster ; *Gastrointestinal Microbiome ; Immunoglobulin Domains ; Invertebrates ; Vertebrates ; },
abstract = {The origins of a "pass-through" gut in early bilaterians facilitated the exploration of new habitats, motivated the innovation of feeding styles and behaviors, and helped drive the evolution of more complex organisms. The gastrointestinal tract has evolved to consist of a series of interwoven exchanges between nutrients, host immunity, and an often microbe-rich environmental interface. Not surprisingly, animals have expanded their immune repertoires to include soluble effectors that can be secreted into luminal spaces, e.g., in the gut, facilitating interactions with microbes in ways that influence their settlement dynamics, virulence, and their interaction with other microbes. The immunoglobulin (Ig) domain, which is also found in some non-immune molecules, is recognized as one of the most versatile recognition domains lying at the interface of innate and adaptive immunity; among vertebrates, secreted Igs are known to play crucial roles in the management of gut microbial communities. In this mini-review, we will focus on secreted immune effectors possessing Ig-like domains in invertebrates, such as the fibrinogen-related effector proteins first described in the gastropod Biomphalaria glabrata, the Down syndrome cellular adhesion molecule first described in the arthropod, Drosophila melanogaster, and the variable region-containing chitin-binding proteins of the protochordates. We will highlight our current understanding of their function and their potential role, if not yet recognized, in the establishment and maintenance of host-microbial interfaces and argue that these Igs are likely also essential to microbiome management.},
}
@article {pmid34983601,
year = {2022},
author = {Maitre, A and Wu-Chuang, A and Aželytė, J and Palinauskas, V and Mateos-Hernández, L and Obregon, D and Hodžić, A and Valiente Moro, C and Estrada-Peña, A and Paoli, JC and Falchi, A and Cabezas-Cruz, A},
title = {Vector microbiota manipulation by host antibodies: the forgotten strategy to develop transmission-blocking vaccines.},
journal = {Parasites &amp; vectors},
volume = {15},
number = {1},
pages = {4},
pmid = {34983601},
issn = {1756-3305},
mesh = {Animals ; Antibodies/blood/*immunology ; Arthropod Vectors/*immunology ; Disease Transmission, Infectious/*prevention &amp; control ; Hemolymph/immunology ; Host-Pathogen Interactions ; Humans ; Salivary Glands/immunology ; Vaccine Development/*methods ; },
abstract = {Human and animal pathogens that are transmitted by arthropods are a global concern, particularly those vectored by ticks (e.g. Borrelia burgdorferi and tick-borne encephalitis virus) and mosquitoes (e.g. malaria and dengue virus). Breaking the circulation of pathogens in permanent foci by controlling vectors using acaricide-based approaches is threatened by the selection of acaricide resistance in vector populations, poor management practices and relaxing of control measures. Alternative strategies that can reduce vector populations and/or vector-mediated transmission are encouraged worldwide. In recent years, it has become clear that arthropod-associated microbiota are involved in many aspects of host physiology and vector competence, prompting research into vector microbiota manipulation. Here, we review how increased knowledge of microbial ecology and vector-host interactions is driving the emergence of new concepts and tools for vector and pathogen control. We focus on the immune functions of host antibodies taken in the blood meal as they can target pathogens and microbiota bacteria within hematophagous arthropods. Anti-microbiota vaccines are presented as a tool to manipulate the vector microbiota and interfere with the development of pathogens within their vectors. Since the importance of some bacterial taxa for colonization of vector-borne pathogens is well known, the disruption of the vector microbiota by host antibodies opens the possibility to develop novel transmission-blocking vaccines.},
}
@article {pmid34982540,
year = {2022},
author = {Vandermaesen, J and Du, S and Daly, AJ and Baetens, JM and Horemans, B and De Baets, B and Boon, N and Springael, D},
title = {Interspecies Interactions of the 2,6-Dichlorobenzamide Degrading Aminobacter sp. MSH1 with Resident Sand Filter Bacteria: Indications for Mutual Cooperative Interactions That Improve BAM Mineralization Activity.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {2},
pages = {1352-1364},
doi = {10.1021/acs.est.1c06653},
pmid = {34982540},
issn = {1520-5851},
mesh = {Bacteria ; Benzamides ; Biodegradation, Environmental ; *Groundwater ; *Phyllobacteriaceae ; *Water Purification/methods ; },
abstract = {Bioaugmentation often involves an invasion process requiring the establishment and activity of a foreign microbe in the resident community of the target environment. Interactions with resident micro-organisms, either antagonistic or cooperative, are believed to impact invasion. However, few studies have examined the variability of interactions between an invader and resident species of its target environment, and none of them considered a bioremediation context. Aminobacter sp. MSH1 mineralizing the groundwater micropollutant 2,6-dichlorobenzamide (BAM), is proposed for bioaugmentation of sand filters used in drinking water production to avert BAM contamination. We examined the nature of the interactions between MSH1 and 13 sand filter resident bacteria in dual and triple species assemblies in sand microcosms. The residents affected MSH1-mediated BAM mineralization without always impacting MSH1 cell densities, indicating effects on cell physiology rather than on cell number. Exploitative competition explained most of the effects (70%), but indications of interference competition were also found. Two residents improved BAM mineralization in dual species assemblies, apparently in a mutual cooperation, and overruled negative effects by others in triple species systems. The results suggest that sand filter communities contain species that increase MSH1 fitness. This opens doors for assisting bioaugmentation through co-inoculation with "helper" bacteria originating from and adapted to the target environment.},
}
@article {pmid34982193,
year = {2023},
author = {Sangodkar, N and Gonsalves, MJ and Nazareth, DR},
title = {Macrofaunal Distribution, Diversity, and Its Ecological Interaction at the Cold Seep Site of Krishna-Godavari Basin, East Coast of India.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {61-75},
pmid = {34982193},
issn = {1432-184X},
mesh = {Animals ; *Ecosystem ; Geologic Sediments/chemistry ; Biodiversity ; Methane/chemistry ; Water ; *Bivalvia ; },
abstract = {Cold seeps are characterized by typical endemic communities with associated microorganisms that depend on sulfide, methane, reduced nitrogenous compounds, and metals as electron donors for their survival through chemosynthesis. The discovery of an active cold seep site in January 2018 in the Krishna-Godavari (K-G) basin of Bay of Bengal was followed by a transit cruise in March 2018 to investigate the distribution and diversity of macrofauna. Further, the ambient sediment and pore water biochemistry were estimated to understand its relationship with macrofauna and the microbial associates of the sediment. Samples were collected at a water depth of around 1750 m at 3 stations: SP1, SP2, and SP3, using the box corer. The benthic fauna at the sites consisted mainly of Bivalvia, shrimps of Caridea family, Gastropoda species, Malacostraca species, Polychaeta, and few species of Echinoidea, Ophiuroidea, and Echiura. A total of 2313 macrofaunal individuals belonging to 8 classes, 18 families, and 20 species were identified from all the three stations. The communities were diverse at these sites with an average Shannon diversity index of 1.64 and are closely related to the lineages previously studied in ecologically similar environments. Most of the macrofauna were found to be filter feeders preferring a low organic carbon environment. Relict vesicomyid clams at the present study site suggest the succession from vesicomyids to the present composition of bivalve mussels and siboglinid worms. The microbial associates in the sediment significantly correlated with methane and hydrogen sulfide concentrations. The study suggests that the K-G basin cold seep serves as a conducive environment for the flourishing of benthic communities and therefore can support a rich biodiversity.},
}
@article {pmid34981145,
year = {2023},
author = {Nabeshima, K and Sato, S and Brinkerhoff, RJ and Amano, M and Kabeya, H and Itou, T and Maruyama, S},
title = {Prevalence and Genetic Diversity of Bartonella Spp. in Northern Bats (Eptesicus nilssonii) and Their Blood-Sucking Ectoparasites in Hokkaido, Japan.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {298-306},
pmid = {34981145},
issn = {1432-184X},
support = {18K06003//japan society for the promotion of science/ ; },
mesh = {Animals ; *Bartonella ; *Chiroptera/microbiology ; Phylogeny ; Prevalence ; Japan/epidemiology ; *Bartonella Infections/epidemiology/veterinary/microbiology ; Genetic Variation ; },
abstract = {We investigated the prevalence of Bartonella in 123 northern bats (Eptesicus nilssonii) and their ectoparasites from Hokkaido, Japan. A total of 174 bat fleas (Ischnopsyllus needhami) and two bat bugs (Cimex japonicus) were collected from the bats. Bartonella bacteria were isolated from 32 (26.0%) of 123 bats. Though Bartonella DNA was detected in 79 (45.4%) of the bat fleas, the bacterium was isolated from only one bat flea (0.6%). The gltA sequences of the isolates were categorized into genotypes I, II, and III, which were found in both bats and their fleas. The gltA sequences of genotypes I and II showed 97.6% similarity with Bartonella strains from a Finnish E. nilssonii and a bat flea from a E. serotinus in the Netherlands. The rpoB sequences of the genotypes showed 98.9% similarity with Bartonella strain 44722 from E. serotinus in Republic of Georgia. The gltA and rpoB sequences of genotype III showed 95.9% and 96.7% similarity with Bartonella strains detected in shrews in Kenya and France, respectively. Phylogenetic analysis revealed that Bartonella isolates of genotypes I and II clustered with Bartonella strains from Eptesicus bats in Republic of Georgia and Finland, Myotis bats in Romania and the UK, and a bat flea from an Eptesicus bat in Finland. In contrast, genotype III formed a clade with B. florencae, B. acomydis, and B. birtlesii. These data suggest that northern bats in Japan harbor two Bartonella species and the bat flea serves as a potential vector of Bartonella transmission among the bats.},
}
@article {pmid34980289,
year = {2022},
author = {Yang, Y and Sun, J and Chen, C and Zhou, Y and Van Dover, CL and Wang, C and Qiu, JW and Qian, PY},
title = {Metagenomic and metatranscriptomic analyses reveal minor-yet-crucial roles of gut microbiome in deep-sea hydrothermal vent snail.},
journal = {Animal microbiome},
volume = {4},
number = {1},
pages = {3},
pmid = {34980289},
issn = {2524-4671},
support = {DY135-E2-1-03//China Ocean Mineral Resources Research and Development Association/ ; GML2019ZD0409//the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 2019B030302004-04//the Major Basic and Applied Basic Research Projects of Guangdong Province/ ; SMSEGL20SC01//the Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 91951201//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Marine animals often exhibit complex symbiotic relationship with gut microbes to attain better use of the available resources. Many animals endemic to deep-sea chemosynthetic ecosystems host chemoautotrophic bacteria endocellularly, and they are thought to rely entirely on these symbionts for energy and nutrition. Numerous investigations have been conducted on the interdependence between these animal hosts and their chemoautotrophic symbionts. The provannid snail Alviniconcha marisindica from the Indian Ocean hydrothermal vent fields hosts a Campylobacterial endosymbiont in its gill. Unlike many other chemosymbiotic animals, the gut of A. marisindica is reduced but remains functional; yet the contribution of gut microbiomes and their interactions with the host remain poorly characterised.<br><br>RESULTS: Metagenomic and metatranscriptomic analyses showed that the gut microbiome of A. marisindica plays key nutritional and metabolic roles. The composition and relative abundance of gut microbiota of A. marisindica were different from those of snails that do not depend on endosymbiosis. The relative abundance of microbial taxa was similar amongst three individuals of A. marisindica with significant inter-taxa correlations. These correlations suggest the potential for interactions between taxa that may influence community assembly and stability. Functional profiles of the gut microbiome revealed thousands of additional genes that assist in the use of vent-supplied inorganic compounds (autotrophic energy source), digest host-ingested organics (carbon source), and recycle the metabolic waste of the host. In addition, members of five taxonomic classes have the potential to form slime capsules&#xa0;to protect themselves from the host immune system, thereby contributing to homeostasis. Gut microbial ecology and its interplay with the host thus contribute to the nutritional and metabolic demands of A. marisindica.<br><br>CONCLUSIONS: The findings advance the understanding of how deep-sea chemosymbiotic animals use available resources through contributions from gut microbiota. Gut microbiota may be critical in the survival of invertebrate hosts with autotrophic endosymbionts in extreme environments.},
}
@article {pmid34979467,
year = {2022},
author = {Lindner, BG and Suttner, B and Zhu, KJ and Conrad, RE and Rodriguez-R, LM and Hatt, JK and Brown, J and Konstantinidis, KT},
title = {Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms.},
journal = {Water research},
volume = {210},
number = {},
pages = {117993},
doi = {10.1016/j.watres.2021.117993},
pmid = {34979467},
issn = {1879-2448},
mesh = {Laboratories ; *Metagenome ; *Metagenomics ; Sewage ; Water Pollution/analysis ; },
abstract = {Little is known about the genomic diversity of the microbial communities associated with raw municipal wastewater (sewage), including whether microbial populations specific to sewage exist and how such populations could be used to improve source attribution and apportioning in contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) to perturb laboratory freshwater mesocosms, simulating sewage contamination events, and followed these mesocosms with shotgun metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inocula yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of the populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster than aerobes under the well-aerated incubation conditions. Notably, a portion of these populations showed decay patterns similar to those of common markers, Enterococcus and HF183. Despite the apparent decay of these populations, the abundance of β-lactamase encoding genes remained high throughout incubation relative to the control. Lastly, we constructed genomic libraries representing several different fecal sources and outline a bioinformatic approach which leverages these libraries for identifying and apportioning contamination signal among multiple probable sources using shotgun metagenomic data.},
}
@article {pmid34977966,
year = {2023},
author = {Vidhate, RP and Dawkar, VV and Punekar, SA and Giri, AP},
title = {Genomic Determinants of Entomopathogenic Fungi and Their Involvement in Pathogenesis.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {49-60},
pmid = {34977966},
issn = {1432-184X},
mesh = {Animals ; *Fungi/genetics ; *Insecta/microbiology ; Plants/microbiology ; Genomics ; Endophytes ; },
abstract = {Entomopathogenic fungi offer an effective and eco-friendly alternative to curb insect populations in biocontrol strategy. The evolutionary history of selected entomopathogenic fungi indicates their ancestral relationship with plant endophytes. During this host shifting, entomopathogenic fungi must have acquired multiple mechanisms, including a combination of various biomolecules that make them distinguishable from other fungi. In this review, we focus on understanding various biochemical and molecular mechanisms involved in entomopathogenesis. In particular, we attempt to explain the indispensable role of enlarged gene families of various virulent factors, viz. chitinases, proteases, lipases, specialized metabolites, and cytochrome P450, in entomopathogenesis. Our analysis suggests that entomopathogenic fungi recruit a different set of gene products during the progression of pathogenesis. Knowledge of these bio-molecular interactions between fungi and insect hosts will allow researchers to execute pointed efforts towards the development of improved entomopathogenic fungal strains.},
}
@article {pmid34976074,
year = {2021},
author = {Cannesson, A and Elenga, N},
title = {Community-Acquired Pneumonia Requiring Hospitalization among French Guianese Children.},
journal = {International journal of pediatrics},
volume = {2021},
number = {},
pages = {4358818},
pmid = {34976074},
issn = {1687-9740},
abstract = {Community-acquired pneumonia remains a leading cause of hospitalizations among children worldwide. The diagnosis is based on the history, the physical examination results in children with fever plus respiratory signs and symptoms, and chest radiography. The microbiological etiology is confirmed by viral testing and hemocultures. The most likely etiology depends on the age of the child. The features of childhood pneumonia vary between countries and territories. The purpose of this study was to describe the epidemiological characteristics and current microbial ecology of community-acquired pneumonia in children in French Guiana. We performed a retrospective, descriptive, and monocentric study between January 1, 2015, and December 31, 2017, in the pediatric ward of the Cayenne Hospital in French Guiana. The studied population was aged from 0 to 15 years and 3 months and hospitalized for acute community-acquired pneumonia. A total of 415 patients (mean age 3.62 years) were included. A pathogen was identifiable in 22.4% of cases, including bacteria in 61.3%, viruses in 43%, and coinfections in 14%. The main pathogens were respiratory syncytial virus (31.2%), Streptococcus pneumoniae (20.4%), Haemophilus influenzae (11.8%), and Mycoplasma pneumoniae (10.8%). The burden of hospitalization for children with community-acquired pneumonia was highest among less than 2 years, in whom respiratory viruses were the most commonly detected causes of pneumonia. The share of vaccine-preventable diseases (S. pneumoniae, H. influenzae, and influenza) remains high. With the vaccination requirement imposed since 1 January 2018 against pneumococcus, Haemophilus influenzae, and whooping cough and the possibility of practicing multiplex PCR in our hospital, it will be interesting to study the impact of this law enforcement on new child generations and compare these new data to our study.},
}
@article {pmid34971998,
year = {2022},
author = {Chen, P and Liu, H and Xing, Z and Wang, Y and Zhang, X and Zhao, T and Zhang, Y},
title = {Cometabolic degradation mechanism and microbial network response of methanotrophic consortia to chlorinated hydrocarbon solvents.},
journal = {Ecotoxicology and environmental safety},
volume = {230},
number = {},
pages = {113110},
doi = {10.1016/j.ecoenv.2021.113110},
pmid = {34971998},
issn = {1090-2414},
abstract = {The cometabolism mechanism of chlorinated hydrocarbon solvents (CHSs) in mixed consortia remains largely unknown. CHS biodegradation characteristics and microbial networks in methanotrophic consortia were studied for the first time. The results showed that all CHSs can efficiently be degraded via cometabolism with a maximum degradation rate of 4.8 mg/(h·gcell). Chloroalkane and chloroethylene were more easily degraded than chlorobenzenes by methanotrophic consortia, especially nonfully chlorinated aliphatic hydrocarbons, which were converted to Cl[-] with a production rate of 0.29-0.36 mg/(h·gcell). In addition, the microecological response results indicated that Methylocystaceae (49.0%), Methylomonas (65.3%) and Methylosarcina (41.9%) may be the major functional degraders in methanotrophic consortia. Furthermore, the results of the microbial correlation network suggested that interactive relationships constructed by type I methanotrophs and heterotrophs determined biodegradability. Additionally, PICRUSt analysis showed that CHSs could increase the relative abundance of CHS degradation genes and reduce the relative abundance of methane oxidation genes, which was in good agreement with the experimental results.},
}
@article {pmid34970700,
year = {2023},
author = {Montiel-Molina, JAM and Sexton, JP and Frank, AC and Beman, JM},
title = {Archaeal and Bacterial Diversity and Distribution Patterns in Mediterranean-Climate Vernal Pools of Mexico and the Western USA.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {24-36},
pmid = {34970700},
issn = {1432-184X},
mesh = {*Archaea/genetics ; Mexico ; Ecosystem ; Soil Microbiology ; Bacteria/genetics ; Soil ; *Microbiota ; Water ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; },
abstract = {Biogeographic patterns in microorganisms are poorly understood, despite the importance of microbial communities for a range of ecosystem processes. Our knowledge of microbial ecology and biogeography is particularly deficient in rare and threatened ecosystems. We tested for three ecological patterns in microbial community composition within ephemeral wetlands-vernal pools-located across Baja California (Mexico) and California (USA): (1) habitat filtering; (2) a latitudinal diversity gradient; and (3) distance decay in community composition. Paired water and soil samples were collected along a latitudinal transect of vernal pools, and bacterial and archaeal communities were characterized using 16S rDNA sequencing. We identified two main microbial communities, with one community present in the soil matrix that included archaeal and bacterial soil taxa, and another community present in the overlying water that was dominated by common freshwater bacterial taxa. Aquatic microbial communities were more diverse in the north, and displayed a significant but inverted latitudinal diversity pattern. Aquatic communities also exhibited a significant distance-decay pattern, with geographic proximity, and precipitation explaining part of the community variation. Collectively these results indicate greater sensitivity to spatial and environmental variation in vernal pool aquatic microbial communities than in soil microbial communities. We conclude that vernal pool aquatic microbial communities can display distribution patterns similar to those exhibited by larger organisms, but differ in some key aspects, such as the latitudinal gradient in diversity.},
}
@article {pmid34968587,
year = {2022},
author = {Wang, D and Huang, K and He, X and Zhang, XX and Meng, Y},
title = {Varied interspecies interactions between anammox and denitrifying bacteria enhanced nitrogen removal in a single-stage simultaneous anammox and denitrification system.},
journal = {The Science of the total environment},
volume = {813},
number = {},
pages = {152519},
doi = {10.1016/j.scitotenv.2021.152519},
pmid = {34968587},
issn = {1879-1026},
mesh = {Anaerobic Ammonia Oxidation ; Bacteria/genetics ; Bioreactors ; *Denitrification ; *Nitrogen ; Oxidation-Reduction ; Sewage ; Wastewater ; },
abstract = {The simultaneous anammox and denitrification (SAD) system has received growing interest for the enhanced nitrogen removal, while the ecological traits of microbial community including spatial distribution characteristics, assembly processes and interspecies interactions have not been fully unraveled. The present study applied metagenomics and ecological analysis methods to gain the ecological traits of microbial communities in the SAD system across different organic substrate loadings. Results showed that organic matter significantly affected the bioreactor performance, and the optimal total nitrogen removal efficiency reached 93.4 ± 0.7% under the COD concentrations of 180 ± 18.2 mg/L. Functional organisms including Candidatus Brocadia (3.9%), Denitratisoma (1.6%), Dokdonella (4.4%) and Thauera (4.6%) obviously enriched under the optimal organic loading conditions. Moreover, microbial communities were significantly governed by deterministic process under high organic concentrations, and the denitrifying organisms displayed important ecological roles in the communities. Although anammox bacteria obviously enriched at the middle of bioreactor, it possessed the highest expression activities at both bottom and middle sites. Denitrifying bacteria that enriched at the bottom sites strongly achieved nitrate reduction and provided nitrite for anammox bacteria, while these organisms trended to compete nitrite with anammox bacteria at the middle site. These findings highlight the importance of microbial ecology in the SAD systems, which may expand our understanding of the synergistic patterns between anammox and denitrifying bacteria.},
}
@article {pmid34966927,
year = {2021},
author = {Scholz, AH and Lange, M and Habekost, P and Oldham, P and Cancio, I and Cochrane, G and Freitag, J},
title = {Myth-busting the provider-user relationship for digital sequence information.},
journal = {GigaScience},
volume = {10},
number = {12},
pages = {},
pmid = {34966927},
issn = {2047-217X},
mesh = {*Biodiversity ; *International Cooperation ; },
abstract = {BACKGROUND: The United Nations Convention on Biological Diversity (CBD) formally recognized the sovereign rights of nations over their biological diversity. Implicit within the treaty is the idea that mega-biodiverse countries will provide genetic resources and grant access to them and scientists in high-income countries will use these resources and share back benefits. However, little research has been conducted on how this framework is reflected in real-life scientific practice.<br><br>RESULT: Currently, parties to the CBD are debating whether digital sequence information (DSI) should be regulated under a new benefit-sharing framework. At this critical time point in the upcoming international negotiations, we test the fundamental hypothesis of provision and use of DSI by looking at the global patterns of access and use in scientific publications.<br><br>CONCLUSION: Our data reject the provider-user relationship and suggest a far more complex information flow for DSI. Therefore, any new policy decisions on DSI should be aware of the high level of use of DSI across low- and middle-income countries and seek to preserve open access to this crucial common good.},
}
@article {pmid34966925,
year = {2021},
author = {Lange, M and Alako, BTF and Cochrane, G and Ghaffar, M and Mascher, M and Habekost, PK and Hillebrand, U and Scholz, U and Schorch, F and Freitag, J and Scholz, AH},
title = {Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature.},
journal = {GigaScience},
volume = {10},
number = {12},
pages = {},
pmid = {34966925},
issn = {2047-217X},
mesh = {Base Sequence ; *Data Mining ; Databases, Nucleic Acid ; Europe ; *Nucleotides ; },
abstract = {BACKGROUND: Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSD provenance, scientific use, and reuse in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level.<br><br>FINDINGS: We extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. We constructed flat data tables and a data warehouse with an interactive web application to enable ad hoc exploration of NSD use and summary statistics.<br><br>CONCLUSIONS: The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enable scientists worldwide to join literature and sequence databases in a multidimensional fashion. As a concrete use case, we visualized statistics of country clusters concerning NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.},
}
@article {pmid34964290,
year = {2021},
author = {Baliarda, A and Winkler, M and Tournier, L and Tinsley, CR and Aymerich, S},
title = {Dynamic interspecies interactions and robustness in a four-species model biofilm.},
journal = {MicrobiologyOpen},
volume = {10},
number = {6},
pages = {e1254},
pmid = {34964290},
issn = {2045-8827},
mesh = {Bacillus cereus/physiology ; Biofilms/*growth &amp; development ; Ecosystem ; *Microbial Interactions ; *Microbiota ; Micrococcaceae/physiology ; Peptides/metabolism ; Plankton/physiology ; Pseudomonas fluorescens/physiology ; Rhodocyclaceae/physiology ; },
abstract = {Interspecific interactions within biofilms determine relative species abundance, growth dynamics, community resilience, and success or failure of invasion by an extraneous organism. However, deciphering interspecific interactions and assessing their contribution to biofilm properties and function remain a challenge. Here, we describe the constitution of a model biofilm composed of four bacterial species belonging to four different genera (Rhodocyclus sp., Pseudomonas fluorescens, Kocuria varians, and Bacillus cereus), derived from a biofilm isolated from an industrial milk pasteurization unit. We demonstrate that the growth dynamics and equilibrium composition of this biofilm are highly reproducible. Based on its equilibrium composition, we show that the establishment of this four-species biofilm is highly robust against initial, transient perturbations but less so towards continuous perturbations. By comparing biofilms formed from different numbers and combinations of the constituent species and by fitting a growth model to the experimental data, we reveal a network of dynamic, positive, and negative interactions that determine the final composition of the biofilm. Furthermore, we reveal that the molecular determinant of one negative interaction is the thiocillin I synthesized by the B. cereus strain, and demonstrate its importance for species distribution and its impact on robustness by mutational analysis of the biofilm ecosystem.},
}
@article {pmid34963611,
year = {2022},
author = {Bouchali, R and Mandon, C and Marti, R and Michalon, J and Aigle, A and Marjolet, L and Vareilles, S and Kouyi, GL and Polomé, P and Toussaint, JY and Cournoyer, B},
title = {Bacterial assemblages of urban microbiomes mobilized by runoff waters match land use typologies and harbor core species involved in pollutant degradation and opportunistic human infections.},
journal = {The Science of the total environment},
volume = {815},
number = {},
pages = {152662},
doi = {10.1016/j.scitotenv.2021.152662},
pmid = {34963611},
issn = {1879-1026},
mesh = {Bacteria/genetics ; *Environmental Pollutants ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/analysis ; },
abstract = {Cities are patchworks of urban catchments divided into functional units according to their commercial, residential and industrial activities, and socio-urbanistic patterns. The hypothesis of city surface microbiomes being structured by socio-urbanistic variables leading to an emergence of synurbic taxa was tested. According to the r/K microbial ecology theory, a gradient of well-adapted synurbic K-strategists and of opportunistic -r-strategists should occur over city surfaces. K-strategists would be core components while r-ones would be transiently detected. To resolve these patterns, sub-catchments (n = 21) of an area of high commercial and industrial activities were investigated over three time periods covering one year. The sub-catchments' land use patterns and associated human behaviors were converted into socio-urbanistic variables and groupings. Bacterial cells mobilized by runoffs per sub-catchment were recovered, and analyzed by classical approaches, microbial source tracking DNA assays and DNA meta-barcoding approaches. Relationships between these datasets, the runoff physico-chemical properties, and descriptors of the socio-urbanistic groupings were investigated. 16S rRNA meta-barcoding analyses showed evidence of the occurrence of K- and r-like strategists. Twenty-eight core genera were identified, and correlation networks revealed large bacterial modules organized around actinobacterial taxa involved in hydrocarbon degradation processes. Other bacterial networks were related to the occurrences of hygienic wastes, and involved bacteria originating from fecal contaminations. Several r-strategists like Sulfurospirillum were recorded and found associated to point source pollutions. The tpm-metabarcoding approach deciphered these r / K strategists at the species level among more than ten genera. Nine core K-like Pseudomomas species were identified. The P. aeruginosa human opportunistic pathogen and P. syringae phytopathogens were part of these K-strategists. Other tpm-harboring bacterial pathogens showed r-like opportunistic distribution patterns. Correlation network analyses indicated a strong incidence of hygienic wastes and hydrocarbon-pollutions on tpm-harboring bacteria. These analyses demonstrated the occurrence of core synurbic bacterial K-strategists over city surfaces.},
}
@article {pmid34959793,
year = {2021},
author = {Binder, C and Schned, H and Longford, N and Schwindt, E and Thanhaeuser, M and Thajer, A and Goeral, K and Tardelli, M and Berry, D and Wisgrill, L and Seki, D and Berger, A and Klebermass-Schrehof, K and Repa, A and Giordano, V},
title = {A Mixed-Lipid Emulsion Containing Fish Oil for the Parenteral Nutrition of Preterm Infants: No Impact on Visual Neuronal Conduction.},
journal = {Nutrients},
volume = {13},
number = {12},
pages = {},
pmid = {34959793},
issn = {2072-6643},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Evoked Potentials, Visual/*drug effects ; Fat Emulsions, Intravenous/*administration &amp; dosage/*chemistry ; Female ; Fish Oils/*administration &amp; dosage ; Humans ; Infant, Newborn ; Infant, Premature/physiology ; Male ; Neural Conduction/*drug effects ; Olive Oil/administration &amp; dosage ; Parenteral Nutrition ; Retrospective Studies ; Soybean Oil/administration &amp; dosage ; Triglycerides/administration &amp; dosage ; },
abstract = {Fish oil is rich in omega-3 fatty acids and essential for neuronal myelination and maturation. The aim of this study was to investigate whether the use of a mixed-lipid emulsion composed of soybean oil, medium-chain triglycerides, olive oil, and fish oil (SMOF-LE) compared to a pure soybean oil-based lipid emulsion (S-LE) for parenteral nutrition had an impact on neuronal conduction in preterm infants. This study is a retrospective matched cohort study comparing preterm infants <1000 g who received SMOF-LE in comparison to S-LE for parenteral nutrition. Visual evoked potentials (VEPs) were assessed longitudinally from birth until discharge. The latencies of the evoked peaks N2 and P2 were analyzed. The analysis included 76 infants (SMOF-LE: n = 41 and S-LE: n = 35) with 344 VEP measurements (SMOF-LE: n= 191 and S-LE n = 153). Values of N2 and P2 were not significantly different between the SMOF-LE and S-LE groups. A possible better treatment effect in the SMOF-LE group was seen as a trend toward a shorter latency, indicating faster neural conduction at around term-equivalent age. Prospective trials and follow-up studies are necessary in order to evaluate the potential positive effect of SMOF-LE on neuronal conduction and visual pathway maturation.},
}
@article {pmid34958387,
year = {2022},
author = {Kable, ME and Chin, EL and Storms, D and Lemay, DG and Stephensen, CB},
title = {Tree-Based Analysis of Dietary Diversity Captures Associations Between Fiber Intake and Gut Microbiota Composition in a Healthy US Adult Cohort.},
journal = {The Journal of nutrition},
volume = {152},
number = {3},
pages = {779-788},
doi = {10.1093/jn/nxab430},
pmid = {34958387},
issn = {1541-6100},
mesh = {Adolescent ; Adult ; Aged ; Cross-Sectional Studies ; Diet ; Dietary Fiber/analysis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Young Adult ; },
abstract = {BACKGROUND: Diet patterns are a significant and modifiable contributing factor to the composition of the human gut microbiota.<br><br>OBJECTIVES: We set out to identify reproducible relationships between diet and gut microbial community composition in a diverse, healthy US adult cohort.<br><br>METHODS: We collected 2 to 3 automated self-administered 24-hour dietary recalls over 10-14 days, together with a single stool sample, from 343 healthy adults in a cross-sectional phenotyping study. This study examined a multi-ethnic cohort balanced for age (18-65 years), sex, and BMI (18.5-45 kg/m2). Dietary data were edited to a tree format according to published methods. The tree structure was annotated with the average total grams of dry weight, fat, protein, carbohydrate, or fiber from each food item reported. The alpha and beta diversity measurements, calculated using the tree structure, were analyzed relative to the microbial community diversity, determined by a Quantitative Insights Into Microbial Ecology (QIIME) 2 analysis of the bacterial 16S ribosomal RNA V4 region, sequenced from stool samples. K-means clustering was used to form groups of individuals consuming similar diets, and gut microbial communities were compared among groups using differential expression analysis for sequence count data.<br><br>RESULTS: The alpha diversity of diet dry weight was significantly correlated with the gut microbial community alpha diversity (r&#xa0;=&#xa0;0.171). The correlation improved when diet was characterized using grams of carbohydrates (r&#xa0;=&#xa0;0.186) or fiber (r&#xa0;=&#xa0;0.213). Bifidobacterium was enriched with diets containing higher levels of total carbohydrate from cooked grains. Lachnospira, was enriched with diet patterns containing high consumption of fiber from fruits excluding berries.<br><br>CONCLUSIONS: The tree structure, annotated with grams of carbohydrate, is a robust analysis method for comparing self-reported diet to the gut microbial community composition. This method identified consumption of fiber from fruit robustly associated with an abundance of pectinolytic bacterial genus, Lachnospira, in the guts of healthy adults. This trial was registered at clinicaltrials.gov as NCT02367287.},
}
@article {pmid34956127,
year = {2021},
author = {Blumberg, KL and Ponsero, AJ and Bomhoff, M and Wood-Charlson, EM and DeLong, EF and Hurwitz, BL},
title = {Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {765268},
pmid = {34956127},
issn = {1664-302X},
abstract = {Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven't been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making 'omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.},
}
@article {pmid34956126,
year = {2021},
author = {Krukenberg, V and Reichart, NJ and Spietz, RL and Hatzenpichler, R},
title = {Microbial Community Response to Polysaccharide Amendment in Anoxic Hydrothermal Sediments of the Guaymas Basin.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {763971},
pmid = {34956126},
issn = {1664-302X},
abstract = {Organic-rich, hydrothermal sediments of the Guaymas Basin are inhabited by diverse microbial communities including many uncultured lineages with unknown metabolic potential. Here we investigated the short-term effect of polysaccharide amendment on a sediment microbial community to identify taxa involved in the initial stage of macromolecule degradation. We incubated anoxic sediment with cellulose, chitin, laminarin, and starch and analyzed the total and active microbial communities using bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Our results show a response of an initially minor but diverse population of Clostridia particularly after amendment with the lower molecular weight polymers starch and laminarin. Thus, Clostridia may readily become key contributors to the heterotrophic community in Guaymas Basin sediments when substrate availability and temperature range permit their metabolic activity and growth, which expands our appreciation of the potential diversity and niche differentiation of heterotrophs in hydrothermally influenced sediments. BONCAT-FACS, although challenging in its application to complex samples, detected metabolic responses prior to growth and thus can provide complementary insight into a microbial community's metabolic potential and succession pattern. As a primary application of BONCAT-FACS on a diverse deep-sea sediment community, our study highlights important considerations and demonstrates inherent limitations associated with this experimental approach.},
}
@article {pmid34956106,
year = {2021},
author = {Onyango, SO and Juma, J and De Paepe, K and Van de Wiele, T},
title = {Oral and Gut Microbial Carbohydrate-Active Enzymes Landscape in Health and Disease.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {653448},
pmid = {34956106},
issn = {1664-302X},
abstract = {Inter-individual variability in the microbial gene complement encoding for carbohydrate-active enzymes (CAZymes) can profoundly regulate how the host interacts with diverse carbohydrate sources thereby influencing host health. CAZy-typing, characterizing the microbiota-associated CAZyme-coding genes within a host individual, can be a useful tool to predict carbohydrate pools that the host can metabolize, or identify which CAZyme families are underrepresented requiring supplementation via microbiota transplantation or probiotics. CAZy-typing, moreover, provides a novel framework to search for disease biomarkers. As a proof of concept, we used publicly available metagenomes (935) representing 310 type strain bacterial genomes to establish the link between disease status and CAZymes in the oral and gut microbial ecosystem. The abundance and distribution of 220 recovered CAZyme families in saliva and stool samples from patients with colorectal cancer, rheumatoid arthritis, and type 1 diabetes were compared with healthy subjects. Based on the multivariate discriminant analysis, the disease phenotype did not alter the CAZyme profile suggesting a functional conservation in carbohydrate metabolism in a disease state. When disease and healthy CAZyme profiles were contrasted in differential analysis, CAZyme markers that were underrepresented in type 1 diabetes (15), colorectal cancer (12), and rheumatoid arthritis (5) were identified. Of interest, are the glycosyltransferase which can catalyze the synthesis of glycoconjugates including lipopolysaccharides with the potential to trigger inflammation, a common feature in many diseases. Our analysis has also confirmed the expansive carbohydrate metabolism in the gut as evidenced by the overrepresentation of CAZyme families in the gut compared to the oral site. Nevertheless, each site exhibited specific CAZyme markers. Taken together, our analysis provides an insight into the CAZyme landscape in health and disease and has demonstrated the diversity in carbohydrate metabolism in host-microbiota which can be a sound basis for optimizing the selection of pre, pro, and syn-biotic candidate products.},
}
@article {pmid34954887,
year = {2022},
author = {Antonelli, P and Salerno, B and Bordin, P and Peruzzo, A and Orsini, M and Arcangeli, G and Barco, L and Losasso, C},
title = {Tetrodotoxin in live bivalve mollusks from Europe: Is it to be considered an emerging concern for food safety?.},
journal = {Comprehensive reviews in food science and food safety},
volume = {21},
number = {1},
pages = {719-737},
doi = {10.1111/1541-4337.12881},
pmid = {34954887},
issn = {1541-4337},
support = {RC IZSVe 01/2019//Ministero della Salute/ ; },
mesh = {Animals ; *Bivalvia ; Europe ; Food Safety ; Shellfish/analysis ; Tetrodotoxin/analysis/toxicity ; },
abstract = {Tetrodotoxins (TTXs) are a group of potent neurotoxins named after the Tetraodontidae fish family (pufferfish). TTXs have been reported in several animal taxa, both terrestrial and marine. The ingestion of TTX-contaminated flesh can cause serious neurotoxic symptomatology and can eventually lead to death. Traditionally, TTXs have been associated with Asian countries, in particular with pufferfish consumption. However, they have also been reported in bivalve mollusks farmed in the Pacific area and, recently, in European seas. In Europe, different countries have reported TTXs, especially those bordering the Mediterranean Sea. As a consequence, in 2017 the European Food Safety Authority (EFSA) released an opinion with reference to TTX present in marine gastropods and bivalves, proposing a safety limit of 44 µg/kg TTXs in shellfish meat, below which no adverse effects should be observed in humans. Nevertheless, this limit has been exceeded on many occasions in European shellfish and, while for bivalves there have been no registered human intoxications, that is not the case for marine gastropods. However, TTXs have not yet been included in the list of marine biotoxins officially monitored in live bivalve mollusks within the European Union (EU). Thus, the aims of this manuscript are to discuss the increasing occurrence of TTXs in live bivalve mollusks from European sea waters, to acknowledge the still ongoing knowledge gaps that should be covered and to stimulate constructive debate on the eventuality of adopting a shared regulatory context, at least in the EU, for monitoring and managing this potential threat to food safety.},
}
@article {pmid34954170,
year = {2022},
author = {Soder-Walz, JM and Torrentó, C and Algora, C and Wasmund, K and Cortés, P and Soler, A and Vicent, T and Rosell, M and Marco-Urrea, E},
title = {Trichloromethane dechlorination by a novel Dehalobacter sp. strain 8M reveals a third contrasting C and Cl isotope fractionation pattern within this genus.},
journal = {The Science of the total environment},
volume = {813},
number = {},
pages = {152659},
doi = {10.1016/j.scitotenv.2021.152659},
pmid = {34954170},
issn = {1879-1026},
mesh = {Biodegradation, Environmental ; Carbon Isotopes/analysis ; Chemical Fractionation ; *Chloroform ; *Groundwater ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Trichloromethane (TCM) is a pollutant frequently detected in contaminated aquifers, and only four bacterial strains are known to respire it. Here, we obtained a novel Dehalobacter strain capable of transforming TCM to dichloromethane, which was denominated Dehalobacter sp. strain 8M. Besides TCM, strain 8M also completely transformed 1,1,2-trichloroethane to vinyl chloride and 1,2-dichloroethane. Quantitative PCR analysis for the 16S rRNA genes confirmed growth of Dehalobacter with TCM and 1,1,2-trichloroethane as electron acceptors. Carbon and chlorine isotope fractionation during TCM transformation was studied in cultured cells and in enzymatic assays with cell suspensions and crude protein extracts. TCM transformation in the three studied systems resulted in small but significant carbon (εC = -2.7 ± 0.1‰ for respiring cells, -3.1 ± 0.1‰ for cell suspensions, and - 4.1 ± 0.5‰ for crude protein extracts) and chlorine (εCl = -0.9 ± 0.1‰, -1.1 ± 0.1‰, and - 1.2 ± 0.2‰, respectively) isotope fractionation. A characteristic and consistent dual CCl isotope fractionation pattern was observed for the three systems (combined Λ[C/Cl] = 2.8 ± 0.3). This Λ[C/Cl] differed significantly from previously reported values for anaerobic dechlorination of TCM by the corrinoid cofactor vitamin B12 and other Dehalobacter strains. These findings widen our knowledge on the existence of different enzyme binding mechanisms underlying TCM-dechlorination within the genus Dehalobacter and demonstrates that dual isotope analysis could be a feasible tool to differentiate TCM degraders at field studies.},
}
@article {pmid34951701,
year = {2022},
author = {Etto, RM and Jesus, EC and Cruz, LM and Schneider, BSF and Tomachewski, D and Urrea-Valencia, S and Gonçalves, DRP and Galvão, F and Ayub, RA and Curcio, GR and Steffens, MBR and Galvão, CW},
title = {Influence of environmental factors on the tropical peatlands diazotrophic communities from the Southern Brazilian Atlantic Rain Forest.},
journal = {Letters in applied microbiology},
volume = {74},
number = {4},
pages = {543-554},
doi = {10.1111/lam.13638},
pmid = {34951701},
issn = {1472-765X},
mesh = {Brazil ; Ecosystem ; *Rainforest ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {The tropical peatlands of southern Brazil are essential for the maintenance of the Atlantic Rain Forest, one of the 25 hotspots of biodiversity in the world. Although diazotrophic micro-organisms are essential for the maintenance of this nitrogen limited ecosystem, so far studies have focused only on micro-organisms involved in the carbon cycle. In this work, peat samples were collected from three tropical peatland regions during dry and rainy seasons and their chemical and microbial characteristics were evaluated. Our results showed that the structure of the diazotrophic communities in the Brazilian tropical peatlands differs in the evaluated seasons. The abundance of the genus Bradyrhizobium showed to be affected by rainfall and peat pH. Despite the shifts of the nitrogen-fixing population in the tropical peatland caused by seasonality it showed to be constantly dominated by α-Proteobacteria followed by Cyanobacteria. In addition, more than 50% of nifH gene sequences have not been classified, indicating the necessity for more studies in tropical peatland, since the reduction of N supply in the peatlands stimulates the recalcitrant organic matter decomposition performed by peatland micro-organisms, influencing the C stock.},
}
@article {pmid34951695,
year = {2021},
author = {Sarker, RK and Chakraborty, P and Sarkar, S and Ghosh, MM and Tribedi, P},
title = {Bioaugmentation of Enterobacter cloacae AKS7 causes an enhanced degradation of low-density polyethylene (LDPE) in soil: a promising approach for the sustainable management of LDPE waste.},
journal = {Archives of microbiology},
volume = {204},
number = {1},
pages = {74},
pmid = {34951695},
issn = {1432-072X},
mesh = {Biodegradation, Environmental ; Ecosystem ; Enterobacter cloacae ; *Polyethylene ; Soil ; Soil Microbiology ; *Soil Pollutants ; },
abstract = {Enterobacter cloacae AKS7 was previously reported to degrade UV-treated low-density polyethylene (LDPE) more efficiently than UV-untreated LDPE. However, the degradation of LDPE by Enterobacter cloacae AKS7 at the LDPE-contaminated soil remained unaddressed. To address this issue, soil microcosms were prepared in which an equal amount of either UV-treated or UV-untreated LDPE was added. Then, the microcosms were either augmented with AKS7 or left non-augmented. We observed that the bioaugmented microcosms exhibited approximately twofold greater polymer degradation than non-bioaugmented microcosms. To investigate the underlying cause, we found that the abundance of LDPE-degrading organisms got increased by approximately fivefold in bioaugmented microcosms than non-bioaugmented microcosms. The microbial biomass carbon and nitrogen content got enhanced by approximately twofold in bioaugmented microcosms as contrasted to non-bioaugmented microcosms. Furthermore, the bioaugmented microcosms showed almost twofold increase in the level of dehydrogenase and fluorescein diacetate (FDA) hydrolyzing activity than the non-bioaugmented microcosms. To add on, Shannon-diversity index and Gini coefficient were determined in each microcosm to measure the microbial richness and evenness, respectively, using the results of carbon source utilization pattern of BiOLOG ECO plate. The bioaugmented microcosms exhibited ~ 30% higher functional richness and ~ 30% enhanced functional evenness than the non-bioaugmented microcosms indicating the formation of an enriched ecosystem that could offer various functions including polymer degradation. Taken together, the results suggested that Enterobacter cloacae AKS7 could be used as a promising bioaugmenting agent for the sustainable degradation of LDPE waste at a contaminated site.},
}
@article {pmid34946990,
year = {2021},
author = {Christopher, Y and Aguilar, C and Gálvez, D and Wcislo, WT and Gerardo, NM and Fernández-Marín, H},
title = {Interactions among Escovopsis, Antagonistic Microfungi Associated with the Fungus-Growing Ant Symbiosis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {7},
number = {12},
pages = {},
pmid = {34946990},
issn = {2309-608X},
support = {FID 18 - 079//Secretar&#xed;a Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; },
abstract = {Fungi in the genus Escovopsis (Ascomycota: Hypocreales) are prevalent associates of the complex symbiosis between fungus-growing ants (Tribe Attini), the ants' cultivated basidiomycete fungi and a consortium of both beneficial and harmful microbes found within the ants' garden communities. Some Escovopsis spp. have been shown to attack the ants' cultivated fungi, and co-infections by multiple Escovopsis spp. are common in gardens in nature. Yet, little is known about how Escovopsis strains impact each other. Since microbe-microbe interactions play a central role in microbial ecology and evolution, we conducted experiments to assay the types of interactions that govern Escovopsis-Escovopsis relationships. We isolated Escovopsis strains from the gardens of 10 attine ant genera representing basal (lower) and derived groups in the attine ant phylogeny. We conducted in vitro experiments to determine the outcome of both intraclonal and interclonal Escovopsis confrontations. When paired with self (intraclonal interactions), Escovopsis isolated from lower attine colonies exhibited antagonistic (inhibitory) responses, while strains isolated from derived attine colonies exhibited neutral or mutualistic interactions, leading to a clear phylogenetic pattern of interaction outcome. Interclonal interactions were more varied, exhibiting less phylogenetic signal. These results can serve as the basis for future studies on the costs and benefits of Escovopsis coinfection, and on the genetic and chemical mechanisms that regulate the compatibility and incompatibility observed here.},
}
@article {pmid34946177,
year = {2021},
author = {Purushotham, N and Jones, E and Monk, J and Ridgway, H},
title = {Fungal Communities in the Native New Zealand Medicinal Plant Pseudowintera colorata (Horopito) Are Determined by Plant Organ Type and Host Maturity with Key Members Promoting Plant Growth.},
journal = {Microorganisms},
volume = {9},
number = {12},
pages = {},
pmid = {34946177},
issn = {2076-2607},
abstract = {The plant Pseudowintera colorata is well known for its antimicrobial and medicinal properties and is endemic to New Zealand. Using PCR-Denaturing gradient gel electrophoresis (DGGE), we investigated the factors influencing the composition of endophytic fungal communities in P. colorata from ten distinct sites across New Zealand. Our results showed that plant organs of P. colorata influenced the diversity and richness of endophytic fungi (PERMANOVA, p < 0.05). In addition, plant maturity and its interactions revealed that endophytic fungal communities formed discrete clusters in leaves, stems, and roots of mature and immature P. colorata plants (PERMANOVA; p = 0.002, p = 0.001 and p = 0.039, respectively). For identifying isolates with biocontrol potential, dual culture tests were set up against four different phytopathogenic fungi. Isolates with high activity (zone of inhibition > 10 mm) were sequenced and identified as Trichoderma harzianum, Pezicula neosporulosa, Fusariumtricinctum, Metarhizium sp., and Chaetomium sp. Applying selected endophytic fungi (n = 7) as soil drenchers significantly increased the growth of P. colorata seedlings and produced more internodes. Seedling shoots treated with Trichoderma sp. PRY2BA21 were 2.2 × longer (8.36 cm) than the untreated controls (3.72 cm). Our results elucidate the main plant factors influencing fungal community composition and demonstrate a role for endophytic fungi in P. colorata growth and further demonstrate that medicinal plants are a rich source of endophytes with potential as biocontrol agents.},
}
@article {pmid34940904,
year = {2021},
author = {Das, S and Paul, P and Chatterjee, S and Chakraborty, P and Sarker, RK and Das, A and Maiti, D and Tribedi, P},
title = {Piperine exhibits promising antibiofilm activity against Staphylococcus aureus by accumulating reactive oxygen species (ROS).},
journal = {Archives of microbiology},
volume = {204},
number = {1},
pages = {59},
pmid = {34940904},
issn = {1432-072X},
support = {R&amp;D/2020/F2//The Neotia University/ ; },
mesh = {*Alkaloids/pharmacology ; Anti-Bacterial Agents/pharmacology ; Benzodioxoles ; Biofilms ; Humans ; Microbial Sensitivity Tests ; Piperidines ; Polyunsaturated Alkamides ; Reactive Oxygen Species ; *Staphylococcus aureus ; },
abstract = {Staphylococcus aureus causes numerous community-acquired and nosocomial infections in humans by exploiting biofilm. In this context, this study aims to impede the formation of Staphylococcus aureus biofilm by exposing the cells to a plant-based alkaloid, piperine. Our study revealed that piperine exhibited considerable antimicrobial activity against the test organism. However, we had tested the lower concentrations (up to 32 µg/mL) of piperine to observe whether they could show any antibiofilm activity against the same organism. Several experiments, like crystal violet (CV) assay, estimation of total biofilm protein, and fluorescence microscopic observations, established that lower concentrations (up to 16 µg/mL) of piperine showed efficient antibiofilm activity against Staphylococcus aureus. In this connection, we also noticed that the lower concentrations (8 and 16 µg/mL) of piperine showed a considerable reduction in microbial metabolic activity. Besides, it was also observed that the mentioned concentrations of piperine did not compromise the microbial growth of the target organism while exhibiting antibiofilm activity. To understand the underlying mechanism of microbial biofilm inhibition under the influence of piperine, we observed that the compound was found to accumulate reactive oxygen species in the bacterial cells that could play an important role in the inhibition of biofilm formation. Furthermore, the tested concentrations (8 and 16 µg/mL) of piperine were able to inhibit the motility of the test organism that might compromise the development of biofilm. Thus, piperine could be considered as a potential agent for the effective management of biofilm threat caused by Staphylococcus aureus.},
}
@article {pmid34939130,
year = {2023},
author = {Trzebny, A and Slodkowicz-Kowalska, A and Björkroth, J and Dabert, M},
title = {Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {247-263},
pmid = {34939130},
issn = {1432-184X},
support = {2020/37/N/NZ8/01735//Narodowe Centrum Nauki/ ; 05/IDUB/2019/94//Initiative of Excellence - Research University at Adam Mickiewicz University, Poznan, Poland/ ; },
mesh = {Animals ; Female ; *Culicidae/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; *Microsporidia/genetics ; },
abstract = {The animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.},
}
@article {pmid34938278,
year = {2021},
author = {Shi, Y and Yang, H and Chu, M and Niu, X and Wang, N and Lin, Q and Lou, K and Zuo, C and Wang, J and Zou, Q and Zhang, Y},
title = {Differentiation and Variability in the Rhizosphere and Endosphere Microbiomes of Healthy and Diseased Cotton (Gossypium sp.).},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {765269},
pmid = {34938278},
issn = {1664-302X},
abstract = {The plant microbiome is a key determinant of health and productivity. However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p < 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. The dominant rhizosphere bacteria were Proteobacteria (29.70%), Acidobacteria (23.14%), Gemmatimonadetes (15.17%), Actinobacteria (8.31%), Chloroflexi (7.99%), and Bacteroidetes (5.15%). The dominant rhizosphere fungi were Ascomycota (83.52%), Mortierellomycota (7.67%), Basidiomycota (2.13%), Chytridiomycota (0.39%), and Olpidiomycota (0.08%). The distribution of dominant bacteria in different cotton rhizosphere soils and roots differed, with the dominant bacteria Pseudomonas (15.54%) and Pantoea (9.19%), and the dominant fungi Alternaria (16.15%) and Cephalotrichum (9.10%) being present in the greatest numbers. At sampling points in different ecological regions, the total numbers of cotton endophytic and rhizosphere microbiome OTUs from southern to northern Xinjiang showed an increasing trend. There were significant differences in the composition and diversity of rhizosphere microbes and endophytes during the entire cotton growth period and in representative ecological regions (p < 0.01), whereas rhizosphere microbes and endophytes showed no significant differences among the four growth periods and in representative ecological regions. RB41, H16, Nitrospira, and Sphingomonas play important roles in the microbial ecology of cotton rhizosphere soil. Pseudomonas accounted for a large proportion of the microbes in the cotton rhizosphere soil. This study provides an in-depth understanding of the complex microbial composition and diversity associated with cotton north and south of the Tianshan Mountains.},
}
@article {pmid34933408,
year = {2022},
author = {Šimek, K and Mukherjee, I and Nedoma, J and de Paula, CCP and Jezberová, J and Sirová, D and Vrba, J},
title = {CARD-FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes.},
journal = {Environmental microbiology},
volume = {24},
number = {9},
pages = {4256-4273},
pmid = {34933408},
issn = {1462-2920},
mesh = {Bacteria/genetics ; *Ciliophora ; Cryptophyta ; Ecosystem ; In Situ Hybridization, Fluorescence ; *Lakes/microbiology ; Phylogeny ; },
abstract = {Heterotrophic nanoflagellates (HNF) and ciliates are major protistan planktonic bacterivores. The term HNF, however, describes a functional guild only and, in contrast to the morphologically distinguishable ciliates, does not reflect the phylogenetic diversity of flagellates in aquatic ecosystems. Associating a function with taxonomic affiliation of key flagellate taxa is currently a major task in microbial ecology. We investigated seasonal changes in the HNF and ciliate community composition as well as taxa-specific bacterivory in four hypertrophic freshwater lakes. Taxa-specific catalyzed reporter deposition-fluorescence in situ hybridization probes assigned taxonomic affiliations to 51%-96% (average ±SD, 75 ± 14%) of total HNF. Ingestion rates of fluorescently labelled bacteria unveiled that HNF contributed to total protist-induced bacterial mortality rates more (56%) than ciliates (44%). Surprisingly, major HNF bacterivores were aplastidic cryptophytes and their Cry1 lineage, comprising on average 53% and 24% of total HNF abundance and 67% and 21% of total HNF bacterivory respectively. Kinetoplastea were important consumers of bacteria during summer phytoplankton blooms, reaching 38% of total HNF. Katablepharidacea (7.5% of total HNF) comprised mainly omnivores, with changing contributions of bacterivorous and algivorous phylotypes. Our results show that aplastidic cryptophytes, accompanied by small omnivorous ciliate genera Halteria/Pelagohalteria, are the major protistan bacterivores in hypertrophic freshwaters.},
}
@article {pmid34933025,
year = {2022},
author = {Qi, P and Li, T and Hu, C and Li, Z and Bi, Z and Chen, Y and Zhou, H and Su, Z and Li, X and Xing, X and Chen, C},
title = {Effects of cast iron pipe corrosion on nitrogenous disinfection by-products formation in drinking water distribution systems via interaction among iron particles, biofilms, and chlorine.},
journal = {Chemosphere},
volume = {292},
number = {},
pages = {133364},
doi = {10.1016/j.chemosphere.2021.133364},
pmid = {34933025},
issn = {1879-1298},
mesh = {Biofilms ; Chlorine ; Corrosion ; Disinfection ; *Drinking Water ; Iron ; Nitrogen ; *Water Purification ; Water Supply ; },
abstract = {The effects of cast iron pipe corrosion on nitrogenous disinfection by-products formation (N-DBPs) in drinking water distribution systems (DWDSs) were investigated. The results verified that in the effluent of corroded DWDSs simulated by annular reactors with corroded cast iron coupons, typical N-DBPs, including haloacetamides, halonitromethanes, and haloacetonitriles, increased significantly compared with the influent of DWDSs. In addition, more dissolved organic carbon, adenosine triphosphate, and iron particles were simultaneously detected in the bulk water of corroded DWDSs, thereby indicating that abundant iron particles acted as a "protective umbrella" for microorganisms. Under the condition of corroded DWDSs, the extracellular polymeric substances gradually exhibited distinct characteristics, including a higher content and lower flocculation efficiency, thereby resulting in a large supply of N-DBPs precursors. Corroded cast iron pipes, equivalent to a unique microbial interface, induced completely distinct microbial community structures and metabolic functions in DWDSs, thereby enhancing the formation of N-DBPs. This is the first study to successfully reveal the interactions among iron particles, biofilms, and chlorine in DWDSs, which may help to fully understand the biofilm transformation and microbial community succession in DWDSs.},
}
@article {pmid34927376,
year = {2022},
author = {Ostermeyer, P and Bonin, L and Leon-Fernandez, LF and Dominguez-Benetton, X and Hennebel, T and Rabaey, K},
title = {Electrified bioreactors: the next power-up for biometallurgical wastewater treatment.},
journal = {Microbial biotechnology},
volume = {15},
number = {3},
pages = {755-772},
pmid = {34927376},
issn = {1751-7915},
mesh = {Biomass ; Bioreactors ; *Wastewater ; *Water Purification ; },
abstract = {Over the past decades, biological treatment of metallurgical wastewaters has become commonplace. Passive systems require intensive land use due to their slow treatment rates, do not recover embedded resources and are poorly controllable. Active systems however require the addition of chemicals, increasing operational costs and possibly negatively affecting safety and the environment. Electrification of biological systems can reduce the use of chemicals, operational costs, surface footprint and environmental impact when compared to passive and active technologies whilst increasing the recovery of resources and the extraction of products. Electrification of low rate applications has resulted in the development of bioelectrochemical systems (BES), but electrification of high rate systems has been lagging behind due to the limited mass transfer, electron transfer and biomass density in BES. We postulate that for high rate applications, the electrification of bioreactors, for example, through the use of electrolyzers, may herald a new generation of electrified biological systems (EBS). In this review, we evaluate the latest trends in the field of biometallurgical and microbial-electrochemical wastewater treatment and discuss the advantages and challenges of these existing treatment technologies. We advocate for future research to focus on the development of electrified bioreactors, exploring the boundaries and limitations of these systems, and their validity upon treating industrial wastewaters.},
}
@article {pmid34927211,
year = {2021},
author = {Islam, MM and Bhattacharya, R and Sarkar, B and Maiti, PK and Mahanty, S and Chaudhuri, P and Biswas, SR and Mandal, S},
title = {Different soil salinity imparts clear alteration in rhizospheric bacterial community dynamics in rice and peanut.},
journal = {Archives of microbiology},
volume = {204},
number = {1},
pages = {36},
pmid = {34927211},
issn = {1432-072X},
mesh = {Arachis ; Metagenomics ; *Oryza ; Salinity ; Soil ; },
abstract = {The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in the overall health of the hostplant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN, whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community structure is related to both the adjoining soil characters and the type of the hosts.},
}
@article {pmid34927107,
year = {2021},
author = {Cáceres, PFF and Vélez, LP and Junca, H and Moreno-Herrera, CX},
title = {Theobroma cacao L. agricultural soils with natural low and high cadmium (Cd) in Santander (Colombia), contain a persistent shared bacterial composition shaped by multiple soil variables and bacterial isolates highly resistant to Cd concentrations.},
journal = {Current research in microbial sciences},
volume = {2},
number = {},
pages = {100086},
pmid = {34927107},
issn = {2666-5174},
abstract = {Heavy metals can be found in soil as natural components or as product of contaminations events; plants growing in soils are prone to bioaccumulate heavy metals on their biomass. Theobroma cacao L. can bioaccumulate cadmium (Cd) in the seed and could be in derived food products, it considered a human health risk; therefore, removal of Cd is desirable but not vet technically and economically feasible; only to avoid Cd in cocoa is by selecting lands plots exhibiting lower Cd concentrations in soils, imposing a serious limitation to farmers and regulators. The study of bacterial communities and isolation bacteria with tolerance and mechanisms to counteract the translocation of Cd to the parts of cocoa plant exhibits high relevance in Colombia economy and especially to companies producing chocolate and derivatives. Here, we explore bacterial communities associated with soils having relatively high natural Cd concentrations in a large agricultural cocoa plot located in the Santander region. We characterized the bacterial communities' compositions by amplicon 16S rRNA sequencing from metagenomics soil DNA and by culturing-based enumeration and isolation approaches. Culture-dependent techniques allowed the isolation of bacteria tolerant to Cd concentration, complement the information for Colombia, and expand the number of strains characterized with adaptive capacity against Cd with tolerance in a concentration of 120 mg/L, which represents the first capacity for Exiguobacterium sp., Ralstonia sp., Serratia sp., Dermacoccus sp., Klebsiella sp., Lactococcus sp. and Staphylococcus sp. In addition to confirming that there is a greater diversity of Cd-tolerant bacteria present in soils of farms cultivated with cocoa in Colombia. As for the results of new generation sequencing, they revealed that, the alpha-diversity in bacterial composition, according to the ANOVA, there are statistically significant differences of the bacterial communities present in the samples. Regarding Pearson correlation analysis, it was found the Shannon Simpson indices, have a positive correlation against OM, C, pH, Mn, C.E.C.I., Ca, P and negatively correlated with S; respect to bacterial community structure, a principal component analysis, which revealed that independent of the concentration of Cd present in soil samples, separates them according to pH value. Phyla to high abundance relative in all samples were Proteobacteria, Acidobacteriota, Actinobacteriota, Verrucomicrobiota, Myxococcota, Chloroflexi, Plactomycetota, Bacteroidota, Gemmatimonadota, Nitrospirota, Firmicutes and NB1_J; the bacteria genera with higher relative abundance (>0.5%) Nitrospira, candidatus Udaeobacter, Haliangium, Cupriavidus, MND1, Bacillus, Kitasatospora, Niveibacterium, Acidothermus, Burkholderia, Acidibacter, Terrimonas, Gaiella, candidatus Solibacter, Kitasatospora, Sphingomonas, Streptomyces, this genus with a relationship with the Cd tolerance process. After it, redundancy analysis was performed between the variation of the bacterial communities identified by dependent and independent techniques and edaphic soil variables, where their positive correlation was found against K, OM, C, Ca, pH (p<0.01) and P, C.E.C.I (p<0.05). For soil samples, the bacterial genera that make up the core community were identified, which are present in all samples as Nitrospira sp., Cupriavidus sp., Burkholderia sp., Haliangium sp., candidatus Udaeobacter, MND1, Kitasatospora, Acidothermus, Acidibacter, Streptomyces, Gaiella, candidatus Solibacter and Terramonas; the genera identified has a different and fundamental role in ecosystem functioning. The combination of different approaches offers new clues regarding the assessment of bacterial communities in soils cultivated with cocoa in soils with elevated Cd content in Colombia, and the ecological role and interplay of soil components and bacterial communities that contribute to modulate the effect of bioaccumulation in products.},
}
@article {pmid34925416,
year = {2021},
author = {Yu, J and Gonzalez, JM and Dong, Z and Shan, Q and Tan, B and Koh, J and Zhang, T and Zhu, N and Dufresne, C and Martin, GB and Chen, S},
title = {Integrative Proteomic and Phosphoproteomic Analyses of Pattern- and Effector-Triggered Immunity in Tomato.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {768693},
pmid = {34925416},
issn = {1664-462X},
abstract = {Plants have evolved a two-layered immune system consisting of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI and ETI are functionally linked, but also have distinct characteristics. Unraveling how these immune systems coordinate plant responses against pathogens is crucial for understanding the regulatory mechanisms underlying plant defense. Here we report integrative proteomic and phosphoproteomic analyses of the tomato-Pseudomonas syringae (Pst) pathosystem with different Pst mutants that allow the dissection of PTI and ETI. A total of 225 proteins and 79 phosphopeptides differentially accumulated in tomato leaves during Pst infection. The abundances of many proteins and phosphoproteins changed during PTI or ETI, and some responses were triggered by both PTI and ETI. For most proteins, the ETI response was more robust than the PTI response. The patterns of protein abundance and phosphorylation changes revealed key regulators involved in Ca[2+] signaling, mitogen-activated protein kinase cascades, reversible protein phosphorylation, reactive oxygen species (ROS) and redox homeostasis, transcription and protein turnover, transport and trafficking, cell wall remodeling, hormone biosynthesis and signaling, suggesting their common or specific roles in PTI and/or ETI. A NAC (NAM, ATAF, and CUC family) domain protein and lipid particle serine esterase, two PTI-specific genes identified from previous transcriptomic work, were not detected as differentially regulated at the protein level and were not induced by PTI. Based on integrative transcriptomics and proteomics data, as well as qRT-PCR analysis, several potential PTI and ETI-specific markers are proposed. These results provide insights into the regulatory mechanisms underlying PTI and ETI in the tomato-Pst pathosystem, and will promote future validation and application of the disease biomarkers in plant defense.},
}
@article {pmid34920315,
year = {2022},
author = {Fu, S and Yang, Q and Sheng, Y and Wang, Q and Wu, J and Qiu, Z and Lan, R and Wang, Y and Liu, Y},
title = {Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off.},
journal = {Water research},
volume = {209},
number = {},
pages = {117941},
doi = {10.1016/j.watres.2021.117941},
pmid = {34920315},
issn = {1879-2448},
abstract = {Early detection of emerging and life-threatening pathogens circulating in complex environments is urgently required to combat infectious diseases. This study proposed a public health risk assessment workflow with three stages, pathogen screening, pathogen genotyping, and risk assessment. In stage one, pathogens were screened with metagenomic sequencing, microfluidic chip, and qPCR. In stage two, pathogens were isolated and genotyped with multi-locus sequence typing (MLST) or conventional PCR. Finally, virulence genes from metagenomic data were assessed for pathogenicity. Two regions (Donggang and Zhanjiang) with potential public health concerns were selected for evaluation, each of which comprised of one urban and one farming wastewater sampling location. Overall, metagenomic sequencing reflected the variation in the relative abundance of medically important bacteria. Over 90 bacterial pathogens were monitored in the metagenomic dataset, of which 56 species harbored virulence genes. In Donggang, a pathogenic Acinetobacter sp. reached high abundances in 2018 and 2020, whereas all pathogenic Vibrio spp. peaked in October 2019. In Zhanjiang, A. baumanni, and other Enterobacteriaceae species were abundantly present in 2019 and 2020, whereas Aeromonas and Vibrio spp. peaked in November-2017. Forty species were subsequently isolated and subtyped by MLST, half of which were prevalent genotypes in clinical data. Additionally, we identified the African Swine Fever Virus (ASFV) in water samples collected in 2017, ahead of the first reported ASFV outbreak in 2018 in China. RNA viruses like Hepatitis A virus (HAV) and Enterovirus 71 (EV71) were also detected, with concentrations peaking in April 2020 and April 2018, respectively. The dynamics of HAV and EV71 were consistent with local epidemic trends. Finally, based on the virulence gene profiles, our study identified the risk level in wastewater of two cities. This workflow illustrates the potential for an early warning of local epidemics, which helps to prioritize the preparedness for specific pathogens locally.},
}
@article {pmid34910570,
year = {2022},
author = {Abramov, SM and Straub, D and Tejada, J and Grimm, L and Schädler, F and Bulaev, A and Thorwarth, H and Amils, R and Kappler, A and Kleindienst, S},
title = {Biogeochemical Niches of Fe-Cycling Communities Influencing Heavy Metal Transport along the Rio Tinto, Spain.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {4},
pages = {e0229021},
pmid = {34910570},
issn = {1098-5336},
mesh = {*Ferric Compounds ; *Fresh Water/microbiology ; Iron ; RNA, Ribosomal, 16S/genetics ; Spain ; },
abstract = {In the mining-impacted Rio Tinto, Spain, Fe-cycling microorganisms influence the transport of heavy metals (HMs) into the Atlantic Ocean. However, it remains largely unknown how spatial and temporal hydrogeochemical gradients along the Rio Tinto shape the composition of Fe-cycling microbial communities and how this in turn affects HM mobility. Using a combination of DNA- and RNA-based 16S rRNA (gene) amplicon sequencing and hydrogeochemical analyses, we explored the impact of pH, Fe(III), Fe(II), and Cl[-] on Fe-cycling microorganisms. We showed that the water column at the acidic (pH 2.2) middle course of the river was colonized by Fe(II) oxidizers affiliated with Acidithiobacillus and Leptospirillum. At the upper estuary, daily fluctuations of pH (2.7 to 3.7) and Cl[-] (6.9 to 16.6 g/L) contributed to the establishment of a unique microbial community, including Fe(II) oxidizers belonging to Acidihalobacter, Marinobacter, and Mariprofundus, identified at this site. Furthermore, DNA- and RNA-based profiles of the benthic community suggested that acidophilic and neutrophilic Fe(II) oxidizers (e.g., Acidihalobacter, Marinobacter, and Mariprofundus), Fe(III) reducers (e.g., Thermoanaerobaculum), and sulfate-reducing bacteria drive the Fe cycle in the estuarine sediments. RNA-based relative abundances of Leptospirillum at the middle course as well as abundances of Acidihalobacter and Mariprofundus at the upper estuary were higher than DNA-based results, suggesting a potentially higher level of activity of these taxa. Based on our findings, we propose a model of how tidal water affects the composition and activity of the Fe-cycling taxa, playing an important role in the transport of HMs (e.g., As, Cd, Cr, and Pb) along the Rio Tinto. IMPORTANCE The estuary of the Rio Tinto is a unique environment in which extremely acidic, heavy metal-rich, and especially iron-rich river water is mixed with seawater. Due to the mixing events, the estuarine water is characterized by a low pH, almost seawater salinity, and high concentrations of bioavailable iron. The unusual hydrogeochemistry maintains unique microbial communities in the estuarine water and in the sediment. These communities include halotolerant iron-oxidizing microorganisms which typically inhabit acidic saline environments and marine iron-oxidizing microorganisms which, in contrast, are not typically found in acidic environments. Furthermore, highly saline estuarine water favored the prosperity of acidophilic heterotrophs, typically inhabiting brackish and saline environments. The Rio Tinto estuarine sediment harbors a diverse microbial community with both acidophilic and neutrophilic members that can mediate the iron cycle and, in turn, can directly impact the mobility and transport of heavy metals in the Rio Tinto estuary.},
}
@article {pmid34908437,
year = {2021},
author = {Kim, J and Hur, JI and Ryu, S and Jeon, B},
title = {Bacteriophage-Mediated Modulation of Bacterial Competition during Selective Enrichment of Campylobacter.},
journal = {Microbiology spectrum},
volume = {9},
number = {3},
pages = {e0170321},
pmid = {34908437},
issn = {2165-0497},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacteriophages ; Campylobacter/*growth &amp; development/*isolation &amp; purification ; Chickens/microbiology ; Culture Media/chemistry ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics/*growth &amp; development/metabolism/*virology ; Food Contamination/analysis ; Food Microbiology/methods ; Meat/*microbiology ; Microbial Sensitivity Tests ; beta-Lactamases/metabolism ; },
abstract = {Selective media using antimicrobial supplements generate unique microbial ecology to facilitate bacterial isolation. However, antibiotic-resistant bacteria indigenous to samples can interfere with the isolation process using selective media. Recent studies showed that extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is highly prevalent on retail raw chicken and compromises the efficacy of Campylobacter isolation because ESBL-producing E. coli are resistant to antimicrobial supplements in Campylobacter-selective media and outgrows Campylobacter. The objective of this study was to improve Campylobacter isolation by inhibiting the growth of ESBL-producing E. coli using bacteriophages (phages). The supplementation of Campylobacter-selective media with E. coli phages reduced the level of ESBL-producing E. coli during the enrichment step. When E. coli phages were combined with the antimicrobial supplements of Campylobacter-selective media, antimicrobial synergy was observed, particularly with rifampicin, an antibiotic used in Preston medium. Although the same materials (i.e., phages and selective media) were used, the sequence of combining the materials markedly influenced the inhibition of ESBL-producing E. coli and the isolation of Campylobacter. These findings indicated that the modulation of microbial competition at the enrichment step was critical to the successful isolation of fastidious bacteria and that phages can be utilized to facilitate the selective enrichment of target bacteria by inhibiting their competitive bacteria. IMPORTANCE Phages are promising antimicrobial alternatives. In this study, we first demonstrated that phages can be used to facilitate selective isolation of fastidious bacteria that are prone to be outgrown by bacterial competitors during isolation. The effectiveness of a phage-based isolation method was primarily dependent on the antimicrobial synergy between phages and antibiotics used in selective media. The same approach could be applied to the development of isolation methods for other fastidious bacteria.},
}
@article {pmid34907449,
year = {2023},
author = {Ghignone, S and Zampieri, E and Tinti, F and Torti, V and Giacoma, C and Mello, A},
title = {Fungal Patterns from Soils in Madagascar: an Insight from Maromizaha Forest (Evergreen Humid Forest) to Outside (Deciduous Forest).},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {184-196},
pmid = {34907449},
issn = {1432-184X},
mesh = {*Ecosystem ; *Soil/chemistry ; Madagascar ; Soil Microbiology ; Forests ; Fungi/genetics ; },
abstract = {Soil fungal diversity was studied by next-generation sequencing and compared in two different Malagasy ecosystems, the first a New Protected Area (Maromizaha NAP) that is a rich humid evergreen forest and the second a degraded and declined deciduous forest (Andaravina) whose area has been also eroded. Both areas, however, have comparable annual rainfalls and soil pH values. So it was of interest to examine the soil fungal diversity in each system and compare them. We detected 1,817,658 reads representing Ascomycota, which were dominant in both habitats (55.9%), followed by unidentified fungi (21.5%), Basidiomycota (12.7%) and Mortierellomycota (6.7%), with Mucoromycota, Chytridiomycota, Glomeromycota and other phyla accounting for less than 5% in total. In detail, 1,142 OTUs out of 1,368 constitute the common core shared by both sampling areas, which are characterized by tropical climate, whereas 185 are Maromizaha specific and 41 Andaravina specific. The most represented guilds involve fungi related to saprotrophic behaviour, with a greater tendency towards pathotrophic mode. A significant variability in terms of richness and abundance is present within Maromizaha, which is a heterogeneous environment for fungi but also for plant composition, as it emerged from the vegetational survey of the investigated sites. A few fungal sequences match taxa from Madagascar, highlighting the scarce representativeness of fungi from this island in the fungal databases and their still low knowledge. Enlarging studies in Madagascar will help not only to unravel its largely unknown fungal biodiversity but also to give a contribution for studies on the reconstruction of the diversity of soil fungi worldwide.},
}
@article {pmid34906246,
year = {2021},
author = {Chaudhari, NM and Overholt, WA and Figueroa-Gonzalez, PA and Taubert, M and Bornemann, TLV and Probst, AJ and Hölzer, M and Marz, M and Küsel, K},
title = {The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers.},
journal = {Environmental microbiome},
volume = {16},
number = {1},
pages = {24},
pmid = {34906246},
issn = {2524-6372},
support = {SFB 1076 -Project Number 218627073//deutsche forschungsgemeinschaft/ ; FZT 118 - 202548816//deutsche forschungsgemeinschaft/ ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//deutsche forschungsgemeinschaft/ ; Nachwuchsgruppe Dr. Alexander Probst//ministerium f&#xfc;r kultur und wissenschaft des landes nordrhein-westfalen/ ; },
abstract = {BACKGROUND: The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges.<br><br>RESULTS: Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1&#xa0;&#xb5;m filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1&#xa0;&#xb5;m fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2&#xa0;&#xb5;m fractions. On average, Patescibacteria enriched in the smaller 0.1&#xa0;&#xb5;m filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2&#xa0;&#xb5;m fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota).<br><br>CONCLUSION: Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to&#xa0;attach multiple hosts just long enough to loot or exchange supplies.},
}
@article {pmid34905647,
year = {2022},
author = {Wang, G and Gao, Q and Yang, Y and Hobbie, SE and Reich, PB and Zhou, J},
title = {Soil enzymes as indicators of soil function: A step toward greater realism in microbial ecological modeling.},
journal = {Global change biology},
volume = {28},
number = {5},
pages = {1935-1950},
doi = {10.1111/gcb.16036},
pmid = {34905647},
issn = {1365-2486},
mesh = {Carbon ; *Ecosystem ; Nitrogen/analysis ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {Soil carbon (C) and nitrogen (N) cycles and their complex responses to environmental changes have received increasing attention. However, large uncertainties in model predictions remain, partially due to the lack of explicit representation and parameterization of microbial processes. One great challenge is to effectively integrate rich microbial functional traits into ecosystem modeling for better predictions. Here, using soil enzymes as indicators of soil function, we developed a competitive dynamic enzyme allocation scheme and detailed enzyme-mediated soil inorganic N processes in the Microbial-ENzyme Decomposition (MEND) model. We conducted a rigorous calibration and validation of MEND with diverse soil C-N fluxes, microbial C:N ratios, and functional gene abundances from a 12-year CO2 × N grassland experiment (BioCON) in Minnesota, USA. In addition to accurately simulating soil CO2 fluxes and multiple N variables, the model correctly predicted microbial C:N ratios and their negative response to enriched N supply. Model validation further showed that, compared to the changes in simulated enzyme concentrations and decomposition rates, the changes in simulated activities of eight C-N-associated enzymes were better explained by the measured gene abundances in responses to elevated atmospheric CO2 concentration. Our results demonstrated that using enzymes as indicators of soil function and validating model predictions with functional gene abundances in ecosystem modeling can provide a basis for testing hypotheses about microbially mediated biogeochemical processes in response to environmental changes. Further development and applications of the modeling framework presented here will enable microbial ecologists to address ecosystem-level questions beyond empirical observations, toward more predictive understanding, an ultimate goal of microbial ecology.},
}
@article {pmid34904179,
year = {2023},
author = {Razak, NA and Gange, AC},
title = {Multitrophic Interactions Between Arbuscular Mycorrhizal Fungi, Foliar Endophytic Fungi and Aphids.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {146-156},
pmid = {34904179},
issn = {1432-184X},
support = {NE/N00244X/1//Natural Environment Research Council/ ; },
mesh = {Animals ; *Mycorrhizae/physiology ; *Aphids ; Plant Roots/microbiology ; Plants ; Endophytes/physiology ; Fungi/physiology ; },
abstract = {Almost all living plants can be simultaneously colonised by arbuscular mycorrhizal fungi in the roots and endophytes in the shoots, while also being attacked by insect herbivores. However, to date, no study has ever examined the multitrophic interactions between these two different fungal groups and insects on any species of forb. Here, we examined the effects of two commercial species mixtures of arbuscular mycorrhizal fungi (AMF) and two foliar endophytes (Colletotrichum acutatum and Cladosporium oxysporum) on the growth of an invasive weed, Impatiens glandulifera, and the aphids that attack it. AMF reduced plant biomass, which was most evident when C. oxysporum was inoculated. Mycorrhizal fungi had few effects on aphids, and these depended on the identity of the endophytes present. Meanwhile, endophytes tended to increase aphid numbers, but this depended on the identity of the AMF inoculum. Throughout, there were differences in the responses of the plant to the two mycorrhizal mixtures, demonstrating clear AMF specificity in this plant. These specific effects were also strongly affected by the endophytes, with a greater number of interactions found between the AMF and endophytes than between the endophytes themselves. In particular, AMF reduced infection levels by the endophytes, while some endophyte inoculations reduced mycorrhizal colonisation. We suggest that both AMF and endophytes could play an important part in future biological control programmes of weeds, but further multitrophic experiments are required to unravel the complexity of interactions between spatially separated parts of the plant microbiome.},
}
@article {pmid34895142,
year = {2021},
author = {Wichmann, S and Scherer, S and Ardern, Z},
title = {Biological factors in the synthetic construction of overlapping genes.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {888},
pmid = {34895142},
issn = {1471-2164},
mesh = {Amino Acid Sequence ; Animals ; *Biological Factors ; *Genes, Overlapping ; Genome ; Open Reading Frames ; },
abstract = {BACKGROUND: Overlapping genes (OLGs) with long protein-coding overlapping sequences are disallowed by standard genome annotation programs, outside of viruses. Recently however they have been discovered in Archaea, diverse Bacteria, and Mammals. The biological factors underlying life's ability to create overlapping genes require more study, and may have important applications in understanding evolution and in biotechnology. A previous study claimed that protein domains from viruses were much better suited to forming overlaps than those from other cellular organisms - in this study we assessed this claim, in order to discover what might underlie taxonomic differences in the creation of gene overlaps.<br><br>RESULTS: After overlapping arbitrary Pfam domain pairs and evaluating them with Hidden Markov Models we find OLG construction to be much less constrained than expected. For instance, close to 10% of the constructed sequences cannot be distinguished from typical sequences in their protein family. Most are also indistinguishable from natural protein sequences regarding identity and secondary structure. Surprisingly, contrary to a previous study, virus domains were much less suitable for designing OLGs than bacterial or eukaryotic domains were. In general, the amount of amino acid change required to force a domain to overlap is approximately equal to the variation observed within a typical domain family. The resulting high similarity between natural sequences and those altered so as to overlap is mostly due to the combination of high redundancy in the genetic code and the evolutionary exchangeability of many amino acids.<br><br>CONCLUSIONS: Synthetic overlapping genes which closely resemble natural gene sequences, as measured by HMM profiles, are remarkably easy to construct, and most arbitrary domain pairs can be altered so as to overlap while retaining high similarity to the original sequences. Future work however will need to assess important factors not considered such as intragenic interactions which affect protein folding. While the analysis here is not sufficient to guarantee functional folding proteins, further analysis of constructed OLGs will improve our understanding of the origin of these remarkable genetic elements across life and opens up exciting possibilities for synthetic biology.},
}
@article {pmid34888738,
year = {2022},
author = {Ryther, CM and Ortmann, AC and Wohlgeschaffen, G and Robinson, BJ},
title = {Temperate Coastal Microbial Communities Rapidly Respond to Low Concentrations of Partially Weathered Diesel.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1122-1132},
pmid = {34888738},
issn = {1432-184X},
mesh = {Biodegradation, Environmental ; Seawater/microbiology ; Bacteria/genetics ; *Microbiota ; Nova Scotia ; *Petroleum ; Hydrocarbons ; },
abstract = {Diesel is frequently encountered in coastal ecosystems due to land run-off from road surfaces. The current study investigates how partially weathered diesel at environmentally relevant concentrations, as may be seen during a run-off event, affect coastal microbial communities. A mesocosm experiment using seawater from the Bedford Basin, Nova Scotia, was followed for 72 h after the addition of partially weathered diesel. Sequencing data suggests partially weathered diesel acts quickly to alter the prokaryotic community, as both opportunistic (Vibrio and Lentibacter) and oil-degrading (Colwellia, Sulfitobacter, and Pseudoalteromonas) bacteria proliferated after 24 h in comparison to the control. In addition, total prokaryotes seemed to recover in abundance after 24 h, where eukaryotes only ceased to decrease slightly at 72 h, likely because of an inability to adapt to the oil-laden conditions, unlike the prokaryotes. Considering there were no highly volatile components (benzene, toluene, ethylbenzene, and xylene) present in the diesel when the communities were exposed, the results indicate that even a relatively small concentration of diesel run-off can cause a drastic change to the microbial community under low energy conditions. Higher energy conditions due to wave action may mitigate the response of the microbial communities by dilution and additional weathering of the diesel.},
}
@article {pmid34887434,
year = {2021},
author = {Goswami, K and Shope, AJ and Tokarev, V and Wright, JR and Unverdorben, LV and Ly, T and Chen See, J and McLimans, CJ and Wong, HT and Lock, L and Clarkson, S and Parvizi, J and Lamendella, R},
title = {Comparative meta-omics for identifying pathogens associated with prosthetic joint infection.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {23749},
pmid = {34887434},
issn = {2045-2322},
mesh = {Aged ; Aged, 80 and over ; Arthritis, Infectious/diagnosis/*etiology ; Biodiversity ; Computational Biology/methods ; Female ; Gene Expression Profiling ; Humans ; Male ; Metagenome ; Metagenomics/*methods ; Middle Aged ; Prosthesis-Related Infections/diagnosis/*etiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Prosthetic joint infections (PJI) are economically and personally costly, and their incidence has been increasing in the United States. Herein, we compared 16S rRNA amplicon sequencing (16S), shotgun metagenomics (MG) and metatranscriptomics (MT) in identifying pathogens causing PJI. Samples were collected from 30 patients, including 10 patients undergoing revision arthroplasty for infection, 10 patients receiving revision for aseptic failure, and 10 patients undergoing primary total joint arthroplasty. Synovial fluid and peripheral blood samples from the patients were obtained at time of surgery. Analysis revealed distinct microbial communities between primary, aseptic, and infected samples using MG, MT, (PERMANOVA p = 0.001), and 16S sequencing (PERMANOVA p < 0.01). MG and MT had higher concordance with culture (83%) compared to 0% concordance of 16S results. Supervised learning methods revealed MT datasets most clearly differentiated infected, primary, and aseptic sample groups. MT data also revealed more antibiotic resistance genes, with improved concordance results compared to MG. These data suggest that a differential and underlying microbial ecology exists within uninfected and infected joints. This study represents the first application of RNA-based sequencing (MT). Further work on larger cohorts will provide opportunities to employ deep learning approaches to improve accuracy, predictive power, and clinical utility.},
}
@article {pmid34878672,
year = {2022},
author = {Wu, L and Yang, F and Feng, J and Tao, X and Qi, Q and Wang, C and Schuur, EAG and Bracho, R and Huang, Y and Cole, JR and Tiedje, JM and Zhou, J},
title = {Permafrost thaw with warming reduces microbial metabolic capacities in subsurface soils.},
journal = {Molecular ecology},
volume = {31},
number = {5},
pages = {1403-1415},
doi = {10.1111/mec.16319},
pmid = {34878672},
issn = {1365-294X},
mesh = {Carbon/metabolism ; Carbon Cycle ; *Permafrost/microbiology ; Soil/chemistry ; Soil Microbiology ; Tundra ; },
abstract = {Microorganisms are major constituents of the total biomass in permafrost regions, whose underlain soils are frozen for at least two consecutive years. To understand potential microbial responses to climate change, here we examined microbial community compositions and functional capacities across four soil depths in an Alaska tundra site. We showed that a 5-year warming treatment increased soil thaw depth by 25.7% (p = .011) within the deep organic layer (15-25 cm). Concurrently, warming reduced 37% of bacterial abundance and 64% of fungal abundances in the deep organic layer, while it did not affect microbial abundance in other soil layers (i.e., 0-5, 5-15, and 45-55 cm). Warming treatment altered fungal community composition and microbial functional structure (p < .050), but not bacterial community composition. Using a functional gene array, we found that the relative abundances of a variety of carbon (C)-decomposing, iron-reducing, and sulphate-reducing genes in the deep organic layer were decreased, which was not observed by the shotgun sequencing-based metagenomics analysis of those samples. To explain the reduced metabolic capacities, we found that warming treatment elicited higher deterministic environmental filtering, which could be linked to water-saturated time, soil moisture, and soil thaw duration. In contrast, plant factors showed little influence on microbial communities in subsurface soils below 15 cm, despite a 25.2% higher (p < .05) aboveground plant biomass by warming treatment. Collectively, we demonstrate that microbial metabolic capacities in subsurface soils are reduced, probably arising from enhanced thaw by warming.},
}
@article {pmid34878610,
year = {2021},
author = {Kumar, V and Kumar, S and Singh, D},
title = {Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {1},
pages = {3},
pmid = {34878610},
issn = {1433-4909},
support = {MLP0143//CSIR-Institute of Himalayan Bioresource Technology/ ; },
mesh = {Geologic Sediments ; *Lakes ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Glacial and kettle lakes in the high-altitude Himalayas are unique habitats with significant scope for microbial ecology. The present study provides insights into bacterial community structure and function of the sediments of two high-altitude lakes using 16S amplicon and whole-genome shotgun (WGS) metagenomics. Microbial communities in the sediments of Parvati kund (glacial lake) and Bhoot ground (kettle lake) majorly consist of bacteria and a small fraction of archaea and eukaryota. The bacterial population has an abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. Despite the common phyla, the sediments from each lake have a distinct distribution of bacterial and archaeal taxa. The analysis of the WGS metagenomes at the functional level provides a broad picture of microbial community metabolism of key elements and suggested chemotrophs as the major primary producers. In addition, the findings also revealed that polyhydroxyalkanoates (PHA) are a crucial stress adaptation molecule. The abundance of PHA metabolism in Alpha- and Betaproteobacteria and less representation in other bacterial and archaeal classes in both metagenomes was disclosed. The metagenomic insights provided an incisive view of the microbiome from Himalayan lake's sediments. It has also opened the scope for further bioprospection from virgin Himalayan niches.},
}
@article {pmid34878336,
year = {2021},
author = {Andrić, S and Meyer, T and Rigolet, A and Prigent-Combaret, C and Höfte, M and Balleux, G and Steels, S and Hoff, G and De Mot, R and McCann, A and De Pauw, E and Argüelles Arias, A and Ongena, M},
title = {Lipopeptide Interplay Mediates Molecular Interactions between Soil Bacilli and Pseudomonads.},
journal = {Microbiology spectrum},
volume = {9},
number = {3},
pages = {e0203821},
pmid = {34878336},
issn = {2165-0497},
mesh = {Bacillus/growth &amp; development/*metabolism ; Lipopeptides/*metabolism ; Microbial Interactions ; Pseudomonas/*metabolism ; Secondary Metabolism ; *Soil Microbiology ; },
abstract = {Some Bacillus species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between B. velezensis and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent in vitro confrontation, a multifaceted macroscopic outcome was observed and characterized by Bacillus growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. Bacillus mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera. IMPORTANCE Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between B. velezensis and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, Bacillus overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow Bacillus to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for Bacillus and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.},
}
@article {pmid34877561,
year = {2021},
author = {Wang, F and Harindintwali, JD and Yuan, Z and Wang, M and Wang, F and Li, S and Yin, Z and Huang, L and Fu, Y and Li, L and Chang, SX and Zhang, L and Rinklebe, J and Yuan, Z and Zhu, Q and Xiang, L and Tsang, DCW and Xu, L and Jiang, X and Liu, J and Wei, N and Kästner, M and Zou, Y and Ok, YS and Shen, J and Peng, D and Zhang, W and Barceló, D and Zhou, Y and Bai, Z and Li, B and Zhang, B and Wei, K and Cao, H and Tan, Z and Zhao, LB and He, X and Zheng, J and Bolan, N and Liu, X and Huang, C and Dietmann, S and Luo, M and Sun, N and Gong, J and Gong, Y and Brahushi, F and Zhang, T and Xiao, C and Li, X and Chen, W and Jiao, N and Lehmann, J and Zhu, YG and Jin, H and Schäffer, A and Tiedje, JM and Chen, JM},
title = {Technologies and perspectives for achieving carbon neutrality.},
journal = {Innovation (Cambridge (Mass.))},
volume = {2},
number = {4},
pages = {100180},
pmid = {34877561},
issn = {2666-6758},
abstract = {Global development has been heavily reliant on the overexploitation of natural resources since the Industrial Revolution. With the extensive use of fossil fuels, deforestation, and other forms of land-use change, anthropogenic activities have contributed to the ever-increasing concentrations of greenhouse gases (GHGs) in the atmosphere, causing global climate change. In response to the worsening global climate change, achieving carbon neutrality by 2050 is the most pressing task on the planet. To this end, it is of utmost importance and a significant challenge to reform the current production systems to reduce GHG emissions and promote the capture of CO2 from the atmosphere. Herein, we review innovative technologies that offer solutions achieving carbon (C) neutrality and sustainable development, including those for renewable energy production, food system transformation, waste valorization, C sink conservation, and C-negative manufacturing. The wealth of knowledge disseminated in this review could inspire the global community and drive the further development of innovative technologies to mitigate climate change and sustainably support human activities.},
}
@article {pmid34877560,
year = {2021},
author = {Xu, Y and Liu, X and Cao, X and Huang, C and Liu, E and Qian, S and Liu, X and Wu, Y and Dong, F and Qiu, CW and Qiu, J and Hua, K and Su, W and Wu, J and Xu, H and Han, Y and Fu, C and Yin, Z and Liu, M and Roepman, R and Dietmann, S and Virta, M and Kengara, F and Zhang, Z and Zhang, L and Zhao, T and Dai, J and Yang, J and Lan, L and Luo, M and Liu, Z and An, T and Zhang, B and He, X and Cong, S and Liu, X and Zhang, W and Lewis, JP and Tiedje, JM and Wang, Q and An, Z and Wang, F and Zhang, L and Huang, T and Lu, C and Cai, Z and Wang, F and Zhang, J},
title = {Artificial intelligence: A powerful paradigm for scientific research.},
journal = {Innovation (Cambridge (Mass.))},
volume = {2},
number = {4},
pages = {100179},
pmid = {34877560},
issn = {2666-6758},
abstract = {Artificial intelligence (AI) coupled with promising machine learning (ML) techniques well known from computer science is broadly affecting many aspects of various fields including science and technology, industry, and even our day-to-day life. The ML techniques have been developed to analyze high-throughput data with a view to obtaining useful insights, categorizing, predicting, and making evidence-based decisions in novel ways, which will promote the growth of novel applications and fuel the sustainable booming of AI. This paper undertakes a comprehensive survey on the development and application of AI in different aspects of fundamental sciences, including information science, mathematics, medical science, materials science, geoscience, life science, physics, and chemistry. The challenges that each discipline of science meets, and the potentials of AI techniques to handle these challenges, are discussed in detail. Moreover, we shed light on new research trends entailing the integration of AI into each scientific discipline. The aim of this paper is to provide a broad research guideline on fundamental sciences with potential infusion of AI, to help motivate researchers to deeply understand the state-of-the-art applications of AI-based fundamental sciences, and thereby to help promote the continuous development of these fundamental sciences.},
}
@article {pmid34875513,
year = {2022},
author = {Iasakov, TR and Kanapatskiy, TA and Toshchakov, SV and Korzhenkov, AA and Ulyanova, MO and Pimenov, NV},
title = {The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation.},
journal = {Marine environmental research},
volume = {173},
number = {},
pages = {105533},
doi = {10.1016/j.marenvres.2021.105533},
pmid = {34875513},
issn = {1879-0291},
mesh = {Anaerobiosis ; Archaea/genetics ; Geologic Sediments ; *Methane ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; Planctomycetes ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.},
}
@article {pmid34875143,
year = {2022},
author = {Verstraete, W and Yanuka-Golub, K and Driesen, N and De Vrieze, J},
title = {Engineering microbial technologies for environmental sustainability: choices to make.},
journal = {Microbial biotechnology},
volume = {15},
number = {1},
pages = {215-227},
pmid = {34875143},
issn = {1751-7915},
mesh = {Animals ; Climate Change ; Humans ; *Microbiota ; *Soil ; },
abstract = {Microbial technologies have provided solutions to key challenges in our daily lives for over a century. In the debate about the ongoing climate change and the need for planetary sustainability, microbial ecology and microbial technologies are rarely considered. Nonetheless, they can bring forward vital solutions to decrease and even prevent long-term effects of climate change. The key to the success of microbial technologies is an effective, target-oriented microbiome management. Here, we highlight how microbial technologies can play a key role in both natural, i.e. soils and aquatic ecosystems, and semi-natural or even entirely human-made, engineered ecosystems, e.g. (waste) water treatment and bodily systems. First, we set forward fundamental guidelines for effective soil microbial resource management, especially with respect to nutrient loss and greenhouse gas abatement. Next, we focus on closing the water circle, integrating resource recovery. We also address the essential interaction of the human and animal host with their respective microbiomes. Finally, we set forward some key future potentials, such as microbial protein and the need to overcome microphobia for microbial products and services. Overall, we conclude that by relying on the wisdom of the past, we can tackle the challenges of our current era through microbial technologies.},
}
@article {pmid34874772,
year = {2021},
author = {Hilts, AS and Hunjan, MS and Hug, LA},
title = {Adapting Macroecology to Microbiology: Using Occupancy Modeling To Assess Functional Profiles across Metagenomes.},
journal = {mSystems},
volume = {6},
number = {6},
pages = {e0079021},
pmid = {34874772},
issn = {2379-5077},
support = {//Canada Research Chairs (Chaires de recherche du Canada)/ ; 2016-03686//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
abstract = {Metagenomic sequencing provides information on the metabolic capacities and taxonomic affiliations for members of a microbial community. When assessing metabolic functions in a community, missing genes in pathways can occur in two ways; the genes may legitimately be missing from the community whose DNA was sequenced, or the genes were missed during shotgun sequencing or failed to assemble, and thus the metabolic capacity of interest is wrongly absent from the sequence data. Here, we borrow and adapt occupancy modeling from macroecology to provide mathematical context to metabolic predictions from metagenomes. We review the five assumptions underlying occupancy modeling through the lens of microbial community sequence data. Using the methane cycle, we apply occupancy modeling to examine the presence and absence of methanogenesis and methanotrophy genes from nearly 10,000 metagenomes spanning global environments. We determine that methanogenesis and methanotrophy are positively correlated across environments, providing a predictive framework for assessing gene absences for these functions. We present this adaptation of macroecology's occupancy modeling to metagenomics as a tool to quantify the uncertainty in predictions of the presence/absence of traits in environmental microbiological surveys. We further initiate a call for stronger metadata standards to accompany metagenome deposition, to enable robust statistical approaches in the future. IMPORTANCE Metagenomics is maturing rapidly as a field but is hampered by a lack of available statistical tools. A primary area of uncertainty is around missing genes or functions from a metagenomic data set. Here, we borrow an established modeling approach from macroecology and adapt it to metagenomic data sets. Rather than multiple sampling trips to a specific area to detect a species of interest (e.g., identifying a cardinal in a forest), we leverage the enormous amount of information within a metagenome and use multiple gene markers for a function of interest (e.g., subunits of an enzyme complex). We applied our adapted occupancy modeling to a case study examining methane cycling capacity. Our models show methanogens and methanotrophs are both more likely to cooccur than be present in the absence of the other guild. The lack of consistent and complete metadata is a significant hurdle for increasing the statistical rigor of metagenomic analyses.},
}
@article {pmid34874481,
year = {2021},
author = {Devi, SP and Jani, K and Sharma, A and Jha, DK},
title = {Bacterial communities and their bioremediation capabilities in oil-contaminated agricultural soils.},
journal = {Environmental monitoring and assessment},
volume = {194},
number = {1},
pages = {9},
doi = {10.1007/s10661-021-09669-9},
pmid = {34874481},
issn = {1573-2959},
mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Ecosystem ; Environmental Monitoring ; Humans ; Hydrocarbons/analysis ; *Petroleum/analysis ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {Rapid industrialization and development in petrochemical industries have resulted in increased hydrocarbon pollution causing substantial damage to the natural ecosystems including agricultural soils. In the recent, past efforts have been made to treat the contaminated soils using microorganisms by natural processes. Soil bacteria, known for their potential to degrade the soil contaminants, play a vital role in maintaining soil health. In the current study, we observed the influence of hydrocarbon contamination on the physicochemical characteristics and enzymatic activities of the soil. Proteobacteria (30.48%), Actinobacteria (13.91%), and Acidobacteria (12.57%) flourished in the non-contaminated soil whereas contaminated sites were dominated by Proteobacteria (44.02 ± 15.65%). In contrast, the sites experiencing the different degrees of exposure to the hydrocarbon pollution allowed specific augmentation of bacterial taxa (in decreasing order of exposure time), viz. Proteobacteria (60.47%), Firmicutes (32.48%), and Bacteroidetes(13.59%), based on culture-independent approach that suggested their potential role in hydrocarbon degradation as compared to the non-contaminated site. The imputation of metabolic function also supported the positive correlation to the exposure to hydrocarbon pollution, with site 2 being highly abundant for gene families involved in xenobiotics biodegradation. The study provides insights into bacterial community structure with special emphasis on their efficiency to degrade hydrocarbons. The results from the study can help in designing appropriate biodegradation strategies to mitigate the serious problems of oil contamination in agricultural soil.},
}
@article {pmid34871418,
year = {2022},
author = {Andreopoulos, WB and Geller, AM and Lucke, M and Balewski, J and Clum, A and Ivanova, NN and Levy, A},
title = {Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.},
journal = {Nucleic acids research},
volume = {50},
number = {3},
pages = {e17},
pmid = {34871418},
issn = {1362-4962},
mesh = {Animals ; Chromosomes, Bacterial/genetics ; *Deep Learning ; *Genome, Bacterial ; *Plasmids/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC-ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.},
}
@article {pmid34867858,
year = {2021},
author = {Ahmed, B and Smart, LB and Hijri, M},
title = {Microbiome of Field Grown Hemp Reveals Potential Microbial Interactions With Root and Rhizosphere Soil.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {741597},
pmid = {34867858},
issn = {1664-302X},
abstract = {Hemp (Cannabis sativa L.) is a crop bred and grown for the production of fiber, grain, and floral extracts that contribute to health and wellness. Hemp plants interact with a myriad of microbiota inhabiting the phyllosphere, endosphere, rhizoplane, and rhizosphere. These microbes offer many ecological services, particularly those of below ground biotopes which are involved in nutrient cycling, uptake, and alleviating biotic and abiotic stress. The microbiota communities of the hemp rhizosphere in the field are not well documented. To discover core microbiota associated with field grown hemp, we cultivated single C. sativa cultivar, "TJ's CBD," in six different fields in New York and sampled hemp roots and their rhizospheric soil. We used Illumina MiSeq amplicon sequencing targeting 16S ribosomal DNA of bacteria and ITS of fungi to study microbial community structure of hemp roots and rhizospheres. We found that Planctobacteria and Ascomycota dominated the taxonomic composition of hemp associated microbial community. We identified potential core microbiota in each community (bacteria: eight bacterial amplicon sequence variant - ASV, identified as Gimesia maris, Pirellula sp. Lacipirellula limnantheis, Gemmata sp. and unclassified Planctobacteria; fungi: three ASVs identified as Fusarium oxysporum, Gibellulopsis piscis, and Mortierella minutissima). We found 14 ASVs as hub taxa [eight bacterial ASVs (BASV) in the root, and four bacterial and two fungal ASVs in the rhizosphere soil], and 10 BASV connected the root and rhizosphere soil microbiota to form an extended microbial communication in hemp. The only hub taxa detected in both the root and rhizosphere soil microbiota was ASV37 (Caulifigura coniformis), a bacterial taxon. The core microbiota and Network hub taxa can be studied further for biocontrol activities and functional investigations in the formulation of hemp bioinoculants. This study documented the microbial diversity and community structure of hemp grown in six fields, which could contribute toward the development of bioinoculants for hemp that could be used in organic farming.},
}
@article {pmid34867834,
year = {2021},
author = {Thomas, P and Sahu, PK},
title = {Vertical Transmission of Diverse Cultivation-Recalcitrant Endophytic Bacteria Elucidated Using Watermelon Seed Embryos.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {635810},
pmid = {34867834},
issn = {1664-302X},
abstract = {Seed transmission of endophytic microorganisms is a growing research area in plant biology and microbiology. We employed cultivation versus cultivation-independent approaches on excised embryos from watermelon seeds (6-12 months in storage) and on embryo-derived in vitro seedlings (EIVS) to assess the vertical transmission of endophytic bacteria. Surface-disinfected watermelon seeds bore abundant residual bacteria in the testa and perisperm tissues, predominantly Bacillus spp. propounding the essentiality of excluding all non-embryonic tissues for vertical transmission studies. Tissue homogenates from re-disinfected seed embryos displayed no cultivable bacteria during the 1-week monitoring. Bright-field live microscopy revealed abundant bacteria in tissue homogenates and in embryo sections as intracellular motile particles. Confocal imaging on embryo sections after SYTO-9 staining and eubacterial fluorescent in situ hybridization (FISH) endorsed enormous bacterial colonization. Quantitative Insights Into Microbial Ecology (QIIME)-based 16S rRNA V3-V4 taxonomic profiling excluding the preponderant chloroplast and mitochondrial sequences revealed a high bacterial diversity in watermelon seed embryos mainly Firmicutes barring spore formers followed by Proteobacteria, Bacteroidetes, and Actinobacteria, and other minor phyla. Embryo-base (comprising the radicle plus plumule parts) and embryo-cotyledon parts differed in bacterial profiles with the abundance of Firmicutes in the former and Proteobacteria dominance in the latter. EIVS displayed a higher bacterial diversity over seed embryos indicating the activation from the dormant stage of more organisms in seedlings or their better amenability to DNA techniques. It also indicated embryo-to-seedling bacterial transmission, varying taxonomic abundances for seed embryos and seedlings, and differing phylogenic profiles for root, hypocotyl, and cotyledon/shoot-tip tissues. Investigations on different watermelon cultivars confirmed the embryo transmission of diverse cultivation recalcitrant endophytic bacteria. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes formed the core phyla across different cultivars with 80-90% similarity at genus to phylum levels. Conversely, freshly harvested seeds displayed a dominance of Proteobacteria. The findings revealed that dicot seeds such as in different watermelon cultivars come packaged with abundant and diverse vertical and seedling-transmissible cultivation recalcitrant endophytic bacteria with significant implications for plant biology.},
}
@article {pmid34867016,
year = {2021},
author = {Chergui, D and Akretche-Kelfat, S and Lamoudi, L and Al-Rshaidat, M and Boudjelal, F and Ait-Amar, H},
title = {Optimization of citric acid production by Aspergillus niger using two downgraded Algerian date varieties.},
journal = {Saudi journal of biological sciences},
volume = {28},
number = {12},
pages = {7134-7141},
pmid = {34867016},
issn = {1319-562X},
abstract = {In the present work, the GHARS and the MECH DEGLA downgraded date varieties were used in a fermentation medium in order to produce citric acid by the Aspergillus niger. The biochemical characteristics of the dates were investigated, along with the chemical and physical characteristics of the solutions of both samples. The analyzed parameters included the moisture and sugar content, the ash residual, the pH values, and the electrical conductivity. The effect of the following fermentation parameters was studied: initial pH, temperature, incubation period, and methanol. For the GHARS and MECH DEGLA date varieties respectively, the ash residual measured at 1.90% and 2.47%. For each date variety, the moisture and total sugars were measured at 11.59% and 85%, for the GHARS, and 12.82% and 80.47% for the MECH DEGLA. Citric acid production using either of the two varieties of dates showed a high yield in a short time. The obtained results showed that the highest production of citric acid by both medium of dates was achieved at the initial pH value of 3.0, temperature 30 °C, and an incubation period of 8 days. Also, the maximum amount of citric acid was produced when both mediums contained 4% of methanol. Both varieties of dates showed a good yield for the citric acid and can be used as a culture medium since they are economic and ensure good growth for the Aspergillus niger.},
}
@article {pmid34865013,
year = {2022},
author = {Kindler, GS and Wong, HL and Larkum, AWD and Johnson, M and MacLeod, FI and Burns, BP},
title = {Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {1},
pages = {},
doi = {10.1093/femsec/fiab158},
pmid = {34865013},
issn = {1574-6941},
mesh = {Animals ; Archaea/genetics ; Bays ; *Metagenomics ; Phylogeny ; Planctomycetes ; *Sharks ; },
abstract = {The present study describes for the first time the community composition and functional potential of the microbial mats found in the supratidal, gypsum-rich and hypersaline region of Blue Holes, Shark Bay. This was achieved via high-throughput metagenomic sequencing of total mat community DNA and complementary analyses using hyperspectral confocal microscopy. Mat communities were dominated by Proteobacteria (29%), followed by Bacteroidetes/Chlorobi group (11%) and Planctomycetes (10%). These mats were found to also harbour a diverse community of potentially novel microorganisms, including members from the DPANN, Asgard archaea and candidate phyla radiation, with highest diversity found in the lower regions (∼14-20 mm depth) of the mat. In addition to pathways for major metabolic cycles, a range of putative rhodopsins with previously uncharacterized motifs and functions were identified along with heliorhodopsins and putative schizorhodopsins. Critical microbial interactions were also inferred, and from 117 medium- to high-quality metagenome-assembled genomes, viral defence mechanisms (CRISPR, BREX and DISARM), elemental transport, osmoprotection, heavy metal resistance and UV resistance were also detected. These analyses have provided a greater understanding of these distinct mat systems in Shark Bay, including key insights into adaptive responses and proposing that photoheterotrophy may be an important lifestyle in Blue Holes.},
}
@article {pmid34864985,
year = {2021},
author = {Voskuhl, L and Akbari, A and Müller, H and Pannekens, M and Brusilova, D and Dyksma, S and Haque, S and Graupner, N and Dunthorn, M and Meckenstock, RU and Brauer, VS},
title = {Indigenous microbial communities in heavy oil show a threshold response to salinity.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {12},
pages = {},
pmid = {34864985},
issn = {1574-6941},
mesh = {Bacteria/genetics ; Lakes ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Salinity ; },
abstract = {Microbial degradation influences the quality of oil resources. The environmental factors that shape the composition of oil microbial communities are largely unknown because most samples from oil fields are impacted by anthropogenic oil production, perturbing the native ecosystem with exogenous fluids and microorganisms. We investigated the relationship between formation water geochemistry and microbial community composition in undisturbed oil samples. We isolated 43 microliter-sized water droplets naturally enclosed in the heavy oil of the Pitch Lake, Trinidad and Tobago. The water chemistry and microbial community composition within the same water droplet were determined by ion chromatography and 16S rRNA gene amplicon sequencing, respectively. The results revealed a high variability in ion concentrations and community composition between water droplets. Microbial community composition was mostly affected by the chloride concentration, which ranged from freshwater to brackish-sea water. Remarkably, microbial communities did not respond gradually to increasing chloride concentration but showed a sudden change to less diverse and uneven communities when exceeding a chloride concentration of 57.3 mM. The results reveal a threshold-regulated response of microbial communities to salinity, offering new insights into the microbial ecology of oil reservoirs.},
}
@article {pmid34864466,
year = {2022},
author = {Kazmi, SSUH and Uroosa, and Warren, A and Zhong, X and Xu, H},
title = {Insights into the ecotoxicity of nitrofurazone in marine ecosystems based on body-size spectra of periphytic ciliates.},
journal = {Marine pollution bulletin},
volume = {174},
number = {},
pages = {113217},
doi = {10.1016/j.marpolbul.2021.113217},
pmid = {34864466},
issn = {1879-3363},
mesh = {Body Size ; *Ciliophora ; Ecosystem ; Ecotoxicology ; *Nitrofurazone/toxicity ; },
abstract = {In ecotoxicological studies, some biological responses known as biomarkers can be used as powerful tools to evaluate the ecotoxicity. In this study, we investigated the disparity of responses shown by body-size spectra of periphytic ciliate communities when used as biomarkers to detect the toxicity of the broad-spectrum veternary antibiotic nitrofurazone. Briefly, in chronic exposure experiments ciliate communities were exposed to different concentrations (0, 1, 2, 4 and 8 mg ml[-1]) of nitrofurazone. Relative Abundance of ciliates in all body-size categories decreased significantly, whereas their frequency of occurrence and probability densities showed hormetic-like responses in a dose dependent manner. Additionally, body-size distinctness indices were influenced by toxic stress and significantly departed from an expectation at higher nitrofurazone concentrations. Taken together, our results demonstrated that body-size spectra and body-size distinctness offered clear evidence of nitrofurazone toxicity in periphytic ciliates. Body-size spectra can therefore be used as a pivotal biomarker to determine the ecotoxicity of nitrofurazone in aquatic environments.},
}
@article {pmid34864020,
year = {2022},
author = {Costa, DPD and Araujo, ASF and Pereira, APA and Mendes, LW and França, RFD and Silva, TDGED and Oliveira, JB and Araujo, JS and Duda, GP and Menezes, RSC and Medeiros, EV},
title = {Forest-to-pasture conversion modifies the soil bacterial community in Brazilian dry forest Caatinga.},
journal = {The Science of the total environment},
volume = {810},
number = {},
pages = {151943},
doi = {10.1016/j.scitotenv.2021.151943},
pmid = {34864020},
issn = {1879-1026},
mesh = {Biodiversity ; Forests ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; },
abstract = {Soils comprise a huge fraction of the world's biodiversity, contributing to several crucial ecosystem functions. However, how the forest-to-pasture conversion impact soil bacterial diversity remains poorly understood, mainly in the Caatinga biome, the largest tropical dry forest of the world. Here, we hypothesized that forest-to-pasture conversion would shape the microbial community. Thus, the soil bacterial community was assessed using the 16S rRNA gene sequencing into the Illumina MiSeq platform. Then, we analyzed ecological patterns and correlated the bacterial community with environmental parameters in forest, and two distinct pastures areas, one less productive and another more productive. The variation in soil properties in pastures and forest influenced the structure and diversity of the bacterial community. Thus, the more productive pasture positively influenced the proportion of specialists and the co-occurrence network compared to the less productive pasture. Also, Proteobacteria, Acidobacteria, and Verrucomicrobia were abundant under forest, while Actinobacteria, Firmicutes, and Chloroflexi were abundant under pastures. Also, the more productive pasture presented a higher bacterial diversity, which is important since that a more stable and connected bacterial community could benefit the agricultural environment and enhance plant performance, as can be observed by the highest network complexity in this pasture. Together, our findings elucidate a significant shift in soil bacterial communities as a consequence of forest-to-pasture conversion and bring important information for the development of preservation strategies.},
}
@article {pmid34863611,
year = {2022},
author = {Nobs, SJ and MacLeod, FI and Wong, HL and Burns, BP},
title = {Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life?.},
journal = {Trends in microbiology},
volume = {30},
number = {5},
pages = {421-431},
doi = {10.1016/j.tim.2021.11.003},
pmid = {34863611},
issn = {1878-4380},
mesh = {Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; },
abstract = {One of the most significant events in the evolution of life is the origin of the eukaryotic cell, an increase in cellular complexity that occurred approximately 2 billion years ago. Ground-breaking research has centered around unraveling the characteristics of the Last Eukaryotic Common Ancestor (LECA) and the nuanced archaeal and bacterial contributions in eukaryogenesis, resulting in fundamental changes in our understanding of the Tree of Life. The archaeal and bacterial roles are covered by theories of endosymbiogenesis wherein an ancestral host archaeon and a bacterial endosymbiont merged to create a new complex cell type - Eukarya - and its mitochondrion. Eukarya is often regarded as a unique and distinct domain due to complex innovations not found in archaea or bacteria, despite housing a chimeric genome containing genes of both archaeal and bacterial origin. However, the discovery of complex cell machineries in recently described Asgard archaeal lineages, and the growing support for diverse bacterial gene transfers prior to and during the time of LECA, is redefining our understanding of eukaryogenesis. Indeed, the uniqueness of Eukarya, as a domain, is challenged. It is likely that many microbial syntrophies, encompassing a 'microbial village', were required to 'raise' a eukaryote during the process of eukaryogenesis.},
}
@article {pmid34862696,
year = {2022},
author = {Jiao, S and Chen, W and Wei, G},
title = {Core microbiota drive functional stability of soil microbiome in reforestation ecosystems.},
journal = {Global change biology},
volume = {28},
number = {3},
pages = {1038-1047},
doi = {10.1111/gcb.16024},
pmid = {34862696},
issn = {1365-2486},
mesh = {Metagenomics ; *Microbiota ; *Soil ; Soil Microbiology ; },
abstract = {Revealing the ecological roles of core microbiota in the maintenance of the functional stability of soil microbiomes is crucial for sustainable ecosystem functioning; however, there is a dearth of whole-soil profile studies on the fundamental topic in microbial ecology, especially in the context of ecological restoration. Here, we explored whether core microbiota influence the temporal changes in the functional stability of soil microbiomes throughout the soil profile (i.e., soil depths of 0-300 cm) during natural succession in restored ex-arable ecosystems, via high-throughput amplicon and metagenomic sequencing. We revealed that core microbiota were essential for the maintenance of the functional stability of soil microbiomes in reforestation ecosystems. Specifically, the core taxa within one cluster of soil network, which had similar ecological preferences, had major contributions to functional stability. Reforestation significantly decreased the functional stability of soil microbiomes, which exhibited significant variations along the vertical soil profile in the reforested soils. Overall, the findings enhance our understanding of the factors driving functional stability in soil microbiomes, and suggests that core microbiota should be considered a key factor and integrated in policy and management activities targeting the enhancement and maintenance of functional stability and ecosystem sustainability in ecological restoration programs.},
}
@article {pmid34862327,
year = {2021},
author = {Neu, AT and Allen, EE and Roy, K},
title = {Defining and quantifying the core microbiome: Challenges and prospects.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {51},
pages = {},
pmid = {34862327},
issn = {1091-6490},
mesh = {Animals ; Environmental Microbiology ; Humans ; *Microbiota ; Phylogeny ; },
abstract = {The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.},
}
@article {pmid34861433,
year = {2022},
author = {Zhu, X and Lee, LW and Song, G and Zhang, X and Gao, Y and Yang, G and Luo, S and Huang, X},
title = {Deciphering mono/multivalent draw solute-induced microbial ecology and membrane fouling in anaerobic osmotic membrane bioreactor.},
journal = {Water research},
volume = {209},
number = {},
pages = {117869},
doi = {10.1016/j.watres.2021.117869},
pmid = {34861433},
issn = {1879-2448},
abstract = {Anaerobic osmotic membrane bioreactor (AnOMBR) attracted attention due to high quality effluent production with low energy demand, and draw solute has significant effect on the system performance. However, the mutual relationship between draw solute-induced salinity accumulation and microbial community had many unknown questions to be solved. This study purpose was to construct two AnOMBR to compare the impact of draw solutes of NaCl and MgCl2 on the dynamic change of microbial ecology and membrane fouling. The result indicated that the draw solute of MgCl2 caused less salinity and more membrane biofouling than that of the draw solute NaCl. Multiple microbiological analysis methods were applied to discover keystone species related to the conductivity change and membrane fouling, especially for the MgCl2-AnOMBR system. It was found that draw solute NaCl could benefit the growth of Proteobacteria to become the most abundant phylum to affect the membrane fouling, while Mg[2+] introduction could stimulate the growth of NS9, Hydrogenphilaceae and Pedosphaeraceae to potentially cause the biofouling. Furthermore, phylogenetic molecular ecological networks (pMENs) deeply analyzed the microbial structure difference under Na[+] and Mg[2+] introduction, and indicated that the family Lentimicrobiaceae and Candidatus_Kaiserbacteria were the keystone species in NaCl-AnOMBR, while two genus Anaerolinea and SWB02, and two families Saprospiraceae and NS9 were discovered to have key effect in MgCl2-AnOMBR due to their strong extracellular polymeric substances (EPS) production ability for survival of other microorganisms. This study was significant to give microbial targets under the impact of various draw solutes, as the reference for the engineers to further investigate how to improve the microbial structure to enhance AnOMBR performance and inhibit the membrane biofouling.},
}
@article {pmid34858369,
year = {2021},
author = {Brüls, T and Baumdicker, F and Smidt, H},
title = {Editorial: Synthetic Microbial Ecology.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {757848},
doi = {10.3389/fmicb.2021.757848},
pmid = {34858369},
issn = {1664-302X},
}
@article {pmid34855091,
year = {2021},
author = {Semenov, AV},
title = {Peptidoglycan of Bacterial Cell Wall Affects Competitive Properties of Microorganisms.},
journal = {Bulletin of experimental biology and medicine},
volume = {172},
number = {2},
pages = {164-168},
pmid = {34855091},
issn = {1573-8221},
mesh = {Antibiosis/*physiology ; Bacillus subtilis/physiology ; Bacterial Proteins/metabolism/physiology ; Bifidobacterium/physiology ; Candida/physiology ; Cell Wall/chemistry/metabolism/*physiology ; Enterobacter/physiology ; Enterococcus faecalis/physiology ; Escherichia coli/physiology ; Female ; Humans ; Lacticaseibacillus casei/physiology ; Microbiological Techniques ; Peptidoglycan/analysis/*metabolism ; Staphylococcus aureus/physiology ; },
abstract = {We studied the effect of bacterial wall peptidoglycan of 7 bacterial species on the competitive properties of human-associated microorganisms. Addition of peptidoglycan to the culture medium did not change the growth characteristics of the test cultures; however, an increase in the antagonism and hydrophobicity of Bifidobacterium sp. and Enterococcus sp. was observed, while the effect on enterobacteria was predominantly indifferent or inhibitory. The effect did not depend much on the source of peptidoglycan and was equally manifested on both indigenous and probiotic strains. The observed new property of peptidoglycan indicates its participation in the formation and functioning of microbiota. The obtained data on the regulation of the properties of microorganisms provide new possibilities for the correction and maintenance of host homeostasis through host-associated microbiota.},
}
@article {pmid34854932,
year = {2023},
author = {Klawonn, I and Dunker, S and Kagami, M and Grossart, HP and Van den Wyngaert, S},
title = {Intercomparison of Two Fluorescent Dyes to Visualize Parasitic Fungi (Chytridiomycota) on Phytoplankton.},
journal = {Microbial ecology},
volume = {85},
number = {1},
pages = {9-23},
pmid = {34854932},
issn = {1432-184X},
support = {KL3332/1-1//german research foundation/ ; WY175/1-1//german research foundation/ ; GR1540/28-1//german research foundation/ ; RA-373/20//german research foundation/ ; },
mesh = {*Phytoplankton ; *Chytridiomycota ; Fluorescent Dyes ; Lakes/microbiology ; Fungi ; },
abstract = {Fungal microparasites (here chytrids) are widely distributed and yet, they are often overlooked in aquatic environments. To facilitate the detection of microparasites, we revisited the applicability of two fungal cell wall markers, Calcofluor White (CFW) and wheat germ agglutinin (WGA), for the direct visualization of chytrid infections on phytoplankton in laboratory-maintained isolates and field-sampled communities. Using a comprehensive set of chytrid-phytoplankton model pathosystems, we verified the staining pattern on diverse morphological structures of chytrids via fluorescence microscopy. Empty sporangia were stained most effectively, followed by encysted zoospores and im-/mature sporangia, while the staining success was more variable for rhizoids, stalks, and resting spores. In a few instances, the staining was unsuccessful (mostly with WGA), presumably due to insufficient cell fixation, gelatinous cell coatings, and multilayered cell walls. CFW and WGA staining could be done in Utermöhl chambers or on polycarbonate filters, but CFW staining on filters seemed less advisable due to high background fluorescence. To visualize chytrids, 1 µg dye mL[-1] was sufficient (but 5 µg mL[-1] are recommended). Using a dual CFW-WGA staining protocol, we detected multiple, mostly undescribed chytrids in two natural systems (freshwater and coastal), while falsely positive or negative stained cells were well detectable. As a proof-of-concept, we moreover conducted imaging flow cytometry, as a potential high-throughput technology for quantifying chytrid infections. Our guidelines and recommendations are expected to facilitate the detection of chytrid epidemics and to unveil their ecological and economical imprint in natural and engineered aquatic systems.},
}
@article {pmid34854719,
year = {2021},
author = {Silveira, SMD and Silva, SD and Macrae, A and Ramos, RTJ and Araújo, FA and Schultz, J and Góes-Neto, A and Costa, MMD and Soares, SC and Azevedo, VAC and Aburjaile, FF and Brenig, B and Rosado, AS and Oliveira, SS},
title = {Genome Sequence of Pseudomonas sp. Strain LAP_36, A Rhizosphere Bacterium Isolated from King George Island, Antarctica.},
journal = {Microbiology resource announcements},
volume = {10},
number = {48},
pages = {e0073121},
pmid = {34854719},
issn = {2576-098X},
abstract = {Pseudomonas sp. strain LAP_36 was isolated from rhizosphere soil from Deschampsia antarctica on King George Island, South Shetland Islands, Antarctica. Here, we report on its draft genome sequence, which consists of 8,794,771 bp with 60.0% GC content and 8,011 protein-coding genes.},
}
@article {pmid34854667,
year = {2021},
author = {Carboni, A and Slomberg, DL and Nassar, M and Santaella, C and Masion, A and Rose, J and Auffan, M},
title = {Aquatic Mesocosm Strategies for the Environmental Fate and Risk Assessment of Engineered Nanomaterials.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {24},
pages = {16270-16282},
doi = {10.1021/acs.est.1c02221},
pmid = {34854667},
issn = {1520-5851},
mesh = {*Ecosystem ; *Nanostructures/toxicity ; Risk Assessment ; },
abstract = {In the past decade, mesocosms have emerged as a useful tool for the environmental study of engineered nanomaterials (ENMs) as they can mimic the relevant exposure scenario of contamination. Herein, we analyzed the scientific outcomes of aquatic mesocosm experiments, with regard to their designs, the ENMs tested, and the end points investigated. Several mesocosm designs were consistently applied in the past decade to virtually mimic various contamination scenarios with regard to ecosystem setting as well as ENMs class, dose, and dosing. Statistical analyses were carried out with the literature data to identify the main parameters driving ENM distribution in the mesocosms and the potential risk posed to benthic and planktonic communities as well as global ecosystem responses. These analyses showed that at the end of the exposure, mesocosm size (water volume), experiment duration, and location indoor/outdoor had major roles in defining the ENMs/metal partitioning. Moreover, a higher exposure of the benthic communities is often observed but did not necessarily translate to a higher risk due to the lower hazard posed by transformed ENMs in the sediments (e.g., aggregated, sulfidized). However, planktonic organisms were generally exposed to lower concentrations of potentially more reactive and toxic ENM species. Hence, mesocosms can be complementary tools to existing standard operational procedures for regulatory purposes and environmental fate and risk assessment of ENMs. To date, the research was markedly unbalanced toward the investigation of metal-based ENMs compared to metalloid- and carbon-based ENMs but also nanoenabled products. Future studies are expected to fill this gap, with special regard to high production volume and potentially hazardous ENMs. Finally, to take full advantage of mesocosms, future studies must be carefully planned to incorporate interdisciplinary approaches and ensure that the large data sets produced are fully exploited.},
}
@article {pmid34852879,
year = {2021},
author = {Cowan, DA and Burton, SG and Rybicki, EP and Wiliamson, AL and Dorrington, RA and Pepper, MS},
title = {Viruses, variants and vaccines.},
journal = {South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde},
volume = {111},
number = {5},
pages = {409-411},
doi = {10.7196/SAMJ.2021.v111i5.15578},
pmid = {34852879},
issn = {2078-5135},
mesh = {*COVID-19/epidemiology/genetics/prevention &amp; control ; *COVID-19 Vaccines ; Humans ; Mutation ; Pandemics/prevention &amp; control ; SARS-CoV-2/*genetics/isolation &amp; purification ; South Africa ; Vaccine Efficacy ; *Vaccines ; *Viruses/pathogenicity ; },
abstract = {The current SARS-CoV-2 pandemic has brought a number of major global clinical, sociological and economic issues into sharp focus. We address some of these issues, focusing on short-term factors such as virus mutations and vaccine efficacy, and also considering the longer-term implications of the current pandemic. We discuss societal responses to the presence of a pathogen that will probably remain in circulation for decades or longer, and to future new emergent viruses.},
}
@article {pmid34851441,
year = {2022},
author = {Oh, HN and Myeong, NR and Kim, T and Min, GS and Kim, S and Sul, WJ},
title = {Changes in Fecal Pellet Microbiome of the Cold-Adapted Antarctic Copepod Tigriopus kingsejongensis at Different Temperatures and Developmental Stages.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1029-1041},
pmid = {34851441},
issn = {1432-184X},
support = {Graduate Research Scholarship in 2016//Chung-Ang University/ ; NRF-2019R1A2C1090861//National Research Foundation of Korea/ ; PE21140//Korea Polar Research Institute/ ; },
mesh = {Animals ; *Copepoda ; Temperature ; Antarctic Regions ; Cold Temperature ; *Microbiota ; },
abstract = {Tigriopus kingsejongensis, a copepod species reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. We cultured T. kingsejongensis at three different temperatures (2 °C, 8 °C, and 15 °C) in a laboratory to observe the changes in its fecal pellet microbiome depending on the cultivation temperatures and developmental stages. We observed that the fecal pellet microbiome of the copepod changed with temperature: a lower microbial diversity, higher abundance of the aquatic bacterium Vibrio, and lower abundance of the psychrophilic bacterium Colwellia were noted at higher temperatures. In addition, the fecal pellet microbiome of the copepod changed according to the developmental stage: a lower microbial diversity was noted in egg-attached copepods than in nauplii at 8 °C. We further analyzed three shotgun metagenomes from the fecal pellet samples of T. kingsejongensis at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolases (GHs) encoding chitinases and virulence factors at a higher relative abundance at 15 °C than at lower temperatures. These results indicate that increasing temperature affects the fecal pellet microbiome and the development of copepods. The findings are helpful to understand the changes in cold-adapted copepods and the effect of temperature on their growth.},
}
@article {pmid34849765,
year = {2021},
author = {Tiwari, DP and Shah, P and Van den Abbeele, P and Marzorati, M and Calatayud, M and Ghyselinck, J and Dubey, AK and Narayanan, S and Jain, M},
title = {Microbial fermentation of Fossence™, a short-chain fructo-oligosaccharide, under simulated human proximal colonic condition and assessment of its prebiotic effects-a pilot study.},
journal = {FEMS microbiology letters},
volume = {368},
number = {21-24},
pages = {},
doi = {10.1093/femsle/fnab147},
pmid = {34849765},
issn = {1574-6968},
mesh = {Bacteria/genetics/metabolism ; Colon/metabolism ; Fatty Acids, Volatile/metabolism ; Feces/chemistry ; *Fermentation ; Humans ; Hydrogen-Ion Concentration ; Lactates/metabolism ; *Microbiota ; *Oligosaccharides/metabolism ; Pilot Projects ; *Prebiotics/analysis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {A short-chain fructo-oligosaccharide (sc-FOS) was tested in a simulator of the human gut microbial ecosystem (SHIME) in vitro model to quantify its prebiotic effects according to Prebiotic Index (PI) and Measure of prebiotic effect (MPE) equations. FossenceTM, (sc-FOS, 0.5%) was fermented in a simulated human proximal colonic condition, using a fecal inoculum from a healthy individual. We analysed the pH reduction, substrate utilization, lactate and short-chain fatty acid (SCFA) production and microbial community modulation. Microbial fermentation of sc-FOS strongly reduced the media pH indicating the production of lactate and SCFA with accumulation of lactate and enhanced levels of acetate (34.38 ± 0.38 mM), propionate (20.93 ± 0.56 mM) and butyrate (4.93 ± 0.03 mM) compared to 18.46 ± 0.20 mM, 6.24 ± 0.10 mM and 3.3 ± 0.06 mM in the blank, respectively. Total SCFA production in test media was 61.91 ± 0.87 mM compared to 33.65 ± 0.36 mM in blank and the contribution of free-sugars present in sc-FOS to SCFAs was negligible. Modulation of the microbial community was analysed through 16S rRNA sequencing and we found that sc-FOS greatly stimulated the beneficial bacteria such as Bifidobacteria and Lactobacillus. We report the PI and MPE values for FossenceTM, as 14.9 and 0.01 respectively at the end of 24 h, which is an indicator of a strong prebiotic effect.},
}
@article {pmid34849757,
year = {2021},
author = {Vargas, P and Bosmans, L and Van Calenberge, B and Van Kerckhove, S and Lievens, B and Rediers, H},
title = {Bacterial community dynamics of tomato hydroponic greenhouses infested with hairy root disease.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {12},
pages = {},
doi = {10.1093/femsec/fiab153},
pmid = {34849757},
issn = {1574-6941},
mesh = {Ecosystem ; Hydroponics ; *Solanum lycopersicum ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil Microbiology ; },
abstract = {The rhizosphere is a complex ecosystem consisting of microbes in the interface between growth medium and plant roots, which affects plant productivity and health. This is one of the few studies analysing bacterial communities present in the rhizosphere of hydroponically grown plants. Tomato grown under hydroponic conditions is prone to hairy root disease (HRD) that is caused by rhizogenic Agrobacterium biovar 1 strains. In this study, using high-throughput amplicon sequencing of partial ribosomal RNA (rRNA) genes, we aimed to characterize bacterial communities in rockwool samples obtained from healthy or HRD-infested tomato during an entire growing season. Alpha diversity of rockwool increased in direct relation with time and samples obtained from healthy greenhouses presented a significantly lower alpha diversity than those from HRD-infested greenhouses. Beta diversity showed that bacterial community composition changed throughout the growing season. Amplicon Sequence Variants (ASVs) identified as rhizogenic Agrobacterium bv. 1 were more prevalent in HRD-infected greenhouses. Conversely, ASVs identified as Paenibacillus, previously identified as biocontrol organisms of rhizogenic agrobacteria, were more prevalent in healthy greenhouses. Altogether, our study greatly contributes to the knowledge of bacterial communities in rockwool hydroponics.},
}
@article {pmid34845558,
year = {2022},
author = {Gao, P and Li, Y and Tian, H and Li, G and Zhao, F and Xia, W and Pan, X and Gu, JD and Le, J and Jia, C and Ma, T},
title = {Bacterial and Archaeal Community Distribution in Oilfield Water Re-injection Facilities and the Influences from Microorganisms in Injected Water.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1011-1028},
pmid = {34845558},
issn = {1432-184X},
mesh = {*Archaea/genetics ; Oil and Gas Fields ; Water ; RNA, Ribosomal, 16S ; *Petroleum/microbiology ; Phylogeny ; Bacteria/genetics ; },
abstract = {Water flooding is widely employed for oil production worldwide. However, there has never been a systematic investigation of the microbial communities occurring in oilfield water re-injection facilities. Here, we investigated the distribution of bacterial and archaeal communities in water re-injection facilities of an oilfield, and illustrated the combined influences of environmental variation and the microorganisms in injected water on the microbial communities. Bacterial communities from the surface injection facilities were dominated by aerobic or facultative anaerobic Betaproteobacteria, Alphaproteobacteria, and Flavobacteria, whereas Clostridia, Deltaproteobacteria, Anaerolineae, and Synergistia predominated in downhole of the injection wells, and Gammaproteobacteria, Betaproteobacteria, and Epsilonproteobacteria predominated in the production wells. Methanosaeta, Methanobacterium, and Methanolinea were dominant archaea in the injection facilities, while Methanosaeta, Methanomethylovorans, and Methanoculleus predominated in the production wells. This study also demonstrated that the microorganisms in injected water could be easily transferred from injection station to wellheads and downhole of injection wells, and environmental variation and diffusion-limited microbial transfer resulted from formation filtration were the main factors determining microbial community assembly in oil-bearing strata. The results provide novel information on the bacterial and archaeal communities and the underlying mechanisms occurring in oilfield water re-injection facilities, and benefit the development of effective microbiologically enhanced oil recovery and microbiologically prevented reservoir souring programs.},
}
@article {pmid34841863,
year = {2021},
author = {Leistenschneider, C and Burkhardt-Holm, P and Mani, T and Primpke, S and Taubner, H and Gerdts, G},
title = {Microplastics in the Weddell Sea (Antarctica): A Forensic Approach for Discrimination between Environmental and Vessel-Induced Microplastics.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {23},
pages = {15900-15911},
doi = {10.1021/acs.est.1c05207},
pmid = {34841863},
issn = {1520-5851},
mesh = {Antarctic Regions ; Environmental Monitoring ; *Microplastics ; Plastics ; *Water Pollutants, Chemical/analysis ; },
abstract = {Microplastic (MP) pollution has been found in the Southern Ocean surrounding Antarctica, but many local regions within this vast area remain uninvestigated. The remote Weddell Sea contributes to the global thermohaline circulation, and one of the two Antarctic gyres is located in that region. In the present study, we evaluate MP (>300 μm) concentration and composition in surface (n = 34) and subsurface water samples (n = 79, ∼11.2 m depth) of the Weddell Sea. All putative MP were analyzed by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. MP was found in 65% of surface and 11.4% of subsurface samples, with mean (±standard deviation (SD)) concentrations of 0.01 (±0.01 SD) MP m[-3] and 0.04 (±0.1 SD) MP m[-3], respectively, being within the range of previously reported values for regions south of the Polar Front. Additionally, we aimed to determine whether identified paint fragments (n = 394) derive from the research vessel. Environmentally sampled fragments (n = 101) with similar ATR-FTIR spectra to reference paints from the research vessel and fresh paint references generated in the laboratory were further subjected to micro-X-ray fluorescence spectroscopy (μXRF) to compare their elemental composition. This revealed that 45.5% of all recovered MP derived from vessel-induced contamination. However, 11% of the measured fragments could be distinguished from the reference paints via their elemental composition. This study demonstrates that differentiation based purely on visual characteristics and FTIR spectroscopy might not be sufficient for accurately determining sample contamination sources.},
}
@article {pmid34841346,
year = {2021},
author = {Sergio, LS and James Michael, K and Fannie Isela, PC and Valeria, VR and Corina, HK and Luis Fernando, GO and James Michael, T and Sheng Yang, H and Juan Jose, PC},
title = {Draft genome sequence of Paraburkholderia sp. strain XV isolated from the rhizosphere of mango (Mangifera indica L.).},
journal = {Current research in microbial sciences},
volume = {2},
number = {},
pages = {100055},
pmid = {34841346},
issn = {2666-5174},
abstract = {Here, we report the draft genome of Paraburkholderia sp. XV. This strain was isolated from the rhizosphere of mango (Mangifera indica L.). Its genome consists of 9,189 coding DNA sequences, 60 tRNAs, a single copy of the 16S rRNA, 5S rRNA, and 23S rRNA gene, and 1 tmRNA. The GC content is 62.6%.},
}
@article {pmid34839952,
year = {2022},
author = {Kazmi, SSUH and Uroosa, and Xu, H and Warren, A},
title = {A community-based approach to analyzing the ecotoxicity of nitrofurazone using periphytic protozoa.},
journal = {Marine pollution bulletin},
volume = {175},
number = {},
pages = {113165},
doi = {10.1016/j.marpolbul.2021.113165},
pmid = {34839952},
issn = {1879-3363},
mesh = {Biodiversity ; *Ciliophora/physiology ; Ecosystem ; Environmental Monitoring ; *Nitrofurazone/toxicity ; },
abstract = {The ecotoxicity of nitrofurazone was analyzed based on a community-based approach using periphytic protozoa. Median lethal concentrations (LC50) within an exposure time of 30 min were determined by an acute toxicity test at 0, 1.5, 3, 6 and 12 mg ml[-1] nitrofurazone. Toxicity curve tests demonstrated a decreasing trend with increasing exposure time and was well fitted to the toxicity equation LC50 = 32.85e[-0.8143t] (t = exposure time; R[2] = 0.91; P < 0.05). Median inhibition concentrations (IC50) for periphytic protozoan growth rates were obtained by chronic tests at 0, 1, 2, 4 and 8 mg ml[-1] nitrofurazone within 10 days exposure and were well fitted to the equation r% = 0.3686e[-0.35Cnit] (Cnit is the concentration of nitrofurazone; R[2] = 0.92 and P < 0.05). These findings suggest that the LC50 and IC50 values of nitrofurazone can be predicted for any exposure time using periphytic protozoan communities as a bioassay model.},
}
@article {pmid34839384,
year = {2022},
author = {Liu, J and Li, C and Ma, W and Liu, W and Wu, W},
title = {Molecular Characterization of Distinct Fungal Communities in the Soil of a Rare Earth Mining Area.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1212-1223},
pmid = {34839384},
issn = {1432-184X},
support = {31760157//national natural science foundation of china/ ; D2019201332//natural science foundation of hebei province/ ; },
mesh = {Soil/chemistry ; *Mycobiome ; Soil Microbiology ; Ecosystem ; Mining ; *Metals, Rare Earth/analysis ; },
abstract = {The exploitation of ion-absorbed rare earth elements (REEs) has caused serious ecological destruction and environmental pollution. Effects on soil fungal structure and diversity exerted by mining activities are usually ignored, although fungus is one of the most important components in soil ecosystems. In the present research, quantitative polymerase chain reaction (qPCR) and high-throughput Illumina MiSeq sequencing were conducted to characterize fungal community composition and structure in soil of a rare earth mining area after in situ leaching. Statistical analyses, network, and FUNGuild were used to conduct in-depth analyses. Ascomycota, Basidiomycota, and Glomeromycota were the most abundant phyla in the mining soils. Fungal community structures were stable after leaching practice, but nutrition contents (organic matter, TC, and TN) significantly and positively contributed to fungal abundances and diversities. Saprotrophs in phyla Ascomycota and Basidiomycota were the dominant fungal trophic mode, and they played critical roles in nutrient cycling, transformation processes, and reducing REE toxicity. Symbiotrophs of phyla Glomeromycota contributed to soil aggregation and slowing down nutrient losses after in situ leaching practice. In addition, fungi could regulate the interactions between species to resist the harsh environment of REE toxicity or ammonium caused by in situ leaching practice.},
}
@article {pmid34836550,
year = {2021},
author = {Ter Horst, AM and Santos-Medellín, C and Sorensen, JW and Zinke, LA and Wilson, RM and Johnston, ER and Trubl, G and Pett-Ridge, J and Blazewicz, SJ and Hanson, PJ and Chanton, JP and Schadt, CW and Kostka, JE and Emerson, JB},
title = {Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {233},
pmid = {34836550},
issn = {2049-2618},
mesh = {*Ecosystem ; Minnesota ; *Soil/chemistry ; Soil Microbiology ; Virome ; },
abstract = {BACKGROUND: Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems.<br><br>RESULTS: Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes.<br><br>CONCLUSIONS: Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.},
}
@article {pmid34836151,
year = {2021},
author = {Calatayud, M and Börner, RA and Ghyselinck, J and Verstrepen, L and Medts, J and Abbeele, PVD and Boulangé, CL and Priour, S and Marzorati, M and Damak, S},
title = {Water Kefir and Derived Pasteurized Beverages Modulate Gut Microbiota, Intestinal Permeability and Cytokine Production In Vitro.},
journal = {Nutrients},
volume = {13},
number = {11},
pages = {},
pmid = {34836151},
issn = {2072-6643},
mesh = {Beverages/*analysis ; Colon/metabolism/microbiology ; Cytokines/*biosynthesis ; Fatty Acids, Volatile/biosynthesis ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism/microbiology ; *Kefir ; Pasteurization ; Permeability ; Water/*pharmacology ; },
abstract = {Fermentation is an ancient food preservation process, and fermented products have been traditionally consumed in different cultures worldwide over the years. The interplay between human gut microbiota, diet and host health is widely recognized. Diet is one of the main factors modulating gut microbiota potentially with beneficial effects on human health. Fermented dairy products have received much attention, but other sources of probiotic delivery through food received far less attention. In this research, a combination of in vitro tools mimicking colonic fermentation and the intestinal epithelium have been applied to study the effect of different pasteurized and non-pasteurized water kefir products on gut microbiota, epithelial barrier function and immunomodulation. Water kefir increased beneficial short-chain fatty acid production at the microbial level, reduced detrimental proteolytic fermentation compounds and increased Bifidobacterium genus abundance. The observed benefits are enhanced by pasteurization. Pasteurized products also had a significant effect at the host level, improving inflammation-induced intestinal epithelial barrier disruption and increasing IL-10 and IL-1β compared to the control condition. Our data support the potential health benefits of water kefir and demonstrate that pasteurization, performed to prolong shelf life and stability of the product, also enhanced these benefits.},
}
@article {pmid34835373,
year = {2021},
author = {Nagoya, M and Kouzuma, A and Watanabe, K},
title = {Codh/Acs-Deficient Methanogens Are Prevalent in Anaerobic Digesters.},
journal = {Microorganisms},
volume = {9},
number = {11},
pages = {},
pmid = {34835373},
issn = {2076-2607},
support = {15H01753//Japan Society for the Promotion of Science/ ; },
abstract = {Methanogens are archaea that grow by producing methane as a catabolic end product and thrive in diverse anaerobic habitats, including soil, sediments, oil reservoirs, digestive tracts, and anaerobic digesters. Methanogens have typically been classified into three types-namely, hydrogenotrophic, acetoclastic, and methylotrophic methanogens. In addition, studies have found methanogens that require both hydrogen/CO2 and organics, such as acetate, for growth. Genomic analyses have shown that these methanogens lack genes for carbon monoxide dehydrogenase/acetyl-CoA synthase (Codh/Acs), one of the oldest enzymes that catalyzes the central step in the Wood-Ljungdahl pathway. Since these methanogens have been found dominant in such habitats as digestive tracts and anaerobic digesters, it is suggested that the loss of Codh/Acs confers ecological advantages on methanogens in these habitats. Comparisons in genomes of methanogens suggest the possibility that these methanogens have emerged recently in anaerobic digesters and are currently under the process of prevalence. We propose that an understanding of the genetic and ecological processes associated with the emergence and prevalence of these methanogens in anaerobic digesters would offer novel evolutionary insights into microbial ecology.},
}
@article {pmid34833075,
year = {2021},
author = {Glasl, B and Haskell, JB and Aires, T and Serrão, EA and Bourne, DG and Webster, NS and Frade, PR},
title = {Microbial Surface Biofilm Responds to the Growth-Reproduction-Senescence Cycle of the Dominant Coral Reef Macroalgae Sargassum spp.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {34833075},
issn = {2075-1729},
support = {SFRH/BDP/110285/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; SFRH/BSAB/150485/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; SFRH/BPD/116774/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; UID/Multi/04326/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; Australian Microbiome Initiative//Bioplatforms Australia &amp; Australian Government National Collaborative Research Infrastructure Strategy/ ; PhD Scholarship BG//Advance Queensland/ ; T 1218//FWF Austrian Science Fund/ ; },
abstract = {Macroalgae play an intricate role in microbial-mediated coral reef degradation processes due to the release of dissolved nutrients. However, temporal variabilities of macroalgal surface biofilms and their implication on the wider reef system remain poorly characterized. Here, we study the microbial biofilm of the dominant reef macroalgae Sargassum over a period of one year at an inshore Great Barrier Reef site (Magnetic Island, Australia). Monthly sampling of the Sargassum biofilm links the temporal taxonomic and putative functional metabolic microbiome changes, examined using 16S rRNA gene amplicon and metagenomic sequencing, to the pronounced growth-reproduction-senescence cycle of the host. Overall, the macroalgal biofilm was dominated by the heterotrophic phyla Firmicutes (35% ± 5.9% SD) and Bacteroidetes (12% ± 0.6% SD); their relative abundance ratio shifted significantly along the annual growth-reproduction-senescence cycle of Sargassum. For example, Firmicutes were 1.7 to 3.9 times more abundant during host growth and reproduction cycles than Bacteroidetes. Both phyla varied in their carbohydrate degradation capabilities; hence, temporal fluctuations in the carbohydrate availability are potentially linked to the observed shift. Dominant heterotrophic macroalgal biofilm members, such as Firmicutes and Bacteroidetes, are implicated in exacerbating or ameliorating the release of dissolved nutrients into the ambient environment, though their contribution to microbial-mediated reef degradation processes remains to be determined.},
}
@article {pmid34828889,
year = {2021},
author = {Bolaños-Núñez, S and Santiago-Urbina, JA and Guyot, JP and Díaz-Ruiz, G and Wacher, C},
title = {Microbial Interactions between Amylolytic and Non-Amylolytic Lactic Acid Bacteria Strains Isolated during the Fermentation of Pozol.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {34828889},
issn = {2304-8158},
support = {CB-2009-131615//CONACYT, M&#xe9;xico/ ; },
abstract = {Pozol is a Mexican beverage prepared from fermented nixtamalized maize dough. To contribute to understanding its complex microbial ecology, the effect of inoculating on MRS-starch pure and mixed cultures of amylolytic Sii-25124 and non-amylolytic W. confusa 17, isolated from pozol, were studied on their interactions and fermentation parameters. These were compared with L. plantarum A6, an amylolytic strain isolated from cassava. Microbial growth, kinetic parameters, amylolytic activity, lactic acid production, and hydrolysis products from starch fermentation were measured. The population dynamics were followed by qPCR. L. plantarum A6 showed higher enzymatic activity, lactic acid, biomass production, and kinetic parameters than pozol LAB in pure cultures. Mixed culture of each pozol LAB with L. plantarum A6 showed a significant decrease in amylolytic activity, lactic acid yield, specific growth rate, and specific rate of amylase production. The interaction between Sii-25124 and W. confusa 17 increased the global maximum specific growth rate (µ), the lactic acid yield from starch (Ylac/s), lactic acid yield from biomass (Ylac/x), and specific rate of lactic acid production (qlac) by 15, 30, 30, and 40%, respectively, compared with the pure culture of Sii-25124. Interactions between the two strains are essential for this fermentation.},
}
@article {pmid34827700,
year = {2021},
author = {Jeon, JS and Etalo, DW and Carreno-Quintero, N and de Vos, RCH and Raaijmakers, JM},
title = {Effects of Sulfur Assimilation in Pseudomonas fluorescens SS101 on Growth, Defense, and Metabolome of Different Brassicaceae.},
journal = {Biomolecules},
volume = {11},
number = {11},
pages = {},
pmid = {34827700},
issn = {2218-273X},
mesh = {*Sulfur/metabolism ; *Pseudomonas fluorescens/metabolism/genetics ; *Metabolome ; *Arabidopsis/metabolism/microbiology/genetics/growth &amp; development ; Brassica/microbiology/metabolism/growth &amp; development/genetics ; Glucosinolates/metabolism ; Brassicaceae/metabolism/microbiology/growth &amp; development/genetics ; Plant Shoots/metabolism/growth &amp; development ; Xanthomonas campestris/metabolism ; },
abstract = {Genome-wide analysis of plant-growth-promoting Pseudomonas fluorescens strain SS101 (PfSS101) followed by site-directed mutagenesis previously suggested that sulfur assimilation may play an important role in growth promotion and induced systemic resistance in Arabidopsis. Here, we investigated the effects of sulfur metabolism in PfSS101 on growth, defense, and shoot metabolomes of Arabidopsis and the Brassica crop, Broccoli. Root tips of seedlings of Arabidopsis and two Broccoli cultivars were treated with PfSS101 or with a mutant disrupted in the adenylsulfate reductase cysH, a key gene in cysteine and methionine biosynthesis. Phenotyping of plants treated with wild-type PfSS101 or its cysH mutant revealed that sulfur assimilation in PfSS101 was associated with enhanced growth of Arabidopsis but with a reduction in shoot biomass of two Broccoli cultivars. Untargeted metabolomics revealed that cysH-mediated sulfur assimilation in PfSS101 had significant effects on shoot chemistry of Arabidopsis, in particular on chain elongation of aliphatic glucosinolates (GLSs) and on indole metabolites, including camalexin and the growth hormone indole-3-acetic acid. In Broccoli, PfSS101 sulfur assimilation significantly upregulated the relative abundance of several shoot metabolites, in particular, indolic GLSs and phenylpropanoids. These metabolome changes in Broccoli plants coincided with PfSS101-mediated suppression of leaf infections by Xanthomonas campestris. Our study showed the metabolic interconnectedness of plants and their root-associated microbiota.},
}
@article {pmid34826030,
year = {2022},
author = {Barbagallo, G and Santagati, M and Guni, A and Torrisi, P and Spitale, A and Stefani, S and Ferlito, S and Nibali, L},
title = {Microbiome differences in periodontal, peri-implant, and healthy sites: a cross-sectional pilot study.},
journal = {Clinical oral investigations},
volume = {26},
number = {3},
pages = {2771-2781},
pmid = {34826030},
issn = {1436-3771},
mesh = {Cross-Sectional Studies ; *Dental Implants/microbiology ; Humans ; *Microbiota/genetics ; *Peri-Implantitis/microbiology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {OBJECTIVES: To explore microbial communities associated with health and disease status around teeth and dental implants.<br><br>MATERIALS AND METHODS: A total of 10 healthy, 24 periodontitis, and 24 peri-implant sites from 24 patients were sequenced by next-generation sequencing. Microbial DNA was extracted and 16S rRNA gene was amplified. Bioinformatic analyses were performed using quantitative insights into microbial ecology (QIIME), linear discriminant analysis effect size (LEfSE), and STAMP.<br><br>RESULTS: Differences in microbial diversity across three types of sites were not statistically significant. Several genera and species were more prevalent in healthy compared with diseased sites, including Lautropia, Rothia and Capnocytophaga and Kingella. Among diseased sites, Peptostreptococcaceae, Dialister, Mongibacterium, Atopobium, and Filifactor were over-represented in peri-implantitis sites, while Bacteroidales was more abundant in periodontitis sites.<br><br>CONCLUSIONS: Diseased periodontal and peri-implant sites and corresponding healthy sites have distinct microbiological profiles. These findings suggest that microbial analyses could identify biomarkers for periodontal health and disease and lead to the development of new strategies to improve periodontal health and treat peri-implant and periodontal diseases.<br><br>CLINICAL RELEVANCE: The study contributes to improving our understanding of healthy, periodontally affected, and peri-implantitis sites which can improve our ability to diagnose, monitor, and manage these oral conditions.},
}
@article {pmid34820729,
year = {2022},
author = {Liu, Q and Pang, Z and Yang, Z and Nyumah, F and Hu, C and Lin, W and Yuan, Z},
title = {Bio-fertilizer Affects Structural Dynamics, Function, and Network Patterns of the Sugarcane Rhizospheric Microbiota.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1195-1211},
pmid = {34820729},
issn = {1432-184X},
support = {CARS- 170208//the Modern Agricultural Industry Technology System of China/ ; 2017J01456//Natural Science Foundation of Fujian Province/ ; KFA17172A//the Special Foundation for Scientific and Technological Innovation of Fujian Agriculture and Forestry University/ ; KFA17528A//the Special Foundation for Scientific and Technological Innovation of Fujian Agriculture and Forestry University/ ; 31771723//the Nature Science Foundation of China/ ; },
mesh = {Fertilizers/analysis ; *Saccharum ; Soil Microbiology ; Soil/chemistry ; *Microbiota ; Fungi/genetics ; Nitrogen/analysis ; Bacteria/genetics ; Phosphorus ; Urea ; Sugars ; },
abstract = {Fertilizers and microbial communities that determine fertilizer efficiency are key to sustainable agricultural development. Sugarcane is an important sugar cash crop in China, and using bio-fertilizers is important for the sustainable development of China's sugar industry. However, information on the effects of bio-fertilizers on sugarcane soil microbiota has rarely been studied. In this study, the effects of bio-fertilizer application on rhizosphere soil physicochemical indicators, microbial community composition, function, and network patterns of sugarcane were discussed using a high-throughput sequencing approach. The experimental design is as follows: CK: urea application (57 kg/ha), CF: compound fertilizer (450 kg/ha), BF1: bio-fertilizer (1500 kg/ha of bio-fertilizer + 57 kg/ha of urea), and BF2: bio-fertilizer (2250 kg/ha of bio-fertilizer + 57 kg/ha of urea). The results showed that the bio-fertilizer was effective in increasing sugarcane yield by 3-12% compared to the CF treatment group, while reducing soil acidification, changing the diversity of fungi and bacteria, and greatly altering the composition and structure of the inter-root microbial community. Variance partitioning canonical correspondence (VPA) analysis showed that soil physicochemical variables explained 80.09% and 73.31% of the variation in bacteria and fungi, respectively. Redundancy analysis and correlation heatmap showed that soil pH, total nitrogen, and available potassium were the main factors influencing bacterial community composition, while total soil phosphorus, available phosphorus, pH, and available nitrogen were the main drivers of fungal communities. Volcano plots showed that using bio-fertilizers contributed to the accumulation of more beneficial bacteria in the sugarcane rhizosphere level and the decline of pathogenic bacteria (e.g., Leifsonia), which may slow down or suppress the occurrence of diseases. Linear discriminant analysis (LDA) and effect size analysis (LEfSe) searched for biomarkers under different fertilizer treatments. Meanwhile, support vector machine (SVM) assessed the importance of the microbial genera contributing to the variability between fertilizers, of interest were the bacteria Anaerolineace, Vulgatibacter, and Paenibacillus and the fungi Cochliobolus, Sordariales, and Dothideomycetes between CF and BF2, compared to the other genera contributing to the variability. Network analysis (co-occurrence network) showed that the network structure of bio-fertilizers was closer to the network characteristics of healthy soils, indicating that bio-fertilizers can improve soil health to some extent, and therefore if bio-fertilizers can be used as an alternative to chemical fertilizers in the future alternative, it is important to achieve green soil development and improve the climate.},
}
@article {pmid34818768,
year = {2022},
author = {He, J and Zhang, N and Muhammad, A and Shen, X and Sun, C and Li, Q and Hu, Y and Shao, Y},
title = {From surviving to thriving, the assembly processes of microbial communities in stone biodeterioration: A case study of the West Lake UNESCO World Heritage area in China.},
journal = {The Science of the total environment},
volume = {805},
number = {},
pages = {150395},
doi = {10.1016/j.scitotenv.2021.150395},
pmid = {34818768},
issn = {1879-1026},
mesh = {Archaea ; Biodiversity ; China ; *Lakes ; *Microbiota ; UNESCO ; },
abstract = {Serious concerns regarding stone biodeterioration have been raised due to the loss of aesthetic value and hidden dangers in stone cultural heritages and buildings. Stone biodeterioration involves a complex ecological interplay among organisms, however, the ecological mechanisms (deterministic or stochastic processes) that determine the microbial community on stone remain poorly understood. Here, using both amplicon and shotgun metagenomic sequencing approaches, we comprehensively investigated the biodiversity, assembly, and function of communities (including prokaryotes, fungi, microfauna, and plants) on various types of deteriorating limestone across different habitats in Feilaifeng. By generalizing classic ecological models to stone habitats, we further uncovered and quantified the mechanisms underlying microbial community assembly processes and microbial interactions within the biodeteriorated limestone. Community profiling revealed stable ecosystem functional potential despite high taxonomic variation across different biodeterioration types, suggesting non-random community assembly. Increased niche differentiation occurred in prokaryotes and fungi but not in microfauna and plant during biodeterioration. Certain microbial groups such as nitrifying archaea and bacteria showed wider niche breadth and likely contributing to the initiation, succession and expansion of stone biodeterioration. Consistently, prokaryotes were more strongly structured by selection-based deterministic processes, while micro-eukaryotes were more influenced by dispersal and drift-based stochastic processes. Importantly, microbial coexistence maintains network robustness within stone microbiotas, highlighting mutual cooperation among functional microorganisms. These results provide new insights into microbial community assembly mechanisms in stone ecosystems and may aid in the sustainable conservation of stone materials of interest.},
}
@article {pmid34818104,
year = {2022},
author = {Albakistani, EA and Nwosu, FC and Furgason, C and Haupt, ES and Smirnova, AV and Verbeke, TJ and Lee, ES and Kim, JJ and Chan, A and Ruhl, IA and Sheremet, A and Rudderham, SB and Lindsay, MBJ and Dunfield, PF},
title = {Seasonal Dynamics of Methanotrophic Bacteria in a Boreal Oil Sands End Pit Lake.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {3},
pages = {e0145521},
pmid = {34818104},
issn = {1098-5336},
mesh = {Bacteria ; *Lakes/microbiology ; Methane ; *Oil and Gas Fields ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; },
abstract = {Base Mine Lake (BML) is the first full-scale demonstration end pit lake for the oil sands mining industry in Canada. We examined aerobic methanotrophic bacteria over all seasons for 5 years in this dimictic lake. Methanotrophs comprised up to 58% of all bacterial reads in 16S rRNA gene amplicon sequencing analyses (median 2.8%), and up to 2.7 × 10[4] cells mL[-1] of water (median 0.5 × 10[3]) based on qPCR of pmoA genes. Methanotrophic activity and populations in the lake water were highest during fall turnover and remained high through the winter ice-covered period into spring turnover. They declined during summer stratification, especially in the epilimnion. Three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus) cycled seasonally, based on both relative and absolute abundance measurements. Methylobacter and Methylovulum populations peaked in winter/spring, when methane oxidation activity was psychrophilic. Methyloparacoccus populations increased in the water column through summer and fall, when methane oxidation was mesophilic, and also predominated in the underlying tailings sediment. Other, less abundant genera grew primarily during summer, possibly due to distinct CH4/O2 microniches created during thermal stratification. These data are consistent with temporal and spatial niche differentiation based on temperature, CH4 and O2. This pit lake displays methane cycling and methanotroph population dynamics similar to natural boreal lakes. IMPORTANCE The study examined methanotrophic bacteria in an industrial end pit lake, combining molecular DNA methods (both quantitative and descriptive) with biogeochemical measurements. The lake was sampled over 5 years, in all four seasons, as often as weekly, and included sub-ice samples. The resulting multiseason and multiyear data set is unique in its size and intensity, and allowed us to document clear and consistent seasonal patterns of growth and decline of three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus). Laboratory experiments suggested that one major control of this succession was niche partitioning based on temperature. The study helps to understand microbial dynamics in engineered end pit lakes, but we propose that the dynamics are typical of boreal stratified lakes and widely applicable in microbial ecology and limnology. Methane-oxidizing bacteria are important model organisms in microbial ecology and have implications for global climate change.},
}
@article {pmid34817641,
year = {2022},
author = {Čanković, M and Dutour-Sikirić, M and Radić, ID and Ciglenečki, I},
title = {Bacterioneuston and Bacterioplankton Structure and Abundance in Two Trophically Distinct Marine Environments - a Marine Lake and the Adjacent Coastal Site on the Adriatic Sea.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {996-1010},
pmid = {34817641},
issn = {1432-184X},
support = {IP-2018-01-1717//hrvatska zaklada za znanost/ ; },
mesh = {*Lakes/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Aquatic Organisms ; Carbon ; Oxygen ; Seawater/microbiology ; },
abstract = {Marine surface microlayer (SML) is a large and extreme marine environment with an important role in biogeochemical cycling and climate regulation. We explored the seasonal structure and abundance of bacterial assemblages in SML (bacterioneuston) and underlying water layer (ULW) (bacterioplankton) in eutrophic marine Rogoznica Lake and more oligotrophic coastal area of the adjacent Adriatic Sea. SML and ULW in each site were similar in pH, salinity, dissolved oxygen, oxygen saturation, and temperature. Rogoznica Lake was colder in winter and warmer in summer compared to the Adriatic Sea. Regarding nutrients, SML and ULW were notably different environments. SML was consistently enriched in nitrate, nitrite, orthophosphate, and total organic carbon than ULW in both investigated environments. Except in spring in Rogoznica Lake, bacterial abundance in SML was also significantly higher (p < 0.05) than in ULW. Both layers and sites show prominent seasonal variability. High-throughput 16S rRNA gene sequencing of DNA and cDNA revealed a considerable difference in bacterial assemblage structure, although study sites were < 200 m apart. Heterotrophs were predominant in both layers with pronounced spatial and temporal structural differences, except in autumn in Rogoznica Lake when, autotrophs became the dominant fraction under oxygen-deprived conditions. All these variations were driven by in situ conditions, the most important ones being total organic carbon and temperature (and additionally dissolved oxygen in Rogoznica Lake). This is especially important in terms of ongoing eutrophication, warming and deoxygenation, noticed not only in the Adriatic Sea and Rogoznica Lake but globally as well. Therefore, further structural and physiological changes in bacterioneuston and bacterioplankton assemblages can be expected.},
}
@article {pmid34817640,
year = {2022},
author = {Wu-Chuang, A and Obregon, D and Estrada-Peña, A and Cabezas-Cruz, A},
title = {Thermostable Keystone Bacteria Maintain the Functional Diversity of the Ixodes scapularis Microbiome Under Heat Stress.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1224-1235},
pmid = {34817640},
issn = {1432-184X},
mesh = {Male ; Animals ; *Ixodes/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Heat-Shock Response ; },
abstract = {Variations in the composition and diversity of tick microbiome due to high temperatures may influence the hierarchy of community members as a response to environmental change. Modifications in the community structure are hypothesized to drive alterations in the presence and/or abundance of functional pathways in the bacterial metagenome. In this study, this hypothesis was tested by using published 16S rRNA datasets of Ixodes scapularis males incubated at different temperatures (i.e., 4, 20, 30, and 37 °C) in a laboratory setting. Changes in community structure and functional profiles in response to temperature shifts were measured using co-occurrence networks and metagenome inference. Results from laboratory-reared ticks were then compared with those of field-collected ticks. The results from laboratory-reared ticks showed that high temperature altered the structure of the microbial community and decreased the number of keystone taxa. Notably, four taxa were identified as keystone in all the temperatures, and the functional diversity of the tick microbiome was contained in the four thermostable keystone their associated bacterial taxa. Three of the thermostable keystone taxa were also found in free-living ticks collected in Massachusetts. Moreover, the comparison of functional profiles of laboratory-reared and field-collected ticks revealed the existence of an important set of metabolic pathways that were common among the different datasets. Similar to the laboratory-reared ticks, the keystone taxa identified in field-collected ticks alongside their consortia (co-occurring taxa) were sufficient to retain the majority of the metabolic pathways in the functional profile. These results suggest that keystone taxa are essential in the stability and the functional resiliency of the tick microbiome under heat stress.},
}
@article {pmid34817235,
year = {2021},
author = {Bulzu, PA and Kavagutti, VS and Chiriac, MC and Vavourakis, CD and Inoue, K and Kandori, H and Andrei, AS and Ghai, R},
title = {Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms.},
journal = {mSphere},
volume = {6},
number = {6},
pages = {e0066121},
pmid = {34817235},
issn = {2379-5042},
mesh = {*Metagenomics ; Models, Molecular ; Oxidative Stress ; Protein Conformation ; Rhodopsins, Microbial/chemistry/*genetics ; },
abstract = {Rhodopsins are light-activated proteins displaying an enormous versatility of function as cation/anion pumps or sensing environmental stimuli and are widely distributed across all domains of life. Even with wide sequence divergence and uncertain evolutionary linkages between microbial (type 1) and animal (type 2) rhodopsins, the membrane orientation of the core structural scaffold of both was presumed universal. This was recently amended through the discovery of heliorhodopsins (HeRs; type 3), that, in contrast to known rhodopsins, display an inverted membrane topology and yet retain similarities in sequence, structure, and the light-activated response. While no ion-pumping activity has been demonstrated for HeRs and multiple crystal structures are available, fundamental questions regarding their cellular and ecological function or even their taxonomic distribution remain unresolved. Here, we investigated HeR function and distribution using genomic/metagenomic data with protein domain fusions, contextual genomic information, and gene coexpression analysis with strand-specific metatranscriptomics. We bring to resolution the debated monoderm/diderm occurrence patterns and show that HeRs are restricted to monoderms. Moreover, we provide compelling evidence that HeRs are a novel type of sensory rhodopsins linked to histidine kinases and other two-component system genes across phyla. In addition, we also describe two novel putative signal-transducing domains fused to some HeRs. We posit that HeRs likely function as generalized light-dependent switches involved in the mitigation of light-induced oxidative stress and metabolic circuitry regulation. Their role as sensory rhodopsins is corroborated by their photocycle dynamics and their presence/function in monoderms is likely connected to the higher sensitivity of these organisms to light-induced damage. IMPORTANCE Heliorhodopsins are enigmatic, novel rhodopsins with a membrane orientation that is opposite to all known rhodopsins. However, their cellular and ecological functions are unknown, and even their taxonomic distribution remains a subject of debate. We provide evidence that HeRs are a novel type of sensory rhodopsins linked to histidine kinases and other two-component system genes across phyla boundaries. In support of this, we also identify two novel putative signal transducing domains in HeRs that are fused with them. We also observe linkages of HeRs to genes involved in mitigation of light-induced oxidative stress and increased carbon and nitrogen metabolism. Finally, we synthesize these findings into a framework that connects HeRs with the cellular response to light in monoderms, activating light-induced oxidative stress defenses along with carbon/nitrogen metabolic circuitries. These findings are consistent with the evolutionary, taxonomic, structural, and genomic data available so far.},
}
@article {pmid34817222,
year = {2021},
author = {Yourstone, SM and Weinstein, I and Ademski, E and Shank, EA and Stasulli, NM},
title = {Selective Bacterial Community Enrichment between the Pitcher Plants Sarracenia minor and Sarracenia flava.},
journal = {Microbiology spectrum},
volume = {9},
number = {3},
pages = {e0069621},
pmid = {34817222},
issn = {2165-0497},
support = {K12 GM000678/GM/NIGMS NIH HHS/United States ; R01 GM112981/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; *Microbiota ; Phylogeny ; Plant Leaves/microbiology ; Sarraceniaceae/classification/*microbiology ; },
abstract = {The interconnected and overlapping habitats present in natural ecosystems remain a challenge in determining the forces driving microbial community composition. The cuplike leaf structures of some carnivorous plants, including those of the family Sarraceniaceae, are self-contained ecological habitats that represent systems for exploring such microbial ecology questions. We investigated whether Sarracenia minor and Sarracenia flava cultivate distinct bacterial communities when sampled at the same geographic location and time. This sampling strategy eliminates many abiotic environmental variables present in other studies that compare samples harvested over time, and it could reveal biotic factors driving the selection of microbes. DNA extracted from the decomposing detritus trapped in each Sarracenia leaf pitcher was profiled using 16S rRNA amplicon sequencing. We identified a surprising amount of bacterial diversity within each pitcher, but we also discovered bacteria whose abundance was specifically enriched in one of the two Sarracenia species. These differences in bacterial community representation suggest some biotic influence of the Sarracenia plant on the bacterial composition of their pitchers. Overall, our results suggest that bacterial selection due to factors other than geographic location, weather, or prey availability is occurring within the pitchers of these two closely related plant species. This indicates that specific characteristics of S. minor and S. flava may play a role in fostering distinct bacterial communities. These confined, naturally occurring microbial ecosystems within Sarracenia pitchers may provide model systems to answer important questions about the drivers of microbial community composition, succession, and response to environmental perturbations. IMPORTANCE This study uses amplicon sequencing to compare the bacterial communities of environmental samples from the detritus of the leaf cavities of Sarracenia minor and Sarracenia flava pitcher plants. We sampled the detritus at the same time and in the same geographic location, eliminating many environmental variables present in other comparative studies. This study revealed that different species of Sarracenia contain distinct bacterial members within their pitchers, suggesting that these communities are not randomly established based on environmental factors and the prey pool but are potentially enriched for by the plants' chemical or physical environment. This study of these naturally occurring, confined microbial ecosystems will help further establish carnivorous pitcher plants as a model system for answering important questions about the development and succession of microbial communities.},
}
@article {pmid34813707,
year = {2022},
author = {Hernández-Reyes, C and Lichtenberg, E and Keller, J and Delaux, PM and Ott, T and Schenk, ST},
title = {NIN-Like Proteins: Interesting Players in Rhizobia-Induced Nitrate Signaling Response During Interaction with Non-Legume Host Arabidopsis thaliana.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {35},
number = {3},
pages = {230-243},
doi = {10.1094/MPMI-10-21-0261-R},
pmid = {34813707},
issn = {0894-0282},
mesh = {*Arabidopsis/genetics/metabolism ; *Fabaceae ; Nitrates/metabolism ; Nitrogen Fixation ; *Rhizobium/physiology ; Root Nodules, Plant/metabolism ; Signal Transduction ; Symbiosis/physiology ; },
abstract = {Nitrogen is an essential macronutrient and a key cellular messenger. Plants have evolved refined molecular systems to sense the cellular nitrogen status. This is exemplified by the root nodule symbiosis between legumes and symbiotic rhizobia, where nitrate availability inhibits this mutualistic interaction. Additionally, nitrate also functions as a metabolic messenger, resulting in nitrate signaling cascades which intensively crosstalk with other physiological pathways. Nodule inception-like proteins (NLPs) are key players in nitrate signaling and regulate nitrate-dependent transcription during legume-rhizobia interactions. Nevertheless, the coordinated interplay between nitrate signaling pathways and rhizobacteria-induced responses remains to be elucidated. In our study, we investigated rhizobia-induced changes in the root system architecture of the non-legume host arabidopsis under different nitrate conditions. We demonstrate that rhizobium-induced lateral root growth and increased root hair length and density are regulated by a nitrate-related signaling pathway. Key players in this process are AtNLP4 and AtNLP5, because the corresponding mutants failed to respond to rhizobia. At the cellular level, AtNLP4 and AtNLP5 control a rhizobia-induced decrease in cell elongation rates, while additional cell divisions occurred independently of AtNLP4. In summary, our data suggest that root morphological responses to rhizobia are coordinated by a newly considered nitrate-related NLP pathway that is evolutionarily linked to regulatory circuits described in legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.},
}
@article {pmid34809998,
year = {2022},
author = {Sutherland, WJ and Atkinson, PW and Butchart, SHM and Capaja, M and Dicks, LV and Fleishman, E and Gaston, KJ and Hails, RS and Hughes, AC and Le Anstey, B and Le Roux, X and Lickorish, FA and Maggs, L and Noor, N and Oldfield, TEE and Palardy, JE and Peck, LS and Pettorelli, N and Pretty, J and Spalding, MD and Tonneijck, FH and Truelove, G and Watson, JEM and Wentworth, J and Wilson, JD and Thornton, A},
title = {A horizon scan of global biological conservation issues for 2022.},
journal = {Trends in ecology &amp; evolution},
volume = {37},
number = {1},
pages = {95-104},
doi = {10.1016/j.tree.2021.10.014},
pmid = {34809998},
issn = {1872-8383},
mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources ; Global Health/*trends ; Policy ; },
abstract = {We present the results of our 13th annual horizon scan of issues likely to impact on biodiversity conservation. Issues are either novel within the biological conservation sector or could cause a substantial step-change in impact, either globally or regionally. Our global panel of 26 scientists and practitioners identified 15 issues that we believe to represent the highest priorities for tracking and action. Many of the issues we identified, including the impact of satellite megaconstellations and the use of long-distance wireless energy transfer, have both elements of threats and emerging opportunities. A recent state-sponsored application to commence deep-sea mining represents a significant step-change in impact. We hope that this horizon scan will increase research and policy attention on the highlighted issues.},
}
@article {pmid34809466,
year = {2021},
author = {Chase, AB and Sweeney, D and Muskat, MN and Guillén-Matus, DG and Jensen, PR},
title = {Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites.},
journal = {mBio},
volume = {12},
number = {6},
pages = {e0270021},
pmid = {34809466},
issn = {2150-7511},
support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; T32 GM067550/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacterial Proteins/genetics/metabolism ; Biosynthetic Pathways ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Micromonosporaceae/classification/*genetics/*metabolism ; *Multigene Family ; Phylogeny ; Recombination, Genetic ; Secondary Metabolism ; },
abstract = {While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving chemical diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) among 118 strains representing all nine currently named species of the marine actinobacterial genus Salinispora. While much attention has been given to the role of horizontal gene transfer (HGT) in structuring BGC distributions, we find that vertical descent facilitates interspecies BGC diversification over evolutionary timescales. Moreover, we identified a distinct phylogenetic signal among Salinispora species at both the BGC and metabolite level, indicating that specialized metabolism represents a conserved phylogenetic trait. Using a combination of genomic analyses and liquid chromatography-high-resolution tandem mass spectrometry (LC-MS/MS) targeting nine experimentally characterized BGCs and their small molecule products, we identified gene gain/loss events, constrained interspecies recombination, and other evolutionary processes associated with vertical inheritance as major contributors to BGC diversification. These evolutionary dynamics had direct consequences for the compounds produced, as exemplified by species-level differences in salinosporamide production. Together, our results support the concept that specialized metabolites, and their cognate BGCs, can represent phylogenetically conserved functional traits with chemical diversification proceeding in species-specific patterns over evolutionary time frames. IMPORTANCE Microbial natural products are traditionally exploited for their pharmaceutical potential, yet our understanding of the evolutionary processes driving BGC evolution and compound diversification remain poorly developed. While HGT is recognized as an integral driver of BGC distributions, we find that the effects of vertical inheritance on BGC diversification had direct implications for species-level specialized metabolite production. As such, understanding the degree of genetic variation that corresponds to species delineations can enhance natural product discovery efforts. Resolving the evolutionary relationships between closely related strains and specialized metabolism can also facilitate our understanding of the ecological roles of small molecules in structuring the environmental distribution of microbes.},
}
@article {pmid34807459,
year = {2022},
author = {Hicks, LC and Frey, B and Kjøller, R and Lukac, M and Moora, M and Weedon, JT and Rousk, J},
title = {Toward a function-first framework to make soil microbial ecology predictive.},
journal = {Ecology},
volume = {103},
number = {2},
pages = {e03594},
doi = {10.1002/ecy.3594},
pmid = {34807459},
issn = {1939-9170},
mesh = {Bacteria ; Ecosystem ; *Microbiota ; Salinity ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial function to community composition and structure. Here, we propose a function-first framework to predict how microbial communities influence ecosystem functions. We first view the microbial community associated with a specific function as a whole and describe the dependence of microbial functions on environmental factors (e.g., the intrinsic temperature dependence of bacterial growth rates). This step defines the aggregate functional response curve of the community. Second, the contribution of the whole community to ecosystem function can be predicted, by combining the functional response curve with current environmental conditions. Functional response curves can then be linked with taxonomic data in order to identify sets of "biomarker" taxa that signal how microbial communities regulate ecosystem functions. Ultimately, such indicator taxa may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition. In this paper, we provide three examples to illustrate the proposed framework, whereby the dependence of bacterial growth on environmental factors, including temperature, pH, and salinity, is defined as the functional response curve used to interlink soil bacterial community structure and function. Applying this framework will make it possible to predict ecosystem functions directly from microbial community composition.},
}
@article {pmid34806699,
year = {2021},
author = {Pioli, R and Stocker, R and Isa, L and Secchi, E},
title = {Patterning of Microorganisms and Microparticles through Sequential Capillarity-assisted Assembly.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {177},
pages = {},
doi = {10.3791/63131},
pmid = {34806699},
issn = {1940-087X},
mesh = {Capillary Action ; *Microfluidic Analytical Techniques/methods ; Microfluidics/methods ; },
abstract = {Controlled patterning of microorganisms into defined spatial arrangements offers unique possibilities for a broad range of biological applications, including studies of microbial physiology and interactions. At the simplest level, accurate spatial patterning of microorganisms would enable reliable, long-term imaging of large numbers of individual cells and transform the ability to quantitatively study distance-dependent microbe-microbe interactions. More uniquely, coupling accurate spatial patterning and full control over environmental conditions, as offered by microfluidic technology, would provide a powerful and versatile platform for single-cell studies in microbial ecology. This paper presents a microfluidic platform to produce versatile and user-defined patterns of microorganisms within a microfluidic channel, allowing complete optical access for long-term, high-throughput monitoring. This new microfluidic technology is based on capillarity-assisted particle assembly and exploits the capillary forces arising from the controlled motion of an evaporating suspension inside a microfluidic channel to deposit individual microsized objects in an array of traps microfabricated onto a polydimethylsiloxane (PDMS) substrate. Sequential depositions generate the desired spatial layout of single or multiple types of micro-sized objects, dictated solely by the geometry of the traps and the filling sequence. The platform has been calibrated using colloidal particles of different dimensions and materials: it has proven to be a powerful tool to generate diverse colloidal patterns and perform surface functionalization of trapped particles. Furthermore, the platform was tested on microbial cells, using Escherichia coli cells as a model bacterium. Thousands of individual cells were patterned on the surface, and their growth was monitored over time. In this platform, the coupling of single-cell deposition and microfluidic technology allows both geometric patterning of microorganisms and precise control of environmental conditions. It thus opens a window into the physiology of single microbes and the ecology of microbe-microbe interactions, as shown by preliminary experiments.},
}
@article {pmid34803951,
year = {2021},
author = {Coton, M and Deniel, F and Mounier, J and Joubrel, R and Robieu, E and Pawtowski, A and Jeuge, S and Taminiau, B and Daube, G and Coton, E and Frémaux, B},
title = {Microbial Ecology of French Dry Fermented Sausages and Mycotoxin Risk Evaluation During Storage.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {737140},
pmid = {34803951},
issn = {1664-302X},
abstract = {Dry fermented sausages are produced worldwide by well-controlled fermentation processes involving complex microbiota including many bacterial and fungal species with key technological roles. However, to date, fungal diversity on sausage casings during storage has not been fully described. In this context, we studied the microbial communities from dry fermented sausages naturally colonized or voluntarily surface inoculated with molds during storage using both culture-dependent and metabarcoding methods. Staphylococci and lactic acid bacteria largely dominated in samples, although some halotolerant genera (e.g., Halomonas, Tetragenococcus, and Celerinatantimonas spp.) were also frequently observed. Fungal populations varied from 7.2 to 9.8 log TFU/cm[2] sausage casing during storage, suggesting relatively low count variability among products. Fungal diversity identified on voluntarily inoculated casings was lower (dominated by Penicillium nalgiovense and Debaryomyces hansenii) than naturally environment-inoculated fermented sausages (colonized by P. nalgiovense, Penicillium nordicum, and other Penicillium spp. and sporadically by Scopulariopsis sp., D. hansenii, and Candida zeylanoïdes). P. nalgiovense and D. hansenii were systematically identified, highlighting their key technological role. The mycotoxin risk was then evaluated, and in situ mycotoxin production of selected mold isolates was determined during pilot-scale sausage productions. Among the identified fungal species, P. nalgiovense was confirmed not to produce mycotoxins. However, some P. nordicum, Penicillium chrysogenum, Penicillium bialowienzense, Penicillium brevicompactum, and Penicillium citreonigrum isolates produced one or more mycotoxins in vitro. P. nordicum also produced ochratoxin A during pilot-scale sausage productions using "worst-case" conditions in the absence of biotic competition. These data provide new knowledge on fermented sausage microbiota and the potential mycotoxin risk during storage.},
}
@article {pmid34803947,
year = {2021},
author = {Runa, V and Wenk, J and Bengtsson, S and Jones, BV and Lanham, AB},
title = {Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {730071},
pmid = {34803947},
issn = {1664-302X},
abstract = {Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.},
}
@article {pmid34803935,
year = {2021},
author = {Hernández-Beltrán, JCR and San Millán, A and Fuentes-Hernández, A and Peña-Miller, R},
title = {Mathematical Models of Plasmid Population Dynamics.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {606396},
pmid = {34803935},
issn = {1664-302X},
abstract = {With plasmid-mediated antibiotic resistance thriving and threatening to become a serious public health problem, it is paramount to increase our understanding of the forces that enable the spread and maintenance of drug resistance genes encoded in mobile genetic elements. The relevance of plasmids as vehicles for the dissemination of antibiotic resistance genes, in addition to the extensive use of plasmid-derived vectors for biotechnological and industrial purposes, has promoted the in-depth study of the molecular mechanisms controlling multiple aspects of a plasmids' life cycle. This body of experimental work has been paralleled by the development of a wealth of mathematical models aimed at understanding the interplay between transmission, replication, and segregation, as well as their consequences in the ecological and evolutionary dynamics of plasmid-bearing bacterial populations. In this review, we discuss theoretical models of plasmid dynamics that span from the molecular mechanisms of plasmid partition and copy-number control occurring at a cellular level, to their consequences in the population dynamics of complex microbial communities. We conclude by discussing future directions for this exciting research topic.},
}
@article {pmid34800493,
year = {2022},
author = {Zhang, X and Yoshihara, K and Miyata, N and Hata, T and Altaisaikhan, A and Takakura, S and Asano, Y and Izuno, S and Sudo, N},
title = {Dietary tryptophan, tyrosine, and phenylalanine depletion induce reduced food intake and behavioral alterations in mice.},
journal = {Physiology &amp; behavior},
volume = {244},
number = {},
pages = {113653},
doi = {10.1016/j.physbeh.2021.113653},
pmid = {34800493},
issn = {1873-507X},
mesh = {Animals ; Diet ; Eating ; Mice ; *Phenylalanine ; *Tryptophan/metabolism ; Tyrosine ; },
abstract = {Important precursors of monoaminergic neurotransmitters, dietary tryptophan (TRP), tyrosine, and phenylalanine (all referred to as TTP), play crucial roles in a wide range of behavioral and emotional functions. In the current study, we investigated whether diets devoid of TTP or diets deficient in TRP alone can affect body weight, behavioral characteristics, and gut microbiota, by comparing mice fed on these amino acids-depleted diets to mice fed on diets containing regular levels of amino acids. Both dietary TTP- and TRP-deprived animals showed a reduction in food intake and body weight. In behavioral analyses, the mice fed TTP-deprived diets were more active than mice fed diets containing regular levels of amino acids. The TRP-deprived group exhibited a reduction in serum TRP levels, concomitant with a decrease in serotonin and 5-hydroxyindoleacetic acid levels in some regions of the brain. The TTP-deprived group showed a reduction in TTP levels in the serum, concomitant with decreases in both phenylalanine and tyrosine levels in the hippocampus, as well as serotonin, norepinephrine, and dopamine concentrations in some regions of the brain. Regarding the effects of TRP or TTP deprivation on gut microbial ecology, the relative abundance of genus Roseburia was significantly reduced in the TTP-deprived group than in the dietary restriction control group. Interestingly, TTP was found even in the feces of mice fed TTP- and TRP-deficient diets, suggesting that TTP is produced by microbial or enzymatic digestion of the host-derived proteins. However, microbe generated TTP did not compensate for the systemic TTP deficiency induced by the lack of dietary TTP intake. Collectively, these results indicate that chronic dietary TTP deprivation induces decreased monoamines and their metabolites in a brain region-specific manner. The altered activities of the monoaminergic systems may contribute to increased locomotor activity.},
}
@article {pmid34799747,
year = {2022},
author = {Zada, S and Sajjad, W and Rafq, M and Ali, S and Hu, Z and Wang, H and Cai, R},
title = {Correction to: Cave Microbes as a Potential Source of Drugs Development in the Modern Era.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {688},
doi = {10.1007/s00248-021-01916-3},
pmid = {34799747},
issn = {1432-184X},
}
@article {pmid34795658,
year = {2021},
author = {Huang, Z and Hou, D and Zhou, R and Zeng, S and Xing, C and Wei, D and Deng, X and Yu, L and Wang, H and Deng, Z and Weng, S and Ning, D and Xiao, C and Yan, Q and Zhou, J and He, Z and He, J},
title = {Environmental Water and Sediment Microbial Communities Shape Intestine Microbiota for Host Health: The Central Dogma in an Anthropogenic Aquaculture Ecosystem.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {772149},
pmid = {34795658},
issn = {1664-302X},
abstract = {From increasing evidence has emerged a tight link among the environment, intestine microbiota, and host health status; moreover, the microbial interaction in different habitats is crucial for ecosystems. However, how the environmental microbial community assembly governs the intestinal microbiota and microbial communities of multiple habitats contribute to the metacommunity remain elusive. Here, we designed two delicate experiments from temporal and spatial scales in a shrimp culture pond ecosystem (SCPE). Of the SCPE metacommunity, the microbial diversity was mainly contributed to by the diversity of[-]β IntraHabitats and β InterHabitats , and water and sediment communities had a large contribution to the shrimp intestine community as shown by SourceTracker and Sloan neutral community model analyses. Also, phylogenetic bin-based null model results show that microbial assembly of three habitats in the SCPE appeared to be largely driven by stochastic processes. These results enrich our understanding of the environment-intestinal microbiota-host health closely linked relationship, making it possible to be the central dogma for an anthropogenic aquaculture ecosystem. Our findings enhance the mechanistic understanding of microbial assembly in the SCPE for further analyzing metacommunities, which has important implications for microbial ecology and animal health.},
}
@article {pmid34795375,
year = {2021},
author = {Van Goethem, MW and Osborn, AR and Bowen, BP and Andeer, PF and Swenson, TL and Clum, A and Riley, R and He, G and Koriabine, M and Sandor, L and Yan, M and Daum, CG and Yoshinaga, Y and Makhalanyane, TP and Garcia-Pichel, F and Visel, A and Pennacchio, LA and O'Malley, RC and Northen, TR},
title = {Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {1302},
pmid = {34795375},
issn = {2399-3642},
support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; },
mesh = {Bacteria/genetics/*metabolism ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; *Secondary Metabolism ; *Soil Microbiology ; Utah ; },
abstract = {Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.},
}
@article {pmid34794517,
year = {2021},
author = {Van Wylick, A and Monclaro, AV and Elsacker, E and Vandelook, S and Rahier, H and De Laet, L and Cannella, D and Peeters, E},
title = {A review on the potential of filamentous fungi for microbial self-healing of concrete.},
journal = {Fungal biology and biotechnology},
volume = {8},
number = {1},
pages = {16},
pmid = {34794517},
issn = {2054-3085},
support = {1SA9721N//FWO-Vlaanderen/ ; 1SC9220N//FWO-Vlaanderen/ ; FNRS-MIS LUX-project F.4502.19//Fonds De La Recherche Scientifique - FNRS/ ; },
abstract = {Concrete is the most used construction material worldwide due to its abundant availability and inherent ease of manufacturing and application. However, the material bears several drawbacks such as the high susceptibility for crack formation, leading to reinforcement corrosion and structural degradation. Extensive research has therefore been performed on the use of microorganisms for biologically mediated self-healing of concrete by means of CaCO3 precipitation. Recently, filamentous fungi have been recognized as high-potential microorganisms for this application as their hyphae grow in an interwoven three-dimensional network which serves as nucleation site for CaCO3 precipitation to heal the crack. This potential is corroborated by the current state of the art on fungi-mediated self-healing concrete, which is not yet extensive but valuable to direct further research. In this review, we aim to broaden the perspectives on the use of fungi for concrete self-healing applications by first summarizing the major progress made in the field of microbial self-healing of concrete and then discussing pioneering work that has been done with fungi. Starting from insights and hypotheses on the types and principles of biomineralization that occur during microbial self-healing, novel potentially promising candidate species are proposed based on their abilities to promote CaCO3 formation or to survive in extreme conditions that are relevant for concrete. Additionally, an overview will be provided on the challenges, knowledge gaps and future perspectives in the field of fungi-mediated self-healing concrete.},
}
@article {pmid34793902,
year = {2022},
author = {Yuan, W and Zeng, X and Cao, Y and Yang, Q and Riaz, L and Wang, Q},
title = {Distribution of antibiotic resistance genes from human and animal origins to their receiving environments: A regional scale survey of urban settings.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {293},
number = {},
pages = {118512},
doi = {10.1016/j.envpol.2021.118512},
pmid = {34793902},
issn = {1873-6424},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Manure ; *Microbiota ; },
abstract = {Antibiotic resistance is a growing problem for ecosystem health and public healthcare. Hence, the transmission of antibiotic resistance from human and animal origins to natural environments requires careful investigation. In this study, nine antibiotic resistance genes (ARGs), three mobile genetic elements (MGEs), and their relations with antibiotics, heavy metals, and microbiota were investigated in 16 sample sites (Xinxiang, China). Fluoroquinolones (0.13-14.22 μg/L) were most abundant in hospital effluent and oxytetracycline (251.86-5817.47 μg/kg) in animal manure. Animal manure showed the highest levels of zinc (80.79-2597.14 mg/kg) and copper (32.47-85.22 mg/kg), possibly affecting the prevalence of intI1 and aac(6')-Ib genes. Aminoglycoside and sulfonamide resistance genes (aac(6')-Ib, aadA, and sul1) were the main ARGs in this area. In addition, the detected ARGs and MGEs were higher in animal manure than in hospital effluent, except for the sul1 gene. On the other hand, the incomplete removal of antibiotics (29.76-100%), heavy metals (31.25-100%), and ARGs (1-3 orders of magnitude) in MWWTPs resulted in the accumulation of these contaminants in the receiving river. Network analysis suggested that the potential hosts (Jeotgalibaca, Atopostipes, Corynebacterium_1, etc.) of ARGs were more predominant in animal manure rather than hospital effluent, indicating a higher ARG transfer potential in animal manure compared with hospital sources. These results provide useful insights into the different migration and dissemination routes of antibiotics, heavy metals, ARGs, and microbiota from anthropogenic and animal origins to their receiving environments via MWWTP discharge and manure fertilization.},
}
@article {pmid34793801,
year = {2022},
author = {Bontemps, Z and Alonso, L and Pommier, T and Hugoni, M and Moënne-Loccoz, Y},
title = {Microbial ecology of tourist Paleolithic caves.},
journal = {The Science of the total environment},
volume = {816},
number = {},
pages = {151492},
doi = {10.1016/j.scitotenv.2021.151492},
pmid = {34793801},
issn = {1879-1026},
mesh = {Animals ; Archaea ; Bacteria ; *Caves ; Fungi ; *Microbiota ; },
abstract = {Microorganisms colonize caves extensively, and in caves open for tourism they may cause alterations on wall surfaces. This is a major concern in caves displaying Paleolithic art, which is usually fragile and may be irremediably damaged by microbial alterations. Therefore, many caves were closed for preservation purposes, e.g. Lascaux (France), Altamira (Spain), while others were never opened to the public to avoid microbial contamination, e.g. Chauvet Cave (France), etc. The recent development of high-throughput sequencing technologies allowed several descriptions of cave microbial diversity and prompted the writing of this review, which focuses on the cave microbiome for the three domains of life (Bacteria, Archaea, microeukaryotes), the impact of tourism-related anthropization on microorganisms in Paleolithic caves, and the development of microbial alterations on the walls of these caves. This review shows that the microbial phyla prevalent in pristine caves are similar to those evidenced in water, soil, plant and metazoan microbiomes, but specificities at lower taxonomic levels remain to be clarified. Most of the data relates to Bacteria and Fungi, while other microeukaryotes and Archaea are poorly documented. Tourism may cause shifts in the microbiota of Paleolithic caves, but larger-scale investigation are required as these shifts may differ from one cave to the next. Finally, different types of alterations can occur in caves, especially in Paleolithic caves. Many microorganisms potentially involved have been identified, but diversity analyses of these alterations have not always included a comparison with neighboring unaltered zones as controls, making such associations uncertain. It is expected that omics technologies will also allow a better understanding of the functional diversities of the cave microbiome. This will be needed to decipher microbiome dynamics in response to touristic frequentation, to guide cave management, and to identify the most appropriate reclamation approaches to mitigate microbial alterations in tourist Paleolithic caves.},
}
@article {pmid34793127,
year = {2022},
author = {Schwarz, C and Mathieu, J and Laverde Gomez, JA and Yu, P and Alvarez, PJJ},
title = {Renaissance for Phage-Based Bacterial Control.},
journal = {Environmental science &amp; technology},
volume = {56},
number = {8},
pages = {4691-4701},
doi = {10.1021/acs.est.1c06232},
pmid = {34793127},
issn = {1520-5851},
mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Computational Biology ; *Microbiota ; Sequence Analysis, DNA ; },
abstract = {Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.},
}
@article {pmid34791400,
year = {2021},
author = {Semon, AK and Keenan, O and Zackular, JP},
title = {Clostridioides difficile and the Microbiota Early in Life.},
journal = {Journal of the Pediatric Infectious Diseases Society},
volume = {10},
number = {Supplement_3},
pages = {S3-S7},
pmid = {34791400},
issn = {2048-7207},
support = {K22 AI137220/AI/NIAID NIH HHS/United States ; //Children's Hospital of Philadelphia/ ; //National Institute of Allergy and Infectious Diseases/ ; R35GM138369/NH/NIH HHS/United States ; L40 AI147162/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; },
mesh = {Adult ; Clostridioides ; *Clostridioides difficile ; *Clostridium Infections/epidemiology ; *Enterocolitis, Pseudomembranous ; Humans ; Infant ; *Microbiota ; },
abstract = {Clostridioides difficile is a spore-forming, obligate anaerobe, and ubiquitous nosocomial pathogen. While C. difficile infection in adults causes a spectrum of disease, including pseudomembranous colitis and toxic megacolon, healthy infants are asymptomatically colonized at high rates. The mechanisms leading to high colonization rates and infant protection from C. difficile are currently unknown; however, the ecology and metabolic state of the intestinal microbiome are factors known to influence C. difficile pathogenesis. In this review, we will examine the aspects of the early-life microbiome that may contribute to the incidence of C. difficile and protection from disease manifestation in infants. We will also discuss whether features of the adult microbiota that enable and restrict C. difficile are prevalent during early-life colonization.},
}
@article {pmid34791198,
year = {2021},
author = {Vannette, RL and McMunn, MS and Hall, GW and Mueller, TG and Munkres, I and Perry, D},
title = {Culturable bacteria are more common than fungi in floral nectar and are more easily dispersed by thrips, a ubiquitous flower visitor.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {12},
pages = {},
doi = {10.1093/femsec/fiab150},
pmid = {34791198},
issn = {1574-6941},
mesh = {Animals ; Bacteria/genetics ; Flowers ; Fungi ; *Microbiota ; Plant Nectar ; Pollination ; *Thysanoptera ; },
abstract = {Variation in dispersal ability among taxa affects community assembly and biodiversity maintenance within metacommunities. Although fungi and bacteria frequently coexist, their relative dispersal abilities are poorly understood. Nectar-inhabiting microbial communities affect plant reproduction and pollinator behavior, and are excellent models for studying dispersal of bacteria and fungi in a metacommunity framework. Here, we assay dispersal ability of common nectar bacteria and fungi in an insect-based dispersal experiment. We then compare these results with the incidence and abundance of culturable flower-inhabiting bacteria and fungi within naturally occurring flowers across two coflowering communities in California across two flowering seasons. Our microbial dispersal experiment demonstrates that bacteria disperse via thrips among artificial habitat patches more readily than fungi. In the field, incidence and abundance of culturable bacteria and fungi were positively correlated, but bacteria were much more widespread. These patterns suggest shared dispersal routes or habitat requirements among culturable bacteria and fungi, but differences in dispersal or colonization frequency by thrips, common flower visitors. The finding that culturable bacteria are more common among nectar sampled here, in part due to superior thrips-mediated dispersal, may have relevance for microbial life history, community assembly of microbes, and plant-pollinator interactions.},
}
@article {pmid34788940,
year = {2022},
author = {Tian, L and Chang, J and Shi, S and Ji, L and Zhang, J and Sun, Y and Li, X and Li, X and Xie, H and Cai, Y and Chen, D and Wang, J and van Veen, JA and Kuramae, EE and Tran, LP and Tian, C},
title = {Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication.},
journal = {The Science of the total environment},
volume = {803},
number = {},
pages = {150131},
doi = {10.1016/j.scitotenv.2021.150131},
pmid = {34788940},
issn = {1879-1026},
mesh = {Domestication ; Methane ; *Oryza/genetics ; Plant Breeding ; Rhizosphere ; },
abstract = {Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.},
}
@article {pmid34787907,
year = {2022},
author = {Ampt, EA and van Ruijven, J and Zwart, MP and Raaijmakers, JM and Termorshuizen, AJ and Mommer, L},
title = {Plant neighbours can make or break the disease transmission chain of a fungal root pathogen.},
journal = {The New phytologist},
volume = {233},
number = {3},
pages = {1303-1316},
pmid = {34787907},
issn = {1469-8137},
mesh = {*Biodiversity ; Nutrients ; Plant Development ; *Plants/microbiology ; },
abstract = {Biodiversity can reduce or increase disease transmission. These divergent effects suggest that community composition rather than diversity per se determines disease transmission. In natural plant communities, little is known about the functional roles of neighbouring plant species in belowground disease transmission. Here, we experimentally investigated disease transmission of a fungal root pathogen (Rhizoctonia solani) in two focal plant species in combinations with four neighbour species of two ages. We developed stochastic models to test the relative importance of two transmission-modifying mechanisms: (1) infected hosts serve as nutrient supply to increase hyphal growth, so that successful disease transmission is self-reinforcing; and (2) plant resistance increases during plant development. Neighbouring plants either reduced or increased disease transmission in the focal plants. These effects depended on neighbour age, but could not be explained by a simple dichotomy between hosts and nonhost neighbours. Model selection revealed that both transmission-modifying mechanisms are relevant and that focal host-neighbour interactions changed which mechanisms steered disease transmission rate. Our work shows that neighbour-induced shifts in the importance of these mechanisms across root networks either make or break disease transmission chains. Understanding how diversity affects disease transmission thus requires integrating interactions between focal and neighbour species and their pathogens.},
}
@article {pmid34784962,
year = {2021},
author = {Tan, FPY and Beltranena, E and Zijlstra, RT},
title = {Resistant starch: Implications of dietary inclusion on gut health and growth in pigs: a review.},
journal = {Journal of animal science and biotechnology},
volume = {12},
number = {1},
pages = {124},
pmid = {34784962},
issn = {1674-9782},
support = {Discovery Grant//natural sciences and engineering research council of canada/ ; },
abstract = {Starch from cereal grains, pulse grains, and tubers is a major energy substrate in swine rations constituting up to 55% of the diet. In pigs, starch digestion is initiated by salivary and then pancreatic α-amylase, and has as final step the digestion of disaccharides by the brush-border enzymes in the small intestine that produce monosaccharides (glucose) for absorption. Resistant starch (RS) is the proportion of starch that escapes the enzymatic digestion and absorption in the small intestine. The undigested starch reaches the distal small intestine and hindgut for microbial fermentation, which produces short-chain fatty acids (SCFA) for absorption. SCFA in turn, influence microbial ecology and gut health of pigs. These fermentative metabolites exert their benefits on gut health through promoting growth and proliferation of enterocytes, maintenance of intestinal integrity and thus immunity, and modulation of the microbial community in part by suppressing the growth of pathogenic bacteria while selectively enhancing beneficial microbes. Thus, RS has the potential to confer prebiotic effects and may contribute to the improvement of intestinal health in pigs during the post-weaning period. Despite these benefits to the well-being of pigs, RS has a contradictory effect due to lower energetic efficiency of fermented vs. digested starch absorption products. The varying amount and type of RS interact differently with the digestion process along the gastrointestinal tract affecting its energy efficiency and host physiological responses including feed intake, energy metabolism, and feed efficiency. Results of research indicate that the use of RS as prebiotic may improve gut health and thereby, reduce the incidence of post-weaning diarrhea (PWD) and associated mortality. This review summarizes our current knowledge on the effects of RS on microbial ecology, gut health and growth performance in pigs.},
}
@article {pmid34783872,
year = {2022},
author = {Berlow, M and Wada, H and Derryberry, EP},
title = {Experimental Exposure to Noise Alters Gut Microbiota in a Captive Songbird.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1264-1277},
pmid = {34783872},
issn = {1432-184X},
support = {IOS-1553657//National Science Foundation/ ; IOS-1827290//National Science Foundation/ ; A18-1243-001//Animal Behavior Society/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Corticosterone ; Noise/adverse effects ; *Sparrows/microbiology ; *Microbiota ; Bacteria ; },
abstract = {Noise pollution is an unprecedented evolutionary pressure on wild animals that can lead to alteration of stress hormone levels and changes in foraging behavior. Both corticosterone and feeding behavior can have direct effects on gut bacteria, as well as indirect effects through changes in gut physiology. Therefore, we hypothesized that exposure to noise will alter gut microbial communities via indirect effects on glucocorticoids and foraging behaviors. We exposed captive white-crowned sparrows to city-like noise and measured each individuals' corticosterone level, food intake, and gut microbial diversity at the end of four treatments (acclimation, noise, recovery, and control) using a balanced repeated measures design. We found evidence that noise acts to increase corticosterone and decrease food intake, adding to a growing body of research indicating noise exposure affects stress hormone levels and foraging behaviors. We also found evidence to support our prediction for a causal, positive relationship between noise exposure and gut microbial diversity, such that birds had higher measures of alpha diversity during noise exposure. These results help to explain previous findings that urban, free-living white-crowned sparrows have higher bacterial richness than rural sparrows. However, noise appeared to act directly on the gut microbiome or, more likely, through an unmeasured variable, rather than through indirect effects via corticosterone and food intake. Altogether, our study indicates that noise affects plasma corticosterone, feeding behavior, and the gut microbiome in a songbird and raises new questions as to the mechanism linking noise exposure to gut microbial diversity.},
}
@article {pmid34782938,
year = {2022},
author = {Liebrenz, K and Gómez, C and Brambilla, S and Frare, R and Stritzler, M and Maguire, V and Ruiz, O and Soldini, D and Pascuan, C and Soto, G and Ayub, N},
title = {Whole-Genome Resequencing of Spontaneous Oxidative Stress-Resistant Mutants Reveals an Antioxidant System of Bradyrhizobium japonicum Involved in Soybean Colonization.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1133-1140},
pmid = {34782938},
issn = {1432-184X},
mesh = {*Glycine max/microbiology ; Antioxidants/metabolism ; Phylogeny ; *Bradyrhizobium/genetics/metabolism ; Symbiosis ; Oxidative Stress ; },
abstract = {Soybean is the most inoculant-consuming crop in the world, carrying strains belonging to the extremely related species Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens. Currently, it is well known that B. japonicum has higher efficiency of soybean colonization than B. diazoefficiens, but the molecular mechanism underlying this differential symbiotic performance remains unclear. In the present study, genome resequencing of four spontaneous oxidative stress-resistant mutants derived from the commercial strain B. japonicum E109 combined with molecular and physiological studies allowed identifying an antioxidant cluster (BjAC) containing a transcriptional regulator (glxA) that controls the expression of a catalase (catA) and a phosphohydrolase (yfbR) related to the hydrolysis of hydrogen peroxide and oxidized nucleotides, respectively. Integrated synteny and phylogenetic analyses supported the fact that BjAC emergence in the B. japonicum lineage occurred after its divergence from the B. diazoefficiens lineage. The transformation of the model bacterium B. diazoefficiens USDA110 with BjAC from E109 significantly increased its ability to colonize soybean roots, experimentally recapitulating the beneficial effects of the occurrence of BjAC in B. japonicum. In addition, the glxA mutation significantly increased the nodulation competitiveness and plant growth-promoting efficiency of E109. Finally, the potential applications of these types of non-genetically modified mutant microbes in soybean production worldwide are discussed.},
}
@article {pmid34782937,
year = {2022},
author = {Banerji, R and Saroj, SD},
title = {Exposure to Acyl Homoserine Lactone Enhances Survival of Streptococcus pyogenes in Murine Macrophages.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1256-1263},
pmid = {34782937},
issn = {1432-184X},
support = {BT/RLF/Re-entry/41/2015//Department of Biotechnology , Ministry of Science and Technology/ ; },
mesh = {Mice ; Humans ; Animals ; *Acyl-Butyrolactones ; *Homoserine ; Streptococcus pyogenes ; 4-Butyrolactone/pharmacology ; Macrophages ; },
abstract = {Streptococcus pyogenes is an opportunistic pathogen causing infections of the skin and upper respiratory tract of the human host. Due to the polymicrobial community present in the human host, S. pyogenes comes across several interspecies signalling molecules. Among these molecules, N-(3-oxododecanoyl)-L-homoserine lactone (Oxo-C12) modulates the morphology, thereby enhancing virulence characteristics of S. pyogenes. After the initial attachment of the bacteria to the host cell, the pathogen needs to invade the host immune system for a successful infection to occur. The host immune system is activated upon infection, where macrophages engulf the pathogen, thereby killing the bacteria. However, S. pyogenes have evolved various strategies to evade the host immune response. In this study, we investigate the role of Oxo-C12 in enhancing the survival of S. pyogenes M3 in murine macrophages. The observed Oxo-C12-mediated increased survival in murine macrophages was through increased lysozyme and acid stress resistance. Moreover, Oxo-C12 increased the survival of S. pyogenes in normal human serum. Thus, understanding the role of interspecies signalling in enhancing the survival strategies of S. pyogenes in the host will further help fill the gap for therapeutics development.},
}
@article {pmid34780015,
year = {2022},
author = {Kazmi, SSUH and Uroosa, and Warren, A and Xu, G and Xu, H},
title = {Use of functional units of periphytic protozoa for monitoring water quality in marine ecosystems: bioindicator redundancy.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {15},
pages = {22139-22150},
pmid = {34780015},
issn = {1614-7499},
support = {31672308//National Natural Science Foundation of China/ ; },
mesh = {Biodiversity ; China ; *Ciliophora ; *Ecosystem ; Environmental Biomarkers ; Environmental Monitoring/methods ; Water Quality ; },
abstract = {Although periphytic protozoan communities have long been used for the bioassessment of water quality, their utility is hampered by functional redundancy, leading to high "signal-to-noise" ratios. In this study, a 1-year baseline survey of periphytic protozoan communities was carried out in coastal waters of the Yellow Sea, northern China, in order to determine redundancy levels in conditions of differing water quality. Samples were collected at four sampling sites along a pollution gradient. Environmental variables such as salinity, chemical oxygen demand (COD), and concentrations of dissolved oxygen (DO), soluble reactive phosphates (SRP), ammonium nitrogen (NH4-N), and nitrate nitrogen (NO3-N) were measured to compare with biotic factors. A total of 53 functional units (FUs) were identified from 144 observed protozoan species based on four biological traits, i.e., feeding type, body size, movement type, and source of food supply. For reducing the "signal-to-noise" ratios of species-abundance/biomass data, the peeling procedure was used to identify the bioindicator redundancy levels based on these FUs. Three consecutive subsets of response units (RU1-RU3) with correlation coefficients > 0.75 of the full FU dataset were identified, comprising 12 FUs, 21 FUs, and 9 FUs, respectively. Algivores and bacterivores were dominant in RU1 and RU2 among the polluted sites, whereas raptors were dominant in RU3 at the unpolluted site. In terms of relative abundance, RU1 was the primary contributor to the protozoan communities during the 1-year cycle and its relative abundance increased with the increasing pollution, whereas RU2 and RU3, with complementary temporal distributions, generally decreased with increasing pollution. Ordinations based on bootstrapped average analyses revealed a significant variation in the functional pattern of all three RUs among the four sampling sites. Biological-environmental match analysis demonstrated that the variability was driven by the increasing concentrations of nutrients (e.g., NH4-N, NO3-N, and PO4-P) and decreasing concentrations of DO (P < 0.05). There were high levels of functional redundancy among periphytic protozoan communities which could be used as bioindicators of marine water quality.},
}
@article {pmid34779881,
year = {2022},
author = {Lee, HB and Jeong, DH and Cho, BC and Park, JS},
title = {The Diversity Patterns of Rare to Abundant Microbial Eukaryotes Across a Broad Range of Salinities in a Solar Saltern.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1103-1121},
pmid = {34779881},
issn = {1432-184X},
support = {NRF-2019R1A2C2002379//National Research Foundation of Korea/ ; NIBR202130203//National Institute of Biological Resources of Korea/ ; },
mesh = {Eukaryota/genetics ; Salinity ; Biodiversity ; DNA, Ribosomal ; *Rhizaria ; *Alveolata ; },
abstract = {Solar salterns are excellent artificial systems for examining species diversity and succession along salinity gradients. Here, the eukaryotic community in surface water of a Korean solar saltern (30 to 380 practical salinity units) was investigated from April 2019 to October 2020 using Illumina sequencing targeting the V4 and V9 regions of 18S rDNA. A total of 926 operational taxonomic units (OTUs) and 1,999 OTUs were obtained with the V4 and V9 regions, respectively. Notably, most of the OTUs were microbial eukaryotes, and the high-abundance groups (> 5% relative abundance (RA), Alveolata, Stramenopila, Archaeplastida, and Opisthokonta) usually accounted for > 90% of the total cumulative read counts and > 80% of all OTUs. Moreover, the high-abundance Alveolata (larger forms) and Stramenopila (smaller forms) groups displayed a significant inverse relationship, probably due to predator-prey interactions. Most of the low-abundance (0.1-5% RA) and rare (< 0.1% RA) groups remained small portion during the field surveys. Taxonomic novelty (at < 90% sequence identity) was high in the Amoebozoa, Cryptista, Haptista, Rhizaria, and Stramenopila groups (69.8% of all novel OTUs), suggesting the presence of a large number of hidden species in hypersaline environments. Remarkably, the high-abundance groups had little overlap with the other groups, implying the weakness of rare-to-prevalent community dynamics. The low-abundance Discoba group alone temporarily became the high-abundance group, suggesting that it is an opportunistic group. Overall, the composition and diversity of the eukaryotic community in hypersaline environments may be persistently stabilized, despite diverse disturbance events.},
}
@article {pmid34777296,
year = {2021},
author = {Long, AM and Jurgensen, SK and Petchel, AR and Savoie, ER and Brum, JR},
title = {Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {748961},
pmid = {34777296},
issn = {1664-302X},
abstract = {Oxygen minimum zones (OMZs) have substantial effects on the global ecology and biogeochemical processes of marine microbes. However, the diversity and activity of OMZ microbes and their trophic interactions are only starting to be documented, especially in regard to the potential roles of viruses and protists. OMZs have expanded over the past 60 years and are predicted to expand due to anthropogenic climate change, furthering the need to understand these regions. This review summarizes the current knowledge of OMZ formation, the biotic and abiotic factors involved in OMZ expansion, and the microbial ecology of OMZs, emphasizing the importance of bacteria, archaea, viruses, and protists. We describe the recognized roles of OMZ microbes in carbon, nitrogen, and sulfur cycling, the potential of viruses in altering host metabolisms involved in these cycles, and the control of microbial populations by grazers and viruses. Further, we highlight the microbial community composition and roles of these organisms in oxic and anoxic depths within the water column and how these differences potentially inform how microbial communities will respond to deoxygenation. Additionally, the current literature on the alteration of microbial communities by other key climate change parameters such as temperature and pH are considered regarding how OMZ microbes might respond to these pressures. Finally, we discuss what knowledge gaps are present in understanding OMZ microbial communities and propose directions that will begin to close these gaps.},
}
@article {pmid34775524,
year = {2022},
author = {Liu, R and Wang, Q and Zhang, K and Wu, H and Wang, G and Cai, W and Yu, K and Sun, Q and Fan, S and Wang, Z},
title = {Analysis of Postmortem Intestinal Microbiota Successional Patterns with Application in Postmortem Interval Estimation.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1087-1102},
pmid = {34775524},
issn = {1432-184X},
support = {81730056//National Natural Science Foundation of China/ ; 2020SF-133//key research and development program of shaanxi/ ; },
mesh = {Mice ; Animals ; *Gastrointestinal Microbiome ; Postmortem Changes ; Bacteria/genetics ; Intestines ; Lactobacillus ; },
abstract = {Microorganisms play a vital role in the decomposition of vertebrate remains in natural nutrient cycling, and the postmortem microbial succession patterns during decomposition remain unclear. The present study used hierarchical clustering based on Manhattan distances to analyze the similarities and differences among postmortem intestinal microbial succession patterns based on microbial 16S rDNA sequences in a mouse decomposition model. Based on the similarity, seven different classes of succession patterns were obtained. Generally, the normal intestinal flora in the cecum was gradually decreased with changes in the living conditions after death, while some facultative anaerobes and obligate anaerobes grew and multiplied upon oxygen consumption. Furthermore, a random forest regression model was developed to predict the postmortem interval based on the microbial succession trend dataset. The model demonstrated a mean absolute error of 20.01 h and a squared correlation coefficient of 0.95 during 15-day decomposition. Lactobacillus, Dubosiella, Enterococcus, and the Lachnospiraceae NK4A136 group were considered significant biomarkers for this model according to the ranked list. The present study explored microbial succession patterns in terms of relative abundances and variety, aiding in the prediction of postmortem intervals and offering some information on microbial behaviors in decomposition ecology.},
}
@article {pmid34767630,
year = {2022},
author = {Wu, G and Miyauchi, S and Morin, E and Kuo, A and Drula, E and Varga, T and Kohler, A and Feng, B and Cao, Y and Lipzen, A and Daum, C and Hundley, H and Pangilinan, J and Johnson, J and Barry, K and LaButti, K and Ng, V and Ahrendt, S and Min, B and Choi, IG and Park, H and Plett, JM and Magnuson, J and Spatafora, JW and Nagy, LG and Henrissat, B and Grigoriev, IV and Yang, ZL and Xu, J and Martin, FM},
title = {Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales.},
journal = {The New phytologist},
volume = {233},
number = {3},
pages = {1383-1400},
doi = {10.1111/nph.17858},
pmid = {34767630},
issn = {1469-8137},
mesh = {*Basidiomycota/genetics ; Biological Evolution ; *Mycorrhizae/genetics ; Phylogeny ; Symbiosis/genetics ; },
abstract = {We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.},
}
@article {pmid34767049,
year = {2022},
author = {Elias, L and Hearn, AM and Blazier, JC and Rogovska, YV and Wang, J and Li, S and Liu, S and Nebogatkin, IV and Rogovskyy, AS},
title = {The Microbiota of Ixodes ricinus and Dermacentor reticulatus Ticks Collected from a Highly Populated City of Eastern Europe.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1072-1086},
pmid = {34767049},
issn = {1432-184X},
mesh = {Male ; Animals ; Female ; *Ixodes/microbiology ; *Dermacentor/microbiology ; RNA, Ribosomal, 16S/genetics ; Europe, Eastern ; *Microbiota ; },
abstract = {Recent investigations have examined, through sequencing the V6 region of 16S rRNA gene, the microbiota of questing Ixodes ricinus and Dermacentor reticulatus ticks collected from rural areas of Central (Dnipropetrovs'k (region D) and Poltava (region P)) and Northeastern (Kharkiv (region K)) Ukraine. In addition to defining the bacterial microbiota of both tick species, the previous investigations also revealed a high degree of inter-sex and inter-regional variations in the tick microbiota. As a continuation of the two studies, the present investigation has analyzed individual microbiota of questing I. ricinus (n = 50) and D. reticulatus (n = 50) ticks originating from Kyiv, the largest city of Ukraine. The Kyiv tick microbiota were compared between males and females for each tick species. Additionally, a cross-regional analysis was performed to compare the microbiota of Kyiv ticks to those from regions D, K, and P. Numerous statistically significant inter-sex and inter-regional variations were detected when alpha diversity, beta diversity, the bacterial relative and differential abundances were assessed. The overall results demonstrated that the microbiota of Kyiv ticks were statistically different compared to the ticks of the other three regions. Besides existing climatic and geographical differences between the four regions, the authors hypothesize that various anthropogenic factors of the megapolis (e.g., animal species translocation, land management, ecology) could have contributed to the distinct microbiota of Kyiv ticks observed in this study.},
}
@article {pmid34767048,
year = {2022},
author = {Zhang, W and Yuan, W and Chen, L and Ye, C and Jiang, Y and Yang, Y},
title = {Uniqueness and Dependence of Bacterial Communities on Microplastics: Comparison with Water, Sediment, and Soil.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {985-995},
pmid = {34767048},
issn = {1432-184X},
support = {32071614//National Natural Science Foundation of China/ ; },
mesh = {*Microplastics ; Plastics ; Soil ; RNA, Ribosomal, 16S/genetics ; Water ; Bacteria/genetics ; *Microbiota ; },
abstract = {Revealing the dependence and uniqueness of microbial communities on microplastics could help us better understand the assembly of the microplastic microbial community in river ecosystems. In this study, we investigated the composition and ecological functions of the bacterial community on microplastics from the Three Gorges Reservoir area compared with those in water, sediment, and soil at species-level via full-length 16S rRNA gene sequencing. The results showed that the full-length 16S rRNA sequencing provided more detail and accurate taxa resolution of the bacterial community in microplastics (100%), water (99.90%), sediment (99.95%), and soil (100%). Betaproteobacteriales were the most abundant bacteria in microplastics (14.1%), water (32.3%), sediments (27.2%), and soil (21.0%). Unexpectedly, oligotrophic SAR11 clade was the third abundant bacteria (8.51%) and dominated the ecological functions of the bacterial community in water, but it was less observed on microplastics, with a relative abundance of 2.73×10[-5]. However, four opportunistic pathogens identified at the species level were selectively enriched on microplastics. Stenotrophomonas maltophilia was the main opportunistic pathogen on microplastics (0.29%). Sediment rather than soil and water may be contributed mostly to pathogens on microplastics. Moreover, some bacteria species with the biodegradation function of microplastics were enriched on microplastics, such as bacteria Rhodobacter sp., and endemic bacteria Luteimonas sp. The distinct bacteria composition on microplastics enhanced several ecological functions, such as xenobiotics biodegradation, which allows screening the bacteria with the biodegradation function of microplastics through long-term exposure.},
}
@article {pmid34766210,
year = {2022},
author = {Sanseverino, I and Pretto, P and António, DC and Lahm, A and Facca, C and Loos, R and Skejo, H and Beghi, A and Pandolfi, F and Genoni, P and Lettieri, T},
title = {Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {850-868},
pmid = {34766210},
issn = {1432-184X},
mesh = {*Cyanobacteria/genetics ; Eutrophication ; Humans ; Lakes/microbiology ; Metagenomics ; *Microbiota/genetics ; Water/analysis ; },
abstract = {Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.},
}
@article {pmid34764222,
year = {2021},
author = {Thamdrup, B and Schauberger, C and Larsen, M and Trouche, B and Maignien, L and Arnaud-Haond, S and Wenzhöfer, F and Glud, RN},
title = {Anammox bacteria drive fixed nitrogen loss in hadal trench sediments.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {46},
pages = {},
pmid = {34764222},
issn = {1091-6490},
mesh = {Anaerobic Ammonia Oxidation/physiology ; Denitrification/physiology ; Geologic Sediments/*microbiology ; Microbiota/physiology ; Nitrates/metabolism ; Nitrification/physiology ; Nitrogen/*metabolism ; Nitrogen Cycle/physiology ; Nitrogen Fixation/*physiology ; Nitrogen-Fixing Bacteria/*metabolism ; Oceans and Seas ; },
abstract = {Benthic N2 production by microbial denitrification and anammox is the largest sink for fixed nitrogen in the oceans. Most N2 production occurs on the continental shelves, where a high flux of reactive organic matter fuels the depletion of nitrate close to the sediment surface. By contrast, N2 production rates in abyssal sediments are low due to low inputs of reactive organics, and nitrogen transformations are dominated by aerobic nitrification and the release of nitrate to the bottom water. Here, we demonstrate that this trend is reversed in the deepest parts of the oceans, the hadal trenches, where focusing of reactive organic matter enhances benthic microbial activity. Thus, at ∼8-km depth in the Atacama Trench, underlying productive surface waters, nitrate is depleted within a few centimeters of the sediment surface, N2 production rates reach those reported from some continental margin sites, and fixed nitrogen loss is mainly conveyed by anammox bacteria. These bacteria are closely related to those known from shallow oxygen minimum zone waters, and comparison of activities measured in the laboratory and in situ suggest they are piezotolerant. Even the Kermadec Trench, underlying oligotrophic surface waters, exhibits substantial fixed N removal. Our results underline the role of hadal sediments as hot spots of deep-sea biological activity, revealing a fully functional benthic nitrogen cycle at high hydrostatic pressure and pointing to hadal sediments as a previously unexplored niche for anaerobic microbial ecology and diagenesis.},
}
@article {pmid34762992,
year = {2022},
author = {Maganha de Almeida Kumlien, AC and Pérez-Vega, C and González-Villalobos, E and Borrego, CM and Balcázar, JL},
title = {Genome analysis of a new Escherichia phage vB_EcoM_C2-3 with lytic activity against multidrug-resistant Escherichia coli.},
journal = {Virus research},
volume = {307},
number = {},
pages = {198623},
doi = {10.1016/j.virusres.2021.198623},
pmid = {34762992},
issn = {1872-7492},
mesh = {*Bacteriophages/genetics ; Escherichia coli/genetics ; Genome, Viral ; Myoviridae/genetics ; *Siphoviridae/genetics ; },
abstract = {In this study, we present the complete, annotated genome of a new member of the Tequatrovirus (T4-like) genus, Escherichia phage vB_EcoM_C2-3. This phage has an isometric head (92 nm in diameter) and a contractile tail (114 nm in length). Its genome consists of a linear, double-stranded DNA of 167,069bp with an average G+C content of 35.3%. There are 267 predicted genes, of which 125 encode functional proteins, including those for DNA replication, transcription and packaging, phage morphogenesis and cell lysis. Neither genes involved in the regulation of lysogeny nor antibiotic resistance genes were identified. Based on our results, its genomic features provide valuable insights into the use of a potential biocontrol agent, as Escherichia phage vB_EcoM_C2-3 exhibited lytic activity against E. coli, including multidrug-resistant strains.},
}
@article {pmid34762695,
year = {2021},
author = {Obusan, MCM and Caras, JAA and Lumang, LSL and Calderon, EJS and Villanueva, RMD and Salibay, CC and Siringan, MAT and Rivera, WL and Masangkay, JS and Aragones, LV},
title = {Bacteriological and histopathological findings in cetaceans that stranded in the Philippines from 2017 to 2018.},
journal = {PloS one},
volume = {16},
number = {11},
pages = {e0243691},
pmid = {34762695},
issn = {1932-6203},
mesh = {Animals ; Cetacea/*microbiology ; Liver/pathology ; Lung/pathology ; Muscle, Skeletal/pathology ; Myocardium/pathology ; Philippines ; },
abstract = {The relatively high frequency of marine mammal stranding events in the Philippines provide many research opportunities. A select set of stranders (n = 21) from 2017 to 2018 were sampled for bacteriology and histopathology. Pertinent tissues and bacteria were collected from individuals representing eight cetacean species (i.e. Feresa attenuata, Kogia breviceps, Globicephala macrorhynchus, Grampus griseus, Lagenodelphis hosei, Peponocephala electra, Stenella attenuata and Stenella longirostris) and were subjected to histopathological examination and antibiotic resistance screening, respectively. The antibiotic resistance profiles of 24 bacteria (belonging to genera Escherichia, Enterobacter, Klebsiella, Proteus, and Shigella) that were isolated from four cetaceans were determined using 18 antibiotics. All 24 isolates were resistant to at least one antibiotic class, and 79.17% were classified as multiple antibiotic resistant (MAR). The MAR index values of isolates ranged from 0.06 to 0.39 with all the isolates resistant to erythromycin (100%; n = 24) and susceptible to imipenem, doripenem, ciprofloxacin, chloramphenicol, and gentamicin (100%; n = 24). The resistance profiles of these bacteria show the extent of antimicrobial resistance in the marine environment, and may inform medical management decisions during rehabilitation of stranded cetaceans. Due to inadequate gross descriptions and limited data gathered by the responders during the stranding events, the significance of histopathological lesions in association with disease diagnosis in each cetacean stranding or mortality remained inconclusive; however, these histopathological findings may be indicative or contributory to the resulting debility and stress during their strandings. The findings of the study demonstrate the challenges faced by cetacean species in the wild, such as but not limited to, biological pollution through land-sea movement of effluents, fisheries interactions, and anthropogenic activities.},
}
@article {pmid34760361,
year = {2021},
author = {Costantini, MS and Medeiros, MCI and Crampton, LH and Reed, FA},
title = {Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12291},
pmid = {34760361},
issn = {2167-8359},
support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawai'i, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored.<br><br>METHODS: We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the 'akikiki (Oreomystis bairdi) and the 'akeke'e (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan.<br><br>RESULTS: A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. 'Akikiki had a more diverse microbiome compared to 'akeke'e. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in 'akikiki.<br><br>CONCLUSION: 'Akikiki and 'akeke'e are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.},
}
@article {pmid34760357,
year = {2021},
author = {Tucker, SJ and Freel, KC and Monaghan, EA and Sullivan, CES and Ramfelt, O and Rii, YM and Rappé, MS},
title = {Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12274},
pmid = {34760357},
issn = {2167-8359},
abstract = {Surveys of microbial communities across transitions coupled with contextual measures of the environment provide a useful approach to dissect the factors determining distributions of microorganisms across ecological niches. Here, monthly time-series samples of surface seawater along a transect spanning the nearshore coastal environment within Kāne'ohe Bay on the island of O'ahu, Hawai'i, and the adjacent offshore environment were collected to investigate the diversity and abundance of SAR11 marine bacteria (order Pelagibacterales) over a 2-year time period. Using 16S ribosomal RNA gene amplicon sequencing, the spatiotemporal distributions of major SAR11 subclades and exact amplicon sequence variants (ASVs) were evaluated. Seven of eight SAR11 subclades detected in this study showed distinct subclade distributions across the coastal to offshore environments. The SAR11 community was dominated by seven (of 106 total) SAR11 ASVs that made up an average of 77% of total SAR11. These seven ASVs spanned five different SAR11 subclades (Ia, Ib, IIa, IV, and Va), and were recovered from all samples collected from either the coastal environment, the offshore, or both. SAR11 ASVs were more often restricted spatially to coastal or offshore environments (64 of 106 ASVs) than they were shared among coastal, transition, and offshore environments (39 of 106 ASVs). Overall, offshore SAR11 communities contained a higher diversity of SAR11 ASVs than their nearshore counterparts, with the highest diversity within the little-studied subclade IIa. This study reveals ecological differentiation of SAR11 marine bacteria across a short physiochemical gradient, further increasing our understanding of how SAR11 genetic diversity partitions into distinct ecological units.},
}
@article {pmid34760346,
year = {2021},
author = {Voigt, E and Rall, BC and Chatzinotas, A and Brose, U and Rosenbaum, B},
title = {Phage strategies facilitate bacterial coexistence under environmental variability.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12194},
pmid = {34760346},
issn = {2167-8359},
abstract = {Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as "Killing the Winner", "Piggyback the loser" (PtL) or "Piggyback the Winner" (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed 'in silico' experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.},
}
@article {pmid34758284,
year = {2022},
author = {Meaden, S and Biswas, A and Arkhipova, K and Morales, SE and Dutilh, BE and Westra, ER and Fineran, PC},
title = {High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems.},
journal = {Current biology : CB},
volume = {32},
number = {1},
pages = {220-227.e5},
pmid = {34758284},
issn = {1879-0445},
mesh = {*Bacteriophages/genetics ; *CRISPR-Cas Systems ; Ecosystem ; Metagenomics ; Prevalence ; },
abstract = {CRISPR-Cas are adaptive immune systems that protect their hosts against viruses and other parasitic mobile genetic elements.[1] Although widely distributed among prokaryotic taxa, CRISPR-Cas systems are not ubiquitous.[2-4] Like most defense-system genes, CRISPR-Cas are frequently lost and gained, suggesting advantages are specific to particular environmental conditions.[5] Selection from viruses is assumed to drive the acquisition and maintenance of these immune systems in nature, and both theory[6-8] and experiments have identified phage density and diversity as key fitness determinants.[9][,][10] However, these approaches lack the biological complexity inherent in nature. Here, we exploit metagenomic data from 324 samples across diverse ecosystems to analyze CRISPR abundance in natural environments. For each metagenome, we quantified viral abundance and diversity to test whether these contribute to CRISPR-Cas abundance across ecosystems. We find a strong positive association between CRISPR-Cas abundance and viral abundance. In addition, when controlling for differences in viral abundance, CRISPR-Cas systems are more abundant when viral diversity is low, suggesting that such adaptive immune systems may offer limited protection when required to target a diverse viral community. CRISPR-Cas abundance also differed among environments, with environmental classification explaining roughly a quarter of the variation in CRISPR-Cas relative abundance. The relationships between CRISPR-Cas abundance, viral abundance, and viral diversity are broadly consistent across environments, providing robust evidence from natural ecosystems that supports predictions of when CRISPR is beneficial. These results indicate that viral abundance and diversity are major ecological factors that drive the selection and maintenance of CRISPR-Cas in microbial ecosystems.},
}
@article {pmid34757460,
year = {2022},
author = {Zhang, W and Wang, X and Li, Y and Wei, P and Sun, N and Wen, X and Liu, Z and Li, D and Feng, Y and Zhang, X},
title = {Differences Between Microbial Communities of Pinus Species Having Differing Level of Resistance to the Pine Wood Nematode.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1245-1255},
pmid = {34757460},
issn = {1432-184X},
support = {ZD202001//major emergency science and technology project of national forestry and grassland administration/ ; 2018YFC1200400//key technology research and development program of shandong/ ; 31901315//national natural science foundation of china/ ; },
mesh = {Animals ; *Pinus/microbiology ; Bacteria/genetics ; *Microbiota ; Introduced Species ; *Nematoda ; Plant Diseases ; },
abstract = {The pine wood nematode (PWN), Bursaphelenchus xylophilus, is a destructive invasive species that exerts devastating effects on most native pines in invaded regions, while many of the non-native pines have resistance to PWN. Recently, increasingly more research is focused on how microbial communities can improve host resistance against pathogens. However, the relationship between the microbial community structures and varying levels of pathogen resistance observed in different pine tree species remains unclear. Here, the bacterial and fungal communities of introduced resistant pines Pinus elliottii, P. caribaea, and P. taeda and native susceptible pines healthy and wilted P. massoniana infected by PWN were analyzed. The results showed that 6057 bacterial and 3931 fungal OTUs were annotated. The pine samples shared 944 bacterial OTUs primarily in the phyla Proteobacteria, Acidobacteria, Firmicutes, Bacteroidetes, and Chloroflexi and 111 fungal OTUs primarily in phyla Ascomycota and Basidiomycota, though different pines had unique OTUs. There were significant differences in microbial community diversity between different pines, especially between the bacterial communities of resistant and susceptible pines, and fungal communities between healthy pines (resistant pines included) and the wilted P. massoniana. Resistant pines had a greater abundance of bacteria in the genera Acidothermus (class unidentified_Actinobacteria) and Prevotellaceae (class Alphaproteobacteria), but a lower abundance of Erwinia (class Gammaproteobacteria). Healthy pines had a higher fungal abundance of Cladosporium (class Dothideomycetes) and class Eurotiomycetes, but a lower abundance of Graphilbum, Sporothrix, Geosmithia (class Sordariomycetes), and Cryptoporus (classes Agaricomycetes and Saccharomycetes). These differences in microbial abundance between resistant and healthy pines might be associated with pathogen resistance of the pines, and the results of this study contribute to the studies exploring microbial-based control of PWN.},
}
@article {pmid34756083,
year = {2021},
author = {Mills, S and Trego, AC and Lens, PNL and Ijaz, UZ and Collins, G},
title = {A Distinct, Flocculent, Acidogenic Microbial Community Accompanies Methanogenic Granules in Anaerobic Digesters.},
journal = {Microbiology spectrum},
volume = {9},
number = {3},
pages = {e0078421},
pmid = {34756083},
issn = {2165-0497},
mesh = {Bacteria, Anaerobic/*metabolism ; Bacterial Adhesion/physiology ; Biofilms/growth &amp; development ; Bioreactors/*microbiology ; Flocculation ; Methane/*biosynthesis ; Microbiota/*physiology ; Sewage/*microbiology ; Streptococcaceae/metabolism ; Water Purification ; },
abstract = {The formation of dense, well-settling methanogenic granules is essential for the operation of high-rate, up-flow anaerobic bioreactors used for wastewater treatment. Granule formation (granulation) mechanisms have been previously proposed, but an ecological understanding of granule formation is still lacking. Additionally, much of the current research on granulation only examines the start-up phase of bioreactor operation, rather than monitoring the fate of established granules and how new granules emerge over time. This paper, therefore, attempts to provide an insight into the microbial ecology of granule formation outside the start-up phase of bioreactor operation and develop an ecological granulation model. The microbial communities of granules actively undergoing growth, breakage, and reformation were examined, and an ecological granulation model was proposed. A distinct pregranular microbial community, with a high proportion of acidogenic organisms, such as the Streptococcaceae, was identified and suggested to have a role in initiating granulation by providing simpler substrates for the methanogenic and syntrophic communities which developed during granule growth. After initial granule formation, deterministic influences on microbial community assembly increased with granule size and indicated that microbial community succession was influenced by granule growth, leading to the formation of a stepwise ecological model for granulation. IMPORTANCE Complex microbial communities in engineered environments can aggregate to form surface-attached biofilms. Others form suspended biofilms, such as methanogenic granules. The formation of dense, methanogenic granules underpins the performance of high-rate, anaerobic bioreactors in industrial wastewater treatment. Granule formation (granulation) has been well studied from a physico-chemical perspective, but the ecological basis is poorly understood. We identified a distinct, flocculent, microbial community, which was present alongside granules, comprising primary consumers likely key in providing simpler substrates to granules. This flocculent community is understudied in anaerobic digestion and may initiate, or perpetuate, granule formation. We propose that it may be possible to influence bioreactor performance (e.g., to regulate volatile fatty acid concentrations) by manipulating this community. The patterns of microbial community diversity and assembly revealed by the study indicate that cycles of granule growth and breakage lead to overall diversification of the bioreactor meta-community, with implications for bioreactor process stability.},
}
@article {pmid34756066,
year = {2021},
author = {Thieringer, PH and Honeyman, AS and Spear, JR},
title = {Spatial and Temporal Constraints on the Composition of Microbial Communities in Subsurface Boreholes of the Edgar Experimental Mine.},
journal = {Microbiology spectrum},
volume = {9},
number = {3},
pages = {e0063121},
pmid = {34756066},
issn = {2165-0497},
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Geologic Sediments/chemistry/*microbiology ; Groundwater/*microbiology ; *Microbiota ; Mining ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. Attention is required to understand the near subsurface and its continuity with surface systems, where numerous novel microbial members with unique physiological modifications remain to be identified. This surface-subsurface relationship raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine (∼150 m below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric groundwater feeding boreholes demonstrated variable recharge rates likely due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined that unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Desulfosporosinus, Candidatus Nitrotoga, and Chelatococcus associated with endemic subsurface communities. Two other boreholes presented sequences related to nonsubsurface-originating microbiota. High concentration of sulfate along with detected sulfur reducing and oxidizing microorganisms suggests that sulfur related metabolic strategies are prominent within these near-subsurface boreholes. Overall, results indicate that microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20 cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments. IMPORTANCE The Edgar Experimental Mine, Idaho Springs, CO, provides inexpensive and open access to borehole investigations for subsurface microbiology studies. Understanding how microbial processes in the near subsurface are connected to surface hydrological influences is lacking. Investigating microbial communities of subsurface mine boreholes provides evidence of how geochemical processes are linked to biogeochemical processes within each borehole and the geochemical connectedness and mobility of surface influences. This study details microbial community composition and fluid geochemistry over spatial and temporal scales from boreholes within the Edgar Mine. These findings are relevant to biogeochemistry of near-surface mines, caves, and other voids across planetary terrestrial systems. In addition, this work can lead to understanding how microbial communities relate to both fluid-rock equilibration, and geochemical influences may enhance our understanding of subsurface molecular biological tools that aid mining economic practices to reflect biological signals for lucrative veins in the near subsurface.},
}
@article {pmid34755197,
year = {2022},
author = {Faghihinia, M and Zou, Y and Bai, Y and Dudáš, M and Marrs, R and Staddon, PL},
title = {Grazing Intensity Rather than Host Plant's Palatability Shapes the Community of Arbuscular Mycorrhizal Fungi in a Steppe Grassland.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1062-1071},
doi = {10.1007/s00248-021-01920-7},
pmid = {34755197},
issn = {1432-184X},
support = {RDF-15-02-13//Xi'an Jiaotong-Liverpool University/ ; },
mesh = {Sheep ; Animals ; *Mycorrhizae/physiology ; Grassland ; Ecosystem ; Soil Microbiology ; Fungi ; Soil ; Poaceae/microbiology ; Plants/microbiology ; Plant Roots/microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are the predominant type of mycorrhizal fungi in roots and rhizosphere soil of grass species worldwide. Grasslands are currently experiencing increasing grazing pressure, but it is not yet clear how grazing intensity and host plant grazing preference by large herbivores interact with soil- and root-associated AMF communities. Here, we tested whether the diversity and community composition of AMF in the roots and rhizosphere soil of two dominant perennial grasses, grazed differently by livestock, change in response to grazing intensity. We conducted a study in a long-term field experiment in which seven levels of field-manipulated grazing intensities were maintained for 13 years in a typical steppe grassland in northern China. We extracted DNA from the roots and rhizosphere soil of two dominant grasses, Leymus chinense (Trin.) Tzvel. and Stipa grandis P. Smirn, with contrasting grazing preference by sheep. AMF DNA from root and soil samples was then subjected to molecular analysis. Our results showed that AMF α-diversity (richness) at the virtual taxa (VT) level varied as a function of grazing intensity. Different VT showed completely different responses along the gradient, one increasing, one decreasing, and others showing no response. Glomeraceae was the most abundant AMF family along the grazing gradient, which fits well with the theory of disturbance tolerance of this group. In addition, sheep-grazing preference for host plants did not explain much of the variation in AMF α-diversity. However, the two grass species exhibited different AMF community composition in their roots and rhizosphere soils. Roots exhibited a lower α-diversity and higher β-diversity within the AMF community than soils. Overall, our results suggest that long-term grazing intensity might have changed the abundance of functionally diverse AMF taxa in favor of those with disturbance-tolerant traits. We suggest our results would be useful in informing the choice of mycorrhizal fungi indicator variables when assessing the impacts of grassland management choices on grassland ecosystem functioning.},
}
@article {pmid34753520,
year = {2021},
author = {Estensmo, ELF and Morgado, L and Maurice, S and Martin-Sanchez, PM and Engh, IB and Mattsson, J and Kauserud, H and Skrede, I},
title = {Spatiotemporal variation of the indoor mycobiome in daycare centers.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {220},
pmid = {34753520},
issn = {2049-2618},
mesh = {Air Microbiology ; *Air Pollution, Indoor/analysis ; Child ; Dust/analysis ; Environmental Monitoring ; Fungi/genetics ; Humans ; *Mycobiome ; Seasons ; },
abstract = {BACKGROUND: Children spend considerable time in daycare centers in parts of the world and are exposed to the indoor micro- and mycobiomes of these facilities. The level of exposure to microorganisms varies within and between buildings, depending on occupancy, climate, and season. In order to evaluate indoor air quality, and the effect of usage and seasonality, we investigated the spatiotemporal variation in the indoor mycobiomes of two daycare centers. We collected dust samples from different rooms throughout a year and analyzed their mycobiomes using DNA metabarcoding.<br><br>RESULTS: The fungal community composition in rooms with limited occupancy (auxiliary rooms) was similar to the outdoor samples, and clearly different from the rooms with higher occupancy (main rooms). The main rooms had higher abundance of Ascomycota, while the auxiliary rooms contained comparably more Basidiomycota. We observed a strong seasonal pattern in the mycobiome composition, mainly structured by the outdoor climate. Most markedly, basidiomycetes of the orders Agaricales and Polyporales, mainly reflecting typical outdoor fungi, were more abundant during summer and fall. In contrast, ascomycetes of the orders Saccharomycetales and Capnodiales were dominant during winter and spring.<br><br>CONCLUSIONS: Our findings provide clear evidences that the indoor mycobiomes in daycare centers are structured by occupancy as well as outdoor seasonality. We conclude that the temporal variability should be accounted for in indoor mycobiome studies and in the evaluation of indoor air quality of buildings. Video abstract.},
}
@article {pmid34753204,
year = {2022},
author = {Figueiredo, ART and Özkaya, &#xd6; and Kümmerli, R and Kramer, J},
title = {Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad.},
journal = {Ecology letters},
volume = {25},
number = {1},
pages = {138-150},
pmid = {34753204},
issn = {1461-0248},
support = {681295//H2020 European Research Council/ ; 31003A_182499//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; KR 5017/2-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Ecosystem ; Humans ; Iron ; Oligopeptides ; Pseudomonas aeruginosa ; *Siderophores ; },
abstract = {Microbial invasions can compromise ecosystem services and spur dysbiosis and disease in hosts. Nevertheless, the mechanisms determining invasion outcomes often remain unclear. Here, we examine the role of iron-scavenging siderophores in driving invasions of Pseudomonas aeruginosa into resident communities of environmental pseudomonads. Siderophores can be 'public goods' by delivering iron to individuals possessing matching receptors; but they can also be 'public bads' by withholding iron from competitors lacking these receptors. Accordingly, siderophores should either promote or impede invasion, depending on their effects on invader and resident growth. Using supernatant feeding and invasion assays, we show that invasion success indeed increased when the invader could use its siderophores to inhibit (public bad) rather than stimulate (public good) resident growth. Conversely, invasion success decreased the more the invader was inhibited by the residents' siderophores. Our findings identify siderophores as a major driver of invasion dynamics in bacterial communities under iron-limited conditions.},
}
@article {pmid34751801,
year = {2022},
author = {LaForgia, ML and Kang, H and Ettinger, CL},
title = {Correction to: Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {509},
doi = {10.1007/s00248-021-01895-5},
pmid = {34751801},
issn = {1432-184X},
}
@article {pmid34750668,
year = {2022},
author = {Deng, W and Yuan, CL and Li, N and Liu, SR and Yang, XY and Xiao, W},
title = {Island Formation History Determines Microbial Species-Area Relationships.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1055-1061},
pmid = {34750668},
issn = {1432-184X},
support = {31360013//National Natural Science Foundation of China/ ; 31760126//National Natural Science Foundation of China/ ; 2019QZKK2002//Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; },
mesh = {Animals ; *Biodiversity ; Trees ; Plants ; Plant Leaves ; *Microbiota ; },
abstract = {The species-area relationship (SAR) and its mechanisms regarding microbes are not as clear as those of plants and animals; this may result from the impact of sampling effects and the confusion between SAR and distance attenuation. We hypothesize that we can find more accurate microbial SAR curve, after removing these two factors. In this study, 27 leaves of three horticultural plants were selected as island models, and microbial biodiversity assessment was done with HTS (high-throughput sequencing). The separate and small systems using leaves as islands allow us to conduct a comprehensive survey of the microbial biodiversity of the leaves, without disturbance from sampling effects and distance attenuation effects. Interestingly, we did not find microbial SAR in those 27 leaves (also not found in evergreen trees Magnolia grandiflora and Eriobotrya japonica), but we did find significant microbial SAR in deciduous tree Ficus altissima. No significant differences were found between the different trees at the alpha diversity level of microbial biodiversity, but quite different on beta diversity. The results of beta diversity partition showed that F. altissima had the highest similarity of the microbial community among the leaves compared to those of M. grandiflora and E. japonica. Since leaf genesis in deciduous plants is more simultaneous than in evergreen plants; the result suggested that inconsistent historical background of leaf islands may mask microbial SAR. Thus, intensive sampling and consistent historical background are important for understanding microbial SAR.},
}
@article {pmid34748071,
year = {2022},
author = {Majaneva, M and Rintala, JM and Blomster, J},
title = {Taxonomically and Functionally Distinct Ciliophora Assemblages Inhabiting Baltic Sea Ice.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {974-984},
pmid = {34748071},
issn = {1432-184X},
mesh = {*Ice Cover/parasitology ; Phylogeny ; *Ciliophora/genetics ; Ecosystem ; Seasons ; },
abstract = {Ciliophora is a phylum of unicellular eukaryotes that are common and have pivotal roles in aquatic environments. Sea ice is a marine habitat, which is composed of a matrix of solid ice and pockets of saline water in which Ciliophora thrive. Here, we used phylogenetic placement to identify Ciliophora 18S ribosomal RNA reads obtained from wintertime water and sea ice, and assigned functions to the reads based on this taxonomic information. Based on our results, sea-ice Ciliophora assemblages are poorer in taxonomic and functional richness than under-ice water and water-column assemblages. Ciliophora diversity stayed stable throughout the ice-covered season both in sea ice and in water, although the assemblages changed during the course of our sampling. Under-ice water and the water column were distinctly predominated by planktonic orders Choreotrichida and Oligotrichida, which led to significantly lower taxonomic and functional evenness in water than in sea ice. In addition to planktonic Ciliophora, assemblages in sea ice included a set of moderately abundant surface-oriented species. Omnivory (feeding on bacteria and unicellular eukaryotes) was the most common feeding type but was not as predominant in sea ice as in water. Sea ice included cytotrophic (feeding on unicellular eukaryotes), bacterivorous and parasitic Ciliophora in addition to the predominant omnivorous Ciliophora. Potentially mixotrophic Ciliophora predominated the water column and heterotrophic Ciliophora sea ice. Our results highlight sea ice as an environment that creates a set of variable habitats, which may be threatened by the diminishing extent of sea ice due to changing climate.},
}
@article {pmid34746021,
year = {2021},
author = {Kang, X and Deng, DM and Crielaard, W and Brandt, BW},
title = {Reprocessing 16S rRNA Gene Amplicon Sequencing Studies: (Meta)Data Issues, Robustness, and Reproducibility.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {720637},
pmid = {34746021},
issn = {2235-2988},
mesh = {*Computational Biology ; Genes, rRNA ; *High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {High-throughput sequencing technology provides an efficient method for evaluating microbial ecology. Different bioinformatics pipelines can be used to convert 16S ribosomal RNA gene amplicon sequencing data into an operational taxonomic unit (OTU) table that is used to analyze microbial communities. It is important to assess the robustness of these pipelines, each with specific algorithms and/or parameters, and their influence on the outcome of statistical tests. Articles with publicly available datasets on the oral microbiome were searched for, and five datasets were retrieved. These were from studies on changes in microbiota related to smoking, oral cancer, caries, diabetes, or periodontitis. Next, the data was processed with four pipelines based on VSEARCH, USEARCH, mothur, and UNOISE3. OTU tables were rarefied, and differences in α-diversity and β-diversity were tested for different groups in a dataset. Finally, these results were checked for consistency among these example pipelines. Of articles that deposited data, only 57% made all sequencing and metadata available. When processing the datasets, issues were encountered, caused by read characteristics and differences between tools and their defaults in combination with a lack of detail in the methodology of the articles. In general, the four mainstream pipelines provided similar results, but importantly, P-values sometimes differed between pipelines beyond the significance threshold. Our results indicated that for published articles, the description of bioinformatics methods and data deposition should be improved, and regarding reproducibility, that analysis of multiple subsamples is required when using rarefying as library-size normalization method.},
}
@article {pmid34745150,
year = {2021},
author = {Zhu, L and Wu, Y and Lin, C and Tang, L and Yu, B and Wan, W and Xuan, J and Du, Y and Chen, Z and Liang, W},
title = {Dynamic Microbial Shifts and Signatures of Long-Term Remission in Allergic Rhinitis After an Herbal Formula Treatment.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {774966},
pmid = {34745150},
issn = {1664-3224},
mesh = {Adolescent ; Adult ; Biomarkers ; Disease Management ; Disease Susceptibility ; Drugs, Chinese Herbal/*adverse effects/therapeutic use ; Dysbiosis/*diagnosis/*etiology ; Female ; Follow-Up Studies ; Gastrointestinal Microbiome/drug effects ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S ; Rhinitis, Allergic/*complications/drug therapy ; Young Adult ; },
abstract = {A mixed Chinese herbal formula, Xiao-Qing-Long-Decoction (XQLD), may contribute to sustained remission in allergic rhinitis (AR), but it is unknown which factors determine such long-term effect. Here, we aimed to identify bacterial signatures associated with sustained remission. To this end, samples from AR patients at four different times were analyzed to compare the dynamic bacterial community and structure shifts. Diversity indices Chao1 showed significant difference across different time (p<0.05), and the Kruskal-Wallis test identified that Dialister (OTU_31), Roseburia (OTU_36), Bacteroides (OTU_22), Bacteroides (OTU_2040), and Prevotella_9 (OTU_5) were the significant differential bacterial taxa (p<0.05). These distinctive genera were significantly associated with the change of AR clinical indices and the predicted functional pathways such as PPAR signaling pathway, peroxisome, and citrate cycle (TCA cycle) (p<0.05), indicating that they may be important bacterial signatures involving in the sustained remission in AR (p<0.05). Besides, lower Firmicutes/Bacteroidetes (F/B) ratio at 6 months follow-up may also contribute to the long-term remission of AR. No seriously adverse events and safety concerns were observed in this study. In conclusion, XQLD is a meaningful, long-term efficient and safe medication for AR treatment. The underlying mechanisms of sustained remission in AR after XQLD treatment may be associated with the dynamic alteration of featured gut bacteria taxa.},
}
@article {pmid34745040,
year = {2021},
author = {Johnston-Monje, D and Gutiérrez, JP and Lopez-Lavalle, LAB},
title = {Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {737616},
pmid = {34745040},
issn = {1664-302X},
abstract = {Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.},
}
@article {pmid34743196,
year = {2021},
author = {Loh, JT and Lee, KG and Lee, AP and Teo, JKH and Lim, HL and Kim, SS and Tan, AH and Lam, KP},
title = {DOK3 maintains intestinal homeostasis by suppressing JAK2/STAT3 signaling and S100a8/9 production in neutrophils.},
journal = {Cell death &amp; disease},
volume = {12},
number = {11},
pages = {1054},
pmid = {34743196},
issn = {2041-4889},
support = {OFYIRG17nov055//MOH | National Medical Research Council (NMRC)/ ; NMRC/OFIRG19may-0083//MOH | National Medical Research Council (NMRC)/ ; NMRC/OFYIRG/083/2018//MOH | National Medical Research Council (NMRC)/ ; NMRC/OFIRG19may-0083//MOH | National Medical Research Council (NMRC)/ ; },
mesh = {Adaptor Proteins, Signal Transducing/deficiency/*metabolism ; Animals ; Calgranulin A/*metabolism ; Calgranulin B/*metabolism ; Colitis/genetics/pathology ; Disease Models, Animal ; Disease Susceptibility ; Dysbiosis/complications/microbiology ; Gene Expression Regulation ; *Homeostasis ; Intestinal Mucosa/pathology ; Intestines/*metabolism/microbiology/pathology ; Janus Kinase 2/*metabolism ; Mice ; Microbiota ; Neutrophils/*metabolism ; STAT3 Transcription Factor/*metabolism ; Signal Transduction ; },
abstract = {How pathogenesis of inflammatory bowel disease (IBD) depends on the complex interplay of host genetics, microbiome and the immune system is not fully understood. Here, we showed that Downstream of Kinase 3 (DOK3), an adapter protein involved in immune signaling, confers protection of mice from dextran sodium sulfate (DSS)-induced colitis. DOK3-deficiency promotes gut microbial dysbiosis and enhanced colitis susceptibility, which can be reversed by the transfer of normal microbiota from wild-type mice. Mechanistically, DOK3 exerts its protective effect by suppressing JAK2/STAT3 signaling in colonic neutrophils to limit their S100a8/9 production, thereby maintaining gut microbial ecology and colon homeostasis. Hence, our findings reveal that the immune system and microbiome function in a feed-forward manner, whereby DOK3 maintains colonic neutrophils in a quiescent state to establish a gut microbiome essential for intestinal homeostasis and protection from IBD.},
}
@article {pmid34743174,
year = {2022},
author = {Sakoula, D and Smith, GJ and Frank, J and Mesman, RJ and Kop, LFM and Blom, P and Jetten, MSM and van Kessel, MAHJ and Lücker, S},
title = {Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria.},
journal = {The ISME journal},
volume = {16},
number = {4},
pages = {958-971},
pmid = {34743174},
issn = {1751-7370},
support = {339880//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; SIAM 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 016.Veni.192.062//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 339880//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; },
mesh = {*Alkanes/metabolism ; *Ammonia/metabolism ; Archaea/genetics ; Bacteria ; In Situ Hybridization, Fluorescence ; Mixed Function Oxygenases/metabolism ; Oxidation-Reduction ; Phylogeny ; },
abstract = {The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.},
}
@article {pmid34742956,
year = {2022},
author = {Fu, Y and Wang, F and Wang, Z and Mei, Z and Jiang, X and Schäffer, A and Virta, M and Tiedje, JM},
title = {Application of magnetic biochar/quaternary phosphonium salt to combat the antibiotic resistome in livestock wastewater.},
journal = {The Science of the total environment},
volume = {811},
number = {},
pages = {151386},
doi = {10.1016/j.scitotenv.2021.151386},
pmid = {34742956},
issn = {1879-1026},
mesh = {Animals ; Anti-Bacterial Agents ; Charcoal ; Genes, Bacterial ; Humans ; *Livestock ; Magnetic Phenomena ; *Wastewater ; },
abstract = {The overuse and misuse of antibiotics in animal breeding for disease treatment and growth enhancement have been major drivers of the occurrence, diffusion, and accumulation of antibiotic resistance genes (ARGs) in wastewater. Strategies to combat ARG dissemination are pressingly needed for human and ecological safety. To achieve this goal, a biochar-based polymer, magnetic biochar/quaternary phosphonium salt (MBQ), was applied in livestock wastewater and displayed a high performance in bacterial deactivation and ARG decrease. Efficient antibacterial effects were achieved by both MBQ and quaternary phosphonium salt; however, the abundance and fold change of ARGs in the MBQ treatment indicated a more powerful ARG dissemination control than quaternary phosphonium salt. The application of MBQ evidently reduced the microbial diversity and may primarily be responsible for altering the ARG profiles in wastewater. Network, redundancy, and variation partitioning analyses were further employed to reveal that the microbial community and the presence of mobile genetic elements were two critical factors shaping the pattern of the antibiotic resistome in livestock wastewater. Considered together, these findings extend the application field of biochar and have important implications for reducing ARG dissemination risks in livestock wastewater.},
}
@article {pmid34741647,
year = {2022},
author = {Rosca, AS and Castro, J and França, &#xc2; and Vaneechoutte, M and Cerca, N},
title = {Gardnerella Vaginalis Dominates Multi-Species Biofilms in both Pre-Conditioned and Competitive In Vitro Biofilm Formation Models.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1278-1287},
pmid = {34741647},
issn = {1432-184X},
mesh = {Humans ; Female ; *Gardnerella vaginalis/genetics ; In Situ Hybridization, Fluorescence ; *Vaginosis, Bacterial/microbiology ; Biofilms ; Vagina/microbiology ; Bacteria ; },
abstract = {Bacterial vaginosis (BV) is one of the most common bacterial vaginal infections worldwide. Despite its high prevalence, BV etiology is still unknown. Nevertheless, a hallmark of BV is the presence of a highly structured polymicrobial biofilm on the vaginal epithelium, formed primarily by Gardnerella spp. and other anaerobic species, of which co-colonization with Fannyhessea vaginae is considered an important diagnostic marker. We previously developed an in vitro biofilm model wherein Gardnerella was first allowed to establish an early biofilm that served as a scaffold for other species to adhere to. To better understand ecological interactions between BV-associated bacteria, we compared triple-species biofilms formed using two distinct models: a pre-conditioned (wherein Gardnerella vaginalis formed the early biofilm) model and a competitive (wherein all three bacteria were co-incubated together) model. Interestingly, synergistic growth interactions were more significant in the competitive model. Furthermore, the biofilm structure and species-specific distribution, as assessed by confocal laser scanning microscopy and using peptide nucleic acid fluorescence in situ hybridization method, revealed two very different triple-species morphotypes, suggesting that different interactions occur in the different models. Interestingly, independent of the model or triple-species consortium tested, we observed that G. vaginalis represented most of the biofilm bacterial composition, further highlighting the relevance of this taxon in BV.},
}
@article {pmid34741646,
year = {2022},
author = {Zakharova, Y and Bashenkhaeva, M and Galachyants, Y and Petrova, D and Tomberg, I and Marchenkov, A and Kopyrina, L and Likhoshway, Y},
title = {Variability of Microbial Communities in Two Long-Term Ice-Covered Freshwater Lakes in the Subarctic Region of Yakutia, Russia.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {958-973},
pmid = {34741646},
issn = {1432-184X},
support = {0297-2021-0023//State Assignments of the Institute for Biological Problems of Cryolithozone/ ; 21-121012190038-0//State Assignments of the Institute for Biological Problems of Cryolithozone/ ; 0279-2021-0008//State Assignments of the Limnological Institute/ ; 121032300186-9//State Assignments of the Limnological Institute/ ; },
mesh = {Humans ; Lakes/microbiology ; RNA, Ribosomal, 16S/genetics ; Ice Cover/microbiology ; *Microbiota ; *Cyanobacteria/genetics ; Proteobacteria/genetics ; Verrucomicrobia/genetics ; },
abstract = {Although under-ice microbial communities are subject to a cold environment, low concentrations of nutrients, and a lack of light, they nevertheless take an active part in biogeochemical cycles. However, we still lack an understanding of how high their diversity is and how these communities are distributed during the long-term ice-cover period. Here, we assessed for the first time the composition and distribution of microbial communities during the ice-cover period in two subarctic lakes (Labynkyr and Vorota) located in the area of the lowest temperature in the Northern Hemisphere. The diversity distribution and abundance of main bacterial taxa as well as the composition of microalgae varied by time and habitat. The 16S rRNA gene sequencing method revealed, in general, a high diversity of bacterial communities where Proteobacteria (~ 45%) and Actinobacteria (~ 21%) prevailed. There were significant differences between the communities of the lakes: Chthoniobacteraceae, Moraxellaceae, and Pirellulaceae were abundant in Lake Labynkyr, while Cyanobiaceae, Oligoflexales, Ilumatobacteraceae, and Methylacidiphilaceae were more abundant in Lake Vorota. The most abundant families were evenly distributed in April, May, and June their contribution was different in different habitats. In April, Moraxellaceae and Ilumatobacteraceae were the most abundant in the water column, while Sphingomonadaceae was abundant both in water column and on the ice bottom. In May, the abundance of Comamonadaceae increased and reached the maximum in June, while Cyanobiaceae, Oxalobacteraceae, and Pirellulaceae followed. We found a correlation of the structure of bacterial communities with snow thickness, pH, Nmin concentration, and conductivity. We isolated psychrophilic heterotrophic bacteria both from dominating and minor taxa of the communities studied. This allowed for specifying their ecological function in the under-ice communities. These findings will advance our knowledge of the under-ice microbial life.},
}
@article {pmid34741645,
year = {2022},
author = {Skrodenytė-Arbačiauskienė, V and Virbickas, T and Lukša, J and Servienė, E and Blažytė-Čereškienė, L and Kesminas, V},
title = {Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1294-1298},
pmid = {34741645},
issn = {1432-184X},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Salmo salar ; Bacteria/genetics ; Firmicutes/genetics ; *Actinobacteria/genetics ; },
abstract = {Gut microbiota of wild Baltic salmon (a sub-population of Atlantic salmon Salmo salar L.) parr was first analyzed using microbial profiling of the 16S rRNA gene (V3-V4 region) and high taxonomic richness was revealed. At the phylum level, the gut microbiota was dominated by Firmicutes, Actinobacteria, and Proteobacteria, the most numerous of which were Firmicutes. The phylum Tenericutes (mainly assigned to Mycoplasmataceae), which is common both in wild North- and East- Atlantic salmon parr, was not detected in Baltic salmon parr. Across all samples, unique amplicon sequence variants (ASVs) belonging to the unclassified Bacilli, Actinomycetales, and Rhizobiales were identified as the major taxa. Fifteen ASVs at the family level were found in all gut samples of Baltic salmon parr, the majority of which were Mycobacteriaceae, Cryptosporangiaceae, Microbacteriaceae, and Planctomycetaceae. At the genus level, Mycobacterium, Clostridium sensu stricto, and Hyphomicrobium were dominant but at low levels in all gut samples. Our study has revealed that the gut microbial community of wild Baltic salmon parr differs from those of wild North- and East-Atlantic salmon parr. This can be due to biogeographical differences or host-selective pressures, as the Baltic salmon population is believed to have split from the Atlantic salmon population in the Ancylian period.},
}
@article {pmid34741194,
year = {2022},
author = {Yang, YZ and Luo, MX and Yan, HX and Gao, RH and Chang, JT and Chao, CT and Liao, PC},
title = {Physicochemical and Biotic Changes and the Phylogenetic Evenness of Microbial Community in Soil Subjected to Phytoreclamation.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1182-1194},
pmid = {34741194},
issn = {1432-184X},
support = {NSFC31760120//national natural science foundation of china/ ; MOST 109-2621-B-003-003-MY3//ministry of science and technology, taiwan/ ; MOST 109-2628-B-003-001//ministry of science and technology, taiwan/ ; },
mesh = {Phylogeny ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Rhizosphere ; *Microbiota/genetics ; Plants ; Plant Roots ; },
abstract = {Phytoreclamation is the intervention of plants to improve degraded soil quality, changing soil biotic and abiotic properties. Many studies have focused on microbial composition and bioactivity, but few explored the changes in phylogenetic assemblages of soil microbiota after phytoreclamation. This study compared microbiomes of bare land to those of planted soils and investigated how the rhizosphere environment affects microbial assemblages from monocot Poa pratensis and eudicot Dianthus plumarius plantings using 16S rRNA metabarcoding. The results showed that the biotic susceptibility of soil to the rhizosphere environment was higher than that of the abiotic. A noticeable change was in some soil physicochemical properties like Na, P, Zn, Cu, C, and sand-to-silt proportion before and after phytoreclamation, but not between the rhizosphere and bulk soil of plantings. Contrastingly, microbial composition and diversity were significantly affected by both turfing and rhizosphere effects and were more susceptible to differences in turfing or not than in planting species. In the turfgrass, the microbiome differences between plants were greater in the rhizosphere than in the surrounding bulk soil, indicating the proximal influence of root exudates. We also found that the main abiotic factors that influenced microbial composition were Na, Zn, NOx, N, and S; as for the phylogenetic assemblages, were by K levels and the increase of silt. Turfgrass decomposes soil aggregates and changes the physicochemical properties, thereby evens the phylogenetic clustering of the soil microbial community. We demonstrated that the deterministic process affects the microbial assemblage and acts as a selective agent of the soil microbiota in fundamental and realized niches. Phytoreclamation may lead to abiotic soil changes that reallocate resources to microbes. This could affect the phylogeny of the microbial assemblages and increase microbial richness.},
}
@article {pmid34740326,
year = {2021},
author = {Ayala-Usma, DA and Cárdenas, M and Guyot, R and Mares, MC and Bernal, A and Muñoz, AR and Restrepo, S},
title = {A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {795},
pmid = {34740326},
issn = {1471-2164},
support = {BB/P027849/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; INV-2018-34-1310//Facultad de Ciencias, Universidad de los Andes/ ; 120471250765//Departamento Administrativo de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n (COLCIENCIAS)/ ; },
mesh = {DNA Transposable Elements ; Evolution, Molecular ; Gene Duplication ; Phylogeny ; *Phytophthora infestans/genetics ; Plant Diseases ; *Solanum tuberosum/genetics ; },
abstract = {BACKGROUND: Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology.<br><br>RESULTS: Our results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270&#xa0;Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/gense-sparse architecture proposed for P. infestans and other filamentous plant pathogens.<br><br>CONCLUSIONS: This study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c.},
}
@article {pmid34739925,
year = {2022},
author = {Leonard, AF and Morris, D and Schmitt, H and Gaze, WH},
title = {Natural recreational waters and the risk that exposure to antibiotic resistant bacteria poses to human health.},
journal = {Current opinion in microbiology},
volume = {65},
number = {},
pages = {40-46},
doi = {10.1016/j.mib.2021.10.004},
pmid = {34739925},
issn = {1879-0364},
support = {MR/S037713/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial ; Drug Resistance, Microbial/genetics ; Humans ; },
abstract = {Antimicrobial resistance (AMR) is widely recognised as a considerable threat to human health, wellbeing and prosperity. Many clinically important antibiotic resistance genes are understood to have originated in the natural environment. However, the complex interactions between humans, animals and the environment makes the health implications of environmental AMR difficult to quantify. This narrative review focuses on the current state of knowledge regarding antibiotic resistant bacteria (ARB) in natural bathing waters and implications for human health. It considers the latest research focusing on the transmission of ARB from bathing waters to humans. The limitations of existing evidence are discussed, as well as research priorities. The authors are of the opinion that future studies should include faecally contaminated bathing waters and people exposed to these environments to accurately parameterise environment-to-human transmission.},
}
@article {pmid34738157,
year = {2022},
author = {Khan, AA and Farooq, F and Jain, SK and Golinska, P and Rai, M},
title = {Comparative Host-Pathogen Interaction Analyses of SARS-CoV2 and Aspergillus fumigatus, and Pathogenesis of COVID-19-Associated Aspergillosis.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1236-1244},
pmid = {34738157},
issn = {1432-184X},
mesh = {Humans ; Aspergillus fumigatus ; RNA, Viral ; *COVID-19 ; SARS-CoV-2 ; *Aspergillosis ; Host-Pathogen Interactions ; },
abstract = {COVID-19 caused a global catastrophe with a large number of cases making it one of the major pandemics of the human history. The clinical presentations of the disease are continuously challenging healthcare workers with the variation of pandemic waves and viral variants. Recently, SARS-CoV2 patients have shown increased occurrence of invasive pulmonary aspergillosis infection even in the absence of traditional risk factors. The mechanism of COVID-19-associated aspergillosis is not completely understood and therefore, we performed this system biological study in order to identify mechanistic implications of aspergillosis susceptibility in COVID-19 patients and the important targets associated with this disease. We performed host-pathogen interaction (HPI) analysis of SARS-CoV2, and most common COVID-19-associated aspergillosis pathogen, Aspergillus fumigatus, using in silico approaches. The known host-pathogen interactions data of SARS-CoV2 was obtained from BIOGRID database. In addition, A. fumigatus host-pathogen interactions were predicted through homology modeling. The human targets interacting with both pathogens were separately analyzed for their involvement in aspergillosis. The aspergillosis human targets were screened from DisGeNet and GeneCards. The aspergillosis targets involved in both HPI were further analyzed for functional overrepresentation analysis using PANTHER. The results indicate that both pathogens interact with a number of aspergillosis targets and altogether they recruit more aspergillosis targets in host-pathogen interaction than alone. Common aspergillosis targets involved in HPI with both SARS-CoV2 and A. fumigatus can indicate strategies for the management of both conditions by modulating these common disease targets.},
}
@article {pmid34737136,
year = {2022},
author = {Lin, Q and De Vrieze, J and Fang, X and Li, L and Li, X},
title = {Labile carbon feedstocks trigger a priming effect in anaerobic digestion: An insight into microbial mechanisms.},
journal = {Bioresource technology},
volume = {344},
number = {Pt B},
pages = {126243},
doi = {10.1016/j.biortech.2021.126243},
pmid = {34737136},
issn = {1873-2976},
mesh = {Anaerobiosis ; Animals ; *Biofuels ; Carbon ; Manure ; *Methane ; Swine ; },
abstract = {The mechanisms underlying the advanced performance in anaerobic co-digestion (AcoD) are crucial but remain elusive. This study conducted AcoD of swine manure, rice straw and apple waste (AW, mainly consisting of labile carbon) or fructose (a pure labile carbon), and monitored microbial community abundances, activities and transcriptional profiles in the digestate and on straw. The transformation efficiencies of manure (not straw) to CH4 were promoted in AcoD co-fed manure and AW (by 39 ± 13%) or fructose (by 65 ± 14%), compared to the control mono-fed manure, implying labile carbon could trigger a priming effect underlying AcoD advantage. Although digestate-associated and straw-associated communities existed in a same bioreactor, the priming effect mainly linked to the former and was attributed to enhancements in deterministic turnover of active communities, in activities of Firmicutes taxa involved in substrate hydrolysis, and in acetoclastic methanogenesis. These findings provide novel insights to elaborate AcoD processes.},
}
@article {pmid34736408,
year = {2021},
author = {Wang, M and Yang, C and Wei, K and Zhao, M and Shen, L and Ji, J and Wang, L and Zhang, D and Guo, J and Zheng, Y and Yu, J and Zhu, M and Liu, H and Li, YF},
title = {Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions.},
journal = {BMC genomics},
volume = {22},
number = {Suppl 3},
pages = {793},
pmid = {34736408},
issn = {1471-2164},
support = {NO.31771703 &amp; 31601241//National Natural Science Foundation of China (CN)/ ; },
mesh = {Gene Expression Profiling ; Gene Expression Regulation, Plant ; Humans ; Meristem ; *MicroRNAs/genetics ; *Triticum/genetics ; },
abstract = {BACKGROUND: Winter wheat requires prolonged exposure to low temperature to initiate flowering (vernalization). Shoot apical meristem of the crown is the site of cold perception, which produces leaf primordia during vegetative growth before developing into floral primordia at the initiation of the reproductive phase. Although many essential genes for winter wheat cold acclimation and floral initiation have been revealed, the importance of microRNA (miRNA) meditated post-transcriptional regulation in crowns is not well understood. To understand the potential roles of miRNAs in crown tissues, we performed a temporal expression study of miRNAs in crown tissues at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage of winter wheat grown under natural growth conditions.<br><br>RESULTS: In total, 348 miRNAs belonging to 298 miRNA families, were identified in wheat crown tissues. Among them, 92 differentially expressed miRNAs (DEMs) were found to be significantly regulated from the three-leaf stage to the jointing stage. Most of these DEMs were highly expressed at the three-leaf stage and winter dormancy stage, and then declined in later stages. Six DEMs, including miR156a-5p were markedly induced during the winter dormancy stage. Eleven DEMs, including miR159a.1, miR390a-5p, miR393-5p, miR160a-5p, and miR1436, were highly expressed at the green-up stage. Twelve DEMs, such as miR172a-5p, miR394a, miR319b-3p, and miR9676-5p were highly induced at the jointing stage. Moreover, 14 novel target genes of nine wheat or Pooideae-specific miRNAs were verified using RLM-5' RACE assay. Notably, six mTERFs and two Rf1 genes, which are associated with mitochondrial gene expression, were confirmed as targets of three wheat-specific miRNAs.<br><br>CONCLUSIONS: The present study not only confirmed the known miRNAs associated with phase transition and floral development, but also identified a number of wheat or Pooideae-specific miRNAs critical for winter wheat cold acclimation and floral development. Most importantly, this study provided experimental evidence that miRNA could regulate mitochondrial gene expression by targeting mTERF and Rf1 genes. Our study provides valuable information for further exploration of the mechanism of miRNA mediated post-transcriptional regulation during winter wheat vernalization and inflorescent initiation.},
}
@article {pmid34735986,
year = {2022},
author = {Schnorr, SL and Berry, D},
title = {Lipid synthesis at the trophic base as the source for energy management to build complex structures.},
journal = {Current opinion in biotechnology},
volume = {73},
number = {},
pages = {364-373},
doi = {10.1016/j.copbio.2021.09.014},
pmid = {34735986},
issn = {1879-0429},
mesh = {Aged ; *Biological Evolution ; *Ecosystem ; Humans ; Lipids ; },
abstract = {The review explores the ecological basis for bacterial lipid metabolism in marine and terrestrial ecosystems. We discuss ecosystem stressors that provoked early organisms to modify their lipid membrane structures, and where these stressors are found across a variety of environments. A major role of lipid membranes is to manage cellular energy utility, including how energy is used for signal propagation. As different environments are imbued with properties that necessitate variation in energy regulation, bacterial lipid synthesis has undergone incalculable permutations of functional trial and error. This may hold clues for how biotechnology can improvise a short-hand version of the evolutionary gauntlet to stimulate latent functional competences for the synthesis of rare lipids. Reducing human reliance on marine resources and deriving solutions for production of essential nutrients is a pressing problem in sustainable agriculture and aquaculture, as well as timely considering the increasing fragility of human health in an aging population.},
}
@article {pmid34735604,
year = {2022},
author = {Wagener, C and du Plessis, M and Measey, J},
title = {Invasive Amphibian Gut Microbiota and Functions Shift Differentially in an Expanding Population but Remain Conserved Across Established Populations.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1042-1054},
pmid = {34735604},
issn = {1432-184X},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; South Africa ; *Microbiota/genetics ; Bufonidae ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Studies of laboratory animals demonstrate extensive variation of host gut microbiomes and their functional capabilities across populations, but how does anthropogenic change impact the microbiomes of non-model species? The anthropogenic movement of species to novel environments can drastically alter animals' microbiomes; however, factors that shape invasive species gut microbiota during introduction remain relatively unexplored. Through 16S amplicon sequencing on guttural toad (Sclerophrys gutturalis) faecal samples, we determine that residence time does not impact microbiome variation between source and introduced populations. The youngest population (~ 20 years in Cape Town) has the most distinct microbiome and associated functional capabilities, whereas longer residence times (~ 100 years in Réunion and Mauritius) produce less divergent microbial compositional, phylogenetic, and predicted functional diversity and differential abundance from source populations (Durban). Additionally, we show extensive variation of microbial and functional diversity, as well as differential abundance patterns in an expanding introduced population (Cape Town) between core and periphery sites. Contrasting previous studies, we suggest that introduction pathways might be an important factor impacting host microbial divergence. These findings also imply that the microbiome can diverge in accordance with host population dynamics.},
}
@article {pmid34734290,
year = {2021},
author = {Higuita Palacio, MF and Montoya, OI and Saldamando, CI and García-Bonilla, E and Junca, H and Cadavid-Restrepo, GE and Moreno-Herrera, CX},
title = {Dry and Rainy Seasons Significantly Alter the Gut Microbiome Composition and Reveal a Key Enterococcus sp. (Lactobacillales: Enterococcaceae) Core Component in Spodoptera frugiperda (Lepidoptera: Noctuidae) Corn Strain From Northwestern Colombia.},
journal = {Journal of insect science (Online)},
volume = {21},
number = {6},
pages = {},
pmid = {34734290},
issn = {1536-2442},
mesh = {Animals ; Colombia ; *Enterococcus ; *Gastrointestinal Microbiome ; Larva ; *Seasons ; Spodoptera/*microbiology ; Zea mays ; },
abstract = {Spodoptera frugiperda is a polyphagous pest of several crops of economic importance. Nowadays, the insect is broadly distributed in America and, recently, in Africa, Asia, and Australia. The species has diverged into corn and rice strains. The role of the gut microbiota in insect physiology is relevant due to its participation in crucial functions. However, knowledge of seasonal variations that alter the gut microbiome in pests is limited. Gut microbiome composition between the dry and rainy seasons was analyzed with cultured and uncultured approaches in S. frugiperda corn strain larvae collected at Northwest Colombia, as seasonal microbiome changes might fluctuate due to environmental changes. On the basis of culture-dependent methods, results show well-defined microbiota with bacterial isolates belonging to Enterococcus, Klebsiella (Enterobacteriales: Enterobacteriaceae), Enterobacter (Enterobacterales: Enterobacteriaceae), and Bacillus (Bacillales: Bacillaceae) genera. The community composition displayed a low bacterial diversity across all samples. The core community detected with uncultured methods was composed of Enterococcus, Erysipelatoclostridium (Erysipelotrichales: Erysipelotrichaceae), Rasltonia (Burkholderiales: Burkholderiaceae), and Rhizobium (Hyphomicrobiales: Rhizobiaceae) genera, and Enterobacteriaceae family members. Significant differences in microbiome diversity were observed between the two seasons. The relative abundance of Erysipelatoclostridium was high in the dry season, while in the phylotype ZOR0006 (Erysipelotrichales: Erysipelotrichaceae) and Tyzzerella (Lachnospirales: Lachnospiraceae) genus, the relative abundance was high in the rainy season. The overall low gut bacterial diversity observed in the S. frugiperda corn strain suggests a strong presence of antagonist activity as a selection factor possibly arising from the host, the dominant bacterial types, or the material ingested. Targeting the stability and predominance of this core microbiome could be an additional alternative to pest control strategies, particularly in this moth.},
}
@article {pmid34732568,
year = {2021},
author = {Ortiz, M and Leung, PM and Shelley, G and Jirapanjawat, T and Nauer, PA and Van Goethem, MW and Bay, SK and Islam, ZF and Jordaan, K and Vikram, S and Chown, SL and Hogg, ID and Makhalanyane, TP and Grinter, R and Cowan, DA and Greening, C},
title = {Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {45},
pages = {},
pmid = {34732568},
issn = {1091-6490},
mesh = {Antarctic Regions ; Autotrophic Processes ; Biodiversity ; *Desert Climate ; Gases/*metabolism ; Hydrogenase/metabolism ; Ice Cover/*microbiology ; Metagenome ; *Microbiota ; Oxidation-Reduction ; Phototrophic Processes ; *Soil Microbiology ; },
abstract = {Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.},
}
@article {pmid34731961,
year = {2022},
author = {Esquivel-Hernández, DA and García-Pérez, JS and López-Pacheco, IY and Iqbal, HMN and Parra-Saldívar, R},
title = {Resource recovery of lignocellulosic biomass waste into lactic acid - Trends to sustain cleaner production.},
journal = {Journal of environmental management},
volume = {301},
number = {},
pages = {113925},
doi = {10.1016/j.jenvman.2021.113925},
pmid = {34731961},
issn = {1095-8630},
mesh = {Biomass ; Fermentation ; Hydrolysis ; *Lactic Acid ; *Lignin/metabolism ; },
abstract = {Biomass waste generation concerns regulatory authorities to develop novel methods to sustain biotransformation processes. Particularly, lactic acid (LA) is a bulk commodity chemical used in diverse industries and holds a growing global market demand. Recently, lignocellulosic waste biomass is preferred for LA bio-production because of its non-edible and inexpensive nature. However, the information about new pretreatment methods for lignocellulosic feedstock, and novel strains capable to produce LA through fermentation is limited. Therefore, this review highlights the advancement of pretreatments methods of lignocellulosic biomass and biotransformation. Herein, we first briefly explored the main sources of lignocellulosic waste biomass, then we explored their latest advances in pretreatment processes particularly supercritical fluid extraction, and microwave-assisted extraction. Approaches for bioconversion were also analyzed, such as consolidated bioprocessing (CBP), simultaneous saccharification and fermentation (SSF), separate hydrolysis fermentation (SHF), among other alternatives. Also, new trends and approaches were documented, such as metagenomics to find novel strains of microorganisms and the use of recombinant strategies for the creation of new strains. Finally, we developed a holistic and sustainable perspective based on novel microbial ecology tools such as next-gen sequencing, bioinformatics, and metagenomics. All these shed light on the needs to culture powerful microbial isolates, co-cultures, and mixed consortia to improve fermentation processes with the aim of optimizing cultures and feedstock pretreatments.},
}
@article {pmid34731271,
year = {2022},
author = {Li, J and Weinberger, F and Saha, M and Majzoub, ME and Egan, S},
title = {Cross-Host Protection of Marine Bacteria Against Macroalgal Disease.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1288-1293},
pmid = {34731271},
issn = {1432-184X},
support = {57381332//Deutscher Akademischer Austauschdienst/ ; },
mesh = {Animals ; *Rhodophyta ; *Seaweed ; *Rhodobacteraceae ; *Microbiota ; *Probiotics ; },
abstract = {Despite an increasing awareness of disease impacts on both cultivated and native seaweed populations, the development of marine probiotics has been limited and predominately focused on farmed animals. Bleaching (loss of thallus pigmentation) is one of the most prevalent diseases observed in marine macroalgae. Endemic probiotic bacteria have been characterized to prevent bleaching disease in red macroalgae Agarophyton vermiculophyllum and Delisea pulchra; however, the extent to which probiotic strains provide cross-protection to non-endemic hosts and the influence of native microbiota remain unknown. Using A. vermiculophyllum as a model, we demonstrate that co-inoculation with the pathogen Pseudoalteromonas arctica G-MAN6 and D. pulchra probiotic strain Phaeobacter sp. BS52 or Pseudoalteromonas sp. PB2-1 reduced the disease risks compared to the pathogen only treatment. Moreover, non-endemic probiotics outperformed the endemic probiotic strain Ralstonia sp. G-NY6 in the presence of the host natural microbiota. This study highlights how the native microbiota can impact the effectiveness of marine probiotics and illustrates the potential of harnessing probiotics that can function across different hosts to mitigate the impact of emerging marine diseases.},
}
@article {pmid34727719,
year = {2021},
author = {Duxbury, SJN and Alderliesten, JB and Zwart, MP and Stegeman, A and Fischer, EAJ and de Visser, JAGM},
title = {Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli.},
journal = {Proceedings. Biological sciences},
volume = {288},
number = {1962},
pages = {20212027},
pmid = {34727719},
issn = {1471-2954},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Drug Resistance, Bacterial/genetics ; *Escherichia coli/genetics ; *Gastrointestinal Microbiome ; Plasmids/genetics ; },
abstract = {Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified in vitro, the influence of interactions with other microbiome members is largely unknown. Here, we investigated the influence of three genera of lactic acid bacteria (LAB) derived from the chicken gastrointestinal microbiome on the spread of an epidemic narrow-range ESBL resistance plasmid, IncI1 carrying blaCTX-M-1, in mixed cultures of isogenic Escherichia coli strains. Secreted products of LAB decreased E. coli growth rates in a genus-specific manner but did not affect plasmid transfer rates. Importantly, we quantified plasmid transfer rates by controlling for density-dependent mating opportunities. Parametrization of a mathematical model with our in vitro estimates illustrated that small fitness costs of plasmid carriage may tip the balance towards plasmid loss under growth conditions in the gastrointestinal tract. This work shows that microbial interactions can influence plasmid success and provides an experimental-theoretical framework for further study of plasmid transfer in a microbiome context.},
}
@article {pmid34727498,
year = {2021},
author = {Wang, X and Prévoteau, A and Rabaey, K},
title = {Impact of Periodic Polarization on Groundwater Denitrification in Bioelectrochemical Systems.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {22},
pages = {15371-15379},
doi = {10.1021/acs.est.1c03586},
pmid = {34727498},
issn = {1520-5851},
mesh = {Autotrophic Processes ; *Bioelectric Energy Sources ; Denitrification ; *Groundwater ; Nitrates ; },
abstract = {Nitrate contamination is a common problem in groundwater around the world. Nitrate can be cathodically reduced in bioelectrochemical systems using autotrophic denitrifiers with low energy investment and without chemical addition. Successful denitrification was demonstrated in previous studies in both microbial fuel cells and microbial electrolysis cells (MECs) with continuous current flow, whereas the impact of intermittent current supply (e.g., in a fluidized-bed system) on denitrification and particularly the electron-storing capacity of the denitrifying electroactive biofilms (EABs) on the cathodes have not been studied in depth. In this study, two continuously fed MECs were operated in parallel under continuous and periodic polarization modes over 280 days, respectively. Under continuous polarization, the maximum denitrification rate reached 233 g NO3[-]-N/m[3]/d with 98% nitrate removal (0.6 mg NO3[-]-N/L in the effluent) with negligible intermediate production, while under a 30 s open-circuit/30 s polarization mode, 86% of nitrate was removed at a maximum rate of 205 g NO3[-]-N/m[3]/d (4.5 mg NO3[-]-N/L in the effluent) with higher N2O production (6.6-9.3 mg N/L in the effluent). Conversely, periodic polarization could be an interesting approach in other bioelectrochemical processes if the generation of chemical intermediates (partially reduced or oxidized) should be favored. Similar microbial communities dominated byGallionellaceaewere found in both MECs; however, swapping the polarization modes and the electrochemical analyses suggested that the periodically polarized EABs probably developed a higher ability for electron storage and transfer, which supported the direct electron transfer pathway in discontinuous operation or fluidized biocathodes.},
}
@article {pmid34727198,
year = {2022},
author = {Floc'h, JB and Hamel, C and Laterrière, M and Tidemann, B and St-Arnaud, M and Hijri, M},
title = {Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1166-1181},
pmid = {34727198},
issn = {1432-184X},
support = {RDC Fund//natural sciences and engineering research council of canada/ ; },
mesh = {Soil ; *Bradyrhizobium ; Soil Microbiology ; Fungi ; Plant Roots/microbiology ; Canada ; *Microbiota ; Rhizosphere ; Bacteria ; Plants ; *Brassica napus ; },
abstract = {The subterranean microbiota of plants is of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere, and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian Prairies. Our aims were to verify whether bacterial and fungal communities of canola roots, rhizosphere, and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification, which was not the case on bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil, and one core bacterium shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.},
}
@article {pmid34726495,
year = {2021},
author = {Georgoulis, SJ and Shalvarjian, KE and Helmann, TC and Hamilton, CD and Carlson, HK and Deutschbauer, AM and Lowe-Power, TM},
title = {Genome-Wide Identification of Tomato Xylem Sap Fitness Factors for Three Plant-Pathogenic Ralstonia Species.},
journal = {mSystems},
volume = {6},
number = {6},
pages = {e0122921},
pmid = {34726495},
issn = {2379-5077},
support = {S10 OD018174/OD/NIH HHS/United States ; 2018-67012-31497//U.S. Department of Agriculture (USDA)/ ; },
abstract = {Plant-pathogenic Ralstonia spp. colonize plant xylem and cause wilt diseases on a broad range of host plants. To identify genes that promote growth of diverse Ralstonia strains in xylem sap from tomato plants, we performed genome-scale genetic screens (random barcoded transposon mutant sequencing screens [RB-TnSeq]) in three strains spanning the genetic, geographical, and physiological range of plant-pathogenic Ralstonia: Ralstonia solanacearum IBSBF1503, Ralstonia pseudosolanacearum GMI1000, and Ralstonia syzygii PSI07. Contrasting mutant fitness phenotypes in culture media versus in xylem sap suggest that Ralstonia strains are adapted to ex vivo xylem sap and that culture media impose foreign selective pressures. Although wild-type Ralstonia grew in sap and in rich medium with similar doubling times and to a similar carrying capacity, more genes were essential for growth in sap than in rich medium. Each strain required many genes associated with envelope remodeling and repair processes for full fitness in xylem sap. These genes were associated with peptidoglycan peptide formation (murI), secretion of periplasmic proteins (tatC), periplasmic protein folding (dsbA), synthesis of osmoregulated periplasmic glucans (mdoGH), and lipopolysaccharide (LPS) biosynthesis. Mutant strains with mutations in four genes had strong, sap-specific fitness defects in all strain backgrounds: murI, thiC, purU, and a lipoprotein (RSc2007). Many amino acid biosynthesis genes were required for fitness in both minimal medium and xylem sap. Multiple mutants with insertions in virulence regulators had gains of fitness in culture media and neutral fitness in sap. Our genome-scale genetic screen identified Ralstonia fitness factors that promote growth in xylem sap, an ecologically relevant condition. IMPORTANCE Traditional transposon mutagenesis genetic screens pioneered molecular plant pathology and identified core virulence traits like the type III secretion system. TnSeq approaches that leverage next-generation sequencing to rapidly quantify transposon mutant phenotypes are ushering in a new wave of biological discovery. Here, we have adapted a genome-scale approach, random barcoded transposon mutant sequencing (RB-TnSeq), to discover fitness factors that promote growth of three related bacterial strains in a common niche, tomato xylem sap. Fitness of the wild type and mutants show that Ralstonia spp. are adapted to grow well in xylem sap from their natural host plant, tomato. Our screen identified multiple sap-specific fitness factors with roles in maintaining the bacterial envelope. These factors include putative adaptations to resist plant defenses that may include antimicrobial proteins and specialized metabolites that damage bacterial membranes.},
}
@article {pmid34725713,
year = {2022},
author = {Kang, H and Lee, J and Zhou, X and Kim, J and Yang, Y},
title = {The Effects of N Enrichment on Microbial Cycling of Non-CO2 Greenhouse Gases in Soils-a Review and a Meta-analysis.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {945-957},
pmid = {34725713},
issn = {1432-184X},
mesh = {Humans ; *Soil ; *Greenhouse Gases ; Ecosystem ; Nitrous Oxide ; Fertilizers ; Methane/analysis ; Carbon Dioxide/analysis ; },
abstract = {Terrestrial ecosystems are typically nitrogen (N) limited, but recent years have witnessed N enrichment in various soil ecosystems caused by human activities such as fossil fuel combustion and fertilizer application. This enrichment may alter microbial processes in soils in a way that would increase the emissions of methane (CH4) and nitrous oxide (N2O), thereby aggravating global climate change. This review focuses on the effects of N enrichment on methanogens and methanotrophs, which play a central role in the dynamics of CH4 at the global scale. We also address the effects of N enrichment on N2O, which is produced in soils mainly by nitrification and denitrification. Overall, N enrichment inhibits methanogenesis in pure culture experiments, while its effects on CH4 oxidation are more complicated. The majority of previous studies reported that N enrichment, especially NH4[+] enrichment, inhibits CH4 oxidation, resulting in higher CH4 emissions from soils. However, both activation and neutral responses have also been reported, particularly in rice paddies and landfill sites, which is well reflected in our meta-analysis. In contrast, N enrichment substantially increases N2O emission by both nitrification and denitrification, which increases proportionally to the amount of N amended. Future studies should address the effects of N enrichment on the active microbes of those functional groups at multiple scales along with parameterization of microbial communities for the application to climate models at the global scale.},
}
@article {pmid34724047,
year = {2021},
author = {Jakus, N and Blackwell, N and Straub, D and Kappler, A and Kleindienst, S},
title = {Presence of Fe(II) and nitrate shapes aquifer-originating communities leading to an autotrophic enrichment dominated by an Fe(II)-oxidizing Gallionellaceae sp.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {11},
pages = {},
doi = {10.1093/femsec/fiab145},
pmid = {34724047},
issn = {1574-6941},
mesh = {Autotrophic Processes ; Denitrification ; Ecosystem ; Ferrous Compounds ; *Gallionellaceae/genetics ; *Groundwater ; Nitrates ; Oxidation-Reduction ; },
abstract = {Autotrophic nitrate reduction coupled to Fe(II) oxidation is an important nitrate removal process in anoxic aquifers. However, it remains unknown how changes of O2 and carbon availability influence the community structure of nitrate-reducing Fe(II)-oxidizing (NRFeOx) microbial assemblages and what the genomic traits of these NRFeOx key players are. We compared three metabolically distinct denitrifying assemblages, supplemented with acetate, acetate/Fe(II) or Fe(II), enriched from an organic-poor, pyrite-rich aquifer. The presence of Fe(II) promoted the growth of denitrifying Burkholderiaceae spp. and an unclassified Gallionellaceae sp. This Gallionellaceae sp. was related to microaerophilic Fe(II) oxidizers; however, it did not grow under microoxic conditions. Furthermore, we explored a metagenome and 15 metagenome-assembled genomes from an aquifer-originating, autotrophic NRFeOx culture. The dominant Gallionellaceae sp. revealed the potential to oxidize Fe(II) (e.g. cyc2), fix CO2 (e.g. rbcL) and perform near-complete denitrification leading to N2O formation (e.g. narGHJI,nirK/S and norBC). In addition, Curvibacter spp.,Methyloversatilis sp. and Thermomonas spp. were identified as novel putative NRFeOx taxa. Our findings provide first insights into the genetic traits of the so far only known autotrophic NRFeOx culture originating from an organic-poor aquifer, providing the genomic basis to study mechanisms of nitrate removal in organic-poor subsurface ecosystems.},
}
@article {pmid34721343,
year = {2021},
author = {Van Eesbeeck, V and Props, R and Mysara, M and Petit, PCM and Rivasseau, C and Armengaud, J and Monsieurs, P and Mahillon, J and Leys, N},
title = {Cyclical Patterns Affect Microbial Dynamics in the Water Basin of a Nuclear Research Reactor.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {744115},
pmid = {34721343},
issn = {1664-302X},
abstract = {The BR2 nuclear research reactor in Mol, Belgium, runs in successive phases of operation (cycles) and shutdown, whereby a water basin surrounding the reactor vessel undergoes periodic changes in physico-chemical parameters such as flow rate, temperature, and radiation. The aim of this study was to explore the microbial community in this unique environment and to investigate its long-term dynamics using a 16S rRNA amplicon sequencing approach. Results from two sampling campaigns spanning several months showed a clear shift in community profiles: cycles were mostly dominated by two Operational Taxonomic Units (OTUs) assigned to unclassified Gammaproteobacterium and Pelomonas, whereas shutdowns were dominated by an OTU assigned to Methylobacterium. Although 1 year apart, both campaigns showed similar results, indicating that the system remained stable over this 2-year period. The community shifts were linked with changes in physico-chemical parameters by Non-metric Multidimensional Scaling (NMDS) and correlation analyses. In addition, radiation was hypothesized to cause a decrease in cell number, whereas temperature had the opposite effect. Chemoautotrophic use of H2 and dead cell recycling are proposed to be used as a strategies for nutrient retrieval in this extremely oligotrophic environment.},
}
@article {pmid34721316,
year = {2021},
author = {Verbeelen, T and Leys, N and Ganigué, R and Mastroleo, F},
title = {Development of Nitrogen Recycling Strategies for Bioregenerative Life Support Systems in Space.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {700810},
pmid = {34721316},
issn = {1664-302X},
abstract = {To enable long-distance space travel, the development of a highly efficient and robust system to recover nutrients from waste streams is imperative. The inability of the current physicochemical-based environmental control and life support system (ECLSS) on the ISS to produce food in situ and to recover water and oxygen at high enough efficiencies results in the need for frequent resupply missions from Earth. Therefore, alternative strategies like biologically-based technologies called bioregenerative life support systems (BLSSs) are in development. These systems aim to combine biological and physicochemical processes, which enable in situ water, oxygen, and food production (through the highly efficient recovery of minerals from waste streams). Hence, minimalizing the need for external consumables. One of the BLSS initiatives is the European Space Agency's (ESA) Micro-Ecological Life Support System Alternative (MELiSSA). It has been designed as a five-compartment bioengineered system able to produce fresh food and oxygen and to recycle water. As such, it could sustain the needs of a human crew for long-term space exploration missions. A prerequisite for the self-sufficient nature of MELiSSA is the highly efficient recovery of valuable minerals from waste streams. The produced nutrients can be used as a fertilizer for food production. In this review, we discuss the need to shift from the ECLSS to a BLSS, provide a summary of past and current BLSS programs and their unique approaches to nitrogen recovery and processing of urine waste streams. In addition, compartment III of the MELiSSA loop, which is responsible for nitrogen recovery, is reviewed in-depth. Finally, past, current, and future related ground and space demonstration and the space-related challenges for this technology are considered.},
}
@article {pmid34719821,
year = {2021},
author = {Beterams, A and De Paepe, K and Maes, L and Wise, IJ and De Keersmaecker, H and Rajkovic, A and Laukens, D and Van de Wiele, T and Calatayud Arroyo, M},
title = {Versatile human in vitro triple coculture model coincubated with adhered gut microbes reproducibly mimics pro-inflammatory host-microbe interactions in the colon.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {35},
number = {12},
pages = {e21992},
doi = {10.1096/fj.202101135R},
pmid = {34719821},
issn = {1530-6860},
mesh = {Coculture Techniques/*methods ; Colon/cytology/*immunology/metabolism/microbiology ; Epithelial Cells/cytology/*immunology/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; Humans ; Intestinal Mucosa/cytology/*immunology/metabolism/microbiology ; Lacticaseibacillus rhamnosus/physiology ; Macrophages/cytology/*immunology/metabolism/microbiology ; Transcriptome ; },
abstract = {The colonic epithelial barrier is vital to preserve gut and host health by maintaining the immune homeostasis between host and microbes. The mechanisms underlying beneficial or harmful host-microbe interactions are poorly understood and impossible to study in vivo given the limited accessibility and ethical constraints. Moreover, existing in vitro models lack the required cellular complexity for the routine, yet profound, analysis of the intricate interplay between different types of host and microbial cells. We developed and characterized a broadly applicable, easy-to-handle in vitro triple coculture model that combines chemically-induced macrophage-like, goblet and epithelial cells covered by a mucus layer, which can be coincubated with complex human-derived gut microbiota samples for 16 h. Comparison with a standard epithelial monolayer model revealed that triple cocultures produce thicker mucus layers, morphologically organize in a network and upon exposure to human-derived gut microbiota samples, respond via pro-inflammatory cytokine production. Both model systems, however, were not suffering from cytotoxic stress or different microbial loads, indicating that the obtained endpoints were caused by the imposed conditions. Addition of the probiotic Lactobacillus rhamnosus GG to assess its immunomodulating capacity in the triple coculture slightly suppressed pro-inflammatory cytokine responses, based on transcriptomic microarray analyses. TNF conditioning of the models prior to microbial exposure did not cause shifts in cytokines, suggesting a strong epithelial barrier in which TNF did not reach the basolateral side. To conclude, the triple coculture model is tolerable towards manipulations and allows to address mechanistic host-microbe research questions in a stable in vitro environment.},
}
@article {pmid34716776,
year = {2022},
author = {Ho, A and Zuan, ATK and Mendes, LW and Lee, HJ and Zulkeflee, Z and van Dijk, H and Kim, PJ and Horn, MA},
title = {Aerobic Methanotrophy and Co-occurrence Networks of a Tropical Rainforest and Oil Palm Plantations in Malaysia.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1154-1165},
pmid = {34716776},
issn = {1432-184X},
support = {HO6234/1-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Rainforest ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Malaysia ; Soil ; Methane ; Bacteria/genetics ; },
abstract = {Oil palm (OP) plantations are gradually replacing tropical rainforest in Malaysia, one of the largest palm oil producers globally. Conversion of lands to OP plantations has been associated with compositional shifts of the microbial community, with consequences on the greenhouse gas (GHG) emissions. While the impact of the change in land use has recently been investigated for microorganisms involved in N2O emission, the response of the aerobic methanotrophs to OP agriculture remains to be determined. Here, we monitored the bacterial community composition, focusing on the aerobic methanotrophs, in OP agricultural soils since 2012, 2006, and 1993, as well as in a tropical rainforest, in 2019 and 2020. High-affinity methane uptake was confirmed, showing significantly lower rates in the OP plantations than in the tropical rainforest, but values increased with continuous OP agriculture. The bacterial, including the methanotrophic community composition, was modified with ongoing OP agriculture. The methanotrophic community composition was predominantly composed of unclassified methanotrophs, with the canonical (Methylocystis) and putative methanotrophs thought to catalyze high-affinity methane oxidation present at higher relative abundance in the oldest OP plantation. Results suggest that the methanotrophic community was relatively more stable within each site, exhibiting less temporal variations than the total bacterial community. Uncharacteristically, a 16S rRNA gene-based co-occurrence network analysis revealed a more complex and connected community in the OP agricultural soil, which may influence the resilience of the bacterial community to disturbances. Overall, we provide a first insight into the ecology and role of the aerobic methanotrophs as a methane sink in OP agricultural soils.},
}
@article {pmid34714368,
year = {2022},
author = {Akbar, S and Li, X and Ding, Z and Liu, Q and Huang, J and Zhou, Q and Gu, L and Yang, Z},
title = {Disentangling Diet- and Medium-Associated Microbes in Shaping Daphnia Gut Microbiome.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {911-921},
pmid = {34714368},
issn = {1432-184X},
support = {31730105//national natural science foundation of china/ ; 31800385//national natural science foundation of china/ ; 2020M681658//postdoctoral research foundation of china/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Daphnia/microbiology ; *Microbiota ; Bacteria/genetics ; Diet ; },
abstract = {Host genotype and environment are considered crucial factors in shaping Daphnia gut microbiome composition. Among the environmental factors, diet is an important factor that regulates Daphnia microbiome. Most of the studies only focused on the use of axenic diet and non-sterile medium to investigate their effects on Daphnia microbiome. However, in natural environment, Daphnia diets such as phytoplankton are associated with microbes and could affect Daphnia microbiome composition and fitness, but remain relatively poorly understood compared to that of axenic diet. To test this, we cultured two Daphnia magna genotypes (genotype-1 and genotype-2) in sterile medium and fed with axenic diet. To check the effects of algal diet-associated microbes versus free water-related microbes, Daphnia were respectively inoculated with three different inoculums: medium microbial inoculum, diet-associated microbial inoculum, and medium and diet-mixed microbial inoculum. Daphnia were cultured for 3 weeks and their gut microbiome and life history traits were recorded. Results showed that Daphnia inoculated with medium microbial inoculum were dominated by Comamonadaceae in both genotypes. In Daphnia inoculated with mixed inoculum, genotype-1 microbiome was highly changed, whereas genotype-2 microbiome was slightly altered. Daphnia inoculated with diet microbial inoculum has almost the same microbiome in both genotypes. The total number of neonates and body size were significantly reduced in Daphnia inoculated with diet microbial inoculum regardless of genotype compared to all other treatments. Overall, this study shows that the microbiome of Daphnia is flexible and varies with genotype and diet- and medium-associated microbes, but not every bacteria is beneficial to Daphnia, and only symbionts can increase Daphnia performance.},
}
@article {pmid34712902,
year = {2021},
author = {Baig, U and Dahanukar, N and Shintre, N and Holkar, K and Pund, A and Lele, U and Gujarathi, T and Patel, K and Jakati, A and Singh, R and Vidwans, H and Tamhane, V and Deshpande, N and Watve, M},
title = {Phylogenetic diversity and activity screening of cultivable Actinobacteria isolated from marine sponges and associated environments from the western coast of India.},
journal = {Access microbiology},
volume = {3},
number = {9},
pages = {000242},
pmid = {34712902},
issn = {2516-8290},
abstract = {The phylogenetic diversity of cultivable actinobacteria isolated from sponges (Haliclona spp.) and associated intertidal zone environments along the northern parts of the western coast of India were studied using 16S rRNA gene sequences. A subset of randomly selected actinobacterial cultures were screened for three activities, namely predatory behaviour, antibacterial activity and enzyme inhibition. We recovered 237 isolates from the phylum Actinobacteria belonging to 19 families and 28 genera, which could be attributed to 95 putative species using maximum-likelihood partition and 100 putative species using Bayesian partition in Poisson tree processes. Although the trends in the discovery of actinobacterial genera isolated from sponges were consistent with previous studies from different study areas, we provide the first report of nine actinobacterial species from sponges. We observed widespread non-obligate epibiotic predatory behaviour in eight actinobacterial genera and we provide the first report of predatory activity in Brevibacterium , Glutamicibacter , Micromonospora , Nocardiopsis , Rhodococcus and Rothia . Sponge-associated actinobacteria showed significantly more predatory behaviour than environmental isolates. While antibacterial activity by actinobacterial isolates mainly affected Gram-positive target bacteria with little or no effect on Gram-negative bacteria, predation targeted both Gram-positive and Gram-negative prey with equal propensity. Actinobacterial isolates from both sponges and associated environments produced inhibitors of serine proteases and angiotensin-converting enzyme. Predatory behaviour was strongly associated with inhibition of trypsin and chymotrypsin. Our study suggests that the sponges and associated environments of the western coast of India are rich in actinobacterial diversity, with widespread predatory activity, antibacterial activity and production of enzyme inhibitors. Understanding the diversity and associations among various actinobacterial activities - with each other and the source of isolation - can provide new insights into marine microbial ecology and provide opportunities to isolate novel therapeutic agents.},
}
@article {pmid34710591,
year = {2022},
author = {Monclaro, AV and Gorgulho Silva, CO and Gomes, HAR and Moreira, LRS and Filho, EXF},
title = {The enzyme interactome concept in filamentous fungi linked to biomass valorization.},
journal = {Bioresource technology},
volume = {344},
number = {Pt A},
pages = {126200},
doi = {10.1016/j.biortech.2021.126200},
pmid = {34710591},
issn = {1873-2976},
mesh = {Biomass ; Cell Wall ; *Fungi ; Hydrolysis ; *Lignin ; },
abstract = {Biomass represents an abundant and inexpensive source of sugars and aromatic compounds that can be used as raw materials for conversion into value-added bioproducts. Filamentous fungi are sources of plant cell wall degrading enzymes in nature. Understanding the interactions between enzymes is crucial for optimizing biomass degradation processes. Herein, the concept of the interactome is presented as a holistic approach that depicts the interactions among enzymes, substrates, metabolites, and inhibitors. The interactome encompasses several stages of biomass degradation, starting with the sensing of the substrate and the subsequent synthesis of hydrolytic and oxidative enzymes (fungus-substrate interaction). Enzyme-enzyme interactions are exemplified in the complex processes of lignocellulosic biomass degradation. The enzyme-substrate-metabolite-inhibitor interaction also provides a better understanding of biomass conversion, allowing bioproduct production from recalcitrant agro-industrial residues, thus bringing greater value to residual biomass. Finally, technological applications are presented for optimizing the interactome at various levels.},
}
@article {pmid34710415,
year = {2022},
author = {Prendergast, DM and O'Doherty, &#xc1; and Burgess, CM and Howe, N and McMahon, F and Murphy, D and Leonard, F and Morris, D and Harrington, C and Carty, A and Moriarty, J and Gutierrez, M},
title = {Critically important antimicrobial resistant Enterobacteriaceae in Irish farm effluent and their removal in integrated constructed wetlands.},
journal = {The Science of the total environment},
volume = {806},
number = {Pt 3},
pages = {151269},
doi = {10.1016/j.scitotenv.2021.151269},
pmid = {34710415},
issn = {1879-1026},
mesh = {Animals ; Anti-Bacterial Agents ; Bacterial Proteins ; *Enterobacteriaceae ; *Escherichia coli ; Farms ; Swine ; Wetlands ; beta-Lactamases ; },
abstract = {This study investigated the ability of Integrated Constructed Wetlands (ICWs) to remove critically important antimicrobial resistant organisms (AROs) from farm wastewater. Influent samples from the untreated farm waste and effluent samples taken at the end of the ICW system were collected monthly from four ICWs, serving four different farm types (suckler, dairy, dairy &amp; poultry and pig). Using selective media to screen for the presence of carbapenemase resistant organisms, plasmid mediated and AmpC β-Lactamase producing organisms (ESBL/pAmpC) and fluoroquinolone resistant organisms, a total of 82 AROs were obtained with the majority being E. coli (n = 79). Statistically significant were the differences on the number of AROs isolated from influent (higher) compared to effluent, as well as a seasonal effect, with less AROs recovered during winter in comparison to other seasons (P < 0.05). On the other hand, there was no significant differences in the recovery of AROs on different farms. The majority of isolates from each of the farms (99%) were multi drug resistant, with 65% resistant to seven or more antimicrobials. A high incidence of tetracycline, trimethoprim/sulfamethoxazole, and ampicillin resistance was common to the isolates from all four farms but there were differences in ESBL levels with 63% of the isolates recovered from Farm 4 (piggery) being ESBLs compared to 18%, 36% and 4.5% recovered from Farms 1 (suckler), 2 (dairy) and 3 (dairy &amp; poultry), respectively. No carbapenemase producing organisms were isolated. Our results showed that ICWs are effective in removing critically important AROs from farm wastewater on all four farm types.},
}
@article {pmid34708599,
year = {2021},
author = {Liu, SJ and Corvini, PF and Rabaey, K},
title = {[ELECTRA: electricity-driven low energy and chemical input technology for accelerated bioremediation].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {37},
number = {10},
pages = {3405-3410},
doi = {10.13345/j.cjb.210431},
pmid = {34708599},
issn = {1872-2075},
mesh = {Biodegradation, Environmental ; Biotechnology ; *COVID-19 ; Electricity ; Humans ; *Pandemics ; SARS-CoV-2 ; },
abstract = {The international cooperation project "electricity-driven low energy and chemical input technology for accelerated bioremediation" (abridged as "ELECTRA") is jointly supported by National Nature Science Foundation of China (NSFC) and European Commission (EC). The ELECTRA consortium consists of 5 research institutions and universities from China and 17 European research institutions and universities, as well as high-tech companies of EC countries. ELECTRA focuses on researches of biodegradation of emerging organic compounds (EOCs) and novel environmental biotechnologies of low-energy and low-chemical inputs. The project has been successfully operated for 2 years, and has made important progresses in obtaining EOCs-degrading microbes, developing weak-electricity-accelerated bioremediation, and 3D-printing techniques for microbial consortium. The ELECTRA has promoted collaborations among the Chinese and European scientists. In the future, ELECTRA will overcome the negative impact of the COVID-19 pandemic and fulfill the scientific objectives through strengthening the international collaboration.},
}
@article {pmid34708598,
year = {2021},
author = {Liu, SJ and Ji, R and Corvini, PF and Rabaey, K},
title = {[Environmental scientists &amp; microbiologists from China &amp; EU: take the responsibility to cherish the Earth homeland].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {37},
number = {10},
pages = {3401-3404},
doi = {10.13345/j.cjb.210754},
pmid = {34708598},
issn = {1872-2075},
mesh = {Biodegradation, Environmental ; China ; *Ecosystem ; *Plastics ; },
abstract = {Humanity shares the common interest to protect the environment and to maintain a healthy global ecosystem. International collaboration is key in this context, to advance the necessary science and technology. The National Science Foundation of China (NSFC) and European Commission (EC) have agreed to collaborate in innovative knowledge and technology in the field of bioremediation of polluted environments and biodegradation of plastics. In this context, projects on bioremediation of soils, wastewater and sediment matrices and on microbial degradation of plastics were supported. This special issue aimed to introduce these projects and their progresses in the related fields. In total, 23 papers have been collected in this issue, covering both fundamental and applied researches.},
}
@article {pmid34707927,
year = {2021},
author = {Schagen, M and Bosch, J and Johnson, J and Duker, R and Lebre, P and Potts, AJ and Cowan, DA},
title = {The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket).},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12176},
pmid = {34707927},
issn = {2167-8359},
abstract = {This study examines the soil bacterial diversity in the Portulacaria afra-dominated succulent thicket vegetation of the Albany Subtropical Thicket biome; this biome is endemic to South Africa. The aim of the study was to compare the soil microbiomes between intact and degraded zones in the succulent thicket and identify environmental factors which could explain the community compositions. Bacterial diversity, using 16S amplicon sequencing, and soil physicochemistry were compared across three zones: intact (undisturbed and vegetated), degraded (near complete removal of vegetation due to browsing) and restored (a previously degraded area which was replanted approximately 11 years before sampling). Amplicon Sequence Variant (ASV) richness was similar across the three zones, however, the bacterial community composition and soil physicochemistry differed across the intact and degraded zones. We identified, via correlation, the potential drivers of microbial community composition as soil density, pH and the ratio of Ca to Mg. The restored zone was intermediate between the intact and degraded zones. The differences in the microbial communities appeared to be driven by the presence of plants, with plant-associated taxa more common in the intact zone. The dominant taxa in the degraded zone were cosmopolitan organisms, that have been reported globally in a wide variety of habitats. This study provides baseline information on the changes of the soil bacterial community of a spatially restricted and threatened biome. It also provides a starting point for further studies on community composition and function concerning the restoration of degraded succulent thicket ecosystems.},
}
@article {pmid34707578,
year = {2021},
author = {Lluansí, A and Llirós, M and Oliver, L and Bahí, A and Elias-Masiques, N and Gonzalez, M and Benejam, P and Cueva, E and Termes, M and Ramió-Pujol, S and Malagón, M and Amoedo, J and Serrano, M and Busquets, D and Torreabla, L and Sabat, M and Buxó, M and Cambra, M and Serra-Pagès, M and Delgado-Aros, S and García-Gil, LJ and Elias, I and Aldeguer, X},
title = {In vitro Prebiotic Effect of Bread-Making Process in Inflammatory Bowel Disease Microbiome.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {716307},
pmid = {34707578},
issn = {1664-302X},
abstract = {Inflammatory bowel disease (IBD), including its two main categories (Crohn's disease and ulcerative colitis), has been linked both to gut microbiota and to diet. Bread is a daily food that has a potential capacity as a prebiotic. Our aim was to evaluate different bread-making processes and their effect on fecal colonic microbiota in IBD patients. The microbial composition of several sourdoughs and dough samples was analyzed by high-throughput sequencing of 16S and 18S rRNA genes. Three types of bread, which followed different bread-making processes, were in vitro digested and incubated with feces from IBD patients. Changes in gut microbiota were assessed by a quantitative polymerase chain reaction using specific bacterial sequence targets. Short-chain fatty acid production was also analyzed by gas chromatography. Lactobacillus sanfranciscensis was the dominant lactic acid bacteria species found in sourdough and bread doughs prepared using sourdough, whereas Saccharomyces cerevisiae was the most dominant yeast in all groups, especially in bread doughs before baking. Differences in microbial composition in raw bread doughs were more related to the type of dough and elaboration than to fermentation time lengths. The analysis of in vitro fecal incubations with bread conditions revealed an increase in most bacterial groups analyzed and short-chain fatty acid production, both in Crohn's disease and ulcerative colitis samples. Most remarkable increases in short-chain fatty acid production mirrored higher abundances of Roseburia species. The potential prebiotic properties observed were mainly obtained when using a high quantity of bread, regardless of bread type. Overall, this study highlights the bacterial dynamics within the bread-making process and the potential prebiotic effect in IBD patients.},
}
@article {pmid34706476,
year = {2021},
author = {Herren, LW and Brewton, RA and Wilking, LE and Tarnowski, ME and Vogel, MA and Lapointe, BE},
title = {Septic systems drive nutrient enrichment of groundwaters and eutrophication in the urbanized Indian River Lagoon, Florida.},
journal = {Marine pollution bulletin},
volume = {172},
number = {},
pages = {112928},
doi = {10.1016/j.marpolbul.2021.112928},
pmid = {34706476},
issn = {1879-3363},
mesh = {Environmental Monitoring ; Eutrophication ; Florida ; *Groundwater ; Harmful Algal Bloom ; Nitrogen/analysis ; Nutrients ; Phosphorus/analysis ; Rivers ; *Water Pollutants, Chemical/analysis ; },
abstract = {Effluent from septic systems can pollute groundwater and surface waters in coastal watersheds. These effects are unknown for the highly urbanized central Indian River Lagoon (CIRL), Florida, where septic systems represent > 50% of wastewater disposal. To better understand these impacts, water quality was assessed along both canals and a tributary that drain into the CIRL. Dissolved nutrient concentrations were higher near septic systems than in natural areas. δ[15]N values of groundwater (+7.2‰), surface water (+5.5‰), and macrophytes (+9.7‰) were within the range for wastewater (>+3‰), as were surface water concentrations of the artificial sweetener sucralose (100 to 1700 ng/L) and fecal indicator bacteria density. These results indicate that septic systems are promoting eutrophication in the CIRL by contributing nutrient pollution to surface water via groundwater. This study demonstrates the need to reduce reliance on septic systems in urbanized coastal communities to improve water quality and subsequently mitigate harmful algal blooms.},
}
@article {pmid34705059,
year = {2023},
author = {Banister, RB and Schwarz, MT and Fine, M and Ritchie, KB and Muller, EM},
title = {Correction to: In stability and Stasis Among the Microbiome of Seagrass Leaves, Roots and Rhizomes, and Nearby Sediments Within a Natural pH Gradient.},
journal = {Microbial ecology},
volume = {85},
number = {4},
pages = {1634},
doi = {10.1007/s00248-021-01903-8},
pmid = {34705059},
issn = {1432-184X},
}
@article {pmid34704828,
year = {2021},
author = {Jensen, M and Wippler, J and Kleiner, M},
title = {Evaluation of RNAlater as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses.},
journal = {Microbiology spectrum},
volume = {9},
number = {2},
pages = {e0142921},
pmid = {34704828},
issn = {2165-0497},
mesh = {Animals ; Annelida/*microbiology/physiology ; Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Phylogeny ; Preservation, Biological/*methods ; Proteomics ; *Symbiosis ; },
abstract = {Field studies are central to environmental microbiology and microbial ecology, because they enable studies of natural microbial communities. Metaproteomics, the study of protein abundances in microbial communities, allows investigators to study these communities "in situ," which requires protein preservation directly in the field because protein abundance patterns can change rapidly after sampling. Ideally, a protein preservative for field deployment works rapidly and preserves the whole proteome, is stable in long-term storage, is nonhazardous and easy to transport, and is available at low cost. Although these requirements might be met by several protein preservatives, an assessment of their suitability under field conditions when targeted for metaproteomic analyses is currently lacking. Here, we compared the protein preservation performance of flash freezing and the preservation solution RNAlater using the marine gutless oligochaete Olavius algarvensis and its symbiotic microbes as a test case. In addition, we evaluated long-term RNAlater storage after 1 day, 1 week, and 4 weeks at room temperature (22°C to 23°C). We evaluated protein preservation using one-dimensional liquid chromatography-tandem mass spectrometry. We found that RNAlater and flash freezing preserved proteins equally well in terms of total numbers of identified proteins and relative abundances of individual proteins, and none of the test time points was altered, compared to time zero. Moreover, we did not find biases against specific taxonomic groups or proteins with particular biochemical properties. Based on our metaproteomic data and the logistical requirements for field deployment, we recommend RNAlater for protein preservation of field-collected samples targeted for metaproteomic analyses. IMPORTANCE Metaproteomics, the large-scale identification and quantification of proteins from microbial communities, provide direct insights into the phenotypes of microorganisms on the molecular level. To ensure the integrity of the metaproteomic data, samples need to be preserved immediately after sampling to avoid changes in protein abundance patterns. In laboratory setups, samples for proteomic analyses are most commonly preserved by flash freezing; however, liquid nitrogen or dry ice is often unavailable at remote field locations, due to their hazardous nature and transport restrictions. Our study shows that RNAlater can serve as a low-hazard, easy-to-transport alternative to flash freezing for field preservation of samples for metaproteomic analyses. We show that RNAlater preserves the metaproteome equally well, compared to flash freezing, and protein abundance patterns remain stable during long-term storage for at least 4 weeks at room temperature.},
}
@article {pmid34703919,
year = {2021},
author = {Grigoryan, AA and Jalique, DR and Stroes-Gascoyne, S and Wolfaardt, GM and Keech, PG and Korber, DR},
title = {Prediction of bacterial functional diversity in clay microcosms.},
journal = {Heliyon},
volume = {7},
number = {10},
pages = {e08131},
pmid = {34703919},
issn = {2405-8440},
abstract = {Microorganisms in clay barriers could affect the long-term performance of waste containers in future deep geological repositories (DGR) for used nuclear fuel through production of corrosive metabolites (e.g., sulfide), which is why clay materials are highly compacted: to reduce both physical space and access to water for microorganisms to grow. However, the highly compacted nature of clays and the resulting low activity or dormancy of microorganisms complicate the extraction of biomarkers (i.e., PLFA, DNA etc.) from such barriers for predictive analysis of microbial risks. In order to overcome these challenges, we have combined culture- and 16S rRNA gene amplicon sequencing-based approaches to describe the functional diversity of microorganisms in several commercial clay products, including two different samples of Wyoming type MX-80 bentonite (Batch 1 and Batch 2), the reference clay for a future Canadian DGR, and Avonlea type Canaprill, a clay sample for comparison. Microorganisms from as-received bentonites were enriched in anoxic 10% w/v clay microcosms for three months at ambient temperature with addition of 10% hydrogen along with presumable indigenous organics and sulfate in the clay. High-throughput sequencing of 16S rRNA gene fragments indicated a high abundance of Gram-positive bacteria of the phylum Firmicutes (82%) in MX-80 Batch 1 incubations. Bacterial libraries from microcosms with MX-80 Batch 2 were enriched with Firmicutes (53%) and Chloroflexi (43%). Firmicutes also significantly contributed (<15%) to the bacterial community in Canaprill clay microcosm, which was dominated by Gram-negative Proteobacteria (>70%). Sequence analysis revealed presence of the bacterial families Peptostreptococcaceae, Clostridiaceae, Peptococcaceae, Bacillaceae, Enterobacteriaceae, Veillonellaceae, Tissierellaceae and Planococcaceae in MX-80 Batch 1 incubations; Bacillaceae, along with unidentified bacteria of the phylum Chloroflexi, in MX-80 Batch 2 clay microcosms, and Pseudomonadaceae, Hydrogenophilaceae, Bacillaceae, Desulfobacteraceae, Desulfobulbaceae, Peptococcaceae, Pelobacteraceae, Alcaligenaceae, Rhodospirillaceae in Canaprill microcosms. Exploration of potential metabolic pathways in the bacterial communities from the clay microcosms suggested variable patterns of sulfur cycling in the different clays with the possible prevalence of bacterial sulfate-reduction in MX-80 bentonite, and probably successive sulfate-reduction/sulfur-oxidation reactions in Canaprill microcosms. Furthermore, analysis of potential metabolic pathways in the bentonite enrichments suggested that bacteria with acid-producing capabilities (i.e., fermenters and acetogens) together with sulfide-producing prokaryotes might perhaps contribute to corrosion risks in clay systems. However, the low activity or dormancy of microorganisms in highly compacted bentonites as a result of severe environmental constraints (e.g., low water activity and high swelling pressure in the confined bentonite) in situ would be expected to largely inhibit bacterial activity in highly compacted clay-based barriers in a future DGR.},
}
@article {pmid34703658,
year = {2021},
author = {Miaow, K and Lacap-Bugler, D and Buckley, HL},
title = {Identifying optimal bioinformatics protocols for aerosol microbial community data.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12065},
pmid = {34703658},
issn = {2167-8359},
abstract = {Microbes are fundamental to Earth's ecosystems, thus understanding ecosystem connectivity through microbial dispersal is key to predicting future ecosystem changes in a warming world. However, aerial microbial dispersal remains poorly understood. Few studies have been performed on bioaerosols (microorganisms and biological fragments suspended in the atmosphere), despite them harboring pathogens and allergens. Most environmental microbes grow poorly in culture, therefore molecular approaches are required to characterize aerial diversity. Bioinformatic tools are needed for processing the next generation sequencing (NGS) data generated from these molecular approaches; however, there are numerous options and choices in the process. These choices can markedly affect key aspects of the data output including relative abundances, diversity, and taxonomy. Bioaerosol samples have relatively little DNA, and often contain novel and proportionally high levels of contaminant organisms, that are difficult to identify. Therefore, bioinformatics choices are of crucial importance. A bioaerosol dataset for bacteria and fungi based on the 16S rRNA gene (16S) and internal transcribed spacer (ITS) DNA sequencing from parks in the metropolitan area of Auckland, Aotearoa New Zealand was used to develop a process for determining the bioinformatics pipeline that would maximize the data amount and quality generated. Two popular tools (Dada2 and USEARCH) were compared for amplicon sequence variant (ASV) inference and generation of an ASV table. A scorecard was created and used to assess multiple outputs and make systematic choices about the most suitable option. The read number and ASVs were assessed, alpha diversity was calculated (Hill numbers), beta diversity (Bray-Curtis distances), differential abundance by site and consistency of ASVs were considered. USEARCH was selected, due to higher consistency in ASVs identified and greater read counts. Taxonomic assignment is highly dependent on the taxonomic database used. Two popular taxonomy databases were compared in terms of number and confidence of assignments, and a combined approach developed that uses information in both databases to maximize the number and confidence of taxonomic assignments. This approach increased the assignment rate by 12-15%, depending on amplicon and the overall assignment was 77% for bacteria and 47% for fungi. Assessment of decontamination using "decontam" and "microDecon" was performed, based on review of ASVs identified as contaminants by each and consideration of the probability of them being legitimate members of the bioaerosol community. For this example, "microDecon's" subtraction approach for removing background contamination was selected. This study demonstrates a systematic approach to determining the optimal bioinformatics pipeline using a multi-criteria scorecard for microbial bioaerosol data. Example code in the R environment for this data processing pipeline is provided.},
}
@article {pmid34703544,
year = {2021},
author = {Schueffl, H and Theiner, S and Hermann, G and Mayr, J and Fronik, P and Groza, D and van Schonhooven, S and Galvez, L and Sommerfeld, NS and Schintlmeister, A and Reipert, S and Wagner, M and Mader, RM and Koellensperger, G and Keppler, BK and Berger, W and Kowol, CR and Legin, A and Heffeter, P},
title = {Albumin-targeting of an oxaliplatin-releasing platinum(iv) prodrug results in pronounced anticancer activity due to endocytotic drug uptake in vivo.},
journal = {Chemical science},
volume = {12},
number = {38},
pages = {12587-12599},
pmid = {34703544},
issn = {2041-6520},
abstract = {Oxaliplatin is a very potent platinum(ii) drug which is frequently used in poly-chemotherapy schemes against advanced colorectal cancer. However, its benefit is limited by severe adverse effects as well as resistance development. Based on their higher tolerability, platinum(iv) prodrugs came into focus of interest. However, comparable to their platinum(ii) counterparts they lack tumor specificity and are frequently prematurely activated in the blood circulation. With the aim to exploit the enhanced albumin consumption and accumulation in the malignant tissue, we have recently developed a new albumin-targeted prodrug, which supposed to release oxaliplatin in a highly tumor-specific manner. In more detail, we designed a platinum(iv) complex containing two maleimide moieties in the axial position (KP2156), which allows selective binding to the cysteine 34. In the present study, diverse cell biological and analytical tools such as laser ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS), isotope labeling, and nano-scale secondary ion mass spectrometry (NanoSIMS) were employed to better understand the in vivo distribution and activation process of KP2156 (in comparison to free oxaliplatin and a non-albumin-binding succinimide analogue). KP2156 forms very stable albumin adducts in the bloodstream resulting in a superior pharmacological profile, such as distinctly prolonged terminal excretion half-life and enhanced effective platinum dose (measured by ICP-MS). The albumin-bound drug is accumulating in the malignant tissue, where it enters the cancer cells via clathrin- and caveolin-dependent endocytosis, and is activated by reduction to release oxaliplatin. This results in profound, long-lasting anticancer activity of KP2156 against CT26 colon cancer tumors in vivo based on cell cycle arrest and apoptotic cell death. Summarizing, albumin-binding of platinum(iv) complexes potently enhances the efficacy of oxaliplatin therapy and should be further developed towards clinical phase I trials.},
}
@article {pmid34700384,
year = {2021},
author = {Zrimec, J and Kokina, M and Jonasson, S and Zorrilla, F and Zelezniak, A},
title = {Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends.},
journal = {mBio},
volume = {12},
number = {5},
pages = {e0215521},
pmid = {34700384},
issn = {2150-7511},
mesh = {Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; *Microbiota ; Plastics/*metabolism ; Seawater/microbiology ; Soil Microbiology ; },
abstract = {Biodegradation is a plausible route toward sustainable management of the millions of tons of plastic waste that have accumulated in terrestrial and marine environments. However, the global diversity of plastic-degrading enzymes remains poorly understood. Taking advantage of global environmental DNA sampling projects, here we constructed hidden Markov models from experimentally verified enzymes and mined ocean and soil metagenomes to assess the global potential of microorganisms to degrade plastics. By controlling for false positives using gut microbiome data, we compiled a catalogue of over 30,000 nonredundant enzyme homologues with the potential to degrade 10 different plastic types. While differences between the ocean and soil microbiomes likely reflect the base compositions of these environments, we find that ocean enzyme abundance increases with depth as a response to plastic pollution and not merely taxonomic composition. By obtaining further pollution measurements, we observed that the abundance of the uncovered enzymes in both ocean and soil habitats significantly correlates with marine and country-specific plastic pollution trends. Our study thus uncovers the earth microbiome's potential to degrade plastics, providing evidence of a measurable effect of plastic pollution on the global microbial ecology as well as a useful resource for further applied research. IMPORTANCE Utilization of synthetic biology approaches to enhance current plastic degradation processes is of crucial importance, as natural plastic degradation processes are very slow. For instance, the predicted lifetime of a polyethylene terephthalate (PET) bottle under ambient conditions ranges from 16 to 48 years. Moreover, although there is still unexplored diversity in microbial communities, synergistic degradation of plastics by microorganisms holds great potential to revolutionize the management of global plastic waste. To this end, the methods and data on novel plastic-degrading enzymes presented here can help researchers by (i) providing further information about the taxonomic diversity of such enzymes as well as understanding of the mechanisms and steps involved in the biological breakdown of plastics, (ii) pointing toward the areas with increased availability of novel enzymes, and (iii) giving a basis for further application in industrial plastic waste biodegradation. Importantly, our findings provide evidence of a measurable effect of plastic pollution on the global microbial ecology.},
}
@article {pmid34700143,
year = {2021},
author = {Yang, Y and Azari, M and Herbold, CW and Li, M and Chen, H and Ding, X and Denecke, M and Gu, JD},
title = {Activities and metabolic versatility of distinct anammox bacteria in a full-scale wastewater treatment system.},
journal = {Water research},
volume = {206},
number = {},
pages = {117763},
doi = {10.1016/j.watres.2021.117763},
pmid = {34700143},
issn = {1879-2448},
mesh = {*Ammonium Compounds ; Anaerobiosis ; Bacteria/genetics ; Bioreactors ; Ecosystem ; Nitrogen ; Oxidation-Reduction ; *Water Purification ; },
abstract = {Anaerobic ammonium oxidation (anammox) is a key N2-producing process in the global nitrogen cycle. Major progress in understanding the core mechanism of anammox bacteria has been made, but our knowledge of the survival strategies of anammox bacteria in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Here, by combining metagenomics with in situ metatranscriptomics, complex anammox-driven nitrogen cycles in an anoxic tank and a granular activated carbon (GAC) biofilm module of a full-scale WWTP treating landfill leachate were constructed. Four distinct anammox metagenome-assembled genomes (MAGs), representing a new genus named Ca. Loosdrechtii, a new species in Ca. Kuenenia, a new species in Ca. Brocadia, and a new strain in "Ca. Kuenenia stuttgartiensis", were simultaneously retrieved from the GAC biofilm. Metabolic reconstruction revealed that all anammox organisms highly expressed the core metabolic enzymes and showed a high metabolic versatility. Pathways for dissimilatory nitrate reduction to ammonium (DNRA) coupled to volatile fatty acids (VFAs) oxidation likely assist anammox bacteria to survive unfavorable conditions and facilitate switches between lifestyles in oxygen fluctuating environments. The new Ca. Kuenenia species dominated the anammox community of the GAC biofilm, specifically may be enhanced by the uniquely encoded flexible ammonium and iron acquisition strategies. The new Ca. Brocadia species likely has an extensive niche distribution that is simultaneously established in the anoxic tank and the GAC biofilm, the two distinct niches. The highly diverse and impressive metabolic versatility of anammox bacteria revealed in this study advance our understanding of the survival and application of anammox bacteria in the full-scale wastewater treatment system.},
}
@article {pmid34697646,
year = {2022},
author = {Tighilt, L and Boulila, F and De Sousa, BFS and Giraud, E and Ruiz-Argüeso, T and Palacios, JM and Imperial, J and Rey, L},
title = {The Bradyrhizobium Sp. LmicA16 Type VI Secretion System Is Required for Efficient Nodulation of Lupinus Spp.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {844-855},
pmid = {34697646},
issn = {1432-184X},
support = {RTI2018-094985-B-100//ministerio de ciencia tecnolog&#xed;a y telecomunicaciones/ ; CNPq-GDE-204842/2018-2//cnpq brazil/ ; Erasmus+ Programme project 2019-1-ES01-KA107-063778//erasmus +/ ; National Exceptional Program (PNE)//ministry of higher education and scientific research of algeria/ ; ANR- 16-CE20-0013//anr grants (fr)/ ; ANR-20-CE20-0012//anr (fr)/ ; },
mesh = {*Bradyrhizobium/genetics ; *Lupinus/microbiology ; *Type VI Secretion Systems/genetics ; Root Nodules, Plant/microbiology ; Phylogeny ; Symbiosis/genetics ; },
abstract = {Many bacteria of the genus Bradyrhizobium are capable of inducing nodules in legumes. In this work, the importance of a type VI secretion system (T6SS) in a symbiotic strain of the genus Bradyrhizobium is described. T6SS of Bradyrhizobium sp. LmicA16 (A16) is necessary for efficient nodulation with Lupinus micranthus and Lupinus angustifolius. A mutant in the gene vgrG, coding for a component of the T6SS nanostructure, induced less nodules and smaller plants than the wild-type (wt) strain and was less competitive when co-inoculated with the wt strain. A16 T6SS genes are organized in a 26-kb DNA region in two divergent gene clusters of nine genes each. One of these genes codes for a protein (Tsb1) of unknown function but containing a methyltransferase domain. A tsb1 mutant showed an intermediate symbiotic phenotype regarding vgrG mutant and higher mucoidity than the wt strain in free-living conditions. T6SS promoter fusions to the lacZ reporter indicate expression in nodules but not in free-living cells grown in different media and conditions. The analysis of nodule structure revealed that the level of nodule colonization was significantly reduced in the mutants with respect to the wt strain.},
}
@article {pmid34696369,
year = {2021},
author = {Hasiów-Jaroszewska, B and Boezen, D and Zwart, MP},
title = {Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities.},
journal = {Viruses},
volume = {13},
number = {10},
pages = {},
pmid = {34696369},
issn = {1999-4915},
mesh = {Biodiversity ; Computational Biology/methods ; DNA Viruses/genetics ; Genome, Viral/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Metagenomics/*methods ; Plant Weeds/*genetics/*virology ; Plants/genetics/virology ; Viruses/classification/genetics ; Viruses, Unclassified/genetics ; },
abstract = {High throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection - often in the absence of disease symptoms - and tend to discover many novel viruses, highlighting the small fraction of virus biodiversity described to date. The majority of the studies using high-throughput sequencing to characterise plant viromes have focused on economically important crops, and only a small number of studies have considered weeds and wild plants. Characterising the viromes of wild plants is highly relevant, as these plants can affect disease dynamics in crops, often by acting as viral reservoirs. Moreover, the viruses in unmanaged systems may also have important effects on wild plant populations and communities. Here, we review metagenomic studies on weeds and wild plants to show the benefits and limitations of this approach and identify knowledge gaps. We consider key genomics developments that are likely to benefit the field in the near future. Although only a small number of HTS studies have been performed on weeds and wild plants, these studies have already discovered many novel viruses, demonstrated unexpected trends in virus distributions, and highlighted the potential of metagenomics as an approach.},
}
@article {pmid34695355,
year = {2021},
author = {Fu, Y and Jia, M and Wang, F and Wang, Z and Mei, Z and Bian, Y and Jiang, X and Virta, M and Tiedje, JM},
title = {Strategy for Mitigating Antibiotic Resistance by Biochar and Hyperaccumulators in Cadmium and Oxytetracycline Co-contaminated Soil.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {24},
pages = {16369-16378},
doi = {10.1021/acs.est.1c03434},
pmid = {34695355},
issn = {1520-5851},
mesh = {Anti-Bacterial Agents/pharmacology ; Biodegradation, Environmental ; Cadmium ; Charcoal ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Manure ; *Oxytetracycline ; Soil ; Soil Microbiology ; },
abstract = {The global prevalence of antibiotic resistance genes (ARGs) is of increasing concern as a serious threat to ecological security and human health. Irrigation with sewage and farmland application of manure or biosolids in agricultural practices introduce substantial selective agents such as antibiotics and toxic metals, aggravating the transfer of ARGs from the soil environment to humans via the food chain. To address this issue, a hyperaccumulator (Sedum plumbizincicola) combined with biochar amendment was first used to investigate the mitigation of the prevalence of ARGs in cadmium and oxytetracycline co-contaminated soil by conducting a pot experiment. The addition of biochar affected the distribution of ARGs in soil and plants differently by enhancing their prevalence in the soil but restraining transmission from the soil to S. plumbizincicola. The planting of S. plumbizincicola resulted in an increase in ARGs in the soil environment. A structural equation model illustrated that mobile genetic elements played a dominant role in shaping the profile of ARGs. Taken together, these findings provide a practical understanding for mitigating the prevalence of ARGs in this soil system with complex contamination and can have profound significance for agricultural management in regard to ARG dissemination control.},
}
@article {pmid34694450,
year = {2022},
author = {Yang, X and Li, Y and Niu, B and Chen, Q and Hu, Y and Yang, Y and Song, L and Wang, J and Zhang, G},
title = {Temperature and Precipitation Drive Elevational Patterns of Microbial Beta Diversity in Alpine Grasslands.},
journal = {Microbial ecology},
volume = {84},
number = {4},
pages = {1141-1153},
doi = {10.1007/s00248-021-01901-w},
pmid = {34694450},
issn = {1432-184X},
support = {41871066//national natural science foundation of china/ ; 41471055//national natural science foundation of china/ ; XDA20050101//strategic priority research program (a) of the chinese academy of sciences/ ; 2019QZKK0503//second tibetan plateau scientific expedition and research program (step)/ ; },
mesh = {*Grassland ; *Ecosystem ; Temperature ; Biodiversity ; Soil/chemistry ; Archaea ; Bacteria/genetics ; },
abstract = {Understanding the mechanisms underlying biodiversity patterns is a central issue in ecology, while how temperature and precipitation jointly control the elevational patterns of microbes is understudied. Here, we studied the effects of temperature, precipitation and their interactions on the alpha and beta diversity of soil archaea and bacteria in alpine grasslands along an elevational gradient of 4300-5200 m on the Tibetan Plateau. Alpha diversity was examined on the basis of species richness and evenness, and beta diversity was quantified with the recently developed metric of local contributions to beta diversity (LCBD). Typical alpine steppe and meadow ecosystems were distributed below and above 4850 m, respectively, which was consistent with the two main constraints of mean annual temperature (MAT) and mean annual precipitation (MAP). Species richness and evenness showed decreasing elevational patterns in archaea and nonsignificant or U-shaped patterns in bacteria. The LCBD of both groups exhibited significant U-shaped elevational patterns, with the lowest values occurring at 4800 m. For the three diversity metrics, soil pH was the primary explanatory variable in archaea, explaining over 20.1% of the observed variation, whereas vegetation richness, total nitrogen and the K/Al ratio presented the strongest effects on bacteria, with relative importance values of 16.1%, 12.5% and 11.6%, respectively. For the microbial community composition of both archaea and bacteria, the moisture index showed the dominant effect, explaining 17.6% of the observed variation, followed by MAT and MAP. Taken together, temperature and precipitation exerted considerable indirect effects on microbial richness and evenness through local environmental and energy supply-related variables, such as vegetation richness, whereas temperature exerted a larger direct influence on LCBD and the community composition. Our findings highlighted the profound influence of temperature and precipitation interactions on microbial beta diversity in alpine grasslands on the Tibetan Plateau.},
}
@article {pmid34693460,
year = {2022},
author = {Zada, S and Sajjad, W and Rafiq, M and Ali, S and Hu, Z and Wang, H and Cai, R},
title = {Cave Microbes as a Potential Source of Drugs Development in the Modern Era.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {676-687},
pmid = {34693460},
issn = {1432-184X},
support = {32070113//national natural science foundation of china/ ; 2019ST023//guangdong science and technology department/ ; 2020PC0052//pifi fellowship from the chinese academy of sciences/ ; },
mesh = {Humans ; *Caves ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The world is constantly facing threats, including the emergence of new pathogens and antibiotic resistance among extant pathogens, which is a matter of concern. Therefore, the need for natural and effective sources of drugs is inevitable. The ancient and pristine ecosystems of caves contain a unique microbial world and could provide a possible source of antimicrobial metabolites. The association between humans and caves is as old as human history itself. Historically, cave environments have been used to treat patients with respiratory tract infections, which is referred to as speleotherapy. Today, the pristine environment of caves that comprise a poorly explored microbial world is a potential source of antimicrobial and anticancer drugs. Oligotrophic conditions in caves enhance the competition among microbial communities, and unique antimicrobial agents may be used in this competition. This review suggests that the world needs a novel and effective source of drug discovery. Therefore, being the emerging spot of modern human civilization, caves could play a crucial role in the current medical crisis, and cave microorganisms may have the potential to produce novel antimicrobial and anticancer drugs.},
}
@article {pmid34693062,
year = {2021},
author = {Lahlali, R and Ibrahim, DSS and Belabess, Z and Kadir Roni, MZ and Radouane, N and Vicente, CSL and Menéndez, E and Mokrini, F and Barka, EA and Galvão de Melo E Mota, M and Peng, G},
title = {High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects.},
journal = {Heliyon},
volume = {7},
number = {10},
pages = {e08142},
pmid = {34693062},
issn = {2405-8440},
abstract = {Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.},
}
@article {pmid34690949,
year = {2021},
author = {Sichert, A and Cordero, OX},
title = {Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {705082},
pmid = {34690949},
issn = {1664-302X},
abstract = {Microbes have the unique ability to break down the complex polysaccharides that make up the bulk of organic matter, initiating a cascade of events that leads to their recycling. Traditionally, the rate of organic matter degradation is perceived to be limited by the chemical and physical structure of polymers. Recent advances in microbial ecology, however, suggest that polysaccharide persistence can result from non-linear growth dynamics created by the coexistence of alternate degradation strategies, metabolic roles as well as by ecological interactions between microbes. This complex "landscape" of degradation strategies and interspecific interactions present in natural microbial communities appears to be far from evolutionarily stable, as frequent gene gain and loss reshape enzymatic repertoires and metabolic roles. In this perspective, we discuss six challenges at the heart of this problem, ranging from the evolution of genetic repertoires, phenotypic heterogeneity in clonal populations, the development of a trait-based ecology, and the impact of metabolic interactions and microbial cooperation on degradation rates. We aim to reframe some of the key questions in the study of polysaccharide-bacteria interactions in the context of eco-evolutionary dynamics, highlighting possible research directions that, if pursued, would advance our understanding of polysaccharide degraders at the interface between biochemistry, ecology and evolution.},
}
@article {pmid34688835,
year = {2022},
author = {Arca-Suárez, J and Rodiño-Janeiro, BK and Pérez, A and Guijarro-Sánchez, P and Vázquez-Ucha, JC and Cruz, F and Gómez-Garrido, J and Alioto, TS and Álvarez-Tejado, M and Gut, M and Gut, I and Oviaño, M and Beceiro, A and Bou, G and , },
title = {Emergence of 16S rRNA methyltransferases among carbapenemase-producing Enterobacterales in Spain studied by whole-genome sequencing.},
journal = {International journal of antimicrobial agents},
volume = {59},
number = {1},
pages = {106456},
doi = {10.1016/j.ijantimicag.2021.106456},
pmid = {34688835},
issn = {1872-7913},
mesh = {Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/*genetics/*metabolism ; Genetic Variation ; Genome-Wide Association Study ; Genotype ; Humans ; Methyltransferases/*genetics/*metabolism ; RNA, Ribosomal, 16S/*genetics ; Spain ; beta-Lactamases/*genetics/*metabolism ; },
abstract = {The emergence of 16S rRNA methyltransferases (RMTs) in Gram-negative pathogens bearing other clinically relevant resistance mechanisms, such as carbapenemase-producing Enterobacterales (CPE), is becoming an alarming concern. We investigated the prevalence, antimicrobial susceptibility, resistance mechanisms, molecular epidemiology and genetic support of RMTs in CPE isolates from Spain. This study included a collection of 468 CPE isolates recovered during 2018 from 32 participating Spanish hospitals. MICs were determined using the broth microdilution method, the agar dilution method (fosfomycin) or MIC gradient strips (plazomicin). All isolates were subjected to hybrid whole-genome sequencing (WGS). Sequence types (STs), core genome phylogenetic relatedness, horizontally acquired resistance mechanisms, plasmid analysis and the genetic environment of RMTs were determined in silico from WGS data in all RMT-positive isolates. Among the 468 CPE isolates evaluated, 24 isolates (5.1%) recovered from nine different hospitals spanning five Spanish regions showed resistance to all aminoglycosides and were positive for an RMT (21 RmtF, 2 ArmA and 1 RmtC). All RMT-producers showed high-level resistance to all aminoglycosides, including plazomicin, and in most cases exhibited an extensively drug-resistant susceptibility profile. The RMT-positive isolates showed low genetic diversity and were global clones of Klebsiella pneumoniae (ST147, ST101, ST395) and Enterobacter cloacae (ST93) bearing blaOXA-48, blaNDM-1 or blaVIM-1 carbapenemase genes. RMTs were harboured in five different multidrug resistance plasmids and linked to efficient mobile genetic elements. Our findings highlight that RMTs are emerging among clinical CPE isolates from Spain and their spread should be monitored to preserve the future clinical utility of aminoglycosides and plazomicin.},
}
@article {pmid34688084,
year = {2021},
author = {Uroosa, and Kazmi, SSUH and Zhong, X and Xu, H},
title = {An approach to evaluating the acute toxicity of nitrofurazone on community functioning using protozoan periphytons.},
journal = {Marine pollution bulletin},
volume = {173},
number = {Pt B},
pages = {113066},
doi = {10.1016/j.marpolbul.2021.113066},
pmid = {34688084},
issn = {1879-3363},
mesh = {Ecosystem ; *Nitrofurazone/toxicity ; *Periphyton ; Phenotype ; },
abstract = {The acute toxicity of nitrofurazone on community functioning was studied using an acute toxicity test. Consequently, 14-day protozoan periphyton assemblages were used as test organism communities, under a range of nitrofurazone concentrations including 0 (control), 0.5, 3, 6, and 12 mg ml[-1] within 0, 2, 4, 6, 8, 10, and 12 h time duration. Fuzzy coding system of functional traits classified the test protozoan periphyton community into six major traits and 15 categories. Briefly, community-weighted means (CWM) were used to identify the community functioning of test protozoan assemblage. Inferences demonstrate a drastic/significant variation in the functional patterns of the test organisms at a high concentration (12 mg ml[-1]) after an exposure time of 12 h, but the functional diversity indices leveled off at the exposure time of 10 h and then dropped sharply. These results suggested that nitrofurazone may significantly influence the community functioning in marine ecosystems.},
}
@article {pmid34687997,
year = {2022},
author = {Macías-Pérez, LA and Levard, C and Barakat, M and Angeletti, B and Borschneck, D and Poizat, L and Achouak, W and Auffan, M},
title = {Contrasted microbial community colonization of a bauxite residue deposit marked by a complex geochemical context.},
journal = {Journal of hazardous materials},
volume = {424},
number = {Pt B},
pages = {127470},
doi = {10.1016/j.jhazmat.2021.127470},
pmid = {34687997},
issn = {1873-3336},
mesh = {*Aluminum Oxide ; Biodegradation, Environmental ; *Microbiota ; Soil ; Soil Microbiology ; },
abstract = {Bauxite residue is the alkaline byproduct generated during alumina extraction and is commonly landfilled in open-air deposits. The growth in global alumina production have raised environmental concerns about these deposits since no large-scale reuses exist to date. Microbial-driven techniques including bioremediation and critical metal bio-recovery are now considered sustainable and cost-effective methods to revalorize bauxite residues. However, the establishment of microbial communities and their active role in these strategies are still poorly understood. We thus determined the geochemical composition of different bauxite residues produced in southern France and explored the development of bacterial and fungal communities using Illumina high-throughput sequencing. Physicochemical parameters were influenced differently by the deposit age and the bauxite origin. Taxonomical analysis revealed an early-stage microbial community dominated by haloalkaliphilic microorganisms and strongly influenced by chemical gradients. Microbial richness, diversity and network complexity increased significantly with the deposit age, reaching an equilibrium community composition similar to typical soils after decades of natural weathering. Our results suggested that salinity, pH, and toxic metals affected the bacterial community structure, while fungal community composition showed no clear correlations with chemical variations.},
}
@article {pmid34686899,
year = {2022},
author = {McLeish, AG and Gong, S and Greenfield, P and Midgley, DJ and Paulsen, IT},
title = {Microbial Community Shifts on Organic Rocks of Different Maturities Reveal potential Catabolisers of Organic Matter in Coal.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {780-793},
pmid = {34686899},
issn = {1432-184X},
support = {2017708//Macquarie University/ ; },
mesh = {*Coal ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; *Microbiota ; Microbial Consortia/genetics ; },
abstract = {The global trend of transiting to more renewable energy sources requires transition fuels, such as coal seam gas, to supplement and secure energy needs. In order to optimise strategies and technologies for enhancing gas production, an understanding of the fundamental microbial processes and interactions would be advantageous. Models have recently begun mapping the microbial roles and interactions in coal seam environments, from direct coal degradation to methanogenesis. This study seeks to expand those models by observing community compositional shifts in the presence of differing organic matter by conducting 16S rRNA microbial surveys using formation water from the Surat and Sydney Basins grown on varying types of organic matter (black and brown coal, oil shale, humic acid, and lignin). A total of 135 microbes were observed to become enriched in the presence of added organic matter in comparison to carbon-free treatments. These surveys allowed detailed analysis of microbial compositions in order to extrapolate which taxa favour growth in the presence of differing organic matter. This study has experimentally demonstrated shifts in the microbial community composition due to differing carbon sources and, for the first time, generated a conceptual model to map putative degradation pathways regarding subsurface microbial consortia.},
}
@article {pmid34686898,
year = {2022},
author = {Qi, R and Xue, N and Zhou, X and Zhao, L and Song, W and Yang, Y},
title = {Distinct Composition and Assembly Processes of Bacterial Communities in a River from the Arid Area: Ecotypes or Habitat Types?.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {769-779},
pmid = {34686898},
issn = {1432-184X},
mesh = {Humans ; *Rivers/microbiology ; Water Microbiology ; Ecotype ; Bacteria/genetics/metabolism ; *Microbiota ; Water/metabolism ; },
abstract = {The composition, function, and assembly mechanism of the bacterial community are the focus of microbial ecology. Unsupervised machine learning may be a better way to understand the characteristics of bacterial metacommunities compared to the empirical habitat types. In this study, the composition, potential function, and assembly mechanism of the bacterial community in the arid river were analysed. The Dirichlet multinomial mixture method recognised four ecotypes across the three habitats (biofilm, water, and sediment). The bacterial communities in water are more sensitive to human activities. Bacterial diversity and richness in water decreased as the intensity of human activities increased from the region of water II to water I. Significant differences in the composition and potential function profile of bacterial communities between water ecotypes were also observed, such as higher relative abundance in the taxonomic composition of Firmicutes and potential function of plastic degradation in water I than those in water II. Habitat filtering may play a more critical role in the assembly of bacterial communities in the river biofilm, while stochastic processes dominate the assembly process of bacterial communities in water and sediment. In water I, salinity and mean annual precipitation were the main drivers shaping the biogeography of taxonomic structure, while mean annual temperature, total organic carbon, and ammonium nitrogen were the main environmental factors influencing the taxonomic structure in water II. These results would provide conceptual frameworks about choosing habitat types or ecotypes for the research of microbial communities among different niches in the aquatic environment.},
}
@article {pmid34683463,
year = {2021},
author = {Van den Abbeele, P and Duysburgh, C and Cleenwerck, I and Albers, R and Marzorati, M and Mercenier, A},
title = {Consistent Prebiotic Effects of Carrot RG-I on the Gut Microbiota of Four Human Adult Donors in the SHIME[®] Model despite Baseline Individual Variability.},
journal = {Microorganisms},
volume = {9},
number = {10},
pages = {},
pmid = {34683463},
issn = {2076-2607},
abstract = {The human gut microbiome is currently recognized to play a vital role in human biology and development, with diet as a major modulator. Therefore, novel indigestible polysaccharides that confer a health benefit upon their fermentation by the microbiome are under investigation. Based on the recently demonstrated prebiotic potential of a carrot-derived pectin extract enriched for rhamnogalacturonan I (cRG-I), the current study aimed to assess the impact of cRG-I upon repeated administration using the M-SHIME technology (3 weeks at 3g cRG-I/d). Consistent effects across four simulated adult donors included enhanced levels of acetate (+21.1 mM), propionate (+17.6 mM), and to a lesser extent butyrate (+4.1 mM), coinciding with a marked increase of OTUs related to Bacteroides dorei and Prevotella species with versatile enzymatic potential likely allowing them to serve as primary degraders of cRG-I. These Bacteroidetes members are able to produce succinate, explaining the consistent increase of an OTU related to the succinate-converting Phascolarctobacterium faecium (+0.47 log10(cells/mL)). While the Bifidobacteriaceae family remained unaffected, a specific OTU related to Bifidobacterium longum increased significantly upon cRG-I treatment (+1.32 log10(cells/mL)). Additional monoculture experiments suggested that Bifidobacterium species are unable to ferment cRG-I structures as such and that B. longum probably feeds on arabinan and galactan side chains of cRG-I, released by aforementioned Bacteroidetes members. Overall, this study confirms the prebiotic potential of cRG-I and additionally highlights the marked consistency of the microbial changes observed across simulated subjects, suggesting the involvement of a specialized consortium in cRG-I fermentation by the human gut microbiome.},
}
@article {pmid34683446,
year = {2021},
author = {Bi, S and Lai, H and Guo, D and Liu, X and Wang, G and Chen, X and Liu, S and Yi, H and Su, Y and Li, G},
title = {The Characteristics of Intestinal Bacterial Community in Three Omnivorous Fishes and Their Interaction with Microbiota from Habitats.},
journal = {Microorganisms},
volume = {9},
number = {10},
pages = {},
pmid = {34683446},
issn = {2076-2607},
support = {31772853//National Natural Science Foundation of China/ ; },
abstract = {Artificial fishery habitats have been extensively used for fishery resource protection and water habitat restoration, and they could attract a large number of omnivorous fishes to gather together. This study intended to reveal the relationship between bacterial communities in the habitats (water and sediment) and intestines of omnivorous fishes (Oreochromis mossambicus, Toxabramis houdemeri and Hemiculter leucisculus). Therefore, we investigated the bacterial communities of samples collected from intestines, water, and sediments in artificial fishery habitats via 16S rRNA metabarcoding high-throughput sequencing technology. The results showed that there were significant differences in the composition, core indicators, diversity and prediction functions in water, sediments, and intestinal microbial communities of the three omnivorous fish. The microbial diversities were significantly higher in habitats than in intestines. The analysis of similarity (ANOSIM) and nonmetric multidimensional scaling (NMDS) results indicated that the intestine microbial communities (T. houdemeri and H. leucisculus) were more similar to the water microbiota, but the intestine microbial communities (O. mossambicus) were more similar to the sediments. Source tracking analysis also confirmed that the contribution of habitat characteristics to omnivorous fish intestinal microorganisms was different; the sediment had a greater contribution than water to the intestinal microbiota of O. mossambicus, which was consistent with their benthic habit. Moreover, the functional prediction results showed that there were unique core indicators and functions between the bacterial community of habitats and intestines. Altogether, these results can enhance our understanding of the bacterial composition and functions about omnivorous fish intestines and their living with habitats, which have provided new information for the ecological benefits of artificial fishery habitats from the perspective of bacterial ecology and contributed to apply artificial fishery habitats in more rivers.},
}
@article {pmid34683378,
year = {2021},
author = {Wang, Y and Brons, JK and van Elsas, JD},
title = {Considerations on the Identity and Diversity of Organisms Affiliated with Sphingobacterium multivorum-Proposal for a New Species, Sphingobacterium paramultivorum.},
journal = {Microorganisms},
volume = {9},
number = {10},
pages = {},
pmid = {34683378},
issn = {2076-2607},
support = {201706240132//China Scholarship Council/ ; },
abstract = {Plant biomass offers great potential as a sustainable resource, and microbial consortia are primordial in its bioconversion. The wheat-straw-biodegradative bacterial strain w15 has drawn much attention as a result of its biodegradative potential and superior degradation performance in bacterial-fungal consortia. Strain w15 was originally assigned to the species Sphingobacterium multivorum based on its 16S ribosomal RNA (rRNA) gene sequence. A closer examination of this taxonomic placement revealed that the sequence used has 98.9% identity with the 'divergent' 16S rRNA gene sequence of S. multivorum NCTC 11343[T], yet lower relatedness with the canonical 16S rRNA sequence. A specific region of the gene, located between positions 186 and 210, was found to be highly variable and determinative for the divergence. To solve the identity of strain w15, genome metrics and analyses of ecophysiological niches were undertaken on a selection of strains assigned to S. multivorum and related species. These analyses separated all strains into three clusters, with strain w15, together with strain BIGb0170, constituting a separate radiation, next to S. multivorum and S. siyangense. Moreover, the strains denoted FDAARGOS 1141 and 1142 were placed inside S. siyangense. We propose the renaming of strains w15 and BIGb0170 as members of the novel species, coined Sphingobacterium paramultivorum.},
}
@article {pmid34683332,
year = {2021},
author = {Amat, S and Holman, DB and Schmidt, K and Menezes, ACB and Baumgaertner, F and Winders, T and Kirsch, JD and Liu, T and Schwinghamer, TD and Sedivec, KK and Dahlen, CR},
title = {The Nasopharyngeal, Ruminal, and Vaginal Microbiota and the Core Taxa Shared across These Microbiomes in Virgin Yearling Heifers Exposed to Divergent In Utero Nutrition during Their First Trimester of Gestation and in Pregnant Beef Heifers in Response to Mineral Supplementation.},
journal = {Microorganisms},
volume = {9},
number = {10},
pages = {},
pmid = {34683332},
issn = {2076-2607},
abstract = {In the present study, we evaluated whether the nasopharyngeal, ruminal, and vaginal microbiota would diverge (1) in virgin yearling beef heifers (9 months old) due to the maternal restricted gain during the first trimester of gestation; and (2) in pregnant beef heifers in response to the vitamin and mineral (VTM) supplementation during the first 6 months of pregnancy. As a secondary objective, using the microbiota data obtained from these two cohorts of beef heifers managed at the same location and sampled at the same time, we performed a holistic assessment of the microbial ecology residing within the respiratory, gastrointestinal, and reproductive tract of cattle. Our 16S rRNA gene sequencing results revealed that both α and β-diversity of the nasopharyngeal, ruminal and vaginal microbiota did not differ between virgin heifers raised from dams exposed to either a low gain (targeted average daily gain of 0.28 kg/d, n = 22) or a moderate gain treatment (0.79 kg/d, n = 23) during the first 84 days of gestation. Only in the vaginal microbiota were there relatively abundant genera that were affected by maternal rate of gain during early gestation. Whilst there was no significant difference in community structure and diversity in any of the three microbiota between pregnant heifers received no VTM (n = 15) and VTM supplemented (n = 17) diets, the VTM supplementation resulted in subtle compositional alterations in the nasopharyngeal and ruminal microbiota. Although the nasopharyngeal, ruminal, and vaginal microbiota were clearly distinct, a total of 41 OTUs, including methanogenic archaea, were identified as core taxa shared across the respiratory, gastrointestinal, and reproductive tracts of both virgin and pregnant heifers.},
}
@article {pmid34678684,
year = {2021},
author = {de Freitas Nunes Oliveira, A and Saboya de Sousa, LI and Silva da Costa, VA and de Andrade, JVT and Lucena Lima, LA and de Sales, PAF and da Silva, DF and de Araujo Pereira, AP and Maciel Melo, VM},
title = {Long-term effects of grazing on the biological, chemical, and physical soil properties of the Caatinga biome.},
journal = {Microbiological research},
volume = {253},
number = {},
pages = {126893},
doi = {10.1016/j.micres.2021.126893},
pmid = {34678684},
issn = {1618-0623},
mesh = {Animals ; Brazil ; *Ecosystem ; *Herbivory ; Microbiota/physiology ; Nitrophenols/analysis ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {Soil degradation is a global issue that affects both plant productivity and human life. Intensive grazing practices can accelerate this process, mainly due to rapid removal of biomass from the soil surface. However, the long-term effects of grazing on biological, chemical, and physical properties remain poorly understood, particularly in tropical drylands, such as the Caatinga biome. Our aim was to evaluate the soil properties and combine both culture-dependent and -independent analyses to assess metabolic activity and bacterial community structure. We collected samples (0-20 cm) of three different types of soil in the Caatinga biome: secondary Caatinga forest (NC), grazing exclusion (GE), and degraded areas by overgrazing (OG). We sought to investigate how grazing affects soil properties to determine the effectiveness of grazing exclusion in the restoration of soil fertility/functions. Redundancy analysis demonstrated NC were positively correlated with organic carbon (λ = 0.18, p = 0.0012) and total nitrogen (λ = 0.16, p = 0.0011), while OG was correlated with harmful soil parameters such as Na[+] (λ = 0.08, p = 0.0400), electric conductivity (λ = 0.13, p = 0.0060) and exchangeable acidity (λ = 0.11, p = 0.0030). In addition, GE showed lower aluminum content and saturation, reducing these harmful parameters by 48 % and 34 %, respectively. Also, GE showed the highest values for the β-glucosidase (63.62 mg ρ-nitrophenol kg[-1] h[-1]) and arylsulfatase (5.8 mg ρ-nitrophenol kg[-1] h[-1]) activities. Changes in bacterial community structure were significant (p = 0.0096), with a higher difference comparing GE and OG (p = 0.0135). The GE area showed 20 % more phosphate solubilizers than OG, but there were no differences for siderophores production. All isolates were halotolerant and had at least 60 % nitrogen fixers. Our findings indicate that while soil recovery is slow, with grazing-exclusion areas presenting 18 years of implantation, it seems to improve in subsequent years. Finally, our results provide evidence that microbe-based technologies can mitigate soil degradation in the Caatinga biome.},
}
@article {pmid34678229,
year = {2022},
author = {Alderliesten, JB and Zwart, MP and de Visser, JAGM and Stegeman, A and Fischer, EAJ},
title = {Second compartment widens plasmid invasion conditions: Two-compartment pair-formation model of conjugation in the gut.},
journal = {Journal of theoretical biology},
volume = {533},
number = {},
pages = {110937},
doi = {10.1016/j.jtbi.2021.110937},
pmid = {34678229},
issn = {1095-8541},
mesh = {Animals ; Bacteria ; *Conjugation, Genetic ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; },
abstract = {Understanding under which conditions conjugative plasmids encoding antibiotic resistance can invade bacterial communities in the gut is of particular interest to combat the spread of antibiotic resistance within and between animals and humans. We extended a one-compartment model of conjugation to a two-compartment model, to analyse how differences in plasmid dynamics in the gut lumen and at the gut wall affect the invasion of plasmids. We compared scenarios with one and two compartments, different migration rates between the lumen and wall compartments, and different population dynamics. We focused on the effect of attachment and detachment rates on plasmid dynamics, explicitly describing pair formation followed by plasmid transfer in the pairs. The parameter space allowing plasmid invasion in the one-compartment model is affected by plasmid costs and intrinsic conjugation rates of the transconjugant, but not by these characteristics of the donor. The parameter space allowing plasmid invasion in the two-compartment model is affected by attachment and detachment rates in the lumen and wall compartment, and by the bacterial density at the wall. The one- and two-compartment models predict the same parameter space for plasmid invasion if the conditions in both compartments are equal to the conditions in the one-compartment model. In contrast, the addition of the wall compartment widens the parameter space allowing invasion compared with the one-compartment model, if the density at the wall is higher than in the lumen, or if the attachment rate at the wall is high and the detachment rate at the wall is low. We also compared the pair-formation models with bulk-conjugation models that describe conjugation by instantaneous transfer of the plasmid at contact between cells, without explicitly describing pair formation. Our results show that pair-formation and bulk-conjugation models predict the same parameter space for plasmid invasion. From our simulations, we conclude that conditions at the gut wall should be taken into account to describe plasmid dynamics in the gut and that transconjugant characteristics rather than donor characteristics should be used to parameterize the models.},
}
@article {pmid34676439,
year = {2022},
author = {Sadiq, FA and Wenwei, L and Wei, C and Jianxin, Z and Zhang, H},
title = {Transcriptional Changes in Bifidobacterium bifidum Involved in Synergistic Multispecies Biofilms.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {922-934},
pmid = {34676439},
issn = {1432-184X},
support = {31871774//National Natural Science Foundation of China/ ; JUSRP51903B//the Fundamental Research Funds for the Central Universities/ ; JUFSTR20180102//the National First-class Discipline Program of Food Science and Technology/ ; },
mesh = {Infant ; Humans ; *Bifidobacterium bifidum/metabolism ; Bifidobacterium/genetics/metabolism ; *Gastrointestinal Microbiome ; Biofilms ; *Microbiota ; },
abstract = {Bifidobacterium bifidum is part of the core microbiota of healthy infant guts where it may form biofilms on epithelial cells, mucosa, and food particles in the gut lumen. Little is known about transcriptional changes in B. bifidum engaged in synergistic multispecies biofilms with ecologically relevant species of the human gut. Recently, we reported prevalence of synergism in mixed-species biofilms formed by the human gut microbiota. This study represents a comparative gene expression analysis of B. bifidum when grown in a single-species biofilm and in two multispecies biofilm consortia with Bifidobacterium longum subsp. infantis, Bacteroides ovatus, and Parabacteroides distasonis in order to identify genes involved in this adaptive process in mixed biofilms and the influence on its metabolic and functional traits. Changes up to 58% and 43% in its genome were found when it grew in three- and four-species biofilm consortia, respectively. Upregulation of genes of B. bifidum involved in carbohydrate metabolism (particularly the galE gene), quorum sensing (luxS and pfs), and amino acid metabolism (especially branched chain amino acids) in both multispecies biofilms, compared to single-species biofilms, suggest that they may be contributing factors for the observed synergistic biofilm production when B. bifidum coexists with other species in a biofilm.},
}
@article {pmid34676060,
year = {2021},
author = {Li, H and Sun, J and Wang, X and Shi, J},
title = {Oral microbial diversity analysis among atrophic glossitis patients and healthy individuals.},
journal = {Journal of oral microbiology},
volume = {13},
number = {1},
pages = {1984063},
pmid = {34676060},
issn = {2000-2297},
abstract = {Atrophic glossitis is a common disease in oral mucosal diseases. The Current studies have found the human oral cavity contains numerous and diverse microorganisms, their composition and diversity can be changed by various oral diseases. To understand the composition and diversity of oral microbiome in atrophic glossitis is better to explore the cause and mechanism of atrophic glossitis. The salivary microbiome is comprised of indigenous oral microorganisms that are specific to each person, exhibits long-term stability. We used llumina MiSeq high-throughput sequencing based on the V3-V4 region of the bacterial 16S rRNA gene and the internal transcribed spacer (ITS) region of fungal rRNA genes from saliva in atrophic glossitis patients and healthy individuals to explore the composition and diversity of oral microbiome. In our reports, it showed a lower diversity of bacteria and fungi in atrophic glossitis patients than in healthy individuals. The data further suggests that Lactobacillus and Saccharomycetales were potential indicators for the initiation and development of atrophic glossitis. Moreover, we also discuss the relationship between the oral microbial ecology and atrophic glossitis.},
}
@article {pmid34674014,
year = {2022},
author = {Agbulu, V and Zaman, R and Ishangulyyeva, G and Cahill, JF and Erbilgin, N},
title = {Host Defense Metabolites Alter the Interactions between a Bark Beetle and its Symbiotic Fungi.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {834-843},
pmid = {34674014},
issn = {1432-184X},
mesh = {Animals ; *Coleoptera/microbiology ; Plant Bark ; *Pinus/microbiology ; Symbiosis ; *Weevils/microbiology ; Monoterpenes/metabolism ; },
abstract = {Successful host plant colonization by tree-killing bark beetle-symbiotic fungal complexes depends on host suitability, which is largely determined by host defense metabolites such as monoterpenes. Studies have shown the ability of specific blends of host monoterpenes to influence bark beetles or their fungal symbionts, but how biologically relevant blends of host monoterpenes influence bark beetle-symbiotic fungal interaction is unknown. We tested how interactions between two host species (lodgepole pine or jack pine) and two fungal symbionts of mountain pine beetle (Grosmannia clavigera or Ophiostoma montium) affect the performance of adult female beetles in vitro. Beetles treated with the propagules of G. clavigera or O. montium or not treated (natural fungal load) were introduced into media amended with a blend of the entire monoterpene profile of either host species and beetle performance was compared. Overall, host blends altered beetle performance depending on the fungal species used in the beetle amendment. When beetles were amended with G. clavigera, their performance was superior over beetles amended with O. montium in either host blend. Furthermore, G. clavigera-amended beetles performed better in media amended with host blends than without a host blend; in contrast, O. montium-amended beetles performed better in media without a host blend than with a host blend. Overall, this study showed that host defense metabolites affect host suitability to bark beetles through influencing their fungal symbionts and that different species of fungal symbionts respond differentlly to host defense metabolites.},
}
@article {pmid34673954,
year = {2021},
author = {Wang, D and Du, Y and Huang, S and You, Z and Zheng, D and Liu, Y},
title = {Combined supplementation of sodium humate and glutamine reduced diarrhea incidence of weaned calves by intestinal microbiota and metabolites changes.},
journal = {Journal of animal science},
volume = {99},
number = {11},
pages = {},
pmid = {34673954},
issn = {1525-3163},
mesh = {Animal Feed/analysis ; Animals ; Cattle ; Diarrhea/prevention &amp; control/veterinary ; Diet/veterinary ; Dietary Supplements ; *Gastrointestinal Microbiome ; *Glutamine ; Incidence ; Sodium ; Weaning ; },
abstract = {This study was conducted to investigate the effects of combined supplementation of sodium humate (HNa) and glutamine (Gln) on growth performance, diarrhea incidence, serum parameters, intestinal microbiome, and metabolites of weaned calves. In Exp. 1, 40 calves were randomly assigned to four treatments: 1) NC (negative control, basal diet), 2) 1% H+1% G (basal diet extra orally gavaged with 1 g of HNa and 1 g of Gln daily), 3) 3% H+1% G (basal diet extra orally gavaged with 3 g of HNa and 1 g of Gln daily), and 4) 5% H+1% G (basal diet extra orally gavaged with 5 g of HNa and 1 g of Gln daily). The HNa and Gln were together mixed with 100 mL of milk replacer (51 to 58 d of age) or water (59 to 72 d of age) and orally administrated to each calf from a bottle before morning feeding. In a 21-d trial, calves on the 5% HNa+1% Gln group had higher (P < 0.05) average daily gain (ADG) and lower (P < 0.05) diarrhea incidence than those in the control group. In Exp. 2, 20 calves were randomly assigned to two treatments fed with a basal diet and a basal diet supplemented with 100 mL of 5% HNa+1% Gln. In a 21-d trial, calves supplemented with HNa and Gln had higher (P < 0.05) ADG, IgG concentration and glutathione peroxidase (GSH-Px), and total antioxidant capacity (T-AOC) activities in the serum, but lower (P < 0.05) diarrhea incidence, as well as serum diamine oxidase (DAO), D-isomer of lactic acid (D-lac), tumor necrosis factor-α (TNF-α), and malondialdehyde (MDA) concentrations compared with control group. Results of intestinal microbiota indicated that supplementation with HNa and Gln significantly increased (P < 0.05) the abundance of intestinal beneficial microbiota. Moreover, supplementation with HNa and Gln altered 18 metabolites and enriched 6 Kyoto Encyclopedia of Genes and Genomes pathways in weaned calves. In conclusion, combined supplementation with HNa and Gln could decrease diarrhea incidence of weaned calves via altering intestinal microbial ecology and metabolism profile.},
}
@article {pmid34672730,
year = {2021},
author = {Hussain, FA and Dubert, J and Elsherbini, J and Murphy, M and VanInsberghe, D and Arevalo, P and Kauffman, K and Rodino-Janeiro, BK and Gavin, H and Gomez, A and Lopatina, A and Le Roux, F and Polz, MF},
title = {Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages.},
journal = {Science (New York, N.Y.)},
volume = {374},
number = {6566},
pages = {488-492},
doi = {10.1126/science.abb1083},
pmid = {34672730},
issn = {1095-9203},
mesh = {Bacteriophages/*pathogenicity ; Evolution, Molecular ; Genetic Variation ; *Interspersed Repetitive Sequences ; Vibrio/*genetics/*virology ; },
abstract = {Although it is generally accepted that phages drive bacterial evolution, how these dynamics play out in the wild remains poorly understood. We found that susceptibility to viral killing in marine Vibrio is mediated by large and highly diverse mobile genetic elements. These phage defense elements display exceedingly fast evolutionary turnover, resulting in differential phage susceptibility among clonal bacterial strains while phage receptors remain invariant. Protection is cumulative, and a single bacterial genome can harbor 6 to 12 defense elements, accounting for more than 90% of the flexible genome among close relatives. The rapid turnover of these elements decouples phage resistance from other genomic features. Thus, resistance to phages in the wild follows evolutionary trajectories alternative to those predicted from laboratory-based evolutionary experiments.},
}
@article {pmid34671827,
year = {2022},
author = {Carbajal-Valenzuela, IA and Muñoz-Sanchez, AH and Hernández-Hernández, J and Barona-Gómez, F and Truong, C and Cibrián-Jaramillo, A},
title = {Microbial Diversity in Cultivated and Feral Vanilla Vanilla planifolia Orchids Affected by Stem and Rot Disease.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {821-833},
pmid = {34671827},
issn = {1432-184X},
support = {285746//consejo nacional de ciencia y tecnolog&#xed;a/ ; 180631//newton fund/ ; },
mesh = {Humans ; *Vanilla/microbiology ; *Microbiota ; DNA, Ribosomal ; Bacteria/genetics ; Mexico ; },
abstract = {The worldwide production of vanilla, a native orchid from Mexico, is greatly affected by stem and root rot disease (SRD), typically associated with Fusarium oxysporum fungi. We hypothesized that the presence of Fusarium species in vanilla is not sufficient for the plant to express symptoms of the disease. We described the taxonomic composition of endophytic microbiomes in symptomatic and asymptomatic vanilla plants using 16S and ITS rDNA metabarcoding, and ITS Sanger sequences generated from fungal isolates. We compared the bacterial and fungal diversity in vanilla plants from a long-term plantation, and from feral plants found near abandoned plantations that did not present SRD symptoms. No significant differences were found in the species richness of the bacterial and fungal microbiome among feral, or asymptomatic and symptomatic cultivated vanilla. However, significant differences were detected in both fungal and bacterial diversity from different organs in the same plant, with roots being more diverse than stems. We found that Proteobacteria and Actinobacteria, as well as the fungal families Nectriaceae and Xylariaceae, constitute the core of the vanilla microbiome that inhabits the root and stem of both cultivated and feral plants. Our work provides information on the microbial diversity associated to root and stem rot in vanilla and lays the groundwork for a better understanding of the role of the microbiome in vanilla fungal diseases.},
}
@article {pmid34671826,
year = {2022},
author = {Neely, WJ and Greenspan, SE and Stahl, LM and Heraghty, SD and Marshall, VM and Atkinson, CL and Becker, CG},
title = {Habitat Disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {901-910},
pmid = {34671826},
issn = {1432-184X},
support = {Start-up fund//the university of alabama/ ; Walter F. Coxe Research Fund//alabama audubon/ ; },
mesh = {Animals ; *Chytridiomycota ; Batrachochytrium ; *Mycoses/microbiology ; *Microbiota ; Ranidae/microbiology ; Bacteria ; Anura ; },
abstract = {Anthropogenic habitat disturbances can dramatically alter ecological community interactions, including host-pathogen dynamics. Recent work has highlighted the potential for habitat disturbances to alter host-associated microbial communities, but the associations between anthropogenic disturbance, host microbiomes, and pathogens are unresolved. Amphibian skin microbial communities are particularly responsive to factors like temperature, physiochemistry, pathogen infection, and environmental microbial reservoirs. Through a field survey on wild populations of Acris crepitans (Hylidae) and Lithobates catesbeianus (Ranidae), we assessed the effects of habitat disturbance and connectivity on environmental bacterial reservoirs, Batrachochytrium dendrobatidis (Bd) infection, and skin microbiome composition. We found higher measures of microbiome dispersion (a measure of community variability) in A. crepitans from more disturbed ponds, supporting the hypothesis that disturbance increases stochasticity in biological communities. We also found that habitat disturbance limited microbiome similarity between locations for both species, suggesting greater isolation of bacterial assemblages in more disturbed areas. Higher disturbance was associated with lower Bd prevalence for A. crepitans, which could signify suboptimal microclimates for Bd in disturbed habitats. Combined, our findings show that reduced microbiome stability stemming from habitat disturbance could compromise population health, even in the absence of pathogenic infection.},
}
@article {pmid34671825,
year = {2022},
author = {Liu, L and Wang, S and Yang, J and Chen, J},
title = {Nutrient Removal in Eutrophic Water Promotes Stability of Planktonic Bacterial and Protist Communities.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {759-768},
pmid = {34671825},
issn = {1432-184X},
support = {31971469//National Natural Science Foundation of China/ ; XDA23040302//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; GXRC-20061//Qishan Scholar Program of Fuzhou University/ ; 2019-JJFDKY-71//Research Project of Development Center of Science and Education Park, Fuzhou University (JinJiang)/ ; },
mesh = {*Plankton/genetics ; *Water ; Ecosystem ; Eutrophication ; Phosphorus ; Eukaryota/genetics ; Nitrogen ; Bacteria/genetics ; Nutrients ; },
abstract = {Nutrient (nitrogen and phosphorus) removal by using bioremediation technologies in eutrophic water alters bacterial and protist community structure and function, but how it changes the stability of community remains unclear. To fill this gap, in this study, bacterial and protist communities were investigated using 16S and 18S rRNA gene high-throughput sequencing during the nutrient removal by using ecological floating beds of Canna indica L. Our results showed that both bacterial and protist community compositions in the treatment group were similar to those in the control group at the beginning of the experiment (day 1 to day 11), but then bacterial and protist community compositions became more stable with the removal of nutrients in the treatment group than those in the control group (day 12 to day 18). We further explored the mechanisms for this increased stability and found that the contribution of the stochastic process to bacterial and protist community variations was higher in the control group than that in the treatment group. This suggests that the high nutrient concentration in the control group might increase the random colonization or extinction, and therefore resulted in the high temporal variability (i.e., unstable) of bacterial and protist communities. Our findings suggest that bioremediation for eutrophication can promote the stability of aquatic communities, and therefore potentially maintain aquatic ecosystem functions and services to humanity.},
}
@article {pmid34671091,
year = {2021},
author = {Song, C and Fu, F and Yang, L and Niu, Y and Tian, Z and He, X and Yang, X and Chen, J and Sun, W and Wan, T and Zhang, H and Yang, Y and Xiao, T and Dossa, K and Meng, X and Cao, F and Van de Peer, Y and Wang, G and Chen, S},
title = {Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {1203},
pmid = {34671091},
issn = {2399-3642},
mesh = {Cycadopsida/*classification ; *Evolution, Molecular ; *Genome, Plant ; Paclitaxel/*biosynthesis ; *Phylogeny ; Taxus/*genetics ; },
abstract = {Taxol, a natural product derived from Taxus, is one of the most effective natural anticancer drugs and the biosynthetic pathway of Taxol is the basis of heterologous bio-production. Here, we report a high-quality genome assembly and annotation of Taxus yunnanensis based on 10.7 Gb sequences assembled into 12 chromosomes with contig N50 and scaffold N50 of 2.89 Mb and 966.80 Mb, respectively. Phylogenomic analyses show that T. yunnanensis is most closely related to Sequoiadendron giganteum among the sampled taxa, with an estimated divergence time of 133.4-213.0 MYA. As with most gymnosperms, and unlike most angiosperms, there is no evidence of a recent whole-genome duplication in T. yunnanensis. Repetitive sequences, especially long terminal repeat retrotransposons, are prevalent in the T. yunnanensis genome, contributing to its large genome size. We further integrated genomic and transcriptomic data to unveil clusters of genes involved in Taxol synthesis, located on the chromosome 12, while gene families encoding hydroxylase in the Taxol pathway exhibited significant expansion. Our study contributes to the further elucidation of gymnosperm relationships and the Taxol biosynthetic pathway.},
}
@article {pmid34669476,
year = {2021},
author = {Zaoli, S and Grilli, J},
title = {A macroecological description of alternative stable states reproduces intra- and inter-host variability of gut microbiome.},
journal = {Science advances},
volume = {7},
number = {43},
pages = {eabj2882},
pmid = {34669476},
issn = {2375-2548},
abstract = {The most fundamental questions in microbial ecology concern the diversity and variability of communities. Their composition varies widely across space and time, as a result of a nontrivial combination of stochastic and deterministic processes. The interplay between nonlinear community dynamics and environmental fluctuations determines the rich statistical structure of community variability. We analyze long time series of individual human gut microbiomes and compare intra- and intercommunity dissimilarity under a macroecological framework. We show that most taxa have large but stationary fluctuations over time, while a minority of taxa display rapid changes in average abundance that cluster in time, suggesting the presence of alternative stable states. We disentangle interindividual variability in a stochastic component and a deterministic one, the latter recapitulated by differences in carrying capacities. Last, by combining environmental fluctuations and alternative stable states, we introduce a model that quantitatively predicts the statistical properties of both intra- and interindividual community variability, therefore summarizing variation in a unique macroecological framework.},
}
@article {pmid34669447,
year = {2022},
author = {Mendiola, SY and Stoy, KS and DiSalvo, S and Wynn, CL and Civitello, DJ and Gerardo, NM},
title = {Competitive Exclusion of Phytopathogenic Serratia marcescens from Squash Bug Vectors by the Gut Endosymbiont Caballeronia.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {1},
pages = {e0155021},
pmid = {34669447},
issn = {1098-5336},
support = {1R01 AI150774-01//HHS | National Institutes of Health (NIH)/ ; R01 AI150774/AI/NIAID NIH HHS/United States ; NIFA 2019-67013-29371//U.S. Department of Agriculture (USDA)/ ; RC Lewontin Graduate Research Excellence//Society for the Study of Evolution (SSE)/ ; NSF IOS-1755002//National Science Foundation (NSF)/ ; DGE-1444932//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Burkholderiaceae ; *Heteroptera ; Insecta ; Serratia marcescens ; Symbiosis ; },
abstract = {Many insects harbor microbial symbiotic partners that offer protection against pathogens, parasitoids, and other natural enemies. Mounting evidence suggests that these symbiotic microbes can play key roles in determining infection outcomes in insect vectors, making them important players in the quest to develop novel vector control strategies. Using the squash bug Anasa tristis, we investigated how the presence of Caballeronia symbionts affected the persistence and intensity of phytopathogenic Serratia marcescens within the insect vector. We reared insects aposymbiotically and with different Caballeronia isolates, infected them with S. marcescens, and then sampled the insects periodically to assess the intensity and persistence of pathogen infection. Squash bugs harboring Caballeronia consistently had much lower-intensity infections and cleared S. marcescens significantly faster than their aposymbiotic counterparts. These patterns held even when we reversed the timing of exposure to symbiont and pathogen. Taken together, these results indicate that Caballeronia symbionts play an essential role in S. marcescens infection outcomes in squash bugs and could be used to alter vector competence to enhance agricultural productivity in the future. IMPORTANCE Insect-microbe symbioses have repeatedly been shown to profoundly impact an insect's ability to vector pathogens to other hosts. The use of symbiotic microbes to control insect vector populations is of growing interest in agricultural settings. Our study examines how symbiotic microbes affect the dynamics of a plant pathogen infection within the squash bug vector Anasa tristis, a well-documented pest of squash and other cucurbit plants and a vector of Serratia marcescens, the causative agent of cucurbit yellow vine disease. We provide evidence that the symbiont Caballeronia prevents successful, long-term establishment of S. marcescens in the squash bug. These findings give us insight into symbiont-pathogen dynamics within the squash bug that could ultimately determine its ability to transmit pathogens and be leveraged to interrupt disease transmission in this system.},
}
@article {pmid34669436,
year = {2022},
author = {Luna, E and Parkar, SG and Kirmiz, N and Hartel, S and Hearn, E and Hossine, M and Kurdian, A and Mendoza, C and Orr, K and Padilla, L and Ramirez, K and Salcedo, P and Serrano, E and Choudhury, B and Paulchakrabarti, M and Parker, CT and Huynh, S and Cooper, K and Flores, GE},
title = {Utilization Efficiency of Human Milk Oligosaccharides by Human-Associated Akkermansia Is Strain Dependent.},
journal = {Applied and environmental microbiology},
volume = {88},
number = {1},
pages = {e0148721},
pmid = {34669436},
issn = {1098-5336},
support = {SC2 GM122620/GM/NIGMS NIH HHS/United States ; T15 LM009451/LM/NLM NIH HHS/United States ; UL1 GM118976/GM/NIGMS NIH HHS/United States ; RL5 GM118975/GM/NIGMS NIH HHS/United States ; TL4 GM118977/GM/NIGMS NIH HHS/United States ; SC1 GM136546/GM/NIGMS NIH HHS/United States ; },
mesh = {Akkermansia ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Milk, Human ; Oligosaccharides ; Verrucomicrobia ; },
abstract = {Akkermansia muciniphila is a mucin-degrading bacterium found in the human gut and is often associated with positive human health. However, despite being detected by as early as 1 month of age, little is known about the role of Akkermansia in the infant gut. Human milk oligosaccharides (HMOs) are abundant components of human milk and are structurally similar to the oligosaccharides that comprise mucin, the preferred growth substrate of human-associated Akkermansia. A limited subset of intestinal bacteria has been shown to grow well on HMOs and mucin. We therefore examined the ability of genomically diverse strains of Akkermansia to grow on HMOs. First, we screened 85 genomes representing the four known Akkermansia phylogroups to examine their metabolic potential to degrade HMOs. Furthermore, we examined the ability of representative isolates to grow on individual HMOs in a mucin background and analyzed the resulting metabolites. All Akkermansia genomes were equipped with an array of glycoside hydrolases associated with HMO deconstruction. Representative strains were all able to grow on HMOs with various efficiencies and growth yields. Strain CSUN-19, belonging to the AmIV phylogroup, grew to the highest level in the presence of fucosylated and sialylated HMOs. This activity may be partially related to the increased copy numbers and/or the enzyme activities of the α-fucosidases, α-sialidases, and β-galactosidases. This study examines the utilization of individual purified HMOs by Akkermansia strains representing all known phylogroups. Further studies are required to examine how HMO ingestion influences gut microbial ecology in infants harboring different Akkermansia phylogroups. IMPORTANCE Human milk oligosaccharides (HMOs) are the third most abundant component of breast milk and provide several benefits to developing infants, including the recruitment of beneficial bacteria to the human gut. Akkermansia strains are largely considered beneficial bacteria and have been detected in colostrum, breast milk, and young infants. A. muciniphila Muc[T], belonging to the AmI phylogroup, contributes to the HMO deconstruction capacity of the infant. Here, using phylogenomics, we examined the genomic capacities of four Akkermansia phylogroups to deconstruct HMOs. Indeed, each phylogroup contained differences in their genomic capacities to deconstruct HMOs, and representative strains of each phylogroup were able to grow using HMOs. These Akkermansia-HMO interactions potentially influence gut microbial ecology in early life, a critical time for the development of the gut microbiome and infant health.},
}
@article {pmid34668755,
year = {2021},
author = {Kim, T and Behrens, S and LaPara, TM},
title = {Microbial Community Composition in Municipal Wastewater Treatment Bioreactors Follows a Distance Decay Pattern Primarily Controlled by Environmental Heterogeneity.},
journal = {mSphere},
volume = {6},
number = {5},
pages = {e0064821},
pmid = {34668755},
issn = {2379-5042},
mesh = {Bioreactors/*microbiology ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Seasons ; Sequence Analysis, DNA ; Sewage/*microbiology ; Wastewater/*microbiology ; Water Purification ; },
abstract = {Understanding spatiotemporal patterns in microbial community composition is a central goal of microbial ecology. The objective of this study was to better understand the biogeography of activated sludge microbial communities, which are important for the protection of surface water quality. Monthly samples were collected from 20 facilities (25 bioreactors) within 442 km of each other for 1 year. Microbial community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Statistically significant distance decay of community similarity was observed in these bioreactors independent of clustering method (operational taxonomic units [OTUs] at 97% similarity, genus-level phylotypes) and community dissimilarity metric (Sørensen, Bray-Curtis, and weighted Unifrac). Universal colonizers (i.e., detected in all samples) and ubiquitous genus-level phylotypes (i.e., detected in every facility at least once) also exhibited a significant distance decay relationship. Variation partitioning analysis of community composition showed that environmental characteristics (temperature, influent characteristics, etc.) explained more of the variance in community composition than geographic distance did, suggesting that environmental heterogeneity is more important than dispersal limitation as a mechanism for determining microbial community composition. Distance decay relationships also became stronger with increasing distance between facilities. Seasonal variation in community composition was also observed from selected bioreactors, but there was no clear seasonal pattern in the distance decay relationships. IMPORTANCE Understanding the spatiotemporal patterns of biodiversity is a central goal of ecology. The distance decay of community similarity is one of the spatial scaling patterns observed in many forms of life, including plants, animals, and microbial communities. Municipal wastewater treatment relies on microorganisms to prevent the release of excessive quantities of nutrients and other pollutants, but relatively few studies have explored distance decay relationships in wastewater treatment bioreactors. Our results demonstrate a strong distance decay pattern in wastewater treatment bioreactors, regardless of the sequence clustering method or the community dissimilarity metric. Our results suggest that microbial communities in wastewater treatment bioreactors are not randomly assembled but rather exhibit a statistically significant spatial pattern.},
}
@article {pmid34668729,
year = {2021},
author = {Coleman, A and Zaugg, J and Wood, A and Cottrell, K and Håkansson, EG and Adams, J and Brown, M and Cervin, A and Bialasiewicz, S},
title = {Upper Respiratory Tract Microbiome of Australian Aboriginal and Torres Strait Islander Children in Ear and Nose Health and Disease.},
journal = {Microbiology spectrum},
volume = {9},
number = {2},
pages = {e0036721},
pmid = {34668729},
issn = {2165-0497},
mesh = {Australia/epidemiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Child ; Child, Preschool ; Ear/*microbiology ; Female ; Health Status ; Humans ; Male ; Microbiota/*genetics/physiology ; Nasal Cavity/*microbiology ; Nasal Mucosa/microbiology ; Nasopharynx/microbiology ; Native Hawaiian or Other Pacific Islander/*statistics &amp; numerical data ; Otitis Media/*epidemiology/microbiology ; Persistent Infection/microbiology ; RNA, Ribosomal, 16S/genetics ; Respiratory System/microbiology ; },
abstract = {The objective of this study was to examine the nasal microbiota in relation to otitis media (OM) status and nose health in Indigenous Australian children. Children 2 to 7 years of age were recruited from two northern Australian (Queensland) communities. Clinical histories were obtained through parent interviews and reviews of the medical records. Nasal cavity swab samples were obtained, and the children's ears, nose, and throat were examined. DNA was extracted and analyzed by 16S rRNA amplicon next-generation sequencing of the V3/V4 region, in combination with previously generated culture data. A total of 103 children were recruited (mean age, 4.7 years); 17 (16.8%) were healthy, i.e., normal examination results and no history of OM. The nasal microbiota differed significantly in relation to OM status and nose health. Children with historical OM had greater relative abundance of Moraxella, compared to healthy children, despite both having healthy ears at the time of swabbing. Children with healthy noses had greater relative abundance of Staphylococcus aureus, compared to those with rhinorrhea. Dolosigranulum was correlated with Corynebacterium in healthy children. Haemophilus and Streptococcus were correlated across phenotypes. Ornithobacterium was absent or was present with low relative abundance in healthy children and clustered around otopathogens. It correlated with Helcococcus and Dichelobacter. Dolosigranulum and Corynebacterium form a synergism that promotes upper respiratory tract (URT)/ear health in Indigenous Australian children. Ornithobacterium likely represents "Candidatus Ornithobacterium hominis" and in this population is correlated with a novel bacterium that appears to be related to poor URT/ear health. IMPORTANCE Recurring and chronic infections of the ear (OM) are disproportionately prevalent in disadvantaged communities across the globe and, in particular, within Indigenous communities. Despite numerous intervention strategies, OM persists as a major health issue and is the leading cause of preventable hearing loss. In disadvantaged communities, this hearing loss is associated with negative educational and social development outcomes, and consequently, poorer employment prospects and increased contact with the justice system in adulthood. Thus, a better understanding of the microbial ecology is needed in order to identify new targets to treat, as well as to prevent the infections. This study used a powerful combination of 16S rRNA gene sequencing and extended culturomics to show that Dolosigranulum pigrum, a bacterium previously identified as a candidate protective species, may require cocolonization with Corynebacterium pseudodiphtheriticum in order to prevent OM. Additionally, emerging and potentially novel pathogens and bacteria were identified.},
}
@article {pmid34665776,
year = {2021},
author = {Abello, JJM and Malajacan, GT and Labrador, KL and Nacario, MAG and Galarion, LH and Obusan, MCM and Rivera, WL},
title = {Library-independent source tracking of fecal contamination in selected stations and tributaries of Laguna Lake, Philippines.},
journal = {Journal of water and health},
volume = {19},
number = {5},
pages = {846-854},
doi = {10.2166/wh.2021.058},
pmid = {34665776},
issn = {1477-8920},
mesh = {Animals ; Cattle ; *Environmental Monitoring ; Feces ; *Lakes ; Philippines ; Rivers ; Swine ; Water Microbiology ; Water Pollution/analysis ; },
abstract = {Laguna Lake is the largest inland freshwater body in the Philippines. Although it is classified to be usable for agricultural and recreational purposes by the country's Department of Environment and Natural Resources (DENR), studies looking at lake ecology revealed severe fecal contamination which contributes to the deterioration of water quality. Determining the sources of fecal contamination is necessary for lake protection and management. This study utilized a library-independent method of microbial source tracking (LIM-MST) to identify sources of fecal contamination in selected Laguna Lake stations and tributaries. Genetic markers of the host-associated Escherichia coli, heat-labile toxin (LTIIA) and heat-stable II (STII), were used to identify cattle and swine fecal contaminations, respectively. Meanwhile, human mitochondrial DNA (mtDNA) was used to identify human fecal contamination. Results identified the presence of agricultural and human fecal contamination in Laguna Lake Stations 1 and 5, Mangangate River, and Alabang River. The selected sites are known to be surrounded by residential and industrial complexes, and most of their discharges find their way into the lake. The identification of the specific sources of fecal contamination will guide management practices that aim to regulate the discharges in order to improve the water quality of Laguna Lake.},
}
@article {pmid34665286,
year = {2022},
author = {Xie, W and Yan, Y and Hu, J and Dong, P and Hou, D and Zhang, H and Yao, Z and Zhu, X and Zhang, D},
title = {Ecological Dynamics and Co-occurrences Among Prokaryotes and Microeukaryotes in a Diatom Bloom Process in Xiangshan Bay, China.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {746-758},
pmid = {34665286},
issn = {1432-184X},
support = {42076158//the National Natural Science Foundation of China/ ; 41706132//the National Natural Science Foundation of China/ ; SJLY2020005//the Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; },
mesh = {*Diatoms ; Bays/microbiology ; *Dinoflagellida ; *Alphaproteobacteria ; *Gammaproteobacteria ; },
abstract = {Diatom blooms can significantly affect the succession of microbial communities, yet little is known about the assembly processes and interactions of microbial communities during autumn bloom events. In this study, we investigated the ecological effects of an autumn diatom bloom on prokaryotic communities (PCCs) and microeukaryotic communities (MECs), focusing on their assembly processes and interactions. The PCCs were largely dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Flavobacteria, while the MECs primarily included Diatomea, Dinoflagellata, and Chlorophyta. The succession of both PCCs and MECs was mainly driven by this diatom bloom and environmental factors, such as nitrate and silicate. Null modeling revealed that homogeneous selection had a more pronounced impact on the structure of PCCs compared with that of MECs. In particular, drift and dispersal limitation cannot be neglected in the assembly processes of MECs. Co-occurrence network analyses showed that Litorimicrobium, Cercozoa, Marine Group I (MGI), Cryptomonadales, Myrionecta, and Micromonas may affect the bloom process. In summary, these results elucidated the complex, robust interactions and obviously distinct assembly mechanisms of PCCs and MECs during a diatom bloom and extend our current comprehension of the ecological mechanisms and microbial interactions involved in an autumn diatom bloom process.},
}
@article {pmid34662276,
year = {2021},
author = {Jones, ML and Rivett, DW and Pascual-García, A and Bell, T},
title = {Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34662276},
issn = {2050-084X},
mesh = {*Microbiota ; Pseudomonas fluorescens/genetics/*physiology ; Pseudomonas putida/genetics/*physiology ; },
abstract = {Common garden experiments that inoculate a standardised growth medium with synthetic microbial communities (i.e. constructed from individual isolates or using dilution cultures) suggest that the ability of the community to resist invasions by additional microbial taxa can be predicted by the overall community productivity (broadly defined as cumulative cell density and/or growth rate). However, to the best of our knowledge, no common garden study has yet investigated the relationship between microbial community composition and invasion resistance in microcosms whose compositional differences reflect natural, rather than laboratory-designed, variation. We conducted experimental invasions of two bacterial strains (Pseudomonas fluorescens and Pseudomonas putida) into laboratory microcosms inoculated with 680 different mixtures of bacteria derived from naturally occurring microbial communities collected in the field. Using 16S rRNA gene amplicon sequencing to characterise microcosm starting composition, and high-throughput assays of community phenotypes including productivity and invader survival, we determined that productivity is a key predictor of invasion resistance in natural microbial communities, substantially mediating the effect of composition on invasion resistance. The results suggest that similar general principles govern invasion in artificial and natural communities, and that factors affecting resident community productivity should be a focal point for future microbial invasion experiments.},
}
@article {pmid34661728,
year = {2022},
author = {Znój, A and Gawor, J and Gromadka, R and Chwedorzewska, KJ and Grzesiak, J},
title = {Root-Associated Bacteria Community Characteristics of Antarctic Plants: Deschampsia antarctica and Colobanthus quitensis-a Comparison.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {808-820},
pmid = {34661728},
issn = {1432-184X},
support = {2016/21/N/NZ9/01536//narodowe centrum nauki/ ; },
mesh = {Antarctic Regions ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Caryophyllaceae/genetics/microbiology ; Plants ; Bacteria/genetics ; },
abstract = {Colobanthus quitensis (Kunth) Bartl. and Deschampsia antarctica Desv. are the only Magnoliophyta to naturally colonize the Antarctic region. The reason for their sole presence in Antarctica is still debated as there is no definitive consensus on how only two unrelated flowering plants managed to establish breeding populations in this part of the world. In this study, we have explored and compared the rhizosphere and root-endosphere dwelling microbial community of C. quitensis and D. antarctica specimens sampled in maritime Antarctica from sites displaying contrasting edaphic characteristics. Bacterial phylogenetic diversity (high-throughput 16S rRNA gene fragment targeted sequencing) and microbial metabolic activity (Biolog EcoPlates) with a geochemical soil background were assessed. Gathered data showed that the microbiome of C. quitensis root system was mostly site-dependent, displaying different characteristics in each of the examined locations. This plant tolerated an active bacterial community only in severe conditions (salt stress and nutrient deprivation), while in other more favorable circumstances, it restricted microbial activity, with a possibility of microbivory-based nutrient acquisition. The microbial communities of D. antarctica showed a high degree of similarity between samples within a particular rhizocompartment. The grass' endosphere was significantly enriched in plant beneficial taxa of the family Rhizobiaceae, which displayed obligatory endophyte characteristics, suggesting that at least part of this community is transmitted vertically. Ultimately, the ecological success of C. quitensis and D. antarctica in Antarctica might be largely attributed to their associations and management of root-associated microbiota.},
}
@article {pmid34654483,
year = {2021},
author = {Gloder, G and Bourne, ME and Verreth, C and Wilberts, L and Bossaert, S and Crauwels, S and Dicke, M and Poelman, EH and Jacquemyn, H and Lievens, B},
title = {Parasitism by endoparasitoid wasps alters the internal but not the external microbiome in host caterpillars.},
journal = {Animal microbiome},
volume = {3},
number = {1},
pages = {73},
pmid = {34654483},
issn = {2524-4671},
support = {FWO//Fonds Wetenschappelijk Onderzoek/ ; G.0961.19N//Fonds Wetenschappelijk Onderzoek/ ; ALWOP.343//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; ALWOP.368//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {BACKGROUND: The microbiome of many insects consists of a diverse community of microorganisms that can play critical roles in the functioning and overall health of their hosts. Although the microbial communities of insects have been studied thoroughly over the past decade, little is still known about how biotic interactions affect the microbial community structure in and on the bodies of insects. In insects that are attacked by parasites or parasitoids, it can be expected that the microbiome of the host insect is affected by the presence of these parasitic organisms that develop in close association with their host. In this study, we used high-throughput amplicon sequencing targeting both bacteria and fungi to test the hypothesis that parasitism by the endoparasitoid Cotesia glomerata affected the microbiome of its host Pieris brassicae. Healthy and parasitized caterpillars were collected from both natural populations and a laboratory culture.<br><br>RESULTS: Significant differences in bacterial community structure were found between field-collected caterpillars and laboratory-reared caterpillars, and between the external and the internal microbiome of the caterpillars. Parasitism significantly altered the internal microbiome of caterpillars, but not the external microbiome. The internal microbiome of all parasitized caterpillars and of the parasitoid larvae in the caterpillar hosts was dominated by a Wolbachia strain, which was completely absent in healthy caterpillars, suggesting that the strain was transferred to the caterpillars during oviposition by the parasitoids.<br><br>CONCLUSION: We conclude that biotic interactions such as parasitism have pronounced effects on the microbiome of an insect host and possibly affect interactions with higher-order insects.},
}
@article {pmid34653799,
year = {2021},
author = {Srinivasan, VN and Li, G and Wang, D and Tooker, NB and Dai, Z and Onnis-Hayden, A and Bott, C and Dombrowski, P and Schauer, P and Pinto, A and Gu, AZ},
title = {Oligotyping and metagenomics reveal distinct Candidatus Accumulibacter communities in side-stream versus conventional full-scale enhanced biological phosphorus removal (EBPR) systems.},
journal = {Water research},
volume = {206},
number = {},
pages = {117725},
doi = {10.1016/j.watres.2021.117725},
pmid = {34653799},
issn = {1879-2448},
mesh = {Bioreactors ; *Metagenomics ; *Phosphorus ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers ; Sewage ; },
abstract = {Candidatus Accumulibacter phosphatis (CAP) and its clade-level micro-diversity has been associated with and implicated in functional differences in phosphorus removal performance in enhanced biological phosphorus removal (EBPR) systems. Side-stream EBPR (S2EBPR) is an emerging process that has been shown to present a suite of advantages over the conventional EBPR design, however, large knowledge gaps remain in terms of its underlying ecological mechanisms. Here, we compared and revealed the higher-resolution differences in microbial ecology of CAP between a full-scale side-stream EBPR configuration and a conventional A2O EBPR process that were operated in parallel and with the same influent feed. Even though the relative abundance of CAP, revealed by 16S rRNA gene amplicon sequencing, was similar in both treatment trains, a clade-level analysis, using combined 16S rRNA-gene based amplicon sequencing and oligotyping analysis and metagenomics analysis, revealed the distinct CAP microdiversity between the S2EBPR and A2O configurations that likely attributed to the improved performance in S2EBPR in comparison to conventional EBPR. Furthermore, genome-resolved metagenomics enabled extraction of three metagenome-assembled genomes (MAGs) belonging to CAP clades IIB (RCAB4-2), IIC (RC14) and II (RC18), from full-scale EBPR sludge for the first time, including a distinct Ca. Accumulibacter clade that is dominant and associated only with the S2EBPR configuration. The results also revealed the temporally increasing predominance of RC14, which belonged to Clade IIC, during the implementation of the S2EBPR configuration. Finally, we also show the existence of previously uncharacterized diversity of clades of CAP, namely the clades IIB and as yet unidentified clade of type II, in full-scale EBPR communities, highlighting the unknown diversity of CAP communities in full-scale EBPR systems.},
}
@article {pmid34653798,
year = {2021},
author = {She, Z and Pan, X and Wang, J and Shao, R and Wang, G and Wang, S and Yue, Z},
title = {Vertical environmental gradient drives prokaryotic microbial community assembly and species coexistence in a stratified acid mine drainage lake.},
journal = {Water research},
volume = {206},
number = {},
pages = {117739},
doi = {10.1016/j.watres.2021.117739},
pmid = {34653798},
issn = {1879-2448},
mesh = {Bacteria/genetics ; *Lakes ; *Microbiota ; Mining ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Acid mine drainage (AMD) lakes are typical hydrologic features caused by open pit mining and represent extreme ecosystems and environmental challenges. Little is known about microbial distribution and community assembly in AMD lakes, especially in deep layers. Here, we investigated prokaryotic microbial diversity and community assembly along a depth profile in a stratified AMD lake using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. The water column in the AMD lake exhibited tight geochemical gradients, with more acidic surface water. Coupled with vertical hydrochemical variations, prokaryotic microbial community structure changed significantly, and was accompanied by increased diversity with depth. In the surface water, heterogeneous selection was the most important assembly process, whereas stochastic processes gained importance with depth. Meanwhile, microbial co-occurrences, especially positive interactions, were more frequent in the stressful surface water with reduced network modularity and keystone taxa. The pH was identified as the key driver of microbial diversity and community assembly along the vertical profile based on random forest analysis. Taken together, environmental effects dominated by acid stress drove the community assembly and species coexistence that underpinned the spatial scaling patterns of AMD microbiota in the lake. These findings demonstrate the distinct heterogeneity of local prokaryotic microbial community in AMD lake, and provide new insights into the mechanism to maintain microbial diversity in extreme acidic environments.},
}
@article {pmid34647148,
year = {2022},
author = {Suyal, DC and Joshi, D and Kumar, S and Bhatt, P and Narayan, A and Giri, K and Singh, M and Soni, R and Kumar, R and Yadav, A and Devi, R and Kaur, T and Kour, D and Yadav, AN},
title = {Himalayan Microbiomes for Agro-environmental Sustainability: Current Perspectives and Future Challenges.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {643-675},
pmid = {34647148},
issn = {1432-184X},
mesh = {Animals ; *Microbiota ; Biodiversity ; Agriculture ; Plant Development ; Crops, Agricultural ; },
abstract = {The Himalayas are one of the most mystical, yet least studied terrains of the world. One of Earth's greatest multifaceted and diverse montane ecosystems is also one of the thirty-four global biodiversity hotspots of the world. These are supposed to have been uplifted about 60-70 million years ago and support, distinct environments, physiography, a variety of orogeny, and great biological diversity (plants, animals, and microbes). Microbes are the pioneer colonizer of the Himalayas that are involved in various bio-geological cycles and play various significant roles. The applications of Himalayan microbiomes inhabiting in lesser to greater Himalayas have been recognized. The researchers explored the applications of indigenous microbiomes in both agricultural and environmental sectors. In agriculture, microbiomes from Himalayan regions have been suggested as better biofertilizers and biopesticides for the crops growing at low temperature and mountainous areas as they help in the alleviation of cold stress and other biotic stresses. Along with alleviation of low temperature, Himalayan microbes also have the capability to enhance plant growth by availing the soluble form of nutrients like nitrogen, phosphorus, potassium, zinc, and iron. These microbes have been recognized for producing plant growth regulators (abscisic acid, auxin, cytokinin, ethylene, and gibberellins). These microbes have been reported for bioremediating the diverse pollutants (pesticides, heavy metals, and xenobiotics) for environmental sustainability. In the current perspectives, present review provides a detailed discussion on the ecology, biodiversity, and adaptive features of the native Himalayan microbiomes in view to achieve agro-environmental sustainability.},
}
@article {pmid34646255,
year = {2021},
author = {Glowacki, RWP and Engelhart, MJ and Ahern, PP},
title = {Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {735562},
pmid = {34646255},
issn = {1664-302X},
abstract = {The profound impact of the gut microbiome on host health has led to a revolution in biomedical research, motivating researchers from disparate fields to define the specific molecular mechanisms that mediate host-beneficial effects. The advent of genomic technologies allied to the use of model microbiomes in gnotobiotic mouse models has transformed our understanding of intestinal microbial ecology and the impact of the microbiome on the host. However, despite incredible advances, our understanding of the host-microbiome dialogue that shapes host physiology is still in its infancy. Progress has been limited by challenges associated with developing model systems that are both tractable enough to provide key mechanistic insights while also reflecting the enormous complexity of the gut ecosystem. Simplified model microbiomes have facilitated detailed interrogation of transcriptional and metabolic functions of the microbiome but do not recapitulate the interactions seen in complex communities. Conversely, intact complex communities from mice or humans provide a more physiologically relevant community type, but can limit our ability to uncover high-resolution insights into microbiome function. Moreover, complex microbiomes from lab-derived mice or humans often do not readily imprint human-like phenotypes. Therefore, improved model microbiomes that are highly defined and tractable, but that more accurately recapitulate human microbiome-induced phenotypic variation are required to improve understanding of fundamental processes governing host-microbiome mutualism. This improved understanding will enhance the translational relevance of studies that address how the microbiome promotes host health and influences disease states. Microbial exposures in wild mice, both symbiotic and infectious in nature, have recently been established to more readily recapitulate human-like phenotypes. The development of synthetic model communities from such "wild mice" therefore represents an attractive strategy to overcome the limitations of current approaches. Advances in microbial culturing approaches that allow for the generation of large and diverse libraries of isolates, coupled to ever more affordable large-scale genomic sequencing, mean that we are now ideally positioned to develop such systems. Furthermore, the development of sophisticated in vitro systems is allowing for detailed insights into host-microbiome interactions to be obtained. Here we discuss the need to leverage such approaches and highlight key challenges that remain to be addressed.},
}
@article {pmid34645520,
year = {2021},
author = {Cobo-Díaz, JF and Alvarez-Molina, A and Alexa, EA and Walsh, CJ and Mencía-Ares, O and Puente-Gómez, P and Likotrafiti, E and Fernández-Gómez, P and Prieto, B and Crispie, F and Ruiz, L and González-Raurich, M and López, M and Prieto, M and Cotter, P and Alvarez-Ordóñez, A},
title = {Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {204},
pmid = {34645520},
issn = {2049-2618},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Food Handling ; Genes, Bacterial ; *Pork Meat ; *Red Meat ; Swine ; },
abstract = {BACKGROUND: The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.<br><br>RESULTS: We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter, Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and &#x3b2;-dispersion of ARGs, which were predominantly assigned to Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum &#x3b2;-lactamase-producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities started. ARGs associated with resistance to &#x3b2;-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.<br><br>CONCLUSIONS: The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility. Video Abstract.},
}
@article {pmid34643439,
year = {2021},
author = {Tan, H and Liu, T and Yu, Y and Tang, J and Jiang, L and Martin, FM and Peng, W},
title = {Morel Production Related to Soil Microbial Diversity and Evenness.},
journal = {Microbiology spectrum},
volume = {9},
number = {2},
pages = {e0022921},
pmid = {34643439},
issn = {2165-0497},
mesh = {Agriculture ; Ascomycota/*metabolism ; Basidiomycota/metabolism ; Crops, Agricultural ; Mycobiome/*physiology ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Black morel is a widely prized ascomycetous mushroom with culinary value. It was once uncultivable but can now be cultivated routinely in ordinary farmland soils. Large-scale morel farming sometimes encounters nonfructification for unknown reasons. In spring 2020, many morel farms in the area of Chengdu-Plain, China, exhibited no fructification at all, causing disastrous economic loss to the farmers. To determine potential ecological factors associated with the different performance of morel production in these farms, 21 affected sites versus 11 sites with normal fructification performance were analyzed to compare soil microbiota and physiochemical characteristics during fructification. The results indicated that soil physiochemical characteristics were unlikely to be a major reason for the difference between successful fructification and nonfructification. The soils with successful fructification had significantly higher diversity in both the fungal and bacterial communities than those with nonfructification. Morel yield was positively correlated with the α-diversity of fungal communities. The higher diversity of the successfully fructified soils was contributed by community evenness rather than taxonomic richness. In contrast, most nonfructification soils were dominated by a high proportion of a certain fungal genus, typically Acremonium or Mortierella, in the fungal communities. Our findings demonstrate the importance of microbial ecology to the large-scale agroindustry of soil-cultivated mushrooms. IMPORTANCE Saprotrophic mushrooms cultivated in soils are subject to complex influences from soil microbial communities. Research on growing edible mushrooms has revealed connections between fungi and a few species of growth-promoting bacteria colonizing the mycosphere. The composition and diversity of the whole microbial community may also have an influence on the growth and production of soil-saprotrophic mushrooms. Morel mushrooms (Morchella spp.) are economically and culturally important and are widely prized throughout the world. This study used the large-scale farming of morels as an example of an agroecosystem for soil-saprotrophic mushroom cultivation. It demonstrated a typical pattern of how the microbial ecology in soil agroecosystems, especially the α-diversity level and community evenness among soil fungal taxa, could affect the production of high-value cash crops and the income of farmers.},
}
@article {pmid34637971,
year = {2021},
author = {Farrell, ML and Joyce, A and Duane, S and Fitzhenry, K and Hooban, B and Burke, LP and Morris, D},
title = {Evaluating the potential for exposure to organisms of public health concern in naturally occurring bathing waters in Europe: A scoping review.},
journal = {Water research},
volume = {206},
number = {},
pages = {117711},
doi = {10.1016/j.watres.2021.117711},
pmid = {34637971},
issn = {1879-2448},
mesh = {*Cryptosporidiosis ; *Cryptosporidium ; Humans ; Public Health ; Water Microbiology ; Water Quality ; },
abstract = {Globally, water-based bathing pastimes are important for both mental and physical health. However, exposure to waterborne organisms could present a substantial public health issue. Bathing waters are shown to contribute to the transmission of illness and disease and represent a reservoir and pathway for the dissemination of antimicrobial resistant (AMR) organisms. Current bathing water quality regulations focus on enumeration of faecal indicator organisms and are not designed for detection of specific waterborne organisms of public health concern (WOPHC), such as antimicrobial resistant (AMR)/pathogenic bacteria, or viruses. This investigation presents the first scoping review of the occurrence of waterborne organisms of public health concern (WOPHC) in identified natural bathing waters across the European Union (EU), which aimed to critically evaluate the potential risk of human exposure and to assess the appropriateness of the current EU bathing water regulations for the protection of public health. Accordingly, this review sought to identify and synthesise all literature pertaining to a selection of bacterial (Campylobacter spp., Escherichia coli, Salmonella spp., Shigella spp., Vibrio spp., Pseudomonas spp., AMR bacteria), viral (Hepatitis spp., enteroviruses, rotavirus, adenovirus, norovirus), and protozoan (Giardia spp., and Cryptosporidium spp.) contaminants in EU bathing waters. Sixty investigations were identified as eligible for inclusion and data was extracted. Peer-reviewed investigations included were from 18 countries across the EU, totalling 87 investigations across a period of 35 years, with 30% published between 2011 and 2015. A variety of water bodies were identified, with 27 investigations exclusively assessing coastal waters. Waterborne organisms were classified into three categories; bacteria, viruses, and protozoa; amounting to 58%, 36% and 17% of the total investigations, respectively. The total number of samples across all investigations was 8,118, with detection of one or more organisms in 2,449 (30%) of these. Viruses were detected in 1281 (52%) of all samples where WOPHC were found, followed by bacteria (865(35%)) and protozoa (303(12%)). Where assessed (442 samples), AMR bacteria had a 47% detection rate, emphasising their widespread occurrence in bathing waters. Results of this scoping review highlight the potential public health risk of exposure to WOPHC in bathing waters that normally remain undetected within the current monitoring parameters.},
}
@article {pmid34636925,
year = {2022},
author = {Manus, MB},
title = {Ecological Processes and Human Behavior Provide a Framework for Studying the Skin Microbial Metacommunity.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {689-702},
pmid = {34636925},
issn = {1432-184X},
mesh = {Animals ; Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Amphibians ; Skin ; },
abstract = {Metacommunity theory dictates that a microbial community is supported both by local ecological processes and the dispersal of microbes between neighboring communities. Studies that apply this perspective to human-associated microbial communities are thus far limited to the gut microbiome. Yet, the skin serves as the primary barrier between the body and the external environment, suggesting frequent opportunities for microbial dispersal to the variable microbial communities that are housed across skin sites. This paper applies metacommunity theory to understand the dispersal of microbes to the skin from the physical and social environment, as well as between different skin sites on an individual's body. This includes highlighting the role of human behavior in driving microbial dispersal, as well as shaping physiological properties of skin that underscore local microbial community dynamics. By leveraging data from research on the skin microbiomes of amphibians and other animals, this paper provides recommendations for future research on the skin microbial metacommunity, including generating testable predictions about the ecological underpinnings of the skin microbiome.},
}
@article {pmid34636672,
year = {2021},
author = {Tran, PQ and Anantharaman, K},
title = {Biogeochemistry Goes Viral: towards a Multifaceted Approach To Study Viruses and Biogeochemical Cycling.},
journal = {mSystems},
volume = {6},
number = {5},
pages = {e0113821},
pmid = {34636672},
issn = {2379-5077},
support = {DBI2047598//National Science Foundation (NSF)/ ; },
abstract = {Viruses are ubiquitous on Earth and are keystone components of environments, ecosystems, and human health. Yet, viruses remain poorly studied because most cannot be isolated in a laboratory. In the field of biogeochemistry, which aims to understand the interactions between biology, geology, and chemistry, there is progress to be made in understanding the different roles played by viruses in nutrient cycling, food webs, and elemental transformations. In this commentary, we outline current microbial ecology frameworks for understanding biogeochemical cycling in aquatic ecosystems. Next, we review some existing experimental and computational techniques that are enabling us to study the role of viruses in biogeochemical cycling, using examples from aquatic environments. Finally, we provide a conceptual model that balances limitations of computational tools when combined with biogeochemistry and ecological data. We envision meeting the grand challenge of understanding how viruses impact biogeochemical cycling by using a multifaceted approach to viral ecology.},
}
@article {pmid34634631,
year = {2021},
author = {Piperagkas, O and Papageorgiou, N},
title = {Changes in (micro and macro) plastic pollution in the sediment of three sandy beaches in the Eastern Mediterranean Sea, in relation to seasonality, beach use and granulometry.},
journal = {Marine pollution bulletin},
volume = {173},
number = {Pt A},
pages = {113014},
doi = {10.1016/j.marpolbul.2021.113014},
pmid = {34634631},
issn = {1879-3363},
mesh = {Environmental Monitoring ; Mediterranean Sea ; Microplastics ; *Plastics ; *Water Pollutants, Chemical/analysis ; },
abstract = {Smaller sized plastics (microplastics or MPs <5 mm) are ubiquitous in nature and have been found to interact in diverse ways with most biotic and abiotic systems globally. Most MPs in the seas have a land-based source, however, little is known about how the transfer occurs. In our study, we used three sandy beaches to describe the process of how MPs travel from accumulation points at the backshore of the beach to the sea, and vice versa. MPs differed significantly in all three beaches (both in quantitative and qualitative terms) between the summer and the winter samplings. During the summer, heavy MPs are the majority, while during the winter, lightweight microplastics are predominant, and the ratio of heavy per lightweight MPs is affected by the sediment median diameter after the summer sampling. Macroplastics follow a similar pattern to MPs and appear to provide a source of MPs for the sea.},
}
@article {pmid34633491,
year = {2022},
author = {Nasreen, T and Islam, MT and Liang, KYH and Johura, FT and Kirchberger, PC and Hill, E and Sultana, M and Case, RJ and Alam, M and Boucher, YF},
title = {Dynamic Subspecies Population Structure of Vibrio cholerae in Dhaka, Bangladesh.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {730-745},
pmid = {34633491},
issn = {1432-184X},
mesh = {Humans ; *Vibrio cholerae/genetics ; *Cholera/epidemiology ; Bangladesh/epidemiology ; Water ; },
abstract = {Cholera has been endemic to the Ganges Delta for centuries. Although the causative agent, Vibrio cholerae, is autochthonous to coastal and brackish water, cholera occurs continually in Dhaka, the inland capital city of Bangladesh which is surrounded by fresh water. Despite the persistence of this problem, little is known about the environmental abundance and distribution of lineages of V. cholerae, the most important being the pandemic generating (PG) lineage consisting mostly of serogroup O1 strains. To understand spatial and temporal dynamics of PG lineage and other lineages belonging to the V. cholerae species in surface water in and around Dhaka City, we used qPCR and high-throughput amplicon sequencing. Seven different freshwater sites across Dhaka were investigated for six consecutive months, and physiochemical parameters were measured in situ. Total abundance of V. cholerae was found to be relatively stable throughout the 6-month sampling period, with 2 × 10[5] to 4 × 10[5] genome copies/L at six sites and around 5 × 10[5] genome copies/L at the site located in the most densely populated part of Dhaka City. PG O1 V. cholerae was present in high abundance during the entire sampling period and composed between 24 and 92% of the total V. cholerae population, only showing occasional but sudden reductions in abundance. In instances where PG O1 lost its dominance, other lineages underwent a rapid expansion while the size of the total V. cholerae population remained almost unchanged. Intraspecies richness of V. cholerae was positively correlated with salinity, conductivity, and total dissolved solids (TDS), while it was negatively correlated with dissolved oxygen (DO) concentration in water. Interestingly, negative correlation was observed specifically between PG O1 and salinity, even though the changes in this variable were minor (0-0.8 ppt). Observations in this study suggest that at the subspecies level, population composition of naturally occurring V. cholerae can be influenced by fluctuations in environmental factors, which can lead to altered competition dynamics among the lineages.},
}
@article {pmid34632704,
year = {2022},
author = {Manning-Berg, A and Selly, T and Bartley, JK},
title = {Actualistic approaches to interpreting the role of biological decomposition in microbial preservation.},
journal = {Geobiology},
volume = {20},
number = {2},
pages = {216-232},
doi = {10.1111/gbi.12475},
pmid = {34632704},
issn = {1472-4669},
mesh = {*Ecosystem ; *Fossils ; Humans ; Siberia ; },
abstract = {Taphonomic processes, especially post-mortem biological decomposition, act as crucial controls on the microbial fossil record. Information loss during the fossilization process obscures interpretation of ancient microbial ecology and limits our view of preserved ecosystems. Conversely, taphonomic information can itself provide insight into fossilization pathways and processes. This information-gain approach requires specific attention to taphonomic patterns in ancient assemblages and robust modern analogue data to serve as points of reference. In this study, we combine experimental taphonomy with decomposition models in order to constrain taphonomic hypotheses regarding Proterozoic microfossil assemblages. Several filamentous and coccoidal prokaryotic and eukaryotic phototrophs were evaluated for taphonomic pattern over the course of a short (~100 days) decomposition experiment. In parallel, simple numerical models were constructed to explain potential taphonomic pathways. These analogue data were then compared to two Mesoproterozoic fossil assemblages, the ~1.5 Ga Kotuikan Formation, Siberia, and the ~1 Ga Angmaat Formation, Canada. Concordant with previous experiments and observations, our results suggest that sheath morphology is more persistent than cell/trichome morphology during early stages of decomposition. These experiments also suggest that taphonomic change in cell morphology may follow one of several trajectories, resulting in distinct taphonomic endpoints. Model output suggests two categories of underlying mechanism and resultant taphonomic trajectory: (1) uniform decomposition, resulting in a low overall taphonomic grade and poor preservation, and (2) faster decomposition of structurally compromised individuals, producing a final population with better overall preservation of very few individuals. In this experiment, cells of coccoidal organisms exhibit the first pattern and trichomes of filamentous organisms and some sheaths exhibit the second. Comparison with preserved microfossil assemblages suggests that differences in taphonomic pattern between parts of an assemblage could be useful in assessing taphonomic processes or degree of taphonomic loss in an entire assemblage.},
}
@article {pmid34628478,
year = {2022},
author = {Bottery, MJ and Matthews, JL and Wood, AJ and Johansen, HK and Pitchford, JW and Friman, VP},
title = {Inter-species interactions alter antibiotic efficacy in bacterial communities.},
journal = {The ISME journal},
volume = {16},
number = {3},
pages = {812-821},
pmid = {34628478},
issn = {1751-7370},
support = {/WT_/Wellcome Trust/United Kingdom ; 204829/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; *Cystic Fibrosis/microbiology ; Humans ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa/genetics ; beta-Lactamases/genetics ; },
abstract = {The efficacy of antibiotic treatments targeting polymicrobial communities is not well predicted by conventional in vitro susceptibility testing based on determining minimum inhibitory concentration (MIC) in monocultures. One reason for this is that inter-species interactions can alter the community members' susceptibility to antibiotics. Here we quantify, and identify mechanisms for, community-modulated changes of efficacy for clinically relevant antibiotics against the pathogen Pseudomonas aeruginosa in model cystic fibrosis (CF) lung communities derived from clinical samples. We demonstrate that multi-drug resistant Stenotrophomonas maltophilia can provide high levels of antibiotic protection to otherwise sensitive P. aeruginosa. Exposure protection to imipenem was provided by chromosomally encoded metallo-β-lactamase that detoxified the environment; protection was dependent upon S. maltophilia cell density and was provided by S. maltophilia strains isolated from CF sputum, increasing the MIC of P. aeruginosa by up to 16-fold. In contrast, the presence of S. maltophilia provided no protection against meropenem, another routinely used carbapenem. Mathematical ordinary differential equation modelling shows that the level of exposure protection provided against different carbapenems can be explained by differences in antibiotic efficacy and inactivation rate. Together, these findings reveal that exploitation of pre-occurring antimicrobial resistance, and inter-specific competition, can have large impacts on pathogen antibiotic susceptibility, highlighting the importance of microbial ecology for designing successful antibiotic treatments for multispecies communities.},
}
@article {pmid34626522,
year = {2022},
author = {Xu, Q and Luo, G and Guo, J and Xiao, Y and Zhang, F and Guo, S and Ling, N and Shen, Q},
title = {Microbial generalist or specialist: Intraspecific variation and dormancy potential matter.},
journal = {Molecular ecology},
volume = {31},
number = {1},
pages = {161-173},
doi = {10.1111/mec.16217},
pmid = {34626522},
issn = {1365-294X},
support = {KYZ201718//Fundamental Research Funds for the Central Universities/ ; 2017YFD0200805//National Key Research and Development Program of China/ ; 41977080//National Natural Science Foundation of China/ ; },
mesh = {Adaptation, Physiological ; Bacteria/genetics ; *Biological Evolution ; Humans ; *Microbiota ; Soil ; },
abstract = {Microbial generalists and specialists coexist in the soil environment while having distinctive impacts on microbial community dynamics. In microbial ecology, the underlying mechanisms as to why a species is a generalist or a specialist remain ambiguous. Herein, we collected soils across a national scale and identified bacterial generalists and specialists according to niche breadth at the species level (OTU level), and the single-nucleotide differences in each species were measured to investigate intraspecific variation (at zero-radius OTU level). Compared with that of the specialists, the intraspecific variation of the generalists was much higher, which ensured their wider niche breadth and lower variability. The higher asynchrony and different niche preferences of conspecific individuals and the higher dormancy potential within the generalists further contributed to their stability in varying environments. Besides, generalists were less controlled by environmental filtering, which was indicated by the stronger signature of stochastic processes in their assembly, and had higher diversification and transition rates that allowed them to adapt to environmental changes to a greater extent than specialists. Overall, this study provides a new comprehensive understanding of the rules of assembly and the evolutionary roles of bacterial generalists and specialists. It also highlights the importance of intraspecific variation and the dormancy potential in the stability of species.},
}
@article {pmid34625829,
year = {2022},
author = {Bouhnik, O and Alami, S and Lamin, H and Lamrabet, M and Bennis, M and Ouajdi, M and Bellaka, M and Antri, SE and Abbas, Y and Abdelmoumen, H and Bedmar, EJ and Idrissi, MME},
title = {The Fodder Legume Chamaecytisus albidus Establishes Functional Symbiosis with Different Bradyrhizobial Symbiovars in Morocco.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {794-807},
pmid = {34625829},
issn = {1432-184X},
mesh = {Symbiosis/genetics ; *Fabaceae ; Root Nodules, Plant ; Phylogeny ; Ecosystem ; Morocco ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics/chemistry ; *Bradyrhizobium/genetics ; *Lupinus/genetics ; Animal Feed ; Soil ; Sequence Analysis, DNA ; },
abstract = {In this work, we analyzed the symbiotic performance and diversity of rhizobial strains isolated from the endemic shrubby legume Chamaecytisus albidus grown in soils of three different agroforestry ecosystems representing arid and semi-arid forest areas in Morocco. The analysis of the rrs gene sequences from twenty-four representative strains selected after REP-PCR fingerprinting showed that all the strains belong to the genus Bradyrhizobium. Following multi-locus sequence analysis (MLSA) using the rrs, gyrB, recA, glnII, and rpoB housekeeping genes, five representative strains, CA20, CA61, CJ2, CB10, and CB61 were selected for further molecular studies. Phylogenetic analysis of the concatenated glnII, gyrB, recA, and rpoB genes showed that the strain CJ2 isolated from Sahel Doukkala soil is close to Bradyrhizobium canariense BTA-1[ T] (96.95%); that strains CA20 and CA61 isolated from the Amhach site are more related to Bradyrhizobium valentinum LmjM3[T], with 96.40 and 94.57% similarity values; and that the strains CB10 and CB60 isolated from soil in the Bounaga site are more related to Bradyrhizobium murdochi CNPSo 4020[ T] and Bradyrhizobium. retamae Ro19[T], with which they showed 95.45 and 97.34% similarity values, respectively. The phylogenetic analysis of the symbiotic genes showed that the strains belong to symbiovars lupini, genistearum, and retamae. All the five strains are able to nodulate Lupinus luteus, Retama monosperma, and Cytisus monspessilanus, but they do not nodulate Glycine max and Phaseolus vulgaris. The inoculation tests showed that the strains isolated from the 3 regions improve significantly the plant yield as compared to uninoculated plants. However, the strains of Bradyrhizobium sp. sv. retamae isolated from the site of Amhach were the most performing. The phenotypic analysis showed that the strains are able to use a wide range of carbohydrates and amino acids as sole carbon and nitrogen source. The strains isolated from the arid areas of Bounaga and Amhach were more tolerant to salinity and drought stress than strains isolated in the semi-arid area of Sahel Doukkala.},
}
@article {pmid34623811,
year = {2021},
author = {Wang, S and De Paepe, K and Van de Wiele, T and Fu, X and Yuan, Y and Zhang, B and Huang, Q},
title = {Starch Microspheres Entrapped with Chitosan Delay In Vitro Fecal Fermentation and Regulate Human Gut Microbiota Composition.},
journal = {Journal of agricultural and food chemistry},
volume = {69},
number = {41},
pages = {12323-12332},
doi = {10.1021/acs.jafc.1c04039},
pmid = {34623811},
issn = {1520-5118},
mesh = {*Chitosan ; Fatty Acids, Volatile ; Feces ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Microspheres ; Starch/metabolism ; },
abstract = {A slow dietary fiber fermentation rate is desirable to obtain a steady metabolite release and even distribution throughout the entire colon, ensuring to meet the energy needs in the distal colon. In this study, we prepared starch-entrapped microspheres with a variable chitosan-to-starch ratio by means of electrospraying and investigated the fermentability by human fecal microbiota in an in vitro batch system. Starch encapsulation reduced microbial gas production and the concentration of short-chain fatty acids. Butyrate production, in particular, gradually decreased with increasing chitosan proportions. Moreover, the starch and chitosan composites induced a synergistic effect on the gut microbiota composition. Roseburia, Lachnospiraceae, and Clostridiales were promoted by all of the microspheres, and the abundance of the aforementioned health-promoting taxa reached a maximum in chitosan/starch microspheres with a 1:6 (w/w) ratio. Our findings highlight the possible benefits of rationally designing functional foods targeting functional and taxonomic gut microbiota modulation.},
}
@article {pmid34623462,
year = {2022},
author = {Ezzedine, JA and Janicot, A and Rasconi, S and Domaizon, I and Jacquet, S},
title = {Short-Term Dynamics of Bdellovibrio and Like Organisms in Lake Geneva in Response to a Simulated Climatic Extreme Event.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {717-729},
pmid = {34623462},
issn = {1432-184X},
mesh = {*Bdellovibrio/genetics ; Lakes ; Phylogeny ; *Deltaproteobacteria/genetics ; },
abstract = {The short time-scale dynamics of three families of Bdellovibrio and like organisms (i.e. Bdellovibrionaceae, Peredibacteraceae, and Bacteriovoracaceae) were studied on the surface waters of Lake Geneva in summer. Using mesocosms deployed nearshore in July 2019, we simulated an extreme climatic event (an input of carbon from the watershed in response to runoff from the catchment, light reduction, and mixing in response to stormy conditions) and aimed to study the impact of both abiotic and biotic factors on their dynamics. The three families of Bdellovibrio and like organisms (BALOs) showed different dynamics during the experiment. Peredibacteraceae was the most abundant group, whereas Bacteriovoracaceae was the least abundant. Compared with the other two families, the abundance of Bdellovibrionaceae did not fluctuate, remaining relatively stable over time. Environmental variables only partially explained the dynamics of these families; in particular, temperature, pH, and chloride concentrations were positively correlated with Bacteriovoracaceae, Bdellovibrionaceae, and Peredibacteraceae abundance, respectively. Prokaryote-like particles (PLPs), such as those with high DNA content (HDNA), were strongly and positively correlated with Peredibacteraceae and Bacteriovoracaceae. In contrast, no relationships were found between Bdellovibrionaceae and PLP abundance, nor between the virus-like particles (VLPs) and the different BALOs. Overall, the experiment revealed that predation was stable in the face of the simulated climatic events. In addition, we observed that Peredibacteraceae and Bacteriovoracaceae share common traits, while Bdellovibrionaceae seems to constitute a distinct category.},
}
@article {pmid34622953,
year = {2022},
author = {Brigham, LM and Bueno de Mesquita, CP and Smith, JG and Sartwell, SA and Schmidt, SK and Suding, KN},
title = {Do plant-soil interactions influence how the microbial community responds to environmental change?.},
journal = {Ecology},
volume = {103},
number = {1},
pages = {e03554},
doi = {10.1002/ecy.3554},
pmid = {34622953},
issn = {1939-9170},
mesh = {Bacteria ; Ecosystem ; Fungi ; *Microbiota ; Nitrogen ; *Soil ; Soil Microbiology ; },
abstract = {Global change alters ecosystems and their functioning, and biotic interactions can either buffer or amplify such changes. We utilized a long-term nitrogen (N) addition and species removal experiment in the Front Range of Colorado, USA to determine whether a codominant forb and a codominant grass, with different effects on nutrient cycling and plant community structure, would buffer or amplify the effects of simulated N deposition on soil bacterial and fungal communities. While the plant community was strongly shaped by both the presence of dominant species and N addition, we did not find a mediating effect of the plant community on soil microbial response to N. In contrast to our hypothesis, we found a decoupling of the plant and microbial communities such that the soil microbial community shifted under N independently of directional shifts in the plant community. These findings suggest there are not strong cascading effects of N deposition across the plant-soil interface in our system.},
}
@article {pmid34622529,
year = {2021},
author = {Li, WL and Dong, X and Lu, R and Zhou, YL and Zheng, PF and Feng, D and Wang, Y},
title = {Microbial ecology of sulfur cycling near the sulfate-methane transition of deep-sea cold seep sediments.},
journal = {Environmental microbiology},
volume = {23},
number = {11},
pages = {6844-6858},
doi = {10.1111/1462-2920.15796},
pmid = {34622529},
issn = {1462-2920},
mesh = {Geologic Sediments/microbiology ; *Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; *Sulfates/metabolism ; Sulfur/metabolism ; },
abstract = {Microbial sulfate reduction is largely associated with anaerobic methane oxidation and alkane degradation in sulfate-methane transition zone (SMTZ) of deep-sea cold seeps. How the sulfur cycling is mediated by microbes near SMTZ has not been fully understood. In this study, we detected a shallow SMTZ in three of eight sediment cores sampled from two cold seep areas in the South China Sea. One hundred ten genomes representing sulfur-oxidizing bacteria (SOB) and sulfur-reducing bacteria (SRB) strains were identified from three SMTZ-bearing cores. In the layers above SMTZ, SOB were mostly constituted by Campylobacterota, Gammaproteobacteria and Alphaproteobacteria that probably depended on nitrogen oxides and/or oxygen for oxidation of sulfide and thiosulfate in near-surface sediment layers. In the layers below the SMTZ, the deltaproteobacterial SRB genomes and metatranscriptomes revealed CO2 fixation by Wood-Ljungdahl pathway, sulfate reduction and nitrogen fixation for syntrophic or fermentative lifestyle. A total of 68% of the metagenome assembled genomes were not adjacent to known species in a phylogenomic tree, indicating a high diversity of bacteria involved in sulfur cycling. With the large number of genomes for SOB and SRB, our study uncovers the microbial populations that potentially mediate sulfur metabolism and associated carbon and nitrogen cycles, which sheds light on complex biogeochemical processes in deep-sea environments.},
}
@article {pmid34618070,
year = {2021},
author = {Thiriet-Rupert, S and Gain, G and Jadoul, A and Vigneron, A and Bosman, B and Carnol, M and Motte, P and Cardol, P and Nouet, C and Hanikenne, M},
title = {Long-term acclimation to cadmium exposure reveals extensive phenotypic plasticity in Chlamydomonas.},
journal = {Plant physiology},
volume = {187},
number = {3},
pages = {1653-1678},
pmid = {34618070},
issn = {1532-2548},
mesh = {*Acclimatization ; *Adaptation, Physiological ; Biomass ; Cadmium/*metabolism ; Chlamydomonas/*drug effects/physiology ; Time Factors ; },
abstract = {Increasing industrial and anthropogenic activities are producing and releasing more and more pollutants in the environment. Among them, toxic metals are one of the major threats for human health and natural ecosystems. Because photosynthetic organisms play a critical role in primary productivity and pollution management, investigating their response to metal toxicity is of major interest. Here, the green microalga Chlamydomonas (Chlamydomonas reinhardtii) was subjected to short (3 d) or chronic (6 months) exposure to 50 µM cadmium (Cd), and the recovery from chronic exposure was also examined. An extensive phenotypic characterization and transcriptomic analysis showed that the impact of Cd on biomass production of short-term (ST) exposed cells was almost entirely abolished by long-term (LT) acclimation. The underlying mechanisms were initiated at ST and further amplified after LT exposure resulting in a reversible equilibrium allowing biomass production similar to control condition. This included modification of cell wall-related gene expression and biofilm-like structure formation, dynamics of metal ion uptake and homeostasis, photosynthesis efficiency recovery and Cd acclimation through metal homeostasis adjustment. The contribution of the identified coordination of phosphorus and iron homeostasis (partly) mediated by the main phosphorus homeostasis regulator, Phosphate Starvation Response 1, and a basic Helix-Loop-Helix transcription factor (Cre05.g241636) was further investigated. The study reveals the highly dynamic physiological plasticity enabling algal cell growth in an extreme environment.},
}
@article {pmid34617123,
year = {2022},
author = {Medeiros, MCI and Seabourn, PS and Rollins, RL and Yoneishi, NM},
title = {Mosquito Microbiome Diversity Varies Along a Landscape-Scale Moisture Gradient.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {893-900},
pmid = {34617123},
issn = {1432-184X},
support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Aedes/microbiology ; Mosquito Vectors/physiology ; *Microbiota ; Disease Vectors ; Urbanization ; },
abstract = {Microorganisms live in close association with metazoan hosts and form symbiotic microbiotas that modulate host biology. Although the function of host-associated microbiomes may change with composition, hosts within a population can exhibit high turnover in microbiome composition among individuals. However, environmental drivers of this variation are inadequately described. Here, we test the hypothesis that this diversity among the microbiomes of Aedes albopictus (a mosquito disease vector) is associated with the local climate and land-use patterns on the high Pacific island of O 'ahu, Hawai 'i. Our principal finding demonstrates that the relative abundance of several bacterial symbionts in the Ae. albopictus microbiome varies in response to a landscape-scale moisture gradient, resulting in the turnover of the mosquito microbiome composition across the landscape. However, we find no evidence that mosquito microbiome diversity is tied to an index of urbanization. This result has implications toward understanding the assembly of host-associated microbiomes, especially during an era of rampant global climate change.},
}
@article {pmid34617072,
year = {2021},
author = {Pace, RM and Chu, DM and Prince, AL and Ma, J and Seferovic, MD and Aagaard, KM},
title = {Complex species and strain ecology of the vaginal microbiome from pregnancy to postpartum and association with preterm birth.},
journal = {Med (New York, N.Y.)},
volume = {2},
number = {9},
pages = {1027-1049},
pmid = {34617072},
issn = {2666-6340},
support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; K12 GM084897/GM/NIGMS NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; R21 ES029462/ES/NIEHS NIH HHS/United States ; R01 DK089201/DK/NIDDK NIH HHS/United States ; T32 GM007330/GM/NIGMS NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; T32 GM088129/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria ; Child ; Female ; Humans ; Infant, Newborn ; Lactobacillus/genetics ; *Microbiota/genetics ; Postpartum Period ; Pregnancy ; *Premature Birth/microbiology ; RNA, Ribosomal, 16S/genetics ; Vagina/chemistry ; },
abstract = {BACKGROUND: Lactobacillus was described as a keystone bacterial taxon in the human vagina over 100 years ago. Using metagenomics, we and others have characterized lactobacilli and other vaginal taxa across health and disease states, including pregnancy. While shifts in community membership have been resolved at the genus/species level, strain dynamics remain poorly characterized.<br><br>METHODS: We performed a metagenomic analysis of the complex ecology of the vaginal econiche during and after pregnancy in a large U.S. based longitudinal cohort of women who were initially sampled in the third trimester of pregnancy, then validated key findings in a second cohort of women initially sampled in the second trimester of pregnancy.<br><br>FINDINGS: First, we resolved microbial species and strains, interrogated their co-occurrence patterns, and probed the relationship between keystone species and preterm birth outcomes. Second, to determine the role of human heredity in shaping vaginal microbial ecology in relation to preterm birth, we performed a mtDNA-bacterial species association analysis. Finally, we explored the clinical utility of metagenomics in detection and co-occurrence patterns for the pathobiont Group B Streptococcus (causative bacterium of invasive neonatal sepsis).<br><br>CONCLUSIONS: Our highly refined resolutions of the vaginal ecology during and post-pregnancy provide insights into not only structural and functional community dynamics, but highlight the capacity of metagenomics to reveal finer aspects of the vaginal microbial ecologic framework.<br><br>FUNDING: NIH-NINR R01NR014792, NIH-NICHD R01HD091731, NIH National Children's Study Formative Research, Burroughs Wellcome Fund Preterm Birth Initiative, March of Dimes Preterm Birth Research Initiative, NIH-NIGMS (K12GM084897, T32GM007330, T32GM088129).},
}
@article {pmid34616379,
year = {2021},
author = {Huang, K and Tang, J and Zou, Y and Sun, X and Lan, J and Wang, W and Xu, P and Wu, X and Ma, R and Wang, Q and Wang, Z and Liu, J},
title = {Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {713462},
pmid = {34616379},
issn = {1664-302X},
abstract = {Alternaria alternata is a pathogen in a wide range of agriculture crops and causes significant economic losses. A strain of A. alternata (Y784-BC03) was isolated and identified from "Hongyang" kiwifruit and demonstrated to cause black spot infections on fruits. The genome sequence of Y784-BC03 was obtained using Nanopore MinION technology. The assembled genome is composed of 33,869,130bp (32.30Mb) comprising 10 chromosomes and 11,954 genes. A total of 2,180 virulence factors were predicted to be present in the obtained genome sequence. The virulence factors comprised genes encoding secondary metabolites, including non-host-specific toxins, cell wall-degrading enzymes, and major transcriptional regulators. The predicted gene clusters encoding genes for the biosynthesis and export of secondary metabolites in the genome of Y784-BC03 were associated with non-host-specific toxins, including cercosporin, dothistromin, and versicolorin B. Major transcriptional regulators of different mycotoxin biosynthesis pathways were identified, including the transcriptional regulators, polyketide synthase, P450 monooxygenase, and major facilitator superfamily transporters.},
}
@article {pmid34615557,
year = {2021},
author = {Wang, Y and Ye, J and Ju, F and Liu, L and Boyd, JA and Deng, Y and Parks, DH and Jiang, X and Yin, X and Woodcroft, BJ and Tyson, GW and Hugenholtz, P and Polz, MF and Zhang, T},
title = {Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {199},
pmid = {34615557},
issn = {2049-2618},
mesh = {Bacteria/genetics ; Bioreactors ; Metagenome ; *Microbiota/genetics ; *Sewage ; },
abstract = {BACKGROUND: Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between states remains poorly understood. We studied monthly activated sludge (AS) samples collected over 9 years from a full-scale wastewater treatment plant to answer how complex AS communities evolve in the long term and how the community functions change when there is a disturbance in operational parameters.<br><br>RESULTS: Here, we show that a microbial community in activated sludge (AS) system fluctuated around a stable average for 3&#xa0;years but was then abruptly pushed into an alternative stable state by a simple transient disturbance (bleaching). While the taxonomic composition rapidly turned into a new state following the disturbance, the metabolic profile of the community and system performance remained remarkably stable. A total of 920 metagenome-assembled genomes (MAGs), representing approximately 70% of the community in the studied AS ecosystem, were recovered from the 97 monthly AS metagenomes. Comparative genomic analysis revealed an increased ability to aggregate in the cohorts of MAGs with correlated dynamics that are dominant after the bleaching event. Fine-scale analysis of dynamics also revealed cohorts that dominated during different periods and showed successional dynamics on seasonal and longer time scales due to temperature fluctuation and gradual changes in mean residence time in the reactor, respectively.<br><br>CONCLUSIONS: Our work highlights that communities can assume different stable states under highly similar environmental conditions and that a specific disturbance threshold may lead to a rapid shift in community composition. Video Abstract.},
}
@article {pmid34612321,
year = {2022},
author = {Avalos, M and Garbeva, P and Vader, L and van Wezel, GP and Dickschat, JS and Ulanova, D},
title = {Biosynthesis, evolution and ecology of microbial terpenoids.},
journal = {Natural product reports},
volume = {39},
number = {2},
pages = {249-272},
doi = {10.1039/d1np00047k},
pmid = {34612321},
issn = {1460-4752},
mesh = {*Biological Products/chemistry ; Ecology ; Humans ; Plants/metabolism ; *Terpenes/chemistry ; },
abstract = {Covering: through June 2021Terpenoids are the largest class of natural products recognised to date. While mostly known to humans as bioactive plant metabolites and part of essential oils, structurally diverse terpenoids are increasingly reported to be produced by microorganisms. For many of the compounds biological functions are yet unknown, but during the past years significant insights have been obtained for the role of terpenoids in microbial chemical ecology. Their functions include stress alleviation, maintenance of cell membrane integrity, photoprotection, attraction or repulsion of organisms, host growth promotion and defense. In this review we discuss the current knowledge of the biosynthesis and evolution of microbial terpenoids, and their ecological and biological roles in aquatic and terrestrial environments. Perspectives on their biotechnological applications, knowledge gaps and questions for future studies are discussed.},
}
@article {pmid34610115,
year = {2021},
author = {Masetti, R and Muratore, E and Leardini, D and Zama, D and Turroni, S and Brigidi, P and Esposito, S and Pession, A},
title = {Gut microbiome in pediatric acute leukemia: from predisposition to cure.},
journal = {Blood advances},
volume = {5},
number = {22},
pages = {4619-4629},
pmid = {34610115},
issn = {2473-9537},
mesh = {*Gastrointestinal Microbiome ; *Hematopoietic Stem Cell Transplantation ; Humans ; *Leukemia, Myeloid, Acute ; *Microbiota ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy ; },
abstract = {The gut microbiome (GM) has emerged as a key factor in the genesis and progression of many diseases. The intestinal bacterial composition also influences treatment-related side effects and even the efficacy of oncological therapies. Acute leukemia (AL) is the most common cancer among children and the most frequent cause of cancer-related death during childhood. Outcomes have improved considerably over the past 4 decades, with the current long-term survival for acute lymphoblastic leukemia being ∼90%. However, several acute toxicities and long-term sequelae are associated with the multimodal therapy protocols applied in these patients. Specific GM configurations could contribute to the multistep developmental hypothesis for leukemogenesis. Moreover, GM alterations occur during the AL therapeutic course and are associated with treatment-related complications, especially during hematopoietic stem cell transplantation. The GM perturbation could last even after the removal of microbiome-modifying factors, like antibiotics, chemotherapeutic drugs, or alloimmune reactions, contributing to several health-related issues in AL survivors. The purpose of this article is to provide a comprehensive review of the chronological changes of GM in children with AL, from predisposition to cure. The underpinning biological processes and the potential interventions to modulate the GM toward a potentially health-promoting configuration are also highlighted.},
}
@article {pmid34609533,
year = {2022},
author = {Bartolomé, C and Buendía-Abad, M and Ornosa, C and De la Rúa, P and Martín-Hernández, R and Higes, M and Maside, X},
title = {Bee Trypanosomatids: First Steps in the Analysis of the Genetic Variation and Population Structure of Lotmaria passim, Crithidia bombi and Crithidia mellificae.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {856-867},
pmid = {34609533},
issn = {1432-184X},
mesh = {Bees ; Animals ; *Crithidia/genetics/parasitology ; *Trypanosomatina/genetics/parasitology ; Genotype ; Genetic Variation ; },
abstract = {Trypanosomatids are among the most prevalent parasites in bees but, despite the fact that their impact on the colonies can be quite important and that their infectivity may potentially depend on their genotypes, little is known about the population diversity of these pathogens. Here we cloned and sequenced three non-repetitive single copy loci (DNA topoisomerase II, glyceraldehyde-3-phosphate dehydrogenase and RNA polymerase II large subunit, RPB1) to produce new genetic data from Crithidia bombi, C. mellificae and Lotmaria passim isolated from honeybees and bumblebees. These were analysed by applying population genetic tools in order to quantify and compare their variability within and between species, and to obtain information on their demography and population structure. The general pattern for the three species was that (1) they were subject to the action of purifying selection on nonsynonymous variants, (2) the levels of within species diversity were similar irrespective of the host, (3) there was evidence of recombination among haplotypes and (4) they showed no haplotype structuring according to the host. C. bombi exhibited the lowest levels of synonymous variation (πS= 0.06 ± 0.04 %) - and a mutation frequency distribution compatible with a population expansion after a bottleneck - that contrasted with the extensive polymorphism displayed by C. mellificae (πS= 2.24 ± 1.00 %), which likely has a more ancient origin. L. passim showed intermediate values (πS= 0.40 ± 0.28 %) and an excess of variants a low frequencies probably linked to the spread of this species to new geographical areas.},
}
@article {pmid34609532,
year = {2022},
author = {Deng, Y and Borewicz, K and van Loo, J and Olabarrieta, MZ and Kokou, F and Sipkema, D and Verdegem, MCJ},
title = {In-Situ Biofloc Affects the Core Prokaryotes Community Composition in Gut and Enhances Growth of Nile Tilapia (Oreochromis niloticus).},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {879-892},
pmid = {34609532},
issn = {1432-184X},
support = {847.13.007//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 201606320215//China Scholarship Council/ ; },
mesh = {Animals ; *Cichlids ; Aquaculture ; *Gastrointestinal Microbiome ; Bacteria ; *Microbiota ; Animal Feed/analysis ; Dietary Supplements/analysis ; },
abstract = {Biofloc technology is commonly applied in intensive tilapia (Oreochromis niloticus) culture to maintain water quality, supply the fish with extra protein, and improve fish growth. However, the effect of dietary supplementation of processed biofloc on the gut prokaryotic (bacteria and archaea) community composition of tilapia is not well understood. In this study one recirculating aquaculture system was used to test how biofloc, including in-situ biofloc, dietary supplementation of ex-situ live or dead biofloc, influence fish gut prokaryotic community composition and growth performance in comparison to a biofloc-free control treatment. A core gut prokaryotic community was identified among all treatments by analyzing the temporal variations in gut prokaryotes. In-situ produced biofloc significantly increased the prokaryotic diversity in the gut by reducing the relative abundance of dominant Cetobacterium and increasing the relative abundance of potentially beneficial bacteria. The in-situ biofloc delivered a unique prokaryotic community in fish gut, while dietary supplementation of tilapias with 5% and 10% processed biofloc (live or dead) only changed the relative abundance of minor prokaryotic taxa outside the gut core microbiota. The modulatory effect of in-situ biofloc on tilapia gut microbiota was associated with the distinct microbial community in the biofloc water and undisturbed biofloc. The growth-promoting effect on tilapia was only detected in the in-situ biofloc treatment, while dietary supplementation of processed biofloc had no effect on fish growth performance as compared to the control treatment.},
}
@article {pmid34609161,
year = {2021},
author = {Wiles, TJ},
title = {Cultivating Healthy Connections: Exploring and Engineering the Microbial Flow That Shapes Microbiomes.},
journal = {mSystems},
volume = {6},
number = {5},
pages = {e0086321},
pmid = {34609161},
issn = {2379-5077},
support = {DP2 AI154420/AI/NIAID NIH HHS/United States ; DP2AI154420//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {Our view of the microbial world has undergone a radical transformation over the past decade. For most of the 20th century, medical microbiological research was focused on understanding the virulent nature of disease-causing pathogens. More recently, advances in DNA sequencing methodologies have exposed a wider diversity of microscopic wildlife that associate with our bodies and the environments around us, and the unexpected roles they play in supporting our health. Our expanding view of the microbial world is now motivating therapeutic interventions that are based not just on the elimination of nefarious pathogens but the nurturing of beneficial microbiomes. In this Commentary, I consider how our historically pathogen-based view of host-microbe interactions may be limiting the scope of new and alternative strategies for engineering microbiomes. I suggest that recognizing the therapeutic potential of the ongoing microbial transmission that connects microbiomes could illuminate unexplored opportunities for cultivating healthy host-microbe relationships.},
}
@article {pmid34608694,
year = {2022},
author = {Bouma-Gregson, K and Crits-Christoph, A and Olm, MR and Power, ME and Banfield, JF},
title = {Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure.},
journal = {Molecular ecology},
volume = {31},
number = {1},
pages = {86-103},
pmid = {34608694},
issn = {1365-294X},
support = {S10 OD018174/OD/NIH HHS/United States ; CZO EAR-1331940//National Science Foundation/ ; DEB-1656009//National Science Foundation/ ; 91767101-0//US Environmental Protection Agency/ ; },
mesh = {*Cyanobacteria/genetics ; Ecosystem ; Metagenomics ; Rivers ; Russia ; },
abstract = {The relative importance of separation by distance and by environment to population genetic diversity can be conveniently tested in river networks, where these two drivers are often independently distributed over space. To evaluate the importance of dispersal and environmental conditions in shaping microbial population structures, we performed genome-resolved metagenomic analyses of benthic Microcoleus-dominated cyanobacterial mats collected in the Eel and Russian River networks (California, USA). The 64 Microcoleus genomes were clustered into three species that shared >96.5% average nucleotide identity (ANI). Most mats were dominated by one strain, but minor alleles within mats were often shared, even over large spatial distances (>300 km). Within the most common Microcoleus species, the ANI between the dominant strains within mats decreased with increasing spatial separation. However, over shorter spatial distances (tens of kilometres), mats from different subwatersheds had lower ANI than mats from the same subwatershed, suggesting that at shorter spatial distances environmental differences between subwatersheds in factors like canopy cover, conductivity, and mean annual temperature decreases ANI. Since mats in smaller creeks had similar levels of nucleotide diversity (π) as mats in larger downstream subwatersheds, within-mat genetic diversity does not appear to depend on the downstream accumulation of upstream-derived strains. The four-gamete test and sequence length bias suggest recombination occurs between almost all strains within each species, even between populations separated by large distances or living in different habitats. Overall, our results show that, despite some isolation by distance and environmental conditions, sufficient gene-flow occurs among cyanobacterial strains to prevent either driver from producing distinctive population structures across the watershed.},
}
@article {pmid34608508,
year = {2022},
author = {Alguacil, MDM and Schlaeppi, K and López-García, &#xc1; and van der Heijden, MGA and Querejeta, JI},
title = {Contrasting Responses of Arbuscular Mycorrhizal Fungal Families to Simulated Climate Warming and Drying in a Semiarid Shrubland.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {941-944},
pmid = {34608508},
issn = {1432-184X},
mesh = {Humans ; *Mycorrhizae/genetics ; Ecosystem ; Soil Microbiology ; Biodiversity ; Soil/chemistry ; *Glomeromycota ; Plant Roots/microbiology ; },
abstract = {We carried out a 4-year manipulative field experiment in a semiarid shrubland in southeastern Spain to assess the impacts of experimental warming (W), rainfall reduction (RR), and their combination (W + RR) on the composition and diversity of arbuscular mycorrhizal fungal (AMF) communities in rhizosphere soil of H. syriacum and G. struthium shrubs using single-molecule real-time (SMRT) DNA sequencing. Across climate treatments, we encountered 109 AMF operational taxonomic units (OTUs) that were assigned to four families: Glomeraceae (93.94%), Gigasporaceae (2.19%), Claroideoglomeraceae (1.95%), and Diversisporaceae (1.92%). AMF community composition and diversity at OTU level were unaffected by the climate manipulation treatments, except for a significant decrease in AMF OTU richness in the W treatment relative to the control. However, we found a significant decrease of AMF family richness in all climate manipulation treatments relative to the control treatment. Members of the Gigasporaceae and Diversisporaceae families appeared to be highly vulnerable to intensification of heat and drought stress, as their abundances decreased by 67% and 77%, respectively, in the W + RR treatment relative to current ambient conditions. In contrast, the relative abundance and dominance of the Glomeraceae family within the AMF community increased significantly under the W + RR treatment, with Glomeraceae being the indicator family for the W + RR treatment. The interaction between warming and rainfall reduction had a significant effect on AMF community structure at family level. These findings provide new insights to help in the conservation of the soil biodiversity facing climate change in dryland ecosystems.},
}
@article {pmid34606240,
year = {2021},
author = {Webster, TM and McFarland, A and Gebert, MJ and Oliverio, AM and Nichols, LM and Dunn, RR and Hartmann, EM and Fierer, N},
title = {Structure and Functional Attributes of Bacterial Communities in Premise Plumbing Across the United States.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {20},
pages = {14105-14114},
doi = {10.1021/acs.est.1c03309},
pmid = {34606240},
issn = {1520-5851},
mesh = {*Drinking Water ; Humans ; *Mycobacterium ; RNA, Ribosomal, 16S/genetics ; Sanitary Engineering ; United States ; Water Microbiology ; },
abstract = {Microbes that thrive in premise plumbing can have potentially important effects on human health. Yet, how and why plumbing-associated microbial communities vary across broad spatial scales remain undetermined. We characterized the bacterial communities in 496 showerheads collected from across the continental United States. The overall community structure, determined by 16S rRNA gene amplicon sequencing, revealed high levels of bacterial diversity. Although a large fraction of the observed variation in community composition could not be explained, differences in bacterial community composition were associated with water supply (private well water vs public municipal water), water source (groundwater vs surface water), and associated differences in water chemistry (pH and chlorine). Most notably, showerheads in homes supplied with public water had higher abundances of Blastomonas, Mycobacterium, and Porphyrobacter, while Pseudorhodoplanes, Novosphingobium, and Nitrospira were more abundant in those receiving private well water. We conducted shotgun metagenomic analyses on 92 of these samples to assess differences in genomic attributes. Public water-sourced showerheads had communities enriched in genes related to lipid and xenobiotic metabolisms, virulence factors, and antibiotic resistance. In contrast, genes associated with oxidative stress and membrane transporters were over-represented in communities from private well water-sourced showerheads compared to those supplied by public water systems. These results highlight the broad diversity of bacteria found in premise plumbing across the United States and the role of the water source and treatment in shaping the microbial community structure and functional potential.},
}
@article {pmid34604105,
year = {2021},
author = {Zöhrer, PA and Hana, CA and Seyed Khoei, N and Mölzer, C and Hörmann-Wallner, M and Tosevska, A and Doberer, D and Marculescu, R and Bulmer, AC and Herbold, CW and Berry, D and Wagner, KH},
title = {Gilbert's Syndrome and the Gut Microbiota - Insights From the Case-Control BILIHEALTH Study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {701109},
pmid = {34604105},
issn = {2235-2988},
mesh = {Case-Control Studies ; Clostridiales ; Female ; *Gastrointestinal Microbiome ; *Gilbert Disease/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The heme catabolite bilirubin has anti-inflammatory, anti-oxidative and anti-mutagenic effects and its relation to colorectal cancer (CRC) risk is currently under evaluation. Although the main metabolic steps of bilirubin metabolism, including the formation of stercobilin and urobilin, take place in the human gastrointestinal tract, potential interactions with the human gut microbiota are unexplored. This study investigated, whether gut microbiota composition is altered in Gilbert's Syndrome (GS), a mild form of chronically elevated serum unconjugated bilirubin (UCB) compared to matched controls. Potential differences in the incidence of CRC-associated bacterial species in GS were also assessed. To this end, a secondary investigation of the BILIHEALTH study was performed, assessing 45 adults with elevated UCB levels (GS) against 45 age- and sex-matched controls (C). Fecal microbiota analysis was performed using 16S rRNA gene sequencing. No association between mildly increased UCB and the composition of the gut microbiota in this healthy cohort was found. The alpha and beta diversity did not differ between C and GS and both groups showed a typical representation of the known dominant phyla. Furthermore, no difference in abundance of Firmicutes and Proteobacteria, which have been associated with the mucosa of CRC patients were observed between the groups. A sequence related to the Christensenella minuta strain YIT 12065 was identified with a weak association value of 0.521 as an indicator species in the GS group. This strain has been previously associated with a lower body mass index, which is typical for the GS phenotype. Overall, sex was the only driver for an identifiable difference in the study groups, as demonstrated by a greater bacterial diversity in women. After adjusting for confounding factors and multiple testing, we can conclude that the GS phenotype does not affect the composition of the human gut microbiota in this generally healthy study group.},
}
@article {pmid34603252,
year = {2021},
author = {Cai, S and Fan, Y and Zhang, B and Lin, J and Yang, X and Liu, Y and Liu, J and Ren, J and Xu, H},
title = {Appendectomy Is Associated With Alteration of Human Gut Bacterial and Fungal Communities.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {724980},
pmid = {34603252},
issn = {1664-302X},
abstract = {Recent research has revealed the importance of the appendix in regulating the intestinal microbiota and mucosal immunity. However, the changes that occur in human gut microbial communities after appendectomy have never been analyzed. We assessed the alterations in gut bacterial and fungal populations associated with a history of appendectomy. In this cross-sectional study, we investigated the association between appendectomy and the gut microbiome using 16S and ITS2 sequencing on fecal samples from 30 healthy individuals with prior appendectomy (HwA) and 30 healthy individuals without appendectomy (HwoA). Analysis showed that the gut bacterial composition of samples from HwA was less diverse than that of samples from HwoA and had a lower abundance of Roseburia, Barnesiella, Butyricicoccus, Odoribacter, and Butyricimonas species, most of which were short-chain fatty acids-producing microbes. The HwA subgroup analysis indicated a trend toward restoration of the HwoA bacterial microbiome over time after appendectomy. HwA had higher gut fungi composition and diversity than HwoA, even 5 years after appendectomy. Compared with those in samples from HwoA, the abundance correlation networks in samples from HwA displayed more complex fungal-fungal and fungal-bacterial community interactions. This study revealed a marked impact of appendectomy on gut bacteria and fungi, which was particularly durable for fungi.},
}
@article {pmid34603220,
year = {2021},
author = {Delago, A and Gregor, R and Dubinsky, L and Dandela, R and Hendler, A and Krief, P and Rayo, J and Aharoni, A and Meijler, MM},
title = {A Bacterial Quorum Sensing Molecule Elicits a General Stress Response in Saccharomyces cerevisiae.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {632658},
pmid = {34603220},
issn = {1664-302X},
abstract = {Bacteria assess their population density through a chemical communication mechanism termed quorum sensing, in order to coordinate group behavior. Most research on quorum sensing has focused primarily on its role as an intraspecies chemical signaling mechanism that enables the regulation of certain phenotypes through targeted gene expression. However, in recent years several seminal studies have revealed important phenomena in which quorum sensing molecules appear to serve additional roles as interspecies signals that may regulate microbial ecology. In this study, we asked whether the budding yeast Saccharomyces cerevisiae can sense chemical signals from prokaryotes. When exposed to a variety of quorum sensing molecules from different bacterial species and from Candida albicans we found that N-(3-oxododecanoyl)-L-homoserine lactone (C12) from the opportunistic human pathogen Pseudomonas aeruginosa induces a remarkable stress response in yeast. Microarray experiments confirmed and aided in interpreting these findings, showing a unique and specific expression pattern that differed significantly from the response to previously described stress factors. We further characterized this response and report preliminary findings on the molecular basis for the recognition of C12 by the yeast.},
}
@article {pmid34602304,
year = {2022},
author = {Mauger, S and Monard, C and Thion, C and Vandenkoornhuyse, P},
title = {Contribution of single-cell omics to microbial ecology.},
journal = {Trends in ecology &amp; evolution},
volume = {37},
number = {1},
pages = {67-78},
doi = {10.1016/j.tree.2021.09.002},
pmid = {34602304},
issn = {1872-8383},
mesh = {Ecology ; Genome ; Genomics ; *Microbiota ; },
abstract = {Micro-organisms play key roles in various ecosystems, but many of their functions and interactions remain undefined. To investigate the ecological relevance of microbial communities, new molecular tools are being developed. Among them, single-cell omics assessing genetic diversity at the population and community levels and linking each individual cell to its functions is gaining interest in microbial ecology. By giving access to a wider range of ecological scales (from individual to community) than culture-based approaches and meta-omics, single-cell omics can contribute not only to micro-organisms' genomic and functional identification but also to the testing of concepts in ecology. Here, we discuss the contribution of single-cell omics to possible breakthroughs in concepts and knowledge on microbial ecosystems and ecoevolutionary processes.},
}
@article {pmid34601412,
year = {2022},
author = {Shi, B and Cheng, C and Zhang, Y and Du, Z and Zhu, L and Wang, J and Wang, J and Li, B},
title = {Effects of 3,6-dichlorocarbazole on microbial ecology and its degradation in soil.},
journal = {Journal of hazardous materials},
volume = {424},
number = {Pt A},
pages = {127315},
doi = {10.1016/j.jhazmat.2021.127315},
pmid = {34601412},
issn = {1873-3336},
mesh = {Carbazoles ; *Dioxins ; *Polychlorinated Dibenzodioxins ; Soil ; Soil Microbiology ; *Soil Pollutants ; },
abstract = {The emerging contaminants polyhalogenated carbazoles (PHCZs) have been verified to be present in soils and sediments globally, and they show dioxin-like toxicity. However, there is a lack of soil ecological risk assessments on PHCZs despite their high detection rate and concentration in soils. The present study investigated the degradation and soil microbial influence of 3,6-dichlorocarbazole (3,6-DCCZ, a frequently detected PHCZ) in soil. The results showed that the half-lives of 3,6-DCCZ at concentrations of 0.100 mg/kg and 1.00 mg/kg were 7.75 d and 16.73 d, respectively. We found that 3,6-DCCZ was transformed into 3-chlorocarbazole (3-CCZ) by dehalogenation in soil. Additionally, intermediate products with higher molecular weights were detected, presumably because the -H on the carbazole ring was replaced by -CH3, -CH2-O-CH3, or -CH2-O-CH2CH3. 3,6-DCCZ exposure slightly increased the soil bacterial abundance and diversity and clearly changed the soil bacterial community structure. Through a comprehensive analysis of FAPROTAX, functional gene qPCR and soil enzyme tests, we concluded that 3,6-DCCZ exposure inhibited nitrification and nitrogen fixation but promoted denitrification, carbon dioxide fixation and hydrocarbon degradation processes in soil. This study provides valuable data for clarifying the PHCZ ecological risk in soil.},
}
@article {pmid34600678,
year = {2021},
author = {Marzorati, M and Van den Abbeele, P and Bubeck, S and Bayne, T and Krishnan, K and Young, A},
title = {Treatment with a spore-based probiotic containing five strains of Bacillus induced changes in the metabolic activity and community composition of the gut microbiota in a SHIME® model of the human gastrointestinal system.},
journal = {Food research international (Ottawa, Ont.)},
volume = {149},
number = {},
pages = {110676},
doi = {10.1016/j.foodres.2021.110676},
pmid = {34600678},
issn = {1873-7145},
mesh = {*Bacillus ; Colon ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Probiotics ; Spores, Bacterial ; Verrucomicrobia ; },
abstract = {MegaSporeBiotic™ is an oral, spore-based probiotic comprised of five Bacillus spp. (Bacillus indicus HU36, Bacillus subtilis HU58, Bacillus coagulans SC208, Bacillus licheniformis SL307, and Bacillus clausii SC109). The effects of MegaSporeBiotic™ on gut microbiota activity and community composition were evaluated for the first time using an in vitro model of the human gastrointestinal tract, the simulator of the human intestinal microbial ecosystem (SHIME®), under healthy conditions. Following a stabilization period and a control period (2 weeks each), the reactor feed was supplemented with daily MegaSporeBiotic™ for 3 weeks (treatment period). Changes in microbial community activity and composition between the control and treatment periods were evaluated for each colon compartment (ascending [AC], transverse [TC], and descending colon [DC]). Propionate levels increased significantly in the TC (week 2, P = 0.02; week 3, P = 0.0019) and DC (week 2, P = 0.03) with treatment while lactate levels significantly decreased in the TC (week 3, P = 0.03). Ammonium levels were significantly decreased during the final week of treatment (TC, P = 0.02; DC, P = 0.03). Overall, Akkermansia muciniphila, Bifidobacteria spp., and Firmicutes increased with treatment while Lactobacillus spp. and Bacteroidetes decreased. The Firmicutes:Bacteroidetes ratio increased with treatment in the AC compartment. MegaSporeProbiotic™ treatment resulted in changes in metabolism and increased bacterial diversity.},
}
@article {pmid34600491,
year = {2021},
author = {Deng, X and Si, J and Qu, Y and Jie, L and He, Y and Wang, C and Zhang, Y},
title = {Vegetarian diet duration's influence on women's gut environment.},
journal = {Genes &amp; nutrition},
volume = {16},
number = {1},
pages = {16},
pmid = {34600491},
issn = {1555-8932},
support = {2018-JYBZZ-JS014//young teacher project of beijing university of chinese medicine/ ; 2017-JYB-JS-022//young teacher project of beijing university of chinese medicine/ ; },
abstract = {BACKGROUND: Nutrient composition of vegetarian diets is greatly different from that of omnivore diets, which may fundamentally influence the gut microbiota and fecal metabolites. The interactions between diet pattern and gut environment need further illustration. This study aims to compare the difference in the gut microbiota and fecal metabolites between vegetarian and omnivore female adults and explore associations between dietary choices/duration and gut environment changes.<br><br>METHODS: In this study, investigations on the fecal metabolome together with the gut microbiome were performed to describe potential interactions with quantitative functional annotation. In order to eliminate the differences brought by factors of gender and living environment, 80 female adults aged 20 to 48 were recruited in the universities in Beijing, China. Quantitative Insights Into Microbial Ecology (QIIME) analysis and Ingenuity Pathway Analysis (IPA) were applied to screen differential data between groups from gut microbiota and fecal metabolites. Furthermore, weighted gene correlation network analysis (WGCNA) was employed as the bioinformatics analysis tool for describing the correlations between gut microbiota and fecal metabolites. Moreover, participants were further subdivided by the vegetarian diet duration for analysis.<br><br>RESULTS: GPCR-mediated integration of enteroendocrine signaling was predicted to be one of the regulatory mechanisms of the vegetarian diet. Intriguingly, changes in the gut environment which occurred along with the vegetarian diet showed attenuated trend as the duration increased. A similar trend of returning to "baseline" after a 10-year vegetarian diet was detected in both gut microbiota and fecal metabolome.<br><br>CONCLUSIONS: The vegetarian diet is beneficial more than harmful to women. Gut microbiota play roles in the ability of the human body to adapt to external changes.},
}
@article {pmid34600011,
year = {2022},
author = {Fehlauer, T and Collin, B and Angeletti, B and Santaella, C and Dentant, C and Chaurand, P and Levard, C and Gonneau, C and Borschneck, D and Rose, J},
title = {Uptake patterns of critical metals in alpine plant species growing in an unimpaired natural site.},
journal = {Chemosphere},
volume = {287},
number = {Pt 4},
pages = {132315},
doi = {10.1016/j.chemosphere.2021.132315},
pmid = {34600011},
issn = {1879-1298},
mesh = {Biodegradation, Environmental ; *Brassicaceae ; Environmental Monitoring ; Metals/analysis ; *Metals, Heavy/analysis ; Soil ; *Soil Pollutants/analysis ; },
abstract = {The range of metals used for industrial purposes - electrical engineering, solar panels, batteries - has increased substantially over the last twenty years. Some of these emerging metals are the subject of geopolitical conflict and are considered critical as their unique properties make them irreplaceable. Many of these elements are poorly studied and their biogeochemical cycles still raise many questions. Aim of this study is to analyse the soil-to-plant transfer of some of these chemical elements and to shed light on their uptake pathways. For this purpose, the geological site of Jas Roux (France) was chosen as this alpine site is naturally rich in critical and potentially toxic elements such as As, Sb, Ba and Tl, but nevertheless is host to a high diversity of plants. Elemental concentrations were analysed in the topsoil and in 12 selected alpine plant species sampled in situ. Statistical tools were used to detect species dependent characteristics in elemental uptake. Our analyses revealed accumulation of rare earth elements by Saxifraga paniculata, selective oxyanion absorption by Hippocrepis comosa, accumulation of Tl by Biscutella laevigata and Galium corrudifolium and an exclusion strategy in Juniperus communis. These findings advance our understanding of the environmental behaviour of critical metals and metalloids such as V, As, Y, Sb, Ce, Ba and Tl and might bare valuable information for phytoremediation applications.},
}
@article {pmid34599659,
year = {2022},
author = {Aivelo, T and Lemoine, M and Tschirren, B},
title = {Elevational Changes in Bacterial Microbiota Structure and Diversity in an Arthropod-Disease Vector.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {868-878},
pmid = {34599659},
issn = {1432-184X},
support = {17_027//Stiftung f&#xfc;r wissenschaftliche Forschung an der Universit&#xe4;t Z&#xfc;rich/ ; PP00P3_128386//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; PP00P3_157455//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {Animals ; Female ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Arthropods ; *Microbiota/genetics ; *Ixodes/microbiology ; Bacteria/genetics ; Disease Vectors ; },
abstract = {Environmental conditions change rapidly along elevational gradients and have been found to affect community composition in macroscopic taxa, with lower diversity typically observed at higher elevations. In contrast, microbial community responses to elevation are still poorly understood. Specifically, the effects of elevation on vector-associated microbiota have not been studied to date, even though the within-vector microbial community is known to influence vector competence for a range of zoonotic pathogens. Here we characterize the structure and diversity of the bacterial microbiota in an important zoonotic disease vector, the sheep tick Ixodes ricinus, along replicated elevational gradient (630-1673 m) in the Swiss Alps. 16S rRNA sequencing of the whole within-tick bacterial microbiota of questing nymphs and adults revealed a decrease in Faith's phylogenetic microbial alpha diversity with increasing elevation, while beta diversity analyses revealed a lower variation in microbial community composition at higher elevations. We also found a higher microbial diversity later in the season and significant differences in microbial diversity among tick life stages and sexes, with lowest microbial alpha diversity observed in adult females. No associations between tick genetic diversity and bacterial diversity were observed. Our study demonstrates systematic changes in tick bacterial microbiota diversity along elevational gradients. The observed patterns mirror diversity changes along elevational gradients typically observed in macroscopic taxa, and they highlight the key role of environmental factors in shaping within-host microbial communities in ectotherms.},
}
@article {pmid34599356,
year = {2022},
author = {Almendras, K and Iannuzzi, S and Carú, M and Orlando, J},
title = {Diversity of Microbial Functional Genes Should Be Considered During the Interpretation of the qPCR Melting Curves.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {935-940},
pmid = {34599356},
issn = {1432-184X},
support = {1181510//fondo nacional de desarrollo cient&#xed;fico y tecnol&#xf3;gico/ ; },
mesh = {*Soil Microbiology ; *Nitrogen/analysis ; Phosphorus ; Bacteria/genetics ; Soil/chemistry ; Real-Time Polymerase Chain Reaction ; },
abstract = {Soil microorganisms play an essential role in biogeochemical cycles. One approach to study these microbial communities is quantifying functional genes by quantitative PCR (qPCR), in which a melting curve analysis is usually assessed to confirm that a single PCR product is being quantified. However, the high diversity of functional genes in environmental samples could generate more than one peak in those curves, so the presence of two or multiple peaks does not always indicate nonspecific amplification. Here, we analyzed the taxonomic diversity of soil microorganisms harboring functional genes involved in nitrogen (N) and phosphorus (P) cycles, based on a database of genomes and metagenomes, and predicted the melting curve profiles of these genes. These functional genes were spread across many bacterial phyla, but mainly Proteobacteria and Actinobacteria. In general, the melting curves exhibited more than one peak or peaks with shoulders, mainly related to the variation of the nucleotide composition of the genes and the expected size of the amplicons. These results indicate that the melting curves of functional genes from environmental samples should be carefully evaluated, being in silico analyses a cost-effective way to identify inherent sequence diversity and avoid interpreting multiple peaks always as unspecific amplifications.},
}
@article {pmid34596724,
year = {2021},
author = {Wang, Y and Elzenga, T and van Elsas, JD},
title = {Effect of culture conditions on the performance of lignocellulose-degrading synthetic microbial consortia.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {20},
pages = {7981-7995},
pmid = {34596724},
issn = {1432-0614},
mesh = {*Ascomycota ; Lignin ; *Microbial Consortia ; Sphingobacterium ; },
abstract = {In this study, we examined a synthetic microbial consortium, composed of two selected bacteria, i.e., Citrobacter freundii so4 and Sphingobacterium multivorum w15, next to the fungus Coniochaeta sp. 2T2.1, with respect to their fate and roles in the degradation of wheat straw (WS). A special focus was placed on the effects of pH (7.2, 6.2, or 5.2), temperature (25 versus 28 °C), and shaking speed (60 versus 180 rpm). Coniochaeta sp. 2T2.1 consistently had a key role in the degradation process, with the two bacteria having additional roles. Whereas temperature exerted only minor effects on the degradation, pH and shaking speed were key determinants of both organismal growth and WS degradation levels. In detail, the three-partner degrader consortium showed significantly higher WS degradation values at pH 6.2 and 5.2 than at pH 7.2. Moreover, the two bacteria revealed up to tenfold enhanced final cell densities (ranging from log8.0 to log9.0 colony forming unit (CFU)/mL) in the presence of Coniochaeta sp. 2T2.1 than when growing alone or in a bacterial bi-culture, regardless of pH range or shaking speed. Conversely, at 180 rpm, fungal growth was clearly suppressed by the presence of the bacteria at pH 5.2 and pH 6.2, but not at pH 7.2. In contrast, at 60 rpm, the presence of the bacteria fostered fungal growth. In these latter cultures, oxygen levels were significantly lowered as compared to the maximal levels found at 180 rpm (about 5.67 mg/L, ~ 62% of saturation). Conspicuous effects on biomass appearance pointed to a fungal biofilm-modulating role of the bacteria.Key points• Coniochaeta sp. 2T2.1 has a key role in wheat straw (WS) degradation.• Bacterial impact shifts when conditions change.• pH and shaking speed are key drivers of the growth dynamics and WS degradation.},
}
@article {pmid34596711,
year = {2022},
author = {Russell, KA and McFrederick, QS},
title = {Elevated Temperature May Affect Nectar Microbes, Nectar Sugars, and Bumble Bee Foraging Preference.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {473-482},
pmid = {34596711},
issn = {1432-184X},
support = {CA- R-ENT-5109-H//National Institute of Food and Agriculture/ ; 2019-67011-29604//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; Bacteria ; Bees ; Flowers/microbiology ; *Plant Nectar ; *Pollination/physiology ; Sugars ; Temperature ; },
abstract = {Floral nectar, an important resource for pollinators, is inhabited by microbes such as yeasts and bacteria, which have been shown to influence pollinator preference. Dynamic and complex plant-pollinator-microbe interactions are likely to be affected by a rapidly changing climate, as each player has their own optimal growth temperatures and phenological responses to environmental triggers, such as temperature. To understand how warming due to climate change is influencing nectar microbial communities, we incubated a natural nectar microbial community at different temperatures and assessed the subsequent nectar chemistry and preference of the common eastern bumble bee, Bombus impatiens. The microbial community in floral nectar is often species-poor, and the cultured Brassica rapa nectar community was dominated by the bacterium Fructobacillus. Temperature increased the abundance of bacteria in the warmer treatment. Bumble bees preferred nectar inoculated with microbes, but only at the lower, ambient temperature. Warming therefore induced an increase in bacterial abundance which altered nectar sugars and led to significant differences in pollinator preference.},
}
@article {pmid34596710,
year = {2022},
author = {Zhang, M and Gao, ZC and Chi, Z and Wang, Z and Liu, GL and Li, XF and Hu, Z and Chi, ZM},
title = {Massoia Lactone Displays Strong Antifungal Property Against Many Crop Pathogens and Its Potential Application.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {376-390},
pmid = {34596710},
issn = {1432-184X},
support = {31970058//innovative research group project of the national natural science foundation of china/ ; },
mesh = {Antifungal Agents/pharmacology ; *Fungicides, Industrial ; *Fusarium/physiology ; Lactones/pharmacology ; Plant Diseases/microbiology/prevention &amp; control ; Triticum/microbiology ; },
abstract = {Massoia lactone could be released from liamocins produced by Aureobasidium melanogenum M39. The obtained Massoia lactone was very stable and highly active against many fungal crop pathogens which cause many plant diseases and food unsafety. Massoia lactone treatment not only could effectively inhibit their hyphal growth and spore germination, but also caused pore formation in cell membrane, reduction of ergosterol content, rise in intracellular ROS levels, and leakage of intracellular components, consequently leading to cellular necrosis and cell death. The direct contact of Massoia lactone with Fusarium graminearum spores could stop the development of Fusarium head blight symptom in the diseased wheats. Therefore, Massoia lactone could be a promising candidate for development as an effective and green bio-fungicide because of its high anti-fungal activity and the multiplicity of mode of its action.},
}
@article {pmid34596709,
year = {2022},
author = {Banister, RB and Schwarz, MT and Fine, M and Ritchie, KB and Muller, EM},
title = {Instability and Stasis Among the Microbiome of Seagrass Leaves, Roots and Rhizomes, and Nearby Sediments Within a Natural pH Gradient.},
journal = {Microbial ecology},
volume = {84},
number = {3},
pages = {703-716},
pmid = {34596709},
issn = {1432-184X},
mesh = {*Rhizome/chemistry ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; Hydrogen-Ion Concentration ; Proton-Motive Force ; *Microbiota ; Bacteria/genetics ; },
abstract = {Seagrass meadows are hotspots of biodiversity with considerable economic and ecological value. The health of seagrass ecosystems is influenced in part by the makeup and stability of their microbiome, but microbiome composition can be sensitive to environmental change such as nutrient availability, elevated temperatures, and reduced pH. The objective of the present study was to characterize the bacterial community of the leaves, bulk samples of roots and rhizomes, and proximal sediment of the seagrass species Cymodocea nodosa along the natural pH gradient of Levante Bay, Vulcano Island, Italy. The bacterial community was determined by characterizing the 16S rRNA amplicon sequencing and analyzing the operational taxonomic unit classification of bacterial DNA within samples. Statistical analyses were used to explore how life-long exposure to different pH/pCO2 conditions may be associated with significant differences in microbial communities, dominant bacterial classes, and microbial diversity within each plant section and sediment. The microbiome of C. nodosa significantly differed among all sample types and site-specific differences were detected within sediment and root/rhizome microbial communities, but not the leaves. These results show that C. nodosa leaves have a consistent microbial community even across a pH range of 8.15 to 6.05. The ability for C. nodosa to regulate and maintain microbial structure may indicate a semblance of resilience within these vital ecosystems under projected changes in environmental conditions such as ocean acidification.},
}
@article {pmid34591681,
year = {2021},
author = {Castillo, DJ and Van Goethem, MW and Makhalanyane, TP},
title = {Three Draft Single-Cell Genome Sequences of Novel SAR324 Strains Isolated from the Abyssopelagic Southern Ocean.},
journal = {Microbiology resource announcements},
volume = {10},
number = {39},
pages = {e0075921},
pmid = {34591681},
issn = {2576-098X},
support = {110717//National Research Foundation (NRF)/ ; },
abstract = {SAR324 is a ubiquitous and phylogenetically distinct clade of Deltaproteobacteria in marine environments. Here, we present three single-cell amplified genome sequences from the SAR324 lineage, obtained from the abyssopelagic zone of the Indian sector of the Southern Ocean.},
}
@article {pmid34591135,
year = {2022},
author = {Villegas-Plazas, M and Sanabria, J and Arbeli, Z and Vasquez, Y and Roldan, F and Junca, H},
title = {Metagenomic Analysis of Biochemical Passive Reactors During Acid Mine Drainage Bioremediation Reveals Key Co-selected Metabolic Functions.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {465-472},
pmid = {34591135},
issn = {1432-184X},
support = {Beca de Estudios Doctorales Nacionales 727//Minciencias/ ; 120377657722//Minciencias/ ; },
mesh = {Acids ; Biodegradation, Environmental ; *Metagenomics ; *Mining ; Sulfates/metabolism ; },
abstract = {Acid mine drainage (AMD) is the major pollutant generated by the mining industry, and it is characterized by low pH and high concentration of metals and sulfate. The use of biochemical passive reactors (BPRs) is a promising strategy for its bioremediation. To date, there are various studies describing the taxonomical composition of BPR microbial communities, generally consisting of an assemblage of sulfate-reducing organisms inside Deltaproteobacteria, and a diverse set of anaerobic (ligno)cellulolytic bacteria; however, insights about its functional metagenomic content are still scarce. In previous studies, a laboratory-scale AMD bioremediation using biochemical passive reactors was designed and performed, tracking operation parameters, chemical composition, and changes, together with taxonomic composition of the microbiomes harbored in these systems. In order to reveal the main functional content of these communities, we used shotgun metagenomics analyses to explore genes of higher relative frequencies and their inferred functions during the AMD bioremediation from three BPRs representing the main microbiome compositions detected in the system. Remarkably, genes encoding for two-component regulatory systems and ABC transporters related to metal and inorganic ions, cellulose degradation enzymes, dicarboxylic acid production, and sulfite reduction complex were all detected at increased frequency. Our results evidenced that higher taxonomic diversity of the microbiome was arising together with a functional redundancy of the specific metabolic roles, indicating its co-selection and suggesting that its enrichment on BPRs may be implicated in the cumulative efficiency of these systems.},
}
@article {pmid34589797,
year = {2021},
author = {Hovens, IB and van Leeuwen, BL and Falcao-Salles, J and de Haan, JJ and Schoemaker, RG},
title = {Enteral enriched nutrition to prevent cognitive dysfunction after surgery; a study in rats.},
journal = {Brain, behavior, &amp; immunity - health},
volume = {16},
number = {},
pages = {100305},
pmid = {34589797},
issn = {2666-3546},
abstract = {BACKGROUND: Inflammation plays an important role in postoperative cognitive dysfunction (POCD), particularly in elderly patients. Enteral enriched nutrition was shown to inhibit the response on inflammatory stimuli. Aim of the present study was to explore the therapeutic potential of enteral enriched nutrition in our rat model for POCD. The anticipated mechanism of action was examined in young rats, while responses in the target group of elderly patients were evaluated in old rats.<br><br>METHODS: Male 3 and 23 months old Wistar rats received a bolus of enteral fat/protein-enriched nutrition 2&#xa0;&#x200b;h and 30&#xa0;&#x200b;min before surgery. The inflammatory response was evaluated by systemic inflammation markers and brain microglia activity. Additionally, in old rats, the role of the gut-brain axis was studied by microbiome analyses of faecal samples. Days 9-14 after surgery, rats were subjected to cognitive testing. Day 16, rats were sacrificed and brains were collected for immunohistochemistry.<br><br>RESULTS: In young rats, enriched nutrition improved long-term spatial learning and memory in the Morris Water Maze, reduced plasma IL1-&#x3b2; and VEGF levels, but left microglia activity and neurogenesis unaffected. In contrast, in old rats, enriched nutrition improved short-term memory in the novel object- and novel location recognition tests, but impaired development of long-term memory in the Morris Water Maze. Systemic inflammation was not affected, but microglia activity seemed even increased. Gut integrity and microbiome were not affected.<br><br>CONCLUSION: Enteral enriched nutrition before surgery in young rats indeed reduced systemic inflammation and improved cognitive performance after surgery, whereas old rats showed a mixed favorable/unfavorable cognitive response, without effect on systemic inflammation. Anti-inflammatory effects of enriched nutrition were not reflected in decreased microglia activity. Neither was an important role for the gut-brain axis observed. Since the relatively straight forward effects of enriched nutrition in young rats could not be shown in old rats, as indicated by a mixed beneficial/detrimental cognitive outcome in the latter, caution is advised by translating effects seen in younger patients to older ones.},
}
@article {pmid34589774,
year = {2021},
author = {Agarwala, S and Naik, B and Ramachandra, NB},
title = {Mucosa-associated specific bacterial species disrupt the intestinal epithelial barrier in the autism phenome.},
journal = {Brain, behavior, &amp; immunity - health},
volume = {15},
number = {},
pages = {100269},
pmid = {34589774},
issn = {2666-3546},
abstract = {Gut-Brain Axis provides a bidirectional communicational route, an imbalance of which can have pathophysiological consequences. Differential gut microbiome studies have become a frontier in autism research, affecting 85% of autistic children. The present study aims to understand how gut microbiota of autism subjects differ from their neurotypical counterparts. This study would help to identify the abundance of bacterial signature species in autism and their associated metabolites. 16S rRNA metagenomic sequence datasets of 30 out of 206 autism subjects were selected from the American Gut Project Archive. First, the taxonomic assignment was inferred by similarity-based methods using the Quantitative Insights into Microbial Ecology (QIIME) toolkit. Next, species abundance was characterized, and a co-occurrence network was built to infer species interaction using measures of diversity. Thirdly, statistical parameters were incorporated to validate the findings. Finally, the identification of metabolites associated with these bacterial signature species connects with biological processes in the host through pathway analysis. Gut microbiome data revealed Akkermansia sp. and Faecalibacterium prausnitzii to be statistically lower in abundance in autistic children than their neurotypical peers with a five and two-fold decrease, respectively. While Prevotella sp. and Sutterella sp. showed a five and a two-fold increase in cases, respectively. The constructed pathway revealed succinate and butyrate as the significant metabolites for the bacterial signature species identified. The present study throws light on the role of mucosa-associated bacterial species: Veillonella sp., Prevotella sp., Akkermansia sp., Sutterella sp., Faecalibacterium prausnitzii, Lactobacillus sp., which can act as diagnostic criteria for detection of gut dysbiosis in autism.},
}
@article {pmid34585291,
year = {2022},
author = {Martínez-López, V and Ruiz, C and Muñoz, I and Ornosa, C and Higes, M and Martín-Hernández, R and De la Rúa, P},
title = {Detection of Microsporidia in Pollinator Communities of a Mediterranean Biodiversity Hotspot for Wild Bees.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {638-642},
pmid = {34585291},
issn = {1432-184X},
support = {21260/PD/19//Fundaci&#xf3;n S&#xe9;neca/ ; 19908/GERM/2015//Fundaci&#xf3;n S&#xe9;neca/ ; JCI2018-036614-I//Ministerio de Econom&#xed;a y Competitividad/ ; FPU13/05115//Ministerio de Educaci&#xf3;n, Cultura y Deporte/ ; },
mesh = {Animals ; Bees ; Biodiversity ; Ecosystem ; *Moths ; *Nosema/genetics ; Phylogeny ; Pollination ; },
abstract = {Insect pollination is crucial for the maintenance of natural and managed ecosystems but the functioning of this ecosystem service is threatened by a worldwide decline of pollinators. Key factors in this situation include the spread and interspecific transmission of pathogens worldwide through the movement of managed pollinators. Research on this field has been mainly conducted in some particular species, while studies assessing the interspecific transmission of pathogens at a community level are scarce. However, this information is pivotal to design strategies to protect pollinators. Herein, we analysed the prevalence of two common microsporidia pathogens of managed honey bees (Nosema ceranae and N. apis) in bee communities of semiarid Mediterranean areas from the Southeast of the Iberian Peninsula. Our results confirm the ability of N. ceranae to disperse across wild bee communities in semiarid Mediterranean ecosystems since it was detected in 36 Apoidea species (39% of the sampling; for the first time in nine genera). The prevalence of the pathogen did not show any phylogenetic signal which suggests a superfamily host range of the pathogen or that wild bees may be acting only as vectors of N. ceranae. In addition, N. apis was detected in an Eucera species, which is the second time it has been detected by molecular techniques in a host other than the honey bee. Our study represents the primary assessment of the prevalence of microsporidia at community level in Mediterranean areas and provides outstanding results on the ability of Nosema pathogens to spread across the landscape.},
}
@article {pmid34585290,
year = {2022},
author = {Kaushal, M and Kolombia, Y and Alakonya, AE and Kuate, AF and Ortega-Beltran, A and Amah, D and Masso, C},
title = {Subterranean Microbiome Affiliations of Plantain (Musa spp.) Under Diverse Agroecologies of Western and Central Africa.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {580-593},
pmid = {34585290},
issn = {1432-184X},
support = {HRST/ST/AURG-II/CALL2/2018//African Union/ ; },
mesh = {Africa, Central ; *Ascomycota/genetics ; Bacteria/genetics ; *Microbiota/physiology ; *Musa/microbiology ; Plant Roots/microbiology ; *Plantago ; Rhizosphere ; Soil Microbiology ; },
abstract = {Plantain (Musa spp.) is a staple food crop and an important source of income for millions of smallholder farmers in sub-Saharan Africa (SSA). However, there is a paucity of knowledge on soil microbial diversity in agroecologies where plantains are grown. Microbial diversity that increases plant performance with multi-trophic interactions involving resiliency to environmental constraints is greatly needed. For this purpose, the bacterial and fungal communities of plantain fields in high rainfall forests (HR) and derived savannas (SV) were studied using Illumina MiSeq for 16S rDNA and ITS amplicon deep sequencing. Microbial richness (α- and β-diversity), operational taxonomic units, and Simpson and Shannon-Wiener indexes (observed species (Sobs), Chao, ACE; P < 0.05) suggested that there were significant differences between HR and SV agroecologies among the most abundant bacterial communities, and some specific dynamic response observed from fungal communities. Proteobacteria formed the predominant bacterial phylum (43.7%) succeeded by Firmicutes (24.7%), and Bacteroidetes (17.6%). Ascomycota, Basidiomycota, and Zygomycota were the three most dominant fungal phyla in both agroecologies. The results also revealed an immense array of beneficial microbes in the roots and rhizosphere of plantain, including Acinetobacter, Bacillus, and Pseudomonas spp. COG and KEGG Orthology database depicted significant variations in the functional attributes of microbes found in the rhizosphere to roots. This result indicates that the different agroecologies and host habitats differentially support the dynamic microbial profile and that helps in altering the structure in the rhizosphere zone for the sake of promoting synergistic host-microbe interactions particularly under resource-poor conditions of SSA.},
}
@article {pmid34585289,
year = {2022},
author = {Cao, X and Zhao, D and Li, C and Röttjers, L and Faust, K and Zhang, H},
title = {Regime transition Shapes the Composition, Assembly Processes, and Co-occurrence Pattern of Bacterioplankton Community in a Large Eutrophic Freshwater Lake.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {336-350},
pmid = {34585289},
issn = {1432-184X},
support = {41871096//National Natural Science Foundation of China/ ; 32171563//National Natural Science Foundation of China/ ; BK20181311//Natural Science Foundation of Jiangsu Province/ ; 2018B43414//Fundamental Research Funds for the Central Universities/ ; B200203051//Fundamental Research Funds for the Central Universities/ ; 201906710009//China Scholarship Council/ ; },
mesh = {Aquatic Organisms ; *Biodiversity ; China ; Ecosystem ; *Lakes/chemistry ; Phylogeny ; Phytoplankton/genetics ; Plankton/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {At certain nutrient concentrations, shallow freshwater lakes are generally characterized by two contrasting ecological regimes with disparate patterns of biodiversity and biogeochemical cycles: a macrophyte-dominated regime (MDR) and a phytoplankton-dominated regime (PDR). To reveal ecological mechanisms that affect bacterioplankton along the regime shift, Illumina MiSeq sequencing of the 16S rRNA gene combined with a novel network clustering tool (Manta) were used to identify patterns of bacterioplankton community composition across the regime shift in Taihu Lake, China. Marked divergence in the composition and ecological assembly processes of bacterioplankton community was observed under the regime shift. The alpha diversity of the bacterioplankton community consistently and continuously decreased with the regime shift from MDR to PDR, while the beta diversity presents differently. Moreover, as the regime shifted from MDR to PDR, the contribution of deterministic processes (such as environmental selection) to the assembly of bacterioplankton community initially decreased and then increased again as regime shift from MDR to PDR, most likely as a consequence of differences in nutrient concentration. The topological properties, including modularity, transitivity and network diameter, of the bacterioplankton co-occurrence networks changed along the regime shift, and the co-occurrences among species changed in structure and were significantly shaped by the environmental variables along the regime transition from MDR to PDR. The divergent environmental state of the regimes with diverse nutritional status may be the most important factor that contributes to the dissimilarity of bacterioplankton community composition along the regime shift.},
}
@article {pmid34584531,
year = {2021},
author = {Ge, W and Zhang, ZY and Dong, CB and Han, YF and Deshmukh, SK and Liang, ZQ},
title = {Bacterial Community Analysis and Potential Functions of Core Taxa in Different Parts of the Fungus Cantharellus cibarius.},
journal = {Polish journal of microbiology},
volume = {70},
number = {3},
pages = {373-385},
pmid = {34584531},
issn = {2544-4646},
mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Basidiomycota ; *Biodiversity ; *Microbial Interactions/physiology ; RNA, Ribosomal, 16S ; },
abstract = {Cantharellus cibarius is a widely distributed, popular, edible fungus with high nutritional and economic value. However, significant challenges persist in the microbial ecology and artificial cultivation of C. cibarius. Based on the 16S rRNA sequencing data, this study analyzed bacterial community structures and diversity of fruit bodies and rhizomorph parts of C. cibarius and mycosphere samples (collected in the Wudang District, Guiyang, Guizhou Province, China). It explored the composition and function of the core bacterial taxa. The analyzed results showed that the rhizomorph bacterial community structure was similar to mycosphere, but differed from the fruit bodies. Members of the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex had the highest abundance in the fruit bodies. However, they were either absent or low in abundance in the rhizomorphs and mycosphere. At the same time, members of the Burkholderia-Caballeronia-Paraburkholderia complex were abundant in the fruit bodies and rhizomorphs parts of C. cibarius, as well as mycosphere. Through functional annotation of core bacterial taxa, we found that there was an apparent trend of potential functional differentiation of related bacterial communities in the fruit body and rhizomorph: potential functional groups of core bacterial taxa in the fruit bodies centered on nitrogen fixation, nitrogen metabolism, and degradation of aromatic compounds, while those in rhizomorphs focused on aerobic chemoheterotrophy, chemoheterotrophy, defense against soil pathogens, decomposition of complex organic compounds, and uptake of insoluble inorganic compounds. The analysis of functional groups of bacteria with different structures is of great significance to understand that bacteria promote the growth and development of C. cibarius.},
}
@article {pmid34581470,
year = {2021},
author = {Wu, MR and Hou, TT and Liu, Y and Miao, LL and Ai, GM and Ma, L and Zhu, HZ and Zhu, YX and Gao, XY and Herbold, CW and Wagner, M and Li, DF and Liu, ZP and Liu, SJ},
title = {Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway.},
journal = {Environmental microbiology},
volume = {23},
number = {11},
pages = {6965-6980},
doi = {10.1111/1462-2920.15751},
pmid = {34581470},
issn = {1462-2920},
mesh = {Aerobiosis ; Alcaligenes/genetics/metabolism ; *Ammonia/metabolism ; Denitrification ; Escherichia coli/metabolism ; Nitrification ; Nitrites/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Sewage ; *Water Purification/methods ; },
abstract = {Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen-rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO-1, oxidizing ammonia to hydroxylamine and ending in the production of N2 gas. Genome analysis revealed that strain HO-1 encoded a complete denitrification pathway but lacks any genes coding for homologous to known ammonia monooxygenases or hydroxylamine oxidoreductases. Our results demonstrated strain HO-1 denitrified nitrite (not nitrate) to N2 and N2 O at anaerobic and aerobic conditions respectively. Further experiments demonstrated that inhibition of aerobic denitrification did not stop ammonia oxidation and N2 production. A gene cluster (dnfT1RT2ABCD) was cloned from strain HO-1 and enabled E. coli accumulated hydroxylamine. Sub-cloning showed that genetic cluster dnfAB or dnfABC already enabled E. coli cells to produce hydroxylamine and further to [15] N2 from ([15] NH4)2 SO4 . Transcriptome analysis revealed these three genes dnfA, dnfB and dnfC were significantly upregulated in response to ammonia stimulation. Taken together, we concluded that strain HO-1 has a novel dnf genetic cluster for ammonia oxidation and this dnf genetic cluster encoded a previously unknown pathway of direct ammonia oxidation (Dirammox) to N2 .},
}
@article {pmid34581434,
year = {2022},
author = {Zayed, N and Boon, N and Bernaerts, K and Chatzigiannidou, I and Van Holm, W and Verspecht, T and Teughels, W},
title = {Differences in chlorhexidine mouthrinses formulations influence the quantitative and qualitative changes in in-vitro oral biofilms.},
journal = {Journal of periodontal research},
volume = {57},
number = {1},
pages = {52-62},
doi = {10.1111/jre.12937},
pmid = {34581434},
issn = {1600-0765},
support = {//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {*Anti-Infective Agents ; *Anti-Infective Agents, Local/pharmacology ; Biofilms ; Cetylpyridinium/pharmacology ; Chlorhexidine/pharmacology ; Mouthwashes/pharmacology ; },
abstract = {OBJECTIVE: Chlorhexidine mouthrinses are marketed in different formulations. This study aimed at investigating qualitative and quantitative changes in in-vitro multispecies oral biofilms, induced by different chlorhexidine-containing mouthrinses.<br><br>BACKGROUND DATA: Earlier studies comparing chlorhexidine mouthrinses are either clinical studies or in-vitro studies assessing the antimicrobial efficacy of the mouthrinses. However, no clear investigations are available regarding ecological impact of different chlorhexidine formulations on in-vitro multispecies oral biofilms after rinsing with different chlorhexidine formulations.<br><br>METHODS: Nine commercially available chlorhexidine mouthrinses were selected. Multispecies oral communities (14&#xa0;species) were grown for 48&#xa0;h in a Biostat-B Twin bioreactor. After that, they were used to develop biofilms on the surface of hydroxyapatite disks in 24-well pates for 48&#xa0;h. Biofilms were then rinsed once or multiple times with the corresponding mouthrinse. Biofilms were collected before starting the rinsing experiment and every 24&#xa0;h for 3&#xa0;days and vitality quantitative PCR was performed. The experiment was repeated 3 independent times on 3 different days and the results were analyzed using a linear mixed model.<br><br>RESULTS: The mouthrinses provoked different effects in terms of change in total viable bacterial load (VBL), ecology, and community structure of the multispecies biofilms. There was no relation between chlorhexidine concentrations, presence, or absence of cetylpyridinium chloride and/or alcohol, and the observed effects. Some tested chlorhexidine mouthrinses (MC, HG, HH, and HI) strongly lowered the total VBL (&#x2248;10[07] Geq/ml), but disrupted biofilm symbiosis (&#x2265;40% of the biofilms communities are pathobionts). On the other hand, other tested chlorhexidine mouthrinses (MD, ME, and HF) had limited impact on total VBL (&#x2265;10[10] Geq/ml), but improved the biofilm ecology and community structure (&#x2264;10% of the biofilms communities are pathobionts).<br><br>CONCLUSION: Not all chlorhexidine mouthrinses have the same effect on oral biofilms. Their effect seems to be strongly product dependent and vary according to their compositions and formulations.},
}
@article {pmid34581127,
year = {2021},
author = {Yang, SH and Qin, ZS and Liang, MC},
title = {[Meta-analysis of Microbial Communities in the Activated Sludge of Wastewater Treatment Plants Under Different Climate Types].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {42},
number = {10},
pages = {4844-4852},
doi = {10.13227/j.hjkx.202101193},
pmid = {34581127},
issn = {0250-3301},
mesh = {China ; *Microbiota ; RNA, Ribosomal, 16S ; Sewage ; Wastewater ; *Water Purification ; },
abstract = {Microbial communities in wastewater treatment plants(WWTPs) are very important for water purification in the context of public drinking water safety and environmental health. Therefore, it is necessary to explore the trends in microbial community structure and diversity in sewage treatment plants and their main environmental impact factors under different climates in China. Based on high-throughput sequencing techniques, a meta-analysis was conducted to screen the 16S rRNA genes in an open database. We analyzed the trends in microbial community structure and diversity in WWTPs under three climate types(Dwa, Cfa, and Cwa) in China. We then constructed cohesion models to examine the core microbial taxa and their interactions within the communities. We also used a piecewise structural equation model(PSEM) to examine the effects of different climate types on microbial community structure. The three climate types significantly affected the structure and diversity of the microbial communities, with patterns correlated with influent pH, mixed liquid temperature, conductivity, and nitrogen concentrations(P<0.05). Based on the PSEM analysis, the β-diversity of the microbial communities was directly correlated with latitude, while α-diversity was indirectly correlated with latitude through conductivity and water temperature. Based on the cohesion modeling, microbial community stability was the highest under Dwa climate followed by the Cfa climate. This could be explained by a small subset of highly connected taxa capable of withstanding disturbance, indicating an important stability role. In contrast, the stability of the microbial communities under the Cwa climate was low, and no species with strong negative cohesion were observed. Overall, the structure, diversity, and stability of microbial community in WWTPs were found to be sensitive to climate, and the responsive mechanisms of α-diversity and β-diversity with respect to latitude were distinct.},
}
@article {pmid34580739,
year = {2022},
author = {Garcia-Vozmediano, A and Tomassone, L and Fonville, M and Bertolotti, L and Heylen, D and Fabri, ND and Medlock, JM and Nijhof, AM and Hansford, KM and Sprong, H and Krawczyk, AI},
title = {The Genetic Diversity of Rickettsiella Symbionts in Ixodes ricinus Throughout Europe.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {613-626},
pmid = {34580739},
issn = {1432-184X},
support = {01KI1720//Federal Ministry of Education and Research (BMBF)/ ; 799609//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; },
mesh = {Animals ; *Coxiellaceae ; Europe ; Genetic Variation ; *Ixodes/microbiology ; Phylogeny ; },
abstract = {Rickettsiella species are bacterial symbionts that are present in a great variety of arthropod species, including ixodid ticks. However, little is known about their genetic diversity and distribution in Ixodes ricinus, as well as their relationship with other tick-associated bacteria. In this study, we investigated the occurrence and the genetic diversity of Rickettsiella spp. in I. ricinus throughout Europe and evaluated any preferential and antagonistic associations with Candidatus Midichloria mitochondrii and the pathogens Borrelia burgdorferi sensu lato and Borrelia miyamotoi. Rickettsiella spp. were detected in most I. ricinus populations investigated, encompassing a wide array of climate types and environments. The infection prevalence significantly differed between geographic locations and was significantly higher in adults than in immature life stages. Phylogenetic investigations and protein characterization disclosed four Rickettsiella clades (I-IV). Close phylogenetic relations were observed between Rickettsiella strains of I. ricinus and other arthropod species. Isolation patterns were detected for Clades II and IV, which were restricted to specific geographic areas. Lastly, although coinfections occurred, we did not detect significant associations between Rickettsiella spp. and the other tick-associated bacteria investigated. Our results suggest that Rickettsiella spp. are a genetically and biologically diverse facultative symbiont of I. ricinus and that their distribution among tick populations could be influenced by environmental components.},
}
@article {pmid34579579,
year = {2021},
author = {Frederickson, ME and Reese, AT},
title = {Microbial Ecology and Evolution Are Essential for Understanding Pandemics.},
journal = {mBio},
volume = {12},
number = {5},
pages = {e0214421},
pmid = {34579579},
issn = {2150-7511},
support = {RGPIN-2021-03711//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Harvard University | Radcliffe Institute for Advanced Study, Harvard University (Radcliffe Institute for Advanced Study)/ ; GBMF9356//Gordon and Betty Moore Foundation | Symbiosis in Aquatic Systems Initiative/ ; },
mesh = {*Biological Evolution ; COVID-19/*epidemiology ; *Ecology ; Humans ; Microbiota/*physiology ; Pandemics ; },
abstract = {Ecology and evolution, especially of microbes, have never been more relevant than in our global fight against SARS-CoV-2, the virus that causes COVID-19. Understanding how populations of SARS-CoV-2 grow, disperse, and evolve is of critical importance to managing the COVID-19 pandemic, and these questions are fundamentally ecological and evolutionary in nature. We compiled data from bioRxiv and medRxiv preprint abstracts and US National Institutes of Health Research Project grant abstracts to visualize the impact that the pivot to COVID-19 research has had on the study of microbes across biological disciplines. Finding that the pivot appears weaker in ecology and evolutionary biology than in other areas of biology, we discuss why the ecology and evolution of microbes, both pathogenic and otherwise, need renewed attention and investment going forward.},
}
@article {pmid34579574,
year = {2021},
author = {Bosch, TCG and Zasloff, M},
title = {Antimicrobial Peptides-or How Our Ancestors Learned to Control the Microbiome.},
journal = {mBio},
volume = {12},
number = {5},
pages = {e0184721},
pmid = {34579574},
issn = {2150-7511},
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Anti-Infective Agents/pharmacology ; Antimicrobial Cationic Peptides/immunology ; Antimicrobial Peptides/*pharmacology ; Bacteria/drug effects ; Drosophila ; Fungi ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hydra ; Immunity, Innate ; Muramidase ; Plant Immunity ; Symbiosis ; Viruses ; },
abstract = {Antimicrobial peptides (AMPs) are short and generally positively charged peptides found in a wide variety of life forms from microorganisms to humans. Their wide range of activity against pathogens, including Gram-positive and -negative bacteria, yeasts, fungi, and enveloped viruses makes them a fundamental component of innate immunity. Marra et al. (A. Marra, M. A. Hanson, S. Kondo, B. Erkosar, B. Lemaitre, mBio 12:e0082421, 2021, https://doi.org/10.1128/mBio.00824-21) use the analytical potential of Drosophila to show that AMPs and lysozymes play a direct role in controlling the composition and abundance of the beneficial gut microbiome. By comparing mutant and wild-type flies, they demonstrated that the specific loss of AMPs and lysozyme production results in changes in microbiome abundance and composition. Furthermore, they established that AMPs and lysozyme are particularly essential in aging flies. Studies of early emerging metazoans, other invertebrates, and humans support the view of an ancestral function of AMPs in controlling microbial colonization.},
}
@article {pmid34579474,
year = {2021},
author = {Smulders, L and Benítez, E and Moreno, B and López-García, &#xc1; and Pozo, MJ and Ferrero, V and de la Peña, E and Alcalá Herrera, R},
title = {Tomato Domestication Affects Potential Functional Molecular Pathways of Root-Associated Soil Bacteria.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {34579474},
issn = {2223-7747},
support = {765290//Horizon 2020 Framework Programme/ ; },
abstract = {While it has been well evidenced that plant domestication affects the structure of the root-associated microbiome, there is a poor understanding of how domestication-mediated differences between rhizosphere microorganisms functionally affect microbial ecosystem services. In this study, we explore how domestication influenced functional assembly patterns of bacterial communities in the root-associated soil of 27 tomato accessions through a transect of evolution, from plant ancestors to landraces to modern cultivars. Based on molecular analysis, functional profiles were predicted and co-occurrence networks were constructed based on the identification of co-presences of functional units in the tomato root-associated microbiome. The results revealed differences in eight metabolic pathway categories and highlighted the influence of the host genotype on the potential functions of soil bacterial communities. In general, wild tomatoes differed from modern cultivars and tomato landraces which showed similar values, although all ancestral functional characteristics have been conserved across time. We also found that certain functional groups tended to be more evolutionarily conserved in bacterial communities associated with tomato landraces than those of modern varieties. We hypothesize that the capacity of soil bacteria to provide ecosystem services is affected by agronomic practices linked to the domestication process, particularly those related to the preservation of soil organic matter.},
}
@article {pmid34579172,
year = {2021},
author = {Ruebel, ML and Gilley, SP and Sims, CR and Zhong, Y and Turner, D and Chintapalli, SV and Piccolo, BD and Andres, A and Shankar, K},
title = {Associations between Maternal Diet, Body Composition and Gut Microbial Ecology in Pregnancy.},
journal = {Nutrients},
volume = {13},
number = {9},
pages = {},
pmid = {34579172},
issn = {2072-6643},
support = {T32 DK007658/DK/NIDDK NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; CRIS 6251-51000-005-00D//U.S. Department of Agriculture/ ; DK007658-30/DK/NIDDK NIH HHS/United States ; R01 DK107516/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; *Body Composition/physiology ; Body Weight ; *Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Gestational Weight Gain/physiology ; Humans ; *Maternal Nutritional Physiological Phenomena ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Maternal body composition, gestational weight gain (GWG) and diet quality influence offspring obesity risk. While the gut microbiome is thought to play a crucial role, it is understudied in pregnancy. Using a longitudinal pregnancy cohort, maternal anthropometrics, body composition, fecal microbiome and dietary intake were assessed at 12, 24 and 36 weeks of gestation. Fecal samples (n = 101, 98 and 107, at each trimester, respectively) were utilized for microbiome analysis via 16S rRNA amplicon sequencing. Data analysis included alpha- and beta-diversity measures and assessment of compositional changes using MaAsLin2. Correlation analyses of serum metabolic and anthropometric markers were performed against bacterial abundance and predicted functional pathways. α-diversity was unaltered by pregnancy stage or maternal obesity status. Actinobacteria, Lachnospiraceae, Akkermansia, Bifidobacterium, Streptococcus and Anaerotuncus abundances were associated with gestation stage. Maternal obesity status was associated with increased abundance of Lachnospiraceae, Bilophila, Dialister and Roseburia. Maternal BMI, fat mass, triglyceride and insulin levels were positively associated with Bilophila. Correlations of bacterial abundance with diet intake showed that Ruminococcus and Paraprevotella were associated with total fat and unsaturated fatty acid intake, while Collinsella and Anaerostipes were associated with protein intake. While causal relationships remain unclear, collectively, these findings indicate pregnancy- and maternal obesity-dependent interactions between dietary factors and the maternal gut microbiome.},
}
@article {pmid34579126,
year = {2021},
author = {Calatayud, M and Verstrepen, L and Ghyselinck, J and Van den Abbeele, P and Marzorati, M and Modica, S and Ranjanoro, T and Maquet, V},
title = {Chitin Glucan Shifts Luminal and Mucosal Microbial Communities, Improve Epithelial Barrier and Modulates Cytokine Production In Vitro.},
journal = {Nutrients},
volume = {13},
number = {9},
pages = {},
pmid = {34579126},
issn = {2072-6643},
support = {ADIPOSTOP project, convention 7366//Gouvernement Wallon/ ; },
mesh = {Bifidobacterium breve/physiology ; Caco-2 Cells ; Chitin/*pharmacology ; Coculture Techniques ; Cytokines/*biosynthesis ; Enterocytes ; Fatty Acids, Volatile/biosynthesis ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects/physiology ; Glucans/*pharmacology ; Humans ; Intestinal Mucosa/*drug effects/physiology ; Prebiotics/*administration &amp; dosage ; Probiotics/administration &amp; dosage ; THP-1 Cells ; },
abstract = {The human gut microbiota has been linked to the health status of the host. Modulation of human gut microbiota through pro- and prebiotic interventions has yielded promising results; however, the effect of novel prebiotics, such as chitin-glucan, on gut microbiota-host interplay is still not fully characterized. We assessed the effect of chitin-glucan (CG) and chitin-glucan plus Bifidobacterium breve (CGB) on human gut microbiota from the luminal and mucosal environments in vitro. Further, we tested the effect of filter-sterilized fecal supernatants from CG and CGB fermentation for protective effects on inflammation-induced barrier disruption and cytokine production using a co-culture of enterocytes and macrophage-like cells. Overall, CG and CGB promote health-beneficial short-chain fatty acid production and shift human gut microbiota composition, with a consistent effect increasing Roseburia spp. and butyrate producing-bacteria. In two of three donors, CG and CGB also stimulated Faecalibacterium prausniitzi. Specific colonization of B. breve was observed in the lumen and mucosal compartment; however, no synergy was detected for different endpoints when comparing CGB and CG. Both treatments included a significant improvement of inflammation-disrupted epithelial barrier and shifts on cytokine production, especially by consistent increase in the immunomodulatory cytokines IL10 and IL6.},
}
@article {pmid34579065,
year = {2021},
author = {Sauvaitre, T and Durif, C and Sivignon, A and Chalancon, S and Van de Wiele, T and Etienne-Mesmin, L and Blanquet-Diot, S},
title = {In Vitro Evaluation of Dietary Fiber Anti-Infectious Properties against Food-Borne Enterotoxigenic Escherichia coli.},
journal = {Nutrients},
volume = {13},
number = {9},
pages = {},
pmid = {34579065},
issn = {2072-6643},
support = {I-SITE Cap2025 WOW//Universit&#xe9; Clermont-Auvergne/ ; European Funding for Regional Developments (FEDER) from the French Region Auvergne Rh&#xf4;ne-Alpes (Pack Ambition Recherche Dysfibre)//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; },
mesh = {Cell Adhesion ; Diarrhea/*microbiology/prevention &amp; control ; Dietary Fiber/*pharmacology/therapeutic use ; Enterotoxigenic Escherichia coli/*drug effects/growth &amp; development/metabolism/pathogenicity ; Enterotoxins/metabolism ; Escherichia coli Infections/*microbiology/prevention &amp; control ; Escherichia coli Proteins/metabolism ; Foodborne Diseases/*microbiology/prevention &amp; control ; Humans ; Intestines/cytology/microbiology ; Lens Plant/chemistry ; Microbial Sensitivity Tests ; Mucins ; Mucus ; Seeds/chemistry ; Travel ; *Virulence Factors ; Yeasts/chemistry ; },
abstract = {Dietary fibers have well-known beneficial effects on human health, but their anti-infectious properties against human enteric pathogens have been poorly investigated. Enterotoxigenic Escherichia coli (ETEC) is the main agent of travelers' diarrhea, against which targeted preventive strategies are currently lacking. ETEC pathogenesis relies on multiple virulence factors allowing interactions with the intestinal mucosal layer and toxins triggering the onset of diarrheal symptoms. Here, we used complementary in vitro assays to study the antagonistic properties of eight fiber-containing products from cereals, legumes or microbes against the prototypical human ETEC strain H10407. Inhibitory effects of these products on the pathogen were tested through growth, toxin production and mucus/cell adhesion inhibition assays. None of the tested compounds inhibited ETEC strain H10407 growth, while lentil extract was able to decrease heat labile toxin (LT) concentration in culture media. Lentil extract and specific yeast cell walls also interfered with ETEC strain H10407 adhesion to mucin beads and human intestinal cells. These results constitute a first step in the use of dietary fibers as a nutritional strategy to prevent ETEC infection. Further work will be dedicated to the study of fiber/ETEC interactions within a complex gut microbial background.},
}
@article {pmid34578249,
year = {2021},
author = {Zhang, D and Verstrepen, L and De Medts, J and Duysburgh, C and Van den Abbeele, P and Marzorati, M and Khoo, C},
title = {A Cranberry Concentrate Decreases Adhesion and Invasion of Escherichia coli (AIEC) LF82 In Vitro.},
journal = {Pathogens (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {34578249},
issn = {2076-0817},
abstract = {While many beneficial host-microbiota interactions have been described, imbalanced microbiota in the gut is speculated to contribute to the progression and recurrence of chronic inflammatory diseases such as Crohn's disease (CD). This in vitro study evaluated the impact of a cranberry concentrate Type M (CTM) on adherent-invasive Escherichia coli (AIEC) LF82, a pathobiont associated with CD. Different stages of pathogenic infection were investigated: (i) colonization of the mucus layer, and (ii) adhesion to and (iii) invasion of the epithelial cells. Following 48 h of fecal batch incubation, 0.5 and 1 mM of CTM significantly altered AIEC LF82 levels in a simulated mucus layer, resulting in a decrease of 50.5% in the untreated blank, down to 43.0% and 11.4%, respectively. At 1 mM of CTM, the significant decrease in the levels of AIEC LF82 coincided with a stimulation of the metabolic activity of the background microbiota. The increased levels of health-associated acetate (+7.9 mM) and propionate levels (+3.5 mM) suggested selective utilization of CTM by host microorganisms. Furthermore, 1 mM of both fermented and unfermented CTM decreased the adhesion and invasion of human-derived epithelial Caco-2 cells by AIEC LF82. Altogether, this exploratory in vitro study demonstrates the prebiotic potential of CTM and supports its antipathogenic effects through direct and/or indirect modulation of the gut microbiome.},
}
@article {pmid34576876,
year = {2021},
author = {Foltz, M and Zahradnik, AC and Van den Abbeele, P and Ghyselinck, J and Marzorati, M},
title = {A Pectin-Rich, Baobab Fruit Pulp Powder Exerts Prebiotic Potential on the Human Gut Microbiome In Vitro.},
journal = {Microorganisms},
volume = {9},
number = {9},
pages = {},
pmid = {34576876},
issn = {2076-2607},
abstract = {Increasing insight into the impact of the gut microbiota on human health has sustained the development of novel prebiotic ingredients. This exploratory study evaluated the prebiotic potential of baobab fruit pulp powder, which consists of pectic polysaccharides with unique composition as compared to other dietary sources, given that it is rich in low methoxylated homogalacturonan (HG). After applying dialysis procedures to remove simple sugars from the product (simulating their absorption along the upper gastrointestinal tract), 48 h fecal batch incubations were performed. Baobab fruit pulp powder boosted colonic acidification across three simulated human adult donors due to the significant stimulation of health-related metabolites acetate (+18.4 mM at 48 h), propionate (+5.5 mM at 48 h), and to a lesser extent butyrate (0.9 mM at 48 h). Further, there was a trend of increased lactate levels (+2.7 mM at 6h) and reduced branched chain fatty acid (bCFA) levels (-0.4 mM at 48 h). While Bacteroidetes levels increased for all donors, donor-dependent increases in Bifidobacteria, Lactobacilli, and Firmicutes were observed, stressing the potential interindividual differences in microbial composition modulation upon Baobab fruit pulp powder treatment. Overall, Baobab fruit pulp powder fermentation displayed features of selective utilization by host microorganisms and, thus, has promising prebiotic potential (also in comparison with the 'gold standard' prebiotic inulin). Further research will be required to better characterize this prebiotic potential, accounting for the interindividual differences, while aiming to unravel the potential resulting health benefits.},
}
@article {pmid34576827,
year = {2021},
author = {Lavoie, C and Wellband, K and Perreault, A and Bernatchez, L and Derome, N},
title = {Artificial Rearing of Atlantic Salmon Juveniles for Supportive Breeding Programs Induces Long-Term Effects on Gut Microbiota after Stocking.},
journal = {Microorganisms},
volume = {9},
number = {9},
pages = {},
pmid = {34576827},
issn = {2076-2607},
support = {RDCPJ 500982-16//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {In supportive breeding programs for wild salmon populations, stocked parr experience higher mortality rates than wild ones. Among other aspects of phenotype, the gut microbiota of artificially raised parr differs from that of wild parr before stocking. Early steps of microbiota ontogeny are tightly dependent upon environmental conditions, both of which exert long-term effects on host physiology. Therefore, our objective was to assess to what extent the resilience capacity of the microbiota of stocked salmon may prevent taxonomic convergence with that of their wild congeners after two months in the same natural environment. Using the 16S SSU rRNA marker gene, we tested the general hypothesis that environmental conditions during the very first steps of microbiota ontogeny imprint a permanent effect on later stages of microbiota recruitment. Our results first showed that gut microbiota composition of stocked and wild parr from the same genetic population, and sharing the same environment, was dependent on the early rearing environment. In contrast, skin microbiota in stocked individuals converged to that of wild individuals. Taxonomic composition and co-occurrence network analyses suggest an impairment of wild bacteria recruitment and a higher instability for the gut microbiota of stocked parr. This study is the first to demonstrate the long-term effect of early microbiota ontogeny in artificial rearing for natural population conservation programs, raising the need to implement microbial ecology.},
}
@article {pmid34576737,
year = {2021},
author = {Gnangui, SLE and Fossou, RK and Ebou, A and Amon, CER and Koua, DK and Kouadjo, CGZ and Cowan, DA and Zézé, A},
title = {The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire.},
journal = {Microorganisms},
volume = {9},
number = {9},
pages = {},
pmid = {34576737},
issn = {2076-2607},
support = {674-AA-2010-A1//United States Agency for International Development/ ; },
abstract = {Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d'Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina's MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.},
}
@article {pmid34572682,
year = {2021},
author = {Gresse, R and Garrido, JJ and Jiménez-Marín, A and Denis, S and Van de Wiele, T and Forano, E and Blanquet-Diot, S and Chaucheyras-Durand, F},
title = {Saccharomyces Cerevisiae Var Boulardii CNCM I-1079 Reduces Expression of Genes Involved in Inflammatory Response in Porcine Cells Challenged by Enterotoxigenic E. Coli and Influences Bacterial Communities in an In Vitro Model of the Weaning Piglet Colon.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {34572682},
issn = {2079-6382},
abstract = {Enterotoxigenic Escherichia coli (ETEC) is the main infectious agent responsible for piglet post-weaning diarrhea with high mortality rates. Antimicrobials represent the current principal strategy for treating ETEC infections in pig farms, but the occurrence of multi-resistant bacterial strains has considerably increased in the last decades. Thus, finding non-antibiotic alternatives becomes a real emergency. In this context, we investigated the effect of a live yeast strain, Saccharomyces cerevisiae var boulardii CNCM I-1079 (SB) in an in vitro model of the weaning piglet colon implemented with a mucus phase (MPigut-IVM) inoculated with ETEC and coupled with an intestinal porcine cell line IPI-2I. We showed that SB was able to modulate the in vitro microbiota through an increase in Bacteroidiaceae and a decrease in Prevotellaceae families. Effluents collected from the SB treated bioreactors were able to mitigate the expression level of genes encoding non-gel forming mucins, tight junction proteins, innate immune pathway, and pro-inflammatory response in IPI-2I cells. Furthermore, SB exerted a significant protective effect against ETEC adhesion on porcine IPEC-J2 intestinal cells in a dose-dependent manner and showed a positive effect on ETEC-challenged IPEC-J2 by lowering expression of genes involved in pro-inflammatory immune responses. Our results showed that the strain SB CNCM I-1079 could prevent microbiota dysbiosis associated with weaning and protect porcine enterocytes from ETEC infections by reducing bacterial adhesion and modulating the inflammatory response.},
}
@article {pmid34570249,
year = {2021},
author = {Pérez, J and Ferreira, V and Graça, MAS and Boyero, L},
title = {Litter Quality Is a Stronger Driver than Temperature of Early Microbial Decomposition in Oligotrophic Streams: a Microcosm Study.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {897-908},
pmid = {34570249},
issn = {1432-184X},
support = {UIDP/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/00129/2014, CEECIND/02484/2018//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {*Ecosystem ; Fungi ; Plant Leaves ; *Rivers ; Temperature ; },
abstract = {Litter decomposition is an ecological process of key importance for forest headwater stream functioning, with repercussions for the global carbon cycle. The process is directly and indirectly mediated by microbial decomposers, mostly aquatic hyphomycetes, and influenced by environmental and biological factors such as water temperature and litter quality. These two factors are forecasted to change globally within the next few decades, in ways that may have contrasting effects on microbial-induced litter decomposition: while warming is expected to enhance microbial performance, the reduction in litter quality due to increased atmospheric carbon dioxide and community composition alteration may have the opposite outcome. We explored this issue through a microcosm experiment focused on early microbial-mediated litter decomposition under stream oligotrophic conditions, by simultaneously manipulating water temperature (10 °C and 15 °C) and litter quality (12 broadleaf plant species classified into 4 categories based on initial concentrations of nitrogen and tannins). We assessed potential changes in microbial-mediated litter decomposition and the performance of fungal decomposers (i.e., microbial respiration, biomass accrual, and sporulation rate) and species richness. We found stronger effects of litter quality, which enhanced the performance of microbial decomposers and decomposition rates, than temperature, which barely influenced any of the studied variables. Our results suggest that poorer litter quality associated with global change will have a major repercussion on stream ecosystem functioning.},
}
@article {pmid34567033,
year = {2021},
author = {Hale, I and Ma, X and Melo, ATO and Padi, FK and Hendre, PS and Kingan, SB and Sullivan, ST and Chen, S and Boffa, JM and Muchugi, A and Danquah, A and Barnor, MT and Jamnadass, R and Van de Peer, Y and Van Deynze, A},
title = {Genomic Resources to Guide Improvement of the Shea Tree.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {720670},
pmid = {34567033},
issn = {1664-462X},
abstract = {A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea's evolutionary past, one prior to the Astrid-Rosid divergence (116-126 Mya) and the other at the root of the order Ericales (65-90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea's more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.},
}
@article {pmid34564670,
year = {2021},
author = {Fournier, C and Riehle, E and Dietrich, DR and Schleheck, D},
title = {Is Toxin-Producing Planktothrix sp. an Emerging Species in Lake Constance?.},
journal = {Toxins},
volume = {13},
number = {9},
pages = {},
pmid = {34564670},
issn = {2072-6651},
mesh = {Environmental Monitoring/*methods ; Germany ; *Harmful Algal Bloom ; Lakes/*microbiology ; Microcystins/*biosynthesis/*toxicity ; Planktothrix/*growth &amp; development/*metabolism ; },
abstract = {Recurring blooms of filamentous, red-pigmented and toxin-producing cyanobacteria Planktothrix rubescens have been reported in numerous deep and stratified prealpine lakes, with the exception of Lake Constance. In a 2019 and 2020 Lake Constance field campaign, we collected samples from a distinct red-pigmented biomass maximum below the chlorophyll-a maximum, which was determined using fluorescence probe measurements at depths between 18 and 20 m. Here, we report the characterization of these deep water red pigment maxima (DRM) as cyanobacterial blooms. Using 16S rRNA gene-amplicon sequencing, we found evidence that the blooms were, indeed, contributed by Planktothrix spp., although phycoerythrin-rich Synechococcus taxa constituted most of the biomass (>96% relative read abundance) of the cyanobacterial DRM community. Through UPLC-MS/MS, we also detected toxic microcystins (MCs) in the DRM in the individual sampling days at concentrations of ≤1.5 ng/L. Subsequently, we reevaluated the fluorescence probe measurements collected over the past decade and found that, in the summer, DRM have been present in Lake Constance, at least since 2009. Our study highlights the need for a continuous monitoring program also targeting the cyanobacterial DRM in Lake Constance, and for future studies on the competition of the different cyanobacterial taxa. Future studies will address the potential community composition changes in response to the climate change driven physiochemical and biological parameters of the lake.},
}
@article {pmid34563431,
year = {2021},
author = {Shalev, O and Ratzke, C},
title = {A holistic view of host-associated microbial evolution.},
journal = {Trends in microbiology},
volume = {29},
number = {11},
pages = {961-962},
doi = {10.1016/j.tim.2021.09.003},
pmid = {34563431},
issn = {1878-4380},
mesh = {*Microbiota ; },
abstract = {Microbes often live associated with other organisms. Whereas the impact of microbes on their hosts is well studied, what such a lifestyle means for the microbes is poorly understood. To address this gap, Bansept et al. explore how microbes could evolve to cope with altering between host-associated and host-free lifestyles.},
}
@article {pmid34562129,
year = {2022},
author = {Zhou, J and Wang, M and Yi, X},
title = {Alteration of Gut Microbiota of a Food-Storing Hibernator, Siberian Chipmunk Tamias sibiricus.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {603-612},
pmid = {34562129},
issn = {1432-184X},
support = {32070447//National Natural Science Foundation of China/ ; 41807053//National Natural Science Foundation of China/ ; 31760156//National Natural Science Foundation of China/ ; 20190601//Youth Talent Introduction and Education Program of Shandong Province/ ; },
mesh = {Animals ; Bacteroidetes ; *Gastrointestinal Microbiome/physiology ; *Hibernation/physiology ; Mammals ; *Microbiota ; Sciuridae ; },
abstract = {Hibernation represents a state of fasting because hibernators cease eating in the torpid periods. Therefore, food deprivation during hibernation is expected to modify the gut microbiota of host. However, there are few reports of gut microbiota in food-storing hibernators that feed during the interbout arousals. Here we collected fecal samples of Siberian chipmunk T. sibiricus to character and examine changes in the gut microbiota at various stages relative to hibernation: pre-hibernation, early-hibernation, mid-hibernation, late-hibernation, and post-hibernation. Compared to the pre-hibernation state, alpha-diversity of gut microbiota was significantly increased during the interbout arousal periods. In addition, beta-diversity of the fecal communities from pre-hibernation and interbout arousal periods grouped together, and post-hibernation gut microbiota resembled the counterpart at late-hibernation. Hibernation significantly decreased the relative abundance of Firmicutes but increased Bacteroidetes, reflecting a shift of microbiota toward taxa in favor of host-derived substrates. The increased abundance of Ruminococcaceae_UCG-014, Lactobacillus, and Christensenellaceae_R-7_group in gut microbiota may help the chipmunks reduce intestinal inflammation and then maintain healthy bowel during hibernation. KEGG pathway indicated that hibernation altered the metabolic function of gut microflora of T. sibiricus. Our study provides evidence that the gut microbiota of food-storing hibernators, despite feeding during the interbout arousals, shows similar response to hibernation that has well documented in fat-storing counterparts, suggesting the potential for a core gut microbiota during hibernation of mammals. Importantly, these results will broaden our understanding of the effects of hibernation on gut microbiota of mammal hibernators.},
}
@article {pmid34561754,
year = {2022},
author = {Varasteh, T and Salazar, V and Tschoeke, D and Francini-Filho, RB and Swings, J and Garcia, G and Thompson, CC and Thompson, FL},
title = {Breviolum and Cladocopium Are Dominant Among Symbiodiniaceae of the Coral Holobiont Madracis decactis.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {325-335},
pmid = {34561754},
issn = {1432-184X},
mesh = {Animals ; *Anthozoa/physiology ; Atlantic Ocean ; Coral Reefs ; DNA, Ribosomal/genetics ; *Dinoflagellida/physiology ; Phylogeny ; Symbiosis ; },
abstract = {The scleractinian reef building coral Madracis decactis is a cosmopolitan species. Understanding host-symbiont associations is critical for assessing coral's habitat requirements and its response to environmental changes. In this study, we performed a fine grained phylogenetic analyses of Symbiodiniaceae associated with Madracis in two locations in the Southwest Atlantic Ocean (Abrolhos Bank and St. Peter and St. Paul Archipelago). Previous studies have argued that Madracis is a specialist coral, with colonies harboring a single symbiont from the genus Breviolum (formerly clade B). However, these previous studies have not precisely addressed if Madracis is colonized by several types of Symbiodiniaceae simultaneously or whether this coral is a specialist. The hypothesis that Madracis is a generalist coral host was evaluated in the present study. A total of 1.9 million reads of ITS2 nuclear ribosomal DNA were obtained by Illumina MiSeq sequencing. While Symbiodiniaceae ITS2 sequences between two sampling depths were almost entirely (62%) from the genus Breviolum (formerly clade B), shallow (10-15 m) populations in Abrolhos had a greater diversity of ITS2 sequences in comparison to deeper (25-35 m) populations of St. Peter and St. Paul Archipelago. Cladocopium (formerly clade C) and Symbiodinium (formerly clade A) were also found in Abrolhos. A single Madracis colony can host different symbiont types with > 30 Symbiodiniaceae ITS2-type profiles. Abrolhos corals presented a higher photosynthetic potential as a possible result of co-occurrence of multiple Symbiodiniaceae in a single coral colony. Multiple genera/clades of Symbiodiniaceae possibly confer coral hosts with broader environmental tolerance and ability to occupy diverse or changing habitats.},
}
@article {pmid34560321,
year = {2021},
author = {Zuo, T and Wu, X and Wen, W and Lan, P},
title = {Gut Microbiome Alterations in COVID-19.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {19},
number = {5},
pages = {679-688},
pmid = {34560321},
issn = {2210-3244},
mesh = {Bacteria ; *COVID-19/complications ; Fungi ; *Gastrointestinal Microbiome ; Humans ; SARS-CoV-2 ; Post-Acute COVID-19 Syndrome ; },
abstract = {Since the outset of the coronavirus disease 2019 (COVID-19) pandemic, the gut microbiome in COVID-19 has garnered substantial interest, given its significant roles in human health and pathophysiology. Accumulating evidence is unveiling that the gut microbiome is broadly altered in COVID-19, including the bacterial microbiome, mycobiome, and virome. Overall, the gut microbial ecological network is significantly weakened and becomes sparse in patients with COVID-19, together with a decrease in gut microbiome diversity. Beyond the existence of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), the gut microbiome of patients with COVID-19 is also characterized by enrichment of opportunistic bacteria, fungi, and eukaryotic viruses, which are also associated with disease severity and presentation. Meanwhile, a multitude of symbiotic bacteria and bacteriophages are decreased in abundance in patients with COVID-19. Such gut microbiome features persist in a significant subset of patients with COVID-19 even after disease resolution, coinciding with 'long COVID' (also known as post-acute sequelae of COVID-19). The broadly-altered gut microbiome is largely a consequence of SARS-CoV-2infection and its downstream detrimental effects on the systemic host immunity and the gut milieu. The impaired host immunity and distorted gut microbial ecology, particularly loss of low-abundance beneficial bacteria and blooms of opportunistic fungi including Candida, may hinder the reassembly of the gut microbiome post COVID-19. Future investigation is necessary to fully understand the role of the gut microbiome in host immunity against SARS-CoV-2 infection, as well as the long-term effect of COVID-19 on the gut microbiome in relation to the host health after the pandemic.},
}
@article {pmid34560288,
year = {2022},
author = {Wang, Z and Liu, M and Ma, H and Lu, B and Shen, Z and Mu, C and Alfarraj, SA and El-Serehy, HA and Warren, A},
title = {Redescription and molecular characterization of two Trichodina species (Ciliophora, Peritrichia, Mobilida) from freshwater fish in China.},
journal = {Parasitology international},
volume = {86},
number = {},
pages = {102470},
doi = {10.1016/j.parint.2021.102470},
pmid = {34560288},
issn = {1873-0329},
mesh = {Animals ; *Carps ; China/epidemiology ; Ciliophora Infections/epidemiology/parasitology/*veterinary ; Fish Diseases/*epidemiology/parasitology ; Oligohymenophorea/*classification/cytology/genetics/isolation &amp; purification ; Phylogeny ; Prevalence ; },
abstract = {During an investigation of parasitic ciliates in northern China, two Trichodina species, T. acuta Lom, 1970 and T. nigra Lom, 1960, were isolated from the freshwater fish Cyprinus carpio Linnaeus, 1758. The morphology of each species was investigated based on dry silver nitrate-stained specimens. In addition, the molecular phylogeny of each was analyzed based on small subunit ribosomal DNA (SSU rDNA) sequence data. Trichodina acuta can be distinguished from its congeners by the undefined periphery of the central circle, the distinct gap between the rays and the central circle, and the distinctly sickle-shaped blades. Trichodina nigra is a cosmopolitan ciliate and is characterized by its densely linked denticles, broad, rounded spatula-shaped blades, robust central parts, and well developed rays. Phylogenetic analyses revealed that T. acuta and T. nigra nest within different clades, supporting the assertion that the GC content of SSU rDNA sequences could reflect evolutionary relationships among Trichodina species.},
}
@article {pmid34559138,
year = {2021},
author = {Tanaka, T and Matsuno, Y and Torisu, T and Shibata, H and Hirano, A and Umeno, J and Kawasaki, K and Fujioka, S and Fuyuno, Y and Moriyama, T and Esaki, M and Kitazono, T},
title = {Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma.},
journal = {Medicine},
volume = {100},
number = {38},
pages = {e27287},
pmid = {34559138},
issn = {1536-5964},
mesh = {Aged ; Case-Control Studies ; Cross-Sectional Studies ; Female ; Gastric Mucosa/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Lymphoma, B-Cell, Marginal Zone/*microbiology ; Male ; Metagenomics ; Middle Aged ; Stomach Neoplasms/*microbiology ; },
abstract = {To investigate the mucosal microbiota in the stomach of patients with Helicobacter pylori-negative mucosa-associated lymphoid tissue (MALT) lymphoma by means of metagenomic analysis.Although some gastric MALT lymphomas are associated with the presence of H. pylori, other gastric MALT lymphomas occur independently of H. pylori infection. The pathogenesis of H. pylori-negative MALT lymphoma remains unclear.Mucosal biopsy specimens were collected from the gastric body from 33 MALT lymphoma patients with gastric lesions, including both H. pylori-infection naïve patients and posteradication patients, as well as 27 control participants without H. pylori infection or cancer. Subsequently, the samples were subjected to 16S rRNA gene sequencing. Quantitative insights into microbial ecology, linear discriminant analysis effect size, and phylogenetic investigation of communities by reconstruction of unobserved states softwares were used to analyze the participants' microbiota.H. pylori-negative MALT lymphoma patients had significantly lower alpha diversity (P = .04), compared with control participants. Significant differences were evident in the microbial composition (P = .04), as determined by comparison of beta diversity between the 2 groups. Taxonomic composition analysis indicated that the genera Burkholderia and Sphingomonas were significantly more abundant in MALT lymphoma patients, while the genera Prevotella and Veillonella were less abundant. Functional microbiota prediction showed that the predicted gene pathways "replication and repair," "translation," and "nucleotide metabolism" were downregulated in MALT lymphoma patients.H. pylori-negative MALT lymphoma patients exhibited altered gastric mucosal microbial compositions, suggesting that altered microbiota might be involved in the pathogenesis of H. pylori-negative MALT lymphoma.},
}
@article {pmid34558584,
year = {2021},
author = {Iglesias-Aguirre, CE and Cortés-Martín, A and Ávila-Gálvez, M&#xc1; and Giménez-Bastida, JA and Selma, MV and González-Sarrías, A and Espín, JC},
title = {Main drivers of (poly)phenol effects on human health: metabolite production and/or gut microbiota-associated metabotypes?.},
journal = {Food &amp; function},
volume = {12},
number = {21},
pages = {10324-10355},
doi = {10.1039/d1fo02033a},
pmid = {34558584},
issn = {2042-650X},
mesh = {Diet/*methods ; Gastrointestinal Microbiome/drug effects/*physiology ; Humans ; Phenols/*metabolism/*pharmacology ; Polyphenols/metabolism/pharmacology ; },
abstract = {Despite the high human interindividual variability in response to (poly)phenol consumption, the cause-and-effect relationship between some dietary (poly)phenols (flavanols and olive oil phenolics) and health effects (endothelial function and prevention of LDL oxidation, respectively) has been well established. Most of the variables affecting this interindividual variability have been identified (food matrix, gut microbiota, single-nucleotide-polymorphisms, etc.). However, the final drivers for the health effects of (poly)phenol consumption have not been fully identified. At least partially, these drivers could be (i) the (poly)phenols ingested that exert their effect in the gastrointestinal tract, (ii) the bioavailable metabolites that exert their effects systemically and/or (iii) the gut microbial ecology associated with (poly)phenol metabolism (i.e., gut microbiota-associated metabotypes). However, statistical associations between health effects and the occurrence of circulating and/or excreted metabolites, as well as cross-sectional studies that correlate gut microbial ecologies and health, do not prove a causal role unequivocally. We provide a critical overview and perspective on the possible main drivers of the effects of (poly)phenols on human health and suggest possible actions to identify the putative actors responsible for the effects.},
}
@article {pmid34557947,
year = {2022},
author = {de Almeida, JCF and da Silva Xavier, A and Cascardo, RS and de Rezende, RR and de Souza, FO and Lopes, CA and Alfenas-Zerbini, P},
title = {Genomic and Biological Characterization of Ralstonia solanacearum Inovirus Brazil 1, an Inovirus that Alters the Pathogenicity of the Phytopathogen Ralstonia pseudosolanacearum.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {527-538},
pmid = {34557947},
issn = {1432-184X},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 2456937/2018//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Estado de Minas Gerais/ ; },
mesh = {*Bacteriophages ; Brazil ; Genomics ; *Inovirus/genetics ; Phylogeny ; Plant Diseases/microbiology ; Ralstonia/genetics ; *Ralstonia solanacearum/genetics ; Virulence/genetics ; },
abstract = {Filamentous bacteriophages contain a single-stranded DNA genome and have a peculiar lifestyle, since they do not cause host cell lysis, but establish a persistent association with the host, often causing behavioral changes, with effects on bacterial ecology. Over the years, a gradual reduction in the incidence of bacterial wilt has been observed in some fields from Brazil. This event, which has been associated with the loss of pathogenicity of Rasltonia spp. isolates due to infection by filamentous viruses of the inovirus group, is widely reported for Ralstonia spp. Asian isolates infected by inoviruses. In an attempt to elucidate which factors are associated with the phenomenon reported in Brazil, we investigated one isolate of R. solanacearum (UB-2014), with unusual characteristics for R. solanacearum, obtained from eggplant with mild wilt symptoms. To verify if the presence of filamentous bacteriophage was related to this phenotype, we performed viral purification and nucleic acid extraction. The phage genome was sequenced, and phylogenetic analyses demonstrated that the virus belongs to the family Inoviridae and was named as Ralstonia solanacerarum inovirus Brazil 1 (RSIBR1). RSIBR1 was transmitted to R. pseudosolanacearum GMI1000, and the virus-infected GMI1000 (GMI1000 VI) isolate showed alterations in phenotypic characteristics, as well as loss of pathogenicity, similarly to that observed in R. solanacearum isolate UB-2014. The presence of virus-infected UB-2014 and GMI1000 VI plants without symptoms, after 3 months, confirms that the infected isolates can colonize the plant without causing disease, which demonstrates that the phage infection changed the behavior of these pathogens.},
}
@article {pmid34555741,
year = {2021},
author = {McDaniel, EA and Wahl, SA and Ishii, S and Pinto, A and Ziels, R and Nielsen, PH and McMahon, KD and Williams, RBH},
title = {Prospects for multi-omics in the microbial ecology of water engineering.},
journal = {Water research},
volume = {205},
number = {},
pages = {117608},
doi = {10.1016/j.watres.2021.117608},
pmid = {34555741},
issn = {1879-2448},
mesh = {Bioreactors ; Metagenomics ; *Microbiota ; Sewage ; *Water ; },
abstract = {Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.},
}
@article {pmid34554284,
year = {2022},
author = {Zhang, L and Lai, JL and Zhang, Y and Luo, XG and Li, ZG},
title = {Degradation of Uranium-Contaminated Decontamination Film by UV Irradiation and Microbial Biodegradation.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {439-450},
pmid = {34554284},
issn = {1432-184X},
support = {No. SKLNBC2019-21//state key laboratory of nbc protection for civilian/ ; },
mesh = {Bacteria ; Biodegradation, Environmental ; Decontamination ; RNA, Ribosomal, 16S/genetics/metabolism ; Ultraviolet Rays ; *Uranium/metabolism ; },
abstract = {This research provides a complete degradation scheme for acrylic copolymer/cellulose acetate butyrate peelable decontamination films. This study analyzed the removal efficiency of uranium by peelable decontamination film. More importantly, the degradability of the films was evaluated by a combined treatment with UV radiation and microbial biodegradation. The results showed that UV radiation would rupture the surface of the decontamination films, which leaded the weight-average molecular weight decreased by 55.3% and number-average molecular weight decreased by 75.83%. Additionally, the microbial flora induced light-degradable decontamination film weight-average molecular weight and number-average molecular weight decreased by 9.3% and 30.73%, respectively. 16S rRNA microbial diversity analysis indicated that Pantoea, Xylella, Cronobacter, and Olivibacter were the major degrading bacteria genera. Among them, 4 key strains that can be stripped of decontamination films have been isolated and identified from the dominant degrading bacteria group. The results show that UV radiation combined with microbial flora can achieve rapid degradation of the decontamination films.},
}
@article {pmid34554283,
year = {2022},
author = {Wu, H and Zhang, Z and Wang, J and Qin, X and Chen, J and Wu, L and Lin, S and Rensing, C and Lin, W},
title = {Bio-fertilizer Amendment Alleviates the Replanting Disease under Consecutive Monoculture Regimes by Reshaping Leaf and Root Microbiome.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {452-464},
pmid = {34554283},
issn = {1432-184X},
support = {U1205021, 81573530//National Science Foundation of China/ ; 82003884//National Science Foundation of China/ ; 2019M650150//Project Funded by China Postdoctoral Science Foundation/ ; },
mesh = {Fertilizers ; *Microbiota ; *Paenibacillus/genetics ; Plant Leaves ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Replanting disease is a growing problem in intensive agricultural systems. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields, and the associated microbiota were characterized by bacterial 16S rRNA gene sequencing and quantitative PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of potential pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the potential beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium. The proportion of positive correlations in the co-occurrence network of bio-fertilizer application was the highest, implying that bio-fertilizer potentially enhanced ecological commensalism or mutualism of the bacterial community across the two compartments. Structural equation models indicated that bio-fertilizer had a positive and indirect effect on both yield and quality by shaping the leaf microbiota and the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving microbe-microbe interactions.},
}
@article {pmid34553243,
year = {2022},
author = {Villalobos-Flores, LE and Espinosa-Torres, SD and Hernández-Quiroz, F and Piña-Escobedo, A and Cruz-Narváez, Y and Velázquez-Escobar, F and Süssmuth, R and García-Mena, J},
title = {The Bacterial and Fungal Microbiota of the Mexican Rubiaceae Family Medicinal Plant Bouvardia ternifolia.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {510-526},
pmid = {34553243},
issn = {1432-184X},
mesh = {Bacteria/genetics ; Endophytes ; Fungi/genetics ; *Mycobiome ; Plant Roots/microbiology ; *Plants, Medicinal/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Rubiaceae/genetics ; Soil Microbiology ; },
abstract = {Bouvardia ternifolia is a medicinal plant considered a source of therapeutic compounds, like the antitumoral cyclohexapeptide bouvardin. It is known that large number of secondary metabolites produced by plants results from the interaction of the host and adjacent or embedded microorganisms. Using high-throughput DNA sequencing of V3-16S and V5-18S ribosomal gene libraries, we characterized the endophytic, endophytic + epiphyte bacterial, and fungal communities associated to flowers, leaves, stems, and roots, as well as the rhizosphere. The Proteobacteria (average 80.7%) and Actinobacteria (average 14.7%) were the most abundant bacterial phyla, while Leotiomycetes (average 54.8%) and Dothideomycetes (average 27.4%) were the most abundant fungal classes. Differential abundance for the bacterial endophyte group showed a predominance of Erwinia, Propionibacterium, and Microbacterium genera, while Sclerotinia, Coccomyces, and Calycina genera predominated for fungi. The predictive metagenome analysis for bacteria showed significative abundance of pathways for secondary metabolite production, while a FUNguild analysis revealed the presence of pathotroph, symbiotroph, and saprotrophs in the fungal community. Intra and inter copresence and mutual exclusion interactions were identified for bacterial and fungal kingdoms in the endophyte communities. This work provides a description of the diversity and composition of bacterial and fungal microorganisms living in flowers, leaves, stems, roots, and the rhizosphere of this medicinal plant; thus, it paves the way towards an integral understanding in the production of therapeutic metabolites.},
}
@article {pmid34550758,
year = {2021},
author = {Moore, MEG and Paulin-Curlee, G and Johnston, BD and Clabots, C and DebRoy, C and Johnson, TJ and Weber, B and Porter, S and Armién, AG and Johnson, JR},
title = {Molecular Characteristics, Ecology, and Zoonotic Potential of Escherichia coli Strains That Cause Hemorrhagic Pneumonia in Animals.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {23},
pages = {e0147121},
pmid = {34550758},
issn = {1098-5336},
support = {//Biomedical Laboratory Research and Development, VA Office of Research and Development (BLR&amp;D, ORD)/ ; },
mesh = {Animals ; *Cat Diseases/microbiology ; Cats ; *Dog Diseases/microbiology ; Dogs ; Escherichia coli/genetics/*pathogenicity ; Phylogeny ; *Pneumonia, Bacterial/veterinary ; },
abstract = {Hemorrhagic pneumonia (HP) is a rare but highly lethal disease, mainly of dogs and cats, caused by hemolytic Escherichia coli strains that contain cnf1 (encoding cytotoxic necrotizing factor 1). After encountering fatal HP in two dogs, we used contemporary molecular methods, including multilocus sequence typing and whole-genome sequencing, to compare the corresponding case isolates with published HP clinical isolates and newly obtained fecal E. coli isolates from 20 humans and animals in the index HP case household. We also compared the aggregated HP clinical isolates, which represented 13 discrete strains, by pulsotype with a large, private pulsotype library of diverse-source E. coli. The HP clinical isolates represented a narrow range of phylogenetic group B2 lineages (mainly sequence types 12 and 127), O types (mainly O4 and O6), and H types (mainly H5 and H31), but diverse fimH alleles (type-1 fimbriae adhesin). Their extensive, highly conserved virulence genotypes, which qualified as extraintestinal pathogenic E. coli (ExPEC), encoded diverse adhesins, toxins, iron uptake systems, and protectins. Household surveillance identified multiple HP-like fecal strains, plus abundant between-host strain sharing, including of the household's index HP strain. The pulsotype library search identified, for five HP clinical strains, same-pulsotype human and animal fecal and clinical (predominantly urine) isolates, from diverse locales and time periods. Thus, E. coli strains that cause HP derive from a narrow range of ExPEC lineages within phylogroup B2, contain multiple virulence genes other than cnf1, are shared extensively between hosts, and likely function in nature mainly as intestinal colonizers and uropathogens. IMPORTANCE This study clarifies the clonal background and extensive virulence genotypes of the E. coli strains that cause hemorrhagic pneumonia in domestic animals (mainly dogs and cats), shows that such strains circulate among animals and humans, identifies a substantial intestinal colonization component to their lifestyle, and extends their known clinical manifestations to include bacteremia and urinary tract infection. The findings place these strains better into context vis-à-vis current understandings of E. coli phylogeny, ecology, and pathogenesis; identify questions for future research; and may prove relevant for surveillance and prevention efforts.},
}
@article {pmid34550753,
year = {2021},
author = {Rothman, JA and Loveless, TB and Kapcia, J and Adams, ED and Steele, JA and Zimmer-Faust, AG and Langlois, K and Wanless, D and Griffith, M and Mao, L and Chokry, J and Griffith, JF and Whiteson, KL},
title = {RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {23},
pages = {e0144821},
pmid = {34550753},
issn = {1098-5336},
support = {S10 OD021718/OD/NIH HHS/United States ; R00RG2814//University of California Office of the President Research Grants Program Office/ ; R01RG3732//University of California Office of the President Research Grants Program Office/ ; S10 RR025496/RR/NCRR NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; //Hewitt Foundation for Biomedical Research/ ; },
mesh = {COVID-19/epidemiology ; California ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Humans ; Polymerase Chain Reaction ; RNA Viruses/classification/genetics/*isolation &amp; purification ; SARS-CoV-2/classification/genetics/*isolation &amp; purification ; Sequence Analysis, RNA ; *Virome ; Wastewater/*virology ; *Wastewater-Based Epidemiological Monitoring ; },
abstract = {Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the coronavirus disease 2019 (COVID-19) pandemic to track disease burden through analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the health care system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven wastewater treatment plants (WTPs), collected from August 2020 to January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single-nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater, and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically important SARS-CoV-2 variants along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. IMPORTANCE Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the coronavirus disease 2019 (COVID-19) pandemic to track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without adding burden to health care systems. In this study, we used metatranscriptomics and reverse transcription-droplet digital PCR (RT-ddPCR) to assay RNA viruses across Southern California wastewater from August 2020 to January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single-nucleotide variants through sequencing. Likewise, wastewater treatment plants (WTPs) harbored different viromes, and we detected other human pathogens, such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.},
}
@article {pmid34550379,
year = {2021},
author = {Garoña, A and Hülter, NF and Romero Picazo, D and Dagan, T},
title = {Segregational Drift Constrains the Evolutionary Rate of Prokaryotic Plasmids.},
journal = {Molecular biology and evolution},
volume = {38},
number = {12},
pages = {5610-5624},
pmid = {34550379},
issn = {1537-1719},
mesh = {Chromosomes ; *Genetic Drift ; Phylogeny ; Plasmids/genetics ; *Prokaryotic Cells ; },
abstract = {Plasmids are extrachromosomal genetic elements in prokaryotes that have been recognized as important drivers of microbial ecology and evolution. Plasmids are found in multiple copies inside their host cell where independent emergence of mutations may lead to intracellular genetic heterogeneity. The intracellular plasmid diversity is thus subject to changes upon cell division. However, the effect of plasmid segregation on plasmid evolution remains understudied. Here, we show that genetic drift during cell division-segregational drift-leads to the rapid extinction of novel plasmid alleles. We established a novel experimental approach to control plasmid allele frequency at the levels of a single cell and the whole population. Following the dynamics of plasmid alleles in an evolution experiment, we find that the mode of plasmid inheritance-random or clustered-is an important determinant of plasmid allele dynamics. Phylogenetic reconstruction of our model plasmid in clinical isolates furthermore reveals a slow evolutionary rate of plasmid-encoded genes in comparison to chromosomal genes. Our study provides empirical evidence that genetic drift in plasmid evolution occurs at multiple levels: the host cell and the population of hosts. Segregational drift has implications for the evolutionary rate heterogeneity of extrachromosomal genetic elements.},
}
@article {pmid34546074,
year = {2021},
author = {Heyse, J and Schattenberg, F and Rubbens, P and Müller, S and Waegeman, W and Boon, N and Props, R},
title = {Predicting the Presence and Abundance of Bacterial Taxa in Environmental Communities through Flow Cytometric Fingerprinting.},
journal = {mSystems},
volume = {6},
number = {5},
pages = {e0055121},
pmid = {34546074},
issn = {2379-5077},
support = {//Onderzoeksprogramma Artifici&#xeb;le Intelligentie (AI) Vlaanderen/ ; 1S80618N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 1221020N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; BOF15/GOA/006//UGent | Bijzonder Onderzoeksfonds UGent (BOF)/ ; },
abstract = {Microbiome management research and applications rely on temporally resolved measurements of community composition. Current technologies to assess community composition make use of either cultivation or sequencing of genomic material, which can become time-consuming and/or laborious in case high-throughput measurements are required. Here, using data from a shrimp hatchery as an economically relevant case study, we combined 16S rRNA gene amplicon sequencing and flow cytometry data to develop a computational workflow that allows the prediction of taxon abundances based on flow cytometry measurements. The first stage of our pipeline consists of a classifier to predict the presence or absence of the taxon of interest, with yielded an average accuracy of 88.13% ± 4.78% across the top 50 operational taxonomic units (OTUs) of our data set. In the second stage, this classifier was combined with a regression model to predict the relative abundances of the taxon of interest, which yielded an average R[2] of 0.35 ± 0.24 across the top 50 OTUs of our data set. Application of the models to flow cytometry time series data showed that the generated models can predict the temporal dynamics of a large fraction of the investigated taxa. Using cell sorting, we validated that the model correctly associates taxa to regions in the cytometric fingerprint, where they are detected using 16S rRNA gene amplicon sequencing. Finally, we applied the approach of our pipeline to two other data sets of microbial ecosystems. This pipeline represents an addition to the expanding toolbox for flow cytometry-based monitoring of bacterial communities and complements the current plating- and marker gene-based methods. IMPORTANCE Monitoring of microbial community composition is crucial for both microbiome management research and applications. Existing technologies, such as plating and amplicon sequencing, can become laborious and expensive when high-throughput measurements are required. In recent years, flow cytometry-based measurements of community diversity have been shown to correlate well with those derived from 16S rRNA gene amplicon sequencing in several aquatic ecosystems, suggesting that there is a link between the taxonomic community composition and phenotypic properties as derived through flow cytometry. Here, we further integrated 16S rRNA gene amplicon sequencing and flow cytometry survey data in order to construct models that enable the prediction of both the presence and the abundances of individual bacterial taxa in mixed communities using flow cytometric fingerprinting. The developed pipeline holds great potential to be integrated into routine monitoring schemes and early warning systems for biotechnological applications.},
}
@article {pmid34546069,
year = {2021},
author = {Liu, J and Villanueva, P and Choi, J and Gunturu, S and Ouyang, Y and Tiemann, LK and Cole, JR and Glanville, KR and Hall, SJ and McDaniel, MD and Lee, J and Howe, A},
title = {MetaFunPrimer: an Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes.},
journal = {mSystems},
volume = {6},
number = {5},
pages = {e0020121},
pmid = {34546069},
issn = {2379-5077},
support = {DE-SC0018420//U.S. Department of Energy (DOE)/ ; DE-SC0014108//U.S. Department of Energy (DOE)/ ; },
abstract = {Genes belonging to the same functional group may include numerous and variable gene sequences, making characterizing and quantifying difficult. Therefore, high-throughput design tools are needed to simultaneously create primers for improved quantification of target genes. We developed MetaFunPrimer, a bioinformatic pipeline, to design primers for numerous genes of interest. This tool also enables gene target prioritization based on ranking the presence of genes in user-defined references, such as environment-specific metagenomes. Given inputs of protein and nucleotide sequences for gene targets of interest and an accompanying set of reference metagenomes or genomes, MetaFunPrimer generates primers for ranked genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 publicly available soil metagenomes. We demonstrate computationally that these amoA-AOB primers can cover 94% of the amoA-AOB genes observed in the 1,550 soil metagenomes compared with a 49% estimated coverage by previously published primers. Finally, we verified the utility of these primer sets in incubation experiments that used long-term nitrogen fertilized or unfertilized soils. High-throughput quantitative PCR (qPCR) results and statistical analyses showed significant differences in relative quantification patterns between the two soils, and subsequent absolute quantifications also confirmed that target genes enumerated by six selected primer pairs were significantly more abundant in the nitrogen-fertilized soils. This new tool gives microbial ecologists a new approach to assess functional gene abundance and related microbial community dynamics quickly and affordably. IMPORTANCE Amplification-based gene characterization allows for sensitive and specific quantification of functional genes. There is often a large diversity of genes represented for functional gene groups, and multiple primers may be necessary to target associated genes. Current primer design tools are limited to designing primers for only a few genes of interest. MetaFunPrimer allows for high-throughput primer design for various genes of interest and also allows for ranking gene targets by their presence and abundance in environmental data sets. Primers designed by this tool improve the characterization and quantification of functional genes in broad gene amplification platforms and can be powerful with high-throughput qPCR approaches.},
}
@article {pmid34545413,
year = {2022},
author = {Wang, L and Wen, Y and Tong, R and Zhang, H and Chen, H and Hu, T and Liu, G and Wang, J and Zhu, L and Wu, T},
title = {Understanding Responses of Soil Microbiome to the Nitrogen and Phosphorus Addition in Metasequoia glyptostroboides Plantations of Different Ages.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {565-579},
pmid = {34545413},
issn = {1432-184X},
mesh = {China ; *Microbiota ; Nitrogen/analysis ; *Phosphorus/analysis ; Soil ; Soil Microbiology ; },
abstract = {Nitrogen (N) and phosphorus (P) have significant effects on soil microbial community diversity, composition, and function. Also, trees of different life stages have different fertilization requirements. In this study, we designed three N additions and three P levels (5 years of experimental treatment) at two Metasequoia glyptostroboides plantations of different ages (young, 6 years old; middle mature, 24 years old) to understand how different addition levels of N and P affect the soil microbiome. Here, the N fertilization of M. glyptostroboides plantation land (5 years of experimental treatment) significantly enriched microbes (e.g., Lysobacter, Luteimonas, and Rhodanobacter) involved in nitrification, denitrification, and P-starvation response regulation, which might further lead to the decreasing in alpha diversity (especially in 6YMP soil). The P addition could impact the genes involved in inorganic P-solubilization and organic P-mineralization by increasing soil AP and TP. Moreover, the functional differences in the soil microbiomes were identified between the 6YMP and 24YMP soil. This study provides valuable information that improves our understanding on the effects of N and P input on the belowground soil microbial community and functional characteristics in plantations of different stand ages.},
}
@article {pmid34545412,
year = {2022},
author = {Chan, J and Geng, D and Pan, B and Zhang, Q and Xu, Q},
title = {Gut Microbial Divergence Between Three Hadal Amphipod Species from the Isolated Hadal Trenches.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {627-637},
pmid = {34545412},
issn = {1432-184X},
support = {2018YFC0310600//the National Key Research and Development Program of China/ ; 2018YFD0900601//the National Key R&amp;D Program of China/ ; 31772826//the National Natural Science Foundation of China/ ; 2017-01-07-00-10-E00060//the major scientific innovation project from Shanghai Committee of Education/ ; },
mesh = {*Amphipoda/genetics ; Animals ; *Gastrointestinal Microbiome ; *Microbiota ; Pacific Ocean ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Amphipods are the dominant scavenging metazoan species in the hadal trenches at water depths below 6,000 m. The gut microbiota have been considered to be contribution to the adaptation of deep-sea organisms; however, few comparative analyses of animal gut microbiota between different isolated hadal environments have been done so far. Here, we employed high-throughput 16S rRNA sequencing to compare the gut microbial taxonomic composition and functional potential diversity of three hadal amphipod species, Hirondellea gigas, Bathycallisoma schellenbergi, and Alicella gigantea, collected from the Mariana Trench, Marceau Trench, and New Britain Trench in the Pacific Ocean, respectively. Results showed that different community compositions were detected across all the amphipod specimens based on the analyses of alpha-diversity, hierarchical cluster tree, and PCoA (principal coordinate analysis). Moreover, almost no correlation was observed between genera overrepresented in different amphipods by microbe-microbe correlations analysis, which suggested that the colonization of symbionts were host-specific. At genus level, Psychromonas was dominant in H. gigas, and Candidatus Hepatoplasma was overall dominant in A. gigantea and B. schellenbergi. Comparison of the functional potential showed that, though three hadal amphipod species shared the same predominant functional pathways, the abundances of those most shared pathways showed distinct differences across all the specimens. These findings pointed to the enrichment of particular functional pathways in the gut microbiota of the different isolated trench amphipods. Moreover, in terms of species relative abundance, alpha-diversity and beta-diversity, there was high similarity of gut microbiota between the two A. gigantea populations, which dwelled in two different localities of the same hadal trench. Altogether, this study provides an initial investigation into the gut-microbial interactions and evolution at the hadal depths within amphipod. Each of these three amphipod species would be a model taxa for future studies investigating the influence habitat difference and geography on gut-microbial communities.},
}
@article {pmid34544390,
year = {2021},
author = {Bento, FMM and Darolt, JC and Merlin, BL and Penã, L and Wulff, NA and Cônsoli, FL},
title = {The molecular interplay of the establishment of an infection - gene expression of Diaphorina citri gut and Candidatus Liberibacter asiaticus.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {677},
pmid = {34544390},
issn = {1471-2164},
mesh = {Animals ; *Citrus ; Gene Expression ; *Hemiptera/genetics ; Insect Vectors/genetics ; Liberibacter ; Plant Diseases ; *Rhizobiaceae/genetics ; },
abstract = {BACKGROUND: Candidatus Liberibacter asiaticus (CLas) is one the causative agents of greening disease in citrus, an unccurable, devastating disease of citrus worldwide. CLas is vectored by Diaphorina citri, and the understanding of the molecular interplay between vector and pathogen will provide additional basis for the development and implementation of successful management strategies. We focused in the molecular interplay occurring in the gut of the vector, a major barrier for CLas invasion and colonization.<br><br>RESULTS: We investigated the differential expression of vector and CLas genes by analyzing a de novo reference metatranscriptome of the gut of adult psyllids fed of CLas-infected and healthy citrus plants for 1-2, 3-4 and 5-6 days. CLas regulates the immune response of the vector affecting the production of reactive species of oxygen and nitrogen, and the production of antimicrobial peptides. Moreover, CLas overexpressed peroxiredoxin, probably in a protective manner. The major transcript involved in immune expression was related to melanization, a CLIP-domain serine protease we believe participates in the wounding of epithelial cells damaged during infection, which is supported by the down-regulation of pangolin. We also detected that CLas modulates the gut peristalsis of psyllids through the down-regulation of titin, reducing the elimination of CLas with faeces. The up-regulation of the neuromodulator arylalkylamine N-acetyltransferase implies CLas also interferes with the double brain-gut communication circuitry of the vector. CLas colonizes the gut by expressing two Type IVb pilin flp genes and several chaperones that can also function as adhesins. We hypothesized biofilm formation occurs by the expression of the cold shock protein of CLas.<br><br>CONCLUSIONS: The thorough detailed analysis of the transcritome of Ca. L. asiaticus and of D. citri at different time points of their interaction in the gut tissues of the host led to the identification of several host genes targeted for regulation by L. asiaticus, but also bacterial genes coding for potential effector proteins. The identified targets and effector proteins are potential targets for the development of new management strategies directed to interfere with the successful utilization of the psyllid vector by this pathogen.},
}
@article {pmid34540837,
year = {2021},
author = {Tudela, H and Claus, SP and Saleh, M},
title = {Next Generation Microbiome Research: Identification of Keystone Species in the Metabolic Regulation of Host-Gut Microbiota Interplay.},
journal = {Frontiers in cell and developmental biology},
volume = {9},
number = {},
pages = {719072},
pmid = {34540837},
issn = {2296-634X},
abstract = {The community of the diverse microorganisms residing in the gastrointestinal tract, known as the gut microbiota, is exceedingly being studied for its impact on health and disease. This community plays a major role in nutrient metabolism, maintenance of the intestinal epithelial barrier but also in local and systemic immunomodulation. A dysbiosis of the gut microbiota, characterized by an unbalanced microbial ecology, often leads to a loss of essential functions that may be associated with proinflammatory conditions. Specifically, some key microbes that are depleted in dysbiotic ecosystems, called keystone species, carry unique functions that are essential for the balance of the microbiota. In this review, we discuss current understanding of reported keystone species and their proposed functions in health. We also elaborate on current and future bioinformatics tools needed to identify missing functions in the gut carried by keystone species. We propose that the identification of such keystone species functions is a major step for the understanding of microbiome dynamics in disease and toward the development of microbiome-based therapeutics.},
}
@article {pmid34540373,
year = {2021},
author = {Rodríguez-Barreras, R and Tosado-Rodríguez, EL and Godoy-Vitorino, F},
title = {Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12084},
pmid = {34540373},
issn = {2167-8359},
support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; },
abstract = {Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species' guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.},
}
@article {pmid34540243,
year = {2021},
author = {Briggs, AA and Brown, AL and Osenberg, CW},
title = {Local versus site-level effects of algae on coral microbial communities.},
journal = {Royal Society open science},
volume = {8},
number = {9},
pages = {210035},
pmid = {34540243},
issn = {2054-5703},
abstract = {Microbes influence ecological processes, including the dynamics and health of macro-organisms and their interactions with other species. In coral reefs, microbes mediate negative effects of algae on corals when corals are in contact with algae. However, it is unknown whether these effects extend to larger spatial scales, such as at sites with high algal densities. We investigated how local algal contact and site-level macroalgal cover influenced coral microbial communities in a field study at two islands in French Polynesia, Mo'orea and Mangareva. At 5 sites at each island, we sampled prokaryotic microbial communities (microbiomes) associated with corals, macroalgae, turf algae and water, with coral samples taken from individuals that were isolated from or in contact with turf or macroalgae. Algal contact and macroalgal cover had antagonistic effects on coral microbiome alpha and beta diversity. Additionally, coral microbiomes shifted and became more similar to macroalgal microbiomes at sites with high macroalgal cover and with algal contact, although the microbial taxa that changed varied by island. Our results indicate that coral microbiomes can be affected by algae outside of the coral's immediate vicinity, and local- and site-level effects of algae can obscure each other's effects when both scales are not considered.},
}
@article {pmid34537690,
year = {2022},
author = {Bai, L and Ju, Q and Wang, C and Tian, L and Wang, C and Zhang, H and Jiang, H},
title = {Responses of steroid estrogen biodegradation to cyanobacterial organic matter biodegradability in the water column of a eutrophic lake.},
journal = {The Science of the total environment},
volume = {805},
number = {},
pages = {150058},
doi = {10.1016/j.scitotenv.2021.150058},
pmid = {34537690},
issn = {1879-1026},
mesh = {*Cyanobacteria ; Estrogens ; Estrone ; *Lakes ; Water ; },
abstract = {The co-occurrence of cyanobacterial harmful algal blooms and contaminants is an increasing environmental concern in freshwater worldwide. Our field investigations coupled with laboratory incubations demonstrated that the microbial degradation potential of 17β-estradiol (E2) with estrone as the intermediate was primarily driven by increased dissolved organic matter (DOM) in the water column of a cyanobacterial bloom. To explain the intrinsic contribution of cyanobacterial-derived DOM (C-DOM) to estrogen biodegradation, a combination of methods including bioassay, ultrahigh-resolution mass spectrometry, and microbial ecology were applied. The results showed that preferential assimilation of highly biodegradable structures, including protein-, carbohydrate-, and unsaturated hydrocarbon-like molecules sustained bacterial growth, selected for more diverse microbes, and resulted in greater estrogen biodegradation compared to less biodegradable molecules (lignin- and tannin-like molecules). The biodegradability of C-DOM decreased from 78% to 1%, whereas the E2 biodegradation rate decreased dramatically at first, then increased with the accumulation of recalcitrant, bio-produced lipid-like molecules in C-DOM. This change was linked to alternative substrate-induced selection of the bacterial community under highly refractory conditions, as suggested by the greater biomass-normalized E2 biodegradation rate after a 24-h lag phase. In addition to the increased frequency of potential degraders, such as Sphingobacterium, the network analysis revealed that C-DOM molecules distributed in high H/C (protein- and lipid-like molecules) were the main drivers structuring the bacterial community, inducing strong deterministic selection of the community assemblage and upregulating the metabolic capacity for contaminants. These findings provide strong evidence that estrogen biodegradation in eutrophic water may be facilitated by cyanobacterial blooms and provide a theoretical basis for ecological remediation of estrogen pollution.},
}
@article {pmid34537275,
year = {2021},
author = {Majlander, J and Anttila, VJ and Nurmi, W and Seppälä, A and Tiedje, J and Muziasari, W},
title = {Routine wastewater-based monitoring of antibiotic resistance in two Finnish hospitals: focus on carbapenem resistance genes and genes associated with bacteria causing hospital-acquired infections.},
journal = {The Journal of hospital infection},
volume = {117},
number = {},
pages = {157-164},
doi = {10.1016/j.jhin.2021.09.008},
pmid = {34537275},
issn = {1532-2939},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; Carbapenems/pharmacology ; Drug Resistance, Microbial ; Finland/epidemiology ; *Genes, Bacterial ; Hospitals ; Humans ; RNA, Ribosomal, 16S ; *Wastewater ; },
abstract = {BACKGROUND: Wastewater-based monitoring represents a useful tool for antibiotic resistance surveillance.<br><br>AIM: To investigate the prevalence and abundance of antibiotic resistance genes (ARGs) in hospital wastewater over time.<br><br>METHODS: Wastewater from two hospitals in Finland (HUS1 and HUS2) was monitored weekly for nine weeks (weeks 25-33) in summer 2020. A high-throughput real-time polymerization chain reaction (HT-qPCR) system was used to detect and quantify 216 ARGs and genes associated with mobile genetic elements (MGEs), integrons, and bacteria causing hospital-acquired infections (HAIs), as well as the 16S rRNA gene. Data from HT-qPCR were analysed and visualized using a novel digital platform, ResistApp. Eight carbapenem resistance genes (blaGES, blaKPC, blaVIM, blaNDM, blaCMY, blaMOX, blaOXA48, and blaOXA51) and three genes associated with bacteria causing HAIs (Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa) were studied.<br><br>FINDINGS: There was a significantly higher number of ARGs at both hospitals in weeks 27-30 (174-191 genes) compared to other sampling weeks (151-171 genes). Our analyses also indicated that the two hospitals, which used different amounts of antibiotics, had significantly different resistance gene profiles. Carbapenem resistance genes were more prevalent and abundant in HUS1 than HUS2. Across both hospitals, blaGES and blaVIM were the most prevalent and abundant. There was also a strong positive association between blaKPC and K.&#xa0;pneumoniae in HUS1 wastewater.<br><br>CONCLUSION: Routine wastewater-based monitoring using ResistApp can provide valuable information on the prevalence and abundance of ARGs in hospitals. This helps hospitals understand the spread of antibiotic resistance in hospitals and identify potential areas for intervention.},
}
@article {pmid34536095,
year = {2022},
author = {Gnat, S and Łagowski, D and Dyląg, M and Nowakiewicz, A},
title = {European Hedgehogs (Erinaceus europaeus L.) as a Reservoir of Dermatophytes in Poland.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {363-375},
pmid = {34536095},
issn = {1432-184X},
mesh = {Animals ; Animals, Wild ; Antifungal Agents/pharmacology ; *Arthrodermataceae/genetics ; Hedgehogs/microbiology ; Humans ; Microbial Sensitivity Tests ; Poland/epidemiology ; *Tinea/epidemiology/microbiology/veterinary ; Trichophyton/genetics ; },
abstract = {The European hedgehog (Erinaceus europaeus Linnaeus) frequently colonises areas located close to human life in cities, as these are more suitable nest sites offering an abundance of food and allowing avoidance of predators. However, urbanisation has a significant impact on the epidemiology of infectious diseases, including dermatophytoses, the primary source of which are wild animals. In this study, we determined the spectrum of dermatophytes isolated from the European hedgehog and assessed their susceptibility profile to antifungal drugs. Symptomatic and asymptomatic dermatophyte infections were observed in 7.7% and 8% of the 182 examined free-living hedgehogs, respectively. In the pool of the isolated dermatophyte strains, Trichophyton erinacei was dominant (29.9%), followed by Trichophyton mentagrophytes (17.9%), Trichophyton benhamiae (13.4%), Nannizzia gypsea (11.9%), Microsporum canis (10.4%), Nannizzia nana (7.5%), Paraphyton cookei (6.0%), and Nannizzia fulva (3.0%). Susceptibility tests revealed the highest activity of luliconazole and the lowest of activity fluconazole among the azole drugs applied. Although terbinafine generally exhibited high efficacy, two Trichophyton mentagrophytes isolates showed resistance to this drug (MIC = 2 µg/ml) resulting from missense mutations in the SQLE gene corresponding to the amino acid substitution Leu393Phe. Summarising, our study has also revealed that such wildlife animals as hedgehogs can be a reservoir of pathogenic human dermatophytes, including harmful strains resistant to commonly used antifungal drugs.},
}
@article {pmid34535834,
year = {2022},
author = {Li, H and Luo, N and Ji, C and Li, J and Zhang, L and Xiao, L and She, X and Liu, Z and Li, Y and Liu, C and Guo, Q and Lai, H},
title = {Liquid Organic Fertilizer Amendment Alters Rhizosphere Microbial Community Structure and Co-occurrence Patterns and Improves Sunflower Yield Under Salinity-Alkalinity Stress.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {423-438},
pmid = {34535834},
issn = {1432-184X},
support = {31600407//National Natural Science Fund Youth Project/ ; K3380220129//Fundamental Research Fund for Shaanxi agriculture department/ ; K3310220056//Shaanxi Provincial Key Technology R&amp;D Program/ ; },
mesh = {Bacteria ; Fertilizers ; *Helianthus ; *Microbiota ; Rhizosphere ; Salinity ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Response of rhizosphere microbial community structure and co-occurrence patterns to liquid organic fertilizer in sunflower cropland was investigated. Moderate and severe saline-alkaline soils were treated with liquid organic fertilizer containing mainly small molecular organic compounds (450 g L[-1]) at a rate of 4500 L ha[-1] year[-1] over 2 years. Compared with the untreated soils, organic fertilizer treatment increased soil nutrient concentrations by 13.8-137.1% while reducing soil pH and salinity by 5.6% and 54.7%, respectively. Organic fertilizer treatment also improved sunflower yield, plant number, and plant height by 28.6-67.3%. Following organic fertilizer treatment, fungal α-diversity was increased, and the effects of salinity-alkalinity stress on rhizosphere microbial communities were alleviated. The relative abundances of some halotolerant microbes and phytopathogenic fungi were reduced in organic fertilizer-treated soils, in contrast to increases in the relative abundances of plant growth-promoting microbes and organic matter decomposers, such as Nocardioides, Rhizophagus, and Stachybotrys. Network analysis revealed that severe salinity-alkalinity stress stimulated cooperation among bacteria, while organic fertilizer treatment tended to stimulate the ecosystem functions of fungi with higher proportions of fungi-bacteria and fungi-fungi links. More keystone taxa (e.g., Amycolatopsis, Variovorax, and Gemmatimonas) were positively correlated with soil nutrient concentrations and crop yield-related traits in organic fertilizer-treated soils. Overall, liquid organic fertilizer amendment could attenuate the adverse effects of salinity-alkalinity stress on sunflower yield by improving soil quality and optimizing rhizosphere microbial community structure and co-occurrence patterns.},
}
@article {pmid34530674,
year = {2021},
author = {Neumann, M and Steimle, A and Grant, ET and Wolter, M and Parrish, A and Willieme, S and Brenner, D and Martens, EC and Desai, MS},
title = {Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1966263},
pmid = {34530674},
issn = {1949-0984},
support = {R01 DK118024/DK/NIDDK NIH HHS/United States ; R01 DK125445/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteria/classification/growth &amp; development/isolation &amp; purification ; Citrobacter rodentium/*growth &amp; development ; Colitis/*microbiology ; Diet, Western/*adverse effects ; Dietary Fiber/*analysis ; Dysbiosis/microbiology ; Enterobacteriaceae Infections/microbiology/pathology ; Fatty Acids, Volatile/metabolism ; Feeding Behavior/physiology ; Female ; Intestinal Mucosa/*microbiology/pathology ; Mice ; Mice, Inbred C57BL ; Specific Pathogen-Free Organisms ; Tight Junctions/*physiology ; },
abstract = {The change of dietary habits in Western societies, including reduced consumption of fiber, is linked to alterations in gut microbial ecology. Nevertheless, mechanistic connections between diet-induced microbiota changes that affect colonization resistance and enteric pathogen susceptibility are still emerging. We sought to investigate how a diet devoid of soluble plant fibers impacts the structure and function of a conventional gut microbiota in specific-pathogen-free (SPF) mice and how such changes alter susceptibility to a rodent enteric pathogen. We show that absence of dietary fiber intake leads to shifts in the abundances of specific taxa, microbiome-mediated erosion of the colonic mucus barrier, a reduction of intestinal barrier-promoting short-chain fatty acids, and increases in markers of mucosal barrier integrity disruption. Importantly, our results highlight that these low-fiber diet-induced changes in the gut microbial ecology collectively contribute to a lethal colitis by the mucosal pathogen Citrobacter rodentium, which is used as a mouse model for enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC, respectively). Our study indicates that modern, low-fiber Western-style diets might make individuals more prone to infection by enteric pathogens via the disruption of mucosal barrier integrity by diet-driven changes in the gut microbiota, illustrating possible implications for EPEC and EHEC infections.},
}
@article {pmid34530278,
year = {2022},
author = {Li, W and Chen, X and Li, M and Cai, Z and Gong, H and Yan, M},
title = {Microplastics as an aquatic pollutant affect gut microbiota within aquatic animals.},
journal = {Journal of hazardous materials},
volume = {423},
number = {Pt B},
pages = {127094},
doi = {10.1016/j.jhazmat.2021.127094},
pmid = {34530278},
issn = {1873-3336},
mesh = {Animals ; *Environmental Pollutants ; *Gastrointestinal Microbiome ; Microplastics ; Plastics/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; },
abstract = {The adverse impact of microplastics (MPs) on gut microbiota within aquatic animals depends on the overall effect of chemicals and biofilm of MPs. Thus, it is ideal to fully understand the influences that arise from each or even all of these characteristics, which should give us a whole picture of consequences that are brought by MPs. Harmful effects of MPs on gut microbiota within aquatic organisms start from the ingestion of MPs by aquatic organisms. According to this, the present review will discuss the ingestion of MPs and its following results on gut microbial communities within aquatic animals, in which chemical components, such as plastic polymers, heavy metals and POPs, and the biofilm of MPs would be involved. This review firstly analyzed the impacts of MPs on aquatic organisms in detail about its chemical components and biofilm based on previous relevant studies. At last, the significance of field studies, functional studies and complex dynamics of gut microbial ecology in the future research of MPs affecting gut microbiota is discussed.},
}
@article {pmid34528105,
year = {2022},
author = {Zhang, J and Peng, S and Li, S and Song, J and Brunel, B and Wang, E and James, EK and Chen, W and Andrews, M},
title = {Arachis hypogaea L. from Acid Soils of Nanyang (China) Is Frequently Associated with Bradyrhizobium guangdongense and Occasionally with Bradyrhizobium ottawaense or Three Bradyrhizobium Genospecies.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {556-564},
pmid = {34528105},
issn = {1432-184X},
mesh = {Arachis ; *Bradyrhizobium/genetics ; DNA, Bacterial/genetics ; *Fabaceae ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rhizobium/genetics ; Root Nodules, Plant ; Sequence Analysis, DNA ; Soil ; Symbiosis ; },
abstract = {Henan Province is a major area of peanut production in China but the rhizobia nodulating the crop in this region have not been described. A collection of 217 strains of peanut rhizobia was obtained from six field sites across four soil types in Henan Province, North China, by using peanut as a trap host under glasshouse conditions. The 217 strains separated into 8 distinct types on PCR-RFLP analysis of their IGS sequences. Phylogenetic analysis of the 16S rRNA, recA, atpD, and glnII genes of 11 representative strains of the 8 IGS types identified Bradyrhizobium guangdongense, B. ottawaense and three novel Bradyrhizobium genospecies. Bradyrhizobium guangdongense was dominant, accounting for 75.0% of the total isolates across the field sites while B. ottawaense covered 5.1% and the three novel Bradyrhizobium genospecies 4.1 to 8.8% of the total. The symbiosis-related nodA and nifH gene sequences were not congruent with the core genes on phylogenetic analysis and separated into three groups, two of which were similar to sequences of Bradyrhizobium spp. isolated from peanut in south-east China and the third identical to that of B. yuanmingense isolated from Lespedeza cuneata in northern China. A canonical correlation analysis between the distribution of IGS genotypes and soil physicochemical characteristics and climatic factors indicated that the occurrence of IGS types/species was mainly associated with soil pH and available phosphorus.},
}
@article {pmid34527661,
year = {2021},
author = {Kerckhof, FM and Sakarika, M and Van Giel, M and Muys, M and Vermeir, P and De Vrieze, J and Vlaeminck, SE and Rabaey, K and Boon, N},
title = {From Biogas and Hydrogen to Microbial Protein Through Co-Cultivation of Methane and Hydrogen Oxidizing Bacteria.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {9},
number = {},
pages = {733753},
pmid = {34527661},
issn = {2296-4185},
abstract = {Increasing efforts are directed towards the development of sustainable alternative protein sources among which microbial protein (MP) is one of the most promising. Especially when waste streams are used as substrates, the case for MP could become environmentally favorable. The risks of using organic waste streams for MP production-the presence of pathogens or toxicants-can be mitigated by their anaerobic digestion and subsequent aerobic assimilation of the (filter-sterilized) biogas. Even though methane and hydrogen oxidizing bacteria (MOB and HOB) have been intensively studied for MP production, the potential benefits of their co-cultivation remain elusive. Here, we isolated a diverse group of novel HOB (that were capable of autotrophic metabolism), and co-cultured them with a defined set of MOB, which could be grown on a mixture of biogas and H2/O2. The combination of MOB and HOB, apart from the CH4 and CO2 contained in biogas, can also enable the valorization of the CO2 that results from the oxidation of methane by the MOB. Different MOB and HOB combinations were grown in serum vials to identify the best-performing ones. We observed synergistic effects on growth for several combinations, and in all combinations a co-culture consisting out of both HOB and MOB could be maintained during five days of cultivation. Relative to the axenic growth, five out of the ten co-cultures exhibited 1.1-3.8 times higher protein concentration and two combinations presented 2.4-6.1 times higher essential amino acid content. The MP produced in this study generally contained lower amounts of the essential amino acids histidine, lysine and threonine, compared to tofu and fishmeal. The most promising combination in terms of protein concentration and essential amino acid profile was Methyloparacoccus murrelli LMG 27482 with Cupriavidus necator LMG 1201. Microbial protein from M. murrelli and C. necator requires 27-67% less quantity than chicken, whole egg and tofu, while it only requires 15% more quantity than the amino acid-dense soybean to cover the needs of an average adult. In conclusion, while limitations still exist, the co-cultivation of MOB and HOB creates an alternative route for MP production leveraging safe and sustainably-produced gaseous substrates.},
}
@article {pmid34526978,
year = {2021},
author = {Marvasi, M and Pangallo, D and Cavalieri, D and Poyatos-Jiménez, F},
title = {Editorial: Multi-Omics Revolution in Microbial Cultural Heritage Conservation.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {720509},
pmid = {34526978},
issn = {1664-302X},
}
@article {pmid34526270,
year = {2021},
author = {Barros, J and Seena, S},
title = {Plastisphere in freshwaters: An emerging concern.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {290},
number = {},
pages = {118123},
doi = {10.1016/j.envpol.2021.118123},
pmid = {34526270},
issn = {1873-6424},
mesh = {Bacteria ; *Ecosystem ; Fresh Water ; Microplastics ; *Plastics ; },
abstract = {Plastisphere, an ecosystem of microbes thriving on floating plastic debris, has been extensively studied in marine waters since 2013. Currently, very little is known about the freshwater plastisphere. This review seeks to provide a broad insight into the freshwater science of plastisphere in the light of marine plastisphere, including research gaps, suggestions, and rising concerns, which would be of interest to the public, policymakers, and stakeholders. Given that freshwaters are endangered ecosystems, it is imperative to understand the role and impact of plastisphere on freshwaters. Plastic debris, especially microplastics (size <5 mm) in freshwater ecosystems, provide a stable, persistent, and buoyant substrate for microbes. Although current evidence suggests that freshwater environmental conditions and microplastics' physical and chemical properties significantly influence microbial colonisation, its role and integration in the aquatic ecosystems are unknown. Considering that the plastisphere biodiversity is unique, we seek to establish why and how many species co-exist in the plastisphere. Evaluating such fundamental questions should advance our basic understanding of the resilience of plastisphere to the changing environment. Plastisphere microbes, including the pathogenic bacteria, were found in both systems demonstrating their ability to survive on the plastic fragments from one ecosystem to another. A significant concern regarding plastisphere is the potential freshwater dispersal of anthropogenic pollutants and invasive or pathogenic species. Notably, microplastics aggregates may serve as a food source for grazers, which opens the question of the extent to which it can impact freshwater food webs. To gain a thorough understanding of the interplay between microplastics and the biogeochemical cycle, further insight into plastisphere microbes' functional role is needed. This would shed light on the unconsidered freshwater elemental cycling pathways. Given the complexity and universal nature of the plastisphere, strong interdisciplinary global research initiatives or networks are required to address the emerging concerns of plastisphere in freshwaters.},
}
@article {pmid34523560,
year = {2021},
author = {Trego, AC and Conall Holohan, B and Keating, C and Graham, A and O'Connor, S and Gerardo, M and Hughes, D and Ijaz, UZ and O'Flaherty, V},
title = {First proof of concept for full-scale, direct, low-temperature anaerobic treatment of municipal wastewater.},
journal = {Bioresource technology},
volume = {341},
number = {},
pages = {125786},
doi = {10.1016/j.biortech.2021.125786},
pmid = {34523560},
issn = {1873-2976},
mesh = {Anaerobiosis ; Bioreactors ; RNA, Ribosomal, 16S/genetics ; Sewage ; Temperature ; *Waste Disposal, Fluid ; *Wastewater ; },
abstract = {Municipal wastewater constitutes the largest fraction of wastewater, and yet treatment processes are largely removal-based. High-rate anaerobic digestion (AD) has revolutionised the sustainability of industrial wastewater treatment and could additionally provide an alternative for municipal wastewater. While AD of dilute municipal wastewater is common in tropical regions, the low temperatures of temperate climates has resulted in slow uptake. Here, we demonstrate for the first time, direct, high-rate, low-temperature AD of low-strength municipal wastewater at full-scale. An 88 m[3] hybrid reactor was installed at the municipal wastewater treatment plant in Builth Wells, UK and operated for 290 days. Ambient temperatures ranged from 2 to 18 °C, but remained below 15 °C for > 100 days. Influent BOD fluctuated between 2 and 200 mg L[-1]. However, BOD removal often reached > 85%. 16S rRNA amplicon sequencing of DNA from the biomass revealed a highly adaptable core microbiome. These findings could provide the basis for the next-generation of municipal wastewater treatment.},
}
@article {pmid34523363,
year = {2023},
author = {De Vuyst, L and Comasio, A and Kerrebroeck, SV},
title = {Sourdough production: fermentation strategies, microbial ecology, and use of non-flour ingredients.},
journal = {Critical reviews in food science and nutrition},
volume = {63},
number = {15},
pages = {2447-2479},
doi = {10.1080/10408398.2021.1976100},
pmid = {34523363},
issn = {1549-7852},
mesh = {*Ecosystem ; Fermentation ; Bread/microbiology ; *Lactobacillales ; Yeasts ; Food Microbiology ; },
abstract = {Sourdough production is an ancient method to ferment flour from cereals for the manufacturing of baked goods. This review deals with the state-of-the-art of current fermentation strategies for sourdough production and the microbial ecology of mature sourdoughs, with a particular focus on the use of non-flour ingredients. Flour fermentation processes for sourdough production are typically carried out by heterogeneous communities of lactic acid bacteria and yeasts. Acetic acid bacteria may also occur, although their presence and role in sourdough production can be criticized. Based on the inoculum used, sourdough productions can be distinguished in fermentation processes using backslopping procedures, originating from a spontaneously fermented flour-water mixture (Type 1), starter culture-initiated fermentation processes (Type 2), and starter culture-initiated fermentation processes that are followed by backslopping (Type 3). In traditional recipes for the initiation and/or propagation of Type 1 sourdough productions, non-flour ingredients are often added to the flour-water mixture. These ingredients may be the source of an additional microbial inoculum and/or serve as (co-)substrates for fermentation. An example of the former is the addition of yoghurt; an example of the latter is the use of fruit juices. The survival of microorganisms transferred from the ingredients to the fermenting flour-water mixture depends on the competitiveness toward particular strains of the microbial species present under the harsh conditions of the sourdough ecosystem. Their survival and growth is also determined by the presence of the appropriate substrates, whether or not carried over by the ingredients added.},
}
@article {pmid34522990,
year = {2022},
author = {Matsumoto, S and Watanabe, K and Imamura, A and Tachibana, M and Shimizu, T and Watarai, M},
title = {Comparative Analysis Between Paramecium Strains with Different Syngens Using the RAPD Method.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {594-602},
pmid = {34522990},
issn = {1432-184X},
support = {19K06383//Japan Society for the Promotion of Science/ ; 17H03914//Japan Society for the Promotion of Science/ ; },
mesh = {*Chlorella ; *Paramecium/genetics ; Random Amplified Polymorphic DNA Technique ; Symbiosis ; },
abstract = {Paramecium spp. are a genus of free-living protists that live mainly in freshwater environments. They are ciliates with high motility and phagocytosis and have been used to analyze cell motility and as a host model for pathogens. Besides such biological characteristics, apart from the usual morphological and genetic classification of species, the existence of taxonomies (such as syngens) and mating types related to Paramecium's unique reproduction is known. In this study, we attempted to develop a simple method to identify Paramecium strains, which are difficult to distinguish morphologically, using random amplified polymorphic DNA (RAPD) analysis. Consequently, we can observe strain-specific band patterns. We also confirm that the presence of endosymbiotic Chlorella cells affects the band pattern of P. bursaria. Furthermore, the results of the RAPD analysis using several P. caudatum strains with different syngens show that it is possible to detect a band specific to a certain syngen. By improving the reaction conditions and random primers, based on the results of this study, RAPD analysis can be applied to the identification of Paramecium strains and their syngen confirmation tests.},
}
@article {pmid34519519,
year = {2021},
author = {Putman, LI and Sabuda, MC and Brazelton, WJ and Kubo, MD and Hoehler, TM and McCollom, TM and Cardace, D and Schrenk, MO},
title = {Microbial Communities in a Serpentinizing Aquifer Are Assembled through Strong Concurrent Dispersal Limitation and Selection.},
journal = {mSystems},
volume = {6},
number = {5},
pages = {e0030021},
pmid = {34519519},
issn = {2379-5077},
support = {NNA15BB02A//NASA | NASA Astrobiology Institute (NAI)/ ; },
abstract = {In recent years, our appreciation of the extent of habitable environments in Earth's subsurface has greatly expanded, as has our understanding of the biodiversity contained within. Most studies have relied on single sampling points, rather than considering the long-term dynamics of subsurface environments and their microbial populations. One such habitat are aquifers associated with the aqueous alteration of ultramafic rocks through a process known as serpentinization. Ecological modeling performed on a multiyear time series of microbiology, hydrology, and geochemistry in an ultrabasic aquifer within the Coast Range Ophiolite reveals that community assembly is governed by undominated assembly (i.e., neither stochastic [random] nor deterministic [selective] processes alone govern assembly). Controls on community assembly were further assessed by characterizing aquifer hydrogeology and microbial community adaptations to the environment. These analyses show that low permeability rocks in the aquifer restrict the transmission of microbial populations between closely situated wells. Alpha and beta diversity measures and metagenomic and metatranscriptomic data from microbial communities indicate that high pH and low dissolved inorganic carbon levels impose strong environmental selection on microbial communities within individual wells. Here, we find that the interaction between strong selection imposed by extreme pH and enhanced ecological drift due to dispersal limitation imposed by slow fluid flow results in the undominated assembly signal observed throughout the site. Strong environmental selection paired with extremely low dispersal in the subsurface results in low diversity microbial communities that are well adapted to extreme pH conditions and subject to enhanced stochasticity introduced by ecological drift over time. IMPORTANCE Microbial communities existing under extreme or stressful conditions have long been thought to be structured primarily by deterministic processes. The application of macroecology theory and modeling to microbial communities in recent years has spurred assessment of assembly processes in microbial communities, revealing that both stochastic and deterministic processes are at play to different extents within natural environments. We show that low diversity microbial communities in a hard-rock serpentinizing aquifer are assembled under the influence of strong selective processes imposed by high pH and enhanced ecological drift that occurs as the result of dispersal limitation due to the slow movement of water in the low permeability aquifer. This study demonstrates the important roles that both selection and dispersal limitation play in terrestrial serpentinites, where extreme pH assembles a microbial metacommunity well adapted to alkaline conditions and dispersal limitation drives compositional differences in microbial community composition between local communities in the subsurface.},
}
@article {pmid34518545,
year = {2021},
author = {Chen, Y and Wang, Y and Paez-Espino, D and Polz, MF and Zhang, T},
title = {Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {5398},
pmid = {34518545},
issn = {2041-1723},
mesh = {Archaea/classification/genetics/virology ; Bacteria/classification/genetics/virology ; *Carbon Cycle ; Energy Metabolism/genetics ; Genes, Viral/genetics ; Genetic Variation ; Host-Pathogen Interactions ; Open Reading Frames/genetics ; Prokaryotic Cells/metabolism/*virology ; Sequence Analysis, DNA/methods ; Sewage/microbiology/*virology ; Virome/*genetics ; Viruses/classification/*genetics/metabolism ; Water Purification/*methods ; },
abstract = {As one of the largest biotechnological applications, activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses, with 10-1,000-fold higher concentrations than in natural environments. However, the compositional variation and host-connections of AS viruses remain poorly explored. Here, we report a catalogue of ~50,000 prokaryotic viruses from six WWTPs, increasing the number of described viral species of AS by 23-fold, and showing the very high viral diversity which is largely unknown (98.4-99.6% of total viral contigs). Most viral genera are represented in more than one AS system with 53 identified across all. Viral infection widely spans 8 archaeal and 58 bacterial phyla, linking viruses with aerobic/anaerobic heterotrophs, and other functional microorganisms controlling nitrogen/phosphorous removal. Notably, Mycobacterium, notorious for causing AS foaming, is associated with 402 viral genera. Our findings expand the current AS virus catalogue and provide reference for the phage treatment to control undesired microorganisms in WWTPs.},
}
@article {pmid34515628,
year = {2021},
author = {Undabarrena, A and Pereira, CF and Kruasuwan, W and Parra, J and Sélem-Mojica, N and Vind, K and Schniete, JK},
title = {Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21.},
journal = {Microbiology (Reading, England)},
volume = {167},
number = {9},
pages = {},
pmid = {34515628},
issn = {1465-2080},
support = {BB/S016651/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Actinobacteria/genetics ; Actinomyces ; Anti-Bacterial Agents ; Multigene Family ; Synthetic Biology ; },
abstract = {Last year ActinoBase, a Wiki-style initiative supported by the UK Microbiology Society, published a review highlighting the research of particular interest to the actinomycete community. Here, we present the second ActinoBase review showcasing selected reports published in 2020 and early 2021, integrating perspectives in the actinomycete field. Actinomycetes are well-known for their unsurpassed ability to produce specialised metabolites, of which many are used as therapeutic agents with antibacterial, antifungal, or immunosuppressive activities. Much research is carried out to understand the purpose of these metabolites in the environment, either within communities or in host interactions. Moreover, many efforts have been placed in developing computational tools to handle big data, simplify experimental design, and find new biosynthetic gene cluster prioritisation strategies. Alongside, synthetic biology has provided advances in tools to elucidate the biosynthesis of these metabolites. Additionally, there are still mysteries to be uncovered in understanding the fundamentals of filamentous actinomycetes' developmental cycle and regulation of their metabolism. This review focuses on research using integrative methodologies and approaches to understand the bigger picture of actinomycete biology, covering four research areas: i) technology and methodology; ii) specialised metabolites; iii) development and regulation; and iv) ecology and host interactions.},
}
@article {pmid34515591,
year = {2023},
author = {Li, Q and Van de Wiele, T},
title = {Gut microbiota as a driver of the interindividual variability of cardiometabolic effects from tea polyphenols.},
journal = {Critical reviews in food science and nutrition},
volume = {63},
number = {11},
pages = {1500-1526},
doi = {10.1080/10408398.2021.1965536},
pmid = {34515591},
issn = {1549-7852},
mesh = {Humans ; Polyphenols/pharmacology/metabolism ; *Gastrointestinal Microbiome ; Tea/metabolism ; *Microbiota ; *Cardiovascular Diseases/prevention &amp; control ; },
abstract = {Tea polyphenols have been extensively studied for their preventive properties against cardiometabolic diseases. Nevertheless, the evidence of these effects from human intervention studies is not always consistent, mainly because of a large interindividual variability. The bioavailability of tea polyphenols is low, and metabolism of tea polyphenols highly depends on individual gut microbiota. The accompanying reciprocal relationship between tea polyphenols and gut microbiota may result in alterations in the cardiometabolic effects, however, the underlying mechanism of which is little explored. This review summarizes tea polyphenols-microbiota interaction and its contribution to interindividual variability in cardiometabolic effects. Currently, only a few bacteria that can biodegrade tea polyphenols have been identified and generated metabolites and their bioactivities in metabolic pathways are not fully elucidated. A deeper understanding of the role of complex interaction necessitates fully individualized data, the ntegration of multiple-omics platforms and development of polyphenol-centered databases. Knowledge of this microbial contribution will enable the functional stratification of individuals in the gut microbiota profile (metabotypes) to clarify interindividual variability in the health effects of tea polyphenols. This could be used to predict individual responses to tea polyphenols consumption, hence bringing us closer to personalized nutrition with optimal dose and additional supplementation of specific microorganisms.},
}
@article {pmid34512595,
year = {2021},
author = {Tavares, TCL and Bezerra, WM and Normando, LRO and Rosado, AS and Melo, VMM},
title = {Brazilian Semi-Arid Mangroves-Associated Microbiome as Pools of Richness and Complexity in a Changing World.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {715991},
pmid = {34512595},
issn = {1664-302X},
abstract = {Mangrove microbiomes play an essential role in the fate of mangroves in our changing planet, but the factors regulating the biogeographical distribution of mangrove microbial communities remain essentially vague. This paper contributes to our understanding of mangrove microbiomes distributed along three biogeographical provinces and ecoregions, covering the exuberant mangroves of Amazonia ecoregion (North Brazil Shelf) as well as mangroves located in the southern limit of distribution (Southeastern ecoregion, Warm Temperate Southwestern Atlantic) and mangroves localized on the drier semi-arid coast (Northeastern ecoregion, Tropical Southwestern Atlantic), two important ecotones where poleward and landward shifts, respectively, are expected to occur related to climate change. This study compared the microbiomes associated with the conspicuous red mangrove (Rhizophora mangle) root soils encompassing soil properties, latitudinal factors, and amplicon sequence variants of 105 samples. We demonstrated that, although the northern and southern sites are over 4,000 km apart, and despite R. mangle genetic divergences between north and south populations, their microbiomes resemble each other more than the northern and northeastern neighbors. In addition, the northeastern semi-arid microbiomes were more diverse and displayed a higher level of complexity than the northern and southern ones. This finding may reflect the endurance of the northeast microbial communities tailored to deal with the stressful conditions of semi-aridity and may play a role in the resistance and growing landward expansion observed in such mangroves. Minimum temperature, precipitation, organic carbon, and potential evapotranspiration were the main microbiota variation drivers and should be considered in mangrove conservation and recovery strategies in the Anthropocene. In the face of changes in climate, land cover, biodiversity, and chemical composition, the richness and complexity harbored by semi-arid mangrove microbiomes may hold the key to mangrove adaptability in our changing planet.},
}
@article {pmid34512593,
year = {2021},
author = {Zhao, J and Ma, J and Yang, Y and Yu, H and Zhang, S and Chen, F},
title = {Response of Soil Microbial Community to Vegetation Reconstruction Modes in Mining Areas of the Loess Plateau, China.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {714967},
pmid = {34512593},
issn = {1664-302X},
abstract = {Vegetation reconstruction and restoration is vital to the health of the mine land ecosystem. Different vegetations might change microbial community structure and function of soil, mediating the biogeochemical cycle and nutrition supply to the soil. To clarify the response of soil microbes to different vegetation reconstruction modes in the mining areas of the Loess Plateau, China, soil microbial community structures and functions were determined by the MiSeq high-throughput sequencing along with PICRUSt2 and FUNGuild tools. The fungal community richness was observed to be the highest in grassland soil and positively correlated with soil organic matter, total nitrogen, and nitrate-nitrogen. The bacterial and fungal community structures were similar in grassland and brushland areas, but were significantly differentiated in the coniferous and broadleaf forest, and the leading factors were soil pH and nitrate-nitrogen. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla under different vegetation reconstruction modes. The dominant phyla of fungi were Ascomycota, Basidiomycota, and Mortierellomycota. Different vegetation reconstruction modes did not affect the bacterial functional communities but shaped different functional groups of fungi. The grassland soil was dominated by saprotrophic fungi, while symbiotrophic fungi dominated the coniferous and broadleaf forests. The results suggested that shifts in vegetation reconstruction modes may alter the mining soil bacterial and fungal community structures and function. These findings improve the understanding of microbial ecology in the reclaimed mine soil and provide a reference for the ecological restoration of fragile mining ecosystems.},
}
@article {pmid34510242,
year = {2022},
author = {Mikhailov, IS and Galachyants, YP and Bukin, YS and Petrova, DP and Bashenkhaeva, MV and Sakirko, MV and Blinov, VV and Titova, LA and Zakharova, YR and Likhoshway, YV},
title = {Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {404-422},
pmid = {34510242},
issn = {1432-184X},
support = {0279-2021-0008//Ministry of Science and Higher Education of Russian Federation/ ; 0279-2021-0009//Ministry of Science and Higher Education of Russian Federation/ ; 0279-2021-0004//Ministry of Science and Higher Education of Russian Federation/ ; &#x410;&#x410;&#x410;&#x410;-&#x410;17-117041250054-8//Integration project of the Irkutsk Scientific Center state/ ; },
mesh = {Bacteria/genetics ; *Lakes/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seasons ; },
abstract = {Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.},
}
@article {pmid34505915,
year = {2022},
author = {LaForgia, ML and Kang, H and Ettinger, CL},
title = {Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {496-508},
pmid = {34505915},
issn = {1432-184X},
mesh = {Bacteria/genetics ; Humans ; *Microbiota/genetics ; Plant Roots/microbiology ; Plants ; Poaceae/genetics ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; },
abstract = {Rhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasion. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plants. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses grown in a shade-house both individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how differentially abundant microbial families correlate to plant biomass under competition. We find that bacterial diversity and structure differ between native forbs and invasive grasses, but fungal diversity and structure do not. Furthermore, bacterial community structures under competition are distinct from individual bacterial community structures. We also identified five bacterial families that varied in normalized abundance between treatments and that were correlated with plant biomass under competition. We speculate that invasive grass dominance over these natives may be partially due to effects on the rhizosphere community, with changes in specific bacterial families potentially benefiting invaders at the expense of natives.},
}
@article {pmid34504476,
year = {2021},
author = {Lammers, A and Zweers, H and Sandfeld, T and Bilde, T and Garbeva, P and Schramm, A and Lalk, M},
title = {Antimicrobial Compounds in the Volatilome of Social Spider Communities.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {700693},
pmid = {34504476},
issn = {1664-302X},
abstract = {Social arthropods such as termites, ants, and bees are among others the most successful animal groups on earth. However, social arthropods face an elevated risk of infections due to the dense colony structure, which facilitates pathogen transmission. An interesting hypothesis is that social arthropods are protected by chemical compounds produced by the arthropods themselves, microbial symbionts, or plants they associate with. Stegodyphus dumicola is an African social spider species, inhabiting communal silk nests. Because of the complex three-dimensional structure of the spider nest antimicrobial volatile organic compounds (VOCs) are a promising protection against pathogens, because of their ability to diffuse through air-filled pores. We analyzed the volatilomes of S. dumicola, their nests, and capture webs in three locations in Namibia and assessed their antimicrobial potential. Volatilomes were collected using polydimethylsiloxane (PDMS) tubes and analyzed using GC/Q-TOF. We showed the presence of 199 VOCs and tentatively identified 53 VOCs. More than 40% of the tentatively identified VOCs are known for their antimicrobial activity. Here, six VOCs were confirmed by analyzing pure compounds namely acetophenone, 1,3-benzothiazole, 1-decanal, 2-decanone, 1-tetradecene, and docosane and for five of these compounds the antimicrobial activity were proven. The nest and web volatilomes had many VOCs in common, whereas the spider volatilomes were more differentiated. Clear differences were identified between the volatilomes from the different sampling sites which is likely justified by differences in the microbiomes of the spiders and nests, the plants, and the different climatic conditions. The results indicate the potential relevance of the volatilomes for the ecological success of S. dumicola.},
}
@article {pmid34499191,
year = {2022},
author = {Yaghoubi Khanghahi, M and Crecchio, C and Verbruggen, E},
title = {Shifts in the Rhizosphere and Endosphere Colonizing Bacterial Communities Under Drought and Salinity Stress as Affected by a Biofertilizer Consortium.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {483-495},
pmid = {34499191},
issn = {1432-184X},
mesh = {Bacteria ; *Droughts ; Endophytes/physiology ; Fertilizers ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Salt Stress ; Soil Microbiology ; },
abstract = {The present research asks how plant growth-promoting bacterial (PGPB) inoculants and chemical fertilizers change rhizosphere and root endophytic bacterial communities in durum wheat, and its dependence on environmental stress. A greenhouse experiment was carried out under drought (at 40% field capacity), or salinity (150 mM NaCl) conditions to investigate the effects of a chemical fertilizer (containing nitrogen, phosphorus, potassium and zinc) or a biofertilizer (a bacterial consortium of four PGPBs). High-throughput amplicon sequencing of the 16S rRNA of the rhizosphere, non-sterilized, or surface-sterilized roots, showed shifts in bacterial communities in response to stress treatments, which were greater for salinity than for drought and tended to show increased oligotrophs relative abundances compared to non-stress controls. The results also showed that Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Thaumarchaeota, Firmicutes, and Verrucomicrobia had a higher relative abundance in the rhizosphere, while Actinobacteria were more abundant on roots, while Candidatus_Saccharibacteria and Planctomycetes inside roots. The results indicated that the root endophytic bacterial communities were more affected by (bio-) fertilization treatments than those in the rhizosphere, particularly as affected by PGPB inoculation. This greater susceptibility of endophytes to (bio-) fertilizers was associated with increased abundance of the 16S rRNA and acdS genes in plant roots, especially under stress conditions. These changes in root endophytes, which coincided with an improvement in grain yield and photosynthetic capacity of plants, may be considered as one of the mechanisms by which PGPB affect plants.},
}
@article {pmid34498120,
year = {2022},
author = {Silva, AMM and Estrada-Bonilla, GA and Lopes, CM and Matteoli, FP and Cotta, SR and Feiler, HP and Rodrigues, YF and Cardoso, EJBN},
title = {Does Organomineral Fertilizer Combined with Phosphate-Solubilizing Bacteria in Sugarcane Modulate Soil Microbial Community and Functions?.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {539-555},
pmid = {34498120},
issn = {1432-184X},
support = {01.13.0209.00//Financiadora de Estudos e Projetos/ ; 2016/18944-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Bacteria ; Fertilizers/analysis ; *Microbiota ; Phosphates ; *Saccharum ; Soil ; Soil Microbiology ; },
abstract = {Soil bacterial and fungal communities are suitable soil ecosystem health indicators due to their sensitivity to management practices and their role in soil ecosystem processes. Here, information on composition and functions of bacterial and fungal communities were evaluated at two phenological stages of sugarcane (six and twelve months, equivalent to the most intensive vegetative stage and to final maturation, respectively) when organomineral fertilizer, combined with phosphate-solubilizing bacteria (PSB), was added into the soil. Organic compost enriched with apatite (C + A) or phosphorite (C + P) and compost without phosphate enrichment (C) were used in the presence or absence of PSB. In addition, we used a control fertilized with soluble triple superphosphate. The differences were more related to the sampling period than to the type of organomineral fertilizer, being observed higher available phosphorus at six months than at twelve months. Only in the C treatment we observed the presence of Bacillaceae and Planococcaceae, while Pseudomonadaceae were only prevalent in inoculated C + A. As for fungi, the genera Chaetomium and Achroiostachys were only present in inoculated C + P, while the genus Naganishia was most evident in inoculated C + A and in uninoculated C + P. Soliccocozyma represented 75% of the total fungal abundance in uninoculated C while in inoculated C, it represented 45%. The bacterial community was more related to the degradation of easily decomposable organic compounds, while the fungal community was more related to degradation of complex organic compounds. Although the microbial community showed a resilient trait, subtle changes were detected in microbial community composition and function, and this may be related to the increase in yield observed.},
}
@article {pmid34498119,
year = {2022},
author = {Yun, J and Jung, JY and Kwon, MJ and Seo, J and Nam, S and Lee, YK and Kang, H},
title = {Temporal Variations Rather than Long-Term Warming Control Extracellular Enzyme Activities and Microbial Community Structures in the High Arctic Soil.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {168-181},
pmid = {34498119},
issn = {1432-184X},
support = {NRF-2019H1A2A1076239//Ministry of Education/ ; NRF-2016M1A5A1901770, PN20081//Ministry of Science and ICT of Korea/ ; NRF-2016M1A5A1901795//Ministry of Science and ICT of Korea/ ; NRF-2020M1A5A1110494//Ministry of Science and ICT of Korea/ ; },
mesh = {Arctic Regions ; *Greenhouse Gases ; Hydrolases ; *Microbiota ; Soil/chemistry ; Soil Microbiology ; },
abstract = {In Arctic soils, warming accelerates decomposition of organic matter and increases emission of greenhouse gases (GHGs), contributing to a positive feedback to climate change. Although microorganisms play a key role in the processes between decomposition of organic matter and GHGs emission, the effects of warming on temporal responses of microbial activity are still elusive. In this study, treatments of warming and precipitation were conducted from 2012 to 2018 in Cambridge Bay, Canada. Soils of organic and mineral layers were collected monthly from June to September in 2018 and analyzed for extracellular enzyme activities and bacterial community structures. The activity of hydrolases was the highest in June and decreased thereafter over summer in both organic and mineral layers. Bacterial community structures changed gradually over summer, and the responses were distinct depending on soil layers and environmental factors; water content and soil temperature affected the shift of bacterial community structures in both layers, whereas bacterial abundance, dissolved organic carbon, and inorganic nitrogen did so in the organic layer only. The activity of hydrolases and bacterial community structures did not differ significantly among treatments but among months. Our results demonstrate that temporal variations may control extracellular enzyme activities and microbial community structure rather than the small effect of warming over a long period in high Arctic soil. Although the effects of the treatments on microbial activity were minor, our study provides insight that microbial activity may increase due to an increase in carbon availability, if the growing season is prolonged in the Arctic.},
}
@article {pmid34498118,
year = {2022},
author = {Minahan, NT and Chen, CH and Shen, WC and Lu, TP and Kallawicha, K and Tsai, KH and Guo, YL},
title = {Fungal Spore Richness in School Classrooms is Related to Surrounding Forest in a Season-Dependent Manner.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {351-362},
pmid = {34498118},
issn = {1432-184X},
support = {MOST 108-2621-M-002-018//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Air Microbiology ; *Allergens/genetics ; Child ; *Forests ; Fungi/genetics ; Humans ; Schools ; Seasons ; Spores, Fungal ; },
abstract = {Airborne fungal spores are important aeroallergens that are remarkably diverse in terms of taxonomic richness. Indoor fungal richness is dominated by outdoor fungi and is geographically patterned, but the influence of natural landscape is unclear. We aimed to elucidate the relationship between indoor fungal spore richness and natural landscape by examining the amount of surrounding forest cover. Passive sampling of airborne fungal spores was conducted in 24 schools in Taiwan during hot and cool seasons, and amplicon sequencing was used to study fungal spore (genus) richness targeting the internal transcribed spacer 2 (ITS2) region. In total, 693 fungal genera were identified, 12 of which were ubiquitous. Despite overall similarity of fungal spore richness between seasons, Basidiomycota and Ascomycota richness increased during the hot and cool seasons, respectively. Fungal spore richness in schools had a strong positive correlation with the amount of surrounding forest cover during the cool season, but not during the hot season. Fungal assemblages in schools were more similar during the hot season due to the increased ubiquity of Agaricomycetes genera. These observations indicate dispersal limitation at the kilometer scale during the cool season and increased long-distance dispersal during the hot season. Several allergenic fungi were commonly identified in schools, including some previously overlooked by conventional methods, which may be targeted as sensitizing agents in future investigations into atopic conditions. More generally, the relative importance of fungal spore richness in the development, chronicity, and severity of atopic conditions in children requires investigation.},
}
@article {pmid34495440,
year = {2021},
author = {Xie, J and Wang, X and Xu, J and Xie, H and Cai, Y and Liu, Y and Ding, X},
title = {Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata).},
journal = {Rice (New York, N.Y.)},
volume = {14},
number = {1},
pages = {79},
pmid = {34495440},
issn = {1939-8425},
support = {81960364//national natural science foundation of china/ ; 31560041//national natural science foundation of china/ ; 81501162//national natural science foundation of china/ ; 20171BCB23020//jiangxi province outstanding young talents funding scheme/ ; 9166-27060003-YB11//interdisciplinary innovation fund of nanchang university/ ; },
abstract = {BACKGROUND: Drought is global environmental stress that limits crop yields. Plant-associated microbiomes play a crucial role in determining plant fitness in response to drought, yet the fundamental mechanisms for maintaining microbial community stability under drought disturbances in wild rice are poorly understood. We make explicit comparisons of leaf, stem, root and rhizosphere microbiomes from the drought-tolerant wild rice (Oryza longistaminata) in response to drought stress.<br><br>RESULTS: We find that the response of the wild rice microbiome to drought was divided into aboveground-underground patterns. Drought reduced the leaf and stem microbial community diversity and networks stability, but not that of the roots and rhizospheres. Contrary to the aboveground microbial networks, the drought-negative response taxa exhibited much closer interconnections than the drought-positive response taxa and were the dominant network hubs of belowground co-occurrence networks, which may contribute to the stability of the belowground network. Notably, drought induces enrichment of Actinobacteria in belowground compartments, but not the aboveground compartment. Additionally, the rhizosphere microbiome exhibited a higher proportion of generalists and broader habitat niche breadth than the microbiome at other compartments, and drought enhanced the proportion of specialists in all compartments. Null model analysis revealed that both the aboveground and belowground-community were governed primarily by the stochastic assembly process, moreover, drought decreased 'dispersal limitation', and enhanced 'drift'.<br><br>CONCLUSIONS: Our results provide new insight into the different strategies and assembly mechanisms of the above and belowground microbial community in response to drought, including enrichment of taxonomic groups, and highlight the important role of the stochastic assembly process in shaping microbial community under drought stress.},
}
@article {pmid34495359,
year = {2022},
author = {Agarwal, R and Gupta, M and Antony, A and Sen, R and Raychoudhury, R},
title = {In Vitro Studies Reveal that Pseudomonas, from Odontotermes obesus Colonies, can Function as a Defensive Mutualist as it Prevents the Weedy Fungus While Keeping the Crop Fungus Unaffected.},
journal = {Microbial ecology},
volume = {84},
number = {2},
pages = {391-403},
pmid = {34495359},
issn = {1432-184X},
mesh = {Animals ; Fungi ; *Isoptera/microbiology ; Plant Weeds/genetics ; Pseudomonas/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; },
abstract = {Insects that farm monocultures of fungi are canonical examples of nutritional symbiosis as well as independent evolution of agriculture in non-human animals. But just like in human agriculture, these fungal crops face constant threat of invasion by weeds which, if unchecked, take over the crop fungus. In fungus-growing termites, the crop fungus (Termitomyces) faces such challenges from the weedy fungus Pseudoxylaria. The mechanism by which Pseudoxylaria is suppressed is not known. However, evidence suggests that some bacterial secondary symbionts can serve as defensive mutualists by preventing the growth of Pseudoxylaria. However, such secondary symbionts must possess the dual, yet contrasting, capabilities of suppressing the weedy fungus while keeping the growth of the crop fungus unaffected. This study describes the isolation, identification, and culture-dependent estimation of the roles of several such putative defensive mutualists from the colonies of the wide-spread fungus-growing termite from India, Odontotermes obesus. From the 38 bacterial cultures tested, a strain of Pseudomonas showed significantly greater suppression of the weedy fungus than the crop fungus. Moreover, a 16S rRNA pan-microbiome survey, using the Nanopore platform, revealed Pseudomonas to be a part of the core microbiota of O. obesus. A meta-analysis of microbiota composition across different species of Odontotermes also confirms the widespread prevalence of Pseudomonas within this termite. These lines of evidence indicate that Pseudomonas could be playing the role of defensive mutualist within Odontotermes.},
}
@article {pmid34494852,
year = {2021},
author = {Ma, L and Huang, X and Wang, H and Yun, Y and Cheng, X and Liu, D and Lu, X and Qiu, X},
title = {Microbial Interactions Drive Distinct Taxonomic and Potential Metabolic Responses to Habitats in Karst Cave Ecosystem.},
journal = {Microbiology spectrum},
volume = {9},
number = {2},
pages = {e0115221},
pmid = {34494852},
issn = {2165-0497},
mesh = {Actinobacteria/classification/isolation &amp; purification/*metabolism ; Bacterial Physiological Phenomena ; Carbon Cycle/physiology ; Caves/*microbiology ; Ecosystem ; Geologic Sediments/*microbiology ; Microbial Interactions/*physiology ; Nitrogen Fixation/physiology ; Proteobacteria/classification/isolation &amp; purification/*metabolism ; Soil Microbiology ; },
abstract = {The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark, humid, and oligotrophic habitat have received far less attention, which is crucial to understanding cave biogeochemistry. Herein, microorganisms from weathered rock and sediment along the Heshang Cave depth were analyzed by random matrix theory-based network and Tax4Fun functional prediction. The results showed that although the cave microbial communities have spatial heterogeneity, differential habitats drove the community structure and diversity. Actinobacteria were predominant in weathered rock, whereas Proteobacteria dominated the sediment. The sediment communities presented significantly higher alpha diversities due to the relatively abundant nutrition from the outside by the intermittent stream. Consistently, microbial interactions in sediment were more complex, as visualized by more nodes and links. The abundant taxa presented more positive correlations with other community members in both of the two networks, indicating that they relied on promotion effects to adapt to the extreme environment. The keystones in weathered rock were mainly involved in the biodegradation of organic compounds, whereas the keystone Nitrospira in sediment contributed to carbon/nitrogen fixation. Collectively, these findings suggest that microbial interactions may lead to distinct taxonomic and functional communities in weathered rock and sediment in the subsurface Heshang Cave. IMPORTANCE In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. There are still many unknowns about the microbial interactions and functions in such a dark environment with little human interference. Two representative habitats, including weathered rock and sediment in Heshang Cave, were selected to give an integrated insight into microbial interactions and potential functions. The cooccurrence network, especially the subnetwork, was used to characterize the cave microbial interactions in detail. We demonstrated that abundant taxa primarily relied on promotion effects rather than inhibition effects to survive in Heshang Cave. Keystone species may play important metabolic roles in sustaining ecological functions. Our study provides improved understanding of microbial interaction patterns and community ecological functions in the karst cave ecosystem.},
}
@article {pmid34493269,
year = {2021},
author = {Hadjirin, NF and Miller, EL and Murray, GGR and Yen, PLK and Phuc, HD and Wileman, TM and Hernandez-Garcia, J and Williamson, SM and Parkhill, J and Maskell, DJ and Zhou, R and Fittipaldi, N and Gottschalk, M and Tucker, AWD and Hoa, NT and Welch, JJ and Weinert, LA},
title = {Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis.},
journal = {BMC biology},
volume = {19},
number = {1},
pages = {191},
pmid = {34493269},
issn = {1741-7007},
support = {MR/N002660/1/MRC_/Medical Research Council/United Kingdom ; MR/R002762/1/MRC_/Medical Research Council/United Kingdom ; BB/L003902/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G019274/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents ; Drug Resistance, Bacterial/genetics ; Genomics ; Microbial Sensitivity Tests ; Pharmaceutical Preparations ; *Streptococcus suis/drug effects/genetics ; Swine ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans.<br><br>RESULTS: We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into 'resistant' and 'susceptible', highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order.<br><br>CONCLUSIONS: We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.},
}
@article {pmid34491099,
year = {2022},
author = {Su, L and Qiu, P and Fang, Z and Sun, J and Mo, X and Liu, Y and Kuramae, EE and Zhang, R and Shen, B and Shen, Q},
title = {Potassium Phosphite Enhances the Antagonistic Capability of Bacillus amyloliquefaciens to Manage Tomato Bacterial Wilt.},
journal = {Plant disease},
volume = {106},
number = {2},
pages = {654-660},
doi = {10.1094/PDIS-08-21-1601-RE},
pmid = {34491099},
issn = {0191-2917},
mesh = {*Bacillus amyloliquefaciens/physiology ; *Biological Control Agents ; *Solanum lycopersicum/microbiology ; Phosphites ; *Plant Diseases/microbiology/prevention &amp; control ; *Potassium Compounds ; *Ralstonia solanacearum/pathogenicity ; },
abstract = {Bacterial wilt caused by Ralstonia solanacearum is a distributed and worldwide soilborne disease. The application of biocontrol microbes or agricultural chemicals has been widely used to manage tomato bacterial wilt. However, whether and how agricultural chemicals affect the antagonistic ability of biocontrol microbes is still unknown. Here, we combined potassium phosphite (K-Phite), an environmentally friendly agricultural chemical, and the biocontrol agent Bacillus amyloliquefaciens QPF8 (strain F8) to manage tomato bacterial wilt disease. First, K-Phite at a concentration of 0.05% (wt/vol) could significantly inhibit the growth of R. solanacearum. Second, 0.05% K-Phite enhanced the antagonistic capability of B. amyloliquefaciens F8. Third, the greenhouse soil experiments showed that the control efficiency for tomato bacterial wilt in the combined treatment was significantly higher than that of the application of B. amyloliquefaciens F8 or K-Phite alone. Overall, our results highlighted a novel strategy for the control of tomato bacterial wilt disease via application and revealed a new integrated pattern depending on the enhancement of the antagonistic capability of biocontrol microbes by K-Phite.},
}
@article {pmid34490209,
year = {2021},
author = {Medvecky, M and Mandalakis, M},
title = {PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems.},
journal = {Frontiers in chemistry},
volume = {9},
number = {},
pages = {722087},
pmid = {34490209},
issn = {2296-2646},
abstract = {The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires a priori knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest.},
}
@article {pmid34487274,
year = {2021},
author = {Benedek, T and Szentgyörgyi, F and Gergócs, V and Menashe, O and Gonzalez, PAF and Probst, AJ and Kriszt, B and Táncsics, A},
title = {Potential of Variovorax paradoxus isolate BFB1_13 for bioremediation of BTEX contaminated sites.},
journal = {AMB Express},
volume = {11},
number = {1},
pages = {126},
pmid = {34487274},
issn = {2191-0855},
support = {TKP2020-IKA-12//ministry of innovation and technology/ ; 2018-2.1.16-T&#xc9;T-IL-2018-00002//nemzeti kutat&#xe1;si fejleszt&#xe9;si &#xe9;s innov&#xe1;ci&#xf3;s hivatal/ ; FK 134439//otka young researcher excellence programme/ ; },
abstract = {Here, we report and discuss the applicability of Variovorax paradoxus strain BFB1_13 in the bioremediation of BTEX contaminated sites. Strain BFB1_13 was capable of degrading all the six BTEX-compounds under both aerobic (O2 conc. 8 mg l[-1]) and micro-aerobic/oxygen-limited (O2 conc. 0.5 mg l[-1]) conditions using either individual (8 mg‧l[-1]) or a mixture of compounds (~ 1.3 mg‧l[-1] of each BTEX compound). The BTEX biodegradation capability of SBP-encapsulated cultures (SBP-Small Bioreactor Platform) was also assessed. The fastest degradation rate was observed in the case of aerobic benzene biodegradation (8 mg l[-1] per 90 h). Complete biodegradation of other BTEX occurred after at least 168 h of incubation, irrespective of the oxygenation and encapsulation. No statistically significant difference was observed between aerobic and microaerobic BTEX biodegradation. Genes involved in BTEX biodegradation were annotated and degradation pathways were predicted based on whole-genome shotgun sequencing and metabolic analysis. We conclude that V. paradoxus strain BFB1_13 could be used for the development of reactive biobarriers for the containment and in situ decontamination of BTEX contaminated groundwater plumes. Our results suggest that V. paradoxus strain BFB1_13-alone or in co-culture with other BTEX degrading bacterial isolates-can be a new and efficient commercial bioremediation agent for BTEX contaminated sites.},
}
@article {pmid34487212,
year = {2022},
author = {Wahdan, SFM and Hossen, S and Tanunchai, B and Sansupa, C and Schädler, M and Noll, M and Dawoud, TM and Wu, YT and Buscot, F and Purahong, W},
title = {Life in the Wheat Litter: Effects of Future Climate on Microbiome and Function During the Early Phase of Decomposition.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {90-105},
pmid = {34487212},
issn = {1432-184X},
mesh = {Bacteria/genetics ; Ecosystem ; Fungi/genetics ; *Microbiota ; Plant Leaves/microbiology ; *Triticum ; },
abstract = {Even though it is widely acknowledged that litter decomposition can be impacted by climate change, the functional roles of microbes involved in the decomposition and their answer to climate change are less understood. This study used a field experimental facility settled in Central Germany to analyze the effects of ambient vs. future climate that is expected in 50-80 years on mass loss and physicochemical parameters of wheat litter in agricultural cropland at the early phase of litter decomposition process. Additionally, the effects of climate change were assessed on microbial richness, community compositions, interactions, and their functions (production of extracellular enzymes), as well as litter physicochemical factors shaping their colonization. The initial physicochemical properties of wheat litter did not change between both climate conditions; however, future climate significantly accelerated litter mass loss as compared with ambient one. Using MiSeq Illumina sequencing, we found that future climate significantly increased fungal richness and altered fungal communities over time, while bacterial communities were more resistant in wheat residues. Changes on fungal richness and/or community composition corresponded to different physicochemical factors of litter under ambient (Ca[2+], and pH) and future (C/N, N, P, K[+], Ca[2+], pH, and moisture) climate conditions. Moreover, highly correlative interactions between richness of bacteria and fungi were detected under future climate. Furthermore, the co-occurrence networks patterns among dominant microorganisms inhabiting wheat residues were strongly distinct between future and ambient climates. Activities of microbial β-glucosidase and N-acetylglucosaminidase in wheat litter were increased over time. Such increased enzymatic activities were coupled with a significant positive correlation between microbial (both bacteria and fungi) richness and community compositions with these two enzymatic activities only under future climate. Overall, we provide evidence that future climate significantly impacted the early phase of wheat litter decomposition through direct effects on fungal communities and through indirect effects on microbial interactions as well as corresponding enzyme production.},
}
@article {pmid34487211,
year = {2022},
author = {Deng, J and Yu, D and Zhou, W and Zhou, L and Zhu, W},
title = {Variations of Phyllosphere and Rhizosphere Microbial Communities of Pinus koraiensis Infected by Bursaphelenchus xylophilus.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {285-301},
pmid = {34487211},
issn = {1432-184X},
support = {E0381601//the Mission of Chinese Academy of Sciences/ ; },
mesh = {Animals ; Bacteria ; *Microbiota ; *Nematoda ; *Pinus/microbiology ; Plant Diseases/microbiology ; Rhizosphere ; Xylophilus ; },
abstract = {Pine wood nematode, Bursaphelenchus xylophilus, as one of the greatest threats to pine trees, is spreading all over the world. Plant microorganisms play an important role in the pathogenesis of nematodes. The phyllosphere and rhizosphere bacterial and fungal communities associated with healthy Pinus koraiensis (PKa) and P. koraiensis infected by B. xylophilus at the early (PKb) and last (PKc) stages were analyzed. Our results demonstrated that pine wood nematode (PWD) could increase the phyllosphere bacterial Pielou_e, Shannon, and Simpson index; phyllosphere fungal Chao 1 index, as well as rhizosphere bacterial Pielou_e, Shannon, and Simpson index; and rhizosphere fungal Pielou_e, Shannon, and Simpson index. What's more, slight shifts of the microbial diversity were observed at the early stage of infection, and the microbial diversity increased significantly as the symptoms of infection worsened. With the infection of B. xylophilus in P. koraiensis, Bradyrhizobium (rhizosphere bacteria), Massilia (phyllosphere bacteria), and Phaeosphaeriaceae (phyllosphere fungi) were the major contributors to the differences in community compositions among different treatments. With the infection of PWD, most of the bacterial groups tended to be co-excluding rather than co-occurring. These changes would correlate with microbial ability to suppress plant pathogen, enhancing the understanding of disease development and providing guidelines to pave the way for its possible management.},
}
@article {pmid34486723,
year = {2021},
author = {Stephen, AS and Dhadwal, N and Nagala, V and Gonzales-Marin, C and Gillam, DG and Bradshaw, DJ and Burnett, GR and Allaker, RP},
title = {Interdental and subgingival microbiota may affect the tongue microbial ecology and oral malodour in health, gingivitis and periodontitis.},
journal = {Journal of periodontal research},
volume = {56},
number = {6},
pages = {1174-1184},
doi = {10.1111/jre.12931},
pmid = {34486723},
issn = {1600-0765},
support = {//GlaxoSmithKline/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Chronic Periodontitis ; *Dental Plaque ; *Gingivitis ; *Halitosis ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Tongue ; },
abstract = {BACKGROUND AND OBJECTIVE: Oral malodour is often observed in gingivitis and chronic periodontitis patients, and the tongue microbiota is thought to play a major role in malodorous gas production, including volatile sulphur compounds (VSCs) such as hydrogen sulphide (H2 S) and methanethiol (CH3 SH). This study aimed to examine the link between the presence of VSCs in mouth air (as a marker of oral malodour) and the oral bacterial ecology in the tongue and periodontal niches of healthy, gingivitis and periodontitis patients.<br><br>METHODS: Participants were clinically assessed using plaque index, bleeding on probing (BOP) and periodontal probing depths, and VSC concentrations in their oral cavity measured using a portable gas chromatograph. Tongue scrapings, subgingival and interdental plaque were collected from healthy individuals (n&#xa0;=&#xa0;22), and those with gingivitis (n&#xa0;=&#xa0;14) or chronic periodontitis (n&#xa0;=&#xa0;15). The bacterial 16S rRNA gene region V3-V4 in these samples was sequenced, and the sequences were analysed using the minimum entropy decomposition pipeline.<br><br>RESULTS: Elevated VSC concentrations and CH3 SH:H2 S were observed in periodontitis compared with health. Significant ecological differences were observed in the tongue microbiota of healthy subjects with high plaque scores compared to low plaque scores, suggesting a possible connection between the microbiota of the tongue and the periodontium and that key dysbiotic changes may be initiated in the clinically healthy individuals who have higher dental plaque accumulation. Greater subgingival bacterial diversity was positively associated with H2 S in mouth air. Periodontopathic bacteria known to be prolific VSC producers increased in abundance on the tongue associated with increased bleeding on probing (BOP) and total percentage of periodontal pockets >6&#xa0;mm, supporting the suggestion that the tongue may become a reservoir for periodontopathogens.<br><br>CONCLUSION: This study highlights the importance of the periodontal microbiota in malodour and has detected dysbiotic changes in the tongue microbiota in periodontitis.},
}
@article {pmid34480872,
year = {2021},
author = {Seki, D and Mayer, M and Hausmann, B and Pjevac, P and Giordano, V and Goeral, K and Unterasinger, L and Klebermaß-Schrehof, K and De Paepe, K and Van de Wiele, T and Spittler, A and Kasprian, G and Warth, B and Berger, A and Berry, D and Wisgrill, L},
title = {Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage.},
journal = {Cell host &amp; microbe},
volume = {29},
number = {10},
pages = {1558-1572.e6},
pmid = {34480872},
issn = {1934-6069},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Brain/growth &amp; development ; Brain Injuries/*immunology/*microbiology/physiopathology ; Female ; *Gastrointestinal Microbiome ; Humans ; Immune System/growth &amp; development ; Infant, Newborn ; Infant, Premature/*growth &amp; development/immunology ; Male ; T-Lymphocytes/immunology ; Vascular Endothelial Growth Factor A/genetics/immunology ; },
abstract = {Premature infants are at substantial risk for suffering from perinatal white matter injury. Though the gut microbiota has been implicated in early-life development, a detailed understanding of the gut-microbiota-immune-brain axis in premature neonates is lacking. Here, we profiled the gut microbiota, immunological, and neurophysiological development of 60 extremely premature infants, which received standard hospital care including antibiotics and probiotics. We found that maturation of electrocortical activity is suppressed in infants with severe brain damage. This is accompanied by elevated γδ T cell levels and increased T cell secretion of vascular endothelial growth factor and reduced secretion of neuroprotectants. Notably, Klebsiella overgrowth in the gut is highly predictive for brain damage and is associated with a pro-inflammatory immunological tone. These results suggest that aberrant development of the gut-microbiota-immune-brain axis may drive or exacerbate brain injury in extremely premature neonates and represents a promising target for novel intervention strategies.},
}
@article {pmid34477968,
year = {2021},
author = {Deepika, S and Kothamasi, D},
title = {Plant hosts may influence arbuscular mycorrhizal fungal community composition in mangrove estuaries.},
journal = {Mycorrhiza},
volume = {31},
number = {6},
pages = {699-711},
pmid = {34477968},
issn = {1432-1890},
support = {894188//h2020 marie sk&#x142;odowska-curie actions/ ; },
mesh = {Ecosystem ; Estuaries ; *Mycobiome ; *Mycorrhizae/genetics ; Plant Roots ; Soil ; Soil Microbiology ; },
abstract = {We investigated the role of plant host and soil variables in determining arbuscular mycorrhizal fungi (AMF) community composition in plant roots of two spatially separated mangrove estuaries on the rivers Aghanashini (14° 30' 30″ N-74° 22' 44″ E) and Gangavali (14° 35' 26″ N-74° 17' 51″ E) on the west coast of India. Both mangrove estuaries had similar plant species composition but differed in soil chemistries.We amplified a 550-bp portion of 18S small subunit (SSU) rDNA from mangrove plant roots and analysed it by restriction fragment length polymorphism (RFLP). Clones representing unique RFLP patterns were sequenced. A total of 736 clones were obtained from roots of seven and five plant species sampled at Aghanashini and Gangavali, respectively. AMF phylotype numbers in plant roots at Aghanashini (12) were higher than at Gangavali (9) indicating quantitative differences in the AMF community composition in plant roots at the two mangrove estuaries. Because both estuaries had similar plant species composition, the quantitative difference in AMF communities between the estuaries could be an attribute of the differences in rhizospheric chemistry between the two sites.Non-metric multidimensional scaling (NMDS) revealed overlap in the AMF communities of the two sites. Three and two AMF phylotypes had significant indicator value indices with specific hosts at Aghanashini and Gangavali, respectively. Environmental vector fitting to NMDS ordination did not reveal a significant effect of any soil variable on AMF composition at the two sites. However, significant effects of both plant hosts and sites were observed on rhizospheric P. Our results indicate that root AMF community composition may be an outcome of plant response to rhizospheric variables. This suggests that plant identity may have a primary role in shaping AMF communities in mangroves.},
}
@article {pmid34477107,
year = {2021},
author = {Mancuso, CP and Lee, H and Abreu, CI and Gore, J and Khalil, AS},
title = {Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34477107},
issn = {2050-084X},
support = {DP2 AI131083/AI/NIAID NIH HHS/United States ; R01 EB027793/EB/NIBIB NIH HHS/United States ; R01 GM102311/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; Bacteriological Techniques ; *Biodiversity ; Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Models, Theoretical ; Population Density ; *Soil Microbiology ; Time Factors ; },
abstract = {Environmental disturbances have long been theorized to play a significant role in shaping the diversity and composition of ecosystems. However, an inability to specify the characteristics of a disturbance experimentally has produced an inconsistent picture of diversity-disturbance relationships (DDRs). Here, using a high-throughput programmable culture system, we subjected a soil-derived bacterial community to dilution disturbance profiles with different intensities (mean dilution rates), applied either constantly or with fluctuations of different frequencies. We observed an unexpected U-shaped relationship between community diversity and disturbance intensity in the absence of fluctuations. Adding fluctuations increased community diversity and erased the U-shape. All our results are well-captured by a Monod consumer resource model, which also explains how U-shaped DDRs emerge via a novel 'niche flip' mechanism. Broadly, our combined experimental and modeling framework demonstrates how distinct features of an environmental disturbance can interact in complex ways to govern ecosystem assembly and offers strategies for reshaping the composition of microbiomes.},
}
@article {pmid34474030,
year = {2022},
author = {Brennerova, MV and Zavala-Meneses, SG and Josefiova, J and Branny, P and Buriankova, K and Vetrovsky, T and Junca, H},
title = {A global survey reveals a divergent extradiol dioxygenase clade as a widespread complementary contributor to the biodegradation of mono- and polycyclic aromatic hydrocarbons.},
journal = {Environmental research},
volume = {204},
number = {Pt A},
pages = {111954},
doi = {10.1016/j.envres.2021.111954},
pmid = {34474030},
issn = {1096-0953},
mesh = {Biodegradation, Environmental ; Oxygenases/genetics ; Phylogeny ; *Polycyclic Aromatic Hydrocarbons ; },
abstract = {Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (EXDOs) with broad substrate specificity, the HrbC EXDOs. The new clade belongs to the XII cluster within family 2 of the vicinal oxygen chelate superfamily (EXDO-VC2), which is typically characterized by a preference for bicyclic substrates. Coding hrbC orthologs were isolated by activity-based screening of fosmid metagenomic libraries from large DNA fragments derived from heavily PAH-contaminated soils. They occurred as solitary genes within conserved sequences encoding enzymes for amino acid metabolism and were stably maintained in the chromosomes of the Betaproteobacteria lineages harboring them. Analysis of contaminated aquifers revealed coexpression of hrbC as a polycistronic mRNA component. The predicted open reading frames were verified by cloning and heterologous expression, confirming the expected molecular mass and meta-cleavage activity of the recombinant enzymes. Evolutionary analysis of the HrbC protein sequences grouped them into a discrete cluster of 1,2-dihydroxynaphthalene dioxygenases represented by a cultured PAH degrader, Rugosibacter aromaticivorans strain Ca6. The ecological importance and relevance of the new EXDO genes were confirmed by PCR-based mapping in different biogeographical localities contaminated with a variety of mono- and polycyclic aromatic compounds. The cosmopolitan distribution of hrbC in PAH-contaminated aquifers supports our hypothesis about its auxiliary role in the degradation of toxic catecholic intermediates, contributing to the composite EXDO catabolic capacity of the world's microbiomes.},
}
@article {pmid34469194,
year = {2021},
author = {Wee, SY and Edgcomb, VP and Beaudoin, D and Yvon-Lewis, S and Sylvan, JB},
title = {Microbial Abundance and Diversity in Subsurface Lower Oceanic Crust at Atlantis Bank, Southwest Indian Ridge.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {22},
pages = {e0151921},
pmid = {34469194},
issn = {1098-5336},
support = {OCE1658118//National Science Foundation (NSF)/ ; OCE1658031//National Science Foundation (NSF)/ ; },
mesh = {Ammonium Compounds ; Atlantic Ocean ; *Expeditions ; Indian Ocean ; *Microbiota ; Phosphates ; Seawater/*microbiology ; },
abstract = {International Ocean Discovery Program Expedition 360 drilled Hole U1473A at Atlantis Bank, an oceanic core complex on the Southwest Indian Ridge, with the aim of recovering representative samples of the lower oceanic crust. Recovered cores were primarily gabbro and olivine gabbro. These mineralogies may host serpentinization reactions that have the potential to support microbial life within the recovered rocks or at greater depths beneath Atlantis Bank. We quantified prokaryotic cells and analyzed microbial community composition for rock samples obtained from Hole U1473A and conducted nutrient addition experiments to assess if nutrient supply influences the composition of microbial communities. Microbial abundance was low (≤10[4] cells cm[-3]) but positively correlated with the presence of veins in rocks within some depth ranges. Due to the heterogeneous nature of the rocks downhole (alternating stretches of relatively unaltered gabbros and more significantly altered and fractured rocks), the strength of the positive correlations between rock characteristics and microbial abundances was weaker when all depths were considered. Microbial community diversity varied at each depth analyzed. Surprisingly, addition of simple organic acids, ammonium, phosphate, or ammonium plus phosphate in nutrient addition experiments did not affect microbial diversity or methane production in nutrient addition incubation cultures over 60 weeks. The work presented here from Site U1473A, which is representative of basement rock samples at ultraslow spreading ridges and the usually inaccessible lower oceanic crust, increases our understanding of microbial life present in this rarely studied environment and provides an analog for basement below ocean world systems such as Enceladus. IMPORTANCE The lower oceanic crust below the seafloor is one of the most poorly explored habitats on Earth. The rocks from the Southwest Indian Ridge (SWIR) are similar to rock environments on other ocean-bearing planets and moons. Studying this environment helps us increase our understanding of life in other subsurface rocky environments in our solar system that we do not yet have the capability to access. During an expedition to the SWIR, we drilled 780 m into lower oceanic crust and collected over 50 rock samples to count the number of resident microbes and determine who they are. We also selected some of these rocks for an experiment where we provided them with different nutrients to explore energy and carbon sources preferred for growth. We found that the number of resident microbes and community structure varied with depth. Additionally, added nutrients did not shape the microbial diversity in a predictable manner.},
}
@article {pmid34468785,
year = {2022},
author = {Bazzicalupo, AL and Erlandson, S and Branine, M and Ratz, M and Ruffing, L and Nguyen, NH and Branco, S},
title = {Fungal Community Shift Along Steep Environmental Gradients from Geothermal Soils in Yellowstone National Park.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {33-43},
pmid = {34468785},
issn = {1432-184X},
mesh = {Fungi/genetics ; *Mycobiome ; *Mycorrhizae ; Parks, Recreational ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Geothermal soils offer unique insight into the way extreme environmental factors shape communities of organisms. However, little is known about the fungi growing in these environments and in particular how localized steep abiotic gradients affect fungal diversity. We used metabarcoding to characterize soil fungi surrounding a hot spring-fed thermal creek with water up to 84 °C and pH 10 in Yellowstone National Park. We found a significant association between fungal communities and soil variable principal components, and we identify the key trends in co-varying soil variables that explain the variation in fungal community. Saprotrophic and ectomycorrhizal fungi community profiles followed, and were significantly associated with, different soil variable principal components, highlighting potential differences in the factors that structure these different fungal trophic guilds. In addition, in vitro growth experiments in four target fungal species revealed a wide range of tolerances to pH levels but not to heat. Overall, our results documenting turnover in fungal species within a few hundred meters suggest many co-varying environmental factors structure the diverse fungal communities found in the soils of Yellowstone National Park.},
}
@article {pmid34468725,
year = {2021},
author = {Varliero, G and Rafiq, M and Singh, S and Summerfield, A and Sgouridis, F and Cowan, DA and Barker, G},
title = {Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {10},
pages = {},
pmid = {34468725},
issn = {1574-6941},
mesh = {Greenland ; Metagenome ; Metagenomics ; *Permafrost ; Soil Microbiology ; },
abstract = {Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.},
}
@article {pmid34468165,
year = {2021},
author = {Iburg, S and Izabel-Shen, D and Austin, &#xc5;N and Hansen, JP and Eklöf, JS and Nascimento, FJA},
title = {Effects of Recreational Boating on Microbial and Meiofauna Diversity in Coastal Shallow Ecosystems of the Baltic Sea.},
journal = {mSphere},
volume = {6},
number = {5},
pages = {e0012721},
pmid = {34468165},
issn = {2379-5042},
mesh = {Animals ; *Biodiversity ; Ecosystem ; Geologic Sediments ; Invertebrates/classification ; Oceans and Seas ; Salinity ; *Water Sports ; },
abstract = {Recreational boating can impact benthic ecosystems in coastal waters. Reduced height and cover of aquatic vegetation in shallow Baltic Sea inlets with high boat traffic have raised concerns about cascading effects on benthic communities in these ecosystems. Here, we characterized the diversity and composition of sediment-associated microbial and meiofaunal communities across five bays subjected to low and high degrees of boating activity and examined the community-environment relationships and association with bay morphometry. We found that recreational boating activity altered meiofauna alpha diversity and the composition of both micro- and meiobenthic communities, and there were strong correlations between community structure and morphometric variables like topographic openness, wave exposure, water surface area, and total phosphorous concentrations. Inlets with high boat traffic showed an increase of bacterial taxa like Hydrogenophilaceae and Burkholderiaceae. Several meiofauna taxa previously reported to respond positively to high levels of suspended organic matter were found in higher relative abundances in the bays with high boat traffic. Overall, our results show that morphometric characteristics of inlets are the strongest drivers of benthic diversity in shallow coastal environments. However, while the effects were small, we found significant effects of recreational boating on benthic community structure that should be considered when evaluating the new mooring projects. IMPORTANCE With the increase of recreational boating activity and development of boating infrastructure in shallow, wave-protected areas, there is growing concern for their impact on coastal ecosystems. In order to properly assess the effects and consider the potential for recovery, it is important to investigate microbial and meiofaunal communities that underpin the functioning of these ecosystems. Here, we present the first study that uses DNA metabarcoding to assess how benthic biodiversity in shallow coastal areas is impacted by recreational boating. Our study shows a relatively small, but significant, effect of recreational boating both on meiofauna alpha diversity and meiofauna and bacterial community composition. However, both meiofauna and bacterial community composition in shallow benthic habitats is mediated to a higher degree by abiotic variables, such as topographic openness, area or size of the inlets, and wave exposure. Despite the fact that the effects were small, such impacts on benthic biodiversity should be considered in the management of coastal shallow habitats.},
}
@article {pmid34467445,
year = {2022},
author = {Gabashvili, E and Kobakhidze, S and Chkhikvishvili, T and Tabatadze, L and Tsiklauri, R and Dadiani, K and Kotetishvili, M},
title = {Bacteriophage-Mediated Risk Pathways Underlying the Emergence of Antimicrobial Resistance via Intrageneric and Intergeneric Recombination of Antibiotic Efflux Genes Across Natural populations of Human Pathogenic Bacteria.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {213-226},
pmid = {34467445},
issn = {1432-184X},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacillus cereus ; *Bacteriophages ; Drug Resistance, Bacterial/genetics ; Humans ; Pilot Projects ; Recombination, Genetic ; },
abstract = {Antimicrobial resistance continues to be a significant and growing threat to global public health, being driven by the emerging drug-resistant and multidrug-resistant strains of human and animal bacterial pathogens. While bacteriophages are generally known to be one of the vehicles of antibiotic resistance genes (ARGs), it remains largely unclear how these organisms contribute to the dissemination of the genetic loci encoding for antibiotic efflux pumps, especially those that confer multidrug resistance, in bacteria. In this study, the in-silico recombination analyses provided strong statistical evidence for bacteriophage-mediated intra-species recombination of ARGs, encoding mainly for the antibiotic efflux proteins from the MF superfamily, as well as from the ABC and RND families, in Salmonella enterica, Staphylococcus aureus, Staphylococcus suis, Pseudomonas aeruginosa, and Burkholderia pseudomallei. Events of bacteriophage-driven intrageneric recombination of some of these genes could be also elucidated among Bacillus thuringiensis, Bacillus cereus and Bacillus tropicus natural populations. Moreover, we could also reveal the patterns of intergeneric recombination, involving the MF superfamily transporter-encoding genetic loci, induced by a Mycobacterium smegmatis phage, in natural populations of Streptomyces harbinensis and Streptomyces chartreusis. The SplitsTree- (fit: 100; bootstrap values: 92.7-100; Phi p ≤ 0.2414), RDP4- (p ≤ 0.0361), and GARD-generated data strongly supported the above genetic recombination inferences in these in-silico analyses. Thus, based on this pilot study, it can be suggested that the above mode of bacteriophage-mediated recombination plays at least some role in the emergence and transmission of multidrug resistance across a fairly broad spectrum of bacterial species and genera including human pathogens.},
}
@article {pmid34466168,
year = {2021},
author = {Crous, PW and Lombard, L and Sandoval-Denis, M and Seifert, KA and Schroers, HJ and Chaverri, P and Gené, J and Guarro, J and Hirooka, Y and Bensch, K and Kema, GHJ and Lamprecht, SC and Cai, L and Rossman, AY and Stadler, M and Summerbell, RC and Taylor, JW and Ploch, S and Visagie, CM and Yilmaz, N and Frisvad, JC and Abdel-Azeem, AM and Abdollahzadeh, J and Abdolrasouli, A and Akulov, A and Alberts, JF and Araújo, JPM and Ariyawansa, HA and Bakhshi, M and Bendiksby, M and Ben Hadj Amor, A and Bezerra, JDP and Boekhout, T and Câmara, MPS and Carbia, M and Cardinali, G and Castañeda-Ruiz, RF and Celis, A and Chaturvedi, V and Collemare, J and Croll, D and Damm, U and Decock, CA and de Vries, RP and Ezekiel, CN and Fan, XL and Fernández, NB and Gaya, E and González, CD and Gramaje, D and Groenewald, JZ and Grube, M and Guevara-Suarez, M and Gupta, VK and Guarnaccia, V and Haddaji, A and Hagen, F and Haelewaters, D and Hansen, K and Hashimoto, A and Hernández-Restrepo, M and Houbraken, J and Hubka, V and Hyde, KD and Iturriaga, T and Jeewon, R and Johnston, PR and Jurjević, &#x17d; and Karalti, I and Korsten, L and Kuramae, EE and Kušan, I and Labuda, R and Lawrence, DP and Lee, HB and Lechat, C and Li, HY and Litovka, YA and Maharachchikumbura, SSN and Marin-Felix, Y and Matio Kemkuignou, B and Matočec, N and McTaggart, AR and Mlčoch, P and Mugnai, L and Nakashima, C and Nilsson, RH and Noumeur, SR and Pavlov, IN and Peralta, MP and Phillips, AJL and Pitt, JI and Polizzi, G and Quaedvlieg, W and Rajeshkumar, KC and Restrepo, S and Rhaiem, A and Robert, J and Robert, V and Rodrigues, AM and Salgado-Salazar, C and Samson, RA and Santos, ACS and Shivas, RG and Souza-Motta, CM and Sun, GY and Swart, WJ and Szoke, S and Tan, YP and Taylor, JE and Taylor, PWJ and Tiago, PV and Váczy, KZ and van de Wiele, N and van der Merwe, NA and Verkley, GJM and Vieira, WAS and Vizzini, A and Weir, BS and Wijayawardene, NN and Xia, JW and Yáñez-Morales, MJ and Yurkov, A and Zamora, JC and Zare, R and Zhang, CL and Thines, M},
title = {Fusarium: more than a node or a foot-shaped basal cell.},
journal = {Studies in mycology},
volume = {98},
number = {},
pages = {100116},
pmid = {34466168},
issn = {0166-0616},
abstract = {Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).},
}
@article {pmid34465761,
year = {2021},
author = {Jia, KH and Liu, H and Zhang, RG and Xu, J and Zhou, SS and Jiao, SQ and Yan, XM and Tian, XC and Shi, TL and Luo, H and Li, ZC and Bao, YT and Nie, S and Guo, JF and Porth, I and El-Kassaby, YA and Wang, XR and Chen, C and Van de Peer, Y and Zhao, W and Mao, JF},
title = {Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome.},
journal = {Horticulture research},
volume = {8},
number = {1},
pages = {177},
pmid = {34465761},
issn = {2662-6810},
support = {31600527//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.},
}
@article {pmid34465293,
year = {2021},
author = {De Vos, S and Rombauts, S and Coussement, L and Dermauw, W and Vuylsteke, M and Sorgeloos, P and Clegg, JS and Nambu, Z and Van Nieuwerburgh, F and Norouzitallab, P and Van Leeuwen, T and De Meyer, T and Van Stappen, G and Van de Peer, Y and Bossier, P},
title = {The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {635},
pmid = {34465293},
issn = {1471-2164},
mesh = {Animals ; *Artemia/genetics ; Extreme Environments ; *Extremophiles ; Heat-Shock Proteins ; Salinity ; },
abstract = {BACKGROUND: Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors.<br><br>RESULTS AND DISCUSSION: Here, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Leaf Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed. Both high salt and anoxia enhanced degradation of erroneous proteins and protein chaperoning. Compared with other branchiopod genomes, Artemia had 0.03% contracted and 6% expanded orthogroups, in which 14% of the genes were differentially expressed under high salinity or anoxia. One phospholipase D gene family, shown to be important in plant stress response, was uniquely present in both extremophiles Artemia and the tardigrade Hypsibius dujardini, yet not differentially expressed under the described experimental conditions.<br><br>CONCLUSIONS: A relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research.},
}
@article {pmid34463583,
year = {2021},
author = {Dekas, AE},
title = {Quantifying Microbial Activity In Situ: the Link between Cells and Cycles.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0075821},
doi = {10.1128/mSystems.00758-21},
pmid = {34463583},
issn = {2379-5077},
abstract = {Metagenomic sequencing of environmental samples has dramatically expanded our knowledge of microbial taxonomic and metabolic diversity and suggests metabolic interdependence is widespread. However, translating these insights into knowledge of ecosystem function and, therefore, implications for local and global chemistry, remains a challenge. In this commentary, I argue that making direct measurements of microbial activity in situ is an essential step to confirm gene-based hypotheses of microbial physiology and bridge advances in microbial ecology with a predicative understanding of global chemistry and climate. Making these measurements across a range of spatial scales and experimentally manipulated conditions contributes to a process-based understanding and, therefore, more robust predictions of how activity will respond to changing environmental conditions. I discuss recent advancements in quantifying microbial activity in situ and highlight several lines of research in marine microbiology that leverage complementary genomic and isotopic methods to connect microbes and global chemistry.},
}
@article {pmid34463567,
year = {2021},
author = {Harrington, V and Lau, L and Seddu, K and Suez, J},
title = {Ecology and Medicine Converge at the Microbiome-Host Interface.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0075621},
doi = {10.1128/mSystems.00756-21},
pmid = {34463567},
issn = {2379-5077},
abstract = {The human body is home to a dense and diverse population of bacteria, viruses, and eukaryotes, collectively termed the microbiome. Research on host-microbiome interactions continuously demonstrates the importance of this microbial community to human physiology and its involvement in a myriad of diseases. This, in turn, sparks great interest in developing means for beneficially modulating the microbiome, such as fecal microbiome transplantation and probiotics. However, these interventions show mixed efficacy in clinical trials and raise safety concerns. How these exogenous microorganisms interact with the microbiome might underlie the efficacy and safety of these therapeutics, yet the signaling mechanisms mediating microbe-microbe interactions between human-dwelling commensals are poorly understood. In this commentary, we discuss known and putative mechanisms of interactions between commensals in the gut and how they can be harnessed for improving microbiome-targeting therapeutics and facilitating translation of microbiome research to the clinic.},
}
@article {pmid34460265,
year = {2021},
author = {Wang, S and Xia, J and De Paepe, K and Zhang, B and Fu, X and Huang, Q and Van de Wiele, T},
title = {Ultra-high Pressure Treatment Controls In Vitro Fecal Fermentation Rate of Insoluble Dietary Fiber from Rosa Roxburghii Tratt Pomace and Induces Butyrogenic Shifts in Microbiota Composition.},
journal = {Journal of agricultural and food chemistry},
volume = {69},
number = {36},
pages = {10638-10647},
doi = {10.1021/acs.jafc.1c03453},
pmid = {34460265},
issn = {1520-5118},
mesh = {Dietary Fiber ; Fermentation ; Fruit ; Humans ; *Microbiota ; *Rosa ; },
abstract = {Dietary fiber has been considered a key element in shaping the beneficial host-microbe symbiosis. In the present study, we identified Rosa roxburghii Tratt fruits as a promising dietary fiber source. The physicochemical properties and in vitro fermentability by human fecal microbes of R. roxburghii pomace water insoluble dietary fiber (RIDF) obtained from ultrasonic extraction and ultrahigh pressure (90 MPa)-treated RIDF (RIDF-90) were compared to those of R. roxburghii Tratt pomace (R). Ultrahigh pressure modification significantly increased the water holding, oil holding, and swelling capacity of RIDF-90 in comparison to R and RIDF. RIDF-90 displayed the slowest fermentation rate yet yielded the highest butyrate production. The superior butyrogenic properties of both RIDF-90 and, in part, RIDF were reflected by increased Coprococcus and Ruminococcus levels, demonstrating that ultrasonic extraction and/or further ultrahigh pressure treatment of insoluble fibers promotes the prebiotic value of R. roxburghii Tratt.},
}
@article {pmid34459553,
year = {2021},
author = {Lindström, S and Timonen, S and Sundström, L},
title = {The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae).},
journal = {MicrobiologyOpen},
volume = {10},
number = {4},
pages = {e1201},
pmid = {34459553},
issn = {2045-8827},
mesh = {Animals ; Ants/*microbiology ; Arctic Regions ; Bacteria/*classification/genetics/metabolism ; Cold Climate ; Cold Temperature ; Fungi/*classification/genetics/metabolism ; Mycobiome/*genetics ; },
abstract = {In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.},
}
@article {pmid34459548,
year = {2021},
author = {Block, KR and O'Brien, JM and Edwards, WJ and Marnocha, CL},
title = {Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake.},
journal = {MicrobiologyOpen},
volume = {10},
number = {4},
pages = {e1228},
pmid = {34459548},
issn = {2045-8827},
mesh = {Chlorobi/classification/genetics/*isolation &amp; purification ; Chromatiaceae/classification/genetics/*isolation &amp; purification ; Cyanobacteria/classification/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; Microbiota/genetics ; New York ; RNA, Ribosomal, 16S/genetics ; Sulfur/*metabolism ; Water Microbiology ; },
abstract = {The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.},
}
@article {pmid34459543,
year = {2021},
author = {Toubes-Rodrigo, M and Potgieter-Vermaak, S and Sen, R and Oddsdóttir, ES and Elliott, D and Cook, S},
title = {Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution-derived hydrogen.},
journal = {MicrobiologyOpen},
volume = {10},
number = {4},
pages = {e1200},
pmid = {34459543},
issn = {2045-8827},
mesh = {Bacteria/classification/genetics/*metabolism ; Carbon Cycle/physiology ; Chemoautotrophic Growth/physiology ; Ecosystem ; Extremophiles/classification/genetics/*metabolism ; Geologic Sediments/chemistry/microbiology ; Hydrogen/*metabolism ; Ice Cover/*microbiology ; Iron/*metabolism ; Methane/biosynthesis/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Silicates/*metabolism ; },
abstract = {The basal zone of glaciers is characterized by physicochemical properties that are distinct from firnified ice due to strong interactions with underlying substrate and bedrock. Basal ice (BI) ecology and the roles that the microbiota play in biogeochemical cycling, weathering, and proglacial soil formation remain poorly described. We report on basal ice geochemistry, bacterial diversity (16S rRNA gene phylogeny), and inferred ecological roles at three temperate Icelandic glaciers. We sampled three physically distinct basal ice facies (stratified, dispersed, and debris bands) and found facies dependent on biological similarities and differences; basal ice character is therefore an important sampling consideration in future studies. Based on a high abundance of silicates and Fe-containing minerals and, compared to earlier BI literature, total C was detected that could sustain the basal ice ecosystem. It was hypothesized that C-fixing chemolithotrophic bacteria, especially Fe-oxidisers and hydrogenotrophs, mutualistically support associated heterotrophic communities. Basal ice-derived rRNA gene sequences corresponding to genera known to harbor hydrogenotrophic methanogens suggest that silicate comminution-derived hydrogen can also be utilized for methanogenesis. PICRUSt-predicted metabolism suggests that methane metabolism and C-fixation pathways could be highly relevant in BI, indicating the importance of these metabolic routes. The nutrients and microbial communities release from melting basal ice may play an important role in promoting pioneering communities establishment and soil development in deglaciating forelands.},
}
@article {pmid34456379,
year = {2020},
author = {Crous, PW and Cowan, DA and Maggs-Kölling, G and Yilmaz, N and Larsson, E and Angelini, C and Brandrud, TE and Dearnaley, JDW and Dima, B and Dovana, F and Fechner, N and García, D and Gené, J and Halling, RE and Houbraken, J and Leonard, P and Luangsa-Ard, JJ and Noisripoom, W and Rea-Ireland, AE and Ševčíková, H and Smyth, CW and Vizzini, A and Adam, JD and Adams, GC and Alexandrova, AV and Alizadeh, A and Duarte, E&#xc1; and Andjic, V and Antonín, V and Arenas, F and Assabgui, R and Ballarà, J and Banwell, A and Berraf-Tebbal, A and Bhatt, VK and Bonito, G and Botha, W and Burgess, TI and Caboň, M and Calvert, J and Carvalhais, LC and Courtecuisse, R and Cullington, P and Davoodian, N and Decock, CA and Dimitrov, R and Di Piazza, S and Drenth, A and Dumez, S and Eichmeier, A and Etayo, J and Fernández, I and Fiard, JP and Fournier, J and Fuentes-Aponte, S and Ghanbary, MAT and Ghorbani, G and Giraldo, A and Glushakova, AM and Gouliamova, DE and Guarro, J and Halleen, F and Hampe, F and Hernández-Restrepo, M and Iturrieta-González, I and Jeppson, M and Kachalkin, AV and Karimi, O and Khalid, AN and Khonsanit, A and Kim, JI and Kim, K and Kiran, M and Krisai-Greilhuber, I and Kučera, V and Kušan, I and Langenhoven, SD and Lebel, T and Lebeuf, R and Liimatainen, K and Linde, C and Lindner, DL and Lombard, L and Mahamedi, AE and Matočec, N and Maxwell, A and May, TW and McTaggart, AR and Meijer, M and Mešić, A and Mileto, AJ and Miller, AN and Molia, A and Mongkolsamrit, S and Cortés, CM and Muñoz-Mohedano, J and Morte, A and Morozova, OV and Mostert, L and Mostowfizadeh-Ghalamfarsa, R and Nagy, LG and Navarro-Ródenas, A and Örstadius, L and Overton, BE and Papp, V and Para, R and Peintner, U and Pham, THG and Pordel, A and Pošta, A and Rodríguez, A and Romberg, M and Sandoval-Denis, M and Seifert, KA and Semwal, KC and Sewall, BJ and Shivas, RG and Slovák, M and Smith, K and Spetik, M and Spies, CFJ and Syme, K and Tasanathai, K and Thorn, RG and Tkalčec, Z and Tomashevskaya, MA and Torres-Garcia, D and Ullah, Z and Visagie, CM and Voitk, A and Winton, LM and Groenewald, JZ},
title = {Fungal Planet description sheets: 1112-1181.},
journal = {Persoonia},
volume = {45},
number = {},
pages = {251-409},
pmid = {34456379},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Austroboletus asper on soil, Cylindromonium alloxyli on leaves of Alloxylon pinnatum, Davidhawksworthia quintiniae on leaves of Quintinia sieberi, Exophiala prostantherae on leaves of Prostanthera sp., Lactifluus lactiglaucus on soil, Linteromyces quintiniae (incl. Linteromyces gen. nov.) on leaves of Quintinia sieberi, Lophotrichus medusoides from stem tissue of Citrus garrawayi, Mycena pulchra on soil, Neocalonectria tristaniopsidis (incl. Neocalonectria gen. nov.) and Xyladictyochaeta tristaniopsidis on leaves of Tristaniopsis collina, Parasarocladium tasmanniae on leaves of Tasmannia insipida, Phytophthora aquae-cooljarloo from pond water, Serendipita whamiae as endophyte from roots of Eriochilus cucullatus, Veloboletus limbatus (incl. Veloboletus gen. nov.) on soil. Austria, Cortinarius glaucoelotus on soil. Bulgaria, Suhomyces rilaensis from the gut of Bolitophagus interruptus found on a Polyporus sp. Canada, Cantharellus betularum among leaf litter of Betula, Penicillium saanichii from house dust. Chile, Circinella lampensis on soil, Exophiala embothrii from rhizosphere of Embothrium coccineum. China, Colletotrichum cycadis on leaves of Cycas revoluta. Croatia, Phialocephala melitaea on fallen branch of Pinus halepensis. Czech Republic, Geoglossum jirinae on soil, Pyrenochaetopsis rajhradensis from dead wood of Buxus sempervirens. Dominican Republic, Amanita domingensis on litter of deciduous wood, Melanoleuca dominicana on forest litter. France, Crinipellis nigrolamellata (Martinique) on leaves of Pisonia fragrans, Talaromyces pulveris from bore dust of Xestobium rufovillosum infesting floorboards. French Guiana, Hypoxylon hepaticolor on dead corticated branch. Great Britain, Inocybe ionolepis on soil. India, Cortinarius indopurpurascens among leaf litter of Quercus leucotrichophora. Iran, Pseudopyricularia javanii on infected leaves of Cyperus sp., Xenomonodictys iranica (incl. Xenomonodictys gen. nov.) on wood of Fagus orientalis. Italy, Penicillium vallebormidaense from compost. Namibia, Alternaria mirabibensis on plant litter, Curvularia moringae and Moringomyces phantasmae (incl. Moringomyces gen. nov.) on leaves and flowers of Moringa ovalifolia, Gobabebomyces vachelliae (incl. Gobabebomyces gen. nov.) on leaves of Vachellia erioloba, Preussia procaviae on dung of Procavia capensis. Pakistan, Russula shawarensis from soil on forest floor. Russia, Cyberlindnera dauci from Daucus carota. South Africa, Acremonium behniae on leaves of Behnia reticulata, Dothiora aloidendri and Hantamomyces aloidendri (incl. Hantamomyces gen. nov.) on leaves of Aloidendron dichotomum, Endoconidioma euphorbiae on leaves of Euphorbia mauritanica, Eucasphaeria proteae on leaves of Protea neriifolia, Exophiala mali from inner fruit tissue of Malus sp., Graminopassalora geissorhizae on leaves of Geissorhiza splendidissima, Neocamarosporium leipoldtiae on leaves of Leipoldtia schultzii, Neocladosporium osteospermi on leaf spots of Osteospermum moniliferum, Neometulocladosporiella seifertii on leaves of Combretum caffrum, Paramyrothecium pituitipietianum on stems of Grielum humifusum, Phytopythium paucipapillatum from roots of Vitis sp., Stemphylium carpobroti and Verrucocladosporium carpobroti on leaves of Carpobrotus quadrifolius, Suttonomyces cephalophylli on leaves of Cephalophyllum pilansii. Sweden, Coprinopsis rubra on cow dung, Elaphomyces nemoreus from deciduous woodlands. Spain, Polyscytalum pini-canariensis on needles of Pinus canariensis, Pseudosubramaniomyces septatus from stream sediment, Tuber lusitanicum on soil under Quercus suber. Thailand, Tolypocladium flavonigrum on Elaphomyces sp. USA, Chaetothyrina spondiadis on fruits of Spondias mombin, Gymnascella minnisii from bat guano, Juncomyces patwiniorum on culms of Juncus effusus, Moelleriella puertoricoensis on scale insect, Neodothiora populina (incl. Neodothiora gen. nov.) on stem cankers of Populus tremuloides, Pseudogymnoascus palmeri from cave sediment. Vietnam, Cyphellophora vietnamensis on leaf litter, Tylopilus subotsuensis on soil in montane evergreen broadleaf forest. Morphological and culture characteristics are supported by DNA barcodes.},
}
@article {pmid34455914,
year = {2021},
author = {Molina Ortiz, JP and McClure, DD and Shanahan, ER and Dehghani, F and Holmes, AJ and Read, MN},
title = {Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1965698},
pmid = {34455914},
issn = {1949-0984},
mesh = {Bacteria/growth &amp; development/metabolism ; *Computer Simulation ; Diet, High-Fat ; Dietary Fiber ; Ecosystem ; Gastrointestinal Microbiome/*physiology ; *Health Status ; Host Microbial Interactions/*physiology ; Humans ; },
abstract = {The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.},
}
@article {pmid34453008,
year = {2021},
author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T},
title = {Reply to Partridge et al.: Complementary bioinformatics and experimental approaches to investigate the transfer of AMR genes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {35},
pages = {},
pmid = {34453008},
issn = {1091-6490},
mesh = {*Computational Biology ; },
}
@article {pmid34451540,
year = {2021},
author = {Dos Santos, IMO and Abe, VY and de Carvalho, K and Barazetti, AR and Simionato, AS and de Almeida Pega, GE and Matis, SH and Cano, BG and Cely, MVT and Marcelino-Guimarães, FC and Chryssafidis, AL and Andrade, G},
title = {Secondary Metabolites of Pseudomonas aeruginosa LV Strain Decrease Asian Soybean Rust Severity in Experimentally Infected Plants.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {8},
pages = {},
pmid = {34451540},
issn = {2223-7747},
abstract = {Asian Soybean Rust (ASR), a disease caused by Phakopsora pachyrhizi, causing yield losses up to 90%. The control is based on the fungicides which may generate resistant fungi. The activation of the plant defense system, should help on ASR control. In this study, secondary metabolites of Pseudomonas aeruginosa LV strain were applied on spore germination and the expression of defense genes in infected soybean plants. The F4A fraction and the pure metabolites were used. In vitro, 10 µg mL[-1] of F4A reduced spore germination by 54%, while 100 µg mL[-1] completely inhibited. Overexpression of phenylalanine ammonia lyase (PAL), O-methyltransferase (OMT) and pathogenesis related protein-2 (PR-2; glucanases) defense-related genes were detected 24 and 72 h after soybean sprouts were sprayed with an organocopper antimicrobial compound (OAC). Under greenhouse conditions, the best control was observed in plants treated with 60 µg mL[-1] of PCA, which reduced ASR severity and lesion frequency by 75% and 43%, respectively. Plants sprayed with 2 and 20 µg mL[-1] of F4A also decreased severity (41%) and lesion frequency (32%). The significant reduction in spore germination ASR in plant suggested that the strain of these metabolites are effective against P. pachyrhizi, and they can be used for ASR control.},
}
@article {pmid34451391,
year = {2021},
author = {Vigsnaes, LK and Ghyselinck, J and Van den Abbeele, P and McConnell, B and Moens, F and Marzorati, M and Bajic, D},
title = {2'FL and LNnT Exert Antipathogenic Effects against C. difficile ATCC 9689 In Vitro, Coinciding with Increased Levels of Bifidobacteriaceae and/or Secondary Bile Acids.},
journal = {Pathogens (Basel, Switzerland)},
volume = {10},
number = {8},
pages = {},
pmid = {34451391},
issn = {2076-0817},
support = {Cut-Off 10: reference number 8404//Eurostars/ ; },
abstract = {Clostridioides difficile (formerly Clostridium difficile) infection (CDI) is one of the most common hospital-acquired infections, which is often triggered by a dysbiosed indigenous gut microbiota (e.g., upon antibiotic therapy). Symptoms can be as severe as life-threatening colitis. The current study assessed the antipathogenic potential of human milk oligosaccharides (HMOs), i.e., 2'-O-fucosyllactose (2'FL), lacto-N-neotetraose (LNnT), and a combination thereof (MIX), against C. difficile ATCC 9689 using in vitro gut models that allowed the evaluation of both direct and, upon microbiota modulation, indirect effects. During a first 48 h fecal batch study, dysbiosis and CDI were induced by dilution of the fecal inoculum. For each of the three donors tested, C. difficile levels strongly decreased (with >4 log CFU/mL) upon treatment with 2'FL, LNnT and MIX versus untreated blanks, coinciding with increased acetate/Bifidobacteriaceae levels. Interindividual differences among donors at an intermediate time point suggested that the antimicrobial effect was microbiota-mediated rather than being a direct effect of the HMOs. During a subsequent 11 week study with the Pathogut[TM] model (specific application of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®])), dysbiosis and CDI were induced by clindamycin (CLI) treatment. Vancomycin (VNC) treatment cured CDI, but the further dysbiosis of the indigenous microbiota likely contributed to CDI recurrence. Upon co-supplementation with VNC, both 2'FL and MIX boosted microbial activity (acetate and to lesser extent propionate/butyrate). Moreover, 2'FL avoided CDI recurrence, potentially because of increased secondary bile acid production. Overall, while not elucidating the exact antipathogenic mechanisms-of-action, the current study highlights the potential of HMOs to combat CDI recurrence, help the gut microbial community recover after antibiotic treatment, and hence counteract the adverse effects of antibiotic therapies.},
}
@article {pmid34447362,
year = {2021},
author = {Isaac, A and Francis, B and Amann, RI and Amin, SA},
title = {Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {718297},
pmid = {34447362},
issn = {1664-302X},
abstract = {The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010-2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.},
}
@article {pmid34444798,
year = {2021},
author = {Homann, CM and Rossel, CAJ and Dizzell, S and Bervoets, L and Simioni, J and Li, J and Gunn, E and Surette, MG and de Souza, RJ and Mommers, M and Hutton, EK and Morrison, KM and Penders, J and van Best, N and Stearns, JC},
title = {Infants' First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts.},
journal = {Nutrients},
volume = {13},
number = {8},
pages = {},
pmid = {34444798},
issn = {2072-6643},
support = {MOP-136811/CAPMC/CIHR/Canada ; IMG-143923/CAPMC/CIHR/Canada ; 529051010//Joint Programming Initiative A healthy diet for a healthy life/ ; },
mesh = {Bacteria/classification ; Biodiversity ; Cohort Studies ; Diet ; Eating ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Infant Food ; Infant Nutritional Physiological Phenomena ; Male ; Netherlands ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {The introduction of solid foods is an important dietary event during infancy that causes profound shifts in the gut microbial composition towards a more adult-like state. Infant gut bacterial dynamics, especially in relation to nutritional intake remain understudied. Over 2 weeks surrounding the time of solid food introduction, the day-to-day dynamics in the gut microbiomes of 24 healthy, full-term infants from the Baby, Food &amp; Mi and LucKi-Gut cohort studies were investigated in relation to their dietary intake. Microbial richness (observed species) and diversity (Shannon index) increased over time and were positively associated with dietary diversity. Microbial community structure (Bray-Curtis dissimilarity) was determined predominantly by individual and age (days). The extent of change in community structure in the introductory period was negatively associated with daily dietary diversity. High daily dietary diversity stabilized the gut microbiome. Bifidobacterial taxa were positively associated, while taxa of the genus Veillonella, that may be the same species, were negatively associated with dietary diversity in both cohorts. This study furthers our understanding of the impact of solid food introduction on gut microbiome development in early life. Dietary diversity seems to have the greatest impact on the gut microbiome as solids are introduced.},
}
@article {pmid34438891,
year = {2021},
author = {You, I and Kim, MJ},
title = {Comparison of Gut Microbiota of 96 Healthy Dogs by Individual Traits: Breed, Age, and Body Condition Score.},
journal = {Animals : an open access journal from MDPI},
volume = {11},
number = {8},
pages = {},
pmid = {34438891},
issn = {2076-2615},
support = {#PJ015274022021//Rural Development Administration, South Korea/ ; },
abstract = {Since dogs are part of many peoples' lives, research and industry related to their health and longevity are becoming a rising topic. Although gut microbiota (GM) is a key contributor to host health, limited information is available for canines. Therefore, this study characterized GM according to individual signatures (e.g., breed, age, and body condition score-BCS) of dogs living in the same environment. Fresh fecal samples from 96 healthy dogs were analyzed by sequencing the V3-V4 region of the 16S rRNA gene. The major microbial phyla were Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, and Actinobacteria. In the comparison by breeds, relative abundance of Fusobacterium was significantly differed. Interestingly, Fusobacterium perfoetens abundance was positively correlated with age (p = 0.018), being significantly more enriched in the 6-10-year-old group (14.3%) than in the 0.5-1-year-old group (7.2%). Moreover, despite the healthy appearance of dogs in all age (0.5-10 years) and BCS (3-6) groups, the gut microbial environment may be disadvantageous in older dogs or in dogs with an abnormal BCS. These findings broaden our understanding of gut microbial ecology according to individual characteristics of dogs and may be used as a reference for providing customized-care to companion animals.},
}
@article {pmid34436641,
year = {2022},
author = {Jan, B and Reshi, ZA and Mohiddin, FA},
title = {Correction to: Site and Organ‑Specific Culture‑Dependent Endophytic Diversity of Crocus sativus L. (Saffron) in Kashmir Himalaya, India.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1007},
doi = {10.1007/s00248-021-01847-z},
pmid = {34436641},
issn = {1432-184X},
}
@article {pmid34436640,
year = {2022},
author = {Möhlmann, TWR and Ter Braak, CJF and Te Beest, DE and Hendriks, M and Nijhuis, EH and Warris, S and Drolet, BS and van Overbeek, L and Koenraadt, CJM},
title = {Species Identity, Life History, and Geographic Distance Influence Gut Bacterial Communities in Lab-Reared and European Field-Collected Culicoides Biting midges.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {267-284},
pmid = {34436640},
issn = {1432-184X},
support = {BBS/E/I/00007039/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 1300018161//ANIHWA-EraNet/ ; Global One Health strategic program//Wageningen University/ ; },
mesh = {Animals ; *Ceratopogonidae ; *Gastrointestinal Microbiome ; Insect Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; *Wolbachia/genetics ; },
abstract = {Bacteria are part of the insect gut system and influence many physiological traits of their host. Gut bacteria may even reduce or block the transmission of arboviruses in several species of arthropod vectors. Culicoides biting midges are important arboviral vectors of several livestock and wildlife diseases, yet limited information is available on their gut bacterial communities. Addressing this gap will help inform how these communities can be manipulated and ultimately used as novel tools to control pathogens. To assess how bacterial communities change during the life stages of lab-reared C. nubeculosus and C. sonorensis, endosymbiotic bacteria were identified using Illumina sequencing of 16S rRNA and taxonomically characterised. Analyses were conducted to determine how gut bacterial communities in adults are influenced by species identity and geographic distance among biting midge populations. Communities of the two lab-reared Culicoides species significantly changed after pupation and with maturation into 6-day-old adults. Pseudomonas, Burkholderiaceae and Leucobacter bacteria were part of a core community that was trans-stadially transmitted and found throughout their life cycle. Among field-collected biting midges, the bacterial communities were unique for almost each species. Cardinium, Rickettsia and Wolbachia were some of the most abundant bacteria in midges collected from wetlands. Only Pseudomonas was present in high relative abundance in all field-collected species. In this study, species identity, as well as geographic distance, influenced the gut bacterial communities and may partly explain known inter- and intra-species variability in vector competence. Additionally, stably associated bacterial species could be candidates for paratransgenic strategies to control vector-borne pathogens.},
}
@article {pmid34434657,
year = {2021},
author = {Leonard, LT and Brodie, EL and Williams, KH and Sharp, JO},
title = {Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11926},
pmid = {34434657},
issn = {2167-8359},
abstract = {Increased drought and temperatures associated with climate change have implications for ecosystem stress with risk for enhanced carbon release in sensitive biomes. Litter decomposition is a key component of biogeochemical cycling in terrestrial ecosystems, but questions remain regarding the local response of decomposition processes to climate change. This is particularly complex in mountain ecosystems where the variable nature of the slope, aspect, soil type, and snowmelt dynamics play a role. Hence, the goal of this study was to determine the role of elevation, soil type, seasonal shifts in soil moisture, and snowmelt timing on litter decomposition processes. Experimental plots containing replicate deployments of harvested lodgepole and spruce needle litter alongside needle-free controls were established in open meadows at three elevations ranging from 2,800-3,500 m in Crested Butte, Colorado. Soil biogeochemistry variables including gas flux, porewater chemistry, and microbial ecology were monitored over three climatically variable years that shifted from high monsoon rains to drought. Results indicated that elevation and soil type influenced baseline soil biogeochemical indicators; however, needle mass loss and chemical composition were consistent across the 700 m elevation gradient. Rates of gas flux were analogously consistent across a 300 m elevation gradient. The additional variable of early snowmelt by 2-3 weeks had little impact on needle chemistry, microbial composition and gas flux; however, it did result in increased dissolved organic carbon in lodgepole porewater collections suggesting a potential for aqueous export. In contrast to elevation, needle presence and seasonal variability of soil moisture and temperature both played significant roles in soil carbon fluxes. During a pronounced period of lower moisture and higher temperatures, bacterial community diversity increased across elevation with new members supplanting more dominant taxa. Microbial ecological resilience was demonstrated with a return to pre-drought structure and abundance after snowmelt rewetting the following year. These results show similar decomposition processes across a 700 m elevation gradient and reveal the sensitivity but resilience of soil microbial ecology to low moisture conditions.},
}
@article {pmid34432600,
year = {2021},
author = {Roussel, C and De Paepe, K and Galia, W and de Bodt, J and Chalancon, S and Denis, S and Leriche, F and Vandekerkove, P and Ballet, N and Blanquet-Diot, S and Van de Wiele, T},
title = {Multi-targeted properties of the probiotic saccharomyces cerevisiae CNCM I-3856 against enterotoxigenic escherichia coli (ETEC) H10407 pathogenesis across human gut models.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1953246},
pmid = {34432600},
issn = {1949-0984},
mesh = {Enterotoxigenic Escherichia coli/*drug effects ; Escherichia coli Infections/*drug therapy/physiopathology ; Foodborne Diseases/*drug therapy ; Gastrointestinal Microbiome/*drug effects ; Humans ; Probiotics/*pharmacology/*therapeutic use ; Saccharomyces cerevisiae/chemistry ; Virulence/*drug effects ; },
abstract = {Enterotoxigenic Escherichia coli (ETEC) is one of the most common causes of acute traveler's diarrhea. Adhesins and enterotoxins constitute the major ETEC virulence traits. With the dramatic increase in antibiotic resistance, probiotics are considered a wholesome alternative to prevent or treat ETEC infections. Here, we examined the antimicrobial properties of the probiotic Saccharomyces cerevisiae CNCM I-3856 against ETEC H10407 pathogenesis upon co-administration in the TNO gastrointestinal Model (TIM-1), simulating the physicochemical and enzymatic conditions of the human upper digestive tract and preventive treatment in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), integrating microbial populations of the ileum and ascending colon. Interindividual variability was assessed by separate M-SHIME experiments with microbiota from six human individuals. The probiotic did not affect ETEC survival along the digestive tract. However, ETEC pathogenicity was significantly reduced: enterotoxin encoding virulence genes were repressed, especially in the TIM-1 system, and a lower enterotoxin production was noted. M-SHIME experiments revealed that 18-days probiotic treatment stimulate the growth of Bifidobacterium and Lactobacillus in different gut regions (mucosal and luminal, ileum and ascending colon) while a stronger metabolic activity was noted in terms of short-chain fatty acids (acetate, propionate, and butyrate) and ethanol production. Moreover, the probiotic pre-treated microbiota displayed a higher robustness in composition following ETEC challenge compared to the control condition. We thus demonstrated the multi-inhibitory properties of the probiotic S. cerevisiae CNCM I-3856 against ETEC in the overall simulated human digestive tract, regardless of the inherent variability across individuals in the M-SHIME.},
}
@article {pmid34432103,
year = {2022},
author = {Allsup, CM and Lankau, RA and Paige, KN},
title = {Herbivory and Soil Water Availability Induce Changes in Arbuscular Mycorrhizal Fungal Abundance and Composition.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {141-152},
pmid = {34432103},
issn = {1432-184X},
mesh = {Herbivory ; *Mycorrhizae ; Plant Roots/microbiology ; Soil ; Soil Microbiology ; Water ; },
abstract = {We tested the prediction that abundance and composition of arbuscular mycorrhizal fungi (AMF) in Ipomopsis aggregata roots and soils are influenced by ungulate herbivory and drought conditions by examining the effects in a field setting over two years. We used a multi-metric approach to quantify AMF root colonization, AMF reproduction, and AMF community composition in roots and soils. We incorporated complimentary community characterization assays by morphologically identifying spores from trap cultures and the use of terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Herbivory caused a twofold increase in spore production, an increase in AMF taxa diversity in roots, and a shift in AMF species composition in rhizosphere soils. The impact of herbivory was dependent on water availability, which differed in the two contrasting years. This study demonstrates that both soil water availability and herbivory shape arbuscular mycorrhizal fungi communities. The changes to mycorrhizal communities may help in understanding mycorrhizal function in changing climates.},
}
@article {pmid34432102,
year = {2022},
author = {Babur, E and Dindaroğlu, T and Riaz, M and Uslu, OS},
title = {Seasonal Variations in Litter Layers' Characteristics Control Microbial Respiration and Microbial Carbon Utilization Under Mature Pine, Cedar, and Beech Forest Stands in the Eastern Mediterranean Karstic Ecosystems.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {153-167},
pmid = {34432102},
issn = {1432-184X},
support = {KSU-2017/5-12D//Scientific Research Projects Commission/ ; },
mesh = {Biomass ; Carbon/metabolism ; *Fagus ; Forests ; *Microbiota ; Nitrogen/metabolism ; *Pinus/metabolism ; Seasons ; Soil/chemistry ; Soil Microbiology ; },
abstract = {The forest floor is hotspot of several functions integral to the stability of forest ecosystems. However, seasonal variations in litter decomposition rate contribute to biochemical and structural heterogeneity in the forest floor carbon (C) and nutrient cycling. We investigated the influence of seasonal variations in litter layers' micro-climate (temperature and moisture content) and chemical characteristics such as pH, electrical conductivity (EC), total organic C (TOC), total nitrogen (TN), and C/N ratio on microbial respiration, biomass, and C use efficiency under mature (> 80 years stage age) pine, beech, and cedar forests in eastern Mediterranean Karstic ecosystems. In contrast to significantly higher microbial respiration in fall, winter, and spring under pine, beech, and cedar forests, the significantly lowest microbial biomass C (MBC) and microbial biomass N (MBN) were observed in winter under each forest. Microbial C use efficiency, measured as the metabolic quotient (qCO2 = CO2/MBC), varied strongly between forest stands and seasons but was generally higher in winter. The significant positive correlations between litter layer and microbial biomass C/N ratios, under beech and cedar forests, suggested strong CN stoichiometric coupling and microbial adaptation to substrate resource stoichiometry. qCO2 correlated significantly negatively with litter layers' temperature, positively with moisture content and EC. However, qCO2 had significant negative relationships with pH in pine and beech forests but significant positive under cedar forest. qCO2 showed significant positive relationships with C/N ratios under all forests but much stronger in beech and cedar forests suggesting higher C respired per unit MBC with an increase in C/N ratio. Despite variations between forest species, the highest MBC/TOC and MBN/TN ratios in fall indicated greater C and N incorporation into microbial biomass. Changes in MBC/MBN ratios under pine (9.62-10.6), beech (8.63-15.6), and cedar (7.32-16.2) forests indicated the shift in microbial communities as fungi have a higher C/N ratio than bacteria. Stepwise regression analysis further revealed that microbial respiration and biomass were controlled differently by litter layer characteristics in each forest. This study suggested that qCO2 independently or with other microbial indices can show litter layers' controls on organic matter turnover in Karst ecosystems and, taking into account the strong seasonal variations, can enhance the predictive potential of decomposition models.},
}
@article {pmid34431694,
year = {2021},
author = {Moreno Morales, N and Patel, MT and Stewart, CJ and Sweeney, K and McClean, MN},
title = {Optogenetic Tools for Control of Public Goods in Saccharomyces cerevisiae.},
journal = {mSphere},
volume = {6},
number = {4},
pages = {e0058121},
pmid = {34431694},
issn = {2379-5042},
support = {P30 CA014520/CA/NCI NIH HHS/United States ; R35 GM128873/GM/NIGMS NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
mesh = {Gene Expression Regulation, Fungal/*radiation effects ; *Light ; Optogenetics/*methods ; Plasmids/*genetics ; Proof of Concept Study ; Saccharomyces cerevisiae/enzymology/*genetics/metabolism/radiation effects ; Sucrose/metabolism ; beta-Fructofuranosidase/genetics/metabolism ; },
abstract = {Microorganisms live in dense and diverse communities, with interactions between cells guiding community development and phenotype. The ability to perturb specific intercellular interactions in space and time provides a powerful route to determining the critical interactions and design rules for microbial communities. Approaches using optogenetic tools to modulate these interactions offer promise, as light can be exquisitely controlled in space and time. We report new plasmids for rapid integration of an optogenetic system into Saccharomyces cerevisiae to engineer light control of expression of a gene of interest. In a proof-of-principle study, we demonstrate the ability to control a model cooperative interaction, namely, the expression of the enzyme invertase (SUC2) which allows S. cerevisiae to hydrolyze sucrose and utilize it as a carbon source. We demonstrate that the strength of this cooperative interaction can be tuned in space and time by modulating light intensity and through spatial control of illumination. Spatial control of light allows cooperators and cheaters to be spatially segregated, and we show that the interplay between cooperative and inhibitory interactions in space can lead to pattern formation. Our strategy can be applied to achieve spatiotemporal control of expression of a gene of interest in S. cerevisiae to perturb both intercellular and interspecies interactions. IMPORTANCE Recent advances in microbial ecology have highlighted the importance of intercellular interactions in controlling the development, composition, and resilience of microbial communities. In order to better understand the role of these interactions in governing community development, it is critical to be able to alter them in a controlled manner. Optogenetically controlled interactions offer advantages over static perturbations or chemically controlled interactions, as light can be manipulated in space and time and does not require the addition of nutrients or antibiotics. Here, we report a system for rapidly achieving light control of a gene of interest in the important model organism Saccharomyces cerevisiae and demonstrate that by controlling expression of the enzyme invertase, we can control cooperative interactions. This approach will be useful for understanding intercellular and interspecies interactions in natural and synthetic microbial consortia containing S. cerevisiae and serves as a proof of principle for implementing this approach in other consortia.},
}
@article {pmid34431166,
year = {2021},
author = {Wang, Y and Chen, L and Xiang, W and Ouyang, S and Zhang, T and Zhang, X and Zeng, Y and Hu, Y and Luo, G and Kuzyakov, Y},
title = {Forest conversion to plantations: A meta-analysis of consequences for soil and microbial properties and functions.},
journal = {Global change biology},
volume = {27},
number = {21},
pages = {5643-5656},
doi = {10.1111/gcb.15835},
pmid = {34431166},
issn = {1365-2486},
mesh = {Carbon ; *Ecosystem ; Forests ; Nitrogen/analysis ; *Soil ; },
abstract = {Primary or secondary forests around the world are increasingly being converted into plantations. Soil microorganisms are critical for all biogeochemical processes in ecosystems, but the effects of forest conversion on microbial communities and their functioning remain unclear. Here, we conducted a meta-analysis to quantify the impacts that converting forests to plantations has on soil microbial communities and functioning as well as on the associated plant and soil properties. We collected 524 paired observations from 138 studies globally. We found that conversion leads to broad range of adverse impacts on soils and microorganisms, including on soil organic carbon (-24%), total nitrogen (-29%), bacterial and fungal biomass (-36% and -42%, respectively), microbial biomass carbon (MBC, -31%) and nitrogen (-33%), and fungi to bacteria ratio (F:B, -16%). In addition, we found impacts on the ratio of MBC to soil organic C (qMBC, -20%), microbial respiration (-18%), N mineralization (-18%), and enzyme activities including β-1,4-glucosidase (-54%), β-1,4-N-acetylglucosaminidase (-39%), and acid phosphatase (ACP; -34%). In contrast, conversion to plantations increases bacterial richness (+21%) and microbial metabolic quotient (qCO2 , +21%). The effects of forest conversion were consistent across stand ages, stand types, and climate zone. Soil C and N contents as well as the C:N ratio were the main factors responsible for the changes of microbial C, F:B, and bacterial richness. The responses of qCO2 , N mineralization, and ACP activity were mainly driven by the reductions in F:B, MBC, and soil C:N. Applying macro-ecology theory on ecosystem disturbance in soil microbial ecology, we show that microbial groups shifted from K to r strategists after conversion to plantations. Our meta-analysis underlines the adverse effects of natural forests conversion to plantations on soil microbial communities and functioning, and suggests that the preservation of soil functions should be a consideration in forest management practices.},
}
@article {pmid34428623,
year = {2021},
author = {Vaezzadeh, V and Yi, X and Rais, FR and Bong, CW and Thomes, MW and Lee, CW and Zakaria, MP and Wang, AJ and Zhong, G and Zhang, G},
title = {Distribution of black carbon and PAHs in sediments of Peninsular Malaysia.},
journal = {Marine pollution bulletin},
volume = {172},
number = {},
pages = {112871},
doi = {10.1016/j.marpolbul.2021.112871},
pmid = {34428623},
issn = {1879-3363},
mesh = {Carbon/analysis ; Environmental Monitoring ; Geologic Sediments ; Malaysia ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Water Pollutants, Chemical/analysis ; },
abstract = {Concentrations, sources and interactions between black carbon (BC) and polycyclic aromatic hydrocarbons (PAHs) were investigated in 42 sediment samples collected from riverine, coastal and shelf areas in Peninsular Malaysia. The concentrations of BC measured by benzene polycarboxylic acid (BPCA) method and PAHs showed broad spatial variations between the relatively pristine environment of the East coast and developed environment of the West and South coast ranging from 0.02 to 0.36% dw and 57.7 ng g[-1] dw to 19,300 ng g[-1] dw, respectively. Among diagnostic ratios of PAHs, the ratios of Ant/(Ant+Phe) and LMW/HMW drew the clearest distinctions between the East coast versus the West and South coast sediments indicating the predominance of petrogenic sources in the former versus pyrogenic sources in the latter. PAHs significantly correlated with BC and total organic carbon (TOC) in the sediments (p < 0.05) having similar correlation coefficients. BC accounted for 6.06 to 30.6% of TOC in sediments.},
}
@article {pmid34427721,
year = {2022},
author = {Basanta, MD and Rebollar, EA and García-Castillo, MG and Parra Olea, G},
title = {Comparative Analysis of Skin Bacterial Diversity and Its Potential Antifungal Function Between Desert and Pine Forest Populations of Boreal Toads Anaxyrus boreas.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {257-266},
pmid = {34427721},
issn = {1432-184X},
support = {CN 18-127//University of California Institute for Mexico and the United States/ ; IN205521//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; },
mesh = {Animals ; Antifungal Agents ; Bacteria ; Bufonidae/microbiology ; *Chytridiomycota ; Forests ; Humans ; Mexico ; *Pinus ; Skin/microbiology ; },
abstract = {The skin microbiome in amphibians has gained a lot of attention as some of its members play a protective role against pathogens such as the fungus Batrachochytrium dendrobatidis (Bd). The composition of skin bacterial communities has been suggested as one of the factors explaining differences in susceptibility to Bd among amphibian species and populations. The boreal toad Anaxyrus boreas is known to be susceptible to Bd, and severe population declines in its southeastern range have been documented. However, throughout A. boreas distribution, populations present differences in susceptibility to Bd infections which may be associated with differences in skin microbial diversity. This study compared the skin bacterial diversity and Bd infection levels of A. boreas in one desert population and one pine forest population from Baja California, Mexico. We found that desert and pine forest toad populations exhibit differences in skin bacterial community structure but show similar Bd infection levels. Using a predictive method, we found that the abundance of bacteria with potential Bd-inhibitory properties differed between uninfected and infected individuals but not between populations. Our data suggest that several bacteria in the skin community may be offering protection from Bd infections in these A. boreas populations. This study provides foundational evidence for future studies seeking to understand the skin-microbial variation among boreal toads' populations and its relation with Bd susceptibility.},
}
@article {pmid34427533,
year = {2021},
author = {Saw, JHW},
title = {Characterizing the Uncultivated Microbial Minority: towards Understanding the Roles of the Rare Biosphere in Microbial Communities.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0077321},
pmid = {34427533},
issn = {2379-5077},
abstract = {Microbial communities are frequently numerically dominated by just a few species. Often, the long "tail" of the rank-abundance plots of microbial communities constitutes the so-called "rare biosphere," microorganisms that are highly diverse but are typically found in low abundance in these communities. Their presence in microbial communities has only recently become apparent with advances in high-throughput sequencing technologies. Despite their low numbers, they are thought to play important roles in their communities and may function as potential members to keep the communities intact and resilient. Their phylogenetic diversity also means that they are important subjects for better understanding the interplay between microbial diversity and evolution. I propose that more efforts should be put into characterizing these poorly understood and mostly unknown microbial lineages that hold vast potentials for our understanding of microbial diversity, ecology, and evolution of life on this planet.},
}
@article {pmid34427532,
year = {2021},
author = {Scanlan, PD},
title = {Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0083221},
pmid = {34427532},
issn = {2379-5077},
support = {//Enterprise Ireland/ ; //Royal Society/ ; //Science Foundation Ireland (SFI)/ ; },
abstract = {How important is adaptive evolution to the unique diversity that we can observe for each individual human gut microbiome? How do gut microbes evolve in response to changes in their environment, and how does evolution in real time impact microbial functionality in the context of host health? My interdisciplinary research uses in vitro microcosm models to test how different abiotic and biotic factors impact microbial evolution in a community context. We complement this approach by tracking focal species as they evolve in real time and in their natural environment of the human gut. Our aim is to provide a better understanding of how the dynamics and outcomes of microbial evolution differ between individual gut environments, and in response to different selection pressures, so that we can move closer to rational gut microbiome treatments that promote host health and prevent and treat human disease.},
}
@article {pmid34427521,
year = {2021},
author = {Rodríguez-Verdugo, A},
title = {Evolving Interactions and Emergent Functions in Microbial Consortia.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0077421},
pmid = {34427521},
issn = {2379-5077},
abstract = {Microbial communities are constantly challenged with environmental stressors, such as antimicrobials, pollutants, and global warming. How do they respond to these changes? Answering this question is crucial given that microbial communities perform essential functions for life on Earth. Our research aims to understand and predict communities' responses to change by addressing the following questions. (i) How do eco-evolutionary feedbacks influence microbial community dynamics? (ii) How do multiple interacting species in a microbial community alter evolutionary processes? (iii) To what extent do microbial communities respond to change by ecological versus evolutionary processes? To answer these questions, we use microbial communities of reduced complexity coupled with experimental evolution, genome sequencing, and mathematical modeling. The overall expectation from this integrative research approach is to generate general concepts that extend beyond specific bacterial species and provide fundamental insights into the consequences of evolution on the functioning of whole microbial communities.},
}
@article {pmid34426366,
year = {2021},
author = {Leite, MFA and Dimitrov, MR and Freitas-Iório, RP and de Hollander, M and Cipriano, MAP and Andrade, SAL and da Silveira, APD and Kuramae, EE},
title = {Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input.},
journal = {The Science of the total environment},
volume = {800},
number = {},
pages = {149493},
doi = {10.1016/j.scitotenv.2021.149493},
pmid = {34426366},
issn = {1879-1026},
mesh = {Bacteria ; Burkholderiaceae ; Enterobacteriaceae ; Herbaspirillum ; Nitrogen ; Plant Roots ; Rhizosphere ; *Saccharum ; Soil Microbiology ; },
abstract = {The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bacterial strains isolated from sugarcane stalks on sugarcane growth and physiology as well as the dynamics of prokaryote community assembly in the rhizosphere and root endosphere under two N fertilization regimes. All six strains, Paraburkholderia caribensis IAC/BECa 88, Kosakonia oryzae IAC/BECa 90, Kosakonia radicincitans IAC/BECa 95, Paraburkholderia tropica IAC/BECa 135, Pseudomonas fluorescens IAC/BECa 141 and Herbaspirillum frisingense IAC/BECa 152, increased in shoot and root dry mass, and influenced the concentration and accumulation of important macro- and micronutrients. However, N input reduced the impact of inoculation by shifting the sugarcane microbiome (rhizosphere and root endosphere) and weakening the co-dependence between soil microbes and sugarcane biomass and nutrients. The results show that these beneficial microbes improved plant nutrient uptake conditioned to a reduced N nutrient input. Therefore, reduced fertilization is not only desirable consequence of bacterial inoculation but essential for higher impact of these beneficial bacteria on the sugarcane microbiome.},
}
@article {pmid34426295,
year = {2022},
author = {Nicomel, NR and Otero-Gonzalez, L and Williamson, A and Ok, YS and Van Der Voort, P and Hennebel, T and Du Laing, G},
title = {Selective copper recovery from ammoniacal waste streams using a systematic biosorption process.},
journal = {Chemosphere},
volume = {286},
number = {Pt 3},
pages = {131935},
doi = {10.1016/j.chemosphere.2021.131935},
pmid = {34426295},
issn = {1879-1298},
mesh = {Adsorption ; Biomass ; *Copper ; Electroplating ; Hydrogen-Ion Concentration ; Kinetics ; *Water Pollutants, Chemical/analysis ; },
abstract = {Cu-NH3 bearing effluents arise from electroplating and metal extraction industries, requiring innovative and sustainable Cu recovery technologies to reduce their adverse environmental impact. CO3[2-] and Zn are often co-occurring, and thus, selective Cu recovery from these complex liquid streams is required for economic viability. This study assessed 23 sustainable biosorbents classified as tannin-rich, lignin-rich, chitosan/chitin, dead biomass, macroalgae or biochar for their Cu adsorption capacity and selectivity in a complex NH3-bearing bioleachate. Under a preliminary screen with 12 mM Cu in 1 M ammoniacal solution, most biosorbents showed optimal Cu adsorption at pH 11, with pinecone remarkably showing high removal efficiencies (up to 68%) at all tested pH values. Further refinements on select biosorbents with pH, contact time, and presence of NH3, Zn and CO3[2-] showed again that pinecone has a high maximum adsorption capacity (1.07 mmol g[-1]), worked over pH 5-12 and was Cu-selective with 3.97 selectivity quotient (KCu/Zn). Importantly, pinecone performance was maintained in a real Cu/NH3/Zn/CO3[2-] bioleachate, with 69.4% Cu removal efficiency. Unlike synthetic adsorbents, pinecones require no pre-treatment, which together with its abundance, selectivity, and efficiency without the need for prior NH3 removal, makes it a competitive and sustainable Cu biosorbent for complex Cu-NH3 bearing streams. Overall, this study demonstrated the potential of integrating bioleaching and biosorption as a clean Cu recovery technology utilizing only sustainable resources (i.e., bio-lixiviant and biosorbents). This presents a closed-loop approach to Cu extraction and recovery from wastes, thus effectively addressing elemental sustainability.},
}
@article {pmid34424345,
year = {2022},
author = {Bacha, L and Ventura, R and Barrios, M and Seabra, J and Tschoeke, D and Garcia, G and Masi, B and Macedo, L and Godoy, JMO and Cosenza, C and de Rezende, CE and Lima, V and Ottoni, AB and Thompson, C and Thompson, F},
title = {Risk of Collapse in Water Quality in the Guandu River (Rio de Janeiro, Brazil).},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {314-324},
pmid = {34424345},
issn = {1432-184X},
mesh = {Brazil ; Environmental Monitoring ; Fresh Water ; Humans ; Phosphorus ; *Rivers ; *Water Pollutants, Chemical/analysis ; Water Quality ; },
abstract = {The Guandu River, one of the main rivers in the state of Rio de Janeiro, provides water for more than nine million people in the metropolitan region. However, the Guandu has suffered from massive domestic and industrial pollution for more than two decades, leading to high levels of dissolved total phosphorus, cyanobacteria, and enteric bacteria observed during the summers of 2020 and 2021. The use of Phoslock, a palliative compound, was not effective in mitigating the levels of phosphorus in the Guandu River. Furthermore, potable water driven from the river had levels of 2-MIB/geosmin and a mud smell/taste. With all these problems, several solutions are proposed for improving the Guandu River water quality, including establishment of (i) sewage treatment plants (STPs), (ii) strict water quality monitoring, (iii) environmental recovery (e.g., reforestation), and (iv) permanent protected areas. The objective of this paper is to verify the poor water quality in the Guandu and the ineffectiveness and undesired effects of Phoslock.},
}
@article {pmid34422537,
year = {2021},
author = {de Siqueira, KA and Liotti, RG and de Sousa, JR and Vendruscullo, SJ and de Souza, GB and de Vasconcelos, LG and Januário, AH and de Oliveira Mendes, TA and Soares, MA},
title = {Streptomyces griseocarneus R132 expresses antimicrobial genes and produces metabolites that modulate Galleria mellonella immune system.},
journal = {3 Biotech},
volume = {11},
number = {9},
pages = {396},
pmid = {34422537},
issn = {2190-572X},
abstract = {UNLABELLED: Actinobacteria is a phylum composed of aerobic, Gram-positive, and filamentous bacteria with a broad spectrum of biological activity, including antioxidant, antitumor, and antibiotic. The crude extract of Streptomyces griseocarneus R132 was fractionated on a C18 silica column and the isolated compound was identified by [1]H and [13]C nuclear magnetic resonance as 3-(phenylprop-2-enoic acid), also known as trans-cinnamic acid. Antimicrobial activity against human pathogens was assayed in vitro (disk-diffusion qualitative test) and in vivo using Galleria mellonella larvae (RT-qPCR). The methanol fractions 132-F30%, 132-F50%, 132-F70%, and 132-F100% inhibited the Escherichia coli (ATCC 25922) and Staphylococcus aureus (MRSA) growth in vitro the most effectively. Compared with the untreated control (60-80% of larvae death), the fractions and isolated trans-cinnamic acid increased the survival rate and modulated the immune system of G. mellonella larvae infected with pathogenic microorganisms. The anti-infection effect of the S. griseocarneus R132 fermentation product led us to sequence its genome, which was assembled and annotated using the Rast and antiSMASH platforms. The assembled genome consisted of 227 scaffolds represented on a linear chromosome of 8.85 Mb and 71.3% of GC. We detected conserved domains typical of enzymes that produce molecules with biological activity, such as polyketides and non-ribosomal and ribosomal peptides, indicating a great potential for obtaining new antibiotics and molecules with biotechnological application.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02942-1.},
}
@article {pmid34421884,
year = {2021},
author = {Carlson, HK and Vuono, DC and Glass, JB and Adams, MWW},
title = {Editorial: Selective Controls on Microbial Energy Metabolisms: From the Microscale to the Macroscale.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {728705},
doi = {10.3389/fmicb.2021.728705},
pmid = {34421884},
issn = {1664-302X},
}
@article {pmid34418848,
year = {2021},
author = {Mei, Z and Xiang, L and Wang, F and Xu, M and Fu, Y and Wang, Z and Hashsham, SA and Jiang, X and Tiedje, JM},
title = {Bioaccumulation of Manure-borne antibiotic resistance genes in carrot and its exposure assessment.},
journal = {Environment international},
volume = {157},
number = {},
pages = {106830},
doi = {10.1016/j.envint.2021.106830},
pmid = {34418848},
issn = {1873-6750},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bioaccumulation ; *Daucus carota ; Drug Resistance, Microbial ; Genes, Bacterial ; *Manure ; Soil ; Soil Microbiology ; Swine ; },
abstract = {The effect of manure application on the distribution and accumulation of antibiotic resistance genes (ARGs) in tissue of root vegetables remains unclear, which poses a bottleneck in assessing the health risks from root vegetables due to application of manure. Towards this goal, experiments were conducted in pots to investigate the distribution and bioaccumulation of ARGs in carrot tissues due to application of pig manure. The 144 ARGs targeting nine types of antibiotics were quantified by high throughput qPCR in the soil and plant samples. The rhizosphere was a hot spot for ARGs enrichment in the manured soil. The abundance, diversity, and bioaccumulation factors of ARGs in the phyllosphere were significantly higher than those of carrot root skin and tuber. Manure application increased bioaccumulation of 12 ARGs and 2 MGEs in carrot tuber with 124 the highest factor. The application of manure increased transfer of 10 ARGs and 3 MGEs from carrot skin to inner tuber by factors of 0.1-11.8. The average gene copy number of ARGs of per gram carrot root was about 4.8 × 10[4] and 1.1 × 10[6] in the control and the manured treatment, respectively. Children and adults may co-ingest 2.7 × 10[7] and 3.2 × 10[7] of ARGs copies/d from carrots grown with pig manure, using estimated human intake values. However, peeling may reduce the intake of ARGs by 28-91% and of MGEs by 46-59%. In conclusion, the application of pig manure increased the accumulation of ARGs in the skin of carrots, whereas peeling was an effective strategy to reduce the risk.},
}
@article {pmid34418788,
year = {2021},
author = {Verstrepen, L and Van den Abbeele, P and Pignataro, G and Ribecco, C and Gramenzi, A and Hesta, M and Marzorati, M},
title = {Inclusion of small intestinal absorption and simulated mucosal surfaces further improve the Mucosal Simulator of the Canine Intestinal Microbial Ecosystem (M-SCIME™).},
journal = {Research in veterinary science},
volume = {140},
number = {},
pages = {100-108},
doi = {10.1016/j.rvsc.2021.08.011},
pmid = {34418788},
issn = {1532-2661},
mesh = {Animals ; Dogs ; *Gastrointestinal Microbiome ; Intestinal Absorption ; Intestine, Small ; *Microbiota ; *Probiotics ; },
abstract = {While a large set of in vitro models are available to study the effects of specific food ingredients (e.g. pre- and probiotics) on the human gut microbiome, the availability of such models for companion animals is limited. Since improving gut health of such animals is an emerging research field, the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME™) was recently developed and validated with in vivo data. The current study presents a further improvement of this model by using an alternative method for feed preparation, i.e. by administering digestive enzymes to mimic upper gastro-intestinal digestion followed by a dialysis approach to mimic small intestinal absorption. As opposed to the previously implemented method, this resulted in a more optimal simulation of protein digestion and absorption. Further, upon entrance in the colon, increased production of the health-promoting butyrate and lower levels of Lactobacillus spp. and Bifidobacterium spp. were observed, which corresponded better with obtained in vivo data. A second model improvement consisted of the implementation of a mucosal environment to not only simulate luminal but also mucosal microbiota. In consistency with the human model for which this technology was previously validated, it was found that for all canine microbiota mucin beads were enriched with members of the Lachnospiraceae (~ Clostridium cluster XIVa), a family containing multiple well-known butyrate producers. The SCIME™ was thus upgraded to a so-called Mucosal SCIME™ (M-SCIME™). In conclusion, the current study presents improvements of the SCIME™, further increasing the relevance of obtained data with this in vitro model for dogs.},
}
@article {pmid34417850,
year = {2021},
author = {Tang, Y and Ma, KY and Cheung, MK and Yang, CH and Wang, Y and Hu, X and Kwan, HS and Chu, KH},
title = {Correction to: Gut Microbiota in Decapod Shrimps: Evidence of Phylosymbiosis.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {1008},
doi = {10.1007/s00248-021-01825-5},
pmid = {34417850},
issn = {1432-184X},
}
@article {pmid34417849,
year = {2022},
author = {Sangwan, S and Prasanna, R},
title = {Mycorrhizae Helper Bacteria: Unlocking Their Potential as Bioenhancers of Plant-Arbuscular Mycorrhizal Fungal Associations.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {1-10},
pmid = {34417849},
issn = {1432-184X},
mesh = {Bacteria/genetics/metabolism ; *Mycorrhizae ; Plant Roots/microbiology ; Plants/microbiology ; Soil ; Soil Microbiology ; Symbiosis ; },
abstract = {The dynamic interactions of plants and arbuscular mycorrhizal fungi (AMF) that facilitate the efficient uptake of minerals from soil and provide protection from various environmental stresses (biotic and abiotic) are now also attributed to a third component of the symbiosis. These are the less investigated mycorrhizae helper bacteria (MHB), which constitute a dense, active bacterial community, tightly associated with AMF, and involved in the development and functioning of AMF. Although AMF spores are known to host several bacteria in their spore walls and cytoplasm, their role in promoting the ecological fitness and establishment of AMF symbiosis by influencing spore germination, mycelial growth, root colonization, metabolic diversity, and biocontrol of soil borne diseases is now being deciphered. MHB also promote the functioning of arbuscular mycorrhizal symbiosis by triggering various plant growth factors, leading to better availability of nutrients in the soil and uptake by plants. In order to develop strategies to promote mycorrhization by AMF, and particularly to stimulate the ability to utilize phosphorus from the soil, there is a need to decipher crucial metabolic signalling pathways of MHB and elucidate their functional significance as mycorrhiza helper bacteria. MHB, also referred to as AMF bioenhancers, also improve agronomic efficiency and formulations using AMF along with enriched population of MHB are a promising option. This review covers the aspects related to the specificity and mechanisms of action of MHB, which positively impact the formation and functioning of AMF in mycorrhizal symbiosis, and the need to advocate MHB as AMF bioenhancers towards their inclusion in integrated nutrient management practices in sustainable agriculture.},
}
@article {pmid34411359,
year = {2021},
author = {Lajoie, G and Kembel, SW},
title = {Plant-bacteria associations are phylogenetically structured in the phyllosphere.},
journal = {Molecular ecology},
volume = {30},
number = {21},
pages = {5572-5587},
doi = {10.1111/mec.16131},
pmid = {34411359},
issn = {1365-294X},
support = {//Canada Research Chairs/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Bacteria/genetics ; Metagenomics ; Phylogeny ; Plant Leaves ; *Plants ; },
abstract = {Determining whether and how global change will lead to novel interactions between hosts and microbes is an important issue in ecology and evolution. Understanding the contribution of host and microbial ecologies and evolutionary histories in driving their contemporary associations is an important step towards addressing this challenge and predicting the fitness consequences of novel associations. Using shotgun metagenomic and amplicon sequencing of bacterial communities from the leaf surfaces (phyllosphere) of trees, we investigated how phylogenetic relatedness among hosts and among their associated bacteria influences the distribution of bacteria among hosts. We also evaluated whether the functional traits of trees and bacteria explained these associations across multiple host species. We show that phylogenetically similar hosts tended to associate with the same bacteria and that phylogenetically similar bacteria tended to associate with the same host species. Phylogenetic interactions between tree and bacterial taxa also explained variation in their associations. The effect of host and symbiont evolutionary histories on bacterial distribution across hosts were observed across phylogenetic scales, but prominently explained variation among higher taxonomic categories of hosts and symbionts. These results suggest that ecological variation arising early in the plant and bacterial phylogenies have been particularly important for driving their contemporary associations. Variation in bacterial functional genes associated with the biosynthesis of aromatic amino acids and compounds and with cell motility were notably important in explaining bacterial community turnover among gymnosperm and angiosperm hosts. Overall, our results suggest an influence of host and bacterial traits and evolutionary histories in driving their contemporary associations.},
}
@article {pmid34410645,
year = {2021},
author = {Baker, JL and Edlund, A},
title = {Identification of Oral Bacterial Biosynthetic Gene Clusters Associated with Caries.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2327},
number = {},
pages = {161-189},
pmid = {34410645},
issn = {1940-6029},
support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; K99 DE029228/DE/NIDCR NIH HHS/United States ; R21 DE028609/DE/NIDCR NIH HHS/United States ; },
mesh = {Biological Products ; *Dental Caries ; Dental Caries Susceptibility ; Humans ; *Microbiota ; Multigene Family ; Streptococcus mutans ; },
abstract = {Small molecules are a primary communication media of the microbial world, and play crucial, yet largely unidentified, roles in microbial ecology and disease pathogenesis. Many small molecules are produced by biosynthetic gene clusters, which can be predicted and analyzed computationally given a genome. A recent study examined the biosynthetic repertoire of the oral microbiome and cross-referenced this information against the disease status of the human host, providing leads for biosynthetic gene clusters, and their natural products, which may be key in the oral microbial ecology affecting dental caries and periodontitis. This chapter provides a step-by-step tutorial to bioinformatically to locate biosynthetic gene clusters within genomes, predict the type of natural products that are produced, and cross-reference the identified biosynthetic gene clusters to microbiomes associated with disease or health.},
}
@article {pmid34410455,
year = {2022},
author = {Atnafu, B and Desta, A and Assefa, F},
title = {Microbial Community Structure and Diversity in Drinking Water Supply, Distribution Systems as well as Household Point of Use Sites in Addis Ababa City, Ethiopia.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {73-89},
pmid = {34410455},
issn = {1432-184X},
mesh = {*Actinobacteria/genetics ; Bacteria/genetics ; *Cryptosporidiosis ; *Cryptosporidium/genetics ; *Drinking Water ; Ethiopia ; Humans ; *Microbiota ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; *Water Purification ; Water Supply ; },
abstract = {Understanding ecology of microbiomes in drinking water distribution systems is the most important notion in delivering safe drinking water. Drinking water distribution systems harbor various microbiota despite efforts made in improving water infrastructures in the water industry, especially, in developing countries. Intermittent water supply, long time of water storage, low water pressure, and contaminated source water are among many of the factors responsible for poor drinking water quality affecting health of people. The aim of this study was to explore microbial diversity and structure in water samples collected from source water, treated water, reservoirs, and household points of use locations (taps). High-throughput Illumina sequencing technology was employed by targeting the V4 region of the 16S rRNA gene and the V1-V3 region of the 18S rRNA gene to analyze the microbial community structure. Proteobacteria followed by Firmicutes, Bacteroidetes, and Actinobacteria were the core dominating taxa. Gammaproteobacteria was also dominant among other proteobacterial classes across all sampling points. Opportunistic bacterial genera such as Pseudomonas, Legionella, Klebsiella, Escherichia, and Actinobacteria, as well as eukaryotic microbes like Cryptosporidium, Hartmannella, Acanthamoeba, Aspergillus, and Candida were also abundant taxa found along the distribution systems. The shift in microbial community structure from source to point of use locations was influenced by basic factors such as residual chlorine, intermittent water supply, and long-time storage at the household. The complex microbiota detected in different sampling sites in this study brings drinking water quality problem which further causes significant health problems to both human and animal health. Treatment ineffectiveness, disinfection inefficiency, poor maintenance actions, leakage of sewage, and other domestic wastes are few among many other factors responsible for degraded drinking water quality in this study putting health at high risk. Findings of this research provide important and baseline information to understand the microbial profiles of drinking water along source water and distribution systems. Moreover, knowing the microbial profile will help to design proper water quality assurance approaches.},
}
@article {pmid34408269,
year = {2022},
author = {Yuan, Z and Druzhinina, IS and Gibbons, JG and Zhong, Z and Van de Peer, Y and Rodriguez, RJ and Liu, Z and Wang, X and Wei, H and Wu, Q and Wang, J and Shi, G and Cai, F and Peng, L and Martin, FM},
title = {Correction: Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus.},
journal = {The ISME journal},
volume = {16},
number = {1},
pages = {321},
doi = {10.1038/s41396-021-01083-w},
pmid = {34408269},
issn = {1751-7370},
}
@article {pmid34406837,
year = {2021},
author = {Cheng, XY and Liu, XY and Wang, HM and Su, CT and Zhao, R and Bodelier, PLE and Wang, WQ and Ma, LY and Lu, XL},
title = {USCγ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves.},
journal = {Microbiology spectrum},
volume = {9},
number = {1},
pages = {e0082021},
pmid = {34406837},
issn = {2165-0497},
mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Caves/*microbiology ; DNA, Bacterial/genetics ; Methane/analysis/metabolism ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {Karst caves have recently been demonstrated to act as a sink for atmospheric methane, due in part to consumption by microbes residing in caves that can oxidize methane at atmospheric levels. However, our knowledge about the responsible atmospheric methane-oxidizing bacteria (atmMOB) in this vast habitat remains limited to date. To address this issue, weathered rock samples from three karst caves were collected in Guilin City and subjected to high-throughput sequencing of pmoA and 16S rRNA genes. The results showed that members of the high-affinity upland soil cluster (USC), especially upland soil cluster gamma (USCγ), with absolute abundances of 10[4] to 10[9] copies · g[-1] dry sample, dominated the atmMOB communities, while Proteobacteria and Actinobacteria dominated the overall bacterial communities. Moreover, USCγ was a keystone taxon in cooccurrence networks of both the atmMOB and the total bacterial community, whereas keystone taxa in the bacterial network also included Gaiella and Aciditerrimonas. Positive links overwhelmingly dominated the cooccurrence networks of both atmMOB and the total bacterial community, indicating a consistent response to environmental disturbances. Our study shed new insights on the diversity and abundances underlining atmMOB and total bacterial communities and on microbial interactions in subterranean karst caves, which increased our understanding about USC and supported karst caves as a methane sink. IMPORTANCE Karst caves have recently been demonstrated to be a potential atmospheric methane sink, presumably due to consumption by methane-oxidizing bacteria. However, the sparse knowledge about the diversity, distribution, and community interactions of methanotrophs requires us to seek further understanding of the ecological significance of methane oxidation in these ecosystems. Our pmoA high-throughput results from weathered rock samples from three karst caves in Guilin City confirm the wide occurrence of atmospheric methane-oxidizing bacteria in this habitat, especially those affiliated with the upland soil cluster, with a gene copy number of 10[4] to 10[9] copies per gram dry sample. Methanotrophs and the total bacterial communities had more positive than negative interactions with each other as indicated by the cooccurrence network, suggesting their consistent response to environmental disturbance. Our results solidly support caves as an atmospheric methane sink, and they contribute to a comprehensive understanding of the diversity, distribution, and interactions of microbial communities in subsurface karst caves.},
}
@article {pmid34406835,
year = {2021},
author = {Li, X and Wang, A and Wan, W and Luo, X and Zheng, L and He, G and Huang, D and Chen, W and Huang, Q},
title = {High Salinity Inhibits Soil Bacterial Community Mediating Nitrogen Cycling.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {21},
pages = {e0136621},
pmid = {34406835},
issn = {1098-5336},
mesh = {Acidobacteria ; Actinobacteria ; Chloroflexi ; Ecosystem ; Nitrogen/metabolism ; *Nitrogen Cycle ; Phylogeny ; Planctomycetes ; RNA, Ribosomal, 16S/genetics ; *Salinity ; *Soil/chemistry ; *Soil Microbiology ; },
abstract = {Salinization is considered a major threat to soil fertility and agricultural productivity throughout the world. Soil microbes play a crucial role in maintaining ecosystem stability and function (e.g., nitrogen cycling). However, the response of bacterial community composition and community-level function to soil salinity remains uncertain. Here, we used multiple statistical analyses to assess the effect of high salinity on bacterial community composition and potential metabolism function in the agricultural ecosystem. Results showed that high salinity significantly altered both bacterial alpha (Shannon-Wiener index and phylogenetic diversity) and beta diversity. Salinity, total nitrogen (TN), and soil organic matter (SOM) were the vital environmental factors shaping bacterial community composition. The relative abundance of Actinobacteria, Chloroflexi, Acidobacteria, and Planctomycetes decreased with salinity, whereas Proteobacteria and Bacteroidetes increased with salinity. The modularity and the ratio of negative to positive links remarkedly decreased, indicating that high salinity destabilized bacterial networks. Variable selection, which belongs to deterministic processes, mediated bacterial community assembly within the saline soils. Function prediction results showed that the key nitrogen metabolism (e.g., ammonification, nitrogen fixation, nitrification, and denitrification processes) was inhibited in high salinity habitats. MiSeq sequencing of 16S rRNA genes revealed that the abundance and composition of the nitrifying community were influenced by high salinity. The consistency of function prediction and experimental verification demonstrated that high salinity inhibited soil bacterial community mediating nitrogen cycling. Our study provides strong evidence for a salinity effect on the bacterial community composition and key metabolism function, which could help us understand how soil microbes respond to ongoing environment perturbation. IMPORTANCE Revealing the response of the soil bacterial community to external environmental disturbances is an important but poorly understood topic in microbial ecology. In this study, we evaluated the effect of high salinity on the bacterial community composition and key biogeochemical processes in salinized agricultural soils (0.22 to 19.98 dS m[-1]). Our results showed that high salinity significantly decreased bacterial diversity, altered bacterial community composition, and destabilized the bacterial network. Moreover, variable selection (61% to 66%) mediated bacterial community assembly within the saline soils. Functional prediction combined with microbiological verification proved that high salinity inhibited soil bacterial community mediating nitrogen turnover. Understanding the impact of salinity on soil bacterial community is of great significance for managing saline soils and maintaining a healthy ecosystem.},
}
@article {pmid34406446,
year = {2022},
author = {Yu, HW and He, WM},
title = {Arbuscular Mycorrhizal Fungi Compete Asymmetrically for Amino Acids with Native and Invasive Solidago.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {131-140},
pmid = {34406446},
issn = {1432-184X},
support = {31971552//National Natural Science Foundation of China/ ; },
mesh = {Amino Acids/metabolism ; *Mycorrhizae/metabolism ; Nitrogen/metabolism ; Plant Roots/metabolism ; Plants/metabolism ; Soil/chemistry ; *Solidago ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) and soil amino acids both affect plant performance. However, little is known about how AMF compete for amino acids with native and invasive congeners. We conducted a factorial experiment (inoculation, native and invasive species, and amino acids) to examine the competition for amino acids between soil microbes and both native and invasive congeners. The competition for amino acids between AMF and invasive Solidago canadensis was weaker than that observed between AMF and native S. decurrens. This asymmetric competition increased the growth advantage of S. canadensis over S. decurrens. The efficacy (biomass production per unit of nitrogen supply) of amino acids compared to ammonium was smaller in S. canadensis than in S. decurrens when both species were grown without inoculation, but the opposite was the case when both species were grown with AMF. AMF and all microbes differentially altered four phenotypic traits (plant height, leaf chlorophyll content, leaf number, and root biomass allocation) and the pathways determining the effects of amino acids on growth advantages. These findings suggest that AMF could enhance plant invasiveness through asymmetric competition for amino acids and that amino acid-driven invasiveness might be differentially regulated by different microbial guilds.},
}
@article {pmid34406445,
year = {2022},
author = {Harris, RL and Vetter, MCYL and van Heerden, E and Cason, E and Vermeulen, JG and Taneja, A and Kieft, TL and DeCoste, CJ and Laevsky, GS and Onstott, TC},
title = {FISH-TAMB, a Fixation-Free mRNA Fluorescent Labeling Technique to Target Transcriptionally Active Members in Microbial Communities.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {182-197},
pmid = {34406445},
issn = {1432-184X},
support = {DGE-1148900//U.S. National Science Foundation/ ; DEB-1441717//U.S. National Science Foundation/ ; EAR-1528492//U.S. National Science Foundation/ ; DEB-1442059//U.S. National Science Foundation/ ; DEB-1441646//U.S. National Science Foundation/ ; P30CA072720-5921//NCI-CCSG/ ; },
mesh = {Archaea ; DNA, Archaeal/genetics ; Escherichia coli/genetics ; In Situ Hybridization, Fluorescence/methods ; *Methane/metabolism ; *Microbiota ; Oxidoreductases/genetics ; Phylogeny ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; },
abstract = {Keystone species or ecological engineers are vital to the health of an ecosystem; however, often, their low abundance or biomass present challenges for their discovery, identification, visualization and selection. We report the development of fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB), a fixation-free protocol that is applicable to archaea and bacteria. The FISH-TAMB method differs from existing FISH methods by the absence of fixatives or surfactants in buffers, the fast hybridization time of as short as 15 min at target cells' growth temperature, and the omission of washing steps. Polyarginine cell-penetrating peptides are employed to deliver molecular beacons (MBs) across prokaryotic cell walls and membranes, fluorescently labeling cells when MBs hybridize to target mRNA sequences. Here, the detailed protocol of the preparation and application of FISH-TAMB is presented. To demonstrate FISH-TAMB's ability to label intracellular mRNA targets, differentiate transcriptional states, detect active and rare taxa, and keep cell viability, labeling experiments were performed that targeted the messenger RNA (mRNA) of methyl-coenzyme M reductase A (mcrA) expressed in (1) Escherichia coli containing a plasmid with a partial mcrA gene of the methanogen Methanosarcina barkeri (E. coli mcrA[+]); (2) M. barkeri; and (3) an anaerobic methanotrophic (ANME) enrichment from a deep continental borehole. Although FISH-TAMB was initially envisioned for mRNA of any functional gene of interest without a requirement of prior knowledge of 16S ribosomal RNA (rRNA)-based taxonomy, FISH-TAMB has the potential for multiplexing and going beyond mRNA and thus is a versatile addition to the molecular ecologist's toolkit, with potentially widespread application in the field of environmental microbiology.},
}
@article {pmid34405252,
year = {2022},
author = {Whitaker, BK and Giauque, H and Timmerman, C and Birk, N and Hawkes, CV},
title = {Local Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 Grass.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {122-130},
pmid = {34405252},
issn = {1432-184X},
support = {HATCH accesssion no 1018688//U.S. Department of Agriculture/ ; SCW1039//U.S. Department of Energy/ ; },
mesh = {Biodiversity ; Fungi/physiology ; *Mycobiome ; *Panicum ; Plants/microbiology ; Soil ; },
abstract = {Microbial communities, like their macro-organismal counterparts, assemble from multiple source populations and by processes acting at multiple spatial scales. However, the relative importance of different sources to the plant microbiome and the spatial scale at which assembly occurs remains debated. In this study, we analyzed how source contributions to the foliar fungal microbiome of a C4 grass differed between locally abundant plants and soils across an abiotic gradient at different spatial scales. Specifically, we used source-sink analysis to assess the likelihood that fungi in leaves from Panicum hallii came from three putative sources: two plant functional groups (C4 grasses and dicots) and soil. We expected that physiologically similar C4 grasses would be more important sources to P. hallii than dicots. We tested this at ten sites in central Texas spanning a steep precipitation gradient. We also examined source contributions at three spatial scales: individual sites (local), local plus adjacent sites (regional), or all sites (gradient-wide). We found that plants were substantially more important sources than soils, but contributions from the two plant functional groups were similar. Plant contributions overall declined and unexplained variation increased as mean annual precipitation increased. This source-sink analysis, combined with partitioning of beta-diversity into nestedness and turnover components, indicated high dispersal limitation and/or strong environmental filtering. Overall, our results suggest that the source-sink dynamics of foliar fungi are primarily local, that foliar fungi spread from plant-to-plant, and that the abiotic environment may affect fungal community sourcing both directly and via changes to host plant communities.},
}
@article {pmid34405251,
year = {2022},
author = {Sharma, R and Gal, L and Garmyn, D and Bru, D and Sharma, S and Piveteau, P},
title = {Plant Growth Promoting Bacterial Consortium Induces Shifts in Indigenous Soil Bacterial Communities and Controls Listeria monocytogenes in Rhizospheres of Cajanus cajan and Festuca arundinacea.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {106-121},
pmid = {34405251},
issn = {1432-184X},
mesh = {*Cajanus/microbiology ; *Festuca ; Humans ; *Listeria monocytogenes ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil ; Soil Microbiology ; },
abstract = {The rhizosphere is a dynamic and complex interface between plant roots and microorganisms. Owing to exudates, a web of interactions establishes among the microbial members of this micro-environment. The present study explored the impact of a bacterial consortium (Azotobacter chroococcum, Bacillus megaterium and Pseudomonas fluorescens, ABP), on the fate of a human pathogen, Listeria monocytogenes EGD-e, in soil and in the rhizospheres of Cajanus cajan and Festuca arundinacea, in addition to its plant growth promoting effect. The study further assessed the impact these bioinoculants exert on the autochthonous soil bacterial communities. Experiments in sterilised soil inoculated with bioinoculants and L. monocytogenes revealed the inhibition of L. monocytogenes by approximately 80-fold compared to that without the consortium. Subsequently, experiments were conducted in non-sterile soil microcosms planted with C. cajan and F. arundinacea, and in bulk soil. The consortium led to a significant increase in plant growth in both plants and prevented growth of L. monocytogenes. However, the presence of resident soil bacterial communities overshadowed this inhibitory effect, and a sharp decline in L. monocytogenes populations (5-6 log reduction) was recorded under non-sterile soil conditions. A shift in the soil resident bacterial communities was observed upon amendment with the bioinoculants. A significant increase of potential Plant Growth Promoting Rhizobacteria (PGPR) and biocontrol agents was observed, while the abundance of potential phytopathogens dropped. The present study opens up new avenues for the application of such a consortium given their dual benefits of plant growth promotion and restricting phytopathogens as well as human pathogen.},
}
@article {pmid34405250,
year = {2022},
author = {Wang, Z and Xiao, R and Huang, J and Qin, X and Hu, D and Guo, E and Liu, C and Lu, F and You, L and Sun, C and Chen, G},
title = {The Diversity of Vaginal Microbiota Predicts Neoadjuvant Chemotherapy Responsiveness in Locally Advanced Cervical Cancer.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {302-313},
pmid = {34405250},
issn = {1432-184X},
support = {81402163//the Nature and Science Foundation of China/ ; 81402164//the Nature and Science Foundation of China/ ; 81572569//the Nature and Science Foundation of China/ ; 81874106//the Nature and Science Foundation of China/ ; 2020JYCXJJ013//the Technology Innovation Foundation of Innovation Institute of Huazhong University of Science and Technology/ ; },
mesh = {Female ; Humans ; *Microbiota/genetics ; Neoadjuvant Therapy ; RNA, Ribosomal, 16S/genetics ; *Uterine Cervical Neoplasms/drug therapy/microbiology ; Vagina/microbiology ; },
abstract = {The vaginal microbiota is closely related to HPV infection and cervical cancer (CC), but its relationship with platinum-based chemotherapy responsiveness is unknown. The study aimed to investigate the vaginal microbiota diversity of women with locally advanced cervical cancer (LACC) and compare the differences between responders and nonresponders. We characterized the 16S rRNA gene sequencing of vaginal microbiome of 66 vaginal samples, including 26 LACC patients before neoadjuvant chemotherapy and 40 healthy controls. Compared with the healthy controls, alpha diversity was significantly increased in CC patients (p <0.05) with more unconventionality bacterial colonization. Beta diversity also significantly differed between cervical cancer patients and controls (p <0.01). Within the CC patients, alpha diversity in vaginal samples was significantly higher in the nonresponders versus the responders (p <0.01), and the Ace index and Chao index were negatively correlated with mass reduction (p <0.001). Moreover, the Bacteroides genus enriched in the nonresponders had a ROC-plot AUC value reaching 0.84. The study suggests the vaginal microbiota in LACC patients is associated with platinum-based chemotherapy responsiveness. Alpha diversity and Bacteroides abundance have the potential of identifying platinum-resistant patients at an early time. These findings provide a basis for further research on the relationship between vaginal microbiome and chemotherapy effect in LACC.},
}
@article {pmid34405249,
year = {2022},
author = {Pascoal, F and Costa, R and Assmy, P and Duarte, P and Magalhães, C},
title = {Exploration of the Types of Rarity in the Arctic Ocean from the Perspective of Multiple Methodologies.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {59-72},
pmid = {34405249},
issn = {1432-184X},
support = {2020.04453.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CTA-AMB/30997/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CTA-AMB/4946/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04423/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/04423/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04565/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; Project N. 007317//Programa Operacional Regional de Lisboa/ ; Arktis 2030//Norwegian Ministries of Foreign Affairs and Climate and Environment/ ; },
mesh = {*Ecosystem ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; },
abstract = {The Arctic Ocean is facing rapid environmental changes with cascading effects on the entire Arctic marine ecosystem. However, we have a limited understanding of the consequences such changes have on bacteria and archaea (prokaryotes) at the base of the marine food web. In this study, we show how the prokaryotic rare biosphere behaves over a range of highly heterogeneous environmental conditions using 16S rRNA gene reads from amplicon and metagenome sequencing data from seawater samples collected during the Norwegian young sea ICE expedition between late winter and early summer. The prokaryotic rare biosphere was analyzed using different approaches: amplicon sequence variants and operational taxonomic units from the 16S rRNA gene amplicons and operational taxonomic units from the 16S rRNA genes of the metagenomes. We found that prokaryotic rare biosphere communities are specific to certain water masses, and that the majority of the rare taxa identified were always rare and disappeared in at least one sample under changing conditions, suggesting their high sensitivity to environmental heterogeneity. In addition, our methodological comparison revealed a good performance of 16S rRNA gene amplicon sequencing in describing rare biosphere patterns, while the metagenome-derived data were better to capture a significant diversity of so-far uncultivated rare taxa. Our analysis on the dynamics of the rare prokaryotic biosphere, by combining different methodological approaches, improves the description of the types of rarity predicted from Community Assembly theory in the Arctic Ocean.},
}
@article {pmid34403645,
year = {2021},
author = {van de Peppel, LJJ and Nieuwenhuis, M and Auxier, B and Grum-Grzhimaylo, AA and Cárdenas, ME and de Beer, ZW and Lodge, DJ and Smith, ME and Kuyper, TW and Franco-Molano, AE and Baroni, TJ and Aanen, DK},
title = {Ancestral predisposition toward a domesticated lifestyle in the termite-cultivated fungus Termitomyces.},
journal = {Current biology : CB},
volume = {31},
number = {19},
pages = {4413-4421.e5},
doi = {10.1016/j.cub.2021.07.070},
pmid = {34403645},
issn = {1879-0445},
mesh = {*Agaricales ; Animals ; Humans ; *Isoptera/microbiology ; Life Style ; Phylogeny ; Symbiosis ; *Termitomyces/genetics ; },
abstract = {The ancestor of termites relied on gut symbionts for degradation of plant material, an association that persists in all termite families.[1][,][2] However, the single-lineage Macrotermitinae has additionally acquired a fungal symbiont that complements digestion of food outside the termite gut.[3] Phylogenetic analysis has shown that fungi grown by these termites form a clade-the genus Termitomyces-but the events leading toward domestication remain unclear.[4] To address this, we reconstructed the lifestyle of the common ancestor of Termitomyces using a combination of ecological data with a phylogenomic analysis of 21 related non-domesticated species and 25 species of Termitomyces. We show that the closely related genera Blastosporella and Arthromyces also contain insect-associated species. Furthermore, the genus Arthromyces produces asexual spores on the mycelium, which may facilitate insect dispersal when growing on aggregated subterranean fecal pellets of a plant-feeding insect. The sister-group relationship between Arthromyces and Termitomyces implies that insect association and asexual sporulation, present in both genera, preceded the domestication of Termitomyces and did not follow domestication as has been proposed previously. Specialization of the common ancestor of these two genera on an insect-fecal substrate is further supported by similar carbohydrate-degrading profiles between Arthromyces and Termitomyces. We describe a set of traits that may have predisposed the ancestor of Termitomyces toward domestication, with each trait found scattered in related taxa outside of the termite-domesticated clade. This pattern indicates that the origin of the termite-fungus symbiosis may not have required large-scale changes of the fungal partner.},
}
@article {pmid34399522,
year = {2021},
author = {Bolívar, A and Tarlak, F and Costa, JCCP and Cejudo-Gómez, M and Bover-Cid, S and Zurera, G and Pérez-Rodríguez, F},
title = {A new expanded modelling approach for investigating the bioprotective capacity of Latilactobacillus sakei CTC494 against Listeria monocytogenes in ready-to-eat fish products.},
journal = {Food research international (Ottawa, Ont.)},
volume = {147},
number = {},
pages = {110545},
doi = {10.1016/j.foodres.2021.110545},
pmid = {34399522},
issn = {1873-7145},
mesh = {Animals ; Coculture Techniques ; Fish Products ; *Lactobacillales ; *Listeria monocytogenes ; Microbial Interactions ; },
abstract = {Understanding the role of food-related factors on the efficacy of protective cultures is essential to attain optimal results for developing biopreservation-based strategies. The aim of this work was to assess and model growth of Latilactobacillus sakei CTC494 and Listeria monocytogenes CTC1034, and their interaction, in two different ready-to-eat fish products (i.e., surimi-based product and tuna pâté) at 2 and 12 °C. The existing expanded Jameson-effect and a new expanded Jameson-effect model proposed in this study were evaluated to quantitatively describe the effect of microbial interaction. The inhibiting effect of the selected lactic acid bacteria strain on the pathogen growth was product dependent. In surimi product, a reduction of lag time of both strains was observed when growing in coculture at 2 °C, followed by the inhibition of the pathogen when the bioprotective L. sakei CTC494 reached the maximum population density, suggesting a mutualism-antagonism continuum phenomenon between populations. In tuna pâté, L. sakei CTC494 exerted a strong inhibition of L. monocytogenes at 2 °C (<0.5 log increase) and limited the growth at 12 °C (<2 log increase). The goodness-of-fit indexes indicated that the new expanded Jameson-effect model performed better and appropriately described the different competition patterns observed in the tested fish products. The proposed expanded competition model allowed for description of not only antagonistic but also mutualism-based interactions based on their influence on lag time.},
}
@article {pmid34399325,
year = {2021},
author = {Barbosa, RG and Oliveira, FC and Andrés-Torres, M and Sleutels, T and Verstraete, W and Boon, N},
title = {Effective orthophosphate removal from surface water using hydrogen-oxidizing bacteria: Moving towards applicability.},
journal = {The Science of the total environment},
volume = {800},
number = {},
pages = {149648},
doi = {10.1016/j.scitotenv.2021.149648},
pmid = {34399325},
issn = {1879-1026},
mesh = {Bacteria ; *Hydrogen ; Nitrogen ; Oxidation-Reduction ; *Phosphates/analysis ; Phosphorus ; Wastewater ; Water ; },
abstract = {Effective orthophosphate removal strategies are needed to counteract eutrophication and guarantee water quality. Previously, we established that hydrogen-oxidizing bacteria (HOB) have the ability to remove orthophosphate from artificial surface water. In the present study, we expand the application of the HOB orthophosphate removal strategy (1) to treat artificial surface water with low initial orthophosphate concentrations, (2) to treat real surface water and real wastewater effluent, and (3) to remove orthophosphate continuously. For synthetic surface water, irrespective of the initial concentration of 0.7, 0.5, 0.3, and 0.1 mg PO4[3-]-P/L, ultra-low concentrations (0.0058 ± 0.0028 mg PO4[3-]-P/L) were obtained. When artificial surface water was replaced by real surface water, without added nutrients or other chemicals, it was shown that over 90% orthophosphate could be removed within 30 min of operation in a batch configuration (0.031 ± 0.023 mg PO4[3-]-P/L). In continuous operation, orthophosphate removal from surface water left an average concentration of 0.040 ± 0.036 for 60 days, and the lowest orthophosphate concentration measured was 0.013 mg PO4[3-]/L. Simultaneously, nitrate was continuously removed for 60 days below 0.1 mg/L. The ability to remove orthophosphate even under nitrogen limiting conditions might be related to the ability of HOB to fix nitrogen. This study brings valuable insights into the potential use of HOB biofilms for nutrient remediation and recovery.},
}
@article {pmid34399219,
year = {2022},
author = {Du, P and He, H and Zhou, L and Dong, F and Liu, X and Zheng, Y},
title = {Different biodegradation potential and the impacted soil functions of epoxiconazole in two soils.},
journal = {Journal of hazardous materials},
volume = {422},
number = {},
pages = {126787},
doi = {10.1016/j.jhazmat.2021.126787},
pmid = {34399219},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; Epoxy Compounds/toxicity ; *Soil ; *Triazoles/analysis/toxicity ; },
abstract = {Epoxiconazole is an effective pesticide to control Fusarium head blight (FHB), and the application will increase. To investigate the ecotoxicity of epoxiconazole to soil microbiome, we carried out an indoor experiment in which soils from two main regions of wheat production in China (Nanjing and Anyang) were treated with epoxiconazole (0, 0.0625, 0.625, or 6.25 mg kg[-1]) and incubated for 90 days. Under epoxiconazole stress, for bacteria and fungi, the abundance was increased and the diversity and community were impacted. In Anyang soil, the half-life of epoxiconazole was short with more increased species (linear discriminant analysis effect size biomarkers) and more increased xenobiotics biodegradation pathways in epoxiconazole treatments. The increased species mostly due to high abundance in initial state and more positive connections of the species. Co-occurrences revealed that epoxiconazole tightened bacterial connection, and increased positive correlations in Anyang soil. The N transformation was influenced with increased nifH and amoA; and the contents of NH4[+]-N and NO3[-]-N were also increased. The functions of C, S, and manganese metabolisms were also impacted by epoxiconazole. This work expands our understanding about epoxiconazole degradation and help us to properly assess the risk of epoxiconazole in soil.},
}
@article {pmid34398256,
year = {2022},
author = {Li, Y and Lin, H and Gao, P and Yang, N and Xu, R and Sun, X and Li, B and Xu, F and Wang, X and Song, B and Sun, W},
title = {Synergistic Impacts of Arsenic and Antimony Co-contamination on Diazotrophic Communities.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {44-58},
pmid = {34398256},
issn = {1432-184X},
support = {U20A20109//National Natural Science Foundation of China/ ; 2020GDASYL-20200102015//GDAS' Project of Science and Technology Development/ ; 2021GDASYL-20210103048//GDAS' Project of Science and Technology Development/ ; 2020GDASYL-20200102014//GDAS' Project of Science and Technology Development/ ; 2021GDASYL-20210103041//GDAS' Project of Science and Technology Development/ ; 2019GDASYL-0103052//GDAS' Project of Science and Technology Development/ ; 2020GDASYL-20200103082//GDAS' Project of Science and Technology Development/ ; 2019GDASYL-0301002//GDAS' Project of Science and Technology Development/ ; 2020GDASYL-20200402003//GDAS' Project of Science and Technology Development/ ; 202002020072//the Science and Technology Planning Project of Guangzhou/ ; 2017GC010570//the High-Level Talents Project of the Pearl River Talents Recruitment Program/ ; 2017BT01Z176//the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; },
mesh = {Antimony/analysis ; *Arsenic/analysis ; Environmental Monitoring ; *Microbiota ; *Soil Pollutants/analysis ; },
abstract = {Nitrogen (N) shortage poses a great challenge to the implementation of in situ bioremediation practices in mining-contaminated sites. Diazotrophs can fix atmospheric N2 into a bioavailable form to plants and microorganisms inhabiting adverse habitats. Increasing numbers of studies mainly focused on the diazotrophic communities in the agroecosystems, while those communities in mining areas are still not well understood. This study compared the variations of diazotrophic communities in composition and interactions in the mining areas with different extents of arsenic (As) and antimony (Sb) contamination. As and Sb co-contamination increased alpha diversities and the abundance of nifH encoding the dinitrogenase reductase, while inhibited the diazotrophic interactions and substantially changed the composition of communities. Based on the multiple lines of evidence (e.g., the enrichment analysis of diazotrophs, microbe-microbe network, and random forest regression), six diazotrophs (e.g., Sinorhizobium, Dechloromonas, Trichormus, Herbaspirillum, Desmonostoc, and Klebsiella) were identified as keystone taxa. Environment-microbe network and random forest prediction demonstrated that these keystone taxa were highly correlated with the As and Sb contamination fractions. All these results imply that the above-mentioned diazotrophs may be resistant to metal(loid)s.},
}
@article {pmid34396460,
year = {2022},
author = {Bamary, Z and Einali, A},
title = {Changes in Carbon Partitioning and Pattern of Antioxidant Enzyme Activity Induced by Arginine Treatment in the Green Microalga Dunaliella salina Under Long-Term Salinity.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {198-212},
pmid = {34396460},
issn = {1432-184X},
support = {27259//University of Sistan and Baluchestan/ ; },
mesh = {*Antioxidants/metabolism/pharmacology ; Arginine/metabolism/pharmacology ; Carbon/metabolism ; Glycerol/metabolism ; Hydrogen Peroxide/metabolism ; *Microalgae/metabolism ; Salinity ; Starch/metabolism ; Sugars/metabolism/pharmacology ; beta Carotene/metabolism/pharmacology ; },
abstract = {In this work, the effects of arginine (Arg) on biochemical responses and antioxidant enzyme activity in the green microalga Dunaliella salina grown at different salt concentrations were investigated. Suspensions adapted with the concentrations of 1, 2, and 3 M NaCl were treated at the exponential growth phase with a concentration of 5 mM Arg. Salt stress was associated with a large decrease in the number of cells and non-reducing sugar levels but accumulated higher amounts of chlorophyll, β-carotene, reducing sugar, starch, total protein, free amino acid, and glycerol. Increased levels of protein carbonylation, lipid peroxidation, proteolysis, hydrogen peroxide, and antioxidant enzyme activity also occurred during salinity. Arg treatment changed the pattern of biochemical responses in the cells grown at high salinity by directing carbon flow to the biosynthesis of non-reducing sugars instead of starch, lowering levels of hydrogen peroxide, and downregulating antioxidant enzyme activity, but the levels of lipid peroxidation, glycerol, and β-carotene remained nearly unchanged. These results suggest that Arg treatment alleviates salinity-induced oxidative stress in D. salina cells by modifying carbon partitioning and inducing signaling molecules rather than antioxidant enzymes.},
}
@article {pmid34394041,
year = {2021},
author = {Chu, XL and Zhang, QG and Buckling, A and Castledine, M},
title = {Interspecific Niche Competition Increases Morphological Diversity in Multi-Species Microbial Communities.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {699190},
pmid = {34394041},
issn = {1664-302X},
abstract = {Intraspecific competition for limited niches has been recognized as a driving force for adaptive radiation, but results for the role of interspecific competition have been mixed. Here, we report the adaptive diversification of the model bacteria Pseudomonas fluorescens in the presence of different numbers and combinations of four competing bacterial species. Increasing the diversity of competitive community increased the morphological diversity of focal species, which is caused by impeding the domination of a single morphotype. Specifically, this pattern was driven by more diverse communities being more likely to contain key species that occupy the same niche as otherwise competitively superior morphotype, and thus preventing competitive exclusion within the focal species. Our results suggest that sympatric adaptive radiation is driven by the presence or absence of niche-specific competitors.},
}
@article {pmid34394013,
year = {2021},
author = {Danko, D and Malli Mohan, GB and Sierra, MA and Rucker, M and Singh, NK and Regberg, AB and Bell, MS and O'Hara, NB and Ounit, R and Mason, CE and Venkateswaran, K},
title = {Characterization of Spacesuit Associated Microbial Communities and Their Implications for NASA Missions.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {608478},
pmid = {34394013},
issn = {1664-302X},
support = {T32 GM083937/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Crewed National Aeronautics and Space Administration (NASA) missions to other solar system bodies are currently being planned. One high-profile scientific focus during such expeditions would be life detection, specifically the discovery of past or present microbial life, if they exist. However, both humans and associated objects typically carry a high microbial burden. Thus, it is essential to distinguish between microbes brought with the expedition and those present on the exploring planets. Modern spacesuits are unique, customized spacecraft which provide protection, mobility and life support to crew during spacewalks, yet they vent, and the mobility of microbes through spacesuits has not been studied.<br><br>RESULTS: To evaluate the microbial colonization of spacesuits, NASA used an Extravehicular Activity swab kit to examine viable microbial populations of 48 samples from spacesuits using both traditional microbiological methods and molecular sequencing methods. The cultivable microbial population ranged from below the detection limit to 9 &#xd7; 10[2] colony forming units per 25 cm[2] of sample and also significantly varied by the location. The cultivable microbial diversity was dominated by members of Bacillus, Arthrobacter, and Ascomycota. However, 16S rRNA-based viable bacterial burden ranged from 10[5] to 10[6] copies per 25 cm[2] of sample. Shotgun metagenome sequencing revealed the presence of a diverse microbial population on the spacesuit surfaces, including Curtobacterium and Methylobacterium from across all sets of spacesuits in high abundance. Among bacterial species identified, higher abundance of Cutibacterium acnes, Methylobacterium oryzae, and M. phyllosphaerae reads were documented.<br><br>CONCLUSION: The results of this study provide evidence that identical microbial strains may live on the wrist joint, inner gauntlet, and outer gauntlet of spacesuits. This raises the possibility, but does not confirm that microbial contaminants on the outside of the suits could contaminate planetary science operations unless additional measures are taken. Overall, these data provide the first estimate of microbial distribution associated with spacesuit surfaces, which will help future mission planners develop effective planetary protection strategies.},
}
@article {pmid34390303,
year = {2021},
author = {Huang, Z and Liu, B and Yin, Y and Liang, F and Xie, D and Han, T and Liu, Y and Yan, B and Li, Q and Huang, Y and Liu, Q},
title = {Impact of biocontrol microbes on soil microbial diversity in ginger (Zingiber officinale Roscoe).},
journal = {Pest management science},
volume = {77},
number = {12},
pages = {5537-5546},
doi = {10.1002/ps.6595},
pmid = {34390303},
issn = {1526-4998},
support = {//National Key R&amp;D Program of China/ ; //Department of Science and Technology of Sichuan Province/ ; },
mesh = {*Zingiber officinale ; Hypocreales ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Soil ; Soil Microbiology ; },
abstract = {BACKGROUND: Bacteria are the most diverse and abundant group of soil organisms that influence plant growth and health. Bacillus and Trichoderma are commonly used as biological control agents (BCA) that directly or indirectly act on soil bacteria. Therefore, it is essential to understand how the applied microbes impact the indigenous microbial community before exploring their activity in the control of soilborne diseases.<br><br>RESULTS: MiSeq sequencing of the 16S rRNA gene was used to decipher the shift of rhizosphere bacterial community in ginger (Zingiber officinale Roscoe) treated with Bacillus subtilus and Trichoderma harzianum at different concentrations. The dominant phyla in treated and nontreated samples were Proteobacteria, Actinobacteria, Acidobacteria and comprised up to 54.7% of the total sequences. There were significant differences between BCA treated and nontreated samples in the bacteria community. BCA treated plants presented higher bacterial diversity than nontreated and higher dosage of BCA had a larger impact on rhizosphere microbiota, but the 'dose-response relationship' varied in different bacterial groups. Potential biomarkers at genus level were found, such as RB41, Pseudomonas, Nitrospira, Candidatus_Udaeobacter.<br><br>CONCLUSION: The combined use of Bacillus subtilus and Trichoderma harzianum could alter bacterial community structure and diversity in rhizosphere soil. BCA-microbes interactions as well as soil microbial ecology should be noticed in plant disease management. &#xa9; 2021 Society of Chemical Industry.},
}
@article {pmid34389059,
year = {2021},
author = {Boeuf, D and Eppley, JM and Mende, DR and Malmstrom, RR and Woyke, T and DeLong, EF},
title = {Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {172},
pmid = {34389059},
issn = {2049-2618},
mesh = {Bacteria/genetics ; *Microbiota ; Oceans and Seas ; Phylogeny ; *Seawater ; },
abstract = {BACKGROUND: Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy in the ocean's interior. SAR324 is a ubiquitous but poorly understood uncultivated clade of Deltaproteobacteria that inhabits the entire water column, from ocean surface waters to its deep interior. Although some progress has been made in elucidating potential metabolic traits of SAR324 in the dark ocean, very little is known about the ecology and the metabolic capabilities of this group in the euphotic and twilight zones. To investigate the comparative genomics, ecology, and physiological potential of the SAR324 clade, we examined the distribution and variability of key genomic features and metabolic pathways in this group from surface waters to the abyss in the North Pacific Subtropical Gyre, one of the largest biomes on Earth.<br><br>RESULTS: We leveraged a pangenomic ecological approach, combining spatio-temporally resolved single-amplified genome, metagenomic, and metatranscriptomic datasets. The data revealed substantial genomic diversity throughout the SAR324 clade, with distinct depth and temporal distributions that clearly differentiated ecotypes. Phylogenomic subclade delineation, environmental distributions, genomic feature similarities, and metabolic capacities revealed strong congruence. The four SAR324 ecotypes delineated in this study revealed striking divergence from one another with respect to their habitat-specific metabolic potentials. The ecotypes living in the dark or twilight oceans shared genomic features and metabolic capabilities consistent with a sulfur-based chemolithoautotrophic lifestyle. In contrast, those inhabiting the sunlit ocean displayed higher plasticity energy-related metabolic pathways, supporting a presumptive photoheterotrophic lifestyle. In epipelagic SAR324 ecotypes, we observed the presence of two types of proton-pumping rhodopsins, as well as genomic, transcriptomic, and ecological evidence for active photoheterotrophy, based on xanthorhodopsin-like light-harvesting proteins.<br><br>CONCLUSIONS: Combining pangenomic and both metagenomic and metatranscriptomic profiling revealed a striking divergence in the vertical distribution, genomic composition, metabolic potential, and predicted lifestyle strategies of geographically co-located members of the SAR324 bacterial clade. The results highlight the utility of metapangenomic approaches employed across environmental gradients, to decipher the properties and variation in function and ecological traits of specific phylogenetic clades within complex microbiomes. Video abstract.},
}
@article {pmid34388922,
year = {2022},
author = {Rogiers, T and Merroun, ML and Williamson, A and Leys, N and Houdt, RV and Boon, N and Mijnendonckx, K},
title = {Cupriavidus metallidurans NA4 actively forms polyhydroxybutyrate-associated uranium-phosphate precipitates.},
journal = {Journal of hazardous materials},
volume = {421},
number = {},
pages = {126737},
doi = {10.1016/j.jhazmat.2021.126737},
pmid = {34388922},
issn = {1873-3336},
mesh = {*Cupriavidus/genetics ; Phosphates ; *Uranium ; },
abstract = {Cupriavidus metallidurans is a model bacterium to study molecular metal resistance mechanisms and its use for the bioremediation of several metals has been shown. However, its mechanisms for radionuclide resistance are unexplored. We investigated the interaction with uranium and associated cellular response to uranium for Cupriavidus metallidurans NA4. Strain NA4 actively captured 98 ± 1% of the uranium in its biomass after growing 24 h in the presence of 100 µM uranyl nitrate. TEM HAADF-EDX microscopy confirmed intracellular uranium-phosphate precipitates that were mainly associated with polyhydroxybutyrate. Furthermore, whole transcriptome sequencing indicated a complex transcriptional response with upregulation of genes encoding general stress-related proteins and several genes involved in metal resistance. More in particular, gene clusters known to be involved in copper and silver resistance were differentially expressed. This study provides further insights into bacterial interactions with and their response to uranium. Our results could be promising for uranium bioremediation purposes with the multi-metal resistant bacterium C. metallidurans NA4.},
}
@article {pmid34387704,
year = {2021},
author = {de Siqueira, KA and Senabio, JA and Pietro-Souza, W and de Oliveira Mendes, TA and Soares, MA},
title = {Aspergillus sp. A31 and Curvularia geniculata P1 mitigate mercury toxicity to Oryza sativa L.},
journal = {Archives of microbiology},
volume = {203},
number = {9},
pages = {5345-5361},
pmid = {34387704},
issn = {1432-072X},
support = {568258/2014//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa&#xa0;do Estado de&#xa0;Mato Grosso/ ; 409062/2018-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Aspergillus/genetics ; Curvularia ; Endophytes ; *Mercury/toxicity ; *Oryza ; Phylogeny ; Plant Roots ; },
abstract = {Aspergillus sp. A31 and Curvularia geniculata P1 are endophytes that colonize the roots of Aeschynomene fluminensis Vell. and Polygonum acuminatum Kunth. in humid environments contaminated with mercury. The two strains mitigated mercury toxicity and promoted Oryza sativa L growth. C. geniculata P1 stood out for increasing the host biomass by fourfold and reducing the negative effects of the metal on photosynthesis. Assembling and annotation of Aspergillus sp. A31 and C. geniculata P1 genomes resulted in 28.60 Mb (CG% 53.1; 10,312 coding DNA sequences) and 32.92 Mb (CG% 50.72; 8,692 coding DNA sequences), respectively. Twelve and 27 genomes of Curvularia/Bipolaris and Aspergillus were selected for phylogenomic analyzes, respectively. Phylogenetic analysis inferred the separation of species from the genus Curvularia and Bipolaris into different clades, and the separation of species from the genus Aspergillus into three clades; the species were distinguished by occupied niche. The genomes had essential gene clusters for the adaptation of microorganisms to high metal concentrations, such as proteins of the phytoquelatin-metal complex (GO: 0090423), metal ion binders (GO: 0046872), ABC transporters (GO: 0042626), ATPase transporters (GO: 0016887), and genes related to response to reactive oxygen species (GO: 0000302) and oxidative stress (GO: 0006979). The results reported here help to understand the unique regulatory mechanisms of mercury tolerance and plant development.},
}
@article {pmid34387702,
year = {2022},
author = {Qin, M and Jiang, L and Kholmatov, BR and Qiao, G and Chen, J},
title = {Phylosymbiotic Structures of the Microbiota in Mollitrichosiphum tenuicorpus (Hemiptera: Aphididae: Greenideinae).},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {227-239},
pmid = {34387702},
issn = {1432-184X},
support = {No. 31772492//National Natural Science Foundation of China/ ; No. XDA19050303//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; Grant No. ANSO-CR-KP-2020-04//Key Collaborative Research Program of the Alliance of International Science Organizations/ ; No. 2020087//Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; },
mesh = {Animals ; *Aphids ; *Buchnera/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; Plants ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; },
abstract = {Aphids harbor an array of symbionts that provide hosts with ecological benefits. Microbial community assembly generally varies with respect to aphid species, geography, and host plants. However, the influence of host genetics and ecological factors on shaping intraspecific microbial community structures has not been fully understood. In the present study, using Illumina sequencing of the V3 - V4 hypervariable region of the 16S rRNA gene, we characterized the microbial compositions associated with Mollitrichosiphum tenuicorpus from different regions and plants in China. The primary symbiont Buchnera aphidicola and the secondary symbiont Arsenophonus dominated the microbial flora in M. tenuicorpus. Ordination analyses and statistical tests suggested that geography and aphid genetics primarily contributed to the variation in the microbiota of M. tenuicorpus. We further confirmed the combined effect of aphid genetics and geography on shaping the structures of symbiont and secondary symbiont communities. Moreover, the significant correlation between aphid genetic divergence and symbiont community dissimilarity provides evidence for intraspecific phylosymbiosis in natural systems. Our study helped to elucidate the eco-evolutionary relationship between symbiont communities and aphids within one given species.},
}
@article {pmid34387003,
year = {2021},
author = {Yang, S and Liebner, S and Svenning, MM and Tveit, AT},
title = {Decoupling of microbial community dynamics and functions in Arctic peat soil exposed to short term warming.},
journal = {Molecular ecology},
volume = {30},
number = {20},
pages = {5094-5104},
doi = {10.1111/mec.16118},
pmid = {34387003},
issn = {1365-294X},
mesh = {Arctic Regions ; Carbon Dioxide/analysis ; Methane ; *Microbiota/genetics ; *Soil ; Soil Microbiology ; Temperature ; },
abstract = {Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH4 and CO2 production rates (Proceedings of the National Academy of Sciences of the United States of America, 112, E2507-E2516). Here, we studied the taxonomic composition and functional potential of samples from the same experiment. We see that along a high-resolution temperature gradient (1-30°C), microbial communities change discretely, but not continuously or stochastically, in response to rising temperatures. The taxonomic variability may thus in part reflect the varied temperature responses of individual taxa and the competition between these taxa for resources. These taxonomic responses contrast the stable functional potential (metagenomic-based) across all temperatures or the previously observed metabolic or trophic shifts at key temperatures. Furthermore, with rising temperatures we observed a progressive decrease in species diversity (Shannon Index) and increased dispersion of greenhouse gas (GHG) production rates. We conclude that the taxonomic variation is decoupled from both the functional potential of the community and the previously observed temperature-dependent changes in microbial function. However, the reduced diversity at higher temperatures might help explain the higher variability in GHG production at higher temperatures.},
}
@article {pmid34385301,
year = {2021},
author = {Shoemaker, WR and Jones, SE and Muscarella, ME and Behringer, MG and Lehmkuhl, BK and Lennon, JT},
title = {Microbial population dynamics and evolutionary outcomes under extreme energy limitation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {33},
pages = {},
pmid = {34385301},
issn = {1091-6490},
mesh = {Bacteria/*classification/*genetics ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Energy Metabolism/*genetics/*physiology ; Mutation ; Species Specificity ; },
abstract = {Microorganisms commonly inhabit energy-limited ecosystems where cellular maintenance and reproduction is highly constrained. To gain insight into how individuals persist under such conditions, we derived demographic parameters from a collection of 21 heterotrophic bacterial taxa by censusing 100 populations in an effectively closed system for 1,000 d. All but one taxon survived prolonged resource scarcity, yielding estimated times to extinction ranging over four orders of magnitude from 10[0] to 10[5] y. Our findings corroborate reports of long-lived bacteria recovered from ancient environmental samples, while providing insight into mechanisms of persistence. As death rates declined over time, lifespan was extended through the scavenging of dead cells. Although reproduction was suppressed in the absence of exogenous resources, populations continued to evolve. Hundreds of mutations were acquired, contributing to genome-wide signatures of purifying selection as well as molecular signals of adaptation. Consistent ecological and evolutionary dynamics indicate that distantly related bacteria respond to energy limitation in a similar and predictable manner, which likely contributes to the stability and robustness of microbial life.},
}
@article {pmid34384885,
year = {2021},
author = {Marzorati, M and Calatayud, M and Rotsaert, C and Van Mele, M and Duysburgh, C and Durkee, S and White, T and Fowler, K and Jannin, V and Bellamine, A},
title = {Comparison of protection and release behavior of different capsule polymer combinations based on L. acidophilus survivability and function and caffeine release.},
journal = {International journal of pharmaceutics},
volume = {607},
number = {},
pages = {120977},
doi = {10.1016/j.ijpharm.2021.120977},
pmid = {34384885},
issn = {1873-3476},
mesh = {*Caffeine ; Capsules ; Chemistry, Pharmaceutical ; Ecosystem ; Humans ; *Polymers ; },
abstract = {Oral administration of active pharmaceutical ingredients, nutraceuticals, enzymes or probiotics requires an appropriate delivery system for optimal bioactivity and absorption. The harsh conditions during the gastrointestinal transit can degrade the administered products, hampering their efficacy. Enteric or delayed-release pharmaceutical formulations may help overcome these issues. In a Simulator of Human Intestinal Microbial Ecosystem model (SHIME) and using caffeine as a marker for release kinetics and L. acidophilus survivability as an indicator for protection, we compared the performance of ten capsule configurations, single or DUOCAP® combinations. The function of L. acidophilus and its impact on the gut microbiota was further tested in three selected capsule types, combinations of DRcaps® capsule in DRcaps® capsule (DR-in-DR) and DRcaps® capsule in Vcaps® capsule (DR-in-VC) and single Vcaps® Plus capsule under colonic conditions. We found that under stomach and small intestine conditions, DR-in-DR and DR-in-VC led to the best performance both under fed and fasted conditions based on the slow caffeine release and the highest L. acidophilus survivability. The Vcaps® Plus capsule however, led to the quickest caffeine and probiotic release. When DR-in-DR, DR-in-VC and single Vcaps® Plus capsules were tested through the whole gastrointestinal tract, including under colonic conditions, caffeine release was found to be slower in capsules containing DRcaps® capsules compared to the single Vcaps® capsules. In addition, colonic survival of L. acidophilus was significantly increased under fasted conditions in DR-in-DR or DR-in-VC formulation compared to Vcaps® Plus capsule. To assess the impact of these formulations on the microbial function, acetate, butyrate and propionate as well as ammonia were measured. L. acidophilus released from DR-in-DR or DR-in-VC induced a significant increase in butyrate and a decrease in ammonia, suggesting a proliferation of butyrate-producing bacteria and reduction in ammonia-producing bacteria. These data suggest that L. acidophilus included in DR-in-DR or DR-in-VC reaching the colon is viable and functional, potentially contributing to changes in colonic microbiota composition and diversity.},
}
@article {pmid34384375,
year = {2021},
author = {Xi, J and Ding, D and Zhu, H and Wang, R and Su, F and Wu, W and Xiao, Z and Liang, X and Zhao, Q and Hong, Z and Fu, H and Xiao, Q},
title = {Disturbed microbial ecology in Alzheimer's disease: evidence from the gut microbiota and fecal metabolome.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {226},
pmid = {34384375},
issn = {1471-2180},
mesh = {Aged ; Aged, 80 and over ; Alzheimer Disease/*microbiology/physiopathology ; Bacteria/*genetics/pathogenicity ; Chromatography, Liquid ; Dysbiosis/complications/*microbiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metabolic Networks and Pathways ; *Metabolome ; Metabolomics/methods ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; },
abstract = {BACKGROUND: Gut microbiota (GMB) alteration has been reported to influence the Alzheimer's disease (AD) pathogenesis through immune, endocrine, and metabolic pathways. This study aims to investigate metabolic output of the dysbiosis of GMB in AD pathogenesis. In this study, the fecal microbiota and metabolome from 21 AD participants and 44 cognitively normal control participants were measured. Untargeted GMB taxa was analyzed through 16S ribosomal RNA gene profiling based on next-generation sequencing and fecal metabolites were quantified by using ultrahigh performance liquid chromatography-mass spectrometry (UPLC-MS).<br><br>RESULTS: Our analysis revealed that AD was characterized by 15 altered gut bacterial genera, of which 46.7% (7/15 general) was significantly associated with a series of metabolite markers. The predicted metabolic profile of altered gut microbial composition included steroid hormone biosynthesis, N-Acyl amino acid metabolism and piperidine metabolism. Moreover, a combination of 2 gut bacterial genera (Faecalibacterium and Pseudomonas) and 4 metabolites (N-Docosahexaenoyl GABA, 19-Oxoandrost-4-ene-3,17-dione, Trigofoenoside F and 22-Angeloylbarringtogenol C) was able to discriminate AD from NC with AUC of 0.955 in these 65 subjects.<br><br>CONCLUSIONS: These findings demonstrate that gut microbial alterations and related metabolic output changes may be associated with pathogenesis of AD, and suggest that fecal markers might be used as a non-invasive examination to assist screening and diagnosis of AD.},
}
@article {pmid34383807,
year = {2021},
author = {Deng, S and Wang, B and Zhang, W and Su, S and Dong, H and Banat, IM and Sun, S and Guo, J and Liu, W and Wang, L and She, Y and Zhang, F},
title = {Elucidate microbial characteristics in a full-scale treatment plant for offshore oil produced wastewater.},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0255836},
pmid = {34383807},
issn = {1932-6203},
mesh = {Anaerobiosis ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Bioreactors ; Oil and Gas Fields/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/metabolism ; Waste Disposal, Fluid/instrumentation/*methods ; Wastewater/*microbiology ; Water Pollutants/isolation &amp; purification/metabolism ; },
abstract = {Oil-produced wastewater treatment plants, especially those involving biological treatment processes, harbor rich and diverse microbes. However, knowledge of microbial ecology and microbial interactions determining the efficiency of plants for oil-produced wastewater is limited. Here, we performed 16S rDNA amplicon sequencing to elucidate the microbial composition and potential microbial functions in a full-scale well-worked offshore oil-produced wastewater treatment plant. Results showed that microbes that inhabited the plant were diverse and originated from oil and marine associated environments. The upstream physical and chemical treatments resulted in low microbial diversity. Organic pollutants were digested in the anaerobic baffled reactor (ABR) dominantly through fermentation combined with sulfur compounds respiration. Three aerobic parallel reactors (APRs) harbored different microbial groups that performed similar potential functions, such as hydrocarbon degradation, acidogenesis, photosynthetic assimilation, and nitrogen removal. Microbial characteristics were important to the performance of oil-produced wastewater treatment plants with biological processes.},
}
@article {pmid34383127,
year = {2022},
author = {Vieira, FR and Pecchia, JA},
title = {Bacterial Community Patterns in the Agaricus bisporus Cultivation System, from Compost Raw Materials to Mushroom Caps.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {20-32},
pmid = {34383127},
issn = {1432-184X},
support = {PEN04741//United States Department of Agriculture (USDA/NIFA - National Institute of Food and Agriculture) and Hatch Appropriations/ ; },
mesh = {*Agaricus/genetics ; Bacteria/genetics ; *Composting ; *Microbiota ; },
abstract = {Different from other fungal species that can be largely cultivated in 'axenic conditions' using plant material (e.g., species of Lentinula and Pleurotus in 'sterile' straw-based substrate), the commercial Agaricus bisporus cultivation system relies heavily on ecological relationships with a broad range of microorganisms present in the system (compost and casing). Since the A. bisporus cultivation system consists of a microbial manipulation process, it is important to know the microbial community dynamics during the entire cultivation cycle to design further studies and/or crop management strategies to optimize this system. To capture the bacterial community 'flow' from compost raw materials to the casing to the formation and maturation of mushroom caps, community snapshots were generated by direct DNA recovery (amplicon sequencing). The 'bacterial community flow' revealed that compost, casing and mushrooms represent different niches for bacteria present in the cultivation system, but at the same time, a bacterial exchange between microenvironments can occur for a portion of the community. Within each microenvironment, compost showed intense bacterial populational dynamics, probably due to the environmental changes imposed by composting conditions. In casing, the colonization of A. bisporus appeared, to reshape the native bacterial community which later, with some other members present in compost, becomes the core community in mushroom caps. The current bacterial survey along with previous results provides more cues of specific bacteria groups that can be in association with A. bisporus development and health.},
}
@article {pmid34378984,
year = {2021},
author = {Liu, D and Pérez-Moreno, J and He, X and Garibay-Orijel, R and Yu, F},
title = {Truffle Microbiome Is Driven by Fruit Body Compartmentalization Rather than Soils Conditioned by Different Host Trees.},
journal = {mSphere},
volume = {6},
number = {4},
pages = {e0003921},
pmid = {34378984},
issn = {2379-5042},
mesh = {Ascomycota/physiology ; Bacteria/classification/*genetics ; Basidiomycota/*physiology ; Fungi/classification/*genetics ; Microbiota/*genetics/physiology ; Phylogeny ; Rhizosphere ; *Soil Microbiology ; *Symbiosis ; *Trees ; },
abstract = {Truffles are among the most expensive edible mushrooms; their value is worth billions of U.S. dollars annually in international markets. They establish ectomycorrhizal symbiotic relationships with diverse host tree roots and produce hypogeous ascomata. Their whole life cycle is closely related to their associated microbiome. However, whether truffle-associated compartments or host tree rhizospheres are the vital driver for truffle ascomata microbiome is unclear. To identify and compare fungal and bacterial communities in four truffle-associated compartments (Tuber indicum: bulk soil, adhering soil to peridium, peridium, and gleba) from three host trees, we sequenced their ITS (fungal) and 16S (bacterial) ribosomal DNA using the Illumina MiSeq high-throughput platform. We further applied the amplicon data to analyze the core microbiome and microbial ecological networks. Tuber indicum microbiome composition was strongly driven by its associated compartments rather than by their symbiotic host trees. Truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex interacting network compared to that of the fungal community. The core fungal community changed from Basidiomycota dominated (bulk soil) to Rozellomycota dominated (interphase soil); the core bacterial community shifted from Bacteroidetes to Proteobacteria dominance from truffle peridium to gleba tissue. Especially, at the truffle and soil interphase, the niche-based selection of truffle microbiome was verified by (i) a clear exclusion of four bacterial phyla (Rokubacteria, Nitrospirae, Chloroflexi, and Planctomycetes) in gleba; (ii) a significant decrease in alpha-diversity (as revealed by Chao 1, Shannon, and Simpson indices); and (iii) the complexity of the network substantially decreased from bulk soil to soil-truffle interphase and further to the peridium and gleba. The network analysis of microbiome showed that the microbial positive interactions were higher in truffle tissues than in both bulk soil and peridium-adhering soil and that Cupriavidus, Bradyrhizobium, Aminobacter, and Mesorhizobium spp. were the keystone network hubs in the truffle gleba. This study provides insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components. IMPORTANCE Currently, the factors that drive the microbiome associated with truffles, the most highly prized fungi in the world, are largely unknown. We demonstrate for the first time here that truffle microbiome composition is strongly driven by associated compartments rather than by symbiotic host trees. The truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex (with the higher numbers of nodes, links, and modules) interacting network compared to that of the fungal community. Network analysis showed a higher number of positive microbial interactions with each other in truffle tissues than in both bulk soil and peridium-adhering soil. For the first time, the fungal community structure associated with truffles using high-throughput sequencing, microbial networks, and keystone species analyses is presented. This study provides novel insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components, showing that they are more complex than previously thought.},
}
@article {pmid34378947,
year = {2021},
author = {Zhang, SY and Xiao, X and Chen, SC and Zhu, YG and Sun, GX and Konstantinidis, KT},
title = {High Arsenic Levels Increase Activity Rather than Diversity or Abundance of Arsenic Metabolism Genes in Paddy Soils.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {20},
pages = {e0138321},
pmid = {34378947},
issn = {1098-5336},
mesh = {Archaea/genetics/metabolism ; Arsenic/analysis/*metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Genes, Archaeal ; *Genes, Bacterial ; Metals, Heavy/analysis ; Oryza ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; },
abstract = {Arsenic (As) metabolism genes are generally present in soils, but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes (ars) including arsR, acr3, arsB, arsC, arsM, arsI, arsP, and arsH as well as energy-generating As respiratory oxidation (aioA) and reduction (arrA) genes. Somewhat unexpectedly, the relative DNA abundances and diversities of ars, aioA, and arrA genes were not significantly different between low and high (∼10 versus ∼100 mg kg[-1]) As soils. Compared to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars gene abundance only when its concentration was higher than 410 mg kg[-1]. In contrast, metatranscriptomics revealed that relative to low-As soils, high-As soils showed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community wide as opposed to taxon specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil or other environments should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level; thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.},
}
@article {pmid34378531,
year = {2021},
author = {Marié, IJ and Brambilla, L and Azzouz, D and Chen, Z and Baracho, GV and Arnett, A and Li, HS and Liu, W and Cimmino, L and Chattopadhyay, P and Silverman, G and Watowich, SS and Khor, B and Levy, DE},
title = {Tonic interferon restricts pathogenic IL-17-driven inflammatory disease via balancing the microbiome.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34378531},
issn = {2050-084X},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 AI133822/AI/NIAID NIH HHS/United States ; R01 AI028900/AI/NIAID NIH HHS/United States ; P50 AR070591/AR/NIAMS NIH HHS/United States ; },
mesh = {Animals ; Dysbiosis/*immunology ; Female ; *Gastrointestinal Microbiome ; Inflammation/*genetics ; Interferons/*administration &amp; dosage ; Interleukin-17/*genetics/metabolism ; Mice ; Mice, Knockout ; STAT1 Transcription Factor/*genetics/metabolism ; },
abstract = {Maintenance of immune homeostasis involves a synergistic relationship between the host and the microbiome. Canonical interferon (IFN) signaling controls responses to acute microbial infection, through engagement of the STAT1 transcription factor. However, the contribution of tonic levels of IFN to immune homeostasis in the absence of acute infection remains largely unexplored. We report that STAT1 KO mice spontaneously developed an inflammatory disease marked by myeloid hyperplasia and splenic accumulation of hematopoietic stem cells. Moreover, these animals developed inflammatory bowel disease. Profiling gut bacteria revealed a profound dysbiosis in the absence of tonic IFN signaling, which triggered expansion of TH17 cells and loss of splenic Treg cells. Reduction of bacterial load by antibiotic treatment averted the TH17 bias and blocking IL17 signaling prevented myeloid expansion and splenic stem cell accumulation. Thus, tonic IFNs regulate gut microbial ecology, which is crucial for maintaining physiologic immune homeostasis and preventing inflammation.},
}
@article {pmid34370735,
year = {2021},
author = {Ghasemian, E and Inic-Kanada, A and Collingro, A and Mejdoubi, L and Alchalabi, H and Keše, D and Elshafie, BE and Hammou, J and Barisani-Asenbauer, T},
title = {Comparison of genovars and Chlamydia trachomatis infection loads in ocular samples from children in two distinct cohorts in Sudan and Morocco.},
journal = {PLoS neglected tropical diseases},
volume = {15},
number = {8},
pages = {e0009655},
pmid = {34370735},
issn = {1935-2735},
mesh = {Adolescent ; Bacterial Outer Membrane Proteins/*genetics ; Case-Control Studies ; Child ; Child, Preschool ; Chlamydia trachomatis/*genetics ; Conjunctivitis, Inclusion/drug therapy/*microbiology/transmission ; Female ; Genotype ; Humans ; Infant ; Male ; Morocco ; Polymerase Chain Reaction ; Sudan ; Trachoma/*genetics ; },
abstract = {Trachoma is a blinding disease caused by repeated conjunctival infection with different Chlamydia trachomatis (Ct) genovars. Ct B genovars have been associated with more severe trachoma symptoms. Here, we investigated associations between Ct genovars and bacterial loads in ocular samples from two distinct geographical locations in Africa, which are currently unclear. We tested ocular swabs from 77 Moroccan children (28 with trachomatous inflammation-follicular (TF) and 49 healthy controls), and 96 Sudanese children (54 with TF and 42 healthy controls) with a Ct-specific real-time polymerase chain reaction (PCR) assay. To estimate bacterial loads, Ct-positive samples were further processed by multiplex real-time qPCR to amplify the chromosomal outer membrane complex B and plasmid open reading frame 2 of Ct. Genotyping was performed by PCR-based amplification of the outer membrane protein A gene (~1120 base pairs) of Ct and Sanger sequencing. Ct-positivities among the Moroccan and Sudanese patient groups were 60·7% and 31·5%, respectively. Significantly more Sudanese patients than Moroccan patients were genovar A-positive. In contrast, B genovars were significantly more prevalent in Moroccan patients than in Sudanese patients. Significantly higher Ct loads were found in samples positive for B genovars (598596) than A genovar (51005). Geographical differences contributed to the distributions of different ocular Ct genovars. B genovars may induce a higher bacterial load than A genovars in trachoma patients. Our findings emphasize the importance of conducting broader studies to elucidate if the noted difference in multiplication abilities are genovar and/or endemicity level dependent.},
}
@article {pmid34370055,
year = {2022},
author = {Travanty, NV and Vargo, EL and Apperson, CS and Ponnusamy, L},
title = {Colonization by the Red Imported Fire Ant, Solenopsis invicta, Modifies Soil Bacterial Communities.},
journal = {Microbial ecology},
volume = {84},
number = {1},
pages = {240-256},
pmid = {34370055},
issn = {1432-184X},
mesh = {Animals ; *Ants/microbiology ; Bacteria/genetics ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Soil ; },
abstract = {The long-standing association between insects and microorganisms has been especially crucial to the evolutionary and ecological success of social insect groups. Notably, research on the interaction of the two social forms (monogyne and polygyne) of the red imported fire ant (RIFA), Solenopsis invicta Buren, with microbes in its soil habitat is presently limited. In this study, we characterized bacterial microbiomes associated with RIFA nest soils and native (RIFA-negative) soils to better understand the effects of colonization of RIFA on soil microbial communities. Bacterial community fingerprints of 16S rRNA amplicons using denaturing gradient gel electrophoresis revealed significant differences in the structure of the bacterial communities between RIFA-positive and RIFA-negative soils at 0 and 10 cm depths. Illumina sequencing of 16S rRNA amplicons provided fine-scale analysis to test for effects of RIFA colonization, RIFA social form, and soil depth on the composition of the bacterial microbiomes of the soil and RIFA workers. Our results showed the bacterial community structure of RIFA-colonized soils to be significantly different from native soil communities and to evidence elevated abundances of several taxa, including Actinobacteria. Colony social form was not found to be a significant factor in nest or RIFA worker microbiome compositions. RIFA workers and nest soils were determined to have markedly different bacterial communities, with RIFA worker microbiomes being characterized by high abundances of a Bartonella-like endosymbiont and Entomoplasmataceae. Cloning and sequencing of the 16S rRNA gene revealed the Bartonella sp. to be a novel bacterium.},
}
@article {pmid34368008,
year = {2021},
author = {Josephs-Spaulding, J and Krogh, TJ and Rettig, HC and Lyng, M and Chkonia, M and Waschina, S and Graspeuntner, S and Rupp, J and Møller-Jensen, J and Kaleta, C},
title = {Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {562525},
pmid = {34368008},
issn = {2235-2988},
mesh = {Anti-Bacterial Agents/therapeutic use ; Humans ; Inflammation/drug therapy ; Urinary Bladder ; *Urinary Tract Infections ; },
abstract = {Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.},
}
@article {pmid34367868,
year = {2021},
author = {Paul, P and Chakraborty, P and Sarker, RK and Chatterjee, A and Maiti, D and Das, A and Mandal, S and Bhattacharjee, S and Dastidar, DG and Tribedi, P},
title = {Tryptophan interferes with the quorum sensing and cell surface hydrophobicity of Staphylococcus aureus: a promising approach to inhibit the biofilm development.},
journal = {3 Biotech},
volume = {11},
number = {8},
pages = {376},
pmid = {34367868},
issn = {2190-572X},
abstract = {UNLABELLED: Staphylococcus aureus, a Gram-positive bacterium has been implicated in a plethora of human infections by virtue of its biofilm-forming ability. Inhibition in microbial biofilm formation has been found to be a promising approach towards compromising microbial pathogenesis. In this regard, various natural and synthetic molecules have been explored to attenuate microbial biofilm. In this study, the role of an amino acid, L-tryptophan was examined against the biofilm-forming ability of S. aureus. The compound did not execute any antimicrobial characteristics, instead, showed strong antibiofilm activity with the highest biofilm inhibition at a concentration of 50 µg/mL. Towards understanding the underlying mechanism of the same, efforts were given to examine whether tryptophan could inhibit biofilm formation by interfering with the quorum-sensing property of S. aureus. A molecular docking analysis revealed an efficient binding between the quorum-sensing protein, AgrA, and tryptophan. Moreover, the expression of the quorum-sensing gene (agrA) got significantly reduced under the influence of the test compound. These results indicated that tryptophan could interfere with the quorum-sensing property of the organism thereby inhibiting its biofilm formation. Further study revealed that tryptophan could also reduce the cell surface hydrophobicity of S. aureus by downregulating the expression of dltA. Moreover, the tested concentrations of tryptophan did not show any significant cytotoxicity. Hence, tryptophan could be recommended as a potential antibiofilm agent to manage the biofilm-associated infections caused by S. aureus.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02924-3.},
}
@article {pmid34367102,
year = {2021},
author = {Rapp, JZ and Sullivan, MB and Deming, JW},
title = {Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {701186},
pmid = {34367102},
issn = {1664-302X},
abstract = {Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼10[5] cells mL[-1]) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼10[8] cells mL[-1]) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.},
}
@article {pmid34365235,
year = {2022},
author = {Bourhane, Z and Lanzén, A and Cagnon, C and Ben Said, O and Mahmoudi, E and Coulon, F and Atai, E and Borja, A and Cravo-Laureau, C and Duran, R},
title = {Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum.},
journal = {Journal of hazardous materials},
volume = {421},
number = {},
pages = {126789},
doi = {10.1016/j.jhazmat.2021.126789},
pmid = {34365235},
issn = {1873-3336},
mesh = {Biomarkers ; Ecosystem ; Environmental Monitoring ; Geologic Sediments ; Humans ; Lakes ; *Polycyclic Aromatic Hydrocarbons/analysis ; RNA, Ribosomal, 16S/genetics ; Rivers ; Soil ; *Water Pollutants, Chemical/analysis ; },
abstract = {Microbial communities inhabiting soil-water-sediment continuum in coastal areas provide important ecosystem services. Their adaptation in response to environmental stressors, particularly mitigating the impact of pollutants discharged from human activities, has been considered for the development of microbial biomonitoring tools, but their use is still in the infancy. Here, chemical and molecular (16S rRNA gene metabarcoding) approaches were combined in order to determine the impact of pollutants on microbial assemblages inhabiting the aquatic network of a soil-water-sediment continuum around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected within the soil-river-lake continuum at three stations in dry (summer) and wet (winter) seasons. The contaminant pressure index (PI), which integrates Polycyclic aromatic hydrocarbons (PAHs), alkanes, Organochlorine pesticides (OCPs) and metal contents, and the microbial pressure index microgAMBI, based on bacterial community structure, showed significant correlation with contamination level and differences between seasons. The comparison of prokaryotic communities further revealed specific assemblages for soil, river and lake sediments. Correlation analyses identified potential "specialist" genera for the different compartments, whose abundances were correlated with the pollutant type found. Additionally, PICRUSt analysis revealed the metabolic potential for pollutant transformation or degradation of the identified "specialist" species, providing information to estimate the recovery capacity of the ecosystem. Such findings offer the possibility to define a relevant set of microbial indicators for assessing the effects of human activities on aquatic ecosystems. Microbial indicators, including the detection of "specialist" and sensitive taxa, and their functional capacity, might be useful, in combination with integrative microbial indices, to constitute accurate biomonitoring tools for the management and restoration of complex coastal aquatic systems.},
}
@article {pmid34364026,
year = {2021},
author = {Rogińska, J and Perdicakis, M and Midoux, C and Bouchez, T and Despas, C and Liu, L and Tian, JH and Chaumont, C and P A Jorand, F and Tournebize, J and Etienne, M},
title = {Electrochemical analysis of a microbial electrochemical snorkel in laboratory and constructed wetlands.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {142},
number = {},
pages = {107895},
doi = {10.1016/j.bioelechem.2021.107895},
pmid = {34364026},
issn = {1878-562X},
mesh = {Bioelectric Energy Sources/*microbiology ; Electrochemical Techniques/*methods ; Nitrates/*chemistry ; Water Purification/*methods ; *Wetlands ; },
abstract = {Microbial electrochemical snorkel (MES) is a short-circuited microbial fuel cell applicable to water treatment that does not produce energy but requires lower cost for its implementation. Few reports have already described its water treatment capabilities but no deeper electrochemical analysis were yet performed. We tested various materials (iron, stainless steel and porous graphite) and configurations of snorkel in order to better understand the rules that will control in a wetland the mixed potential of this self-powered system. We designed a model snorkel that was studied in laboratory and on the field. We confirmed the development of MES by identifying anodic and cathodic parts, by measuring the current between them and by analyzing microbial ecology in laboratory and field experiments. An important application is denitrification of surface water. Here we discuss the influence of nitrate on its electrochemical response and denitrification performances. Introducing nitrate caused the increase of the mixed potential of MES and of current at a potential value relatively more positive than for nitrate-reducing biocathodes described in the literature. The major criteria for promoting application of MES in artificial wetland dedicated to mitigation of non-point source nitrate pollution from agricultural water are considered.},
}
@article {pmid34363579,
year = {2022},
author = {Ghosh, A and Bhadury, P},
title = {Exploring changes in bacterioplankton community structure in response to tannic acid, a major component of mangrove litterfall of Sundarbans mangrove ecosystem: a laboratory mesocosm approach.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {2},
pages = {2107-2121},
pmid = {34363579},
issn = {1614-7499},
mesh = {Aquatic Organisms ; *Ecosystem ; Estuaries ; Humans ; *Laboratories ; RNA, Ribosomal, 16S/genetics ; Tannins ; },
abstract = {Tannic acid is a secondary compound produced by vascular plants and is a major component of mangrove litterfall. Tannic acid is water soluble, leaches out from mangrove litterfall and contributes to DOC and DON pools in adjacent estuaries. About 50% of the litterfall may be degraded and channelized into the marine microbial loop. The influence of tannic acid on bacterioplankton community structure was tested by setting up laboratory-based barrel experiments. Estuarine water from Stn3 of Sundarbans Biological Observatory Time Series (SBOTS) was enriched with tannic acid, and the change in concentration of dissolved nutrients was determined on a daily basis over a span of 15 days. Concentrations of tannic acid, gallic acid and other dissolved nutrients such as nitrate and ortho-phosphate were determined using a UV-Vis spectrophotometer. Tannic acid significantly affected the concentrations of gallic acid and dissolved nitrate in the barrels. Degradation of tannic acid was tracked by a decrease in concentration of tannic acid and generation of gallic acid. The influence of tannic acid on bacterioplankton community structure was analysed on the start (day 0), intermediate (day 3, day 5, day 7 and day 9) and end (day 15) of the experiment. Bacterioplankton community structure was elucidated by sequencing the V3-V4 region of 16S ribosomal RNA on an Illumina MiSeq platform. Proteobacteria was found to be the most dominant bacterial phylum in control and tannic acid-enriched barrels (barrels 1 and 2) on day 0. With the progression of experiment, the abundance of Proteobacteria altered significantly in the control barrel indicating the possible role of this phylum in the breakdown of tannic acid within estuarine mangroves. The abundance of Proteobacteria in the tannic acid-enriched barrels remained high, indicating that members of Proteobacteria may be capable of using tannic acid as a source of carbon and nitrogen. Tannic acid appeared to inhibit most of the other bacterioplankton phyla including Actinobacteria, Acidobacteria and Verrucomicrobia that existed in large abundance in the control barrel on day 15 but were almost absent in the tannic acid-enriched barrels. At class level, Bacteroides was found to be present in highest abundance in the tannic acid-enriched barrels. Tannic acid appeared to strongly influence the abundant bacterioplankton phyla and families as indicated by Pearson's correlation coefficient and non-metric multidimensional scaling ordination plots. Gallic acid is one of the final products of tannic acid degradation. Breakdown of tannic acid could influence the marine nitrogen and carbon cycling by releasing DON and DOC, respectively, into the adjacent estuaries. Information of breakdown and remineralization of components of litterfall such as tannic acid would also be important for calculation of carbon and nitrogen budgets of coastal ecosystems including in mangroves.},
}
@article {pmid34363516,
year = {2022},
author = {Su, Y and Du, Y and Xing, P},
title = {The Light-to-Nutrient Ratio in Alpine Lakes: Different Scenarios of Bacterial Nutrient Limitation and Community Structure in Lakes Above and Below the Treeline.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {837-849},
pmid = {34363516},
issn = {1432-184X},
support = {31971475//National Natural Science Foundation of China/ ; 31722008//National Natural Science Foundation of China/ ; 31670461//National Natural Science Foundation of China/ ; },
mesh = {Bacteria ; Chlorophyll A ; *Ecosystem ; *Lakes/chemistry ; Nitrogen ; Nutrients ; Phosphorus ; },
abstract = {The light-to-nutrient hypothesis proposes that under high light-to-nutrient conditions, bacteria tend to be limited by phosphorus (P), while under relatively low light-to-nutrient conditions, bacteria are likely driven towards carbon (C) limitation. Exploring whether this light-to-nutrient hypothesis is fitting for alpine lakes has profound implications for predicting the impacts of climatic and environmental changes on the structures and processes of aquatic ecosystems in climate-sensitive regions. We investigated the environmental conditions and bacterioplankton community compositions of 15 high-elevation lakes (7 above and 8 below treeline). High light-to-nutrient conditions (denoted by the reciprocal value of the attenuation coefficient (1/K) to total phosphorus (TP)), high chlorophyll a (Chl a) concentrations, low TP concentrations and low ratios of the dissolved organic carbon concentration to the dissolved total nitrogen concentration (DOC:DTN) were detected in above-treeline lakes. Significant positive correlations between the bacterioplankton community compositions with 1/K:TP ratios and Chl a concentrations indicated that not only high light energy but also nutrient competition between phytoplankton and bacteria could induce P limitation for bacteria. In contrast, low light-to-nutrient conditions and high allochthonous DOC input in below-treeline lakes lessen P limitation and C limitation. The most abundant genus, Polynucleobacter, was significantly enriched, and more diverse oligotypes of Polynucleobacter operational taxonomic units were identified in the below-treeline lakes, indicating the divergence of niche adaptations among Polynucleobacter oligotypes. The discrepancies in the light-to-P ratio and the components of organic matter between the above-treeline and below-treeline lakes have important implications for the nutrient limitation of bacterioplankton and their community compositions.},
}
@article {pmid34363515,
year = {2022},
author = {Perera, IA and Abinandan, S and Subashchandrabose, SR and Venkateswarlu, K and Naidu, R and Megharaj, M},
title = {Impact of Nitrate and Ammonium Concentrations on Co-Culturing of Tetradesmus obliquus IS2 with Variovorax paradoxus IS1 as Revealed by Phenotypic Responses.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {951-959},
pmid = {34363515},
issn = {1432-184X},
mesh = {*Ammonium Compounds/metabolism ; Coculture Techniques ; Comamonadaceae ; Nitrates/metabolism ; Nitrogen/metabolism ; },
abstract = {Mutual interactions in co-cultures of microalgae and bacteria are well known for establishing consortia and nutrient uptake in aquatic habitats, but the phenotypic changes in terms of morphological, physiological, and biochemical attributes that drive these interactions have not been clearly understood. In this novel study, we demonstrated the phenotypic response in a co-culture involving a microalga, Tetradesmus obliquus IS2, and a bacterium, Variovorax paradoxus IS1, grown with varying concentrations of two inorganic nitrogen sources. Modified Bold's basal medium was supplemented with five ratios (%) of NO3-N:NH4-N (100:0, 75:25, 50:50, 25:75, and 0:100), and by maintaining N:P Redfield ratio of 16:1. The observed morphological changes in microalga included an increase in granularity and a broad range of cell sizes under the influence of increased ammonium levels. Co-culturing in presence of NO3-N alone or combination with NH4-N up to equimolar concentrations resulted in complete nitrogen uptake, increased growth in both the microbial strains, and enhanced accumulation of carbohydrates, proteins, and lipids. Total chlorophyll content in microalga was also significantly higher when it was grown as a co-culture with NO3-N and NH4-N up to a ratio of 50:50. Significant upregulation in the synthesis of amino acids and sugars and downregulation of organic acids were evident with higher ammonium uptake in the co-culture, indicating the regulation of carbon and nitrogen assimilation pathways and energy synthesis. Our data suggest that the co-culture of strains IS1 and IS2 could be exploited for effluent treatment by considering the concentrations of inorganic sources, particularly ammonium, in the wastewaters.},
}
@article {pmid34361657,
year = {2021},
author = {Al-Shaibani, MM and Radin Mohamed, RMS and Sidik, NM and Enshasy, HAE and Al-Gheethi, A and Noman, E and Al-Mekhlafi, NA and Zin, NM},
title = {Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications.},
journal = {Molecules (Basel, Switzerland)},
volume = {26},
number = {15},
pages = {},
pmid = {34361657},
issn = {1420-3049},
mesh = {Actinobacteria/*metabolism ; Anti-Bacterial Agents/isolation &amp; purification/metabolism ; Biological Products ; Enzymes/isolation &amp; purification/metabolism ; Secondary Metabolism ; },
abstract = {The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities' well-being.},
}
@article {pmid34360485,
year = {2021},
author = {Ramli, NA and Md Yusof, NFF and Zarkasi, KZ and Suroto, A},
title = {Chemical, Biological and Morphological Properties of Fine Particles during Local Rice Straw Burning Activities.},
journal = {International journal of environmental research and public health},
volume = {18},
number = {15},
pages = {},
pmid = {34360485},
issn = {1660-4601},
mesh = {*Air Pollutants/analysis ; Bacillus ; Deltaproteobacteria ; Environmental Monitoring ; Humans ; *Oryza ; Particle Size ; Particulate Matter/analysis ; },
abstract = {Rice straw is commonly burned openly after harvesting in Malaysia and many other Asian countries where rice is the main crop. This operation emits a significant amount of air pollution, which can have severe consequences for indoor air quality, public health, and climate change. Therefore, this study focuses on determining the compositions of trace elements and the morphological properties of fine particles. Furthermore, the species of bacteria found in bioaerosol from rice burning activities were discovered in this study. For morphological observation of fine particles, FESEM-EDX was used in this study. Two main categories of particles were found, which were natural particles and anthropogenic particles. The zinc element was found during the morphological observation and was assumed to come from the fertilizer used by the farmers. ICP-OES identifies the concentration of trace elements in the fine particle samples. A cultured method was used in this study by using nutrient agar. From this study, several bacteria were identified: Exiguobavterium indicum, Bacillus amyloliquefaciens, Desulfonema limicola str. Jadabusan, Exiguobacterium acetylicum, Lysinibacillus macrolides, and Bacillus proteolyticus. This study is important, especially for human health, and further research on the biological composition of aerosols should be conducted to understand the effect of microorganisms on human health.},
}
@article {pmid34358486,
year = {2021},
author = {Wauters, L and Slaets, H and De Paepe, K and Ceulemans, M and Wetzels, S and Geboers, K and Toth, J and Thys, W and Dybajlo, R and Walgraeve, D and Biessen, E and Verbeke, K and Tack, J and Van de Wiele, T and Hellings, N and Vanuytsel, T},
title = {Efficacy and safety of spore-forming probiotics in the treatment of functional dyspepsia: a pilot randomised, double-blind, placebo-controlled trial.},
journal = {The lancet. Gastroenterology &amp; hepatology},
volume = {6},
number = {10},
pages = {784-792},
doi = {10.1016/S2468-1253(21)00226-0},
pmid = {34358486},
issn = {2468-1253},
mesh = {Adult ; Bacillus coagulans ; Bacillus subtilis ; Belgium/epidemiology ; Case-Control Studies ; Dietary Supplements/*adverse effects ; Double-Blind Method ; Dyspepsia/*diet therapy/epidemiology/*physiopathology ; Female ; Humans ; Male ; Middle Aged ; Pilot Projects ; Placebos/administration &amp; dosage ; Prevalence ; Probiotics/administration &amp; dosage/adverse effects/*therapeutic use ; Proton Pump Inhibitors/therapeutic use ; Safety ; Spores/chemistry ; Treatment Outcome ; },
abstract = {BACKGROUND: Current treatments for functional dyspepsia have limited efficacy or present safety issues. We aimed to assess spore-forming probiotics in functional dyspepsia as monotherapy or add-on therapy to long-term treatment with proton-pump inhibitors.<br><br>METHODS: In this single-centre, randomised, double-blind, placebo-controlled pilot trial that took place at University Hospitals Leuven (Leuven, Belgium), adult patients (&#x2265;18 years) with functional dyspepsia (as defined by Rome IV criteria, on proton-pump inhibitors or off proton-pump inhibitors) were randomly assigned (1:1) via computer-generated blocked lists, stratified by proton-pump inhibitor status, to receive 8 weeks of treatment with probiotics (Bacillus coagulans MY01 and Bacillus subtilis MY02, 2&#xb7;5&#x2009;&#xd7;&#x2009;10[9] colony-forming units per capsule) or placebo consumed twice per day, followed by an open-label extension phase of 8 weeks. Individuals with a history of abdominal surgery, diabetes, coeliac or inflammatory bowel disease, active psychiatric conditions, and use of immunosuppressant drugs, antibiotics, or probiotics in the past 3 months were excluded. All patients and on-site study personnel were masked to treatment allocation in the first 8 weeks. Symptoms, immune activation, and faecal microbiota were assessed and recorded. The primary endpoint was a decrease of at least 0&#xb7;7 in the postprandial distress syndrome (PDS) score of the Leuven Postprandial Distress Scale in patients with a baseline PDS score of 1 or greater (at least mild symptoms), assessed in the intention-to-treat population. This study is registered with ClinicalTrials.gov, NCT04030780.<br><br>FINDINGS: Between June 3, 2019, and March 11, 2020, of 93 individuals assessed for eligibility, we included 68 patients with functional dyspepsia (51 [75%] women, mean age 40&#xb7;1 years [SD 14&#xb7;4], 34 [50%] on proton-pump inhibitors). We randomly assigned 32 participants to probiotics and 36 to placebo. The proportion of clinical responders was higher with probiotics (12 [48%] of 25) than placebo (six [20%] of 30; relative risk 1&#xb7;95 [95% CI 1&#xb7;07-4&#xb7;11]; p=0&#xb7;028). The number of patients with adverse events was similar with probiotics (five [16%] of 32) and placebo (12 [33%] of 36). Two serious adverse events occurring during the open-label phase (appendicitis and syncope in two separate patients) were assessed as unlikely to be related to the study product.<br><br>INTERPRETATION: In this exploratory study, B coagulans MY01 and B subtilis MY02 were efficacious and safe in the treatment of functional dyspepsia. Participants had potentially beneficial immune and microbial changes, which could provide insights into possible underlying mechanisms as future predictors or treatment targets.<br><br>FUNDING: MY HEALTH.},
}
@article {pmid34356506,
year = {2021},
author = {Bapteste, E and Gérard, P and Larose, C and Blouin, M and Not, F and Campos, L and Aïdan, G and Selosse, MA and Adénis, MS and Bouchard, F and Dutreuil, S and Corel, E and Vigliotti, C and Huneman, P and Lapointe, FJ and Lopez, P},
title = {The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View.},
journal = {Biology},
volume = {10},
number = {7},
pages = {},
pmid = {34356506},
issn = {2079-7737},
support = {REVMICNAT//Centre National de la Recherche Scientifique/ ; },
abstract = {Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appear as novel major biological players, offer new artistic frontiers, new uses from medicine to laws, and inspire novel ontologies. We identify several convergent emerging themes across ecosystem studies, microbial and evolutionary ecology, arts, medicine, forensic analyses, law and philosophy of science, as well as some outstanding issues raised by microbiome studies across these disciplines and practices. An 'epistemic revolution induced by microbiome studies' seems to be ongoing, characterized by four features: (i) an ecologization of pre-existing concepts within disciplines, (ii) a growing interest in systemic analyses of the investigated or represented phenomena and a greater focus on interactions as their root causes, (iii) the intent to use openly multi-scalar interaction networks as an explanatory framework to investigate phenomena to acknowledge the causal effects of microbiomes, (iv) a reconceptualization of the usual definitions of which individuals are worth considering as an explanans or as an explanandum by a given field, which result in a fifth strong trend, namely (v) a de-anthropocentrification of our perception of the world.},
}
@article {pmid34354050,
year = {2021},
author = {Cheng, SP and Jia, KH and Liu, H and Zhang, RG and Li, ZC and Zhou, SS and Shi, TL and Ma, AC and Yu, CW and Gao, C and Cao, GL and Zhao, W and Nie, S and Guo, JF and Jiao, SQ and Tian, XC and Yan, XM and Bao, YT and Yun, QZ and Wang, XZ and Porth, I and El-Kassaby, YA and Wang, XR and Li, Z and Van de Peer, Y and Mao, JF},
title = {Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger.},
journal = {Horticulture research},
volume = {8},
number = {1},
pages = {188},
pmid = {34354050},
issn = {2662-6810},
support = {31600527//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.},
}
@article {pmid34353114,
year = {2021},
author = {Czajkowski, R and Rabalski, L and Kosinski, M and de Neergaard, E and Harding, S},
title = {High-Quality Complete Genome Resource of Pathogenic Bacterium Pectobacterium atrosepticum Strain Green1 Isolated from Potato (Solanum tuberosum L.) in Greenland.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {34},
number = {11},
pages = {1328-1333},
doi = {10.1094/MPMI-06-21-0130-A},
pmid = {34353114},
issn = {0894-0282},
mesh = {Greenland ; *Pectobacterium/genetics ; Plant Diseases ; *Solanum tuberosum ; },
abstract = {Pectobacterium atrosepticum is a narrow-host-range, pectinolytic, plant-pathogenic bacterium causing blackleg of potato (Solanum tuberosum L.) worldwide. Till present, several P. atrosepticum genomes have been sequenced and characterized in detail; however, all of these genomes have come from P. atrosepticum isolates from plants grown in temperate zones, not from hosts cultivated under different climatic conditions. Herewith, we present the first complete, high-quality genome of the P. atrosepticum strain Green1 isolated from potato plants grown under a subarctic climate in Greenland. The genome of P. atrosepticum strain Green1 consists of one chromosome of 4,959,719 bp, with a GC content of 51% and no plasmids. The genome contains 4,531 annotated features, including 4,179 protein-coding genes, 22 ribosomal RNA genes, 70 transfer RNA genes, 8 noncoding RNA genes, 2 CRISPRs, and 126 pseudogenes. We believe that the information in this first high-quality, complete, closed genome of P. atrosepticum strains isolated from host plants grown in a subarctic agricultural region will provide resources for comparative genomic studies and for analyses targeting climatic adaptation and ecological fitness mechanisms present in P. atrosepticum.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
}
@article {pmid34351469,
year = {2022},
author = {Vora, SM and Ankati, S and Patole, C and Podile, AR and Archana, G},
title = {Alterations of Primary Metabolites in Root Exudates of Intercropped Cajanus cajan-Zea mays Modulate the Adaptation and Proteome of Ensifer (Sinorhizobium) fredii NGR234.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1008-1025},
pmid = {34351469},
issn = {1432-184X},
mesh = {*Cajanus ; Exudates and Transudates ; *Fabaceae/microbiology ; Proteome/metabolism ; *Rhizobium ; *Sinorhizobium fredii/metabolism ; Zea mays/microbiology ; },
abstract = {Legume-cereal intercropping systems, in the context of diversity, ecological function, and better yield have been widely studied. Such systems enhance nutrient phytoavailability by balancing root-rhizosphere interactions. Root exudates (RE) play an important role in the rhizospheric interactions of plant-plant and/or plant-microbiome interaction. However, the influence of the primary metabolites of RE on plant-rhizobia interactions in a legume-cereal intercrop system is not known. To understand the plant communication with rhizobia, Cajanus cajan-Zea mays intercropped plants and the broad host range legume nodulating Ensifer fredii NGR234 as the model plants and rhizobium used respectively. A metabolomics-based approach revealed a clear separation between intercropped and monocropped RE of the two plants. Intercropped C. cajan showed an increase in the myo-inositol, and proline, while intercropped Z. mays showed enhanced galactose, D-glucopyranoside, and arginine in the RE. Physiological assays of NGR234 with the RE of intercropped C. cajan exhibited a significant enhancement in biofilm formation, while intercropped Z. mays RE accelerated the bacterial growth in the late log phase. Further, using label-free proteomics, we identified a total of 2570 proteins of NGR234 covering 50% annotated protein sequences upon exposure to Z. mays RE. Furthermore, intercropped Z. mays RE upregulated bacterioferritin comigratory protein (BCP), putative nitroreductase, IlvD, LeuC, D (branched-chain amino acid proteins), and chaperonin proteins GroEL2. Identification offered new insights into the metabolome of the legume-cereal intercrop and proteome of NGR234-Z. mays interactions that underline the new molecular candidates likely to be involved in the fitness of rhizobium in the intercropping system.},
}
@article {pmid34349744,
year = {2021},
author = {Gresse, R and Chaucheyras-Durand, F and Garrido, JJ and Denis, S and Jiménez-Marín, A and Beaumont, M and Van de Wiele, T and Forano, E and Blanquet-Diot, S},
title = {Pathogen Challenge and Dietary Shift Alter Microbiota Composition and Activity in a Mucin-Associated in vitro Model of the Piglet Colon (MPigut-IVM) Simulating Weaning Transition.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {703421},
pmid = {34349744},
issn = {1664-302X},
abstract = {Enterotoxigenic Escherichia coli (ETEC) is the principal pathogen responsible for post-weaning diarrhea in newly weaned piglets. Expansion of ETEC at weaning is thought to be the consequence of various stress factors such as transient anorexia, dietary change or increase in intestinal inflammation and permeability, but the exact mechanisms remain to be elucidated. As the use of animal experiments raise more and more ethical concerns, we used a recently developed in vitro model of piglet colonic microbiome and mucobiome, the MPigut-IVM, to evaluate the effects of a simulated weaning transition and pathogen challenge at weaning. Our data suggested that the tested factors impacted the composition and functionality of the MPigut-IVM microbiota. The simulation of weaning transition led to an increase in relative abundance of the Prevotellaceae family which was further promoted by the presence of the ETEC strain. In contrast, several beneficial families such as Bacteroidiaceae or Ruminococcaceae and gut health related short chain fatty acids like butyrate or acetate were reduced upon simulated weaning. Moreover, the incubation of MPigut-IVM filtrated effluents with porcine intestinal cell cultures showed that ETEC challenge in the in vitro model led to an increased expression of pro-inflammatory genes by the porcine cells. This study provides insights about the etiology of a dysbiotic microbiota in post-weaning piglets.},
}
@article {pmid34347817,
year = {2021},
author = {Menden-Deuer, S and Rowlett, J and Nursultanov, M and Collins, S and Rynearson, T},
title = {Biodiversity of marine microbes is safeguarded by phenotypic heterogeneity in ecological traits.},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0254799},
pmid = {34347817},
issn = {1932-6203},
mesh = {Aquatic Organisms/*physiology ; Bacteria/*metabolism ; *Biodiversity ; Computer Simulation ; Phenotype ; },
abstract = {Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both phenomena by investigating a non-cooperative game that interpolates between individual-level competitions and species-level outcomes. We identified all equilibrium strategies of the game. These strategies represent the probability distribution of competitive abilities (e.g. traits) and are characterized by maximal phenotypic heterogeneity. They are also neutral towards each other in the sense that an unlimited number of species can co-exist while competing according to the equilibrium strategies. Whereas prior theory predicts that natural selection would minimize trait variation around an optimum value, here we obtained a mathematical proof that species with maximally variable traits are those that endure. This discrepancy may reflect a disparity between predictions from models developed for larger organisms in contrast to our microbe-centric model. Rigorous mathematics proves that phenotypic heterogeneity is itself a mechanistic underpinning of microbial diversity. This discovery has fundamental ramifications for microbial ecology and may represent an adaptive reservoir sheltering biodiversity in changing environmental conditions.},
}
@article {pmid34347524,
year = {2021},
author = {Kim, T and Behrens, S and LaPara, TM},
title = {Direct Evidence for Deterministic Assembly of Bacterial Communities in Full-Scale Municipal Wastewater Treatment Facilities.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {20},
pages = {e0108621},
pmid = {34347524},
issn = {1098-5336},
mesh = {Bacteria ; Bioreactors/*microbiology ; Microbiota ; Wastewater/*microbiology ; Water Purification ; },
abstract = {In this study, we investigated whether bacterial community composition in full-scale wastewater treatment bioreactors can be better explained by niche- or neutral-based theory (deterministic or stochastic) and whether bioreactor design (continuous flow versus fill and draw) affected community assembly. Four wastewater treatment facilities (one with quadruplicated continuous-flow bioreactors, two with one continuous-flow bioreactor each, and one with triplicate fill-and-draw bioreactors) were investigated. Bioreactor community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Replicate bioreactors at the same wastewater treatment facility had largely reproducible (i.e., deterministic) bacterial community composition, although bacterial community composition in continuous-flow bioreactors was significantly more reproducible (P < 0.001) than in fill-and-draw bioreactors (Bray-Curtis dissimilarity, μ = 0.48 ± 0.06 versus 0.58 ± 0.08). Next, we compared our results to previously used indirect methods for distinguishing between deterministic and stochastic community assembly mechanisms. Synchronicity was observed in the bacterial community composition among bioreactors within the same metropolitan region, consistent with deterministic community assembly. Similarly, a null model-based analysis also indicated that all wastewater bioreactor communities were controlled by deterministic factors and that continuous-flow bioreactors were significantly more deterministic (P < 0.001) than fill-and-draw bioreactors (nearest-taxon index, μ = 3.8 ± 0.6 versus 2.7 ± 0.8). Our results indicate that bacterial community composition in wastewater treatment bioreactors is better explained by deterministic community assembly theory; simultaneously, our results validate previously used but indirect methods to quantify whether microbial communities were assembled via deterministic or stochastic mechanisms. IMPORTANCE Understanding the mechanisms of bacterial community assembly is one of the grand challenges of microbial ecology. In environmental systems, this challenge is exacerbated because replicate experiments are typically impossible; that is, microbial ecologists cannot fabricate multiple field-scale experiments of identical, natural ecosystems. Our results directly demonstrate that deterministic mechanisms are more prominent than stochastic mechanisms in the assembly of wastewater treatment bioreactor communities. Our results also suggest that wastewater treatment bioreactor design is pertinent, such that the imposition of feast-famine conditions (i.e., fill-and-draw bioreactors) nudge bacterial community assembly more toward stochastic mechanisms than the imposition of stringent nutrient limitation (i.e., continuous-flow bioreactors). Our research also validates the previously used indirect methods (synchronous community dynamics and an application of a null model) for characterizing the relative importance of deterministic versus stochastic mechanisms of community assembly.},
}
@article {pmid34347349,
year = {2021},
author = {Bosch, J and Varliero, G and Hallsworth, JE and Dallas, TD and Hopkins, D and Frey, B and Kong, W and Lebre, P and Makhalanyane, TP and Cowan, DA},
title = {Microbial anhydrobiosis.},
journal = {Environmental microbiology},
volume = {23},
number = {11},
pages = {6377-6390},
doi = {10.1111/1462-2920.15699},
pmid = {34347349},
issn = {1462-2920},
mesh = {Adaptation, Physiological ; *Desiccation ; *Eukaryota/metabolism ; Water/metabolism ; },
abstract = {The loss of cellular water (desiccation) and the resulting low cytosolic water activity are major stress factors for life. Numerous prokaryotic and eukaryotic taxa have evolved molecular and physiological adaptions to periods of low water availability or water-limited environments that occur across the terrestrial Earth. The changes within cells during the processes of desiccation and rehydration, from the activation (and inactivation) of biosynthetic pathways to the accumulation of compatible solutes, have been studied in considerable detail. However, relatively little is known on the metabolic status of organisms in the desiccated state; that is, in the sometimes extended periods between the drying and rewetting phases. During these periods, which can extend beyond decades and which we term 'anhydrobiosis', organismal survival could be dependent on a continued supply of energy to maintain the basal metabolic processes necessary for critical functions such as macromolecular repair. Here, we review the state of knowledge relating to the function of microorganisms during the anhydrobiotic state, highlighting substantial gaps in our understanding of qualitative and quantitative aspects of molecular and biochemical processes in desiccated cells.},
}
@article {pmid34346368,
year = {2021},
author = {Tulumello, J and Chabert, N and Rodriguez, J and Long, J and Nalin, R and Achouak, W and Heulin, T},
title = {Rhizobium alamii improves water stress tolerance in a non-legume.},
journal = {The Science of the total environment},
volume = {797},
number = {},
pages = {148895},
doi = {10.1016/j.scitotenv.2021.148895},
pmid = {34346368},
issn = {1879-1026},
mesh = {Dehydration ; Humans ; Plant Roots ; *Rhizobium ; Soil Microbiology ; *Water ; },
abstract = {With the increasing demand for alternative solutions to replace or optimize the use of synthetic fertilizers and pesticides, the inoculation of bacteria that can contribute to the growth and health of plants (PGPR) is essential. The properties classically sought in PGPR are the production of phytohormones and other growth-promoting molecules, and more rarely the production of exopolysaccharides. We compared the effect of two strains of exopolysaccharide-producing Rhizobium alamii on rapeseed grown in a calcareous silty-clay soil under water stress conditions or not. The effect of factors 'water stress' and 'inoculation' were evaluated on plant growth parameters and the diversity of microbiota associated to root and root-adhering soil compartments. Water stress resulted in a significant decrease in leaf area, shoot biomass and RAS/RT ratio (root-adhering soil/root tissues), as well as overall beta-diversity. Inoculation with R. alamii YAS34 and GBV030 under water-stress conditions produced the same shoot dry biomass compared to uninoculated treatment in absence of water stress, and both strains increased shoot biomass under water-stressed conditions (+7% and +15%, respectively). Only R. alamii GBV030 significantly increased shoot biomass under unstressed or water-stressed conditions compared to the non-inoculated control (+39% and +15%, respectively). Alpha-diversity of the root-associated microbiota after inoculation with R. alamii YAS34 was significantly reduced. Beta-diversity was significantly modified after inoculation with R. alamii GBV030 under unstressed conditions. LEfSe analysis identified characteristic bacterial families, Flavobacteriaceae and Comamonadaceae, in the RT and RAS compartments for the treatment inoculated by R. alamii GBV030 under unstressed conditions, as well as Halomonadaceae (RT) and several species belonging to Actinomycetales (RAS). We showed that R. alamii GBV030 had a PGPR effect on rapeseed growth, increasing its tolerance to water stress, probably involving its capacity to produce exopolysaccharides, and other plant growth-promoting (PGP) traits.},
}
@article {pmid34345962,
year = {2022},
author = {Chaitra, HS and Singh, A and Pandiyan, K and Kalia, VK},
title = {Sex Biased Variance in the Structural and Functional Diversity of the Midgut Bacterial Community of Last Instar Larvae of Pectinophora gossypiella (Lepidoptera: Gelechiidae).},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1112-1122},
pmid = {34345962},
issn = {1432-184X},
mesh = {Animals ; Bacteria/genetics ; Bacterial Proteins ; *Endotoxins ; Female ; Gossypium ; Hemolysin Proteins ; Larva/physiology ; Male ; *Moths/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Elucidating the midgut bacterial diversity in an important cotton bollworm Pectinophora gossypiella can be a stepping stone in understanding the possible role of midgut bacteria in field evolved resistance against Bt cotton as well as to commonly used insecticides. Present study targeted metagenomics of 16S rRNA V3-V4 region to understand the influence of sex, if exists, in community diversity of gut microbes vis a vis their function in pink bollworm larvae. The results of the present study revealed that Proteobacteria, Firmicutes, and Actinobacteria were the predominant phyla in the midgut of pink bollworm. Distinctive differences were found in the Shannon and Simpson diversity indices, ChaoI and ACE richness estimates in male and female larvae. The alpha diversity analysis showed that the gut bacteria of male were diverse and rich as compared to that of female. Further, beta diversity analysis indicated that the gut bacterial communities of both larval groups were unique from each other. These findings are the maiden report on sex-based variation in gut bacteria in P. gossypiella larvae. Role of candidate phyla OD1 (Parcubacteria) and TM7 (Saccharibacteria) in the living organisms needs to be studied, and their fairly significant composition in male and negligible composition in female larva raises question on their obvious role. Taxonomic to phenotypic mapping revealed that these gut bacteria play vital role in many metabolic and physiological activities of pink bollworm. Difference in potential functions of gut bacteria also varied with the sex.},
}
@article {pmid34342700,
year = {2022},
author = {Chen, H and Verplaetse, E and Jauslin, T and Cosson, P and Slamti, L and Lereclus, D},
title = {The Fate of Bacteria of the Bacillus cereus Group in the Amoeba Environment.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1088-1104},
pmid = {34342700},
issn = {1432-184X},
mesh = {*Amoeba ; *Bacillus ; *Bacillus anthracis/genetics ; Bacillus cereus/genetics ; *Bacillus thuringiensis ; Soil ; },
abstract = {The Bacillus cereus sensu lato group consists of several closely related species, including B. anthracis, B. cereus sensu stricto, and B. thuringiensis. Spores of these pathogenic bacteria are commonly found in the soil but evidence suggests that they are unable to grow in such a natural environment in the absence of nutrient input. Amoebas have been reported to be an amplifier for several species of pathogenic bacteria and their potential involvement to explain the large amount of B. thuringiensis and B. cereus spores in soil has been frequently proposed. Here, we studied the fate of Bacillus and amoebas when cultured together. We show that the virulence factors produced by B. thuringiensis and B. cereus do not affect the amoeba Acanthamoeba castellanii, which, on the contrary, can phagocytose and effectively digest vegetative Bacillus cells to grow and prevent the formation of cysts. Bacterial spores can germinate in the amoeba environment and the vegetative cells can then form chains or aggregates that appear to be less efficiently phagocyted by the amoeba. The use of transcriptional fusions between fluorescent reporter genes and stationary phase- and sporulation-specific promoters showed that the sporulation process occurs more efficiently in the presence of amoebas than in their absence. Moreover, our results showed the amoeba environment to promote spore germination and allow the bacteria to complete their developmental cycle. Overall, this study suggests that the amoeba-Bacillus interaction creates a virtuous circle in which each protagonist helps the other to develop.},
}
@article {pmid34342699,
year = {2022},
author = {Ke, L and Yan, WY and Zhang, LZ and Zeng, ZJ and Evans, JD and Huang, Q},
title = {Honey Bee Habitat Sharing Enhances Gene Flow of the Parasite Nosema ceranae.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1105-1111},
pmid = {34342699},
issn = {1432-184X},
mesh = {Animals ; Bees ; Ecosystem ; Gene Flow ; *Nosema/genetics ; *Parasites ; },
abstract = {Host-parasite co-evolution is a process of reciprocal, adaptive genetic change. In natural conditions, parasites can shift to other host species, given both host and parasite genotypes allow this. Even though host-parasite co-evolution has been extensively studied both theoretically and empirically, few studies have focused on parasite gene flow between native and novel hosts. Nosema ceranae is a native parasite of the Asian honey bee Apis cerana, which infects epithelial cells of mid-guts. This parasite successfully switched to the European honey bee Apis mellifera, where high virulence has been reported. In this study, we used the parasite N. ceranae and both honey bee species as model organisms to study the impacts of two-host habitat sharing on parasite diversity and virulence. SNVs (Single Nucleotide Variants) were identified from parasites isolated from native and novel hosts from sympatric populations, as well as novel hosts from a parapatric population. Parasites isolated from native hosts showed the highest levels of polymorphism. By comparing the parasites isolated from novel hosts between sympatric and parapatric populations, habitat sharing with the native host significantly enhanced parasite diversity, suggesting there is continuing gene flow of parasites between the two host species in sympatric populations.},
}
@article {pmid34342698,
year = {2022},
author = {Jan, B and Reshi, ZA and Mohiddin, FA},
title = {Site and Organ-Specific Culture-Dependent Endophytic Diversity of Crocus sativus L. (Saffron) in Kashmir Himalaya, India.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {989-1006},
pmid = {34342698},
issn = {1432-184X},
mesh = {Bacteria ; *Crocus/genetics/microbiology ; DNA, Ribosomal/genetics ; Endophytes ; Phylogeny ; },
abstract = {The endophytic diversity of a host plant has been shown to vary across various spatio-temporal scales and between different organs of a plant, but no such study has been carried out on the economically important plant Crocus sativus (saffron). To fill this knowledge gap, the present study was undertaken to document the diversity of culturable bacterial, actinomycete and fungal endophytes at multiple sites from vegetative and reproductive organs of C. sativus. A total of 1170 culturable endophytic isolates were recovered from 6480 tissue segments of C. sativus collected from six different study sites in Pampore region of Kashmir valley in India. These isolates were identified using 16S and ITS (internal transcribed spacer) rDNA barcode sequence analysis and were classified into 84 operational taxonomic units (OTUs), including 52 bacterial OTUs, 7 actinomycete OTUs and 25 fungal OTUs. The phylogenetic analysis of sequences separated them into four phyla, namely, Firmicutes (46%), Ascomycota (30%), Proteobacteria (16%) and Actinobacteria (8%). Significant differences were observed in the diversity of endophytic assemblages across various study sites and different plant organs (P ≤ 0.001). Species richness was highest at the Baroosa site and lowest at the Chandhar site while the Shannon index was highest at the Baroosa site and lowest at the Letpur site. Among organs, species richness was highest in stigma and lowest in leaf. Similarly, Shannon index was highest for root and lowest for leaf. Further, 15 culturable endophytic OTUs showed organ specificity. The present study is the first comprehensive report that not only brings out differences in the diversity of endophytes associated with different organs and at different sites but also highlights the complexity of host-endophyte interaction at multiple scales.},
}
@article {pmid34340552,
year = {2021},
author = {Munoz-Munoz, J and Ndeh, D and Fernandez-Julia, P and Walton, G and Henrissat, B and Gilbert, HJ},
title = {Sulfation of Arabinogalactan Proteins Confers Privileged Nutrient Status to Bacteroides plebeius.},
journal = {mBio},
volume = {12},
number = {4},
pages = {e0136821},
pmid = {34340552},
issn = {2150-7511},
support = {/WT_/Wellcome Trust/United Kingdom ; WT097907MA/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Bacteroides/enzymology/genetics/growth &amp; development/*metabolism ; Dietary Carbohydrates/metabolism ; Gastrointestinal Microbiome/physiology ; Mucoproteins/*metabolism ; Nutrients/*metabolism ; Plant Proteins/metabolism ; Polysaccharide-Lyases/genetics/metabolism ; Polysaccharides/metabolism ; Sulfatases/*metabolism ; },
abstract = {The human gut microbiota (HGM) contributes to the physiology and health of its host. The health benefits provided by dietary manipulation of the HGM require knowledge of how glycans, the major nutrients available to this ecosystem, are metabolized. Arabinogalactan proteins (AGPs) are a ubiquitous feature of plant polysaccharides available to the HGM. Although the galactan backbone and galactooligosaccharide side chains of AGPs are conserved, the decorations of these structures are highly variable. Here, we tested the hypothesis that these variations in arabinogalactan decoration provide a selection mechanism for specific Bacteroides species within the HGM. The data showed that only a single bacterium, B. plebeius, grew on red wine AGP (Wi-AGP) and seaweed AGP (SW-AGP) in mono- or mixed culture. Wi-AGP thus acts as a privileged nutrient for a Bacteroides species within the HGM that utilizes marine and terrestrial plant glycans. The B. plebeius polysaccharide utilization loci (PULs) upregulated by AGPs encoded a polysaccharide lyase, located in the enzyme family GH145, which hydrolyzed Rha-Glc linkages in Wi-AGP. Further analysis of GH145 identified an enzyme with two active sites that displayed glycoside hydrolase and lyase activities, respectively, which conferred substrate flexibility for different AGPs. The AGP-degrading apparatus of B. plebeius also contained a sulfatase, BpS1_8, active on SW-AGP and Wi-AGP, which played a pivotal role in the utilization of these glycans by the bacterium. BpS1_8 enabled other Bacteroides species to access the sulfated AGPs, providing a route to introducing privileged nutrient utilization into probiotic and commensal organisms that could improve human health. IMPORTANCE Dietary manipulation of the HGM requires knowledge of how glycans available to this ecosystem are metabolized. The variable structures that decorate the core component of plant AGPs may influence their utilization by specific organisms within the HGM. Here, we evaluated the ability of Bacteroides species to utilize a marine and terrestrial AGP. The data showed that a single bacterium, B. plebeius, grew on Wi-AGP and SW-AGP in mono- or mixed culture. Wi-AGP is thus a privileged nutrient for a Bacteroides species that utilizes marine and terrestrial plant glycans. A key component of the AGP-degrading apparatus of B. plebeius is a sulfatase that conferred the ability of the bacterium to utilize these glycans. The enzyme enabled other Bacteroides species to access the sulfated AGPs, providing a route to introducing privileged nutrient utilization into probiotic and commensal organisms that could improve human health.},
}
@article {pmid34340550,
year = {2021},
author = {Goordial, J and D'Angelo, T and Labonté, JM and Poulton, NJ and Brown, JM and Stepanauskas, R and Früh-Green, GL and Orcutt, BN},
title = {Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif.},
journal = {mBio},
volume = {12},
number = {4},
pages = {e0049021},
pmid = {34340550},
issn = {2150-7511},
mesh = {Genomics ; Geologic Sediments/*microbiology ; Microbiota/*genetics ; *Oceans and Seas ; },
abstract = {The marine lithospheric subsurface is one of the largest biospheres on Earth; however, little is known about the identity and ecological function of microorganisms found in low abundance in this habitat, though these organisms impact global-scale biogeochemical cycling. Here, we describe the diversity and metabolic potential of sediment and endolithic (within rock) microbial communities found in ultrasmall amounts (10[1] to 10[4] cells cm[-3]) in the subsurface of the Atlantis Massif, an oceanic core complex on the Mid-Atlantic Ridge that was sampled on International Ocean Discovery Program (IODP) Expedition 357. This study used fluorescence-activated cell sorting (FACS) to enable the first amplicon, metagenomic, and single-cell genomic study of the shallow (<20 m below seafloor) subsurface of an actively serpentinizing marine system. The shallow subsurface biosphere of the Atlantis Massif was found to be distinct from communities observed in the nearby Lost City alkaline hydrothermal fluids and chimneys, yet similar to other low-temperature, aerobic subsurface settings. Genes associated with autotrophy were rare, although heterotrophy and aerobic carbon monoxide and formate cycling metabolisms were identified. Overall, this study reveals that the shallow subsurface of an oceanic core complex hosts a biosphere that is not fueled by active serpentinization reactions and by-products. IMPORTANCE The subsurface rock beneath the ocean is one of the largest biospheres on Earth, and microorganisms within influence global-scale nutrient cycles. This biosphere is difficult to study, in part due to the low concentrations of microorganisms that inhabit the vast volume of the marine lithosphere. In spite of the global significance of this biosphere, little is currently known about the microbial ecology of such rock-associated microorganisms. This study describes the identity and genomic potential of microorganisms in the subsurface rock and sediment at the Atlantis Massif, an underwater mountain near the Mid-Atlantic Ridge. To enable our analyses, fluorescence-activated cell sorting (FACS) was used as a means to concentrate cells from low biomass environmental samples for genomic analyses. We found distinct rock-associated microorganisms and found that the capacity for microorganisms to utilize organic carbon was the most prevalent form of carbon cycling. We additionally identified a potential role for carbon monoxide metabolism in the subsurface.},
}
@article {pmid34339990,
year = {2022},
author = {Zhang, S and Lu, J and Wang, Y and Verstraete, W and Yuan, Z and Guo, J},
title = {Insights of metallic nanoparticles and ions in accelerating the bacterial uptake of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {421},
number = {},
pages = {126728},
doi = {10.1016/j.jhazmat.2021.126728},
pmid = {34339990},
issn = {1873-3336},
mesh = {Acinetobacter/genetics ; Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Humans ; *Ions/toxicity ; *Metal Nanoparticles/toxicity ; },
abstract = {The increasing release of nanomaterials has attracted significant concerns for human and environmental health. Similarly, the dissemination of antimicrobial resistance (AMR) is a global health crisis affecting approximately 700,000 people a year. However, a knowledge gap persists between the spread of AMR and nanomaterials. This study aims to fill this gap by investigating whether and how nanomaterials could directly facilitate the dissemination of AMR through horizontal gene transfer. Our results show that commonly-used nanoparticles (NPs) (Ag, CuO and ZnO NPs) and their ion forms (Ag[+], Cu[2+] and Zn[2+]) at realistic concentrations within aquatic environments can significantly promote the transformation of extracellular antibiotic resistance genes in Acinetobacter baylyi ADP1 by a factor of 11.0-folds, which is comparable to the effects of antibiotics. The enhanced transformation by Ag NPs/Ag[+] and CuO NPs/Cu[2+] was primarily associated with the overproduction of reactive oxygen species and cell membrane damage. ZnO NPs/Zn[2+] might increase the natural transformation rate by stimulating the stress response and ATP synthesis. All tested NPs/ions resulted in upregulating the competence and SOS response-associated genes. These findings highlight a new concern that nanomaterials can speed up the spread of AMR, which should not be ignored when assessing the holistic risk of nanomaterials.},
}
@article {pmid34339704,
year = {2022},
author = {Torun, F and Hostins, B and De Schryver, P and Boon, N and De Vrieze, J},
title = {Molybdate effectively controls sulphide production in a shrimp pond model.},
journal = {Environmental research},
volume = {203},
number = {},
pages = {111797},
doi = {10.1016/j.envres.2021.111797},
pmid = {34339704},
issn = {1096-0953},
mesh = {Animals ; *Geologic Sediments ; Molybdenum ; *Ponds ; Seawater ; Sulfides ; },
abstract = {The production of shrimp is often performed in earthen outdoor ponds in which the high input of feed and faeces on the bottom can result in deterioration of the water quality, which negatively impacts the animals and the environment. Here, we investigate the potential of sodium molybdate (Na2MoO4·2H2O), sodium nitrate (NaNO3) and sodium percarbonate (Na2CO3·1.5H2O2) to control sulphide production in a simulated shrimp pond bottom system that included the sediment, overlaying artificial seawater and organic matter input in the form of shrimp feed and shrimp faeces. Sediment depth gradient measurements of oxygen, H2S and pH were obtained during 7 days of incubation using microelectrodes. The most significant impact in terms of H2S, was observed for 50 mg/L sodium molybdate. At the water-sediment interface, there was up to 73% less H2S detected for this treatment in comparison to a control treatment, while in the deeper layers of the sediment it was up to 47% less H2S. The residual sulphate concentrations in the molybdate treated samples were 16 ± 4% higher than the control, indicating an inhibition in sulphate reduction. Nitrate and sodium percarbonate treatments also showed a limited capacity to decrease H2S entering in the water column, yet no clear difference in H2S concentrations in the sediment compared to the control were observed. Molybdate treatment appears to work through the inhibition of sulphate reducing bacteria in situ for the control of H2S production better than the chemical oxygen boosters or nitrate treatment.},
}
@article {pmid34339295,
year = {2021},
author = {Göing, S and Gasperotti, AF and Yang, Q and Defoirdt, T and Jung, K},
title = {Insights into a Pyruvate Sensing and Uptake System in Vibrio campbellii and Its Importance for Virulence.},
journal = {Journal of bacteriology},
volume = {203},
number = {20},
pages = {e0029621},
pmid = {34339295},
issn = {1098-5530},
mesh = {Animals ; Artemia/microbiology ; Bacterial Proteins/genetics/metabolism ; Biological Transport ; Carrier Proteins/genetics/*metabolism ; Culture Media/chemistry ; Gene Expression Regulation, Bacterial ; Genotype ; Larva/microbiology ; Pyruvic Acid/chemistry/*metabolism ; Vibrio/genetics/*metabolism/*pathogenicity ; Virulence ; },
abstract = {Pyruvate is a key metabolite in living cells and has been shown to play a crucial role in the virulence of several bacterial pathogens. The bioluminescent Vibrio campbellii, a severe infectious burden for marine aquaculture, excretes extraordinarily large amounts of pyruvate during growth and rapidly retrieves it by an as-yet-unknown mechanism. We have now identified the responsible pyruvate transporter, here named BtsU, and our results show that it is the only pyruvate transporter in V. campbellii. Expression of btsU is tightly regulated by the membrane-integrated LytS-type histidine kinase BtsS, a sensor for extracellular pyruvate, and the LytTR-type response regulator BtsR. Cells lacking either the pyruvate transporter or sensing system show no chemotactic response toward pyruvate, indicating that intracellular pyruvate is required to activate the chemotaxis system. Moreover, pyruvate sensing and uptake were found to be important for the resuscitation of V. campbellii from the viable but nonculturable state and the bacterium's virulence against brine shrimp larvae. IMPORTANCE Bacterial infections are a serious threat to marine aquaculture, one of the fastest growing food sectors on earth. Therefore, it is extremely important to learn more about the pathogens responsible, one of which is Vibrio campbellii. This study sheds light on the importance of pyruvate sensing and uptake for V. campbellii, and reveals that the bacterium possesses only one pyruvate transporter, which is activated by a pyruvate-responsive histidine kinase/response regulator system. Without the ability to sense or take up pyruvate, the virulence of V. campbellii toward gnotobiotic brine shrimp larvae is strongly reduced.},
}
@article {pmid34338516,
year = {2021},
author = {Tang, JS and Cait, A and Li, Y and Abolins-Thompson, H and Gell, K and Herst, PM and O'Sullivan, D and Gasser, O},
title = {Practical Approach To Explore the Effects of Polyphenols on Aryl Hydrocarbon Receptor Regulated Immune Function.},
journal = {Journal of agricultural and food chemistry},
volume = {69},
number = {31},
pages = {8625-8633},
doi = {10.1021/acs.jafc.1c02095},
pmid = {34338516},
issn = {1520-5118},
mesh = {Humans ; *Immunity ; Ligands ; *Polyphenols/pharmacology ; *Receptors, Aryl Hydrocarbon/genetics ; Tryptophan ; },
abstract = {The ligand-activated aryl hydrocarbon receptor (AhR) is an important molecular regulator of immune function, whose activity can be modulated by dietary glucosinolate- and tryptophan-derived metabolites. In contrast, the potential use of polyphenols as dietary regulators of AhR-dependent immunity remains unclear. In this perspective, we discuss how cellular metabolism may alter the net effect of polyphenols on AhR, thus potentially reconciling some of the conflicting observations reported in the literature. We further provide a methodological roadmap, across the fields of immunology, metabolomics, and gut microbial ecology, to explore the potential effects of polyphenol-rich diets on AhR-regulated immune function in humans.},
}
@article {pmid34335540,
year = {2021},
author = {Zhang, J and Zeng, R and Labes, A},
title = {Editorial: Marine Microbial-Derived Molecules and Their Potential Medical and Cosmetic Applications.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {706152},
doi = {10.3389/fmicb.2021.706152},
pmid = {34335540},
issn = {1664-302X},
}
@article {pmid34333553,
year = {2022},
author = {Howard, MM and Bass, E and Chautá, A and Mutyambai, D and Kessler, A},
title = {Integrating plant-to-plant communication and rhizosphere microbial dynamics: ecological and evolutionary implications and a call for experimental rigor.},
journal = {The ISME journal},
volume = {16},
number = {1},
pages = {5-9},
pmid = {34333553},
issn = {1751-7370},
mesh = {Plant Roots ; Plants ; *Rhizosphere ; *Soil Microbiology ; },
abstract = {The perception of airborne chemical signals by plants can trigger reconfigurations of their metabolism that alter their biotic interactions. While plant-to-plant chemical communication has primarily been studied in the context of eliciting defenses to herbivores and pathogens, recent work suggests that it can also affect plants’ interactions with their rhizosphere microbiomes. In this perspective, we discuss the potential for integrating the fields of plant-to-plant communication and microbial ecology to understand the chemical ecology of plant−microbiome interactions. As an introduction for microbial ecologists, we highlight mechanistic knowledge gaps in plant volatile organic compound (VOC) perception and provide recommendations for avoiding common experimental errors that have plagued the plant communication field. Lastly, we discuss potential implications of plant VOCs structuring rhizosphere microbiomes, particularly effects on plant community and evolutionary dynamics. As we continue to discover links between plant metabolism and their microbiomes—from molecular to community scales—we hope that this perspective will provide both motivation and words of caution for researchers working at the intersection of these two fields.},
}
@article {pmid34333428,
year = {2021},
author = {Boada, E and Santos-Clotas, E and Cabrera-Codony, A and Martín, MJ and Bañeras, L and Gich, F},
title = {The core microbiome is responsible for volatile silicon and organic compounds degradation during anoxic lab scale biotrickling filter performance.},
journal = {The Science of the total environment},
volume = {798},
number = {},
pages = {149162},
doi = {10.1016/j.scitotenv.2021.149162},
pmid = {34333428},
issn = {1879-1026},
mesh = {Biodegradation, Environmental ; Bioreactors ; Filtration ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Silicon ; *Volatile Organic Compounds ; },
abstract = {Volatile silicon compounds present in the biogas of anaerobic digesters can cause severe problems in the energy recovery systems, inducing costly damages. Herein, the microbial community of a lab-scale biotrickling filter (BTF) was studied while testing its biodegradation capacity on octamethylcyclotetrasiloxane (D4) and decamethylcyclopentasiloxane (D5), in the presence of toluene, limonene and hexane. The reactor performance was tested at different empty bed residence times (EBRT) and packing materials. Community structure was analysed by bar-coded amplicon sequencing of the 16S rRNA gene. Microbial diversity and richness were higher in the inoculum and progressively decreased during BTF operation (Simpson's diversity index changing from 0.98-0.90 and Richness from 900 to 200 OTUs). Minimum diversity was found when reactor was operated at relatively low EBRT (7.3 min) using a multicomponent feed. The core community was composed of 36 OTUs (accounting for 55% of total sequences). Packing material played a key role in the community structure. Betaproteobacteriales were dominant in the presence of lava rock and were partially substituted by Corynebacteriales and Rhizobiales when activated carbon was added to the BTF. Despite these changes, a stable and resilient core microbiome was selected defining a set of potentially degrading bacteria for siloxane bioremoval as a complementary alternative to non-regenerative adsorption onto activated carbon.},
}
@article {pmid34333046,
year = {2021},
author = {Hunt, KA and Forbes, J and Taub, F and Elliott, N and Hardwicke, J and Petersen, R and Stopnisek, N and Beck, DAC and Stahl, DA},
title = {An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates.},
journal = {Journal of microbiological methods},
volume = {188},
number = {},
pages = {106294},
doi = {10.1016/j.mimet.2021.106294},
pmid = {34333046},
issn = {1872-8359},
mesh = {Bacteria, Anaerobic/*growth &amp; development ; Bacteriological Techniques/instrumentation/*methods ; Data Collection/instrumentation/*methods ; Environmental Monitoring/instrumentation/methods ; *Gases ; High-Throughput Screening Assays ; Kinetics ; Methanococcus/growth &amp; development ; Optical Devices ; Symbiosis ; },
abstract = {Standard methods of monitoring the growth kinetics of anaerobic microorganisms are generally impractical when there is a protracted or indeterminate period of active growth, and when high numbers of samples or replications are required. As part of our studies of the adaptive evolution of a simple anaerobic syntrophic mutualism, requiring the characterization of many isolates and alternative syntrophic pairings, we developed a multiplexed growth monitoring system using a combination of commercially available electronics and custom designed circuitry and materials. This system automatically monitors up to 64 sealed, and as needed pressurized, culture tubes and reports the growth data in real-time through integration with a customized relational database. The utility of this system was demonstrated by resolving minor differences in growth kinetics associated with the adaptive evolution of a simple microbial community comprised of a sulfate reducing bacterium, Desulfovibrio vulgaris, grown in syntrophic association with Methanococcus maripaludis, a hydrogenotrophic methanogen.},
}
@article {pmid34331150,
year = {2021},
author = {de Freitas, F and Vendruscolo, SJ and Soares, MA and Battirola, LD and de Andrade, RLT},
title = {Biomass of the macrophyte remedies and detoxifies Cd(II) and Pb(II) in aqueous solution.},
journal = {Environmental monitoring and assessment},
volume = {193},
number = {8},
pages = {537},
pmid = {34331150},
issn = {1573-2959},
mesh = {Adsorption ; Biomass ; *Cadmium/analysis ; Environmental Monitoring ; Hydrogen-Ion Concentration ; Kinetics ; Lead ; Water ; *Water Pollutants, Chemical/analysis/toxicity ; },
abstract = {Aquatic plants are considered to be important remedial agents in aquatic environments contaminated by metals. The Salvinia biloba macrophyte was evaluated in relation to its removal kinetics, adsorption capacity, and toxicology, aiming at its application in the removal of Cd[+2] and Pb[+2] ions from aqueous solutions. A batch-type system was used, in which the plants were cultivated in microcosms containing nutritive solution and metallic ions, stored in a controlled environment (pH, temperature, and luminosity). The removal kinetics consisted in the analysis of efficiency, varying the concentrations of the metals, and time of cultivation of plants in solution. To describe the process, adsorption isotherms were constructed with the equilibrium data, which were later adjusted to Langmuir and Freundlich models. The toxicological trial was performed by sub-acute exposure test of Caenorhabditis elegans nematode to phytoremediated solutions. The results highlight the remedial effect of the plant in solutions contaminated with both metals. The kinetic study demonstrated that the plant responds differently to metals, and physical-chemical and biological processes can be attributed to the removal of metals from the solution by the plant. The equilibrium time obtained was 48 h for both metals, and the adsorption capacity was higher for Cd[2+]. The toxicological evaluation indicates that there was a reduction in toxicity after the remediation of the solutions by S. biloba, for all times and concentrations evaluated. Salvinia biloba was efficient for the removal of Cd[2+] and Pb[2+] metals from aqueous solution. The plant is a low-cost metal biosorbent and can be considered promising for phytoremediation strategies in liquid effluents and water bodies.},
}
@article {pmid34331071,
year = {2022},
author = {Haydon, TD and Suggett, DJ and Siboni, N and Kahlke, T and Camp, EF and Seymour, JR},
title = {Temporal Variation in the Microbiome of Tropical and Temperate Octocorals.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1073-1087},
pmid = {34331071},
issn = {1432-184X},
mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Biodiversity ; Coral Reefs ; *Gammaproteobacteria/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.},
}
@article {pmid34330907,
year = {2021},
author = {Rahlff, J and Turzynski, V and Esser, SP and Monsees, I and Bornemann, TLV and Figueroa-Gonzalez, PA and Schulz, F and Woyke, T and Klingl, A and Moraru, C and Probst, AJ},
title = {Lytic archaeal viruses infect abundant primary producers in Earth's crust.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {4642},
pmid = {34330907},
issn = {2041-1723},
mesh = {Archaea/classification/*genetics/virology ; Archaeal Viruses/*genetics/metabolism/physiology ; Biofilms/growth &amp; development ; Ecosystem ; Genome, Viral/*genetics ; Genomics/methods ; Host-Pathogen Interactions/genetics ; Lysogeny/genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microscopy, Fluorescence ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Virus Activation/genetics ; },
abstract = {The continental subsurface houses a major portion of life's abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.},
}
@article {pmid34326823,
year = {2021},
author = {Gu, Q and Chen, M and Zhang, J and Guo, W and Wu, H and Sun, M and Wei, L and Wang, J and Wei, X and Zhang, Y and Ye, Q and Xue, L and Pang, R and Ding, Y and Wu, Q},
title = {Genomic Analysis and Stability Evaluation of the Phenol-Degrading Bacterium Acinetobacter sp. DW-1 During Water Treatment.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {687511},
pmid = {34326823},
issn = {1664-302X},
abstract = {Phenol is a toxic organic molecule that is widely detected in the natural environment, even in drinking water sources. Biological methods were considered to be a good tool for phenol removal, especially microbial immobilized technology. However, research on the "seed" bacteria along with microbial community analysis in oligotrophic environment such as drinking water system has not been addressed. In this study, Acinetobacter sp. DW-1 with high phenol degradation ability had been isolated from a drinking water biofilter was used as seeded bacteria to treat phenol micro-polluted drinking water source. Meanwhile, the whole genome of strain DW-1 was sequenced using nanopore technology. The genomic analysis suggests that Acinetobacter sp. DW-1 could utilize phenol via the β-ketoadipate pathway, including the catechol and protocatechuate branches. Subsequently, a bio-enhanced polyhedral hollow polypropylene sphere (BEPHPS) filter was constructed to investigate the stability of the seeded bacteria during the water treatment process. The denatured gradient gel electrophoresis (DGGE) profile and the quantification of phenol hydroxylase gene results indicate that when the BEPHPS filter was operated for 56 days, Acinetobacter sp. was still a persistent and competitive bacterium in the treatment group. In addition, 16S rRNA gene amplicon sequencing results indicate that Acinetobacter sp., as well as Pseudomonas sp., Nitrospira sp., Rubrivivax sp. were the predominant bacteria in the treatment group, which were different from that in the CK group. This study provides a better understanding of the mechanisms of phenol degradation by Acinetobacter sp. DW-1 at the gene level, and provides new insights into the stability of seeded bacteria and its effects on microbial ecology during drinking water treatment.},
}
@article {pmid34324834,
year = {2021},
author = {Christensen, SM and Munkres, I and Vannette, RL},
title = {Nectar bacteria stimulate pollen germination and bursting to enhance microbial fitness.},
journal = {Current biology : CB},
volume = {31},
number = {19},
pages = {4373-4380.e6},
doi = {10.1016/j.cub.2021.07.016},
pmid = {34324834},
issn = {1879-0445},
mesh = {Animals ; Bacteria ; Bees ; Flowers ; *Plant Nectar ; Pollen ; *Pollination/physiology ; },
abstract = {Many organisms consume pollen, yet mechanisms of its digestion remain a fundamental enigma in pollination biology,[1-3] as pollen is protected by a recalcitrant outer shell.[4-8] Pollen is commonly found in floral nectar,[9][,][10] as are nectar microbes, which are nearly ubiquitous among flowers.[11-13] Nectar specialist bacteria, like Acinetobacter, can reach high densities (up to 10[9] cells/mL), despite the fact that floral nectar is nitrogen poor.[14-17] Here, we show evidence that the genus Acinetobacter, prevalent nectar- and bee-associated bacteria,[12][,][18-20] can induce pollen germination and bursting, gain access to protoplasm nutrients, and thereby grow to higher densities. Although induced germination had been suggested as a potential method in macroscopic pollen consumers,[2][,][21-23] and fungal inhibition of pollen germination has been shown,[24-27] direct biological induction of germination has not been empirically documented outside of plants.[28-32]Acinetobacter pollinis SCC477[19] induced over 5× greater pollen germination and 20× greater pollen bursting than that of uninoculated pollen by 45 min. When provided with germinable pollen, A. pollinis stimulates protein release and grows to nearly twice the density compared to growth with ungerminable pollen, indicating that stimulation of germination benefits bacterial fitness. In contrast, a common nectar-inhabiting yeast (Metschnikowia)[33] neither induced nor benefited from pollen germination. We conclude that Acinetobacter both specifically causes and benefits from inducing pollen germination and bursting. Further study of microbe-pollen interactions may inform many aspects of pollination ecology, including floral microbial ecology,[34][,][35] pollinator nutrient acquisition from pollen,[2][,][3][,][21][,][36] and cues of pollen germination for plant reproduction.[37-39].},
}
@article {pmid34320736,
year = {2021},
author = {Rimboud, M and Etcheverry, L and Barakat, M and Achouak, W and Bergel, A and Délia, ML},
title = {Hypersaline microbial fuel cell equipped with an oxygen-reducing microbial cathode.},
journal = {Bioresource technology},
volume = {337},
number = {},
pages = {125448},
doi = {10.1016/j.biortech.2021.125448},
pmid = {34320736},
issn = {1873-2976},
mesh = {*Bioelectric Energy Sources ; Electricity ; Electrodes ; Oxidation-Reduction ; Oxygen ; },
abstract = {Microbial anodes and oxygen reducing microbial cathodes were designed separately under constant polarization at + 0.1 V/SCE in a hypersaline medium (NaCl 45 g/L). They were then associated to design two-compartment microbial fuel cells (MFCs). These MFCs produced up to 209 ± 24 mW m[-2] during a week. This was the first demonstration that hypersaline MFCs equipped with microbial cathodes can produce power density at this level. Desulfuromonas sp. were confirmed to be key species of the anodes. The efficiency of the cathodes was linked to the development of a redox system centred at + 0.2 V/SCE and to the presence of Gammaproteobacteria (Alteromonadales and Oceanospirillales), especially an unclassified order phylogenetically linked to the genus Thioalobacter. Comparing the different performance of the four MFCs with the population analyses suggested that polarization at + 0.1 V/SCE should be maintained longer to promote the growth of Thioalobacter on the cathode and thus increase the MFC performance.},
}
@article {pmid34320208,
year = {2021},
author = {Minnebo, Y and De Paepe, K and Raes, J and de Wiele, TV},
title = {Nutrient load acts as a driver of gut microbiota load, community composition and metabolic functionality in the simulator of the human intestinal microbial ecosystem.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {9},
pages = {},
doi = {10.1093/femsec/fiab111},
pmid = {34320208},
issn = {1574-6941},
mesh = {Fatty Acids, Volatile ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Nutrients ; Verrucomicrobia ; },
abstract = {A recently introduced quantitative framework for gut microbiota analysis indicated that microbial load alterations can be linked to various diseases, making it essential to pinpoint its determinants. We identified nutrient load as a main driver of the quantitative microbial community composition and functionality in vitro by stepwise decreasing standardized feed concentrations from 100% to 33%, 20% and 10% in 5-day intervals. While the proportional composition and metabolic profile were mainly determined by the inter-individual variability (35% and 41%), nutrient load accounted for 58%, 23% and 65% of the observed variation in the microbial load, quantitative composition and net daily metabolite production, respectively. After the 10-fold nutrient reduction, the microbial load decreased by 79.72 ± 9% and 82.96 ± 1.66% in the proximal and distal colon, respectively, while the net total short-chain fatty acid production dropped by 79.42 ± 4.42% and 84.58 ± 2.42%, respectively. The majority of microbial taxa quantitatively decreased, whereas a select group of nutritional specialists, such as Akkermansia muciniphila and Bilophila wadsworthia, and a number of opportunistic pathogens remained unaffected. This shows that nutrient load is an important driver of the human gut microbiome and should be considered in future in vitro and in vivo dietary research.},
}
@article {pmid34313080,
year = {2021},
author = {Zou, WX and Shen, JP and Zhang, LM and Hu, A and Wang, JJ and He, JZ},
title = {Quantitative stable isotope probing technique and its applications in microbial ecology.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {32},
number = {7},
pages = {2615-2622},
doi = {10.13287/j.1001-9332.202107.032},
pmid = {34313080},
issn = {1001-9332},
mesh = {Carbon Isotopes ; DNA ; High-Throughput Nucleotide Sequencing ; Isotope Labeling ; *Microbiota ; },
abstract = {Quantitative stable isotope probing (qSIP) is a powerful tool, which links microbial taxon with functional metabolism in ecosystems and quantitatively determines the metabolic activity or growth rate of individual microbial taxa exposed to isotope tracers in the environment. qSIP technique employs quantitative PCR, high-throughput sequencing and stable isotope probing (SIP) techniques. The procedure involves adding labeled substrates to environmental samples for cultivation, separating labeled heavy fraction from unlabeled light fraction via isopycnic ultracentrifugation, making absolute quantification and sequencing analysis for microbial populations in all fractions, and then quantifying the isotope abundance of DNA involved in uptake and transformation based on the DNA density curve of unlabeled treatment and GC content. Here, we reviewed the rationale, data analysis and application of qSIP in microbial ecology, and discussed the existing problems and prospects of qSIP.},
}
@article {pmid34312710,
year = {2022},
author = {Islam, MS and Sobur, MA and Rahman, S and Ballah, FM and Ievy, S and Siddique, MP and Rahman, M and Kafi, MA and Rahman, MT},
title = {Detection of blaTEM, blaCTX-M, blaCMY, and blaSHV Genes Among Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Migratory Birds Travelling to Bangladesh.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {942-950},
pmid = {34312710},
issn = {1432-184X},
support = {2019/8/BAU//Bangladesh Agricultural University Research System/ ; 2020/28/UGC//University Grants Commission/ ; },
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bangladesh ; Chickens ; *Escherichia coli/genetics ; *Escherichia coli Infections/veterinary ; Humans ; beta-Lactamases/genetics ; },
abstract = {Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli cause severe health hazards. Migratory birds are reservoirs and transmitters of many pathogens including ESBL-producing E. coli. To examine migratory birds as potential carriers of ESBL-producing E. coli and E. coli-carrying antibiotic resistance genes, 55 PCR-positive E. coli isolates were screened using the disk diffusion method, double-disk synergy test, and further polymerase chain reaction (PCR) tests. Genes encoding resistance to tetracycline [tetA, 100% (35/35); tetB, 31.43% (11/35)], fluoroquinolone [qnrA, 35.71% (10/28); qnrB, 25% (7/28)], and streptomycin [aadA1, 90.24% (37/41)] were detected in the isolated E. coli. Of the 55 E. coli isolates, 21 (38.18%) were ESBL producers, and all of them were multidrug resistant. All the ESBL-producing E. coli isolates harbored at least two or more beta-lactamase genes, of which blaTEM, blaCMY, blaCTX-M, and blaSHV were detected in 95.24%, 90.48%, 85.71%, and 42.86% of isolates, respectively. All the beta-lactamase genes were present in four of the ESBL-producing E. coli isolates. Furthermore, 95.24% of ESBL-producing E. coli isolates were positive for one or more antibiotic resistance genes. To the best of our knowledge, this is the first study to detect E. coli-carrying antibiotic resistance genes including beta-lactamase blaCMY and blaSHV originating from migratory birds in Bangladesh. These results suggest that migratory birds are potential carriers of ESBL-producing E. coli along with other clinically important antibiotic resistance genes which may have detrimental impacts on human health.},
}
@article {pmid34312709,
year = {2022},
author = {de Los Ríos, A and Garrido-Benavent, I and Limón, A and Cason, ED and Maggs-Kölling, G and Cowan, D and Valverde, A},
title = {Novel lichen-dominated hypolithic communities in the Namib Desert.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1036-1048},
pmid = {34312709},
issn = {1432-184X},
support = {CTM2015-64728-C2-2-R//(MINECO/FEDER, EU)/ ; PID2019-105469RB-C22//MICINN-AEI/ ; },
mesh = {*Cyanobacteria/genetics ; Desert Climate ; Ecosystem ; *Lichens ; Soil Microbiology ; },
abstract = {The ventral surfaces of translucent rocks from hot desert pavements often harbor hypolithic microbial communities, which are mostly dominated by cyanobacteria. The Namib Desert fog belt supports extensive hypolithic colonization of quartz rocks, which are also colonized by lichens on their dorsal surfaces. Here, we aim to evaluate whether lichens colonize the ventral surface of the rocks (i.e., show hypolithic lifestyle) and compare the bacterial composition of these coastal hypolithic communities with those found inland. Fungal DNA barcoding and fungal and bacterial Illumina metabarcoding were combined with electron microscopy to characterize the composition and spatial structure of hypolithic communities from two (coastal and inland) areas in the Namib Desert. We report, for the first time, the structure and composition of lichen-dominated hypolithic communities found in the coastal zone of the Namib Desert with extensive epilithic lichen cover. Lichen modified areoles with inverted morphology of the genus Stellarangia (three lineages) and Buellia (two lineages) were the main components of these hypolithic communities. Some of these lineages were also found in epilithic habitats. These lichen-dominated hypolithic communities differed in structural organization and bacterial community composition from those found in inland areas. The hypolithic lichen colonization characterized here seems not to be an extension of epilithic or biological soil crust lichen growths but the result of specific sublithic microenvironmental conditions. Moisture derived from fog and dew could be the main driver of this unique colonization.},
}
@article {pmid34312335,
year = {2021},
author = {Wanner, J},
title = {The development in biological wastewater treatment over the last 50 years.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {84},
number = {2},
pages = {274-283},
doi = {10.2166/wst.2021.095},
pmid = {34312335},
issn = {0273-1223},
mesh = {Bioreactors ; Nitrogen ; Phosphorus ; Sewage ; *Waste Disposal, Fluid ; Wastewater ; *Water Purification ; },
abstract = {The paper summarizes the development in the understanding and practical application of the activated sludge process over the last 50 years. Since its invention, the activated sludge process has been a big challenge to design engineers. Traditionally, the technology was covered by sanitary engineers. However, with the development in the understanding of activated sludge process principles, further progress was not possible without knowledge of reaction kinetics and reactor theory. The shift from BOD removal only to combined removal of organic pollution, nitrogen and phosphorus required a chemical engineering approach with outputs of activated sludge microbiology and microbial ecology. Molecular biology enabled more accurate identification of important activated sludge microorganisms. The development in activated sludge process also required more efficient activated sludge separation and thickening. The paper describes the development from secondary clarifiers to membrane separation. Increasing water stress around the globe has also changed the main wastewater paradigm from wastewater treatment and safe discharge to safe reuse.},
}
@article {pmid34311495,
year = {2021},
author = {Pascual, J and Tanner, K and Vilanova, C and Porcar, M and Delgado, A},
title = {The microbial terroir: open questions on the Nagoya protocol applied to microbial resources.},
journal = {Microbial biotechnology},
volume = {14},
number = {5},
pages = {1878-1880},
pmid = {34311495},
issn = {1751-7915},
mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; *Environmental Microbiology ; },
abstract = {The Nagoya Protocol on Access and Benefit-sharing (https://www.cbd.int/abs/), primarily designed for vascular plant and animal resources, is also extended to the use of microbial resources, but its application to the microbiological realm has raised many doubts and provoked criticisms. This is because of the particularities of microbial ecology and the technical and legal difficulties encompassed in its application.},
}
@article {pmid34311349,
year = {2021},
author = {Williams, MR and Stedtfeld, RD and Stedtfeld, TM and Crawford, RB and Kuwahara, T and Kaminski, NE and Tiedje, JM and Hashsham, SA},
title = {MicroRNA-based host response to toxicant exposure is influenced by the presence of gut microbial populations.},
journal = {The Science of the total environment},
volume = {797},
number = {},
pages = {149130},
pmid = {34311349},
issn = {1879-1026},
support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Immunity ; Mice ; Mice, Inbred C57BL ; *MicroRNAs/genetics ; *Polychlorinated Dibenzodioxins/toxicity ; Receptors, Aryl Hydrocarbon/genetics ; },
abstract = {Segmented filamentous bacteria (SFB) and Bacteroides fragilis are known to interact with the host immune response through the aryl hydrocarbon receptor (Ahr). 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), an environmental toxicant and a high-affinity Ahr ligand has the potential to modify the effect of SFB and B. fragilis. MicroRNAs (miRNA) with their role in regulating gene expression post-transcriptionally, may potentially be used to observe such interactions between SFB, B. fragilis, and TCDD. However, little is known regarding the impact of gut microbial members on miRNA expression or its modulation in the presence of an environmental toxicant. This information is important in understanding toxicant-mediated dysbiosis in gut microbiome and the resulting human health impacts. In this study, C57BL/6 germ-free (GF) mice were colonized with SFB and B. fragilis and administered 30 μg/kg TCDD every 4 d for 28 d and miRNA were measured. Compared to GF mice, colonization with SFB resulted in an increase in up- and down-regulated Ileal miRNAs. TCDD treatment of this group decreased the number of upregulated miRNA and increased the number of down-regulated miRNAs. Association with SFB and B. fragilis together had a similar but less pronounced effect in response to TCDD treatment. TCDD treatment of GF mice had no miRNA expression response. Immune and inflammatory responses and T-cell differentiation were the key functions impacted by these miRNAs. Overall, these results reveal that the host response to toxicants may also depend on the presence of specific gut microbial populations.},
}
@article {pmid34309697,
year = {2022},
author = {Begum, N and Wang, L and Ahmad, H and Akhtar, K and Roy, R and Khan, MI and Zhao, T},
title = {Co-inoculation of Arbuscular Mycorrhizal Fungi and the Plant Growth-Promoting Rhizobacteria Improve Growth and Photosynthesis in Tobacco Under Drought Stress by Up-Regulating Antioxidant and Mineral Nutrition Metabolism.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {971-988},
pmid = {34309697},
issn = {1432-184X},
mesh = {Antioxidants/metabolism ; Chlorophyll A/metabolism ; Droughts ; Electrolytes/metabolism ; Minerals/metabolism ; *Mycorrhizae/physiology ; Nutritional Status ; Photosynthesis ; Plant Roots/microbiology ; Nicotiana ; },
abstract = {Drought stress is a major environmental concern that limits crop growth on a large scale around the world. Significant efforts are required to overcome this issue in order to improve crop production. Therefore, the exciting role of beneficial microorganisms under stress conditions needs to be deeply explored. In this study, the role of two biotic entities, i.e., Arbuscular mycorrhizal fungi (AMF, Glomus versiforme) and plant growth-promoting rhizobacteria (PGPR, Bacillus methylotrophicus) inoculation in drought tolerance of tobacco (Nicotiana tabacum L.), was investigated. The present results showed that drought stress considerably reduced tobacco plant's growth and their physiological attributes. However, the plants co-inoculated with AMF and PGPR showed higher drought tolerance by bringing up significant improvement in the growth and biomass of tobacco plants. Moreover, the co-inoculation of AMF and PGPR considerably increased chlorophyll a, b, total chlorophylls, carotenoids, photosynthesis, and PSII efficiency by 96.99%, 76.90%, and 67.96% and 56.88%, 53.22%, and 33.43% under drought stress conditions, respectively. Furthermore, it was observed that drought stress enhanced lipid peroxidation and electrolyte leakage. However, the co-inoculation of AMF and PGPR reduced the electrolyte leakage and lipid peroxidation and significantly enhanced the accumulation of phenols and flavonoids by 57.85% and 71.74%. Similarly, the antioxidant enzymatic activity and the plant nutrition status were also considerably improved in co-inoculated plants under drought stress. Additionally, the AMF and PGPR inoculation also enhanced abscisic acid (ABA) and indole-3-acetic acid (IAA) concentrations by 67.71% and 54.41% in the shoots of tobacco plants. The current findings depicted that inoculation of AMF and PGPR (alone or in combination) enhanced the growth and mitigated the photosynthetic alteration with the consequent up-regulation of secondary metabolism, osmolyte accumulation, and antioxidant system.},
}
@article {pmid34305833,
year = {2021},
author = {Hernández, R and Jimenez, H and Vargas-Garcia, C and Caro-Quintero, A and Reyes, A},
title = {Disentangling the Complexity of the Rumen Microbial Diversity Through Fractionation Using a Sucrose Density Gradient.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {664754},
pmid = {34305833},
issn = {1664-302X},
abstract = {The ruminal microbial community is an important element in health, nutrition, livestock productivity, and climate impact. Despite the historic and current efforts to characterize this microbial diversity, many of its members remain unidentified, making it challenging to associate microbial groups with functions. Here we present a low-cost methodology for rumen sample treatment that separates the microbial community based on cell size, allowing for the identification of subtle compositional changes. In brief, the sample is centrifuged through a series of sucrose density gradients, and cells migrate to their corresponding density fraction. From each fraction, DNA is extracted and 16S rRNA gene amplicons are sequenced. We tested our methodology on four animals under two different conditions, fasting, and post-feeding. Each fraction was examined by confocal microscopy showing that the same sucrose fraction consistently separated similar cell-sized microorganisms independent of the animal or treatment. Microbial composition analysis using metabarcoding showed that our methodology detected low abundance bacterial families and population changes between fasting and post-feeding treatments that could not be observed by bulk DNA analysis. In conclusion, the sucrose-based method is a powerful low-cost approximation to untwine, enrich, and potentially isolate uncharacterized members of the ruminal microbiome.},
}
@article {pmid34305582,
year = {2021},
author = {Chen, Z and Lv, Y and Xu, H and Deng, L},
title = {Herbal Medicine, Gut Microbiota, and COVID-19.},
journal = {Frontiers in pharmacology},
volume = {12},
number = {},
pages = {646560},
pmid = {34305582},
issn = {1663-9812},
abstract = {Coronavirus Disease 19 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has grown to a worldwide pandemic with substantial mortality. The symptoms of COVID-19 range from mild flu-like symptoms, including cough and fever, to life threatening complications. There are still quite a number of patients with COVID-19 showed enteric symptoms including nausea, vomiting, and diarrhea. The gastrointestinal tract may be one of the target organs of SARS-CoV-2. Angiotensin converting enzyme 2 (ACE2) is the main receptor of SARS-CoV-2 virus, which is significantly expressed in intestinal cells. ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation. Intestinal flora imbalance and endotoxemia may accelerate the progression of COVID-19. Many herbs have demonstrated properties relevant to the treatment of COVID-19, by supporting organs and systems of the body affected by the virus. Herbs can restore the structure of the intestinal flora, which may further modulate the immune function after SARS-CoV-2 infection. Regulation of intestinal flora by herbal medicine may be helpful for the treatment and recovery of the disease. Understanding the role of herbs that regulate intestinal flora in fighting respiratory virus infections and maintaining intestinal flora balance can provide new ideas for preventing and treating COVID-19.},
}
@article {pmid34304501,
year = {2021},
author = {Liu, X and Liu, H and Li, C},
title = {[Advances in the study of chronic sinusitis microbiology using 16SrRNA gene sequencing technology].},
journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery},
volume = {35},
number = {7},
pages = {658-661},
pmid = {34304501},
issn = {2096-7993},
mesh = {Bacteria/genetics ; Chronic Disease ; Humans ; *Rhinitis ; *Sinusitis ; Technology ; },
abstract = {Traditional conventional bacterial culture techniques can cultivate fewer types of bacteria, aiming to isolate and identify specific pathogens, guide antibiotic treatment and eradicate pathogens.Macrogenomics techniques can simultaneously identify both cultured and uncultured bacteria in the flora, providing the possibility for the study of symbiotic flora. With the vigorous development of SrRNA and application of 16 gene sequencing technology, the microbial ecology research of chronic sinusitis （chronic rhinosinusitis,CRS） has once again become a hot topic.And the CRS view of microbial community composition and microbial diversity were presented. This review describes the use of 16 SrRNA gene sequencing in recent years advances in technical studies CRS microbial ecology.},
}
@article {pmid34304356,
year = {2021},
author = {Araujo, ASF and de Pereira, APA and Antunes, JEL and Oliveira, LMS and de Melo, WJ and Rocha, SMB and do Amorim, MR and Araujo, FF and Melo, VMM and Mendes, LW},
title = {Dynamics of bacterial and archaeal communities along the composting of tannery sludge.},
journal = {Environmental science and pollution research international},
volume = {28},
number = {45},
pages = {64295-64306},
doi = {10.1007/s11356-021-15585-9},
pmid = {34304356},
issn = {1614-7499},
support = {305069/2018-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {*Archaea/genetics ; *Bacteria/genetics ; *Composting ; *Industrial Waste ; RNA, Ribosomal, 16S/genetics ; Sewage ; Soil ; Tanning ; },
abstract = {The process of composting has been proposed as a biological alternative to improve the quality of tannery sludge (TS) by the action of microbial communities. However, there is limited knowledge about the dynamic of these microbial communities during the composting process. This study assessed the responses of bacterial and archaeal communities during TS composting using the 16S rRNA sequencing. The composting process occurred within 90 days, and samples of compost were collected on day 7 (d7; mesophilic stage), 30 (d30; thermophilic stage), 60 (d60; cooling stage), and 90 (d90; maturation stage). The results showed a succession of microbial phyla during the composting with enrichment of Synergistetes, WS1, and Euryarchaeota at the mesophilic stage, while at the thermophilic stage, there was an enrichment of Hydrogenedentes, WPS-2, Chloroflexi, and Deinococcus-Thermus. At the cooling stage, there was an enrichment of Kiritimatiellaeota, and at the maturation stage, there was an enrichment of Entotheonellaeota, Dadabacteria, Nitrospirae, Dependiatiae, and Fibrobacteres. When analyzing the drivers influencing microbial communities, Cr and pH presented more negative correlations with general phyla. In contrast, S, C, K, temperature, and N presented more positive correlations, while Ni, Cd, and P showed fewer correlations. According to niche occupancy, we observed a decreased proportion of generalists with a consequently increased proportion of specialists following the composting process. This study showed that different stages of the composting present a specific microbial community structure and dynamics, which are related to some specific composting characteristics.},
}
@article {pmid34304060,
year = {2021},
author = {Sepúlveda-Correa, A and Daza-Giraldo, LV and Polanía, J and Arenas, NE and Muñoz-García, A and Sandoval-Figueredo, AV and Vanegas, J},
title = {Genes associated with antibiotic tolerance and synthesis of antimicrobial compounds in a mangrove with contrasting salinities.},
journal = {Marine pollution bulletin},
volume = {171},
number = {},
pages = {112740},
doi = {10.1016/j.marpolbul.2021.112740},
pmid = {34304060},
issn = {1879-3363},
mesh = {Anti-Bacterial Agents ; Ecosystem ; Metagenomics ; *Salinity ; *Wetlands ; },
abstract = {Salinity and wastewater pollution in mangrove ecosystems can affect microorganisms and the abundance of genes involved in response to these stressors. This research aimed to identify genes associated with resistance and biosynthesis of antimicrobial compounds in mangrove soils subjected to contrasting salinities and wastewater pollution. Samples of rhizospheric soil were taken from a mangrove at the mouth of the Ranchería River in La Guajira, Colombia. A functional analysis was performed using Illumina HiSeq 2500 sequencing data obtained from total DNA extracted. Increased salt concentration influenced metabolic pathways and differential abundance of genes associated with the synthesis of antimicrobial compounds (e.g., rfbB/rffG, INO1/ISYNA1, rfbA/rffH, sat/met3, asd). Also, among 33 genes involved in intrinsic antibiotic resistance, 16 were significantly influenced by salinity (e.g., cusR/copR/silR, vgb, tolC). We concluded that salt stress tolerance and adaptive mechanisms could favor the biosynthesis of antimicrobial compounds in mangroves contaminated by sewage.},
}
@article {pmid34303166,
year = {2021},
author = {Li, C and Wang, L and Ji, S and Chang, M and Wang, L and Gan, Y and Liu, J},
title = {The ecology of the plastisphere: Microbial composition, function, assembly, and network in the freshwater and seawater ecosystems.},
journal = {Water research},
volume = {202},
number = {},
pages = {117428},
doi = {10.1016/j.watres.2021.117428},
pmid = {34303166},
issn = {1879-2448},
mesh = {*Ecosystem ; Fresh Water ; *Microbiota ; Plastics ; Rivers ; Seawater ; },
abstract = {Microplastics provide a unique habitat for microorganisms, forming the plastisphere. Yet the ecology of the plastisphere, including the microbial composition, functions, assembly processes, and interaction networks, needs to be understood. Here, we collected microplastics and their surrounding water samples in freshwater and seawater ecosystems. The bacterial and fungal communities of the plastisphere and the aquatic environment were studied based on 16S and internal transcribed spacer (ITS) high-throughput sequencing. We found that the plastisphere had a distinct microbial community and recruited a noteworthy proportion of unique species compared to the aquatic environment community, potentially altering ecosystem microbial community and causing microbial invasion. Using a random-forest machine-learning model, we identified a group of biomarkers that could best distinguish the plastisphere from the aquatic environment. Significant differences exist in microbial functions between the plastisphere and the aquatic environment, including functions of pathogenicity, compound degradation, as well as functions related to the cycling of carbon, nitrogen, and sulfur. And these functional differences were expressed differently in freshwater and seawater ecosystems. The oxidation-reduction potential, salinity, the concentrations of nitrogen-related ions (NO3[-], NO2[-], and NH4[+]), and the concentration of dissolved organic carbon in the surrounding environment drive the variation of the plastisphere. But environmental physicochemical properties explain less of the microbial community variation in the plastisphere than that in the aquatic environment. Niche-based processes govern the assembly of the plastisphere community, while neutral-based processes dominate the community assembly of the aquatic environment. Furthermore, compared to the aquatic environment, the plastisphere has a network of less complexity, more modules, higher modularity, and more competitive links in freshwater ecosystems, but the pattern is reversed in seawater ecosystems. Altogether, the microbial ecology of the new anthropogenic ecosystem-plastisphere-is unique and exerts different effects in freshwater and seawater ecosystems.},
}
@article {pmid34302509,
year = {2022},
author = {Ren, Z and Zhang, Y and Cai, T and Mao, K and Xu, Y and Li, C and He, S and Li, J and Wan, H},
title = {Dynamics of Microbial Communities across the Life Stages of Nilaparvata lugens (Stål).},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1049-1058},
pmid = {34302509},
issn = {1432-184X},
support = {32072462//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Bacteria/genetics ; *Hemiptera/microbiology ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Nymph/microbiology ; },
abstract = {Understanding the composition of microorganismal communities hosted by insect pests is an important prerequisite for revealing their functions and developing new pest control strategies. Although studies of the structure of the microbiome of Nilaparvata lugens have been published, little is known about the dynamic changes in this microbiome across different developmental stages, and an understanding of the core microbiota is still lacking. In this study, we investigated the dynamic changes in bacteria and fungi in different developmental stages of N. lugens using high-throughput sequencing technology. We observed that the microbial diversity in eggs and mated adults was higher than that in nymphs and unmated adults. We also observed a notable strong correlation between fungal and bacterial α-diversity, which suggests that fungi and bacteria are closely linked and may perform functions collaboratively during the whole developmental period. Arsenophonus and Hirsutella were the predominant bacterial and fungal taxa, respectively. Bacteria were more conserved than fungi during the transmission of the microbiota between developmental stages. Compared with that in the nymph and unmated adult stages of N. lugens, the correlation between bacterial and fungal communities in the mated adult and egg stages was stronger. Moreover, the core microbiota across all developmental stages in N. lugens was identified, and there were more bacterial genera than fungal genera; notably, the core microbiota of eggs, nymphs, and mated and unmated adults showed distinctive functional enrichment. These findings highlight the potential value of further exploring microbial functions during different developmental stages and developing new pest management strategies.},
}
@article {pmid34302348,
year = {2021},
author = {Dong, X and Zhang, C and Li, W and Weng, S and Song, W and Li, J and Wang, Y},
title = {Functional diversity of microbial communities in inactive seafloor sulfide deposits.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {8},
pages = {},
doi = {10.1093/femsec/fiab108},
pmid = {34302348},
issn = {1574-6941},
mesh = {Bacteria/genetics ; *Hydrothermal Vents ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides ; },
abstract = {The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.},
}
@article {pmid34302194,
year = {2022},
author = {Zhang, SK and Wang, Y and Li, ZK and Xue, HJ and Zhou, XD and Huang, JH},
title = {Two Apriona Species Sharing a Host Niche Have Different Gut Microbiome Diversity.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1059-1072},
doi = {10.1007/s00248-021-01799-4},
pmid = {34302194},
issn = {1432-184X},
support = {2020SY08//Cooperation Project of Zhejiang Province and Chinese Academy of Forestry/ ; },
mesh = {Animals ; Bacteria/genetics ; *Coleoptera ; *Gastrointestinal Microbiome/genetics ; Insecta ; Plants ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The adaptability of herbivorous insects to toxic plant defense compounds is partly related to the structure of the gut microbiome. To overcome plant resistance, the insect gut microbiome should respond to a wide range of allelochemicals derived from dietary niches. Nevertheless, for sibling herbivorous insect species, whether the gut microbiome contributes to success in food niche competition is unclear. Based on 16S rDNA high-throughput sequencing, the gut microbiomes of two Apriona species that share the same food niche were investigated in this study to determine whether the gut microbiome contributes to insect success in food-niche competition. Our observations indicated that the gut microbiome tended to play a part in host niche competition between the two Apriona species. The gut microbiome of Apriona swainsoni had many enriched pathways that can help degrade plant toxic secondary compounds, including xenobiotic biodegradation and metabolism, terpenoid and polyketide metabolism, and secondary metabolite biosynthesis. Meanwhile, A. swainsoni hosted a much greater variety of microorganisms and had more viable bacteria than A. germari. We conclude that gut microbes may influence the coevolution of herbivores and host plants. Gut bacteria may not only serve to boost nutritional relationships, but may also play an important role in insect food niche competition.},
}
@article {pmid34301298,
year = {2021},
author = {Wang, Q and Zhang, Y and Yang, Q and Fu, S and Qu, B and Defoirdt, T},
title = {One health pathogen surveillance demonstrated the dissemination of gut pathogens within the two coastal regions associated with intensive farming.},
journal = {Gut pathogens},
volume = {13},
number = {},
pages = {47},
pmid = {34301298},
issn = {1757-4749},
support = {81903372//Young Scientists Fund/ ; },
abstract = {BACKGROUND: Intensive aquaculture farming has caused significant degradation of coastal wetlands and has been proposed as a reservoir for pathogenic Vibrio spp.<br><br>RESULTS: Gut pathogens including Vibrio spp., Salmonella spp., and Klebsiella spp. were isolated from bird feces, shrimp and wetland water in two typical coastal regions of China in 2015 and 2017 and were subsequently subjected to whole-genome sequencing. Meanwhile, local patient isolates were also selected to confirm the epidemiological links. Bacterial community composition analyses of the sediments that were sampled in 2015 and 2017 were conducted by the hypervariable region 4 of the 16S rRNA gene. Together with the local clinical isolates, we observed highly related Vibrio isolates from waterbirds, wetlands and shrimp. Phylogenetic genome comparisons also demonstrated that sequence types ST3 and ST2414 Vibrio parahaemolyticus isolates obtained from aquatic animals were clonally related to patient isolates. Likewise, three Salmonella typhimurium isolates were also genomically related to one clinical strain. The results showed that farming activities significantly altered the community composition and resulted in the emergence of several pathogens, including Acinetobacter, Mycobacterium and Legionella.<br><br>CONCLUSIONS: In conclusion, our results demonstrated that intensive shrimp farming in wetlands has two devastating impacts: pathogen dissemination from aquatic animals into migratory birds and transmission of foodborne pathogens into local communities.},
}
@article {pmid34298185,
year = {2021},
author = {Zhao, L and Xu, M and Pan, X and Zhang, B and Dou, Q},
title = {Binding and detoxification ability of lactobacillus acidophilus towards di-n-butyl phthalate: Change of MAPK pathway in Caco-2 cell model.},
journal = {Journal of proteomics},
volume = {247},
number = {},
pages = {104333},
doi = {10.1016/j.jprot.2021.104333},
pmid = {34298185},
issn = {1876-7737},
mesh = {Caco-2 Cells ; Dibutyl Phthalate ; Humans ; Lactobacillus ; *Lactobacillus acidophilus ; *Probiotics ; },
abstract = {Di-n-butyl phthalate (DBP), a common compound of phthalates, can pose a risk to humans as a contaminant in the food industry. At present, the molecular mechanism of gene and protein toxicity caused by DBP in human cells is unclear. This in vitro study investigated the potential of inactivated Lactobacillus acidophilus NCFM in alleviating the damage caused by DBP in Caco-2 cells. According to the results from transcriptome and proteome analyses, the Caco-2 cells treated by DBP was resulted finally endoplasmic reticulum stress and mitochondrial oxidative damage. The most important differentially expressed genes and proteins involved in Caco-2 cells treated with NCFM to relieve DBP's cytotoxicity were TNF, NF-κB, CREB, P21, GADD45, FOS and CASP3. The molecular mechanism of DBP toxicity alleviated by strain NCFM was involved the MAPK pathway, via DBP bind to strain NCFM and avoid the activation of TNF receptor by DBP, so down-regulated the NF-κB, CREB, P21, GADD45, and CASP3, relieving the apoptosis of Caco-2 cells. Overall, our data provide new insights into detoxification of phthalate by using Lactobacillus. SIGNIFICANCE: Here we sequenced and assembled the transcriptome from Caco-2 cells which were treated with 4 groups: Control, DBP, strain NCFM, and strain NCFM+DBP groups, and combined it with proteome to characterize DBP detoxification genes/proteins through multiomics analysis. The cell viability in DBP treated groups were significantly increased by NCFM strain, indicating NCFM strain has the ability to alleviate the cytotoxicity of DBP via their binding ability with toxins. Furthermore, the results of transcriptome and proteome analysis showed that the signaling pathway of strain NCFM can alleviate DBP toxicity through MAPK pathway, and the potential biomarkers were identified too. This research may provided new information for developing new detoxification strategies for DBP.},
}
@article {pmid34297464,
year = {2022},
author = {Zhang, S and Yang, Q and Defoirdt, T},
title = {Indole decreases the virulence of pathogenic vibrios belonging to the Harveyi clade.},
journal = {Journal of applied microbiology},
volume = {132},
number = {1},
pages = {167-176},
doi = {10.1111/jam.15227},
pmid = {34297464},
issn = {1365-2672},
mesh = {Animals ; Artemia ; Indoles/pharmacology ; *Penaeidae ; *Vibrio/genetics ; *Vibrio parahaemolyticus ; Virulence/genetics ; Virulence Factors ; },
abstract = {AIM: Indole is a signaling molecule secreted by over 85 species of bacteria, including several Vibrio species, and it has been reported to affect different bacterial phenotypes such as biofilm formation, motility, and virulence. In this study, we aimed at investigating the inter-strain variability of the effect of indole in 12 different strains belonging to the Harveyi clade of vibrios.<br><br>METHODS AND RESULTS: Indole reduced the virulence of all strains towards gnotobiotic brine shrimp larvae. The survival rate of brine shrimp larvae challenged with vibrios pretreated with indole was increased by 1.3-fold to 1.8-fold. Additionally, indole significantly decreased the biofilm formation in all of the strains, decreased the swimming motility in eight of the strains, and decreased swarming motility in five of the strains. When cultured in the presence of exogenous indole, the mRNA level of the pirA and pirB toxin genes were down-regulated to 65% and 46%, and to 62% and 55% in the AHPND-causing strains Vibrio parahaemolyticus M0904 and Vibrio campbellii S01, respectively.<br><br>CONCLUSIONS: These data indicate that indole has a significant impact on the virulence of different strains belonging to the Harveyi clade of vibrios.<br><br>Our results suggest that indole signaling is a valid target for the development of novel therapeutics in order to control infections caused by Harveyi clade vibrios in aquaculture.},
}
@article {pmid34294810,
year = {2021},
author = {Verspecht, T and Van Holm, W and Boon, N and Bernaerts, K and Daep, CA and Zayed, N and Quirynen, M and Teughels, W},
title = {Comparison of the modulatory effects of three structurally similar potential prebiotic substrates on an in vitro multi-species oral biofilm.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15033},
pmid = {34294810},
issn = {2045-2322},
mesh = {Biodiversity ; *Biofilms/drug effects/growth &amp; development ; Host Microbial Interactions ; Metagenome ; Metagenomics/methods ; Microbiota ; Mouth/*microbiology ; Prebiotics/*administration &amp; dosage ; Virulence/genetics ; },
abstract = {Previous research identified potential prebiotic substrates for oral health like the structural analogues N-acetyl-D-mannosamine (NADM) and N-acetyl-D-glucosamine (NADG). The main hypothesis of the current study was twofold. Firstly, it was hypothesized that the modulatory effects of NADM are not limited to changes in multi-species oral biofilm composition, but also include effects on metabolism, virulence, and inflammatory potential. Secondly, the presence and orientation of their N-acetyl group could play a role. Therefore, a comparison was made between the effects of NADM, NADG and D-(+)-mannose on multi-species oral biofilms. Besides a beneficial compositional shift, NADM-treated biofilms also showed an altered metabolism, a reduced virulence and a decreased inflammatory potential. At a substrate concentration of 1 M, these effects were pronounced for all biofilm aspects, whereas at ~ 0.05 M (1%(w/v)) only the effects on virulence were pronounced. When comparing between substrates, both the presence and orientation of the N-acetyl group played a role. However, this was generally only at 1 M and dependent on the biofilm aspect. Overall, NADM was found to have different effects at two concentrations that beneficially modulate in vitro multi-species oral biofilm composition, metabolism, virulence and inflammatory potential. The presence and orientation of the N-acetyl group influenced these effects.},
}
@article {pmid34290548,
year = {2021},
author = {Do, H and Kim, SH and Cho, G and Kim, DR and Kwak, YS},
title = {Investigation of Fungal Strains Composition in Fruit Pollens for Artificial Pollination.},
journal = {Mycobiology},
volume = {49},
number = {3},
pages = {249-257},
pmid = {34290548},
issn = {1229-8093},
abstract = {Plants pollination are conducted through various pollinators such as wind, animals, and insects. Recently, the necessity for artificial pollination is drawing attention as the proportion of natural pollinators involved is decreasing over the years. Likewise, the trade in pollen for artificial pollination is also increasing worldwide. Through these imported pollens, many unknown microorganisms can flow from foreign countries. Among them, spores of various fungi present in the particles of pollen can be dispersed throughout the orchard. Therefore, in this study, the composition of fungal communities in imported pollen was revealed, and potential ecological characteristics of the fungi were investigated in four types of imported pollen. Top 10 operational taxonomic unit (OTU) of fungi were ranked among the following groups: Alternaria sp., Cladosporium sp., and Didymella glomerata which belong to many pathogenic species. Through FUNGuild analysis, the proportion of OTUs, which is assumed to be potentially plant pathogens, was higher than 50%, except for apple pollen in 2018. Based on this study of fungal structure, this information can suggest the direction of the pollen quarantine process and contribute to fungal biology in pollen.},
}
@article {pmid34288928,
year = {2021},
author = {Harlow, BE and Flythe, MD and Klotz, JL and Harmon, DL and Aiken, GE},
title = {Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge.},
journal = {PloS one},
volume = {16},
number = {7},
pages = {e0253754},
pmid = {34288928},
issn = {1932-6203},
mesh = {Acidosis/*drug therapy/microbiology ; *Animal Feed ; Animals ; Bacteria/drug effects/isolation &amp; purification ; Bacterial Load ; Cattle/*microbiology ; Cattle Diseases/*drug therapy/microbiology ; Cellulose/metabolism ; Deoxyglucose/pharmacology ; Dietary Carbohydrates/metabolism ; *Dietary Fiber/metabolism ; Dietary Proteins/metabolism ; Fermentation ; Gastrointestinal Contents/*microbiology ; Gastrointestinal Microbiome/*drug effects ; Genistein/pharmacology/*therapeutic use ; Hydrogen-Ion Concentration ; Ionophores/pharmacology ; Male ; Random Allocation ; Rumen/*microbiology ; Silage ; Starch/metabolism ; },
abstract = {Subacute rumen acidosis (SARA) occurs when highly fermentable carbohydrates are introduced into the diet, decreasing pH and disturbing the microbial ecology of the rumen. Rumen amylolytic bacteria rapidly catabolize starch, fermentation acids accumulate in the rumen and reduce environmental pH. Historically, antibiotics (e.g., monensin, MON) have been used in the prevention and treatment of SARA. Biochanin A (BCA), an isoflavone produced by red clover (Trifolium pratense), mitigates changes associated with starch fermentation ex vivo. The objective of the study was to determine the effect of BCA on amylolytic bacteria and rumen pH during a SARA challenge. Twelve rumen fistulated steers were assigned to 1 of 4 treatments: HF CON (high fiber control), SARA CON, MON (200 mg d-1), or BCA (6 g d-1). The basal diet consisted of corn silage and dried distiller's grains ad libitum. The study consisted of a 2-wk adaptation, a 1-wk HF period, and an 8-d SARA challenge (d 1-4: 40% corn; d 5-8: 70% cracked corn). Samples for pH and enumeration were taken on the last day of each period (4 h). Amylolytic, cellulolytic, and amino acid/peptide-fermenting bacteria (APB) were enumerated. Enumeration data were normalized by log transformation and data were analyzed by repeated measures ANOVA using the MIXED procedure of SAS. The SARA challenge increased total amylolytics and APB, but decreased pH, cellulolytics, and in situ DMD of hay (P < 0.05). BCA treatment counteracted the pH, microbiological, and fermentative changes associated with SARA challenge (P < 0.05). Similar results were also observed with MON (P < 0.05). These results indicate that BCA may be an effective alternative to antibiotics for mitigating SARA in cattle production systems.},
}
@article {pmid34287300,
year = {2021},
author = {Santschi, PH and Chin, WC and Quigg, A and Xu, C and Kamalanathan, M and Lin, P and Shiu, RF},
title = {Marine Gel Interactions with Hydrophilic and Hydrophobic Pollutants.},
journal = {Gels (Basel, Switzerland)},
volume = {7},
number = {3},
pages = {},
pmid = {34287300},
issn = {2310-2861},
abstract = {Microgels play critical roles in a variety of processes in the ocean, including element cycling, particle interactions, microbial ecology, food web dynamics, air-sea exchange, and pollutant distribution and transport. Exopolymeric substances (EPS) from various marine microbes are one of the major sources for marine microgels. Due to their amphiphilic nature, many types of pollutants, especially hydrophobic ones, have been found to preferentially associate with marine microgels. The interactions between pollutants and microgels can significantly impact the transport, sedimentation, distribution, and the ultimate fate of these pollutants in the ocean. This review on marine gels focuses on the discussion of the interactions between gel-forming EPS and pollutants, such as oil and other hydrophobic pollutants, nanoparticles, and metal ions.},
}
@article {pmid34287003,
year = {2021},
author = {Schloss, PD},
title = {Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters.},
journal = {mSphere},
volume = {6},
number = {4},
pages = {e0019121},
pmid = {34287003},
issn = {2379-5042},
support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA215574/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; },
mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; *Genetic Variation ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Amplicon sequencing variants (ASVs) have been proposed as an alternative to operational taxonomic units (OTUs) for analyzing microbial communities. ASVs have grown in popularity, in part because of a desire to reflect a more refined level of taxonomy since they do not cluster sequences based on a distance-based threshold. However, ASVs and the use of overly narrow thresholds to identify OTUs increase the risk of splitting a single genome into separate clusters. To assess this risk, I analyzed the intragenomic variation of 16S rRNA genes from the bacterial genomes represented in an rrn copy number database, which contained 20,427 genomes from 5,972 species. As the number of copies of the 16S rRNA gene increased in a genome, the number of ASVs also increased. There was an average of 0.58 ASVs per copy of the 16S rRNA gene for full-length 16S rRNA genes. It was necessary to use a distance threshold of 5.25% to cluster full-length ASVs from the same genome into a single OTU with 95% confidence for genomes with 7 copies of the 16S rRNA, such as Escherichia coli. This research highlights the risk of splitting a single bacterial genome into separate clusters when ASVs are used to analyze 16S rRNA gene sequence data. Although there is also a risk of clustering ASVs from different species into the same OTU when using broad distance thresholds, these risks are of less concern than artificially splitting a genome into separate ASVs and OTUs. IMPORTANCE 16S rRNA gene sequencing has engendered significant interest in studying microbial communities. There has been tension between trying to classify 16S rRNA gene sequences to increasingly lower taxonomic levels and the reality that those levels were defined using more sequence and physiological information than is available from a fragment of the 16S rRNA gene. Furthermore, the naming of bacterial taxa reflects the biases of those who name them. One motivation for the recent push to adopt ASVs in place of OTUs in microbial community analyses is to allow researchers to perform their analyses at the finest possible level that reflects species-level taxonomy. The current research is significant because it quantifies the risk of artificially splitting bacterial genomes into separate clusters. Far from providing a better representation of bacterial taxonomy and biology, the ASV approach can lead to conflicting inferences about the ecology of different ASVs from the same genome.},
}
@article {pmid34285323,
year = {2021},
author = {Mafla-Endara, PM and Arellano-Caicedo, C and Aleklett, K and Pucetaite, M and Ohlsson, P and Hammer, EC},
title = {Microfluidic chips provide visual access to in situ soil ecology.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {889},
pmid = {34285323},
issn = {2399-3642},
mesh = {*Bacterial Physiological Phenomena ; Ecology/*instrumentation ; Fungi/*physiology ; Hyphae/physiology ; Lab-On-A-Chip Devices ; Microbiota/*physiology ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Microbes govern most soil functions, but investigation of these processes at the scale of their cells has been difficult to accomplish. Here we incubate microfabricated, transparent 'soil chips' with soil, or bury them directly in the field. Both soil microbes and minerals enter the chips, which enables us to investigate diverse community interdependences, such as inter-kingdom and food-web interactions, and feedbacks between microbes and the pore space microstructures. The presence of hyphae ('fungal highways') strongly and frequently increases the dispersal range and abundance of water-dwelling organisms such as bacteria and protists across air pockets. Physical forces such as water movements, but also organisms and especially fungi form new microhabitats by altering the pore space architecture and distribution of soil minerals in the chip. We show that soil chips hold a large potential for studying in-situ microbial interactions and soil functions, and to interconnect field microbial ecology with laboratory experiments.},
}
@article {pmid34283261,
year = {2022},
author = {Xu, R and Tao, W and Lin, H and Huang, D and Su, P and Gao, P and Sun, X and Yang, Z and Sun, W},
title = {Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {929-941},
doi = {10.1007/s00248-021-01808-6},
pmid = {34283261},
issn = {1432-184X},
support = {Grant No. 42007357 and 41771301//National Natural Science Foundation of China (CN)/ ; Grant Nos. 2020T130127 and 2019M662825//postdoctoral research foundation of china/ ; Grant Nos. 202002030271//the Science and Technology Planning Project of Guangzhou/ ; Grant No. 2019A1515110351//Guangdong Basic and Applied Basic Research Foundation/ ; Grant Nos. 2020GDASYL-20200103086, 2020GDASYL-20200102015, 2020GDASYL-20200102014 and 2019GDASYL-0301002//GDAS' Project of Science and Technology Development/ ; Grant No. 2017GC010570//Guangdong Introducing Innovative and Entrepreneurial Talents/ ; Grant No. 2019B121205006//Guangdong Foundation for Program of Science and Technology Research/ ; },
mesh = {Alkanesulfonic Acids ; Caprylates ; *Fluorocarbons/analysis/chemistry ; *Microbiota ; Soil/chemistry ; },
abstract = {The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. In this work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their effects on soil microorganisms. Microbial community structure and microbe-microbe relationships were investigated by high-throughput sequencing and co-occurrence network analysis. Under 90 days of exposure, the alpha-diversity of soil microbial communities was increased with the PFOS treatment, followed by the PFOA treatment. The exposure of PFASs substantially changed the compositions of soil microbial communities, leading to the enrichment of more PFASs-tolerant bacteria, such as Proteobacteria, Burkholderiales, and Rhodocyclales. Comparative co-occurrence networks were constructed to investigate the microbe-microbe interactions under different PFASs treatments. The majority of nodes in the PFOA and PFOS networks were associated with the genus Azospirillum and Hydrogenophaga, respectively. The LEfSe analysis further identified a set of biomarkers in the soil microbial communities, such as Azospirillum, Methyloversatilis, Hydrogenophaga, Pseudoxanthomonas, and Fusibacter. The relative abundances of these biomarkers were also changed by different PFASs treatments. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be inhibited under PFAS exposure, which may further affect soil ecological services.},
}
@article {pmid34282938,
year = {2021},
author = {Cruz-Loya, M and Tekin, E and Kang, TM and Cardona, N and Lozano-Huntelman, N and Rodriguez-Verdugo, A and Savage, VM and Yeh, PJ},
title = {Antibiotics Shift the Temperature Response Curve of Escherichia coli Growth.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0022821},
pmid = {34282938},
issn = {2379-5077},
support = {UL1TR001881//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; //Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACYT)/ ; //James S. McDonnell Foundation (JSMF)/ ; //Hellman Foundation/ ; //University of California Institute for Mexico and the United States (UC MEXUS)/ ; UL1 TR001881/TR/NCATS NIH HHS/United States ; },
abstract = {Temperature variation-through time and across climatic gradients-affects individuals, populations, and communities. Yet how the thermal response of biological systems is altered by environmental stressors is poorly understood. Here, we quantify two key features-optimal temperature and temperature breadth-to investigate how temperature responses vary in the presence of antibiotics. We use high-throughput screening to measure growth of Escherichia coli under single and pairwise combinations of 12 antibiotics across seven temperatures that range from 22°C to 46°C. We find that antibiotic stress often results in considerable changes in the optimal temperature for growth and a narrower temperature breadth. The direction of the optimal temperature shifts can be explained by the similarities between antibiotic-induced and temperature-induced damage to the physiology of the bacterium. We also find that the effects of pairs of stressors in the temperature response can often be explained by just one antibiotic out of the pair. Our study has implications for a general understanding of how ecological systems adapt and evolve to environmental changes. IMPORTANCE The growth of living organisms varies with temperature. This dependence is described by a temperature response curve that is described by an optimal temperature where growth is maximized and a temperature range (termed breadth) across which the organism can grow. Because an organism's temperature response evolves or acclimates to its environment, it is often assumed to change over only evolutionary or developmental timescales. Counter to this, we show here that antibiotics can quickly (over hours) change the optimal growth temperature and temperature breadth for the bacterium Escherichia coli. Moreover, our results suggest a shared-damage hypothesis: when an antibiotic damages similar cellular components as hot (or cold) temperatures do, this shared damage will combine and compound to more greatly reduce growth when that antibiotic is administered at hot (or cold) temperatures. This hypothesis could potentially also explain how temperature responses are modified by stressors other than antibiotics.},
}
@article {pmid34282310,
year = {2021},
author = {Wasmund, K and Pelikan, C and Schintlmeister, A and Wagner, M and Watzka, M and Richter, A and Bhatnagar, S and Noel, A and Hubert, CRJ and Rattei, T and Hofmann, T and Hausmann, B and Herbold, CW and Loy, A},
title = {Publisher Correction: Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments.},
journal = {Nature microbiology},
volume = {6},
number = {8},
pages = {1102},
doi = {10.1038/s41564-021-00936-6},
pmid = {34282310},
issn = {2058-5276},
support = {P29426//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; P25111//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; },
}
@article {pmid34280807,
year = {2021},
author = {De Vrieze, J and Heyer, R and Props, R and Van Meulebroek, L and Gille, K and Vanhaecke, L and Benndorf, D and Boon, N},
title = {Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles.},
journal = {Water research},
volume = {202},
number = {},
pages = {117422},
doi = {10.1016/j.watres.2021.117422},
pmid = {34280807},
issn = {1879-2448},
mesh = {Anaerobiosis ; *Bioreactors ; Methane ; *Microbiota ; RNA, Ribosomal, 16S ; Sewage ; },
abstract = {The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.},
}
@article {pmid34279697,
year = {2022},
author = {Zhou, D and Wang, R and Li, X and Peng, B and Yang, G and Zhang, KQ and Zhang, Y and Xu, J},
title = {Genetic Diversity and Azole Resistance Among Natural Aspergillus fumigatus Populations in Yunnan, China.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {869-885},
pmid = {34279697},
issn = {1432-184X},
support = {31760010//National Natural Science Foundation of China/ ; 2020R3//McMaster University/ ; KY2018412//Department of Education of Guizhou Province/ ; },
mesh = {Antifungal Agents/pharmacology ; *Aspergillus fumigatus/genetics ; *Azoles/pharmacology ; China ; Genetic Variation ; Humans ; },
abstract = {The emergence and spread of azole resistance alleles in clinical and environmental isolates of Aspergillus fumigatus is a global human health concern and endangers the "One Health" approach in our fight against antifungal resistance (AFR) in this pathogen. A major challenge to combat AFR in A. fumigatus is the massive aerial dispersal ability of its asexual spores. Our recent fine-scale survey of greenhouse populations of A. fumigatus near Kunming, Yunnan, China, suggested that the use of azole fungicides for plant protection was likely a major driver of the high-frequency azole-resistant A. fumigatus (ARAF) in greenhouses. Here, we investigated the potential spread of those ARAF and the structure of geographic populations of A. fumigatus by analyzing 452 isolates from 19 geographic locations across Yunnan. We found lower frequencies of ARAF in these outdoor populations than those in greenhouses near Kunming, but there were abundant new alleles and new genotypes, including those associated with azole resistance, consistent with multiple independent origins of ARAF across Yunnan. Interestingly, among the four ecological niches, the sediments of a large lake near Kunming were found to have the highest frequency of ARAF (~ 43%). While most genetic variations were observed within the 19 local populations, statistically significant genetic differentiations were found between many subpopulations within Yunnan. Furthermore, similar to greenhouse populations, these outdoor populations of A. fumigatus in Yunnan were significantly different from those in other parts of the world. Our results call for increased attention to local and regional studies of this fungal pathogen to help develop targeted control strategies against ARAF.},
}
@article {pmid34279696,
year = {2022},
author = {Adomako, MO and Xue, W and Du, DL and Yu, FH},
title = {Soil Microbe-Mediated N:P Stoichiometric Effects on Solidago canadensis Performance Depend on Nutrient Levels.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {960-970},
doi = {10.1007/s00248-021-01814-8},
pmid = {34279696},
issn = {1432-184X},
mesh = {Biomass ; Ecosystem ; Humans ; Nitrogen/analysis ; Nutrients ; Soil ; *Solidago ; },
abstract = {Both soil microbes and soil N:P ratios can affect plant growth, but it is unclear whether they can interact to alter plant growth and whether such an interactive effect depends on nutrient levels. Here, we tested the hypothesis that soil microbes can ameliorate the negative effects of nutrient imbalance caused by low or high N:P ratios on plant growth and that such an ameliorative effect of soil microbes depends on nutrient supply levels. We grew individuals of six populations of the clonal plant Solidago canadensis at three N:P ratios (low (1.7), intermediate (15), and high (135)), under two nutrient levels (low versus high) and in the presence versus absence of soil microbes. The presence of soil microbes significantly increased biomass of S. canadensis at all three N:P ratios and under both nutrient levels. Under the low-nutrient level, biomass, height, and leaf number of S. canadensis did not differ significantly among the three N:P ratio treatments in the absence of soil microbes, but they were higher at the high than at the low and the intermediate N:P ratio in the presence of soil microbes. Under the high-nutrient level, by contrast, biomass, height, and leaf number of S. canadensis were significantly higher at the low than at the high and the intermediate N:P ratio in the absence of soil microbes, but increased with increasing the N:P ratio in the presence of soil microbes. In the presence of soil microbes, number of ramets (asexual individuals) and the accumulation of N and P in plants were significantly higher at the high than at the low and the intermediate N:P ratio under both nutrient levels, whereas in the absence of soil microbes, they did not differ significantly among the three N:P ratio regardless of the nutrient levels. Our results provide empirical evidence that soil microbes can alter effects of N:P ratios on plant performance and that such an effect depends on nutrient availability. Soil microbes may, therefore, play a role in modulating ecosystem functions such as productivity and carbon and nutrient cycling via modulating nutrient imbalance caused by low and high N:P ratios.},
}
@article {pmid34277691,
year = {2021},
author = {Calatayud, M and Van den Abbeele, P and Ghyselinck, J and Marzorati, M and Rohs, E and Birkett, A},
title = {Comparative Effect of 22 Dietary Sources of Fiber on Gut Microbiota of Healthy Humans in vitro.},
journal = {Frontiers in nutrition},
volume = {8},
number = {},
pages = {700571},
pmid = {34277691},
issn = {2296-861X},
abstract = {Human gut microbiota has a fundamental role in human health, and diet is one of the most relevant factors modulating the gut microbial ecosystem. Fiber, fat, proteins, and micronutrients can shape microbial activity and structure. Much information is available on the role of defined prebiotic fibers on gut microbiota, but less known are the effects of intact dietary fiber sources on healthy gut ecosystems. This research investigated in vitro the short-term effect of 22 commercially available food sources of dietary fiber on gut microbiota activity [pH, gas, short-chain fatty acids (SCFA), branched fatty acids (BCFA), lactate] and specific composition of Firmicutes, Bacteroidetes, bifidobacteria, and lactobacilli populations. More than 80% (19 of 22) of the products were highly fermentable and induced SCFAs production, with specific product differences. In general, all the whole grain cereals had a similar effect on gut microbiota modulation, inducing acetate and butyrate production and increasing bifidobacteria levels. Incorporating and comparing a large variety of products, including "non-conventional" fiber sources, like konjac, bamboo fiber, or seeds fiber, about which there is little information, contributes to our knowledge on the modulatory activity of diverse food fiber sources on human gut microbiota, and therefore potential health promotion through dietary fiber diversification.},
}
@article {pmid34277527,
year = {2021},
author = {Larroya, A and Pantoja, J and Codoñer-Franch, P and Cenit, MC},
title = {Towards Tailored Gut Microbiome-Based and Dietary Interventions for Promoting the Development and Maintenance of a Healthy Brain.},
journal = {Frontiers in pediatrics},
volume = {9},
number = {},
pages = {705859},
pmid = {34277527},
issn = {2296-2360},
abstract = {Mental health is determined by a complex interplay between the Neurological Exposome and the Human Genome. Multiple genetic and non-genetic (exposome) factors interact early in life, modulating the risk of developing the most common complex neurodevelopmental disorders (NDDs), with potential long-term consequences on health. To date, the understating of the precise etiology underpinning these neurological alterations, and their clinical management pose a challenge. The crucial role played by diet and gut microbiota in brain development and functioning would indicate that modulating the gut-brain axis may help protect against the onset and progression of mental-health disorders. Some nutritional deficiencies and gut microbiota alterations have been linked to NDDs, suggesting their potential pathogenic implications. In addition, certain dietary interventions have emerged as promising alternatives or adjuvant strategies for improving the management of particular NDDs, at least in particular subsets of subjects. The gut microbiota can be a key to mediating the effects of other exposome factors such as diet on mental health, and ongoing research in Psychiatry and Neuropediatrics is developing Precision Nutrition Models to classify subjects according to a diet response prediction based on specific individual features, including microbiome signatures. Here, we review current scientific evidence for the impact of early life environmental factors, including diet, on gut microbiota and neuro-development, emphasizing the potential long-term consequences on health; and also summarize the state of the art regarding the mechanisms underlying diet and gut microbiota influence on the brain-gut axis. Furthermore, we describe the evidence supporting the key role played by gut microbiota, diet and nutrition in neurodevelopment, as well as the effectiveness of certain dietary and microbiome-based interventions aimed at preventing or treating NDDs. Finally, we emphasize the need for further research to gain greater insight into the complex interplay between diet, gut microbiome and brain development. Such knowledge would help towards achieving tailored integrative treatments, including personalized nutrition.},
}
@article {pmid34276734,
year = {2021},
author = {Yoshiura, CA and Venturini, AM and Braga, LPP and da França, AG and de Lyra, MDCCP and Tsai, SM and Rodrigues, JLM},
title = {Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {683658},
pmid = {34276734},
issn = {1664-462X},
abstract = {The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.},
}
@article {pmid34276600,
year = {2021},
author = {Liu, J and Su, J and Zhang, M and Luo, Z and Li, X and Chai, B},
title = {Bacterial Community Spacing Is Mainly Shaped by Unique Species in the Subalpine Natural Lakes of China.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {669131},
pmid = {34276600},
issn = {1664-302X},
abstract = {Bacterial communities have been described as early indicators of both regional and global climatic change and play a critical role in the global biogeochemical cycle. Exploring the mechanisms that determine the diversity patterns of bacterial communities and how they share different habitats along environmental gradients are, therefore, a central theme in microbial ecology research. We characterized the diversity patterns of bacterial communities in Pipahai Lake (PPH), Mayinghai Lake (MYH), and Gonghai Lake (GH), three subalpine natural lakes in Ningwu County, Shanxi, China, and analyzed the distribution of their shared and unique taxa (indicator species). Results showed that the species composition and structure of bacterial communities were significantly different among the three lakes. Both the structure of the entire bacterial community and the unique taxa were significantly influenced by the carbon content (TOC and IC) and space distance; however, the structure of the shared taxa was affected by conductivity (EC), pH, and salinity. The structure of the entire bacterial community and unique taxa were mainly affected by the same factors, suggesting that unique taxa may be important in maintaining the spatial distribution diversity of bacterial communities in subalpine natural freshwater lakes. Our results provide new insights into the diversity maintenance patterns of the bacterial communities in subalpine lakes, and suggest dispersal limitation on bacterial communities between adjacent lakes, even in a small local area. We revealed the importance of unique taxa in maintaining bacterial community structure, and our results are important in understanding how bacterial communities in subalpine lakes respond to environmental change in local habitats.},
}
@article {pmid34273695,
year = {2021},
author = {Ntagia, E and Chatzigiannidou, I and Carvajal-Arroyo, JM and Arends, JBA and Rabaey, K},
title = {Continuous H2/CO2 fermentation for acetic acid production under transient and continuous sulfide inhibition.},
journal = {Chemosphere},
volume = {285},
number = {},
pages = {131536},
doi = {10.1016/j.chemosphere.2021.131536},
pmid = {34273695},
issn = {1879-1298},
mesh = {*Acetic Acid ; Bioreactors ; *Carbon Dioxide ; Fermentation ; Hydrogen ; Sulfides ; },
abstract = {Waste gas fermentation powered by renewable H2 is reaching kiloton scale. The presence of sulfide, inherent to many waste gases, can cause inhibition, requiring additional gas treatment. In this work, acetogenesis and methanogenesis inhibition by sulfide were studied in a 10-L mixed-culture fermenter, supplied with CO2 and connected with a water electrolysis unit for electricity-powered H2 supply. Three cycles of inhibition (1.3 mM total dissolved sulfide (TDS)) and recovery were applied, then the fermenter was operated at 0.5 mM TDS for 35 days. During operation at 0.5 mM TDS the acetate production rate reached 7.1 ± 1.5 mmol C L[-1] d[-1]. Furthermore, 43.7 ± 15.6% of the electrons, provided as H2, were distributed to acetate and 7.7 ± 4.1% to butyrate, the second most abundant fermentation product. Selectivity of sulfide as inhibitor was demonstrated by a 7 days lag-phase of methanogenesis recovery, compared to 48 h for acetogenesis and by the less than 1% electrons distribution to CH4, under 0.5 mM TDS. The microbial community was dominated by Eubacterium, Proteiniphilum and an unclassified member of the Eggerthellaceae family. The taxonomic diversity of the community decreased and conversely the phenotypic diversity increased, during operation. This work illustrated the scale-up potential of waste gas fermentations, by elucidating the effect of sulfide as a common gas impurity, and by demonstrating continuous, potentially renewable supply of electrons.},
}
@article {pmid34272992,
year = {2022},
author = {Lu, Y and Zhang, Y and Wang, J and Zhang, M and Wu, Y and Xiao, X and Xu, J},
title = {Dynamics in Bacterial Community Affected by Mesoscale Eddies in the Northern Slope of the South China Sea.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {823-836},
pmid = {34272992},
issn = {1432-184X},
support = {2014CB441503//National Basic Research Program of China (973 Program)/ ; },
mesh = {Bacteria/genetics ; *Cyclonic Storms ; Ecosystem ; *Seawater/microbiology ; Water ; },
abstract = {Mesoscale eddies are common oceanographic processes that can enhance primary productivity by transporting nutrients to the euphotic zone. In the northern South China Sea (SCS), eddies were frequently found to promote the exchange between the nutrient-rich shelf water and the oligotrophic water at the slope area. However, the response of bacterial community to eddy perturbations remains unclear. In the present study, we examined the variation of bacterial community under the impact of eddies in early spring and summer. The results showed that both the summer cyclonic eddy and spring anticyclonic eddy enhanced the bacterial abundance in surface water. The bacterial community composition and their functional potentials of surface samples were also influenced by the summer cyclonic eddy, while no significant change was observed in the case of spring anticyclonic eddy. Salinity and nutrients, which varied between the inside and outside of the eddies, were the significant factors explaining the differentiation of the community composition and related functions. Taken together, the results of our present study reveal the effects of mesoscale eddies on the bacterial community and associated metagenomes, providing a better understanding of the dynamics of bacteria in the slope ecosystem of the SCS.},
}
@article {pmid34272991,
year = {2021},
author = {Paul, P and Das, S and Chatterjee, S and Shukla, A and Chakraborty, P and Sarkar, S and Maiti, D and Das, A and Tribedi, P},
title = {1,4-Naphthoquinone disintegrates the pre-existing biofilm of Staphylococcus aureus by accumulating reactive oxygen species.},
journal = {Archives of microbiology},
volume = {203},
number = {8},
pages = {4981-4992},
pmid = {34272991},
issn = {1432-072X},
mesh = {Biofilms ; Humans ; Naphthoquinones ; Reactive Oxygen Species ; *Staphylococcal Infections ; *Staphylococcus aureus/genetics ; },
abstract = {Staphylococcus aureus causes several nosocomial and community-acquired infections in human host involving biofilm. Thus, strategies need to be explored to curb biofilm threats by either inhibiting the formation of biofilm or disintegrating the pre-existing biofilm. Towards this direction, we had already revealed the biofilm inhibiting properties of 1,4-naphthoquinone against S. aureus. In this study, we have investigated whether this compound can act on pre-existing biofilm. Hence, biofilm of S. aureus was developed first and challenged further with 1,4-naphthoquinone. Experiments such as crystal violet assay, fluorescence microscopy, and estimation of total biofilm protein were performed to confirm the biofilm disintegration properties of 1,4-naphthoquinone. The disintegration of pre-existing biofilm could be attributed to the generation of reactive oxygen species (ROS). To investigate further, we observed that extracellular DNA (eDNA) was found to play an important role in holding the biofilm network as DNaseI treatment could cause an efficient disintegration of the same. To examine the effect of ROS on the eDNA, we exposed pre-existing biofilm to either 1,4-naphthoquinone or a combination of both 1,4-naphthoquinone and ascorbic acid for different length of time. Post-incubation, ROS generation and the amount of eDNA associated with the biofilm were determined wherein an inversely proportional relationship was observed between them. The result indicated that with the increase of ROS generation, the amount of eDNA associated with biofilm got decreased substantially. Thus, the results indicated that the generation of ROS could degrade the eDNA thereby compromising the integrity of biofilm which lead to the disintegration of pre-existing biofilm.},
}
@article {pmid34272569,
year = {2022},
author = {Martínez-Reyes, CM and Rodríguez-Zaragoza, S and Cabirol, N and Alarcón, A and Mendoza-López, MR},
title = {Effect of Predation by Colpoda sp. in Nitrogen Fixation Rate of Two Free-Living Bacteria.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1026-1035},
pmid = {34272569},
issn = {1432-184X},
support = {IN222618//PAPIIT/ ; },
mesh = {Animals ; Bacteria ; *Ciliophora ; Nitrogen ; *Nitrogen Fixation ; Predatory Behavior ; },
abstract = {Biological nitrogen fixation is limited to several groups of prokaryotes, some of them reduce nitrogen as free-living nitrogen-fixing bacteria. Protozoa predation on these latter releases sequestered nitrogen that may enhance the formation of new bacterial biomass and possibly increase nitrogen fixation within soil microbial communities. We aim to evaluate the predation effect of Colpoda sp. on two nitrogen fixers: Azospirillum lipoferum and Stenotrophomonas sp. during their lag, early exponential, and exponential phases. The kinetics of bacterial population growth was determined in the predators' presence or absence and the effect of predation on the rate of N fixation was evaluated through the reduction of acetylene to ethylene technique. Colpoda sp. showed a non-significant difference in preferences between the two species offered as prey. Consequently, the abundance of A. lipoferum and Stenotrophomonas sp. decreased significantly due to predator's pressure and both species responded by increasing their specific growth rate. Likewise, predation promoted greater nitrogen fixation rate by CFU during the lag phase in A. lipoferum (0.20 nM/CFU with predation vs 0.09 nM/CFU without predation) and Stenotrophomonas sp. (0.22 nM/CFU vs 0.09 nM/CFU respectively). During early exponential phase (29 h), the rate diminished to 0.13 and 0.05 nM/CFU in A. lipoferum and to 0.09 nM/CFU and 0.05 nM/CFU in Stenotrophomonas sp. Finally, during the exponential phase (52 h), only A. lipoferum without predation produced 0.003 nM/CFU of ethylene. Thus, the nitrogenase activity was higher in the lag and the early exponential phases when predator activity was involved.},
}
@article {pmid34269959,
year = {2021},
author = {Đurović, G and Van Neerbos, FAC and Bossaert, S and Herrera-Malaver, B and Steensels, J and Arnó, J and Wäckers, F and Sobhy, IS and Verstrepen, KJ and Jacquemyn, H and Lievens, B},
title = {The Pupal Parasitoid Trichopria drosophilae Is Attracted to the Same Yeast Volatiles as Its Adult Host.},
journal = {Journal of chemical ecology},
volume = {47},
number = {8-9},
pages = {788-798},
pmid = {34269959},
issn = {1573-1561},
support = {722642 (INTERFUTURE)//Horizon 2020 Framework Programme/ ; PID2019-107030RB-C21//CERCA Programme/ ; },
mesh = {Animals ; Behavior, Animal/drug effects ; Esters/chemistry/metabolism/pharmacology ; Host-Parasite Interactions/drug effects ; Hymenoptera/growth &amp; development/*physiology ; Principal Component Analysis ; Proteins/genetics/metabolism ; Pupa/drug effects/physiology ; Saccharomyces cerevisiae/*chemistry/metabolism ; Volatile Organic Compounds/*chemistry/pharmacology ; },
abstract = {There is increasing evidence that microorganisms, particularly fungi and bacteria, emit volatile compounds that mediate the foraging behaviour of insects and therefore have the potential to affect key ecological relationships. However, to what extent microbial volatiles affect the olfactory response of insects across different trophic levels remains unclear. Adult parasitoids use a variety of chemical stimuli to locate potential hosts, including those emitted by the host's habitat, the host itself, and microorganisms associated with the host. Given the great capacity of parasitoids to utilize and learn odours to increase foraging success, parasitoids of eggs, larvae, or pupae may respond to the same volatiles the adult stage of their hosts use when locating their resources, but compelling evidence is still scarce. In this study, using Saccharomyces cerevisiae we show that Trichopria drosophilae, a pupal parasitoid of Drosophila species, is attracted to the same yeast volatiles as their hosts in the adult stage, i.e. acetate esters. Parasitoids significantly preferred the odour of S. cerevisiae over the blank medium in a Y-tube olfactometer. Deletion of the yeast ATF1 gene, encoding a key acetate ester synthase, decreased attraction of T. drosophilae, while the addition of synthetic acetate esters to the fermentation medium restored parasitoid attraction. Bioassays with individual compounds revealed that the esters alone were not as attractive as the volatile blend of S. cerevisiae, suggesting that other volatile compounds also contribute to the attraction of T. drosophilae. Altogether, our results indicate that pupal parasitoids respond to the same volatiles as the adult stage of their hosts, which may aid them in locating oviposition sites.},
}
@article {pmid34269858,
year = {2022},
author = {Lin, YC and Chin, CP and Yang, JW and Chiang, KP and Hsieh, CH and Gong, GC and Shih, CY and Chen, SY},
title = {How Communities of Marine Stramenopiles Varied with Environmental and Biological Variables in the Subtropical Northwestern Pacific Ocean.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {916-928},
pmid = {34269858},
issn = {1432-184X},
support = {104-2811-M-019- 003//Ministry of Science and Technology, Taiwan/ ; 109-2611-M-019 -018//Ministry of Science and Technology, Taiwan/ ; 107-2611-M-019 -002 -MY3//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Biodiversity ; Nitrites ; Pacific Ocean ; Phylogeny ; Seawater ; *Stramenopiles ; *Synechococcus ; Water ; },
abstract = {MArine STramenopiles (MASTs) have been recognized as parts of heterotrophic protists and contribute substantially to protist abundances in the ocean. However, little is known about their spatiotemporal variations with respect to environmental and biological factors. The objectives of this study are to use canonical correspondence analysis to investigate how MASTs communities are shaped by environmental variables, and co-occurrence networks to examine their potential interactions with prokaryotic communities. Our dataset came from the southern East China Sea (sECS) in the subtropical northwestern Pacific, and involved 14 cruises along a coastal-oceanic transect, each of which sampled surface water from 4 to 7 stations. MASTs communities were revealed by metabarcoding of 18S rDNA V4 region. Most notably, MAST-9 had a high representation in warm waters in terms of read number and diversity. Subclades of MAST-9C and -9D showed slightly different niches, with MAST-9D dominating in more coastal waters where concentrations of nitrite and Synechococcus were higher. MAST-1C was a common component of colder water during spring. Overall, canonical correspondence analysis showed that MASTs communities were significantly influenced by temperature, nitrite and Synechococcus concentrations. The co-occurrence networks showed that certain other minor prokaryotic taxa can influence MAST communities. This study provides insight into how MASTs communities varied with environmental and biological variables.},
}
@article {pmid34267209,
year = {2021},
author = {Chen, F and Chen, Z and Chen, M and Chen, G and Huang, Q and Yang, X and Yin, H and Chen, L and Zhang, W and Lin, H and Ou, M and Wang, L and Chen, Y and Lin, C and Xu, W and Yin, G},
title = {Reduced stress-associated FKBP5 DNA methylation together with gut microbiota dysbiosis is linked with the progression of obese PCOS patients.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {60},
pmid = {34267209},
issn = {2055-5008},
mesh = {Adult ; Biodiversity ; Biomarkers ; Case-Control Studies ; Computational Biology ; *DNA Methylation ; Disease Susceptibility ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; Metabolomics/methods ; Middle Aged ; Obesity ; Polycystic Ovary Syndrome/diagnosis/*etiology/*metabolism ; *Stress, Physiological ; Tacrolimus Binding Proteins/*genetics ; Young Adult ; },
abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disease in females that is characterized by hyperandrogenemia, chronic anovulation, and polycystic ovaries. However, the exact etiology and pathogenesis of PCOS are still unknown. The aim of this study was to clarify the bacterial, stress status, and metabolic differences in the gut microbiomes of healthy individuals and patients with high body mass index (BMI) PCOS (PCOS-HB) and normal BMI PCOS (PCOS-LB), respectively. Here, we compared the gut microbiota characteristics of PCOS-HB, PCOS-LB, and healthy controls by 16S rRNA gene sequencing, FK506-binding protein 5 (FKBP5) DNA methylation and plasma metabolite determination. Clinical parameter comparisons indicated that PCOS patients had higher concentrations of total testosterone, androstenedione, dehydroepiandrosterone sulfate, luteinizing hormone, and HOMA-IR while lower FKBP5 DNA methylation. Significant differences in bacterial diversity and community were observed between the PCOS and healthy groups but not between the PCOS-HB and PCOS-LB groups. Bacterial species number was negatively correlated with insulin concentrations (both under fasting status and 120 min after glucose load) and HOMA-IR but positively related to FKBP5 DNA methylation. Compared to the healthy group, both PCOS groups had significant changes in bacterial genera, including Prevotella_9, Dorea, Maihella, and Slackia, and plasma metabolites, including estrone sulfate, lysophosphatidyl choline 18:2, and phosphatidylcholine (22:6e/19:1). The correlation network revealed the complicated interaction of the clinical index, bacterial genus, stress indices, and metabolites. Our work links the stress responses and gut microbiota characteristics of PCOS disease, which might afford perspectives to understand the progression of PCOS.},
}
@article {pmid34263935,
year = {2021},
author = {Amini, S and Arsova, B and Gobert, S and Carnol, M and Bosman, B and Motte, P and Watt, M and Hanikenne, M},
title = {Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply.},
journal = {Plant, cell &amp; environment},
volume = {44},
number = {10},
pages = {3376-3397},
doi = {10.1111/pce.14151},
pmid = {34263935},
issn = {1365-3040},
mesh = {Brachypodium/*genetics/*metabolism ; Plant Proteins/*genetics/metabolism ; Plant Shoots/metabolism ; Transcription, Genetic ; Zinc/*deficiency/metabolism ; },
abstract = {The biological processes underlying zinc homeostasis are targets for genetic improvement of crops to counter human malnutrition. Detailed phenotyping, ionomic, RNA-Seq analyses and flux measurements with [67] Zn isotope revealed whole-plant molecular events underlying zinc homeostasis upon varying zinc supply and during zinc resupply to starved Brachypodium distachyon (Brachypodium) plants. Although both zinc deficiency and excess hindered Brachypodium growth, accumulation of biomass and micronutrients into roots and shoots differed depending on zinc supply. The zinc resupply dynamics involved 1,893 zinc-responsive genes. Multiple zinc-regulated transporter and iron-regulated transporter (IRT)-like protein (ZIP) transporter genes and dozens of other genes were rapidly and transiently down-regulated in early stages of zinc resupply, suggesting a transient zinc shock, sensed locally in roots. Notably, genes with identical regulation were observed in shoots without zinc accumulation, pointing to root-to-shoot signals mediating whole-plant responses to zinc resupply. Molecular events uncovered in the grass model Brachypodium are useful for the improvement of staple monocots.},
}
@article {pmid34263341,
year = {2022},
author = {González-Dominici, LI and Saati-Santamaría, Z and García-Fraile, P},
title = {Correction to: Genome Analysis and Genomic Comparison of the Novel Species Arthrobacter ipis Reveal Its Potential Protective Role in Its Bark Beetle Host.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {1123},
doi = {10.1007/s00248-021-01811-x},
pmid = {34263341},
issn = {1432-184X},
abstract = {A Correction to this paper has been published: https://doi.org/10.1007/s00248-021-01811-x.},
}
@article {pmid34262548,
year = {2021},
author = {Leinberger, J and Holste, J and Bunk, B and Freese, HM and Spröer, C and Dlugosch, L and Kück, AC and Schulz, S and Brinkhoff, T},
title = {High Potential for Secondary Metabolite Production of Paracoccus marcusii CP157, Isolated From the Crustacean Cancer pagurus.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {688754},
pmid = {34262548},
issn = {1664-302X},
abstract = {Secondary metabolites are key components in microbial ecology by mediating interactions between bacteria and their environment, neighboring species or host organisms. Bioactivities can be beneficial for both interaction partners or provide a competitive advantage only for the producer. Colonizers of confined habitats such as biofilms are known as prolific producers of a great number of bioactive secondary metabolites and are a potential source for novel compounds. We investigated the strain Paracoccus marcusii CP157, which originates from the biofilm on the carapace of a shell disease-affected Cancer pagurus specimen, for its potential to produce bioactive secondary metabolites. Its closed genome contains 22 extrachromosomal elements and several gene clusters potentially involved in biosynthesis of bioactive polyketides, bacteriocins, and non-ribosomal peptides. Culture extracts of CP157 showed antagonistic activities against bacteria from different phyla, but also against microalgae and crustacean larvae. Different HPLC-fractions of CP157 culture extracts had antibacterial properties, indicating that several bioactive compounds are produced by CP157. The bioactive extract contains several small, antibacterial compounds that partially withstand elevated temperatures, extreme pH values and exposure to proteolytic enzymes, providing high stability toward environmental conditions in the natural habitat of CP157. Further, screening of 17 Paracoccus spp. revealed that antimicrobial activity, hemolysis and production of N-acyl homoserine lactones are common features within the genus. Taking into account the large habitat diversity and phylogenetic distance of the tested strains, we hypothesize that bioactive secondary metabolites play a central role in the ecology of Paracoccus spp. in their natural environments.},
}
@article {pmid34260793,
year = {2022},
author = {Yang, Q and Wang, Q and Wu, J and Zhang, Y and Wei, D and Qu, B and Liu, Y and Fu, S},
title = {Distinct dynamics of Vibrio parahaemolyticus populations in two farming models.},
journal = {Journal of applied microbiology},
volume = {133},
number = {3},
pages = {1146-1155},
doi = {10.1111/jam.15217},
pmid = {34260793},
issn = {1365-2672},
support = {81903372//National Natural Science Foundation of China/ ; QL202005//Youth Fund of Liaoning Provincial Department of Education/ ; 2019B020215001//Key R&amp;D Program of Guangdong Province/ ; GML2019ZD0402//Key R&amp;D Program of Guangdong Province/ ; //Special Research Fund of Ghent University/ ; },
mesh = {Aquaculture ; Humans ; Multilocus Sequence Typing ; *Vibrio Infections/microbiology ; *Vibrio parahaemolyticus/genetics ; Water ; },
abstract = {AIMS: Despite the recent prosperity of shrimp cultivation in China, very little is known about how different shrimp farming models influence the dynamics of Vibrio parahaemolyticus populations and the antibiotic resistance of this bacterium.<br><br>METHODS AND RESULTS: To this end, we conducted continuous surveillance of V. parahaemolyticus on four farms over 3&#xa0;years: two traditional shrimp farms with daily water exchange and two farms operated in the recirculating aquaculture systems (RAS). No antibiotics were used in these farms to exclude the potential impacts of antibiotics on the emergence of antibacterial resistance. Multilocus sequence typing was utilized to characterize the dynamics of V. parahaemolyticus populations. Whole-genome sequencing (WGS) was conducted to determine the representative sequence types (STs) at each farm. Results revealed that the population structure of V. parahaemolyticus remained stable over time in both RAS farms, with only nine and four STs observed at each. In contrast, annual replacement of V. parahaemolyticus populations was observed in traditional farms with 26 and 28 STs identified in rearing water. WGS of 50 isolates divided them into five clusters, of which ST917a isolates harboured a genomic island that disrupted the gene recA. Pair-wised genomic comparison of isolates from the same STs showed that they were genetically related but belonged to different clones associated with geographical distribution.<br><br>CONCLUSIONS: These results suggested that RAS presented a specific ecological niche by minimizing the water exchanges with the external environment. In contrast, traditional farming might pose a food safety issue by introducing new V. parahaemolyticus populations with antibiotic resistance genes.<br><br>Our results expose the potential food safety issue associated with conventional agriculture and should encourage the development of preventive strategies to reduce the emergence of resistant V. parahaemolyticus populations.},
}
@article {pmid34258685,
year = {2021},
author = {Carpio, LE and Sanz, Y and Gozalbes, R and Barigye, SJ},
title = {Computational strategies for the discovery of biological functions of health foods, nutraceuticals and cosmeceuticals: a review.},
journal = {Molecular diversity},
volume = {25},
number = {3},
pages = {1425-1438},
pmid = {34258685},
issn = {1573-501X},
support = {INNTAL32/19/002//Agencia Valenciana de la Investigaci&#xf3;n/ ; 893810//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; },
mesh = {Algorithms ; Cheminformatics/*methods ; Cosmeceuticals/*chemistry/pharmacology ; Databases, Chemical ; Dietary Supplements/*analysis ; Functional Food/*analysis ; Humans ; Machine Learning ; *Models, Molecular ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; *Quantitative Structure-Activity Relationship ; },
abstract = {Scientific and consumer interest in healthy foods (also known as functional foods), nutraceuticals and cosmeceuticals has increased in the recent years, leading to an increased presence of these products in the market. However, the regulations across different countries that define the type of claims that may be made, and the degree of evidence required to support these claims, are rather inconsistent. Moreover, there is also controversy on the effectiveness and biological mode of action of many of these products, which should undergo an exhaustive approval process to guarantee the consumer rights. Computational approaches constitute invaluable tools to facilitate the discovery of bioactive molecules and provide biological plausibility on the mode of action of these products. Indeed, methodologies like QSAR, docking or molecular dynamics have been used in drug discovery protocols for decades and can now aid in the discovery of bioactive food components. Thanks to these approaches, it is possible to search for new functions in food constituents, which may be part of our daily diet, and help to prevent disorders like diabetes, hypercholesterolemia or obesity. In the present manuscript, computational studies applied to this field are reviewed to illustrate the potential of these approaches to guide the first screening steps and the mechanistic studies of nutraceutical, cosmeceutical and functional foods.},
}
@article {pmid34255112,
year = {2022},
author = {Pavlova, ON and Izosimova, ON and Chernitsyna, SM and Ivanov, VG and Pogodaeva, TV and Khabuev, AV and Gorshkov, AG and Zemskaya, TI},
title = {Anaerobic oxidation of petroleum hydrocarbons in enrichment cultures from sediments of the Gorevoy Utes natural oil seep under methanogenic and sulfate-reducing conditions.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {899-915},
pmid = {34255112},
issn = {1432-184X},
support = {0279-2021-0006 (121032300223-1)//Ministry of Education and Science of the Russian Federation/ ; },
mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Euryarchaeota/genetics ; Geologic Sediments/microbiology ; Hydrocarbons/metabolism ; *Microbiota ; *Petroleum ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Sulfates/metabolism ; },
abstract = {This article presents the first experimental data on the ability of microbial communities from sediments of the Gorevoy Utes natural oil seep to degrade petroleum hydrocarbons under anaerobic conditions. Like in marine ecosystems associated with oil discharge, available electron acceptors, in particular sulfate ions, affect the composition of the microbial community and the degree of hydrocarbon conversion. The cultivation of the surface sediments under sulfate-reducing conditions led to the formation of a more diverse bacterial community and greater loss of n-alkanes (28%) in comparison to methanogenic conditions (6%). Microbial communities of both surface and deep sediments are more oriented to degrade polycyclic aromatic hydrocarbons (PAHs), to which the degree of the PAH conversion testifies (up to 46%) irrespective of the present electron acceptors. Microorganisms with the uncultured closest homologues from thermal habitats, sediments of mud volcanoes, and environments contaminated with hydrocarbons mainly represented microbial communities of enrichment cultures. The members of the phyla Firmicutes, Chloroflexi, and Caldiserica (OP5), as well as the class Deltaproteobacteria and Methanomicrobia, were mostly found in enrichment cultures. The influence of gas-saturated fluids may be responsible for the presence in the bacterial 16S rRNA gene libraries of the sequences of "rare taxa": Planctomycetes, Ca. Atribacteria (OP9), Ca. Armatimonadetes (OP10), Ca. Latescibacteria (WS3), Ca. division (AC1), Ca. division (OP11), and Ca. Parcubacteria (OD1), which can be involved in hydrocarbon oxidation.},
}
@article {pmid34254828,
year = {2021},
author = {Harrison, JG and Randolph, GD and Buerkle, CA},
title = {Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0029421},
pmid = {34254828},
issn = {2379-5077},
support = {EPS-1655726//National Science Foundation (NSF)/ ; },
abstract = {New approaches to characterizing microbiomes via high-throughput sequencing provide impressive gains in efficiency and cost reduction compared to approaches that were standard just a few years ago. However, the speed of method development has been such that staying abreast of the latest technological advances is challenging. Moreover, shifting laboratory protocols to include new methods can be expensive and time consuming. To facilitate adoption of new techniques, we provide a guide and review of recent advances that are relevant for single-locus sequence-based study of microbiomes-from extraction to library preparation-including a primer regarding the use of liquid-handling automation in small-scale academic settings. Additionally, we describe several amendments to published techniques to improve throughput, track contamination, and reduce cost. Notably, we suggest adding synthetic DNA molecules to each sample during nucleic acid extraction, thus providing a method of documenting incidences of cross-contamination. We also describe a dual-indexing scheme for Illumina sequencers that allows multiplexing of many thousands of samples with minimal PhiX input. Collectively, the techniques that we describe demonstrate that laboratory technology need not impose strict limitations on the scale of molecular microbial ecology studies. IMPORTANCE New methods to characterize microbiomes reduce technology-imposed limitations to study design, but many new approaches have not been widely adopted. Here, we present techniques to increase throughput and reduce contamination alongside a thorough review of current best practices.},
}
@article {pmid34254826,
year = {2021},
author = {Ha, AD and Moniruzzaman, M and Aylward, FO},
title = {High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0029321},
pmid = {34254826},
issn = {2379-5077},
support = {Early Career Award in Marine Microbial Ecology and Evolution//Simons Foundation (SF)/ ; 1918271//National Science Foundation (NSF)/ ; },
abstract = {Viruses belonging to the Nucleocytoviricota phylum are globally distributed and include members with notably large genomes and complex functional repertoires. Recent studies have shown that these viruses are particularly diverse and abundant in marine systems, but the magnitude of actively replicating Nucleocytoviricota present in ocean habitats remains unclear. In this study, we compiled a curated database of 2,431 Nucleocytoviricota genomes and used it to examine the gene expression of these viruses in a 2.5-day metatranscriptomic time-series from surface waters of the California Current. We identified 145 viral genomes with high levels of gene expression, including 90 Imitervirales and 49 Algavirales viruses. In addition to recovering high expression of core genes involved in information processing that are commonly expressed during viral infection, we also identified transcripts of diverse viral metabolic genes from pathways such as glycolysis, the TCA cycle, and the pentose phosphate pathway, suggesting that virus-mediated reprogramming of central carbon metabolism is common in oceanic surface waters. Surprisingly, we also identified viral transcripts with homology to actin, myosin, and kinesin domains, suggesting that viruses may use these gene products to manipulate host cytoskeletal dynamics during infection. We performed phylogenetic analysis on the virus-encoded myosin and kinesin proteins, which demonstrated that most belong to deep-branching viral clades, but that others appear to have been acquired from eukaryotes more recently. Our results highlight a remarkable diversity of active Nucleocytoviricota in a coastal marine system and underscore the complex functional repertoires expressed by these viruses during infection. IMPORTANCE The discovery of giant viruses has transformed our understanding of viral complexity. Although viruses have traditionally been viewed as filterable infectious agents that lack metabolism, giant viruses can reach sizes rivalling cellular lineages and possess genomes encoding central metabolic processes. Recent studies have shown that giant viruses are widespread in aquatic systems, but the activity of these viruses and the extent to which they reprogram host physiology in situ remains unclear. Here, we show that numerous giant viruses consistently express central metabolic enzymes in a coastal marine system, including components of glycolysis, the TCA cycle, and other pathways involved in nutrient homeostasis. Moreover, we found expression of several viral-encoded actin, myosin, and kinesin genes, indicating viral manipulation of the host cytoskeleton during infection. Our study reveals a high activity of giant viruses in a coastal marine system and indicates they are a diverse and underappreciated component of microbial diversity in the ocean.},
}
@article {pmid34253727,
year = {2021},
author = {Wan, T and Liu, Z and Leitch, IJ and Xin, H and Maggs-Kölling, G and Gong, Y and Li, Z and Marais, E and Liao, Y and Dai, C and Liu, F and Wu, Q and Song, C and Zhou, Y and Huang, W and Jiang, K and Wang, Q and Yang, Y and Zhong, Z and Yang, M and Yan, X and Hu, G and Hou, C and Su, Y and Feng, S and Yang, J and Yan, J and Chu, J and Chen, F and Ran, J and Wang, X and Van de Peer, Y and Leitch, AR and Wang, Q},
title = {The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {4247},
pmid = {34253727},
issn = {2041-1723},
mesh = {Africa ; Cycadopsida/*genetics ; DNA Methylation/genetics ; *Desert Climate ; Evolution, Molecular ; *Genome, Plant ; Geography ; Meristem/genetics ; Molecular Sequence Annotation ; Plant Leaves/genetics ; Rain ; Sequence Analysis, DNA ; Species Specificity ; Transcriptome/genetics ; },
abstract = {The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and transcriptome data to explore its astonishing biology. We also present a refined, high-quality assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant's longevity and tolerance to temperature, nutrient and water stress.},
}
@article {pmid34252564,
year = {2022},
author = {Fournier, E and Roussel, C and Dominicis, A and Ley, D and Peyron, MA and Collado, V and Mercier-Bonin, M and Lacroix, C and Alric, M and Van de Wiele, T and Chassard, C and Etienne-Mesmin, L and Blanquet-Diot, S},
title = {In vitro models of gut digestion across childhood: current developments, challenges and future trends.},
journal = {Biotechnology advances},
volume = {54},
number = {},
pages = {107796},
doi = {10.1016/j.biotechadv.2021.107796},
pmid = {34252564},
issn = {1873-1899},
mesh = {Animals ; Child ; Digestion ; *Environmental Pollutants ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/physiology ; Humans ; },
abstract = {The human digestion is a multi-step and multi-compartment process essential for human health, at the heart of many issues raised by academics, the medical world and industrials from the food, nutrition and pharma fields. In the first years of life, major dietary changes occur and are concomitant with an evolution of the whole child digestive tract anatomy and physiology, including colonization of gut microbiota. All these phenomena are influenced by child exposure to environmental compounds, such as drugs (especially antibiotics) and food pollutants, but also childhood infections. Due to obvious ethical, regulatory and technical limitations, in vivo approaches in animal and human are more and more restricted to favor complementary in vitro approaches. This review summarizes current knowledge on the evolution of child gut physiology from birth to 3 years old regarding physicochemical, mechanical and microbial parameters. Then, all the available in vitro models of the child digestive tract are described, ranging from the simplest static mono-compartmental systems to the most sophisticated dynamic and multi-compartmental models, and mimicking from the oral phase to the colon compartment. Lastly, we detail the main applications of child gut models in nutritional, pharmaceutical and microbiological studies and discuss the limitations and challenges facing this field of research.},
}
@article {pmid34252020,
year = {2021},
author = {Doll, EV and Staib, L and Huptas, C and Scherer, S and Wenning, M},
title = {Facklamia lactis sp. nov., isolated from raw milk.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {71},
number = {7},
pages = {},
doi = {10.1099/ijsem.0.004869},
pmid = {34252020},
issn = {1466-5034},
mesh = {Aerococcaceae/*classification/isolation &amp; purification ; Animals ; Bacterial Typing Techniques ; Base Composition ; Cattle ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Germany ; Glycolipids/chemistry ; Milk/*microbiology ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Two strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus Facklamia but could not be assigned to any species with a validly published name. Facklamia miroungae ATCC BAA-466[T] (97.3 % 16S rRNA sequence similarity), Facklamia languida CCUG 37842[T] (96.9 %), and Facklamia hominis CCUG 36813[T] (96.6 %) are the closest relatives. In the 16S rRNA phylogeny and in the core-genome phylogeny strains WS 5301[T] and WS 5302 form a well-supported, separate lineage. Pairwise average nucleotide identity calculated using MUMmer (ANIm) between WS 5301[T] and type strains of other Facklamia species is well below the species cut-off (95 %) and ranges from 83.4 to 87.7 %. The DNA G+C content of the type strain is 36.4 mol% and the assembly size of the genome is 2.2 Mb. Cells of WS 5301[T] are non-motile, non-endospore-forming, oxidase-negative, catalase-negative and facultatively anaerobic cocci. The fastidious species grows at 10-40 °C and with up to 7.0 % (w/v) NaCl in BHI supplemented with 5 g l[-1] yeast extract. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and two glycolipids. Predominant fatty acids are C16 : 1ω9c and C18 : 1ω9c. On the basis of their genomic, physiological and chemotaxonomic characteristics the strains examined in this study represent the same, hitherto unknown species. We propose the name Facklamia lactis sp. nov. for which WS 5301[T] (=DSM 111018[T]=LMG 31861[T]) is the type strain and WS 5302 (=DSM 111019=LMG 31862) is an additional strain of this novel species.},
}
@article {pmid34251452,
year = {2021},
author = {Nguyen, MP and Lehosmaa, K and Martz, F and Koskimäki, JJ and Pirttilä, AM and Häggman, H},
title = {Host species shape the community structure of culturable endophytes in fruits of wild berry species (Vaccinium myrtillus L., Empetrum nigrum L. and Vaccinium vitis-idaea L.).},
journal = {FEMS microbiology ecology},
volume = {97},
number = {8},
pages = {},
pmid = {34251452},
issn = {1574-6941},
mesh = {Basidiomycota ; Endophytes/genetics ; Fruit ; Humans ; *Vaccinium myrtillus ; *Vaccinium vitis-idaea ; },
abstract = {Wild berries are interesting research subjects due to their rich sources of health-beneficial phenolic compounds. However, the internal microbial communities, endophytes, associated with the wild berry fruits are currently unknown. Endophytes are bacteria or fungi inhabiting inside plant tissues, and their functions vary depending on the host species and environmental parameters. The present study aimed to examine community composition of fungal and bacterial endophytes in fruits of three wild berry species (bilberry Vaccinium myrtillus L., lingonberry Vaccinium vitis-idaea L. and crowberry Empetrum nigrum L.) and the effects of host plant species and their growth sites on shaping the endophytic communities. We found that the endophytic community structures differed between the berry species, and fungi were predominant over bacteria in the total endophytic taxa. We identified previously unknown endophytic fungal taxa including Angustimassarina, Dothidea, Fellozyma, Pseudohyphozyma, Hannaella coprosmae and Oberwinklerozyma straminea. A role of soluble phenolic compounds, the intracellular components in wild berry fruits, in shaping the endophytic communities is proposed. Overall, our study demonstrates that each berry species harbors a unique endophytic community of microbes.},
}
@article {pmid34251412,
year = {2021},
author = {Collins, SM and Gibson, GR and Kennedy, OB and Walton, G and Rowland, I and Commane, DM},
title = {Development of a prebiotic blend to influence in vitro fermentation effects, with a focus on propionate, in the gut.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {8},
pages = {},
doi = {10.1093/femsec/fiab101},
pmid = {34251412},
issn = {1574-6941},
mesh = {Fatty Acids, Volatile ; Feces ; Fermentation ; Humans ; Inulin/metabolism ; *Prebiotics ; *Propionates ; },
abstract = {Short chain fatty acids (SCFAs) derived from the human gut microbiota, and in particular propionate, may beneficially influence metabolic processes such as appetite regulation. Development of prebiotics that induce high propionate levels during fermentation is desirable. A total of 11 candidate prebiotics were screened to investigate their fermentation characteristics, with a focus on propionate production in mixed anaerobic batch culture of faecal bacteria. Further to this, a continuous 3-stage colonic fermentation model (simulating the human colon) was used to evaluate changes in microbial ecology, lactate and SCFA production of three 50:50 blends, comprising both slow and rapidly fermented prebiotics. In mixed batch culture: xylo-oligosaccharide, polydextrose and α-gluco-oligosaccharide were associated with the greatest increase in propionate. Polydextrose, α-gluco-oligosaccharide, β-1,4 glucan and oat fibre induced the greatest reductions in the acetate to propionate ratio. The most bifidogenic prebiotics were the oligosaccharides. Fermentation of a 50:50 blend of inulin and arabinoxylan, through the continuous 3-stage colonic fermentation model, induced a substantial and sustained release of propionate. The sustained release of propionate through the colon, if replicable in vivo, could potentially influence blood glucose, blood lipids and appetite regulation, however, dietary intervention studies are needed. Bifidogenic effects were also observed for the inulin and arabinoxylan blend and an increase synthesis of butyrate and lactate, thus indicating wider prebiotic potential.},
}
@article {pmid34249520,
year = {2021},
author = {Priest, T and Orellana, LH and Huettel, B and Fuchs, BM and Amann, R},
title = {Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e11721},
pmid = {34249520},
issn = {2167-8359},
abstract = {The impacts of climate change on the Arctic Ocean are manifesting throughout the ecosystem at an unprecedented rate. Of global importance are the impacts on heat and freshwater exchange between the Arctic and North Atlantic Oceans. An expanding Atlantic influence in the Arctic has accelerated sea-ice decline, weakened water column stability and supported the northward shift of temperate species. The only deep-water gateway connecting the Arctic and North Atlantic and thus, fundamental for these exchange processes is the Fram Strait. Previous research in this region is extensive, however, data on the ecology of microbial communities is limited, reflecting the wider bias towards temperate and tropical latitudes. Therefore, we present 14 metagenomes, 11 short-read from Illumina and three long-read from PacBio Sequel II, of the 0.2-3 µm fraction to help alleviate such biases and support future analyses on changing ecological patterns. Additionally, we provide 136 species-representative, manually refined metagenome-assembled genomes which can be used for comparative genomics analyses and addressing questions regarding functionality or distribution of taxa.},
}
@article {pmid34249034,
year = {2021},
author = {Kaur, J and Sharma, J},
title = {Orchid Root Associated Bacteria: Linchpins or Accessories?.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {661966},
pmid = {34249034},
issn = {1664-462X},
abstract = {Besides the plant-fungus symbiosis in arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) plants, many endorhizal and rhizosphere bacteria (Root Associated Bacteria, or RAB) also enhance plant fitness, diversity, and coexistence among plants via bi- or tripartite interactions with plant hosts and mycorrhizal fungi. Assuming that bacterial associations are just as important for the obligate mycorrhizal plant family Orchidaceae, surprisingly little is known about the RAB associated with orchids. Herein, we first present the current, underwhelming state of RAB research including their interactions with fungi and the influence of holobionts on plant fitness. We then delineate the need for novel investigations specifically in orchid RAB ecology, and sketch out questions and hypotheses which, when addressed, will advance plant-microbial ecology. We specifically discuss the potential effects of beneficial RAB on orchids as: (1) Plant Growth Promoting Rhizobacteria (PGPR), (2) Mycorrhization Helper Bacteria (MHB), and (3) constituents of an orchid holobiont. We further posit that a hologenomic view should be considered as a framework for addressing co-evolution of the plant host, their obligate Orchid Mycorrhizal Fungi (OMF), and orchid RAB. We conclude by discussing implications of the suggested research for conservation of orchids, their microbial partners, and their collective habitats.},
}
@article {pmid34247483,
year = {2021},
author = {Jakus, N and Mellage, A and Höschen, C and Maisch, M and Byrne, JM and Mueller, CW and Grathwohl, P and Kappler, A},
title = {Anaerobic Neutrophilic Pyrite Oxidation by a Chemolithoautotrophic Nitrate-Reducing Iron(II)-Oxidizing Culture Enriched from a Fractured Aquifer.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {14},
pages = {9876-9884},
doi = {10.1021/acs.est.1c02049},
pmid = {34247483},
issn = {1520-5851},
mesh = {Anaerobiosis ; Ferric Compounds ; Ferrous Compounds ; *Groundwater ; Iron ; *Nitrates ; Oxidation-Reduction ; Sulfides ; },
abstract = {Neutrophilic microbial pyrite (FeS2) oxidation coupled to denitrification is thought to be an important natural nitrate attenuation pathway in nitrate-contaminated aquifers. However, the poor solubility of pyrite raises questions about its bioavailability and the mechanisms underlying its oxidation. Here, we investigated direct microbial pyrite oxidation by a neutrophilic chemolithoautotrophic nitrate-reducing Fe(II)-oxidizing culture enriched from a pyrite-rich aquifer. We used pyrite with natural abundance (NA) of Fe isotopes ([NA]Fe-pyrite) and [57]Fe-labeled siderite to evaluate whether the oxidation of the more soluble Fe(II)-carbonate (FeCO3) can indirectly drive abiotic pyrite oxidation. Our results showed that in setups where only pyrite was incubated with bacteria, direct microbial pyrite oxidation contributed ca. 26% to overall nitrate reduction. The rest was attributed to the oxidation of elemental sulfur (S[0]), present as a residue from pyrite synthesis. Pyrite oxidation was evidenced in the [NA]Fe-pyrite/[57]Fe-siderite setups by maps of [56]FeO and [32]S obtained using a combination of SEM with nanoscale secondary ion MS (NanoSIMS), which showed the presence of [56]Fe(III) (oxyhydr)oxides that could solely originate from [56]FeS2. Based on the fit of a reaction model to the geochemical data and the Fe-isotope distributions from NanoSIMS, we conclude that anaerobic oxidation of pyrite by our neutrophilic enrichment culture was mainly driven by direct enzymatic activity of the cells. The contribution of abiotic pyrite oxidation by Fe[3+] appeared to be negligible in our experimental setup.},
}
@article {pmid34245330,
year = {2022},
author = {Fall, F and Sanguin, H and Fall, D and Tournier, E and Bakhoum, N and Ndiaye, C and Diouf, D and Bâ, AM},
title = {Changes in Intraspecific Diversity of the Arbuscular Mycorrhizal Community Involved in Plant-Plant Interactions Between Sporobolus robustus Kunth and Prosopis juliflora (Swartz) DC Along an Environmental Gradient.},
journal = {Microbial ecology},
volume = {83},
number = {4},
pages = {886-898},
pmid = {34245330},
issn = {1432-184X},
support = {I-1-D-6153-1//International Foundation for Science/ ; },
mesh = {Cebinae ; *Mycorrhizae ; Plants/microbiology ; Poaceae/microbiology ; *Prosopis ; Soil/chemistry ; Soil Microbiology ; },
abstract = {The intensification of biological processes coping with salt stress became a major issue to mitigate land degradation. The Sine-Saloum Delta in Senegal is characterized by salt-affected soils with vegetation dominated by salt-tolerant grass Sporobolus robustus and shrubs like Prosopis juliflora. Plant experiments in controlled conditions suggested that arbuscular mycorrhizal (AM) fungi might be the key actors of facilitation process observed between S. robustus and P. juliflora, but the AM fungal community determinants are largely unknown. The current field-based study aimed at (1) characterizing the environmental drivers (rhizosphere physico-chemical properties, plant type and season) of the AM fungal community along an environmental gradient and (2) identifying the AM fungal taxa that might explain the S. robustus-mediated benefits to P. juliflora. Glomeraceae predominated in the two plants, but a higher richness was observed for S. robustus. The pH and salinity were the main drivers of AM fungal community associated with the two plants, negatively impacting richness and diversity. However, while a negative impact was also observed on mycorrhizal colonization for S. robustus, P. juliflora showed opposite colonization patterns. Furthermore, no change was observed in terms of AM fungal community dissimilarity between the two plants along the environmental gradient as would be expected according to the stress-gradient and complementary hypotheses when a facilitation process occurs. However, changes in intraspecific diversity of shared AM fungal community between the two plants were observed, highlighting 23 AM fungal OTUs associated with both plants and the highest salinity levels. Consequently, the increase of their abundance and frequency along the environmental gradient might suggest their potential role in the facilitation process that can take place between the two plants. Their use in ecological engineering could also represent promising avenues for improving vegetation restoration in saline Senegalese's lands.},
}
@article {pmid34245329,
year = {2022},
author = {Rosado, D and Pérez-Losada, M and Severino, R and Xavier, R},
title = {Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {789-797},
pmid = {34245329},
issn = {1432-184X},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Aquaculture/methods ; *Bass/genetics/microbiology ; *Fish Diseases/drug therapy/microbiology ; *Microbiota ; Photobacterium/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The microbiota of fish skin, the primary barrier against disease, is highly dynamic and modulated by several factors. In fish aquaculture, disease outbreaks occur mainly during early-life stages, with associated high economic losses. Antibiotic treatments sometimes remain the best option to control bacterial diseases, despite many reported negative impacts of its use on fish and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of fingerlings are scarce. We sequenced the bacterial 16S rRNA V4 gene region using a metabarcoding approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with flumequine, on the skin microbiota of farmed seabass (Dicentrarchus labrax) fingerlings. Both infection and antibiotic treatment led to a significant increase in bacterial diversity and core microbial communities and impacted microbiome structure. Dysbiosis was confirmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also significantly affected by flumequine administration, suggesting a detriment to fish skin health. Our results add to an increasing body of literature, showing how fish microbiome response to infection and antibiotics cannot be easily predicted.},
}
@article {pmid34244148,
year = {2021},
author = {Delgado-Baquerizo, M and Eldridge, DJ and Liu, YR and Sokoya, B and Wang, JT and Hu, HW and He, JZ and Bastida, F and Moreno, JL and Bamigboye, AR and Blanco-Pastor, JL and Cano-Díaz, C and Illán, JG and Makhalanyane, TP and Siebe, C and Trivedi, P and Zaady, E and Verma, JP and Wang, L and Wang, J and Grebenc, T and Peñaloza-Bojacá, GF and Nahberger, TU and Teixido, AL and Zhou, XQ and Berdugo, M and Duran, J and Rodríguez, A and Zhou, X and Alfaro, F and Abades, S and Plaza, C and Rey, A and Singh, BK and Tedersoo, L and Fierer, N},
title = {Global homogenization of the structure and function in the soil microbiome of urban greenspaces.},
journal = {Science advances},
volume = {7},
number = {28},
pages = {},
pmid = {34244148},
issn = {2375-2548},
abstract = {The structure and function of the soil microbiome of urban greenspaces remain largely undetermined. We conducted a global field survey in urban greenspaces and neighboring natural ecosystems across 56 cities from six continents, and found that urban soils are important hotspots for soil bacterial, protist and functional gene diversity, but support highly homogenized microbial communities worldwide. Urban greenspaces had a greater proportion of fast-growing bacteria, algae, amoebae, and fungal pathogens, but a lower proportion of ectomycorrhizal fungi than natural ecosystems. These urban ecosystems also showed higher proportions of genes associated with human pathogens, greenhouse gas emissions, faster nutrient cycling, and more intense abiotic stress than natural environments. City affluence, management practices, and climate were fundamental drivers of urban soil communities. Our work paves the way toward a more comprehensive global-scale perspective on urban greenspaces, which is integral to managing the health of these ecosystems and the well-being of human populations.},
}
@article {pmid34243050,
year = {2021},
author = {Favere, J and Waegenaar, F and Boon, N and De Gusseme, B},
title = {Online microbial monitoring of drinking water: How do different techniques respond to contaminations in practice?.},
journal = {Water research},
volume = {202},
number = {},
pages = {117387},
doi = {10.1016/j.watres.2021.117387},
pmid = {34243050},
issn = {1879-2448},
mesh = {Bacteria ; *Drinking Water ; *Groundwater ; Water Microbiology ; Water Quality ; },
abstract = {Safeguarding the microbial water quality remains a challenge for drinking water utilities, and because of population growth and climate change, new issues arise regularly. To overcome these problems, biostable drinking water production and water reuse will become increasingly important. In this respect, high-resolution online microbial monitoring during treatment and distribution could prove essential. Here, we present the first scientific and practical comparison of multiple online microbial monitoring techniques in which six commercially available devices were set up in a full-scale drinking water production plant. Both the devices' response towards operational changes and contaminations, as well as their detection limit for different contaminations were evaluated and compared. During normal operation, all devices were able to detect abrupt operational changes such as backwashing of activated carbon filters and interruption of the production process in a fast and sensitive way. To benchmark their response to contaminations, the calculation of a dynamic baseline for sensitive separation between noise and events is proposed. In order of sensitivity, enzymatic analysis, ATP measurement, and flow cytometric fingerprinting were the most performant for detection of rain- and groundwater contaminations (0.01 - 0.1 v%). On the other hand, optical classification and flow cytometric cell counts showed to be more robust techniques, requiring less maintenance and providing direct information about the cell concentration, even though they were still more sensitive than plate counting. The choice for a certain technology will thus depend on the type of application and is a balance between sensitivity, price and maintenance. All things considered, a combination of several devices and use of advanced data analysis such as fingerprinting may be of added value. In general, the strategic implementation of online microbial monitoring as early-warning system will allow for intensive quality control by high-frequency sampling as well as a short event response timeframe.},
}
@article {pmid34242738,
year = {2021},
author = {Thompson, RS and Gaffney, M and Hopkins, S and Kelley, T and Gonzalez, A and Bowers, SJ and Vitaterna, MH and Turek, FW and Foxx, CL and Lowry, CA and Vargas, F and Dorrestein, PC and Wright, KP and Knight, R and Fleshner, M},
title = {Ruminiclostridium 5, Parabacteroides distasonis, and bile acid profile are modulated by prebiotic diet and associate with facilitated sleep/clock realignment after chronic disruption of rhythms.},
journal = {Brain, behavior, and immunity},
volume = {97},
number = {},
pages = {150-166},
doi = {10.1016/j.bbi.2021.07.006},
pmid = {34242738},
issn = {1090-2139},
mesh = {Animals ; Bacteroidetes ; *Bile Acids and Salts ; Chromatography, Liquid ; Circadian Rhythm ; Diet ; Male ; *Prebiotics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Sleep ; Tandem Mass Spectrometry ; },
abstract = {Chronic disruption of rhythms (CDR) impacts sleep and can result in circadian misalignment of physiological systems which, in turn, is associated with increased disease risk. Exposure to repeated or severe stressors also disturbs sleep and diurnal rhythms. Prebiotic nutrients produce favorable changes in gut microbial ecology, the gut metabolome, and reduce several negative impacts of acute severe stressor exposure, including disturbed sleep, core body temperature rhythmicity, and gut microbial dysbiosis. In light of previous compelling evidence that prebiotic diet broadly reduces negative impacts of acute, severe stressors, we hypothesize that prebiotic diet will also effectively mitigate the negative impacts of chronic disruption of circadian rhythms on physiology and sleep/wake behavior. Male, Sprague Dawley rats were fed diets enriched in prebiotic substrates or calorically matched control chow. After 5 weeks on diet, rats were exposed to CDR (12 h light/dark reversal, weekly for 8 weeks) or remained on undisturbed normal light/dark cycles (NLD). Sleep EEG, core body temperature, and locomotor activity were recorded via biotelemetry in freely moving rats. Fecal samples were collected on experimental days -33, 0 (day of onset of CDR), and 42. Taxonomic identification and relative abundances of gut microbes were measured in fecal samples using 16S rRNA gene sequencing and shotgun metagenomics. Fecal primary, bacterially modified secondary, and conjugated bile acids were measured using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Prebiotic diet produced rapid and stable increases in the relative abundances of Parabacteroides distasonis and Ruminiclostridium 5. Shotgun metagenomics analyses confirmed reliable increases in relative abundances of Parabacteroides distasonis and Clostridium leptum, a member of the Ruminiclostridium genus. Prebiotic diet also modified fecal bile acid profiles; and based on correlational and step-wise regression analyses, Parabacteroides distasonis and Ruminiclostridium 5 were positively associated with each other and negatively associated with secondary and conjugated bile acids. Prebiotic diet, but not CDR, impacted beta diversity. Measures of alpha diversity evenness were decreased by CDR and prebiotic diet prevented that effect. Rats exposed to CDR while eating prebiotic, compared to control diet, more quickly realigned NREM sleep and core body temperature (ClockLab) diurnal rhythms to the altered light/dark cycle. Finally, both cholic acid and Ruminiclostridium 5 prior to CDR were associated with time to realign CBT rhythms to the new light/dark cycle after CDR; whereas both Ruminiclostridium 5 and taurocholic acid prior to CDR were associated with NREM sleep recovery after CDR. These results support our hypothesis and suggest that ingestion of prebiotic substrates is an effective strategy to increase the relative abundance of health promoting microbes, alter the fecal bile acid profile, and facilitate the recovery and realignment of sleep and diurnal rhythms after circadian disruption.},
}
@article {pmid34242413,
year = {2021},
author = {Tuganbaev, T and Honda, K},
title = {Non-zero-sum microbiome immune system interactions.},
journal = {European journal of immunology},
volume = {51},
number = {9},
pages = {2120-2136},
pmid = {34242413},
issn = {1521-4141},
mesh = {Adaptive Immunity/immunology ; Enteric Nervous System/*physiology ; Gastrointestinal Microbiome/*immunology ; Gastrointestinal Tract/*immunology/innervation/*microbiology/physiology ; Humans ; Immunity, Innate/immunology ; Symbiosis/immunology ; },
abstract = {Fundamental asymmetries between the host and its microbiome in enzymatic activities and nutrient storage capabilities have promoted mutualistic adaptations on both sides. As a result, the enteric immune system has evolved so as not to cause a zero-sum sterilization of non-self, but rather achieve a non-zero-sum self-reinforcing cooperation with its evolutionary partner the microbiome. In this review, we attempt to integrate the accumulated knowledge of immune-microbiome interactions into an evolutionary framework and trace the pattern of positive immune-microbiome feedback loops across epithelial, enteric nervous system, innate, and adaptive immune circuits. Indeed, the immune system requires commensal signals for its development and function, and reciprocally protects the microbiome from nutrient shortage and pathogen outgrowth. In turn, a healthy microbiome is the result of immune system curatorship as well as microbial ecology. The paradigms of host-microbiome asymmetry and the cooperative nature of their interactions identified in the gut are applicable across all tissues influenced by microbial activities. Incorporation of immune system influences into models of microbiome ecology will be a step forward toward defining what constitutes a healthy human microbiome and guide discoveries of novel host-microbiome mutualistic adaptations that may be harnessed for the promotion of human health.},
}
@article {pmid34241654,
year = {2022},
author = {Ahmad, T and Farooq, S and Mirza, DN and Kumar, A and Mir, RA and Riyaz-Ul-Hassan, S},
title = {Insights into the Endophytic Bacterial Microbiome of Crocus sativus: Functional Characterization Leads to Potential Agents that Enhance the Plant Growth, Productivity, and Key Metabolite Content.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {669-688},
pmid = {34241654},
issn = {1432-184X},
mesh = {*Crocus/microbiology ; Endophytes ; Fungi ; *Microbiota ; Plant Development ; },
abstract = {The study was undertaken to unravel the culturable endophytic bacterial microbiome of Crocus sativus L. (saffron crocus) and consequently obtain potential leads to develop plant growth-promoting and biocontrol agents for increased productivity and sustainable cultivation. The endophytes formed 47 different operational taxonomic units (OTUs), spanning over 28 genera. The host was preferentially colonized by the genus Bacillus, followed by Burkholderia and Pantoea, respectively. Several endophytes possessed potential plant growth-promoting properties and inhibitory activities against the specific fungal pathogens of saffron. The endophytes, except for Microbacterium oxydans, did not cause any disease symptoms in the pot experiments. The selected cultures, Burkholderia gladioli, Streptomyces achromogenes, and three species of Bacillus, enhanced the host plant growth significantly. Based on the pot experiment results, two isolates, Bacillus mojavensis CS4EB32 and Burkholderia gladioli E39CS3, were selected for the field experiments. We obtained an increase of 67.5%, 69.8%, and 68.3% in the production of flowers with the individual and collective treatments, respectively. The treatments also enhanced the biomass of the plant and the length and weight of stigmas significantly. The endophyte treatments induced the expression of the pathway genes, resulting in a marked increase in the concentration of apocarotenoids. The study indicates that the dominant endophytes support plant growth and development in nature and present an opportunity for developing microbial formulations for the sustainability of saffron cultivation.},
}
@article {pmid34240513,
year = {2021},
author = {Shi, Y and Wang, J and Ao, Y and Han, J and Guo, Z and Liu, X and Zhang, J and Mu, C and Le Roux, X},
title = {Responses of soil N2 O emissions and their abiotic and biotic drivers to altered rainfall regimes and co-occurring wet N deposition in a semi-arid grassland.},
journal = {Global change biology},
volume = {27},
number = {19},
pages = {4894-4908},
doi = {10.1111/gcb.15792},
pmid = {34240513},
issn = {1365-2486},
mesh = {Ecosystem ; *Grassland ; Nitrogen/analysis ; Nitrous Oxide/analysis ; *Soil ; },
abstract = {Global change factors such as changed rainfall regimes and nitrogen (N) deposition contribute to increases in the emission of the greenhouse gas nitrous oxide (N2 O) from the soil. In previous research, N deposition has often been simulated by using a single or a series of N addition events over the course of a year, but wet N deposition actually co-occurs with rainfall. How soil N2 O emissions respond to altered rainfall amount and frequency, wet N deposition, and their interactions is still not fully understood. We designed a three-factor, fully factorial experiment with factors of rainfall amounts (ambient, -30%) rainfall frequency (ambient, ±50%) and wet N deposition (with/without) co-occurring with rainfall in semi-arid grassland mesocosms, and measured N2 O emissions and their possible biotic and abiotic drivers. Across all treatments, reduced rainfall amount and N deposition increased soil N2 O emissions by 35% and 28%, respectively. A significant interactive effect was observed between rainfall amount and N deposition, and to a lesser extent between rainfall frequency and N deposition. Without N deposition, reduced rainfall amount and altered rainfall frequency indirectly affected soil N2 O emissions by changing the abundance of nirK and soil net N mineralization, and the changes in nirK abundance were indirectly driven by soil N availability rather than directly by soil moisture. With N deposition, both the abundance of nirK and the level of soil water-filled pore space contributed to changes in N2 O emissions in response to altered rainfall regimes, and the changes in the abundance of nirK were indirectly driven by plant N uptake and nitrifier (ammonia-oxidizing bacteria) abundance. Our results imply that unlike wetter grassland ecosystems, reduced precipitation may increase N2 O emissions, and N deposition may only slightly increase N2 O emissions in arid and semi-arid N-limited ecosystems that are dominated by grasses with high soil N uptake capacity.},
}
@article {pmid34238491,
year = {2021},
author = {Schweyer, L and Pougnet, L},
title = {[Microbial ecology, the understanding of the invisible living].},
journal = {Revue de l'infirmiere},
volume = {70},
number = {272},
pages = {25-26},
doi = {10.1016/j.revinf.2021.04.007},
pmid = {34238491},
issn = {1293-8505},
mesh = {*Ecology ; *Ecosystem ; Humans ; Hygiene ; },
abstract = {Microorganisms are invisible to the naked eye. Hospital hygiene practices are therefore based on the representation that caregivers have of them. This difficulty can generate irrational behavior and fear of blame. Conversely, a better knowledge of the specificities of this invisible living world favors a rationalization of care practices. To do this, caregivers will be able to appropriate the major concepts of microbiology, particularly microbial ecology.},
}
@article {pmid34238316,
year = {2021},
author = {Oberman, K and Hovens, I and de Haan, J and Falcao-Salles, J and van Leeuwen, B and Schoemaker, R},
title = {Acute pre-operative ibuprofen improves cognition in a rat model for postoperative cognitive dysfunction.},
journal = {Journal of neuroinflammation},
volume = {18},
number = {1},
pages = {156},
pmid = {34238316},
issn = {1742-2094},
mesh = {Animals ; Anti-Inflammatory Agents, Non-Steroidal/*administration &amp; dosage ; Cognition/*drug effects/physiology ; Hippocampus/drug effects/metabolism ; Ibuprofen/*administration &amp; dosage ; Male ; Maze Learning/drug effects/physiology ; Postoperative Cognitive Complications/*drug therapy/metabolism/psychology ; Preoperative Care/*methods ; Rats ; Rats, Wistar ; },
abstract = {BACKGROUND: Inflammation is considered a key factor in the development of postoperative cognitive dysfunction (POCD). Therefore, we hypothesized that pre-operative anti-inflammatory treatment with ibuprofen would inhibit POCD in our rat-model.<br><br>METHODS: Male Wistar rats of 3 or 23 months old received a single injection of ibuprofen (15 mg/kg i.p.) or were control handled before abdominal surgery. Timed blood and fecal samples were collected for analyses of inflammation markers and gut microbiome changes. Behavioral testing was performed from 9 to 14 days after surgery, in the open field, novel object- and novel location-recognition tests and Morris water maze. Neuroinflammation and neurogenesis were assessed by immune histochemistry after sacrifice on postoperative day 14.<br><br>RESULTS: Ibuprofen improved short-term spatial memory in the novel location recognition test, and increased hippocampal neurogenesis. However, these effects were associated with increased hippocampal microglia activity. Whereas plasma cytokine levels (IL1-&#x3b2;, IL6, IL10, and TNF&#x3b1;) were not significantly affected, VEGF levels increased and IFABP levels decreased after ibuprofen. Long-term memory in the Morris water maze was not significantly improved by ibuprofen. The gut microbiome was neither significantly affected by surgery nor by ibuprofen treatment. In general, effects in aged rats appeared similar to those in young rats, though less pronounced.<br><br>CONCLUSION: A single injection of ibuprofen before surgery improved hippocampus-associated short-term memory after surgery and increased neurogenesis. However, this favorable outcome seemed not attributable to inhibition of (neuro)inflammation. Potential contributions of intestinal and blood-brain barrier integrity need further investigation. Although less pronounced compared to young rats, effects in aged rats indicate that even elderly individuals could benefit from ibuprofen treatment.},
}
@article {pmid34235554,
year = {2022},
author = {Buysse, M and Binetruy, F and Leibson, R and Gottlieb, Y and Duron, O},
title = {Ecological Contacts and Host Specificity Promote Replacement of Nutritional Endosymbionts in Ticks.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {776-788},
pmid = {34235554},
issn = {1432-184X},
support = {EVOSYM//Ministry of Science and Technology, Israel/ ; EVOSYM//centre national de la recherche scientifique (CNRS)/ ; ANR-10-LAX-25-01//Agence Nationale de la Recherche (FR)/ ; ISF No. 1074/18//Israel science foundation/ ; },
mesh = {Animals ; *Francisella ; Host Specificity ; Phylogeny ; Symbiosis ; *Ticks ; },
abstract = {Symbiosis with vitamin-provisioning microbes is essential for the nutrition of animals with some specialized feeding habits. While coevolution favors the interdependence between symbiotic partners, their associations are not necessarily stable: Recently acquired symbionts can replace ancestral symbionts. In this study, we demonstrate successful replacement by Francisella-like endosymbionts (-LE), a group of B-vitamin-provisioning endosymbionts, across tick communities driven by horizontal transfers. Using a broad collection of Francisella-LE-infected tick species, we determined the diversity of Francisella-LE haplotypes through a multi-locus strain typing approach and further characterized their phylogenetic relationships and their association with biological traits of their tick hosts. The patterns observed showed that Francisella-LE commonly transfer through similar ecological networks and geographic distributions shared among different tick species and, in certain cases, through preferential shuffling across congeneric tick species. Altogether, these findings reveal the importance of geographic, ecological, and phylogenetic proximity in shaping the replacement pattern in which new nutritional symbioses are initiated.},
}
@article {pmid34232732,
year = {2021},
author = {Malki, K and Sawaya, NA and Tisza, MJ and Coutinho, FH and Rosario, K and Székely, AJ and Breitbart, M},
title = {Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida).},
journal = {Applied and environmental microbiology},
volume = {87},
number = {18},
pages = {e0064621},
pmid = {34232732},
issn = {1098-5336},
mesh = {Florida ; Fresh Water/microbiology ; Genome, Viral ; Natural Springs/*microbiology ; *Prokaryotic Cells ; RNA, Ribosomal, 16S ; *Viruses/genetics ; Water Microbiology ; },
abstract = {Flow from high-magnitude springs fed by the Floridan aquifer system contributes hundreds of liters of water per second to rivers, creating unique lotic systems. Despite their importance as freshwater sources and their contributions to the state's major rivers, little is known about the composition and spatiotemporal variability of prokaryotic and viral communities of these spring systems or their influence on downstream river sites. At four time points throughout a year, we determined the abundance and diversity of prokaryotic and viral communities at three sites within the first-magnitude Manatee Springs system (the spring head where water emerges from the aquifer, a mixed region where the spring run ends, and a downstream site in the Suwannee River). The abundance of prokaryotes and virus-like particles increased 100-fold from the spring head to the river and few members from the head communities persisted in the river at low abundance, suggesting the springs play a minor role in seeding downstream communities. Prokaryotic and viral communities within Manatee Springs clustered by site, with seasonal variability likely driven by flow. As water flowed through the system, microbial community composition was affected by changes in physiochemical parameters and community coalescence. Evidence of species sorting and mass effects could be seen in the assemblages. Greater temporal fluctuations were observed in prokaryotic and viral community composition with increasing distance from the spring outflow, reflecting the relative stability of the groundwater environment, and comparisons to springs from prior work reaffirmed that distinct first-magnitude springs support unique communities. IMPORTANCE Prokaryotic and viral communities are central to food webs and biogeochemical processes in aquatic environments, where they help maintain ecosystem health. The Floridan aquifer system (FAS), which is the primary drinking water source for millions of people in the southeastern United States, contributes large amounts of freshwater to major river systems in Florida through its springs. However, there is a paucity of information regarding the spatiotemporal dynamics of microbial communities in these essential flowing freshwater systems. This work explored the prokaryotic and viral communities in a first-magnitude spring system fed by the FAS that discharges millions of liters of water per day into the Suwannee River. This study examined microbial community composition through space and time as well as the environmental parameters and metacommunity assembly mechanisms that shape these communities, providing a foundational understanding for monitoring future changes.},
}
@article {pmid34231344,
year = {2021},
author = {Ossowicki, A and Raaijmakers, JM and Garbeva, P},
title = {Disentangling soil microbiome functions by perturbation.},
journal = {Environmental microbiology reports},
volume = {13},
number = {5},
pages = {582-590},
pmid = {34231344},
issn = {1758-2229},
mesh = {Bacteria ; Microbial Consortia ; *Microbiota/genetics ; *Soil ; Soil Microbiology ; },
abstract = {Soil biota contribute to diverse soil ecosystem services such as greenhouse gas mitigation, carbon sequestration, pollutant degradation, plant disease suppression and nutrient acquisition for plant growth. Here, we provide detailed insight into different perturbation approaches to disentangle soil microbiome functions and to reveal the underlying mechanisms. By applying perturbation, one can generate compositional and functional shifts of complex microbial communities in a controlled way. Perturbations can reduce microbial diversity, diminish the abundance of specific microbial taxa and thereby disturb the interactions within the microbial consortia and with their eukaryotic hosts. Four different microbiome perturbation approaches, namely selective heat, specific biocides, dilution-to-extinction and genome editing are the focus of this mini-review. We also discuss the potential of perturbation approaches to reveal the tipping point at which specific soil functions are lost and to link this change to key microbial taxa involved in specific microbiome-associated phenotypes.},
}
@article {pmid34231036,
year = {2022},
author = {Viana, TA and Barbosa, WF and Jojoa, LLB and Bernardes, RC and da Silva, JS and Jacobs-Lorena, M and Martins, GF},
title = {A Genetically Modified Anti-Plasmodium Bacterium Is Harmless to the Foragers of the Stingless Bee Partamona helleri.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {766-775},
pmid = {34231036},
issn = {1432-184X},
support = {CBB-APQ-00247-14//Funda&#xe7;&#xe3;o de Apoio ao Ensino, Pesquisa e Assist&#xea;ncia do Hospital das Cl&#xed;nicas da Faculdade de Medicina de Ribeir&#xe3;o Preto da Universidade de S&#xe3;o Paulo (BR)/ ; R01 AI031478/AI/NIAID NIH HHS/United States ; R01AI031478/NH/NIH HHS/United States ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 301725/2019-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; R01 AI051366/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Bees ; Brazil ; *Mosquito Vectors ; *Serratia/genetics ; },
abstract = {Paratransgenesis consists of genetically engineering an insect symbiont to control vector-borne diseases. Biosafety assessments are a prerequisite for the use of genetically modified organisms (GMOs). Assessments rely on the measurement of the possible impacts of GMOs on different organisms, including beneficial organisms, such as pollinators. The bacterium Serratia AS1 has been genetically modified to express anti-Plasmodium effector proteins and does not impose a fitness cost on mosquitoes that carry it. In the present study, we assessed the impact of this bacterium on the native bee Partamona helleri (Meliponini), an ecologically important species in Brazil. Serratia eGFP AS1 (recombinant strain) or a wild strain of Serratia marcescens were suspended in a sucrose solution and fed to foragers, followed by measurements of survival, feeding rate, and behavior (walking and flying). These bacteria did not change any of the variables measured at 24, 72, and 144 h after the onset of the experiment. Recombinant and wild bacteria were detected in the homogenates of digestive tract during the 144 h period analyzed, but their numbers decreased with time. The recombinant strain was detected in the midgut at 24 h and in the hindgut at 72 h and 144 h after the onset of the experiment under the fluorescent microscope. As reported for mosquitoes, Serratia eGFP AS1 did not compromise the foragers of P. helleri, an ecologically relevant bee.},
}
@article {pmid34229570,
year = {2022},
author = {Rizwan, T and Kothidar, A and Meghwani, H and Sharma, V and Shobhawat, R and Saini, R and Vaishnav, HK and Singh, V and Pratap, M and Sihag, H and Kumar, S and Dey, JK and Dey, SK},
title = {Comparative analysis of SARS-CoV-2 envelope viroporin mutations from COVID-19 deceased and surviving patients revealed implications on its ion-channel activities and correlation with patient mortality.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {40},
number = {20},
pages = {10454-10469},
doi = {10.1080/07391102.2021.1944319},
pmid = {34229570},
issn = {1538-0254},
mesh = {Humans ; *COVID-19/mortality/virology ; Mutation ; *SARS-CoV-2/genetics ; *Viroporin Proteins/genetics ; },
abstract = {One major obstacle in designing a successful therapeutic regimen to combat COVID-19 pandemic is the frequent occurrence of mutations in the SARS-CoV-2 resulting in patient to patient variations. Out of the four structural proteins of SARS-CoV-2 namely, spike, envelope, nucleocapsid and membrane, envelope protein governs the virus pathogenicity and induction of acute-respiratory-distress-syndrome which is the major cause of death in COVID-19 patients. These effects are facilitated by the viroporin (ion-channel) like activities of the envelope protein. Our current work reports metagenomic analysis of envelope protein at the amino acid sequence level through mining all the available SARS-CoV-2 genomes from the GISAID and coronapp servers. We found majority of mutations in envelope protein were localized at or near PDZ binding motif. Our analysis also demonstrates that the acquired mutations might have important implications on its structure and ion-channel activity. A statistical correlation between specific mutations (e.g. F4F, R69I, P71L, L73F) with patient mortalities were also observed, based on the patient data available for 18,691 SARS-CoV-2-genomes in the GISAID database till 30 April 2021. Albeit, whether these mutations exist as the cause or the effect of co-infections and/or co-morbid disorders within COVID-19 patients is still unclear. Moreover, most of the current vaccine and therapeutic interventions are revolving around spike protein. However, emphasizing on envelope protein's (1) conserved epitopes, (2) pathogenicity attenuating mutations, and (3) mutations present in the deceased patients, as reported in our present study, new directions to the ongoing efforts of therapeutic developments against COVID-19 can be achieved by targeting envelope viroporin.},
}
@article {pmid34228269,
year = {2021},
author = {Agustí, A and Campillo, I and Balzano, T and Benítez-Páez, A and López-Almela, I and Romaní-Pérez, M and Forteza, J and Felipo, V and Avena, NM and Sanz, Y},
title = {Bacteroides uniformis CECT 7771 Modulates the Brain Reward Response to Reduce Binge Eating and Anxiety-Like Behavior in Rat.},
journal = {Molecular neurobiology},
volume = {58},
number = {10},
pages = {4959-4979},
pmid = {34228269},
issn = {1559-1182},
support = {AGL2014-52101-P//Ministry of Science, Innovationa and Universities (MCIU, Spain)/ ; AGL2017-88801-P//Ministry of Science, Innovation and Universities (MCIU,Spain)/ ; PROMETEO/2019/015//Conselleria de Educaci&#xf3;n, Investigaci&#xf3;n, Cultura y Deporte de la Comunidad valenciana/ ; AGL2017-88801-P//Ministry of Science, Innovation and Universities (MCIU, Spain)/ ; PTA//Ministry of Science, Innovation and Univesities (MCIU, Spain)/ ; },
mesh = {Animals ; Anxiety/*metabolism/therapy ; Bacteroides/isolation &amp; purification/*metabolism ; Binge-Eating Disorder/*metabolism/therapy ; Brain/*metabolism ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant, Newborn ; Male ; Microdialysis/methods ; Rats ; Rats, Inbred WKY ; *Reward ; },
abstract = {Food addiction (FA) is characterized by behavioral and neurochemical changes linked to loss of food intake control. Gut microbiota may influence appetite and food intake via endocrine and neural routes. The gut microbiota is known to impact homeostatic energy mechanisms, but its role in regulating the reward system is less certain. We show that the administration of Bacteroides uniformis CECT 7771 (B. uniformis) in a rat FA model impacts on the brain reward response, ameliorating binge eating and decreasing anxiety-like behavior. These effects are mediated, at least in part, by changes in the levels of dopamine, serotonin, and noradrenaline in the nucleus accumbens and in the expression of dopamine D1 and D2 receptors in the prefrontal cortex and intestine. B. uniformis reverses the fasting-induced microbiota changes and increases the abundance of species linked to healthy metabolotypes. Our data indicate that microbiota-based interventions might help to control compulsive overeating by modulating the reward response.},
}
@article {pmid34228196,
year = {2022},
author = {de Menezes, GCA and Câmara, PEAS and Pinto, OHB and Convey, P and Carvalho-Silva, M and Simões, JC and Rosa, CA and Rosa, LH},
title = {Fungi in the Antarctic Cryosphere: Using DNA Metabarcoding to Reveal Fungal Diversity in Glacial Ice from the Antarctic Peninsula Region.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {647-657},
pmid = {34228196},
issn = {1432-184X},
mesh = {Animals ; Antarctic Regions ; *Basidiomycota/genetics ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Fungi/genetics ; Ice ; },
abstract = {We assessed fungal diversity present in glacial from the Antarctic Peninsula using DNA metabarcoding through high-throughput sequencing (HTS). We detected a total of 353,879 fungal DNA reads, representing 94 genera and 184 taxa, in glacial ice fragments obtained from seven sites in the north-west Antarctic Peninsula and South Shetland Islands. The phylum Ascomycota dominated the sequence diversity, followed by Basidiomycota and Mortierellomycota. Penicillium sp., Cladosporium sp., Penicillium atrovenetum, Epicoccum nigrum, Pseudogymnoascus sp. 1, Pseudogymnoascus sp. 2, Phaeosphaeriaceae sp. and Xylaria grammica were the most dominant taxa, respectively. However, the majority of the fungal diversity comprised taxa of rare and intermediate relative abundance, predominately known mesophilic fungi. High indices of diversity and richness were calculated, along with moderate index of dominance, which varied among the different sampling sites. Only 26 (14%) of the total fungal taxa detected were present at all sampling sites. The identified diversity was dominated by saprophytic taxa, followed by known plant and animal pathogens and a low number of symbiotic fungi. Our data suggest that Antarctic glacial ice may represent a hotspot of previously unreported fungal diversity; however, further studies are required to integrate HTS and culture approaches to confirm viability of the taxa detected.},
}
@article {pmid34227830,
year = {2021},
author = {McDaniel, EA and Moya-Flores, F and Keene Beach, N and Camejo, PY and Oyserman, BO and Kizaric, M and Khor, EH and Noguera, DR and McMahon, KD},
title = {Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0047421},
pmid = {34227830},
issn = {2379-5077},
support = {//MINEDUC | Comisi&#xf3;n Nacional de Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (CONICYT)/ ; MCB-1518130//National Science Foundation (NSF)/ ; Department of Bacteriology//University of Wisconsin-Madison (UW)/ ; },
abstract = {Natural microbial communities consist of closely related taxa that may exhibit phenotypic differences and inhabit distinct niches. However, connecting genetic diversity to ecological properties remains a challenge in microbial ecology due to the lack of pure cultures across the microbial tree of life. "Candidatus Accumulibacter phosphatis" (Accumulibacter) is a polyphosphate-accumulating organism that contributes to the enhanced biological phosphorus removal (EBPR) biotechnological process for removing excess phosphorus from wastewater and preventing eutrophication from downstream receiving waters. Distinct Accumulibacter clades often coexist in full-scale wastewater treatment plants and laboratory-scale enrichment bioreactors and have been hypothesized to inhabit distinct ecological niches. However, since individual strains of the Accumulibacter lineage have not been isolated in pure culture to date, these predictions have been made solely on genome-based comparisons and enrichments with varying strain compositions. Here, we used genome-resolved metagenomics and metatranscriptomics to explore the activity of coexisting Accumulibacter strains in an engineered bioreactor environment. We obtained four high-quality genomes of Accumulibacter strains that were present in the bioreactor ecosystem, one of which is a completely contiguous draft genome scaffolded with long Nanopore reads. We identified core and accessory genes to investigate how gene expression patterns differed among the dominating strains. Using this approach, we were able to identify putative pathways and functions that may confer distinct functions to Accumulibacter strains and provide key functional insights into this biotechnologically significant microbial lineage. IMPORTANCE "Candidatus Accumulibacter phosphatis" is a model polyphosphate-accumulating organism that has been studied using genome-resolved metagenomics, metatranscriptomics, and metaproteomics to understand the EBPR process. Within the Accumulibacter lineage, several similar but diverging clades are defined by the shared sequence identity of the polyphosphate kinase (ppk1) locus. These clades are predicted to have key functional differences in acetate uptake rates, phage defense mechanisms, and nitrogen-cycling capabilities. However, such hypotheses have largely been made based on gene content comparisons of sequenced Accumulibacter genomes, some of which were obtained from different systems. Here, we performed time series genome-resolved metatranscriptomics to explore gene expression patterns of coexisting Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.},
}
@article {pmid34227829,
year = {2021},
author = {Trojan, D and Garcia-Robledo, E and Meier, DV and Hausmann, B and Revsbech, NP and Eichorst, SA and Woebken, D},
title = {Microaerobic Lifestyle at Nanomolar O2 Concentrations Mediated by Low-Affinity Terminal Oxidases in Abundant Soil Bacteria.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0025021},
pmid = {34227829},
issn = {2379-5077},
support = {P26392-B20//Austrian Science Fund (FWF)/ ; FEDER-UCA18-107225//EC | European Regional Development Fund (ERDF)/ ; },
abstract = {High-affinity terminal oxidases (TOs) are believed to permit microbial respiration at low oxygen (O2) levels. Genes encoding such oxidases are widespread, and their existence in microbial genomes is taken as an indicator for microaerobic respiration. We combined respiratory kinetics determined via highly sensitive optical trace O2 sensors, genomics, and transcriptomics to test the hypothesis that high-affinity TOs are a prerequisite to respire micro- and nanooxic concentrations of O2 in environmentally relevant model soil organisms: acidobacteria. Members of the Acidobacteria harbor branched respiratory chains terminating in low-affinity (caa3-type cytochrome c oxidases) as well as high-affinity (cbb3-type cytochrome c oxidases and/or bd-type quinol oxidases) TOs, potentially enabling them to cope with varying O2 concentrations. The measured apparent Km (Km(app)) values for O2 of selected strains ranged from 37 to 288 nmol O2 liter[-1], comparable to values previously assigned to low-affinity TOs. Surprisingly, we could not detect the expression of the conventional high-affinity TO (cbb3 type) at micro- and nanomolar O2 concentrations but detected the expression of low-affinity TOs. To the best of our knowledge, this is the first observation of microaerobic respiration imparted by low-affinity TOs at O2 concentrations as low as 1 nM. This challenges the standing hypothesis that a microaerobic lifestyle is exclusively imparted by the presence of high-affinity TOs. As low-affinity TOs are more efficient at generating ATP than high-affinity TOs, their utilization could provide a great benefit, even at low-nanomolar O2 levels. Our findings highlight energy conservation strategies that could promote the success of Acidobacteria in soil but might also be important for as-yet-unrevealed microorganisms. IMPORTANCE Low-oxygen habitats are widely distributed on Earth, ranging from the human intestine to soils. Microorganisms are assumed to have the capacity to respire low O2 concentrations via high-affinity terminal oxidases. By utilizing strains of a ubiquitous and abundant group of soil bacteria, the Acidobacteria, and combining respiration kinetics, genomics, and transcriptomics, we provide evidence that these microorganisms use the energetically more efficient low-affinity terminal oxidases to respire low-nanomolar O2 concentrations. This questions the standing hypothesis that the ability to respire traces of O2 stems solely from the activity of high-affinity terminal oxidases. We propose that this energetically efficient strategy extends into other, so-far-unrevealed microbial clades. Our findings also demonstrate that physiological predictions regarding the utilization of different O2 concentrations based solely on the presence or absence of terminal oxidases in bacterial genomes can be misleading.},
}
@article {pmid34226946,
year = {2022},
author = {Tan, MH and Loke, S and Croft, LJ and Gleason, FH and Lange, L and Pilgaard, B and Trevathan-Tackett, SM},
title = {Correction to: First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {822},
doi = {10.1007/s00248-021-01807-7},
pmid = {34226946},
issn = {1432-184X},
}
@article {pmid34225812,
year = {2021},
author = {Stothart, MR and Newman, AEM},
title = {Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal.},
journal = {Animal microbiome},
volume = {3},
number = {1},
pages = {46},
pmid = {34225812},
issn = {2524-4671},
abstract = {BACKGROUND: Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate).<br><br>RESULTS: Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations.<br><br>CONCLUSIONS: Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.},
}
@article {pmid34223947,
year = {2022},
author = {Jiao, L and Kourkoumpetis, T and Hutchinson, D and Ajami, NJ and Hoffman, K and White, DL and Graham, DY and Hair, C and Shah, R and Kanwal, F and Jarbrink-Sehgal, M and Husain, N and Hernaez, R and Hou, J and Cole, R and Velez, M and Ketwaroo, G and Kramer, J and El-Serag, HB and Petrosino, JF},
title = {Spatial Characteristics of Colonic Mucosa-Associated Gut Microbiota in Humans.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {811-821},
pmid = {34223947},
issn = {1432-184X},
support = {P30 DK56338/DK/NIDDK NIH HHS/United States ; I01 CX001430/CX/CSRD VA/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; },
mesh = {Adult ; Colon/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Intestinal Mucosa/microbiology ; RNA, Ribosomal, 16S/genetics ; Verrucomicrobia/genetics ; },
abstract = {Limited data exist on the spatial distribution of the colonic bacteria in humans. We collected the colonic biopsies from five segments of 27 polyp-free adults and collected feces from 13 of them. We sequenced the V4 region of the bacterial 16S rRNA gene using the MiSeq platform. The sequencing data were assigned to the amplicon sequence variant (ASV) using SILVA. Biodiversity and the relative abundance of the ASV were compared across the colonic segments and between the rectal and fecal samples. Bacterial functional capacity was assessed using Tax4fun. Each individual had a unique bacterial community composition (Weighted Bray-Curtis P value = 0.001). There were no significant differences in richness, evenness, community composition, and the taxonomic structure across the colon segments in all the samples. Firmicutes (47%), Bacteroidetes (39%), and Proteobacteria (6%) were the major phyla in all segments, followed by Verrucomicrobia, Fusobacteria, Desulfobacterota, and Actinobacteria. There were 15 genera with relative abundance > 1%, including Bacteroides, Faecalibacterium, Escherichia/Shigella, Sutterella, Akkermansia, Parabacteroides, Prevotella, Lachnoclostridium, Alistipes, Fusobacterium, Erysipelatoclostridium, and four Lachnospiraceae family members. Intra-individually, the community compositional dissimilarity was the greatest between the cecum and the rectum. There were significant differences in biodiversity and the taxonomic structure between the rectal and fecal bacteria. The bacterial community composition and structure were homogeneous across the large intestine in adults. The inter-individual variability of the bacteria was greater than inter-segment variability. The rectal and fecal bacteria differed in the community composition and structure.},
}
@article {pmid34223869,
year = {2021},
author = {Smercina, DN and Bailey, VL and Hofmockel, KS},
title = {Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {7},
pages = {},
doi = {10.1093/femsec/fiab091},
pmid = {34223869},
issn = {1574-6941},
mesh = {Climate Change ; Ecology ; *Ecosystem ; *Soil ; Soil Microbiology ; },
abstract = {Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.},
}
@article {pmid34220760,
year = {2021},
author = {Ceron-Chafla, P and Chang, YT and Rabaey, K and van Lier, JB and Lindeboom, REF},
title = {Directional Selection of Microbial Community Reduces Propionate Accumulation in Glycerol and Glucose Anaerobic Bioconversion Under Elevated pCO2.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {675763},
pmid = {34220760},
issn = {1664-302X},
abstract = {Volatile fatty acid accumulation is a sign of digester perturbation. Previous work showed the thermodynamic limitations of hydrogen and CO2 in syntrophic propionate oxidation under elevated partial pressure of CO2 (pCO2). Here we study the effect of directional selection under increasing substrate load as a strategy to restructure the microbial community and induce cross-protection mechanisms to improve glucose and glycerol conversion performance under elevated pCO2. After an adaptive laboratory evolution (ALE) process, viable cell density increased and predominant microbial groups were modified: an increase in Methanosaeta and syntrophic propionate oxidizing bacteria (SPOB) associated with the Smithella genus was found with glycerol as the substrate. A modest increase in SPOB along with a shift in the predominance of Methanobacterium toward Methanosaeta was observed with glucose as the substrate. The evolved inoculum showed affected diversity within archaeal spp. under 5 bar initial pCO2; however, higher CH4 yield resulted from enhanced propionate conversion linked to the community shifts and biomass adaptation during the ALE process. Moreover, the evolved inoculum attained increased cell viability with glucose and a marginal decrease with glycerol as the substrate. Results showed differences in terms of carbon flux distribution using the evolved inoculum under elevated pCO2: glucose conversion resulted in a higher cell density and viability, whereas glycerol conversion led to higher propionate production whose enabled conversion reflected in increased CH4 yield. Our results highlight that limited propionate conversion at elevated pCO2 resulted from decreased cell viability and low abundance of syntrophic partners. This limitation can be mitigated by promoting alternative and more resilient SPOB and building up biomass adaptation to environmental conditions via directional selection of microbial community.},
}
@article {pmid34219185,
year = {2021},
author = {Jani, K and Bandal, J and Shouche, Y and Shafi, S and Azhar, EI and Zumla, A and Sharma, A},
title = {Extended Ecological Restoration of Bacterial Communities in the Godavari River During the COVID-19 Lockdown Period: a Spatiotemporal Meta-analysis.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {365-376},
pmid = {34219185},
issn = {1432-184X},
support = {IA/E/17/1/503700/WTDBT_/DBT-Wellcome Trust India Alliance/India ; BT/Coord.II/01/03/2016//Department of Biotechnology , Ministry of Science and Technology/ ; },
mesh = {Bacteria/classification/*isolation &amp; purification ; COVID-19/epidemiology/prevention &amp; control ; Communicable Disease Control/*legislation &amp; jurisprudence ; Drug Resistance, Bacterial ; *Ecosystem ; Environmental Monitoring ; Hinduism ; Human Activities ; India/epidemiology ; Principal Component Analysis ; Rivers/*microbiology ; },
abstract = {The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz. Proteobacteria (70.6%), Bacteroidetes (22.5%), Verrucomicrobia (1.8%), Actinobacteria (1.2%) and Cyanobacteria (1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by - 0.71-fold and - 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.},
}
@article {pmid34218293,
year = {2022},
author = {Németh, JB and Knapp, DG and Kósa, A and Hegedűs, P&#xc1; and Herczeg, G and Vági, P and Kovács, GM},
title = {Micro-scale Experimental System Coupled with Fluorescence-based Estimation of Fungal Biomass to Study Utilisation of Plant Substrates.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {714-723},
pmid = {34218293},
issn = {1432-184X},
support = {J&#xe1;nos Bolyai Research Scholarship//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; K109102//Hungarian Scientific Research Fund/ ; K105517//Hungarian Scientific Research Fund/ ; ELTE Thematic Excellence Program 2020 (TKP2020-IKA-05)//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal/ ; },
mesh = {Biomass ; *Ecosystem ; *Endophytes ; Fluorescence ; Fungi/metabolism ; Plant Roots/microbiology ; },
abstract = {The degradation capacity and utilisation of complex plant substrates are crucial for the functioning of saprobic fungi and different plant symbionts with fundamental functions in ecosystems. Measuring the growth capacity and biomass of fungi on such systems is a challenging task. We established a new micro-scale experimental setup using substrates made of different plant species and organs as media for fungal growth. We adopted and tested a reliable and simple titration-based method for the estimation of total fungal biomass within the substrates using fluorescence-labelled lectin. We found that the relationship between fluorescence intensity and fungal dry weight was strong and linear but differed among fungi. The effect of the plant organ (i.e. root vs. shoot) used as substrate on fungal growth differed among plant species and between root endophytic fungal species. The novel microscale experimental system is useful for screening the utilisation of different substrates, which can provide insight into the ecological roles and functions of fungi. Furthermore, our fungal biomass estimation method has applications in various fields. As the estimation is based on the fungal cell wall, it measures the total cumulative biomass produced in a certain environment.},
}
@article {pmid34218232,
year = {2021},
author = {Huang, YM and Straub, D and Kappler, A and Smith, N and Blackwell, N and Kleindienst, S},
title = {A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction.},
journal = {Microbial physiology},
volume = {31},
number = {3},
pages = {280-295},
doi = {10.1159/000517083},
pmid = {34218232},
issn = {2673-1673},
mesh = {Carbon Cycle ; *Ferrous Compounds ; *Nitrates ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Fe(II) oxidation coupled to nitrate reduction (NRFO) has been described for many environments. Yet very few autotrophic microorganisms catalysing NRFO have been cultivated and their diversity, as well as their mechanisms for NRFO in situ remain unclear. A novel autotrophic NRFO enrichment culture, named culture BP, was obtained from freshwater sediment. After more than 20 transfers, culture BP oxidized 8.22 mM of Fe(II) and reduced 2.42 mM of nitrate within 6.5 days under autotrophic conditions. We applied metagenomic, metatranscriptomic, and metaproteomic analyses to culture BP to identify the microorganisms involved in autotrophic NRFO and to unravel their metabolism. Overall, twelve metagenome-assembled genomes (MAGs) were constructed, including a dominant Gallionellaceae sp. MAG (≥71% relative abundance). Genes and transcripts associated with potential Fe(II) oxidizers in culture BP, identified as a Gallionellaceae sp., Noviherbaspirillum sp., and Thiobacillus sp., were likely involved in metal oxidation (e.g., cyc2, mtoA), denitrification (e.g., nirK/S, norBC), carbon fixation (e.g., rbcL), and oxidative phosphorylation. The putative Fe(II)-oxidizing protein Cyc2 was detected for the Gallionellaceae sp. Overall, a complex network of microbial interactions among several Fe(II) oxidizers and denitrifiers was deciphered in culture BP that might resemble NRFO mechanisms in situ. Furthermore, 16S rRNA gene amplicon sequencing from environmental samples revealed 36 distinct Gallionellaceae taxa, including the key player of NRFO from culture BP (approx. 0.13% relative abundance in situ). Since several of these in situ-detected Gallionellaceae taxa were closely related to the key player in culture BP, this suggests that the diversity of organisms contributing to NRFO might be higher than currently known.},
}
@article {pmid34214906,
year = {2021},
author = {Desiderio, TM and Stacy, NI and Ossiboff, RJ and Iredale, M and Archer, LL and Alexander, AB and Heard, DJ and Crevasse, SE and Craft, WF and Fredholm, DVE and Donnelly, KA and Rosenberg, JF and Childress, AL and Russell, K and Wellehan, JFX},
title = {Identification of a novel mortality-associated Helicobacter species in gopher tortoises (Gopherus polyphemus), qPCR test development and validation, and correlation with mortality in a wildlife rehabilitation population.},
journal = {Veterinary microbiology},
volume = {259},
number = {},
pages = {109136},
doi = {10.1016/j.vetmic.2021.109136},
pmid = {34214906},
issn = {1873-2542},
mesh = {Animals ; Animals, Wild/*microbiology ; DNA Primers/genetics ; Female ; Helicobacter/*genetics/*pathogenicity ; Nasal Mucosa ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction/*methods/*veterinary ; Respiratory Tract Infections/microbiology/*mortality/*veterinary ; Turtles/*microbiology ; },
abstract = {The genus Helicobacter includes spiral-shaped bacteria in the phylum Proteobacteria, class Epsilonproteobacteria, order Campylobacteriales, that have been associated with disease in animals, including reptiles. Three wild gopher tortoise (Gopherus polyphemus) index cases presented between 2012 and 2019 with nasal discharge, lethargy, and weight loss. Cytological examination of nasal discharge from all 3 tortoises identified marked heterophilic and mild histiocytic rhinitis with abundant extracellular and phagocytized spiral shaped bacteria that stained positive with Warthin-Starry stain. Polymerase chain reaction (PCR) and sequencing of the 16S rRNA gene revealed this to be a novel Helicobacter species. Two tortoises died despite treatment attempts, and the third was moribund and was euthanized. Histological examination of the nasal mucosa (n = 3) showed granulocytic to lymphocytic rhinitis with variable mucosal hyperplasia, erosion, and ulceration; Warthin-Starry staining highlighted the presence of spiral bacteria in the untreated tortoise. Genus-specific primers were designed, and the gyrA and groEL genes were amplified by PCR and sequenced. Phylogenetic analysis shows that this organism and other previously characterized Helicobacter from tortoises form a clade. Development and cross-validation of two qPCR diagnostic assays for the gyrA and groEL genes showed significant correlation of the results of two assays (P < 0.0001). These assays were used to survey nasal wash samples from 31 rehabilitating gopher tortoises. Mortality of tortoises significantly correlated with higher Helicobacter loads detected by qPCR (P = 0.028). Appropriate quarantine protocols for tortoises during rehabilitation should consider this organism. Upper respiratory disease in tortoises may involve complex microbial ecology; factors beyond Mycoplasmopsis (Mycoplasma) agassizii should be taken into account.},
}
@article {pmid34214230,
year = {2021},
author = {Gyeong, H and Hyun, CU and Kim, SC and Tripathi, BM and Yun, J and Kim, J and Kang, H and Kim, JH and Kim, S and Kim, M},
title = {Contrasting early successional dynamics of bacterial and fungal communities in recently deglaciated soils of the maritime Antarctic.},
journal = {Molecular ecology},
volume = {30},
number = {17},
pages = {4231-4244},
doi = {10.1111/mec.16054},
pmid = {34214230},
issn = {1365-294X},
mesh = {Antarctic Regions ; Bacteria/genetics ; *Mycobiome/genetics ; *Soil ; Soil Microbiology ; },
abstract = {Although microorganisms are the very first colonizers of recently deglaciated soils even prior to plant colonization, the drivers and patterns of microbial community succession at early-successional stages remain poorly understood. The successional dynamics and assembly processes of bacterial and fungal communities were compared on a glacier foreland in the maritime Antarctic across the ~10-year soil-age gradient from bare soil to sparsely vegetated area. Bacterial communities shifted more rapidly than fungal communities in response to glacial retreat; species turnover (primarily the transition from glacier- to soil-favouring taxa) contributed greatly to bacterial beta diversity, but this pattern was less clear in fungi. Bacterial communities underwent more predictable (more deterministic) changes along the soil-age gradient, with compositional changes paralleling the direction of changes in soil physicochemical properties following deglaciation. In contrast, the compositional shift in fungal communities was less associated with changes in deglaciation-induced changes in soil geochemistry and most fungal taxa displayed mosaic abundance distribution across the landscape, suggesting that the successional dynamics of fungal communities are largely governed by stochastic processes. A co-occurrence network analysis revealed that biotic interactions between bacteria and fungi are very weak in early succession. Taken together, these results collectively suggest that bacterial and fungal communities in recently deglaciated soils are largely decoupled from each other during succession and exert very divergent trajectories of succession and assembly under different selective forces.},
}
@article {pmid34213774,
year = {2021},
author = {Kiesewetter, KN and Afkhami, ME},
title = {Microbiome-mediated effects of habitat fragmentation on native plant performance.},
journal = {The New phytologist},
volume = {232},
number = {4},
pages = {1823-1838},
doi = {10.1111/nph.17595},
pmid = {34213774},
issn = {1469-8137},
mesh = {Bacteria ; Biodiversity ; *Ecosystem ; *Microbiota ; *Pinus ; Soil Microbiology ; },
abstract = {Habitat fragmentation is a leading cause of biodiversity and ecosystem function loss in the Anthropocene. Despite the importance of plant-microbiome interactions to ecosystem productivity, we have limited knowledge of how fragmentation affects microbiomes and even less knowledge of its consequences for microbial interactions with plants. Combining field surveys, microbiome sequencing, manipulative experiments, and random forest models, we investigated fragmentation legacy effects on soil microbiomes in imperiled pine rocklands, tested how compositional shifts across 14 fragmentation-altered soil microbiomes affected performance and resource allocation of three native plant species, and identified fragmentation-responding microbial families underpinning plant performance. Legacies of habitat fragmentation were associated with significant changes in microbial diversity and composition (across three of four community axes). Experiments showed plants often strongly benefited from the microbiome's presence, but fragmentation-associated changes in microbiome composition also significantly affected plant performance and resource allocation across all seven metrics examined. Finally, random forest models identified ten fungal and six bacterial families important for plant performance that changed significantly with fragmentation. Our findings not only support the existence of significant fragmentation effects on natural microbiomes, but also demonstrate for the first time that fragmentation-associated changes in microbiomes can have meaningful consequences for native plant performance and investment.},
}
@article {pmid34209897,
year = {2021},
author = {Hugoni, M and Galland, W and Lecomte, S and Bruto, M and Barakat, M and Piola, F and Achouak, W and Haichar, FEZ},
title = {Effects of the Denitrification Inhibitor "Procyanidins" on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome.},
journal = {Microorganisms},
volume = {9},
number = {7},
pages = {},
pmid = {34209897},
issn = {2076-2607},
support = {ANR-18-CE32-0005, DIORE//The French National Research Agency/ ; },
abstract = {Some plant secondary metabolites, such as procyanidins, have been demonstrated to cause biological denitrification inhibition (BDI) of denitrifiers in soils concomitantly with a gain in plant biomass. The present work evaluated whether procyanidins had an impact on the diversity of nontarget microbial communities that are probably involved in soil fertility and ecosystem services. Lettuce plants were grown in two contrasting soils, namely Manziat (a loamy sand soil) and Serail (a sandy clay loam soil) with and without procyanidin amendment. Microbial diversity was assessed using Illumina sequencing of prokaryotic 16S rRNA gene and fungal ITS regions. We used a functional inference to evaluate the putative microbial functions present in both soils and reconstructed the microbial interaction network. The results showed a segregation of soil microbiomes present in Serail and Manziat that were dependent on specific soil edaphic variables. For example, Deltaproteobacteria was related to total nitrogen content in Manziat, while Leotiomycetes and Firmicutes were linked to Ca[2+] in Serail. Procyanidin amendment did not affect the diversity and putative activity of microbial communities. In contrast, microbial interactions differed according to procyanidin amendment, with the results showing an enrichment of Entotheonellaeota and Mucoromycota in Serail soil and of Dependentiae and Rozellomycetes in Manziat soil.},
}
@article {pmid34209778,
year = {2021},
author = {Vanwijnsberghe, S and Peeters, C and De Ridder, E and Dumolin, C and Wieme, AD and Boon, N and Vandamme, P},
title = {Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.},
journal = {International journal of molecular sciences},
volume = {22},
number = {13},
pages = {},
pmid = {34209778},
issn = {1422-0067},
support = {/WT_/Wellcome Trust/United Kingdom ; BOF15/GOA/006//Geconcerteerde Onderzoeksacties (GOA) of Ghent University/ ; },
mesh = {Bacterial Typing Techniques ; Burkholderiaceae/*classification/*genetics/isolation &amp; purification/metabolism ; Coumaric Acids/metabolism/pharmacokinetics ; DNA, Bacterial/analysis/genetics ; Environmental Restoration and Remediation/methods ; Forests ; Genome, Bacterial ; Hydrocarbons, Aromatic/*metabolism/pharmacokinetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rec A Recombinases/analysis/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; },
abstract = {We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderiaaspalathi, Paraburkholderiamadseniana, Paraburkholderiasediminicola, Paraburkholderiacaffeinilytica, Paraburkholderiasolitsugae and Paraburkholderiaelongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA-DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia&amp;nbsp;domus with LMG 31832[T] (=CECT 30334) as the type strain, Paraburkholderia&amp;nbsp;nemoris with LMG 31836[T] (=CECT 30335) as the type strain and Paraburkholderia&amp;nbsp;haematera with LMG 31837[T] (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.},
}
@article {pmid34209491,
year = {2021},
author = {Inui, T and Hanley, B and Tee, ES and Nishihira, J and Tontisirin, K and Van Dael, P and Eggersdorfer, M},
title = {The Role of Micronutrients in Ageing Asia: What Can Be Implemented with the Existing Insights.},
journal = {Nutrients},
volume = {13},
number = {7},
pages = {},
pmid = {34209491},
issn = {2072-6643},
mesh = {Aged ; Aged, 80 and over ; *Aging ; Asia, Southeastern/epidemiology ; Dietary Supplements ; Elder Nutritional Physiological Phenomena ; Fatty Acids, Omega-3 ; Female ; Humans ; Life Expectancy/trends ; Male ; *Micronutrients ; Minerals ; Noncommunicable Diseases/*epidemiology ; *Nutrition Policy ; Nutritional Status ; *Population Health ; Quality of Life ; Trace Elements ; Vitamins ; },
abstract = {Life expectancy as a measure of population health does not reflect years of healthy life. The average life expectancy in the Asia-Pacific region has more than doubled since 1900 and is now above 70 years. In the Asia-Pacific region, the proportion of aged people in the population is expected to double between 2017 and 2050. Increased life expectancy leads to an increase in non-communicable diseases, which consequently affects quality of life. Suboptimal nutritional status is a contributing factor to the prevalence and severity of non-communicable diseases, including cardiovascular, cognitive, musculoskeletal, immune, metabolic and ophthalmological functions. We have reviewed the published literature on nutrition and healthy ageing as it applies to the Asia-Pacific region, focusing on vitamins, minerals/trace elements and omega-3 fatty acids. Optimal nutritional status needs to start before a senior age is reached and before the consequences of the disease process are irreversible. Based on the nutritional status and health issues in the senior age in the region, micronutrients of particular importance are vitamins A, D, E, C, B-12, zinc and omega-3 fatty acids. The present paper substantiates the creation of micronutrient guidelines and proposes actions to support the achievement of optimal nutritional status as contribution to healthy ageing for Asia-Pacific populations.},
}
@article {pmid34207561,
year = {2021},
author = {Abellan-Schneyder, I and Siebert, A and Hofmann, K and Wenning, M and Neuhaus, K},
title = {Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34207561},
issn = {2076-2607},
support = {n/a (grant for a scientist//Research Foundation of Dairy Science at the Technical University of Munich (VFMF)/ ; n/a (grant for a doctorate position)//ZIEL-Institute for Food &amp; Health at the Technical University of Munich/ ; 281A105616//Federal Ministry of Food and Agriculture (BMEL)/ ; AiF 20027N//IGF Project of the FEI via AiF/ ; },
abstract = {Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.},
}
@article {pmid34207412,
year = {2021},
author = {Lopes, LD and Chai, YN and Marsh, EL and Rajewski, JF and Dweikat, I and Schachtman, DP},
title = {Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34207412},
issn = {2076-2607},
support = {DE-SC0014395//U.S. Department of Energy/ ; },
abstract = {The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of seven sweet sorghum genotypes differing in sensitivity to N-stress. Sorghum genotypes were grown in fields with no (low-N) or sufficient (high-N) N. The dry shoot weight ratio (low-N/high-N) was used to determine N-stress sensitivity. Our hypothesis was that genotypes tolerant and sensitive to N-stress select distinct bacterial communities. The endosphere and rhizosphere bacterial community structure were significantly different between the N-stress sensitive and tolerant genotypes in the high-N field, but not in the low-N field. However, significant changes in the relative abundance of specific bacterial taxa were observed in both fields. Streptomyces, a bacterial genus known to alleviate plant abiotic stresses, was enriched in the endosphere and rhizosphere of the tolerant genotypes in the low-N field. Our study indicates that sweet sorghum genotypes tolerant to N-stress select taxa that can potentially mitigate the N-stress, suggesting that the interactions between N-stress tolerant lines and the root-associated microbiome might be vital for coping with N-stress.},
}
@article {pmid34207399,
year = {2021},
author = {Van Gerrewey, T and El-Nakhel, C and De Pascale, S and De Paepe, J and Clauwaert, P and Kerckhof, FM and Boon, N and Geelen, D},
title = {Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34207399},
issn = {2076-2607},
support = {Not applicable//MELiSSA/ ; },
abstract = {Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO3[-]/NH4[+] ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions.},
}
@article {pmid34206618,
year = {2021},
author = {Rilling, JI and Maruyama, F and Sadowsky, MJ and Acuña, JJ and Jorquera, MA},
title = {CRISPR loci-PCR as Tool for Tracking Azospirillum sp. Strain B510.},
journal = {Microorganisms},
volume = {9},
number = {7},
pages = {},
pmid = {34206618},
issn = {2076-2607},
support = {1201386//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 1181050//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; },
abstract = {Azospirillum-based plant and soil inoculants are widely used in agriculture. The inoculated Azospirillum strains are commonly tracked by both culture-dependent and culture-independent methods, which are time-consuming or expensive. In this context, clustered regularly interspaced short palindromic repeats (CRISPR) loci structure is unique in the bacterial genome, including some Azospirillum species. Here, we investigated the use of CRISPR loci to track specific Azospirillum strains in soils systems by PCR. Primer sets for Azospirillum sp. strain B510 were designed and evaluated by colony and endpoint PCR. The CRISPRloci-PCR approach was standardized for Azospirillum sp. strain B510, and its specificity was observed by testing against 9 different Azospirillum strains, and 38 strains of diverse bacterial genera isolated from wheat plants. The CRISPRloci-PCR approach was validated in assays with substrate and wheat seedlings. Azospirillum sp. strain B510 was detected after of two weeks of inoculation in both sterile and nonsterile substrates as well as rhizosphere grown in sterile substrate. The CRISPRloci-PCR approach was found to be a useful molecular tool for specific tracking of Azospirillum at the strain level. This technique can be easily adapted to other microbial inoculants carrying CRISPR loci and can be used to complement other microbiological techniques.},
}
@article {pmid34206081,
year = {2021},
author = {Lai, CC and Ko, CY and Austria, E and Shiah, FK},
title = {Extreme Weather Events Enhance DOC Consumption in a Subtropical Freshwater Ecosystem: A Multiple-Typhoon Analysis.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34206081},
issn = {2076-2607},
abstract = {Empirical evidence suggests that the frequency/intensity of extreme weather events might increase in a warming climate. It remains unclear how these events quantitatively impact dissolved organic carbon (DOC), a pool approximately equal to CO2 in the atmosphere. This study conducted a weekly-to-biweekly sampling in a deep subtropical reservoir in the typhoon-prevailing season (June to September) from 2004 to 2009, at which 33 typhoons with distinctive precipitation (<1~362 mm d[-1]) had passed the study site. Our analyses indicated that the phosphate (i.e., DIP; <10~181 nMP) varied positively with the intensity of the accumulated rainfall 2-weeks prior; bacteria growth rate (0.05~3.68 d[-1]) behaved as a positive function of DIP, and DOC concentrations (54~119 µMC) changed negatively with bacterial production (1.2~26.1 mgC m[-3] d[-1]). These implied that the elevated DIP-loading in the hyperpycnal flow induced by typhoons could fuel bacteria growth and cause a significant decline of DOC concentrations. As the typhoon's intensity increases, many mineral-limited lentic freshwater ecosystems might become more like a CO2 source injecting more CO2 back to the atmosphere, creating a positive feedback loop that might generate severer extreme weather events.},
}
@article {pmid34204924,
year = {2021},
author = {Blanchette, ML and Lund, MA},
title = {Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34204924},
issn = {2076-2607},
support = {C27043//Australian Coal Association Research Program/ ; },
abstract = {Mine pit lakes ('pit lakes') are new aquatic ecosystems of the Anthropocene. Potentially hundreds of meters deep, these lakes are prominent in the landscape and in the public consciousness. However, the ecology of pit lakes is underrepresented in the literature. The broad goal of this research was to determine the environmental drivers of pelagic microbe assemblages in Australian coal pit lakes. The overall experimental design was four lakes sampled three times, top and bottom, in 2019. Instrument chains were installed in lakes and measurements of in situ water quality and water samples for metals, metalloids, nutrients and microbe assemblage were collected. Lakes were monomictic and the timing of mixing was influenced by high rainfall events. Water quality and microbial assemblages varied significantly across space and time, and most taxa were rare. Lakes were moderately saline and circumneutral; Archeans were not prevalent. Richness also varied by catchment. Microbial assemblages correlated to environmental variables, and no one variable was consistently significant, spatially or temporally. Study lakes were dominated by 'core' taxa exhibiting temporal turnover likely driven by geography, water quality and interspecific competition, and the presence of water chemistry associated with an artificial aquifer likely influenced microbial community composition. Pit lakes are deceptively complex aquatic ecosystems that host equally complex pelagic microbial communities. This research established links between microbial assemblages and environmental variables in pit lakes and determined core communities; the first steps towards developing a monitoring program using microbes.},
}
@article {pmid34204724,
year = {2021},
author = {Clocchiatti, A and Hannula, SE and Rizaludin, MS and Hundscheid, MPJ and Klein Gunnewiek, PJA and Schilder, MT and Postma, J and de Boer, W},
title = {Impact of Cellulose-Rich Organic Soil Amendments on Growth Dynamics and Pathogenicity of Rhizoctonia solani.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34204724},
issn = {2076-2607},
support = {14012//Stichting voor de Technische Wetenschappen/ ; },
abstract = {Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable substrate for R. solani, whereas its performance on wood sawdusts varied with tree species. In two pot experiments, the effects of amendment of R. solani-infected soil with cellulose-rich materials on performance of beetroot seedlings were tested. All deciduous sawdusts and paper pulp stimulated soil fungal biomass, but only oak, elder and beech sawdusts reduced damping-off of beetroot. Oak sawdust amendment gave a consistent stimulation of saprotrophic Sordariomycetes fungi and of seedling performance, independently of the time between amendment and sowing. In contrast, paper pulp caused a short-term increase in R. solani abundance, coinciding with increased disease severity for beet seedlings sown immediately after amendment. However, damping-off of beetroot was reduced if plants were sown two or four weeks after paper pulp amendment. Cellulolytic bacteria, including Cytophagaceae, responded to paper pulp during the first two weeks and may have counteracted further spread of R. solani. The results showed that fungus-stimulating, cellulose-rich amendments have potential to be used for suppression of R. solani. However, such amendments require a careful consideration of material choice and application strategy.},
}
@article {pmid34201311,
year = {2021},
author = {Šulčius, S and Alzbutas, G and Juknevičiūtė, V and Šimoliūnas, E and Venckus, P and Šimoliūnienė, M and Paškauskas, R},
title = {Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics.},
journal = {Genes},
volume = {12},
number = {6},
pages = {},
pmid = {34201311},
issn = {2073-4425},
mesh = {Bacterial Proteins/genetics/metabolism ; Bacteriophages/*genetics/isolation &amp; purification/pathogenicity ; Calcium Sulfate/analysis/metabolism ; Chlorobium/genetics/metabolism/*virology ; Genomics/methods ; Host-Pathogen Interactions ; Lakes/chemistry/*microbiology/virology ; Metagenome ; Single-Cell Analysis/methods ; Sulfur/metabolism ; *Virome ; },
abstract = {Little is known about the diversity and distribution of viruses infecting green sulfur bacteria (GSB) thriving in euxinic (sulfuric and anoxic) habitats, including gypsum karst lake ecosystems. In this study, we used targeted cell sorting combined with single-cell sequencing to gain insights into the gene content and genomic potential of viruses infecting sulfur-oxidizing bacteria Chlorobium clathratiforme, obtained from water samples collected during summer stratification in gypsum karst Lake Kirkilai (Lithuania). In total, 82 viral contigs were bioinformatically identified in 62 single amplified genomes (SAGs) of C. clathratiforme. The majority of viral gene and protein sequences showed little to no similarity with phage sequences in public databases, uncovering the vast diversity of previously undescribed GSB viruses. We observed a high level of lysogenization in the C. clathratiforme population, as 87% SAGs contained intact prophages. Among the thirty identified auxiliary metabolic genes (AMGs), two, thiosulfate sulfurtransferase (TST) and thioredoxin-dependent phosphoadenosine phosphosulfate (PAPS) reductase (cysH), were found to be involved in the oxidation of inorganic sulfur compounds, suggesting that viruses can influence the metabolism and cycling of this essential element. Finally, the analysis of CRISPR spacers retrieved from the consensus C. clathratiforme genome imply persistent and active virus-host interactions for several putative phages prevalent among C. clathratiforme SAGs. Overall, this study provides a glimpse into the diversity of phages associated with naturally occurring and highly abundant sulfur-oxidizing bacteria.},
}
@article {pmid34199628,
year = {2021},
author = {Rizaludin, MS and Stopnisek, N and Raaijmakers, JM and Garbeva, P},
title = {The Chemistry of Stress: Understanding the 'Cry for Help' of Plant Roots.},
journal = {Metabolites},
volume = {11},
number = {6},
pages = {},
pmid = {34199628},
issn = {2218-1989},
abstract = {Plants are faced with various biotic and abiotic stresses during their life cycle. To withstand these stresses, plants have evolved adaptive strategies including the production of a wide array of primary and secondary metabolites. Some of these metabolites can have direct defensive effects, while others act as chemical cues attracting beneficial (micro)organisms for protection. Similar to aboveground plant tissues, plant roots also appear to have evolved "a cry for help" response upon exposure to stress, leading to the recruitment of beneficial microorganisms to help minimize the damage caused by the stress. Furthermore, emerging evidence indicates that microbial recruitment to the plant roots is, at least in part, mediated by quantitative and/or qualitative changes in root exudate composition. Both volatile and water-soluble compounds have been implicated as important signals for the recruitment and activation of beneficial root-associated microbes. Here we provide an overview of our current understanding of belowground chemical communication, particularly how stressed plants shape its protective root microbiome.},
}
@article {pmid34198081,
year = {2021},
author = {Yuan, H and Yuan, J and You, Y and Zhang, B and Wu, Y and Huang, S and Zhang, Y},
title = {Simultaneous ammonium and sulfate biotransformation driven by aeration: Nitrogen/sulfur metabolism and metagenome-based microbial ecology.},
journal = {The Science of the total environment},
volume = {794},
number = {},
pages = {148650},
doi = {10.1016/j.scitotenv.2021.148650},
pmid = {34198081},
issn = {1879-1026},
mesh = {*Ammonium Compounds ; Bioreactors ; Biotransformation ; Denitrification ; Metagenome ; Nitrification ; *Nitrogen ; Sewage ; Sulfates ; Sulfur ; },
abstract = {The present study aimed to clarify the effect of oxygen respiration on biotransformation of alternative electron acceptors (e.g., nitrate and sulfate) underlying the simultaneous removal of ammonium and sulfate in a single aerated sequencing batch reactor. Complete nitrification was achieved in feast condition, while denitrification was carried out in both feast and famine conditions when aeration intensity (AI) was higher than 0.22 L/(L·min). Reactors R1 [0.56 L/(L·min)], R2 [0.22 L/(L·min)], and R3 [0.08 L/(L·min)] achieved 72.39% sulfate removal efficiency in feast condition, but H2S release occurred in R3. Following exogenous substrate depletion, sulfate concentration increased again and exceeded the influent value in R1, indicating that sulfate transformation was affected by oxygen intrusion. Metagenomic analysis showed that a higher AI promoted sulfate reduction by switching from dissimilatory to assimilatory pathway. Lower AI-acclimated microorganisms (R3) produced H2S and ammonium, while higher AI-acclimated microorganisms (R1) accumulated nitrite, which confirmed that biotransformation of N and S was strongly regulated by redox imbalance driven by aeration. This implied that respiration control, a microbial self-regulation mechanism, was linked to the dynamic imbalance between electron donors and electron acceptors. Aerobic nitrate (sulfate) reduction, as one of the effects of respiration control, could be used as an alternative strategy to compensate for dynamic imbalance, when supported by efficient endogenous metabolism. Moderate aeration induced microorganisms to change their energy conservation and survival strategy through respiration control and inter-genus protection of respiratory activity among keystone taxa (including Azoarcus in R1, Thauera in R2, and Thiobacillus, Ottowia, and Geoalkalibacter in R3) to form an optimal niche in response to oxygen intrusion and achieve benign biotransformation of C, N, and S without toxic intermediate accumulation. This study clarified the biotransformation mechanism of ammonium and sulfate driven by aeration and provided theoretical guidance for optimizing existing aeration-based techniques.},
}
@article {pmid34195856,
year = {2022},
author = {McGirr, S and Clarke, D and Kilcoyne, J and Silke, J and Touzet, N},
title = {Co-localisation of Azaspiracid Analogs with the Dinoflagellate Species Azadinium spinosum and Amphidoma languida in the Southwest of Ireland.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {635-646},
pmid = {34195856},
issn = {1432-184X},
support = {CF/15/01//Marine Research Sub-programme by the Irish Government/ ; },
mesh = {*Dinoflagellida/genetics ; Humans ; Ireland ; Marine Toxins ; *Spiro Compounds/analysis ; },
abstract = {Phytoplankton and biotoxin monitoring programmes have been implemented in many countries to protect human health and to mitigate the impacts of harmful algal blooms (HABs) on the aquaculture industry. Several amphidomatacean species have been confirmed in Irish coastal waters, including the azaspiracid-producing species Azadinium spinosum and Amphidoma languida. Biogeographic distribution studies have been hampered by the fact that these small, armoured dinoflagellates share remarkably similar morphologies when observed by light microscopy. The recent releases of species-specific molecular detection assays have, in this context, been welcome developments. A survey of the south west and west coasts of Ireland was carried out in August 2017 to investigate the late summer distribution of toxic amphidomataceans and azaspiracid toxins. Azadinium spinosum and Am. languida were detected in 83% of samples in the southwest along the Crease Line and Bantry Bay transects between 20 and 70 m depth, with maximal cell concentrations of 7000 and 470,000 cells/L, respectively. Azaspiracid concentrations were well aligned with the distributions of Az. spinosum and Am. languida, up to 1.1 ng/L and 4.9 ng/L for combined AZA-1, -2, -33, and combined AZA-38, -39, respectively. Although a snapshot in time, this survey provides new insights in the late summer prominence of AZAs and AZA-producing species in the southwest of Ireland, where major shellfish aquaculture operations are located. Results showed a substantial overlap in the distribution of amphidomatacean species in the area and provide valuable baseline information in the context of ongoing monitoring efforts of toxigenic amphidomataceans in the region.},
}
@article {pmid34192775,
year = {2022},
author = {Vadaq, N and Schirmer, M and Tunjungputri, RN and Vlamakis, H and Chiriac, C and Ardiansyah, E and Gasem, MH and Joosten, LAB and de Groot, PG and Xavier, RJ and Netea, MG and van der Ven, AJ and de Mast, Q},
title = {Untargeted Plasma Metabolomics and Gut Microbiome Profiling Provide Novel Insights into the Regulation of Platelet Reactivity in Healthy Individuals.},
journal = {Thrombosis and haemostasis},
volume = {122},
number = {4},
pages = {529-539},
doi = {10.1055/a-1541-3706},
pmid = {34192775},
issn = {2567-689X},
mesh = {Adult ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Metabolome ; Metabolomics/methods ; Plasma ; },
abstract = {BACKGROUND: Considerable variation exists in platelet reactivity to stimulation among healthy individuals. Various metabolites and metabolic pathways influence platelet reactivity, but a comprehensive overview of these associations is missing. The gut microbiome has a strong influence on the plasma metabolome. Here, we investigated the association of platelet reactivity with results of untargeted plasma metabolomics and gut microbiome profiling.<br><br>METHODS: We used data from a cohort of 534 healthy adult Dutch volunteers (the 500 Functional Genomics study). Platelet activation and reactivity were measured by the expression of the alpha-granule protein P-selectin and the binding of fibrinogen to the activated integrin &#x3b1;IIb&#x3b2;3, both in unstimulated blood and after ex vivo stimulation with platelet agonists. Plasma metabolome was measured using an untargeted metabolic profiling approach by quadrupole time-of-flight mass spectrometry. Gut microbiome data were measured by shotgun metagenomic sequencing from stool samples.<br><br>RESULTS: Untargeted metabolomics yielded 1,979 metabolites, of which 422 were identified to play a role in a human metabolic pathway. Overall, 92/422 (21.8%) metabolites were significantly associated with at least one readout of platelet reactivity. The majority of associations involved lipids, especially members of eicosanoids, including prostaglandins and leukotrienes. Dietary-derived polyphenols were also found to inhibit platelet reactivity. Validation of metabolic pathways with functional microbial profiles revealed two overlapping metabolic pathways ("alanine, aspartate, and glutamate metabolism" and "arginine biosynthesis") that were associated with platelet reactivity.<br><br>CONCLUSION: This comprehensive overview is an resource for understanding the regulation of platelet reactivity by the plasma metabolome and the possible contribution of the gut microbiota.},
}
@article {pmid34192637,
year = {2021},
author = {Li, P and Li, K and Xu, P and Liu, X and Pu, Y},
title = {Treatment of wastewater with high carbon-to-nitrogen ratio using a waterfall aeration biofilm reactor combined with sequencing batch reactor: Microbial community structure and metabolism analysis.},
journal = {Bioresource technology},
volume = {337},
number = {},
pages = {125450},
doi = {10.1016/j.biortech.2021.125450},
pmid = {34192637},
issn = {1873-2976},
mesh = {Biofilms ; Bioreactors ; Carbon ; Denitrification ; *Microbiota ; Nitrification ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Wastewater ; },
abstract = {A low-cost and high-efficiency waterfall aeration biofilm reactor (WABR) combined with a sequencing batch reactor (SBR) was established to treat wastewater with a C/N ratio of 50. Three WABR-SBR systems with different fillers were used. In the stable operation phase, the removal efficiency of chemical oxygen demand was R1 (approximately 99%), R2 (97-99%), and R3 (96-99%); the effluent concentration of NH4[+]-N was 0.5 mg/L without nitrite or nitrate accumulation. High-throughput 16S rRNA sequencing revealed that the dominant phyla in the microbial community structure were Proteobacteria, Bacteroidetes, and Planctomycetes. Quantitative PCR was used to quantify the nitrification and denitrification gene expressions (Nitrobacter, nirS, and nirK) to evaluate the simultaneous nitrification and denitrification processes. Both anammox and denitrifying bacteria were abundant. Metagenomic annotation of genes that revealed the metabolic pathways of carbohydrates, amino acids, and the two dominant enzymes (GH and GT) provide valuable information for microbial ecology analysis.},
}
@article {pmid34191105,
year = {2022},
author = {Paolinelli, M and Escoriaza, G and Cesari, C and Garcia-Lampasona, S and Hernandez-Martinez, R},
title = {Characterization of Grapevine Wood Microbiome Through a Metatranscriptomic Approach.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {658-668},
pmid = {34191105},
issn = {1432-184X},
support = {PRET-1251101//Instituto Nacional de Tecnolog&#xed;a Agropecuaria/ ; },
mesh = {*Ascomycota ; *Microbiota/genetics ; Plant Diseases/microbiology ; *Vitis/microbiology ; Wood/microbiology ; },
abstract = {Grapevine trunk diseases threaten wine and table grape production worldwide, primarily by reducing yields and, in its advanced stages, causing plant death. Among those diseases, the complex etiology disease known as hoja de malvón (HDM) significantly concerns Argentinian and Uruguayan viticulture. At least four different fungi are associated with this disease, but their role and interactions with other wood microorganisms are understudied. In this sense, analyzing grapevine wood microbiome composition could help understand microbial interactions occurring in HDM onset. Hence, a metatranscriptomic study was performed for the microbiome characterization of mature field-grown Vitis vinifera cv. Malbec, leaf-symptomatic or leaf-asymptomatic. The microbiome was mainly represented by Dothideomycetes and Actinobacteria. In the plant with more marked symptoms, higher levels of the Basidiomycota Arambarria destruens and Phellinus laevigatus were detected. Despite this particular difference, discriminating symptomatic from asymptomatic plants based on the presence or abundance of HDM pathogens was not possible. Alpha diversity and rank-abundance curve analyses indicated that plants with foliar symptoms have lower microbial evenness than asymptomatic plants. The co-occurrence network modeled microbial interkingdom interactions. Molecular data generated in this study will help develop future targeted molecular quantification for specific taxa.},
}
@article {pmid34190973,
year = {2021},
author = {Sadiq, FA and Wenwei, L and Heyndrickx, M and Flint, S and Wei, C and Jianxin, Z and Zhang, H},
title = {Synergistic interactions prevail in multispecies biofilms formed by the human gut microbiota on mucin.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {8},
pages = {},
doi = {10.1093/femsec/fiab096},
pmid = {34190973},
issn = {1574-6941},
mesh = {Bacteroides ; Bacteroidetes ; Bifidobacterium bifidum ; Bifidobacterium longum subspecies infantis ; *Biofilms ; *Gastrointestinal Microbiome ; Humans ; *Mucins ; },
abstract = {Bacterial species in the human gut predominantly exist in the form of mixed-species biofilms on mucosal surfaces. In this study, the biofilm-forming ability of many human gut bacterial strains (133 strains recovered from human faeces) on mucin-coated and non-coated polystyrene surfaces was determined. A significant variation (P < 0.05) in the biofilm-forming ability of many bacterial species on both surfaces was noticed. Based on some preliminary trials, four bacterial species were selected (Bifidobacterium bifidum, Bifidobacterium longum subsp. infantis, Parabacteroides distasonis and Bacteroides ovatus), which could not form any abundant biofilm individually under the in vitro conditions investigated, but produced abundant biofilms when co-cultured in different combinations of two, three and four species, giving an evidence of synergistic interactions in multispecies biofilm formation. There was a 4.74-fold increase in the biofilm mass when all strains developed a biofilm together. Strain-specific qPCR analysis showed that B. bifidum was the most dominant species (56%) in the four-species biofilm after 24 h, followed by B. longum subsp. infantis (36.2%). Study involving cell free supernatant of the cooperating strains showed that cell viability as well as physical presence of cooperating cells were prerequisites for the observed synergy in biofilms. The molecular mechanism behind these interactions and subsequent effects on the functionality of the strains involved were not determined in our study but merit further work.},
}
@article {pmid34190389,
year = {2021},
author = {Barnes, EM and Kutos, S and Naghshineh, N and Mesko, M and You, Q and Lewis, JD},
title = {Assembly of the amphibian microbiome is influenced by the effects of land-use change on environmental reservoirs.},
journal = {Environmental microbiology},
volume = {23},
number = {8},
pages = {4595-4611},
doi = {10.1111/1462-2920.15653},
pmid = {34190389},
issn = {1462-2920},
mesh = {Amphibians ; Animals ; Bacteria/genetics ; Fungi/genetics ; Humans ; *Microbiota ; Soil Microbiology ; },
abstract = {A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land-use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land-use associated factors creating site-specific compositions. By employing a quantitative, null-based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function.},
}
@article {pmid34190033,
year = {2021},
author = {Duysburgh, C and Van den Abbeele, P and Morera, M and Marzorati, M},
title = {Lacticaseibacillus rhamnosus GG and Saccharomyces cerevisiae boulardii supplementation exert protective effects on human gut microbiome following antibiotic administration in vitro.},
journal = {Beneficial microbes},
volume = {12},
number = {4},
pages = {59-73},
doi = {10.3920/BM2020.0180},
pmid = {34190033},
issn = {1876-2891},
mesh = {Amoxicillin/adverse effects ; Anti-Bacterial Agents/adverse effects ; Clavulanic Acid/adverse effects ; Dysbiosis/chemically induced ; Fatty Acids, Volatile/analysis ; *Gastrointestinal Microbiome ; Humans ; In Vitro Techniques ; *Lacticaseibacillus rhamnosus ; *Probiotics ; *Saccharomyces boulardii ; },
abstract = {Antibiotic-induced dysbiosis of the microbial community has been associated with several gastrointestinal symptoms. The impact of repeated administration of Lacticaseibacillus rhamnosus GG (CNCM-I-4798) (formerly known as Lactobacillus rhamnosus GG), Saccharomyces cerevisiae boulardii (CNCM-I-1079) and their combination (associated in Smebiocta/Smectaflora Protect®) in supporting recovery of gut microbiota functionality and composition during and following amoxicillin:clavulanic acid administration was evaluated in vitro. Antibiotic dosage negatively affected SCFA production, coinciding with detrimental effects on Bacteroidetes, Firmicutes and Bifidobacterium spp. in the simulated proximal colon, while Akkermansia muciniphila was significantly reduced in the distal colon. L. rhamnosus GG and S. boulardii were able to thrive in both colon regions upon dosing, with S. boulardii even showing protective effects on the survival of L. rhamnosus GG during antibiotic administration. The impact of the probiotic strains on microbiome recovery revealed that supplementation with L. rhamnosus GG and/or S. boulardii resulted in a stimulating effect on the most abundant bacterial groups within the bacterial community of each donor. For one of the donors tested, co-dosing of L. rhamnosus GG and S. boulardii resulted in superior short-chain fatty acid recovery accompanied by a stronger increase in abundance of Bifidobacteriaceae. Overall, the current study provides first evidence that combined supplementation of L. rhamnosus GG and S. boulardii might be an interesting candidate in limiting detrimental effects of amoxicillin:clavulanic acid on the human gut microbiome, though further studies are warranted to confirm these findings.},
}
@article {pmid34189610,
year = {2022},
author = {Wang, X and Shang, Y and Wei, Q and Wu, X and Dou, H and Zhang, H and Zhou, S and Sha, W and Sun, G and Ma, S and Zhang, H},
title = {Comparative Analyses of the Gut Microbiome of Two Fox Species, the Red Fox (Vulpes Vulpes) and Corsac Fox (Vulpes Corsac), that Occupy Different Ecological Niches.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {753-765},
pmid = {34189610},
issn = {1432-184X},
support = {31872242//the national natural science foundation of china/ ; 31672313//the national natural science foundation of china/ ; 32070405//the national natural science foundation of china/ ; 32001228//the national natural science foundation of china/ ; 32000291//the national natural science foundation of china/ ; 61902368//the national natural science foundation of china/ ; 201404420//the Special Fund for Forest Scientific Research in the Public Welfare/ ; },
mesh = {Animals ; Ecosystem ; *Foxes ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; },
abstract = {The gut microbiome is integral for the host's living and environmental adaptation and crucially important for understanding host adaptive mechanisms. The red fox (Vulpes vulpes) dominates a wider ecological niche and more complicated habitat than that of the corsac fox (V. corsac). However, the adaptive mechanisms (in particular, the gut microbiome responsible for this kind of difference) are still unclear. Therefore, we investigated the gut microbiome of these two species in the Hulunbuir grassland, China, and evaluated their microbiome composition, function, and adaptive mechanisms. We profiled the gut microbiome and metabolism function of red and corsac foxes via 16S rRNA gene and metagenome sequencing. The foxes harbored species-specific microbiomes and functions that were related to ecological niche and habitat. The red fox had abundant Bacteroides, which leads to significant enrichment of metabolic pathways (K12373 and K21572) and enzymes related to chitin and carbohydrate degradation that may help the red fox adapt to a wider niche. The corsac fox harbored large proportions of Blautia, Terrisporobacter, and ATP-binding cassette (ABC) transporters (K01990, K02003, and K06147) that can help maintain corsac fox health, allowing it to live in harsh habitats. These results indicate that the gut microbiome of the red and corsac foxes may have different abilities which may provide these species with differing capabilities to adapt to different ecological niches and habitats, thus providing important microbiome data for understanding the mechanisms of host adaptation to different niches and habitats.},
}
@article {pmid34185360,
year = {2021},
author = {Jiao, S and Zhang, B and Zhang, G and Chen, W and Wei, G},
title = {Stochastic community assembly decreases soil fungal richness in arid ecosystems.},
journal = {Molecular ecology},
volume = {30},
number = {17},
pages = {4338-4348},
doi = {10.1111/mec.16047},
pmid = {34185360},
issn = {1365-294X},
mesh = {Desert Climate ; *Ecosystem ; Fungi/genetics ; *Soil ; Soil Microbiology ; },
abstract = {Uncovering the linkages between community assembly and species diversity is a fundamental issue in microbial ecology. In this study, a large-scale (transect intervals of 1257.6 km) cross-biome soil survey was conducted, which ranged over agricultural fields, forests, wetlands, grasslands and desert, in the arid regions of northwest China. The aim was to investigate the biogeographic distribution, community assembly and species co-occurrence of soil fungi. The fungal communities in agricultural soils exhibited a steeper distance-decay slope and wider niche breadths, and were more strongly affected by stochastic assembly processes, than fungi in other natural habitats. A strong relationship was revealed between soil fungal richness and community assembly in arid ecosystems, with the influence of stochastic assembly processes decreasing with increasing fungal richness. Moreover, aridity was the most important environmental factor influencing fungal richness, β-diversity and species co-occurrence patterns. Specifically, the predicted increase in arid conditions will probably reduce fungal richness and network complexity. These findings represent a considerable advance in linking fungal richness to mechanisms underlying the biogeographic patterns and assembly processes of fungal communities in arid ecosystems. These results can thus be used to forecast species co-occurrence and diversities pattern of soil fungi under climate aridity and land-use change scenarios.},
}
@article {pmid34184914,
year = {2021},
author = {Savoie, ER and Lanclos, VC and Henson, MW and Cheng, C and Getz, EW and Barnes, SJ and LaRowe, DE and Rappé, MS and Thrash, JC},
title = {Ecophysiology of the Cosmopolitan OM252 Bacterioplankton (Gammaproteobacteria).},
journal = {mSystems},
volume = {6},
number = {3},
pages = {e0027621},
pmid = {34184914},
issn = {2379-5077},
abstract = {Among the thousands of species that comprise marine bacterioplankton communities, most remain functionally obscure. One key cosmopolitan group in this understudied majority is the OM252 clade of Gammaproteobacteria. Although frequently found in sequence data and even previously cultured, the diversity, metabolic potential, physiology, and distribution of this clade has not been thoroughly investigated. Here, we examined these features of OM252 bacterioplankton using a newly isolated strain and genomes from publicly available databases. We demonstrated that this group constitutes a globally distributed novel genus ("Candidatus Halomarinus"), sister to Litoricola, comprising two subclades and multiple distinct species. OM252 organisms have small genomes (median, 2.21 Mbp) and are predicted obligate aerobes capable of alternating between chemoorganoheterotrophic and chemolithotrophic growth using reduced sulfur compounds as electron donors. Subclade I genomes encode genes for the Calvin-Benson-Bassham cycle for carbon fixation. One representative strain of subclade I, LSUCC0096, had extensive halotolerance and a mesophilic temperature range for growth, with a maximum rate of 0.36 doublings/h at 35°C. Cells were curved rod/spirillum-shaped, ∼1.5 by 0.2 μm. Growth yield on thiosulfate as the sole electron donor under autotrophic conditions was roughly one-third that of heterotrophic growth, even though calculations indicated similar Gibbs energies for both catabolisms. These phenotypic data show that some "Ca. Halomarinus" organisms can switch between serving as carbon sources or sinks and indicate the likely anabolic cost of lithoautotrophic growth. Our results thus provide new hypotheses about the roles of these organisms in global biogeochemical cycling of carbon and sulfur. IMPORTANCE Marine microbial communities are teeming with understudied taxa due to the sheer numbers of species in any given sample of seawater. One group, the OM252 clade of Gammaproteobacteria, has been identified in gene surveys from myriad locations, and one isolated organism has even been genome sequenced (HIMB30). However, further study of these organisms has not occurred. Using another isolated representative (strain LSUCC0096) and publicly available genome sequences from metagenomic and single-cell genomic data sets, we examined the diversity within the OM252 clade and the distribution of these taxa in the world's oceans, reconstructed the predicted metabolism of the group, and quantified growth dynamics in LSUCC0096. Our results generate new knowledge about the previously enigmatic OM252 clade and point toward the importance of facultative chemolithoautotrophy for supporting some clades of ostensibly "heterotrophic" taxa.},
}
@article {pmid34182782,
year = {2021},
author = {Murareanu, BM and Sukhdeo, R and Qu, R and Jiang, J and Reinke, AW},
title = {Generation of a Microsporidia Species Attribute Database and Analysis of the Extensive Ecological and Phenotypic Diversity of Microsporidia.},
journal = {mBio},
volume = {12},
number = {3},
pages = {e0149021},
pmid = {34182782},
issn = {2150-7511},
mesh = {Animals ; *Databases, Factual ; *Ecology ; *Genetic Variation ; Host Specificity ; Humans ; Microsporidia/classification/*genetics ; *Phenotype ; },
abstract = {Microsporidia are a large group of fungus-related obligate intracellular parasites. Though many microsporidia species have been identified over the past 160 years, depiction of the full diversity of this phylum is lacking. To systematically describe the characteristics of these parasites, we created a database of 1,440 species and their attributes, including the hosts they infect and spore characteristics. We find that microsporidia have been reported to infect 16 metazoan and 4 protozoan phyla, with smaller phyla being underrepresented. Most species are reported to infect only a single host, but those that are generalists are also more likely to infect a broader set of host tissues. Strikingly, polar tubes are threefold longer in species that infect tissues besides the intestine, suggesting that polar tube length is a determinant of tissue specificity. Phylogenetic analysis revealed four clades which each contain microsporidia that infect hosts from all major habitats. Although related species are more likely to infect similar hosts, we observe examples of changes in host specificity and convergent evolution. Taken together, our results show that microsporidia display vast diversity in their morphology and the hosts they infect, illustrating the flexibility of these parasites to evolve new traits. IMPORTANCE Microsporidia are a large group of parasites that cause death and disease in humans and many agriculturally important animal species. To fully understand the diverse properties of these parasites, we curated species reports from the last 160 years. Using these data, we describe when and where microsporidia were identified and what types of animals and host tissues these parasites infect. Microsporidia infect hosts using a conserved apparatus known as the polar tube. We observe that the length of this tube is correlated with the tissues that are being infected, suggesting that the polar tube controls where within the animals that the parasite infects. Finally, we show that microsporidia species often exist in multiple environments and are flexible in their ability to evolve new traits. Our study provides insight into the ecology and evolution of microsporidia and provides a useful resource to further understand these fascinating parasites.},
}
@article {pmid34180595,
year = {2021},
author = {Suleiman, M and Choffat, Y and Daugaard, U and Petchey, OL},
title = {Large and interacting effects of temperature and nutrient addition on stratified microbial ecosystems in a small, replicated, and liquid-dominated Winogradsky column approach.},
journal = {MicrobiologyOpen},
volume = {10},
number = {3},
pages = {e1189},
pmid = {34180595},
issn = {2045-8827},
mesh = {Cyanobacteria/growth &amp; development/*metabolism ; *Ecological Systems, Closed ; Nutrients/*metabolism ; Sulfur/metabolism ; Temperature ; },
abstract = {Aquatic ecosystems are often stratified, with cyanobacteria in oxic layers and phototrophic sulfur bacteria in anoxic zones. Changes in stratification caused by the global environmental change are an ongoing concern. Increasing understanding of how such aerobic and anaerobic microbial communities, and associated abiotic conditions, respond to multifarious environmental changes is an important endeavor in microbial ecology. Insights can come from observational and experimental studies of naturally occurring stratified aquatic ecosystems, theoretical models of ecological processes, and experimental studies of replicated microbial communities in the laboratory. Here, we demonstrate a laboratory-based approach with small, replicated, and liquid-dominated Winogradsky columns, with distinct oxic/anoxic strata in a highly replicable manner. Our objective was to apply simultaneous global change scenarios (temperature, nutrient addition) on this micro-ecosystem to report how the microbial communities (full-length 16S rRNA gene seq.) and the abiotic conditions (O2 , H2 S, TOC) of the oxic/anoxic layer responded to these environmental changes. The composition of the strongly stratified microbial communities was greatly affected by temperature and by the interaction of temperature and nutrient addition, demonstrating the need of investigating global change treatments simultaneously. Especially phototrophic sulfur bacteria dominated the water column at higher temperatures and may indicate the presence of alternative stable states. We show that the establishment of such a micro-ecosystem has the potential to test global change scenarios in stratified eutrophic limnic systems.},
}
@article {pmid34179320,
year = {2021},
author = {Hoogenkamp, MA and Brandt, BW and Laheij, AMGA and de Soet, JJ and Crielaard, W},
title = {16S rDNA sequencing and metadata of Dutch dental unit water.},
journal = {Data in brief},
volume = {37},
number = {},
pages = {107221},
pmid = {34179320},
issn = {2352-3409},
abstract = {Dental practices were approached to fill out a questionnaire on the infection control protocols in use to control biofilm growth in the dental unit and to send two types of water sample. Sampling of the dental units had to be performed prior to any infection control measures and on the second day of operation, to avoid residual effects of biofilm disinfection protocols performed in the weekend. Instructions were given on how to sample the units. Only samples, accompanied with a completed questionnaire and returned within two days by regular mail, were analysed. Samples were processed for heterotrophic plate counts, 16S (V4) rDNA microbiome sequencing and q-PCR for the concentration of bacterial 16S rDNA, fungal 18S rDNA, Legionella spp. and the presence of amoeba. The files contain the metadata needed to interpret and analyse the microbiome data. This dataset can be used by other scientists, members of infection control units, (trainee) bioinformaticians and policy makers. This dataset can provide leads to further unexplored parameters which could influence the microbial ecology of the dental unit.},
}
@article {pmid34177846,
year = {2021},
author = {Tláskal, V and Pylro, VS and Žifčáková, L and Baldrian, P},
title = {Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {668644},
pmid = {34177846},
issn = {1664-302X},
abstract = {The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.},
}
@article {pmid34177841,
year = {2021},
author = {Selari, PJRG and Olchanheski, LR and Ferreira, AJ and Paim, TDP and Calgaro Junior, G and Claudio, FL and Alves, EM and Santos, DC and Araújo, WL and Silva, FG},
title = {Short-Term Effect in Soil Microbial Community of Two Strategies of Recovering Degraded Area in Brazilian Savanna: A Pilot Case Study.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {661410},
pmid = {34177841},
issn = {1664-302X},
abstract = {The Brazilian Cerrado is a highland tropical savanna considered a biodiversity hotspot with many endemic species of plants and animals. Over the years, most of the native areas of this biome became arable areas, and with inadequate management, some are nowadays at varying levels of degradation stage. Crop-livestock integrated systems (CLIS) are one option for the recovery of areas in degradation, improving the physicochemical and biological characteristics of the soil while increasing income and mitigating risks due to product diversification. Little is known about the effect of CLIS on the soil microbial community. Therefore, we perform this pilot case study to support further research on recovering degraded areas. The bacterial and fungal soil communities in the area with CLIS were compared to an area under moderate recovery (low-input recovering - LI) and native savanna (NS) area. Bacterial and fungal communities were investigated by 16S and ITS rRNA gene sequencing (deep rRNA sequencing). Ktedonobacteraceae and AD3 families were found predominantly in LI, confirming the relationship of the members of the Chloroflexi phylum in challenging environmental conditions, which can be evidenced in LI. The CLIS soil presented 63 exclusive bacterial families that were not found in LI or NS and presented a higher bacterial richness, which can be related to good land management. The NS area shared 21 and 6 families with CLIS and LI, respectively, suggesting that the intervention method used in the analyzed period brings microbial diversity closer to the conditions of the native area, demonstrating a trend of approximation between NS and CLIS even in the short term. The most abundant fungal phylum in NS treatment was Basidiomycota and Mucoromycota, whereas Ascomycota predominated in CLIS and LI. The fungal community needs more time to recover and to approximate from the native area than the bacterial community. However, according to the analysis of bacteria, the CLIS area behaved differently from the LI area, showing that this treatment induces a faster response to the increase in species richness, tending to more accelerated recovery. Results obtained herein encourage CLIS as a sustainable alternative for recovery and production in degraded areas.},
}
@article {pmid34173031,
year = {2022},
author = {Zhang, W and Zhang, YC and Wang, ZG and Gu, QY and Niu, JZ and Wang, JJ},
title = {The Diversity of Viral Community in Invasive Fruit Flies (Bactrocera and Zeugodacus) Revealed by Meta-transcriptomics.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {739-752},
pmid = {34173031},
issn = {1432-184X},
support = {2019YFD1002100//National Key R&amp;D Program of China/ ; 31701846//National Natural Science Foundation of China/ ; CARS-26//earmarked fund for Modern Agro-industry (Citrus) Technology Research System of China/ ; B18044//111 Project/ ; },
mesh = {Animals ; Ecosystem ; Kenya ; *RNA Viruses/genetics ; *Tephritidae ; Transcriptome ; },
abstract = {RNA viruses are extremely diverse and rapidly evolving in various organisms. Our knowledge on viral evolution with interacted hosts in the manner of ecology is still limited. In the agricultural ecosystem, invasive insect species are posing a great threat to sustainable crop production. Among them, fruit flies (Diptera: Tephritidae Bactrocera and Zeugodacus) are destructive to fruits and vegetables, which are also closely related and often share similar ecological niches. Thus, they are ideal models for investigating RNA virome dynamics in host species. Using meta-transcriptomics, we found 39 viral sequences in samples from 12 fly species. These viral species represented the diversity of the viromes including Dicistroviridae, negev-like virus clades, Thika virus clades, Solemoviridae, Narnaviridae, Nodaviridae, Iflaviridae, Orthomyxoviridae, Bunyavirales, Partitiviridae, and Reoviridae. In particular, dicistrovirus, negev-like virus, orthomyxovirus, and orbivirus were common in over four of the fly species, which suggests a positive interaction between fly viromes that exist under the same ecological conditions. For most of the viruses, the virus-derived small RNAs displayed significantly high peaks in 21 nt and were symmetrically distributed throughout the viral genome. These results suggest that infection by these viruses can activate the host's RNAi immunity. Our study provides RNA virome diversity and evidence on their infection activity in ecologically associated invasive fruit fly species, which could help our understanding of interactions between complex species and viruses.},
}
@article {pmid34170682,
year = {2021},
author = {Mamet, SD and Jimmo, A and Conway, A and Teymurazyan, A and Talebitaher, A and Papandreou, Z and Chang, YF and Shannon, W and Peak, D and Siciliano, SD},
title = {Soil Buffering Capacity Can Be Used To Optimize Biostimulation of Psychrotrophic Hydrocarbon Remediation.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {14},
pages = {9864-9875},
doi = {10.1021/acs.est.1c01113},
pmid = {34170682},
issn = {1520-5851},
mesh = {Biodegradation, Environmental ; Hydrocarbons ; *Petroleum ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {Effective bioremediation of hydrocarbons requires innovative approaches to minimize phosphate precipitation in soils of different buffering capacities. Understanding the mechanisms underlying sustained stimulation of bacterial activity remains a key challenge for optimizing bioremediation-particularly in northern regions. Positron emission tomography (PET) can trace microbial activity within the naturally occurring soil structure of intact soils. Here, we use PET to test two hypotheses: (1) optimizing phosphate bioavailability in soil will outperform a generic biostimulatory solution in promoting hydrocarbon remediation and (2) oligotrophic biostimulation will be more effective than eutrophic approaches. In so doing, we highlight the key bacterial taxa that underlie aerobic and anaerobic hydrocarbon degradation in subarctic soils. In particular, we showed that (i) optimized phosphate bioavailability outperformed generic biostimulatory solutions in promoting hydrocarbon degradation, (ii) oligotrophic biostimulation is more effective than eutrophic approaches, and (iii) optimized biostimulatory solutions stimulated specific soil regions and bacterial consortia. The knowledge gleaned from this study will be crucial in developing field-scale biodegradation treatments for sustained stimulation of bacterial activity in northern regions.},
}
@article {pmid34169333,
year = {2022},
author = {Cobo-Díaz, JF and Legrand, F and Le Floch, G and Picot, A},
title = {Influence of Maize Residues in Shaping Soil Microbiota and Fusarium spp. Communities.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {702-713},
pmid = {34169333},
issn = {1432-184X},
support = {Grant#9097 MycoRes//R&#xe9;gion Bretagne/ ; },
mesh = {*Ascomycota ; *Fusarium/genetics ; *Microbiota ; Plant Diseases/microbiology ; Soil/chemistry ; Zea mays/microbiology ; },
abstract = {Fusarium head blight (FHB) is a devastating fungal disease of small grain cereals including wheat. Causal fungal agents colonize various components of the field during their life cycle including previous crop residues, soil, and grains. Although soil and residues constitute the main inoculum source, these components have received much less attention than grains. This study aimed at disentangling the role of previous crop residues in shaping soil microbiota, including Fusarium spp. communities, in fields under wheat-maize rotation. Such knowledge may contribute to better understand the complex interactions between Fusarium spp. and soil microbiota. Dynamics of bacterial and fungal communities, with a special focus on Fusarium spp., were monitored in soils at 3 time points: during wheat cultivation (April 2015 and 2017) and after maize harvest (November 2016) and in maize residues taken from fields after harvest. Shifts in microbiota were also evaluated under mesocosm experiments using soils amended with maize residues. Fusarium graminearum and F. avenaceum were predominant on maize residues but did not remain in soils during wheat cultivation. Differences in soil bacterial diversity and compositions among years were much lower than variation between fields, suggesting that bacterial communities are field-specific and more conserved over time. In contrast, soil fungal diversity and compositions were more influenced by sampling time. Maize residues, left after harvest, led to a soil enrichment with several fungal genera, including Epicoccum, Fusarium, Vishniacozyma, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus, and Bullera, but not with bacterial genera. Likewise, under mesocosm conditions, the addition of maize residues had a stronger influence on fungal communities than on bacterial communities. In particular, addition of maize significantly increased soil fungal richness, while bacteria were much less prone to changes. Based on co-occurrence networks, OTUs negatively correlated to Fusarium spp. were identified, such as those assigned to Epicoccum and Vishniacozyma. Altogether, our results allowed to gain a deeper insight into the complex microbiota interactions in soils, with bacteria and fungi responding differently to environmental disturbances.},
}
@article {pmid34169332,
year = {2022},
author = {Djemai, K and Drancourt, M and Tidjani Alou, M},
title = {Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {536-554},
pmid = {34169332},
issn = {1432-184X},
support = {M&#xe9;diterran&#xe9;e Infection 10-IAHU-03//National Research Agency/ ; },
mesh = {Archaea/metabolism ; Bacteria/genetics/metabolism ; *Euryarchaeota/metabolism ; Humans ; Methane/metabolism ; *Microbiota ; },
abstract = {Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.},
}
@article {pmid34168166,
year = {2021},
author = {Gan, L and Xu, WH and Xiong, Y and Lv, Z and Zheng, J and Zhang, Y and Lin, J and Liu, J and Chen, S and Chen, M and Guo, Q and Wu, J and Chen, J and Su, Z and Sun, J and He, Y and Liu, C and Wang, W and Verstraete, W and Sorgeloos, P and Defoirdt, T and Qin, Q and Liu, Y},
title = {Probiotics: their action against pathogens can be turned around.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {13247},
pmid = {34168166},
issn = {2045-2322},
mesh = {Animals ; Disease Susceptibility/diet therapy ; Fish Diseases/diet therapy/microbiology ; Metabolome ; Microbiota/drug effects ; Probiotics/*therapeutic use ; Vibrio/*drug effects ; Vibrio Infections/diet therapy/microbiology/*veterinary ; Zebrafish/microbiology ; },
abstract = {Probiotics when applied in complex evolving (micro-)ecosystems, might be selectively beneficial or detrimental to pathogens when their prophylactic efficacies are prone to ambient interactions. Here, we document a counter-intuitive phenomenon that probiotic-treated zebrafish (Danio rerio) were respectively healthy at higher but succumbed at lower level of challenge with a pathogenic Vibrio isolate. This was confirmed by prominent dissimilarities in fish survival and histology. Based upon the profiling of the zebrafish microbiome, and the probiotic and the pathogen shared gene orthogroups (genetic niche overlaps in genomes), this consequently might have modified the probiotic metabolome as well as the virulence of the pathogen. Although it did not reshuffle the architecture of the commensal microbiome of the vertebrate host, it might have altered the probiotic-pathogen inter-genus and intra-species communications. Such in-depth analyses are needed to avoid counteractive phenomena of probiotics and to optimise their efficacies to magnify human and animal well-being. Moreover, such studies will be valuable to improve the relevant guidelines published by organisations such as FAO, OIE and WHO.},
}
@article {pmid34161269,
year = {2021},
author = {Qian, X and Gunturu, S and Sun, W and Cole, JR and Norby, B and Gu, J and Tiedje, JM},
title = {Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {25},
pages = {},
pmid = {34161269},
issn = {1091-6490},
mesh = {Animals ; Anti-Bacterial Agents ; Base Sequence ; Cattle ; Drug Resistance, Microbial/*genetics ; Environmental Microbiology ; Feces/*microbiology ; Gene Regulatory Networks ; Genes, Bacterial ; Genetic Linkage ; Genetic Variation ; Host Specificity/*genetics ; Microbiota/genetics ; Phylogeny ; Plasmids/genetics ; *Sequence Analysis, DNA ; },
abstract = {While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the inability to culture many environmental organisms, and it is difficult to evaluate risk from current sequence-based environmental methods. The four most important criteria to determine risk are whether the antibiotic-resistance genes (ARGs) are a complete, potentially functional complement; if they are linked with other resistances; whether they are mobile; and the identity of their host. Long-read sequencing fills this important gap between culture and short sequence-based methods. To address these criteria, we collected feces from a ceftiofur-treated cow, enriched the samples in the presence of antibiotics to favor ARG functionality, and sequenced long reads using Nanopore and PacBio technologies. Multidrug-resistance genes comprised 58% of resistome abundance, but only 0.8% of them were plasmid associated; fluroquinolone-, aminoglycoside-, macrolide-lincosamide-streptogramin (MLS)-, and β-lactam-resistance genes accounted for 2.7 to 12.3% of resistome abundance but with 19 to 78% located on plasmids. A variety of plasmid types were assembled, some of which share low similarity to plasmids in current databases. Enterobacteriaceae were dominant hosts of antibiotic-resistant plasmids; physical linkage of extended-spectrum β-lactamase genes (CTX-M, TEM, CMY, and CARB) was largely found with aminoglycoside-, MLS-, tetracycline-, trimethoprim-, phenicol-, sulfonamide-, and mercury-resistance genes. A draft circular chromosome of Vagococcus lutrae was assembled; it carries MLS-, tetracycline- (including tetM and tetL on an integrative conjugative element), and trimethoprim-resistance genes flanked by many transposase genes and insertion sequences, implying that they remain transferrable.},
}
@article {pmid34160245,
year = {2021},
author = {Shi, X and Oliveira, DAF and Holsten, L and Steinhauer, K and de Rezende, JR},
title = {Long-Term Biocide Efficacy and Its Effect on a Souring Microbial Community.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {17},
pages = {e0084221},
pmid = {34160245},
issn = {1098-5336},
mesh = {Acids/analysis/metabolism ; Bacteria/classification/*drug effects/isolation &amp; purification/metabolism ; Disinfectants/*pharmacology ; Microbiota/*drug effects ; Oil and Gas Fields/chemistry/microbiology ; Oxidation-Reduction ; Sulfates/analysis/metabolism ; Time Factors ; },
abstract = {Reservoir souring, which is the production of H2S mainly by sulfate-reducing microorganisms (SRM) in oil reservoirs, has been a long-standing issue for the oil industry. While biocides have been frequently applied to control biogenic souring, the effects of biocide treatment are usually temporary, and biocides eventually fail. The reasons for biocide failure and the long-term response of the microbial community remain poorly understood. In this study, one-time biocide treatments with glutaraldehyde (GA) and an aldehyde-releasing biocide (ARB) at low (100 ppm) and high (750 ppm) doses were individually applied to a complex SRM community, followed by 1 year of monitoring of the chemical responses and the microbial community succession. The chemical results showed that souring control failed after 7 days at a dose of 100 ppm regardless of the biocide type and lasting souring control for the entire 1-year period was achieved only with ARB at 750 ppm. Microbial community analyses suggested that the high-dose biocide treatments resulted in 1 order of magnitude lower average total microbial abundance and average SRM abundance, compared to the low-dose treatments. The recurrence of souring was associated with reduction of alpha diversity and with long-term microbial community structure changes; therefore, monitoring changes in microbial community metrics may provide early warnings of the failure of a biocide-based souring control program in the field. Furthermore, spore-forming sulfate reducers (Desulfotomaculum and Desulfurispora) were enriched and became dominant in both GA-treated groups, which could cause challenges for the design of long-lasting remedial souring control strategies. IMPORTANCE Reservoir souring is a problem for the oil and gas industry, because H2S corrodes the steel infrastructure, downgrades oil quality, and poses substantial risks to field personnel and the environment. Biocides have been widely applied to remedy souring, but the long-term performance of biocide treatments is hard to predict or to optimize due to limited understanding of the microbial ecology affected by biocide treatment. This study investigates the long-term biocide performance and associated changes in the abundance, diversity, and structure of the souring microbial community, thus advancing the knowledge toward a deeper understanding of the microbial ecology of biocide-treated systems and contributing to the improvement of current biocide-based souring control practices. The study showcases the potential application of incorporating microbial community analyses to forecast souring, and it highlights the long-term consequences of biocide treatment in the microbial communities, with relevance to both operators and regulators.},
}
@article {pmid34157595,
year = {2021},
author = {Volpiano, CG and Sant'Anna, FH and da Mota, FF and Sangal, V and Sutcliffe, I and Munusamy, M and Saravanan, VS and See-Too, WS and Passaglia, LMP and Rosado, AS},
title = {Proposal of Carbonactinosporaceae fam. nov. within the class Actinomycetia. Reclassification of Streptomyces thermoautotrophicus as Carbonactinospora thermoautotrophica gen. nov., comb. nov.},
journal = {Systematic and applied microbiology},
volume = {44},
number = {4},
pages = {126223},
doi = {10.1016/j.syapm.2021.126223},
pmid = {34157595},
issn = {1618-0984},
mesh = {Actinobacteria ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; *Phylogeny ; Proteomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Streptomyces/classification ; },
abstract = {Streptomyces thermoautotrophicus UBT1[T] has been suggested to merit generic status due to its phylogenetic placement and distinctive phenotypes among Actinomycetia. To evaluate whether 'S. thermoautotrophicus' represents a higher taxonomic rank, 'S. thermoautotrophicus' strains UBT1[T] and H1 were compared to Actinomycetia using 16S rRNA gene sequences and comparative genome analyses. The UBT1[T] and H1 genomes each contain at least two different 16S rRNA sequences, which are closely related to those of Acidothermus cellulolyticus (order Acidothermales). In multigene-based phylogenomic trees, UBT1[T] and H1 typically formed a sister group to the Streptosporangiales-Acidothermales clade. The Average Amino Acid Identity, Percentage of Conserved Proteins, and whole-genome Average Nucleotide Identity (Alignment Fraction) values were ≤58.5%, ≤48%, ≤75.5% (0.3) between 'S. thermoautotrophicus' and Streptosporangiales members, all below the respective thresholds for delineating genera. The values for genomics comparisons between strains UBT1[T] and H1 with Acidothermales, as well as members of the genus Streptomyces, were even lower. A review of the 'S. thermoautotrophicus' proteomic profiles and KEGG orthology demonstrated that UBT1[T] and H1 present pronounced differences, both tested and predicted, in phenotypic and chemotaxonomic characteristics compared to its sister clades and Streptomyces. The distinct phylogenetic position and the combination of genotypic and phenotypic characteristics justify the proposal of Carbonactinospora gen. nov., with the type species Carbonactinospora thermoautotrophica comb. nov. (type strain UBT1[T], = DSM 100163[T] = KCTC 49540[T]) belonging to Carbonactinosporaceae fam. nov. within Actinomycetia.},
}
@article {pmid34156270,
year = {2021},
author = {Zhu, M and Duan, X and Guo, H and Huang, W and Quan, K and Yan, X and Ji, J and Li, Y and Li, Z},
title = {Occurrence of Powdery Mildew Caused by Erysiphe buhrii on Dianthus chinensis in Inner Mongolia, China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-01-21-0048-PDN},
pmid = {34156270},
issn = {0191-2917},
abstract = {Dianthus chinensis is widely cultivated for ornamental and medicinal use in China (Guo et al. 2017). The plant has been used in traditional Chinese medicine for the treatment of urinary problems such as strangury and diuresis (Han et al. 2015). In June and July 2020, powdery mildew-like signs and symptoms were seen on leaves of D. chinensis cultivated on the campus of Inner Mongolia Agricultural University, Hohhot city, Inner Mongolia Province, China. White powder-like masses occurred in irregular shaped lesions on both leaf surfaces and covered up to 50% of leaf area. Some infected leaves were deformed on their edges and some leaf senescence occurred. More than 40 % of plants (n = 180) exhibited these signs and symptoms. Conidiophores (n = 50) of the suspect fungus were unbranched and measured 70 to 140 µm long × 6 to 10 µm wide and had foot cells that were 25 to 48 µm long. Conidia (n = 50) were produced singly, elliptical to cylindrical shaped, 30 to 45 µm long × 12 to 19 µm wide, with length/width ratio of 2.0 to 3.2, and lacked fibrosin bodies. No chasmothecia were found. Based on these morphological characteristics, the fungus was tentatively identified as an Erysiphe sp. (Braun and Cook 2012). Fungal structures were isolated from diseased leaves and genomic DNA of the pathogen extracted utilizing the method described by Zhu et al. (2019). The internal transcribed spacer (ITS) region was amplified by PCR employing the primers PMITS1/PMITS2 (Cunnington et al. 2003) and the amplicon sequenced by Invitrogen (Shanghai, China). The sequence for the powdery mildew fungus (deposited into GenBank under Accession No. MW144997) showed 100 % identity (558/558 bp) with E. buhrii (Accession No. LC009898) that was reported on Dianthus sp. in Japan (Takamatsu et al. 2015). Pathogenicity tests were done by collecting fungal conidia from infected D. chinensis leaves and brushing them onto leaves of four healthy plants. Four uninoculated plants served as controls. Inoculated and uninoculated plants were placed in separate growth chambers maintained at 19 ℃, 65 % humidity, with a 16 h/8 h light/dark period. Nine-days post-inoculation, powdery mildew disease signs appeared on inoculated plants, whereas control plants remained asymptomatic. The same results were obtained for two repeated pathogenicity experiments. The powdery mildew fungus was identified and confirmed as E. buhrii based on morphological and molecular analysis. An Oidium sp. causing powdery mildew on D. chinensis previously was reported in Xinjiang Province, China (Zheng and Yu 1987). This, to the best of our knowledge, is the first report of powdery mildew caused by E. buhrii on D. chinensis in China (Farr and Rossman 2020). The sudden occurrence of this destructive powdery mildew disease on D. chinensis may adversely affect the health, ornamental value and medicinal uses of the plant in China. Identifying the cause of the disease will support efforts for its future control and management.},
}
@article {pmid34154406,
year = {2021},
author = {Guo, H and Rischer, M and Westermann, M and Beemelmanns, C},
title = {Two Distinct Bacterial Biofilm Components Trigger Metamorphosis in the Colonial Hydrozoan Hydractinia echinata.},
journal = {mBio},
volume = {12},
number = {3},
pages = {e0040121},
pmid = {34154406},
issn = {2150-7511},
mesh = {Animals ; *Biofilms ; Coral Reefs ; Ecosystem ; Hydrozoa/*microbiology/*physiology ; Larva/*microbiology ; *Metamorphosis, Biological ; },
abstract = {In marine environments, the bacterially induced metamorphosis of larvae is a widespread cross-kingdom communication phenomenon that is critical for the persistence of many marine invertebrates. However, the majority of inducing bacterial signals and underlying cellular mechanisms remain enigmatic. The marine hydroid Hydractinia echinata is a well-known model system for investigating bacterially stimulated larval metamorphosis, as larvae transform into the colonial adult stage within 24 h of signal detection. Although H. echinata has served as a cell biological model system for decades, the identity and influence of bacterial signals on the morphogenic transition remained largely unexplored. Using a bioassay-guided analysis, we first determined that specific bacterial (lyso)phospholipids, naturally present in bacterial membranes and vesicles, elicit metamorphosis in Hydractinia larvae in a dose-response manner. Lysophospholipids, as single compounds or in combination (50 μM), induced metamorphosis in up to 50% of all larvae within 48 h. Using fluorescence-labeled bacterial phospholipids, we demonstrated that phospholipids are incorporated into the larval membranes, where interactions with internal signaling cascades are proposed to occur. Second, we identified two structurally distinct exopolysaccharides of bacterial biofilms, the new Rha-Man polysaccharide from Pseudoalteromonas sp. strain P1-9 and curdlan from Alcaligenes faecalis, to induce metamorphosis in up to 75% of tested larvae. We also found that combinations of (lyso)phospholipids and curdlan induced transformation within 24 h, thereby exceeding the morphogenic activity observed for single compounds and bacterial biofilms. Our results demonstrate that two structurally distinct, bacterium-derived metabolites converge to induce high transformation rates of Hydractinia larvae and thus may help ensure optimal habitat selection. IMPORTANCE Bacterial biofilms profoundly influence the recruitment and settlement of marine invertebrates, critical steps for diverse marine processes such as the formation of coral reefs, the maintenance of marine fisheries, and the fouling of submerged surfaces. However, the complex composition of biofilms often makes the characterization of individual signals and regulatory mechanisms challenging. Developing tractable model systems to characterize these coevolved interactions is the key to understanding fundamental processes in evolutionary biology. Here, we characterized two types of bacterial signaling molecules, phospholipids and polysaccharides, that induce the morphogenic transition. We then analyzed their abundance and combinatorial activity. This study highlights the general importance of multiple bacterial signal converging activity in development-related cross-kingdom signaling and poses the question of whether complex lipids and polysaccharides are general metamorphic cues for cnidarian larvae.},
}
@article {pmid34148108,
year = {2022},
author = {Rosado-Porto, D and Ratering, S and Cardinale, M and Maisinger, C and Moser, G and Deppe, M and Müller, C and Schnell, S},
title = {Elevated Atmospheric CO2 Modifies Mostly the Metabolic Active Rhizosphere Soil Microbiome in the Giessen FACE Experiment.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {619-634},
pmid = {34148108},
issn = {1432-184X},
mesh = {Carbon Dioxide/metabolism ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere.},
}
@article {pmid34148107,
year = {2022},
author = {Deignan, LK and McDougald, D},
title = {Differential Response of the Microbiome of Pocillopora acuta to Reciprocal Transplantation Within Singapore.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {608-618},
pmid = {34148107},
issn = {1432-184X},
support = {MSRDP-03//National Research Foundation Singapore/ ; },
mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Singapore ; },
abstract = {As corals continue to decline globally, particularly due to climate change, it is vital to understand the extent to which their microbiome may confer an adaptive resilience against environmental stress. Corals that survive on the urban reefs of Singapore are ideal candidates to study the association of scleractinians with their microbiome, which in turn can inform reef conservation and management. In this study, we monitored differences in the microbiome of Pocillopora acuta colonies reciprocally transplanted between two reefs, Raffles and Kusu, within the Port of Singapore, where corals face intense anthropogenic impacts. Pocillopora acuta had previously been shown to host distinct microbial communities between these two reefs. Amplicon sequencing (16S rRNA) was used to assess the coral microbiomes at 1, 2, 4, and 10 days post-transplantation. Coral microbiomes responded rapidly to transplantation, becoming similar to those of the local corals at the destination reef within one day at Raffles and within two days at Kusu. Elevated nitrate concentrations were detected at Raffles for the duration of the study, potentially influencing the microbiome's response to transplantation. The persistence of corals within the port of Singapore highlights the ability of corals to adapt to stressful environments. Further, coral resilience appears to coincide with a dynamic microbiome which can undergo shifts in composition without succumbing to dysbiosis.},
}
@article {pmid34146566,
year = {2021},
author = {Baumgartner, M and Lang, M and Holley, H and Crepaz, D and Hausmann, B and Pjevac, P and Moser, D and Haller, F and Hof, F and Beer, A and Orgler, E and Frick, A and Khare, V and Evstatiev, R and Strohmaier, S and Primas, C and Dolak, W and Köcher, T and Klavins, K and Rath, T and Neurath, MF and Berry, D and Makristathis, A and Muttenthaler, M and Gasche, C},
title = {Mucosal Biofilms Are an Endoscopic Feature of Irritable Bowel Syndrome and Ulcerative Colitis.},
journal = {Gastroenterology},
volume = {161},
number = {4},
pages = {1245-1256.e20},
pmid = {34146566},
issn = {1528-0012},
support = {714366/ERC_/European Research Council/International ; },
mesh = {Austria ; Bacteria/*growth &amp; development/metabolism/ultrastructure ; Biofilms/*growth &amp; development ; Case-Control Studies ; Colitis, Ulcerative/metabolism/*microbiology/pathology ; Colon/metabolism/*microbiology/pathology ; *Colonoscopy ; Deep Learning ; *Gastrointestinal Microbiome ; Germany ; Humans ; Image Interpretation, Computer-Assisted ; Intestinal Mucosa/metabolism/*microbiology/pathology ; Irritable Bowel Syndrome/metabolism/*microbiology/pathology ; Metabolomics ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Predictive Value of Tests ; Ribotyping ; },
abstract = {BACKGROUND &amp; AIMS: Irritable bowel syndrome (IBS) and inflammatory bowel diseases result in a substantial reduction in quality of life and a considerable socioeconomic impact. In IBS, diagnosis and treatment options are limited, but evidence for involvement of the gut microbiome in disease pathophysiology is emerging. Here we analyzed the prevalence of endoscopically visible mucosal biofilms in gastrointestinal disease and associated changes in microbiome composition and metabolism.<br><br>METHODS: The presence of mucosal biofilms was assessed in 1426 patients at 2 European university-based endoscopy centers. One-hundred and seventeen patients were selected for in-depth molecular and microscopic analysis using 16S ribosomal RNA gene amplicon-sequencing of colonic biopsies and fecal samples, confocal microscopy with deep learning-based image analysis, scanning electron microscopy, metabolomics, and in&#xa0;vitro biofilm formation assays.<br><br>RESULTS: Biofilms were present in 57% of patients with IBS and 34% of patients with ulcerative colitis compared with 6% of controls (P < .001). These yellow-green adherent layers of the ileum and right-sided colon were microscopically confirmed to be dense bacterial biofilms. 16S-sequencing links the presence of biofilms to a dysbiotic gut microbiome, including overgrowth of Escherichia coli and Ruminococcus gnavus. R. gnavus isolates cultivated from patient biofilms also formed biofilms in&#xa0;vitro. Metabolomic analysis found an accumulation of bile acids within biofilms that correlated with fecal bile acid excretion, linking this phenotype with a mechanism of diarrhea.<br><br>CONCLUSIONS: The presence of mucosal biofilms is an endoscopic feature in a subgroup of IBS and ulcerative colitis with disrupted bile acid metabolism and bacterial dysbiosis. They provide novel insight into the pathophysiology of IBS and ulcerative colitis, illustrating that biofilm can be seen as a tipping point in the development of dysbiosis and disease.},
}
@article {pmid34145482,
year = {2022},
author = {González-Olalla, JM and Medina-Sánchez, JM and Carrillo, P},
title = {Fluctuation at High Temperature Combined with Nutrients Alters the Thermal Dependence of Phytoplankton.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {555-567},
pmid = {34145482},
issn = {1432-184X},
mesh = {*Ecosystem ; Heterotrophic Processes ; Nutrients/metabolism ; *Phytoplankton/metabolism ; Temperature ; },
abstract = {The Metabolic Theory of Ecology (MTE) predicts that the temperature increases exert a common effect on organisms stimulating metabolic rates, this being stronger for a heterotrophic than for an autotrophic metabolism. However, no available studies within the MTE framework have focused on organisms' response under fluctuation at high temperature interacting with factors such as nutrient availability, or how this interaction could affect the coexistence between mixotrophic and strict autotrophic phytoplankton. Hence, we assess how the phytoplankton metabolism and species composition are affected under scenarios of high temperature and fluctuation at high temperature, and how nutrients alter the direction and magnitude of such impact. For that, we use a mixed culture composed of two phytoplankton species: a strict autotrophic species and a mixotrophic species. Our results indicate that, in agreement with the MTE, only fluctuation at high temperature treatment registered a greater activation energy (Ea) value for respiration than for primary production and stimulated mixotrophic over strict autotrophic species abundance compared to control treatment. Remarkably, fluctuation at high temperature had a strong negative impact on the total abundance of the mixed-culture. The interaction between nutrient enrichment and fluctuation at high temperature increased abundance of the strict autotrophic species and overall species abundance, and led to Ea values that were higher in primary production than in respiration. Changes in community composition, enhanced by nutrient enrichment, could be behind this response, which can have implications in ecosystem functioning in a changing world.},
}
@article {pmid34143976,
year = {2021},
author = {Yang, JY and Fang, W and Miranda-Sanchez, F and Brown, JM and Kauffman, KM and Acevero, CM and Bartel, DP and Polz, MF and Kelly, L},
title = {Degradation of host translational machinery drives tRNA acquisition in viruses.},
journal = {Cell systems},
volume = {12},
number = {8},
pages = {771-779.e5},
pmid = {34143976},
issn = {2405-4720},
support = {K99 GM123230/GM/NIGMS NIH HHS/United States ; R35 GM118135/GM/NIGMS NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacteriophages/genetics ; Codon/genetics ; Codon Usage ; RNA, Transfer/genetics/metabolism ; *Viruses/genetics ; },
abstract = {Viruses are traditionally thought to be under selective pressure to maintain compact genomes and thus depend on host cell translational machinery for reproduction. However, some viruses encode abundant tRNA and other translation-related genes, potentially optimizing for codon usage differences between phage and host. Here, we systematically interrogate selective advantages that carrying 18 tRNAs may convey to a T4-like Vibriophage. Host DNA and RNA degrade upon infection, including host tRNAs, which are replaced by those of the phage. These tRNAs are expressed at levels slightly better adapted to phage codon usage, especially that of late genes. The phage is unlikely to randomly acquire as diverse an array of tRNAs as observed (p = 0.0017). Together, our results support that the main driver behind phage tRNA acquisition is pressure to sustain translation as host machinery degrades, a process resulting in a dynamically adapted codon usage strategy during the course of infection.},
}
@article {pmid34143648,
year = {2021},
author = {Hawkes, CV and Kjøller, R and Raaijmakers, JM and Riber, L and Christensen, S and Rasmussen, S and Christensen, JH and Dahl, AB and Westergaard, JC and Nielsen, M and Brown-Guedira, G and Hestbjerg Hansen, L},
title = {Extension of Plant Phenotypes by the Foliar Microbiome.},
journal = {Annual review of plant biology},
volume = {72},
number = {},
pages = {823-846},
doi = {10.1146/annurev-arplant-080620-114342},
pmid = {34143648},
issn = {1545-2123},
mesh = {Ecology ; *Microbiota ; Phenotype ; Plant Development ; Plants ; },
abstract = {The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.},
}
@article {pmid34143451,
year = {2021},
author = {Romaní-Pérez, M and López-Almela, I and Bullich-Vilarrubias, C and Rueda-Ruzafa, L and Gómez Del Pulgar, EM and Benítez-Páez, A and Liebisch, G and Lamas, JA and Sanz, Y},
title = {Holdemanella biformis improves glucose tolerance and regulates GLP-1 signaling in obese mice.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {35},
number = {7},
pages = {e21734},
doi = {10.1096/fj.202100126R},
pmid = {34143451},
issn = {1530-6860},
mesh = {Animals ; Blood Glucose/metabolism ; Diabetes Mellitus, Type 2/*metabolism/*microbiology ; Disease Models, Animal ; Firmicutes/*physiology ; Glucagon-Like Peptide 1/*metabolism ; Gluconeogenesis/physiology ; Glucose/metabolism ; Glucose Tolerance Test/methods ; Hyperglycemia/metabolism ; Insulin/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Obese/*metabolism/*microbiology ; Obesity/metabolism/microbiology ; },
abstract = {Impaired glucose homeostasis in obesity is mitigated by enhancing the glucoregulatory actions of glucagon-like peptide 1 (GLP-1), and thus, strategies that improve GLP-1 sensitivity and secretion have therapeutic potential for the treatment of type 2 diabetes. This study shows that Holdemanella biformis, isolated from the feces of a metabolically healthy volunteer, ameliorates hyperglycemia, improves oral glucose tolerance and restores gluconeogenesis and insulin signaling in the liver of obese mice. These effects were associated with the ability of H. biformis to restore GLP-1 levels, enhancing GLP-1 neural signaling in the proximal and distal small intestine and GLP-1 sensitivity of vagal sensory neurons, and to modify the cecal abundance of unsaturated fatty acids and the bacterial species associated with metabolic health. Our findings overall suggest the potential use of H biformis in the management of type 2 diabetes in obesity to optimize the sensitivity and function of the GLP-1 system, through direct and indirect mechanisms.},
}
@article {pmid34142402,
year = {2021},
author = {Simonin, M and Rocca, JD and Gerson, JR and Moore, E and Brooks, AC and Czaplicki, L and Ross, MRV and Fierer, N and Craine, JM and Bernhardt, ES},
title = {Consistent declines in aquatic biodiversity across diverse domains of life in rivers impacted by surface coal mining.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {31},
number = {6},
pages = {e02389},
doi = {10.1002/eap.2389},
pmid = {34142402},
issn = {1051-0761},
mesh = {Animals ; Biodiversity ; *Coal Mining ; Ecosystem ; Environmental Monitoring ; Invertebrates ; Mining ; Rivers ; *Water Pollutants, Chemical/analysis ; },
abstract = {The rivers of Appalachia (United States) are among the most biologically diverse freshwater ecosystems in the temperate zone and are home to numerous endemic aquatic organisms. Throughout the Central Appalachian ecoregion, extensive surface coal mines generate alkaline mine drainage that raises the pH, salinity, and trace element concentrations in downstream waters. Previous regional assessments have found significant declines in stream macroinvertebrate and fish communities after draining these mined areas. Here, we expand these assessments with a more comprehensive evaluation across a broad range of organisms (bacteria, algae, macroinvertebrates, all eukaryotes, and fish) using high-throughput amplicon sequencing of environmental DNA (eDNA). We collected water samples from 93 streams in Central Appalachia (West Virginia, United States) spanning a gradient of mountaintop coal mining intensity and legacy to assess how this land use alters downstream water chemistry and affects aquatic biodiversity. For each group of organisms, we identified the sensitive and tolerant taxa along the gradient and calculated stream specific conductivity thresholds in which large synchronous declines in diversity were observed. Streams below mining operations had steep declines in diversity (-18 to -41%) and substantial shifts in community composition that were consistent across multiple taxonomic groups. Overall, large synchronous declines in bacterial, algal, and macroinvertebrate communities occurred even at low levels of mining impact at stream specific conductivity thresholds of 150-200 µS/cm that are substantially below the current U.S. Environmental Protection Agency aquatic life benchmark of 300 µS/cm for Central Appalachian streams. We show that extensive coal surface mining activities led to the extirpation of 40% of biodiversity from impacted rivers throughout the region and that current water quality criteria are likely not protective for many groups of aquatic organisms.},
}
@article {pmid34141244,
year = {2021},
author = {Boynton, PJ and Wloch-Salamon, D and Landermann, D and Stukenbrock, EH},
title = {Forest Saccharomyces paradoxus are robust to seasonal biotic and abiotic changes.},
journal = {Ecology and evolution},
volume = {11},
number = {11},
pages = {6604-6619},
pmid = {34141244},
issn = {2045-7758},
abstract = {Microorganisms are famous for adapting quickly to new environments. However, most evidence for rapid microbial adaptation comes from laboratory experiments or domesticated environments, and it is unclear how rates of adaptation scale from human-influenced environments to the great diversity of wild microorganisms. We examined potential monthly-scale selective pressures in the model forest yeast Saccharomyces paradoxus. Contrary to expectations of seasonal adaptation, the S. paradoxus population was stable over four seasons in the face of abiotic and biotic environmental changes. While the S. paradoxus population was diverse, including 41 unique genotypes among 192 sampled isolates, there was no correlation between S. paradoxus genotypes and seasonal environments. Consistent with observations from other S. paradoxus populations, the forest population was highly clonal and inbred. This lack of recombination, paired with population stability, implies that selection is not acting on the forest S. paradoxus population on a seasonal timescale. Saccharomyces paradoxus may instead have evolved generalism or phenotypic plasticity with regard to seasonal environmental changes long ago. Similarly, while the forest population included diversity among phenotypes related to intraspecific interference competition, there was no evidence for active coevolution among these phenotypes. At least ten percent of the forest S. paradoxus individuals produced "killer toxins," which kill sensitive Saccharomyces cells, but the presence of a toxin-producing isolate did not predict resistance to the toxin among nearby isolates. How forest yeasts acclimate to changing environments remains an open question, and future studies should investigate the physiological responses that allow microbial cells to cope with environmental fluctuations in their native habitats.},
}
@article {pmid34141209,
year = {2021},
author = {Li, Y and Chesters, D and Wang, MQ and Wubet, T and Schuldt, A and Anttonen, P and Guo, PF and Chen, JT and Zhou, QS and Zhang, NL and Ma, KP and Bruelheide, H and Wu, CS and Zhu, CD},
title = {Tree diversity and functional leaf traits drive herbivore-associated microbiomes in subtropical China.},
journal = {Ecology and evolution},
volume = {11},
number = {11},
pages = {6153-6166},
pmid = {34141209},
issn = {2045-7758},
abstract = {Herbivorous insects acquire microorganisms from host plants or soil, but it remains unclear how the diversity and functional composition of host plants contribute to structuring herbivore microbiomes. Within a controlled tree diversity setting, we used DNA metabarcoding of 16S rRNA to assess the contribution of Lepidoptera species and their local environment (particularly, tree diversity, host tree species, and leaf traits) to the composition of associated bacterial communities. In total, we obtained 7,909 bacterial OTUs from 634 caterpillar individuals comprising 146 species. Tree diversity was found to drive the diversity of caterpillar-associated bacteria both directly and indirectly via effects on caterpillar communities, and tree diversity was a stronger predictor of bacterial diversity than diversity of caterpillars. Leaf toughness and dry matter content were important traits of the host plant determining bacterial species composition, while leaf calcium and potassium concentration influenced bacterial richness. Our study reveals previously unknown linkages between trees and their characteristics, herbivore insects, and their associated microbes, which contributes to developing a more nuanced understanding of functional dependencies between herbivores and their environment, and has implications for the consequences of plant diversity loss for trophic interactions.},
}
@article {pmid34137824,
year = {2021},
author = {Abiriga, D and Jenkins, A and Alfsnes, K and Vestgarden, LS and Klempe, H},
title = {Spatiotemporal and seasonal dynamics in the microbial communities of a landfill-leachate contaminated aquifer.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {7},
pages = {},
pmid = {34137824},
issn = {1574-6941},
mesh = {*Groundwater ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seasons ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; },
abstract = {The microbiome of an aquifer contaminated by landfill leachate and undergoing intrinsic remediation was characterised using 16S rRNA metabarcoding. The archaeal/bacterial V3-V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina MiSeq, and multivariate statistics were applied to make inferences. Results indicate that the aquifer recharge and aquifer sediment samples harbour different microbial communities compared to the groundwater samples. While Proteobacteria dominated both the recharge and groundwater samples, Acidobacteria dominated the aquifer sediment. The most abundant genera detected from the contaminated aquifer were Polynucleobacter, Rhodoferax, Pedobacter, Brevundimonas, Pseudomonas, Undibacterium, Sulfurifustis, Janthinobacterium, Rhodanobacter, Methylobacter and Aquabacterium. The result also shows that the microbial communities of the groundwater varied spatially, seasonally and interannually, although the interannual variation was significant for only one of the wells. Variation partitioning analysis indicates that water chemistry and well distance are intercorrelated and they jointly accounted for most of the variation in microbial composition. This implies that the species composition and water chemistry characteristics have a similar spatial structuring, presumably caused by the landfill leachate plume. The study improves our understanding of the dynamics in subsurface microbial communities in space and time.},
}
@article {pmid34136953,
year = {2022},
author = {Nair, A and Ghugare, GS and Khairnar, K},
title = {An Appraisal of Bacteriophage Isolation Techniques from Environment.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {519-535},
pmid = {34136953},
issn = {1432-184X},
mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; *Phage Therapy/methods ; },
abstract = {Researchers have recently renewed interest in bacteriophages. Being valuable models for the study of eukaryotic viruses, and more importantly, natural killers of bacteria, bacteriophages are being tapped for their potential role in multiple applications. Bacteriophages are also being increasingly sought for bacteriophage therapy due to rising antimicrobial resistance among pathogens. Reports show that there is an increasing trend in therapeutic application of natural bacteriophages, genetically engineered bacteriophages, and bacteriophage-encoded products as antimicrobial agents. In view of these applications, the isolation and characterization of bacteriophages from the environment has caught attention. In this review, various methods for isolation of bacteriophages from environmental sources like water, soil, and air are comprehensively described. The review also draws attention towards a handful on-field bacteriophage isolation techniques and the need for their further rapid development.},
}
@article {pmid34136952,
year = {2022},
author = {Jorge, F and Dheilly, NM and Froissard, C and Wainwright, E and Poulin, R},
title = {Consistency of Bacterial Communities in a Parasitic Worm: Variation Throughout the Life Cycle and Across Geographic Space.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {724-738},
pmid = {34136952},
issn = {1432-184X},
mesh = {Animals ; Bacteria/genetics ; Birds ; Life Cycle Stages ; Snails ; *Trematoda/genetics ; },
abstract = {Microbial communities within metazoans are increasingly linked with development, health and behaviour, possibly functioning as integrated evolutionary units with the animal in which they live. This would require microbial communities to show some consistency both ontogenetically (across life stages) and geographically (among populations). We characterise the bacteriome of the parasitic trematode Philophthalmus attenuatus, which undergoes major life cycle transitions, and test whether its bacteriome remains consistent on developmental and spatial scales. Based on sequencing the prokaryotic 16S SSU rRNA gene, we compared the parasite bacteriome (i) across three life stages (rediae in snails, cercariae exiting snails, adults in birds) in one locality and (ii) among three geographic localities for rediae only. We found that each life stage harbours a bacteriome different from that of its host (except the adult stage) and the external environment. Very few bacterial taxa were shared among life stages, suggesting substantial ontogenetic turnover in bacteriome composition. Rediae from the three different localities also had different bacteriomes, with dissimilarities increasing with geographical distance. However, rediae from different localities nevertheless shared more bacterial taxa than did different life stages from the same locality. Changes in the bacteriome along the parasite's developmental history but some degree of geographical stability within a given life stage point toward non-random, stage-specific acquisition, selection and/or propagation of bacteria.},
}
@article {pmid34135464,
year = {2021},
author = {Ware, IM and Van Nuland, ME and Yang, ZK and Schadt, CW and Schweitzer, JA and Bailey, JK},
title = {Climate-driven divergence in plant-microbiome interactions generates range-wide variation in bud break phenology.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {748},
pmid = {34135464},
issn = {2399-3642},
mesh = {*Climate Change ; *Ecosystem ; Genetic Variation ; Microbiota ; Populus/*microbiology ; Rhizosphere ; Soil/*chemistry ; *Soil Microbiology ; Trees/microbiology ; United States ; },
abstract = {Soil microbiomes are rapidly becoming known as an important driver of plant phenotypic variation and may mediate plant responses to environmental factors. However, integrating spatial scales relevant to climate change with plant intraspecific genetic variation and soil microbial ecology is difficult, making studies of broad inference rare. Here we hypothesize and show: 1) the degree to which tree genotypes condition their soil microbiomes varies by population across the geographic distribution of a widespread riparian tree, Populus angustifolia; 2) geographic dissimilarity in soil microbiomes among populations is influenced by both abiotic and biotic environmental variation; and 3) soil microbiomes that vary in response to abiotic and biotic factors can change plant foliar phenology. We show soil microbiomes respond to intraspecific variation at the tree genotype and population level, and geographic variation in soil characteristics and climate. Using a fully reciprocal plant population by soil location feedback experiment, we identified a climate-based soil microbiome effect that advanced and delayed bud break phenology by approximately 10 days. These results demonstrate a landscape-level feedback between tree populations and associated soil microbial communities and suggest soil microbes may play important roles in mediating and buffering bud break phenology with climate warming, with whole ecosystem implications.},
}
@article {pmid34134353,
year = {2021},
author = {Guo, X and Akram, S and Stedtfeld, R and Johnson, M and Chabrelie, A and Yin, D and Mitchell, J},
title = {Distribution of antimicrobial resistance across the overall environment of dairy farms - A case study.},
journal = {The Science of the total environment},
volume = {788},
number = {},
pages = {147489},
doi = {10.1016/j.scitotenv.2021.147489},
pmid = {34134353},
issn = {1879-1026},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; Drug Resistance, Bacterial/genetics ; Farms ; Genes, Bacterial ; Manure ; Michigan ; Soil ; Soil Microbiology ; },
abstract = {The environmental implications of antimicrobial resistance arising from food animal farm practice are still a knowledge gap. This study investigates the fate and transport of antimicrobial resistance genes related to the use of antibiotics on a dairy farm in Michigan. Manure, soil, animal feed, animal drinking water, surface and groundwater samples were taken and the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were subsequently measured using high parallel quantitative PCR targeting 136 genes. The total abundance and detected numbers of ARGs were found to be highest in the stagnant lagoon. Up to 44 ARG subtypes with high abundance were found in drinking water in pen which was very close to those in manure compost. The ARGs pattern clustered by soil depth although they were treated by different manure. ARGs and MGEs were detected in surface and groundwater surrounded by dairy farmlands, with the occurrence of carbapenemase-encoding KPC gene in two waters, which may be due to transport of ARGs through runoff or other sources. Overall, the results of the study suggest high prevalence of ARGs both inside and outside the animal raising area and their potential contribution to environmental ARGs.},
}
@article {pmid34133848,
year = {2021},
author = {Stella, R and Bovo, D and Mastrorilli, E and Pezzolato, M and Bozzetta, E and Biancotto, G},
title = {Anabolic treatments in bovines: quantification of plasma protein markers of dexamethasone administration.},
journal = {Proteomics},
volume = {21},
number = {16},
pages = {e2000238},
doi = {10.1002/pmic.202000238},
pmid = {34133848},
issn = {1615-9861},
mesh = {Animals ; Biomarkers ; Blood Proteins ; Cattle ; *Dexamethasone ; Male ; Proteome ; *Proteomics ; },
abstract = {The aim of this study was to profile plasma proteome responses in bulls experimentally treated with dexamethasone at anabolic dosage. Illicit use of active substances in animal husbandry remains a matter of concern in Europe. Corticosteroids are probably one of the most widespread growth promoter family illegally used in beef cattle and veal calves. Testing for corticosteroids relies on detection of drug residues or their metabolites in biological fluids or tissues. Their indirect detection by mapping altered physiological parameters may overcome limits linked to route of administration, dosage, biotransformation and elimination kinetics that can lower residual drug concentration, hampering official controls. A set of 11 proteins proposed in literature as potential markers of anabolic treatments with dexamethasone, was quantified in bovine plasma by targeted proteomics based on liquid chromatography-high resolution tandem mass spectrometry. Among investigated proteins, sex hormone-binding globulin (SHBG), histidine-rich glycoprotein (HRG) and paraoxonase-1 (PON1) were found to be biomarkers of treatment. To investigate further such biomarkers, an additional group of veal calves was experimentally treated with dexamethasone at anabolic. These animals also demonstrated a significant alteration in SHBG, HRG and PON1 concentration, suggesting that quantification of plasma markers have the potential to detect animals illegally exposed to dexamethasone.},
}
@article {pmid34133817,
year = {2022},
author = {Mitiku, AA and Vandeweyer, D and Lievens, B and Bossaert, S and Crauwels, S and Aernouts, B and Kechero, Y and Van Campenhout, L},
title = {Microbial profile during fermentation and aerobic stability of ensiled mixtures of maize stover and banana pseudostem in South Ethiopia.},
journal = {Journal of applied microbiology},
volume = {132},
number = {1},
pages = {126-139},
doi = {10.1111/jam.15183},
pmid = {34133817},
issn = {1365-2672},
support = {AMU 2017IUC035A10//Flemish Interuniversity Council for University Development Cooperation (VLIR-UOS)/ ; },
mesh = {Aerobiosis ; Ethiopia ; Fermentation ; *Musa ; Silage/analysis ; *Zea mays ; },
abstract = {AIMS: This study evaluated pH reduction and microbial growth during fermentation of maize stover (MS) mixed with banana pseudostem (BPS) under South Ethiopian conditions.<br><br>MATERIALS AND RESULTS: The MS and BPS were chopped and mixed into six treatments (T): 80% BPS plus 20% DMS (T1), 70% BPS plus 30% DMS (T2), 40% BPS plus 60% FMS (fresh MS) (T3), 20% BPS plus 80% FMS (T4), 100% FMS (T5), and 95% BPS plus 5% molasses (T6). At 0, 7, 14, 30, 60, and 90&#xa0;days, pH and dry matter were determined. Microbiological quality was assessed using plate counts and Illumina MiSeq sequencing. On day 60 and 90, aerobic stability was investigated. The results showed a significant reduction in pH in all mixtures, except in T1 and T2. Lactic acid bacteria counts reached a maximum in all treatments within 14&#xa0;days. Sequencing showed marked changes in dominant bacteria, such as Buttiauxella and Acinetobacter to Lactobacillus and Bifidobacterium.<br><br>CONCLUSIONS: The fresh MS and BPS mixtures and fresh maize showed significant pH reduction and dominance of desirable microbial groups.<br><br>The study enables year-round livestock feed supplementation to boost milk and meat production in South Ethiopia.},
}
@article {pmid34132846,
year = {2022},
author = {Perera, IA and Abinandan, S and Subashchandrabose, SR and Venkateswarlu, K and Cole, N and Naidu, R and Megharaj, M},
title = {Extracellular Polymeric Substances Drive Symbiotic Interactions in Bacterial‒Microalgal Consortia.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {596-607},
pmid = {34132846},
issn = {1432-184X},
support = {RTP//Australian Government/ ; },
mesh = {Extracellular Polymeric Substance Matrix/metabolism ; *Microalgae ; Symbiosis ; Wastewater/microbiology ; },
abstract = {The importance of several factors that drive the symbiotic interactions between bacteria and microalgae in consortia has been well realised. However, the implication of extracellular polymeric substances (EPS) released by the partners remains unclear. Therefore, the present study focused on the influence of EPS in developing consortia of a bacterium, Variovorax paradoxus IS1, with a microalga, Tetradesmus obliquus IS2 or Coelastrella sp. IS3, all isolated from poultry slaughterhouse wastewater. The bacterium increased the specific growth rates of microalgal species significantly in the consortia by enhancing the uptake of nitrate (88‒99%) and phosphate (92‒95%) besides accumulating higher amounts of carbohydrates and proteins. The EPS obtained from exudates, collected from the bacterial or microalgal cultures, contained numerous phytohormones, vitamins, polysaccharides and amino acids that are likely involved in interspecies interactions. The addition of EPS obtained from V. paradoxus IS1 to the culture medium doubled the growth of both the microalgal strains. The EPS collected from T. obliquus IS2 significantly increased the growth of V. paradoxus IS1, but there was no apparent change in bacterial growth when it was cultured in the presence of EPS from Coelastrella sp. IS3. These observations indicate that the interaction between V. paradoxus IS1 and T. obliquus IS2 was mutualism, while commensalism was the interaction between the bacterial strain and Coelastrella sp. IS3. Our present findings thus, for the first time, unveil the EPS-induced symbiotic interactions among the partners involved in bacterial‒microalgal consortia.},
}
@article {pmid34132589,
year = {2021},
author = {Tedersoo, L and Albertsen, M and Anslan, S and Callahan, B},
title = {Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {17},
pages = {e0062621},
pmid = {34132589},
issn = {1098-5336},
support = {R35 GM133745/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Microbiota ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such as rapid molecular diagnostics and direct RNA sequencing, and both Pacific Biosciences (PacBio) and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long-read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.},
}
@article {pmid34130083,
year = {2021},
author = {Yan, L and Hermans, SM and Totsche, KU and Lehmann, R and Herrmann, M and Küsel, K},
title = {Groundwater bacterial communities evolve over time in response to recharge.},
journal = {Water research},
volume = {201},
number = {},
pages = {117290},
doi = {10.1016/j.watres.2021.117290},
pmid = {34130083},
issn = {1879-2448},
mesh = {Bacteria/genetics ; *Groundwater ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Water Wells ; },
abstract = {Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than surface oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in bacterial communities of shallow fractured bedrock groundwater, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n = 230) along a hillslope recharge area. We showed that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and exhibited non-linear dissimilarity patterns which corresponded to periods of groundwater recharge. Further, we observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The sampling period was able to explain up to 29.5% of the variability in bacterial community composition and the impact of recharge events on the groundwater microbiome was linked to the strength of the recharge and local environmental selection. Many groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, the microbiomes in shallow fractured-rock groundwater vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the dynamics of bacterial communities in groundwater, which is an essential resource for the provision of clean drinking water; understanding the biological complexities of these systems is therefore crucial.},
}
@article {pmid34128692,
year = {2021},
author = {Zhang, ZF and Pan, J and Pan, YP and Li, M},
title = {Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {e0138120},
pmid = {34128692},
issn = {2379-5077},
support = {31970105//National Natural Science Foundation of China (NSFC)/ ; 91851105//National Natural Science Foundation of China (NSFC)/ ; JCYJ20200109105010363//Shenzhen Science and Technology Program/ ; 2019FY100700//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2020KCXTD023//Innovation Team Project of Universities in Guangdong Province/ ; 2020M672779//China Postdoctoral Science Foundation/ ; },
abstract = {Archaea are a major part of Earth's life. They are believed to play important roles in nutrient biogeochemical cycling in the mangrove. However, only a few studies on the archaeal community in mangroves have been reported. In particular, the assembly processes and interaction patterns that impact the archaeal communities in mangroves have not been investigated to date. Here, the biogeography, assembly patterns, and driving factors of archaeal communities in seven representative mangroves across southeastern China were systematically analyzed. The analysis revealed that the archaeal community is more diverse in surface sediments than in subsurface sediments, and more diverse in mangroves at low latitudes than at high latitudes, with Woesearchaeota and Bathyarchaeota as the most diverse and most abundant phyla, respectively. Beta nearest-taxon index analysis suggested a determinant role of homogeneous selection on the overall archaeon community in all mangroves and in each individual mangrove. In addition, the conditionally rare taxon community was strongly shaped by homogeneous selection, while stochastic processes shaped the dominant taxon and always-rare taxon communities. Further, a moderate effect of environmental selection on the archaeal community was noted, with the smallest effect on the always-rare taxon community. Mangrove location, mean annual temperature, and salinity were the major factors that greatly affected the community composition. Finally, network analysis revealed comprehensive cooccurrence relationships in the archaeal community, with a crucial role of Bathyarchaeota. This study expands the understanding of the biogeography, assembly patterns, driving factors, and cooccurrence relationships of the mangrove archaeal community and inspires functional exploration of archaeal resources in mangrove sediments. IMPORTANCE As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood. Mangroves are located at the land-ocean interface and are an ideal environment for examining the above questions. We here provided the first-ever overview of archaeal community structure and biogeography in mangroves located along an over-9,000-km coastline of southeastern China. We observed that archaeal diversity in low-latitude mangroves was higher than that in high-latitude mangroves. Furthermore, our data indicated that homogeneous selection strongly controlled the assembly of the overall and conditionally rare taxon communities in mangrove sediments, while the dominant taxon and always-rare taxon communities were mainly controlled by dispersal limitation.},
}
@article {pmid34127845,
year = {2021},
author = {Wasmund, K and Pelikan, C and Schintlmeister, A and Wagner, M and Watzka, M and Richter, A and Bhatnagar, S and Noel, A and Hubert, CRJ and Rattei, T and Hofmann, T and Hausmann, B and Herbold, CW and Loy, A},
title = {Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments.},
journal = {Nature microbiology},
volume = {6},
number = {7},
pages = {885-898},
pmid = {34127845},
issn = {2058-5276},
mesh = {Anaerobiosis ; Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics ; Biodegradation, Environmental ; Biosynthetic Pathways ; Carbon Isotopes/metabolism ; Cold Temperature ; DNA/*metabolism ; Genome, Bacterial/genetics ; Geologic Sediments/*microbiology ; Metagenomics ; Nucleosides/metabolism ; Phylogeny ; Seawater/*microbiology ; },
abstract = {Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. [13]C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to [13]CO2. SIP probing of DNA revealed diverse 'Candidatus Izemoplasma', Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived [13]C-carbon. NanoSIMS confirmed incorporation of [13]C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the [13]C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse 'Candidatus Izemoplasmatales' (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed.},
}
@article {pmid34126927,
year = {2021},
author = {Shao, K and Yao, X and Wu, Z and Jiang, X and Hu, Y and Tang, X and Xu, Q and Gao, G},
title = {The bacterial community composition and its environmental drivers in the rivers around eutrophic Chaohu Lake, China.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {179},
pmid = {34126927},
issn = {1471-2180},
support = {41930760//the National Natural Science Foundation of China/ ; 41977322//the National Natural Science Foundation of China/ ; 2017ZX07603-001//the Major Science and Technology Program for Water Pollution Control and Treatment, China/ ; QYZDJSSWDQC008//the Key Research Program of Frontier Sciences, Chinese Academy of Sciences/ ; ZDRW-ZS-2017-3-4//the Key Program of the Chinese Academy of Sciences/ ; },
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; China ; Ecosystem ; Environmental Monitoring ; Eutrophication ; Lakes/*microbiology ; *Microbiota ; Rivers/*microbiology ; Sewage/microbiology ; },
abstract = {BACKGROUND: Bacterial community play a key role in environmental and ecological processes in river ecosystems. Rivers are used as receiving body for treated and untreated urban wastewaters that brings high loads of sewage and excrement bacteria. However, little is known about the bacterial community structure and functional files in the rivers around the eutrophic Chaohu Lake, the fifth largest freshwater lake in China, has been subjected to severe eutrophication and cyanobacterial blooms over the past few decades. Therefore, understanding the taxonomic and functional compositions of bacterial communities in the river will contribute to understanding aquatic microbial ecology. The main aims were to (1) examine the structure of bacterial communities and functional profiles in this system; (2) find the environmental factors of bacterial community variations.<br><br>RESULTS: We studied 88 sites at rivers in the Chaohu Lake basin, and determined bacterial communities using Illumina Miseq sequencing of the 16&#xa0;S rRNA gene, and predicted functional profiles using PICRUSt2. A total of 3,390,497 bacterial 16&#xa0;S rRNA gene sequences were obtained, representing 17 phyla, and 424 genera; The dominant phyla present in all samples were Bacteroidetes (1.4-82.50&#x2009;%), followed by Proteobacteria (12.6-97.30&#x2009;%), Actinobacteria (0.1-17.20&#x2009;%). Flavobacterium was the most numerous genera, and accounted for 0.12-80.34&#x2009;% of assigned 16&#xa0;S reads, followed by Acinetobacter (0.33-49.28&#x2009;%). Other dominant bacterial genera including Massilia (0.06-25.40&#x2009;%), Psychrobacter (0-36.23&#x2009;%), Chryseobacterium (0.01-22.86&#x2009;%), Brevundimonas (0.01-12.82&#x2009;%), Pseudomonas (0-59.73&#x2009;%), Duganella (0.08-23.37&#x2009;%), Unidentified Micrococcaceae (0-8.49&#x2009;%). The functional profiles of the bacterial populations indicated an relation with many human diseases, including infectious diseases. Overall results, using the &#x3b2; diversity measures, coupled with heatmap and RDA showed that there were spatial variations in the bacterial community composition at river sites, and Chemical oxygen demand (CODMn) and (NH4[+])were the dominant environmental drivers affecting the bacterial community variance.<br><br>CONCLUSIONS: The high proportion of the opportunistic pathogens (Acinetobacter, Massilia, Brevundimonas) indicated that the discharge of sewage without adequate treatment into the rivers around Chaohu Lake. We propose that these bacteria could be more effective bioindicators for long-term sewage monitoring in eutrophic lakes.},
}
@article {pmid34126067,
year = {2022},
author = {Li, J and Morrow, C and Barnes, S and Wilson, L and Womack, ED and McLain, A and Yarar-Fisher, C},
title = {Gut Microbiome Composition and Serum Metabolome Profile Among Individuals With Spinal Cord Injury and Normal Glucose Tolerance or Prediabetes/Type 2 Diabetes.},
journal = {Archives of physical medicine and rehabilitation},
volume = {103},
number = {4},
pages = {702-710},
doi = {10.1016/j.apmr.2021.03.043},
pmid = {34126067},
issn = {1532-821X},
support = {R01 NR016443/NR/NINR NIH HHS/United States ; K01 HD087463/HD/NICHD NIH HHS/United States ; },
mesh = {Adult ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome/genetics ; Glucose ; Humans ; Metabolome ; *Prediabetic State ; RNA, Ribosomal, 16S/genetics ; *Spinal Cord Injuries ; },
abstract = {OBJECTIVE: To compare the gut microbiome composition and serum metabolome profile among individuals with spinal cord injury (SCI) and normal glucose tolerance (NGT) or prediabetes/type 2 diabetes (preDM/T2D).<br><br>DESIGN: Cross-sectional design.<br><br>SETTING: Research university.<br><br>PARTICIPANTS: A total of 25 adults (N=25) with SCI were included in the analysis and categorized as NGT (n=16) or preDM/T2D (n=9) based on their glucose concentration at minute 120 during a 75-g oral glucose tolerance test. The American Diabetes Association diagnosis guideline was used for grouping participants.<br><br>INTERVENTIONS: Not applicable.<br><br>MAIN OUTCOME MEASURES: A stool sample was collected and used to assess the gut microbiome composition (alpha and beta diversity, microbial abundance) via the 16s ribosomal RNA sequencing technique. A fasting serum sample was used for liquid chromatography-mass spectrometry-based untargeted metabolomics analysis, the results from which reflect the relative quantity of metabolites detected and identified. Gut microbiome and metabolomics data were analyzed by the Quantitative Insights into Microbial Ecology 2 and Metaboanalyst platforms, respectively.<br><br>RESULTS: Gut microbiome alpha diversity (Pielou's evenness index, Shannon's index) and beta diversity (weighted UniFrac distances) differed between groups. Compared with participants with NGT, participants with preDM/T2D had less evenness in microbial communities. In particular, those with preDM/T2D had a lower abundance of the Clostridiales order and higher abundance of the Akkermansia genus, as well as higher serum levels of gut-derived metabolites, including indoxyl sulfate and phenylacetylglutamine (P < .05 for all).<br><br>CONCLUSIONS: Our results provide evidence for altered gut microbiome composition and dysregulation of gut-derived metabolites in participants with SCI and preDM/T2D. Both indoxyl sulfate and phenylacetylglutamine have been implicated in the development of cardiovascular diseases in the able-bodied population. These findings may inform future investigations in the field of SCI and cardiometabolic health.},
}
@article {pmid34124627,
year = {2021},
author = {Crous, PW and Hernández-Restrepo, M and Schumacher, RK and Cowan, DA and Maggs-Kölling, G and Marais, E and Wingfield, MJ and Yilmaz, N and Adan, OCG and Akulov, A and Duarte, E&#xc1; and Berraf-Tebbal, A and Bulgakov, TS and Carnegie, AJ and de Beer, ZW and Decock, C and Dijksterhuis, J and Duong, TA and Eichmeier, A and Hien, LT and Houbraken, JAMP and Khanh, TN and Liem, NV and Lombard, L and Lutzoni, FM and Miadlikowska, JM and Nel, WJ and Pascoe, IG and Roets, F and Roux, J and Samson, RA and Shen, M and Spetik, M and Thangavel, R and Thanh, HM and Thao, LD and van Nieuwenhuijzen, EJ and Zhang, JQ and Zhang, Y and Zhao, LL and Groenewald, JZ},
title = {New and Interesting Fungi. 4.},
journal = {Fungal systematics and evolution},
volume = {7},
number = {},
pages = {255-343},
pmid = {34124627},
issn = {2589-3831},
abstract = {An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: Superstratomycetales and Superstratomycetaceae (based on Superstratomyces). New genera: Haudseptoria (based on Haudseptoria typhae); Hogelandia (based on Hogelandia lambearum); Neoscirrhia (based on Neoscirrhia osmundae); Nothoanungitopsis (based on Nothoanungitopsis urophyllae); Nothomicrosphaeropsis (based on Nothomicrosphaeropsis welwitschiae); Populomyces (based on Populomyces zwinianus); Pseudoacrospermum (based on Pseudoacrospermum goniomae). New species: Apiospora sasae on dead culms of Sasa veitchii (Netherlands); Apiospora stipae on dead culms of Stipa gigantea (Spain); Bagadiella eucalyptorum on leaves of Eucalyptus sp. (Australia); Calonectria singaporensis from submerged leaf litter (Singapore); Castanediella neomalaysiana on leaves of Eucalyptus sp. (Malaysia); Colletotrichum pleopeltidis on leaves of Pleopeltis sp. (South Africa); Coniochaeta deborreae from soil (Netherlands); Diaporthe durionigena on branches of Durio zibethinus (Vietnam); Floricola juncicola on dead culm of Juncus sp. (France); Haudseptoria typhae on leaf sheath of Typha sp. (Germany); Hogelandia lambearum from soil (Netherlands); Lomentospora valparaisensis from soil (Chile); Neofusicoccum mystacidii on dead stems of Mystacidium capense (South Africa); Neomycosphaerella guibourtiae on leaves of Guibourtia sp. (Angola); Niesslia neoexosporioides on dead leaves of Carex paniculata (Germany); Nothoanungitopsis urophyllae on seed capsules of Eucalyptus urophylla (South Africa); Nothomicrosphaeropsis welwitschiae on dead leaves of Welwitschia mirabilis (Namibia); Paracremonium bendijkiorum from soil (Netherlands); Paraphoma ledniceana on dead wood of Buxus sempervirens (Czech Republic); Paraphoma salicis on leaves of Salix cf. alba (Ukraine); Parasarocladium wereldwijsianum from soil (Netherlands); Peziza ligni on masonry and plastering (France); Phyllosticta phoenicis on leaves of Phoenix reclinata (South Africa); Plectosphaerella slobbergiarum from soil (Netherlands); Populomyces zwinianus from soil (Netherlands); Pseudoacrospermum goniomae on leaves of Gonioma kamassi (South Africa); Pseudopyricularia festucae on leaves of Festuca californica (USA); Sarocladium sasijaorum from soil (Netherlands); Sporothrix hypoxyli in sporocarp of Hypoxylon petriniae on Fraxinus wood (Netherlands); Superstratomyces albomucosus on Pycnanthus angolensis (Netherlands); Superstratomyces atroviridis on Pinus sylvestris (Netherlands); Superstratomyces flavomucosus on leaf of Hakea multilinearis (Australia); Superstratomyces tardicrescens from human eye specimen (USA); Taeniolella platani on twig of Platanus hispanica (Germany), and Tympanis pini on twigs of Pinus sylvestris (Spain). Citation: Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. Fungal Systematics and Evolution 7: 255-343. doi: 10.3114/fuse.2021.07.13.},
}
@article {pmid34123319,
year = {2021},
author = {Prothiwa, M and Filz, V and Oehler, S and Böttcher, T},
title = {Inhibiting quinolone biosynthesis of Burkholderia.},
journal = {Chemical science},
volume = {12},
number = {20},
pages = {6908-6912},
pmid = {34123319},
issn = {2041-6520},
abstract = {2-Alkylquinolones are important signalling molecules of Burkholderia species. We developed a substrate-based chemical probe against the central quinolone biosynthesis enzyme HmqD and applied it in competitive profiling experiments to discover the first known HmqD inhibitors. The most potent inhibitors quantitatively blocked quinolone production in Burkholderia cultures with single-digit micromolar efficacy.},
}
@article {pmid34122370,
year = {2021},
author = {Cyriaque, V and Madsen, JS and Fievez, L and Leroy, B and Hansen, LH and Bureau, F and Sørensen, SJ and Wattiez, R},
title = {Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {655903},
pmid = {34122370},
issn = {1664-302X},
abstract = {Plasmids carrying metal resistance genes (MRGs) have been suggested to be key ecological players in the adaptation of metal-impacted microbial communities, making them promising drivers of bio-remediation processes. However, the impact of metals on plasmid-mediated spread of MRGs through selection, plasmid loss, and transfer is far from being fully understood. In the present study, we used two-member bacterial communities to test the impact of lead on the dispersal of the IncP plasmid pKJK5 from a Pseudomonas putida KT2440 plasmid donor and two distinct recipients, Variovorax paradoxus B4 or Delftia acidovorans SPH-1 after 4 and 10 days of mating. Two versions of the plasmid were used, carrying or not carrying the lead resistance pbrTRABCD operon, to assess the importance of fitness benefit and conjugative potential for the dispersal of the plasmid. The spread dynamics of metal resistance conveyed by the conjugative plasmid were dependent on the recipient and the lead concentration: For V. paradoxus, the pbr operon did not facilitate neither lead resistance nor variation in plasmid spread. The growth gain brought by the pbr operon to D. acidovorans SPH-1 and P. putida KT2440 at 1 mM Pb enhanced the spread of the plasmid. At 1.5 mM Pb after 4 days, the proteomics results revealed an oxidative stress response and an increased abundance of pKJK5-encoded conjugation and partitioning proteins, which most likely increased the transfer of the control plasmid to D. acidovorans SPH-1 and ensured plasmid maintenance. As a consequence, we observed an increased spread of pKJK5-gfp. Conversely, the pbr operon reduced the oxidative stress response and impeded the rise of conjugation- and partitioning-associated proteins, which slowed down the spread of the pbr carrying plasmid. Ultimately, when a fitness gain was recorded in the recipient strain, the spread of MRG-carrying plasmids was facilitated through positive selection at an intermediate metal concentration, while a high lead concentration induced oxidative stress with positive impacts on proteins encoding plasmid conjugation and partitioning.},
}
@article {pmid34119873,
year = {2021},
author = {Batool, M and Blazier, JC and Rogovska, YV and Wang, J and Liu, S and Nebogatkin, IV and Rogovskyy, AS},
title = {Metagenomic analysis of individually analyzed ticks from Eastern Europe demonstrates regional and sex-dependent differences in the microbiota of Ixodes ricinus.},
journal = {Ticks and tick-borne diseases},
volume = {12},
number = {5},
pages = {101768},
doi = {10.1016/j.ttbdis.2021.101768},
pmid = {34119873},
issn = {1877-9603},
mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Female ; Geography ; Ixodes/*microbiology ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Sex Factors ; Ukraine ; },
abstract = {Understanding the microbial ecology of disease vectors may be useful for development of novel strategies aimed at preventing transmission of vector-borne pathogens. Although Ixodes ricinus is one of the most important tick vectors, the microbiota of this tick has been examined for only limited parts of the globe. To date, the microbiota of I. ricinus ticks collected from Eastern Europe has not been defined. The objective of this study was to compare microbiota of I. ricinus ticks within (males vs. females) and between collection sites that represented three administrative regions of Ukraine, Dnipropetrovs'k (D), Kharkiv (K), and Poltava (P). A total of 89 questing I. ricinus adults were collected from region D (number of ticks, n = 29; 14 males and 15 females), region K (n = 30; 15 males and 15 females) and region P (n = 30; 15 males and 15 females). Each tick was subjected to metagenomic analysis by targeting the V6 region of 16S rRNA gene through the Illumina 4000 Hiseq sequencing. The alpha diversity analysis demonstrated that, regardless of tick sex, patterns of bacterial diversity in ticks from regions K and P were similar, whereas the microbiota of region D ticks was quite distinct. A number of inter-regional differences were detected by most beta diversity metrics for both males and females. The inter-regional variations were also supported by the principal coordinate analysis based on the unweighted UniFrac metrics with three region-specific clusters of female ticks and one distinct cluster of region D males. Lastly, numerous region- and sex-specific differences were also identified in the relative abundance of various bacterial taxa. Collectively, the present findings demonstrate that the microbiota of the I. ricinus tick can exhibit a high degree of variation between tick sexes and geographical regions.},
}
@article {pmid34118665,
year = {2021},
author = {Zhang, L and Gong, X and Wang, L and Guo, K and Cao, S and Zhou, Y},
title = {Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system.},
journal = {The Science of the total environment},
volume = {791},
number = {},
pages = {148096},
doi = {10.1016/j.scitotenv.2021.148096},
pmid = {34118665},
issn = {1879-1026},
mesh = {Anaerobiosis ; Bioreactors ; Hydrolysis ; *Metagenomics ; Methane ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sewage ; },
abstract = {Thermal hydrolysis process (THP) is an effective pre-treatment method to reduce solids volume and improve biogas production during anaerobic digestion (AD) via increasing the biodegradability of waste activated sludge (WAS). However, the effects of THP pre-treated sludge on microbial diversity, interspecies interactions, and metabolism in AD systems remain largely unknown. We therefore setup and operated an anaerobic digester during a long-term period to shed light on the effect of THP pre-treatment on AD microbial ecology in comparison to conventional AD via Illumina based 16S rRNA gene amplicon sequencing and genome-centric metagenomics analysis. Results showed THP sludge significantly reduced the microbial diversity, shaped the microbial community structure, and resulted in more intense microbial interactions. Compared to WAS as the feed sludge, THP sludge shaped the core functional groups, but functional redundancy ensured the system's stability. The metabolic interactions between methanogens and syntrophic bacteria as well as the specific metabolic pathways were further elucidated. Hydrogenotrophic methanogens, Methanospirillum sp. and Methanolinea sp., were the primary contributors for methane production when treating THP and WAS, respectively, which also have potential for acetate oxidation to methane. Collectively, this study provides in-depth information on the interspecies interactions to better understand how THP pre-treatment influences AD microbial community.},
}
@article {pmid34117524,
year = {2022},
author = {Morales Medina, WR and Eramo, A and Fahrenfeld, NL},
title = {Metabolically Active Prokaryotes and Actively Transcribed Antibiotic Resistance Genes in Sewer Systems: Implications for Public Health and Microbially Induced Corrosion.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {583-595},
pmid = {34117524},
issn = {1432-184X},
support = {1510461//National Science Foundation (US)/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; Corrosion ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Public Health ; RNA, Ribosomal, 16S/genetics ; Wastewater/microbiology ; },
abstract = {Sewer systems are reservoirs of pathogens and bacteria carrying antibiotic resistance genes (ARGs). However, most recent high-throughput studies rely on DNA-based techniques that cannot provide information on the physiological state of the cells nor expression of ARGs. In this study, wastewater and sewer sediment samples were collected from combined and separate sanitary sewer systems. The metabolically active prokaryote community was evaluated using 16S rRNA amplicon sequencing and actively transcribed ARG abundance was measured using mRNA RT-qPCR. Three (sul1, blaTEM, tet(G)) of the eight tested ARGs were quantifiable in select samples. Sewer sediment samples had greater abundance of actively transcribed ARGs compared to wastewater. Microbiome analysis showed the presence of metabolically active family taxa that contain clinically relevant pathogens (Pseudomonadaceae, Enterobacteraceae, Streptococcaceae, Arcobacteraceae, and Clostridiaceae) and corrosion-causing prokaryotes (Desulfobulbaceae and Desulfovibrionaceae) in both matrices. Spirochaetaceae and methanogens were more common in the sediment matrix while Mycobacteraceae were more common in wastewater. The microbiome obtained from 16S rRNA sequencing had a significantly different structure from the 16S rRNA gene microbiome. Overall, this study demonstrates active transcription of ARGs in sewer systems and provides insight into the abundance and physiological state of taxa of interest in the different sewer matrices and sewer types relevant for wastewater-based epidemiology, corrosion, and understanding the hazard posed by different matrices during sewer overflows.},
}
@article {pmid34112519,
year = {2021},
author = {Vaezzadeh, V and Thomes, MW and Kunisue, T and Tue, NM and Zhang, G and Zakaria, MP and Affendi, YA and Yap, FC and Chew, LL and Teoh, HW and Lee, CW and Bong, CW},
title = {Corrigendum to "Examination of barnacles' potential to be used as bioindicators of persistent organic pollutants in coastal ecosystem: A Malaysia case study" [Chemosphere 263 (2021) 128272].},
journal = {Chemosphere},
volume = {281},
number = {},
pages = {131081},
doi = {10.1016/j.chemosphere.2021.131081},
pmid = {34112519},
issn = {1879-1298},
}
@article {pmid34112387,
year = {2021},
author = {Vissenaekens, H and Smagghe, G and Criel, H and Grootaert, C and Raes, K and Rajkovic, A and Goeminne, G and Boon, N and De Schutter, K and Van Camp, J},
title = {Intracellular quercetin accumulation and its impact on mitochondrial dysfunction in intestinal Caco-2 cells.},
journal = {Food research international (Ottawa, Ont.)},
volume = {145},
number = {},
pages = {110430},
doi = {10.1016/j.foodres.2021.110430},
pmid = {34112387},
issn = {1873-7145},
mesh = {Caco-2 Cells ; Humans ; Membrane Potential, Mitochondrial ; *Mitochondria/metabolism ; *Quercetin/metabolism ; Reactive Oxygen Species/metabolism ; },
abstract = {PURPOSE: Flavonoid bioavailability and bioactivity is associated with interindividual variability, which is partially due to differences in health status. Previously, it was demonstrated that cellular stress, especially mitochondrial stress, increases intracellular quercetin uptake and this is associated with beneficial health effects. Here, the impact of quercetin on mitochondrial dysfunction, induced by stressors targeting different sites of the electron transport chain, is investigated. The influence of the mitochondrial stress on quercetin uptake and subcellular location is studied and the accumulated quercetin metabolites in intestinal Caco-2 cells and mitochondria are characterized.<br><br>PRINCIPAL RESULTS: It was observed that quercetin counteracted (i) the carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP)-induced decrease in maximum oxygen consumption, (ii) the valinomycin-, oligomycin- and FCCP-induced reactive oxygen species production and (iii) the valinomycin-induced disruption of mitochondrial membrane potential. Using confocal microscopy, it was found that upon mitochondrial stress, the intracellular quercetin accumulation increased and was partially located in the mitochondria. Finally, it was demonstrated that quercetin was present as O-methyl, O-methylglucuronide and O-methylsulfate conjugates in the cell lysate and mitochondria-enriched fraction.<br><br>MAJOR CONCLUSIONS: This study shows that quercetin can partially restore, especially FCCP-induced, mitochondrial dysfunction and this protective effect was linked with an intracellular quercetin accumulation in the mitochondria of intestinal cells.},
}
@article {pmid34110473,
year = {2021},
author = {Rivera, AJ and Tyx, RE},
title = {Microbiology of the American Smokeless Tobacco.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {12},
pages = {4843-4853},
pmid = {34110473},
issn = {1432-0614},
mesh = {Carcinogens ; Humans ; Metagenomics ; *Microbiota ; Nicotiana ; *Tobacco, Smokeless ; United States ; },
abstract = {Smokeless tobacco products (STP) contain diverse microbial communities that contribute to the formation of harmful chemical byproducts. This is concerning since 300 million individuals around the globe are users of smokeless tobacco. Significant evidence has shown that microbial metabolic activities mediate the formation of carcinogens during manufacturing. In recent years, studies have revealed a series of additional health impacts that include lesions and inflammation of the oral mucosa and the gastrointestinal tract, as well as alterations of the endogenous microbiota. These findings are due to recent developments in molecular technologies that allowed researchers to better examine the microbial component of these products. This new information illustrates the scale of the STP microbiota and its diversity in the finished product that is sold for consumption. Additionally, the application of metagenomics and metatranscriptomics has provided the tools to look at phylogenies across bacterial, viral, and eukaryotic groups, their functional capacities, and viability. Here we present key examples of tobacco microbiology research that utilizes newer approaches and strategies to define the microbial component of smokeless tobacco products. We also highlight challenges in these approaches, the knowledge gaps being filled, and those gaps that warrant further study. A better understanding of the microbiology of STP brings vast public health benefits. It will provide important information for the product consumer, impact manufacturing practices, and provide support for the development of attainable and more meaningful regulatory goals. KEY POINTS: Newer technologies allowed quicker and more comprehensive identification of microbes in tobacco samples, encapsulating microorganisms difficult or impossible to culture. Current research in smokeless tobacco microbiology is filling knowledge gaps previously unfilled due to the lack of suitable approaches. The microbial ecology of smokeless tobacco presents a clearer picture of diversity and variability not considered before.},
}
@article {pmid34110072,
year = {2022},
author = {Nir, I and Barak, H and Kramarsky-Winter, E and Kushmaro, A and de Los Ríos, A},
title = {Microscopic and biomolecular complementary approaches to characterize bioweathering processes at petroglyph sites from the Negev Desert, Israel.},
journal = {Environmental microbiology},
volume = {24},
number = {2},
pages = {967-980},
doi = {10.1111/1462-2920.15635},
pmid = {34110072},
issn = {1462-2920},
mesh = {*Bacteria ; Israel ; *Metagenomics ; Microscopy, Electron, Scanning ; },
abstract = {Throughout the Negev Desert highlands, thousands of ancient petroglyphs sites are susceptible to deterioration processes that may result in the loss of this unique rock art. Therefore, the overarching goal of the current study was to characterize the composition, diversity and effects of microbial colonization of the rocks to find ways of protecting these unique treasures. The spatial organization of the microbial colonizers and their relationships with the lithic substrate were analysed using scanning electron microscopy. This approach revealed extensive epilithic and endolithic colonization and close microbial-mineral interactions. Shotgun sequencing analysis revealed various taxa from the archaea, bacteria and some eukaryotes. Metagenomic coding sequences (CDS) of these microbial lithobionts exhibited specific metabolic pathways involved in the rock elements' cycles and uptake processes. Thus, our results provide evidence for the potential participation of the microorganisms colonizing these rocks during different solubilization and mineralization processes. These damaging actions may contribute to the deterioration of this extraordinary rock art and thus threaten this valuable heritage. Shotgun metagenomic sequencing, in conjunction with the in situ scanning electron microscopy study, can thus be considered an effective strategy to understand the complexity of the weathering processes occurring at petroglyph sites and other cultural heritage assets.},
}
@article {pmid34108667,
year = {2021},
author = {Yuan, Z and Druzhinina, IS and Gibbons, JG and Zhong, Z and Van de Peer, Y and Rodriguez, RJ and Liu, Z and Wang, X and Wei, H and Wu, Q and Wang, J and Shi, G and Cai, F and Peng, L and Martin, FM},
title = {Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus.},
journal = {The ISME journal},
volume = {15},
number = {12},
pages = {3468-3479},
pmid = {34108667},
issn = {1751-7370},
mesh = {*Ascomycota/genetics ; *Chenopodiaceae/microbiology ; Endophytes/genetics ; *Genomic Islands ; Melanins ; Pigmentation ; Salt-Tolerant Plants/*microbiology ; },
abstract = {Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila-S. salsa symbiosis.},
}
@article {pmid34108452,
year = {2021},
author = {Zhao, T and Zwaenepoel, A and Xue, JY and Kao, SM and Li, Z and Schranz, ME and Van de Peer, Y},
title = {Whole-genome microsynteny-based phylogeny of angiosperms.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3498},
pmid = {34108452},
issn = {2041-1723},
mesh = {Evolution, Molecular ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Magnoliopsida/classification/*genetics ; Models, Genetic ; Multigene Family/genetics ; *Phylogeny ; *Synteny ; },
abstract = {Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny-the conservation of local gene content and order-is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on microsynteny information. Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of a large-scale whole-genome data set for angiosperms, including more than 120 available high-quality genomes, representing more than 50 different plant families and 30 orders. Our 'microsynteny-based' tree is largely congruent with phylogenies proposed based on more traditional sequence alignment-based methods and current phylogenetic classifications but differs for some long-contested and controversial relationships. For instance, our synteny-based tree finds Vitales as early diverging eudicots, Saxifragales within superasterids, and magnoliids as sister to monocots. We discuss how synteny-based phylogenetic inference can complement traditional methods and could provide additional insights into some long-standing controversial phylogenetic relationships.},
}
@article {pmid34107988,
year = {2021},
author = {Flachs, A and Orkin, JD},
title = {On pickles: biological and sociocultural links between fermented foods and the human gut microbiome.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {17},
number = {1},
pages = {39},
pmid = {34107988},
issn = {1746-4269},
support = {Global Synergy Grant//College of Liberal Arts, Purdue University/ ; },
mesh = {Fermentation ; *Fermented Foods/microbiology ; *Food Microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; },
abstract = {BACKGROUND: The composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa.<br><br>METHODS: In this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews with eleven people and participated in a four-day craft fermentation workshop. We also collected 46 fermented food products and 46 stool samples from workshop participants eating those fermented foods.<br><br>RESULTS: We identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 amplicon sequence variants (ASVs) shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes.<br><br>CONCLUSIONS: By combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.},
}
@article {pmid34106771,
year = {2021},
author = {Scales, BS and Cable, RN and Duhaime, MB and Gerdts, G and Fischer, F and Fischer, D and Mothes, S and Hintzki, L and Moldaenke, L and Ruwe, M and Kalinowski, J and Kreikemeyer, B and Pedrotti, ML and Gorsky, G and Elineau, A and Labrenz, M and Oberbeckmann, S},
title = {Cross-Hemisphere Study Reveals Geographically Ubiquitous, Plastic-Specific Bacteria Emerging from the Rare and Unexplored Biosphere.},
journal = {mSphere},
volume = {6},
number = {3},
pages = {e0085120},
pmid = {34106771},
issn = {2379-5042},
mesh = {Bacteria/*genetics/*isolation &amp; purification/metabolism ; Biofilms/growth &amp; development ; Geography ; *Microbiota ; *Plastics ; RNA, Ribosomal, 16S ; Seawater/*microbiology ; Water Pollutants, Chemical/analysis ; },
abstract = {While it is now appreciated that the millions of tons of plastic pollution travelling through marine systems carry complex communities of microorganisms, it is still unknown to what extent these biofilm communities are specific to the plastic or selected by the surrounding ecosystem. To address this, we characterized and compared the microbial communities of microplastic particles, nonplastic (natural and wax) particles, and the surrounding waters from three marine ecosystems (the Baltic, Sargasso and Mediterranean seas) using high-throughput 16S rRNA gene sequencing. We found that biofilm communities on microplastic and nonplastic particles were highly similar to one another across this broad geographical range. The similar temperature and salinity profiles of the Sargasso and Mediterranean seas, compared to the Baltic Sea, were reflected in the biofilm communities. We identified plastic-specific operational taxonomic units (OTUs) that were not detected on nonplastic particles or in the surrounding waters. Twenty-six of the plastic-specific OTUs were geographically ubiquitous across all sampled locations. These geographically ubiquitous plastic-specific OTUs were mostly low-abundance members of their biofilm communities and often represented uncultured members of marine ecosystems. These results demonstrate the potential for plastics to be a reservoir of rare and understudied microbes, thus warranting further investigations into the dynamics and role of these microbes in marine ecosystems. IMPORTANCE This study represents one of the largest comparisons of biofilms from environmentally sampled plastic and nonplastic particles from aquatic environments. By including particles sampled through three separate campaigns in the Baltic, Sargasso, and Mediterranean seas, we were able to make cross-geographical comparisons and discovered common taxonomical signatures that define the plastic biofilm. For the first time, we identified plastic-specific bacteria that reoccur across marine regions. Our data reveal that plastics have selective properties that repeatedly enrich for similar bacteria regardless of location, potentially shifting aquatic microbial communities in areas with high levels of plastic pollution. Furthermore, we show that bacterial communities on plastic do not appear to be strongly influenced by polymer type, suggesting that other properties, such as the absorption and/or leaching of chemicals from the surface, are likely to be more important in the selection and enrichment of specific microorganisms.},
}
@article {pmid34106767,
year = {2021},
author = {Dove, NC and Veach, AM and Muchero, W and Wahl, T and Stegen, JC and Schadt, CW and Cregger, MA},
title = {Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors.},
journal = {mSphere},
volume = {6},
number = {3},
pages = {e0131620},
pmid = {34106767},
issn = {2379-5042},
mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Fungi/classification/*genetics ; *Genotype ; Microbiota/*genetics/physiology ; Plant Leaves/microbiology ; Populus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Seasons ; Soil Microbiology ; },
abstract = {Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors. IMPORTANCE The initial assembly of the plant microbiome may establish the trajectory of forthcoming microbiome states, which could determine the overall future health of the plant. However, while much is known about the initial microbiome assembly of grasses and agricultural crops, less is known about the initial microbiome of long-lived trees, such as poplar (Populus spp.). Thus, a greater understanding of initial plant microbiome assembly in an ecologically and economically important plant such as Populus is highly desirable. Here, we show that the initial microbiome community composition and assembly in the first growing season of Populus is temporally dynamic and is determined by a combination of both selective and stochastic factors. Our findings could be used to prescribe ecologically informed microbial inoculations and better predict the composition of the Populus microbiome into the future and to better understand its influence on plant health.},
}
@article {pmid34105010,
year = {2022},
author = {Naidoo, Y and Valverde, A and Pierneef, RE and Cowan, DA},
title = {Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {689-701},
pmid = {34105010},
issn = {1432-184X},
support = {Free standing//National Research Foundation/ ; },
mesh = {Desert Climate ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.},
}
@article {pmid34105009,
year = {2022},
author = {Febinia, CA and Malik, SG and Djuwita, R and Weta, IW and Wihandani, DM and Maulida, R and Sudoyo, H and Holmes, AJ},
title = {Distinctive Microbiome Type Distribution in a Young Adult Balinese Cohort May Reflect Environmental Changes Associated with Modernization.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {798-810},
pmid = {34105009},
issn = {1432-184X},
mesh = {Cohort Studies ; Diet ; Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Young Adult ; },
abstract = {An important public health question is understanding how changes in human environments can drive changes in the gut microbiota that influence risks associated with human health and wellbeing. It is well-documented that the modernization of societies is strongly correlated with intergenerational change in the frequency of nutrition-related chronic diseases in which microbial dysbiosis is implicated. The population of Bali, Indonesia, is well-positioned to study the interconnection between a changing food environment and microbiome patterns in its early stages, because of a recent history of modernization. Here, we characterize the fecal microbiota and diet history of the young adult women in Bali, Indonesia (n = 41) in order to compare microbial patterns in this generation with those of other populations with different histories of a modern food environment (industrialized supply chain). We found strong support for two distinct fecal microbiota community types in our study cohort at similar frequency: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community (p < 0.001, analysis of similarity, Wilcoxon test). Although Type-P individuals had lower alpha diversity (p < 0.001, Shannon) and higher incidence of obesity, multivariate analyses with diet data showed that community types significantly influenced associations with BMI. In a multi-country dataset (n = 257), we confirmed that microbial beta diversity across subsistent and industrial populations was significantly associated with Prevotella and Bacteroides abundance (p < 0.001, generalized additive model) and that the prevalence of community types differs between societies. The young adult Balinese microbiota was distinctive in having an equal prevalence of two community types. Collectively, our study showed that the incorporation of community types as an explanatory factor into study design or modeling improved the ability to identify microbiome associations with diet and health metrics.},
}
@article {pmid34105008,
year = {2022},
author = {Sun, Y and Huang, Y and Xu, S and Li, J and Yin, M and Tian, H},
title = {Seasonal Variations in the Characteristics of Microbial Community Structure and Diversity in Atmospheric Particulate Matter from Clean Days and Smoggy Days in Beijing.},
journal = {Microbial ecology},
volume = {83},
number = {3},
pages = {568-582},
pmid = {34105008},
issn = {1432-184X},
mesh = {*Air Pollutants ; Beijing ; China ; Environmental Monitoring/methods ; Humans ; *Microbiota ; Particulate Matter ; Seasons ; },
abstract = {Microorganisms are an important part of atmospheric particulate matter and are closely related to human health. In this paper, the variations in the characteristics of the chemical components and bacterial communities in PM10 and PM2.5 grouped according to season, pollution degree, particle size, and winter heating stage were studied. The influence of environmental factors on community structure was also analyzed. The results showed that seasonal variations were significant. NO3[-] contributed the most to the formation of particulate matter in spring and winter, while SO4[2-] contributed the most in summer and autumn. The community structures in summer and autumn were similar, while the community structure in spring was significantly different. The dominant phyla were similar among seasons, but their proportions were different. The dominant genera were no-rank_c_Cyanobacteria, Acidovorax, Escherichia-Shigella and Sphingomonas in spring; Massilia, Bacillus, Acinetobacter, Rhodococcus, and Brevibacillus in summer and autumn; and Rhodococcus in winter. The atmospheric microorganisms in Beijing mainly came from soil, water, and plants. The few pathogens detected were mainly affected by the microbial source on the sampling day, regardless of pollution level. RDA (redundancy analysis) showed that the bacterial community was positively correlated with the concentration of particulate matter and that the wind speed in spring was positively correlated with NO3[-] levels, NH4[+] levels, temperature, and relative humidity in summer and autumn, but there was no clear consistency among winter samples. This study comprehensively analyzed the variations in the characteristics of the airborne bacterial community in Beijing over one year and provided a reference for understanding the source, mechanism, and assessment of the health effects of different air qualities.},
}
@article {pmid34100639,
year = {2021},
author = {Rochefort, A and Simonin, M and Marais, C and Guillerm-Erckelboudt, AY and Barret, M and Sarniguet, A},
title = {Transmission of Seed and Soil Microbiota to Seedling.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {e0044621},
pmid = {34100639},
issn = {2379-5077},
support = {//INRAE Metaomics and Ecosystems Metaprogram/ ; //INRAE Plant Health and Environment division/ ; //Conseil R&#xe9;gional de Bretagne (Brittany Council)/ ; },
abstract = {The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa. IMPORTANCE Seed microbiota can have a crucial role for crop installation by modulating dormancy, germination, seedling development, and recruitment of plant symbionts. Little knowledge is available on the fraction of the plant microbiota that is acquired through seeds. We characterize the encounter between seed and soil communities and how they colonize the seedling together. Transmission success and seedling community assemblage can be influenced by the variation of initial microbial pools, i.e., plant genotype and cropping year for seeds and diversity level for soils. Despite a supposed resident advantage of the seed microbiota, we show that transmission success is in favor of the soil microbiota. Our results also suggest that successful plant-microbiome engineering based on native seed or soil microbiota must include rare taxa.},
}
@article {pmid34100635,
year = {2021},
author = {Tracanna, V and Ossowicki, A and Petrus, MLC and Overduin, S and Terlouw, BR and Lund, G and Robinson, SL and Warris, S and Schijlen, EGWM and van Wezel, GP and Raaijmakers, JM and Garbeva, P and Medema, MH},
title = {Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {e0111620},
pmid = {34100635},
issn = {2379-5077},
support = {ALWGR. 2015.1//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; },
abstract = {Disease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10× metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotype. IMPORTANCE Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops. Our approach to develop novel sustainable strategies to control this fungal root pathogen is to explore and exploit an effective, yet poorly understood naturally occurring protection, i.e., disease-suppressive soils. After screening 28 agricultural soils, we recently identified four soils that were suppressive to root disease of wheat caused by Fusarium culmorum. We also confirmed, via sterilization and transplantation, that the microbiomes of these soils play a significant role in the suppressive phenotype. By adopting nonribosomal peptide synthetase (NRPS) functional amplicon screening of suppressive and conducive soils, we here show how computationally driven comparative analysis of combined functional amplicon and metagenomic data can unravel putative mechanisms underlying microbiome-associated plant phenotypes.},
}
@article {pmid34099808,
year = {2021},
author = {Timmers, LFSM and Peixoto, JV and Ducati, RG and Bachega, JFR and de Mattos Pereira, L and Caceres, RA and Majolo, F and da Silva, GL and Anton, DB and Dellagostin, OA and Henriques, JAP and Xavier, LL and Goettert, MI and Laufer, S},
title = {SARS-CoV-2 mutations in Brazil: from genomics to putative clinical conditions.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {11998},
pmid = {34099808},
issn = {2045-2322},
mesh = {Brazil ; COVID-19/*genetics ; Genome, Viral ; Genomics ; Humans ; Mutation/*genetics ; SARS-CoV-2/*genetics/pathogenicity ; Severity of Illness Index ; Viral Proteins/*genetics ; },
abstract = {Due to the high rate of transmissibility, Brazil became the new COVID-19 outbreak epicenter and, since then, is being monitored to understand how SARS-CoV-2 mutates and spreads. We combined genomic and structural analysis to evaluate genomes isolated from different regions of Brazil and show that the most prevalent mutations were located in the S, N, ORF3a and ORF6 genes, which are involved in different stages of viral life cycle and its interaction with the host cells. Structural analysis brought to light the positions of these mutations on protein structures, contributing towards studies of selective structure-based drug discovery and vaccine development.},
}
@article {pmid34097120,
year = {2021},
author = {Hou, D and Zhou, R and Zeng, S and Wei, D and Deng, X and Xing, C and Weng, S and He, J and Huang, Z},
title = {Stochastic processes shape the bacterial community assembly in shrimp cultural pond sediments.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {12},
pages = {5013-5022},
pmid = {34097120},
issn = {1432-0614},
support = {31902392//National Natural Science Foundation of China/ ; CARS-48//China Agriculture Research System/ ; 2019A1515011557//Natural Science Foundation of Guangdong Province/ ; 19lgpy103//Fundamental Research Funds for the Central Universities/ ; 2020B0202010009//Key Research and Development Projects in Guangdong Province/ ; },
mesh = {Animals ; Bacteria/genetics ; *Geologic Sediments ; *Ponds ; RNA, Ribosomal, 16S ; Stochastic Processes ; },
abstract = {Sediment environments harbor a repertoire of microorganisms that contribute to animal health and the microecosystem in aquaculture ecosystems, but their community diversity and the potential factors that control it remain unclear. Here, we applied 16S rRNA gene amplicon sequencing to investigate bacterial diversity and assembly mechanisms in the sediments of shrimp cultural ponds at the mesoscale. Our results showed that sediment bacterial communities contained 10,333 operational taxonomic units (OTUs) but had only 34 core OTUs and that the relative abundances of these core OTUs were significantly correlated with the physicochemical properties of the sediments. Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Acidobacteria, Firmicutes, Actinobacteria, Ignavibacteriae, Spirochaetae and Planctomycetes were the ten most abundant bacterial phyla. Notably, some opportunistic pathogens (e.g. Vibrio and Photobacterium) and potential functional microbes (e.g. Nitrospira, Nitrosomonas, Desulfobulbus and Desulfuromusa) were widely distributed in shrimp cultural pond sediments. More importantly, we found that there was a significant negative but weak distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and that the spatial turnover of these bacterial communities appeared to be largely driven by stochastic processes. Additionally, environmental factors, such as pH and total nitrogen, also played important roles in influencing the sediment bacterial structure. Our findings enhance our understanding of microbial ecology in aquatic ecosystems and facilitate sediment microbiota management in aquaculture. KEY POINTS: • Core bacterial taxa in cultural pond sediments contributed to the shrimp health and element cycling. • There was a significant negative distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and its spatial turnover appeared to be largely driven by stochastic processes. • Environmental factors (e.g. pH and total nitrogen) played important roles in influencing bacterial structure in shrimp cultural pond sediments.},
}
@article {pmid34094994,
year = {2021},
author = {Kumar, S and Kumari, N and Talukdar, D and Kothidar, A and Sarkar, M and Mehta, O and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and Desiraju, BK and Nair, GB and Bhatnagar, S and Mukherjee, S and Das, B and , },
title = {The Vaginal Microbial Signatures of Preterm Birth Delivery in Indian Women.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {622474},
pmid = {34094994},
issn = {2235-2988},
mesh = {Female ; Fusobacteria ; Humans ; India ; Infant, Newborn ; Lactobacillus ; Pregnancy ; *Premature Birth/epidemiology ; RNA, Ribosomal, 16S/genetics ; Vagina ; },
abstract = {BACKGROUND: The incidence of preterm birth (PTB) in India is around 13%. Specific bacterial communities or individual taxon living in the vaginal milieu of pregnant women is a potential risk factor for PTB and may play an important role in its pathophysiology. Besides, bacterial taxa associated with PTB vary across populations.<br><br>OBJECTIVE: Conduct a comparative analysis of vaginal microbiome composition and microbial genomic repertoires of women who enrolled in the Interdisciplinary Group for Advanced Research on Birth Outcomes - A DBT India Initiative (GARBH-Ini) pregnancy cohort to identify bacterial taxa associated with term birth (TB) and PTB in Indian women.<br><br>METHODS: Vaginal swabs were collected during all three trimesters from 38 pregnant Indian women who delivered spontaneous term (n=20) and preterm (n=18) neonates. Paired-end sequencing of V3-V4 region of 16S rRNA gene was performed using the metagenomic DNA isolated from vaginal swabs (n=115). Whole genome sequencing of bacterial species associated with birth outcomes was carried out by shotgun method. Lactobacillus species were grown anaerobically in the De Man, Rogosa and Sharpe (MRS) agar culture medium for isolation of genomic DNA and whole genome sequencing.<br><br>RESULTS: Vaginal microbiome of both term and preterm samples reveals similar alpha diversity indices. However, significantly higher abundance of Lactobacillus iners (p-value All_Trimesters<0.02), Megasphaera sp (p-value1st_Trimester <0.05), Gardnerella vaginalis (p-value2nd_Trimester= 0.01) and Sneathia sanguinegens (p-value2nd_Trimester <0.0001) were identified in preterm samples whereas higher abundance of L. gasseri (p-value3rd_Trimester =0.010) was observed in term samples by Wilcoxon rank-sum test. The relative abundance of L. iners, and Megasphaera sp. were found to be significantly different over time between term and preterm mothers. Analyses of the representative genomes of L. crispatus and L. gasseri indicate presence of secretory transcriptional regulator and several ribosomally synthesized antimicrobial peptides correlated with anti-inflammatory condition in the vagina. These findings indicate protective role of L. crispatus and L. gasseri in reducing the risk of PTB.<br><br>CONCLUSION: Our findings indicate that the dominance of specific Lactobacillus species and few other facultative anaerobes are associated with birth outcomes.},
}
@article {pmid34093488,
year = {2021},
author = {Pjevac, P and Hausmann, B and Schwarz, J and Kohl, G and Herbold, CW and Loy, A and Berry, D},
title = {An Economical and Flexible Dual Barcoding, Two-Step PCR Approach for Highly Multiplexed Amplicon Sequencing.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {669776},
pmid = {34093488},
issn = {1664-302X},
abstract = {In microbiome research, phylogenetic and functional marker gene amplicon sequencing is the most commonly-used community profiling approach. Consequently, a plethora of protocols for the preparation and multiplexing of samples for amplicon sequencing have been developed. Here, we present two economical high-throughput gene amplification and sequencing workflows that are implemented as standard operating procedures at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna. These workflows are based on a previously-published two-step PCR approach, but have been updated to either increase the accuracy of results, or alternatively to achieve orders of magnitude higher numbers of samples to be multiplexed in a single sequencing run. The high-accuracy workflow relies on unique dual sample barcoding. It allows the same level of sample multiplexing as the previously-published two-step PCR approach, but effectively eliminates residual read missasignments between samples (crosstalk) which are inherent to single barcoding approaches. The high-multiplexing workflow is based on combinatorial dual sample barcoding, which theoretically allows for multiplexing up to 299,756 amplicon libraries of the same target gene in a single massively-parallelized amplicon sequencing run. Both workflows presented here are highly economical, easy to implement, and can, without significant modifications or cost, be applied to any target gene of interest.},
}
@article {pmid34091718,
year = {2022},
author = {Girolamini, L and Salaris, S and Pascale, MR and Mazzotta, M and Cristino, S},
title = {Dynamics of Legionella Community Interactions in Response to Temperature and Disinfection Treatment: 7 Years of Investigation.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {353-362},
pmid = {34091718},
issn = {1432-184X},
mesh = {Disinfection/methods ; Humans ; Hydrogen Peroxide ; *Legionella ; *Legionella pneumophila/genetics ; Temperature ; Water Microbiology ; },
abstract = {In man-made water distribution systems, Legionella community interactions remain unknown, due to their ability to change from sessile to planktonic states or live in viable but non-culturable forms, in response to anthropic and environmental stress. During 7 years of hospital Legionella surveillance, in 191 hot water positive samples, the interactions among the Legionella species, temperature, and disinfection treatment were evaluated. Legionella was isolated following ISO 11731:2017, and identification was performed by mip gene sequencing and sequence-based typing (SBT) for L. anisa or L. rubrilucens and L. pneumophila, respectively. The species with the higher frequency of isolation was L. pneumophila serogroup 1 (78.53%; 4865.36 ± 25,479.11 cfu/L), followed by L. anisa (54.45%; 558.79 ± 2637.41 cfu/L) and L. rubrilucens (21.99%; 307.73 ± 1574.95 cfu/L), which were sometimes present together. Spearman's rho correlation test was conducted among the species with respect to temperature and disinfectant (H2O2/Ag[+]). The results showed a generally positive interaction among these species sharing the same environment, except for competition between L. anisa and L. rubrilucens. High temperature (48.83 ± 2.59 °C) and disinfection treatment (11.58 ± 4.99 mg/L) affected the presence of these species. An exception was observed with L. anisa, which showed disinfection treatment resistance. For the purposes of environmental surveillance, it is fundamental to better understand the interactions and dynamic of the Legionella community in man-made water systems in order to choose the proper physical or chemical treatments. The simultaneous presence of different Legionella species could result in an increased resistance to high temperature and disinfectant treatment, leading to changes in contamination level and species diversity.},
}
@article {pmid34091717,
year = {2022},
author = {Jaskulska, A and Šulčius, S and Kokociński, M and Koreivienė, J and Nájera, AF and Mankiewicz-Boczek, J},
title = {Cyanophage Distribution Across European Lakes of the Temperate-Humid Continental Climate Zone Assessed Using PCR-Based Genetic Markers.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {284-295},
pmid = {34091717},
issn = {1432-184X},
mesh = {*Bacteriophages/genetics ; Genetic Markers ; *Lakes ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Studies of the diversity and distribution of freshwater cyanophages are generally limited to the small geographical areas, in many cases including only one or few lakes. Data from dozens of various lakes distributed at a larger distance are necessary to understand their spatial distribution and sensitivity to biotic and abiotic factors. Thus, the objective of this study was to analyze the diversity and distribution of cyanophages within the infected cells using marker genes (psbA, nblA, and g91) in 21 Polish and Lithuanian lakes. Physicochemical factors that might be related to them were also analyzed. The results demonstrated that genetic markers representing cyanophages were observed in most lakes studied. The frequently detected gene was psbA with 88% of cyanophage-positive samples, while nblA and g91 were found in approximately 50% of lakes. The DNA sequence analyses for each gene demonstrated low variability between them, although the psbA sequences branched within the larger cluster of marine Synechoccocuss counterparts. The principal component analysis allowed to identify significant variation between the lakes that presented high and low cyanobacterial biomass. The lakes with high cyanobacterial biomass were further separated by country and the different diversity of cyanobacteria species, particularly Planktothrix agardhii, was dominant in the Polish lakes and Planktolyngbya limnetica in the Lithuanian lakes. The total phosphorous and the presence of cyanophage genes psbA and nblA were the most important factors that allowed differentiation for the Polish lakes, while the pH and the genes g91 and nblA for the Lithuanian lakes.},
}
@article {pmid34091223,
year = {2021},
author = {Sun, C and Zhang, B and Ning, D and Zhang, Y and Dai, T and Wu, L and Li, T and Liu, W and Zhou, J and Wen, X},
title = {Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern.},
journal = {Water research},
volume = {200},
number = {},
pages = {117295},
doi = {10.1016/j.watres.2021.117295},
pmid = {34091223},
issn = {1879-2448},
mesh = {*Microbiota ; Phylogeny ; Seasons ; Sewage ; *Water Purification ; },
abstract = {The optimal operation and functional stability of a wastewater treatment plant (WWTP) strongly depend on the properties of its microbial community. However, a knowledge gap remains regarding the seasonal dynamics of microbial community properties, especially phylogenetic group based assembly and co-occurrence patterns. Accordingly, in this study, influent and activated sludge (AS) samples were weekly collected from 2 full-scale WWTPs for one year (89 influent and 103 AS samples in total) and examined by high-throughput Illumina-MiSeq sequencing. The results suggested that the microbial community diversity and composition in the influent fluctuated substantially with season, while those in the AS had a relatively more stable pattern throughout the year. The phylogenetic group based assembly mechanisms of AS community were identified by using "Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP)". The results showed that drift accounted for the largest proportion (52.8%), while homogeneous selection (18.2%) was the most important deterministic process. Deterministic processes dominated in 47 microbial groups (bins), which were also found (~40%) in the AS core taxa dataset. Moreover, the results suggested that Nitrospira were more susceptible to stochastic processes in winter, which may provide a possible explanation for nitrification failure in winter. Network analysis results suggested that the network structure of the AS community could be more stable in summer and autumn. In addition, there were no identical keystone taxa found in different networks (constructed from different plants, sources, and seasons), which supported the context dependency theory. The results of this study deepened our understanding of the microbial ecology in AS systems and provided a foundation for further studies on the community regulation strategy of WWTPs.},
}
@article {pmid34089088,
year = {2022},
author = {Zhao, Z and Cheng, M and Li, Y and Song, X and Wang, Y and Zhang, Y},
title = {A Novel Constructed Wetland Combined with Microbial Desalination Cells and its Application.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {340-352},
pmid = {34089088},
issn = {1432-184X},
support = {51909157//National Natural Science Foundation of China/ ; 2019YFC0408604//National Key Research and Development Project/ ; 19QC1401100//Shanghai Rising-Star Program/ ; hklk201912//Open Foundation of Hebei Key Laboratory of Wetland Ecology and Conservation/ ; SZGXZS2020068//Research project of ecological environment protection and restoration of Yangtze River in Zhoushan/ ; },
mesh = {*Bioelectric Energy Sources/microbiology ; Electrodes ; Wastewater ; *Water Purification/methods ; Wetlands ; },
abstract = {Wastewater recycling can alleviate the shortage of water resources. Saline water is seldom treated with biological processes, and its recycling rate is low. Constructed wetland (CW) is a safe, economical, and ecological water treatment method. However, the saline water treatment performance of CW is not good. Microbial desalination cells (MDC) utilizing a bioelectrochemical approach achieve functions of desalination and power generation. In this study, MDC was used to strengthen CW to form a composite system, MDC-CW. Through optimization of design parameters, MDC-CW was applied in the treatment of salt-containing water. The average total nitrogen removal rate in MDC-CW-P1 reached 87.33% and the average COD removal rate was 92.79%. The average desalination rate of MDC-CW-P1 was 55.78% and the average voltage of MDC-CW-P1 reached 0.40 mV. Planting Canna indica in the MDC-CW was conducive to the functions of desalination and power generation. The above results were also verified by the microbial analysis results of gravels in the substrate, plant rhizosphere, and electrodes. In addition, the decontamination of the device mainly depended on the function of the bacteria commonly used in water treatment, such as Proteobacteria and Bacteroidetes, whereas the generation of power depended on the function of Geobacter. Salt ions moved spontaneously to the cathode and anode under the influence of current generation so that the desalination function was realized under the selective isolation function of exchange membranes. The device design and laboratory applications of MDC-CW experimentally achieved the electrochemical function and broadened the treatment scale of CW.},
}
@article {pmid34086451,
year = {2021},
author = {De Paepe, J and Clauwaert, P and Gritti, MC and Ganigué, R and Sas, B and Vlaeminck, SE and Rabaey, K},
title = {Electrochemical In Situ pH Control Enables Chemical-Free Full Urine Nitrification with Concomitant Nitrate Extraction.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {12},
pages = {8287-8298},
doi = {10.1021/acs.est.1c00041},
pmid = {34086451},
issn = {1520-5851},
mesh = {Ammonia ; Bioreactors ; Hydrogen-Ion Concentration ; *Nitrates ; *Nitrification ; Nitrogen ; },
abstract = {Urine is a valuable resource for nutrient recovery. Stabilization is, however, recommended to prevent urea hydrolysis and the associated risk for ammonia volatilization, uncontrolled precipitation, and malodor. This can be achieved by alkalinization and subsequent biological conversion of urea and ammonia into nitrate (nitrification) and organics into CO2. Yet, without pH control, the extent of nitrification is limited as a result of insufficient alkalinity. This study explored the feasibility of an integrated electrochemical cell to obtain on-demand hydroxide production through water reduction at the cathode, compensating for the acidification caused by nitritation, thereby enabling full nitrification. To deal with the inherent variability of the urine influent composition and bioprocess, the electrochemical cell was steered via a controller, modulating the current based on the pH in the bioreactor. This provided a reliable and innovative alternative to base addition, enabling full nitrification while avoiding the use of chemicals, the logistics associated with base storage and dosing, and the associated increase in salinity. Moreover, the electrochemical cell could be used as an in situ extraction and concentration technology, yielding an acidic concentrated nitrate-rich stream. The make-up of the end product could be tailored by tweaking the process configuration, offering versatility for applications on Earth and in space.},
}
@article {pmid34085863,
year = {2021},
author = {Jakus, N and Blackwell, N and Osenbrück, K and Straub, D and Byrne, JM and Wang, Z and Glöckler, D and Elsner, M and Lueders, T and Grathwohl, P and Kleindienst, S and Kappler, A},
title = {Nitrate Removal by a Novel Lithoautotrophic Nitrate-Reducing, Iron(II)-Oxidizing Culture Enriched from a Pyrite-Rich Limestone Aquifer.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {16},
pages = {e0046021},
pmid = {34085863},
issn = {1098-5336},
mesh = {Autotrophic Processes ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Calcium Carbonate/analysis/metabolism ; Ferrous Compounds/*metabolism ; Geologic Sediments/analysis/microbiology ; Groundwater/chemistry/*microbiology ; Iron/analysis/metabolism ; Nitrates/*metabolism ; Oxidation-Reduction ; Sulfides/analysis/metabolism ; },
abstract = {Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially mediated nitrate reduction by Fe(II)-oxidizing (NRFeOx) microorganisms. However, lithoautotrophic NRFeOx cultures have never been enriched from any aquifer, and as such, there are no model cultures available to study the physiology and geochemistry of this potentially environmentally relevant process. Using iron(II) as an electron donor, we enriched a lithoautotrophic NRFeOx culture from nitrate-containing groundwater of a pyrite-rich limestone aquifer. In the enriched NRFeOx culture that does not require additional organic cosubstrates for growth, within 7 to 11 days, 0.3 to 0.5 mM nitrate was reduced and 1.3 to 2 mM iron(II) was oxidized, leading to a stoichiometric NO3[-]/Fe(II) ratio of 0.2, with N2 and N2O identified as the main nitrate reduction products. Short-range ordered Fe(III) (oxyhydr)oxides were the product of iron(II) oxidation. Microorganisms were observed to be closely associated with formed minerals, but only few cells were encrusted, suggesting that most of the bacteria were able to avoid mineral precipitation at their surface. Analysis of the microbial community by long-read 16S rRNA gene sequencing revealed that the culture is dominated by members of the Gallionellaceae family that are known as autotrophic, neutrophilic, and microaerophilic iron(II) oxidizers. In summary, our study suggests that NRFeOx mediated by lithoautotrophic bacteria can lead to nitrate removal in anthropogenically affected aquifers. IMPORTANCE Removal of nitrate by microbial denitrification in groundwater is often limited by low concentrations of organic carbon. In these carbon-poor ecosystems, nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate removal. However, no lithoautotrophic NRFeOx culture has been successfully isolated or enriched from this type of environment, and as such, there are no model cultures available to study the rate-limiting factors of this potentially important process. Here, we present the physiology and microbial community composition of a novel lithoautotrophic NRFeOx culture enriched from a fractured aquifer in southern Germany. The culture is dominated by a putative Fe(II) oxidizer affiliated with the Gallionellaceae family and performs nitrate reduction coupled to Fe(II) oxidation leading to N2O and N2 formation without the addition of organic substrates. Our analyses demonstrate that lithoautotrophic NRFeOx can potentially lead to nitrate removal in nitrate-contaminated aquifers.},
}
@article {pmid34083720,
year = {2021},
author = {Cao, YL and Li, YL and Fan, YF and Li, Z and Yoshida, K and Wang, JY and Ma, XK and Wang, N and Mitsuda, N and Kotake, T and Ishimizu, T and Tsai, KC and Niu, SC and Zhang, D and Sun, WH and Luo, Q and Zhao, JH and Yin, Y and Zhang, B and Wang, JY and Qin, K and An, W and He, J and Dai, GL and Wang, YJ and Shi, ZG and Jiao, EN and Wu, PJ and Liu, X and Liu, B and Liao, XY and Jiang, YT and Yu, X and Hao, Y and Xu, XY and Zou, SQ and Li, MH and Hsiao, YY and Lin, YF and Liang, CK and Chen, YY and Wu, WL and Lu, HC and Lan, SR and Wang, ZW and Zhao, X and Zhong, WY and Yeh, CM and Tsai, WC and Van de Peer, Y and Liu, ZJ},
title = {Wolfberry genomes and the evolution of Lycium (Solanaceae).},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {671},
pmid = {34083720},
issn = {2399-3642},
mesh = {Africa ; Asia ; Chromosomes, Plant/*genetics ; Evolution, Molecular ; Fruit/genetics/metabolism ; Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Geography ; Lycium/classification/*genetics/metabolism ; North America ; Phylogeny ; Polyploidy ; Polysaccharides/metabolism ; Solanaceae/classification/*genetics/metabolism ; Species Specificity ; Whole Genome Sequencing/*methods ; },
abstract = {Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.},
}
@article {pmid34083551,
year = {2021},
author = {Fabersani, E and Portune, K and Campillo, I and López-Almela, I and la Paz, SM and Romaní-Pérez, M and Benítez-Páez, A and Sanz, Y},
title = {Bacteroides uniformis CECT 7771 alleviates inflammation within the gut-adipose tissue axis involving TLR5 signaling in obese mice.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {11788},
pmid = {34083551},
issn = {2045-2322},
mesh = {Adaptive Immunity ; Adipose Tissue/metabolism ; Animals ; Bacteroides/*physiology ; Bacteroides Infections/*metabolism/*microbiology/pathology ; Cytokines/metabolism ; Disease Models, Animal ; Energy Metabolism ; Gastroenteritis/*metabolism/*microbiology/pathology ; Gastrointestinal Microbiome ; Immunity, Innate ; Inflammation Mediators/metabolism ; Mice ; Mice, Obese ; Phenotype ; *Signal Transduction ; Toll-Like Receptor 5/*metabolism ; },
abstract = {This study investigated the immune mechanisms whereby administration of Bacteroides uniformis CECT 7771 reduces metabolic dysfunction in obesity. C57BL/6 adult male mice were fed a standard diet or a Western diet high in fat and fructose, supplemented or not with B. uniformis CECT 7771 for 14 weeks. B. uniformis CECT 7771 reduced body weight gain, plasma cholesterol, triglyceride, glucose, and leptin levels; and improved oral glucose tolerance in obese mice. Moreover, B. uniformis CECT 7771 modulated the gut microbiota and immune alterations associated with obesity, increasing Tregs and reducing B cells, total macrophages and the M1/M2 ratio in both the gut and epididymal adipose tissue (EAT) of obese mice. B. uniformis CECT 7771 also increased the concentration of the anti-inflammatory cytokine IL-10 in the gut, EAT and peripheral blood, and protective cytokines TSLP and IL-33, involved in Treg induction and type 2 innate lymphoid cells activation, in the EAT. It also restored the obesity-reduced TLR5 expression in the ileum and EAT. The findings indicate that the administration of a human intestinal bacterium with immunoregulatory properties on the intestinal mucosa helps reverse the immuno-metabolic dysfunction caused by a Western diet acting over the gut-adipose tissue axis.},
}
@article {pmid34081148,
year = {2022},
author = {Mezzasoma, A and Coleine, C and Sannino, C and Selbmann, L},
title = {Endolithic Bacterial Diversity in Lichen-Dominated Communities Is Shaped by Sun Exposure in McMurdo Dry Valleys, Antarctica.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {328-339},
pmid = {34081148},
issn = {1432-184X},
mesh = {Antarctic Regions ; Biodiversity ; *Cyanobacteria/genetics ; Humans ; *Lichens ; Sunlight ; },
abstract = {The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon sequencing, targeting the V3 and V4 of the 16S region. Despite the increasing interest in edaphic factors that drive bacterial community composition in Antarctic rocky communities, few researchers focused attention on the direct effects of sun exposure on bacterial diversity; we herein reported significant differences in the northern and southern communities. The analysis of β-diversity showed significant differences among sampled localities. For instance, the most abundant genera found in the north-exposed rocks were Rhodococcus and Blastococcus in Knobhead Mt.; Ktedonobacter and Cyanobacteria Family I Group I in Finger Mt.; Rhodococcus and Endobacter in University Valley; and Segetibacter and Tetrasphaera in Siegfried Peak samples. In south-exposed rocks, instead, the most abundant genera were Escherichia/Shigella and Streptococcus in Knobhead Mt.; Ktedonobacter and Rhodococcus in Finger Mt.; Ktedonobacter and Roseomonas in University Valley; and Blastocatella, Cyanobacteria Family I Group I and Segetibacter in Siegfried Peak. Significant biomarkers, detected by the Linear discriminant analysis Effect Size, were also found among north- and south-exposed communities. Besides, the large number of positive significant co-occurrences may suggest a crucial role of positive associations over competitions under the harsher conditions where these rock-inhabiting microorganisms spread. Although the effect of geographic distances in these extreme environments play a significant role in shaping biodiversity, the study of an edaphic factor, such as solar exposure, adds an important contribution to the mosaic of microbial biodiversity of Antarctic bacterial cryptoendolithic communities.},
}
@article {pmid34081147,
year = {2021},
author = {Zhang, T and Wang, NF and Yu, LY},
title = {Geographic Distance and Habitat Type Influence Fungal Communities in the Arctic and Antarctic Sites.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {224-232},
pmid = {34081147},
issn = {1432-184X},
support = {31670025//National Natural Science Foundation of China/ ; },
mesh = {Antarctic Regions ; Arctic Regions ; Ecosystem ; *Mycobiome ; Soil Microbiology ; },
abstract = {The Antarctic and Arctic regions are collectively referred to as the "Two Poles" of the earth and have extremely harsh climate conditions and fragile ecosystems. Until now, the biogeography of the fungal communities in the bipolar regions is not well known. In this study, we focused on the fungal communities in 110 samples collected from four habitat types (i.e., soil, vascular plant, freshwater, moss) in the Antarctic and Arctic sites using high-throughput sequencing. The data showed that the diversity and composition of fungal communities were both geographically patterned and habitat-patterned. ANOSIM tests revealed statistically significant differences among fungal communities in the eight sample types (R = 0.5035, p < 0.001) and those in the bipolar regions (R = 0.32859, p < 0.001). Only 396 OTUs (14.8%) were shared between the bipolar sites. Fungal communities in the four habitat types clustered together in the Arctic site but were separate from those of the Antarctic site, indicating that geographic distance was a more important determinant of fungal communities in the bipolar sites. These findings offer insights into the present-day biogeography of fungal communities in the bipolar sites.},
}
@article {pmid34080061,
year = {2021},
author = {Carbonero, F and Strobel, G},
title = {Fungal Ecology Special Issue: Editorial.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {1-4},
pmid = {34080061},
issn = {1432-184X},
mesh = {*Ecology ; *Fungi/genetics ; },
}
@article {pmid34078434,
year = {2021},
author = {Gresse, R and Chaucheyras-Durand, F and Denis, S and Beaumont, M and Van de Wiele, T and Forano, E and Blanquet-Diot, S},
title = {Weaning-associated feed deprivation stress causes microbiota disruptions in a novel mucin-containing in vitro model of the piglet colon (MPigut-IVM).},
journal = {Journal of animal science and biotechnology},
volume = {12},
number = {1},
pages = {75},
pmid = {34078434},
issn = {1674-9782},
abstract = {BACKGROUND: Risk factors for the etiology of post-weaning diarrhea, a major problem in swine industry associated with enormous economic losses, remain to be fully elucidated. In concordance with the ethical concerns raised by animal experiments, we developed a new in vitro model of the weaning piglet colon (MPigut-IVM) including a mucin bead compartment to reproduce the mucus surface from the gut to which gut microbes can adhere.<br><br>RESULTS: Our results indicated that the MPigut-IVM is able to establish a representative piglet archaeal and bacterial colon microbiota in terms of taxonomic composition and function. The MPigut-IVM was consequently used to investigate the potential effects of feed deprivation, a common consequence of weaning in piglets, on the microbiota. The lack of nutrients in the MPigut-IVM led to an increased abundance of Prevotellaceae and Escherichia-Shigella and a decrease in Bacteroidiaceae and confirms previous in vivo findings. On top of a strong increase in redox potential, the feed deprivation stress induced modifications of microbial metabolite production such as a decrease in acetate and an increase in proportional valerate, isovalerate and isobutyrate production.<br><br>CONCLUSIONS: The MPigut-IVM is able to simulate luminal and mucosal piglet microbiota and represent an innovative tool for comparative studies to investigate the impact of weaning stressors on piglet microbiota. Besides, weaning-associated feed deprivation in piglets provokes disruptions of MPigut-IVM microbiota composition and functionality and could be implicated in the onset of post-weaning dysbiosis in piglets.},
}
@article {pmid34077260,
year = {2021},
author = {Cornell, CR and Zhang, Y and Van Nostrand, JD and Wagle, P and Xiao, X and Zhou, J},
title = {Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils.},
journal = {mSphere},
volume = {6},
number = {3},
pages = {e0116020},
pmid = {34077260},
issn = {2379-5042},
mesh = {Crops, Agricultural/*virology ; *Grassland ; *Metagenome ; Metagenomics ; *Soil Microbiology ; Spatio-Temporal Analysis ; Virome/*genetics ; Viruses/*genetics ; },
abstract = {During the last several decades, viruses have been increasingly recognized for their abundance, ubiquity, and important roles in different ecosystems. Despite known contributions to aquatic systems, few studies examine viral abundance and community structure over time in terrestrial ecosystems. The effects of land conversion and land management on soil microbes have been previously investigated, but their effects on virus population are not well studied. This study examined annual dynamics of viral abundance in soils from a native tallgrass prairie and two croplands, conventional till winter wheat and no-till canola, in Oklahoma. Virus-like particle (VLP) abundance varied across sites, and showed clear seasonal shifts. VLP abundance significantly correlated with environmental variables that were generally reflective of land use, including air temperature, soil nitrogen, and plant canopy coverage. Structural equation modeling supported the effects of land use on soil communities by emphasizing interactions between management, environmental factors, and viral and bacterial abundance. Between the viral metagenomes from the prairie and tilled wheat field, 1,231 unique viral operational taxonomic units (vOTUs) were identified, and only five were shared that were rare in the contrasting field. Only 13% of the vOTUs had similarity to previously identified viruses in the RefSeq database, with only 7% having known taxonomic classification. Together, our findings indicated land use and tillage practices influence virus abundance and community structure. Analyses of viromes over time and space are vital to viral ecology in providing insight on viral communities and key information on interactions between viruses, their microbial hosts, and the environment. IMPORTANCE Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution. Therefore, viruses are considered an important part of soil functions in terrestrial ecosystems. In aquatic environments, virus abundance generally exceeds bacterial counts by an order of magnitude, and they are thought to be one of the greatest genetic reservoirs on the planet. However, data are extremely limited on viruses in soils, and even less is known about their responses to the disturbances associated with land use and management. The study provides important insights into the temporal dynamics of viral abundance and the structure of viral communities in response to the common practice of turning native habitats into arable soils.},
}
@article {pmid34073029,
year = {2021},
author = {Broadhead, R and Craeye, L and Callewaert, C},
title = {The Future of Functional Clothing for an Improved Skin and Textile Microbiome Relationship.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34073029},
issn = {2076-2607},
support = {F2019/IOF-STARTT/261//Ghent University/ ; },
abstract = {The skin microbiome has become a hot field of research in the last few years. The emergence of next-generation sequencing has given unprecedented insights into the impact and involvement of microbiota in skin conditions. More and more cosmetics contain probiotics or bacteria as an active ingredient, with or without scientific data. This research is also acknowledged by the textile industry. There has been a more holistic approach on how the skin and textile microbiome interacts and how they influence the pH, moisture content and odour generation. To date, most of the ingredients have a broad-spectrum antibacterial action. This manuscript covers the current research and industry developments in the field of skin and textiles. It explores the nature of antimicrobial finishing in textiles which can disrupt the skin microbiome, and the benefits of more natural and microbiome friendly therapies to combat skin conditions, malodour and skin infection.},
}
@article {pmid34072450,
year = {2021},
author = {Romaní-Pérez, M and Bullich-Vilarrubias, C and López-Almela, I and Liébana-García, R and Olivares, M and Sanz, Y},
title = {The Microbiota and the Gut-Brain Axis in Controlling Food Intake and Energy Homeostasis.},
journal = {International journal of molecular sciences},
volume = {22},
number = {11},
pages = {},
pmid = {34072450},
issn = {1422-0067},
support = {797297//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; AGL2017-88801-P//Spanish Ministry of Science and Innovation/ ; },
mesh = {Brain/*physiology ; Circadian Rhythm ; Diet ; Disease Susceptibility ; Eating ; *Energy Metabolism ; Feeding Behavior ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*physiology ; *Homeostasis ; Humans ; Microbiota/*physiology ; Micronutrients ; Nutrients ; Obesity/etiology/metabolism ; },
abstract = {Obesity currently represents a major societal and health challenge worldwide. Its prevalence has reached epidemic proportions and trends continue to rise, reflecting the need for more effective preventive measures. Hypothalamic circuits that control energy homeostasis in response to food intake are interesting targets for body-weight management, for example, through interventions that reinforce the gut-to-brain nutrient signalling, whose malfunction contributes to obesity. Gut microbiota-diet interactions might interfere in nutrient sensing and signalling from the gut to the brain, where the information is processed to control energy homeostasis. This gut microbiota-brain crosstalk is mediated by metabolites, mainly short chain fatty acids, secondary bile acids or amino acids-derived metabolites and subcellular bacterial components. These activate gut-endocrine and/or neural-mediated pathways or pass to systemic circulation and then reach the brain. Feeding time and dietary composition are the main drivers of the gut microbiota structure and function. Therefore, aberrant feeding patterns or unhealthy diets might alter gut microbiota-diet interactions and modify nutrient availability and/or microbial ligands transmitting information from the gut to the brain in response to food intake, thus impairing energy homeostasis. Herein, we update the scientific evidence supporting that gut microbiota is a source of novel dietary and non-dietary biological products that may beneficially regulate gut-to-brain communication and, thus, improve metabolic health. Additionally, we evaluate how the feeding time and dietary composition modulate the gut microbiota and, thereby, the intraluminal availability of these biological products with potential effects on energy homeostasis. The review also identifies knowledge gaps and the advances required to clinically apply microbiome-based strategies to improve the gut-brain axis function and, thus, combat obesity.},
}
@article {pmid34068093,
year = {2021},
author = {Zhu, J and Sun, X and Zhang, ZD and Tang, QY and Gu, MY and Zhang, LJ and Hou, M and Sharon, A and Yuan, HL},
title = {Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianum.},
journal = {Microorganisms},
volume = {9},
number = {5},
pages = {},
pmid = {34068093},
issn = {2076-2607},
support = {31760009//National Natural Science Foundation of China/ ; 2021SKLAB6-9//Project for Extramural Scientists of State Key Laboratory of Agrobiotechnology/ ; nkypt005//Improvement Project of Agricultural Science and Capacity of Technology Innovation Platform in Xinjiang Academy of Agricultural Sciences/ ; KY2019021//Special Project for Basic Scientific Activities of Non-profit Institutes Supported the Government of Xinjiang Uyghur Autonomous Region/ ; },
abstract = {Endophytic bacteria and fungi colonize plants that grow in various types of terrestrial and aquatic ecosystems. Our study investigates the communities of endophytic bacteria and fungi of halophyte Kalidium schrenkianum growing in stressed habitats with ionizing radiation. The geochemical factors and radiation (at low, medium, high level and control) both affected the structure of endophytic communities. The bacterial class Actinobacteria and the fungal class Dothideomycetes predominated the endophytic communities of K. schrenkianum. Aerial tissues of K. schrenkianum had higher fungal diversity, while roots had higher bacterial diversity. Radiation had no significant effect on the abundance of bacterial classes. Soil pH, total nitrogen, and organic matter showed significant effects on the diversity of root endophytes. Radiation affected bacterial and fungal community structure in roots but not in aerial tissues, and had a strong effect on fungal co-occurrence networks. Overall, the genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments, however negative correlations were found between endophytic bacteria and fungi in the plant. The genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments. Our findings suggest that radiation affects root endophytes, and that the endophytes associated with aerial tissues and roots of K. schrenkianum follow different mechanisms for community assembly and different paradigms in stress response.},
}
@article {pmid34064714,
year = {2021},
author = {Park, T and Yoon, J and Kim, A and Unno, T and Yun, Y},
title = {Comparison of the Gut Microbiota of Jeju and Thoroughbred Horses in Korea.},
journal = {Veterinary sciences},
volume = {8},
number = {5},
pages = {},
pmid = {34064714},
issn = {2306-7381},
support = {2016R1A6A1A03012862//National Research Foundation of Korea/ ; },
abstract = {(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoroughbred horses, respectively; (3) Results: The gut microbiota belonged to 23 phyla and 159 families. Firmicutes and Bacteroidetes were the most abundant and predominant phyla, followed by Verrucomicrobia, Euryachaeota, and Spirochaete. The ratio of Firmicutes to Bacteroidetes (F/B), which is known as a relevant marker of gut dysbiosis, was 1.84 for Jeju horses, whereas it was 1.76 for Thoroughbred horses. Moreover, at the genus level, 21 genera were significantly different between the Jeju and Thoroughbred horses (p < 0.05); (4) Conclusions: The Thoroughbred horse's gut microbiotas had significantly higher diversity than the Jeju horses (p < 0.05). In addition, beneficial commensal bacteria that produce short-chain fatty acids thus providing a significant source of energy are also more abundant in Thoroughbred horses. These results provide novel information on the horse gut microbiota and insights for further studies related to the horse gut microbiota.},
}
@article {pmid34064045,
year = {2021},
author = {Uriot, O and Kebouchi, M and Lorson, E and Galia, W and Denis, S and Chalancon, S and Hafeez, Z and Roux, E and Genay, M and Blanquet-Diot, S and Dary-Mourot, A},
title = {Identification of Streptococcus thermophilus Genes Specifically Expressed under Simulated Human Digestive Conditions Using R-IVET Technology.},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34064045},
issn = {2076-2607},
abstract = {Despite promising health effects, the probiotic status of Streptococcus thermophilus, a lactic acid bacterium widely used in dairy industry, requires further documentation of its physiological status during human gastrointestinal passage. This study aimed to apply recombinant-based in vivo technology (R-IVET) to identify genes triggered in a S. thermophilus LMD-9 reference strain under simulated digestive conditions. First, the R-IVET chromosomal cassette and plasmid genomic library were designed to positively select activated genes. Second, recombinant clones were introduced into complementary models mimicking the human gut, the Netherlands Organization for Applied Scientific Research (TNO) gastrointestinal model imitating the human stomach and small intestine, the Caco-2 TC7 cell line as a model of intestinal epithelium, and anaerobic batch cultures of human feces as a colon model. All inserts of activated clones displayed a promoter activity that differed from one digestive condition to another. Our results also showed that S. thermophilus adapted its metabolism to stressful conditions found in the gastric and colonic competitive environment and modified its surface proteins during adhesion to Caco-2 TC7 cells. Activated genes were investigated in a collection of S. thermophilus strains showing various resistance levels to gastrointestinal stresses, a first stage in the identification of gut resistance markers and a key step in probiotic selection.},
}
@article {pmid34063014,
year = {2021},
author = {Weiss, B and Souza, ACO and Constancio, MTL and Alvarenga, DO and Pylro, VS and Alves, LMC and Varani, AM},
title = {Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics.},
journal = {Microorganisms},
volume = {9},
number = {5},
pages = {},
pmid = {34063014},
issn = {2076-2607},
support = {Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior - Brasil (CAPES)/ ; [16/16624-1] and [10/17520-9]//S&#xe3;o Paulo Research Foundation (FAPESP)/ ; [303061/2019-7] and [302085/2017-3]//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {Second-generation biofuel production is in high demand, but lignocellulosic biomass' complexity impairs its use due to the vast diversity of enzymes necessary to execute the complete saccharification. In nature, lignocellulose can be rapidly deconstructed due to the division of biochemical labor effectuated in bacterial communities. Here, we analyzed the lignocellulolytic potential of a bacterial consortium obtained from soil and dry straw leftover from a sugarcane milling plant. This consortium was cultivated for 20 weeks in aerobic conditions using sugarcane bagasse as a sole carbon source. Scanning electron microscopy and chemical analyses registered modification of the sugarcane fiber's appearance and biochemical composition, indicating that this consortium can deconstruct cellulose and hemicellulose but no lignin. A total of 52 metagenome-assembled genomes from eight bacterial classes (Actinobacteria, Alphaproteobacteria, Bacilli, Bacteroidia, Cytophagia, Gammaproteobacteria, Oligoflexia, and Thermoleophilia) were recovered from the consortium, in which ~46% of species showed no relevant modification in their abundance during the 20 weeks of cultivation, suggesting a mostly stable consortium. Their CAZymes repertoire indicated that many of the most abundant species are known to deconstruct lignin (e.g., Chryseobacterium) and carry sequences related to hemicellulose and cellulose deconstruction (e.g., Chitinophaga, Niastella, Niabella, and Siphonobacter). Taken together, our results unraveled the bacterial diversity, enzymatic potential, and effectiveness of this lignocellulose-decomposing bacterial consortium.},
}
@article {pmid34059942,
year = {2021},
author = {Siebert, A and Hofmann, K and Staib, L and Doll, EV and Scherer, S and Wenning, M},
title = {Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {11},
pages = {4761-4773},
pmid = {34059942},
issn = {1432-0614},
support = {Projekt DEAL (German DEAL agreement)//Technische Universit&#xe4;t M&#xfc;nchen/ ; },
mesh = {Animals ; Cattle ; DNA, Bacterial/genetics ; Female ; *Microbiota ; *Milk ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy[®] PowerFood[®] Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. KEY POINTS: • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR.},
}
@article {pmid34059936,
year = {2022},
author = {Zhao, XF and Shu, WS and Hao, YQ},
title = {Seasonal Climate Variations Promote Bacterial α-Diversity in Soil.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {513-517},
pmid = {34059936},
issn = {1432-184X},
support = {31901113//National Natural Science Foundation of China/ ; 31901112//National Natural Science Foundation of China/ ; 2019M662951//China Postdoctoral Science Foundation/ ; 2019A1515011879//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Bacteria/genetics ; Seasons ; *Soil ; *Soil Microbiology ; Triticum ; },
abstract = {Ecological theory suggests that temporal environmental fluctuations can contribute greatly to diversity maintenance. Given bacteria's short generation time and rapid responses to environmental change, seasonal climate fluctuations are very likely to play an important role in maintaining the extremely high α-diversity of soil bacterial community, which has been unfortunately neglected in previous studies. Here, with in-depth analyses of two previously published soil bacterial datasets at global scale, we found that soil bacterial α-diversity was positively correlated with both seasonal variations of temperature and precipitation. Furthermore, piecewise structural equation models showed that seasonal variations of temperature or precipitation had weak but significant positive effect on soil bacterial α-diversity in each dataset. However, it is noteworthy that the importance of seasonal climate variations might be underestimated in the above analyses, due to the potential confounding factors (such as vegetation type) and the lack of sampling across seasons. As a supplement, we analyzed a previously published wheat cropland dataset with samples collected in both winter and the following summer across North China Plain. As expected, bacterial α-diversity was positively correlated with seasonal climate variations in the cropland dataset, and climate seasonality explained a larger proportion of variations in bacterial α-diversity. Collectively, these findings implied that fluctuation-dependent mechanisms of diversity maintenance presumably operate in soil bacterial communities. Based on existing evidence, we speculated that the storage effect may be the main mechanism responsible for diversity maintenance in soil bacterial community, but rigorous experimental tests are needed in the future.},
}
@article {pmid34058098,
year = {2021},
author = {Paredes, GF and Viehboeck, T and Lee, R and Palatinszky, M and Mausz, MA and Reipert, S and Schintlmeister, A and Maier, A and Volland, JM and Hirschfeld, C and Wagner, M and Berry, D and Markert, S and Bulgheresi, S and König, L},
title = {Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {e0118620},
pmid = {34058098},
issn = {2379-5077},
support = {P 28743/FWF_/Austrian Science Fund FWF/Austria ; P28953//Austrian Science Fund (FWF)/ ; P28743//Austrian Science Fund (FWF)/ ; DK plus grant W1257: Microbial Nitrogen Cycling//Austrian Science Fund (FWF)/ ; },
abstract = {Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on "Candidatus Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of [13]C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that "Ca. T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. IMPORTANCE Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of "Candidatus Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.},
}
@article {pmid34054786,
year = {2021},
author = {Guerrero-Cruz, S and Vaksmaa, A and Horn, MA and Niemann, H and Pijuan, M and Ho, A},
title = {Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {678057},
pmid = {34054786},
issn = {1664-302X},
abstract = {Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.},
}
@article {pmid34054772,
year = {2021},
author = {Trego, AC and McAteer, PG and Nzeteu, C and Mahony, T and Abram, F and Ijaz, UZ and O'Flaherty, V},
title = {Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {666584},
pmid = {34054772},
issn = {1664-302X},
abstract = {Advances in null-model approaches have resulted in a deeper understanding of community assembly mechanisms for a variety of complex microbiomes. One under-explored application is assembly of communities from the built-environment, especially during process disturbances. Anaerobic digestion for biological wastewater treatment is often underpinned by retaining millions of active granular biofilm aggregates. Flotation of granules is a major problem, resulting in process failure. Anaerobic aggregates were sampled from three identical bioreactors treating dairy wastewater. Microbiome structure was analysed using qPCR and 16S rRNA gene amplicon sequencing from DNA and cDNA. A comprehensive null-model approach quantified assembly mechanisms of floating and settled communities. Significant differences in diversity were observed between floating and settled granules, in particular, we highlight the changing abundances of Methanosaeta and Lactococcus. Both stochastic and deterministic processes were important for community assembly. Homogeneous selection was the primary mechanism for all categories, but dispersal processes also contributed. The lottery model was used to identify clade-level competition driving community assembly. Lottery "winners" were identified with different winners between floating and settled groups. Some groups changed their winner status when flotation occurred. Spirochaetaceae, for example, was only a winner in settled biomass (cDNA-level) and lost its winner status during flotation. Alternatively, Arcobacter butzerli gained winner status during flotation. This analysis provides a deeper understanding of changes that occur during process instabilities and identified groups which may be washed out-an important consideration for process control.},
}
@article {pmid34054757,
year = {2021},
author = {Rocha, FYO and Negrisoli Júnior, AS and de Matos, GF and Gitahy, PM and Rossi, CN and Vidal, MS and Baldani, JI},
title = {Endophytic Bacillus Bacteria Living in Sugarcane Plant Tissues and Telchin licus licus Larvae (Drury) (Lepidoptera: Castniidae): The Symbiosis That May Open New Paths in the Biological Control.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {659965},
pmid = {34054757},
issn = {1664-302X},
abstract = {Bacteria of the genus Bacillus can colonize endophytically and benefit several crops including the control of some pest orders. In view of the benefits provided by these microorganisms and in order to find out an efficient biotechnological control for the giant borer, our interest in studying the microorganisms in symbiosis with sugarcane and the giant borer has arisen, since there is no efficient chemical or biological control method for this pest. Therefore, endophytic Bacillus strains were isolated from three sugarcane niches (apoplast fluid, central internode cylinder and roots) and also from the giant borer larvae living inside sugarcane varieties grown in the Northeast region of Brazil. The taxonomical characterization (16S rRNA) of 157 Gram-positive isolates showed that 138 strains belonged to the Bacillus genus. The most representative species were phylogenetically closely related to B. megaterium (11.5%) followed by B. safensis (10.8%), B. cereus (8.9%), B. oleronius (8.9%), B. amyloliquefaciens (7.0%), and B. pacificus (6.4%). BOX-PCR analyses showed very distinct band pattern profiles suggesting a great diversity of Bacillus species within the sugarcane niches and the digestive tract, while the B. cereus group remained very closely clustered in the dendrogram. According to XRE biomarker analysis, eleven strains (FORCN005, 007, 008, 011, 012, 014, 067, 076, 092, 093, and 135) correspond to B. thuringiensis species. Additional studies using conserved genes (glp, gmk, pta, and tpi) indicated that most of these strains were phylogenetically closely related to B. thuringiensis and may be considered different subspecies. In conclusion, this study suggests that the culturable Bacillus species are greatly diversified within the plant niches and showed Bacillus species in the digestive tract of the giant borer for the first time. These results open new perspectives to understand the role and functions played by these microorganisms in symbiosis with this pest and also the possibility of developing an efficient biological control method for the giant borer using strains identified as the B. thuringiensis species.},
}
@article {pmid34053521,
year = {2021},
author = {Jang, MJ and Kim, SY and Ricke, SC and Rhee, MS and Kim, SA},
title = {Microbial ecology of alfalfa, radish, and rapeseed sprouts based on culture methods and 16S rRNA microbiome sequencing.},
journal = {Food research international (Ottawa, Ont.)},
volume = {144},
number = {},
pages = {110316},
doi = {10.1016/j.foodres.2021.110316},
pmid = {34053521},
issn = {1873-7145},
mesh = {*Brassica napus ; Colony Count, Microbial ; Food Microbiology ; Medicago sativa ; *Microbiota ; RNA, Ribosomal, 16S ; *Raphanus ; },
abstract = {Sprouts harbor high populations of bacteria and cause numerous foodborne disease outbreaks, yet little is known about their microbial composition. The present study aimed to define the microbiological ecology of sprouts using 16S rRNA microbiome sequencing and culture-dependent methods. Different types (radish, alfalfa, and rapeseed), brands (A, B, and C), and distribution routes (online and offline) of sprouts (n = 70) were considered for microbiome analysis, as well as quantitative (aerobic plate count and coliforms) and qualitative analyses (Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella Typhimurium). The aerobic plate count ranged from 7 to 8 CFU/g, and the coliforms ranged from 6 to 7 log CFU/g. Microbiome analysis revealed that Proteobacteria was the dominant phylum, accounting for 79.0% in alfalfa sprouts, 68.5% in rapeseed sprouts, and 61.9% in radish sprouts. Enterobacteriaceae was the dominant family in alfalfa sprouts (33.9%) and rapeseed sprouts (14.6%), while Moraxellaceae (11.9%) were prevalent on radish sprouts. The majority of the dominant genera were common in the environment, such as soil or water. Alfalfa sprouts yielded the lowest aerobic plate count but the highest relative abundance of Enterobacteriaceae compared to the other sprouts. These results could explain why alfalfa sprouts are a leading cause of sprout-related foodborne disease outbreaks. Alpha-diversity results (Chao1 and Shannon indices) suggested that species richness was greater on radish sprouts than the other sprout types. Beta-diversity results showed samples were clustered by types, indicating dissimilarity in microbial communities. However, the distribution route had a limited influence on microbial composition. The present study provides a comparative examination of the microbial profiles of sprouts. Microbiome analyses contribute to an in-depth understanding of the microbial ecology of sprouts, leading to potential control measures for ensuring food safety.},
}
@article {pmid34052880,
year = {2022},
author = {Fernández, LD and Seppey, CVW and Singer, D and Fournier, B and Tatti, D and Mitchell, EAD and Lara, E},
title = {Niche Conservatism Drives the Elevational Diversity Gradient in Major Groups of Free-Living Soil Unicellular Eukaryotes.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {459-469},
pmid = {34052880},
issn = {1432-184X},
mesh = {Biodiversity ; *Ciliophora/genetics ; Ecosystem ; Phylogeny ; *Soil ; },
abstract = {Ancestral adaptations to tropical-like climates drive most multicellular biogeography and macroecology. Observational studies suggest that this niche conservatism could also be shaping unicellular biogeography and macroecology, although evidence is limited to Acidobacteria and testate amoebae. We tracked the phylogenetic signal of this niche conservatism in far related and functionally contrasted groups of common soil protists (Bacillariophyta, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida) along a humid but increasingly cold elevational gradient in Switzerland. Protist diversity decreased, and the size of the geographic ranges of taxa increased with elevation and associated decreasing temperature (climate), which is consistent with a macroecological pattern known as the Rapoport effect. Bacillariophyta exhibited phylogenetically overdispersed communities assembled by competitive exclusion of closely related taxa with shared (conserved) niches. By contrast, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida exhibited phylogenetically clustered communities assembled by habitat filtering, revealing the coexistence of closely related taxa with shared (conserved) adaptations to cope with the humid but temperate to cold climate of the study site. Phylobetadiversity revealed that soil protists exhibit a strong phylogenetic turnover among elevational sites, suggesting that most taxa have evolutionary constraints that prevent them from colonizing the colder and higher sites of the elevation gradient. Our results suggest that evolutionary constraints determine how soil protists colonize climates departing from warm and humid conditions. We posit that these evolutionary constraints are linked to an ancestral adaptation to tropical-like climates, which limits their survival in exceedingly cold sites. This niche conservatism possibly drives their biogeography and macroecology along latitudinal and altitudinal climatic gradients.},
}
@article {pmid34052601,
year = {2021},
author = {Chandler, L and Harford, AJ and Hose, GC and Humphrey, CL and Chariton, A and Greenfield, P and Davis, J},
title = {Saline mine-water alters the structure and function of prokaryote communities in shallow groundwater below a tropical stream.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {284},
number = {},
pages = {117318},
doi = {10.1016/j.envpol.2021.117318},
pmid = {34052601},
issn = {1873-6424},
mesh = {Archaea/genetics ; Bacteria/genetics ; *Ecosystem ; *Groundwater ; Water ; },
abstract = {Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated putative functional processes were examined in a shallow sandy aquifer in a wet-dry tropical environment. The aquifer had a contaminated gradient of saline mine-water, which primarily consisted of elevated magnesium (Mg[2+]) and sulfate (SO4[2-]), although other major ions and trace metals were also present. Groundwaters were sampled from piezometers, approximately 2 m in depth, located in the creek channel upstream and downstream of the mine-water influence. Sampling occurred during the dry-season when only subsurface water flow was present. Next generation sequencing was used to analyse the prokaryote assemblages using 16S rDNA and metabolic functions were predicted with FAPROTAX. Significant changes in community composition and functional processes were observed with exposure to mine-waters. Communities in the exposed sites had significantly lower relative abundance of methanotrophs such as Methylococcaceae and methanogens (Methanobacteriaceae), but higher abundance in Nitrososphaeraceae, associated with nitrification, indicating potentially important changes in the biogeochemistry of the exposed sites. The changes were most strongly correlated with concentrations of SO4[2-], Mg[2+] and Na[+]. This knowledge allows an assessment of the risk of mine-water contamination to groundwater ecosystem function and aids mine-water management.},
}
@article {pmid34049069,
year = {2021},
author = {Lim, JH and Lee, CW and Bong, CW and Kudo, I},
title = {The impact of eutrophication towards selected bacterial process rates in tropical coastal waters.},
journal = {Marine pollution bulletin},
volume = {169},
number = {},
pages = {112524},
doi = {10.1016/j.marpolbul.2021.112524},
pmid = {34049069},
issn = {1879-3363},
mesh = {Bacteria ; *Bacterial Physiological Phenomena ; Carbon/analysis ; *Eutrophication ; Malaysia ; Nitrogen/analysis ; },
abstract = {The dissolved organic nutrient conditions and bacterial process rates at two tropical coastal sites in Peninsular Malaysia (Port Klang and Port Dickson) were initially studied in 2004-2005 period and later revisited in 2010-2011. We observed that dissolved organic nitrogen (DON) increased about two- and ten-fold at Port Klang and Port Dickson, respectively and resulted in a significant change in DOC:DON ratio (t ≥ 2.077, p < 0.05). Among the bacterial processes measured, bacterial respiration (BR) was lower in the 2010-2011 period at both stations (t ≥ 3.390, p < 0.01). BR also correlated to the DOC:DON ratio (R[2] ≥ 0.259, p < 0.01). The increase in substrate quality enabled the bacteria to respire less in the dissolved organic matter degradation. As a result, the average bacterial growth efficiency increased slightly in the 2010-2011 period.},
}
@article {pmid34039416,
year = {2021},
author = {Leung, MHY and Tong, X and Bøifot, KO and Bezdan, D and Butler, DJ and Danko, DC and Gohli, J and Green, DC and Hernandez, MT and Kelly, FJ and Levy, S and Mason-Buck, G and Nieto-Caballero, M and Syndercombe-Court, D and Udekwu, K and Young, BG and Mason, CE and Dybwad, M and Lee, PKH},
title = {Characterization of the public transit air microbiome and resistome reveals geographical specificity.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {112},
pmid = {34039416},
issn = {2049-2618},
support = {U01 DA053941/DA/NIDA NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; R21 AI129851/AI/NIAID NIH HHS/United States ; R01 NS076465/NS/NINDS NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; R25 EB020393/EB/NIBIB NIH HHS/United States ; },
mesh = {Bacteria/genetics ; Geography ; Hong Kong ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; },
abstract = {BACKGROUND: The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized.<br><br>RESULTS: City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes.<br><br>CONCLUSIONS: Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.},
}
@article {pmid34037999,
year = {2021},
author = {Petje, LM and Jensen, SA and Szikora, S and Sulzbacher, M and Bartosik, T and Pjevac, P and Hausmann, B and Hufnagl, K and Untersmayr, E and Fischer, L and Vyskocil, E and Eckl-Dorna, J and Jensen-Jarolim, E and Hofstetter, G and Afify, SM and Krenn, CG and Roth, GA and Rivelles, E and Hann, S and Roth-Walter, F},
title = {Functional iron-deficiency in women with allergic rhinitis is associated with symptoms after nasal provocation and lack of iron-sequestering microbes.},
journal = {Allergy},
volume = {76},
number = {9},
pages = {2882-2886},
pmid = {34037999},
issn = {1398-9995},
mesh = {Allergens ; *Anemia, Iron-Deficiency ; Female ; Humans ; Iron ; Nasal Mucosa ; Nasal Provocation Tests ; Nose ; *Rhinitis, Allergic/diagnosis ; },
}
@article {pmid34031701,
year = {2022},
author = {Ao, L and Zhao, M and Li, X and Sun, G},
title = {Different Urban Forest Tree Species Affect the Assembly of the Soil Bacterial and Fungal Community.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {447-458},
pmid = {34031701},
issn = {1432-184X},
support = {41701289//National Natural Science Foundation of China/ ; 31870373//National Natural Science Foundation of China/ ; 2018M640287//Postdoctoral Research Foundation of China/ ; },
mesh = {China ; Forests ; *Microbiota ; *Mycobiome ; Soil/chemistry ; Soil Microbiology ; Trees ; },
abstract = {The selection of tree species used for the afforestation of urban forests is very important for maintaining the urban ecosystem, while soil microbe is one of the driving factors of material cycling in the urban forest ecosystem and for health of forests. In this study, the characteristics of surface soil bacterial and fungal community structure in four urban forests (primarily composed of Fraxinus mandshurica (Fm), Quercus mongolica (Qm), Pinus sylvestris var. mongolica (Ps), and Pinus tabulaeformis var. Mukdensis (Pt) as the main dominant tree species, respectively) were investigated by high-throughput sequencing. Our results showed that the alpha diversity of the soil microbial community in the Fm urban forest was the highest, while the lowest was in the Ps urban forest. In the bacterial community, Proteobacteria was the most predominant phylum in soils from Fm, Ps, and Pt urban forests. The most relatively abundant phylum of the Qm urban forest soil was Acidobacteria. The relative abundances of the bacterial communities at the genus level in the soil of four urban forests were significantly different. The soil bacterial communities in Ps and Pt urban forests were more similar, and Qm and Fm were also more similar. In the fungal community, Basidiomycota was the most predominant phylum in soils from Qm, Ps, and Pt urban forests. The phylum with the greatest relative abundance in the Fm urban forest soil was Ascomycota. There were differences in the fungal community between Qm, Fm, Ps, and Pt urban forests. Soil microbial community composition was affected by environmental factors: soil bacterial and fungal community compositions were significantly related to soil electrical conductivity (EC), alkali hydrolysable nitrogen (AHN), total nitrogen (TN), and total phosphorus (TP). In conclusion, the soil microbial community structure was related to both forest's tree species and soil properties.},
}
@article {pmid34030967,
year = {2021},
author = {Yang, Y},
title = {Emerging Patterns of Microbial Functional Traits.},
journal = {Trends in microbiology},
volume = {29},
number = {10},
pages = {874-882},
doi = {10.1016/j.tim.2021.04.004},
pmid = {34030967},
issn = {1878-4380},
mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Ecosystem ; Environment ; Phenotype ; },
abstract = {Functional traits are measurable characteristics that affect an organism's fitness under certain environmental conditions. The use of functional traits in microbial ecology holds great promise for improving our ability to develop biogeochemical models and predict ecosystem responses to global changes. Notably, functional traits could be decoupled from taxonomic relatedness, owing to horizontal gene transfer among microorganisms and adaptive evolution. In recent years, our knowledge about microbial functional traits has been substantially enhanced, thereby revealing the multitude of ecological processes in driving community assembly and dynamics. Here, I summarize the emerging patterns of how microbial functional traits respond to changing environments, which considerably differ from better-studied microbial taxonomy. I use niche and neutral theories to explain microbial functional traits. Finally, I highlight future challenges to analyze, elucidate, and utilize functional traits in microbial ecology.},
}
@article {pmid34030400,
year = {2021},
author = {Hildebrandt, L and Zimmermann, T and Primpke, S and Fischer, D and Gerdts, G and Pröfrock, D},
title = {Comparison and uncertainty evaluation of two centrifugal separators for microplastic sampling.},
journal = {Journal of hazardous materials},
volume = {414},
number = {},
pages = {125482},
doi = {10.1016/j.jhazmat.2021.125482},
pmid = {34030400},
issn = {1873-3336},
abstract = {For commonly applied microplastic sampling approaches based on filtration, high throughput and no size-discrimination are conflicting goals. Therefore, we propose two efficient centrifugal separators for small microplastic sampling, namely the utilization of a hydrocyclone as well as a continuous flow centrifuge. Thorough method optimization was followed by application in an extensive sampling study to investigate the separators' retention behavior for particulate plastics from estuarine waters. Microplastic concentrations ranged from 193 to 2072 particles m[-3]. The most dominant identified polymer types were polypropylene, acrylates, polyvinyl chloride and polyethylene. More than 95% of particles were < 100 µm. For the first time in microplastic research, an expanded uncertainty was calculated according to the "Guide to the expression of Uncertainty in Measurement" (JCGM 100:2008). Bottom-up uncertainty evaluation revealed the different sampling methods (~ 44%), sample replicates (~ 26%) and the different detection techniques (~ 16%) as the major sources of uncertainty. Depending on the number of particles detected in the samples, the relative expanded uncertainty (Urel (k = 2)) ranged from 24% up to > 200% underpinning tremendous importance of sound uncertainty evaluation. Our results indicate that scientist should rethink many "observed patterns" in the literature due to being insignificant and herewith not real.},
}
@article {pmid34030262,
year = {2021},
author = {Glodowska, M and Schneider, M and Eiche, E and Kontny, A and Neumann, T and Straub, D and Berg, M and Prommer, H and Bostick, BC and Nghiem, AA and Kleindienst, S and Kappler, A},
title = {Fermentation, methanotrophy and methanogenesis influence sedimentary Fe and As dynamics in As-affected aquifers in Vietnam.},
journal = {The Science of the total environment},
volume = {779},
number = {},
pages = {146501},
doi = {10.1016/j.scitotenv.2021.146501},
pmid = {34030262},
issn = {1879-1026},
mesh = {*Arsenic/analysis ; Fermentation ; Ferric Compounds ; *Groundwater ; Humans ; Oxidation-Reduction ; Vietnam ; *Water Pollutants, Chemical/analysis ; },
abstract = {High arsenic (As) concentrations in groundwater are a worldwide problem threatening the health of millions of people. Microbial processes are central in the (trans)formation of the As-bearing ferric and ferrous minerals, and thus regulate dissolved As levels in many aquifers. Mineralogy, microbiology and dissolved As levels can vary sharply within aquifers, making high-resolution measurements particularly valuable in understanding the linkages between them. We conducted a high spatial resolution geomicrobiological study in combination with analysis of sediment chemistry and mineralogy in an alluvial aquifer system affected by geogenic As in the Red River delta in Vietnam. Microbial community analysis revealed a dominance of fermenters, methanogens and methanotrophs whereas sediment mineralogy along a 46 m deep core showed a diversity of Fe minerals including poorly crystalline Fe (II/III) and Fe(III) (oxyhydr)oxides such as goethite, hematite, and magnetite, but also the presence of Fe(II)-bearing carbonates and sulfides which likely formed as a result of microbially driven organic carbon (OC) degradation. A potential important role of methane (CH4) as electron donor for reductive Fe mineral (trans)formation was supported by the high abundance of Candidatus Methanoperedens, a known Fe(III)-reducing methanotroph. Overall, these results imply that OC turnover including fermentation, methanogenesis and CH4 oxidation are important mechanisms leading to Fe mineral (trans)formation, dissolution and precipitation, and thus indirectly affecting As mobility by changing the Fe-mineral inventory.},
}
@article {pmid34029817,
year = {2021},
author = {Zhang, Y and Chen, M and Zhao, YY and Zhang, AY and Peng, DH and Lu, F and Dai, CC},
title = {Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern.},
journal = {The Science of the total environment},
volume = {788},
number = {},
pages = {147794},
doi = {10.1016/j.scitotenv.2021.147794},
pmid = {34029817},
issn = {1879-1026},
mesh = {Animals ; Astacoidea ; China ; *Oryza ; *Soil ; Soil Microbiology ; },
abstract = {The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.},
}
@article {pmid34025695,
year = {2021},
author = {Li, T and Wu, S and Yang, W and Selosse, MA and Gao, J},
title = {How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {647114},
pmid = {34025695},
issn = {1664-462X},
abstract = {Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.},
}
@article {pmid34025597,
year = {2021},
author = {Suominen, S and van Vliet, DM and Sánchez-Andrea, I and van der Meer, MTJ and Sinninghe Damsté, JS and Villanueva, L},
title = {Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {628301},
pmid = {34025597},
issn = {1664-302X},
abstract = {Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of [13]C and/or [15]N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.},
}
@article {pmid34025590,
year = {2021},
author = {You, Y and Aho, K and Lohse, KA and Schwabedissen, SG and Ledbetter, RN and Magnuson, TS},
title = {Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {569791},
pmid = {34025590},
issn = {1664-302X},
support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; },
abstract = {Numerous studies have examined bacterial communities in biological soil crusts (BSCs) associated with warm arid to semiarid ecosystems. Few, however, have examined bacterial communities in BSCs associated with cold steppe ecosystems, which often span a wide range of climate conditions and are sensitive to trends predicted by relevant climate models. Here, we utilized Illumina sequencing to examine BSC bacterial communities with respect to climatic gradients (elevation), land management practices (grazing vs. non-grazing), and shrub/intershrub patches in a cold sagebrush steppe ecosystem in southwestern Idaho, United States. Particular attention was paid to shifts in bacterial community structure and composition. BSC bacterial communities, including keystone N-fixing taxa, shifted dramatically with both elevation and shrub-canopy microclimates within elevational zones. BSC cover and BSC cyanobacteria abundance were much higher at lower elevation (warmer and drier) sites and in intershrub areas. Shrub-understory BSCs were significantly associated with several non-cyanobacteria diazotrophic genera, including Mesorhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. High elevation (wetter and colder) sites had distinct, highly diverse, but low-cover BSC communities that were significantly indicated by non-cyanobacterial diazotrophic taxa including families in the order Rhizobiales and the family Frankiaceae. Abiotic soil characteristics, especially pH and ammonium, varied with both elevation and shrub/intershrub level, and were strongly associated with BSC community composition. Functional inference using the PICRUSt pipeline identified shifts in putative N-fixing taxa with respect to both the elevational gradient and the presence/absence of shrub canopy cover. These results add to current understanding of biocrust microbial ecology in cold steppe, serving as a baseline for future mechanistic research.},
}
@article {pmid34023922,
year = {2022},
author = {Kaur, M and Kumari, A and Singh, R},
title = {The Indigenous Volatile Inhibitor 2-Methyl-2-butene Impacts Biofilm Formation and Interspecies Interaction of the Pathogenic Mucorale Rhizopus arrhizus.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {506-512},
pmid = {34023922},
issn = {1432-184X},
support = {ECR/2016/000102//Early Career Research Award, Science and Engineering Research Board (SERB), Department of Science and Technology (DST), Govt. of India/ ; DST/INSPIRE Faculty Award/2013/DST/INSPIRE/04/2013/000925//DST-INSPIRE Faculty Scheme, Govt. of India/ ; },
mesh = {Alkenes ; Biofilms ; *Rhizopus ; *Rhizopus oryzae ; Staphylococcus aureus ; },
abstract = {2-Methyl-2-butene has recently been reported to be a quorum-based volatile self-inhibitor of spore germination and growth in pathogenic Mucorale Rhizopus arrhizus. The present study aimed to elucidate if this compound can influence R. arrhizus biofilm formation and interspecies interaction. The compound was found to significantly decrease R. arrhizus biofilm formation (p < 0.001), with nearly 25% and 50% lesser biomass in the biofilms cultured with exposure to 4 and 32 µg/ml of 2-methyl-2-butene, respectively. The growth of pre-formed biofilms was also impacted, albeit to a lesser extent. Additionally, 2-methyl-2-butene was found to self-limit R. arrhizus growth during interspecies interaction with Staphylococcus aureus and was detected at a substantially greater concentration in the headspace of co-cultures (2338.75 µg/ml) compared with monocultures (69.52 µg/ml). Some of the C5 derivatives of this compound (3-methyl-1-butanol, 2-methyl-2-butanol, and 3-methyl-1-butyne) were also observed to partially mimic its action, such as inhibition of spore germination, but did not impact R. arrhizus biofilm formation. Finally, the treated R. arrhizus displayed changes in fungal morphology suggestive of cytoskeletal alterations, such as filopodia formation, blebs, increased longitudinal folds and/or corrugations, and finger-like and sheet-like surface protrusions, depending upon the concentration of the compound(s) and the planktonic or biofilm growth mode.},
}
@article {pmid34021563,
year = {2021},
author = {Wright, ES and Gupta, R and Vetsigian, KH},
title = {Multi-stable bacterial communities exhibit extreme sensitivity to initial conditions.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {6},
pages = {},
doi = {10.1093/femsec/fiab073},
pmid = {34021563},
issn = {1574-6941},
mesh = {Bacteria/genetics ; *Microbiota ; *Models, Biological ; Population Dynamics ; },
abstract = {Microbial communities can have dramatically different compositions even among similar environments. This might be due to the existence of multiple alternative stable states, yet there exists little experimental evidence supporting this possibility. Here, we gathered a large collection of absolute population abundances capturing population dynamics in one- to four-strain communities of soil bacteria with a complex life cycle in a feast-or-famine environment. This dataset led to several observations: (i) some pairwise competitions resulted in bistability with a separatrix near a 1:1 initial ratio across a range of population densities; (ii) bistability propagated to multi-stability in multispecies communities; and (iii) replicate microbial communities reached different stable states when starting close to initial conditions separating basins of attraction, indicating finite-sized regions where the dynamics are unpredictable. The generalized Lotka-Volterra equations qualitatively captured most competition outcomes but were unable to quantitatively recapitulate the observed dynamics. This was partly due to complex and diverse growth dynamics in monocultures that ranged from Allee effects to nonmonotonic behaviors. Overall, our results highlight that multi-stability might be generic in multispecies communities and, combined with ecological noise, can lead to unpredictable community assembly, even in simple environments.},
}
@article {pmid34020935,
year = {2021},
author = {Huang, YM and Straub, D and Blackwell, N and Kappler, A and Kleindienst, S},
title = {Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {15},
pages = {e0049621},
pmid = {34020935},
issn = {1098-5336},
mesh = {Autotrophic Processes ; Gallionellaceae/genetics/*metabolism ; Gammaproteobacteria/genetics/*metabolism ; Gene Expression Profiling ; Heterotrophic Processes ; Iron/*metabolism ; Metagenome ; Metagenomics ; Nitrates/*metabolism ; Oxidation-Reduction ; Proteomics ; },
abstract = {Nitrate reduction coupled to Fe(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing Fe(II)-oxidizing bacteria are rare, and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics, and metaproteomics) to the nitrate-reducing Fe(II)-oxidizing enrichment culture KS growing under autotrophic or heterotrophic conditions and originating from freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of ≥95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in Fe(II) oxidation (e.g., mtoAB, cyc2, and mofA), denitrification (e.g., napGHI), and oxidative phosphorylation (e.g., respiratory chain complexes I to V) along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be performed by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb3- and aa3-type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and Fe(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments. IMPORTANCE Nitrate-reducing Fe(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing Fe(II)-oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of study is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to Fe(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic, and metaproteomic analyses of culture KS and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key Fe(II) oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to Fe(II) oxidation is not performed by an individual strain but is a cooperation of at least two members of the bacterial community in culture KS. These findings serve as a foundation for our understanding of nitrate-reducing Fe(II)-oxidizing bacteria in the environment.},
}
@article {pmid34020712,
year = {2021},
author = {Silva, DP and Villela, HDM and Santos, HF and Duarte, GAS and Ribeiro, JR and Ghizelini, AM and Vilela, CLS and Rosado, PM and Fazolato, CS and Santoro, EP and Carmo, FL and Ximenes, DS and Soriano, AU and Rachid, CTCC and Vega Thurber, RL and Peixoto, RS},
title = {Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {118},
pmid = {34020712},
issn = {2049-2618},
mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Petroleum ; *Petroleum Pollution ; *Probiotics ; },
abstract = {BACKGROUND: Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities.<br><br>RESULTS: The selected multi-domain microbial&#xa0;consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome.<br><br>CONCLUSIONS: Our&#xa0;results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and&#xa0;their associated microbiome&#xa0;than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs. Video abstract.},
}
@article {pmid34017060,
year = {2021},
author = {Kim, JH and Kim, K and Kim, W},
title = {Gut microbiota restoration through fecal microbiota transplantation: a new atopic dermatitis therapy.},
journal = {Experimental &amp; molecular medicine},
volume = {53},
number = {5},
pages = {907-916},
pmid = {34017060},
issn = {2092-6413},
mesh = {Animals ; Antibodies/pharmacology ; Biomarkers ; Dermatitis, Atopic/etiology/*therapy ; Disease Management ; Disease Models, Animal ; Disease Susceptibility ; Fatty Acids, Volatile/metabolism ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/drug effects/immunology ; Immunoglobulin E/blood/immunology ; Immunomodulation ; Lymphocyte Count ; Metagenome ; Metagenomics ; Mice ; T-Lymphocyte Subsets/immunology/metabolism ; Treatment Outcome ; },
abstract = {The pathogenesis of atopic dermatitis (AD) involves complex factors, including gut microbiota and immune modulation, which remain poorly understood. The aim of this study was to restore gut microbiota via fecal microbiota transplantation (FMT) to ameliorate AD in mice. FMT was performed using stool from donor mice. The gut microbiota was characterized via 16S rRNA sequencing and analyzed using Quantitative Insights into Microbial Ecology 2 with the DADA2 plugin. Gut metabolite levels were determined by measuring fecal short-chain fatty acid (SCFA) contents. AD-induced allergic responses were evaluated by analyzing blood parameters (IgE levels and eosinophil percentage, eosinophil count, basophil percentage, and monocyte percentage), the levels of Th1 and Th2 cytokines, dermatitis score, and the number of mast cells in the ileum and skin tissues. Calprotectin level was measured to assess gut inflammation after FMT. FMT resulted in the restoration of gut microbiota to the donor state and increases in the levels of SCFAs as gut metabolites. In addition, FMT restored the Th1/Th2 balance, modulated Tregs through gut microbiota, and reduced IgE levels and the numbers of mast cells, eosinophils, and basophils. FMT is associated with restoration of gut microbiota and immunologic balance (Th1/Th2) along with suppression of AD-induced allergic responses and is thus a potential new therapy for AD.},
}
@article {pmid34016155,
year = {2021},
author = {LaMartina, EL and Mohaimani, AA and Newton, RJ},
title = {Urban wastewater bacterial communities assemble into seasonal steady states.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {116},
pmid = {34016155},
issn = {2049-2618},
support = {R01 AI091829/AI/NIAID NIH HHS/United States ; R01AI091829/NH/NIH HHS/United States ; },
mesh = {Ecosystem ; Humans ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Sewage ; *Wastewater ; },
abstract = {BACKGROUND: Microorganisms in urban sanitary sewers exhibit community properties that suggest sewers are a novel ecosystem. Sewer microorganisms present both an opportunity as a control point for wastewater treatment and a risk to human health. If treatment processes are to be improved and health risks quantified, then it is necessary to understand microbial distributions and dynamics within this community. Here, we use 16S rRNA gene sequencing to characterize raw influent wastewater bacterial communities in a 5-year time series from two wastewater treatment plants in Milwaukee, WI; influent wastewater from 77 treatment plants across the USA; and wastewater in 12 Milwaukee residential sewers.<br><br>RESULTS: In Milwaukee, we find that in transit from residences to treatment plants, the human bacterial component of wastewater decreases in proportion and exhibits stochastic temporal variation. In contrast, the resident sewer community increases in abundance during transit and cycles seasonally according to changes in wastewater temperature. The result is a bacterial community that assembles into two distinct community states each year according to the extremes in wastewater temperature. Wastewater bacterial communities from other northern US cities follow temporal trends that mirror those in Milwaukee, but southern US cities have distinct community compositions and differ in their seasonal patterns.<br><br>CONCLUSIONS: Our findings provide evidence that environmental conditions associated with seasonal change and climatic differences related to geography predictably structure the bacterial communities residing in below-ground sewer pipes. Video abstract.},
}
@article {pmid34016152,
year = {2021},
author = {Dwużnik-Szarek, D and Mierzejewska, EJ and Rodo, A and Goździk, K and Behnke-Borowczyk, J and Kiewra, D and Kartawik, N and Bajer, A},
title = {Monitoring the expansion of Dermacentor reticulatus and occurrence of canine babesiosis in Poland in 2016-2018.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {267},
pmid = {34016152},
issn = {1756-3305},
mesh = {Animal Distribution ; Animals ; Babesia/genetics/isolation &amp; purification/physiology ; Babesiosis/epidemiology/parasitology/*transmission ; Dermacentor/*parasitology/physiology ; Dog Diseases/epidemiology/parasitology/*transmission ; Dogs ; Female ; Male ; Poland/epidemiology ; Seasons ; Tick Infestations/epidemiology/parasitology/*veterinary ; Tick-Borne Diseases/epidemiology/parasitology/transmission/*veterinary ; },
abstract = {BACKGROUND: The significance of tick-borne diseases has increased considerably in recent years. Because of the unique distribution of the tick species Dermacentor reticulatus in Poland, comprising two expanding populations, Eastern and Western that are separated by a Dermacentor-free zone, it is important to conduct studies on the process of tick expansion and emergence of canine babesiosis. The main aim of the current study was to monitor the expansion of D. reticulatus populations from spring 2016 to autumn 2018 to determine (1) the actual geographical range of this tick species, and (2) and the seasonal/annual shift in range limits and changes in distance between Western and Eastern populations of ticks (the size of the non-endemic area).<br><br>METHODS: Ticks were collected in spring/autumn during a 3-year study. From each season and year at least three pairs of sites from the Western and Eastern populations were selected. Then the mean distance between paired sites was calculated for each season and year. We collected and analyzed data from veterinary clinics on the number of canine babesiosis cases treated in the clinic during a whole year (2018).<br><br>RESULTS: Accordingly, further expansion of the two D. reticulatus populations was recorded, mainly along river basins. Marked colonization of the gap zone was observed, with a mean annual shift in the range of 2.5-10 km and a steadily decreasing distance between the two tick populations. The occurrence of babesiosis in different regions revealed low numbers of cases in Western Poland (19 cases/year) and the gap area (only 7 cases/year) and high incidence (up to 250 cases/1000 dogs) and fatality (total 3.65%) in Central and Eastern Poland. Strong associations were found geographically between tick and babesiosis occurrence and temporally in the seasonal patterns of occurrence of ticks and outbreaks of babesiosis.<br><br>CONCLUSIONS: We documented the shift in range limits and continued process of colonization of the gap zone accompanied by the emergence of canine babesiosis in the Eastern expansion zone. Updated maps of the distribution of ticks and occurrence of babesiosis in different regions of Poland have allowed us to predict of the emergence of pathogens vectored by D. reticulatus. Incidence (per 1000 dogs) of canine babesiosis in veterinary clinics by current range of D. reticulatus.},
}
@article {pmid34014937,
year = {2021},
author = {Tibatá, VM and Sanchez, A and Palmer-Young, E and Junca, H and Solarte, VM and Madella, S and Ariza, F and Figueroa, J and Corona, M},
title = {Africanized honey bees in Colombia exhibit high prevalence but low level of infestation of Varroa mites and low prevalence of pathogenic viruses.},
journal = {PloS one},
volume = {16},
number = {5},
pages = {e0244906},
pmid = {34014937},
issn = {1932-6203},
mesh = {Animals ; Bees/*microbiology/virology ; Colombia ; Insect Viruses/*pathogenicity ; Varroidae/*pathogenicity ; },
abstract = {The global spread of the ectoparasitic mite Varroa destructor has promoted the spread and virulence of highly infectious honey bee viruses. This phenomenon is considered the leading cause for the increased number of colony losses experienced by the mite-susceptible European honey bee populations in the Northern hemisphere. Most of the honey bee populations in Central and South America are Africanized honey bees (AHBs), which are considered more resistant to Varroa compared to European honey bees. However, the relationship between Varroa levels and the spread of honey bee viruses in AHBs remains unknown. In this study, we determined Varroa prevalence and infestation levels as well as the prevalence of seven major honey bee viruses in AHBs from three regions of Colombia. We found that although Varroa exhibited high prevalence (92%), its infestation levels were low (4.5%) considering that these populations never received acaricide treatments. We also detected four viruses in the three regions analyzed, but all colonies were asymptomatic, and virus prevalence was considerably lower than those found in other countries with higher rates of mite-associated colony loss (DWV 19.88%, BQCV 17.39%, SBV 23.4%, ABPV 10.56%). Our findings indicate that AHBs possess a natural resistance to Varroa that does not prevent the spread of this parasite among their population, but restrains mite population growth and suppresses the prevalence and pathogenicity of mite-associated viruses.},
}
@article {pmid34013437,
year = {2021},
author = {Romero-Olivares, AL and Morrison, EW and Pringle, A and Frey, SD},
title = {Correction to: Linking Genes to Traits in Fungi.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {156},
doi = {10.1007/s00248-021-01776-x},
pmid = {34013437},
issn = {1432-184X},
}
@article {pmid34009446,
year = {2021},
author = {Antunes, VDC and Freitag, D and Serrato, RV},
title = {Differential exopolysaccharide production and composition by Herbaspirillum strains from diverse ecological environments.},
journal = {Archives of microbiology},
volume = {203},
number = {7},
pages = {3883-3892},
pmid = {34009446},
issn = {1432-072X},
mesh = {*Bacteria/metabolism ; *Environment ; *Herbaspirillum/chemistry/genetics/metabolism ; *Polysaccharides, Bacterial/biosynthesis/chemistry ; },
abstract = {Bacteria belonging to the genus Herbaspirillum are found in many different ecological niches. Some species are typically endophytic, while others were reported as free-living organisms that occupy various environments. Also, opportunistic herbaspirilli have been found infecting humans affected by several diseases. We have analyzed the production of exopolysaccharides (EPS) by Herbaspirillum strains isolated from different sources and with distinct ecological characteristics. The monosaccharide composition was determined for the EPS obtained for selected strains including free-living, plant-associated and clinical isolates, and the relationship with the ecological niches occupied by Herbaspirillum spp. is proposed.},
}
@article {pmid34008895,
year = {2021},
author = {Ketchum, RN and Smith, EG and Vaughan, GO and McParland, D and Al-Mansoori, N and Burt, JA and Reitzel, AM},
title = {Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients.},
journal = {Molecular ecology},
volume = {30},
number = {15},
pages = {3869-3881},
doi = {10.1111/mec.15990},
pmid = {34008895},
issn = {1365-294X},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Microbiota/genetics ; Sea Urchins ; Seasons ; Temperature ; },
abstract = {Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species' range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20℃ - 37℃) and is connected to the Gulf of Oman which experiences more typical oceanic conditions (<32℃ in the summer). This system is an informative model for understanding how symbiotic microbial assemblages respond to thermal variation across temporal and spatial scales. Here, we elucidate the role of temperature on the microbial gut community of the sea urchin Echinometra sp. EZ and identify microbial taxa that are tightly correlated with the thermal environment. We generated two independent datasets with a high degree of geographic and temporal resolution. The results show that microbial communities vary across thermally variable habitats, display temporal shifts that correlate with temperature, and can become more disperse as temperatures rise. The relative abundances of several ASVs significantly correlate with temperature in both independent datasets despite the >300 km distance between the furthest sites and the extreme seasonal variations. Notably, over 50% of the temperature predictive ASVs identified from the two datasets belonged to the family Vibrionaceae. Together, our results identify temperature as a robust predictor of community-level variation and highlight specific microbial taxa putatively involved in the response to thermal environment.},
}
@article {pmid34006626,
year = {2021},
author = {Hwang, Y and Rahlff, J and Schulze-Makuch, D and Schloter, M and Probst, AJ},
title = {Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {},
pmid = {34006626},
issn = {2379-5077},
abstract = {Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.},
}
@article {pmid34003315,
year = {2022},
author = {Kim, J and Heo, YM and Yun, J and Lee, H and Kim, JJ and Kang, H},
title = {Changes in Archaeal Community and Activity by the Invasion of Spartina anglica Along Soil Depth Profiles of a Coastal Wetland.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {436-446},
pmid = {34003315},
issn = {1432-184X},
support = {2019R1A6A3A01091184//Ministry of Education (KR)/ ; 2020R1I1A2072824//Ministry of Education (KR)/ ; 2018K2A9A1A01090455, 2019K1A3A1A74107424, 2019K1A3A1A80113041//Ministry of Science and ICT (KR)/ ; 20170318//Ministry of Oceans and Fisheries (KR)/ ; 2019H1A2A1076239//Ministry of Education/ ; },
mesh = {Archaea ; Ecosystem ; Introduced Species ; Poaceae/physiology ; *Soil ; *Wetlands ; },
abstract = {Invasion of Spartina spp. in tidal salt marshes may affect the function and characteristics of the ecosystem. Previous studies reported that the invasion alters biogeochemical and microbial processes in marsh ecosystems, yet our knowledge of changing archaeal community due to the invasion is still limited, whereas archaeal communities play a pivotal role in biogeochemical cycles within highly reduced marsh soils. In this study, we aimed to illustrate the influences of the Spartina anglica invasion on soil archaeal community and the depth profile of the influences. The relative abundance of archaeal phyla demonstrated that the invasion substantially shifted the characteristics of tidal salt marsh from marine to terrestrial soil only in surface layer, while the influences indirectly propagated to the deeper soil layer. In particular, two archaeal phyla, Asgardaeota and Diapherotrites, were strongly influenced by the invasion, indicating a shift from marine to terrestrial archaeal communities. The shifts in soil characteristics spread to the deeper soil layer that results in indirect propagation of the influences of the invasion down to the deeper soil, which was underestimated in previous studies. The changes in the concentration of dissolved organic carbon and salinity were the substantial regulating factors for that. Therefore, changes in biogeochemical and microbial characteristics in the deep soil layer, which is below the root zone of the invasive plant, should be accounted for a more accurate illustration of the consequences of the invasion.},
}
@article {pmid33993638,
year = {2021},
author = {Ng, CK and Putra, SL and Kennerley, J and Habgood, R and Roy, RA and Raymond, JL and Thompson, IP and Huang, WE},
title = {Genetic engineering biofilms in situ using ultrasound-mediated DNA delivery.},
journal = {Microbial biotechnology},
volume = {14},
number = {4},
pages = {1580-1593},
pmid = {33993638},
issn = {1751-7915},
support = {SGRF-2017-471//Commonwealth Scholarship Commission/ ; EP/M002403/1//Engineering and Physical Sciences Research Council/ ; EP/N009746/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {*Bioelectric Energy Sources ; Biofilms ; DNA ; Genetic Engineering ; *Shewanella/genetics ; },
abstract = {The ability to directly modify native and established biofilms has enormous potential in understanding microbial ecology and application of biofilm in 'real-world' systems. However, efficient genetic transformation of established biofilms at any scale remains challenging. In this study, we applied an ultrasound-mediated DNA delivery (UDD) technique to introduce plasmid to established non-competent biofilms in situ. Two different plasmids containing genes coding for superfolder green fluorescent protein (sfGFP) and the flavin synthesis pathway were introduced into established bacterial biofilms in microfluidic flow (transformation efficiency of 3.9 ± 0.3 × 10[-7] cells in biofilm) and microbial fuel cells (MFCs), respectively, both employing UDD. Gene expression and functional effects of genetically modified bacterial biofilms were observed, where some cells in UDD-treated Pseudomonas putida UWC1 biofilms expressed sfGFP in flow cells and UDD-treated Shewanella oneidensis MR-1 biofilms generated significantly (P < 0.05) greater (61%) bioelectricity production (21.9 ± 1.2 µA cm[-2]) in MFC than a wild-type control group (~ 13.6 ± 1.6 µA cm[-2]). The effects of UDD were amplified in subsequent growth under selection pressure due to antibiotic resistance and metabolism enhancement. UDD-induced gene transfer on biofilms grown in both microbial flow cells and MFC systems was successfully demonstrated, with working volumes of 0.16 cm[3] and 300 cm[3] , respectively, demonstrating a significant scale-up in operating volume. This is the first study to report on a potentially scalable direct genetic engineering method for established non-competent biofilms, which can be exploited in enhancing their capability towards environmental, industrial and medical applications.},
}
@article {pmid33992330,
year = {2021},
author = {Battistelli, N and Perpetuini, G and Piva, A and Pepe, A and Sidari, R and Wache, Y and Tofalo, R},
title = {Cultivable microbial ecology and aromatic profile of "mothers" for Vino cotto wine production.},
journal = {Food research international (Ottawa, Ont.)},
volume = {143},
number = {},
pages = {110311},
doi = {10.1016/j.foodres.2021.110311},
pmid = {33992330},
issn = {1873-7145},
mesh = {Fermentation ; Hanseniaspora ; Metschnikowia ; Saccharomycetales ; *Wine/analysis ; },
abstract = {The aim of the present study was to assess the cultivable microbiota of "mothers" of Vino cotto collected from production of different years 1890, 1895, 1920, 1975, 2008. A total of 73 yeasts and 81 bacteria were isolated. Starmerella lactis-condensi, Starmerella bacillaris, Hanseniaspora uvarum, Saccharomyces cerevisiae, Hanseniaspora guillermondi and Metschnikowia pulcherrima were identified. Bacteria isolates belonged to lactic acid bacteria (Lactiplantibacillus plantarum and Pediococcus pentosaceus) and acetic acid bacteria (Gluconobacter oxydans). Remarkable biodiversity was observed for Starm. bacillaris, as well as L. plantarum and G. oxydans. Organic acids and volatile compounds were also determined. Malic and succinic acids were the main ones with values ranging from 8.49 g/L to 11.76 g/L and from 4.15 g/L to 7.73 g/L respectively, while citric acid was present at low concentrations (<0.2 g/L) in all samples. Esters and higher alcohols were the main volatile compounds detected followed by alkanes. This study permits to better understand the microbial communities associated to this product and could be considered a starting point for the definition of tailored starter cultures to improve the quality of Vino cotto preserving its typical traits.},
}
@article {pmid33990304,
year = {2021},
author = {Hartwick, MA and Berenson, A and Whistler, CA and Naumova, EN and Jones, SH},
title = {The Seasonal Microbial Ecology of Plankton and Plankton-Associated Vibrio parahaemolyticus in the Northeast United States.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {15},
pages = {e0297320},
pmid = {33990304},
issn = {1098-5336},
mesh = {Animals ; Bays/*microbiology ; *Microbial Interactions ; New England ; *Phytoplankton ; Seasons ; Seawater/microbiology ; *Vibrio parahaemolyticus ; Water Microbiology ; *Zooplankton ; },
abstract = {Microbial ecology studies have proven to be important resources for improving infectious disease response and outbreak prevention. Vibrio parahaemolyticus is an ongoing source of shellfish-borne food illness in the Northeast United States, and there is keen interest in understanding the environmental conditions that coincide with V. parahaemolyticus disease risk, in order to aid harvest management and prevent further illness. Zooplankton and chitinous phytoplankton are associated with V. parahaemolyticus dynamics elsewhere; however, this relationship is undetermined for the Great Bay estuary (GBE), an important emerging shellfish growing region in the Northeast United States. A comprehensive evaluation of the microbial ecology of V. parahaemolyticus associated with plankton was conducted in the GBE using 3 years of data regarding plankton community, nutrient concentration, water quality, and V. parahaemolyticus concentration in plankton. The concentrations of V. parahaemolyticus associated with plankton were highly seasonal, and the highest concentrations of V. parahaemolyticus cultured from zooplankton occurred approximately 1 month before the highest concentrations of V. parahaemolyticus from phytoplankton. The two V. parahaemolyticus peaks corresponded with different water quality variables and a few highly seasonal plankton taxa. Importantly, V. parahaemolyticus concentrations and plankton community dynamics were poorly associated with nutrient concentrations and chlorophyll a, commonly applied proxy variables for assessing ecological health risks and human health risks from harmful plankton and V. parahaemolyticus elsewhere. Together, these statistical associations (or lack thereof) provide valuable insights to characterize the plankton-V. parahaemolyticus dynamic and inform approaches for understanding the potential contribution of plankton to human health risks from V. parahaemolyticus for the Northeast United States. IMPORTANCE The Vibrio-plankton interaction is a focal relationship in Vibrio disease research; however, little is known about this dynamic in the Northeast United States, where V. parahaemolyticus is an established public health issue. We integrated phototactic plankton separation with seasonality analysis to determine the dynamics of the plankton community, water quality, and V. parahaemolyticus concentrations. Distinct bimodal peaks in the seasonal timing of V. parahaemolyticus abundance from phyto- versus zooplankton and differing associations with water quality variables and plankton taxa indicate that monitoring and forecasting approaches should consider the source of exposure when designing predictive methods for V. parahaemolyticus. Helicotheca tamensis has not been previously reported in the GBE. Its detection during this study provides evidence of the changes occurring in the ecology of regional estuaries and potential mechanisms for changes in V. parahaemolyticus populations. The Vibrio monitoring approaches can be translated to aid other areas facing similar public health challenges.},
}
@article {pmid33990222,
year = {2021},
author = {Qian, X and Gunturu, S and Guo, J and Chai, B and Cole, JR and Gu, J and Tiedje, JM},
title = {Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {108},
pmid = {33990222},
issn = {2049-2618},
mesh = {Anti-Bacterial Agents ; Ecosystem ; Genes, Bacterial ; Grassland ; Humans ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; Tropical Climate ; Tundra ; },
abstract = {BACKGROUND: Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively.<br><br>RESULTS: High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition.<br><br>CONCLUSIONS: Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.},
}
@article {pmid33989956,
year = {2021},
author = {Zhong, X and Yu, S and Xu, H},
title = {Influence of tidal events on the body-size spectrum of periphytic ciliates for marine bioassessment using artificial substrata.},
journal = {Marine pollution bulletin},
volume = {168},
number = {},
pages = {112435},
doi = {10.1016/j.marpolbul.2021.112435},
pmid = {33989956},
issn = {1879-3363},
mesh = {Body Size ; *Ciliophora ; *Ecosystem ; Environmental Monitoring ; Water Quality ; },
abstract = {As an internal functional trait of a community, the body-size spectrum is a highly informative indicator for bioassessment of water/environmental quality in aquatic ecosystems. To determine the influence of tidal events on body-size spectra of protozoan periphytons, a 3-month baseline survey was conducted in Korean coastal waters using the polyurethane foam enveloped slide system (PFES) and conventional slide system (CS). The body-size spectrum of the protozoans showed a clear temporal pattern during the study period using both sampling systems. However, the temporal dynamics showed significantly different trajectories in the body-size spectrum between the two sampling methods during the study period. The bootstrapped average analysis revealed that the patterns of the body-size spectrum were significantly different between the PFES and CS systems, especially in terms of frequency of occurrence. These findings suggest that the tidal events may significantly influence body-size spectrum of periphytic ciliates for bioassessment in marine ecosystems.},
}
@article {pmid33989624,
year = {2021},
author = {Singh, NS and Sharma, R and Singh, SK and Singh, DK},
title = {A comprehensive review of environmental fate and degradation of fipronil and its toxic metabolites.},
journal = {Environmental research},
volume = {199},
number = {},
pages = {111316},
doi = {10.1016/j.envres.2021.111316},
pmid = {33989624},
issn = {1096-0953},
mesh = {Agriculture ; *Insecticides/toxicity ; *Pesticides ; Pyrazoles ; },
abstract = {The use of pesticides to increase crop production has become one of the inevitable components of modern agriculture. Fipronil, a phenylpyrazoles insecticide, is one of the most widely used, systemic, broad-spectrum insecticides. Owing to its unique mode of action and selective toxicity, it was once regarded as safer alternatives to more toxic and persistent organochlorine insecticides. However, with the increased use, many studies have reported the toxicity of fipronil and its metabolites in various non-target organisms during the last two decades. Currently, it is regarded as one of the most persistent and lipophilic insecticides in the market. In the environment, fipronil can undergo oxidation, reduction, hydrolysis, or photolysis to form fipronil sulfone, fipronil sulfide, fipronil amide, or fipronil desulfinyl respectively. These metabolites except fipronil amide are more or less toxic and persistent than fipronil and have been reported from diverse environmental samples. Recently many studies have focused on the degradation and removal of fipronil residues from the environment. However, a comprehensive review summarizing and combining these recent findings is lacking. In the present review, we evaluate, summarize, and combine important findings from recent degradation studies of fipronil and its metabolites. An attempt has been made to elucidate the possible mechanism and pathways of degradation of fipronil and its toxic metabolites.},
}
@article {pmid33987687,
year = {2022},
author = {Figueiredo, G and Gomes, M and Covas, C and Mendo, S and Caetano, T},
title = {The Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {470-481},
pmid = {33987687},
issn = {1432-184X},
support = {SFRH/BD/98446/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECIND/01463/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/50017/2020+UIDB/50017/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {*Actinobacteria/genetics ; *Bacteroidetes/genetics ; Computational Biology ; Genomics/methods ; Humans ; Multigene Family ; },
abstract = {Research on secondary metabolites (SMs) has been mostly focused on Gram-positive bacteria, especially Actinobacteria. The association of genomics with robust bioinformatics tools revealed the neglected potential of Gram-negative bacteria as promising sources of new SMs. The family Sphingobacteriaceae belongs to the phylum Bacteroidetes having representatives in practically all environments including humans, rhizosphere, soils, wastewaters, among others. Some genera of this family have demonstrated great potential as plant growth promoters, bioremediators and producers of some value-added compounds such as carotenoids and antimicrobials. However, to date, Sphingobacteriaceae's SMs are still poorly characterized, and likewise, little is known about their chemistry. This study revealed that Sphingobacteriaceae pangenome encodes a total of 446 biosynthetic gene clusters (BGCs), which are distributed across 85 strains, highlighting the great potential of this bacterial family to produce SMs. Pedobacter, Mucilaginibacter and Sphingobacterium were the genera with the highest number of BGCs, especially those encoding the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), terpenes, polyketides and nonribosomal peptides (NRPs). In Mucilaginibacter and Sphingobacterium genera, M. lappiensis ATCC BAA-1855, Mucilaginibacter sp. OK098 (both with 11 BGCs) and Sphingobacterium sp. 21 (6 BGCs) are the strains with the highest number of BGCs. Most of the BGCs found in these two genera did not have significant hits with the MIBiG database. These results strongly suggest that the bioactivities and environmental functions of these compounds, especially RiPPs, PKs and NRPs, are still unknown. Among RiPPs, two genera encoded the production of class I and class III lanthipeptides. The last are associated with LanKC proteins bearing uncommon lyase domains, whose dehydration mechanism deserves further investigation. This study translated genomics into functional information that unveils the enormous potential of environmental Gram-negative bacteria to produce metabolites with unknown chemistries, bioactivities and, more importantly, unknown ecological roles.},
}
@article {pmid33986093,
year = {2021},
author = {Girolamini, L and Salaris, S and Orsini, M and Pascale, MR and Mazzotta, M and Grottola, A and Cristino, S},
title = {Draft Genome Sequences of Legionella Presumptive Novel Species Isolated during Environmental Surveillance in Artificial Water Systems.},
journal = {Microbiology resource announcements},
volume = {10},
number = {19},
pages = {},
pmid = {33986093},
issn = {2576-098X},
abstract = {We present the draft genome sequences of three Legionella strains that were isolated from a hotel water distribution system. Legionella species identification was performed by macrophage infectivity potentiator (mip) and RNA polymerase β subunit (rpoB) gene sequencing. Whole-genome sequencing and average nucleotide identity results supported the hypothesis of new Legionella species isolation.},
}
@article {pmid33984318,
year = {2021},
author = {Stevens, BR and Pepine, CJ and Richards, EM and Kim, S and Raizada, MK},
title = {Depressive hypertension: A proposed human endotype of brain/gut microbiome dysbiosis.},
journal = {American heart journal},
volume = {239},
number = {},
pages = {27-37},
doi = {10.1016/j.ahj.2021.05.002},
pmid = {33984318},
issn = {1097-6744},
mesh = {Adult ; Affect/*physiology ; Biobehavioral Sciences ; Biota/*genetics ; *Depression/diagnosis/metabolism/physiopathology ; *Dysbiosis/diagnosis/physiopathology/psychology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Gastrointestinal Tract/microbiology/physiopathology ; Humans ; *Hypertension/diagnosis/metabolism/psychology ; Machine Learning ; Male ; Metabolic Networks and Pathways ; Metagenome ; },
abstract = {BACKGROUND: Hypertension (HTN) is frequently linked with depression (DEP) in adults with cardiovascular disease (CVD), yet the underlying mechanism and successful management remain elusive. We approached this knowledge gap through the lens that humans are eukaryote-prokaryote "meta-organisms," such that cardiovascular disease dysregulation is a mosaic disorder involving dysbiosis of the gut. We hypothesized that patients diagnosed with hypertension plus depression harbor a unique gut microbial ecology with attending functional genomics engaged with their hosts' gut/brain axis physiology.<br><br>METHODS: Stool microbiome DNA was analyzed by whole metagenome shotgun sequencing in 54 subjects parsed into cohorts diagnosed with HTN only (N&#x202f;=&#x202f;18), DEP only (N&#x202f;=&#x202f;7), DEP plus HTN (DEP-HTN) (N&#x202f;=&#x202f;8), or reference subjects with neither HTN nor DEP (N&#x202f;=&#x202f;21). A novel battery of machine-learning multivariate analyses of de-noised data yielded effect sizes and permutational covariance-based dissimilarities that significantly differentiated the cohorts (false discovery rate (FDR)-adjusted P &#x2264; .05); data clustering within 95% confidence interval).<br><br>RESULTS: Metagenomic significant differences extricated the four cohorts. Data of the cohort exhibiting DEP-HTN were germane to the interplay of central control of blood pressure concomitant with the neuropathology of depressive disorders. DEP-HTN gut bacterial community ecology was defined by co-occurrence of Eubacterium siraeum, Alistipes obesi, Holdemania filiformis, and Lachnospiraceae bacterium 1.1.57FAA with Streptococcus salivariu. The corresponding microbial functional genomics of DEP-HTN engaged pathways degrading GABA and beneficial short chain fatty acids (SCFA), and are associated with enhanced sodium absorption and inflammasome induction.<br><br>CONCLUSIONS: These data suggest a new putative endotype of hypertension, which we denote "depressive-hypertension" (DEP-HTN), for which we posit a model that is distinctive from either HTN alone or DEP alone. An "endotype" is a subtype of a heterogeneous pathophysiological mechanism. The DEP-HTN model incorporates a unique signature of microbial taxa and functional genomics with crosstalk that putatively intertwines host pathophysiology involving the gastrointestinal tract with disruptions in central control of blood pressure and mood. The DEP-HTN endotype model engages cardiology with gastroenterology and psychiatry, providing a proof-of-concept foundation to explore future treatments, diagnosis, and prevention of HTN-coupled mood disorders.},
}
@article {pmid33981000,
year = {2021},
author = {Flieder, M and Buongiorno, J and Herbold, CW and Hausmann, B and Rattei, T and Lloyd, KG and Loy, A and Wasmund, K},
title = {Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling.},
journal = {The ISME journal},
volume = {15},
number = {11},
pages = {3159-3180},
pmid = {33981000},
issn = {1751-7370},
mesh = {*Geologic Sediments ; *Hydrogensulfite Reductase/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur ; },
abstract = {Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.},
}
@article {pmid33980683,
year = {2021},
author = {De Leόn, KB},
title = {mSphere of Influence: Surface Sensing in Biofilm Formation.},
journal = {mSphere},
volume = {6},
number = {3},
pages = {},
pmid = {33980683},
issn = {2379-5042},
mesh = {Bacteria/*metabolism ; Bacterial Adhesion ; Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; Pseudomonas aeruginosa/growth &amp; development/physiology ; Surface Properties ; },
abstract = {Kara B. De Leόn works in the field of microbial ecology, environmental biofilms, and microbial genetics. In this mSphere of Influence article, she reflects on how the paper "Multigenerational memory and adaptive adhesion in early bacterial biofilm communities" by C. K. Lee et al. (C. K. Lee, J. de Anda, A. E. Baker, R. R. Bennett, et al., Proc Natl Acad Sci U S A 115:4471-4476, 2018, https://dx.doi.org/10.1073/pnas.1720071115) made an impact on her by changing the way she thinks about initial cell attachment to a surface in an environment.},
}
@article {pmid33980476,
year = {2021},
author = {Liébana-García, R and Olivares, M and Bullich-Vilarrubias, C and López-Almela, I and Romaní-Pérez, M and Sanz, Y},
title = {The gut microbiota as a versatile immunomodulator in obesity and associated metabolic disorders.},
journal = {Best practice &amp; research. Clinical endocrinology &amp; metabolism},
volume = {35},
number = {3},
pages = {101542},
doi = {10.1016/j.beem.2021.101542},
pmid = {33980476},
issn = {1878-1594},
mesh = {Diet ; *Gastrointestinal Microbiome ; Humans ; Immunologic Factors ; *Metabolic Diseases/etiology ; Obesity ; },
abstract = {Obesity has reached epidemic proportions and is associated with chronic-low-grade inflammation and metabolic morbidities. Energy-dense diets and a sedentary lifestyle are determinants of obesity. The gut microbiome is a novel biological factor involved in obesity via interactions with the host and the diet. The gut microbiome act as a synergistic force protecting or aggravating the effects of the diet on the metabolic phenotype. The role of the microbiome in the regulation of intestinal and systemic immunity is one of the mechanisms by which it contributes to the host's response to the diet and to the pathophysiology of diet-induced obesity. Here, we review the mechanisms whereby "obesogenic" diets and the microbiome impact immunity, locally and systemically, focusing on the consequences in the gut-adipose tissue axis. We also review the structural and microbial metabolites that influence immunity and how advances in this field could help design microbiome-informed strategies to tackle obesity-related disorders more effectively.},
}
@article {pmid33978602,
year = {2022},
author = {Jung, CE and Estaki, M and Chopyk, J and Taylor, BC and Gonzalez, A and McDonald, D and Shin, J and Ferrante, K and Wasenda, E and Lippmann, Q and Knight, R and Pride, D and Lukacz, ES},
title = {Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection.},
journal = {Female pelvic medicine &amp; reconstructive surgery},
volume = {28},
number = {1},
pages = {20-26},
pmid = {33978602},
issn = {2154-4212},
mesh = {Estrogens ; Female ; Humans ; *Microbiota ; Postmenopause ; RNA, Ribosomal, 16S/genetics ; *Urinary Tract Infections/drug therapy ; Vagina ; },
abstract = {OBJECTIVE: The aim of this study was to describe effects of vaginal estrogen (VE) on the urogenital microbiome in postmenopausal women with recurrent urinary tract infections (rUTIs).<br><br>METHODS: This is a secondary analysis of 17 participants enrolled in a randomized controlled trial of VE versus placebo on urinary tract infection recurrence in postmenopausal women with rUTIs. Paired clean-catch urine samples were collected at baseline and after 6 months of VE and sequenced using 16S rRNA gene sequencing. Sequence reads were analyzed using Quantitative Insights Into Microbial Ecology 2. Changes in &#x3b1; diversity, &#x3b2; diversity, and differentially abundant genera were measured between paired baseline and 6-month samples and between those with a urinary tract infection at 6 months (failures) and those without (successes).<br><br>RESULTS: Of the 17 women, 11 were successes and 6 were failures after 6 months of VE treatment. There was a significant change in &#x3b1; diversity from baseline to month 6 in samples overall (Kruskal-Wallis &#x3c7;2 = 3.47, P = 0.037) and in the treatment success group (Yuen T = -2.53, P = 0.035). The increase in relative abundance of Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners AB-1 was correlated with month 6. A relative bloom of L. crispatus compared with L. gasseri was associated with treatment success (Kruskal-Wallis &#x3c7;2 = 4.9, P = 0.0014).<br><br>CONCLUSIONS: Lactobacillus increases in the urogenital microbiome of postmenopausal women with rUTI after 6 months of VE. However, only the relative increase in L. crispatus specifically may be associated with treatment success.},
}
@article {pmid33976843,
year = {2021},
author = {Eliades, SJ and Brown, JC and Colston, TJ and Fisher, RN and Niukula, JB and Gray, K and Vadada, J and Rasalato, S and Siler, CD},
title = {Gut microbial ecology of the Critically Endangered Fijian crested iguana (Brachylophus vitiensis): Effects of captivity status and host reintroduction on endogenous microbiomes.},
journal = {Ecology and evolution},
volume = {11},
number = {9},
pages = {4731-4743},
pmid = {33976843},
issn = {2045-7758},
abstract = {Animals often exhibit distinct microbial communities when maintained in captivity as compared to when in the wild. Such differentiation may be significant in headstart and reintroduction programs where individuals spend some time in captivity before release into native habitats. Using 16S rRNA gene sequencing, we (i) assessed differences in gut microbial communities between captive and wild Fijian crested iguanas (Brachylophus vitiensis) and (ii) resampled gut microbiota in captive iguanas released onto a native island to monitor microbiome restructuring in the wild. We used both cloacal swabs and fecal samples to further increase our understanding of gut microbial ecology in this IUCN Critically Endangered species. We found significant differentiation in gut microbial community composition and structure between captive and wild iguanas in both sampling schemes. Approximately two months postrelease, microbial communities in cloacal samples from formerly captive iguanas closely resembled wild counterparts. Interestingly, microbial communities in fecal samples from these individuals remained significantly distinct from wild conspecifics. Our results indicate that captive upbringings can lead to differences in microbial assemblages in headstart iguanas as compared to wild individuals even after host reintroduction into native conditions. This investigation highlights the necessity of continuous monitoring of reintroduced animals in the wild to ensure successful acclimatization and release.},
}
@article {pmid33975968,
year = {2021},
author = {Sieradzki, ET and Morando, M and Fuhrman, JA},
title = {Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {},
pmid = {33975968},
issn = {2379-5077},
abstract = {Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs)-toxic and recalcitrant components of crude oil as well as by-products of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by chronic inputs responds to acute pollution. We investigated the diversity and functional potential of a similar seed community in the chronically polluted Port of Los Angeles (POLA), using stable isotope probing with naphthalene, deep-sequenced metagenomes, and carbon incorporation rate measurements at the port and in two sites in the San Pedro Channel. We demonstrate the ability of the community of degraders at the POLA to incorporate carbon from naphthalene, leading to a quick shift in microbial community composition to be dominated by the normally rare Colwellia and Cycloclasticus We show that metagenome-assembled genomes (MAGs) belonged to these naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes, even when combining genes from the entire microbial community, leading us to hypothesize that promiscuous dehydrogenases replace canonical naphthalene degradation enzymes in this site. We compared metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate genomic-based recommendations for future optimization of PAH bioremediation at the POLA, e.g., ammonium as opposed to urea, heme or hemoproteins as an iron source, and polar amino acids.IMPORTANCE Oil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles through bioaccumulation of toxic hydrocarbons and oxygen depletion by hydrocarbon-degrading bacteria. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil or other organic carbon sources, and have a significant role in degradation of oil spills. Polycyclic aromatic hydrocarbons are the most persistent and toxic component of crude oil. Therefore, the bacteria that can break those molecules down are of particular importance. We identified such bacteria at the Port of Los Angeles (POLA), one of the busiest ports worldwide, and characterized their metabolic capabilities. We propose chemical targets based on those analyses to stimulate the activity of these bacteria in case of an oil spill in the Port POLA.},
}
@article {pmid33975966,
year = {2021},
author = {Chuckran, PF and Fofanov, V and Hungate, BA and Morrissey, EM and Schwartz, E and Walkup, J and Dijkstra, P},
title = {Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {},
pmid = {33975966},
issn = {2379-5077},
abstract = {Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four time points that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased the transcription of genes encoding ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen-fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes.IMPORTANCE A large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for an improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.},
}
@article {pmid33975908,
year = {2021},
author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T},
title = {Reply to Shaw: Challenges for enrichment analysis of AMR gene-bearing plasmids.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {21},
pages = {},
pmid = {33975908},
issn = {1091-6490},
mesh = {*Drug Resistance, Bacterial ; Plasmids/genetics ; },
}
@article {pmid33974954,
year = {2021},
author = {Lima, J and Manning, T and Rutherford, KM and Baima, ET and Dewhurst, RJ and Walsh, P and Roehe, R},
title = {Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.},
journal = {Journal of microbiological methods},
volume = {186},
number = {},
pages = {106235},
doi = {10.1016/j.mimet.2021.106235},
pmid = {33974954},
issn = {1872-8359},
support = {BB/N01720X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S006567/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; Computational Biology/*methods ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Molecular Sequence Annotation/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine/microbiology ; },
abstract = {Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification.},
}
@article {pmid33973345,
year = {2021},
author = {Clocchiatti, A and Hannula, SE and Hundscheid, MPJ and Klein Gunnewiek, PJA and de Boer, W},
title = {Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings.},
journal = {Environmental microbiology},
volume = {23},
number = {10},
pages = {6056-6073},
pmid = {33973345},
issn = {1462-2920},
mesh = {Fungi/genetics ; *Microbiota ; *Mycorrhizae ; Plant Roots/microbiology ; Rhizosphere ; Seedlings ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here, we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust-amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following [13] CO2 -pulse-labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA-SIP) and nucleic acids (DNA-SIP). Sawdust-stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α-Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate-consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root-associated microbiomes.},
}
@article {pmid33973200,
year = {2021},
author = {Moossavi, S and Fehr, K and Maleki, H and Seyedpour, S and Keshavarz-Fathi, M and Tabasi, F and Heravi, M and Sharifian, R and Shafiei, G and Badihian, N and Kelishadi, R and Nematollahi, S and Almasi, M and Popescu, S and Keshavarz-Fathi, M and Rezaei, N},
title = {Prevention of COVID-19: Preventive Strategies for General Population, Healthcare Setting, and Various Professions.},
journal = {Advances in experimental medicine and biology},
volume = {1318},
number = {},
pages = {575-604},
pmid = {33973200},
issn = {0065-2598},
mesh = {*COVID-19 ; *Cancer Vaccines ; Delivery of Health Care ; Humans ; Immunotherapy ; SARS-CoV-2 ; },
abstract = {The disease 2019 (COVID-19) made a public health emergency in early 2020. Despite attempts for the development of therapeutic modalities, there is no effective treatment yet. Therefore, preventive measures in various settings could help reduce the burden of disease. In this chapter, the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19, non-pharmaceutical approaches at individual and population level, chemoprevention, immunoprevention, preventive measures in different healthcare settings and other professions, special considerations in high-risk groups, and the role of organizations to hamper the psychosocial effects will be discussed.},
}
@article {pmid33973059,
year = {2022},
author = {Castelli, L and Branchiccela, B and Romero, H and Zunino, P and Antúnez, K},
title = {Seasonal Dynamics of the Honey Bee Gut Microbiota in Colonies Under Subtropical Climate : Seasonal Dynamics of Honey Bee Gut Microbiota.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {492-500},
pmid = {33973059},
issn = {1432-184X},
mesh = {Animals ; Bacteria/genetics ; Bees ; Biodiversity ; *Gastrointestinal Microbiome/genetics ; Pollination ; Seasons ; },
abstract = {Honey bees (Apis mellifera) provide invaluable benefits for food production and maintenance of biodiversity of natural environments through pollination. They are widely spread across the world, being adapted to different climatic conditions. To survive the winter in cold temperate regions, honey bees developed different strategies including storage of honey and pollen, confinement of individuals during the winter, and an annual cycle of colony growth and reproduction. Under these conditions, winter honey bees experience physiological changes, including changes in immunity and the composition of honey bee gut microbiota. However, under tropical or subtropical climates, the life cycle can experience alterations, i.e., queens lay eggs during almost all the year and new honey bees emerge constantly. In the present study, we characterized nurses' honey bee gut microbiota in colonies under subtropical region through a year, combining qPCR, PCR-DGGE, and 16S rDNA high-throughput sequencing. We also identified environmental variables involved in those changes. Our results showed that under the mentioned conditions, the number of bacteria is stable throughout the year. Diversity of gut microbiota is higher in spring and lower in summer and winter. Gradual changes in compositions occur between seasons: Lactobacillus spp. predominate in spring while Gilliamella apicola and Snodgrasella alvi predominate in summer and winter. Environmental variables (mainly precipitations) affected the composition of the honey bee gut microbiota. Our findings provide new insights into the dynamics of honey bee gut microbiota and may be useful to understand the adaptation of bees to different environmental conditions.},
}
@article {pmid33970854,
year = {2021},
author = {Alvarez-Perez, S and Baker, LJ and Morris, MM and Tsuji, K and Sanchez, VA and Fukami, T and Vannette, RL and Lievens, B and Hendry, TA},
title = {Acinetobacter pollinis sp. nov., Acinetobacter baretiae sp. nov. and Acinetobacter rathckeae sp. nov., isolated from floral nectar and honey bees.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {71},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.004783},
pmid = {33970854},
issn = {1466-5034},
mesh = {Acinetobacter/*classification/isolation &amp; purification ; Animals ; Bacterial Typing Techniques ; Base Composition ; Bees/*microbiology ; California ; DNA, Bacterial/genetics ; Flowers ; Nucleic Acid Hybridization ; *Phylogeny ; *Plant Nectar ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {A detailed evaluation of eight bacterial isolates from floral nectar and animal visitors to flowers shows evidence that they represent three novel species in the genus Acinetobacter. Phylogenomic analysis shows the closest relatives of these new isolates are Acinetobacter apis, Acinetobacter boissieri and Acinetobacter nectaris, previously described species associated with floral nectar and bees, but high genome-wide sequence divergence defines these isolates as novel species. Pairwise comparisons of the average nucleotide identity of the new isolates compared to known species is extremely low (<83 %), thus confirming that these samples are representative of three novel Acinetobacter species, for which the names Acinetobacter pollinis sp. nov., Acinetobacter baretiae sp. nov. and Acinetobacter rathckeae sp. nov. are proposed. The respective type strains are SCC477[T] (=TSD-214[T]=LMG 31655[T]), B10A[T] (=TSD-213[T]=LMG 31702[T]) and EC24[T] (=TSD-215[T]=LMG 31703[T]=DSM 111781[T]).},
}
@article {pmid33970312,
year = {2022},
author = {Zhao, J and Wang, B and Zhou, X and Alam, MS and Fan, J and Guo, Z and Zhang, H and Gubry-Rangin, C and Zhongjun, J},
title = {Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {424-435},
pmid = {33970312},
issn = {1432-184X},
support = {41530857//National Natural Science Foundation of China/ ; 91751204//National Natural Science Foundation of China/ ; 41977056//National Natural Science Foundation of China/ ; URF150571//The Royal Society/ ; NE/ K016342/1//Natural Environment Research Council/ ; },
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; Ecosystem ; Fertilization ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems.},
}
@article {pmid33969432,
year = {2022},
author = {Nasehi, SF and Fathipour, Y and Asgari, S and Mehrabadi, M},
title = {Environmental Temperature, but Not Male Age, Affects Wolbachia and Prophage WO Thereby Modulating Cytoplasmic Incompatibility in the Parasitoid Wasp, Habrobracon Hebetor.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {482-491},
pmid = {33969432},
issn = {1432-184X},
support = {98008582//Iran National Science Foundation/ ; },
mesh = {Animals ; Cytoplasm/metabolism ; Female ; Male ; Prophages/genetics ; Temperature ; *Wasps/microbiology ; *Wolbachia/genetics/metabolism ; },
abstract = {Wolbachia is an endosymbiotic bacterium found in many species of arthropods and manipulates its host reproduction. Cytoplasmic incompatibility (CI) is one of the most common manipulations that is induced when an uninfected female mates with a Wolbachia-infected male. The CI factors (cifA and cifB genes) are encoded by phage WO that naturally infects Wolbachia. Here, we questioned whether an environmental factor (temperature) or host factor (male age) affected the strength of the CI phenotype in the ectoparasitoid wasp, Habrobracon hebetor. We found that temperature, but not male age, results in reduced CI penetrance. Consistent with these results, we also found that the expression of the cif CI factors decreased in temperature-exposed males but was consistent across aging male wasps. Similar to studies of other insect systems, cifA showed a higher expression level than cifB, and male hosts showed increased cif expression relative to females. Our results suggest that prophage WO is present in the Wolbachia-infected wasps and expression of cif genes contributes to the induction of CI in this insect. It seems that male aging has no effect on the intensity of CI; however, temperature affects Wolbachia and prophage WO titers as well as expression levels of cif genes, which modulate the CI level.},
}
@article {pmid33968313,
year = {2021},
author = {Verspecht, T and Van Holm, W and Boon, N and Bernaerts, K and Daep, CA and Masters, JG and Zayed, N and Quirynen, M and Teughels, W},
title = {Potential prebiotic substrates modulate composition, metabolism, virulence and inflammatory potential of an in vitro multi-species oral biofilm.},
journal = {Journal of oral microbiology},
volume = {13},
number = {1},
pages = {1910462},
pmid = {33968313},
issn = {2000-2297},
abstract = {Background: Modulation of the commensal oral microbiota constitutes a promising preventive/therapeutic approach in oral healthcare. The use of prebiotics for maintaining/restoring the health-associated homeostasis of the oral microbiota has become an important research topic. Aims: This study hypothesised that in vitro 14-species oral biofilms can be modulated by (in)direct stimulation of beneficial/commensal bacteria with new potential prebiotic substrates tested at 1 M and 1%(w/v), resulting in more host-compatible biofilms with fewer pathogens, decreased virulence and less inflammatory potential. Methods: Established biofilms were repeatedly rinsed with N-acetyl-D-glucosamine, α-D-lactose, D-(+)-trehalose or D-(+)-raffinose at 1 M or 1%(w/v). Biofilm composition, metabolic profile, virulence and inflammatory potential were eventually determined. Results: Repeated rinsing caused a shift towards a more health-associated microbiological composition, an altered metabolic profile, often downregulated virulence gene expression and decreased the inflammatory potential on oral keratinocytes. At 1 M, the substrates had pronounced effects on all biofilm aspects, whereas at 1%(w/v) they had a pronounced effect on virulence gene expression and a limited effect on inflammatory potential. Conclusion: Overall, this study identified four new potential prebiotic substrates that exhibit different modulatory effects at two different concentrations that cause in vitro multi-species oral biofilms to become more host-compatible.},
}
@article {pmid33966095,
year = {2022},
author = {Frare, R and Pascuan, C and Galindo-Sotomonte, L and McCormick, W and Soto, G and Ayub, N},
title = {Exploring the Role of the NO-Detoxifying Enzyme HmpA in the Evolution of Domesticated Alfalfa Rhizobia.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {501-505},
pmid = {33966095},
issn = {1432-184X},
mesh = {Genomics ; Hempa ; Medicago sativa ; *Rhizobium/genetics ; Symbiosis ; },
abstract = {We have previously shown the extensive loss of genes during the domestication of alfalfa rhizobia and the high nitrous oxide emission associated with the extreme genomic instability of commercial inoculants. In the present note, we describe the molecular mechanism involved in the evolution of alfalfa rhizobia. Genomic analysis showed that most of the gene losses in inoculants are due to large genomic deletions rather than to small deletions or point mutations, a fact consistent with recurrent DNA double-strand breaks (DSBs) at numerous locations throughout the microbial genome. Genetic analysis showed that the loss of the NO-detoxifying enzyme HmpA in inoculants results in growth inhibition and high DSB levels under nitrosative stress, and large genomic deletions in planta but not in the soil. Therefore, besides its known function in the effective establishment of the symbiosis, HmpA can play a critical role in the preservation of the genomic integrity of alfalfa rhizobia under host-derived nitrosative stress.},
}
@article {pmid33959106,
year = {2021},
author = {Parks, DH and Rigato, F and Vera-Wolf, P and Krause, L and Hugenholtz, P and Tyson, GW and Wood, DLA},
title = {Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {643682},
pmid = {33959106},
issn = {1664-302X},
abstract = {A fundamental goal of microbial ecology is to accurately determine the species composition in a given microbial ecosystem. In the context of the human microbiome, this is important for establishing links between microbial species and disease states. Here we benchmark the Microba Community Profiler (MCP) against other metagenomic classifiers using 140 moderate to complex in silico microbial communities and a standardized reference genome database. MCP generated accurate relative abundance estimates and made substantially fewer false positive predictions than other classifiers while retaining a high recall rate. We further demonstrated that the accuracy of species classification was substantially increased using the Microba Genome Database, which is more comprehensive than reference datasets used by other classifiers and illustrates the importance of including genomes of uncultured taxa in reference databases. Consequently, MCP classifies appreciably more reads than other classifiers when using their recommended reference databases. These results establish MCP as best-in-class with the ability to produce comprehensive and accurate species profiles of human gastrointestinal samples.},
}
@article {pmid33958420,
year = {2021},
author = {McDaniel, EA and Wever, R and Oyserman, BO and Noguera, DR and McMahon, KD},
title = {Genome-Resolved Metagenomics of a Photosynthetic Bioreactor Performing Biological Nutrient Removal.},
journal = {Microbiology resource announcements},
volume = {10},
number = {18},
pages = {},
pmid = {33958420},
issn = {2576-098X},
abstract = {Enhanced biological phosphorus removal (EBPR) is an economically and environmentally significant wastewater treatment process for removing excess phosphorus by harnessing the metabolic physiologies of enriched microbial communities. We present a genome-resolved metagenomic data set consisting of 86 metagenome-assembled genome sequences from a photosynthetically operated lab-scale bioreactor simulating EBPR.},
}
@article {pmid33957514,
year = {2021},
author = {Zhao, Z and Li, H and Sun, Y and Yang, Q and Fan, J},
title = {Contrasting the assembly of phytoplankton and zooplankton communities in a polluted semi-closed sea: Effects of marine compartments and environmental selection.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {285},
number = {},
pages = {117256},
doi = {10.1016/j.envpol.2021.117256},
pmid = {33957514},
issn = {1873-6424},
mesh = {Animals ; Ecosystem ; Food Chain ; *Phytoplankton ; Plankton ; *Zooplankton ; },
abstract = {Understanding the underlying mechanisms of community assembly is a major challenge in microbial ecology, particularly in communities composed of diverse organisms with different ecological characteristics. However, very little is known about the effects of marine compartments in shaping marine planktonic communities; primarily, how they are related to organism types and environmental variables. In this study, we used multiple statistical methods to explore the mechanisms driving phytoplankton and zooplankton metacommunity dynamics at the regional scale in the Bohai Sea, China. Clear geographic patterns were observed in both phytoplankton and zooplankton communities. Zooplankton showed a stronger distance-decay of similarity than phytoplankton, which had greater community differences between locations with further distances. Our analyses indicated that the zooplankton communities were primarily governed by species sorting versus dispersal limitation than the phytoplankton communities. Furthermore, we detected that zooplankton exhibited wider habitat niche breadths and dispersal abilities than phytoplankton. Our findings also showed that environmental pollution affected high trophic organisms via food webs; the presence of heavy metals in the Bohai Sea altered the abundance of some phytoplankton, and thus modified the zooplankton that feed on them.},
}
@article {pmid33956174,
year = {2022},
author = {Zhou, Q and He, R and Zhao, D and Zeng, J and Yu, Z and Wu, QL},
title = {Contrasting Patterns of the Resident and Active Rhizosphere Bacterial Communities of Phragmites Australis.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {314-327},
pmid = {33956174},
issn = {1432-184X},
support = {32022050 and 31971478//National Natural Science Foundation of China/ ; U2040201//National Natural Science Foundation of China/ ; 41871096//National Natural Science Foundation of China/ ; 2021NIGLAS-CJH01//the Project of Young Scientist Group of NIGLAS/ ; 2017FY100300//Science &amp; Technology Basic Resources Investigation Program of China/ ; BK20181311//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {Bacteria/genetics ; Poaceae/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; },
abstract = {Rhizosphere microbes play a key role in maintaining plant health and regulating biogeochemical cycles. The active bacterial community (ABC) in rhizosphere, as a small fraction of the rhizosphere resident bacterial community (RBC), has the potential to actively participate in nutrient cycling processes at the root-sediment interface. Here, we investigated the ABC and RBC within the rhizosphere of Phragmites australis (P. australis) subjected to different environmental conditions (i.e., seasons and flooding conditions) in Lake Taihu, China. Our results indicated that RBC exhibited significantly higher alpha diversity as well as lower beta diversity than ABC. The active ratios of 16S rRNA to 16S rDNA (also RNA/DNA) of the bacterial communities in summer and winter suggested a lower proportion of potential active taxa in the rhizosphere bacterial community during summer. Network analysis showed that negative correlations in each network were observed to dominate the species correlations between the rhizosphere and bulk sediment bacterial communities. Our results revealed that niche differentiation and seasonal variation played crucial roles in driving the assembly of ABC and RBC associated with the rhizospheres of P. australis. These findings broaden our knowledge about how rhizosphere bacterial communities respond to environmental variations through changing their diversity and composition.},
}
@article {pmid33954842,
year = {2022},
author = {Fernández-Juárez, V and Jaén-Luchoro, D and Brito-Echeverría, J and Agawin, NSR and Bennasar-Figueras, A and Echeveste, P},
title = {Everything Is Everywhere: Physiological Responses of the Mediterranean Sea and Eastern Pacific Ocean Epiphyte Cobetia Sp. to Varying Nutrient Concentration.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {296-313},
pmid = {33954842},
issn = {1432-184X},
support = {11170837//Fondecyt Iniciaci&#xf3;n/ ; EQM120137//FONDEQUIP/ ; 170403//REDI/ ; CTM2016-75457-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; },
mesh = {*Alismatales/physiology ; Ecosystem ; Mediterranean Sea ; Nutrients ; Pacific Ocean ; },
abstract = {Bacteria are essential in the maintenance and sustainment of marine environments (e.g., benthic systems), playing a key role in marine food webs and nutrient cycling. These microorganisms can live associated as epiphytic or endophytic populations with superior organisms with valuable ecological functions, e.g., seagrasses. Here, we isolated, identified, sequenced, and exposed two strains of the same species (i.e., identified as Cobetia sp.) from two different marine environments to different nutrient regimes using batch cultures: (1) Cobetia sp. UIB 001 from the endemic Mediterranean seagrass Posidonia oceanica and (2) Cobetia sp. 4B UA from the endemic Humboldt Current System (HCS) seagrass Heterozostera chilensis. From our physiological studies, both strains behaved as bacteria capable to cope with different nutrient and pH regimes, i.e., N, P, and Fe combined with different pH levels, both in long-term (12 days (d)) and short-term studies (4 d/96 h (h)). We showed that the isolated strains were sensitive to the N source (inorganic and organic) at low and high concentrations and low pH levels. Low availability of phosphorus (P) and Fe had a negative independent effect on growth, especially in the long-term studies. The strain UIB 001 showed a better adaptation to low nutrient concentrations, being a potential N2-fixer, reaching higher growth rates (μ) than the HCS strain. P-acquisition mechanisms were deeply investigated at the enzymatic (i.e., alkaline phosphatase activity, APA) and structural level (e.g., alkaline phosphatase D, PhoD). Finally, these results were complemented with the study of biochemical markers, i.e., reactive oxygen species (ROS). In short, we present how ecological niches (i.e., MS and HCS) might determine, select, and modify the genomic and phenotypic features of the same bacterial species (i.e., Cobetia spp.) found in different marine environments, pointing to a direct correlation between adaptability and oligotrophy of seawater.},
}
@article {pmid33953314,
year = {2021},
author = {Melkonian, C and Fillinger, L and Atashgahi, S and da Rocha, UN and Kuiper, E and Olivier, B and Braster, M and Gottstein, W and Helmus, R and Parsons, JR and Smidt, H and van der Waals, M and Gerritse, J and Brandt, BW and Röling, WFM and Molenaar, D and van Spanning, RJM},
title = {High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {530},
pmid = {33953314},
issn = {2399-3642},
mesh = {Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Benzene/*metabolism ; *Biodegradation, Environmental ; *Biodiversity ; *Metagenome ; Nitrates/*metabolism ; },
abstract = {A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.},
}
@article {pmid33952668,
year = {2021},
author = {Lesniak, NA and Schubert, AM and Sinani, H and Schloss, PD},
title = {Clearance of Clostridioides difficile Colonization Is Associated with Antibiotic-Specific Bacterial Changes.},
journal = {mSphere},
volume = {6},
number = {3},
pages = {},
pmid = {33952668},
issn = {2379-5042},
support = {T32 AI007528/AI/NIAID NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage/classification/*therapeutic use ; Bacteria/drug effects/*metabolism ; Cefoperazone/therapeutic use ; Clindamycin/therapeutic use ; Clostridioides difficile/*drug effects/*physiology ; Clostridium Infections/*drug therapy/microbiology/prevention &amp; control ; Disease Susceptibility ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/physiology ; Mice ; Streptomycin/therapeutic use ; },
abstract = {The gut bacterial community prevents many pathogens from colonizing the intestine. Previous studies have associated specific bacteria with clearing Clostridioides difficile colonization across different community perturbations. However, those bacteria alone have been unable to clear C. difficile colonization. To elucidate the changes necessary to clear colonization, we compared differences in bacterial abundance between communities able and unable to clear C. difficile colonization. We treated mice with titrated doses of antibiotics prior to C. difficile challenge, resulting in no colonization, colonization and clearance, or persistent colonization. Previously, we observed that clindamycin-treated mice were susceptible to colonization but spontaneously cleared C. difficile Therefore, we investigated whether other antibiotics would show the same result. We found that reduced doses of cefoperazone and streptomycin permitted colonization and clearance of C. difficile Mice that cleared colonization had antibiotic-specific community changes and predicted interactions with C. difficile Clindamycin treatment led to a bloom in populations related to Enterobacteriaceae Clearance of C. difficile was concurrent with the reduction of those blooming populations and the restoration of community members related to the Porphyromonadaceae and Bacteroides Cefoperazone created a susceptible community characterized by drastic reductions in the community diversity and interactions and a sustained increase in the abundance of many facultative anaerobes. Lastly, clearance in streptomycin-treated mice was associated with the recovery of multiple members of the Porphyromonadaceae, with little overlap in the specific Porphyromonadaceae observed in the clindamycin treatment. Further elucidation of how C. difficile colonization is cleared from different gut bacterial communities will improve C. difficile infection treatments.IMPORTANCE The community of microorganisms, or microbiota, in our intestines prevents pathogens like C. difficile from colonizing and causing infection. However, antibiotics can disturb the gut microbiota, which allows C. difficile to colonize. C. difficile infections (CDI) are primarily treated with antibiotics, which frequently leads to recurrent infections because the microbiota has not yet returned to a resistant state. The recurrent infection cycle often ends when the fecal microbiota from a presumed resistant person is transplanted into the susceptible person. Although this treatment is highly effective, we do not understand the mechanism. We hope to improve the treatment of CDI through elucidating how the bacterial community eliminates CDI. We found that C. difficile colonized susceptible mice but was spontaneously eliminated in an antibiotic treatment-specific manner. These data indicate that each community had different requirements for clearing colonization. Understanding how different communities clear colonization will reveal targets to improve CDI treatments.},
}
@article {pmid33952552,
year = {2021},
author = {Tang, H and Bohannon, L and Lew, M and Jensen, D and Jung, SH and Zhao, A and Sung, AD and Wischmeyer, PE},
title = {Randomised, double-blind, placebo-controlled trial of Probiotics To Eliminate COVID-19 Transmission in Exposed Household Contacts (PROTECT-EHC): a clinical trial protocol.},
journal = {BMJ open},
volume = {11},
number = {5},
pages = {e047069},
pmid = {33952552},
issn = {2044-6055},
support = {R03 AG064260/AG/NIA NIH HHS/United States ; },
mesh = {*COVID-19 ; Double-Blind Method ; Humans ; Pandemics ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Randomized Controlled Trials as Topic ; SARS-CoV-2 ; Treatment Outcome ; },
abstract = {INTRODUCTION: The COVID-19 pandemic has proven to be an unprecedented challenge to worldwide health, and strategies to mitigate the spread and severity of COVID-19 infection are urgently needed. Emerging evidence suggests that the composition of the gut microbiome and modification of microbial ecology via probiotics can affect susceptibility to a wide range of infections, including respiratory tract infections. In this study, we aim to evaluate the effects of the probiotic Lactobacillus rhamnosus GG (LGG) versus placebo on COVID-19 infection status and the gut microbiome in subjects with a household contact who has tested positive for COVID-19.<br><br>METHODS AND ANALYSIS: In this double-blinded, randomised, placebo-controlled trial, we will randomise 1132 subjects having a household contact who has recently (&#x2264;7&#x2009;days) tested positive for COVID-19 to daily oral LGG or placebo for 28 days. We hypothesise that taking LGG as a probiotic will protect against COVID-19 infection and reduce the severity of disease in those who become infected (primary endpoint: decreased symptoms), and will be associated with beneficial changes in the composition of the gut microbiome. Stool samples and nasal swabs will be collected to evaluate the microbiome by 16S rRNA sequencing and the presence of SARS-CoV-2 by PCR, respectively. We will also conduct multivariate analysis of demographic, behavioural, temporal, and other variables that may predict development of symptoms and other outcomes.<br><br>ETHICS AND DISSEMINATION: This trial is conducted under a Food and Drug Administration Investigational New Drug for LGG, has received ethics approval by the institutional review board of Duke University and enrolment has begun. We plan to disseminate the results in peer-reviewed journals and at national and international conferences.<br><br>TRIAL REGISTRATION NUMBER: NCT04399252.},
}
@article {pmid33952355,
year = {2021},
author = {Baker, JM and Hinkle, KJ and McDonald, RA and Brown, CA and Falkowski, NR and Huffnagle, GB and Dickson, RP},
title = {Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {99},
pmid = {33952355},
issn = {2049-2618},
support = {R01 AI138348/AI/NIAID NIH HHS/United States ; R01 HL121774/HL/NHLBI NIH HHS/United States ; R01 HL144599/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Bacteria/genetics ; DNA, Bacterial/genetics ; Female ; Lung ; Mice ; *Microbiota/genetics ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Low-biomass microbiome studies (such as those of the lungs, placenta, and skin) are vulnerable to contamination and sequencing stochasticity, which obscure legitimate microbial signal. While human lung microbiome studies have rigorously identified sampling strategies that reliably capture microbial signal from these low-biomass microbial communities, the optimal sampling strategy for characterizing murine lung microbiota has not been empirically determined. Performing accurate, reliable characterization of murine lung microbiota and distinguishing true microbial signal from noise in these samples will be critical for further mechanistic microbiome studies in mice.<br><br>RESULTS: Using an analytic approach grounded in microbial ecology, we compared bacterial DNA from the lungs of healthy adult mice collected via two common sampling approaches: homogenized whole lung tissue and bronchoalveolar lavage (BAL) fluid. We quantified bacterial DNA using droplet digital PCR, characterized bacterial communities using 16S rRNA gene sequencing, and systematically assessed the quantity and identity of bacterial DNA in both specimen types. We compared bacteria detected in lung specimens to each other and to potential source communities: negative (background) control specimens and paired oral samples. By all measures, whole lung tissue in mice contained greater bacterial signal and less evidence of contamination than did BAL fluid. Relative to BAL fluid, whole lung tissue exhibited a greater quantity of bacterial DNA, distinct community composition, decreased sample-to-sample variation, and greater biological plausibility when compared to potential source communities. In contrast, bacteria detected in BAL fluid were minimally different from those of procedural, reagent, and sequencing controls.<br><br>CONCLUSIONS: An ecology-based analytical approach discriminates signal from noise in this low-biomass microbiome study and identifies whole lung tissue as the preferred specimen type for murine lung microbiome studies. Sequencing, analysis, and reporting of potential source communities, including negative control specimens and contiguous biological sites, are crucial for biological interpretation of low-biomass microbiome studies, independent of specimen type. Video abstract.},
}
@article {pmid33948706,
year = {2022},
author = {Stabili, L and Di Salvo, M and Alifano, P and Talà, A},
title = {An Integrative, Multiparametric Approach for the Comprehensive Assessment of Microbial Quality and Pollution in Aquaculture Systems.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {271-283},
pmid = {33948706},
issn = {1432-184X},
support = {LIFE16 ENV/IT/000343//LIFE Environment and Resource Efficiency 2016/ ; },
mesh = {Animals ; *Aquaculture/methods ; Humans ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; *Vibrio/genetics ; Water Quality ; },
abstract = {As the aquaculture sector significantly expanded worldwide in the past decades, the concept of sustainable aquaculture has developed with the challenge of not only maximizing benefits but also minimizing the negative impacts on the environment assuring, at the same time, food security. In this framework, monitoring and improving the microbiological water quality and animal health are a central topic. In the present study, we evaluated the seawater microbiological quality in a mariculture system located in a Mediterranean coastal area (Northern Ionian Sea, Italy). We furnished, for the first time, a microbial inventory based on conventional culture-based methods, integrated with the 16S rRNA gene metabarcoding approach for vibrios identification and diversity analyses, and further implemented with microbial metabolic profiling data obtained from the Biolog EcoPlate system. Microbiological pollution indicators, vibrios diversity, and microbial metabolism were determined in two different times of the year (July and December). All microbial parameters measured in July were markedly increased compared to those measured in December. The presence of potentially pathogenic vibrios is discussed concerning the risk of fish disease and human infections. Thus, the microbial inventory here proposed might represent a new multiparametric approach for the suitable surveillance of the microbial quality in a mariculture system. Consequently, it could be useful for ensuring the safety of both the reared species and the consumers in the light of sustainable, eco-friendly aquaculture management.},
}
@article {pmid33947808,
year = {2021},
author = {Boysen, AK and Carlson, LT and Durham, BP and Groussman, RD and Aylward, FO and Ribalet, F and Heal, KR and White, AE and DeLong, EF and Armbrust, EV and Ingalls, AE},
title = {Particulate Metabolites and Transcripts Reflect Diel Oscillations of Microbial Activity in the Surface Ocean.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {},
pmid = {33947808},
issn = {2379-5077},
abstract = {Light fuels photosynthesis and organic matter production by primary producers in the sunlit ocean. The quantity and quality of the organic matter produced influence community function, yet in situ measurements of metabolites, the products of cellular metabolism, over the diel cycle are lacking. We evaluated community-level biochemical consequences of oscillations of light in the North Pacific Subtropical Gyre by quantifying 79 metabolites in particulate organic matter from 15 m every 4 h over 8 days. Total particulate metabolite concentration peaked at dusk and represented up to 2% of total particulate organic carbon (POC). The concentrations of 55/79 (70%) individual metabolites exhibited significant 24-h periodicity, with daily fold changes from 1.6 to 12.8, often greater than those of POC and flow cytometry-resolvable biomass, which ranged from 1.2 to 2.8. Paired metatranscriptome analysis revealed the taxa involved in production and consumption of a subset of metabolites. Primary metabolites involved in anabolism and redox maintenance had significant 24-h periodicity and diverse organisms exhibited diel periodicity in transcript abundance associated with these metabolites. Compounds with osmotic properties displayed the largest oscillations in concentration, implying rapid turnover and supporting prior evidence of functions beyond cell turgor maintenance. The large daily oscillation of trehalose paired with metatranscriptome and culture data showed that trehalose is produced by the nitrogen-fixing cyanobacterium Crocosphaera, likely to store energy for nighttime metabolism. Together, paired measurements of particulate metabolites and transcripts resolve strategies that microbes use to manage daily energy and redox oscillations and highlight dynamic metabolites with cryptic roles in marine microbial ecosystems.IMPORTANCE Fueled by light, phytoplankton produce the organic matter that supports ocean ecosystems and carbon sequestration. Ocean change impacts microbial metabolism with repercussions for biogeochemical cycling. As the small molecule products of cellular metabolism, metabolites often change rapidly in response to environmental conditions and form the basis of energy and nutrient management and storage within cells. By pairing measurements of metabolites and gene expression in the stratified surface ocean, we reveal strategies of microbial energy management over the day-night cycle and hypothesize that oscillating metabolites are important substrates for dark respiration by phytoplankton. These high-resolution diel measurements of in situ metabolite concentrations form the basis for future work into the specific roles these compounds play in marine microbial communities.},
}
@article {pmid33947800,
year = {2021},
author = {Heal, KR and Durham, BP and Boysen, AK and Carlson, LT and Qin, W and Ribalet, F and White, AE and Bundy, RM and Armbrust, EV and Ingalls, AE},
title = {Marine Community Metabolomes Carry Fingerprints of Phytoplankton Community Composition.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {},
pmid = {33947800},
issn = {2379-5077},
abstract = {Phytoplankton transform inorganic carbon into thousands of biomolecules that represent an important pool of fixed carbon, nitrogen, and sulfur in the surface ocean. Metabolite production differs between phytoplankton, and the flux of these molecules through the microbial food web depends on compound-specific bioavailability to members of a wider microbial community. Yet relatively little is known about the diversity or concentration of metabolites within marine plankton. Here, we compare 313 polar metabolites in 21 cultured phytoplankton species and in natural planktonic communities across environmental gradients to show that bulk community metabolomes reflect the chemical composition of the phytoplankton community. We also show that groups of compounds have similar patterns across space and taxonomy, suggesting that the concentrations of these compounds in the environment are controlled by similar sources and sinks. We quantify several compounds in the surface ocean that represent substantial understudied pools of labile carbon. For example, the N-containing metabolite homarine was up to 3% of particulate carbon and is produced in high concentrations by cultured Synechococcus, and S-containing gonyol accumulated up to 2.5 nM in surface particles and likely originates from dinoflagellates or haptophytes. Our results show that phytoplankton composition directly shapes the carbon composition of the surface ocean. Our findings suggest that in order to access these pools of bioavailable carbon, the wider microbial community must be adapted to phytoplankton community composition.IMPORTANCE Microscopic phytoplankton transform 100 million tons of inorganic carbon into thousands of different organic compounds each day. The structure of each chemical is critical to its biological and ecosystem function, yet the diversity of biomolecules produced by marine microbial communities remained mainly unexplored, especially small polar molecules which are often considered the currency of the microbial loop. Here, we explore the abundance and diversity of small biomolecules in planktonic communities across ecological gradients in the North Pacific and within 21 cultured phytoplankton species. Our work demonstrates that phytoplankton diversity is an important determinant of the chemical composition of the highly bioavailable pool of organic carbon in the ocean, and we highlight understudied yet abundant compounds in both the environment and cultured organisms. These findings add to understanding of how the chemical makeup of phytoplankton shapes marine microbial communities where the ability to sense and use biomolecules depends on the chemical structure.},
}
@article {pmid33940748,
year = {2021},
author = {Guarin, TC and Pagilla, KR},
title = {Microbial community in biofilters for water reuse applications: A critical review.},
journal = {The Science of the total environment},
volume = {773},
number = {},
pages = {145655},
doi = {10.1016/j.scitotenv.2021.145655},
pmid = {33940748},
issn = {1879-1026},
mesh = {*Drinking Water ; Filtration ; *Microbiota ; Reproducibility of Results ; *Water Purification ; },
abstract = {The combination of ozonation (O3) and biofiltration processes has become practical and desirable in advanced water reclamation for water reuse applications. However, the role of microbial community and its characteristics (source, abundance, composition, viability, structure) on treatment performance has not received the same attention in water reclamation biofilters as in other applications, such as in drinking water biofilters. Microbial community characterization of biofilters used in water reuse applications will add evidence to better understand the potential microorganisms, consequent risks, and mechanisms that will populate drinking water sources and ultimately influence public health and the environment. This critical review provides insights into O3-biofiltration as a treatment barrier with a focus on development, structure, and composition of the microbial community characteristics involved in the process. The effect of microorganism seeding by the influent before and after the biofilter and ozone oxidation effects are explored to capture the microbial ecology interactions and environmental factors affecting the media ecosystem. The findings of reviewed studies concurred in identifying Proteobacteria as the most dominant phylum. However, Proteobacteria and other phyla relative abundance differ substantially depending upon environmental factors (e.g., pH, temperature, nutrients availability, among others) gradients. In general, we found significant gaps to relate and explain the biodegradation performance and metabolic processes within the biofilter, and hence deserve future attention. We highlighted and identified key challenges and future research ideas to assure O3-biofiltration reliability as a promising barrier in advanced water treatment applications.},
}
@article {pmid33935412,
year = {2021},
author = {Sergaliev, NK and Kakishev, MG and Ginayatov, NS and Nurzhanova, FK and Andronov, EE},
title = {Microbiome structure in a recirculating aquaculture system and its connection to infections in sturgeon fish.},
journal = {Veterinary world},
volume = {14},
number = {3},
pages = {661-668},
pmid = {33935412},
issn = {0972-8988},
abstract = {AIM: This study aimed to determine the bacterial composition at various stages of the temperature regime in a recirculating aquaculture system (RAS) to assess the pathological risk of a group of opportunistic pathogenic microflora.<br><br>MATERIALS AND METHODS: Water temperature, incidences of illnesses, and fish mortality were monitored, during the research period to identify the causes of pathogens in sturgeons. Analysis of the nucleotide sequences was performed using the quantitative insights into microbial ecology module. Sequence alignment in the analysis of the distribution of gene libraries was performed using the Unclust method. The RDP database was used for the taxonomic identification of operational taxonomic units.<br><br>RESULTS: The pattern of the contraction of infection among sturgeons bred in the RAS was established. A detailed analysis of the microbiome structure's taxonomic features showed dominant taxa during the "artificial wintering" period and at a temperature optimum in industrial aquaculture. It was found that the main outbreaks of pseudomonosis occurred during this period in the RAS. With a decrease in temperature of the aquatic environment, the incidence of illness increased by 75% compared with the optimum temperature period. Pseudomonas, Cetobacterium, and Lactococcus were specific taxa characteristic for the "artificial wintering" period. Xanthomonadaceae and Flavobacterium were specific taxa characteristic for the optimum temperature.<br><br>CONCLUSION: Consequently, the microbial structure was determined at different temperature regimes in a RAS, and the dominant communities were identified. The pattern of the contraction of infection caused by an opportunistic microflora (pseudomonosis) among sturgeons was established, allowing for the development and correction of treatment and preventive measures.},
}
@article {pmid33933764,
year = {2021},
author = {Vermeire, ML and Thoresen, J and Lennard, K and Vikram, S and Kirkman, K and Swemmer, AM and Te Beest, M and Siebert, F and Gordijn, P and Venter, Z and Brunel, C and Wolfaard, G and Krumins, JA and Cramer, MD and Hawkins, HJ},
title = {Fire and herbivory drive fungal and bacterial communities through distinct above- and belowground mechanisms.},
journal = {The Science of the total environment},
volume = {785},
number = {},
pages = {147189},
doi = {10.1016/j.scitotenv.2021.147189},
pmid = {33933764},
issn = {1879-1026},
mesh = {Bacteria ; Biomass ; Ecosystem ; *Fires ; Fungi ; Grassland ; *Herbivory ; Soil ; Soil Microbiology ; },
abstract = {Fire and herbivory are important natural disturbances in grassy biomes. Both drivers are likely to influence belowground microbial communities but no studies have unravelled the long-term impact of both fire and herbivory on bacterial and fungal communities. We hypothesized that soil bacterial communities change through disturbance-induced shifts in soil properties (e.g. pH, nutrients) while soil fungal communities change through vegetation modification (biomass and species composition). To test these ideas, we characterised soil physico-chemical properties (pH, acidity, C, N, P and exchangeable cations content, texture, bulk density, moisture), plant species richness and biomass, microbial biomass and bacterial and fungal community composition and diversity (using 16S and ITS rRNA amplicon sequencing, respectively) in six long-term (18 to 70 years) ecological research sites in South African savanna and grassland ecosystems. We found that fire and herbivory regimes profoundly modified soil physico-chemical properties, plant species richness and standing biomass. In all sites, an increase in woody biomass (ranging from 12 to 50%) was observed when natural disturbances were excluded. The intensity and direction of changes in soil properties were highly dependent on the topo-pedo-climatic context. Overall, fire and herbivory shaped bacterial and fungal communities through distinct driving forces: edaphic properties (including Mg, pH, Ca) for bacteria, and vegetation (herbaceous biomass and woody cover) for fungi. Fire and herbivory explained on average 7.5 and 9.8% of the fungal community variability, respectively, compared to 6.0 and 5.6% for bacteria. The relatively small changes in microbial communities due to natural disturbance is in stark contrast to dramatic vegetation and edaphic changes and suggests that soil microbial communities, having evolved with disturbance, are resistant to change. This represents both a buffer to short-term anthropogenic-induced changes and a restoration challenge in the face of long-term changes.},
}
@article {pmid33931358,
year = {2021},
author = {Lucas, SK and Feddema, E and Boyer, HC and Hunter, RC},
title = {Diversity of cystic fibrosis chronic rhinosinusitis microbiota correlates with different pathogen dominance.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {20},
number = {4},
pages = {678-681},
pmid = {33931358},
issn = {1873-5010},
support = {R01 HL136919/HL/NHLBI NIH HHS/United States ; T90 DE022732/DE/NIDCR NIH HHS/United States ; },
mesh = {Bacteria/classification/isolation &amp; purification ; Chronic Disease ; Correlation of Data ; Cystic Fibrosis/complications/*microbiology ; Humans ; Microbiota ; Rhinitis/complications/*microbiology ; Sinusitis/complications/*microbiology ; },
abstract = {Chronic rhinosinusitis (CRS) affects nearly all individuals with cystic fibrosis (CF) and is thought to serve as a reservoir for microbiota that subsequently colonize the lung. To better understand the microbial ecology of CRS, we generated a 16S rRNA gene sequencing profile of sinus mucus from CF-CRS patients. We show that CF-CRS sinuses harbor bacterial diversity not entirely captured by clinical culture. Culture data consistently identified the dominant organism in most patients, though lower abundance bacteria were not always identified. We also demonstrate that bacterial communities dominated by Staphylococcus spp. were significantly more diverse compared to those dominated by Pseudomonas spp. Diversity was not significantly associated with clinical factors or patient age, however, younger subjects yielded a much wider range of bacterial diversity. These data mirror bacterial community dynamics in the lung and provide additional insight into the role of sinus microbiota in chronic airway disease progression.},
}
@article {pmid33930130,
year = {2021},
author = {Co, R and Hug, LA},
title = {Prediction, enrichment and isolation identify a responsive, competitive community of cellulolytic microorganisms from a municipal landfill.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {5},
pages = {},
doi = {10.1093/femsec/fiab065},
pmid = {33930130},
issn = {1574-6941},
mesh = {Bacteria/genetics ; Metagenome ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Waste Disposal Facilities ; },
abstract = {Landfills are engineered, heterogeneously contaminated sites containing large reservoirs of paper waste. Cellulose degradation is an important process within landfill microbial ecology, and these anoxic, saturated environments are prime locations for discovery of cellulases that may offer improvements on industrial cellulose degradation efforts. We sampled leachate from three locations within a municipal landfill, a leachate collection cistern, and groundwater from an adjacent aquifer to identify cellulolytic populations and their associated cellulases. Metagenomic sequencing identified wide-spread and taxonomically diverse cellulolytic potential, with a notable scarcity of predicted exocellulases. 16S rRNA amplicon sequencing detected nine landfill microorganisms enriched in a customized leachate medium amended with microcrystalline cellulose or common paper stocks. Paper-enrichment cultures showed competition dynamics in response to the specific composition (lignin: hemi-cellulose: cellulose) of the different paper stocks. From leachate biomass, four novel cellulolytic bacteria were isolated, including two with the capacity for cellulolysis at industrially relevant temperatures. None of the isolates demonstrated exocellulase activity, consistent with the metagenome-based predictions. However, there was very little overlap between metagenome-derived predicted cellulolytic organisms, organisms enriched on paper sources, or the isolates, suggesting the landfill cellulolytic community is at low abundance but able to rapidly respond to introduced substrates.},
}
@article {pmid33928415,
year = {2022},
author = {Solans, M and Pelliza, YI and Tadey, M},
title = {Inoculation with Native Actinobacteria May Improve Desert Plant Growth and Survival with Potential Use for Restoration Practices.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {380-392},
pmid = {33928415},
issn = {1432-184X},
support = {PIP 0235.//Conicet/ ; PICT 3478//FONCYT/ ; },
mesh = {*Actinobacteria ; *Ecosystem ; Plant Development ; Seedlings/microbiology ; Soil ; },
abstract = {Soil microorganisms, together with water, play a key role in arid ecosystems, being responsible for the nutrient cycle, facilitating nutrient incorporation into plants, influencing plant drought tolerance, and enhancing their establishment. Therefore, their use for restoration practices is promising. We tested the potential of native strains of Actinobacteria from Monte Desert as growth promoters of native vegetation, isolating them from two substrates from their habitat (bare soil and leaf-cutting ant refuse dumps). Strains were inoculated into the soil where seedlings of three native plant species (Atriplex lampa, Grindelia chiloensis, Gutierrezia solbrigii) were growing. Seedlings were grown following a full factorial design experiment under greenhouse and field conditions comparing native Actinobacteria effects with a known growth-promoting strain, Streptomyces sp. (BCRU-MM40 GenBank accession number: FJ771041), and control treatments. Seedlings survived greenhouse condition but species survival and growth were different among treatments at field conditions, varying over time. The highest survival was observed in a native soil strain (S20) while the lowest in MM40. The low survival in MM40 and in the other treatments may be explained by the higher herbivory observed in those seedlings compared to control ones, suggesting a higher nutritional status in inoculated plants. Strains from refuse dumps were the best at enhancing seedling growth, while strains from soil were the best at maintaining their survival. Native Actinobacteria studied may increase plant species survival and growth by improving their nutritional status, suggesting their potential to facilitate vegetation establishment and, therefore, being good candidates for restoration practices. Furthermore, plant species respond differently to different strains, highlighting the importance of microorganism diversity for ecosystem functioning.},
}
@article {pmid33927711,
year = {2021},
author = {Griggs, RG and Steenwerth, KL and Mills, DA and Cantu, D and Bokulich, NA},
title = {Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {673810},
pmid = {33927711},
issn = {1664-302X},
abstract = {Microbiomes are integral to viticulture and winemaking - collectively termed winegrowing - where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.},
}
@article {pmid33927707,
year = {2021},
author = {Orevi, T and Kashtan, N},
title = {Life in a Droplet: Microbial Ecology in Microscopic Surface Wetness.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {655459},
pmid = {33927707},
issn = {1664-302X},
abstract = {While many natural and artificial surfaces may appear dry, they are in fact covered by thin liquid films and microdroplets invisible to the naked eye known as microscopic surface wetness (MSW). Central to the formation and the retention of MSW are the deliquescent properties of hygroscopic salts that prevent complete drying of wet surfaces or that drive the absorption of water until dissolution when the relative humidity is above a salt-specific level. As salts are ubiquitous, MSW occurs in many microbial habitats, such as soil, rocks, plant leaf, and root surfaces, the built environment, and human and animal skin. While key properties of MSW, including very high salinity and segregation into droplets, greatly affect microbial life therein, it has been scarcely studied, and systematic studies are only in their beginnings. Based on recent findings, we propose that the harsh micro-environment that MSW imposes, which is very different from bulk liquid, affects key aspects of bacterial ecology including survival traits, antibiotic response, competition, motility, communication, and exchange of genetic material. Further research is required to uncover the fundamental principles that govern microbial life and ecology in MSW. Such research will require multidisciplinary science cutting across biology, physics, and chemistry, while incorporating approaches from microbiology, genomics, microscopy, and computational modeling. The results of such research will be critical to understand microbial ecology in vast terrestrial habitats, affecting global biogeochemical cycles, as well as plant, animal, and human health.},
}
@article {pmid33925970,
year = {2021},
author = {Saw, NMMT and Suwanchaikasem, P and Zuniga-Montanez, R and Qiu, G and Marzinelli, EM and Wuertz, S and Williams, RBH},
title = {Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR).},
journal = {Metabolites},
volume = {11},
number = {5},
pages = {},
pmid = {33925970},
issn = {2218-1989},
support = {1102-IRIS-10-02//National Research Foundation, Republic of Singapore/ ; },
abstract = {Metabolome profiling is becoming more commonly used in the study of complex microbial communities and microbiomes; however, to date, little information is available concerning appropriate extraction procedures. We studied the influence of different extraction solvent mixtures on untargeted metabolomics analysis of two continuous culture enrichment communities performing enhanced biological phosphate removal (EBPR), with each enrichment targeting distinct populations of polyphosphate-accumulating organisms (PAOs). We employed one non-polar solvent and up to four polar solvents for extracting metabolites from biomass. In one of the reactor microbial communities, we surveyed both intracellular and extracellular metabolites using the same set of solvents. All samples were analysed using ultra-performance liquid chromatography mass spectrometry (UPLC-MS). UPLC-MS data obtained from polar and non-polar solvents were analysed separately and evaluated using extent of repeatability, overall extraction capacity and the extent of differential abundance between physiological states. Despite both reactors demonstrating the same bioprocess phenotype, the most appropriate extraction method was biomass specific, with methanol: water (50:50 v/v) and methanol: chloroform: water (40:40:20 v/v) being chosen as the most appropriate for each of the two different bioreactors, respectively. Our approach provides new data on the influence of solvent choice on the untargeted surveys of the metabolome of PAO enriched EBPR communities and suggests that metabolome extraction methods need to be carefully tailored to the specific complex microbial community under study.},
}
@article {pmid33923841,
year = {2021},
author = {van der Linde, C and Barone, M and Turroni, S and Brigidi, P and Keleszade, E and Swann, JR and Costabile, A},
title = {An In Vitro Pilot Fermentation Study on the Impact of Chlorella pyrenoidosa on Gut Microbiome Composition and Metabolites in Healthy and Coeliac Subjects.},
journal = {Molecules (Basel, Switzerland)},
volume = {26},
number = {8},
pages = {},
pmid = {33923841},
issn = {1420-3049},
mesh = {*Chlorella ; Enterobacteriaceae/classification/genetics ; Fermentation/physiology ; Gastrointestinal Microbiome/*physiology ; RNA, Ribosomal, 16S ; },
abstract = {The response of a coeliac and a healthy gut microbiota to the green algae Chlorella pyrenoidosa was evaluated using an in vitro continuous, pH controlled, gut model system, which simulated the human colon. The effect of C. pyrenoidosa on the microbial structure was determined by 16S rRNA gene sequencing and inferred metagenomics, whereas the metabolic activitywas determined by[1]H-nuclear magnetic resonancespectroscopic analysis. The addition of C. pyrenoidosa significantly increased the abundance of the genera Prevotella, Ruminococcus and Faecalibacterium in the healthy donor, while an increase in Faecalibacterium, Bifidobacterium and Megasphaera and a decrease in Enterobacteriaceae were observed in the coeliac donor. C. pyrenoidosa also altered several microbial pathways including those involved in short-chain fatty acid (SCFA) production. At the metabolic level, a significant increase from baseline was seen in butyrate and propionate (p < 0.0001) in the healthy donor, especially in vessels 2 and 3. While acetate was significantly higher in the healthy donor at baseline in vessel 3 (p < 0.001) compared to the coeliac donor, this was markedly decreased after in vitro fermentation with C. pyrenoidosa. This is the first in vitro fermentation study of C. pyrenoidosa and human gut microbiota, however, further in vivo studies are needed to prove its efficacy.},
}
@article {pmid33922357,
year = {2021},
author = {Oh, RM and Bollati, E and Maithani, P and Huang, D and Wainwright, BJ},
title = {The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore.},
journal = {Microorganisms},
volume = {9},
number = {5},
pages = {},
pmid = {33922357},
issn = {2076-2607},
abstract = {The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.},
}
@article {pmid33920240,
year = {2021},
author = {Skliros, D and Kalatzis, PG and Kalloniati, C and Komaitis, F and Papathanasiou, S and Kouri, ED and Udvardi, MK and Kokkari, C and Katharios, P and Flemetakis, E},
title = {The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy.},
journal = {Viruses},
volume = {13},
number = {4},
pages = {},
pmid = {33920240},
issn = {1999-4915},
mesh = {*Adaptation, Physiological ; Bacteriophages/*genetics/pathogenicity ; Drug Resistance, Bacterial ; Gene Expression Profiling ; Genome, Viral ; Genomics ; Host Microbial Interactions/*genetics ; Metabolic Networks and Pathways/genetics ; Metabolomics ; Phage Therapy ; Phylogeny ; Vibrio alginolyticus/*genetics/*metabolism/virology ; },
abstract = {Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine Vibrios has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. The results of our multi-omics approach, incorporating transcriptome and metabolome analyses of Vibrio alginolyticus phage-resistant strains, corroborate this prospect. Our results provide insights into phage-tolerant strains diminishing the expression of phage receptors ompF, lamB, and btuB. The same pattern was observed for genes encoding natural nutrient channels, such as rbsA, ptsG, tryP, livH, lysE, and hisp, meaning that the cell needs to readjust its biochemistry to achieve phage resistance. The results showed reprogramming of bacterial metabolism by transcript regulations in key-metabolic pathways, such as the tricarboxylic acid cycle (TCA) and lysine biosynthesis, as well as the content of intracellular metabolites belonging to processes that could also significantly affect the cell physiology. Finally, SNP analysis in resistant strains revealed no evidence of amino acid alterations in the studied putative bacterial phage receptors, but several SNPs were detected in genes involved in transcriptional regulation. This phenomenon appears to be a phage-specific, fine-tuned metabolic engineering, imposed by the different phage genera the bacteria have interacted with, updating the role of lytic phages in microbial marine ecology.},
}
@article {pmid33919845,
year = {2021},
author = {Thompson, HJ and Levitt, JO and McGinley, JN and Chandler, P and Guenther, PM and Huybrechts, I and Playdon, MC},
title = {Measuring Dietary Botanical Diversity as a Proxy for Phytochemical Exposure.},
journal = {Nutrients},
volume = {13},
number = {4},
pages = {},
pmid = {33919845},
issn = {2072-6643},
support = {001/WHO_/World Health Organization/International ; 5R00CA218694-03/CA/NCI NIH HHS/United States ; },
mesh = {Aged ; Algorithms ; Chronic Disease/prevention &amp; control ; Diet Surveys/*methods/statistics &amp; numerical data ; Feeding Behavior/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; *Phytochemicals ; Plants, Edible/*chemistry ; },
abstract = {The study of natural plant molecules and their medicinal properties, pharmacognosy, provides a taxonomy for botanical families that represent diverse chemical groupings with potentially distinct functions in relation to human health. Yet, this reservoir of knowledge has not been systematically applied to elucidating the role of patterns of plant food consumption on gut microbial ecology and function. All chemical classes of dietary phytochemicals can affect the composition of the microbes that colonize the gut and their function. In turn, the gut microbiome affects the host via multiple mechanisms including gut barrier function, immune function, satiety and taste regulation and the activity of biological signaling pathways that influence health and disease. Herein, we report the development of a botanical diversity index (BDI) to evaluate plant food consumption as a novel metric for identifying and quantifying phytochemicals to which an individual is exposed. A rationale is advanced for using the BDI to investigate how plant food diversity impacts gut microbial ecology and functionality.},
}
@article {pmid33918726,
year = {2021},
author = {Khomutovska, N and de Los Ríos, A and Syczewski, MD and Jasser, I},
title = {Connectivity of Edaphic and Endolithic Microbial Niches in Cold Mountain Desert of Eastern Pamir (Tajikistan).},
journal = {Biology},
volume = {10},
number = {4},
pages = {},
pmid = {33918726},
issn = {2079-7737},
support = {DSM501-D114-86-0117600-16//Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw/ ; PID2019-105469RB-C22//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2015/19/B/NZ9/00473//Narodowe Centrum Nauki/ ; },
abstract = {Microbial communities found in arid environments are commonly represented by biological soil crusts (BSCs) and endolithic assemblages. There is still limited knowledge concerning endoliths and BSCs occurring in the cold mountain desert of Pamir. The aim of the study was to investigate the composition and structure of endolithic bacterial communities in comparison to surrounding BSCs in three subregions of the Eastern Pamir (Tajikistan). The endolithic and BSC communities were studied using culture-independent and culture-dependent techniques. The structure of the endolithic bacterial communities can be characterized as Actinobacteria-Proteobacteria-Bacteroidetes-Chloroflexi-Cyanobacteria, while the BSCs' can be described as Proteobacteria-Actinobacteria-Bacteroidetes-Cyanobacteria assemblages with low representation of other bacteria. The endolithic cyanobacterial communities were characterized by the high percentage of Chroococcidiopsaceae, Nodosilineaceae, Nostocaceae and Thermosynechococcaceae, while in the BSCs were dominated by Nodosilineaceae, Phormidiaceae and Nostocaceae. The analysis of 16S rRNA genes of the cyanobacterial cultures revealed the presence of possibly novel species of Chroococcidiopsis, Gloeocapsopsis and Wilmottia. Despite the niches' specificity, which is related to the influence of microenvironment factors on the composition and structure of endolithic communities, our results illustrate the interrelation between the endoliths and the surrounding BSCs in some regions. The structure of cyanobacterial communities from BSC was the only one to demonstrate some subregional differences.},
}
@article {pmid33911260,
year = {2021},
author = {Kremer, JM and Sohrabi, R and Paasch, BC and Rhodes, D and Thireault, C and Schulze-Lefert, P and Tiedje, JM and He, SY},
title = {Peat-based gnotobiotic plant growth systems for Arabidopsis microbiome research.},
journal = {Nature protocols},
volume = {16},
number = {5},
pages = {2450-2470},
pmid = {33911260},
issn = {1750-2799},
support = {R01 GM109928/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Arabidopsis/*growth &amp; development/*microbiology ; Culture Techniques/*methods ; Germ-Free Life ; Industry ; *Microbiota ; Soil/*chemistry ; },
abstract = {The complex structure and function of a plant microbiome are driven by many variables, including the environment, microbe-microbe interactions and host factors. Likewise, resident microbiota can influence many host phenotypes. Gnotobiotic growth systems and controlled environments empower researchers to isolate these variables, and standardized methods equip a global research community to harmonize protocols, replicate experiments and collaborate broadly. We developed two easily constructed peat-based gnotobiotic growth platforms: the FlowPot system and the GnotoPot system. Sterile peat is amenable to colonization by microbiota and supports growth of the model plant Arabidopsis thaliana in the presence or absence of microorganisms. The FlowPot system uniquely allows one to flush the substrate with water, nutrients and/or suspensions of microbiota via an irrigation port, and a mesh retainer allows for the inversion of plants for dip or vacuum infiltration protocols. The irrigation port also facilitates passive drainage, preventing root anoxia. In contrast, the GnotoPot system utilizes a compressed peat pellet, widely used in the horticultural industry. GnotoPot construction has fewer steps and requires less user handling, thereby reducing the risk of contamination. Both protocols take up to 4 d to complete with 4-5 h of hands-on time, including substrate and seed sterilization. In this protocol, we provide detailed assembly and inoculation procedures for the two systems. Both systems are modular, do not require a sterile growth chamber, and cost less than US$2 per vessel.},
}
@article {pmid33906488,
year = {2022},
author = {García-González, I and Corona-Cervantes, K and Hernández-Quiroz, F and Villalobos-Flores, LE and Galván-Rodríguez, F and Romano, MC and Miranda-Brito, C and Piña-Escobedo, A and Borquez-Arreortúa, FG and Rangel-Calvillo, MN and García-Mena, J},
title = {The Influence of Holder Pasteurization on the Diversity of the Human Milk Bacterial Microbiota Using High-Throughput DNA Sequencing.},
journal = {Journal of human lactation : official journal of International Lactation Consultant Association},
volume = {38},
number = {1},
pages = {118-130},
doi = {10.1177/08903344211011946},
pmid = {33906488},
issn = {1552-5732},
mesh = {Bacteria/genetics ; Breast Feeding ; Cross-Sectional Studies ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; *Microbiota/genetics ; *Milk Banks ; Milk, Human/microbiology ; Pasteurization ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Human milk is the best food for infants; however, when breastfeeding is not possible, pasteurized milk from human milk banks is the best alternative. Little has been reported about variations in the bacterial microbiota composition of human milk after pasteurization.<br><br>RESEARCH AIM: To characterize and compare the bacterial microbiota composition and diversity within human milk among Mexican mothers before and after the Holder pasteurization process.<br><br>METHODS: A cross-sectional, observational, and comparative design was used. The effect of the pasteurization process on the bacterial composition and diversity of human milk samples of donors (N = 42) from a public milk bank was assessed before and after pasteurization by high throughput deoxyribonucleic acid sequencing of V3-16S rRNA gene libraries. Sequencing data were examined using the Quantitative Insights into Microbial Ecology software and Phyloseq in R environment.<br><br>RESULTS: A varied community of bacteria was found in both raw and pasteurized human milk. The bacterial diversity of the milk samples was increased by the pasteurization, where some thermoduric bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were more abundant. The source tracker analysis indicated that at most 1.0% of bacteria may have come from another source, showing the safety of the process used to treat milk samples.<br><br>CONCLUSION: The pasteurization process increased the bacterial diversity. We selected taxa capable of surviving the process, which could proliferate after the treatment without being a risk for infants.},
}
@article {pmid33903927,
year = {2022},
author = {Kajan, K and Cukrov, N and Cukrov, N and Bishop-Pierce, R and Orlić, S},
title = {Microeukaryotic and Prokaryotic Diversity of Anchialine Caves from Eastern Adriatic Sea Islands.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {257-270},
pmid = {33903927},
issn = {1432-184X},
support = {KK.01.1.1.01//European Regional Development Fund/ ; },
mesh = {*Biodiversity ; *Ecosystem ; Geography ; Islands ; Salinity ; },
abstract = {Anchialine ecosystems in the eastern Adriatic Sea are diverse both morphologically and biologically. In this study, for the first time, we explored the microeukaryotic and prokaryotic community of anchialine caves in the Mediterranean region using high-throughput sequencing. Four anchialine caves located on nearby islands with a well-pronounced salinity gradient were sampled at the surface freshwater area, halocline area, and seawater area. Sequencing revealed a surprisingly wide diversity of the microeukaryotic and prokaryotic community with the relative abundance of major phyla differing within the salinity gradient and between the caves. Interestingly, microeukaryotic and prokaryotic communities clustered into four groups based on location, pointing out that sampled anchialine caves have different microbial community patterns and high microbial endemism. Our results indicate that even with the halocline acting as a selecting barrier, the salinity is not the only community structuring factor. Despite the short geographical distance, the isolation of anchialine caves facilitated high microbial community adaptation and endemism. Our study suggests that anchialine caves represent reservoirs of new biodiversity, maintaining unique and complex microbial diversity influenced by biotic interactions and abiotic environmental conditions.},
}
@article {pmid33902741,
year = {2021},
author = {Zhou, X and Leite, MFA and Zhang, Z and Tian, L and Chang, J and Ma, L and Li, X and van Veen, JA and Tian, C and Kuramae, EE},
title = {Facilitation in the soil microbiome does not necessarily lead to niche expansion.},
journal = {Environmental microbiome},
volume = {16},
number = {1},
pages = {4},
pmid = {33902741},
issn = {2524-6372},
support = {XDA23070501, XDB15030103//Science Foundation of the Chinese Academy of Sciences/ ; 2016YFC0501202//National Key Research and Development Program of China/ ; KFZD-SW-112//Key Research Project of the Chinese Academy of Sciences/ ; 41571255//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown.<br><br>RESULTS: Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent.<br><br>CONCLUSIONS: Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.},
}
@article {pmid33902740,
year = {2020},
author = {Chopyk, J and Nasko, DJ and Allard, S and Bui, A and Pop, M and Mongodin, EF and Sapkota, AR},
title = {Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond.},
journal = {Environmental microbiome},
volume = {15},
number = {1},
pages = {18},
pmid = {33902740},
issn = {2524-6372},
support = {2016-68007-25064//United States Department of Agriculture-National Institute of Food and Agriculture/ ; 1632976//National Science Foundation/ ; },
abstract = {BACKGROUND: Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond.<br><br>RESULTS: Water samples (n&#x2009;=&#x2009;14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2&#x2009;&#x3bc;m filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae.<br><br>CONCLUSIONS: Overall, this study provides one of the&#xa0;largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.},
}
@article {pmid33902721,
year = {2020},
author = {Tang, X and Xie, G and Shao, K and Hu, Y and Cai, J and Bai, C and Gong, Y and Gao, G},
title = {Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China.},
journal = {Environmental microbiome},
volume = {15},
number = {1},
pages = {10},
pmid = {33902721},
issn = {2524-6372},
support = {NIGLAS2017GH05//"One-Three-Five" Strategic Planning of NGLAS, CAS/ ; 41971062//National Natural Science Foundation of China/ ; 41790423//National Natural Science Foundation of China/ ; 41621002//National Natural Science Foundation of China/ ; QYZDJ-SSW-DQC008//Key Research Program of Frontier Sciences, CAS/ ; },
abstract = {BACKGROUND: Microorganisms in rivers and lakes are essential for nutrient recycling in aquatic ecosystems. Understanding the ecological processes shaping microbial communities is of crucial importance for aquatic microbial ecology and biogeography. However, the diversity of microorganisms and the forces that control this diversity are poorly understood. This is particularly true within the framework of the river-lake continuum in arid regions.<br><br>RESULTS: Using a whole catchment-sampling effort, we explored biogeographical patterns and mechanisms of microbial community (bacteria and archaea) assembly within the catchment of the largest inland once&#xa0;freshwater&#xa0;lake (Lake Bosten) in China. Water samples from headstream tributaries, the mainstream of the River Kaidu to downstream Lake Bosten were characterized using amplicon sequencing of 16S rRNA genes. Higher &#x3b1;-diversity was found in mainstream of River Kaidu and in the tributaries compared with Lake Bosten. And the microbial community composition was also significantly different between the&#xa0;lake and its connected river habitats. Canonical correspondence analysis demonstrated that salinity and total suspended solids were the most important environmental factors shaping the community variations. Overall, pure environmental and pure spatial factors explained 13.7 and 5.6% of the community variation, respectively, while 32.0% of the variation was explained by combined environmental and spatial variables. These observations suggested that spatially structured environmental variations mainly shaped the microbial biogeography in this region. Both deterministic and stochastic processes influenced the microbial community assembly in river and lake habitats, and the stochastic pattern was particularly pronounced for microbiome in river habitat. Co-occurrence network analysis revealed more abundant and complicated correlations among frequently occurred taxa in lake habitat compared with the river habitat, implying that ecological multispecies interactions (e.g., competition) shaped lake microbial community structures.<br><br>CONCLUSIONS: Our findings demonstrate an ecological succession along the river-lake continuum of microbial communities across the largest inland once&#xa0;freshwater lake basin in China, and highlight the effects of spatially structured environmental factors on regional microbial &#x3b2;-diversity and species interactions on local community assembly.},
}
@article {pmid33902717,
year = {2020},
author = {Bagnaro, A and Baltar, F and Brownstein, G and Lee, WG and Morales, SE and Pritchard, DW and Hepburn, CD},
title = {Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems - focus on the pelagic environment.},
journal = {Environmental microbiome},
volume = {15},
number = {1},
pages = {16},
pmid = {33902717},
issn = {2524-6372},
abstract = {BACKGROUND: One of the central objectives of microbial ecology is to study the distribution of microbial communities and their association with their environments. Biogeographical studies have partitioned the oceans into provinces and regions, but the identification of their boundaries remains challenging, hindering our ability to study transition zones (i.e. ecotones) and microbial ecosystem heterogeneity. Fuzzy clustering is a promising method to do so, as it creates overlapping sets of clusters. The outputs of these analyses thus appear both structured (into clusters) and gradual (due to the overlaps), which aligns with the inherent continuity of the pelagic environment, and solves the issue of defining ecosystem boundaries.<br><br>RESULTS: We show the suitability of applying fuzzy clustering to address the patchiness of microbial ecosystems, integrating environmental (Sea Surface Temperature, Salinity) and bacterioplankton data (Operational Taxonomic Units (OTUs) based on 16S rRNA gene) collected during six cruises over 1.5&#x2009;years from the subtropical frontal zone off New Zealand. The technique was able to precisely identify ecological heterogeneity, distinguishing both the patches and the transitions between them. In particular we show that the subtropical front is a distinct, albeit transient, microbial ecosystem. Each water mass harboured a specific microbial community, and the characteristics of their ecotones matched the characteristics of the environmental transitions, highlighting that environmental mixing lead to community mixing. Further explorations into the OTU community compositions revealed that, although only a small proportion of the OTUs explained community variance, their associations with given water mass were consistent through time.<br><br>CONCLUSION: We demonstrate recurrent associations between microbial communities and dynamic oceanic features. Fuzzy clusters can be applied to any ecosystem (terrestrial, human, marine, etc) to solve uncertainties regarding the position of microbial ecological boundaries and to refine the relation between the distribution of microorganisms and their environment.},
}
@article {pmid33901904,
year = {2021},
author = {Rahman, MS and Kazmi, SSUH and Uroosa, and Xu, H},
title = {Insights into seasonal shift in the homogeneity of periphytic protozoan fauna in coastal waters of the Yellow Sea, northern China.},
journal = {Marine pollution bulletin},
volume = {168},
number = {},
pages = {112367},
doi = {10.1016/j.marpolbul.2021.112367},
pmid = {33901904},
issn = {1879-3363},
mesh = {Biodiversity ; China ; *Ciliophora ; *Ecosystem ; Environmental Monitoring ; Seasons ; },
abstract = {The seasonal shift in the homogeneity of the periphytic protozoan fauna was studied based on a four-season baseline survey in the coastal waters of the Yellow Sea, northern China. Samples were collected using glass microscope slides as an artificial substratum at a depth of 2 m after the immersion time of 14 days during each of the four seasons (winter, spring, summer, and autumn, 2017). The protozoan fauna showed a clear seasonal shift in species composition and a significant variation in homogeneity in terms of both compositional and community structure during four seasons. The dispersion measures and β-diversity index represented an increase in the trend from spring to winter. These findings suggest that the homogeneity of the periphytic protozoan fauna was subject to a significant variability shaped mainly by species composition during a four-season cycle in marine ecosystems.},
}
@article {pmid33899919,
year = {2021},
author = {Lin, Q and Dini-Andreote, F and Li, L and Umari, R and Novotny, V and Kukla, J and Heděnec, P and Frouz, J},
title = {Soil microbial interconnections along ecological restoration gradients of lowland forests after slash-and-burn agriculture.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {5},
pages = {},
doi = {10.1093/femsec/fiab063},
pmid = {33899919},
issn = {1574-6941},
mesh = {Agriculture ; Basidiomycota ; *Burns ; Ecosystem ; Forests ; Fungi/genetics ; Humans ; Papua New Guinea ; *Soil ; Soil Microbiology ; },
abstract = {Microbial interconnections in soil are pivotal to ecosystem services and restoration. However, little is known about how soil microbial interconnections respond to slash-and-burn agriculture and to the subsequent ecosystem restoration after the practice. Here, we used amplicon sequencing and co-occurrence network analyses to explore the interconnections within soil bacterial and fungal communities in response to slash-and-burn practice and a spontaneous restoration (spanning ca. 60 years) of tropical forests after the practice, in Papua New Guinea. We found significantly higher complexity and greater variations in fungal networks than in those of bacteria, despite no significant changes observed in bacterial or fungal networks across successional stages. Within most successional stages, bacterial core co-occurrences (co-occurrences consistently present across all sub-networks in a stage) were more frequent than those of fungi, indicating higher stability of interconnections between bacteria along succession. The stable interconnections occurred frequently between bacterial taxa (i.e. Sporosarcina, Acidimicrobiale and Bacillaceae) and between ectomycorrhizal fungi (Boletaceae and Russula ochroleuca), implying important ecological roles of these taxa in the ecosystem restoration. Collectively, our results provide new insight into microbial interconnections in response to slash-and-burn agriculture and the subsequent ecosystem restoration, thus promoting a better understanding of microbial roles in ecosystem services and restoration.},
}
@article {pmid33897672,
year = {2021},
author = {Estrela, S and Sánchez, &#xc1; and Rebolleda-Gómez, M},
title = {Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {657467},
pmid = {33897672},
issn = {1664-302X},
support = {R35 GM133467/GM/NIGMS NIH HHS/United States ; },
abstract = {Recent advances in robotics and affordable genomic sequencing technologies have made it possible to establish and quantitatively track the assembly of enrichment communities in high-throughput. By conducting community assembly experiments in up to thousands of synthetic habitats, where the extrinsic sources of variation among replicates can be controlled, we can now study the reproducibility and predictability of microbial community assembly at different levels of organization, and its relationship with nutrient composition and other ecological drivers. Through a dialog with mathematical models, high-throughput enrichment communities are bringing us closer to the goal of developing a quantitative predictive theory of microbial community assembly. In this short review, we present an overview of recent research on this growing field, highlighting the connection between theory and experiments and suggesting directions for future work.},
}
@article {pmid33893533,
year = {2022},
author = {Ding, L and Zhou, J and Li, Q and Tang, J and Chen, X},
title = {Effects of Land-Use Type and Flooding on the Soil Microbial Community and Functional Genes in Reservoir Riparian Zones.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {393-407},
pmid = {33893533},
issn = {1432-184X},
support = {2016YFC0502703//the National Key Research and Development Program of China/ ; 31470483//National Natural Science Foundation of China/ ; 31570411//National Natural Science Foundation of China/ ; },
mesh = {Archaea/genetics ; *Microbiota/genetics ; Nitrogen Cycle ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {Ecological processes (e.g., nutrient cycling) in riparian zones are often affected by land-use type and flooding. The extent to which land-use types and flooding conditions affect soil microorganisms and their ecological functions in riparian zones is not well known. By using high-throughput sequencing and quantitative PCR (q-PCR), we tested the effects of three land-use types (i.e., forest, wetland, and grassland) and two flooding conditions (i.e., landward locations and waterward locations within the land-use types) on soil microbial communities and microbial functional genes in the riparian zones of a reservoir. Land-use type but not flooding significantly affected soil microbial community composition at the phylum level, while both land-use type and flooding significantly affected the orders Nitrosotaleales and Nitrososphaerales. Alpha diversity was higher in the wetland and forest regardless of flooding conditions. Functional gene abundance differed among the three land-use types. Archaeal amoA (AOA) and nirS genes were more abundant in the wetland than in the grassland or forest. Bacterial amoA (AOB), nirK, nirS, and nosZ genes were more abundant in the waterward location than in the landward location but only in the wetland. Soil pH, moisture, and concentrations of soil organic matter and total soil nitrogen were significantly associated with the composition of archaeal and bacterial communities as well as with their gene abundance. This study revealed that soil microorganisms putatively involved in nitrogen cycling in riparian zones were more affected by land-use type than flooding.},
}
@article {pmid33893532,
year = {2022},
author = {Maltsev, Y and Maltseva, S and Maltseva, I},
title = {Diversity of Cyanobacteria and Algae During Primary Succession in Iron Ore Tailing Dumps.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {408-423},
pmid = {33893532},
issn = {1432-184X},
mesh = {*Cyanobacteria ; *Ecosystem ; Iron ; Soil/chemistry ; Soil Microbiology ; },
abstract = {The extraction of commercial minerals is often accompanied by the formation of large areas of quarry and dump technogenic ecosystems. This stimulates the search for measures to reduce their negative impact on the environment, as well as a detailed study of all the constituent elements of ecosystems that spontaneously or after reclamation form on them. Primary stages of syngenesis on the tailing dumps of iron ore mines in Kryvorizhzhia took place involving cyanobacteria and eukaryotic algae. The dynamics of the community structures of algae and cyanobacteria depends on the mineralogical composition of tailings, salinity conditions, pH, and content of particles of physical clay and humus. The assessment of the features of the dynamics of algae communities was carried out based on the ordination procedure because of the method of non-metric multidimensional scaling. The considered environmental variables were statistically significant predictors of community structure and could explain 47-90% of the variation in measurements. Diagnostic signs of the species composition of communities of algae and cyanobacteria tailing dumps were established by physical and chemical parameters. An increase in the content of physical clay particles in the substrate and a pH shift towards the alkaline side increased the species richness of cyanobacteria, while an increase in the humus content increased the total species diversity. Based on the specificity of the type of growth and the species composition of algae communities, when describing the primary successions, it is proposed to allocate the following stages of development of algae and cyanobacteria communities: dispersal aerophyton, stratose epilitophyton, algal crust, mixed moss and algal crust, and edaphone.},
}
@article {pmid33892834,
year = {2021},
author = {Delikan, E and Caliskan, S and Cankilic, MY and Aksu, S and Kesim, B and Ulger, ST},
title = {Microbiota of Endodontically Infected Primary and Permanent Teeth.},
journal = {Pediatric dentistry},
volume = {43},
number = {2},
pages = {102-110},
pmid = {33892834},
issn = {1942-5473},
mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Tooth, Deciduous ; },
abstract = {Purpose: Differences in the endodontic microbiome of permanent and primary teeth during the mixed dentition period are still unknown. The purpose of this study was to examine bacterial diversity in endodontically infected primary and permanent teeth using 16S rRNA gene sequencing and the QIIME 2 (Quantitative Insights Into Microbial Ecology 2) bioinformatics pipeline. Methods: Microbial samples from endodontically infected primary (n equals 15) and permanent (n equals 15) maxillary or mandibular molar teeth were subjected to next-generation sequencing analysis based on examination of the hypervariable V3 to V4 region of the 16S rRNA gene. Statistical analysis was performed using R software. Results: Of 1,664,926 reads and 2,237 operational taxonomic units, 14 phyla, 89 families, and 236 genera were identified. Firmicutes were the most commonly detected phyla in both endodontically infected primary and permanent root canals. Bacteroides and Proteobacteria were more common in primary teeth, whereas Actinobacteria and Verrucomicrobia were more common in permanent teeth. The overall canal microbiota composition was similar in endodontically infected primary and permanent teeth (P=0.338). Conclusions: This study provides a comprehensive assessment of microbiota composition in endodontically infected primary and permanent teeth and gives a deeper insight into the origin of the root canal infections.},
}
@article {pmid33891367,
year = {2021},
author = {Wang, T and Persson, P and Tunlid, A},
title = {A widespread mechanism in ectomycorrhizal fungi to access nitrogen from mineral-associated proteins.},
journal = {Environmental microbiology},
volume = {23},
number = {10},
pages = {5837-5849},
doi = {10.1111/1462-2920.15539},
pmid = {33891367},
issn = {1462-2920},
mesh = {Fungi/metabolism ; Minerals/metabolism ; *Mycorrhizae/metabolism ; Nitrogen/metabolism ; Soil/chemistry ; Soil Microbiology ; },
abstract = {A large fraction of nitrogen (N) in forest soils is present in mineral-associated proteinaceous compounds. The strong association between proteins and minerals limits microbial accessibility to this source, which is a relatively stable reservoir of soil N. We have shown that the ectomycorrhizal (ECM) fungus Paxillus involutus can acquire N from iron oxide-associated proteins. Using tightly controlled isotopic, spectroscopic and chromatographic experiments, we demonstrated that the capacity to access N from iron oxide-associated bovine serum albumin (BSA) is shared with the ECM fungi Hebeloma cylindrosporum and Piloderma olivaceum. Despite differences in evolutionary history, growth rates, exploration types and the decomposition mechanisms of organic matter, their N acquisition mechanisms were similar to those described for P. involutus. The fungi released N from mineral-associated BSA by direct action of extracellular aspartic proteases on the mineral-associated BSA, without initial desorption of the protein. Hydrolysis was suppressed by the adsorption of proteases to minerals, but this adverse effect was counteracted by the secretion of compounds that conditioned the mineral surface. These data suggest that the enzymatic exudate-driven mechanism to access N from mineral-associated proteins is found in ECM fungi of multiple lineages and exploration types.},
}
@article {pmid33890146,
year = {2022},
author = {Kanjanapruthipong, T and Sukphopetch, P and Reamtong, O and Isarangkul, D and Muangkaew, W and Thiangtrongjit, T and Sansurin, N and Fongsodsri, K and Ampawong, S},
title = {Cytoskeletal Alteration Is an Early Cellular Response in Pulmonary Epithelium Infected with Aspergillus fumigatus Rather than Scedosporium apiospermum.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {216-235},
pmid = {33890146},
issn = {1432-184X},
support = {CU_FRB640001_01_33_1//TSRI Fund/ ; },
mesh = {A549 Cells ; Animals ; *Aspergillus fumigatus ; Cytoskeleton/*microbiology ; Epithelium/*microbiology ; Humans ; Lung ; Mice ; *Mycoses ; *Scedosporium ; },
abstract = {Invasive aspergillosis and scedosporiosis are life-threatening fungal infections with similar clinical manifestations in immunocompromised patients. Contrarily, Scedosporium apiospermum is susceptible to some azole derivative but often resistant to amphotericin B. Histopathological examination alone cannot diagnose these two fungal species. Pathogenesis studies could contribute to explore candidate protein markers for new diagnosis and treatment methods leading to a decrease in mortality. In the present study, proteomics was conducted to identify significantly altered proteins in A549 cells infected with or without Aspergillus fumigatus and S. apiospermum as measured at initial invasion. Protein validation was performed with immunogold labelling alongside immunohistochemical techniques in infected A549 cells and lungs from murine models. Further, cytokine production was measured, using the Bio-Plex-Multiplex immunoassay. The cytoskeletal proteins HSPA9, PA2G4, VAT1, PSMA2, PEX1, PTGES3, KRT1, KRT9, CLIP1 and CLEC20A were mainly changed during A. fumigatus infection, while the immunologically activated proteins WNT7A, GAPDH and ANXA2 were principally altered during S. apiospermum infection. These proteins are involved in fungal internalisation and structural destruction leading to pulmonary disorders. Interleukin (IL)-21, IL-1α, IL-22, IL-2, IL-8, IL-12, IL-17A, interferon-γ and tumour necrosis factor-α were upregulated in both aspergillosis and scedosporiosis, although more predominately in the latter, in accordance with chitin synthase-1 and matrix metalloproteinase levels. Our results demonstrated that during invasion, A. fumigatus primarily altered host cellular integrity, whereas S. apiospermum chiefly induced and extensively modulated host immune responses.},
}
@article {pmid33890145,
year = {2022},
author = {Fisol, AFBC and Saidi, NB and Al-Obaidi, JR and Lamasudin, DU and Atan, S and Razali, N and Sajari, R and Rahmad, N and Hussin, SNIS and Mr, NH},
title = {Differential Analysis of Mycelial Proteins and Metabolites From Rigidoporus Microporus During In Vitro Interaction With Hevea Brasiliensis.},
journal = {Microbial ecology},
volume = {83},
number = {2},
pages = {363-379},
pmid = {33890145},
issn = {1432-184X},
support = {S16IPDM0533//Malaysian Rubber Board/ ; },
mesh = {Gene Expression Regulation, Plant ; *Hevea/chemistry/microbiology ; Plant Diseases/microbiology ; *Polyporales ; Tandem Mass Spectrometry ; },
abstract = {Rigidoporus microporus is the fungus accountable for the white root rot disease that is detrimental to the rubber tree, Hevea brasiliensis. The pathogenicity mechanism of R. microporus and the identity of the fungal proteins and metabolites involved during the infection process remain unclear. In this study, the protein and metabolite profiles of two R. microporus isolates, Segamat (SEG) and Ayer Molek (AM), were investigated during an in vitro interaction with H. brasiliensis. The isolates were used to inoculate H. brasiliensis clone RRIM 2025, and mycelia adhering to the roots of the plant were collected for analysis. Transmission electron microscope (TEM) images acquired confirms the hyphae attachment and colonization of the mycelia on the root of the H. brasiliensis clones after 4 days of inoculation. The protein samples were subjected to 2-DE analysis and analyzed using MALDI-ToF MS/MS, while the metabolites were extracted using methanol and analyzed using LC/MS-QTOF. Based on the differential analyses, upregulation of proteins that are essential for fungal evolution such as malate dehydrogenase, fructose 1,6-biphosphate aldolase, and glyceraldehyde-3-phosphate dehydrogenase hints an indirect role in fungal pathogenicity, while metabolomic analysis suggests an increase in acidic compounds which may lead to increased cell wall degrading enzyme activity. Bioinformatics analyses revealed that the carbohydrate and amino acid metabolisms were prominently affected in response to the fungal pathogenicity. In addition to that, other pathways that were significantly affected include "Protein Ubiquitination Pathway," Unfolded Protein Response," "HIFα Signaling," and "Sirtuin Signaling Pathway." The identification of responsive proteins and metabolites from this study promotes a better understanding of mechanisms underlying R. microporus pathogenesis and provides a list of potential biological markers for early recognition of the white root rot disease.},
}
@article {pmid33886659,
year = {2021},
author = {Han, XY},
title = {Effects of climate changes and road exposure on the rapidly rising legionellosis incidence rates in the United States.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0250364},
pmid = {33886659},
issn = {1932-6203},
mesh = {Adolescent ; Adult ; Aged ; Centers for Disease Control and Prevention, U.S. ; Child ; Child, Preschool ; Female ; *Global Warming ; *Hot Temperature ; Humans ; Incidence ; Infant ; Infant, Newborn ; Legionella pneumophila/*pathogenicity ; Legionellosis/*epidemiology/microbiology ; Male ; Middle Aged ; Rural Population ; *Sunlight ; *Ultraviolet Rays ; United States/epidemiology ; Urban Population ; Young Adult ; },
abstract = {Legionellosis is an infection acquired through inhalation of aerosols that are contaminated with environmental bacteria Legionella spp. The bacteria require warm temperature for proliferation in bodies of water and moist soil. The legionellosis incidence in the United States has been rising rapidly in the past two decades without a clear explanation. In the meantime, the US has recorded consecutive years of above-norm temperature since 1997 and precipitation surplus since 2008. The present study analyzed the legionellosis incidence in the US during the 20-year period of 1999 to 2018 and correlated with concurrent temperature, precipitation, solar ultraviolet B (UVB) radiation, and vehicle mileage data. The age-adjusted legionellosis incidence rates rose exponentially from 0.40/100,000 in 1999 (with 1108 cases) to 2.69/100,000 in 2018 (with 9933 cases) at a calculated annual increase of 110%. In regression analyses, the rise correlated with an increase in vehicle miles driven and with temperature and precipitation levels that have been above the 1901-2000 mean since 1997 and 2008, respectively, suggesting more road exposure to traffic-generated aerosols and promotive effects of anomalous climate. Remarkably, the regressions with cumulative anomalies of temperature and precipitation were robust (R2 ≥ 0.9145, P ≤ 4.7E-11), implying possible changes to microbial ecology in the terrestrial and aquatic environments. An interactive synergy between annual precipitation and vehicle miles was also found in multiple regressions. Meanwhile, the bactericidal UVB radiation has been decreasing, which also contributed to the rising incidence in an inverse correlation. The 2018 legionellosis incidence peak corresponded to cumulative effects of the climate anomalies, vast vehicle miles (3,240 billion miles, 15904 km per capita), record high precipitation (880.1 mm), near record low UVB radiation (7488 kJ/m2), and continued above-norm temperature (11.96°C). These effects were examined and demonstrated in California, Florida, New Jersey, Ohio, and Wisconsin, states that represent diverse incidence rates and climates. The incidence and above-norm temperature both rose most in cold Wisconsin. These results suggest that warming temperature and precipitation surplus have likely elevated the density of Legionella bacteria in the environment, and together with road exposure explain the rapidly rising incidence of legionellosis in the United States. These trends are expected to continue, warranting further research and efforts to prevent infection.},
}
@article {pmid33886638,
year = {2021},
author = {Colda, A and Bossaert, S and Verreth, C and Vanhoutte, B and Honnay, O and Keulemans, W and Lievens, B},
title = {Inoculation of pear flowers with Metschnikowia reukaufii and Acinetobacter nectaris enhances attraction of honeybees and hoverflies, but does not increase fruit and seed set.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0250203},
pmid = {33886638},
issn = {1932-6203},
mesh = {Animals ; Bees ; Flowers/*microbiology ; Fruit ; *Plant Nectar ; *Pollination ; Pyrus/*microbiology ; },
abstract = {Currently, one of the most important challenges is to provide sufficient and affordable food and energy for a fast-growing world population, alongside preserving natural habitats and maintaining biodiversity. About 35% of the global food production depends on animals for pollination. In recent years, an alarming worldwide decline in pollinators has been reported, putting our food production under additional pressure. Therefore, there is an urgent need to find sustainable ways to ensure this crucial ecosystem service. Recent studies have shown that floral nectar is generally colonized by microorganisms, specifically yeasts and bacteria, which may alter nectar chemistry and enhance attraction of pollinators. In this study, we investigated changes in pollinator foraging behavior and pollination success in European pear (Pyrus communis L.) cultivars 'Regal Red' and 'Sweet Sensation' (red sports of 'Doyenné de Comice') after flower inoculation with the typical nectar-inhabiting microorganisms Metschnikowia reukaufii and Acinetobacter nectaris, and a combination of both. Pollination success was monitored by measuring the number of flower visits, fruit set and seed set in two consecutive years, 2019 and 2020. Results revealed that application of a mixture of M. reukaufii and A. nectaris resulted in significantly higher visitation rates of honeybees and hoverflies. By contrast, no effects on flower visits were found when yeasts and bacteria were applied separately. Fruit set and seed set were not significantly affected by any of the inoculation treatments. The only factors affecting fruit set were initial number of flower clusters on the trees and the year. The absence of treatment effects can most likely be attributed to the fact that pollination was not a limiting factor for fruit set in our experiments. Altogether, our results show that inoculation of flowers with nectar microbes can modify pollinator foraging patterns, but did not lead to increased pollination success under the conditions tested.},
}
@article {pmid33886557,
year = {2021},
author = {Hewson, I and Sewell, MA},
title = {Surveillance of densoviruses and mesomycetozoans inhabiting grossly normal tissues of three Aotearoa New Zealand asteroid species.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0241026},
pmid = {33886557},
issn = {1932-6203},
mesh = {Animals ; Densovirus/genetics/*isolation &amp; purification ; Mesomycetozoea/genetics/*isolation &amp; purification ; Metagenome ; Metagenomics ; Microbiota ; New Zealand ; Starfish/*parasitology/*virology ; },
abstract = {Asteroid wasting events and mass mortality have occurred for over a century. We currently lack a fundamental understanding of the microbial ecology of asteroid disease, with disease investigations hindered by sparse information about the microorganisms associated with grossly normal specimens. We surveilled viruses and protists associated with grossly normal specimens of three asteroid species (Patiriella regularis, Stichaster australis, Coscinasterias muricata) on the North Island / Te Ika-a-Māui, Aotearoa New Zealand, using metagenomes prepared from virus and ribosome-sized material. We discovered several densovirus-like genome fragments in our RNA and DNA metagenomic libraries. Subsequent survey of their prevalence within populations by quantitative PCR (qPCR) demonstrated their occurrence in only a few (13%) specimens (n = 36). Survey of large and small subunit rRNAs in metagenomes revealed the presence of a mesomycete (most closely matching Ichthyosporea sp.). Survey of large subunit prevalence and load by qPCR revealed that it is widely detectable (80%) and present predominately in body wall tissues across all 3 species of asteroid. Our results raise interesting questions about the roles of these microbiome constituents in host ecology and pathogenesis under changing ocean conditions.},
}
@article {pmid33885917,
year = {2022},
author = {Wallenborn, JT and Gunier, RB and Pappas, DJ and Chevrier, J and Eskenazi, B},
title = {Breastmilk, Stool, and Meconium: Bacterial Communities in South Africa.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {246-251},
pmid = {33885917},
issn = {1432-184X},
support = {R01 ES020360/ES/NIEHS NIH HHS/United States ; U24 ES028529/ES/NIEHS NIH HHS/United States ; 1R01ES020360-01//Foundation for the National Institutes of Health/ ; },
mesh = {Feces/microbiology ; Humans ; Infant ; Infant, Newborn ; *Meconium/microbiology ; *Milk, Human/microbiology ; RNA, Ribosomal, 16S/genetics ; South Africa ; },
abstract = {Human milk optimizes gut microbial richness and diversity, and is critical for proper immune development. Research has shown differing microbial composition based on geographic location, providing evidence that diverse biospecimen data is needed when studying human bacterial communities. Yet, limited research describes human milk and infant gut microbial communities in Africa. Our study uses breastmilk, stool, and meconium samples from a South African birth cohort to describe the microbial diversity, identify distinct taxonomic units, and determine correlations between bacterial abundance in breastmilk and stool samples. Mother-infant dyads (N = 20) were identified from a longitudinal birth cohort in the Vhembe district of Limpopo Province, South Africa. Breastmilk, meconium, and stool samples were analyzed using 16S ribosomal RNA sequencing of the V4-V5 gene region using the MiSeq platform for identification and relative quantification of bacterial taxa. A non-metric multidimensional scaling using Bray-Curtis distances of sample Z-scores showed that meconium, stool, and breastmilk microbial communities are distinct with varying genus. Breastmilk was mostly comprised of Streptococcus, Staphylococcus, Veillonella, and Corynebacterium. Stool samples showed the highest levels of Bifidobacterium, Faecalibacterium, Bacteroides, and Streptococcus. Alpha diversity measures found that stool samples have the highest Shannon index score compared to breastmilk and meconium. The abundance of Bifidobacterium (r = 0.57), Blautia (r = 0.59), and Haemophilus (r = 0.69) was correlated (p < 0.1) between breastmilk and stool samples. Despite the importance of breastmilk in seeding the infant gut microbiome, we found evidence of distinct bacterial communities between breastmilk and stool samples from South African mother-infant dyads.},
}
@article {pmid33880762,
year = {2021},
author = {Zeng, T and Yu, X and Chen, Z},
title = {Applying artificial intelligence in the microbiome for gastrointestinal diseases: A review.},
journal = {Journal of gastroenterology and hepatology},
volume = {36},
number = {4},
pages = {832-840},
doi = {10.1111/jgh.15503},
pmid = {33880762},
issn = {1440-1746},
support = {2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; 61803360//National Natural Science Foundation of China/ ; 11871456//National Natural Science Foundation of China/ ; XDB38050200//Strategic Priority Research Program of Chinese Academy of Sciences/ ; },
mesh = {Artificial Intelligence/*trends ; *Big Data ; Datasets as Topic ; Gastrointestinal Diseases/*etiology/*microbiology ; *Gastrointestinal Microbiome ; Information Storage and Retrieval/*methods ; },
abstract = {For a long time, gut bacteria have been recognized for their important roles in the occurrence and progression of gastrointestinal diseases like colorectal cancer, and the ever-increasing amounts of microbiome data combined with other high-quality clinical and imaging datasets are leading the study of gastrointestinal diseases into an era of biomedical big data. The "omics" technologies used for microbiome analysis continuously evolve, and the machine learning or artificial intelligence technologies are key to extract the relevant information from microbiome data. This review intends to provide a focused summary of recent research and applications of microbiome big data and to discuss the use of artificial intelligence to combat gastrointestinal diseases.},
}
@article {pmid33880565,
year = {2021},
author = {Golob, JL and Rao, K},
title = {Signal Versus Noise: How to Analyze the Microbiome and Make Progress on Antimicrobial Resistance.},
journal = {The Journal of infectious diseases},
volume = {223},
number = {12 Suppl 2},
pages = {S214-S221},
pmid = {33880565},
issn = {1537-6613},
support = {R01 HS027431/HS/AHRQ HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/adverse effects ; Clostridioides difficile/growth &amp; development/pathogenicity ; Clostridium Infections/etiology/microbiology ; Disease Models, Animal ; Drug Resistance, Microbial/drug effects/*genetics ; Gastrointestinal Microbiome/drug effects/*genetics/immunology ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Humans ; },
abstract = {Antimicrobial resistance has become a worldwide medical challenge [1], so impactful that vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have entered the common vernacular. We have attempted to reduce the selective pressure through antimicrobial stewardship, curtail the spread by identifying and isolating carriers and individuals with symptomatic infection, and treat antibiotic-resistant organisms (AROs) by developing novel antimicrobials. Despite these extraordinary measures, the challenge of AROs continues to grow. The gut microbiome, the ecosystem of microbes (ie, the microbiota) and metabolites present upon and within all humans, is an emerging target for both the risk for colonization and defense against infection with AROs. Here, informed from experiences and successes with understanding the role of the microbiome in mediating risk of Clostridioides difficile infection (CDI), we (1) review our understanding of the risk from ARO acquisition; (2) review our current understanding of the gut microbiome's ability to resist colonization with AROs; (3) describe how experimental model systems can test these initial, global insights to arrive at more granular, mechanistic ones; and (4) suggest a path forward to make further progress in the field.},
}
@article {pmid33879498,
year = {2021},
author = {Taylor, M and Vega, NM},
title = {Host Immunity Alters Community Ecology and Stability of the Microbiome in a Caenorhabditis elegans Model.},
journal = {mSystems},
volume = {6},
number = {2},
pages = {},
pmid = {33879498},
issn = {2379-5077},
abstract = {A growing body of data suggests that the microbiome of a species can vary considerably from individual to individual, but the reasons for this variation-and the consequences for the ecology of these communities-remain only partially explained. In mammals, the emerging picture is that the metabolic state and immune system status of the host affect the composition of the microbiome, but quantitative ecological microbiome studies are challenging to perform in higher organisms. Here, we show that these phenomena can be quantitatively analyzed in the tractable nematode host Caenorhabditis elegans Mutants in innate immunity, in particular the DAF-2/insulin growth factor (IGF) pathway, are shown to contain a microbiome that differs from that of wild-type nematodes. We analyzed the underlying basis of these differences from the perspective of community ecology by comparing experimental observations to the predictions of a neutral sampling model and concluded that fundamental differences in microbiome ecology underlie the observed differences in microbiome composition. We tested this hypothesis by introducing a minor perturbation into the colonization conditions, allowing us to assess stability of communities in different host strains. Our results show that altering host immunity changes the importance of interspecies interactions within the microbiome, resulting in differences in community composition and stability that emerge from these differences in host-microbe ecology.IMPORTANCE Here, we used a Caenorhabditis elegans microbiome model to demonstrate how genetic differences in innate immunity alter microbiome composition, diversity, and stability by changing the ecological processes that shape these communities. These results provide insight into the role of host genetics in controlling the ecology of the host-associated microbiota, resulting in differences in community composition, successional trajectories, and response to perturbation.},
}
@article {pmid33876556,
year = {2021},
author = {Mihajlovic, J and Leutner, M and Hausmann, B and Kohl, G and Schwarz, J and Röver, H and Stimakovits, N and Wolf, P and Maruszczak, K and Bastian, M and Kautzky-Willer, A and Berry, D},
title = {Combined hormonal contraceptives are associated with minor changes in composition and diversity in gut microbiota of healthy women.},
journal = {Environmental microbiology},
volume = {23},
number = {6},
pages = {3037-3047},
doi = {10.1111/1462-2920.15517},
pmid = {33876556},
issn = {1462-2920},
mesh = {Animals ; Contraceptive Agents ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Menstrual Cycle ; *Microbiota ; },
abstract = {Recent human and animal studies have found associations between gut microbiota composition and serum levels of sex hormones, indicating that they could be an important factor in shaping the microbiota. However, little is known about the effect of regular hormonal fluctuations over the menstrual cycle or CHC-related changes of hormone levels on gut microbiota structure, diversity and dynamics. The aim of this study was to investigate the effect of CHCs on human gut microbiota composition. The effect of CHC pill intake on gut microbiota composition was studied in a group of seven healthy pre-menopausal women using the CHC pill, compared to the control group of nine age-matched healthy women that have not used hormonal contraceptives in the 6 months prior to the start of the study. By analysing the gut microbiota composition in both groups during one menstrual cycle, we found that CHC usage is associated with a minor decrease in gut microbiota diversity and differences in the abundance of several bacterial taxa. These results call for further investigation of the mechanisms underlying hormonal and hormonal contraceptive-related changes of the gut microbiota and the potential implications of these changes for women's health.},
}
@article {pmid35021714,
year = {2020},
author = {Ghosh, P and Bera, A and Ghosh, A and Bhadury, P and De, P},
title = {Side-Chain Proline-Based Polymers as Effective Inhibitors for In Vitro Aggregation of Insulin.},
journal = {ACS applied bio materials},
volume = {3},
number = {8},
pages = {5407-5419},
doi = {10.1021/acsabm.0c00709},
pmid = {35021714},
issn = {2576-6422},
abstract = {Insulin fibril formation is considered as the hallmark of several debilitating pathological conditions. To develop effective therapeutics that are able to control the amyloidogenesis process and inhibit fibril formation, herein we have designed a side-chain proline (Pro)-based homopolymer and block copolymers through the reversible addition-fragmentation chain transfer (RAFT) polymerization technique and further explored their obligatory role in the in vitro insulin fibrillation process. Using a variety of biophysical tools, including turbidity measurements, thioflavin T (ThT) fluorescence kinetics, tyrosine (Tyr) fluorescence study, Nile red (NR) fluorescence assay, dynamic light scattering (DLS) study, circular dichroism (CD) measurements, and isothermal titration calorimetry (ITC) techniques, we demonstrated that Pro-based polymers can significantly inhibit the insulin fibrillation process. Among them, the Pro-based homopolymer acts as the most potent inhibitor of insulin fibrillation as confirmed by ThT assay, CD study, and transmission electron microscopic (TEM) analysis. Tyrosine fluorescence measurements and NR fluorescence assay revealed that hydrophobic interactions are the crucial factor that mainly controls the inhibition process. Apart from hydrophobic interactions, polar interactions may also be responsible for the inhibition process as evaluated by ITC study.},
}
@article {pmid35122045,
year = {2020},
author = {Slowicka, K and Petta, I and Blancke, G and Hoste, E and Dumas, E and Sze, M and Vikkula, H and Radaelli, E and Haigh, JJ and Jonckheere, S and Taminau, J and Vandamme, N and Wullaert, A and Tulchinsky, E and Nittner, D and Van Vlierberghe, P and De Hertogh, G and Baldin, P and Etlioglu, E and Wirapati, P and Boon, L and Lambrecht, BN and Callewaert, C and Tejpar, S and Goossens, S and Berx, G and Vereecke, L and van Loo, G},
title = {Publisher Correction: Zeb2 drives invasive and microbiota-dependent colon carcinoma.},
journal = {Nature cancer},
volume = {1},
number = {7},
pages = {750},
doi = {10.1038/s43018-020-0097-4},
pmid = {35122045},
issn = {2662-1347},
}
@article {pmid35047975,
year = {2020},
author = {Belibasakis, GN},
title = {Grand Challenges in Oral Infections and Microbes.},
journal = {Frontiers in oral health},
volume = {1},
number = {},
pages = {2},
pmid = {35047975},
issn = {2673-4842},
}
@article {pmid35121975,
year = {2020},
author = {Slowicka, K and Petta, I and Blancke, G and Hoste, E and Dumas, E and Sze, M and Vikkula, H and Radaelli, E and Haigh, JJ and Jonckheere, S and Taminau, J and Vandamme, N and Wullaert, A and Tulchinsky, E and Nittner, D and Van Vlierberghe, P and De Hertogh, G and Baldin, P and Etlioglu, E and Wirapati, P and Boon, L and Lambrecht, BN and Callewaert, C and Tejpar, S and Goossens, S and Berx, G and Vereecke, L and van Loo, G},
title = {Zeb2 drives invasive and microbiota-dependent colon carcinoma.},
journal = {Nature cancer},
volume = {1},
number = {6},
pages = {620-634},
pmid = {35121975},
issn = {2662-1347},
mesh = {Animals ; *Carcinoma/metabolism ; Colon/metabolism ; Mice ; *Microbiota ; },
abstract = {Colorectal cancer (CRC) is highly prevalent in Western society, and increasing evidence indicates strong contributions of environmental factors and the intestinal microbiota to CRC initiation, progression and even metastasis. We have identified a synergistic inflammatory tumor-promoting mechanism through which the resident intestinal microbiota boosts invasive CRC development in an epithelial-to-mesenchymal transition-prone tissue environment. Intestinal epithelial cell (IEC)-specific transgenic expression of the epithelial-to-mesenchymal transition regulator Zeb2 in mice (Zeb2[IEC-Tg/+]) leads to increased intestinal permeability, myeloid cell-driven inflammation and spontaneous invasive CRC development. Zeb2[IEC-Tg/+] mice develop a dysplastic colonic epithelium, which progresses to severely inflamed neoplastic lesions while the small intestinal epithelium remains normal. Zeb2[IEC-Tg/+] mice are characterized by intestinal dysbiosis, and microbiota depletion with broad-spectrum antibiotics or germ-free rederivation completely prevents cancer development. Zeb2[IEC-Tg/+] mice represent the first mouse model of spontaneous microbiota-dependent invasive CRC and will help us to better understand host-microbiome interactions driving CRC development in humans.},
}
@article {pmid33997168,
year = {2021},
author = {Rai, SN and Qian, C and Pan, J and Rai, JP and Song, M and Bagaitkar, J and Merchant, M and Cave, M and Egilmez, NK and McClain, CJ},
title = {Microbiome data analysis with applications to pre-clinical studies using QIIME2: Statistical considerations.},
journal = {Genes &amp; diseases},
volume = {8},
number = {2},
pages = {215-223},
pmid = {33997168},
issn = {2352-3042},
abstract = {Diversity analysis and taxonomic profiles can be generated from marker-gene sequence data with the help of many available computational tools. The Quantitative Insights into Microbial Ecology Version 2 (QIIME2) has been widely used for 16S rRNA data analysis. While many articles have demonstrated the use of QIIME2 with suitable datasets, the application to pre-clinical data has rarely been talked about. The issues involved in the pre-clinical data include the low-quality score and small sample size that should be addressed properly during analysis. In addition, there are few articles that discuss the detailed statistical methods behind those alpha and beta diversity significance tests that researchers are eager to find. Running the program without knowing the logic behind it is extremely risky. In this article, we first provide a guideline for analyzing 16S rRNA data using QIIME2. Then we will talk about issues in pre-clinical data, and how they could impact the outcome. Finally, we provide brief explanations of statistical methods such as group significance tests and sample size calculation.},
}
@article {pmid33902718,
year = {2019},
author = {Voříšková, J and Elberling, B and Priemé, A},
title = {Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils.},
journal = {Environmental microbiome},
volume = {14},
number = {1},
pages = {6},
pmid = {33902718},
issn = {2524-6372},
support = {5298507//Danish Geocenter Grant/ ; CENPERM DNRF100//Danish National Research Foundation/ ; },
abstract = {BACKGROUND: Climate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore the short-term effect of increased snow cover on soil fungal, bacterial and archaeal communities in two tundra sites with contrasting water regimes in Greenland. In order to assess seasonal variation of microbial communities, we collected soil samples four times during the plant-growing season.<br><br>RESULTS: The analysis revealed that soil microbial communities from two tundra sites differed from each other due to contrasting soil chemical properties. Fungal communities showed higher richness at the dry site whereas richness of prokaryotes was higher at the wet tundra site. We demonstrated that fungal and bacterial communities at both sites were significantly affected by short-term increased snow cover manipulation. Our results showed that fungal community composition was more affected by deeper snow cover compared to prokaryotes. The fungal communities showed changes in both taxonomic and ecological groups in response to climate manipulation. However, the changes were not pronounced at all sampling times which points to the need of multiple sampling in ecosystems where environmental factors show seasonal variation. Further, we showed that effects of increased snow cover were manifested after snow had melted.<br><br>CONCLUSIONS: We demonstrated rapid response of soil fungal and bacterial communities to short-term climate manipulation simulating increased winter precipitation at two tundra sites. In particular, we provide evidence that fungal community composition was more affected by increased snow cover compared to prokaryotes indicating fast adaptability to changing environmental conditions. Since fungi are considered the main decomposers of complex organic matter in terrestrial ecosystems, the stronger response of fungal communities may have implications for organic matter turnover in tundra soils under future climate.},
}
@article {pmid33902719,
year = {2019},
author = {Breider, S and Sehar, S and Berger, M and Thomas, T and Brinkhoff, T and Egan, S},
title = {Genome sequence of Epibacterium ulvae strain DSM 24752[T], an indigoidine-producing, macroalga-associated member of the marine Roseobacter group.},
journal = {Environmental microbiome},
volume = {14},
number = {1},
pages = {4},
pmid = {33902719},
issn = {2524-6372},
support = {FT130100828//Australian Research Council/ ; Transregio TRR 51//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Strain U95[T] (= DSM 24752[T] = LMG 26464[T]) is the type strain of Epibacterium ulvae, which is the type species of the genus Epibacterium. This genus belongs to the marine Roseobacter group. E. ulvae Strain U95[T] was isolated from the macroalga Ulva australis, is Gram-negative, rod-shaped and motile. Here we describe the permanent draft genome sequence and annotation of E. ulvae U95[T] with a focus on secondary metabolite production and interaction with its host. The genome contains 4,092,893 bp, 3977 protein-coding genes and 60 RNA genes. The genome encodes a gene cluster for synthesis of the blue-pigmented secondary metabolite indigoidine and contains several genes for adhesion mechanisms, putative bacteriocin, siderophores, a type VI secretion system, and enzymes that confer oxidative stress resistance. Combined, these features may aid in the successful colonization and persistence of E. ulvae on host surfaces and in competition with the surrounding microbial consortium.},
}
@article {pmid34179235,
year = {2018},
author = {McLeod, KH and Mason, L and Mariño, E},
title = {Transplantation of Fecal Microbiota Shaped by Diet.},
journal = {Bio-protocol},
volume = {8},
number = {1},
pages = {e2683},
pmid = {34179235},
issn = {2331-8325},
abstract = {Alterations in diet and gut microbial ecology underlie the pathogenesis of type 1 diabetes (T1D). In the non-obese diabetic (NOD) mouse, we found high concentrations of bacterial metabolites acetate and butyrate in blood and faeces correlated with protection from disease. We reconstituted germ free (GF) NOD mice with fecal bacteria from protected NOD mice fed with high acetate- and butyrate-yielding diets, to test whether the transferred gut microbiota protect against the development of T1D. GF NOD mice that received a microbiota shaped by high acetate- but not butyrate-yielding diet showed a marked protection against diabetes. This fecal transplantation assay demonstrated the potential for a dietary technology to reshape the gut microbiota that enables specific bacteria to transfer protection against T1D.},
}
@article {pmid34541249,
year = {2017},
author = {Stuart, RK and Mayali, X and Thelen, MP and Pett-Ridge, J and Weber, PK},
title = {Measuring Cyanobacterial Metabolism in Biofilms with NanoSIMS Isotope Imaging and Scanning Electron Microscopy (SEM).},
journal = {Bio-protocol},
volume = {7},
number = {9},
pages = {e2263},
pmid = {34541249},
issn = {2331-8325},
abstract = {To advance the understanding of microbial interactions, it is becoming increasingly important to resolve the individual metabolic contributions of microorganisms in complex communities. Organisms from biofilms can be especially difficult to separate, image and analyze, and methods to address these limitations are needed. High resolution imaging secondary ion mass spectrometry (NanoSIMS) generates single cell isotopic composition measurements, and can be used to quantify incorporation and exchange of an isotopically labeled substrate among individual organisms. Here, incorporation of cyanobacterial extracellular organic matter (EOM) by members of a cyanobacterial mixed species biofilm is used as a model to illustrate this method. Incorporation of stable isotope labeled ([15]N and [13]C) EOM by two groups, cyanobacteria and associated heterotrophic microbes, are quantified. Methods for generating, preparing, and analyzing samples for quantifying uptake of stable isotope-labeled EOM in the biofilm are described.},
}
@article {pmid33870123,
year = {2021},
author = {Ciobanu, D and Clum, A and Ahrendt, S and Andreopoulos, WB and Salamov, A and Chan, S and Quandt, CA and Foster, B and Meier-Kolthoff, JP and Tang, YT and Schwientek, P and Benny, GL and Smith, ME and Bauer, D and Deshpande, S and Barry, K and Copeland, A and Singer, SW and Woyke, T and Grigoriev, IV and James, TY and Cheng, JF},
title = {A single-cell genomics pipeline for environmental microbial eukaryotes.},
journal = {iScience},
volume = {24},
number = {4},
pages = {102290},
pmid = {33870123},
issn = {2589-0042},
abstract = {Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.},
}
@article {pmid33868801,
year = {2021},
author = {Vikram, S and Arneodo, JD and Calcagno, J and Ortiz, M and Mon, ML and Etcheverry, C and Cowan, DA and Talia, P},
title = {Diversity structure of the microbial communities in the guts of four neotropical termite species.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10959},
pmid = {33868801},
issn = {2167-8359},
abstract = {The termite gut microbiome is dominated by lignocellulose degrading microorganisms. This study describes the intestinal microbiota of four Argentinian higher termite species with different feeding habits: Microcerotermes strunckii (hardwood), Nasutitermes corniger (softwood), Termes riograndensis (soil organic matter/grass) and Cornitermes cumulans (grass) by deep sequencing of amplified 16S rRNA and ITS genes. In addition, we have performed a taxonomic and gut community structure comparison incorporating into the analysis the previously reported microbiomes of additional termite species with varied diets. The bacterial phylum Spirochaetes was dominant in the guts of M. strunckii, N. corniger and C. cumulans, whereas Firmicutes predominated in the T. riograndensis gut microbiome. A single bacterial genus, Treponema (Spirochaetes), was dominant in all termite species, except for T. riograndensis. Both in our own sequenced samples and in the broader comparison, prokaryotic α-diversity was higher in the soil/grass feeders than in the wood feeders. Meanwhile, the β-diversity of prokaryotes and fungi was highly dissimilar among strict wood-feeders, whereas that of soil- and grass-feeders grouped more closely. Ascomycota and Basidiomycota were the only fungal phyla that could be identified in all gut samples, because of the lack of reference sequences in public databases. In summary, higher microbial diversity was recorded in termites with more versatile feeding sources, providing further evidence that diet, along with other factors (e.g., host taxonomy), influences the microbial community assembly in the termite gut.},
}
@article {pmid33866059,
year = {2021},
author = {Hu, R and Zhao, H and Xu, X and Wang, Z and Yu, K and Shu, L and Yan, Q and Wu, B and Mo, C and He, Z and Wang, C},
title = {Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities.},
journal = {Environment international},
volume = {154},
number = {},
pages = {106560},
doi = {10.1016/j.envint.2021.106560},
pmid = {33866059},
issn = {1873-6750},
mesh = {Bacteria ; Biodegradation, Environmental ; *Esters ; Humans ; *Phthalic Acids ; Prospective Studies ; },
abstract = {The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.},
}
@article {pmid33864491,
year = {2022},
author = {Rojas-Gätjens, D and Fuentes-Schweizer, P and Rojas-Jiménez, K and Pérez-Pantoja, D and Avendaño, R and Alpízar, R and Coronado-Ruíz, C and Chavarría, M},
title = {Methylotrophs and Hydrocarbon-Degrading Bacteria Are Key Players in the Microbial Community of an Abandoned Century-Old Oil Exploration Well.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {83-99},
pmid = {33864491},
issn = {1432-184X},
support = {809-B8-518//Vicerrector&#xed;a de Investigaci&#xf3;n, Universidad de Costa Rica/ ; ANID PIA/Anillo ACT172128, ANID PIA/BASAL FB0002 and FONDECYT 1201741.//Chilean government/ ; },
mesh = {Bacteria ; Biodegradation, Environmental ; Hydrocarbons/metabolism ; *Microbiota ; Oil and Gas Fields ; *Petroleum ; RNA, Ribosomal, 16S/genetics/metabolism ; },
abstract = {In this work, we studied the microbial community and the physicochemical conditions prevailing in an exploratory oil well, abandoned a century ago, located in the Cahuita National Park (Costa Rica). According to our analysis, Cahuita well is characterized by a continuous efflux of methane and the presence of a mixture of hydrocarbons including phenanthrene/anthracene, fluoranthene, pyrene, dibenzothiophene, tricyclic terpanes, pyrene, sesquiterpenes, sterane, and n-alkanes. Based on the analysis of 16S rRNA gene amplicons, we detected a significant abundance of methylotrophic bacteria such as Methylobacillus (6.3-26.0% of total reads) and Methylococcus (4.1-30.6%) and the presence of common genera associated with hydrocarbon degradation, such as Comamonas (0.8-4.6%), Hydrogenophaga (1.5-3.3%) Rhodobacter (1.0-4.9%), and Flavobacterium (1.1-6.5%). The importance of C1 metabolism in this niche was confirmed by amplifying the methane monooxygenase (MMO)-encoding gene (pmo) from environmental DNA and the isolation of two strains closely related to Methylorubrum rhodesianum and Paracoccus communis with the ability to growth using methanol and formate as sole carbon source respectively. In addition, we were able to isolated 20 bacterial strains from the genera Pseudomonas, Acinetobacter, and Microbacterium which showed the capability to grow using the hydrocarbons detected in the oil well as sole carbon source. This work describes the physicochemical properties and microbiota of an environment exposed to hydrocarbons for 100 years, and it not only represents a contribution to the understanding of microbial communities in environments with permanently high concentrations of these compounds but also has biotechnological implications for bioremediation of petroleum-polluted sites.},
}
@article {pmid33864130,
year = {2022},
author = {Álvarez-Pérez, S and Tsuji, K and Donald, M and Van Assche, A and Vannette, RL and Herrera, CM and Jacquemyn, H and Fukami, T and Lievens, B},
title = {Correction to: Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {256},
doi = {10.1007/s00248-021-01755-2},
pmid = {33864130},
issn = {1432-184X},
}
@article {pmid33864129,
year = {2021},
author = {Pereira, A and Figueiredo, A and Ferreira, V},
title = {Invasive Acacia Tree Species Affect Instream Litter Decomposition Through Changes in Water Nitrogen Concentration and Litter Characteristics.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {257-273},
pmid = {33864129},
issn = {1432-184X},
support = {SFRH/BD/118069/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/00129/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {*Acacia ; Ecosystem ; Introduced Species ; Nitrogen ; Plant Leaves ; Rivers ; *Trees ; Water ; },
abstract = {Non-native nitrogen-fixing Acacia species have been invading riparian ecosystems worldwide, potentially threatening stream communities that strongly depend on allochthonous litter. We examined the effects of the invasion of native deciduous temperate forests by Acacia species on litter decomposition and associated fungal decomposers in streams. Litter of native (Alnus glutinosa and Quercus robur) and invasive (Acacia melanoxylon) species were enclosed in fine-mesh bags and immersed in three native and three invaded streams, for 14-98 days. Litter decomposition rates, fungal biomass, and aquatic hyphomycete sporulation rates were higher in invaded than in native streams, likely due to the higher water nitrogen concentration found in invaded streams. Alnus glutinosa litter had higher aquatic hyphomycete sporulation rates and species richness, and higher decomposition rates, probably because they were soft and nitrogen rich. Quercus robur litter also had high aquatic hyphomycete sporulation rates but lower decomposition rates than Al. glutinosa, probably due to high polyphenol concentration and carbon:nitrogen ratio. Acacia melanoxylon litter had lower aquatic hyphomycete sporulation rates and species richness, and lower decomposition rates, most likely because it was very tough. Thus, litter decomposition rates varied in the order: Al. glutinosa > Q. robur > Ac. melanoxylon. The aquatic hyphomycete community structure strongly differed between native and invaded streams, and among litter species, suggesting that microbes were sensitive to water nitrogen concentration and litter characteristics. Overall, increases in water nitrogen concentration and alterations in litter characteristics promoted by the invasion of native riparian forests by Acacia species may affect the activity and community structure of microbial decomposers, and instream litter decomposition, thus altering the functioning of stream ecosystems.},
}
@article {pmid33863892,
year = {2021},
author = {Luhung, I and Uchida, A and Lim, SBY and Gaultier, NE and Kee, C and Lau, KJX and Gusareva, ES and Heinle, CE and Wong, A and Premkrishnan, BNV and Purbojati, RW and Acerbi, E and Kim, HL and Junqueira, ACM and Longford, S and Lohar, SR and Yap, ZH and Panicker, D and Koh, Y and Kushwaha, KK and Ang, PN and Putra, A and Drautz-Moses, DI and Schuster, SC},
title = {Experimental parameters defining ultra-low biomass bioaerosol analysis.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {37},
pmid = {33863892},
issn = {2055-5008},
mesh = {Air Microbiology ; *Biomass ; *Ecosystem ; *Environmental Microbiology ; Environmental Monitoring ; Metagenome ; Metagenomics/methods ; *Microbiota ; Soil Microbiology ; Water Microbiology ; },
abstract = {Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical challenge that is confounded by temporal fluctuations in community structure. Our ultra-low biomass pipeline advances the field of bioaerosol research by significantly reducing sampling times from days/weeks/months to minutes/hours, while maintaining the ability to perform species-level identification through direct metagenomic sequencing. The study further addresses all experimental factors contributing to analysis outcome, such as amassment, storage and extraction, as well as factors that impact on nucleic acid analysis. Quantity and quality of nucleic acid extracts from each optimisation step are evaluated using fluorometry, qPCR and sequencing. Both metagenomics and marker gene amplification-based (16S and ITS) sequencing are assessed with regard to their taxonomic resolution and inter-comparability. The pipeline is robust across a wide range of climatic settings, ranging from arctic to desert to tropical environments. Ultimately, the pipeline can be adapted to environmental settings, such as dust and surfaces, which also require ultra-low biomass analytics.},
}
@article {pmid33860847,
year = {2022},
author = {Caragata, EP and Otero, LM and Tikhe, CV and Barrera, R and Dimopoulos, G},
title = {Microbial Diversity of Adult Aedes aegypti and Water Collected from Different Mosquito Aquatic Habitats in Puerto Rico.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {182-201},
pmid = {33860847},
issn = {1432-184X},
support = {CC999999/ImCDC/Intramural CDC HHS/United States ; R21AI136456/NH/NIH HHS/United States ; BAA 2017-N-18041/CC/CDC HHS/United States ; },
mesh = {*Aedes ; Animals ; Humans ; Larva ; *Microbiota ; Mosquito Vectors ; Puerto Rico ; Water ; },
abstract = {Mosquitoes, the major vectors of viruses like dengue, are naturally host to diverse microorganisms, which play an important role in their development, fecundity, immunity, and vector competence. The composition of their microbiota is strongly influenced by the environment, particularly their aquatic larval habitat. In this study, we used 2×300 bp 16s Illumina sequencing to compare the microbial profiles of emerging adult Aedes aegypti mosquitoes and the water collected from common types of aquatic habitat containers in Puerto Rico, which has endemic dengue transmission. We sequenced 141 mosquito and 46 water samples collected from plastic containers, septic tanks, discarded tires, underground trash cans, tree holes, or water meters. We identified 9 bacterial genera that were highly prevalent in the mosquito microbiome, and 77 for the microbiome of the aquatic habitat. The most abundant mosquito-associated bacterial OTUs were from the families Burkholderiaceae, Pseudomonadaceae, Comamonadaceae, and Xanthomonadaceae. Microbial profiles varied greatly between mosquitoes, and there were few major differences explained by container type; however, the microbiome of mosquitoes from plastic containers was more diverse and contained more unique taxa than the other groups. Container water was significantly more diverse than mosquitoes, and our data suggest that mosquitoes filter out many bacteria, with Alphaproteobacteria in particular being far more abundant in water. These findings provide novel insight into the microbiome of mosquitoes in the region and provide a platform to improve our understanding of the fundamental mosquito-microbe interactions.},
}
@article {pmid33859339,
year = {2021},
author = {Parras-Moltó, M and Aguirre de Cárcer, D},
title = {Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {8299},
pmid = {33859339},
issn = {2045-2322},
mesh = {Bacteria/*classification/*genetics ; Genes, Bacterial/*genetics ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxon and taxonomic rank. Subsequently, we employ the same data to assess the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. The results presented here can be used to guide the exploration of results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data (https://git.io/Jec5U).},
}
@article {pmid33858359,
year = {2021},
author = {Xue, H and Kurokawa, M and Ying, BW},
title = {Correlation between the spatial distribution and colony size was common for monogenetic bacteria in laboratory conditions.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {114},
pmid = {33858359},
issn = {1471-2180},
mesh = {Demography ; Escherichia coli/*growth &amp; development ; Laboratories ; },
abstract = {BACKGROUND: Geographically separated population growth of microbes is a common phenomenon in microbial ecology. Colonies are representative of the morphological characteristics of this structured population growth. Pattern formation by single colonies has been intensively studied, whereas the spatial distribution of colonies is poorly investigated.<br><br>RESULTS: The present study describes a first trial to address the questions of whether and how the spatial distribution of colonies determines the final colony size using the model microorganism Escherichia coli, colonies of which can be grown under well-controlled laboratory conditions. A computational tool for image processing was developed to evaluate colony density, colony size and size variation, and the Voronoi diagram was applied for spatial analysis of colonies with identical space resources. A positive correlation between the final colony size and the Voronoi area was commonly identified, independent of genomic and nutritional differences, which disturbed the colony size and size variation.<br><br>CONCLUSIONS: This novel finding of a universal correlation between the spatial distribution and colony size not only indicated the fair distribution of spatial resources for monogenetic colonies growing with identical space resources but also indicated that the initial localization of the microbial colonies decided by chance determined the fate of the subsequent population growth. This study provides a valuable example for quantitative analysis of the complex microbial ecosystems by means of experimental ecology.},
}
@article {pmid33857526,
year = {2021},
author = {Diego, D and Hannisdal, B and Dahle, H},
title = {On how the power supply shapes microbial survival.},
journal = {Mathematical biosciences},
volume = {338},
number = {},
pages = {108615},
doi = {10.1016/j.mbs.2021.108615},
pmid = {33857526},
issn = {1879-3134},
mesh = {Electric Power Supplies ; *Microbial Viability ; *Microbiota/physiology ; *Models, Biological ; Population Dynamics ; },
abstract = {Understanding how environmental factors affect microbial survival is an important open problem in microbial ecology. Patterns of microbial community structure have been characterized across a wide range of different environmental settings, but the mechanisms generating these patterns remain poorly understood. Here, we use mathematical modelling to investigate fundamental connections between chemical power supply to a system and patterns of microbial survival. We reveal a complex set of interdependences between power supply and distributions of survival probability across microbial habitats, in a case without interspecific resource competition. We also find that different properties determining power supply, such as substrate fluxes and Gibbs energies of reactions, affect microbial survival in fundamentally different ways. Moreover, we show how simple connections between power supply and growth can give rise to complex patterns of microbial survival across physicochemical gradients, such as pH gradients. Our findings show the importance of taking energy fluxes into account in order to reveal fundamental connections between microbial survival and environmental conditions, and to obtain a better understanding of microbial population dynamics in natural environments.},
}
@article {pmid33854112,
year = {2021},
author = {Mahjoubi, M and Aliyu, H and Neifar, M and Cappello, S and Chouchane, H and Souissi, Y and Masmoudi, AS and Cowan, DA and Cherif, A},
title = {Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {8124},
pmid = {33854112},
issn = {2045-2322},
mesh = {Bacterial Proteins/genetics/metabolism ; Chromatography, Gas ; Dioxins/chemistry/metabolism ; *Genome, Bacterial ; Geologic Sediments/microbiology ; Hydrocarbons/chemistry/metabolism ; Naphthalenes/metabolism ; Phylogeny ; Pseudomonas/classification/*genetics/isolation &amp; purification/metabolism ; Surface-Active Agents/metabolism ; Tunisia ; },
abstract = {Bioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974[T] and P. chloritidismutans AW-1[T]. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1[T]. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments.},
}
@article {pmid33851256,
year = {2021},
author = {Birhane, E and Gebregergs, T and Hailemariam, M and Norgrove, L and Aynekulu, E},
title = {Root Colonization and Spore Abundance of Arbuscular Mycorrhizal Fungi Along Altitudinal Gradients in Fragmented Church Natural Forest Remnants in Northern Ethiopia.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {233-242},
pmid = {33851256},
issn = {1432-184X},
support = {ETH 13/0018//NORAD/NORHED/ ; },
mesh = {Ethiopia ; Forests ; *Mycorrhizae ; Plant Roots ; Soil Microbiology ; Spores, Fungal ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) spore density and root colonization are considered sensitive to host species and abiotic factors such as climate and soil. However, there is a knowledge gap about how fragmented native forest remnants might contribute to AMF conservation, what is the AMF spore density and root colonization, and to what extent climate change, particularly warming, might impact AMF. The aim of the study was to quantify the AMF spore density and root colonization along altitudinal gradients in three agro-ecological zones of nine church forests in northern Ethiopia. Data were collected from 45 plots. All the surveyed church forest species were colonized by AMF. However, we found a significant (p < 0.05) decrease in root colonization and AMF abundance in forests at high elevation. The topsoil had significantly (p < 0.05) higher root colonization and AMF abundance than subsurface soil. We found strong negative correlations between altitude and both spore density and root colonization and soil fertility. While we cannot separate whether spore density was temperature or soil limited, we can demonstrate the importance of conserving certain tree species, particularly Ficus species, which harbor high spore densities, in both lowland and midland church forests. In the highland, no Ficus species were found. However, Hagenia abyssinica, another Rosales, had the highest spore density in the highland ecoregion.},
}
@article {pmid33850046,
year = {2021},
author = {Altamia, MA and Lin, Z and Trindade-Silva, AE and Uy, ID and Shipway, JR and Wilke, DV and Concepcion, GP and Distel, DL and Schmidt, EW and Haygood, MG},
title = {Correction for Altamia et al., "Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes".},
journal = {mSystems},
volume = {6},
number = {2},
pages = {},
doi = {10.1128/mSystems.00288-21},
pmid = {33850046},
issn = {2379-5077},
}
@article {pmid33848236,
year = {2021},
author = {Perez-Mon, C and Qi, W and Vikram, S and Frossard, A and Makhalanyane, T and Cowan, D and Frey, B},
title = {Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps).},
journal = {Microbial genomics},
volume = {7},
number = {4},
pages = {},
pmid = {33848236},
issn = {2057-5858},
mesh = {Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Carbon/metabolism ; Carbon Cycle ; Metagenome ; Metagenomics ; *Microbiota ; Nitrogen/metabolism ; Permafrost/chemistry/*microbiology ; Phylogeny ; Soil Microbiology ; Switzerland ; },
abstract = {The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.},
}
@article {pmid33846820,
year = {2022},
author = {Valencia, EY and Barros, JP and Ferenci, T and Spira, B},
title = {A Broad Continuum of E. coli Traits in Nature Associated with the Trade-off Between Self-preservation and Nutritional Competence.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {68-82},
pmid = {33846820},
issn = {1432-184X},
support = {2016/11547-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {*Escherichia coli/physiology ; *Escherichia coli Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Phenotype ; Sigma Factor/genetics ; },
abstract = {A trade-off between reproduction and survival is a characteristic of many organisms. In bacteria, growth is constrained when cellular resources are channelled towards environmental stress protection. At the core of this trade-off in Escherichia coli is RpoS, a sigma factor that diverts transcriptional resources towards general stress resistance. The constancy of RpoS levels in natural isolates is unknown. A uniform RpoS content in E. coli would impart a narrow range of resistance properties to the species, whereas a diverse set of RpoS levels in nature should result in a diverse range of stress susceptibilities. We explore the diversity of trade-off settings and phenotypes by measuring the level of RpoS protein in strains of E. coli cohabiting in a natural environment. Strains from a stream polluted with domestic waste were investigated in monthly samples. Analyses included E. coli phylogroup classification, RpoS protein level, RpoS-dependent stress phenotypes and the sequencing of rpoS mutations. The most striking finding was the continuum of RpoS levels, with a 100-fold range of RpoS amounts consistently found in individuals in the stream. Approximately 1.8% of the sampled strains carried null or non-synonymous mutations in rpoS. The natural isolates also exhibited a broad (>100-fold) range of stress resistance responses. Our results are consistent with the view that a multiplicity of survival-multiplication trade-off settings is a feature of the species E. coli. The phenotypic diversity resulting from the trade-off permits bet-hedging and the adaptation of E. coli strains to a very broad range of environments.},
}
@article {pmid33846334,
year = {2021},
author = {Deng, X and Zhang, N and Shen, Z and Zhu, C and Liu, H and Xu, Z and Li, R and Shen, Q and Salles, JF},
title = {Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {33},
pmid = {33846334},
issn = {2055-5008},
mesh = {*Antibiosis ; Bacterial Load ; Biodiversity ; Fusarium/*physiology ; Host-Pathogen Interactions ; Solanum lycopersicum/microbiology ; *Microbiota ; Plant Diseases/microbiology/therapy ; Ralstonia solanacearum/*physiology ; *Soil Microbiology ; },
abstract = {Soil microbiome manipulation can potentially reduce the use of pesticides by improving the ability of soils to resist or recover from pathogen infestation, thus generating natural suppressiveness. We simulated disturbance through soil fumigation and investigated how the subsequent application of bio-organic and organic amendments reshapes the taxonomic and functional potential of the soil microbiome to suppress the pathogens Ralstonia solanacearum and Fusarium oxysporum in tomato monocultures. The use of organic amendment alone generated smaller shifts in bacterial and fungal community composition and no suppressiveness. Fumigation directly decreased F. oxysporum and induced drastic changes in the soil microbiome. This was further converted from a disease conducive to a suppressive soil microbiome due to the application of organic amendment, which affected the way the bacterial and fungal communities were reassembled. These direct and possibly indirect effects resulted in a highly efficient disease control rate, providing a promising strategy for the control of the diseases caused by multiple pathogens.},
}
@article {pmid33841364,
year = {2021},
author = {Lui, LM and Majumder, EL and Smith, HJ and Carlson, HK and von Netzer, F and Fields, MW and Stahl, DA and Zhou, J and Hazen, TC and Baliga, NS and Adams, PD and Arkin, AP},
title = {Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {642422},
pmid = {33841364},
issn = {1664-302X},
abstract = {Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.},
}
@article {pmid33834428,
year = {2021},
author = {Iturbe-Espinoza, P and Brandt, BW and Braster, M and Bonte, M and Brown, DM and van Spanning, RJM},
title = {Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil.},
journal = {Folia microbiologica},
volume = {66},
number = {4},
pages = {597-606},
pmid = {33834428},
issn = {1874-9356},
support = {216-2015-FONDECYT//FONDECYT-CONCYTEC/ ; },
mesh = {*DNA, Bacterial/genetics/isolation &amp; purification ; *Environmental Monitoring/methods ; *Genetic Techniques/standards ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {Microbial community profiling using high-throughput sequencing relies in part on the preservation of the DNA and the effectiveness of the DNA extraction method. This study aimed at understanding to what extent these parameters affect the profiling. We obtained samples treated with and without a preservation solution. Also, we compared DNA extraction kits from Qiagen and Zymo-Research. The types of samples were defined strains, both as single species and mixtures, as well as undefined indigenous microbial communities from soil. We show that the use of a preservation solution resulted in substantial changes in the 16S rRNA gene profiles either due to an overrepresentation of Gram-positive bacteria or to an underrepresentation of Gram-negative bacteria. In addition, 16S rRNA gene profiles were substantially different depending on the type of kit that was used for extraction. The kit from Zymo extracted DNA from different types of bacteria in roughly equal amounts. In contrast, the kit from Qiagen preferentially extracted DNA from Gram-negative bacteria while DNA from Gram-positive bacteria was extracted less effectively. These differences in kit performance strongly influenced the interpretation of our microbial ecology studies.},
}
@article {pmid33834254,
year = {2021},
author = {Conacher, CG and Luyt, NA and Naidoo-Blassoples, RK and Rossouw, D and Setati, ME and Bauer, FF},
title = {The ecology of wine fermentation: a model for the study of complex microbial ecosystems.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {8},
pages = {3027-3043},
pmid = {33834254},
issn = {1432-0614},
support = {83471//South African National Research Foundation/ ; 118505//South African National Research Foundation/ ; FLAIR//The Royal Society/ ; },
mesh = {Ecosystem ; Fermentation ; *Microbiota ; Models, Biological ; *Wine ; },
abstract = {The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. In research, next generation sequencing allows accurate mapping of the microbiomes that characterise ecosystems of biotechnological and/or medical relevance. But the gap between mapping and understanding, to be filled by "functional microbiomics", requires the collection and integration of many different layers of complex data sets, from molecular multi-omics to spatial imaging technologies to online ecosystem monitoring tools. Holistically, studying the complexity of most microbial ecosystems, consisting of hundreds of species in specific spatial arrangements, is beyond our current technical capabilities, and simpler model systems with fewer species and reduced spatial complexity are required to establish the fundamental rules of ecosystem functioning. One such ecosystem, the ecosystem responsible for natural alcoholic fermentation, can provide an excellent tool to study evolutionarily relevant interactions between multiple species within a relatively easily controlled environment. This review will critically evaluate the approaches that are currently implemented to dissect the cellular and molecular networks that govern this ecosystem. KEY POINTS: • Evolutionarily isolated fermentation ecosystem can be used as an ecological model. • Experimental toolbox is gearing towards mechanistic understanding of this ecosystem. • Integration of multidisciplinary datasets is key to predictive understanding.},
}
@article {pmid33830034,
year = {2021},
author = {Zama, D and Gori, D and Muratore, E and Leardini, D and Rallo, F and Turroni, S and Prete, A and Brigidi, P and Pession, A and Masetti, R},
title = {Enteral versus Parenteral Nutrition as Nutritional Support after Allogeneic Hematopoietic Stem Cell Transplantation: a Systematic Review and Meta-Analysis.},
journal = {Transplantation and cellular therapy},
volume = {27},
number = {2},
pages = {180.e1-180.e8},
doi = {10.1016/j.jtct.2020.11.006},
pmid = {33830034},
issn = {2666-6367},
mesh = {Enteral Nutrition ; *Graft vs Host Disease/prevention &amp; control ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Nutritional Support ; Parenteral Nutrition ; },
abstract = {Nutritional support for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) has been widely debated. Enteral nutrition (EN) is recommended as first-line nutritional support by the main international guidelines. However, these recommendations are based on weak evidence, and there is wide variability in the types of nutritional support among transplantation centers, with the majority providing parenteral nutrition (PN) instead of EN. Here we provide an up-to-date systematic review and meta-analysis of studies comparing EN and PN for nutritional support during the neutropenic period after allo-HSCT. The literature search strategy identified 13 papers, of which 10 compared clinical transplantation outcomes, 2 compared gut microbiota (GM) compositions, and 1 compared systemic metabolic profiles. For the meta-analysis, among the 10 clinical studies, 8 studies in which 2 groups were compared were selected: in 1 group, EN was provided as primary nutritional support in the neutropenic phase after allo-HSCT with or without the addition of PN (EN group), whereas in the other group, only PN was provided as nutritional support. The incidence rates of acute graft-versus-host disease (aGVHD) (relative risk [RR], 0.69; 95% confidence interval [CI], 0.56 to 0.86; P = .0007), aGVHD grade III-IV (RR, 0.44; 95% CI, 0.30 to 0.64; P < .0001), and gut aGVHD (RR, 0.44; 95% CI, 0.30 to 0.66; P < .0001) were lower in the EN group than in the PN group. No differences were found between the 2 groups with regard to the incidence of severe oral mucositis (RR, 0.95; 95% CI, 0.83 to 1.09; P = .46) or overall survival at day +100 (RR, 1.07; 95% CI, 0.95 to 1.21; P = .29). Other variables were too heterogeneous to perform quantitative analyses. The results of the meta-analysis showed that EN reduced the incidence of aGVHD, specifically grade III-IV and gut aGVHD. This result should prompt improved efforts to implement EN as first-line nutritional support in patients undergoing allo-HSCT. Considering the emerging evidence regarding the association between GM dysbiosis and aGVHD onset, we speculate that this protective effect could be attributed to the improved gut eubiosis observed in enterally fed patients. Further studies are warranted to better address the relationship between the GM composition, aGVHD, and the nutritional administration route during HSCT.},
}
@article {pmid33827912,
year = {2021},
author = {Gauthier, J and Derome, N},
title = {Evenness-Richness Scatter Plots: a Visual and Insightful Representation of Shannon Entropy Measurements for Ecological Community Analysis.},
journal = {mSphere},
volume = {6},
number = {2},
pages = {},
pmid = {33827912},
issn = {2379-5042},
mesh = {*Biodiversity ; *Biota ; *Entropy ; Mathematical Concepts ; },
abstract = {Shannon's entropy is a popular alpha diversity metric because it estimates both richness and evenness in a single equation. However, since its value is dependent on both those parameters, there is theoretically an infinite number of richness/evenness value combinations translating into the same index score. By decoupling both components measured by Shannon's entropy, two communities having identical indices can be differentiated by mapping richness and evenness coordinates on a scatter plot. In such graphs, confidence ellipses would allow testing significant differences between groups of samples. Multivariate statistical tests such as permutational multivariate analysis of variance (PERMANOVA) can be performed on distance matrices calculated from richness and evenness coordinates and detect statistically significant differences that would have remained unforeseen otherwise. Therefore, plotting richness and evenness on two-dimensional (2D) graphs gives a more thorough understanding of how alpha diversity differs between groups of samples.},
}
@article {pmid33827413,
year = {2021},
author = {Shanmugam, G and Lee, SH and Jeon, J},
title = {EzMAP: Easy Microbiome Analysis Platform.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {179},
pmid = {33827413},
issn = {1471-2105},
support = {918017-04//Ministry of Agriculture, Food, and Rural Affairs/ ; PJ013178//Rural Development Administration , Korea/ ; NRF-2018R1A5A1023599//National Research Foundation of Korea/ ; },
mesh = {*High-Throughput Nucleotide Sequencing ; *Microbiota ; Phylogeny ; Programming Languages ; *Software ; },
abstract = {BACKGROUND: The rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability to understand diversity of microbes in a given sample. Over the past decade, several computational pipelines have been developed to efficiently process and annotate these microbiome data. However, most of these pipelines require an implementation of additional tools for downstream analyses as well as advanced programming skills.<br><br>RESULTS: Here we introduce a user-friendly microbiome analysis platform, EzMAP (Easy Microbiome Analysis Platform), which was developed using Java Swings, Java Script and R programming language. EzMAP is a standalone package providing graphical user interface, enabling easy access to all the functionalities of QIIME2 (Quantitative Insights Into Microbial Ecology) as well as streamlined downstream analyses using QIIME2 output as input. This platform is designed to give users the detailed reports and the intermediate output files that are generated progressively. The users are allowed to download the features/OTU table (.biom;.tsv;.xls), representative sequences (.fasta) and phylogenetic tree (.nwk), taxonomy assignment file (optional). For downstream analyses, users are allowed to perform relative abundances (at all taxonomical levels), community comparison (alpha and beta diversity, core microbiome), differential abundances (DESeq2 and linear discriminant analysis) and functional prediction (PICRust, Tax4Fun and FunGuilds). Our case study using a published rice microbiome dataset demonstrates intuitive user interface and great accessibility of the EzMAP.<br><br>CONCLUSIONS: This EzMAP allows users to consolidate the microbiome analysis processes from raw sequence processing to downstream analyses specific for individual projects. We believe that this will be an invaluable tool for the beginners in their microbiome data analysis. This platform is freely available at https://github.com/gnanibioinfo/EzMAP and will be continually updated for adoption of changes in methods and approaches.},
}
@article {pmid33824198,
year = {2021},
author = {Cooper, RO and Vavra, JM and Cressler, CE},
title = {Targeted Manipulation of Abundant and Rare Taxa in the Daphnia magna Microbiota with Antibiotics Impacts Host Fitness Differentially.},
journal = {mSystems},
volume = {6},
number = {2},
pages = {},
pmid = {33824198},
issn = {2379-5077},
abstract = {Host-associated microbes contribute to host fitness, but it is unclear whether these contributions are from rare keystone taxa, numerically abundant taxa, or interactions among community members. Experimental perturbation of the microbiota can highlight functionally important taxa; however, this approach is primarily applied in systems with complex communities where the perturbation affects hundreds of taxa, making it difficult to pinpoint contributions of key community members. Here, we use the ecological model organism Daphnia magna to examine the importance of rare and abundant taxa by perturbing its relatively simple microbiota with targeted antibiotics. We used sublethal antibiotic doses to target either rare or abundant members across two temperatures and then measured key host life history metrics and shifts in microbial community composition. We find that removal of abundant taxa had greater impacts on host fitness than did removal of rare taxa and that the abundances of nontarget taxa were impacted by antibiotic treatment, suggesting that no rare keystone taxa exist in the Daphnia magna microbiota but that microbe-microbe interactions may play a role in host fitness. We also find that microbial community composition was impacted by antibiotics differently across temperatures, indicating that ecological context shapes within-host microbial responses and effects on host fitness.IMPORTANCE Understanding the contributions of rare and abundant taxa to host fitness is an outstanding question in host microbial ecology. In this study, we use the model zooplankton Daphnia magna and its relatively simple cohort of bacterial taxa to disentangle the roles of distinct taxa in host life history metrics, using a suite of antibiotics to selectively reduce the abundance of functionally important taxa. We also examine how environmental context shapes the importance of these bacterial taxa in host fitness.},
}
@article {pmid33824193,
year = {2021},
author = {Daisley, BA and Reid, G},
title = {BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities.},
journal = {mSystems},
volume = {6},
number = {2},
pages = {},
pmid = {33824193},
issn = {2379-5077},
abstract = {High-throughput 16S rRNA gene sequencing technologies have robust potential to improve our understanding of bee (Hymenoptera: Apoidea)-associated microbial communities and their impact on hive health and disease. Despite recent computation algorithms now permitting exact inferencing of high-resolution exact amplicon sequence variants (ASVs), the taxonomic classification of these ASVs remains a challenge due to inadequate reference databases. To address this, we assemble a comprehensive data set of all publicly available bee-associated 16S rRNA gene sequences, systematically annotate poorly resolved identities via inclusion of 618 placeholder labels for uncultivated microbial dark matter, and correct for phylogenetic inconsistencies using a complementary set of distance-based and maximum likelihood correction strategies. To benchmark the resultant database (BEExact), we compare performance against all existing reference databases in silico using a variety of classifier algorithms to produce probabilistic confidence scores. We also validate realistic classification rates on an independent set of ∼234 million short-read sequences derived from 32 studies encompassing 50 different bee types (36 eusocial and 14 solitary). Species-level classification rates on short-read ASVs range from 80 to 90% using BEExact (with ∼20% due to "bxid" placeholder names), whereas only ∼30% at best can be resolved with current universal databases. A series of data-driven recommendations are developed for future studies. We conclude that BEExact (https://github.com/bdaisley/BEExact) enables accurate and standardized microbiota profiling across a broad range of bee species-two factors of key importance to reproducibility and meaningful knowledge exchange within the scientific community that together, can enhance the overall utility and ecological relevance of routine 16S rRNA gene-based sequencing endeavors.IMPORTANCE The failure of current universal taxonomic databases to support the rapidly expanding field of bee microbiota research has led to many investigators relying on "in-house" reference sets or manual classification of sequence reads (usually based on BLAST searches), often with vague identity thresholds and subjective taxonomy choices. This time-consuming, error- and bias-prone process lacks standardization, cripples the potential for comparative cross-study analysis, and in many cases is likely to incorrectly sway study conclusions. BEExact is structured on and leverages several complementary bioinformatic techniques to enable refined inference of bee host-associated microbial communities without any other methodological modifications necessary. It also bridges the gap between current practical outcomes (i.e., phylotype-to-genus level constraints with 97% operational taxonomic units [OTUs]) and the theoretical resolution (i.e., species-to-strain level classification with 100% ASVs) attainable in future microbiota investigations. Other niche habitats could also likely benefit from customized database curation via implementation of the novel approaches introduced in this study.},
}
@article {pmid33820946,
year = {2021},
author = {Deng, Y and Huang, Y and Che, Y and Yang, Y and Yin, X and Yan, A and Dai, L and Liu, YY and Polz, M and Zhang, T},
title = {Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants.},
journal = {The ISME journal},
volume = {15},
number = {10},
pages = {2817-2829},
pmid = {33820946},
issn = {1751-7370},
support = {R01 AI141529/AI/NIAID NIH HHS/United States ; },
mesh = {Bacteria/genetics ; Drug Resistance, Microbial ; Humans ; Metagenome ; *Microbiota/genetics ; Sulfonamides ; },
abstract = {Antibiotic subsistence in bacteria represents an alternative resistance machinery, while paradoxically, it is also a cure for environmental resistance. Antibiotic-subsisting bacteria can detoxify antibiotic-polluted environments and prevent the development of antibiotic resistance in environments. However, progress toward efficient in situ engineering of antibiotic-subsisting bacteria is hindered by the lack of mechanistic and predictive understanding of the assembly of the functioning microbiome. By top-down manipulation of wastewater microbiomes using sulfadiazine as the single limiting source, we monitored the ecological selection process that forces the wastewater microbiome to perform efficient sulfadiazine subsistence. We found that the community-level assembly selects for the same three families rising to prominence across different initial pools of microbiomes. We further analyzed the assembly patterns using a linear model. Detailed inspections of the sulfonamide metabolic gene clusters in individual genomes of isolates and assembled metagenomes reveal limited transfer potential beyond the boundaries of the Micrococcaceae lineage. Our results open up new possibilities for engineering specialist bacteria for environmental applications.},
}
@article {pmid33817951,
year = {2021},
author = {Gwizdala, M and Lebre, PH and Maggs-Kölling, G and Marais, E and Cowan, DA and Krüger, TPJ},
title = {Sub-lithic photosynthesis in hot desert habitats.},
journal = {Environmental microbiology},
volume = {23},
number = {7},
pages = {3867-3880},
doi = {10.1111/1462-2920.15505},
pmid = {33817951},
issn = {1462-2920},
mesh = {*Cyanobacteria/genetics ; *Desert Climate ; Ecosystem ; Photosynthesis ; Soil Microbiology ; },
abstract = {In hyper-arid soil environments, photosynthetic microorganisms are largely restricted to hypolithic (sub-lithic) habitats: i.e., on the ventral surfaces of translucent pebbles in desert pavements. Here, we combined fluorometric, spectroscopic, biochemical and metagenomic approaches to investigate in situ the light transmission properties of quartz stones in the Namib Desert, and assess the photosynthetic activity of the underlying hypolithic cyanobacterial biofilms. Quartz pebbles greatly reduced the total photon flux to the ventral surface biofilms and filtered out primarily the short wavelength portion of the solar spectrum. Chlorophylls d and f were not detected in biofilm pigment extracts; however, hypolithic cyanobacterial communities showed some evidence of adaptation to sub-lithic conditions, including the prevalence of genes encoding Helical Carotenoid Proteins, which are associated with desiccation stress. Under water-saturated conditions, hypolithic communities showed no evidence of light stress, even when the quartz stones were exposed to full midday sunlight. This initial study creates a foundation for future in-situ and laboratory exploration of various adaptation mechanisms employed by photosynthetic organisms forming hypolithic microbial communities.},
}
@article {pmid33813729,
year = {2021},
author = {Camacho-Montealegre, CM and Rodrigues, EM and Morais, DK and Tótola, MR},
title = {Prokaryotic community diversity during bioremediation of crude oil contaminated oilfield soil: effects of hydrocarbon concentration and salinity.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {52},
number = {2},
pages = {787-800},
pmid = {33813729},
issn = {1678-4405},
mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Carbon Dioxide/metabolism ; Hydrocarbons/metabolism ; *Microbiota/genetics ; Oil and Gas Fields/*microbiology ; Petroleum/*metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sodium Chloride/metabolism ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Crude oil extracted from oilfield reservoirs brings together hypersaline produced water. Failure in pipelines transporting this mixture causes contamination of the soil with oil and hypersaline water. Soil salinization is harmful to biological populations, impairing the biodegradation of contaminants. We simulated the contamination of a soil from an oilfield with produced water containing different concentrations of NaCl and crude oil, in order to evaluate the effect of salinity and hydrocarbon concentration on prokaryote community structure and biodegradation activity. Microcosms were incubated in CO2-measuring respirometer. After the incubation, residual aliphatic hydrocarbons were quantified and were performed 16S rRNA gene sequencing. An increase in CO2 emission and hydrocarbon biodegradation was observed with increasing oil concentration up to 100 g kg[-1]. Alpha diversity decreased in oil-contaminated soils with an increase in the relative abundance of Actinobacteria and reduction of Bacteroidetes with increasing oil concentration. In the NaCl-contaminated soils, alpha diversity, CO2 emission, and hydrocarbon biodegradation decreased with increasing NaCl concentration. There was an increase in the relative abundance of Firmicutes and Proteobacteria and a reduction of Actinobacteria with increasing salt concentration. Our results highlight the need to adopt specific bioremediation strategies in soils impacted by mixtures of crude oil and hypersaline produced water.},
}
@article {pmid33813189,
year = {2021},
author = {Glodowska, M and Schneider, M and Eiche, E and Kontny, A and Neumann, T and Straub, D and , and Kleindienst, S and Kappler, A},
title = {Microbial transformation of biogenic and abiogenic Fe minerals followed by in-situ incubations in an As-contaminated vs. non-contaminated aquifer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {281},
number = {},
pages = {117012},
doi = {10.1016/j.envpol.2021.117012},
pmid = {33813189},
issn = {1873-6424},
mesh = {*Arsenic ; Ferric Compounds ; *Groundwater ; Iron ; Minerals ; Oxidation-Reduction ; },
abstract = {Fe(III) minerals play a crucial role for arsenic (As) mobility in aquifers as they usually represent the main As-bearing phases. Microbial reductive dissolution of As-bearing Fe(III) minerals is responsible for the release of As and the resulting groundwater contamination in many sites worldwide. So far, in most studies mainly abiogenic iron minerals have been considered. Yet, biogenic minerals that possess different properties to their abiogenic counterparts are also present in the environment. In some environments they dominate the iron mineral inventory but so far, it is unclear what this means for the As mobility. We, therefore, performed an in-situ aquifer Fe(III) minerals exposure experiment i) to evaluate how different biogenic and abiogenic Fe(III) minerals are transformed in a strongly reducing, As-contaminated aquifer (25 m) compared to As-free moderately reducing aquifer (32 m) and ii) to assess which microbial taxa are involved in these Fe(III) minerals transformations. We found that higher numbers of bacteria and archaea were associated with the minerals incubated in the As-contaminated compared to the non-contaminated aquifer and that all Fe(III) minerals were mainly colonized by Fe(III)-reducing bacteria, with Geobacter being the most abundant taxon. Additionally, fermenting microorganisms were abundant on minerals incubated in the As-contaminated aquifer, while methanotrophs were identified on the minerals incubated in the As-free moderately reducing aquifer, implying involvement of these microorganisms in Fe(III) reduction. We observed that biogenic Fe(III) minerals generally tend to become more reduced and when incubated in the As-contaminated aquifer sorbed more As than the abiogenic ones. Most of abiogenic and biogenic Fe(III) minerals were transformed into magnetite while biogenic more crystalline mixed phases were not subjected to visible transformation. This in-situ Fe(III) minerals incubation approach shows that biogenic minerals are more prone to be colonized by (Fe(III)-reducing) microorganisms and bind more As, although ultimately produce similar minerals during Fe(III) reduction.},
}
@article {pmid33811505,
year = {2022},
author = {Han, Y and Guo, C and Guan, X and McMinn, A and Liu, L and Zheng, G and Jiang, Y and Liang, Y and Shao, H and Tian, J and Wang, M},
title = {Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {34-47},
pmid = {33811505},
issn = {1432-184X},
support = {2018YFC1406704//National Key Research and Development Program of China/ ; No. 2018SDKJ0406-6//Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao), China/ ; 41906126//Natural Science Foundation of China/ ; 41976117//Natural Science Foundation of China/ ; 201912003//Research Funds for the Central Universities/ ; 201812002//Research Funds for the Central Universities/ ; LMB20091001//Open Research Fund of LMB, SCSIO/ ; },
mesh = {*Alveolata/classification ; Pacific Ocean ; RNA, Ribosomal, 18S/genetics ; *Rhizaria/classification ; Seawater/*microbiology ; *Stramenopiles/classification ; },
abstract = {Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.},
}
@article {pmid33811029,
year = {2021},
author = {Rupp, DL and Lamit, LJ and Techtmann, SM and Kane, ES and Lilleskov, EA and Turetsky, MR},
title = {The Rhizosphere Responds: Rich Fen Peat and Root Microbial Ecology after Long-Term Water Table Manipulation.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {12},
pages = {e0024121},
pmid = {33811029},
issn = {1098-5336},
mesh = {Alaska ; Archaea/genetics/isolation &amp; purification/metabolism ; Bacteria/genetics/isolation &amp; purification/metabolism ; Carbon Cycle ; *Groundwater ; Iron/metabolism ; Magnoliopsida/*microbiology ; Methane/metabolism ; Microbiota ; Plant Roots/*microbiology ; *Rhizosphere ; Soil ; *Soil Microbiology ; },
abstract = {Hydrologic shifts due to climate change will affect the cycling of carbon (C) stored in boreal peatlands. Carbon cycling in these systems is carried out by microorganisms and plants in close association. This study investigated the effects of experimentally manipulated water tables (lowered and raised) and plant functional groups on the peat and root microbiomes in a boreal rich fen. All samples were sequenced and processed for bacterial, archaeal (16S DNA genes; V4), and fungal (internal transcribed spacer 2 [ITS2]) DNA. Depth had a strong effect on microbial and fungal communities across all water table treatments. Bacterial and archaeal communities were most sensitive to the water table treatments, particularly at the 10- to 20-cm depth; this area coincides with the rhizosphere or rooting zone. Iron cyclers, particularly members of the family Geobacteraceae, were enriched around the roots of sedges, horsetails, and grasses. The fungal community was affected largely by plant functional group, especially cinquefoils. Fungal endophytes (particularly Acephala spp.) were enriched in sedge and grass roots, which may have underappreciated implications for organic matter breakdown and cycling. Fungal lignocellulose degraders were enriched in the lowered water table treatment. Our results were indicative of two main methanogen communities, a rooting zone community dominated by the archaeal family Methanobacteriaceae and a deep peat community dominated by the family Methanomicrobiaceae. IMPORTANCE This study demonstrated that roots and the rooting zone in boreal fens support organisms likely capable of methanogenesis, iron cycling, and fungal endophytic association and are directly or indirectly affecting carbon cycling in these ecosystems. These taxa, which react to changes in the water table and associate with roots and, particularly, graminoids, may gain greater biogeochemical influence, as projected higher precipitation rates could lead to an increased abundance of sedges and grasses in boreal fens.},
}
@article {pmid33809442,
year = {2021},
author = {Jesus, HE and Carreira, RS and Paiva, SSM and Massone, C and Enrich-Prast, A and Peixoto, RS and Rodrigues, JLM and Lee, CK and Cary, C and Rosado, AS},
title = {Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil.},
journal = {Microorganisms},
volume = {9},
number = {3},
pages = {},
pmid = {33809442},
issn = {2076-2607},
support = {001//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; CNE2017//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; },
abstract = {The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze-thaw cycle (FTC) alternating between -20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.},
}
@article {pmid33807581,
year = {2021},
author = {Maes, PW and Floyd, AS and Mott, BM and Anderson, KE},
title = {Overwintering Honey Bee Colonies: Effect of Worker Age and Climate on the Hindgut Microbiota.},
journal = {Insects},
volume = {12},
number = {3},
pages = {},
pmid = {33807581},
issn = {2075-4450},
support = {2022-21000-021-00D//Agricultural Research Service/ ; },
abstract = {Honey bee overwintering health is essential to meet the demands of spring pollination. Managed honey bee colonies are overwintered in a variety of climates, and increasing rates of winter colony loss have prompted investigations into overwintering management, including indoor climate controlled overwintering. Central to colony health, the worker hindgut gut microbiota has been largely ignored in this context. We sequenced the hindgut microbiota of overwintering workers from both a warm southern climate and controlled indoor cold climate. Congruently, we sampled a cohort of known chronological age to estimate worker longevity in southern climates, and assess age-associated changes in the core hindgut microbiota. We found that worker longevity over winter in southern climates was much lower than that recorded for northern climates. Workers showed decreased bacterial and fungal load with age, but the relative structure of the core hindgut microbiome remained stable. Compared to cold indoor wintering, collective microbiota changes in the southern outdoor climate suggest compromised host physiology. Fungal abundance increased by two orders of magnitude in southern climate hindguts and was positively correlated with non-core, likely opportunistic bacteria. Our results contribute to understanding overwintering honey bee biology and microbial ecology and provide insight into overwintering strategies.},
}
@article {pmid33807233,
year = {2021},
author = {Mulholland, KA and Robinson, MG and Keeler, SJ and Johnson, TJ and Weber, BW and Keeler, CL},
title = {Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing.},
journal = {Microorganisms},
volume = {9},
number = {4},
pages = {},
pmid = {33807233},
issn = {2076-2607},
support = {2015-68004-23131//U.S. Department of Agriculture/ ; },
abstract = {Elucidating the complex microbial interactions in biological environments requires the identification and characterization of not only the bacterial component but also the eukaryotic viruses, bacteriophage, and fungi. In a proof of concept experiment, next generation sequencing approaches, accompanied by the development of novel computational and bioinformatics tools, were utilized to examine the evolution of the microbial ecology of the avian trachea during the growth of a healthy commercial broiler flock. The flock was sampled weekly, beginning at placement and concluding at 49 days, the day before processing. Metagenomic sequencing of DNA and RNA was utilized to examine the bacteria, virus, bacteriophage, and fungal components during flock growth. The utility of using a metagenomic approach to study the avian respiratory virome was confirmed by detecting the dysbiosis in the avian respiratory virome of broiler chickens diagnosed with infection with infectious laryngotracheitis virus. This study provides the first comprehensive analysis of the ecology of the avian respiratory microbiome and demonstrates the feasibility for the use of this approach in future investigations of avian respiratory diseases.},
}
@article {pmid33805552,
year = {2021},
author = {Pham, VT and Calatayud, M and Rotsaert, C and Seifert, N and Richard, N and Van den Abbeele, P and Marzorati, M and Steinert, RE},
title = {Antioxidant Vitamins and Prebiotic FOS and XOS Differentially Shift Microbiota Composition and Function and Improve Intestinal Epithelial Barrier In Vitro.},
journal = {Nutrients},
volume = {13},
number = {4},
pages = {},
pmid = {33805552},
issn = {2072-6643},
mesh = {Adult ; Antioxidants/*pharmacology ; Bacteria/classification/drug effects ; Caco-2 Cells ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Glucuronates/*pharmacology ; HT29 Cells ; Humans ; Intestinal Mucosa/drug effects/microbiology ; Male ; Oligosaccharides/*pharmacology ; Oxidation-Reduction ; *Prebiotics ; Vitamins/*pharmacology ; },
abstract = {Human gut microbiota (HGM) play a significant role in health and disease. Dietary components, including fiber, fat, proteins and micronutrients, can modulate HGM. Much research has been performed on conventional prebiotics such as fructooligosaccharides (FOS) and galactooligosaccharides (GOS), however, novel prebiotics or micronutrients still require further validation. We assessed the effect of FOS, xylooligosaccharides (XOS) and a mixture of an antioxidant vitamin blend (AOB) on gut microbiota composition and activity, and intestinal barrier in vitro. We used batch fermentations and tested the short-term effect of different products on microbial activity in six donors. Next, fecal inocula from two donors were used to inoculate the simulator of the human microbial ecosystem (SHIME) and after long-term exposure of FOS, XOS and AOB, microbial activity (short- and branched-chain fatty acids and lactate) and HGM composition were evaluated. Finally, in vitro assessment of intestinal barrier was performed in a Transwell setup of differentiated Caco-2 and HT29-MTX-E12 cells exposed to fermentation supernatants. Despite some donor-dependent differences, all three tested products showed beneficial modulatory effects on microbial activity represented by an increase in lactate and SCFA levels (acetate, butyrate and to a lesser extent also propionate), while decreasing proteolytic markers. Bifidogenic effect of XOS was consistent, while AOB supplementation appears to exert a specific impact on reducing F. nucleatum and increasing butyrate-producing B. wexlerae. Functional and compositional microbial changes were translated to an in vitro host response by increases of the intestinal barrier integrity by all the products and a decrease of the redox potential by AOB supplementation.},
}
@article {pmid33800578,
year = {2021},
author = {Panteli, N and Mastoraki, M and Lazarina, M and Chatzifotis, S and Mente, E and Kormas, KA and Antonopoulou, E},
title = {Configuration of Gut Microbiota Structure and Potential Functionality in Two Teleosts under the Influence of Dietary Insect Meals.},
journal = {Microorganisms},
volume = {9},
number = {4},
pages = {},
pmid = {33800578},
issn = {2076-2607},
support = {MIS 5045857//the European Union and Greek national funds through the National Strategic Reference Framework 2014-2020 (GR &amp; EU), Special Actions Aquaculture-Industrial Materials-Open innovation in culture/ ; },
abstract = {Insect meals are considered promising, eco-friendly, alternative ingredients for aquafeed. Considering the dietary influence on establishment of functioning gut microbiota, the effect of the insect meal diets on the microbial ecology should be addressed. The present study assessed diet- and species-specific shifts in gut resident bacterial communities of juvenile reared Dicentrarchus labrax and Sparus aurata in response to three experimental diets with insect meals from three insects (Hermetia illucens, Tenebrio molitor, Musca domestica), using high-throughput Illumina sequencing of the V3-V4 region of the 16S rRNA gene. The dominant phyla were Firmicutes, Proteobacteria and Actinobacteria in all dietary treatments. Anaerococcus sp., Cutibacterium sp. and Pseudomonas sp. in D. labrax, and Staphylococcus sp., Hafnia sp. and Aeromonas sp. in S. aurata were the most enriched shared species, following insect-meal inclusion. Network analysis of the dietary treatments highlighted diet-induced changes in the microbial community assemblies and revealed unique and shared microbe-to-microbe interactions. PICRUSt-predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly differentiated, including genes associated with metabolic pathways. The present findings strengthen the importance of diet in microbiota configuration and underline that different insects as fish feed ingredients elicit species-specific differential responses of structural and functional dynamics in gut microbial communities.},
}
@article {pmid33799457,
year = {2021},
author = {Rao, Z and Li, J and Shi, B and Zeng, Y and Liu, Y and Sun, Z and Wu, L and Sun, W and Tang, Z},
title = {Dietary Tryptophan Levels Impact Growth Performance and Intestinal Microbial Ecology in Weaned Piglets via Tryptophan Metabolites and Intestinal Antimicrobial Peptides.},
journal = {Animals : an open access journal from MDPI},
volume = {11},
number = {3},
pages = {},
pmid = {33799457},
issn = {2076-2615},
support = {31772610, 31872370//National Natural Science Foundation of China/ ; cx2017024//Chongqing key innovation project for overseas students/ ; 2018YFD0501000//National Key R&amp;D Program of China/ ; },
abstract = {Tryptophan (Trp) plays an important role in piglet growth. However, the effect of dietary Trp on microbial flora is still poorly understood. A total of 40 28-d weaned piglets were allocated to four groups with 10 barrows per group and one pig per replicate. Piglets were fed a corn and soybean meal-based diet with 0.14%, 0.21%, 0.28%, or 0.35% Trp for four weeks. Five piglets from each diet group were euthanized, and blood and tissue samples were collected. The average daily body weight gain, average daily feed intake, feed conversion ratio, spleen index, pancreas index, longissimus dorsi muscle index, plasma insulin, 5-hydroxytryptamine, kynurenine, and Trp concentrations of weaned piglets increased in a dose-dependent manner (p < 0.05). Compared with the 0.14% Trp diet, the adequate-Trp diets (0.21%, 0.28%, or 0.35%) down-regulated the relative abundances of 12 genera including Turicibacter, Prevotella, Mitsuokella, Anaerovibrio, Megasphaera, Succinivibrio, Sutterella, Desulfovibrio, and Methanobrevibacter (p < 0.05); up-regulated the abundances of Ruminococcaceae, Lactobacillus, and Muribaculaceae in the colon (p < 0.05); and augmented the mRNA level and concentration of porcine β-defensin 2 in the small intestinal mucosa (p < 0.05). Moreover, Trp-adequate diets increased the abundances of Trp hydroxylase, indoleamine 2,3-dioxygenase, porcine β-defensin 2, phosphorylated mammalian target of rapamycin, and phosphorylated protein kinase B in the small intestinal mucosa (p < 0.05). We noted that a corn and soybean meal-based diet with 0.35% Trp may be a nutritional strategy to improve growth performance, intestinal mucosal barrier integrity, and intestinal microbial ecology in weaned piglets.},
}
@article {pmid33797563,
year = {2022},
author = {Frankel-Bricker, J and Frankel, LK},
title = {Re-Analysis of 16S rRNA Gene Sequence Data Sets Uncovers Disparate Laboratory-Specific Microbiomes Associated with the Yellow Fever Mosquito (Aedes aegypti).},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {167-181},
pmid = {33797563},
issn = {1432-184X},
mesh = {*Aedes/microbiology ; Animals ; Female ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Host-microbiome dynamics occurring in the yellow fever mosquito (Aedes aegypti) contribute to host life history traits, and particular bacterial taxa are proposed to comprise a "core" microbiota that influences host physiology. Laboratory-based studies are frequently performed to investigate these processes; however, experimental results are often presumed to be generalizable across laboratories, and few efforts have been made to independently reproduce and replicate significant findings. A recent study by Muturi et al. (FEMS Microbiol Ecol 95 (1):213, 2019) demonstrated the food source imbibed by laboratory-reared adult female mosquitoes significantly impacted the host-associated microbiota-a foundational finding in the field of mosquito biology worthy of independent evaluation. Here, we coalesce these data with two additional mosquito-derived 16S rRNA gene sequence data sets using a unifying bioinformatics pipeline to reproduce the characterization of these microbiota, test for a significant food source effect when independent samples were added to the analyses, assess whether similarly fed mosquito microbiomes were comparable across laboratories, and identify conserved bacterial taxa. Our pipeline characterized similar microbiome composition and structure from the data published previously, and a significant food source effect was detected with the addition of independent samples, increasing the robustness of this previously discovered component of mosquito biology. However, distinct microbial communities were identified from similarly fed but independently reared mosquitoes, and surveys across all samples did not identify conserved bacterial taxa. These findings demonstrated that while the main effect of the food source was supported, laboratory-specific conditions may produce inherently differential microbiomes across independent laboratory environments.},
}
@article {pmid33792742,
year = {2022},
author = {Xu, Q and Ling, N and Quaiser, A and Guo, J and Ruan, J and Guo, S and Shen, Q and Vandenkoornhuyse, P},
title = {Rare Bacteria Assembly in Soils Is Mainly Driven by Deterministic Processes.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {137-150},
pmid = {33792742},
issn = {1432-184X},
support = {2016YFD0200900//National Key Research and Development Program of China/ ; },
mesh = {Bacteria/genetics ; China ; *Soil ; *Soil Microbiology ; },
abstract = {Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules.},
}
@article {pmid33790426,
year = {2021},
author = {Hanson, BT and Dimitri Kits, K and Löffler, J and Burrichter, AG and Fiedler, A and Denger, K and Frommeyer, B and Herbold, CW and Rattei, T and Karcher, N and Segata, N and Schleheck, D and Loy, A},
title = {Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut.},
journal = {The ISME journal},
volume = {15},
number = {9},
pages = {2779-2791},
pmid = {33790426},
issn = {1751-7370},
support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Bacteria/genetics ; Feces ; Humans ; *Hydrogen Sulfide ; Methylglucosides ; Nutrients ; },
abstract = {Responses of the microbiota to diet are highly personalized but mechanistically not well understood because many metabolic capabilities and interactions of human gut microorganisms are unknown. Here we show that sulfoquinovose (SQ), a sulfonated monosaccharide omnipresent in green vegetables, is a selective yet relevant substrate for few but ubiquitous bacteria in the human gut. In human feces and in defined co-culture, Eubacterium rectale and Bilophila wadsworthia used recently identified pathways to cooperatively catabolize SQ with 2,3-dihydroxypropane-1-sulfonate as a transient intermediate to hydrogen sulfide (H2S), a key intestinal metabolite with disparate effects on host health. SQ-degradation capability is encoded in almost half of E. rectale genomes but otherwise sparsely distributed among microbial species in the human intestine. However, re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and H2S production (mostly from B. wadsworthia) pathways were expressed abundantly across various health states, demonstrating that these microbial functions are core attributes of the human gut. The discovery of green-diet-derived SQ as an exclusive microbial nutrient and an additional source of H2S in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and has implications for precision editing of the gut microbiota by dietary and prebiotic interventions.},
}
@article {pmid33783701,
year = {2021},
author = {Muñoz-Palazon, B and Rodriguez-Sanchez, A and Hurtado-Martinez, M and Gonzalez-Lopez, J and Vahala, R and Gonzalez-Martinez, A},
title = {Evaluating the nitrogen-contaminated groundwater treatment by a denitrifying granular sludge bioreactor: effect of organic matter loading.},
journal = {Environmental science and pollution research international},
volume = {28},
number = {30},
pages = {41351-41364},
pmid = {33783701},
issn = {1614-7499},
mesh = {Bioreactors ; Denitrification ; *Groundwater ; Nitrogen/analysis ; *Sewage ; },
abstract = {A sequential bed granular bioreactor was adapted to treat nitrate-polluted synthetic groundwater under anaerobic conditions and agitation with denitrification gas, achieving very efficient performance in total nitrogen removal at influent organic carbon concentrations of 1 g L[-1] (80-90%) and 0.5 g L[-1] (70-80%) sodium acetate, but concentrations below 0.5 g L[-1] caused accumulation of nitrite and nitrate and led to system failure (30-40% removal). Biomass size and settling velocity were higher above 0.5 g L[-1] sodium acetate. Trichosporonaceae dominated the fungal populations at all times, while a dominance of terrestrial group Thaumarchaeota and Acidovorax at 1 and 0.5 g L[-1] passed to a domination of Methanobrevibacter and an unclassified Comamonadaceae clone for NaAc lower than 0.5 g L[-1]. The results obtained pointed out that the denitrifying granular sludge technology is a feasible solution for the treatment of nitrogen-contaminated groundwater, and that influent organic matter plays an important role on the conformation of microbial communities within it and, therefore, on the overall efficiency of the system.},
}
@article {pmid33782710,
year = {2022},
author = {Khan, S and Hill, JE},
title = {Population Density Affects the Outcome of Competition in Co-cultures of Gardnerella Species Isolated from the Human Vaginal Microbiome.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {236-245},
pmid = {33782710},
issn = {1432-184X},
mesh = {Coculture Techniques ; Female ; Gardnerella/genetics ; Humans ; *Microbiota ; Population Density ; RNA, Ribosomal, 16S/genetics ; Vagina ; },
abstract = {Negative frequency-dependent selection is one possible mechanism for maintenance of rare species in communities, but the selective advantage of rare species may be checked at lower overall population densities where resources are abundant. Gardnerella spp. belonging to cpn60 subgroup D, are detected at low levels in vaginal microbiomes and are nutritional generalists relative to other more abundant Gardnerella spp., making them good candidates for negative frequency-dependent selection. The vaginal microbiome is a dynamic environment, and the resulting changes in density of the microbiota may explain why subgroup D never gains dominance. To test this, we co-cultured subgroup D isolates with isolates from the more common and abundant subgroup C. Deep amplicon sequencing of rpoB was used to determine proportional abundance of each isolate at 0 h and 72 h in 152 co-cultures and to calculate change in proportion. D isolates had a positive change in proportional abundance in most co-cultures regardless of initial proportion. Initial density affected the change in proportion of subgroup D isolates either positively or negatively depending on the particular isolates combined, suggesting that growth rate, population density and other intrinsic features of the isolates influenced the outcome. Our results demonstrate that population density is an important factor influencing the outcome of competition between Gardnerella spp. isolated from the human vaginal microbiome.},
}
@article {pmid33782568,
year = {2021},
author = {Scoma, A},
title = {Functional groups in microbial ecology: updated definitions of piezophiles as suggested by hydrostatic pressure dependence on temperature.},
journal = {The ISME journal},
volume = {15},
number = {7},
pages = {1871-1878},
pmid = {33782568},
issn = {1751-7370},
mesh = {*Hydrostatic Pressure ; Temperature ; },
}
@article {pmid33777336,
year = {2021},
author = {Gutiérrez-Chávez, C and Benaud, N and Ferrari, BC},
title = {The ecological roles of microbial lipopeptides: Where are we going?.},
journal = {Computational and structural biotechnology journal},
volume = {19},
number = {},
pages = {1400-1413},
pmid = {33777336},
issn = {2001-0370},
abstract = {Lipopeptides (LPs) are secondary metabolites produced by a diversity of bacteria and fungi. Their unique chemical structure comprises both a peptide and a lipid moiety. LPs are of major biotechnological interest owing to their emulsification, antitumor, immunomodulatory, and antimicrobial activities. To date, these versatile compounds have been applied across multiple industries, from pharmaceuticals through to food processing, cosmetics, agriculture, heavy metal, and hydrocarbon bioremediation. The variety of LP structures and the diversity of the environments from which LP-producing microorganisms have been isolated suggest important functions in their natural environment. However, our understanding of the ecological role of LPs is limited. In this review, the mode of action and the role of LPs in motility, antimicrobial activity, heavy metals removal and biofilm formation are addressed. We include discussion on the need to characterise LPs from a diversity of microorganisms, with a focus on taxa inhabiting 'extreme' environments. We introduce the use of computational target fishing and molecular dynamics simulations as powerful tools to investigate the process of interaction between LPs and cell membranes. Together, these advances will provide new understanding of the mechanism of action of novel LPs, providing greater insights into the roles of LPs in the natural environment.},
}
@article {pmid33777079,
year = {2021},
author = {Stice, SP and Shin, GY and De Armas, S and Koirala, S and Galván, GA and Siri, MI and Severns, PM and Coutinho, T and Dutta, B and Kvitko, BH},
title = {The Distribution of Onion Virulence Gene Clusters Among Pantoea spp.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {643787},
pmid = {33777079},
issn = {1664-462X},
abstract = {Pantoea ananatis is a gram-negative bacterium and the primary causal agent of center rot of onions in Georgia. Previous genomic studies identified two virulence gene clusters, HiVir and alt, associated with center rot. The HiVir gene cluster is required to induce necrosis on onion tissues via synthesis of pantaphos, (2-hydroxy[phosphono-methyl)maleate), a phosphonate phytotoxin. The alt gene cluster aids in tolerance to thiosulfinates generated during onion tissue damage. Whole genome sequencing of other Pantoea species suggests that these gene clusters are present outside of P. ananatis. To assess the distribution of these gene clusters, two PCR primer sets were designed to detect the presence of HiVir and alt. Two hundred fifty-two strains of Pantoea spp. were phenotyped using the red onion scale necrosis (RSN) assay and were genotyped using PCR for the presence of these virulence genes. A diverse panel of strains from three distinct culture collections comprised of 24 Pantoea species, 41 isolation sources, and 23 countries, collected from 1946-2019, was tested. There is a significant association between the alt PCR assay and Pantoea strains recovered from symptomatic onion (P < 0.001). There is also a significant association of a positive HiVir PCR and RSN assay among P. ananatis strains but not among Pantoea spp., congeners. This may indicate a divergent HiVir cluster or different pathogenicity and virulence mechanisms. Last, we describe natural alt positive [RSN[+]/HiVir[+]/alt [+]] P. ananatis strains, which cause extensive bulb necrosis in a neck-to-bulb infection assay compared to alt negative [RSN[+]/HiVir[+]/alt [-]] P. ananatis strains. A combination of assays that include PCR of virulence genes [HiVir and alt] and an RSN assay can potentially aid in identification of onion-bulb-rotting pathogenic P. ananatis strains.},
}
@article {pmid33776147,
year = {2021},
author = {Nakato, GV and Studholme, DJ and Blomme, G and Grant, M and Coutinho, TA and Were, EM and Wicker, E and Mahuku, G},
title = {SNP-based genotyping and whole-genome sequencing reveal previously unknown genetic diversity in Xanthomonas vasicola pv. musacearum, causal agent of banana xanthomonas wilt, in its presumed Ethiopian origin.},
journal = {Plant pathology},
volume = {70},
number = {3},
pages = {534-543},
pmid = {33776147},
issn = {0032-0862},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {For decades, Xanthomonas vasicola pv. musacearum (Xvm) has been an economically important bacterial pathogen on enset in Ethiopia. Since 2001, Xvm has also been responsible for significant losses to banana crops in several East and Central African countries, with devastating consequences for smallholder farmers. Understanding the genetic diversity within Xvm populations is essential for the smart design of transnationally reasoned, durable, and effective management practices. Previous studies have revealed limited genetic diversity in Xvm, with East African isolates from banana each falling into one of two closely related clades previously designated as sublineages SL 1 and SL 2, the former of which had also been detected on banana and enset in Ethiopia. Given the presumed origin of Xvm in Ethiopia, we hypothesized that both clades might be found in that country, along with additional genotypes not seen in Central and East African bananas. Genotyping of 97 isolates and whole-genome sequencing of 15 isolates revealed not only the presence of SL 2 in Ethiopia, but additional diversity beyond SL 1 and SL 2 in four new clades. Moreover, SL 2 was detected in the Democratic Republic of Congo, where previously SL 1 was the only clade reported. These results demonstrate a greater range of genetic diversity among Xvm isolates than previously reported, especially in Ethiopia, and further support the hypothesis that the East/Central Africa xanthomonas wilt epidemic has been caused by a restricted set of genotypes drawn from a highly diverse pathogen pool in Ethiopia.},
}
@article {pmid33774510,
year = {2021},
author = {Jungreis, I and Nelson, CW and Ardern, Z and Finkel, Y and Krogan, NJ and Sato, K and Ziebuhr, J and Stern-Ginossar, N and Pavesi, A and Firth, AE and Gorbalenya, AE and Kellis, M},
title = {Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution.},
journal = {Virology},
volume = {558},
number = {},
pages = {145-151},
pmid = {33774510},
issn = {1096-0341},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 HG004037/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; },
mesh = {*Open Reading Frames ; SARS-CoV-2/*genetics/immunology ; *Spike Glycoprotein, Coronavirus/classification/genetics ; *Terminology as Topic ; },
abstract = {At least six small alternative-frame open reading frames (ORFs) overlapping well-characterized SARS-CoV-2 genes have been hypothesized to encode accessory proteins. Researchers have used different names for the same ORF or the same name for different ORFs, resulting in erroneous homological and functional inferences. We propose standard names for these ORFs and their shorter isoforms, developed in consultation with the Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. We recommend calling the 39 codon Spike-overlapping ORF ORF2b; the 41, 57, and 22 codon ORF3a-overlapping ORFs ORF3c, ORF3d, and ORF3b; the 33 codon ORF3d isoform ORF3d-2; and the 97 and 73 codon Nucleocapsid-overlapping ORFs ORF9b and ORF9c. Finally, we document conflicting usage of the name ORF3b in 32 studies, and consequent erroneous inferences, stressing the importance of reserving identical names for homologs. We recommend that authors referring to these ORFs provide lengths and coordinates to minimize ambiguity caused by prior usage of alternative names.},
}
@article {pmid33773678,
year = {2021},
author = {Van Hecke, T and Vossen, E and Goethals, S and Boon, N and De Vrieze, J and De Smet, S},
title = {In vitro and in vivo digestion of red cured cooked meat: oxidation, intestinal microbiota and fecal metabolites.},
journal = {Food research international (Ottawa, Ont.)},
volume = {142},
number = {},
pages = {110203},
doi = {10.1016/j.foodres.2021.110203},
pmid = {33773678},
issn = {1873-7145},
mesh = {Animals ; Cattle ; Cooking ; Digestion ; *Gastrointestinal Microbiome ; Meat/analysis ; Rats ; *Red Meat/analysis ; },
abstract = {Mechanisms explaining epidemiological associations between red (processed) meat consumption and chronic disease risk are not yet elucidated, but may involve oxidative reactions, microbial composition alterations, inflammation and/or the formation of toxic bacterial metabolites. First, in vitro gastrointestinal digestion of 23 cooked beef-lard minces, to which varying doses of nitrite salt (range 0-40 g/kg) and sodium ascorbate (range 0-2 g/kg) were added, showed that nitrite salt decreased protein carbonylation up to 3-fold, and inhibited lipid oxidation, demonstrated by up to 4-fold lower levels of 'thiobarbituric acid reactive substances', 32-fold lower 4-hydroxynonenal, and 21-fold lower hexanal values. The use of ascorbate increased the antioxidant effect of low nitrite salt levels, whereas it slightly increased protein carbonylation at higher doses of nitrite salt. The addition of a low dose of ascorbate without nitrite salt slightly promoted oxidation during digestion, whereas higher doses had varying antioxidant effects. Second, 40 rats were fed a diet of cooked chicken- or beef-lard minces, either or not cured, for three weeks. Beef, compared to chicken, consumption increased lipid oxidation (2- to 4-fold) during digestion, and gut protein fermentation (cecal iso-butyrate, (iso-)valerate, and fecal indole, cresol), but oxidative stress and inflammation were generally not affected. Cured, compared to fresh, meat consumption significantly increased stomach protein carbonylation (+16%), colonic Ruminococcaceae (2.1-fold) and cecal propionate (+18%), whereas it decreased cecal butyrate (-25%), fecal phenol (-69%) and dimethyl disulfide (-61%) levels. Fecal acetaldehyde and diacetyl levels were increased in beef-fed rats by 2.8-fold and 5.9-fold respectively, and fecal carbon disulfide was 4-fold higher in rats consuming cured beef vs. fresh chicken. Given their known toxicity, the role of acetaldehyde and carbon disulfide in the relation between meat consumption and health should be investigated in future studies.},
}
@article {pmid33772660,
year = {2021},
author = {El Alaoui, A and Raklami, A and Bechtaoui, N and El Gharmali, A and Ouhammou, A and Imziln, B and Achouak, W and Pajuelo, E and Oufdou, K},
title = {Use of native plants and their associated bacteria rhizobiomes to remediate-restore Draa Sfar and Kettara mining sites, Morocco.},
journal = {Environmental monitoring and assessment},
volume = {193},
number = {4},
pages = {232},
doi = {10.1007/s10661-021-08977-4},
pmid = {33772660},
issn = {1573-2959},
mesh = {Bacteria ; Biodegradation, Environmental ; Environmental Monitoring ; *Metals, Heavy/analysis ; Morocco ; Plant Roots/chemistry ; Soil ; *Soil Pollutants/analysis ; },
abstract = {Soil and mine tailings are unreceptive to plant growth representing an imminent threat to the environment and resource sustainability. Using indigenous plants and their associated rhizobacteria to restore mining sites would be an eco-friendly solution to mitigate soil-metal toxicity. Soil prospection from Draa Sfar and Kettara mining sites in Morocco was carried out during different seasons for native plant sampling and rhizobacteria screening. The sites have been colonized by fifteen tolerant plant species having different capacities to accumulate Cu, Zn, and P in their shoots/root systems. In Draa Sfar mine, Suaeda vera J.F. Gmel., Sarcocornia fruticosa (L.) A.J. Scott., and Frankenia corymbosa Desf. accumulated mainly Cu (more than 90 mg kg[-1]), Atriplex halimus L. accumulated Zn (mg kg[-1]), and Frankenia corymbosa Desf. accumulated Pb (14 mg kg[-1]). As for Kettara mine, Aizoon canariense L. mainly accumulated Zn (270 mg kg[-1]), whereas Forsskalea tenacissima L. was the best shoot Cu accumulator with up to 50 mg kg[-1], whereas Cu accumulation in roots was 21 mg kg[-1]. The bacterial screening revealed the strains' abilities to tolerate heavy metals up to 50 mg kg[-1] Cu, 250 mg kg[-1] Pb, and 150 mg kg[-1] Zn. Isolated strains belonged mainly to Bacillaceae (73.33%) and Pseudomonadaceae (10%) and expressed different plant growth-promoting traits, alongside their antifungal activity. Results from this study will provide an insight into the ability of native plants and their associated rhizobacteria to serve as a basis for remediation-restoration strategies.},
}
@article {pmid33771785,
year = {2021},
author = {Andreo-Jimenez, B and Schilder, MT and Nijhuis, EH and Te Beest, DE and Bloem, J and Visser, JHM and van Os, G and Brolsma, K and de Boer, W and Postma, J},
title = {Chitin- and Keratin-Rich Soil Amendments Suppress Rhizoctonia solani Disease via Changes to the Soil Microbial Community.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {11},
pages = {},
pmid = {33771785},
issn = {1098-5336},
mesh = {Bacterial Physiological Phenomena ; Chitin/*analysis ; Fertilizers/*analysis ; Fungi/physiology ; Keratins/*analysis ; Microbiota/physiology ; Plant Diseases/*prevention &amp; control ; Rhizoctonia/drug effects/*physiology ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Enhancing soil suppressiveness against plant pathogens or pests is a promising alternative strategy to chemical pesticides. Organic amendments have been shown to reduce crop diseases and pests, with chitin products the most efficient against fungal pathogens. To study which characteristics of organic products are correlated with disease suppression, an experiment was designed in which 10 types of organic amendments with different physicochemical properties were tested against the soilborne pathogen Rhizoctonia solani in sugar beet seedlings. Organic amendments rich in keratin or chitin reduced Rhizoctonia solani disease symptoms in sugar beet plants. The bacterial and fungal microbial communities in amended soils were distinct from the microbial communities in nonamended soil, as well as those in soils that received other nonsuppressive treatments. The Rhizoctonia-suppressive amended soils were rich in saprophytic bacteria and fungi that are known for their keratinolytic and chitinolytic properties (i.e., Oxalobacteraceae and Mortierellaceae). The microbial community in keratin- and chitin-amended soils was associated with higher zinc, copper, and selenium, respectively.IMPORTANCE Our results highlight the importance of soil microorganisms in plant disease suppression and the possibility to steer soil microbial community composition by applying organic amendments to the soil.},
}
@article {pmid33771784,
year = {2021},
author = {Yang, X and Wang, H and Hrycauk, S and Klassen, MD},
title = {Effects of Peroxyacetic Acid Spray and Storage Temperature on the Microbiota and Sensory Properties of Vacuum-Packed Subprimal Cuts of Meat.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {11},
pages = {},
pmid = {33771784},
issn = {1098-5336},
mesh = {Disinfectants/*pharmacology ; *Food Microbiology ; *Food Packaging/methods ; *Food Storage/methods ; Meat/analysis/*microbiology ; Microbiota/physiology ; Peracetic Acid/*pharmacology ; *Temperature ; Vacuum ; },
abstract = {We investigated the impact of peroxyacetic acid (PAA; 200 ppm) spray on the microbiota and shelf life of commercial, vacuum-packed beef stored at chiller temperatures. Ribeye cuts (n = 147) were collected from a local beef plant on the day of production for two consecutive days, with one set collected at the start of work with the PAA spray nozzles turned off (control) and during routine production with the PAA spray nozzles turned on (PAA) each day. Packs were stored at 4, 2, and -1°C for up to 34, 104, and 180 days and sampled at appropriate intervals for sensory assessment, microbial enumeration, and microbial profiling by 16S rRNA gene amplicon analysis. Treatment with PAA did not affect the initial meat pH, the initial numbers of total aerobes, lactic acid bacteria, or Enterobacteriaceae (P > 0.05) before storage; however, it delayed the onset of spoilage by 7, 21, and 54 days at 4, 2, and -1°C, respectively. Square-root models of the variation of growth rate with temperature indicated lactic acid bacteria grew faster and Enterobacteriaceae grew slower on PAA-treated than on untreated meat. Negative associations between pH and deterioration of meat during storage were observed for PAA-treated meat. During storage, the microbiota were primarily dominated by Carnobacterium and Lactobacillus/Lactococcus on control meat but by Leuconostoc on PAA-treated meat. Serratia, Yersinia, and Clostridium were identified by linear discriminant effect size analysis as biomarkers for control meat; Clostridium was found in high abundance in samples that had the highest spoilage scores.IMPORTANCE The findings of this study show that PAA solutions applied at low concentrations under commercial settings positively modulated the meat microbiota. It did not have bactericidal effects for beef subprimals with very low microbial loads. However, it differentially impacted the members of the microbiota, which resulted in delayed onset of spoilage of vacuum-packed beef subprimal stored at all three temperatures (4, 2, and -1°C). This differential impact could be through one or a combination of the following factors: favoring the growth of lactic acid bacteria, which may in turn exert a competitive exclusion that might be due to production of antimicrobial compounds such as organic acids and bacteriocins; exerting synergistic antimicrobial effects with low temperatures against members of Enterobacteriaceae; and direct or indirect inhibitory effects against members of the clostridia. These findings not only advance our understanding of the microbial ecology of vacuum-packed meat stored at chiller temperatures but also suggest that bacteriostatic concentrations of antimicrobial interventions can be explored for shelf-life extension.},
}
@article {pmid33768626,
year = {2021},
author = {Wang, Y and Xue, K},
title = {Linkage between microbial shift and ecosystem functionality.},
journal = {Global change biology},
volume = {27},
number = {14},
pages = {3197-3199},
pmid = {33768626},
issn = {1365-2486},
mesh = {Carbon ; *Ecosystem ; *Permafrost ; },
abstract = {Exploring the linkage between microbial shifts and ecological processes or ecosystem functionality is a central focus in microbial ecology, but faces considerable obstacles, including the gap between DNA-based information and biochemical processes, as well as the asynchronization in microbial taxonomic shifts and their functionality change. Despite these issues, the well-established linkage between functional genes (reflecting genetic potential) and carbon release via laboratory incubation (reflecting field potential) is a good preliminary step that provides clues about the magnitude of in situ permafrost carbon release under permafrost thaw on the basis of microbial functional gene changes.},
}
@article {pmid33766138,
year = {2021},
author = {Pascual-García, A},
title = {Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework : Comment to ``A conceptual framework for the phylogenetically-constrained assembly of microbial communities''.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {73},
pmid = {33766138},
issn = {2049-2618},
mesh = {*Microbiota/genetics ; Phylogeny ; },
abstract = {In this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology. Video Abstract.},
}
@article {pmid33758981,
year = {2022},
author = {Campos, AB and Cavalcante, LC and de Azevedo, AR and Loiola, M and Silva, AET and Ara, A and Meirelles, PM},
title = {CPR and DPANN Have an Overlooked Role in Corals' Microbial Community Structure.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {252-255},
pmid = {33758981},
issn = {1432-184X},
support = {11268//Minist&#xe9;rio da Ci&#xea;ncia, Tecnologia, Inova&#xe7;&#xf5;es e Comunica&#xe7;&#xf5;es/ ; Serra-1709-17818//Instituto Serrapilheira/ ; 132261/2018-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 88887.301758/2018-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Animals ; *Anthozoa/microbiology ; Archaea/genetics ; Bacteria/genetics ; *Microbiota ; },
abstract = {Understanding how microbial communities are structured in coral holobionts is important to estimate local and global impacts and provide efficient environment management strategies. Several studies investigated the relationship between corals and their microbial communities, including the environmental drivers of shifts in this relationship, associated with diseases and coral cover loss. However, these studies are often geographically or taxonomically restricted and usually focused on the most abundant microbial groups, neglecting the rare biosphere, including archaea in the group DPANN and the recently discovered bacterial members of the candidate phyla radiation (CPR). Although it is known that rare microbes can play essential roles in several environments, we still lack understanding about which taxa comprise the rare biosphere of corals' microbiome. Here, we investigated the host-related and technical factors influencing coral microbial community structure and the importance of CPR and DPANN in this context by analyzing more than a hundred coral metagenomes from independent studies worldwide. We show that coral genera are the main biotic factor shaping coral microbial communities. We also detected several CPR and DPANN phyla comprising corals' rare biosphere for the first time and showed that they significantly contribute to shaping coral microbial communities.},
}
@article {pmid33758980,
year = {2022},
author = {Liu, Y and Xu, L and Zhang, Z and Huang, Z and Fang, D and Zheng, X and Yang, Z and Lu, M},
title = {Isolation, Identification, and Analysis of Potential Functions of Culturable Bacteria Associated with an Invasive Gall Wasp, Leptocybe invasa.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {151-166},
pmid = {33758980},
issn = {1432-184X},
support = {2017YFD0600101//the National Key Research and Development Program/ ; 31870634//National Natural Science Foundation of China/ ; 2018GXNSFDA281004//Key projects of Guangxi Natural Science Foundation/ ; },
mesh = {Animals ; Bacteria/genetics ; *Eucalyptus ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Wasps/microbiology ; },
abstract = {Symbioses between invasive insects and bacteria are one of the key drivers of insect invasion success. Gall-inducing insects stimulate host plants to produce galls, which affects the normal growth of plants. Leptocybe invasa Fisher et La Salle, an invasive gall-inducing wasp, mainly damages Eucalyptus plantations in Southern China, but little is known about its associated bacteria. The aim of this study was to assess the diversity of bacterial communities at different developmental stages of L. invasa and to identify possible ecological functions of the associated bacteria. Bacteria associated with L. invasa were isolated using culture-dependent methods and their taxonomic statuses were determined by sequencing the 16S rRNA gene. A total of 88 species belonging to four phyla, 27 families, and 44 genera were identified by phylogenetic analysis. The four phyla were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, mainly from the genera Pantoea, Enterobacter, Pseudomonas, Bacillus, Acinetobacter, Curtobacterium, Sphingobium, Klebsiella, and Rhizobium. Among them, 72 species were isolated in the insect gall stage and 46 species were isolated from the adult stage. The most abundant bacterial species were γ-Proteobacteria. We found significant differences in total bacterial counts and community compositions at different developmental stages, and identified possible ecological roles of L. invasa-associated bacteria. This study is the first to systematically investigate the associated bacteria of L. invasa using culture-dependent methods, and provides a reference for other gall-inducing insects and associated bacteria.},
}
@article {pmid33758979,
year = {2022},
author = {Norte, AC and Araújo, PM and Augusto, L and Guímaro, H and Santos, S and Lopes, RJ and Núncio, MS and Ramos, JA and Lopes de Carvalho, I},
title = {Effects of stress exposure in captivity on physiology and infection in avian hosts: no evidence of increased Borrelia burgdorferi s.l. infectivity to vector ticks.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {202-215},
pmid = {33758979},
issn = {1432-184X},
support = {MARE - UID/MAR/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BPD/108197/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL57/2016/CP1370/CT89//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/31569/2017 - NORTE -01-0145- FEDER-30288//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL57/2016/CP1440/CT0006//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; na//Portuguese National Institute of Health Doutor Ricardo Jorge (PT)/ ; },
mesh = {Animals ; *Borrelia ; *Borrelia burgdorferi ; *Borrelia burgdorferi Group/physiology ; *Ixodes/microbiology ; *Lyme Disease/microbiology/veterinary ; *Songbirds/microbiology ; },
abstract = {Exposure to environmental stressors, an increasingly recurring event in natural communities due to anthropogenic-induced environmental change, profoundly impacts disease emergence and spread. One mechanism through which this occurs is through stress-induced immunosuppression increasing disease susceptibility, prevalence, intensity and reactivation in hosts. We experimentally evaluated how exposure to stressors affected both the physiology of avian hosts and the prevalence of the zoonotic bacteria Borrelia burgdorferi sensu lato (s.l.), in two model species-the blackbird Turdus merula and the robin Erithacus rubecula captured in the wild, using xenodiagnoses and analysis of skin biopsies and blood. Although exposure to stressors in captivity induced physiological stress in birds (increased the number of circulating heterophils), there was no evidence of increased infectivity to xenodiagnostic ticks. However, Borrelia detection in the blood for both experimental groups of blackbirds was higher by the end of the captivity period. The infectivity and efficiency of transmission were higher for blackbirds than robins. When comparing different methodologies to determine infection status, xenodiagnosis was a more sensitive method than skin biopsies and blood samples, which could be attributed to mild levels of infection in these avian hosts and/or dynamics and timing of Borrelia infection relapses and redistribution in tissues.},
}
@article {pmid33758030,
year = {2021},
author = {Jiao, S and Peng, Z and Qi, J and Gao, J and Wei, G},
title = {Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling.},
journal = {mSystems},
volume = {6},
number = {2},
pages = {},
pmid = {33758030},
issn = {2379-5077},
abstract = {Biodiversity is important for supporting ecosystem functioning. To evaluate the factors contributing to the strength of microbial diversity-function relationships in complex terrestrial ecosystems, we conducted a soil survey over different habitats, including an agricultural field, forest, wetland, grassland, and desert. Soil microbial multidiversity was estimated by the combination of bacterial and fungal diversity. Soil ecosystem functions were evaluated using a multinutrient cycling index (MNC) in relation to carbon, nitrate, phosphorus, and potassium cycling. Significant positive relationships between soil multidiversity and multinutrient cycling were observed in all habitats, except the grassland and desert. Specifically, community compositions showed stronger correlations with multinutrient cycling than α-diversity, indicating the crucial role of microbial community composition differences on soil nutrient cycling. Importantly, we revealed that changes in both the neutral processes (Sloan neutral modeling) and the proportion of negative bacterial-fungal associations were linked to the magnitude and direction of the diversity-MNC relationships. The habitats less governed by neutral processes and dominated by negative bacterial-fungal associations exhibited stronger negative microbial α-diversity-MNC relationships. Our findings suggested that the balance between positive and negative bacterial-fungal associations was connected to the link between soil biodiversity and ecosystem function in complex terrestrial ecosystems. This study elucidates the potential factors influencing diversity-function relationships, thereby enabling future studies to forecast the effects of belowground biodiversity on ecosystem function.IMPORTANCE The relationships between soil biodiversity and ecosystem functions are an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the factors driving the relationships between microbial diversity and potential soil nutrient cycling in complex terrestrial ecosystems. Our structural equation modeling and random forest analysis revealed that the balance between positive and negative bacterial-fungal associations was clearly linked to the strength of the relationships between soil microbial diversity and multiple nutrients cycling across different habitats. This study revealed the potential factors underpinning diversity-function relationships in terrestrial ecosystems and thus helps us to manage soil microbial communities for better provisioning of key ecosystem services.},
}
@article {pmid33755773,
year = {2021},
author = {Gorfer, M and Mayer, M and Berger, H and Rewald, B and Tallian, C and Matthews, B and Sandén, H and Katzensteiner, K and Godbold, DL},
title = {High Fungal Diversity but Low Seasonal Dynamics and Ectomycorrhizal Abundance in a Mountain Beech Forest.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {243-256},
pmid = {33755773},
issn = {1432-184X},
support = {C-Alp I//&#xd6;sterreichischen Akademie der Wissenschaften/ ; C-Alp II//&#xd6;sterreichischen Akademie der Wissenschaften/ ; },
mesh = {*Fagus ; Forests ; Fungi/genetics ; *Mycorrhizae/genetics ; Seasons ; Soil ; Soil Microbiology ; },
abstract = {Forests on steep slopes constitute a significant proportion of European mountain areas and are important as production and protection forests. This study describes the soil fungal community structure in a European beech-dominated mountain forest stands in the Northern Calcareous Alps and investigates how it is determined by season and soil properties. Samples were collected at high spatial resolution in an area of ca. 100 m × 700 m in May (spring) and August (summer). Illumina MiSeq high-throughput sequencing of the ITS2-region revealed distinct patterns for the soil fungal communities. In contrast to other studies from temperate European beech forest stands, Ascomycota dominated the highly diverse fungal community, while ectomycorrhizal fungi were of lower abundance. Russulaceae, which are often among the dominant ectomycorrhizal fungi associated with European beech, were absent from all samples. Potentially plant pathogenic fungi were more prevalent than previously reported. Only subtle seasonal differences were found between fungal communities in spring and summer. Especially, dominant saprotrophic taxa were largely unaffected by season, while slightly stronger effects were observed for ectomycorrhizal fungi. Soil characteristics like pH and organic carbon content, on the other hand, strongly shaped abundant taxa among the saprotrophic fungal community.},
}
@article {pmid33752014,
year = {2021},
author = {Aponte, H and Mondaca, P and Santander, C and Meier, S and Paolini, J and Butler, B and Rojas, C and Diez, MC and Cornejo, P},
title = {Enzyme activities and microbial functional diversity in metal(loid) contaminated soils near to a copper smelter.},
journal = {The Science of the total environment},
volume = {779},
number = {},
pages = {146423},
doi = {10.1016/j.scitotenv.2021.146423},
pmid = {33752014},
issn = {1879-1026},
mesh = {Copper/analysis ; Environmental Monitoring ; Environmental Pollution ; Metals/analysis ; *Metals, Heavy/analysis ; Soil ; *Soil Pollutants/analysis ; },
abstract = {The monitoring of soil metal(loid) contamination is of global significance due to deleterious effects that metal(loid)s have on living organisms. Soil biological properties such as enzyme activities (EAs) are good indicators of metal(loid) contamination due to their high sensitivity, fast response, and low-cost. Here, the effect of metal(loid) contamination on physicochemical properties and microbial functionality in soils sampled from within 10 km of a Cu smelter is investigated. Soil composite samples were randomly taken within 2, 4, 6, 8 and10 km zones from a mining industry Cu smelter. The EAs of dehydrogenase (DHA), arylsulfatase (ARY), β-glucosidase, urease, and arginine ammonification (AA) were studied as indicators of metal(loid) contamination, which included the ecological dose (ED50) with respect to Cu and As contents. The community level physiological profile (CLPP), functional diversity, and catabolic evenness were evaluated based on the C-substrate utilisation. All EAs decreased in zones with high degrees of metal(loid) contamination, which also had low TOC and clay contents, reflecting long term processes of soil degradation. Positive and strong relationships between EAs and TOC were found. DHA and ARY activities decreased by approximately 85-90% in highly metal(loid) contaminated soils. DHA and AA showed significant ED50 values associated with available Cu (112.8 and 121.6 mg CuDTPA kg[-1], respectively) and total As contents (30.8 and 31.8 mg As kg[-1], respectively). The CLPP showed different metabolic profiles along the metal(loid) contamination gradients. Long-term stress conditions in soils close to industrial areas resulted in the decreasing of general biological activity, catabolic capacity, and functional diversity.},
}
@article {pmid33751575,
year = {2021},
author = {Matysik, S and Krautbauer, S and Liebisch, G and Schött, HF and Kjølbaek, L and Astrup, A and Blachier, F and Beaumont, M and Nieuwdorp, M and Hartstra, A and Rampelli, S and Pagotto, U and Iozzo, P},
title = {Short-chain fatty acids and bile acids in human faeces are associated with the intestinal cholesterol conversion status.},
journal = {British journal of pharmacology},
volume = {178},
number = {16},
pages = {3342-3353},
doi = {10.1111/bph.15440},
pmid = {33751575},
issn = {1476-5381},
mesh = {*Bile Acids and Salts ; Cholesterol ; Chromatography, Liquid ; Fatty Acids, Volatile ; Feces ; Humans ; *Tandem Mass Spectrometry ; },
abstract = {BACKGROUND AND PURPOSE: The analysis of human faecal metabolites can provide an insight into metabolic interactions between gut microbiota and the host organism. The creation of metabolic profiles in faeces has received little attention until now, and reference values, especially in the context of dietary and therapeutic interventions, are missing. Exposure to xenobiotics significantly affects the physiology of the microbiome, and microbiota manipulation and short-chain fatty acid administration have been proposed as treatment targets for several diseases. The aim of the present study is to give concomitant concentration ranges of faecal sterol species, bile acids and short-chain fatty acids, based on a large cohort.<br><br>EXPERIMENTAL APPROACH: Sterol species, bile acids and short-chain fatty acids in human faeces from 165 study participants were quantified by LC-MS/MS. For standardization, we refer all values to dry weight of faeces. Based on the individual intestinal sterol conversion, we classified participants into low and high converters according to their coprostanol/cholesterol ratio.<br><br>KEY RESULTS: Low converters excrete more straight-chain fatty acids and bile acids than high converters; 5th and 95th percentile and median of bile acids and short-chain fatty acids were calculated for both groups.<br><br>CONCLUSION AND IMPLICATIONS: We give concentration ranges for 16 faecal metabolites that can serve as reference values. Patient stratification into high or low sterol converter groups is associated with significant differences in faecal metabolites with biological activities. Such stratification should then allow better assessment of faecal metabolites before therapeutic interventions.<br><br>LINKED ARTICLES: This article is part of a themed issue on Oxysterols, Lifelong Health and Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v178.16/issuetoc.},
}
@article {pmid33751165,
year = {2022},
author = {Foley, KM and Beard, KH and Atwood, TB and Waring, BG},
title = {Herbivory changes soil microbial communities and greenhouse gas fluxes in a high-latitude wetland.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {127-136},
pmid = {33751165},
issn = {1432-184X},
support = {ARC-1304523//National Science Foundation/ ; ARCCS-1932889//NSF/ ; },
mesh = {Carbon Dioxide/analysis ; *Greenhouse Gases ; Herbivory ; Methane/analysis ; *Microbiota ; Nitrous Oxide ; Soil/chemistry ; Wetlands ; },
abstract = {Herbivory can have strong impacts on greenhouse gas fluxes in high-latitude ecosystems. For example, in the Yukon-Kuskokwim (Y-K) Delta in western Alaska, migratory goose grazing affects the magnitude of soil carbon dioxide (CO2) and methane (CH4) fluxes. However, the underlying drivers of this relationship are unclear, as few studies systematically tease apart the processes by which herbivores influences soil biogeochemistry. To examine these mechanisms in detail, we conducted a laboratory incubation experiment to quantify changes in greenhouse gas fluxes in response to three parameters altered by herbivores in situ: temperature, soil moisture content, and nutrient inputs. These treatments were applied to soils collected in grazing lawns and nearby ungrazed habitat, allowing us to assess how variation in microbial community structure influenced observed responses. We found pronounced differences in both fungal and prokaryotic community composition between grazed and ungrazed areas. In the laboratory incubation experiment, CO2 and CH4 fluxes increased with temperature, soil moisture, and goose fecal addition, suggesting that grazing-related changes in the soil abiotic environment may enhance soil C losses. Yet, these abiotic drivers were insufficient to explain variation in fluxes between soils with and without prior grazing. Differences in trace gas fluxes between grazed and ungrazed areas may result both from herbivore-induced shifts in abiotic parameters and grazing-related alterations in microbial community structure. Our findings suggest that relationships among herbivores and soil microbial communities could mediate carbon-climate feedbacks in rapidly changing high-latitude ecosystems.},
}
@article {pmid33750865,
year = {2021},
author = {Wang, S and Tang, W and Delage, E and Gifford, S and Whitby, H and González, AG and Eveillard, D and Planquette, H and Cassar, N},
title = {Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {5508},
pmid = {33750865},
issn = {2045-2322},
abstract = {Variation in the microbial cycling of nutrients and carbon in the ocean is an emergent property of complex planktonic communities. While recent findings have considerably expanded our understanding of the diversity and distribution of nitrogen (N2) fixing marine diazotrophs, knowledge gaps remain regarding ecological interactions between diazotrophs and other community members. Using quantitative 16S and 18S V4 rDNA amplicon sequencing, we surveyed eukaryotic and prokaryotic microbial communities from samples collected in August 2016 and 2017 across the Western North Atlantic. Leveraging and significantly expanding an earlier published 2015 molecular dataset, we examined microbial community structure and ecological co-occurrence relationships associated with intense hotspots of N2 fixation previously reported at sites off the Southern New England Shelf and Mid-Atlantic Bight. Overall, we observed a negative relationship between eukaryotic diversity and both N2 fixation and net community production (NCP). Maximum N2 fixation rates occurred at sites with high abundances of mixotrophic stramenopiles, notably Chrysophyceae. Network analysis revealed such stramenopiles to be keystone taxa alongside the haptophyte diazotroph host Braarudosphaera bigelowii and chlorophytes. Our findings highlight an intriguing relationship between marine stramenopiles and high N2 fixation coastal sites.},
}
@article {pmid33745062,
year = {2022},
author = {Glaeser, SP and Silva, LMR and Prieto, R and Silva, MA and Franco, A and Kämpfer, P and Hermosilla, C and Taubert, A and Eisenberg, T},
title = {A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {18-33},
pmid = {33745062},
issn = {1432-184X},
mesh = {Animals ; *Balaenoptera ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sperm Whale/microbiology ; },
abstract = {Large baleen and toothed whales play crucial ecological roles in oceans; nonetheless, very little is known about their intestinal microbiomes. Based on striking differences in natural history and thus in feeding behaviours, it can be expected that intestinal microbiomes of large baleen whales and toothed whales are different. To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea. Faecal samples from free-ranging large whales collected off the Azores Archipelago (Portugal) were used, comprising 13 individual baleen whales (one sei, two blue and ten fin whales) and four sperm whales. The phylogenetic composition of the Bacteria faecal microbiomes of baleen and toothed whales showed no significant differences at the phylum level. However, significant differences were detected at the family and genus levels. Most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes and Spirochaeta. Few highly abundant bacterial genera were identified as key taxa with a high contribution to differences among baleen and toothed whales microbiomes. Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea. This is the first study that directly compares the faecal bacterial and archaeal microbiomes of free-ranging baleen and toothed whales which represent the two parvorders of Cetacea which members are fully aquatic large mammals which were evolutionary split millions of years ago.},
}
@article {pmid33743015,
year = {2022},
author = {Xu, MP and Wang, JY and Zhu, YF and Han, XH and Ren, CJ and Yang, GH},
title = {Plant Biomass and Soil Nutrients Mainly Explain the Variation of Soil Microbial Communities During Secondary Succession on the Loess Plateau.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {114-126},
pmid = {33743015},
issn = {1432-184X},
support = {2020132111//Forest and Grass Technology Innovation Development and Research Project of the State Forestry and Grassland Administration/ ; 2018JZ4002//Key project of Shaanxi Provincial Natural Science Foundation/ ; 2019HBGC-13//Shaanxi Engineering Research Center of Circular Agriculture/ ; },
mesh = {Biomass ; China ; *Microbiota ; Nutrients ; *Soil/chemistry ; Soil Microbiology ; },
abstract = {Soil microorganisms play an important role in the circulation of materials and nutrients between plants and soil ecosystems, but the drivers of microbial community composition and diversity remain uncertain in different vegetation restoration patterns. We studied soil physicochemical properties (i.e., soil moisture, bulk density, pH, soil nutrients, available nutrients), plant characteristics (i.e., Shannon index [HPlant] and Richness index [SPlant], litter biomass [LB], and fine root biomass [FRB]), and microbial variables (biomass, enzyme activity, diversity, and composition of bacterial and fungal communities) in different plant succession patterns (Robinia pseudoacacia [MF], Caragana korshinskii [SF], and grassland [GL]) on the Loess Plateau. The herb communities, soil microbial biomass, and enzyme activities were strongly affected by vegetation restoration, and soil bacterial and fungal communities were significantly different from each other at the sites. Correlation analysis showed that LB and FRB were significantly positively correlated with the Chao index of soil bacteria, soil microbial biomass, enzyme activities, Proteobacteria, Zygomycota, and Cercozoa, while negatively correlated with Actinobacteria and Basidiomycota. In addition, soil water content (SW), pH, and nutrients have important effects on the bacterial and fungal diversities, as well as Acidobacteria, Proteobacteria, Actinobacteria, Nitrospirae, Zygomycota, and microbial biomass. Furthermore, plant characteristics and soil properties modulated the composition and diversity of soil microorganisms, respectively. Overall, the relative contribution of vegetation and soil to the diversity and composition of soil bacterial and fungal communities illustrated that plant characteristics and soil properties may synergistically modulate soil microbial communities, and the composition and diversity of soil bacterial and fungal communities mainly depend on plant biomass and soil nutrients.},
}
@article {pmid33742230,
year = {2022},
author = {Tipton, L and Zahn, GL and Darcy, JL and Amend, AS and Hynson, NA},
title = {Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {48-57},
pmid = {33742230},
issn = {1432-184X},
mesh = {*Ecosystem ; *Fungi/genetics ; Hawaii ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {To study biogeography and other ecological patterns of microorganisms, including fungi, scientists have been using operational taxonomic units (OTUs) as representations of species or species hypotheses. However, when defined by 97% sequence similarity cutoff at an accepted barcode locus such as 16S in bacteria or ITS in fungi, these OTUs can obscure biogeographic patterns, mask taxonomic diversity, and hinder meta-analyses. Amplicon sequence variants (ASVs) have been proposed to alleviate all of these issues and have been shown to do so in bacteria. Analyzing ASVs is just emerging as a common practice among fungal studies, and it is unclear whether the benefits found in bacterial studies of using such an approach carryover to fungi. Here, we conducted a meta-analysis of Hawaiian fungi by analyzing ITS1 amplicon sequencing data as ASVs and exploring ecological patterns. These surveys spanned three island groups and five ecosystems combined into the first comprehensive Hawaiian Mycobiome ASV Database. Our results show that ASVs can be used to combine fungal ITS surveys, increase reproducibility, and maintain the broad ecological patterns observed with OTUs, including diversity orderings. Additionally, the ASVs that comprise some of the most common OTUs in our database reveals some island specialists, indicating that traditional OTU clustering can obscure important biogeographic patterns. We recommend that future fungal studies, especially those aimed at assessing biogeography, analyze ASVs rather than OTUs. We conclude that similar to bacterial studies, ASVs improve reproducibility and data sharing for fungal studies.},
}
@article {pmid33741616,
year = {2021},
author = {Zhu, X and Feng, X and Liang, C and Li, J and Jia, J and Feng, L and Tao, Y and Chen, Y},
title = {Microbial Ecological Mechanism for Long-Term Production of High Concentrations of n-Caproate via Lactate-Driven Chain Elongation.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {11},
pages = {},
pmid = {33741616},
issn = {1098-5336},
mesh = {*Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Bioreactors/*microbiology ; Caproates/*metabolism ; Clostridiales/*physiology ; Fermentation ; Lactic Acid/*chemistry ; *Microbiota ; },
abstract = {Lactate-driven chain elongation (LCE) has emerged as a new biotechnology to upgrade organic waste streams into a valuable biochemical and fuel precursor, medium-chain carboxylate, n-caproate. Considering that a low cost of downstream extraction is critical for biorefinery technology, a high concentration of n-caproate production is very important to improve the scale-up of the LCE process. We report here that in a nonsterile open environment, the n-caproate concentration was increased from the previous record of 25.7 g·liter[-1] to a new high level of 33.7 g·liter[-1] (76.8 g chemical oxygen demand [COD]·liter [-][1]), with the highest production rate being 11.5 g·liter[-1]·day[-1] (26.2 g COD·liter [-][1]·day[-1]). In addition, the LCE process remained stable, with an average concentration of n-caproate production of 20.2 ± 5.62 g·liter[-1] (46.1 ± 12.8 g COD·liter [-][1]) for 780 days. Dynamic changes in taxonomic composition integrated with metagenomic data reveal the microbial ecology for long-term production of high concentrations of n-caproate: (i) the core microbiome is related to efficient functional groups, such as Ruminococcaceae (with functional strain CPB6); (ii) the core bacteria can maintain stability for long-term operation; (iii) the microbial network has relatively low microbe-microbe interaction strength; and (iv) low relative abundance and variety of competitors. The network structure could be shaped by hydraulic retention time (HRT) over time, and long-term operation at an HRT of 8 days displayed higher efficacy.IMPORTANCE Our research revealed the microbial network of the LCE reactor microbiome for n-caproate production at high concentrations, which will provide a foundation for designing or engineering the LCE reactor microbiome to recover n-caproate from organic waste streams in the future. In addition, the hypothetical model of the reactor microbiome that we proposed may offer guidance for researchers to find the underlying microbial mechanism when they encounter low-efficiency n-caproate production from the LCE process. We anticipate that our research will rapidly advance LCE biotechnology with the goal of promoting the sustainable development of human society.},
}
@article {pmid33734553,
year = {2021},
author = {Ruuskanen, MO and Sommeria-Klein, G and Havulinna, AS and Niiranen, TJ and Lahti, L},
title = {Modelling spatial patterns in host-associated microbial communities.},
journal = {Environmental microbiology},
volume = {23},
number = {5},
pages = {2374-2388},
doi = {10.1111/1462-2920.15462},
pmid = {33734553},
issn = {1462-2920},
mesh = {Ecology ; Humans ; *Microbiota ; },
abstract = {Microbial communities exhibit spatial structure at different scales, due to constant interactions with their environment and dispersal limitation. While this spatial structure is often considered in studies focusing on free-living environmental communities, it has received less attention in the context of host-associated microbial communities or microbiota. The wider adoption of methods accounting for spatial variation in these communities will help to address open questions in basic microbial ecology as well as realize the full potential of microbiome-aided medicine. Here, we first overview known factors affecting the composition of microbiota across diverse host types and at different scales, with a focus on the human gut as one of the most actively studied microbiota. We outline a number of topical open questions in the field related to spatial variation and patterns. We then review the existing methodology for the spatial modelling of microbiota. We suggest that methodology from related fields, such as systems biology and macro-organismal ecology, could be adapted to obtain more accurate models of spatial structure. We further posit that methodological developments in the spatial modelling and analysis of microbiota could in turn broadly benefit theoretical and applied ecology and contribute to the development of novel industrial and clinical applications.},
}
@article {pmid33733305,
year = {2022},
author = {da Silva, TH and Câmara, PEAS and Pinto, OHB and Carvalho-Silva, M and Oliveira, FS and Convey, P and Rosa, CA and Rosa, LH},
title = {Diversity of Fungi Present in Permafrost in the South Shetland Islands, Maritime Antarctic.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {58-67},
pmid = {33733305},
issn = {1432-184X},
mesh = {Animals ; Antarctic Regions ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Fungi/genetics ; Humans ; Islands ; *Permafrost ; },
abstract = {We assess the fungal diversity present in permafrost from different islands in the South Shetland Islands archipelago, maritime Antarctic, using next-generation sequencing (NGS). We detected 1,003,637 fungal DNA reads representing, in rank abundance order, the phyla Ascomycota, Mortierellomycota, Basidiomycota, Chytridiomycota, Rozellomycota, Mucoromycota, Calcarisporiellomycota and Zoopagomycota. Ten taxa were dominant these being, in order of abundance, Pseudogymnoascus appendiculatus, Penicillium sp., Pseudogymnoascus roseus, Penicillium herquei, Curvularia lunata, Leotiomycetes sp., Mortierella sp. 1, Mortierella fimbricystis, Fungal sp. 1 and Fungal sp. 2. A further 38 taxa had intermediate abundance and 345 were classified as rare. The total fungal community detected in the permafrost showed high indices of diversity, richness and dominance, although these varied between the sampling locations. The use of a metabarcoding approach revealed the presence of DNA of a complex fungal assemblage in the permafrost of the South Shetland Islands including taxa with a range of ecological functions among which were multiple animal, human and plant pathogenic fungi. Further studies are required to determine whether the taxa identified are present in the form of viable cells or propagules and which might be released from melting permafrost to other Antarctic habitats and potentially dispersed more widely.},
}
@article {pmid33733304,
year = {2022},
author = {Yang, H and Hu, C},
title = {Soil Chemistry and Nutrients Influence the Distribution of Aerobic Anoxygenic Phototrophic Bacteria and Eukaryotic Phototrophic Microorganisms of Physical Soil Crusts at Different Elevations on the Tibetan Plateau.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {100-113},
pmid = {33733304},
issn = {1432-184X},
support = {Grant No. XDA17010502//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. 31900237//National Natural Science Foundation of China/ ; },
mesh = {Bacteria, Aerobic/genetics ; *Eukaryota ; Nutrients ; *Soil/chemistry ; Soil Microbiology ; Tibet ; },
abstract = {Photosynthetic microorganisms are widely distributed in the soil and play an important role in plant-free soil crusts. However, the distribution and environmental drivers of phototrophic microbial communities in physical soil crusts, where the abundance of cyanobacteria is low, are scarcely understood. Here, we performed high-throughput sequencing of pufM and 18S rRNA genes in soil crusts at different elevations on the Tibetan Plateau and used the data combined with environmental variables to analyze the diversity and structure of phototrophic microbial communities. We found that the dominant taxa of aerobic anoxygenic phototrophic bacteria (AAPB) and eukaryotic phototrophic microorganisms (EPM) were shown to shift with elevation. The phototrophic microbial diversity showed a single-peak pattern, with the lowest diversity of AAPB and highest diversity of EPM at middle elevations. Moreover, the elevation and soil property determined the phototrophic microbial community. Soil salts, especially Cl[-], were the most important for AAPB. Likewise, soil nutrients, especially carbon, were the most important for EPM. The relationship between high-abundance taxa and environmental variables showed that Rhizobiales was significantly negatively correlated with salt ions and positively correlated with chlorophyll. Rhodobacterales showed the strongest and significant positive associations with Cl[-]. Chlorophyceae and Bacillariophyceae were positively correlated with CO3[2-]. These results indicated that salinity and soil nutrients affected the diversity and structure of microbial communities. This study contributes to our understanding of the diversity, composition, and structure of photosynthetic microorganisms in physical soil crusts and helps in developing new approaches for controlling desertification and salinization and improving the desert ecological environment.},
}
@article {pmid33730193,
year = {2022},
author = {Vignale, FA and Lencina, AI and Stepanenko, TM and Soria, MN and Saona, LA and Kurth, D and Guzmán, D and Foster, JS and Poiré, DG and Villafañe, PG and Albarracín, VH and Contreras, M and Farías, ME},
title = {Lithifying and Non-Lithifying Microbial Ecosystems in the Wetlands and Salt Flats of the Central Andes.},
journal = {Microbial ecology},
volume = {83},
number = {1},
pages = {1-17},
pmid = {33730193},
issn = {1432-184X},
support = {PICT 2013/0730 and PICT V 2015/3825//CONICET-FONCyT/ ; },
mesh = {Geologic Sediments/chemistry ; Lakes/chemistry ; *Microbiota ; Salinity ; *Wetlands ; },
abstract = {The wetlands and salt flats of the Central Andes region are unique extreme environments as they are located in high-altitude saline deserts, largely influenced by volcanic activity. Environmental factors, such as ultraviolet (UV) radiation, arsenic content, high salinity, low dissolved oxygen content, extreme daily temperature fluctuation, and oligotrophic conditions, resemble the early Earth and potentially extraterrestrial conditions. The discovery of modern microbialites and microbial mats in the Central Andes during the past decade has increased the interest in this area as an early Earth analog. In this work, we review the current state of knowledge of Central Andes region environments found within lakes, small ponds or puquios, and salt flats of Argentina, Chile, and Bolivia, many of them harboring a diverse range of microbial communities that we have termed Andean Microbial Ecosystems (AMEs). We have integrated the data recovered from all the known AMEs and compared their biogeochemistry and microbial diversity to achieve a better understanding of them and, consequently, facilitate their protection.},
}
@article {pmid33727400,
year = {2021},
author = {Mujakić, I and Andrei, A&#x15e; and Shabarova, T and Fecskeová, LK and Salcher, MM and Piwosz, K and Ghai, R and Koblížek, M},
title = {Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes.},
journal = {mSystems},
volume = {6},
number = {2},
pages = {},
pmid = {33727400},
issn = {2379-5077},
abstract = {Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes' epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments.IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.},
}
@article {pmid33727399,
year = {2021},
author = {Cantrell, K and Fedarko, MW and Rahman, G and McDonald, D and Yang, Y and Zaw, T and Gonzalez, A and Janssen, S and Estaki, M and Haiminen, N and Beck, KL and Zhu, Q and Sayyari, E and Morton, JT and Armstrong, G and Tripathi, A and Gauglitz, JM and Marotz, C and Matteson, NL and Martino, C and Sanders, JG and Carrieri, AP and Song, SJ and Swafford, AD and Dorrestein, PC and Andersen, KG and Parida, L and Kim, HC and Vázquez-Baeza, Y and Knight, R},
title = {EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets.},
journal = {mSystems},
volume = {6},
number = {2},
pages = {},
pmid = {33727399},
issn = {2379-5077},
support = {U19 AG063744/AG/NIA NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; },
abstract = {Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality-including ordination integration and animations-alongside many standard tree visualization features and thus simplifies exploratory analyses of many forms of 'omic data.IMPORTANCE Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research. The ever-growing scale of modern microbiome surveys has led to numerous challenges in visualizing these data. In this paper we used five diverse data sets to showcase the versatility and scalability of EMPress, an interactive web visualization tool. EMPress addresses the growing need for exploratory analysis tools that can accommodate large, complex multi-omic data sets.},
}
@article {pmid33727395,
year = {2021},
author = {Sun, M and Zhan, Y and Marsan, D and Páez-Espino, D and Cai, L and Chen, F},
title = {Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale.},
journal = {mSystems},
volume = {6},
number = {2},
pages = {},
pmid = {33727395},
issn = {2379-5077},
abstract = {Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii ("Iraqibacter") was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment.IMPORTANCE This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples. Our results indicate that there exists a large pool of abundant and diverse viruses in estuaries that have not yet been cultivated, their genomes only available thanks to single-cell genomics or single-molecule sequencing, demonstrating the importance of these methods for viral discovery. The spatiotemporal pattern of these abundant uncultivated viruses is more variable than that of cultured viruses. Despite strong environmental gradients, season and location had surprisingly little impact on the viral community within an estuary, but we saw a significant distinction between the two estuaries and also between estuarine and open ocean viromes.},
}
@article {pmid33725151,
year = {2021},
author = {Menéndez-Serra, M and Triadó-Margarit, X and Casamayor, EO},
title = {Ecological and Metabolic Thresholds in the Bacterial, Protist, and Fungal Microbiome of Ephemeral Saline Lakes (Monegros Desert, Spain).},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {885-896},
pmid = {33725151},
issn = {1432-184X},
support = {BRIDGES CGL2015-69043-P and INTERACTOMA RTI2018-101205-B-I00//Agencia Estatal de Investigaci&#xf3;n/ ; FPI PhD scholarships program (BRIDGES-MINECO)//Agencia Estatal de Investigaci&#xf3;n/ ; BRIDGES CGL2015-69043-P and INTERACTOMA RTI2018-101205-B-I00//FEDER/ ; },
mesh = {Eukaryota ; *Lakes ; *Mycobiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Spain ; },
abstract = {We studied the 16S and 18S rRNA genes of the bacterial, protist, and fungal microbiomes of 131 samples collected in 14 ephemeral small inland lakes located in the endorheic area of the Monegros Desert (NE Spain). The sampling covered different temporal flooding/desiccation cycles that created natural salinity gradients between 0.1% (w/v) and salt saturation. We aimed to test the hypothesis of a lack of competitive advantage for microorganisms using the "salt-in" strategy in highly fluctuating hypersaline environments where temperature and salinity transitions widely vary within short time periods, as in ephemeral inland lakes. Overall, 5653 bacterial zOTUs and 2658 eukaryal zOTUs were detected heterogeneously distributed with significant variations on taxonomy and general energy-yielding metabolisms and trophic strategies along the gradient. We observed a more diverse bacterial assembly than initially expected at extreme salinities and a lack of dominance of a few "salt-in" organisms. Microbial thresholds were unveiled for these highly fluctuating hypersaline environments with high selective pressures. We conclude that the extremely high dynamism observed in the ephemeral lakes of Monegros may have given a competitive advantage for more versatile ("salt-out") organisms compared to those better adapted to stable high salinities usually more common in solar salterns. Ephemeral inland saline lakes offered a well-suited natural framework for highly detailed evolutionary and ecological studies.},
}
@article {pmid33723621,
year = {2021},
author = {Chen, X and Krug, L and Yang, M and Berg, G and Cernava, T},
title = {The Himalayan Onion (Allium wallichii Kunth) Harbors Unique Spatially Organized Bacterial Communities.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {909-918},
pmid = {33723621},
issn = {1432-184X},
support = {31701836//National Natural Science Foundation of China/ ; 31960555//National Natural Science Foundation of China/ ; 32050410297//National Natural Science Foundation of China/ ; 2018-1050//Guizhou Science and Technology Department/ ; SQ2020YFE010090//National Key Research and Development Program of China/ ; D20023//Program for Introducing Talents to Chinese Universities (111 Program)/ ; },
mesh = {*Allium ; *Microbiota ; Onions ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil Microbiology ; },
abstract = {Plant-associated microorganisms are known to contribute with various beneficial functions to the health and productivity of their hosts, yet the microbiome of most plants remains unexplored. This especially applies to wild relatives of cultivated plants, which might harbor beneficial microorganisms that were lost during intensive breeding. We studied bacterial communities of the Himalayan onion (Allium wallichii Kunth), a wild relative of onion native to mountains in East Asia. The bacterial community structure was assessed in different plant microhabitats (rhizosphere, endosphere, anthosphere) by sequencing of 16S rRNA gene fragment amplicons. Targeted bioinformatic analyses were implemented in order to identify unique features in each habitat and to map the overall community in the first representative of the Amaryllidaceae plant family. The highest bacterial diversity was found for bulk soil (Shannon index, H' 9.3) at the high-altitude sampling location. It was followed by the plant rhizosphere (H' 8.9) while communities colonizing flowers (H' 6.1) and the endosphere (H' 6.5 and 5.6) where less diverse. Interestingly, we observed a non-significant rhizosphere effect. Another specificity of the microbiome was its high evenness in taxonomic distribution, which was so far not observed in plant microbiomes. Pseudomonas was identified among additional 10 bacterial genera as a plant-specific signature. The first insights into the microbiome of a plant in the widespread Allium genus will facilitate upcoming comparisons with its domesticated relatives while additionally providing a detailed microbiome mapping of the plant's microhabitats to facilitate bioresource mining.},
}
@article {pmid33723620,
year = {2021},
author = {Sidrim, JJC and de Maria, GL and Paiva, MAN and Araújo, GDS and da Graça-Filho, RV and de Oliveira, JS and Sales, JA and Pereira-Neto, WA and Guedes, GMM and Castelo-Branco, DSCM and Cordeiro, RA and Brilhante, RSN and Rocha, MFG},
title = {Azole-Resilient Biofilms and Non-wild Type C. albicans Among Candida Species Isolated from Agricultural Soils Cultivated with Azole Fungicides: an Environmental Issue?.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {1080-1083},
pmid = {33723620},
issn = {1432-184X},
support = {Grant 428737/2018-8//CNPQ/ ; },
mesh = {Antifungal Agents/pharmacology ; Azoles/pharmacology ; Biofilms ; *Candida/genetics ; Candida albicans ; *Fungicides, Industrial/pharmacology ; Microbial Sensitivity Tests ; Soil ; },
abstract = {This study aimed to identify Candida spp. from agricultural soils cultivated with azole fungicides and investigate their susceptibility to clinical (fluconazole, itraconazole, voriconazole, and amphotericin B) and agricultural (tetraconazole and tebuconazole) antifungals in planktonic form. Additionally, Candida biofilm-forming ability and biofilm susceptibility to agricultural antifungals and voriconazole were analyzed. Species identification was performed by phenotypic and molecular assays. The susceptibility of planktonic cells was evaluated by the broth microdilution method. The biofilm metabolic activity was evaluated by the XTT reduction assay. The recovered Candida spp. were identified as C. parapsilosis sensu stricto (n = 14), C. albicans (n = 5), C. tropicalis (n = 2), C. fermentati (n = 1), and C. metapsilosis (n = 2). Minimum inhibitory concentration ranges for clinical and agricultural antifungals were ≤ 0.03-4 μg/mL and 1-128 μg/mL, respectively. Two and one C. albicans strains were considered non-wild type for voriconazole and fluconazole, respectively. All strains were biofilm producers. The minimum biofilm inhibitory concentration ranges for tetraconazole and tebuconazole were 128-> 1024 μg/mL, while for voriconazole was 512-> 1024 μg/mL. In summary, this study shows that non-wild type and azole-resilient biofilm-producing Candida species colonize agricultural soils cultivated with azole fungicides.},
}
@article {pmid33723574,
year = {2021},
author = {Castilleux, R and Plancot, B and Vicré, M and Nguema-Ona, E and Driouich, A},
title = {Extensin, an underestimated key component of cell wall defence?.},
journal = {Annals of botany},
volume = {127},
number = {6},
pages = {709-713},
pmid = {33723574},
issn = {1095-8290},
mesh = {*Arabidopsis/genetics ; *Cell Wall ; Peroxidases ; Plant Proteins ; },
abstract = {BACKGROUND: Extensins are plant cell wall hydroxyproline-rich glycoproteins known to be involved in cell wall reinforcement in higher plants, and in defence against pathogen attacks. The ability of extensins to form intra- and intermolecular cross-links is directly related to their role in cell wall reinforcement. Formation of such cross-links requires appropriate glycosylation and structural conformation of the glycoprotein.<br><br>SCOPE: Although the role of cell wall components in plant defence has drawn increasing interest over recent years, relatively little focus has been dedicated to extensins. Nevertheless, new insights were recently provided regarding the structure and the role of extensins and their glycosylation in plant-microbe interactions, stimulating an interesting debate from fellow cell wall community experts. We have previously revealed a distinct distribution of extensin epitopes in Arabidopsis thaliana wild-type roots and in mutants impaired in extensin arabinosylation, in response to elicitation with flagellin 22. That study was recently debated in a Commentary by Tan and Mort (Tan L, Mort A. 2020. Extensins at the front line of plant defence. A commentary on: 'Extensin arabinosylation is involved in root response to elicitors and limits oomycete colonization'. Annals of Botany 125: vii-viii) and several points regarding our results were discussed. As a response, we herein clarify the points raised by Tan and Mort, and update the possible epitope structure recognized by the anti-extensin monoclonal antibodies. We also provide additional data showing differential distribution of LM1 extensin epitopes in roots between a mutant defective in PEROXIDASES 33 and 34 and the wild type, similarly to previous observations from the rra2 mutant defective in extensin arabinosylation. We propose these two peroxidases as potential candidates to specifically catalyse the cross-linking of extensins within the cell wall.<br><br>CONCLUSIONS: Extensins play a major role within the cell wall to ensure root protection. The cross-linking of extensins, which requires correct glycosylation and specific peroxidases, is most likely to result in modulation of cell wall architecture that allows enhanced protection of root cells against invading pathogens. Study of the relationship between extensin glycosylation and their cross-linking is a very promising approach to further understand how the cell wall influences root immunity.},
}
@article {pmid33720954,
year = {2021},
author = {Paul, B and Sierra, MA and Xu, F and Crystal, YO and Li, X and Saxena, D and Ruff, RR},
title = {Microbial population shift and metabolic characterization of silver diamine fluoride treatment failure on dental caries.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0242396},
pmid = {33720954},
issn = {1932-6203},
support = {R56 DE028933/DE/NIDCR NIH HHS/United States ; },
mesh = {Carnobacteriaceae/genetics/isolation &amp; purification ; Child ; Cross-Sectional Studies ; DNA, Bacterial/chemistry/metabolism ; Dental Caries/*drug therapy/pathology ; Dental Plaque/microbiology ; Discriminant Analysis ; Fluorides, Topical/therapeutic use ; Humans ; Leptotrichia/genetics/isolation &amp; purification ; *Microbiota ; Pilot Projects ; Principal Component Analysis ; Quaternary Ammonium Compounds/*therapeutic use ; Saliva/microbiology ; Sequence Analysis, DNA ; Silver Compounds/*therapeutic use ; Treatment Failure ; },
abstract = {The objective of this pilot study was to describe the microbial profiles present in the plaque and saliva of children who continued to develop new carious lesions following treatment with silver diamine fluoride ("nonresponders") compared to caries active, caries-free, and children immediately receiving SDF treatment for untreated caries in order to identify potential microbial differences that may relate to a re-incidence of caries. Saliva and plaque samples from infected and contralateral sites were obtained from twenty children who were either caries free, had active carious lesions, were caries active and received SDF treatment immediately before sampling, or had previously received SDF treatment and developed new caries. In total, 8,057,899 Illumina-generated sequence reads from 60 samples were obtained. Reads were processed using the Quantitative Insights Into Microbial Ecology pipeline. Group differences were assessed using Analysis of Variance Models and Tukey Honest Significant Differences. To identify significant taxa between treatment groups, Linear discriminant analysis Effect Size (LefSe) and Analysis of Differential Abundance Taking Sample Variation Into Account were used. Differential abundant analysis indicated that members of the Lachnospiraceae family were significantly enriched in non-responders and the genus Tannerella and species Granulicatella adiances were also highly abundant in this group. LefSe analysis between non-responders and SDF-treated groups revealed that genera Leptotrichia and Granulicatella were enriched in non-responders. We observed the highest abundance of phosphotransferase system and lowest abundance of lipopolysaccharide synthesis in non-responders. The microbiome in dental biofilms is responsible for initiation and progression of dental caries. SDF has been shown to be effective in arresting the progression carious lesions, in part due to its antimicrobial properties. Findings suggest that the differential abundance of select microbiota and specific pathway functioning in individuals that present with recurrent decay after SDF treatment may contribute to a potential failure of silver diamine fluoride to arrest dental caries. However, the short duration of sample collection following SDF application and the small sample size emphasize the need for further data and additional analysis.},
}
@article {pmid33719323,
year = {2021},
author = {Wang, L and Yin, Y and Jing, X and Wang, M and Zhao, M and Yu, J and Qiu, Z and Li, YF},
title = {Profiling of MicroRNAs Involved in Mepiquat Chloride-Mediated Inhibition of Internode Elongation in Cotton (Gossypium hirsutum L.) Seedlings.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {643213},
pmid = {33719323},
issn = {1664-462X},
abstract = {Mepiquat chloride (MC) is the most important plant growth retardant that is widely used in cotton (Gossypium hirsutum L.) production to suppress excessive vegetative growth and improve plant architecture. MicroRNAs (miRNAs) are important gene expression regulators that control plant growth and development. However, miRNA-mediated post-transcriptional regulation in MC-induced growth inhibition remains unclear. In this study, the dynamic expression profiles of miRNAs responsive to MC in cotton internodes were investigated. A total of 508 known miRNAs belonging to 197 families and five novel miRNAs were identified. Among them, 104 miRNAs were differentially expressed at 48, 72, or 96 h post MC treatment compared with the control (0 h); majority of them were highly conserved miRNAs. The number of differentially expressed miRNAs increased with time after treatment. The expression of 14 known miRNAs was continuously suppressed, whereas 12 known miRNAs and one novel miRNA were continuously induced by MC. The expression patterns of the nine differentially expressed miRNAs were verified using qRT-PCR. The targets of the known and novel miRNAs were predicted. Four conserved and six novel targets were validated using the RLM-5' RACE assay. This study revealed that miRNAs play crucial regulatory roles in the MC-induced inhibition of internode elongation. It can improve our understanding of post-transcriptional gene regulation in MC-mediated growth inhibition and could potentially facilitate the breeding of dwarf cotton.},
}
@article {pmid33719058,
year = {2021},
author = {Esquivel-Hernández, DA and García-Pérez, JS and Xu, X and Metha, S and Maldonado, J and Xia, S and Zhao, HP and Rittmann, BE and Ontiveros-Valencia, A},
title = {Microbial ecology in selenate-reducing biofilm communities: Rare biosphere and their interactions with abundant phylotypes.},
journal = {Biotechnology and bioengineering},
volume = {118},
number = {7},
pages = {2460-2471},
doi = {10.1002/bit.27754},
pmid = {33719058},
issn = {1097-0290},
mesh = {*Bacteria/classification/growth &amp; development ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; *Bioreactors ; Microbial Consortia/*physiology ; *Phylogeny ; Selenic Acid/*metabolism ; },
abstract = {Selenate (SeO4[2-]) reduction in hydrogen (H2)-fed membrane biofilm reactors (H2 -MBfRs) was studied in combinations with other common electron acceptors. We employed H2 -MBfRs with two distinctly different conditions: R1, with ample electron-donor availability and acceptors SeO4[2-] and sulfate (SO4[2-]), and R2, with electron-donor limitation and the presence of electron acceptors SeO4[2-] , nitrate (NO3[-]), and SO4[2-] . Even though H2 was available to reduce all input SeO4[2-] and SO4[2-] in R1, SeO4[2-] reduction was preferred over SO4[2-] reduction. In R2, co-reduction of NO3[-] and SeO4[2-] occurred, and SO4[2-] reduction was mostly suppressed. Biofilms in all MBfRs had high microbial diversity that was influenced by the "rare biosphere" (RB), phylotypes with relative abundance less than 1%. While all MBfR biofilms had abundant members, such as Dechloromonas and Methyloversatilis, the bacterial communities were significantly different between R1 and R2. For R1, abundant genera were Methyloversatilis, Melioribacter, and Propionivibrio; for R2, abundant genera were Dechloromonas, Hydrogenophaga, Cystobacter, Methyloversatilis, and Thauera. Although changes in electron-acceptor or -donor loading altered the phylogenetic structure of the microbial communities, the biofilm communities were resilient in terms of SeO4[2-] and NO3[-] reductions, because interacting members of the RB had the capacity of respiring these electron acceptors.},
}
@article {pmid33717676,
year = {2021},
author = {Messer, LF and Brown, MV and Van Ruth, PD and Doubell, M and Seymour, JR},
title = {Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10809},
pmid = {33717676},
issn = {2167-8359},
abstract = {Biological dinitrogen (N2) fixation is one mechanism by which specific microorganisms (diazotrophs) can ameliorate nitrogen (N) limitation. Historically, rates of N2 fixation were believed to be limited outside of the low nutrient tropical and subtropical open ocean; however, emerging evidence suggests that N2 fixation is also a significant process within temperate coastal waters. Using a combination of amplicon sequencing, targeting the nitrogenase reductase gene (nifH), quantitative nifH PCR, and [15]N2 stable isotope tracer experiments, we investigated spatial patterns of diazotroph assemblage structure and N2 fixation rates within the temperate coastal waters of southern Australia during Austral autumn and summer. Relative to previous studies in open ocean environments, including tropical northern Australia, and tropical and temperate estuaries, our results indicate that high rates of N2 fixation (10-64 nmol L[-1] d[-1]) can occur within the large inverse estuary Spencer Gulf, while comparatively low rates of N2 fixation (2 nmol L[-1] d[-1]) were observed in the adjacent continental shelf waters. Across the dataset, low concentrations of NO3/NO2 were significantly correlated with the highest N2 fixation rates, suggesting that N2 fixation could be an important source of new N in the region as dissolved inorganic N concentrations are typically limiting. Overall, the underlying diazotrophic community was dominated by nifH sequences from Cluster 1 unicellular cyanobacteria of the UCYN-A clade, as well as non-cyanobacterial diazotrophs related to Pseudomonas stutzeri, and Cluster 3 sulfate-reducing deltaproteobacteria. Diazotroph community composition was significantly influenced by salinity and SiO4 concentrations, reflecting the transition from UCYN-A-dominated assemblages in the continental shelf waters, to Cluster 3-dominated assemblages in the hypersaline waters of the inverse estuary. Diverse, transitional diazotrophic communities, comprised of a mixture of UCYN-A and putative heterotrophic bacteria, were observed at the mouth and southern edge of Spencer Gulf, where the highest N2 fixation rates were observed. In contrast to observations in other environments, no seasonal patterns in N2 fixation rates and diazotroph community structure were apparent. Collectively, our findings are consistent with the emerging view that N2 fixation within temperate coastal waters is a previously overlooked dynamic and potentially important component of the marine N cycle.},
}
@article {pmid33710327,
year = {2021},
author = {Wang, X and Chen, S and Ma, X and Yssel, AEJ and Chaluvadi, SR and Johnson, MS and Gangashetty, P and Hamidou, F and Sanogo, MD and Zwaenepoel, A and Wallace, J and Van de Peer, Y and Bennetzen, JL and Van Deynze, A},
title = {Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis).},
journal = {GigaScience},
volume = {10},
number = {3},
pages = {},
pmid = {33710327},
issn = {2047-217X},
mesh = {*Digitaria/genetics ; Genetic Variation ; Genome, Plant ; Humans ; *Plant Breeding ; Plant Preparations ; },
abstract = {BACKGROUND: Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry, and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered, however, by a low degree of plant breeding and improvement.<br><br>FINDINGS: We sequenced the fonio genome with long-read SMRT-cell technology, yielding a &#x223c;761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a high level of completion, with a BUSCO score of >99%. The fonio genome was found to be a tetraploid, with most of the genome retained as homoeologous duplications that differ overall by &#x223c;4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence &#x223c;3.1 million years ago. The repeat content (>49%) is fairly standard for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (&#x223c;6.7) was found to be exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant height, and grain size. Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains.<br><br>CONCLUSIONS: We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.},
}
@article {pmid33709229,
year = {2021},
author = {Yang, ZW and Men, Y and Zhang, J and Liu, ZH and Luo, JY and Wang, YH and Li, WJ and Xie, Q},
title = {Evaluation of Sample Preservation Approaches for Better Insect Microbiome Research According to Next-Generation and Third-Generation Sequencing.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {971-980},
pmid = {33709229},
issn = {1432-184X},
support = {31222051, 31772425//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Biodiversity ; High-Throughput Nucleotide Sequencing ; Insecta ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The microbial communities associated with insects play critical roles in many physiological functions such as digestion, nutrition, and defense. Meanwhile, with the development of sequencing technology, more and more studies begin to focus on broader biodiversity of insects and the corresponding mechanisms of insect microbial symbiosis, which need longer time collecting in the field. However, few studies have evaluated the effect of insect microbiome sample preservation approaches especially in different time durations or have assessed whether these approaches are appropriate for both next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies. Here, we used Tessaratoma papillosa (Hemiptera: Tessaratomidae), an important litchi pest, as the model insect and adopted two sequencing technologies to evaluate the effect of four different preservation approaches (cetyltrimethylammonium bromide (CTAB), ethanol, air dried, and RNAlater). We found the samples treated by air dried method, which entomologists adopted for morphological observation and classical taxonomy, would get worse soon. RNAlater as the most expensive approaches for insect microbiome sample preservation did not suit for field works longer than 1 month. We recommended CTAB and ethanol as better preservatives in longer time field work for their effectiveness and low cost. Comparing with the full-length 16S rRNA gene sequenced by TGS, the V4 region of 16S rRNA gene sequenced by NGS has a lower resolution trait and may misestimate the composition of microbial communities. Our results provided recommendations for suitable preservation approaches applied to insect microbiome studies based on two sequencing technologies, which can help researchers properly preserve samples in field works.},
}
@article {pmid33706038,
year = {2021},
author = {Hooban, B and Fitzhenry, K and Cahill, N and Joyce, A and O' Connor, L and Bray, JE and Brisse, S and Passet, V and Abbas Syed, R and Cormican, M and Morris, D},
title = {A Point Prevalence Survey of Antibiotic Resistance in the Irish Environment, 2018-2019.},
journal = {Environment international},
volume = {152},
number = {},
pages = {106466},
doi = {10.1016/j.envint.2021.106466},
pmid = {33706038},
issn = {1873-6750},
mesh = {Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Ireland ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Prevalence ; *beta-Lactamases/genetics ; },
abstract = {Water bodies worldwide have proven to be vast reservoirs of clinically significant antibiotic resistant organisms. Contamination of waters by anthropogenic discharges is a significant contributor to the widespread dissemination of antibiotic resistance. The aim of this research was to investigate multiple different anthropogenic sources on a national scale for the role they play in the environmental propagation of antibiotic resistance. A total of 39 water and 25 sewage samples were collected across four local authority areas in the West, East and South of Ireland. In total, 211 Enterobacterales were isolated (139 water, 72 sewage) and characterised. A subset of isolates (n=60) were chosen for whole genome sequencing. Direct comparisons of the water versus sewage isolate collections revealed a higher percentage of sewage isolates displayed resistance to cefoxitin (46%) and ertapenem (32%), while a higher percentage of water isolates displayed resistance to tetracycline (55%) and ciprofloxacin (71%). Half of all isolates displayed extended spectrum beta-lactamase (ESBL) production phenotypically (n = 105/211; 50%), with blaCTX-M detected in 99/105 isolates by PCR. Carbapenemase genes were identified in 11 isolates (6 sewage, 5 water). The most common variant was blaOXA-48 (n=6), followed by blaNDM-5 (n=2) and blaKPC-2 (n=2). Whole genome sequencing analysis revealed numerous different sequence types in circulation in both waters and sewage including E. coli ST131 (n=15), ST38 (n=8), ST10 (n=4) along with Klebsiella ST405 (n=3) and ST11 (n=2). Core genome MLST (cgMLST) comparisons uncovered three highly similar Klebsiella isolates originating from hospital sewage and two nearby waters. The Klebsiella isolates from an estuary and seawater displayed 99.1% and 98.8% cgMLST identity to the hospital sewage isolate respectively. In addition, three pairs of E. coli isolates from different waters also revealed cgMLST similarities, indicating widespread dissemination and persistence of certain strains in the aquatic environment. These findings highlight the need for routine monitoring of water bodies used for recreational and drinking purposes for the presence of multi-drug resistant organisms.},
}
@article {pmid33705567,
year = {2021},
author = {Hicks, LC and Lajtha, K and Rousk, J},
title = {Nutrient limitation may induce microbial mining for resources from persistent soil organic matter.},
journal = {Ecology},
volume = {102},
number = {6},
pages = {e03328},
doi = {10.1002/ecy.3328},
pmid = {33705567},
issn = {1939-9170},
support = {2020-03858//Vetenskapsr&#xe5;det/ ; 2020-04083//Vetenskapsr&#xe5;det/ ; KAW 1017.0171//The Knut and Alice Wallenberg Foundation/ ; 2018-01315//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {Ecosystem ; Fungi ; Nutrients ; *Soil ; *Soil Microbiology ; },
abstract = {Fungi and bacteria are the two principal microbial groups in soil, responsible for the breakdown of organic matter (OM). The relative contribution of fungi and bacteria to decomposition is thought to impact biogeochemical cycling at the ecosystem scale, whereby bacterially dominated decomposition supports the fast turnover of easily available substrates, whereas fungal-dominated decomposition leads to the slower turnover of more complex OM. However, empirical support for this is lacking. We used soils from a detritus input and removal treatment experiment in an old-growth coniferous forest, where above- and belowground litter inputs have been manipulated for 20 yr. These manipulations have generated variation in OM quality, as defined by energetic content and proxied as respiration per g soil organic matter (SOM) and the δ[13] C signature in respired CO2 and microbial PLFAs. Respiration per g SOM reflects the availability and lability of C substrate to microorganisms, and the δ[13] C signature indicates whether the C used by microorganisms is plant derived and higher quality (more δ[13] C depleted) or more microbially processed and lower quality (more δ[13] C enriched). Surprisingly, higher quality C did not disproportionately benefit bacterial decomposers. Both fungal and bacterial growth increased with C quality, with no systematic change in the fungal-to-bacterial growth ratio, reflecting the relative contribution of fungi and bacteria to decomposition. There was also no difference in the quality of C targeted by bacterial and fungal decomposers either for catabolism or anabolism. Interestingly, respired CO2 was more δ[13] C enriched than soil C, suggesting preferential use of more microbially processed C, despite its lower quality. Gross N mineralization and consumption were also unaffected by differences in the ratio of fungal-to-bacterial growth. However, the ratio of C to gross N mineralization was lower than the average C/N of SOM, meaning that microorganisms specifically targeted N-rich components of OM, indicative of selective microbial N-mining. Consistent with the δ[13] C data, this reinforces evidence for the use of more microbially processed OM with a lower C/N ratio, rather than plant-derived OM. These results challenge the widely held assumption that microorganisms favor high-quality C sources and suggest that there is a trade-off in OM use that may be related to the growth-limiting factor for microorganisms in the ecosystem.},
}
@article {pmid33704553,
year = {2021},
author = {Sochard, C and Dupont, C and Simon, JC and Outreman, Y},
title = {Secondary Symbionts Affect Foraging Capacities of Plant-Specialized Genotypes of the Pea Aphid.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {1009-1019},
pmid = {33704553},
issn = {1432-184X},
support = {ANR Hmicmac 16-CE02-0014//ANR/ ; },
mesh = {Animals ; *Aphids ; Genotype ; Pisum sativum ; Phenotype ; Symbiosis ; },
abstract = {Ecological specialization is widespread in animals, especially in phytophagous insects, which have often a limited range of host plant species. This host plant specialization results from divergent selection on insect populations, which differ consequently in traits like behaviors involved in plant use. Although recent studies highlighted the influence of symbionts on dietary breadth of their insect hosts, whether these microbial partners influence the foraging capacities of plant-specialized insects has received little attention. In this study, we used the pea aphid Acyrthosiphon pisum, which presents distinct plant-specialized lineages and several secondary bacterial symbionts, to examine the possible effects of symbionts on the different foraging steps from plant searching to host plant selection. In particular, we tested the effect of secondary symbionts on the aphid capacity (1) to explore habitat at long distance (estimated through the production of winged offspring), (2) to explore habitat at short distance, and (3) to select its host plant. We found that secondary symbionts had a variable influence on the production of winged offspring in some genotypes, with potential consequences on dispersal and survival. By contrast, symbionts influenced both short-distance exploration and host plant selection only marginally. The implication of symbionts' influence on insect foraging capacities is discussed.},
}
@article {pmid33690989,
year = {2021},
author = {Wade, WG},
title = {Resilience of the oral microbiome.},
journal = {Periodontology 2000},
volume = {86},
number = {1},
pages = {113-122},
doi = {10.1111/prd.12365},
pmid = {33690989},
issn = {1600-0757},
support = {R37 DE016937/DE/NIDCR NIH HHS/United States ; },
mesh = {*Dental Caries/prevention &amp; control ; Humans ; *Microbiota ; Mouth ; *Mouth Diseases ; Saliva ; },
abstract = {The human mouth harbors a complex microbiota, the composition of which is potentially influenced by a wide range of factors, including the intake of food and drink, the availability of endogenous nutrients, the host immune system, drug treatments, and systemic diseases. Despite these possible influences, the oral microbiota is remarkably resilient, particularly in comparison with the microbiota of the large intestine. Diet, with the exception of excessive and/or frequent consumption of fermentable carbohydrate or supplementation with nitrate, has minimal impact on the composition of the oral bacterial community. The common oral diseases dental caries and the periodontal diseases is associated with modification of the oral microbiota primarily as a result of the ecological changes induced by excessive acid production and inflammation, respectively. Systemically-administered antimicrobials have only a small effect on the composition of the oral bacterial community, and while locally delivered antimicrobials can have some clinical benefits, the biofilm lifestyle of oral bacteria lends them substantial resistance to the agents used. Saliva plays an important role in oral microbial ecology, by supplying nutrients and providing protection against colonization by nonoral organisms. Dry mouth is one condition that has a major effect on the microbiota, resulting in increased colonization by opportunistic pathogens. Some systemic diseases do affect the oral microbiome, notably diabetes, in which raised levels of glucose in saliva and tissue impact on bacterial nutrition.},
}
@article {pmid33688007,
year = {2021},
author = {Huang, S and He, T and Yue, F and Xu, X and Wang, L and Zhu, P and Teng, F and Sun, Z and Liu, X and Jing, G and Su, X and Jin, L and Liu, J and Xu, J},
title = {Longitudinal Multi-omics and Microbiome Meta-analysis Identify an Asymptomatic Gingival State That Links Gingivitis, Periodontitis, and Aging.},
journal = {mBio},
volume = {12},
number = {2},
pages = {},
pmid = {33688007},
issn = {2150-7511},
mesh = {*Aging ; Cohort Studies ; Cytokines/*analysis/immunology ; Dysbiosis ; Genomics ; Gingiva/*microbiology/pathology ; Gingivitis/*microbiology ; Humans ; Longitudinal Studies ; Metabolomics ; *Metagenome ; *Microbiota ; Periodontitis/*microbiology ; Proteomics ; Saliva/immunology ; },
abstract = {Most adults experience episodes of gingivitis, which can progress to the irreversible, chronic state of periodontitis, yet roles of plaque in gingivitis onset and progression to periodontitis remain elusive. Here, we longitudinally profiled the plaque metagenome, the plaque metabolome, and salivary cytokines in 40 adults who transited from naturally occurring gingivitis (NG) to healthy gingivae (baseline) and then to experimental gingivitis (EG). During EG, rapid and consistent alterations in plaque microbiota, metabolites, and salivary cytokines emerged as early as 24 to 72 h after oral-hygiene pause, defining an asymptomatic suboptimal health (SoH) stage of the gingivae. SoH features a swift, full activation of 11 salivary cytokines but a steep synergetic decrease of plaque-derived betaine and Rothia spp., suggesting an anti-gum inflammation mechanism by health-promoting symbionts. Global, cross-cohort meta-analysis revealed, at SoH, a greatly elevated microbiome-based periodontitis index driven by its convergence of both taxonomical and functional profiles toward the periodontitis microbiome. Finally, post-SoH gingivitis development accelerates oral microbiota aging by over 1 year within 28 days, with Rothia spp. depletion and Porphyromonas gingivalis elevation as hallmarks. Thus, the microbiome-defined, transient gum SoH stage is a crucial link among gingivitis, periodontitis, and aging.IMPORTANCE A significant portion of world population still fails to brush teeth daily. As a result, the majority of the global adult population is afflicted with chronic gingivitis, and if it is left untreated, some of them will eventually suffer from periodontitis. Here, we identified periodontitis-like microbiome dysbiosis in an asymptomatic SoH stage as early as 24 to 72 h after oral-hygiene pause. SoH features a swift, full activation of multiple salivary cytokines but a steep synergetic decrease of plaque-derived betaine and Rothia spp. The microbial ecology during early gingivitis is highly similar to that in periodontitis under both taxonomical and functional contexts. Unexpectedly, exposures to gingivitis can accelerate over 10-fold the normal rate of oral microbiota aging. Our findings underscore the importance of intervening at the SoH stage of gingivitis via proper oral-hygiene practices on a daily basis, so as to maintain a periodontitis-preventive plaque and ensure the healthy aging of the oral ecosystem.},
}
@article {pmid33685679,
year = {2021},
author = {Lietaer, L and Bogado Pascottini, O and Hernandez-Sanabria, E and Kerckhof, FM and Lacoere, T and Boon, N and Vlaminck, L and Opsomer, G and Van de Wiele, T},
title = {Low microbial biomass within the reproductive tract of mid-lactation dairy cows: A study approach.},
journal = {Journal of dairy science},
volume = {104},
number = {5},
pages = {6159-6174},
doi = {10.3168/jds.2020-19554},
pmid = {33685679},
issn = {1525-3198},
mesh = {Animals ; Cattle ; Female ; Biomass ; *Lactation ; Reproducibility of Results ; RNA, Ribosomal, 16S ; *Uterus ; },
abstract = {The microbiome from the reproductive tract is being investigated for its putative effect on fertility, embryo development, and health status of the human or animal host postpartum. Besides the presence of a vaginal microbiome, recent studies have claimed the existence and putative role of the uterine microbiome. Yet, the extremely low bacterial numbers and high eukaryotic/prokaryotic DNA ratio make this a highly challenging environment to study with next-generation sequencing (NGS) techniques. Here, we describe the methodological challenges that are typically encountered when performing an accurate analysis of low microbial biomass samples, illustrated by data of our own observational study. In terms of the research question, we compared the microbial composition throughout different parts of the reproductive tract of clinically healthy, mid-lactation Holstein-Friesian cows. Samples were collected from 5 dairy cows immediately after killing. Swabs were taken from the vagina, and from 4 pre-established locations of the uterine endometrium. In addition to the conventional DNA extraction blank controls, sterile swabs rubbed over disinfected disposable gloves and the disinfected surface of the uterus (tunica serosa) before incision were taken as sampling controls. The DNA extraction, DNA quantification, quantitative PCR of the 16S rRNA genes, and 16S rRNA gene sequencing were performed. In terms of NGS data analysis, we performed prevalence-based filtering of putative contaminant operational taxonomic units (OTU) using the decontam R package. Although the bacterial composition differed between the vagina and uterus, no differences in bacterial community structure (α and β diversity) were found among the different locations in the uterus. At phylum level, uterine samples had a greater relative abundance of Proteobacteria, and a lesser relative abundance of Firmicutes than vaginal samples. The number of shared OTU between vagina and uterus was limited, suggesting the existence of bacterial transmission routes other than the transcervical one to the uterus. The mid-lactation bovine genital tract is a low microbial biomass environment, which makes it difficult to distinguish between its constitutive versus contaminant microbiome. The integration of key controls is therefore strictly necessary to decrease the effect of accidentally introduced contaminant sequences and improve the reliability of results in samples with low microbial biomass.},
}
@article {pmid33685393,
year = {2021},
author = {Zhang, X and Shi, L and Sun, T and Guo, K and Geng, S},
title = {Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {78},
pmid = {33685393},
issn = {1471-2180},
support = {51707149//National Natural Science Foundation of China/ ; XJJ2017071//Xi'an Jiaotong University/ ; SKLIPR.1609//State Key Laboratory of Intense Pulsed Radiation Simulation and Effect/ ; },
mesh = {Biodiversity ; Cytokines/*genetics ; Dysbiosis/*complications/immunology ; Feces/microbiology ; Gastrointestinal Microbiome/*immunology ; Humans ; Psoriasis/*complications/immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients' quality of life. The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies. Our objective was to identify differences in the fecal microbial composition of patients with psoriasis compared with healthy individuals to unravel the microbiota profiling in this autoimmune disease.<br><br>RESULTS: We collected fecal samples from 30 psoriasis patients and 30 healthy controls, sequenced them by 16S rRNA high-throughput sequencing, and identified the gut microbial composition using bioinformatic analyses including Quantitative Insights into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our results showed that different relative abundance of certain bacterial taxa between psoriasis patients and healthy individuals, including Faecalibacterium and Megamonas, were increased in patients with psoriasis. It's also implicated that many cytokines act as main effect molecules in the pathology of psoriasis. We selected the inflammation-related indicators that were abnormal in psoriasis patients and found the microbiome variations were associated with the level of them, especially interleukin-2 receptor showed a positive relationship with Phascolarctobacterium and a negative relationship with the Dialister. The relative abundance of Phascolarctobacterium and Dialister can be regard as predictors of psoriasis activity. The correlation analysis based on microbiota and Inflammation-related indicators showed that microbiota dysbiosis might induce an abnormal immune response in psoriasis.<br><br>CONCLUSIONS: We concluded that the gut microbiome composition in psoriasis patients has been altered markedly and provides evidence to understand the relationship between gut microbiota and psoriasis. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of psoriasis and whether the relationship between gut microbiota and cytokines was involved.},
}
@article {pmid33684884,
year = {2021},
author = {Song, C and Jin, K and Raaijmakers, JM},
title = {Designing a home for beneficial plant microbiomes.},
journal = {Current opinion in plant biology},
volume = {62},
number = {},
pages = {102025},
doi = {10.1016/j.pbi.2021.102025},
pmid = {33684884},
issn = {1879-0356},
mesh = {Agriculture ; *Microbiota/genetics ; *Plant Breeding ; Plant Development ; Plants ; },
abstract = {The plant microbiome comprises a highly diverse community of saprotrophic, mutualistic, and pathogenic microbes that can affect plant growth and plant health. There is substantial interest to exploit beneficial members of plant microbiomes for new sustainable management strategies in crop production. However, poor survival and colonization of plant tissues by introduced microbial isolates as well as lack of expression of the plant growth-promoting or disease-suppressive traits at the right time and place are still major limitations for successful implementation of microbiomes in future agricultural practices and plant breeding programs. Similar to building a home for humans, we discuss different strategies of building a home for beneficial plant microbiomes, here referred to as the 'MicrobiHome'.},
}
@article {pmid33682183,
year = {2021},
author = {Sperlea, T and Kreuder, N and Beisser, D and Hattab, G and Boenigk, J and Heider, D},
title = {Quantification of the covariation of lake microbiomes and environmental variables using a machine learning-based framework.},
journal = {Molecular ecology},
volume = {30},
number = {9},
pages = {2131-2144},
doi = {10.1111/mec.15872},
pmid = {33682183},
issn = {1365-294X},
mesh = {Ecology ; *Lakes ; Machine Learning ; *Microbiota/genetics ; },
abstract = {It is known that microorganisms are essential for the functioning of ecosystems, but the extent to which microorganisms respond to different environmental variables in their natural habitats is not clear. In the current study, we present a methodological framework to quantify the covariation of the microbial community of a habitat and environmental variables of this habitat. It is built on theoretical considerations of systems ecology, makes use of state-of-the-art machine learning techniques and can be used to identify bioindicators. We apply the framework to a data set containing operational taxonomic units (OTUs) as well as more than twenty physicochemical and geographic variables measured in a large-scale survey of European lakes. While a large part of variation (up to 61%) in many environmental variables can be explained by microbial community composition, some variables do not show significant covariation with the microbial lake community. Moreover, we have identified OTUs that act as "multitask" bioindicators, i.e., that are indicative for multiple environmental variables, and thus could be candidates for lake water monitoring schemes. Our results represent, for the first time, a quantification of the covariation of the lake microbiome and a wide array of environmental variables for lake ecosystems. Building on the results and methodology presented here, it will be possible to identify microbial taxa and processes that are essential for functioning and stability of lake ecosystems.},
}
@article {pmid33680353,
year = {2021},
author = {Ghannam, RB and Techtmann, SM},
title = {Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring.},
journal = {Computational and structural biotechnology journal},
volume = {19},
number = {},
pages = {1092-1107},
pmid = {33680353},
issn = {2001-0370},
abstract = {Advances in nucleic acid sequencing technology have enabled expansion of our ability to profile microbial diversity. These large datasets of taxonomic and functional diversity are key to better understanding microbial ecology. Machine learning has proven to be a useful approach for analyzing microbial community data and making predictions about outcomes including human and environmental health. Machine learning applied to microbial community profiles has been used to predict disease states in human health, environmental quality and presence of contamination in the environment, and as trace evidence in forensics. Machine learning has appeal as a powerful tool that can provide deep insights into microbial communities and identify patterns in microbial community data. However, often machine learning models can be used as black boxes to predict a specific outcome, with little understanding of how the models arrived at predictions. Complex machine learning algorithms often may value higher accuracy and performance at the sacrifice of interpretability. In order to leverage machine learning into more translational research related to the microbiome and strengthen our ability to extract meaningful biological information, it is important for models to be interpretable. Here we review current trends in machine learning applications in microbial ecology as well as some of the important challenges and opportunities for more broad application of machine learning to understanding microbial communities.},
}
@article {pmid33678886,
year = {2021},
author = {Muandze-Nzambe, JU and Onanga, R and Yala, JF and Somda, NS and Cissé, H and Zongo, C and Mavoungou, JF and Savadogo, A},
title = {Technological and microbiological characteristics of indigenous food produced in Gabon.},
journal = {Journal of food science and technology},
volume = {58},
number = {3},
pages = {1027-1041},
pmid = {33678886},
issn = {0022-1155},
abstract = {The purpose of this study was to provide contextual information on indigenous food's technologies and safety from Gabon. The strategic focus being to promote local food with enhanced nutritional value and improved safety. An investigation and monitoring were carried out to elucidate their process flow diagrams and to identify safety failures. Samples were taken for microbiological analysis using conventional culture-based techniques. Detection and identification of Salmonella in samples were confirmed using PCR based method by targeting invasion plasmid antigen B (IpaB) gene. The investigation shows that women play a protagonist role in the technical know-how of Gabonese indigenous foods in a context that is evolving towards the disappearance of this knowledge. The food production process remains archaic, which makes the environment impact on food safety. Indeed, the proximity of food manufacturing environment to animals, waste, or latrines coupled with the lack of hygiene and manufacturing practices affect the quality of these foods. This is reflected in our study's microbiological results, namely, Aerobic Mesophilic Bacteria ranged from 3.53 to 11.96 log CFU/g and indicators of fecal contaminations of up to 8.21 log CFU/g. Salmonella is detected in 18.69% of samples. The presence of these bacteria is a risk for consumer health. Although some of these foods can be considered as a fermented food, the producers should be further educated and encouraged to take preventive measures to ensure the quality of these food products. A much more subtle approach based on microbial ecology of these foods should be explored for better exploitation.},
}
@article {pmid33678560,
year = {2021},
author = {Acosta, N and Duh Kang, I and Rabaey, K and De Vrieze, J},
title = {Cow manure stabilizes anaerobic digestion of cocoa waste.},
journal = {Waste management (New York, N.Y.)},
volume = {126},
number = {},
pages = {508-516},
doi = {10.1016/j.wasman.2021.02.010},
pmid = {33678560},
issn = {1879-2456},
mesh = {Anaerobiosis ; Animals ; *Biofuels ; Bioreactors ; Cattle ; Female ; Food ; *Manure ; Methane ; },
abstract = {Anaerobic digestion of a mono-feedstock often causes low methane yields and process instability. An effective strategy to overcome these barriers is co-digestion with animal manure. The obtained process improvement is often attributed to buffer capacity, nutrients, vitamins and trace metals, and microorganisms present in manure, but it remains unknown which factor plays the key role in digester performance. Here, we investigated anaerobic digestion of cocoa waste in four different treatments: mono-digestion, addition of synthetic nutrients, co-digestion with sterile cow manure, and co-digestion with raw cow manure. Co-digestion with raw manure resulted in the highest methane yield of 181 ± 39 L kg[-1] VS (volatile solids), similar to the co-digestion with sterile manure, i.e., 162 ± 52 L kg[-1] VS. The supplementation of synthetic nutrients to the anaerobic digestion of cocoa waste only temporarily increased methane yield, indicating that this will tackle a lack of nutrients in the short term, but has a limited long-term contribution to the stabilization of the process. Hence, because of the inability of synthetic nutrients to stabilize the digestion process and the similarity between the digesters fed sterile and raw manure, both at the physico-chemical and microbial level, the key contribution of manure co-digestion with cocoa seems to be the provision of buffering capacity.},
}
@article {pmid33677560,
year = {2021},
author = {Vázquez-Ucha, JC and Seoane-Estévez, A and Rodiño-Janeiro, BK and González-Bardanca, M and Conde-Pérez, K and Martínez-Guitián, M and Alvarez-Fraga, L and Arca-Suárez, J and Lasarte-Monterrubio, C and Gut, M and Gut, I and Álvarez-Tejado, M and Oviaño, M and Beceiro, A and Bou, G and , },
title = {Activity of imipenem/relebactam against a Spanish nationwide collection of carbapenemase-producing Enterobacterales.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {76},
number = {6},
pages = {1498-1510},
doi = {10.1093/jac/dkab043},
pmid = {33677560},
issn = {1460-2091},
mesh = {Anti-Bacterial Agents/pharmacology ; *Azabicyclo Compounds/pharmacology ; Bacterial Proteins ; Ceftazidime ; Drug Combinations ; *Imipenem/pharmacology ; Microbial Sensitivity Tests ; Spain ; beta-Lactamases/genetics ; },
abstract = {BACKGROUND: Imipenem/relebactam is a novel carbapenem/β-lactamase inhibitor combination, developed to act against carbapenemase-producing Enterobacterales (CPE).<br><br>OBJECTIVES: To assess the in vitro activity of imipenem/relebactam against a Spanish nationwide collection of CPE by testing the susceptibility of these isolates to 16 widely used antimicrobials and to determine the underlying &#x3b2;-lactam resistance mechanisms involved and the molecular epidemiology of carbapenemases in Spain.<br><br>MATERIALS AND METHODS: Clinical CPE isolates (n&#x200a;=&#x200a;401) collected for 2&#x2009;months from 24 hospitals in Spain were tested. MIC50, MIC90 and susceptibility/resistance rates were interpreted in accordance with the EUCAST guidelines. &#x3b2;-Lactam resistance mechanisms and molecular epidemiology were characterized by WGS.<br><br>RESULTS: For all isolates, high rates of susceptibility to colistin (86.5%; MIC50/90&#x200a;=&#x200a;0.12/8&#x2009;mg/L), imipenem/relebactam (85.8%; MIC50/90&#x200a;=&#x200a;0.5/4&#x2009;mg/L) and ceftazidime/avibactam (83.8%, MIC50/90&#x200a;=&#x200a;1/&#x2265;256&#x2009;mg/L) were observed. The subgroups of isolates producing OXA-48-like (n&#x200a;=&#x200a;305, 75.1%) and KPC-like enzymes (n&#x200a;=&#x200a;44, 10.8%) were highly susceptible to ceftazidime/avibactam (97.7%, MIC50/90&#x200a;=&#x200a;1/2&#x2009;mg/L) and imipenem/relebactam (100.0%, MIC50/90&#x200a;=&#x200a;&#x2264;0.25/1&#x2009;mg/L), respectively.The most widely disseminated high-risk clones of carbapenemase-producing Klebsiella pneumoniae across Spain were found to be ST11, ST147, ST392 and ST15 (mostly associated with OXA-48) and ST258/512 (in all cases producing KPC).<br><br>CONCLUSIONS: Imipenem/relebactam, colistin and ceftazidime/avibactam were the most active antimicrobials against all CPEs. Imipenem/relebactam is a valuable addition to the antimicrobial arsenal used in the fight against CPE, particularly against KPC-producing isolates, which in all cases were susceptible to this combination.},
}
@article {pmid33676244,
year = {2021},
author = {Du, B and Wang, Q and Yang, Q and Wang, R and Yuan, W and Yan, L},
title = {Responses of bacterial and bacteriophage communities to long-term exposure to antimicrobial agents in wastewater treatment systems.},
journal = {Journal of hazardous materials},
volume = {414},
number = {},
pages = {125486},
doi = {10.1016/j.jhazmat.2021.125486},
pmid = {33676244},
issn = {1873-3336},
mesh = {Anti-Bacterial Agents ; *Anti-Infective Agents ; Bacteria/genetics ; *Bacteriophages/genetics ; Humans ; *Microbiota ; *Water Purification ; },
abstract = {The occurrence of antibacterial agents has received increasing concern due to their possible threats to human health. However, the effects of antibacterial residues on the evolution and dynamics between bacteria and bacteriophages in wastewater treatment systems have seldom been researched. Especially for phages, little is known about their response to antimicrobial exposure. In this study, two identical anoxic-aerobic wastewater treatment systems were established to evaluate the responses of bacterial and phage communities to long-term exposure to antimicrobial agents. The results indicated simultaneous exposure to combined antimicrobials significantly inhibited (p < 0.05) the abundance of phages and bacteria. Metagenomic sequencing analysis indicated the community of bacteria and phages changed greatly at the genus level due to combined antibacterial exposure. Additionally, long-term exposure to antimicrobial agents promoted the attachment of receptor-binding protein genes to Klebsiella, Escherichia and Salmonella (which were all members of Enterobacteriaceae). Compared to that in the control system, the numbers of receptor-binding protein genes on their possible phages (such as Lambdalikevirus and P2likevirus) were also obviously higher when the microorganisms were exposed to antimicrobials. The results are helpful to understanding the microbial communities and tracking the relationship of phage-bacterial host systems, especially under the pressure of antimicrobial exposure.},
}
@article {pmid33674901,
year = {2021},
author = {Ghosh, A and Bhadury, P},
title = {Correction to: Vibrio chemaguriensis sp. nov., from Sundarbans, Bay of Bengal.},
journal = {Current microbiology},
volume = {78},
number = {3},
pages = {1068},
doi = {10.1007/s00284-021-02363-6},
pmid = {33674901},
issn = {1432-0991},
}
@article {pmid33673660,
year = {2021},
author = {Madoroba, E and Magwedere, K and Chaora, NS and Matle, I and Muchadeyi, F and Mathole, MA and Pierneef, R},
title = {Microbial Communities of Meat and Meat Products: An Exploratory Analysis of the Product Quality and Safety at Selected Enterprises in South Africa.},
journal = {Microorganisms},
volume = {9},
number = {3},
pages = {},
pmid = {33673660},
issn = {2076-2607},
support = {21.1.1/VPH-01/OVI and 21.1.1/VPH-02/OVI//the Department of Agriculture, Land Reform and Rural Development (DALRRD) under project number 21.1.1/VPH-01/OVI and 21.1.1/VPH-02/OVI/ ; },
abstract = {Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms.},
}
@article {pmid33671218,
year = {2021},
author = {Dumolin, C and Peeters, C and De Canck, E and Boon, N and Vandamme, P},
title = {Network Analysis Based on Unique Spectral Features Enables an Efficient Selection of Genomically Diverse Operational Isolation Units.},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {},
pmid = {33671218},
issn = {2076-2607},
support = {//Wellcome Trust/United Kingdom ; GOH3817N//European Marine Biological Resource Centre Belgium/ ; BOF15/GOA/006//Universiteit Gent/ ; },
abstract = {Culturomics-based bacterial diversity studies benefit from the implementation of MALDI-TOF MS to remove genomically redundant isolates from isolate collections. We previously introduced SPeDE, a novel tool designed to dereplicate spectral datasets at an infraspecific level into operational isolation units (OIUs) based on unique spectral features. However, biological and technical variation may result in methodology-induced differences in MALDI-TOF mass spectra and hence provoke the detection of genomically redundant OIUs. In the present study, we used three datasets to analyze to which extent hierarchical clustering and network analysis allowed to eliminate redundant OIUs obtained through biological and technical sample variation and to describe the diversity within a set of spectra obtained from 134 unknown soil isolates. Overall, network analysis based on unique spectral features in MALDI-TOF mass spectra enabled a superior selection of genomically diverse OIUs compared to hierarchical clustering analysis and provided a better understanding of the inter-OIU relationships.},
}
@article {pmid33670965,
year = {2021},
author = {Lambrecht, E and Coillie, EV and Boon, N and Heyndrickx, M and Wiele, TV},
title = {Transfer of Antibiotic Resistance Plasmid from Commensal E. coli Towards Human Intestinal Microbiota in the M-SHIME: Effect of E. coli dosis, Human Individual and Antibiotic Use.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
pmid = {33670965},
issn = {2075-1729},
support = {BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; RF 13/9 TRAMRISK//FOD Volksgezondheid, Veiligheid van de Voedselketen en Leefmilieu/ ; },
abstract = {Along with (in) direct contact with animals and a contaminated environment, humans are exposed to antibiotic-resistant bacteria by consumption of food. The implications of ingesting antibiotic-resistant commensal bacteria are unknown, as dose-response data on resistance transfer and spreading in our gut is lacking. In this study, transfer of a resistance plasmid (IncF), harbouring several antibiotic resistance genes, from a commensal E. coli strain towards human intestinal microbiota was assessed using a Mucosal Simulator of the Human Intestinal Ecosystem (M-SHIME). More specifically, the effect of the initial E. coli plasmid donor concentration (10[5] and 10[7] CFU/meal), antibiotic treatment (cefotaxime) and human individual (n = 6) on plasmid transfer towards lumen coliforms and anaerobes was determined. Transfer of the resistance plasmid to luminal coliforms and anaerobes was observed shortly after the donor strain arrived in the colon and was independent of the ingested dose. Transfer occurred in all six simulated colons and despite their unique microbial community composition, no differences could be detected in antibiotic resistance transfer rates between the simulated human colons. After 72 h, resistant coliform transconjugants levels ranged from 7.6 × 10[4] to 7.9 × 10[6] CFUcefotaxime resistant/Ml colon lumen. Presence of the resistance plasmid was confirmed and quantified by PCR and qPCR. Cefotaxime treatment led to a significant reduction (85%) in resistant coliforms, however no significant effect on the total number of cultivable coliforms and anaerobes was observed.},
}
@article {pmid33670234,
year = {2021},
author = {Vigneron, A and Cruaud, P and Ducellier, F and Head, IM and Tsesmetzis, N},
title = {Syntrophic Hydrocarbon Degradation in a Decommissioned Off-Shore Subsea Oil Storage Structure.},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {},
pmid = {33670234},
issn = {2076-2607},
support = {-//Shell Global Solutions International/ ; },
abstract = {Over the last decade, metagenomic studies have revealed the impact of oil production on the microbial ecology of petroleum reservoirs. However, despite their fundamental roles in bioremediation of hydrocarbons, biocorrosion, biofouling and hydrogen sulfide production, oil field and oil production infrastructure microbiomes are poorly explored. Understanding of microbial activities within oil production facilities is therefore crucial for environmental risk mitigation, most notably during decommissioning. The analysis of the planktonic microbial community from the aqueous phase of a subsea oil-storage structure was conducted. This concrete structure was part of the production platform of the Brent oil field (North Sea), which is currently undergoing decommissioning. Quantification and sequencing of microbial 16S rRNA genes, metagenomic analysis and reconstruction of metagenome assembled genomes (MAGs) revealed a unique microbiome, strongly dominated by organisms related to Dethiosulfatibacter and Cloacimonadetes. Consistent with the hydrocarbon content in the aqueous phase of the structure, a strong potential for degradation of low molecular weight aromatic hydrocarbons was apparent in the microbial community. These degradation pathways were associated with taxonomically diverse microorganisms, including the predominant Dethiosulfatibacter and Cloacimonadetes lineages, expanding the list of potential hydrocarbon degraders. Genes associated with direct and indirect interspecies exchanges (multiheme type-C cytochromes, hydrogenases and formate/acetate metabolism) were widespread in the community, suggesting potential syntrophic hydrocarbon degradation processes in the system. Our results illustrate the importance of genomic data for informing decommissioning strategies in marine environments and reveal that hydrocarbon-degrading community composition and metabolisms in man-made marine structures might differ markedly from natural hydrocarbon-rich marine environments.},
}
@article {pmid33670115,
year = {2021},
author = {De Pessemier, B and Grine, L and Debaere, M and Maes, A and Paetzold, B and Callewaert, C},
title = {Gut-Skin Axis: Current Knowledge of the Interrelationship between Microbial Dysbiosis and Skin Conditions.},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {},
pmid = {33670115},
issn = {2076-2607},
abstract = {The microbiome plays an important role in a wide variety of skin disorders. Not only is the skin microbiome altered, but also surprisingly many skin diseases are accompanied by an altered gut microbiome. The microbiome is a key regulator for the immune system, as it aims to maintain homeostasis by communicating with tissues and organs in a bidirectional manner. Hence, dysbiosis in the skin and/or gut microbiome is associated with an altered immune response, promoting the development of skin diseases, such as atopic dermatitis, psoriasis, acne vulgaris, dandruff, and even skin cancer. Here, we focus on the associations between the microbiome, diet, metabolites, and immune responses in skin pathologies. This review describes an exhaustive list of common skin conditions with associated dysbiosis in the skin microbiome as well as the current body of evidence on gut microbiome dysbiosis, dietary links, and their interplay with skin conditions. An enhanced understanding of the local skin and gut microbiome including the underlying mechanisms is necessary to shed light on the microbial involvement in human skin diseases and to develop new therapeutic approaches.},
}
@article {pmid33669689,
year = {2021},
author = {Duysburgh, C and Van den Abbeele, P and Kamil, A and Fleige, L and De Chavez, PJ and Chu, Y and Barton, W and O'Sullivan, O and Cotter, PD and Quilter, K and Joyce, SA and Murphy, M and DunnGalvin, G and Dinan, TG and Marzorati, M},
title = {In vitro-in vivo Validation of Stimulatory Effect of Oat Ingredients on Lactobacilli.},
journal = {Pathogens (Basel, Switzerland)},
volume = {10},
number = {2},
pages = {},
pmid = {33669689},
issn = {2076-0817},
abstract = {The prebiotic activity of a commercially available oat product and a novel oat ingredient, at similar β-glucan loads, was tested using a validated in vitro gut model (M-SHIME[®]). The novel oat ingredient was tested further at lower β-glucan loads in vitro, while the commercially available oat product was assessed in a randomised, single-blind, placebo-controlled, and cross-over human study. Both approaches focused on healthy individuals with mild hypercholesterolemia. In vitro analysis revealed that both oat products strongly stimulated Lactobacillaceae and Bifidobacteriaceae in the intestinal lumen and the simulated mucus layer, and corresponded with enhanced levels of acetate and lactate with cross-feeding interactions leading to an associated increase in propionate and butyrate production. The in vitro prebiotic activity of the novel oat ingredient remained at lower β-glucan levels, indicating the prebiotic potential of the novel oat product. Finally, the stimulation of Lactobacillus spp. was confirmed during the in vivo trial, where lactobacilli abundance significantly increased in the overall population at the end of the intervention period with the commercially available oat product relative to the control product, indicating the power of in vitro gut models in predicting in vivo response of the microbial community to dietary modulation.},
}
@article {pmid33669125,
year = {2021},
author = {Ugalde-Salas, P and Ramírez C, H and Harmand, J and Desmond-Le Quéméner, E},
title = {Microbial Interactions as Drivers of a Nitrification Process in a Chemostat.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {8},
number = {3},
pages = {},
pmid = {33669125},
issn = {2306-5354},
support = {16-CE04-0003//Agence Nationale de la Recherche/ ; 1200355//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 170001//Basal Program CMM-AFB/ ; },
abstract = {This article deals with the inclusion of microbial ecology measurements such as abundances of operational taxonomic units in bioprocess modelling. The first part presents the mathematical analysis of a model that may be framed within the class of Lotka-Volterra models fitted to experimental data in a chemostat setting where a nitrification process was operated for over 500 days. The limitations and the insights of such an approach are discussed. In the second part, the use of an optimal tracking technique (developed within the framework of control theory) for the integration of data from genetic sequencing in chemostat models is presented. The optimal tracking revisits the data used in the aforementioned chemostat setting. The resulting model is an explanatory model, not a predictive one, it is able to reconstruct the different forms of nitrogen in the reactor by using the abundances of the operational taxonomic units, providing some insights into the growth rate of microbes in a complex community.},
}
@article {pmid33669086,
year = {2021},
author = {Cipriano, MAP and Freitas-Iório, RP and Dimitrov, MR and de Andrade, SAL and Kuramae, EE and Silveira, APDD},
title = {Plant-Growth Endophytic Bacteria Improve Nutrient Use Efficiency and Modulate Foliar N-Metabolites in Sugarcane Seedling.},
journal = {Microorganisms},
volume = {9},
number = {3},
pages = {},
pmid = {33669086},
issn = {2076-2607},
support = {456420-2013-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2008/56147-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; PNPD//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {Beneficial plant-microbe interactions lead to physiological and biochemical changes that may result in plant-growth promotion. This study evaluated the effect of the interaction between sugarcane and endophytic bacterial strains on plant physiological and biochemical responses under two levels of nitrogen (N) fertilization. Six strains of endophytic bacteria, previously selected as plant growth-promoting bacteria (PGPB), were used to inoculate sugarcane mini stalks, with and without N fertilization. After 45 days, biomass production; shoot nutrient concentrations; foliar polyamine and free amino acid profiles; activities of nitrate reductase and glutamine synthase; and the relative transcript levels of the GS1, GS2, and SHR5 genes in sugarcane leaves were determined. All six endophytic strains promoted sugarcane growth, increasing shoot and root biomass, plant nutritional status, and the use efficiency of most nutrients. The inoculation-induced changes at the biochemical level altered the foliar free amino acid and polyamine profiles, mainly regarding the relative concentrations of citrulline, putrescine, glycine, alanine, glutamate, glutamine, proline, and aspartate. The transcription of GS1, GS2, and SHR5 was higher in the N fertilized seedlings, and almost not altered by endophytic bacterial strains. The endophytic strains promoted sugarcane seedlings growth mainly by improving nutrient efficiency. This improvement could not be explained by their ability to induce the production of amino acid and polyamine composts, or GS1, GS2, and SHR5, showing that complex interactions may be associated with enhancement of the sugarcane seedlings' performance by endophytic bacteria. The strains demonstrated biotechnological potential for sugarcane seedling production.},
}
@article {pmid33668823,
year = {2021},
author = {Van den Abbeele, P and Sprenger, N and Ghyselinck, J and Marsaux, B and Marzorati, M and Rochat, F},
title = {A Comparison of the In Vitro Effects of 2'Fucosyllactose and Lactose on the Composition and Activity of Gut Microbiota from Infants and Toddlers.},
journal = {Nutrients},
volume = {13},
number = {3},
pages = {},
pmid = {33668823},
issn = {2072-6643},
mesh = {Bifidobacterium ; Breast Feeding ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Infant Nutritional Physiological Phenomena ; Lactose/*pharmacology ; Milk, Human/*chemistry ; Trisaccharides/*pharmacology ; },
abstract = {Because of the recognized health benefits of breast milk, it is recommended as the sole nutrition source during the first 6 months of life. Among the bioactive components are human milk oligosaccharides (HMOs) that exert part of their activity via the gut microbiota. Here, we investigated the gut microbiota fermentation of HMO 2'fucosyllactose (2'-FL), using two in vitro models (48 h fecal incubations and the long-term mucosal simulator of the human intestinal microbial ecosystem [M-SHIME[®]]) with fecal samples from 3-month-old breastfed (BF) infants as well as 2-3 year old toddlers. The short-term model allowed the screening of five donors for each group and provided supportive data for the M-SHIME[®] study. A key finding was the strong and immediate increase in the relative abundance of Bifidobacteriaceae following 2'-FL fermentation by both the BF infant and toddler microbiota in the M-SHIME[®]. At the metabolic level, while decreasing branched-chain fatty acids, 2'-FL strongly increased acetate production together with increases in the health-related propionate and butyrate whilst gas production only mildly increased. Notably, consistently lower gas production was observed with 2'-FL fermentation as compared to lactose, suggesting that reduced discomfort during the dynamic microbiome establishment in early life may be an advantage along with the bifidogenic effect observed.},
}
@article {pmid33668312,
year = {2021},
author = {Becker, AAMJ and Hill, KC and Butaye, P},
title = {Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean.},
journal = {Microorganisms},
volume = {9},
number = {3},
pages = {},
pmid = {33668312},
issn = {2076-2607},
support = {41001-2016//One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine/ ; },
abstract = {Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5[TM] XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator's impact throughout the Caribbean.},
}
@article {pmid33667294,
year = {2021},
author = {Ranallo, RT and McDonald, LC and Halpin, AL and Hiltke, T and Young, VB},
title = {The State of Microbiome Science at the Intersection of Infectious Diseases and Antimicrobial Resistance.},
journal = {The Journal of infectious diseases},
volume = {223},
number = {12 Suppl 2},
pages = {S187-S193},
pmid = {33667294},
issn = {1537-6613},
support = {U01 AI124255/AI/NIAID NIH HHS/United States ; U54 CK000481/CK/NCEZID CDC HHS/United States ; U54 CK000607/CK/NCEZID CDC HHS/United States ; },
mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Stewardship ; Communicable Diseases/diagnosis/immunology/*microbiology/therapy ; *Drug Resistance, Microbial ; Fecal Microbiota Transplantation ; Homeostasis ; Host-Pathogen Interactions ; Humans ; Immunity ; *Microbiota/drug effects ; },
abstract = {Along with the rise in modern chronic diseases, ranging from diabetes to asthma, there are challenges posed by increasing antibiotic resistance, which results in difficult-to-treat infections, as well as sepsis. An emerging and unifying theme in the pathogenesis of these diverse public health threats is changes in the microbial communities that inhabit multiple body sites. Although there is great promise in exploring the role of these microbial communities in chronic disease pathogenesis, the shorter timeframe of most infectious disease pathogenesis may allow early translation of our basic scientific understanding of microbial ecology and host-microbiota-pathogen interactions. Likely translation avenues include development of preventive strategies, diagnostics, and therapeutics. For example, as basic research related to microbial pathogenesis continues to progress, Clostridioides difficile infection is already being addressed clinically through at least 2 of these 3 avenues: targeted antibiotic stewardship and treatment of recurrent disease through fecal microbiota transplantation.},
}
@article {pmid33666710,
year = {2021},
author = {Fitzgerald, RS and Sanderson, IR and Claesson, MJ},
title = {Paediatric Inflammatory Bowel Disease and its Relationship with the Microbiome.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {833-844},
pmid = {33666710},
issn = {1432-184X},
support = {GOIPG/2017/1573//Irish Research Council/ ; 510264//Crohn's and Colitis Foundation/ ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Child ; *Colitis, Ulcerative ; *Crohn Disease ; Humans ; *Inflammatory Bowel Diseases ; *Microbiota ; *Mycobiome ; },
abstract = {Paediatric inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the digestive tract, comprising of Crohn's disease (CD), ulcerative colitis (UC), and, where classification is undetermined, inflammatory bowel disease unclassified (IBDU). Paediatric IBD incidence is increasing globally, with prevalence highest in the developed world. Though no specific causative agent has been identified for paediatric IBD, it is believed that a number of factors may contribute to the development of the disease, including genetics and the environment. Another potential component in the development of IBD is the microbiota in the digestive tract, particularly the gut. While the exact role that the microbiome plays in IBD is unclear, many studies acknowledge the complex relationship between the gut bacteria and pathogenesis of IBD. In this review, we look at the increasing number of studies investigating the role the microbiome and other biomes play in paediatric patients with IBD, particularly changes associated with IBD, varying disease states, and therapeutics. The paediatric IBD microbiome is significantly different to that of healthy children, with decreased diversity and differences in bacterial composition (such as a decrease in Firmicutes). Changes in the microbiome relating to various treatments of IBD and disease severity have also been observed in multiple studies. Changes in diversity and composition may also extend to other biomes in paediatric IBD, such as the virome and the mycobiome. Research into biome differences in IBD paediatric patients may help progress our understanding of the aetiology of the disease.},
}
@article {pmid33665722,
year = {2021},
author = {Cureau, N and Threlfall, R and Marasini, D and Lavefve, L and Carbonero, F},
title = {Year, Location, and Variety Impact on Grape-Associated Mycobiota of Arkansas-Grown Wine Grapes for Wine Production.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {845-858},
pmid = {33665722},
issn = {1432-184X},
mesh = {Arkansas ; *Ascomycota ; *Vitis ; *Wine ; Yeasts ; },
abstract = {Wine grape berries (Vitis spp.) harbor a wide variety of yeasts and filamentous fungi that impact grapevine health and the winemaking process. Identification of these fungi could be important for controlling and improving wine production. The use of high-throughput sequencing (HTS) strategies has enabled identification and quantification of bacterial and fungal species in vineyards. The aims of this study were to identify mycobiota from Cabernet Sauvignon and Zinfandel (V. vinifera), Carlos and Noble muscadines (V. rotundifolia), Cynthiana (V. aestivalis), and Vignoles hybrid (cross of different Vitis spp.) grapes, and investigate the effect of grape variety, location, and year on grape fungal communities. Grape berries were collected in 2016 and 2017 from four vineyards located in Arkansas. The HTS of the Internal Transcribed Spacer 1 region was used to identify grape indigenous epiphytic and endophytic fungal communities. The predominant genera identified on the Arkansas wine grapes were Uwebraunia, Zymoseptoria, Papiliotrema, Meyerozyma, Filobasidium, and Curvibasidium. Overall, the data suggested that grape fungal community distribution and relative abundance were influenced by grape variety, year, and location, but each was influenced to a different extent. Not only were grape mycobiota influenced by year, variety, and location but also it appeared that communities from the previous year impacted microbial communities the following year. For example, an increase of the mycoparasite Ampelomyces quisqualis was noticed in 2017 on grapes that carried the causal agent of powdery mildew, Erysiphe necator, in 2016, thus, amplifying the importance of vineyard microbiota knowledge for disease management and winemaking.},
}
@article {pmid33665721,
year = {2021},
author = {Zhou, X and Li, B and Wei, J and Ye, Y and Xu, J and Chen, L and Lu, C},
title = {Temperature Influenced the Comammox Community Composition in Drinking Water and Wastewater Treatment Plants.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {870-884},
pmid = {33665721},
issn = {1432-184X},
support = {41807029//National Natural Science Foundation of China/ ; 51679067//National Natural Science Foundation of China/ ; 51879088//National Natural Science Foundation of China/ ; 51709085//National Natural Science Foundation of China/ ; B200201028//Fundamental Research Funds for the Central Universities/ ; B200204002//Fundamental Research Funds for the Central Universities/ ; B200202158//Fundamental Research Funds for the Central Universities/ ; B200204033//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Ammonia ; Archaea ; Bacteria/genetics ; *Drinking Water ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Temperature ; *Water Purification ; },
abstract = {Nitrification is a pivotal step applied in water engineered systems for nitrogen removal. Temperature variation due to seasonal changes is a great challenge for maintaining nitrogen removal efficiency in water engineered ecosystems by affecting nitrifier activities. Research on the abundance, activity, and metabolic characteristics of nitrifiers can provide information for selecting suitable design parameters to ensure efficient nitrogen removal in different seasons. To date, the temperature-related niche separation of comammox, a newly discovered nitrifier with potential high-growth yield, has been rarely investigated. This study addressed the distribution of comammox and canonical nitrifying guilds in drinking water treatment plants (DWTPs) and wastewater treatment plants (WWTPs) in different seasons. qPCR-based surveys showed that comammox ubiquitously distributed and greatly outnumbered other ammonia-oxidizing prokaryotes in both DWTPs and WWTPs, except in Aug samples from DWTPs, suggesting the potential competitive advantage of AOA in summer. The nitrificans-like comammox and nitrosa-like comammox comprised the majority of the comammox community in DWTPs and WWTPs, respectively, and COD and NH4[+] concentrations significantly contributed to the distinct comammox phylotype distribution between DWTPs and WWTPs. The temperature-related distribution pattern of the comammox community was observed at each site. Moreover, the network complex of comammox communities was highest in Dec at all the sites, possibly contributing to the survival of comammox community in low temperature conditions.},
}
@article {pmid33664141,
year = {2021},
author = {de Assis Costa, OY and Meima-Franke, M and Bodelier, PLE},
title = {Complete and Draft Genome Sequences of Aerobic Methanotrophs Isolated from a Riparian Wetland.},
journal = {Microbiology resource announcements},
volume = {10},
number = {9},
pages = {},
pmid = {33664141},
issn = {2576-098X},
abstract = {Wetlands are important sources of methane emissions, and the impacts of these emissions can be mitigated by methanotrophic bacteria. The genomes of methanotrophs Methylomonas sp. strain LL1 and Methylosinus sp. strain H3A, as well as Methylocystis sp. strains H4A, H15, H62, and L43, were sequenced and are reported here.},
}
@article {pmid33663865,
year = {2021},
author = {Petri, RM and Aditya, S and Humer, E and Zebeli, Q},
title = {Effect of an intramammary lipopolysaccharide challenge on the hindgut microbial composition and fermentation of dairy cattle experiencing intermittent subacute ruminal acidosis.},
journal = {Journal of dairy science},
volume = {104},
number = {5},
pages = {5417-5431},
doi = {10.3168/jds.2020-19496},
pmid = {33663865},
issn = {1525-3198},
mesh = {*Acidosis/metabolism/veterinary ; Animals ; Cattle ; *Cattle Diseases/metabolism ; Diet/veterinary ; Female ; Fermentation ; Hydrogen-Ion Concentration ; Lactation ; Lipopolysaccharides/metabolism ; Pregnancy ; Rumen/metabolism ; },
abstract = {Feeding grain-rich diets often results in subacute ruminal acidosis (SARA), a condition associated with ruminal dysbiosis and systemic inflammation. Yet, the effect of SARA on hindgut microbiota, and whether this condition is aggravated by exogenous immune stimuli, is less understood. Therefore, the aims of this study were to determine the effects of an intermittent high-grain SARA model on the hindgut microbial community, and to evaluate whether the effects of SARA on the fecal microbiome and fermentation were further affected by an intramammary lipopolysaccharide (LPS) challenge. A total of 18 early-lactating Simmental cows were divided into 3 groups (n = 6); 2 were fed a SARA-inducing feeding regimen (60% concentrate), 1 was fed a control (CON) diet (40% concentrate). On d 30, 1 SARA group (SARA-LPS) and the CON group (CON-LPS) were intramammarily challenged with a single dose of 50 µg of LPS from Escherichia coli O26:B6, whereas the remaining 6 SARA cows (SARA-PLA) received a placebo. Using a longitudinal randomized controlled design, with grouping according to parity and days in milk), statistical analysis was performed with baseline measurements used as a covariate in a mixed model procedure. The SARA-inducing feeding challenge resulted in decreased fecal pH and increased butyrate as a proportion of total short-chain fatty acids in the feces. On d 30, SARA-challenged cows had decreased fecal diversity as shown by the Shannon and Chao1 indices and a decrease in the relative abundance of Euryarchaeota and cellulolytic genera, and numerical increases in the relative abundance of several Firmicutes associated with starch and secondary fermentation. The LPS challenge did not affect the fecal pH and short-chain fatty acids, but increased the Chao1 richness index in an interaction with the SARA challenge, and affected the relative abundance of Verrucomicrobia (1.13%), Actinobacteria (0.19%), and Spirochaetes (0.002%), suggesting an effect on the microbial ecology of the hindgut during SARA conditions. In conclusion, the SARA-inducing feeding regimen promoted important microbial changes at d 30, including reduced diversity and evenness compared with CON, whereas the external LPS challenge led to changes in the microbial community without affecting fecal fermentation properties.},
}
@article {pmid33661311,
year = {2021},
author = {González-Olalla, JM and Medina-Sánchez, JM and Norici, A and Carrillo, P},
title = {Regulation of Phagotrophy by Prey, Low Nutrients, and Low Light in the Mixotrophic Haptophyte Isochrysis galbana.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {981-993},
pmid = {33661311},
issn = {1432-184X},
support = {CGL2015-67682-R//Ministerio de Econom&#xed;a y Competitividad/ ; GA&#x10c;R 16-16343S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; FPU14/00977//Ministerio de Educaci&#xf3;n of Spanish Government/ ; },
mesh = {Autotrophic Processes ; Bacteria ; *Haptophyta ; Light ; Nutrients ; Phosphorus ; },
abstract = {Mixotrophy combines autotrophy and phagotrophy in the same cell. However, it is not known to what extent the phagotrophy influences metabolism, cell composition, and growth. In this work, we assess, on the one hand (first test), the role of phagotrophy on the elemental and biochemical composition, cell metabolism, and enzymes related to C, N, and S metabolism of Isochrysis galbana Parke, 1949. On the other hand, we study how a predicted increase of phagotrophy under environmental conditions of low nutrients (second test) and low light (third test) can affect its metabolism and growth. Our results for the first test revealed that bacterivory increased the phosphorous and iron content per cell, accelerating cell division and improving the cell fitness; in addition, the stimulation of some C and N enzymatic routes help to maintain, to some degree, compositional homeostasis. Under nutrient or light scarcity, I. galbana grew more slowly despite greater bacterial consumption, and the activities of key enzymes involved in C, N, and S metabolism changed according to a predominantly phototrophic strategy of nutrition in this alga. Contrary to recent studies, the stimulation of phagotrophy under low nutrient and low irradiance did not imply greater and more efficient C flux.},
}
@article {pmid33660069,
year = {2021},
author = {Wang, H and Li, X and Li, X and Li, F and Su, Z and Zhang, H},
title = {Community Composition and Co-Occurrence Patterns of Diazotrophs along a Soil Profile in Paddy Fields of Three Soil Types in China.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {961-970},
pmid = {33660069},
issn = {1432-184X},
support = {XDB15010101//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. 41671258//National Natural Science Foundation of China/ ; },
mesh = {*Bradyrhizobium ; Nitrogen/analysis ; Nitrogen Fixation ; *Soil ; Soil Microbiology ; },
abstract = {Diazotrophs play a key role in biological nitrogen (N2) fixation. However, we know little about the distribution of the diazotrophic community along the soil profile in paddy fields. Here, we used Illumina MiSeq sequencing, targeting the nitrogenase reductase (nifH) gene, to investigate changes with depth (0-100 cm) in the diazotrophic community in paddy soils of three regions (Changshu, Hailun, and Yingtan) in China. The results indicated that most diazotrophs belonged to the phylum Proteobacteria, accounting for 78.05% of the total number of sequences. The diazotrophic diversity was generally highest in the 10-20 cm layer, and then significantly decreased with soil depth. Principal coordinate analysis and PERMANOVA indicated that the diazotrophic community structure was significantly affected by region and soil depth. There were obvious differences in the composition of the diazotrophic community between the topsoil (0-40 cm) and the subsoil (40-100 cm). Anaeromyxobacter, Sideroxydans, Methylomonas, Nostoc, Methanocella, and Methanosaeta were enriched in the topsoil, while Geobacter, Azoarcus, Bradyrhizobium, and Dechloromonas were concentrated in the subsoil. Furthermore, co-occurrence network analysis showed that the diazotrophic network in the topsoil was more complex than that in the subsoil. Distance-based redundancy analysis indicated that soil total C and N content and pH were the main factors influencing the vertical variation in the diazotrophic community. These results highlighted that depth has a great impact on the diazotrophic diversity, community composition, and co-occurrence patterns in paddy soil.},
}
@article {pmid33659955,
year = {2020},
author = {Ross, BN and Whiteley, M},
title = {Ignoring social distancing: advances in understanding multi-species bacterial interactions.},
journal = {Faculty reviews},
volume = {9},
number = {},
pages = {23},
pmid = {33659955},
issn = {2732-432X},
abstract = {Almost every ecosystem on this planet is teeming with microbial communities made of diverse bacterial species. At a reductionist view, many of these bacteria form pairwise interactions, but, as the field of view expands, the neighboring organisms and the abiotic environment can play a crucial role in shaping the interactions between species. Over the years, a strong foundation of knowledge has been built on isolated pairwise interactions between bacteria, but now the field is advancing toward understanding how cohabitating bacteria and natural surroundings affect these interactions. Use of bottom-up approaches, piecing communities together, and top-down approaches that deconstruct communities are providing insight on how different species interact. In this review, we highlight how studies are incorporating more complex communities, mimicking the natural environment, and recurring findings such as the importance of cooperation for stability in harsh environments and the impact of bacteria-induced environmental pH shifts. Additionally, we will discuss how omics are being used as a top-down approach to identify previously unknown interspecies bacterial interactions and the challenges of these types of studies for microbial ecology.},
}
@article {pmid33659338,
year = {2020},
author = {Marinkovic, ZS and Vulin, C and Acman, M and Song, X and Di Meglio, JM and Lindner, AB and Hersen, P},
title = {Observing Nutrient Gradients, Gene Expression and Growth Variation Using the "Yeast Machine" Microfluidic Device.},
journal = {Bio-protocol},
volume = {10},
number = {13},
pages = {e3668},
pmid = {33659338},
issn = {2331-8325},
abstract = {The natural environment of microbial cells like bacteria and yeast is often a complex community in which growth and internal organization reflect morphogenetic processes and interactions that are dependent on spatial position and time. While most of research is performed in simple homogeneous environments (e.g., bulk liquid cultures), which cannot capture full spatiotemporal community dynamics, studying biofilms or colonies is complex and usually does not give access to the spatiotemporal dynamics at single cell level. Here, we detail a protocol for generation of a microfluidic device, the "yeast machine", with arrays of long monolayers of yeast colonies to advance the global understanding of how intercellular metabolic interactions affect the internal structure of colonies within defined and customizable spatial dimensions. With Saccharomyces cerevisiae as a model yeast system we used the "yeast machine" to demonstrate the emergence of glucose gradients by following expression of fluorescently labelled hexose transporters. We further quantified the expression spatial patterns with intra-colony growth rates and expression of other genes regulated by glucose availability. In addition to this, we showed that gradients of amino acids also form within a colony, potentially opening similar approaches to study spatiotemporal formation of gradients of many other nutrients and metabolic waste products. This approach could be used in the future to decipher the interplay between long-range metabolic interactions, cellular development, and morphogenesis in other same species or more complex multi-species systems at single-cell resolution and timescales relevant to ecology and evolution.},
}
@article {pmid33658719,
year = {2021},
author = {Graf, JS and Schorn, S and Kitzinger, K and Ahmerkamp, S and Woehle, C and Huettel, B and Schubert, CJ and Kuypers, MMM and Milucka, J},
title = {Anaerobic endosymbiont generates energy for ciliate host by denitrification.},
journal = {Nature},
volume = {591},
number = {7850},
pages = {445-450},
pmid = {33658719},
issn = {1476-4687},
mesh = {Adenosine Triphosphate/metabolism ; *Anaerobiosis ; Bacteria/genetics/*metabolism ; Biological Evolution ; Cell Respiration ; Ciliophora/chemistry/cytology/*metabolism ; Citric Acid Cycle/genetics ; *Denitrification ; Electron Transport/genetics ; *Energy Metabolism ; Genome, Bacterial/genetics ; *Host Microbial Interactions/genetics ; Mitochondria ; Nitrates/metabolism ; Oxygen/metabolism ; Phylogeny ; *Symbiosis ; },
abstract = {Mitochondria are specialized eukaryotic organelles that have a dedicated function in oxygen respiration and energy production. They evolved about 2 billion years ago from a free-living bacterial ancestor (probably an alphaproteobacterium), in a process known as endosymbiosis[1,2]. Many unicellular eukaryotes have since adapted to life in anoxic habitats and their mitochondria have undergone further reductive evolution[3]. As a result, obligate anaerobic eukaryotes with mitochondrial remnants derive their energy mostly from fermentation[4]. Here we describe 'Candidatus Azoamicus ciliaticola', which is an obligate endosymbiont of an anaerobic ciliate and has a dedicated role in respiration and providing energy for its eukaryotic host. 'Candidatus A. ciliaticola' contains a highly reduced 0.29-Mb genome that encodes core genes for central information processing, the electron transport chain, a truncated tricarboxylic acid cycle, ATP generation and iron-sulfur cluster biosynthesis. The genome encodes a respiratory denitrification pathway instead of aerobic terminal oxidases, which enables its host to breathe nitrate instead of oxygen. 'Candidatus A. ciliaticola' and its ciliate host represent an example of a symbiosis that is based on the transfer of energy in the form of ATP, rather than nutrition. This discovery raises the possibility that eukaryotes with mitochondrial remnants may secondarily acquire energy-providing endosymbionts to complement or replace functions of their mitochondria.},
}
@article {pmid33656687,
year = {2021},
author = {Ceola, G and Goss-Souza, D and Alves, J and Alves da Silva, A and Stürmer, SL and Baretta, D and Sousa, JP and Klauberg-Filho, O},
title = {Biogeographic Patterns of Arbuscular Mycorrhizal Fungal Communities Along a Land-Use Intensification Gradient in the Subtropical Atlantic Forest Biome.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {942-960},
pmid = {33656687},
issn = {1432-184X},
support = {CNPq-SisBiota 563251/2010-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Biodiversity ; Ecosystem ; Forests ; Fungi ; *Mycobiome ; *Mycorrhizae/genetics ; Soil ; Soil Microbiology ; },
abstract = {Information concerning arbuscular mycorrhizal (AM) fungal geographical distribution in tropical and subtropical soils from the Atlantic Forest (a global hotspot of biodiversity) are scarce and often restricted to the evaluation of richness and abundance of AM fungal species at specific ecosystems or local landscapes. In this study, we hypothesized that AM fungal diversity and community composition in subtropical soils would display fundamental differences in their geographical patterns, shaped by spatial distance and land-use change, at local and regional scales. AM fungal community composition was examined by spore-based taxonomic analysis, using soil trap cultures. Acaulospora koskei and Glomus were found as generalists, regardless of mesoregions and land uses. Other Acaulospora species were also found generalists within mesoregions. Land-use change and intensification did not influence AM fungal composition, partially rejecting our first hypothesis. We then calculated the distance-decay of similarities among pairs of AM fungal communities and the distance-decay relationship within and over mesoregions. We also performed the Mantel test and redundancy analysis to discriminate the main environmental drivers of AM fungal diversity and composition turnover. Overall, we found significant distance-decays for all land uses. We also observed a distance-decay relationship within the mesoregion scale (< 104 km) and these changes were correlated mainly to soil type (not land use), with the secondary influence of both total organic carbon and clay contents. AM fungal species distribution presented significant distance-decays, regardless of land uses, which was indicative of dispersal limitation, a stochastic neutral process. Although, we found evidence that, coupled with dispersal limitation, niche differentiation also played a role in structuring AM fungal communities, driven by long-term historical contingencies, as represented by soil type, resulting from different soil origin and mineralogy across mesoregions.},
}
@article {pmid33656686,
year = {2021},
author = {Salawu-Rotimi, A and Lebre, PH and Vos, HC and Fister, W and Kuhn, N and Eckardt, FD and Cowan, DA},
title = {Gone with the Wind: Microbial Communities Associated with Dust from Emissive Farmlands.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {859-869},
pmid = {33656686},
issn = {1432-184X},
support = {107803//National Research Foundation (ZA)/ ; },
mesh = {Bacteria/genetics ; *Dust/analysis ; Farms ; *Microbiota ; Soil Microbiology ; },
abstract = {Dust is a major vehicle for the dispersal of microorganisms across the globe. While much attention has been focused on microbial dispersal in dust plumes from major natural dust sources, very little is known about the fractionation processes that select for the "dust microbiome." The recent identification of highly emissive, agricultural land dust sources in South Africa has provided the opportunity to study the displacement of microbial communities through dust generation and transport. In this study, we aimed to document the microbial communities that are carried in the dust from one of South Africa's most emissive locations, and to investigate the selective factors that control the partitioning of microbial communities from soil to dust. For this purpose, dust samples were generated at different emission sources using a Portable In-Situ Wind Erosion Lab (PI-SWERL), and the taxonomic composition of the resulting microbiomes was compared with the source soils. Dust emission processes resulted in the clear fractionation of the soil bacterial community, where dust samples were significantly enriched in spore-forming taxa. Conversely, little fractionation was observed in the soil fungal communities, such that the dust fungal fingerprint could be used to identify the source soil. Dust microbiomes were also found to vary according to the emission source, suggesting that land use significantly affected the structure and fractionation of microbial communities transported in dust plumes. In addition, several potential biological allergens of fungal origin were detected in the dust microbiomes, highlighting the potential detrimental effects of dust plumes emitted in South Africa. This study represents the first description of the fractionation of microbial taxa occurring at the source of dust plumes and provides a direct link between land use and its impact on the dust microbiome.},
}
@article {pmid33653941,
year = {2021},
author = {Belk, AD and Duarte, T and Quinn, C and Coil, DA and Belk, KE and Eisen, JA and Quinn, JC and Martin, JN and Yang, X and Metcalf, JL},
title = {Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics.},
journal = {mSystems},
volume = {6},
number = {2},
pages = {},
pmid = {33653941},
issn = {2379-5077},
abstract = {The United States' large-scale poultry meat industry is energy and water intensive, and opportunities may exist to improve sustainability during the broiler chilling process. By USDA regulation, after harvest the internal temperature of the chicken must be reduced to 40°F or less within 16 h to inhibit bacterial growth that would otherwise compromise the safety of the product. This step is accomplished most commonly by water immersion chilling in the United States, while air chilling methods dominate other global markets. A comprehensive understanding of the differences between these chilling methods is lacking. Therefore, we assessed the meat quality, shelf-life, microbial ecology, and techno-economic impacts of chilling methods on chicken broilers in a university meat laboratory setting. We discovered that air chilling methods resulted in superior chicken odor and shelf-life, especially prior to 14 days of dark storage. Moreover, we demonstrated that air chilling resulted in a more diverse microbiome that we hypothesize may delay the dominance of the spoilage organism Pseudomonas Finally, a techno-economic analysis highlighted potential economic advantages to air chilling compared to water chilling in facility locations where water costs are a more significant factor than energy costs.IMPORTANCE As the poultry industry works to become more sustainable and to reduce the volume of food waste, it is critical to consider points in the processing system that can be altered to make the process more efficient. In this study, we demonstrate that the method used during chilling (air versus water chilling) influences the final product microbial community, quality, and physiochemistry. Notably, the use of air chilling appears to delay the bloom of Pseudomonas spp. that are the primary spoilers in packaged meat products. By using air chilling to reduce carcass temperatures instead of water chilling, producers may extend the time until spoilage of the products and, depending on the cost of water in the area, may have economic and sustainability advantages. As a next step, a similar experiment should be done in an industrial setting to confirm these results generated in a small-scale university lab facility.},
}
@article {pmid33653887,
year = {2021},
author = {Yanuka-Golub, K and Dubinsky, V and Korenblum, E and Reshef, L and Ofek-Lalzar, M and Rishpon, J and Gophna, U},
title = {Anode Surface Bioaugmentation Enhances Deterministic Biofilm Assembly in Microbial Fuel Cells.},
journal = {mBio},
volume = {12},
number = {2},
pages = {},
pmid = {33653887},
issn = {2150-7511},
mesh = {Bacteria/genetics/growth &amp; development ; *Biodegradation, Environmental ; Bioelectric Energy Sources/microbiology ; Biofilms/*growth &amp; development ; *Electrodes ; *Microbiota ; Wastewater/microbiology ; Water Purification/*methods ; },
abstract = {Microbial fuel cells (MFCs) generate energy while aiding the biodegradation of waste through the activity of an electroactive mixed biofilm. Metabolic cooperation is essential for MFCs' efficiency, especially during early colonization. Thus, examining specific ecological processes that drive the assembly of anode biofilms is highly important for shortening startup times and improving MFC performance, making this technology cost-effective and sustainable. Here, we use metagenomics to show that bioaugmentation of the anode surface with a taxonomically defined electroactive consortium, dominated by Desulfuromonas, resulted in an extremely rapid current density generation. Conversely, the untreated anode surface resulted in a highly stochastic and slower biofilm assembly. Remarkably, an efficient anode colonization process was obtained only if wastewater was added, leading to a nearly complete replacement of the bioaugmented community by Geobacter lovleyi Although different approaches to improve MFC startup have been investigated, we propose that only the combination of anode bioaugmentation with wastewater inoculation can reduce stochasticity. Such an approach provides the conditions that support the growth of specific newly arriving species that positively support the fast establishment of a highly functional anode biofilm.IMPORTANCE Mixed microbial communities play important roles in treating wastewater, in producing renewable energy, and in the bioremediation of pollutants in contaminated environments. While these processes are well known, especially the community structure and biodiversity, how to efficiently and robustly manage microbial community assembly remains unknown. Moreover, it has been shown that a high degree of temporal variation in microbial community composition and structure often occurs even under identical environmental conditions. This heterogeneity is directly related to stochastic processes involved in microbial community organization, similarly during the initial stages of biofilm formation on surfaces. In this study, we show that anode surface pretreatment alone is not sufficient for a substantial improvement in startup times in microbial fuel cells (MFCs), as previously thought. Rather, we have discovered that the combination of applying a well-known consortium directly on the anode surface together with wastewater (including the bacteria that they contain) is the optimized management scheme. This allowed a selected colonization process by the wastewater species, which improved the functionality relative to that of untreated systems.},
}
@article {pmid33652267,
year = {2021},
author = {Pavlovic, J and Cavalieri, D and Mastromei, G and Pangallo, D and Perito, B and Marvasi, M},
title = {MinION technology for microbiome sequencing applications for the conservation of cultural heritage.},
journal = {Microbiological research},
volume = {247},
number = {},
pages = {126727},
doi = {10.1016/j.micres.2021.126727},
pmid = {33652267},
issn = {1618-0623},
mesh = {Bacteria/classification/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Metagenomics/instrumentation/*methods ; Microbiota/*genetics ; Paintings ; Sequence Analysis, DNA ; Textiles ; },
abstract = {The MinION single-molecule sequencing system has been attracting the attention of the community of microbiologists involved in the conservation of cultural heritage. The use of MinION for the conservation of cultural heritage is extremely recent, but surprisingly the only few applications available have been exploring many different substrates: stone, textiles, paintings and wax. The use of MinION sequencing is mainly used to address the metataxonomy (with special emphasis on non-cultivable microorganisms) with the effort to identify species involved in the degradation of the substrates. In this review, we show the current applications available on different artworks, showing how this technology can be a useful tool for microbiologists and conservators also in light of its low cost and the easy chemistry.},
}
@article {pmid33649554,
year = {2021},
author = {Li, Z and Pan, D and Wei, G and Pi, W and Zhang, C and Wang, JH and Peng, Y and Zhang, L and Wang, Y and Hubert, CRJ and Dong, X},
title = {Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity.},
journal = {The ISME journal},
volume = {15},
number = {8},
pages = {2366-2378},
pmid = {33649554},
issn = {1751-7370},
support = {TPR 15-229/HX/HSRD VA/United States ; },
mesh = {*Geologic Sediments ; Methane ; *Microbiota ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.},
}
@article {pmid33643242,
year = {2021},
author = {Rüger, L and Feng, K and Dumack, K and Freudenthal, J and Chen, Y and Sun, R and Wilson, M and Yu, P and Sun, B and Deng, Y and Hochholdinger, F and Vetterlein, D and Bonkowski, M},
title = {Assembly Patterns of the Rhizosphere Microbiome Along the Longitudinal Root Axis of Maize (Zea mays L.).},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {614501},
pmid = {33643242},
issn = {1664-302X},
abstract = {It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil - their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize (Zea mays L.). We grew maize plants in an agricultural loamy soil and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of operational taxonomic unit (OTU) richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Further up the root where lateral roots emerged processes of community assembly appeared to be more deterministic (e.g., through competition and predation). This shift toward significance of deterministic processes was revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Such patterns were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is crucially important.},
}
@article {pmid33638074,
year = {2021},
author = {Koroleva, E and Mqulwa, AZ and Norris-Jones, S and Reed, S and Tambe, Z and Visagie, A and Jacobs, K},
title = {Impact of cigarette butts on bacterial community structure in soil.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {33638074},
issn = {1614-7499},
abstract = {Cigarette butts contribute significantly to global pollution present on the planet. The filters found in cigarette butts contain a microplastic, cellulose acetate, as well as toxic metals and metalloids which are responsible for pollution in the environment. Although cigarette butt litter is prevalent in many soils, research on the effects of these cigarette butts is limited. In this study, we used Automated Ribosomal Intergenic Spacer Analysis (ARISA) to generate DNA fingerprints of bacterial communities in soil before and after the addition of cigarette butt leachate treatments. An ICP-MS analysis of the biodegradable and non-biodegradable cigarette butts revealed the presence of various elements: Al, As, B, Ba, Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Pb, Sb, Se, Sn, Sr, V, and Zn. The analysis also specified which metals were present at the highest concentrations in the biodegradable and non-biodegradable cigarette butts, and these were, respectively, Al (1,31 g/kg and 2,35 g/kg), Fe (2,03 g/kg and 1,11 g/kg), and Zn (3,18 mg/kg and 15,70 mg/kg). Our results show that biodegradable cigarette butts had a significant effect on bacterial community composition (beta diversity), unlike the non-biodegradable butts. This effect can be attributed to higher concentrations of certain metals and metalloids in the leachate of biodegradable cigarette butts compared to the non-biodegradable ones. Our findings suggest that biodegradable and non-biodegradable cigarette butts can significantly affect bacterial communities in soil as a result of the leaching of significant quantities of certain elements into the surrounding soils.},
}
@article {pmid33637782,
year = {2021},
author = {Vashistha, G and Mungi, NA and Lang, JW and Ranjan, V and Dhakate, PM and Khudsar, FA and Kothamasi, D},
title = {Gharial nesting in a reservoir is limited by reduced river flow and by increased bank vegetation.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {4805},
pmid = {33637782},
issn = {2045-2322},
abstract = {The gharial (Gavialis gangeticus Gmelin) is a fish-eating specialist crocodylian, endemic to south Asia, and critically endangered in its few remaining wild localities. A secondary gharial population resides in riverine-reservoir habitat adjacent to the Nepal border, within the Katerniaghat Wildlife Sanctuary (KWS), and nests along a 10 km riverbank of the Girwa River. A natural channel shift in the mainstream Karnali River (upstream in Nepal) has reduced seasonal flow in the Girwa stretch where gharials nest, coincident with a gradual loss of nest sites, which in turn was related to an overall shift to woody vegetation at these sites. To understand how these changes in riparian vegetation on riverbanks were related to gharial nesting, we sampled vegetation at these sites from 2017 to 2019, and derived an Enhanced Vegetation Index (EVI) from LANDSAT 8 satellite data to quantify riverside vegetation from 1988 through 2019. We found that sampled sites transitioned to woody cover, the number of nesting sites declined, and the number of nests were reduced by > 40%. At these sites, after the channel shift, woody vegetation replaced open sites that predominated prior to the channel shift. Our findings indicate that the lack of open riverbanks and the increase in woody vegetation at potential nesting sites threatens the reproductive success of the KWS gharial population. This population persists today in a regulated river ecosystem, and nests in an altered riparian habitat which appears to be increasingly unsuitable for the continued successful recruitment of breeding adults. This second-ranking, critically endangered remnant population may have incurred an "extinction debt" by living in a reservoir that will lead to its eventual extirpation.},
}
@article {pmid33637572,
year = {2021},
author = {Wang, Z and Chen, Z and Kowalchuk, GA and Xu, Z and Fu, X and Kuramae, EE},
title = {Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {9},
pages = {},
pmid = {33637572},
issn = {1098-5336},
mesh = {*Agricultural Inoculants ; Bacteria/classification/genetics ; Hydrogen-Ion Concentration ; Juglandaceae/*growth &amp; development ; *Microbiota ; RNA, Ribosomal, 16S ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {To maintain the beneficial effects of microbial inoculants on plants and soil, repeated inoculation represents a promising option. Until now, the impacts of one-off inoculation on the native microbiome have been explored, but it remains unclear how long and to what extent the periodic inoculations would affect the succession of the resident microbiome in bulk soil. Here, we examined the dynamic responses of plant growth, soil functions, and the resident bacterial community in the bulk soil to periodic inoculations of phosphate-solubilizing and N2-fixing bacteria alone or in combination. Compared to single-strain inoculation, coinoculation better stimulated plant growth and soil nutrients. However, the benefits from inoculants did not increase with repeated inoculations and were not maintained after transplantation to a different site. In response to microbial inoculants, three patterns of shifts in the bacterial composition were observed: fold increase, fold decrease, and resilience. The periodic inoculations impacted the succession course of resident bacterial communities in bulk soil, mainly driven by changes in soil pH and nitrate, resulting in the development of three main cluster types throughout the investigation. The single and mixed inoculants transiently modulated the variation in the resident community in association with soil pH and the C/N ratio, but finally, the community established and showed resilience to subsequent inoculations. Consequently, the necessity of repeated inoculations should be reconsidered, and while the different microbial inoculants showed distinct impacts on resident microbiome succession, the communities ultimately exhibited resilience.IMPORTANCE Introducing beneficial microbes to the plant-soil system is an environmentally friendly approach to improve the crop yield and soil environment. Numerous studies have attempted to reveal the impacts of inoculation on the rhizosphere microbiome. However, little is known about the effectiveness of periodic inoculations on soil functioning. In addition, the long-term impact of repeated inoculations on the native community remains unclear. Here, we track the succession traits of the resident microbiome in the bulk soil across a growing season and identify the taxon clusters that respond differently to periodic inoculation. Crucially, we compare the development of the resident community composition with and without inoculation, thus providing new insight into the interactions between resident microbes and intruders. Finally, we conclude that initial inoculation plays a more important role in influencing the whole system, and the native microbial community exhibits traits of resilience, but no resistance, to the subsequent inoculations.},
}
@article {pmid33634334,
year = {2021},
author = {Srivastava, A and Mishra, S and Verma, D},
title = {Characterization of Oral Bacterial Composition of Adult Smokeless Tobacco Users from Healthy Indians Using 16S rDNA Analysis.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {1061-1073},
pmid = {33634334},
issn = {1432-184X},
support = {SB/YS/LS-102/2014//Science and Engineering Research Board/ ; F 30-442/2018/BSR//University Grants Commission/ ; },
mesh = {Adult ; Bacteria/genetics ; DNA, Ribosomal/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Tobacco, Smokeless ; },
abstract = {The present investigation is aiming to report the oral bacterial composition of smokeless tobacco (SLT) users and to determine the influence of SLT products on the healthy Indian population. With the aid of the V3 hypervariable region of the 16S rRNA gene, a total of 8,080,889 high-quality reads were clustered into 15 phyla and 180 genera in the oral cavity of the SLT users. Comparative analysis revealed a more diverse microbiome where two phyla and sixteen genera were significantly different among the SLT users as compared to the control group (p-value < 0.05). The prevalence of Fusobacteria-, Porphyromonas-, Desulfobulbus-, Enterococcus-, and Parvimonas-like genera among SLT users indicates altered bacterial communities among SLT users. Besides, the depletion of health-compatible bacteria such as Lactobacillus and Haemophilus also suggests poor oral health. Here, the majority of the altered genera belong to Gram-negative anaerobes that have been reported for assisting biofilm formation that leads in the progression of several oral diseases. The PICRUSt analysis further supports the hypothesis where a significant increase in the count of the genes involved in the metabolism of nitrogen, amino acids, and nicotinate/nicotinamide was observed among tobacco chewers. Moreover, this study has a high significance in Indian prospects where the SLT consumers are prevalent but we are deficient in information on their oral microbiome.},
}
@article {pmid33629948,
year = {2019},
author = {Cho, GY and Whang, KS},
title = {Sandarakinorhabdus rubra sp. nov., and Sandarakinorhabdus oryzae sp. nov., isolated from oxidized rice paddy soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {71},
number = {3},
pages = {},
doi = {10.1099/ijsem.0.004722},
pmid = {33629948},
issn = {1466-5034},
abstract = {Three Gram-stain-negative, motile or non-motile, rod-shaped, facultatively aerobic strains, designated MO-4[T], NP-34 and NM-18[T], were isolated from oxidized rice paddy soil in Chungbuk, Republic of Korea. Colonies were circular and convex with entire margins, red in colour on R2A after 3 days at 30 °C. The three strains grew at pH 5.0-10.0 (optimum, pH 8.0), at 15-45 °C (optimum, 30 °C) and at salinities of 0-1.5 % (w/v) NaCl (optimum, 0.4 % NaCl). The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the three isolates represent members of the genus Sandarakinorhabdus and strains MO-4[T] and NP-34 were most closely related to Sandarakinorhabdus cyanobacteriorum TH057[T] (97.7 %) and Sandarakinorhabdus limnophila DSM 17366[T] (97.1 %). NM-18[T] showed highest 16S rRNA gene sequence similarities to Sandarakinorhabdus limnophila DSM 17366[T] (98.7 %) and Sandarakinorhabdus cyanobacteriorum TH057[T] (96.7 %). Genomic similarities between strains MO-4[T] and NM-18[T] and the two type strains of species of the genus Sandarakinorhabdus based on average nucleotide identity and digital DNA-DNA hybridization values were lower than the species delineation thresholds. The major fatty acids were iso-C18 : 1 ω7c and summed feature 3. The DNA G+C contents of strains MO-4[T] and NM-18[T], obtained from genome sequencing data, were 67.6 and 66.6 mol%, respectively. On the basis of these genotypic and phenotypic characteristics, the three strains are assigned to two novel species of the genus Sandarakinorhabdus, for which the names Sandarakinorhabdus rubra sp. nov. (type strain MO-4[T] =KACC 21378=NBRC 114106) and Sandarakinorhabdus oryzae sp. nov. (type strain NM-18[T]=KACC 21379=NBRC 113957) are proposed.},
}
@article {pmid33629529,
year = {2021},
author = {Phillips, AA and Speth, DR and Miller, LG and Wang, XT and Wu, F and Medeiros, PM and Monteverde, DR and Osburn, MR and Berelson, WM and Betts, HL and Wijker, RS and Mullin, SW and Johnson, HA and Orphan, VJ and Fischer, WW and , and , and Sessions, AL},
title = {Microbial succession and dynamics in meromictic Mono Lake, California.},
journal = {Geobiology},
volume = {19},
number = {4},
pages = {376-393},
pmid = {33629529},
issn = {1472-4669},
mesh = {Bacteria ; California ; *Ecosystem ; *Lakes ; Phylogeny ; },
abstract = {Mono Lake is a closed-basin, hypersaline, alkaline lake located in Eastern Sierra Nevada, California, that is dominated by microbial life. This unique ecosystem offers a natural laboratory for probing microbial community responses to environmental change. In 2017, a heavy snowpack and subsequent runoff led Mono Lake to transition from annually mixed (monomictic) to indefinitely stratified (meromictic). We followed microbial succession during this limnological shift, establishing a two-year (2017-2018) water-column time series of geochemical and microbiological data. Following meromictic conditions, anoxia persisted below the chemocline and reduced compounds such as sulfide and ammonium increased in concentration from near 0 to ~400 and ~150 µM, respectively, throughout 2018. We observed significant microbial succession, with trends varying by water depth. In the epilimnion (above the chemocline), aerobic heterotrophs were displaced by phototrophic genera when a large bloom of cyanobacteria appeared in fall 2018. Bacteria in the hypolimnion (below the chemocline) had a delayed, but systematic, response reflecting colonization by sediment "seed bank" communities. Phototrophic sulfide-oxidizing bacteria appeared first in summer 2017, followed by microbes associated with anaerobic fermentation in spring 2018, and eventually sulfate-reducing taxa by fall 2018. This slow shift indicated that multi-year meromixis was required to establish a sulfate-reducing community in Mono Lake, although sulfide oxidizers thrive throughout mixing regimes. The abundant green alga Picocystis remained the dominant primary producer during the meromixis event, abundant throughout the water column including in the hypolimnion despite the absence of light and prevalence of sulfide. Our study adds to the growing literature describing microbial resistance and resilience during lake mixing events related to climatic events and environmental change.},
}
@article {pmid33629506,
year = {2021},
author = {Benítez-Páez, A and Hess, AL and Krautbauer, S and Liebisch, G and Christensen, L and Hjorth, MF and Larsen, TM and Sanz, Y and , },
title = {Sex, Food, and the Gut Microbiota: Disparate Response to Caloric Restriction Diet with Fiber Supplementation in Women and Men.},
journal = {Molecular nutrition &amp; food research},
volume = {65},
number = {8},
pages = {e2000996},
doi = {10.1002/mnfr.202000996},
pmid = {33629506},
issn = {1613-4133},
mesh = {Bacteroidetes ; Bile Acids and Salts/metabolism ; Biomarkers ; *Caloric Restriction ; Dietary Fiber/*pharmacology ; Dietary Supplements ; Fatty Acids, Volatile/blood/metabolism ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Multivariate Analysis ; Sex Factors ; Weight Loss ; },
abstract = {SCOPE: Dietary-based strategies are regularly explored in controlled clinical trials to provide cost-effective therapies to tackle obesity and its comorbidities. The article presents a complementary analysis based on a multivariate multi-omics approach of a caloric restriction intervention (CRD) with fiber supplementation to unveil synergic effects on body weight control, lipid metabolism, and gut microbiota.<br><br>METHODS AND RESULTS: The study explores fecal bile acids (BAs) and short-chain fatty acids (SCFAs), plasma BAs, and fecal shotgun metagenomics on 80 overweight participants of a 12-week caloric restriction clinical trial (-500&#xa0;kcal day[-1]) randomly allocated into fiber (10&#xa0;g day[-1] inulin + 10&#xa0;g day[-1] resistant maltodextrin) or placebo (maltodextrin) supplementation groups. The multi-omic data integration analysis uncovered the benefits of the fiber supplementation and/or the CRD (e.g., increase of Parabacteroides distasonis and fecal propionate), showing sex-specific effects on either adiposity and fasting insulin; effects thought to be linked to changes of specific gut microbiota species, functional genes, and bacterially produced metabolites like SCFAs and secondary BAs.<br><br>CONCLUSIONS: This study identifies diet-microbe-host interactions helping to design personalised interventions. It also suggests that sex perspective should be considered routinely in future studies on dietary interventions efficacy. All in all, the study uncovers that the dietary intervention is more beneficial for women than men.},
}
@article {pmid33629169,
year = {2021},
author = {Tang, Y and Ma, KY and Cheung, MK and Yang, CH and Wang, Y and Hu, X and Kwan, HS and Chu, KH},
title = {Gut Microbiota in Decapod Shrimps: Evidence of Phylosymbiosis.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {994-1007},
pmid = {33629169},
issn = {1432-184X},
support = {C4042-14G//Research Grants Council, Hong Kong SAR and the Hong Kong Branch of Southern Marine Science and Technology Guangdong Laboratory (Guangzhou), China/ ; },
mesh = {Animals ; *Decapoda ; *Gastrointestinal Microbiome ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; },
abstract = {Gut microbiota have long attracted the interest of scientists due to their profound impact on the well-being of animals. A non-random pattern of microbial assembly that results in a parallelism between host phylogeny and microbial similarity is described as phylosymbiosis. Phylosymbiosis has been consistently observed in different clades of animal hosts, but there have been no studies on crustaceans. In this study, we investigated whether host phylogeny has an impact on the gut microbiota assemblages in decapod shrimps. We examined the gut microbial communities in 20 shrimp species from three families inhabiting distinct environments, using metabarcoding analyses of the V1-V3 hypervariable region of the 16S rRNA gene. Gut microbial communities varied within each shrimp group but were generally dominated by Proteobacteria. A prevalent phylosymbiotic pattern in shrimps was evidenced for the first time by the observations of (1) the distinguishability of microbial communities among species within each group, (2) a significantly lower intraspecific than interspecific gut microbial beta diversity across shrimp groups, (3) topological congruence between host phylogenetic trees and gut microbiota dendrograms, and (4) a correlation between host genetic distances and microbial dissimilarities. Consistent signals of phylosymbiosis were observed across all groups in dendrograms based on the unweighted UniFrac distances at 99% operational taxonomic units (OTUs) level and in Mantel tests based on the weighted UniFrac distances based on 97% OTUs and amplicon sequence variants. Penaeids exhibited phylosymbiosis in most tests, while phylosymbiotic signals in atyids and pandalids were only detected in fewer than half of the tests. A weak phylogenetic signal was detected in the predicted functions of the penaeid gut microbiota. However, the functional diversities of the two caridean groups were not significantly related to host phylogeny. Our observations of a parallelism in the taxonomy of the gut microbiota with host phylogeny for all shrimp groups examined and in the predicted functions for the penaeid shrimps indicate a tight host-microbial relationship during evolution.},
}
@article {pmid33624262,
year = {2021},
author = {Cho, JC},
title = {Omics-based microbiome analysis in microbial ecology: from sequences to information.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {59},
number = {3},
pages = {229-232},
pmid = {33624262},
issn = {1976-3794},
mesh = {Bacteria/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Microbial Interactions ; *Microbiota ; },
abstract = {Microbial ecology is the study of microorganisms present in nature. It particularly focuses on microbial interactions with any biota and with surrounding environments. Microbial ecology is entering its golden age with innovative multi-omics methods triggered by next-generation sequencing technologies. However, the extraction of ecologically relevant information from ever-increasing omics data remains one of the most challenging tasks in microbial ecology. This special issue includes 11 review articles that provide an overview of the state of the art of omics-based approaches in the field of microbial ecology, with particular emphasis on the interpretation of omics data, environmental pollution tracking, interactions in microbiomes, and viral ecology.},
}
@article {pmid33624137,
year = {2021},
author = {Hyun, HR and Yoon, H and Lyou, ES and Kim, JJ and Kwon, SY and Lee, TK},
title = {Short-Term Legacy Effects of Mercury Contamination on Plant Growth and nifH-Harboring Microbial Community in Rice Paddy Soil.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {932-941},
pmid = {33624137},
issn = {1432-184X},
support = {918014-4//Strategic Initiative for Microbiomes in Agriculture and Food, Ministry of Agriculture, Food and Rural Affairs/ ; 2020002480003//Korea Ministry of Environment as Subsurface Environment Management Projects/ ; },
mesh = {*Mercury ; *Microbiota ; *Oryza ; Soil ; *Soil Pollutants/analysis ; },
abstract = {Methylmercury (MeHg), which is formed in rice paddy soil, exhibits strong neurotoxicity through bioaccumulation in the food chain. A few groups of microorganisms drive both mercury methylation and nitrogen fixation in the rhizosphere. Little is known about how the shifted soil microbial community by Hg contamination affects nitrogen fixation rate and plant growth in paddy soil. Here, we examined how stimulated short-term Hg amendment affects the nitrogen fixing microbial community and influences plant-microbe interactions. Soil was treated with low (0.2 mg/kg) and high (1.1 mg/kg) concentrations of Hg for 4 weeks; then, rice (Oryza sativa) was planted and grown for 12 weeks. The nitrogen-fixation rate and rice growth were measured. The diversity and structure of the microbial community were analyzed by sequencing the nifH gene before and after rice cultivation. Hg treatments significantly decreased the nitrogen fixation rate and dry weight of the rice plants. The structure of the nifH-harboring community was remarkably changed after rice cultivation depending on Hg treatments. Iron- or sulfate-reducing bacteria, including Desulfobacca, Desulfoporosimus, and Geobacter, were observed as legacy response groups; their abundances increased in the soil after Hg treatment. The high abundance of those groups were maintained in control, but the abundance drastically decreased after rice cultivation in the soil treated with Hg, indicating that symbiotic behavior of rice plants changes according to the legacy effects on Hg contamination. These results suggested that Hg contamination can persist in soil microbial communities, affecting their nitrogen-fixation ability and symbiosis with rice plants in paddy soil.},
}
@article {pmid33614160,
year = {2021},
author = {Zwart, MP and Blanc, S and Johnson, M and Manrubia, S and Michalakis, Y and Sofonea, MT},
title = {Unresolved advantages of multipartitism in spatially structured environments.},
journal = {Virus evolution},
volume = {7},
number = {1},
pages = {veab004},
pmid = {33614160},
issn = {2057-1577},
abstract = {Multipartite viruses have segmented genomes and package each of their genome segments individually into distinct virus particles. Multipartitism is common among plant viruses, but why this apparently costly genome organization and packaging has evolved remains unclear. Recently Zhang and colleagues developed network epidemiology models to study the epidemic spread of multipartite viruses and their distribution over plant and animal hosts (Phys. Rev. Lett. 2019, 123, 138101). In this short commentary, we call into question the relevance of these results because of key model assumptions. First, the model of plant hosts assumes virus transmission only occurs between adjacent plants. This assumption overlooks the basic but imperative fact that most multipartite viruses are transmitted over variable distances by mobile animal vectors, rendering the model results irrelevant to differences between plant and animal hosts. Second, when not all genome segments of a multipartite virus are transmitted to a host, the model assumes an incessant latent infection occurs. This is a bold assumption for which there is no evidence to date, making the relevance of these results to understanding multipartitism questionable.},
}
@article {pmid33613641,
year = {2021},
author = {Gil, J and Andrade-Martínez, JS and Duitama, J},
title = {Accurate, Efficient and User-Friendly Mutation Calling and Sample Identification for TILLING Experiments.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {624513},
pmid = {33613641},
issn = {1664-8021},
abstract = {TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful reverse genetics method in plant functional genomics and breeding to identify mutagenized individuals with improved behavior for a trait of interest. Pooled high throughput sequencing (HTS) of the targeted genes allows efficient identification and sample assignment of variants within genes of interest in hundreds of individuals. Although TILLING has been used successfully in different crops and even applied to natural populations, one of the main issues for a successful TILLING experiment is that most currently available bioinformatics tools for variant detection are not designed to identify mutations with low frequencies in pooled samples or to perform sample identification from variants identified in overlapping pools. Our research group maintains the Next Generation Sequencing Experience Platform (NGSEP), an open source solution for analysis of HTS data. In this manuscript, we present three novel components within NGSEP to facilitate the design and analysis of TILLING experiments: a pooled variants detector, a sample identifier from variants detected in overlapping pools and a simulator of TILLING experiments. A new implementation of the NGSEP calling model for variant detection allows accurate detection of low frequency mutations within pools. The samples identifier implements the process to triangulate the mutations called within overlapping pools in order to assign mutations to single individuals whenever possible. Finally, we developed a complete simulator of TILLING experiments to enable benchmarking of different tools and to facilitate the design of experimental alternatives varying the number of pools and individuals per pool. Simulation experiments based on genes from the common bean genome indicate that NGSEP provides similar accuracy and better efficiency than other tools to perform pooled variants detection. To the best of our knowledge, NGSEP is currently the only tool that generates individual assignments of the mutations discovered from the pooled data. We expect that this development will be of great use for different groups implementing TILLING as an alternative for plant breeding and even to research groups performing pooled sequencing for other applications.},
}
@article {pmid33613482,
year = {2021},
author = {Chang, J and Sun, Y and Tian, L and Ji, L and Luo, S and Nasir, F and Kuramae, EE and Tian, C},
title = {The Structure of Rhizosphere Fungal Communities of Wild and Domesticated Rice: Changes in Diversity and Co-occurrence Patterns.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {610823},
pmid = {33613482},
issn = {1664-302X},
abstract = {The rhizosphere fungal community affects the ability of crops to acquire nutrients and their susceptibility to pathogen invasion. However, the effects of rice domestication on the diversity and interactions of rhizosphere fungal community still remain largely unknown. Here, internal transcribed spacer amplicon sequencing was used to systematically analyze the structure of rhizosphere fungal communities of wild and domesticated rice. The results showed that domestication increased the alpha diversity indices of the rice rhizosphere fungal community. The changes of alpha diversity index may be associated with the enrichment of Acremonium, Lecythophora, and other specific rare taxa in the rhizosphere of domesticated rice. The co-occurrence network showed that the complexity of wild rice rhizosphere fungal community was higher than that of the domesticated rice rhizosphere fungal community. Arbuscular mycorrhizal fungi (AMF) and soilborne fungi were positively and negatively correlated with more fungi in the wild rice rhizosphere, respectively. For restructuring the rhizomicrobial community of domesticated crops, we hypothesize that microbes that hold positive connections with AMF and negative connections with soilborne fungi can be used as potential sources for bio-inoculation. Our findings provide a scientific basis for reshaping the structure of rhizomicrobial community and furthermore create potential for novel intelligent and sustainable agricultural solutions.},
}
@article {pmid33612832,
year = {2021},
author = {Patin, NV and Dietrich, ZA and Stancil, A and Quinan, M and Beckler, JS and Hall, ER and Culter, J and Smith, CG and Taillefert, M and Stewart, FJ},
title = {Gulf of Mexico blue hole harbors high levels of novel microbial lineages.},
journal = {The ISME journal},
volume = {15},
number = {8},
pages = {2206-2232},
pmid = {33612832},
issn = {1751-7370},
mesh = {*Archaea ; Bacteria/genetics ; Florida ; Gulf of Mexico ; *Metagenomics ; },
abstract = {Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole's rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.},
}
@article {pmid33609143,
year = {2021},
author = {Green, EA and Smedley, SR and Klassen, JL},
title = {North American Fireflies Host Low Bacterial Diversity.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {793-804},
pmid = {33609143},
issn = {1432-184X},
mesh = {Animals ; Bacteria/genetics ; Female ; *Fireflies ; Male ; *Microbiota ; North America ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Although there are numerous studies of firefly mating flashes, lantern bioluminescence, and anti-predation lucibufagin metabolites, almost nothing is known about their microbiome. We therefore used 16S rRNA community amplicon sequencing to characterize the gut and body microbiomes of four North American firefly taxa: Ellychnia corrusca, the Photuris versicolor species complex, Pyractomena borealis, and Pyropyga decipiens. These firefly microbiomes all have very low species diversity, often dominated by a single species, and each firefly type has a characteristic microbiome. Although the microbiomes of male and female fireflies did not differ from each other, Ph. versicolor gut and body microbiomes did, with their gut microbiomes being enriched in Pseudomonas and Acinetobacter. Ellychnia corrusca egg and adult microbiomes were unique except for a single egg microbiome that shared a community type with E. corrusca adults, which could suggest microbial transmission from mother to offspring. Mollicutes that had been previously isolated from fireflies were common in our firefly microbiomes. These results set the stage for further research concerning the function and transmission of these bacterial symbionts.},
}
@article {pmid33606088,
year = {2021},
author = {Tatsumi, C and Azuma, WA and Ogawa, Y and Komada, N},
title = {Nitrogen Availability and Microbial Communities of Canopy Soils in a Large Cercidiphyllum japonicum Tree of a Cool-Temperate Old Growth Forest.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {919-931},
pmid = {33606088},
issn = {1432-184X},
support = {17J07686//Grant-in-Aid for JSPS Research Fellow/ ; },
mesh = {Forests ; *Microbiota ; Nitrogen/analysis ; Soil ; Soil Microbiology ; *Trees ; },
abstract = {Canopy soils on large trees are important for supporting the lives of many canopy plants, and thereby increasing regional biodiversity. However, because of the less accessibility to canopy soils, there is insufficient knowledge on how canopy soils produce available nitrogen (N) for canopy plants through the activity of canopy soil microbes. Canopy soils usually have different soil properties from ground soils, so we hypothesized that canopy soils would have unique microbial communities compared to ground soils, but still provide available N for canopy plants. Here, we compared soil N availability, including net N mineralization and nitrification rate, and microbial communities between canopy soils (organic soils) collected at various heights of a large Cercidiphyllum japonicum tree and ground soils (organic and mineral soils) in a cool-temperate old-growth forest of Japan. The canopy soils had significantly different N availability (mass-based higher but volume-based lower) and microbial communities from the ground mineral soils. Among organic soils, the height of the soil had an impact on the microbial communities but not on the N availability, which agreed with our hypothesis. Despite the decrease in fungal abundance in the higher soils, the increase in certain components of the cellulose-decomposing fungi and oligotrophic bacteria may contribute to the available N production. Also, the abundance of ammonia-oxidizers did not change with the height, which would be important for the nitrification rate. Our study implied canopy soils could provide N to canopy plants partly through the functional redundancy within different microbial communities and constant population of ammonia-oxidizers.},
}
@article {pmid33606087,
year = {2021},
author = {Dlamini, ST and Jaiswal, SK and Mohammed, M and Dakora, FD},
title = {Studies of Phylogeny, Symbiotic Functioning and Ecological Traits of Indigenous Microsymbionts Nodulating Bambara Groundnut (Vigna subterranea L. Verdc) in Eswatini.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {688-703},
pmid = {33606087},
issn = {1432-184X},
mesh = {Bradyrhizobium ; Eswatini ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant ; *Vigna ; },
abstract = {Rhizobial microsymbionts of grain legumes are ubiquitous in soils and exhibit a wide range of diversity with respect to colony morphology, genetic variability, biochemical characteristics, and phylogenetic relationships. This study assessed the phylogenetic positions of rhizobial microsymbionts of Bambara groundnut from Eswatini exhibiting variations in morpho-physiology, adaptive characteristics, and N2-fixing efficiency. The isolates' ERIC-PCR profiles revealed the presence of high genetic variation among them. These test isolates also exhibited differences in pH tolerance and IAA production. Multilocus sequence analysis based on the 16S rRNA, atpD, glnII, gyrB, and recA gene sequences of representative test isolates closely aligned them to the type strains of Bradyrhizobium arachidis, B. manausense, B. guangdongense, B. elkanii, and B. pachyrhizi. However, some isolates showed a high divergence from the known reference type strains, indicating that they may represent species yet to be properly characterized and described. Functional characterization in the glasshouse revealed that most of the isolates from the contrasting Agro-ecologies of Eswatini were efficient in N2 fixation, and therefore elicited greater stomatal conductance and photosynthetic rates in the homologous Bambara groundnut. Of the 75 isolates tested, 51% were more effective than the commercial Bradyrhizobium sp. strain CB756, with relative symbiotic effectiveness ranging from 138 to 308%. The findings of this study indicated that the analysis of housekeeping genes and functional traits of Bambara-nodulating microsymbionts can provide a clear view for understanding and predicting rhizobial community structure across environmental gradients.},
}
@article {pmid33604703,
year = {2021},
author = {Ritter, CD and Forster, D and Azevedo, JAR and Antonelli, A and Nilsson, RH and Trujillo, ME and Dunthorn, M},
title = {Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {746-760},
pmid = {33604703},
issn = {1432-184X},
mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Forests ; Rainforest ; Soil Microbiology ; },
abstract = {Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here, we used DNA metabarcoding data from litter and mineral soils collected from a longitudinal transect in Amazonia to explore patterns of co-occurrence. We compared data from different Amazonian habitat types, each with a characteristic biota and environmental conditions. These included non-flooded rainforests (terra-firme), forests seasonally flooded by fertile white waters (várzeas) or by unfertile black waters (igapós), and open areas associated with white sand soil (campinas). We ran co-occurrence network analyses based on null models and Spearman correlation for all samples and for each habitat separately. We found that one third of all operational taxonomic units (OTUs) were bacteria and two thirds were eukaryotes. The resulting networks were nevertheless mostly composed of bacteria, with fewer fungi, protists, and metazoans. Considering the functional traits of the OTUs, there is a combination of metabolism modes including respiration and fermentation for bacteria, and a high frequency of saprotrophic fungi (those that feed on dead organic matter), indicating a high turnover of organic material. The organic carbon and base saturation indices were important in the co-occurrences in Amazonian networks, whereas several other soil properties were important for the co-exclusion. Different habitats had similar network properties with some variation in terms of modularity, probably associated with flooding pulse. We show that Amazonian microorganism communities form highly interconnected co-occurrence and co-exclusion networks, which highlights the importance of complex biotic and abiotic interactions in explaining the outstanding biodiversity of the region.},
}
@article {pmid33600877,
year = {2021},
author = {Verspecht, T and Ghesquière, J and Bernaerts, K and Boon, N and Teughels, W},
title = {Evaluating the intrinsic capacity of oral bacteria to produce hydrogen peroxide (H2O2) in liquid cultures: Interference by bacterial growth media.},
journal = {Journal of microbiological methods},
volume = {182},
number = {},
pages = {106170},
doi = {10.1016/j.mimet.2021.106170},
pmid = {33600877},
issn = {1872-8359},
mesh = {*Culture Media ; Hydrogen Peroxide/*metabolism ; *Streptococcus pneumoniae/growth &amp; development/metabolism ; },
abstract = {This work highlights the issue of interference by growth media when measuring bacterial H2O2 production. H2O2 was shown to be stable in phosphate buffered saline (PBS) but not in growth media. The protocol used for evaluating the intrinsic capacity of oral streptococci to produce H2O2 was shown to be reliable.},
}
@article {pmid33598748,
year = {2021},
author = {Nava-González, B and Suazo-Ortuño, I and López, PB and Maldonado-López, Y and Lopez-Toledo, L and Raggi, L and Parra-Olea, G and Alvarado-Díaz, J and Gómez-Gil, B},
title = {Inhibition of Batrachochytrium dendrobatidis Infection by Skin Bacterial Communities in Wild Amphibian Populations.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {666-676},
pmid = {33598748},
issn = {1432-184X},
support = {2015-259173//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 444637//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Programa 2019//Coordinaci&#xf3;n de la Investigaci&#xf3;n Cient&#xed;fica/ ; },
mesh = {Animals ; Bacteria/genetics ; Batrachochytrium ; *Chytridiomycota ; Humans ; *Microbiota ; Ranidae ; Skin ; },
abstract = {Skin-associated bacteria are known to inhibit infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd) in amphibians. It has also been postulated that skin-associated bacterial community is related to Bd infection intensity. However, our understanding of host microbial dynamics and their importance in regulating Bd intensity is limited. We analyzed Bd infection and skin-associated bacteria from two amphibian species, the salamander Ambystoma rivulare and the frog Lithobates spectabilis that co-occurred in a tropical high-altitude site in central Mexico. Sixty-three percent of sampled salamander individuals and 80% of frog individuals tested positive for Bd. Overall, we registered 622 skin-associated bacterial genera, from which 73 are known to have Bd inhibitory effects. These inhibitory taxa represented a relative abundance of 50% in relation to total relative bacterial abundance. Our results indicated that, although sharing some bacterial taxa, bacterial community from the skin of both species was different in taxonomic composition and in relative abundance. Pseudomonas spp. and Stenotrophomonas spp. were among the five most abundant bacterial taxa of both species. Both bacterial taxa inhibit Bd infection. We detected that bacterial richness and relative abundance of inhibitory Bd bacteria were negatively related to intensity of Bd infection independent of species and seasons. Despite the high Bd prevalence in both host species, no dead or sick individuals were registered during field surveys. The relatively low levels of Bd load apparently do not compromise survival of host species. Therefore, our results suggested that individuals analyzed were able to survive and thrive under a dynamic relation with enzootic infections of Bd and their microbiota.},
}
@article {pmid33598747,
year = {2021},
author = {Zhang, W and Bahadur, A and Sajjad, W and Wu, X and Zhang, G and Liu, G and Chen, T},
title = {Seasonal Variation in Fungal Community Composition Associated with Tamarix chinensis Roots in the Coastal Saline Soil of Bohai Bay, China.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {652-665},
pmid = {33598747},
issn = {1432-184X},
support = {31870479, 31570498//the National Science Foundation of China/ ; 2021PB0072//CAS-President`s International Fellowship Initiative, Postdoctoral Fellowship/ ; },
mesh = {Bays ; China ; Fungi/genetics ; *Mycobiome ; Seasons ; Soil ; Soil Microbiology ; *Tamaricaceae ; },
abstract = {Coastal salinity typically alters the soil microbial communities, which subsequently affect the biogeochemical cycle of nutrients in the soil. The seasonal variation of the soil fungal communities in the coastal area, closely associated with plant population, is poorly understood. This study provides an insight into the fungal community's variations from autumn to winter and spring to summer at a well-populated area of salt-tolerant Tamarix chinensis and beach. The richness and diversity of fungal community were higher in the spring season and lower in the winter season, as showed by high throughput sequencing of the 18S rRNA gene. Ascomycota was the predominant phylum reported in all samples across the region, and higher difference was reported at order level across the seasonal variations. The redundancy analysis suggested that the abundance and diversity of fungal communities in different seasons are mainly correlated to total organic carbon and total nitrogen. Additionally, the saprotrophic and pathotrophic fungi decreased while symbiotic fungi increased in the autumn season. This study provides a pattern of seasonal variation in fungal community composition that further broadens our limited understanding of how the density of the salt-tolerant T. chinensis population of the coastal saline soil could respond to their seasonal variations.},
}
@article {pmid33598162,
year = {2021},
author = {Lyu, W and Jia, H and Deng, C and Yamada, S and Kato, H},
title = {Zeolite-containing mixture alleviates microbial dysbiosis in dextran sodium sulfate-induced colitis in mice.},
journal = {Food science &amp; nutrition},
volume = {9},
number = {2},
pages = {772-780},
pmid = {33598162},
issn = {2048-7177},
abstract = {Inflammatory bowel disease (IBD) is a multifactorial immunomodulatory disorder. In relative nosogenesis, gut microbiota has been the focus of research on IBD. In our previous study, we demonstrated the ameliorating effect of zeolite-containing mixture (Hydryeast[®], HY) on dextran sodium sulfate (DSS)-induced colitis, through transcriptomics and proteomics. In the present study, we performed further investigation from the perspective of metagenomics using the gut microbiota. C57BL6 mice were provided an AIN-93G basal diet or a 0.8% HY-containing diet, and sterilized tap water for 11 days. Thereafter, colitis was induced by providing 1.5% (w/v) DSS-containing water for 9 days. DNA was extracted from the cecal contents and pooled into libraries in a single Illumina MiSeq run. The resulting sequences were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) software. According to the alterations in the relative abundance of certain bacteria, and the related gene and protein expressions, HY supplementation could improve the gut microbiota composition, ameliorate the degree of inflammation, inhibit the colonic mucosal microbial growth, and, to some extent, promote energy metabolism in the colon compared with the DSS treatment. Thus, we believe that HY may be a candidate to prevent and treat IBD.},
}
@article {pmid33598106,
year = {2021},
author = {Izabel-Shen, D},
title = {Understanding response of microbial communities to saltwater intrusion through microcosms.},
journal = {Computational and structural biotechnology journal},
volume = {19},
number = {},
pages = {929-933},
pmid = {33598106},
issn = {2001-0370},
abstract = {A central pursuit of microbial ecology is to accurately describe and explain the shifts in microbial community composition and function that occur in response to environmental changes. This goal requires a thorough understanding of the individual responses of different species and of the processes guiding the assembly of microbial populations similar in their response traits and corresponding functional traits. These research topics are addressed and synthesized in this Highlights, in four studies applying a trait-based framework to assess how environmental change affected the composition and functional performance of bacterioplankton of natural origin in microcosm experiments. The salinity of many aquatic environments is currently changing, due to climate change and anthropogenic activities. The mechanisms by which salinity influences community assembly, functional redundancy and functional genes involved in nitrogen cycle, and how dispersal modifies community outcome are explored in the four studies. Together, the findings of these case studies demonstrate the feasibility of using novel experiments in combination with integrative analyses of 16S rRNA and meta-'omic' data to address ecological questions. This combined approach has the potential to elucidate both the processes contributing to bacterial community assembly and the possible links between the compositional and functional changes that occur under shifting environmental conditions.},
}
@article {pmid33597941,
year = {2021},
author = {Wahdan, SFM and Heintz-Buschart, A and Sansupa, C and Tanunchai, B and Wu, YT and Schädler, M and Noll, M and Purahong, W and Buscot, F},
title = {Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {629169},
pmid = {33597941},
issn = {1664-302X},
abstract = {The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.},
}
@article {pmid33597669,
year = {2021},
author = {Gupta, S and Shariff, M and Chaturvedi, G and Sharma, A and Goel, N and Yadav, M and Mortensen, MS and Sørensen, SJ and Mukerji, M and Chauhan, NS},
title = {Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {3963},
pmid = {33597669},
issn = {2045-2322},
mesh = {Aged ; Bacteria/genetics ; Bronchoalveolar Lavage ; Diagnosis, Differential ; Female ; Humans ; Lung/microbiology ; Lung Diseases, Interstitial/*microbiology ; Male ; Microbiota/genetics ; Middle Aged ; Pulmonary Disease, Chronic Obstructive/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sarcoidosis/*microbiology ; },
abstract = {Studying respiratory illness-specific microbial signatures and their interaction with other micro-residents could provide a better understanding of lung microbial ecology. Each respiratory illness has a specific disease etiology, however, so far no study has revealed disease-specific microbial markers. The present study was designed to determine disease-specific microbial features and their interactions with other residents in chronic obstructive pulmonary diseases (stable and exacerbated), sarcoidosis, and interstitial lung diseases. Broncho-alveolar lavage samples (n = 43) were analyzed by SSU rRNA gene sequencing to study the alveolar microbiome in these diseases. A predominance of Proteobacteria followed by Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria was observed in all the disease subsets. Shannon diversity was significantly higher in stable COPD when compared to exacerbated chronic obstructive pulmonary disease (ECOPD) (p = 0.0061), and ILD patient samples (p = 0.037). The lung microbiome of the patients with stable COPD was more diverse in comparison to ECOPD and ILD patients (p < 0.001). Lefse analysis identified 40 disease-differentiating microbial features (LDA score (log10) > 4). Species network analysis indicated a significant correlation (p < 0.05) of diseases specific microbial signature with other lung microbiome members. The current study strengthens the proposed hypothesis that each respiratory illness has unique microbial signatures. These microbial signatures could be used as diagnostic markers to differentiate among various respiratory illnesses.},
}
@article {pmid33597173,
year = {2021},
author = {Keller, CM and Kendra, CG and Bruna, RE and Craft, D and Pontes, MH},
title = {Genetic Modification of Sodalis Species by DNA Transduction.},
journal = {mSphere},
volume = {6},
number = {1},
pages = {},
pmid = {33597173},
issn = {2379-5042},
support = {R21 AI148774/AI/NIAID NIH HHS/United States ; },
mesh = {Bacteriophages/genetics/metabolism ; DNA, Bacterial/*genetics ; Enterobacteriaceae/classification/*genetics/*virology ; Escherichia coli/genetics ; *Gene Transfer Techniques ; *Genome, Bacterial ; Host Specificity ; Phylogeny ; Symbiosis ; *Transduction, Genetic ; },
abstract = {Bacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation of Escherichia coli and a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing, and promoting transduction in members of the bacterial genus Sodalis, including the maternally inherited insect endosymbiont Sodalis glossinidius While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram-negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms.IMPORTANCE A large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherent nature of these associations, insect endosymbionts cannot be usually isolated in pure culture or genetically manipulated. Here we use a broad-host-range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad-host-range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.},
}
@article {pmid33596519,
year = {2021},
author = {Kleerebezem, R and Stouten, G and Koehorst, J and Langenhoff, A and Schaap, P and Smidt, H},
title = {Experimental infrastructure requirements for quantitative research on microbial communities.},
journal = {Current opinion in biotechnology},
volume = {67},
number = {},
pages = {158-165},
doi = {10.1016/j.copbio.2021.01.017},
pmid = {33596519},
issn = {1879-0429},
mesh = {Bacteria/genetics ; *Ecosystem ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; },
abstract = {Natural microbial communities are composed of a large diversity of interacting microorganisms, each with a specific role in the functional properties of the ecosystem. The objectives in microbial ecology research are related to identifying, understanding and exploring the role of these different microorganisms. Because of the rapidly increasing power of DNA sequencing and the rapid increase of genomic data, main attention of microbial ecology research shifted from cultivation-oriented studies towards metagenomic studies. Despite these efforts, the direct link between the molecular properties and the measurable changes in the functional performance of the ecosystem is often poorly documented. A quantitative understanding of functional properties in relation to the molecular changes requires effective integration, standardization, and parallelization of experiments. High-resolution functional characterization is a prerequisite for interpretation of changes in metagenomic properties, and will improve our understanding of microbial communities and facilitate their exploration for health and circular economy related objectives.},
}
@article {pmid33594548,
year = {2021},
author = {Labrador, MDM and Doña, J and Serrano, D and Jovani, R},
title = {Correction to: Quantitative Interspecific Approach to the Stylosphere: Patterns of Bacteria and Fungi Abundance on Passerine Bird Feathers.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {831},
doi = {10.1007/s00248-021-01713-y},
pmid = {33594548},
issn = {1432-184X},
}
@article {pmid33594547,
year = {2021},
author = {Katsoula, A and Vasileiadis, S and Karamanoli, K and Vokou, D and Karpouzas, DG},
title = {Factors Structuring the Epiphytic Archaeal and Fungal Communities in a Semi-arid Mediterranean Ecosystem.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {638-651},
pmid = {33594547},
issn = {1432-184X},
support = {-//State Scholarship Foundation of Greece/ ; -//European Social Fund (ESF) and National Resources/ ; -//General Secretariat of Research and Technology, Greece/ ; //State Scholarship Foundation of Greece/ ; //European Social Fund (ESF) and National Resources/ ; //General Secretariat of Research and Technology, Greece/ ; },
mesh = {Archaea/genetics ; Biodiversity ; Ecosystem ; Fungi/genetics ; *Microbiota ; *Mycobiome ; },
abstract = {The phyllosphere microbiome exerts a strong effect on plants' productivity, and its composition is determined by various factors. To date, most phyllosphere studies have focused on bacteria, while fungi and especially archaea have been overlooked. We studied the effects of plant host and season on the abundance and diversity of the epiphytic archaeal and fungal communities in a typical semi-arid Mediterranean ecosystem. We collected leaves in two largely contrasting seasons (summer and winter) from eight perennial species of varying attributes which could be grouped into the following: (i) high-canopy, evergreen sclerophyllοus shrubs with leathery leaves, and low-canopy, either semi-deciduous shrubs or non-woody perennials with non-leathery leaves, and (ii) aromatic and non-aromatic plants. We determined the abundance of epiphytic Crenarchaea, total fungi, Alternaria and Cladosporium (main airborne fungi) via q-PCR and the structure of the epiphytic archaeal and fungal communities via amplicon sequencing. We observed a strong seasonal effect with all microbial groups examined showing higher abundance in summer. Plant host and season were equally important determinants of the composition of the fungal community consisted mostly of Ascomycota, with Hypocreales dominating in winter and Capnodiales and Pleosporales in summer. In contrast, the archaeal community showed plant host driven patterns dominated by the Soil Crenarchaeotic Group (SCG) and Aenigmarchaeota. Plant habit and aromatic nature exhibited filtering effects only on the epiphytic fungal communities. Our study provides a first in-depth analysis of the key determinants shaping the phyllosphere archaeal and fungal communities of a semi-arid Mediterranean ecosystem.},
}
@article {pmid33592536,
year = {2021},
author = {Taş, N and de Jong, AE and Li, Y and Trubl, G and Xue, Y and Dove, NC},
title = {Metagenomic tools in microbial ecology research.},
journal = {Current opinion in biotechnology},
volume = {67},
number = {},
pages = {184-191},
doi = {10.1016/j.copbio.2021.01.019},
pmid = {33592536},
issn = {1879-0429},
mesh = {Ecology ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; },
abstract = {Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.},
}
@article {pmid33591419,
year = {2021},
author = {Luzzi, G and Brinks, E and Fritsche, J and Franz, CMAP},
title = {Effect of reduction of sodium content on the microbial ecology of Edam cheese samples.},
journal = {AMB Express},
volume = {11},
number = {1},
pages = {28},
pmid = {33591419},
issn = {2191-0855},
support = {2819107716//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft/ ; },
abstract = {Sodium intake is a major risk factor for non-communicable diseases. Consequently, reformulation of cheeses such as Edam to contain less sodium may contribute to lowering disease risk. However, sodium is essential for cheese manufacture, influencing starter culture bacteria activity and abundance during fermentation. This study aimed to assess the microbial diversity of reformulated Edam cheese samples with a reduced sodium content using culture-independent technique. The microbial diversity of samples produced using simple sodium reduction, as well as by substituting salt with a mineral salt compound containing potassium, were analysed in comparison to regular control Edam samples during manufacture and the subsequent 6-week ripening period using 16S rDNA metagenomics. In addition, a challenge test using Listeria (List.) innocua as a surrogate species for List. monocytogenes was performed. Reducing sodium content did not influence the microbiological composition of reformulated samples in comparison to that of regular samples. The starter culture bacteria dominated the microbial diversity and no increase in spoilage or potentially pathogenic bacterial growth was detected, including that of List. innocua. From a microbiological perspective, it can be concluded that lowering sodium content in Edam samples without affecting the microbial composition is achievable through simple sodium reduction and through implementation of a mineral salt replacement approach.},
}
@article {pmid33589842,
year = {2021},
author = {Schorn, MA and Verhoeven, S and Ridder, L and Huber, F and Acharya, DD and Aksenov, AA and Aleti, G and Moghaddam, JA and Aron, AT and Aziz, S and Bauermeister, A and Bauman, KD and Baunach, M and Beemelmanns, C and Beman, JM and Berlanga-Clavero, MV and Blacutt, AA and Bode, HB and Boullie, A and Brejnrod, A and Bugni, TS and Calteau, A and Cao, L and Carrión, VJ and Castelo-Branco, R and Chanana, S and Chase, AB and Chevrette, MG and Costa-Lotufo, LV and Crawford, JM and Currie, CR and Cuypers, B and Dang, T and de Rond, T and Demko, AM and Dittmann, E and Du, C and Drozd, C and Dujardin, JC and Dutton, RJ and Edlund, A and Fewer, DP and Garg, N and Gauglitz, JM and Gentry, EC and Gerwick, L and Glukhov, E and Gross, H and Gugger, M and Guillén Matus, DG and Helfrich, EJN and Hempel, BF and Hur, JS and Iorio, M and Jensen, PR and Kang, KB and Kaysser, L and Kelleher, NL and Kim, CS and Kim, KH and Koester, I and König, GM and Leao, T and Lee, SR and Lee, YY and Li, X and Little, JC and Maloney, KN and Männle, D and Martin H, C and McAvoy, AC and Metcalf, WW and Mohimani, H and Molina-Santiago, C and Moore, BS and Mullowney, MW and Muskat, M and Nothias, LF and O'Neill, EC and Parkinson, EI and Petras, D and Piel, J and Pierce, EC and Pires, K and Reher, R and Romero, D and Roper, MC and Rust, M and Saad, H and Saenz, C and Sanchez, LM and Sørensen, SJ and Sosio, M and Süssmuth, RD and Sweeney, D and Tahlan, K and Thomson, RJ and Tobias, NJ and Trindade-Silva, AE and van Wezel, GP and Wang, M and Weldon, KC and Zhang, F and Ziemert, N and Duncan, KR and Crüsemann, M and Rogers, S and Dorrestein, PC and Medema, MH and van der Hooft, JJJ},
title = {A community resource for paired genomic and metabolomic data mining.},
journal = {Nature chemical biology},
volume = {17},
number = {4},
pages = {363-368},
pmid = {33589842},
issn = {1552-4469},
support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R35 GM138002/GM/NIGMS NIH HHS/United States ; R01 AT009143/AT/NCCIH NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; DP2 AT010401/AT/NCCIH NIH HHS/United States ; F32 CA221327/CA/NCI NIH HHS/United States ; U01 GM110706/GM/NIGMS NIH HHS/United States ; },
mesh = {Data Mining/*methods ; Databases, Factual ; Genomics/*methods ; Metabolomics/*methods ; },
abstract = {Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.},
}
@article {pmid33587250,
year = {2021},
author = {Zheng, R and Wu, M and Wang, H and Chai, L and Peng, J},
title = {Copper-induced sublethal effects in Bufo gargarizans tadpoles: growth, intestinal histology and microbial alternations.},
journal = {Ecotoxicology (London, England)},
volume = {30},
number = {3},
pages = {502-513},
doi = {10.1007/s10646-021-02356-y},
pmid = {33587250},
issn = {1573-3017},
support = {No. 42077370//National Natural Science Foundation of China/ ; No. 2020JM232//Natural Science Foundation of Shaanxi Province/ ; },
mesh = {Animals ; Bufonidae ; *Copper/toxicity ; *Gastrointestinal Microbiome ; Intestines ; Larva ; },
abstract = {Copper (Cu) is one of the environmental contaminations which can pose significant risks for organisms. The current study explores the effects of Cu exposure on the growth, intestinal histology and microbial ecology in Bufo gargarizans. The results revealed that 0.5-1 μM Cu exposure induced growth retardation (including reduction of total body length and wet weight) and intestinal histological injury (including disordered enterocyte, changes in the villi and vacuoles) of tadpoles. Also, high-throughput sequencing analysis showed that Cu exposure caused changes in richness, diversity and structure of intestinal microbiota. Moreover, the composition of intestinal microbiota was altered in tadpoles exposed to different concentrations of Cu. At the phylum level, we observed the abundance of proteobacteria was increased, while the abundance of fusobacteria was decreased in the intestinal microbiota of tadpoles exposed to 1 μM Cu. At the genus level, a reduced abundance of kluyvera and aeromonas was observed in the intestinal microbiota of tadpoles under the exposure of 0-0.5 μM Cu. Finally, functional predictions revealed that tadpoles exposed to copper may be at a higher risk of developing metabolic disorders or diseases. Above all, our results will develop a comprehensive view of the Cu exposure in amphibians and will yield a new consideration for sublethal effects of Cu on aquatic organisms.},
}
@article {pmid33584618,
year = {2021},
author = {George, SF and Fierer, N and Levy, JS and Adams, B},
title = {Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {616730},
pmid = {33584618},
issn = {1664-302X},
abstract = {Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5-10 km[2]) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.},
}
@article {pmid33584606,
year = {2021},
author = {Walker, AM and Leigh, MB and Mincks, SL},
title = {Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {581124},
pmid = {33584606},
issn = {1664-302X},
support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; },
abstract = {The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.},
}
@article {pmid33584565,
year = {2020},
author = {Rain-Franco, A and de Moraes, GP and Beier, S},
title = {Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {597653},
pmid = {33584565},
issn = {1664-302X},
abstract = {Experimental reproducibility in aquatic microbial ecology is critical to predict the dynamics of microbial communities. However, controlling the initial composition of naturally occurring microbial communities that will be used as the inoculum in experimental setups is challenging, because a proper method for the preservation of those communities is lacking. To provide a feasible method for preservation and resuscitation of natural aquatic prokaryote assemblages, we developed a cryopreservation procedure applied to natural aquatic prokaryotic communities. We studied the impact of inoculum size, processing time, and storage time on the success of resuscitation. We further assessed the effect of different growth media supplemented with dissolved organic matter (DOM) prepared from naturally occurring microorganisms on the recovery of the initially cryopreserved communities obtained from two sites that have contrasting trophic status and environmental heterogeneity. Our results demonstrated that the variability of the resuscitation process among replicates decreased with increasing inoculum size. The degree of similarity between initial and resuscitated communities was influenced by both the growth medium and origin of the community. We further demonstrated that depending on the inoculum source, 45-72% of the abundant species in the initially natural microbial communities could be detected as viable cells after cryopreservation. Processing time and long-term storage up to 12 months did not significantly influence the community composition after resuscitation. However, based on our results, we recommend keeping handling time to a minimum and ensure identical incubation conditions for repeated resuscitations from cryo-preserved aliquots at different time points. Given our results, we recommend cryopreservation as a promising tool to advance experimental research in the field of microbial ecology.},
}
@article {pmid33584558,
year = {2020},
author = {Oyserman, BO and Cordovez, V and Flores, SS and Leite, MFA and Nijveen, H and Medema, MH and Raaijmakers, JM},
title = {Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {574053},
pmid = {33584558},
issn = {1664-302X},
abstract = {One of the fundamental tenets of biology is that the phenotype of an organism (Y) is determined by its genotype (G), the environment (E), and their interaction (GE). Quantitative phenotypes can then be modeled as Y = G + E + GE + e, where e is the biological variance. This simple and tractable model has long served as the basis for studies investigating the heritability of traits and decomposing the variability in fitness. The importance and contribution of microbe interactions to a given host phenotype is largely unclear, nor how this relates to the traditional GE model. Here we address this fundamental question and propose an expansion of the original model, referred to as GEM, which explicitly incorporates the contribution of the microbiome (M) to the host phenotype, while maintaining the simplicity and tractability of the original GE model. We show that by keeping host, environment, and microbiome as separate but interacting variables, the GEM model can capture the nuanced ecological interactions between these variables. Finally, we demonstrate with an in vitro experiment how the GEM model can be used to statistically disentangle the relative contributions of each component on specific host phenotypes.},
}
@article {pmid33582117,
year = {2021},
author = {Petrin, S and Orsini, M and Mastrorilli, E and Longo, A and Cozza, D and Olsen, JE and Ricci, A and Losasso, C and Barco, L},
title = {Identification and characterization of a spreadable IncI1 plasmid harbouring a blaCTX-M-15 gene in an Italian human isolate of Salmonella serovar Napoli.},
journal = {Plasmid},
volume = {114},
number = {},
pages = {102566},
doi = {10.1016/j.plasmid.2021.102566},
pmid = {33582117},
issn = {1095-9890},
mesh = {Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Humans ; Italy ; Plasmids/genetics ; *Salmonella/genetics ; Serogroup ; beta-Lactamases/genetics ; },
abstract = {Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) ranks among the top serovars causing human infections in Italy, although not common in other European countries. Isolates are generally pan-susceptible or resistant to aminoglycosides only, however data on antimicrobial resistance genes in strains of S. Napoli are limited. Recently an isolate encoding resistance to third generation cephalosporins was reported. This study aimed to characterize plasmid-encoded cephalosporin resistance due to the blaCTX-M-15 gene in a human S. Napoli isolate in Italy, and to investigate plasmid stability over time. S. Napoli 16/174478 was confirmed to be ESBL-producing. The blaCTX-M-15 gene was shown to be located on an IncI1α plasmid of 90,272 bp (50.03 GC%) encoding for 107 coding sequences (CDS). The plasmid was successfully transferred by conjugation to an E. coli 1816 recipient strain (conjugation frequency 3.9 × 10[-2] transconjugants per donor). Transconjugants were confirmed to carry the IncI1α plasmid, and to be ESBL-producing strains as well. Moreover, transconjugant colonies maintained the plasmid for up to 10 passages. The identification of S. Napoli isolates able to produce ESBLs is of great concern, as this pathogen is frequently associated with invasive infections and a higher risk of bacteraemia, and its reservoir has not yet been clearly identified.},
}
@article {pmid33581524,
year = {2021},
author = {Cordovez, V and Rotoni, C and Dini-Andreote, F and Oyserman, B and Carrión, VJ and Raaijmakers, JM},
title = {Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome.},
journal = {The Science of the total environment},
volume = {772},
number = {},
pages = {144825},
doi = {10.1016/j.scitotenv.2020.144825},
pmid = {33581524},
issn = {1879-1026},
mesh = {Genotype ; *Solanum lycopersicum ; *Microbiota ; Plant Roots ; Rhizosphere ; Soil Microbiology ; },
abstract = {Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root microbiome is relatively small or, for many plant species, still largely unknown. Here we cultivated modern and wild tomato genotypes for four successive cycles and showed that divergence in microbiome assembly between the two genotypes was significantly amplified over time. Also, we show that the composition of the rhizosphere microbiome of modern and wild plants became more dissimilar from the initial bulk soil and from each other. Co-occurrence analyses further identified amplicon sequence variants (ASVs) associated with early and late successions of the tomato rhizosphere microbiome. Among the members of the Late Successional Rhizosphere microbiome, we observed an enrichment of ASVs belonging to the genera Acidovorax, Massilia and Rhizobium in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseudomonas. Collectively, our approach allowed us to study the dynamics of rhizosphere microbiome over successional cultivation as well as to categorize rhizobacterial taxa for their ability to form transient or long-term associations with their host plants.},
}
@article {pmid33581124,
year = {2021},
author = {Liu, W and Zhang, X and Xu, H and Li, S and Lau, HC and Chen, Q and Zhang, B and Zhao, L and Chen, H and Sung, JJ and Yu, J},
title = {Microbial Community Heterogeneity Within Colorectal Neoplasia and its Correlation With Colorectal Carcinogenesis.},
journal = {Gastroenterology},
volume = {160},
number = {7},
pages = {2395-2408},
doi = {10.1053/j.gastro.2021.02.020},
pmid = {33581124},
issn = {1528-0012},
mesh = {Adenoma/*microbiology ; Aged ; Biopsy ; Carcinogenesis/*genetics ; Colon/microbiology/pathology ; Colorectal Neoplasms/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; *Genetic Heterogeneity ; Humans ; Male ; Microsatellite Instability ; Middle Aged ; Proto-Oncogene Proteins p21(ras)/genetics ; RNA, Ribosomal, 16S/analysis ; },
abstract = {BACKGROUND &amp; AIMS: Gut microbial dysbiosis has pivotal involvement in colorectal cancer (CRC). However, the intratumoral microbiota and its association with CRC progression remain elusive. We aimed to determine the microbial community architecture within a neoplasia (CRC or adenoma) and its contribution to colorectal carcinogenesis.<br><br>METHODS: We collected 436 tissue biopsies from patients with CRC (n&#xa0;= 36) or adenoma (n&#xa0;= 32) (2-6 biopsies from a neoplasia plus 2-5 biopsies from adjacent normal tissues per individual). Microbial profiling was performed using 16S ribosomal RNA gene sequencing with subsequent investigation of microbiota diversities and heterogeneity. The correlation between microbial dysbiosis and host genetic alterations (KRAS mutation and microsatellite instability) in all neoplasia biopsies was also analyzed.<br><br>RESULTS: We discovered that intra-neoplasia microbial communities are heterogeneous. Abundances of some CRC-associated pathobionts (eg, Fusobacterium, Bacteroides, Parvimonas, and Prevotella) were found to be highly varied within a single neoplasia. Correlation of such heterogeneity with CRC development revealed alterations in microbial communities involving microbes with high intra-neoplasia variation in abundance. Moreover, we found that the intra-neoplasia variation in abundance of individual microbes changed along the adenoma-carcinoma sequence. We further determined that there was a significant difference in intra-neoplasia microbiota between biopsies with and without KRAS mutation (P < .001) or microsatellite instability (P < .001), and illustrated the association of intratumoral microbial heterogeneity with genetic alteration.<br><br>CONCLUSIONS: We demonstrated that intra-neoplasia microbiota is heterogeneous and correlated with colorectal carcinogenesis. Our findings provide new insights on the contribution of gut microbiota heterogeneity to CRC progression.},
}
@article {pmid33580950,
year = {2021},
author = {Lopes, LD and Hao, J and Schachtman, DP},
title = {Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {4},
pages = {},
doi = {10.1093/femsec/fiab028},
pmid = {33580950},
issn = {1574-6941},
mesh = {Bacteria/genetics ; Hydrogen-Ion Concentration ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil ; Soil Microbiology ; },
abstract = {Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.},
}
@article {pmid33580815,
year = {2021},
author = {Kellogg, JA and Reganold, JP and Murphy, KM and Carpenter-Boggs, LA},
title = {A Plant-Fungus Bioassay Supports the Classification of Quinoa (Chenopodium quinoa Willd.) as Inconsistently Mycorrhizal.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {135-144},
pmid = {33580815},
issn = {1432-184X},
support = {2016-51300-25808//USDA National Institute of Food and Agriculture (US)/ ; n/a//Lundberg Family Farms, Richvale, California (US)/ ; 1014754//USDA National Institute of Food and Agriculture Hatch project (US)/ ; },
mesh = {Biological Assay ; *Chenopodium quinoa ; Fungi ; *Mycorrhizae/genetics ; Plant Roots ; },
abstract = {Quinoa (Chenopodium quinoa Willd.) is becoming an increasingly important food crop. Understanding the microbiome of quinoa and its relationships with soil microorganisms may improve crop yield potential or nutrient use efficiency. Whether quinoa is a host or non-host of a key soil symbiont, arbuscular mycorrhizal fungi (AMF), is suddenly up for debate with recent field studies reporting root colonization and presence of arbuscules. This research seeks to add evidence to the mycorrhizal classification of quinoa as we investigated additional conditions not previously explored in quinoa that may affect root colonization. A greenhouse study used six AMF species, two AMF commercial inoculant products, and a diverse set of 10 quinoa genotypes. Results showed 0 to 3% quinoa root colonization by AMF when grown under greenhouse conditions. Across quinoa genotypes, AMF inoculant affected shoot dry weight (p = 0.066) and height (p = 0.031). Mykos Gold produced greater dry biomass than Claroideoglomus eutunicatum (27% increase), Rhizophagus clarus (26% increase), and within genotype CQ119, the control (21% increase). No treatment increased plant height compared to control, but Funneliformis mosseae increased height compared to C. eutunicatum (25% increase) and Rhizophagus intraradices (25% increase). Although quinoa plants were minimally colonized by AMF, plant growth responses fell along the mutualism-parasitism continuum. Individual AMF treatments increased leaf greenness in quinoa genotypes 49ALC and QQ87, while R. clarus decreased greenness in CQ119 compared to the control. Our research findings support the recommendation to classify quinoa as non-mycorrhizal when no companion plant is present and inconsistently mycorrhizal when conditional colonization occurs.},
}
@article {pmid33580272,
year = {2021},
author = {He, Y and Huang, D and Li, S and Shi, L and Sun, W and Sanford, RA and Fan, H and Wang, M and Li, B and Li, Y and Tang, X and Dong, Y},
title = {Profiling of Microbial Communities in the Sediments of Jinsha River Watershed Exposed to Different Levels of Impacts by the Vanadium Industry, Panzhihua, China.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {623-637},
pmid = {33580272},
issn = {1432-184X},
support = {92051111//National Natural Science Foundation of China/ ; 91851211//National Natural Science Foundation of China/ ; 41877321//National Natural Science Foundation of China/ ; JG/18011B//China Three Gorges Projects Development Co. Ltd/ ; },
mesh = {China ; Environmental Monitoring ; Geologic Sediments ; *Metals, Heavy/analysis ; *Microbiota ; Mining ; RNA, Ribosomal, 16S/genetics ; Rivers ; Vanadium/analysis ; },
abstract = {The mining, smelting, manufacturing, and disposal of vanadium (V) and associated products have caused serious environmental problems. Although the microbial ecology in V-contaminated soils has been intensively studied, the impacted watershed ecosystems have not been systematically investigated. In this study, geochemistry and microbial structure were analyzed along ~30 km of the Jinsha River and its two tributaries across the industrial areas in Panzhihua, one of the primary V mining and production cities in China. Geochemical analyses showed different levels of contamination by metals and metalloids in the sediments, with high degrees of contamination observed in one of the tributaries close to the industrial park. Analyses of the V4 hypervariable region of 16S rRNA genes of the microbial communities in the sediments showed significant decrease in microbial diversity and microbial structure in response to the environmental gradient (e.g., heavy metals, total sulfur, and total nitrogen). Strong association of the taxa (e.g., Thauera, Algoriphagus, Denitromonas, and Fontibacter species) with the metals suggested selection for these potential metal-resistant and/or metabolizing populations. Further co-occurrence network analysis showed that many identified potential metal-mediating species were among the keystone taxa that were closely associated in the same module, suggesting their strong inter-species interactions but relative independence from other microorganisms in the hydrodynamic ecosystems. This study provided new insight into the microbe-environment interactions in watershed ecosystems differently impacted by the V industries. Some of the phylotypes identified in the highly contaminated samples exhibited potential for bioremediation of toxic metals (e.g., V and Cr).},
}
@article {pmid33579680,
year = {2021},
author = {Coban, O and Rasigraf, O and de Jong, AEE and Spott, O and Bebout, BM},
title = {Quantifying potential N turnover rates in hypersaline microbial mats by [15]N tracer techniques.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {8},
pages = {},
pmid = {33579680},
issn = {1098-5336},
abstract = {Microbial mats, due to stratification of the redox zones, have a potential to include a complete N cycle, however an attempt to evaluate a complete N cycle in these ecosystems has not been yet made. In this study, occurrence and rates of major N cycle processes were evaluated in intact microbial mats from Elkhorn Slough, Monterey Bay, CA, USA, and Baja California Sur, Mexico under oxic and anoxic conditions using [15]N-labeling techniques. All of the major N transformation pathways, with the exception of anammox, were detected in both microbial mats. Nitrification rates were found to be low at both sites for both seasons investigated. The highest rates of ammonium assimilation were measured in Elkhorn Slough mats in April and corresponded to high in situ ammonium concentration in the overlying water. Baja mats featured higher ammonification than ammonium assimilation rates and this, along with their higher affinity for nitrate compared to ammonium and low dissimilatory nitrate reduction to ammonium rates, characterized their differences from Elkhorn Slough mats. Nitrogen fixation rates in Elkhorn Slough microbial mats were found to be low implying that other processes such as recycling and assimilation from water are main sources of N for these mats at the times sampled. Denitrification in all of the mats was incomplete with nitrous oxide as end product and not dinitrogen. Our findings highlight N cycling features not previously quantified in microbial mats and indicate a need of further investigations in these microbial ecosystems.Importance: Nitrogen is essential for life. The nitrogen cycle on Earth is mediated by microbial activity and has had a profound impact on both the atmosphere and the biosphere throughout geologic time. Microbial mats, present in many modern environments, have been regarded as living records of the organisms, genes, and phylogenies of microbes, as they are one of the most ancient ecosystems on Earth. While rates of major nitrogen metabolic pathways have been evaluated in a number of ecosystems, it remains elusive in microbial mats. In particular it is unclear what factors affect nitrogen cycling in these ecosystems and how morphological differences between mats impact nitrogen transformations. In this study we investigate nitrogen cycling in two microbial mats having morphological differences. Our findings provide insight for further understanding of biogeochemistry and microbial ecology of microbial mats.},
}
@article {pmid33578056,
year = {2021},
author = {Jiang, C and Peces, M and Andersen, MH and Kucheryavskiy, S and Nierychlo, M and Yashiro, E and Andersen, KS and Kirkegaard, RH and Hao, L and Høgh, J and Hansen, AA and Dueholm, MS and Nielsen, PH},
title = {Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers.},
journal = {Water research},
volume = {193},
number = {},
pages = {116871},
doi = {10.1016/j.watres.2021.116871},
pmid = {33578056},
issn = {1879-2448},
mesh = {Anaerobiosis ; Archaea/genetics ; Bioreactors ; Denmark ; Methane ; *Microbiota ; Sewage ; *Water Purification ; },
abstract = {Anaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting primary and surplus activated sludge to methane-rich biogas. However, the limited number of surveys and the lack of comprehensive datasets have hindered a deeper understanding of the characteristics and associations between key variables and the microbial community composition. Here, we present a six-year survey of 46 anaerobic digesters, located at 22 WWTPs in Denmark, which is the first and largest known study of the microbial ecology of AD at WWTPs at a regional scale. For three types of AD (mesophilic, mesophilic with thermal hydrolysis pretreatment, and thermophilic), we present the typical value range of 12 key parameters including operational variables and performance parameters. High-resolution bacterial and archaeal community analyses were carried out at species level using amplicon sequencing of >1,000 samples and the new ecosystem-specific MiDAS 3 reference database. We detected 42 phyla, 1,600 genera, and 3,584 species in the bacterial community, where 70% of the genera and 93% of the species represented environmental taxa that were only classified based on MiDAS 3 de novo placeholder taxonomy. More than 40% of the bacterial species were found not to grow in the mesophilic and thermophilic digesters and were only present due to immigration with the feed sludge. Ammonium concentration was the main driver shaping the bacterial community while temperature and pH were main drivers for the archaea in the three types of ADs. Sub-setting for the growing microbes improved significantly the correlation analyses and revealed the main drivers for the presence of specific species. Within mesophilic digesters, feed sludge composition and other key parameters (organic loading rate, biogas yield, and ammonium concentration) correlated with specific growing species. This survey provides a comprehensive insight into community structure at species level, providing a foundation for future studies of the ecological significance/characteristics and function of the many novel or poorly described taxa.},
}
@article {pmid33576997,
year = {2021},
author = {Pratscher, J},
title = {Extraction of Microbial Cells from Environmental Samples for FISH Approaches.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2246},
number = {},
pages = {291-299},
pmid = {33576997},
issn = {1940-6029},
mesh = {Environmental Microbiology ; In Situ Hybridization, Fluorescence/*methods ; Microbiota/genetics ; },
abstract = {Fluorescent in situ hybridization (FISH) on environmental samples has become a standard technique to identify and enumerate microbial populations. However, visualization and quantification of cells in environmental samples with complex matrices is often challenging to impossible, and downstream protocols might also require the absence of organic and inorganic particles for analysis. Therefore, quite often microbial cells have to be detached and extracted from the sample matrix prior to use in FISH. Here, details are given for a routine protocol to extract intact microbial cells from environmental samples using density gradient centrifugation. This protocol is suitable and adaptable for a wide range of environmental samples.},
}
@article {pmid33576992,
year = {2021},
author = {Nielsen, JL},
title = {Assigning Function to Phylogeny: MAR-FISH.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2246},
number = {},
pages = {225-236},
pmid = {33576992},
issn = {1940-6029},
mesh = {Autoradiography/*methods ; Biomass ; Electrons ; In Situ Hybridization, Fluorescence/*methods ; Microbiota/genetics ; Phylogeny ; },
abstract = {Microautoradiography (MAR) is a technique by which assimilated radioactive tracers incorporated into the biomass can be detected by a film emulsion. This allows for the testing of cellular preferences in electron donors and acceptors of individual cells in complex microbial assemblages, as well as the ability to take up substrates under diverse environmental exposures.Combination with staining techniques such as fluorescence in situ hybridization (FISH) can be used to identify the involved cells. Here, the practical aspects of a combined microautoradiography and fluorescence in situ hybridization (MAR-FISH) approach are described.},
}
@article {pmid33576852,
year = {2021},
author = {Zhou, G and Tong, H and Cai, L and Huang, H},
title = {Transgenerational Effects on the Coral Pocillopora damicornis Microbiome Under Ocean Acidification.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {572-580},
pmid = {33576852},
issn = {1432-184X},
support = {41876192//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Anthozoa ; Coral Reefs ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; Oceans and Seas ; Seawater ; },
abstract = {Reef-building corals are inhabited by functionally diverse microorganisms which play important roles in coral health and persistence in the Anthropocene. However, our understanding of the complex associations within coral holobionts is largely limited, particularly transgenerational exposure to environmental stress, like ocean acidification. Here we investigated the microbiome development of an ecologically important coral Pocillopora damicornis following transgenerational exposure to moderate and high pCO2 (partial pressure of CO2) levels, using amplicon sequencing and analysis. Our results showed that the Symbiodiniaceae community structures in adult and juvenile had similar patterns, all of which were dominated by Durusdinium spp., previously known as clade D. Conversely, prokaryotic communities varied between adults and juveniles, possibly driven by the effect of host development. Surprisingly, there were no significant changes in both Symbiodiniaceae and prokaryotic communities with different pCO2 treatments, which was independent of the life history stage. This study shows that ocean acidification has no significant effect on P. damicornis microbiome, and warrants further research to test whether transgenerational acclimation exists in coral holobiont to projected future climate change.},
}
@article {pmid33575595,
year = {2020},
author = {Yang, P and Tan, C and Han, M and Cheng, L and Cui, X and Ning, K},
title = {Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology.},
journal = {NAR genomics and bioinformatics},
volume = {2},
number = {2},
pages = {lqaa042},
pmid = {33575595},
issn = {2631-9268},
abstract = {Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species-species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.},
}
@article {pmid33570667,
year = {2021},
author = {Franco-Frías, E and Mercado-Guajardo, V and Merino-Mascorro, A and Pérez-Garza, J and Heredia, N and León, JS and Jaykus, LA and Dávila-Aviña, J and García, S},
title = {Analysis of Bacterial Communities by 16S rRNA Gene Sequencing in a Melon-Producing Agro-environment.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {613-622},
pmid = {33570667},
issn = {1432-184X},
support = {A1-S-250//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 2018-07410, 2019-67017-29642//National Institute of Food and Agriculture/ ; HHSF223201710406P//U.S. Food and Drug Administration/ ; },
mesh = {Bacteria/genetics ; *Cucurbitaceae ; Genes, rRNA ; RNA, Ribosomal, 16S/genetics ; Salmonella ; },
abstract = {Cantaloupe melons, which have been responsible of an increasing number of foodborne disease outbreaks, may become contaminated with microbial pathogens during production. However, little information is available on the microbial populations in the cantaloupe farm environment. The purpose of this work was to characterize the bacterial communities present on cantaloupe farms. Fruit, soil, and harvester hand rinsates were collected from two Mexican cantaloupe farms, each visited three times. Microbiome analysis was performed by sequencing 16sRNA and analyzed using qiime2 software. Correlations were determined between sample type and microbial populations. The α and β diversity analysis identified 2777 sequences across all samples. The soil samples had the highest number and diversity of unique species (from 130 to 1329 OTUs); cantaloupe (from 112 to 205 OTUs), and hands (from 67 to 151 OTUs) had similar diversity. Collectively, Proteobacteria was the most abundant phyla (from 42 to 95%), followed by Firmicutes (1-47%), Actinobacteria (< 1 to 23%), and Bacteroidetes (< 1 to 4.8%). The most abundant genera were Acinetobacter (20-58%), Pseudomonas (14.5%), Erwinia (13%), and Exiguobacterium (6.3%). Genera with potential to be pathogenic included Bacillus (4%), Salmonella (0.85%), Escherichia-Shigella (0.38%), Staphylococcus (0.32%), Listeria (0.29%), Clostridium (0.28%), and Cronobacter (0.27%), which were found at lower frequencies. This study provides information on the cantaloupe production microbiome, which can inform future research into critical food safety issues such as antimicrobial resistance, virulence, and genomic epidemiology.},
}
@article {pmid33568638,
year = {2021},
author = {Aubry, F and Jacobs, S and Darmuzey, M and Lequime, S and Delang, L and Fontaine, A and Jupatanakul, N and Miot, EF and Dabo, S and Manet, C and Montagutelli, X and Baidaliuk, A and Gámbaro, F and Simon-Lorière, E and Gilsoul, M and Romero-Vivas, CM and Cao-Lormeau, VM and Jarman, RG and Diagne, CT and Faye, O and Faye, O and Sall, AA and Neyts, J and Nguyen, L and Kaptein, SJF and Lambrechts, L},
title = {Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {916},
pmid = {33568638},
issn = {2041-1723},
mesh = {Aedes/physiology/virology ; Africa ; Animals ; Asia ; Female ; Humans ; Male ; Mice ; Phylogeny ; Virulence ; Zika Virus/classification/genetics/*pathogenicity/*physiology ; Zika Virus Infection/*mortality/transmission/*virology ; },
abstract = {The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compare seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We find that recent African ZIKV strains display higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice than their Asian counterparts. We emphasize the high epidemic potential of African ZIKV strains and suggest that they could more easily go unnoticed by public health surveillance systems than Asian strains due to their propensity to cause fetal loss rather than birth defects.},
}
@article {pmid33563841,
year = {2021},
author = {Westhoff, S and Kloosterman, AM and van Hoesel, SFA and van Wezel, GP and Rozen, DE},
title = {Competition Sensing Changes Antibiotic Production in Streptomyces.},
journal = {mBio},
volume = {12},
number = {1},
pages = {},
pmid = {33563841},
issn = {2150-7511},
mesh = {Anti-Bacterial Agents/*biosynthesis/metabolism ; Antibiosis/*genetics ; *Gene Expression Regulation, Bacterial ; *Microbial Interactions ; Multigene Family ; Secondary Metabolism/genetics/physiology ; Streptomyces/classification/*genetics/growth &amp; development/*physiology ; },
abstract = {One of the most important ways that bacteria compete for resources and space is by producing antibiotics that inhibit competitors. Because antibiotic production is costly, the biosynthetic gene clusters coordinating their synthesis are under strict regulatory control and often require "elicitors" to induce expression, including cues from competing strains. Although these cues are common, they are not produced by all competitors, and so the phenotypes causing induction remain unknown. By studying interactions between 24 antibiotic-producing strains of streptomycetes, we show that strains commonly inhibit each other's growth and that this occurs more frequently if strains are closely related. Next, we show that antibiotic production is more likely to be induced by cues from strains that are closely related or that share secondary metabolite biosynthetic gene clusters (BGCs). Unexpectedly, antibiotic production is less likely to be induced by competitors that inhibit the growth of a focal strain, indicating that cell damage is not a general cue for induction. In addition to induction, antibiotic production often decreases in the presence of a competitor, although this response was not associated with genetic relatedness or overlap in BGCs. Finally, we show that resource limitation increases the chance that antibiotic production declines during competition. Our results reveal the importance of social cues and resource availability in the dynamics of interference competition in streptomycetes.IMPORTANCE Bacteria secrete antibiotics to inhibit their competitors, but the presence of competitors can determine whether these toxins are produced. Here, we study the role of the competitive and resource environment on antibiotic production in Streptomyces, bacteria renowned for their production of antibiotics. We show that Streptomyces cells are more likely to produce antibiotics when grown with competitors that are closely related or that share biosynthetic pathways for secondary metabolites, but not when they are threatened by competitor's toxins, in contrast to predictions of the competition sensing hypothesis. Streptomyces cells also often reduce their output of antibiotics when grown with competitors, especially under nutrient limitation. Our findings highlight that interactions between the social and resource environments strongly regulate antibiotic production in these medicinally important bacteria.},
}
@article {pmid33563788,
year = {2021},
author = {Otwell, AE and Carr, AV and Majumder, ELW and Ruiz, MK and Wilpiszeski, RL and Hoang, LT and Webb, B and Turkarslan, S and Gibbons, SM and Elias, DA and Stahl, DA and Siuzdak, G and Baliga, NS},
title = {Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33563788},
issn = {2379-5077},
support = {R35 GM130385/GM/NIGMS NIH HHS/United States ; },
abstract = {Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater, and sediment and therefore may play important roles in competitive interactions. Here, through comparative transcriptomic and metabolomic analyses, we have uncovered mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of nitrate respiratory growth for the NRB Intrasporangium calvum C5. Specifically, the systems analysis predicted that cysteine and hydrogen sulfide inhibit growth of I. calvum C5 by disrupting distinct steps across multiple pathways, including branched-chain amino acid (BCAA) biosynthesis, utilization of specific carbon sources, and cofactor metabolism. We have validated these predictions by demonstrating that complementation with BCAAs and specific carbon sources relieves the growth inhibitory effects of cysteine and hydrogen sulfide. We discuss how these mechanistic insights give new context to the interplay and stratification of NRB and SRB in diverse environments.IMPORTANCE Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts. For instance, the removal of reactive nitrogen species by NRB is desirable for wastewater treatment, but in agricultural soils, NRB can drive the conversion of nitrates from fertilizers into nitrous oxide, a potent greenhouse gas. Similarly, the hydrogen sulfide produced by SRB can help sequester and immobilize toxic heavy metals but is undesirable in oil wells where competition between SRB and NRB has been exploited to suppress hydrogen sulfide production. By characterizing how reduced sulfur compounds inhibit growth and activity of NRB, we have gained systems-level and mechanistic insight into the interplay of these two important groups of organisms and drivers of their stratification in diverse environments.},
}
@article {pmid33563787,
year = {2021},
author = {de la Cuesta-Zuluaga, J and Spector, TD and Youngblut, ND and Ley, RE},
title = {Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33563787},
issn = {2379-5077},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Archaea of the order Methanomassiliicoccales use methylated amines such as trimethylamine as the substrates for methanogenesis. They form two large phylogenetic clades and reside in diverse environments, from soil to the human gut. Two genera, one from each clade, inhabit the human gut: Methanomassiliicoccus, which has one cultured representative, and "Candidatus Methanomethylophilus," which has none. Questions remain regarding their distribution across biomes and human populations, their association with other taxa in the gut, and whether host genetics correlate with their abundance. To gain insight into the Methanomassiliicoccales clade, particularly its human-associated members, we performed a genomic comparison of 72 Methanomassiliicoccales genomes and assessed their presence in metagenomes derived from the human gut (n = 4,472, representing 22 populations), nonhuman animal gut (n = 145), and nonhost environments (n = 160). Our analyses showed that all taxa are generalists; they were detected in animal gut and environmental samples. We confirmed two large clades, one enriched in the gut and the other enriched in the environment, with notable exceptions. Genomic adaptations to the gut include genome reduction and genes involved in the shikimate pathway and bile resistance. Genomic adaptations differed by clade, not habitat preference, indicating convergent evolution between the clades. In the human gut, the relative abundance of Methanomassiliicoccales spp. correlated with trimethylamine-producing bacteria and was unrelated to host genotype. Our results shed light on the microbial ecology of this group and may help guide Methanomassiliicoccales-based strategies for trimethylamine mitigation in cardiovascular disease.IMPORTANCE Methanomassiliicoccales are less-known members of the human gut archaeome. Members of this order use methylated amines, including trimethylamine, in methane production. This group has only one cultured representative; how its members adapted to inhabit the mammalian gut and how they interact with other microbes is largely unknown. Using bioinformatics methods applied to DNA from a wide range of samples, we profiled the abundances of these Archaea spp. in environmental and host-associated microbial communities. We observed two groups of Methanomassiliicoccales, one largely host associated and one largely found in environmental samples, with some exceptions. When host associated, these Archaea have smaller genomes and possess genes related to bile resistance and aromatic amino acid precursors. We did not detect Methanomassiliicoccales in all human populations tested, but when present, they were correlated with bacteria known to produce trimethylamine. Due to their metabolism of trimethylamine, these intriguing Archaea may form the basis of novel therapies for cardiovascular disease.},
}
@article {pmid33562402,
year = {2021},
author = {Maillet, A and Denojean, P and Bouju-Albert, A and Scaon, E and Leuillet, S and Dousset, X and Jaffrès, E and Combrisson, J and Prévost, H},
title = {Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {2},
pages = {},
pmid = {33562402},
issn = {2304-8158},
support = {2016-06930//Conseil R&#xe9;gional des Pays de la Loire/ ; 2016/1546//Association Nationale de la Recherche et de la Technologie/ ; },
abstract = {Cold-smoked salmon is a widely consumed ready-to-eat seafood product that is a fragile commodity with a long shelf-life. The microbial ecology of cold-smoked salmon during its shelf-life is well known. However, to our knowledge, no study on the microbial ecology of cold-smoked salmon using next-generation sequencing has yet been undertaken. In this study, cold-smoked salmon microbiotas were investigated using a polyphasic approach composed of cultivable methods, V3-V4 16S rRNA gene metabarcoding and chemical analyses. Forty-five cold-smoked salmon products processed in three different factories were analyzed. The metabarcoding approach highlighted 12 dominant genera previously reported as fish spoilers: Firmicutes Staphylococcus, Carnobacterium, Lactobacillus, β-Proteobacteria Photobacterium, Vibrio, Aliivibrio, Salinivibrio, Enterobacteriaceae Serratia,Pantoea, γ-Proteobacteria Psychrobacter, Shewanella and Pseudomonas. Specific operational taxonomic units were identified during the 28-day storage study period. Operational taxonomic units specific to the processing environment were also identified. Although the 45 cold-smoked salmon products shared a core microbiota, a processing plant signature was found. This suggest that the bacterial communities of cold-smoked salmon products are impacted by the processing environment, and this environment could have a negative effect on product quality. The use of a polyphasic approach for seafood products and food processing environments could provide better insights into residential bacteria dynamics and their impact on food safety and quality.},
}
@article {pmid33562194,
year = {2021},
author = {Szczypta, A and Talaga-Ćwiertnia, K and Kielar, M and Krzyściak, P and Gajewska, A and Szura, M and Bulanda, M and Chmielarczyk, A},
title = {Investigation of Acinetobacter baumannii Activity in Vascular Surgery Units through Epidemiological Management Based on the Analysis of Antimicrobial Resistance, Biofilm Formation and Genotyping.},
journal = {International journal of environmental research and public health},
volume = {18},
number = {4},
pages = {},
pmid = {33562194},
issn = {1660-4601},
mesh = {*Acinetobacter Infections/drug therapy/epidemiology ; *Acinetobacter baumannii/genetics ; Anti-Bacterial Agents/pharmacology ; Biofilms ; *Cross Infection/drug therapy/epidemiology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial ; Genotype ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; beta-Lactamases/genetics ; },
abstract = {BACKGROUND/OBJECTIVES: The genus Acinetobacter demonstrates resistance to antibiotics and has been shown to spread in the hospital environment causing epidemic outbreaks among hospitalized patients. The objectives of the present study was to investigate the antibiotic resistance, biofilm formation, and clonality among Acinetobacter baumannii strains.<br><br>MATERIALS AND METHODS: The study involved 6 (I Outbreak) and 3 (II Outbreak) A. baumannii strains isolated from patients hospitalized in vascular surgery unit.<br><br>RESULTS: All tested A. baumannii strains were extensively drug resistant (XDR) and all the isolates were carbapenem-resistant and among them, all carried the blaOXA-51 gene, the blaOXA-24 gene, as well as the blaOXA-23 gene. All of the investigated strains had the ability to form a biofilm, but all of them produced less biofilm than the reference strain. Multi-locus sequence typing (MLST) showed that all strains belonged to the ST2 clone. Pulsed-field gel electrophoresis (PFGE) divided the tested outbreak strains into two clones (A and B).<br><br>CONCLUSION: This study shows a nosocomial spread of XDR A. baumannii ST2 having the blaOXA-51 gene, the blaOXA-24 gene, as well as the blaOXA-23 gene, low biofilm formers, that was prevalent in the vascular surgery unit. To identify the current situation of vascular surgery departments targeted epidemiological investigation was needed. Effective implementation of infection control prevented the spread of the epidemic outbreaks.},
}
@article {pmid33561237,
year = {2021},
author = {Higgins, P and Grace, CA and Lee, SA and Goddard, MR},
title = {Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion.},
journal = {G3 (Bethesda, Md.)},
volume = {11},
number = {1},
pages = {},
pmid = {33561237},
issn = {2160-1836},
mesh = {Fermentation ; Genome, Fungal ; Genomics ; New Zealand ; *Saccharomyces cerevisiae/genetics ; *Wine ; },
abstract = {Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.},
}
@article {pmid33559710,
year = {2021},
author = {Ayyasamy, A and Kempraj, V and Pagadala Damodaram, KJ},
title = {Endosymbiotic Bacteria Aid to Overcome Temperature Induced Stress in the Oriental Fruit Fly, Bactrocera dorsalis.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {783-792},
pmid = {33559710},
issn = {1432-184X},
support = {NICRA//Indian Council of Agricultural Research/ ; },
mesh = {Animals ; Bacteria/genetics ; DNA, Ribosomal ; Female ; *Gastrointestinal Microbiome ; Male ; Temperature ; *Tephritidae ; },
abstract = {Endosymbiotic microbiota are known to have an enormous impact on their host, influencing its physiology, behavior, fitness, and various other aspects. The present study hypothesizes that certain bacterial symbionts aid the Oriental fruit fly, Bactrocera dorsalis in its adaptation to survive thermal stress encountered in the environment. Investigative studies on the change in gut and reproductive tract microbiota diversity of male and female B. dorsalis revealed that certain genera of Acinetobacter, Brevibacillus, Bacillus, Enterobacter, Enterococcus, Pseudomonas, and Staphylococcus were involved in the adaptation of B. dorsalis to temperature stresses. The intestinal and reproductive tract bacterial community of B. dorsalis varied depending on the temperature the insects were reared at. We hypothesized that the microbiota present in B. dorsalis' gut helped it endure temperature stresses over prolonged periods. Out of 54 bacterial isolates, 25, 15, and 14 isolates were obtained from flies reared at 27 °C, 18 °C, and 35 °C, respectively. A 16S rDNA analysis revealed that the bacterial isolates (reared at different temperatures) belonged to different genera. The flies were supplemented with antibiotics to suppress the existing gut microbiota and subsequently fed with bacterial isolates from flies reared at 18 °C, 27 °C (control) or 35 °C separately. When these flies were placed in incubators pre-set at the above temperatures, the survival rate exhibited by the flies differed significantly. The flies fed with bacterial isolates from 18 °C could survive only in incubators pre-set at 18 °C, while flies fed with bacterial isolates from 35 °C could survive only at 35 °C and not vice versa. The microbiota supplementation assay established that the presence of specific bacterial isolates aided the flies' survival under varied thermal stresses.},
}
@article {pmid33558687,
year = {2021},
author = {Joshi, S and Robles, A and Aguiar, S and Delgado, AG},
title = {The occurrence and ecology of microbial chain elongation of carboxylates in soils.},
journal = {The ISME journal},
volume = {15},
number = {7},
pages = {1907-1918},
pmid = {33558687},
issn = {1751-7370},
mesh = {Acetates ; Anaerobiosis ; *Clostridium kluyveri ; Fermentation ; *Soil ; Soil Microbiology ; },
abstract = {Chain elongation is a growth-dependent anaerobic metabolism that combines acetate and ethanol into butyrate, hexanoate, and octanoate. While the model microorganism for chain elongation, Clostridium kluyveri, was isolated from a saturated soil sample in the 1940s, chain elongation has remained unexplored in soil environments. During soil fermentative events, simple carboxylates and alcohols can transiently accumulate up to low mM concentrations, suggesting in situ possibility of microbial chain elongation. Here, we examined the occurrence and microbial ecology of chain elongation in four soil types in microcosms and enrichments amended with chain elongation substrates. All soils showed evidence of chain elongation activity with several days of incubation at high (100 mM) and environmentally relevant (2.5 mM) concentrations of acetate and ethanol. Three soils showed substantial activity in soil microcosms with high substrate concentrations, converting 58% or more of the added carbon as acetate and ethanol to butyrate, butanol, and hexanoate. Semi-batch enrichment yielded hexanoate and octanoate as the most elongated products and microbial communities predominated by C. kluyveri and other Firmicutes genera not known to undergo chain elongation. Collectively, these results strongly suggest a niche for chain elongation in anaerobic soils that should not be overlooked in soil microbial ecology studies.},
}
@article {pmid33555369,
year = {2021},
author = {Dou, W and Miao, Y and Xiao, J and Huang, D},
title = {Association of Wolbachia with Gene Expression in Drosophila Testes.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {805-817},
pmid = {33555369},
issn = {1432-184X},
support = {31830084//National Natural Science Foundation of China/ ; 31970440//National Natural Science Foundation of China/ ; 31672336//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Drosophila ; Drosophila melanogaster/genetics ; Male ; Testis ; Transcriptome ; *Wolbachia/genetics ; },
abstract = {Wolbachia is a genus of intracellular symbiotic bacteria that are widely distributed in arthropods and nematodes. These maternally inherited bacteria regulate host reproductive systems in various ways to facilitate their vertical transmission. Since the identification of Wolbachia in many insects, the relationship between Wolbachia and the host has attracted great interest. Numerous studies have indicated that Wolbachia modifies a variety of biological processes in the host. Previous studies in Drosophila melanogaster (D. melanogaster) have demonstrated that Wolbachia can affect spermatid differentiation, chromosome deposition, and sperm activity in the early stages of spermatogenesis, leading to sperm dysfunction. Here, we explored the putative effect of Wolbachia in sperm maturation using transcriptomic approaches to compare gene expression in Wolbachia-infected and Wolbachia-free D. melanogaster adult testes. Our findings show that Wolbachia affects many biological processes in D. melanogaster adult testes, and most of the differentially expressed genes involved in carbohydrate metabolism, lysosomal degradation, proteolysis, lipid metabolism, and immune response were upregulated in the presence of Wolbachia. In contrast, some genes that are putatively associated with cutin and wax biosynthesis and peroxisome pathways were downregulated. We did not find any differentially expressed genes that are predicted to be related to spermatogenesis in the datasets. This work provides additional information for understanding the Wolbachia-host intracellular relationships.},
}
@article {pmid33555368,
year = {2021},
author = {Grzesiak, J and Woltyńska, A and Zdanowski, MK and Górniak, D and Świątecki, A and Olech, MA and Aleksandrzak-Piekarczyk, T},
title = {Metabolic fingerprinting of the Antarctic cyanolichen Leptogium puberulum-associated bacterial community (Western Shore of Admiralty Bay, King George Island, Maritime Antarctica).},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {818-829},
pmid = {33555368},
issn = {1432-184X},
support = {2017/25/B/NZ8/01915//Narodowe Centrum Nauki/ ; },
mesh = {Antarctic Regions ; Ascomycota ; Bacteria/genetics ; Bays ; *Lichens ; *Microbiota ; },
abstract = {Lichens are presently regarded as stable biotopes, small ecosystems providing a safe haven for the development of a diverse and numerous microbiome. In this study, we conducted a functional diversity assessment of the microbial community residing on the surface and within the thalli of Leptogium puberulum, a eurytopic cyanolichen endemic to Antarctica, employing the widely used Biolog EcoPlates which test the catabolism of 31 carbon compounds in a colorimetric respiration assay. Lichen thalli occupying moraine ridges of differing age within a proglacial chronosequence, as well as those growing in sites of contrasting nutrient concentrations, were procured from the diverse landscape of the western shore of Admiralty Bay in Maritime Antarctica. The L. puberulum bacterial community catabolized photobiont- (glucose-containing carbohydrates) and mycobiont-specific carbon compounds (D-Mannitol). The bacteria also had the ability to process degradation products of lichen thalli components (D-cellobiose and N-acetyl-D-glucosamine). Lichen thalli growth site characteristics had an impact on metabolic diversity and respiration intensity of the bacterial communities. While high nutrient contents in lichen specimens from "young" proglacial locations and in those from nitrogen enriched sites stimulated bacterial catabolic activity, in old proglacial locations and in nutrient-lacking sites, a metabolic activity restriction was apparent, presumably due to lichen-specific microbial control mechanisms.},
}
@article {pmid33553003,
year = {2020},
author = {Yang, Q and Zou, P and Cao, Z and Wang, Q and Fu, S and Xie, G and Huang, J},
title = {QseC Inhibition as a Novel Antivirulence Strategy for the Prevention of Acute Hepatopancreatic Necrosis Disease (AHPND)-Causing Vibrio parahaemolyticus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {594652},
pmid = {33553003},
issn = {2235-2988},
mesh = {Animals ; Aquaculture ; Necrosis ; *Penaeidae ; *Type VI Secretion Systems/genetics ; *Vibrio parahaemolyticus ; },
abstract = {Acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus resulted in great economic losses in global shrimp aquaculture. There is an urgent need for development of novel strategies to combat AHPND-causing V. parahaemolyticus (VpAHPND), given that one of the greatest challenges currently is the widespread use of antibiotics and subsequent emergence of multidrug-resistant bacteria. Here, we proposed a broad-spectrum antivirulence approach targeting a conserved histidine kinase, QseC, which has been demonstrated to activate virulence expression in several Gram-negative pathogens. Our results showed that QseC mediated the catecholamine stimulated effects on growth and flagellar motility of VpAHPND. Transcriptome analysis revealed that QseC was involved in the global regulation of the virulence of VpAHPND as the ΔqseC mutant exhibited a decreased expression of genes related to type IV pilin, flagellar motility, and biofilm formation, while an overexpression of type VI secretion system and cell wall biosynthesis. Subsequently, the bacterial catecholamine receptor antagonist LED209 not only neutralized the stimulatory effects of host catecholamines on the growth and motility of VpAHPNDin vitro, but also attenuated the virulence of VpAHPND towards brine shrimp larvae and white shrimp in vivo. Additionally, LED209 presented no interference with pathogen growth, nor the toxicity to the experimental animals. These results suggest that QseC can be an attractive antivirulence therapy target, and LED209 is a promising candidate for development of broad-spectrum antivirulence agents. This is the first study that demonstrated the role of QseC in the global regulation of VpAHPND infection and demonstrated the antivirulence potential of LED209, which provides insight into the use of an antivirulence approach for targeting not only VpAHPND, but also a much larger collection of pathogenic bacteria.},
}
@article {pmid33552017,
year = {2020},
author = {Bovio-Winkler, P and Cabezas, A and Etchebehere, C},
title = {Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {603234},
pmid = {33552017},
issn = {1664-302X},
abstract = {Although microbial communities of anaerobic bioreactors have been extensively studied using DNA-based tools, there are still several knowledge gaps regarding the microbiology of the process, in particular integration of all generated data is still limited. One understudied core phylum within anaerobic bioreactors is the phylum Chloroflexi, despite being one of the most abundant groups in anaerobic reactors. In order to address the abundance, diversity and phylogeny of this group in full-scale methanogenic reactors globally distributed, a compilation of 16S ribosomal RNA gene sequence data from 62 full-scale methanogenic reactors studied worldwide, fed either with wastewater treatment anaerobic reactors (WTARs) or solid-waste treatment anaerobic reactors (STARs), was performed. One of the barriers to overcome was comparing data generated using different primer sets and different sequencing platforms. The sequence analysis revealed that the average abundance of Chloroflexi in WTARs was higher than in STARs. Four genera belonging to the Anaerolineae class dominated both WTARs and STARs but the core populations were different. According to the phylogenetic analysis, most of the sequences formed clusters with no cultured representatives. The Anaerolineae class was more abundant in reactors with granular biomass than in reactors with disperse biomass supporting the hypothesis that Anaerolineae play an important role in granule formation and structure due to their filamentous morphology. Cross-study comparisons can be fruitfully used to understand the complexity of the anaerobic digestion process. However, more efforts are needed to standardize protocols and report metadata information.},
}
@article {pmid33552002,
year = {2020},
author = {García-Ulloa, MI and Escalante, AE and Moreno-Letelier, A and Eguiarte, LE and Souza, V},
title = {Evolutionary Rescue of an Environmental Pseudomonas otitidis in Response to Anthropogenic Perturbation.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {563885},
pmid = {33552002},
issn = {1664-302X},
abstract = {Anthropogenic perturbations introduce novel selective pressures to natural environments, impacting the genomic variability of organisms and thus altering the evolutionary trajectory of populations. Water overexploitation for agricultural purposes and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire hydrological systems to the brink of extinction along with their native populations. Here, we studied the effects of continuous water overexploitation on an environmental aquatic lineage of Pseudomonas otitidis over a 13-year period which encompasses three desiccation events. By comparing the genomes of a population sample from 2003 (original state) and 2015 (perturbed state), we analyzed the demographic history and evolutionary response to perturbation of this lineage. Through coalescent simulations, we obtained a demographic model of contraction-expansion-contraction which points to the occurrence of an evolutionary rescue event. Loss of genomic and nucleotide variation alongside an increment in mean and variance of Tajima's D, characteristic of sudden population expansions, support this observation. In addition, a significant increase in recombination rate (R/θ) was observed, pointing to horizontal gene transfer playing a role in population recovery. Furthermore, the gain of phosphorylation, DNA recombination, small-molecule metabolism and transport and loss of biosynthetic and regulatory genes suggest a functional shift in response to the environmental perturbation. Despite subsequent sampling events in the studied site, no pseudomonad was found until the lagoon completely dried in 2017. We speculate about the causes of P. otitidis final decline or possible extinction. Overall our results are evidence of adaptive responses at the genomic level of bacterial populations in a heavily exploited aquifer.},
}
@article {pmid33551270,
year = {2021},
author = {Lemos, LN and Mendes, LW and Baldrian, P and Pylro, VS},
title = {Genome-Resolved Metagenomics Is Essential for Unlocking the Microbial Black Box of the Soil.},
journal = {Trends in microbiology},
volume = {29},
number = {4},
pages = {279-282},
doi = {10.1016/j.tim.2021.01.013},
pmid = {33551270},
issn = {1878-4380},
mesh = {Bacteria/*genetics ; *Genetic Variation ; *Genome, Bacterial ; Metagenomics/*methods ; *Soil Microbiology ; },
abstract = {Despite several efforts to unravel the microbial diversity of soil, most microbes are still unknown. A recent large-scale effort based on genome-resolved metagenomics by Nayfach et al. has demonstrated how this approach can expand our understanding of novel bacterial lineages, including those from soils. Genomic catalogs of soil microbiomes are now enabling a deeper investigation of the evolutionary and functional role of high-complex soil microbiomes, promoting new knowledge from the reuse and sharing of multi-omics data.},
}
@article {pmid33547531,
year = {2021},
author = {Lesiczka, PM and Hrazdilová, K and Majerová, K and Fonville, M and Sprong, H and Hönig, V and Hofmannová, L and Papežík, P and Růžek, D and Zurek, L and Votýpka, J and Modrý, D},
title = {The Role of Peridomestic Animals in the Eco-Epidemiology of Anaplasma phagocytophilum.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {602-612},
pmid = {33547531},
issn = {1432-184X},
support = {17-16009S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; CZ.02.1.01/16_019/0000759//CePaViP/ ; },
mesh = {*Anaplasma phagocytophilum/genetics ; Animals ; Ecosystem ; Hedgehogs ; Humans ; *Ixodes ; *Tick-Borne Diseases ; },
abstract = {Anaplasma phagocytophilum is an important tick-borne zoonotic agent of human granulocytic anaplasmosis (HGA). In Europe, the Ixodes ticks are the main vector responsible for A. phagocytophilum transmission. A wide range of wild animals is involved in the circulation of this pathogen in the environment. Changes in populations of vertebrates living in different ecosystems impact the ecology of ticks and the epidemiology of tick-borne diseases. In this study, we investigated four species, Western European hedgehog (Erinaceus europaeus), northern white-breasted hedgehog (Erinaceus roumanicus), Eurasian red squirrel (Sciurus vulgaris), and the common blackbird (Turdus merula), to describe their role in the circulation of A. phagocytophilum in urban and periurban ecosystems. Ten different tissues were collected from cadavers of the four species, and blood and ear/skin samples from live blackbirds and hedgehogs. Using qPCR, we detected a high rate of A. phagocytophilum: Western European hedgehogs (96.4%), northern white-breasted hedgehogs (92.9%), Eurasian red squirrels (60%), and common blackbirds (33.8%). In the groEL gene, we found nine genotypes belonging to three ecotypes; seven of the genotypes are associated with HGA symptoms. Our findings underline the role of peridomestic animals in the ecology of A. phagocytophilum and indicate that cadavers are an important source of material for monitoring zoonotic pathogens. Concerning the high prevalence rate, all investigated species play an important role in the circulation of A. phagocytophilum in municipal areas; however, hedgehogs present the greatest anaplasmosis risk for humans. Common blackbirds and squirrels carry different A. phagocytophilum variants some of which are responsible for HGA.},
}
@article {pmid33545473,
year = {2021},
author = {Wei, H and Lin, X},
title = {Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum.},
journal = {The Science of the total environment},
volume = {771},
number = {},
pages = {144824},
doi = {10.1016/j.scitotenv.2020.144824},
pmid = {33545473},
issn = {1879-1026},
mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Estuaries ; Humans ; Oxidation-Reduction ; Phylogeny ; Rivers ; Soil Microbiology ; },
abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g[-1] d[-1], mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 10[6] and 2.4 ± 3.54 × 10[6] copies g[-1], respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4[+]) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4[+] consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.},
}
@article {pmid33542279,
year = {2021},
author = {Meale, SJ and Popova, M and Saro, C and Martin, C and Bernard, A and Lagree, M and Yáñez-Ruiz, DR and Boudra, H and Duval, S and Morgavi, DP},
title = {Early life dietary intervention in dairy calves results in a long-term reduction in methane emissions.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {3003},
pmid = {33542279},
issn = {2045-2322},
mesh = {Animal Feed ; Animals ; Archaea/isolation &amp; purification ; Body Fluids ; Body Weight ; Cattle ; Diet ; *Ecosystem ; Female ; Fermentation ; Lactation/*metabolism ; Methane/*metabolism ; Propanols/pharmacology ; Rumen/metabolism/*microbiology ; Weaning ; },
abstract = {Recent evidence suggests that changes in microbial colonization of the rumen prior to weaning may imprint the rumen microbiome and impact phenotypes later in life. We investigated how dietary manipulation from birth influences growth, methane production, and gastrointestinal microbial ecology. At birth, 18 female Holstein and Montbéliarde calves were randomly assigned to either treatment or control (CONT). Treatment was 3-nitrooxypropanol (3-NOP), an investigational anti-methanogenic compound that was administered daily from birth until three weeks post-weaning (week 14). Samples of rumen fluid and faecal content were collected at weeks 1, 4, 11, 14, 23, and 60 of life. Calves were tested for methane emissions using the GreenFeed system during the post-weaning period (week 11-23 and week 56-60 of life). Calf physiological parameters (BW, ADG and individual VFA) were similar across groups throughout the trial. Treated calves showed a persistent reduction in methane emissions (g CH4/d) throughout the post-weaning period up to at least 1 year of life, despite treatment ceasing three weeks post-weaning. Similarly, despite variability in the abundance of individual taxa across weeks, the rumen bacterial, archaeal and fungal structure differed between CONT and 3-NOP calves across all weeks, as visualised using sparse-PLS-DA. Similar separation was also observed in the faecal bacterial community. Interestingly, despite modest modifications to the abundance of rumen microbes, the reductive effect of 3-NOP on methane production persisted following cessation of the treatment period, perhaps indicating a differentiation of the ruminal microbial ecosystem or a host response triggered by the treatment in the early development phase.},
}
@article {pmid33542245,
year = {2021},
author = {Grum-Grzhimaylo, AA and Bastiaans, E and van den Heuvel, J and Berenguer Millanes, C and Debets, AJM and Aanen, DK},
title = {Somatic deficiency causes reproductive parasitism in a fungus.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {783},
pmid = {33542245},
issn = {2041-1723},
mesh = {Cell Fusion ; DNA Mutational Analysis ; *Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; Gene Knockout Techniques ; Genes, Fungal/genetics ; Hyphae/*physiology ; Mutation ; Neurospora crassa/*physiology ; },
abstract = {Some multicellular organisms can fuse because mergers potentially provide mutual benefits. However, experimental evolution in the fungus Neurospora crassa has demonstrated that free fusion of mycelia favours cheater lineages, but the mechanism and evolutionary dynamics of this exploitation are unknown. Here we show, paradoxically, that all convergently evolved cheater lineages have similar fusion deficiencies. These mutants are unable to initiate fusion but retain access to wild-type mycelia that fuse with them. This asymmetry reduces cheater-mutant contributions to somatic substrate-bound hyphal networks, but increases representation of their nuclei in the aerial reproductive hyphae. Cheaters only benefit when relatively rare and likely impose genetic load reminiscent of germline senescence. We show that the consequences of somatic fusion can be unequally distributed among fusion partners, with the passive non-fusing partner profiting more. We discuss how our findings may relate to the extensive variation in fusion frequency of fungi found in nature.},
}
@article {pmid33539603,
year = {2021},
author = {Fernandes, MF and Lopes, LD and Dick, RP},
title = {Microbial dynamics associated with the decomposition of coconut and maize residues in a microcosm experiment with tropical soils under two nitrogen fertilization levels.},
journal = {Journal of applied microbiology},
volume = {131},
number = {3},
pages = {1261-1273},
doi = {10.1111/jam.15021},
pmid = {33539603},
issn = {1365-2672},
support = {//Empresa Brasileira de Pesquisa Agropecu&#xe1;ria/ ; //Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Carbon ; *Cocos ; Fertilization ; *Nitrogen/analysis ; *Soil ; *Soil Microbiology ; *Zea mays ; },
abstract = {AIMS: The microbial dynamics associated with the decomposition of maize (Zea mays) and coconut (Cocos nucifera) residues were investigated to assess the feasibility of using them as mulch in tropical soils.<br><br>METHODS AND RESULTS: Phospholipid fatty-acid (PLFA) profiling, microbial biomass (MB-C), basal respiration, C-cycle enzyme activities and inorganic N dynamics were monitored in a microcosm experiment incubating soil samples with plant residues for 425&#xa0;days. Maize stover (MS) showed a higher decomposition, respiration rate, MB-C, enzymes activities and shift in microbial community structure than coconut husk (CH), which was barely changed. In MS, the lower N level increased C losses and decreased N mineralization compared to the higher N level.<br><br>CONCLUSIONS: Maize stover is suitable for mulching and has a high potential of increasing soil quality if the proper N fertilization level is used, avoiding excessive C mineralization and N immobilization. Coconut husk decomposition was mostly impaired, indicating that a pre-processing is necessary to improve the benefits of this residue.<br><br>Tropical soils are prone to degradation. Mulching can promote soil conservation, but depends on residue type and soil chemistry. Our study showed that MS managed under the recommended N fertilization level is suitable for mulching while CH is highly inaccessible for microbial degradation.},
}
@article {pmid33538855,
year = {2021},
author = {Lyautey, E and Billard, E and Tissot, N and Jacquet, S and Domaizon, I},
title = {Seasonal Dynamics of Abundance, Structure, and Diversity of Methanogens and Methanotrophs in Lake Sediments.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {559-571},
pmid = {33538855},
issn = {1432-184X},
mesh = {Archaea/genetics ; *Euryarchaeota/genetics ; Geologic Sediments ; Lakes ; Methane ; *Methylococcaceae/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; },
abstract = {Understanding temporal and spatial microbial community abundance and diversity variations is necessary to assess the functional roles played by microbial actors in the environment. In this study, we investigated spatial variability and temporal dynamics of two functional microbial sediment communities, methanogenic Archaea and methanotrophic bacteria, in Lake Bourget, France. Microbial communities were studied from 3 sites sampled 4 times over a year, with one core sampled at each site and date, and 5 sediment layers per core were considered. Microbial abundance in the sediment were determined using flow cytometry. Methanogens and methanotrophs community structures, diversity, and abundance were assessed using T-RFLP, sequencing, and real-time PCR targeting mcrA and pmoA genes, respectively. Changes both in structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics. Methanogen diversity was dominated by Methanomicrobiales (mainly Methanoregula) members, followed by Methanosarcinales and Methanobacteriales. For methanotrophs, diversity was dominated by Methylobacter in the deeper area and by Methylococcus in the shallow area. Organic matter appeared to be the main environmental parameter controlling methanogens, while oxygen availability influenced both the structure and abundance of the methanotrophic community.},
}
@article {pmid33538813,
year = {2021},
author = {Ruiz-González, C and Rodellas, V and Garcia-Orellana, J},
title = {The microbial dimension of submarine groundwater discharge: current challenges and future directions.},
journal = {FEMS microbiology reviews},
volume = {45},
number = {5},
pages = {},
pmid = {33538813},
issn = {1574-6976},
support = {//MICINN/ ; RTI2018-099740-J-I00//GRAMMY Foundation/ ; },
mesh = {Environmental Monitoring ; *Groundwater ; *Microbiota ; Seawater ; },
abstract = {Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land-ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater-marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.},
}
@article {pmid33538648,
year = {2021},
author = {Hennebique, A and Peyroux, J and Brunet, C and Martin, A and Henry, T and Knezevic, M and Santic, M and Boisset, S and Maurin, M},
title = {Amoebae can promote the survival of Francisella species in the aquatic environment.},
journal = {Emerging microbes &amp; infections},
volume = {10},
number = {1},
pages = {277-290},
pmid = {33538648},
issn = {2222-1751},
mesh = {Amoeba/*microbiology ; Francisella tularensis/*growth &amp; development ; Fresh Water/*microbiology ; Microbial Viability ; },
abstract = {Francisella tularensis, a tier 1 select agent, is the causative bacterium of tularemia, a zoonosis with a large animal reservoir. However, F. tularensis, like many other Francisella species, is assumed to have an aquatic reservoir. The mechanisms of Francisella species persistence in surface water remain poorly characterized. In this study, we deeply investigated the long-term interactions of the tularemia agent F. tularensis subsp. holarctica, F. novicida or F. philomiragia with amoebae of the Acanthamoeba species. In amoeba plate screening tests, all the Francisella species tested resisted the attack by amoebae. In in vitro infection models, intra-amoebic growth of Francisella varied according to the involved bacterial species and strains, but also the amoeba culture medium used. In co-culture models, the amoebae favoured Francisella survival over 16 days, which was likely dependent on direct contact between bacteria and amoebae for F. novicida and on amoeba-excreted compounds for F. novicida and for F. tularensis. In a spring water co-culture model, amoebae again enhanced F. novicida survival and preserved bacterial morphology. Overall, our results demonstrate that amoebae likely promote Francisella survival in aquatic environments, including the tularemia agent F. tularensis. However, bacteria-amoebae interactions are complex and depend on the Francisella species considered.},
}
@article {pmid33537111,
year = {2021},
author = {Salek, MM and Fernandez, V and D'souza, G and Puigmartí-Luis, J and Stocker, R and Secchi, E},
title = {An interdisciplinary and application-oriented approach to teach microfluidics.},
journal = {Biomicrofluidics},
volume = {15},
number = {1},
pages = {014104},
pmid = {33537111},
issn = {1932-1058},
abstract = {Microfluidics is a relatively novel interdisciplinary research area with broad applications in chemistry, physics, material science, and biology. Despite the rapid growth of the field, students' exposure to microfluidic technologies is still limited and often insufficient to appreciate the advantages over other commonly used technologies. To this end, we designed a five-day course, "Microfluidics for microbial ecology," in which students with very different backgrounds learn the basics of microfluidic technologies and sample a range of applications in microbial ecology. The course was created for Master and Ph.D. students interested in applying microfluidics to their research and, therefore, followed an application-oriented approach. The presentation of critical aspects of fluid flow phenomena at the microscale and an outline of the advantages and constraints of the technology provide students with the background to design and perform microfluidics-based experiments. In order to improve the effectiveness of learning in a class with diverse interests and backgrounds, two active learning exercises were implemented. The first comprised the design of an individualized microfluidics experiment in parallel with the lectures: students were guided to apply each module to their personalized application and discuss it in groups. The second was a group experimental activity, in which students jointly set up, performed, analyzed, and presented a microfluidics-based experiment. Given the multidisciplinary teaching context, the course was able to foster common conceptual ground and promote discussion among students. This application-oriented approach built upon experimental activities and in-class discussion is well suited to promote learning in a technology-related subject such as microfluidics.},
}
@article {pmid33537022,
year = {2020},
author = {Haber, M and Burgsdorf, I and Handley, KM and Rubin-Blum, M and Steindler, L},
title = {Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {622824},
pmid = {33537022},
issn = {1664-302X},
abstract = {Sponges are among the oldest metazoans and their success is partly due to their abundant and diverse microbial symbionts. They are one of the few animals that have Thaumarchaeota symbionts. Here we compare genomes of 11 Thaumarchaeota sponge symbionts, including three new genomes, to free-living ones. Like their free-living counterparts, sponge-associated Thaumarchaeota can oxidize ammonia, fix carbon, and produce several vitamins. Adaptions to life inside the sponge host include enrichment in transposases, toxin-antitoxin systems and restriction modifications systems, enrichments previously reported also from bacterial sponge symbionts. Most thaumarchaeal sponge symbionts lost the ability to synthesize rhamnose, which likely alters their cell surface and allows them to evade digestion by the host. All but one archaeal sponge symbiont encoded a high-affinity, branched-chain amino acid transporter system that was absent from the analyzed free-living thaumarchaeota suggesting a mixotrophic lifestyle for the sponge symbionts. Most of the other unique features found in sponge-associated Thaumarchaeota, were limited to only a few specific symbionts. These features included the presence of exopolyphosphatases and a glycine cleavage system found in the novel genomes. Thaumarchaeota have thus likely highly specific interactions with their sponge host, which is supported by the limited number of host sponge species to which each of these symbionts is restricted.},
}
@article {pmid33536337,
year = {2021},
author = {Zakem, EJ and Cael, BB and Levine, NM},
title = {A unified theory for organic matter accumulation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {6},
pages = {},
pmid = {33536337},
issn = {1091-6490},
mesh = {Carbon/*metabolism ; Climate ; Microbiota/*genetics ; *Models, Theoretical ; Organic Chemicals/*metabolism ; Temperature ; },
abstract = {Organic matter constitutes a key reservoir in global elemental cycles. However, our understanding of the dynamics of organic matter and its accumulation remains incomplete. Seemingly disparate hypotheses have been proposed to explain organic matter accumulation: the slow degradation of intrinsically recalcitrant substrates, the depletion to concentrations that inhibit microbial consumption, and a dependency on the consumption capabilities of nearby microbial populations. Here, using a mechanistic model, we develop a theoretical framework that explains how organic matter predictably accumulates in natural environments due to biochemical, ecological, and environmental factors. Our framework subsumes the previous hypotheses. Changes in the microbial community or the environment can move a class of organic matter from a state of functional recalcitrance to a state of depletion by microbial consumers. The model explains the vertical profile of dissolved organic carbon in the ocean and connects microbial activity at subannual timescales to organic matter turnover at millennial timescales. The threshold behavior of the model implies that organic matter accumulation may respond nonlinearly to changes in temperature and other factors, providing hypotheses for the observed correlations between organic carbon reservoirs and temperature in past earth climates.},
}
@article {pmid33536320,
year = {2021},
author = {Rubbens, P and Props, R and Kerckhof, FM and Boon, N and Waegeman, W},
title = {PhenoGMM: Gaussian Mixture Modeling of Cytometry Data Quantifies Changes in Microbial Community Structure.},
journal = {mSphere},
volume = {6},
number = {1},
pages = {},
pmid = {33536320},
issn = {2379-5042},
mesh = {Biodiversity ; Flow Cytometry/*methods ; *Microbiota ; *Normal Distribution ; },
abstract = {Microbial flow cytometry can rapidly characterize the status of microbial communities. Upon measurement, large amounts of quantitative single-cell data are generated, which need to be analyzed appropriately. Cytometric fingerprinting approaches are often used for this purpose. Traditional approaches either require a manual annotation of regions of interest, do not fully consider the multivariate characteristics of the data, or result in many community-describing variables. To address these shortcomings, we propose an automated model-based fingerprinting approach based on Gaussian mixture models, which we call PhenoGMM. The method successfully quantifies changes in microbial community structure based on flow cytometry data, which can be expressed in terms of cytometric diversity. We evaluate the performance of PhenoGMM using data sets from both synthetic and natural ecosystems and compare the method with a generic binning fingerprinting approach. PhenoGMM supports the rapid and quantitative screening of microbial community structure and dynamics.IMPORTANCE Microorganisms are vital components in various ecosystems on Earth. In order to investigate the microbial diversity, researchers have largely relied on the analysis of 16S rRNA gene sequences from DNA. Flow cytometry has been proposed as an alternative technology to characterize microbial community diversity and dynamics. The technology enables a fast measurement of optical properties of individual cells. So-called fingerprinting techniques are needed in order to describe microbial community diversity and dynamics based on flow cytometry data. In this work, we propose a more advanced fingerprinting strategy based on Gaussian mixture models. We evaluated our workflow on data sets from both synthetic and natural ecosystems, illustrating its general applicability for the analysis of microbial flow cytometry data. PhenoGMM supports a rapid and quantitative analysis of microbial community structure using flow cytometry.},
}
@article {pmid33535686,
year = {2021},
author = {M'hir, S and Filannino, P and Mejri, A and Tlais, AZA and Di Cagno, R and Ayed, L},
title = {Functional Exploitation of Carob, Oat Flour, and Whey Permeate as Substrates for a Novel Kefir-Like Fermented Beverage: An Optimized Formulation.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {2},
pages = {},
pmid = {33535686},
issn = {2304-8158},
abstract = {This study investigated the fortification of a carob-based kefir-like beverage (KLB) with whey permeate (WP) and oat flour (OF). The response surface method was used to show the effect of WP and OF concentrations on lactic acid bacteria and yeast cell densities, pH, total titratable acidity (TTA), total phenolics content (TCP), DPPH radical scavenging activity, and overall acceptability (OA) in KLB. The statistical design provided thirteen formulations where OF concentration varied from 3% to 5% and WP from 10% to 15%. The enrichment of carob pods decoction with WP and OF had a positive effect on biomass production. Overall fermentation was shown to increase TPC of KLB. Furthermore, OF supplementation led to the higher levels of TPC and antiradical activity. WP negatively affected OA at linear and quadratic levels, whereas no effect of OF was observed at the linear level. The optimum point was found by using WP at 11.51% and OF at 4.77%. Optimized KLB resulted in an enrichment of bioavailable phenolics derivatives and highly digestible proteins.},
}
@article {pmid33535657,
year = {2021},
author = {Bourigault, Y and Chane, A and Barbey, C and Jafra, S and Czajkowski, R and Latour, X},
title = {Biosensors Used for Epifluorescence and Confocal Laser Scanning Microscopies to Study Dickeya and Pectobacterium Virulence and Biocontrol.},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {},
pmid = {33535657},
issn = {2076-2607},
support = {-//Minist&#xe8;re de l'Enseignement Sup&#xe9;rieur, de la Recherche et de l'innovation, the R&#xe9;gion Normandie and the Evreux Portes de Normandie agglom&#xe9;ration, the P&#xf4;le de Comp&#xe9;tivit&#xe9; Valorial, and FEDER (European Union)/ ; DS 531-N105-D786-20//Polish Ministry of Science and Higher Education (Ministerstwo Nauki i Szkolnictwa Wy&#x17c;szego, Polska)/ ; DS 531-N104-D800-20//Polish Ministry of Higher Education (Ministers two Nauki i Szkolnictwa Wy&#x17c;szego, Polska)/ ; },
abstract = {Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot Pectobacteriaceae biosensors, often inoculated in potato Solanum tuberosum, are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, Dickeya and Pectobacterium-tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence in planta, in the near future.},
}
@article {pmid33533410,
year = {2021},
author = {Min, D and Doxey, AC and Neufeld, JD},
title = {AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology.},
journal = {GigaScience},
volume = {10},
number = {2},
pages = {},
pmid = {33533410},
issn = {2047-217X},
mesh = {Automation ; Data Visualization ; *High-Throughput Nucleotide Sequencing ; Phylogeny ; *Software ; },
abstract = {BACKGROUND: Advances in high-throughput sequencing accessibility have democratized small subunit ribosomal RNA gene sequence data collection, coincident with an increasing availability of computational tools for sequence data processing, multivariate statistics, and data visualization. However, existing tools often require programming ability and frequent user intervention that may not be suitable for fast-paced and large-scale data analysis by end user microbiologists who are unfamiliar with the Linux command line environment or who prefer interactions with a GUI. Here we present AXIOME3, which is a completely redeveloped AXIOME pipeline that streamlines small subunit ribosomal RNA data analysis by managing QIIME2, R, and Python-associated analyses through an interactive web interface.<br><br>FINDINGS: AXIOME3 comes with web GUI to improve usability by simplifying configuration processes and task status tracking. Internally, it uses an automated pipeline that is wrapped around QIIME2 to generate a range of outputs including amplicon sequence variant tables, taxonomic classifications, phylogenetic trees, biodiversity metrics, and ordinations. The extension module for AXIOME3 provides advanced data visualization tools such as principal coordinate analysis, bubble plots, and triplot ordinations that can be used to visualize interactions between a distance matrix, amplicon sequence variant taxonomy, and sample metadata.<br><br>CONCLUSIONS: Because repeat analysis of small subunit ribosomal RNA amplicon sequence data is challenging for those who have limited experience in command line environments, AXIOME3 now offers rapid and user-friendly options within an automated pipeline, with advanced data visualization tools and the ability for users to incorporate additional analyses easily through extension. AXIOME3 is completely open source (https://github.com/neufeld/AXIOME3, https://github.com/neufeld/AXIOME3-GUI), and researchers are encouraged to modify and redistribute the package.},
}
@article {pmid33532913,
year = {2021},
author = {Caillon, F and Besemer, K and Peduzzi, P and Schelker, J},
title = {Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {591-601},
pmid = {33532913},
issn = {1432-184X},
mesh = {Bacteria/genetics ; Floods ; *Microbiota ; *Soil ; Soil Microbiology ; },
abstract = {Flood events are now recognized as potentially important occasions for the transfer of soil microbes to stream ecosystems. Yet, little is known about these "dynamic pulses of microbial life" for stream bacterial community composition (BCC) and diversity. In this study, we explored the potential alteration of stream BCC by soil inoculation during high flow events in six pre-alpine first order streams and the larger Oberer Seebach. During 1 year, we compared variations of BCC in soil water, stream water and in benthic biofilms at different flow conditions (low to intermediate flows versus high flow). Bacterial diversity was lowest in biofilms, followed by soils and highest in headwater streams and the Oberer Seebach. In headwater streams, bacterial diversity was significantly higher during high flow, as compared to low flow (Shannon diversity: 7.6 versus 7.9 at low versus high flow, respectively, p < 0.001). Approximately 70% of the bacterial operational taxonomic units (OTUs) from streams and stream biofilms were the same as in soil water, while in the latter one third of the OTUs were specific to high flow conditions. These soil high-flow OTUs were also found in streams and biofilms at other times of the year. These results demonstrate the relevance of floods in generating short and reoccurring inoculation events for flowing waters. Moreover, they show that soil microbial inoculation during high flow enhances microbial diversity and shapes fluvial BCC even during low flow. Hence, soil microbial inoculation during floods could act as a previously overlooked driver of microbial diversity in headwater streams.},
}
@article {pmid33531553,
year = {2021},
author = {Jeon, JS and Carreno-Quintero, N and van Eekelen, HDLM and De Vos, RCH and Raaijmakers, JM and Etalo, DW},
title = {Impact of root-associated strains of three Paraburkholderia species on primary and secondary metabolism of Brassica oleracea.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {2781},
pmid = {33531553},
issn = {2045-2322},
mesh = {*Brassica/metabolism/microbiology ; Burkholderiaceae/*metabolism ; Plant Diseases/*prevention &amp; control ; Plant Leaves/*metabolism ; *Plant Roots/metabolism/microbiology ; Severity of Illness Index ; },
abstract = {Several root-colonizing bacterial species can simultaneously promote plant growth and induce systemic resistance. How these rhizobacteria modulate plant metabolism to accommodate the carbon and energy demand from these two competing processes is largely unknown. Here, we show that strains of three Paraburkholderia species, P. graminis PHS1 (Pbg), P. hospita mHSR1 (Pbh), and P. terricola mHS1 (Pbt), upon colonization of the roots of two Broccoli cultivars led to cultivar-dependent increases in biomass, changes in primary and secondary metabolism and induced resistance against the bacterial leaf pathogen Xanthomonas campestris. Strains that promoted growth led to greater accumulation of soluble sugars in the shoot and particularly fructose levels showed an increase of up to 280-fold relative to the non-treated control plants. Similarly, a number of secondary metabolites constituting chemical and structural defense, including flavonoids, hydroxycinnamates, stilbenoids, coumarins and lignins, showed greater accumulation while other resource-competing metabolite pathways were depleted. High soluble sugar generation, efficient sugar utilization, and suppression or remobilization of resource-competing metabolites potentially contributed to curb the tradeoff between the carbon and energy demanding processes induced by Paraburkholderia-Broccoli interaction. Collectively, our results provide a comprehensive and integrated view of the temporal changes in plant metabolome associated with rhizobacteria-mediated plant growth promotion and induced resistance.},
}
@article {pmid33531404,
year = {2021},
author = {Cazares, D and Cazares, A and Figueroa, W and Guarneros, G and Edwards, RA and Vinuesa, P},
title = {A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33531404},
issn = {2379-5077},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Phages are generally described as species specific or even strain specific, implying an inherent limitation for some to be maintained and spread in diverse bacterial communities. Moreover, phage isolation and host range determination rarely consider the phage ecological context, likely biasing our notion on phage specificity. Here we isolated and characterized a novel group of six promiscuous phages, named Atoyac, existing in rivers and sewage by using a diverse collection of over 600 bacteria retrieved from the same environments as potential hosts. These podophages isolated from different regions in Mexico display a remarkably broad host range, infecting bacteria from six genera: Aeromonas, Pseudomonas, Yersinia, Hafnia, Escherichia, and Serratia Atoyac phage genomes are ∼42 kb long and highly similar to each other, but not to those currently available in genome and metagenome public databases. Detailed comparison of the phages' efficiency of plating (EOP) revealed variation among bacterial genera, implying a cost associated with infection of distant hosts, and between phages, despite their sequence similarity. We show, through experimental evolution in single or alternate hosts of different genera, that efficiency of plaque production is highly dynamic and tends toward optimization in hosts rendering low plaque formation. However, adaptation to distinct hosts differed between similar phages; whereas one phage optimized its EOP in all tested hosts, the other reduced plaque production in one host, suggesting that propagation in multiple bacteria may be key to maintain promiscuity in some viruses. Our study expands our knowledge of the virosphere and uncovers bacterium-phage interactions overlooked in natural systems.IMPORTANCE In natural environments, phages coexist and interact with a broad variety of bacteria, posing a conundrum for narrow-host-range phage maintenance in diverse communities. This context is rarely considered in the study of host-phage interactions, typically focused on narrow-host-range viruses and their infectivity in target bacteria isolated from sources distinct to where the phages were retrieved from. By studying phage-host interactions in bacteria and viruses isolated from river microbial communities, we show that novel phages with promiscuous host range encompassing multiple bacterial genera can be found in the environment. Assessment of hundreds of interactions in diverse hosts revealed that similar phages exhibit different infection efficiency and adaptation patterns. Understanding host range is fundamental in our knowledge of bacterium-phage interactions and their impact on microbial communities. The dynamic nature of phage promiscuity revealed in our study has implications in different aspects of phage research such as horizontal gene transfer or phage therapy.},
}
@article {pmid33530561,
year = {2021},
author = {Lalaouna, D and Fochesato, S and Harir, M and Ortet, P and Schmitt-Kopplin, P and Heulin, T and Achouak, W},
title = {Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments.},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {},
pmid = {33530561},
issn = {2076-2607},
abstract = {In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.},
}
@article {pmid33530464,
year = {2021},
author = {Masetti, R and Zama, D and Leardini, D and Muratore, E and Turroni, S and Brigidi, P and Pession, A},
title = {Microbiome-Derived Metabolites in Allogeneic Hematopoietic Stem Cell Transplantation.},
journal = {International journal of molecular sciences},
volume = {22},
number = {3},
pages = {},
pmid = {33530464},
issn = {1422-0067},
support = {GR-2013-02357136//Ministero della Salute/ ; },
mesh = {Amino Acids/metabolism ; Animals ; Dietary Fiber/metabolism ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome ; *Hematopoietic Stem Cell Transplantation ; Humans ; *Metabolome ; *Microbiota ; Polyamines/metabolism ; Riboflavin/metabolism ; Transplantation, Homologous ; },
abstract = {The gut microbiome has emerged as a major character in the context of hematopoietic stem cell transplantation. The biology underpinning this relationship is still to be defined. Recently, mounting evidence has suggested a role for microbiome-derived metabolites in mediating crosstalk between intestinal microbial communities and the host. Some of these metabolites, such as fiber-derived short-chain fatty acids or amino acid-derived compounds, were found to have a role also in the transplant setting. New interesting data have been published on this topic, posing a new intriguing perspective on comprehension and treatment. This review provides an updated comprehensive overview of the available evidence in the field of gut microbiome-derived metabolites and hematopoietic stem cell transplantation.},
}
@article {pmid33530338,
year = {2021},
author = {Fiedler, G and Herbstmann, AD and Doll, E and Wenning, M and Brinks, E and Kabisch, J and Breitenwieser, F and Lappann, M and Böhnlein, C and Franz, CMAP},
title = {Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences.},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {},
pmid = {33530338},
issn = {2076-2607},
support = {281A105616//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft/ ; },
abstract = {The genetic heterogeneity of Heyndrickxia sporothermodurans (formerly Bacillussporothermodurans) was evaluated using whole genome sequencing. The genomes of 29 previously identified Heyndrickxiasporothermodurans and two Heyndrickxia vini strains isolated from ultra-high-temperature (UHT)-treated milk were sequenced by short-read (Illumina) sequencing. After sequence analysis, the two H. vini strains could be reclassified as H. sporothermodurans. In addition, the genomes of the H.sporothermodurans type strain (DSM 10599[T]) and the closest phylogenetic neighbors Heyndrickxiaoleronia (DSM 9356[T]) and Heyndrickxia vini (JCM 19841[T]) were also sequenced using both long (MinION) and short-read (Illumina) sequencing. By hybrid sequence assembly, the genome of the H. sporothermodurans type strain was enlarged by 15% relative to the short-read assembly. This noticeable increase was probably due to numerous mobile elements in the genome that are presumptively related to spore heat tolerance. Phylogenetic studies based on 16S rDNA gene sequence, core genome, single-nucleotide polymorphisms and ANI/dDDH, showed that H. vini is highly related to H. sporothermodurans. When examining the genome sequences of all H.sporothermodurans strains from this study, together with 4 H. sporothermodurans genomes available in the GenBank database, the majority of the 36 strains examined occurred in a clonal lineage with less than 100 SNPs. These data substantiate previous reports on the existence and spread of a genetically highly homogenous and heat resistant spore clone, i.e., the HRS-clone.},
}
@article {pmid33529974,
year = {2021},
author = {Candry, P and Ganigué, R},
title = {Chain elongators, friends, and foes.},
journal = {Current opinion in biotechnology},
volume = {67},
number = {},
pages = {99-110},
doi = {10.1016/j.copbio.2021.01.005},
pmid = {33529974},
issn = {1879-0429},
mesh = {Carbohydrates ; Fermentation ; *Friends ; Humans ; Lactic Acid ; *Microbiota/genetics ; },
abstract = {Bioproduction of medium chain carboxylic acids has recently emerged as an alternative strategy to valorize low-value organic waste and side-streams. Key to this route is chain elongation, an anaerobic microbial process driven by ethanol, lactic acid, or carbohydrates. Because these technologies use wastes as feedstocks, mixed microbial communities are often considered as biocatalysts. Understanding and steering these microbiomes is key to optimize bioprocess performance. From a meta-analysis of publicly available sequencing data, we (i) explore how the current collection of isolated chain elongators compares to microbiome members, (ii) discuss the main beneficial and antagonistic interactions with community partners, and (iii) identify the key research gaps and needs to help understand chain elongation microbiomes, and design/steer these novel bioproduction processes.},
}
@article {pmid33529447,
year = {2021},
author = {Miantezila Basilua, J and Mesia Kahunu, G and Pochart, P and Tona Lutete, G},
title = {Overview of HIV treatment failure in Africa using the WHO Pharmacovigilance data.},
journal = {Tropical medicine &amp; international health : TM &amp; IH},
volume = {26},
number = {5},
pages = {530-534},
doi = {10.1111/tmi.13556},
pmid = {33529447},
issn = {1365-3156},
mesh = {Adolescent ; Africa ; Anti-Retroviral Agents/*therapeutic use ; Child ; Child, Preschool ; Databases, Factual ; Female ; HIV Infections/*drug therapy ; Humans ; Infant ; Male ; *Pharmacovigilance ; Retrospective Studies ; Treatment Failure ; World Health Organization ; },
abstract = {OBJECTIVE: To characterise the factors associated with HIV treatment failure (HIVTF) from reported pharmacovigilance data in Africa.<br><br>MATERIALS AND METHODS: This is an observational pharmacovigilance analysis of the safety data of HIVTF available in the WHO International Pharmacovigilance database 'VigiBase[&#xae;] '. We used the Standardised MedDRA Queries (SMQ) to identify all the terms corresponding to HIVTF. To identify all relevant molecules and classes of antiretroviral therapy, we used the anatomic, therapeutic, and chemical classification. We presented results as a percentage or an adjusted Reporting Odds Ratio (aROR) with a 95% confidence interval (95% CI).<br><br>RESULTS: HIVTF was more reported in Africa compared with the rest of the world with 19.1% (18.1%-20.1%) corresponding to 1206 of all 6304 HIVTF reports. Among all the 37 WHO country members in Africa, South Africa was the main source of origin for these HIVTF reports with 86.8% (84.9%-88.7%). Compared to adults, children and adolescents were the most population groups affected by HIVTF, aROR&#xa0;=&#xa0;2.7, (95% CI) 1.7-4.2 and aROR&#xa0;=&#xa0;7.9, (95% CI) 4.5-13.9, respectively.<br><br>CONCLUSION: South Africa was the leading country of the reporting of HIVTF in Africa. The proportion of HIVTF was higher in both HIV-infected children and adolescents than in adults. There is a need for the improvement of medical care for children and adolescents with HIV infection in Africa.},
}
@article {pmid33529050,
year = {2021},
author = {Poveda, J and Martínez-Gómez, &#xc1; and Fenoll, C and Escobar, C},
title = {The Use of Biochar for Plant Pathogen Control.},
journal = {Phytopathology},
volume = {111},
number = {9},
pages = {1490-1499},
doi = {10.1094/PHYTO-06-20-0248-RVW},
pmid = {33529050},
issn = {0031-949X},
mesh = {*Charcoal ; Nutrients ; *Plant Diseases/prevention &amp; control ; Soil ; },
abstract = {To support the search for alternative, nonchemical plant disease control strategies, we present a review of the pathogen-suppressive effects of biochar, a product derived from agricultural and other organic wastes, used as a soil amendment. A wide range of biochar effects contribute to the control of root or foliar fungal pathogens through modification of root exudates, soil properties, and nutrient availability, which influence the growth of antagonist microorganisms. The induction of systemic plant defenses by biochar in the roots to reduce foliar pathogenic fungi, the activation of stress-hormone responses, as well as changes in active oxygen species are indicative of a coordinated hormonal signaling within the plant. Although scarce data are available for oomycetes and bacterial pathogens, reports indicate that biochar promotes changes in the soil microbiota influencing pathogen motility and colonization, and the induction of plant systemic defenses, both contributing to disease suppression. Biochar also suppresses nematode and insect pests. For plant-parasitic nematodes, the primary modes of action are changes in soil microbial community diversity, the release of nematicidal compounds, and the induction of plant defenses. Use of biochar-based soil amendments is a promising strategy compatible with a circular economy, based on zero waste, as part of integrated pathogen and pest management. Since biochars exert complex and distinct modes of action for the control of plant pathogens, its nature and application regimes should be designed for particular pathogens and its effects studied locally.},
}
@article {pmid33527233,
year = {2021},
author = {Din, GMU and Du, Z and Zhang, H and Zhao, S and Liu, T and Chen, W and Gao, L},
title = {Effects of Tilletia foetida on Microbial Communities in the Rhizosphere Soil of Wheat Seeds Coated with Different Concentrations of Jianzhuang.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {736-745},
pmid = {33527233},
issn = {1432-184X},
mesh = {Basidiomycota ; *Microbiota ; Plant Diseases ; Rhizosphere ; Seeds ; Soil ; Soil Microbiology ; *Triticum ; },
abstract = {Tilletia foetida (syn. T. laevis) leads to wheat common bunt, a worldwide disease that can lead to 80% yield loss and even total loss of production, together with degrading the quality of grains and flour by producing a rotten fish smell. To explore the potential microbial community that may contribute to the control of soil- and seed-borne pathogens, in this study, we analyzed the effects of the plant pathogenic fungus T. foetida on rhizosphere soil microorganisms in wheat seeds coated with different concentrations of a fungicide (Jianzhuang) used to control the disease. To analyze the bacterial and fungal abundance in T. foetida-infected and mock-infected plants, the microorganisms were sequenced using high-throughput HiSeq 2500 gene sequencing. The results showed that bacterial communities, including Verrucomicrobia, Patescibacteria, Armatimonadetes, Nitrospirae, Fibrobacteres, Chlamydiae, and Hydrogenedentes, and fungal communities, including Basidiomycota and Ciliophora, were more prevalent in the mock group than in the T. foetida-infected group, which may contribute to the control of wheat common bunt. Moreover, cluster and PCoA analysis revealed that replicates of the same samples were clustered together, and these results were also found in the distance index within-group analysis for bacterial and fungal communities in the T. foetida-infected and mock groups.},
}
@article {pmid33526910,
year = {2021},
author = {Weisskopf, L and Schulz, S and Garbeva, P},
title = {Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions.},
journal = {Nature reviews. Microbiology},
volume = {19},
number = {6},
pages = {391-404},
pmid = {33526910},
issn = {1740-1534},
mesh = {Animals ; Archaea/*metabolism ; Bacteria/*metabolism ; Fungi/*metabolism ; Plants/metabolism ; Volatile Organic Compounds/chemistry/*metabolism ; },
abstract = {Microorganisms produce and excrete a versatile array of metabolites with different physico-chemical properties and biological activities. However, the ability of microorganisms to release volatile compounds has only attracted research attention in the past decade. Recent research has revealed that microbial volatiles are chemically very diverse and have important roles in distant interactions and communication. Microbial volatiles can diffuse fast in both gas and water phases, and thus can mediate swift chemical interactions. As well as constitutively emitted volatiles, microorganisms can emit induced volatiles that are triggered by biological interactions or environmental cues. In this Review, we highlight recent discoveries concerning microbial volatile compounds and their roles in intra-kingdom microbial interactions and inter-kingdom interactions with plants and insects. Furthermore, we indicate the potential biotechnological applications of microbial volatiles and discuss challenges and perspectives in this emerging research field.},
}
@article {pmid33526659,
year = {2021},
author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T},
title = {Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {6},
pages = {},
pmid = {33526659},
issn = {1091-6490},
mesh = {Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genes, Bacterial ; Mosaicism ; Mutagenesis, Insertional/*genetics ; Phylogeny ; Plasmids/*genetics ; Synteny/genetics ; },
abstract = {It is well established that plasmids play an important role in the dissemination of antimicrobial resistance (AMR) genes; however, little is known about the role of the underlying interactions between different plasmid categories and other mobile genetic elements (MGEs) in shaping the promiscuous spread of AMR genes. Here, we developed a tool designed for plasmid classification, AMR gene annotation, and plasmid visualization and found that most plasmid-borne AMR genes, including those localized on class 1 integrons, are enriched in conjugative plasmids. Notably, we report the discovery and characterization of a massive insertion sequence (IS)-associated AMR gene transfer network (245 combinations covering 59 AMR gene subtypes and 53 ISs) linking conjugative plasmids and phylogenetically distant pathogens, suggesting a general evolutionary mechanism for the horizontal transfer of AMR genes mediated by the interaction between conjugative plasmids and ISs. Moreover, our experimental results confirmed the importance of the observed interactions in aiding the horizontal transfer and expanding the genetic range of AMR genes within complex microbial communities.},
}
@article {pmid33526186,
year = {2021},
author = {Brandenburg, KM and Krock, B and Klip, HCL and Sluijs, A and Garbeva, P and Van de Waal, DB},
title = {Intraspecific variation in multiple trait responses of Alexandrium ostenfeldii towards elevated pCO2.},
journal = {Harmful algae},
volume = {101},
number = {},
pages = {101970},
doi = {10.1016/j.hal.2020.101970},
pmid = {33526186},
issn = {1878-1470},
mesh = {Carbon ; *Dinoflagellida ; Nitrogen ; Oceans and Seas ; Phytoplankton ; },
abstract = {Dissolved oceanic CO2 concentrations are rising as result of increasing atmospheric partial pressure of CO2 (pCO2), which has large consequences for phytoplankton. To test how higher CO2 availability affects different traits of the toxic dinoflagellate Alexandrium ostenfeldii, we exposed three strains of the same population to 400 and 1,000 µatm CO2, and measured traits including growth rate, cell volume, elemental composition, [13]C fractionation, toxin content, and volatile organic compounds (VOCs). Strains largely increased their growth rates and particulate organic carbon and nitrogen production with higher pCO2 and showed significant changes in their VOC profile. One strain showed a significant decrease in both PSP and cyclic imine content and thereby in cellular toxicity. Fractionation against [13]C increased in response to elevated pCO2, which may point towards enhanced CO2 acquisition and/or a downscaling of the carbon concentrating mechanisms. Besides consistent responses in some traits, other traits showed large variation in both direction and strength of responses towards elevated pCO2. The observed intraspecific variation in phenotypic plasticity of important functional traits within the same population may help A. ostenfeldii to negate the effects of immediate environmental fluctuations and allow populations to adapt more quickly to changing environments.},
}
@article {pmid33522965,
year = {2021},
author = {Dada, N and Jupatanakul, N and Minard, G and Short, SM and Akorli, J and Villegas, LM},
title = {Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {36},
pmid = {33522965},
issn = {2049-2618},
mesh = {Animals ; Culicidae/*microbiology ; *Metagenomics ; *Microbiota ; Reproducibility of Results ; Research/*organization &amp; administration/*trends ; },
abstract = {In the past decade, there has been increasing interest in mosquito microbiome research, leading to large amounts of data on different mosquito species, with various underlying physiological characteristics, and from diverse geographical locations. However, guidelines and standardized methods for conducting mosquito microbiome research are lacking. To streamline methods in mosquito microbiome research and optimize data quality, reproducibility, and comparability, as well as facilitate data curation in a centralized location, we are establishing the Mosquito Microbiome Consortium, a collaborative initiative for the advancement of mosquito microbiome research. Our overall goal is to collectively work on unraveling the role of the mosquito microbiome in mosquito biology, while critically evaluating its potential for mosquito-borne disease control. This perspective serves to introduce the consortium and invite broader participation. It highlights the issues we view as most pressing to the community and proposes guidelines for conducting mosquito microbiome research. We focus on four broad areas in this piece: (1) sampling/experimental design for field, semi-field, or laboratory studies; (2) metadata collection; (3) sample processing, sequencing, and use of appropriate controls; and (4) data handling and analysis. We finally summarize current challenges and highlight future directions in mosquito microbiome research. We hope that this piece will spark discussions around this area of disease vector biology, as well as encourage careful considerations in the design and implementation of mosquito microbiome research. Video Abstract.},
}
@article {pmid33517091,
year = {2021},
author = {Uroosa, and Kazmi, SSUH and Rahman, MS and Xu, H},
title = {Use of biological trait analysis of periphytic protozoan assemblages for evaluating effects of harmful algal blooms on ecological quality status in marine ecosystem.},
journal = {Marine pollution bulletin},
volume = {164},
number = {},
pages = {112083},
doi = {10.1016/j.marpolbul.2021.112083},
pmid = {33517091},
issn = {1879-3363},
mesh = {*Dinoflagellida ; Ecosystem ; *Harmful Algal Bloom ; },
abstract = {The effects of two harmful algal bloom (HAB) species Alexandrium tamarense and Gymnodinium catenatum on ecological quality status were studied using 14-day protozoan samples as test organisms. A fuzzy coding system with four traits and 11 categories of the test organisms was used for biological trait analysis. Five treatments were designed following the concentrations of 10[0], 10[2], 10[3], 10[4] and 10[5] cell ml[-][1] of each algal species. The community-weighted means were used to summarize the functioning process of the test organism assemblages. The community functioning of the protozoa showed a significant change in the treatments with high algal concentrations (10[4] and 10[5] cell ml[-1]). The functional richness of the test organisms showed continuous increasing trend from 10[2] to 10[4] cell ml[-1], and sharply dropped. These findings suggest that the BTA may be used as a useful tool for assessing the effects of HABs on ecological quality status in marine ecosystems.},
}
@article {pmid33515051,
year = {2021},
author = {Keet, JH and Ellis, AG and Hui, C and Novoa, A and Le Roux, JJ},
title = {Impacts of Invasive Australian Acacias on Soil Bacterial Community Composition, Microbial Enzymatic Activities, and Nutrient Availability in Fynbos Soils.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {704-721},
pmid = {33515051},
issn = {1432-184X},
support = {89967//South Africa National Research Foundation/ ; 109244//South African National Research Foundation/ ; 109683//South African National Research Foundation/ ; EXPRO 19-28807X//Czech Science Foundation/ ; RVO 67985939//The Czech Academy of Sciences/ ; },
mesh = {*Acacia ; Australia ; *Microbiota ; Nutrients ; Soil ; Soil Microbiology ; },
abstract = {Invasive plants often impact soil conditions, notably through changes in soil chemistry and microbial community composition, potentially leading to altered soil functionality. We determine the impacts of invasive nitrogen-fixing Australian Acacia trees on soil chemistry and function (carbon, nitrogen, and phosphorus cycling) in South Africa's Core Cape Subregion, and whether any differences in soil function are linked to differences in soil chemical properties and bacterial community composition between neighbouring acacia-invaded and uninvaded sites. We do so by using Illumina MiSeq sequencing data together with soil chemistry and soil enzyme activity profiles. Acacias significantly increased levels of soil nitrogen (NO3[-], NH4[+], and total N), C, and pH. Although we did not find evidence that acacias affected soil bacterial community diversity, we did find them to alter bacterial community composition. Acacias also significantly elevated microbial phosphatase activity, but not β-glucosidase, whilst having contrasting effects on urease. Changes in soil chemical properties under acacia invasion were found to correlate with changes in enzyme activities for urease and phosphatase. Similarly, changes in soil bacterial community composition were correlated to changes in phosphatase enzymatic activity levels under acacia invasion. Whilst we found evidence for acacias altering soil function by changing soil chemical properties and bacterial community composition, these impacts appear to be specific to local site conditions.},
}
@article {pmid33515050,
year = {2021},
author = {Cureau, N and Threlfall, R and Savin, M and Marasini, D and Lavefve, L and Carbonero, F},
title = {Year, Location, and Variety Impact on Grape-, Soil-, and Leaf-Associated Fungal Microbiota of Arkansas-Grown Table Grapes.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {73-86},
pmid = {33515050},
issn = {1432-184X},
mesh = {Arkansas ; *Mycobiome ; Plant Leaves ; Soil ; *Vitis ; },
abstract = {With the recent advancement of next-generation sequencing methods, there has been an increase in studies on identification of vineyard microbiota, winery-associated microbiota, and microbiota in wine fermentation. However, there have been few studies investigating the fungal microbiota of table grapes which present distinct spoilage and food safety challenges. The aims of this study were to identify and compare the impact of year, variety, and vineyard location on grape, leaf, and soil fungal communities of two varieties of table grapes, Faith and Gratitude, grown in two open-air vineyards and one high tunnel vineyard. The grape, leaf, and soil mycobiota were analyzed using high throughput amplicon sequencing of the ITS region. The sampling year and location of table grapes had an impact on grape, leaf, and soil mycobiota. Fungal diversity of grape, leaf, and soil was greater in 2017 than in 2016. Grape and leaf samples presented strong similarities in fungal communities with abundance of Sporidiobolaceae and Filobasidium in two vineyards and Cladosporium in another one. The high tunnel structure had distinct grape and leaf fungal communities compared to the two other vineyard locations. Mortierella was the predominant genus (27%) in soil samples for the three locations; however, genera of lower abundance varied between locations. These results provide extensive description of fungal communities in less-studied table grape vineyards and high tunnels, providing useful insight of potential threats and preventive strategies to help improve the production and marketability of table grapes.},
}
@article {pmid33512536,
year = {2021},
author = {Adhikari, P and Jain, R and Sharma, A and Pandey, A},
title = {Plant Growth Promotion at Low Temperature by Phosphate-Solubilizing Pseudomonas Spp. Isolated from High-Altitude Himalayan Soil.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {677-687},
pmid = {33512536},
issn = {1432-184X},
support = {NA//Ministry of Environment, Forest and Climate Change, Govt of India/ ; },
mesh = {Altitude ; Ecosystem ; *Phosphates ; Pseudomonas/genetics ; *Soil ; Soil Microbiology ; Temperature ; },
abstract = {Scarcity of arable land, limited soil nutrient availability, and low-temperature conditions in the Himalayan regions need to be smartly managed using sustainable approaches for better crop yields. Microorganisms, able to efficiently solubilize phosphate at low temperatures, provide an opportunity to promote plant growth in an ecofriendly way. In this study, we have investigated the ability of psychrotolerant Pseudomonas spp., isolated from high altitudes of Indian Himalaya to solubilize P at low temperature. Quantitative estimation of phosphate solubilization and production of relevant enzymes at two different temperatures (15 and 25 °C) was performed for 4 out of 11 selected isolates, namely, GBPI_506 (Pseudomonas sp.), GBPI_508 (Pseudomonas palleroniana), GBPI_Hb61 (Pseudomonas proteolytica), and GBPI_CDB143 (Pseudomonas azotoformans). Among all, isolate GBPI_CDB143 showed highest efficiency to solubilize tri-calcium phosphate (110.50 ± 3.44 μg/mL) at 25 °C after 6 days while the culture supernatants of isolate GBPI_506 displayed the highest phytase activity (15.91 ± 0.35 U/mL) at 15 °C and alkaline phosphatase (3.09 ± 0.07 U/mL) at 25 °C in 6 and 9 days, respectively. Out of five different organic acids quantified, oxalic acid and malic acid were produced in maximum quantity by all four isolates. With the exception of GBPI_508, inoculation of bacteria promoted overall growth (rosette diameter, leaf area, and biomass) of Arabidopsis thaliana plants as compared to uninoculated control plants in growth chamber conditions. The plant growth promotion by each bacterial isolate was further validated by monitoring root colonization in the inoculated plants. These bacterial isolates with low-temperature phosphate solubilization potential along with phosphatases and phytase activity at low temperature could be harnessed for sustainable crop production in P-deficient agricultural soils under mountain ecosystems.},
}
@article {pmid33512248,
year = {2021},
author = {Shaffer, JP and Marotz, C and Belda-Ferre, P and Martino, C and Wandro, S and Estaki, M and Salido, RA and Carpenter, CS and Zaramela, LS and Minich, JJ and Bryant, M and Sanders, K and Fraraccio, S and Ackermann, G and Humphrey, G and Swafford, AD and Miller-Montgomery, S and Knight, R},
title = {A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.},
journal = {BioTechniques},
volume = {70},
number = {3},
pages = {149-159},
pmid = {33512248},
issn = {1940-9818},
support = {K12 GM068524/GM/NIGMS NIH HHS/United States ; U01 AI124316/AI/NIAID NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; R01 HL134887/HL/NHLBI NIH HHS/United States ; RF1 AG058942/AG/NIA NIH HHS/United States ; R01 DK102932/DK/NIDDK NIH HHS/United States ; 1RF1-AG058942-01,R01DK102932,R01HL134887,R01HL140976,U01AI124316,U19AG063744/GF/NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Biodiversity ; Cats ; Chemical Fractionation/methods ; DNA, Viral/*isolation &amp; purification ; Feces/microbiology/virology ; Female ; Fermented Foods/microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Limit of Detection ; Male ; Metagenomics/methods ; Mice ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*isolation &amp; purification ; SARS-CoV-2/*genetics ; Saliva/microbiology/virology ; Skin/microbiology/virology ; },
abstract = {One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here the authors present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection and well-to-well contamination between these protocols.},
}
@article {pmid33511438,
year = {2021},
author = {Sabino-Pinto, J and Bletz, MC and Islam, MM and Shimizu, N and Bhuju, S and Geffers, R and Jarek, M and Kurabayashi, A and Vences, M},
title = {Correction to: Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {830},
doi = {10.1007/s00248-021-01693-z},
pmid = {33511438},
issn = {1432-184X},
}
@article {pmid33511437,
year = {2021},
author = {Cao, C and Tao, S and Cui, Z and Zhang, Y},
title = {Response of Soil Properties and Microbial Communities to Increasing Salinization in the Meadow Grassland of Northeast China.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {722-735},
pmid = {33511437},
issn = {1432-184X},
support = {41877536//National Natural Science Foundation of China/ ; 41403063//National Natural Science Foundation of China/ ; 41371505//National Natural Science Foundation of China/ ; },
mesh = {China ; Grassland ; *Microbiota ; *Soil ; Soil Microbiology ; },
abstract = {Secondary salinization is a serious environmental issue and a major threat to the sustainable use of grasslands. Information about the response of microbial communities and soil properties in already saline soils to increasing salinity is lacking. We investigated soil properties and the structures of soil bacterial and fungal communities across a gradient of salinization in the Horqin Grassland, China. Three sites with relatively lightly (average soluble salt content = 0.11%), relatively moderately (average soluble salt content = 0.44%), and heavily (average soluble salt content = 1.07%) degraded grassland, were selected as experimental sites. We examined variations in the composition and structure of the soil bacterial and fungal communities by using high-throughput sequencing of the 16S and 18S rRNA genes, respectively. We found degrading effects of salinization on soil properties, i.e., decreased soil moisture, organic matter, total N, NH4-N, and NO3-N and increased soil bulk density, pH, and electrical conductivity. The bacterial and fungal community structures changed with increasing salinity. However, dominant microbial taxa (including phylum, genus, and operational taxonomic unit levels) were similar among experimental sites, indicating that increasing salinization slightly affected the basic compositions of microbial communities in already saline grasslands. Furthermore, the relative abundances of most dominant taxa sensitively responded to the soil salt content. Acidobacteria, Actinobacteria, Chloroflexi, RB4, Rubrobacter, Blastocatella, H16, Glomeromycota, and Aspergillus linearly increased with increasing salinization, suggesting that they could be used as bioindicators for salt-tolerant communities. Overall, the changes in the structures of soil bacterial and fungal communities were determined by the relative quantities of dominant taxa rather than community composition. The structures of soil bacterial and fungal communities were linked to soil properties and vegetation. Increasing soil salt content, and thereby varied pH and organic matter, were likely the direct influencing factors of microbial communities in these saline grasslands.},
}
@article {pmid33511436,
year = {2021},
author = {Lu, XM and Liu, XP},
title = {Distribution of Metal Resistance Genes in Estuarine Sediments and Associated Key Impact Factors.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {581-590},
pmid = {33511436},
issn = {1432-184X},
support = {GY-Z19042//Fujian University of Technology/ ; 2020J01880//Fujian Provincial Natural Science Foundation/ ; },
mesh = {Environmental Monitoring ; Estuaries ; Geologic Sediments ; *Metals, Heavy/analysis ; Rivers ; Seawater ; *Water Pollutants, Chemical/analysis ; },
abstract = {Currently, little is known about the distribution of metal resistance genes (MRGs) in estuarine sediments. In this study, we used the high-throughput quantitative real-time polymerase chain reaction (HT-qPCR) to determine the distribution of MRGs in the sediments of an estuary system and the associated key impact factors. The relative abundance of the detected MRGs showed a decreasing trend from the river inlet toward the sea and a decrease from the middle area of the estuary to the near-shore areas on both sides; these decreases were higher in the summer than in the winter. In the estuary system during the summer, the abundance of Zn- and Cu-MRGs from the river inlet to the sea decreased by 99.5% and 93.6%, whereas those of Hg- and Cd-Zn-Co-MRGs increased by 51.5% and 16.7%, respectively. Moreover, the abundance of Zn- and Cu-MRGs in the winter decreased by 88.6% and 97.7%, respectively, whereas that of Cd-Bi-Zn-Pb-MRGs increased by 729.6%. Furthermore, the abundances of MRGs and mobile genetic elements (MGEs) were significantly positively correlated with the levels of antibiotic residues and heavy metals as well as with the particle size and total organic carbon content of the sediment; however, they were significantly negatively correlated with seawater salinity and the oxidation and reduction potential (Eh) and pH of the sediment. The abundance of MGEs was significantly positively correlated with the abundance of MRGs in the sediment. Our findings suggest that antibiotic residues facilitated the proliferation and propagation of MRGs by promoting MGEs in estuarine sediments.},
}
@article {pmid33510866,
year = {2021},
author = {Callewaert, C and Knödlseder, N and Karoglan, A and Güell, M and Paetzold, B},
title = {Skin microbiome transplantation and manipulation: Current state of the art.},
journal = {Computational and structural biotechnology journal},
volume = {19},
number = {},
pages = {624-631},
pmid = {33510866},
issn = {2001-0370},
abstract = {Many skin conditions are associated with an imbalance in the skin microbiome. In recent years, the skin microbiome has become a hot topic, for both therapeutic and cosmetic purposes. The possibility of manipulating the human skin microbiome to address skin conditions has opened exciting new paths for therapy. Here we review the skin microbiome manipulation strategies, ranging from skin microbiome transplantation, over skin bacteriotherapy to the use of prebiotics, probiotics and postbiotics. We summarize all efforts undertaken to exchange, manipulate, transplant or selectively apply the skin microbiome to date. Multiple microbial groups have been targeted, since they have been proven to be beneficial for skin health. We focus on the most common skin disorders and their associated skin microbiome dysbiosis and we review the existing scientific data and clinical trials undertaken to combat these skin conditions. The skin microbiome represents a novel platform for therapy. Transplantation of a complete microbiome or application of single strains has demonstrated beneficial therapeutic application.},
}
@article {pmid33510747,
year = {2020},
author = {Favero, VO and Carvalho, RH and Motta, VM and Leite, ABC and Coelho, MRR and Xavier, GR and Rumjanek, NG and Urquiaga, S},
title = {Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean (Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {602645},
pmid = {33510747},
issn = {1664-462X},
abstract = {The mung bean has a great potential under tropical conditions given its high content of grain protein. Additionally, its ability to benefit from biological nitrogen fixation (BNF) through association with native rhizobia inhabiting nodule microbiome provides most of the nitrogen independence on fertilizers. Soil microbial communities which are influenced by biogeographical factors and soil properties, represent a source of rhizobacteria capable of stimulating plant growth. The objective of this study is to support selection of beneficial bacteria that form positive interactions with mung bean plants cultivated in tropical soils, as part of a seed inoculation program for increasing grain yield based on the BNF and other mechanisms. Two mung bean genotypes (Camaleão and Esmeralda) were cultivated in 10 soil samples. Nodule microbiome was characterized by next-generation sequencing using Illumina MiSeq 16S rRNA. More than 99% of nodule sequences showed similarity with Bradyrhizobium genus, the only rhizobial present in nodules in our study. Higher bacterial diversity of soil samples collected in agribusiness areas (MW_MT-I, II or III) was associated with Esmeralda genotype, while an organic agroecosystem soil sample (SE_RJ-V) showed the highest bacterial diversity independent of genotype. Furthermore, OTUs close to Bradyrhizobium elkanii have dominated in all soil samples, except in the sample from the organic agroecosystem, where just B. japonicum was present. Bacterial community of mung bean nodules is mainly influenced by soil pH, K, Ca, and P. Besides a difference on nodule colonization by OTU sequences close to the Pseudomonas genus regarding the two genotypes was detected too. Although representing a small rate, around 0.1% of the total, Pseudomonas OTUs were only retrieved from nodules of Esmeralda genotype, suggesting a different trait regarding specificity between macro- and micro-symbionts. The microbiome analysis will guide the next steps in the development of an inoculant for mung bean aiming to promote plant growth and grain yield, composed either by an efficient Bradyrhizobium strain on its own or co-inoculated with a Pseudomonas strain. Considering the results achieved, the assessment of microbial ecology parameters is a potent coadjuvant capable to accelerate the inoculant development process and to improve the benefits to the crop by soil microorganisms.},
}
@article {pmid33509983,
year = {2021},
author = {Rachek, S and Nikpoor, N and Gómez Del Pulgar, EM and Gonzaga, A and Sanz, Y and Tompkins, TA},
title = {Complete Genome Sequence of Phascolarctobacterium faecium G 104, Isolated from the Stools of a Healthy Lean Donor.},
journal = {Microbiology resource announcements},
volume = {10},
number = {4},
pages = {},
pmid = {33509983},
issn = {2576-098X},
abstract = {Phascolarctobacterium faecium is a strict anaerobe belonging to the Firmicutes phylum that is found abundantly in the human gastrointestinal tract. Here, we report the complete genome sequence of P. faecium G 104, a strain isolated from a fresh stool sample from a healthy lean donor.},
}
@article {pmid33508898,
year = {2021},
author = {Babaahmadifooladi, M and Jacxsens, L and Van de Wiele, T and Carlos da Silva Júnior, E and Du Laing, G},
title = {Assessment of bioaccessible and dialyzable fractions of nickel in food products and their impact on the chronic exposure of Belgian population to nickel.},
journal = {Food chemistry},
volume = {342},
number = {},
pages = {128210},
doi = {10.1016/j.foodchem.2020.128210},
pmid = {33508898},
issn = {1873-7072},
mesh = {Belgium ; Dialysis ; Digestion ; Edible Grain/chemistry ; *Food Analysis ; Fruit/chemistry/metabolism ; Humans ; Nickel/*analysis/metabolism ; Tea/chemistry/metabolism ; Triticum/chemistry/metabolism ; },
abstract = {This study aimed to investigate bioaccessible/dialyzable fractions of nickel in selected foods and to clarify the impact of the food digestion/absorption on the final exposure of consumers to nickel. In vitro gastrointestinal incubation experiments were conducted to estimate the bioaccessibility of nickel in different foods. For estimation of a dialyzable fraction, dialysis filtration was conducted. Highest bioaccessibility (99.6%) was observed for wheat-based breakfast cereals. Lowest bioaccessibilities was observed for dried-fruits (on average 20.4%). Highest (61.5%) and lowest (24.5%) dialyzable fractions were observed for wheat-based breakfast cereal and chocolate respectively. Bioaccessible/dialyzable fractions based exposure assessments were highlighted the overestimation of exposures calculated based on total nickel concentrations in foods. This is particularly important when exposure values were compared with toxicological thresholds in a risk characterization study. When threshold values have been obtained through animal studies in which nickel was dosed at 100% accessibility/availability, e.g. nickel salts this is even more important.},
}
@article {pmid33508664,
year = {2021},
author = {Durán, J and Rodríguez, A and Fangueiro, D and De Los Ríos, A},
title = {In-situ soil greenhouse gas fluxes under different cryptogamic covers in maritime Antarctica.},
journal = {The Science of the total environment},
volume = {770},
number = {},
pages = {144557},
doi = {10.1016/j.scitotenv.2020.144557},
pmid = {33508664},
issn = {1879-1026},
mesh = {Antarctic Regions ; Carbon Dioxide/analysis ; Ecosystem ; *Greenhouse Gases/analysis ; Methane/analysis ; Nitrous Oxide/analysis ; Soil ; },
abstract = {Soils can influence climate by sequestering or emitting greenhouse gases (GHG) such as carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). We are far from understanding the direct influence of cryptogamic covers on soil GHG fluxes, particularly in areas free of potential anthropogenic confounding factors. We assessed the role of well-developed cryptogamic covers in soil attributes, as well as in the in-situ exchange of GHG between Antarctic soils and the atmosphere during the austral summer. We found lower values of soil organic matter, total organic carbon, and total nitrogen in bare areas than in soils covered by mosses and, particularly, lichens. These differences, together with concomitant decreases and increases in soil temperature and moisture, respectively, resulted in increases in in-situ CO2 emission (i.e. ecosystem respiration) and decreases in CH4 uptake but no significant changes in N2O fluxes. We found consistent linear positive and negative relationships between soil attributes (i.e. soil organic matter, total organic carbon and total nitrogen) and CO2 emissions and CH4 uptake, respectively, and polynomial relationships between these soil attributes and net N2O fluxes. Our results indicate that any increase in the area occupied by cryptogams in terrestrial Antarctic ecosystems (due to increased growing season and increasingly warming conditions) will likely result in parallel increases in soil fertility as well as in an enhanced capacity to emit CO2 and a decreased capacity to uptake CH4. Such changes, unless offset by parallel C uptake processes, would represent a paradigmatic example of a positive climate change feedback. Further, we show that the fate of these terrestrial ecosystems under future climate scenarios, as well as their capacity to exchange GHG with the atmosphere might depend on the relative ability of different aboveground cryptogams to thrive under the new conditions.},
}
@article {pmid33507249,
year = {2021},
author = {Del Moral, &#xc1; and Garrido-Benavent, I and Durán, J and Lehmann, JR and Rodríguez, A and Heiðmarsson, S and de Los Ríos, A},
title = {Are recently deglaciated areas at both poles colonised by the same bacteria?.},
journal = {FEMS microbiology letters},
volume = {368},
number = {3},
pages = {},
doi = {10.1093/femsle/fnab011},
pmid = {33507249},
issn = {1574-6968},
mesh = {Antarctic Regions ; Arctic Regions ; Bacteria/classification/*genetics ; *Biodiversity ; Ice Cover/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {Polar glacier forefields offer an unprecedented framework for studying community assembly processes in regions that are geographically and climatically isolated. Through amplicon sequence variant (ASV) inference, we compared the composition and structure of soil bacterial communities from glacier forefields in Iceland and Antarctica to assess overlap between communities and the impact of established cryptogamic covers on the uniqueness of their taxa. These pioneer microbial communities were found to share only 8% of ASVs and each taxonomic group's contribution to the shared ASV data subset was heterogeneous and independent of their relative abundance. Although the presence of ASVs specific to one glacier forefield and/or different cryptogam cover values confirms the existence of habitat specialist bacteria, our data show that the influence of cryptogams on the edaphic bacterial community structure also varied also depending on the taxonomic group. Hence, the establishment of distinct cryptogamic covers is probably not the only factor driving the uniqueness of bacterial communities at both poles. The structure of bacterial communities colonising deglaciated areas seems also conditioned by lineage-specific limitations in their dispersal capacity and/or their establishment and persistence in these isolated and hostile regions.},
}
@article {pmid33505795,
year = {2021},
author = {Chica Cardenas, LA and Clavijo, V and Vives, M and Reyes, A},
title = {Bacterial meta-analysis of chicken cecal microbiota.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10571},
pmid = {33505795},
issn = {2167-8359},
abstract = {Poultry production is an industry that generates 90,000 metric tons of chicken meat worldwide. Thus, optimizing chicken growth and sustainable production is of great importance. A central factor determining not only production parameters, but also stability of the immune system and chicken health, is the diversity and variability of the microbiota present throughout the gastrointestinal tract. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on studies using amplicon sequencing with Illumina sequencing technologies in order to build a baseline for comparison in future analyses of the cecal bacterial composition in chicken. A systematic literature review was performed (SYRF ID: e84f0468-e418-4eec-9da4-b517f1b4809d. Full project URL: https://app.syrf.org.uk/projects/e84f0468-e418-4eec-9da4-b517f1b4809d/detail). From all the available and analyzed manuscripts only nine contained full raw-sequence data available and the corresponding metadata. A total of 324 samples, comprising three different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 11 phyla, with Firmicutes as the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 109 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. Despite the large number of parameters that were taken into account, the identification of common bacteria showed five genera to be common for all sets in at least 50% of the samples. These genera are highly associated to cellulose degradation and short chain fatty acids synthesis. In general, it was possible to identify some commonalities in the bacterial cecal microbial community despite the extensive variability and factors differing from one study to another.},
}
@article {pmid33505541,
year = {2021},
author = {Shen, G and Wu, J and Ye, BC and Qi, N},
title = {Gut Microbiota-Derived Metabolites in the Development of Diseases.},
journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2021},
number = {},
pages = {6658674},
pmid = {33505541},
issn = {1712-9532},
abstract = {Gut microbiota is increasingly recognized as a metabolic organ essential for human health. Compelling evidences show a variety set of links between diets and gut microbial homeostasis. Changes in gut microbial flora would probably contribute to the development of certain diseases such as diabetes, heart disease, allergy, and psychiatric diseases. In addition to the composition of gut microbiota, the metabolites derived from gut microbiota have emerged as a pivotal regulator in diseases development. Since high-fat and high-protein diets substantially affect the gut microbial ecology and human health, the current review summarizes the gut microbiota-derived metabolites such as short-chain fatty acids (SCFAs), amino acids, and their derivatives and highlights the mechanisms underlying the host responses to these bioactive substances.},
}
@article {pmid33505386,
year = {2020},
author = {Borda-Molina, D and Mátis, G and Mackei, M and Neogrády, Z and Huber, K and Seifert, J and Camarinha-Silva, A},
title = {Caeca Microbial Variation in Broiler Chickens as a Result of Dietary Combinations Using Two Cereal Types, Supplementation of Crude Protein and Sodium Butyrate.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {617800},
pmid = {33505386},
issn = {1664-302X},
abstract = {The intestinal microbiome can influence the efficiency and the health status of its host's digestive system. Indigestible non-starch polysaccharides (NSP) serve as substrates for bacterial fermentation, resulting in short-chain fatty acids like butyrate. In broiler's nutrition, dietary crude protein (CP) and butyrate's presence is of particular interest for its impact on intestinal health and growth performance. In this study, we evaluated the effect on the microbial ecology of the ceca of dietary supplementations, varying the cereal type (maize and wheat), adequate levels of CP and supplementation of sodium butyrate on broiler chickens with 21 days. The overall structure of bacterial communities was statistically affected by cereal type, CP, and sodium butyrate (p = 0.001). Wheat in the diet promoted the presence of Lactobacillaceae, Bifidobacteriaceae and Bacteroides xylanisolvens, which can degrade complex carbohydrates. Maize positively affected the abundance of Bacteroides vulgatus. The addition of CP promoted the family Rikenellaceae, while sodium butyrate as feed supplement was positively related to the family Lachnospiraceae. Functional predictions showed an effect of the cereal type and a statistical significance across all supplementations and their corresponding interactions. The composition of diets affected the overall structure of broilers' intestinal microbiota. The source of NSP as a substrate for bacterial fermentation had a stronger stimulus on bacterial communities than CP content or supplementation of butyrate.},
}
@article {pmid33505154,
year = {2021},
author = {Rahayu, ES and Mariyatun, M and Putri Manurung, NE and Hasan, PN and Therdtatha, P and Mishima, R and Komalasari, H and Mahfuzah, NA and Pamungkaningtyas, FH and Yoga, WK and Nurfiana, DA and Liwan, SY and Juffrie, M and Nugroho, AE and Utami, T},
title = {Effect of probiotic Lactobacillus plantarum Dad-13 powder consumption on the gut microbiota and intestinal health of overweight adults.},
journal = {World journal of gastroenterology},
volume = {27},
number = {1},
pages = {107-128},
pmid = {33505154},
issn = {2219-2840},
mesh = {Adult ; Child ; Double-Blind Method ; Escherichia coli ; Feces ; *Gastrointestinal Microbiome ; Humans ; Indonesia/epidemiology ; *Lactobacillus plantarum ; Powders ; *Probiotics/therapeutic use ; },
abstract = {BACKGROUND: Shifting on lifestyle, diet, and physical activity contributed on increasing number of obese people around the world. Multiple factors influence the development of obesity. Some research suggested that gut microbiota (GM) plays an important role in nutrient absorption and energy regulation of individuals, thus affecting their nutritional status. Report of Indonesia Basic Health Research showed that the prevalence of obesity in every province tended to increase. Although the root cause of obesity is excessive calorie intake compared with expenditure, the differences in gut microbial ecology between healthy and obese humans may affect energy homeostasis. GM affect body weight, especially obesity. Probiotics that are consumed while alive and able to colonize in the intestine are expected to increase the population of good bacteria, especially Bifidobacteria and Lactobacilli, and suppress pathogens such as Enterobacteriaceae and Staphylococcus. The strain of L. plantarum Dad-13 has been demonstrated to survive and colonize in the gastrointestinal tract of healthy Indonesian adults who consume fermented milk containing L. plantarum Dad-13. The consumption of probiotic L. plantarum Dad-13 powder decreased E. coli and non-E. coli coliform bacteria in school-aged children in Indonesia. L. plantarum is a dominant bacterium in the average Indonesian's GM. For this reason, this bacterium is probably a more suitable probiotic for Indonesians.<br><br>AIM: To determine the effect of the consumption of indigenous probiotic Lactobacillus plantarum Dad-13 powder in overweight adults in Yogyakarta (Indonesia).<br><br>METHODS: Sixty overweight volunteers with a body mass index (BMI) equal to or greater than 25 consume indigenous probiotic powder L. plantarum Dad-13 (2 &#xd7; 10[9] CFU/gram/sachet) for 90 d. The study was a randomized, double-blind, placebo-controlled study. The volunteers filled in a diary on a daily basis, which consisted of questions on study product intake (only during ingestion period), other food intake, number of bowel movements, fecal quality (consistency and color), any medications received, and any symptom of discomfort, such as diarrhea, constipation, vomiting, gassing, sensation of illness, etc. Fecal samples and the subjects' diaries were collected on the morning of day 10 + 1, which was marked as the end of the baseline period and the start of the ingestion period. During the ingestion period (from day 11 to day 101), several parameters to measure and analyze the results included body weight and height (once a month), the lipid profile, GM analysis using MiSeq, short-chain fatty acid (SCFA) analysis using gas chromatography, and the measurement of fecal pH using a pH meter.<br><br>RESULTS: The consumption of indigenous probiotic powder L. plantarum Dad-13 caused the average body weight and BMI of the probiotic group to decrease from 84.54 &#xb1; 17.64 kg to 83.14 &#xb1; 14.71 kg and 33.10 &#xb1; 6.15 kg/m[2] to 32.57 &#xb1; 5.01 kg/m[2], respectively. No significant reduction of body weight and BMI in the placebo group was observed. An analysis of the microbiota showed that the number of Bacteroidetes, specifically Prevotella, increased significantly, while that of Firmicutes significantly decreased. No significant change in lipid profile in both groups was found. Also, no significant change in SCFAs (e.g., butyrate, propionate, acetic acid) and pH level was found after the consumption of the probiotic.<br><br>CONCLUSION: No significant differences in pH before and after ingestion were observed in both the probiotic and placebo groups as well as in the lipid profile of both cholesterol and triglyceride, high-density lipoprotein (HDL), low-density lipoprotein (LDL), and the LDL/HDL ratio. In addition, no significant changes in the concentration of SCFAs (e.g., acetic acid, propionate, and butyrate) were found after con-sumption. Interestingly, a significant decrease in body weight and BMI (P < 0.05) was determined in the treatment group. An analysis of GM shows that L. plantarum Dad-13 caused the Firmicutes population to decrease and the Bacteroidetes population (especially Prevotella) to increase.},
}
@article {pmid33502573,
year = {2021},
author = {Terlova, EF and Holzinger, A and Lewis, LA},
title = {Terrestrial Green Algae Show Higher Tolerance to Dehydration than Do Their Aquatic Sister-Species.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {770-782},
pmid = {33502573},
issn = {1432-184X},
support = {I 1951/FWF_/Austrian Science Fund FWF/Austria ; I 1951-B16//Austrian Science Fund (AT)/ ; },
mesh = {*Chlorophyta ; *Dehydration ; Desiccation ; Ecosystem ; Photosystem II Protein Complex ; },
abstract = {Diverse algae possess the ability to recover from extreme desiccation without forming specialized resting structures. Green algal genera such as Tetradesmus (Sphaeropleales, Chlorophyceae) contain temperate terrestrial, desert, and aquatic species, providing an opportunity to compare physiological traits associated with the transition to land in closely related taxa. We subjected six species from distinct habitats to three dehydration treatments varying in relative humidity (RH 5%, 65%, 80%) followed by short- and long-term rehydration. We tested the capacity of the algae to recover from dehydration using the effective quantum yield of photosystem II as a proxy for physiological activity. The degree of recovery was dependent both on the habitat of origin and the dehydration scenario, with terrestrial, but not aquatic, species recovering from dehydration. Distinct strains of each species responded similarly to dehydration and rehydration, with the exception of one aquatic strain that recovered from the mildest dehydration treatment. Cell ultrastructure was uniformly maintained in both aquatic and desert species during dehydration and rehydration, but staining with an amphiphilic styryl dye indicated damage to the plasma membrane from osmotically induced water loss in the aquatic species. These analyses demonstrate that terrestrial Tetradesmus possess a vegetative desiccation tolerance phenotype, making these species ideal for comparative omics studies.},
}
@article {pmid33500192,
year = {2021},
author = {Maganha de Almeida Kumlien, AC and Borrego, CM and Balcázar, JL},
title = {Antimicrobial Resistance and Bacteriophages: An Overlooked Intersection in Water Disinfection.},
journal = {Trends in microbiology},
volume = {29},
number = {6},
pages = {517-527},
doi = {10.1016/j.tim.2020.12.011},
pmid = {33500192},
issn = {1878-4380},
mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; *Bacteriophages ; Disinfection/*methods ; *Drug Resistance, Bacterial ; Feces ; Genes, Bacterial ; Humans ; Water Purification/*methods ; },
abstract = {This article focuses on how bacteriophages (phages), antibiotic-resistance genes (ARGs), and disinfection practices intersect. Phages are considered to be the most abundant biological entities on Earth and they have the potential to transfer genes (including ARGs) among their bacterial hosts. In the urban water cycle, phages are used as indicators of fecal pollution and surrogates for human viral pathogens but they are also known to withstand common disinfection treatments deployed to produce safe drinking/reclaimed water. Recent studies also suggest that phages have the potential to become an additional footprint to monitor water safety. A precautionary approach should therefore include phages in surveillance programs aimed at monitoring antimicrobial resistance (AMR) in the urban water cycle. This article argues that phages ought to be used to assess the efficiency of disinfection treatments (both classical and novel) on reducing the risk associated with antibiotic resistance. Finally, this article discusses contributions to the advancement of AMR stewardship in aquatic settings and is relevant for researchers and water industry practitioners.},
}
@article {pmid33499970,
year = {2020},
author = {van Veelen, HPJ and Falcão Salles, J and Matson, KD and van der Velde, M and Tieleman, BI},
title = {Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata.},
journal = {Animal microbiome},
volume = {2},
number = {1},
pages = {21},
pmid = {33499970},
issn = {2524-4671},
support = {Vidi 864.10.012//NWO/ ; },
abstract = {BACKGROUND: The relevance of the host microbiota to host ecology and evolution is well acknowledged. However, the effect of the microbial environment on host immune function and host microbiota dynamics is understudied in terrestrial vertebrates. Using a novel experimental approach centered on the manipulation of the microbial environment of zebra finches Taeniopygia guttata, we carried out a study to investigate effects of the host's microbial environment on: 1) constitutive immune function, 2) the resilience of the host cloacal microbiota; and 3) the degree to which immune function and host microbiota covary in microbial environments that differ in diversity.<br><br>RESULTS: We explored immune indices (hemagglutination, hemolysis, IgY levels and haptoglobin concentration) and host-associated microbiota (diversity and composition) in birds exposed to two experimental microbial environments differing in microbial diversity. According to our expectations, exposure to experimental microbial environments led to differences related to specific antibodies: IgY levels were elevated in the high diversity treatment, whereas we found no effects for the other immune indices. Furthermore, according to predictions, we found significantly increased richness of dominant OTUs for cloacal microbiota of birds of the high diversity compared with the low diversity group. In addition, cloacal microbiota of individual females approached their baseline state sooner in the low diversity environment than females in the high diversity environment. This result supported a direct phenotypically plastic response of host microbiota, and suggests that its resilience depends on environmental microbial diversity. Finally, immune indices and cloacal microbiota composition tend to covary within treatment groups, while at the same time, individuals exhibited consistent differences of immune indices and microbiota characteristics.<br><br>CONCLUSION: We show that microbes in the surroundings of terrestrial vertebrates can influence immune function and host-associated microbiota dynamics over relatively short time scales. We suggest that covariation between immune indices and cloacal microbiota, in addition to large and consistent differences among individuals, provides potential for evolutionary adaptation. Ultimately, our study highlights that linking environmental and host microbiotas may help unravelling immunological variation within and potentially among species, and together these efforts will advance the integration of microbial ecology and ecological immunology.},
}
@article {pmid33499721,
year = {2021},
author = {López-Almela, I and Romaní-Pérez, M and Bullich-Vilarrubias, C and Benítez-Páez, A and Gómez Del Pulgar, EM and Francés, R and Liebisch, G and Sanz, Y},
title = {Bacteroides uniformis combined with fiber amplifies metabolic and immune benefits in obese mice.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-20},
pmid = {33499721},
issn = {1949-0984},
mesh = {Adipose Tissue/metabolism ; Animals ; *Bacteroides ; Cecum/metabolism/microbiology ; Diet, High-Fat/adverse effects ; *Dietary Fiber ; Epididymis/metabolism ; Fatty Acids/metabolism ; Gastrointestinal Microbiome ; Inflammation ; Insulin/metabolism ; Interleukins/metabolism ; Intestinal Mucosa/immunology ; Liver/metabolism ; Lymphocytes/metabolism ; Male ; Mice ; Obesity/*diet therapy/etiology/immunology/metabolism ; Signal Transduction ; Thermogenesis ; Weight Gain ; Interleukin-22 ; },
abstract = {Gut microbiota represents a therapeutic target for obesity. We hypothesize that B. uniformis CECT 7771 combined with wheat bran extract (WBE), its preferred carbon source, may exert superior anti-obesity effects. We performed a 17-week intervention in diet-induced obese mice receiving either B. uniformis, WBE, or their combination to identify interactions and independent actions on metabolism and immunity. B. uniformis combined with WBE was the most effective intervention, curbing weight gain and adiposity, while exerting more modest effects separately. The combination restored insulin-dependent metabolic routes in fat and liver, although the bacterium was the primary driver for improving whole-body glucose disposal. Moreover, B. uniformis-combined with WBE caused the highest increases in butyrate and restored the proportion of induced intraepithelial lymphocytes and type-3 innate lymphoid cells in the intestinal epithelium. Thus, strengthening the first line of immune defense against unhealthy diets and associated dysbiosis in the intestine. This intervention also attenuated the altered IL22 signaling and liver inflammation. Our study shows opportunities for employing B. uniformis, combined with WBE, to aid in the treatment of obesity.},
}
@article {pmid33499060,
year = {2021},
author = {Patuzzi, I and Orsini, M and Cibin, V and Petrin, S and Mastrorilli, E and Tiengo, A and Gobbo, F and Catania, S and Barco, L and Ricci, A and Losasso, C},
title = {The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time.},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {},
pmid = {33499060},
issn = {2076-2607},
support = {IZS VE 04/13 RC//Ministero della Salute/ ; },
abstract = {Campylobacter is the most frequent foodborne zoonotic bacteria worldwide, with chicken meat being overwhelmingly the most important reservoir for human infections. Control measures implemented at the farm level (i.e., biosecurity or vaccination), which have been successfully applied to limit other pathogens, such as Salmonella, have not been effective in reducing Campylobacter occurrence. Thus, new approaches are needed to fully understand the ecological interactions of Campylobacter with host animals to effectively comprehend its epidemiology. The objective of this study was to analyse longitudinally the gut microbiota composition of Campylobacter-infected and non-infected farms to identify any difference that could potentially be indicative of gut colonization by Campylobacter spp. Differences in the colonization rate and timing were observed at the farms that became positive for Campylobacter jejuni over the investigated time points, even though in positive tests, the occurrence of Campylobacter jejuni gut colonization was not observed before the second week of the life of the birds. Significant differences were observed in the abundances of specific bacterial taxa between the microbiota of individuals belonging to farms that became Campylobacter positive during the study and those who remained negative with particular reference to Bacteroidales and Clostridiales, respectively. Moreover, Campylobacter colonization dramatically influenced the microbiota richness, although to a different extent depending on the infection timing. Finally, a key role of Faecalibacterium and Lactobacillus genera on the Campylobacter microbial network was observed. Understanding the ecology of the Campylobacter interaction with host microbiota during infection could support novel approaches for broiler microbial barrier restoration. Therefore, evidence obtained through this study can be used to identify options to reduce the incidence of infection at a primary production level based on the targeted influence of the intestinal microbiota, thus helping develop new control strategies in order to mitigate the risk of human exposure to Campylobacter by chicken meat consumption.},
}
@article {pmid33498531,
year = {2021},
author = {do Espirito Santo Pereira, A and Caixeta Oliveira, H and Fernandes Fraceto, L and Santaella, C},
title = {Nanotechnology Potential in Seed Priming for Sustainable Agriculture.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {11},
number = {2},
pages = {},
pmid = {33498531},
issn = {2079-4991},
support = {#88881.191767/2018-01//CAPES-COFECUB/ ; (#88887.363975/2010-00//CAPES-COFECUB/ ; #2017/21004-5//FAPESP/ ; },
abstract = {Our agriculture is threatened by climate change and the depletion of resources and biodiversity. A new agriculture revolution is needed in order to increase the production of crops and ensure the quality and safety of food, in a sustainable way. Nanotechnology can contribute to the sustainability of agriculture. Seed nano-priming is an efficient process that can change seed metabolism and signaling pathways, affecting not only germination and seedling establishment but also the entire plant lifecycle. Studies have shown various benefits of using seed nano-priming, such as improved plant growth and development, increased productivity, and a better nutritional quality of food. Nano-priming modulates biochemical pathways and the balance between reactive oxygen species and plant growth hormones, resulting in the promotion of stress and diseases resistance outcoming in the reduction of pesticides and fertilizers. The present review provides an overview of advances in the field, showing the challenges and possibilities concerning the use of nanotechnology in seed nano-priming, as a contribution to sustainable agricultural practices.},
}
@article {pmid33495891,
year = {2021},
author = {Fuentes, E and Prieto, B},
title = {Recovery Capacity of Subaerial Biofilms Grown on Granite Buildings Subjected to Simulated Drought in a Climate Change Context.},
journal = {Microbial ecology},
volume = {82},
number = {3},
pages = {761-769},
pmid = {33495891},
issn = {1432-184X},
support = {BES-2017-079927//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CGL2016-79778-R//Agencia Estatal de Investigaci&#xf3;n/ ; CGL2016-79778-R//European Regional Development Fund/ ; },
mesh = {Biofilms ; *Climate Change ; *Droughts ; Extracellular Polymeric Substance Matrix ; Silicon Dioxide ; },
abstract = {Variations in environmental conditions in the context of climate change are expected to affect biofilm-associated organisms on granite heritage buildings. The number and duration of drought periods should be considered, as these factors will affect the availability of water for the microorganisms. In this study, mature biofilms were exposed to various drying-rewetting cycles, and the effects of water stress on the SAB and their resilience were evaluated in terms of the variation in microbial composition, extracellular polymeric substance production, and photosynthetic efficiency. The structure of the biofilm changed after exposure to drought, becoming more heterogeneous and with an increase in the carbohydrate to protein ratio, especially after the second day of total drought. YMAX and YEF parameters proved to be the most informative, showing that the photosynthetic efficiency and recovery capacity were inversely related to the duration of the drought period. Furthermore, cyanobacteria resisted drought better than algae, giving rise to a decrease in the algae to cyanobacteria ratio.},
}
@article {pmid33494899,
year = {2021},
author = {Hollander, A and Yaron, S},
title = {Pore-forming treatments induce aggregation of Salmonella Senftenberg through protein leakage.},
journal = {Food microbiology},
volume = {96},
number = {},
pages = {103721},
doi = {10.1016/j.fm.2020.103721},
pmid = {33494899},
issn = {1095-9998},
mesh = {Acyclic Monoterpenes/pharmacology ; Bacterial Proteins/*metabolism ; Cell Membrane Permeability/drug effects ; Ocimum ; Ocimum basilicum/chemistry ; Oils, Volatile/*pharmacology ; Plant Oils/*pharmacology ; Salmonella/cytology/*drug effects/metabolism ; },
abstract = {Fresh herbs are not commonly associated with foodborne pathogens, due to the production of essential oils with antimicrobial activity. Recalls of contaminated basil, and basil outbreaks caused by Salmonella motivated studies aimed to comprehend the antimicrobial activity of basil essential oils, and to explore the mechanisms in which Salmonella can overcome them. Linalool, a major constituent of basil oil, increases the permeability of Salmonella Senftenberg cells by damaging their membrane. Linalool also induces bacterial aggregation. We hypothesized that the membrane perforation effect triggers cell aggregation through leakage of intracellular substances from live and dead cells. By exposing S. Senftenberg to additional physical (sonication) or chemical (eugenol, Triton-X-100) treatments, we showed that the aggregation is caused by various membrane-targeted treatments. Enzymatic degradation of leaked proteins restricted the bacterial aggregation, and disassembled existing aggregates. Moreover, supplemented proteins such as bacterial intracellular proteins or BSA also caused aggregation, further supporting the hypothesis that non-specific proteins trigger the bacterial aggregation. This study provides a novel understanding of the role of protein leakage in promoting bacterial aggregation. Since aggregation has significant roles in food safety and microbial ecology, this finding may establish future studies about microbial resistance via formation of clusters similar to biofilm development.},
}
@article {pmid33491139,
year = {2021},
author = {Parada-Pinilla, MP and Ferreira, MA and Roncallo, JC and Santos, SN and Melo, IS and Assef, ANB and Wilke, DV and Silva, LF and Garrido, LM and Araújo, WL and Padilla, G},
title = {Biopolymer production by halotolerant bacteria isolated from Caatinga biome.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {52},
number = {2},
pages = {547-559},
pmid = {33491139},
issn = {1678-4405},
support = {2009/52665-4; 2010/51458-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biopolymers/*metabolism ; Brazil ; Phylogeny ; Polyhydroxyalkanoates/metabolism ; Polysaccharides, Bacterial/metabolism ; Sodium Chloride/analysis/*metabolism ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Saline environments are extreme habitats with a high diversity of microorganisms source of a myriad of biomolecules. These microorganisms are assigned as extremophiles recognized to be producers of new natural compounds, which can be synthesized by helping to survive under harshness and extreme conditions. In Brazil, in the saline and semi-arid region of Areia Branca (Caatinga biome), halotolerant bacteria (able to growth at high NaCl concentrations) were isolated from rhizosphere of native plants Blutaparon portulacoides and Spergularia sp. and their biopolymer production was studied. A total of 25 bacterial isolates were identified at genus level based on 16S rRNA gene sequence analysis. Isolates were mainly Gram-positive bacteria from Bacillaceae, Staphylococcaceae, Microbacteriaceae, and Bacillales XII incertae sedis families, affiliates to Bacillus, Staphylococcus, Curtobacterium, and Exiguobacterium genera, respectively. One of the Gram-negative isolates was identified as member of the Pseudomonadaceae family, genus Pseudomonas. All the identified strains were halotolerant bacteria with optimum growth at 0.6-2.0 M salt concentrations. Assays for biopolymer production showed that the halotolerant strains are a rich source of compounds as polyhydroxyalkanoates (PHA), biodegradable biopolymer, such as poly(3-hydroxybutyrate) (PHB) produced from low-cost substrates, and exopolysaccharides (EPS), such as hyaluronic acid (HA), metabolite of great interest to the cosmetic and pharmaceutical industry. Also, eight bacterial EPS extracts showed immunostimulatory activity, promising results that can be used in biomedical applications. Overall, our findings demonstrate that these biomolecules can be produced in culture medium with 0.6-2.0 M NaCl concentrations, relevant feature to avoid costly production processes. This is the first report of biopolymer-producing bacteria from a saline region of Caatinga biome that showed important biological activities.},
}
@article {pmid33490051,
year = {2020},
author = {Shahsavari, E and Rouch, D and Khudur, LS and Thomas, D and Aburto-Medina, A and Ball, AS},
title = {Challenges and Current Status of the Biological Treatment of PFAS-Contaminated Soils.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {8},
number = {},
pages = {602040},
pmid = {33490051},
issn = {2296-4185},
abstract = {Per- and polyfluoroalkyl substances (PFAS) are Synthetic Organic Compounds (SOCs) which are of current concern as they are linked to a myriad of adverse health effects in mammals. They can be found in drinking water, rivers, groundwater, wastewater, household dust, and soils. In this review, the current challenge and status of bioremediation of PFAs in soils was examined. While several technologies to remove PFAS from soil have been developed, including adsorption, filtration, thermal treatment, chemical oxidation/reduction and soil washing, these methods are expensive, impractical for in situ treatment, use high pressures and temperatures, with most resulting in toxic waste. Biodegradation has the potential to form the basis of a cost-effective, large scale in situ remediation strategy for PFAS removal from soils. Both fungal and bacterial strains have been isolated that are capable of degrading PFAS; however, to date, information regarding the mechanisms of degradation of PFAS is limited. Through the application of new technologies in microbial ecology, such as stable isotope probing, metagenomics, transcriptomics, and metabolomics there is the potential to examine and identify the biodegradation of PFAS, a process which will underpin the development of any robust PFAS bioremediation technology.},
}
@article {pmid33489789,
year = {2021},
author = {Macchi, M and Festa, S and Nieto, E and Irazoqui, JM and Vega-Vela, NE and Junca, H and Valacco, MP and Amadio, AF and Morelli, IS and Coppotelli, BM},
title = {Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {29},
number = {},
pages = {e00588},
pmid = {33489789},
issn = {2215-017X},
abstract = {Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.},
}
@article {pmid33484740,
year = {2021},
author = {Costa, OYA and Kuramae, EE},
title = {The influence of agar brands and micronutrients in the growth optimization of Granulicella sp. (Acidobacteriota).},
journal = {Journal of microbiological methods},
volume = {181},
number = {},
pages = {106148},
doi = {10.1016/j.mimet.2021.106148},
pmid = {33484740},
issn = {1872-8359},
mesh = {Acidobacteria/*growth &amp; development ; Agar/metabolism ; *Culture Media/chemistry/metabolism ; Micronutrients/*metabolism ; },
abstract = {Acidobacteriota are highly abundant in soils, however, few cultured representatives are available. The purity of the reagents can influence microbial growth in laboratory conditions and successful isolation. Here we investigated the impact of different agar brands in culture medium and advocate that agar origin should be carefully considered for Acidobacteriota strains growth and microbial isolation.},
}
@article {pmid33483845,
year = {2021},
author = {Romero-Olivares, AL and Morrison, EW and Pringle, A and Frey, SD},
title = {Linking Genes to Traits in Fungi.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {145-155},
pmid = {33483845},
issn = {1432-184X},
support = {Hatch 1016142//Agricultural Research Service/ ; Diversity &amp; Innovation Scholars program//University of New Hampshire/ ; },
mesh = {*Ecosystem ; Fungi/genetics ; *Mycorrhizae ; Nitrogen ; Soil ; Soil Microbiology ; },
abstract = {Fungi are mediators of the nitrogen and carbon cycles in terrestrial ecosystems. Examining how nitrogen uptake and organic matter decomposition potential differs in fungi can provide insight into the underlying mechanisms driving fungal ecological processes and ecosystem functioning. In this study, we assessed the frequency of genes encoding for specific enzymes that facilitate nitrogen uptake and organic matter decomposition in 879 fungal genomes with fungal taxa grouped into trait-based categories. Our linked gene-trait data approach revealed that gene frequencies vary across and within trait-based groups and that trait-based categories differ in trait space. We present two examples of how this linked gene-trait approach can be used to address ecological questions. First, we show that this type of approach can help us better understand, and potentially predict, how fungi will respond to environmental stress. Specifically, we found that trait-based categories with high nitrogen uptake gene frequency increased in relative abundance when exposed to high soil nitrogen enrichment. Second, by comparing frequencies of nitrogen uptake and organic matter decomposition genes, we found that most ectomycorrhizal fungi in our dataset have similar gene frequencies to brown rot fungi. This demonstrates that gene-trait data approaches can shed light on potential evolutionary trajectories of life history traits in fungi. We present a framework for exploring nitrogen uptake and organic matter decomposition gene frequencies in fungal trait-based groups and provide two concise examples on how to use our framework to address ecological questions from a mechanistic perspective.},
}
@article {pmid33482922,
year = {2021},
author = {Okazaki, Y and Fujinaga, S and Salcher, MM and Callieri, C and Tanaka, A and Kohzu, A and Oyagi, H and Tamaki, H and Nakano, SI},
title = {Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {24},
pmid = {33482922},
issn = {2049-2618},
mesh = {Aquatic Organisms/classification/genetics/isolation &amp; purification ; *Biodiversity ; Europe ; *Fresh Water ; Japan ; Phylogeny ; *Phylogeography ; Plankton/classification/*genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe.<br><br>RESULTS: Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion.<br><br>CONCLUSIONS: Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future. Video abstract.},
}
@article {pmid33482213,
year = {2021},
author = {Vinothkanna, A and Sathiyanarayanan, G and Balaji, P and Mathivanan, K and Pugazhendhi, A and Ma, Y and Sekar, S and Thirumurugan, R},
title = {Structural characterization, functional and biological activities of an exopolysaccharide produced by probiotic Bacillus licheniformis AG-06 from Indian polyherbal fermented traditional medicine.},
journal = {International journal of biological macromolecules},
volume = {174},
number = {},
pages = {144-152},
doi = {10.1016/j.ijbiomac.2021.01.117},
pmid = {33482213},
issn = {1879-0003},
mesh = {A549 Cells ; Antineoplastic Agents/pharmacology ; Antioxidants/chemistry/pharmacology ; Bacillus licheniformis/*metabolism ; Chromatography, High Pressure Liquid/methods ; Fermentation/physiology ; Free Radicals ; Humans ; Magnetic Resonance Spectroscopy/methods ; Medicine, Traditional/methods ; Polysaccharides, Bacterial/*chemistry/isolation &amp; purification/*metabolism ; Probiotics/metabolism ; Spectroscopy, Fourier Transform Infrared/methods ; },
abstract = {An exopolysaccharide (EPS) was purified from the probiotic bacterium Bacillus licheniformis AG-06 isolated from the polyherbal fermented traditional medicine (Ashwagandharishta) of Indian Ayurveda. High-performance liquid chromatography (HPLC) based compositional analysis exhibits the heteropolymeric nature of the EPS consisting of galactose, rhamnose, xylose, mannose, and glucose, as the monomeric units. Fourier-transform infrared (FT-IR) and nuclear magnetic resonance (NMR) spectroscopic analyses confirm the presence of typical carbohydrate polymer functional groups and structural units, respectively. The purified EPS demonstrates the web-like fibrous and porous nature in scanning electron microscopic and atomic force microscopic studies. The purified EPS had shown 71.83% and 67.79% of flocculation and emulsification activities, respectively. Antioxidant activity was evaluated against 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), nitric oxide, and superoxide free radicals and the scavenging actions were increased in a dose-dependent manner. Moreover, the purified EPS exhibits a significant cytotoxic activity against the human lung carcinoma cells (A549), which strongly suggests the anticancer potential of the EPS derived from B. licheniformis AG-06.},
}
@article {pmid33480992,
year = {2021},
author = {Baunach, M and Chowdhury, S and Stallforth, P and Dittmann, E},
title = {The Landscape of Recombination Events That Create Nonribosomal Peptide Diversity.},
journal = {Molecular biology and evolution},
volume = {38},
number = {5},
pages = {2116-2130},
pmid = {33480992},
issn = {1537-1719},
mesh = {*Evolution, Molecular ; *Models, Genetic ; Multigene Family ; Peptide Biosynthesis, Nucleic Acid-Independent/*genetics ; Peptide Synthases/*genetics ; *Recombination, Genetic ; },
abstract = {Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing and matching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the Acore domains, yet domain interfaces and the flexible Asub domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches.},
}
@article {pmid33477842,
year = {2021},
author = {Ruiz-Roldán, L and de Toro, M and Sáenz, Y},
title = {Whole Genome Analysis of Environmental Pseudomonas mendocina Strains: Virulence Mechanisms and Phylogeny.},
journal = {Genes},
volume = {12},
number = {1},
pages = {},
pmid = {33477842},
issn = {2073-4425},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Proteins/genetics ; Drug Resistance, Microbial/genetics ; Ducks/microbiology ; Endocarditis/drug therapy/*microbiology ; Endodeoxyribonucleases/genetics ; Feces/microbiology ; Food Microbiology ; *Genome, Bacterial ; Humans ; Lactuca/microbiology ; Phylogeny ; Pseudomonas mendocina/genetics/*pathogenicity ; Sepsis/drug therapy/*microbiology ; Virulence Factors/*genetics ; Whole Genome Sequencing ; },
abstract = {Pseudomonas mendocina is an environmental bacterium, rarely isolated in clinical specimens, although it has been described as producing endocarditis and sepsis. Little is known about its genome. Whole genome sequencing can be used to learn about the phylogeny, evolution, or pathogenicity of these isolates. Thus, the aim of this study was to analyze the resistome, virulome, and phylogenetic relationship of two P. mendocina strains, Ps542 and Ps799, isolated from a healthy Anas platyrhynchos fecal sample and a lettuce, respectively. Among all of the small number of P.mendocina genomes available in the National Center for Biotechnology Information (NCBI) repository, both strains were placed within one of two well-defined phylogenetic clusters. Both P. mendocina strains lacked antimicrobial resistance genes, but the Ps799 genome showed a MOBP3 family relaxase. Nevertheless, this study revealed that P. mendocina possesses an important number of virulence factors, including a leukotoxin, flagella, pili, and the Type 2 and Type 6 Secretion Systems, that could be responsible for their pathogenesis. More phenotypical and in vivo studies are needed to deepen the association with human infections and the potential P. mendocina pathogenicity.},
}
@article {pmid33477775,
year = {2021},
author = {Zerva, I and Remmas, N and Kagalou, I and Melidis, P and Ariantsi, M and Sylaios, G and Ntougias, S},
title = {Effect of Chlorination on Microbiological Quality of Effluent of a Full-Scale Wastewater Treatment Plant.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
pmid = {33477775},
issn = {2075-1729},
abstract = {The evaluation of effluent wastewater quality mainly relies on the assessment of conventional bacterial indicators, such as fecal coliforms and enterococci; however, little is known about opportunistic pathogens, which can resist chlorination and may be transmitted in aquatic environments. In contrast to conventional microbiological methods, high-throughput molecular techniques can provide an accurate evaluation of effluent quality, although a limited number of studies have been performed in this direction. In this work, high-throughput amplicon sequencing was employed to assess the effectiveness of chlorination as a disinfection method for secondary effluents. Common inhabitants of the intestinal tract, such as Bacteroides, Arcobacter and Clostridium, and activated sludge denitrifiers capable of forming biofilms, such as Acidovorax, Pseudomonas and Thauera, were identified in the chlorinated effluent. Chloroflexi with dechlorination capability and the bacteria involved in enhanced biological phosphorus removal, i.e., Candidatus Accumulibacter and Candidatus Competibacter, were also found to resist chlorination. No detection of Escherichia indicates the lack of fecal coliform contamination. Mycobacterium spp. were absent in the chlorinated effluent, whereas toxin-producing cyanobacteria of the genera Anabaena and Microcystis were identified in low abundances. Chlorination significantly affected the filamentous bacteria Nocardioides and Gordonia, whereas Zoogloea proliferated in the disinfected effluent. Moreover, perchlorate/chlorate- and organochlorine-reducing bacteria resisted chlorination.},
}
@article {pmid33476328,
year = {2021},
author = {Mariani, N and Borsini, A and Cecil, CAM and Felix, JF and Sebert, S and Cattaneo, A and Walton, E and Milaneschi, Y and Cochrane, G and Amid, C and Rajan, J and Giacobbe, J and Sanz, Y and Agustí, A and Sorg, T and Herault, Y and Miettunen, J and Parmar, P and Cattane, N and Jaddoe, V and Lötjönen, J and Buisan, C and González Ballester, MA and Piella, G and Gelpi, JL and Lamers, F and Penninx, BWJH and Tiemeier, H and von Tottleben, M and Thiel, R and Heil, KF and Järvelin, MR and Pariante, C and Mansuy, IM and Lekadir, K},
title = {Identifying causative mechanisms linking early-life stress to psycho-cardio-metabolic multi-morbidity: The EarlyCause project.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0245475},
pmid = {33476328},
issn = {1932-6203},
support = {G108/603/MRC_/Medical Research Council/United Kingdom ; MR/N029488/1/MRC_/Medical Research Council/United Kingdom ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Adult ; Adverse Childhood Experiences/psychology ; Biomarkers/metabolism ; Cardiovascular Diseases/*epidemiology/*etiology/metabolism/psychology ; Child ; Depression/*epidemiology/*etiology/metabolism/psychology ; Diabetes Mellitus/*epidemiology/*etiology/metabolism/psychology ; Environment ; Humans ; Longitudinal Studies ; Morbidity ; Risk Factors ; Stress, Psychological/*complications ; },
abstract = {INTRODUCTION: Depression, cardiovascular diseases and diabetes are among the major non-communicable diseases, leading to significant disability and mortality worldwide. These diseases may share environmental and genetic determinants associated with multimorbid patterns. Stressful early-life events are among the primary factors associated with the development of mental and physical diseases. However, possible causative mechanisms linking early life stress (ELS) with psycho-cardio-metabolic (PCM) multi-morbidity are not well understood. This prevents a full understanding of causal pathways towards the shared risk of these diseases and the development of coordinated preventive and therapeutic interventions.<br><br>METHODS AND ANALYSIS: This paper describes the study protocol for EarlyCause, a large-scale and inter-disciplinary research project funded by the European Union's Horizon 2020 research and innovation programme. The project takes advantage of human longitudinal birth cohort data, animal studies and cellular models to test the hypothesis of shared mechanisms and molecular pathways by which ELS shapes an individual's physical and mental health in adulthood. The study will research in detail how ELS converts into biological signals embedded simultaneously or sequentially in the brain, the cardiovascular and metabolic systems. The research will mainly focus on four biological processes including possible alterations of the epigenome, neuroendocrine system, inflammatome, and the gut microbiome. Life-course models will integrate the role of modifying factors as sex, socioeconomics, and lifestyle with the goal to better identify groups at risk as well as inform promising strategies to reverse the possible mechanisms and/or reduce the impact of ELS on multi-morbidity development in high-risk individuals. These strategies will help better manage the impact of multi-morbidity on human health and the associated risk.},
}
@article {pmid33471175,
year = {2021},
author = {Fernandes, NM and Campello-Nunes, PH and Paiva, TS and Soares, CAG and Silva-Neto, ID},
title = {Correction to: Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {644},
doi = {10.1007/s00248-021-01691-1},
pmid = {33471175},
issn = {1432-184X},
}
@article {pmid33471174,
year = {2021},
author = {Borruso, L and Checcucci, A and Torti, V and Correa, F and Sandri, C and Luise, D and Cavani, L and Modesto, M and Spiezio, C and Mimmo, T and Cesco, S and Di Vito, M and Bugli, F and Randrianarison, RM and Gamba, M and Rarojoson, NJ and Zaborra, CA and Mattarelli, P and Trevisi, P and Giacoma, C},
title = {I Like the Way You Eat It: Lemur (Indri indri) Gut Mycobiome and Geophagy.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {215-223},
pmid = {33471174},
issn = {1432-184X},
mesh = {Animals ; Ecosystem ; *Indriidae ; *Lemur ; *Mycobiome ; Pica ; Soil Microbiology ; },
abstract = {Here, we investigated the possible linkages among geophagy, soil characteristics, and gut mycobiome of indri (Indri indri), an endangered lemur species able to survive only in wild conditions. The soil eaten by indri resulted in enriched secondary oxide-hydroxides and clays, together with a high concentration of specific essential micronutrients. This could partially explain the role of the soil in detoxification and as a nutrient supply. Besides, we found that soil subject to geophagy and indris' faeces shared about 8.9% of the fungal OTUs. Also, several genera (e.g. Fusarium, Aspergillus and Penicillium) commonly associated with soil and plant material were found in both geophagic soil and indri samples. On the contrary, some taxa with pathogenic potentials, such as Cryptococcus, were only found in indri samples. Further, many saprotrophs and plant-associated fungal taxa were detected in the indri faeces. These fungal species may be involved in the digestion processes of leaves and could have a beneficial role in their health. In conclusion, we found an intimate connection between gut mycobiome and soil, highlighting, once again, the potential consequent impacts on the wider habitat.},
}
@article {pmid33469721,
year = {2021},
author = {Kim, MS and Kim, KH and Hwang, SJ and Lee, TK},
title = {Role of Algal Community Stability in Harmful Algal Blooms in River-Connected Lakes.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {309-318},
pmid = {33469721},
issn = {1432-184X},
mesh = {Ecosystem ; *Harmful Algal Bloom ; Lakes ; *Microcystis ; Rivers ; },
abstract = {Harmful algal blooms (HABs) in freshwater produce toxins that pose a threat to public health and aquatic ecosystems. Although algal communities have been studied globally to understand the characteristics of HABs, the occurrence of toxic cyanobacteria in freshwater ecosystems is rarely understood. Unlike abiotic factors, the effects of biotic factors (e.g., interaction, dominance, and variability) on the occurrence of toxic cyanobacteria were overlooked due to the intricate interaction of microorganisms under different environmental conditions. To address this problem, a comprehensive ecological concept stability, which encompasses variations in species or communities due to changing biological interactions or environmental fluctuations, was applied in this study. The algal communities in six river-connected lakes in the North Han River, South Korea, were classified into high and low stability groups. The algal species belonging to diatoms and green algae groups played a major role in the interaction within the algal community in highly stable lakes, but the frequency of Microcystis led the interaction within the algal community at the center of the network in low-stability lakes. These results indicate that the interaction within the cluster is easily changed by Microcystis, where the abundance explosively increases in lakes with low algal community stability. Water quality is more strongly associated with the occurrence of toxic cyanobacteria (Microcystis and Dolichospermum). In low-stability lakes, more diverse water quality indicators are correlated with the development of toxic algae than in high-stability lakes. This paper is the first report on the importance of algal community stability in freshwater in the occurrence of toxic cyanobacteria and offers a new perspective on Microcystis monitoring and management.},
}
@article {pmid33468708,
year = {2021},
author = {Fu, S and Yang, Q and Wang, Q and Pang, B and Lan, R and Wei, D and Qu, B and Liu, Y},
title = {Continuous Genomic Surveillance Monitored the In Vivo Evolutionary Trajectories of Vibrio parahaemolyticus and Identified a New Virulent Genotype.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33468708},
issn = {2379-5077},
abstract = {Our ability to predict evolutionary trajectories of pathogens is one of the promising leverages to fight against the pandemic disease, yet few studies have addressed this question in situ, due to the difficulty in monitoring the milestone evolutionary events for a given pathogen and in understanding the evolutionary strategies. In this study, we monitored the real-time evolution of Vibrio parahaemolyticus in response to successive antibiotic treatment in three shrimp farms in North China from 2011 to 2018 by whole-genome sequencing. Results showed that the stepwise emergence of resistance was associated with the antibiotic usage. Genomic analysis of resistant isolates showed that the acquisition of the resistant mobile genetic elements flanked by an insertion sequence (ISVal1) closely mirrored the antibiotics used in shrimp farms since 2014. Next, we also identified 50 insertion sites of ISVal1 in the chromosome, which facilitated the formation of pathogenicity islands (PAIs) and fitness islands in the following years. Further, horizontal transfers of a virulent trh-nik-ure genomic island (GI) and two GIs improving the fitness have been observed in two farms since 2016. In this case study, we proposed that the insertion sequence triggered four major evolutionary events during the outbreaks of shrimp disease in three farms, including horizontal transfer of transposon (HTT) (stage 1), the formation of resistance islands (stage 2) and the PAIs (stage 3), and horizontal transfer of the PAIs (stage 4). This study presented the first in vivo evolutionary trajectories for a given bacterial pathogen, which helps us to understand the emergence mechanisms of new genotypes.IMPORTANCE Most human infectious diseases originate from animals. Thus, how to reduce or prevent pandemic zoonoses before they emerge in people is becoming a critical issue. Continuous genomic surveillance of the evolutionary trajectories of potential human pathogens on farms is a promising strategy to realize early warning. Here, we conducted an 8-year surveillance of Vibrio parahaemolyticus in three shrimp farms. The results showed that the use of antibiotics and horizontal transfer of transposons (HTT) drove the evolution of V. parahaemolyticus, which could be divided into four stages: HTT, formation of resistance islands, formation of pathogenicity islands (PAIs), and horizontal transfer of PAIs. This study presented the first in vivo monitoring of evolutionary trajectories for a given bacterial pathogen, providing valuable information for the prevention of pandemic zoonoses.},
}
@article {pmid33468704,
year = {2021},
author = {Rubbens, P and Props, R},
title = {Computational Analysis of Microbial Flow Cytometry Data.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33468704},
issn = {2379-5077},
abstract = {Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution. The complexity and amount of data necessitate an objective and streamlined data processing workflow that extends beyond commercial instrument software. No full overview of the necessary steps regarding the computational analysis of microbial flow cytometry data currently exists. In this review, we provide an overview of the full data analysis pipeline, ranging from measurement to data interpretation, tailored toward studies in microbial ecology. At every step, we highlight computational methods that are potentially useful, for which we provide a short nontechnical description. We place this overview in the context of a number of open challenges to the field and offer further motivation for the use of standardized flow cytometry in microbial ecology research.},
}
@article {pmid33468585,
year = {2021},
author = {Swaney, MH and Kalan, LR},
title = {Living in Your Skin: Microbes, Molecules, and Mechanisms.},
journal = {Infection and immunity},
volume = {89},
number = {4},
pages = {},
pmid = {33468585},
issn = {1098-5522},
support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; },
mesh = {*Biomarkers ; Cell Communication ; Energy Metabolism ; Homeostasis ; Host-Pathogen Interactions ; Humans ; Immune System/immunology/metabolism ; *Microbiota ; Organ Specificity ; Skin/*microbiology ; *Skin Physiological Phenomena ; Wound Healing ; },
abstract = {Human skin functions as a physical, chemical, and immune barrier against the external environment while also providing a protective niche for its resident microbiota, known as the skin microbiome. Cooperation between the microbiota, host skin cells, and the immune system is responsible for maintenance of skin health, and a disruption to this delicate balance, such as by pathogen invasion or a breach in the skin barrier, may lead to impaired skin function. In this minireview, we describe the role of the microbiome in microbe, host, and immune interactions under distinct skin states, including homeostasis, tissue repair, and wound infection. Furthermore, we highlight the growing number of diverse microbial metabolites and products that have been identified to mediate these interactions, particularly those involved in host-microbe communication and defensive symbiosis. We also address the contextual pathogenicity exhibited by many skin commensals and provide insight into future directions in the skin microbiome field.},
}
@article {pmid33467504,
year = {2021},
author = {Chang, J and Shi, S and Tian, L and Leite, MFA and Chang, C and Ji, L and Ma, L and Tian, C and Kuramae, EE},
title = {Self-Crossing Leads to Weak Co-Variation of the Bacterial and Fungal Communities in the Rice Rhizosphere.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
pmid = {33467504},
issn = {2076-2607},
support = {41920104008//the National Natural Science Foundation of China/ ; 2016YFC0501202//the National Key Research and Development Program of China/ ; XDA23070501//the Science Foundation of Chinese Academy of Sciences/ ; 2019SYHZ0039//the Cooperative Project between CAS and Jilin Province of China/ ; 20190303070SF//the Science and Technology Development Project of Jilin Province of China/ ; },
abstract = {The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipogon wild rice; male parent Oryza sativa cultivated rice; their F1 progeny; and the F2, F3 and F4 self-crossing generations. Our results showed that the bacterial and fungal α-diversities of the hybrid F1 and self-crossing generations (F2, F3, F4) were closer to one of the two parental lines, which may indicate a role of the parental line in the diversity of the rhizosphere microbial community assembly. Self-crossing from F1 to F4 led to weak co-variation of the bacterial and fungal communities and distinct rhizosphere microbiomes. In the parental and self-crossing progenies, the reduction of community dissimilarity was higher for the fungal community than for the bacterial community.},
}
@article {pmid33462700,
year = {2021},
author = {Moroenyane, I and Mendes, L and Tremblay, J and Tripathi, B and Yergeau, &#xc9;},
title = {Plant Compartments and Developmental Stages Modulate the Balance between Niche-Based and Neutral Processes in Soybean Microbiome.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {416-428},
pmid = {33462700},
issn = {1432-184X},
support = {RGPIN 2014-05274//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Bacteria/genetics ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Glycine max ; },
abstract = {Understanding the dynamics of plant-associated microbial communities within agriculture is well documented. However, the ecological processes that assemble the plant microbiome are not well understood. This study elucidates the relative dominance of assembly processes across plant compartments (root, stem, and leaves) and developmental stages (emergence, growth, flowering, and maturation). Bacterial community composition and assembly processes were assessed using 16S rRNA gene amplicon sequencing. Null models that couple phylogenetic community composition and species distribution models were used to evaluate ecological assembly processes of bacterial communities. All models highlighted that the balance between the assembly process was modulated by compartments and developmental stages. Dispersal limitation dominated amongst the epiphytic communities and at the maturation stage. Homogeneous selection dominated assembly across plant compartments and development stages. Overall, both sets of models were mostly in agreement in predicting the prevailing assembly processes. Our results show, for the first time, that even though niche-based processes dominate in the plant environment, the relative influence of dispersal limitation in community assembly is important.},
}
@article {pmid33461083,
year = {2021},
author = {Xiao, R and Ni, BJ and Liu, S and Lu, H},
title = {Impacts of organics on the microbial ecology of wastewater anammox processes: Recent advances and meta-analysis.},
journal = {Water research},
volume = {191},
number = {},
pages = {116817},
doi = {10.1016/j.watres.2021.116817},
pmid = {33461083},
issn = {1879-2448},
mesh = {*Ammonium Compounds ; Anaerobiosis ; Bioreactors ; Denitrification ; Nitrogen ; Oxidation-Reduction ; *Wastewater ; },
abstract = {Anaerobic ammonium oxidation (anammox) represents a promising technology for wastewater nitrogen removal. Organics management is critical to achieving efficient and stable performance of anammox or integrated processes, e.g., denitratation-anammox. The aim of this systematic review is to synthesize the state-of-the-art knowledge on the multifaceted impacts of organics on wastewater anammox community structure and function. Both exogenous and endogenous organics are discussed with respect to their effects on the biofilm/granule structure and function, as well as the interactions between anammox bacteria (AnAOB) and a broad range of coexisting functional groups. A global core community consisting of 19 taxa is identified and a co-occurrence network is constructed by meta-analysis on the 16S rDNA sequences of 149 wastewater anammox samples. Correlations between core taxa, keystone taxa, and environmental factors, including COD, nitrogen loading rate (NLR) and C/N ratio are obtained. This review provides a holistic understanding of the microbial responses to different origins and types of organics in wastewater anammox reactors, which will facilitate the design and operation of more efficient anammox-based wastewater nitrogen removal process.},
}
@article {pmid33459836,
year = {2021},
author = {Arias, A and Selander, E and Saiz, E and Calbet, A},
title = {Predator Chemical Cue Effects on the Diel Feeding Behaviour of Marine Protists.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {356-364},
pmid = {33459836},
issn = {1432-184X},
support = {BES-2015-074092//MICINN/ ; },
mesh = {Animals ; *Ciliophora ; Cues ; *Dinoflagellida ; Feeding Behavior ; Predatory Behavior ; },
abstract = {We have assessed the effect of copepod chemical cues on the diel feeding rhythms of heterotrophic and mixotrophic marine protists. All phagotrophic protists studied exhibited relatively high diurnal feeding rates. The magnitude of the diel feeding rhythm, expressed as the quotient of day and night ingestion rates, was inversely related to the time that phagotrophic protists were maintained in the laboratory in an environment without predators. In the case of the recently isolated ciliate Strombidium arenicola, the rhythm was lost after a few months. When challenged with chemical alarm signals (copepodamides) from the copepod Calanus finmarchicus at realistic concentrations (0.6-6 pM), S. arenicola partially re-established diurnal feeding. Conversely, the amplitude of the diel feeding rhythm for the ciliate Mesodinium rubrum was not affected by copepodamides, although the 24-h integrated food intake increased by approximately 23%. For the dinoflagellates Gyrodinium dominans and Karlodinium armiger, copepodamides significantly reduced the amplitude of their diel feeding rhythms; significant positive effects on total daily ingestion were only observed in G. dominans. Finally, the dinoflagellate Oxyrrhis marina, isolated >20 years ago, showed inconsistent responses to copepodamides, except for an average 6% increase in its total ingestion over 24 h. Our results demonstrate that the predation risk by copepods affects the diel feeding rhythm of marine protists and suggests a species-specific response to predation threats.},
}
@article {pmid33459817,
year = {2021},
author = {Kumar, M and Sodhi, KK and Singh, DK},
title = {Addressing the potential role of curcumin in the prevention of COVID-19 by targeting the Nsp9 replicase protein through molecular docking.},
journal = {Archives of microbiology},
volume = {203},
number = {4},
pages = {1691-1696},
pmid = {33459817},
issn = {1432-072X},
support = {NASF/CA-6030/2017-2018//NASF, ICAR/ ; },
mesh = {Curcumin/*pharmacology ; *Molecular Docking Simulation ; RNA-Binding Proteins/*antagonists &amp; inhibitors ; SARS-CoV-2/*drug effects/physiology ; Viral Nonstructural Proteins/*antagonists &amp; inhibitors ; Virus Replication/*drug effects ; },
abstract = {The pandemics have always been a destructive carrier to living organisms. Humans are the ultimate victims, as now we are facing the SARS CoV-2 virus caused COVID-19 since its emergence in Dec 2019, at Wuhan (China). Due to the new coronavirus' unexplored nature, we shed light on curcumin for its potential role against the disease. The Nsp9 replicase protein, which plays an essential role in virus replication, was extracted online, followed by 3D PDB model prediction with its validation. The in silico molecular docking of curcumin with the replicase enzyme gave insights into the preventive measures against the virus as curcumin showed multiple interactions with Nsp9 replicase. The current study showed the use of curcumin against the coronavirus and its possible role in developing medicine against it.},
}
@article {pmid33459471,
year = {2021},
author = {DeLong, EF},
title = {Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats.},
journal = {Environmental microbiology},
volume = {23},
number = {3},
pages = {1301-1321},
pmid = {33459471},
issn = {1462-2920},
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Genome ; Humans ; Metagenomics ; Phylogeny ; },
abstract = {As a young bacteriologist just launching my career during the early days of the 'microbial revolution' in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize 'wild' bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited 'How we did it' perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!},
}
@article {pmid33454808,
year = {2021},
author = {Takano, SI and Gotoh, Y and Hayashi, T},
title = {"Candidatus Mesenet longicola": Novel Endosymbionts of Brontispa longissima that Induce Cytoplasmic Incompatibility.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {512-522},
pmid = {33454808},
issn = {1432-184X},
support = {18H02207//Japan Society for the Promotion of Science/ ; 16H06279//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Coleoptera ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; *Wolbachia/genetics ; },
abstract = {Intracellular bacteria that are mainly transmitted maternally affect their arthropod hosts' biology in various ways. One such effect is known as cytoplasmic incompatibility (CI), and three bacterial species are known to induce CI: Wolbachia, Cardinium hertigii, and a recently found alphaproteobacterial symbiont. To clarify the taxonomic status and provide the foundation for future studies to reveal CI mechanisms and other phenotypes, we investigated genetic and morphological properties of the third CI inducer that we have previously reported inducing CI in the coconut beetle Brontispa longissima. The draft genome of the bacteria was obtained from the oocytes of two isofemale lines of B. longissima infected with the bacteria: one from Japan (GL2) and the other from Vietnam (L5). Genome features of the symbionts (sGL2 and sL5) were highly similar, showing 1.3 Mb in size, 32.1% GC content, and 99.83% average nucleotide sequence. A phylogenetic study based on 43 universal and single-copy phylogenetic marker genes indicates that they formed a distinct clade in the family Anaplasmataceae. 16S rRNA gene sequences indicate that they are different from the closest known relatives, at least at the genus level. Therefore, we propose a new genus and species, "Candidatus Mesenet longicola", for the symbionts of B. longissima. Morphological analyses showed that Ca. M. longicola is an intracellular bacterium that is ellipsoidal to rod-shaped and 0.94 ± 0.26 μm (mean ± SD) in length, and accumulated in the anterior part of the oocyte. Candidates for the Ca. M. longicola genes responsible for CI induction are also described.},
}
@article {pmid33452897,
year = {2021},
author = {Dahl, MB and Peršoh, D and Jentsch, A and Kreyling, J},
title = {Root-Associated Mycobiomes of Common Temperate Plants (Calluna vulgaris and Holcus lanatus) Are Strongly Affected by Winter Climate Conditions.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {403-415},
pmid = {33452897},
issn = {1432-184X},
support = {DFG JE 282/5-1//Deutsche Forschungsgemeinschaft/ ; RTG 2010//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Ascomycota ; *Calluna ; Climate Change ; *Holcus ; *Mycobiome ; Seasons ; Soil ; },
abstract = {Winter temperatures are projected to increase in Central Europe. Subsequently, snow cover will decrease, leading to increased soil temperature variability, with potentially different consequences for soil frost depending on e.g. altitude. Here, we experimentally evaluated the effects of increased winter soil temperature variability on the root associated mycobiome of two plant species (Calluna vulgaris and Holcus lanatus) at two sites in Germany; a colder and wetter upland site with high snow accumulation and a warmer and drier lowland site, with low snow accumulation. Mesocosm monocultures were set-up in spring 2010 at both sites (with soil and plants originating from the lowland site). In the following winter, an experimental warming pulse treatment was initiated by overhead infrared heaters and warming wires at the soil surface for half of the mesocosms at both sites. At the lowland site, the warming treatment resulted in a reduced number of days with soil frost as well as increased the average daily temperature amplitude. Contrary, the treatment caused no changes in these parameters at the upland site, which was in general a much more frost affected site. Soil and plant roots were sampled before and after the following growing season (spring and autumn 2011). High-throughput sequencing was used for profiling of the root-associated fungal (ITS marker) community (mycobiome). Site was found to have a profound effect on the composition of the mycobiome, which at the upland site was dominated by fast growing saprotrophs (Mortierellomycota), and at the lowland site by plant species-specific symbionts (e.g. Rhizoscyphus ericae and Microdochium bolleyi for C. vulgaris and H. lanatus respectively). The transplantation to the colder upland site and the temperature treatment at the warmer lowland site had comparable consequences for the mycobiome, implying that winter climate change resulting in higher temperature variability has large consequences for mycobiome structures regardless of absolute temperature of a given site.},
}
@article {pmid33452896,
year = {2021},
author = {Bergo, NM and Bendia, AG and Ferreira, JCN and Murton, BJ and Brandini, FP and Pellizari, VH},
title = {Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {344-355},
pmid = {33452896},
issn = {1432-184X},
support = {14/50820-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {*Archaea/genetics ; Atlantic Ocean ; Geologic Sediments ; Iron ; *Manganese ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe-Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.},
}
@article {pmid33452613,
year = {2021},
author = {Vingiani, GM and Gasulla, F and Barón-Sola, &#xc1; and Sobrino-Plata, J and Henández, LE and Casano, LM},
title = {Physiological and Molecular Alterations of Phycobionts of Genus Trebouxia and Coccomyxa Exposed to Cadmium.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {334-343},
pmid = {33452613},
issn = {1432-184X},
support = {CGL2016- 80259-P//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; AGL2014-53771-R//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; AGL2017-87591-R//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
mesh = {Cadmium/toxicity ; *Chlorophyta/genetics ; *Lichens ; *Microalgae/genetics ; Oxidative Stress ; },
abstract = {Several studies on aeroterrestrial microalgae are unravelling their resistance mechanisms to different abiotic stressors, including hazardous metals, pointing to their future role as bioremediation microorganisms. In the present study, physiological and molecular alterations of four phycobionts of genus Trebouxia (T. TR1 and T. TR9) and Coccomyxa (C. subellipsoidea and C. simplex) exposed to Cd were studied. Cd accumulation and subcellular distribution, cell wall structure, production of biothiols (GSH and phytochelatins), reactive oxygen species (ROS) formation, expression of key antioxidant genes and ROS-related enzymes were evaluated to determine the physiological differences among the four microalgae, with the aim to identify the most suitable microorganism for further biotechnological applications. After 7 days of Cd exposure, Coccomyxa algae showed higher capacity of Cd intake than Trebouxia species, with C. subellipsoidea being the highest Cd accumulator at both intracellular and, especially, cell wall level. Cd induced ROS formation in the four microalgae, but to a greater extent in both Coccomyxa algae. Trebouxia TR9 showed the lowest Cd-dependent oxidative stress probably due to glutathione reductase induction. All microalgae synthetized phytochelatins in response to Cd but in a species-specific and a dose-dependent manner. Results from this study agree with the notion that each microalga has evolved a distinct strategy to detoxify hazardous metals like Cd and to cope with oxidative stress associated with them. Coccomyxa subellipsoidea and Trebouxia TR9 appear as the most interesting candidates for further applications.},
}
@article {pmid33449130,
year = {2021},
author = {Zai, X and Luo, W and Bai, W and Li, Y and Xiao, X and Gao, X and Wang, E and Wei, G and Chen, W},
title = {Effect of Root Diameter on the Selection and Network Interactions of Root-Associated Bacterial Microbiomes in Robinia pseudoacacia L.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {391-402},
pmid = {33449130},
issn = {1432-184X},
support = {31870476//the National Natural Science Foundation of China/ ; 41830755//the National Natural Science Foundation of China/ ; },
mesh = {*Microbiota ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Robinia ; Soil Microbiology ; },
abstract = {The high plasticity of root morphology, physiology, and function influences root-associated microbiomes. However, the variation in root-associated microbiome diversity and structures in response to root diameter at different root depths remains poorly understood. Here, we selected black locust (Robinia pseudoacacia L.) as a model plant to investigate the selection and network interactions of rhizospheric and root endophytic bacterial microbiomes associated with roots of different diameters (1, 1-2, and > 2 mm) among root depths of 0-100 cm via the Illumina sequencing of the 16S rRNA gene. The results showed that the alpha diversity of the root-associated bacterial communities decreased with increasing root diameters among different root depths; fewer orders with higher relative abundance, especially in the endosphere, were enriched in association with coarse roots (> 2 mm) than fine roots among root depths. Furthermore, the variation in the enriched bacterial orders associated with different root diameters was explained by bulk soil properties. Higher co-occurrence network complexity and stability emerged in the rhizosphere microbiomes of fine roots than those of coarse roots, in contrast to the situation in the endosphere microbiomes. In particular, the endosphere of roots with a diameter of 1-2 mm exhibited the lowest network complexity and stability and a high proportion of keystone taxa (e.g., Cytophagia, Flavobacteriia, Sphingobacteriia, β-Proteobacteria, and γ-Proteobacteria), suggesting a keystone taxon-reliant strategy in this transitional stage. In summary, this study indicated that root diameter at different root depths differentially affects rhizospheric and endophytic bacterial communities, which implies a close relationship between the bacterial microbiome, root function, and soil properties.},
}
@article {pmid33448446,
year = {2020},
author = {Moraes, LC and Lang, PM and Arcanjo, RA and Rampelotto, PH and Fatturi-Parolo, CC and Ferreira, MBC and Montagner, F},
title = {Microbial ecology and predicted metabolic pathways in various oral environments from patients with acute endodontic infections.},
journal = {International endodontic journal},
volume = {53},
number = {12},
pages = {1603-1617},
doi = {10.1111/iej.13389},
pmid = {33448446},
issn = {1365-2591},
support = {//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul/ ; },
mesh = {Adult ; Cross-Sectional Studies ; DNA, Bacterial ; Humans ; Metabolic Networks and Pathways ; *Microbiota ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {AIM: To assess in a cross-sectional clinical study the effect of antibiotics on the diversity, structure and metabolic pathways of bacterial communities in various oral environments in patients with acute primary infections.<br><br>METHODOLOGY: Samples of saliva (SA), supragingival biofilm (SB) and from the pulp cavity (PC) were collected from teeth with acute primary infections and then grouped according to previous use of antibiotics (NoAtb&#xa0;=&#xa0;no antibiotics [n&#xa0;=&#xa0;6]; Atb&#xa0;=&#xa0;antibiotics [n&#xa0;=&#xa0;6]). DNA sequencing was conducted using MiSeq (Illumina, San Diego, CA, USA). The V1-V3 hyper-variable region of the 16S rRNA gene was amplified. A custom Mothur pipeline was used for 16S rRNA processing. Subsequent analyses of the sequence dataset were performed in R (using vegan, phyloseq and ggplot2 packages) or QIIME.<br><br>RESULTS: Twelve patients aged from 22 to 56&#xa0;years were recruited. Participants in the Atb group had taken the beta-lactamics amoxicillin (5/6) or cephalexin (1/6) for 2-3&#xa0;days. A total of 332 bacterial taxa (OTUs) were identified, belonging to 120 genera, 60 families and nine phyla. Firmicutes (41%) and Bacteroidetes (38%) were the most abundant phyla in all samples. Taxa clustered significantly by oral site (PCoA analysis; P&#xa0;<&#xa0;0.05, ANOSIM). Use of antibiotics had little effect on this clustering. However, SA, SB and PC had different degrees of richness, diversity and evenness. The greatest diversity was observed in SB samples and the least diversity was observed in PC samples. Metabolic prediction identified 163 pathways and previous use of antibiotics had a major effect on the estimated functional clustering in SA and PC samples.<br><br>CONCLUSION: The ecological niche had a strong influence on the bacterial content of samples from various oral sites. Previous exposure to antibiotics may exert an effect on the phylogenetic composition of SA. Metabolic pathways appear to be modulated by antimicrobial agents in SA and PC samples. The dynamics of host/microbial interactions in the apical region and the functional ecology of the infected pulp cavity should be revisited.},
}
@article {pmid33447808,
year = {2020},
author = {Lories, B and Belpaire, TER and Yssel, A and Ramon, H and Steenackers, HP},
title = {Agaric acid reduces Salmonella biofilm formation by inhibiting flagellar motility.},
journal = {Biofilm},
volume = {2},
number = {},
pages = {100022},
pmid = {33447808},
issn = {2590-2075},
abstract = {Salmonella biofilms are a common cause of contaminations in the food or feed industry. In a screening for novel compounds to combat biofilm-associated foodborne outbreaks, we identified agaric acid as a Salmonella Typhimurium biofilm inhibitor that does not affect planktonic growth. Importantly, the remaining biofilm cells after preventive treatment with agaric acid were significantly more sensitive to the common disinfectant hydrogen peroxide. Screening of a GFP-promoter fusion library of biofilm related genes revealed that agaric acid downregulates the transcription of genes responsible for flagellar motility. Concurrently, swimming motility was completely abrogated in the presence of agaric acid, indicating that biofilm inhibition occurs via interference with the motility phenotype. Moreover, agaric acid also reduced biofilm formation of Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli. Agaric acid thus shows potential as an anti-virulence compound that inhibits both motility and biofilm formation.},
}
@article {pmid33446998,
year = {2020},
author = {Li, M and Shao, D and Zhou, J and Gu, J and Qin, J and Chen, W and Wei, W},
title = {Signatures within esophageal microbiota with progression of esophageal squamous cell carcinoma.},
journal = {Chinese journal of cancer research = Chung-kuo yen cheng yen chiu},
volume = {32},
number = {6},
pages = {755-767},
pmid = {33446998},
issn = {1000-9604},
abstract = {OBJECTIVE: Esophageal squamous cell carcinoma (ESCC) is one of the dominant malignances worldwide, but currently there is less focus on the microbiota with ESCC and its precancerous lesions.<br><br>METHODS: Paired esophageal biopsy and swab specimens were obtained from 236 participants in Linzhou, China. Data from 16S ribosomal RNA gene sequencing were processed using quantitative insights into microbial ecology (QIIME2) and R Studio to evaluate differences. The Wilcoxon rank sum test and Kruskal-Wallis rank sum test were used to compare diversity and characteristic genera by specimens and participant groups. Ordinal logistic regression model was used to build microbiol prediction model.<br><br>RESULTS: Microbial diversity was similar between biopsy and swab specimens, including operational taxonomic unit (OTU) numbers and Shannon index. There were variations and similarities of esophageal microbiota among different pathological characteristics of ESCC. Top 10 relative abundance genera in all groups include Streptococcus, Prevotella, Veillonella, Actinobacillus, Haemophilus, Neisseria, Alloprevotella, Rothia, Gemella and Porphyromonas. Genus Streptococcus, Haemophilus, Neisseria and Porphyromonas showed significantly difference in disease groups when compared to normal control, whereas Streptococcus showed an increasing tendency with the progression of ESCC and others showed a decreasing tendency. About models based on all combinations of characteristic genera, only taken Streptococcus and Neisseria into model, the prediction performance was the ideal one, of which the area under the curve (AUC) was 0.738.<br><br>CONCLUSIONS: Esophageal biopsy and swab specimens could yield similar microbial characterization. The combination of Streptococcus and Neisseria has the potential to predict the progression of ESCC, which is needed to confirm by large-scale, prospective cohort studies.},
}
@article {pmid33446818,
year = {2021},
author = {McGill, SL and Yung, Y and Hunt, KA and Henson, MA and Hanley, L and Carlson, RP},
title = {Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1457},
pmid = {33446818},
issn = {2045-2322},
support = {U01 EB019416/EB/NIBIB NIH HHS/United States ; },
mesh = {Bacterial Proteins/*metabolism ; Humans ; *Models, Biological ; Pseudomonas aeruginosa/*metabolism/pathogenicity ; },
abstract = {Pseudomonas aeruginosa is a globally-distributed bacterium often found in medical infections. The opportunistic pathogen uses a different, carbon catabolite repression (CCR) strategy than many, model microorganisms. It does not utilize a classic diauxie phenotype, nor does it follow common systems biology assumptions including preferential consumption of glucose with an 'overflow' metabolism. Despite these contradictions, P. aeruginosa is competitive in many, disparate environments underscoring knowledge gaps in microbial ecology and systems biology. Physiological, omics, and in silico analyses were used to quantify the P. aeruginosa CCR strategy known as 'reverse diauxie'. An ecological basis of reverse diauxie was identified using a genome-scale, metabolic model interrogated with in vitro omics data. Reverse diauxie preference for lower energy, nonfermentable carbon sources, such as acetate or succinate over glucose, was predicted using a multidimensional strategy which minimized resource investment into central metabolism while completely oxidizing substrates. Application of a common, in silico optimization criterion, which maximizes growth rate, did not predict the reverse diauxie phenotypes. This study quantifies P. aeruginosa metabolic strategies foundational to its wide distribution and virulence including its potentially, mutualistic interactions with microorganisms found commonly in the environment and in medical infections.},
}
@article {pmid33446769,
year = {2021},
author = {Berger, C and Rückert, C and Blom, J and Rabaey, K and Kalinowski, J and Rosenbaum, MA},
title = {Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1370},
pmid = {33446769},
issn = {2045-2322},
support = {864669/ERC_/European Research Council/International ; },
mesh = {*Genome, Bacterial ; Genomics ; Pseudomonas Infections/*genetics ; Pseudomonas aeruginosa/*genetics/isolation &amp; purification/*pathogenicity ; Sequence Analysis, DNA ; Virulence ; },
abstract = {The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.},
}
@article {pmid33445025,
year = {2021},
author = {González-Martínez, A and Muñoz-Palazon, B and Kruglova, A and Vilpanen, M and Kuokkanen, A and Mikola, A and Heinonen, M},
title = {Performance and microbial community structure of a full-scale ANITA[TM]Mox bioreactor for treating reject water located in Finland.},
journal = {Chemosphere},
volume = {271},
number = {},
pages = {129526},
doi = {10.1016/j.chemosphere.2020.129526},
pmid = {33445025},
issn = {1879-1298},
mesh = {Anaerobiosis ; Bioreactors ; Finland ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; Wastewater ; *Water ; },
abstract = {The aim of this work was to study the operational performance and the microbial community dynamics during the start-up of ANITA[TM]Mox technology implemented at full-scale wastewater treatment plant in Finland to treat reject water from anaerobic digesters. The average ammonium removal in the studied setup reached around 90%, withstanding ammonium loads up to 0.13 g N m[-2]h[-1]. The nitrite concentration in the effluent did not exceed 10 mg L[-1], and there was a slight accumulation of NO3[-]-N during the operation which was controlled. Thus, the result showed a robust success to high ammonium loading in presence of organic matter. The sequencing showed a heterogeneous microbial population where Methanosaeta, WCHA1-57 genus, Sphingobacteriia, Chlorobia and diverse unknown fungi were found as dominant phylotypes. Moreover, members of the Brocadiaceae family were dominant in the adhered biomass, mostly represented by Candidatus Scalindua, rarely reported in WWTPs. Overall, the results demonstrated a drastic effect of region-specific operational conditions on carrier biofilm microbial communities as it was demonstrated by the microbial studies.},
}
@article {pmid33444853,
year = {2021},
author = {Yang, Y and Herbold, CW and Jung, MY and Qin, W and Cai, M and Du, H and Lin, JG and Li, X and Li, M and Gu, JD},
title = {Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration.},
journal = {Water research},
volume = {191},
number = {},
pages = {116798},
doi = {10.1016/j.watres.2020.116798},
pmid = {33444853},
issn = {1879-2448},
mesh = {Ammonia ; *Archaea/genetics ; Bacteria ; Copper ; Ions ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; *Water Pollutants, Chemical ; },
abstract = {Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.},
}
@article {pmid33444433,
year = {2021},
author = {Kerkhof, LJ},
title = {Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {3},
pages = {},
pmid = {33444433},
issn = {1574-6941},
mesh = {High-Throughput Nucleotide Sequencing ; *Microbiota ; *Nanopore Sequencing ; *Nanopores ; Sequence Analysis, DNA ; },
abstract = {This minireview will discuss the improvements in Oxford Nanopore (Oxford; sequencing technology that make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65 to 96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.},
}
@article {pmid33443587,
year = {2021},
author = {Hugoni, M and Nunan, N and Thioulouse, J and Dubost, A and Abrouk, D and Martins, JMF and Goffner, D and Prigent-Combaret, C and Grundmann, G},
title = {Small-Scale Variability in Bacterial Community Structure in Different Soil Types.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {470-483},
pmid = {33443587},
issn = {1432-184X},
support = {779949//EC2CO MicrobiEn/ ; ANR-11-LABX-0010//LabEx Chimie des Syst&#xe8;mes Complexes (FR)/ ; },
mesh = {Biodiversity ; Ecosystem ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; },
abstract = {Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.},
}
@article {pmid33442763,
year = {2021},
author = {Mutnale, MC and Reddy, GS and Vasudevan, K},
title = {Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {554-558},
pmid = {33442763},
issn = {1432-184X},
support = {BSC0207//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/ ; },
mesh = {Animals ; Anura ; Bacteria/genetics ; *Chytridiomycota/genetics ; *Microbiota ; *Mycoses ; Skin ; },
abstract = {Chytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.},
}
@article {pmid33442762,
year = {2021},
author = {Qin, Y and Puppe, D and Zhang, L and Sun, R and Li, P and Xie, S},
title = {How Does Sphagnum Growing Affect Testate Amoeba Communities and Corresponding Protozoic Si Pools? Results from Field Analyses in SW China.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {459-469},
pmid = {33442762},
issn = {1432-184X},
mesh = {*Amoeba ; Biodiversity ; Ecosystem ; *Sphagnopsida ; },
abstract = {The policy and practice of ecological restoration and conservation in China obtained some remarkable results. For example, Sphagnum moss growing on abandoned farmland, which was peatland before agricultural use, has rapidly expanded the wetland area in SW China. Microorganisms such as testate amoebae are sensitive to environmental change and thus have been widely used as ecological indicators in various habitats. We analyzed differently aged Sphagnum growing plots on a Sphagnum growing farmland and natural Sphagnum plots in SW China to examine how Sphagnum-dwelling testate amoeba communities and corresponding protozoic silicon (Si) pools respond to ecological restoration practice. We found that abundance, taxon richness, and diversity of testate amoebae were higher in Sphagnum growing farmland plots compared to natural Sphagnum plots. Protozoic Si pools showed an increase with Sphagnum growing time representing increased Si accumulation by idiosomic testate amoeba shells. However, protozoic Si pools were negatively correlated with taxon richness and diversity of testate amoebae. Our results showed that (i) natural Sphagnum plots were not characterized by the expected higher biodiversity of testate amoebae compared to Sphagnum growing plots and (ii) consequently protozoic Si pool quantity in natural Sphagnum plots was less driven by biodiversity of testate amoebae than expected. We concluded our results to underline the value of (i) environmental restoration policy in general and (ii) testate amoeba communities and corresponding protozoic Si pools for Si cycling in restoration areas of peatlands in particular. Based on our results, we recommend a sustainable cultivation of Sphagnum moss and an additional establishment of protected areas, where no Sphagnum harvesting occurs. These protected Sphagnum areas might represent hot spots of undisturbed testate amoeba communities and corresponding protozoic Si pools and thus of microbial Si cycling.},
}
@article {pmid33441489,
year = {2021},
author = {Fritts, RK and McCully, AL and McKinlay, JB},
title = {Extracellular Metabolism Sets the Table for Microbial Cross-Feeding.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {85},
number = {1},
pages = {},
pmid = {33441489},
issn = {1098-5557},
mesh = {Bacteria/*metabolism ; Biofilms/*growth &amp; development ; Biological Transport/*physiology ; Extracellular Vesicles/physiology ; Microbiota/physiology ; Quorum Sensing/*physiology ; Signal Transduction ; Symbiosis/*physiology ; },
abstract = {The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.},
}
@article {pmid33441406,
year = {2021},
author = {Hu, J and Jin, VL and Konkel, JYM and Schaeffer, SM and Schneider, LG and DeBruyn, JM},
title = {Soil Health Management Enhances Microbial Nitrogen Cycling Capacity and Activity.},
journal = {mSphere},
volume = {6},
number = {1},
pages = {},
pmid = {33441406},
issn = {2379-5042},
mesh = {Agriculture/*methods ; Bacteria/*genetics ; Bacterial Physiological Phenomena/genetics ; Nitrification ; Nitrogen/metabolism ; Nitrogen Cycle/*genetics/physiology ; Soil/chemistry ; *Soil Microbiology ; Vicia/microbiology ; },
abstract = {Soil microbial transformations of nitrogen (N) can be affected by soil health management practices. Here, we report in situ seasonal dynamics of the population size (gene copy abundances) and functional activity (transcript copy abundances) of five bacterial genes involved in soil N cycling (ammonia-oxidizing bacteria [AOB] amoA, nifH, nirK, nirS, and nosZ) in a long-term continuous cotton production system under different management practices (cover crops, tillage, and inorganic N fertilization). Hairy vetch (Vicia villosa Roth), a leguminous cover crop, most effectively promoted the expression of N cycle genes, which persisted after cover crop termination throughout the growing season. Moreover, we observed similarly high or even higher N cycle gene transcript abundances under vetch with no fertilizer as no cover crop with N fertilization throughout the cover crop peak and cotton growing seasons (April, May, and October). Further, both the gene and transcript abundances of amoA and nosZ were positively correlated to soil nitrous oxide (N2O) emissions. We also found that the abundances of amoA genes and transcripts both positively correlated to field and incubated net nitrification rates. Together, our results revealed relationships between microbial functional capacity and activity and in situ soil N transformations under different agricultural seasons and soil management practices.IMPORTANCE Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer. Hairy vetch also left a legacy on soil nutrient capacity by promoting the continued activity of N cycling microbes after cover crop termination and into the main growing season. By examining both genes and transcripts involved in soil N cycling, we showed different responses of functional capacity (i.e., gene abundances) and functional activity (i.e., transcript abundances) to agricultural seasons and management practices, adding to our understanding of the effects of soil health management practices on microbial ecology.},
}
@article {pmid33440279,
year = {2021},
author = {Zhong, Q and Cruz-Paredes, C and Zhang, S and Rousk, J},
title = {Can heavy metal pollution induce bacterial resistance to heavy metals and antibiotics in soils from an ancient land-mine?.},
journal = {Journal of hazardous materials},
volume = {411},
number = {},
pages = {124962},
doi = {10.1016/j.jhazmat.2020.124962},
pmid = {33440279},
issn = {1873-3336},
mesh = {Ancient Lands ; Anti-Bacterial Agents/toxicity ; China ; Ecosystem ; Environmental Monitoring ; Humans ; *Metals, Heavy/analysis/toxicity ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; },
abstract = {Microbial resistance to antibiotics is a growing challenge to human health. Recent evidence has indicated that antibiotic resistance can be co-selected for by exposure to heavy metals in agricultural soils. It remains unknown if this is a concern in other environments contaminated by metals. We here investigated soil microbial activities, composition and tolerance to heavy metals and antibiotics in a mining soil survey. We found that microbial respiration, growth, and biomass were affected by available metal concentrations. Most of the variation in microbial PLFA composition was explained by differences in heavy metal and pH. Additionally, pollution-induced bacterial community tolerance to toxicants including Cu, Pb, Zn, tetracycline and vancomycin was determined. Although only bacterial tolerance to Pb increased with higher levels of metals, the links between bacterial metal tolerance and soil metal concentrations were clear when considered together with previously published reports, suggesting that bacterial metal tolerance were universally elevated in the surveyed soils. The induced levels of heavy metal tolerance coincided with elevated levels of tolerance to vancomycin, but not to tetracycline. Our study showed that heavy metals can co-select for resistance to clinically important antibiotics also in ecosystems without manure input or antibiotic pollution.},
}
@article {pmid33438074,
year = {2021},
author = {Shen, J and Wyness, AJ and Claire, MW and Zerkle, AL},
title = {Spatial Variability of Microbial Communities and Salt Distributions Across a Latitudinal Aridity Gradient in the Atacama Desert.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {442-458},
pmid = {33438074},
issn = {1432-184X},
support = {678812//H2020 European Research Council/ ; 60501//John Templeton Foundation/ ; 201708060070//Chinese Scholarship Council/ ; },
mesh = {Bacteria/genetics ; Bacteroidetes ; *Desert Climate ; *Microbiota ; Soil Microbiology ; },
abstract = {Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.},
}
@article {pmid33437426,
year = {2021},
author = {Petrén, H and Gloder, G and Posledovich, D and Wiklund, C and Friberg, M},
title = {Innate preference hierarchies coupled with adult experience, rather than larval imprinting or transgenerational acclimation, determine host plant use in Pieris rapae.},
journal = {Ecology and evolution},
volume = {11},
number = {1},
pages = {242-251},
pmid = {33437426},
issn = {2045-7758},
abstract = {The evolution of host range drives diversification in phytophagous insects, and understanding the female oviposition choices is pivotal for understanding host specialization. One controversial mechanism for female host choice is Hopkins' host selection principle, where females are predicted to increase their preference for the host species they were feeding upon as larvae. A recent hypothesis posits that such larval imprinting is especially adaptive in combination with anticipatory transgenerational acclimation, so that females both allocate and adapt their offspring to their future host. We study the butterfly Pieris rapae, for which previous evidence suggests that females prefer to oviposit on host individuals of similar nitrogen content as the plant they were feeding upon as larvae, and where the offspring show higher performance on the mother's host type. We test the hypothesis that larval experience and anticipatory transgenerational effects influence female host plant acceptance (no-choice) and preference (choice) of two host plant species (Barbarea vulgaris and Berteroa incana) of varying nitrogen content. We then test the offspring performance on these hosts. We found no evidence of larval imprinting affecting female decision-making during oviposition, but that an adult female experience of egg laying in no-choice trials on the less-preferred host Be. incana slightly increased the P. rapae propensity to oviposit on Be. incana in subsequent choice trials. We found no transgenerational effects on female host acceptance or preference, but negative transgenerational effects on larval performance, because the offspring of P. rapae females that had developed on Be. incana as larvae grew slower on both hosts, and especially on Be. incana. Our results suggest that among host species, preferences are guided by hard-wired preference hierarchies linked to species-specific host traits and less affected by larval experience or transgenerational effects, which may be more important for females evaluating different host individuals of the same species.},
}
@article {pmid33436516,
year = {2021},
author = {Fu, S and Wang, Q and Zhang, Y and Yang, Q and Hao, J and Liu, Y and Pang, B},
title = {Dynamics and Microevolution of Vibrio parahaemolyticus Populations in Shellfish Farms.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33436516},
issn = {2379-5077},
abstract = {Vibrio parahaemolyticus is becoming the leading cause of acute bacterial gastroenteritis, but its population dynamics in aquafarms have received limited attention. To address this research gap, we selected three shellfish farms to examine the impacts of ocean currents and the transport of live aquatic animals on the transmission and microevolution of V. parahaemolyticus by using multilocus sequence typing (MLST) and whole-genome sequencing. MLST and genomic analysis revealed that the community structure of V. parahaemolyticus in Dalian and Donggang was relatively stable in the presence of ocean currents; however, horizontal gene transfer of mobile genetic elements (MGEs) between Dalian and Donggang was very common. Further analysis indicated that the transport of live aquatic animals from Dalian to Xiamen not only introduced new V. parahaemolyticus populations but also allowed the exchange of genetic material between the two sites. More interestingly, Dalian-originated strain ST722 was introduced to Xiamen farms, resulting in one MLST allele change and the acquisition of two genomic islands from indigenous isolates in Xiamen within 8 months; such alterations are thought to promote the adaptation of V. parahaemolyticus These results provide direct observations of how ocean currents and the transport of live aquatic animals contribute to the dissemination and genetic mixture of V. parahaemolyticus, which provides insights into the dynamics and microevolution of V. parahaemolyticus in aquacultural environments.IMPORTANCE Globally, V. parahaemolyticus-related gastroenteritis outbreaks caused by seafood consumption represent an increasing threat to human health. Despite advances in our understanding of the global epidemiology of pandemic V. parahaemolyticus, fundamental questions about the key driving forces for the spread of V. parahaemolyticus at regional and national scales remain unanswered. This study revealed that the transregional transport of aquatic animals and the movement of ocean currents both contributed to the mixing of V. parahaemolyticus populations. More importantly, this study demonstrated how genetic mixture occurred between introduced and endemic V. parahaemolyticus populations via the transport of aquatic animals, which accelerated bacterial adaptation by transferring ecologically important functions. These results suggest that human activities entail a risk of the emergence of new virulent populations for both aquatic animals and humans by horizontal gene transfer and provide important insights into the microevolution and population mixing of V. parahaemolyticus.},
}
@article {pmid33436509,
year = {2021},
author = {Meier, DV and Imminger, S and Gillor, O and Woebken, D},
title = {Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33436509},
issn = {2379-5077},
abstract = {Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.},
}
@article {pmid33436507,
year = {2021},
author = {Wang, H and Beier, N and Boedeker, C and Sztajer, H and Henke, P and Neumann-Schaal, M and Mansky, J and Rohde, M and Overmann, J and Petersen, J and Klawonn, F and Kucklick, M and Engelmann, S and Tomasch, J and Wagner-Döbler, I},
title = {Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33436507},
issn = {2379-5077},
abstract = {Outer membrane vesicles (OMVs) are universally produced by prokaryotes and play important roles in symbiotic and pathogenic interactions. They often contain DNA, but a mechanism for its incorporation is lacking. Here, we show that Dinoroseobacter shibae, a dinoflagellate symbiont, constitutively secretes OMVs containing DNA. Time-lapse microscopy captured instances of multiple OMV production at the septum during cell division. DNA from the vesicle lumen was up to 22-fold enriched for the region around the terminus of replication (ter). The peak of coverage was located at dif, a conserved 28-bp palindromic sequence required for binding of the site-specific tyrosine recombinases XerC/XerD. These enzymes are activated at the last stage of cell division immediately prior to septum formation when they are bound by the divisome protein FtsK. We suggest that overreplicated regions around the terminus have been repaired by the FtsK-dif-XerC/XerD molecular machinery. The vesicle proteome was clearly dominated by outer membrane and periplasmic proteins. Some of the most abundant vesicle membrane proteins were predicted to be required for direct interaction with peptidoglycan during cell division (LysM, Tol-Pal, Spol, lytic murein transglycosylase). OMVs were 15-fold enriched for the saturated fatty acid 16:00. We hypothesize that constitutive OMV secretion in D. shibae is coupled to cell division. The footprint of the FtsK-dif-XerC/XerD molecular machinery suggests a novel potentially highly conserved route for incorporation of DNA into OMVs. Clearing the division site from small DNA fragments might be an important function of vesicles produced during exponential growth under optimal conditions.IMPORTANCE Gram-negative bacteria continually form vesicles from their outer membrane (outer membrane vesicles [OMVs]) during normal growth. OMVs frequently contain DNA, and it is unclear how DNA can be shuffled from the cytoplasm to the OMVs. We studied OMV cargo in Dinoroseobacter shibae, a symbiont of dinoflagellates, using microscopy and a multi-omics approach. We found that vesicles formed during undisturbed exponential growth contain DNA which is enriched for genes around the replication terminus, specifically, the binding site for an enzyme complex that is activated at the last stage of cell division. We suggest that the enriched genes are the result of overreplication which is repaired by their excision and excretion via membrane vesicles to clear the divisome from waste DNA.},
}
@article {pmid33435231,
year = {2021},
author = {Cohen Kadosh, K and Muhardi, L and Parikh, P and Basso, M and Jan Mohamed, HJ and Prawitasari, T and Samuel, F and Ma, G and Geurts, JM},
title = {Nutritional Support of Neurodevelopment and Cognitive Function in Infants and Young Children-An Update and Novel Insights.},
journal = {Nutrients},
volume = {13},
number = {1},
pages = {},
pmid = {33435231},
issn = {2072-6643},
mesh = {Brain/*growth &amp; development ; Child, Preschool ; *Cognition ; Cognitive Aging ; Emotions ; Fatty Acids ; Food ; Gastrointestinal Microbiome ; Humans ; Infant ; Kynurenine ; Minerals ; Nutrients ; *Nutritional Support ; Prebiotics ; Probiotics ; Quality of Life ; },
abstract = {Proper nutrition is crucial for normal brain and neurocognitive development. Failure to optimize neurodevelopment early in life can have profound long-term implications for both mental health and quality of life. Although the first 1000 days of life represent the most critical period of neurodevelopment, the central and peripheral nervous systems continue to develop and change throughout life. All this time, development and functioning depend on many factors, including adequate nutrition. In this review, we outline the role of nutrients in cognitive, emotional, and neural development in infants and young children with special attention to the emerging roles of polar lipids and high quality (available) protein. Furthermore, we discuss the dynamic nature of the gut-brain axis and the importance of microbial diversity in relation to a variety of outcomes, including brain maturation/function and behavior are discussed. Finally, the promising therapeutic potential of psychobiotics to modify gut microbial ecology in order to improve mental well-being is presented. Here, we show that the individual contribution of nutrients, their interaction with other micro- and macronutrients and the way in which they are organized in the food matrix are of crucial importance for normal neurocognitive development.},
}
@article {pmid33432372,
year = {2021},
author = {Nguyen, TTT and Foysal, MJ and Fotedar, R and Gupta, SK and Siddik, MAB and Tay, CY},
title = {The Effect of Two Dietary Protein Sources on Water Quality and the Aquatic Microbial Communities in Marron (Cherax cainii) Culture.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {299-308},
pmid = {33432372},
issn = {1432-184X},
support = {CIPRS) (No. 18508848 - Curtin)//Curtin University of Technology/ ; },
mesh = {Animal Feed/analysis ; Animals ; *Astacoidea ; Dietary Proteins ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Water Quality ; },
abstract = {Feeding freshwater crayfish species with different diets not only affects the water quality but also induces the abundance of various microbial communities in their digestive tracts. In this context, very limited research has been undertaken to understand the impacts of various protein incorporated aqua-diets on the characteristics of water and its microbial communities. In this study, we have critically analysed the water quality parameters including pH, dissolved oxygen, nitrate, nitrite, ammonia and phosphorus, as well as bacterial communities under marron (Cherax cainii) aquaculture, fed fishmeal (FM) and poultry by-product meal (PBM)-based diets for 60 days. The results unveiled that over the time, feeding has significant impacts on organic waste accumulation, especially ammonia, nitrate, nitrite and phosphate, while no effects were observed on pH and dissolved oxygen. Analysis of 16S rRNA sequence data of water sample indicated significant (P < 0.05) shift of microbial abundance in post-fed FM and PBM water with the evidence of microbial transmission from the gut of marron. Post-fed marron resulted in a significant correlation of Hafnia, Enterobacter, Candidatus Bacilloplasma and Aquitella with the quality and microbial population of water. The results of this study generated valuable knowledge database of microbes-water relationship for better health management practices and production of marron aquaculture fed with FM and PBM diets in under restricted feeding regime with the feeding ratios provided.},
}
@article {pmid33429312,
year = {2021},
author = {Fu, Y and Wang, F and Sheng, H and Hu, F and Wang, Z and Xu, M and Bian, Y and Jiang, X and Tiedje, JM},
title = {Removal of extracellular antibiotic resistance genes using magnetic biochar/quaternary phosphonium salt in aquatic environments: A mechanistic study.},
journal = {Journal of hazardous materials},
volume = {411},
number = {},
pages = {125048},
doi = {10.1016/j.jhazmat.2021.125048},
pmid = {33429312},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology ; Charcoal ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Humans ; Magnetic Phenomena ; Wastewater ; },
abstract = {The proliferation and spread of antibiotic resistance genes (ARGs) is becoming a worldwide crisis. Extracellular DNA encoding ARGs (eARGs) in aquatic environment plays a critical role in the dispersion of antimicrobial resistance genes. Strategies to control the dissemination of eARGs are urgently required for ecological safety and human health. Towards this goal, magnetic biochar/quaternary phosphonium salt (MBQ), was used to investigate the efficiency and removal mechanism for eARGs. Magnetic biochar modified by quaternary phosphonium salt enhanced the adsorption capacity of extracellular DNA to approximately 9 folds, compared to that of the unmodified. DNA adsorption by MBQ was mainly dominated by chemisorption in heterogeneous systems and was promoted in acidic and low-salt environment. The generation of •OH and MBQ colloid jointly cleaved DNA into fragments, facilitating the adsorption of the phosphate backbone of DNA onto MBQ through electrostatic force as well as the conformational transition of DNA. Furthermore, quantification of extracellular DNA after MBQ was applied in water demonstrated that over 92.7% of resistance genes were removed, indicating a significantly reduced risk of propagation of antimicrobial resistance in aquatic environments. These findings have a practical significance in the application of MBQ in mitigating the spread of ARGs in aquatic environment.},
}
@article {pmid33429117,
year = {2021},
author = {Forés, E and Bofill-Mas, S and Itarte, M and Martínez-Puchol, S and Hundesa, A and Calvo, M and Borrego, CM and Corominas, LL and Girones, R and Rusiñol, M},
title = {Evaluation of two rapid ultrafiltration-based methods for SARS-CoV-2 concentration from wastewater.},
journal = {The Science of the total environment},
volume = {768},
number = {},
pages = {144786},
pmid = {33429117},
issn = {1879-1026},
mesh = {Animals ; *COVID-19 ; Communicable Disease Control ; Humans ; Mice ; *SARS-CoV-2 ; Ultrafiltration ; Wastewater ; },
abstract = {Quantitative measurements of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in raw wastewater have been implemented worldwide since the beginning of the pandemic. Recent efforts are being made to evaluate different viral concentration methodologies to overcome supplier shortages during lockdowns. A set of 22-wastewater samples seeded with murine hepatitis virus (MHV), a member of the Coronaviridae family, and the bacteriophage MS2, were used to characterize and compare two ultrafiltration-based methods: a centrifugal ultrafiltration device (Centricon® Plus-70) and the automated concentrating pipette CP-Select™. Based on the recovery efficiencies, significant differences were observed for MHV, with Centricon® Plus-70 (24%) being the most efficient method. Nevertheless, concentrations of naturally occurring SARS-CoV-2, Human adenoviruses and JC polyomaviruses in these samples did not result in significant differences between methods suggesting that testing naturally occurring viruses may complement the evaluation of viral concentration methodologies. Based on the virus adsorption to solids and the necessity of a pre-centrifugation step to remove larger particles and avoid clogging when using ultrafiltration methods, we assessed the percentage of viruses not quantified after ultrafiltration. Around 23% of the detected SARS-CoV-2 would be discarded during the debris removal step. The CP-Select™ provided the highest concentration factor (up to 333×) and the lowest LoD (6.19 × 10[3] GC/l) for MHV and proved to be fast, automatic, highly reproducible and suitable to work under BSL-2 measures.},
}
@article {pmid33428723,
year = {2021},
author = {Laursen, MF and Bahl, MI and Licht, TR},
title = {Settlers of our inner surface - factors shaping the gut microbiota from birth to toddlerhood.},
journal = {FEMS microbiology reviews},
volume = {45},
number = {4},
pages = {},
pmid = {33428723},
issn = {1574-6976},
support = {NNF19OC0056246//Novo Nordic Foundation/ ; },
mesh = {Adult ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; },
abstract = {During the first 3 years of life, the microbial ecosystem within the human gut undergoes a process that is unlike what happens in this ecosystem at any other time of our life. This period in time is considered a highly important developmental window, where the gut microbiota is much less resilient and much more responsive to external and environmental factors than seen in the adult gut. While advanced bioinformatics and clinical correlation studies have received extensive focus within studies of the human microbiome, basic microbial growth physiology has attracted much less attention, although it plays a pivotal role to understand the developing gut microbiota during early life. In this review, we will thus take a microbial ecology perspective on the analysis of factors that influence the temporal development of the infant gut microbiota. Such factors include sources of microbes that seed the intestinal environment, physico-chemical (abiotic) conditions influencing microbial growth and the availability of nutrients needed by the intestinal microbes.},
}
@article {pmid33424787,
year = {2020},
author = {Figueroa-Gonzalez, PA and Bornemann, TLV and Adam, PS and Plewka, J and Révész, F and von Hagen, CA and Táncsics, A and Probst, AJ},
title = {Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {587782},
pmid = {33424787},
issn = {1664-302X},
abstract = {Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.},
}
@article {pmid33422757,
year = {2021},
author = {Vázquez-Blanco, R and Arias-Estévez, M and Bååth, E and Fernández-Calviño, D},
title = {Comparing the effect of Cu-based fungicides and pure Cu salts on microbial biomass, microbial community structure and bacterial community tolerance to Cu.},
journal = {Journal of hazardous materials},
volume = {409},
number = {},
pages = {124960},
doi = {10.1016/j.jhazmat.2020.124960},
pmid = {33422757},
issn = {1873-3336},
mesh = {Biomass ; Fatty Acids ; *Fungicides, Industrial/toxicity ; *Microbiota ; Salts ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; },
abstract = {The effect of Cu on three different microbial endpoints was studied using different Cu sources, in order to check the usefulness of pure Cu salts to estimate the toxicity of commercial Cu fungicides on soil microbes. Cu additions caused similar dose-response curves of substrate induced respiration (SIR) decreases regardless of Cu source, i.e. the use of pure Cu salts to estimate the effect of Cu fungicides on microbial biomass using SIR may be useful. Phospholipid fatty acid (PLFA) analysis showed that the Cu source was more important for the microbial community structure than Cu concentration. Thus, the use of Cu salts to infer the effects of Cu fungicides on microbial community structure using PLFA analysis is not recommended, since effects of Cu concentration will be confounded with Cu source. Analyzing pollution induced community tolerance (PICT) to Cu showed that the use of pure Cu salts may overestimate Cu effects if Cu salt additions modified the soil pH. The highest doses of Cu salts increased bacterial community tolerance to Cu between 300 and 600 times, while commercial Cu fungicide increases were between 20 and 160 times. Therefore, the use of pure Cu salts to estimate the Cu fungicides effects on soil microbes is not recommended for PLFAs analyses, not suitable for PICT at high Cu concentrations, while useful for SIR.},
}
@article {pmid33420911,
year = {2021},
author = {Doliwa, A and Dunthorn, M and Rassoshanska, E and Mahé, F and Bass, D and Duarte Ritter, C},
title = {Identifying Potential Hosts of Short-Branch Microsporidia.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {549-553},
pmid = {33420911},
issn = {1432-184X},
support = {#DU1319/5-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Cercozoa ; *Microsporidia/genetics ; Phylogeny ; Rainforest ; Soil ; },
abstract = {Microsporidia are obligate parasites that are closely related to Fungi. While the widely known "long-branch" Microsporidia infect mostly metazoans, the hosts of "short-branch" Microsporidia are only partially characterized or not known at all. Here, we used network analyses from Neotropical rainforest soil metabarcoding data, to infer co-occurrences between environmental lineages of short-branch microsporidians and their potential hosts. We found significant co-occurrences with several taxa, especially with Apicomplexa, Cercozoa, and Fungi, as well as some Metazoa. Our results are the first step to identify potential hosts of the environmental lineages of short-branch microsporidians, which can be targeted in future molecular and microscopic studies.},
}
@article {pmid33420910,
year = {2021},
author = {García Hernández, E and Berg, MP and Van Oosten, AR and Smit, C and Falcão Salles, J},
title = {Linking Bacterial Communities Associated with the Environment and the Ecosystem Engineer Orchestia gammarellus at Contrasting Salt Marsh Elevations.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {537-548},
pmid = {33420910},
issn = {1432-184X},
support = {484425//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; ALWOP.219.00179028//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Bacteria/genetics ; Ecosystem ; *Microbiota ; Phylogeny ; Soil ; Soil Microbiology ; *Wetlands ; },
abstract = {The digestive tract of animals harbors microbiota important for the host's fitness and performance. The interaction between digestive tract bacteria and soil animal hosts is still poorly explored despite the importance of soil fauna for ecosystem processes. In this study, we investigated the interactions between the bacterial communities from the digestive tract of the litter-feeding, semi-terrestrial crustacean Orchestia gammarellus and those obtained from the environment; these organisms thrive in, i.e., soil and plant litter from salt marshes. We hypothesized that elevation is an important driver of soil and litter bacterial communities, which indirectly (via ingested soil and litter bacteria) influences the bacterial communities in the digestive tract of O. gammarellus. Indeed, our results revealed that elevation modulated soil and litter bacterial community composition along with soil organic matter content and the C:N ratio. Soil and plant litter differed in alpha diversity indexes (richness and diversity), and in the case of plant litter, both indexes increased with elevation. In contrast, elevation did not affect the composition of bacterial communities associated with O. gammarellus' digestive tract, suggesting selection by the host, despite the fact that a large component of the bacterial community was also detected in external sources. Importantly, Ca. Bacilloplasma and Vibrio were highly prevalent and abundant in the host. The taxonomic comparison of Ca. Bacilloplasma amplicon sequence variants across the host at different elevations suggested a phylogenetic divergence due to host habitat (i.e., marine or semi-terrestrial), thus supporting their potential functional role in the animal physiology. Our study sheds light on the influence of the environment on soil animal-bacteria interactions and provides insights into the resilience of the O. gammarellus-associated bacteria to increased flooding frequency.},
}
@article {pmid33420625,
year = {2021},
author = {Win, PM and Matsumura, E and Fukuda, K},
title = {Effects of Pesticides on the Diversity of Endophytic Fungi in Tea Plants.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {62-72},
pmid = {33420625},
issn = {1432-184X},
mesh = {Ascomycota ; Biodiversity ; *Colletotrichum ; Endophytes/genetics ; Fungi/genetics ; *Pesticides ; Plant Leaves ; Tea ; },
abstract = {We examined the effects of agrochemicals on the endophytic fungal community associated with tea plants. Endophytic fungi were isolated from four different tea plant tissues (bark, xylem, old leaves, new leaves) collected from pesticide-treated and untreated plots. In pesticide-treated plot, the acaricides, fungicides, and insecticides are typically applied 3 times each year. The infection rate was slightly lower in the pesticide-treated plot, but the difference between plots was not statistically significant. Colletotrichum camelliae, Phyllosticta capitalensis, and Pleosporales sp. were common endophytes in both plots. Among a total of 41 fungal species, only 21 were considered common endophytes. Colletotrichum pseudomajus was the predominant endophyte in the bark tissue in the untreated plot, whereas C. camelliae was predominant in the pesticide-treated plot. Paraphaeosphaeria neglecta and Phoma bellendis were predominant in the xylem tissues of samples from the untreated and treated plots, respectively. Colletotrichum camelliae was the most commonly found species in leaf tissues in both plots, but the colonization frequency was significantly lower in the pesticide-treated plot. Species richness was not affected by pesticide treatment. The community structure of endophytic fungi in stem tissues (bark and xylem) differed significantly between plots, but leaf tissue endophytic fungal community structure was not significantly influenced by pesticide treatment.},
}
@article {pmid33420624,
year = {2021},
author = {Eraqi, WA and ElRakaiby, MT and Megahed, SA and Yousef, NH and Elshahed, MS and Yassin, AS},
title = {Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {288-298},
pmid = {33420624},
issn = {1432-184X},
support = {2016423//National Science Foundation/ ; 3046//Academy of Scientific Research and Technology/ ; },
mesh = {Animals ; *Cyanobacteria ; Geologic Sediments ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rivers ; Spatio-Temporal Analysis ; Water ; },
abstract = {Assessing microbial identity, diversity, and community structure could be a valuable tool for monitoring the impact of xenobiotics and anthropogenic inputs in rivers, especially in urban and industrial settings. Here, we characterize the Nile River microbial community in water and sediments in summer and winter at five locations that span its natural flow through the Cairo metropolis. 16S rRNA gene datasets were analyzed to identify the role played by sample type (sediment versus water), season, and location in shaping the community, as well as to predict functional potential of the Nile River microbiome. Microbial communities were mostly influenced by sampling type (sediments versus water), while seasonal effects were only observed in water samples. Spatial differences did not represent a significant factor in shaping the community in either summer or winter seasons. Proteobacteria was the most abundant phylum in both water and sediment samples, with the order Betaproteobacteriales being the abundant one. Chloroflexi and Bacteroidetes were also prevalent in sediment samples, while Cyanobacteria and Actinobacteria were abundant in water samples. The linear discriminative analysis effect size (LEfSe) identified the cyanobacterial genus Cyanobium PCC-6307 as the main variable between summer and winter water. Sequences representing human and animal potential pathogens, as well as toxin-producing Cyanobacteria, were identified in low abundance within the Nile microbiome. Functionally predicted metabolic pathways predicted the presence of antibiotic biosynthesis, as well as aerobic xenobiotic degradation pathways in the river microbiome.},
}
@article {pmid33417698,
year = {2021},
author = {Moossavi, S and Fontes, ME and Rossi, L and Fusch, G and Surette, MG and Azad, MB},
title = {Capturing the diversity of the human milk microbiota through culture-enriched molecular profiling: a feasibility study.},
journal = {FEMS microbiology letters},
volume = {368},
number = {3},
pages = {},
doi = {10.1093/femsle/fnab001},
pmid = {33417698},
issn = {1574-6968},
mesh = {Bacteria/classification/genetics/*growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Culture Techniques ; *Food Microbiology ; Humans ; Milk, Human/*microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Previous human milk studies have confirmed the existence of a highly diverse bacterial community using culture-independent and targeted culture-dependent techniques. However, culture-enriched molecular profiling of milk microbiota has not been done. Additionally, the impact of storage conditions and milk fractionation on microbiota composition is not understood. In this feasibility study, we optimized and applied culture-enriched molecular profiling to study culturable milk microbiota in eight milk samples collected from mothers of infants admitted to a neonatal intensive care unit. Fresh samples were immediately plated or stored at -80°C for 2 weeks (short-term frozen). Long-term samples were stored at -20°C for >6 months. Samples were cultured using 10 different culture media and incubated both aerobically and anaerobically. We successfully isolated major milk bacteria, including Streptococcus, Staphylococcus and Bifidobacterium, from fresh milk samples, but were unable to culture any bacteria from the long-term frozen samples. Short-term freezing shifted the composition of viable milk bacteria from the original composition in fresh samples. Nevertheless, the inter-individual variability of milk microbiota composition was observed even after short-term storage. There was no major difference in the overall milk microbiota composition between milk fractions in this feasibility study. This is among the first studies on culture-enriched molecular profiling of the milk microbiota demonstrating the effect of storage and fractionation on milk microbiota composition.},
}
@article {pmid33415825,
year = {2021},
author = {Rogiers, T and Claesen, J and Van Gompel, A and Vanhoudt, N and Mysara, M and Williamson, A and Leys, N and Van Houdt, R and Boon, N and Mijnendonckx, K},
title = {Soil microbial community structure and functionality changes in response to long-term metal and radionuclide pollution.},
journal = {Environmental microbiology},
volume = {23},
number = {3},
pages = {1670-1683},
pmid = {33415825},
issn = {1462-2920},
mesh = {*Metals, Heavy ; *Microbiota ; Radioisotopes ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {Microbial communities are essential for a healthy soil ecosystem. Metals and radionuclides can exert a persistent pressure on the soil microbial community. However, little is known on the effect of long-term co-contamination of metals and radionuclides on the microbial community structure and functionality. We investigated the impact of historical discharges of the phosphate and nuclear industry on the microbial community in the Grote Nete river basin in Belgium. Eight locations were sampled along a transect to the river edge and one location further in the field. Chemical analysis demonstrated a metal and radionuclide contamination gradient and revealed a distinct clustering of the locations based on all metadata. Moreover, a relation between the chemical parameters and the bacterial community structure was demonstrated. Although no difference in biomass was observed between locations, cultivation-dependent experiments showed that communities from contaminated locations survived better on singular metals than communities from control locations. Furthermore, nitrification, a key soil ecosystem process seemed affected in contaminated locations when combining metadata with microbial profiling. These results indicate that long-term metal and radionuclide pollution impacts the microbial community structure and functionality and provides important fundamental insights into microbial community dynamics in co-metal-radionuclide contaminated sites.},
}
@article {pmid33415385,
year = {2021},
author = {Colin, Y and Berthe, T and Molbert, N and Guigon, E and Vivant, AL and Alliot, F and Collin, S and Goutte, A and Petit, F},
title = {Urbanization Constrains Skin Bacterial Phylogenetic Diversity in Wild Fish Populations and Correlates with the Proliferation of Aeromonads.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {523-536},
pmid = {33415385},
issn = {1432-184X},
mesh = {Animals ; *Bacteria/genetics ; Cell Proliferation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Urbanization ; },
abstract = {Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.},
}
@article {pmid33415384,
year = {2021},
author = {Shi, Y and Yang, H and Chu, M and Niu, X and Huo, X and Gao, Y and Zeng, J and Lin, Q and Lou, K},
title = {Diversity and Spatiotemporal Dynamics of Fungal Communities in the Rhizosphere Soil of Cotton in the Arid Region of Northwest China.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {87-99},
pmid = {33415384},
issn = {1432-184X},
support = {41471220//the National Natural Science Foundation of China/ ; 31860024//National Natural Science Foundation of China/ ; 2017YFD0200608-05//Nation Key Research Program of China/ ; 2018D01A44//National Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2016M602953XB//China Postdoctoral Science Foundation Funded the Sixtieth Batch/ ; qn2005yx023//Xinjiang Uygur Autonomous Region Outstanding Young Talent Training Program/ ; },
mesh = {Biodiversity ; Fungi/genetics ; Gossypium ; *Mycobiome ; *Rhizosphere ; Soil ; Soil Microbiology ; },
abstract = {This study aimed to investigate the fungal diversity and its temporal and spatial dynamics in the rhizosphere soil of healthy cotton by high-throughput sequencing. We studied species richness, composition, and distribution of cotton rhizosphere fungal community with respect to location (Alaer, Kuerle, Tumushuke, Hami, Shihezi, Wusu, and Jinghe) and plant growth period (seedling stage, bud stage, flowering stage, and boll-opening stage) using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. A total of 1,838,454 fungal nuclear ribosomal internal transcribed spacer region sequences (rRNA ITS) were obtained from all cotton plants sampled at different growth stages in the seven locations in Xinjiang. The most abundant fungal group in the cotton rhizosphere was the Ascomycota (78.72%), followed by the Zygomycota (9.56%) and Basidiomycota (2.77%). These sequences revealed an enormous number of operational taxonomic units (OTUs) in cotton (1802 unique OTUs), with 67-464 OTUs in a single cotton sample, at a 3% threshold and a sequencing depth of 30,000 sequences. We identified 33 classes and 389 genera from the resulting 1,800,714 sequences. Sordariomycetes was the most frequent class in all samples, followed by Leotiomycetes and Eurotiomycetes. There were some differences in OTUs among different growth stages, but the differences were not significant, with 382 OTUs (14.66%) being common to each of the stages. A marked difference in the diversity of fungi in the rhizosphere soil of cotton was evident among the different locations, with the highest number of OTUs being detected in Jinghe (1084 OTUs) and clusters of OTUs representative of northern and eastern Xinjiang being detected. There were significantly more tags of Mortierella in Jinghe and Wusu than in the other sampling sites. The dynamics of the rhizosphere fungal communities were influenced by sampling sites. To the best of our knowledge, the current study is the first application of PCR-based Illumina to characterize and compare the fungal biodiversity in multiple rhizosphere soil samples from cotton.},
}
@article {pmid33414351,
year = {2021},
author = {Verdera, AB and Montecillo, AD and Obusan, MCM},
title = {Draft Genome Sequence of Streptomyces sp. Isolate H28 from the Meycauayan River, Philippines.},
journal = {Microbiology resource announcements},
volume = {10},
number = {1},
pages = {},
pmid = {33414351},
issn = {2576-098X},
abstract = {In this paper, we report the draft genome sequence of Streptomyces sp. isolate H28, isolated from sediments of the Meycauayan River in the Philippines. This species exhibits production of melanin as well as the ability to utilize and degrade both high-density polyethylene (HDPE) and low-density polyethylene (LDPE).},
}
@article {pmid33414343,
year = {2021},
author = {Mori, JF and Kanaly, RA},
title = {Complete Genome Sequence of Sphingobium barthaii KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Soil Bacterium.},
journal = {Microbiology resource announcements},
volume = {10},
number = {1},
pages = {},
pmid = {33414343},
issn = {2576-098X},
abstract = {Sphingobium barthaii KK22[T] is a high-molecular-weight polycyclic aromatic hydrocarbon-degrading soil bacterium that has been investigated in biotransformation, microbial ecology, and DNA damage studies. The complete genome sequence of S. barthaii revealed four closed circular sequences, including two chromosomes, a megaplasmid, and a smaller plasmid, by hybrid assembly using short- and long-read sequencing technologies.},
}
@article {pmid33414017,
year = {2021},
author = {Riber, L and Hansen, LH},
title = {Epigenetic Memories: The Hidden Drivers of Bacterial Persistence?.},
journal = {Trends in microbiology},
volume = {29},
number = {3},
pages = {190-194},
doi = {10.1016/j.tim.2020.12.005},
pmid = {33414017},
issn = {1878-4380},
mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; DNA Methylation ; *Epigenesis, Genetic ; Gene Expression Regulation, Bacterial ; },
abstract = {Epigenetic modifications, including DNA methylation, stably alter gene expression without modifying genomic sequences. Recent evidence suggests that epigenetic regulation coupled with a long-term 'memory' effect plays a major role within bacterial persistence formation. Today, emerging high-resolution, single-molecule sequencing technologies allow an increased focus on DNA modifications as regulatory epigenetic marks, which presents a unique opportunity to identify possible epigenetic drivers of bacterial persistence.},
}
@article {pmid33412377,
year = {2021},
author = {Wang, B and Ma, J and Zhang, L and Su, Y and Xie, Y and Ahmad, Z and Xie, B},
title = {The synergistic strategy and microbial ecology of the anaerobic co-digestion of food waste under the regulation of domestic garbage classification in China.},
journal = {The Science of the total environment},
volume = {765},
number = {},
pages = {144632},
doi = {10.1016/j.scitotenv.2020.144632},
pmid = {33412377},
issn = {1879-1026},
mesh = {Anaerobiosis ; Bioreactors ; China ; Digestion ; Food ; *Garbage ; Methane ; *Refuse Disposal ; Sewage ; },
abstract = {With the implementation of new domestic garbage classification policy in China, attention is growing to improve the treatment efficiency of municipal 'wet' waste. Combing with the new regulation, the synergistic strategy and the microbial ecology of the anaerobic co-digestion (AcoD) of cooked food waste (CFW), uncooked food waste (UCFW) and rice straw (RS) were analyzed in current study. Results showed that the maximum cumulative methane yield (CMY) and synergic index were obtained when CFW and UCFW were mixed at the ratio of 1:1 (based on volatile solid content). The highest CMY 452.94 ± 0.99 mL/g-VS was obtained when the ratio of CFW, UCFW and RS was 0.81:0.09:0.10, which was 16.29%, 36.20% and 121.84% higher than their mono-digestion, respectively. The AcoD promoted the methane potential by prolonging the release time of organic matter and slowing down the hydrolysis rate. Furthermore, the AcoD increased the species diversification and relative abundance of fermentation bacteria in digesters, and Methanosaeta predominated the methanogen communities. This study demonstrated a clean and sustainable AcoD strategy for safe disposal of urban food waste and revealed the variation of microbial community, which can provide a base for efficient bioenergy recovery from urban domestic garbage.},
}
@article {pmid33411249,
year = {2021},
author = {Chakraborty, P and Paul, P and Kumari, M and Bhattacharjee, S and Singh, M and Maiti, D and Dastidar, DG and Akhter, Y and Kundu, T and Das, A and Tribedi, P},
title = {Attenuation of Pseudomonas aeruginosa biofilm by thymoquinone: an individual and combinatorial study with tetrazine-capped silver nanoparticles and tryptophan.},
journal = {Folia microbiologica},
volume = {66},
number = {2},
pages = {255-271},
pmid = {33411249},
issn = {1874-9356},
mesh = {Anti-Bacterial Agents/pharmacology ; Benzoquinones ; Biofilms ; *Metal Nanoparticles ; Microbial Sensitivity Tests ; *Pseudomonas aeruginosa ; Silver/pharmacology ; Tryptophan ; },
abstract = {Microbial biofilm indicates a cluster of microorganisms having the capability to display drug resistance property, thereby increasing its proficiency in spreading diseases. In the present study, the antibiofilm potential of thymoquinone, a black seed-producing natural molecule, was contemplated against the biofilm formation by Pseudomonas aeruginosa. Substantial antimicrobial activity was exhibited by thymoquinone against the test organism wherein the minimum inhibitory concentration of the compound was found to be 20 μg/mL. Thereafter, an array of experiments (crystal violet staining, protein count, and microscopic observation, etc.) were carried out by considering the sub-MIC doses of thymoquinone (5 and 10 μg/mL), each of which confirmed the biofilm attenuating capacity of thymoquinone. However, these concentrations did not show any antimicrobial activity. Further explorations on understanding the underlying mechanism of the same revealed that thymoquinone accumulated reactive oxygen species (ROS) and also inhibited the expression of the quorum sensing gene (lasI) in Pseudomonas aeruginosa. Furthermore, by taking up a combinatorial approach with two other reported antibiofilm agents (tetrazine-capped silver nanoparticles and tryptophan), the antibiofilm efficiency of thymoquinone was expanded. In this regard, the highest antibiofilm activity was observed when thymoquinone, tryptophan, and tetrazine-capped silver nanoparticles were applied together against Pseudomonas aeruginosa. These combinatorial applications of antibiofilm molecules were found to accumulate ROS in cells that resulted in the inhibition of biofilm formation. Thus, the combinatorial study of these antibiofilm molecules could be applied to control biofilm threats as the tested antibiofilm molecules alone or in combinations showed negligible or very little cytotoxicity.},
}
@article {pmid33410938,
year = {2021},
author = {Oita, S and Carey, J and Kline, I and Ibáñez, A and Yang, N and Hom, EFY and Carbone, I and U'Ren, JM and Arnold, AE},
title = {Methodological Approaches Frame Insights into Endophyte Richness and Community Composition.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {21-34},
pmid = {33410938},
issn = {1432-184X},
mesh = {*Endophytes/genetics ; *Fungi/genetics ; Phylogeny ; Plant Leaves ; Plants ; },
abstract = {Isolating microbes is vital to study microbiomes, but insights into microbial diversity and ecology can be constrained by recalcitrant or unculturable strains. Culture-free methods (e.g., next-generation sequencing, NGS) have become popular in part because they detect greater richness than culturing alone. Both approaches are used widely to characterize microfungi within healthy leaves (foliar endophytes), but methodological differences among studies can constrain large-scale insights into endophyte ecology. We examined endophytes in a temperate plant community to quantify how certain methodological factors, such as the choice of cultivation media for culturing and storage period after leaf collection, affect inferences regarding endophyte communities; how such effects vary among plant taxa; and how complementary culturing and NGS can be when subsets of the same plant tissue are used for each. We found that endophyte richness and composition from culturing were consistent across five media types. Insights from culturing and NGS were largely robust to differences in storage period (1, 5, and 10 days). Although endophyte richness, composition, and taxonomic diversity identified via culturing vs. NGS differed markedly, both methods revealed host-structured communities. Studies differing only in cultivation media or storage period thus can be compared to estimate endophyte richness, composition, and turnover at scales larger than those of individual studies alone. Our data show that it is likely more important to sample more host species, rather than sampling fewer species more intensively, to quantify endophyte diversity in given locations, with the richest insights into endophyte ecology emerging when culturing and NGS are paired.},
}
@article {pmid33410937,
year = {2021},
author = {Rodrigues, LA and da Silva, DKA and Yano-Melo, AM},
title = {Arbuscular Mycorrhizal Fungal Assemblages in Conservation Unit of Atlantic Forest Areas Under Native Vegetation and Natural Regeneration.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {122-134},
pmid = {33410937},
issn = {1432-184X},
support = {CNPq 421241 / 2017-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 131015/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; APQ-0003- 2.03/18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; },
mesh = {Biodiversity ; Forests ; *Mycorrhizae ; Plant Roots ; Soil Microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) play an important role in the dynamic of plant community in the south American Atlantic Rainforest biome. Even in protected areas, this biome is under several anthropic impacts, which can cause shifts in the soil microbiota, including AMF. This study aimed to determine the structure and composition of AMF community in areas of native Atlantic Forest and in natural regeneration and to identify which abiotic factors are influencing this community in these areas. Soil samples were collected at Monte Pascoal National and Historical Park, in Southern Bahia, in native and natural regeneration areas of Atlantic Forest in two seasons (rainy and dry). Greater number of glomerospores and richness and diversity of AMF were found in the area under regeneration, with differences between seasons being observed only for the number of glomerospores. Seventy-seven species of AMF were recorded, considering all areas and seasons, with Acaulospora and Glomus being the most representative genera. Greater abundance of species of the genera Acaulospora, Claroideoglomus, and Septoglomus was found in the regeneration area. The AMF community differed between the study areas, but not between seasons, with soil attributes (pH, K, Al, Mg, m, and clay) structuring factors for this difference in the AMF community. Atlantic Forest areas in natural regeneration and the soil edaphic factors provide changes in the structure and composition of the AMF community, increasing the richness and diversity of these fungi in conservation units.},
}
@article {pmid33410936,
year = {2021},
author = {St James, AR and Lin, J and Richardson, RE},
title = {Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {429-441},
pmid = {33410936},
issn = {1432-184X},
mesh = {Carbon ; *Microbiota ; Soil ; *Sphagnopsida ; Wetlands ; },
abstract = {Peatland microbial community composition varies with respect to a range of biological and physicochemical variables. While the extent of peat degradation (humification) has been linked to microbial community composition along vertical stratification gradients within peatland sites, across-site variations have been relatively unexplored. In this study, we compared microbial communities across ten pristine Sphagnum-containing peatlands in the Adirondack Mountains, NY, which represented three different peat types-humic fen peat, humic bog peat, and fibric bog peat. Using 16S amplicon sequencing and network correlation analysis, we demonstrate that microbial community composition is primarily linked to peat type, and that distinct taxa networks distinguish microbial communities in each type. Shotgun metagenomic sequencing of the active water table region (mesotelm) from two Sphagnum-dominated bogs-one with fibric peat and one with humic peat-revealed differences in primary carbon degradation pathways, with the fibric peat being dominated by carbohydrate metabolism and hydrogenotrophic methanogenesis, and the humic peat being dominated by aliphatic carbon metabolism and aceticlastic methanogenesis. Our results suggest that peat humification is a major factor driving microbial community dynamics across peatland ecosystems.},
}
@article {pmid33410935,
year = {2021},
author = {Li, W and Nelson, KE},
title = {Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {1074-1079},
pmid = {33410935},
issn = {1432-184X},
mesh = {Adult ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; *Human Body ; Humans ; Infant, Newborn ; Metagenome ; Metagenomics ; Twins, Dizygotic/genetics ; },
abstract = {In recent years, many studies have described the composition and function of the human microbiome at different body sites and suggested a role for the microbiome in various diseases and health conditions. Some studies, using longitudinal samples, have also suggested how the microbiome changes over time due to disease, diet, development, travel, and other environmental factors. However, to date, no study has demonstrated whether the microorganisms established at birth or in early childhood, either transmitted from parents or obtained from the environment, can stay in the human body until adult or senior age. To directly answer this question is difficult, because microbiome samples at childhood and at later adulthood for the same individual will need to be compared and the field is not old enough to have allowed for that type of sample collection. Here, using a metagenomic approach, we analyzed 1004 gut microbiome samples from senior adults (65 ± 7.8 years) from the TwinsUK cohort. Our data indicate that many species in the human gut acquired in early childhood can stay for a lifetime until senior ages. We identified the rare genomic variants (single nucleotide variation and indels) for 27 prevalent species with enough sequencing coverage for confident genomic variant identification. We found that for some species, twin pairs, including both monozygotic (MZ) and dizygotic (DZ) twins, share significantly more rare variants than unrelated subject pairs. But no significant difference is found between MZ and DZ twin pairs. These observations strongly suggest that these species acquired in early childhood remained in these persons until senior adulthood.},
}
@article {pmid33410934,
year = {2021},
author = {Tan, MH and Loke, S and Croft, LJ and Gleason, FH and Lange, L and Pilgaard, B and Trevathan-Tackett, SM},
title = {First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {498-511},
pmid = {33410934},
issn = {1432-184X},
support = {ADPRF//Deakin University/ ; },
mesh = {Ecology ; Phylogeny ; *Stramenopiles ; Virulence ; },
abstract = {Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula spp. virulence and ecology. Given these uncertainties, we investigated the Labyrinthula genus from a novel genomic perspective by presenting the first draft genome and predicted proteome of a pathogenic isolate Labyrinthula SR_Ha_C, generated from a hybrid assembly of Nanopore and Illumina sequences. Phylogenetic and cross-phyla comparisons revealed insights into the evolutionary history of Stramenopiles. Genome annotation showed evidence of glideosome-type machinery and an apicoplast protein typically found in protist pathogens and parasites. Proteins involved in Labyrinthula SR_Ha_C's actin-myosin mode of transport, as well as carbohydrate degradation were also prevalent. Further, CAZyme functional predictions revealed a repertoire of enzymes involved in breakdown of cell-wall and carbohydrate storage compounds common to seagrasses. The relatively low number of CAZymes annotated from the genome of Labyrinthula SR_Ha_C compared to other Labyrinthulea species may reflect the conservative annotation parameters, a specialized substrate affinity and the scarcity of characterized protist enzymes. Inherently, there is high probability for finding both unique and novel enzymes from Labyrinthula spp. This study provides resources for further exploration of Labyrinthula spp. ecology and evolution, and will hopefully be the catalyst for new hypothesis-driven SWD research revealing more details of molecular interactions between the Labyrinthula genus and its host substrate.},
}
@article {pmid33410933,
year = {2021},
author = {Luo, Y and Wang, H and Liang, J and Qian, H and Ye, J and Chen, L and Yang, X and Chen, Z and Wang, F and Octavia, S and Payne, M and Song, X and Jiang, J and Jin, D and Lan, R},
title = {Population Structure and Multidrug Resistance of Non-O1/Non-O139 Vibrio cholerae in Freshwater Rivers in Zhejiang, China.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {319-333},
pmid = {33410933},
issn = {1432-184X},
support = {2019JZZY011018//Key Technology Research and Development Program of Shandong/ ; },
mesh = {Drug Resistance, Multiple ; Humans ; Multilocus Sequence Typing ; *Rivers ; *Vibrio cholerae non-O1/genetics ; Virulence/genetics ; },
abstract = {To understand the environmental reservoirs of Vibrio cholerae and their public health significance, we surveyed freshwater samples from rivers in two cities (Jiaxing [JX] and Jiande [JD]) in Zhejiang, China. A total of 26 sampling locations were selected, and river water was sampled 456 times from 2015 to 2016 yielding 200 V. cholerae isolates, all of which were non-O1/non-O139. The average isolation rate was 47.3% and 39.1% in JX and JD, respectively. Antibiotic resistance profiles of the V. cholerae isolates were examined with nonsusceptibility to cefazolin (68.70%, 79/115) being most common, followed by ampicillin (47.83%, 55/115) and imipenem (27.83%, 32/115). Forty-two isolates (36.52%, 42/115) were defined as multidrug resistant (MDR). The presence of virulence genes was also determined, and the majority of the isolates were positive for toxR (198/200, 99%) and hlyA (196/200, 98%) with few other virulence genes observed. The population structure of the V. cholerae non-O1/non-O139 sampled was examined using multilocus sequence typing (MLST) with 200 isolates assigned to 128 STs and 6 subpopulations. The non-O1/non-O139 V. cholerae population in JX was more varied than in JD. By clonal complexes (CCs), 31 CCs that contained isolates from this study were shared with other parts of China and/or other countries, suggesting widespread presence of some non-O1/non-O139 clones. Drug resistance profiles differed between subpopulations. The findings suggest that non-O1/non-O139 V. cholerae in the freshwater environment is a potential source of human infections. Routine surveillance of non-O1/non-O139 V. cholerae in freshwater rivers will be of importance to public health.},
}
@article {pmid33410932,
year = {2021},
author = {Hutchinson, MI and Bell, TAS and Gallegos-Graves, V and Dunbar, J and Albright, M},
title = {Merging Fungal and Bacterial Community Profiles via an Internal Control.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {484-497},
pmid = {33410932},
issn = {1432-184X},
support = {F255LANL2018//Office of Science/ ; },
mesh = {Bacteria/genetics ; DNA, Fungal/genetics ; *Fungi/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; },
abstract = {Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.},
}
@article {pmid33410931,
year = {2021},
author = {Gomez, JA and Primm, TP},
title = {A Slimy Business: the Future of Fish Skin Microbiome Studies.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {275-287},
pmid = {33410931},
issn = {1432-184X},
mesh = {Animals ; *Bacteria/genetics ; Fishes ; Metagenomics ; *Microbiota/genetics ; Skin ; },
abstract = {Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.},
}
@article {pmid33408702,
year = {2020},
author = {Riva, A and Kolimár, D and Spittler, A and Wisgrill, L and Herbold, CW and Abrankó, L and Berry, D},
title = {Conversion of Rutin, a Prevalent Dietary Flavonol, by the Human Gut Microbiota.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {585428},
pmid = {33408702},
issn = {1664-302X},
abstract = {The gut microbiota plays a pivotal role in the conversion of dietary flavonoids, which can affect their bioavailability and bioactivity and thereby their health-promoting properties. The ability of flavonoids to metabolically-activate the microbiota has, however, not been systematically evaluated. In the present study, we used a fluorescence-based single-cell activity measure [biorthogonal non-canonical ammino acid-tagging (BONCAT)] combined with fluorescence activated cell sorting (FACS) to determine which microorganisms are metabolically-active after amendment of the flavonoid rutin. We performed anaerobic incubations of human fecal microbiota amended with rutin and in the presence of the cellular activity marker L-azidohomoalanine (AHA) to detect metabolically-active cells. We found that 7.3% of cells in the gut microbiota were active after a 6 h incubation and 26.9% after 24 h. We then sorted BONCAT-positive cells and observed an enrichment of Lachnospiraceae (Lachnoclostridium and Eisenbergiella), Enterobacteriaceae, Tannerellaceae, and Erysipelotrichaceae species in the rutin-responsive fraction of the microbiota. There was marked inter-individual variability in the appearance of rutin conversion products after incubation with rutin. Consistent with this, there was substantial variability in the abundance of rutin-responsive microbiota among different individuals. Specifically, we observed that Enterobacteriaceae were associated with conversion of rutin into quercetin-3-glucoside (Q-glc) and Lachnospiraceae were associated with quercetin (Q) production. This suggests that individual microbiotas differ in their ability to metabolize rutin and utilize different conversion pathways.},
}
@article {pmid33408369,
year = {2021},
author = {Meisner, A and Snoek, BL and Nesme, J and Dent, E and Jacquiod, S and Classen, AT and Priemé, A},
title = {Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles.},
journal = {The ISME journal},
volume = {15},
number = {4},
pages = {1207-1221},
pmid = {33408369},
issn = {1751-7370},
mesh = {Climate Change ; Desiccation ; Freezing ; *Soil ; *Soil Microbiology ; },
abstract = {Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.},
}
@article {pmid33406784,
year = {2021},
author = {Mayta-Apaza, AC and García-Cano, I and Dabrowski, K and Jiménez-Flores, R},
title = {Bacterial Diversity Analysis and Evaluation Proteins Hydrolysis During the Acid Whey and Fish Waste Fermentation.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
pmid = {33406784},
issn = {2076-2607},
abstract = {The disposal of acid whey (Aw), a by-product from fermented products, is a problem for the dairy industry. The fishery industry faces a similar dilemma, disposing of nearly 50% of fish processed for human consumption. Economically feasible and science-based alternatives are needed to overcome this problem. One possible solution is to add value to the remaining nutrients from these by-products. This study focuses on the breakdown of nutrients in controlled fermentations of Aw, fish waste (F), molasses (M), and a lactic acid bacteria (LAB) strain (Lr). The aim was to assess the dynamic variations in microbial diversity and the biochemical changes that occur during fermentation. Four treatments were compared (AwF, AwFM, AwFLr, and AwFMLr), and the fermentation lasted 14 days at 22.5 °C. Samples were taken every other day. Colorimetric tests for peptide concentrations, pH, and microbial ecology by 16S-v4 rRNA amplicon using Illumina MiSeq were conducted. The results of the microbial ecology showed elevated levels of alpha and beta diversity in the samples at day zero. By day 2 of fermentation, pH dropped, and the availability of a different set of nutrients was reflected in the microbial diversity. The fermentation started to stabilize and was driven by the Firmicutes phylum, which dominated the microbial community by day 14. Moreover, there was a significant increase (3.6 times) in peptides when comparing day 0 with day 14, making this treatment practical and feasible for protein hydrolysis. This study valorizes two nutrient-dense by-products and provides an alternative to the current handling of these materials.},
}
@article {pmid33406135,
year = {2021},
author = {Kanzaki, N and Ekino, T and Hamaguchi, K and Takeuchi-Kaneko, Y},
title = {Three Seinura species from Japan with a description of S. shigaensis n. sp. (Tylenchomorpha: Aphelenchoididae).},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244653},
pmid = {33406135},
issn = {1932-6203},
mesh = {Animals ; Electron Transport Complex IV/genetics ; *Genes, Mitochondrial ; Japan ; Rhabditida/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; },
abstract = {A preliminary survey of Seinura spp. was conducted in the Kyoto area, Western Japan. The survey yielded four new strains of Seinura spp., including two strains of S. caverna, a strain of S. italiensis, and a strain of an undescribed species. Molecularly, the two strains of S. caverna were nearly identical to the type strain but showed some minor variations, particularly in the mitochondrial cytochrome oxidase subunit I gene. The small subunit and D2-D3 large subunit sequences of the Japanese strain of S. italiensis were nearly identical and identical to its original description, respectively, and the difference in the small subunit was due to mis-reading of the sequences. The new species, S. shigaensis n. sp., was phylogenetically close to S. caverna and S. persica, although these three species were clearly different phylogenetically. The new species was typologically similar or nearly identical to several other Seinura spp., including S. chertkovi, S. christiei, S. italiensis, S. steineri, and S. tenuicaudata, but it can be distinguished from those species by the morphometric values. Because the new species is phylogenetically very close to S. caverna, it could be a good comparative system for S. caverna as a potential satellite model for the predatory nematode.},
}
@article {pmid33404822,
year = {2021},
author = {Álvarez-Pérez, S and Tsuji, K and Donald, M and Van Assche, A and Vannette, RL and Herrera, CM and Jacquemyn, H and Fukami, T and Lievens, B},
title = {Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {990-1003},
pmid = {33404822},
issn = {1432-184X},
support = {742964//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; DEB 1737758//National Science Foundation/ ; RYC2018-023847-I//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; },
mesh = {Acinetobacter ; Animals ; Bees ; Insecta ; *Nitrogen ; Phylogeny ; *Plant Nectar ; },
abstract = {Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understood, it is reasonable to assume that they are efficient nitrogen scavengers that can consume a wide range of nitrogen sources in nectar. Furthermore, it can be hypothesized that phylogenetically closely related strains have more similar phenotypic characteristics than distant relatives. We tested these hypotheses by investigating the growth performance on different nitrogen-rich substrates of a collection of 82 acinetobacters isolated from nectar and honeybees, representing members of five species (Acinetobacter nectaris, A. boissieri, A. apis, and the recently described taxa A. bareti and A. pollinis). We also analyzed possible links between growth performance and phylogenetic affiliation of the isolates, while taking into account their geographical origin. Results demonstrated that the studied isolates could utilize a wide variety of nitrogen sources, including common metabolic by-products of yeasts (e.g., ammonium and urea), and that phylogenetic relatedness was associated with the variation in nitrogen assimilation among the studied acinetobacters. Finally, nutrient source and the origin (sample type and country) of isolates also predicted the ability of the acinetobacters to assimilate nitrogen-rich compounds. Overall, these results demonstrate inter-clade variation in the potential of the acinetobacters as nitrogen scavengers and suggest that nutritional dependences might influence interactions between bacteria and yeasts in floral nectar.},
}
@article {pmid33404821,
year = {2021},
author = {Shar, S and Reith, F and Ball, AS and Shahsavari, E},
title = {Long-term Impact of Gold and Platinum on Microbial Diversity in Australian Soils.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {977-989},
pmid = {33404821},
issn = {1432-184X},
support = {ARC-FT100150200//Australian Research Council/ ; },
mesh = {Australia ; Gold ; Platinum ; *Soil ; *Soil Microbiology ; },
abstract = {The effects of platinum (Pt) and gold (Au) and on the soil bacterial community was evaluated in four different Australian soil types (acidic Burn Grounds (BGR), organic matter-rich Fox Lane, high silt/metal Pinpinio (PPN), and alkali Minnipa (MNP) spiked with either Pt or Au at 1, 25, and 100 mg kg[-1] using a next-generation sequencing approach (amplicon-based, MiSeq). Soil type and metal concentrations were observed to be key drivers of Pt and Au effects on soil microbial community structure. Different trends were therefore observed in the response of the bacterial community to Pt and Au amendments; however in each soil type, Pt and Au amendment caused a detectable shift in community structure that in most samples was positively correlated with increasing metal concentrations. New dominant groups were only observed in BGR and PPN soils at 100 mg kg[-1] (Kazan-3B-28 and Verrucomicrobia groups (BGR, Pt) and Firmicutes and Caldithrix groups (PPN, Pt) and WS2 (BGR, Au). The effects of Pt on soil microbial diversity were largely adverse at 100 mg kg[-1] and were pronounced in acidic, basic, and metal/silt-rich soils. However, this effect was concentration-related; Au appeared to be more toxic to soil bacterial communities than Pt at 25 mg kg[-1] but Pt was more toxic at 100 mg kg[-1]. More bacterial groups such as those belonging to Burkholderiales/Burkholderiaceae, Alicyclobacillaceae, Rubrobacteraceae, Cytophagaceae, Oxalobacteraceae were selectively enriched by Pt compared to Au (Sphingomonadaceae and Rhodospirillaceae) amendments irrespective of soil type. The research outcomes have important implications in the management (remediation) of Pt- and Au-contaminated environments.},
}
@article {pmid33404820,
year = {2021},
author = {Leiva, D and Fernández-Mendoza, F and Acevedo, J and Carú, M and Grube, M and Orlando, J},
title = {The Bacterial Community of the Foliose Macro-lichen Peltigera frigida Is More than a Mere Extension of the Microbiota of the Subjacent Substrate.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {965-976},
pmid = {33404820},
issn = {1432-184X},
support = {1181510//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; },
mesh = {*Ascomycota ; *Cyanobacteria ; *Lichens ; *Microbiota ; },
abstract = {Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates.},
}
@article {pmid33404819,
year = {2021},
author = {Ogaki, MB and Pinto, OHB and Vieira, R and Neto, AA and Convey, P and Carvalho-Silva, M and Rosa, CA and Câmara, PEAS and Rosa, LH},
title = {Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {157-164},
pmid = {33404819},
issn = {1432-184X},
mesh = {Animals ; Antarctic Regions ; *Ascomycota ; DNA ; DNA Barcoding, Taxonomic ; Fungi/genetics ; Geologic Sediments ; Humans ; *Mycobiome ; },
abstract = {We assessed fungal diversity in deep-sea sediments obtained from different depths in the Southern Ocean using the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA by metabarcoding through high-throughput sequencing (HTS). We detected 655,991 DNA reads representing 263 fungal amplicon sequence variants (ASVs), dominated by Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Chytridiomycota and Rozellomycota, confirming that deep-sea sediments can represent a hotspot of fungal diversity in Antarctica. The community diversity detected included 17 dominant fungal ASVs, 62 intermediate and 213 rare. The dominant fungi included taxa of Mortierella, Penicillium, Cladosporium, Pseudogymnoascus, Phaeosphaeria and Torula. Despite the extreme conditions of the Southern Ocean benthos, the total fungal community detected in these marine sediments displayed high indices of diversity and richness, and moderate dominance, which varied between the different depths sampled. The highest diversity indices were obtained in sediments from 550 m and 250 m depths. Only 49 ASVs (18.63%) were detected at all the depths sampled, while 16 ASVs were detected only in the deepest sediment sampled at 1463 m. Based on sequence identities, the fungal community included some globally distributed taxa, primarily recorded otherwise from terrestrial environments, suggesting transport from these to deep marine sediments. The assigned taxa included symbionts, decomposers and plant-, animal- and human-pathogenic fungi, suggesting that deep-sea sediments host a complex fungal diversity, although metabarcoding does not itself confirm that living or viable organisms are present.},
}
@article {pmid33404818,
year = {2021},
author = {Liu, Y and Anastacio, GR and Ishangulyyeva, G and Rodriguez-Ramos, JC and Erbilgin, N},
title = {Mutualistic Ophiostomatoid Fungi Equally Benefit from Both a Bark Beetle Pheromone and Host Tree Volatiles as Nutrient Sources.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {1106-1110},
pmid = {33404818},
issn = {1432-184X},
mesh = {Animals ; *Coleoptera ; Nutrients ; Ophiostoma ; *Ophiostomatales ; Pheromones ; *Pinus ; Plant Bark ; Trees ; },
abstract = {Interactions between mutualistic bark beetles and ophiostomatoid fungi have received considerable attention in recent years. Studies have shown how volatile organic compounds emitted from mutualist fungi affect the behaviors of several bark beetle species. However, we currently lack sufficient knowledge regarding whether bark beetle pheromones can influence mutualist fungi. Here, we measured growth and biomass of two mutualistic fungi of the mountain pine beetle in response to headspace of a beetle pheromone (trans-verbenol), a blend of host tree volatiles, the combination of both, or control (no volatile source) in vitro experiments consisting of a nitrogen-based medium. The surface area and ergosterol content of the mycelia were used as surrogates for fungal growth and biomass respectively. We found that both growth and biomass of Grosmannia clavigera and Ophiostoma montium were greater in medium exposed to any type of volatile sources than the control. While growth and ergosterol content of G. clavigera were highest in the combination treatment, there were no differences in growth or biomass among the types of volatiles introduced for O. montium. These results suggest that both mutualistic fungi can utilize both bark beetle pheromone and host tree volatiles as nutrient sources. Overall, these results support the on-going studies on the role of volatile organic compounds mediating mutualistic bark beetle-fungi interactions.},
}
@article {pmid33401417,
year = {2021},
author = {Savadova-Ratkus, K and Mazur-Marzec, H and Karosienė, J and Kasperovičienė, J and Paškauskas, R and Vitonytė, I and Koreivienė, J},
title = {Interplay of Nutrients, Temperature, and Competition of Native and Alien Cyanobacteria Species Growth and Cyanotoxin Production in Temperate Lakes.},
journal = {Toxins},
volume = {13},
number = {1},
pages = {},
pmid = {33401417},
issn = {2072-6651},
support = {European Network for Algal Bioproducts (EUALGAE).//European Cooperation in Science and Technology (COST) Action ES1408/International ; },
mesh = {Cyanobacteria/*classification/*physiology ; Harmful Algal Bloom ; Lakes/chemistry/*microbiology ; Saxitoxin/*chemistry/metabolism ; Species Specificity ; Temperature ; Water Pollutants, Chemical/*chemistry ; },
abstract = {Global warming and eutrophication contribute to formation of HABs and distribution of alien cyanobacteria northward. The current study assessed how alien to Europe Sphaerospermopsis aphanizomenoides and Chrysosporum bergii will co-occur with dominant native Planktothrix agardhii and Aphanizomenon gracile species under changing conditions in temperate freshwaters. The experiments were carried out to examine the effect of nutrients and temperature on the growth rate of cyanobacteria, production of cyanotoxins, and interspecies competition. The highest growth rate was determined for A. gracile (0.43 day[-1]) and S. aphanizomenoides (0.40 day[-1]) strains at all the tested nutrient concentrations (IP and IN were significant factors). S. aphanizomenoides adapted to the wide range of nutrient concentrations and temperature due to high species ecological plasticity; however, A. gracile was able to suppress its dominance under changing conditions. Regularity between tested variables and STX concentration in A. gracile was not found, but IP concentration negatively correlated with the amount of dmMC-RR and other non-ribosomal peptides (NRPs) in P. agardhii strains. The relative concentration of NRPs in nontoxic P. agardhii strain was up to 3-fold higher than in MC-producing strain. Our study indicated that nutrients, temperature, and species had significant effects on interspecies competition. A. gracile had a negative effect on biomass of both alien species and P. agardhii.},
}
@article {pmid33399932,
year = {2021},
author = {Aguero, CM and Eyer, PA and Crippen, TL and Vargo, EL},
title = {Reduced Environmental Microbial Diversity on the Cuticle and in the Galleries of a Subterranean Termite Compared to Surrounding Soil.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {1054-1063},
pmid = {33399932},
issn = {1432-184X},
mesh = {Animals ; Fungi/genetics ; Humans ; *Isoptera ; *Microbiota ; Soil ; *Streptomyces ; },
abstract = {Termites are intimately tied to the microbial world, as they utilize their gut microbiome for the conversion of plant cellulose into necessary nutrients. Subterranean termites must also protect themselves from the vast diversity of harmful microbes found in soil. However, not all soil microbes are harmful, such as Streptomyces and methanotrophic bacteria that some species of termites harbor in complex nest structures made of fecal material. The eastern subterranean termite, Reticulitermes flavipes, has a simple nest structure consisting of fecal lined galleries. We tested the hypothesis that R. flavipes maintains a select microbial community in its nests to limit the penetration of harmful soilborne pathogens and favor the growth of beneficial microbes. Using Illumina sequencing, we characterized the bacterial and fungal communities in the surrounding soil, in the nest galleries, and on the cuticle of workers. We found that the galleries provide a more beneficial microbial community than the surrounding soil. Bacterial and fungal diversity was highest in the soil, lower in the galleries, and least on the cuticle. Bacterial communities clustered together according to the substrate from which they were sampled, but this clustering was less clear in fungal communities. Most of the identified bacterial and fungal taxa were unique to one substrate, but the soil and gallery communities had very similar phylum-level taxonomic profiles. Notably, the galleries of R. flavipes also harbored both the potentially beneficial Streptomyces and the methanotrophic Methylacidiphilales, indicating that these microbial associations in fecal material pre-date the emergence of complex fecal nest structures. Surprisingly, several pathogenic groups were relatively abundant in the galleries and on the cuticle, suggesting that pathogens may accumulate within termite nests over time while putatively remaining at enzootic level during the lifetime of the colony.},
}
@article {pmid33399931,
year = {2021},
author = {Shih, CM and Ophine, L and Chao, LL},
title = {Molecular Detection and Genetic Identification of Wolbachia Endosymbiont in Wild-Caught Culex quinquefasciatus (Diptera: Culicidae) Mosquitoes from Sumatera Utara, Indonesia.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {1064-1074},
pmid = {33399931},
issn = {1432-184X},
support = {MOST 109-2314-B-037-077//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Animals ; *Culex ; *Culicidae ; Female ; Indonesia ; Male ; Phylogeny ; *Wolbachia/genetics ; },
abstract = {The genetic identity of Wolbachia endosymbiont in wild-caught Culex quinquefasciatus was determined for the first time in Indonesia. A total of 314 Cx. quinquefasciatus were examined for Wolbachia by PCR assay targeting the Wolbachia surface protein (wsp) gene. The prevalence of Wolbachia infection was detected in 29.94% of Cx. specimens (45.86% female and 8.27% male). The group-specific infection was detected with an infection rate of 0.32%, 28.98%, and 0.64% in groups A, B, and A&amp;B, respectively. Phylogenetic analysis revealed all Wolbachia strains from Indonesia were genetically affiliated to the supergroup A and B with the high sequence similarity of 97.9-100% and 99.7-100%, respectively. Phylogenetic relationships can be easily distinguished by neighbor-joining analysis and were congruent by maximum likelihood method. The genetic distance (GD) values of intra- and inter-group analysis indicated a lower level (GD < 0.007 for group A and GD < 0.003 for group B) within the Indonesia strains and a higher level (GD > 1.125 for group A and GD > 1.129 for group B) as compared with other Wolbachia strains. Our results provide the first genetic identification of Wolbachia endosymbiont in Cx. quinquefasciatus collected from Indonesia, and the phylogenetic analysis revealed a new discovery of group A Wolbachia in wild-caught Cx. quinquefasciatus mosquitoes.},
}
@article {pmid33399896,
year = {2021},
author = {Asha, K and Bhadury, P},
title = {Myceligenerans indicum sp. nov., an actinobacterium isolated from mangrove sediment of Sundarbans, India.},
journal = {Archives of microbiology},
volume = {203},
number = {4},
pages = {1577-1585},
pmid = {33399896},
issn = {1432-072X},
mesh = {*Actinobacteria/chemistry/classification/genetics ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Genome, Bacterial/genetics ; *Geologic Sediments/microbiology ; Glycolipids/analysis ; India ; Peptidoglycan/chemistry ; Phospholipids/analysis ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Species Specificity ; Wetlands ; },
abstract = {A new actinobacterial species of the genus Myceligenerans has been isolated from the intertidal sediment of Indian Sundarbans mangrove ecosystem. The isolate has been characterized based on polyphasic approaches. The isolate exhibit well-developed substrate mycelia along with the presence of cocci- and rod-shaped elements. The organism can grow across a wide range of temperature, salinity, and pH as well as on different carbon sources. Phylogenetic analyses based on 16S rRNA showed that this isolate is closely related to Myceligenerans salitolerans XHU 5031 (99% identity; 100% coverage). Presence of ketosynthase domain representing polyketide synthases in the isolate provides evidence of its potential ability to produce secondary metabolites. Multigene phylogeny based on atpD and rpoB gene sequences confirmed it as a new species within the family Promicromonosporaceae (Phylum Actinobacteria). The DNA G + C content of the isolate has been determined as 72 mol%. The peptidoglycan type was A4α and the whole-cell hydrolysates contained glucose, galactose, and mannose. The polar lipids were represented by diphosphatidylglycerol, one unknown phospholipid and one unknown glycolipid. Major fatty acids present in the isolate are anteiso-C15, iso-C15, iso-C16, and anteiso-C17. Whole-genome sequence indicates the size of genome is ~ 5 Mbp. GGDC (%), orthoANIu (%), and AAI of I2 genome indicated 28.9%, 77.44% and 0.859 identity with the genome of Myceligenerans xiligouense strain DSM 15,700. The isolate I2 has been proposed as a new species, Myceligenerans indicum sp. nov. The genome sequence has been deposited to GenBank/ENA/DDBJ under the accession number JABBYC000000000.},
}
@article {pmid33398112,
year = {2021},
author = {Marco, ML and Sanders, ME and Gänzle, M and Arrieta, MC and Cotter, PD and De Vuyst, L and Hill, C and Holzapfel, W and Lebeer, S and Merenstein, D and Reid, G and Wolfe, BE and Hutkins, R},
title = {The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {18},
number = {3},
pages = {196-208},
pmid = {33398112},
issn = {1759-5053},
mesh = {Consensus ; *Fermented Foods ; Humans ; *Nutrition Policy ; *Prebiotics ; *Probiotics ; },
abstract = {An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term 'fermented' led the panel to define fermented foods and beverages as "foods made through desired microbial growth and enzymatic conversions of food components". This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines.},
}
@article {pmid33396683,
year = {2020},
author = {Kuramae, EE and Dimitrov, MR and da Silva, GHR and Lucheta, AR and Mendes, LW and Luz, RL and Vet, LEM and Fernandes, TV},
title = {On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
pmid = {33396683},
issn = {2076-2607},
support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 2013/50351-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 206884/2014-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 99999.008090/2015-07;0622/2014//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.},
}
@article {pmid33392630,
year = {2021},
author = {Oliveira, MM and Proenca, AM and Moreira-Silva, E and de Castro, AM and Dos Santos, FM and Marconatto, L and Medina-Silva, R},
title = {Biofilms of Pseudomonas and Lysinibacillus Marine Strains on High-Density Polyethylene.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {833-846},
pmid = {33392630},
issn = {1432-184X},
support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 0050.0096017.15.9//Petrobras/ ; },
mesh = {Bacteria ; Biodegradation, Environmental ; Biofilms ; *Polyethylene ; *Pseudomonas ; },
abstract = {Environmental pollution by plastic debris is estimated on a scale of 100 million metric tons, a portion of which is fragmented into micro- and nanoplastics. These fragments are often colonized by bacterial species in marine environments, possibly contributing to the biodegradation of such materials. However, further investigations are necessary to determine the impact of abiotic polymer weathering on biofilm adhesion, as well as the specific biofilm formation strategies employed by marine isolates. Here, we evaluate deep-sea sediment bacterial isolates for biofilm adhesion, extracellular matrix production, and polymer degradation ability. Our study focuses on high-density polyethylene (HDPE) fragments for their high durability and environmental persistence, subjecting fragments to abiotic weathering prior to bacterial colonization. Marine isolates identified as Pseudomonas sp. and Lysinibacillus sp. exhibited decreasing biofilm formation on weathered HDPE, especially over the first 24 h of incubation. This effect was countered by increased extracellular matrix production, likely improving cell adhesion to surfaces roughened by abiotic degradation. These adhesion strategies were contrasted with a reference Pseudomonas aeruginosa strain, which displayed high levels of biofilm formation on non-weathered HDPE and lower extracellular matrix production over the first 24 h of incubation. Furthermore, our results suggest that an increase in biofilm biomass correlated with changes to HDPE structure, indicating that these strains have a potential for biodegradation of plastic fragments. Therefore, this work provides a detailed account of biofilm formation strategies and bacteria-plastic interactions that represent crucial steps in the biodegradation of plastic fragments in marine environments.},
}
@article {pmid33392629,
year = {2021},
author = {do Carmo Linhares, D and Saia, FT and Duarte, RTD and Nakayama, CR and de Melo, IS and Pellizari, VH},
title = {Methanotrophic Community Detected by DNA-SIP at Bertioga's Mangrove Area, Southeast Brazil.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {954-964},
pmid = {33392629},
issn = {1432-184X},
support = {04/13910-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2009/06601-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Brazil ; DNA ; Isotopes ; *Methane ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; },
abstract = {Methanotrophic bacteria can use methane as sole carbon and energy source. Its importance in the environment is related to the mitigation of methane emissions from soil and water to the atmosphere. Brazilian mangroves are highly productive, have potential to methane production, and it is inferred that methanotrophic community is of great importance for this ecosystem. The scope of this study was to investigate the functional and taxonomic diversity of methanotrophic bacteria present in the anthropogenic impacted sediments from Bertioga´s mangrove (SP, Brazil). Sediment sample was cultivated with methane and the microbiota actively involved in methane oxidation was identified by DNA-based stable isotope probing (DNA-SIP) using methane as a labeled substrate. After 4 days (96 h) of incubation and consumption of 0.7 mmol of methane, the most active microorganisms were related to methanotrophs Methylomonas and Methylobacter as well as to methylotrophic Methylotenera, indicating a possible association of these bacterial groups within a methane-derived food chain in the Bertioga mangrove. The abundance of genera Methylomonas, able to couple methane oxidation to nitrate reduction, may indicate that under low dissolved oxygen tensions, some aerobic methanotrophs could shift to intraerobic methane oxidation to avoid oxygen starvation.},
}
@article {pmid33392628,
year = {2021},
author = {Vega, L and Jaimes, J and Morales, D and Martínez, D and Cruz-Saavedra, L and Muñoz, M and Ramírez, JD},
title = {Microbial Communities' Characterization in Urban Recreational Surface Waters Using Next Generation Sequencing.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {847-863},
pmid = {33392628},
issn = {1432-184X},
support = {Direcci&#xf3;n de Investigaci&#xf3;n e Innovaci&#xf3;n//Universidad del Rosario/ ; },
mesh = {*Cyanobacteria/genetics ; Eutrophication ; High-Throughput Nucleotide Sequencing ; Humans ; Lakes ; *Microbiota ; Water Microbiology ; },
abstract = {Microbial communities in surface waters used for recreational purposes are indicators of contamination and risk of contact with human pathogens. Hence, monitoring microbial communities in recreational waters is important for potential public health threats to humans. Such monitoring is rare in Colombia, even in its capital, Bogotá, the most populous city in the country. This city encompasses metropolitan and linear parks with recreational water bodies that are used frequently by the public, and the presence of pathogens can compromise the health of the citizens. Therefore, we examined the bacterial, and eukaryotic communities in urban recreational lakes (URL) in four metropolitan parks in Bogotá, Colombia. Samples from four metropolitan parks (Los Novios, Simon Bolivar, El Tunal, and Timiza) and one stream contaminated with sewage from a linear park (El Virrey) were collected. We used amplicon next-generation sequencing of the 16S-rRNA gene and 18S-rRNA gene to characterize microbial communities followed by bioinformatics analyses. In addition, general water quality parameters-pH, hardness, acidity, alkalinity, dissolved oxygen, and nitrites-were recorded using a commercial kit. Genera of pathogens, including Legionella, Pseudomonas, Mycobacterium, Candida, and Naegleria, were found in lake waters. The stream El Virrey was, however, the only surface water that showed an abundance of fecal bacteria, often associated with low oxygen concentrations. All water bodies showed a predominance of fungal phyla, except for the lake at Timiza. This lake showed the highest pH, and its ecological dynamics are likely different from other water bodies. Likewise, some URLs displayed a greater abundance of cyanobacteria, including toxin-producing species. Algal genera associated with eutrophication were predominant among primary producing microorganisms. This study shows for the first time the description of the bacterial and eukaryotic communities of some URLs and a stream in Bogotá. The URLs and the stream harbored various pathogens that might pose a risk to the citizen's health.},
}
@article {pmid33392158,
year = {2020},
author = {Cerruti, M and Stevens, B and Ebrahimi, S and Alloul, A and Vlaeminck, SE and Weissbrodt, DG},
title = {Enrichment and Aggregation of Purple Non-sulfur Bacteria in a Mixed-Culture Sequencing-Batch Photobioreactor for Biological Nutrient Removal From Wastewater.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {8},
number = {},
pages = {557234},
pmid = {33392158},
issn = {2296-4185},
abstract = {Mixed-culture biotechnologies are widely used to capture nutrients from wastewater. Purple non-sulfur bacteria (PNSB), a guild of anoxygenic photomixotrophic organisms, rise interest for their ability to directly assimilate nutrients in the biomass. One challenge targets the aggregation and accumulation of PNSB biomass to separate it from the treated water. Our aim was to enrich and produce a concentrated, fast-settling PNSB biomass with high nutrient removal capacity in a 1.5-L, stirred-tank, anaerobic sequencing-batch photobioreactor (SBR). PNSB were rapidly enriched after inoculation with activated sludge at 0.1 gVSS L[-1] in a first batch of 24 h under continuous irradiance of infrared (IR) light (>700 nm) at 375 W m[-2], with Rhodobacter reaching 54% of amplicon sequencing read counts. SBR operations with decreasing hydraulic retention times (48 to 16 h, i.e., 1-3 cycles d[-1]) and increasing volumetric organic loading rates (0.2-1.3 kg COD d[-1] m[-3]) stimulated biomass aggregation, settling, and accumulation in the system, reaching as high as 3.8 g VSS L[-1]. The sludge retention time (SRT) increased freely from 2.5 to 11 days. Acetate, ammonium, and orthophosphate were removed up to 96% at a rate of 1.1 kg COD d[-1] m[-3], 77% at 113 g N d[-1] m[-3], and 73% at 15 g P d[-1] m[-3], respectively, with COD:N:P assimilation ratio of 100:6.7:0.9 m/m/m. SBR regime shifts sequentially selected for Rhodobacter (90%) under shorter SRT and non-limiting concentration of acetate during reaction phases, for Rhodopseudomonas (70%) under longer SRT and acetate limitation during reaction, and Blastochloris (10%) under higher biomass concentrations, underlying competition for substrate and photons in the PNSB guild. With SBR operations we produced a fast-settling biomass, highly (>90%) enriched in PNSB. A high nutrient removal was achieved by biomass assimilation, reaching the European nutrient discharge limits. We opened further insights on the microbial ecology of PNSB-based processes for water resource recovery.},
}
@article {pmid33391698,
year = {2020},
author = {Kroetsch, SA and Kidd, KA and Monk, WA and Culp, JM and Compson, ZG and Pavey, SA},
title = {The effects of taxonomy, diet, and ecology on the microbiota of riverine macroinvertebrates.},
journal = {Ecology and evolution},
volume = {10},
number = {24},
pages = {14000-14019},
pmid = {33391698},
issn = {2045-7758},
abstract = {Freshwater macroinvertebrates play key ecological roles in riverine food webs, such as the transfer of nutrients to consumers and decomposition of organic matter. Although local habitat quality drives macroinvertebrate diversity and abundance, little is known about their microbiota. In most animals, the microbiota provides benefits, such as increasing the rate at which nutrients are metabolized, facilitating immune system development, and defending against pathogenic attack. Our objectives were to identify the bacteria within aquatic invertebrates and determine whether their composition varied with taxonomy, habitat, diet, and time of sample collection. In 2016 and 2017, we collected 264 aquatic invertebrates from the mainstem Saint John (Wolastoq) River in New Brunswick, Canada, representing 15 orders. We then amplified the V3-V4 hypervariable region of the 16S rRNA gene within each individual, which revealed nearly 20,000 bacterial operational taxonomic units (OTUs). The microbiota across all aquatic invertebrates were dominated by Proteobacteria (69.25% of the total sequence reads), but they differed significantly in beta diversity, both among host invertebrate taxa (genus-, family-, and order-levels) and temporally. In contrast to previous work, we observed no microbiota differences among functional feeding groups or traditional feeding habits, and neither water velocity nor microhabitat type structured microbiota variability. Our findings suggest that host invertebrate taxonomy was the most important factor in modulating the composition of the microbiota, likely through a combination of vertical and horizontal bacterial transmission, and evolutionary processes. This is one of the most comprehensive studies of freshwater invertebrate microbiota to date, and it underscores the need for future studies of invertebrate microbiota evolution and linkages to environmental bacteria and physico-chemical conditions.},
}
@article {pmid33388944,
year = {2021},
author = {Saona, LA and Soria, M and Durán-Toro, V and Wörmer, L and Milucka, J and Castro-Nallar, E and Meneses, C and Contreras, M and Farías, ME},
title = {Phosphate-Arsenic Interactions in Halophilic Microorganisms of the Microbial Mat from Laguna Tebenquiche: from the Microenvironment to the Genomes.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {941-953},
pmid = {33388944},
issn = {1432-184X},
support = {1200834//ANID-FONDECYT/ ; ACT192057//ANID-PIA-Anillo INACH/ ; PICT 3825//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; },
mesh = {*Arsenic ; Geologic Sediments ; Lakes ; *Microbiota ; Phosphates ; },
abstract = {Arsenic (As) is a metalloid present in the earth's crust and widely distributed in the environment. Due to its high concentrations in the Andean valleys and its chemical similarity with phosphorus (P), its biological role in Andean Microbial Ecosystems (AMEs) has begun to be studied. The AMEs are home to extremophilic microbial communities that form microbial mats, evaporites, and microbialites inhabiting Andean lakes, puquios, or salt flats. In this work, we characterize the biological role of As and the effect of phosphate in AMEs from the Laguna Tebenquiche (Atacama Desert, Chile). Using micro X-ray fluorescence, the distribution of As in microbial mat samples was mapped. Taxonomic and inferred functional profiles were obtained from enriched cultures of microbial mats incubated under As stress and different phosphate conditions. Additionally, representative microorganisms highly resistant to As and able to grow under low phosphate concentration were isolated and studied physiologically. Finally, the genomes of the isolated Salicola sp. and Halorubrum sp. were sequenced to analyze genes related to both phosphate metabolism and As resistance. The results revealed As as a key component of the microbial mat ecosystem: (i) As was distributed across all sections of the microbial mat and represented a significant weight percentage of the mat (0.17 %) in comparison with P (0.40%); (ii) Low phosphate concentration drastically changed the microbial community in microbial mat samples incubated under high salinity and high As concentrations; (iii) Archaea and Bacteria isolated from the microbial mat were highly resistant to arsenate (up to 500 mM), even under low phosphate concentration; (iv) The genomes of the two isolates were predicted to contain key genes in As metabolism (aioAB and arsC/acr3) and the genes predicted to encode the phosphate-specific transport operon (pstSCAB-phoU) are next to the arsC gene, suggesting a functional relationship between these two elements.},
}
@article {pmid33387813,
year = {2021},
author = {Bossaert, S and Winne, V and Van Opstaele, F and Buyse, J and Verreth, C and Herrera-Malaver, B and Van Geel, M and Verstrepen, KJ and Crauwels, S and De Rouck, G and Lievens, B},
title = {Description of the temporal dynamics in microbial community composition and beer chemistry in sour beer production via barrel ageing of finished beers.},
journal = {International journal of food microbiology},
volume = {339},
number = {},
pages = {109030},
doi = {10.1016/j.ijfoodmicro.2020.109030},
pmid = {33387813},
issn = {1879-3460},
mesh = {Bacteria/*classification/*genetics ; Beer/*microbiology ; Biodiversity ; Fermentation ; Flavoring Agents ; *Food Microbiology ; *Microbiota ; Pediococcus ; Polyphenols/analysis ; RNA, Ribosomal, 16S/genetics ; Taste ; Time Factors ; },
abstract = {Currently, there is a strong interest in barrel ageing of finished, conventionally fermented beers, as a novel way to produce sour beers with a rich and complex flavour profile. The production process, however, remains largely a process of trial and error, often resulting in profit losses and inconsistency in quality. To improve product quality and consistency, a better understanding of the interactions between microorganisms, wood and maturing beer is needed. The aim of this study was to describe the temporal dynamics in microbial community composition, beer chemistry and sensory characteristics during barrel ageing of three conventionally fermented beers that differed in parameters like alcohol content and bitterness. Beers were matured for 38 weeks in new (two types of wood) and used (one type of wood) oak barrels. Beer samples were taken at the start of the maturation and after 2, 12 and 38 weeks. Microbial community composition, determined using amplicon sequencing of the V4 region of the bacterial 16S rRNA gene and the fungal ITS1 region, beer chemistry and sensory characteristics substantially changed throughout the maturation process. Likewise, total bacterial and fungal population densities generally increased during maturation. PerMANOVA revealed significant differences in the bacterial and fungal community composition of the three beers and across time points, but not between the different wood types. By contrast, significant differences in beer chemistry were found across the different beers, wood types and sampling points. Results also indicated that the outcome of the maturation process likely depends on the initial beer properties. Specifically, results suggested that beer bitterness may restrain the bacterial community composition, thereby having an impact on beer souring. While the bacterial community composition of moderately-hopped beers shifted to a dominance of lactic acid bacteria, the bacterial community of the high-bitterness beer remained fairly constant, with low population densities. Bacterial community composition of the moderate-bitterness beers also resembled those of traditional sours like lambic beers, hosting typical lambic brewing species like Pediococcus damnosus, Lactobacillus brevis and Acetobacter sp. Furthermore, results suggested that alcohol level may have affected the fungal community composition and extraction of wood compounds. More specifically, the concentration of wood compounds like cis-3-methyl-4-octanolide, trans-3-methyl-4-octanolide, eugenol and total polyphenols was higher in beers with a high alcohol content. Altogether, our results provide novel insights into the barrel ageing process of beer, and may pave the way for a new generation of sour beers.},
}
@article {pmid33385649,
year = {2021},
author = {Park, Y and Yu, J and Nguyen, VK and Park, S and Kim, J and Lee, T},
title = {Understanding complete ammonium removal mechanism in single-chamber microbial fuel cells based on microbial ecology.},
journal = {The Science of the total environment},
volume = {764},
number = {},
pages = {144231},
doi = {10.1016/j.scitotenv.2020.144231},
pmid = {33385649},
issn = {1879-1026},
mesh = {*Ammonium Compounds ; *Bioelectric Energy Sources ; Biofilms ; Bioreactors ; Humans ; Nitrites ; Nitrogen ; Wastewater ; },
abstract = {The removal of organics and ammonium from domestic wastewater was successfully achieved by a flat-panel air-cathode microbial fuel cell (FA-MFC). To elucidate the reason for complete ammonium removal in the single-chamber MFCs, microbial communities were analyzed in biofilms on the surface of each anode, separator, and cathode of separator-electrode assemblies (SEAs). The spatial distribution of bacterial families related to the nitrogen cycle varied based on local conditions. Since oxygen diffusing from the air-cathode created a locally aerobic condition, ammonia-oxidizing bacteria (AOB) Nitrosomonadacea and nitrite-oxidizing bacteria (NOB) Nitrospiraceae were present near the cathode. NOB (~12.1%) was more abundant than AOB (~4.4%), suggesting that the nitrate produced by NOB may be reduced back to nitrite by heterotrophic denitrifiers such as Rhodocyclaceae (~21.7%) and Comamonadaceae (~5%) in the anoxic zone close to the NOB layer. Near that zone, the "nitrite loop" also substantially enriched two nitrite-reducing bacterial families: Ignavibacteriaceae (~18.1%), facultative heterotrophs, and Brocadiaceae (~11.2%), anaerobic ammonium oxidizing autotrophs. A larger inner area of biofilm contained abundant heterotrophic denitrifiers and fermentation bacteria. These results indicate that the large-surface SEA of FA-MFC allows counter-diffusion between substrates and oxygen, resulting in interactions of bacteria involved in the nitrogen cycle for complete ammonium removal.},
}
@article {pmid33384680,
year = {2020},
author = {Amacker, N and Gao, Z and Agaras, BC and Latz, E and Kowalchuk, GA and Valverde, CF and Jousset, A and Weidner, S},
title = {Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {614194},
pmid = {33384680},
issn = {1664-302X},
abstract = {Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.},
}
@article {pmid33384676,
year = {2020},
author = {Assis, JM and Abreu, F and Villela, HMD and Barno, A and Valle, RF and Vieira, R and Taveira, I and Duarte, G and Bourne, DG and Høj, L and Peixoto, RS},
title = {Delivering Beneficial Microorganisms for Corals: Rotifers as Carriers of Probiotic Bacteria.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {608506},
pmid = {33384676},
issn = {1664-302X},
abstract = {The use of Beneficial Microorganisms for Corals (BMCs) to increase the resistance of corals to environmental stress has proven to be effective in laboratory trials. Because direct inoculation of BMCs in larger tanks or in the field can be challenging, a delivery mechanism is needed for efficient transmission of the BMC consortium. Packaged delivery mechanisms have been successfully used to transmit probiotics to other organisms, including humans, lobsters, and fish. Here, we tested a method for utilizing rotifers of the species Brachionus plicatilis for delivery of BMCs to corals of the species Pocillopora damicornis. Epifluorescence microscopy combined with a live/dead cell staining assay was used to evaluate the viability of the BMCs and monitor their in vivo uptake by the rotifers. The rotifers efficiently ingested BMCs, which accumulated in the digestive system and on the body surface after 10 min of interaction. Scanning electron microscopy confirmed the adherence of BMCs to the rotifer surfaces. BMC-enriched rotifers were actively ingested by P. damicornis corals, indicating that this is a promising technique for administering coral probiotics in situ. Studies to track the delivery of probiotics through carriers such as B. plicatilis, and the provision or establishment of beneficial traits in corals are the next proof-of-concept research priorities.},
}
@article {pmid33382858,
year = {2020},
author = {Lequime, S and Dehecq, JS and Matheus, S and de Laval, F and Almeras, L and Briolant, S and Fontaine, A},
title = {Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus.},
journal = {PLoS pathogens},
volume = {16},
number = {12},
pages = {e1009068},
pmid = {33382858},
issn = {1553-7374},
mesh = {Aedes/metabolism/virology ; Animals ; Disease Outbreaks ; Disease Vectors ; Epidemics ; Humans ; Models, Theoretical ; Mosquito Vectors/*metabolism/*virology ; Saliva/virology ; Viral Load ; Viremia/transmission ; Zika Virus/pathogenicity ; Zika Virus Infection/epidemiology/*transmission/virology ; },
abstract = {Originating from African forests, Zika virus (ZIKV) has now emerged worldwide in urbanized areas, mainly transmitted by Aedes aegypti mosquitoes. Although Aedes albopictus can transmit ZIKV experimentally and was suspected to be a ZIKV vector in Central Africa, the potential of this species to sustain virus transmission was yet to be uncovered until the end of 2019, when several autochthonous transmissions of the virus vectored by Ae. albopictus occurred in France. Aside from these few locally acquired ZIKV infections, most territories colonized by Ae. albopictus have been spared so far. The risk level of ZIKV emergence in these areas remains however an open question. To assess Ae. albopictus' vector potential for ZIKV and identify key virus outbreak predictors, we built a complete framework using the complementary combination of (i) dose-dependent experimental Ae. albopictus exposure to ZIKV followed by time-dependent assessment of infection and systemic infection rates, (ii) modeling of intra-human ZIKV viremia dynamics, and (iii) in silico epidemiological simulations using an Agent-Based Model. The highest risk of transmission occurred during the pre-symptomatic stage of the disease, at the peak of viremia. At this dose, mosquito infection probability was estimated to be 20%, and 21 days were required to reach the median systemic infection rates. Mosquito population origin, either temperate or tropical, had no impact on infection rates or intra-host virus dynamic. Despite these unfavorable characteristics for transmission, Ae. albopictus was still able to trigger and yield large outbreaks in a simulated environment in the presence of sufficiently high mosquito biting rates. Our results reveal a low but existing epidemic potential of Ae. albopictus for ZIKV, that might explain the absence of large scale ZIKV epidemics so far in territories occupied only by Ae. albopictus. They nevertheless support active surveillance and eradication programs in these territories to maintain the risk of emergence to a low level.},
}
@article {pmid33382250,
year = {2021},
author = {Kirchner, N and Cano-Prieto, C and Schulz-Fincke, AC and Gütschow, M and Ortlieb, N and Moschny, J and Niedermeyer, THJ and Horak, J and Lämmerhofer, M and van der Voort, M and Raaijmakers, JM and Gross, H},
title = {Discovery of Thanafactin A, a Linear, Proline-Containing Octalipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining.},
journal = {Journal of natural products},
volume = {84},
number = {1},
pages = {101-109},
doi = {10.1021/acs.jnatprod.0c01174},
pmid = {33382250},
issn = {1520-6025},
mesh = {Genome, Bacterial ; Multigene Family ; Peptide Synthases/*chemistry/metabolism ; Proline/*chemistry ; Pseudomonas/*chemistry/drug effects ; Pseudomonas fluorescens/genetics ; },
abstract = {Genome mining of the bacterial strains Pseudomonas sp. SH-C52 and Pseudomonas fluorescens DSM 11579 showed that both strains contained a highly similar gene cluster encoding an octamodular nonribosomal peptide synthetase (NRPS) system which was not associated with a known secondary metabolite. Insertional mutagenesis of an NRPS component followed by comparative profiling led to the discovery of the corresponding novel linear octalipopeptide thanafactin A, which was subsequently isolated and its structure determined by two-dimensional NMR and further spectroscopic and chromatographic methods. In bioassays, thanafactin A exhibited weak protease inhibitory activity and was found to modulate swarming motility in a strain-specific manner.},
}
@article {pmid33381966,
year = {2021},
author = {Yu, Z and Schwarz, C and Zhu, L and Chen, L and Shen, Y and Yu, P},
title = {Hitchhiking Behavior in Bacteriophages Facilitates Phage Infection and Enhances Carrier Bacteria Colonization.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {4},
pages = {2462-2472},
doi = {10.1021/acs.est.0c06969},
pmid = {33381966},
issn = {1520-5851},
mesh = {Bacillus cereus ; *Bacteriophages ; Biofilms ; Coliphages ; Escherichia coli ; },
abstract = {Interactions between bacteriophages (phages) and biofilms remain poorly understood despite the broad implications for microbial ecology, water quality, and microbiome engineering. Here, we demonstrate that lytic coliphage PHH01 can hitchhike on carrier bacteria Bacillus cereus to facilitate its infection of host bacteria, Escherichia coli, in biofilms. Specifically, PHH01 could adsorb onto the flagella of B. cereus, and thus phage motility was increased, resulting in 4.36-fold more effective infection of E. coli in biofilm relative to free PHH01 alone. Moreover, phage infection mitigated interspecies competition and enhanced B. cereus colonization; the fraction of B. cereus in the final biofilm increased from 9% without phages to 43% with phages. The mutualistic relationship between the coliphage and carrier bacteria was substantiated by migration tests on an E. coli lawn: the conjugation of PHH01 and B. cereus enhanced B. cereus colonization by 6.54-fold compared to B. cereus alone (6.15 vs 0.94 cm[2] in 24 h) and PHH01 migration by 5.15-fold compared to PHH01 alone (10.3 vs 2.0 mm in 24 h). Metagenomic and electron microscopic analysis revealed that the phages of diverse taxonomies and different morphologies could be adsorbed by the flagella of B. cereus, suggesting hitchhiking on flagellated bacteria might be a widespread strategy in aquatic phage populations. Overall, our study highlights that hitchhiking behavior in phages can facilitate phage infection of biofilm bacteria, promote carrier bacteria colonization, and thus significantly influence biofilm composition, which holds promise for mediating biofilm functions and moderating associated risks.},
}
@article {pmid33378450,
year = {2021},
author = {Metze, D and Popp, D and Schwab, L and Keller, NS and da Rocha, UN and Richnow, HH and Vogt, C},
title = {Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {2},
pages = {},
doi = {10.1093/femsec/fiaa261},
pmid = {33378450},
issn = {1574-6941},
mesh = {Carbon ; *Groundwater ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Temperature ; },
abstract = {High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediment sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate a potential loss of ecosystem functioning, functional redundancy and resilience, while heat storage at 80°C bears the risk of ecological collapse.},
}
@article {pmid33378284,
year = {2020},
author = {Afolayan, AO and Ayeni, FA},
title = {Metagenomic Analysis of Bacterial Communities in Water and Soil of the Fulani and non-Fulani in Nigeria.},
journal = {Journal of infection in developing countries},
volume = {14},
number = {12},
pages = {},
doi = {10.3855/jidc.12975},
pmid = {33378284},
issn = {1972-2680},
mesh = {DNA, Bacterial ; Humans ; Metagenomics ; *Microbiota ; Nigeria ; Proteobacteria/classification/genetics ; Pseudomonas/classification/genetics ; Public Health ; RNA, Ribosomal, 16S ; Rural Population ; *Soil Microbiology ; *Water Microbiology ; },
abstract = {INTRODUCTION: Interactions between environmental factors (water and soil) and humans are inevitable, particularly in rural and semi-urbanized regions. As such, knowledge on the microbial constituents of these environmental factors is key to understanding potential risk to public health. However, the microbial profile of soil and water present in vulnerable human communities in Nigeria is currently unknown. This study sought to investigate the composition of soil and water microbiota in the environment inhabited by recently studied human communities (the Fulani nomadic group and the urbanized Jarawa ethnic group) and estimate the contribution of these environmental factors to the microbiome of the aforementioned human communities.<br><br>METHODOLOGY: Soil and water samples were collected from the Fulani and non-Fulani community in Jengre (Plateau State, Nigeria) and Jos (Plateau State, Nigeria), respectively. Genomic DNA was extracted from these environmental samples, followed by Illumina sequencing of the V4 region of the 16S rRNA gene and bioinformatics analysis via Quantitative Insights into Microbial Ecology QIIME.<br><br>RESULTS: There is abundance of Proteobacteria (43%) signature members in soil samples obtained from both human communities. Analysis of the water samples revealed the abundance of Proteobacteria, particularly in water sourced from the borehole (Fulani). Pseudomonas (30%) had higher relative abundance in the drinking water of the Fulani.<br><br>CONCLUSIONS: The drinking water of the Fulani could be a potential health risk to the studied Fulani community. Factors that increase the abundance of public health threats and health risk, such as hygiene practices, soil and water quality need to be studied further for the improvement of health in vulnerable populations.},
}
@article {pmid33375064,
year = {2020},
author = {Duranti, S and Longhi, G and Ventura, M and van Sinderen, D and Turroni, F},
title = {Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
pmid = {33375064},
issn = {2076-2607},
support = {SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P1/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. Amongst these latter microorganisms, bifidobacteria represent a key model to study host-microbe interaction within the mammalian gut. Remarkably, bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract. They constitute one of the dominant bacterial members of the intestinal microbiota and are among the first colonizers of the mammalian gut. Notably, the presence of bifidobacteria in the gut has been associated with several health-promoting activities. In this review, we aim to provide an overview of current knowledge on the genetic diversity and ecology of bifidobacteria. Furthermore, we will discuss how this important group of gut bacteria is able to colonize and survive in the mammalian gut, so as to facilitate host interactions.},
}
@article {pmid33375046,
year = {2020},
author = {Khomutovska, N and de Los Ríos, A and Jasser, I},
title = {Diversity and Colonization Strategies of Endolithic Cyanobacteria in the Cold Mountain Desert of Pamir.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
pmid = {33375046},
issn = {2076-2607},
abstract = {Microorganisms can survive in extreme environments and oligotrophic habitats thanks to their specific adaptive capacity. Due to its severe and contrasting climate conditions, the cold mountain desert in Eastern Pamir provides a unique environment for analyzing microbial adaptation mechanisms occurring within colonization of endolithic habitats. This study aims to investigate the composition and structure of endolithic microbial communities and analyze the interactions between microorganisms and colonized lithic substrates. Endolithic biofilms were examined using scanning electron microscopy in backscattered electron mode (SEM-BSE) and next-generation sequencing (NGS) applying amplicon sequence variants (ASVs) approach. The investigation of the V3-V4 region of 16S rRNA gene revealed that endolithic communities are dominated by Actinobacteria (26%), Proteobacteria (23%), and Cyanobacteria (11.4%). Cyanobacteria were represented by Oxyphotobacteria with a predominance of subclasses of Oscillatoriophycidae, Synechococcophycideae, and Nostocophycidae as well as the rarely occurring Sericytochromatia. The positive correlation between the contribution of the orders Synechococcales and Rhizobiales to community structure suggests that some functionally closed taxa of Cyanobacteria and Proteobacteria can complement each other, for example, in nitrogen fixation in endolithic communities. The endolithic communities occurring in Eastern Pamir were identified as complex systems whose composition and structure seem to be influenced by the architecture of microhabitats and related microenvironmental conditions.},
}
@article {pmid33374976,
year = {2020},
author = {Rughöft, S and Jehmlich, N and Gutierrez, T and Kleindienst, S},
title = {Comparative Proteomics of Marinobacter sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
pmid = {33374976},
issn = {2076-2607},
support = {Elite Program for Postdocs//Baden-W&#xfc;rttemberg Stiftung/ ; 326028733//Deutsche Forschungsgemeinschaft/ ; },
abstract = {The application of chemical dispersants during marine oil spills can affect the community composition and activity of marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as Marinobacter spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced biodegradation rates. However, a major knowledge gap exists regarding the mechanisms underlying these physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate Marinobacter sp. TT1 grown under different conditions. Strain TT1 received different carbon sources (pyruvate vs. n-hexadecane) with and without added dispersant (Corexit EC9500A). Additional treatments contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF; with Corexit). For the first time, we identified the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a protein-based proposed metabolism of Corexit components as carbon substrates. Our findings revealed that Corexit exposure affects hydrocarbon metabolism, chemotactic motility, biofilm formation, and induces solvent tolerance mechanisms, like efflux pumps, in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions.},
}
@article {pmid33374225,
year = {2020},
author = {Shah, F and Gressler, M and Nehzati, S and Op De Beeck, M and Gentile, L and Hoffmeister, D and Persson, P and Tunlid, A},
title = {Secretion of Iron(III)-Reducing Metabolites during Protein Acquisition by the Ectomycorrhizal Fungus Paxillus involutus.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
pmid = {33374225},
issn = {2076-2607},
support = {P41 GM103393/GM/NIGMS NIH HHS/United States ; 2013.0073//Knut and Alice Wallenberg Foundation/ ; 2016-04561 and 2017-04261//Swedish Research Council/ ; },
abstract = {The ectomycorrhizal fungus Paxillus involutus decomposes proteins using a two-step mechanism, including oxidation and proteolysis. Oxidation involves the action of extracellular hydroxyl radicals (•OH) generated by the Fenton reaction. This reaction requires the presence of iron(II). Here, we monitored the speciation of extracellular iron and the secretion of iron(III)-reducing metabolites during the decomposition of proteins by P. involutus. X-ray absorption spectroscopy showed that extracellular iron was mainly present as solid iron(III) phosphates and oxides. Within 1 to 2 days, these compounds were reductively dissolved, and iron(II) complexes were formed, which remained in the medium throughout the incubation. HPLC and mass spectrometry detected five extracellular iron(III)-reducing metabolites. Four of them were also secreted when the fungus grew on a medium containing ammonium as the sole nitrogen source. NMR identified the unique iron(III)-reductant as the diarylcyclopentenone involutin. Involutin was produced from day 2, just before the elevated •OH production, preceding the oxidation of BSA. The other, not yet fully characterized iron(III)-reductants likely participate in the rapid reduction and dissolution of solid iron(III) complexes observed on day one. The production of these metabolites is induced by other environmental cues than for involutin, suggesting that they play a role beyond the Fenton chemistry associated with protein oxidation.},
}
@article {pmid33374112,
year = {2020},
author = {LeBrun, ES and Nighot, M and Dharmaprakash, V and Kumar, A and Lo, CC and Chain, PSG and Ma, TY},
title = {The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {1},
pages = {},
pmid = {33374112},
issn = {2075-1729},
support = {R01 DK121073/DK/NIDDK NIH HHS/United States ; R01Dk121073/NH/NIH HHS/United States ; R01DK106072/NH/NIH HHS/United States ; J. Lloyd Huck Chair in Medicine//Penn State College of Medicine/ ; },
abstract = {Phenotypic health effects, both positive and negative, have been well studied in association with the consumption of alcohol in humans as well as several other mammals including mice. Many studies have also associated these same health effects and phenotypes to specific members of gut microbiome communities. Here we utilized a chronic plus binge ethanol feed model (Gao-binge model) to explore microbiome community changes across three independent experiments performed in mice. We found significant and reproducible differences in microbiome community assemblies between ethanol-treated mice and control mice on the same diet absent of ethanol. We also identified significant differences in gut microbiota occurring temporally with ethanol treatment. Peak shift in communities was observed 4 days after the start of daily alcohol consumption. We quantitatively identified many of the bacterial genera indicative of these ethanol-induced shifts including 20 significant genera when comparing ethanol treatments with controls and 14 significant genera based on temporal investigation. Including overlap of treatment with temporal shifts, we identified 25 specific genera of interest in ethanol treatment microbiome shifts. Shifts coincide with observed presentation of fatty deposits in the liver tissue, i.e., Alcoholic Liver Disease-associated phenotype. The evidence presented herein, derived from three independent experiments, points to the existence of a common, reproducible, and characterizable "mouse ethanol gut microbiome".},
}
@article {pmid33370423,
year = {2020},
author = {Parks, M and Kedy, C and Skalla, C},
title = {Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemys scripta).},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0244489},
pmid = {33370423},
issn = {1932-6203},
mesh = {Animal Shells/*microbiology ; Animals ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; DNA, Bacterial/isolation &amp; purification ; Fresh Water/microbiology ; Iowa ; Microbiota/*genetics ; Oklahoma ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Turtles/*microbiology ; },
abstract = {Microbial communities associated with freshwater aquatic habitats and resident species are both critical to and indicative of ecosystem status and organismal health. External surfaces of turtle shells readily accumulate microbial growth and could carry representation of habitat-wide microbial diversity, since they are in regular contact with multiple elements of freshwater environments. Yet, microbial diversity residing on freshwater turtle shells is poorly understood. We applied 16S and 18S metabarcoding to characterize microbiota associated with external shell surfaces of 20 red-eared slider (Trachemys scripta) turtles collected from varied habitats in central and western Oklahoma, and ranging to southeast Iowa. Shell-associated microbial communities were highly diverse, with samples dominated by Bacteroidia and alpha-/gamma-proteobacteria, and ciliophoran alveolates. Alpha diversity was lower on turtle shells compared to shallow-water-associated environmental samples, likely resulting from basking-drying behavior and seasonal scute shedding, while alpha diversity was higher on carapace than plastron surfaces. Beta diversity of turtle shells was similarly differentiated from environmental samples, although sampling site was consistently a significant factor. Deinococcus-Thermus bacteria and ciliophoran alveolates were recovered with significantly higher abundance on turtle shells versus environmental samples, while bacterial taxa known to include human-pathogenic species were variably more abundant between shell and environmental samples. Microbial communities from a single, shared-site collection of the ecologically similar river cooter (P. concinna) largely overlapped with those of T. scripta. These data add to a foundation for further characterization of turtle shell microbial communities across species and habitats, with implications for freshwater habitat assessment, microbial ecology and wildlife conservation efforts.},
}
@article {pmid33363527,
year = {2020},
author = {Smith, PE and Waters, SM and Gómez Expósito, R and Smidt, H and Carberry, CA and McCabe, MS},
title = {Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {606825},
pmid = {33363527},
issn = {1664-302X},
abstract = {Our understanding of complex microbial communities, such as those residing in the rumen, has drastically advanced through the use of high throughput sequencing (HTS) technologies. Indeed, with the use of barcoded amplicon sequencing, it is now cost effective and computationally feasible to identify individual rumen microbial genera associated with ruminant livestock nutrition, genetics, performance and greenhouse gas production. However, across all disciplines of microbial ecology, there is currently little reporting of the use of internal controls for validating HTS results. Furthermore, there is little consensus of the most appropriate reference database for analyzing rumen microbiota amplicon sequencing data. Therefore, in this study, a synthetic rumen-specific sequencing standard was used to assess the effects of database choice on results obtained from rumen microbial amplicon sequencing. Four DADA2 reference training sets (RDP, SILVA, GTDB, and RefSeq + RDP) were compared to assess their ability to correctly classify sequences included in the rumen-specific sequencing standard. In addition, two thresholds of phylogenetic bootstrapping, 50 and 80, were applied to investigate the effect of increasing stringency. Sequence classification differences were apparent amongst the databases. For example the classification of Clostridium differed between all databases, thus highlighting the need for a consistent approach to nomenclature amongst different reference databases. It is hoped the effect of database on taxonomic classification observed in this study, will encourage research groups across various microbial disciplines to develop and routinely use their own microbiome-specific reference standard to validate analysis pipelines and database choice.},
}
@article {pmid33362871,
year = {2020},
author = {Setubal, JC and Stoye, J and Dutilh, BE},
title = {Editorial: Computational Methods for Microbiome Analysis.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {623897},
doi = {10.3389/fgene.2020.623897},
pmid = {33362871},
issn = {1664-8021},
}
@article {pmid33361365,
year = {2021},
author = {Van Holm, W and Ghesquière, J and Boon, N and Verspecht, T and Bernaerts, K and Zayed, N and Chatzigiannidou, I and Teughels, W},
title = {A Viability Quantitative PCR Dilemma: Are Longer Amplicons Better?.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {5},
pages = {e0265320},
pmid = {33361365},
issn = {1098-5336},
support = {C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; G0B2719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G091219N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; FWO-1SA5719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; },
mesh = {DNA, Bacterial ; *Microbial Viability ; *Polymerase Chain Reaction ; },
abstract = {The development of viability quantitative PCR (v-qPCR) has allowed for a more accurate assessment of the viability of a microbial sample by limiting the amplification of DNA from dead cells. Although valuable, v-qPCR is not infallible. One of the most limiting factors for accurate live/dead distinction is the length of the qPCR amplicon used. However, no consensus or guidelines exist for selecting and designing amplicon lengths for optimal results. In this study, a wide range of incrementally increasing amplicon lengths (68 to 906 base pairs [bp]) was used on live and killed cells of nine bacterial species treated with a viability dye (propidium monoazide [PMA]). Increasing amplicon lengths up to approximately 200 bp resulted in increasing quantification cycle (Cq) differences between live and killed cells while maintaining a good qPCR efficiency. Longer amplicon lengths, up to approximately 400 bp, further increased the Cq difference but at the cost of qPCR efficiency. Above 400 bp, no valuable increase in Cq differences was observed. IMPORTANCE Viability quantitative PCR (v-qPCR) has evolved into a valuable, mainstream technique for determining the number of viable microorganisms in samples by qPCR. Amplicon length is known to be positively correlated with the ability to distinguish between live and dead bacteria but is negatively correlated with qPCR efficiency. This trade-off is often not taken into account and might have an impact on the accuracy of v-qPCR data. Currently, there is no consensus on the optimal amplicon length. This paper provides methods to determine the optimal amplicon length and suggests an amplicon length range for optimal v-qPCR, taking into consideration the trade-off between qPCR efficiency and live/dead distinction.},
}
@article {pmid33360128,
year = {2021},
author = {Yuan, W and Wei, Y and Zhang, Y and Riaz, L and Yang, Q and Wang, Q and Wang, R},
title = {Resistance of multidrug resistant Escherichia coli to environmental nanoscale TiO2 and ZnO.},
journal = {The Science of the total environment},
volume = {761},
number = {},
pages = {144303},
doi = {10.1016/j.scitotenv.2020.144303},
pmid = {33360128},
issn = {1879-1026},
mesh = {Anti-Bacterial Agents/toxicity ; Ecosystem ; Escherichia coli ; *Metal Nanoparticles/toxicity ; *Nanoparticles ; Titanium/toxicity ; *Zinc Oxide/toxicity ; },
abstract = {Excessive production and utilization of nanoparticles (NPs) at industrial and household levels releases substantial quantities of NPs into the environment. These can be harmful to different types of organisms and cause adverse effects on ecosystems. Purchased TiO2 and ZnO NPs were characterized via XRD, XPS, FESEM, and Zeta potential. This study elucidates how multidrug resistant Escherichia coli LM13, which was recovered from livestock manure, counteracts the antibacterial activities of TiO2 and ZnO NPs to survive in the environment. E. coli ATCC25922, which is susceptible to antibiotics, was used as control. A dose-response experiment showed that the antibacterial activity of TiO2 was lower than that of ZnO NPs and, LM13 was more resistant to NPs than ATCC25922. An AcrAB-TolC efflux pump along with its regulation genes helped LM13 to minimize NP toxicity. Flow cytometry findings also indicated that the intensity of the side-scatter light parameter increased with TiO2 and ZnO NPs in a dose dependent manner, suggesting NP uptake by the both strains. The generation of reactive oxygen species in LM13 was several-fold lower than in ATCC25922, suggesting that reactive oxygen species mainly contribute to the toxicity mechanism. These results illustrate the necessity to evaluate the impacts of NPs on the survival capacity of bacteria and on the resistance genes in bacteria with higher NP resistance than NP susceptible bacteria.},
}
@article {pmid33360101,
year = {2021},
author = {Ngo, KN and Van Winckel, T and Massoudieh, A and Wett, B and Al-Omari, A and Murthy, S and Takács, I and De Clippeleir, H},
title = {Towards more predictive clarification models via experimental determination of flocculent settling coefficient value.},
journal = {Water research},
volume = {190},
number = {},
pages = {116294},
doi = {10.1016/j.watres.2020.116294},
pmid = {33360101},
issn = {1879-2448},
mesh = {Calibration ; Flocculation ; Models, Theoretical ; Sewage ; *Waste Disposal, Fluid ; *Water Purification ; },
abstract = {Improved settleability has become an essential feature of new wastewater treatment innovations. To accelerate adoption of such new technologies, improved clarifier models are needed to help with designing and predicting improvement in settleability. In general, the level of mathematics of settling clarifier models has gone far beyond the level of existing experimental methods available to support these models. To date, even for simple one-dimensional (1D) clarifier models, no experimental method has been described for flocculent settling coefficient (rp). As a consequence, rp cannot be considered as a sludge characteristic and is used as a calibration parameter to achieve observed effluent quality. In this study, we focused on the development of an empirical function based on a simple and practical experimental approach for the calculation of the rp value from sludge characteristics. This approach provided a similar approach as currently taken for hindered settling coefficient calculations (Veslind equation) and allowed for the model to predict effluent quality, thus increasing the power of the 1D model. The threshold of flocculation (TOF), which describes the collision efficiency of particles, directly correlated with the effluent quality of the five tested activated sludge systems and was selected as experimental method. The proposed empirical function between TOF and rp was validated for four years of validating data with five different sludge types operated under different operational conditions and configurations. The good effluent quality prediction with this approach brings us one step closer in making the clarification models more predictive towards effluent quality and clarifier performance.},
}
@article {pmid33360100,
year = {2021},
author = {Ceballos-Escalera, A and Pous, N and Chiluiza-Ramos, P and Korth, B and Harnisch, F and Bañeras, L and Balaguer, MD and Puig, S},
title = {Electro-bioremediation of nitrate and arsenite polluted groundwater.},
journal = {Water research},
volume = {190},
number = {},
pages = {116748},
doi = {10.1016/j.watres.2020.116748},
pmid = {33360100},
issn = {1879-2448},
mesh = {*Arsenic ; *Arsenites ; Biodegradation, Environmental ; *Groundwater ; Nitrates/analysis ; Oxidation-Reduction ; *Water Pollutants, Chemical/analysis ; },
abstract = {The coexistence of different pollutants in groundwater is a common threat. Sustainable and resilient technologies are required for their treatment. The present study aims to evaluate microbial electrochemical technologies (METs) for treating groundwater contaminated with nitrate (NO3[-]) while containing arsenic (in form of arsenite (As(III)) as a co-contaminant. The treatment was based on the combination of nitrate reduction to dinitrogen gas and arsenite oxidation to arsenate (exhibiting less toxicity, solubility, and mobility), which can be removed more easily in further post-treatment. We operated a bioelectrochemical reactor at continuous-flow mode with synthetic contaminated groundwater (33 mg N-NO3[-] L[-1] and 5 mg As(III) L[-1]) identifying the key operational conditions. Different hydraulic retention times (HRT) were evaluated, reaching a maximum nitrate reduction rate of 519 g N-NO3[-] m[3]Net Cathodic Compartment d[-1] at HRT of 2.3 h with a cathodic coulombic efficiency of around 100 %. Simultaneously, arsenic oxidation was complete at all HRT tested down to 1.6 h reaching an oxidation rate of up to 90 g As(III) m[-3]Net Reactor Volume d [-1]. Electrochemical and microbiological characterization of single granules suggested that arsenite at 5 mg L[-1] did not have an inhibitory effect on a denitrifying biocathode mainly represented by Sideroxydans sp. Although the coexistence of abiotic and biotic arsenic oxidation pathways was shown to be likely, microbial arsenite oxidation linked to denitrification by Achromobacter sp. was the most probable pathway. This research paves the ground towards a real application for treating groundwater with widespread pollutants.},
}
@article {pmid33355923,
year = {2021},
author = {Lofgren, LA and Nguyen, NH and Vilgalys, R and Ruytinx, J and Liao, HL and Branco, S and Kuo, A and LaButti, K and Lipzen, A and Andreopoulos, W and Pangilinan, J and Riley, R and Hundley, H and Na, H and Barry, K and Grigoriev, IV and Stajich, JE and Kennedy, PG},
title = {Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi.},
journal = {The New phytologist},
volume = {230},
number = {2},
pages = {774-792},
pmid = {33355923},
issn = {1469-8137},
support = {S10 OD016290/OD/NIH HHS/United States ; },
mesh = {Evolution, Molecular ; Fungi/genetics ; Genome, Fungal ; Genomics ; *Mycorrhizae/genetics ; *Pinus ; Specialization ; },
abstract = {While there has been significant progress characterizing the 'symbiotic toolkit' of ectomycorrhizal (ECM) fungi, how host specificity may be encoded into ECM fungal genomes remains poorly understood. We conducted a comparative genomic analysis of ECM fungal host specialists and generalists, focusing on the specialist genus Suillus. Global analyses of genome dynamics across 46 species were assessed, along with targeted analyses of three classes of molecules previously identified as important determinants of host specificity: small secreted proteins (SSPs), secondary metabolites (SMs) and G-protein coupled receptors (GPCRs). Relative to other ECM fungi, including other host specialists, Suillus had highly dynamic genomes including numerous rapidly evolving gene families and many domain expansions and contractions. Targeted analyses supported a role for SMs but not SSPs or GPCRs in Suillus host specificity. Phylogenomic-based ancestral state reconstruction identified Larix as the ancestral host of Suillus, with multiple independent switches between white and red pine hosts. These results suggest that like other defining characteristics of the ECM lifestyle, host specificity is a dynamic process at the genome level. In the case of Suillus, both SMs and pathways involved in the deactivation of reactive oxygen species appear to be strongly associated with enhanced host specificity.},
}
@article {pmid33351643,
year = {2021},
author = {Oesterle, I and Braun, D and Berry, D and Wisgrill, L and Rompel, A and Warth, B},
title = {Polyphenol Exposure, Metabolism, and Analysis: A Global Exposomics Perspective.},
journal = {Annual review of food science and technology},
volume = {12},
number = {},
pages = {461-484},
doi = {10.1146/annurev-food-062220-090807},
pmid = {33351643},
issn = {1941-1421},
mesh = {Humans ; Mass Spectrometry ; *Metabolomics ; *Polyphenols ; },
abstract = {Polyphenols are generally known for their health benefits and estimating actual exposure levels in health-related studies can be improved by human biomonitoring. Here, the application of newly available exposomic and metabolomic technology, notably high-resolution mass spectrometry, in the context of polyphenols and their biotransformation products, is reviewed. Comprehensive workflows for investigating these important bioactives in biological fluids or microbiome-related experiments are scarce. Consequently, this new era of nontargeted analysis and omic-scale exposure assessment offers a unique chance for better assessing exposure to, as well as metabolism of, polyphenols. In clinical and nutritional trials, polyphenols can be investigated simultaneously with the plethora of other chemicals to which we are exposed, i.e., the exposome, which may interact abundantly and modulate bioactivity. This research direction aims at ultimately eluting into atrue systems biology/toxicology evaluation of health effects associated with polyphenol exposure, especially during early life, to unravel their potential for preventing chronic diseases.},
}
@article {pmid33350826,
year = {2021},
author = {Kosgey, K and Chandran, K and Gokal, J and Kiambi, SL and Bux, F and Kumari, S},
title = {Critical Analysis of Biomass Retention Strategies in Mainstream and Sidestream ANAMMOX-Mediated Nitrogen Removal Systems.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {1},
pages = {9-24},
doi = {10.1021/acs.est.0c00276},
pmid = {33350826},
issn = {1520-5851},
mesh = {*Ammonium Compounds ; Anaerobiosis ; Biomass ; Bioreactors ; Denitrification ; *Nitrogen ; Oxidation-Reduction ; Wastewater ; },
abstract = {ANAMMOX (anaerobic ammonium oxidation) represents an energy-efficient process for biological nitrogen removal, particularly from wastewater streams with low chemical oxygen demand (COD) to nitrogen (C/N) ratios. Its widespread application, however, is still hampered by a lack of access to biomass-enriched with ANAMMOX bacteria (AMX), slow growth rates of AMX, and their sensitivity to inhibition. Although the coupling of ANAMMOX processes with partial nitrification is already widespread, especially for sidestream treatment, maintaining a functional population density of AMX remains a challenge in these systems. Therefore, strategies that maximize retention of AMX-rich biomass are essential to promote process stability. This paper reviews existing methods of biomass retention in ANAMMOX-mediated systems, focusing on (i) granulation; (ii) biofilm formation on carrier materials; (iii) gel entrapment; and (iv) membrane technology in mainstream and sidestream systems. In addition, the microbial ecology of different ANAMMOX-mediated systems is reviewed.},
}
@article {pmid33350010,
year = {2021},
author = {Peñalver, L and Schmid, P and Szamosvári, D and Schildknecht, S and Globisch, C and Sawade, K and Peter, C and Böttcher, T},
title = {A Ligand Selection Strategy Identifies Chemical Probes Targeting the Proteases of SARS-CoV-2.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {60},
number = {12},
pages = {6799-6806},
pmid = {33350010},
issn = {1521-3773},
support = {Emmy Noether//Deutsche Forschungsgemeinschaft/ ; SFB969//Deutsche Forschungsgemeinschaft/ ; Zukunftskolleg Incomming Felowship (ZIF)//FP7 People: Marie-Curie Actions/ ; },
mesh = {Catalytic Domain ; Coronavirus 3C Proteases/*chemistry/metabolism ; Coronavirus Papain-Like Proteases/*chemistry/metabolism ; Cysteine Proteinase Inhibitors/*chemistry/metabolism ; Hep G2 Cells ; Humans ; Ligands ; Molecular Docking Simulation ; *Molecular Probe Techniques ; Molecular Probes/*chemistry ; Molecular Structure ; Proof of Concept Study ; Protein Binding ; SARS-CoV-2/*enzymology ; Small Molecule Libraries/*chemistry/metabolism ; Structure-Activity Relationship ; },
abstract = {Activity-based probes are valuable tools for chemical biology. However, finding probes that specifically target the active site of an enzyme remains a challenging task. Herein, we present a ligand selection strategy that allows to rapidly tailor electrophilic probes to a target of choice and showcase its application for the two cysteine proteases of SARS-CoV-2 as proof of concept. The resulting probes were specific for the active site labeling of 3CL[pro] and PL[pro] with sufficient selectivity in a live cell model as well as in the background of a native human proteome. Exploiting the probes as tools for competitive profiling of a natural product library identified salvianolic acid derivatives as promising 3CL[pro] inhibitors. We anticipate that our ligand selection strategy will be useful to rapidly develop customized probes and discover inhibitors for a wide range of target proteins also beyond corona virus proteases.},
}
@article {pmid33349634,
year = {2020},
author = {Molinaro, A and Bel Lassen, P and Henricsson, M and Wu, H and Adriouch, S and Belda, E and Chakaroun, R and Nielsen, T and Bergh, PO and Rouault, C and André, S and Marquet, F and Andreelli, F and Salem, JE and Assmann, K and Bastard, JP and Forslund, S and Le Chatelier, E and Falony, G and Pons, N and Prifti, E and Quinquis, B and Roume, H and Vieira-Silva, S and Hansen, TH and Pedersen, HK and Lewinter, C and Sønderskov, NB and , and Køber, L and Vestergaard, H and Hansen, T and Zucker, JD and Galan, P and Dumas, ME and Raes, J and Oppert, JM and Letunic, I and Nielsen, J and Bork, P and Ehrlich, SD and Stumvoll, M and Pedersen, O and Aron-Wisnewsky, J and Clément, K and Bäckhed, F},
title = {Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {6448},
doi = {10.1038/s41467-020-20412-9},
pmid = {33349634},
issn = {2041-1723},
}
@article {pmid33348645,
year = {2020},
author = {Álvarez-Mena, A and Cámara-Almirón, J and de Vicente, A and Romero, D},
title = {Multifunctional Amyloids in the Biology of Gram-Positive Bacteria.},
journal = {Microorganisms},
volume = {8},
number = {12},
pages = {},
pmid = {33348645},
issn = {2076-2607},
support = {BacBio 637971//H2020 European Research Council/ ; AGL2016-78662-R//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PID2019-107724GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
abstract = {Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.},
}
@article {pmid33341792,
year = {2020},
author = {ElNaker, NA and Sallam, AM and El-Sayed, EM and El Ghandoor, H and Talaat, MS and Yousef, AF and Hasan, SW},
title = {A conceptual framework modeling of functional microbial communities in wastewater treatment electro-bioreactors.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {82},
number = {12},
pages = {3047-3061},
doi = {10.2166/wst.2020.553},
pmid = {33341792},
issn = {0273-1223},
mesh = {Bioreactors ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Waste Disposal, Fluid ; Wastewater ; *Water Purification ; },
abstract = {Understanding the microbial ecology of a system allows linking members of the community and their metabolic functions to the performance of the wastewater bioreactor. This study provided a comprehensive conceptual framework for microbial communities in wastewater treatment electro-bioreactors (EBRs). The model was based on data acquired from monitoring the effect of altering different bioreactor operational parameters, such as current density and hydraulic retention time, on the microbial communities of an EBR and its nutrient removal efficiency. The model was also based on the 16S rRNA gene high-throughput sequencing data analysis and bioreactor efficiency data. The collective data clearly demonstrated that applying various electric currents affected the microbial community composition and stability and the reactor efficiency in terms of chemical oxygen demand, N and P removals. Moreover, a schematic that recommends operating conditions that are tailored to the type of wastewater that needs to be treated based on the functional microbial communities enriched at specific operating conditions was suggested. In this study, a conceptual model as a simplified representation of the behavior of microbial communities in EBRs was developed. The proposed conceptual model can be used to predict how biological treatment of wastewater in EBRs can be improved by varying several operating conditions.},
}
@article {pmid33332530,
year = {2021},
author = {Liu, C and Cui, Y and Li, X and Yao, M},
title = {microeco: an R package for data mining in microbial community ecology.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {2},
pages = {},
doi = {10.1093/femsec/fiaa255},
pmid = {33332530},
issn = {1574-6941},
mesh = {Computational Biology ; Data Mining ; Ecology ; *Microbiota ; *Software ; },
abstract = {A large amount of sequencing data is produced in microbial community ecology studies using the high-throughput sequencing technique, especially amplicon-sequencing-based community data. After conducting the initial bioinformatic analysis of amplicon sequencing data, performing the subsequent statistics and data mining based on the operational taxonomic unit and taxonomic assignment tables is still complicated and time-consuming. To address this problem, we present an integrated R package-'microeco' as an analysis pipeline for treating microbial community and environmental data. This package was developed based on the R6 class system and combines a series of commonly used and advanced approaches in microbial community ecology research. The package includes classes for data preprocessing, taxa abundance plotting, venn diagram, alpha diversity analysis, beta diversity analysis, differential abundance test and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis. Each class is designed to provide a set of approaches that can be easily accessible to users. Compared with other R packages in the microbial ecology field, the microeco package is fast, flexible and modularized to use and provides powerful and convenient tools for researchers. The microeco package can be installed from CRAN (The Comprehensive R Archive Network) or github (https://github.com/ChiLiubio/microeco).},
}
@article {pmid33329631,
year = {2020},
author = {Robles-Aguilar, AA and Grunert, O and Hernandez-Sanabria, E and Mysara, M and Meers, E and Boon, N and Jablonowski, ND},
title = {Effect of Applying Struvite and Organic N as Recovered Fertilizers on the Rhizosphere Dynamics and Cultivation of Lupine (Lupinus angustifolius).},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {572741},
pmid = {33329631},
issn = {1664-462X},
abstract = {Intensive agriculture and horticulture heavily rely on the input of fertilizers to sustain food (and feed) production. However, high carbon footprint and pollution are associated with the mining processes of P and K, and the artificial nitrogen fixation for the production of synthetic fertilizers. Organic fertilizers or recovered nutrients from different waste sources can be used to reduce the environmental impact of fertilizers. We tested two recovered nutrients with slow-release patterns as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as a nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in lupine plants. Plant performance was not affected by the fertilizer applied; however, N recovery was higher from the organic fertilizer than from struvite. As root architecture is fundamental for plant productivity, variations in root structure and length as a result of soil nutrient availability driven by plant-bacteria interactions were compared showing also no differences between fertilizers. However, fertilized plants were considerably different in the root length and morphology compared with the no fertilized plants. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed that the fertilizer applied had a significant impact on the associations and functionality of the bacteria inhabiting the growing medium used. The type of fertilizer significantly influenced the interindividual dissimilarities in the most abundant genera between treatments. This means that different plant species have a distinct effect on modulating the associated microbial community, but in the case of lupine, the fertilizer had a bigger effect than the plant itself. These novel insights on interactions between recovered fertilizers, plant, and associated microbes can contribute to developing sustainable crop production systems.},
}
@article {pmid33329472,
year = {2020},
author = {Kohler, TJ and Peter, H and Fodelianakis, S and Pramateftaki, P and Styllas, M and Tolosano, M and de Staercke, V and Schön, M and Busi, SB and Wilmes, P and Washburne, A and Battin, TJ},
title = {Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {591465},
pmid = {33329472},
issn = {1664-302X},
abstract = {Glacier-fed streams (GFSs) exhibit near-freezing temperatures, variable flows, and often high turbidities. Currently, the rapid shrinkage of mountain glaciers is altering the delivery of meltwater, solutes, and particulate matter to GFSs, with unknown consequences for their ecology. Benthic biofilms dominate microbial life in GFSs, and play a major role in their biogeochemical cycling. Mineralization is likely an important process for microbes to meet elemental budgets in these systems due to commonly oligotrophic conditions, and extracellular enzymes retained within the biofilm enable the degradation of organic matter and acquisition of carbon (C), nitrogen (N), and phosphorus (P). The measurement and comparison of these extracellular enzyme activities (EEA) can in turn provide insight into microbial elemental acquisition effort relative to environmental availability. To better understand how benthic biofilm communities meet resource demands, and how this might shift as glaciers vanish under climate change, we investigated biofilm EEA in 20 GFSs varying in glacier influence from New Zealand's Southern Alps. Using turbidity and distance to the glacier snout normalized for glacier size as proxies for glacier influence, we found that bacterial abundance (BA), chlorophyll a (Chl a), extracellular polymeric substances (EPS), and total EEA per gram of sediment increased with decreasing glacier influence. Yet, when normalized by BA, EPS decreased with decreasing glacier influence, Chl a still increased, and there was no relationship with total EEA. Based on EEA ratios, we found that the majority of GFS microbial communities were N-limited, with a few streams of different underlying bedrock geology exhibiting P-limitation. Cell-specific C-acquiring EEA was positively related to the ratio of Chl a to BA, presumably reflecting the utilization of algal exudates. Meanwhile, cell-specific N-acquiring EEA were positively correlated with the concentration of dissolved inorganic nitrogen (DIN), and both N- and P-acquiring EEA increased with greater cell-specific EPS. Overall, our results reveal greater glacier influence to be negatively related to GFS biofilm biomass parameters, and generally associated with greater microbial N demand. These results help to illuminate the ecology of GFS biofilms, along with their biogeochemical response to a shifting habitat template with ongoing climate change.},
}
@article {pmid33329469,
year = {2020},
author = {Shintani, M and Nour, E and Elsayed, T and Blau, K and Wall, I and Jechalke, S and Spröer, C and Bunk, B and Overmann, J and Smalla, K},
title = {Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {590776},
pmid = {33329469},
issn = {1664-302X},
abstract = {IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn501, IS1071, Tn402, or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a mer operon with Tn501-like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.},
}
@article {pmid33329459,
year = {2020},
author = {Ruiz-Lopez, S and Foster, L and Boothman, C and Cole, N and Morris, K and Lloyd, JR},
title = {Identification of a Stable Hydrogen-Driven Microbiome in a Highly Radioactive Storage Facility on the Sellafield Site.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {587556},
pmid = {33329459},
issn = {1664-302X},
abstract = {The use of nuclear power has been a significant part of the United Kingdom's energy portfolio with the Sellafield site being used for power production and more recently reprocessing and decommissioning of spent nuclear fuel activities. Before being reprocessed, spent nuclear fuel is stored in water ponds with significant levels of background radioactivity and in high alkalinity (to minimize fuel corrosion). Despite these challenging conditions, the presence of microbial communities has been detected. To gain further insight into the microbial communities present in extreme environments, an indoor, hyper-alkaline, oligotrophic, and radioactive spent fuel storage pond (INP) located on the Sellafield site was analyzed. Water samples were collected from sample points within the INP complex, and also the purge water feeding tank (FT) that supplies water to the pond, and were screened for the presence of the 16S and 18S rRNA genes to inform sequencing requirements over a period of 30 months. Only 16S rRNA genes were successfully amplified for sequencing, suggesting that the microbial communities in the INP were dominated by prokaryotes. Quantitative Polymerase Chain Reaction (qPCR) analysis targeting 16S rRNA genes suggested that bacterial cells in the order of 10[4]-10[6] mL[-1] were present in the samples, with loadings rising with time. Next generation Illumina MiSeq sequencing was performed to identify the dominant microorganisms at eight sampling times. The 16S rRNA gene sequence analysis suggested that 70% and 91% from of the OTUs samples, from the FT and INP respectively, belonged to the phylum Proteobacteria, mainly from the alpha and beta subclasses. The remaining OTUs were assigned primarily to the phyla Acidobacteria, Bacteroidetes, and, Cyanobacteria. Overall the most abundant genera identified were Hydrogenophaga, Curvibacter, Porphyrobacter, Rhodoferax, Polaromonas, Sediminibacterium, Roseococcus, and Sphingomonas. The presence of organisms most closely related to Hydrogenophaga species in the INP areas, suggests the metabolism of hydrogen as an energy source, most likely linked to hydrolysis of water caused by the stored fuel. Isolation of axenic cultures using a range of minimal and rich media was also attempted, but only relatively minor components (from the phylum Bacteroidetes) of the pond water communities were obtained, emphasizing the importance of DNA-based, not culture-dependent techniques, for assessing the microbiome of nuclear facilities.},
}
@article {pmid33329422,
year = {2020},
author = {Mony, C and Vandenkoornhuyse, P and Bohannan, BJM and Peay, K and Leibold, MA},
title = {A Landscape of Opportunities for Microbial Ecology Research.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {561427},
pmid = {33329422},
issn = {1664-302X},
abstract = {Microbes encompass tremendous biodiversity, provide support to all living forms, including humans, and play an important role in many ecosystem services. The rules that govern microorganism community assembly are increasingly revealed due to key advances in molecular and analytical methods but their understanding remain a key challenge in microbial ecology. The existence of biogeographic patterns within microbial communities has been established and explained in relation to landscape-scale processes, including selection, drift, dispersal and mutation. The effect of habitat patchiness on microorganisms' assembly rules remains though incompletely understood. Here, we review how landscape ecology principles can be adapted to explore new perspectives on the mechanisms that determine microbial community structure. To provide a general overview, we characterize microbial landscapes, the spatial and temporal scales of the mechanisms that drive microbial assembly and the feedback between microorganisms and landscape structure. We provide evidence for the effects of landscape heterogeneity, landscape fragmentation and landscape dynamics on microbial community structure, and show that predictions made for macro-organisms at least partly also apply to microorganisms. We explain why emerging metacommunity approaches in microbial ecology should include explicit characterization of landscape structure in their development and interpretation. We also explain how biotic interactions, such as competition, prey-predator or mutualist relations may influence the microbial landscape and may be involved in the above-mentioned feedback process. However, we argue that the application of landscape ecology to the microbial world cannot simply involve transposing existing theoretical frameworks. This is due to the particularity of these organisms, in terms of size, generation time, and for some of them, tight interaction with hosts. These characteristics imply dealing with unusual and dependent space and time scales of effect. Evolutionary processes have also a strong importance in microorganisms' response to their landscapes. Lastly, microorganisms' activity and distribution induce feedback effects on the landscape that have to be taken into account. The transposition of the landscape ecology framework to microorganisms provides many challenging research directions for microbial ecology.},
}
@article {pmid33329414,
year = {2020},
author = {Mullin, SW and Wanger, G and Kruger, BR and Sackett, JD and Hamilton-Brehm, SD and Bhartia, R and Amend, JP and Moser, DP and Orphan, VJ},
title = {Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {536535},
pmid = {33329414},
issn = {1664-302X},
abstract = {The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57°C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter, Methyloversatilis, and Pseudomonas. Subsequent experimental deployments included a methanogen-dominated stage (Methanobacteriales and Methanomicrobiales) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells.},
}
@article {pmid33323508,
year = {2020},
author = {Brooks, CN and Field, EK},
title = {Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats.},
journal = {mBio},
volume = {11},
number = {6},
pages = {},
pmid = {33323508},
issn = {2150-7511},
mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Fresh Water/chemistry/*microbiology ; Iron/chemistry/*metabolism ; Microbial Interactions ; Microbiota ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.},
}
@article {pmid33321044,
year = {2021},
author = {Peixoto, RS and Sweet, M and Villela, HDM and Cardoso, P and Thomas, T and Voolstra, CR and Høj, L and Bourne, DG},
title = {Coral Probiotics: Premise, Promise, Prospects.},
journal = {Annual review of animal biosciences},
volume = {9},
number = {},
pages = {265-288},
doi = {10.1146/annurev-animal-090120-115444},
pmid = {33321044},
issn = {2165-8110},
mesh = {Animals ; Anthozoa/*microbiology/physiology ; Dinoflagellida ; Microbiota ; *Probiotics ; Symbiosis ; },
abstract = {The use of Beneficial Microorganisms for Corals (BMCs) has been proposed recently as a tool for the improvement of coral health, with knowledge in this research topic advancing rapidly. BMCs are defined as consortia of microorganisms that contribute to coral health through mechanisms that include (a) promoting coral nutrition and growth, (b) mitigating stress and impacts of toxic compounds, (c) deterring pathogens, and (d) benefiting early life-stage development. Here, we review the current proposed BMC approach and outline the studies that have proven its potential to increase coral resilience to stress. We revisit and expand the list of putative beneficial microorganisms associated with corals and their proposed mechanismsthat facilitate improved host performance. Further, we discuss the caveats and bottlenecks affecting the efficacy of BMCs and close by focusing on the next steps to facilitate application at larger scales that can improve outcomes for corals and reefs globally.},
}
@article {pmid33319645,
year = {2020},
author = {Christensen, L and Sørensen, CV and Wøhlk, FU and Kjølbæk, L and Astrup, A and Sanz, Y and Hjorth, MF and Benítez-Páez, A},
title = {Microbial enterotypes beyond genus level: Bacteroides species as a predictive biomarker for weight change upon controlled intervention with arabinoxylan oligosaccharides in overweight subjects.},
journal = {Gut microbes},
volume = {12},
number = {1},
pages = {1847627},
pmid = {33319645},
issn = {1949-0984},
mesh = {Adolescent ; Adult ; Bacteroides/classification/genetics/*growth &amp; development/isolation &amp; purification ; Biomarkers/metabolism ; Body Weight ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Oligosaccharides/*metabolism ; Overweight/*diet therapy/*microbiology/physiopathology ; Xylans/*metabolism ; Young Adult ; },
abstract = {Recent studies indicate that microbial enterotypes may influence the beneficial effects of wholegrain enriched diets including bodyweight regulation. In a 4-week intervention trial, overweight subjects were randomized to consume either arabinoxylan-oligosaccharides (AXOS) (10.4 g/d) from wheat bran or polyunsaturated fatty acids (PUFA) (3.6 g/d). In the present study, we have stratified the subjects participating in the intervention (n = 29) according to the baseline Prevotella-to-Bacteroides (P/B) ratios through a post-hoc analysis and applied a linear mixed model analysis to identify the influence of this P/B ratio on the differences in weight changes in the intervention arms. Following AXOS consumption (n = 15), the high P/B group showed no bodyweight changes [-0.14 kg (95% CI: -0.67; 0.38, p = .59)], while the low P/B group gained 0.65 kg (95% CI: 0.16; 1.14, p = .009). Consequently, a difference of -0.79 kg was found between P/B groups (95% CI: -1.51; -0.08, p = .030). No differences were found between P/B groups following PUFA consumption (0.61 kg, 95% CI: -0.13; 1.35, p = .10). Among the Bacteroides species, B. cellulosilyticus relative abundance exhibited the highest positive rank correlation (Kendall's tau = 0.51, FDR p = .070) with 4-week weight change on AXOS, and such association was further supported by using supervised classification methods (Random Forest). We outlined several carbohydrate-active enzyme (CAZy) genes involved in xylan-binding and degradation to be enriched in B. cellulosilyticus genomes, as well as multiple accessory genes, suggesting a supreme AXOS-derived glycan scavenging role of such species. This post-hoc analysis, ensuring species and strain demarcation at the human gut microbiota, permitted to uncover the predictive role of Bacteroides species over P/B enterotype in weight gain during a fiber-based intervention. The results of this pilot trial pave the way for future assessments on fiber fermentation outputs from Bacteroides species affecting lipid metabolism in the host and with direct impact on adiposity, thus helping to design personalized interventions.},
}
@article {pmid33315910,
year = {2020},
author = {Oyuela Aguilar, M and Gobbi, A and Browne, PD and Ellegaard-Jensen, L and Hansen, LH and Semorile, L and Pistorio, M},
title = {Influence of vintage, geographic location and cultivar on the structure of microbial communities associated with the grapevine rhizosphere in vineyards of San Juan Province, Argentina.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0243848},
pmid = {33315910},
issn = {1932-6203},
mesh = {Argentina ; Bacteria/classification ; Biodiversity ; Climate ; Fungi/classification ; *Geography ; *Microbiota ; *Rhizosphere ; Soil/chemistry ; Vitis/*microbiology ; },
abstract = {Soil microbiomes, as a primary reservoir for plant colonizing fungi and bacteria, play a major role in determining plant productivity and preventing invasion by pathogenic microorganisms. The use of 16S rRNA and ITS high-throughput amplicon sequencing for analysis of complex microbial communities have increased dramatically in recent years, establishing links between wine specificity and, environmental and viticultural factors, which are framed into the elusive terroir concept. Given the diverse and complex role these factors play on microbial soil structuring of agricultural crops, the main aim of this study is to evaluate how external factors, such as vintage, vineyard location, cultivar and soil characteristics, may affect the diversity of the microbial communities present. Additionally, we aim to compare the influence these factors have on the structuring of bacterial and fungal populations associated with Malbec grapevine rhizosphere with that of the more widespread Cabernet Sauvignon grapevine cultivar. Samples were taken from Malbec and Cabernet Sauvignon cultivars from two different vineyards in the San Juan Province of Argentina. Total DNA extracts from the rhizosphere soil samples were sequenced using Illumina's Miseq technology, targeting the V3-V4 hypervariable 16S rRNA region in prokaryotes and the ITS1 region in yeasts. The major bacterial taxa identified were Proteobacteria, Bacteroidetes and Firmicutes, while the major fungal taxa were Ascomycetes, Basidiomycetes, Mortierellomycetes and a low percentage of Glomeromycetes. Significant differences in microbial community composition were found between vintages and vineyard locations, whose soils showed variances in pH, organic matter, and content of carbon, nitrogen, and absorbable phosphorus.},
}
@article {pmid33311714,
year = {2021},
author = {Lee, KS and Pereira, FC and Palatinszky, M and Behrendt, L and Alcolombri, U and Berry, D and Wagner, M and Stocker, R},
title = {Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions.},
journal = {Nature protocols},
volume = {16},
number = {2},
pages = {634-676},
pmid = {33311714},
issn = {1750-2799},
support = {GBMF3783//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; P26127-B20//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; P27831-B28//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 2019-04401//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; },
mesh = {Cell Separation/methods ; Flow Cytometry/*methods ; Genome/genetics ; Genomics/methods ; In Situ Hybridization, Fluorescence/methods ; Isotope Labeling/methods ; Metagenomics/methods ; Microbiota/genetics ; Microfluidics/methods ; Optical Tweezers ; Optogenetics/methods ; Single-Cell Analysis/methods ; Spectrum Analysis, Raman/*methods ; },
abstract = {Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question "who does what?" in complex microbial communities when coupled with fluorescence in situ hybridization or downstream 'omics' analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 ± 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required.},
}
@article {pmid33310220,
year = {2021},
author = {Thwaites, BJ and Stuetz, R and Short, M and Reeve, P and Alvarez-Gaitan, JP and Dinesh, N and Philips, R and van den Akker, B},
title = {Analysis of nitrous oxide emissions from aerobic granular sludge treating high saline municipal wastewater.},
journal = {The Science of the total environment},
volume = {756},
number = {},
pages = {143653},
doi = {10.1016/j.scitotenv.2020.143653},
pmid = {33310220},
issn = {1879-1026},
mesh = {Bioreactors ; Denitrification ; Nitrification ; Nitrogen/analysis ; Nitrous Oxide/analysis ; *Sewage ; Waste Disposal, Fluid ; *Wastewater ; },
abstract = {Conventional activated sludge (CAS)-based wastewater treatment processes have the potential to emit high concentrations of nitrous oxide (N2O) during nitrification and denitrification, which can significantly impact the environmental performance and carbon footprint of wastewater treatment operations. While N2O emissions from CAS have been extensively studied, there is little knowledge of N2O emissions from aerobic granular sludge (AGS) which is now an increasingly popular secondary treatment alternative. The N2O emissions performance of AGS needs to be investigated to ensure that the positive benefits of AGS, such as increased capacity and stable nutrient removal, are not offset by higher emissions. This study quantified N2O emissions from a pilot-scale AGS reactor operated under a range of organic loading rates. A second CAS pilot plant was operated in parallel and under identical loading rates to allow for side-by-side comparison of N2O emissions from floc-based activated sludge. Under low loadings of <0.6 kg COD/m[3]/d the N2O emission factor from AGS and CAS were similar, at around 1.46 ± 0.1% g N2Oemitted/g ammonium loaded. A step increase in the organic loading rate increased N2O emissions from AGS more so than CAS which appeared to be attributed to the reactor feeding strategy that was required for AGS formation. The use of a separate anaerobic feeding phase which was followed by the aeration phase, resulted in extended periods of low dissolved oxygen (DO) concentrations combined with an initial high biomass ammonium loading rate, which favours N2O production and was exacerbated at higher organic loads. Conversely, the combined feeding plus aeration operation (aerobic feed) employed by the CAS system enabled a more even biomass ammonium loading rate and DO supply. This work has shown that while AGS has many operational benefits, the impacts that aeration profile, loading rate and feeding strategy have on N2O emissions must be considered.},
}
@article {pmid33308279,
year = {2020},
author = {Yulandi, A and Suwanto, A and Waturangi, DE and Wahyudi, AT},
title = {Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh.},
journal = {BMC research notes},
volume = {13},
number = {1},
pages = {562},
pmid = {33308279},
issn = {1756-0500},
mesh = {Enterococcus ; *Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Soy Foods ; },
abstract = {OBJECTIVE: Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used to profile the microbial community from fermented food samples. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in estimating microbial community composition. As potential paraprobiotics sources, a comprehensive profiling study of tempeh microbial ecology could contribute to tempeh product development. This study employed a shotgun metagenomic approach, where metagenome fragments from tempeh samples were sequenced directly for taxonomic and functional profiling analysis.<br><br>RESULTS: Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the shotgun metagenomic analysis in all tempeh samples. In terms of composition, this shotgun metagenomic study revealed that Proteobacteria was the most abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed gene based on this metagenomic analysis. The metagenome-assembled genomes (MAGs) results from the binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.},
}
@article {pmid33305821,
year = {2021},
author = {Leininger, A and Yates, MD and Ramirez, M and Kjellerup, B},
title = {Biofilm structure, dynamics, and ecology of an upscaled biocathode wastewater microbial fuel cell.},
journal = {Biotechnology and bioengineering},
volume = {118},
number = {3},
pages = {1305-1316},
doi = {10.1002/bit.27653},
pmid = {33305821},
issn = {1097-0290},
mesh = {*Bioelectric Energy Sources ; *Biofilms ; Electrodes ; *Microbiota ; Wastewater/*microbiology ; },
abstract = {A microbial fuel cell (MFC) system containing modular half-submerged biocathode was operated for 6 months in an 800 L flow-through system with domestic wastewater. For the first time, spatial and temporal differences in biofilm communities were examined on large three-dimensional electrodes in a wastewater MFC. Biocathode microbial community analysis showed a specialized biofilm community with electrogenic and electrotrophic taxa forming during operation, suggesting potentially opposing electrode reactions. The anodic community structure shifted during operation, but no spatial differences were observed along the length of the electrode. Power output from the system was most strongly influenced by pH. Higher power densities were associated with the use of solids-dewatering filtrate with increased organic matter, conductivity, and pH. The results show that the biocathode was the rate-limiting step and that future MFC design should consider the effect of size, shape, and orientation of biocathodes on their community assembly and electrotrophic ability.},
}
@article {pmid33305411,
year = {2021},
author = {Cheng, J and Yang, Y and Yuan, MM and Gao, Q and Wu, L and Qin, Z and Shi, ZJ and Schuur, EAG and Cole, JR and Tiedje, JM and Zhou, J},
title = {Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stability.},
journal = {Molecular ecology},
volume = {30},
number = {4},
pages = {926-937},
doi = {10.1111/mec.15773},
pmid = {33305411},
issn = {1365-294X},
mesh = {Carbon ; Climate Change ; Ecosystem ; *Mycobiome ; *Soil ; Soil Microbiology ; Tundra ; },
abstract = {High-latitude tundra ecosystems are increasingly affected by climate warming. As an important fraction of soil microorganisms, fungi play essential roles in carbon degradation, especially the old, chemically recalcitrant carbon. However, it remains obscure how fungi respond to climate warming and whether fungi, in turn, affect carbon stability of tundra. In a 2-year winter soil warming experiment of 2°C by snow fences, we investigated responses of fungal communities to warming in the active layer of an Alaskan tundra. Although fungal community composition, revealed by the 28S rRNA gene amplicon sequencing, remained unchanged (p > .05), fungal functional gene composition, revealed by a microarray named GeoChip, was altered (p < .05). Changes in functional gene composition were linked to winter soil temperature, thaw depth, soil moisture, and gross primary productivity (canonical correlation analysis, p < .05). Specifically, relative abundances of fungal genes encoding invertase, xylose reductase and vanillin dehydrogenase significantly increased (p < .05), indicating higher carbon degradation capacities of fungal communities under warming. Accordingly, we detected changes in fungal gene networks under warming, including higher average path distance, lower average clustering coefficient and lower percentage of negative links, indicating that warming potentially changed fungal interactions. Together, our study reveals higher carbon degradation capacities of fungal communities under short-term warming and highlights the potential impacts of fungal communities on tundra ecosystem respiration, and consequently future carbon stability of high-latitude tundra.},
}
@article {pmid33304469,
year = {2020},
author = {Bassani, I and Larousse, M and Tran, QD and Attard, A and Galiana, E},
title = {Phytophthora zoospores: From perception of environmental signals to inoculum formation on the host-root surface.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {3766-3773},
pmid = {33304469},
issn = {2001-0370},
abstract = {To explore moist soils and to target host plants, phytopathogenic Phytophthora species utilize the sensory and propulsion capabilities of the biflagellate unicellular zoospores they produce. Zoospore motion and interactions with the microenvironment are of primary importance for Phytophthora physiology. These are also of critical significance for plant pathology in early infection sequential events and their regulation: the directed zoospore migration toward the host, the local aggregation and adhesion at the host penetration site. In the soil, these early events preceding the root colonization are orchestrated by guidance factors, released from the soil particles in water films, or emitted within microbiota and by host plants. This signaling network is perceived by zoospores and results in coordinated behavior and preferential localization in the rhizosphere. Recent computational and structural studies suggest that rhizospheric ion and plant metabolite sensing is a key determinant in driving zoospore motion, orientation and aggregation. To reach their target, zoospores respond to various molecular, chemical and electrical stimuli. However, it is not yet clear how these signals are generated in local soil niches and which gene functions govern the sensing and subsequent responses of zoospores. Here we review studies on the soil, microbial and host-plant factors that drive zoospore motion, as well as the adaptations governing zoospore behavior. We propose several research directions that could be explored to characterize the role of zoospore microbial ecology in disease.},
}
@article {pmid33303324,
year = {2021},
author = {Molderez, TR and Prévoteau, A and Ceyssens, F and Verhelst, M and Rabaey, K},
title = {A chip-based 128-channel potentiostat for high-throughput studies of bioelectrochemical systems: Optimal electrode potentials for anodic biofilms.},
journal = {Biosensors &amp; bioelectronics},
volume = {174},
number = {},
pages = {112813},
doi = {10.1016/j.bios.2020.112813},
pmid = {33303324},
issn = {1873-4235},
mesh = {*Bioelectric Energy Sources ; Biofilms ; *Biosensing Techniques ; Electrodes ; Electron Transport ; *Geobacter ; Reproducibility of Results ; },
abstract = {The presence of microorganisms performing extracellular electron transfer has been established in many environments. Research to determine their role is moving slowly due to the high cost of potentiostats and the variance of data with small number of replicates. Here, we present a 128-channel potentiostat, connected to a 128 gold electrode array. Whereas the system is able to perform simultaneously 128 (bio)electrochemical measurements with an independent electrical signal input, the present manufacturing of the array limited the number of effective channels for this study to 77. We assessed the impact of 11 electrode potentials ranging from -0.45V to +0.2V vs. Ag/AgCl (7 replicates per potential) on the growth and electrochemical characteristics of anodic electroactive biofilms (EABs) formed by acetate-fed microbial communities. After 7 days of growth, maximum current was reached for electrodes poised at -0.3V, closely followed by -0.25V and -0.1V to +0.1V, a range well-fitting the midpoint potential of minerals naturally reduced by electroactive bacteria such as Geobacter Sulfurreducens. There was no significant difference in apparent midpoint potential of the EABs (-0.35V), suggesting that the mechanism of heterogeneous electron transfer was not affected by the electrode potential. The EABs poised below current plateau potential (≤-0.3V) exhibited slower growth but higher charge transfer parameters. The high-throughput and high reproducibility provided by the array may have a major facilitating impact on the field of electromicrobiology. Key aspects to improve are data processing algorithms to deal with the vast amount of generated data, and manufacturing of the electrode array itself.},
}
@article {pmid33297305,
year = {2020},
author = {Nikolausz, M and Kretzschmar, J},
title = {Anaerobic Digestion in the 21st Century.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {7},
number = {4},
pages = {},
pmid = {33297305},
issn = {2306-5354},
abstract = {Despite being a mature biotechnological process, anaerobic digestion is still attracting considerable research attention, mainly due to its versatility both in substrate and product spectra, as well as being a perfect test system for the microbial ecology of anaerobes [...].},
}
@article {pmid33297216,
year = {2021},
author = {Vaezzadeh, V and Thomes, MW and Kunisue, T and Tue, NM and Zhang, G and Zakaria, MP and Affendi, YA and Yap, FC and Chew, LL and Teoh, HW and Lee, CW and Bong, CW},
title = {Examination of barnacles' potential to be used as bioindicators of persistent organic pollutants in coastal ecosystem: A Malaysia case study.},
journal = {Chemosphere},
volume = {263},
number = {},
pages = {128272},
doi = {10.1016/j.chemosphere.2020.128272},
pmid = {33297216},
issn = {1879-1298},
mesh = {Animals ; Ecosystem ; Environmental Biomarkers ; Environmental Monitoring ; Halogenated Diphenyl Ethers/analysis ; *Hydrocarbons, Chlorinated/analysis ; Malaysia ; Persistent Organic Pollutants ; *Pesticides/analysis ; *Polychlorinated Biphenyls/analysis ; *Thoracica ; },
abstract = {Barnacles are ubiquitous in coastal ecosystems of different geographical regions worldwide. This is the first study attempting to assess the suitability of barnacles as bioindicators of persistent organic pollutants (POPs) in coastal environments. Barnacles were collected from the coasts around Peninsular Malaysia and analyzed for POPs including polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and organochlorine pesticides (OCPs). Among POPs, PCBs showed the highest concentrations with elevated contributions of CB28 and CB153. As for PBDEs, BDE47 was the most frequently detected congener, while BDE209 was detected in barnacles from two stations in Port Klang and the levels reached up to >70% of total PBDE concentrations. Concentrations of OCPs detected in barnacles were in the order of CHLs > DDTs > HCHs > HCB and 4,4'-DDE and cis- and trans-chlordane were the predominant OCP compounds. A comparison with previous studies in Malaysia showed consistent levels of POPs. Green mussels collected from selected barnacles' habitats, for the sake of a comparison, showed almost similar profiles but lower concentrations of POPs. The spatial distribution of POPs observed in barnacles and comparison of POP levels and profiles with mussels indicated that barnacles can be useful bioindicators for monitoring POPs contamination in the coastal ecosystems.},
}
@article {pmid33296424,
year = {2020},
author = {Fiedler, S and Wünnemann, H and Hofmann, I and Theobalt, N and Feuchtinger, A and Walch, A and Schwaiger, J and Wanke, R and Blutke, A},
title = {A practical guide to unbiased quantitative morphological analyses of the gills of rainbow trout (Oncorhynchus mykiss) in ecotoxicological studies.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0243462},
pmid = {33296424},
issn = {1932-6203},
mesh = {Animals ; Female ; Gills/*anatomy &amp; histology/drug effects/physiology/ultrastructure ; Male ; Microscopy, Fluorescence ; Oncorhynchus mykiss/*anatomy &amp; histology/physiology ; Reproducibility of Results ; Water Pollutants, Chemical/chemistry/*toxicity ; },
abstract = {Rainbow trout (Oncorhynchus mykiss) are frequently used as experimental animals in ecotoxicological studies, in which they are experimentally exposed to defined concentrations of test substances, such as heavy metals, pesticides, or pharmaceuticals. Following exposure to a broad variety of aquatic pollutants, early morphologically detectable toxic effects often manifest in alterations of the gills. Suitable methods for an accurate and unbiased quantitative characterization of the type and the extent of morphological gill alterations are therefore essential prerequisites for recognition, objective evaluation and comparison of the severity of gill lesions. The aim of the present guidelines is to provide practicable, standardized and detailed protocols for the application of unbiased quantitative stereological analyses of relevant morphological parameters of the gills of rainbow trout. These gill parameters inter alia include the total volume of the primary and secondary gill lamellae, the surface area of the secondary gill lamellae epithelium (i.e., the respiratory surface) and the thickness of the diffusion barrier. The featured protocols are adapted to fish of frequently used body size classes (300-2000 g). They include well-established, conventional sampling methods, probes and test systems for unbiased quantitative stereological analyses of light- and electron microscopic 2-D gill sections, as well as the application of modern 3-D light sheet fluorescence microscopy (LSFM) of optically cleared gill samples as an innovative, fast and efficient quantitative morphological analysis approach. The methods shown here provide a basis for standardized and representative state-of-the-art quantitative morphological analyses of trout gills, ensuring the unbiasedness and reproducibility, as well as the intra- and inter-study comparability of analyses results. Their broad implementation will therefore significantly contribute to the reliable identification of no observed effect concentration (NOEC) limits in ecotoxicological studies and, moreover, to limit the number of experimental animals by reduction of unnecessary repetition of experiments.},
}
@article {pmid33295059,
year = {2021},
author = {Li, J and Bååth, E and Pei, J and Fang, C and Nie, M},
title = {Temperature adaptation of soil microbial respiration in alpine, boreal and tropical soils: An application of the square root (Ratkowsky) model.},
journal = {Global change biology},
volume = {27},
number = {6},
pages = {1281-1292},
doi = {10.1111/gcb.15476},
pmid = {33295059},
issn = {1365-2486},
support = {2020M670975//The Postdoctoral Science Foundation of China/ ; 31830009//The National Science Foundation of China/ ; 32030067//The National Science Foundation of China/ ; 91951112//The National Science Foundation of China/ ; 2020PJD003//The Shanghai Pujiang Program/ ; },
mesh = {Carbon ; China ; Ecosystem ; Respiration ; *Soil ; *Soil Microbiology ; Temperature ; },
abstract = {Warming is expected to stimulate soil microbial respiration triggering a positive soil carbon-climate feedback loop while a consensus remains elusive regarding the magnitude of this feedback. This is partly due to our limited understanding of the temperature-adaptive response of soil microbial respiration, especially over broad climatic scales. We used the square root (Ratkowsky) model to calculate the minimum temperature for soil microbial respiration (Tmin , which describes the temperature adaptation of soil microbial respiration) of 298 soil samples from alpine grasslands on the Tibetan Plateau and forest ecosystems across China with a mean annual temperature (MAT) range from -6°C to +25°C. The instantaneous soil microbial respiration was determined between 4°C and 28°C. The square root model could well fit the temperature effect on soil microbial respiration for each individual soil, with R[2] higher than 0.98 for all soils. Tmin ranged from -8.1°C to -0.1°C and increased linearly with increasing MAT (R[2] = 0.68). MAT dominantly regulated Tmin variation when accounting simultaneously for multiple other drivers (mean annual precipitation, soil pH and carbon quality); an independent experiment showed that carbon availability had no significant effect on Tmin . Using the relationship between Tmin and MAT, soil microbial respiration after an increased MAT could be estimated, resulting in a relative increase in respiration with decreasing MAT. Thus, soil microbial respiration responses are adapted to long-term temperature differences in MAT. We suggest that Tmin = -5 + 0.2 × MAT, that is, every 1°C rise in MAT is estimated to increase Tmin of respiration by approximately 0.2°C, could be used as a first approximation to incorporate temperature adaptation of soil microbial respiration in model predictions. Our results can be used to predict future changes in the response of soil microbial respiration to temperature over different levels of warming and across broad geographic scales with different MAT.},
}
@article {pmid33294135,
year = {2020},
author = {Tobias, NJ and Eberhard, FE and Guarneri, AA},
title = {Enzymatic biosynthesis of B-complex vitamins is supplied by diverse microbiota in the Rhodnius prolixus anterior midgut following Trypanosoma cruzi infection.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {3395-3401},
pmid = {33294135},
issn = {2001-0370},
abstract = {Trypanosoma cruzi, the causative agent of Chagas disease, colonizes the gut of triatomine insects, including Rhodnius prolixus. It is believed that this colonization upsets the microbiota that are normally present, presumably switching the environment to one more favorable for parasite survival. It was previously thought that one particular bacterium, Rhodococcus rhodnii, was essential for insect survival due to its ability to produce vital B-complex vitamins. However, these bacteria are not always identified in great abundance in studies on R. prolixus microbiota. Here we sequenced the microbiota of the insect anterior midgut using shotgun metagenomic sequencing in order to obtain a high-resolution snapshot of the microbes inside at two different time points and under two conditions; in the presence or absence of parasite and immediately following infection, or three days post-infection. We identify a total of 217 metagenomic bins, and recovered one metagenome-assembled genome, which we placed in the genus Dickeya. We show that, despite Rhodococcus being present, it is not the only microbe capable of synthesizing B-complex vitamins, with the genes required for biosynthesis present in a number of different microbes. This work helps to gain a new insight into the microbial ecology of R. prolixus.},
}
@article {pmid33292591,
year = {2020},
author = {Zhang, W and Bao, C and Wang, J and Zang, J and Cao, Y},
title = {Administration of Saccharomyces boulardii mafic-1701 improves feed conversion ratio, promotes antioxidant capacity, alleviates intestinal inflammation and modulates gut microbiota in weaned piglets.},
journal = {Journal of animal science and biotechnology},
volume = {11},
number = {1},
pages = {112},
pmid = {33292591},
issn = {1674-9782},
abstract = {BACKGROUND: Probiotics are used as a means to improve animal health and intestinal development. Saccharomyces boulardii is a well-known probiotic; however, few studies have examined the effects of S. boulardii on weaned piglet performance. Therefore, this 28-day study compared the effects of S. boulardii mafic-1701 and aureomycin in diets for weaned piglets on growth performance, antioxidant parameters, inflammation and intestinal microbiota. One hundred and eight piglets, weaned at 28 d of age (8.5 ± 1.1 kg), were randomly divided into the three dietary treatment groups with six pens and six piglets per pen (half male and half female). The dietary treatment groups were as follows: 1) basal diet (CON); 2) basal diet supplemented with 75 mg/kg aureomycin (ANT); 3) basal diet supplemented with 1 × 10[8] CFU/kg S. boulardii mafic-1701 (SB).<br><br>RESULTS: Compared to CON group, SB group had higher feed efficiency (P&#x2009;<&#x2009;0.05) in the last 14&#x2009;d and lower diarrhea rate (P&#x2009;<&#x2009;&#xa0;0.05) over the entire 28&#x2009;d. Total superoxide dismutase in serum was markedly increased in SB group (P&#x2009;<&#x2009;0.05). Moreover, compared with CON group, SB group decreased the levels of pro-inflammatory cytokines interleukin-6 (P&#x2009;<&#x2009;&#xa0;0.01) and Tumor necrosis factor-&#x3b1; (P&#x2009;<&#x2009;0.05) in jejunum. Supplementation of S. boulardii mafic-1701 increased the abundance of Ruminococcaceae_UCG_009 and Turicibacter (P&#x2009;<&#x2009;0.05), whereas the abundance of unclassified_Clostridiaceae_4 was decreased (P&#x2009;<&#x2009;0.05). Furthermore, S. boulardii mafic-1701 administration increased cecal concentration of microbial metabolites, isobutyrate and valerate (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: The improvement in feed conversion ratio, reduction in diarrhea rate in weaned piglets provided diets supplemented with S. boulardii mafic-1701 may be associated with enhanced antioxidant activity, anti-inflammatory responses and improved intestinal microbial ecology.},
}
@article {pmid33290744,
year = {2020},
author = {Songailiene, I and Juozapaitis, J and Tamulaitiene, G and Ruksenaite, A and Šulčius, S and Sasnauskas, G and Venclovas, &#x10c; and Siksnys, V},
title = {HEPN-MNT Toxin-Antitoxin System: The HEPN Ribonuclease Is Neutralized by OligoAMPylation.},
journal = {Molecular cell},
volume = {80},
number = {6},
pages = {955-970.e7},
doi = {10.1016/j.molcel.2020.11.034},
pmid = {33290744},
issn = {1097-4164},
mesh = {Adenosine Monophosphate/genetics ; Antidotes/chemistry ; Antitoxins/*genetics/metabolism ; Aphanizomenon/chemistry/genetics ; Bacterial Toxins/*genetics ; CRISPR-Cas Systems/genetics ; Nucleotidyltransferases/genetics/metabolism ; Ribonucleases/*genetics/metabolism ; Toxin-Antitoxin Systems/*genetics ; Tyrosine/genetics ; },
abstract = {Prokaryotic toxin-antitoxin (TA) systems are composed of a toxin capable of interfering with key cellular processes and its neutralizing antidote, the antitoxin. Here, we focus on the HEPN-MNT TA system encoded in the vicinity of a subtype I-D CRISPR-Cas system in the cyanobacterium Aphanizomenon flos-aquae. We show that HEPN acts as a toxic RNase, which cleaves off 4 nt from the 3' end in a subset of tRNAs, thereby interfering with translation. Surprisingly, we find that the MNT (minimal nucleotidyltransferase) antitoxin inhibits HEPN RNase through covalent di-AMPylation (diadenylylation) of a conserved tyrosine residue, Y109, in the active site loop. Furthermore, we present crystallographic snapshots of the di-AMPylation reaction at different stages that explain the mechanism of HEPN RNase inactivation. Finally, we propose that the HEPN-MNT system functions as a cellular ATP sensor that monitors ATP homeostasis and, at low ATP levels, releases active HEPN toxin.},
}
@article {pmid33289627,
year = {2021},
author = {Hofmann, K and Woller, A and Huptas, C and Wenning, M and Scherer, S and Doll, EV},
title = {Pseudomonas cremoris sp. nov., a novel proteolytic species isolated from cream.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {71},
number = {1},
pages = {},
doi = {10.1099/ijsem.0.004597},
pmid = {33289627},
issn = {1466-5034},
mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Genes, Bacterial ; Germany ; Milk/*microbiology ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Proteolysis ; Pseudomonas/*classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Ubiquinone/chemistry ; },
abstract = {During a study investigating the microbiota of raw milk and its semi-finished products, strains WS 5106[T] and WS 5096 were isolated from cream and skimmed milk concentrate. They could be assigned to the genus Pseudomonas by their 16S rRNA sequences, but not to any validly named species. In this work, a polyphasic approach was used to characterize the novel strains and to investigate their taxonomic status. Examinations based on the topology of core genome phylogenomy as well as average nucleotide identity (ANIm) comparisons suggested a novel Pseudomonas species within the Pseudomonas fluorescens subgroup. With pairwise ANIm values of 90.1 and 89.8 %, WS 5106[T] was most closely related to Pseudomonas nabeulensis CECT 9765[T] and Pseudomonas kairouanensis CECT 9766[T]. The G+C content of strain WS 5106[T] was 60.1 mol%. Morphologic analyses revealed Gram-stain-negative, aerobic, catalase and oxidase positive, rod-shaped and motile cells. Proteolysis on skimmed milk agar as well as lipolysis on tributyrin agar occurred at both 28 and 6 °C. Tolerated growth conditions were temperatures between 4 and 34 °C, pH values between 6.0 and 8.0, and salt concentrations of up to 5 %. Fatty acid profiles showed a pattern typical for Pseudomonas, with C16 : 0 as the dominant component. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol and the dominating quinone was Q-9. Based on these results, it is proposed to classify the strains as a novel species, Pseudomonas cremoris sp. nov., with WS 5106[T] (=DSM 111143[T]=LMG 31863[T]) as type strain and WS 5096 (=DSM 111129=LMG 31864) as an additional strain.},
}
@article {pmid33289410,
year = {2020},
author = {Zhu, M and Ji, J and Duan, X and Li, Y},
title = {First Report of Golovinomyces cichoracearum Causing Powdery Mildew on Zinnia elegans in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-11-20-2333-PDN},
pmid = {33289410},
issn = {0191-2917},
abstract = {Zinnia elegans, common zinnia, is an annual plant with highly ornamental values. It is widely planted in many nurseries, city parks, universities and home gardens in China. From August to October 2020, powdery mildew-like signs and symptoms were observed on leaves of Z. elegans growing on the campus of Henan Normal University, Henan Province, China. White powdery colonies in circular- or irregularly shaped-lesions were abundant on both surfaces of leaves and covered up to 95 % of the leaf area. Any infected leaves were chlorotic, deformed or senescence. More than 70 % of the monitored Z. elegans plants showed these signs and symptoms. Conidiophores (n = 20) were 100 to 200 × 9 to 13 μm and composed of foot cells, followed by straight cells and conidia. Mycelial appressoria were single and nipple-shaped. The oval-shaped conidia (n = 30) were 22 to 36 × 12 to 18 μm, with a length/width ratio of 1.4 to 2.7, and produced germ tubes from the polar ends of the spore. No chasmothecia were found. Based on these morphological characteristics, the pathogen was initially identified morphologically as Golovinomyces cichoracearum (Braun and Cook 2012). Structures of the pathogen were scraped from infected leaves and total genomic DNA was isolated using the method previously described by Zhu et al. (2019). The internal transcribed spacer (ITS) region of rDNA was amplified by PCR using the primers ITS1/ITS4 (White et al. 1990) and the amplicon was sequenced by Invitrogen (Shanghai, China). The sequence for the fungus was deposited into GenBank under Accession No. MW029904 and was 99.83 % identical (595/596 bp) to G. cichoracearum on Symphyotrichum novi-belgii (HM769725)(Mørk et al. 2011). To perform pathogenicity analysis, leaf surfaces of five healthy plants were fixed in a settling tower and then inoculated by blowing fungal conidia from mildew-infested leaves using pressurized air. Five non-inoculated plants served as a control. The inoculated and non-inoculated plants were separately maintained in two growth chambers (humidity, 60 %; light/dark, 16 h/8 h; temperature, 18 ℃). Eleven- to twelve-days post-inoculation, powdery mildew signs were conspicuous on inoculated plants, while control plants remained healthy. Similar results were obtained by conducting two repeated pathogenicity assays. Thus, based on the morphological characteristics and molecular analysis, the pathogen was identified and confirmed as G. cichoracearum. This pathogen has been reported on Z. elegans in India, Israel, Jordan, Korea, Nepal, Sri Lanka, Switzerland, and Turkey (Farr and Rossman 2020). To our best knowledge, this is the first report of G. cichoracearum on Z. elegans in China. The sudden outbreak of powdery mildew caused by G. cichoracearum on Z. elegans may adversely impact the plant health and ornamental value in China. Therefore, the confirmation of G. cichoracearum infecting Z. elegans expands the understanding of this pathogen and provides the fundamental knowledge for future powdery mildew control.},
}
@article {pmid33288837,
year = {2020},
author = {Busti, S and Rossi, B and Volpe, E and Ciulli, S and Piva, A and D'Amico, F and Soverini, M and Candela, M and Gatta, PP and Bonaldo, A and Grilli, E and Parma, L},
title = {Effects of dietary organic acids and nature identical compounds on growth, immune parameters and gut microbiota of European sea bass.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21321},
pmid = {33288837},
issn = {2045-2322},
mesh = {Animals ; Bass/*metabolism ; Biodiversity ; Gastrointestinal Microbiome/genetics/*physiology ; High-Throughput Nucleotide Sequencing ; Interleukin-10/metabolism ; Interleukin-8/metabolism ; Transforming Growth Factor beta/metabolism ; },
abstract = {A 71-day study was conducted to explore the effect of increasing dietary levels (0, 250, 500, 1000 mg kg feed[-1]; D0, D250, D500 and D1000, respectively) of a blend of microencapsulated organic acids (OA, specifically citric and sorbic acid) and nature identical compounds (NIC, specifically thymol and vanillin), on growth, intestinal immune parameters and gut microbiota (GM) of European sea bass juveniles reared under normal and subsequently suboptimal environmental conditions (high temperature, 30.0 ± 0.4 °C and low oxygen, 4.6 ± 0.6 mg L[-1]). OA and NIC did not promote growth, feed utilisation and feed intake at the inclusion tested but induced a significantly upregulation of IL-8, IL-10 and TGFβ. GM analyzed by next-generation sequencing showed that OA and NIC were able to exert prebiotic properties stimulating the development of beneficial bacteria taxa such as Lactobacillus, Leuconostoc, and Bacillus sp. Picrust analyses displayed a significant potential functional reconfiguration of GM promoting a decrease in inflammation-promoting and homeostatic functions at increasing OA and NIC administration. For the first time on this species the exposure to suboptimal rearing conditions was able to modify GM structure reducing LAB and increasing Proteobacteria, findings which were consistent with the inflammatory process observed at mRNA level.},
}
@article {pmid33282266,
year = {2020},
author = {Zhao, L and Li, X and Yang, Q and Zhuang, D and Pan, X and Li, L},
title = {Adsorption kinetics and mechanism of di-n-butyl phthalate by Leuconostoc mesenteroides.},
journal = {Food science &amp; nutrition},
volume = {8},
number = {11},
pages = {6153-6163},
pmid = {33282266},
issn = {2048-7177},
abstract = {Di-n-butyl phthalate (DBP) poses a risk to humans as a ubiquitous environmental contaminant. A strain of Leuconostoc mesenteroides DM12 was chosen from lactic acid bacteria strains to study the DBP binding mechanisms. Adsorption of DBP by strain DM12 reached the highest binding rate of 87% after 11 hr of incubation, which could be explained by pseudo-second-order kinetics. The adsorption isotherm coincided with the model of Langmuir-Freundlich, indicating physical and chemical adsorption processes involved. Further, NaIO4 and TCA treatments were used to analyze the DBP binding mechanism of strain DM12, which indicated that peptidoglycan on the bacterial cell wall was involved in the process. The O-H, C-O, and N-H bonds were possibly involved in the binding process as the main functional groups.},
}
@article {pmid33281127,
year = {2020},
author = {Nakajima, Y and Kojima, K and Kashiyama, Y and Doi, S and Nakai, R and Sudo, Y and Kogure, K and Yoshizawa, S},
title = {Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins.},
journal = {Microbes and environments},
volume = {35},
number = {4},
pages = {},
pmid = {33281127},
issn = {1347-4405},
mesh = {Actinobacteria/chemistry/genetics/*metabolism/radiation effects ; Bacterial Proteins/*genetics/metabolism ; Biosynthetic Pathways ; Chromatography, High Pressure Liquid ; Light ; Rhodopsin/*biosynthesis/chemistry ; Tandem Mass Spectrometry ; },
abstract = {Microbial rhodopsins, comprising a protein moiety (rhodopsin apoprotein) bound to the light-absorbing chromophore retinal, function as ion pumps, ion channels, or light sensors. However, recent genomic and metagenomic surveys showed that some rhodopsin-possessing prokaryotes lack the known genes for retinal biosynthesis. Since rhodopsin apoproteins cannot absorb light energy, rhodopsins produced by prokaryotic strains lacking genes for retinal biosynthesis are hypothesized to be non-functional in cells. In the present study, we investigated whether Aurantimicrobium minutum KNC[T], which is widely distributed in terrestrial environments and lacks any previously identified retinal biosynthesis genes, possesses functional rhodopsin. We initially measured ion transport activity in cultured cells. A light-induced pH change in a cell suspension of rhodopsin-possessing bacteria was detected in the absence of exogenous retinal. Furthermore, spectroscopic analyses of the cell lysate and HPLC-MS/MS analyses revealed that this strain contained an endogenous retinal. These results confirmed that A. minutum KNC[T] possesses functional rhodopsin and, hence, produces retinal via an unknown biosynthetic pathway. These results suggest that rhodopsin-possessing prokaryotes lacking known retinal biosynthesis genes also have functional rhodopsins.},
}
@article {pmid33279744,
year = {2021},
author = {Agrawal, S and Weissbrodt, DG and Annavajhala, M and Jensen, MM and Arroyo, JMC and Wells, G and Chandran, K and Vlaeminck, SE and Terada, A and Smets, BF and Lackner, S},
title = {Time to act-assessing variations in qPCR analyses in biological nitrogen removal with examples from partial nitritation/anammox systems.},
journal = {Water research},
volume = {190},
number = {},
pages = {116604},
doi = {10.1016/j.watres.2020.116604},
pmid = {33279744},
issn = {1879-2448},
mesh = {*Ammonium Compounds ; Bacteria/genetics ; Bioreactors ; Denitrification ; *Microbiota ; Nitrification ; Nitrogen ; Oxidation-Reduction ; },
abstract = {Quantitative PCR (qPCR) is broadly used as the gold standard to quantify microbial community fractions in environmental microbiology and biotechnology. Benchmarking efforts to ensure the comparability of qPCR data for environmental bioprocesses are still scarce. Also, for partial nitritation/anammox (PN/A) systems systematic investigations are still missing, rendering meta-analysis of reported trends and generic insights potentially precarious. We report a baseline investigation of the variability of qPCR-based analyses for microbial communities applied to PN/A systems. Round-robin testing was performed for three PN/A biomass samples in six laboratories, using the respective in-house DNA extraction and qPCR protocols. The concentration of extracted DNA was significantly different between labs, ranged between 2.7 and 328 ng mg[-1] wet biomass. The variability among the qPCR abundance data of different labs was very high (1-7 log fold) but differed for different target microbial guilds. DNA extraction caused maximum variation (3-7 log fold), followed by the primers (1-3 log fold). These insights will guide environmental scientists and engineers as well as treatment plant operators in the interpretation of qPCR data.},
}
@article {pmid33279588,
year = {2021},
author = {Huang, L and Duan, C and Xia, X and Wang, H and Wang, Y and Zhong, Z and Wang, B and Ding, W and Yang, Y},
title = {Commensal microbe-derived propionic acid mediates juvenile social isolation-induced social deficits and anxiety-like behaviors.},
journal = {Brain research bulletin},
volume = {166},
number = {},
pages = {161-171},
doi = {10.1016/j.brainresbull.2020.12.001},
pmid = {33279588},
issn = {1873-2747},
mesh = {Animals ; Anxiety/*metabolism ; Behavior, Animal ; Gastrointestinal Microbiome/*physiology ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Prefrontal Cortex/*metabolism ; Propionates/*metabolism ; Receptors, Oxytocin/*metabolism ; *Social Isolation ; },
abstract = {Social experiences during early life are thought to be critical for proper social and emotional development. Conversely, social insults during development causes long-lasting behavioral abnormalities later in life. However, how juvenile social deprivation influences social and emotional behaviors remains poorly understood. Here, we show that juvenile social isolation induces a shift in microbial ecology that negatively impacts social and emotional behaviors in adulthood. These behavioral changes, which occur during this critical period are transferable to antibiotic pre-treated mice by fecal microbiota transplant. In addition, juvenile social isolation decreases the expression of oxytocin receptor (OXTR) in the medial prefrontal cortex (mPFC), and increases the amounts of fecal propionic acid (PA), a short-chain fatty acid derived from gut micobiota. Accordingly, infusion with an OXTR antagonist (OXTR-A, l-368,899) specifically in the mPFC or supplementation of PA both can cause social deficits and anxiety-like behaviors in group housed mice. Collectively, our findings reveal that juvenile social experience regulates prefrontal cortical OXTR expression through gut microbiota-produced PA and that is essential for normal social and emotional behaviors, thus providing a cellular and molecular context to understand the consequences of juvenile social deprivation.},
}
@article {pmid33279067,
year = {2021},
author = {Kim, E and Cho, EJ and Yang, SM and Kim, MJ and Kim, HY},
title = {Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing.},
journal = {Food microbiology},
volume = {94},
number = {},
pages = {103641},
doi = {10.1016/j.fm.2020.103641},
pmid = {33279067},
issn = {1095-9998},
mesh = {Bacteria/chemistry/classification/genetics/*isolation &amp; purification ; Brassica/*microbiology ; Fermentation ; Fermented Foods/*microbiology ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Vegetables/microbiology ; Yeasts/classification/genetics/*isolation &amp; purification/metabolism ; },
abstract = {Complex interactions occur within microbial communities during the fermentation process of kimchi. Identification of these microorganisms provides the essential information required to improve food quality and to understand their role in this process. This was the first study to compare two methods for accuracy in the identification of microbial community changes during the fermentation of kimchi by comparing a culture-dependent (MALDI-TOF MS analysis) and a culture-independent method (high-throughput sequencing) of 16S rRNA gene fragment). Members of the Lactobacillus-related genera, Leuconostoc, and Weissella were identified as the predominant microorganisms by both methods. The culture-independent method was able to additionally identify non-lactic acid bacteria and yeasts, such as Kazachstania in kimchi. However, high-throughput sequencing failed to accurately recognize Latilactobacillus sakei, Latilactobacillus curvatus, Lactiplantibacillus plantarum, and W. cibaria, which played an important role in kimchi fermentation, as this method only allowed for identification at the genus level. Conversely, MALDI-TOF MS analysis could identify the isolates at the species level. Also, culture-dependent method could identify predominant species in viable cell communities. The culture-dependent method and culture-independent method provided complementary information by producing a more comprehensive view of the microbial ecology in fermented kimchi.},
}
@article {pmid33277271,
year = {2021},
author = {Van Herreweghen, F and De Paepe, K and Marzorati, M and Van de Wiele, T},
title = {Mucin as a Functional Niche is a More Important Driver of in Vitro Gut Microbiota Composition and Functionality than Supplementation of Akkermansia m uciniphila.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {4},
pages = {},
pmid = {33277271},
issn = {1098-5336},
abstract = {IMPORTANCE SECTION Research into identification of biomarkers for gut health and ways to modulate the microbiota composition and activity to improve health, has put Akkermansia muciniphila in the spotlight. As a mucin degrader, A. muciniphila colonizes the interesting but not-fully described host-glycan degradation niche., . Plenty of research concerning A. muciniphila has been done, but little is known about its behavior in the complex microbial ecosystem in the colon, about the potential role of mucins to influence A. muciniphila behavior and the impact of its probiotic administration on the microbial ecosystem.This study aimed at investigating the impact of A. muciniphila administration on the endogenous community while also taking into account its nutritional specificity. As such, the effect of A.mucinihpila administration was investigated with and without addition of mucin. This allowed us to elucidate the importance of mucin presence to modulate the efficiency of the probiotic supplementation with A. muciniphila Akkermansia muciniphila is an abundantly present commensal mucin degrading gut bacterium (1 - 4%) , widely distributed among healthy individuals. It has been positioned as a health biomarker and is currently explored as a biotherapeutic agent and next generation probiotic. Preliminary and ongoing research is mostly based on in vivo mouse models and human intervention trials. While these allow the assessment of physiologically relevant endpoints, the analysis of fecal samples presents limitations with respect to the in-depth mechanistic characterization of Akkermansia effects at the level of the microbiome. We aimed to evaluate the effect of A. muciniphila treatment on the endogenous community from four different donors in a validated, controlled in vitro model of the gut microbial ecosystem (SHIME). Taking into account the nutritional specificity of A. muciniphila, and the prebiotic-like action of mucins in the colon environment, the interplay between mucin, A. muciniphila and the endogenous community was investigated. The effects on the microbial community composition and functionality of A. muciniphila supplementation without mucin were limited, whereas mucin addition successfully induced compositional and metabolic changes in the gut microbiota. Indeed, mucin addition resulted in significantly higher acetate, propionate and butyrate production for all four donors, and the increase of several species, including A. muciniphila, Ruminococcus, Clostridium cluster XIVa, and Lachnospiraceae This study revealed that the supplementation of A. muciniphila together with mucin limited the observed prebiotic-like effect of mucin in inducing compositional changes.},
}
@article {pmid33274397,
year = {2021},
author = {Bien, T and Hambleton, EA and Dreisewerd, K and Soltwisch, J},
title = {Molecular insights into symbiosis-mapping sterols in a marine flatworm-algae-system using high spatial resolution MALDI-2-MS imaging with ion mobility separation.},
journal = {Analytical and bioanalytical chemistry},
volume = {413},
number = {10},
pages = {2767-2777},
pmid = {33274397},
issn = {1618-2650},
support = {Drei2/018/17//Interdisciplinary Center for Clinical Research, M&#xfc;nster, Germany/ ; SO976/5-1, project number 400912714//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Dinoflagellida/*chemistry/physiology ; Ion Mobility Spectrometry/methods ; Platyhelminths/*chemistry/physiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Sterols/*analysis/metabolism ; Symbiosis ; },
abstract = {Waminoa sp. acoel flatworms hosting Symbiodiniaceae and the related Amphidinium dinoflagellate algae are an interesting model system for symbiosis in marine environments. While the host provides a microhabitat and safety, the algae power the system by photosynthesis and supply the worm with nutrients. Among these nutrients are sterols, including cholesterol and numerous phytosterols. While it is widely accepted that these compounds are produced by the symbiotic dinoflagellates, their transfer to and fate within the sterol-auxotrophic Waminoa worm host as well as their role in its metabolism are unknown. Here we used matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging combined with laser-induced post-ionization and trapped ion mobility spectrometry (MALDI-2-TIMS-MSI) to map the spatial distribution of over 30 different sterol species in sections of the symbiotic system. The use of laser post-ionization crucially increased ion yields and allowed the recording of images with a pixel size of 5 μm. Trapped ion mobility spectrometry (TIMS) helped with the tentative assignment of over 30 sterol species. Correlation with anatomical features of the worm, revealed by host-derived phospholipid signals, and the location of the dinoflagellates, revealed by chlorophyll a signal, disclosed peculiar differences in the distribution of different sterol species (e.g. of cholesterol versus stigmasterol) within the receiving host. These findings point to sterol species-specific roles in the metabolism of Waminoa beyond a mere source of energy. They also underline the value of the MALDI-2-TIMS-MSI method to future research in the spatially resolved analysis of sterols.},
}
@article {pmid33272988,
year = {2020},
author = {Singh, RP and Johri, AK and Dua, M},
title = {Metagenomic Analysis of Microbial Diversity in Cotton Rhizosphere Soil in Alwar, India.},
journal = {Microbiology resource announcements},
volume = {9},
number = {49},
pages = {},
pmid = {33272988},
issn = {2576-098X},
abstract = {Cotton is an important cash crop for both the Indian economy and rural livelihoods. In the present study, metagenomic analysis is used to characterize microbial diversity in cotton rhizosphere soil from the Alwar district, located in the semiarid northeast region of the state of Rajasthan in India.},
}
@article {pmid33266447,
year = {2020},
author = {Martucci, M and Conte, M and Bucci, L and Giampieri, E and Fabbri, C and Palmas, MG and Izzi, M and Salvioli, S and Zambrini, AV and Orsi, C and Brigidi, P and Santoro, A and Capri, M and Monti, D and Franceschi, C},
title = {Twelve-Week Daily Consumption of ad hoc Fortified Milk with ω-3, D, and Group B Vitamins Has a Positive Impact on Inflammaging Parameters: A Randomized Cross-Over Trial.},
journal = {Nutrients},
volume = {12},
number = {11},
pages = {},
pmid = {33266447},
issn = {2072-6643},
support = {00088MI01//Italian Ministry of Agriculture/ ; },
mesh = {Aged ; Aged, 80 and over ; Animals ; Cross-Over Studies ; Double-Blind Method ; Fatty Acids, Omega-3/*administration &amp; dosage ; Female ; *Food, Fortified ; Health Status ; Humans ; Inflammation/*epidemiology ; Male ; Micronutrients/blood ; Middle Aged ; *Milk ; Placebos ; Vitamin B Complex/*administration &amp; dosage ; Vitamin D/administration &amp; dosage/*analogs &amp; derivatives ; },
abstract = {BACKGROUND AND AIM: A state of chronic, subclinical inflammation known as inflammaging is present in elderly people and represents a risk factor for all age-related diseases. Dietary supplementation with ad hoc fortified foods seems an appealing strategy to counteract inflammaging. The purpose of this study was to test the efficacy of elderly-tailored fortified milk on inflammaging and different health parameters.<br><br>METHODS: A double-blind randomized cross-over study was performed on forty-eight volunteers aged 63-80 years. The fortified milk was enriched with &#x3c9;-3 polyunsaturated fatty acids (eicosapentaenoic acid, EPA; docosahexaenoic acid, DHA), vitamins (25-hydroxyvitamin D, E, C, B6, B9, B12), and trace elements (zinc, selenium). The two intervention periods lasted for 12 weeks, with a 16-week washout intermission.<br><br>RESULTS: Compared to placebo, the consumption of fortified milk increased the circulating levels of different micronutrients, including vitamins and the &#x3c9;-3 index of erythrocyte membranes. Conversely, it reduced the amount of arachidonic acid, homocysteine, and &#x3c9;-6/&#x3c9;-3 ratio.<br><br>CONCLUSION: Twelve-week daily consumption of adhoc fortified milk has an overall positive impact on different health parameters related to inflammaging in the elderly.},
}
@article {pmid33264963,
year = {2021},
author = {Rai, PK and Lee, J and Brown, RJC and Kim, KH},
title = {Environmental fate, ecotoxicity biomarkers, and potential health effects of micro- and nano-scale plastic contamination.},
journal = {Journal of hazardous materials},
volume = {403},
number = {},
pages = {123910},
doi = {10.1016/j.jhazmat.2020.123910},
pmid = {33264963},
issn = {1873-3336},
mesh = {Animals ; Biomarkers ; Environmental Pollution ; Humans ; Microplastics ; *Plastics/toxicity ; *Water Pollutants, Chemical/analysis ; },
abstract = {In recent decades, the quantity of plastic waste products has increased tremendously. As plastic wastes are released into the environment, they exert harmful effects on biota and human health. In this work, a comprehensive review is offered to describe the physical and chemical characteristics of microplastics and nanoplastics in relation to their fate, microbial ecology, transport, and ecotoxic behavior. Present discussion is expanded further to cover the biochemical, physiological, and molecular mechanisms controlling the environmental fate, ecotoxicity, and human health hazards of micro- and nanoplastics. The risks of their exposure to microbes, plants, animals, and human health are also reviewed with special emphasis. Finally, a direction for future interdisciplinary research in materials and polymer science is also discussed to help control the pollution caused by micro- and nanoplastics.},
}
@article {pmid33264923,
year = {2021},
author = {Williamson, AJ and Verbruggen, F and Chavez Rico, VS and Bergmans, J and Spooren, J and Yurramendi, L and Laing, GD and Boon, N and Hennebel, T},
title = {Selective leaching of copper and zinc from primary ores and secondary mineral residues using biogenic ammonia.},
journal = {Journal of hazardous materials},
volume = {403},
number = {},
pages = {123842},
doi = {10.1016/j.jhazmat.2020.123842},
pmid = {33264923},
issn = {1873-3336},
mesh = {Ammonia ; Bacillaceae ; *Copper ; Minerals ; *Zinc ; },
abstract = {With the number of easily accessible ores depleting, alternate primary and secondary sources are required to meet the increasing demand of economically important metals. Whilst highly abundant, these materials are of lower grade with respect to traditional ores, thus highly selective and sustainable metal extraction technologies are needed to reduce processing costs. Here, we investigated the metal leaching potential of biogenic ammonia produced by a ureolytic strain of Lysinibacillus sphaericus on eight primary and secondary materials, comprised of mining and metallurgical residues, sludges and automotive shredder residues (ASR). For the majority of materials, moderate to high yields (30-70%) and very high selectivity (>97% against iron) of copper and zinc were obtained with 1 mol L[-1] total ammonia. Optimal leaching was achieved and further refined for the ASR in a two-step indirect leaching system with biogenic ammonia. Copper leaching was the result of local corrosion and differences in leaching against the synthetic (NH4)2CO3 control could be accounted for by pH shifts from microbial metabolism, subsequently altering free NH3 required for coordination. These results provide important findings for future sustainable metal recovery technologies from secondary materials.},
}
@article {pmid33264383,
year = {2021},
author = {Ghuneim, LJ and Distaso, MA and Chernikova, TN and Bargiela, R and Lunev, EA and Korzhenkov, AA and Toshchakov, SV and Rojo, D and Barbas, C and Ferrer, M and Golyshina, OV and Golyshin, PN and Jones, DL},
title = {Utilization of low-molecular-weight organic compounds by the filterable fraction of a lotic microbiome.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {2},
pages = {},
pmid = {33264383},
issn = {1574-6941},
mesh = {Carbon ; Fresh Water ; *Microbiota ; *Organic Chemicals ; RNA, Ribosomal, 16S/genetics ; Rivers ; },
abstract = {Filterable microorganisms participate in dissolved organic carbon (DOC) cycling in freshwater systems, however their exact functional role remains unknown. We determined the taxonomic identity and community dynamics of prokaryotic microbiomes in the 0.22 µm-filtered fraction and unfiltered freshwater from the Conwy River (North Wales, UK) in microcosms and, using targeted metabolomics and 14C-labelling, examined their role in the utilization of amino acids, organic acids and sugars spiked at environmentally-relevant (nanomolar) concentrations. To identify changes in community structure, we used 16S rRNA amplicon and shotgun sequencing. Unlike the unfiltered water samples where the consumption of DOC was rapid, the filtered fraction showed a 3-day lag phase before the consumption started. Analysis of functional categories of clusters of orthologous groups of proteins (COGs) showed that COGs associated with energy production increased in number in both fractions with substrate addition. The filtered fraction utilized low-molecular-weight (LMW) DOC at much slower rates than the whole community. Addition of nanomolar concentrations of LMW DOC did not measurably influence the composition of the microbial community nor the rate of consumption across all substrate types in either fraction. We conclude that due to their low activity, filterable microorganisms play a minor role in LMW DOC processing within a short residence time of lotic freshwater systems.},
}
@article {pmid33262758,
year = {2020},
author = {Batista, MA and Calvo-Fortes, F and Silveira-Nunes, G and Camatta, GC and Speziali, E and Turroni, S and Teixeira-Carvalho, A and Martins-Filho, OA and Neretti, N and Maioli, TU and Santos, RR and Brigidi, P and Franceschi, C and Faria, AMC},
title = {Inflammaging in Endemic Areas for Infectious Diseases.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {579972},
pmid = {33262758},
issn = {1664-3224},
mesh = {Aging/*physiology ; Animals ; Communicable Diseases/epidemiology/*immunology/microbiology ; Diet, Western ; Endemic Diseases ; Frailty ; Healthy Aging ; Humans ; Immunosenescence ; Inflammation/epidemiology/*immunology/microbiology ; Italy/epidemiology ; Microbiota/*immunology ; },
abstract = {Immunosenescence is marked by a systemic process named inflammaging along with a series of defects in the immunological activity that results in poor responses to infectious agents and to vaccination. Inflammaging, a state of low-grade chronic inflammation, usually leads to chronic inflammatory diseases and frailty in the elderly. However, some elderly escape from frailty and reach advanced age free of the consequences of inflammaging. This process has been called immunological remodeling, and it is the hallmark of healthy aging as described in the studies of centenarians in Italy. The biological markers of healthy aging are still a matter of debate, and the studies on the topic have focused on inflammatory versus remodeling processes and molecules. The sub-clinical inflammatory status associated with aging might be a deleterious event for populations living in countries where chronic infectious diseases are not prevalent. Nevertheless, in other parts of the world where they are, two possibilities may occur. Inflammatory responses may have a protective effect against these infectious agents. At the same time, the long-term consequences of protective immune responses during chronic infections may result in accelerated immunosenescence in these individuals. Therefore, the biological markers of healthy aging can vary according to environmental, cultural, and geographical settings that reflect worldwide, and in a non-biased, non-westernized perspective, the changes that we experience regarding our contacts with microorganisms and the outcomes of such contacts.},
}
@article {pmid33262754,
year = {2020},
author = {Baksi, KD and Kuntal, BK and Mande, SS},
title = {Corrigendum: 'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {605295},
doi = {10.3389/fmicb.2020.605295},
pmid = {33262754},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2018.00036.].},
}
@article {pmid33262240,
year = {2020},
author = {Khanolkar, RA and Clark, ST and Wang, PW and Hwang, DM and Yau, YCW and Waters, VJ and Guttman, DS},
title = {Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways.},
journal = {mSystems},
volume = {5},
number = {6},
pages = {},
pmid = {33262240},
issn = {2379-5077},
abstract = {Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical focus on the dominant pathogens ignores potentially important community-level interactions in disease pathology, perhaps explaining why these treatments are often less effective than predicted based on in vitro testing. A better understanding of the ecological dynamics of this ecosystem may enable clinicians to harness these interactions and thereby improve treatment outcomes. Like all ecosystems, the CF lung microbial community develops through a series of stages, each of which may present with distinct microbial communities that generate unique host-microbe and microbe-microbe interactions, metabolic profiles, and clinical phenotypes. While insightful models have been developed to explain some of these stages and interactions, there is no unifying model to describe how these infections develop and persist. Here, we review current perspectives on the ecology of the CF airway and present the CF Ecological Succession (CFES) model that aims to capture the spatial and temporal complexity of CF lung infection, address current challenges in disease management, and inform the development of ecologically driven therapeutic strategies.},
}
@article {pmid33261862,
year = {2021},
author = {Liu, D and Legras, JL and Zhang, P and Chen, D and Howell, K},
title = {Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine.},
journal = {International journal of food microbiology},
volume = {338},
number = {},
pages = {108983},
doi = {10.1016/j.ijfoodmicro.2020.108983},
pmid = {33261862},
issn = {1879-3460},
mesh = {Agriculture ; *Biodiversity ; Farms ; *Fermentation ; Fungi/chemistry/*classification/metabolism ; *Microbiota ; Odorants ; Saccharomyces cerevisiae ; Vitis/microbiology ; Wine/*microbiology ; },
abstract = {Microbial ecology is an integral part of an agricultural ecosystem and influences the quality of agricultural commodities. Microbial activity influences grapevine health and crop production, conversion of sugar to ethanol during fermentation, thus forming wine aroma and flavour. There are regionally differentiated microbial patterns in grapevines and must but how microbial patterns contribute to wine regional distinctiveness (terroir) at small scale (<100 km) is not well defined. Here we characterise fungal communities, yeast populations, and Saccharomyces cerevisiae populations during spontaneous fermentation using metagenomics and population genetics to investigate microbial distribution and fungal contributions to the resultant wine. We found differentiation of fungi, yeasts, and S. cerevisiae between geographic origins (estate/vineyard), with influences from the grape variety. Growth and dominance of S. cerevisiae during fermentation reshaped the fungal community and showed geographic structure at the strain level. Associations between fungal microbiota diversity and wine chemicals suggest that S. cerevisiae plays a primary role in determining wine aroma profiles at a sub-regional scale. The geographic distribution at scales of less than 12 km supports that differential microbial communities, including the dominant fermentative yeast S. cerevisiae can be distinct in a local setting. These findings provide further evidence for microbial contributions to wine terroir, and perspectives for sustainable agricultural practices to maintain microbial diversity and optimise fermentation function to craft beverage quality.},
}
@article {pmid33258525,
year = {2021},
author = {Gweon, HS and Bowes, MJ and Moorhouse, HL and Oliver, AE and Bailey, MJ and Acreman, MC and Read, DS},
title = {Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum.},
journal = {Environmental microbiology},
volume = {23},
number = {1},
pages = {484-498},
pmid = {33258525},
issn = {1462-2920},
support = {NE/N018125/1//Natural Environment Research Council/ ; NE/R016429/1//Natural Environment Research Council/ ; },
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Ecosystem ; *Microbiota ; Phylogeny ; Rivers/chemistry/*microbiology ; United Kingdom ; },
abstract = {The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological assembly processes differ between lotic habitats by examining community composition and inferring community assembly processes across four major habitat types (free-living, particle-associated, biofilm on benthic stones and rocks, and sediment). This was conducted at 12 river sites from headwater streams to the main river in the River Thames, UK. Our results indicate that there are distinct differences in the bacterial communities between four major habitat types, with contrasting ecological processes shaping their community assembly processes. While the mobile free-living and particle-associated communities were consistently less diverse than the fixed sediment and biofilm communities, the latter two communities displayed higher homogeneity across the sampling sites. This indicates that the relative influence of deterministic environmental filtering is elevated in sediment and biofilm communities compared with free-living and particle-associated communities, where stochastic processes play a larger role.},
}
@article {pmid33257312,
year = {2021},
author = {Barbosa, RG and van Veelen, HPJ and Pinheiro, V and Sleutels, T and Verstraete, W and Boon, N},
title = {Enrichment of Hydrogen Oxidizing Bacteria from High Temperature and Salinity Environments.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {4},
pages = {},
pmid = {33257312},
issn = {1098-5336},
abstract = {There is an urgent need for sustainable protein supply routes with low environmental footprint. Recently, the use of hydrogen oxidizing bacteria (HOB) as a platform for high quality microbial protein (MP) production has regained interest. This study aims to investigate the added value of using conditions such as salt and temperature to steer HOB communities to lower diversities, while maintaining a high protein content and a high quality amino acid profile. Pressure drop and hydrogen consumption were measured for 56 days to evaluate autotrophy of a total of six communities in serum flasks. Of the six communities, four were enriched under saline (0.0, 0.25, 0.5 and 1.0 mol NaCl l[-1]) and two under thermophilic conditions (65°C). Five communities enriched for HOB were subsequently cultivated in continuously stirred reactors under the same conditions to evaluate their potential as microbial protein producers. The protein percentages ranged from 41 to 80%. The highest protein content was obtained for the thermophilic enrichments. Amino acid profiles were comparable to protein sources commonly used for feed purposes. Members of the genus Achromobacter were found to dominate the saline enrichments while members of the genus Hydrogenibacillus were found to dominate the thermophilic enrichments. Here we show that enriching for HOB while steering the community toward low diversity and maintaining a high quality protein content can be successfully achieved, both in saline and thermophilic conditions.IMPORTANCE Alternative feed and food supply chains are required to decrease water and land use. HOB offer a promising substitute for traditional agricultural practice to produce microbial protein (MP) from residual materials and renewable energy. To safeguard product stability, the composition of the HOB community should be controlled. Defining strategies to maintain the stability of the communities is therefore key for optimization purposes. In this study, we use salt and temperature as independent conditions to stabilize the composition of the HOB communities. Based on the results presented, we conclude that HOB communities can be steered to have low diversity using the presented conditions while producing a desirable protein content with a valuable amino acid profile.},
}
@article {pmid33257152,
year = {2021},
author = {Abel, SM and Primpke, S and Int-Veen, I and Brandt, A and Gerdts, G},
title = {Systematic identification of microplastics in abyssal and hadal sediments of the Kuril Kamchatka trench.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {269},
number = {},
pages = {116095},
doi = {10.1016/j.envpol.2020.116095},
pmid = {33257152},
issn = {1873-6424},
mesh = {Environmental Monitoring ; Geologic Sediments ; *Microplastics ; Oceans and Seas ; Pacific Ocean ; Plastics ; *Water Pollutants, Chemical/analysis ; },
abstract = {The occurrence of microplastics throughout marine environments worldwide, from pelagic to benthic habitats, has become serious cause for concern. Hadal zones were recently described as the "trash bins of the oceans" and ultimate sink for marine plastic debris. The Kuril region covers a substantial area of the North Pacific Ocean and is characterised by high biological productivity, intense marine traffic through the Kuril straits, and anthropogenic activity. Moreover, strong tidal currents and eddy activity, as well as the influence of Pacific currents, have the potential for long distance transport and retention of microplastics in this area. To verify the hypothesis that the underlying Kuril Kamchatka Trench might accumulate microplastics from the surrounding environments and act as the final sink for high quantities of microplastics, we analysed eight sediment samples collected in the Kuril Kamchatka Trench at a depth range of 5143-8250 m during the Kuril Kamchatka Biodiversity Studies II (KuramBio II) expedition in summer 2016. Microplastics were characterised via Micro Fourier Transform Infrared spectroscopy. All samples were analysed in their entirety to avoid inaccuracies due to extrapolations of microplastic concentrations and polymer diversities, which would otherwise be based on commonly applied representative aliquots. The number of microplastic particles detected ranged from 14 to 209 kg[-1] sediment (dry weight) with a total of 15 different plastic polymers detected. Polypropylene accounted for the largest proportion (33.2%), followed by acrylates/polyurethane/varnish (19%) and oxidized polypropylene (17.4%). By comparing extrapolated sample aliquots with in toto results, it was shown that aliquot-based extrapolations lead to severe under- or overestimations of microplastic concentrations, and an underestimation of polymer diversity.},
}
@article {pmid33256756,
year = {2020},
author = {Gao, S and Kong, Y and Yu, J and Miao, L and Ji, L and Song, L and Zeng, C},
title = {Isolation of axenic cyanobacterium and the promoting effect of associated bacterium on axenic cyanobacterium.},
journal = {BMC biotechnology},
volume = {20},
number = {1},
pages = {61},
pmid = {33256756},
issn = {1472-6750},
support = {No.2013AA102805-04//National High-tech Research and Development Program/International ; No. 2019EC61-15//Key Project of Jingzhou Science and Technology/International ; No. 2016M591832//Postdoctoral Research Foundation of China/International ; No. BK20150165//Natural Science Foundation of Jiangsu Province/International ; No. KJ15ZB01//General Administration of Quality Supervision, Inspection and Quarantine of the People's Republic of China (CN)/International ; No. 2018ZJSHKF06//Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province/International ; },
mesh = {Chryseobacterium ; Cyanobacteria/classification/genetics/*isolation &amp; purification/*physiology ; Ecology ; Ecosystem ; Heterotrophic Processes ; Microcystis/classification/genetics/isolation &amp; purification/physiology ; Phylogeny ; Symbiosis ; },
abstract = {BACKGROUND: Harmful cyanobacterial blooms have attracted wide attention all over the world as they cause water quality deterioration and ecosystem health issues. Microcystis aeruginosa associated with a large number of bacteria is one of the most common and widespread bloom-forming cyanobacteria that secret toxins. These associated bacteria are considered to benefit from organic substrates released by the cyanobacterium. In order to avoid the influence of associated heterotrophic bacteria on the target cyanobacteria for physiological and molecular studies, it is urgent to obtain an axenic M. aeruginosa culture and further investigate the specific interaction between the heterotroph and the cyanobacterium.<br><br>RESULTS: A traditional and reliable method based on solid-liquid alternate cultivation was carried out to purify the xenic cyanobacterium M. aeruginosa FACHB-905. On the basis of 16S rDNA gene sequences, two associated bacteria named strain B905-1 and strain B905-2, were identified as Pannonibacter sp. and Chryseobacterium sp. with a 99 and 97% similarity value, respectively. The axenic M. aeruginosa FACHB-905A (Microcystis 905A) was not able to form colonies on BG11 agar medium without the addition of strain B905-1, while it grew well in BG11 liquid medium. Although the presence of B905-1 was not indispensable for the growth of Microcystis 905A, B905-1 had a positive effect on promoting the growth of Microcystis 905A.<br><br>CONCLUSIONS: The associated bacteria were eliminated by solid-liquid alternate cultivation method and the axenic Microcystis 905A was successfully purified. The associated bacterium B905-1 has the potentiality to promote the growth of Microcystis 905A. Moreover, the purification technique for cyanobacteria described in this study is potentially applicable to a wider range of unicellular cyanobacteria.},
}
@article {pmid33256601,
year = {2020},
author = {Wagner, E and Zaiser, A and Leitner, R and Quijada, NM and Pracser, N and Pietzka, A and Ruppitsch, W and Schmitz-Esser, S and Wagner, M and Rychli, K},
title = {Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {847},
pmid = {33256601},
issn = {1471-2164},
support = {P 27920/FWF_/Austrian Science Fund FWF/Austria ; P27920-B22//Austrian Science Fund/ ; n.a.//Bundesministerium f&#xfc;r Verkehr, Innovation und Technologie/ ; },
mesh = {Bacterial Proteins ; Caco-2 Cells ; Food Microbiology ; Genomics ; Humans ; *Listeria monocytogenes/genetics ; *Listeriosis ; Virulence/genetics ; Virulence Factors/genetics ; },
abstract = {BACKGROUND: Listeria (L.) monocytogenes strains show a high diversity regarding stress tolerance and virulence potential. Genome studies have mainly focused on specific sequence types (STs) predominantly associated with either food or human listeriosis. This study focused on the prevalent ST155, showing equal distribution among clinical and food isolates. We evaluated the virulence potential of 20 ST155 strains and performed comparative genomic analysis of 130 ST155 strains isolated from food, food processing environments and human listeriosis cases in different countries and years.<br><br>RESULTS: The in vitro virulence assays using human intestinal epithelial Caco2 and hepatocytic HEPG2 cells showed an impaired virulence phenotype for six of the 20 selected ST155 strains. Genome analysis revealed no distinct clustering of strains from the same source category (food, food processing environment, and clinical isolates). All strains harbored an intact inlA and inlB locus, except four strains, which had an internal deletion in the inlA gene. All strains harbored LIPI-1, but prfA was present in a longer variant in six strains, all showing impaired virulence. The longer PrfA variant resulted in lower expression of inlA, inlB, and prfA, and no expression of hly and actA. Regarding stress-related gene content, SSI-1 was present, whereas qacH was absent in all strains. 34.6% of the strains harbored a plasmid. All but one ST155 plasmids showed high conservation and harbored cadA2, bcrABC, and a triphenylmethane reductase.<br><br>CONCLUSIONS: This study contributes to an enhanced understanding of L. monocytogenes ST155 strains, being equally distributed among isolates from humans, food, and food processing environments. The conservation of the present genetic traits and the absence of unique inherent genetic features makes these types of STs especially interesting since they are apparently equally adapted to the conditions in food processing environments,&#xa0;as well as in food as to the human host environment. However, a ST155-specific mutation resulting in a longer PrfA variant impaired the virulence potential of several ST155 strains.},
}
@article {pmid33254950,
year = {2021},
author = {Del Olmo, G and Husband, S and Sánchez Briones, C and Soriano, A and Calero Preciado, C and Macian, J and Douterelo, I},
title = {The microbial ecology of a Mediterranean chlorinated drinking water distribution systems in the city of Valencia (Spain).},
journal = {The Science of the total environment},
volume = {754},
number = {},
pages = {142016},
doi = {10.1016/j.scitotenv.2020.142016},
pmid = {33254950},
issn = {1879-1026},
mesh = {Animals ; Biofilms ; *Cyprinodontiformes ; *Drinking Water ; *Mycobiome ; Spain ; Water Microbiology ; Water Quality ; Water Supply ; },
abstract = {Drinking water distribution systems host extensive microbiomes with diverse biofilm communities regardless of treatment, disinfection, or operational practices. In Mediterranean countries higher temperatures can accelerate reactions and microbial growth that may increase aesthetic water quality issues, particularly where material deposits can develop as a result of net zero flows within looped urban networks. This study investigated the use of flow and turbidity monitoring to hydraulically manage mobilisation of pipe wall biofilms and associated material from the Mediterranean city of Valencia (Spain). Pipe sections of different properties were subjected to controlled incremental flushing with monitoring and sample collection for physico-chemical and DNA analysis with Illumina sequencing of bacterial and fungal communities. A core microbial community was detected throughout the network with microorganisms like Pseudomonas, Aspergillus or Alternaria increasing during flushing, indicating greater abundance in underlying and more consolidated material layers. Bacterial and fungal communities were found to be highly correlated, with bacteria more diverse and dynamic during flushing whilst fungi were more dominant and less variable between sampling sites. Results highlight that water quality management can be achieved through hydraulic strategies yet understanding community dynamics, including the fungal component, will be key to maintaining safe and ultimately beneficial microbiomes in drinking water distribution systems.},
}
@article {pmid33254908,
year = {2021},
author = {Dong, J and Hunt, J and Delhaize, E and Zheng, SJ and Jin, CW and Tang, C},
title = {Impacts of elevated CO2 on plant resistance to nutrient deficiency and toxic ions via root exudates: A review.},
journal = {The Science of the total environment},
volume = {754},
number = {},
pages = {142434},
doi = {10.1016/j.scitotenv.2020.142434},
pmid = {33254908},
issn = {1879-1026},
mesh = {Biological Transport ; Biomass ; *Carbon Dioxide/toxicity ; Ions ; *Nutrients ; Plant Exudates ; Plant Roots ; },
abstract = {Elevated atmospheric CO2 (eCO2) concentration can increase root exudation into soils, which improves plant tolerance to abiotic stresses. This review used a meta-analysis to assess effect sizes of eCO2 on both efflux rates and total amounts of some specific root exudates, and dissected whether eCO2 enhances plant's resistance to nutrient deficiency and ion toxicity via root exudates. Elevated CO2 did not affect efflux rates of total dissolved organic carbon, a measure of combined root exudates per unit of root biomass or length, but increased the efflux amount of root systems per plant by 31% which is likely attributed to increased root biomass (29%). Elevated CO2 increased efflux rates of soluble-sugars, carboxylates, and citrate by 47%, 111%, and 16%, respectively, but did not affect those of amino acids and malate. The increased carbon allocation to roots, increased plant requirements of mineral nutrients, and heightened detoxification responses to toxic ions under eCO2 collectively contribute to the increased efflux rates despite lacking molecular evidence. The increased efflux rates of root exudates under eCO2 were closely associated with improved nutrient uptake whilst less studies have validated the associations between root exudates and resistance to toxic ions of plants when grown under eCO2. Future studies are required to reveal how climate change (eCO2) affect the efflux of specific root exudates, particularly organic anions, the corresponding nutrient uptake and toxic ion resistance from plant molecular biology and soil microbial ecology perspectives.},
}
@article {pmid33254807,
year = {2021},
author = {Yuan, W and Zhang, Y and Riaz, L and Yang, Q and Du, B and Wang, R},
title = {Multiple antibiotic resistance and DNA methylation in Enterobacteriaceae isolates from different environments.},
journal = {Journal of hazardous materials},
volume = {402},
number = {},
pages = {123822},
doi = {10.1016/j.jhazmat.2020.123822},
pmid = {33254807},
issn = {1873-3336},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *DNA Methylation ; Drug Resistance, Microbial ; *Enterobacteriaceae/genetics ; Humans ; Integrons ; Microbial Sensitivity Tests ; beta-Lactamases/genetics ; },
abstract = {Antibiotic resistant bacteria with diverse resistance phenotypes and genotypes are ubiquitous in the environments that have become a global health concern. The role of DNA methylation in the dissemination of antibiotic resistance among different environments is currently unclear. We recovered 646 Enterobacteriaceae (Eb) isolates from hospital, livestock manure, municipal wastewater-treatment plants, river sediment and soil for comprehensive analysis of resistance phenotypes, β-lactamase genes, integrons, integron-associated gene cassettes and the levels of DNA methylation. Antibiotic susceptibility testing revealed that approximately 87.31 % isolates were multidrug resistant Eb. The β-lactamase genes were positively detected in 473 isolates with greater diversity in human or animal sourced Eb, while its prevalence was found to be highest in the Eb isolates from the natural environments. Forty-three gene cassettes (28 different types mediated by intI1) were detected in 53 (19.63 %) isolates, with greater diversity in Eb isolates from hospital and livestock manure. The multiple antibiotic resistance index of single strain was positively correlated with the 5-methylcytosine and showed a negative correlation with 6-methylademine. We conclude that the development of antibiotic resistance could possibly be coupled with DNA methylation, which might enhance the antimicrobial resistance and survival capacity of Eb.},
}
@article {pmid33254460,
year = {2021},
author = {Ghysels, S and Buffel, S and Rabaey, K and Ronsse, F and Ganigué, R},
title = {Biochar and activated carbon enhance ethanol conversion and selectivity to caproic acid by Clostridium kluyveri.},
journal = {Bioresource technology},
volume = {319},
number = {},
pages = {124236},
doi = {10.1016/j.biortech.2020.124236},
pmid = {33254460},
issn = {1873-2976},
mesh = {Caproates ; Charcoal ; *Clostridium kluyveri ; Ethanol ; },
abstract = {Syngas from biomass or steel mills can be fermented into a dilute stream of ethanol and acetic acid, which requires energy intensive distillation for product recovery. This can be circumvented by selective secondary fermentation of the syngas fermentation effluent to caproic acid as easier recoverable platform chemical with Clostridium kluyveri. Here, we explore the impact of biochar and activated carbon on this process. Changes during the fermentation with biochar or activated carbon were monitored, different doses were tested and the recyclability of biochar and activated carbon was assessed. Biochar decreased the lag phase and increased the caproic acid production rate (up to 0.50 g·L[-1]·h[-1]). Upon recycling for subsequent fermentation, biochar retained this property largely. Activated carbon addition, especially at high dose, could potentially increase the conversion and selectivity towards caproic acid to 14.15 g·L[-1] (control: 11.01 g·L[-1]) and 92% (control: 84%), respectively.},
}
@article {pmid33253458,
year = {2021},
author = {Ndhlovu, A and Durand, PM and Ramsey, G},
title = {Programmed cell death as a black queen in microbial communities.},
journal = {Molecular ecology},
volume = {30},
number = {5},
pages = {1110-1119},
doi = {10.1111/mec.15757},
pmid = {33253458},
issn = {1365-294X},
mesh = {*Apoptosis ; *Microbiota/genetics ; },
abstract = {Programmed cell death (PCD) in unicellular organisms is in some instances an altruistic trait. When the beneficiaries are clones or close kin, kin selection theory may be used to explain the evolution of the trait, and when the trait evolves in groups of distantly related individuals, group or multilevel selection theory is invoked. In mixed microbial communities, the benefits are also available to unrelated taxa. But the evolutionary ecology of PCD in communities is poorly understood. Few hypotheses have been offered concerning the community role of PCD despite its far-reaching effects. The hypothesis we consider here is that PCD is a black queen. The Black Queen Hypothesis (BQH) outlines how public goods arising from a leaky function are exploited by other taxa in the community. Black Queen (BQ) traits are essential for community survival, but only some members bear the cost of possessing them, while others lose the trait In addition, BQ traits have been defined in terms of adaptive gene loss, and it is unknown whether this has occurred for PCD. Our conclusion is that PCD fulfils the two most important criteria of a BQ (leakiness and costliness), but that more empirical data are needed for assessing the remaining two criteria. In addition, we hold that for viewing PCD as a BQ, the original BQH needs to include social traits. Thus, despite some empirical and conceptual shortcomings, the BQH provides a helpful avenue for investigating PCD in microbial communities.},
}
@article {pmid33252774,
year = {2021},
author = {Lee, JC and Whang, KS},
title = {Altererythrobacter segetis sp. nov., Isolated from Farmland Soil.},
journal = {Current microbiology},
volume = {78},
number = {1},
pages = {389-396},
pmid = {33252774},
issn = {1432-0991},
mesh = {Alphaproteobacteria ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Farms ; Fatty Acids ; Phospholipids ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil ; *Soil Microbiology ; },
abstract = {A Gram-stain-negative bacterium, designated YJ20[T], was isolated from rhizosphere soil of a spinach farmland at Shinan in Korea. Strain YJ20[T] was found to be aerobic, non-motile rods which can grow at 10-33 °C (optimum, 28 °C), at pH 6.5-8.5 (optimum, pH 6.5-7.5) and in the absence of NaCl. The 16S rRNA gene sequence analysis showed that strain YJ20[T] belongs to the genus Altererythrobacter with moderate sequence similarities to Altererythrobacter dongtanensis KCTC 22672[T] (96.8%), Altererythrobacter soli MN-1[T] (96.6%) and Altererythrobacter xinjiangensis S3-63[T] (96.5%). The phylogenomic analysis based on the whole-genome sequence demonstrated that strain YJ20[T] formed a distinct phyletic line with Altererythrobacter soli MN-1[T] and Altererythrobacter salegens XY-R17[T] showing average nucleotide identity (ANI) values of 79.4 and 77.5%, respectively. The predominant ubiquinone was identified as Q-10, and the major fatty acids were C17:1 ω6c, C18:1 ω7c and C15:0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidycholin, sphingoglycolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. The G+C content of the genome was determined to be 66.3 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic and phylogenomic analyses in this study, strain YJ20[T] is considered to represent a novel species in the genus Altererythrobacter, for which the name Altererythrobacter segetis sp. nov. is proposed. The type strain is YJ20[T] (= KACC 19554[T] = NBRC 113199[T]).},
}
@article {pmid33252655,
year = {2020},
author = {Weißbecker, C and Schnabel, B and Heintz-Buschart, A},
title = {Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.},
journal = {GigaScience},
volume = {9},
number = {12},
pages = {},
pmid = {33252655},
issn = {2047-217X},
mesh = {High-Throughput Nucleotide Sequencing ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Software ; },
abstract = {BACKGROUND: Amplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources.<br><br>RESULTS: We present dadasnake, a user-friendly, 1-command Snakemake pipeline that wraps the preprocessing of sequencing reads and the delineation of exact sequence variants by using the favorably benchmarked and widely used DADA2 algorithm with a taxonomic classification and the post-processing of the resultant tables, including hand-off in standard formats. The suitability of the provided default configurations is demonstrated using mock community data from bacteria and archaea, as well as fungi.<br><br>CONCLUSIONS: By use of Snakemake, dadasnake makes efficient use of high-performance computing infrastructures. Easy user configuration guarantees flexibility of all steps, including the processing of data from multiple sequencing platforms. It is easy to install dadasnake via conda environments. dadasnake is available at https://github.com/a-h-b/dadasnake.},
}
@article {pmid33250870,
year = {2020},
author = {Miclotte, L and De Paepe, K and Rymenans, L and Callewaert, C and Raes, J and Rajkovic, A and Van Camp, J and Van de Wiele, T},
title = {Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota in vitro, Irrespective of Chemical or Natural Emulsifier Origin.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {577474},
pmid = {33250870},
issn = {1664-302X},
abstract = {The use of additives in food products has become an important public health concern. In recent reports, dietary emulsifiers have been shown to affect the gut microbiota, contributing to a pro-inflammatory phenotype and metabolic syndrome. So far, it is not yet known whether similar microbiome shifts are observable for a more diverse set of emulsifier types and to what extent these effects vary with the unique features of an individual's microbiome. To bridge this gap, we investigated the effect of five dietary emulsifiers on the fecal microbiota from 10 human individuals upon a 48 h exposure. Community structure was assessed with quantitative microbial profiling, functionality was evaluated by measuring fermentation metabolites, and pro-inflammatory properties were assessed with the phylogenetic prediction algorithm PICRUSt, together with a TLR5 reporter cell assay for flagellin. A comparison was made between two mainstream chemical emulsifiers (carboxymethylcellulose and P80), a natural extract (soy lecithin), and biotechnological emulsifiers (sophorolipids and rhamnolipids). While fecal microbiota responded in a donor-dependent manner to the different emulsifiers, profound differences between emulsifiers were observed. Rhamnolipids, sophorolipids, and soy lecithin eliminated 91 ± 0, 89 ± 1, and 87 ± 1% of the viable bacterial population after 48 h, yet they all selectively increased the proportional abundance of putative pathogens. Moreover, profound shifts in butyrate (-96 ± 6, -73 ± 24, and -34 ± 25%) and propionate (+13 ± 24, +88 ± 50, and +29 ± 16%) production were observed for these emulsifiers. Phylogenetic prediction indicated higher motility, which was, however, not confirmed by increased flagellin levels using the TLR5 reporter cell assay. We conclude that dietary emulsifiers can severely impact the gut microbiota, and this seems to be proportional to their emulsifying strength, rather than emulsifier type or origin. As biotechnological emulsifiers were especially more impactful than chemical emulsifiers, caution is warranted when considering them as more natural alternatives for clean label strategies.},
}
@article {pmid33250307,
year = {2021},
author = {Ostermeyer, P and Bonin, L and Folens, K and Verbruggen, F and García-Timermans, C and Verbeken, K and Rabaey, K and Hennebel, T},
title = {Effect of speciation and composition on the kinetics and precipitation of arsenic sulfide from industrial metallurgical wastewater.},
journal = {Journal of hazardous materials},
volume = {409},
number = {},
pages = {124418},
doi = {10.1016/j.jhazmat.2020.124418},
pmid = {33250307},
issn = {1873-3336},
abstract = {Precipitation of arsenic as As2S3 produces little waste sludge, has the potential for low chemical consumption and for selective metal(loid) removal. In this study, arsenic removal from acidic (pH 2), metallurgical wastewater was tested in industrially relevant conditions. Sulfides added at a S:As molar ratio of 2.5 and 5 resulted in removal of 99% and 84% of As(III) and As(V). Precipitation of As2S3 from the As(III) and industrial wastewater containing 17% As(V) was nearly instantaneous. For the synthetic As(V) solution, reduction to As(III) was the rate limiting step. At a S:As ratio of 20 and an observed removal rate (k2 = 4.8 (mol L[-1]) h[-1]), two hours were required to remove of 93% of arsenic from a 1 g As L[-1] solution. In the case of As(V) in industrial samples this time lag was not observed, showing that components in the industrial wastewater affected the removal and reduction of arsenate. Speciation also affected flocculation and coagulation characteristics of As2S3 particles: As(V) reduction resulted in poor coagulation and flocculation. Selective precipitation of arsenic was possible, but depended on speciation, S:As ratio and other metals present.},
}
@article {pmid33247364,
year = {2021},
author = {Burtseva, O and Baulina, O and Zaytseva, A and Fedorenko, T and Chekanov, K and Lobakova, E},
title = {In vitro Biofilm Formation by Bioluminescent Bacteria Isolated from the Marine Fish Gut.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {932-940},
pmid = {33247364},
issn = {1432-184X},
mesh = {Animals ; Bacteria/genetics ; *Biofilms ; *Enterobacteriaceae ; Fimbriae, Bacterial ; },
abstract = {The internal surface of the animal gastrointestinal tract is covered by microbial biofilms. They play an important role in the development and functioning of the host organism and protect it against pathogens. Microbial communities of gastrointestinal biofilms are less elucidated than luminal microbiota. Therefore, the studies of biofilm formation by gastrointestinal microorganisms are a topical issue. For the first time, we report the formation of a biofilm in vitro by the strains of bioluminescent bacteria isolated from the intestines of marine fish. These bacteria exhibit co-aggregation and tend to attach to solid surfaces. The attachment of cells is accompanied by appearance of the pili. Then, we observed the formation of microcolonies and the production of extracellular polymer substances (EPSs) connecting bacterial cells into an integrated system. The presence of acidic polysaccharides is shown in the EPS when using the ruthenium red staining. Acidic polysaccharides in this matrix is a biochemical evidence of microbial biofilms. On the fibers of the polymer matrix, these bacteria form the "mushroom body"-type structures. Matured biofilms exhibit a specific three-dimensional architecture with pores and channels formed by cells and EPS. We also demonstrated the formation of a biofilm by binary culture of the luminous enterobacterium Kosakonia cowanii and a Gram-positive Macrococcus sp. The data obtained help to understand the role of these bacteria in the intestines of fish. They lead to a new study in the field of investigation of the intestinal microbiome of fish.},
}
@article {pmid33244619,
year = {2021},
author = {Mathai, PP and Bertram, JH and Padhi, SK and Singh, V and Tolo, IE and Primus, A and Mor, SK and Phelps, NBD and Sadowsky, MJ},
title = {Influence of Environmental Stressors on the Microbiota of Zebra Mussels (Dreissena polymorpha).},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {1042-1053},
pmid = {33244619},
issn = {1432-184X},
support = {Minnesota Agricultural Experiment Station.//Minnesota Agricultural Experiment Station./ ; },
mesh = {Animals ; *Bivalvia ; *Dreissena ; Lakes ; *Microbiota ; Temperature ; },
abstract = {Host-associated microbiota play a critical role in host fitness by providing nutrition, enhancing digestion capabilities, and by providing protection from pathogens. Here, we investigated the effects of two environmental stressors, temperature, and salinity, on the microbiota associated with zebra mussels (ZMs), a highly invasive bivalve in North America. To examine this in detail, lake-collected ZMs were acclimated to laboratory conditions, and subjected to temperature and salinity stress conditions. The impact of these stressors on the diversity, composition, and dynamics of ZM-associated microbiota were assessed by using amplicon- and shotgun-based sequencing, and qPCR-based approaches. Elevated temperature was found to be the primary driver of ZM mortality, although salinity alone also increased its likelihood. Stressor-induced ZM mortality, which ranged between 53 and 100%, was concomitant with significant increases in the relative abundance of several genera of putative opportunistic pathogens including Aeromonas. These genera were only present in low relative abundance in ZMs obtained from the control tank with 0% mortality. Shotgun sequencing and qPCR analyses indicated that the relative and absolute abundances of pathogenic Aeromonas species (particularly A. veronii) were significantly greater in temperature-induced dead ZMs. Taken together, our results show that environmental stress, especially elevated temperature (> 25 °C), is associated with the rapid mortality of ZMs as well as the proliferation of putative opportunistic bacterial pathogens.},
}
@article {pmid33244064,
year = {2020},
author = {Shilts, MH and Rosas-Salazar, C and Lynch, CE and Tovchigrechko, A and Boone, HH and Russell, PB and Connolly, AS and Costello, KM and McCollum, MD and Mai, A and Wiggins, DA and Rajagopala, SV and Yooseph, S and Peebles, RS and Hartert, TV and Das, SR},
title = {Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {20618},
pmid = {33244064},
issn = {2045-2322},
support = {K24AI77930//National Institute of Allergy and Infectious Diseases/International ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; K12HD087023//Eunice Kennedy Shriver National Institute of Child Health and Human Development/International ; U19AI095227//NIAID, NIH/International ; U2CDK059637/DK/NIDDK NIH HHS/United States ; P30DK020593/DK/NIDDK NIH HHS/United States ; R21 AI149262/AI/NIAID NIH HHS/United States ; R21 AI154016/AI/NIAID NIH HHS/United States ; U19 AI110819/AI/NIAID NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; P30 EY008126/EY/NEI NIH HHS/United States ; G20 RR030956/RR/NCRR NIH HHS/United States ; },
mesh = {Adult ; Child ; Female ; Humans ; Immunity/genetics/immunology ; Male ; Metagenome/genetics/immunology ; Microbiota/*genetics/*immunology ; Nasal Absorption/immunology ; Nasal Cavity/immunology/microbiology ; Nasal Lavage Fluid/*immunology/*microbiology ; Nose/*immunology/*microbiology ; RNA, Ribosomal, 16S/genetics/immunology ; Specimen Handling/methods ; },
abstract = {Despite being commonly used to collect upper airway epithelial lining fluid, nasal washes are poorly reproducible, not suitable for serial sampling, and limited by a dilution effect. In contrast, nasal filters lack these limitations and are an attractive alternative. To examine whether nasal filters are superior to nasal washes as a sampling method for the characterization of the upper airway microbiome and immune response, we collected paired nasal filters and washes from a group of 40 healthy children and adults. To characterize the upper airway microbiome, we used 16S ribosomal RNA and shotgun metagenomic sequencing. To characterize the immune response, we measured total protein using a BCA assay and 53 immune mediators using multiplex magnetic bead-based assays. We conducted statistical analyses to compare common microbial ecology indices and immune-mediator median fluorescence intensities (MFIs) between sample types. In general, nasal filters were more likely to pass quality control in both children and adults. There were no significant differences in microbiome community richness, α-diversity, or structure between pediatric samples types; however, these were all highly dissimilar between adult sample types. In addition, there were significant differences in the abundance of amplicon sequence variants between sample types in children and adults. In adults, total proteins were significantly higher in nasal filters than nasal washes; consequently, the immune-mediator MFIs were not well detected in nasal washes. Based on better quality control sequencing metrics and higher immunoassay sensitivity, our results suggest that nasal filters are a superior sampling method to characterize the upper airway microbiome and immune response in both children and adults.},
}
@article {pmid33243511,
year = {2021},
author = {Xu, M and Wang, F and Sheng, H and Stedtfeld, RD and Li, Z and Hashsham, SA and Jiang, X and Tiedje, JM},
title = {Does anaerobic condition play a more positive role in dissipation of antibiotic resistance genes in soil?.},
journal = {The Science of the total environment},
volume = {757},
number = {},
pages = {143737},
doi = {10.1016/j.scitotenv.2020.143737},
pmid = {33243511},
issn = {1879-1026},
mesh = {Anaerobiosis ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Soil ; Soil Microbiology ; },
abstract = {The persistence of antibiotic resistance genes (ARGs) under the aerobic vs. anaerobic conditions is unknown, especially under different fertilization. Towards this goal, a microcosm experiment was carried out with chemical fertilized and manured soil under aerobic and anaerobic conditions. High throughput qPCR was used to analyze ARGs with 144 primer sets and sequencing for microorganisms. Completely different dynamics of ARGs were observed in soil under aerobic and anaerobic conditions, regardless of the fertilization type. ARGs had different half-lives, even though they confer resistance to the same type of antibiotics. Aminoglycoside, chloramphenicol, macrolide - lincosamide - streptogramin B (MLSB) and tetracycline resistance genes were significantly accumulated in the aerobic soils. Anaerobic soil possessed a higher harboring capacity for exogenous microorganisms and ARGs than aerobic soil. The interaction between ARGs and mobile genetic elements (MGEs) in manured soil under aerobic condition was more pronounced than the anaerobic condition. These findings unveil that anaerobic soil could play a more positive role in reducing potential risk of ARGs in the farmland environment.},
}
@article {pmid33242583,
year = {2021},
author = {Garrido-Benavent, I and Pérez-Ortega, S and de Los Ríos, A and Mayrhofer, H and Fernández-Mendoza, F},
title = {Neogene speciation and Pleistocene expansion of the genus Pseudephebe (Parmeliaceae, lichenized fungi) involving multiple colonizations of Antarctica.},
journal = {Molecular phylogenetics and evolution},
volume = {155},
number = {},
pages = {107020},
doi = {10.1016/j.ympev.2020.107020},
pmid = {33242583},
issn = {1095-9513},
mesh = {Antarctic Regions ; Ecosystem ; *Genetic Speciation ; Haplotypes/genetics ; Lichens/*classification ; Parmeliaceae/*classification ; Phylogeny ; Phylogeography ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; },
abstract = {Widespread geographic distributions in lichens have been usually explained by the high dispersal capacity of their tiny diaspores. However, recent phylogenetic surveys have challenged this assumption and provided compelling evidence for cryptic speciation and more restricted distribution ranges in diverse lineages of lichen-forming fungi. To evaluate these scenarios, we focus on the fungal genus Pseudephebe (Parmeliaceae) which includes amphitropical species, a distribution pattern whose origin has been a matter of debate since first recognized in the nineteenth century. In our study, a six-locus dataset and a broad specimen sampling covering almost all Earth's continents is used to investigate species delimitation in Pseudephebe. Population structure, gene flow and dating analyses, as well as genealogical reconstruction methods, are employed to disentangle the most plausible transcontinental migration routes, and estimate the timing of the origin of the amphitropical distribution and the Antarctic populations. Our results demonstrate the existence of three partly admixed phylogenetic species that diverged between the Miocene and Pliocene, and whose Quaternary distribution has been strongly driven by glacial cycles. Pseudephebe minuscula is the only species showing an amphitropical distribution, with populations in Antarctica, whereas the restricted distribution of P. pubescens and an undescribed Alaskan species might reflect the survival of these species in European and North American refugia. Our microevolutionary analyses suggest a Northern Hemisphere origin for P. minuscula, which could have dispersed into the Southern Hemisphere directly and/or through "mountain-hopping" during the Pleistocene. The Antarctic populations of this species are sorted into two genetic clusters: populations of the Antarctic Peninsula were grouped together with South American ones, and the Antarctic Continental populations formed a second cluster with Bolivian and Svalbard populations. Therefore, our data strongly suggest that the current distribution of P. minuscula in Antarctica is the outcome of multiple, recent colonizations. In conclusion, our results stress the need for integrating species delimitation and population analyses to properly approach historical biogeography in lichen-forming fungi.},
}
@article {pmid33242086,
year = {2021},
author = {Yue, L and Kong, W and Li, C and Zhu, G and Zhu, L and Makhalanyane, TP and Cowan, DA},
title = {Dissolved inorganic carbon determines the abundance of microbial primary producers and primary production in Tibetan Plateau lakes.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {2},
pages = {},
doi = {10.1093/femsec/fiaa242},
pmid = {33242086},
issn = {1574-6941},
mesh = {*Carbon ; Ecosystem ; *Lakes ; Salinity ; Tibet ; },
abstract = {Climate change globally accelerates the shrinkage of inland lakes, resulting in increases in both water salinity and dissolved inorganic carbon (DIC). The increases of salinity and DIC generate contrasting effects on microbial primary producers and primary production, however, their combined effects remain unclear in aquatic ecosystems. We hypothesized that increased DIC mitigates the constraints of enhanced salinity on microbial primary producers and primary production. To test this, we employed isotope labeling and molecular methods to explore primary production and four dominant types of microbial primary producers (form IA, IB, IC and ID) in lakes on the Tibetan Plateau. Results showed that DIC was positively correlated with the abundance of the form IAB and ID microbial primary producers and primary production (all P < 0.001) and offset salinity constraints. Structural equation models elucidated that DIC substantially enhanced primary production by stimulating the abundance of form ID microbial primary producers. The abundance of form ID primary producers explained more variations (14.6%) of primary production than form IAB (6%) and physicochemical factors (6.8%). Diatoms (form ID) played a determinant role in primary production in the lakes by adapting to high DIC and high salinity. Our findings suggest that inland lakes may support higher primary productivity in future climate change scenarios.},
}
@article {pmid33242082,
year = {2020},
author = {Stahl, LM and Olson, JB},
title = {Environmental abiotic and biotic factors affecting the distribution and abundance of Naegleria fowleri.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {1},
pages = {},
pmid = {33242082},
issn = {1574-6941},
mesh = {*Amoeba ; *Central Nervous System Protozoal Infections ; Fresh Water ; Humans ; *Naegleria fowleri ; Water ; },
abstract = {Naegleria fowleri is a free-living protozoan that resides in soil and freshwater. Human intranasal amoebae exposure through water or potentially dust particles can culminate in primary amoebic meningoencephalitis, which generally causes death. While many questions remain regarding pathogenesis, the microbial ecology of N. fowleri is even less understood. This review outlines current knowledge of the environmental abiotic and biotic factors that affect the distribution and abundance of N. fowleri. Although the impacts of some abiotic factors remain poorly investigated or inconclusive, N. fowleri appears to have a wide pH range, low salinity tolerance and thermophilic preference. From what is known about biotic factors, the amoebae preferentially feed upon bacteria and are preyed upon by other free-living amoebae. Additional laboratory and environmental studies are needed to fill in knowledge gaps, which are crucial for surveillance and management of N. fowleri in freshwaters. As surface water temperatures increase with climate change, it is likely that this amoeba will pose a greater threat to human health, suggesting that identifying its abiotic and biotic preferences is critical to mitigating this risk.},
}
@article {pmid33240229,
year = {2020},
author = {Shaw, C and Brooke, C and Hawley, E and Connolly, MP and Garcia, JA and Harmon-Smith, M and Shapiro, N and Barton, M and Tringe, SG and Glavina Del Rio, T and Culley, DE and Castenholz, R and Hess, M},
title = {Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {572131},
pmid = {33240229},
issn = {1664-302X},
abstract = {Cyanobacteria are found in most illuminated environments and are key players in global carbon and nitrogen cycling. Although significant efforts have been made to advance our understanding of this important phylum, still little is known about how members of the cyanobacteria affect and respond to changes in complex biological systems. This lack of knowledge is in part due to our dependence on pure cultures when determining the metabolism and function of a microorganism. We took advantage of the Culture Collection of Microorganisms from Extreme Environments (CCMEE), a collection of more than 1,000 publicly available photosynthetic co-cultures maintained at the Pacific Northwest National Laboratory, and assessed via 16S rRNA amplicon sequencing if samples readily available from public culture collection could be used in the future to generate new insights into the role of microbial communities in global and local carbon and nitrogen cycling. Results from this work support the existing notion that culture depositories in general hold the potential to advance fundamental and applied research. Although it remains to be seen if co-cultures can be used at large scale to infer roles of individual organisms, samples that are publicly available from existing co-cultures depositories, such as the CCMEE, might be an economical starting point for such studies. Access to archived biological samples, without the need for costly field work, might in some circumstances be one of the few remaining ways to advance the field and to generate new insights into the biology of ecosystems that are not easily accessible. The current COVID-19 pandemic, which makes sampling expeditions almost impossible without putting the health of the participating scientists on the line, is a very timely example.},
}
@article {pmid33239370,
year = {2020},
author = {Props, R and Monsieurs, P and Vandamme, P and Leys, N and Denef, VJ and Boon, N},
title = {Correction for Props et al., "Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions".},
journal = {mSphere},
volume = {5},
number = {6},
pages = {},
doi = {10.1128/mSphere.01143-20},
pmid = {33239370},
issn = {2379-5042},
}
@article {pmid33238123,
year = {2020},
author = {Zhang, H and Madi, A and Yosef, N and Chihara, N and Awasthi, A and Pot, C and Lambden, C and Srivastava, A and Burkett, PR and Nyman, J and Christian, E and Etminan, Y and Lee, A and Stroh, H and Xia, J and Karwacz, K and Thakore, PI and Acharya, N and Schnell, A and Wang, C and Apetoh, L and Rozenblatt-Rosen, O and Anderson, AC and Regev, A and Kuchroo, VK},
title = {An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets.},
journal = {Cell reports},
volume = {33},
number = {8},
pages = {108433},
pmid = {33238123},
issn = {2211-1247},
support = {R01 NS030843/NS/NINDS NIH HHS/United States ; 677251/ERC_/European Research Council/International ; P01 AI129880/AI/NIAID NIH HHS/United States ; P01 AI056299/AI/NIAID NIH HHS/United States ; R01 CA229400/CA/NCI NIH HHS/United States ; P01 AI039671/AI/NIAID NIH HHS/United States ; U19 AI133524/AI/NIAID NIH HHS/United States ; R01 AI144166/AI/NIAID NIH HHS/United States ; P01 AI073748/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Gene Regulatory Networks/*genetics ; Humans ; Interleukin-10/*metabolism ; Interleukin-27/*metabolism ; Mice ; Mice, Knockout ; Th1 Cells/*metabolism ; },
abstract = {Interleukin-27 (IL-27) is an immunoregulatory cytokine that suppresses inflammation through multiple mechanisms, including induction of IL-10, but the transcriptional network mediating its diverse functions remains unclear. Combining temporal RNA profiling with computational algorithms, we predict 79 transcription factors induced by IL-27 in T cells. We validate 11 known and discover 5 positive (Cebpb, Fosl2, Tbx21, Hlx, and Atf3) and 2 negative (Irf9 and Irf8) Il10 regulators, generating an experimentally refined regulatory network for Il10. We report two central regulators, Prdm1 and Maf, that cooperatively drive the expression of signature genes induced by IL-27 in type 1 regulatory T cells, mediate IL-10 expression in all T helper cells, and determine the regulatory phenotype of colonic Foxp3[+] regulatory T cells. Prdm1/Maf double-knockout mice develop spontaneous colitis, phenocopying ll10-deficient mice. Our work provides insights into IL-27-driven transcriptional networks and identifies two shared Il10 regulators that orchestrate immunoregulatory programs across T helper cell subsets.},
}
@article {pmid33237956,
year = {2020},
author = {Buranarom, N and Komin, O and Matangkasombut, O},
title = {Hyposalivation, oral health, and Candida colonization in independent dentate elders.},
journal = {PloS one},
volume = {15},
number = {11},
pages = {e0242832},
pmid = {33237956},
issn = {1932-6203},
mesh = {Aged ; Candida albicans/pathogenicity ; Candidiasis, Oral/epidemiology/*microbiology/pathology/prevention &amp; control ; Dental Prosthesis/*microbiology ; Female ; Humans ; Male ; Middle Aged ; Mouth/*microbiology ; Mouth, Edentulous/epidemiology/*microbiology/pathology ; Oral Health ; Risk Factors ; Saliva/microbiology ; Secretory Rate ; Xerostomia/epidemiology/microbiology/pathology ; },
abstract = {Hyposalivation is an important problem in elders and could interfere with several oral functions and microbial ecology. While the number of independent elders who retain more natural teeth increases worldwide, few studies examined hyposalivation in this population. Thus, this study aims to examine relationships between hyposalivation, oral health conditions and oral Candida colonization in independent dentate elders and evaluate factors associated with salivary flow and Candida carriage. We conducted a cross-sectional study in fifty-three dentate elders (≥65 years old with at least 4 pairs of posterior occlusal contacts) with no, or well-controlled, systemic conditions. Participants were interviewed for medical history, subjective dry mouth symptoms, oral hygiene practices and denture information. Unstimulated and stimulated salivary flow rates, objective dry mouth signs, gingival, tongue-coating, and root-caries indices were recorded. Stimulated saliva was cultured on Sabouraud-dextrose agar for Candida counts. Candida species were identified using chromogenic Candida agar and polymerase chain reaction. Statistical significance level was set at p<0.05. The results showed that hyposalivation was associated with higher gingival and tongue-coating indices (p = 0.003 and 0.015, respectively), but not root-caries index. Hyposalivation was also associated with higher prevalence of oral Candida colonization (p = 0.010; adjusted OR = 4.36, 95% confidence interval = 1.29-14.72). These two indices and Candida load were negatively correlated with unstimulated and stimulated salivary flow rates. Interestingly, non-albicans Candida species were more prevalent in denture wearers (p = 0.017). Hence, hyposalivation is a risk factor for poorer oral health and oral Candida colonization in independent dentate elders. Because of its potential adverse effects on oral and systemic health, hyposalivation should be carefully monitored in elders.},
}
@article {pmid33236218,
year = {2021},
author = {Saxena, S and Strobel, GA},
title = {Marvellous Muscodor spp.: Update on Their Biology and Applications.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {5-20},
pmid = {33236218},
issn = {1432-184X},
mesh = {Ascomycota ; Biology ; Endophytes ; Humans ; *Volatile Organic Compounds ; *Xylariales ; },
abstract = {Nearly 20 years ago, the first report appeared on the discovery of a novel genus-Muscodor. This organism was isolated as an endophyte from a cinnamon tree that had been introduced to Honduras from Sri Lanka in the early part of the last century. Characteristically, the original Muscodor albus, and all of its species isolated since that time are non-spore producers and each one exudes a characteristic spectrum of volatile bioactive compounds. The majority have a whitish mycelium, which is sometimes coiling, intertwined and decorated with variously shaped structures. Presently, there are at least 22 type species known/documented and each has been described as an endophyte from various plant families with widely varying habitats. An enormous variety of volatile organic compounds (VOCs) are produced by Muscodor spp. and some of these include esters, acids, aldehydes, ketones, aromatics, alkanes, alcohols, nitrosamides and terpenoids. The VOCs are both inhibitory and lethal to a wide variety of fungi and bacteria including some major pathogens of plants and humans. Interestingly, in almost all cases studied, no one compound by itself can mimic the bioactivity of the complete gas mixture, suggesting that the volatiles are acting in a synergistic manner and this has been tested with individual as well as the VOCs in various mixtures and concentrations. This review will discuss some of the recent findings in all aspects of this unique fungal genus whilst at the same time pointing out some of the major questions that remain about its biology, ecology and its applications in agriculture, medicine and other sectors. Most importantly, the authors provide arguments supporting the claim that Muscodor is taxonomically distinct from Induratia, a recently proposed change to its nomenclature.},
}
@article {pmid33233106,
year = {2020},
author = {Lianou, A and Nychas, GE and Koutsoumanis, KP},
title = {Strain variability in biofilm formation: A food safety and quality perspective.},
journal = {Food research international (Ottawa, Ont.)},
volume = {137},
number = {},
pages = {109424},
doi = {10.1016/j.foodres.2020.109424},
pmid = {33233106},
issn = {1873-7145},
mesh = {*Biofilms ; *Food Microbiology ; Food Safety ; },
abstract = {The inherent differences in microbial behavior among identically treated strains of the same microbial species, referred to as "strain variability", are regarded as an important source of variability in microbiological studies. Biofilms are defined as the structured multicellular communities with complex architecture that enable microorganisms to grow adhered to abiotic or living surfaces and constitute a fundamental aspect of microbial ecology. The research studies assessing the strain variability in biofilm formation are relatively few compared to the ones evaluating other aspects of microbial behavior such as virulence, growth and stress resistance. Among the available research data on intra-species variability in biofilm formation, compiled and discussed in the present review, most of them refer to foodborne pathogens as compared to spoilage microorganisms. Molecular and physiological aspects of biofilm formation potentially related to strain-specific responses, as well as information on the characterization and quantitative description of this type of biological variability are presented and discussed. Despite the considerable amount of available information on the strain variability in biofilm formation, there are certain data gaps and still-existing challenges that future research should cover and address. Current and future advances in systems biology and omics technologies are expected to aid significantly in the explanation of phenotypic strain variability, including biofilm formation variability, allowing for its integration in microbiological risk assessment.},
}
@article {pmid33232448,
year = {2021},
author = {d'Enfert, C and Kaune, AK and Alaban, LR and Chakraborty, S and Cole, N and Delavy, M and Kosmala, D and Marsaux, B and Fróis-Martins, R and Morelli, M and Rosati, D and Valentine, M and Xie, Z and Emritloll, Y and Warn, PA and Bequet, F and Bougnoux, ME and Bornes, S and Gresnigt, MS and Hube, B and Jacobsen, ID and Legrand, M and Leibundgut-Landmann, S and Manichanh, C and Munro, CA and Netea, MG and Queiroz, K and Roget, K and Thomas, V and Thoral, C and Van den Abbeele, P and Walker, AW and Brown, AJP},
title = {The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives.},
journal = {FEMS microbiology reviews},
volume = {45},
number = {3},
pages = {},
pmid = {33232448},
issn = {1574-6976},
support = {MR/V033417/1/MRC_/Medical Research Council/United Kingdom ; MR/N006364/2/MRC_/Medical Research Council/United Kingdom ; MR/M026663/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/N006364/1/MRC_/Medical Research Council/United Kingdom ; MR/M026663/2/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Candida albicans/immunology/pathogenicity ; Candidiasis/*immunology/*microbiology ; Host Microbial Interactions/*physiology ; Humans ; Microbial Interactions/*physiology ; },
abstract = {Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.},
}
@article {pmid33232202,
year = {2021},
author = {Coleine, C and Stajich, JE and de Los Ríos, A and Selbmann, L},
title = {Beyond the extremes: Rocks as ultimate refuge for fungi in drylands.},
journal = {Mycologia},
volume = {113},
number = {1},
pages = {108-133},
doi = {10.1080/00275514.2020.1816761},
pmid = {33232202},
issn = {1557-2536},
mesh = {Adaptation, Physiological ; Antarctic Regions ; Biodiversity ; Climate Change ; *Desert Climate ; Droughts ; *Extreme Environments ; *Fungi/classification/isolation &amp; purification ; Geologic Sediments/microbiology ; Lichens ; },
abstract = {In an era of rapid climate change and expansion of desertification, the extremely harsh conditions of drylands are a true challenge for microbial life. Under drought conditions, where most life forms cannot survive, rocks represent the main refuge for life. Indeed, the endolithic habitat provides thermal buffering, physical stability, and protection against incident ultraviolet (UV) radiation and solar radiation and, to some extent, ensures water retention to microorganisms. The study of these highly specialized extreme-tolerant and extremophiles may provide tools for understanding microbial interactions and processes that allow them to keep their metabolic machinery active under conditions of dryness and oligotrophy that are typically incompatible with active life, up to the dry limits for life. Despite lithobiontic communities being studied all over the world, a comprehensive understanding of their ecology, evolution, and adaptation is still nascent. Herein, we survey the fungal component of these microbial ecosystems. We first provide an overview of the main defined groups (i.e., lichen-forming fungi, black fungi, and yeasts) of the most known and studied Antarctic endolithic communities that are almost the only life forms ensuring ecosystem functionality in the ice-free areas of the continent. For each group, we discuss their main traits and their diversity. Then, we focus on the fungal taxonomy and ecology of other worldwide endolithic communities. Finally, we highlight the utmost importance of a global rock survey in order to have a comprehensive view of the diversity, distribution, and functionality of these fungi in drylands, to obtain tools in desert area management, and as early alarm systems to climate change.},
}
@article {pmid33231332,
year = {2021},
author = {Stothart, MR and Greuel, RJ and Gavriliuc, S and Henry, A and Wilson, AJ and McLoughlin, PD and Poissant, J},
title = {Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters.},
journal = {Molecular ecology},
volume = {30},
number = {2},
pages = {555-571},
doi = {10.1111/mec.15747},
pmid = {33231332},
issn = {1365-294X},
mesh = {Animals ; Bacteria/genetics ; Canada ; Female ; Horses ; Islands ; *Microbiota/genetics ; Phylogeny ; },
abstract = {Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.},
}
@article {pmid33230594,
year = {2021},
author = {Paul, P and Chakraborty, P and Chatterjee, A and Sarker, RK and Dastidar, DG and Kundu, T and Sarkar, N and Das, A and Tribedi, P},
title = {1,4-Naphthoquinone accumulates reactive oxygen species in Staphylococcus aureus: a promising approach towards effective management of biofilm threat.},
journal = {Archives of microbiology},
volume = {203},
number = {3},
pages = {1183-1193},
pmid = {33230594},
issn = {1432-072X},
mesh = {Anti-Bacterial Agents/pharmacology ; Biofilms/*drug effects ; Humans ; Microbial Sensitivity Tests ; Naphthoquinones/*pharmacology ; Reactive Oxygen Species/*metabolism ; Staphylococcal Infections/prevention &amp; control ; Staphylococcus aureus/*drug effects ; },
abstract = {Staphylococcus aureus, a Gram-positive opportunistic microorganism, promotes pathogenicity in the human host through biofilm formation. Microorganisms associated with biofilm often exhibit drug-resistance property that poses a major threat to public healthcare. Thus, the exploration of new therapeutic approaches is the need of the hour to manage biofilm-borne infections. In the present study, efforts are put together to test the antimicrobial as well as antibiofilm activity of 1,4-naphthoquinone against Staphylococcus aureus. The result showed that the minimum bactericidal concentration (MBC) of this compound was found to be 100 µg/mL against Staphylococcus aureus. In this regard, an array of experiments (crystal violet, biofilm protein measurement, and microscopic analysis) related to biofilm assay were conducted with the sub-MBC concentrations (1/20 and 1/10 MBC) of 1,4-naphthoquinone. All the results of biofilm assay demonstrated that these tested concentrations (1/20 and 1/10 MBC) of the compound (1,4-naphthoquinone) showed a significant reduction in biofilm development by Staphylococcus aureus. Moreover, the tested concentrations (1/20 and 1/10 MBC) of the compound (1,4-naphthoquinone) were able to reduce the microbial motility of Staphylococcus aureus that might affect the development of biofilm. Further studies revealed that the treatment of 1,4-naphthoquinone to the organism was found to increase the cellular accumulation of reactive oxygen species (ROS) that resulted in the inhibition of biofilm formation by Staphylococcus aureus. Hence, it can be concluded that 1,4-naphthoquinone might be considered as a promising compound towards biofilm inhibition caused by Staphylococcus aureus.},
}
@article {pmid33228011,
year = {2020},
author = {Cano-Ortiz, A and Laborda-Illanes, A and Plaza-Andrades, I and Membrillo Del Pozo, A and Villarrubia Cuadrado, A and Rodríguez Calvo de Mora, M and Leiva-Gea, I and Sanchez-Alcoholado, L and Queipo-Ortuño, MI},
title = {Connection between the Gut Microbiome, Systemic Inflammation, Gut Permeability and FOXP3 Expression in Patients with Primary Sjögren's Syndrome.},
journal = {International journal of molecular sciences},
volume = {21},
number = {22},
pages = {},
pmid = {33228011},
issn = {1422-0067},
support = {CPI13/00003//Miguel Servet Type II" program, ISCIII, Spain/ ; C-0030-2018//"Nicolas Monardes" research program of the Consejer&#xed;a de Salud (C-0030-2018, Junta de Andaluc&#xed;a, Spain/ ; PE-0106-2019//Predoctoral grant from Consejer&#xed;a de Salud y Familia, Andalucia, Spain/ ; FI19-00112//predoctoral grant PFIS-ISCIII, Madrid, Spain/ ; },
mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Adolescent ; Adult ; Aged ; Bacteroides/classification/genetics/isolation &amp; purification ; Body Mass Index ; Case-Control Studies ; Dysbiosis/genetics/immunology/*microbiology/pathology ; Feces/microbiology ; Female ; Firmicutes/classification/genetics/isolation &amp; purification ; Forkhead Transcription Factors/genetics/*immunology ; Gastrointestinal Microbiome/*immunology ; Genetic Variation ; Humans ; Inflammation ; Interleukin-10/genetics/immunology ; Intestines/immunology/*microbiology ; Middle Aged ; Permeability ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sjogren's Syndrome/genetics/immunology/*microbiology/pathology ; T-Lymphocytes, Regulatory/microbiology ; },
abstract = {The aims of this study were to explore intestinal microbial composition and functionality in primary Sjögren's syndrome (pSS) and to relate these findings to inflammation, permeability and the transcription factor Forkhead box protein P3 (FOXP3) gene expression in peripheral blood. The study included 19 pSS patients and 19 healthy controls matched for age, sex, and body mass index. Fecal bacterial DNA was extracted and analyzed by 16S rRNA sequencing using an Ion S5 platform followed by a bioinformatics analysis using Quantitative Insights into Microbial Ecology (QIIME II) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our data suggest that the gut microbiota of pSS patients differs at both the taxonomic and functional levels with respect to healthy controls. The gut microbiota profile of our pSS patients was characterized by a lower diversity and richness and with Bacteroidetes dominating at the phylum level. The pSS patients had less beneficial or commensal butyrate-producing bacteria and a higher proportion of opportunistic pathogens with proinflammatory activity, which may impair intestinal barrier function and therefore contribute to inflammatory processes associated with pSS by increasing the production of proinflammatory cytokines and decreasing the release of the anti-inflammatory cytokine IL-10 and the peripheral FOXP3 mRNA expression, implicated in the development and function of regulatory T cells (Treg) cells. Further studies are needed to better understand the real impact of dysbiosis on the course of pSS and to conceive preventive or therapeutic strategies to counteract microbiome-driven inflammation.},
}
@article {pmid33226191,
year = {2020},
author = {Gonçalves E Silva, F and Dos Santos, HF and de Assis Leite, DC and Lutfi, DS and Vianna, M and Rosado, AS},
title = {Skin and stinger bacterial communities in two critically endangered rays from the South Atlantic in natural and aquarium settings.},
journal = {MicrobiologyOpen},
volume = {9},
number = {12},
pages = {e1141},
pmid = {33226191},
issn = {2045-8827},
mesh = {Animals ; Atlantic Ocean ; Bacteria/*classification/*genetics/isolation &amp; purification ; Brazil ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Skates, Fish/classification/*microbiology ; Skin/*microbiology ; },
abstract = {Bacterial communities of two critically endangered rays from the South Atlantic, the butterfly ray (Gymnura altavela) and the groovebelly ray (Dasyatis hypostigma), were described using 16S rRNA gene metabarcoding. The study characterized the bacterial communities associated with (i) G. altavela in natural (in situ) and aquarium (ex situ) settings, (ii) skin and stinger of G. altavela, and D. hypostigma in aquaria, and (iii) newborns and adults of D. hypostigma. The results revealed potentially antibiotic-producing bacterial groups on the skin of rays from the natural environment, and some taxa with the potential to benefit ray health, mainly in rays from the natural environment, as well as possible pathogens to other animals, including fish and humans. Differences were observed between the G. altavela and D. hypostigma bacteria composition, as well as between the skin and stinger bacterial composition. The bacterial community associated with D. hypostigma changed with the age of the ray. The aquarium environment severely impacted the G. altavela bacteria composition, which changed from a complex bacterial community to one dominated almost exclusively by two taxa, Oceanimonas sp. and Sediminibacterium sp. on the skin and stinger, respectively.},
}
@article {pmid33225409,
year = {2021},
author = {Labrador, MDM and Doña, J and Serrano, D and Jovani, R},
title = {Quantitative Interspecific Approach to the Stylosphere: Patterns of Bacteria and Fungi Abundance on Passerine Bird Feathers.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {1088-1097},
pmid = {33225409},
issn = {1432-184X},
mesh = {Animals ; Bacteria/genetics ; *Bird Diseases ; Feathers ; Fungi/genetics ; Humans ; *Mites ; *Passeriformes ; },
abstract = {Feathers are the habitat of a myriad of organisms, from fungi and bacteria to lice and mites. Although most studies focus on specific taxa and their interaction with the bird host, anecdotal data glimpse feathers as holders of a system with its own ecology, what we call here the stylosphere. A major gap in our knowledge of the stylosphere is the ecology of the total abundance of microorganisms, being also rare to find studies that analyze abundance of more than one group of microorganisms at the bird interspecific level. Here, we quantified bacterial and fungi abundances through qPCR on the wing feathers of 144 birds from 24 passerine and one non-passerine bird species from three localities in Southern Spain. Bacteria and fungi abundances spanned three orders of magnitude among individual birds, but were consistent when comparing the right and the left wing feathers of individuals. Sampling locality explained ca. 14% of the variation in both bacteria and fungi abundances. Even when statistically controlling for sampling locality, microbial abundances consistently differed between birds from different species, but these differences were not explained by bird phylogeny. Finally, bird individuals and species having more bacteria also tended to held larger abundances of fungi. Our results suggest a quite complex explanation for stylosphere microorganisms' abundance, being shaped by bird individual and species traits, as well as environmental factors, and likely bacteria-fungi interactions.},
}
@article {pmid33220680,
year = {2020},
author = {Hall, MA and Brettell, LE and Liu, H and Nacko, S and Spooner-Hart, R and Riegler, M and Cook, JM},
title = {Temporal changes in the microbiome of stingless bee foragers following colony relocation.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {1},
pages = {},
doi = {10.1093/femsec/fiaa236},
pmid = {33220680},
issn = {1574-6941},
mesh = {Animals ; Bacteria/genetics ; Bees ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Maintaining beneficial interactions with microbial symbionts is vital for animal health. Yet, for social insects, the stability of microbial associations within and between cohorts is largely unknown. We investigated temporal changes in the microbiomes of nine stingless bee (Tetragonula carbonaria) colonies at seven timepoints across a 10-month period when moved between two climatically and florally different sites. Bacterial 16S rRNA gene and fungal ITS amplicon sequencing confirmed that microbiomes varied considerably between colonies initially at site one. However, following relocation, considerable changes occurred in bacterial community composition within each colony, and the microbiome composition became more similar across colonies. Notably, Snodgrassella disappeared and Zymobacter appeared as relatively abundant taxa. Remarkably, bacterial communities within colonies continued to shift over time but remained similar across colonies, becoming dominated by Acinetobacter six months after returning to the original site. Our results indicate that the stingless bee microbiome can undergo major changes in response to the environment, and that these changes can be long-lasting. Such legacy effects have not been reported for corbiculate bees. Further understanding the microbial ecology of stingless bees will aid future management of colonies used in agricultural production.},
}
@article {pmid33220679,
year = {2020},
author = {Nilsson, JF and Castellani, LG and Draghi, WO and Mogro, EG and Wibberg, D and Winkler, A and Hansen, LH and Schlüter, A and Pühler, A and Kalinowski, J and Torres Tejerizo, GA and Pistorio, M},
title = {Global transcriptome analysis of Rhizobium favelukesii LPU83 in response to acid stress.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {1},
pages = {},
doi = {10.1093/femsec/fiaa235},
pmid = {33220679},
issn = {1574-6941},
mesh = {Acids/toxicity ; Gene Expression Profiling ; *Rhizobium/genetics ; Symbiosis ; },
abstract = {Acidic environments naturally occur worldwide and inappropriate agricultural management may also cause acidification of soils. Low soil pH values are an important barrier in the plant-rhizobia interaction. Acidic conditions disturb the establishment of the efficient rhizobia usually used as biofertilizer. This negative effect on the rhizobia-legume symbiosis is mainly due to the low acid tolerance of the bacteria. Here, we describe the identification of relevant factors in the acid tolerance of Rhizobium favelukesii using transcriptome sequencing. A total of 1924 genes were differentially expressed under acidic conditions, with ∼60% underexpressed. Rhizobium favelukesii acid response mainly includes changes in the energy metabolism and protein turnover, as well as a combination of mechanisms that may contribute to this phenotype, including GABA and histidine metabolism, cell envelope modifications and reverse proton efflux. We confirmed the acid-sensitive phenotype of a mutant in the braD gene, which showed higher expression under acid stress. Remarkably, 60% of the coding sequences encoded in the symbiotic plasmid were underexpressed and we evidenced that a strain cured for this plasmid featured an improved performance under acidic conditions. Hence, this work provides relevant information in the characterization of genes associated with tolerance or adaptation to acidic stress of R. favelukesii.},
}
@article {pmid33219851,
year = {2021},
author = {Sun, M and Li, T and Li, D and Zhao, Y and Gao, F and Sun, L and Li, X},
title = {Conversion of Land Use from Upland to Paddy Field Changes Soil Bacterial Community Structure in Mollisols of Northeast China.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {1018-1028},
pmid = {33219851},
issn = {1432-184X},
support = {41701289//National Natural Science Foundation of China/ ; 2018M640287//China Postdoctoral Science Foundation/ ; },
mesh = {Agriculture ; Carbon/analysis ; China ; *Oryza ; RNA, Ribosomal, 16S ; *Soil ; Soil Microbiology ; },
abstract = {Mollisols are extremely important soil resource for crop and forage production. In northeast China, it is a major land use management practice from dry land crops to irrigated rice. However, there is few data regarding soil quality and microbial composition in Mollisols during land use transition. Here, we analyzed the upper 30 cm of soil from land with more than 30 years of paddy use and from adjacent areas with upland crops. Our results showed that land use and soil depth had a significant effect on soil properties and enzyme activities. Soil moisture (SM) and soil organic carbon (SOC) contents were substantially higher in paddy fields than in upland crop lands, while nitrogen-related enzyme activities were lower. Following the land use change, bacterial diversity was increased and bacterial community composition changed. Taxonomic analyses showed that Proteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes were the dominant phyla present. At family level, Gemmatimonadaceae decreased with land use change, while Syntrophorhabdaceae and Syntrophacea that play a part in methane cycling and nitrifying bacteria such as Nitrospiraceae increased, indicating that the structure and composition of the bacterial community might be a promising indicator of Mollisol health. Redundancy analysis indicated that land use type had a stronger effect on the soil bacterial community composition than soil depth. Additionally, bacterial community composition was closely associated with soil parameters such as soil moisture, pH, SOC, NO3[-]-N, and NH4[+]-N. Overall, land use change affects the physical and chemical properties of the soil, resulting in changes in the composition of the soil bacterial community and flora. These changes could provide a view of the bacterial community assembly and functional shifts following land use change.},
}
@article {pmid33219400,
year = {2021},
author = {Torralba, MG and Aleti, G and Li, W and Moncera, KJ and Lin, YH and Yu, Y and Masternak, MM and Golusinski, W and Golusinski, P and Lamperska, K and Edlund, A and Freire, M and Nelson, KE},
title = {Correction to: Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {1047},
doi = {10.1007/s00248-020-01641-3},
pmid = {33219400},
issn = {1432-184X},
}
@article {pmid33219399,
year = {2021},
author = {Khan, S and Vancuren, SJ and Hill, JE},
title = {A Generalist Lifestyle Allows Rare Gardnerella spp. to Persist at Low Levels in the Vaginal Microbiome.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {1048-1060},
pmid = {33219399},
issn = {1432-184X},
mesh = {Female ; Gardnerella ; Humans ; Life Style ; *Microbiota/genetics ; Vagina ; *Vaginosis, Bacterial ; },
abstract = {Gardnerella spp. are considered a hallmark of bacterial vaginosis, a dysbiosis of the vaginal microbiome. There are four cpn60 sequence-based subgroups within the genus (A, B, C and D), and thirteen genome species have been defined recently. Gardnerella spp. co-occur in the vaginal microbiome with varying abundance, and these patterns are shaped by a resource-dependent, exploitative competition, which affects the growth rate of subgroups A, B and C negatively. The growth rate of rarely abundant subgroup D, however, increases with the increasing number of competitors, negatively affecting the growth rate of others. We hypothesized that a nutritional generalist lifestyle and minimal niche overlap with the other more abundant Gardnerella spp. facilitate the maintenance of subgroup D in the vaginal microbiome through negative frequency-dependent selection. Using 40 whole-genome sequences from isolates representing all four subgroups, we found that they could be distinguished based on the content of their predicted proteomes. Proteins associated with carbohydrate and amino acid uptake and metabolism were significant contributors to the separation of subgroups. Subgroup D isolates had significantly more of their proteins assigned to amino acid metabolism than the other subgroups. Subgroup D isolates were also significantly different from others in terms of number and type of carbon sources utilized in a phenotypic assay, while the other three could not be distinguished. Overall, the results suggest that a generalist lifestyle and lack of niche overlap with other Gardnerella spp. leads to subgroup D being favoured by negative frequency-dependent selection in the vaginal microbiome.},
}
@article {pmid33218996,
year = {2021},
author = {Hansen, ML and He, Z and Wibowo, M and Jelsbak, L},
title = {A Whole-Cell Biosensor for Detection of 2,4-Diacetylphloroglucinol (DAPG)-Producing Bacteria from Grassland Soil.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {3},
pages = {},
pmid = {33218996},
issn = {1098-5336},
mesh = {*Biosensing Techniques ; Grassland ; Pest Control, Biological ; Phloroglucinol/*analogs &amp; derivatives/metabolism ; Pseudomonas/*isolation &amp; purification/*metabolism ; Soil ; Soil Microbiology ; },
abstract = {Fluorescent Pseudomonas spp. producing the antibiotic 2,4-diacetylphloroglucinol (DAPG) are ecologically important in the rhizosphere, as they can control phytopathogens and contribute to disease suppression. DAPG can also trigger a systemic resistance response in plants and stimulate root exudation and branching as well as induce plant-beneficial activities in other rhizobacteria. While studies of DAPG-producing Pseudomonas have predominantly focused on rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments, such as bulk soil and grassland, where the level of DAPG producers are predicted to be low. In this study, we constructed a whole-cell biosensor for detection of DAPG and DAPG-producing bacteria from environmental samples. The constructed biosensor contains a phlF response module and either lacZ or lux genes as output modules assembled on a pSEVA plasmid backbone for easy transfer to different host species and to enable easy future genetic modifications. We show that the sensor is highly specific toward DAPG, with a sensitivity in the low nanomolar range (>20 nM). This sensitivity is comparable to the DAPG levels identified in rhizosphere samples by chemical analysis. The biosensor enables guided isolation of DAPG-producing Pseudomonas Using the biosensor, we probed the same grassland soil sampling site to isolate genetically related DAPG-producing Pseudomonas kilonensis strains over a period of 12 months. Next, we used the biosensor to determine the frequency of DAPG-producing pseudomonads within three different grassland soil sites and showed that DAPG producers can constitute part of the Pseudomonas population in the range of 0.35 to 17% at these sites. Finally, we showed that the biosensor enables detection of DAPG produced by non-Pseudomonas species. Our study shows that a whole-cell biosensor for DAPG detection can facilitate isolation of bacteria that produce this important secondary metabolite and provide insight into the population dynamics of DAPG producers in natural grassland soil.IMPORTANCE The interest in bacterial biocontrol agents as biosustainable alternatives to pesticides to increase crop yields has grown. To date, we have a broad knowledge of antimicrobial compounds, such as DAPG, produced by bacteria growing in the rhizosphere surrounding plant roots. However, compared to the rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments, such as bulk and grassland soil. Currently, we are restricted to chemical methods with detection limits and time-consuming PCR-based and probe hybridization approaches to detect DAPG and its respective producer. In this study, we developed a whole-cell biosensor, which can circumvent the labor-intensive screening process as well as increase the sensitivity at which DAPG can be detected. This enables quantification of relative amounts of DAPG producers, which, in turn, increases our understanding of the dynamics and ecology of these producers in natural soil environments.},
}
@article {pmid33218113,
year = {2020},
author = {Sperling, JLH and Fitzgerald, D and Sperling, FAH and Magor, KE},
title = {Microbiome Composition and Borrelia Detection in Ixodes scapularis Ticks at the Northwestern Edge of Their Range.},
journal = {Tropical medicine and infectious disease},
volume = {5},
number = {4},
pages = {},
pmid = {33218113},
issn = {2414-6366},
support = {RGPIN-2015-05045//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04668//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2018-04920//Natural Sciences and Engineering Research Council of Canada/ ; Grant in Biodiversity to J. Sperling//Alberta Conservation Association/ ; scholarship to J. Sperling//Alberta Innovates - Technology Futures/ ; },
abstract = {Lyme disease-causing Borrelia burgdorferi has been reported in 10-19% of Ixodes ticks from Alberta, Canada, where the tick vector Ixodes scapularis is at the northwestern edge of its range. However, the presence of Borrelia has not been verified independently, and the bacterial microbiome of these ticks has not been described. We performed 16S rRNA bacterial surveys on female I. scapularis from Alberta that were previously qPCR-tested in a Lyme disease surveillance program. Both 16S and qPCR methods were concordant for the presence of Borrelia. The 16S studies also provided a profile of associated bacteria that showed the microbiome of I. scapularis in Alberta was similar to other areas of North America. Ticks that were qPCR-positive for Borrelia had significantly greater bacterial diversity than Borrelia-negative ticks, on the basis of generalized linear model testing. This study adds value to ongoing tick surveillance and is a foundation for deeper understanding of tick microbial ecology and disease transmission in a region where I. scapularis range expansion, induced by climate and land use changes, is likely to have increasing public health implications.},
}
@article {pmid33218015,
year = {2020},
author = {Koller, G and Foschi, F and Mitchell, P and Witherden, E and Bruce, K and Mannocci, F},
title = {Amoebae in Chronic, Polymicrobial Endodontic Infections Are Associated with Altered Microbial Communities of Increased Virulence.},
journal = {Journal of clinical medicine},
volume = {9},
number = {11},
pages = {},
pmid = {33218015},
issn = {2077-0383},
abstract = {BACKGROUND: Infections of the root canal space involve polymicrobial biofilms and lead to chronic, low grade inflammatory responses arising from the seeding of microbes and by-products. Acute exacerbation and/or disseminating infections occur when established microbial communities undergo sudden changes in phenotypic behaviour.<br><br>METHODS: Within clinical endodontic infections, we assessedcategorical determinants comprising, and changing microbial composition of, chronic polymicrobial infections and their association with amoebae. After standardised assessment, primary or secondary infections underwent sampling and DNA processing, targeting bacteria, fungi and amoebae, including 16S high-throughput sequencing. After taxonomic assignment, community composition was correlated with clinical signs and symptoms. Diversity and abundance analyses were carried out in relation to the presence of non-bacterial amplicons.<br><br>RESULTS: Clinical specimens revealed two distinct community clusters, where specific changes correlated with clinical signs. An association between the compositions of microbiomes was found between these groups and the presence of Entamoeba gingivalis in 44% of cases. When amoebae were present in endodontic infections, we demonstrate changes in microbial community structure that mirror those observed in treatment-resistant or recurrent infections.<br><br>CONCLUSIONS: Amoeba are present in endodontic infections at a high prevalence, and may promote increased virulence by enrichment for phagocytosis-resistant bacteria.},
}
@article {pmid33217780,
year = {2021},
author = {Ontiveros, VJ and Capitán, JA and Casamayor, EO and Alonso, D},
title = {The characteristic time of ecological communities.},
journal = {Ecology},
volume = {102},
number = {2},
pages = {e03247},
pmid = {33217780},
issn = {1939-9170},
mesh = {*Biodiversity ; Biota ; *Ecosystem ; Islands ; },
abstract = {A simple description of temporal dynamics of ecological communities may help us understand how community assembly proceeds, predict ecological responses to environmental disturbances, and improve the performance of biological conservation actions. Although community changes take place at multiple temporal scales, the variation of species composition and richness over time across communities and habitats shows general patterns that may potentially reveal the main drivers of community dynamics. We used the simplest stochastic model of island biogeography to propose two quantities to characterize community dynamics: the community characteristic time, as a measure of the typical time scale of species-richness change, and the characteristic Jaccard index, as a measure of temporal β diversity, that is, the variation of community composition over time. In addition, the community characteristic time, which sets the temporal scale at which null, noninteracting species assemblages operate, allowed us to define a relative sampling frequency (to the characteristic time). Here we estimate these quantities across microbial and macroscopic species assemblages to highlight two related results. First, we illustrated both characteristic time and Jaccard index and their relation with classic time-series in ecology, and found that the most thoroughly sampled communities, relative to their characteristic time, presented the largest similarity between consecutive samples. Second, our analysis across a variety of habitats and taxa show that communities span a large range of species turnover, from potentially very fast (short characteristic times) to rather slow (long characteristic times) communities. This was in agreement with previous knowledge, but indicated that some habitats may have been sampled less frequently than required. Our work provides new perspectives to explore the temporal component in ecological studies and highlights the usefulness of simple approximations to the complex dynamics of ecological communities.},
}
@article {pmid33215610,
year = {2020},
author = {Madi, N and Vos, M and Murall, CL and Legendre, P and Shapiro, BJ},
title = {Does diversity beget diversity in microbiomes?.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
pmid = {33215610},
issn = {2050-084X},
mesh = {*Biodiversity ; Biota/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; },
abstract = {Microbes are embedded in complex communities where they engage in a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested to explain how species interactions could influence diversity. 'Ecological Controls' (EC) predicts a negative relationship, where the evolution or migration of novel types is constrained as niches become filled. In contrast, 'Diversity Begets Diversity' (DBD) predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Using high-throughput amplicon sequencing data from the Earth Microbiome Project, we provide evidence that DBD is strongest in low-diversity biomes, but weaker in more diverse biomes, consistent with biotic interactions initially favouring the accumulation of diversity (as predicted by DBD). However, as niches become increasingly filled, diversity hits a plateau (as predicted by EC).},
}
@article {pmid33213979,
year = {2021},
author = {Glodowska, M and Stopelli, E and Straub, D and Vu Thi, D and Trang, PTK and Viet, PH and AdvectAs Team Members, and Berg, M and Kappler, A and Kleindienst, S},
title = {Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling.},
journal = {Journal of hazardous materials},
volume = {407},
number = {},
pages = {124398},
doi = {10.1016/j.jhazmat.2020.124398},
pmid = {33213979},
issn = {1873-3336},
abstract = {The fate of arsenic (As) in groundwater is determined by multiple interrelated microbial and abiotic processes that contribute to As (im)mobilization. Most studies to date have investigated individual processes related to As (im)mobilization rather than the complex networks present in situ. In this study, we used RNA-based microbial community analysis in combination with groundwater hydrogeochemical measurements to elucidate the behavior of As along a 2 km transect near Hanoi, Vietnam. The transect stretches from the riverbank across a strongly reducing and As-contaminated Holocene aquifer, followed by a redox transition zone (RTZ) and a Pleistocene aquifer, at which As concentrations are low. Our analyses revealed fermentation and methanogenesis as important processes providing electron donors, fueling the microbially mediated reductive dissolution of As-bearing Fe(III) minerals and ultimately promoting As mobilization. As a consequence of high CH4 concentrations, methanotrophs thrive across the Holocene aquifer and the redox transition zone. Finally, our results underline the role of SO4[2-]-reducing and putative Fe(II)-/As(III)-oxidizing bacteria as a sink for As, particularly at the RTZ. Overall, our results suggest that a complex network of microbial and biogeochemical processes has to be considered to better understand the biogeochemical behavior of As in groundwater.},
}
@article {pmid33213887,
year = {2021},
author = {Sutherland, WJ and Atkinson, PW and Broad, S and Brown, S and Clout, M and Dias, MP and Dicks, LV and Doran, H and Fleishman, E and Garratt, EL and Gaston, KJ and Hughes, AC and Le Roux, X and Lickorish, FA and Maggs, L and Palardy, JE and Peck, LS and Pettorelli, N and Pretty, J and Spalding, MD and Tonneijck, FH and Walpole, M and Watson, JEM and Wentworth, J and Thornton, A},
title = {A 2021 Horizon Scan of Emerging Global Biological Conservation Issues.},
journal = {Trends in ecology &amp; evolution},
volume = {36},
number = {1},
pages = {87-97},
doi = {10.1016/j.tree.2020.10.014},
pmid = {33213887},
issn = {1872-8383},
mesh = {Biodiversity ; Climate Change ; *Conservation of Natural Resources ; Coral Reefs ; *Ecosystem ; Forecasting ; Humans ; },
abstract = {We present the results from our 12th annual horizon scan of issues likely to impact biological conservation in the future. From a list of 97 topics, our global panel of 25 scientists and practitioners identified the top 15 issues that we believe society may urgently need to address. These issues are either novel in the biological conservation sector or represent a substantial positive or negative step-change in impact at global or regional level. Six issues, such as coral reef deoxygenation and changes in polar coastal productivity, affect marine or coastal ecosystems and seven relate to human and ecosystem-level responses to climate change. Identification of potential forthcoming issues for biological conservation may enable increased preparedness by researchers, practitioners, and decision-makers.},
}
@article {pmid33208892,
year = {2021},
author = {Pelikan, C and Wasmund, K and Glombitza, C and Hausmann, B and Herbold, CW and Flieder, M and Loy, A},
title = {Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment.},
journal = {The ISME journal},
volume = {15},
number = {3},
pages = {833-847},
pmid = {33208892},
issn = {1751-7370},
support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 29426/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Anaerobiosis ; *Fusobacteria ; *Geologic Sediments ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria that degraded [13]C-labeled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within 5 days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed [13]C-labeling of various Deltaproteobacteria within 10 days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions, and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.},
}
@article {pmid33208748,
year = {2020},
author = {Molinaro, A and Bel Lassen, P and Henricsson, M and Wu, H and Adriouch, S and Belda, E and Chakaroun, R and Nielsen, T and Bergh, PO and Rouault, C and André, S and Marquet, F and Andreelli, F and Salem, JE and Assmann, K and Bastard, JP and Forslund, S and Le Chatelier, E and Falony, G and Pons, N and Prifti, E and Quinquis, B and Roume, H and Vieira-Silva, S and Hansen, TH and Pedersen, HK and Lewinter, C and Sønderskov, NB and , and Køber, L and Vestergaard, H and Hansen, T and Zucker, JD and Galan, P and Dumas, ME and Raes, J and Oppert, JM and Letunic, I and Nielsen, J and Bork, P and Ehrlich, SD and Stumvoll, M and Pedersen, O and Aron-Wisnewsky, J and Clément, K and Bäckhed, F},
title = {Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5881},
pmid = {33208748},
issn = {2041-1723},
support = {/DH_/Department of Health/United Kingdom ; },
mesh = {Adult ; Aged ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cohort Studies ; Diabetes Mellitus, Type 2/blood/metabolism/*microbiology ; Female ; *Gastrointestinal Microbiome ; Histidine/metabolism ; Humans ; Imidazoles/*blood ; Male ; Middle Aged ; },
abstract = {Microbiota-host-diet interactions contribute to the development of metabolic diseases. Imidazole propionate is a novel microbially produced metabolite from histidine, which impairs glucose metabolism. Here, we show that subjects with prediabetes and diabetes in the MetaCardis cohort from three European countries have elevated serum imidazole propionate levels. Furthermore, imidazole propionate levels were increased in subjects with low bacterial gene richness and Bacteroides 2 enterotype, which have previously been associated with obesity. The Bacteroides 2 enterotype was also associated with increased abundance of the genes involved in imidazole propionate biosynthesis from dietary histidine. Since patients and controls did not differ in their histidine dietary intake, the elevated levels of imidazole propionate in type 2 diabetes likely reflects altered microbial metabolism of histidine, rather than histidine intake per se. Thus the microbiota may contribute to type 2 diabetes by generating imidazole propionate that can modulate host inflammation and metabolism.},
}
@article {pmid33207956,
year = {2022},
author = {de Melo Pereira, GV and de Carvalho Neto, DP and Maske, BL and De Dea Lindner, J and Vale, AS and Favero, GR and Viesser, J and de Carvalho, JC and Góes-Neto, A and Soccol, CR},
title = {An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?.},
journal = {Critical reviews in food science and nutrition},
volume = {62},
number = {7},
pages = {1870-1889},
doi = {10.1080/10408398.2020.1848787},
pmid = {33207956},
issn = {1549-7852},
mesh = {Bacteria/genetics ; *Cultured Milk Products/microbiology ; Fermentation ; High-Throughput Nucleotide Sequencing ; Lactobacillus ; Phylogeny ; },
abstract = {The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.},
}
@article {pmid33205286,
year = {2021},
author = {Fernandez-Gonzalez, N and Braz, GHR and Regueiro, L and Lema, JM and Carballa, M},
title = {Microbial invasions in sludge anaerobic digesters.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {1},
pages = {21-33},
pmid = {33205286},
issn = {1432-0614},
support = {2014-CE224//Centre for Industrial Technological Development/ ; ED431C 2017/29//Secretaria Xeral de Investigaci&#xf3;n e Desenvolvemento, Xunta de Galicia/ ; AGRUP2017/01//Secretaria Xeral de Investigaci&#xf3;n e Desenvolvemento, Xunta de Galicia/ ; BEX-2160/2015-03//Minist&#xe9;rio da Educa&#xe7;&#xe3;o/ ; },
mesh = {Anaerobiosis ; Bioreactors ; Methane ; *Microbiota ; *Sewage ; },
abstract = {Among processes that control microbial community assembly, microbial invasion has received little attention until recently, especially in the field of anaerobic digestion. However, knowledge of the principles regulating the taxonomic and functional stability of microbial communities is key to truly develop better predictive models and effective management strategies for the anaerobic digestion process. To date, available studies focus on microbial invasions in digesters feed with activated sludge from municipal wastewater treatment plants. Herein, this review summarizes the importance of invasions for anaerobic digestion management, the ecological theories about microbial invasions, the traits of activated sludge microorganisms entering the digesters, and the resident communities of anaerobic reactors that are relevant for invasions and the current knowledge about the success and impacts of invasions, and discusses the research needs on this topic. The initial data indicate that the impact of invasions is low and only a small percentage of the mostly aerobic microorganisms present in the activated sludge feed are able to become stablished in the anaerobic digesters. However, there are still numerous unknowns about microbial invasions in anaerobic digestion including the influence of anaerobic feedstocks or process perturbances that new approaches on microbial ecology could unveil. KEY POINTS: • Microbial invasions are key processes to develop better strategies for digesters management. • Knowledge on pathogen invasions can improve anaerobic digestion microbial safety. • To date, the number of successful invasions on anaerobic digesters from activated sludge organisms is low. • Feed organisms detected in digesters are mostly inactive residual populations. • Need to expand the range of invaders and operational scenarios studied.},
}
@article {pmid33204208,
year = {2020},
author = {Naseer, A and Garrido-Benavent, I and Khan, J and Ballarà, J and Mahiques, R and Khalid, AN and Sher, H},
title = {Cortinarius pakistanicus and C. pseudotorvus: two new species in oak forests in the Pakistan Himalayas.},
journal = {MycoKeys},
volume = {74},
number = {},
pages = {91-108},
pmid = {33204208},
issn = {1314-4049},
abstract = {The genus of basidiomycetous fungi Cortinarius occurs worldwide, from subtropical to boreal latitudes. Although molecular systematics has triggered the study of these fungi in the Americas and Europe in the last two decades, there is still limited research on its diversity in large portions of the planet, such as the high mountain ranges of Asia. Several collections of Cortinarius were made during mycological field trips conducted between 2014 and 2018 in pure oak forests in the Pakistan Himalayas. An integrative framework combining morphological and phylogenetic data was employed for their study. As a result, the two species C. pakistanicus and C. pseudotorvus are here described as new to science. Detailed macro- and micro-morphological descriptions, including SEM images of spores, and a molecular phylogenetic reconstruction based on nrITS sequence data are provided and used to discriminate the new species from morphologically and phylogenetically close taxa. Whereas our phylogenetic tree inference gave unequivocal support for the inclusion of C. pseudotorvus within C. sect. Telamonia, the assignment of C. pakistanicus to any known sections remained elusive. These species likely establish ectomycorrhizal associations with trees in the genus Quercus, making this type of forest in the Pakistan Himalayas a promising focus for future research on the diversity of Cortinarius.},
}
@article {pmid33203691,
year = {2020},
author = {Jordaan, K and Lappan, R and Dong, X and Aitkenhead, IJ and Bay, SK and Chiri, E and Wieler, N and Meredith, LK and Cowan, DA and Chown, SL and Greening, C},
title = {Hydrogen-Oxidizing Bacteria Are Abundant in Desert Soils and Strongly Stimulated by Hydration.},
journal = {mSystems},
volume = {5},
number = {6},
pages = {},
pmid = {33203691},
issn = {2379-5077},
abstract = {How the diverse bacterial communities inhabiting desert soils maintain energy and carbon needs is much debated. Traditionally, most bacteria are thought to persist by using organic carbon synthesized by photoautotrophs following transient hydration events. Recent studies focused on Antarctic desert soils have revealed, however, that some bacteria use atmospheric trace gases, such as hydrogen (H2), to conserve energy and fix carbon independently of photosynthesis. In this study, we investigated whether atmospheric H2 oxidation occurs in four nonpolar desert soils and compared this process to photosynthesis. To do so, we first profiled the distribution, expression, and activities of hydrogenases and photosystems in surface soils collected from the South Australian desert over a simulated hydration-desiccation cycle. Hydrogenase-encoding sequences were abundant in the metagenomes and metatranscriptomes and were detected in actinobacterial, acidobacterial, and cyanobacterial metagenome-assembled genomes. Native dry soil samples mediated H2 oxidation, but rates increased 950-fold following wetting. Oxygenic and anoxygenic phototrophs were also detected in the community but at lower abundances. Hydration significantly stimulated rates of photosynthetic carbon fixation and, to a lesser extent, dark carbon assimilation. Hydrogenase genes were also widespread in samples from three other climatically distinct deserts, the Namib, Gobi, and Mojave, and atmospheric H2 oxidation was also greatly stimulated by hydration at these sites. Together, these findings highlight that H2 is an important, hitherto-overlooked energy source supporting bacterial communities in desert soils. Contrary to our previous hypotheses, however, H2 oxidation occurs simultaneously rather than alternately with photosynthesis in such ecosystems and may even be mediated by some photoautotrophs.IMPORTANCE Desert ecosystems, spanning a third of the earth's surface, harbor remarkably diverse microbial life despite having a low potential for photosynthesis. In this work, we reveal that atmospheric hydrogen serves as a major previously overlooked energy source for a large proportion of desert bacteria. We show that both chemoheterotrophic and photoautotrophic bacteria have the potential to oxidize hydrogen across deserts sampled across four continents. Whereas hydrogen oxidation was slow in native dry deserts, it increased by three orders of magnitude together with photosynthesis following hydration. This study revealed that continual harvesting of atmospheric energy sources may be a major way that desert communities adapt to long periods of water and energy deprivation, with significant ecological and biogeochemical ramifications.},
}
@article {pmid33200135,
year = {2020},
author = {Shaffer, JP and Marotz, C and Belda-Ferre, P and Martino, C and Wandro, S and Estaki, M and Salido, RA and Carpenter, CS and Zaramela, LS and Minich, JJ and Bryant, M and Sanders, K and Fraraccio, S and Ackermann, G and Humphrey, G and Swafford, AD and Miller-Montgomery, S and Knight, R},
title = {A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2020.11.13.370387},
pmid = {33200135},
issn = {2692-8205},
abstract = {UNLABELLED: One goal among microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods we previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, we compare the relative performance of two total nucleic acid extraction protocols and our previously benchmarked protocol. We included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here we present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection, and well-to-well contamination, between these protocols.<br><br>ACCESSION NUMBERS: Raw sequence data were deposited at the European Nucleotide Archive (accession#: ERP124610) and raw and processed data are available at Qiita (Study ID: 12201). All processing and analysis code is available on GitHub (github.com/justinshaffer/Extraction_test_MagMAX).<br><br>METHODS SUMMARY: To allow for downstream applications involving RNA-based organisms such as SARS-CoV-2, we compared the two extraction protocols designed to extract DNA and RNA against our previously established protocol for extracting only DNA for microbial community analyses. Across 10 diverse sample types, one of the two protocols was equivalent or better than our established DNA-based protocol. Our conclusion is based on per-sample comparisons of DNA and RNA yield, the number of quality sequences generated, microbial community alpha- and beta-diversity and taxonomic composition, the limit of detection, and extent of well-to-well contamination.},
}
@article {pmid33199799,
year = {2020},
author = {Perona-Vico, E and Feliu-Paradeda, L and Puig, S and Bañeras, L},
title = {Bacteria coated cathodes as an in-situ hydrogen evolving platform for microbial electrosynthesis.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {19852},
pmid = {33199799},
issn = {2045-2322},
mesh = {Bacteria/genetics/*growth &amp; development/metabolism ; Bacterial Physiological Phenomena ; Bioelectric Energy Sources/*microbiology ; Biofilms ; Biosensing Techniques/instrumentation ; Electrochemical Techniques ; Hydrogen/*analysis ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological ; },
abstract = {Hydrogen is a key intermediate element in microbial electrosynthesis as a mediator of the reduction of carbon dioxide (CO2) into added value compounds. In the present work we aimed at studying the biological production of hydrogen in biocathodes operated at - 1.0 V vs. Ag/AgCl, using a highly comparable technology and CO2 as carbon feedstock. Ten bacterial strains were chosen from genera Rhodobacter, Rhodopseudomonas, Rhodocyclus, Desulfovibrio and Sporomusa, all described as hydrogen producing candidates. Monospecific biofilms were formed on carbon cloth cathodes and hydrogen evolution was constantly monitored using a microsensor. Eight over ten bacteria strains showed electroactivity and H2 production rates increased significantly (two to eightfold) compared to abiotic conditions for two of them (Desulfovibrio paquesii and Desulfovibrio desulfuricans). D. paquesii DSM 16681 exhibited the highest production rate (45.6 ± 18.8 µM min[-1]) compared to abiotic conditions (5.5 ± 0.6 µM min[-1]), although specific production rates (per 16S rRNA copy) were similar to those obtained for other strains. This study demonstrated that many microorganisms are suspected to participate in net hydrogen production but inherent differences among strains do occur, which are relevant for future developments of resilient biofilm coated cathodes as a stable hydrogen production platform in microbial electrosynthesis.},
}
@article {pmid33196853,
year = {2021},
author = {Sánchez-Soto, MF and Cerqueda-García, D and Alcántara-Hernández, RJ and Falcón, LI and Pech, D and Árcega-Cabrera, F and Aguirre-Macedo, ML and García-Maldonado, JQ},
title = {Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {908-921},
pmid = {33196853},
issn = {1432-184X},
support = {201441//Mexican National Council for Science and Technology - Mexican Ministry of Energy Hydrocarbon Fund/ ; 251622 - 2015//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {*Bacteria/genetics ; Geologic Sediments ; Gulf of Mexico ; High-Throughput Nucleotide Sequencing ; Phylogeny ; *Sulfates ; },
abstract = {This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.},
}
@article {pmid33194800,
year = {2020},
author = {Jaiswal, S and Kumar, M and Mandeep, and Sunita, and Singh, Y and Shukla, P},
title = {Systems Biology Approaches for Therapeutics Development Against COVID-19.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {560240},
pmid = {33194800},
issn = {2235-2988},
mesh = {Animals ; Antiviral Agents/pharmacology ; COVID-19/immunology/virology ; COVID-19 Vaccines/administration &amp; dosage/genetics/immunology ; Humans ; SARS-CoV-2/drug effects/genetics/immunology/*physiology ; Systems Biology ; *COVID-19 Drug Treatment ; },
abstract = {Understanding the systems biology approaches for promoting the development of new therapeutic drugs is attaining importance nowadays. The threat of COVID-19 outbreak needs to be vanished for global welfare, and every section of research is focusing on it. There is an opportunity for finding new, quick, and accurate tools for developing treatment options, including the vaccine against COVID-19. The review at this moment covers various aspects of pathogenesis and host factors for exploring the virus target and developing suitable therapeutic solutions through systems biology tools. Furthermore, this review also covers the extensive details of multiomics tools i.e., transcriptomics, proteomics, genomics, lipidomics, immunomics, and in silico computational modeling aiming towards the study of host-virus interactions in search of therapeutic targets against the COVID-19.},
}
@article {pmid33193238,
year = {2020},
author = {Abdelhamid, MK and Quijada, NM and Dzieciol, M and Hatfaludi, T and Bilic, I and Selberherr, E and Liebhart, D and Hess, C and Hess, M and Paudel, S},
title = {Co-infection of Chicken Layers With Histomonas meleagridis and Avian Pathogenic Escherichia coli Is Associated With Dysbiosis, Cecal Colonization and Translocation of the Bacteria From the Gut Lumen.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {586437},
pmid = {33193238},
issn = {1664-302X},
abstract = {Histomonosis in chickens often appears together with colibacillosis in the field. Thus, we have experimentally investigated consequences of the co-infection of birds with Histomonas meleagridis and avian pathogenic Escherichia coli (APEC) on the pathology, host microbiota and bacterial translocation from the gut. Commercial chicken layers were infected via oral and cloacal routes with lux-tagged APEC with or without H. meleagridis whereas negative controls were left uninfected. Except one bird, which died due to colibacillosis, no clinical signs were recorded in birds infected with bioluminescence lux gene tagged E. coli. In co-infected birds, depression and ruffled feathers were observed in 4 birds and average body weight gain significantly decreased. Typhlitis caused by H. meleagridis was present only in co-infected birds, which also had pronounced microscopic lesions in systemic organs such as liver, heart and spleen. The 16S rRNA gene amplicon sequencing showed that in co-infected birds, corresponding to the severity of cecal lesions, microbial species richness and diversity in caeca greatly decreased and the abundance of the Escherichia group, Helicobacter and Bacteroides was relatively higher with a reduction of commensals. Most of the shared Amplicon Sequencing Variants between cecum and blood in co-infected birds belonged to Pseudomonas, Staphylococcus, and members of Enterobacteriaceae while those assigned as Lactobacillus and members of Ruminococcaceae and Lachnospiraceae were found mainly in negative controls. In infected birds, E. coli in the cecal lumen penetrated into deeper layers, a phenomenon noticed with higher incidence in the dead and co-infected birds. Furthermore, numbers of lux-tagged E. coli in caeca were significantly higher at every sampling date in co-infected birds. Altogether, infection of layers with H. meleagridis and E. coli resulted in more severe pathological changes, dramatic shift in the cecal mucosa-associated microbiota, higher tissue colonization of pathogenic bacteria such as avian pathogenic E. coli in the gut and increased penetration of E. coli from the cecal lumen toward peritoneum. This study provides novel insights into the parasite-bacteria interaction in vivo highlighting the role of H. meleagridis to support E. coli in the pathogenesis of colibacillosis in chickens.},
}
@article {pmid33193131,
year = {2020},
author = {Straub, D and Blackwell, N and Langarica-Fuentes, A and Peltzer, A and Nahnsen, S and Kleindienst, S},
title = {Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {550420},
pmid = {33193131},
issn = {1664-302X},
abstract = {One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination with bioinformatics analyses. However, focusing on environmental samples from contrasting habitats, it was not systematically evaluated (i) which analysis methods provide results that reflect reality most accurately, (ii) how the interpretations of microbial community studies are biased by different analysis methods and (iii) if the most optimal analysis workflow can be implemented in an easy-to-use pipeline. Here, we compared the performance of 16S rRNA (gene) amplicon sequencing analysis tools (i.e., Mothur, QIIME1, QIIME2, and MEGAN) using three mock datasets with known microbial community composition that differed in sequencing quality, species number and abundance distribution (i.e., even or uneven), and phylogenetic diversity (i.e., closely related or well-separated amplicon sequences). Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), suggesting that this approach is able to reflect the in situ microbial community most accurately. Further analysis of 24 environmental datasets obtained from four contrasting terrestrial and freshwater sites revealed dramatic differences in the resulting microbial community composition for all pipelines at genus level. For instance, at the investigated river water sites Sphaerotilus was only reported when using QIIME1 (8% abundance) and Agitococcus with QIIME1 or QIIME2 (2 or 3% abundance, respectively), but both genera remained undetected when analyzed with Mothur or MEGAN. Since these abundant taxa probably have implications for important biogeochemical cycles (e.g., nitrate and sulfate reduction) at these sites, their detection and semi-quantitative enumeration is crucial for valid interpretations. A high-performance computing conformant workflow was constructed to allow FAIR (Findable, Accessible, Interoperable, and Re-usable) 16S rRNA (gene) amplicon sequence analysis starting from raw sequence files, using the most optimal methods identified in our study. Our presented workflow should be considered for future studies, thereby facilitating the analysis of high-throughput 16S rRNA (gene) sequencing data substantially, while maximizing reliability and confidence in microbial community data analysis.},
}
@article {pmid33193120,
year = {2020},
author = {Rosen, GL and Hammrich, P},
title = {Teaching Microbiome Analysis: From Design to Computation Through Inquiry.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {528051},
pmid = {33193120},
issn = {1664-302X},
abstract = {In this article, we present our three-class course sequence to educate students about microbiome analysis and metagenomics through experiential learning by taking them from inquiry to analysis of the microbiome: Molecular Ecology Lab, Bioinformatics, and Computational Microbiome Analysis. Students developed hypotheses, designed lab experiments, sequenced the DNA from microbiomes, learned basic python/R scripting, became proficient in at least one microbiome analysis software, and were able to analyze data generated from the microbiome experiments. While over 150 students (graduate and undergraduate) were impacted by the development of the series of courses, our assessment was only on undergraduate learning, where 45 students enrolled in at least one of the three courses and 4 students took all three. Students gained skills in bioinformatics through the courses, and several positive comments were received through surveys and private correspondence. Through a summative assessment, general trends show that students became more proficient in comparative genomic techniques and had positive attitudes toward their abilities to bridge biology and bioinformatics. While most students took individual or 2 of the courses, we show that pre- and post-surveys of these individual classes still showed progress toward learning objectives. It is expected that students trained will enter the workforce with skills needed to innovate in the biotechnology, health, and environmental industries. Students are trained to maximize impact and tackle real world problems in biology and medicine with their learned knowledge of data science and machine learning. The course materials for the new microbiome analysis course are available on Github: https://github.com/EESI/Comp_Metagenomics_resources.},
}
@article {pmid33190166,
year = {2021},
author = {Yi, X and Guo, J and Wang, M and Xue, C and Ju, M},
title = {Inter-trophic Interaction of Gut Microbiota in a Tripartite System.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {1075-1087},
pmid = {33190166},
issn = {1432-184X},
support = {3207047 and 31760156//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Quercus ; Sciuridae ; Seeds ; *Weevils ; },
abstract = {Gut microbiota can be transmitted either environmentally or socially and vertically at intraspecific level; however, whether gut microbiota interact along trophic levels has been largely overlooked. Here, we characterized the gut bacterial communities of weevil larvae of Curculio arakawai that infest acorns of Mongolian oak (Quercus mongolica) as well as acorn-eating mammals, Siberian chipmunk (Tamias sibiricus), to test whether consumption of seed-borne larvae remodels the gut bacterial communities of T. sibiricus. Ingestion of weevil larvae of C. arakawai significantly altered the gut bacterial communities of T. sibiricus. Consequently, T. sibiricus fed larvae of C. arakawai showed higher capability to counter the negative effects of tannins, in terms of body weight maintenance, acorn consumption, N content in feces, urine pH, and blood ALT activity. Our results may first show that seed-borne insects as hidden players have a potential to alter the gut microbiota of seed predators in the tripartite system.},
}
@article {pmid33189472,
year = {2021},
author = {Miao, Y and Heintz, MB and Bell, CH and Johnson, NW and Polasko, AL and Favero, D and Mahendra, S},
title = {Profiling microbial community structures and functions in bioremediation strategies for treating 1,4-dioxane-contaminated groundwater.},
journal = {Journal of hazardous materials},
volume = {408},
number = {},
pages = {124457},
doi = {10.1016/j.jhazmat.2020.124457},
pmid = {33189472},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; Dioxanes ; *Groundwater ; *Microbiota ; Rhodococcus ; *Water Pollutants, Chemical ; },
abstract = {Microbial community compositions and functional profiles were analyzed in microcosms established using aquifer materials from a former automobile factory site, where 1,4-dioxane was identified as the primary contaminant of concern. Propane or oxygen biostimulation resulted in limited 1,4-dioxane degradation, which was markedly enhanced with the addition of nutrients, resulting in abundant Mycobacterium and Methyloversatilis taxa and high expressions of propane monooxygenase gene, prmA. In bioaugmented treatments, Pseudonocardia dioxanivorans CB1190 or Rhodococcus ruber ENV425 strains dominated immediately after augmentation and degraded 1,4-dioxane rapidly which was consistent with increased representation of xenobiotic and lipid metabolism-related functions. Although the bioaugmented microbes decreased due to insufficient growth substrates and microbial competition, they did continue to degrade 1,4-dioxane, presumably by indigenous propanotrophic and heterotrophic bacteria, inducing similar community structures across bioaugmentation conditions. In various treatments, functional redundancy acted as buffer capacity to ensure a stable microbiome, drove the restoration of the structure and microbial functions to original levels, and induced the decoupling between basic metabolic functions and taxonomy. The results of this study provided valuable information for design and decision-making for ex-situ bioreactors and in-situ bioremediation applications. A metagenomics-based understanding of the treatment process will enable efficient and accurate adjustments when encountering unexpected issues in bioremediation.},
}
@article {pmid33188444,
year = {2021},
author = {Xu, Z and Wu, C and Lv, Y and Meng, F and Ban, Y},
title = {Effects of Aeration on the Formation of Arbuscular Mycorrhiza under a Flooded State and Copper Oxide Nanoparticle Removal in Vertical Flow Constructed Wetlands.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {922-931},
pmid = {33188444},
issn = {1432-184X},
mesh = {Copper ; Fungi ; *Mycorrhizae ; *Nanoparticles ; Oxides ; Wetlands ; },
abstract = {In this study, six vertical flow constructed wetlands (VFCWs) planted with Phragmites australis were operated at different aeration times (4 h day[-1] and 8 h day[-1]), aeration modes (continuous and intermittent), and arbuscular mycorrhizal fungi (AMF) inoculation treatments (inoculation with Rhizophagus intraradices and no inoculation) to explore the effects of different aeration strategies on the formation of arbuscular mycorrhiza under a flooded state in VFCWs. In addition, these VFCWs were further used to treat copper oxide nanoparticle (CuO-NP) wastewater to evaluate the correlations among aeration, colonization, growth, and CuO-NP removal. The highest AMF 28S copy number (1.99×10[5]) and colonization in reed roots, with values of 67%, 21%, and 1% for frequency (F%), intensity (M%), and arbuscule abundance (A%), were observed in the treatment with intermittent aeration for 4 h day[-1]. Aeration significantly increased the dissolved oxygen (DO) concentration and AMF colonization in VFCWs, thereby promoting plant growth and the purification of the CuO-NPs. However, excessive and continuous aeration had little positive effect on AMF colonization. This study provides a theoretical basis for the application of AMF for improving pollutant removal performance in constructed wetlands.},
}
@article {pmid33188298,
year = {2021},
author = {Sakoula, D and Koch, H and Frank, J and Jetten, MSM and van Kessel, MAHJ and Lücker, S},
title = {Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification.},
journal = {The ISME journal},
volume = {15},
number = {4},
pages = {1010-1024},
pmid = {33188298},
issn = {1751-7370},
mesh = {Ammonia ; *Ammonium Compounds ; Bacteria/genetics ; Ecosystem ; *Nitrification ; Nitrites ; Oxidation-Reduction ; },
abstract = {The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Additionally, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named "Candidatus Nitrospira kreftii", and performed a detailed genomic and physiological characterization. The complete genome of "Ca. N. kreftii" allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3 ≈ 0.040 ± 0.01 µM), but a higher nitrite affinity (Km(app)_NO2- = 12.5 ± 4.0 µM), indicating an adaptation to highly oligotrophic environments. Furthermore, we observed partial inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This inhibition of "Ca. N. kreftii" indicates that differences in ammonium tolerance rather than affinity could potentially be a niche determining factor for different comammox Nitrospira.},
}
@article {pmid33188000,
year = {2021},
author = {Coe, GL and Pinkham, NV and Celis, AI and Johnson, C and DuBois, JL and Walk, ST},
title = {Dynamic Gut Microbiome Changes in Response to Low-Iron Challenge.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {3},
pages = {},
pmid = {33188000},
issn = {1098-5336},
support = {R01 GM086755/GM/NIGMS NIH HHS/United States ; R21 DK114607/DK/NIDDK NIH HHS/United States ; R35 GM136390/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bacteria/drug effects/genetics/isolation &amp; purification ; Feces/chemistry ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Iron/*administration &amp; dosage/blood/pharmacokinetics ; Male ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S ; Mice ; },
abstract = {Iron is an essential micronutrient for life. In mammals, dietary iron is absorbed primarily in the small intestine. Currently, the impacts of dietary iron on the taxonomic structure and function of the gut microbiome and reciprocal effects on the animal host are not well understood. Here, we establish a mouse model of low-iron challenge in which intestinal biomarkers and reduced fecal iron reveal iron stress while serum iron and mouse behavioral markers indicate maintenance of iron homeostasis. We show that the diversity of the gut microbiome in conventional C57BL/6 mice changes dramatically during 2 weeks on a low-iron diet. We also show the effects of a low-iron diet on microbiome diversity are long lasting and not easily recovered when iron is returned to the diet. Finally, after optimizing taxon association methods, we show that some bacteria are unable to fully recover after the low-iron challenge and appear to be extirpated from the gut entirely. In particular, operational taxonomic units (OTUs) from the Prevotellaceae and Porphyromonadaceae families and Bacteroidales order are highly sensitive to low-iron conditions, while other seemingly insensitive OTUs recover. These results provide new insights into the iron requirements of gut microbiome members and add to the growing understanding of mammalian iron cycling.IMPORTANCE All cells need iron. Both too much and too little iron lead to diseases and unwanted outcomes. Although the impact of dietary iron on human cells and tissues has been well studied, there is currently a lack of understanding about how different levels of iron influence the abundant and diverse members of the human microbiome. This study develops a well-characterized mouse model for studying low-iron levels and identifies key groups of bacteria that are most affected. We found that the microbiome undergoes large changes when iron is removed from the diet but that many individual bacteria are able to rebound when iron levels are changed back to normal. That said, a select few members, referred to as iron-sensitive bacteria, seem to be lost. This study begins to identify individual members of the mammalian microbiome most affected by changes in dietary iron levels.},
}
@article {pmid33187698,
year = {2021},
author = {Zheng, Z and Li, L and Makhalanyane, TP and Xu, C and Li, K and Xue, K and Xu, C and Qian, R and Zhang, B and Du, J and Yu, H and Cui, X and Wang, Y and Hao, Y},
title = {The composition of antibiotic resistance genes is not affected by grazing but is determined by microorganisms in grassland soils.},
journal = {The Science of the total environment},
volume = {761},
number = {},
pages = {143205},
doi = {10.1016/j.scitotenv.2020.143205},
pmid = {33187698},
issn = {1879-1026},
mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; Ecosystem ; Genes, Bacterial ; *Grassland ; *Soil ; Soil Microbiology ; },
abstract = {Grazing is expected to exert a substantial influence on antibiotic resistance genes (ARGs) in grassland ecosystems. However, the precise effects of grazing on the composition of ARGs in grassland soils remain unclear. This is especially the case for grassland soils subject to long-term grazing. Here, we investigated ARGs and bacterial community composition in soils subject to long-term historic grazing (13-39 years) and corresponding ungrazed samples. Using a combination of shotgun metagenomics, amplicon analyses and associated soil physicochemical data, we provide novel insights regarding the structure of ARGs in grassland soils. Interestingly, our analysis revealed that long-term historic grazing had no impacts on the composition of ARGs in grassland soils. An average of 378 ARGs, conferring resistance to 14 major categories of antibiotics (80%), were identified in both grazing and ungrazed sites. Actinobacteria, Proteobacteria and Acidobacteria were the most prevalent predicted hosts in these soils and were also shown to harbour genetic capacity for multiple-resistant ARGs. Our results suggested that positive effects of bacterial community composition on ARGs could potentially be controlled by affecting MGEs. Soil properties had direct effects on the composition of ARGs through affecting the frequency of horizontal gene transfer among bacteria. Twelve novel ARGs were found in S. grandis steppe grasslands, indicating that different vegetation types might induce shifts in soil ARGs. Collectively, these findings suggest that soil properties, plants and microorganisms play critical roles in shaping ARG patterns in grasslands. Together, these data establish a solid baseline for understanding environmental antibiotic resistance in grasslands.},
}
@article {pmid33184503,
year = {2021},
author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Yarza, P and Hedlund, BP and Reysenbach, AL},
title = {Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.},
journal = {Nature microbiology},
volume = {6},
number = {1},
pages = {136},
doi = {10.1038/s41564-020-00827-2},
pmid = {33184503},
issn = {2058-5276},
support = {DEB-1841658//National Science Foundation (NSF)/ ; },
}
@article {pmid33184155,
year = {2020},
author = {Yadav, B and Johri, AK and Dua, M},
title = {Metagenomic Analysis of the Microbial Diversity in Solid Waste from Okhla Landfill, New Delhi, India.},
journal = {Microbiology resource announcements},
volume = {9},
number = {46},
pages = {},
pmid = {33184155},
issn = {2576-098X},
abstract = {The Okhla landfill site is consistently in the news for having pollution levels higher than the city average. Here, we report the taxonomic characterization of the microbial diversity of Okhla landfill solid waste. The metagenome analyses revealed the microbial and metabolic diversity of the site.},
}
@article {pmid33183698,
year = {2021},
author = {Chow, LKM and Ghaly, TM and Gillings, MR},
title = {A survey of sub-inhibitory concentrations of antibiotics in the environment.},
journal = {Journal of environmental sciences (China)},
volume = {99},
number = {},
pages = {21-27},
doi = {10.1016/j.jes.2020.05.030},
pmid = {33183698},
issn = {1001-0742},
mesh = {*Anti-Bacterial Agents ; Bacteria ; *Environmental Pollutants ; Humans ; Surveys and Questionnaires ; },
abstract = {Antibiotics are poorly metabolized, and can enter the environment via human waste streams, agricultural run-off and pharmaceutical effluent. We consequently expect to see a concentration gradient of antibiotic compounds radiating from areas of human population. Such antibiotics should be thought of as pollutants, as they can accumulate, and have biological effects. These antibiotic pollutants can increase rates of mutation and lateral transfer events, and continue to exert selection pressure even at sub-inhibitory concentrations. Here, we conducted a literature survey on environmental concentrations of antibiotics. We collated 887 data points from 40 peer-reviewed papers. We then determined whether these concentrations were biologically relevant by comparing them to their minimum selective concentrations, usually defined as between 1/4 and 1/230 of the minimum inhibitory concentration. Environmental concentrations of antibiotics surveyed often fall into this range. In general, the antibiotic concentrations recorded in aquatic and sediment samples were similar. These findings indicate that environmental concentrations of antibiotics are likely to be influencing microbial ecology, and to be driving the selection of antibiotic resistant bacteria.},
}
@article {pmid33182220,
year = {2021},
author = {Li, M and Mi, T and He, H and Chen, Y and Zhen, Y and Yu, Z},
title = {Active bacterial and archaeal communities in coastal sediments: Biogeography pattern, assembly process and co-occurrence relationship.},
journal = {The Science of the total environment},
volume = {750},
number = {},
pages = {142252},
doi = {10.1016/j.scitotenv.2020.142252},
pmid = {33182220},
issn = {1879-1026},
mesh = {*Archaea/genetics ; *Bacteria/genetics ; China ; Geologic Sediments ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The biogeography of active microbial communities and the underlying mechanisms in marine sediments are important in microbial ecology but remain unclear. Here, using qPCR and high-throughput sequencing, we investigated bacterial and archaeal community abundances and activities by quantifying the abundance and expression of the 16S rRNA gene respectively, RNA-derived bacterial and archaeal community biogeography, assembly mechanisms and co-occurrence relationships in surface sediment samples from the Bohai Sea (BS), South Yellow Sea (SYS) and the north East China Sea (NECS) of the eastern Chinese marginal seas. The results revealed a higher heterogeneity of bacterial and archaeal community activities than of abundances and heterogeneous ecological functions among areas reflected by community compositions. Furthermore, clear geographic groups (i.e., the BS, SYS and NECS groups) were observed for all, abundant and rare active bacterial and archaeal communities, accompanied by significant distance-decay patterns. However, the abundant and rare taxa showed inconsistent geographic patterns. More importantly, deterministic processes played a greater role than stochastic processes in active bacterial and archaeal community assembly. The rare taxa had weaker abilities to disperse and/or adapt and more complex ecological processes than the abundant taxa. In addition, this study also showed that intertaxa competition was the dominant interaction between active bacterial and archaeal members, which could greatly contribute to dispersal limitation. Moreover, active bacterial and archaeal co-occurrence patterns showed significant distance-decay patterns, which were consistent with the community compositions.},
}
@article {pmid33178725,
year = {2020},
author = {Vadopalas, L and Ruzauskas, M and Lele, V and Starkute, V and Zavistanaviciute, P and Zokaityte, E and Bartkevics, V and Pugajeva, I and Reinolds, I and Badaras, S and Klupsaite, D and Mozuriene, E and Dauksiene, A and Gruzauskas, R and Bartkiene, E},
title = {Combination of Antimicrobial Starters for Feed Fermentation: Influence on Piglet Feces Microbiota and Health and Growth Performance, Including Mycotoxin Biotransformation in vivo.},
journal = {Frontiers in veterinary science},
volume = {7},
number = {},
pages = {528990},
pmid = {33178725},
issn = {2297-1769},
abstract = {The aim of this study was to apply a combination of the microbial starters Lactobacillus uvarum LUHS245, Lactobacillus casei LUHS210, Pediococcus acidilactici LUHS29, and Pediococcus pentosaceus LUHS183 for feed fermentation and to evaluate the influence of fermentation on feed acidity and microbiological characteristics, as well as on the piglet feces microbiota, health, and growth performance. Additionally, mycotoxin biotransformation was analyzed, including masked mycotoxins, in feed and piglet feces samples. The 36-day experiment was conducted using 25-day-old Large White/Norwegian Landrace (LW/NL) piglets with an initial body weight of 6.9-7.0 kg, which were randomly distributed into two groups (in each 100 piglets): control group, fed with basal diet (based on barley, wheat, potato protein, soybean protein concentrate, and whey powder), and treated group, fed with fermented feed at 500 g kg[-1] of total feed. Compared to a commercially available lactic acid bacteria (LAB) combination, the novel LAB mixture effectively reduced feed pH (on average pH 3.65), produced a 2-fold higher content of L(+) lactic acid, increased viable LAB count [on average 8.8 log10 colony-forming units (CFU) g[-1]], and led to stable feed fermentation during the entire test period (36 days). Fecal microbiota analysis showed an increased number of probiotic bacteria in the treated group, particularly Lactobacillus, when compared with the control group at the end of experiment. This finding indicates that fermented feed can modify microbial profile change in the gut of pigs. In treated piglets' blood (at day 61), the serum high-density lipoprotein (HDL) cholesterol and triglycerides (TG) were significantly higher, but the levels of T4, glucose, K, alkaline phosphatase (AP), and urea were significantly decreased (p ≤ 0.05) compared with the control group. Mycotoxin analysis showed that alternariol monomethyl ether (AME) and altenuene were found in 61-day-old control piglets' feces and in fermented feed samples. However, AME was not found in treated piglets' feces. Feed fermentation with the novel LAB combination is a promising means to modulate piglets' microbiota, which is essential to improve nutrient absorption, growth performance, and health parameters. The new LAB composition suggests a novel dietary strategy to positively manipulate fermented feed chemicals and bio-safety and the piglet gut microbial ecology to reduce antimicrobials use in pig production and increase local feed stock uses and economical effectiveness of the process.},
}
@article {pmid33175111,
year = {2021},
author = {Pascoal, F and Costa, R and Magalhães, C},
title = {The microbial rare biosphere: current concepts, methods and ecological principles.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {1},
pages = {},
doi = {10.1093/femsec/fiaa227},
pmid = {33175111},
issn = {1574-6941},
mesh = {*Biodiversity ; *Microbiota ; Phylogeny ; },
abstract = {Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.},
}
@article {pmid33174822,
year = {2021},
author = {Fu, B and Olawole, O and Beattie, GA},
title = {Biological Control and Microbial Ecology Draft Genome Sequence Data of Glutamicibacter sp. FBE-19, a Bacterium Antagonistic to the Plant Pathogen Erwinia tracheiphila.},
journal = {Phytopathology},
volume = {111},
number = {4},
pages = {765-768},
doi = {10.1094/PHYTO-09-20-0380-A},
pmid = {33174822},
issn = {0031-949X},
mesh = {*Cucurbita ; *Cucurbitaceae ; *Erwinia/genetics ; Genome, Bacterial/genetics ; Plant Diseases ; },
abstract = {Glutamicibacter sp. FBE-19 was isolated based on its strong antagonism to the cucurbit bacterial blight pathogen Erwinia tracheiphila on plates. Members of the Glutamicibacter genus can promote plant growth under saline conditions and antagonize fungi on plates via chitinolytic activity; however, their production of antibacterial compounds has not been examined. Here, we report the genome sequence of strain FBE-19. The genome is 3.85 Mbp with a G+C content of 60.1% and comprises 3,791 genes. Genes that may contribute to its antagonistic activity include genes for the secondary metabolites stenothricin, salinosporamide A, a second β-lactone compound, and a carotenoid. The Glutamicibacter sp. FBE-19 genome data may be a useful resource if this strain proves to be an effective biocontrol agent against E. tracheiphila.},
}
@article {pmid33173062,
year = {2020},
author = {Zakem, EJ and Polz, MF and Follows, MJ},
title = {Redox-informed models of global biogeochemical cycles.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5680},
pmid = {33173062},
issn = {2041-1723},
mesh = {Bacteria/metabolism ; *Computer Simulation ; Ecology ; Ecosystem ; *Global Warming ; *Greenhouse Effect ; Greenhouse Gases/metabolism ; Methane/metabolism ; Models, Theoretical ; Nitrous Oxide/metabolism ; *Oxidation-Reduction ; },
abstract = {Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments."Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things." -Georgia O'Keefe.},
}
@article {pmid33171770,
year = {2020},
author = {Rico-Reséndiz, F and Cervantes-Pérez, SA and Espinal-Centeno, A and Dipp-Álvarez, M and Oropeza-Aburto, A and Hurtado-Bautista, E and Cruz-Hernández, A and Bowman, JL and Ishizaki, K and Arteaga-Vázquez, MA and Herrera-Estrella, L and Cruz-Ramírez, A},
title = {Transcriptional and Morpho-Physiological Responses of Marchantia polymorpha upon Phosphate Starvation.},
journal = {International journal of molecular sciences},
volume = {21},
number = {21},
pages = {},
pmid = {33171770},
issn = {1422-0067},
support = {PhD scholarships (No. 629985), (No. 420770), (No. 487660).//CONACYT/ ; (19H03247)//JSPS KAKENHI grant/ ; 19941-44//UCMEXUS/ ; 158550 &amp; A1-S-38383//CONACYT Ciencia B&#xe1;sica/ ; NA150181//Royal Society Newton Advanced Fellowship/ ; },
mesh = {Ecosystem ; Gene Expression Regulation, Plant/drug effects/genetics ; Gene Regulatory Networks/drug effects/genetics ; Hepatophyta/metabolism ; Marchantia/*genetics/*metabolism ; Phosphates/*metabolism ; Phylogeny ; Transcription Factors/metabolism ; },
abstract = {Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phylogeny. To shed light on how early divergent plants respond to Pi limitation, we analyzed the morpho-physiological and transcriptional dynamics of Marchantia polymorpha upon Pi starvation. Our phylogenomic analysis highlights some gene networks present since the Chlorophytes and others established in the Streptophytes (e.g., PHR1-SPX1 and STOP1-ALMT1, respectively). At the morpho-physiological level, the response is characterized by the induction of phosphatase activity, media acidification, accumulation of auronidins, reduction of internal Pi concentration, and developmental modifications of rhizoids. The transcriptional response involves the induction of MpPHR1, Pi transporters, lipid turnover enzymes, and MpMYB14, which is an essential transcription factor for auronidins biosynthesis. MpSTOP2 up-regulation correlates with expression changes in genes related to organic acid biosynthesis and transport, suggesting a preference for citrate exudation. An analysis of MpPHR1 binding sequences (P1BS) shows an enrichment of this cis regulatory element in differentially expressed genes. Our study unravels the strategies, at diverse levels of organization, exerted by M. polymorpha to cope with low Pi availability.},
}
@article {pmid33170351,
year = {2021},
author = {Rose, A and Padovan, A and Christian, K and van de Kamp, J and Kaestli, M and Tsoukalis, S and Bodrossy, L and Gibb, K},
title = {The Diversity of Nitrogen-Cycling Microbial Genes in a Waste Stabilization Pond Reveals Changes over Space and Time that Is Uncoupled to Changing Nitrogen Chemistry.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {1029-1041},
pmid = {33170351},
issn = {1432-184X},
support = {Australian Postgraduate Awards Scheme (APA)//Australian Government/ ; D2012/55671//PowerWater Corporation/ ; R-04202//OCE Science Leader Fellowship/ ; Environmental Genomics grant (R-02412)//CSIRO Oceans and Atmosphere/ ; },
mesh = {Archaea/genetics ; Denitrification ; Genes, Microbial ; *Nitrogen/analysis ; Nitrogen Cycle ; Oxidation-Reduction ; *Ponds ; Wastewater ; },
abstract = {Nitrogen removal is an important process for wastewater ponds prior to effluent release. Bacteria and archaea can drive nitrogen removal if they possess the genes required to metabolize nitrogen. In the tropical savanna of northern Australia, we identified the previously unresolved microbial communities responsible for nitrogen cycling in a multi-pond wastewater stabilization system by measuring genomic DNA and cDNA for the following: nifH (nitrogen fixation); nosZ (denitrification); hzsA (anammox); archaeal AamoA and bacterial BamoA (ammonia oxidation); nxrB (nitrite oxidation); and nrfA (dissimilatory NO3 reduction to NH3). By collecting 160 DNA and 40 cDNA wastewater samples and measuring nitrogen (N)-cycling genes using a functional gene array, we found that genes from all steps of the N cycle were present and, except for nxrB, were also expressed. As expected, N-cycling communities showed daily, seasonal, and yearly shifts. However, contrary to our prediction, probes from most functional groups, excluding nosZ and AamoA, were different between ponds. Further, different genes that perform the same N-cycling role sometimes had different trends over space and time, resulting in only weak correlations between the different functional communities. Although N-cycling communities were correlated with wastewater nitrogen levels and physico-chemistry, the relationship was not strong enough to reliably predict the presence or diversity of N-cycling microbes. The complex and dynamic response of these genes to other functional groups and the changing physico-chemical environment provides insight into why altering wastewater pond conditions can result an abundance of some gene variants while others are lost.},
}
@article {pmid33169932,
year = {2021},
author = {Heyse, J and Props, R and Kongnuan, P and De Schryver, P and Rombaut, G and Defoirdt, T and Boon, N},
title = {Rearing water microbiomes in white leg shrimp (Litopenaeus vannamei) larviculture assemble stochastically and are influenced by the microbiomes of live feed products.},
journal = {Environmental microbiology},
volume = {23},
number = {1},
pages = {281-298},
doi = {10.1111/1462-2920.15310},
pmid = {33169932},
issn = {1462-2920},
support = {20180033//European Asian aquaculture Technology and innovation Platform (EURASTiP)/ ; 20180045//European Asian aquaculture Technology and innovation Platform (EURASTiP)/ ; 1S80618N//Flemish Fund for Scientific research (FWO-Vlaanderen)/ ; },
mesh = {Animal Feed/*microbiology ; Animals ; Aquaculture ; Artemia/*microbiology ; Bacteria/*growth &amp; development/*metabolism ; Fish Diseases/epidemiology/microbiology/prevention &amp; control ; Microbiota ; Penaeidae/*microbiology ; Water ; Water Microbiology ; },
abstract = {The development of effective management strategies to reduce the occurrence of diseases in aquaculture is hampered by the limited knowledge on the microbial ecology of these systems. In this study, the dynamics and dominant community assembly processes in the rearing water of Litopenaeus vannamei larviculture tanks were determined. Additionally, the contribution of peripheral microbiomes, such as those of live and dry feeds, to the rearing water microbiome were quantified. The community assembly in the hatchery rearing water over time was dominated by stochasticity, which explains the observed heterogeneity between replicate cultivations. The community undergoes two shifts that match with the dynamics of the algal abundances in the rearing water. Source tracking analysis revealed that 37% of all bacteria in the hatchery rearing water were introduced either by the live or dry feeds, or during water exchanges. The contribution of the microbiome from the algae was the largest, followed by that of the Artemia, the exchange water and the dry feeds. Our findings provide fundamental knowledge on the assembly processes and dynamics of rearing water microbiomes and illustrate the crucial role of these peripheral microbiomes in maintaining health-promoting rearing water microbiomes.},
}
@article {pmid33169788,
year = {2021},
author = {Ionescu, D and Zoccarato, L and Zaduryan, A and Schorn, S and Bizic, M and Pinnow, S and Cypionka, H and Grossart, HP},
title = {Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems.},
journal = {Molecular biology and evolution},
volume = {38},
number = {3},
pages = {1040-1059},
pmid = {33169788},
issn = {1537-1719},
mesh = {*Biological Evolution ; Ecosystem ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Gram-Negative Aerobic Bacteria/*genetics/metabolism ; Heterozygote ; Phylogeny ; Polyploidy ; *Water Microbiology ; },
abstract = {Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell's hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.},
}
@article {pmid33169034,
year = {2021},
author = {Aksenov, AA and Laponogov, I and Zhang, Z and Doran, SLF and Belluomo, I and Veselkov, D and Bittremieux, W and Nothias, LF and Nothias-Esposito, M and Maloney, KN and Misra, BB and Melnik, AV and Smirnov, A and Du, X and Jones, KL and Dorrestein, K and Panitchpakdi, M and Ernst, M and van der Hooft, JJJ and Gonzalez, M and Carazzone, C and Amézquita, A and Callewaert, C and Morton, JT and Quinn, RA and Bouslimani, A and Orio, AA and Petras, D and Smania, AM and Couvillion, SP and Burnet, MC and Nicora, CD and Zink, E and Metz, TO and Artaev, V and Humston-Fulmer, E and Gregor, R and Meijler, MM and Mizrahi, I and Eyal, S and Anderson, B and Dutton, R and Lugan, R and Boulch, PL and Guitton, Y and Prevost, S and Poirier, A and Dervilly, G and Le Bizec, B and Fait, A and Persi, NS and Song, C and Gashu, K and Coras, R and Guma, M and Manasson, J and Scher, JU and Barupal, DK and Alseekh, S and Fernie, AR and Mirnezami, R and Vasiliou, V and Schmid, R and Borisov, RS and Kulikova, LN and Knight, R and Wang, M and Hanna, GB and Dorrestein, PC and Veselkov, K},
title = {Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data.},
journal = {Nature biotechnology},
volume = {39},
number = {2},
pages = {169-173},
pmid = {33169034},
issn = {1546-1696},
support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R01 AR073324/AR/NIAMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; U19 AG063744/AG/NIA NIH HHS/United States ; R21 AA028432/AA/NIAAA NIH HHS/United States ; T32 AR069515/AR/NIAMS NIH HHS/United States ; T32 AR064194/AR/NIAMS NIH HHS/United States ; R03 AR072182/AR/NIAMS NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; U01 CA235507/CA/NCI NIH HHS/United States ; R24 AA022057/AA/NIAAA NIH HHS/United States ; },
mesh = {*Algorithms ; Animals ; Anura ; *Gas Chromatography-Mass Spectrometry ; Humans ; *Metabolomics ; },
abstract = {We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.},
}
@article {pmid33167488,
year = {2020},
author = {Oba, PM and Holscher, HD and Mathai, RA and Kim, J and Swanson, KS},
title = {Diet Influences the Oral Microbiota of Infants during the First Six Months of Life.},
journal = {Nutrients},
volume = {12},
number = {11},
pages = {},
pmid = {33167488},
issn = {2072-6643},
support = {USDA Hatch #ILLU 538-937//U.S. Department of Agriculture/ ; },
mesh = {Bacteria ; Breast Feeding ; *Diet ; Fungi ; Humans ; Infant ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; Species Specificity ; },
abstract = {Background: Oral microorganisms contribute to oral health and disease, but few have studied how infant feeding methods affect their establishment. Methods: Infant (n = 12) feeding records and tongue and cheek swabs were collected within 48 h of birth, and after 2, 4, and 6 mo. DNA was extracted from samples, bacterial and fungal amplicons were generated and sequenced using Illumina MiSeq, and sequences were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and Statistical Analysis System (SAS) to evaluate differences over time and among breast-fed, formula-fed, mixed-fed, and solid food-fed infants. Results: Considering all time points, breast milk- and mixed-fed infants had lower oral species richness than solid food-fed infants (p = 0.006). Regardless of feeding mode, species richness was lower at birth than at other time points (p = 0.006). Principal coordinates analysis (PCoA) of unique fraction metric (UniFrac) distances indicated that bacterial communities were impacted by feeding method (p < 0.005). Considering all time points, breast-fed infants had higher Streptococcus, while formula-fed infants had higher Actinomyces and Prevotella. Regardless of feeding mode, Propionibacterium, Porphyromonas, Prevotella, Gemella, Granulicatella, Veillonella, Fusobacterium, Leptotrichia, Neisseria, and Haemophilus increased with age, while Cloacibacterium and Dechloromonas decreased with age. Oral fungi were detected in infants but were not impacted by diet. Conclusions: These findings demonstrate that the establishment of oral bacteria depends on dietary composition and age. More research is necessary to determine whether this affects risk of oral caries and other health outcomes later in life.},
}
@article {pmid33166536,
year = {2021},
author = {Goraj, W and Pytlak, A and Kowalska, B and Kowalski, D and Grządziel, J and Szafranek-Nakonieczna, A and Gałązka, A and Stępniewska, Z and Stępniewski, W},
title = {Influence of pipe material on biofilm microbial communities found in drinking water supply system.},
journal = {Environmental research},
volume = {196},
number = {},
pages = {110433},
doi = {10.1016/j.envres.2020.110433},
pmid = {33166536},
issn = {1096-0953},
mesh = {Biofilms ; *Drinking Water ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Water Supply ; },
abstract = {The biofilms and water samples from a model installation built of PVC-U, PE-HD and cast iron pipes were investigated using standard heterotrophic plate count and 16S rRNA Next Generation Sequencing. The results of the high throughput identification imply that the construction material strongly influences the microbiome composition. PVC-U and PE-HD pipes were dominated with Proteobacteria (54-60%) while the cast pipe was overgrown by Nitrospirae (64%). It was deduced that the plastic pipes create a more convenient environment for the potentially pathogenic taxa than the cast iron. The 7-year old biofilms were described as complex habitats with sharp oxidation-reduction gradients, where co-existence of methanogenic and methanotrophic microbiota takes place. Furthermore, it was found that the drinking water distribution systems (DWDS) are a useful tool for studying the ecology of rare bacterial phyla. New ecophysiological aspects were described for Aquihabitans, Thermogutta and Vampirovibrio. The discrepancy between identity of HPC-derived bacteria and NGS-revealed composition of biofilm and water microbiomes point to the need of introducing new diagnostical protocols to enable proper assessment of the drinking water safety, especially in DWDSs operating without disinfection.},
}
@article {pmid33166079,
year = {2021},
author = {Nie, Y and Wu, XL},
title = {Getting back to the nature of the microbial world: from the description and inductive reasoning to deductive study after 'meta-omics'.},
journal = {Microbial biotechnology},
volume = {14},
number = {1},
pages = {22-25},
pmid = {33166079},
issn = {1751-7915},
mesh = {Databases, Factual ; *Microbiota ; },
abstract = {'Omics' studies have by now deposited massive amounts of data into the databases, and it is now time to return to the question as to what can we actually learn from them. Increased application of the deductive approach in synthetic microbial ecology and synthetic microbiome research will undoubtedly provide exciting new opportunities for advancing our understanding of microbial ecology.},
}
@article {pmid33164669,
year = {2020},
author = {Zhu, M and Ji, J and Duan, X and Shi, W and Li, Y},
title = {First Report of Powdery Mildew Caused by Blumeria graminis f. sp. bromi on Bromus catharticus in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-09-20-1983-PDN},
pmid = {33164669},
issn = {0191-2917},
abstract = {Bromus catharticus, rescuegrass, is a brome grass that has been cultivated for herbage production, and been widely naturalized in many provinces of China, including Henan province. During April and May 2020, powdery mildew was found on leaves of Br. catharticus on the campus of Henan Normal University, Xinxiang city (35.3°N; 113.9°E), Henan Province, China. Abundant white or grayish irregular or coalesced circular powdery colonies were scattered on the adaxial surface of leaves and 70% of the leaf areas were affected. Some of the infected leaves either were chlorotic or senescent. About 60% of the observed plants showed powdery mildew symptoms. Conidiophores (n = 25) were 32 to 45 μm × 7 to 15 μm and composed of foot cells and conidia (mostly 6 conidia) in chains. Conidia (n = 50) were 25 to 35 μm × 10 to 15 μm, on average 30 × 13 μm, with a length/width ratio of 2.3. Chasmothecia were not found. Based on these morphologic characteristics, the pathogen was initially identified as Blumeria graminis f. sp. bromi (Braun and Cook 2012; Troch et al. 2014). B. graminis mycelia and conidia were collected, and total genomic DNA was extracted (Zhu et al. 2019). The rDNA internal transcribed spacer (ITS) region was amplified with primer pairs ITS1/ITS4. The amplicon was cloned and sequenced. The sequence (574 bp) was deposited into GenBank under Accession No. MT892940. BLASTn analysis revealed that MT892940 was 100% identical to B. graminis f. sp. bromi on Br. catharticus (AB000935, 550 of 550 nucleotides) (Takamatsu et al. 1998). Phylogenetic analysis of MT892940 and ITS of other B. graminis ff. spp. clearly indicated least two phylogenetically distinct clades of B. graminis f. sp. bromi and that MT892940 clustered with the Takamatsu vouchers. Leaf surfaces of five healthy plants were fixed at the base of a settling tower and then inoculated by blowing conidia from diseased leaves using pressurized air. Five non-inoculated plants served as controls. The inoculated and non-inoculated plants were maintained separately in two growth chambers (humidity, 60%; light/dark, 16 h/8 h; temperature, 18℃). Thirteen- to fifteen-days after inoculation, B. graminis signs and symptoms were visible on inoculated leaves, whereas control plants remained asymptomatic. The pathogenicity assays were repeated twice with the same results. The observed signs and symptoms were morphologically identical to those of the originally infected leaves. Accordingly, the causal organism of the powdery mildew was confirmed as B. graminis f. sp. bromi by morphological characteristics and ITS sequence data. B. graminis has been reported on Br. catharticus in the United States (Klingeman et al. 2018), Japan (Inuma et al. 2007) and Argentina (Delhey et al. 2003). To our best knowledge, this is the first report of B. graminis on Br. catharticus in China. Since hybridization of B. graminis ff. spp. is a mechanism of adaptation to new hosts, Br. catharticus may serve as a primary inoculum reservoir of B. graminis to infect other species (Menardo et al. 2016). This report provides fundamental information for the powdery mildew that can be used to develop control management of the disease in Br. catharticus herbage production.},
}
@article {pmid33162209,
year = {2021},
author = {Hou, D and Hong, M and Wang, K and Yan, H and Wang, Y and Dong, P and Li, D and Liu, K and Zhou, Z and Zhang, D},
title = {Prokaryotic community succession and assembly on different types of microplastics in a mariculture cage.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {268},
number = {Pt A},
pages = {115756},
doi = {10.1016/j.envpol.2020.115756},
pmid = {33162209},
issn = {1873-6424},
mesh = {China ; Microplastics ; *Plastics ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/analysis ; },
abstract = {Microplastics have emerged as a new anthropogenic substrate that can readily be colonized by microorganisms. Nevertheless, microbial community succession and assembly among different microplastics in nearshore mariculture cages remains poorly understood. Using an in situ incubation experiment, 16S rRNA gene amplicon sequencing, and the neutral model, we investigated the prokaryotic communities attached to polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) in a mariculture cage in Xiangshan Harbor, China. The α-diversities and compositions of microplastic-attached prokaryotic communities were significantly distinct from free-living and small particle-attached communities in the surrounding water but relatively similar to the large particle-attached communities. Although a distinct prokaryotic community was developed on each type of microplastic, the communities on PE and PP more closely resembled each other. Furthermore, the prokaryotic community dissimilarity among all media (microplastics and water fractions) tended to decrease over time. Hydrocarbon-degrading bacteria Alcanivorax preferentially colonized PE, and the genus Vibrio with opportunistically pathogenic members has the potential to colonize PET. Additionally, neutral processes dominated the prokaryotic community assembly on PE and PP, while selection was more responsible for the prokaryotic assembly on PET. The assembly of Planctomycetaceae and Thaumarchaeota Marine Group I taxa on three microplastics were mainly governed by selection and neutral processes, respectively. Our study provides further understanding of microplastic-associated microbial ecology in mariculture environments.},
}
@article {pmid33161552,
year = {2021},
author = {Navarrete, AA and de Cássia Bonassi, R and Américo-Pinheiro, JHP and Vazquez, GH and Mendes, LW and de Souza Loureiro, E and Kuramae, EE and Tsai, SM},
title = {Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2232},
number = {},
pages = {251-263},
doi = {10.1007/978-1-0716-1040-4_19},
pmid = {33161552},
issn = {1940-6029},
mesh = {Agriculture/*methods ; Biofuels/microbiology ; Biomass ; Carbon/metabolism ; Crops, Agricultural/*genetics/microbiology ; Environmental Biomarkers/genetics ; Greenhouse Effect ; *Soil Microbiology ; },
abstract = {Here we describe a suite of methods to identify potential taxonomic and functional soil microbial indicators of soil quality and plant health in biofuel crops in various areas and land types. This approach draws on tools to assess microbial diversity, greenhouse gas fluxes, and soil physicochemical properties in bioenergy cropping systems. Integrative statistical models are then used to identify potential microbial indicators for sustainable management of bioenergy crops.},
}
@article {pmid33161546,
year = {2021},
author = {Yeoh, YK},
title = {Removing Host-derived DNA Sequences from Microbial Metagenomes via Mapping to Reference Genomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2232},
number = {},
pages = {147-153},
doi = {10.1007/978-1-0716-1040-4_13},
pmid = {33161546},
issn = {1940-6029},
mesh = {Animals ; Arthropods/microbiology ; Base Sequence/*genetics ; Eukaryota/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota ; Plants/microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; },
abstract = {DNA sequencing has become a common tool in environmental microbial ecology, facilitating characterization of microbial populations as well as complex microbial communities by circumventing culture bottlenecks. However, certain samples especially from host-associated environments (rhizosphere, human tissue) or complex communities (soils) can contain a high degree of DNA sequences derived from hosts (plants, human) or other organisms of non-interest (arthropods, unicellular eukaryotes). This chapter presents a simple in silico method to remove contaminating sequences in metagenomes based on aligning sequences to reference genomes of the target organism.},
}
@article {pmid33161522,
year = {2021},
author = {Rosa, LH and Pinto, OHB and Convey, P and Carvalho-Silva, M and Rosa, CA and Câmara, PEAS},
title = {DNA Metabarcoding to Assess the Diversity of Airborne Fungi Present over Keller Peninsula, King George Island, Antarctica.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {165-172},
pmid = {33161522},
issn = {1432-184X},
mesh = {Animals ; Antarctic Regions ; *Ascomycota ; Basidiomycota ; DNA Barcoding, Taxonomic ; *Ecosystem ; Fungi/genetics ; Mortierella ; },
abstract = {We assessed fungal diversity present in air samples obtained from King George Island, Antarctica, using DNA metabarcoding through high-throughput sequencing. We detected 186 fungal amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, and Chytridiomycota. Fungi sp. 1, Agaricomycetes sp. 1, Mortierella parvispora, Mortierella sp. 2, Penicillium sp., Pseudogymnoascus roseus, Microdochium lycopodinum, Mortierella gamsii, Arrhenia sp., Cladosporium sp., Mortierella fimbricystis, Moniliella pollinis, Omphalina sp., Mortierella antarctica, and Pseudogymnoascus appendiculatus were the most dominant ASVs. In addition, several ASVs could only be identified at higher taxonomic levels and may represent previously unknown fungi and/or new records for Antarctica. The fungi detected in the air displayed high indices of diversity, richness, and dominance. The airborne fungal diversity included saprophytic, mutualistic, and plant and animal opportunistic pathogenic taxa. The diversity of taxa detected reinforces the hypothesis that the Antarctic airspora includes fungal propagules of both intra- and inter-continental origin. If regional Antarctic environmental conditions ameliorate further in concert with climate warming, these fungi might be able to reactivate and colonize different Antarctic ecosystems, with as yet unknown consequences for ecosystem function in Antarctica. Further aeromycological studies are necessary to understand how and from where these fungi arrive and move within Antarctica and if environmental changes will encourage the development of non-native fungal species in Antarctica.},
}
@article {pmid33161521,
year = {2021},
author = {Tanuwidjaja, I and Vogel, C and Pronk, GJ and Schöler, A and Kublik, S and Vestergaard, G and Kögel-Knabner, I and Mrkonjic Fuka, M and Schloter, M and Schulz, S},
title = {Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {897-907},
pmid = {33161521},
issn = {1432-184X},
support = {SCHL 446/4-2//Deutsche Forschungsgemeinschaft (DE)/ ; KO 1035/33-1//Deutsche Forschungsgemeinschaft/ ; KO 1035/33-2//Deutsche Forschungsgemeinschaft/ ; 031B0509 B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {Bacteria/genetics ; Clay ; Minerals ; *Soil ; *Soil Microbiology ; },
abstract = {Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for accessing P pools. We used a metagenomic approach to analyze the microbial potential to access P after 842 days of incubation in artificial soils with a clay mineral composition of either non-expandable illite (IL) or expandable montmorillonite (MT), which differ in their surface characteristics like soil surface area and surface charge. Our data indicate that microorganisms of the two soils developed different strategies to overcome P depletion, resulting in similar total P concentrations. Genes predicted to encode inorganic pyrophosphatase (ppa), exopolyphosphatase (ppx), and the pstSCAB transport system were higher in MT, suggesting effective P uptake and the use of internal poly-P stores. Genes predicted to encode enzymes involved in organic P turnover like alkaline phosphatases (phoA, phoD) and glycerophosphoryl diester phosphodiesterase were detected in both soils in comparable numbers. In addition, Po concentrations did not differ significantly. Most identified genes were assigned to microbial lineages generally abundant in agricultural fields, but some were assigned to lineages known to include oligotrophic specialists, such as Bacillaceae and Microchaetaceae.},
}
@article {pmid33160238,
year = {2021},
author = {Gao, Y and Zhang, W and Li, Y and Wu, H and Yang, N and Hui, C},
title = {Dams shift microbial community assembly and imprint nitrogen transformation along the Yangtze River.},
journal = {Water research},
volume = {189},
number = {},
pages = {116579},
doi = {10.1016/j.watres.2020.116579},
pmid = {33160238},
issn = {1879-2448},
mesh = {China ; *Microbiota ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Rivers ; },
abstract = {Dams are important for flood control, water storage, irrigation, electric generation, navigation, and have been regarded as the largest anthropogenic disturbance in aquatic ecosystems. However, how dams impact nitrogen transformation on a large watershed scale remained less studied. To explicitly address the impact of dams on nitrogen transformation, we used 16S rRNA gene sequencing to investigate the microbial dynamics and ecological processes under different dam conditions along the Yangtze River, as microbial communities are playing a key role in aquatic nitrogen transformation. Compared with landforms, dams exerted a more significant impact on the distribution patterns of microbial communities along the Yangtze River. The results showed that, by controlling suspended sand concentration, dams filtered keystone species, reshaped distribution of metacommunities, and mediated ecological assembly processes of microbial communities. Moreover, direct causal relationships between dams and nitrogen transformation were chained via microbial communities. To summarize, by combining knowledge in hydrology, microbial ecology, and biogeochemistry, this research exhibited the impact of different dams on the nitrogen transformation along a large river, and the key roles of suspended sand and microbial communities were emphasized. We anticipate a more precise modelling and prediction of nitrogen transformation in large watersheds, which may provide new perspectives for controlling the nitrogen in aquatic environments.},
}
@article {pmid33158898,
year = {2021},
author = {Jiang, Y and Brandt, BW and Buijs, MJ and Cheng, L and Exterkate, RAM and Crielaard, W and Deng, DM},
title = {Manipulation of Saliva-Derived Microcosm Biofilms To Resemble Dysbiotic Subgingival Microbiota.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {3},
pages = {},
pmid = {33158898},
issn = {1098-5336},
mesh = {Biofilms ; Butyric Acid/metabolism ; Dipeptidyl Peptidase 4/metabolism ; Dysbiosis/*microbiology ; Gingiva/*microbiology ; Humans ; Microbiota/genetics/physiology ; Porphyromonas gingivalis/enzymology/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; },
abstract = {Periodontitis is a highly prevalent oral inflammatory disease triggered by dysbiotic subgingival microbiota. For the development of microbiome modulators that can reverse the dysbiotic state and reestablish a health-associated microbiota, a high-throughput in vitro multispecies biofilm model is needed. Our aim is to establish a model that resembles a dysbiotic subgingival microbial biofilm by incorporating the major periodontal pathogen Porphyromonas gingivalis into microcosm biofilms cultured from pooled saliva of healthy volunteers. The biofilms were grown for 3, 7, and 10 days and analyzed for their microbial composition by 16S rRNA gene amplicon sequencing as well as measurement of dipeptidyl peptidase IV (DPP4) activity and butyric acid production. The addition of P. gingivalis increased its abundance in saliva-derived microcosm biofilms from 2.7% on day 3 to >50% on day 10, which significantly reduced the Shannon diversity but did not affect the total number of operational taxonomic units (OTUs). The P. gingivalis-enriched biofilms displayed altered microbial composition as revealed by principal-component analysis and reduced interactions among microbial species. Moreover, these biofilms exhibited enhanced DPP4 activity and butyric acid production. In conclusion, by adding P. gingivalis to saliva-derived microcosm biofilms, we established an in vitro pathogen-enriched dysbiotic microbiota which resembles periodontitis-associated subgingival microbiota in terms of increased P. gingivalis abundance and higher DPP4 activity and butyric acid production. This model may allow for investigating factors that accelerate or hinder a microbial shift from symbiosis to dysbiosis and for developing microbiome modulation strategies.IMPORTANCE In line with the new paradigm of the etiology of periodontitis, an inflammatory disorder initiated by dysbiotic subgingival microbiota, novel therapeutic strategies have been proposed targeting reversing dysbiosis and restoring host-compatible microbiota rather than eliminating the biofilms unselectively. Thus, appropriate laboratory models are required to evaluate the efficacy of potential microbiome modulators. In the present study, we used the easily obtainable saliva as an inoculum, spiked the microcosm biofilms with the periodontal pathogen Porphyromonas gingivalis, and obtained a P. gingivalis-enriched microbiota, which resembles the in vivo pathogen-enriched subgingival microbiota in severe periodontitis. This biofilm model circumvents the difficulties encountered when using subgingival plaque as the inoculum and achieves microbiota in a dysbiotic state in a controlled and reproducible manner, which is required for high-throughput and large-scale evaluation of strategies that can potentially modulate microbial ecology.},
}
@article {pmid33158547,
year = {2021},
author = {Rahman, MS and Sikder, MNA and Xu, H},
title = {Insights into β-diversity of periphytic protozoan fauna along the water column of marine ecosystems.},
journal = {Marine pollution bulletin},
volume = {162},
number = {},
pages = {111801},
doi = {10.1016/j.marpolbul.2020.111801},
pmid = {33158547},
issn = {1879-3363},
mesh = {Biodiversity ; China ; *Ciliophora ; *Ecosystem ; Environmental Monitoring ; Water ; },
abstract = {It has been increasingly recognized that there is high relevance in determining the β-diversity of communities along an environmental gradient for bioassessment of environmental quality status. To evaluate the vertical variations in β-diversity of periphytic protozoan fauna, in response to environmental heterogeneity in marine ecosystems, a baseline survey was conducted at the four water depths in the coastal waters of the Yellow Sea, northern China. Results demonstrated that (1) the species distribution presented different patterns at four water depths; (2) both compositional and community structure showed a significant vertical variation in multivariate dispersions from surface layer to the deeper layers; and (3) β-diversity measures generally increased from depths of 1 m to 5 m. These findings suggest that the homogeneity in the periphytic communities are of a high variability along the water column of marine ecosystems.},
}
@article {pmid33158546,
year = {2020},
author = {Gui, Y and Uroosa, and Bai, X and Wang, Z and Xu, G and Xu, H},
title = {An approach to assessing ecological quality status due to microalgae bloom using biofilm-dwelling protozoa based on biological trait analysis.},
journal = {Marine pollution bulletin},
volume = {161},
number = {Pt A},
pages = {111795},
doi = {10.1016/j.marpolbul.2020.111795},
pmid = {33158546},
issn = {1879-3363},
mesh = {Biofilms ; *Biological Products ; Environmental Monitoring ; *Microalgae ; Water Quality ; },
abstract = {Functional diversity/distinctness measure based trait has been proved to be a robust indicator to summarize the description of community structures and to assess water quality in different types of aquatic environment. In this study, for identifying the shielding effect of microalgae against protozoan grazing, a nine-day survey was conducted by exposing protozoan communities to a series of concentration gradients (10[0] (control), 10[4], 10[5], 10[6] and 10[7] cells ml[-1]) of two microalgae, respectively. Our results showed clear resistance of two test microalgae against protozoan grazing in five treatments. The functional distinctness measures commonly represented a decreasing trend along the gradient of concentrations of both microalgae. Ellipse tests based on the paired functional distinctness indices revealed that community functioning represented an uptrend departure from the expected pattern with the concentrations of both microalgae increase. Therefore, we suggest that the functional distinctness measures might be a reliable approach to detect the ecological effect of microalgae against protozoan grazing.},
}
@article {pmid33158141,
year = {2020},
author = {Syrokou, MK and Themeli, C and Paramithiotis, S and Mataragas, M and Bosnea, L and Argyri, AA and Chorianopoulos, NG and Skandamis, PN and Drosinos, EH},
title = {Microbial Ecology of Greek Wheat Sourdoughs, Identified by a Culture-Dependent and a Culture-Independent Approach.},
journal = {Foods (Basel, Switzerland)},
volume = {9},
number = {11},
pages = {},
pmid = {33158141},
issn = {2304-8158},
support = {T1EDK-05339//European Union and Greek national funds/ ; },
abstract = {The aim of the present study was to assess the microecosystem of 13 homemade spontaneously fermented wheat sourdoughs from different regions of Greece, through the combined use of culture-dependent (classical approach; clustering by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) and identification by PCR species-specific for Lactiplantibacillus plantarum, and sequencing of the 16S-rRNA and 26S-rRNA gene, for Lactic Acid Bacteria (LAB) and yeasts, respectively) and independent approaches [DNA- and RNA-based PCR-Denaturing Gradient Gel Electrophoresis (DGGE)]. The pH and Total Titratable Acidity (TTA) values ranged from 3.64-5.05 and from 0.50-1.59% lactic acid, respectively. Yeast and lactic acid bacteria populations ranged within 4.60-6.32 and 6.28-9.20 log CFU/g, respectively. The yeast: LAB ratio varied from 1:23-1:10,000. A total of 207 bacterial and 195 yeast isolates were obtained and a culture-dependent assessment of their taxonomic affiliation revealed dominance of Lb. plantarum in three sourdoughs, Levilactobacillus brevis in four sourdoughs and co-dominance of these species in two sourdoughs. In addition, Companilactobacillusparalimentarius dominated in two sourdoughs and Fructilactobacillussanfranciscensis and Latilactobacillus sakei in one sourdough each. Lactococcus lactis, Lb. curvatus, Leuconostoc citreum, Ln. mesenteroides and Lb. zymae were also recovered from some samples. Regarding the yeast microbiota, it was dominated by Saccharomyces cerevisiae in 11 sourdoughs and Pichia membranifaciens and P. fermentans in one sourdough each. Wickerhamomyces anomalus and Kazachstania humilis were also recovered from one sample. RNA-based PCR-DGGE provided with nearly identical results with DNA-based one; in only one sample the latter provided an additional band. In general, the limitations of this approach, namely co-migration of amplicons from different species to the same electrophoretic position and multiband profile of specific isolates, greatly reduced resolution capacity, which resulted in only partial verification of the microbial ecology detected by culture-dependent approach in the majority of sourdough samples. Our knowledge regarding the microecosystem of spontaneously fermented Greek wheat-based sourdoughs was expanded, through the study of sourdoughs originating from regions of Greece that were not previously assessed.},
}
@article {pmid33157349,
year = {2021},
author = {Kiewra, D and Szymanowski, M and Czułowska, A and Kolanek, A},
title = {The local-scale expansion of Dermacentor reticulatus ticks in Lower Silesia, SW Poland.},
journal = {Ticks and tick-borne diseases},
volume = {12},
number = {1},
pages = {101599},
doi = {10.1016/j.ttbdis.2020.101599},
pmid = {33157349},
issn = {1877-9603},
mesh = {*Animal Distribution ; Animals ; Dermacentor/*physiology ; Female ; Male ; Models, Biological ; Poland ; },
abstract = {The range of D. reticulatus is discontinuous in Europe, with a gap between the Western and Eastern European populations. Recent studies have shown, however, a decrease in the gap as a consequence of D. reticulatus spreading to new areas. This study aims to analyze the dynamic of local-scale changes in the D. reticulatus range in Lower Silesia, SW Poland. All sites of D. reticulatus presence recognized in our research were located in the north-western part of the study area (Wroclaw and its surroundings), whereas the south-eastern part was found to be free of these ticks. However, a five-year observation period (2014-2019) indicates the expansion of D. reticulatus on a local scale, with a general tendency to expand to the east, with northerly or southerly deviations from year to year. The settled sites differed in distance to the nearest built-up area, the density of resident population, as well as land development intensity in the immediate vicinity. The 100% probability isolines of D. reticulatus presence in Wroclaw and its surroundings allowed the determination of the rate of range change, which turned out to be uneven in terms of direction and speed. The average rate of change in the range of tick occurrence was estimated at 7 km in 3 years. A more accurate analysis of the estimated range changes-made using modeling and verification of predicted changes in the field-showed that the likely rate of range change can be estimated at around 0.6-2.3 km/year.},
}
@article {pmid33157023,
year = {2021},
author = {Köstlbacher, S and Collingro, A and Halter, T and Domman, D and Horn, M},
title = {Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria.},
journal = {Current biology : CB},
volume = {31},
number = {2},
pages = {346-357.e3},
pmid = {33157023},
issn = {1879-0445},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Adaptation, Physiological/*genetics ; Chlamydia/*genetics/pathogenicity ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; *Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Host Microbial Interactions/genetics ; Plasmids/*genetics ; },
abstract = {Plasmids are important in microbial evolution and adaptation to new environments. Yet, carrying a plasmid can be costly, and long-term association of plasmids with their hosts is poorly understood. Here, we provide evidence that the Chlamydiae, a phylum of strictly host-associated intracellular bacteria, have coevolved with their plasmids since their last common ancestor. Current chlamydial plasmids are amalgamations of at least one ancestral plasmid and a bacteriophage. We show that the majority of plasmid genes are also found on chromosomes of extant chlamydiae. The most conserved plasmid gene families are predominantly vertically inherited, while accessory plasmid gene families show significantly increased mobility. We reconstructed the evolutionary history of plasmid gene content of an entire bacterial phylum over a period of around one billion years. Frequent horizontal gene transfer and chromosomal integration events illustrate the pronounced impact of coevolution with these extrachromosomal elements on bacterial genome dynamics in host-dependent microbes.},
}
@article {pmid33156501,
year = {2021},
author = {Trabelsi, ABH and Zaafouri, K and Friaa, A and Abidi, S and Naoui, S and Jamaaoui, F},
title = {Municipal sewage sludge energetic conversion as a tool for environmental sustainability: production of innovative biofuels and biochar.},
journal = {Environmental science and pollution research international},
volume = {28},
number = {8},
pages = {9777-9791},
pmid = {33156501},
issn = {1614-7499},
support = {Project : "Thermo-chemical conversion of solid wastes into renewable biofuels and bio-products"//Ministry of Higher Education and Scientific Research (MESRST) in Tunisia/ ; },
mesh = {*Biofuels/analysis ; Charcoal ; Hot Temperature ; Pyrolysis ; *Sewage ; },
abstract = {In this study, municipal sewage sludge (MSS) is converted simultaneously into renewable biofuels (bio-oil, syngas) and high value-added products (biochar) using a fixed bed pyrolyzer. This work examines the combined effect of two factors: final pyrolysis temperature (°C) and MSS moisture content (%) on pyrogenic product yields and characteristics. A centered composite experimental design (CCD) is established for pyrolysis process optimization by adopting the response surface methodology (RSM). The statistical results indicate that the optimal conditions considering all studied factors and responses are 550 °C as final pyrolysis temperature and 15% as MSS moisture content. In these optimal conditions, biofuels yield is around 48 wt%, whereas biochar yield is about 52 wt%. The pyrolysis products characterizations reveal that (i) pyrolytic oil has a complex molecular composition rich with n-alkanes, n-alkenes, carboxylic acids, and aromatic compounds; (ii) bio-oil presents a high-energy content (high heating value HHV around 30.6 MJ/kg); (iii) syngas mixture has a good calorific value (HHV up to 8 MJ/kg), which could be used as renewable energy vector or for pyrolysis reactor heating; and (iv) biochar residue has good aliphatic and oxygenated group contents favoring its application as biofertilizer. These findings suggest that MSS conversion into biofuels and biochar is an appropriate approach for MSS treatment. MSS-to-energy could be proposed as an element for circular economy concept due to its effectiveness in producing high value-added and sustainable products and reducing environmental problems linked to MSS disposal.},
}
@article {pmid33156395,
year = {2021},
author = {Addesso, R and Gonzalez-Pimentel, JL and D'Angeli, IM and De Waele, J and Saiz-Jimenez, C and Jurado, V and Miller, AZ and Cubero, B and Vigliotta, G and Baldantoni, D},
title = {Microbial Community Characterizing Vermiculations from Karst Caves and Its Role in Their Formation.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {884-896},
pmid = {33156395},
issn = {1432-184X},
support = {MINECO [CGL2016-75590-P]//European Regional Development Fund/ ; },
mesh = {Acidobacteria ; Bacteria/genetics ; *Caves ; *Microbiota ; Proteobacteria ; },
abstract = {The microbiota associated with vermiculations from karst caves is largely unknown. Vermiculations are enigmatic deposits forming worm-like patterns on cave walls all over the world. They represent a precious focus for geomicrobiological studies aimed at exploring both the microbial life of these ecosystems and the vermiculation genesis. This study comprises the first approach on the microbial communities thriving in Pertosa-Auletta Cave (southern Italy) vermiculations by next-generation sequencing. The most abundant phylum in vermiculations was Proteobacteria, followed by Acidobacteria > Actinobacteria > Nitrospirae > Firmicutes > Planctomycetes > Chloroflexi > Gemmatimonadetes > Bacteroidetes > Latescibacteria. Numerous less-represented taxonomic groups (< 1%), as well as unclassified ones, were also detected. From an ecological point of view, all the groups co-participate in the biogeochemical cycles in these underground environments, mediating oxidation-reduction reactions, promoting host rock dissolution and secondary mineral precipitation, and enriching the matrix in organic matter. Confocal laser scanning microscopy and field emission scanning electron microscopy brought evidence of a strong interaction between the biotic community and the abiotic matrix, supporting the role of microbial communities in the formation process of vermiculations.},
}
@article {pmid33155101,
year = {2021},
author = {Torralba, MG and Aleti, G and Li, W and Moncera, KJ and Lin, YH and Yu, Y and Masternak, MM and Golusinski, W and Golusinski, P and Lamperska, K and Edlund, A and Freire, M and Nelson, KE},
title = {Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {1030-1046},
pmid = {33155101},
issn = {1432-184X},
support = {R00 DE023584/DE/NIDCR NIH HHS/United States ; },
mesh = {*Carcinoma, Squamous Cell ; *Head and Neck Neoplasms ; Humans ; *Mouth Neoplasms ; RNA, Ribosomal, 16S/genetics ; Squamous Cell Carcinoma of Head and Neck ; Virulence Factors/genetics ; },
abstract = {The human microbiome has been the focus of numerous research efforts to elucidate the pathogenesis of human diseases including cancer. Oral cancer mortality is high when compared with other cancers, as diagnosis often occurs during late stages. Its prevalence has increased in the USA over the past decade and accounts for over 40,000 new cancer patients each year. Additionally, oral cancer pathogenesis is not fully understood and is likely multifactorial. To unravel the relationships that are associated with the oral microbiome and their virulence factors, we used 16S rDNA and metagenomic sequencing to characterize the microbial composition and functional content in oral squamous cell carcinoma (OSCC) tumor tissue, non-tumor tissue, and saliva from 18 OSCC patients. Results indicate a higher number of bacteria belonging to the Fusobacteria, Bacteroidetes, and Firmicutes phyla associated with tumor tissue when compared with all other sample types. Additionally, saliva metaproteomics revealed a significant increase of Prevotella in five OSCC subjects, while Corynebacterium was mostly associated with ten healthy subjects. Lastly, we determined that there are adhesion and virulence factors associated with Streptococcus gordonii as well as from known oral pathogens belonging to the Fusobacterium genera found mostly in OSCC tissues. From these results, we propose that not only will the methods utilized in this study drastically improve OSCC diagnostics, but the organisms and specific virulence factors from the phyla detected in tumor tissue may be excellent biomarkers for characterizing disease progression.},
}
@article {pmid33153747,
year = {2021},
author = {Gu, Z and Liu, K and Pedersen, MW and Wang, F and Chen, Y and Zeng, C and Liu, Y},
title = {Community assembly processes underlying the temporal dynamics of glacial stream and lake bacterial communities.},
journal = {The Science of the total environment},
volume = {761},
number = {},
pages = {143178},
doi = {10.1016/j.scitotenv.2020.143178},
pmid = {33153747},
issn = {1879-1026},
mesh = {Bacteria/genetics ; Ice Cover ; *Lakes ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Community assembly processes are important in structuring aquatic microbial communities; however, the influence of these processes on the dynamics of bacterial communities in glacial streams and lakes remains largely unstudied. To investigate the assembly processes underlying the temporal variation of the bacterial community, we collected 50 water samples over five months in an ephemeral glacial stream and its downstream lake at the terminus of the Qiangyong glacier on the Tibetan Plateau. Using the V4 hypervariable region of the bacterial 16S rRNA gene combined with environmental measurements, such as water temperature, pH, total nitrogen (TN), dissolved organic carbon (DOC) and water conductivity, we found that temporal variation in the environmental factors promoted the shift in the proglacial stream and the lake bacterial communities. The quantification of ecological processes showed that the stream microbial communities were influenced by the ecological drift (40%) in June, then changed to homogeneous selection (40%) in July and variable selection (60%) in September, while the dynamic pattern of proglacial lake bacterioplankton was governed by homogeneous selection (≥ 50%) over the time. Overall, the dynamic of bacterial community in the proglacial stream and lake water is influenced by environmental factors, and the community composition assembly of the Qiangyong glacial stream and lake could be dynamic and primarily governed by deterministic processes.},
}
@article {pmid33151560,
year = {2021},
author = {Yang, Q and Fu, S and Zou, P and Hao, J and Wei, D and Xie, G and Huang, J},
title = {Coordination of primary metabolism and virulence factors expression mediates the virulence of Vibrio parahaemolyticus towards cultured shrimp (Penaeus vannamei).},
journal = {Journal of applied microbiology},
volume = {131},
number = {1},
pages = {50-67},
doi = {10.1111/jam.14922},
pmid = {33151560},
issn = {1365-2672},
support = {31702385//National Natural Science Foundation of China/ ; 81903372//National Natural Science Foundation of China/ ; QL202005//Youth Program of Education Department of Liaoning Province/ ; QNLM201706//Pilot National Laboratory for Marine Science and Technology (Qingdao)/ ; },
mesh = {Animals ; Bacterial Toxins/genetics/metabolism ; DNA Transposable Elements/genetics ; Penaeidae/*microbiology ; Plasmids/genetics ; Seafood/microbiology ; Vibrio Infections/microbiology/mortality/*veterinary ; Vibrio parahaemolyticus/genetics/metabolism/*pathogenicity ; Virulence/genetics ; Virulence Factors/genetics/*metabolism ; },
abstract = {AIMS: Acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus has emerged as a severe bacterial disease of cultured shrimp. To identify the key virulence factors, two AHPND-causing V. parahaemolyticus (VpAHPND) strains (123 and 137) and two non-VpAHPND strains (HZ56 and ATCC 17082) were selected.<br><br>METHODS AND RESULTS: Challenge tests showed that the four strains exhibited different virulence towards shrimp with cumulative mortalities at 48&#xa0;h postinfection (hpi) ranging from 10 to 92%. The expression of pirAB[VP] in strain 123 and 137 was not significantly different. Genomic analysis revealed that the two VpAHPND strains contain a plasmid with the PirAB[VP] toxins (pirAB[VP]) flanked by the insertion sequence (ISVal1) that has been identified in various locations of chromosomes in VpAHPND strains. The two VpAHPND strains possessed almost identical virulence factors, while ISVal1 disrupted three genes related to flagellar motility in strain 137. Phenotype assay showed that strain 123 possessed the highest growth rate and swimming motility, followed by strain 137, suggesting that the disruption of essential genes mediated by ISVal1 significantly affected the virulence level. Transcriptome analysis of two VpAHPND strains (123 and 137) further suggested that virulence genes related to the capsule, flagella and primary metabolism were highly expressed in strain 123.<br><br>CONCLUSIONS: Here for the first time, it is demonstrated that the virulence of VpAHPND is not only determined by the expression of pirAB[VP] , but also is mediated by ISVal1 which affects the genes involved in flagellar motility and primary metabolism.<br><br>The genomic and transcriptomic analysis of VpAHPND strains provides valuable information on the virulence factors affecting the pathogenicity of VpAHPND.},
}
@article {pmid33151140,
year = {2020},
author = {Waite, DW and Chuvochina, M and Pelikan, C and Parks, DH and Yilmaz, P and Wagner, M and Loy, A and Naganuma, T and Nakai, R and Whitman, WB and Hahn, MW and Kuever, J and Hugenholtz, P},
title = {Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {11},
pages = {5972-6016},
doi = {10.1099/ijsem.0.004213},
pmid = {33151140},
issn = {1466-5034},
support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Bacteria/*classification ; Deltaproteobacteria/*classification ; Phylogeny ; Proteobacteria/*classification ; Terminology as Topic ; },
abstract = {The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class Deltaproteobacteria encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the Oligoflexia. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes Deltaproteobacteria and Oligoflexia in the phylum Proteobacteria. Instead, the great majority of currently recognized members of the class Deltaproteobacteria are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class Oligoflexia represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum Thermodesulfobacteria, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the Thermodesulfobacteria rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.},
}
@article {pmid33150937,
year = {2020},
author = {Hopkins, JR and Semenova-Nelsen, T and Sikes, BA},
title = {Fungal community structure and seasonal trajectories respond similarly to fire across pyrophilic ecosystems.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {1},
pages = {},
doi = {10.1093/femsec/fiaa219},
pmid = {33150937},
issn = {1574-6941},
mesh = {Ecosystem ; *Fires ; *Mycobiome ; Seasons ; Soil ; },
abstract = {Fire alters microbial community composition, and is expected to increase in frequency due to climate change. Testing whether microbes in different ecosystems will respond similarly to increased fire disturbance is difficult though, because fires are often unpredictable and hard to manage. Fire recurrent or pyrophilic ecosystems, however, may be useful models for testing the effects of frequent disturbance on microbes. We hypothesized that across pyrophilic ecosystems, fire would drive similar alterations to fungal communities, including altering seasonal community dynamics. We tested fire's effects on fungal communities in two pyrophilic ecosystems, a longleaf pine savanna and tallgrass prairie. Fire caused similar fungal community shifts, including (i) driving immediate changes that favored taxa able to survive fire and take advantage of post-fire environments and (ii) altering seasonal trajectories due to fire-associated changes to soil nutrient availability. This suggests that fire has predictable effects on fungal community structure and intra-annual community dynamics in pyrophilic ecosystems, and that these changes could significantly alter fungal function. Parallel fire responses in these key microbes may also suggest that recurrent fires drive convergent changes across ecosystems, including less fire-frequented systems that may start burning more often due to climate change.},
}
@article {pmid33150935,
year = {2020},
author = {Landazuri, CFG and Gomez, JS and Raaijmakers, JM and Oyserman, BO},
title = {Restoring degraded microbiome function with self-assembled communities.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {12},
pages = {},
doi = {10.1093/femsec/fiaa225},
pmid = {33150935},
issn = {1574-6941},
mesh = {Bacteria/genetics ; Microbial Consortia ; *Microbiota ; Soil ; *Soil Microbiology ; },
abstract = {The natural microbial functions of many soils are severely degraded. Current state-of-the-art technology to restore these functions is through the isolation, screening, formulation and application of microbial inoculants and synthetic consortia. These approaches have inconsistent success, in part due to the incompatibility between the biofertilizer, crop, climate, existing soil microbiome and physicochemical characteristics of the soils. Here, we review the current state of the art in biofertilization and identify two key deficiencies in current strategies: the difficulty in designing complex multispecies biofertilizers and the bottleneck in scaling the production of complex multispecies biofertilizers. To address the challenge of producing scalable, multispecies biofertilizers, we propose to merge ecological theory with bioprocess engineering to produce 'self-assembled communities' enriched for particular functional guilds and adapted to a target soil and host plant. Using the nitrogen problem as an anchor, we review relevant ecology (microbial, plant and environmental), as well as reactor design strategies and operational parameters for the production of functionally enriched self-assembled communities. The use of self-assembled communities for biofertilization addresses two major hurdles in microbiome engineering: the importance of enriching microbes indigenous to (and targeted for) a specific environment and the recognized potential benefits of microbial consortia over isolates (e.g. functional redundancy). The proposed community enrichment model could also be instrumental for other microbial functions such as phosphorus solubilization, plant growth promotion or disease suppression.},
}
@article {pmid33150499,
year = {2021},
author = {Rasmussen, AN and Damashek, J and Eloe-Fadrosh, EA and Francis, CA},
title = {In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {601-616},
pmid = {33150499},
issn = {1432-184X},
support = {OCE-0847266//Division of Ocean Sciences/ ; },
mesh = {*Archaea/genetics ; Bays ; *Plankton/genetics ; RNA, Ribosomal, 16S/genetics ; San Francisco ; },
abstract = {Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.},
}
@article {pmid33150498,
year = {2021},
author = {Pino-Bodas, R and Stenroos, S},
title = {Global Biodiversity Patterns of the Photobionts Associated with the Genus Cladonia (Lecanorales, Ascomycota).},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {173-187},
pmid = {33150498},
issn = {1432-184X},
support = {FLF program//Royal Botanical Gardens, Kew/ ; Juan de la Cierva-Incorporaci&#xf3;n 2015-23526//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
mesh = {*Ascomycota/genetics ; Biodiversity ; *Chlorophyta/genetics ; *Lichens ; Phylogeny ; Symbiosis ; },
abstract = {The diversity of lichen photobionts is not fully known. We studied here the diversity of the photobionts associated with Cladonia, a sub-cosmopolitan genus ecologically important, whose photobionts belong to the green algae genus Asterochloris. The genetic diversity of Asterochloris was screened by using the ITS rDNA and actin type I regions in 223 specimens and 135 species of Cladonia collected all over the world. These data, added to those available in GenBank, were compiled in a dataset of altogether 545 Asterochloris sequences occurring in 172 species of Cladonia. A high diversity of Asterochloris associated with Cladonia was found. The commonest photobiont lineages associated with this genus are A. glomerata, A. italiana, and A. mediterranea. Analyses of partitioned variation were carried out in order to elucidate the relative influence on the photobiont genetic variation of the following factors: mycobiont identity, geographic distribution, climate, and mycobiont phylogeny. The mycobiont identity and climate were found to be the main drivers for the genetic variation of Asterochloris. The geographical distribution of the different Asterochloris lineages was described. Some lineages showed a clear dominance in one or several climatic regions. In addition, the specificity and the selectivity were studied for 18 species of Cladonia. Potentially specialist and generalist species of Cladonia were identified. A correlation was found between the sexual reproduction frequency of the host and the frequency of certain Asterochloris OTUs. Some Asterochloris lineages co-occur with higher frequency than randomly expected in the Cladonia species.},
}
@article {pmid33149844,
year = {2020},
author = {Skelly, E and Johnson, NW and Kapellas, K and Kroon, J and Lalloo, R and Weyrich, L},
title = {Response of Salivary Microbiota to Caries Preventive Treatment in Aboriginal and Torres Strait Islander Children.},
journal = {Journal of oral microbiology},
volume = {12},
number = {1},
pages = {1830623},
pmid = {33149844},
issn = {2000-2297},
abstract = {A once-annual caries preventive (Intervention) treatment was offered to Aboriginal and Torres Strait Islander schoolchildren-a population with disproportionately poorer oral health than non-Indigenous Australian children-in the Northern Peninsula Area (NPA) of Far North Queensland (FNQ), which significantly improved their oral health. Here, we examine the salivary microbiota of these children (mean age = 10 ± 2.96 years; n = 103), reconstructing the bacterial community composition with high-throughput sequencing of the V4 region of bacterial 16S rRNA gene. Microbial communities of children who received the Intervention had lower taxonomic diversity than those who did not receive treatment (Shannon, p < 0.05). Moreover, the Intervention resulted in further decreased microbial diversity in children with active carious lesions existing at the time of saliva collection. Microbial species associated with caries were detected; Lactobacillus salivarius, Lactobacillus reuteri, Lactobacillus gasseri, Prevotella multisaccharivorax, Parascardovia denticolens, and Mitsuokella HMT 131 were significantly increased (p < 0.05) in children with severe caries, especially in children who did not receive the Intervention. These insights into microbial associations and community differences prompt future considerations to the mechanisms behind caries-preventive therapy induced change; important for understanding the long-term implications of like treatment to improve oral health disparities within Australia. Trial registration: ANZCTR, ACTRN12615000693527. Registered 3 July 2015, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=368750&amp;isReview=true.},
}
@article {pmid33149734,
year = {2020},
author = {Pereira, LM and Messias, EA and Sorroche, BP and Oliveira, ADN and Arantes, LMRB and de Carvalho, AC and Tanaka-Azevedo, AM and Grego, KF and Carvalho, AL and Melendez, ME},
title = {In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland.},
journal = {The journal of venomous animals and toxins including tropical diseases},
volume = {26},
number = {},
pages = {e20190058},
pmid = {33149734},
issn = {1678-9199},
abstract = {BACKGROUND: Lack of complete genomic data of Bothrops jararaca impedes molecular biology research focusing on biotechnological applications of venom gland components. Identification of full-length coding regions of genes is crucial for the correct molecular cloning design.<br><br>METHODS: RNA was extracted from the venom gland of one adult female specimen of Bothrops jararaca. Deep sequencing of the mRNA library was performed using Illumina NextSeq 500 platform. De novo assembly of B. jararaca transcriptome was done using Trinity. Annotation was performed using Blast2GO. All predicted proteins after clustering step were blasted against non-redundant protein database of NCBI using BLASTP. Metabolic pathways present in the transcriptome were annotated using the KAAS-KEGG Automatic Annotation Server. Toxins were identified in the B. jararaca predicted proteome using BLASTP against all protein sequences obtained from Animal Toxin Annotation Project from Uniprot KB/Swiss-Pro database. Figures and data visualization were performed using ggplot2 package in R language environment.<br><br>RESULTS: We described the in-depth transcriptome analysis of B. jararaca venom gland, in which 76,765 de novo assembled isoforms, 96,044 transcribed genes and 41,196 unique proteins were identified. The most abundant transcript was the zinc metalloproteinase-disintegrin-like jararhagin. Moreover, we identified 78 distinct functional classes of proteins, including toxins, inhibitors and tumor suppressors. Other venom proteins identified were the hemolytic lethal factors stonustoxin and verrucotoxin.<br><br>CONCLUSION: It is believed that the application of deep sequencing to the analysis of snake venom transcriptomes may represent invaluable insight on their biotechnological potential focusing on candidate molecules.},
}
@article {pmid33149208,
year = {2021},
author = {Du, Q and Ren, B and He, J and Peng, X and Guo, Q and Zheng, L and Li, J and Dai, H and Chen, V and Zhang, L and Zhou, X and Xu, X},
title = {Candida albicans promotes tooth decay by inducing oral microbial dysbiosis.},
journal = {The ISME journal},
volume = {15},
number = {3},
pages = {894-908},
pmid = {33149208},
issn = {1751-7370},
mesh = {Acids ; Animals ; Biofilms ; *Candida albicans ; Carbohydrate Metabolism ; *Dental Caries ; Dysbiosis ; Rats ; },
abstract = {Candida albicans has been detected in root carious lesions. The current study aimed to explore the action of this fungal species on the microbial ecology and the pathogenesis of root caries. Here, by analyzing C. albicans in supragingival dental plaque collected from root carious lesions and sound root surfaces of root-caries subjects as well as caries-free individuals, we observed significantly increased colonization of C. albicans in root carious lesions. Further in vitro and animal studies showed that C. albicans colonization increased the cariogenicity of oral biofilm by altering its microbial ecology, leading to a polymicrobial biofilm with enhanced acidogenicity, and consequently exacerbated tooth demineralization and carious lesion severity. More importantly, we demonstrated that the cariogenicity-promoting activity of C. albicans was dependent on PHR2. Deletion of PHR2 restored microbial equilibrium and led to a less cariogenic biofilm as demonstrated by in vitro artificial caries model or in vivo root-caries rat model. Our data indicate the critical role of C. albicans infection in the occurrence of root caries. PHR2 is the major factor that determines the ecological impact and caries-promoting activity of C. albicans in a mixed microbial consortium.},
}
@article {pmid33145650,
year = {2021},
author = {Albornoz, FE and Orchard, S and Standish, RJ and Dickie, IA and Bending, GD and Hilton, S and Lardner, T and Foster, KJ and Gleeson, DB and Bougoure, J and Barbetti, MJ and You, MP and Ryan, MH},
title = {Evidence for Niche Differentiation in the Environmental Responses of Co-occurring Mucoromycotinian Fine Root Endophytes and Glomeromycotinian Arbuscular Mycorrhizal Fungi.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {864-873},
pmid = {33145650},
issn = {1432-184X},
support = {DP180103157//Australian Research Council (ARC) Discovery/ ; NE/S010270/1//Natural Environment Research Council/ ; FT140100103//ARC Future Fellowship/ ; ON-279//Australian Wool Innovation Ltd/ ; },
mesh = {Carbon ; Endophytes/genetics ; Fungi ; *Mycorrhizae ; Plant Roots ; Soil ; Soil Microbiology ; },
abstract = {Fine root endophytes (FRE) were traditionally considered a morphotype of arbuscular mycorrhizal fungi (AMF), but recent genetic studies demonstrate that FRE belong within the subphylum Mucoromycotina, rather than in the subphylum Glomeromycotina with the AMF. These findings prompt enquiry into the fundamental ecology of FRE and AMF. We sampled FRE and AMF in roots of Trifolium subterraneum from 58 sites across temperate southern Australia. We investigated the environmental drivers of composition, richness, and root colonization of FRE and AMF by using structural equation modelling and canonical correspondence analyses. Root colonization by FRE increased with increasing temperature and rainfall but decreased with increasing phosphorus (P). Root colonization by AMF increased with increasing soil organic carbon but decreased with increasing P. Richness of FRE decreased with increasing temperature and soil pH. Richness of AMF increased with increasing temperature and rainfall but decreased with increasing soil aluminium (Al) and pH. Aluminium, soil pH, and rainfall were, in decreasing order, the strongest drivers of community composition of FRE; they were also important drivers of community composition of AMF, along with temperature, in decreasing order: rainfall, Al, temperature, and soil pH. Thus, FRE and AMF showed the same responses to some (e.g. soil P, soil pH) and different responses to other (e.g. temperature) key environmental factors. Overall, our data are evidence for niche differentiation among these co-occurring mycorrhizal associates.},
}
@article {pmid33144313,
year = {2020},
author = {Manus, MB and Kuthyar, S and Perroni-Marañón, AG and Núñez-de la Mora, A and Amato, KR},
title = {Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States.},
journal = {mSystems},
volume = {5},
number = {6},
pages = {},
pmid = {33144313},
issn = {2379-5077},
abstract = {Daily practices put humans in close contact with the surrounding environment, and differences in these practices have an impact on human physiology, development, and health. There is mounting evidence that the microbiome represents an interface that mediates interactions between the human body and the environment. In particular, the skin microbiome serves as the primary interface with the external environment and aids in host immune function by contributing as the first line of defense against pathogens. Despite these important connections, we have only a basic understanding of how the skin microbiome is first established, or which environmental factors contribute to its development. To this end, this study compared the skin bacterial communities of infants (n = 47) living in four populations in Mexico and the United States that span the socioeconomic gradient, where we predicted that variation in physical and social environments would shape the infant skin microbiome. Results of 16S rRNA bacterial gene sequencing on 119 samples (armpit, hand, and forehead) showed that infant skin bacterial diversity and composition are shaped by population-level factors, including those related to socioeconomic status and household composition, and vary by skin site and infant age. Differences in infant-environment interactions, including with other people, appear to vary across the populations, likely influencing infant microbial exposures and, in turn, the composition of infant skin bacterial communities. These findings suggest that variation in microbial exposures stemming from the local environment in infancy can impact the establishment of the skin microbiome across body sites, with implications for developmental and health outcomes.IMPORTANCE This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).},
}
@article {pmid33142974,
year = {2020},
author = {Sánchez-Clemente, R and Guijo, MI and Nogales, J and Blasco, R},
title = {Carbon Source Influence on Extracellular pH Changes along Bacterial Cell-Growth.},
journal = {Genes},
volume = {11},
number = {11},
pages = {},
pmid = {33142974},
issn = {2073-4425},
mesh = {Bacteria/genetics/*growth &amp; development/*metabolism ; Bacterial Proteins/genetics ; Carbon/*metabolism ; Culture Media/chemistry/metabolism ; Escherichia coli/genetics/growth &amp; development/metabolism ; Gene Expression Regulation, Bacterial/genetics ; Hydrogen-Ion Concentration ; Pseudomonas pseudoalcaligenes/genetics/growth &amp; development/metabolism ; Pseudomonas putida/genetics/growth &amp; development/metabolism ; },
abstract = {The effect of initial pH on bacterial cell-growth and its change over time was studied under aerobic heterotrophic conditions by using three bacterial strains: Escherichia coli ATCC 25922, Pseudomonas putida KT2440, and Pseudomonas pseudoalcaligenes CECT 5344. In Luria-Bertani (LB) media, pH evolved by converging to a certain value that is specific for each bacterium. By contrast, in the buffered Minimal Medium (MM), pH was generally more stable along the growth curve. In MM with glucose as carbon source, a slight acidification of the medium was observed for all strains. In the case of E. coli, a sudden drop in pH was observed during exponential cell growth that was later recovered at initial pH 7 or 8, but was irreversible below pH 6, thus arresting further cell-growth. When using other carbon sources in MM at a fixed initial pH, pH changes depended mainly on the carbon source itself. While glucose, glycerol, or octanoate slightly decreased extracellular pH, more oxidized carbon sources, such as citrate, 2-furoate, 2-oxoglutarate, and fumarate, ended up with the alkalinization of the medium. These observations are in accordance with pH change predictions using genome-scale metabolic models for the three strains, thus revealing the metabolic reasons behind pH change. Therefore, we conclude that the composition of the medium, specifically the carbon source, determines pH change during bacterial growth to a great extent and unravel the main molecular mechanism behind this phenotype. These findings pave the way for predicting pH changes in a given bacterial culture and may anticipate the interspecies interactions and fitness of bacteria in their environment.},
}
@article {pmid33142874,
year = {2020},
author = {Van Herreweghen, F and Amberg, C and Marques, R and Callewaert, C},
title = {Biological and Chemical Processes that Lead to Textile Malodour Development.},
journal = {Microorganisms},
volume = {8},
number = {11},
pages = {},
pmid = {33142874},
issn = {2076-2607},
abstract = {The development of malodour on clothing is a well-known problem with social, economic and ecological consequences. Many people still think malodour is the result of a lack of hygiene, which causes social stigma and embarrassment. Clothing is washed more frequently due to odour formation or even discarded when permastink develops. The malodour formation process is impacted by many variables and processes throughout the textile lifecycle. The contact with the skin with consequent transfer of microorganisms, volatiles and odour precursors leads to the formation of a distinctive textile microbiome and volatilome. The washing and drying processes further shape the textile microbiome and impact malodour formation. These processes are impacted by interindividual differences and fabric type as well. This review describes the current knowledge on the volatilome and microbiome of the skin, textile and washing machine, the multiple factors that determine malodour formation on textiles and points out what information is still missing.},
}
@article {pmid33141643,
year = {2020},
author = {Zhu, M and Ji, J and Shi, W and Li, Y},
title = {Occurrence of Powdery Mildew Caused by Blumeria graminis f. sp. poae on Poa pratensis in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-09-20-2051-PDN},
pmid = {33141643},
issn = {0191-2917},
abstract = {Poa pratensis, known as bluegrass, is a perennial grass and one of the best varieties with highly valued pasture and turf grass uses. It is widely grown on golf courses and used for lawns in squares and parks (Luo et al. 2020). During April and May 2020, powdery mildew-like signs and symptoms were observed on leaves of P. pratensis in Muye Park, Xinxiang city (35.3°N; 113.9°E), Henan Province, China. White or grayish powdery masses in spots- or coalesced lesions were abundant on the adaxial surfaces of leaves and covered up to 90 % of the leaf area. Some of the mildew-infested leaves appeared chlorotic or began senescence. Mildew-infested leaves were collected to microscopically observe the morphological characteristics of this pathogen. Conidiophores were composed of foot cells, followed by one or two cells, and conidia. The ellipsoid- shaped conidia (n = 50) were 25 - 36 × 10 - 15 μm (length × width), on average 30 × 13 μm, with a length/width ratio of 2.3. Foot-cells (n = 15) were 30 - 44 μm long and 7 - 15 μm wide. On leaf surfaces, germinated conidia produced a short primary germ tube and then a long secondary germ tube that finally differentiated into a hooked appressorium. Chasmothecia were not found. Based on these morphological characteristics, the pathogen was initially identified as B. graminis f. sp. poae, the known forma specialis (f. sp.) of B. graminis on P. pratensis (Braun and Cook 2012; Troch et al. 2014). Mycelia of the pathogen were scraped from infected leaves and total genomic DNA was isolated using the method described previously (Zhu et al. 2019). The rDNA internal transcribed spacer (ITS) region was amplified applying primer pairs ITS1/ITS4 (White et al. 1990). The amplicon was cloned and sequenced by Invitrogen (Shanghai, China). The obtained sequence for the pathogen was deposited into GenBank under Accession No. MT892956 and was 100 % identical (549/549 bp) to B. graminis on P. pratensis (AB273530) (Inuma et al. 2007). In addition, the phylogenetic analysis clearly showed that the identified fungus and B. graminis f. sp. poae were clustered in the same branch. To perform pathogenicity analysis, leaf surfaces of eight healthy plants were inoculated by dusting fungal conidia from diseased leaves. Eight non-inoculated plants served as a control. The non-inoculated and inoculated plants were separately maintained in two growth chambers (humidity, 60 %; light/dark, 16 h/8 h; temperature, 18 ℃). Twelve to fourteen days after inoculation, B. graminis signs were visible on inoculated leaves, while control plants remained healthy. The pathogenicity assays were repeated twice and showed same results. Therefore, based on the morphological characteristics and molecular analysis, the pathogen was identified and confirmed as B. graminis f. sp. poae. This pathogen has been reported on P. pratensis in Switzerland and Japan (Inuma et al. 2007). This is, to our best knowledge, the first disease note reporting B. graminis on P. pratensis in China. Because the hybridization of B. graminis formae speciales (ff. spp.). allow the pathogens to adapt to new hosts, P. pratensis may serve as a primary inoculum reservoir of B. graminis to threaten other species, including cereal crops (Klingeman et al. 2018; Menardo et al. 2016). In addition, powdery mildew may negatively affect the yield and quality of grasses. Our report expands the knowledge of B. graminis f. sp. poae and provides the fundamental information for future powdery mildew control.},
}
@article {pmid33140722,
year = {2020},
author = {Sharma, K and Palatinszky, M and Nikolov, G and Berry, D and Shank, EA},
title = {Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
pmid = {33140722},
issn = {2050-084X},
support = {DE-SC0013887//Biological and Environmental Research/International ; DE-SC0019012//Biological and Environmental Research/International ; FunKeyGut 741623/ERC_/European Research Council/International ; },
mesh = {Bacillus subtilis ; Bacteria ; Carbon Isotopes ; Deuterium Oxide ; Dimethylpolysiloxanes ; Fluorescent Dyes/chemistry ; Fluorocarbon Polymers/chemistry ; Fungi ; Isotope Labeling/*methods ; Mucor ; Particle Size ; Sodium Fluoride/chemistry ; Soil/*chemistry ; *Soil Microbiology ; Spectrum Analysis, Raman ; },
abstract = {Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil's opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.},
}
@article {pmid33140283,
year = {2021},
author = {Zhao, Y and Chen, J and Bai, B and Wang, Y and Zheng, J and Yu, Z and Deng, Q and Li, P},
title = {Pathogen determination from clinical abscess fluids using metagenomic next-generation sequencing.},
journal = {Folia microbiologica},
volume = {66},
number = {2},
pages = {197-202},
pmid = {33140283},
issn = {1874-9356},
support = {2020A1515010979//Natural Science Foundation of Guangdong Province/ ; JCYJ20170412143551332//Science, Technology and Innovation Commission of Shenzhen Municipality of key funds/ ; JCYJ20180302144721183//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; JCYJ20180302144340004//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; JCYJ20180302144345028//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; JCYJ20180302144431923//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; 2019001//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; 2019004//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; 2019005//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; 2019027//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; A2018163//provincial medical funds of Guangdong/ ; SZXK06162//Shenzhen Key Medical Discipline Construction Fund/ ; },
mesh = {*Abscess/diagnosis ; Firmicutes ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Sensitivity and Specificity ; },
abstract = {Abscesses are often clinically manifested as local necrotic tissues in various organs or systems of the human body, which is commonly caused by microbial infection. Rapid and accurate identification of pathogens from clinical abscetic samples would greatly guide a clinician to make the precise choices of the antimicrobial treatment. Here, this study aimed to investigate the application of metagenomic next-generation sequencing (mNGS) in the microbial detection of clinical samples of abscess fluids from various organs or systems. Nine patients with abscess from various organs or systems were enrolled in this study. The pathogenic bacteria in abscess fluid were detected and compared by the conventional bacterial culture and mNGS respectively. The dominant pathogens of abscess fluids in 8 cases can be found directly from mNGS, dominating over 80% of the total reads abundance of the microbiome. Although the pathogens from 6 cases detected by mNGS were consistent with that from the conventional bacteria culture method, the fastidious obligate anaerobic bacteria in 2 cases additionally detected by mNGS were not found by the conventional culture method. Moreover, complex polymicrobial infection containing Parvimonas micra in one case negatively with conventional bacterial culture were demonstrated by the mNGS method. And the mNGS method can directly reflect the diversity of microbial ecology in the abscess fluids from the different parts of the human body. Conclusively, mNGS can be used as a supplemental method for the pathogen detection of clinically abscess fluids.},
}
@article {pmid33139872,
year = {2021},
author = {Lecoeuvre, A and Ménez, B and Cannat, M and Chavagnac, V and Gérard, E},
title = {Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge).},
journal = {The ISME journal},
volume = {15},
number = {3},
pages = {818-832},
pmid = {33139872},
issn = {1751-7370},
mesh = {Archaea/genetics ; Carbon ; *Ecosystem ; *Hydrothermal Vents ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Lost City (mid-Atlantic ridge) is a unique oceanic hydrothermal field where carbonate-brucite chimneys are colonized by a single phylotype of archaeal Methanosarcinales, as well as sulfur- and methane-metabolizing bacteria. So far, only one submarine analog of Lost City has been characterized, the Prony Bay hydrothermal field (New Caledonia), which nonetheless shows more microbiological similarities with ecosystems associated with continental ophiolites. This study presents the microbial ecology of the 'Lost City'-type Old City hydrothermal field, recently discovered along the southwest Indian ridge. Five carbonate-brucite chimneys were sampled and subjected to mineralogical and geochemical analyses, microimaging, as well as 16S rRNA-encoding gene and metagenomic sequencing. Dominant taxa and metabolisms vary between chimneys, in conjunction with the predicted redox state, while potential formate- and CO-metabolizing microorganisms as well as sulfur-metabolizing bacteria are always abundant. We hypothesize that the variable environmental conditions resulting from the slow and diffuse hydrothermal fluid discharge that currently characterizes Old City could lead to different microbial populations between chimneys that utilize CO and formate differently as carbon or electron sources. Old City discovery and this first description of its microbial ecology opens up attractive perspectives for understanding environmental factors shaping communities and metabolisms in oceanic serpentinite-hosted ecosystems.},
}
@article {pmid33139480,
year = {2021},
author = {Sibinelli-Sousa, S and Hespanhol, JT and Bayer-Santos, E},
title = {Targeting the Achilles' Heel of Bacteria: Different Mechanisms To Break Down the Peptidoglycan Cell Wall during Bacterial Warfare.},
journal = {Journal of bacteriology},
volume = {203},
number = {7},
pages = {},
pmid = {33139480},
issn = {1098-5530},
mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biological Warfare ; Cell Wall/genetics/*metabolism ; Peptidoglycan/*metabolism ; },
abstract = {Bacteria commonly live in dense polymicrobial communities and compete for scarce resources. Consequently, they employ a diverse array of mechanisms to harm, inhibit, and kill their competitors. The cell wall is essential for bacterial survival by providing mechanical strength to resist osmotic stress. Because peptidoglycan is the major component of the cell wall and its synthesis is a complex multistep pathway that requires the coordinate action of several enzymes, it provides a target for rival bacteria, which have developed a large arsenal of antibacterial molecules to attack the peptidoglycan of competitors. These molecules include antibiotics, bacteriocins, and contact-dependent effectors that are either secreted into the medium or directly translocated into a target cell. In this minireview, we summarize the diversity of these molecules and highlight distinct mechanisms to disrupt the peptidoglycan, giving special attention to molecules that are known or have the potential to be used during interbacterial competitions.},
}
@article {pmid33138291,
year = {2020},
author = {Lyu, Y and Debevere, S and Bourgeois, H and Ran, M and Broeckx, BJG and Vanhaecke, L and Wiele, TV and Hesta, M},
title = {Dose-Dependent Effects of Dietary Xylooligosaccharides Supplementation on Microbiota, Fermentation and Metabolism in Healthy Adult Cats.},
journal = {Molecules (Basel, Switzerland)},
volume = {25},
number = {21},
pages = {},
pmid = {33138291},
issn = {1420-3049},
mesh = {*Animal Feed ; Animals ; *Bacteria/classification/growth &amp; development ; Cats ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Glucuronates/*pharmacology ; Oligosaccharides/*pharmacology ; },
abstract = {In order to investigate the effect and appropriate dose of prebiotics, this study evaluated the effect of two levels of xylooligosaccharides (XOS) in cats. Twenty-four healthy adult cats were divided into three groups: no-XOS control diet with 1% cellulose; low XOS supplementation (LXOS) with 0.04% XOS and 0.96% cellulose; and high XOS supplementation (HXOS) with 0.40% XOS and 0.60% cellulose. Both XOS groups increased blood 3-hydroxybutyryl carnitine levels and decreased hexadecanedioyl carnitine levels. Both XOS treatments displayed an increased bacterial abundance of Blautia, Clostridium XI, and Collinsella and a decreased abundance of Megasphaera and Bifidobacterium. LXOS groups increased fecal pH and bacterial abundance of Streptococcus and Lactobacillus, decreased blood glutaryl carnitine concentration, and Catenibacterium abundance. HXOS group showed a more distinct microbiome profile and higher species richness, and an increased bacterial abundance of Subdoligranulum, Ruminococcaceae genus (unassigned genus), Erysipelotrichaceae genus, and Lachnospiraceae. Correlations between bacterial abundances and blood and fecal parameters were also observed. In conclusion, XOS could benefit feline gut health by altering microbiota; its effects dependant on the dose. The higher-dose XOS increased bacterial populations that possibly promoted intestinal fermentation, while the lower dose altered populations of carbohydrate-metabolic microbiota and possibly modulated host metabolism. Low-dose prebiotics may become a trend in future studies.},
}
@article {pmid33134552,
year = {2020},
author = {Latorre-Pérez, A and Pascual, J and Porcar, M and Vilanova, C},
title = {A lab in the field: applications of real-time, in situ metagenomic sequencing.},
journal = {Biology methods &amp; protocols},
volume = {5},
number = {1},
pages = {bpaa016},
pmid = {33134552},
issn = {2396-8923},
abstract = {High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.},
}
@article {pmid33133427,
year = {2020},
author = {Harvey, HJ and Wildman, RD and Mooney, SJ and Avery, SV},
title = {Challenges and approaches in assessing the interplay between microorganisms and their physical micro-environments.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {2860-2866},
pmid = {33133427},
issn = {2001-0370},
abstract = {Spatial structure over scales ranging from nanometres to centimetres (and beyond) varies markedly in diverse habitats and the industry-relevant settings that support microbial activity. Developing an understanding of the interplay between a structured environment and the associated microbial processes and ecology is fundamental, but challenging. Several novel approaches have recently been developed and implemented to help address key questions for the field: from the use of imaging tools such as X-ray Computed Tomography to explore microbial growth in soils, to the fabrication of scratched materials to examine microbial-surface interactions, to the design of microfluidic devices to track microbial biofilm formation and the metabolic processes therein. This review discusses new approaches and challenges for incorporating structured elements into the study of microbial processes across different scales. We highlight how such methods can be pivotal for furthering our understanding of microbial interactions with their environments.},
}
@article {pmid33133035,
year = {2020},
author = {Colby, GA and Ruuskanen, MO and St Pierre, KA and St Louis, VL and Poulain, AJ and Aris-Brosou, S},
title = {Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {561194},
pmid = {33133035},
issn = {1664-302X},
abstract = {Temperatures in the Arctic are expected to increase dramatically over the next century, and transform high latitude watersheds. However, little is known about how microbial communities and their underlying metabolic processes will be affected by these environmental changes in freshwater sedimentary systems. To address this knowledge gap, we analyzed sediments from Lake Hazen, NU Canada. Here, we exploit the spatial heterogeneity created by varying runoff regimes across the watershed of this uniquely large high-latitude lake to test how a transition from low to high runoff, used as one proxy for climate change, affects the community structure and functional potential of dominant microbes. Based on metagenomic analyses of lake sediments along these spatial gradients, we show that increasing runoff leads to a decrease in taxonomic and functional diversity of sediment microbes. Our findings are likely to apply to other, smaller, glacierized watersheds typical of polar or high latitude ecosystems; we can predict that such changes will have far reaching consequences on these ecosystems by affecting nutrient biogeochemical cycling, the direction and magnitude of which are yet to be determined.},
}
@article {pmid33131854,
year = {2021},
author = {Durán, J and Rodríguez, A and Heiðmarsson, S and Lehmann, JRK and Del Moral, &#xc1; and Garrido-Benavent, I and De Los Ríos, A},
title = {Cryptogamic cover determines soil attributes and functioning in polar terrestrial ecosystems.},
journal = {The Science of the total environment},
volume = {762},
number = {},
pages = {143169},
doi = {10.1016/j.scitotenv.2020.143169},
pmid = {33131854},
issn = {1879-1026},
mesh = {Biodiversity ; Climate Change ; *Ecosystem ; *Soil ; Soil Microbiology ; },
abstract = {We still lack studies that provide evidence for direct links between the development of soil surface cryptogamic communities and soil attributes and functioning. This is particularly true in areas free of potentially confounding factors such as different soil types, land uses, or anthropogenic disturbances. Despite the ecological importance of polar ecosystems and their sensitivity to climate change, we are far from understanding how their soils function and will respond to climate change-driven alterations in above- and belowground features. We used two complementary approaches (i.e. cover gradients in the forefront of retreating glaciers as well as long-time deglaciated areas with well-developed cryptogamic cover types) to evaluate the role of cryptogams driving multiple soil biotic and abiotic attributes and functioning rates in polar terrestrial ecosystems. Increases in cryptogamic cover were consistently related to increases in organic matter accumulation, soil fertility, and bacterial diversity, but also in enhanced soil functioning rates in both sampling areas. However, we also show that the ability to influence soil attributes varies among different polar cryptogamic covers, indicating that their differential ability to thrive under climate-change scenarios will largely determine the fate of polar soils in coming decades.},
}
@article {pmid33130421,
year = {2020},
author = {Boulard, L and Parrhysius, P and Jacobs, B and Dierkes, G and Wick, A and Buchmeier, G and Koschorreck, J and Ternes, TA},
title = {Development of an analytical method to quantify pharmaceuticals in fish tissues by liquid chromatography-tandem mass spectrometry detection and application to environmental samples.},
journal = {Journal of chromatography. A},
volume = {1633},
number = {},
pages = {461612},
doi = {10.1016/j.chroma.2020.461612},
pmid = {33130421},
issn = {1873-3778},
mesh = {Animals ; *Chromatography, Liquid ; Drug Residues/*analysis ; Environmental Monitoring/*methods ; *Fishes/metabolism ; Food Analysis/*methods ; Limit of Detection ; Rivers/*chemistry ; Solid Phase Extraction ; *Tandem Mass Spectrometry ; Wastewater/analysis ; Water Pollutants, Chemical/analysis ; },
abstract = {A sensitive multiresidue method was developed to quantify 35 pharmaceuticals and 28 metabolites/transformation products (TPs) in fish liver, fish fillet and fish plasma via LC-MS/MS. The method was designed to cover a broad range of substance polarities. This objective was realized by using non-discriminating sample clean-ups including separation technique based on size exclusion, namely restricted access media (RAM) chromatography. This universal clean-up allows for an easy integration of further organic micropollutants into the analytical method. Limits of quantification (LOQ) ranged from 0.05 to 5.5 ng/mL in fish plasma, from 0.1 to 19 ng/g d.w. (dry weight) in fish fillet and from 0.46 to 48 ng/g d.w. in fish liver. The method was applied for the analysis of fillets and livers of breams from the rivers Rhine and Saar, the Teltow Canal as well as carps kept in fish monitoring ponds fed by effluent from municipal wastewater treatment plants. This allowed for the first detection of 17 analytes including 10 metabolites/TPs such as gabapentin lactam and norlidocaine in fish tissues. These results highlight the importance of including metabolites and transformation products of pharmaceuticals in fish monitoring campaigns and further investigating their potential effects.},
}
@article {pmid33129268,
year = {2020},
author = {Djemiel, C and Dequiedt, S and Karimi, B and Cottin, A and Girier, T and El Djoudi, Y and Wincker, P and Lelièvre, M and Mondy, S and Chemidlin Prévost-Bouré, N and Maron, PA and Ranjard, L and Terrat, S},
title = {BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons.},
journal = {BMC bioinformatics},
volume = {21},
number = {1},
pages = {492},
pmid = {33129268},
issn = {1471-2105},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biodiversity ; Cluster Analysis ; Computational Biology/*methods ; Computer Simulation ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Fungi/*genetics ; *Genes, rRNA ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; *Software ; Soil Microbiology ; },
abstract = {BACKGROUND: The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.<br><br>RESULTS: BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups.<br><br>CONCLUSIONS: The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.},
}
@article {pmid33125668,
year = {2020},
author = {Kim, S and Park, MS and Song, J and Kang, I and Cho, JC},
title = {High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {58},
number = {11},
pages = {893-905},
doi = {10.1007/s12275-020-0452-2},
pmid = {33125668},
issn = {1976-3794},
mesh = {*Bacteria/classification/isolation &amp; purification ; Bacteriological Techniques/*methods ; Culture Media/*chemistry ; Ecosystem ; Lakes/*microbiology ; Metagenomics ; *Water Microbiology ; },
abstract = {Multi-omics approaches, including metagenomics and single-cell amplified genomics, have revolutionized our understanding of the hidden diversity and function of microbes in nature. Even in the omics age, cultivation is an essential discipline in microbial ecology since microbial cultures are necessary to assess the validity of an in silico prediction about the microbial metabolism and to isolate viruses infecting bacteria and archaea. However, the ecophysiological characteristics of predominant freshwater bacterial lineages remain largely unknown due to the scarcity of cultured representatives. In an ongoing effort to cultivate the uncultured majority of freshwater bacteria, the most abundant freshwater Actinobacteria acI clade has recently been cultivated from Lake Soyang through catalase-supplemented high-throughput cultivation based on dilution-to-extinction. This method involves physical isolation of target microbes from mixed populations, culture media simulating natural habitats, and removal of toxic compounds. In this protocol, we describe detailed procedures for isolating freshwater oligotrophic microbes, as well as the essence of the dilution-to-extinction culturing. As a case study employing the catalase-supplemented dilution-to-extinction protocol, we also report a cultivation trial using a water sample collected from Lake Soyang. Of the 480 cultivation wells inoculated with a single lake-water sample, 75 new acI strains belonging to 8 acI tribes (acI-A1, A2, A4, A5, A6, A7, B1, B4, C1, and C2) were cultivated, and each representative strain per subclade could be revived from glycerol stocks. These cultivation results demonstrate that the protocol described in this study is efficient in isolating freshwater bacterioplankton harboring streamlined genomes.},
}
@article {pmid33123759,
year = {2021},
author = {Janiszewska, M and Sobkowiak, S and Stefańczyk, E and Śliwka, J},
title = {Population Structure of Phytophthora infestans from a Single Location in Poland Over a Long Period of Time in Context of Weather Conditions.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {746-757},
pmid = {33123759},
issn = {1432-184X},
support = {PW Task 3.1//Polish Ministry of Agriculture and Rural Development/ ; 1-3-00-1-02//Polish Ministry of Science and Higher Education/ ; MN 1-3-00-3-01//Polish Ministry of Science and Higher Education/ ; },
mesh = {*Phytophthora infestans/genetics ; Plant Diseases ; Poland ; *Solanum tuberosum ; Weather ; },
abstract = {Phytophthora infestans (Mont.) de Bary is a destructive potato pathogen. Changing weather conditions are among the factors that influence the pathogen population structure. In this study, 237 P. infestans isolates were collected from a single unprotected experimental field in an area with high late-blight pressure located in Boguchwała in the southeastern part of Poland during 15 growing seasons (2000-2014). The isolates were assessed for mating type, mitochondrial haplotype, resistance to metalaxyl, virulence, and polymorphism of 14 single-sequence repeat markers (SSRs). The results revealed 89 unique genotypes among the 237 P. infestans isolates. Eighty-seven isolates belonged to genotype 34_A1, which was detected in all the years of research except 2012. Isolates of P. infestans from individual years were very similar to each other, as shown by Nei's genetic identity based on 14 SSR markers. The obtained results on isolate characteristics were analyzed in terms of meteorological data (air temperature and precipitation) and indicated that frost, long winters, and hot, dry summers did not directly affect the P. infestans population structure. We described the variability in metalaxyl resistance and virulence among isolates of the P. infestans genotype 34_A1.},
}
@article {pmid33123758,
year = {2021},
author = {Tzuri, N and Caspi-Fluger, A and Betelman, K and Rohkin Shalom, S and Chiel, E},
title = {Horizontal Transmission of Microbial Symbionts Within a Guild of Fly Parasitoids.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {818-827},
pmid = {33123758},
issn = {1432-184X},
support = {435/2018//Israel science Foundation/ ; },
mesh = {Animals ; Host-Parasite Interactions ; Larva ; Pupa ; *Wasps ; *Wolbachia/genetics ; },
abstract = {Many insects harbor facultative microbial symbionts which affect the ecology of their hosts in diverse ways. Most symbionts are transmitted vertically with high fidelity, whereas horizontal transmission occurs rarely. Parasitoid larvae feed on a single host and are in close physical contact with it, providing an ecological opportunity for symbionts' horizontal transmission, but there is little empirical evidence documenting this. Here we studied horizontal transmission of three bacterial symbionts-Rickettsia, Sodalis, and Wolbachia-between three fly pupal ectoparasitoid species: Spalangia cameroni, S. endius, and Muscidifurax raptor. Muscidifurax raptor readily parasitized and successfully developed on the Spalangia spp., while the inverse did not happen. The two Spalangia spp. attacked each other and conspecifics in very low rates. Symbiont horizontal transmissions followed by stable vertical transmission in the recipient species were achieved, in low percentages, only between conspecifics: Wolbachia from infected to uninfected M. raptor, Rickettsia in S. endius, and Sodalis in S. cameroni. Low frequency of horizontal transmissions occurred in the interspecific combinations, but none of them persisted in the recipient species beyond F4, at most. Our study is one of few to demonstrate symbionts' horizontal transmission between hosts within the same trophic level and guild and highlights the rarity of such events.},
}
@article {pmid33123113,
year = {2020},
author = {Mitchell, K and Ronas, J and Dao, C and Freise, AC and Mangul, S and Shapiro, C and Moberg Parker, J},
title = {PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {584699},
pmid = {33123113},
issn = {1664-302X},
abstract = {Improvements in high-throughput sequencing makes targeted amplicon analysis an ideal method for the study of human and environmental microbiomes by undergraduates. Multiple bioinformatics programs are available to process and interpret raw microbial diversity datasets, and the choice of programs to use in curricula is largely determined by student learning goals. Many of the most commonly used microbiome bioinformatics platforms offer end-to-end data processing and data analysis using a command line interface (CLI), but the downside for novice microbiome researchers is the steep learning curve often required. Alternatively, some sequencing providers include processing of raw data and taxonomy assignments as part of their pipelines. This, when coupled with available web-based or graphical user interface (GUI) analysis and visualization tools, eliminates the need for students or instructors to have extensive CLI experience. However, lack of universal data formats can make integration of these tools challenging. For example, tools for upstream and downstream analyses frequently use multiple different data formats which then require writing custom scripts or hours of manual work to make the files compatible. Here, we describe a microbial ecology bioinformatics curriculum that focuses on data analysis, visualization, and statistical reasoning by taking advantage of existing web-based and GUI tools. We created the Program for Unifying Microbiome Analysis Applications (PUMAA), which solves the problem of inconsistent files by formatting the output files from several raw data processing programs to seamlessly transition to a suite of GUI programs for analysis and visualization of microbiome taxonomic and inferred functional profiles. Additionally, we created a series of tutorials to accompany each of the microbiome analysis curricular modules. From pre- and post-course surveys, students in this curriculum self-reported conceptual and confidence gains in bioinformatics and data analysis skills. Students also demonstrated gains in biologically relevant statistical reasoning based on rubric-guided evaluations of open-ended survey questions and the Statistical Reasoning in Biology Concept Inventory. The PUMAA program and associated analysis tutorials enable students and researchers with no computational experience to effectively analyze real microbiome datasets to investigate real-world research questions.},
}
@article {pmid33123105,
year = {2020},
author = {Navarro, MOP and Dilarri, G and Simionato, AS and Grzegorczyk, K and Dealis, ML and Cano, BG and Barazetti, AR and Afonso, L and Chryssafidis, AL and Ferreira, H and Andrade, G},
title = {Corrigendum: Determining the Targets of Fluopsin C Action on Gram-Negative and Gram-Positive Bacteria.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {574002},
doi = {10.3389/fmicb.2020.574002},
pmid = {33123105},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2020.01076.].},
}
@article {pmid33118857,
year = {2021},
author = {Patel, D and Shittu, TA and Baroncelli, R and Muthumeenakshi, S and Osborne, TH and Janganan, TK and Sreenivasaprasad, S},
title = {Genome Sequence of the Biocontrol Agent Coniothyrium minitans Conio (IMI 134523).},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {34},
number = {2},
pages = {222-225},
doi = {10.1094/MPMI-05-20-0124-A},
pmid = {33118857},
issn = {0894-0282},
mesh = {*Ascomycota/genetics ; Crops, Agricultural/microbiology ; *Genome, Fungal/genetics ; Microbial Interactions/genetics ; },
abstract = {Coniothyrium minitans (synonym, Paraphaeosphaeria minitans) is a highly specific mycoparasite of the wide host range crop pathogen Sclerotinia sclerotiorum. The capability of C. minitans to destroy the sclerotia of S. sclerotiorum has been well recognized and it is available as a widely used biocontrol product Contans WG. We present the draft genome sequence of C. minitans Conio (IMI 134523), which has previously been used in extensive studies that formed part of a registration package of the commercial product. This work provides a distinctive resource for further research into the molecular basis of mycoparasitism to harness the biocontrol potential of C. minitans.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
}
@article {pmid33117398,
year = {2020},
author = {Pirr, S and Viemann, D},
title = {Host Factors of Favorable Intestinal Microbial Colonization.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {584288},
pmid = {33117398},
issn = {1664-3224},
mesh = {Animals ; Gastrointestinal Microbiome/*immunology ; Homeostasis/immunology ; Humans ; Immune System/immunology ; Immunity, Mucosal/*immunology ; Symbiosis/immunology ; },
abstract = {Gut microbial colonization starts with birth and initiates a complex process between the host and the microbiota. Successful co-development of both establishes a symbiotic mutual relationship and functional homeostasis, while alterations thereof predispose the individual life-long to inflammatory and metabolic diseases. Multiple data have been provided how colonizing microbes induce a reprogramming and maturation of immunity by providing crucial instructing information to the newborn immune system. Less is known about what host factors have influence on the interplay between intestinal immunity and the composition of the gut microbial ecology. Here we review existing evidence regarding host factors that contribute to a favorable development of the gut microbiome and thereby successful maturation of gut mucosal immunity.},
}
@article {pmid33116344,
year = {2020},
author = {Crous, PW and Wingfield, MJ and Chooi, YH and Gilchrist, CLM and Lacey, E and Pitt, JI and Roets, F and Swart, WJ and Cano-Lira, JF and Valenzuela-Lopez, N and Hubka, V and Shivas, RG and Stchigel, AM and Holdom, DG and Jurjević, &#x17d; and Kachalkin, AV and Lebel, T and Lock, C and Martín, MP and Tan, YP and Tomashevskaya, MA and Vitelli, JS and Baseia, IG and Bhatt, VK and Brandrud, TE and De Souza, JT and Dima, B and Lacey, HJ and Lombard, L and Johnston, PR and Morte, A and Papp, V and Rodríguez, A and Rodríguez-Andrade, E and Semwal, KC and Tegart, L and Abad, ZG and Akulov, A and Alvarado, P and Alves, A and Andrade, JP and Arenas, F and Asenjo, C and Ballarà, J and Barrett, MD and Berná, LM and Berraf-Tebbal, A and Bianchinotti, MV and Bransgrove, K and Burgess, TI and Carmo, FS and Chávez, R and Čmoková, A and Dearnaley, JDW and de A Santiago, ALCM and Freitas-Neto, JF and Denman, S and Douglas, B and Dovana, F and Eichmeier, A and Esteve-Raventós, F and Farid, A and Fedosova, AG and Ferisin, G and Ferreira, RJ and Ferrer, A and Figueiredo, CN and Figueiredo, YF and Reinoso-Fuentealba, CG and Garrido-Benavent, I and Cañete-Gibas, CF and Gil-Durán, C and Glushakova, AM and Gonçalves, MFM and González, M and Gorczak, M and Gorton, C and Guard, FE and Guarnizo, AL and Guarro, J and Gutiérrez, M and Hamal, P and Hien, LT and Hocking, AD and Houbraken, J and Hunter, GC and Inácio, CA and Jourdan, M and Kapitonov, VI and Kelly, L and Khanh, TN and Kisło, K and Kiss, L and Kiyashko, A and Kolařík, M and Kruse, J and Kubátová, A and Kučera, V and Kučerová, I and Kušan, I and Lee, HB and Levicán, G and Lewis, A and Liem, NV and Liimatainen, K and Lim, HJ and Lyons, MN and Maciá-Vicente, JG and Magaña-Dueñas, V and Mahiques, R and Malysheva, EF and Marbach, PAS and Marinho, P and Matočec, N and McTaggart, AR and Mešić, A and Morin, L and Muñoz-Mohedano, JM and Navarro-Ródenas, A and Nicolli, CP and Oliveira, RL and Otsing, E and Ovrebo, CL and Pankratov, TA and Paños, A and Paz-Conde, A and Pérez-Sierra, A and Phosri, C and Pintos, &#xc1; and Pošta, A and Prencipe, S and Rubio, E and Saitta, A and Sales, LS and Sanhueza, L and Shuttleworth, LA and Smith, J and Smith, ME and Spadaro, D and Spetik, M and Sochor, M and Sochorová, Z and Sousa, JO and Suwannasai, N and Tedersoo, L and Thanh, HM and Thao, LD and Tkalčec, Z and Vaghefi, N and Venzhik, AS and Verbeken, A and Vizzini, A and Voyron, S and Wainhouse, M and Whalley, AJS and Wrzosek, M and Zapata, M and Zeil-Rolfe, I and Groenewald, JZ},
title = {Fungal Planet description sheets: 1042-1111.},
journal = {Persoonia},
volume = {44},
number = {},
pages = {301-459},
pmid = {33116344},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.) from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis. USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.) on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.) from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes.},
}
@article {pmid33115951,
year = {2020},
author = {Khan, S and Waliullah, S and Godfrey, V and Khan, MAW and Ramachandran, RA and Cantarel, BL and Behrendt, C and Peng, L and Hooper, LV and Zaki, H},
title = {Dietary simple sugars alter microbial ecology in the gut and promote colitis in mice.},
journal = {Science translational medicine},
volume = {12},
number = {567},
pages = {},
doi = {10.1126/scitranslmed.aay6218},
pmid = {33115951},
issn = {1946-6242},
support = {P30 CA142543/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Colitis/chemically induced ; Dextran Sulfate ; Diet ; *Dietary Sugars/adverse effects ; Disease Models, Animal ; Mice ; Mice, Inbred C57BL ; Monosaccharides ; },
abstract = {The higher prevalence of inflammatory bowel disease (IBD) in Western countries points to Western diet as a possible IBD risk factor. High sugar, which is linked to many noncommunicable diseases, is a hallmark of the Western diet, but its role in IBD remains unknown. Here, we studied the effects of simple sugars such as glucose and fructose on colitis pathogenesis in wild-type and Il10[-/-] mice. Wild-type mice fed 10% glucose in drinking water or high-glucose diet developed severe colitis induced by dextran sulfate sodium. High-glucose-fed Il10[-/-] mice also developed a worsened colitis compared to glucose-untreated Il10[-/-] mice. Short-term intake of high glucose or fructose did not trigger inflammatory responses in healthy gut but markedly altered gut microbiota composition. In particular, the abundance of the mucus-degrading bacteria Akkermansia muciniphila and Bacteroides fragilis was increased. Consistently, bacteria-derived mucolytic enzymes were enriched leading to erosion of the colonic mucus layer of sugar-fed wild-type and Il10[-/-] mice. Sugar-induced exacerbation of colitis was not observed when mice were treated with antibiotics or maintained in a germ-free environment, suggesting that altered microbiota played a critical role in sugar-induced colitis pathogenesis. Furthermore, germ-free mice colonized with microbiota from sugar-treated mice showed increased colitis susceptibility. Together, these data suggest that intake of simple sugars predisposes to colitis and enhances its pathogenesis via modulation of gut microbiota in mice.},
}
@article {pmid33115836,
year = {2020},
author = {García-Timermans, C and Props, R and Zacchetti, B and Sakarika, M and Delvigne, F and Boon, N},
title = {Raman Spectroscopy-Based Measurements of Single-Cell Phenotypic Diversity in Microbial Populations.},
journal = {mSphere},
volume = {5},
number = {5},
pages = {},
pmid = {33115836},
issn = {2379-5042},
mesh = {Biodiversity ; Escherichia coli/drug effects/metabolism ; Ethanol/pharmacology ; *Microbiota ; Phenotype ; Saccharomyces cerevisiae/metabolism ; Single-Cell Analysis/instrumentation/*methods ; Spectrum Analysis, Raman/*methods ; Stress, Physiological/drug effects ; },
abstract = {Microbial cells experience physiological changes due to environmental change, such as pH and temperature, the release of bactericidal agents, or nutrient limitation. This has been shown to affect community assembly and physiological processes (e.g., stress tolerance, virulence, or cellular metabolic activity). Metabolic stress is typically quantified by measuring community phenotypic properties such as biomass growth, reactive oxygen species, or cell permeability. However, bulk community measurements do not take into account single-cell phenotypic diversity, which is important for a better understanding and the subsequent management of microbial populations. Raman spectroscopy is a nondestructive alternative that provides detailed information on the biochemical makeup of each individual cell. Here, we introduce a method for describing single-cell phenotypic diversity using the Hill diversity framework of Raman spectra. Using the biomolecular profile of individual cells, we obtained a metric to compare cellular states and used it to study stress-induced changes. First, in two Escherichia coli populations either treated with ethanol or nontreated and then in two Saccharomyces cerevisiae subpopulations with either high or low expression of a stress reporter. In both cases, we were able to quantify single-cell phenotypic diversity and to discriminate metabolically stressed cells using a clustering algorithm. We also described how the lipid, protein, and nucleic acid compositions changed after the exposure to the stressor using information from the Raman spectra. Our results show that Raman spectroscopy delivers the necessary resolution to quantify phenotypic diversity within individual cells and that this information can be used to study stress-driven metabolic diversity in microbial populations.IMPORTANCE Microbial cells that live in the same community can exist in different physiological and morphological states that change as a function of spatiotemporal variations in environmental conditions. This phenomenon is commonly known as phenotypic heterogeneity and/or diversity. Measuring this plethora of cellular expressions is needed to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behavior of the sampled community. In this work, we present a way to quantify the phenotypic diversity of microbial samples by inferring the (bio)molecular profile of its constituent cells using Raman spectroscopy. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. Raman spectroscopy holds potential for the detection of stressed cells in bioproduction.},
}
@article {pmid33114469,
year = {2020},
author = {Cornejo-Pareja, I and Ruiz-Limón, P and Gómez-Pérez, AM and Molina-Vega, M and Moreno-Indias, I and Tinahones, FJ},
title = {Differential Microbial Pattern Description in Subjects with Autoimmune-Based Thyroid Diseases: A Pilot Study.},
journal = {Journal of personalized medicine},
volume = {10},
number = {4},
pages = {},
pmid = {33114469},
issn = {2075-4426},
support = {CP16/00163, PI18/01160//Carlos III Health Institute-co-founded by Fondo Europeo de Desarrollo Regional - FEDER/ ; },
abstract = {The interaction between genetic susceptibility, epigenetic, endogenous, and environmental factors play a key role in the initiation and progression of autoimmune thyroid diseases (AITDs). Studies have shown that gut microbiota alterations take part in the development of autoimmune diseases. We have investigated the possible relationship between gut microbiota composition and the most frequent AITDs. A total of nine Hashimoto's thyroiditis (HT), nine Graves-Basedow's disease (GD), and 11 otherwise healthy donors (HDs) were evaluated. 16S rRNA pyrosequencing and bioinformatics analysis by Quantitative Insights into Microbial Ecology and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) were used to analyze the gut microbiota. Beta diversity analysis showed that gut microbiota from our groups was different. We observed an increase in bacterial richness in HT and a lower evenness in GD in comparison to the HDs. GD showed a significant increase of Fusobacteriaceae, Fusobacterium and Sutterella compared to HDs and the core microbiome features showed that Prevotellaceae and Prevotella characterized this group. Victivallaceae was increased in HT and was part of their core microbiome. Streptococcaceae, Streptococcus and Rikenellaceae were greater in HT compared to GD. Core microbiome features of HT were represented by Streptococcus, Alistipes, Anaerostipes, Dorea and Haemophilus. Faecalibacterium decreased in both AITDs compared to HDs. PICRUSt analysis demonstrated enrichment in the xenobiotics degradation, metabolism, and the metabolism of cofactors and vitamins in GD patients compared to HDs. Moreover, correlation studies showed that some bacteria were widely correlated with autoimmunity parameters. A prediction model evaluated a possible relationship between predominant concrete bacteria such as an unclassified genus of Ruminococcaceae, Sutterella and Faecalibacterium in AITDs. AITD patients present altered gut microbiota compared to HDs. These alterations could be related to the immune system development in AITD patients and the loss of tolerance to self-antigens.},
}
@article {pmid33111499,
year = {2020},
author = {Zrimec, J},
title = {Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens.},
journal = {MicrobiologyOpen},
volume = {9},
number = {12},
pages = {e1129},
pmid = {33111499},
issn = {2045-8827},
mesh = {Algorithms ; Bacteria/drug effects/*genetics ; Conjugation, Genetic/*genetics ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Nucleic Acid Conformation ; Plasmids/*genetics ; Sequence Alignment ; Transformation, Bacterial/*genetics ; },
abstract = {Antimicrobial resistance poses a great danger to humanity, in part due to the widespread horizontal gene transfer of plasmids via conjugation. Modeling of plasmid transfer is essential to uncovering the fundamentals of resistance transfer and for the development of predictive measures to limit the spread of resistance. However, a major limitation in the current understanding of plasmids is the incomplete characterization of the conjugative DNA transfer mechanisms, which conceals the actual potential for plasmid transfer in nature. Here, we consider that the plasmid-borne origin-of-transfer substrates encode specific DNA structural properties that can facilitate finding these regions in large datasets and develop a DNA structure-based alignment procedure for typing the transfer substrates that outperforms sequence-based approaches. Thousands of putative DNA transfer substrates are identified, showing that plasmid mobility can be twofold higher and span almost twofold more host species than is currently known. Over half of all putative mobile plasmids contain the means for mobilization by conjugation systems belonging to different mobility groups, which can hypothetically link previously confined host ranges across ecological habitats into a robust plasmid transfer network. This hypothetical network is found to facilitate the transfer of antimicrobial resistance from environmental genetic reservoirs to human pathogens, which might be an important driver of the observed rapid resistance development in humans and thus an important point of focus for future prevention measures.},
}
@article {pmid33110109,
year = {2020},
author = {Bellone, R and Lequime, S and Jupille, H and Göertz, GP and Aubry, F and Mousson, L and Piorkowski, G and Yen, PS and Gabiane, G and Vazeille, M and Sakuntabhai, A and Pijlman, GP and de Lamballerie, X and Lambrechts, L and Failloux, AB},
title = {Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {18404},
pmid = {33110109},
issn = {2045-2322},
mesh = {*Adaptation, Physiological ; Aedes/*virology ; Animals ; Dengue/epidemiology/transmission ; Dengue Virus/*physiology ; Epistasis, Genetic ; Humans ; Mosquito Vectors/*virology ; },
abstract = {In most of the world, Dengue virus (DENV) is mainly transmitted by the mosquito Aedes aegypti while in Europe, Aedes albopictus is responsible for human DENV cases since 2010. Identifying mutations that make DENV more competent for transmission by Ae. albopictus will help to predict emergence of epidemic strains. Ten serial passages in vivo in Ae. albopictus led to select DENV-1 strains with greater infectivity for this vector in vivo and in cultured mosquito cells. These changes were mediated by multiple adaptive mutations in the virus genome, including a mutation at position 10,418 in the DENV 3'UTR within an RNA stem-loop structure involved in subgenomic flavivirus RNA production. Using reverse genetics, we showed that the 10,418 mutation alone does not confer a detectable increase in transmission efficiency in vivo. These results reveal the complex adaptive landscape of DENV transmission by mosquitoes and emphasize the role of epistasis in shaping evolutionary trajectories of DENV variants.},
}
@article {pmid33108474,
year = {2021},
author = {Sahu, KP and Kumar, A and Patel, A and Kumar, M and Gopalakrishnan, S and Prakash, G and Rathour, R and Gogoi, R},
title = {Rice Blast Lesions: an Unexplored Phyllosphere Microhabitat for Novel Antagonistic Bacterial Species Against Magnaporthe oryzae.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {731-745},
pmid = {33108474},
issn = {1432-184X},
support = {09/083(0367)/2016-EMR-I//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/ ; },
mesh = {Actinobacteria ; Ascomycota ; *Magnaporthe/genetics ; *Oryza ; Pantoea ; Plant Diseases ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Dark brown necrotic lesions caused by Magnaporthe oryzae on rice foliage is a contrasting microhabitat for leaf-colonizing microbiome as compared with the surrounding healthy chlorophyll-rich tissues. We explored culturable bacterial communities of blast lesions by adopting microbiological tools for isolating effective biocontrol bacterial strains against M. oryzae. 16S rRNA gene sequencing-based molecular identification revealed a total of 17 bacterial species belonging to Achromobacter (2), Comamonas (1), Curtobacterium (1), Enterobacter (1), Leclercia (2), Microbacterium (1), Pantoea (3), Sphingobacterium (1), and Stenotrophomonas (5) found colonizing the lesion. Over 50% of the bacterial isolates were able to suppress the mycelial growth of M. oryzae either by secretory or volatile metabolites. Volatiles released by Achromobacter sp., Curtobacterium luteum, Microbacterium oleivorans, Pantoea ananatis, Stenotrophomonas maltophilia, and Stenotrophomonas sp., and were found to be fungicidal while others showed fungistatic action. In planta pathogen challenged evaluation trial revealed the biocontrol potential of Stenotrophomonas sp. and Microbacterium oleivorans that showed over 60% blast severity suppression on the rice leaf. The lesion-associated bacterial isolates were found to trigger expression of defense genes such as OsCEBiP, OsCERK1, OsEDS1, and OsPAD4 indicating their capability to elicit innate defense in rice against blast disease. The investigation culminated in the identification of potential biocontrol agents for the management of rice blast disease.},
}
@article {pmid33105583,
year = {2020},
author = {Rabieh, S and Bayaraa, O and Romeo, E and Amosa, P and Calnek, K and Idaghdour, Y and Ochsenkühn, MA and Amin, SA and Goldstein, G and Bromage, TG},
title = {MH-ICP-MS Analysis of the Freshwater and Saltwater Environmental Resources of Upolu Island, Samoa.},
journal = {Molecules (Basel, Switzerland)},
volume = {25},
number = {21},
pages = {},
pmid = {33105583},
issn = {1420-3049},
support = {S10 OD026989/OD/NIH HHS/United States ; UN-India Development Partnership Fund//United Nations Development Programme, United Nations United Nations Educational, Scientific and Cultural Organisation/ ; },
mesh = {Coral Reefs ; Environmental Monitoring/*methods ; Fresh Water/chemistry ; Geologic Sediments/chemistry ; Herbicides/analysis ; Humans ; Islands ; Mass Spectrometry/*methods ; Pesticides/analysis ; Samoa ; Seawater/chemistry ; Water Pollutants, Chemical/*analysis ; Water Quality ; },
abstract = {The elemental composition of freshwater and saltwater samples around the South Pacific island of Upolu, Samoa has been investigated together with other indicators of water quality. Up to 69 elements from Li (3) to U (92) are measured in each sample, analyzed by Mattauch-Herzog-inductively coupled plasma-mass spectrometry (MH-ICP-MS). One hundred and seventy-six samples were collected from surface freshwater sources (24 rivers, two volcanic lakes, one dam) and from seawater sources from the surface to 30 m depth (45 inner reef, reef, and outer reef locations) around Upolu Island, including river mouths and estuaries. Principal component and hierarchical clustering correlation analyses were performed on quantile normalized log transformed elemental composition data to identify groups of samples with similar characteristics and to improve the visualization of the full spectrum of elements. Human activities, such as the use of herbicides and pesticides, may relate to observed elevated concentrations of some elements contained in chemicals known to have deleterious obesogenic effects on humans that may also cause coral reef decline. Furthermore, the salinity of some saltwater samples tested were very high, possibly due to climate variability, which may additionally harm the health and biodiversity of coral reefs.},
}
@article {pmid33099662,
year = {2021},
author = {Sepehri, M and Khatabi, B},
title = {Combination of Siderophore-Producing Bacteria and Piriformospora indica Provides an Efficient Approach to Improve Cadmium Tolerance in Alfalfa.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {717-730},
pmid = {33099662},
issn = {1432-184X},
mesh = {Basidiomycota ; Biodegradation, Environmental ; Cadmium/toxicity ; Humans ; Medicago sativa ; Plant Roots ; *Rhizobium ; Siderophores ; *Soil Pollutants ; },
abstract = {Application of siderophore-producing microorganisms (SPMs), as an environmentally friendly approach, facilitates plant growth and survival under heavy metals toxicity. This study evaluated the effectiveness of SPMs, belonging to the bacterial genera Rhizobium and Pseudomonas and a root endophytic fungus (Piriformospora indica) to improve the fitness of alfalfa under cadmium (Cd) stress. A greenhouse experiment was performed as a randomized design with factorial arrangement of treatments. Treatments included microbial inoculations (Sinorhizobium meliloti, Pseudomonas fluorescence, and P. indica) and different Cd concentrations (0, 2, 5, 10 mg/kg) with three replications in potting media containing sand and sterile perlite (v/v, 2:1). The effect of Cd on plant growth and development, antioxidant enzymes activities, and accumulation of Cd and nutrients in alfalfa plant was investigated. Alfalfa inoculated with SPMs showed significantly higher biomass and nutrients uptake under both normal and Cd stress conditions than the controls. Under the highest Cd concentration (10 mg/kg), alfalfa plants inoculated with P. fluorescens and P. indica, either alone or in combination, showed the highest shoot dry weights. Cd-induced oxidative stress was mitigated by SPMs through enhanced antioxidant enzyme activities of catalase, ascorbate peroxidase, and guaiacol peroxidase. We showed that P. indica either alone or in combination with the siderophore producing bacteria (SPB) minimized the toxicity of Cd by enhanced growth rate and the lower Cd concentration in the shoots. In conclusion, metal-resistant SPMs could assist alfalfa to survive in Cd-contaminated soil by enhancing plant growth and development. Application of plant-associated microbes is an efficient, environmentally friendly approach to surmount the adverse effects of heavy metals toxicity on plants, animals, and humans. Graphical abstract.},
}
@article {pmid33099661,
year = {2021},
author = {Kubera, &#x141;},
title = {Spread Patterns of Antibiotic Resistance in Faecal Indicator Bacteria Contaminating an Urbanized Section of the Brda River.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {592-600},
pmid = {33099661},
issn = {1432-184X},
support = {Grant No. 008/RID/2018/19//Ministerstwo Nauki i Szkolnictwa Wy&#x17c;szego/ ; },
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Microbial ; *Enterococcus ; Feces ; Microbial Sensitivity Tests ; *Rivers ; },
abstract = {This paper presents the spatio-temporal distribution of faecal indicator bacteria (FIB) in the river section subject to anthropogenic stress and describes spread patterns of antibiotic resistance in the studied bacterial groups. The analysis involved 58 strains of Escherichia coli and 61 strains of enterococci. Antibiotic resistance profiles were prepared in accordance with the recommendations of the European Committee on Antimicrobial Susceptibility Testing (EUCAST). The results indicated a correlation between the location of a sampling site and the concentration of faecal bacteria. The highest average concentrations were recorded at the site located in the city centre, where the river is used mainly for recreation. Antibiotic resistance profiles showed that Escherichia coli had 100% sensitivity to tigecycline, levofloxacin and imipenem. The highest percentaage of strains (17%) were resistant to piperacillin. Enterococci were 100% sensitive to levofloxacin. No strains were vancomycin-resistant (VRE). The highest percentage of strains was resistant to imipenem (23%), and the lowest, to ampicillin (2%). The spatio-temporal distribution of antibiotic-resistant strains (ARS) indicated a high concentration of drug-resistant Escherichia coli (47%) in the summer season at the sampling site located in the last part of the river. At the same time, drug resistance in enterococci increased along the river course and was considerably higher in spring. There were no significant relationships between physico-chemical parameters of water and the levels of faecal bacteria. On the other hand, strong relationships were observed between the percentage of strains showing resistance to the applied antibiotics and physico-chemical and biological parameters of water. The percentage of antibiotic resistant strains of Escherichia coli was negatively correlated with dissolved oxygen concentration (r = - 0.9; p < 0.001) and BOD5 (r = - 0.85; p < 0.05). The percentage of antibiotic resistant strains of enterococci was most strongly correlated with water pH (r = - 0.92; p < 0.001).},
}
@article {pmid33099264,
year = {2021},
author = {Gao, R and Bonin, L and Arroyo, JMC and Logan, BE and Rabaey, K},
title = {Separation and recovery of ammonium from industrial wastewater containing methanol using copper hexacyanoferrate (CuHCF) electrodes.},
journal = {Water research},
volume = {188},
number = {},
pages = {116532},
doi = {10.1016/j.watres.2020.116532},
pmid = {33099264},
issn = {1879-2448},
mesh = {*Ammonium Compounds ; Copper ; Electrodes ; Ferrocyanides ; Methanol ; *Wastewater ; },
abstract = {Ammonium is typically removed from wastewater by converting it to nitrogen gas using microorganisms, precluding its recovery. Copper hexacyanoferrate (CuHCF) is known to reversibly intercalate alkali cations in aqueous electrolytes due to the Prussian Blue crystal structure. We used this property to create a carbon-based intercalation electrode within an electrochemical cell. Depending on the electrode potential, it can recover NH4[+] from wastewater via insertion/regeneration while leaving organics. In the first phase, different binders were evaluated towards creating a stable electrode matrix, with sodium carboxymethyl cellulose giving the best performance. Subsequently, based on voltammetry, we determined an intercalation potential for NH4[+] removal of + 0.3 V vs. Ag/AgCl, while the regeneration potential of the electrode was + 1.1 V (vs. Ag/AgCl). Using the CuHCF electrodes 95% of the NH4[+] in a synthetic wastewater containing 56 mM NH4[+] and 68 mM methanol was removed with an energy input of 0.34 ± 0.01 Wh g[-1] NH4[+]. A similar removal of 93% was obtained using an actual industrial wastewater (56 mM NH4[+], 68 mM methanol, 0.02 mM NO2[-], 0.05 mM NO3[-], 0.04 mM SO4[2-] and 0.34 mM ethanol), with an energy input of 0.40 ± 0.01 Wh g[-1] NH4[+]. In both cases, there was negligible removal of organics. The stability of CuHCF electrodes was evaluated either by open circuit potential monitoring (61 h) or by cyclic voltammetry (50 h, 116 cycles). The stability during cycling of the electrode was determined in both synthetic and real streams for 25 h (125 cycles). The charge density (C cm[-1]) of the CuHCF electrodes declined by 17 % and 19% after 125 cycles in the synthetic stream and the actual wastewater, respectively. This study highlights the possibility of low-cost CuHCF coated electrodes for achieving separation of NH4[+] from streams containing methanol. The stability of electrodes has been improved but needs to be further enhanced for large-scale applications and long-term operation.},
}
@article {pmid33098438,
year = {2021},
author = {Gunnabo, AH and van Heerwaarden, J and Geurts, R and Wolde-Meskel, E and Degefu, T and Giller, KE},
title = {Phylogeography and Symbiotic Effectiveness of Rhizobia Nodulating Chickpea (Cicer arietinum L.) in Ethiopia.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {703-716},
pmid = {33098438},
issn = {1432-184X},
mesh = {*Cicer ; DNA, Bacterial ; Ethiopia ; *Mesorhizobium/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S ; *Rhizobium ; Sequence Analysis, DNA ; Symbiosis ; },
abstract = {Chickpea (Cicer arietinum L.) used to be considered a restrictive host that nodulated and fixed nitrogen only with Mesorhizobium ciceri and M. mediterraneum. Recent analysis revealed that chickpea can also establish effective symbioses with strains of several other Mesorhizobium species such as M. loti, M. haukuii, M. amorphae, M. muleiense, etc. These strains vary in their nitrogen fixation potential inviting further exploration. We characterized newly collected mesorhizobial strains isolated from various locations in Ethiopia to evaluate genetic diversity, biogeographic structure and symbiotic effectiveness. Symbiotic effectiveness was evaluated in Leonard Jars using a locally released chickpea cultivar "Nattoli". Most of the new isolates belonged to a clade related to M. plurifarium, with very few sequence differences, while the total collection of strains contained three additional mesorhizobial genospecies associated with M. ciceri, M. abyssinicae and an unidentified Mesorhizobium species isolated from a wild host in Eritrea. The four genospecies identified represented a subset of the eight major Mesorhizobium clades recently reported for Ethiopia based on metagenomic data. All Ethiopian strains had nearly identical symbiotic genes that grouped them in a single cluster with M. ciceri, M. mediterraneum and M. muleiense, but not with M. plurifarium. Some phylogeographic structure was observed, with elevation and geography explaining some of the genetic differences among strains, but the relation between genetic identity and symbiotic effectiveness was observed to be weak.},
}
@article {pmid33096434,
year = {2021},
author = {Prévoteau, A and Kerckhof, FM and Clauwaert, P and Rabaey, K},
title = {Electrochemical and phylogenetic comparisons of oxygen-reducing electroautotrophic communities.},
journal = {Biosensors &amp; bioelectronics},
volume = {171},
number = {},
pages = {112700},
doi = {10.1016/j.bios.2020.112700},
pmid = {33096434},
issn = {1873-4235},
mesh = {Biofilms ; *Biosensing Techniques ; Electrodes ; Oxidation-Reduction ; *Oxygen ; *Phylogeny ; },
abstract = {The mechanisms of extracellular electron transfer and the microbial taxa associated with the observed electroactivity are fundamental to oxygen-reducing microbial cathodes. Here we confirmed the apparent 'electroautotrophic' behavior of electroactive biofilms (EABs) grown on carbon electrodes at + 0.20V vs. Ag/AgCl under air. The EABs catalyzed O2 electroreduction into water ─ as demonstrated by a rotating ring disc experiment ─ and performed quasi-reversible heterogeneous electron transfer (HET). By using electrodes of low surface capacitance, we report for the first time nonturnover redox peaks that are very likely intrinsic to the redox protein(s) performing the HET. Because the formal potential of redox proteins is pH-dependent, we investigated the evolution of characteristic potentials of the EABs with the solution pH: (i) open circuit potential, (ii) half-wave potential, and (iii) averaged peak potential of nonturnover cyclic voltammograms, which is presumably the formal potential of the primary electron acceptor(s) for the community. In addition to describing the redox thermodynamics behind HET, we suggest that the corresponding data provides an electrochemical fingerprint that could help in comparing the electroactivity of diverse microbial communities. The taxon with the highest relative abundance in our EABs was an unclassified member of the Gammaproteobacteria that was phylogenetically closely related to most other abundant unclassified Gammaproteobacteria commonly reported in EABs reducing O2 at high potentials, further suggesting that those taxa are responsible for the bioelectroactivity. Phylogenetic and electrochemical similarities between reported EABs jointly support the hypothesis that similar biomolecular mechanisms may be responsible for this highly probable electroautotrophic metabolism.},
}
@article {pmid33096247,
year = {2020},
author = {Pelusio, NF and Rossi, B and Parma, L and Volpe, E and Ciulli, S and Piva, A and D'Amico, F and Scicchitano, D and Candela, M and Gatta, PP and Bonaldo, A and Grilli, E},
title = {Effects of increasing dietary level of organic acids and nature-identical compounds on growth, intestinal cytokine gene expression and gut microbiota of rainbow trout (Oncorhynchus mykiss) reared at normal and high temperature.},
journal = {Fish &amp; shellfish immunology},
volume = {107},
number = {Pt A},
pages = {324-335},
doi = {10.1016/j.fsi.2020.10.021},
pmid = {33096247},
issn = {1095-9947},
mesh = {Animal Feed/analysis ; Animals ; Bacterial Physiological Phenomena/drug effects ; Benzaldehydes/administration &amp; dosage/*metabolism ; Citric Acid/administration &amp; dosage/*metabolism ; Cytokines/drug effects/metabolism ; Diet/veterinary ; Eating/*drug effects ; Gastrointestinal Microbiome/physiology ; Gene Expression/drug effects/immunology ; Hot Temperature ; Intestines/*drug effects/microbiology/physiology ; Oncorhynchus mykiss/genetics/growth &amp; development/*immunology/microbiology ; Sorbic Acid/administration &amp; dosage/*metabolism ; Thymol/administration &amp; dosage/*metabolism ; Time Factors ; },
abstract = {Organic acids (OA) and nature-identical compounds (NIC) such as monoterpenes and aldehydes are well-known growth and health promoters in terrestrial livestock while their application for fish production is recent and their mechanisms of action require further study. Hence, this study tested the increasing dietary level (D0, D250, D500, D1000; 0, 250, 500 and 1000 mg kg feed[-1] respectively) of a microencapsulated blend containing citric and sorbic acid, thymol and vanillin over 82 days on rainbow trout to assess the effects on growth, feed utilization, intestine cytokine gene expression and gut microbiota (GM). Furthermore, the effects on intestinal cytokine gene expression and GM were also explored after one week at high water temperature (23 °C). OA and NIC improved specific growth rate (SGR) and feed conversion rate (FCR) during the second half (day 40-82) of the feeding trial, while at the end of the trial protein (PER) and lipid efficiency (LER) increased with increasing dietary level. GM diversity and composition and cytokine gene expression analysis showed no significant differences in fish fed with increasing doses of OA and NIC (82 days) demonstrating the absence of inflammatory activity in the intestinal mucosa. Although there were no statistical differences, GM structure showed a tendency in clustering D0 group separately from the other dietary groups and a trend towards reduction of Streptococcus spp. was observed in the D250 and D1000 groups. After exposure to high water temperature, lower GM diversity and increased gene expression of inflammatory intestinal cytokines were observed for both inclusions (D0 vs. D1000) compared to groups in standard condition. However, the gene up-regulation involved a limited number of cytokines showing the absence of a substantial inflammation process able to compromise the functional activity of the intestine. Despite further study should be conducted to fully clarify this mechanism, cytokines up-regulation seems to be concomitant to the reduction of the GM diversity and, particularly, to the reduction of specific lactic acid bacteria such as Leuconostoc. The application of the microencapsulate blend tested can be a useful strategy to improve growth and feed utilization in rainbow trout under normal temperature conditions. According to the results organic acids and nature-identical compounds did not revert the effects triggered by the increased temperature of water.},
}
@article {pmid33095158,
year = {2020},
author = {Greenhalgh, R and Dermauw, W and Glas, JJ and Rombauts, S and Wybouw, N and Thomas, J and Alba, JM and Pritham, EJ and Legarrea, S and Feyereisen, R and Van de Peer, Y and Van Leeuwen, T and Clark, RM and Kant, MR},
title = {Genome streamlining in a minute herbivore that manipulates its host plant.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
pmid = {33095158},
issn = {2050-084X},
support = {773902-SuperPests//Horizon 2020 - Research and Innovation Framework Programme/International ; STW-GAP/13550//Netherlands Organisation for Scientific Research/International ; 12T9818N//Research Foundation Flanders/International ; 772026-POLYADAPT//European Union Horizon 2020 research and innovation program/International ; 1457346//USA National Science Foundation/International ; 1274917N//Research Foundation Flanders/International ; 1457346//National Science Foundation/International ; T32 GM007464/GM/NIGMS NIH HHS/United States ; STW-VIDI/13492//Netherlands Organisation for Scientific Research/International ; 773902-SuperPests//European Union Horizon 2020 research and innovation program/International ; },
mesh = {Animals ; Evolution, Molecular ; *Genome ; *Herbivory ; Host-Pathogen Interactions ; Solanum lycopersicum/*parasitology ; Mites/*genetics ; Phylogeny ; },
abstract = {The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host's natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species' highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.},
}
@article {pmid33094372,
year = {2021},
author = {Jeong, SY and Kim, TG},
title = {Effects of Plants on Metacommunities and Correlation Networks of Soil Microbial Groups in an Ecologically Restored Wetland.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {657-672},
pmid = {33094372},
issn = {1432-184X},
support = {2018R1D1A1B07048872//Ministry of Education/ ; },
mesh = {Fungi/genetics ; *Microbiota ; Plants ; Soil ; Soil Microbiology ; *Wetlands ; },
abstract = {Plants may influence different aspects of the belowground microorganisms, including abundance, distribution, and interaction, in wetlands. Microbial communities were scrutinized in a 4-year-old restored wetland ecosystem with 5 distinct sites: a bare-soil site (10 local patches) and sites dominated by Miscanthus, Phragmites, Typha, and Zizania (20 patches per site). Ordination analysis revealed that plant-induced attributes (e.g., organic matter and total carbon and nitrogen) could explain the total environmental variance. Community comparisons showed that all groups (Bacteria, Fungi, Protista, and Metazoa) differed in community structure among the 5 sites (P < 0.05). Comparisons between the community and environmental ordination plots revealed that community structural variation among the sites correlated with the environmental change across all groups (R[2] ≥ 0.61). This indicates that all groups were primarily influenced by plant detritus. In addition, correlation networks markedly varied in topology and composition among the sites across all groups. There was a strong coupling between the metacommunity and correlation network for both Bacteria and Fungi (R[2] ≥ 0.58), indicating that the plants determined the spatial covariation patterns of microbial populations. Multi-group networks and group synchrony results revealed that Bacteria, Fungi, and Protista were synchronized with each other (R[2] ≥ 0.52) as the key founders of the microbial systems, while Metazoa participated in the system only under Miscanthus. Our findings concluded that the plants shaped the communities by controlling the abundance and interaction of their populations.},
}
@article {pmid33087520,
year = {2020},
author = {Tomkovich, S and Stough, JMA and Bishop, L and Schloss, PD},
title = {The Initial Gut Microbiota and Response to Antibiotic Perturbation Influence Clostridioides difficile Clearance in Mice.},
journal = {mSphere},
volume = {5},
number = {5},
pages = {},
pmid = {33087520},
issn = {2379-5042},
support = {U01 AI124255/AI/NIAID NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/classification/*drug effects ; Breeding ; Clostridioides difficile ; Clostridium Infections/*drug therapy/microbiology ; Disease Models, Animal ; Feces ; Female ; Gastrointestinal Microbiome/*drug effects ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The gut microbiota has a key role in determining susceptibility to Clostridioides difficile infections (CDIs). However, much of the mechanistic work examining CDIs in mouse models uses animals obtained from a single source. We treated mice from 6 sources (2 University of Michigan colonies and 4 commercial vendors) with clindamycin, followed by a C. difficile challenge, and then measured C. difficile colonization levels throughout the infection. The microbiota were profiled via 16S rRNA gene sequencing to examine the variation across sources and alterations due to clindamycin treatment and C. difficile challenge. While all mice were colonized 1 day postinfection, variation emerged from days 3 to 7 postinfection with animals from some sources colonized with C. difficile for longer and at higher levels. We identified bacteria that varied in relative abundance across sources and throughout the experiment. Some bacteria were consistently impacted by clindamycin treatment in all sources of mice, including Lachnospiraceae, Ruminococcaceae, and Enterobacteriaceae To identify bacteria that were most important to colonization regardless of the source, we created logistic regression models that successfully classified mice based on whether they cleared C. difficile by 7 days postinfection using community composition data at baseline, post-clindamycin treatment, and 1 day postinfection. With these models, we identified 4 bacterial taxa that were predictive of whether C. difficile cleared. They varied across sources (Bacteroides) or were altered by clindamycin (Porphyromonadaceae) or both (Enterobacteriaceae and Enterococcus). Allowing for microbiota variation across sources better emulates human interindividual variation and can help identify bacterial drivers of phenotypic variation in the context of CDIs.IMPORTANCEClostridioides difficile is a leading nosocomial infection. Although perturbation to the gut microbiota is an established risk, there is variation in who becomes asymptomatically colonized, develops an infection, or has adverse infection outcomes. Mouse models of C. difficile infection (CDI) are widely used to answer a variety of C. difficile pathogenesis questions. However, the interindividual variation between mice from the same breeding facility is less than what is observed in humans. Therefore, we challenged mice from 6 different breeding colonies with C. difficile We found that the starting microbial community structures and C. difficile persistence varied by the source of mice. Interestingly, a subset of the bacteria that varied across sources were associated with how long C. difficile was able to colonize. By increasing the interindividual diversity of the starting communities, we were able to better model human diversity. This provided a more nuanced perspective of C. difficile pathogenesis.},
}
@article {pmid33083833,
year = {2021},
author = {Arca-Suárez, J and Lasarte-Monterrubio, C and Rodiño-Janeiro, BK and Cabot, G and Vázquez-Ucha, JC and Rodríguez-Iglesias, M and Galán-Sánchez, F and Beceiro, A and González-Bello, C and Oliver, A and Bou, G},
title = {Molecular mechanisms driving the in vivo development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR Pseudomonas aeruginosa infections.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {76},
number = {1},
pages = {91-100},
doi = {10.1093/jac/dkaa396},
pmid = {33083833},
issn = {1460-2091},
mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Azabicyclo Compounds/pharmacology/therapeutic use ; *Ceftazidime/pharmacology ; Cephalosporins/pharmacology ; Drug Combinations ; Humans ; Microbial Sensitivity Tests ; *Pseudomonas Infections/drug therapy ; Pseudomonas aeruginosa/genetics ; Tazobactam/pharmacology ; beta-Lactamases/genetics ; },
abstract = {BACKGROUND: The development of resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of Pseudomonas aeruginosa infections is concerning.<br><br>OBJECTIVES: Characterization of the mechanisms leading to the development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR P. aeruginosa infections.<br><br>METHODS: Four paired ceftolozane/tazobactam- and ceftazidime/avibactam-susceptible/resistant isolates were evaluated. MICs were determined by broth microdilution. STs, resistance mechanisms and genetic context of &#x3b2;-lactamases were determined by genotypic methods, including WGS. The OXA-10 variants were cloned in PAO1 to assess their impact on resistance. Models for the OXA-10 derivatives were constructed to evaluate the structural impact of the amino acid changes.<br><br>RESULTS: The same XDR ST253 P. aeruginosa clone was detected in all four cases evaluated. All initial isolates showed OprD deficiency, produced an OXA-10 enzyme and were susceptible to ceftazidime, ceftolozane/tazobactam, ceftazidime/avibactam and colistin. During treatment, the isolates developed resistance to all cephalosporins. Comparative genomic analysis revealed that the evolved resistant isolates had acquired mutations in the OXA-10 enzyme: OXA-14 (Gly157Asp), OXA-794 (Trp154Cys), OXA-795 (&#x394;Phe153-Trp154) and OXA-824 (Asn143Lys). PAO1 transformants producing the evolved OXA-10 derivatives showed enhanced ceftolozane/tazobactam and ceftazidime/avibactam resistance but decreased meropenem MICs in a PAO1 background. Imipenem/relebactam retained activity against all strains. Homology models revealed important changes in regions adjacent to the active site of the OXA-10 enzyme. The blaOXA-10 gene was plasmid borne and acquired due to transposition of Tn6746 in the pHUPM plasmid scaffold.<br><br>CONCLUSIONS: Modification of OXA-10 is a mechanism involved in the in vivo acquisition of resistance to cephalosporin/&#x3b2;-lactamase inhibitor combinations in P. aeruginosa.},
}
@article {pmid33082281,
year = {2020},
author = {Allard, SM and Costa, MT and Bulseco, AN and Helfer, V and Wilkins, LGE and Hassenrück, C and Zengler, K and Zimmer, M and Erazo, N and Mazza Rodrigues, JL and Duke, N and Melo, VMM and Vanwonterghem, I and Junca, H and Makonde, HM and Jiménez, DJ and Tavares, TCL and Fusi, M and Daffonchio, D and Duarte, CM and Peixoto, RS and Rosado, AS and Gilbert, JA and Bowman, J},
title = {Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems.},
journal = {mSystems},
volume = {5},
number = {5},
pages = {},
pmid = {33082281},
issn = {2379-5077},
abstract = {Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.},
}
@article {pmid33078238,
year = {2021},
author = {Jayakumar, A and Nair, IC and Radhakrishnan, EK},
title = {Environmental Adaptations of an Extremely Plant Beneficial Bacillus subtilis Dcl1 Identified Through the Genomic and Metabolomic Analysis.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {687-702},
pmid = {33078238},
issn = {1432-184X},
mesh = {*Bacillus subtilis/genetics ; Endophytes ; Genomics ; *Plant Diseases ; Plants ; },
abstract = {Bacterial endophytes ubiquitously colonize the internal tissues of plants and promote the plant growth through diverse mechanisms. The current study describes the mechanistic basis of plant-specific adaptations present in an extremely beneficial endophytic bacterium. Here, the endophytic Bacillus subtilis Dcl1 isolated from the dried rhizome of Curcuma longa was found to have the drought tolerance, IAA and ACC deaminase production and phosphate solubilization properties. The whole genome sequencing and annotation further showed the genome of B. subtilis Dcl1 to have the size of 4,321,654 bp. This also showed the presence of genes for IAA, H2S, acetoin, butanediol, flagella and siderophore production along with phosphate solubilization and biofilm formation for the B. subtilis Dcl1. In addition, the genes responsible for the synthesis of surfactin, iturin, fengycin, bacillibactin, bacillaene, bacilysin, chitinase, chitosanase, protease and glycoside hydrolase could also be annotated from the genome of B. subtilis Dcl1. Identification of genes for the glycine betaine, glutamate and trehalose further indicated the drought stress tolerance features of B. subtilis Dcl1. The presence of the genetic basis to produce the catalase, superoxide dismutase, peroxidases, gamma-glutamyltranspeptidase, glutathione and glycolate oxidase also indicated the plant oxidative stress protective effect of B. subtilis Dcl1. Identification of these properties and the demonstration of its plant probiotic effect in Vigna unguiculata confirmed the applicability of B. subtilis Dcl1 as a biofertilizer, biocontrol and bioremediator agent to enhance the agricultural productivity.},
}
@article {pmid33077749,
year = {2020},
author = {Yang, FS and Nie, S and Liu, H and Shi, TL and Tian, XC and Zhou, SS and Bao, YT and Jia, KH and Guo, JF and Zhao, W and An, N and Zhang, RG and Yun, QZ and Wang, XZ and Mannapperuma, C and Porth, I and El-Kassaby, YA and Street, NR and Wang, XR and Van de Peer, Y and Mao, JF},
title = {Chromosome-level genome assembly of a parent species of widely cultivated azaleas.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5269},
pmid = {33077749},
issn = {2041-1723},
mesh = {Anthocyanins/biosynthesis ; Biosynthetic Pathways ; Carotenoids/metabolism ; Chromosomes, Plant/*genetics/metabolism ; Flowers/genetics/growth &amp; development/metabolism ; Gene Expression Regulation, Plant ; *Genome, Plant ; Multigene Family ; Plant Proteins/*genetics/metabolism ; Rhododendron/*genetics/growth &amp; development/metabolism ; Transcription Factors/genetics/metabolism ; },
abstract = {Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.},
}
@article {pmid33075580,
year = {2021},
author = {Francis, JS and Tatarko, AR and Richman, SK and Vaudo, AD and Leonard, AS},
title = {Microbes and pollinator behavior in the floral marketplace.},
journal = {Current opinion in insect science},
volume = {44},
number = {},
pages = {16-22},
doi = {10.1016/j.cois.2020.10.003},
pmid = {33075580},
issn = {2214-5753},
mesh = {Animals ; *Behavior, Animal ; Flowers/*microbiology ; *Pollination ; },
abstract = {Pollinator foraging decisions shape microbial dispersal, and microbes change floral phenotypes in ways perceivable by pollinators. Yet, the role microbes play in the cognitive ecology of pollination is relatively unexplored. Reviewing recent literature on floral microbial ecology and pollinator behavior, we advocate for further integration between these two fields. Insights into pollinator learning, memory, and decision-making can help explain their responses to microbially-altered floral phenotypes. Specifically, considering how pollinators forage for multiple nutrients, cope with uncertainty, structure foraging bouts, and move through their environment could inform predictions about microbial dispersal within plant communities. We highlight how behavior connects microbial changes in floral phenotype to downstream effects on both microbial dispersal and plant fitness.},
}
@article {pmid33072042,
year = {2020},
author = {Sabino, YNV and de Araújo, KC and de Assis, FGDV and Moreira, SM and Lopes, TDS and Mendes, TAO and Huws, SA and Mantovani, HC},
title = {In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {576738},
pmid = {33072042},
issn = {1664-302X},
abstract = {Studies of rumen microbial ecology suggest that the capacity to produce antimicrobial peptides could be a useful trait in species competing for ecological niches in the ruminal ecosystem. However, little is known about the synthesis of lasso peptides by ruminal microorganisms. Here we analyzed the distribution and diversity of lasso peptide gene clusters in 425 bacterial genomes from the rumen ecosystem. Genome mining was performed using antiSMASH 5, BAGEL4, and a database of well-known precursor sequences. The genomic context of the biosynthetic clusters was investigated to identify putative lasA genes and protein sequences from enzymes of the biosynthetic machinery were evaluated to identify conserved motifs. Metatranscriptome analysis evaluated the expression of the biosynthetic genes in the rumen microbiome. Several incomplete (n = 23) and complete (n = 11) putative lasso peptide clusters were detected in the genomes of ruminal bacteria. The complete gene clusters were exclusively found within the phylum Firmicutes, mainly (48%) in strains of the genus Butyrivibrio. The analysis of the genetic organization of complete putative lasso peptide clusters revealed the presence of co-occurring genes, including kinases (85%), transcriptional regulators (49%), and glycosyltransferases (36%). Moreover, a conserved pattern of cluster organization was detected between strains of the same genus/species. The maturation enzymes LasB, LasC, and LasD showed regions highly conserved, including the presence of a transglutaminase core in LasB, an asparagine synthetase domain in LasC, and an ABC-type transporter system in LasD. Phylogenetic trees of the essential biosynthetic proteins revealed that sequences split into monophyletic groups according to their shared single common ancestor. Metatranscriptome analyses indicated the expression of the lasso peptides biosynthetic genes within the active rumen microbiota. Overall, our in silico screening allowed the discovery of novel biosynthetic gene clusters in the genomes of ruminal bacteria and revealed several strains with the genetic potential to synthesize lasso peptides, suggesting that the ruminal microbiota represents a potential source of these promising peptides.},
}
@article {pmid33072023,
year = {2020},
author = {Dias, T and Pimentel, V and Cogo, AJD and Costa, R and Bertolazi, AA and Miranda, C and de Souza, SB and Melo, J and Carolino, M and Varma, A and Eutrópio, F and Olivares, FL and Ramos, AC and Cruz, C},
title = {The Free-Living Stage Growth Conditions of the Endophytic Fungus Serendipita indica May Regulate Its Potential as Plant Growth Promoting Microbe.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {562238},
pmid = {33072023},
issn = {1664-302X},
abstract = {Serendipita indica (former Piriformospora indica) is a non-obligate endophytic fungus and generally a plant growth and defence promoter with high potential to be used in agriculture. However, S. indica may switch from biotrophy to saprotrophy losing its plant growth promoting traits. Our aim was to understand if the free-living stage growth conditions (namely C availability) regulate S. indica's phenotype, and its potential as plant-growth-promoting-microbe (PGPM). We grew S. indica in its free-living stage under increasing C availabilities (2-20 g L[-1] of glucose or sucrose). We first characterised the effect of C availability during free-living stage growth on fungal phenotype: colonies growth and physiology (plasma membrane proton pumps, stable isotopic signatures, and potential extracellular decomposing enzymes). The effect of the C availability during the free-living stage of the PGPM was evaluated on wheat. We observed that C availability during the free-living stage regulated S. indica's growth, ultrastructure and physiology, resulting in two distinct colony phenotypes: compact and explorer. The compact phenotype developed at low C, used peptone as the major C and N source, and displayed higher decomposing potential for C providing substrates; while the explorer phenotype developed at high C, used glucose and sucrose as major C sources and casein and yeast extract as major N sources, and displayed higher decomposing potential for N and P providing substrates. The C availability, or the C/N ratio, during the free-living stage left a legacy to the symbiosis stage, regulating S. indica's potential to promote plant growth: wheat growth promotion by the explorer phenotype was ± 40% higher than that by the compact phenotype. Our study highlights the importance of considering microbial ecology in designing PGPM/biofertilizers. Further studies are needed to test the phenotypes under more extreme conditions, and to understand if the in vitro acquired characteristics persist under field conditions.},
}
@article {pmid33072015,
year = {2020},
author = {Zhu, C and Bass, D and Wang, Y and Shen, Z and Song, W and Yi, Z},
title = {Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {555795},
pmid = {33072015},
issn = {1664-302X},
abstract = {Microeukaryotes are key components of aquatic ecosystems and play crucial roles in aquatic food webs. However, influencing factors and potential assembly mechanisms for microeukaryotic community on biofilms are rarely studied. Here, those of microeukaryotic biofilms in subtropical eutrophic freshwaters were investigated for the first time based on 2,585 operational taxonomic units (OTUs) from 41 samples, across different environmental conditions and substrate types. Following conclusions were drawn: (1) Environmental parameters were more important than substrate types in structuring microeukaryotic community of biofilms in subtropical eutrophic freshwaters. (2) In the fluctuating river, there was a higher diversity of OTUs and less predictability of community composition than in the stable lake. Sessile species were more likely to be enriched on smooth surfaces of glass slides, while both free-swimming and attached organisms occurred within holes inside PFUs (polyurethane foam units). (3) Both species sorting and neutral process were mechanisms for assembly of microeukaryotic biofilms, but their importance varied depending on different habitats and substrates. (4) The effect of species sorting was slightly higher than the neutral process in river biofilms due to stronger environmental filtering. Species sorting was a stronger force structuring communities on glass slides than PFUs with more niche availability. Our study sheds light on assembly mechanisms for microeukaryotic community on different habitat and substrate types, showing that the resulting communities are determined by both sets of variables, in this case primarily habitat type. The balance of neutral process and species sorting differed between habitats, but the high alpha diversity of microeukaryotes in both led to similar sets of lifecycle traits being selected for in each case.},
}
@article {pmid33072010,
year = {2020},
author = {Shang, Y and Wu, X and Wei, Q and Dou, H and Wang, X and Chen, J and Zhang, H and Ma, S and Zhang, H},
title = {Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {548607},
pmid = {33072010},
issn = {1664-302X},
abstract = {Bacteria have the metabolic potential to produce a diverse array of secondary metabolites, which have important roles in biogeochemical cycling processes. However, for Hulun Lake and the rivers that enter into it, the bacterial community structures and their effects have not previously been widely studied, limiting our ecological understanding of this habitat. To address this, we have analyzed the bacterial communities in the water ecosystem of the Hulun Lake Basin. 16S rRNA high-throughput sequencing identified 64 phyla, 165 classes, 218 orders, 386 families, and 740 genera of bacteria across all samples. The dominant phyla in the central area of the lake were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, while in all other areas, Proteobacteria, Actinobacteria, and Bacteroidetes were dominant. The microbial community structures were significantly affected by environmental factors [arsenic (As), pH, and sulfate (SO4 [2-])] and their location in the lake. The species richness in the sediments of Hulun Lake was higher than in the water, and this ecosystem harbored the highest proportion of unclassified sequences, representing unclassified bacteria. This study provides basic data for future investigations into the Hulun lake ecosystem and for water microbial monitoring and protection measures.},
}
@article {pmid33072003,
year = {2020},
author = {Brown, JM and Labonté, JM and Brown, J and Record, NR and Poulton, NJ and Sieracki, ME and Logares, R and Stepanauskas, R},
title = {Single Cell Genomics Reveals Viruses Consumed by Marine Protists.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {524828},
pmid = {33072003},
issn = {1664-302X},
abstract = {The predominant model of the role of viruses in the marine trophic web is that of the "viral shunt," where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, planktonic protists in the Gulf of Maine (GoM) and the Mediterranean Sea. We found viral DNA associated with a substantial fraction cells from the GoM (51%) and the Mediterranean Sea (35%). While Mediterranean SAGs contained a larger proportion of cells containing bacterial sequences (49%), a smaller fraction of cells contained bacterial sequences in the GoM (19%). In GoM cells, nearly identical bacteriophage and ssDNA virus sequences where found across diverse lineages of protists, suggesting many of these viruses are non-infective. The fraction of cells containing viral DNA varied among protistan lineages and reached 100% in Picozoa and Choanozoa. These two groups also contained significantly higher numbers of viral sequences than other identified taxa. We consider mechanisms that may explain the presence of viral DNA in protistan cells and conclude that protistan predation on free viral particles contributed to the observed patterns. These findings confirm prior experiments with protistan isolates and indicate that the viral shunt is complemented by a viral link in the marine microbial food web. This link may constitute a sink of viral particles in the ocean and has implications for the flow of carbon through the microbial food web.},
}
@article {pmid33070212,
year = {2021},
author = {Xu, S and Jiang, L and Qiao, G and Chen, J},
title = {Diversity of bacterial symbionts associated with Myzus persicae (Sulzer) (Hemiptera: Aphididae: Aphidinae) revealed by 16S rRNA Illumina sequencing.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {784-794},
pmid = {33070212},
issn = {1432-184X},
support = {2016YFE0203100//National Key R &amp; D Program of China/ ; 31620103916//National Natural Science Foundation of China (CN)/ ; 31772492//National Natural Science Foundation of China/ ; XDA19050303//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2020087//Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; },
mesh = {Animals ; *Aphids ; Bacteria/genetics ; *Buchnera/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; },
abstract = {Aphids are known to be associated with a variety of symbiotic bacteria. To improve our knowledge of the bacterial diversity of polyphagous aphids, in the present study, we investigated the microbiota of the cosmopolitan agricultural pest Myzus persicae (Sulzer). Ninety-two aphid samples collected from different host plants in various regions of China were examined using high-throughput amplicon sequencing. We comprehensively characterized the symbiont diversity of M. persicae and assessed the variations in aphid-associated symbiont communities. We detected a higher diversity of symbionts than has been previously observed. M. persicae hosted the primary endosymbiont Buchnera aphidicola and seven secondary symbionts, among which Wolbachia was the most prevalent and Rickettsia, Arsenophonus, and Spiroplasma were reported for the first time. Ordination analyses and statistical tests revealed that the symbiont flora associated with M. persicae did not change with respect to host plant or geography, which may be due to frequent migrations between different aphid populations. These findings will advance our knowledge of the microbiota of polyphagous insects and will enrich our understanding of assembly of host-microbiome systems.},
}
@article {pmid33069997,
year = {2021},
author = {Dai, H and Gao, J and Li, D and Wang, Z and Duan, W},
title = {Metagenomics combined with DNA-based stable isotope probing provide comprehensive insights of active triclosan-degrading bacteria in wastewater treatment.},
journal = {Journal of hazardous materials},
volume = {404},
number = {Pt B},
pages = {124192},
doi = {10.1016/j.jhazmat.2020.124192},
pmid = {33069997},
issn = {1873-3336},
mesh = {Beijing ; DNA ; Isotopes ; Metagenomics ; *Triclosan ; *Water Purification ; },
abstract = {The biotransformation of triclosan (TCS) during wastewater treatment occurred frequently, while little researches are known the identity of microorganisms involved in the biodegradation process. In this work, DNA-based stable isotope probing (DNA-SIP) was occupied to investigate the TCS assimilation microbes originated from a full-scale cyclic activated sludge system in Beijing. Results of TCS removal pathway showed that the TCS removal in nitrification process was mainly contributed by the metabolism of heterotrophic bacteria, accounting for about 18.54%. DNA-SIP assay indicated that Sphingobium dominated the degradation of TCS. Oligotyping analysis further indicated that oligotype GCTAAT and ATGTTA of Sphingobium played important roles in degrading TCS. Furthermore, the Kyoto Encyclopedia of Genes and Genomes functional abundance statistics based on PICRUSt2 showed that glutathione transferase was the most prevalent enzyme involved in TCS metabolism, and TCS might be removed through microbial carbon metabolism. Metagenomics made clear that Sphingobium might play irrelevant role on the propagation of antibiotics resistance genes (ARGs), even though, it could degrade TCS. Thauera and Dechloromonas were identified as the key hosts of most ARGs. This study revealed the potential metabolic pathway and microbial ecology of TCS biodegradation in nitrification process of wastewater treatment system.},
}
@article {pmid33068395,
year = {2020},
author = {Lebre, PH and Bottos, E and Makhalanyane, TP and Hogg, I and Cowan, DA},
title = {Islands in the sand: are all hypolithic microbial communities the same?.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {1},
pages = {},
doi = {10.1093/femsec/fiaa216},
pmid = {33068395},
issn = {1574-6941},
mesh = {Antarctic Regions ; Islands ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sand ; *Soil Microbiology ; },
abstract = {Hypolithic microbial communities (hypolithons) are complex assemblages of phototrophic and heterotrophic organisms associated with the ventral surfaces of translucent minerals embedded in soil surfaces. Past studies on the assembly, structure and function of hypolithic communities have tended to use composite samples (i.e. bulked hypolithic biomass) with the underlying assumption that samples collected from within a 'homogeneous' locality are phylogenetically homogeneous. In this study, we question this assumption by analysing the prokaryote phylogenetic diversity of multiple individual hypolithons: i.e. asking the seemingly simple question of 'Are all hypolithons the same'? Using 16S rRNA gene-based phylogenetic analysis of hypolithons recovered for a localized moraine region in the Taylor Valley, McMurdo Dry Valleys, Antarctica, we demonstrate that these communities are heterogeneous at very small spatial scales (<5 m). Using null models of phylogenetic turnover, we showed that this heterogeneity between hypolithons is probably due to stochastic effects such as dispersal limitations, which is entirely consistent with the physically isolated nature of the hypolithic communities ('islands in the sand') and the almost complete absence of a liquid continuum as a mode of microbial transport between communities.},
}
@article {pmid33067657,
year = {2021},
author = {Han, D and Richter-Heitmann, T and Kim, IN and Choy, E and Park, KT and Unno, T and Kim, J and Nam, SI},
title = {Survey of Bacterial Phylogenetic Diversity During the Glacier Melting Season in an Arctic Fjord.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {579-591},
pmid = {33067657},
issn = {1432-184X},
support = {NRF-2015M1A5A1037243//National Research Foundation of Korea/ ; NRF-2018R1D1A3B07041743//National Research Foundation of Korea/ ; NRF-2019R1I1A1A01058140//National Research Foundation of Korea/ ; },
mesh = {Arctic Regions ; *Estuaries ; *Ice Cover ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; },
abstract = {To understand bacterial biogeography in response to the hydrographic impact of climate change derived from the Arctic glacier melting, we surveyed bacterial diversity and community composition using bacterial 16S rRNA gene metabarcoding in the seawaters of Kongsfjorden, Svalbard, during summer 2016. In the present study, bacterial biogeography in the Kongsfjorden seawaters showed distinct habitat patterns according to water mass classification and habitat transition between Atlantic and fjord surface waters. Moreover, we estimated phylogenetic diversity of bacterial communities using the net relatedness, nearest taxon, and beta nearest taxon indices. We found the influence of freshwater input from glacier melting in shaping bacterial assemblage composition through the stochastic model. We further evaluated bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) using a quantitative PCR (qPCR) measurement with demethylation (dmdA) and cleavage (dddP) genes of two fundamentally different processes. Our qPCR results imply that bacterial DMSP degradation follows the Atlantic inflow during summer in Kongsfjorden. These findings suggest that the Atlantic inflow and glacial melting influence bacterial community composition and assembly processes and thus affect the degradation of phytoplankton-derived organic matter in an Arctic fjord.},
}
@article {pmid33067588,
year = {2021},
author = {Mueller, AJ and Jung, MY and Strachan, CR and Herbold, CW and Kirkegaard, RH and Wagner, M and Daims, H},
title = {Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting.},
journal = {The ISME journal},
volume = {15},
number = {3},
pages = {732-745},
pmid = {33067588},
issn = {1751-7370},
support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Bacteria/genetics ; Genomics ; Kinetics ; *Nitrites ; Oceans and Seas ; Oxidation-Reduction ; },
abstract = {Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named "Candidatus Nitrohelix vancouverensis" and "Candidatus Nitronauta litoralis", shed light on the niche differentiation and potential ecological roles of Nitrospinae.},
}
@article {pmid33067398,
year = {2020},
author = {Shibl, AA and Isaac, A and Ochsenkühn, MA and Cárdenas, A and Fei, C and Behringer, G and Arnoux, M and Drou, N and Santos, MP and Gunsalus, KC and Voolstra, CR and Amin, SA},
title = {Diatom modulation of select bacteria through use of two unique secondary metabolites.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {44},
pages = {27445-27455},
pmid = {33067398},
issn = {1091-6490},
mesh = {Animals ; Bacteria/genetics/*growth &amp; development ; Cinnamates/metabolism ; Depsides/metabolism ; Diatoms/genetics/*metabolism ; Dicarboxylic Acids/metabolism ; Gene Expression Profiling ; Metabolomics ; Metagenome ; Metagenomics ; Microbiota/*physiology ; Oceans and Seas ; Phytoplankton/genetics/*metabolism ; Secondary Metabolism/physiology ; *Water Microbiology ; Rosmarinic Acid ; },
abstract = {Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world's oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.},
}
@article {pmid33067195,
year = {2020},
author = {Co, R and Hug, LA},
title = {A Need for Improved Cellulase Identification from Metagenomic Sequence Data.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {1},
pages = {},
pmid = {33067195},
issn = {1098-5336},
mesh = {Bacteria/*isolation &amp; purification ; Cellulase/*analysis ; *Environmental Microbiology ; *Metagenome ; Metagenomics/*methods ; },
abstract = {Improved sequencing technologies and the maturation of metagenomic approaches allow the identification of gene variants with potential industrial applications, including cellulases. Cellulase identification from metagenomic environmental surveys is complicated by inconsistent nomenclature and multiple categorization systems. Here, we summarize the current classification and nomenclature systems, with recommendations for improvements to these systems. Addressing the issues described will strengthen the annotation of cellulose-active enzymes from environmental sequence data sets-a rapidly growing resource in environmental and applied microbiology.},
}
@article {pmid33066774,
year = {2020},
author = {Yan, H and Yu, B and Degroote, J and Spranghers, T and Van Noten, N and Majdeddin, M and Van Poucke, M and Peelman, L and De Vrieze, J and Boon, N and Gielen, I and Smet, S and Chen, D and Michiels, J},
title = {Antibiotic affects the gut microbiota composition and expression of genes related to lipid metabolism and myofiber types in skeletal muscle of piglets.},
journal = {BMC veterinary research},
volume = {16},
number = {1},
pages = {392},
pmid = {33066774},
issn = {1746-6148},
support = {CARS-36//earmarked fund for the China Agriculture Research System/ ; 31672436//National Natural Science Foundation of China/ ; 31730091//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Lipid Metabolism/drug effects/*genetics ; Muscle, Skeletal/*drug effects/metabolism ; Myofibrils/chemistry/*drug effects ; *Swine/genetics/metabolism ; Tylosin/*pharmacology ; },
abstract = {BACKGROUND: Early-life antibiotic administration is known to affect gut microbiota and host adiposity, but the effects of antibiotic exposure on skeletal muscle properties remain unknown. The present study evaluated the changes in skeletal muscle properties including myofiber characteristics and composition, as well as intramuscular fat (IMF) content in skeletal muscle of piglets when exposed to a tylosin-containing diet.<br><br>RESULTS: A total of 18 piglets (28&#x2009;days of age) were randomly allocated into two groups: control basal diet (Control) and Control +&#x2009;100&#x2009;mg tylosin phosphate/kg of feed (Antibiotic). The trial lasted for 39&#x2009;days. High-throughput amplicon sequencing revealed that no significant difference in initial gut microbiota composition was existed between Control and Antibiotic groups. Antibiotic administration increased body weight and growth rate and decreased feed to gain ratio of pigs (P&#x2009;<&#x2009;0.05). The carcass lean and fat volumes of pigs were increased by the tylosin administration (P&#x2009;<&#x2009;0.05). Antibiotic treatment increased myofiber density and the expression of genes related to type I and type IIb myofibers in longissimus muscle (P&#x2009;<&#x2009;0.05). The IMF content in longissimus muscle was increased by antibiotic exposure (P&#x2009;<&#x2009;0.05). Antibiotic administration increased expression of genes related to fatty acid uptake and de novo synthesis, and decreased expression of genes related to triglyceride hydrolysis (P&#x2009;<&#x2009;0.05). Tylosin administration affected taxonomic distribution and beta diversity of the caecal and colonic microbiota of piglets.<br><br>CONCLUSION: These results confirm that the growth performance, myofiber composition and muscle lipid metabolism are affected by antibiotic administration, which may be associated with an altered gut microbiota, suggesting that the gut microbiota could be served as a potential target for modulating skeletal muscle properties of host.},
}
@article {pmid33066697,
year = {2020},
author = {Amat, S and Lantz, H and Munyaka, PM and Willing, BP},
title = {Prevotella in Pigs: The Positive and Negative Associations with Production and Health.},
journal = {Microorganisms},
volume = {8},
number = {10},
pages = {},
pmid = {33066697},
issn = {2076-2607},
abstract = {A diverse and dynamic microbial community (known as microbiota) resides within the pig gastrointestinal tract (GIT). The microbiota contributes to host health and performance by mediating nutrient metabolism, stimulating the immune system, and providing colonization resistance against pathogens. Manipulation of gut microbiota to enhance growth performance and disease resilience in pigs has recently become an active area of research in an era defined by increasing scrutiny of antimicrobial use in swine production. In order to develop microbiota-targeted strategies, or to identify potential next-generation probiotic strains originating from the endogenous members of GIT microbiota in pigs, it is necessary to understand the role of key commensal members in host health. Many, though not all, correlative studies have associated members of the genus Prevotella with positive outcomes in pig production, including growth performance and immune response; therefore, a comprehensive review of the genus in the context of pig production is needed. In the present review, we summarize the current state of knowledge about the genus Prevotella in the intestinal microbial community of pigs, including relevant information from other animal species that provide mechanistic insights, and identify gaps in knowledge that must be addressed before development of Prevotella species as next-generation probiotics can be supported.},
}
@article {pmid33065340,
year = {2021},
author = {Jacquemyn, H and Pozo, MI and Álvarez-Pérez, S and Lievens, B and Fukami, T},
title = {Yeast-nectar interactions: metacommunities and effects on pollinators.},
journal = {Current opinion in insect science},
volume = {44},
number = {},
pages = {35-40},
doi = {10.1016/j.cois.2020.09.014},
pmid = {33065340},
issn = {2214-5753},
mesh = {Animals ; *Behavior, Animal ; Genetic Fitness ; Mycobiome ; Plant Nectar/*chemistry ; *Pollination ; *Yeasts ; },
abstract = {About 90% of all flowering plant species are pollinated by animals. Animals are attracted to flowers because they often provide food in the form of nectar and pollen. While floral nectar is assumed to be initially sterile, it commonly becomes colonized by yeasts after animals have visited the flowers. Although yeast communities in floral nectar appear simple, community assembly depends on a complex interaction between multiple factors. Yeast colonization has a significant effect on the scent of floral nectar, foraging behavior of insects and nectar consumption. Consumption of nectar colonized by yeasts has been shown to improve bee fitness, but effects largely depended on yeast species. Altogether, these results indicate that dispersal, colonization history and nectar chemistry strongly interact and have pronounced effects on yeast metacommunities and, as a result, on bee foraging behavior and fitness. Future research directions to better understand the dynamics of plant-microbe-pollinator interactions are discussed.},
}
@article {pmid33062716,
year = {2020},
author = {Almugadam, BS and Liu, Y and Chen, SM and Wang, CH and Shao, CY and Ren, BW and Tang, L},
title = {Alterations of Gut Microbiota in Type 2 Diabetes Individuals and the Confounding Effect of Antidiabetic Agents.},
journal = {Journal of diabetes research},
volume = {2020},
number = {},
pages = {7253978},
pmid = {33062716},
issn = {2314-6753},
mesh = {Adult ; Bacteria/classification ; Biodiversity ; Blood Glucose ; Case-Control Studies ; DNA/analysis ; Diabetes Mellitus, Type 2/*complications ; Faecalibacterium ; Feces/microbiology ; Female ; Fusobacterium ; Gastrointestinal Microbiome/*drug effects ; Glycated Hemoglobin/biosynthesis ; Humans ; Hypoglycemic Agents/*pharmacology ; Intestines ; Male ; Metformin/therapeutic use ; Microbiology ; Middle Aged ; RNA, Ribosomal, 16S/metabolism ; Risk ; Sudan/epidemiology ; },
abstract = {Type 2 diabetes is a leading cause of morbidity and a common risk of several disorders. Identifying the microbial ecology changes is essential for disease prediction, therapy, and prevention. Thus, our study is aimed at investigating the intestinal microbiota among healthy and type 2 diabetes individuals and exploring the effect of antidiabetic agents on gut bacterial flora. 24 type 2 diabetes (metformin, glimepiride, and nontherapeutic subgroups; N = 8) and 24 healthy control subjects were enrolled in this study, and intestinal bacterial microbiota was investigated by analyzing V3-V4 regions of 16S rRNA gene sequence. Numerous alterations were observed in the gut microbial community of diabetic individuals. These changes were characterized by a significant lowered abundance of Faecalibacterium, Fusobacterium, Dialister, and Elusimicrobium in the nontherapeutic subgroup compared to the healthy control group. Likewise, correlation analysis showed a substantial decline in gut microbiota richness and diversity with the duration of illness. Furthermore, antidiabetic agents restored to some extent the richness and diversity of gut microbiota and improved the abundance of many beneficial bacteria with a significant increase of Methanobrevibacter in the metformin subcategory compared to the nontherapeutic subgroup. In return, they decreased the abundance of some opportunistic pathogens. The findings of this study have added a novel understanding about the pathogenesis of the disease and the mechanisms underlying antidiabetic therapy, which are of potential interest for therapeutic lines and further studies.},
}
@article {pmid33059158,
year = {2021},
author = {Chique, C and Hynds, P and Burke, LP and Morris, D and Ryan, MP and O'Dwyer, J},
title = {Contamination of domestic groundwater systems by verotoxigenic escherichia coli (VTEC), 2003-2019: A global scoping review.},
journal = {Water research},
volume = {188},
number = {},
pages = {116496},
doi = {10.1016/j.watres.2020.116496},
pmid = {33059158},
issn = {1879-2448},
mesh = {*Groundwater ; Humans ; Prospective Studies ; *Shiga-Toxigenic Escherichia coli ; Water Supply ; *Waterborne Diseases ; },
abstract = {Verocytotoxin-producing E. coli (VTEC) are important agents of diarrhoeal disease in humans globally. As a noted waterborne disease, emphasis has been given to the study VTEC in surface waters, readily susceptible to microbial contamination. Conversely, the status of VTEC in potable groundwater sources, generally regarded as a "safe" drinking-water supply remains largely understudied. As such, this investigation presents the first scoping review seeking to determine the global prevalence of VTEC in groundwater supply sources intended for human consumption. Twenty-three peer-reviewed studies were identified and included for data extraction. Groundwater sample and supply detection rates (estimated 0.6 and 1.3%, respectively) indicate VTEC is infrequently present in domestic groundwater sources. However, where generic (fecal indicator) E. coli are present, the VTEC to E. coli ratio was found to be 9.9%, representing a latent health concern for groundwater consumers. Geographically, extracted data indicates higher VTEC detection rates in urban (5.4%) and peri‑urban (4.9%) environments than in rural areas (0.9%); however, this finding is confounded by the predominance of research studies in lower income regions. Climate trends indicate local environments classified as 'temperate' (14/554; 2.5%) and 'cold' (8/392; 2%) accounted for a majority of supply sources with VTEC present, with similar detection rates encountered among supplies sampled during periods typically characterized by 'high' precipitation (15/649; 2.3%). Proposed prevalence figures may find application in preventive risk-based catchment and groundwater quality management including development of Quantitative Microbial Risk Assessments (QMRA). Notwithstanding, to an extent, a large geographical disparity in available investigations, lack of standardized reporting, and bias in source selection, restrict the transferability of research findings. Overall, the mechanisms responsible for VTEC transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between hydrogeological and public health research. Key recommendations and guidelines are provided for prospective studies directed at increasingly integrative and multi-disciplinary research.},
}
@article {pmid33059136,
year = {2021},
author = {Ávila, C and García-Galán, MJ and Borrego, CM and Rodríguez-Mozaz, S and García, J and Barceló, D},
title = {New insights on the combined removal of antibiotics and ARGs in urban wastewater through the use of two configurations of vertical subsurface flow constructed wetlands.},
journal = {The Science of the total environment},
volume = {755},
number = {Pt 2},
pages = {142554},
doi = {10.1016/j.scitotenv.2020.142554},
pmid = {33059136},
issn = {1879-1026},
mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; Waste Disposal, Fluid ; *Wastewater/analysis ; *Wetlands ; },
abstract = {The occurrence and removal of 49 antibiotics and 11 selected antibiotic resistance genes (ARGs) were investigated in 2 vertical subsurface flow (VF) constructed wetlands (1.5 m[2] each): an unsaturated (UVF) unit and a partially saturated (SVF) unit (0.35 m saturated out of 0.8 m) operating in parallel and treating urban wastewater. Thirteen antibiotics were detected in influent wastewater, 6 of which were present in all samples. The SVF showed statistical significance on the removal of 4 compounds (namely ciprofloxacin, ofloxacin, pipemidic acid and azithromycin), suggesting that the wider range of pH and/or redox conditions of this configuration might promote the microbial degradation of some antibiotics. In contrast, the concentration of the latter (except pipemidic acid) and also clindamycin was higher in the effluent than in the influent of the UVF. Five ARGs were detected in influent wastewater, sul1 and sul2, blaTEM, ermB and qnrS. All of them were detected also in the biofilm of both wetlands, except qnrS. Average removal rates of ARGs showed no statistical differences between both wetland units, and ranged between 46 and 97% for sul1, 33 and 97% for sul2, 9 and 99% for ermB, 18 and 97% for qnrS and 11 and 98% for blaTEM.},
}
@article {pmid33054775,
year = {2020},
author = {Roussel, C and De Paepe, K and Galia, W and De Bodt, J and Chalancon, S and Leriche, F and Ballet, N and Denis, S and Alric, M and Van de Wiele, T and Blanquet-Diot, S},
title = {Spatial and temporal modulation of enterotoxigenic E. coli H10407 pathogenesis and interplay with microbiota in human gut models.},
journal = {BMC biology},
volume = {18},
number = {1},
pages = {141},
pmid = {33054775},
issn = {1741-7007},
mesh = {Colon, Ascending/microbiology ; Enterotoxigenic Escherichia coli/*pathogenicity/*physiology ; Escherichia coli Infections/*microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Ileum/microbiology ; Microbial Viability ; },
abstract = {BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) substantially contributes to the burden of diarrheal illnesses in developing countries. With the use of complementary in vitro models of the human digestive environment, TNO gastrointestinal model (TIM-1), and Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), we provided the first detailed report on the spatial-temporal modulation of ETEC H10407 survival, virulence, and its interplay with gut microbiota. These systems integrate the main physicochemical parameters of the human upper digestion (TIM-1) and simulate the ileum vs ascending colon microbial communities and luminal vs mucosal microenvironments, captured from six fecal donors (M-SHIME).<br><br>RESULTS: A loss of ETEC viability was noticed upon gastric digestion, while a growth renewal was found at the end of jejunal and ileal digestion. The remarkable ETEC mucosal attachment helped to maintain luminal concentrations above 6&#xa0;log10&#xa0;mL[-1] in the ileum and ascending colon up to 5&#x2009;days post-infection. Seven ETEC virulence genes were monitored. Most of them were switched on in the stomach and switched off in the TIM-1 ileal effluents and in a late post-infectious stage in the M-SHIME ascending colon. No heat-labile enterotoxin production was measured in the stomach in contrast to the ileum and ascending colon. Using 16S rRNA gene-based amplicon sequencing, ETEC infection modulated the microbial community structure of the ileum mucus and ascending colon lumen.<br><br>CONCLUSIONS: This study provides a better understanding of the interplay between ETEC and gastrointestinal cues and may serve to complete knowledge on ETEC pathogenesis and inspire novel prophylactic strategies for diarrheal diseases.},
}
@article {pmid33054212,
year = {2020},
author = {Li, Y and Wang, T and Camps-Arbestain, M and Suárez-Abelenda, M and Whitby, CP},
title = {Lime and/or Phosphate Application Affects the Stability of Soil Organic Carbon: Evidence from Changes in Quantity and Chemistry of the Soil Water-Extractable Organic Matter.},
journal = {Environmental science &amp; technology},
volume = {54},
number = {21},
pages = {13908-13916},
doi = {10.1021/acs.est.0c01341},
pmid = {33054212},
issn = {1520-5851},
mesh = {Calcium Compounds ; *Carbon ; Oxides ; Phosphates ; *Soil ; Water ; },
abstract = {The mechanisms by which lime and/or phosphate addition impacts the preservation of soil organic matter (OM) are poorly understood. We explored the changes in quantity and chemistry of water-extractable organic matter (WEOM) in the bulk soil and its heavy density fraction (>1.6 g/cm[3]) of an unmanaged C-rich volcanic soil caused by lime and/or phosphate application. The addition of lime or phosphate caused (i) a significant increase in the WEOM, along with a decrease in its C/N ratio and an increase in its aromaticity, and (ii) changes in the WEOM chemical composition, measured with pyrolysis-gas chromatography/mass spectrometry, this being most impacted by lime application. The combined effect of lime and phosphate addition on the quantity and chemistry of WEOM was larger than the effects of separate lime and phosphate additions. By comparing the response of the bulk soil and the heavy fraction, we infer that phosphate has a greater contribution to the destabilization of vulnerable particulate OM, while lime causes a comparable disruption in the particulate OM and that in the heavy fraction. These findings provide a mechanistic insight into the decreased OM stability after liming and/or P fertilizing Andosols. They have implications for designing climate-smart management practices for these soils.},
}
@article {pmid33051738,
year = {2021},
author = {Zhang, W and Wang, X and Li, Y and Liu, Z and Li, D and Wen, X and Feng, Y and Zhang, X},
title = {Pinewood Nematode Alters the Endophytic and Rhizospheric Microbial Communities of Pinus massoniana.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {807-817},
pmid = {33051738},
issn = {1432-184X},
support = {2018YFC1200400//National Key R &amp; D Program of China/ ; 31901315//Young Scientists Fund/ ; },
mesh = {Animals ; Bacteria/genetics ; China ; *Microbiota ; *Nematoda ; *Pinus ; },
abstract = {Pinewood nematode, Bursaphelenchus xylophilus, is one of the greatest threats to pine trees and is spreading all over the world. During the nematode's pathogenesis, plant microorganisms play important roles. However, many microbial communities, such as that in Pinus massoniana, a major host of B. xylophilus that is widely distributed in China, are not well studied, especially the fungal communities. Here, the endophytic and rhizospheric bacterial and fungal communities associated with healthy and B. xylophilus-infected P. massoniana were analyzed. The results showed that 7639 bacterial and 3108 fungal OTUs were annotated from samples of P. massoniana, the rhizosphere, and B. xylophilus. There were significant diversity differences of endophytic microbes between healthy and infected P. massoniana. The abundances of endophytic bacteria Paenibacillus, unidentified_Burkholderiaceae, Serratia, Erwinia, and Pseudoxanthomonas and fungi Penicillifer, Zygoascus, Kirschsteiniothelia, Cyberlindnera, and Sporothrix in infected pines were greater than those in healthy pines, suggesting an association of particular microbial abundances with the pathogenesis of B. xylophilus in pines. Meanwhile, the abundances of microbes of unidentified_Burkholderiaceae, Saitozyma, and Pestalotiopsis were greater and Acidothermus and Trichoderma were lower in the rhizosphere under infected pines than those under healthy pines and the differences might be caused by B. xylophilus-induced weakening of the health of pines. Our study explored the endophytic and rhizospheric microbial community changes potentially caused by B. xylophilus infection of pines.},
}
@article {pmid33049639,
year = {2021},
author = {Ni, N and Li, X and Yao, S and Shi, R and Kong, D and Bian, Y and Jiang, X and Song, Y},
title = {Biochar applications combined with paddy-upland rotation cropping systems benefit the safe use of PAH-contaminated soils: From risk assessment to microbial ecology.},
journal = {Journal of hazardous materials},
volume = {404},
number = {Pt A},
pages = {124123},
doi = {10.1016/j.jhazmat.2020.124123},
pmid = {33049639},
issn = {1873-3336},
mesh = {Charcoal ; Humans ; *Oryza ; *Polycyclic Aromatic Hydrocarbons/analysis ; Risk Assessment ; Rotation ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {This study aimed to establish a method allowing the safe use of polycyclic aromatic hydrocarbon (PAH)-contaminated soils through the combination of biochar applications and different cropping systems. The impact of biochar applications under different cropping systems on the human health risks of PAHs and soil microbiology was elucidated. The residual PAHs were the lowest in rhizosphere soils amended with 2% corn straw-derived biochar pyrolyzed at 300 °C (CB300) under the paddy-upland rotation cropping (PURC) system. Human health risks resulting from the ingestion of PAH-contaminated carrot roots / rice grains under the PURC system were significantly lower than those under continuous upland cropping systems. The greatest diversity, richness and network complexity of soil microbial communities occurred under the PURC system combined with the 2% CB300 treatment. Soil microbial functions associated with soil health and PAH biodegradation were enhanced under this strategy, while the pathogen group was inhibited. Primarily owing to its high sorption capacity, bamboo-derived biochar pyrolyzed at 700 °C realized in the reduction of PAHs, but weakly influenced shifts in soil microbial communities. Overall, the combination of PURC systems and low-temperature-pyrolyzed nutrient-rich biochar could efficiently reduce the human health risks of PAHs and improve soil microbial ecology in agricultural fields.},
}
@article {pmid33047413,
year = {2021},
author = {Dini-Andreote, F and Kowalchuk, GA and Prosser, JI and Raaijmakers, JM},
title = {Towards meaningful scales in ecosystem microbiome research.},
journal = {Environmental microbiology},
volume = {23},
number = {1},
pages = {1-4},
doi = {10.1111/1462-2920.15276},
pmid = {33047413},
issn = {1462-2920},
}
@article {pmid33043868,
year = {2020},
author = {Seto, M and Iwasa, Y},
title = {Microbial material cycling, energetic constraints and ecosystem expansion in subsurface ecosystems.},
journal = {Proceedings. Biological sciences},
volume = {287},
number = {1931},
pages = {20200610},
pmid = {33043868},
issn = {1471-2954},
mesh = {*Ecological and Environmental Phenomena ; *Ecosystem ; *Environmental Microbiology ; },
abstract = {To harvest energy from chemical reactions, microbes engage in diverse catabolic interactions that drive material cycles in the environment. Here, we consider a simple mathematical model for cycling reactions between alternative forms of an element (A and Ae), where reaction 1 converts A to Ae and reaction 2 converts Ae to A. There are two types of microbes: type 1 microbes harness reaction 1, and type 2 microbes harness reaction 2. Each type receives its own catabolic resources from the other type and provides the other type with the by-products as the catabolic resources. Analyses of the model show that each type increases its steady-state abundance in the presence of the other type. The flux of material flow becomes faster in the presence of microbes. By coupling two catabolic reactions, types 1 and 2 can also expand their realized niches through the abundant resource premium, the effect of relative quantities of products and reactants on the available chemical energy, which is especially important for microbes under strong energetic limitations. The plausibility of mutually beneficial interactions is controlled by the available chemical energy (Gibbs energy) of the system. We conclude that mutualistic catabolic interactions can be an important factor that enables microbes in subsurface ecosystems to increase ecosystem productivity and expand the ecosystem.},
}
@article {pmid33042180,
year = {2020},
author = {Otlewska, A and Migliore, M and Dybka-Stępień, K and Manfredini, A and Struszczyk-Świta, K and Napoli, R and Białkowska, A and Canfora, L and Pinzari, F},
title = {When Salt Meddles Between Plant, Soil, and Microorganisms.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {553087},
pmid = {33042180},
issn = {1664-462X},
abstract = {In extreme environments, the relationships between species are often exclusive and based on complex mechanisms. This review aims to give an overview of the microbial ecology of saline soils, but in particular of what is known about the interaction between plants and their soil microbiome, and the mechanisms linked to higher resistance of some plants to harsh saline soil conditions. Agricultural soils affected by salinity is a matter of concern in many countries. Soil salinization is caused by readily soluble salts containing anions like chloride, sulphate and nitrate, as well as sodium and potassium cations. Salinity harms plants because it affects their photosynthesis, respiration, distribution of assimilates and causes wilting, drying, and death of entire organs. Despite these life-unfavorable conditions, saline soils are unique ecological niches inhabited by extremophilic microorganisms that have specific adaptation strategies. Important traits related to the resistance to salinity are also associated with the rhizosphere-microbiota and the endophytic compartments of plants. For some years now, there have been studies dedicated to the isolation and characterization of species of plants' endophytes living in extreme environments. The metabolic and biotechnological potential of some of these microorganisms is promising. However, the selection of microorganisms capable of living in association with host plants and promoting their survival under stressful conditions is only just beginning. Understanding the mechanisms of these processes and the specificity of such interactions will allow us to focus our efforts on species that can potentially be used as beneficial bioinoculants for crops.},
}
@article {pmid33040164,
year = {2021},
author = {Wisnoski, NI and Lennon, JT},
title = {Microbial community assembly in a multi-layer dendritic metacommunity.},
journal = {Oecologia},
volume = {195},
number = {1},
pages = {13-24},
pmid = {33040164},
issn = {1432-1939},
support = {DEB-1442246//National Science Foundation (US)/ ; W911NF-14-1-0411//Army Research Office/ ; },
mesh = {*Ecosystem ; *Microbiota ; Phylogeny ; },
abstract = {A major goal of metacommunity ecology is to infer the local- and regional-scale processes that underlie community assembly. In dendritic ecological networks, branching patterns and directional flow can alter the balance between local and regional factors during assembly. Vertical habitat structure may further affect community assembly in dendritic metacommunities. In this study, we analyzed the bacterial metacommunity of a fifth-order mountain stream network to assess differences in community assembly (1) between planktonic and benthic habitats, (2) across spatial scales, and (3) between headwater and downstream regions of the network. Using taxonomic and phylogenetic null modeling, we found habitat-specific spatial patterns of community assembly across the dendritic network. Compositional differences between planktonic and benthic communities were maintained by variable selection, but we also found evidence of local dispersal limitation between the two habitats. Planktonic community assembly was scale dependent, transitioning from homogeneous selection at local scales to variable selection at regional scales, while benthic community assembly was less scale dependent. Variable selection structured headwaters in both habitat types, but downstream communities were primarily structured by homogeneous selection, especially in sediments. Taken together, our results show that vertical habitat structure contributes to the scale-dependent processes of community assembly across the dendritic metacommunity.},
}
@article {pmid33039899,
year = {2020},
author = {Douterelo, I and Dutilh, BE and Calero, C and Rosales, E and Martin, K and Husband, S},
title = {Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks.},
journal = {Water research},
volume = {187},
number = {},
pages = {116416},
doi = {10.1016/j.watres.2020.116416},
pmid = {33039899},
issn = {1879-2448},
mesh = {Biofilms ; *Drinking Water ; Phosphates ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Water Quality ; Water Supply ; },
abstract = {Phosphate is routinely dosed to ensure regulatory compliance for lead in drinking water distribution systems. Little is known about the impact of the phosphate dose on the microbial ecology in these systems and in particular the endemic biofilms. Disturbance of the biofilms and embedded material in distribution can cause regulatory failures for turbidity and metals. To investigate the impact of phosphate on developing biofilms, pipe wall material from four independent pipe sections was mobilised and collected using two twin-flushing operations a year apart in a chlorinated UK network pre- and post-phosphate dosing. Intensive monitoring was undertaken, including turbidity and water physico-chemistry, traditional microbial culture-based indicators, and microbial community structure via sequencing the 16S rRNA gene for bacteria and the ITS2 gene for fungi. Whole metagenome sequencing was used to study shifts in functional characteristics following the addition of phosphate. As an operational consequence, turbidity responses from the phosphate-enriched water were increased, particularly from cast iron pipes. Differences in the taxonomic composition of both bacteria and fungi were also observed, emphasising a community shift towards microorganisms able to use or metabolise phosphate. Phosphate increased the relative abundance of bacteria such as Pseudomonas, Paenibacillus, Massilia, Acinetobacter and the fungi Cadophora, Rhizophagus and Eupenicillium. Whole metagenome sequencing showed with phosphate a favouring of sequences related to Gram-negative bacterium type cell wall function, virions and thylakoids, but a reduction in the number of sequences associated to vitamin binding, methanogenesis and toxin biosynthesis. With current faecal indicator tests only providing risk detection in bulk water samples, this work improves understanding of how network changes effect microbial ecology and highlights the potential for new approaches to inform future monitoring or control strategies to protect drinking water quality.},
}
@article {pmid33039841,
year = {2021},
author = {Alloul, A and Muys, M and Hertoghs, N and Kerckhof, FM and Vlaeminck, SE},
title = {Cocultivating aerobic heterotrophs and purple bacteria for microbial protein in sequential photo- and chemotrophic reactors.},
journal = {Bioresource technology},
volume = {319},
number = {},
pages = {124192},
doi = {10.1016/j.biortech.2020.124192},
pmid = {33039841},
issn = {1873-2976},
mesh = {Kinetics ; *Proteobacteria ; Rhodobacter ; *Rhodopseudomonas ; Wastewater ; },
abstract = {Aerobic heterotrophic bacteria (AHB) and purple non-sulfur bacteria (PNSB) are typically explored as two separate types of microbial protein, yet their properties as respectively a bulk and added-value feed ingredient make them appealing for combined use. The feasibility of cocultivation in a sequential photo- and chemotrophic approach was investigated. First, mapping the chemotrophic growth kinetics for four Rhodobacter, Rhodopseudomonas and Rhodospirillum species on different carbon sources showed a preference for fructose (µmax 2.4-3.9 d[-1] 28 °C; protein 36-59%DW). Secondly, a continuous photobioreactor inoculated with Rhodobacter capsulatus (VFA as C-source) delivered the starter culture for an aerobic batch reactor (fructose as C-source). This two-stage system showed an improved nutritional quality compared to AHB production: higher protein content (45-71%DW), more attractive amino/fatty acid profile and contained up to 10% PNSB. The findings strengthen protein production with cocultures and might enable the implementation of the technology for resource recovery on streams such as wastewater.},
}
@article {pmid33037304,
year = {2020},
author = {De Rudder, C and Garcia-Tímermans, C and De Boeck, I and Lebeer, S and Van de Wiele, T and Calatayud Arroyo, M},
title = {Lacticaseibacillus casei AMBR2 modulates the epithelial barrier function and immune response in a donor-derived nasal microbiota manner.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {16939},
pmid = {33037304},
issn = {2045-2322},
mesh = {Cells, Cultured ; Cytokines/immunology ; Epithelial Cells/immunology/microbiology ; Epithelium ; Host Microbial Interactions/immunology ; Humans ; Immunity/immunology ; Inflammation/immunology/microbiology ; Lacticaseibacillus casei/*immunology ; Macrophages/immunology ; Microbiota/*immunology ; Nose/immunology/*microbiology ; Respiratory Mucosa/*immunology/*microbiology ; },
abstract = {Live biotherapeutic products (LBP) are emerging as alternative treatment strategies for chronic rhinosinusitis. The selection of interesting candidate LBPs often involves model systems that do not include the polymicrobial background (i.e. the host microbiota) in which they will be introduced. Here, we performed a screening in a simplified model system of upper respiratory epithelium to assess the effect of nasal microbiota composition on the ability to attach and grow of a potential LBP, Lacticaseibacillus casei AMBR2, in this polymicrobial background. After selecting the most permissive and least permissive donor, L. casei AMBR2 colonisation in their respective polymicrobial backgrounds was assessed in more physiologically relevant model systems. We examined cytotoxicity, epithelial barrier function, and cytokine secretion, as well as bacterial cell density and phenotypic diversity in differentiated airway epithelium based models, with or without macrophage-like cells. L. casei AMBR2 could colonize in the presence of both selected donor microbiota and increased epithelial barrier resistance in presence of donor-derived nasal bacteria, as well as anti-inflammatory cytokine secretion in the presence of macrophage-like cells. This study highlights the potential of L. casei AMBR2 as LBP and the necessity to employ physiologically relevant model systems to investigate host-microbe interaction in LBP research.},
}
@article {pmid33033618,
year = {2020},
author = {Medina, WRM and Eramo, A and Tu, M and Fahrenfeld, NL},
title = {Sewer biofilm microbiome and antibiotic resistance genes as function of pipe material, source of microbes, and disinfection: field and laboratory studies.},
journal = {Environmental science : water research &amp; technology},
volume = {6},
number = {8},
pages = {2122-2137},
pmid = {33033618},
issn = {2053-1400},
support = {R25 GM058389/GM/NIGMS NIH HHS/United States ; },
abstract = {Wastewater systems are recognized pathways for the spread of antibiotic resistant bacteria, but relatively little is known about the microbial ecology of the sewer environment. Sewer biofilm colonization by antibiotic resistance gene (ARG) carrying bacteria may impact interpretations of sewage epidemiology data, water quality during sewer overflows, and hazard to utility workers. The objectives of this research were to evaluate the (1) microbiome of real and simulated sewer biofilms and their potential to accumulate ARGs and (2) susceptibility of simulated sewer biofilms to bleach disinfection. First, biofilm samples were collected from sewer municipal systems. Next, an annular biofilm reactor was used to simulate the sewer environment while controlling the pipe material (concrete vs. PVC). The reactor was operated either as fed semi-batch with sewer sediment and synthetic wastewater (Sed-SB) or fed with a continuous flow of raw sewage (WW-CF). The abundance of ARGs, human fecal marker HF183, and 16S rRNA gene copies in these biofilm samples was measured with qPCR. Amplicon sequencing was performed to compare the prokaryotic diversity between samples. Finally, the susceptibility of reactor biofilm to a 4.6% bleach disnfection protocol was evaluated using viability qPCR and amplicon sequencing. Field and WW-CF biofilms contained the most ARG copies and the microbial community compositions varied between the different biofilm samples (field, Sed-SB, and WW-CF). Pipe material did not affect the abundance of ARGs in the reactor samples. However, log removal following bleach treatment suggested that the biofilm grown on PVC surface was primarily dislodged from the surface by the bleach treatment whereas more bacteria were lysed within the biofilm that remained on the concrete surface. Viable bacteria carrying ARGs were observed following 10 minutes of treatment. This study showed that sewer biofilms can accumulate bacteria carrying ARGs and that while bleach can reduce sewer biofilm density, the protocol tested here will not completely remove the biofilms.},
}
@article {pmid33033140,
year = {2020},
author = {Peruzzo, A and Salerno, B and Tiengo, A and Petrin, S and Barco, L and Losasso, C and Orsini, M},
title = {Genome Sequence of a Persistent Campylobacter jejuni Strain, 2016-IZSVE-19-111250.},
journal = {Microbiology resource announcements},
volume = {9},
number = {41},
pages = {},
pmid = {33033140},
issn = {2576-098X},
abstract = {In this report, we present the whole-genome sequence of a Campylobacter jejuni strain isolated recursively for the last 3 years from an Italian poultry farm.},
}
@article {pmid33032584,
year = {2020},
author = {Zhu, L and Xu, F and Wan, W and Yu, B and Tang, L and Yang, Y and Du, Y and Chen, Z and Xu, H},
title = {Correction to: Gut microbial characteristics of adult patients with allergy rhinitis.},
journal = {Microbial cell factories},
volume = {19},
number = {1},
pages = {192},
pmid = {33032584},
issn = {1475-2859},
abstract = {An amendment to this paper has been published and can be accessed via the original article.},
}
@article {pmid33032128,
year = {2021},
author = {Zhang, S and Xia, X and Ke, Y and Song, S and Shen, Z and Cheung, S and Liu, H},
title = {Population dynamics and interactions of Noctiluca scintillans and Mesodinium rubrum during their successive blooms in a subtropical coastal water.},
journal = {The Science of the total environment},
volume = {755},
number = {Pt 1},
pages = {142349},
doi = {10.1016/j.scitotenv.2020.142349},
pmid = {33032128},
issn = {1879-1026},
mesh = {*Dinoflagellida ; Environmental Monitoring ; *Phytoplankton ; Population Dynamics ; Water ; },
abstract = {A time series field survey were conducted in Port Shelter, a subtropical coastal water in NW Pacific, beginning before the onset of a chain of Noctiluca scintillans and/or Mesodinium rubrum blooms, and ending after the blooms had declined. At the first mixed bloom stage, seed of N. scintillans and the consequent outbreak of both N. scintillans and M. rubrum were largely due to the physical forcing. Plenty food supply and their different feeding habits supported N. scintillans and M. rubrum to bloom massively and concomitantly. Following that, there was a small N. scintillans bloom followed by a small crest of M. rubrum. Their initiation and scale were mainly affected by limited food supply and/or the inferior food source. Sudden change of wind from mild northeast wind to strong southeast wind might contribute to the termination of N. scintillans bloom. Finally, physical accumulation was the most important driving factors of the formation and dispersal of the third and largest bloom of N. scintillans. Formation of these bloom events may involve vertical migration and/or the concentrating mechanism of M. rubrum and N. scintillans. Meanwhile, biotic interactions such as mutual supportive relationship between N. scintillans and M. rubrum, and O. hongkongense fed on the progametes of N. scintillans, as well as other abiotic factors like seawater temperature and rainfall, also play important roles in this series of bloom events. Our findings have important implications for coastal zones worldwide, which are affected recurrently by these two ubiquitous red tide-forming species.},
}
@article {pmid33031481,
year = {2020},
author = {Klaps, J and de Vega, C and Herrera, CM and Junker, RR and Lievens, B and Álvarez-Pérez, S},
title = {Candida metrosideri pro tempore sp. nov. and Candida ohialehuae pro tempore sp. nov., two antifungal-resistant yeasts associated with Metrosideros polymorpha flowers in Hawaii.},
journal = {PloS one},
volume = {15},
number = {10},
pages = {e0240093},
pmid = {33031481},
issn = {1932-6203},
mesh = {Amphotericin B/pharmacology ; Antifungal Agents/pharmacology ; Candida/*classification/drug effects/genetics/isolation &amp; purification ; Drug Resistance, Fungal ; Flowers/microbiology ; Hawaii ; Microbial Sensitivity Tests ; Myrtaceae/*microbiology ; Phenotype ; Phylogeny ; RNA, Ribosomal/classification/genetics/metabolism ; },
abstract = {Flowers produce an array of nutrient-rich exudates in which microbes can thrive, making them hotspots for microbial abundance and diversity. During a diversity study of yeasts inhabiting the flowers of Metrosideros polymorpha (Myrtaceae) in the Hawai'i Volcanoes National Park (HI, USA), five isolates were found to represent two novel species. Morphological and physiological characterization, and sequence analysis of the small subunit ribosomal RNA (rRNA) genes, the D1/D2 domains of the large subunit rRNA genes, the internal transcribed spacer (ITS) regions, and the genes encoding the largest and second largest subunits of the RNA polymerase II (RPB1 and RPB2, respectively), classified both species in the family Metschnikowiaceae, and we propose the names Candida metrosideri pro tempore sp. nov. (JK22T = CBS 16091 = MUCL 57821) and Candida ohialehuae pro tempore sp. nov. (JK58.2T = CBS 16092 = MUCL 57822) for such new taxa. Both novel Candida species form a well-supported subclade in the Metschnikowiaceae containing species associated with insects, flowers, and a few species of clinical importance. The ascosporic state of the novel species was not observed. The two novel yeast species showed elevated minimum inhibitory concentrations to the antifungal drug amphotericin B (>4 μg/mL). The ecology and phylogenetic relationships of C. metrosideri and C. ohialehuae are also discussed.},
}
@article {pmid33027736,
year = {2020},
author = {Dettling, A and Wedel, C and Huptas, C and Hinrichs, J and Scherer, S and Wenning, M},
title = {High counts of thermophilic spore formers in dairy powders originate from persisting strains in processing lines.},
journal = {International journal of food microbiology},
volume = {335},
number = {},
pages = {108888},
doi = {10.1016/j.ijfoodmicro.2020.108888},
pmid = {33027736},
issn = {1879-3460},
mesh = {Animals ; Colony Count, Microbial ; Dairy Products/*microbiology ; Endospore-Forming Bacteria/classification/genetics/*isolation &amp; purification ; *Food Handling ; Food Microbiology ; Genome, Bacterial/genetics ; Germany ; Milk/microbiology ; Spores, Bacterial/classification/genetics/*isolation &amp; purification ; },
abstract = {During the last decades, thermophilic spore counts became a very important quality parameter for manufacturers with regard to powdered dairy products. Low-spore count powders are highly demanded but challenging to produce when high production volume and long process times are intended. In this study a detailed monitoring of microbial levels in three skim milk powder plants was conducted. Anoxybacillus flavithermus was found to be primarily responsible for increased spore levels with increasing spore numbers being detected after 6-8 h already during initial processing steps. Simultaneously, the species composition shifted from a diverse bulk tank milk microbiota where different Bacillus species represented around 90% of the thermophilic bacteria to a dominance of A. flavithermus in the end product. The analysis of A. flavithermus isolates from different powder batches with RAPD PCR revealed recurring patterns in each of the eight German manufacturers sampled over several months. The high relatedness of isolates exhibiting identical RAPD patterns was exemplified by cgMLST based on whole genome sequences. We assume that A. flavithermus strains persisted in production plants and were not eliminated by cleaning. It is concluded that such persisting strains recurrently recontaminated subsequent powder productions. The data highlight that a targeted optimization of cleaning and disinfection procedures is the most promising measure to effectively reduce thermophilic spore counts in German dairy powders.},
}
@article {pmid33026073,
year = {2021},
author = {Sauvaitre, T and Etienne-Mesmin, L and Sivignon, A and Mosoni, P and Courtin, CM and Van de Wiele, T and Blanquet-Diot, S},
title = {Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections.},
journal = {FEMS microbiology reviews},
volume = {45},
number = {2},
pages = {},
doi = {10.1093/femsre/fuaa052},
pmid = {33026073},
issn = {1574-6976},
mesh = {Dietary Fiber/*metabolism ; Gastrointestinal Diseases/*prevention &amp; control ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestines/*microbiology ; Mucus/*metabolism ; },
abstract = {The human gut is inhabited by a large variety of microorganims involved in many physiological processes and collectively referred as to gut microbiota. Disrupted microbiome has been associated with negative health outcomes and especially could promote the onset of enteric infections. To sustain their growth and persistence within the human digestive tract, gut microbes and enteric pathogens rely on two main polysaccharide compartments, namely dietary fibers and mucus carbohydrates. Several evidences suggest that the three-way relationship between gut microbiota, dietary fibers and mucus layer could unravel the capacity of enteric pathogens to colonise the human digestive tract and ultimately lead to infection. The review starts by shedding light on similarities and differences between dietary fibers and mucus carbohydrates structures and functions. Next, we provide an overview of the interactions of these two components with the third partner, namely, the gut microbiota, under health and disease situations. The review will then provide insights into the relevance of using dietary fibers interventions to prevent enteric infections with a focus on gut microbial imbalance and impaired-mucus integrity. Facing the numerous challenges in studying microbiota-pathogen-dietary fiber-mucus interactions, we lastly describe the characteristics and potentialities of currently available in vitro models of the human gut.},
}
@article {pmid33025063,
year = {2021},
author = {Gomard, Y and Flores, O and Vittecoq, M and Blanchon, T and Toty, C and Duron, O and Mavingui, P and Tortosa, P and McCoy, KD},
title = {Changes in Bacterial Diversity, Composition and Interactions During the Development of the Seabird Tick Ornithodoros maritimus (Argasidae).},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {770-783},
pmid = {33025063},
issn = {1432-184X},
support = {ESPEVEC (ANR blanc ANR-13-BSV7-0018-01)//Agence Nationale de la Recherche/ ; DISTIC//Labex CeMEB (Centre M&#xe9;diterran&#xe9;en de l'Environnement et de la Biodiversit&#xe9;)/ ; },
mesh = {Animals ; *Argasidae ; Birds ; Female ; Male ; *Ornithodoros ; RNA, Ribosomal, 16S/genetics ; *Rickettsia/genetics ; },
abstract = {Characterising within-host microbial interactions is essential to understand the drivers that shape these interactions and their consequences for host ecology and evolution. Here, we examined the bacterial microbiota hosted by the seabird soft tick Ornithodoros maritimus (Argasidae) in order to uncover bacterial interactions within ticks and how these interactions change over tick development. Bacterial communities were characterised through next-generation sequencing of the V3-V4 hypervariable region of the bacterial 16S ribosomal RNA gene. Bacterial co-occurrence and co-exclusion were determined by analysing networks generated from the metagenomic data obtained at each life stage. Overall, the microbiota of O. maritimus was dominated by four bacterial genera, namely Coxiella, Rickettsia, Brevibacterium and Arsenophonus, representing almost 60% of the reads. Bacterial diversity increased over tick development, and adult male ticks showed higher diversity than did adult female ticks. Bacterial networks showed that co-occurrence was more frequent than co-exclusion and highlighted substantial shifts across tick life stages; interaction networks changed from one stage to the next with a steady increase in the number of interactions through development. Although many bacterial interactions appeared unstable across life stages, some were maintained throughout development and were found in both sexes, such as Coxiella and Arsenophonus. Our data support the existence of a few stable interactions in O. maritimus ticks, on top of which bacterial taxa accumulate from hosts and/or the environment during development. We propose that stable associations delineate core microbial interactions, which are likely to be responsible for key biological functions.},
}
@article {pmid33025062,
year = {2021},
author = {Baeza, N and Mercade, E},
title = {Relationship Between Membrane Vesicles, Extracellular ATP and Biofilm Formation in Antarctic Gram-Negative Bacteria.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {645-656},
pmid = {33025062},
issn = {1432-184X},
support = {CTQ2014-59632-R//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; BES-2015-074582//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2014SGR1017//Departament d'Innovaci&#xf3;, Universitats i Empresa, Generalitat de Catalunya/ ; },
mesh = {Adenosine Triphosphate ; Antarctic Regions ; Biofilms ; *Extracellular Vesicles ; Gram-Negative Bacteria ; *Shewanella ; },
abstract = {Biofilms offer a safe environment that favors bacterial survival; for this reason, most pathogenic and environmental bacteria live integrated in biofilm communities. The development of biofilms is complex and involves many factors, which need to be studied in order to understand bacterial behavior and control biofilm formation when necessary. We used a collection of cold-adapted Antarctic Gram-negative bacteria to study whether their ability to form biofilms is associated with a capacity to produce membrane vesicles and secrete extracellular ATP. In most of the studied strains, no correlation was found between biofilm formation and these two factors. Only Shewanella vesiculosa M7[T] secreted high levels of extracellular ATP, and its membrane vesicles caused a significant increase in the speed and amount of biofilm formation. In this strain, an important portion of the exogenous ATP was contained in membrane vesicles, where it was protected from apyrase treatment. These results confirm that ATP influences biofilm formation. Although the role of extracellular ATP in prokaryotes is still not well understood, the metabolic cost of its production suggests it has an important function, such as a role in biofilm formation. Thus, the liberation of extracellular ATP through membrane vesicles and its function deserve further study.},
}
@article {pmid33025061,
year = {2021},
author = {Boraks, A and Plunkett, GM and Doro, TM and Alo, F and Sam, C and Tuiwawa, M and Ticktin, T and Amend, AS},
title = {Scale-Dependent Influences of Distance and Vegetation on the Composition of Aboveground and Belowground Tropical Fungal Communities.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {874-883},
pmid = {33025061},
issn = {1432-184X},
support = {1555793//National Science Foundation (US)/ ; 1555657//National Science Foundation/ ; },
mesh = {Biodiversity ; *Ecosystem ; Fungi/genetics ; *Mycobiome ; Soil Microbiology ; Trees ; },
abstract = {Fungi provide essential ecosystem services and engage in a variety of symbiotic relationships with trees. In this study, we investigate the spatial relationship of trees and fungi at a community level. We characterized the spatial dynamics for above- and belowground fungi using a series of forest monitoring plots, at nested spatial scales, located in the tropical South Pacific, in Vanuatu. Fungal communities from different habitats were sampled using metagenomic analysis of the nuclear ribosomal ITS1 region. Fungal communities exhibited strong distance-decay of similarity across our entire sampling range (3-110,000 m) and also at small spatial scales (< 50 m). Unexpectedly, this pattern was inverted at an intermediate scale (3.7-26 km). At large scales (80-110 km), belowground and aboveground fungal communities responded inversely to increasing geographic distance. Aboveground fungal community turnover (beta diversity) was best explained, at all scales, by geographic distance. In contrast, belowground fungal community turnover was best explained by geographic distance at small scales and tree community composition at large scales. Fungal communities from various habitats respond differently to the influences of habitat and geographic distance. At large geographic distances (80-110 km), community turnover for aboveground fungi is better explained by spatial distance, whereas community turnover for belowground fungi is better explained by plant community turnover. Future syntheses of spatial dynamics among fungal communities must explicitly consider geographic scale to appropriately contextualize community turnover.},
}
@article {pmid33025060,
year = {2021},
author = {Fernandes, NM and Campello-Nunes, PH and Paiva, TS and Soares, CAG and Silva-Neto, ID},
title = {Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {630-643},
pmid = {33025060},
issn = {1432-184X},
support = {E-26/202.325/2018//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; E-26/202.326/2018//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 426648/2016-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {*Ciliophora/genetics ; *Ecosystem ; Forests ; High-Throughput Nucleotide Sequencing ; Phylogeny ; },
abstract = {Rainforest aquatic ecosystems include complex habitats with scarce information on their unicellular eukaryote diversity and community structure. We have investigated the diversity of ciliates in freshwater and brackish environments along the Brazilian Atlantic Forest, based on the hypervariable V4 region of the 18S-rDNA obtained by high-throughput DNA sequencing. Our analyses detected 409 ciliate taxonomic units (OTUs), mostly attributed to the classes Oligohymenophorea and Spirotrichea. A total of 11 classes, 12 subclasses, 112 genera, and 144 species were reported. We found the following: (a) the ciliate communities are more diverse in freshwater- than in Atlantic Forest-associated brackish environments; (b) the ciliate communities are composed by a small amount of highly abundant OTUs, but a high number of low-abundant or rare OTUs; (c) nearly one-third of the ciliate OTUs share less than 97% sequence identity to reference sequences and (d) phylogenetic inference supports the hypothesis that the V4 region of the Ciliophora 18S-rDNA is a suitable marker for accurate evolutionary inferences at class level. Our results showed that a considerable fraction of the HTS-detected diversity of ciliates from Brazilian Atlantic Forest is not represented in the currently available molecular databases.},
}
@article {pmid33024291,
year = {2021},
author = {Giguere, AT and Eichorst, SA and Meier, DV and Herbold, CW and Richter, A and Greening, C and Woebken, D},
title = {Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils.},
journal = {The ISME journal},
volume = {15},
number = {2},
pages = {363-376},
pmid = {33024291},
issn = {1751-7370},
support = {P 26392/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Acidobacteria/metabolism ; Hydrogen ; *Hydrogenase/genetics/metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; },
abstract = {Significant rates of atmospheric dihydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.},
}
@article {pmid33022257,
year = {2020},
author = {Koskella, B},
title = {The phyllosphere.},
journal = {Current biology : CB},
volume = {30},
number = {19},
pages = {R1143-R1146},
doi = {10.1016/j.cub.2020.07.037},
pmid = {33022257},
issn = {1879-0445},
mesh = {Bacteria/classification/*growth &amp; development ; *Biodiversity ; *Ecosystem ; *Host Microbial Interactions ; *Microbiota ; Plant Leaves/*microbiology ; Plants/*microbiology ; Soil Microbiology ; },
abstract = {There is longstanding interest in studying microbial communities below ground, while little attention has historically been paid to the above ground portions of plants (the phyllosphere). The phyllosphere has been estimated to make up around 60% of the biomass across all taxa on Earth, making it a key habitat for microbial organisms. The more we study these complex and dynamic communities, the more we come to realize their importance to the health of plant hosts. Overall, the phyllosphere is proving to be both an important microbial habitat and a tractable model system for asking questions in microbial ecology and evolution.},
}
@article {pmid33021904,
year = {2021},
author = {Taparia, T and Hendrix, E and Hendriks, M and Krijger, M and de Boer, W and van der Wolf, J},
title = {Comparative Studies on the Disease Prevalence and Population Dynamics of Ginger Blotch and Brown Blotch Pathogens of Button Mushrooms.},
journal = {Plant disease},
volume = {105},
number = {3},
pages = {542-547},
doi = {10.1094/PDIS-06-20-1260-RE},
pmid = {33021904},
issn = {0191-2917},
mesh = {Agaricus ; Europe ; *Zingiber officinale ; Population Dynamics ; Prevalence ; Pseudomonas ; },
abstract = {Bacterial blotch is one of the most economically important diseases of button 'mushroom. Knowledge of mechanisms of disease expression, inoculum thresholds, and disease management is limited to the most well-known pathogen, Pseudomonas tolaasii. Recent outbreaks in Europe have been attributed to 'P. gingeri' and P. salomonii for ginger and brown blotch, respectively. Information about their identity, infection dynamics, and pathogenicity is largely lacking. The disease pressure in an experimental mushroom cultivation facility was evaluated for 'P. gingeri' and P. salomonii over varying inoculation densities, casing soil types, environmental humidity, and cultivation cycles. The pathogen population structures in the casing soils were simultaneously tracked across the cropping cycle using highly specific and sensitive TaqMan-quantitative PCR assays. 'P. gingeri' caused disease outbreaks at lower inoculum thresholds (10[4] CFU/g) in the soil than P. salomonii (10[5] CFU/g). Ginger blotch generically declined in later harvest cycles, although brown blotch did not. Casing soils were differentially suppressive to blotch diseases, based on their composition and supplementation. Endemic pathogen populations increased across the cultivation cycle although the inoculated pathogen populations were consistent between the first and second flush. In conclusion, 'P. gingeri' and P. salomonii have unique infection and population dynamics that vary over soil types. Their endemic populations are also differently abundant in peat-based casing soils. This knowledge is essential for interpreting diagnostic results from screening mushroom farms and designing localized disease control strategies.},
}
@article {pmid33021677,
year = {2021},
author = {Kolátková, V and Čepička, I and Hoffman, R and Vohník, M},
title = {Marinomyxa Gen. Nov. Accommodates Gall-Forming Parasites of the Tropical to Subtropical Seagrass Genus Halophila and Constitutes a Novel Deep-Branching Lineage Within Phytomyxea (Rhizaria: Endomyxa).},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {673-686},
pmid = {33021677},
issn = {1432-184X},
support = {1308218//Grantov&#xe1; Agentura, Univerzita Karlova/ ; },
mesh = {Animals ; *Hydrocharitaceae ; *Parasites ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; *Rhizaria ; },
abstract = {Marine representatives of Phytomyxea (SAR: Rhizaria: Endomyxa), a peculiar class of obligate endobiotic parasites, are a greatly understudied ecological group of protists infecting many algal, diatom, and seagrass species. Very little is known about the actual diversity, ecology, and pathogenic potential of these organisms and their taxonomic treatment in many cases follows outdated morphotaxonomic concepts. Here we focused on resolving the phylogenetic relations of the phytomyxean parasites of the widespread seagrass genus Halophila. We report the first finding of Plasmodiophora halophilae, the parasite of ovate-leaf Halophila species, after more than 100 years since its original description in 1913. We provide additional information on its anatomy, morphology, distribution, and host range, together with a phylogenetic evidence that it is congeneric with the recently rediscovered species infecting the invasive seagrass Halophila stipulacea in the Mediterranean Sea. Despite the previously hypothesized affiliation of the latter to Tetramyxa, our phylogenetic analyses of the 18S rRNA gene place Tetramyxa parasitica (a parasite of brackish water phanerogams and the type species of the genus) in the freshwater/terrestrial phytomyxean order Plasmodiophorida and reveal that phytomyxids associated with Halophila spp. form a separate deep-branching clade within the class proposed here as Marinomyxa gen. nov. We further argue that M. marina infecting H. stipulacea is most likely a species-specific parasite and implies their comigration through the Suez Canal.},
}
@article {pmid33013993,
year = {2020},
author = {Jueterbock, A and Boström, C and Coyer, JA and Olsen, JL and Kopp, M and Dhanasiri, AKS and Smolina, I and Arnaud-Haond, S and Van de Peer, Y and Hoarau, G},
title = {The Seagrass Methylome Is Associated With Variation in Photosynthetic Performance Among Clonal Shoots.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {571646},
pmid = {33013993},
issn = {1664-462X},
abstract = {Evolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management considers genetic variation as the ultimate measure of a population's ability to survive over time. However, clonal plants are among the oldest living organisms on our planet. Here, we test the hypothesis that clonal seagrass meadows display epigenetic variation that complements genetic variation as a source of phenotypic variation. In a clonal meadow of the seagrass Zostera marina, we characterized DNA methylation among 42 shoots. We also sequenced the whole genome of 10 shoots to correlate methylation patterns with photosynthetic performance under exposure to and recovery from 27°C, while controlling for somatic mutations. Here, we show for the first time that clonal seagrass shoots display DNA methylation variation that is independent from underlying genetic variation, and associated with variation in photosynthetic performance under experimental conditions. It remains unknown to what degree this association could be influenced by epigenetic responses to transplantation-related stress, given that the methylomes showed a strong shift under acclimation to laboratory conditions. The lack of untreated control samples in the heat stress experiment did not allow us to distinguish methylome shifts induced by acclimation from such induced by heat stress. Notwithstanding, the co-variation in DNA methylation and photosynthetic performance may be linked via gene expression because methylation patterns varied in functionally relevant genes involved in photosynthesis, and in the repair and prevention of heat-induced protein damage. While genotypic diversity has been shown to enhance stress resilience in seagrass meadows, we suggest that epigenetic variation plays a similar role in meadows dominated by a single genotype. Consequently, conservation management of clonal plants should consider epigenetic variation as indicator of resilience and stability.},
}
@article {pmid33013873,
year = {2020},
author = {Ou, J and Liang, S and Guo, XK and Hu, X},
title = {α-Defensins Promote Bacteroides Colonization on Mucosal Reservoir to Prevent Antibiotic-Induced Dysbiosis.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {2065},
pmid = {33013873},
issn = {1664-3224},
mesh = {Animals ; Anti-Bacterial Agents/*adverse effects/therapeutic use ; Bacteroides/*physiology ; Bacteroides Infections/*immunology ; Drug-Related Side Effects and Adverse Reactions/*immunology ; Dysbiosis/*immunology ; Homeostasis ; Intestinal Mucosa/*immunology ; Matrix Metalloproteinase 7/genetics ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; alpha-Defensins/*metabolism ; },
abstract = {In addition to their established functions in host defense, accumulating evidence has suggested an emerging role for antimicrobial proteins (AMPs) in shaping commensal microbiota. However, the role of α-defensins, the most abundant AMPs of intestine, in regulating microbial ecology remains inconclusive. Here, we report that α-defensins promote commensal Bacteroides colonization by enhancing bacterial adhesion to the mucosal reservoir. Experiments utilizing mice deficient in matrix metalloproteinase 7 (MMP7), the α-defensin-activating enzyme, with rigorous littermate controls showed that α-defensin deficiency did not significantly influence steady-state intestinal microbiota. In contrast, α-defensins are essential for replenishment of commensal Bacteroides from the mucosal reservoir following antibiotics-induced dysbiosis, shown by markedly compromised recovery of Bacteroides in Mmp7[-/-] animals. Mechanistically, α-defensins promote Bacteroides colonization on epithelial surfaces in vivo and adhesion to epithelial cells in vitro. Moreover, α-defensins unexpectedly does not show any microbicidal activities against Bacteroides. Together, we propose that α-defensins promote commensal bacterial colonization and recovery to maintain microbial diversity upon environmental challenges.},
}
@article {pmid33013780,
year = {2020},
author = {Yang, Y and Zhang, Y and Cápiro, NL and Yan, J},
title = {Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {546063},
pmid = {33013780},
issn = {1664-302X},
abstract = {Dehalococcoidia (Dia) class microorganisms are frequently found in various pristine and contaminated environments. Metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) studies have substantially improved the understanding of Dia microbial ecology and evolution; however, an updated thorough investigation on the genomic and evolutionary characteristics of Dia microorganisms distributed in geographically distinct environments has not been implemented. In this study, we analyzed available genomic data to unravel Dia evolutionary and metabolic traits. Based on the phylogeny of 16S rRNA genes retrieved from sixty-seven genomes, Dia microorganisms can be categorized into three groups, the terrestrial cluster that contains all Dehalococcoides and Dehalogenimonas strains, the marine cluster I, and the marine cluster II. These results reveal that a higher ratio of horizontally transferred genetic materials was found in the Dia marine clusters compared to that of the Dia terrestrial cluster. Pangenome analysis further suggests that Dia microorganisms have evolved cluster-specific enzymes (e.g., dehalogenase in terrestrial Dia, sulfite reductase in marine Dia) and biosynthesis capabilities (e.g., siroheme biosynthesis in marine Dia). Marine Dia microorganisms are likely adapted to versatile metabolisms for energy conservation besides organohalide respiration. The genomic differences between marine and terrestrial Dia may suggest distinct functions and roles in element cycling (e.g., carbon, sulfur, chlorine), which require interdisciplinary approaches to unravel the physiology and evolution of Dia in various environments.},
}
@article {pmid33013755,
year = {2020},
author = {Whitworth, DE and Jurkevitch, E and Pérez, J and Fuhrmann, G and Koval, SF},
title = {Editorial: Mechanisms of Prokaryotic Predation.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {2071},
doi = {10.3389/fmicb.2020.02071},
pmid = {33013755},
issn = {1664-302X},
}
@article {pmid33013480,
year = {2020},
author = {Turroni, S and Magnani, M and Kc, P and Lesnik, P and Vidal, H and Heer, M},
title = {Gut Microbiome and Space Travelers' Health: State of the Art and Possible Pro/Prebiotic Strategies for Long-Term Space Missions.},
journal = {Frontiers in physiology},
volume = {11},
number = {},
pages = {553929},
pmid = {33013480},
issn = {1664-042X},
abstract = {The upcoming exploration missions will imply a much longer duration than any of the missions flown so far. In these missions, physiological adaptation to the new environment leads to changes in different body systems, such as the cardiovascular and musculoskeletal systems, metabolic and neurobehavioral health and immune function. To keep space travelers healthy on their trip to Moon, Mars and beyond and their return to Earth, a variety of countermeasures need to be provided to maintain body functionality. From research on the International Space Station (ISS) we know today, that for instance prescribing an adequate training regime for each individual with the devices available in the respective spacecraft is still a challenge. Nutrient supply is not yet optimal and must be optimized in exploration missions. Food intake is intrinsically linked to changes in the gut microbiome composition. Most of the microbes that inhabit our body supply ecosystem benefit to the host-microbe system, including production of important resources, bioconversion of nutrients, and protection against pathogenic microbes. The gut microbiome has also the ability to signal the host, regulating the processes of energy storage and appetite perception, and influencing immune and neurobehavioral function. The composition and functionality of the microbiome most likely changes during spaceflight. Supporting a healthy microbiome by respective measures in space travelers might maintain their health during the mission but also support rehabilitation when being back on Earth. In this review we are summarizing the changes in the gut microbiome observed in spaceflight and analog models, focusing particularly on the effects on metabolism, the musculoskeletal and immune systems and neurobehavioral disorders. Since space travelers are healthy volunteers, we focus on the potential of countermeasures based on pre- and probiotics supplements.},
}
@article {pmid33008820,
year = {2020},
author = {Stracke, C and Meyer, BH and Hagemann, A and Jo, E and Lee, A and Albers, SV and Cha, J and Bräsen, C and Siebers, B},
title = {Salt Stress Response of Sulfolobus acidocaldarius Involves Complex Trehalose Metabolism Utilizing a Novel Trehalose-6-Phosphate Synthase (TPS)/Trehalose-6-Phosphate Phosphatase (TPP) Pathway.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {24},
pages = {},
pmid = {33008820},
issn = {1098-5336},
mesh = {Archaeal Proteins/*genetics/metabolism ; Glucosyltransferases/genetics/metabolism ; Metabolic Networks and Pathways ; Phosphoric Monoester Hydrolases/genetics/metabolism ; Salt Stress/*genetics ; Sulfolobus acidocaldarius/*enzymology ; Trehalose/*metabolism ; },
abstract = {The crenarchaeon Sulfolobus acidocaldarius has been described to synthesize trehalose via the maltooligosyltrehalose synthase (TreY) and maltooligosyltrehalose trehalohydrolase (TreZ) pathway, and the trehalose glycosyltransferring synthase (TreT) pathway has been predicted. Deletion mutant analysis of strains with single and double deletions of ΔtreY and ΔtreT in S. acidocaldarius revealed that in addition to these two pathways, a third, novel trehalose biosynthesis pathway is operative in vivo: the trehalose-6-phosphate (T6P) synthase/T6P phosphatase (TPS/TPP) pathway. In contrast to known TPS proteins, which belong to the GT20 family, the S. acidocaldarius TPS belongs to the GT4 family, establishing a new function within this group of enzymes. This novel GT4-like TPS was found to be present mainly in the Sulfolobales The ΔtreY ΔtreT Δtps triple mutant of S. acidocaldarius, which lacks the ability to synthesize trehalose, showed no altered phenotype under standard conditions or heat stress but was unable to grow under salt stress. Accordingly, in the wild-type strain, a significant increase of intracellular trehalose formation was observed under salt stress. Quantitative real-time PCR showed a salt stress-mediated induction of all three trehalose-synthesizing pathways. This demonstrates that in Archaea, trehalose plays an essential role for growth under high-salt conditions.IMPORTANCE The metabolism and function of trehalose as a compatible solute in Archaea was not well understood. This combined genetic and enzymatic approach at the interface of microbiology, physiology, and microbial ecology gives important insights into survival under stress, adaptation to extreme environments, and the role of compatible solutes in Archaea Here, we unraveled the complexity of trehalose metabolism, and we present a comprehensive study on trehalose function in stress response in S. acidocaldarius This sheds light on the general microbiology and the fascinating metabolic repertoire of Archaea, involving many novel biocatalysts, such as glycosyltransferases, with great potential in biotechnology.},
}
@article {pmid33007535,
year = {2021},
author = {Wang, H and Chen, J and Ren, P and Zhang, Y and Omondi Onyango, S},
title = {Ultrasound irradiation alters the spatial structure and improves the antioxidant activity of the yellow tea polysaccharide.},
journal = {Ultrasonics sonochemistry},
volume = {70},
number = {},
pages = {105355},
pmid = {33007535},
issn = {1873-2828},
mesh = {Antioxidants/*pharmacology ; Camellia/*chemistry ; Carbohydrate Conformation ; Molecular Weight ; Polysaccharides/*chemistry/pharmacology ; *Ultrasonic Waves ; },
abstract = {In this study, the impact of ultrasound irradiation on the structural characteristics and antioxidant properties of yellow tea polysaccharides with different molecular weights (Mw) were investigated. Native yellow tea polysaccharide containing YTPS-3N, YTPS-5N and YTPS-7N were prepared through precipitation with ethanol at various concentrations of 30%, 50%, and 70%, respectively, and irradiated with high intensity ultrasound (20 kHz) for 55 min to yield yellow tea polysaccharide including YTPS-3U, YTPS-5U and YTPS-7U. The molecular weight (Mw) of YTPS-3N (from 37.7 to 15.1 kDa) and YTPS-5N (from 14.6 to 5.2 kDa) sharply decreased upon ultrasound irradiation, coincidentally particle size (Zavg) was also significantly reduced for YTPS-3N (40%), YTPS-5N (48%) and YTPS-7N (54%). The high-performance liquid chromatography and Fourier transform-infrared spectroscopy analysis revealed a partial degradation of native yellow tea polysaccharide treated with ultrasound, though the monosaccharide composition was not altered. Furthermore, changes in morphology and the breakdown of native yellow tea polysaccharide upon irradiation was confirmed with the circular dichroism spectrum, atomic force and scanning electron microscopy. As a consequence, irradiation of yellow tea polysaccharide increased free radical scavenging activity with YTPS-7U exhibiting the highest levels of 2, 2-diphenyl-1-picrylhydrazyl free radical, superoxide and hydroxyl radicals scavenging activity. These results suggest that the alteration of the spatial structure of yellow tea polysaccharide can enhance its antioxidant activity which is an important property for functional foods or medicines.},
}
@article {pmid33006023,
year = {2021},
author = {Gao, X and Xu, H and Yuan, X},
title = {The Overlooked Genetic Diversity in the Dryland Soil Surface-Dwelling Cyanobacterium Nostoc flagelliforme as Revealed by the Marker Gene wspA.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {828-831},
pmid = {33006023},
issn = {1432-184X},
support = {31670104//the National Natural Science Foundation of China/ ; 2020JZ-51//Natural Science Foundation of Shaanxi Province (CN)/ ; },
mesh = {Ecosystem ; Genetic Variation ; *Nostoc/genetics ; Phylogeny ; *Soil ; },
abstract = {Biodiversity is recognized to be relatively low in the dryland ecosystem. However, we might overlook the accumulating genetic variation in those dryland micro-populations, which should eventually increase the dryland biodiversity. In the xeric steppes of western and northwestern China, there are two soil surface-dwelling and genetically close cyanobacterial species, Nostoc commune and Nostoc flagelliforme. They respectively exhibit lamellate and filamentous colony shapes. Their individual colony is consisted of hundreds of trichomes and the common exopolysaccharide matrix. N. flagelliforme is exclusively distributed in the dryland and supposed to be evolved from N. commune. We previously reported that the morphological diversity of N. flagelliforme colonies was very limited, being either cylindrical or strip-like. In this communication, we performed single-nucleotide polymorphism (SNP) analysis of the marker gene wspA as well as phylogenetic analysis of the WspA protein in N. flagelliforme colonies to gain insights into its genetic diversity. SNP analysis suggested that there existed plentiful nucleotide variations in the individual colonies and meanwhile these variations shared certain evolutionary regularity. Phylogenetic analysis of the deduced proteins from the cloned wspA sequences suggested that the relatively regular variations were possibly dispersed in the N. flagelliforme populations of different regions. Thus, these results presented a scenario of the underestimated genetic diversity hidden behind the limited morphotype of dryland cyanobacteria. Maybe, we can consider the individual cyanobacterial colony as a potential biodiversity pool in the drylands.},
}
@article {pmid33004967,
year = {2020},
author = {Walker, SP and Barrett, M and Hogan, G and Flores Bueso, Y and Claesson, MJ and Tangney, M},
title = {Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {16356},
pmid = {33004967},
issn = {2045-2322},
support = {12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 15/CDA/3630/SFI_/Science Foundation Ireland/Ireland ; MRCG2016-25/HRBI_/Health Research Board/Ireland ; },
mesh = {Bacteria/genetics ; Breast Neoplasms/genetics ; DNA, Bacterial/*genetics ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; RNA, Ribosomal, 16S/*analysis ; Sequence Analysis, DNA/*methods ; },
abstract = {The targeted sequencing of the 16S rRNA gene is one of the most frequently employed techniques in the field of microbial ecology, with the bacterial communities of a wide variety of niches in the human body have been characterised in this way. This is performed by targeting one or more hypervariable (V) regions within the 16S rRNA gene in order to produce an amplicon suitable in size for next generation sequencing. To date, all technical research has focused on the ability of different V regions to accurately resolve the composition of bacterial communities. We present here an underreported artefact associated with 16S rRNA gene sequencing, namely the off-target amplification of human DNA. By analysing 16S rRNA gene sequencing data from a selection of human sites we highlighted samples susceptible to this off-target amplification when using the popular primer pair targeting the V3-V4 region of the gene. The most severely affected sample type identified (breast tumour samples) were then re-analysed using the V1-V2 primer set, showing considerable reduction in off target amplification. Our data indicate that human biopsy samples should preferably be amplified using primers targeting the V1-V2 region. It is shown here that these primers result in on average 80% less human genome aligning reads, allowing for more statistically significant analysis of the bacterial communities residing in these samples.},
}
@article {pmid33002118,
year = {2020},
author = {Song, J and Klümper, U and Riber, L and Dechesne, A and Smets, BF and Sørensen, SJ and Brandt, KK},
title = {A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {11},
pages = {},
doi = {10.1093/femsec/fiaa200},
pmid = {33002118},
issn = {1574-6941},
mesh = {*Conjugation, Genetic ; *Copper ; Permissiveness ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; },
abstract = {Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) toward a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526 mg kg-1) soil compared to corresponding communities extracted from moderately (458 mg kg-1) Cu contaminated soil and a low Cu reference soil (15 mg kg-1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.},
}
@article {pmid33001506,
year = {2020},
author = {Beier, S and Andersson, AF and Galand, PE and Hochart, C and Logue, JB and McMahon, K and Bertilsson, S},
title = {The environment drives microbial trait variability in aquatic habitats.},
journal = {Molecular ecology},
volume = {29},
number = {23},
pages = {4605-4617},
doi = {10.1111/mec.15656},
pmid = {33001506},
issn = {1365-294X},
mesh = {*Bacteriophages/genetics ; Lakes ; Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.},
}
@article {pmid33001224,
year = {2021},
author = {Yavitt, JB and Roco, CA and Debenport, SJ and Barnett, SE and Shapleigh, JP},
title = {Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {758-769},
pmid = {33001224},
issn = {1432-184X},
support = {1007286//Agricultural Research Service/ ; },
mesh = {Bacteria/genetics ; Biodiversity ; Ecosystem ; Forests ; *Metagenomics ; Proton-Motive Force ; *Soil ; Soil Microbiology ; },
abstract = {Soil pH has shown to predict bacterial diversity, but mechanisms are still poorly understood. To investigate how bacteria distribute themselves as a function of soil pH, we assessed community composition, diversity, assembly, and gene abundance across local (ca. 1 km) scale gradients in soil pH from ~ 3.8 to 6.5 created by differences in soil parent material in three northern forests. Plant species were the same on all sites, with no evidence of agriculture in the past. Concentrations of extractable calcium, iron, and phosphorus also varied significantly across the pH gradients. Among taxa, Alphaproteobacteria and Acidobacteria were more common in soils with acidic pH values. Overall richness and diversity of OTUs peaked at intermediate pH values. Variations in OTU richness and diversity also had a quadratic fit with concentrations of extractable calcium and phosphorus. Community assembly was via homogeneous deterministic processes in soils with acidic pH values, whereas stochastic processes dominated in soils with near-neutral pH values. Although we expected selection via genes for acid tolerance response in acidic soils, genes for genetic information processing were more selective. Taxa in higher pH soils had differential abundance of transporter genes, suggesting adaptation to acquire metabolic substrates from soils. Soil bacterial communities in northern forest soils are incredibly diverse, and we still have much to learn about how soil pH and co-varying soil parameters directly drive gene selection in this critical component of ecosystem structure.},
}
@article {pmid33001029,
year = {2020},
author = {Nelson, CW and Ardern, Z and Goldberg, TL and Meng, C and Kuo, CH and Ludwig, C and Kolokotronis, SO and Wei, X},
title = {Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
pmid = {33001029},
issn = {2050-084X},
support = {Postdoctoral Research Fellowship//Academia Sinica/International ; Grant//National Philanthropic Trust/International ; John D. MacArthur Professorship Chair//University of Wisconsin-Madison/International ; IOS grants #1755370 and #1758800//National Science Foundation/International ; John D MacArthur Professorship Chair//University of Wisconsin-Madison/International ; },
mesh = {Amino Acid Sequence ; Animals ; Antibodies, Viral/immunology ; Antibody Specificity ; Antigens, Viral/biosynthesis/genetics/immunology ; Betacoronavirus/*genetics/pathogenicity/physiology ; COVID-19 ; China/epidemiology ; Chiroptera/virology ; Coronavirus/genetics ; Coronavirus Infections/epidemiology/*virology ; Epitopes/genetics/immunology ; Europe/epidemiology ; Eutheria/virology ; *Evolution, Molecular ; Gene Expression Regulation, Viral ; *Genes, Overlapping ; *Genes, Viral ; Genetic Variation ; Haplotypes/genetics ; Host Specificity/*genetics ; Humans ; Models, Molecular ; Mutation ; Open Reading Frames/*genetics ; *Pandemics ; Phylogeny ; Pneumonia, Viral/epidemiology/*virology ; Protein Biosynthesis ; Protein Conformation ; RNA, Viral/genetics ; SARS-CoV-2 ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Viral Proteins/*genetics/immunology ; },
abstract = {Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.},
}
@article {pmid33000311,
year = {2021},
author = {Silva-Lima, AW and Froes, AM and Garcia, GD and Tonon, LAC and Swings, J and Cosenza, CAN and Medina, M and Penn, K and Thompson, JR and Thompson, CC and Thompson, FL},
title = {Mussismilia braziliensis White Plague Disease Is Characterized by an Affected Coral Immune System and Dysbiosis.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {795-806},
pmid = {33000311},
issn = {1432-184X},
support = {Biocomp, IODP//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; PQ//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (BR)/ ; CNE//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {Animals ; *Anthozoa ; Coral Reefs ; Dysbiosis ; Immune System ; Symbiosis ; },
abstract = {Infectious diseases are one of the major drivers of coral reef decline worldwide. White plague-like disease (WPL) is a widespread disease with a complex etiology that infects several coral species, including the Brazilian endemic species Mussismilia braziliensis. Gene expression profiles of healthy and WPL-affected M. braziliensis were analyzed in winter and summer seasons. The de novo assembly of the M. braziliensis transcriptome from healthy and white plague samples produced a reference transcriptome containing 119,088 transcripts. WPL-diseased samples were characterized by repression of immune system and cellular defense processes. Autophagy and cellular adhesion transcripts were also repressed in WPL samples, suggesting exhaustion of the coral host defenses. Seasonal variation leads to plasticity in transcription with upregulation of intracellular signal transduction, apoptosis regulation, and oocyte development in the summer. Analysis of the active bacterial rRNA indicated that Pantoea bacteria were more abundant in WPL corals, while Tistlia, Fulvivirga, and Gammaproteobacteria Ga0077536 were more abundant in healthy samples. Cyanobacteria proliferation was also observed in WPL, mostly in the winter. These results indicate a scenario of dysbiosis in WPL-affected M. braziliensis, with the loss of potentially symbiotic bacteria and proliferation of opportunistic microbes after the start of the infection process.},
}
@article {pmid32998695,
year = {2020},
author = {Soverini, M and Rampelli, S and Turroni, S and Brigidi, P and Biagi, E and Candela, M},
title = {Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {678},
pmid = {32998695},
issn = {1471-2164},
mesh = {*Gastrointestinal Microbiome ; *Genes, Bacterial ; Genes, Essential ; Humans ; Intestinal Mucosa/metabolism/microbiology ; *Metagenome ; Metagenomics/methods/standards ; },
abstract = {BACKGROUND: Advances in bioinformatics recently allowed for the recovery of 'metagenomes assembled genomes' from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits.<br><br>RESULTS: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.<br><br>CONCLUSIONS: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.},
}
@article {pmid32996612,
year = {2021},
author = {Moisan, K and Raaijmakers, JM and Dicke, M and Lucas-Barbosa, D and Cordovez, V},
title = {Volatiles from soil-borne fungi affect directional growth of roots.},
journal = {Plant, cell &amp; environment},
volume = {44},
number = {1},
pages = {339-345},
pmid = {32996612},
issn = {1365-3040},
mesh = {Brassica rapa/*growth &amp; development/metabolism ; Gas Chromatography-Mass Spectrometry ; Plant Roots/*growth &amp; development/metabolism ; *Soil Microbiology ; Volatile Organic Compounds/*metabolism ; },
abstract = {Volatiles play major roles in mediating ecological interactions between soil (micro)organisms and plants. It is well-established that microbial volatiles can increase root biomass and lateral root formation. To date, however, it is unknown whether microbial volatiles can affect directional root growth. Here, we present a novel method to study belowground volatile-mediated interactions. As proof-of-concept, we designed a root Y-tube olfactometer, and tested the effects of volatiles from four different soil-borne fungi on directional growth of Brassica rapa roots in soil. Subsequently, we compared the fungal volatile organic compounds (VOCs) previously profiled with Gas Chromatography-Mass Spectrometry (GC-MS). Using our newly designed setup, we show that directional root growth in soil is differentially affected by fungal volatiles. Roots grew more frequently toward volatiles from the root pathogen Rhizoctonia solani, whereas volatiles from the other three saprophytic fungi did not impact directional root growth. GC-MS profiling showed that six VOCs were exclusively emitted by R. solani. These findings verify that this novel method is suitable to unravel the intriguing chemical cross-talk between roots and soil-borne fungi and its impact on root growth.},
}
@article {pmid32996237,
year = {2021},
author = {Barbera, P and Czech, L and Lutteropp, S and Stamatakis, A},
title = {SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements.},
journal = {Molecular ecology resources},
volume = {21},
number = {1},
pages = {340-349},
pmid = {32996237},
issn = {1755-0998},
support = {//Klaus Tschira Stiftung/ ; },
mesh = {*Algorithms ; *Microbiota ; *Phylogeny ; Sequence Analysis, DNA ; *Software ; },
abstract = {Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample remains challenging, as traditional methods do not scale well with the increasing data volumes and/or do not leverage the phylogenetic placement information. Here, we present scrapp, a highly parallel and scalable tool that uses a molecular species delimitation algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic placement of the sample. scrapp employs a novel approach to cluster phylogenetic placements, called placement space clustering, to efficiently perform dimensionality reduction, so as to scale on large data volumes. Furthermore, it uses the phylogeny-aware molecular species delimitation method mPTP to quantify diversity. We evaluated scrapp using both, simulated and empirical data sets. We use simulated data to verify our approach. Tests on an empirical data set show that scrapp-derived metrics can classify samples by their diversity-correlated features equally well or better than existing, commonly used approaches. scrapp is available at https://github.com/pbdas/scrapp.},
}
@article {pmid32995929,
year = {2021},
author = {Wang, H and Zhang, Y and Bartlett, DH and Xiao, X},
title = {Transcriptomic Analysis Reveals Common Adaptation Mechanisms Under Different Stresses for Moderately Piezophilic Bacteria.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {617-629},
pmid = {32995929},
issn = {1432-184X},
support = {2018YFC0309800//National Key Research and Development Program of China/ ; 41776173//National Natural Science Foundation of China/ ; 41530967//National Natural Science Foundation of China/ ; 91951117//National Natural Science Foundation of China/ ; 41921006//National Natural Science Foundation of China/ ; },
mesh = {*Adaptation, Physiological/genetics ; Bacillaceae ; Bacteria/genetics ; Sporosarcina ; *Transcriptome ; },
abstract = {Piezophiles, by the commonly accepted definition, grow faster under high hydrostatic pressure (HHP) than under ambient pressure and are believed to exist only in pressurized environments where life has adapted to HHP during evolution. However, recent findings suggest that piezophiles have developed a common adaptation strategy to cope with multiple types of stresses including HHP. These results raise a question on the ecological niches of piezophiles: are piezophiles restricted to habitats with HHP? In this study, we observed that the bacterial strains Sporosarcina psychrophila DSM 6497 and Lysinibacillus sphaericus LMG 22257, which were isolated from surface environments and then transferred under ambient pressure for half a century, possess moderately piezophilic characteristics with optimal growth pressures of 7 and 20 MPa, respectively. Their tolerance to HHP was further enhanced by MgCl2 supplementation under the highest tested pressure of 50 MPa. Transcriptomic analysis was performed to compare gene expression with and without MgCl2 supplementation under 50 MPa for S. psychrophila DSM 6497. Among 4390 genes or transcripts obtained, 915 differentially expressed genes (DEGs) were identified. These DEGs are primarily associated with the antioxidant defense system, intracellular compatible solute accumulation, and membrane lipid biosynthesis, which have been reported to be essential for cells to cope with HHP. These findings indicate no in situ pressure barrier for piezophile isolation, and cells may adopt a common adaptation strategy to cope with different stresses.},
}
@article {pmid32994415,
year = {2020},
author = {Guo, X and Gao, Q and Yuan, M and Wang, G and Zhou, X and Feng, J and Shi, Z and Hale, L and Wu, L and Zhou, A and Tian, R and Liu, F and Wu, B and Chen, L and Jung, CG and Niu, S and Li, D and Xu, X and Jiang, L and Escalas, A and Wu, L and He, Z and Van Nostrand, JD and Ning, D and Liu, X and Yang, Y and Schuur, EAG and Konstantinidis, KT and Cole, JR and Penton, CR and Luo, Y and Tiedje, JM and Zhou, J},
title = {Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {4897},
pmid = {32994415},
issn = {2041-1723},
mesh = {Acclimatization/genetics ; Archaea/genetics/isolation &amp; purification/metabolism ; Bacteria/genetics/isolation &amp; purification/metabolism ; Carbon/*analysis/metabolism ; Carbon Cycle ; Cellulose/metabolism ; DNA, Environmental/genetics/isolation &amp; purification ; Fungi/genetics/isolation &amp; purification/metabolism ; Global Warming ; Grassland ; Hot Temperature/adverse effects ; Metagenome/*genetics ; Metagenomics ; Microbiota/*physiology ; Models, Genetic ; Plant Roots/chemistry ; Poaceae/chemistry ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q10) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.},
}
@article {pmid32994285,
year = {2020},
author = {Trego, AC and O'Sullivan, S and Quince, C and Mills, S and Ijaz, UZ and Collins, G},
title = {Size Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life Cycle.},
journal = {mSystems},
volume = {5},
number = {5},
pages = {},
pmid = {32994285},
issn = {2379-5077},
support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Methanogenic archaea are key players in cycling organic matter in nature but also in engineered waste treatment systems, where they generate methane, which can be used as a renewable energy source. In such systems in the built environment, complex methanogenic consortia are known to aggregate into highly organized, spherical granular biofilms comprising the interdependent microbial trophic groups mediating the successive stages of the anaerobic digestion (AD) process. This study separated methanogenic granules into a range of discrete size fractions, hypothesizing different biofilm growth stages, and separately supplied each with specific substrates to stimulate the activity of key AD trophic groups, including syntrophic acid oxidizers and methanogens. Rates of specific methanogenic activity were measured, and amplicon sequencing of 16S rRNA gene transcripts was used to resolve phylotranscriptomes across the series of size fractions. Increased rates of methane production were observed in each of the size fractions when hydrogen was supplied as the substrate compared with those of volatile fatty acids (acetate, propionate, and butyrate). This was connected to a shift toward hydrogenotrophic methanogenesis dominated by Methanobacterium and Methanolinea Interestingly, the specific active microbiomes measured in this way indicated that size was significantly more important than substrate in driving the structure of the active community in granules. Multivariate integration studywise discriminant analysis identified 56 genera shaping changes in the active community across both substrate and size. Half of those were found to be upregulated in the medium-sized granules, which were also the most active and potentially of the most important size, or life stage, for precision management of AD systems.IMPORTANCE Biological wastewater conversion processes collectively constitute one of the single biggest worldwide applications of microbial communities. There is an obvious requirement, therefore, to study the microbial systems central to the success of such technologies. Methanogenic granules, in particular, are architecturally fascinating biofilms that facilitate highly organized cooperation within the metabolic network of the anaerobic digestion (AD) process and, thus, are especially intriguing model systems for microbial ecology. This study, in a way not previously reported, provoked syntrophic and methanogenic activity and the structure of the microbial community, using specific substrates targeting the key trophic groups in AD. Unexpectedly, granule size more strongly than substrate shaped the active portion of the microbial community. Importantly, the findings suggest the size, or age, of granules inherently shapes the active microbiome linked to a life cycle. This provides exciting insights into the function of, and the potential for additional modeling of biofilm development in, methanogenic granules.},
}
@article {pmid32993824,
year = {2021},
author = {Hanley-Cook, GT and Argaw, AA and de Kok, BP and Vanslambrouck, KW and Toe, LC and Kolsteren, PW and Jones, AD and Lachat, CK},
title = {EAT-Lancet diet score requires minimum intake values to predict higher micronutrient adequacy of diets in rural women of reproductive age from five low- and middle-income countries.},
journal = {The British journal of nutrition},
volume = {126},
number = {1},
pages = {92-100},
doi = {10.1017/S0007114520003864},
pmid = {32993824},
issn = {1475-2662},
mesh = {Democratic Republic of the Congo ; *Developing Countries ; *Diet ; Eating ; Ecuador ; Female ; Humans ; Kenya ; Micronutrients/*administration &amp; dosage ; Rural Population ; Sri Lanka ; *Trace Elements/administration &amp; dosage ; Vietnam ; },
abstract = {The EAT-Lancet Commission promulgated a universal reference diet. Subsequently, researchers constructed an EAT-Lancet diet score (0-14 points), with minimum intake values for various dietary components set at 0 g/d, and reported inverse associations with risks of major health outcomes in a high-income population. We assessed associations between EAT-Lancet diet scores, without or with lower bound values, and the mean probability of micronutrient adequacy (MPA) among nutrition-insecure women of reproductive age (WRA) from low- and middle-income countries (LMIC). We analysed single 24-h diet recall data (n 1950) from studies in rural DRC, Ecuador, Kenya, Sri Lanka and Vietnam. Associations between EAT-Lancet diet scores and MPA were assessed by fitting linear mixed-effects models. Mean EAT-Lancet diet scores were 8·8 (SD 1·3) and 1·9 (SD 1·1) without or with minimum intake values, respectively. Pooled MPA was 0·58 (SD 0·22) and energy intake was 10·5 (SD 4·6) MJ/d. A one-point increase in the EAT-Lancet diet score, without minimum intake values, was associated with a 2·6 (SD 0·7) percentage points decrease in MPA (P < 0·001). In contrast, the EAT-Lancet diet score, with minimum intake values, was associated with a 2·4 (SD 1·3) percentage points increase in MPA (P = 0·07). Further analysis indicated positive associations between EAT-Lancet diet scores and MPA adjusted for energy intake (P < 0·05). Our findings indicate that the EAT-Lancet diet score requires minimum intake values for nutrient-dense dietary components to avoid positively scoring non-consumption of food groups and subsequently predicting lower MPA of diets, when applied to rural WRA in LMIC.},
}
@article {pmid32993503,
year = {2020},
author = {De Maayer, P and Pillay, T and Coutinho, TA},
title = {Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {670},
pmid = {32993503},
issn = {1471-2164},
support = {SFH180109299856//National Research Foundation/ ; },
mesh = {Conserved Sequence ; Enterobacteriaceae/classification/*genetics ; Evolution, Molecular ; Flagella/*genetics ; Flagellin/*genetics ; Phylogeny ; Sequence Homology ; },
abstract = {BACKGROUND: Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of flagella is highly energy intensive and therefore flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility.<br><br>RESULTS: Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode predicted peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4028 (~&#x2009;20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales.<br><br>CONCLUSIONS: Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.},
}
@article {pmid32992776,
year = {2020},
author = {García-Vega, &#xc1;S and Corrales-Agudelo, V and Reyes, A and Escobar, JS},
title = {Diet Quality, Food Groups and Nutrients Associated with the Gut Microbiota in a Nonwestern Population.},
journal = {Nutrients},
volume = {12},
number = {10},
pages = {},
pmid = {32992776},
issn = {2072-6643},
mesh = {Adolescent ; Adult ; Animals ; *Diet ; Dietary Fiber ; Fatty Acids, Volatile ; Female ; *Food Quality ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Middle Aged ; *Nutrients ; Obesity ; Overweight ; RNA, Ribosomal, 16S/analysis ; Vegetables ; Young Adult ; },
abstract = {Diet plays an important role in shaping gut microbiota. However, much remains to be learned regarding this association. We analyzed dietary intake and gut microbiota in a community-dwelling cohort of 441 Colombians. Diet quality, intake of food groups and nutrient consumption were paired with microbial diversity and composition using linear regressions, Procrustes analyses and a random-forest machine-learning algorithm. Analyses were adjusted for potential confounders, including the five cities from where the participants originated, sex (male, female), age group (18-40 and 41-62 years), BMI (lean, overweight, obese) and socioeconomic status. Microbial diversity was higher in individuals with increased intake of nutrients obtained from plant-food sources, whereas the intake of food groups and nutrients correlated with microbiota structure. Random-forest regressions identified microbial communities associated with different diet components. Two remarkable results confirmed previous expectations regarding the link between diet and microbiota: communities composed of short-chain fatty acid (SCFA) producers were more prevalent in the microbiota of individuals consuming diets rich in fiber and plant-food sources, such as fruits, vegetables and beans. In contrast, an inflammatory microbiota composed of bile-tolerant and putrefactive microorganisms along with opportunistic pathogens thrived in individuals consuming diets enriched in animal-food sources and of low quality, i.e., enriched in ultraprocessed foods and depleted in dietary fiber. This study expands our understanding of the relationship between dietary intake and gut microbiota. We provide evidence that diet is strongly associated with the gut microbial community and highlight generalizable connections between them.},
}
@article {pmid32990279,
year = {2020},
author = {Zhu, Y and Xiong, Y and Gu, Y and Li, Q and Liu, Y},
title = {Chiropractic Therapy Modulated Gut Microbiota and Attenuated Allergic Airway Inflammation in an Immature Rat Model.},
journal = {Medical science monitor : international medical journal of experimental and clinical research},
volume = {26},
number = {},
pages = {e926039},
pmid = {32990279},
issn = {1643-3750},
mesh = {Animals ; *Asthma/microbiology/physiopathology/therapy ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Male ; *Manipulation, Chiropractic ; Rats ; Rats, Sprague-Dawley ; },
abstract = {BACKGROUND As a type of traditional Chinese massage, chiropractic therapy is applied to prevent and treat children with asthma in China. However, its mechanism of action is unclear. Allergic airway inflammation plays a key role in the occurrence and development of asthma, in which changes in gut microbiota are involved. The present study investigated the influence of chiropractic therapy on allergic airway inflammation (AAI) and gut microbiota in an immature rat model. MATERIAL AND METHODS Three-week-old male Sprague-Dawley rats were divided randomly into control (CN), AAI, and chiropractic (CP) groups. AAI and CP groups were sensitized and challenged with ovalbumin (OVA) to induce AAI. The CP group received chiropractic therapy during AAI modelling. AAI was assessed by cell counts in bronchoalveolar lavage fluid and HE staining of lung tissues. Plasma OVA-sIgE, IFN-γ, IL-4, and IL-10 levels were detected by ELISA. DNA extraction from feces samples was used for 16S rRNA gene sequencing and analyzed for gut microbiota by Quantitative Insights Into Microbial Ecology (QIIME). RESULTS AAI group had significantly lower richness and diversity of gut microbiota along with Th2 response and allergic airway inflammation. Moreover, the AAI group had lower abundance of butyrate-producing bacterial taxa with more Lactobacillus. Chiropractic therapy significantly increased the richness and diversity of gut microbiota and increased butyrate-producing bacterial taxa and decreased Lactobacillus, along with attenuating Th2 response and allergic airway inflammation during AAI modelling. CONCLUSIONS Chiropractic therapy attenuated allergic airway inflammation and optimized gut microbiota in an immature rat model, which might promote the development of adult-like butyrogenic milieu, immunotolerance, and inflammation attenuation.},
}
@article {pmid32989484,
year = {2021},
author = {González-Hourcade, M and Del Campo, EM and Casano, LM},
title = {The Under-explored Extracellular Proteome of Aero-Terrestrial Microalgae Provides Clues on Different Mechanisms of Desiccation Tolerance in Non-Model Organisms.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {437-453},
pmid = {32989484},
issn = {1432-184X},
support = {CGL2016-80259-P//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
mesh = {*Acclimatization ; Algal Proteins/metabolism ; Cell Wall/metabolism ; Chlorophyta/classification/metabolism/physiology ; Desiccation ; Extracellular Polymeric Substance Matrix/*metabolism ; Lichens/classification/metabolism/physiology ; Microalgae/classification/metabolism/*physiology ; Plant Proteins/metabolism ; Proteome/*metabolism ; Species Specificity ; Water/metabolism ; },
abstract = {Trebouxia sp. (TR9) and Coccomyxa simplex (Csol) are desiccation-tolerant lichen microalgae with different adaptive strategies in accordance with the prevailing conditions of their habitats. The remodelling of cell wall and extracellular polysaccharides depending on water availability are key elements in the tolerance to desiccation of both microalgae. Currently, there is no information about the extracellular proteins of these algae and other aero-terrestrial microalgae in response to limited water availability. To our knowledge, this is the first report on the proteins associated with the extracellular polymeric substances (EPS) of aero-terrestrial microalgae subjected to cyclic desiccation/rehydration. LC-MS/MS and bioinformatic analyses of the EPS-associated proteins in the two lichen microalgae submitted to four desiccation/rehydration cycles allowed the compilation of 111 and 121 identified proteins for TR9 and Csol, respectively. Both sets of EPS-associated proteins shared a variety of predicted biological functions but showed a constitutive expression in Csol and partially inducible in TR9. In both algae, the EPS-associated proteins included a number of proteins of unknown functions, some of which could be considered as small intrinsically disordered proteins related with desiccation-tolerant organisms. Differences in the composition and the expression pattern between the studied EPS-associated proteins would be oriented to preserve the biochemical and biophysical properties of the extracellular structures under the different conditions of water availability in which each alga thrives.},
}
@article {pmid32984478,
year = {2020},
author = {Hassen, AI and Pierneef, R and Swanevelder, ZH and Bopape, FL},
title = {Microbial and functional diversity of Cyclopia intermedia rhizosphere microbiome revealed by analysis of shotgun metagenomics sequence data.},
journal = {Data in brief},
volume = {32},
number = {},
pages = {106288},
pmid = {32984478},
issn = {2352-3409},
abstract = {Cyclopia spp., commonly referred to as honeybush due to the honey scented flowers, are indigenous legumes mainly growing in the Cape Floristic Region of the Western Cape, South Africa. Dozens of species, including Cyclopia intermedia, C. subternata, C. plicata, C. genistoides are used to make the well-known, popular and widely enjoyed beverage called 'honeybush tea'. In the past, most rhizosphere microbial studies associated with Cyclopia spp. focused mainly on the taxonomy and diversity of the root nodule associated symbiotic nitrogen fixing rhizobia. The work presented here is the first report on the microbial and functional diversity of rhizosphere microbiome associated with Cyclopia intermedia. Metagenomic shotgun sequencing was performed on the rhizosphere soil sample collected from this Cyclopia sp. using illumina Hiseq 2500 platform which resulted in an α- diversity of 312 species. Analysis of the metagenome sequence using the Metagenomic analysis server (MG-RAST) indicated that bacteria constitute the dominant domain followed by Eukaryota, Archaea and other sequences derived from fungi and viruses. Functional diversity of the metagenome based on analysis using the Cluster Orthologous Group (COG) method showed metabolism as the most important function in the community. The raw sequence data is uploaded in FASTQ format on MG-RAST server with ID mgm4855911.3 which can be accessed at http://www.mg-rast.org/linkin.cgi?project=mgp90368. The data on the microbial and functional diversity of the rhizosphere community of Cyclopia intermedia generates a baseline information about the microbial ecology of this indigenous legume. The microbial profile data can also be used as indicators of soil health characteristic of the rhizosphere of this important legume.},
}
@article {pmid32983401,
year = {2020},
author = {Lequime, S and Bastide, P and Dellicour, S and Lemey, P and Baele, G},
title = {nosoi: A stochastic agent-based transmission chain simulation framework in r.},
journal = {Methods in ecology and evolution},
volume = {11},
number = {8},
pages = {1002-1007},
pmid = {32983401},
issn = {2041-210X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The transmission process of an infectious agent creates a connected chain of hosts linked by transmission events, known as a transmission chain. Reconstructing transmission chains remains a challenging endeavour, except in rare cases characterized by intense surveillance and epidemiological inquiry. Inference frameworks attempt to estimate or approximate these transmission chains but the accuracy and validity of such methods generally lack formal assessment on datasets for which the actual transmission chain was observed.We here introduce nosoi, an open-source r package that offers a complete, tunable and expandable agent-based framework to simulate transmission chains under a wide range of epidemiological scenarios for single-host and dual-host epidemics. nosoi is accessible through GitHub and CRAN, and is accompanied by extensive documentation, providing help and practical examples to assist users in setting up their own simulations.Once infected, each host or agent can undergo a series of events during each time step, such as moving (between locations) or transmitting the infection, all of these being driven by user-specified rules or data, such as travel patterns between locations. nosoi is able to generate a multitude of epidemic scenarios, that can-for example-be used to validate a wide range of reconstruction methods, including epidemic modelling and phylodynamic analyses. nosoi also offers a comprehensive framework to leverage empirically acquired data, allowing the user to explore how variations in parameters can affect epidemic potential. Aside from research questions, nosoi can provide lecturers with a complete teaching tool to offer students a hands-on exploration of the dynamics of epidemiological processes and the factors that impact it. Because the package does not rely on mathematical formalism but uses a more intuitive algorithmic approach, even extensive changes of the entire model can be easily and quickly implemented.},
}
@article {pmid32983187,
year = {2020},
author = {de Souza, RSC and Armanhi, JSL and Arruda, P},
title = {From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {1179},
pmid = {32983187},
issn = {1664-462X},
abstract = {Plants teem with microorganisms, whose tremendous diversity and role in plant-microbe interactions are being increasingly explored. Microbial communities create a functional bond with their hosts and express beneficial traits capable of enhancing plant performance. Therefore, a significant task of microbiome research has been identifying novel beneficial microbial traits that can contribute to crop productivity, particularly under adverse environmental conditions. However, although knowledge has exponentially accumulated in recent years, few novel methods regarding the process of designing inoculants for agriculture have been presented. A recently introduced approach is the use of synthetic microbial communities (SynComs), which involves applying concepts from both microbial ecology and genetics to design inoculants. Here, we discuss how to translate this rationale for delivering stable and effective inoculants for agriculture by tailoring SynComs with microorganisms possessing traits for robust colonization, prevalence throughout plant development and specific beneficial functions for plants. Computational methods, including machine learning and artificial intelligence, will leverage the approaches of screening and identifying beneficial microbes while improving the process of determining the best combination of microbes for a desired plant phenotype. We focus on recent advances that deepen our knowledge of plant-microbe interactions and critically discuss the prospect of using microbes to create SynComs capable of enhancing crop resiliency against stressful conditions.},
}
@article {pmid32983012,
year = {2020},
author = {Hounmanou, YMG and Dalsgaard, A and Sopacua, TF and Uddin, GMN and Leekitcharoenphon, P and Hendriksen, RS and Olsen, JE and Larsen, MH},
title = {Molecular Characteristics and Zoonotic Potential of Salmonella Weltevreden From Cultured Shrimp and Tilapia in Vietnam and China.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1985},
pmid = {32983012},
issn = {1664-302X},
abstract = {Salmonella Weltevreden is increasingly reported from aquatic environments, seafood, and patients in several Southeast Asian countries. Using genome-wide analysis, we characterized S. Weltevreden isolated from cultured shrimp and tilapia from Vietnam and China to study their genetic characteristics and relatedness to clinical isolates of S. Weltevreden ST-365. The phylogenetic analysis revealed up to 312 single-nucleotide polymorphism (SNP) difference between tilapia isolates, whereas isolates from shrimp were genetically more closely related. Epidemiologically unrelated isolates from Vietnam were closely related to isolates from China, e.g., 20 SNPs differences between strains 28V and 75C. In comparison with strains from other parts of the world, our environmental isolates predominantly clustered within the continental South Asia lineage, constituted mostly of strains from human stool with as low as seven SNPs difference, e.g., 30V versus Cont_ERR495254. All sequenced isolates were MLST type ST-365 and contained the major virulence-related genes encoded by the Salmonella Pathogenicity Islands 1-5. Ten of the isolates harbored the IncFII(S) plasmid similar to the virulence genes-mediated plasmid pSPCV of S. Paratyphi C, and one isolate had the IncQ1 plasmid on the same contig with strA/B, sul2, and tetA resistance genes similar to the IncQ1 type, pNUC of S. Typhimurium. A pangenomic analysis yielded 7891 genes including a core genome of 4892 genes, with a closely related accessory genome content between clinical and environmental isolates (Benjamini p > 0.05). In a search for differences that could explain the higher prevalence of S. Weltevreden in aquatic samples, genomes were compared with those of other Salmonella enterica serovars. S. Weltevreden revealed specific regions harboring glpX (Fructose-1;6-bisphosphatase; class II), rfbC (dTDP-4-dehydrorhamnose 3;5-epimerase), and cmtB (PTS Mannitol-specific cryptic phosphotransferase enzyme IIA component) involved in carbohydrate biosynthesis pathways. Our study builds grounds for future experiments to determine genes or pathways that are essential when S. Weltevreden are in aquatic environments and microbial interactions providing survival advantages to S. Weltevreden in such environments.},
}
@article {pmid32982988,
year = {2020},
author = {van der Goot, E and van Spronsen, FJ and Falcão Salles, J and van der Zee, EA},
title = {A Microbial Community Ecology Perspective on the Gut-Microbiome-Brain Axis.},
journal = {Frontiers in endocrinology},
volume = {11},
number = {},
pages = {611},
pmid = {32982988},
issn = {1664-2392},
mesh = {Brain/*microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Microbiota/*physiology ; },
}
@article {pmid32979812,
year = {2020},
author = {Meyer, KM and Morris, AH and Webster, K and Klein, AM and Kroeger, ME and Meredith, LK and Brændholt, A and Nakamura, F and Venturini, A and Fonseca de Souza, L and Shek, KL and Danielson, R and van Haren, J and Barbosa de Camargo, P and Tsai, SM and Dini-Andreote, F and de Mauro, JMS and Barlow, J and Berenguer, E and Nüsslein, K and Saleska, S and Rodrigues, JLM and Bohannan, BJM},
title = {Belowground changes to community structure alter methane-cycling dynamics in Amazonia.},
journal = {Environment international},
volume = {145},
number = {},
pages = {106131},
doi = {10.1016/j.envint.2020.106131},
pmid = {32979812},
issn = {1873-6750},
mesh = {Animals ; Brazil ; Cattle ; Forests ; *Methane ; *Soil ; Soil Microbiology ; },
abstract = {Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6 ± 9482.3 μg CH4 m[-2] d[-1]), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8 ± 120.5 μg CH4 m[-2] d[-1]), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2 ± 35.7 μg CH4 m[-2] d[-1]), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.},
}
@article {pmid32978127,
year = {2020},
author = {Xia, WW and Zhao, J and Zheng, Y and Zhang, HM and Zhang, JB and Chen, RR and Lin, XG and Jia, ZJ},
title = {Active Soil Nitrifying Communities Revealed by In Situ Transcriptomics and Microcosm-Based Stable-Isotope Probing.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {23},
pages = {},
pmid = {32978127},
issn = {1098-5336},
mesh = {Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Fertilizers/analysis ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Nitrogen/*metabolism ; RNA, Archaeal/analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Real-Time Polymerase Chain Reaction ; *Soil Microbiology ; Transcription, Genetic ; },
abstract = {Long-term nitrogen field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes in communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to those of [13]C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimens for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N-fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable-isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and Nitrosospira viennensis-like AOA, despite the strong advantage of AOB over AOA in the N-fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was the opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidence that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in [13]C-labeled microcosms.IMPORTANCE The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results for active AOA and AOB, although an apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that the soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosms can serve as powerful tools to test the theory of environmental filtering on the key functional microbial guilds.},
}
@article {pmid32975888,
year = {2021},
author = {Goelen, T and Vuts, J and Sobhy, IS and Wäckers, F and Caulfield, JC and Birkett, MA and Rediers, H and Jacquemyn, H and Lievens, B},
title = {Identification and application of bacterial volatiles to attract a generalist aphid parasitoid: from laboratory to greenhouse assays.},
journal = {Pest management science},
volume = {77},
number = {2},
pages = {930-938},
doi = {10.1002/ps.6102},
pmid = {32975888},
issn = {1526-4998},
support = {HBC.2018/2022//Agentschap Innoveren en Ondernemen/ ; 1S15116316N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; *Aphids ; Bacteria ; Biological Assay ; Laboratories ; *Volatile Organic Compounds/pharmacology ; },
abstract = {BACKGROUND: Recent studies have shown that microorganisms emit volatile compounds that affect insect behaviour. However, it remains largely unclear whether microbes can be exploited as a source of attractants to improve biological control of insect pests. In this study, we used a combination of coupled gas chromatography-electroantennography (GC-EAG) and Y-tube olfactometer bioassays to identify attractive compounds in the volatile extracts of three bacterial strains that are associated with the habitat of the generalist aphid parasitoid Aphidius colemani, and to create mixtures of synthetic compounds to find attractive blends for A. colemani. Subsequently, the most attractive blend was evaluated in two-choice cage experiments under greenhouse conditions.<br><br>RESULTS: GC-EAG analysis revealed 20 compounds that were linked to behaviourally attractive bacterial strains. A mixture of two EAG-active compounds, styrene and benzaldehyde applied at a respective dose of 1 &#x3bc;g and 10 ng, was more attractive than the single compounds or the culture medium of the bacteria in Y-tube olfactometer bioassays. Application of this synthetic mixture under greenhouse conditions resulted in significant attraction of the parasitoids, and outperformed application of the bacterial culture medium.<br><br>CONCLUSION: Compounds isolated from bacterial blends were capable of attracting parasitoids both in laboratory and greenhouse assays, indicating that microbial cultures are an effective source of insect attractants. This opens new opportunities to attract and retain natural enemies of pest species and to enhance biological pest control.},
}
@article {pmid32975751,
year = {2020},
author = {Garbisu, C and Alkorta, I and Kidd, P and Epelde, L and Mench, M},
title = {Keep and promote biodiversity at polluted sites under phytomanagement.},
journal = {Environmental science and pollution research international},
volume = {27},
number = {36},
pages = {44820-44834},
pmid = {32975751},
issn = {1614-7499},
support = {SOE1/P5/E0189//Interreg/ ; },
mesh = {Biodegradation, Environmental ; Biodiversity ; Biomass ; Ecosystem ; Soil ; *Soil Pollutants/analysis ; },
abstract = {The phytomanagement concept combines a sustainable reduction of pollutant linkages at risk-assessed contaminated sites with the generation of both valuable biomass for the (bio)economy and ecosystem services. One of the potential benefits of phytomanagement is the possibility to increase biodiversity in polluted sites. However, the unique biodiversity present in some polluted sites can be severely impacted by the implementation of phytomanagement practices, even resulting in the local extinction of endemic ecotypes or species of great conservation value. Here, we highlight the importance of promoting measures to minimise the potential adverse impact of phytomanagement on biodiversity at polluted sites, as well as recommend practices to increase biodiversity at phytomanaged sites without compromising its effectiveness in terms of reduction of pollutant linkages and the generation of valuable biomass and ecosystem services.},
}
@article {pmid32975677,
year = {2021},
author = {Ouarabi, L and Drider, D and Taminiau, B and Daube, G and Bendali, F and Lucau-Danila, A},
title = {Vaginal Microbiota: Age Dynamic and Ethnic Particularities of Algerian Women.},
journal = {Microbial ecology},
volume = {82},
number = {4},
pages = {1020-1029},
pmid = {32975677},
issn = {1432-184X},
mesh = {*Ethnicity ; Female ; Humans ; Lactobacillus/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Vagina ; },
abstract = {The composition of the vaginal microbiota is a key element for maintaining gynecological and reproductive health. With the aim of obtaining an accurate overview of the vaginal microbiota of Algerian women, in terms of their age and ethnic group, we conducted a 16S rRNA gene targeted metagenomic analysis of 100 vaginal samples taken from healthy childbearing and menopausal women. These data were used to establish the pattern of the vaginal microbiota during reproductive and postreproductive phases. Hormone levels were correlated to changes in microbial composition for menopausal women. The ethnic comparison revealed a particular microbiota profile for Algerian women, with a dominance of CST III and CST I. A rapid qPCR method developed by the authors was successfully used to identify the vaginal bacterial pattern for a customized gynecological management.},
}
@article {pmid32975666,
year = {2020},
author = {Lee, CW and Lim, JH and Heng, PL and Marican, NF and Narayanan, K and Sim, EUH and Bong, CW},
title = {Influence of elevated river flow on hypoxia occurrence, nutrient concentration and microbial dynamics in a tropical estuary.},
journal = {Environmental monitoring and assessment},
volume = {192},
number = {10},
pages = {660},
pmid = {32975666},
issn = {1573-2959},
support = {HiCOE (IOES-2014D)//Ministry of Higher Education/ ; FRGS (FP061-2018A)//Ministry of Higher Education/ ; },
mesh = {Chlorophyll A ; Environmental Monitoring ; *Estuaries ; Humans ; Hypoxia ; Nutrients ; *Rivers ; Seasons ; },
abstract = {We sampled the Klang estuary during the inter-monsoon and northeast monsoon period (July-Nov 2011, Oct-Nov 2012), which coincided with higher rainfall and elevated Klang River flow. The increased freshwater inflow into the estuary resulted in water column stratification that was observed during both sampling periods. Dissolved oxygen (DO) dropped below 63 μM, and hypoxia was observed. Elevated river flow also transported dissolved inorganic nutrients, chlorophyll a and bacteria to the estuary. However, bacterial production did not correlate with DO concentration in this study. As hypoxia was probably not due to in situ heterotrophic processes, deoxygenated waters were probably from upstream. We surmised this as DO correlated with salinity (R[2] = 0.664, df = 86, p < 0.001). DO also decreased with increasing flushing time (R[2] = 0.556, df = 11, p < 0.01), suggesting that when flushing time (> 6.7 h), hypoxia could occur at the Klang estuary. Here, we presented a model that related riverine flow rate to the post-heavy rainfall hypoxia that explicated the episodic hypoxia at Klang estuary. As Klang estuary supports aquaculture and cockle culture, our results could help protect the aquaculture and cockle culture industry here.},
}
@article {pmid32975419,
year = {2021},
author = {Trueba-Santiso, A and Wasmund, K and Soder-Walz, JM and Marco-Urrea, E and Adrian, L},
title = {Genome Sequence, Proteome Profile, and Identification of a Multiprotein Reductive Dehalogenase Complex in Dehalogenimonas alkenigignens Strain BRE15M.},
journal = {Journal of proteome research},
volume = {20},
number = {1},
pages = {613-623},
pmid = {32975419},
issn = {1535-3907},
support = {P 29426/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Bacterial Proteins/genetics/metabolism ; *Chloroflexi ; Halogenation ; *Proteome/genetics ; *Proteomics ; },
abstract = {Bacteria of the genus Dehalogenimonas respire with vicinally halogenated alkanes via dihaloelimination. We aimed to describe involved proteins and their supermolecular organization. Metagenomic sequencing of a Dehalogenimonas-containing culture resulted in a 1.65 Mbp draft genome of Dehalogenimonas alkenigignens strain BRE15M. It contained 31 full-length reductive dehalogenase homologous genes (rdhA), but only eight had cognate rdhB gene coding for membrane-anchoring proteins. Shotgun proteomics of cells grown with 1,2-dichloropropane as an electron acceptor identified 1152 proteins representing more than 60% of the total proteome. Ten RdhA proteins were detected, including a DcpA ortholog, which was the strongest expressed RdhA. Blue native gel electrophoresis (BNE) demonstrating maximum activity was localized in a protein complex of 146-242 kDa. Protein mass spectrometry revealed the presence of DcpA, its membrane-anchoring protein DcpB, two hydrogen uptake hydrogenase subunits (HupL and HupS), an iron-sulfur protein (HupX), and subunits of a redox protein with a molybdopterin-binding motif (OmeA and OmeB) in the complex. BNE after protein solubilization with different detergent concentrations revealed no evidence for an interaction between the putative respiratory electron input module (HupLS) and the OmeA/OmeB/HupX module. All detected RdhAs comigrated with the organohalide respiration complex. Based on genomic and proteomic analysis, we propose quinone-independent respiration in Dehalogenimonas.},
}
@article {pmid32974747,
year = {2021},
author = {Souza, UA and Webster, A and Dall'Agnol, B and Morel, AP and Peters, FB and Favarini, MO and Mazim, FD and Soares, JBG and Tirelli, FP and Tortato, MA and de Lemos, ERS and Trigo, TC and Soares, JF and Reck, J},
title = {Molecular and Serological Survey of the Cat-Scratch Disease Agent (Bartonella henselae) in Free-Ranging Leopardus geoffroyi and Leopardus wiedii (Carnivora: Felidae) From Pampa Biome, Brazil.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {483-492},
pmid = {32974747},
issn = {1432-184X},
mesh = {Animals ; Animals, Wild ; Antibodies, Bacterial/blood ; Bacterial Proteins/genetics ; Bartonella/classification/genetics/immunology/isolation &amp; purification ; Bartonella henselae/classification/genetics/immunology/*isolation &amp; purification ; Brazil ; Cat-Scratch Disease/microbiology/*veterinary ; DNA, Bacterial/genetics ; Felidae/*microbiology ; Grassland ; Nucleotidyltransferases/genetics ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Phylogeny ; },
abstract = {The genus Bartonella comprises emerging bacteria that affect humans and other mammals worldwide. Felids represent an important reservoir for several Bartonella species. Domestic cats are the main reservoir of Bartonella henselae, the agent of cat scratch disease (CSD). It can be transmitted directly by scratches and bites from infected cats and via cat fleas. This study aims to investigate the circulation of Bartonella spp. in free-ranging Neotropical wild felids from Southern Brazil using serological and molecular methods. In this study, 53 live-trapped free-ranging wild felids were sampled, 39 Leopardus geoffroyi and 14 Leopardus wiedii, from five municipalities in the Rio Grande, do Sul state, southern Brazil. All captured animals were clinically healthy. Two blood samples of L. geoffroyi were positive, by PCR, for the presence of B. henselae DNA. Conversely, none of L. wiedii blood samples were positive when tested using PCR. Indirect immunofluorescence assay (IFA) showed that 28% of serum samples of wild felids were reactive (seropositive) for B. henselae by immunofluorescence, with titers ranging from 64 to 256. The results presented here provide the first evidence of a Bartonella-enzootic cycle involving L. geoffroyi and L. wiedii, which may account for the spillover of the emerging zoonotic pathogen B. henselae for the indigenous fauna in Southern Brazil.},
}
@article {pmid32974213,
year = {2020},
author = {de Souza-Basqueira, M and Ribeiro, RM and de Oliveira, LC and Moreira, CHV and Martins, RCR and Franco, DC and Amado, PPP and Mayer, MPA and Sabino, EC},
title = {Gut Dysbiosis in Chagas Disease. A Possible Link to the Pathogenesis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {402},
pmid = {32974213},
issn = {2235-2988},
support = {P50 AI098461/AI/NIAID NIH HHS/United States ; U19 AI098461/AI/NIAID NIH HHS/United States ; },
mesh = {*Chagas Disease ; Dysbiosis ; Feces ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; *Trypanosoma cruzi ; },
abstract = {Chagas disease is caused by the flagellate protozoan Trypanosoma cruzi. Cardiomyopathy and damage to gastrointestinal tissue are the main disease manifestations. There are data suggesting that the immune response to T. cruzi depends on the intestinal microbiota. We hypothesized that Chagas disease is associated with an altered gut microbiome and that these changes are related to the disease phenotype. The stool microbiome from 104 individuals, 73 with Chagas disease (30 with the cardiac, 11 with the digestive, and 32 with the indeterminate form), and 31 healthy controls was characterized using 16S rRNA amplification and sequencing. The QIIME (Quantitative Insights Into Microbial Ecology) platform was used to analyze the data. Alpha and beta diversity indexes did not indicate differences between the groups. However, the relative abundance of Verrucomicrobia, represented primarily by the genus Akkermansia, was significantly lower in the Chagas disease groups, especially the cardiac group, compared to the controls. Furthermore, differences in the relative abundances of Alistipes, Bilophila, and Dialister were observed between the groups. We conclude that T. cruzi infection results in changes in the gut microbiome that may play a role in the myocardial and intestinal inflammation seen in Chagas disease.},
}
@article {pmid32974121,
year = {2020},
author = {Lee, NLY and Huang, D and Quek, ZBR and Lee, JN and Wainwright, BJ},
title = {Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula.},
journal = {IMA fungus},
volume = {11},
number = {},
pages = {17},
pmid = {32974121},
issn = {2210-6340},
abstract = {Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems.},
}
@article {pmid32973727,
year = {2020},
author = {Kuznecova, J and Šulčius, S and Vogts, A and Voss, M and Jürgens, K and Šimoliūnas, E},
title = {Nitrogen Flow in Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Is Altered by Cyanophage Infection.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {2010},
pmid = {32973727},
issn = {1664-302X},
abstract = {Viruses can significantly influence cyanobacteria population dynamics and activity, and through this the biogeochemical cycling of major nutrients. However, surprisingly little attention has been given to understand how viral infections alter the ability of diazotrophic cyanobacteria for atmospheric nitrogen fixation and its release to the environment. This study addressed the importance of cyanophages for net [15]N2 assimilation rate, expression of nitrogenase reductase gene (nifH) and changes in nitrogen enrichment ([15]N/[14]N) in the diazotrophic cyanobacterium Aphanizomenon flos-aquae during infection by the cyanophage vB_AphaS-CL131. We found that while the growth of A. flos-aquae was inhibited by cyanophage addition (decreased from 0.02 h[-1] to 0.002 h[-1]), there were no significant differences in nitrogen fixation rates (control: 22.7 × 10[-7] nmol N heterocyte[-1]; infected: 23.9 × 10[-7] nmol N heterocyte[-1]) and nifH expression level (control: 0.6-1.6 transcripts heterocyte[-1]; infected: 0.7-1.1 transcripts heterocyte[-1]) between the infected and control A. flos-aquae cultures. This implies that cyanophage genome replication and progeny production within the vegetative cells does not interfere with the N2 fixation reactions in the heterocytes of these cyanobacteria. However, higher [15]N enrichment at the poles of heterocytes of the infected A. flos-aquae, revealed by NanoSIMS analysis indicates the accumulation of fixed nitrogen in response to cyanophage addition. This suggests reduced nitrogen transport to vegetative cells and the alterations in the flow of fixed nitrogen within the filaments. In addition, we found that cyanophage lysis resulted in a substantial release of ammonium into culture medium. Cyanophage infection seems to substantially redirect N flow from cyanobacterial biomass to the production of N storage compounds and N release.},
}
@article {pmid32973299,
year = {2020},
author = {Hernández-Del Amo, E and Dolinová, I and la Ramis-Jorba, G and Gich, F and Bañeras, L},
title = {Limited effect of radial oxygen loss on ammonia oxidizers in Typha angustifolia root hairs.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {15694},
pmid = {32973299},
issn = {2045-2322},
mesh = {Ammonia/*metabolism ; Microbiota ; Nitrification/*physiology ; Oxygen/metabolism ; Plant Roots/*metabolism ; RNA, Ribosomal, 16S/genetics ; Typhaceae/*metabolism ; },
abstract = {The benefits of plant-microbe interactions have been exploited extensively for nutrient removal. Radial oxygen loss in aquatic macrophytes potentially promotes nitrification and accelerates nitrogen removal through coupled nitrification-denitrification process. Nitrification is likely the limiting activity for an effective nitrogen removal in wetlands. In this work, we have quantified the effect of radial oxygen losses in Typha angustifolia plants in environments of contrasting salinities, including a temporary lagoon, a constructed wetland, and a river estuary. In all sites, radial oxygen diffusion occurred mainly at a narrow band, from 1 to 5 cm from the root tip, and were almost absent at the tip and basal sections of the root (> 5 cm). Root sections with active oxygen diffusion tended to show higher bacterial and archaeal densities in the rhizoplane according to 16S rRNA gene abundance data, except at higher salinities. Archaeal amoA /bacterial amoA gene ratios were highly variable among sites. Archaeal nitrifiers were only favoured over bacteria on the root surface of Typha collected from the constructed wetland. Collectively, radial oxygen loss had little effect on the nitrifying microbial community at the smaller scale (differences according to root-section), and observed differences were more likely related to prevailing physicochemical conditions of the studied environments or to long-term effects of the root microenvironment (root vs sediment comparisons).},
}
@article {pmid32970805,
year = {2020},
author = {Sakarika, M and Sosa, DAT and Depoortere, M and Rottiers, H and Ganigué, R and Dewettinck, K and Rabaey, K},
title = {The type of microorganism and substrate determines the odor fingerprint of dried bacteria targeting microbial protein production.},
journal = {FEMS microbiology letters},
volume = {367},
number = {18},
pages = {},
doi = {10.1093/femsle/fnaa138},
pmid = {32970805},
issn = {1574-6968},
mesh = {Bacteria/classification/growth &amp; development/*metabolism ; Bacterial Proteins/analysis/*metabolism ; Culture Media/chemistry/*metabolism ; Electronic Nose ; Food Microbiology ; Microbiota ; Odorants/*analysis ; Volatile Organic Compounds/analysis/metabolism ; },
abstract = {The rapidly increasing demand for protein has led to the pursuit of new protein sources, among which microbial protein (MP) is one of the most promising. Although the nutritional properties of MP are important and often well-studied, the sensory properties of the microbial cells will in part determine the commercial success of the product and are much less investigated. Here we assessed the odor fingerprint of dried bacteria originating from pure cultures and enriched mixed microbial communities using an electronic nose (e-nose). The e-nose discriminated between the different MP sources, while the choice of culture and substrate substantially affected their volatile organic compound (VOC) profile. The most dominant odor descriptors (>20% of VOC peak area) were sweet, fruity and fishy, while the mixed cultures presented higher peak areas indicating potentially more intense aromas than the pure cultures. The e-nose can detect the suitability of new MP sources and determine their best end-use.},
}
@article {pmid32969526,
year = {2021},
author = {Niemeier-Walsh, C and Ryan, PH and Meller, J and Ollberding, NJ and Adhikari, A and Indugula, R and Reponen, T},
title = {The mycobiomes and bacteriomes of sputum, saliva, and home dust.},
journal = {Indoor air},
volume = {31},
number = {2},
pages = {357-368},
doi = {10.1111/ina.12750},
pmid = {32969526},
issn = {1600-0668},
support = {T42OH008432/OH/NIOSH CDC HHS/United States ; R21ES024807/ES/NIEHS NIH HHS/United States ; },
mesh = {Adolescent ; Air Microbiology ; *Air Pollution, Indoor ; Bacteria ; Cohort Studies ; DNA, Bacterial ; DNA, Fungal ; Dust/analysis ; *Environmental Monitoring ; Fungi ; Housing ; Humans ; *Microbiota ; *Mycobiome ; RNA, Ribosomal, 16S ; Respiratory System ; Saliva/microbiology ; },
abstract = {Respiratory microbiome is an understudied area of research compared to other microbiomes of the human body. The respiratory tract is exposed to an array of environmental pollutants, including microbes. Yet, we know very little about the relationship between environmental and respiratory microbiome. The primary aim of our study was to compare the mycobiomes and bacteriomes between three sample types from the same participants, including home dust, saliva, and sputum. Samples were collected from 40 adolescents in a longitudinal cohort. We analyzed the samples using 16s bacterial rDNA and ITS fungal rDNA gene sequencing, as well as quantitative PCR with universal fungal and bacterial primers. Results showed that home dust had the greatest alpha diversity between the three sample types for both bacteria and fungi. Dust had the highest total fungal load and the lowest total bacterial load. Sputum had greater bacterial diversity than saliva, but saliva had greater fungal diversity than sputum. The distribution of major bacterial phyla differed between all sample types. However, the distribution of major fungal classes differed only between sputum and saliva. Future research should examine the biological significance of the taxa found in each sample type based on microbial ecology and associations with health effects.},
}
@article {pmid32968841,
year = {2021},
author = {Zhao, D and Zhang, Z and Niu, H and Guo, H},
title = {Win by Quantity: a Striking Rickettsia-Bias Symbiont Community Revealed by Seasonal Tracking in the Whitefly Bemisia tabaci.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {523-534},
pmid = {32968841},
issn = {1432-184X},
support = {31701797//the National Natural Science Foundation of China/ ; BK20170598//the Natural Science Foundation of Jiangsu Province, China/ ; BE2010342//the Key Research and Development Program of Jiangsu Province, China/ ; },
mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; China ; Cucumis sativus/parasitology ; Gossypium/parasitology ; Hemiptera/*microbiology ; Microbial Interactions ; *Microbiota ; Rickettsia/classification/genetics/*isolation &amp; purification ; Seasons ; *Symbiosis ; },
abstract = {Maintaining an adaptive seasonality is a basic ecological requisite for cold-blooded organism insects which usually harbor various symbionts. However, how coexisting symbionts coordinate in insects during seasonal progress is still unknown. The whitefly Bemisia tabaci in China harbors the obligate symbiont Portiera that infects each individual, as well as various facultative symbionts. In this study, we investigated whitefly populations in cucumber and cotton fields from May to December 2019, aiming to reveal the fluctuations of symbiont infection frequencies, symbiont coordination in multiple infected individuals, and host plants effects on symbiont infections. The results indicated that the facultative symbionts Hamiltonella (H), Rickettsia (R), and Cardinium (C) exist in field whiteflies, with single (H) and double (HC and HR) infections occurring frequently. Infection frequencies of Hamiltonella (always 100%) and Cardinium (29.50-34.38%) remained steady during seasonal progression. Rickettsia infection frequency in the cucumber whitefly population decreased from 64.47% in summer to 35.29% in winter. Significantly lower Rickettsia infection frequency (15.55%) was identified in cotton whitefly populations and was not subject to seasonal fluctuation. Nevertheless, Rickettsia had a significantly quantitative advantage in the symbiont community of whitefly individuals and populations from both cucumber and cotton field all through the seasons. Moreover, higher Portiera and Hamiltonella densities were found in HC and HR whitefly than in H whitefly, suggesting these symbionts may contribute to producing nutrients for their symbiont partners. These results provide ample cues to further explore the interactions between coexisting symbionts, the coevolutionary relationship between symbionts and host symbiont-induced effects on host plant use.},
}
@article {pmid32967081,
year = {2020},
author = {Ortiz, M and Bosch, J and Coclet, C and Johnson, J and Lebre, P and Salawu-Rotimi, A and Vikram, S and Makhalanyane, T and Cowan, D},
title = {Microbial Nitrogen Cycling in Antarctic Soils.},
journal = {Microorganisms},
volume = {8},
number = {9},
pages = {},
pmid = {32967081},
issn = {2076-2607},
abstract = {The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more "hospitable" maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.},
}
@article {pmid32963580,
year = {2020},
author = {Floková, K and Shimels, M and Andreo Jimenez, B and Bardaro, N and Strnad, M and Novák, O and Bouwmeester, HJ},
title = {An improved strategy to analyse strigolactones in complex sample matrices using UHPLC-MS/MS.},
journal = {Plant methods},
volume = {16},
number = {},
pages = {125},
pmid = {32963580},
issn = {1746-4811},
abstract = {BACKGROUND: Strigolactones represent the most recently described group of plant hormones involved in many aspects of plant growth regulation. Simultaneously, root exuded strigolactones mediate rhizosphere signaling towards beneficial arbuscular mycorrhizal fungi, but also attract parasitic plants. The seed germination of parasitic plants induced by host strigolactones leads to serious agricultural problems worldwide. More insight in these signaling molecules is hampered by their extremely low concentrations in complex soil and plant tissue matrices, as well as their instability. So far, the combination of tailored isolation-that would replace current unspecific, time-consuming and labour-intensive processing of large samples-and a highly sensitive method for the simultaneous profiling of a broad spectrum of strigolactones has not been reported.<br><br>RESULTS: Depending on the sample matrix, two different strategies for the rapid extraction of the seven structurally similar strigolactones and highly efficient single-step pre-concentration on polymeric RP SPE sorbent were developed and validated. Compared to conventional methods, controlled temperature during the extraction and the addition of an organic modifier (acetonitrile, acetone) to the extraction solvent helped to tailor strigolactone isolation from low initial amounts of root tissue (150&#xa0;mg fresh weight, FW) and root exudate (20&#xa0;ml), which improved both strigolactone stability and sample purity. We have designed an efficient UHPLC separation with sensitive MS/MS detection for simultaneous analysis of seven natural strigolactones including their biosynthetic precursors-carlactone and carlactonoic acid. In combination with the optimized UHPLC-MS/MS method, attomolar detection limits were achieved. The new method allowed successful profiling of seven strigolactones in small exudate and root tissue samples of four different agriculturally important plant species-sorghum, rice, pea and tomato.<br><br>CONCLUSION: The established method provides efficient strigolactone extraction with aqueous mixtures of less nucleophilic organic solvents from small root tissue and root exudate samples, in combination with rapid single-step pre-concentration. This method improves strigolactone stability and eliminates the co-extraction and signal of matrix-associated contaminants during the final UHPLC-MS/MS analysis with an electrospray interface, which dramatically increases the overall sensitivity of the analysis. We show that the method can be applied to a variety of plant species.},
}
@article {pmid32963001,
year = {2020},
author = {Dueholm, MS and Andersen, KS and McIlroy, SJ and Kristensen, JM and Yashiro, E and Karst, SM and Albertsen, M and Nielsen, PH},
title = {Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax).},
journal = {mBio},
volume = {11},
number = {5},
pages = {},
pmid = {32963001},
issn = {2150-7511},
mesh = {Automation, Laboratory ; Bacteria/*classification ; DNA Primers ; *Databases, Nucleic Acid ; *Ecosystem ; *High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Reference Values ; Sequence Analysis, DNA ; Wastewater/microbiology ; },
abstract = {High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene amplicon sequence variant (FL-ASV) resolved reference databases that include high-identity references (>98.7% identity) for nearly all abundant bacteria (>0.01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an example. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for amplicon sequencing, allowing researchers to choose those that are ideal for their ecosystem. Reference databases processed with AutoTax greatly improves the classification of short-read 16S rRNA ASVs at the genus- and species-level, compared with the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.},
}
@article {pmid32962223,
year = {2020},
author = {Rothman, JA and Cox-Foster, DL and Andrikopoulos, C and McFrederick, QS},
title = {Diet Breadth Affects Bacterial Identity but Not Diversity in the Pollen Provisions of Closely Related Polylectic and Oligolectic Bees.},
journal = {Insects},
volume = {11},
number = {9},
pages = {},
pmid = {32962223},
issn = {2075-4450},
support = {NNX15AP99A/NASA/NASA/United States ; 2018-67011- 28123//U.S. Department of Agriculture/ ; CA-R-ENT-5109-H//U.S. Department of Agriculture/ ; 1929572//National Science Foundation/ ; Pollinating Insect Research Unit Base Funds//U.S. Department of Agriculture/ ; },
abstract = {Mounting evidence suggests that microbes found in the pollen provisions of wild and solitary bees are important drivers of larval development. As these microbes are also known to be transmitted via the environment, most likely from flowers, the diet breadth of a bee may affect the diversity and identity of the microbes that occur in its pollen provisions. Here, we tested the hypothesis that, due to the importance of floral transmission of microbes, diet breadth affects pollen provision microbial community composition. We collected pollen provisions at four sites from the polylectic bee Osmia lignaria and the oligolectic bee Osmia ribifloris. We used high-throughput sequencing of the bacterial 16S rRNA gene to characterize the bacteria found in these provisions. We found minimal overlap in the specific bacterial variants in pollen provisions across the host species, even when the bees were constrained to foraging from the same flowers in cages at one site. Similarly, there was minimal overlap in the specific bacterial variants across sites, even within the same host species. Together, these findings highlight the importance of environmental transmission and host specific sorting influenced by diet breadth for microbes found in pollen provisions. Future studies addressing the functional consequences of this filtering, along with tests for differences between more species of oligoletic and polylectic bees will provide rich insights into the microbial ecology of solitary bees.},
}
@article {pmid32962069,
year = {2020},
author = {Cold, F and Kousgaard, SJ and Halkjaer, SI and Petersen, AM and Nielsen, HL and Thorlacius-Ussing, O and Hansen, LH},
title = {Fecal Microbiota Transplantation in the Treatment of Chronic Pouchitis: A Systematic Review.},
journal = {Microorganisms},
volume = {8},
number = {9},
pages = {},
pmid = {32962069},
issn = {2076-2607},
support = {7076-00129B//Danish Innovation Fund/ ; },
abstract = {The objective was to evaluate available literature on treatment of chronic pouchitis with fecal microbiota transplantation (FMT) focusing on clinical outcomes, safety, and different approaches to FMT preparation and delivery. A systematic review of electronic databases was conducted using Medline, EMBASE, and the Cochrane Central Register of Controlled Trials Library from inception through April 2020. Human studies of all study types reporting results of FMT to treat chronic pouchitis were included. Nine studies, reporting FMT treatment of 69 patients with chronic pouchitis were found eligible for the review. Most studies were case series and cohort studies rated as having fair to poor quality due to high risk of bias and small sample size. Only one randomized controlled trial was included, finding no beneficial effect of FMT. In total clinical response after FMT was reported in 14 (31.8%) out of 44 evaluated patients at various timepoints after FMT, and clinical remission in ten (22.7%) patients. Only minor self-limiting adverse events were reported. FMT varied greatly regarding preparation, length of treatment, and route of delivery. The effects of FMT on symptoms of chronic pouchitis are not established, though some studies show promising results. Future controlled well-designed studies are warranted.},
}
@article {pmid32962009,
year = {2020},
author = {Pantanella, F and Lekunberri, I and Gagliardi, A and Venuto, G and Sànchez-Melsió, A and Fabiani, M and Balcázar, JL and Schippa, S and De Giusti, M and Borrego, C and Solimini, A},
title = {Effect of Urban Wastewater Discharge on the Abundance of Antibiotic Resistance Genes and Antibiotic-Resistant Escherichia coli in Two Italian Rivers.},
journal = {International journal of environmental research and public health},
volume = {17},
number = {18},
pages = {},
pmid = {32962009},
issn = {1660-4601},
mesh = {Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; *Escherichia coli/drug effects/genetics ; *Genes, Bacterial ; Italy ; RNA, Ribosomal, 16S ; *Wastewater/analysis ; },
abstract = {BACKGROUND: Wastewater treatment plants (WWTPs) are microbial factories aimed to reduce the amount of nutrients and pathogenic microorganisms in the treated wastewater before its discharge into the environment. We studied the impact of urban WWTP effluents on the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant Escherichia coli (AR-E. coli) in the last stretch of two rivers (Arrone and Tiber) in Central Italy that differ in size and flow volume.<br><br>METHODS: Water samples were collected in three seasons upstream and downstream of the WWTP, at the WWTP outlet, and at sea sites near the river mouth, and analyzed for the abundance of ARGs by qPCR and AR-E. coli using cultivation followed by disk diffusion assays.<br><br>RESULTS: For all studied genes (16S rRNA, intI1, sul1, ermB, blaTEM, tetW and qnrS), absolute concentrations were significantly higher in the Tiber than in the Arrone at all sampling sites, despite their collection date, but the prevalence of target ARGs within bacterial communities in both rivers was similar. The absolute concentrations of most ARGs were also generally higher in the WWTP effluent with median levels between log 4 and log 6 copies per ml but did not show differences along the studied stretches of rivers. Statistically significant site effect was found for E. coli phenotypic resistance to tetracycline and ciprofloxacin in the Arrone but not in the Tiber.<br><br>CONCLUSIONS: In both rivers, diffuse or point pollution sources other than the studied WWTP effluents may account for the observed resistance pattern, although the Arrone appears as more sensitive to the wastewater impact considering its lower flow volume.},
}
@article {pmid32961710,
year = {2020},
author = {Yacoub, A and Magnin, N and Gerbore, J and Haidar, R and Bruez, E and Compant, S and Guyoneaud, R and Rey, P},
title = {The Biocontrol Root-Oomycete, Pythium Oligandrum, Triggers Grapevine Resistance and Shifts in the Transcriptome of the Trunk Pathogenic Fungus, Phaeomoniella Chlamydospora.},
journal = {International journal of molecular sciences},
volume = {21},
number = {18},
pages = {},
pmid = {32961710},
issn = {1422-0067},
mesh = {Ascomycota/*growth &amp; development ; *Disease Resistance ; *Pest Control, Biological ; Plant Diseases/*microbiology ; Pythium/*growth &amp; development ; Vitis/*microbiology ; },
abstract = {The worldwide increase in grapevine trunk diseases, mainly esca, represents a major threat for vineyard sustainability. Biocontrol of a pioneer fungus of esca, Phaeomoniella chlamydospora, was investigated here by deciphering the tripartite interaction between this trunk-esca pathogen, grapevine and the biocontrol-oomycete, Pythium oligandrum. When P. oligandrum colonizes grapevine roots, it was observed that the wood necroses caused by P. chlamydospora were significantly reduced. Transcriptomic analyses of plant and fungus responses were performed to determine the molecular events occurring, with the aim to relate P.chlamydospora degradation of wood to gene expression modulation. Following P. oligandrum-root colonization, major transcriptomic changes occurred both, in the grapevine-defense system and in the P. chlamydospore-virulence factors. Grapevine-defense was enhanced in response to P. chlamydospora attacks, with P. oligandrum acting as a plant-systemic resistance inducer, promoting jasmonic/ethylene signaling pathways and grapevine priming. P. chlamydospora pathogenicity genes, such as those related to secondary metabolite biosynthesis, carbohydrate-active enzymes and transcription regulators, were also affected in their expression. Shifts in grapevine responses and key-fungal functions were associated with the reduction of P. chlamydospora wood necroses. This study provides evidence of wood fungal pathogen transcriptional changes induced by a root biocontrol agent, P. oligandrum, in which there is no contact between the two microorganisms.},
}
@article {pmid32961324,
year = {2020},
author = {de Souza, CM and Garcia, MT and de Barros, PP and Pedroso, LLC and Ward, RADC and Strixino, JF and Melo, VMM and Junqueira, JC},
title = {Chitosan enhances the antimicrobial photodynamic inactivation mediated by Photoditazine® against Streptococcus mutans.},
journal = {Photodiagnosis and photodynamic therapy},
volume = {32},
number = {},
pages = {102001},
doi = {10.1016/j.pdpdt.2020.102001},
pmid = {32961324},
issn = {1873-1597},
mesh = {*Anti-Infective Agents ; Biofilms ; *Chitosan ; *Dental Caries/drug therapy ; Humans ; *Photochemotherapy/methods ; Photosensitizing Agents/pharmacology ; Streptococcus mutans ; },
abstract = {Chitosan (CS), a biopolymer with intrinsic antimicrobial activity, can increase antimicrobial photodynamic inactivation (aPDI). The aim of this study was to evaluate the capacity of CS to potentiate the efficacy of Photoditazine® (PDZ)-mediated aPDI of the cariogenic bacterium Streptococcus mutans. CS effectively augmented the effects of aPDI, with reductions of approximately 4.5 logs in both planktonic and biofilm states. The combined treatment was also capable of reducing the number of S. mutans cells and amount of extracellular matrix in biofilms formed on enamel surfaces, which were characterized using scanning electron microscopy analysis. Furthermore, CS increased the absorption of PDZ by S. mutans cells. The combination of CS with PDZ-mediated aPDI is hence a promising antimicrobial approach against S. mutans and may be useful to control dental caries.},
}
@article {pmid32960315,
year = {2021},
author = {Sodhi, KK and Kumar, M and Singh, DK},
title = {Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing.},
journal = {Archives of microbiology},
volume = {203},
number = {1},
pages = {367-375},
pmid = {32960315},
issn = {1432-072X},
mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; DNA, Bacterial/genetics ; *High-Throughput Nucleotide Sequencing ; Industrial Waste ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; },
abstract = {A small percentage of the total freshwater on Earth is represented by river water. Microbes have an essential role to play in the biogeochemical cycles, mineralization of organic water, along with xenobiotics degradation. Microbial dynamics are susceptible to environmental stressors which includes pollutants such as antibiotics, metals, and other degradants. River Yamuna is polluted extensively by domestic and industrial wastes. Xenobiotics, when released into the environment, can lead to water pollution. The present study evaluates the microbial diversity in Yamuna River (28°40'5.53'' N, 77°15'0.35'' E) along with the prediction of the metagenome function. In this context, the metagenomic DNA was extracted and sequencing was done on Illumina@MiSeq platform. The total number of OTUs picked was 41,994, out of which 74% were classified within the kingdom Bacteria. 35% of the OTUs were assigned to phylum Proteobacteria, followed by Bacteriodetes (22%), whereas 26% of OTUs were unassigned. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to predict metagenomic functions using 16S rDNA as a marker. Metagenomic reads were assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous (COG), and Gene Ontology (GO). Functional characterization reveals the presence of methyl-accepting chemotaxis protein which is an important adaptation for the microbes in the environment. The enzymes can be mapped for the bioremediation of xenobiotics. Information obtained from the amplicon sequencing of River Yamuna, collaborated with "omic" studies, may help in the design of bioremediation strategies and can be used for environmental clean-up of pollutants.},
}
@article {pmid32958725,
year = {2020},
author = {Wünsch, D and Strijkstra, A and Wöhlbrand, L and Freese, HM and Scheve, S and Hinrichs, C and Trautwein, K and Maczka, M and Petersen, J and Schulz, S and Overmann, J and Rabus, R},
title = {Global Response of Phaeobacter inhibens DSM 17395 to Deletion of Its 262-kb Chromid Encoding Antibiotic Synthesis.},
journal = {Microbial physiology},
volume = {30},
number = {1-6},
pages = {9-24},
doi = {10.1159/000508591},
pmid = {32958725},
issn = {2673-1673},
mesh = {Amino Acids ; Anti-Bacterial Agents/*biosynthesis ; Bacterial Proteins/genetics/metabolism ; Biological Transport ; Bioreactors ; Carbon Dioxide ; Chromosomes ; Proteome ; Replicon ; Rhodobacteraceae/*genetics/*metabolism ; Transcriptome ; Tropolone/analogs &amp; derivatives ; },
abstract = {The marine alphaproteobacterium Phaeobacter inhibens DSM 17395, a member of the Roseobacter group, was recently shown to markedly enhance growth upon deletion of its 262-kb chromid encoding biosynthesis of tropodithietic acid (TDA). To scrutinize the metabolic/regulatory adaptations that underlie enhanced growth of the Δ262 mutant, its transcriptome and proteome compared to the wild type were investigated in process-controlled bioreactors with Casamino Acids as growth substrate. Genome resequencing revealed only few additional genetic changes (a heterogenic insertion, prophage activation, and several point mutations) between wild type and Δ262 mutant, albeit with no conceivable effect on the studied growth physiology. The abundances of the vast majority of transcripts and proteins involved in the catabolic network for complete substrate oxidation to CO2 were found to be unchanged, suggesting that the enhanced amino acid utilization of the Δ262 mutant did not require elevated synthesis of most enzymes of the catabolic network. Similarly, constituents of genetic information processing and cellular processes remained mostly unchanged. In contrast, 426 genes displayed differential expression, of which 410 were localized on the 3.2-Mb chromosome, 5 on the 65-kb chromid, and 11 on the 78-kb chromid. Notably, the branched-chain amino transferase IlvE acting on rapidly utilized Val, Ile, and Leu was upregulated. Moreover, the transportome was reconfigured, as evidenced from increased abundances of transcripts and proteins of several uptake systems for amino acids and inorganic nutrients (e.g., phosphate). Some components of the respiratory chain were also upregulated, which correlates with the higher respiration rates of the Δ262 mutant. Furthermore, chromosomally encoded transcripts and proteins that are peripherally related to TDA biosynthesis (e.g., the serine acyl transferase CysE) were strongly downregulated in the Δ262 mutant. Taken together, these observations reflect adaptations to enhanced growth as well as the functional interconnectivity of the replicons of P. inhibens DSM 17395.},
}
@article {pmid32957572,
year = {2020},
author = {Wang, Q and Fu, S and Yang, Q and Hao, J and Zhou, C and Liu, Y},
title = {The Impact of Water Intrusion on Pathogenic Vibrio Species to Inland Brackish Waters of China.},
journal = {International journal of environmental research and public health},
volume = {17},
number = {18},
pages = {},
pmid = {32957572},
issn = {1660-4601},
mesh = {China ; Multilocus Sequence Typing ; *Seawater/virology ; *Vibrio cholerae ; *Vibrio parahaemolyticus/genetics ; Water ; Water Microbiology ; Water Movements ; },
abstract = {The estuary is the ecological niche of pathogenic Vibrio spp. as it provides abundant organic and inorganic nutrients from seawater and rivers. However, little is known about the ecology of these Vibrio species in the inland brackish water area. In this study, their co-occurrence and relationships to key environmental constraints (salinity and temperature) in the Hun-Tai River of China were examined using the most probable number polymerase chain reaction (MPN-PCR) approach. We hereby report 2-year continuous surveillance based on six water indices of the Hun-Tai River. The results showed that seawater intrusion maximally reached inland as far as 26.5 km for the Hun-Tai River. Pathogenic Vibrio spp. were detected in 21.9% of the water samples. In particular, V. cholerae, V. parahaemolyticus, and V. vulnificus were isolated in 10 (10.4%), 20 (20.8.5%), and 2 (2.08%) samples, respectively. All V. parahaemolyticus strains were tdh gene negative, 10% were positive for the trh gene. Multi-locus sequence typing (MLST) divided V. parahaemolyticus strains into 12 sequence types (STs) for the Hun-Tai River. Five STs were respectively present in various locations along the Hun-Tai River. The PCR assay for detecting six virulence genes and Vibrio seventh pandemic island I and II revealed three genotypes in 12 V. cholerae isolates. The results of our study showed that seawater intrusion and salinity have profound effects on the distribution of pathogenic Vibrio spp. in the inland river, suggesting a potential health risk associated with the waters of the Hun-Tai River used for irrigation and drinking.},
}
@article {pmid32950135,
year = {2020},
author = {Peruzy, MF and Aponte, M and Proroga, YTR and Capuano, F and Cristiano, D and Delibato, E and Houf, K and Murru, N},
title = {Yersinia enterocolitica detection in pork products: Evaluation of isolation protocols.},
journal = {Food microbiology},
volume = {92},
number = {},
pages = {103593},
doi = {10.1016/j.fm.2020.103593},
pmid = {32950135},
issn = {1095-9998},
mesh = {Animals ; Culture Media/chemistry/metabolism ; Food Contamination/analysis ; Meat Products/analysis/*microbiology ; Swine ; Yersinia enterocolitica/classification/genetics/*isolation &amp; purification/metabolism ; },
abstract = {Conventional methods for Yersinia enterocolitica detection in food samples are generally considered inadequate. Problems arise from the presence of the so-called "background flora", coupled to the low contamination level of the pathogen. Since, data on the microbial ecology occurring in competitive microflora are still lacking, MALDI TOF MS was used for strains 'identification after enrichment in PSB or ITC broths, and after plating on selective CIN medium at different incubation times. SYBR Green Real time PCR was used for the Y. enterocolitica strains' detection (4/O:3, 1A/O:5) in experimentally contaminated foods, as well as in naturally contaminated samples. A higher number of different bacterial genera (10 on CIN and 18 on PCA) was recorded after enrichment in PSB, whilst enrichment in ITC led to recovery of 6 and 10 genera on CIN and PCA, respectively. Yersiniaceae was the dominant family on the first day of incubation, but on the second day the percentage of isolation considerably decreased. By testing experimentally contaminated samples, substantial difficulties were encountered. The biotype 1A was always detected, whereas strain 4/O:3 proved to be poorly competitive. Based on the data, the enrichment media PSB and ITC, currently proposed for Y. enterocolitica detection, need to be improved to promote a successful pathogen's recovery.},
}
@article {pmid32949457,
year = {2020},
author = {Hermans, SM and Buckley, HL and Curran-Cournane, F and Taylor, M and Lear, G},
title = {Temporal variation in soil bacterial communities can be confounded with spatial variation.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {12},
pages = {},
doi = {10.1093/femsec/fiaa192},
pmid = {32949457},
issn = {1574-6941},
mesh = {Bacteria/genetics ; Biodiversity ; *Ecosystem ; Forests ; Humans ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; },
abstract = {Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13-24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.},
}
@article {pmid32948906,
year = {2021},
author = {Jeong, SY and Kim, TG},
title = {Spatial Variance of Species Distribution Predicts the Interspecies Interactions within a Microbial Metacommunity.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {549-552},
pmid = {32948906},
issn = {1432-184X},
support = {2018R1D1A1B07048872//Ministry of Education/ ; },
mesh = {Bacteria ; Biofilms ; *Ecosystem ; Lakes/microbiology ; *Microbial Interactions ; *Microbiota ; Reproducibility of Results ; Soil Microbiology ; },
abstract = {Interspecies interactions have a profound influence on spatial distribution of coexisting microbial species. We explored whether spatial variance of species distribution (SVSD) predicts the degree of interspecies interactions within a microbial metacommunity. Simulations were used to determine the relationships from random, lake, soil, and biofilm metacommunity datasets (1,000 times). All of the bacterial datasets showed a negative correlation between the habitat breadth (inverse to SVSD) and the numbers of total, positive, and negative interspecies interactions (P < 0.05); the only exception was the relationship between habitat breadth and negative interactions in the biofilm dataset. The random dataset had no significant relationships (P > 0.05). We repeated the simulations to determine the degree of correlation and reproducibility (100 times). Habitat breadth was negatively correlated with the total and positive interactions in all of the real datasets (P < 0.05), and the negative relationships persisted across repetitions. Despite variability in the slope of total interactions, the slope values of positive interactions were similar for the real datasets (- 19.9, - 19.2, and - 25.8 for lake, soil, and biofilm, respectively). In conclusion, our results demonstrate the patterns of species interaction-distribution and show that interspecies interactions are positively correlated with the SVSD.},
}
@article {pmid32948905,
year = {2020},
author = {Mars Brisbin, M and Conover, AE and Mitarai, S},
title = {Influence of Regional Oceanography and Hydrothermal Activity on Protist Diversity and Community Structure in the Okinawa Trough.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {746-761},
doi = {10.1007/s00248-020-01583-w},
pmid = {32948905},
issn = {1432-184X},
mesh = {*Biodiversity ; Eukaryota/*isolation &amp; purification ; *Hydrothermal Vents ; *Oceans and Seas ; Pacific Ocean ; Seawater/*chemistry ; },
abstract = {Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but the relative importance of factors shaping protist diversity, such as environmental selection and dispersal, remains difficult to parse. Water masses of a back-arc basin with hydrothermal activity provide a unique opportunity for studying the effects of dispersal and environmental selection on protist communities. In this study, we used metabarcoding to characterize protist communities in the Okinawa Trough, a back-arc spreading basin containing at least twenty-five active hydrothermal vent fields. Water was sampled from four depths at fourteen stations spanning the length of the Okinawa Trough, including three sites influenced by nearby hydrothermal vent sites. While significant differences in community structure reflecting water depth were present, protist communities were mostly homogeneous horizontally. Protist communities in the bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.},
}
@article {pmid32948266,
year = {2020},
author = {Morimoto, D and Šulčius, S and Tominaga, K and Yoshida, T},
title = {Predetermined clockwork microbial worlds: Current understanding of aquatic microbial diel response from model systems to complex environments.},
journal = {Advances in applied microbiology},
volume = {113},
number = {},
pages = {163-191},
doi = {10.1016/bs.aambs.2020.06.001},
pmid = {32948266},
issn = {0065-2164},
mesh = {Aquatic Organisms/metabolism/*physiology ; Carbon/metabolism ; Energy Metabolism ; Food Chain ; Microbial Interactions ; Microbiota/*physiology ; Models, Biological ; *Periodicity ; Photosynthesis ; Sunlight ; },
abstract = {In the photic zone of aquatic ecosystems, microorganisms with different metabolisms and their viruses form complex interactions and food webs. Within these interactions, phototrophic microorganisms such as eukaryotic microalgae and cyanobacteria interact directly with sunlight, and thereby generate circadian rhythms. Diel cycling originally generated in microbial phototrophs is directly transmitted toward heterotrophic microorganisms utilizing the photosynthetic products as they are excreted or exuded. Such diel cycling seems to be indirectly propagated toward heterotrophs as a result of complex biotic interactions. For example, cell death of phototrophic microorganisms induced by viral lysis and protistan grazing provides additional resources of dissolved organic matter to the microbial community, and so generates diel cycling in other heterotrophs with different nutrient dependencies. Likewise, differences in the diel transmitting pathway via complex interactions among heterotrophs, and between heterotrophs and their viruses, may also generate higher variation and time lag diel rhythms in different heterotrophic taxa. Thus, sunlight and photosynthesis not only contribute energy and carbon supply, but also directly or indirectly control diel cycling of the microbial community through complex interactions in the photic zone of aquatic ecosystems.},
}
@article {pmid32945836,
year = {2020},
author = {Pajdak-Stós, A and Fiałkowski, W and Fiałkowska, E},
title = {Rotifers weaken the efficiency of the cyanobacterium defence against ciliate grazers.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {11},
pages = {},
pmid = {32945836},
issn = {1574-6941},
mesh = {Animals ; *Ciliophora ; *Cyanobacteria ; *Rotifera ; },
abstract = {Cyanobacteria can protect themselves through limited dispersion and by increasing the compactness of the mucilage-covered cyanobacterial mat as well as by producing sheaths covering their trichomes. These features have been used in research to measure their degree of inducible defence. The influence of the presence of the rotifers Lecane inermis on the effectiveness of Phormidium sp. (Ph2) cyanobacterium defence was investigated. Experiments were conducted on the ciliates Pseudomicrothorax dubius and Furgasonia blochmanni, specialised in the ingestion of filamentous cyanobacteria. The most compact were cyanobacterial mats that were subjected exclusively to ciliates and the most dispersed were mats in the presence of rotifers alone. The presence of rotifers feeding on cyanobacterial mucilage led to the decreased effectiveness of the defence in two ways, by increasing the dispersion of cyanobacterial trichomes, thus loosening the cyanobacterial mat, and through the ingestion of the exopolysaccharide material covering the trichomes. As a result, in the presence of rotifers and the high density of ciliates, almost all the trichomes were removed. Moreover, in comparison with other treatments, a higher number of ciliates and rotifers remained active until the end of the experiments. This is the first report to show how rotifers can weaken the defence of cyanobacteria.},
}
@article {pmid32941745,
year = {2021},
author = {Fu, S and Ni, P and Yang, Q and Hu, H and Wang, Q and Ye, S and Liu, Y},
title = {Delineating the key virulence factors and intraspecies divergence of Vibrio harveyi via whole-genome sequencing.},
journal = {Canadian journal of microbiology},
volume = {67},
number = {3},
pages = {231-248},
doi = {10.1139/cjm-2020-0079},
pmid = {32941745},
issn = {1480-3275},
mesh = {Animals ; Biofilms/growth &amp; development ; Fishes/microbiology ; Genetic Variation ; Genome, Bacterial/*genetics ; Movement ; Multilocus Sequence Typing ; Phylogeny ; Type VI Secretion Systems/genetics ; Vibrio/classification/*genetics/*pathogenicity ; Virulence Factors/*genetics ; Whole Genome Sequencing ; },
abstract = {Vibrio harveyi is one of the major pathogens in aquaculture. To identify the key virulence factors affecting pathogenesis of V. harveyi towards fish, we conducted a field investigation for three representative fish farms infected with V. harveyi. Multilocus sequence typing (MLST) and whole-genome sequencing were conducted to delineate the phylogenetic relationship and genetic divergence of V. harveyi. A total of 25 V. harveyi strains were isolated from the diseased fish and groundwater and were subtyped into 12 sequence types by MLST. Five virulence genes, mshB, pilA, hutR, ureB, and ureG, were variably presented in the sequenced strains. The virulence gene profiles strongly correlated with the distinct pathogenicity of V. harveyi strains, with a strain harboring all five genes exhibiting the highest virulence towards fish. Phenotype assay confirmed that reduced virulence correlated with decreased motility and biofilm formation ability. Additionally, three types of type VI secretion system, namely T6SS1, T6SS2, and T6SS3, were identified in V. harveyi strains, which can be classified into six, four, and 12 subtypes, respectively. In conclusion, the results indicated that the virulence level of V. harveyi is mainly determined by the above virulence genes, which may play vital roles in environmental adaptation for V. harveyi.},
}
@article {pmid32939928,
year = {2020},
author = {Masetti, R and Zama, D and Leardini, D and Muratore, E and Turroni, S and Prete, A and Brigidi, P and Pession, A},
title = {The gut microbiome in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation.},
journal = {Pediatric blood &amp; cancer},
volume = {67},
number = {12},
pages = {e28711},
doi = {10.1002/pbc.28711},
pmid = {32939928},
issn = {1545-5017},
mesh = {Gastrointestinal Microbiome/*immunology ; Graft vs Host Disease/*etiology/pathology ; Hematologic Neoplasms/*therapy ; Hematopoietic Stem Cell Transplantation/*adverse effects ; Humans ; Transplantation, Homologous ; },
abstract = {The gut microbiome (GM) has been associated with different clinical outcomes in the context of allogeneic hematopoietic stem cell transplantation (HSCT). Large multicenter cohort studies in adults have found significant correlations with overall survival, relapse, and incidence of complications. Moreover, GM is already a promising target for therapeutic interventions. However, few data are available in children, a population presenting unique features and challenges. During childhood, the GM evolves rapidly with large structural fluctuations, alongside with the maturation of the immune system. Furthermore, the HSCT procedure presents significant differences in children. These considerations underline the importance of a specific focus on the pediatric setting, and the role of GM and its age-dependent trajectory in influencing the immunity reconstitution and clinical outcomes. This review provides a comprehensive overview of the available evidence in the field of GM and pediatric HSCT, highlighting age-specific issues and discussing GM-based therapeutic approaches.},
}
@article {pmid32935184,
year = {2021},
author = {He, Y and Zhou, Y and Weng, R and Wang, J and Chen, J and Huang, M},
title = {Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {314-322},
pmid = {32935184},
issn = {1432-184X},
support = {41877477//National Natural Science Foundation of China/ ; 18DZ1203806//Shanghai Science and Technology Development Funds/ ; 2017ZX07207001//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; 2018ZX07208008//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; },
mesh = {Ammonia/analysis/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Calcium Compounds/analysis ; Environmental Restoration and Remediation/*methods ; Geologic Sediments/chemistry/*microbiology ; Nitrates/analysis ; Oxidation-Reduction ; Oxygen/analysis ; Rivers/chemistry/*microbiology ; Species Specificity ; Water Pollutants, Chemical/metabolism ; },
abstract = {In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO3)2 injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO3)2 injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO3)2 injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO3)2 runs. Taken together, Ca(NO3)2 was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.},
}
@article {pmid32935183,
year = {2021},
author = {Phoma, BS and Makhalanyane, TP},
title = {Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {396-409},
pmid = {32935183},
issn = {1432-184X},
mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Enzymes/analysis/metabolism ; Indian Ocean ; Microbiota/genetics/*physiology ; Nutrients/analysis/metabolism ; Plankton/classification/genetics/isolation &amp; purification ; Prince Edward Island ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; },
abstract = {Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.},
}
@article {pmid32930890,
year = {2020},
author = {Gupta, D and Guzman, MS and Bose, A},
title = {Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {47},
number = {9-10},
pages = {863-876},
pmid = {32930890},
issn = {1476-5535},
support = {MCB2021822//National Science Foundation/ ; 201563111//David and Lucile Packard Foundation/ ; DESC0014613//U.S. Department of Energy/ ; W911NF-18-1-0037//U.S. Department of Defense/ ; },
mesh = {*Autotrophic Processes ; Biological Transport ; Carbon Cycle ; Electrodes ; Electron Transport ; *Electrons ; Oxidation-Reduction ; Photosynthesis/physiology ; },
abstract = {Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation-reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.},
}
@article {pmid32929739,
year = {2021},
author = {Raymond, NS and Gómez-Muñoz, B and van der Bom, FJT and Nybroe, O and Jensen, LS and Müller-Stöver, DS and Oberson, A and Richardson, AE},
title = {Phosphate-solubilising microorganisms for improved crop productivity: a critical assessment.},
journal = {The New phytologist},
volume = {229},
number = {3},
pages = {1268-1277},
doi = {10.1111/nph.16924},
pmid = {32929739},
issn = {1469-8137},
mesh = {Agriculture ; Crops, Agricultural ; *Phosphates ; Phosphorus ; *Soil ; Soil Microbiology ; },
abstract = {Phosphate-solubilising microorganisms (PSM) are often reported to have positive effects on crop productivity through enhanced phosphorus (P) nutrition. Our aim was to evaluate the validity of this concept. Most studies that report 'positive effects' of PSM on plant growth have been conducted under controlled conditions, whereas field experiments more frequently fail to demonstrate a positive response. Many studies have indicated that the mechanisms seen in vitro do not translate into improved crop P nutrition in complex soil-plant systems. Furthermore, associated mechanisms are often not rigorously assessed. We suggest that PSM do not mobilise sufficient P to change the crops' nutritional environment under field conditions. The current concept, in which PSM solubilise P 'for the plant' should thus be revised. Although PSM have the capacity to solubilise P to meet their own needs, it is the turnover of the microbial biomass that subsequently provides P to plants over a longer time. Therefore, the existing concept of PSM function is unlikely to deliver a reliable strategy for increasing crop P nutrition. A further mechanistic understanding is needed to determine how P mobilisation by PSM as a component of the whole soil community can be manipulated to become more effective for plant P nutrition.},
}
@article {pmid32925728,
year = {2020},
author = {Berentsen, B and Nagaraja, BH and Teige, EP and Lied, GA and Lundervold, AJ and Lundervold, K and Steinsvik, EK and Hillestad, ER and Valeur, J and Brønstad, I and Gilja, OH and Osnes, B and Hatlebakk, JG and Haász, J and Labus, J and Gupta, A and Mayer, EA and Benitez-Páez, A and Sanz, Y and Lundervold, A and Hausken, T},
title = {Study protocol of the Bergen brain-gut-microbiota-axis study: A prospective case-report characterization and dietary intervention study to evaluate the effects of microbiota alterations on cognition and anatomical and functional brain connectivity in patients with irritable bowel syndrome.},
journal = {Medicine},
volume = {99},
number = {37},
pages = {e21950},
pmid = {32925728},
issn = {1536-5964},
mesh = {Adolescent ; Adult ; Aged ; Brain/microbiology/physiopathology ; Case-Control Studies ; Cognition/physiology ; Diet, Carbohydrate-Restricted/*methods ; Female ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Humans ; Irritable Bowel Syndrome/*diet therapy/*microbiology/psychology ; Male ; Middle Aged ; Prospective Studies ; Young Adult ; },
abstract = {INTRODUCTION: Irritable bowel syndrome (IBS) is a common clinical label for medically unexplained gastrointestinal (GI) symptoms, recently described as a disturbance of the brain-gut-microbiota (BGM) axis. To gain a better understanding of the mechanisms underlying the poorly understood etiology of IBS, we have designed a multifaceted study that aim to stratify the complex interaction and dysfunction between the brain, the gut, and the microbiota in patients with IBS.<br><br>METHODS: Deep phenotyping data from patients with IBS (n&#x200a;=&#x200a;100) and healthy age- (between 18 and 65) and gender-matched controls (n&#x200a;=&#x200a;40) will be collected between May 2019 and December 2021. Psychometric tests, questionnaires, human biological tissue/samples (blood, faeces, saliva, and GI biopsies from antrum, duodenum, and sigmoid colon), assessment of gastric accommodation and emptying using transabdominal ultrasound, vagal activity, and functional and structural magnetic resonance imaging (MRI) of the brain, are included in the investigation of each participant. A subgroup of 60 patients with IBS-D will be further included in a 12-week low FODMAP dietary intervention-study to determine short and long-term effects of diet on GI symptoms, microbiota composition and functions, molecular GI signatures, cognitive, emotional and social functions, and structural and functional brain signatures. Deep machine learning, prediction tools, and big data analyses will be used for multivariate analyses allowing disease stratification and diagnostic biomarker detection.<br><br>DISCUSSION: To our knowledge, this is the first study to employ unsupervised machine learning techniques and incorporate systems-based interactions between the central and the peripheral components of the brain-gut-microbiota axis at the levels of the multiomics, microbiota profiles, and brain connectome of a cohort of 100 patients with IBS and matched controls; study long-term safety and efficacy of the low-FODMAP diet on changes in nutritional status, gut microbiota composition, and metabolites; and to investigate changes in the brain and gut connectome after 12 weeks strict low-FODMAP-diet in patients with IBS. However, there are also limitations to the study. As a restrictive diet, the low-FODMAP diet carries risks of nutritional inadequacy and may foster disordered eating patterns. Strict FODMAP restriction induces a potentially unfavourable gut microbiota, although the health effects are unknown.<br><br>TRIAL REGISTRATION NUMBER: NCT04296552 (ClinicalTrials.gov).},
}
@article {pmid32923720,
year = {2020},
author = {Giongo, A and Dos Anjos Borges, LG and Marconatto, L and de Lara Palhano, P and Serbent, MP and Moreira-Silva, E and de Abreu Siqueira, T and Martinho, CT and Barili, R and Paz, LV and Moser, LI and De Marco Veríssimo, C and Ketzer, JMM and Medina-Silva, R},
title = {Adaption of microbial communities to the hostile environment in the Doce River after the collapse of two iron ore tailing dams.},
journal = {Heliyon},
volume = {6},
number = {8},
pages = {e04778},
pmid = {32923720},
issn = {2405-8440},
abstract = {In November 2015, two iron ore tailing dams collapsed in the city of Mariana, Brazil. The dams' collapse generated a wave of approximately 50 million m[3] of a mixture of mining waste and water. It was a major environmental tragedy in Brazilian history, which damaged rivers, and cities 660 km away in the Doce River basin until it reached the ocean coast. Shortly after the incident, several reports informed that the concentration of metals in the water was above acceptable legal limits under Brazilian laws. Here the microbial communities in samples of water, mud, foam, and rhizosphere of Eichhornia from Doce River were analyzed for 16S and 18S rRNA-based amplicon sequencing, along with microbial isolation, chemical and mineralogical analyses. Samples were collected one month and thirteen months after the collapse. Prokaryotic communities from mud shifted drastically over time (33% Bray-Curtis similarity), while water samples were more similar (63% Bray-Curtis similarity) in the same period. After 12 months, mud samples remained with high levels of heavy metals and a reduction in the diversity of microeukaryotes was detected. Amoebozoans increased in mud samples, reaching 49% of microeukaryote abundance, with Discosea and Lobosa groups being the most abundant. The microbial communities' structure in mud samples changed adapting to the new environment condition. The characterization of microbial communities and metal-tolerant organisms from such impacted environments is essential for understanding the ecological consequences of massive anthropogenic impacts and strategies for the restoration of contaminated sites such as the Doce River.},
}
@article {pmid32923454,
year = {2020},
author = {Ardern, Z and Neuhaus, K and Scherer, S},
title = {Are Antisense Proteins in Prokaryotes Functional?.},
journal = {Frontiers in molecular biosciences},
volume = {7},
number = {},
pages = {187},
pmid = {32923454},
issn = {2296-889X},
abstract = {Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes. Across bacterial species hundreds of short open reading frames antisense to annotated genes show evidence of both transcription and translation, for instance in ribosome profiling data. Determining the functional fraction of these protein products awaits further research, including insights from studies of molecular interactions and detailed evolutionary analysis. There are multiple lines of evidence, however, that many of these newly discovered proteins are of use to the organism. Condition-specific phenotypes have been characterized for a few. These proteins should be added to genome annotations, and the methods for predicting them standardized. Evolutionary analysis of these typically young sequences also may provide important insights into gene evolution. This research should be prioritized for its exciting potential to uncover large numbers of novel proteins with extremely diverse potential practical uses, including applications in synthetic biology and responding to pathogens.},
}
@article {pmid32920672,
year = {2021},
author = {Valverde, A and Cason, ED and Gómez-Arias, A and Bozkale, D and Govender, D and Riddell, E and Cowan, D},
title = {Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa.},
journal = {Archives of microbiology},
volume = {203},
number = {1},
pages = {295-303},
pmid = {32920672},
issn = {1432-072X},
mesh = {Archaea/*drug effects/genetics ; Bacteria/*drug effects/genetics ; Geologic Sediments/chemistry/*microbiology ; Microbiota/*drug effects ; Mining ; RNA, Ribosomal, 16S/genetics ; Rivers/chemistry/*microbiology ; South Africa ; Water Pollutants/*toxicity ; },
abstract = {Human activities such as agriculture and mining are leading causes of water pollution worldwide. Individual contaminants are known to negatively affect microbial communities. However, the effect of multifaceted pollution on these communities is less well understood. We investigated, using next-generation sequencing of the 16S rRNA genes, the effects of multisource (i.e., fertilizer industry and mining) chronic pollution on bacterial and archaeal communities in water and sediments from the Olifants River catchment, South Africa. Water samples showed less microbial species diversity than sediments and both habitats displayed different microbial communities. Within each of these habitats, pollution had no effect on alpha diversity but shaped the microbial composition and taxonomy-based predicted functions. Certain prokaryotic taxa and functional groups were indicative of different degrees of pollution. Heterotrophic taxa (e.g., Flavobacterium sp.) and sulphur-oxidizing bacteria (i.e., Thiobacillus sp.) were indicators of pollution in water and sediments, respectively. Ultimately, this information could be used to develop microbial indicators of water quality degradation.},
}
@article {pmid32920671,
year = {2021},
author = {Lee, JC and Whang, KS},
title = {Lysobacter telluris sp. nov., isolated from Korean rhizosphere soil.},
journal = {Archives of microbiology},
volume = {203},
number = {1},
pages = {287-293},
pmid = {32920671},
issn = {1432-072X},
mesh = {DNA, Bacterial/genetics ; Lysobacter/*classification/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Rhizosphere ; *Soil Microbiology ; Species Specificity ; },
abstract = {A Gram-stain-negative, aerobic, non-motile, non-spore-forming light-yellow-coloured rod-shaped bacterial strain, designated YJ15[T], was isolated from soil at Bigeum island in Korea. Growth was observed at 10-37 °C (optimum, 28 °C), at pH 6.0-7.5 (optimum, pH 7.0) and in the absence of NaCl. Based on 16S rRNA gene sequence analysis, strain YJ15[T] was closely related to 'Lysobacter tongrenensis' YS037[T] (97.8%), Lysobacter pocheonensis Gsoil193[T] (96.5%) and Lysobacter daecheongensis Dae08[T] (95.8%) and phylogenetically grouped together with 'Lysobacter tongrenensis' YS037[T], Lysobacter dokdonensis DS-58[T] and Lysobacter pocheonensis Gsoil 193[T]. The DNA-DNA relatedness between strain YJ15[T] and 'Lysobacter tongrenensis' KCTC 52206[T] was 12% and the phylogenomic analysis based on the whole genome sequence demonstrated that strain YJ20[T] formed a distinct phyletic line with Lysobacterlter dokdonensis DS-58[T] showing average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of 76.3 and 21.3%, respectively. The predominant ubiquinone was identified as Q-8, and polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified aminolipids. The major fatty acids were iso-C17:1 ω9c, iso-C15:0, iso-C16:0 and iso-C17:0. The genomic DNA G + C content was 68.2 mol %. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ15[T] is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter telluris sp. nov. is proposed. The type strain is YJ15[T] (= KACC 19552[T] = NBRC 113197[T]).},
}
@article {pmid32920663,
year = {2021},
author = {Paz, C and Öpik, M and Bulascoschi, L and Bueno, CG and Galetti, M},
title = {Dispersal of Arbuscular Mycorrhizal Fungi: Evidence and Insights for Ecological Studies.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {283-292},
pmid = {32920663},
issn = {1432-184X},
support = {2018/16697-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/00212-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {Animals ; Biota ; Environment ; Geography ; Hyphae/cytology/physiology ; Mycorrhizae/cytology/isolation &amp; purification/*physiology ; Plant Roots/microbiology ; Spores, Fungal/cytology/physiology ; },
abstract = {Dispersal is a critical ecological process that modulates gene flow and contributes to the maintenance of genetic and taxonomic diversity within ecosystems. Despite an increasing global understanding of the arbuscular mycorrhizal (AM) fungal diversity, distribution and prevalence in different biomes, we have largely ignored the main dispersal mechanisms of these organisms. To provide a geographical and scientific overview of the available data, we systematically searched for the direct evidence on the AM fungal dispersal agents (abiotic and biotic) and different propagule types (i.e. spores, extraradical hyphae or colonized root fragments). We show that the available data (37 articles) on AM fungal dispersal originates mostly from North America, from temperate ecosystems, from biotic dispersal agents (small mammals) and AM fungal spores as propagule type. Much lesser evidence exists from South American, Asian and African tropical systems and other dispersers such as large-bodied birds and mammals and non-spore propagule types. We did not find strong evidence that spore size varies across dispersal agents, but wind and large animals seem to be more efficient dispersers. However, the data is still too scarce to draw firm conclusions from this finding. We further discuss and propose critical research questions and potential approaches to advance the understanding of the ecology of AM fungi dispersal.},
}
@article {pmid32920539,
year = {2021},
author = {Zhang, R and Weinbauer, MG and Peduzzi, P},
title = {Aquatic Viruses and Climate Change.},
journal = {Current issues in molecular biology},
volume = {41},
number = {},
pages = {357-380},
doi = {10.21775/cimb.041.357},
pmid = {32920539},
issn = {1467-3045},
mesh = {Carbon/metabolism ; Climate Change ; Ecosystem ; Host Microbial Interactions/physiology ; Humans ; Viruses/*metabolism ; },
abstract = {The viral component in aquatic systems clearly needs to be incorporated into future ocean and inland water climate models. Viruses have the potential to influence carbon and nutrient cycling in aquatic ecosystems significantly. Changing climate likely has both direct and indirect influence on virus-mediated processes, among them an impact on food webs, biogeochemical cycles and on the overall metabolic performance of whole ecosystems. Here we synthesise current knowledge on potential climate-related consequences for viral assemblages, virus-host interactions and virus functions, and in turn, viral processes contributing to climate change. There is a need to increase the accuracy of predictions of climate change impacts on virus- driven processes, particularly of those linked to biological production and biogeochemical cycles. Comprehension of the relationships between microbial/viral processes and global phenomena is essential to predict the influence on as well as the response of the biosphere to global change.},
}
@article {pmid32920408,
year = {2021},
author = {Soh, YNA and Kunacheva, C and Menon, S and Webster, RD and Stuckey, DC},
title = {Comparison of soluble microbial product (SMP) production in full-scale anaerobic/aerobic industrial wastewater treatment and a laboratory based synthetic feed anaerobic membrane system.},
journal = {The Science of the total environment},
volume = {754},
number = {},
pages = {142173},
doi = {10.1016/j.scitotenv.2020.142173},
pmid = {32920408},
issn = {1879-1026},
mesh = {Anaerobiosis ; Bioreactors ; Sewage ; *Waste Disposal, Fluid ; *Wastewater ; },
abstract = {This study focused on the characterisation of soluble microbial products (SMPs) produced from a full-scale multi-stage (anaerobic/aerobic) industrial wastewater treatment plant, and contrasted them to the SMPs detected in the effluent of a lab-scale AnMBR treating synthetic wastewater to determine if there were any common solutes detected irrespective of the feed organics. Recently developed analytical methods using gas chromatography coupled mass spectrometry (GC-MS) and liquid chromatography coupled quadrupole-time-of-flight (LC-Q-ToF) for SMP characterisation in a wide molecular weight (MW) range of 30-2000 Da (Da) were applied. Samples collected from the Industrial Wastewater plant were the upflow anaerobic sludge blanket (UASB) influent and effluent, and aerobic membrane bioreactor (MBR) effluent before discharge. The GC-MS detected a spike in cyclooctasulphur in the UASB effluent, an indicator of shock-loading, which disappeared after the MBR process. Alkanes, acids and nitrogenous compounds were found to be the end-products from the GC-MS results, while LC-Q-ToF analysis revealed that eicosanoids, a group of cell-signalling molecules, were produced in the aerobic MBR, and made up 71% of its effluent. A comparison of the submerged anaerobic membrane bioreactor (SAMBR) and aerobic MBR effluents using GC-MS showed that there was only a small degree of similarity between the SMPs, comprising mainly long chain alkanes and phthalate. On the other hand, LC-Q-ToF showed a large contrast in compound composition, mostly having cell-signalling functions, which deepened our understanding of the different metabolic processes occurring in aerobic and anaerobic systems. These data could be useful for future work in various areas such as controlling quorum-sensing and biofilm formation, process optimisation and control, and microbial ecology.},
}
@article {pmid32920334,
year = {2020},
author = {Candry, P and Radić, L and Favere, J and Carvajal-Arroyo, JM and Rabaey, K and Ganigué, R},
title = {Mildly acidic pH selects for chain elongation to caproic acid over alternative pathways during lactic acid fermentation.},
journal = {Water research},
volume = {186},
number = {},
pages = {116396},
doi = {10.1016/j.watres.2020.116396},
pmid = {32920334},
issn = {1879-2448},
mesh = {*Caproates ; Carbohydrates ; Fermentation ; Hydrogen-Ion Concentration ; *Lactic Acid ; },
abstract = {Carbohydrate-rich waste streams can be used for bioproduction of medium-chain carboxylic acids (MCCA) such as caproic acid. The carbohydrates in these streams can be converted to lactic acid as the initial fermentation product, which can then be fermented to MCCA by chain elongation. In this process, chain elongators compete for lactic acid with other bacterial groups that, for instance, ferment lactic acid to propionic and acetic acid. Understanding the drivers that control the competition between these two pathways is essential to maximizing MCCA production. This study aimed to investigate the competition between chain elongating and propionic acid producing organisms as a function of operational pH. Operation of long-term lactic acid fermenting reactors with varying pH values showed that pH values above 6 resulted in a propionic acid producing community dominated by Veillonella and Aminobacterium. At pH values below 6, the community moved towards chain elongation, with communities dominated by Caproiciproducens. Short-term incubations showed that rates of lactic acid consumption were strongly reduced at pH below 6 (7.7 ± 1.2 mM lactic acid·h[-1] at pH 6.5; 0.74 ± 0.33 mM lactic acid·h[-1] at pH 5.5). Similar to observations in long-term reactors, when a chain elongating community adapted to pH 5.5 was used for short-term incubations at pH 6.5, propionic acid was the dominant product. The results of this study show that pH below 6 stimulate lactic acid chain elongators through kinetic effects, and potentially improved energetics, providing a tool for microbial management of MCCA-producing systems.},
}
@article {pmid32919387,
year = {2021},
author = {Casterline, BW and Paller, AS},
title = {Early development of the skin microbiome: therapeutic opportunities.},
journal = {Pediatric research},
volume = {90},
number = {4},
pages = {731-737},
pmid = {32919387},
issn = {1530-0447},
support = {F30 AI126791/AI/NIAID NIH HHS/United States ; },
mesh = {Child ; Humans ; *Microbiota ; Skin/*microbiology ; },
abstract = {As human skin hosts a diverse microbiota in health and disease, there is an emerging consensus that dysregulated interactions between host and microbiome may contribute to chronic inflammatory disease of the skin. Neonatal skin is a unique habitat, structurally similar to the adult but with a different profile of metabolic substrates, environmental stressors, and immune activity. The surface is colonized within moments of birth with a bias toward maternal strains. Initial colonists are outcompeted as environmental exposures increase and host skin matures. Nonetheless, early life microbial acquisitions may have long-lasting effects on health through modulation of host immunity and competitive interactions between bacteria. Microbial ecology and its influence on health have been of interest to dermatologists for >50 years, and an explosion of recent interest in the microbiome has prompted ongoing investigations of several microbial therapeutics for dermatological disease. In this review, we consider how recent insight into the host and microbial factors driving development of the skin microbiome in early life offers new opportunities for therapeutic intervention. IMPACT: Advancement in understanding molecular mechanisms of bacterial competition opens new avenues of investigation into dermatological disease. Primary development of the skin microbiome is determined by immunological features of the cutaneous habitat. Understanding coordinated microbial and immunological development in the pediatric patient requires a multidisciplinary synthesis of primary literature.},
}
@article {pmid32919372,
year = {2020},
author = {Frommeyer, B and Fiedler, AW and Oehler, SR and Hanson, BT and Loy, A and Franchini, P and Spiteller, D and Schleheck, D},
title = {Environmental and Intestinal Phylum Firmicutes Bacteria Metabolize the Plant Sugar Sulfoquinovose via a 6-Deoxy-6-sulfofructose Transaldolase Pathway.},
journal = {iScience},
volume = {23},
number = {9},
pages = {101510},
pmid = {32919372},
issn = {2589-0042},
support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Bacterial degradation of the sugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) produced by plants, algae, and cyanobacteria, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a third biochemical pathway for primary SQ degradation in an aerobic Bacillus aryabhattai strain. An isomerase converts SQ to 6-deoxy-6-sulfofructose (SF). A novel transaldolase enzyme cleaves the SF to 3-sulfolactaldehyde (SLA), while the non-sulfonated C3-(glycerone)-moiety is transferred to an acceptor molecule, glyceraldehyde phosphate (GAP), yielding fructose-6-phosphate (F6P). Intestinal anaerobic bacteria such as Enterococcus gilvus, Clostridium symbiosum, and Eubacterium rectale strains also express transaldolase pathway gene clusters during fermentative growth with SQ. The now three known biochemical strategies for SQ catabolism reflect adaptations to the aerobic or anaerobic lifestyle of the different bacteria. The occurrence of these pathways in intestinal (family) Enterobacteriaceae and (phylum) Firmicutes strains further highlights a potential importance of metabolism of green-diet SQ by gut microbial communities to, ultimately, hydrogen sulfide.},
}
@article {pmid32918562,
year = {2021},
author = {Ennis, NJ and Dharumaduri, D and Bryce, JG and Tisa, LS},
title = {Metagenome Across a Geochemical Gradient of Indian Stone Ruins Found at Historic Sites in Tamil Nadu, India.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {385-395},
pmid = {32918562},
issn = {1432-184X},
mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Climate ; India ; *Metagenome ; Microbiota/*genetics ; Minerals/analysis ; Quartz/analysis ; Silicon Dioxide/*chemistry ; },
abstract = {Although stone surfaces seem unlikely to be habitable, they support microbial life. Life on these surfaces are subjected to many varying harsh conditions and require the inhabitants to exhibit resistance to environmental factors including UV irradiation, toxic metal exposure, and fluctuating temperatures and humidity. Here we report the effect of hosting stone geochemistry on the microbiome of stone ruins found in Tamil Nadu, India. The microbial communities found on the two lithologies, granite and granodiorite, hosted distinct populations of bacteria. Geochemical composition analysis of sampled stones revealed quartz mineral content as a major driver of microbial community structure, particularly promoting community richness and proportions of Cyanobacteria and Deinococcus-Thermus. Other geochemical parameters including ilmenite, albite, anorthite, and orthoclase components or elemental concentrations (Ti, Fe, Mn, Na, and K) also influenced community structure to a lesser degree than quartz. Core members of the stone microbiome community found on both lithologies were also identified and included Cyanobacteria (Chroococcidiopsaceae and Dapisostemonum CCIBt 3536), Rubrobacter, and Deinococcus. A cluster of taxa including Sphingomonas, Geodermatophilus, and Truepera were mostly found in the granodiorite samples. Community diversity correlated with quartz mineral content in these samples may indicate that the microbial communities that attach to quartz surfaces may be transient and regularly changing. This work has expanded our understanding of built-stone microbial community structure based on lithology and geochemistry.},
}
@article {pmid32918153,
year = {2021},
author = {Sajjad, W and Ali, B and Bahadur, A and Ghimire, PS and Kang, S},
title = {Bacterial Diversity and Communities Structural Dynamics in Soil and Meltwater Runoff at the Frontier of Baishui Glacier No.1, China.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {370-384},
pmid = {32918153},
issn = {1432-184X},
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; China ; Ecosystem ; Ice Cover/chemistry/*microbiology ; *Microbiota ; Soil/chemistry ; *Soil Microbiology ; Water/chemistry ; *Water Microbiology ; },
abstract = {Comprehensive knowledge of bacterial ecology mainly in supraglacial habitats is pivotal particularly at the frontier of accelerated glacier retreat. In this study, bacterial diversity and community composition in glacial soil and meltwater runoff at the frontier of Baishui Glacier No.1 were evaluated using high throughput sequencing. Significant variations in the physiochemical parameters formed an ecological gradient between soil and meltwater runoff. Based on the richness and evenness indexes, the bacterial diversity was relatively higher in soil compared with meltwater runoff. Hierarchical clustering and bi-plot ordination revealed that the taxonomic composition of soil samples was highly similar and significantly influenced by the ecological parameters than the meltwater runoff. The overall relative abundance trend of bacterial phyla and genera were greatly varied in soil and water samples. The relative abundance of Proteobacteria was higher in water runoff samples (40.5-87%) compared with soil samples (32-52.7%). Proteobacteria, Firmicutes, and a little part of Cyanobacteria occupied a major portion of water runoff while the soil was dominated by Acidobacteria (6-16.2%), Actinobacteria (5-16%), Bacteroidetes (0.5-8.8%), and Cyanobacteria (0.1-8.3%) besides Proteobacteria and Firmicutes. Higher numbers of biomarkers were found in soil group compared with the water group. The study area is diverse in terms of richness, while community structures are not evenly distributed. This study provides a preliminary understanding of the bacterial diversity and shifts in community structure in soil and meltwater runoff at the frontier of the glacial. The findings revealed that the environmental factors are a significantly strong determinant of bacterial community structures in such a closely linked ecosystem.},
}
@article {pmid32917751,
year = {2020},
author = {Park, SJ and Andrei, A&#x15e; and Bulzu, PA and Kavagutti, VS and Ghai, R and Mosier, AC},
title = {Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {22},
pages = {},
pmid = {32917751},
issn = {1098-5336},
mesh = {Bacteria/*classification/isolation &amp; purification/*metabolism ; Geologic Sediments/microbiology ; Metabolic Networks and Pathways ; *Microbiota ; Nitrites/*metabolism ; Oxidation-Reduction ; Republic of Korea ; Seawater/microbiology ; },
abstract = {Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 μM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats.IMPORTANCE Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to various nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB) yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.},
}
@article {pmid32917275,
year = {2020},
author = {Modin, O and Liébana, R and Saheb-Alam, S and Wilén, BM and Suarez, C and Hermansson, M and Persson, F},
title = {Hill-based dissimilarity indices and null models for analysis of microbial community assembly.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {132},
pmid = {32917275},
issn = {2049-2618},
mesh = {Archaea/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; *Computer Simulation ; *Microbiota ; *Software ; },
abstract = {BACKGROUND: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases, and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.<br><br>RESULTS: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.<br><br>CONCLUSIONS: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines. Video Abstract.},
}
@article {pmid32916620,
year = {2020},
author = {Lukumbuzya, M and Kristensen, JM and Kitzinger, K and Pommerening-Röser, A and Nielsen, PH and Wagner, M and Daims, H and Pjevac, P},
title = {A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria.},
journal = {Water research},
volume = {186},
number = {},
pages = {116372},
doi = {10.1016/j.watres.2020.116372},
pmid = {32916620},
issn = {1879-2448},
mesh = {*Ammonia ; *Ecosystem ; In Situ Hybridization, Fluorescence ; Oligonucleotide Probes/genetics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.},
}
@article {pmid32915303,
year = {2021},
author = {Chan, YF and Chiang, PW and Tandon, K and Rogozin, D and Degermendzhi, A and Zykov, V and Tang, SL},
title = {Spatiotemporal Changes in the Bacterial Community of the Meromictic Lake Uchum, Siberia.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {357-369},
pmid = {32915303},
issn = {1432-184X},
support = {No. 19-05-00428//&#x420;&#x43e;&#x441;&#x441;&#x438;&#x439;&#x441;&#x43a;&#x438;&#x439; &#x424;&#x43e;&#x43d;&#x434; &#x424;&#x443;&#x43d;&#x434;&#x430;&#x43c;&#x435;&#x43d;&#x442;&#x430;&#x43b;&#x44c;&#x43d;&#x44b;&#x445; &#x418;&#x441;&#x441;&#x43b;&#x435;&#x434;&#x43e;&#x432;&#x430;&#x43d;&#x438;&#x439; (&#x420;&#x424;&#x424;&#x418;) (RU)/ ; No. 18-45-243002//Krasnoyarsk Regional Fund of Science/ ; 105-2923-B-001-001-MY3//Ministry of Science and Technology, Taiwan/ ; 108-2811-M-001-603//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Hydrogen Sulfide/analysis/metabolism ; Lakes/chemistry/*microbiology ; *Microbiota ; Oxidation-Reduction ; Oxygen/analysis ; Seasons ; Siberia ; Sulfates/metabolism ; Sulfur/metabolism ; },
abstract = {Lake Uchum is a newly defined meromictic lake in Siberia with clear seasonal changes in its mixolimnion. This study characterized the temporal dynamics and vertical profile of bacterial communities in oxic and anoxic zones of the lake across all four seasons: October (autumn), March (winter), May (spring), and August (summer). Bacterial richness and diversity in the anoxic zone varied widely between time points. Proteobacteria was the dominant bacterial phylum throughout the oxic and anoxic zones across all four seasons. Alphaproteobacteria (Loktanella) and Gammaproteobacteria (Aliidiomarina) exhibited the highest abundance in the oxic and anoxic zone, respectively. Furthermore, there was a successional shift in sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria in the anoxic zone across the seasons. The most dominant SRB, Desulfonatronovibrio sp., is likely one of the main producers of hydrogen sulfide (H2S) and typically accumulates the most H2S in winter. The representative anoxygenic phototrophic bacterial group in Lake Uchum was purple sulfur bacteria (PSB). PSB were dominant (60.76%) in summer, but only had 0.2-1.5% relative abundance from autumn to spring. Multivariate analysis revealed that the abundance of these SRB and PSB correlated to the concentration of H2S in Lake Uchum. Taken together, this study provides insights into the relationships between changes in bacterial community and environmental features in Lake Uchum.},
}
@article {pmid32914254,
year = {2021},
author = {Chen, J and Xie, P and Yu, D and Xie, L and Zeng, C and Chen, J},
title = {Dynamic Change of Sedimental Microbial Community During Black Bloom-an In Situ Enclosure Simulation Study.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {304-313},
pmid = {32914254},
issn = {1432-184X},
support = {2012ZX07101-010//Major Science and Technology Program for Water Pollution Control and Treatment/ ; 2014FBZ02, 2014FB15//State Key Laboratory of Freshwater Ecology and Biotechnology/ ; 31901081//National Natural Science Foundation of China/ ; },
mesh = {Cluster Analysis ; Cyanobacteria/classification/genetics/isolation &amp; purification ; *Eutrophication ; Geologic Sediments/chemistry/*microbiology ; Lakes/chemistry/microbiology ; *Microbiota/genetics ; Odorants/analysis ; Phylogeny ; Water Pollutants, Chemical/analysis ; },
abstract = {Black bloom is a worldwide environmental problem. Sediment microbes play important roles in the process of black bloom. The dynamic change of sedimental microbial community and their potential link between taste and odor compounds during black bloom was investigated in an in situ black bloom enclosure simulation experiment. Through high-throughput sequencing and analysis, pronounced shifts of sedimental microbial community were observed on the 3rd and 7th day in the black bloom group. Microbes in Cyanobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria were obviously increased, while microbes from the phyla OP8, Chloroflexi, and Acidobacteria were decreased significantly. RDA analysis revealed that the concentrations of chlorophyll a (Chla), total phosphorus (TP), and turbidity (NTU) in the water and the TP, TN concentrations in the sediment were the main environmental factors that affect the microbial community in the sediment. Correlation analysis revealed that microbes Dechloromonas sp. (OTU003567 and OTU000093), Desulfococcus sp. (OTU000911), Chromatiaceae (OTU001222), and Methanosaeta sp. (OTU004809) were positively correlated with the taste and odor substances in the sediment, such as dimethyl sulfide (DMS), β-ionone, β-cyclocitral and geosmin. The sedimental microbial community gradually recovered in the late phase of black bloom, indicating the stability and self-recovery ability of the sedimental microbial community during black bloom. Noteworthily, we observed many possible pathogens increased significantly during the black bloom, which alerts us to keep away from contaminated sediment when black bloom occurred.},
}
@article {pmid32911871,
year = {2020},
author = {Mbareche, H and Dumont-Leblond, N and Bilodeau, GJ and Duchaine, C},
title = {An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists.},
journal = {Life (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {32911871},
issn = {2075-1729},
abstract = {High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the "dos and don'ts" involved in conducting a precise microbial ecology study.},
}
@article {pmid32910439,
year = {2020},
author = {Callewaert, C and Ravard Helffer, K and Lebaron, P},
title = {Skin Microbiome and its Interplay with the Environment.},
journal = {American journal of clinical dermatology},
volume = {21},
number = {Suppl 1},
pages = {4-11},
pmid = {32910439},
issn = {1179-1888},
mesh = {Animals ; Humans ; Humpback Whale/*microbiology ; Microbiota/*physiology ; Phylogeny ; Skin/*microbiology ; *Water Microbiology ; },
abstract = {Advances in sequencing, bioinformatics and analytics now allow the structure, function and interrelations of whole microbial communities to be studied in greater detail. Collaborative efforts and multidisciplinary studies, crossing the boundary between environmental and medical microbiology, have allowed specific environmental, animal and human microbiomes to be characterized. One of the main challenges for microbial ecology is to link the phylogenetic diversity of host-associated microbes to their functional roles within the community. Much remains to be learned on the way microbes colonize the skin of different living organisms and the way the skin microbiome reacts to the surrounding environment (air, water, etc.). In this review, we discuss examples of recent studies that have used modern technology to provide insights into microbial communities in water and on skin, such as those in natural resources (thermal spring water), large mammals (humpback whales) and humans (the skin microbiome). The results of these studies demonstrate how a greater understanding of the structure and functioning of microbiota, together with their interactions with the environment, may facilitate the discovery of new probiotics or postbiotics, provide indicators for the quality of the environment, and show how changes in lifestyle and living environment, such as urbanization, can impact on the skin microbiome and skin health and disease in humans.},
}
@article {pmid32909073,
year = {2021},
author = {Mootapally, C and Mahajan, MS and Nathani, NM},
title = {Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {540-548},
pmid = {32909073},
issn = {1432-184X},
support = {PDF/2016/001239//Science and Engineering Research Board/ ; PDF/2016/000190//Science and Engineering Research Board/ ; },
mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Genes, Bacterial/genetics ; Geologic Sediments/*microbiology ; Metagenome/*genetics ; Oceans and Seas ; Plasmids/*genetics ; Seawater/*microbiology ; Virulence Factors/genetics ; },
abstract = {Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.},
}
@article {pmid32906802,
year = {2020},
author = {Nakai, R and Naganuma, T and Tazato, N and Morohoshi, S and Koide, T},
title = {Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage.},
journal = {Microorganisms},
volume = {8},
number = {9},
pages = {},
pmid = {32906802},
issn = {2076-2607},
support = {KAKENHI Grant Number JP13J03441//Japan Society for the Promotion of Science/ ; KAKENHI Grant Number JP15H05620//Japan Society for the Promotion of Science/ ; KAKENHI Grant Number JP19H05683//Ministry of Education, Culture, Sports, Science and Technology/ ; KAKENHI Grant Number JP19H05679//Ministry of Education, Culture, Sports, Science and Technology/ ; KAKENHI Grant Number JP23570117//Japan Society for the Promotion of Science/ ; },
abstract = {Rhizobiales bacterium strain IZ6 is a novel filterable bacterium that was isolated from a suspension filtrate (<0.22 µm) of soil collected in Shimane Prefecture, western Japan. Additional closely related isolates were recovered from filterable fractions of terrestrial environmental samples collected from other places in Japan; the Gobi Desert, north-central China; and Svalbard, Arctic Norway. These findings indicate a wide distribution of this lineage. This study reports the cell variation and genomic structure of IZ6. When cultured at lower temperatures (4 °C and 15 °C), this strain contained ultra-small cells and cell-like particles in the filtrate. PacBio sequencing revealed that this chromosome (3,114,641 bp) contained 3150 protein-coding, 51 tRNA, and three rRNA genes. IZ6 showed low 16S rRNA gene sequence identity (<97%) and low average nucleotide identity (<76%) with its closest known relative, Flaviflagellibacter deserti. Unlike the methylotrophic bacteria and nitrogen-fixing bacteria in related genera, there were no genes that encoded enzymes for one-carbon-compound utilization and nitrogen fixation in the IZ6 genome; the genes related to nitrate and nitrite reductase are retained and those related to the cell membrane function tend to be slightly enriched in the genome. This genomic information helps elucidate the eco-physiological function of a phenotypically heterogeneous and diverse Rhizobiales group.},
}
@article {pmid32903459,
year = {2020},
author = {Álvarez-Rodríguez, I and Arana, L and Ugarte-Uribe, B and Gómez-Rubio, E and Martín-Santamaría, S and Garbisu, C and Alkorta, I},
title = {Type IV Coupling Proteins as Potential Targets to Control the Dissemination of Antibiotic Resistance.},
journal = {Frontiers in molecular biosciences},
volume = {7},
number = {},
pages = {201},
pmid = {32903459},
issn = {2296-889X},
abstract = {The increase of infections caused by multidrug-resistant bacteria, together with the loss of effectiveness of currently available antibiotics, represents one of the most serious threats to public health worldwide. The loss of human lives and the economic costs associated to the problem of the dissemination of antibiotic resistance require immediate action. Bacteria, known by their great genetic plasticity, are capable not only of mutating their genes to adapt to disturbances and environmental changes but also of acquiring new genes that allow them to survive in hostile environments, such as in the presence of antibiotics. One of the major mechanisms responsible for the horizontal acquisition of new genes (e.g., antibiotic resistance genes) is bacterial conjugation, a process mediated by mobile genetic elements such as conjugative plasmids and integrative conjugative elements. Conjugative plasmids harboring antibiotic resistance genes can be transferred from a donor to a recipient bacterium in a process that requires physical contact. After conjugation, the recipient bacterium not only harbors the antibiotic resistance genes but it can also transfer the acquired plasmid to other bacteria, thus contributing to the spread of antibiotic resistance. Conjugative plasmids have genes that encode all the proteins necessary for the conjugation to take place, such as the type IV coupling proteins (T4CPs) present in all conjugative plasmids. Type VI coupling proteins constitute a heterogeneous family of hexameric ATPases that use energy from the ATP hydrolysis for plasmid transfer. Taking into account their essential role in bacterial conjugation, T4CPs are attractive targets for the inhibition of bacterial conjugation and, concomitantly, the limitation of antibiotic resistance dissemination. This review aims to compile present knowledge on T4CPs as a starting point for delving into their molecular structure and functioning in future studies. Likewise, the scientific literature on bacterial conjugation inhibitors has been reviewed here, in an attempt to elucidate the possibility of designing T4CP-inhibitors as a potential solution to the dissemination of multidrug-resistant bacteria.},
}
@article {pmid32903319,
year = {2020},
author = {Møller, TE and van der Bilt, WGM and Roerdink, DL and Jørgensen, SL},
title = {Microbial Community Structure in Arctic Lake Sediments Reflect Variations in Holocene Climate Conditions.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1520},
pmid = {32903319},
issn = {1664-302X},
abstract = {The reconstruction of past climate variability using physical and geochemical parameters from lake sedimentary records is a well-established and widely used approach. These geological records are also known to contain large and active microbial communities, believed to be responsive to their surroundings at the time of deposition, and proceed to interact intimately with their physical and chemical environment for millennia after deposition. However, less is known about the potential legacy of past climate conditions on the contemporary microbial community structure. We analysed two Holocene-length (past 10 ka BP) sediment cores from the glacier-fed Ymer Lake, located in a highly climate-sensitive region on south-eastern Greenland. By combining physical proxies, solid as well as fluid geochemistry, and microbial population profiling in a comprehensive statistical framework, we show that the microbial community structure clusters according to established lithological units, and thus captures past environmental conditions and climatic transitions. Further, comparative analyses of the two sedimentary records indicates that the manifestation of regional climate depends on local settings such as water column depth, which ultimately constrains microbial variability in the deposited sediments. The strong coupling between physical and geochemical shifts in the lake and microbial variation highlights the potential of molecular microbiological data to strengthen and refine existing sedimentological classifications of past environmental conditions and transitions. Furthermore, this coupling implies that microbially controlled transformation and partitioning of geochemical species (e.g., manganese and sulphate) in Ymer lake today is still affected by climatic conditions that prevailed thousands of years back in time.},
}
@article {pmid32901388,
year = {2021},
author = {González-Dominici, LI and Saati-Santamaría, Z and García-Fraile, P},
title = {Genome Analysis and Genomic Comparison of the Novel Species Arthrobacter ipsi Reveal Its Potential Protective Role in Its Bark Beetle Host.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {471-482},
pmid = {32901388},
issn = {1432-184X},
support = {19-09072S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; CLU-2018-04//Junta de Castilla y Le&#xf3;n (ES)/ ; },
mesh = {Animals ; Antibiosis ; Arthrobacter/classification/genetics/*physiology ; Coleoptera/*microbiology ; DNA, Bacterial/genetics ; Fungi/growth &amp; development ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Host Microbial Interactions ; Phenotype ; Phylogeny ; Pinus/parasitology ; Plant Bark/*parasitology ; Plant Diseases/parasitology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The pine engraver beetle, Ips acuminatus Gyll, is a bark beetle that causes important damages in Scots pine (Pinus sylvestris) forests and plantations. As almost all higher organisms, Ips acuminatus harbours a microbiome, although the role of most members of its microbiome is not well understood. As part of a work in which we analysed the bacterial diversity associated to Ips acuminatus, we isolated the strain Arthrobacter sp. IA7. In order to study its potential role within the bark beetle holobiont, we sequenced and explored its genome and performed a pan-genome analysis of the genus Arthrobacter, showing specific genes of strain IA7 that might be related with its particular role in its niche. Based on these investigations, we suggest several potential roles of the bacterium within the beetle. Analysis of genes related to secondary metabolism indicated potential antifungal capability, confirmed by the inhibition of several entomopathogenic fungal strains (Metarhizium anisopliae CCF0966, Lecanicillium muscarium CCF6041, L. muscarium CCF3297, Isaria fumosorosea CCF4401, I. farinosa CCF4808, Beauveria bassiana CCF4422 and B. brongniartii CCF1547). Phylogenetic analyses of the 16S rRNA gene, six concatenated housekeeping genes (tuf-secY-rpoB-recA-fusA-atpD) and genome sequences indicated that strain IA7 is closely related to A. globiformis NBRC 12137[T] but forms a new species within the genus Arthrobacter; this was confirmed by digital DNA-DNA hybridization (37.10%) and average nucleotide identity (ANIb) (88.9%). Based on phenotypic and genotypic features, we propose strain IA7[T] as the novel species Arthrobacter ipsi sp. nov. (type strain IA7[T] = CECT 30100[T] = LMG 31782[T]) and suggest its protective role for its host.},
}
@article {pmid32901387,
year = {2021},
author = {Wu, C and Wei, X and Hu, Z and Liu, Y and Hu, Y and Qin, H and Chen, X and Wu, J and Ge, T and Zhran, M and Su, Y},
title = {Diazotrophic Community Variation Underlies Differences in Nitrogen Fixation Potential in Paddy Soils Across a Climatic Gradient in China.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {425-436},
pmid = {32901387},
issn = {1432-184X},
support = {2017YFD0800104//National Key Research and Development program/ ; 41977100//National Natural Science Foundation of China/ ; 41771300//National Natural Science Foundation of China/ ; 2018WK4012//Hunan Province Base for Scientific and Technological Innovation Cooperation/ ; 2017QNCXTD_GTD//Youth Innovation Team Project of Institute of Subtropical Agriculture, Chinese Academy of Sciences/ ; 2019JJ10003//Natural Science Foundation of&#xa0;Hunan Province/ ; },
mesh = {Carbon/analysis ; *Climate ; Hydrogen-Ion Concentration ; Microbiota/genetics/*physiology ; Nitrogen/analysis/metabolism ; Nitrogen Fixation/*physiology ; Nitrogenase/analysis/metabolism ; Oryza ; Oxidoreductases/genetics ; Phosphates/analysis ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Biological nitrogen (N2) fixation as a source of new N input into the soil by free-living diazotrophs is important for achieving sustainable rice agriculture. However, the dominant environmental drivers or factors influencing N2 fixation and the functional significance of the diazotroph community structure in paddy soil across a climatic gradient are not yet well understood. Thus, we characterized the diazotroph community and identified the ecological predictors of N2 fixation potential in four different climate zones (mid-temperate, warm-temperate, subtropical, and tropical paddy soils) in eastern China. Comprehensive nifH gene sequencing, functional activity detection, and correlation analysis with environmental factors were estimated. The potential nitrogenase activity (PNA) was highest in warm-temperate regions, where it was 6.2-, 2.9-, and 2.2-fold greater than in the tropical, subtropical, and mid-temperate regions, respectively; nifH gene abundance was significantly higher in warm-temperate and subtropical zones than in the tropical or mid-temperate zones. Diazotroph diversity was significantly higher in the tropical climate zone and significantly lower in the mid-temperate zone. Non-metric multidimensional scaling and canonical correlation analysis indicated that paddy soil diazotroph populations differed significantly among the four climate zones, mainly owing to differences in climate and soil pH. Structural equation models and automatic linear models revealed that climate and nutrients indirectly affected PNA by affecting soil pH and diazotroph community, respectively, while diazotroph community, C/P, and nifH gene abundance directly affected PNA. And C/P ratio, pH, and the diazotroph community structure were the main predictors of PNA in paddy soils. Collectively, the differences in diazotroph community structure have ecological significance, with important implications for the prediction of soil N2-fixing functions under climate change scenarios.},
}
@article {pmid32901386,
year = {2021},
author = {Petrzik, K and Lukavský, J and Koloniuk, I},
title = {Novel Virus on Filamentous Arthronema africanum Cyanobacterium.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {454-459},
pmid = {32901386},
issn = {1432-184X},
support = {RVO60077344//institutional support/ ; RVO67985939//institutional support/ ; Biocirtech T01000048//Technologick&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; },
mesh = {Amino Acid Sequence ; Bacteriophages/classification/genetics/*physiology ; Base Composition ; Cyanobacteria/*virology ; DNA, Viral/genetics ; Fresh Water/microbiology ; Genome Size ; Genome, Viral/genetics ; Host Specificity ; Lysogeny ; Phylogeny ; Podoviridae/classification/genetics/*physiology ; Sequence Analysis, DNA ; Viral Proteins/genetics ; },
abstract = {Widely distributed in water environments and in soil, cyanobacteria are hosts of lysogenic or lytic bacterioviruses. A novel, probably lysogenic virus (phage) for which the name Arthronema africanum virus TR020 (Aa-TR020) is proposed, has been isolated from filamentous freshwater cyanobacterium Arthronema africanum. The virus formed turbid plaques on plate culture of A. africanum strain 1980/01 but not on other Arthronema strain and other bacterial species. The genome of Aa-TR020 is linear molecule of dsDNA, 44,805 bp in length with 216 bp long terminal repeats and with G + C content of 46%. Fifty-five genes organized on plus and minus strands were predicted there. The genome size, gene arrangement, and selected protein sequences showed relatedness to Phormidium virus Pf-WMP3 and other viruses known to infect cyanobacteria and classified in the family Podoviridae.},
}
@article {pmid32897365,
year = {2020},
author = {Rodrigues, GR and Pinto, OHB and Schroeder, LF and Fernandes, GDR and Costa, OYA and Quirino, BF and Kuramae, EE and Barreto, CC},
title = {Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils.},
journal = {FEMS microbiology letters},
volume = {367},
number = {18},
pages = {},
doi = {10.1093/femsle/fnaa149},
pmid = {32897365},
issn = {1574-6968},
mesh = {Acidobacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Brazil ; Cellulose/metabolism ; Genome, Bacterial/genetics ; Hydrolysis ; Pectins/metabolism ; Phylogeny ; Polysaccharides/metabolism ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Xylans/*metabolism ; },
abstract = {The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occallatibacter and Telmatobacter. However, AB60 grew on xylan as carbon source, which was not observed in Occallatibacter species; but growth was not detected on medium containing carboxymethyl cellulose, as observed in Telmatobacter. Nevertheless, the genome analysis of AB60 revealed genes for the enzymes involved in cellulose as well as xylan degradation. In addition to enzymes involved in xylan degradation, α-l-rhamnosidase was detected in the cultures of AB60. Functional screening of a small-insert genomic library did not identify any clones capable of carboxymethyl cellulose degradation, but open reading frames coding α-l-arabinofuranosidase and α-l-rhamnosidase were present in clones showing xylan degradation halos. Both enzymes act on the lateral chains of heteropolymers such as pectin and some hemicelluloses. These results indicate that the hydrolysis of α-linked sugars may offer a metabolic niche for slow-growing Acidobacteria, allowing them to co-exist with other plant-degrading microbes that hydrolyze β-linked sugars from cellulose or hemicellulose backbones.},
}
@article {pmid32897356,
year = {2020},
author = {Bandini, F and Misci, C and Taskin, E and Cocconcelli, PS and Puglisi, E},
title = {Biopolymers modulate microbial communities in municipal organic waste digestion.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {10},
pages = {},
doi = {10.1093/femsec/fiaa183},
pmid = {32897356},
issn = {1574-6941},
mesh = {Anaerobiosis ; Biopolymers ; Bioreactors ; Digestion ; *Microbiota ; Phylogeny ; *Refuse Disposal ; },
abstract = {The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. Starch-based bioplastic showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.},
}
@article {pmid32896070,
year = {2020},
author = {Fei, C and Ochsenkühn, MA and Shibl, AA and Isaac, A and Wang, C and Amin, SA},
title = {Quorum sensing regulates 'swim-or-stick' lifestyle in the phycosphere.},
journal = {Environmental microbiology},
volume = {22},
number = {11},
pages = {4761-4778},
pmid = {32896070},
issn = {1462-2920},
support = {AD179//New York University Abu Dhabi/ ; NA19NOS4780183//National Oceanic and Atmospheric Administration (NOAA)/ ; },
mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism ; Bacteria/classification/genetics/metabolism ; *Bacterial Adhesion/genetics ; Diatoms/*microbiology ; Genes, Bacterial ; *Locomotion/genetics ; Microbiota ; Oceans and Seas ; Phytoplankton/*microbiology ; Quorum Sensing/genetics/*physiology ; },
abstract = {Interactions between phytoplankton and bacteria play major roles in global biogeochemical cycles and oceanic nutrient fluxes. These interactions occur in the microenvironment surrounding phytoplankton cells, known as the phycosphere. Bacteria in the phycosphere use either chemotaxis or attachment to benefit from algal excretions. Both processes are regulated by quorum sensing (QS), a cell-cell signalling mechanism that uses small infochemicals to coordinate bacterial gene expression. However, the role of QS in regulating bacterial attachment in the phycosphere is not clear. Here, we isolated a Sulfitobacter pseudonitzschiae F5 and a Phaeobacter sp. F10 belonging to the marine Roseobacter group and an Alteromonas macleodii F12 belonging to Alteromonadaceae, from the microbial community of the ubiquitous diatom Asterionellopsis glacialis. We show that only the Roseobacter group isolates (diatom symbionts) can attach to diatom transparent exopolymeric particles. Despite all three bacteria possessing genes involved in motility, chemotaxis, and attachment, only S. pseudonitzschiae F5 and Phaeobacter sp. F10 possessed complete QS systems and could synthesize QS signals. Using UHPLC-MS/MS, we identified three QS molecules produced by both bacteria of which only 3-oxo-C16:1 -HSL strongly inhibited bacterial motility and stimulated attachment in the phycosphere. These findings suggest that QS signals enable colonization of the phycosphere by algal symbionts.},
}
@article {pmid32894355,
year = {2021},
author = {He, W and Zhang, M and Jin, G and Sui, X and Zhang, T and Song, F},
title = {Effects of Nitrogen Deposition on Nitrogen-Mineralizing Enzyme Activity and Soil Microbial Community Structure in a Korean Pine Plantation.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {410-424},
pmid = {32894355},
issn = {1432-184X},
support = {31971527//National Natural Science Foundation of China/ ; TD2019C002//Natural Science Foudation of Heilongjiang Province/ ; },
mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; China ; Forests ; Fungi/classification/genetics/isolation &amp; purification/metabolism ; *Microbiota ; Nitrates/analysis/metabolism ; Nitrogen/analysis/*metabolism ; Peptide Hydrolases/metabolism ; Pinus/microbiology ; Soil/chemistry ; *Soil Microbiology ; Urease/metabolism ; },
abstract = {To predict the effects of nitrogen deposition on nitrogen-mineralizing enzyme activity and soil microbial community structure in artificial temperate forests in northern China, we studied the soil properties, nitrogen-mineralizing enzyme activity, and microbial community structure in the soil of a Korean pine plantation in which different concentrations (0, 20, 40, 80 kg N ha[-1] year[-1]) of ammonium nitrate were applied for 5 consecutive years. The results showed that nitrogen addition at different concentrations did not significantly affect the soil pH. High nitrogen addition (80 kg N ha[-1] year[-1]) significantly increased the soil organic matter, ammonium nitrogen, and nitrate nitrogen content in the Korean pine plantation, and ammonium nitrogen was the key factor that influenced the soil fungal community structure. The urease activity under the moderate nitrogen addition treatment (40 kg N ha[-1] year[-1]) was significantly lower than that under the control (0 kg N ha[-1] year[-1]), and the protease activity in the three treatments was also significantly lower than that in the control. There was no significant correlation between microbial community structure and the four mineralizing enzymes. After nitrogen addition at different concentrations, the Simpson and Shannon indexes of soil bacteria decreased significantly under low nitrogen addition (20 kg N ha[-1] year[-1]), but the α-diversity index of soil fungi did not show significant differences under nitrogen addition. The microbial community composition was significantly changed by the different treatments. PLS-DA analysis showed that Tardiphaga was an important genus that made the greatest contribution to the differences in bacterial community composition among treatments, as was Taeniolella for fungal community composition. The low level of nitrogen addition inhibited nitrogen mineralization in the Korean pine plantation by reducing the relative abundances of Nitrosomonadaceae and Betaproteobacteriales and by reducing the abundances of symbiotrophic fungi. Berkelbacteria and Polyporales were bacteria and fungi, respectively, that changed significantly under the high nitrogen addition treatment (80 kg N ha[-1] year[-1]). This study provides more data to support predictions of the changes in nitrogen-mineralizing enzyme activity and microbial community structure in artificial temperate forest soils in response to increased nitrogen deposition.},
}
@article {pmid32893477,
year = {2020},
author = {Castledine, M and Padfield, D and Buckling, A},
title = {Experimental (co)evolution in a multi-species microbial community results in local maladaptation.},
journal = {Ecology letters},
volume = {23},
number = {11},
pages = {1673-1681},
doi = {10.1111/ele.13599},
pmid = {32893477},
issn = {1461-0248},
support = {BB/T002522/1//NERC National Environmental research council/ ; NE/S000771/1//NERC National Environmental research council/ ; NE/P001130/1//NERC National Environmental research council/ ; },
mesh = {Acclimatization ; Adaptation, Physiological ; Biological Evolution ; *Microbiota ; },
abstract = {Interspecific coevolutionary interactions can result in rapid biotic adaptation, but most studies have focused only on species pairs. Here, we (co)evolved five microbial species in replicate polycultures and monocultures and quantified local adaptation. Specifically, growth rate assays were used to determine adaptations of each species' populations to (1) the presence of the other four species in general and (2) sympatric vs. allopatric communities. We found that species did not show an increase in net biotic adaptation:ancestral, polyculture- and monoculture-evolved populations did not have significantly different growth rates within communities. However, 4/5 species' growth rates were significantly lower within the community they evolved in relative to an allopatric community. 'Local maladaptation' suggests that species evolved increased competitive interactions to sympatric species' populations. This increased competition did not affect community stability or productivity. Our results suggest that (co)evolution within communities can increase competitive interactions that are specific to (co)evolved community members.},
}
@article {pmid32892232,
year = {2021},
author = {Dwidar, M and Jang, H and Sangwan, N and Mun, W and Im, H and Yoon, S and Choi, S and Nam, D and Mitchell, RJ},
title = {Diffusible Signaling Factor, a Quorum-Sensing Molecule, Interferes with and Is Toxic Towards Bdellovibrio bacteriovorus 109J.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {347-356},
pmid = {32892232},
issn = {1432-184X},
support = {2020R1A2C2012158//National Research Foundation of Korea/ ; 2017M1A3A3A02016642//National Research Foundation of Korea/ ; },
mesh = {4-Butyrolactone/analogs &amp; derivatives/toxicity ; Antibiosis/drug effects ; Bdellovibrio bacteriovorus/*drug effects/genetics/metabolism/physiology ; Cell Membrane/drug effects/metabolism ; Fatty Acids, Monounsaturated/*toxicity ; Flagella/genetics ; *Quorum Sensing ; Serine Proteases/genetics/metabolism ; Stress, Physiological/drug effects ; Transcriptome/drug effects ; },
abstract = {Bdellovibrio bacteriovorus 109J is a predatory bacterium which lives by predating on other Gram-negative bacteria to obtain the nutrients it needs for replication and survival. Here, we evaluated the effects two classes of bacterial signaling molecules (acyl homoserine lactones (AHLs) and diffusible signaling factor (DSF)) have on B. bacteriovorus 109J behavior and viability. While AHLs had a non-significant impact on predation rates, DSF considerably delayed predation and bdelloplast lysis. Subsequent experiments showed that 50 μM DSF also reduced the motility of attack-phase B. bacteriovorus 109J cells by 50% (38.2 ± 14.9 vs. 17 ± 8.9 μm/s). Transcriptomic analyses found that DSF caused genome-wide changes in B. bacteriovorus 109J gene expression patterns during both the attack and intraperiplasmic phases, including the significant downregulation of the flagellum assembly genes and numerous serine protease genes. While the former accounts for the reduced speeds observed, the latter was confirmed experimentally with 50 μM DSF completely blocking protease secretion from attack-phase cells. Additional experiments found that 30% of the total cellular ATP was released into the supernatant when B. bacteriovorus 109J was exposed to 200 μM DSF, implying that this QS molecule negatively impacts membrane integrity.},
}
@article {pmid32889760,
year = {2021},
author = {Harrison, JG and John Calder, W and Shuman, B and Alex Buerkle, C},
title = {The quest for absolute abundance: The use of internal standards for DNA-based community ecology.},
journal = {Molecular ecology resources},
volume = {21},
number = {1},
pages = {30-43},
doi = {10.1111/1755-0998.13247},
pmid = {32889760},
issn = {1755-0998},
support = {EPS-1655726//National Science Foundation/ ; },
mesh = {Bacteria/classification ; DNA ; *High-Throughput Nucleotide Sequencing ; *Microbiota ; *Sequence Analysis, DNA ; },
abstract = {To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional data are inherently constrained and difficult to interpret. The incorporation of internal standards (ISDs; colloquially referred to as 'spike-ins') into DNA pools can ameliorate the problems posed by relative abundance data and allow absolute abundances to be approximated. Unfortunately, many laboratory and sampling biases cause ISDs to underperform or fail. Here, we discuss how careful deployment of ISDs can avoid these complications and be an integral component of well-designed studies seeking to characterize ecological assemblages via sequencing of DNA.},
}
@article {pmid32888042,
year = {2020},
author = {Dickey, JR and Fordyce, JA and Lebeis, SL},
title = {Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {846-858},
doi = {10.1007/s00248-020-01594-7},
pmid = {32888042},
issn = {1432-184X},
support = {DEB1638922//National Science Foundation (USA)/ ; },
mesh = {Bacteria/*isolation &amp; purification ; *Microbiota ; *Rhizosphere ; Salvia/*microbiology ; Sample Size ; Soil Microbiology ; Spatial Analysis ; Tennessee ; },
abstract = {Advancements in molecular technology have reduced the constraints that the grain of observation, or the spatial resolution and volume of the sampling unit, has on the characterization of plant-associated microbiomes. With discrete ecological sampling and massive parallel sequencing, we can more precisely portray microbiome community assembly and microbial recruitment to host tissue over space and time. Here, we differentiate rarefied community richness and relative abundance in bacterial microbiomes of Salvia lyrata dependent on three spatial depths, which are discrete physical distances from the soil surface within the rhizosphere microhabitat as a proxy for the root system zones. To assess the impact of sampling grain on rarefied community richness and relative abundance, we evaluated the variation of these metrics between samples pooled prior to DNA extraction and samples pooled after sequencing. A distance-based redundancy analysis with the quantitative Jaccard distance revealed that rhizosphere microbiomes vary in richness between rhizosphere soil depths. At all orders of diversity, rarefied microbial richness was consistently lowest at the deepest samples taken (approximately 4 cm from soil surface) in comparison with other rhizosphere soil depths. We additionally show that finer grain sampling (i.e., three samples of equal volume pooled after sequencing) recovers greater microbial richness when using 16S rRNA gene sequencing to describe microbial communities found within the rhizosphere system. In summary, to further elucidate the extent host-specific microbiomes assemble within the rhizosphere, the grain at which bacterial communities are sampled should reflect and encompass fine-scale heterogeneity of the system.},
}
@article {pmid32887945,
year = {2021},
author = {Gao, CH and Cao, H and Cai, P and Sørensen, SJ},
title = {The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity.},
journal = {The ISME journal},
volume = {15},
number = {1},
pages = {29-40},
pmid = {32887945},
issn = {1751-7370},
mesh = {*Bacteria/genetics ; *Carbon ; Coculture Techniques ; Reproducibility of Results ; },
abstract = {Coculture is an important model system in microbial ecology studies. As a key experimental parameter, the initial inoculation ratio has a crucial impact on the results of the coculture system. However, such an effect has never been investigated under multiple niche conditions. In this study, we established a simple coculture system with two model bacteria in various carbon sources and investigated the influence of initial inoculum ratios of 1:1000 to 1000:1 on community structure, function, and bacterial interaction. We found that the final ratio of the cocultures with different initial inoculum ratios differed in approximately five-sixths of the carbon sources, suggesting that the final ratio is highly dependent on the initial inoculum ratio, while the carbon source preferences of bacteria could not predict the final ratio of cocultures. Furthermore, we found that the initial ratio could regulate the metabolic capacity of the coculture, as only cocultures with initial ratios of 1:1 and 1000:1 gained high capacity on 14 specific carbon sources. The underlying reason may be that the pattern of species interaction is changed by the initial ratio. In conclusion, we showed that the initial ratio can induce emergent properties in coculture. These findings suggest that the initial ratio not only impacts the reproducibility of coculture experiments but also can influence our understanding of generic microbial ecology.},
}
@article {pmid32887010,
year = {2020},
author = {Oliveira, BB and Veigas, B and Carlos, FF and Sánchez-Melsió, A and Balcázar, JL and Borrego, CM and Baptista, PV},
title = {Water safety screening via multiplex LAMP-Au-nanoprobe integrated approach.},
journal = {The Science of the total environment},
volume = {741},
number = {},
pages = {140447},
doi = {10.1016/j.scitotenv.2020.140447},
pmid = {32887010},
issn = {1879-1026},
mesh = {*Escherichia coli ; Feces ; *Nucleic Acid Amplification Techniques ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; },
abstract = {Contaminated water resources remain a major global concern regarding public health. The majority of water safety protocols include indicators of microbial contamination to evaluate the potential risk to public health and are key elements of quality guidelines. Among these, markers for total coliforms and fecal coliforms are strong indicators of co-contamination with other pathogens. Traditional methods, recurring to slow and cumbersome culture-based approaches, have been gradually replaced by molecular methods, capable of faster and more specific screening. These are usually PCR-based methods that may allow for multiple pathogen detection but require dedicated laboratory equipment, hindering the rapid on-site assessment. Here, we used a multiplex Loop-Mediated Isothermal Amplification (mLAMP) strategy for the amplification of two markers associated with the contamination by total and fecal coliforms (e.g. Escherichia coli) - lacZ and uidA genes, respectively - thus allowing for single tube multiplex detection. The mLAMP products were then subject to an Au-nanoprobe colorimetric detection assay for precise discrimination of targets. This approach was validated in 22 water samples that were also screened for the presence of lacZ and uidA using standard and quantitative PCR, with the capability for discriminating the contamination level, e.g. a semi-quantitative evaluation of water quality.},
}
@article {pmid32885507,
year = {2020},
author = {Wall, CB and Egan, CP and Swift, SIO and Hynson, NA},
title = {Three decades post-reforestation has not led to the reassembly of arbuscular mycorrhizal fungal communities associated with remnant primary forests.},
journal = {Molecular ecology},
volume = {29},
number = {21},
pages = {4234-4247},
doi = {10.1111/mec.15624},
pmid = {32885507},
issn = {1365-294X},
mesh = {Ecosystem ; Forests ; Hawaii ; *Mycobiome ; *Mycorrhizae/genetics ; Soil ; Soil Microbiology ; },
abstract = {The negative effects of deforestation can potentially be ameliorated through ecological restoration. However, reforestation alone may not reassemble the same ecological communities or functions as primary forests. In part, this failure may be owed to forest ecosystems inherently involving complex interactions among guilds of organisms. Plants, which structure forest food webs, rely on intimate associations with symbiotic microbes such as root-inhabiting mycorrhizal fungi. Here, we leverage a large-scale reforestation project on Hawai'i Island underway for over three decades to assess whether arbuscular mycorrhizal (AM) fungal communities have concurrently been restored. The reference ecosystem for this restoration project is a remnant montane native Hawaiian forest that provides critical habitat for endangered birds. We sampled soils from 12 plots within remnant and restored forest patches and characterized AM fungal communities using high-throughput amplicon sequencing. While some AM fungal community metrics were comparable between remnant and restored forest (e.g. species richness), other key characteristics were not. Specifically, community membership and the identity of AM fungal keystone species differed between the two habitat types, as well as the primary environmental factors influencing community composition. Remnant forest AM fungal communities were strongly associated with soil chemical properties, especially pH, while restored forest communities were influenced by the spatial proximity to remnant forests. We posit that combined, these differences in soil AM fungal communities could be negatively affecting the recruitment of native plant hosts and that future restoration efforts should consider plant-microbe interactions as an important facet of forest health.},
}
@article {pmid32884655,
year = {2020},
author = {Duplouy, A and Minard, G and Saastamoinen, M},
title = {The gut bacterial community affects immunity but not metabolism in a specialist herbivorous butterfly.},
journal = {Ecology and evolution},
volume = {10},
number = {16},
pages = {8755-8769},
pmid = {32884655},
issn = {2045-7758},
abstract = {Plant tissues often lack essential nutritive elements and may contain a range of secondary toxic compounds. As nutritional imbalance in food intake may affect the performances of herbivores, the latter have evolved a variety of physiological mechanisms to cope with the challenges of digesting their plant-based diet. Some of these strategies involve living in association with symbiotic microbes that promote the digestion and detoxification of plant compounds or supply their host with essential nutrients missing from the plant diet. In Lepidoptera, a growing body of evidence has, however, recently challenged the idea that herbivores are nutritionally dependent on their gut microbial community. It is suggested that many of the herbivorous Lepidopteran species may not host a resident microbial community, but rather a transient one, acquired from their environment and diet. Studies directly testing these hypotheses are however scarce and come from an even more limited number of species.By coupling comparative metabarcoding, immune gene expression, and metabolomics analyses with experimental manipulation of the gut microbial community of prediapause larvae of the Glanville fritillary butterfly (Melitaea cinxia, L.), we tested whether the gut microbial community supports early larval growth and survival, or modulates metabolism or immunity during early stages of development.We successfully altered this microbiota through antibiotic treatments and consecutively restored it through fecal transplants from conspecifics. Our study suggests that although the microbiota is involved in the up-regulation of an antimicrobial peptide, it did not affect the life history traits or the metabolism of early instars larvae.This study confirms the poor impact of the microbiota on diverse life history traits of yet another Lepidoptera species. However, it also suggests that potential eco-evolutionary host-symbiont strategies that take place in the gut of herbivorous butterfly hosts might have been disregarded, particularly how the microbiota may affect the host immune system homeostasis.},
}
@article {pmid32882545,
year = {2021},
author = {Li, L and Ning, D and Jeon, Y and Ryu, H and Santo Domingo, JW and Kang, DW and Kadudula, A and Seo, Y},
title = {Ecological insights into assembly processes and network structures of bacterial biofilms in full-scale biologically active carbon filters under ozone implementation.},
journal = {The Science of the total environment},
volume = {751},
number = {},
pages = {141409},
pmid = {32882545},
issn = {1879-1026},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
mesh = {Bacteria ; Biofilms ; Charcoal ; *Ozone ; *Water Purification ; },
abstract = {To address the adverse effects of harmful algal blooms, there are increased demands over the implementation of ozone coupled with biologically active carbon (BAC) filters in the drinking water treatment plants. Although the microbial biofilms are vital elements to support the proper performance of BAC filters, except for taxonomic affiliations, little is known about the assembly mechanisms of microbial communities in the full-scale BAC filters. This study aimed to examine how the assembly processes and their associated factors (e.g., influent characteristics, biological interactions) drive the temporal dynamics of bacterial communities in full-scale BAC filters, which underwent ozone implementation (five consecutive seasons from 2017 to 2018). The results revealed that along with the increase of bacterial taxonomic richness and evenness, stochastic processes became more crucial to determine the bacterial community assembly in the summer and autumn after ozone implementation (relative contribution: 61.23% and 83.75%, respectively). Moreover, their corresponding networks possessed simple network structures with lower modularity than other seasons, which implied lesser biological interactions among bacterial populations. The correlation between taxonomic and predicted functional diversities using functional redundancy index indicated that relatively high levels of bacterial functional redundancy (>0.83) were generally present in BAC filters. However, compared to other seasons, significantly higher degrees of functional redundancy existed in the summer and autumn after ozone implementation (0.85 ± 0.01 and 0.86 ± 0.01, respectively). Overall, this work improves our understanding of the microbial ecology of full-scale BAC filters by providing a conceptual framework that characterizes bacterial biofilm assembly processes relevant to performance optimization of full-scale BAC filters.},
}
@article {pmid32880700,
year = {2021},
author = {Sabu, EA and Gonsalves, MJ and Sreepada, RA and Shivaramu, MS and Ramaiah, N},
title = {Evaluation of the Physiological Bacterial Groups in a Tropical Biosecured, Zero-Exchange System Growing Whiteleg Shrimp, Litopenaeus vannamei.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {335-346},
pmid = {32880700},
issn = {1432-184X},
support = {PSC 0206//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/ ; },
mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Aquaculture ; Bacteria/classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; *Ecosystem ; Nitrogen/analysis/chemistry ; Penaeidae/*growth &amp; development ; Phytoplankton/classification/genetics/metabolism ; Ponds/chemistry/microbiology ; Water Quality ; },
abstract = {To elucidate the individual and multiple roles of physiological bacterial groups involved in biogeochemical cycles of carbon, nitrogen, phosphorus and sulfur, the changes in the abundance of aerobic bacteria (heterotrophs, methane oxidizers, ammonia oxidizers, sulfur oxidizers, phosphate solubilizers, phosphate accumulators) and anaerobic bacteria (total anaerobes, nitrate reducers, denitrifiers and sulfate reducers) were investigated in a biosecured, zero-exchange system stocked with whiteleg shrimp, Litopenaeus vannamei for one production cycle. Key water quality parameters during the 96-day production cycle fell within the normal range for L. vannamei culture. Results of Spearman's correlation matrix revealed that different sets of variables correlated at varying levels of significance of the interrelationships between bacterial abundances and water quality parameters. The three nitrogenous species (ammonia, nitrite and nitrate) strongly influenced the physiological bacterial groups' abundance. The strong relationship of bacterial groups with phytoplankton biomass and abundance clearly showed the trophic interconnections in nutrient exchange/recycling. Canonical correspondence analysis performed to assess the total variation revealed that the three dissolved nitrogen species followed by salinity, temperature, phytoplankton biomass and pH collectively accounted for as much as 82% of the total variation. In conclusion, the results of the study revealed that the major drivers that interweaved biogeochemical cycles are the three dissolved nitrogen species, which microbially mediated various aerobic-anaerobic assimilation/dissimilation processes in the pond ecosystem. Considering the pond microbial ecology becoming an important management tool where applied research could improve the economic and environmental sustainability of the aquaculture industry, the findings of the present study are practically relevant.},
}
@article {pmid32880699,
year = {2020},
author = {Wei, J and Segraves, KA and Li, WZ and Yang, XK and Xue, HJ},
title = {Gut bacterial communities and their contribution to performance of specialist Altica flea beetles.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {946-959},
doi = {10.1007/s00248-020-01590-x},
pmid = {32880699},
issn = {1432-184X},
support = {31672334//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Bacteria/classification/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Coleoptera/*microbiology/physiology ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; },
abstract = {Host plant shifts are a common mode of speciation in herbivorous insects. Although insects can evolve adaptations to successfully incorporate a new host plant, it is becoming increasingly recognized that the gut bacterial community may play a significant role in allowing insects to detoxify novel plant chemical defenses. Here, we examined differences in gut bacterial communities between Altica flea beetle species that feed on phylogenetically unrelated host plants in sympatry. We surveyed the gut bacterial communities of three closely related flea beetles from multiple locations using 16S rRNA amplicon sequencing. The results showed that the beetle species shared a high proportion (80.7%) of operational taxonomic units. Alpha-diversity indicators suggested that gut bacterial diversity did not differ among host species, whereas geography had a significant effect on bacterial diversity. In contrast, analyses of beta-diversity showed significant differences in gut bacterial composition among beetle species when we used species composition and relative abundance metrics, but there was no difference in composition when species presence/absence and phylogenetic distance indices were used. Within host beetle species, gut bacterial composition varied significantly among sites. A metagenomic functionality analysis predicted that the gut microbes had functions involved in xenobiotic biodegradation and metabolism as well as metabolism of terpenoids and polyketides. These predictions, however, did not differ among beetle host species. Antibiotic curing experiments showed that development time was significantly prolonged, and there was a significant decline in body weight of newly emerged adults in beetles lacking gut bacteria, suggesting the beetles may receive a potential benefit from the gut microbe-insect interaction. On the whole, our results suggest that although the gut bacterial community did not show clear host-specific patterns among Altica species, spatiotemporal variability is an important determinant of gut bacterial communities. Furthermore, the similarity of communities among these beetle species suggests that microbial facilitation may not be a determinant of host plant shifts in Altica.},
}
@article {pmid32879989,
year = {2020},
author = {Gonzalo, M and Deveau, A and Aigle, B},
title = {Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {872-884},
doi = {10.1007/s00248-020-01579-6},
pmid = {32879989},
issn = {1432-184X},
support = {ANR-11-LABX 0002 01//ANR/ ; },
mesh = {Bacteria/*growth &amp; development/isolation &amp; purification ; Forests ; France ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Rhizosphere ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Soil is a complex environment made of multiple microhabitats in which a wide variety of microorganisms co-exist and interact to form dynamic communities. While the abiotic factors that regulate the structure of these communities are now quite well documented, our knowledge of how bacteria interact with each other within these communities is still insufficient. Literature reveals so far contradictory results and is mainly focused on antagonistic interactions. To start filling this gap, we isolated 35 different bacterial isolates from grains of soil assuming that, at this scale, these bacteria would have been likely interacting in their natural habitat. We tested pairwise interactions between all isolates from each grain and scored positive and negative interactions. We compared the effects of simultaneous versus delayed co-inoculations, allowing or not to a strain to modify first its environment. One hundred fifty-seven interactions, either positive or negative, were recorded among the 525 possible one's. Members of the Bacillus subtilis, Pseudomonas and Streptomyces genera were responsible for most inhibitions, while positive interactions occurred between isolates of the Bacillales order and only in delayed inoculation conditions. Antagonist isolates had broad spectral abilities to acquire nutrients from organic and inorganic matter, while inhibited isolates tended to have little potentials. Despite an overall domination of antagonistic interactions (87%), a third of the isolates were able to stimulate or rescue the growth of other isolates, suggesting that cooperation between bacteria may be underestimated.},
}
@article {pmid32879459,
year = {2021},
author = {Rubbens, P and Props, R and Kerckhof, FM and Boon, N and Waegeman, W},
title = {Cytometric fingerprints of gut microbiota predict Crohn's disease state.},
journal = {The ISME journal},
volume = {15},
number = {1},
pages = {354-358},
pmid = {32879459},
issn = {1751-7370},
mesh = {*Crohn Disease/diagnosis ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Variations in the gut microbiome have been associated with changes in health state such as Crohn's disease (CD). Most surveys characterize the microbiome through analysis of the 16S rRNA gene. An alternative technology that can be used is flow cytometry. In this report, we reanalyzed a disease cohort that has been characterized by both technologies. Changes in microbial community structure are reflected in both types of data. We demonstrate that cytometric fingerprints can be used as a diagnostic tool in order to classify samples according to CD state. These results highlight the potential of flow cytometry to perform rapid diagnostics of microbiome-associated diseases.},
}
@article {pmid32879458,
year = {2021},
author = {Mooshammer, M and Kitzinger, K and Schintlmeister, A and Ahmerkamp, S and Nielsen, JL and Nielsen, PH and Wagner, M},
title = {Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities.},
journal = {The ISME journal},
volume = {15},
number = {1},
pages = {348-353},
pmid = {32879458},
issn = {1751-7370},
mesh = {Carbon Isotopes/analysis ; Food Chain ; Isotope Labeling ; Isotopes ; *Microbiota ; },
abstract = {Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and [13]C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.},
}
@article {pmid32877326,
year = {2020},
author = {Lee, HJ and Kim, SY and Whang, KS},
title = {Cellulomonas citrea sp. nov., isolated from paddy soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {10},
pages = {5304-5311},
doi = {10.1099/ijsem.0.004409},
pmid = {32877326},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Base Composition ; Cellulomonas/*classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; *Oryza ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; },
abstract = {Two Gram-stain-positive, facultatively anaerobic, motile, aerobic, rod-shaped and non-spore-forming actinobacteria, strains AO-9[T] and AO-18, were isolated from paddy soil collected from Daejeon, Republic of Korea. Colonies were smooth, lemon-yellow and circular and 0.5-0.8×2.0-2.4 µm in diameter after 3 days of incubation at 28 °C on tryptic soy agar. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains AO-9[T] and AO-18 belonged to the genus Cellulomonas, showing the highest sequence similarities to Cellulomonas marina FXJ8.089[T] (96.6 %), Cellulomonas endophytica SYSUP0004[T] (96.5 %), Cellulomonas gelida DSM 20111[T] (96.2 %), Cellulomonas uda DSM 20107[T] (96.1 %), Cellulomonas rhizosphaerae NEAU-TCZ24[T] (96.1 %), Cellulomonas composti TR7-06[T] (96.0 %), Cellulomonas persica JCM 18111[T] (96.0 %) and less than 96 % to other closely related species. The DNA-DNA hybridization values between strains AO-9[T] and AO-18 were 87 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain AO-9[T] and type strains of related species of the genus Cellulomonas were 84.0-85.8 % and 20.3-20.9 %, respectively. The major cellular fatty acids are anteiso-C15:0 (49.9 %), C14:0 (12.9 %) and iso-C14:0 (12.1 %). The predominant isoprenoid quinone was MK-9 (H4). The polar lipid profile consists of diphosphatidylglycerol, phosphatidylglycerol and one unidentified lipid. The DNA G+C content was 72.9 mol%. Based on its distinctive phenotypic, phylogenetic and chemotaxonomic characteristics, the two strains are considered to represent novel species of the genus Cellulomonas, for which the name Cellulomonas citrea sp. nov. is proposed. The type strain is AO-9[T] (=KACC 19069[T]=NBRC 112523[T]).},
}
@article {pmid32875141,
year = {2020},
author = {Corbin, KD and Krajmalnik-Brown, R and Carnero, EA and Bock, C and Emerson, R and Rittmann, BE and Marcus, AK and Davis, T and Dirks, B and Ilhan, ZE and Champagne, C and Smith, SR},
title = {Integrative and quantitative bioenergetics: Design of a study to assess the impact of the gut microbiome on host energy balance.},
journal = {Contemporary clinical trials communications},
volume = {19},
number = {},
pages = {100646},
pmid = {32875141},
issn = {2451-8654},
support = {R01 DK105829/DK/NIDDK NIH HHS/United States ; },
abstract = {UNLABELLED: The literature is replete with clinical studies that characterize the structure, diversity, and function of the gut microbiome and correlate the results to different disease states, including obesity. Whether the microbiome has a direct impact on obesity has not been established. To address this gap, we asked whether the gut microbiome and its bioenergetics quantitatively change host energy balance. This paper describes the design of a randomized crossover clinical trial that combines outpatient feeding with precisely controlled metabolic phenotyping in an inpatient metabolic ward. The target population was healthy, weight-stable individuals, age 18-45 and with a body mass index ≤30 kg/m[2]. Our primary objective was to determine within-participant differences in energy balance after consuming a control Western Diet versus a Microbiome Enhancer Diet intervention specifically designed to optimize the gut microbiome for positive impacts on host energy balance. We assessed the complete energy-balance equation via whole-room calorimetry, quantified energy intake, fecal energy losses, and methane production. We implemented conditions of tight weight stability and balance between metabolizable energy intake and predicted energy expenditure. We explored key factors that modulate the balance between host and microbial nutrient accessibility by measuring enteroendocrine hormone profiles, appetite/satiety, gut transit and gastric emptying. By integrating these clinical measurements with future bioreactor experiments, gut microbial ecology analysis, and mathematical modeling, our goal is to describe initial cause-and-effect mechanisms of gut microbiome metabolism on host energy balance. Our innovative methods will enable subsequent studies on the interacting roles of diet, the gut microbiome, and human physiology.<br><br>CLINICALTRIALSGOV IDENTIFIER: NCT02939703. The present study reference can be found here: https://clinicaltrials.gov/ct2/show/NCT02939703.},
}
@article {pmid32874778,
year = {2020},
author = {Marchioro, GM and Glasl, B and Engelen, AH and Serrão, EA and Bourne, DG and Webster, NS and Frade, PR},
title = {Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9644},
pmid = {32874778},
issn = {2167-8359},
abstract = {Corals are associated with diverse microbial assemblages; however, the spatial-temporal dynamics of intra-species microbial interactions are poorly understood. The coral-associated microbial community varies substantially between tissue and mucus microhabitats; however, the factors controlling the occurrence, abundance, and distribution of microbial taxa over time have rarely been explored for different coral compartments simultaneously. Here, we test (1) differentiation in microbiome diversity and composition between coral compartments (surface mucus and tissue) of two Acropora hosts (A. tenuis and A. millepora) common along inshore reefs of the Great Barrier Reef, as well as (2) the potential linkage between shifts in individual coral microbiome families and underlying host and environmental parameters. Amplicon based 16S ribosomal RNA gene sequencing of 136 samples collected over 14 months, revealed significant differences in bacterial richness, diversity and community structure among mucus, tissue and the surrounding seawater. Seawater samples were dominated by members of the Synechococcaceae and Pelagibacteraceae bacterial families. The mucus microbiome of Acropora spp. was dominated by members of Flavobacteriaceae, Synechococcaceae and Rhodobacteraceae and the tissue was dominated by Endozoicimonaceae. Mucus microbiome in both Acropora species was primarily correlated with seawater parameters including levels of chlorophyll a, ammonium, particulate organic carbon and the sum of nitrate and nitrite. In contrast, the correlation of the tissue microbiome to the measured environmental (i.e., seawater parameters) and host health physiological factors differed between host species, suggesting host-specific modulation of the tissue-associated microbiome to intrinsic and extrinsic factors. Furthermore, the correlation between individual coral microbiome members and environmental factors provides novel insights into coral microbiome-by-environment dynamics and hence has potential implications for current reef restoration and management efforts (e.g. microbial monitoring and observatory programs).},
}
@article {pmid32873609,
year = {2020},
author = {Kloosterman, AM and Shelton, KE and van Wezel, GP and Medema, MH and Mitchell, DA},
title = {RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery.},
journal = {mSystems},
volume = {5},
number = {5},
pages = {},
pmid = {32873609},
issn = {2379-5077},
support = {R01 AI144967/AI/NIAID NIH HHS/United States ; T32 GM070421/GM/NIGMS NIH HHS/United States ; },
abstract = {Many ribosomally synthesized and posttranslationally modified peptide classes (RiPPs) are reliant on a domain called the RiPP recognition element (RRE). The RRE binds specifically to a precursor peptide and directs the posttranslational modification enzymes to their substrates. Given its prevalence across various types of RiPP biosynthetic gene clusters (BGCs), the RRE could theoretically be used as a bioinformatic handle to identify novel classes of RiPPs. In addition, due to the high affinity and specificity of most RRE-precursor peptide complexes, a thorough understanding of the RRE domain could be exploited for biotechnological applications. However, sequence divergence of RREs across RiPP classes has precluded automated identification based solely on sequence similarity. Here, we introduce RRE-Finder, a new tool for identifying RRE domains with high sensitivity. RRE-Finder can be used in precision mode to confidently identify RREs in a class-specific manner or in exploratory mode to assist in the discovery of novel RiPP classes. RRE-Finder operating in precision mode on the UniProtKB protein database retrieved ∼25,000 high-confidence RREs spanning all characterized RRE-dependent RiPP classes, as well as several yet-uncharacterized RiPP classes that require future experimental confirmation. Finally, RRE-Finder was used in precision mode to explore a possible evolutionary origin of the RRE domain. The results suggest RREs originated from a co-opted DNA-binding transcriptional regulator domain. Altogether, RRE-Finder provides a powerful new method to probe RiPP biosynthetic diversity and delivers a rich data set of RRE sequences that will provide a foundation for deeper biochemical studies into this intriguing and versatile protein domain.IMPORTANCE Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary structure prediction. Depending on user goals, RRE-Finder can operate in precision mode to accurately identify RREs present in known RiPP classes or in exploratory mode to assist with novel RiPP discovery. Employing RRE-Finder on the UniProtKB database revealed several high-confidence RREs in novel RiPP-like clusters, suggesting that many new RiPP classes remain to be discovered.},
}
@article {pmid32873292,
year = {2020},
author = {Zhu, L and Xu, F and Wan, W and Yu, B and Tang, L and Yang, Y and Du, Y and Chen, Z and Xu, H},
title = {Gut microbial characteristics of adult patients with allergy rhinitis.},
journal = {Microbial cell factories},
volume = {19},
number = {1},
pages = {171},
pmid = {32873292},
issn = {1475-2859},
support = {81900541//National Natural Science Foundation of China/ ; 2019J05005//Natural Science Foundation of Fujian Province/ ; },
mesh = {Adult ; *Biodiversity ; China/epidemiology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Male ; Metagenome ; Quality of Life ; RNA, Ribosomal, 16S ; Rhinitis, Allergic/*microbiology ; Severity of Illness Index ; Surveys and Questionnaires ; Young Adult ; },
abstract = {BACKGROUND: Although recent studies have indicated that intestinal microbiota dweller are involved in the pathogenesis of allergy rhinitis (AR), the influence of gut microbiota on AR adult has not been fully elucidated yet. Hence, we carried out this study to uncover the distinctive bacterial taxa that differentiate allergy rhinitis patients from healthy individuals. Feces samples from thirty three AR patients and thirty one healthy individuals were analyzed by 16S rRNA gene sequencing.<br><br>RESULTS: Results showed that the bacterial diversity in AR group was significantly higher than that of the non-AR group. Bacterial communities between AR and non-AR group were significantly differentiated as revealed by Principal coordinates analysis (PCoA) and the variation within non-AR were higher than that of the counterpart. Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria and Chloroflexi were the significantly differed phyla taxa and the top significantly distinguished bacterial genus included Prevotella_9, Phascolarctobacterium, Roseburia, Megamonas, Alistipes, Lachnoclostridium and Fusobacterium. The higher network complexity in AR group were dominated by taxa belonging to Firmicutes. The predicted function, alpha linolenic acid metabolism and bacterial invasion of epithelial cells pathway were higher in non-AR group while gonadotropin-releasing hormone (GnRH) signaling pathway, Fc &#x3b3;-R mediated phagocytosis and endocytosis were higher in AR patients. Although the bacterial diversity between moderate and severe AR patients showed no significant difference, the significant correlation between featured genus and total nasal symptom score or rhinoconjunctivitis quality of life questionnaire, such as Butyricicoccus and Eisenbergiella, revealed the potential to intervene the AR status by means of gut microbiota.<br><br>CONCLUSIONS: In conclusion, patients with allergy rhinitis had distinguished gut microbiota characteritics in comparison with healthy controls. The results suggest that gut microbiota might play crucial roles in influencing the course and different symptoms of AR. Trial registration ChiCTR, ChiCTR1900028613. Registered 29 December 2019, https://www.chictr.org.cn/showproj.aspx?proj=47650 .},
}
@article {pmid32870508,
year = {2021},
author = {Kedia, S and Ghosh, TS and Jain, S and Desigamani, A and Kumar, A and Gupta, V and Bopanna, S and Yadav, DP and Goyal, S and Makharia, G and Travis, SPL and Das, B and Ahuja, V},
title = {Gut microbiome diversity in acute severe colitis is distinct from mild to moderate ulcerative colitis.},
journal = {Journal of gastroenterology and hepatology},
volume = {36},
number = {3},
pages = {731-739},
doi = {10.1111/jgh.15232},
pmid = {32870508},
issn = {1440-1746},
support = {//Intramural THSTI research funds/ ; //Scheme for Promotion of Academic and Research Collaboration (SPARC)/ ; },
mesh = {Acute Disease ; Adolescent ; Adult ; Colitis/*microbiology ; Colitis, Ulcerative/*microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Microbiological Techniques ; Middle Aged ; Nucleic Acid Amplification Techniques ; RNA, Ribosomal, 16S ; Severity of Illness Index ; },
abstract = {BACKGROUND AND AIM: Although the gut microbiome of patients with ulcerative colitis (UC) has been characterized, no study has characterized the gut microbiome in acute severe colitis (ASC). We compared the gut microbiome of patients with UC, ASC, and healthy controls (HCs).<br><br>METHODS: Patients with mild to moderate UC (n&#xa0;=&#xa0;24), ASC (n&#xa0;=&#xa0;19 with 21 episodes) and HCs (n&#xa0;=&#xa0;50) were recruited prospectively. A 16SrDNA amplicon approach was used to explore gut microbial diversity and taxonomic repertoires. UC was diagnosed using European Crohn's and Colitis Organization guidelines, and ASC was diagnosed using Truelove and Witts' criteria.<br><br>RESULTS: The normalized alpha diversity was significantly lower in ASC than mild-moderately active UC (P&#xa0;<&#xa0;0.05) or HC (P&#xa0;<&#xa0;0.001). The gut microbiome in ASC was highly unstable, as characterized by high intracohort variation (analyzed using J-divergence measure), which was significantly greater than in UC or HC. On principal coordinate analysis, the microbiome of HC and UC were similar, with the ASC cohort being distinct from both. Comparison of ranked abundances identified four distinct clusters of genera (G1, G2, G3, and G4), with specific trends in their abundance across three groups: G1/G2A clusters had the least, whereas G3 had the highest abundance in the ASC cohort.<br><br>CONCLUSIONS: Gut microbial diversity is lower in ASC than mild-moderate UC or HCs. Gut microbiome composition is increasingly unstable in ASC, with a distinct abundance of specific genera varying between HCs and ASC. Mild-moderate UC lies within the spectrum.},
}
@article {pmid32862246,
year = {2021},
author = {Starke, R and Pylro, VS and Morais, DK},
title = {16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {535-539},
pmid = {32862246},
issn = {1432-184X},
support = {18-25706S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-02022Y//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; },
mesh = {Gene Dosage ; Gene Library ; Metagenome/genetics ; Metagenomics/*standards ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.},
}
@article {pmid32861933,
year = {2020},
author = {Uroosa, and Kazmi, SSUH and Xu, G and Xu, H},
title = {Insights into the effects of harmful algal bloom on ecological quality status using body-size spectrum of biofilm-dwelling ciliates in marine ecosystems.},
journal = {Marine pollution bulletin},
volume = {160},
number = {},
pages = {111596},
doi = {10.1016/j.marpolbul.2020.111596},
pmid = {32861933},
issn = {1879-3363},
mesh = {Biofilms ; *Ciliophora ; *Dinoflagellida ; Ecosystem ; Harmful Algal Bloom ; },
abstract = {The effects of two harmful algae Alexandrium tamarense and Gymnodinium catenatum on ecological quality status were identified using biofilm-dwelling ciliate assemblage as test organism communities. The body-size spectra of the test ciliates were observed at a gradient of cell concentrations of both algal species: 10[0] (control), followed by10[2], 10[3], 10[4] and 10[5] cells ml[-1]. The test ciliates showed clear variations in body-size spectra along the concentration gradients of both algal species. In terms of probability density, the ciliates generally peaked at low levels of algal concentrations (10[0]-10[4] cells ml[-1]) in small size forms, followed by the forms with large sizes at the concentration of 10[5] cells ml[-1] of both algal species. Bootstrapped-average analysis demonstrated a significant change in body-size spectrum when algal concentrations were higher than 10[4] cells ml[-1]. It is suggested that the body-size spectrum of the ciliates may be used to indicate the effects of harmful algal bloom.},
}
@article {pmid32860516,
year = {2021},
author = {Virta, L and Soininen, J and Norkko, A},
title = {Biodiversity Loss Threatens the Current Functional Similarity of Beta Diversity in Benthic Diatom Communities.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {293-303},
pmid = {32860516},
issn = {1432-184X},
support = {294853//Academy of Finland/ ; },
mesh = {*Biodiversity ; Diatoms/classification/*isolation &amp; purification ; Environment ; Estuaries ; Water Microbiology ; },
abstract = {The global biodiversity loss has increased the need to understand the effects of decreasing diversity, but our knowledge on how species loss will affect the functioning of communities and ecosystems is still very limited. Here, the levels of taxonomic and functional beta diversity and the effect of species loss on functional beta diversity were investigated in an estuary that provides a naturally steep environmental gradient. The study was conducted using diatoms that are among the most important microorganisms in all aquatic ecosystems and globally account for 40% of marine primary production. Along the estuary, the taxonomic beta diversity of diatom communities was high (Bray-Curtis taxonomic similarity 0.044) and strongly controlled by the environment, particularly wind exposure, salinity, and temperature. In contrast, the functional beta diversity was low (Bray-Curtis functional similarity 0.658) and much less controlled by the environment. Thus, the diatom communities stayed functionally almost similar despite large changes in species composition and environment. This may indicate that, through high taxonomic diversity and redundancy in functions, microorganisms provide an insurance effect against environmental change. However, when studying the effect of decreasing species richness on functional similarity of communities, simulated species loss to 45% of the current species richness decreased functional similarity significantly. This suggests that decreasing species richness may increase variability and reduce the stability and resilience of communities. These results highlight the importance of high taxonomic biodiversity for the stable functioning of benthic communities.},
}
@article {pmid32860076,
year = {2021},
author = {Câmara, PEAS and Carvalho-Silva, M and Pinto, OHB and Amorim, ET and Henriques, DK and da Silva, TH and Pellizzari, F and Convey, P and Rosa, LH},
title = {Diversity and Ecology of Chlorophyta (Viridiplantae) Assemblages in Protected and Non-protected Sites in Deception Island (Antarctica, South Shetland Islands) Assessed Using an NGS Approach.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {323-334},
pmid = {32860076},
issn = {1432-184X},
support = {23/2018//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Antarctic Regions ; *Biodiversity ; Chlorophyta/classification/genetics/*growth &amp; development ; Ecosystem ; Geography ; Humans ; Introduced Species ; *Islands ; Soil Microbiology ; },
abstract = {Assessment of the diversity of algal assemblages in Antarctica has until now largely relied on traditional microbiological culture approaches. Here we used DNA metabarcoding through high-throughput sequencing (HTS) to assess the uncultured algal diversity at two sites on Deception Island, Antarctica. The first was a relatively undisturbed site within an Antarctic Specially Protected Area (ASPA 140), and the second was a site heavily impacted by human visitation, the Whalers Bay historic site. We detected 65 distinct algal taxa, 50 from within ASPA 140 and 61 from Whalers Bay. Of these taxa, 46 were common to both sites, and 19 only occurred at one site. Algal richness was about six times greater than reported in previous studies using culture methods. A high proportion of DNA reads obtained was assigned to the highly invasive species Caulerpa webbiana at Whalers Bay, and the potentially pathogenic genus Desmodesmus was found at both sites. Our data demonstrate that important differences exist between these two protected and human-impacted sites on Deception Island in terms of algal diversity, richness, and abundance. The South Shetland Islands have experienced considerable effects of climate change in recent decades, while warming through geothermal activity on Deception Island itself makes this island one of the most vulnerable to colonization by non-native species. The detection of DNA of non-native taxa highlights concerns about how human impacts, which take place primarily through tourism and national research operations, may influence future biological colonization processes in Antarctica.},
}
@article {pmid32859925,
year = {2020},
author = {Jurburg, SD and Konzack, M and Eisenhauer, N and Heintz-Buschart, A},
title = {The archives are half-empty: an assessment of the availability of microbial community sequencing data.},
journal = {Communications biology},
volume = {3},
number = {1},
pages = {474},
pmid = {32859925},
issn = {2399-3642},
mesh = {Databases, Nucleic Acid ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; },
abstract = {As DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.},
}
@article {pmid32859275,
year = {2020},
author = {Lu, J and Salzberg, SL},
title = {Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {124},
pmid = {32859275},
issn = {2049-2618},
support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/*genetics/*isolation &amp; purification ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Software ; Time Factors ; },
abstract = {BACKGROUND: For decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying bacterial genera from simulated human gut, ocean, and soil metagenomes, although QIIME 2 also proved to be the most computationally expensive. Kraken, first released in 2014, has been shown to provide exceptionally fast and accurate classification for shotgun metagenomics sequencing projects. Bracken, released in 2016, then provided users with the ability to accurately estimate species or genus relative abundances using Kraken classification results. Kraken 2, which matches the accuracy and speed of Kraken 1, now supports 16S rRNA databases, allowing for direct comparisons to QIIME and similar systems.<br><br>METHODS: For a comprehensive assessment of each tool, we compare the computational resources and speed of QIIME 2's q2-feature-classifier, Kraken 2, and Bracken in generating the three main 16S rRNA databases: Greengenes, SILVA, and RDP. For an evaluation of accuracy, we evaluated each tool using the same simulated 16S rRNA reads from human gut, ocean, and soil metagenomes that were previously used to compare QIIME, MAPseq, mothur, and QIIME 2. We evaluated accuracy based on the accuracy of the final genera read counts assigned by each tool. Finally, as Kraken 2 is the only tool providing per-read taxonomic assignments, we evaluate the sensitivity and precision of Kraken 2's per-read classifications.<br><br>RESULTS: For both the Greengenes and SILVA database, Kraken 2 and Bracken are up to 100 times faster at database generation. For classification, using the same data as previous studies, Kraken 2 and Bracken are up to 300 times faster, use 100x less RAM, and generate results that more accurate at 16S rRNA profiling than QIIME 2's q2-feature-classifier.<br><br>CONCLUSION: Kraken 2 and Bracken provide a very fast, efficient, and accurate solution for 16S rRNA metataxonomic data analysis. Video Abstract.},
}
@article {pmid32857837,
year = {2020},
author = {Ho, A and Mendes, LW and Lee, HJ and Kaupper, T and Mo, Y and Poehlein, A and Bodelier, PLE and Jia, Z and Horn, MA},
title = {Response of a methane-driven interaction network to stressor intensification.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {10},
pages = {},
doi = {10.1093/femsec/fiaa180},
pmid = {32857837},
issn = {1574-6941},
mesh = {*Methane ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; },
abstract = {Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.},
}
@article {pmid32855435,
year = {2021},
author = {Fodelianakis, S and Valenzuela-Cuevas, A and Barozzi, A and Daffonchio, D},
title = {Direct quantification of ecological drift at the population level in synthetic bacterial communities.},
journal = {The ISME journal},
volume = {15},
number = {1},
pages = {55-66},
pmid = {32855435},
issn = {1751-7370},
mesh = {*Bacteria/genetics ; *Microbiota ; },
abstract = {In community ecology, drift refers to random births and deaths in a population. In microbial ecology, drift is estimated indirectly via community snapshots but in this way, it is almost impossible to distinguish the effect of drift from the effect of other ecological processes. Controlled experiments where drift is quantified in isolation from other processes are still missing. Here we isolate and quantify drift in a series of controlled experiments on simplified and tractable bacterial communities. We detect drift arising randomly in the populations within the communities and resulting in a 1.4-2% increase in their growth rate variability on average. We further use our experimental findings to simulate complex microbial communities under various conditions of selection and dispersal. We find that the importance of drift increases under high selection and low dispersal, where it can lead to ~5% of species loss and to ~15% increase in β-diversity. The species extinct by drift are mainly rare, but they become increasingly less rare when selection increases, and dispersal decreases. Our results provide quantitative insights regarding the properties of drift in bacterial communities and suggest that it accounts for a consistent fraction of the observed stochasticity in natural surveys.},
}
@article {pmid32854141,
year = {2020},
author = {Altinli, M and Lequime, S and Atyame, C and Justy, F and Weill, M and Sicard, M},
title = {Wolbachia modulates prevalence and viral load of Culex pipiens densoviruses in natural populations.},
journal = {Molecular ecology},
volume = {29},
number = {20},
pages = {4000-4013},
doi = {10.1111/mec.15609},
pmid = {32854141},
issn = {1365-294X},
mesh = {Animals ; *Culex/genetics ; *Densovirus/genetics ; Phylogeny ; Prevalence ; Viral Load ; *Wolbachia/genetics ; },
abstract = {The inadequacy of standard mosquito control strategies calls for ecologically safe novel approaches, for example the use of biological agents such as the endosymbiotic α-proteobacteria Wolbachia or insect-specific viruses (ISVs). Understanding the ecological interactions between these "biocontrol endosymbionts" is thus a fundamental step. Wolbachia are transmitted vertically from mother to offspring and modify their hosts' phenotypes, including reproduction (e.g., cytoplasmic incompatibility) and survival (e.g., viral interference). In nature, Culex pipiens (sensu lato) mosquitoes are always found infected with genetically diverse Wolbachia called wPip that belong to five phylogenetic groups. In recent years, ISVs have also been discovered in these mosquito species, although their interactions with Wolbachia in nature are unknown. Here, we studied the interactions between a widely prevalent ISV, the Culex pipiens densovirus (CpDV, Densovirinae), and Wolbachia in northern Tunisian C. pipiens populations. We showed an influence of different Wolbachia groups on CpDV prevalence and a general positive correlation between Wolbachia and CpDV loads. By investigating the putative relationship between CpDV diversification and wPip groups in the different sites, we detected a signal linked to wPip groups in CpDV phylogeny in sites where all larvae were infected by the same wPip group. However, no such signal was detected where the wPip groups coexisted, suggesting CpDV horizontal transfer between hosts. Overall, our results provide good evidence for an ecological influence of Wolbachia on an ISV, CpDV, in natural populations and highlight the importance of integrating Wolbachia in our understanding of ISV ecology in nature.},
}
@article {pmid32853201,
year = {2020},
author = {Buongiorno, J and Sipes, K and Wasmund, K and Loy, A and Lloyd, KG},
title = {Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0234839},
pmid = {32853201},
issn = {1932-6203},
support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 29426/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Arctic Regions ; Bacterial Proteins/genetics ; Estuaries ; Gammaproteobacteria/classification/*genetics/metabolism ; Genome, Bacterial ; Geologic Sediments/*microbiology ; Heat-Shock Proteins/genetics ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Svalbard ; Transcriptome ; },
abstract = {Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.},
}
@article {pmid32852571,
year = {2021},
author = {Hubert, J and Nesvorna, M and Green, SJ and Klimov, PB},
title = {Microbial Communities of Stored Product Mites: Variation by Species and Population.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {506-522},
pmid = {32852571},
issn = {1432-184X},
support = {GA19-09998S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-14-00004//Russian Science Foundation/ ; },
mesh = {Acaridae/classification/growth &amp; development/*microbiology ; Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Diet ; Feces/microbiology ; Host Microbial Interactions ; *Microbiota ; Ovum/microbiology ; Phylogeny ; },
abstract = {Arthropod-associated microorganisms are important because they affect host fitness, protect hosts from pathogens, and influence the host's ability to vector pathogens. Stored product mites (Astigmata) often establish large populations in various types of food items, damaging the food by direct feeding and introducing contaminants, including their own bodies, allergen-containing feces, and associated microorganisms. Here we access the microbial structure and abundance in rearing diets, eggs, feces fraction, and mite bodies of 16 mite populations belonging to three species (Carpoglyphus lactis, Acarus siro, and Tyrophagus putrescentiae) using quantitative PCR and 16S ribosomal RNA (rRNA) gene amplicon sequencing. The mite microbiomes had a complex structure dominated by the following bacterial taxa (OTUs): (a) intracellular symbionts of the genera Cardinium and Wolbachia in the mite bodies and eggs; (b) putative gut symbionts of the genera Solitalea, Bartonella, and Sodalis abundant in mite bodies and also present in mite feces; (c) feces-associated or environmental bacteria of the genera Bacillus, Staphylococcus, and Kocuria in the diet, mite bodies, and feces. Interestingly and counterintuitively, the differences between microbial communities in various conspecific mite populations were higher than those between different mite species. To explain some of these differences, we hypothesize that the intracellular bacterial symbionts can affect microbiome composition in mite bodies, causing differences between microbial profiles. Microbial profiles differed between various sample types, such as mite eggs, bodies, and the environment (spent growth medium-SPGM). Low bacterial abundances in eggs may result in stochastic effects in parent-offspring microbial transmission, except for the intracellular symbionts. Bacteria in the rearing diet had little effect on the microbial community structure in SPGM and mite bodies. Mite fitness was positively correlated with bacterial abundance in SPGM and negatively correlated with bacterial abundances in mite bodies. Our study demonstrates critical host-microbe interactions, affecting all stages of mite growth and leading to alteration of the environmental microbiome. Correlational evidence based on absolute quantitation of bacterial 16S rRNA gene copies suggests that mite-associated microorganisms are critical for modulating important pest properties of mites by altering population growth.},
}
@article {pmid32850972,
year = {2020},
author = {Álvarez-Rodríguez, I and Ugarte-Uribe, B and de la Arada, I and Arrondo, JLR and Garbisu, C and Alkorta, I},
title = {Conjugative Coupling Proteins and the Role of Their Domains in Conjugation, Secondary Structure and in vivo Subcellular Location.},
journal = {Frontiers in molecular biosciences},
volume = {7},
number = {},
pages = {185},
pmid = {32850972},
issn = {2296-889X},
abstract = {Type IV Coupling Proteins (T4CPs) are essential elements in many type IV secretion systems (T4SSs). The members of this family display sequence, length, and domain architecture heterogeneity, being the conserved Nucleotide-Binding Domain the motif that defines them. In addition, most T4CPs contain a Transmembrane Domain (TMD) in the amino end and an All-Alpha Domain facing the cytoplasm. Additionally, a few T4CPs present a variable domain at the carboxyl end. The structural paradigm of this family is TrwBR388, the T4CP of conjugative plasmid R388. This protein has been widely studied, in particular the role of the TMD on the different characteristics of TrwBR388. To gain knowledge about T4CPs and their TMD, in this work a chimeric protein containing the TMD of TraJpKM101 and the cytosolic domain of TrwBR388 has been constructed. Additionally, one of the few T4CPs of mobilizable plasmids, MobBCloDF13 of mobilizable plasmid CloDF13, together with its TMD-less mutant MobBΔTMD have been studied. Mating studies showed that the chimeric protein is functional in vivo and that it exerted negative dominance against the native proteins TrwBR388 and TraJpKM101. Also, it was observed that the TMD of MobBCloDF13 is essential for the mobilization of CloDF13 plasmid. Analysis of the secondary structure components showed that the presence of a heterologous TMD alters the structure of the cytosolic domain in the chimeric protein. On the contrary, the absence of the TMD in MobBCloDF13 does not affect the secondary structure of its cytosolic domain. Subcellular localization studies showed that T4CPs have a unipolar or bipolar location, which is enhanced by the presence of the remaining proteins of the conjugative system. Unlike what has been described for TrwBR388, the TMD is not an essential element for the polar location of MobBCloDF13. The main conclusion is that the characteristics described for the paradigmatic TrwBR388 T4CP should not be ascribed to the whole T4CP family. Specifically, it has been proven that the mobilizable plasmid-related MobBCloDF13 presents different characteristics regarding the role of its TMD. This work will contribute to better understand the T4CP family, a key element in bacterial conjugation, the main mechanism responsible for antibiotic resistance spread.},
}
@article {pmid32850744,
year = {2020},
author = {Song, C and Zhu, F and Carrión, VJ and Cordovez, V},
title = {Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {8},
number = {},
pages = {896},
pmid = {32850744},
issn = {2296-4185},
abstract = {Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has been focusing on the description of the taxonomic composition of the microbiome. Therefore, a focus on the plant-associated microbiome functions is pivotal for the development of novel agricultural practices which, in turn, will increase plant fitness. Recent advances in microbiome research using model plant species started to shed light on the functions of specific microorganisms and the underlying mechanisms of plant-microbial interaction. Here, we review (1) microbiome-mediated functions associated with plant growth and protection, (2) insights from native and agricultural habitats that can be used to improve soil health and crop productivity, (3) current -omics and new approaches for studying the plant microbiome, and (4) challenges and future perspectives for exploiting the plant microbiome for beneficial outcomes. We posit that integrated approaches will help in translating fundamental knowledge into agricultural practices.},
}
@article {pmid32849473,
year = {2020},
author = {Sedlacek, CJ},
title = {It Takes a Village: Discovering and Isolating the Nitrifiers.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1900},
pmid = {32849473},
issn = {1664-302X},
support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a "founder of microbiology" and "the founder of microbial ecology." Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.},
}
@article {pmid32849470,
year = {2020},
author = {Nagler, M and Podmirseg, SM and Mayr, M and Ascher-Jenull, J and Insam, H},
title = {Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1894},
pmid = {32849470},
issn = {1664-302X},
abstract = {Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool. Our results showed that this fine-tuned DNA approach coupled with the interpretation of the ratio between free exDNA and iDNA considerably improved microbial activity tracking compared to the classical extraction/quantification of total DNA. Additionally, it allowed to identify and quantify methanogenic populations that are inactive and those that are strongly influenced by cell lysis. We argue that despite the need of further studies, this method represents a novel approach to gain specific physiological information from a complex environmental sample and holds the potential to be applied to other microbes of interest.},
}
@article {pmid32849423,
year = {2020},
author = {Moonga, HB and Schoustra, SE and van den Heuvel, J and Linnemann, AR and Samad, MS and Shindano, J and Smid, EJ},
title = {Composition and Diversity of Natural Bacterial Communities in Mabisi, a Traditionally Fermented Milk.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1816},
pmid = {32849423},
issn = {1664-302X},
abstract = {Many traditionally fermented milk products such as mabisi involve spontaneous fermentation, which can result in bacterial community composition variation due to selection pressure. The aim of this study was to determine the composition of bacterial communities in the different types of mabisi produced across Zambia and identify the factors that influence their composition. Samples of mabisi were collected across the country, and analyzed for pH and bacterial communities using 16S rRNA amplicon sequencing. We found that the bacterial community composition was dominated by members of two phyla, i.e., Firmicutes and Proteobacteria, from which the top 10 most abundant genera were Lactococcus, Lactobacillus, Streptococcus, Enterobacter, Citrobacter, Klebsiella, Kluyvera, Buttiauxella, Aeromonas, and Acinetobacter. The most dominant genus was Lactococcus, which was present in all types of mabisi produced from all regions. The mabisi products from traditional mabisi production regions (TMPRs) were dominated by lactic acid bacteria (LAB) whereas products from non-TMPRs were dominated by non-LAB species. Tonga mabisi, the most popular type of mabisi produced in non-TMPRs, had the most complex and diverse bacterial community composition compared to the other types, which included barotse, backslopping, creamy, and thick-tonga mabisi. Other factors that influenced bacterial community composition were geographical location, fermentation duration and pH while the type of fermentation container and producer did not. This study provides new insights that can be applied in starter culture development as well as microbial functionality studies.},
}
@article {pmid32849396,
year = {2020},
author = {Huang, J and Yang, J and Jiang, H and Wu, G and Liu, W and Wang, B and Xiao, H and Han, J},
title = {Microbial Responses to Simulated Salinization and Desalinization in the Sediments of the Qinghai-Tibetan Lakes.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1772},
pmid = {32849396},
issn = {1664-302X},
abstract = {Uncovering microbial response to salinization or desalinization is of great importance to understanding of the influence of global climate change on lacustrine microbial ecology. In this study, to simulate salinization and desalinization, sediments from Erhai Lake (salinity 0.3-0.8 g/L) and Chaka Lake (salinity 299.3-350.7 g/L) on the Qinghai-Tibetan Plateau were transplanted into different lakes with a range of salinity of 0.3-299.3 g/L, followed by in situ incubation for 50 days and subsequent geochemical and microbial analyses. Desalinization was faster than salinization in the transplanted sediments. The salinity of the transplanted sediment increased and decreased in the salinization and desalinization simulation experiments, respectively. The TOC contents of the transplanted sediments were lower than that of their undisturbed counterparts in the salinization experiments, whereas they had a strong negative linear relationship with salinity in the desalinization experiments. Microbial diversity decreased in response to salinization and desalinization, and microbial community dissimilarity significantly (P < 0.01) increased with salinity differences between the transplanted sediments and their undisturbed counterparts. Microbial groups belonging to Gammaproteobacteria and Actinobacteria became abundant in salinization whereas Bacteroidetes and Chloroflexi became dominant in desalinization. Among the predicted microbial functions, hydrogenotrophic methanogenesis, methanogenesis through CO2 reduction with H2, nitrate/nitrogen respiration, and nitrification increased in salinization; in desalinization, enhancement was observed for respiration of sulfur compounds, sulfate respiration, sulfur respiration, thiosulfate respiration, hydrocarbon degradation, chemoheterotrophy, and fermentation, whereas depressing was found for aerobic ammonia oxidation, nitrate/nitrogen respiration, nitrification, nitrite respiration, manganese oxidation, aerobic chemoheterotrophy, and phototrophy. Such microbial variations could be explained by changes of transplantation, salinity, and covarying variables. In summary, salinization and desalinization had profound influence on the geochemistry, microbial community, and function in lakes.},
}
@article {pmid32849356,
year = {2020},
author = {Arbour, TJ and Gilbert, B and Banfield, JF},
title = {Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1694},
pmid = {32849356},
issn = {1664-302X},
abstract = {Extracellular electron transfer (EET) between microbes and iron minerals, and syntrophically between species, is a widespread process affecting biogeochemical cycles and microbial ecology. The distribution of this capacity among microbial taxa, and the thermodynamic controls on EET in complex microbial communities, are not fully known. Microbial electrochemical cells (MXCs), in which electrodes serve as the electron acceptor or donor, provide a powerful approach to enrich for organisms capable of EET and to study their metabolism. We used MXCs coupled with genome-resolved metagenomics to investigate the capacity for EET in microorganisms present in a well-studied aquifer near Rifle, CO. Electroactive biofilms were established and maintained for almost 4 years on anodes poised mostly at -0.2 to -0.25 V vs. SHE, a range that mimics the redox potential of iron-oxide minerals, using acetate as the sole carbon source. Here we report the metagenomic characterization of anode-biofilm and planktonic microbial communities from samples collected at timepoints across the study period. From two biofilm and 26 planktonic samples we reconstructed draft-quality and near-complete genomes for 84 bacteria and 2 archaea that represent the majority of organisms present. A novel Geobacter sp. with at least 72 putative multiheme c-type cytochromes (MHCs) was the dominant electrode-attached organism. However, a diverse range of other electrode-associated organisms also harbored putative MHCs with at least 10 heme-binding motifs, as well as porin-cytochrome complexes and e-pili, including Actinobacteria, Ignavibacteria, Chloroflexi, Acidobacteria, Firmicutes, Beta- and Gammaproteobacteria. Our results identify a small subset of the thousands of organisms previously detected in the Rifle aquifer that may have the potential to mediate mineral redox transformations.},
}
@article {pmid32849338,
year = {2020},
author = {Presley, GN and Zhang, J and Purvine, SO and Schilling, JS},
title = {Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1646},
pmid = {32849338},
issn = {1664-302X},
abstract = {Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth's largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.},
}
@article {pmid32849330,
year = {2020},
author = {Floc'h, JB and Hamel, C and Lupwayi, N and Harker, KN and Hijri, M and St-Arnaud, M},
title = {Bacterial Communities of the Canola Rhizosphere: Network Analysis Reveals a Core Bacterium Shaping Microbial Interactions.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1587},
pmid = {32849330},
issn = {1664-302X},
abstract = {The rhizosphere hosts a complex web of prokaryotes interacting with one another that may modulate crucial functions related to plant growth and health. Identifying the key factors structuring the prokaryotic community of the plant rhizosphere is a necessary step toward the enhancement of plant production and crop yield with beneficial associative microorganisms. We used a long-term field experiment conducted at three locations in the Canadian prairies to verify that: (1) the level of cropping system diversity influences the α- and β-diversity of the prokaryotic community of canola (Brassica napus) rhizosphere; (2) the canola rhizosphere community has a stable prokaryotic core; and (3) some highly connected taxa of this community fit the description of hub-taxa. We sampled the rhizosphere of canola grown in monoculture, in a 2-phase rotation (canola-wheat), in a 3-phase rotation (pea-barley-canola), and in a highly diversified 6-phase rotation, five and eight years after cropping system establishment. We detected only one core bacterial Amplicon Sequence Variant (ASV) in the prokaryotic component of the microbiota of canola rhizosphere, a hub taxon identified as cf. Pseudarthrobacter sp. This ASV was also the only hub taxon found in the networks of interactions present in both years and at all three sites. We highlight a cohort of bacteria and archaea that were always connected with the core taxon in the network analyses.},
}
@article {pmid32846525,
year = {2020},
author = {Jilani, H and Cilla, A and Barberá, R and Hamdi, M},
title = {Antiproliferative activity of green, black tea and olive leaves polyphenols subjected to biosorption and in vitro gastrointestinal digestion in Caco-2 cells.},
journal = {Food research international (Ottawa, Ont.)},
volume = {136},
number = {},
pages = {109317},
doi = {10.1016/j.foodres.2020.109317},
pmid = {32846525},
issn = {1873-7145},
mesh = {Apoptosis/drug effects ; Biological Availability ; Caco-2 Cells ; Camellia sinensis/*chemistry ; Cell Cycle/drug effects ; Cell Proliferation/*drug effects ; Cell Survival/drug effects ; *Digestion ; Humans ; Olea/*chemistry ; Plant Leaves/*chemistry ; Polyphenols/metabolism/pharmacokinetics/*pharmacology ; Saccharomyces cerevisiae/metabolism ; Tea/chemistry ; },
abstract = {Olive (Olea europaea L.) leaves and tea (Camellia sinensis) are rich sources of bioactive compounds, especially polyphenols. Our previous studies have evidenced the potential use of Saccharomyces cerevisiae as a natural delivery system for these antioxidants and a means to improve their bioaccessibility in the human gut. In the present work, the antiproliferative effect of green tea (GT), black tea (BT) and olive leaves (OL) infusions and suspensions of S. cerevisiae were evaluated, for the first time, in human colon cancer cells (Caco-2) after biosorption and in vitro gastrointestinal digestion. The bioaccessible fractions (BF) were not overtly cytotoxic, not affecting cell viability. ROS and mitochondrial membrane potential changes (Δψm) values were reduced compared with control cells. Moreover, all the BF after biosorption induced a significant (p < 0.05) increase in cell proportions in S-phase. The arrest of the cell cycle was reversible without induction of apoptosis, suggesting that the biosorbed phenolics in both infusions and suspensions act as cytostatic agents.},
}
@article {pmid32845305,
year = {2020},
author = {Imchen, M and Kumavath, R},
title = {Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {10},
pages = {},
doi = {10.1093/femsec/fiaa173},
pmid = {32845305},
issn = {1574-6941},
mesh = {*Anti-Bacterial Agents/pharmacology ; Brazil ; China ; Drug Resistance, Microbial/genetics ; Humans ; India ; Malaysia ; *Metagenomics ; Saudi Arabia ; Wetlands ; },
abstract = {Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.},
}
@article {pmid32845128,
year = {2020},
author = {Ceron-Chafla, P and Kleerebezem, R and Rabaey, K and van Lier, JB and Lindeboom, REF},
title = {Direct and Indirect Effects of Increased CO2 Partial Pressure on the Bioenergetics of Syntrophic Propionate and Butyrate Conversion.},
journal = {Environmental science &amp; technology},
volume = {54},
number = {19},
pages = {12583-12592},
pmid = {32845128},
issn = {1520-5851},
mesh = {Anaerobiosis ; Bioreactors ; *Butyrates ; Carbon Dioxide ; Energy Metabolism ; Methane ; Partial Pressure ; *Propionates ; },
abstract = {Simultaneous digestion and in situ biogas upgrading in high-pressure bioreactors will result in elevated CO2 partial pressure (pCO2). With the concomitant increase in dissolved CO2, microbial conversion processes may be affected beyond the impact of increased acidity. Elevated pCO2 was reported to affect the kinetics and thermodynamics of biochemical conversions because CO2 is an intermediate and end-product of the digestion process and modifies the carbonate equilibrium. Our results showed that increasing pCO2 from 0.3 to 8 bar in lab-scale batch reactors decreased the maximum substrate utilization rate (rsmax) for both syntrophic propionate and butyrate oxidation. These kinetic limitations are linked to an increased overall Gibbs free energy change (ΔGOverall) and a potential biochemical energy redistribution among syntrophic partners, which showed interdependence with hydrogen partial pressure (pH2). The bioenergetics analysis identified a moderate, direct impact of elevated pCO2 on propionate oxidation and a pH-mediated effect on butyrate oxidation. These constraints, combined with physiological limitations on growth exerted by increased acidity and inhibition due to higher concentrations of undissociated volatile fatty acids, help to explain the observed phenomena. Overall, this investigation sheds light on the role of elevated pCO2 in delicate biochemical syntrophic conversions by connecting kinetic, bioenergetic, and physiological effects.},
}
@article {pmid32844509,
year = {2020},
author = {Zhu, X and Jackson, RD and DeLucia, EH and Tiedje, JM and Liang, C},
title = {The soil microbial carbon pump: From conceptual insights to empirical assessments.},
journal = {Global change biology},
volume = {26},
number = {11},
pages = {6032-6039},
doi = {10.1111/gcb.15319},
pmid = {32844509},
issn = {1365-2486},
support = {31930070//National Natural Science Foundation of China/ ; 41977051//National Natural Science Foundation of China/ ; GJTD-2019-10//K.C. Wong Education Foundation/ ; },
mesh = {Agriculture ; *Carbon ; Crops, Agricultural ; *Soil ; Soil Microbiology ; },
abstract = {The global soil carbon (C) pool is massive, so relatively small changes in soil organic carbon (SOC) stocks can significantly alter atmospheric C and global climate. The recently proposed concept of the soil microbial carbon pump (MCP) emphasizes the active role of soil microbes in SOC storage by integrating the continual microbial transformation of organic C from labile to persistent anabolic forms. However, the concept has not been evaluated with data. Here, we combine datasets, including microbial necromass biomarker amino sugars and SOC, from two long-term agricultural field studies conducted by large United States bioenergy research programs. We interrogate the soil MCP concept by investigating the asynchronous responses of microbial necromass and SOC to land-use change. Microbial necromass appeared to preferentially accumulate in soil and be the dominant contributor to SOC accrual in diversified perennial bioenergy crops. Specifically, ~92% of the additional SOC enhanced by plant diversity was estimated to be microbial necromass C, and >76% of the additional SOC enhanced by land-use transition from annual to perennial crops was estimated to be microbial necromass. This suggests that the soil MCP was stimulated in diversified perennial agroecosystems. We further delineate and suggest two parameters-soil MCP capacity and efficacy-reflecting the conversion of plant C into microbial necromass and the contribution of microbial necromass to SOC, respectively, that should serve as valuable metrics for future studies evaluating SOC storage under alternative management in changing climates.},
}
@article {pmid32843743,
year = {2021},
author = {Khoruts, A and Staley, C and Sadowsky, MJ},
title = {Faecal microbiota transplantation for Clostridioides difficile: mechanisms and pharmacology.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {18},
number = {1},
pages = {67-80},
pmid = {32843743},
issn = {1759-5053},
mesh = {Anti-Bacterial Agents/adverse effects/therapeutic use ; *Clostridioides difficile/metabolism/pathogenicity/physiology ; Clostridium Infections/etiology/*physiopathology/*therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Recurrence ; Treatment Outcome ; },
abstract = {Faecal microbiota transplantation (FMT) has emerged as a remarkably successful treatment for recurrent Clostridioides difficile infection that cannot be cured with antibiotics alone. Understanding the complex biology and pathogenesis of C. difficile infection, which we discuss in this Perspective, is essential for understanding the potential mechanisms by which FMT cures this disease. Although FMT has already entered clinical practice, different microbiota-based products are currently in clinical trials and are vying for regulatory approval. However, all these therapeutics belong to an entirely new class of agents that require the development of a new branch of pharmacology. Characterization of microbiota therapeutics uses novel and rapidly evolving technologies and requires incorporation of microbial ecology concepts. Here, we consider FMT within a pharmacological framework, including its essential elements: formulation, pharmacokinetics and pharmacodynamics. From this viewpoint, multiple gaps in knowledge become apparent, identifying areas that require systematic research. This knowledge is needed to help clinical providers use microbiota therapeutics appropriately and to facilitate development of next-generation microbiota products with improved safety and efficacy. The discussion here is limited to FMT as a representative of microbiota therapeutics and recurrent C. difficile as the indication; however, consideration of the intrinsic basic principles is relevant to this entire class of microbiota-based therapeutics.},
}
@article {pmid32843539,
year = {2020},
author = {Santillan, E and Constancias, F and Wuertz, S},
title = {Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors.},
journal = {mSystems},
volume = {5},
number = {4},
pages = {},
pmid = {32843539},
issn = {2379-5077},
abstract = {Press disturbances are of interest in microbial ecology, as they can drive microbial communities to alternative stable states. However, the effect of press disturbances in community assembly mechanisms, particularly with regard to taxa and functional genes at different levels of abundance (i.e., common and rare), remains largely unknown. Here, we tested the effect of a continuous alteration in substrate feeding scheme on the structure, function, and assembly of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loads for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Disturbed reactors exhibited different community function, structure, and assembly compared to undisturbed reactors. Bacterial taxa and functional genes showed dissimilar α-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors and in common fractions compared to rare ones. Function quickly recovered after the disturbance was removed, but community structure did not. Our results highlight that functional gene data from metagenomics can indicate patterns of community assembly that differ from those obtained from taxon data. This study reveals how a joint evaluation of assembly mechanisms and community structure of bacterial taxa and functional genes as well as ecosystem function can unravel the response of complex microbial systems to a press disturbance.IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. This work provides a glimpse of the changes in assembly mechanisms found in microbial communities exposed to sustained changes in their environment. These mechanisms, deterministic or stochastic, can cause communities to reach a similar or variable composition and function. For a comprehensive view, we use a joint evaluation of temporal dynamics in assembly mechanisms and community structure for both bacterial taxa and their functional genes at different abundance levels, in both disturbed and undisturbed states. We further reverted the disturbance state to contrast recovery of function with community structure. Our findings are relevant, as very few studies have employed such an approach, while there is a need to assess the relative importance of assembly mechanisms for microbial communities across different spatial and temporal scales, environmental gradients, and types of disturbance.},
}
@article {pmid32842646,
year = {2020},
author = {Finore, I and Vigneron, A and Vincent, WF and Leone, L and Di Donato, P and Schiano Moriello, A and Nicolaus, B and Poli, A},
title = {Novel Psychrophiles and Exopolymers from Permafrost Thaw Lake Sediments.},
journal = {Microorganisms},
volume = {8},
number = {9},
pages = {},
pmid = {32842646},
issn = {2076-2607},
support = {UMI-MicroMeNu//Program Sentinel North financed by the Canada First Research Excellence Fund (CFREF); the Natural Sciences and Engineering Research Council of Canada (NSERC); the CNR (Italy)-Universit&#xe9; Laval UMI-MicroMeNu program; the Fonds de Recherche du Qu&#xe9;bec-Nature/ ; },
abstract = {Thermokarst lakes are one of the most abundant types of microbial ecosystems in the circumpolar North. These shallow basins are formed by the thawing and collapse of ice-rich permafrost, with subsequent filling by snow and ice melt. Until now, permafrost thaw lakes have received little attention for isolation of microorganisms by culture-based analysis. The discovery of novel psychrophiles and their biomolecules makes these extreme environments suitable sources for the isolation of new strains, including for potential biotechnological applications. In this study, samples of bottom sediments were collected from three permafrost thaw lakes in subarctic Québec, Canada. Their diverse microbial communities were characterized by 16S rRNA gene amplicon analysis, and subsamples were cultured for the isolation of bacterial strains. Phenotypic and genetic characterization of the isolates revealed affinities to the genera Pseudomonas, Paenibacillus, Acinetobacter,Staphylococcus and Sphingomonas. The isolates were then evaluated for their production of extracellular enzymes and exopolymers. Enzymes of potential biotechnological interest included α and β-glucosidase, α and β-maltosidase, β-xylosidase and cellobiohydrolase. One isolate, Pseudomonas extremaustralis strain 2ASCA, also showed the capability to produce, in the loosely bound cell fraction, a levan-type polysaccharide with a yield of 613 mg/L of culture, suggesting its suitability as a candidate for eco-sustainable alternatives to commercial polymers.},
}
@article {pmid32841483,
year = {2020},
author = {Mammola, S and Amorim, IR and Bichuette, ME and Borges, PAV and Cheeptham, N and Cooper, SJB and Culver, DC and Deharveng, L and Eme, D and Ferreira, RL and Fišer, C and Fišer, &#x17d; and Fong, DW and Griebler, C and Jeffery, WR and Jugovic, J and Kowalko, JE and Lilley, TM and Malard, F and Manenti, R and Martínez, A and Meierhofer, MB and Niemiller, ML and Northup, DE and Pellegrini, TG and Pipan, T and Protas, M and Reboleira, ASPS and Venarsky, MP and Wynne, JJ and Zagmajster, M and Cardoso, P},
title = {Fundamental research questions in subterranean biology.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {95},
number = {6},
pages = {1855-1872},
doi = {10.1111/brv.12642},
pmid = {32841483},
issn = {1469-185X},
support = {eLTER//Horizon 2020 Framework Programme/International ; N1-0069//Javna Agencija za Raziskovalno Dejavnost RS/International ; 15471//Villum Fonden/International ; 678193//Horizon 2020 Framework Programme/International ; RDP 00092-18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/International ; 882221//H2020 Marie Sk&#x142;odowska-Curie Actions/International ; ANR-15-CE32-0005//Agence Nationale de la Recherche/International ; 745530//H2020 Marie Sk&#x142;odowska-Curie Actions/International ; CF19-0609//Carlsbergfondet/International ; },
mesh = {Adaptation, Physiological ; *Caves ; *Ecology ; Genomics ; },
abstract = {Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well-established methodology of 'horizon scanning' to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation, evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top-priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis-driven studies likely to resonate broadly from the traditional boundaries of this field.},
}
@article {pmid32840670,
year = {2021},
author = {Nikouli, E and Meziti, A and Smeti, E and Antonopoulou, E and Mente, E and Kormas, KA},
title = {Gut Microbiota of Five Sympatrically Farmed Marine Fish Species in the Aegean Sea.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {460-470},
pmid = {32840670},
issn = {1432-184X},
mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Diet/veterinary ; *Fisheries ; Fishes/classification/growth &amp; development/*microbiology ; *Gastrointestinal Microbiome ; Greece ; Mediterranean Sea ; RNA, Ribosomal, 16S ; Species Specificity ; },
abstract = {In this study, we hypothesized that sympatrically grown farmed fish, i.e. fish which experience similar environmental conditions and nutritionally similar diets, would have more convergent gut microbiota. Using a "common garden" approach, we identified the core microbiota and bacterial community structure differences between five fish species farmed in the same aquaculture site on the west coast of the Aegean Sea, Greece. The investigated individuals were at similar developmental stages and reared in adjacent (< 50 m) aquaculture cages; each cage had 15 kg fish m[-3]. The diets were nutritionally similar to support optimal growth for each fish species. DNA from the midgut of 3-6 individuals per fish species was extracted and sequenced for the V3-V4 region of the bacterial 16S rRNA. Only 3.9% of the total 181 operational taxonomic units (OTUs) were shared among all fish. Between 5 and 74 OTUs were unique to each fish species. Each of the investigated fish species had a distinct profile of dominant OTUs, i.e. cumulative relative abundance of ≥ 80%. Co-occurrence network analysis for each fish species showed that all networks were strongly dominated by positive correlations between the abundances of their OTUs. However, each fish species had different network characteristics suggesting the differential significance of the OTUs in each of the five fish species midgut. The results of the present study may provide evidence that adult fish farmed in the Mediterranean Sea have a rather divergent and species-specific gut microbiota profile, which are shaped independently of the similar environmental conditions under which they grow.},
}
@article {pmid32840024,
year = {2020},
author = {Sizikov, S and Burgsdorf, I and Handley, KM and Lahyani, M and Haber, M and Steindler, L},
title = {Characterization of sponge-associated Verrucomicrobia: microcompartment-based sugar utilization and enhanced toxin-antitoxin modules as features of host-associated Opitutales.},
journal = {Environmental microbiology},
volume = {22},
number = {11},
pages = {4669-4688},
doi = {10.1111/1462-2920.15210},
pmid = {32840024},
issn = {1462-2920},
support = {1243/16//Israel Science Foundation/ ; },
mesh = {Animals ; Mediterranean Sea ; Microbiota ; Phylogeny ; Porifera/*microbiology ; Seawater/microbiology ; Sugars/*metabolism ; *Symbiosis ; Toxin-Antitoxin Systems/*genetics ; Verrucomicrobia/classification/genetics/metabolism/*physiology ; },
abstract = {Bacteria of the phylum Verrucomicrobia are ubiquitous in marine environments and can be found as free-living organisms or as symbionts of eukaryotic hosts. Little is known about host-associated Verrucomicrobia in the marine environment. Here we reconstructed two genomes of symbiotic Verrucomicrobia from bacterial metagenomes derived from the Atlanto-Mediterranean sponge Petrosia ficiformis and three genomes from strains that we isolated from offshore seawater of the Eastern Mediterranean Sea. Phylogenomic analysis of these five strains indicated that they are all members of Verrucomicrobia subdivision 4, order Opitutales. We compared these novel sponge-associated and seawater-isolated genomes to closely related Verrucomicrobia. Genomic analysis revealed that Planctomycetes-Verrucomicrobia microcompartment gene clusters are enriched in the genomes of symbiotic Opitutales including sponge symbionts but not in free-living ones. We hypothesize that in sponge symbionts these microcompartments are used for degradation of l-fucose and l-rhamnose, which are components of algal and bacterial cell walls and therefore may be found at high concentrations in the sponge tissue. Furthermore, we observed an enrichment of toxin-antitoxin modules in symbiotic Opitutales. We suggest that, in sponges, verrucomicrobial symbionts utilize these modules as a defence mechanism against antimicrobial activity deriving from the abundant microbial community co-inhabiting the host.},
}
@article {pmid32839879,
year = {2021},
author = {Noskov, YA and Kabilov, MR and Polenogova, OV and Yurchenko, YA and Belevich, OE and Yaroslavtseva, ON and Alikina, TY and Byvaltsev, AM and Rotskaya, UN and Morozova, VV and Glupov, VV and Kryukov, VY},
title = {A Neurotoxic Insecticide Promotes Fungal Infection in Aedes aegypti Larvae by Altering the Bacterial Community.},
journal = {Microbial ecology},
volume = {81},
number = {2},
pages = {493-505},
pmid = {32839879},
issn = {1432-184X},
support = {18-74-00090//Russian Science Foundation (RU)/ ; },
mesh = {Aedes/*microbiology ; Animals ; Antibiosis/drug effects ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; Bacterial Load ; Insecticides/*pharmacology ; Ivermectin/analogs &amp; derivatives/pharmacology ; Larva/microbiology ; Metarhizium/*physiology ; Microbiota/*drug effects ; Mosquito Control ; Spores, Fungal/physiology ; },
abstract = {Symbiotic bacteria have a significant impact on the formation of defensive mechanisms against fungal pathogens and insecticides. The microbiome of the mosquito Aedes aegypti has been well studied; however, there are no data on the influence of insecticides and pathogenic fungi on its structure. The fungus Metarhizium robertsii and a neurotoxic insecticide (avermectin complex) interact synergistically, and the colonization of larvae with hyphal bodies is observed after fungal and combined (conidia + avermectins) treatments. The changes in the bacterial communities (16S rRNA) of Ae. aegypti larvae under the influence of fungal infection, avermectin toxicosis, and their combination were studied. In addition, we studied the interactions between the fungus and the predominant cultivable bacteria in vitro and in vivo after the coinfection of the larvae. Avermectins increased the total bacterial load and diversity. The fungus decreased the diversity and insignificantly increased the bacterial load. Importantly, avermectins reduced the relative abundance of Microbacterium (Actinobacteria), which exhibited a strong antagonistic effect towards the fungus in in vitro and in vivo assays. The avermectin treatment led to an increased abundance of Chryseobacterium (Flavobacteria), which exerted a neutral effect on mycosis development. In addition, avermectin treatment led to an elevation of some subdominant bacteria (Pseudomonas) that interacted synergistically with the fungus. We suggest that avermectins change the bacterial community to favor the development of fungal infection.},
}
@article {pmid32836127,
year = {2020},
author = {Li, X and Wang, T and Chang, SX and Jiang, X and Song, Y},
title = {Biochar increases soil microbial biomass but has variable effects on microbial diversity: A meta-analysis.},
journal = {The Science of the total environment},
volume = {749},
number = {},
pages = {141593},
doi = {10.1016/j.scitotenv.2020.141593},
pmid = {32836127},
issn = {1879-1026},
mesh = {Biomass ; *Carbon ; Charcoal ; *Soil ; Soil Microbiology ; },
abstract = {Biochar has been extensively studied as a soil amendment for carbon sequestration and for improving soil quality; however, a systematic understanding of the responses of soil microbial biomass and diversity to biochar addition is lacking. Here, a meta-analysis of 999 paired data points from 194 studies shows that biochar increases microbial biomass but has variable effects on microbial diversity. Generally, the effects of biochar on microbial biomass are dependent on biochar properties, while that on microbial diversity is dependent on soil properties. The application of biochar, particularly that produced under low temperature and from nutrient-rich feedstocks, could better increase soil microbial biomass (based on phospholipid fatty acid analysis (MBCPLFA)) and diversity. The increases of total microbial biomass with biochar addition are greater in the field than in laboratory studies, in sandy than in clay soils, and when measured by fumigation-extraction (MBCFE) than by MBCPLFA. The bacterial biomass only significantly increases in laboratory studies and fungal biomass only in soils with pH ≤ 7.5 and soil organic carbon ≤30 g kg[-1]. The increases in total microbial diversity with biochar addition were greater in acidic and sandy soils with low soil organic carbon content and in laboratory incubation studies. In addition, long-term and low-rate addition of biochar always increases microbial diversity. To better guide the use of biochar as a soil amendment, we suggest that establishing long-term and field studies, using a standard method for measuring microbial communities, on different soil types should be our emphasis in future research.},
}
@article {pmid32835181,
year = {2020},
author = {Kirubakaran, R and ArulJothi, KN and Revathi, S and Shameem, N and Parray, JA},
title = {Emerging priorities for microbial metagenome research.},
journal = {Bioresource technology reports},
volume = {11},
number = {},
pages = {100485},
pmid = {32835181},
issn = {2589-014X},
abstract = {Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.},
}
@article {pmid32834061,
year = {2020},
author = {D'Abramo, F and Neumeyer, S},
title = {A historical and political epistemology of microbes.},
journal = {Centaurus; international magazine of the history of science and medicine},
volume = {62},
number = {2},
pages = {321-330},
pmid = {32834061},
issn = {0008-8994},
abstract = {This article traces the historical co-evolution of microbiology, bacteriology, and virology, framed within industrial and agricultural contexts, as well as their role in colonial and national history between the end of the 19th century and the first decades of the 20th century. The epistemology of germ theory, coupled with the economic interests of European colonies, has shaped the understanding of human-microbial relationships in a reductionist way. We explore a brief history of the medical and biological sciences, focusing on microbes and the difficulty of implementing germ theory outside of biology laboratories. Furthermore, we highlight the work of Lynn Margulis, who conceptualized microbes within their ecological contexts. Such research shows the active role microbes play in handling life-sustaining biological and biochemical processes. We outline how the industrial and technological advancements of the last two centuries not only impacted almost all human societies, but also changed the world on microbial, biological, and geological levels. The narration of these histories is a complex task, and depends on how national, international, and intergovernmental institutions (such as the World Health Organization) conceive of the selective environmental pressures exerted by industry and biotechnological companies.},
}
@article {pmid32832265,
year = {2020},
author = {Li, X and Li, Z and He, Y and Li, P and Zhou, H and Zeng, N},
title = {Regional distribution of Christensenellaceae and its associations with metabolic syndrome based on a population-level analysis.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9591},
pmid = {32832265},
issn = {2167-8359},
abstract = {The link between the gut microbiota and metabolic syndrome (MetS) has attracted widespread attention. Christensenellaceae was recently described as an important player in human health, while its distribution and relationship with MetS in Chinese population is still unknown. This study sought to observe the association between Christensenellaceae and metabolic indexes in a large sample of residents in South China. A total of 4,781 people from the GGMP project were included, and the fecal microbiota composition of these individuals was characterized by 16S rRNA sequencing and analyzed the relation between Christensenellaceae and metabolism using QIIME (Quantitative Insight Into Microbial Ecology, Version 1.9.1). The results demonstrated that microbial richness and diversity were increased in the group with a high abundance of Christensenellaceae, who showed a greater complexity of the co-occurrence network with other bacteria than residents who lacked Christensenellaceae. The enriched bacterial taxa were predominantly represented by Oscillospira, Ruminococcaceae, RF39, Rikenellaceae and Akkermansia as the Christensenellaceae abundance increased, while the abundances of Veillonella, Fusobacterium and Klebsiella were significantly reduced. Furthermore, Christensenellaceae was negatively correlated with the pathological features of MetS, such as obesity, hypertriglyceridemia and body mass index (BMI). We found reduced levels of lipid biosynthesis and energy metabolism pathways in people with a high abundance of Christensenellaceae, which may explain the negative relationship between body weight and Christensenellaceae. In conclusion, we found a negative correlation between Christensenellaceae and MetS in a large Chinese population and reported the geographical distribution of Christensenellaceae in the GGMP study. The association data from this population-level research support the investigation of strains within Christensenellaceae as potentially beneficial gut microbes.},
}
@article {pmid32830554,
year = {2020},
author = {Van Hul, M and Karnik, K and Canene-Adams, K and De Souza, M and Van den Abbeele, P and Marzorati, M and Delzenne, NM and Everard, A and Cani, PD},
title = {Comparison of the effects of soluble corn fiber and fructooligosaccharides on metabolism, inflammation, and gut microbiome of high-fat diet-fed mice.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {319},
number = {4},
pages = {E779-E791},
doi = {10.1152/ajpendo.00108.2020},
pmid = {32830554},
issn = {1522-1555},
mesh = {Animals ; Body Composition ; Body Weight ; Diet, High-Fat/*adverse effects ; Dietary Fiber/*pharmacology ; Energy Metabolism/drug effects ; Gastrointestinal Microbiome/*drug effects ; *Inflammation ; Insulin Resistance ; Male ; Metabolism/*drug effects ; Mice ; Mice, Inbred C57BL ; Oligosaccharides/*pharmacology ; Probiotics ; *Zea mays ; },
abstract = {Dietary fibers are essential components of a balanced diet and have beneficial effects on metabolic functions. To gain insight into their impact on host physiology and gut microbiota, we performed a direct comparison of two specific prebiotic fibers in mice. During an 8-wk follow up, mice fed a high-fat diet (HFD) were compared with mice on a normal diet (basal condition, controls) and to mice fed the HFD but treated with one of the following prebiotics: fructooligosaccharides (FOS) or soluble corn fiber (SCF). Both prebiotic fibers led to a similar reduction of body weight and fat mass, lower inflammation and improved metabolic parameters. However, these health benefits were the result of different actions of the fibers, as SCF impacted energy excretion, whereas FOS did not. Interestingly, both fibers had very distinct gut microbial signatures with different short-chain fatty acid profiles, indicating that they do not favor the growth of the same bacterial communities. Although the prebiotic potential of different fibers may seem physiologically equivalent, our data show that the underlying mechanisms of action are different, and this by targeting different gut microbes. Altogether, our data provide evidence that beneficial health effects of specific dietary fibers must be documented to be considered a prebiotic and that studies devoted to understanding how structures relate to specific microbiota modulation and metabolic effects are warranted.},
}
@article {pmid32830371,
year = {2020},
author = {Mukherjee, I and Salcher, MM and Andrei, A&#x15e; and Kavagutti, VS and Shabarova, T and Grujčić, V and Haber, M and Layoun, P and Hodoki, Y and Nakano, SI and Šimek, K and Ghai, R},
title = {A freshwater radiation of diplonemids.},
journal = {Environmental microbiology},
volume = {22},
number = {11},
pages = {4658-4668},
doi = {10.1111/1462-2920.15209},
pmid = {32830371},
issn = {1462-2920},
support = {MSM200961801//Akademie V&#x11b;d &#x10c;esk&#xe9; Republiky/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 19-23469S//Grant Agency of the Czech Republic/ ; 20-12496X//Grant Agency of the Czech Republic/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 116/2019/P//Grant Agency of the University of South Bohemia/ ; JSPS-17-17//JSPS Bilateral Japanese-Czech Joint Research Project/ ; 310030_185108/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Biodiversity ; Ecosystem ; Euglenozoa/*classification/cytology/genetics/*isolation &amp; purification ; In Situ Hybridization, Fluorescence ; Japan ; Lakes/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; },
abstract = {Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and catalysed reporter deposition-fluorescent in situ hybridization (CARD-FISH). We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to a marine clade, which are mainly isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single-cell genomes of marine diplonemids show they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.},
}
@article {pmid32829442,
year = {2021},
author = {Cabrerizo, MJ and Marañón, E},
title = {Grazing Pressure Is Independent of Prey Size in a Generalist Herbivorous Protist: Insights from Experimental Temperature Gradients.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {553-562},
pmid = {32829442},
issn = {1432-184X},
support = {PGC2018-094553B-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; FJCI2017-32318//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
mesh = {*Dinoflagellida ; *Food Chain ; Phytoplankton ; Plankton ; Temperature ; },
abstract = {Grazing by herbivorous protists contributes to structuring plankton communities through its effect on the growth, biomass, and competitiveness of prey organisms and also impacts the transfer of primary production towards higher trophic levels. Previous evidence shows that heterotrophic processes (grazing rates, g) are more sensitive to temperature than autotrophic ones (phytoplankton growth rates, μ) and also that small cells tend to be more heavily predated than larger ones; however, it remains unresolved how the interplay between changes in temperature and cell size modulates grazing pressure (i.e., g:μ ratio). We addressed this problem by conducting an experiment with four phytoplankton populations, from pico- to microphytoplankton, over a 12 °C gradient and in the presence/absence of a generalist herbivorous protist, Oxyrrhis marina. We found that highest g rates coincided with highest μ rates, which corresponded to intermediate cell sizes. There were no significant differences in either μ or g between the smallest and largest cell sizes considered. The g:μ ratio was largely independent of cell size and C:N ratios, and its thermal dependence was low although species-specific differences were large. We suggest that the similar g:μ found could be the consequence that the energetic demand imposed by rising temperatures would be a more important issue than the mechanical constriction to ingestion derived from prey cell size. Despite the difficulty of quantifying μ and g in natural planktonic communities, we suggest that the g:μ ratio is a key response variable to evaluate thermal sensitivity of food webs because it gives a more integrative view of trophic functioning than both rates separately.},
}
@article {pmid32829441,
year = {2021},
author = {Silveira, R and Silva, MRSS and de Roure Bandeira de Mello, T and Alvim, EACC and Marques, NCS and Kruger, RH and da Cunha Bustamante, MM},
title = {Bacteria and Archaea Communities in Cerrado Natural Pond Sediments.},
journal = {Microbial ecology},
volume = {81},
number = {3},
pages = {563-578},
pmid = {32829441},
issn = {1432-184X},
support = {process number 193.000.567/2009//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Distrito Federal/ ; },
mesh = {*Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Geologic Sediments ; Phylogeny ; *Ponds ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Natural ponds in the Brazilian Cerrado harbor high biodiversity but are still poorly studied, especially their microbial assemblage. The characterization of the microbial community in aquatic environments is fundamental for understanding its functioning, particularly under the increasing pressure posed by land conversion and climate change. Here, we aim to characterize the structure (abundance, richness, and diversity) and composition of the Bacteria and Archaea in the sediment of two natural ponds belonging to different basins that primarily differ in size and depth in the Cerrado. Sediment samples were collected in the dry and rainy seasons and the transition periods between both. The structure and composition of Bacteria and Archaea were assessed by 16S rRNA gene pyrosequencing. We identified 45 bacterial and four archaeal groups. Proteobacteria and Acidobacteria dominated the bacterial community, while Euryarchaeota and Thaumarchaeota dominated the archaeal community. Seasonal fluctuations in the relative abundance of microbial taxa were observed, but pond characteristics were more determinant to community composition differences. Microbial communities are highly diverse, and local variability could partially explain the microbial structure's main differences. Functional predictions based in 16S rRNA gene accessed with Tax4Fun indicated an enriched abundance of predicted methane metabolism in the deeper pond, where higher abundance of methanogenic archaea Methanocella, Methanosaeta, and Methanomicrobiaceae was detected. Our dataset encompasses the more comprehensive survey of prokaryotic microbes in Cerrado's aquatic environments. Here, we present basic and essential information about composition and diversity, for initial insights into the ecology of Bacteria and Archaea in these environments.},
}
@article {pmid32829154,
year = {2021},
author = {Jamwal, R and Amit, and Kumari, S and Balan, B and Kelly, S and Cannavan, A and Singh, DK},
title = {Rapid and non-destructive approach for the detection of fried mustard oil adulteration in pure mustard oil via ATR-FTIR spectroscopy-chemometrics.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {244},
number = {},
pages = {118822},
doi = {10.1016/j.saa.2020.118822},
pmid = {32829154},
issn = {1873-3557},
abstract = {Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy integrated with chemometrics was effectively applied for the rapid detection and accurate quantification of fried mustard oil (FMO) adulteration in pure mustard oil (PMO). PMO was adulterated with FMO in the range of 0.5-50% v/v. Principal component analysis (PCA) elucidated the studied adulteration using two components with an explained variance of 97%. The linear discriminant analysis (LDA) was adopted to classify the adulterated PMO samples with FMO. LDA model showed 100% accuracy initially, as well as when cross-validated. To enhance the overall quality of models, characteristic spectral regions were optimized, and principal component regression (PCR) and partial least square regression (PLS-R) models were constructed with high accuracy and precision. PLS-R model for the 2nd derivative of the optimized spectral region 1260-1080 cm[-1] showed best results for prediction sample sets in terms of high R[2] and residual predictive deviation (RPD) value of 0.999 and 31.91 with low root mean square error (RMSE) and relative prediction error (RE %) of 0.53% v/v and 3.37% respectively. Thus, the suggested method can detect up to 0.5% v/v of adulterated FMO in PMO in a short time interval.},
}
@article {pmid32829116,
year = {2020},
author = {Sakarika, M and Candry, P and Depoortere, M and Ganigué, R and Rabaey, K},
title = {Impact of substrate and growth conditions on microbial protein production and composition.},
journal = {Bioresource technology},
volume = {317},
number = {},
pages = {124021},
doi = {10.1016/j.biortech.2020.124021},
pmid = {32829116},
issn = {1873-2976},
mesh = {Biomass ; *Carbon ; },
abstract = {Production of microbial protein (MP) from recovered resources - e.g. CO2-sourced formate and acetate - could provide protein while enabling CO2 capture. To assess the protein quality obtained from this process, pure cultures and enriched communities were selected and characterized kinetically, stoichiometrically and nutritionally. Growth on acetate resulted in up to 5.3 times higher maximum specific growth rate (μmax) than formate (i.e. 0.15-0.41 h[-1] for acetate compared to 0.061-0.29 h[-1] for formate at pH = 7). The protein content was a function of the growth phase, with the highest values during stationary phase, ranging between 18 and 82%CDW protein depending on the organism and substrate. The negative correlation between biomass productivity and protein content indicated a trade-off between production rate and product quality. The final product (i.e. dried MP) quality was in most cases superior to soybean and all cultures were rich in threonine, phenylalanine and tyrosine, regardless of the carbon source.},
}
@article {pmid32827977,
year = {2020},
author = {Dai, H and Gao, J and Wang, S and Li, D and Wang, Z},
title = {The key active degrader, metabolic pathway and microbial ecology of triclosan biodegradation in an anoxic/oxic system.},
journal = {Bioresource technology},
volume = {317},
number = {},
pages = {124014},
doi = {10.1016/j.biortech.2020.124014},
pmid = {32827977},
issn = {1873-2976},
mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Drug Resistance, Microbial ; Metabolic Networks and Pathways ; *Triclosan ; },
abstract = {A lab-scale anoxic/oxic (A/O) system was used to reveal the key active triclosan-degrading bacteria (TCS-DB) in this study. The results showed that TCS was mainly removed by metabolism of heterotrophic bacteria (accounting for about 62%), and the potential metabolic pathway was the break of ether bond in TCS formed 2,4-dichlorophenol, and further dechlorination formed phenol or other metabolic end products. DNA-based stable isotope probing (DNA-SIP) assay further revealed that Methylobacillus accounting for 20.75% in [13]C sample was the key active TCS-DB. Furthermore, methylotrophy and methanol oxidation were found to be the potential metabolic routes of TCS degradation by functional annotation of prokaryotic taxa analysis. Interestingly, TCS accelerated the propagation of antibiotic resistance genes (fabI) and intI1 which positively correlated with several functional microorganisms (p < 0.05). This study contributes to comprehend the potential mechanism, metabolic pathway and microbial ecology of TCS biodegradation in A/O system.},
}
@article {pmid32827089,
year = {2021},
author = {Maher, AMD and Asaiyah, M and Quinn, S and Burke, R and Wolff, H and Bode, HB and Griffin, CT},
title = {Competition and Co-existence of Two Photorhabdus Symbionts with a Nematode Host.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {223-239},
pmid = {32827089},
issn = {1432-184X},
support = {16/RI/3399/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Animals ; Anthraquinones/metabolism ; Grassland ; Luminescent Measurements ; Photorhabdus/growth &amp; development/*metabolism ; Secondary Metabolism/physiology ; Strongyloidea/*microbiology ; Symbiosis/*physiology ; },
abstract = {Photorhabdus spp. (Enterobacteriales: Morganellaceae) occur exclusively as symbionts of Heterorhabditis nematodes for which they provide numerous services, including killing insects and providing nutrition and defence within the cadavers. Unusually, two species (Photorhabdus cinerea and Photorhabdus temperata) associate with a single population of Heterorhabditis downesi at a dune grassland site. Building on previous work, we investigated competition between these two Photorhabdus species both at the regional (between insects) and local (within insect) level by trait comparison and co-culture experiments. There was no difference between the species with respect to supporting nematode reproduction and protection of cadavers against invertebrate scavengers, but P. cinerea was superior to P. temperata in several traits: faster growth rate, greater antibacterial and antifungal activity and colonisation of a higher proportion of nematodes in co-culture. Moreover, where both bacterial symbionts colonised single nematode infective juveniles, P. cinerea tended to dominate in numbers. Differences between Photorhabdus species were detected in the suite of secondary metabolites produced: P. temperata produced several compounds not produced by P. cinerea including anthraquinone pigments. Bioluminescence emitted by P. temperata also tended to be brighter than that from P. cinerea. Bioluminescence and pigmentation may protect cadavers against scavengers that rely on sight. We conclude that while P. cinerea may show greater local level (within-cadaver) competitive success, co-existence of the two Photorhabdus species in the spatially heterogeneous environment of the dunes is favoured by differing specialisations in defence of the cadaver against differing locally important threats.},
}
@article {pmid32826215,
year = {2020},
author = {Gofstein, TR and Perkins, M and Field, J and Leigh, MB},
title = {The Interactive Effects of Crude Oil and Corexit 9500 on Their Biodegradation in Arctic Seawater.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {21},
pages = {},
pmid = {32826215},
issn = {1098-5336},
support = {RL5 GM118990/GM/NIGMS NIH HHS/United States ; TL4 GM118992/GM/NIGMS NIH HHS/United States ; UL1 GM118991/GM/NIGMS NIH HHS/United States ; },
mesh = {Arctic Regions ; Bacteria/*metabolism ; Biodegradation, Environmental ; *Lipids ; *Microbiota ; Petroleum/*metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seawater/microbiology ; },
abstract = {The risk of petroleum spills coupled with the potential application of chemical dispersants as a spill response strategy necessitates further understanding of the fate of oil and dispersants and their interactive effects during biodegradation. Using Arctic seawater mesocosms amended with either crude oil, Corexit 9500, or both together, we quantified the chemical losses of crude oil and Corexit 9500 and identified microbial taxa implicated in their biodegradation based on shifts in the microbial community structure over a 30-day time course. Chemical analyses included total petroleum hydrocarbons (TPH), n-alkanes, branched alkanes, and polycyclic aromatic hydrocarbons (PAHs) for oil loss and the surfactant components dioctyl sodium sulfosuccinate (DOSS), Span 80, Tween 80, Tween 85, and the DOSS metabolite ethylhexyl sulfosuccinate (EHSS) for Corexit loss. Changes to the microbial communities and identification of key taxa were determined by 16S rRNA gene amplicon sequencing. The nonionic surfactants of Corexit 9500 (Span 80 and Tweens 80 and 85) biodegraded rapidly, dropping to below the limits of detection within 5 days and prior to any detectable initiation of oil biodegradation. This resulted in no observable suppression of petroleum biodegradation in the presence of Corexit compared to that of oil alone. In contrast, biodegradation of DOSS was delayed in the presence of oil, based on the prolonged presence of DOSS and accumulation of the degradation intermediate EHSS that did not occur in the absence of oil. Microbial analyses revealed that oil and Corexit enriched different overall microbial communities, with the presence of both resulting in a community composition that shifted from one more similar to that of Corexit only to one reflecting the oil-only community over time, in parallel with the degradation of predominantly Corexit and then oil components. Some microbial taxa (Oleispira, Pseudofulvibacter, and Roseobacter) responded to either oil or Corexit, suggesting that some organisms may be capable of utilizing both substrates. Together, these findings reveal interactive effects of crude oil and Corexit 9500 on chemical losses and microbial communities as they biodegrade, providing further insight into their fate when copresent in the environment.IMPORTANCE Chemical dispersants such as Corexit 9500 are commonly used in oil spill response and are currently under consideration for use in the Arctic, where their fate and effects have not been well studied. This research was performed to determine the interactive effects of the copresence of crude oil and Corexit 9500 on the degradation of components from each mixture and the associated microbial community structure over time in Arctic seawater. These findings will help yield a better understanding of the biodegradability of dispersant components applied to an oil spill, the temporal microbial community response to dispersed oil, and the fundamental microbial ecology of organic contaminant biodegradation processes in the Arctic marine environment.},
}
@article {pmid32825355,
year = {2020},
author = {Floyd, AS and Mott, BM and Maes, P and Copeland, DC and McFrederick, QS and Anderson, KE},
title = {Microbial Ecology of European Foul Brood Disease in the Honey Bee (Apis mellifera): Towards a Microbiome Understanding of Disease Susceptibility.},
journal = {Insects},
volume = {11},
number = {9},
pages = {},
pmid = {32825355},
issn = {2075-4450},
abstract = {European honey bees (Apis mellifera Linnaeus) are beneficial insects that provide essential pollination services for agriculture and ecosystems worldwide. Modern commercial beekeeping is plagued by a variety of pathogenic and environmental stressors often confounding attempts to understand colony loss. European foulbrood (EFB) is considered a larval-specific disease whose causative agent, Melissococcus plutonius, has received limited attention due to methodological challenges in the field and laboratory. Here, we improve the experimental and informational context of larval disease with the end goal of developing an EFB management strategy. We sequenced the bacterial microbiota associated with larval disease transmission, isolated a variety of M.plutonius strains, determined their virulence against larvae in vitro, and explored the potential for probiotic treatment of EFB disease. The larval microbiota was a low diversity environment similar to honey, while worker mouthparts and stored pollen contained significantly greater bacterial diversity. Virulence of M. plutonius against larvae varied markedly by strain and inoculant concentration. Our chosen probiotic, Parasaccharibacter apium strain C6, did not improve larval survival when introduced alone, or in combination with a virulent EFB strain. We discuss the importance of positive and negative controls for in vitro studies of the larval microbiome and disease.},
}
@article {pmid32824323,
year = {2020},
author = {Rutere, C and Knoop, K and Posselt, M and Ho, A and Horn, MA},
title = {Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments.},
journal = {Microorganisms},
volume = {8},
number = {8},
pages = {},
pmid = {32824323},
issn = {2076-2607},
support = {641939//European Commission/ ; },
abstract = {Ibuprofen, a non-steroidal anti-inflammatory pain reliever, is among pharmaceutical residues of environmental concern ubiquitously detected in wastewater effluents and receiving rivers. Thus, ibuprofen removal potentials and associated bacteria in the hyporheic zone sediments of an impacted river were investigated. Microbially mediated ibuprofen degradation was determined in oxic sediment microcosms amended with ibuprofen (5, 40, 200, and 400 µM), or ibuprofen and acetate, relative to an un-amended control. Ibuprofen was removed by the original sediment microbial community as well as in ibuprofen-enrichments obtained by re-feeding of ibuprofen. Here, 1-, 2-, 3-hydroxy- and carboxy-ibuprofen were the primary transformation products. Quantitative real-time PCR analysis revealed a significantly higher 16S rRNA abundance in ibuprofen-amended relative to un-amended incubations. Time-resolved microbial community dynamics evaluated by 16S rRNA gene and 16S rRNA analyses revealed many new ibuprofen responsive taxa of the Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Latescibacteria, and Proteobacteria. Two ibuprofen-degrading strains belonging to the genera Novosphingobium and Pseudomonas were isolated from the ibuprofen-enriched sediments, consuming 400 and 300 µM ibuprofen within three and eight days, respectively. The collective results indicated that the hyporheic zone sediments sustain an efficient biotic (micro-)pollutant degradation potential, and hitherto unknown microbial diversity associated with such (micro)pollutant removal.},
}
@article {pmid32823898,
year = {2020},
author = {Francis, F and Jacquemyn, H and Delvigne, F and Lievens, B},
title = {From Diverse Origins to Specific Targets: Role of Microorganisms in Indirect Pest Biological Control.},
journal = {Insects},
volume = {11},
number = {8},
pages = {},
pmid = {32823898},
issn = {2075-4450},
abstract = {Integrated pest management (IPM) is today a widely accepted pest management strategy to select and use the most efficient control tactics and at the same time reduce over-dependence on chemical insecticides and their potentially negative environmental effects. One of the main pillars of IPM is biological control. While biological control programs of pest insects commonly rely on natural enemies such as predatory insects, parasitoids and microbial pathogens, there is increasing evidence that plant, soil and insect microbiomes can also be exploited to enhance plant defense against herbivores. In this mini-review, we illustrate how microorganisms from diverse origins can contribute to plant fitness, functional traits and indirect defense responses against pest insects, and therefore be indirectly used to improve biological pest control practices. Microorganisms in the rhizosphere, phyllosphere and endosphere have not only been shown to enhance plant growth and plant strength, but also promote plant defense against herbivores both above- and belowground by providing feeding deterrence or antibiosis. Also, herbivore associated molecular patterns may be induced by microorganisms that come from oral phytophagous insect secretions and elicit plant-specific responses to herbivore attacks. Furthermore, microorganisms that inhabit floral nectar and insect honeydew produce volatile organic compounds that attract beneficial insects like natural enemies, thereby providing indirect pest control. Given the multiple benefits of microorganisms to plants, we argue that future IPMs should consider and exploit the whole range of possibilities that microorganisms offer to enhance plant defense and increase attraction, fecundity and performance of natural enemies.},
}
@article {pmid32823755,
year = {2020},
author = {Quijada, NM and Bodas, R and Lorenzo, JM and Schmitz-Esser, S and Rodríguez-Lázaro, D and Hernández, M},
title = {Dietary Supplementation with Sugar Beet Fructooligosaccharides and Garlic Residues Promotes Growth of Beneficial Bacteria and Increases Weight Gain in Neonatal Lambs.},
journal = {Biomolecules},
volume = {10},
number = {8},
pages = {},
pmid = {32823755},
issn = {2218-273X},
support = {IDMICRO//Consejer&#xed;a de Agricultura y Ganader&#xed;a, Castilla y Le&#xf3;n/International ; },
mesh = {Animals ; Animals, Newborn ; Bacteria/*classification/genetics/growth &amp; development/isolation &amp; purification ; Beta vulgaris/*chemistry ; Bifidobacterium/classification/genetics/growth &amp; development/isolation &amp; purification ; Body Weight/*drug effects ; Dietary Supplements ; Garlic/*chemistry ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Lactobacillus/classification/genetics/growth &amp; development/isolation &amp; purification ; Milk/chemistry ; Oligosaccharides/*administration &amp; dosage/pharmacology ; Plant Extracts/*administration &amp; dosage/pharmacology ; Prebiotics/administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sheep ; Veillonella/classification/genetics/growth &amp; development/isolation &amp; purification ; },
abstract = {The proper development of the early gastrointestinal tract (GIT) microbiota is critical for newborn ruminants. This microbiota is susceptible to modification by diverse external factors (such as diet) that can lead to long-lasting results when occurring in young ruminants. Dietary supplementation with prebiotics, ingredients nondigestible and nonabsorbable by the host that stimulate the growth of beneficial GIT bacteria, has been applied worldwide as a potential approach in order to improve ruminant health and production yields. However, how prebiotics affect the GIT microbiota during ruminants' early life is still poorly understood. We investigated the effect of milk supplementation with a combination of two well-known prebiotics, fructooligosaccharides (FOS) from sugar beet and garlic residues (all together named as "additive"), exerted on preweaned lamb growth and the composition of their fecal microbiota, by using 16S rRNA gene amplicon high-throughput sequencing. The results showed a significant increase in the mean daily weight gain of lambs fed with the additive. Lamb fecal microbiota was also influenced by the additive intake, as additive-diet lambs showed lower bacterial diversity and were significantly more abundant in Bifidobacterium, Enterococcus, Lactobacillus and Veillonella. These bacteria have been previously reported to confer beneficial properties to the ruminant, including promotion of growth and health status, and our results showed that they were strongly linked to the additive intake and the increased weight gain of lambs. This study points out the combination of FOS from sugar beet and garlic residues as a potential prebiotic to be used in young ruminants' nutrition in order to improve production yields.},
}
@article {pmid32819450,
year = {2020},
author = {Berg, G and Rybakova, D and Fischer, D and Cernava, T and Vergès, MC and Charles, T and Chen, X and Cocolin, L and Eversole, K and Corral, GH and Kazou, M and Kinkel, L and Lange, L and Lima, N and Loy, A and Macklin, JA and Maguin, E and Mauchline, T and McClure, R and Mitter, B and Ryan, M and Sarand, I and Smidt, H and Schelkle, B and Roume, H and Kiran, GS and Selvin, J and de Souza, RSC and van Overbeek, L and Singh, BK and Wagner, M and Walsh, A and Sessitsch, A and Schloter, M},
title = {Correction to: Microbiome definition re-visited: old concepts and new challenges.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {119},
pmid = {32819450},
issn = {2049-2618},
abstract = {An amendment to this paper has been published and can be accessed via the original article.},
}
@article {pmid32818149,
year = {2020},
author = {Kaplan, F and Shapiro-Ilan, D and Schiller, KC},
title = {Dynamics of entomopathogenic nematode foraging and infectivity in microgravity.},
journal = {NPJ microgravity},
volume = {6},
number = {},
pages = {20},
pmid = {32818149},
issn = {2373-8065},
abstract = {Microgravity is a unique environment to elucidate host-parasite biology. Entomopathogenic nematodes (EPNs), model parasites, kill host insects with mutualistic bacteria and provide environmentally friendly pest control. It is unknown how microgravity affects a multistep insect invasion by parasites with mutualistic bacteria. EPNs respond directionally to electromagnetic cues and their sinusoidal locomotion is affected by various physical factors. Therefore, we expected microgravity to impact EPN functionality. Microgravity experiments during space flight on the International Space Station (ISS) indicated that EPNs successfully emerged from consumed insect host cadavers, moved through soil, found and infected bait insects in a manner equivalent to Earth controls. However, nematodes that developed entirely in space, from the egg stage, died upon return to Earth, unlike controls in microgravity and on Earth. This agricultural biocontrol experiment in space gives insight to long-term space flight for symbiotic organisms, parasite biology, and the potential for sustainable crop protection in space.},
}
@article {pmid32817104,
year = {2020},
author = {Miller, JI and Techtmann, S and Joyner, D and Mahmoudi, N and Fortney, J and Fordyce, JA and GaraJayeva, N and Askerov, FS and Cravid, C and Kuijper, M and Pelz, O and Hazen, TC},
title = {Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth.},
journal = {mBio},
volume = {11},
number = {4},
pages = {},
pmid = {32817104},
issn = {2150-7511},
mesh = {Bacteria/*classification ; Biodegradation, Environmental ; *Genetic Variation ; *Microbiota ; Petroleum/metabolism ; Phylogeny ; Seawater/*microbiology ; },
abstract = {The environmental surveys following the 2010 Deepwater Horizon (DWH) spill identified a variety of hydrocarbon-degrading microorganisms, and laboratory studies with field-collected water samples then demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Knowledge about microbial community composition, diversity, and functional metabolic capabilities aids in understanding and predicting petroleum biodegradation by microbial communities in situ and is therefore an important component of the petroleum spill response decision-making process. This study investigates the taxonomic composition of microbial communities in six different global basins where petroleum and gas activities occur. Shallow-water communities were strikingly similar across basins, while deep-water communities tended to show subclusters by basin, with communities from the epipelagic, mesopelagic, and bathypelagic zones sometimes appearing within the same cluster. Microbial taxa that were enriched in the water column in the Gulf of Mexico following the DWH spill were found across marine basins. Several hydrocarbon-degrading genera (e.g., Actinobacteria, Pseudomonas, and Rhodobacteriacea) were common across all basins. Other genera such as Pseudoalteromonas and Oleibacter were highly enriched in specific basins.IMPORTANCE Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole carbon source). This study quantifies the subpopulations of microorganisms that are expected to be involved in petroleum hydrocarbon biodegradation, which is important information during the decision-making process in the event of a petroleum spill accident.},
}
@article {pmid32816051,
year = {2021},
author = {Zhang, Q and Campos, M and Larama, G and Acuña, JJ and Valenzuela, B and Solis, F and Zamorano, P and Araya, R and Sadowsky, MJ and Jorquera, MA},
title = {Composition and predicted functions of the bacterial community in spouting pool sediments from the El Tatio Geyser field in Chile.},
journal = {Archives of microbiology},
volume = {203},
number = {1},
pages = {389-397},
pmid = {32816051},
issn = {1432-072X},
support = {1201386//FONDECYT/ ; NSFC190012//CONICYT/ ; },
mesh = {Bacteria/*classification/genetics/metabolism ; *Biodiversity ; Chile ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The El Tatio Geyser Field (ETGF), located in Northern Chile, is the main geyser field in the southern hemisphere. Despite this, details of its microbial ecology are still unknown. Here, we briefly report on the composition and predicted functions of the bacterial community in spouting pool sediments from the ETGF as revealed by high-throughput sequencing of 16S rRNA genes. Results of this analysis showed that while there were differences in richness and diversity between samples, bacterial communities were primarily dominated by the phyla Proteobacteria, followed Firmicutes, Bacteroidetes, Acidobacteria, and Chloroflexi. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by sulfur (respiration of sulfur compounds and sulfate) and nitrogen (nitrate reduction, respiration of nitrogen and nitrate) cycling. Taken together, our results suggest a high diversity in taxonomy and predictive functions of bacterial communities in sediments from spouting pools. This study provides fundamentally important information on the structure and function predictive functions of microbiota communities in spouting pools. Moreover, since the ETGF is intensively visited and impacted by tens of thousands of tourists every year, our results can be used to help guide the design of sustainable conservation strategies.},
}
@article {pmid32816010,
year = {2020},
author = {Vestrum, RI and Attramadal, KJK and Vadstein, O and Gundersen, MS and Bakke, I},
title = {Bacterial community assembly in Atlantic cod larvae (Gadus morhua): contributions of ecological processes and metacommunity structure.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {9},
pages = {},
pmid = {32816010},
issn = {1574-6941},
mesh = {Animals ; Bacteria/genetics ; *Gadus morhua ; *Gastrointestinal Microbiome ; Larva ; *Microbiota ; },
abstract = {Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental conditions affect the community assembly. We investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed to quantify ecological processes influencing community assembly in cod larvae and to elucidate the complex relationship between the bacteria of the environment and the fish. Selection within the fish was the major determinant for community assembly, but drift resulted in inter-individual variation. The environmental bacterial communities were highly dissimilar from those associated with the fish. Still, differences in the environmental bacterial communities strongly influenced the fish communities. The most striking difference was an excessive dominance of a single OTU (Arcobacter) for larvae reared in two of the three systems. These larvae were exposed to environments with higher fractions of opportunistic bacteria, and we hypothesise that detrimental host-microbe interactions might have made the fish susceptible to Arcobacter colonisation. Despite strong selection within the host, this points to a possibility to steer the metacommunity towards mutualistic host-microbe interactions and improved fish health and survival.},
}
@article {pmid32815317,
year = {2020},
author = {Nascimento Lemos, L and Manoharan, L and William Mendes, L and Monteiro Venturini, A and Satler Pylro, V and Tsai, SM},
title = {Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.},
journal = {Environmental microbiology reports},
volume = {12},
number = {6},
pages = {651-655},
doi = {10.1111/1758-2229.12880},
pmid = {32815317},
issn = {1758-2229},
support = {//Brazilian Microbiome Project/International ; 140032/2015-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/International ; 161931/2015-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/International ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/International ; 2014/50320-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; 2015/13546-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; 2016/18215-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; 2017/09643-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; 2017/24037-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; //Coordination for the Improvement of Higher Education Personnel/International ; //National Council for Scientific and Technological Development/International ; //S&#xe3;o Paulo Research Foundation/International ; },
mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Databases, Genetic ; Genome Size ; *Genome, Bacterial ; Metagenome ; Microbiota ; Phylogeny ; *Soil Microbiology ; },
abstract = {Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.},
}
@article {pmid32814025,
year = {2020},
author = {Alexander, M and Turnbaugh, PJ},
title = {Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions.},
journal = {Immunity},
volume = {53},
number = {2},
pages = {264-276},
pmid = {32814025},
issn = {1097-4180},
support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; M01 RR001271/RR/NCRR NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; F32 AI147456/AI/NIAID NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; },
mesh = {*Diet ; Gastrointestinal Microbiome/*physiology ; Humans ; Immunity/physiology ; Immunomodulation/*physiology ; Inflammation/pathology ; },
abstract = {Emerging evidence suggests that the effect of dietary intake on human health and disease is linked to both the immune system and the microbiota. Yet, we lack an integrated mechanistic model for how these three complex systems relate, limiting our ability to understand and treat chronic and infectious disease. Here, we review recent findings at the interface of microbiology, immunology, and nutrition, with an emphasis on experimentally tractable models and hypothesis-driven mechanistic work. We outline emerging mechanistic concepts and generalizable approaches to bridge the gap between microbial ecology and molecular mechanism. These set the stage for a new era of precision human nutrition informed by a deep and comprehensive knowledge of the diverse cell types in and on the human body.},
}
@article {pmid32812858,
year = {2020},
author = {Lee, JC and Whang, KS},
title = {Agriterribacter humi gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from soil of a farming field.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {9},
pages = {5123-5130},
doi = {10.1099/ijsem.0.004397},
pmid = {32812858},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Bacteroidetes/*classification/isolation &amp; purification ; Base Composition ; DNA, Bacterial/genetics ; *Farms ; Fatty Acids/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; },
abstract = {A Gram-stain-negative bacterium, designated strain YJ03[T], was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ03[T] was found to be an aerobic, non-motile and non-spore-forming bacterium which can grow at 10-33 °C (optimum, 25-28 °C), at pH 6.6-9.5 (optimum, pH 7.0-7.5) and at salinities of 0-1.0 % (w/v) NaCl (optimum, 0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ03[T] with the closely related relatives were in the range 93.9-92.2 %, and the results of phylogenomic analysis indicated that strain YJ03[T] was clearly separated from species of the genera in the family Chitinophagaceae, showing average nucleotide identity values of 68.8-64.3 %. The predominant isoprenoid quinone was identified as MK-7 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and an unidentified fatty acid with an equivalent chain-length of 13.565. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and six unidentified lipids. The G+C content of the genome was determined to be 41.8 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences in this study, strain YJ03[T] is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Agriterribacter humi gen. nov., sp. nov., is proposed. The type strain of Agriterribacter humi is YJ03[T] (=KACC 19548[T]=NBRC 113195[T]).},
}
@article {pmid32807105,
year = {2020},
author = {Kabwe, MH and Vikram, S and Mulaudzi, K and Jansson, JK and Makhalanyane, TP},
title = {The gut mycobiota of rural and urban individuals is shaped by geography.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {257},
pmid = {32807105},
issn = {1471-2180},
mesh = {Adult ; DNA, Fungal/genetics ; DNA, Intergenic/*genetics ; Diet/adverse effects/classification ; Feces/*microbiology ; Female ; Fungi/*classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/drug effects ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Phylogeny ; Phylogeography ; Rural Population ; Sequence Analysis, DNA/*methods ; Smoking/adverse effects ; South Africa ; Urban Population ; Young Adult ; },
abstract = {BACKGROUND: Understanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape the human gut microbiota. However, most of these studies have focused on the more abundant bacterial component and comparatively less is known regarding fungi in the human gut. This knowledge deficit is especially true for rural and urban African populations. Therefore, we assessed the structure and drivers of rural and urban gut mycobiota.<br><br>RESULTS: Our participants (n&#x2009;=&#x2009;100) were balanced by geography and sex. The mycobiota of these geographically separated cohorts was characterized using amplicon analysis of the Internal Transcribed Spacer (ITS) gene. We further assessed biomarker species specific to rural and urban cohorts. In addition to phyla which have been shown to be ubiquitous constituents of gut microbiota, Pichia were key constituents of the mycobiota. We found that geographic location was a major driver of gut mycobiota. Other factors such as smoking where also determined gut mycobiota albeit to a lower extent, as explained by the small proportion of total variation. Linear discriminant and the linear discriminant analysis effect size analysis revealed several distinct urban and rural biomarkers.<br><br>CONCLUSIONS: Together, our analysis reveals distinct community structure in urban and rural South African individuals. Geography was shown to be a key driver of rural and urban gut mycobiota.},
}
@article {pmid32806693,
year = {2020},
author = {Martin-Rivilla, H and Gutierrez-Mañero, FJ and Gradillas, A and P Navarro, MO and Andrade, G and Lucas, JA},
title = {Identifying the Compounds of the Metabolic Elicitors of Pseudomonas fluorescens N 21.4 Responsible for Their Ability to Induce Plant Resistance.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {8},
pages = {},
pmid = {32806693},
issn = {2223-7747},
support = {AGL-2013-45189-R//Ministerio de Econom&#xed;a y Competitividad of Spain/ ; },
abstract = {In this work, the metabolic elicitors extracted from the beneficial rhizobacterium Pseudomonas fluorescens N 21.4 were sequentially fragmented by vacuum liquid chromatography to isolate, purify and identify the compounds responsible for the extraordinary capacities of this strain to induce systemic resistance and to elicit secondary defensive metabolism in diverse plant species. To check if the fractions sequentially obtained were able to increase the synthesis of isoflavones and if, therefore, they still maintained the eliciting capacity of the live strain, rapid and controlled experiments were done with soybean seeds. The optimal action concentration of the fractions was established and all of them elicited isoflavone secondary metabolism-the fractions that had been extracted with n-hexane being more effective. The purest fraction was the one with the highest eliciting capacity and was also tested in Arabidopsis thaliana seedlings to induce systemic resistance against the pathogen Pseudomonas syringae pv. tomato DC 3000. This fraction was then analyzed by UHPLC/ESI-QTOF-MS, and an alkaloid, two amino lipids, three arylalkylamines and a terpenoid were tentatively identified. These identified compounds could be part of commercial plant inoculants of biological and sustainable origin to be applied in crops, due to their potential to enhance the plant immune response and since many of them have putative antibiotic and/or antifungal potential.},
}
@article {pmid32804245,
year = {2021},
author = {Wei, X and Chi, Z and Liu, GL and Hu, Z and Chi, ZM},
title = {The Genome-Wide Mutation Shows the Importance of Cell Wall Integrity in Growth of the Psychrophilic Yeast Metschnikowia australis W7-5 at Different Temperatures.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {52-66},
pmid = {32804245},
issn = {1432-184X},
support = {31970058//Major Research Plan/ ; },
mesh = {Acclimatization/*genetics ; Cell Wall/*physiology ; Cold Temperature ; Gene Editing/methods ; Gene Expression Regulation, Fungal ; Genome, Fungal/genetics ; Glucosyltransferases/genetics ; Glycerol/metabolism ; Glycerol-3-Phosphate Dehydrogenase (NAD+)/genetics ; Glycogen/metabolism ; Integrases/metabolism ; Metschnikowia/*genetics/*growth &amp; development/physiology ; Mitogen-Activated Protein Kinases/genetics ; Signal Transduction/genetics ; Transcription Factors/*genetics ; Trehalose/metabolism ; },
abstract = {In this study, it was found that a Cre/loxP system could be successfully used as a tool for editing the genome of the psychrophilic yeast Metschnikowia australis W7-5 isolated from Antarctica. The deletion and over-expression of the TPS1 gene for trehalose biosynthesis, the GSY gene for glycogen biosynthesis, and the GPD1 and GPP genes for glycerol biosynthesis had no influence on cell growth of the mutants and transformants compared to cell growth of their wild-type strain M. australis W7-5, indicating that trehalose, glycogen, and glycerol had no function in growth of the psychrophilic yeast at different temperatures. However, removal of the SLT2 gene encoding the mitogen-activated protein kinase in the cell wall integrity (CWI) signaling pathway and the SWI4 and SWI6 genes encoding the transcriptional activators Swi4/6 had the crucial influence on cell growth of the psychrophilic yeast at the low temperature, especially at 25 °C and expression of the genes related to cell wall and lipid biosynthesis. Therefore, the cell wall could play an important role in growth of the psychrophilic yeast at different temperatures and biosynthesis of cell wall was actively regulated by the CWI signaling pathway. This was the first time to show that the genome of the psychrophilic yeast was successfully edited and the molecular evidences were obtained to elucidate mechanisms of low temperature growth of the psychrophilic yeast from Antarctica.},
}
@article {pmid32804239,
year = {2020},
author = {Andras, JP and Rodriguez-Reillo, WG and Truchon, A and Blanchard, JL and Pierce, EA and Ballantine, KA},
title = {Rewilding the small stuff: the effect of ecological restoration on prokaryotic communities of peatland soils.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {10},
pages = {},
doi = {10.1093/femsec/fiaa144},
pmid = {32804239},
issn = {1574-6941},
mesh = {Carbon ; Carbon Sequestration ; *Microbiota ; *Soil ; Soil Microbiology ; Wetlands ; },
abstract = {To investigate the effect that restoration has on the microbiome of wetland soils, we used 16S amplicon sequencing to characterize the soil prokaryotic communities of retired cranberry farms that were restored to approximate the peat wetlands they once were. For comparison, we also surveyed the soil communities of active cranberry farms, retired cranberry farms and natural peat wetlands that were never farmed. Our results show that the prokaryotic communities of active cranberry farms are distinct from those of natural peat wetlands. Moreover, 4 years after restoration, the prokaryotic community structure of restored cranberry farms had shifted, resulting in a community more similar to natural peat wetlands than to active farms. Meanwhile, the prokaryotic communities of retired cranberry farms remained similar to those of active farms. The observed differences in community structure across site types corresponded with significant differences in inferred capacity for denitrification, methanotrophy and methanogenesis, and community composition was also correlated with previously published patterns of denitrification and carbon sequestration measured from the same soil samples. Taken together, these results suggest that ecological restoration efforts have the potential to restore ecosystem functions of soils and that they do so by 'rewilding' the communities of resident soil microbes.},
}
@article {pmid32803365,
year = {2020},
author = {Li, CX and Fan, YF and Luan, W and Dai, Y and Wang, MX and Wei, CM and Wang, Y and Tao, X and Mao, P and Ma, XR},
title = {Correction to: Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {960},
doi = {10.1007/s00248-020-01572-z},
pmid = {32803365},
issn = {1432-184X},
abstract = {We request that the following corrections be made in our article.},
}
@article {pmid32803364,
year = {2021},
author = {Berlow, M and Phillips, JN and Derryberry, EP},
title = {Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {253-266},
pmid = {32803364},
issn = {1432-184X},
mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; Gastrointestinal Microbiome/*genetics ; Male ; Noise/adverse effects ; RNA, Ribosomal, 16S/genetics ; Rural Population/statistics &amp; numerical data ; San Francisco ; Sparrows/*microbiology ; Urban Population/statistics &amp; numerical data ; *Urbanization ; Wilderness ; },
abstract = {Habitats are changing rapidly around the globe and urbanization is one of the primary drivers. Urbanization changes food availability, environmental stressors, and the prevalence of disease for many species. These changes can lead to divergence in phenotypic traits, including behavioral, physiological, and morphological features between urban and rural populations. Recent research highlights that urbanization is also changing the gut microbial communities found in a diverse group of host species. These changes have not been uniform, leaving uncertainty as to how urban habitats are shaping gut microbial communities. To better understand these effects, we investigated the gut bacterial communities of White-Crowned Sparrow (Zonotrichia leucophrys) populations along an urbanization gradient in the San Francisco Bay area. We examined how gut bacterial communities vary with the local environment and host morphological characteristics. We found direct effects of environmental factors, including urban noise levels and territory land cover, as well as indirect effects through body size and condition, on alpha and beta diversity of gut microbial communities. We also found that urban and rural birds' microbiomes differed in which variables predicted their diversity, with urban communities driven by host morphology, and rural communities driven by environmental factors. Elucidating these effects provides a better understanding of how urbanization affects wild avian physiology.},
}
@article {pmid32803363,
year = {2020},
author = {Cai, Y and Zhou, X and Shi, L and Jia, Z},
title = {Atmospheric Methane Oxidizers Are Dominated by Upland Soil Cluster Alpha in 20 Forest Soils of China.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {859-871},
doi = {10.1007/s00248-020-01570-1},
pmid = {32803363},
issn = {1432-184X},
support = {41401294//National Natural Science Foundation of China/ ; 41877062//National Natural Science Foundation of China/ ; 91751204//National Natural Science Foundation of China/ ; 2019311//Youth Innovation Promotion Association, CAS/ ; },
mesh = {Bacteria/isolation &amp; purification/*metabolism ; China ; Forests ; Genes, Bacterial ; Methane/*metabolism ; Methylocystaceae/isolation &amp; purification/metabolism ; *Microbiota ; Oxidation-Reduction ; Polymerase Chain Reaction ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; },
abstract = {Upland soil clusters alpha and gamma (USCα and USCγ) are considered a major biological sink of atmospheric methane and are often detected in forest and grassland soils. These clusters are phylogenetically classified using the particulate methane monooxygenase gene pmoA because of the difficulty of cultivation. Recent studies have established a direct link of pmoA genes to 16S rRNA genes based on their isolated strain or draft genomes. However, whether the results of pmoA-based assays could be largely represented by 16S rRNA gene sequencing in upland soils remains unclear. In this study, we collected 20 forest soils across China and compared methane-oxidizing bacterial (MOB) communities by high-throughput sequencing of 16S rRNA and pmoA genes using different primer sets. The results showed that 16S rRNA gene sequencing and the semi-nested polymerase chain reaction (PCR) of the pmoA gene (A189/A682r nested with a mixture of mb661 and A650) consistently revealed the dominance of USCα (accounting for more than 50% of the total MOB) in 12 forest soils. A189f/A682r successfully amplified pmoA genes (mainly RA14 of USCα) in only three forest soils. A189f/mb661 could amplify USCα (mainly JR1) in several forest soils but showed a strong preferential amplification of Methylocystis and many other type I MOB groups. A189f/A650 almost exclusively amplified USCα (mainly JR1) and largely discriminated against Methylocystis and most of the other MOB groups. The semi-nested PCR approach weakened the bias of A189f/mb661 and A189f/A650 for JR1 and balanced the coverage of all USCα members. The canonical correspondence analysis indicated that soil NH4[+]-N and pH were the main environmental factors affecting the MOB community of Chinese forest soils. The RA14 of the USCα group prefers to live in soils with low pH, low temperature, low elevation, high precipitation, and rich in nitrogen. JR1's preferences for temperature and elevation were opposite to RA14. Our study suggests that combining the deep sequencing of 16S rRNA and pmoA genes to characterize MOB in forest soils is the best choice.},
}
@article {pmid32803362,
year = {2021},
author = {Zilius, M and Samuiloviene, A and Stanislauskienė, R and Broman, E and Bonaglia, S and Meškys, R and Zaiko, A},
title = {Depicting Temporal, Functional, and Phylogenetic Patterns in Estuarine Diazotrophic Communities from Environmental DNA and RNA.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {36-51},
pmid = {32803362},
issn = {1432-184X},
support = {P-MIP-17-126//Lietuvos Mokslo Taryba/ ; },
mesh = {Cyanobacteria/*genetics/*metabolism ; DNA, Environmental/genetics ; Estuaries ; Fresh Water/*microbiology ; Heterotrophic Processes ; Microbiota ; Nitrogen Cycle/*physiology ; Nitrogen Fixation/*physiology ; Oxidoreductases/genetics ; Phylogeny ; RNA/genetics ; Seasons ; Water Microbiology ; },
abstract = {Seasonally nitrogen-limited and phosphorus-replete temperate coastal waters generally host dense and diverse diazotrophic communities. Despite numerous studies in marine systems, little is known about diazotrophs and their functioning in oligohaline estuarine environments. Here we applied a combination of nifH transcript and metagenomic shotgun sequencing approaches to investigate temporal shifts in taxonomic composition and nifH activity of size-fractionated diazotrophic communities in a shallow and mostly freshwater coastal lagoon. Patterns in active nifH phylotypes exhibited a clear seasonal succession, which reflected their different tolerances to temperature change and nitrogen (N) availability. Thus, in spring, heterotrophic diazotrophs (Proteobacteria) dominated the nifH phylotypes, while increasing water temperature and depletion of inorganic N fostered heterocystous Cyanobacteria in summer. Metagenomic data demonstrated four main N-cycling pathways and three of them with a clear seasonal pattern: denitrification (spring) → N2 fixation (summer) → assimilative NO3[-] reduction (fall), with NH4[+] uptake into cells occurring across all seasons. Although a substantial denitrification signal was observed in spring, it could have originated from the re-suspended benthic rather than planktonic community. Our results contribute to a better understanding of the realized genetic potential of pelagic N2 fixation and its seasonal dynamics in oligohaline estuarine ecosystems, which are natural coastal biogeochemical reactors.},
}
@article {pmid32801177,
year = {2020},
author = {Pilgrim, J and Siozios, S and Baylis, M and Hurst, GDD},
title = {Tissue Tropisms and Transstadial Transmission of a Rickettsia Endosymbiont in the Highland Midge, Culicoides impunctatus (Diptera: Ceratopogonidae).},
journal = {Applied and environmental microbiology},
volume = {86},
number = {20},
pages = {},
pmid = {32801177},
issn = {1098-5336},
support = {BBS/E/I/00001701/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M012441/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Ceratopogonidae/*microbiology ; Female ; In Situ Hybridization, Fluorescence ; Insect Vectors/*microbiology ; Male ; Phylogeny ; Rickettsia/*physiology ; *Symbiosis ; Tropism ; },
abstract = {Rickettsia is a genus of intracellular bacteria which can manipulate host reproduction and alter sensitivity to natural enemy attack in a diverse range of arthropods. The maintenance of Rickettsia endosymbionts in insect populations can be achieved through both vertical and horizontal transmission routes. For example, the presence of the symbiont in the follicle cells and salivary glands of Bemisia whiteflies allows Belli group Rickettsia transmission via the germ line and plants, respectively. However, the transmission routes of other Rickettsia bacteria, such as those in the Torix group of the genus, remain underexplored. Through fluorescence in situ hybridization (FISH) and transmission electron microscopy (TEM) screening, this study describes the pattern of Torix Rickettsia tissue tropisms in the highland midge, Culicoides impunctatus (Diptera: Ceratopogonidae). Of note is the high intensity of infection of the ovarian suspensory ligament, suggestive of a novel germ line targeting strategy. Additionally, localization of the symbiont in tissues of several developmental stages suggests transstadial transmission is a major route for ensuring maintenance of Rickettsia within C. impunctatus populations. Aside from providing insights into transmission strategies, the presence of Rickettsia bacteria in the fat body of larvae indicates potential host fitness and vector capacity impacts to be investigated in the future.IMPORTANCE Microbial symbionts of disease vectors have garnered recent attention due to their ability to alter vectorial capacity. Their consideration as a means of arbovirus control depends on symbiont vertical transmission, which leads to spread of the bacteria through a population. Previous work has identified a Rickettsia symbiont present in several species of biting midges (Culicoides spp.), which transmit bluetongue and Schmallenberg arboviruses. However, symbiont transmission strategies and host effects remain underexplored. In this study, we describe the presence of Rickettsia in the ovarian suspensory ligament of Culicoides impunctatus Infection of this organ suggests the connective tissue surrounding developing eggs is important for ensuring vertical transmission of the symbiont in midges and possibly other insects. Additionally, our results indicate Rickettsia localization in the fat body of Culicoides impunctatus As the arboviruses spread by midges often replicate in the fat body, this location implies possible symbiont-virus interactions to be further investigated.},
}
@article {pmid32801031,
year = {2020},
author = {Hodges, JK and Sasaki, GY and Bruno, RS},
title = {Anti-inflammatory activities of green tea catechins along the gut-liver axis in nonalcoholic fatty liver disease: lessons learned from preclinical and human studies.},
journal = {The Journal of nutritional biochemistry},
volume = {85},
number = {},
pages = {108478},
doi = {10.1016/j.jnutbio.2020.108478},
pmid = {32801031},
issn = {1873-4847},
mesh = {Animals ; Anti-Inflammatory Agents/pharmacology/*therapeutic use ; Catechin/pharmacology/*therapeutic use ; Gastrointestinal Microbiome/drug effects ; Humans ; Liver/drug effects/metabolism/pathology ; NF-kappa B/metabolism ; Non-alcoholic Fatty Liver Disease/*drug therapy/metabolism/pathology ; Plant Extracts/pharmacology/therapeutic use ; *Tea/chemistry ; Toll-Like Receptor 4/metabolism ; },
abstract = {Nonalcoholic fatty liver disease (NAFLD), which is the most prevalent hepatic disorder worldwide, affecting 25% of the general population, describes a spectrum of progressive liver conditions ranging from relatively benign liver steatosis and advancing to nonalcoholic steatohepatitis (NASH), fibrosis, and cirrhosis. Hallmark features of NASH are fatty hepatocytes and inflammatory cell infiltrates in association with increased activation of hepatic nuclear factor kappa-B (NFκB) that exacerbates liver injury. Because no pharmacological treatments exist for NAFLD, emphasis has been placed on dietary approaches to manage NASH risk. Anti-inflammatory bioactivities of catechin-rich green tea extract (GTE) have been well-studied, especially in preclinical models that have detailed its effects on inflammatory responses downstream of NFκB activation. This review will therefore discuss the experimental evidence that has advanced an understanding of the mechanisms by which GTE, either directly through its catechins or potentially indirectly through microbiota-derived metabolites, limits NFκB activation and NASH-associated liver injury. Specifically, it will describe the hepatic-level benefits of GTE that attenuate intracellular redox distress and pro-inflammatory signaling from extracellular receptors that otherwise activate NFκB. In addition, it will discuss the anti-inflammatory activities of GTE on gut barrier function as well as prebiotic and antimicrobial effects on gut microbial ecology that help to limit the translocation of gut-derived endotoxins (e.g. lipopolysaccharides) to the liver where they otherwise upregulate NFκB activation by Toll-like receptor-4 signaling. This summary is therefore expected to advance research translation of the hepatic- and intestinal-level benefits of GTE and its catechins to help manage NAFLD-associated morbidity.},
}
@article {pmid32800221,
year = {2020},
author = {Yadav, R and Rajput, V and Gohil, K and Khairnar, K and Dharne, M},
title = {Comprehensive metagenomic insights into a unique mass gathering and bathing event reveals transient influence on a riverine ecosystem.},
journal = {Ecotoxicology and environmental safety},
volume = {202},
number = {},
pages = {110938},
doi = {10.1016/j.ecoenv.2020.110938},
pmid = {32800221},
issn = {1090-2414},
mesh = {Drug Resistance, Microbial ; Ecosystem ; *Environmental Monitoring ; Humans ; India ; Metagenome ; Microbiota ; Rivers/*chemistry ; Water Pollution/*statistics &amp; numerical data ; Water Quality ; },
abstract = {The religious mass gathering and bathing can pose a multitude of significant public health challenges and lead to severe alterations in the river microbial ecology. The Pandharpur Wari is an annual pilgrimage of Maharashtra, India, where millions of devotees carry the footprints of the saint-poets and pay their obeisance to Lord Vitthal on the 11th day of moon's waxing phase (Ashadi Ekadashi). As a part of the ritual, the engrossed devotees, walk over 250 km, take a first holy dip in a sacred river Indrayani at Alandi and secondly in Bhima River at Pandharpur. The MinION-based shotgun metagenomic approach was employed to examine the impact of spiritual mass bathing on environmental changes (concerning the river microbial community structure and functions); and public health aspects (in terms of changes in the pathogenic potential and antibiotic resistance). The analysis of bathing and post-bathing samples of both the rivers revealed alterations in the alpha and beta diversity, indicating significant spatiotemporal variations in the overall microbial structure and function. Furthermore, the analysis revealed up to 80% of differences in the abundance of virulence genes between the bathing and post bathing samples. We observed parallel increase of priority skin and enteric pathogens (ranging from 11% to 80%) such as Acinetobacter baumannii, Staphylococcus aureus, Streptococcus pyogenes, Mycobacterium tuberculosis, and Pseudomonas aeruginosa during the bathing event. Moreover, we observed a significant increase in the antibiotic resistance in the bathing samples of Bhima and Indrayani rivers respectively. Altogether, this is the first comprehensive metagenomic study unravelling the influence of religious mass-bathing on the riverine ecosystem.},
}
@article {pmid32798895,
year = {2020},
author = {Rabaey, K and Vandekerckhove, T and de Walle, AV and Sedlak, DL},
title = {The third route: Using extreme decentralization to create resilient urban water systems.},
journal = {Water research},
volume = {185},
number = {},
pages = {116276},
doi = {10.1016/j.watres.2020.116276},
pmid = {32798895},
issn = {1879-2448},
mesh = {Humans ; Politics ; Public Health ; *Sanitation ; *Water ; Water Supply ; },
abstract = {For much of the world's urban population, centralized treatment plants and pipe networks built in the nineteenth and twentieth centuries provide homes with water and a means of disposing of the resulting wastewater. Due to the real or perceived inability of existing systems to deliver safe and palatable water, many users apply additional treatment prior to consumption. Where piped water supply is lacking, drinking water is obtained through water vendors at considerable cost. Despite economic inefficiencies and public health risks inherent in these two water supply systems, the high sunk costs of existing water infrastructure along with low returns on investment and the inflexible nature of the institutions involved in water provision have slowed down the diffusion of alternative approaches that may prove to be less expensive, more adaptable and safer than the current system. We advocate a third, complementary route: household-based personalized water systems. Initially, relatively affluent people expecting more functionality and sustainability from water systems will invest in personalized water systems that allow them to tailor their water to their personal preferences. This approach will tap into the tremendous creativity-base of individual users and entrepreneurs, facilitating the type of co-creation that accelerated the rapid development of consumer electronics. Competition among manufacturers and economies of scale that accrue as these systems become more popular will lead to rapid innovation that drives down costs, improves performance and expands access. These solutions complement emerging approaches for sanitation and resource recovery that do not rely upon sewers for the management of human waste.},
}
@article {pmid32795675,
year = {2020},
author = {Fernández-Murga, ML and Olivares, M and Sanz, Y},
title = {Bifidobacterium pseudocatenulatum CECT 7765 reverses the adverse effects of diet-induced obesity through the gut-bone axis.},
journal = {Bone},
volume = {141},
number = {},
pages = {115580},
doi = {10.1016/j.bone.2020.115580},
pmid = {32795675},
issn = {1873-2763},
mesh = {Animals ; *Bifidobacterium pseudocatenulatum ; Bone Density ; Diet, High-Fat/adverse effects ; Dietary Supplements ; Male ; Mice ; Mice, Inbred C57BL ; Obesity ; },
abstract = {Obesity and the associated chronic metabolic diseases (e.g., type-2 diabetes) adversely affect bone metabolism and health. Gut microbiota is considered to be involved in the pathophysiology of obesity and also represents a therapeutic target. This study has investigated the contribution of diet-induced obesity to alterations in bone health and metabolism and whether these could be restored by oral administration of Bifidobacterium pseudocatenulatum CECT 7765. To do so, adult male wild-type C57BL-6 mice were fed either a standard or high-fat diet (HFD), supplemented or not with B. pseudocatenulatum CECT 7765 (10[9] CFU/day) for 14 weeks. Effects on bone mass density (BMD), bone mineral content, bone remodeling, bone structure and gene expression were assessed. In HFD-fed mice, bone microstructural properties at the distal femur showed deteriorated trabecular architecture in bone volumetric fraction, trabecular number and trabecular pattern factor. Besides, the HFD reduced the volumetric bone mineral density in the trabecular bone, but not in the cortical bone. All these bone microstructural alterations found in obese mice were reversed by B. pseudocatenulatum CECT 7765. Administration of the bacterium increased (p < .05) the Wnt/β-catenin pathway gene expression, which could mediate effects on BMD. Bifidobacterium pseudocatenulatum CECT 7765 supplementation increased (p < .05) serum osteocalcin (OC, bone formation parameter), and decreased serum C-terminal telopeptide (CTX) (p < .01) and parathormone (PTH) (p < .05) (both bone resorption parameters). It also altered the microstructure of the femur. In summary, HFD interfered with the normal bone homeostasis leading to increased bone loss. In obese mice, B. pseudocatenulatum CECT 7765 lowered bone mass loss and enhanced BMD by decreasing bone resorption and increasing bone formation.},
}
@article {pmid32795263,
year = {2020},
author = {Puente-Sánchez, F and García-García, N and Tamames, J},
title = {SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o.},
journal = {BMC bioinformatics},
volume = {21},
number = {1},
pages = {358},
pmid = {32795263},
issn = {1471-2105},
support = {CTM2016-80095-C2-1-R//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; PID2019-110011RB-C31//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; IJC2018-035180-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; SEV-2013-0347-17-2//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
mesh = {Computational Biology/*methods ; Contig Mapping ; Databases, Factual ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Software ; },
abstract = {BACKGROUND: The dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. Nowadays even small research groups can easily obtain raw sequencing data. After that, however, non-specialists are faced with the double challenge of choosing among an ever-increasing array of analysis methodologies, and navigating the vast amounts of results returned by these approaches.<br><br>RESULTS: Here we present a workflow that relies on the SqueezeMeta software for the automated processing of raw reads into annotated contigs and reconstructed genomes (bins). A set of custom scripts seamlessly integrates the output into the anvi'o analysis platform, allowing filtering and visual exploration of the results. Furthermore, we provide a software package with utility functions to expose the SqueezeMeta results to the R analysis environment.<br><br>CONCLUSIONS: Altogether, our workflow allows non-expert users to go from raw sequencing reads to custom plots with only a few powerful, flexible and well-documented commands.},
}
@article {pmid32793165,
year = {2020},
author = {Guyet, U and Nguyen, NA and Doré, H and Haguait, J and Pittera, J and Conan, M and Ratin, M and Corre, E and Le Corguillé, G and Brillet-Guéguen, L and Hoebeke, M and Six, C and Steglich, C and Siegel, A and Eveillard, D and Partensky, F and Garczarek, L},
title = {Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1707},
pmid = {32793165},
issn = {1664-302X},
abstract = {Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.},
}
@article {pmid32793158,
year = {2020},
author = {Procopio, N and Ghignone, S and Voyron, S and Chiapello, M and Williams, A and Chamberlain, A and Mello, A and Buckley, M},
title = {Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1686},
pmid = {32793158},
issn = {1664-302X},
support = {MR/S032878/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Decomposition of animal bodies in the burial environment plays a key role in the biochemistry of the soil, altering the balance of the local microbial populations present before the introduction of the carcass. Despite the growing number of studies on decomposition and soil bacterial populations, less is known on its effects on fungal communities. Shifts in the fungal populations at different post-mortem intervals (PMIs) could provide insights for PMI estimation and clarify the role that specific fungal taxa have at specific decomposition stages. In this study, we buried pig carcasses over a period of 1- to 6-months, and we sampled the soil in contact with each carcass at different PMIs. We performed metabarcoding analysis of the mycobiome targeting both the internal transcribed spacer (ITS) 1 and 2, to elucidate which one was more suitable for this purpose. Our results showed a decrease in the fungal taxonomic richness associated with increasing PMIs, and the alteration of the soil fungal signature even after 6 months post-burial, showing the inability of soil communities to restore their original composition within this timeframe. The results highlighted taxonomic trends associated with specific PMIs, such as the increase of the Mortierellomycota after 4- and 6-months and of Ascomycota particularly after 2 months, and the decrease of Basidiomycota from the first to the last time point. We have found a limited number of taxa specifically associated with the carrion and not present in the control soil, showing that the major contributors to the recorded changes are originated from the soil and were not introduced by the carrion. As this is the first study conducted on burial graves, it sets the baseline for additional studies to investigate the role of fungal communities on prolonged decomposition periods and to identify fungal biomarkers to improve the accuracy of PMI prediction for forensic applications.},
}
@article {pmid32793152,
year = {2020},
author = {Lyu, Y and Su, C and Verbrugghe, A and Van de Wiele, T and Martos Martinez-Caja, A and Hesta, M},
title = {Past, Present, and Future of Gastrointestinal Microbiota Research in Cats.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1661},
pmid = {32793152},
issn = {1664-302X},
abstract = {The relationship between microbial community and host has profound effects on the health of animals. A balanced gastrointestinal (GI) microbial population provides nutritional and metabolic benefits to its host, regulates the immune system and various signaling molecules, protects the intestine from pathogen invasion, and promotes a healthy intestinal structure and an optimal intestinal function. With the fast development of next-generation sequencing, molecular techniques have become standard tools for microbiota research, having been used to demonstrate the complex intestinal ecosystem. Similarly to other mammals, the vast majority of GI microbiota in cats (over 99%) is composed of the predominant bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Many nutritional and clinical studies have shown that cats' microbiota can be affected by several different factors including body condition, age, diet, and inflammatory diseases. All these factors have different size effects, and some of these may be very minor, and it is currently unknown how important these are. Further research is needed to determine the functional variations in the microbiome in disease states and in response to environmental and/or dietary modulations. Additionally, further studies are also needed to explain the intricate relationship between GI microbiota and the genetics and immunity of its host. This review summarizes past and present knowledge of the feline GI microbiota and looks into the future possibilities and challenges of the field.},
}
@article {pmid32790601,
year = {2020},
author = {Lee, JC and Whang, KS},
title = {Agromyces humi sp. nov., actinobacterium isolated from farm soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {9},
pages = {5032-5039},
doi = {10.1099/ijsem.0.004376},
pmid = {32790601},
issn = {1466-5034},
mesh = {Actinobacteria/*classification/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Farms ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Spinacia oleracea ; Vitamin K 2/chemistry ; },
abstract = {A Gram-stain-positive actinobacterial strain, designated ANK073[T], was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073[T] were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20-40 °C (optimum, 30 °C), at pH 6.0-10.0 (optimum, pH 6.5-7.5) and at salinities of 0-4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073[T] belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5[T] (98.8 %), Agromyces tardus SJ-23[T] (98.5 %) and Agromyces iriomotensis IY07-20[T] (98.4 %). The phylogenetic analysis indicated that strain ANK073[T] formed a distinct phyletic line in the genus Agromyces and the results of DNA-DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073[T] could be separated from its closest relatives in the genus Agromyces. The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073[T] is considered to represent a novel species in the genus Agromyces, for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073[T] (=KACC 18683[T]=NBRC 111825[T]).},
}
@article {pmid32789440,
year = {2021},
author = {Kim, JW and Jeong, Y and Park, SJ and Jin, H and Lee, J and Ju, JH and Ji, GE and Park, SH},
title = {Influence of proton pump inhibitor or rebamipide use on gut microbiota of rheumatoid arthritis patients.},
journal = {Rheumatology (Oxford, England)},
volume = {60},
number = {2},
pages = {708-716},
doi = {10.1093/rheumatology/keaa316},
pmid = {32789440},
issn = {1462-0332},
mesh = {Alanine/*analogs &amp; derivatives/pharmacology ; Arthritis, Rheumatoid/complications/*drug therapy ; Bacteria/genetics/*isolation &amp; purification ; DNA, Bacterial/analysis ; Enzyme Inhibitors/pharmacology ; Female ; Gastrointestinal Diseases/etiology/microbiology/*prevention &amp; control ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Middle Aged ; Prognosis ; Proton Pump Inhibitors/*therapeutic use ; Quinolones/*pharmacology ; },
abstract = {OBJECTIVE: Patients with RA commonly use gastrointestinal (GI) protective drugs for treatment and prevention of drug-associated GI injuries. However, how these drugs affect the gut microbiota in RA patients remains unknown. The objective of this study was to examine the gut microbiota of RA patients according to use of GI protective drugs such as proton pump inhibitors (PPIs), histamine 2-receptor antagonists and rebamipide.<br><br>METHODS: Faecal samples were obtained from 15 healthy controls and 32 RA patients who were receiving PPI, histamine 2-receptor antagonist or rebamipide. Bacterial DNA was extracted from the faecal samples and 16S rRNA sequencing was performed. Microbial composition and function were analysed using Quantitative Insights Into Microbial Ecology and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.<br><br>RESULTS: RA patients exhibited reduced diversity and altered composition of the gut microbiota compared with healthy controls. The gut microbiota of RA patients receiving acid-suppressing drugs, particularly PPIs, was distinct from that of RA patients receiving rebamipide (PPI vs rebamipide, P&#x2009;=&#x2009;0.005). Streptococcus was enriched in RA patients receiving PPI, while Clostridium bolteae was enriched in RA patients receiving rebamipide. The gut microbiota of PPI users was abundant with microbial functional pathway involved in the production of virulence factors. This featured microbial function was positively correlated with relative abundance of Streptococcus, the differentially abundant taxa of PPI users.<br><br>CONCLUSION: The gut microbiota of RA patients receiving PPIs was distinguishable from that of those receiving rebamipide. The enriched virulent function in the gut microbiota of PPI users suggests that inappropriate PPI use may be harmful in RA patients.},
}
@article {pmid32785735,
year = {2021},
author = {Balan, B and Dhaulaniya, AS and Varma, DA and Sodhi, KK and Kumar, M and Tiwari, M and Singh, DK},
title = {Microbial biofilm ecology, in silico study of quorum sensing receptor-ligand interactions and biofilm mediated bioremediation.},
journal = {Archives of microbiology},
volume = {203},
number = {1},
pages = {13-30},
pmid = {32785735},
issn = {1432-072X},
mesh = {Bacteria/*metabolism ; Bacterial Proteins/*metabolism ; *Biodegradation, Environmental ; *Biofilms ; Computer Simulation ; *Ligands ; Quorum Sensing/*physiology ; },
abstract = {Biofilms are structured microbial communities of single or multiple populations in which microbial cells adhere to a surface and get embedded in extracellular polymeric substances (EPS). This review attempts to explain biofilm architecture, development phases, and forces that drive bacteria to promote biofilm mode of growth. Bacterial chemical communication, also known as Quorum sensing (QS), which involves the production, detection, and response to small molecules called autoinducers, is highlighted. The review also provides a brief outline of interspecies and intraspecies cell-cell communication. Additionally, we have performed docking studies using Discovery Studio 4.0, which has enabled our understanding of the prominent interactions between autoinducers and their receptors in different bacterial species while also scoring their interaction energies. Receptors, such as LuxN (Phosphoreceiver domain and RecA domain), LuxP, and LuxR, interacted with their ligands (AI-1, AI-2, and AHL) with a CDocker interaction energy of - 31.6083 kcal/mole; - 34.5821 kcal/mole, - 48.2226 kcal/mole and - 41.5885 kcal/mole, respectively. Since biofilms are ideal for the remediation of contaminants due to their high microbial biomass and their potential to immobilize pollutants, this article also provides an overview of biofilm-mediated bioremediation.},
}
@article {pmid32785584,
year = {2020},
author = {Nardi, P and Laanbroek, HJ and Nicol, GW and Renella, G and Cardinale, M and Pietramellara, G and Weckwerth, W and Trinchera, A and Ghatak, A and Nannipieri, P},
title = {Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications.},
journal = {FEMS microbiology reviews},
volume = {44},
number = {6},
pages = {874-908},
doi = {10.1093/femsre/fuaa037},
pmid = {32785584},
issn = {1574-6976},
mesh = {Bacteria/*metabolism ; Host Microbial Interactions/*physiology ; Nitrification/*physiology ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.},
}
@article {pmid32784779,
year = {2020},
author = {Kumar, H and Jang, YN and Kim, K and Park, J and Jung, MW and Park, JE},
title = {Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach.},
journal = {Animals : an open access journal from MDPI},
volume = {10},
number = {8},
pages = {},
pmid = {32784779},
issn = {2076-2615},
support = {PJ01252102//Rural Development Administration/ ; },
abstract = {Traditionally slurry is used as source of nitrogen, phosphorous, and potassium in bio fertilizers to improve crop production. However, poorly managed slurry causes a hazardous effect to the environment by producing greenhouse gases, causing the eutrophication of water bodies, and polluting the groundwater. It has been largely reported that the microbial presence in slurry causing a diverse effect on its storage and disposal system. However, the diversity of bacterial populations in pig slurries remains largely unexplored. Here we report the bacterial diversity present in the slurry from slurry pits, and the effect of storage time on bacterial population. We collected 42 samples from three different pig slurry pits, as three replicates from each one until the 14th week. We used the 16S rRNA, Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) protocols for the metagenomic downstream analysis. Taxonomic annotation using the Greengenes metagenomic database indicated that on an average 76.2% Firmicutes, 14.4% Bacteroidetes, 4.9% Proteobacteria, etc. microbial populations were present. Comparative microbial analysis showed that the population of Firmicutes decreased from the first to the 14th week, whereas the population of Bacteroidetes increased from the first to the 14th week. Through principal coordinate analysis (PCoA), (linear discriminant analysis effect size (LEfSe), and Pearson's correlation analysis, we found microbial biomarkers according to the storage time point. All bacterial populations were well clustered according to the early, middle, and last weeks of storage. LEfSe showed that Actinobacteria, Lachnospiraceae, Ruminococcaceae, and Bacteroidia are dominantly present in first, seventh, ninth, and 14th week, respectively. Lachnospiraceae and Ruminococcaceae are ubiquitous gastrointestinal non-pathogenic bacteria. KEGG pathways, such as membrane transport, carbohydrate and amino acid metabolism, genetic replication and repair, were significant among all samples. Such a KEGG pathway may indicate the association between the host organism's metabolic activity and the microbes present in the gastro intestinal tract (GIT).},
}
@article {pmid32783779,
year = {2021},
author = {Belibasakis, GN and Manoil, D},
title = {Microbial Community-Driven Etiopathogenesis of Peri-Implantitis.},
journal = {Journal of dental research},
volume = {100},
number = {1},
pages = {21-28},
pmid = {32783779},
issn = {1544-0591},
mesh = {*Dental Implants ; Humans ; *Microbiota ; *Peri-Implantitis/etiology ; *Periodontitis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Osseointegrated dental implants are a revolutionary tool in the armament of reconstructive dentistry, employed to replace missing teeth and restore masticatory, occlusal, and esthetic functions. Like natural teeth, the orally exposed part of dental implants offers a pristine nonshedding surface for salivary pellicle-mediated microbial adhesion and biofilm formation. In early colonization stages, these bacterial communities closely resemble those of healthy periodontal sites, with lower diversity. Because the peri-implant tissues are more susceptible to endogenous oral infections, understanding of the ecological triggers that underpin the microbial pathogenesis of peri-implantitis is central to developing improved prevention, diagnosis, and therapeutic strategies. The advent of next-generation sequencing (NGS) technologies, notably applied to 16S ribosomal RNA gene amplicons, has enabled the comprehensive taxonomic characterization of peri-implant bacterial communities in health and disease, revealing a differentially abundant microbiota between these 2 states, or with periodontitis. With that, the peri-implant niche is highlighted as a distinct ecosystem that shapes its individual resident microbial community. Shifts from health to disease include an increase in diversity and a gradual depletion of commensals, along with an enrichment of classical and emerging periodontal pathogens. Metatranscriptomic profiling revealed similarities in the virulence characteristics of microbial communities from peri-implantitis and periodontitis, nonetheless with some distinctive pathways and interbacterial networks. Deeper functional assessment of the physiology and virulence of the well-characterized microbial communities of the peri-implant niche will elucidate further the etiopathogenic mechanisms and drivers of the disease.},
}
@article {pmid32780919,
year = {2020},
author = {Robles-Vera, I and de la Visitación, N and Toral, M and Sánchez, M and Romero, M and Gómez-Guzmán, M and Yang, T and Izquierdo-García, JL and Guerra-Hernández, E and Ruiz-Cabello, J and Raizada, MK and Pérez-Vizcaíno, F and Jiménez, R and Duarte, J},
title = {Probiotic Bifidobacterium breve prevents DOCA-salt hypertension.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {34},
number = {10},
pages = {13626-13640},
doi = {10.1096/fj.202001532R},
pmid = {32780919},
issn = {1530-6860},
support = {HL102033//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
mesh = {Animals ; *Bifidobacterium breve ; *Blood Pressure ; Desoxycorticosterone Acetate ; *Gastrointestinal Microbiome ; Hypertension/chemically induced/*therapy ; Male ; Probiotics/*therapeutic use ; Rats ; Rats, Wistar ; *Vasodilation ; },
abstract = {Many probiotics that affect gut microbial ecology have been shown to produce beneficial effects on renin-angiotensin-dependent rodent models and human hypertension. We hypothesized that Bifidobacterium breve CECT7263 (BFM) would attenuate hypertension in deoxycorticosterone acetate (DOCA)-salt rats, a renin-independent model of hypertension. Rats were randomly divided into five groups: control, DOCA-salt, treated DOCA-salt-BFM, treated DOCA-salt-butyrate, and treated DOCA-salt-acetate, for 5 weeks. BFM prevented the increase in systolic blood pressure, cardiac weight, and renal damage induced by DOCA-salt. BFM increased acetate-producing bacterial population and gut acetate levels, improved colonic integrity, normalized endotoxemia, plasma trimethylamine (TMA) levels, and restored the Th17 and Treg content in mesenteric lymph nodes and aorta. Furthermore, BFM improved nitric oxide-dependent vasorelaxation induced by acetylcholine in aortic rings and reduced NADPH oxidase activity in DOCA-salt animals. These protective effects were mimicked by acetate, but not by butyrate supplementation. These data demonstrate that BFM induces changes in gut microbiota linked with attenuation of endothelial dysfunction and increase in blood pressure in this low-renin form of hypertension. These beneficial effects seem to be mediated by increased acetate and reduced TMA production by gut microbiota, thus, improving gut integrity and restoring Th17/Tregs polarization and endotoxemia.},
}
@article {pmid32780840,
year = {2020},
author = {Looby, CI and Martin, PH},
title = {Diversity and function of soil microbes on montane gradients: the state of knowledge in a changing world.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {9},
pages = {},
doi = {10.1093/femsec/fiaa122},
pmid = {32780840},
issn = {1574-6941},
mesh = {Archaea/genetics ; Biodiversity ; Fungi/genetics ; *Soil ; *Soil Microbiology ; },
abstract = {Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here, we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike flora and fauna that often display a mid-elevation peak in diversity, we found a decline (34% of the time) or no trend (33%) in total microbial diversity with increasing elevation. Diversity of functional groups also varied with elevation (e.g. saprotrophic fungi declined 83% of the time). Most studies (82%) found that climate and soils (especially pH) were the primary mechanisms driving shifts in composition, and drivers differed across taxa-fungi were mostly determined by climate, while bacteria (48%) and archaea (71%) were structured primarily by soils. We hypothesize that the central role of soils-which can vary independently of other abiotic and geographic gradients-in structuring microbial communities weakens diversity patterns expected on montane gradients. Moving forward, we need improved cross-study comparability of microbial diversity indices (i.e. standardizing sequencing) and more geographic replication using experiments to broaden our knowledge of microbial biogeography on global gradients.},
}
@article {pmid32778917,
year = {2020},
author = {Gamez, RM and Ramirez, S and Montes, M and Cardinale, M},
title = {Complementary Dynamics of Banana Root Colonization by the Plant Growth-Promoting Rhizobacteria Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006 at Spatial and Temporal Scales.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {656-668},
pmid = {32778917},
issn = {1432-184X},
support = {Public resources from Ministerio de Agricultura y Desarrollo Rural [Ministry of Agriculture and Rural Development] (MADR)//Corporaci&#xf3;n Colombiana de Investigaci&#xf3;n Agropecuaria - Agrosavia/ ; },
mesh = {Bacillus amyloliquefaciens/*physiology ; Colombia ; Musa/*microbiology ; Plant Roots/*microbiology ; Pseudomonas/*physiology ; Rhizosphere ; Spatio-Temporal Analysis ; },
abstract = {Banana (Musa acuminata) growth for commercial purposes requires high amounts of chemical fertilizers, generating high costs and deleterious effects on the environment. In a previous study, we demonstrated that two plant growth-promoting rhizobacteria (PGPR), Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006, isolated in Colombia, could partially replace chemical fertilizers for banana seedling growth. In a second work, the effects of the two inoculants on banana transcripts were found to occur at different times, earlier for Bs006 and later for Ps006. This leads to the hypothesis that the two rhizobacteria have different colonization dynamics. Accordingly, the aim of this work was to analyze the dynamics of root colonization of the two PGPR, Bs006 and Ps006, on banana growth over a time frame of 30 days. We used fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM), followed by three-dimensional reconstruction and quantitative image analysis. Bacillus amyloliquefaciens Bs006 abundantly colonized banana roots earlier (from 1 to 48 h), ectophytically on the rhizoplane, and then decreased. Pseudomonas palleroniana Ps006 was initially scarce, but after 96 h it increased dramatically and became clearly endophytic. Here we identify and discuss the potential genetic factors responsible for this complementary behavior. This information is crucial for optimizing the formulation of an effective biofertilizer for banana and its inoculation strategy.},
}
@article {pmid32771820,
year = {2020},
author = {Elhalis, H and Cox, J and Frank, D and Zhao, J},
title = {The crucial role of yeasts in the wet fermentation of coffee beans and quality.},
journal = {International journal of food microbiology},
volume = {333},
number = {},
pages = {108796},
doi = {10.1016/j.ijfoodmicro.2020.108796},
pmid = {32771820},
issn = {1879-3460},
mesh = {Acetaldehyde/metabolism ; Acetates/metabolism ; Acetic Acid/metabolism ; Anti-Infective Agents/pharmacology ; Bacteria/classification/*metabolism ; Bioreactors/microbiology ; Coffee/*metabolism/microbiology ; Ethanol/metabolism ; Fermentation/*physiology ; Hanseniaspora/*metabolism ; Lactic Acid/metabolism ; Natamycin/pharmacology ; Odorants/analysis ; Pentanols/metabolism ; Pichia/*metabolism ; Taste ; Yeasts/*metabolism ; },
abstract = {The objective of this study was to investigate the role of yeasts in the wet fermentation of coffee beans and their contribution to coffee quality using a novel approach. Natamycin (300 ppm) was added to the fermentation mass to suppress yeast growth and their metabolic activities, and the resultant microbial ecology, bean chemistry and sensory quality were analyzed and compared to non-treated spontaneous fermentation we reported previously. The yeast community was dominated by Hanseniaspora uvarum and Pichia kudriavzevii and grew to a maximum population of about 5.5 log CFU/g in the absence of Natamycin, while when Natamycin was added yeasts were suppressed. The major bacterial species in both the spontaneous and yeast-suppressed fermentations included the lactic acid bacteria Leuconostoc mesenteroides and Lactococcus lactis, the acetic acid bacteria Gluconobacter cerinus and Acetobacter persici and the Enterobacteriaceae Enterobacter, Citrobacter and Erwinia. For both fermentations, the mucilage layers were completely degraded by the end of the process and the absence of yeast activities had no significant impact on mucilage degradation. During fermentation, reducing sugars were consumed while lactic acid was accumulated inside the beans, and its concentration was significantly higher in the spontaneous fermentation (3 times) than that where yeasts were suppressed by Natamycin. Glycerol was detected with a concentration of 0.08% in the absence of Natamycin and was not identified when Natamycin was added. Green beans fermented with yeast growth contained a higher amount of isoamyl alcohol (21 times), ethanol (3.7 times), acetaldehyde (8 times), and ethyl acetate (25 times) compared to beans fermented in the absence of yeast activities, which remained higher in the former after roasting. Beans fermented without yeast activities had a mild fruity aroma, and lower sensory scores of fragrances (7.0), flavor (6.5), acidity (6.3), body (7.0) and overall score (6.5) compared to the former. These findings demonstrated the crucial roles of yeasts in wet fermentation of coffee beans and for producing high quality coffee.},
}
@article {pmid32770272,
year = {2021},
author = {Thongprem, P and Davison, HR and Thompson, DJ and Lorenzo-Carballa, MO and Hurst, GDD},
title = {Incidence and Diversity of Torix Rickettsia-Odonata Symbioses.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {203-212},
pmid = {32770272},
issn = {1432-184X},
support = {CGL2008-02799//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Infectious Disease Transmission, Vertical ; Odonata/*microbiology ; Ovary/microbiology ; Rickettsia/classification/genetics/*physiology ; Rickettsia Infections/*transmission ; Symbiosis/*physiology ; },
abstract = {Heritable microbes are an important component of invertebrate biology, acting both as beneficial symbionts and reproductive parasites. Whilst most previous research has focussed on the 'Wolbachia pandemic', recent work has emphasised the importance of other microbial symbionts. In this study, we present a survey of odonates (dragonflies and damselflies) for torix group Rickettsia, following previous research indicating that this clade can be common in other aquatic insect groups. PCR assays were used to screen a broad range of odonates from two continents and revealed 8 of 76 species tested were infected with Rickettsia. We then conducted further deeper screening of UK representatives of the Coenagrionidae damselfly family, revealing 6 of 8 UK coenagrionid species to be positive for torix Rickettsia. Analysis of Rickettsia gene sequences supported multiple establishments of symbiosis in the group. Some strains were shared between UK coenagrionid species that shared mtDNA barcodes, indicating a likely route for mitochondrial introgression between sister species. There was also evidence of coinfecting Rickettsia strains in two species. FISH analysis indicated Rickettsia were observed in the ovarioles, consistent with heritable symbiosis. We conclude that torix Rickettsia represent an important associate of odonates, being found in a broad range of species from both Europe and South America. There is evidence that coinfection can occur, vertical transmission is likely, and that symbiont movement following hybridisation may underpin the lack of 'barcoding gap' between well-established species pairs in the genus. Future work should establish the biological significance of the symbioses observed.},
}
@article {pmid32770154,
year = {2020},
author = {Cichocki, N and Hübschmann, T and Schattenberg, F and Kerckhof, FM and Overmann, J and Müller, S},
title = {Bacterial mock communities as standards for reproducible cytometric microbiome analysis.},
journal = {Nature protocols},
volume = {15},
number = {9},
pages = {2788-2812},
pmid = {32770154},
issn = {1750-2799},
mesh = {Bacteria/*cytology ; Computational Biology ; Cytological Techniques/*standards ; *Microbiota ; Reference Standards ; Reproducibility of Results ; },
abstract = {Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.},
}
@article {pmid32770005,
year = {2020},
author = {Yang, S and Lv, Y and Liu, X and Wang, Y and Fan, Q and Yang, Z and Boon, N and Wang, F and Xiao, X and Zhang, Y},
title = {Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {3941},
pmid = {32770005},
issn = {2041-1723},
mesh = {Acetates/*metabolism ; Anaerobiosis ; Archaea/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Carbon Cycle/physiology ; Coenzyme A Ligases/genetics/*metabolism ; Genome, Archaeal ; Geologic Sediments/microbiology ; Metabolic Networks and Pathways/genetics ; Methane/*metabolism ; Oxidation-Reduction ; Seawater/microbiology ; },
abstract = {Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.},
}
@article {pmid32767092,
year = {2020},
author = {Greer, JA and Swei, A and Vredenburg, VT and Zink, AG},
title = {Parental Care Alters the Egg Microbiome of Maritime Earwigs.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {920-934},
doi = {10.1007/s00248-020-01558-x},
pmid = {32767092},
issn = {1432-184X},
support = {IOS-1258133//National Science Foundation/ ; DBI-1427772//National Science Foundation/ ; DEB-1745411//National Science Foundation/ ; DEB-175037//National Science Foundation/ ; R25-GM059298//Foundation for the National Institutes of Health/ ; },
mesh = {Animals ; Female ; Insecta/microbiology/*physiology ; Maternal Behavior ; *Microbiota ; Ovum/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; },
abstract = {Recruitment of beneficial microbes to protect offspring, often reducing the energetic costs of care, is now recognized as an important component of parental care in many animals. Studies on earwigs (order Dermaptera) have revealed that removal of females from egg tending increases mortality of eggs due to fungal infections, possibly caused by changes in the bacterial microbiome on the egg surface. We used a controlled female-removal experiment to evaluate whether female nest attendance in the maritime earwig, Anisolabis maritima, influences the bacterial microbiome on the egg surface. Further, we analyzed the microbiomes of mothers and their eggs to determine if there are a core set of bacteria transferred to eggs through female care. Microbiomes were analyzed using 16S rRNA bacterial DNA sequencing, revealing that bacterial operational taxonomic unit (OTU) richness and diversity were both significantly higher for female attended versus unattended eggs. The core microbiome of adult females contained bacteria which have the potential to carry anti-fungal characteristics; these bacteria were found in higher presence and relative abundance on eggs where females were allowed to provide care. These results demonstrate that female egg attendance significantly impacts the bacterial microbiome of A. maritima eggs, and identifies specific bacteria within the egg microbiome that should be investigated further for beneficial anti-fungal properties in this system.},
}
@article {pmid32767091,
year = {2021},
author = {Vargas, S and Leiva, L and Wörheide, G},
title = {Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {213-222},
pmid = {32767091},
issn = {1432-184X},
mesh = {Animals ; Bacteroidetes/*classification/genetics/isolation &amp; purification ; Biodiversity ; Climate ; Climate Change ; Cyanobacteria/*classification/genetics/isolation &amp; purification ; Hot Temperature ; Microbiota/*genetics ; Planctomycetales/*classification/genetics/isolation &amp; purification ; Porifera/*microbiology ; Proteobacteria/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Thermotolerance/genetics ; },
abstract = {Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.},
}
@article {pmid32765428,
year = {2020},
author = {Zhang, H and Sekar, R and Visser, PM},
title = {Editorial: Microbial Ecology in Reservoirs and Lakes.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1348},
pmid = {32765428},
issn = {1664-302X},
}
@article {pmid32763579,
year = {2021},
author = {Gong, L and Wang, J and Abbas, T and Zhang, Q and Cai, M and Tahir, M and Wu, D and Di, H},
title = {Immobilization of exchangeable Cd in soil using mixed amendment and its effect on soil microbial communities under paddy upland rotation system.},
journal = {Chemosphere},
volume = {262},
number = {},
pages = {127828},
doi = {10.1016/j.chemosphere.2020.127828},
pmid = {32763579},
issn = {1879-1298},
mesh = {Agriculture/methods ; Cadmium/analysis/*chemistry/toxicity ; Calcium Compounds ; Charcoal ; Crops, Agricultural ; Environmental Pollution ; Environmental Restoration and Remediation/methods ; Fertilizers ; Humans ; Microbiota/*drug effects/physiology ; Oryza/drug effects ; Oxides ; Phosphates ; Rotation ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*chemistry/toxicity ; Triticum ; },
abstract = {Cadmium (Cd) pollution is a widespread environmental problem that decreases crop production, destroys the microbial ecology of soil, and poses a severe risk to human health. Organo-chemical amendment is a cost-effective, eco-friendly, and community-acceptable widely applied an in situ technique for metal-contaminated farmland. In this study, we mixed lime, zeolite, calcium magnesium phosphate fertilizer, and biochar in a mixture ratio of 71:23:5:1 to form a mixed amendment. Field and laboratory experiments were conducted to study the effects of the mixed amendment on soil exchangeable Cd content, plant Cd accumulation, and soil microbial community. It was found that the application of 0.5% mixed amendment decreased exchangeable soil Cd by more than 85% and 64% in wheat and rice season, respectively, compared with control (CK), without increasing pH. Moreover, the application of 0.5% mixed amendment decreased Cd accumulation in grains by 22.9% and 41.2% in wheat and rice season, respectively, compared to CK. The result of phospholipid fatty acids (PLFAs) shows that the level of soil microbial diversity and species richness under mixed amendment treatments were higher than in lime treatment, indicating more copiotrophic conditions and faster rate of nutrient turnover in mixed amendment than pure lime treatment. Hence, it concluded that the mixed amendment has a strong effect on fixing exchangeable soil Cd and reducing the accumulation of Cd in crops. Finally, it was observed that the mixed amendment improved the soil microbial community structure and accelerate the rate of nutrient turnover by microbes under this favorable condition comparative to individual treatments.},
}
@article {pmid32761502,
year = {2021},
author = {Herrmann, M and Geesink, P and Richter, R and Küsel, K},
title = {Canopy Position Has a Stronger Effect than Tree Species Identity on Phyllosphere Bacterial Diversity in a Floodplain Hardwood Forest.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {157-168},
pmid = {32761502},
issn = {1432-184X},
support = {FZT 118//Deutsche Forschungsgemeinschaft/ ; CRC1076 AquaDiva//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Acer/*microbiology ; Actinobacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Forests ; Germany ; High-Throughput Nucleotide Sequencing ; Microbiota/physiology ; Plant Leaves/*microbiology ; Quercus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Tilia/*microbiology ; Trees/microbiology ; },
abstract = {The phyllosphere is a challenging microbial habitat in which microorganisms can flourish on organic carbon released by plant leaves but are also exposed to harsh environmental conditions. Here, we assessed the relative importance of canopy position-top, mid, and bottom at a height between 31 and 20 m-and tree species identity for shaping the phyllosphere microbiome in a floodplain hardwood forest. Leaf material was sampled from three tree species-maple (Acer pseudoplatanus L.), oak (Quercus robur L.), and linden (Tilia cordata MILL.)-at the Leipzig canopy crane facility (Germany). Estimated bacterial species richness (Chao1) and bacterial abundances approximated by quantitative PCR of 16S rRNA genes exhibited clear vertical trends with a strong increase from the top to the mid and bottom position of the canopy. Thirty operational taxonomic units (OTUs) formed the core microbiome, which accounted for 77% of all sequence reads. These core OTUs showed contrasting trends in their vertical distribution within the canopy, pointing to different ecological preferences and tolerance to presumably more extreme conditions at the top position of the canopy. Co-occurrence analysis revealed distinct tree species-specific OTU networks, and 55-57% of the OTUs were unique to each tree species. Overall, the phyllosphere microbiome harbored surprisingly high fractions of Actinobacteria of up to 66%. Our results clearly demonstrate strong effects of the position in the canopy on phyllosphere bacterial communities in a floodplain hardwood forest and-in contrast to other temperate or tropical forests-a strong predominance of Actinobacteria.},
}
@article {pmid32761501,
year = {2021},
author = {Dos Passos, JH and Maia, LC and de Assis, DMA and da Silva, JA and Oehl, F and da Silva, IR},
title = {Arbuscular Mycorrhizal Fungal Community Structure in the Rhizosphere of Three Plant Species of Crystalline and Sedimentary Areas in the Brazilian Dry Forest.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {104-121},
pmid = {32761501},
issn = {1432-184X},
support = {420.129/2018-9; 307.129/2015-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 100.900/2018-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; Financie Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; IBPG-0010-2.03/18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; APV-0014-2.03/19//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; },
mesh = {Biodiversity ; Forests ; *Mycobiome ; *Mycorrhizae ; Plant Roots ; Rhizosphere ; Soil Microbiology ; },
abstract = {The Brazilian dry forest (Caatinga) is located in one of the world's largest tropical semiarid regions, and it occurs on two large geological environments named the crystalline and sedimentary basins. In order to determine the structure and the main drivers of the composition of communities of arbuscular mycorrhizal fungi (AMF) in the Caatinga, we collected soil samples from the rhizosphere of Jatropha mollissima, J. mutabilis, and Mimosa tenuiflora, species that occur in crystalline and sedimentary areas. Ninety-six AMF taxa were identified from soils collected directly in the field and trap cultures. Acaulospora, Glomus, and Rhizoglomus represented almost 49% of the taxon richness. The composition of the AMF communities differed between the crystalline and sedimentary areas and between the rhizospheres of the three plant species. Coarse sand, total sand, natural clay, calcium, soil particles density, flocculation, pH, and base saturation were the principal edaphic variables related to the distribution of these organisms. We registered nine and 17 AMF species classified as indicators, for the geological environments and plant species, respectively. Glomerospores of Glomerales predominated in crystalline basins, whereas glomerospores of Gigasporales prevailed in sedimentary areas; among the plant species, lower number of glomerospores of Archaeosporales and Glomerales was recorded in the rhizosphere of J. mollissima. The results show that the AMF community composition is shaped by geological environments and plant hosts. In addition, soil characteristics, mainly physical attributes, significantly influence the structure of Glomeromycota communities occurring in areas of the Brazilian semiarid.},
}
@article {pmid32760678,
year = {2020},
author = {Celis Ramírez, AM and Amézquita, A and Cardona Jaramillo, JEC and Matiz-Cerón, LF and Andrade-Martínez, JS and Triana, S and Mantilla, MJ and Restrepo, S and Barrios, AFG and de Cock, H},
title = {Analysis of Malassezia Lipidome Disclosed Differences Among the Species and Reveals Presence of Unusual Yeast Lipids.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {338},
pmid = {32760678},
issn = {2235-2988},
mesh = {Animals ; Humans ; Lipidomics ; Lipids ; *Malassezia/genetics ; Saccharomyces cerevisiae ; },
abstract = {Malassezia yeasts are lipid dependent and part of the human and animal skin microbiome. However, they are also associated with a variety of dermatological conditions and even cause systemic infections. How these yeasts can live as commensals on the skin and switch to a pathogenic stage has long been a matter of debate. Lipids are important cellular molecules, and understanding the lipid metabolism and composition of Malassezia species is crucial to comprehending their biology and host-microbe interaction. Here, we investigated the lipid composition of Malassezia strains grown to the stationary phase in a complex Dixon medium broth. In this study, we perform a lipidomic analysis of a subset of species; in addition, we conducted a gene prediction analysis for the detection of lipid metabolic proteins. We identified 18 lipid classes and 428 lipidic compounds. The most commonly found lipids were triglycerides (TAG), sterol (CH), diglycerides (DG), fatty acids (FAs), phosphatidylcholine (PC), phosphatidylethanolamine (PE), ceramides, cholesteryl ester (CE), sphingomyelin (SM), acylcarnitine, and lysophospholipids. Particularly, we found a low content of CEs in Malassezia furfur, atypical M. furfur, and Malassezia pachydermatis and undetectable traces of these components in Malassezia globosa, Malassezia restricta, and Malassezia sympodialis. Remarkably, uncommon lipids in yeast, like diacylglyceryltrimethylhomoserine and FA esters of hydroxyl FAs, were found in a variable concentration in these Malassezia species. The latter are bioactive lipids recently reported to have antidiabetic and anti-inflammatory properties. The results obtained can be used to discriminate different Malassezia species and offer a new overview of the lipid composition of these yeasts. We could confirm the presence and the absence of certain lipid-biosynthesis genes in specific species. Further analyses are necessary to continue disclosing the complex lipidome of Malassezia species and the impact of the lipid metabolism in connection with the host interaction.},
}
@article {pmid32760379,
year = {2020},
author = {Podar, PT and Yang, Z and Björnsdóttir, SH and Podar, M},
title = {Comparative Analysis of Microbial Diversity Across Temperature Gradients in Hot Springs From Yellowstone and Iceland.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1625},
pmid = {32760379},
issn = {1664-302X},
abstract = {Geothermal hot springs are a natural setting to study microbial adaptation to a wide range of temperatures reaching up to boiling. Temperature gradients lead to distinct microbial communities that inhabit their optimum niches. We sampled three alkaline, high temperature (80-100°C) hot springs in Yellowstone and Iceland that had cooling outflows and whose microbial communities had not been studied previously. The microbial composition in sediments and mats was determined by DNA sequencing of rRNA gene amplicons. Over three dozen phyla of Archaea and Bacteria were identified, representing over 1700 distinct organisms. We observed a significant non-linear reduction in the number of microbial taxa as the temperature increased from warm (38°C) to boiling. At high taxonomic levels, the community structure was similar between the Yellowstone and Iceland hot springs. We identified potential endemism at the genus level, especially in thermophilic phototrophs, which may have been potentially driven by distinct environmental conditions and dispersal limitations.},
}
@article {pmid32757814,
year = {2020},
author = {Zhu, Y and Guo, J},
title = {Impact of dichlorprop on soil microbial community structure and diversity during its enantioselective biodegradation in agricultural soils.},
journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes},
volume = {55},
number = {11},
pages = {974-982},
doi = {10.1080/03601234.2020.1802186},
pmid = {32757814},
issn = {1532-4109},
mesh = {2,4-Dichlorophenoxyacetic Acid/*analogs &amp; derivatives/analysis/chemistry/pharmacokinetics/pharmacology ; Agriculture ; Bacteria/drug effects/genetics/metabolism ; Biodegradation, Environmental ; Kinetics ; Michigan ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/chemistry/pharmacokinetics/*pharmacology ; Stereoisomerism ; },
abstract = {Enantioselective biodegradation of racemic dichlorprop in two soils was investigated in the laboratory. Chiral separation of racemic dichlorprop was achieved by using HPLC with Phenomenex Lux Amylose-2. The first-order kinetic model fitted well the dissipation data of racemic dichlorprop and its pure R- and S-enantiomers. S-dichlorprop was preferentially degraded in both soils and enantioselectivity was affected by soil pH. The half-lives (DT50) of S-dichlorprop were 8.22 days in soil A and 8.06 days in soil D, while R-dichlorprop was more persistent with DT50 of 12.93 days in soil A and 12.38 days in soil D, respectively. Dichlorprop dissipated faster in soil D with lower organic matter content. In sterilized soils, neglected dissipation was observed and enantiomer fraction values remained constant, indicating that the enantioselective degradation was mainly controlled by soil microorganisms. Soil microbial community structure and diversity was assessed by Illumina MiSeq sequencing of 16S rRNA genes from dichlorprop and no dichlorprop contaminated microcosms. Compared with controls, dichlorprop application had no significant effect on microbial community structures at phylum level, but increased bacterial diversity and dichlorprop degradation related taxa in both soils. S-dichlorprop preferential degradation might be attributed to the S-enantiomer preferred degraders in the family of Sphingomonadaceae.},
}
@article {pmid32757488,
year = {2021},
author = {Xu, Y and Tandon, R and Ancheta, C and Arroyo, P and Gilbert, JA and Stephens, B and Kelley, ST},
title = {Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions.},
journal = {Indoor air},
volume = {31},
number = {1},
pages = {188-205},
doi = {10.1111/ina.12727},
pmid = {32757488},
issn = {1600-0668},
support = {F32 GM020013/GM/NIGMS NIH HHS/United States ; },
mesh = {Air Pollution, Indoor ; Bacteria ; *Built Environment ; Construction Materials ; *Environmental Microbiology ; Fungi ; Humans ; Humidity ; Microbial Interactions ; Microbiota ; Mycobiome ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Indoor microbial communities vary in composition and diversity depending on material type, moisture levels, and occupancy. In this study, we integrated bacterial cell counting, fungal biomass estimation, and fluorescence-assisted cell sorting (FACS) with amplicon sequencing of bacterial (16S rRNA) and fungal (ITS) communities to investigate the influence of wetting on medium density fiberboard (MDF) and gypsum wallboard. Surface samples were collected longitudinally from wetted materials maintained at high relative humidity (~95%). Bacterial and fungal growth patterns were strongly time-dependent and material-specific. Fungal growth phenotypes differed between materials: spores dominated MDF surfaces while fungi transitioned from spores to hyphae on gypsum. FACS confirmed that most of the bacterial cells were intact (viable) on both materials over the course of the study. Integrated cell count and biomass data (quantitative profiling) revealed that small changes in relative abundance often resulted from large changes in absolute abundance, while negative correlations in relative abundances were explained by rapid growth of only one group of bacteria or fungi. Comparisons of bacterial-bacterial and fungal-bacterial networks suggested a top-down control of fungi on bacterial growth, possibly via antibiotic production. In conclusion, quantitative profiling provides novel insights into microbial growth dynamics on building materials with potential implications for human health.},
}
@article {pmid32756341,
year = {2020},
author = {Sierra, MA and Li, Q and Pushalkar, S and Paul, B and Sandoval, TA and Kamer, AR and Corby, P and Guo, Y and Ruff, RR and Alekseyenko, AV and Li, X and Saxena, D},
title = {The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community.},
journal = {Genes},
volume = {11},
number = {8},
pages = {},
pmid = {32756341},
issn = {2073-4425},
support = {R01 LM012517/LM/NLM NIH HHS/United States ; CA206105/NH/NIH HHS/United States ; DE025992/NH/NIH HHS/United States ; DE027074/NH/NIH HHS/United States ; },
mesh = {Computational Biology/methods/*standards ; DNA Barcoding, Taxonomic/methods/standards ; Databases, Genetic/*standards ; Humans ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.},
}
@article {pmid32754956,
year = {2020},
author = {Morimoto, D and Šulčius, S and Yoshida, T},
title = {Viruses of freshwater bloom-forming cyanobacteria: genomic features, infection strategies and coexistence with the host.},
journal = {Environmental microbiology reports},
volume = {12},
number = {5},
pages = {486-502},
doi = {10.1111/1758-2229.12872},
pmid = {32754956},
issn = {1758-2229},
support = {//Bilateral Open Partnership Joint Research Project/International ; 16H06437//JSPS Scientific Research on Innovative Areas/International ; 203143100025//The Canon Foundation/International ; //Research Council of Lithuania/International ; S-MIP-17-28//Japan Society for the Promotion of Science/International ; 17H03850//Japan Society for the Promotion of Science/International ; },
mesh = {Bacteriophages/classification/*genetics/isolation &amp; purification/metabolism ; Cyanobacteria/classification/genetics/growth &amp; development/*virology ; Fresh Water/*microbiology/*virology ; Genome, Viral ; Genomics ; Phylogeny ; Viruses/classification/*genetics/isolation &amp; purification/metabolism ; },
abstract = {Freshwater bloom-forming cyanobacteria densely grow in the aquatic environments, leading to an increase in the viral-contact rate. They possess numerous antiviral genes, as well as cell differentiation- and physiological performance-related genes, owing to genome expansion. Their genomic features and unique lifestyles suggest that they coexist with cyanoviruses in ways different from marine cyanobacteria. Furthermore, genome contents of isolated freshwater bloom-forming cyanobacterial viruses have little in common with those of marine cyanoviruses studied to date. They lack the marine cyanoviral hallmark genes that sustain photosynthetic activity and redirect host metabolism to viral reproduction; therefore, they are predicted to share metabolisms and precursor pools with host cyanobacteria to ensure efficient viral reproduction and avoid nutrient deficiencies and antiviral response. Additionally, cyanovirus-cyanobacteria coexistence strategies may change as bloom density increases. Diverse genotypic populations of cyanoviruses and hosts coexist and fluctuate under high viral-contact rate conditions, leading to their rapid coevolution through antiviral responses. The ancestral and newly evolved genotypes coexist, thereby expanding the diversity levels of host and viral populations. Bottleneck events occurring due to season-related decreases in bloom-forming species abundance provide each genotype within cyanobacterial population an equal chance to increase in prevalence during the next bloom and enhance further diversification.},
}
@article {pmid32751149,
year = {2020},
author = {Marsaux, B and Van den Abbeele, P and Ghyselinck, J and Prioult, G and Marzorati, M and Bogićević, B},
title = {Synbiotic Effect of Bifidobacterium lactis CNCM I-3446 and Bovine Milk-Derived Oligosaccharides on Infant Gut Microbiota.},
journal = {Nutrients},
volume = {12},
number = {8},
pages = {},
pmid = {32751149},
issn = {2072-6643},
mesh = {Animals ; *Bifidobacterium animalis ; Cattle ; Feces/microbiology ; Female ; Fermentation/drug effects ; Gastrointestinal Microbiome/drug effects ; Humans ; Infant ; Male ; Milk/*chemistry ; Oligosaccharides/*pharmacology ; Probiotics/*pharmacology ; RNA, Ribosomal, 16S/analysis ; *Synbiotics ; },
abstract = {BACKGROUND: This study evaluated the impact of Bifidobacterium animalis ssp. lactis CNCM I-3446, Bovine Milk-derived OligoSaccharides (BMOS) and their combination on infant gut microbiota in vitro. In addition, a novel strategy consisting of preculturing B. lactis with BMOS to further enhance their potential synbiotic effects was assessed.<br><br>METHOD: Short-term fecal batch fermentations (48 h) were used to assess the microbial composition and activity modulated by BMOS alone, B. lactis grown on BMOS or dextrose alone, or their combinations on different three-month-old infant microbiota.<br><br>RESULTS: BMOS alone significantly induced acetate and lactate production (leading to pH decrease) and stimulated bifidobacterial growth in 10 donors. A further in-depth study on two different donors proved B. lactis ability to colonize the infant microbiota, regardless of the competitiveness of the environment. BMOS further enhanced this engraftment, suggesting a strong synbiotic effect. This was also observed at the microbiota activity level, especially in a donor containing low initial levels of bifidobacteria. In this donor, preculturing B. lactis with BMOS strengthened further the early modulation of microbiota activity observed after 6 h.<br><br>CONCLUSION: This study demonstrated the strong synbiotic effect of BMOS and B. lactis on the infant gut microbiota, and suggests a strategy to improve its effectiveness in an otherwise low-Bifidobacterium microbiota.},
}
@article {pmid32748335,
year = {2020},
author = {Maal-Bared, R},
title = {Operational impacts of heavy metals on activated sludge systems: the need for improved monitoring.},
journal = {Environmental monitoring and assessment},
volume = {192},
number = {9},
pages = {560},
doi = {10.1007/s10661-020-08529-2},
pmid = {32748335},
issn = {1573-2959},
mesh = {Environmental Monitoring ; Metals, Heavy/*analysis ; *Microbiota ; Sewage ; Wastewater/analysis ; },
abstract = {Biological nutrient removal is highly reliant on maintaining a heterogeneous, balanced, and metabolically active microbial community that can adapt to the fluctuating composition of influent wastewater and encompassing environmental conditions. Maintaining this balance can be challenging in municipal wastewater systems that sporadically receive wastewater from industrial facilities due to the impact of heavy metals and other contaminants on the microbial ecology of the activated sludge. A thorough understanding of the impacts of heavy metals on activated sludge and of practical monitoring options is needed to support decision-making at the wastewater utility level. This paper is divided into two parts. In the first part, the review explains what happens when heavy metals interact with activated sludge systems by highlighting biosorption and bioaccumulation processes, and when an activated sludge system switches from bioaccumulation to toxic shock. Here, it also summarizes the impacts of heavy metal exposure on plant performance. In the second part, the review summarizes practical approaches that can be used at the plant outside the realm of traditional toxicological bioassays testing to determine the possible impacts of influent heavy metal concentrations on the BNR process. These approaches include the following: monitoring operational parameters for major shifts; respirometry; microscopy; ATP; chemical analyses of heavy metals with a focus on synergistic impacts and inhibitory limits; and other novel approaches, such as EPS chemical analyses, molecular techniques, and quorum sensing.},
}
@article {pmid32747713,
year = {2020},
author = {Pieper, R and Dadi, TH and Pieper, L and Vahjen, W and Franke, A and Reinert, K and Zentek, J},
title = {Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire.},
journal = {The ISME journal},
volume = {14},
number = {11},
pages = {2783-2793},
pmid = {32747713},
issn = {1751-7370},
mesh = {Animal Feed/analysis ; Animals ; *Anti-Bacterial Agents ; Colon ; Diet ; Drug Resistance, Microbial ; Swine ; Weaning ; *Zinc ; },
abstract = {Despite a well-documented effect of high dietary zinc oxide on the pig intestinal microbiota composition less is it yet known about changes in microbial functional properties or the effect of organic zinc sources. Forty weaning piglets in four groups were fed diets supplemented with 40 or 110 ppm zinc as zinc oxide, 110 ppm as Zn-Lysinate, or 2500 ppm as zinc oxide. Host zinc homeostasis, intestinal zinc fractions, and ileal nutrient digestibility were determined as main nutritional and physiological factors putatively driving colon microbial ecology. Metagenomic sequencing of colon microbiota revealed only clear differences at genus level for the group receiving 2500 ppm zinc oxide. However, a clear group differentiation according to dietary zinc concentration and source was observed at species level. Functional analysis revealed significant differences in genes related to stress response, mineral, and carbohydrate metabolism. Taxonomic and functional gene differences were accompanied with clear effects in microbial metabolite concentration. Finally, a selection of certain antibiotic resistance genes by dietary zinc was observed. This study sheds further light onto the consequences of concentration and chemical form of dietary zinc on microbial ecology measures and the resistome in the porcine colon.},
}
@article {pmid32747679,
year = {2020},
author = {Hach, PF and Marchant, HK and Krupke, A and Riedel, T and Meier, DV and Lavik, G and Holtappels, M and Dittmar, T and Kuypers, MMM},
title = {Rapid microbial diversification of dissolved organic matter in oceanic surface waters leads to carbon sequestration.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {13025},
pmid = {32747679},
issn = {2045-2322},
abstract = {The pool of dissolved organic matter (DOM) in the deep ocean represents one of the largest carbon sinks on the planet. In recent years, studies have shown that most of this pool is recalcitrant, because individual compounds are present at low concentrations and because certain compounds seem resistant to microbial degradation. The formation of the diverse and recalcitrant deep ocean DOM pool has been attributed to repeated and successive processing of DOM by microorganisms over time scales of weeks to years. Little is known however, about the transformation and cycling that labile DOM undergoes in the first hours upon its release from phytoplankton. Here we provide direct experimental evidence showing that within hours of labile DOM release, its breakdown and recombination with ambient DOM leads to the formation of a diverse array of new molecules in oligotrophic North Atlantic surface waters. Furthermore, our results reveal a preferential breakdown of N and P containing molecules versus those containing only carbon. Hence, we show the preferential breakdown and molecular diversification are the crucial first steps in the eventual formation of carbon rich DOM that is resistant to microbial remineralization.},
}
@article {pmid32747621,
year = {2020},
author = {Guerra, CA and Heintz-Buschart, A and Sikorski, J and Chatzinotas, A and Guerrero-Ramírez, N and Cesarz, S and Beaumelle, L and Rillig, MC and Maestre, FT and Delgado-Baquerizo, M and Buscot, F and Overmann, J and Patoine, G and Phillips, HRP and Winter, M and Wubet, T and Küsel, K and Bardgett, RD and Cameron, EK and Cowan, D and Grebenc, T and Marín, C and Orgiazzi, A and Singh, BK and Wall, DH and Eisenhauer, N},
title = {Blind spots in global soil biodiversity and ecosystem function research.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {3870},
pmid = {32747621},
issn = {2041-1723},
mesh = {Animals ; Bacteria/classification/metabolism ; *Biodiversity ; Biomass ; Climate ; *Ecosystem ; Fungi/classification/metabolism ; Geography ; Hydrogen-Ion Concentration ; Nematoda/classification/metabolism ; Oligochaeta/classification/metabolism ; Soil/chemistry/*parasitology ; *Soil Microbiology ; Temperature ; },
abstract = {Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.},
}
@article {pmid32744986,
year = {2020},
author = {Siebert, A and Huptas, C and Wenning, M and Scherer, S and Doll, EV},
title = {Fundicoccus ignavus gen. nov., sp. nov., a novel genus of the family Aerococcaceae isolated from bulk tank milk.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {8},
pages = {4774-4781},
doi = {10.1099/ijsem.0.004344},
pmid = {32744986},
issn = {1466-5034},
mesh = {Aerococcaceae/*classification/isolation &amp; purification ; Animals ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Glycolipids/chemistry ; Milk/*microbiology ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Three strains of a Gram-stain-positive, catalase-negative, facultative anaerobic, and coccoid species were isolated from German bulk tank milk. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that the three strains (WS4937[T], WS4759 and WS5303) constitute an independent phylogenetic lineage within the family Aerococcaceae with Facklamia hominis CCUG 36813[T] (93.7-94.1 %) and Eremococcus coleocola M1831/95/2[T] (93.5 %) as most closely related type species. The unclassified strains demonstrated variable growth with 6.5 % (w/v) NaCl and tolerated pH 6.5-9.5. Growth was observed from 12 to 39 °C. Their cell-wall peptidoglycan belongs to the A1α type (l-Lys-direct) consisting of alanine, glutamic acid and lysine. The predominant fatty acids were C16 : 1 ω9c, C16 : 0 and C18 : 1 ω9c and in the polar lipids profile three glycolipids, a phospholipid, phosphatidylglycerol, phosphoglycolipid and diphosphatidylglycerol were found. The G+C content of strain WS4937[T] was 37.4 mol% with a genome size of ~3.0 Mb. Based on phylogenetic, phylogenomic and biochemical characterizations, the isolates can be demarcated from all other genera of the family Aerococcaceae and, therefore, the novel genus Fundicoccus gen. nov. is proposed. The type species of the novel genus is Fundicoccus ignavus gen. nov., sp. nov. WS4937[T] (=DSM 109652[T]=LMG 31441[T]).},
}
@article {pmid32742267,
year = {2020},
author = {Breitenwieser, F and Doll, EV and Clavel, T and Scherer, S and Wenning, M},
title = {Complementary Use of Cultivation and High-Throughput Amplicon Sequencing Reveals High Biodiversity Within Raw Milk Microbiota.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1557},
pmid = {32742267},
issn = {1664-302X},
abstract = {Raw milk microbiota are complex communities with a significant impact on the hygienic, sensory and technological quality of milk products. However, there is a lack of knowledge on factors determining their composition. In the present study, four bulk tank milk samples of two farms at two different time points were analyzed in detail for their microbiota using cultivation and 16S rRNA amplicon sequencing. Diversity in samples from the first time point was assessed via cultivation of 500 aerobic mesophilic bacterial isolates in each sample. A high biodiversity of 70 and 110 species per sample was determined, of which 25-28% corresponded to yet unknown taxa. The isolates were dominated by Gram-positive members of the genera Staphylococcus, Corynebacterium, Streptococcus, or Janibacter, whilst Chryseobacterium and Acinetobacter were most abundant among the Gram-negative taxa. At the second time point, samples of the same farms were analyzed via both cultivation (1,500 individual colonies each) and high-throughput 16S rRNA gene amplicon sequencing. The latter revealed a threefold higher biodiversity at the genus level, as anaerobic or fastidious species were also detected. However, cultivation identified genera not captured by sequencing, indicating that both approaches are complementary. Using amplicon sequencing, the relative abundance of a few genera was distorted, which seems to be an artifact of sample preparation. Therefore, attention needs to be paid to the library preparation procedure with special emphasis on cell lysis and PCR.},
}
@article {pmid32740757,
year = {2021},
author = {Bose, T and Wingfield, MJ and Roux, J and Vivas, M and Burgess, TI},
title = {Phytophthora Species Associated with Roots of Native and Non-native Trees in Natural and Managed Forests.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {122-133},
pmid = {32740757},
issn = {1432-184X},
mesh = {Acacia/parasitology ; Biodiversity ; Eucalyptus/parasitology ; Forests ; Phytophthora/*classification/genetics/*isolation &amp; purification ; Plant Diseases/parasitology ; Plant Roots/*parasitology ; Soil/*parasitology ; South Africa ; Trees/*parasitology ; },
abstract = {Roots act as a biological filter that exclusively allows only a portion of the soil-associated microbial diversity to infect the plant. This microbial diversity includes organisms both beneficial and detrimental to plants. Phytophthora species are among the most important groups of detrimental microbes that cause various soil-borne plant diseases. We used a metabarcoding approach with Phytophthora-specific primers to compare the diversity and richness of Phytophthora species associated with roots of native and non-native trees, using different types of soil inocula collected from native and managed forests. Specifically, we analysed (1) roots of two non-native tree species (Eucalyptus grandis and Acacia mearnsii) and native trees, (2) roots of two non-native tree species from an in vivo plant baiting trial, (3) roots collected from the field versus those from the baiting trial, and (4) roots and soil samples collected from the field. The origin of the soil and the interaction between root and soil significantly influenced Phytophthora species richness. Moreover, species richness and community composition were significantly different between the field root samples and field soil samples with a higher number of Phytophthora species in the soil than in the roots. The results also revealed a substantial and previously undetected diversity of Phytophthora species from South Africa.},
}
@article {pmid32740714,
year = {2020},
author = {Xian, L and Wan, T and Cao, Y and Sun, J and Wu, T and Apudo, AA and Li, W and Liu, F},
title = {Structural Variability and Functional Prediction in the Epiphytic Bacteria Assemblies of Myriophyllum spicatum.},
journal = {Current microbiology},
volume = {77},
number = {11},
pages = {3582-3594},
pmid = {32740714},
issn = {1432-0991},
support = {31370262//National Natural Science Foundation of China/ ; 31670368//National Natural Science Foundation of China/ ; 31670369//National Natural Science Foundation of China/ ; 31500296//National Natural Science Foundation of China/ ; 2016YFA0601001//National Key R &amp; D Program of China/ ; },
mesh = {Aquatic Organisms ; *Bacteria/genetics ; *Microbiota ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The underlying principles influencing bacteria community assembly have long been of interest in the field of microbial ecology. Environmental heterogeneity is believed to be important in controlling the uniqueness and variability of communities. However, little is known about the influence of the host macrophytes on epiphytic bacteria assembly. In this study, we used two contrasting artificial water environments (eutrophic and oligotrophic) for reciprocal transplant experiment of Myriophyllum spicatum to examine the colonization of epiphytic bacteria accompanied with plants growth. Comparative analysis addressed a higher species diversity in epiphytic bacteria than in bacterioplankton, and the highest microbiome richness in sediment. Our data revealed that the organization of epiphytic bacterial community was affected by both plant status (i.e. branch number, net photosynthesis rate etc.) and water bodies (i.e. total phosphate, total nitrogen, pH etc.). Moreover, plant status effected the assembly in priority to water. 16S rRNA gene sequencing further indicated that the epiphytic assemblies were motivated by functionalization and interplay with hosts as a whole. The results complemented new evidences for the 'lottery process' in the epiphytic bacteria assembly traits and shed insights into the assembly patterns referring to functional adaptation across epiphytic bacteria and macrophytes.},
}
@article {pmid32739699,
year = {2020},
author = {De Paepe, J and De Paepe, K and Gòdia, F and Rabaey, K and Vlaeminck, SE and Clauwaert, P},
title = {Bio-electrochemical COD removal for energy-efficient, maximum and robust nitrogen recovery from urine through membrane aerated nitrification.},
journal = {Water research},
volume = {185},
number = {},
pages = {116223},
doi = {10.1016/j.watres.2020.116223},
pmid = {32739699},
issn = {1879-2448},
mesh = {Biofilms ; Bioreactors ; Denitrification ; Humans ; *Nitrification ; *Nitrogen ; Nitrosomonas ; Waste Disposal, Fluid ; },
abstract = {Resource recovery from source-separated urine can shorten nutrient cycles on Earth and is essential in regenerative life support systems for deep-space exploration. In this study, a robust two-stage, energy-efficient, gravity-independent urine treatment system was developed to transform fresh real human urine into a stable nutrient solution. In the first stage, up to 85% of the COD was removed in a microbial electrolysis cell (MEC), converting part of the energy in organic compounds (27-46%) into hydrogen gas and enabling full nitrogen recovery by preventing nitrogen losses through denitrification in the second stage. Besides COD removal, all urea was hydrolysed in the MEC, resulting in a stream rich in ammoniacal nitrogen and alkalinity, and low in COD. This stream was fed into a membrane-aerated biofilm reactor (MABR) in order to convert the volatile and toxic ammoniacal nitrogen to non-volatile nitrate by nitrification. Bio-electrochemical pre-treatment allowed to recover all nitrogen as nitrate in the MABR at a bulk-phase dissolved oxygen level below 0.1 mg O2 L[-1]. In contrast, feeding the MABR directly with raw urine (omitting the first stage), at the same nitrogen loading rate, resulted in nitrogen loss (18%) due to denitrification. The MEC and MABR were characterised by very distinct and diverse microbial communities. While (strictly) anaerobic genera, such as Geobacter (electroactive bacteria), Thiopseudomonas, a Lentimicrobiaceae member, Alcaligenes and Proteiniphilum prevailed in the MEC, the MABR was dominated by aerobic genera, including Nitrosomonas (a known ammonium oxidiser), Moheibacter and Gordonia. The two-stage approach yielded a stable nitrate-rich, COD-low nutrient solution, suitable for plant and microalgae cultivation.},
}
@article {pmid32737846,
year = {2021},
author = {Adeleke, BS and Babalola, OO},
title = {The endosphere microbial communities, a great promise in agriculture.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {24},
number = {1},
pages = {1-17},
pmid = {32737846},
issn = {1618-1905},
support = {123634//National Research Foundation/ ; },
mesh = {Agriculture ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Endophytes/classification/genetics/*isolation &amp; purification/metabolism ; Fertilizers/analysis/microbiology ; *Microbiota ; *Soil Microbiology ; },
abstract = {Agricultural food production and sustainability need intensification to address the current global food supply to meet human demand. The continuous human population increase and other anthropogenic activities threaten food security. Agrochemical inputs have long been used in conventional agricultural systems to boost crop productivity, but they are disadvantageous to a safe environment. Towards developing environmentally friendly agriculture, efforts are being directed in exploring biological resources from soil and plant microbes. The survival of the rhizosphere and endosphere microbiota is influenced by biotic and abiotic factors. Plant microbiota live interdependently with the host plants. Endophytes are regarded as colonizer microbes inhabiting and establishing microbial communities within the plant tissue. Their activities are varied and include fixing atmospheric nitrogen, solubilizing phosphate, synthesis of siderophores, secretion of metabolite-like compounds containing active biocontrol agents in the control of phytopathogens, and induced systemic resistance that stimulates plant response to withstand stress. Exploring beneficial endophyte resources in the formulation of bio-inoculants, such as biofertilizers, as an alternative to agrochemicals (fertilizers and pesticides) in developing environmentally friendly agriculture and for incorporation into crop breeding and disease control program is promising. Therefore, in this review, endosphere microbial ecology, associating environmental factors, and their roles that contribute to their effectiveness in promoting plant growth for maximum agricultural crop productivity were highlighted.},
}
@article {pmid32737539,
year = {2021},
author = {Takamatsu, T and Arai, H and Abe, N and Nakai, M and Kunimi, Y and Inoue, MN},
title = {Coexistence of Two Male-Killers and Their Impact on the Development of Oriental Tea Tortrix Homona magnanima.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {193-202},
pmid = {32737539},
issn = {1432-184X},
support = {24580076//Japan Society for the Promotion of Science/ ; 19J13123//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; Female ; Male ; Moths/*microbiology ; RNA Virus Infections/*mortality ; RNA Viruses/*pathogenicity ; Reproduction/*physiology ; Spiroplasma/*physiology ; Wolbachia/metabolism ; },
abstract = {Male-killing, the death of male offspring induced by maternally transmitted microbes, is classified as early, or late, male-killing. The primary advantage afforded by early male-killing, which typically occurs during embryogenesis, is the reallocation of resources to females, that would have otherwise been consumed by males. Meanwhile, the key advantage of late male-killing, which typically occurs during late larval development, is the maximized potential for horizontal transmission. To date, no studies have reported on the associated developmental and physiological effects of host coinfection with early and late male-killers, which may have a significant impact on the population dynamics of the male-killers. Here we used a lepidopteran tea pest Homona magnanima as a model, which is a unique system wherein an early male-killer (a Spiroplasma bacterium) and a late male-killer (an RNA virus) can coexist in nature. An artificially established matriline, coinfected with both Spiroplasma and RNA virus, exhibited embryonic death (early male-killing) as seen in the host line singly infected with Spiroplasma. Moreover, the coinfected line also exhibited developmental retardation and low pupal weight similar to the host line singly infected with the RNA virus. A series of field surveys revealed that Spiroplasma-RNA virus coinfection occurs in nature at a low frequency. Hence, although the two male-killers are capable of coexisting within the H. magnanima population independently, high associated fitness cost appears to limit the prevalence of male-killer coinfection in the field host population.},
}
@article {pmid32737538,
year = {2021},
author = {Stone, BWG and Jackson, CR},
title = {Seasonal Patterns Contribute More Towards Phyllosphere Bacterial Community Structure than Short-Term Perturbations.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {146-156},
pmid = {32737538},
issn = {1432-184X},
support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; Cellular Senescence/physiology ; Climate ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; Plant Leaves/*microbiology ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; Rain ; Seasons ; Typhaceae/*microbiology ; },
abstract = {Phyllosphere microorganisms are sensitive to fluctuations in wind, temperature, solar radiation, and rain. However, recent explorations of patterns in phyllosphere communities across time often focus on seasonal shifts and leaf senescence without measuring the contribution of environmental drivers and leaf traits. Here, we focus on the effects of rain on the phyllosphere bacterial community of the wetland macrophyte broadleaf cattail (Typha latifolia) across an entire year, specifically targeting days before and 1, 3, and 5 days after rain events. To isolate the contribution of precipitation from other factors, we covered a subset of plants to shield them from rainfall. We used targeted Illumina sequencing of the V4 region of the bacterial 16S rRNA gene to characterize phyllosphere community composition. Rain events did not have a detectable effect on phyllosphere community richness or evenness regardless of whether the leaves were covered from rain or not, suggesting that foliar microbial communities are robust to such disturbances. While climatic and leaf-based variables effectively modeled seasonal trends in phyllosphere diversity and composition, they provided more limited explanatory value at shorter time scales. These findings underscore the dominance of long-term seasonal patterns related to climatic variation as the main factor influencing the phyllosphere community.},
}
@article {pmid32733460,
year = {2020},
author = {Saresella, M and Marventano, I and Barone, M and La Rosa, F and Piancone, F and Mendozzi, L and d'Arma, A and Rossi, V and Pugnetti, L and Roda, G and Casagni, E and Cas, MD and Paroni, R and Brigidi, P and Turroni, S and Clerici, M},
title = {Alterations in Circulating Fatty Acid Are Associated With Gut Microbiota Dysbiosis and Inflammation in Multiple Sclerosis.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {1390},
pmid = {32733460},
issn = {1664-3224},
mesh = {Adult ; Biodiversity ; Biomarkers ; Butyric Acid/blood ; Caproates/blood ; Chromatography, Liquid ; Cytokines/metabolism ; Disease Susceptibility ; Dysbiosis/*blood ; Fatty Acids/*blood ; Female ; Flow Cytometry ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism/microbiology ; Male ; Middle Aged ; Multiple Sclerosis/*blood/*etiology ; Permeability ; T-Lymphocyte Subsets/immunology/metabolism ; Tandem Mass Spectrometry ; Transcription Factors/metabolism ; },
abstract = {Background: Butyric acid (BA) is a short-chain fatty acid (SCFA) with anti-inflammatory properties, which promotes intestinal barrier function. Medium-chain fatty acids (MCFA), including caproic acid (CA), promote TH1 and TH17 differentiation, thus supporting inflammation. Aim: Since most SCFAs are absorbed in the cecum and colon, the measurement of BA in peripheral blood could provide information on the health status of the intestinal ecosystem. Additionally, given the different immunomodulatory properties of BA and CA the evaluation of their serum concentration, as well as their ratio could be as a simple and rapid biomarker of disease activity and/or treatment efficacy in MS. Methods: We evaluated serum BA and CA concentrations, immune parameters, intestinal barrier integrity and the gut microbiota composition in patients with multiple sclerosis (MS) comparing result to those obtained in healthy controls. Results: In MS, the concentration of BA was reduced and that of CA was increased. Concurrently, the microbiota was depleted of BA producers while it was enriched in mucin-degrading, pro-inflammatory components. The reduced serum concentration of BA seen in MS patients correlated with alterations of the barrier permeability, as evidenced by the higher plasma concentrations of lipopolysaccharide and intestinal fatty acid-binding protein, and inflammation. Specifically, CA was positively associated with CD4+/IFNγ+ T lymphocytes, and the BA/CA ratio correlated positively with CD4+/CD25[high]/Foxp3+ and negatively with CD4+/IFNγ+ T lymphocytes. Conclusion: The gut microbiota dysbiosis found in MS is possibly associated with alterations of the SCFA/MCFA ratio and of the intestinal barrier; this could explain the chronic inflammation that characterizes this disease. SCFA and MCFA quantification could be a simple biomarker to evaluate the efficacy of therapeutic and rehabilitation procedures in MS.},
}
@article {pmid32733417,
year = {2020},
author = {Dove, NC and Rogers, TJ and Leppanen, C and Simberloff, D and Fordyce, JA and Brown, VA and LeBude, AV and Ranney, TG and Cregger, MA},
title = {Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1528},
pmid = {32733417},
issn = {1664-302X},
abstract = {The hemlock woolly adelgid (Adelges tsugae, HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii, that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.},
}
@article {pmid32728091,
year = {2020},
author = {Gulati, S and Ballhausen, MB and Kulkarni, P and Grosch, R and Garbeva, P},
title = {A non-invasive soil-based setup to study tomato root volatiles released by healthy and infected roots.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12704},
pmid = {32728091},
issn = {2045-2322},
mesh = {Bacillus/genetics/growth &amp; development/*isolation &amp; purification ; Chromatography, Gas ; DNA, Bacterial/genetics ; Fusarium/*pathogenicity ; Solanum lycopersicum/chemistry/*growth &amp; development/microbiology ; Metabolomics ; Plant Extracts/analysis ; Plant Roots/chemistry/growth &amp; development/microbiology ; Soil Microbiology ; Volatile Organic Compounds/*analysis ; },
abstract = {The role of root exudates in mediating plant-microbe interactions has been well documented. However, the function of volatile organic compounds (VOCs) emitted by plant roots has only recently begun to attract attention. This newly recognized relevance of belowground VOCs has so far mostly been tested using systems limited to a two-compartment Petri-dish design. Furthermore, many of the plant-microbe interaction studies have only investigated the effects of microbial VOCs on plant growth. Here, we go two steps further. First we investigated the volatile profile of healthy and pathogen (Fusarium oxysporum) infected tomato roots grown in soil. We then used a unique soil-based olfactometer-choice assay to compare the migration pattern of four beneficial bacteria (Bacillus spp.) towards the roots of the tomato plants. We demonstrate that the blend of root-emitted VOCs differs between healthy and diseased plants. Our results show that VOCs are involved in attracting bacteria to plant roots.},
}
@article {pmid32727863,
year = {2020},
author = {Salcher, MM and Andrei, A&#x15e; and Bulzu, PA and Keresztes, ZG and Banciu, HL and Ghai, R},
title = {Visualization of Lokiarchaeia and Heimdallarchaeia (Asgardarchaeota) by Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition (CARD-FISH).},
journal = {mSphere},
volume = {5},
number = {4},
pages = {},
pmid = {32727863},
issn = {2379-5042},
mesh = {Archaea/classification/*genetics ; Geologic Sediments/microbiology ; In Situ Hybridization, Fluorescence/*methods ; Microscopy, Fluorescence ; Oligonucleotide Probes/*genetics ; Phylogeny ; },
abstract = {Metagenome-assembled genomes (MAGs) of Asgardarchaeota have been recovered from a variety of habitats, broadening their environmental distribution and providing access to the genetic makeup of this archaeal lineage. The recent success in cultivating the first representative of Lokiarchaeia was a breakthrough in science at large and gave rise to new hypotheses about the evolution of eukaryotes. Despite their singular phylogenetic position at the base of the eukaryotic tree of life, the morphology of these bewildering organisms remains a mystery, except for the report of an unusual morphology with long, branching protrusions of the cultivated Lokiarchaeion strain "Candidatus Prometheoarchaeum syntrophicum" MK-D1. In order to visualize this elusive group, we applied a combination of fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed CARD-FISH probes for Heimdallarchaeia and Lokiarchaeia lineages, and provide the first visual evidence for Heimdallarchaeia and new images of a lineage of Lokiarchaeia that is different from the cultured representative. Here, we show that while Heimdallarchaeia are characterized by a uniform cellular morphology typified by a centralized DNA localization, Lokiarchaeia display a plethora of shapes and sizes that likely reflect their broad phylogenetic diversity and ecological distribution.IMPORTANCE Asgardarchaeota are considered to be the closest relatives to modern eukaryotes. These enigmatic microbes have been mainly studied using metagenome-assembled genomes (MAGs). Only very recently, a first member of Lokiarchaeia was isolated and characterized in detail; it featured a striking morphology with long, branching protrusions. In order to visualize additional members of the phylum Asgardarchaeota, we applied a fluorescence in situ hybridization technique and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed probes for Heimdallarchaeia and Lokiarchaeia lineages. We provide the first visual evidence for Heimdallarchaeia that are characterized by a uniform cellular morphology typified by an apparently centralized DNA localization. Further, we provide new images of a lineage of Lokiarchaeia that is different from the cultured representative and with multiple morphologies, ranging from small ovoid cells to long filaments. This diversity in observed cell shapes is likely owing to the large phylogenetic diversity within Asgardarchaeota, the vast majority of which remain uncultured.},
}
@article {pmid32727027,
year = {2020},
author = {Pédron, J and Guyon, L and Lecomte, A and Blottière, L and Chandeysson, C and Rochelle-Newall, E and Raynaud, X and Berge, O and Barny, MA},
title = {Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa.},
journal = {Microorganisms},
volume = {8},
number = {8},
pages = {},
pmid = {32727027},
issn = {2076-2607},
support = {Ec2co-CARTOBACTER//Centre National de la Recherche Scientifique/ ; CE32-2017-SPREE//Agence Nationale de la Recherche/ ; },
abstract = {To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3-V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.},
}
@article {pmid32723798,
year = {2020},
author = {Xu, L and Xiang, M and Zhu, W and Zhang, M and Chen, H and Huang, J and Chen, Y and Chang, Q and Jiang, J and Zhu, L},
title = {The Behavior of Amphibians Shapes Their Symbiotic Microbiomes.},
journal = {mSystems},
volume = {5},
number = {4},
pages = {},
pmid = {32723798},
issn = {2379-5077},
abstract = {Seasonal dynamics in symbiotic microbiomes have been investigated in a number of vertebrates and are mainly caused by changes in the diet (in the gut microbiome) or the living environment (in the skin microbiome). Most amphibian microbiome studies focus on the skin, whereas internal microbiome structure and dynamics are often overlooked. The present study investigated the seasonal dynamics in three types of symbiotic microbiomes (the skin, stomach, and gut) across four wild frog species, belonging to different families, in May and October. The frogs harbored more water source microbes in May than in October. On the contrary, the frogs harbored more soil source microbes in October than in May. The frog species investigated tend to live in a water environment in May to maintain body surface humidity at high environmental temperatures and to breed. In October, these four species prefer to live on the land, as the environmental temperature decreases, to prepare for hibernation in caves or under stones. Thus, seasonal changes in the wild amphibian symbiotic microbiome may be caused by the difference in microbe transmission from their living environment due to specific behaviors. This study demonstrated that the behavior and living environment of wild amphibians shape their symbiotic microbiome externally (on the skin) and internally (in the stomach and gut). We revealed the potential association between specific behaviors in poikilothermic animals and host symbiotic microbiomes.IMPORTANCE Understanding the interactions between host behavior and microbiome dynamics remains an outstanding priority in the field of microbial ecology. Here, we provide the reader with a simple example of how the behavior and living environment of wild amphibians shape their symbiotic microbiome externally (on the skin) and internally (in the stomach and gut).},
}
@article {pmid32723791,
year = {2020},
author = {Malli Mohan, GB and Parker, CW and Urbaniak, C and Singh, NK and Hood, A and Minich, JJ and Knight, R and Rucker, M and Venkateswaran, K},
title = {Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation.},
journal = {mSystems},
volume = {5},
number = {4},
pages = {},
pmid = {32723791},
issn = {2379-5077},
abstract = {Microbial contamination during long-term confinements of space exploration presents potential risks for both crew members and spacecraft life support systems. A novel swab kit was used to sample various surfaces from a submerged, closed, analog habitat to characterize the microbial populations. Samples were collected from various locations across the habitat which were constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal), and microbial populations were examined by culture, quantitative PCR (qPCR), microbiome 16S rRNA gene sequencing, and shotgun metagenomics. Propidium monoazide (PMA)-treated samples identified the viable/intact microbial population of the habitat. The cultivable microbial population ranged from below the detection limit to 10[6] CFU/sample, and their identity was characterized using Sanger sequencing. Both 16S rRNA amplicon and shotgun sequencing were used to characterize the microbial dynamics, community profiles, and functional attributes (metabolism, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable (after PMA treatment) Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia, and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus, and Oceanobacillus), and Proteobacteria (especially Acinetobacter) on linoleum, dry wall, and particle board (LDP) surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Nonmetric multidimensional scaling determined from both 16S rRNA and metagenomic analyses revealed differential microbial species on LDP surfaces and glass/metal surfaces. The shotgun metagenomic sequencing of samples after PMA treatment showed bacterial predominance of viable Brevibacterium (53.6%), Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus (2.1%), while fungal analyses revealed Aspergillus and Penicillium dominance.IMPORTANCE This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged analog habitat differs greatly from that of previously studied analog habitats.},
}
@article {pmid32721842,
year = {2020},
author = {Pascual-Benito, M and Ballesté, E and Monleón-Getino, T and Urmeneta, J and Blanch, AR and García-Aljaro, C and Lucena, F},
title = {Impact of treated sewage effluent on the bacterial community composition in an intermittent mediterranean stream.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {266},
number = {Pt 1},
pages = {115254},
doi = {10.1016/j.envpol.2020.115254},
pmid = {32721842},
issn = {1873-6424},
mesh = {Bacteria/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Sewage ; Wastewater ; },
abstract = {Water quality monitoring is essential to safeguard human and environmental health. The advent of next-generation sequencing techniques in recent years, which allow a more in-depth study of environmental microbial communities in the environment, could broaden the perspective of water quality monitoring to include impact of faecal pollution bacteria on ecosystem. In this study, 16 S rRNA amplicon sequencing was used to evaluate the impact of wastewater treatment plant (WWTP) effluent on autochthonous microbial communities of a temporary Mediterranean stream characterized by high flow seasonality (from 0.02 m[3]/s in winter to 0.006 m[3]/s in summer). Seven sampling campaigns were performed under different temperatures and streamflow conditions (winter and summer). Water samples were collected upstream (Upper) of the WWTP, the secondary effluent (EF) discharge and 75 m (P75) and 1000 m (P1000) downstream of the WWTP. A total of 5,593,724 sequences were obtained, giving rise to 20,650 amplicon sequence variants (ASV), which were further analysed and classified into phylum, class, family and genus. Each sample presented different distribution and abundance of taxa. Although taxon distribution and abundance differed in each sample, the microbial community structure of P75 resembled that of EF samples, and Upper and P1000 samples mostly clustered together. Alpha diversity showed the highest values for Upper and P1000 samples and presented seasonal differences, being higher in winter conditions of high streamflow and low temperature. Our results suggest the microbial ecology re-establishment, since autochthonous bacterial communities were able to recover from the impact of the WWTP effluent in 1 km. Alpha diversity results indicates a possible influence of environmental factors on the bacterial community structure. This study shows the potential of next-generation sequencing techniques as useful tools in water quality monitoring and management within the climate change scenario.},
}
@article {pmid32720097,
year = {2020},
author = {Zou, P and Yang, Q and Wang, H and Xie, G and Cao, Z and Chen, X and Gao, W and Huang, J},
title = {In vitro disinfection efficacy and clinical protective effects of common disinfectants against acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio isolates in Pacific white shrimp Penaeus vannamei.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {58},
number = {8},
pages = {675-686},
doi = {10.1007/s12275-020-9537-1},
pmid = {32720097},
issn = {1976-3794},
mesh = {Animals ; Anti-Infective Agents, Local/*pharmacology ; Aquaculture/methods ; Biguanides/pharmacology ; Disinfection/*methods ; Hepatopancreas/microbiology/pathology ; Hydrogen Peroxide/pharmacology ; Penaeidae/*microbiology ; Seafood/microbiology ; Vibrio/*drug effects/isolation &amp; purification ; Vibrio parahaemolyticus/*drug effects/isolation &amp; purification ; },
abstract = {Acute hepatopancreatic necrosis disease (AHPND) is one of the most significant bacterial diseases in global shrimp culture, causing severe economic losses. In the present study, we carried out in vitro antimicrobial tests to investigate the disinfection efficacy of 14 common disinfectants toward different AHPND-causing Vibrio spp., including eight isolates of V. parahaemolyticus, four isolates of V. campbellii, and one isolate of V. owensii. Polyhexamethylene biguanidine hydrochloride (PHMB) was revealed to possess the strongest inhibitory activity. Through analyzing and evaluating the results of antimicrobial tests and acute toxicity test, we selected PHMB and hydrogen peroxide (H2O2) for further clinical protection test. Clinical manifestations indicated that both PHMB (2 mg/L and 4 mg/L) and H2O2 (12 mg/L) could effectively protect juvenile Penaeus vannamei from the infection of V. parahaemolyticus isolate Vp362 at 10[6] CFU/ml, and the survival rate was over 80%. When the bacterial concentration was reduced to 10[5] CFU/ml, 10[4] CFU/ml, and 10[3] CFU/ml, the survival rate after treated by 1 mg/L PHMB was 64.44%, 93.33%, and 100%, respectively. According to the results, PHMB and H2O2 showed a lower toxicity while a better protection activity, particularly against a lower concentration of the pathogens. Therefore, these two disinfectants are proved to be promising disinfectants that can be applied to prevent and control AHPND in shrimp culture. Moreover, the methods of this study also provided valuable information for the prevention of other important bacterial diseases and suggested a reliable means for screening potential drugs in aquaculture.},
}
@article {pmid32719667,
year = {2020},
author = {Geelhoed, JS and van de Velde, SJ and Meysman, FJR},
title = {Quantification of Cable Bacteria in Marine Sediments via qPCR.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1506},
pmid = {32719667},
issn = {1664-302X},
abstract = {Cable bacteria (Deltaproteobacteria, Desulfobulbaceae) are long filamentous sulfur-oxidizing bacteria that generate long-distance electric currents running through the bacterial filaments. This way, they couple the oxidation of sulfide in deeper sediment layers to the reduction of oxygen or nitrate near the sediment-water interface. Cable bacteria are found in a wide range of aquatic sediments, but an accurate procedure to assess their abundance is lacking. We developed a qPCR approach that quantifies cable bacteria in relation to other bacteria within the family Desulfobulbaceae. Primer sets targeting cable bacteria, Desulfobulbaceae and the total bacterial community were applied in qPCR with DNA extracted from marine sediment incubations. Amplicon sequencing of the 16S rRNA gene V4 region confirmed that cable bacteria were accurately enumerated by qPCR, and suggested novel diversity of cable bacteria. The conjoint quantification of current densities and cell densities revealed that individual filaments carry a mean current of ∼110 pA and have a cell specific oxygen consumption rate of 69 fmol O2 cell[-1] day[-1]. Overall, the qPCR method enables a better quantitative assessment of cable bacteria abundance, providing new metabolic insights at filament and cell level, and improving our understanding of the microbial ecology of electrogenic sediments.},
}
@article {pmid32719401,
year = {2020},
author = {Huber, P and Metz, S and Unrein, F and Mayora, G and Sarmento, H and Devercelli, M},
title = {Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system.},
journal = {The ISME journal},
volume = {14},
number = {12},
pages = {2951-2966},
pmid = {32719401},
issn = {1751-7370},
mesh = {Aquatic Organisms ; Bacteria/genetics ; *Ecosystem ; Phylogeny ; *Rivers ; },
abstract = {How diversity is structured has been a central goal of microbial ecology. In freshwater ecosystems, selection has been found to be the main driver shaping bacterial communities. However, its relative importance compared with other processes (dispersal, drift, diversification) may depend on spatial heterogeneity and the dispersal rates within a metacommunity. Still, a decrease in the role of selection is expected with increasing dispersal homogenization. Here, we investigate the main ecological processes modulating bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the floodplain system of the Paraná River. The bacterioplankton metacommunity was studied using both statistical inferences based on phylogenetic and taxa turnover as well as co-occurrence networks. We found that selection was the main process determining community assembly even at both extremes of environmental heterogeneity and homogeneity, challenging the general view that the strength of selection is weakened due to dispersal homogenization. The ecological processes acting on the community also determined the connectedness of bacterial networks associations. Heterogeneous selection promoted more interconnected networks increasing β-diversity. Finally, spatiotemporal heterogeneity was an important factor determining the number and identity of the most highly connected taxa in the system. Integrating all these empirical evidences, we propose a new conceptual model that elucidates how the environmental heterogeneity determines the action of the ecological processes shaping the bacterial metacommunity.},
}
@article {pmid32717345,
year = {2020},
author = {Ahlawat, S and Asha, and Sharma, KK},
title = {Immunological co-ordination between gut and lungs in SARS-CoV-2 infection.},
journal = {Virus research},
volume = {286},
number = {},
pages = {198103},
pmid = {32717345},
issn = {1872-7492},
mesh = {Angiotensin-Converting Enzyme 2 ; Antibodies, Monoclonal/therapeutic use ; Antiviral Agents/therapeutic use ; Betacoronavirus/immunology/*pathogenicity ; COVID-19 ; Coronavirus Infections/drug therapy/*immunology/microbiology/virology ; Cytokine Release Syndrome/drug therapy/*immunology/microbiology/virology ; Cytokines/antagonists &amp; inhibitors/genetics/immunology ; Dysbiosis/drug therapy/*immunology/microbiology/virology ; Gastrointestinal Microbiome/immunology ; Gastrointestinal Tract/drug effects/*immunology/microbiology/virology ; Gene Expression ; Host-Pathogen Interactions/immunology ; Humans ; Inflammatory Bowel Diseases/drug therapy/*immunology/microbiology/virology ; Lung/drug effects/*immunology/microbiology/virology ; Pandemics ; Peptidyl-Dipeptidase A/genetics/immunology ; Pneumonia, Viral/drug therapy/*immunology/microbiology/virology ; Receptors, Virus/genetics/immunology ; SARS-CoV-2 ; },
abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into a major pandemic called coronavirus disease 2019 (COVID-19) that has created unprecedented global health emergencies, and emerged as a serious threat due to its strong ability for human-to-human transmission. The reports indicate the ability of SARS-CoV-2 to affect almost any organ due to the presence of a receptor known as angiotensin converting enzyme 2 (ACE2) across the body. ACE2 receptor is majorly expressed in the brush border of gut enterocytes along with the ciliated cells and alveolar epithelial type II cells in the lungs. The amino acid transport function of ACE2 has been linked to gut microbial ecology in gastrointestinal (GI) tract, thereby suggesting that COVID-19 may, to some level, be linked to the enteric microbiota. The significant number of COVID-19 patients shows extra-pulmonary symptoms in the GI tract. Many subsequent studies revealed viral RNA of SARS-CoV-2 in fecal samples of COVID-19 patients. This presents a new challenge in the diagnosis and control of COVID-19 infection with a caution for proper sanitation and hygiene. Here, we aim to discuss the immunological co-ordination between gut and lungs that facilitates SARS-CoV-2 to infect and multiply in the inflammatory bowel disease (IBD) and non-IBD patients.},
}
@article {pmid32710789,
year = {2020},
author = {Zhang, QF and Laanbroek, HJ},
title = {Tannins from senescent Rhizophora mangle mangrove leaves have a distinctive effect on prokaryotic and eukaryotic communities in a Distichlis spicata salt marsh soil.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {9},
pages = {},
doi = {10.1093/femsec/fiaa148},
pmid = {32710789},
issn = {1574-6941},
mesh = {Eukaryota ; Plant Leaves ; RNA, Ribosomal, 16S/genetics ; *Rhizophoraceae ; Soil ; Soil Microbiology ; Tannins ; Wetlands ; },
abstract = {Due to climate warming, tannin-rich Rhizophora mangle migrates into tannin-poor salt marshes, where the tannins interfere with the biogeochemistry in the soil. Changes in biogeochemistry are likely associated with changes in microbial communities. This was studied in microcosms filled with salt marsh soil and amended with leaf powder, crude condensed tannins, purified condensed tannins (PCT), all from senescent R. mangle leaves, or with tannic acid. Size and composition of the microbial communities were determined by denaturing gradient gel electrophoresis, high-throughput sequencing and real-time PCR based on the 16S and 18S rRNA genes. Compared with the control, the 16S rRNA gene abundance was lowered by PCT, while the 18S rRNA gene abundance was enhanced by all treatments. The treatments also affected the composition of the 16S rRNA and 18S rRNA gene assemblies, but the effects on the 18S rRNA gene were greater. The composition of the 18S rRNA gene, but not of the 16S rRNA gene, was significantly correlated with the mineralization of carbon, nitrogen and phosphorus. Distinctive microbial groups emerged during the different treatments. This study revealed that migration of mangroves may affect both the prokaryotic and the eukaryotic communities in salt marsh soils, but that the effects on the eukaryotes will likely be greater.},
}
@article {pmid32710756,
year = {2020},
author = {Pedrinho, A and Mendes, LW and Merloti, LF and Andreote, FD and Tsai, SM},
title = {The natural recovery of soil microbial community and nitrogen functions after pasture abandonment in the Amazon region.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {9},
pages = {},
doi = {10.1093/femsec/fiaa149},
pmid = {32710756},
issn = {1574-6941},
mesh = {Forests ; *Microbiota ; Nitrogen/analysis ; *Soil ; Soil Microbiology ; },
abstract = {We assessed the impacts of forest-to-pasture conversion on the dynamic of soil microbial communities, especially those involved in the N-cycle, and their potential functions, using DNA-metagenomic sequencing coupled with the quantification of marker genes for N-cycling. We also evaluated whether the community's dynamic was reestablished with secondary forest growth. In general, the microbial community structure was influenced by changes in soil chemical properties. Aluminum and nitrate significantly correlated to community structure and with 12 out of 21 microbial phyla. The N-related microbial groups and their potential functions were also affected by land-use change, with pasture being clearly different from primary and secondary forest systems. The microbial community analysis demonstrated that forest-to-pasture conversion increased the abundance of different microbial groups related to nitrogen fixation, including Bacteroidetes, Chloroflexi and Firmicutes. In contrast, after pasture abandonment and with the secondary forest regeneration, there was an increase in the abundance of Proteobacteria taxa and denitrification genes. Our multi-analytical approach indicated that the secondary forest presented some signs of resilience, suggesting that the N-related microbial groups and their potential functions can be recovered over time with implications for future ecological restoration programs.},
}
@article {pmid32710182,
year = {2020},
author = {Luzzi, G and Brinks, E and Fritsche, J and Franz, CMAP},
title = {Microbial composition of sweetness-enhanced yoghurt during fermentation and storage.},
journal = {AMB Express},
volume = {10},
number = {1},
pages = {131},
pmid = {32710182},
issn = {2191-0855},
support = {2819107616//Bundesanstalt f&#xfc;r Landwirtschaft und Ern&#xe4;hrung/ ; },
abstract = {The reformulation of dairy products to contain less added sugar can contribute to reducing sugar consumption, thereby reducing the risk of non-communicable diseases. The objective of this study was to investigate the microbial ecology of reformulated yoghurt, which was produced using bi-enzymatic modification of lactose to increase its sweetness by a factor of 2-3. Ultimately, this reformulation strategy could reduce the amount of added sugar needed for equal sweetness of the end product. The bi-enzymatic modification relied on utilisation of a β-galactosidase enzyme to convert the milk sugar lactose to galactose and glucose, followed by the enzymatic conversion of the glucose moiety to fructose using a glucose isomerase. The microbial ecology of reformulated yoghurt produced with two mixed starter culture preparations containing either Streptococcus (S.) thermophilus and Lactobacillus (Lb.) delbrueckii or S. thermophilus, Lb. acidophilus and Bifidobacterium sp. strains, was analysed during fermentation and cool storage using 16S rRNA based metagenomics. None of the yoghurt samples showed a significant difference in microbial composition between sweetness-enhanced and regular milk at all sampling time points during manufacture and storage of yoghurt. However, a significant difference between the microbiota of inoculated milk before and after fermentation was observed. In both types of yoghurt, the starter culture genera dominated the microbial ecology at the end of fermentation as expected, reducing the possibility of growth of potentially pathogenic or spoilage bacteria possibly resulting from a changed carbohydrate spectrum.},
}
@article {pmid32709974,
year = {2020},
author = {Daebeler, A and Kitzinger, K and Koch, H and Herbold, CW and Steinfeder, M and Schwarz, J and Zechmeister, T and Karst, SM and Albertsen, M and Nielsen, PH and Wagner, M and Daims, H},
title = {Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira.},
journal = {The ISME journal},
volume = {14},
number = {12},
pages = {2967-2979},
pmid = {32709974},
issn = {1751-7370},
mesh = {*Bacteria/genetics ; Hydrogen-Ion Concentration ; Metagenome ; *Nitrites ; Nitrogen Cycle ; Oxidation-Reduction ; },
abstract = {Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, "Candidatus Nitrospira alkalitolerans", revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. "Ca. Nitrospira alkalitolerans" also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.},
}
@article {pmid32709258,
year = {2020},
author = {Nobu, MK and Narihiro, T and Mei, R and Kamagata, Y and Lee, PKH and Lee, PH and McInerney, MJ and Liu, WT},
title = {Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {111},
pmid = {32709258},
issn = {2049-2618},
support = {DE-AC02-05CH1123//Department of Energy/International ; DE-FG02-96ER20214//Department of Energy/International ; },
mesh = {Acetates/metabolism ; Anaerobiosis ; Archaea/*metabolism ; *Chemoautotrophic Growth ; *Ecosystem ; Formates/metabolism ; Methane/*metabolism ; Thermodynamics ; },
abstract = {BACKGROUND: Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H2 accumulation and can be inhibited by H2 produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic environments remain unexplored.<br><br>RESULTS: To uncover how anaerobes combat this H2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology-methanogenic bioreactors. Through analysis of 17 anaerobic digesters, we recovered 1343 high-quality metagenome-assembled genomes and corresponding gene expression profiles for uncultured lineages spanning 66 phyla and reconstructed their metabolic capacities. We discovered that diverse uncultured populations can drive H2-sensitive metabolisms through (i) metabolic coupling with concurrent H2-tolerant catabolism, (ii) forgoing H2 generation in favor of interspecies transfer of formate and electrons (cytochrome- and pili-mediated) to avoid thermodynamic conflict, and (iii) integration of low-concentration O2 metabolism as an ancillary thermodynamics-enhancing electron sink. Archaeal populations support these processes through unique methanogenic metabolisms-highly favorable H2 oxidation driven by methyl-reducing methanogenesis and tripartite uptake of formate, electrons, and acetate.<br><br>CONCLUSION: Integration of omics and eco-thermodynamics revealed overlooked behavior and interactions of uncultured organisms, including coupling favorable and unfavorable metabolisms, shifting from H2 to formate transfer, respiring low-concentration O2, performing direct interspecies electron transfer, and interacting with high H2-affinity methanogenesis. These findings shed light on how microorganisms overcome a&#xa0;critical obstacle in methanogenic carbon cycles we had hitherto disregarded&#xa0;and provide foundational&#xa0;insight into anaerobic microbial&#xa0;ecology. Video Abstract.},
}
@article {pmid32708991,
year = {2020},
author = {Swarte, JC and Eelderink, C and Douwes, RM and Said, MY and Hu, S and Post, A and Westerhuis, R and Bakker, SJL and Harmsen, HJM},
title = {Effect of High versus Low Dairy Consumption on the Gut Microbiome: Results of a Randomized, Cross-Over Study.},
journal = {Nutrients},
volume = {12},
number = {7},
pages = {},
pmid = {32708991},
issn = {2072-6643},
mesh = {Aged ; Body Composition ; Body Mass Index ; Body Weight ; Cholesterol/blood ; Constipation/microbiology ; Cross-Over Studies ; *Dairy Products ; *Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Middle Aged ; Overweight/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; Surveys and Questionnaires ; Triglycerides/blood ; },
abstract = {The influence of dairy on the gut microbiome has not been studied extensively. We performed a randomized cross-over study to analyze the effect of high dairy intake on the gut microbiome. Subjects were randomly assigned to a high-dairy diet (HDD) (5-6 dairy portions per day) and a low-dairy diet (LDD) (≤1 dairy portion per day) for 6 weeks with a washout period of 4 weeks in between both diets. The gut microbiome was assessed using 16S rRNA gene sequencing. Compositionality and functionality of the gut microbiome was assessed using Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Stool consistency was evaluated using the Bristol stool chart. In total, 46 healthy overweight subjects (BMI range 25-30 kg/m[2]) completed both intervention periods. During the HDD, there was a significantly higher abundance of the genera Streptococcus, Leuconostoc, and Lactococcus, and the species Streptococcus thermophilus, Erysipelatoclostridium ramosum and Leuconostoc mesenteroides (pFDR < 0.10). Furthermore, during the HDD, there was a significantly lower abundance of the genera Faecalibacterium and Bilophila, and the species Faecalibacterium prausnitzii, Clostridium aldenense, Acetivibrio ethanolgignens, Bilophila wadsworthia and Lactococcus lactis (pFDR < 0.10). There were eight subjects who became constipated during the HDD and these subjects all had a lower abundance of F. prausnitzii. This is the first cross-over study in which the effect of an HDD compared to an LDD on the gut microbiome has been studied. An HDD led to a significantly different composition of the gut microbiome, with a particularly lower abundance of F. prausnitzii and a higher abundance of S. thermophilus. Constipation was observed in several subjects during the HDD. Predicted metabolic pathways were not significantly altered due to an HDD.},
}
@article {pmid32706331,
year = {2020},
author = {Pérez-Cobas, AE and Gomez-Valero, L and Buchrieser, C},
title = {Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.},
journal = {Microbial genomics},
volume = {6},
number = {8},
pages = {},
pmid = {32706331},
issn = {2057-5858},
mesh = {Computational Biology/methods ; Genetic Markers/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Software ; Whole Genome Sequencing/*methods ; },
abstract = {Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.},
}
@article {pmid32705812,
year = {2020},
author = {Mitiku, AA and Andeta, AF and Borremans, A and Lievens, B and Bossaert, S and Crauwels, S and Aernouts, B and Kechero, Y and Van Campenhout, L},
title = {Silage making of maize stover and banana pseudostem under South Ethiopian conditions: evolution of pH, dry matter and microbiological profile.},
journal = {Microbial biotechnology},
volume = {13},
number = {5},
pages = {1477-1488},
pmid = {32705812},
issn = {1751-7915},
mesh = {Fermentation ; Hydrogen-Ion Concentration ; *Musa ; *Silage ; Zea mays ; },
abstract = {The study was conducted to evaluate the microbial dynamics during silage of maize stover and banana pseudostem in the environmental conditions of southern Ethiopia. To meet this objective, microsilos containing either maize stover or banana pseudostem, both with and without molasses, were prepared. Subsequently, samples were analysed on day 0, 7, 14, 30, 60 and 90 of the fermentation process. As a result, on day 7, all treatments except banana pseudostem without molasses showed a significant reduction in pH. It was also this silage type that supported the growth of Enterobacteriaceae longer than three other silage types, i.e. until 30 days. The yeasts and moulds and the Clostridum endospore counts also showed a reducing trend in early fermentation and afterwards remained constant until day 90. Illumina MiSeq sequencing revealed that Leuconostoc, Buttiauxella species and Enterobacteriaceae were the most abundant bacteria in the initial phases of the fermentation. Later on, Buttiauxella, Lactobacillus, Weissella and Bifidobacterium species were found to be dominant. In conclusion, silage of the two crop by-products is possible under South Ethiopian conditions. For banana pseudostem, the addition of molasses is crucial for a fast fermentation, in contrast to maize. Upscaling needs to be investigated for the two by-products.},
}
@article {pmid32705311,
year = {2021},
author = {Mateus-Barros, E and de Melo, ML and Bagatini, IL and Caliman, A and Sarmento, H},
title = {Local and Geographic Factors Shape the Occupancy-Frequency Distribution of Freshwater Bacteria.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {26-35},
pmid = {32705311},
issn = {1432-184X},
support = {2014/14139-3//S&#xe3;o Paulo Research Foundation - FAPESP/ ; 2011/50054-4//S&#xe3;o Paulo Research Foundation - FAPESP/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior - Brasil (CAPES)/ ; 309514/2017-7//National Council for Scientific and Technological Development - CNPq/ ; },
mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Bacterial Load ; Biodiversity ; Brazil ; Demography ; Ecosystem ; Fresh Water/*microbiology ; Geography ; Microbial Consortia/*physiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Species prevalence across the landscape is related to their local abundance, which is a result of deterministic and stochastic processes that select organisms capable of recolonizing sites where they were once extinct, a process known as the rescue effect. The occupancy-frequency distribution (OFD) describes these patterns and has been extensively used to understand organism's distribution but has been poorly tested on microorganisms. In order to test OFD on freshwater bacteria, we collected data from 60 shallow lakes distributed across a wide area in southeastern Brazil, to determine the bacterial operational taxonomic units (OTUs) that were present in all sites (core) and at only one site (satellite). Then, we analyzed the spatial abundance distributions of individual OTUs to understand the influence of local abundances on regional occupancy patterns. Finally, we tested the environmental factors that influenced occupancy and abundance. We found a significant bimodal OFD for freshwater bacteria using both OTUs (97% clustering) and amplicon sequence variants (ASVs, unique sequences), with 13 core OTUs and 1169 satellite OTUs, but only three core ASVs. Core organisms had a bimodal or gamma abundance distribution. The main driver of the core community was pH, while nutrients were key when the core community was excluded and the rest of the community (mild and satellite taxa) was considered. This study demonstrates the close relationship between local environmental conditions and the abundance and dispersion of microorganisms, which shapes their distribution across the landscape.},
}
@article {pmid32704052,
year = {2020},
author = {González-Ramos, S and Paz-García, M and Fernández-García, V and Portune, KJ and Acosta-Medina, EF and Sanz, Y and Castrillo, A and Martín-Sanz, P and Obregon, MJ and Boscá, L},
title = {NOD1 deficiency promotes an imbalance of thyroid hormones and microbiota homeostasis in mice fed high fat diet.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12317},
pmid = {32704052},
issn = {2045-2322},
mesh = {Adipocytes/metabolism ; Adipose Tissue, White/pathology ; Animals ; Biodiversity ; Body Weight ; *Diet, High-Fat ; Fatty Liver/pathology ; *Feeding Behavior ; *Gastrointestinal Microbiome ; Glucose Tolerance Test ; *Homeostasis ; Inflammation/pathology ; Intestines/pathology ; Lipids/chemistry ; Liver/pathology ; Metabolomics ; Mice, Inbred C57BL ; Mice, Knockout ; Nod1 Signaling Adaptor Protein/*deficiency/metabolism ; Obesity/blood/microbiology/pathology ; Thyroid Gland/pathology/physiopathology ; Thyroid Hormones/blood/*metabolism ; },
abstract = {The contribution of the nucleotide-binding oligomerization domain protein NOD1 to obesity has been investigated in mice fed a high fat diet (HFD). Absence of NOD1 accelerates obesity as early as 2 weeks after feeding a HFD. The obesity was due to increases in abdominal and inguinal adipose tissues. Analysis of the resting energy expenditure showed an impaired function in NOD1-deficient animals, compatible with an alteration in thyroid hormone homeostasis. Interestingly, free thyroidal T4 increased in NOD1-deficient mice fed a HFD and the expression levels of UCP1 in brown adipose tissue were significantly lower in NOD1-deficient mice than in the wild type animals eating a HFD, thus contributing to the observed adiposity in NOD1-deficient mice. Feeding a HFD resulted in an alteration of the proinflammatory profile of these animals, with an increase in the infiltration of inflammatory cells in the liver and in the white adipose tissue, and an elevation of the circulating levels of TNF-α. In addition, alterations in the gut microbiota in NOD1-deficient mice correlate with increased vulnerability of their ecosystem to the HFD challenge and affect the immune-metabolic phenotype of obese mice. Together, the data are compatible with a protective function of NOD1 against low-grade inflammation and obesity under nutritional conditions enriched in saturated lipids. Moreover, one of the key players of this early obesity onset is a dysregulation in the metabolism and release of thyroid hormones leading to reduced energy expenditure, which represents a new role for these hormones in the metabolic actions controlled by NOD1.},
}
@article {pmid32702578,
year = {2020},
author = {Zhang, Q and Chen, X and Zhang, Z and Luo, W and Wu, H and Zhang, L and Zhang, X and Zhao, T},
title = {Performance and microbial ecology of a novel moving bed biofilm reactor process inoculated with heterotrophic nitrification-aerobic denitrification bacteria for high ammonia nitrogen wastewater treatment.},
journal = {Bioresource technology},
volume = {315},
number = {},
pages = {123813},
doi = {10.1016/j.biortech.2020.123813},
pmid = {32702578},
issn = {1873-2976},
mesh = {Ammonia ; Biofilms ; Bioreactors ; Denitrification ; *Nitrification ; Nitrogen/analysis ; *Wastewater ; },
abstract = {To overcome long start-up time, poor ammonia tolerance and removal performance of traditional moving bed biofilm reactor (MBBR) inoculated with activated sludge for high-ammonia wastewater treatment, a novel MBBR based on heterotrophic nitrification-aerobic denitrification (HN-AD) was proposed. Start-up of MBBR was firstly performed via inoculated with HN-AD bacteria. Start-up time was shortened from 39 d to 15 d, NH4[+] tolerance was enhanced from 200 mg/L to 1000 mg/L, and TN removal was increased from 30.4% to 80.7%. The carrier types and NH4[+] concentration had significant effects on nitrogen removal and microbial ecology. When the NH4[+] concentration was increased to 900 mg/L in MBBR using polyvinyl alcohol gel as carrier, the TN removal, the abundance of HN-AD bacteria Acinetobacter, Pseudomonas and Paracoccus, which played a key role in TN removal and ammonia tolerance, and the abundance of genes related to nitrogen removal were much higher than those of MBBR using kaldness.},
}
@article {pmid32699992,
year = {2020},
author = {Hopkins, JR and Huffman, JM and Platt, WJ and Sikes, BA},
title = {Frequent fire slows microbial decomposition of newly deposited fine fuels in a pyrophilic ecosystem.},
journal = {Oecologia},
volume = {193},
number = {3},
pages = {631-643},
doi = {10.1007/s00442-020-04699-5},
pmid = {32699992},
issn = {1432-1939},
support = {DEB-1557000//National Science Foundation/ ; DEB-1556837//National Science Foundation/ ; 1451148//National Science Foundation/ ; },
mesh = {Ecosystem ; *Fires ; *Pinus ; Soil ; },
abstract = {Frequent fires maintain nearly 50% of terrestrial ecosystems, and drive ecosystem changes that govern future fires. Since fires are dependent on available plant or fine fuels, ecosystem processes that alter fine fuel loads like microbial decomposition are particularly important and could modify future fires. We hypothesized that variation in short-term fire history would influence fuel dynamics in such ecosystems. We predicted that frequent fires within a short-time period would slow microbial decomposition of new fine fuels. We expected that fire effects would differ based on dominant substrates and that fire history would also alter soil nutrient availability, indirectly slowing decomposition. We measured decomposition of newly deposited fine fuels in a Longleaf pine savanna, comparing plots that burned 0, 1, 2, or 3 times between 2014 and 2016, and which were located in either close proximity to or away from overstory pines (Longleaf pine, Pinus palustris). Microbial decomposition was slower in plots near longleaf pines and, as the numbers of fires increased, decomposition slowed. We then used structural equation modeling to assess pathways for these effects (number of fires, 2016 fuel/fire characteristics, and soil chemistry). Increased fire frequency was directly associated with decreased microbial decomposition. While increased fires decreased nutrient availability, changes in nutrients were not associated with decomposition. Our findings indicate that increasing numbers of fires over short-time intervals can slow microbial decomposition of newly deposited fine fuels. This could favor fine fuel accumulation and drive positive feedbacks on future fires.},
}
@article {pmid32698767,
year = {2020},
author = {Taparia, T and Krijger, M and Haynes, E and Elphinstone, JG and Noble, R and van der Wolf, J},
title = {Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {505},
pmid = {32698767},
issn = {1471-2164},
support = {KV1509-050//Dutch Ministry of Economic Affairs (NL)/ ; M063//Agriculture and Horticulture Development Board/ ; },
mesh = {*Agaricus/genetics ; Belgium ; Europe ; Phylogeny ; Pseudomonas/genetics ; United Kingdom ; },
abstract = {BACKGROUND: Bacterial blotch is a group of economically important diseases affecting the cultivation of common button mushroom, Agaricus bisporus. Despite being studied for more than a century, the identity and nomenclature of blotch-causing Pseudomonas species is still unclear. This study aims to molecularly characterize the phylogenetic and phenotypic diversity of blotch pathogens in Western Europe.<br><br>METHODS: In this study, blotched mushrooms were sampled from farms across the Netherlands, United Kingdom and Belgium. Bacteria were isolated from symptomatic cap tissue and tested in pathogenicity assays on fresh caps and in pots. Whole genome sequences of pathogenic and non-pathogenic isolates were used to establish phylogeny via multi-locus sequence alignment (MLSA), average nucleotide identity (ANI) and in-silico DNA:DNA hybridization (DDH) analyses.<br><br>RESULTS: The known pathogens "Pseudomonas gingeri", P. tolaasii, "P. reactans" and P. costantinii were recovered from blotched mushroom caps. Seven novel pathogens were also identified, namely, P. yamanorum, P. edaphica, P. salomonii and strains that clustered with Pseudomonas sp. NC02 in one genomic species, and three non-pseudomonads, i.e. Serratia liquefaciens, S. proteamaculans and a Pantoea sp. Insights on the pathogenicity and symptom severity of these blotch pathogens were also generated.<br><br>CONCLUSION: A detailed overview of genetic and regional diversity and the virulence of blotch pathogens in Western Europe, was obtained via the phylogenetic and phenotypic analyses. This information has implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management.},
}
@article {pmid32697840,
year = {2020},
author = {Cary, C and Cowan, DA and McMinn, A and Häggblom, MM},
title = {Editorial: Thematic issue on polar and alpine microbiology.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {8},
pages = {},
doi = {10.1093/femsec/fiaa136},
pmid = {32697840},
issn = {1574-6941},
}
@article {pmid32696567,
year = {2020},
author = {Kuranaga, T and Matsuda, K and Takaoka, M and Tachikawa, C and Sano, A and Itoh, K and Enomoto, A and Fujita, K and Abe, I and Wakimoto, T},
title = {Total Synthesis and Structural Revision of Kasumigamide, and Identification of a New Analogue.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {21},
number = {23},
pages = {3329-3332},
doi = {10.1002/cbic.202000409},
pmid = {32696567},
issn = {1439-7633},
mesh = {Biological Products/*analysis/*chemical synthesis/metabolism ; Molecular Conformation ; Oligopeptides/*analysis/biosynthesis/*chemical synthesis ; },
abstract = {Kasumigamide is an antialgal hybrid peptide-polyketide isolated from the freshwater cyanobacterium Microcystis aeruginosa (NIES-87). The biosynthetic gene cluster was identified from not only the cyanobacterium but also Candidatus "Entotheonella", associated with the Japanese marine sponge Discodermia calyx. Therefore, kasumigamide is considered to play a key role in microbial ecology, regardless of the terrestrial and marine habitats. We now report synthetic studies on this intriguing natural product that have led to a structural revision and the first total synthesis. During this study, a new analogue, deoxykasumigamide, was also isolated and structurally validated. This study confirmed the presence of the unusual pathway in the biosynthesis of a hybrid peptide-polyketide natural product.},
}
@article {pmid32696239,
year = {2021},
author = {Cassán, F and López, G and Nievas, S and Coniglio, A and Torres, D and Donadio, F and Molina, R and Mora, V},
title = {What Do We Know About the Publications Related with Azospirillum? A Metadata Analysis.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {278-281},
pmid = {32696239},
issn = {1432-184X},
support = {PICT-2017-0572//FONCyT-MINCYT/ ; },
mesh = {Azospirillum/classification/*metabolism ; Host Microbial Interactions/*physiology ; Plant Development ; *Plant Growth Regulators ; Plant Roots/microbiology ; Plants/*microbiology ; },
abstract = {Azospirillum is one of the most successful plant growth-promoting bacteria (PGPB) genera and it is considered a study model for plant-bacteria interactions. Because of that, a wide broad of topics has been boarded and discussed in a significant number of publications in the last four decades. Using the Scopus® database, we conducted a bibliographic search in order to analyze the number and type of publications, the authors responsible of these contributions, and the origin of the researchers, as well as the keywords and journals selected by the authors, among other related characteristics, with the aim to understand some less addressed details about the work done with Azospirillum worldwide since its discovery in 1925. Despite that the largest numbers of publications about this bacterium were obtained between the 1970 and 1980s, there is still a linear increase tendency in the number of published works. Understanding the mechanisms involved in the ability of these bacteria to promote growth in a wide broad of plant species under both laboratory and field conditions has been a preferential target for these published articles. This tendency could be considered a cause or consequence of the current increase in the number of commercial products formulated with Azospirillum around the world and a catalyzer for the increase of published articles along time.},
}
@article {pmid32694129,
year = {2020},
author = {Wang, S and Xiong, W and Wang, Y and Nie, Y and Wu, Q and Xu, Y and Geisen, S},
title = {Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System.},
journal = {mSystems},
volume = {5},
number = {4},
pages = {},
pmid = {32694129},
issn = {2379-5077},
abstract = {We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.IMPORTANCE We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.},
}
@article {pmid32694124,
year = {2020},
author = {Sieradzki, ET and Koch, BJ and Greenlon, A and Sachdeva, R and Malmstrom, RR and Mau, RL and Blazewicz, SJ and Firestone, MK and Hofmockel, KS and Schwartz, E and Hungate, BA and Pett-Ridge, J},
title = {Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design.},
journal = {mSystems},
volume = {5},
number = {4},
pages = {},
pmid = {32694124},
issn = {2379-5077},
abstract = {Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets-from soil and seawater microbiomes-to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon's abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.IMPORTANCE One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about their genomic content and potential functions but may not reflect an organism's activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of community interactions but often fail to link the two. Quantitative stable isotope probing (qSIP) is a method that can link the identity and functional activity of specific microbes within a naturally occurring community. Here, we explore how the resolution of density gradient fractionation affects the error and precision of qSIP results, how they may be improved via additional experimental replication, and discuss cost-benefit balanced scenarios for SIP experimental design.},
}
@article {pmid32691599,
year = {2020},
author = {Elsayed, SS and Genta-Jouve, G and Carrión, VJ and Nibbering, PH and Siegler, MA and de Boer, W and Hankemeier, T and van Wezel, GP},
title = {Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus.},
journal = {The Journal of organic chemistry},
volume = {85},
number = {16},
pages = {10648-10657},
pmid = {32691599},
issn = {1520-6904},
mesh = {Anti-Bacterial Agents ; *Polyketides ; *Streptomyces/genetics ; *Streptomycetaceae ; },
abstract = {More than half of all antibiotics and many other bioactive compounds are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have been described for its sister genus Streptacidiphilus within Streptomycetaceae. Here, we describe an unusual family of spirotetronate polyketides, called streptaspironates, which are produced by Streptacidiphilus sp. P02-A3a, isolated from decaying pinewood. The characteristic structural and genetic features delineating spirotetronate polyketides could be identified in streptaspironates A (1) and B (2). Conversely, streptaspironate C (3) showed an unprecedented tetronate-less macrocycle-less structure, which was likely produced from an incomplete polyketide chain, together with an intriguing decarboxylation step, indicating a hypervariable biosynthetic machinery. Taken together, our work enriches the chemical space of actinobacterial natural products and shows the potential of Streptacidiphilus as producers of new compounds.},
}
@article {pmid32690378,
year = {2020},
author = {Zhang, X and Fan, L and Wu, J and Xu, H and Leung, WY and Fu, K and Wu, J and Liu, K and Man, K and Yang, X and Han, J and Ren, J and Yu, J},
title = {Erratum to: "Macrophage p38 alpha promotes nutritional steatohepatitis through M1 polarization (J Hepatol 2019; 71(1):163-174)".},
journal = {Journal of hepatology},
volume = {73},
number = {3},
pages = {742-743},
doi = {10.1016/j.jhep.2020.06.019},
pmid = {32690378},
issn = {1600-0641},
}
@article {pmid32688217,
year = {2020},
author = {Dey, P and Olmstead, BD and Sasaki, GY and Vodovotz, Y and Yu, Z and Bruno, RS},
title = {Epigallocatechin gallate but not catechin prevents nonalcoholic steatohepatitis in mice similar to green tea extract while differentially affecting the gut microbiota.},
journal = {The Journal of nutritional biochemistry},
volume = {84},
number = {},
pages = {108455},
doi = {10.1016/j.jnutbio.2020.108455},
pmid = {32688217},
issn = {1873-4847},
mesh = {Animals ; Catechin/*analogs &amp; derivatives/pharmacology/*therapeutic use ; Gastrointestinal Microbiome/*drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/microbiology/pathology/*prevention &amp; control ; Protective Agents/pharmacology/*therapeutic use ; *Tea/chemistry ; },
abstract = {Catechin-rich green tea extract (GTE) protects against nonalcoholic steatohepatitis (NASH) by alleviating gut-derived endotoxin translocation and hepatic Toll-like receptor-4 (TLR4)-nuclear factor κB (NFκB) inflammation. We hypothesized that intact GTE would attenuate NASH-associated responses along the gut-liver axis to a greater extent than purified (-)-epigallocatechin gallate (EGCG) or (+)-catechin (CAT). Male C57BL/6J mice were fed a low-fat diet, a high-fat (HF) diet, or the HF diet with 2% GTE, 0.3% EGCG or 0.3% CAT for 8 weeks prior to assessing NASH relative to endotoxemia, hepatic and intestinal inflammation, intestinal tight junction proteins (TJPs) and gut microbial ecology. GTE prevented HF-induced obesity to a greater extent than EGCG and CAT, whereas GTE and EGCG more favorably attenuated insulin resistance. GTE, EGCG and CAT similarly attenuated serum alanine aminotransferase and serum endotoxin, but only GTE and EGCG fully alleviated HF-induced NASH. However, hepatic TLR4/NFκB inflammatory responses that were otherwise increased in HF mice were similarly attenuated by GTE, EGCG and CAT. Each treatment also similarly prevented the HF-induced loss in expression of intestinal TJPs and hypoxia inducible factor-1α and the otherwise increased levels of ileal and colonic TNFα mRNA and fecal calprotectin protein concentrations. Gut microbial diversity that was otherwise lowered in HF mice was maintained by GTE and CAT only. Further, microbial metabolic functions were more similar between GTE and CAT. Collectively, GTE catechins similarly protect against endotoxin-TLR4-NFκB inflammation in NASH, but EGCG and CAT exert differential prebiotic and antimicrobial activities suggesting that catechin-mediated shifts in microbiota composition are not entirely responsible for their benefits along the gut-liver axis.},
}
@article {pmid32688002,
year = {2020},
author = {Zhou, WH and Wang, YT and Lian, ZH and Yang, TT and Zeng, QW and Feng, SW and Fang, Z and Shu, WS and Huang, LN and Ye, ZH and Liao, B and Li, JT},
title = {Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond.},
journal = {The Science of the total environment},
volume = {744},
number = {},
pages = {140793},
doi = {10.1016/j.scitotenv.2020.140793},
pmid = {32688002},
issn = {1879-1026},
mesh = {Biodegradation, Environmental ; *Microbiota ; Ponds ; Soil ; Soil Microbiology ; Soil Pollutants/*analysis ; },
abstract = {Owing to its sustainability and low cost, direct revegetation (DR) has been considered a promising alternative to capped revegetation (CR) for dealing with the serious environmental problem derived from various types of mine wastelands that are widespread in the world. However, a direct comparison of the performance of these two revegetation approaches for reclamation of extremely acidic mine wastelands and the underlying mechanisms is still lacking. To bridge this critical knowledge gap, we established 5000 m[2] of vegetation on a highly acidified (pH < 3) Pb/Zn mine tailings pond employing both CR and DR schemes (2500 m[2] for each scheme). We then profiled the structure, ecological network and function of soil microbial communities associated with two dominant plant species of the vegetations via high-throughput sequencing. Our results showed that CR and DR achieved a vegetation coverage of 59.7% and 90.5% within two years, respectively. This pattern was accompanied by higher concentrations of plant nutrients and lower acidification potentials in topsoils of the rhizospheres of the vegetation established by DR compared to those of CR. Revegetation approach, rather than plant identity, mostly affected the structure, ecological network and function of soil microbial community in the mine tailings pond. Rhizosphere soils of the vegetation established by DR generally had higher microbial diversity, higher relative abundances of dominant microbial phyla (e.g. Nitrospirae) that can aid plant uptake of nutrients, more complicated microbial interactive networks and more microbial genes responsible for nutrient cycling than those by CR. As the first report on a direct comparison of CR and DR schemes for reclamation of an extremely acidic mine wasteland, our study has important implications for not only the understanding of microbial ecology in revegetated mine wastelands but also the further development of sustainable revegetation schemes.},
}
@article {pmid32686214,
year = {2021},
author = {Liu, D and Howell, K},
title = {Community succession of the grapevine fungal microbiome in the annual growth cycle.},
journal = {Environmental microbiology},
volume = {23},
number = {4},
pages = {1842-1857},
doi = {10.1111/1462-2920.15172},
pmid = {32686214},
issn = {1462-2920},
mesh = {Fungi/classification/*physiology ; *Mycobiome ; *Vitis/microbiology ; *Wine ; },
abstract = {Microbial ecology and activity in wine production influences grapevine health and productivity, conversion of sugar to ethanol during fermentation, wine aroma, wine quality and distinctiveness. Fungi in the vineyard ecosystem are not well described. Here, we characterized the spatial and temporal dynamics of fungal communities associated with the grapevine (grapes, flowers, leaves, and roots) and soils over an annual growth cycle in two vineyards to investigate the influences of grape habitat, plant developmental stage (flowering, fruit set, veraison, and harvest), vineyards, and climatic conditions. Fungi were influenced by both the grapevine habitat and plant development stage. The core microbiome was prioritized over space and time, and the identified core members drove seasonal community succession. The developmental stage of veraison, where the grapes undergo a dramatic change in metabolism and start accumulating sugar, coincided with a distinct shift in fungal communities. Co-occurrence networks showed strong correlations between the plant microbiome, the soil microbiome, and weather indices. Our study describes the complex ecological dynamics that occur in microbial assemblages over a growing season and highlight succession of the core community in vineyards.},
}
@article {pmid32685479,
year = {2020},
author = {Li, Z and Ni, M and Yu, H and Wang, L and Zhou, X and Chen, T and Liu, G and Gao, Y},
title = {Gut Microbiota and Liver Fibrosis: One Potential Biomarker for Predicting Liver Fibrosis.},
journal = {BioMed research international},
volume = {2020},
number = {},
pages = {3905130},
pmid = {32685479},
issn = {2314-6141},
mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Biomarkers/analysis ; Carbon Tetrachloride/toxicity ; Disease Models, Animal ; Feces/microbiology ; *Gastrointestinal Microbiome ; Liver Cirrhosis/chemically induced/*microbiology/*pathology ; Male ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; Rats ; Rats, Wistar ; },
abstract = {PURPOSE: To investigate the relationship between gut microbiota and liver fibrosis and establish a microbiota biomarker for detecting and staging liver fibrosis.<br><br>METHODS: 131 Wistar rats were used in our study, and liver fibrosis was induced by carbon tetrachloride. Stool samples were collected within 72 hours after the last administration. The V4 regions of 16S rRNA gene were amplified. The sequencing data was processed using the Quantitative Insights Into Microbial Ecology (QIIME version 1.9). The diversity, principal coordinate analysis (PCoA), nonmetric multidimensional scaling (NMDS), and linear discriminant analysis (LDA) effect size (LEfSe) were performed. Random-Forest classification was performed for discriminating the samples from different groups. Microbial function was assessed using the PICRUST.<br><br>RESULTS: The Simpson in the control group was lower than that in the liver fibrosis group (p = 0.048) and differed significantly among different fibrosis stages (p = 0.047). The Chao1 index in the control group was higher than that in the liver fibrosis group (p < 0.001). NMDS analysis showed a marked difference between the control and liver fibrosis groups (p < 0.001). PCoA analysis indicated the different community composition between the control and liver fibrosis groups with variances of PC1 13.76% and PC2 5.89% and between different liver fibrosis stages with variances of PC1 10.51% and PC2 7.78%. LEfSe analysis showed alteration of gut microbiota in the liver fibrosis group. Biomarkers obtained from Random-Forest classification showed excellent diagnostic accuracy in prediction of liver fibrosis with AUROCs of 0.99. The AUROCs were 0.77~0.84 in prediction of stage F4. There were six increased and 17 decreased metabolic functions in the liver fibrosis group and 6 metabolic functions significantly differed among four liver fibrosis stages.<br><br>CONCLUSION: Gut microbiota is a potential biomarker for detecting and staging liver fibrosis with high diagnostic accuracies.},
}
@article {pmid32681284,
year = {2021},
author = {Varasteh, T and Hamerski, L and Tschoeke, D and Lima, AS and Garcia, G and Cosenza, CAN and Thompson, C and Thompson, F},
title = {Conserved Pigment Profiles in Phylogenetically Diverse Symbiotic Bacteria Associated with the Corals Montastraea cavernosa and Mussismilia braziliensis.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {267-277},
pmid = {32681284},
issn = {1432-184X},
mesh = {Animals ; Anthozoa/*microbiology ; Antioxidants/*metabolism ; Bacteroidetes/genetics/isolation &amp; purification/*metabolism ; Brazil ; Carotenoids/metabolism ; Catalase/biosynthesis ; DNA, Bacterial/genetics ; Genome, Bacterial/genetics ; Oxidoreductases/biosynthesis ; Paracoccus/genetics/isolation &amp; purification/*metabolism ; Peroxidase/biosynthesis ; Pigments, Biological/genetics/*metabolism ; Pseudoalteromonas/genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; },
abstract = {Pigmented bacterial symbionts play major roles in the health of coral holobionts. However, there is scarce knowledge on the diversity of these microbes for several coral species. To gain further insights into holobiont health, pigmented bacterial isolates of Fabibacter pacificus (Bacteroidetes; n = 4), Paracoccus marcusii (Alphaproteobacteria; n = 1), and Pseudoalteromonas shioyasakiensis (Gammaproteobacteria; n = 1) were obtained from the corals Mussismilia braziliensis and Montastraea cavernosa in Abrolhos Bank, Brazil. Cultures of these bacterial symbionts produced strong antioxidant activity (catalase, peroxidase, and oxidase). To explore these bacterial isolates further, we identified their major pigments by HPLC and mass spectrometry. The six phylogenetically diverse symbionts had similar pigment patterns and produced myxol and keto-carotene. In addition, similar carotenoid gene clusters were confirmed in the whole genome sequences of these symbionts, which reinforce their antioxidant potential. This study highlights the possible roles of bacterial symbionts in Montastraea and Mussismilia holobionts.},
}
@article {pmid32681144,
year = {2020},
author = {Hylling, O and Carstens, AB and Kot, W and Hansen, M and Neve, H and Franz, CMAP and Johansen, A and Ellegaard-Jensen, L and Hansen, LH},
title = {Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {11879},
pmid = {32681144},
issn = {2045-2322},
mesh = {Bacteriophages/*classification/genetics/isolation &amp; purification/ultrastructure ; Ecology ; Gene Order ; Genome, Viral ; Genomics/methods ; Groundwater/*microbiology ; Phylogeny ; Virion ; *Water Microbiology ; },
abstract = {Although bacteriophages are central entities in bacterial ecology and population dynamics, there is currently no literature on the genomes of bacteriophages isolated from groundwater. Using a collection of bacterial isolates from an aquifer as hosts, this study isolated, sequenced and characterised two bacteriophages native to the groundwater reservoir. Host phylogenetic analyses revealed that the phages targeted B. mycoides and a novel Pseudomonas species. These results suggest that both bacteriophages represent new genera, highlighting that groundwater reservoirs, and probably other subsurface environments as well, are underexplored biotopes in terms of the presence and ecology of bacteriophages.},
}
@article {pmid32680791,
year = {2020},
author = {Daisley, BA and Chmiel, JA and Pitek, AP and Thompson, GJ and Reid, G},
title = {Missing Microbes in Bees: How Systematic Depletion of Key Symbionts Erodes Immunity.},
journal = {Trends in microbiology},
volume = {28},
number = {12},
pages = {1010-1021},
doi = {10.1016/j.tim.2020.06.006},
pmid = {32680791},
issn = {1878-4380},
mesh = {Animals ; Bees/*immunology/*microbiology ; Disease Resistance/physiology ; Ecology ; Host Microbial Interactions/*physiology ; *Immunity ; Lactobacillus ; Microbiota ; Nutrients/deficiency ; Pesticides/pharmacology ; Probiotics ; Stress, Physiological ; Symbiosis ; },
abstract = {Pesticide exposure, infectious disease, and nutritional stress contribute to honey bee mortality and a high rate of colony loss. This realization has fueled a decades-long investigation into the single and combined effects of each stressor and their overall bearing on insect physiology. However, one element largely missing from this research effort has been the evaluation of underlying microbial communities in resisting environmental stressors and their influence on host immunity and disease tolerance. In humans, multigenerational bombardment by antibiotics is linked with many contemporary diseases. Here, we draw a parallel conclusion for the case in honey bees and suggest that chronic exposure to antimicrobial xenobiotics can systematically deplete honey bees of their microbes and hamper cross-generational preservation of host-adapted symbionts that are crucial to health.},
}
@article {pmid32679495,
year = {2020},
author = {Moopantakath, J and Imchen, M and Siddhardha, B and Kumavath, R},
title = {16s rRNA metagenomic analysis reveals predominance of Crtl and CruF genes in Arabian Sea coast of India.},
journal = {The Science of the total environment},
volume = {743},
number = {},
pages = {140699},
doi = {10.1016/j.scitotenv.2020.140699},
pmid = {32679495},
issn = {1879-1026},
mesh = {Archaea/*genetics ; Bacteria/genetics ; Geologic Sediments ; India ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.},
}
@article {pmid32678322,
year = {2020},
author = {Li, L and Wang, S and Wang, H and Sahu, SK and Marin, B and Li, H and Xu, Y and Liang, H and Li, Z and Cheng, S and Reder, T and Çebi, Z and Wittek, S and Petersen, M and Melkonian, B and Du, H and Yang, H and Wang, J and Wong, GK and Xu, X and Liu, X and Van de Peer, Y and Melkonian, M and Liu, H},
title = {Author Correction: The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.},
journal = {Nature ecology &amp; evolution},
volume = {4},
number = {9},
pages = {1280},
pmid = {32678322},
issn = {2397-334X},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32677880,
year = {2020},
author = {Zhang, Q and Xu, J and Warren, A and Yang, R and Shen, Z and Yi, Z},
title = {Assessing the utility of Hsp90 gene for inferring evolutionary relationships within the ciliate subclass Hypotricha (Protista, Ciliophora).},
journal = {BMC evolutionary biology},
volume = {20},
number = {1},
pages = {86},
pmid = {32677880},
issn = {1471-2148},
support = {31772440//National Natural Science Foundation of China/International ; 31970486//National Natural Science Foundation of China/International ; 31672279//National Natural Science Foundation of China/International ; 2018SDKJ0406-1//Marine S&amp;T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao)/International ; GDOE(2019)A23//Guangdong MEPP Fund/International ; },
mesh = {Amino Acid Sequence ; Base Sequence ; Ciliophora/classification/*genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Databases, Protein ; *Evolution, Molecular ; HSP90 Heat-Shock Proteins/chemistry/*genetics ; Phylogeny ; },
abstract = {BACKGROUND: Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates for inferring phylogenies within this group. In this study, we investigate the utility of the heat-shock protein 90 gene (Hsp90) as a marker for inferring phylogenetic relationships among hypotrich ciliates.<br><br>RESULTS: A total of 87 novel Hsp90 gene sequences of 10 hypotrich species were generated. Of these, 85 were distinct sequences. Phylogenetic analyses based on these data showed that: (1) the Hsp90 gene amino acid trees are comparable to the small subunit rDNA tree for recovering phylogenetic relationships at the rank of class, but lack sufficient phylogenetic signal for inferring evolutionary relationships at the genus level; (2) Hsp90 gene paralogs are recent and therefore unlikely to pose a significant problem for recovering hypotrich clades; (3) definitions of some hypotrich orders and families need to be revised as their monophylies are not supported by various gene markers; (4) The order Sporadotrichida is paraphyletic, but the monophyly of the "core" Urostylida is supported; (5) both the subfamily Oxytrichinae and the genus Urosoma seem to be non-monophyletic, but monophyly of Urosoma is not rejected by AU tests.<br><br>CONCLUSIONS: Our results for the first time demonstrate that the Hsp90 gene is comparable to SSU rDNA for recovering phylogenetic relationships at the rank of class, and its paralogs are unlikely to pose a significant problem for recovering hypotrich clades. This study shows the value of careful gene marker selection for phylogenomic analyses of ciliates.},
}
@article {pmid32673982,
year = {2020},
author = {Ali, M and Yue, D},
title = {Population dynamics of microbial species under high and low ammonia nitrogen in the alternate layer bioreactor landfill (ALBL) approach.},
journal = {Bioresource technology},
volume = {315},
number = {},
pages = {123787},
doi = {10.1016/j.biortech.2020.123787},
pmid = {32673982},
issn = {1873-2976},
mesh = {*Ammonia ; Bioreactors ; Ecosystem ; Methane ; Nitrogen ; Population Dynamics ; *Refuse Disposal ; Waste Disposal Facilities ; },
abstract = {Anaerobic landfill process is still believed to be a complex ecosystem due to the lack of knowledge on the functional activities of microbial species. This research sought to introduce a novel landfill bioreactor, named here as the alternate layer bioreactor landfill (ALBL) of fresh MSW (FW) and stabilized waste (CT) to avoid inhibitory conditions for the microbial species in anaerobic landfill. The stabilized waste layer in the bottom of landfill cell significantly changed microbial ecology of fresh MSW which in turn reduced the concentrations of NH4-N (29-31%) and VFAs (33-38%) in the ALBL approach, compared to fresh MSW disposal in sanitary landfill. The reduction of NH4-N favored early onset of methanogenesis within 6 weeks and methane (CH4) content of landfill gas increased from 11% to 40-50% (v/v), owing to the coexistence of Methanosarcinales (36-50%) and Methanomicrobiales (26-28%) archaea. The acetoclastic methanogenesis was achieved by reducing NH4-N toxicity in the ALBL.},
}
@article {pmid32670501,
year = {2020},
author = {Khot, V and Strous, M and Hawley, AK},
title = {Computational approaches in viral ecology.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {1605-1612},
pmid = {32670501},
issn = {2001-0370},
abstract = {Dynamic virus-host interactions play a critical role in regulating microbial community structure and function. Yet for decades prior to the genomics era, viruses were largely overlooked in microbial ecology research, as only low-throughput culture-based methods of discovering viruses were available. With the advent of metagenomics, culture-independent techniques have provided exciting opportunities to discover and study new viruses. Here, we review recently developed computational methods for identifying viral sequences, exploring viral diversity in environmental samples, and predicting hosts from metagenomic sequence data. Methods to analyze viruses in silico utilize unconventional approaches to tackle challenges unique to viruses, such as vast diversity, mosaic viral genomes, and the lack of universal marker genes. As the field of viral ecology expands exponentially, computational advances have become increasingly important to gain insight into the role viruses in diverse habitats.},
}
@article {pmid32666305,
year = {2020},
author = {Castelli, L and Branchiccela, B and Garrido, M and Invernizzi, C and Porrini, M and Romero, H and Santos, E and Zunino, P and Antúnez, K},
title = {Impact of Nutritional Stress on Honeybee Gut Microbiota, Immunity, and Nosema ceranae Infection.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {908-919},
doi = {10.1007/s00248-020-01538-1},
pmid = {32666305},
issn = {1432-184X},
support = {CSIC 6406//Comisi&#xf3;n Sectorial de Investigaci&#xf3;n Cient&#xed;fica (UY)/ ; POS_NAC_2013_1_12228//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; },
mesh = {Animal Nutritional Physiological Phenomena/immunology/physiology ; Animals ; Bees/*immunology/*microbiology ; *Gastrointestinal Microbiome ; *Immunity, Innate ; Nosema/*physiology ; },
abstract = {Honeybees are important pollinators, having an essential role in the ecology of natural and agricultural environments. Honeybee colony losses episodes reported worldwide and have been associated with different pests and pathogens, pesticide exposure, and nutritional stress. This nutritional stress is related to the increase in monoculture areas which leads to a reduction of pollen availability and diversity. In this study, we examined whether nutritional stress affects honeybee gut microbiota, bee immunity, and infection by Nosema ceranae, under laboratory conditions. Consumption of Eucalyptus grandis pollen was used as a nutritionally poor-quality diet to study nutritional stress, in contraposition to the consumption of polyfloral pollen. Honeybees feed with Eucalyptus grandis pollen showed a lower abundance of Lactobacillus mellifer and Lactobacillus apis (Firm-4 and Firm-5, respectively) and Bifidobacterium spp. and a higher abundance of Bartonella apis, than honeybees fed with polyfloral pollen. Besides the impact of nutritional stress on honeybee microbiota, it also decreased the expression levels of vitellogenin and genes associated to immunity (glucose oxidase, hymenoptaecin and lysozyme). Finally, Eucalyptus grandis pollen favored the multiplication of Nosema ceranae. These results show that nutritional stress impacts the honeybee gut microbiota, having consequences on honeybee immunity and pathogen development. Those results may be useful to understand the influence of modern agriculture on honeybee health.},
}
@article {pmid32666084,
year = {2020},
author = {Zhang, T and Fukuda, K and Topp, E and Zhu, YG and Smalla, K and Tiedje, JM and Larsson, DGJ},
title = {Editorial: The Environmental Dimension of Antibiotic Resistance.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {8},
pages = {},
doi = {10.1093/femsec/fiaa130},
pmid = {32666084},
issn = {1574-6941},
}
@article {pmid32664604,
year = {2020},
author = {Marzorati, M and Abbeele, PVD and Bubeck, SS and Bayne, T and Krishnan, K and Young, A and Mehta, D and DeSouza, A},
title = {Bacillus subtilis HU58 and Bacillus coagulans SC208 Probiotics Reduced the Effects of Antibiotic-Induced Gut Microbiome Dysbiosis in An M-SHIME[®] Model.},
journal = {Microorganisms},
volume = {8},
number = {7},
pages = {},
pmid = {32664604},
issn = {2076-2607},
abstract = {Benefits associated with probiotic use have been reported; however, the mechanisms behind these benefits are poorly understood. The effects of a probiotic formulation (MegaDuo™) containing Bacillus coagulans SC208 and Bacillus subtilis HU58 on intestinal permeability and immune markers was assessed using a combination of the in vitro gut model, the mucosal simulator of the human intestinal microbial ecosystem (M-SHIME[®]), and an in vitro inflammatory bowel disease-like Caco-2/THP1 co-culture model in both healthy and antibiotic-induced dysbiosis conditions. Established M-SHIME[®] proximal colon vessels were treated with/without clindamycin (1 week) and then with/without daily MegaDuo™ treatment (2 weeks). The mucosal and luminal microbial communities were sampled weekly. Suspensions were removed from the proximal colon vessels after 1 and 2 weeks of MegaDuo™ treatment and added to the co-culture system. Transepithelial resistance (membrane barrier function), cytokine/chemokine release, and NFκB activity were then measured. Under conditions of antibiotic-induced dysbiosis, suspensions from MegaDuo™ treated vessels showed reduced gut membrane barrier damage and decreased levels of TNFα and IL-6 compared with suspensions from untreated vessels; no appreciable differences were observed under healthy conditions. MegaDuo™ treatment had no effect on NFκB activity of THP1-Blue™ cells. The potential benefits of MegaDuo™ treatment appeared most evident after 2 weeks of treatment.},
}
@article {pmid32661888,
year = {2020},
author = {Szczepańska, A and Kiewra, D and Plewa-Tutaj, K and Dyczko, D and Guz-Regner, K},
title = {Sensitivity of Ixodes ricinus (L., 1758) and Dermacentor reticulatus (Fabr., 1794) ticks to entomopathogenic fungi isolates: preliminary study.},
journal = {Parasitology research},
volume = {119},
number = {11},
pages = {3857-3861},
pmid = {32661888},
issn = {1432-1955},
mesh = {Animals ; Biological Assay ; Dermacentor/*microbiology ; Europe ; Female ; Fungi/*pathogenicity ; Ixodes/*microbiology ; Metarhizium/pathogenicity ; Pest Control, Biological ; Sensitivity and Specificity ; Survival Analysis ; },
abstract = {Entomopathogenic fungi of the genus Beauveria and Metarhizium play an important role in controlling the population of arthropods. However, the data on their effectiveness against ticks focus mainly on species that do not occur in Europe. The aim of the study was to assess the effectiveness of entomopathogenic fungi against two of the most important tick species in Europe: Ixodes ricinus and Dermacentor reticulatus. In our study, the majority of tested entomopathogenic fungi strains showed potential efficacy against both tick species; however, D. reticulatus was less susceptible in comparison to I. ricinus. The observed mortality of ticks was up to 100% by using all commercial strains as well as three out of nine of the environmental strains. Among all tested fungi, the most effective against both tick species was environmental strain Metarhizium anisopliae LO4(1) with LC50 values: 2.6 × 10[3] cfu/ml-5.7 × 10[5] cfu/ml. Botanigard proved to be more effective than MET52 with LC50 values: 6.8 × 10[3] cfu/ml-3.3 × 10[6] cfu/ml. The conducted bioassays indicate the potential possibility of using the environmental isolates of entomopathogenic fungi, as well as commercial strains in control of local populations of I. ricinus and D. reticulatus; however, the possibility of using them in vivo requires more research.},
}
@article {pmid32659564,
year = {2020},
author = {Ray, D and Leary, P and Livens, F and Gray, N and Morris, K and Law, KA and Fuller, AJ and Abrahamsen-Mills, L and Howe, J and Tierney, K and Muir, G and Law, GTW},
title = {Controls on anthropogenic radionuclide distribution in the Sellafield-impacted Eastern Irish Sea.},
journal = {The Science of the total environment},
volume = {743},
number = {},
pages = {140765},
doi = {10.1016/j.scitotenv.2020.140765},
pmid = {32659564},
issn = {1879-1026},
abstract = {Understanding anthropogenic radionuclide biogeochemistry and mobility in natural systems is key to improving the management of radioactively contaminated environments and radioactive wastes. Here, we describe the contemporary depth distribution and phase partitioning of [137]Cs, Pu, and [241]Am in two sediment cores taken from the Irish Sea (Site 1: the Irish Sea Mudpatch; Site 2: the Esk Estuary). Both sites are located ~10 km from the Sellafield nuclear site. Low-level aqueous radioactive waste has been discharged from the Sellafield site into the Irish Sea for >50 y. We compare the depth distribution of the radionuclides at each site to trends in sediment and porewater redox chemistry, using trace element abundance, microbial ecology, and sequential extractions, to better understand the relative importance of sediment biogeochemistry vs. physical controls on radionuclide distribution/post-depositional mobility in the sediments. We highlight that the distribution of [137]Cs, Pu, and [241]Am at both sites is largely controlled by physical mixing of the sediments, physical transport processes, and sediment accumulation. Interestingly, at the Esk Estuary, microbially-mediated redox processes (considered for Pu) do not appear to offer significant controls on Pu distribution, even over decadal timescales. We also highlight that the Irish Sea Mudpatch likely still acts as a source of historical pollution to other areas in the Irish Sea, despite ever decreasing levels of waste output from the Sellafield site.},
}
@article {pmid32658690,
year = {2020},
author = {Bai, X and Zhong, X and Guo, C and Gui, Y and Xu, H},
title = {Colonization dynamics of protozoan communities in marine bioassessment surveys using two modified sampling systems.},
journal = {Marine pollution bulletin},
volume = {157},
number = {},
pages = {111325},
doi = {10.1016/j.marpolbul.2020.111325},
pmid = {32658690},
issn = {1879-3363},
mesh = {Biodiversity ; China ; *Ciliophora ; Ecosystem ; Environmental Monitoring ; Surveys and Questionnaires ; },
abstract = {Colonization dynamics of protozoan communities were investigated at a depth of 1 m in the coastal waters of the Yellow Sea, northern China from May to June 2019, using modified glass slide (mGS) and modified polyurethane foam unit (mPFU) systems. The colonization process and growth curves of protozoa were well fitted to the MacArthur-Wilson and logistic models in both systems, respectively. However, they showed significant differences in both colonization dynamics and biodiversity/functional parameters between the mGS and mPFU systems. The H' (species diversity), the G (colonization rate), and Amax (maximum abundance) were higher, while the value of T90% (the time for reaching 90% equilibrium species number) was lower in the mGS system than those in the mPFU system. Multivariate analyses demonstrated that protozoa showed different models of colonization dynamics in both systems. The results suggest that the mGS system might be more effective than the mPFU system in marine bioassessment surveys.},
}
@article {pmid32656607,
year = {2021},
author = {Xie, XG and Zhao, YY and Yang, Y and Lu, F and Dai, CC},
title = {Endophytic Fungus Alleviates Soil Sickness in Peanut Crops by Improving the Carbon Metabolism and Rhizosphere Bacterial Diversity.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {49-61},
pmid = {32656607},
issn = {1432-184X},
support = {31870478//National Natural Science Foundation of China/ ; 17CXTD00014//Program for Jiangsu Excellent Scientific and Technological Innovation Team/ ; },
mesh = {Arachis ; Carbon ; Fungi ; Plant Roots ; *Rhizosphere ; *Soil ; Soil Microbiology ; },
abstract = {Endophytic fungi can profoundly affect host productivity, but the underlying mechanisms of these effects are only partly understood. As the most important regulators of plant-soil feedback, root exudates can easily cause soil sickness in continuous monoculture systems by reducing certain microbes in the rhizosphere. In this study, exudates from roots colonized by the endophytic fungus Phomopsis liquidambaris significantly increased rhizosphere bacterial abundance, soil respiration, microbial biomass and enzyme activities in a long-term continuously cropped peanut soil. Further analysis revealed that P. liquidambaris-colonized root exudates clearly altered the carbon metabolism and rhizosphere bacterial diversity, which were closely correlated with changes in soil chemical properties caused by the exudates from the colonized roots. Finally, a synthetic root exudate experiment further confirmed that the root exudates derived from P. liquidambaris colonization can indeed play an important role in promoting peanut growth. Therefore, these results show that this endophytic fungus could improve the carbon metabolism and rhizosphere bacterial community in long-term monoculture soils via exudates from colonized roots, which contribute to the alleviation of soil sickness.},
}
@article {pmid32656252,
year = {2020},
author = {Adhikari, B and Jun, SR and Kwon, YM and Kiess, AS and Adhikari, P},
title = {Effects of Housing Types on Cecal Microbiota of Two Different Strains of Laying Hens During the Late Production Phase.},
journal = {Frontiers in veterinary science},
volume = {7},
number = {},
pages = {331},
pmid = {32656252},
issn = {2297-1769},
abstract = {Due to animal welfare issues, European Union has banned the use of conventional cages (CC) and non-EU countries including the US are also under constant public pressure to restrict their use in egg production. Very limited information is available on the composition of the microbial community of hens raised in different housing environments. This study was conducted to determine the effects of CC and enriched colony cages (EC) on cecal microbiota of two commercial laying hen strains, Hy-Line W36 (W36) and Hy-Line Brown (HB) during the late production stage (53, 58, 67, and 72 weeks of age). Cecal microbiota was studied by analyzing 16S rRNA gene sequences with Quantitative Insights Into Microbial Ecology (QIIME) 2 ver. 2018.8. Differentially abundant taxa were identified by Linear discriminant analysis Effect Size (LEfSe) analysis (P < 0.05, LDA score > 2.0). At phylum level, Actinobacteria was significantly enriched in W36 at all time points while Synergistetes (53 weeks), Spirochaetes (58 weeks), and Synergistetes and Spirochaetes (67 weeks) were significantly higher in HB. At genus level, Bifidobacterium (at all time points) and butyric acid producing genera such as Butyricicoccus and Subdoligranulum (58 and 72 weeks) were significantly higher in W36 as compared to HB. Moreover, Proteobacteria (72 weeks) and its associated genus Campylobacter (67 and 72 weeks) were significantly enriched in EC as compared to CC. Alpha diversity was significantly higher in HB (at all time points) and in EC (67 weeks) as compared to W36 and CC, respectively. Similarly, there was a significant difference in community structure (beta diversity) between W36 and HB (all time points) as well as between EC and CC (67 weeks). The effect of housing and strains was not only seen at the bacterial composition and structure but also reflected at their functional level. Notably, KEGG metabolic pathways predicted to be involved in carbohydrates degradation and amino acids biosynthesis by PICRUSt analysis were significantly different between W36 and HB housed at CC and EC. In sum, cecal microbiota composition, diversities, and their functional pathways were affected by housing type which further varied between two commercial laying hen strains, HB and W36. This suggests that both housing and genetic strains of laying hens should be considered for selection of the alternative housing systems such as enriched colony cage.},
}
@article {pmid32655529,
year = {2020},
author = {Benítez-Páez, A and Olivares, M and Szajewska, H and Pieścik-Lech, M and Polanco, I and Castillejo, G and Nuñez, M and Ribes-Koninckx, C and Korponay-Szabó, IR and Koletzko, S and Meijer, CR and Mearin, ML and Sanz, Y},
title = {Breast-Milk Microbiota Linked to Celiac Disease Development in Children: A Pilot Study From the PreventCD Cohort.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1335},
pmid = {32655529},
issn = {1664-302X},
abstract = {Celiac disease (CeD) is an immune-mediated disorder triggered by exposure to dietary gluten proteins in genetically predisposed individuals. In addition to the host genome, the microbiome has recently been linked to CeD risk and pathogenesis. To progress in our understanding of the role of breast milk microbiota profiles in CeD, we have analyzed samples from a sub-set of mothers (n = 49) included in the PreventCD project, whose children did or did not develop CeD. The results of the microbiota data analysis indicated that neither the BMI, HLA-DQ genotype, the CeD condition nor the gluten-free diet of the mothers could explain the human milk microbiota profiles. Nevertheless, we found that origin country, the offspring's birth date and, consequently, the milk sampling date influenced the abundance and prevalence of microbes in human milk, undergoing a transition from an anaerobic to a more aerobic microbiota, including potential pathogenic species. Furthermore, certain microbial species were more abundant in milk samples from mothers whose children went on to develop CeD compared to those that remained healthy. These included increases in facultative methylotrophs such as Methylobacterium komagatae and Methylocapsa palsarum as well as in species such as Bacteroides vulgatus, that consumes fucosylated-oligosaccharides present in human milk, and other breast-abscess associated species. Theoretically, these microbiota components could be vertically transmitted from mothers-to-infants during breastfeeding, thereby influencing CeD risk.},
}
@article {pmid32655525,
year = {2020},
author = {Raes, EJ and Karsh, K and Kessler, AJ and Cook, PLM and Holmes, BH and van de Kamp, J and Bodrossy, L and Bissett, A},
title = {Can We Use Functional Genetics to Predict the Fate of Nitrogen in Estuaries?.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1261},
pmid = {32655525},
issn = {1664-302X},
abstract = {Increasing nitrogen (N) loads present a threat to estuaries, which are among the most heavily populated and perturbed parts of the world. N removal is largely mediated by the sediment microbial process of denitrification, in direct competition to dissimilatory nitrate reduction to ammonium (DNRA), which recycles nitrate to ammonium. Molecular proxies for N pathways are increasingly measured and analyzed, a major question in microbial ecology, however, is whether these proxies can add predictive power around the fate of N. We analyzed the diversity and community composition of sediment nirS and nrfA genes in 11 temperate estuaries, covering four types of land use in Australia, and analyzed how these might be used to predict N removal. Our data suggest that sediment microbiomes play a central role in controlling the magnitude of the individual N removal rates in the 11 estuaries. Inclusion, however, of relative gene abundances of 16S, nirS, nrfA, including their ratios did not improve physicochemical measurement-based regression models to predict rates of denitrification or DNRA. Co-occurrence network analyses of nirS showed a greater modularity and a lower number of keystone OTUs in pristine sites compared to urban estuaries, suggesting a higher degree of niche partitioning in pristine estuaries. The distinctive differences between the urban and pristine network structures suggest that the nirS gene could be a likely gene candidate to understand the mechanisms by which these denitrifying communities form and respond to anthropogenic pressures.},
}
@article {pmid32651453,
year = {2020},
author = {Sauder, LA and Albertsen, M and Engel, K and Schwarz, J and Nielsen, PH and Wagner, M and Neufeld, JD},
title = {Correction: Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.},
journal = {The ISME journal},
volume = {14},
number = {9},
pages = {2366},
doi = {10.1038/s41396-020-0714-3},
pmid = {32651453},
issn = {1751-7370},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32651355,
year = {2020},
author = {Lian, Y and Yan, C and Lian, Y and Yang, R and Chen, Q and Ma, D and Lian, W and Liu, J and Luo, C and Ren, J and Xu, H},
title = {Long intergenic non-protein-coding RNA 01446 facilitates the proliferation and metastasis of gastric cancer cells through interacting with the histone lysine-specific demethylase LSD1.},
journal = {Cell death &amp; disease},
volume = {11},
number = {7},
pages = {522},
pmid = {32651355},
issn = {2041-4889},
mesh = {Cell Proliferation/physiology ; Disease Progression ; Female ; Histone Demethylases/*metabolism ; Humans ; Male ; Middle Aged ; Neoplasm Metastasis ; RNA, Long Noncoding/*genetics ; Stomach Neoplasms/genetics/*metabolism/pathology ; },
abstract = {Growing evidences illustrated that long non-coding RNAs (lncRNAs) exhibited widespread effects on the progression of human cancers via various mechanisms. Long intergenic non-protein-coding RNA 01446 (LINC01446), a 3484-bp ncRNA, is known to locate at chromosome 7p12.1. However, its biological functions and specific action mechanism in gastric cancer (GC) are still unclear. In our study, LINC01446 was proved to be markedly upregulated in GC tissues relative to the normal tissues, and positively correlated with the poor survival of GC patients. The multivariate Cox regression model showed that LINC01446 functioned as an independent prognostic factor for the survival of GC patients. Functionally, LINC01446 facilitated the proliferation and metastasis of GC cells. Moreover, RNA-seq analysis demonstrated that LINC01446 knockdown primarily regulated the genes relating to the growth and migration of GC. Mechanistically, LINC01446 could widely interact with histone lysine-specific demethylase LSD1 and recruit LSD1 to the Ras-related dexamethasone-induced 1 (RASD1) promoter, thereby suppressing RASD1 transcription. Overall, these findings suggest that LINC01446/LSD1/RASD1 regulatory axis may provide bona fide targets for anti-GC therapies.},
}
@article {pmid32647153,
year = {2020},
author = {Borrego, C and Sabater, S and Proia, L},
title = {Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {11288},
pmid = {32647153},
issn = {2045-2322},
mesh = {Archaea/*classification ; Bacteria/*classification ; Biota ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rivers/*microbiology ; Spain ; Water Microbiology ; },
abstract = {Spatial heterogeneity along river networks is interrupted by dams, affecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil differences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Differences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir.},
}
@article {pmid32638044,
year = {2021},
author = {Lukoseviciute, L and Lebedeva, J and Kuisiene, N},
title = {Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {110-121},
pmid = {32638044},
issn = {1432-184X},
mesh = {Acidobacteria/genetics ; Actinobacteria/genetics ; Bacteria/classification/*genetics/metabolism ; Caves/*microbiology ; Chloroflexi/genetics ; Firmicutes/genetics ; Geologic Sediments/*microbiology ; Georgia (Republic) ; Metagenome/genetics ; Microbiota/genetics ; Peptide Synthases/*genetics ; Polyketide Synthases/*genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Secondary Metabolism/*genetics ; Soil Microbiology ; },
abstract = {Caves are considered to be extreme and challenging environments. It is believed that the ability of microorganisms to produce secondary metabolites enhances their survivability and adaptiveness in the energy-starved cave environment. Unfortunately, information on the genetic potential for the production of secondary metabolites, such as polyketides and nonribosomal peptides, is limited. In the present study, we aimed to identify and characterize genes responsible for the production of secondary metabolites in the microbial community of one of the deepest caves in the world, Krubera-Voronja Cave (43.4184 N 40.3083 E, Western Caucasus). The analysed sample materials included sediments, drinkable water from underground camps, soil and clay from the cave walls, speleothems and coloured spots from the cave walls. The type II polyketide synthases (PKSs) ketosynthases α and β and the adenylation domains of nonribosomal peptide synthetases (NRPSs) were investigated using a metagenomic approach. Taxonomic diversity analysis showed that most PKS sequences could be attributed to Actinobacteria followed by unclassified bacteria and Acidobacteria, while the NRPS sequences were more taxonomically diverse and could be assigned to Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Chloroflexi, etc. Only three putative metabolites could be predicted: an angucycline group polyketide, a massetolide A-like cyclic lipopeptide and a surfactin-like lipopeptide. The absolute majority of PKS and NRPS sequences showed low similarity with the sequences of the reference biosynthetic pathways, suggesting that these sequences could be involved in the production of novel secondary metabolites.},
}
@article {pmid32638043,
year = {2021},
author = {Griffin, TW and Baer, JG and Ward, JE},
title = {Direct Comparison of Fecal and Gut Microbiota in the Blue Mussel (Mytilus edulis) Discourages Fecal Sampling as a Proxy for Resident Gut Community.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {180-192},
pmid = {32638043},
issn = {1432-184X},
support = {1559180//Directorate for Biological Sciences/ ; },
mesh = {Animals ; Feces/*microbiology ; Food Microbiology ; Gastrointestinal Microbiome/*genetics ; Mytilus edulis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Stomach/*microbiology ; },
abstract = {Bivalves have ecological and economic importance but information regarding their associated microbiomes is lacking. As suspension feeders, bivalves capture and ingest a myriad of particles, and their digestive organs have a high throughput of particle-associated microbiota. To better understand the complement of transient and resident microbial communities, standard methods need to be developed. For example, fecal sampling could represent a convenient proxy for the gut microbiome and is simple, nondestructive, and allows for sampling of individuals through time. The goal of this study was to evaluate fecal sampling as a reliable proxy for gut microbiome assessment in the blue mussel (Mytilus edulis). Mussels were collected from the natural environment and placed into individual sterilized microcosms for 6 h to allow for fecal egestion. Feces and gut homogenates from the same individuals were sampled and subjected to 16S rRNA gene amplicon sequencing. Fecal communities of different mussels resembled each other but did not resemble gut communities. Fecal communities were significantly more diverse, in terms of amplicon sequence variant (ASV) richness and evenness, than gut communities. Results suggested a mostly transient nature for fecal microbiota. Nonetheless, mussels retained a distinct resident microbial community in their gut after fecal egestion that was dominated by ASVs belonging to Mycoplasma. The use of fecal sampling as a nondestructive substitute for direct sampling of the gut is strongly discouraged. Experiments that aim to study solely resident bivalve gut microbiota should employ an egestion period prior to gut sampling to allow time for voidance of transient microbes.},
}
@article {pmid32629308,
year = {2020},
author = {Qi, Y and Beriot, N and Gort, G and Huerta Lwanga, E and Gooren, H and Yang, X and Geissen, V},
title = {Impact of plastic mulch film debris on soil physicochemical and hydrological properties.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {266},
number = {Pt 3},
pages = {115097},
doi = {10.1016/j.envpol.2020.115097},
pmid = {32629308},
issn = {1873-6424},
mesh = {Agriculture ; Ecosystem ; Hydrology ; Plastics ; *Soil ; *Soil Pollutants ; },
abstract = {The plastic mulch films used in agriculture are considered to be a major source of the plastic residues found in soil. Mulching with low-density polyethylene (LDPE) is widely practiced and the resulting macro- and microscopic plastic residues in agricultural soil have aroused concerns for years. Over the past decades, a variety of biodegradable (Bio) plastics have been developed in the hope of reducing plastic contamination of the terrestrial ecosystem. However, the impact of these Bio plastics in agroecosystems have not been sufficiently studied. Therefore, we investigated the impact of macro (around 5 mm) and micro (<1 mm) sized plastic debris from LDPE and one type of starch-based Bio mulch film on soil physicochemical and hydrological properties. We used environmentally relevant concentrations of plastics, ranging from 0 to 2% (w/w), identified by field studies and literature review. We studied the effects of the plastic residue on a sandy soil for one month in a laboratory experiment. The bulk density, porosity, saturated hydraulic conductivity, field capacity and soil water repellency were altered significantly in the presence of the four kinds of plastic debris, while pH, electrical conductivity and aggregate stability were not substantially affected. Overall, our research provides clear experimental evidence that microplastics affect soil properties. The type, size and content of plastic debris as well as the interactions between these three factors played complex roles in the variations of the measured soil parameters. Living in a plastic era, it is crucial to conduct further interdisciplinary studies in order to have a comprehensive understanding of plastic debris in soil and agroecosystems.},
}
@article {pmid32628807,
year = {2020},
author = {Rejeb, IB and Dhen, N and Gargouri, M and Boulila, A},
title = {Chemical Composition, Antioxidant Potential and Enzymes Inhibitory Properties of Globe Artichoke By-Products.},
journal = {Chemistry &amp; biodiversity},
volume = {17},
number = {9},
pages = {e2000073},
doi = {10.1002/cbdv.202000073},
pmid = {32628807},
issn = {1612-1880},
mesh = {Acetylcholinesterase/metabolism ; Antioxidants/chemistry/isolation &amp; purification/*pharmacology ; Benzothiazoles/antagonists &amp; inhibitors ; Biphenyl Compounds/antagonists &amp; inhibitors ; Butyrylcholinesterase/metabolism ; Cynara scolymus/*chemistry ; Enzyme Inhibitors/chemistry/isolation &amp; purification/*pharmacology ; Flavonoids/chemistry/isolation &amp; purification/*pharmacology ; Fluorescence Recovery After Photobleaching ; Phenols/chemistry/isolation &amp; purification/*pharmacology ; Picrates/antagonists &amp; inhibitors ; Plant Components, Aerial/chemistry ; Plant Extracts/chemistry/isolation &amp; purification/*pharmacology ; Sulfonic Acids/antagonists &amp; inhibitors ; alpha-Amylases/antagonists &amp; inhibitors/metabolism ; },
abstract = {In this study, chemical composition and in vitro biological activities of artichoke by-products (leaves, floral stems and bracts) issued from two Tunisian varieties were evaluated. Analysis was performed by means of high-performance liquid chromatography with diode array detection coupled to electrospray ionization mass spectrometric (LC/DAD/ESI-MS). Total phenolic (TPC) and flavonoid (TFC) contents as well as the antioxidant activity conducted by three complementary methods, DPPH, ABTS and FRAP tests, were performed for each sample. Enzyme inhibitory effects against acetylcholinesterase, butyrylcholinesterase and α-amylase were also studied. Results showed that TPC and TFC varied according to variety as well as the plant part. Bracts presented the highest TPC values (10-15 mg GAE/g DW), while leaves were distinguished by the highest TFC values (52-58 mg EQ/g DW). In vitro assays showed that Violet d'Hyères bracts and Blanc d'Oran leaves present the most antioxidant activities (30.040 and 20.428 mgET/gDW, respectively, by the DPPH method). Leaves demonstrated the highest acetylcholinesterase and butyrylcholinesterase inhibitory effects. Moreover, all organs displayed a noticeable inhibition towards α-amylase. LC/DAD/MS analysis revealed that artichoke by-products are a potential source of biopharmaceuticals such as luteolin derivatives from leaves and mono/dicaffeoylquinic acids in the other parts. This research demonstrates that globe artichoke by-products, unexploited in our country, are a promising source of natural health promoting compounds with potential applications in the food and pharmaceutical industries.},
}
@article {pmid32628343,
year = {2020},
author = {Aguilar, P and Sommaruga, R},
title = {The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time.},
journal = {Molecular ecology},
volume = {29},
number = {16},
pages = {3117-3130},
pmid = {32628343},
issn = {1365-294X},
mesh = {Aquatic Organisms ; *Lakes ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Stochastic Processes ; },
abstract = {One major goal in microbial ecology is to establish the importance of deterministic and stochastic processes for community assembly. This is relevant to explain and predict how diversity changes at different temporal scales. However, understanding of the relative quantitative contribution of these processes and particularly of how they may change over time is limited. Here, we assessed the importance of deterministic and stochastic processes based on the analysis of the bacterial microbiome in one alpine oligotrophic and in one subalpine mesotrophic lake, which were sampled over two consecutive years at different time scales. We found that in both lakes, homogeneous selection (i.e., a deterministic process) was the main assembly process at the annual scale and explained 66.7% of the bacterial community turnover, despite differences in diversity and temporal variability patterns between ecosystems. However, in the alpine lake, homogenizing dispersal (i.e., a stochastic process) was the most important assembly process at the short-term (daily and weekly) sampling scale and explained 55% of the community turnover. Alpha diversity differed between lakes, and seasonal stability of the bacterial community was more evident in the oligotrophic lake than in the mesotrophic one. Our results demonstrate how important forces that govern temporal changes in bacterial communities act at different time scales. Overall, our study validates on a quantitative basis, the importance and dominance of deterministic processes in structuring bacterial communities in freshwater environments over long time scales.},
}
@article {pmid32625179,
year = {2020},
author = {Costa, OYA and Oguejiofor, C and Zühlke, D and Barreto, CC and Wünsche, C and Riedel, K and Kuramae, EE},
title = {Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia".},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1227},
pmid = {32625179},
issn = {1664-302X},
abstract = {Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated.},
}
@article {pmid32623832,
year = {2020},
author = {Morvan, S and Meglouli, H and Lounès-Hadj Sahraoui, A and Hijri, M},
title = {Into the wild blueberry (Vaccinium angustifolium) rhizosphere microbiota.},
journal = {Environmental microbiology},
volume = {22},
number = {9},
pages = {3803-3822},
doi = {10.1111/1462-2920.15151},
pmid = {32623832},
issn = {1462-2920},
support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council of Canada/International ; },
mesh = {Ascomycota/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Blueberry Plants/chemistry/*microbiology ; *Microbiota ; Mycorrhizae/classification/genetics/isolation &amp; purification/metabolism ; Nitrogen/analysis ; Plant Leaves/chemistry/microbiology ; *Rhizosphere ; Symbiosis ; },
abstract = {The ability of wild blueberries to adapt to their harsh environment is believed to be closely related to their symbiosis with ericoid mycorrhizal fungi, which produce enzymes capable of organic matter mineralization. Although some of these fungi have been identified and characterized, we still know little about the microbial ecology of wild blueberry. Our study aims to characterize the fungal and bacterial rhizosphere communities of Vaccinium angustifolium (the main species encountered in wild blueberry fields). Our results clearly show that the fungal order Helotiales was the most abundant taxon associated with V. angustifolium. Helotiales contains most of the known ericoid mycorrhizal fungi which are expected to dominate in such a biotope. Furthermore, we found the dominant bacterial order was the nitrogen-fixing Rhizobiales. The Bradyrhizobium genus, whose members are known to form nodules with legumes, was among the 10 most abundant genera in the bacterial communities. In addition, Bradyrhizobium and Roseiarcus sequences significantly correlated with higher leaf-nitrogen content. Overall, our data documented fungal and bacterial community structure differences in three wild blueberry production fields.},
}
@article {pmid32623497,
year = {2021},
author = {Pereira, A and Ferreira, V},
title = {Invasion of Native Riparian Forests by Acacia Species Affects In-Stream Litter Decomposition and Associated Microbial Decomposers.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {14-25},
pmid = {32623497},
issn = {1432-184X},
support = {SFRH/BD/118069/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/00129/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/MAR/04292/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Acacia/*metabolism ; Alnus/microbiology ; Bacteria/*growth &amp; development ; Biomass ; Ecology ; Forests ; Fungi/*growth &amp; development ; *Introduced Species ; Microbiota ; Nitrogen Fixation/physiology ; Portugal ; Quercus/microbiology ; Rivers/*chemistry/*microbiology ; },
abstract = {The invasion of native riparian forests by exotic tree species can lead to profound changes in the ecological integrity of freshwater ecosystems. We assessed litter decomposition of native (Alnus glutinosa and Quercus robur) and invasive (Acacia melanoxylon and Acacia dealbata) tree species, and associated microbial activity and community structure, after being immersed for conditioning in 3 reference and 3 "invaded" streams in Serra da Lousã (central Portugal) and used in microcosms simulating stream conditions. Litter decomposition differed among species, in the order: Al. glutinosa > Q. robur > (Ac. melanoxylon ~ Ac. dealbata). Alnus glutinosa litter decomposed faster probably because it was soft and had high nitrogen concentration for decomposers. Quercus robur litter decomposed slower most likely because it was tough and had high polyphenol and low nitrogen concentrations. Acacia melanoxylon litter was the toughest and had a thick cuticle that likely acted as a physical barrier for microbial colonization. In Ac. dealbata, the small-sized leaflets and high lignin concentration may have limited microbial litter decomposition. Litter decomposition was faster in "invaded" streams, probably because they were N-limited and increases in nitrogen concentration in water, promoted by Acacia species invasion, stimulated microbial activity on litter. The aquatic hyphomycete community structure differed among litter species and between stream types, further suggesting that microbes were sensitive to litter characteristics and water nutrient concentrations. Overall, the invasion of native riparian forests by Acacia species may affect microbial decomposer activity, thus altering important stream ecosystem processes, such as litter decomposition and nutrient cycles.},
}
@article {pmid32622275,
year = {2020},
author = {Seuntjens, D and Carvajal Arroyo, JM and Van Tendeloo, M and Chatzigiannidou, I and Molina, J and Nop, S and Boon, N and Vlaeminck, SE},
title = {Mainstream partial nitritation/anammox with integrated fixed-film activated sludge: Combined aeration and floc retention time control strategies limit nitrate production.},
journal = {Bioresource technology},
volume = {314},
number = {},
pages = {123711},
doi = {10.1016/j.biortech.2020.123711},
pmid = {32622275},
issn = {1873-2976},
mesh = {*Ammonium Compounds ; Bioreactors ; Nitrites ; Nitrogen ; Oxidation-Reduction ; *Sewage ; },
abstract = {Implementation of mainstream partial nitritation/anammox (PN/A) can lead to more sustainable and cost-effective sewage treatment. For mainstream PN/A reactor, an integrated fixed-film activated sludge (IFAS) was operated (26 °C). The effects of floccular aerobic sludge retention time (AerSRTfloc), a novel aeration strategy, and N-loading rate were tested to optimize the operational strategy. The best performance was observed with a low, but sufficient AerSRTfloc (~7d) and continuous aeration with two alternating dissolved oxygen setpoints: 10 min at 0.07-0.13 mg O2 L[-1] and 5 min at 0.27-0.43 mg O2 L[-1]. Nitrogen removal rates were 122 ± 23 mg N L[-1] d[-1], and removal efficiencies 73 ± 13%. These conditions enabled flocs to act as nitrite sources while the carriers were nitrite sinks, with low abundance of nitrite oxidizing bacteria. The operational strategies in the source-sink framework can serve as a guideline for successful operation of mainstream PN/A reactors.},
}
@article {pmid32621211,
year = {2021},
author = {Stricker, E and Crain, G and Rudgers, J and Sinsabaugh, R and Fernandes, V and Nelson, C and Giraldo-Silva, A and Garcia-Pichel, F and Belnap, J and Darrouzet-Nardi, A},
title = {What Could Explain δ[13]C Signatures in Biocrust Cyanobacteria of Drylands?.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {134-145},
pmid = {32621211},
issn = {1432-184X},
support = {1557135//Directorate for Biological Sciences/ ; 1557162//Directorate for Biological Sciences/ ; 1832194//Directorate for Biological Sciences/ ; 1655499//National Science Foundation/ ; },
mesh = {Carbon Cycle/*physiology ; Carbon Isotopes/*analysis ; Cyanobacteria/*metabolism ; Desert Climate ; Ecosystem ; Microbiota/physiology ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plants/*microbiology ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Dryland ecosystems are increasing in geographic extent and contribute greatly to interannual variability in global carbon dynamics. Disentangling interactions among dominant primary producers, including plants and autotrophic microbes, can help partition their contributions to dryland C dynamics. We measured the δ[13]C signatures of biological soil crust cyanobacteria and dominant plant species (C3 and C4) across a regional scale in the southwestern USA to determine if biocrust cyanobacteria were coupled to plant productivity (using plant-derived C mixotrophically), or independent of plant activity (and therefore purely autotrophic). Cyanobacterial assemblages located next to all C3 plants and one C4 species had consistently more negative δ[13]C (by 2‰) than the cyanobacteria collected from plant interspaces or adjacent to two C4 Bouteloua grass species. The differences among cyanobacterial assemblages in δ[13]C could not be explained by cyanobacterial community composition, photosynthetic capacity, or any measured leaf or root characteristics (all slopes not different from zero). Thus, microsite differences in abiotic conditions near plants, rather than biotic interactions, remain a likely mechanism underlying the observed δ[13]C patterns to be tested experimentally.},
}
@article {pmid32621210,
year = {2021},
author = {Hery, L and Guidez, A and Durand, AA and Delannay, C and Normandeau-Guimond, J and Reynaud, Y and Issaly, J and Goindin, D and Legrave, G and Gustave, J and Raffestin, S and Breurec, S and Constant, P and Dusfour, I and Guertin, C and Vega-Rúa, A},
title = {Natural Variation in Physicochemical Profiles and Bacterial Communities Associated with Aedes aegypti Breeding Sites and Larvae on Guadeloupe and French Guiana.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {93-109},
pmid = {32621210},
issn = {1432-184X},
support = {Grant ACIP 01-2016//Action Concert&#xe9;es Inter Pasteuriennes/ ; grant 2015-FED-192//Programme Op&#xe9;rationnel FEDER-Guadeloupe-Conseil R&#xe9;gional 2014-2020/ ; Stage-2018//Calmette &amp; Yersin/ ; 2017-2020//La R&#xe9;gion Guadeloupe/ ; },
mesh = {Aedes/*growth &amp; development/*microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; French Guiana ; Guadeloupe ; Larva/growth &amp; development/microbiology ; Microbiota/*genetics ; Mosquito Vectors/growth &amp; development/microbiology ; RNA, Ribosomal, 16S/genetics ; Water/*chemistry ; },
abstract = {Aedes aegypti develop in aquatic habitats in which mosquito larvae are exposed to physicochemical elements and microorganisms that may influence their life cycle and their ability to transmit arboviruses. Little is known about the natural bacterial communities associated with A. aegypti or their relation to the biotic and abiotic characteristics of their aquatic habitats. We characterized the physicochemical properties and bacterial microbiota of A. aegypti breeding sites and larvae on Guadeloupe and in French Guiana. In addition, we explored whether geographic location, the type of breeding site and physicochemical parameters influenced the microbiota associated with this mosquito species. We used large-scale 16S rRNA gene sequencing of 160 breeding sites and 147 pools of A. aegypti larvae and recorded 12 physicochemical parameters at the sampled breeding sites. Ordination plots and multiple linear regression were used to assess the influence of environmental factors on the bacterial microbiota of water and larvae. We found territory-specific differences in physicochemical properties (dissolved oxygen, conductivity) and the composition of bacterial communities in A. aegypti breeding sites that influenced the relative abundance of several bacteria genera (e.g., Methylobacterium, Roseoccocus) on the corresponding larvae. A significant fraction of the bacterial communities identified on larvae, dominated by Herbiconiux and Microvirga genera, were consistently enriched in mosquitoes regardless the location. In conclusion, territory-specific differences observed in the biotic and abiotic properties of A. aegypti breeding sites raise concern about the impact of these changes on pathogen transmission by different A. aegypti populations.},
}
@article {pmid32621209,
year = {2021},
author = {Shahraki, AH and Chaganti, SR and Heath, DD},
title = {Diel Dynamics of Freshwater Bacterial Communities at Beaches in Lake Erie and Lake St. Clair, Windsor, Ontario.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {1-13},
pmid = {32621209},
issn = {1432-184X},
mesh = {Actinobacteria/genetics/*isolation &amp; purification ; Bathing Beaches ; Biodiversity ; *Environmental Monitoring ; Escherichia coli/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Humans ; Lakes/*microbiology ; Microbiota/*genetics ; Ontario ; Population Dynamics ; Proteobacteria/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seasons ; Time Factors ; Water Microbiology ; },
abstract = {Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla. Moreover, relative abundance of Enterobacteriaceae (associated with potential health risk) was significantly high at night in some dial cycles. Diversity was significantly high at night across most of the diel sampling events. qPCR assays showed a substantial bi-hourly variation of Escherichia coli levels with a significant high level of E. coli at night hours in comparison with day hours and the lowest levels at noon and during the afternoon hours. Taken together, these findings highlighted a considerable short-term temporal variation of bacterial communities which helps better understanding of freshwater bacterial dynamics and their ecology. E. coli monitoring showed that multiple samples in different hours will provide more accurate picture of freshwater safety and human health risk. Graphical abstract.},
}
@article {pmid32620132,
year = {2020},
author = {Wang, Y and Wang, K and Huang, L and Dong, P and Wang, S and Chen, H and Lu, Z and Hou, D and Zhang, D},
title = {Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {106},
pmid = {32620132},
issn = {2049-2618},
support = {LY18C030002//Zhejiang Provincial Natural Science Foundation of China/International ; 31672658//National Natural Science Foundation of China/International ; 2017C110001//Agricultural Major Project of Ningbo, China/International ; LGN20C190008//Basic Public Welfare Research Project of Zhejiang Province/International ; },
mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Larva/*microbiology ; Penaeidae/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using a high-frequency sampling strategy and 16S rRNA gene amplicon sequencing, we investigated dynamics of larval shrimp bacterial community and its relationship with bacterioplankton in the rearing water across the whole developmental cycle in a realistic aquaculture practice.<br><br>RESULTS: Alpha-diversity of larval shrimp bacteria showed a U-shaped pattern across the developmental cycle with the stages zoea and mysis as the valley. Correspondingly, the compositions of dominant bacterial taxa at the stages nauplius and early postlarvae were more complex than other stages. Remarkably, Rhodobacteraceae maintained the overwhelming dominance after the mouth opening of larvae (zoea I~early postlarvae). The taxonomic and phylogenetic compositions of larval bacterial community both showed stage-dependent patterns with higher rate of taxonomic turnover, suggesting that taxonomic turnover was mainly driven by temporal switching among closely related taxa (such as Rhodobacteraceae taxa). The assembly of larval bacteria was overall governed by neutral processes (dispersal among individuals and ecological drift) at all the stages, but bacterioplankton also had certain contribution during three sub-stages of zoea, when larval and water bacterial communities were most associated. Furthermore, the positive host selection for Rhodobacteraceae taxa from the rearing water during the zoea stage and its persistent dominance and large predicted contribution to metabolic potentials of organic matters at post-mouth opening stages suggest a crucial role of this family in larval microbiome and thus a potential source of probiotic candidates for shrimp larval nursery.<br><br>CONCLUSIONS: Our results reveal pronounced succession patterns and dynamic assembly processes of larval shrimp bacterial communities during the developmental cycle, highlighting the importance of the mouth opening stage from the perspective of microbial ecology. We also suggest the possibility and potential timing in microbial management of the rearing water for achieving the beneficial larval microbiota in the nursery practice. Video Abstract.},
}
@article {pmid32617619,
year = {2021},
author = {Pinto, OHB and Costa, FS and Rodrigues, GR and da Costa, RA and da Rocha Fernandes, G and Júnior, ORP and Barreto, CC},
title = {Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {169-179},
pmid = {32617619},
issn = {1432-184X},
support = {88881.062152/2014-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Acidobacteria/drug effects/*genetics/isolation &amp; purification/*metabolism ; Carotenoids/metabolism ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Genome, Bacterial/genetics ; Hydrogen Peroxide/*toxicity ; Multigene Family/genetics ; Oxidative Stress/*physiology ; Soil/chemistry ; Soil Microbiology ; },
abstract = {Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.},
}
@article {pmid32615432,
year = {2020},
author = {Yang, L and Hou, K and Zhang, B and Ouyang, C and Lin, A and Xu, S and Ke, D and Fang, L and Chen, Q and Wu, J and Yan, C and Lian, Y and Jiang, T and He, J and Wang, H and Fu, Y and Xiao, C and Chen, Z},
title = {Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut.},
journal = {The Science of the total environment},
volume = {741},
number = {},
pages = {140423},
doi = {10.1016/j.scitotenv.2020.140423},
pmid = {32615432},
issn = {1879-1026},
mesh = {Cost-Benefit Analysis ; Feces ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Specimen Handling ; Temperature ; },
abstract = {With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of -80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and -80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.},
}
@article {pmid32615392,
year = {2020},
author = {Kassaian, N and Feizi, A and Rostami, S and Aminorroaya, A and Yaran, M and Amini, M},
title = {The effects of 6 mo of supplementation with probiotics and synbiotics on gut microbiota in the adults with prediabetes: A double blind randomized clinical trial.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {79-80},
number = {},
pages = {110854},
doi = {10.1016/j.nut.2020.110854},
pmid = {32615392},
issn = {1873-1244},
mesh = {Adult ; Double-Blind Method ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Prediabetic State/therapy ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; *Synbiotics ; },
abstract = {OBJECTIVES: The evidence of 16S rRNA genes in the gut microbiota distinguished a higher Firmicutes-to-Bacteroidetes ratio in individuals who were obese and had diabetes than in a healthy cohort. So, it seems that the modulation of intestinal microbial ecology by pro-/pre-/synbiotics may contribute to the progression and prevention of metabolic diseases. The aim of this study was to assess the effects of probiotics and synbiotic supplementation on the modification of the intestinal microbiome in adults with prediabetes.<br><br>METHODS: In a randomized, double-blinded, placebo-controlled clinical trial, 120 patients with prediabetes were randomly assigned to consume 6 g/d of either a placebo containing maltodextrin (control) or multispecies probiotic or inulin-based synbiotic for 6 mo. Fecal samples were obtained at baseline and after 6 mo of supplementation. Dietary intake was assessed throughout the study (at baseline and after 3 and 6 mo). Total energy, macronutrients, and dietary fiber were calculated using a dietary program Nutritionist 4. DNA was extracted from fecal samples and the numbers of Clostridium perfringens (the represent of phylum Firmicutes), Bacteroides fragilis (the representative of Bacteroidetes) and Escherichia coli (as universal bacteria) were determined by quantitative real-time polymerase chain reactions (qPCR). The changes in the relative abundance of the two fecal bacteria before and after supplementation were analyzed and compared within and between groups.<br><br>RESULTS: There were no significant changes in dietary intake during the study. Six mo of supplementation with probiotics resulted in a statistically significant increase in the abundance of the B. fragilis-to-E.coli ratio (mean difference [MD] &#xb1; SE 0.47 &#xb1; 0.37, P&#xa0;=&#xa0;0.04) and decrease of the relative proportion of Firmicutes-to-Bacteroidetes representatives (MD &#xb1; SE -118.8 &#xb1; 114.6, P&#xa0;=&#xa0;0.02). Synbiotic had no significant effect on the changes in the bacteria. There were no significant differences between the three groups.<br><br>CONCLUSION: The results of this study suggest that manipulation of the human gut microbiome by using probiotics could provide a potential therapeutic approach in the prevention and management of obesity and metabolic disorders such as diabetes.},
}
@article {pmid32614521,
year = {2020},
author = {Cheng, XS and Huo, YN and Fan, YY and Xiao, CX and Ouyang, XM and Liang, LY and Lin, Y and Wu, JF and Ren, JL and Guleng, B},
title = {Mindin serves as a tumour suppressor gene during colon cancer progression through MAPK/ERK signalling pathway in mice.},
journal = {Journal of cellular and molecular medicine},
volume = {24},
number = {15},
pages = {8391-8404},
pmid = {32614521},
issn = {1582-4934},
mesh = {Animals ; Cell Cycle/genetics ; Cell Line ; Cell Line, Tumor ; Cell Proliferation/genetics ; Colitis/genetics/pathology ; Colon/pathology ; Colonic Neoplasms/*genetics/pathology ; Disease Models, Animal ; Disease Progression ; Extracellular Matrix Proteins/*genetics ; Genes, Tumor Suppressor/*physiology ; Humans ; MAP Kinase Signaling System/*genetics ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; RAW 264.7 Cells ; Signal Transduction/*genetics ; },
abstract = {Mindin is important in broad spectrum of immune responses. On the other hand, we previously reported that mindin attenuated human colon cancer development by blocking angiogenesis through Egr-1-mediated regulation. However, the mice original mindin directly suppressed the syngenic colorectal cancer (CRC) growth in our recent study and we aimed to further define the role of mindin during CRC development in mice. We established the mouse syngeneic CRC CMT93 and CT26 WT cell lines with stable mindin knock-down or overexpression. These cells were also subcutaneously injected into C57BL/6 and BALB/c mice as well as established a colitis-associated colorectal cancer (CAC) mouse model treated with lentiviral-based overexpression and knocked-down of mindin. Furthermore, we generated mindin knockout mice using a CRISPR-Cas9 system with CAC model. Our data showed that overexpression of mindin suppressed cell proliferation in both of CMT93 and CT26 WT colon cancer cell lines, while the silencing of mindin promoted in vitro cell proliferation via the ERK and c-Fos pathways and cell cycle control. Moreover, the overexpression of mindin significantly suppressed in vivo tumour growth in both the subcutaneous transplantation and the AOM/DSS-induced CAC models. Consistently, the silencing of mindin reversed these in vivo observations. Expectedly, the tumour growth was promoted in the CAC model on mindin-deficient mice. Thus, mindin plays a direct tumour suppressive function during colon cancer progression and suggesting that mindin might be exploited as a therapeutic target for CRC.},
}
@article {pmid32613267,
year = {2021},
author = {Douglas, AJ and Hug, LA and Katzenback, BA},
title = {Composition of the North American Wood Frog (Rana sylvatica) Bacterial Skin Microbiome and Seasonal Variation in Community Structure.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {78-92},
pmid = {32613267},
issn = {1432-184X},
support = {RGPIN-2017-04218//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification ; Animals ; Bacteroidetes/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Microbiota/genetics ; Ponds ; Proteobacteria/classification/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Ranidae/*microbiology ; Seasons ; Skin/*microbiology ; United States ; },
abstract = {While a number of amphibian skin microbiomes have been characterized, it is unclear how these communities might vary in response to seasonal changes in the environment and the corresponding behaviors that many amphibians exhibit. Given recent studies demonstrating the importance of the skin microbiome in frog innate immune defense against pathogens, investigating how changes in the environment impact the microbial species present will provide a better understanding of conditions that may alter host susceptibility to pathogens in their environment. We sampled the bacterial skin microbiome of North American wood frogs (Rana sylvatica) from two breeding ponds in the spring, along with the bacterial community present in their vernal breeding pools, and frogs from the nearby forest floor in the summer and fall to determine whether community composition differs by sex, vernal pond site, or temporally across season (spring, summer, fall). Taxon relative abundance data reveals a profile of bacterial phyla similar to those previously described on anuran skin, with Proteobacteria, Bacteroidetes, and Actinobacteria dominating the wood frog skin microbiome. Our results indicate that sex had no significant effect on skin microbiota diversity; however, this may be due to our limited female frog sample size. Vernal pool site had a small but significant effect on skin microbiota, but skin-associated communities were more similar to each other than to the communities observed in the frogs' respective pond water. Across seasons, diversity analyses suggest that there are significant differences between the bacterial skin microbiome of frogs from spring and summer/fall groups while the average α-diversity per frog remained consistent. These results illustrate seasonal variation in wood frog skin microbiome structure and highlight the importance of considering temporal trends in an amphibian microbiome, particularly for species whose life history requires recurrent shifts in habitat and behavior.},
}
@article {pmid32610452,
year = {2020},
author = {Van den Abbeele, P and Verstrepen, L and Ghyselinck, J and Albers, R and Marzorati, M and Mercenier, A},
title = {A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated in Vitro Approach.},
journal = {Nutrients},
volume = {12},
number = {7},
pages = {},
pmid = {32610452},
issn = {2072-6643},
support = {SMEi 811592//Horizon 2020/ ; Eurostars E! 10574-NIMF//European Commission/ ; },
mesh = {Bifidobacterium/metabolism ; Colon/metabolism ; Daucus carota/*chemistry ; Digestion/*drug effects ; Electric Impedance ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Host Microbial Interactions/drug effects ; Humans ; Intestinal Mucosa/drug effects ; Pectins/*pharmacology ; Prebiotics/*analysis/microbiology ; },
abstract = {Modulation of the gut microbiome as a means to improve human health has recently gained increasing interest. In this study, it was investigated whether cRG-I, a carrot-derived pectic polysaccharide, enriched in rhamnogalacturonan-I (RG-I) classifies as a potential prebiotic ingredient using novel in vitro models. First, digestion methods involving α-amylase/brush border enzymes demonstrated the non-digestibility of cRG-I by host-derived enzymes versus digestible (starch/maltose) and non-digestible controls (inulin). Then, a recently developed short-term (48 h) colonic incubation strategy was applied and revealed that cRG-I fermentation increased levels of health-promoting short-chain fatty acids (SCFA; mainly acetate and propionate) and lactate comparable but not identical to the reference prebiotic inulin. Upon upgrading this fermentation model by inclusion of a simulated mucosal environment while applying quantitative 16S-targeted Illumina sequencing, cRG-I was additionally shown to specifically stimulate operational taxonomic units (OTUs) related to health-associated species such as Bifidobacterium longum, Bifidobacterium adolescentis, Bacteroides dorei, Bacteroides ovatus, Roseburia hominis, Faecalibacterium prausnitzii, and Eubacterium hallii. Finally, in a novel model to assess host-microbe interactions (Caco-2/peripheral blood mononuclear cells (PBMC) co-culture) fermented cRG-I increased barrier integrity while decreasing markers for inflammation. In conclusion, by using novel in vitro models, cRG-I was identified as a promising prebiotic candidate to proceed to clinical studies.},
}
@article {pmid32607236,
year = {2020},
author = {Skarżyńska, E and Wilczyńska, P and Kiersztyn, B and Żytyńska-Daniluk, J and Jakimiuk, A and Lisowska-Myjak, B},
title = {Comparison of protease and aminopeptidase activities in meconium: A pilot study.},
journal = {Biomedical reports},
volume = {13},
number = {2},
pages = {7},
pmid = {32607236},
issn = {2049-9434},
abstract = {The successive accumulation of proteases and aminopeptidases in meconium are important physiological components of the intrauterine environment in which a fetus develops. The aim of the present study was to assess the changes in the activities of these enzymes in meconium of healthy infants, and to investigate whether there were any statistically significant associations between activity of the enzymes of interest and the mode of delivery. The activities of proteases and aminopeptidases were determined in meconium portions (n=110) using the substrates BODIPY FL casein and L-leucine-7-amido-4-methylcoumarin hydrochloride, respectively. Serial meconium samples (2-5 per neonate) were collected from healthy infants born vaginally (n=14), and by a cesarean section (n=16). Protease activity (10[4] RFU/h) was lower in the first meconium sample compared with the final sample from the same infant (3.99±2.03 vs. 5.76±2.24, respectively, mean ± standard deviation; P=0.004). Conversely, there was no significant difference in aminopeptidase activity (10[3] nM/l/h) between consecutive meconium samples (P=0.702). The ratios of the first-meconium sample enzyme activity to the last-meconium sample enzyme activity were lower for proteases compared with aminopeptidases (0.76±0.48 vs. 1.35±1.04, respectively mean ± standard deviation; P=0.014), and sustained in the infants born by a cesarean section (P=0.008). Spearman's correlation coefficient analysis between the first and last meconium samples showed the correlation increased in the infants born vaginally compared with the rest of the infants (proteases, R=0.618 vs. R=0.314; aminopeptidases, R=0.688 vs. R=0.566). Aminopeptidase activity did not exhibit any notable dynamic changes during meconium accumulation in the fetal intestine. In infants born vaginally compared with those born by a cesarean section, the activity of both proteases and aminopeptidases in the first meconium sample showed an improved correlation with the activity of the final meconium sample. This may suggest that in the intrauterine environment, during accumulation of meconium in the digestive tract of the fetus, the activity and/or levels of these enzymes and the substrates they catalyze were more stable in newborns born vaginally compared with infants born by caesarean section.},
}
@article {pmid32606027,
year = {2020},
author = {Altamia, MA and Lin, Z and Trindade-Silva, AE and Uy, ID and Shipway, JR and Wilke, DV and Concepcion, GP and Distel, DL and Schmidt, EW and Haygood, MG},
title = {Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes.},
journal = {mSystems},
volume = {5},
number = {3},
pages = {},
pmid = {32606027},
issn = {2379-5077},
support = {R35 GM122521/GM/NIGMS NIH HHS/United States ; U01 TW008163/TW/FIC NIH HHS/United States ; U19 TW008163/TW/FIC NIH HHS/United States ; },
abstract = {Shipworms play critical roles in recycling wood in the sea. Symbiotic bacteria supply enzymes that the organisms need for nutrition and wood degradation. Some of these bacteria have been grown in pure culture and have the capacity to make many secondary metabolites. However, little is known about whether such secondary metabolite pathways are represented in the symbiont communities within their hosts. In addition, little has been reported about the patterns of host-symbiont co-occurrence. Here, we collected shipworms from the United States, the Philippines, and Brazil and cultivated symbiotic bacteria from their gills. We analyzed sequences from 22 shipworm gill metagenomes from seven shipworm species and from 23 cultivated symbiont isolates. Using (meta)genome sequencing, we demonstrate that the cultivated isolates represent all the major bacterial symbiont species and strains in shipworm gills. We show that the bacterial symbionts are distributed among shipworm hosts in consistent, predictable patterns. The symbiotic bacteria harbor many gene cluster families (GCFs) for biosynthesis of bioactive secondary metabolites, only <5% of which match previously described biosynthetic pathways. Because we were able to cultivate the symbionts and to sequence their genomes, we can definitively enumerate the biosynthetic pathways in these symbiont communities, showing that ∼150 of ∼200 total biosynthetic gene clusters (BGCs) present in the animal gill metagenomes are represented in our culture collection. Shipworm symbionts occur in suites that differ predictably across a wide taxonomic and geographic range of host species and collectively constitute an immense resource for the discovery of new biosynthetic pathways corresponding to bioactive secondary metabolites.IMPORTANCE We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis.},
}
@article {pmid32605663,
year = {2020},
author = {Berg, G and Rybakova, D and Fischer, D and Cernava, T and Vergès, MC and Charles, T and Chen, X and Cocolin, L and Eversole, K and Corral, GH and Kazou, M and Kinkel, L and Lange, L and Lima, N and Loy, A and Macklin, JA and Maguin, E and Mauchline, T and McClure, R and Mitter, B and Ryan, M and Sarand, I and Smidt, H and Schelkle, B and Roume, H and Kiran, GS and Selvin, J and Souza, RSC and van Overbeek, L and Singh, BK and Wagner, M and Walsh, A and Sessitsch, A and Schloter, M},
title = {Microbiome definition re-visited: old concepts and new challenges.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {103},
pmid = {32605663},
issn = {2049-2618},
support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; European Union's Horizon 2020//Horizon 2020/International ; },
mesh = {*Microbiota ; Surveys and Questionnaires ; *Terminology as Topic ; },
abstract = {The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.},
}
@article {pmid32599485,
year = {2020},
author = {Balan, B and Dhaulaniya, AS and Jamwal, R and Yadav, A and Kelly, S and Cannavan, A and Singh, DK},
title = {Rapid detection and quantification of sucrose adulteration in cow milk using Attenuated total reflectance-Fourier transform infrared spectroscopy coupled with multivariate analysis.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {240},
number = {},
pages = {118628},
doi = {10.1016/j.saa.2020.118628},
pmid = {32599485},
issn = {1873-3557},
mesh = {Animals ; Cattle ; Female ; *Food Contamination/analysis ; Least-Squares Analysis ; *Milk ; Multivariate Analysis ; Spectroscopy, Fourier Transform Infrared ; Sucrose ; },
abstract = {Adulteration of milk to gain economic benefit has become a common practice in recent years. Sucrose is illegally added in milk to reconstitute its compositional requirement by improving the total solid contents. The present study is aimed to use FTIR spectroscopy in combination with multivariate chemometric modelling for the differentiation and quantification of sucrose in cow milk. Pure milk and adulterated milk spectra (0.5-7.5% w/v) were observed in the spectral region 4000-400 cm[-1]. Principal component analysis (PCA) was used for the discrimination of pure milk and adulterated milk. Soft independent modelling of class analogy (SIMCA) was able to classify test samples with a classification efficiency of 100%. Partial least square regression (PLS-R) and principle component regression (PCR) models were established for normal spectra, 1st derivative and 2nd derivative for the quantification of sucrose in milk. PLS-R model (normal spectra) in the combined wavenumber range of 1070-980 cm[-1] showed the best prediction based on parameters like coefficient of determination (R[2]) (Cal: 0.996; Val: 0.993), RMSE (Cal: 0.15% w/v; Val: 0.20% w/v), RE% (Cal: 4.9% w/v; Val: 5.1% w/v) and RPD (13.40). This method has a detection level of 0.5% w/v sucrose adulteration.},
}
@article {pmid32595912,
year = {2020},
author = {Hernández, M and Planells, P and Martínez, E and Mira, A and Carda-Diéguez, M},
title = {Microbiology of molar-incisor hypomineralization lesions. A pilot study.},
journal = {Journal of oral microbiology},
volume = {12},
number = {1},
pages = {1766166},
pmid = {32595912},
issn = {2000-2297},
abstract = {Objective: An insufficient mineralization (hypomineralization) in the teeth during the maturation stage of amelogenesis cause defects in 3-44% of children. Here, we describe for the first time the microbiota associated with these defects and compared it to healthy teeth within the same subjects. Methods: Supragingival dental plaque was sampled from healthy and affected teeth from 25 children with molar-incisor hypomineralization (MIH). Total DNA was extracted and the 16S rRNA gene was sequenced by Illumina sequencing in order to describe the bacterial composition. Results: We detected a higher bacterial diversity in MIH samples, suggesting better bacterial adhesion or higher number of niches in those surfaces. We found the genera Catonella, Fusobacterium, Campylobacter, Tannerella, Centipeda, Streptobacillus, Alloprevotella and Selenomonas associated with hypomineralized teeth, whereas Rothia and Lautropia were associated with healthy sites. Conclusion: The higher protein content of MIH-affected teeth could favour colonization by proteolytic microorganisms. The over-representation of bacteria associated with endodontic infections and periodontal pathologies suggests that, in addition to promote caries development, MIH could increase the risk of other oral diseases.},
}
@article {pmid32595184,
year = {2020},
author = {Morono, Y and Kubota, K and Tsukagoshi, D and Terada, T},
title = {EDTA-FISH: A Simple and Effective Approach to Reduce Non-specific Adsorption of Probes in Fluorescence in situ Hybridization (FISH) for Environmental Samples.},
journal = {Microbes and environments},
volume = {35},
number = {3},
pages = {},
pmid = {32595184},
issn = {1347-4405},
mesh = {Adsorption ; Edetic Acid/*chemistry ; Fluorescence ; Geologic Sediments/microbiology ; In Situ Hybridization, Fluorescence/*methods ; Indicators and Reagents/chemistry ; Oligonucleotide Probes/*chemistry ; Seawater/microbiology ; },
abstract = {Fluorescence in situ hybridization (FISH) is a widely used molecular technique in microbial ecology. However, the non-specific adsorption of fluorescent probes and resulting high intensity of background signals from mineral particles hampers the specific detection of microbial cells in grain-rich environmental samples, such as subseafloor sediments. We herein demonstrated that a new buffer composition containing EDTA efficiently reduced the adsorption of probes without compromising the properties of the FISH-based probing of microbes. The inclusion of a high concentration of EDTA in the buffer in our protocol provides a simple and effective approach for reducing the background in FISH for environmental samples.},
}
@article {pmid32594248,
year = {2021},
author = {Sugden, S and St Clair, CC and Stein, LY},
title = {Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {240-252},
pmid = {32594248},
issn = {1432-184X},
support = {RGPIN-2017-05915//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-04399//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Coyotes/*microbiology ; DNA, Bacterial/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Most knowledge of the vertebrate gut microbiota comes from fecal samples; due to difficulties involved in sample collection, the upper intestinal microbiota is poorly understood in wild animals despite its potential to inform broad interpretations about host-gut microbe relationships under natural conditions. Here, we used 16S rRNA gene sequencing to characterize the microbiota of wild coyotes (Canis latrans) along the gastrointestinal tract, including samples from the duodenum, jejunum, ileum, caecum, ascending and descending colon, and feces. We used this intestinal profile to (1) quantify how intestinal site and individual identity interact to shape the microbiota in an uncontrolled setting, and (2) evaluate whether the fecal microbiota adequately represent other intestinal sites. Microbial communities in the large intestine were distinct from those in the small intestine, with higher diversity and a greater abundance of anaerobic taxa. Within each of the small and large intestine, individual identity explained significantly more among-sample variation than specific intestinal sites, revealing the importance of individual variation in the microbiota of free-living animals. Fecal samples were not an adequate proxy for studying upper intestinal environments, as they contained only half the amplicon sequence variants (ASVs) present in the small intestine at three- to four-fold higher abundances. Our study is a unique biogeographical investigation of the microbiota using free-living mammals rather than livestock or laboratory organisms and provides a foundational understanding of the gastrointestinal microbiota in a wild canid.},
}
@article {pmid32592942,
year = {2020},
author = {Valencia, A and Ordonez, D and Wen, D and McKenna, AM and Chang, NB and Wanielista, MP},
title = {The interaction of dissolved organic nitrogen removal and microbial abundance in iron-filings based green environmental media for stormwater treatment.},
journal = {Environmental research},
volume = {188},
number = {},
pages = {109815},
doi = {10.1016/j.envres.2020.109815},
pmid = {32592942},
issn = {1096-0953},
mesh = {*Denitrification ; Filing ; Iron ; Nitrogen ; Oxidation-Reduction ; Rain ; *Water Purification ; Water Supply ; },
abstract = {Nonpoint sources pollution from agricultural crop fields and urbanized regions oftentimes have elevated concentrations of dissolved organic nitrogen (DON) in stormwater runoff, which are difficult for microbial communities to decompose. The impact of elevated DON can be circumvented through the use of green sorption media, such as Biosorption Activated Media (BAM) and Iron-Filing Green Environmental Media (IFGEM), which, as integral parts of microbial ecology, can contribute to the decomposition of DON. To compare the fate, transport, and transformation of DON in green sorption media relative to natural soil (control), a series of fixed-bed columns, which contain natural soil, BAM, and two types of IFGEM, respectively, were constructed to compare nutrient removal efficiency under three distinct stormwater influent conditions containing nitrogen and phosphorus. The interactions among six microbial species, including ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, complete ammonia oxidation (comammox) bacteria, anaerobic ammonium oxidation (anammox) bacteria, dissimilatory nitrate reduction to ammonium bacteria, and iron-reducing bacteria, were further analyzed from microbial ecology perspectives to determine the DON impact on nutrient removal in BAM and IFGEM. Natural soil was only able to achieve adequate DON transformation at the influent condition of lower nutrient concentration. However, the two types of IFGEM showed satisfactory nutrient removals and achieved greater transformation of DON relative to BAM when treating stormwater in all three influent conditions.},
}
@article {pmid32591381,
year = {2020},
author = {Luo, Y and Huang, Y and Xu, RX and Qian, B and Zhou, JW and Xia, XL},
title = {Primary and Secondary Succession Mediate the Accumulation of Biogenic Amines during Industrial Semidry Chinese Rice Wine Fermentation.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {17},
pages = {},
pmid = {32591381},
issn = {1098-5336},
mesh = {Bacteria/isolation &amp; purification ; Biogenic Amines/*metabolism ; China ; *Fermentation ; Microbiota/*physiology ; Wine/*microbiology ; },
abstract = {The use of exogenous functional microorganisms to regulate biogenic amine (BA) content is a common approach in fermentation systems. Here, to better understand the microbial traits of succession trajectories in resource-based and biotic interference systems, the BA-related primary and secondary succession were tracked during industrial semidry Chinese rice wine (CRW) fermentation. Dominant abundance and BA-associated microbial functionality based on phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that Citrobacter, Acinetobacter, Lactobacillus, Exiguobacterium, Bacillus, Pseudomonas, and Enterobacter spp. prominently contributed to the decarboxylase gene family in CRW. The expression levels of tyrosine decarboxylase (tyrDC), ornithine decarboxylase (odc), and agmatine deiminase (aguA) genes were assessed by quantitative PCR (qPCR). The transcription levels of these genes did not correlate with the BA formation rate during postfermentation, indicating that acidification and carbon source depletion upregulated the expression and microbes launch the dormancy strategy to respond to unfavorable conditions. Furthermore, microbial interference with CRW fermentation by Lactobacillus plantarum (ACBC271) and Staphylococcus xylosus (CGMCC1.8382) coinoculated at a ratio of 1:2 exhibited the best synergetic control of BA content. Spearman correlations revealed that Lactobacillus and Staphylococcus exhibited influence on BA-associated microbiota (|ρ| > 0), Exiguobacterium and Pseudomonas were strongly suppressed by Lactobacillus (ρ = -0.867 and ρ = -0.782, respectively; P < 0.05), and Staphylococcus showed the strongest inhibitory effect toward Lactobacillus (ρ = -0.115) and Citrobacter (ρ = -0.188) in the coinoculated 1:2 group. The high inhibitory effect of exogenous added strains on specific bacteria presented evidence for the obtained BA-associated contributors. Overall, this work provides important insight into the microbial traits that rely on resource usage and functional microbiota within food microbial ecology.IMPORTANCE Understanding the shifting patterns of substance usage and microbial interactions is a fundamental objective within microbiology and ecology. Analyses of primary and secondary microbial succession allow for determinations of taxonomic diversity, community traits, and functional transformations over time or after a disturbance. The kinetics of BA generation and the patterns of resource consumption, functional metagenome prediction, and microbial interactions were profiled to elucidate the equilibrium mechanism of microbial systems. Secondary succession after a disturbance triggers a change in resource usage, which in turn affects primary succession and metabolism. In this study, the functional potential of exogenous microorganisms under disturbance synergized with secondary succession strategies, including rebalancing and dormancy, which ultimately reduced BA accumulation. Thus, this succession system could facilitate the settling of essential issues with respect to microbial traits that rely on resource usage and microbial interactions that occur in natural ecosystems.},
}
@article {pmid32588072,
year = {2021},
author = {Zhou, X and Wang, JT and Wang, WH and Tsui, CK and Cai, L},
title = {Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {1004-1017},
pmid = {32588072},
issn = {1432-184X},
support = {NSFC 31725001//National Natural Science Foundation of China/ ; QYZDB-SSW-SMC044//Key Research Program of Frontier Sciences,CAS/ ; },
mesh = {Bacteria/genetics ; *Fusarium/genetics ; *Solanum lycopersicum ; *Mycobiome ; Plant Diseases ; },
abstract = {Fusarium wilt of tomato caused by the pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is one of the most devastating soilborne diseases of tomato. To evaluate whether microbial community composition associated with Fol-infected tomato is different from healthy tomato, we analyzed the tomato-associated microbes in both healthy and Fol-infected tomato plants at both the taxonomic and functional levels; both bacterial and fungal communities have been characterized from bulk soil, rhizosphere, rhizoplane, and endosphere of tomatoes using metabarcoding and metagenomics approaches. The microbial community (bacteria and fungi) composition of healthy tomato was significantly different from that of diseased tomato, despite similar soil physicochemical characteristics. Both fungal and bacterial diversities were significantly higher in the tomato plants that remained healthy than in those that became diseased; microbial diversities were also negatively correlated with the concentration of Fol pathogen. Network analysis revealed the microbial community of healthy tomato formed a larger and more complex network than that of diseased tomato, probably providing a more stable community beneficial to plant health. Our findings also suggested that healthy tomato contained significantly greater microbial consortia, including some well-known biocontrol agents (BCAs), and enriched more functional genes than diseased tomato. The microbial taxa enriched in healthy tomato plants are recognized as potential suppressors of Fol pathogen invasion.},
}
@article {pmid32583006,
year = {2020},
author = {Mapelli, F and Riva, V and Vergani, L and Choukrallah, R and Borin, S},
title = {Unveiling the Microbiota Diversity of the Xerophyte Argania spinosa L. Skeels Root System and Residuesphere.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {822-836},
pmid = {32583006},
issn = {1432-184X},
support = {688320//Horizon 2020 Framework Programme (Research and Innovation)/ ; 20172TZHYX//MIUR-PRIN2017/ ; },
mesh = {Bacteria/*isolation &amp; purification ; *Microbiota ; Morocco ; Plant Roots/*microbiology ; *Rhizosphere ; Sapotaceae/*microbiology ; *Soil Microbiology ; Trees/microbiology ; },
abstract = {The microbiota associated to xerophyte is a "black box" that might include microbes involved in plant adaptation to the extreme conditions that characterize their habitat, like water shortage. In this work, we studied the bacterial communities inhabiting the root system of Argania spinosa L. Skeels, a tree of high economic value and ecological relevance in Northern Africa. Illumina 16S rRNA gene sequencing and cultivation techniques were applied to unravel the bacterial microbiota's structure in environmental niches associated to argan plants (i.e., root endosphere, rhizosphere, root-surrounding soil), not associated to the plant (i.e., bulk soil), and indirectly influenced by the plant being partially composed by its leafy residue and the associated microbes (i.e., residuesphere). Illumina dataset indicated that the root system portions of A. spinosa hosted different bacterial communities according to their degree of association with the plant, enriching for taxa typical of the plant microbiome. Similar alpha- and beta-diversity trends were observed for the total microbiota and its cultivable fraction, which included 371 isolates. In particular, the residuesphere was the niche with the highest bacterial diversity. The Plant Growth Promotion (PGP) potential of 219 isolates was investigated in vitro, assessing several traits related to biofertilization and biocontrol, besides the production of exopolysaccharides. Most of the multivalent isolates showing the higher PGP score were identified in the residuesphere, suggesting it as a habitat that favor their proliferation. We hypothesized that these bacteria can contribute, in partnership with the argan root system, to the litter effect played by this tree in its native arid lands.},
}
@article {pmid32582085,
year = {2020},
author = {Trego, AC and Galvin, E and Sweeney, C and Dunning, S and Murphy, C and Mills, S and Nzeteu, C and Quince, C and Connelly, S and Ijaz, UZ and Collins, G},
title = {Growth and Break-Up of Methanogenic Granules Suggests Mechanisms for Biofilm and Community Development.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1126},
pmid = {32582085},
issn = {1664-302X},
support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Methanogenic sludge granules are densely packed, small, spherical biofilms found in anaerobic digesters used to treat industrial wastewaters, where they underpin efficient organic waste conversion and biogas production. Each granule theoretically houses representative microorganisms from all of the trophic groups implicated in the successive and interdependent reactions of the anaerobic digestion (AD) process. Information on exactly how methanogenic granules develop, and their eventual fate will be important for precision management of environmental biotechnologies. Granules from a full-scale bioreactor were size-separated into small (0.6-1 mm), medium (1-1.4 mm), and large (1.4-1.8 mm) size fractions. Twelve laboratory-scale bioreactors were operated using either small, medium, or large granules, or unfractionated sludge. After >50 days of operation, the granule size distribution in each of the small, medium, and large bioreactor sets had diversified beyond-to both bigger and smaller than-the size fraction used for inoculation. Interestingly, extra-small (XS; <0.6 mm) granules were observed, and retained in all of the bioreactors, suggesting the continuous nature of granulation, and/or the breakage of larger granules into XS bits. Moreover, evidence suggested that even granules with small diameters could break. "New" granules from each emerging size were analyzed by studying community structure based on high-throughput 16S rRNA gene sequencing. Methanobacterium, Aminobacterium, Propionibacteriaceae, and Desulfovibrio represented the majority of the community in new granules. H2-using, and not acetoclastic, methanogens appeared more important, and were associated with abundant syntrophic bacteria. Multivariate integration (MINT) analyses identified distinct discriminant taxa responsible for shaping the microbial communities in different-sized granules.},
}
@article {pmid32582065,
year = {2020},
author = {Navarro, MOP and Dilarri, G and Simionato, AS and Grzegorczyk, K and Dealis, ML and Cano, BG and Barazetti, AR and Afonso, L and Chryssafidis, AL and Ferreira, H and Andrade, G},
title = {Determining the Targets of Fluopsin C Action on Gram-Negative and Gram-Positive Bacteria.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {1076},
pmid = {32582065},
issn = {1664-302X},
abstract = {The antibiotic activity of metalloantibiotic compounds has been evaluated since the 90s, and many different modes of action were characterized. In the last decade, the effects of secondary metabolites produced by Pseudomonas aeruginosa LV strain, including a cupric compound identified as Fluopsin C, were tested against many pathogenic bacteria strains, proving their high antibiotic activity. In the present study, the bactericidal mechanisms of action of Fluopsin C and the semi-purified fraction F4A were elucidated. The results found in electron microscopy [scanning electron microscopy (SEM) and transmission electronic microscopy (TEM)] demonstrated that both Fluopsin C and F4A are affecting the cytoplasmatic membrane of Gram-positive and Gram-negative bacteria. These results were confirmed by fluorescence microscopy, where these bacteria presented permeabilization of their cytoplasmatic membranes after contact with the semi-purified fraction and pure compound. Using electronic and fluorescence microscopy, along with bacterial mutant strains with marked divisional septum, the membrane was defined as the primary target of Fluopsin C in the tested bacteria.},
}
@article {pmid32582043,
year = {2020},
author = {Gill, AS and Purnell, K and Palmer, MI and Stein, J and McGuire, KL},
title = {Microbial Composition and Functional Diversity Differ Across Urban Green Infrastructure Types.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {912},
pmid = {32582043},
issn = {1664-302X},
abstract = {Functional and biogeographical properties of soil microbial communities in urban ecosystems are poorly understood despite their role in metabolic processes underlying valuable ecosystem services. The worldwide emergence of engineered habitats in urban landscapes-green roofs, bioswales, and other types of soil-based green infrastructure-highlights the importance of understanding how environmental changes affect the community assembly processes that shape urban microbial diversity and function. In this study we investigated (1) whether engineered green roofs and bioswales in New York City had distinct microbial community composition and trait-associated diversity compared to non-engineered soils in parks and tree pits, and (2) if these patterns were consistent with divergent community assembly processes associated with engineered specifications of green infrastructure habitats not present in conventional, non-engineered green infrastructure; specifically, tree pit and park lawn soils. We found that green roofs and bioswales each had distinct bacterial and fungal communities, but that community composition and diversity were not significantly associated with geographic distance, suggesting that the processes structuring these differences are related to aspects of the habitats themselves. Bioswales, and to a lesser extent green roofs, also contained increased functional potential compared to conventional GI soils, based on the diversity and abundance of taxa associated with nitrogen cycling, biodegradation, decomposition, and traits positively associated with plant growth. We discuss these results in the context of community assembly theory, concluding that urban soil microbial community composition and diversity in engineered habitats are driven largely by environmental filtering, whereas stochastic processes are more important among non-engineered soils.},
}
@article {pmid32580805,
year = {2020},
author = {Garber, A and Hastie, PM and Farci, V and McGuinness, D and Bulmer, L and Alzahal, O and Murray, JMD},
title = {The effect of supplementing pony diets with yeast on 2. The faecal microbiome.},
journal = {Animal : an international journal of animal bioscience},
volume = {14},
number = {12},
pages = {2493-2502},
doi = {10.1017/S1751731120001512},
pmid = {32580805},
issn = {1751-732X},
mesh = {Animal Feed/analysis ; Animals ; Diet/veterinary ; Feces ; Horses ; Male ; *Microbiota ; *Saccharomyces cerevisiae ; },
abstract = {There is a need to develop feeding strategies to prevent the adverse effect of concentrate feeding in high-performance horses fed energy-dense diets aiming to maintain their health and welfare. The objective of this study is to determine the effect of a VistaEQ product containing 4% live yeast Saccharomyces cerevisiae (S. cerevisiae), with activity 5 × 108 colony-forming unit/g and fed 2 g/pony per day, on faecal microbial populations when supplemented with high-starch and high-fibre diets using Illumina next generation sequencing of the V3-V4 region of the 16S ribosomal RNA gene. The four treatments were allocated to eight mature Welsh section A pony geldings enrolled in a 4-period × 8 animal crossover design. Each 19-day experimental period consisted of an 18-day adaptation phase and a single collection day, followed by a 7-day wash out period. After DNA extraction from faeces and library preparation, α-diversity and linear discriminant analysis effect size were performed using 16S metagenomics pipeline in Quantitative Insights Into Microbial Ecology (QIIME™) and Galaxy/Hutlab. Differences between the groups were considered significant when linear discriminant analysis score was >2 corresponding to P < 0.05. The present study showed that S. cerevisiae used was able to induce positive changes in the equine microbiota when supplemented to a high-fibre diet: it increased relative abundance (RA) of Lachnospiraceae and Dehalobacteriaceae family members associated with a healthy core microbiome. Yeast supplementation also increased the RA of fibrolytic bacteria (Ruminococcus) when fed with a high-fibre diet and reduced the RA of lactate producing bacteria (Streptococcus) when a high-starch diet was fed. In addition, yeast increased the RA of acetic, succinic acid producing bacterial family (Succinivibrionaceae) and butyrate producing bacterial genus (Roseburia) when fed with high-starch and high-fibre diets, respectively. VistaEQ supplementation to equine diets can be potentially used to prevent acidosis and increase fibre digestibility. It may help to meet the energy requirements of performance horses while maintaining gut health.},
}
@article {pmid32577778,
year = {2020},
author = {Huang, R and Zeng, J and Zhao, D and Yong, B and Yu, Z},
title = {Co-association of Two nir Denitrifiers Under the Influence of Emergent Macrophytes.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {809-821},
doi = {10.1007/s00248-020-01545-2},
pmid = {32577778},
issn = {1432-184X},
support = {31730013, 41621002, 41871096, and 31971478//National Natural Science Foundation of China/ ; 2018B43414, 2019B17814//Fundamental Research Funds for the Central Universities/ ; 2018M642147//China Postdoctoral Science Foundation/ ; 2017FY100300//Science &amp; Technology Basic Resources Investigation Program of China/ ; },
mesh = {Bacteria/*enzymology ; *Bacterial Physiological Phenomena ; China ; *Denitrification ; Lakes/*microbiology ; *Microbiota ; Nitrate Reductase/*metabolism ; Poaceae ; },
abstract = {Diverse microorganisms perform similar metabolic process in biogeochemical cycles, whereas they are found of highly genomic differentiation. Biotic interactions should be considered in any community survey of these functional groups, as they contribute to community assembly and ultimately alter ecosystem properties. Current knowledge has mainly been achieved based on functional community characterized by a single gene using co-occurrence network analysis. Biotic interactions between functionally equivalent microorganisms, however, have received much less attention. Herein, we propose the nirK- and nirS-type denitrifier communities represented by these two nitrite reductase (nir)-encoding genes, as model communities to investigate the potential interactions of two nir denitrifiers. We evaluated co-occurrence patterns and co-association network structures of nir denitrifier community from an emergent macrophyte-dominated riparian zone of highly active denitrification in Lake Taihu, China. We found a more segregated pattern in combined nir communities than in individual communities. Network analyses revealed a modularized structure of associating nir denitrifiers. An increased proportion of negative associations among combined communities relative to those of individual communities indicated potential interspecific competition between nirK and nirS denitrifiers. pH and NH4[+]-N were the most important factors driving co-occurrence and mutual exclusion between nirK and nirS denitrifiers. We also showed the topological importance of nirK denitrifiers acting as module hubs for constructing entire association networks. We revealed previously unexplored co-association relationships between nirK and nirS denitrifiers, which were previously neglected in network analyses of individual communities. Using nir denitrifier community as a model, these findings would be helpful for us to understand the biotic interactions and mechanisms underlying how functional groups co-exist in performing biogeochemical cycles.},
}
@article {pmid32576522,
year = {2020},
author = {Lopetuso, LR and Quagliariello, A and Schiavoni, M and Petito, V and Russo, A and Reddel, S and Del Chierico, F and Ianiro, G and Scaldaferri, F and Neri, M and Cammarota, G and Putignani, L and Gasbarrini, A},
title = {Towards a disease-associated common trait of gut microbiota dysbiosis: The pivotal role of Akkermansia muciniphila.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {52},
number = {9},
pages = {1002-1010},
doi = {10.1016/j.dld.2020.05.020},
pmid = {32576522},
issn = {1878-3562},
mesh = {Akkermansia/physiology ; Case-Control Studies ; Dysbiosis/metabolism/*physiopathology ; Feces/*microbiology ; Gastrointestinal Diseases/metabolism/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestinal Mucosa/*metabolism/microbiology ; Permeability ; Phenotype ; },
abstract = {BACKGROUND: Gut microbiota exerts a crucial role in gastrointestinal (GI) and extra-intestinal (EI) disorders. In this context, Akkermansia muciniphila is pivotal for the maintenance of host health and has been correlated with several disorders.<br><br>AIM: To explore the potential role of A. muciniphila as common dysbiotic marker linked to the disease status.<br><br>METHODS: A cohort of patients affected by GI and EI disorders was enrolled and compared to healthy controls (CTRLs). A targeted-metagenomics approach combined to unsupervised cluster and machine learning (ML) analyses provided microbiota signatures.<br><br>RESULTS: Microbiota composition was associated to disease phenotype, therapies, diet and anthropometric features, identifying phenotype and therapies as the most impacting variables on microbiota ecology. Unsupervised cluster analyses identified one cluster composed by the majority of patients. DESeq2 algorithm identified ten microbial discriminatory features of patients and CTRLs clusters. Among these microbes, Akkermansia muciniphila resulted the discriminating ML node between patients and CTRLs, independently of specific GI/EI disease or confounding effects. A. muciniphila decrease represented a transversal signature of gut microbiota alteration, showing also an inverse correlation with &#x3b1;-diversity.<br><br>CONCLUSION: Overall, A. muciniphila decline may have a crucial role in affecting microbial ecology and in discriminating patients from healthy subjects. Its grading may be considered as a gut dysbiosis feature associated to disease-related microbiota profile.},
}
@article {pmid32574158,
year = {2020},
author = {Desai, C and Handley, SA and Rodgers, R and Rodriguez, C and Ordiz, MI and Manary, MJ and Holtz, LR},
title = {Growth velocity in children with Environmental Enteric Dysfunction is associated with specific bacterial and viral taxa of the gastrointestinal tract in Malawian children.},
journal = {PLoS neglected tropical diseases},
volume = {14},
number = {6},
pages = {e0008387},
pmid = {32574158},
issn = {1935-2735},
support = {R21 AI121939/AI/NIAID NIH HHS/United States ; },
mesh = {Bacteria/*classification/genetics/isolation &amp; purification/virology ; Bacteriophages/*classification/genetics/growth &amp; development/isolation &amp; purification ; Child, Preschool ; Female ; Gastrointestinal Diseases/microbiology/virology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology/*virology ; Growth Disorders/*microbiology/*virology ; Humans ; Infant ; Intestine, Small/microbiology/virology ; Malawi ; Male ; Microbial Viability ; Permeability ; RNA, Ribosomal, 16S ; },
abstract = {Environmental enteric dysfunction (EED) is characterized by diffuse villous atrophy of the small bowel. EED is strongly associated with stunting, a major public health problem linked to increased childhood morbidity and mortality. EED and subsequent stunting of linear growth are surmised to have microbial origins. To interrogate this relationship, we defined the comprehensive virome (eukaryotic virus and bacteriophage) and bacterial microbiome of a longitudinal cohort of rural Malawian children with extensive metadata and intestinal permeability testing at each time point. We found thirty bacterial taxa differentially associated with linear growth. We detected many eukaryotic viruses. Neither the total number of eukaryotic families nor a specific viral family was statistically associated with improved linear growth. We identified 3 differentially abundant bacteriophage among growth velocities. Interestingly, there was a positive correlation between bacteria and bacteriophage richness in children with subsequent adequate/moderate growth which children with subsequent poor growth lacked. This suggests that a disruption in the equilibrium between bacteria and bacteriophage communities might be associated with subsequent poor growth. Future studies of EED and stunting should include the evaluation of viral communities in addition to bacterial microbiota to understand the complete microbial ecology of these poorly understood entities.},
}
@article {pmid32572536,
year = {2020},
author = {Díaz-García, L and Bugg, TDH and Jiménez, DJ},
title = {Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {885-896},
doi = {10.1007/s00248-020-01546-1},
pmid = {32572536},
issn = {1432-184X},
support = {PR.3.2018.5287//Universidad de Los Andes/ ; BB/P01738X/1//BBSRC/ ; },
mesh = {Bacteria/*enzymology/genetics ; Biomass ; Lignin/*metabolism ; *Metagenome ; Metagenomics ; *Microbial Consortia ; Panicum/microbiology ; *Soil Microbiology ; Triticum/microbiology ; Zea mays/microbiology ; },
abstract = {An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.},
}
@article {pmid32572535,
year = {2020},
author = {Cohen, H and McFrederick, QS and Philpott, SM},
title = {Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria : RRH: Environmental Drivers of Bee Microbiome.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {897-907},
doi = {10.1007/s00248-020-01549-y},
pmid = {32572535},
issn = {1432-184X},
support = {2016-67019-25185//USDA-NIFA/ ; },
mesh = {Animals ; Bees/*microbiology ; Biodiversity ; California ; *Ecosystem ; Gardening/*methods ; *Gardens/classification ; *Microbiota ; },
abstract = {Wild bees encounter environmental microbes while foraging. While environmental context affects bee diversity, little is known about it how affects the wild bee microbiome. We used field surveys in 17 urban gardens to examine whether and how variation in local and landscape habitat features shapes the microbiome of the solitary Blue Orchard Bee, Osmia lignaria. We installed O. lignaria cocoons at each site, allowed bees to emerge and forage, then collected them. We measured local features of gardens using vegetation transects and landscape features with GIS. We found that in microbiome composition between bee individuals varied by environmental features such as natural habitat, floral resources, and bee species richness. We also found that environmental features were associated with the abundance of bacterial groups important for bee health, such as Lactobacillus. Our study highlights complex interactions between environment context, bee species diversity, and the bee-associated microbes.},
}
@article {pmid32572534,
year = {2020},
author = {Arce-Rodríguez, A and Puente-Sánchez, F and Avendaño, R and Libby, E and Mora-Amador, R and Rojas-Jimenez, K and Martínez, M and Pieper, DH and Chavarría, M},
title = {Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {793-808},
doi = {10.1007/s00248-020-01530-9},
pmid = {32572534},
issn = {1432-184X},
support = {VI 809-B6-524//Vicerrector&#xed;a de Investigaci&#xf3;n, Universidad de Costa Rica/ ; No FI-255B-17//The Costa Rican Ministry of Science, Technology and Telecommunication (MICITT) and Federal Ministry of Education and Research (BMBF)/ ; ERC250350-IPBSL//ERC grant IPBSL/ ; CTM2016-80095-C2-1-R//Spanish Economy and Competitiveness Ministry (MINECO)/ ; },
mesh = {Archaea/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; Costa Rica ; Hydrogen-Ion Concentration ; Microbiota/*physiology ; Oxygen/*analysis ; RNA, Archaeal/analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Rivers ; Volcanic Eruptions ; },
abstract = {We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L[-1], iron ~ 35-61 mg L[-1] (waters), and ~ 8-293 g kg[-1] (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L[-1]) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.},
}
@article {pmid32572216,
year = {2020},
author = {Li, L and Wang, S and Wang, H and Sahu, SK and Marin, B and Li, H and Xu, Y and Liang, H and Li, Z and Cheng, S and Reder, T and Çebi, Z and Wittek, S and Petersen, M and Melkonian, B and Du, H and Yang, H and Wang, J and Wong, GK and Xu, X and Liu, X and Van de Peer, Y and Melkonian, M and Liu, H},
title = {The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.},
journal = {Nature ecology &amp; evolution},
volume = {4},
number = {9},
pages = {1220-1231},
pmid = {32572216},
issn = {2397-334X},
mesh = {*Chlorophyta/genetics ; Genome ; Phylogeny ; },
abstract = {Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C4 photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B1, B7 and B12 auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution.},
}
@article {pmid32572143,
year = {2020},
author = {Ren, FR and Sun, X and Wang, TY and Yao, YL and Huang, YZ and Zhang, X and Luan, JB},
title = {Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits.},
journal = {The ISME journal},
volume = {14},
number = {10},
pages = {2542-2553},
pmid = {32572143},
issn = {1751-7370},
mesh = {Animals ; Bacteria/genetics ; *Biotin ; Escherichia coli ; *Hemiptera ; Symbiosis ; },
abstract = {Insect symbionts are widespread in nature and lateral gene transfer is prevalent in insect symbiosis. However, the function of horizontally transferred genes (HTGs) in insect symbiosis remains speculative, including the mechanism that enables insects to feed on plant phloem deficient in B vitamins. Previously, we found there is redundancy in biotin synthesis pathways from both whitefly Bemisia tabaci and symbiotic Hamiltonella due to the presence of whitefly HTGs. Here, we demonstrate that elimination of Hamiltonella decreased biotin levels but elevated the expression of horizontally transferred biotin genes in whiteflies. HTGs proteins exhibit specific expression patterns in specialized insect cells called bacteriocytes housing symbionts. Complementation with whitefly HTGs rescued E. coli biotin gene knockout mutants. Furthermore, silencing whitefly HTGs in Hamiltonella-infected whiteflies reduced biotin levels and hindered adult survival and fecundity, which was partially rescued by biotin supplementation. Each of horizontally transferred biotin genes are conserved in various laboratory cultures and species of whiteflies with geographically diverse distributions, which shares an evolutionary origin. We provide the first experimental evidence that biotin synthesized through acquired HTGs is important in whiteflies and may be as well in other animals. Our findings suggest that B vitamin provisioning in animal-microbe symbiosis frequently evolved from bacterial symbionts to animal hosts through horizontal gene transfer events. This study will also shed light on how the animal genomes evolve through functional transfer of genes with bacterial origin in the wider contexts of microbial ecology.},
}
@article {pmid32568403,
year = {2020},
author = {Toe, LC and Kerckhof, FM and De Bodt, J and Morel, FB and Ouedraogo, JB and Kolsteren, P and Van de Wiele, T},
title = {A prebiotic-enhanced lipid-based nutrient supplement (LNSp) increases Bifidobacterium relative abundance and enhances short-chain fatty acid production in simulated colonic microbiota from undernourished infants.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {7},
pages = {},
doi = {10.1093/femsec/fiaa105},
pmid = {32568403},
issn = {1574-6941},
mesh = {Bifidobacterium ; Child ; Fatty Acids, Volatile ; Humans ; Infant ; Lipids ; *Microbiota ; Nutrients ; *Prebiotics/analysis ; },
abstract = {Undernutrition remains a public health problem in the developing world with an attributable under-five death proportion of 45%. Lower gut microbiota diversity and poor metabolic output are associated with undernutrition and new therapeutic paths may come from steering gut microbiota composition and functionality. Using a dynamic gut model, the Simulator of Human Intestinal Microbial Ecosystem (SHIME®), we investigated the effect of a lipid-based nutrient supplement enriched with prebiotics (LNSp), compared to LNS alone and control treatment, on the composition and metabolic functionality of fecal microbiota from three infants suffering from undernutrition. LNS elicited a significant increase in acetate and branched-chain fatty acid production, and a higher relative abundance of the genera Prevotella, Megasphaera, Acinetobacter, Acidaminococcus and Pseudomonas. In contrast, LNSp treatment resulted in a significant 9-fold increase in Bifidobacterium relative abundance and a decrease in that of potential pathogens and detrimental bacteria such as Enterobacteriaceae spp. and Bilophila sp. Moreover, the LNSp treatment resulted in a significantly higher production of acetate, butyrate and propionate, as compared to control and LNS. Our results suggest that provision of prebiotic-enhanced LNS to undernourished children could be a possible strategy to steer the microbiota toward a more beneficial composition and metabolic activity. Further in vivo investigations are needed to assess these effects and their repercussion on nutritional status.},
}
@article {pmid32562995,
year = {2020},
author = {Rowles Iii, LS and Hossain, AI and Ramirez, I and Durst, NJ and Ward, PM and Kirisits, MJ and Araiza, I and Lawler, DF and Saleh, NB},
title = {Seasonal contamination of well-water in flood-prone colonias and other unincorporated U.S. communities.},
journal = {The Science of the total environment},
volume = {740},
number = {},
pages = {140111},
doi = {10.1016/j.scitotenv.2020.140111},
pmid = {32562995},
issn = {1879-1026},
mesh = {*Floods ; Humans ; Seasons ; Southwestern United States ; Texas ; United States ; Water Supply ; *Water Wells ; },
abstract = {Many of the six million residents of unincorporated communities in the United States depend on well-water to meet their needs. One group of unincorporated communities is the colonias, located primarily in several southwestern U.S. states. Texas is home to the largest number of these self-built communities, of mostly low-income families, lacking basic infrastructure. While some states have regulations that mandate minimum infrastructure for these communities, water and sewage systems are still lacking for many of their residents. Unprotected wells and self-built septic/cesspool systems serve as the primary infrastructure for many such colonias. This research was designed to probe how wells and septic/cesspool systems are influenced by heavy rainfall events. Such events are hypothesized to impact water quality with regard to human health. Inorganic and microbiological water quality of the wells in nine colonias located in Nueces County, Texas, were evaluated during dry and wet periods. Nueces County was selected as an example based on its flooding history and the fact that many colonias there depend entirely on well-water and septic/cesspool systems. The results demonstrate that well-water quality in these communities varies seasonally with respect to arsenic (up to 35 μg/L) and bacterial contamination (Escherichia coli), dependent on the amount of rainfall, which leaves this population vulnerable to health risks during both wet and dry periods. Microbial community analyses were also conducted on selected samples. To explore similar seasonal contamination of well-water, an analysis of unincorporated communities, flooding frequency, and arsenic contamination in wells was conducted by county throughout the United States. This nationwide analysis indicates that unincorporated communities elsewhere in the United States are likely experiencing comparable challenges for potable water access because of a confluence of socioeconomic, infrastructural, and policy realities.},
}
@article {pmid32561945,
year = {2021},
author = {Rapp, D and Ross, CM and Maclean, P and Cave, VM and Brightwell, G},
title = {Investigation of On-Farm Transmission Routes for Contamination of Dairy Cows with Top 7 Escherichia coli O-Serogroups.},
journal = {Microbial ecology},
volume = {81},
number = {1},
pages = {67-77},
pmid = {32561945},
issn = {1432-184X},
mesh = {Animals ; Animals, Wild/microbiology ; Cattle ; Dairying ; Escherichia coli Infections/*transmission ; Farms ; Feces/microbiology ; Foodborne Diseases/*microbiology ; Molecular Typing/methods ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Shiga-Toxigenic Escherichia coli/genetics/*isolation &amp; purification ; },
abstract = {Shiga toxin-producing Escherichia coli (STEC) are foodborne bacterial pathogens, with cattle a significant reservoir for human infection. This study evaluated environmental reservoirs, intermediate hosts and key pathways that could drive the presence of Top 7 STEC (O157:H7, O26, O45, O103, O111, O121 and O145) on pasture-based dairy herds, using molecular and culture-based methods. A total of 235 composite environmental samples (including soil, bedding, pasture, stock drinking water, bird droppings and flies and faecal samples of dairy animals) were collected from two dairy farms, with four sampling events on each farm. Molecular detection revealed O26, O45, O103 and O121 as the most common O-serogroups, with the greatest occurrence in dairy animal faeces (> 91%), environments freshly contaminated with faeces (> 73%) and birds and flies (> 71%). STEC (79 isolates) were a minor population within the target O-serogroups in all sample types but were widespread in the farm environment in the summer samplings. Phylogenetic analysis of whole genome sequence data targeting single nucleotide polymorphisms revealed the presence of several clonal strains on a farm; a single STEC clonal strain could be found in several sample types concurrently, indicating the existence of more than one possible route for transmission to dairy animals and a high rate of transmission of STEC between dairy animals and wildlife. Overall, the findings improved the understanding of the ecology of the Top 7 STEC in open farm environments, which is required to develop on-farm intervention strategies controlling these zoonoses.},
}
@article {pmid32561944,
year = {2020},
author = {Adomako, MO and Xue, W and Tang, M and Du, DL and Yu, FH},
title = {Synergistic Effects of Soil Microbes on Solidago canadensis Depend on Water and Nutrient Availability.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {837-845},
doi = {10.1007/s00248-020-01537-2},
pmid = {32561944},
issn = {1432-184X},
mesh = {*Microbiota ; Nutrients/*metabolism ; Soil/*chemistry ; *Soil Microbiology ; Solidago/*growth &amp; development ; Water/*metabolism ; },
abstract = {Soil microbes may greatly affect plant growth. While plants are commonly associated with diverse communities of soil microbes, complementary roles of different microbial communities that may stimulate synergistic effects on plant growth are not adequately tested. Also, such synergistic effects may vary with environmental conditions such as soil nutrient and water availability. We conducted a greenhouse experiment with a widespread clonal plant Solidago canadensis. The experiment was a factorial design with four levels of soil microbial inoculation (fresh soil inocula from grasslands in northern and southern China that were expected to differ in soil microbial composition, a mixture of the two fresh soil inocula, and a sterilized mixed inoculum control), two levels of nutrient availability (low vs. high), and two levels of water supply (low vs. high, i.e., 1376 vs. 352 mm per year). Irrespective of water supply and nutrient availability, total, aboveground, and belowground mass of S. canadensis were generally higher when the plant grew in soil inoculated with a mixture of soil microbes from the south and north of China (in the mixed inoculum treatment) than when it grew in soil inoculated with soil microbes from only the north or the south or the sterilized control. Such effects of soil microbes on total and aboveground mass were stronger under high than under low nutrient availability and also under high than under low water supply. Our results suggest that interactions of different soil microbial communities can result in a synergistic effect on plant growth and such a synergistic effect depends on environmental conditions. The findings shed light on the importance of plant-microbe interactions during the spreading of some plant species in face of increased atmospheric nutrient deposition coupled with altered rainfall pattern due to global change.},
}
@article {pmid32561583,
year = {2020},
author = {Henson, MW and Lanclos, VC and Pitre, DM and Weckhorst, JL and Lucchesi, AM and Cheng, C and Temperton, B and Thrash, JC},
title = {Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {17},
pages = {},
pmid = {32561583},
issn = {1098-5336},
mesh = {Bacteria/*isolation &amp; purification ; Bacteriological Techniques/*methods ; *Biodiversity ; Models, Biological ; Phytoplankton/*isolation &amp; purification ; },
abstract = {Cultivated bacterioplankton representatives from diverse lineages and locations are essential for microbiology, but the large majority of taxa either remain uncultivated or lack isolates from diverse geographic locales. We paired large-scale dilution-to-extinction (DTE) cultivation with microbial community analysis and modeling to expand the phylogenetic and geographic diversity of cultivated bacterioplankton and to evaluate DTE cultivation success. Here, we report results from 17 DTE experiments totaling 7,820 individual incubations over 3 years, yielding 328 repeatably transferable isolates. Comparison of isolates to microbial community data for source waters indicated that we successfully isolated 5% of the observed bacterioplankton community throughout the study; 43% and 26% of our isolates matched operational taxonomic units and amplicon single-nucleotide variants, respectively, within the top 50 most abundant taxa. Isolates included those from previously uncultivated clades such as SAR11 LD12 and Actinobacteria acIV, as well as geographically novel members from other ecologically important groups like SAR11 subclade IIIa, SAR116, and others, providing isolates in eight putatively new genera and seven putatively new species. Using a newly developed DTE cultivation model, we evaluated taxon viability by comparing relative abundance with cultivation success. The model (i) revealed the minimum attempts required for successful isolation of taxa amenable to growth on our media and (ii) identified possible subpopulation viability variation in abundant taxa such as SAR11 that likely impacts cultivation success. By incorporating viability in experimental design, we can now statistically constrain the effort necessary for successful cultivation of specific taxa on a defined medium.IMPORTANCE Even before the coining of the term "great plate count anomaly" in the 1980s, scientists had noted the discrepancy between the number of microorganisms observed under the microscope and the number of colonies that grew on traditional agar media. New cultivation approaches have reduced this disparity, resulting in the isolation of some of the "most wanted" bacterial lineages. Nevertheless, the vast majority of microorganisms remain uncultured, hampering progress toward answering fundamental biological questions about many important microorganisms. Furthermore, few studies have evaluated the underlying factors influencing cultivation success, limiting our ability to improve cultivation efficacy. Our work details the use of dilution-to-extinction (DTE) cultivation to expand the phylogenetic and geographic diversity of available axenic cultures. We also provide a new model of the DTE approach that uses cultivation results and natural abundance information to predict taxon-specific viability and iteratively constrain DTE experimental design to improve cultivation success.},
}
@article {pmid32561582,
year = {2020},
author = {Blackwell, N and Bryce, C and Straub, D and Kappler, A and Kleindienst, S},
title = {Genomic Insights into Two Novel Fe(II)-Oxidizing Zetaproteobacteria Isolates Reveal Lifestyle Adaption to Coastal Marine Sediments.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {17},
pages = {},
pmid = {32561582},
issn = {1098-5336},
mesh = {*Adaptation, Biological ; Environment ; Ferrous Compounds/*metabolism ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; Phylogeny ; Proteobacteria/*genetics ; Seawater/microbiology ; },
abstract = {The discovery of the novel Zetaproteobacteria class greatly expanded our understanding of neutrophilic, microaerophilic microbial Fe(II) oxidation in marine environments. Despite molecular techniques demonstrating their global distribution, relatively few isolates exist, especially from low-Fe(II) environments. Furthermore, the Fe(II) oxidation pathways used by Zetaproteobacteria remain poorly understood. Here, we present the genomes (>99% genome completeness) of two Zetaproteobacteria, which are the only cultivated isolates originating from typical low-Fe [porewater Fe(II), 70 to 100 μM] coastal marine sediments. The two strains share <90% average nucleotide identity (ANI) with each other and <80% ANI with any other Zetaproteobacteria genome. The closest relatives were Mariprofundus aestuarium strain CP-5 and Mariprofundus ferrinatatus strain CP-8 (96 to 98% 16S rRNA gene sequence similarity). Fe(II) oxidation of strains KV and NF is most likely mediated by the putative Fe(II) oxidase Cyc2. Interestingly, the genome of strain KV also encodes a putative multicopper oxidase, PcoAB, which could play a role in Fe(II) oxidation, a pathway found only in two other Zetaproteobacteria genomes (Ghiorsea bivora TAG-1 and SCGC AB-602-C20). The strains show potential adaptations to fluctuating O2 concentrations, indicated by the presence of both cbb3- and aa3-type cytochrome c oxidases, which are adapted to low and high O2 concentrations, respectively. This is further supported by the presence of several oxidative-stress-related genes. In summary, our results reveal the potential Fe(II) oxidation pathways employed by these two novel chemolithoautotrophic Fe(II)-oxidizing species and the lifestyle adaptations which enable the Zetaproteobacteria to survive in coastal environments with low Fe(II) and regular redox fluctuations.IMPORTANCE Until recently, the importance and relevance of Zetaproteobacteria were mainly thought to be restricted to high-Fe(II) environments, such as deep-sea hydrothermal vents. The two novel Mariprofundus isolates presented here originate from typical low-Fe(II) coastal marine sediments. As well as being low in Fe(II), these environments are often subjected to fluctuating O2 concentrations and regular mixing by wave action and bioturbation. The discovery of two novel isolates highlights the importance of these organisms in such environments, as Fe(II) oxidation has been shown to impact nutrients and trace metals. Genome analysis of these two strains further supported their lifestyle adaptation and therefore their potential preference for coastal marine sediments, as genes necessary for surviving dynamic O2 concentrations and oxidative stress were identified. Furthermore, our analyses also expand our understanding of the poorly understood Fe(II) oxidation pathways used by neutrophilic, microaerophilic Fe(II) oxidizers.},
}
@article {pmid32561577,
year = {2020},
author = {Onyango, SO and De Clercq, N and Beerens, K and Van Camp, J and Desmet, T and Van de Wiele, T},
title = {Oral Microbiota Display Profound Differential Metabolic Kinetics and Community Shifts upon Incubation with Sucrose, Trehalose, Kojibiose, and Xylitol.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {16},
pages = {},
pmid = {32561577},
issn = {1098-5336},
mesh = {Bacteria/*metabolism ; Disaccharides/metabolism ; Humans ; Kinetics ; *Microbiota ; Mouth/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sucrose/metabolism ; Sugars/*metabolism ; Trehalose/metabolism ; Xylitol/*metabolism ; },
abstract = {This study compares the metabolic properties of kojibiose, trehalose, sucrose, and xylitol upon incubation with representative oral bacteria as monocultures or synthetic communities or with human salivary bacteria in a defined medium. Compared to sucrose and trehalose, kojibiose resisted metabolism during a 48-h incubation with monocultures, except for Actinomyces viscosus Incubations with Lactobacillus-based communities, as well as salivary bacteria, displayed kojibiose metabolism, yet to a lesser extent than sucrose and trehalose. Concurring with our in vitro findings, screening for carbohydrate-active enzymes revealed that only Lactobacillus spp. and A. viscosus possess enzymes from glycohydrolase (GH) families GH65 and GH15, respectively, which are associated with kojibiose metabolism. Donor-dependent differences in salivary microbiome composition were noted, and differences in pH drop during incubation indicated different rates of sugar metabolism. However, functional analysis indicated that lactate, acetate, and formate evenly dominated the metabolic profile for all sugars except for xylitol. 16S rRNA gene sequencing analysis and α-diversity markers revealed that a significant shift of the microbiome community by sugars was more pronounced in sucrose and trehalose than in kojibiose and xylitol. In Streptococcus spp., a taxon linked to cariogenesis dominated in sucrose (mean ± standard deviation, 91.8 ± 6.4%) and trehalose (55.9 ± 38.6%), representing a high diversity loss. In contrast, Streptococcus (5.1 ± 3.7%) was less abundant in kojibiose, which instead was dominated by Veillonella (26.8 ± 19.6%), while for xylitol, Neisseria (29.4 ± 19.1%) was most abundant. Overall, kojibiose and xylitol incubations stimulated cariogenic species less yet closely maintained an abundance of key phyla and genera of the salivary microbiome, suggesting that kojibiose has low cariogenic properties.IMPORTANCE This study provides a detailed scientific insight on the metabolism of a rare disaccharide, kojibiose, whose mass production has recently been made possible. While the resistance of kojibiose was established with monocultures, delayed utilization of kojibiose was observed with communities containing lactobacilli and A. viscosus as well as with complex communities of bacteria from human saliva. Kojibiose is, therefore, less metabolizable than sucrose and trehalose. Moreover, although conventional sugars cause distinct shifts in salivary microbial communities, our study has revealed that kojibiose is able to closely maintain the salivary microbiome composition, suggesting its low cariogenic properties. This study furthermore underscores the importance and relevance of microbial culture and ex vivo mixed cultures to study cariogenicity and substrate utilization; this is in sharp contrast with tests that solely rely on monocultures such as Streptococcus mutans, which clearly fail to capture complex interactions between oral microbiota.},
}
@article {pmid32558638,
year = {2020},
author = {Prudence, SMM and Addington, E and Castaño-Espriu, L and Mark, DR and Pintor-Escobar, L and Russell, AH and McLean, TC},
title = {Advances in actinomycete research: an ActinoBase review of 2019.},
journal = {Microbiology (Reading, England)},
volume = {166},
number = {8},
pages = {683-694},
pmid = {32558638},
issn = {1465-2080},
support = {BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Actinobacteria/genetics/growth &amp; development/metabolism/*physiology ; Animals ; Bacteriological Techniques ; Biological Products/metabolism ; Biomedical Research/instrumentation/organization &amp; administration ; *Databases, Factual ; Environmental Microbiology ; Gene Expression Regulation, Bacterial ; Streptomyces/genetics/growth &amp; development/metabolism/physiology ; Symbiosis ; },
abstract = {The actinomycetes are Gram-positive bacteria belonging to the order Actinomycetales within the phylum Actinobacteria. They include members with significant economic and medical importance, for example filamentous actinomycetes such as Streptomyces species, which have a propensity to produce a plethora of bioactive secondary metabolites and form symbioses with higher organisms, such as plants and insects. Studying these bacteria is challenging, but also fascinating and very rewarding. As a Microbiology Society initiative, members of the actinomycete research community have been developing a Wikipedia-style resource, called ActinoBase, the purpose of which is to aid in the study of these filamentous bacteria. This review will highlight 10 publications from 2019 that have been of special interest to the ActinoBase community, covering 4 major components of actinomycete research: (i) development and regulation; (ii) specialized metabolites; (iii) ecology and host interactions; and (iv) technology and methodology.},
}
@article {pmid32556417,
year = {2020},
author = {Fuster, M and Billard, H and Mandart, M and Steiger, J and Sime-Ngando, T and Colombet, J},
title = {Trophic Conditions Influence Widespread Distribution of Aster-Like Nanoparticles Within Aquatic Environments.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {741-745},
doi = {10.1007/s00248-020-01541-6},
pmid = {32556417},
issn = {1432-184X},
mesh = {*Ecosystem ; France ; Nanoparticles/*analysis ; Prokaryotic Cells/*physiology ; *Rivers ; },
abstract = {Aster-like nanoparticles (ALNs) are newly described femto-entities. Their ecology (e.g., geographic distribution, spatial dynamic, preferences, forcing factors) is still unknown. Here, we report that these entities, which have largely been ignored until now, can develop or maintain themselves in most aquatic environments in the Loire River catchment, France. We observed a significant influence of the trophic state on ALN ecological distributions. A positive relationship between prokaryotic abundance and ALN (r[2] = 0.72, p < 0.01) has been identified, but its exact nature remains to be clarified. Combined with their ubiquitous distribution and high abundances (up to 7.9 × 10[6] ALNs mL[-1]) recorded in our samples, this probably makes ALNs an overlooked functional component in aquatic ecosystems.},
}
@article {pmid32556393,
year = {2021},
author = {Carteron, A and Beigas, M and Joly, S and Turner, BL and Laliberté, E},
title = {Temperate Forests Dominated by Arbuscular or Ectomycorrhizal Fungi Are Characterized by Strong Shifts from Saprotrophic to Mycorrhizal Fungi with Increasing Soil Depth.},
journal = {Microbial ecology},
volume = {82},
number = {2},
pages = {377-390},
pmid = {32556393},
issn = {1432-184X},
support = {RGPIN-2014-06106, RGPIN-2019-04537//Natural Sciences and Engineering Research Council of Canada/ ; 2016-NC-188823//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies/ ; },
mesh = {Forests ; Fungi/genetics ; *Mycorrhizae/genetics ; Soil ; Soil Microbiology ; Trees ; },
abstract = {In temperate and boreal forests, competition for soil resources between free-living saprotrophs and ectomycorrhizal (EcM) fungi has been suggested to restrict saprotrophic fungal dominance to the most superficial organic soil horizons in forests dominated by EcM trees. By contrast, lower niche overlap with arbuscular mycorrhizal (AM) fungi could allow fungal saprotrophs to maintain this dominance into deeper soil horizons in AM-dominated forests. Here we used a natural gradient of adjacent forest patches that were dominated by either AM or EcM trees, or a mixture of both to determine how fungal communities characterized with high-throughput amplicon sequencing change across organic and mineral soil horizons. We found a general shift from saprotrophic to mycorrhizal fungal dominance with increasing soil depth in all forest mycorrhizal types, especially in organic horizons. Vertical changes in soil chemistry, including pH, organic matter, exchangeable cations, and extractable phosphorus, coincided with shifts in fungal community composition. Although fungal communities and soil chemistry differed among adjacent forest mycorrhizal types, variations were stronger within a given soil profile, pointing to the importance of considering horizons when characterizing soil fungal communities. Our results also suggest that in temperate forests, vertical shifts from saprotrophic to mycorrhizal fungi within organic and mineral horizons occur similarly in both ectomycorrhizal and arbuscular mycorrhizal forests.},
}
@article {pmid32551196,
year = {2020},
author = {Coil, DA and Neches, RY and Lang, JM and Jospin, G and Brown, WE and Cavalier, D and Hampton-Marcell, J and Gilbert, JA and Eisen, JA},
title = {Bacterial communities associated with cell phones and shoes.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9235},
pmid = {32551196},
issn = {2167-8359},
abstract = {BACKGROUND: Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively.<br><br>FINDINGS: We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States.<br><br>CONCLUSIONS: We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of "environmental" taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.},
}
@article {pmid32547588,
year = {2020},
author = {Rantsiou, K and Giacosa, S and Pugliese, M and Englezos, V and Ferrocino, I and Río Segade, S and Monchiero, M and Gribaudo, I and Gambino, G and Gullino, ML and Rolle, L},
title = {Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Microbial Ecology and Chemical-Physical Grape Characteristics at Harvest.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {700},
pmid = {32547588},
issn = {1664-462X},
abstract = {Viticulture is a cropping system in which treatment against fungal diseases (in particular powdery and downy mildews) can be extremely frequent. Accordingly, a reduction in antimicrobial treatments and the application of environmentally-friendly compounds are becoming increasingly important for a more sustainable viticulture. In addition to their effect against pathogens, the impact of these products on the quality of the grapes is very important for the oenological industries, but unfortunately at present few data are available. We evaluated the effect of the application of biocontrol products and resistance inducers in the vineyard on the mechanical properties, microbial ecology, technological and phenolic maturity of Vitis vinifera "Nebbiolo" grapes at harvest. The yield and vigor of vines were not influenced by the treatments, nor were the production of primary and secondary metabolites. However, the active ingredients influenced the mechanical properties of the skin (hardness and thickness). A significant hardening of the skin was detected when laminarin and chito-oligosaccharides were used, and sulfur induced a thickening of the skin with potential consequences for wine quality. Furthermore, the yeast community present on grape berries was influenced by the treatments. The abundance of Aureobasidium pullulans, the dominant species on the grape berry, changed in response to the compounds used. In addition, Alternaria sp. was reduced in some treatments with a potentially positive effect on the quality and the safety of the grapes. This study provides an overview of the effect of biocontrol products and resistance inducers on microbial ecology and "Nebbiolo" grape quality, contributing to the establishment of more sustainable and effective defense strategies in viticulture.},
}
@article {pmid32546676,
year = {2020},
author = {Gulino, K and Rahman, J and Badri, M and Morton, J and Bonneau, R and Ghedin, E},
title = {Initial Mapping of the New York City Wastewater Virome.},
journal = {mSystems},
volume = {5},
number = {3},
pages = {},
pmid = {32546676},
issn = {2379-5077},
abstract = {Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments.IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.},
}
@article {pmid32540743,
year = {2020},
author = {Cahill, N and Morris, D},
title = {Recreational waters - A potential transmission route for SARS-CoV-2 to humans?.},
journal = {The Science of the total environment},
volume = {740},
number = {},
pages = {140122},
pmid = {32540743},
issn = {1879-1026},
mesh = {*Betacoronavirus ; COVID-19 ; *Coronavirus Infections/transmission ; Humans ; Pandemics ; Pneumonia, Viral ; *Recreation ; SARS-CoV-2 ; *Water Microbiology ; },
abstract = {Coronavirus disease 2019 (COVID-19), the respiratory illness caused by the novel virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has lead to high morbidity and mortality rates worldwide, has been causing major public health concerns since first detected in late 2019. Following identification of novel pathogens, questions in relation to dissemination of the pathogen and transmission routes begin to emerge. This rapidly spreading SARS-CoV-2 virus has been detected in both faecal and wastewater samples across the globe, highlighting the potential for faecal-oral transmission of the virus. As a result, concerns regarding the transmission of the virus in the environment and the risk associated with contracting the virus in recreational waters, particularly where inadequately treated wastewater is discharged, have been emerging in recent weeks. This paper highlights the need for further research to be carried out to investigate the presence, infectivity and viability of this newly identified SARS-CoV-2 virus in wastewater effluent and receiving recreational waters.},
}
@article {pmid32540193,
year = {2020},
author = {Candry, P and Ulcar, B and Petrognani, C and Rabaey, K and Ganigué, R},
title = {Ethanol:propionate ratio drives product selectivity in odd-chain elongation with Clostridium kluyveri and mixed communities.},
journal = {Bioresource technology},
volume = {313},
number = {},
pages = {123651},
doi = {10.1016/j.biortech.2020.123651},
pmid = {32540193},
issn = {1873-2976},
mesh = {Caproates ; *Clostridium kluyveri ; Ethanol ; Fermentation ; Propionates ; },
abstract = {Microbial production of valerate, a five-carbon carboxylate, can occur from propionate and ethanol through a process called odd-chain elongation. The generation of even-chain compounds in this process lowers product selectivity, forming a key challenge. This study investigated factors determining product selectivity during odd-chain elongation in an odd-chain elongating mixed community and the pure culture Clostridium kluyveri DSM555. Incubations at different ratios of ethanol:propionate showed that increasing ratios (from 0.5 to 7) lowered product specificity, as evidenced by a decrease in the odd:even product ratio from 5.5 to 1.5 for C. kluyveri and from 15 to 0.8 for the mixed community. The consistency of these observations with literature data suggests that control of ethanol:propionate ratio offers a robust tool for process control in odd-chain elongation, while the flexible metabolism can also have implications for efficient use of ethanol during even-chain elongation processes.},
}
@article {pmid32539984,
year = {2020},
author = {Zagdoun, M and Coeuret, G and N'Dione, M and Champomier-Vergès, MC and Chaillou, S},
title = {Large microbiota survey reveals how the microbial ecology of cooked ham is shaped by different processing steps.},
journal = {Food microbiology},
volume = {91},
number = {},
pages = {103547},
doi = {10.1016/j.fm.2020.103547},
pmid = {32539984},
issn = {1095-9998},
mesh = {Acids/analysis/metabolism ; Animals ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cooking ; Ethanol/analysis/metabolism ; Food Handling/*methods ; Food Microbiology ; Meat Products/analysis/*microbiology ; *Microbiota/genetics ; Pork Meat/*microbiology ; Seasons ; Swine ; },
abstract = {Cooked ham production involves numerous steps shaping the microbial communities of the final product, with consequences on spoilage metabolites production. To identify the main factors driving the ecology of ham and its spoilage, we designed a study encompassing five variables related to ham production: type of storage during meat transportation, churning speed, drain-off time, slicing line and O2 packaging permeability. About 200 samples from the same facility were obtained and characterized with respect to i) their microbiota based on gyrB amplicon sequencing ii) their production of spoilage-related metabolites based on E-Nose analysis and enzymatic assays. The slicing was the most critical step, shaping two general types of microbiota according to the slicing line: one dominated by Carnobacterium divergens and another one dominated by Leuconostoc carnosum and Serratia proteamaculans. Regarding metabolites production, L. carnosum was associated to d-lactic acid, ethanol and acetic acid production, whereas Serratia proteamaculans was associated to acetic acid production. This last species prevailed with highly O2-permeable packaging. Within a given slicing line, campaign-based variations were observed, with Lactobacillus sakei, Leuconostoc mesenteroides and Carnobacterium maltaromaticum prevalent in summer. L. sakei was associated with l-lactic acid production and C. maltaromaticum with formic and acetic acid productions.},
}
@article {pmid32539232,
year = {2021},
author = {Hussan, JR and Hunter, PJ},
title = {Our natural "makeup" reveals more than it hides: Modeling the skin and its microbiome.},
journal = {WIREs mechanisms of disease},
volume = {13},
number = {1},
pages = {e1497},
doi = {10.1002/wsbm.1497},
pmid = {32539232},
issn = {2692-9368},
mesh = {*Microbiota ; Skin ; },
abstract = {Skin is our primary interface with the environment. A structurally and functionally complex organ that hosts a dynamic ecosystem of microbes, and synthesizes many compounds that affect our well-being and psychosocial interactions. It is a natural platform of signal exchange between internal organs, skin resident microbes, and the environment. These interactions have gained a great deal of attention due to the increased prevalence of atopic diseases, and the co-occurrence of multiple allergic diseases related to allergic sensitization in early life. Despite significant advances in experimentally characterizing the skin, its microbial ecology, and disease phenotypes, high-levels of variability in these characteristics even for the same clinical phenotype are observed. Addressing this variability and resolving the relevant biological processes requires a systems approach. This review presents some of our current understanding of the skin, skin-immune, skin-neuroendocrine, skin-microbiome interactions, and computer-based modeling approaches to simulate this ecosystem in the context of health and disease. The review highlights the need for a systems-based understanding of this sophisticated ecosystem. This article is categorized under: Infectious Diseases > Computational Models.},
}
@article {pmid32535638,
year = {2020},
author = {Cardarelli, EL and Bargar, JR and Francis, CA},
title = {Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {778-792},
doi = {10.1007/s00248-020-01534-5},
pmid = {32535638},
issn = {1432-184X},
support = {DE-AC02-76SF00515//Office of Science/ ; DE-SC0019119//U.S. Department of Energy/ ; },
mesh = {Ammonia/*metabolism ; Archaea/isolation &amp; purification/*physiology ; Colorado ; Ecosystem ; Floods ; Microbiota/*physiology ; New Mexico ; Oxidation-Reduction ; *Soil Microbiology ; Wyoming ; },
abstract = {Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.},
}
@article {pmid32529471,
year = {2020},
author = {López-López, A and Mira, A},
title = {Shifts in Composition and Activity of Oral Biofilms After Fluoride Exposure.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {729-738},
doi = {10.1007/s00248-020-01531-8},
pmid = {32529471},
issn = {1432-184X},
support = {RTI 2018-102032-B-100//Ministerio de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {Adult ; Bacteria/classification/*drug effects/genetics/metabolism ; Bacterial Physiological Phenomena/*drug effects ; Biofilms/*drug effects ; Cariostatic Agents/*pharmacology ; Dental Caries/*prevention &amp; control ; Humans ; Sodium Fluoride/*pharmacology ; Species Specificity ; },
abstract = {Oral diseases are biofilm-mediated diseases caused by imbalances in the ecology of resident microflora. Among them, dental caries (tooth decay) is considered the most common disease worldwide, and toothbrushing, which physically eliminates the oral biofilm, is the most widespread prevention strategy. Although it is well established that fluoride increases enamel resistance to acidic pH and promotes tooth remineralization, its effect on the biofilm bacterial communities' composition and metabolism is not fully understood. We have grown in vitro oral biofilms and used 16S rRNA Illumina sequencing to study the effect of fluoride on DNA- and RNA-based bacterial populations. In addition, a metatranscriptomic approach has also been performed, in which total RNA has been sequenced to study gene expression profiles in the presence/absence of 500 ppm sodium fluoride. Our data show a lower pH drop and a clear shift in total and metabolically active bacterial composition after fluoride exposure. Streptococcus oralis was the species most affected, with a 10-fold reduction in both DNA and RNA samples, whereas Rothia mucilaginosa underwent an 8-fold increase in the DNA and S. salivarius a 4- and 5-fold increase in the RNA and DNA samples, respectively. The metatranscriptomes indicated that fluoride exposure induced a dramatic shutdown of sugar metabolism, including significant under-expression of different sugar transporters, fucosidases, and a pyruvate oxidase, among others. The reduction in saccharolytic organisms and the inhibition of sugar fermentation pathways by fluoride may therefore be considered instrumental for the beneficial effect of fluoride-containing oral hygiene products.},
}
@article {pmid32525738,
year = {2020},
author = {Aszalós, JM and Szabó, A and Megyes, M and Anda, D and Nagy, B and Borsodi, AK},
title = {Bacterial Diversity of a High-Altitude Permafrost Thaw Pond Located on Ojos del Salado (Dry Andes, Altiplano-Atacama Region).},
journal = {Astrobiology},
volume = {20},
number = {6},
pages = {754-765},
doi = {10.1089/ast.2018.2012},
pmid = {32525738},
issn = {1557-8070},
mesh = {*Altitude ; Bacteria/*genetics/growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; *Genetic Variation ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing ; Permafrost/*microbiology ; Phylogeny ; Ponds/*microbiology ; Principal Component Analysis ; South America ; Water ; },
abstract = {Microbial ecology of permafrost, due to its ecological and astrobiological importance, has been in the focus of studies in past decades. Although permafrost is an ancient and stable environment, it is also subjected to current climate changes. Permafrost degradation often results in generation of thaw ponds, a phenomenon not only reported mainly from polar regions but also present in high-altitude permafrost environments. Our knowledge about microbial communities of thaw ponds in these unique, remote mountain habitats is sparse. This study presents the first culture collection and results of the next-generation DNA sequencing (NGS) analysis of bacterial communities inhabiting a high-altitude permafrost thaw pond. In February 2016, a permafrost thaw pond on the Ojos del Salado at 5900 m a.s.l. (meters above sea level) was sampled as part of the Hungarian Dry Andes Research Programme. A culture collection of 125 isolates was established, containing altogether 11 genera belonging to phyla Bacteroidetes, Actinobacteria, and Proteobacteria. Simplified bacterial communities with a high proportion of candidate and hitherto uncultured bacteria were revealed by Illumina MiSeq NGS. Water of the thaw pond was dominated by Bacteroidetes and Proteobacteria, while in the sediment of the lake and permafrost, members of Acidobacteria, Actinobacteria, Bacteroidetes, Patescibacteria, Proteobacteria, and Verrucomicrobia were abundant. This permafrost habitat can be interesting as a potential Mars analog.},
}
@article {pmid32525284,
year = {2021},
author = {Verbeeck, K and De Vrieze, J and Pikaar, I and Verstraete, W and Rabaey, K},
title = {Assessing the potential for up-cycling recovered resources from anaerobic digestion through microbial protein production.},
journal = {Microbial biotechnology},
volume = {14},
number = {3},
pages = {897-910},
pmid = {32525284},
issn = {1751-7915},
mesh = {Anaerobiosis ; Animals ; *Biofuels ; Bioreactors ; *Manure ; Methane ; Swine ; },
abstract = {Anaerobic digesters produce biogas, a mixture of predominantly CH4 and CO2 , which is typically incinerated to recover electrical and/or thermal energy. In a context of circular economy, the CH4 and CO2 could be used as chemical feedstock in combination with ammonium from the digestate. Their combination into protein-rich bacterial, used as animal feed additive, could contribute to the ever growing global demand for nutritive protein sources and improve the overall nitrogen efficiency of the current agro- feed/food chain. In this concept, renewable CH4 and H2 can serve as carbon-neutral energy sources for the production of protein-rich cellular biomass, while assimilating and upgrading recovered ammonia from the digestate. This study evaluated the potential of producing sustainable high-quality protein additives in a decentralized way through coupling anaerobic digestion and microbial protein production using methanotrophic and hydrogenotrophic bacteria in an on-farm bioreactor. We show that a practical case digester handling liquid piggery manure, of which the energy content is supplemented for 30% with co-substrates, provides sufficient biogas to allow the subsequent microbial protein as feed production for about 37% of the number of pigs from which the manure was derived. Overall, producing microbial protein on the farm from available methane and ammonia liberated by anaerobic digesters treating manure appears economically and technically feasible within the current range of market prices existing for high-quality protein. The case of producing biomethane for grid injection and upgrading the CO2 with electrolytic hydrogen to microbial protein by means of hydrogen-oxidizing bacteria was also examined but found less attractive at the current production prices of renewable hydrogen. Our calculations show that this route is only of commercial interest if the protein value equals the value of high-value protein additives like fishmeal and if the avoided costs for nutrient removal from the digestate are taken into consideration.},
}
@article {pmid32523566,
year = {2020},
author = {Taparia, T and Krijger, M and Hodgetts, J and Hendriks, M and Elphinstone, JG and van der Wolf, J},
title = {Six Multiplex TaqMan[TM]-qPCR Assays for Quantitative Diagnostics of Pseudomonas Species Causative of Bacterial Blotch Diseases of Mushrooms.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {989},
pmid = {32523566},
issn = {1664-302X},
abstract = {Bacterial blotch is a group of economically important diseases of the common button mushroom (Agaricus bisporus). Once the pathogens are introduced to a farm, mesophilic growing conditions (that are optimum for mushroom production) result in severe and widespread secondary infections. Efficient, timely and quantitative detection of the pathogens is hence critical for the design of localized control strategies and prediction of disease risk. This study describes the development of real-time TaqMan[TM] assays that allow molecular diagnosis of three currently prevalent bacterial blotch pathogens: "Pseudomonas gingeri," Pseudomonas tolaasii and (as yet uncharacterized) Pseudomonas strains (belonging to Pseudomonas salomonii and Pseudomonas edaphica). For each pathogen, assays targeting specific DNA markers on two different loci, were developed for primary detection and secondary verification. All six developed assays showed high diagnostic specificity and sensitivity when tested against a panel of 63 Pseudomonas strains and 40 other plant pathogenic bacteria. The assays demonstrated good analytical performance indicated by linearity across calibration curve (>0.95), amplification efficiency (>90%) and magnitude of amplification signal (>2.1). The limits of detection were optimized for efficient quantification in bacterial cultures, symptomatic tissue, infected casing soil and water samples from mushroom farms. Each target assay was multiplexed with two additional assays. Xanthomonas campestris was detected as an extraction control, to account for loss of DNA during sample processing. And the total Pseudomonas population was detected, to quantify the proportion of pathogenic to beneficial Pseudomonas in the soil. This ratio is speculated to be an indicator for blotch outbreaks. The multiplexed assays were successfully validated and applied by routine testing of diseased mushrooms, peat sources, casing soils, and water from commercial production units.},
}
@article {pmid32518182,
year = {2020},
author = {Topçuoğlu, BD and Lesniak, NA and Ruffin, MT and Wiens, J and Schloss, PD},
title = {A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems.},
journal = {mBio},
volume = {11},
number = {3},
pages = {},
pmid = {32518182},
issn = {2150-7511},
support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA215574/CA/NCI NIH HHS/United States ; },
mesh = {Colonic Neoplasms/diagnosis ; Feces/microbiology ; Gastrointestinal Diseases/*diagnosis ; Humans ; Linear Models ; Logistic Models ; Machine Learning/*standards ; Microbiota/*genetics ; Predictive Value of Tests ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Machine learning (ML) modeling of the human microbiome has the potential to identify microbial biomarkers and aid in the diagnosis of many diseases such as inflammatory bowel disease, diabetes, and colorectal cancer. Progress has been made toward developing ML models that predict health outcomes using bacterial abundances, but inconsistent adoption of training and evaluation methods call the validity of these models into question. Furthermore, there appears to be a preference by many researchers to favor increased model complexity over interpretability. To overcome these challenges, we trained seven models that used fecal 16S rRNA sequence data to predict the presence of colonic screen relevant neoplasias (SRNs) (n = 490 patients, 261 controls and 229 cases). We developed a reusable open-source pipeline to train, validate, and interpret ML models. To show the effect of model selection, we assessed the predictive performance, interpretability, and training time of L2-regularized logistic regression, L1- and L2-regularized support vector machines (SVM) with linear and radial basis function kernels, a decision tree, random forest, and gradient boosted trees (XGBoost). The random forest model performed best at detecting SRNs with an area under the receiver operating characteristic curve (AUROC) of 0.695 (interquartile range [IQR], 0.651 to 0.739) but was slow to train (83.2 h) and not inherently interpretable. Despite its simplicity, L2-regularized logistic regression followed random forest in predictive performance with an AUROC of 0.680 (IQR, 0.625 to 0.735), trained faster (12 min), and was inherently interpretable. Our analysis highlights the importance of choosing an ML approach based on the goal of the study, as the choice will inform expectations of performance and interpretability.IMPORTANCE Diagnosing diseases using machine learning (ML) is rapidly being adopted in microbiome studies. However, the estimated performance associated with these models is likely overoptimistic. Moreover, there is a trend toward using black box models without a discussion of the difficulty of interpreting such models when trying to identify microbial biomarkers of disease. This work represents a step toward developing more-reproducible ML practices in applying ML to microbiome research. We implement a rigorous pipeline and emphasize the importance of selecting ML models that reflect the goal of the study. These concepts are not particular to the study of human health but can also be applied to environmental microbiology studies.},
}
@article {pmid32515051,
year = {2020},
author = {Koch, C and Kuchenbuch, A and Marosvölgyi, M and Weisshart, K and Harnisch, F},
title = {Label-Free Four-Dimensional Visualization of Anaerobically Growing Electroactive Biofilms.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {97},
number = {7},
pages = {737-741},
doi = {10.1002/cyto.a.24169},
pmid = {32515051},
issn = {1552-4930},
mesh = {*Biofilms ; Microscopy, Fluorescence ; },
abstract = {Light sheet fluorescence microscopy (LSFM) allows nondestructive, label-free and in vivo imaging of large specimen, even at nontransparent surfaces. We show that LSFM can be applied for label-free analyses of prokaryotes on the example of electroactive biofilms. Biofilm growth is linked to the production of current serving as measure of metabolic activity in vivo by monitoring with high spatial and temporal resolution. After 35 h of exponential growth, a homogeneous biofilm with a thickness of 9 μm was formed. This was followed by a stratification of the biofilm including the formation of 3D structures over the next 100 h. Light reflection was sufficient to visualize the biofilm structure and development over time and the terminal morphology was confirmed using fluorescence staining. This proof of concept on using LSFM for investigation of biofilms opens the door for its application in the entire field of microbial ecology. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.},
}
@article {pmid32514926,
year = {2020},
author = {McGee, CF},
title = {The effects of silver nanoparticles on the microbial nitrogen cycle: a review of the known risks.},
journal = {Environmental science and pollution research international},
volume = {27},
number = {25},
pages = {31061-31073},
doi = {10.1007/s11356-020-09548-9},
pmid = {32514926},
issn = {1614-7499},
mesh = {*Metal Nanoparticles ; Nitrogen Cycle ; Sewage ; Silver/*analysis ; Soil ; },
abstract = {The nitrogen cycle is an integral biogeochemical function for maintaining healthy environments. Nitrogen is a key nutrient that must be continuously replenished through recycling mechanisms to sustain ecosystems, disruption to which can result in compromised ecosystem functioning. Certain stages in the microbial conversion of nitrogen compounds are performed by a limited range of micro-organisms making these key functional species in ecosystems. The growing industrial use of silver nanoparticles (AgNPs) potentially poses significant risks for microbial nitrogen cycling species. AgNPs possess potent antimicrobial properties and are expected to reach a range of natural environments through several routes of exposure. Certain functional nitrogen cycling microbes have been shown to be highly susceptible to AgNP toxicity. The current literature indicates that AgNPs can negatively affect certain nitrogen fixing, nitrifying and denitrifying microbes in vitro. In vivo studies investigating the effect of AgNPs on nitrogen cycling microbial communities and nitrogen transformation rates in soil, sediment and sludge environments have also indicated disruption of these functional processes. This review provides a comprehensive description of the current state of knowledge regarding the toxicity of AgNPs to nitrogen cycling communities. The aim of the review is to highlight the most susceptible stages in the nitrogen cycle and the implications for the affected ecosystems.},
}
@article {pmid32514604,
year = {2020},
author = {Ruan, Y and Wang, T and Guo, S and Ling, N and Shen, Q},
title = {Plant Grafting Shapes Complexity and Co-occurrence of Rhizobacterial Assemblages.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {643-655},
doi = {10.1007/s00248-020-01532-7},
pmid = {32514604},
issn = {1432-184X},
support = {IRT_17R56//Innovative Research Team Development Plan of the Ministry of Education of China/ ; KYT201802//Fundamental Research Funds for the Central Universities/ ; 31772398//National Nature Science Foundation of China/ ; },
mesh = {Bacteria/*isolation &amp; purification ; Citrullus/microbiology ; Cucurbitaceae/*microbiology ; Microbiota/*physiology ; Plant Roots/*microbiology ; *Rhizosphere ; *Soil Microbiology ; },
abstract = {Grafting is a basic technique which is widely used to increase yield and enhance biotic and abiotic stress tolerance in plant production. The diversity and interactions of rhizobacterial assemblages shaped by grafting are important for the growth of their hosts but remain poorly understood. To test the hypothesis that plant grafting shapes complexity and co-occurrence of rhizobacterial assemblage, four types of plants, including ungrafted bottle gourd (B), ungrafted watermelon (W), grafted watermelon with bottle gourd rootstock (W/B), and grafted bottle gourd with watermelon rootstock (B/W), were cultivated in two soil types in a greenhouse, and the rhizosphere bacterial communities were analyzed by 16S rRNA gene high-throughput sequencing. Both the soil type and grafting significantly influenced the bacterial community composition. Grafting increased bacterial within-sample diversity in both soils. Core enriched operational taxonomic units (OTUs) in the W/B rhizosphere compared with the other three treatments (B, W, and B/W) were mainly affiliated with Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which are likely related to methanol oxidation, methylotrophy, fermentation, and ureolysis. Co-occurrence network analysis proved that grafting increased network complexity, including the number of nodes, edges, and modules. Moreover, grafting strengthened the structural robustness of the network in the rhizosphere, while ungrafted watermelon had the lowest network robustness. Homogeneous selection played a predominant role in bacterial community assembly, and the contribution of dispersal limitation was increased in grafted watermelon with bottle gourd rootstock. Grafting increased the diversity and transformed the network topology of the bacterial community, which indicated that grafting could improve species coexistence in the watermelon rhizosphere.},
}
@article {pmid32514073,
year = {2020},
author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Yarza, P and Hedlund, BP and Reysenbach, AL},
title = {Roadmap for naming uncultivated Archaea and Bacteria.},
journal = {Nature microbiology},
volume = {5},
number = {8},
pages = {987-994},
pmid = {32514073},
issn = {2058-5276},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Bacterial ; Metagenome ; Phylogeny ; Prokaryotic Cells/classification ; Sequence Analysis, DNA ; Terminology as Topic ; },
abstract = {The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.},
}
@article {pmid32512474,
year = {2020},
author = {Di Cesare, A and Pjevac, P and Eckert, E and Curkov, N and Miko Šparica, M and Corno, G and Orlić, S},
title = {The role of metal contamination in shaping microbial communities in heavily polluted marine sediments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {265},
number = {Pt B},
pages = {114823},
doi = {10.1016/j.envpol.2020.114823},
pmid = {32512474},
issn = {1873-6424},
mesh = {Croatia ; Environmental Monitoring ; Environmental Pollution ; Geologic Sediments ; Metals, Heavy/*analysis ; *Microbiota ; Water Pollutants, Chemical/*analysis ; },
abstract = {Microorganisms in coastal sediments are fundamental for ecosystem functioning, and regulate processes relevant in global biogeochemical cycles. Still, our understanding of the effects anthropogenic perturbation and pollution can have on microbial communities in marine sediments is limited. We surveyed the microbial diversity, and the occurrence and abundance of metal and antibiotic resistance genes is sediments collected from the Pula Bay (Croatia), one of the most significantly polluted sites along the Croatian coast. With a collection of 14 samples from the bay area, we were able to generate a detailed status quo picture of a site that only recently started a cleaning and remediation process (closing of sewage pipes and reduction of industrial activity). The concentrations of heavy metals in Pula Bay sediments are significantly higher than in pristine sediments from the Adriatic Sea, and in some cases, manifold exceed international sediment quality guidelines. While the sedimentary concentrations of heavy metals did significantly influence the abundance of the tested metal resistance genes, no strong effect of heavy metal pollution on the overall microbial community composition was observed. Like in many other marine sediments, Gammaproteobacteria, Bacteroidota and Desulfobacterota dominated the microbial community composition in most samples, and community assembly was primarily driven by water column depth and nutrient (carbon and nitrogen) availability, regardless of the degree of heavy metal pollution.},
}
@article {pmid32511085,
year = {2020},
author = {Gurney, J and Azimi, S and Brown, SP and Diggle, SP},
title = {Combinatorial quorum sensing in Pseudomonas aeruginosa allows for novel cheating strategies.},
journal = {Microbiology (Reading, England)},
volume = {166},
number = {8},
pages = {777-784},
doi = {10.1099/mic.0.000941},
pmid = {32511085},
issn = {1465-2080},
mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; Culture Media/metabolism ; Genetic Fitness ; Microbial Interactions ; Mutation ; Pseudomonas aeruginosa/*physiology ; Quorum Sensing/genetics/*physiology ; Signal Transduction/genetics ; },
abstract = {In the opportunistic pathogen Pseudomonas aeruginosa, quorum sensing (QS) is a social trait that is exploitable by non-cooperating cheats. Previously it has been shown that by linking QS to the production of both public and private goods, cheats can be prevented from invading populations of cooperators and this was described by Dandekar et al. (Science 2012;338:264-266) as 'a metabolic incentive to cooperate'. We hypothesized that P. aeruginosa could evolve novel cheating strategies to circumvent private goods metabolism by rewiring its combinatorial response to two QS signals (3O-C12-HSL and C4-HSL). We performed a selection experiment that cycled P. aeruginosa between public and private goods growth media and evolved an isolate that rewired its control of cooperative protease expression from a synergistic (AND-gate) response to dual-signal input to a 3O-C12-HSL-only response. We show that this isolate circumvents metabolic incentives to cooperate and acts as a combinatorial signalling cheat, with higher fitness in competition with its ancestor. Our results show three important principles: first, combinatorial QS allows for diverse social strategies to emerge; second, restrictions levied by private goods are not sufficient to explain the maintenance of cooperation in natural populations; and third, modifying combinatorial QS responses could result in important physiological outcomes in bacterial populations.},
}
@article {pmid32510910,
year = {2020},
author = {Iddins, BO and Waugh, MH and Robbins, T and Cunningham, J and Graham, DE and Finn, MT},
title = {Antimicrobial Silver Touch Surfaces in an Occupational Medicine Clinic.},
journal = {Journal of occupational and environmental medicine},
volume = {62},
number = {6},
pages = {e287-e288},
pmid = {32510910},
issn = {1536-5948},
mesh = {*Anti-Infective Agents/pharmacology ; Health Facilities ; Humans ; *Occupational Medicine ; Silver/*pharmacology ; },
}
@article {pmid32510000,
year = {2020},
author = {Chopra, S and Kumar, D},
title = {Ibuprofen as an emerging organic contaminant in environment, distribution and remediation.},
journal = {Heliyon},
volume = {6},
number = {6},
pages = {e04087},
pmid = {32510000},
issn = {2405-8440},
abstract = {Pharmaceutical and personal care products (PPCPs) are the one of sub-class under emerging organic contaminants (EOCs). Ibuprofen is the world's third most consumable drug. This drug enters into our water system through human pharmaceutical use. It attracts the attention of environmentalist on the basis of risk associated, presence and transformation in the environment. The detection and removal are the two key area where we need to focus. The concentration of such compounds in waterbodies detected through conventional and also by the advanced methods. This review we described the available technologies including chemical, physical and biological methods, etc used the for removal of Ibuprofen. The pure culture based method, mixed culture approach and activated sludge culture approach focused and pathway of degradation of ibuprofen was deciphered by using the various methods of structure determination. The various degradation methods used for Ibuprofen are discussed. The advanced methods coupled with physical, chemical, biological, chemical methods like ozonolysis, oxidation and adsorption, nanotechnology based methods, nanocatalysis and use of nonosensors to detect the presence of small amount in waterbodies can enhance the future degradation of this drug. It is necessary to develop the new detection methods to enhance the detection of such pollutants. With the developments in new detection methods based on GC-MS//MS, HPLC, LC/MS and nanotechnology based sensors makes easier detection of these compounds which can detect even very minute amount with great sensitivity and in less time. Also, the isolation and characterization of more potent microbial strains and nano-photocatalysis will significantly increase the future degradation of such harmful compounds from the environment.},
}
@article {pmid32508155,
year = {2020},
author = {Mercer, KE and Yeruva, L and Pack, L and Graham, JL and Stanhope, KL and Chintapalli, SV and Wankhade, UD and Shankar, K and Havel, PJ and Adams, SH and Piccolo, BD},
title = {Xenometabolite signatures in the UC Davis type 2 diabetes mellitus rat model revealed using a metabolomics platform enriched with microbe-derived metabolites.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {319},
number = {2},
pages = {G157-G169},
pmid = {32508155},
issn = {1522-1547},
support = {RC1DK087307//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; 6026-51000-010-05S//U.S. Department of Agriculture (USDA)/International ; R01 HL121324/HL/NHLBI NIH HHS/United States ; R01HL107256//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; R01DK095060//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; U24DK092933//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; R01HL091333//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; RO1HL121324//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; },
mesh = {Animals ; Bacteria/classification/isolation &amp; purification ; Cecum/microbiology ; Diabetes Mellitus, Type 2/*metabolism ; Gastrointestinal Microbiome/*physiology ; Male ; Metabolic Networks and Pathways ; *Metabolomics ; Rats ; Rats, Sprague-Dawley ; },
abstract = {The gut microbiome has the potential to create or modify xenometabolites (i.e., nonhost-derived metabolites) through de novo synthesis or modification of exogenous and endogenous compounds. While there are isolated examples of xenometabolites influencing host health and disease, wide-scale characterization of these metabolites remains limited. We developed a metabolomics platform ("XenoScan") using liquid chromatography-mass spectrometry to characterize a range of known and suspected xenometabolites and their derivatives. This assay currently applies authentic standards for 190 molecules, enriched for metabolites of microbial origin. As a proof-of-principle, we characterized the cecal content xenometabolomics profile in adult male lean Sprague-Dawley (LSD) and University of California, Davis type 2 diabetes mellitus (UCD-T2DM) rats at different stages of diabetes. These results were correlated to specific bacterial species generated via shotgun metagenomic sequencing. UCD-T2DM rats had a unique xenometabolite profile compared with LSD rats, regardless of diabetes status, suggesting that at least some of the variation is associated with host genetics. Furthermore, modeling approaches revealed that several xenometabolites discriminated UCD-T2DM rats at early stages of diabetes versus those at 3 mo postdiabetes onset. Several xenometabolite hubs correlated with specific bacterial species in both LSD and UCD-T2DM rats. For example, indole-3-propionic acid negatively correlated with species within the Oscillibacter genus in UCD-T2DM rats considered to be prediabetic or recently diagnosed diabetic, in contrast to gluconic acid and trimethylamine, which were positively correlated with Oscillibacter species. The application of a xenometabolite-enriched metabolomics assay in relevant milieus will enable rapid identification of a wide variety of gut-derived metabolites, their derivatives, and their potential biochemical origins of xenometabolites in relationship to host gastrointestinal microbial ecology.NEW &amp; NOTEWORTHY We debut a liquid chromatography-mass spectrometry (LC/MS) platform called the XenoScan, which is a metabolomics platform for xenometabolites (nonself-originating metabolites). This assay has 190 in-house standards with the majority enriched for microbe-derived metabolites. As a proof-of-principle, we used the XenoScan to discriminate genetic differences from cecal samples associated with different rat lineages, in addition to characterizing diabetes progression in rat model of type 2 diabetes. Complementing microbial sequencing data with xenometabolites uncovered novel microbial metabolism in targeted organisms.},
}
@article {pmid32504423,
year = {2020},
author = {Lacalle, RG and Garbisu, C and Becerril, JM},
title = {Effects of the application of an organic amendment and nanoscale zero-valent iron particles on soil Cr(VI) remediation.},
journal = {Environmental science and pollution research international},
volume = {27},
number = {25},
pages = {31726-31736},
pmid = {32504423},
issn = {1614-7499},
support = {AGL2015-64481-C2-1-R//Ministerio de Econom&#xed;a y Competitividad/ ; AGL2016-76592-R//Ministerio de Econom&#xed;a y Competitividad/ ; GV IT1018-16//Eusko Jaurlaritza/ ; PhytoSUDOE-SOE1/P5/E0189//Interreg/ ; },
mesh = {Chromium/analysis ; *Environmental Restoration and Remediation ; Iron ; Soil ; Soil Pollutants/*analysis ; },
abstract = {Chromium is considered an environmental pollutant of much concern whose toxicity depends, to a great extent, on its valence state, with Cr(VI) being more soluble, bioavailable, and toxic, compared to Cr(III). Nanoremediation is a promising strategy for the remediation of metal pollutants by changing their valence state. However, among other aspects, its effectiveness for soil remediation is seriously hampered by the interaction of nanoparticles with soil organic matter. In this study, soil was (i) amended with two doses of a municipal solid organic waste and (ii) artificially polluted with 300 mg Cr(VI) kg[-1] DW soil. After a period of aging, a nanoremediation treatment with nanoscale zero-valent iron particles (1 g nZVI kg[-1] DW soil) was applied. The efficiency of the remediation treatment was assessed in terms of Cr(VI) immobilization and recovery of soil health. The presence of the organic amendment caused (i) a decrease of redox potential, (ii) Cr(VI) immobilization via its reduction to Cr(III), (iii) a stimulation of soil microbial communities, and (iv) an improvement of soil health, compared to unamended soil. By contrast, nZVI did not have any impact on Cr(VI) immobilization nor on soil health. It was concluded that, unlike the presence of the organic amendment, nanoremediation with nZVI was not a valid option for soils polluted with Cr(VI) under our experimental conditions.},
}
@article {pmid32503635,
year = {2020},
author = {Tao, X and Feng, J and Yang, Y and Wang, G and Tian, R and Fan, F and Ning, D and Bates, CT and Hale, L and Yuan, MM and Wu, L and Gao, Q and Lei, J and Schuur, EAG and Yu, J and Bracho, R and Luo, Y and Konstantinidis, KT and Johnston, ER and Cole, JR and Penton, CR and Tiedje, JM and Zhou, J},
title = {Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {84},
pmid = {32503635},
issn = {2049-2618},
support = {DE-SC0004601//U.S. Department of Energy/International ; DE-SC0010715//U.S. Department of Energy/International ; 41430856//National Natural Science Foundation of China/International ; 41877048//National Natural Science Foundation of China/International ; 41825016//National Natural Science Foundation of China/International ; },
mesh = {Alaska ; Burkholderia/metabolism ; Climate Change ; Hot Temperature ; *Lignin/metabolism ; Permafrost ; *Proteobacteria/metabolism ; Soil/chemistry ; *Soil Microbiology ; Tundra ; },
abstract = {BACKGROUND: In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed.<br><br>RESULTS: The &#x3b2;-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2&#x2009;&#xb0;C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, &#x3b1;-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling.<br><br>CONCLUSIONS: Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.},
}
@article {pmid33447802,
year = {2020},
author = {Payne, AT and Davidson, AJ and Kan, J and Peipoch, M and Bier, R and Williamson, K},
title = {Widespread cryptic viral infections in lotic biofilms.},
journal = {Biofilm},
volume = {2},
number = {},
pages = {100016},
pmid = {33447802},
issn = {2590-2075},
abstract = {Viruses have important impacts on aquatic microbial ecology and have been studied at length in the global ocean. However, the roles of bacteriophages in lotic ecosystems, particularly in benthic biofilms, have been largely under-studied. The main goals of this work were to determine whether viruses are consistent members of natural benthic biofilm communities of freshwater streams; whether temperate phages are present and active in such biofilms; and whether community profiling approaches like RAPD-PCR can be adapted to characterize biofilm virus communities. Results from both field and laboratory experiments suggest that viruses are consistent members of lotic biofilm communities. Interestingly, prophage induction was statistically significant but only a small percentage of the total bacterial population appeared to harbor prophage or engaged in induction. Finally, while the use of RAPD-PCR for the community level profiling of biofilm viral communities suggests temporal change in response to biofilm maturity, further refinements are required for broad-scale quantitative application.},
}
@article {pmid33654882,
year = {2019},
author = {Chaudhary, DK and Kim, J},
title = {Experimental Setup for a Diffusion Bioreactor to Isolate Unculturable Soil Bacteria.},
journal = {Bio-protocol},
volume = {9},
number = {19},
pages = {e3388},
pmid = {33654882},
issn = {2331-8325},
abstract = {Unculturable bacteria are those bacteria which proliferate in their native habitat but unable to grow or thrive in the normal laboratory media and conditions. The molecular techniques have revealed the significance of these uncultured bacteria in terms of their functional diversity and potential to produce secondary metabolites. To achieve these benefits, scientists have attempted to isolate and cultivate unculturable bacteria in the laboratory using transwell plates, optical tweezers, laser microdissection, microbioreactors, and diffusions bioreactors. However, these techniques are still inadequate to resolve the difficulties of cultivating unculturable bacteria. Therefore, it is essential to develop new cultivation method that enables growth of diverse range of bacteria in the laboratory conditions. Diffusion bioreactor is a membrane bound chamber which allows microbes to proliferate in their native environment by providing the excess to naturally occurring nutrients and signaling compounds. This paper presents efficient and reliable protocol to construct a diffusion bioreactor and its utilization to isolate and cultivate unculturable soil bacteria in laboratory.},
}
@article {pmid33336908,
year = {2019},
author = {Cui, J and Lian, Y and Zhao, C and Du, H and Han, Y and Gao, W and Xiao, H and Zheng, J},
title = {Dietary Fibers from Fruits and Vegetables and Their Health Benefits via Modulation of Gut Microbiota.},
journal = {Comprehensive reviews in food science and food safety},
volume = {18},
number = {5},
pages = {1514-1532},
doi = {10.1111/1541-4337.12489},
pmid = {33336908},
issn = {1541-4337},
support = {CAAS-XTCX201605-1&#x223c;6//Collaborative Innovation of Chinese Academy of Agricultural Sciences/ ; 31401581//National Natural Science Foundation of China/ ; 31428017//National Natural Science Foundation of China/ ; },
abstract = {Dietary fibers (DFs) regulate host health through various mechanisms related to their dietary sources, specific physicochemical structures, fermentability, and physiological properties in the gut. Considering the numerous types and sources of DFs and their different physicochemical and physiological properties, it is challenging yet important to establish the key mechanisms for the beneficial health effects of DFs. In this review, the types and structures of DFs from different fruits and vegetables were summarized and the effects of different processing methods on DF properties were discussed. Moreover, the impacts of DFs on gut microbial ecology, host physiology, and health were described. Understanding the complex interaction between different DFs and gut microbiota is vital for personalized nutrition. It is also important to comprehend factors influencing gut microbiota and strategies to regulate the microbiota, thereby augmenting beneficial health responses. The exploration of molecular mechanism linking DFs, gut microbiota, and host physiology may allow for the identification of effective targets to fight against major chronic diseases.},
}
@article {pmid33654784,
year = {2019},
author = {Hennessy, RC and Stougaard, P and Olsson, S},
title = {Imaging Gene Expression Dynamics in Pseudomonas fluorescens In5 duringInteractions with the Fungus Fusarium graminearum PH-1.},
journal = {Bio-protocol},
volume = {9},
number = {12},
pages = {e3264},
pmid = {33654784},
issn = {2331-8325},
abstract = {Genomics, transcriptomics and metabolomics are powerful technologies for studying microbial interactions. The main drawback of these methods is the requirement for destructive sampling. We have established an alternative but complementary technique based on a microplate system combined with promoter fusions for visualizing gene expression in space and time. Here we provide a protocol for measuring spatial and temporal gene expression of a bacterial reporter strain interacting with a fungus on a solid surface.},
}
@article {pmid33354438,
year = {2018},
author = {Reyes, VC and Merino, N and Gedalanga, PB and Van Nostrand, JD and Keely, SP and De Long, SK and Zhou, J and Mahendra, S},
title = {Differential Sensitivity of Wetland-Derived Nitrogen Cycling Microorganisms to Copper Nanoparticles.},
journal = {ACS sustainable chemistry &amp; engineering},
volume = {6},
number = {9},
pages = {11642-11652},
pmid = {33354438},
issn = {2168-0485},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {Metallic nanoparticles (NPs), the most abundant nanomaterials in consumer and industrial products, are the most probable class to enter the environment. In this study, wetland-derived microcosms were incubated with copper nanoparticles (Cu-NP) and ionic CuCl2 to investigate acute (10 days) and chronic (100 days) exposure towards nitrogen cycling microorganisms. The microbial ecology of wetlands play a crucial role in balancing nitrogen in pristine environments as well as in areas impacted by high nutrient loads (e.g., at wastewater effluent discharges). Gene abundance and expression changes were monitored using the GeoChip 5.0 high throughput functional gene microarray and metatranscriptomic shotgun sequencing (RNA-seq), respectively. After 10 days, the Cu-NP impacted microbial communities experienced structural shifts within microorganisms associated with dissimilatory nitrogen reduction accompanied by lower nitrate removal as compared to the unexposed controls. By day 100, these differences were largely resolved and nitrate removal was similar to the unexposed control. Furthermore, the Cu-NP exposed microcosms tolerated copper and were more resilient and adaptive than the unexposed controls based on the abundance and expression of other functions, including electron transfer, metal homeostasis, and stress response. These findings suggest sudden influxes of Cu-NPs into wetland systems may impair nitrogen removal initially, but long-term microbial shifts and functional redundancy would promote the net flux of total nitrogen out of the wetlands.},
}
@article {pmid32624887,
year = {2018},
author = {Tzirita, M and Papanikolaou, S and Chatzifragkou, A and Quilty, B},
title = {Waste fat biodegradation and biomodification by Yarrowia lipolytica and a bacterial consortium composed of Bacillus spp. and Pseudomonas putida.},
journal = {Engineering in life sciences},
volume = {18},
number = {12},
pages = {932-942},
pmid = {32624887},
issn = {1618-0240},
abstract = {Fats, oils, and greases (FOGs) are a particular environmental threat. Biodegradation of FOGs is a challenge and in this study the biodegradation of waste cooking fats, namely butter and olive oil, was studied using a non-conventional yeast, Yarrowia lipolytica strain LFMB 20, and a bioaugmentation product consisting of Bacillus spp. and Pseudomonas putida CP1 strain. The microorganisms were grown aerobically in shake-flask experiments in an enriched medium supplemented with ca 0.85% w/v of waste fat. Analysis of the remaining substrate showed a removal of ca 90% of the fat by the yeast at the end of the incubation, while the bacteria removed ca 95% of both fats. Growth rate, biomass production and biomass yield per unit of fat consumed were all higher for the yeast compared to the bacterial consortium. The bacterial consortium exhibited autolysis and a significant decrease in its DCW value at the late growth phases of both fat substrate cultures. The main fatty acids (FAs) present in both fats were linoleic (Δ9,12C18:2), oleic (Δ9C18:1), palmitic (C16:0), palmitoleic (Δ9C16:1) and stearic (C18:0) acid. Both the bacterial consortium and Y. lipolytica preferentially removed Δ9C18:1 from the medium, while a negative selectivity against C18:0 was reported. Both inocula produced microbial mass that contained intra-cellular lipid quantities, but the bacterial consortium gave significantly higher lipid in DCW values compared with the yeast (maximum values up to ca 63% w/w for the butter and ca 42% w/w for the olive oil while the respective values for both lipids were 22% ± 2% w/w for Y. lipolytica). In all cases, intra-cellular lipids in DCW values decreased during the late growth phases, while their FA composition differed with those of the substrate fat.},
}
@article {pmid33525774,
year = {2017},
author = {Rogers, GB},
title = {The lung microbiome.},
journal = {Emerging topics in life sciences},
volume = {1},
number = {4},
pages = {313-324},
doi = {10.1042/ETLS20170043},
pmid = {33525774},
issn = {2397-8554},
abstract = {Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.},
}
@article {pmid32846721,
year = {2014},
author = {Yang, LH and Gratton, C},
title = {Insects as drivers of ecosystem processes.},
journal = {Current opinion in insect science},
volume = {2},
number = {},
pages = {26-32},
doi = {10.1016/j.cois.2014.06.004},
pmid = {32846721},
issn = {2214-5753},
abstract = {Insects and other small invertebrates are ubiquitous components of all terrestrial and freshwater food webs, but their cumulative biomass is small relative to plants and microbes. As a result, it is often assumed that these animals make relatively minor contributions to ecosystem processes. Despite their small sizes and cumulative biomass, we suggest that these animals may commonly have important effects on carbon and nutrient cycling by modulating the quality and quantity of resources that enter the detrital food web, with consequences at the ecosystem level. These effects can occur through multiple pathways, including direct inputs of insect biomass, the transformation of detrital biomass, and the indirect effects of predators on herbivores and detritivores. In virtually all cases, the ecosystem effects of these pathways are ultimately mediated through interactions with plants and soil microbes. Merging our understanding of insect, plant and microbial ecology will offer a valuable way to better integrate community-level interactions with ecosystem processes.},
}
@article {pmid33412651,
year = {2014},
author = {Clodoveo, ML and Hbaieb, RH and Kotti, F and Mugnozza, GS and Gargouri, M},
title = {Mechanical Strategies to Increase Nutritional and Sensory Quality of Virgin Olive Oil by Modulating the Endogenous Enzyme Activities.},
journal = {Comprehensive reviews in food science and food safety},
volume = {13},
number = {2},
pages = {135-154},
doi = {10.1111/1541-4337.12054},
pmid = {33412651},
issn = {1541-4337},
abstract = {This monograph is a critical review of the biological activities that occur during virgin olive oil (VOO) extraction process. Strategic choices of plant engineering systems and of processing technologies should be made to condition the enzymatic activities, in order to modulate the nutritional and the sensory quality of the product toward the consumer expectations. "Modulation" of the product quality properties has the main aim to predetermine the quantity and the quality of 2 classes of substances: polyphenols and volatile compounds responsible of VOO nutritional and sensory characteristics. In the 1st section, a systematic analysis of the literature has been carried out to investigate the main olive enzymatic activities involved in the complex biotransformation that occurs during the mechanical extraction process. In the 2nd section, a critical and interpretative discussion of the influence of each step of the extraction process on the polyphenols and the volatile compounds has been performed. The effect of the different mechanical devices that are part of the extraction process is analyzed and recommendations, strategies, and possible avenues for future researches are suggested.},
}
@article {pmid33873560,
year = {2004},
author = {Piotrowski, JS and Denich, T and Klironomos, JN and Graham, JM and Rillig, MC},
title = {The effects of arbuscular mycorrhizas on soil aggregation depend on the interaction between plant and fungal species.},
journal = {The New phytologist},
volume = {164},
number = {2},
pages = {365-373},
doi = {10.1111/j.1469-8137.2004.01181.x},
pmid = {33873560},
issn = {1469-8137},
abstract = {• Arbuscular mycorrhizal fungi (AMF) and roots mediate soil stabilization, although the mechanisms and how their interactions affect soil stabilization are not known. We tested the effects of specific plant-fungus combinations on aggregate stabilization, and whether hyphal length and root biomass determine stabilization, predicting that fungi producing more hyphae, and plants with higher root biomasses, would better stabilize soils. • The percentage of water-stable aggregates (%WSA1-2 mm), hyphal lengths, and root biomass were measured from a five AMF × nine plant factorial experiment. Arbuscular mycorrhizal fungi with greater extradical mycelium production were represented by the Gigasporaceae and plants of high root biomass by grasses. Other taxa represented lower hyphal lengths and root biomass. • An interaction between symbionts with respect to %WSA1-2 mm was observed. Root biomass and total hyphal lengths were not positively correlated with %WSA. Combinations of grasses with Gigasporaceae fungi had the lowest %WSA. • Mechanisms underlying aggregation were not elucidated by measuring root biomass and total hyphal lengths alone, suggesting other physiological or architectural mechanisms may be responsible.},
}
@article {pmid33873615,
year = {2004},
author = {Leake, JR and McKendrick, SL and Bidartondo, M and Read, DJ},
title = {Symbiotic germination and development of the myco-heterotroph Monotropa hypopitys in nature and its requirement for locally distributed Tricholoma spp.},
journal = {The New phytologist},
volume = {163},
number = {2},
pages = {405-423},
pmid = {33873615},
issn = {1469-8137},
abstract = {• Germination and symbiotic development of the myco-heterotrophic plant Monotropa hypopitys were studied by sequential recovery of packets of seed buried in dune slacks in relation to distance from mature M. hypopitys and presence and absence of shoots of its autotrophic coassociate Salix repens. • Fungal associates of M. hypopitys growing under S. repens in the dune slacks, and under S. caprea and Pinus sylvestris at two other locations in the UK, were identified by molecular analysis. • While the earliest stage of germination could be found in the absence both of mature M. hypopitys, and S. repens, further development was dependent upon mycorrhizal colonisation, which was most common close to these plants. Molecular analysis showed that when growing with Salix, M. hypopitys associated with the Salix-specific ectomycorrhizal fungus Tricholoma cingulatum, whereas under Pinus it was colonised by the closely related, Pinaceae-specific, T. terreum. • We establish the first definitive chronology of development of M. hypopitys and highlight its critical dependence upon, and specificity for, locally distributed Tricholoma species that link the myco-heterotroph to its autotrophic coassociates.},
}
@article {pmid33873541,
year = {2003},
author = {Högberg, MN and Bååth, E and Nordgren, A and Arnebrant, K and Högberg, P},
title = {Contrasting effects of nitrogen availability on plant carbon supply to mycorrhizal fungi and saprotrophs - a hypothesis based on field observations in boreal forest.},
journal = {The New phytologist},
volume = {160},
number = {1},
pages = {225-238},
pmid = {33873541},
issn = {1469-8137},
abstract = {• Soil microorganisms are considered C-limited, while plant productivity is frequently N-limited. Large stores of organic C in boreal forest soils are attributed to negative effects of low temperature, soil acidity and plant residue recalcitrance upon microbial activity. • We examined microbial activity, biomass and community composition along a natural 90-m-long soil N supply gradient, where plant species composition varies profoundly, forest productivity three-fold and soil pH by three units. • There was, however, no significant variation in soil respiration in the field across the gradient. Neither did microbial biomass C determined by fumigation-extraction vary, while other estimates of activity and biomass showed a weak increase with increasing N supply and soil pH. Simultaneously, a phospholipid fatty acid attributed mainly to mycorrhizal fungi declined drastically, while bacterial biomass increased. • We hypothesize that low N supply and plant productivity, and hence low litter C supply to saprotrophs is associated with a high plant C supply to mycorrhizal fungi, while the reverse occurs under high N supply. This should mean that effects of N availability on C supply to these functional groups of microbes acts in opposing directions.},
}
@article {pmid33873670,
year = {2003},
author = {Olsson, PA and Larsson, L and Bago, B and Wallander, H and Van Aarle, IM},
title = {Ergosterol and fatty acids for biomass estimation of mycorrhizal fungi.},
journal = {The New phytologist},
volume = {159},
number = {1},
pages = {7-10},
pmid = {33873670},
issn = {1469-8137},
}
@article {pmid33873298,
year = {2002},
author = {Van Aarle, IM and Olsson, PA and Söderström, B},
title = {Arbuscular mycorrhizal fungi respond to the substrate pH of their extraradical mycelium by altered growth and root colonization.},
journal = {The New phytologist},
volume = {155},
number = {1},
pages = {173-182},
pmid = {33873298},
issn = {1469-8137},
abstract = {• To test the response of arbuscular mycorrhizal (AM) fungi to a difference in soil pH, the extraradical mycelium of Scutellospora calospora or Glomus intraradices, in association with Plantago lanceolata, was exposed to two different pH treatments, while the root substrate pH was left unchanged. • Seedlings of P. lanceolata, colonized by one or other of the fungal symbionts, and nonmycorrhizal controls, were grown in mesh bags placed in pots containing pH-buffered sand (pH around 5 or 6). The systems were harvested at approximately 2-wk intervals between 20 and 80 d. • Both fungi formed more extraradical mycelium at the higher pH. Glomus intraradices formed almost no detectable extraradical mycelium at lower pH. The extraradical mycelium of S. calospora had higher acid phosphatase activity than that of G. intraradices. Total AM root colonization decreased for both fungi at the higher pH, and high pH also reduced arbuscule and vesicle formation in G. intraradices. • In conclusion, soil pH influences AM root colonization as well as the growth and phosphatase activities of extraradical mycelium, although the two fungi responded differently.},
}
@article {pmid33873464,
year = {2002},
author = {Gavito, ME and Bruhn, D and Jakobsen, I},
title = {Phosphorus uptake by arbuscular mycorrhizal hyphae does not increase when the host plant grows under atmospheric CO2 enrichment.},
journal = {The New phytologist},
volume = {154},
number = {3},
pages = {751-760},
pmid = {33873464},
issn = {1469-8137},
abstract = {• We conducted an experiment to test whether phosphorus (P) uptake by mycorrhizal hyphae could be enhanced by growing the host plant under [CO2 ] enrichment and whether any response to [CO2 ] was dependent on C source-sink relationships. • Plant C assimilation, mass allocation, growth and P uptake were measured in pea (Pisum sativum) plants inoculated with 0, 1 or 5% of a mixture of three Glomus spp. Intra- and extra-radical mycorrhizal development was followed and hyphal [33] P uptake from a root-exclusion compartment was measured. • Total P and [33] P content measurements indicated that root, not hyphal, P uptake was increased by elevated [CO2 ] in the mycorrhizal treatments and that hyphal P uptake was actually reduced by elevated [CO2 ] after 57 d. Neither intra- nor extraradical mycorrhizal development was related to this response. • Plant and fungal measurements suggested positive interactions in plant growth and P uptake only when C source-sink relationships were balanced; high C source (enhanced assimilation at elevated [CO2 ]) and high C sink (increasing mycorrhizal development). The results also indicated that enhanced plant C supply does not alter growth or function of arbuscular mycorrhizal fungi.},
}
@article {pmid33873431,
year = {2002},
author = {Bordallo, JJ and Lopez-Llorca, LV and Jansson, HB and Salinas, J and Persmark, L and Asensio, L},
title = {Colonization of plant roots by egg-parasitic and nematode-trapping fungi.},
journal = {The New phytologist},
volume = {154},
number = {2},
pages = {491-499},
pmid = {33873431},
issn = {1469-8137},
abstract = {• The ability of the nematode-trapping fungus Arthrobotrys oligospora and the nematode egg parasite Verticillium chlamydosporium to colonize barley (Hordeum vulgare) and tomato (Lycopersicum esculentum) roots was examined, together with capability of the fungi to induce cell wall modifications in root cells. • Chemotropism was studied using an agar plate technique. Root colonization was investigated with light microscopy and scanning electron microscopy, while compounds involved in fungus-plant interactions were studied histochemically. • Only A. oligospora responded chemotropically to roots. Colonization of barley and tomato by both fungi involved appressoria to facilitate epidermis penetration. V. chlamydosporium colonized tomato root epidermis and produced chlamydospores. Papillae, appositions and lignitubers ensheathing hyphae on tomato were also found. Phenolics (including lignin), protein deposits and callose were present in papillae in both hosts. Both fungi were still present in epidermal cells 3 months after inoculation. • Nematophagous fungi colonized endophytically monocotyledon and dicotyledon plant roots. Arthrobotrys oligospora seemed to be more aggressive than V. chlamydosporium on barley roots. Both fungi induced cell wall modifications, but these did not prevent growth. The response of root cells to colonization by nematophagous fungi may have profound implications in the performance of these organisms as biocontrol agents of plant parasitic nematodes.},
}
@article {pmid33853251,
year = {2001},
author = {Wallander, H and Nilsson, LO and Hagerberg, D and Bååth, E},
title = {Estimation of the biomass and seasonal growth of external mycelium of ectomycorrhizal fungi in the field.},
journal = {The New phytologist},
volume = {151},
number = {3},
pages = {753-760},
pmid = {33853251},
issn = {1469-8137},
abstract = {• In-growth mesh bags were used to quantify the production of external mycelium of ectomycorrhizal (EM) fungi in the field. • Colonization of the mesh bags was followed by visual estimation of the amount of mycelium, and by measuring fungal biomarkers (the phospholipid fatty acid (PLFA) 18 : 2ω6,9 and ergosterol). Mesh bags were placed inside and outside plots that were root isolated in order to estimate the amount of saprotrophic mycelium in relation to EM mycelium. The majority of mycelium in the mesh bags were EM, and this was confirmed by analysis of the δ[13] C value in mycelia. • Fungal colonization of mesh bags peaked during autumn. The total amount of EM mycelium produced in the mesh bags during a year was calculated to be between 125 and 200 kg ha[-1] . The total amount of EM mycelium (including EM mantles) in the humus was estimated to be 700-900 kg ha[-1] . • The biomass of EM mycelium in the soil was in the same range as the biomass of fine roots and peaks of mycelial growth coincided with periods of maximum growth of fine-roots.},
}
@article {pmid33863172,
year = {1997},
author = {Ulrich, K and Lentzsch, P and Seyfarth, W},
title = {Identification of cultivar-specific leghaemoglobin components in Pisum sativum.},
journal = {The New phytologist},
volume = {137},
number = {2},
pages = {285-291},
doi = {10.1046/j.1469-8137.1997.00797.x},
pmid = {33863172},
issn = {1469-8137},
abstract = {The components of leghaemoglobin (Lb) from twelve different Pisum sativum L. cvs and three near-isogenic foliar mutants were investigated by anion-exchange high-performance liquid chromatography (HPLC). Five different Lb component profiles could he found. The number of components varied from four to six dependent on cultivar used. An Lb pattern composed of four Lb components could be detected in thirteen P. sativum cultivars and lines. Ten of them showed an identical profile. In nodules of each cultivar, the two known major components, LbI and LbV, but also LbIV, could be detected. Additionally, cultivar-specific Lb components could be identified, each representing up to 10%, of total Lb. One of these components, LbIII, has been described previously, but three new Lb components (LbII, LbVI, and LbVII) were found. The presence of all Lb components detected by HPLC was confirmed by analytical isoelectric focusing. Further, it was shown that age-dependent changes in the relative concentrations of LbI and LbV are common in P. sativum and that these variations are independent of breeding lines and cultivars.},
}
@article {pmid33657731,
year = {1997},
author = {Rosén, S and Sjollema, K and Veenhuis, M and Tunlid, A},
title = {A cytoplasmic lectin produced by the fungus Arthrobotrys oligospora functions as a storage protein during saprophytic and parasitic growth.},
journal = {Microbiology (Reading, England)},
volume = {143},
number = {8},
pages = {2593-2604},
doi = {10.1099/00221287-143-8-2593},
pmid = {33657731},
issn = {1465-2080},
abstract = {It was recently shown that the nematode-infecting fungus Arthrobotrys oligospora contains a saline-soluble lectin (designated AOL) that is a member of a novel family of fungal lectins sharing similar primary sequences and binding specificities. During saprophytic growth in liquid cultures, levels of AOL and AOL mRNA were found to vary depending on the growth phase of the mycelium and the carbon/nitrogen (C/N) ratio of the medium. AOL was not detected in young mycelium. In older mycelium (stationary growth phase) grown in media with low C/N ratios (1 or 6), AOL comprised 5-20% of the total amount of saline-soluble proteins present in the mycelium. Neither the lectin nor its transcript was detected in mycelia grown in medium with higher C/N ratios (≥150). Under conditions of nitrogen starvation, AOL was preferentially degraded in relation to the total amount of saline-soluble proteins present in the mycelium. During the infection of nematodes, the level of AOL protein and AOL mRNA increased significantly once the nematodes had been penetrated and digested. Large amounts of AOL accumulated in the trophic hyphae growing inside the nematode as visualized by immunofluorescence microscopy. Later, AOL labelling was detected outside the digested nematodes, preferentially in strands of aggregated hyphae and in newly developed trap cells. Electron microscopy showed that AOL was localized to the cytoplasm and the nucleus of both vegetative mycelium and trap cells, and in the trophic hyphae growing inside the infected nematodes. These results indicate that AOL functions as a storage protein during both saprophytic and parasitic growth.},
}
@article {pmid33657740,
year = {1996},
author = {Langdahl, BR and Bisp, P and Ingvorsen, K},
title = {Nitrile hydrolysis by Rhodococcus erythropolis BL1, an acetonitrile-tolerant strain isolated from a marine sediment.},
journal = {Microbiology (Reading, England)},
volume = {142},
number = {1},
pages = {145-154},
doi = {10.1099/13500872-142-1-145},
pmid = {33657740},
issn = {1465-2080},
abstract = {A number of physiologically different nitrile-hydrolysing bacteria were isolated from coastal marine sediments in Denmark by enrichment culture. One strain, BL1, identified as Rhodococcus erythropolis, grew on acetonitrile as sole carbon and nitrogen source in a defined medium. Growth occurred between 0 and 8% NaCl with an optimum around 2%, thus reflecting the marine origin of the isolate. Intact cells of R. erythropolis BL1 could hydrolyse a large variety of saturated and unsaturated aliphatic nitriles to their corresponding acids. Benzonitrile and benzylcyanide were not hydrolysed, whereas some aromatic compounds containing a -CN group attached to a C3 or C4 aliphatic side chain were accepted as substrates. The substrate spectrum of R. erythropolis BL1 was thus markedly different from those of other Grampositive nitrile-hydrolysing bacteria isolated from non-marine environments. Nitrile hydrolysis during growth and in resting cell suspensions usually occurred without intermediate accumulation of amide outside the cells. Detailed studies, however, showed that nitrile hydrolysis by strain BL1 was due to a nitrile hydratase/amidase enzyme system. Nitrile hydratase activity was found to be inducible whereas amidase activity was constitutive. The amidase activity of cells could, however, be enhanced manyfold by growth in media containing acetamide or acetonitrile. In most cases amides were hydrolysed at a much higher rate than the corresponding nitriles, which explained why amides were rarely detected in the surrounding medium during nitrile hydrolysis. R. erythropolis BL1 exhibited the highest tolerance towards acetonitrile ever reported for a nitrile-hydrolysing bacterium, as demonstrated by its ability to grow exponentially in the presence of 900 mM acetonitrile.},
}
@article {pmid33874368,
year = {1994},
author = {Wingler, A and Einig, W and Schaeffer, C and Wallenda, T and Hampp, R and Wallander, H and Nylund, JE},
title = {Influence of different nutrient regimes on the regulation of carbon metabolism in Norway spruce [Picea abies (L.) Karst.] seedlings.},
journal = {The New phytologist},
volume = {128},
number = {2},
pages = {323-330},
doi = {10.1111/j.1469-8137.1994.tb04016.x},
pmid = {33874368},
issn = {1469-8137},
abstract = {Phosphoenolpyruvate carboxylase (PEPC) activity, fructose 2, 6-bisphosphate (F26BP), starch and soluble sugar contents were determined m needles and roots of Norway spruce seedlings grown in a semi-hydroponic cultivation system under different nutrient regimes, tn needles, a surplus of nitrogen caused an increase in specific PEPC activity (up to six times control activity) and F26BP content (up to three times control level) while starch content was reduced. Sucrose contents were not affected. Basically, the responses in root samples were similar. Here, PEPC was highest at an imbalance in nutrition (+ N/ -P) F26BP, with root contents being 3- to 11 -times higher than those in needles, significantly exceeded control values at + N/+ P. The results show that alteration of nitrogen supply leads to marked changes in allocation of carbon between pathways, which is also influenced by P-nutrition. Pool sizes of F26BP and activity of PEPC are indicators for these changes in leaf as well as in root tissues of Norway spruce.},
}
@article {pmid33874472,
year = {1994},
author = {Erland, S and Henrion, B and Martin, F and Glover, LA and Alexanders, IJ},
title = {Identification of the ectomycorrhizal basidiomycete Tylospora fibrillosa Donk by RFLP analysis of the PCR-amplified ITS and IGS regions of ribosomal DNA.},
journal = {The New phytologist},
volume = {126},
number = {3},
pages = {525-532},
doi = {10.1111/j.1469-8137.1994.tb04251.x},
pmid = {33874472},
issn = {1469-8137},
abstract = {Sitka spruce mycorrhizas, macroscopically identified as being formed by Tylospora fibritiosa Donk, were sampled from a young and on old plantation and the mycobionts were isolated into pure culture. DNA was extracted and fragments of the ribosomal DNA (rDNA) were amplified using the polymerase chain reaction (PCR). The primers were directed to conserved regions of fungal rDXA and hybridize to a wide range of fungi. One amplified region includes the internal spacer (ITS) region which has a low degree of conservation. The JTS amplification products, which were approximately 600 base pairs (bp), were digested with a variety of restriction endonucleases in order to detect restriction fragment length polymorphisms (RFLPs). The RFLPs clearly separated T. fibrillosa from other ectomycorrhizal species but there were only minor differences between the T. fibrillosa isolates. PCR amplification of the ITS region, digestion with the endonudeasc HinfI and examination of the RFLPs produced proved to be a rapid method by which to distinguish T. fibriHosa from a large number of other basidiomyictes. The method was also applied to DNA extracted, from single mycotrhizal root tips. The imergenic spacer region (1GS) of the rDNA is more variable than the ITS region in several fungal species. The 5'end of the 25S and the intergenic region between the 25S and the 5S genes were amplified and analyzed as above. Polymorphisms between T. fibritiosa isolates within this region were limited and RFLPs were not useful m discriminating between isolates, suggesting a low genetic variability in this species.},
}
@article {pmid33874350,
year = {1993},
author = {Arnebrant, K and Ek, H and Finlay, RD and Söderström, B},
title = {Nitrogen translocation between Alnus glutinosa (L.) Gaertn. seedlings inoculated with Frankia sp. and Pinus contorta Doug, ex Loud seedlings connected by a common ectomycorrhizal mycelium.},
journal = {The New phytologist},
volume = {124},
number = {2},
pages = {231-242},
doi = {10.1111/j.1469-8137.1993.tb03812.x},
pmid = {33874350},
issn = {1469-8137},
abstract = {Uptake and translocation of nitrogen was studied in laboratory microcosms consisting of Alnus glutinosa (L.) Gaertn., Frankia sp., Paxillus involutus (Fr.) Fr. and Pinus contorta Dougl. ex Loud. P. involutus was shown to form a fully functional ectomycorrhizal association with alder as well as pine, and the seedlings thus became interconnected by a common mycelium. When microcosms were exposed to [15] N2 gas, interplant translocation of [15] N was observed in two out of three experiments. [15] N2 was fixed by Frankia and translocated to all other parts of the system. In the two experiments in which interplant translocation occurred, between 5 and 15% of the [15] N recovered was found in the pine seedlings. Within seven days, fixed N2 was incorporated into amino acids in the Frankia nodules, translocated to both the A. glutinosa and P. contorta seedlings and incorporated into macromolecules. In alder seedlings, citrulline and ornithine were the free amino acids that had both the highest [15] N enrichment levels and concentrations. In pine, glutamine and citrulline had the highest [15] N concentrations, and glutamine had the highest level of [15] N enrichment. [15] N enrichment levels were greatest in the nodules, at between 5.5 and 29% in the different amino acids and 12% in the macromolecular fraction. Enrichment levels decreased with increasing distance from the nodules. The uptake and translocation of [15] N applied as [15] NH4 Cl to the mycelium was also studied. [15] N was incorporated into amino acids in the mycelium and translocated further in this form. Generally, free amino acids had high [15] N enrichment levels in the mycelium, decreasing along the translocation pathway. Citrulline and glutamine were the amino acids with highest [15] N concentrations in all parts of the system. [15] N was also found in the macromolecular fraction.},
}
@article {pmid33874136,
year = {1991},
author = {Erland, S and Finlay, R and Söderström, B},
title = {The influence of substrate pH on carbon translocation in ectomycorrhizal and non-mycorrhizal pine seedlings.},
journal = {The New phytologist},
volume = {119},
number = {2},
pages = {235-242},
doi = {10.1111/j.1469-8137.1991.tb01026.x},
pmid = {33874136},
issn = {1469-8137},
abstract = {The effects of changed substrate pH on translocation and partitioning of [14] C-labeled plant assimilates were examined in laboratory microcosms containing mycorrhizal (unidentified fungal isolate 'Pink FMT 87:2') and non-mycorrhizal seedlings of Pinus sylvestris L. and Pinus contorta Dougl. ex Loud. The mycorrhizal plants had intact mycelial systems at different developmental stages, and microcosms contained non-sterile peat (pH 3.8) or peat adjusted to different pH values with CaO. In systems with mycorrhizal mycelium which had just started to colonize the peat no significant differences in [14] C assimilation were found, either with respect to substrate pH or mycorrhizal status of the plant. Loss of activity from the mycorrhizal plants was more rapid, however, probably mainly as a result of increased respiration from the infected root systems. After 8 wk growth in peat at pH 3.8 and 5.2 shoot weights of all seedlings were the same, whereas non-mycorrhizal plants had root systems twice the size of the mycorrhizal ones. In plants with well developed extramatrical mycelia translocation of labeled carbon to the mycelium growing at pH 3.8 was faster than that to mycelium growing at pH 5.2. After 4 d incubation, however, the percentage of the originally supplied carbon present in the mycelium was 5% regardless of substrate pH. Activity found in the peat surrounding non-mycorrhizal plants rarely exceeded 0.3%.},
}
@article {pmid33874309,
year = {1991},
author = {Erland, S and Söerström, B},
title = {Effects of liming on ectomycorrhizal fungi infecting Pinus sylvestris L.: III. Saprophytic growth and host plant infection at different pH values in unsterile humus.},
journal = {The New phytologist},
volume = {117},
number = {3},
pages = {405-411},
doi = {10.1111/j.1469-8137.1991.tb00004.x},
pmid = {33874309},
issn = {1469-8137},
abstract = {Five ectomycorrhizal fungi were studied in relation to the effects of applications of lime and wood ash to the growth substrate. Growth and survival of inoculated fungi in unsterile humus and relative root colonization frequency by inoculated and indigenous ectomycorrhizal fungi were measured. Growth of the fungi was tested in Petri dish systems with humus taken from a field site treated with lime and wood ash. The infection potential of the fungi was tested by introducing Pinus sylvestris L. seedlings into the growth systems. Paxillus involutus (Fr.) Fr. was the only fungus affected both by the pH increase, and by the different treatments applied, in all aspects of its ecology tested (growth and survival in humus, infection potential and competitive ability). No other fungus grew saprophytically, but they showed the similar changes in infection potential in response to pH whether lime or ash had been used.},
}
@article {pmid32731678,
year = {1989},
author = {Corpet, DE},
title = {Microbial ecology of the intestine. In vitro, in vivo and mathematical models.},
journal = {Revue scientifique et technique (International Office of Epizootics)},
volume = {8},
number = {2},
pages = {391-403},
doi = {10.20506/rst.8.2.419},
pmid = {32731678},
issn = {0253-1933},
}
@article {pmid33874008,
year = {1989},
author = {},
title = {Reviews.},
journal = {The New phytologist},
volume = {111},
number = {3},
pages = {559-565},
doi = {10.1111/j.1469-8137.1989.tb00718.x},
pmid = {33874008},
issn = {1469-8137},
abstract = {The Flavonoids. Advances in Research since 1980. Ed. by J. B. Harborne. Hungry crops: a guide to nutrient deficiencies in field crops By N. J. Grundon. Microbial ecology: organisms, habitats, activities. By Heinz Stolp. Evolutionary Biology of the Fungi. Ed. by A. D. M. Rayner, C. M. Brasier and D. Moore. Micro-algal Biotechnology. Edited by M.A. Borowitzka and L. J. Borowitzka and L. J. Borowitzka. Experimental Phycology: A laboratory manual Edited by Christopher S. Lobban, David J. Chapman, and Bruno P. Kremer. 100 Families of Flowering Plants. By M. Hickey and C. King. Differentiation Patterns in Higher Plants. Edited by K. M. Urbanska. The Living Tundra. By Yu. I. Chernov, Translated by D. Löve. North American Terrestrial Vegetation. Edited by M. G. Barbour &amp; W. D. Billings. Biogeography and Quaternary History in Tropical Latin America. By T. C. Whitmore and G. T. Prance (Editors). Biogeographical Evolution of the Malay Archipelago. By T. C. Whitmore (Editor). Postglacial Vegetation of Canada. By J. C. Richie.},
}
@article {pmid32502166,
year = {2020},
author = {Lu, GS and LaRowe, DE and Fike, DA and Druschel, GK and Gilhooly, WP and Price, RE and Amend, JP},
title = {Bioenergetic characterization of a shallow-sea hydrothermal vent system: Milos Island, Greece.},
journal = {PloS one},
volume = {15},
number = {6},
pages = {e0234175},
pmid = {32502166},
issn = {1932-6203},
mesh = {*Energy Metabolism ; Greece ; *Hydrothermal Vents/microbiology ; Islands ; Thermodynamics ; },
abstract = {Shallow-sea hydrothermal systems, like their deep-sea and terrestrial counterparts, can serve as relatively accessible portals into the microbial ecology of subsurface environments. In this study, we determined the chemical composition of 47 sediment porewater samples along a transect from a diffuse shallow-sea hydrothermal vent to a non-thermal background area in Paleochori Bay, Milos Island, Greece. These geochemical data were combined with thermodynamic calculations to quantify potential sources of energy that may support in situ chemolithotrophy. The Gibbs energies (ΔGr) of 730 redox reactions involving 23 inorganic H-, O-, C-, N-, S-, Fe-, Mn-, and As-bearing compounds were calculated. Of these reactions, 379 were exergonic at one or more sampling locations. The greatest energy yields were from anaerobic CO oxidation with NO2- (-136 to -162 kJ/mol e-), followed by reactions in which the electron acceptor/donor pairs were O2/CO, NO3-/CO, and NO2-/H2S. When expressed as energy densities (where the concentration of the limiting reactant is taken into account), a different set of redox reactions are the most exergonic: in sediments affected by hydrothermal input, sulfide oxidation with a range of electron acceptors or nitrite reduction with different electron donors provide 85~245 J per kg of sediment, whereas in sediments less affected or unaffected by hydrothermal input, various S0 oxidation reactions and aerobic respiration reactions with several different electron donors are most energy-yielding (80~95 J per kg of sediment). A model that considers seawater mixing with hydrothermal fluids revealed that there is up to ~50 times more energy available for microorganisms that can use S0 or H2S as electron donors and NO2- or O2 as electron acceptors compared to other reactions. In addition to revealing likely metabolic pathways in the near-surface and subsurface mixing zones, thermodynamic calculations like these can help guide novel microbial cultivation efforts to isolate new species.},
}
@article {pmid32501785,
year = {2020},
author = {Lee, JC and Whang, KS},
title = {Sphingomonas segetis sp. nov., isolated from spinach farming field soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {6},
pages = {3905-3911},
doi = {10.1099/ijsem.0.004257},
pmid = {32501785},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Farms ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Spermidine/chemistry ; Sphingomonas/*classification ; Spinacia oleracea ; Ubiquinone/analogs &amp; derivatives/chemistry ; },
abstract = {A Gram-stain-negative bacterium, designated strain YJ09[T], was isolated from spinach farming field soil at Shinan in the Republic of Korea. Cells of strain YJ09[T] were found to be strictly aerobic, non-motile, non-spore-forming creamy-yellow rods which can grow at 20-37 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-0.5 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain YJ09[T] belongs to the genus Sphingomonas with high sequence similarities to Sphingomonas parvus GP20-2 [T] (98.0 %), Sphingomonas agri HKS-06[T] (97.7 %) and Sphingomonas lutea JS5[T] (97.4 %). The results of phylogenetic analysis indicated that strain YJ09[T] formed a distinct phyletic line in the genus Sphingomonas and the results of DNA-DNA relatedness studies demonstrated that strain YJ09[T] could be separated from its closest relatives in the genus Sphingomonas. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, an unidentified phospholipid and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18:1 ω7c, C16 : 0 and C16:1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of this novel isolate was 65.9 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ09[T] is considered to represent a novel species in the genus Sphingomonas, for which the name Sphingomonas segetis sp. nov. is proposed. The type strain is YJ09[T] (=KACC 19551[T]=NBRC 113247[T]).},
}
@article {pmid32500958,
year = {2020},
author = {Kundu, K and Weber, N and Griebler, C and Elsner, M},
title = {Phenotypic heterogeneity as key factor for growth and survival under oligotrophic conditions.},
journal = {Environmental microbiology},
volume = {22},
number = {8},
pages = {3339-3356},
doi = {10.1111/1462-2920.15106},
pmid = {32500958},
issn = {1462-2920},
mesh = {Adaptation, Physiological/*physiology ; Computer Simulation ; Energy Metabolism/physiology ; *Genetic Speciation ; *Micrococcaceae/cytology/growth &amp; development/metabolism ; Phenotype ; },
abstract = {Productivity-poor oligotrophic environments are plentiful on earth. Yet it is not well understood how organisms maintain population sizes under these extreme conditions. Most scenarios consider the adaptation of a single microorganism (isogenic) at the cellular level, which increases their fitness in such an environment. However, in oligotrophic environments, the adaptation of microorganisms at population level - that is, the ability of living cells to differentiate into subtypes with specialized attributes leading to the coexistence of different phenotypes in isogenic populations - remains a little-explored area of microbiology research. In this study, we performed experiments to demonstrate that an isogenic population differentiated to two subpopulations under low energy-flux in chemostats. Fluorescence cytometry and turnover rates revealed that these subpopulations differ in their nucleic acid content and metabolic activity. A mechanistic modelling framework for the dynamic adaptation of microorganisms with the consideration of their ability to switch between different phenotypes was experimentally calibrated and validated. Simulation of hypothetical scenarios suggests that responsive diversification upon a change in energy availability offers a competitive advantage over homogenous adaptation for maintaining viability and metabolic activity with time.},
}
@article {pmid32500269,
year = {2020},
author = {Yang, Y and Liu, W and Zhang, Z and Grossart, HP and Gadd, GM},
title = {Microplastics provide new microbial niches in aquatic environments.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {15},
pages = {6501-6511},
pmid = {32500269},
issn = {1432-0614},
support = {2015282 and 2017388//Chinese Academy of Sciences/ ; },
mesh = {*Biofilms ; Ecosystem ; Lakes/microbiology ; *Microbial Interactions ; Microbiota/*physiology ; *Microplastics ; Rivers/microbiology ; *Water Microbiology ; Water Pollutants, Chemical ; },
abstract = {Microplastics in the biosphere are currently of great environmental concern because of their potential toxicity for aquatic biota and human health and association with pathogenic microbiota. Microplastics can occur in high abundance in all aquatic environments, including oceans, rivers and lakes. Recent findings have highlighted the role of microplastics as important vectors for microorganisms, which can form fully developed biofilms on this artificial substrate. Microplastics therefore provide new microbial niches in the aquatic environment, and the developing biofilms may significantly differ in microbial composition compared to natural free-living or particle-associated microbial populations in the surrounding water. In this article, we discuss the composition and ecological function of the microbial communities found in microplastic biofilms. The potential factors that influence the richness and diversity of such microbial microplastic communities are also evaluated. Microbe-microbe and microbe-substrate interactions in microplastic biofilms have been little studied and are not well understood. Multiomics tools together with morphological, physiological and biochemical analyses should be combined to provide a more comprehensive overview on the ecological role of microplastic biofilms. These new microbial niches have so far unknown consequences for microbial ecology and environmental processes in aquatic ecosystems. More knowledge is required on the microbial community composition of microplastic biofilms and their ecological functions in order to better evaluate consequences for the environment and animal health, including humans, especially since the worldwide abundance of microplastics is predicted to dramatically increase. Key Points • Bacteria are mainly studied in community analyses: fungi are neglected. • Microbial colonization of microplastics depends on substrate, location and time. • Community ecology is a promising approach to investigate microbial colonization. • Biodegradable plastics, and ecological roles of microplastic biofilms, need analysis.},
}
@article {pmid32499774,
year = {2020},
author = {Hallin, S and Bodelier, PLE},
title = {Grand Challenges in Terrestrial Microbiology: Moving on From a Decade of Progress in Microbial Biogeochemistry.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {981},
pmid = {32499774},
issn = {1664-302X},
}
@article {pmid32499764,
year = {2020},
author = {Liu, W and Graham, EB and Zhong, L and Zhang, J and Li, S and Lin, X and Feng, Y},
title = {Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {873},
pmid = {32499764},
issn = {1664-302X},
abstract = {Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.},
}
@article {pmid32498175,
year = {2020},
author = {Benidire, L and El Khalloufi, F and Oufdou, K and Barakat, M and Tulumello, J and Ortet, P and Heulin, T and Achouak, W},
title = {Phytobeneficial bacteria improve saline stress tolerance in Vicia faba and modulate microbial interaction network.},
journal = {The Science of the total environment},
volume = {729},
number = {},
pages = {139020},
doi = {10.1016/j.scitotenv.2020.139020},
pmid = {32498175},
issn = {1879-1026},
mesh = {Bacteria ; Humans ; Microbial Consortia ; Microbial Interactions ; Plant Roots ; RNA, Ribosomal, 16S ; Soil Microbiology ; *Vicia faba ; },
abstract = {Increased global warming, caused by climate change and human activities, will seriously hinder plant development, such as increasing salt concentrations in soils, which will limit water availability for plants. To ensure optimal plant growth under such changing conditions, microorganisms that improve plant growth and health must be integrated into agricultural practices. In the present work, we examined the fate of Vicia faba microbiota structure and interaction network upon inoculation with plant-nodulating rhizobia (Rhizobium leguminosarum RhOF125) and non-nodulating strains (Paenibacillus mucilaginosus BLA7 and Ensifer meliloti RhOL1) in the presence (or absence) of saline stress. Inoculated strains significantly improved plant tolerance to saline stress, suggesting either a direct or indirect effect on the plant response to such stress. To determine the structure of microbiota associated with V. faba, samples of the root-adhering soil (RAS), and the root tissues (RT) of seedlings inoculated (or not) with equal population size of RhOF125, BLA7 and RhOL1 strains and grown in the presence (or absence) of salt, were used to profile the microbial composition by 16S rRNA gene sequencing. The inoculation did not show a significant impact on the composition of the RT microbiota or RAS microbiota. The saline stress shifted the RAS microbiota composition, which correlated with a decrease in Enterobacteriaceae and an increase in Sphingobacterium, Chryseobacterium, Stenotrophomonas, Agrobacterium and Sinorhizobium. When the microbiota of roots and RAS are considered together, the interaction networks for each treatment are quite different and display different key populations involved in community assembly. These findings indicate that upon seed inoculation, community interaction networks rather than their composition may contribute to helping plants to better tolerate environmental stresses. The way microbial populations interfere with each other can have an impact on their functions and thus on their ability to express the genes required to help plants tolerate stresses.},
}
@article {pmid32497654,
year = {2020},
author = {Nardello, LCL and Amado, PPP and Franco, DC and Cazares, RXR and Nogales, CG and Mayer, MPA and Karygianni, L and Thurnheer, T and Pinheiro, ET},
title = {Next-Generation Sequencing to Assess Potentially Active Bacteria in Endodontic Infections.},
journal = {Journal of endodontics},
volume = {46},
number = {8},
pages = {1105-1112},
doi = {10.1016/j.joen.2020.05.004},
pmid = {32497654},
issn = {1878-3554},
mesh = {Actinobacteria ; Bacteria ; *Bacterial Infections ; Clostridiales ; DNA, Bacterial ; *High-Throughput Nucleotide Sequencing ; Humans ; RNA, Ribosomal, 16S ; },
abstract = {INTRODUCTION: Because active bacteria present a higher abundance of ribosomal RNA (rRNA) than DNA (rRNA gene), the rRNA/DNA ratio of next-generation sequencing (NGS) data was measured to search for active bacteria in endodontic infections.<br><br>METHODS: Paired complementary DNA and DNA samples from 5 root canals of teeth with apical periodontitis were subjected to polymerase chain reaction with bar-coded primers amplifying the 16S rRNA gene hypervariable regions V4-V5. High-throughput sequencing was performed using MiSeq (Illumina, San Deigo, CA), and data were analyzed using Quantitative Insights Into Microbial Ecology and Human Oral Microbiome Database. Statistical analysis was performed for relative abundance of bacteria in the DNA- and rRNA-based NGS data using the Mann-Whitney test, whereas differences in the diversity and richness indexes were assessed using a nonparametric 2-sample t test (P < .05). For bacterial taxa detected in both approaches, the rRNA/DNA ratios were calculated by dividing the average abundance of individual species in the respective analysis.<br><br>RESULTS: Although no significant difference was found in the indexes of bacterial richness and diversity, the relative abundance of bacterial members varied in both analyses. Comparing rRNA with DNA data, there was a significant decrease in the relative abundance of Firmicutes (P < .05). The bacterial taxa Bacteroidales [G-2] bacterium HMT 274, Porphyromonas endodontalis, Tannerella forsythia, Alloprevotella tannerae, Prevotella intermedia, Pseudoramibacter alactolyticus, Olsenella sp. HMT 809, Olsenella sp. HMT 939, Olsenella uli, and Fusobacterium nucleatum subsp. animalis were both dominant (DNA &#x2265; 1%) and active (rRNA/DNA &#x2265; 1).<br><br>CONCLUSIONS: The integrated DNA- and rRNA-based NGS strategy was particularly important to disclose the activity of as-yet-uncultivated or difficult-to-culture bacteria in endodontic infections.},
}
@article {pmid32497185,
year = {2020},
author = {Van den Abbeele, P and Duysburgh, C and Rakebrandt, M and Marzorati, M},
title = {Dried yeast cell walls high in beta-glucan and mannan-oligosaccharides positively affect microbial composition and activity in the canine gastrointestinal tract in vitro.},
journal = {Journal of animal science},
volume = {98},
number = {6},
pages = {},
pmid = {32497185},
issn = {1525-3163},
mesh = {Animals ; Cell Wall/chemistry ; Diet/veterinary ; Dietary Supplements/*analysis ; Dogs/microbiology/*physiology ; Enterobacteriaceae/drug effects/growth &amp; development ; Fermentation ; Fusobacteria/drug effects/growth &amp; development ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/metabolism/microbiology ; Mannans/*pharmacology ; Oligosaccharides/*pharmacology ; Saccharomyces cerevisiae/*chemistry ; Yeast, Dried/chemistry ; beta-Glucans/*pharmacology ; },
abstract = {The outer cell wall of yeast is characterized by high levels of β-glucans and mannan-oligosaccharides (MOS), which have been linked with beneficial effects on intestinal health and immune status in dogs. In this study, a standardized in vitro simulation of the canine gastrointestinal tract (Simulator of the Canine Intestinal Microbial Ecosystem; SCIME) was used to evaluate the effect of a Saccharomyces cerevisiae-based product, consisting of 27.5% β-glucans and 22.5% MOS, on the activity (as assessed by measurement of fermentative metabolites) and composition (as assessed by 16S-targeted Illumina sequencing) of canine intestinal microbiota. The S. cerevisiae-based product was tested at three different dosages, i.e., 0.5, 1.0, and 2.0 g/d. A dose-dependent fermentation pattern was observed along the entire length of the colon, as shown by the increased production of the health-related acetate, propionate, and butyrate for the three concentrations tested (0.5, 1.0, and 2.0 g/d). A consistent finding for all three tested concentrations was the increased propionate production (P < 0.05) in the simulated proximal and distal colon. These changes in terms of fermentative metabolites could be linked to specific microbial alterations at the family level, such as the specific stimulation of the propionate-producing families Porphyromonadaceae and Prevotellaceae upon in vitro exposure to the S. cerevisiae-based product. Other consistent changes in community composition upon repeated exposure included the decrease in the Enterobacteriaceae and the Fusobacteriaceae families, which both contain several potentially opportunistic pathogens. Altogether, the generated data support a possible health-promoting role of a product high in β-glucans and MOS when supplemented to the dogs' diet.},
}
@article {pmid32494840,
year = {2020},
author = {Xiong, J and Li, X and Yan, M and Lu, J and Qiu, Q and Chen, J},
title = {Comparable Ecological Processes Govern the Temporal Succession of Gut Bacteria and Microeukaryotes as Shrimp Aged.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {935-945},
doi = {10.1007/s00248-020-01533-6},
pmid = {32494840},
issn = {1432-184X},
support = {31872693//the National Natural Science Foundation of China/ ; LR19C030001//Natural Science Fund for Distinguished Young Scholars of Zhejiang Province/ ; 2015C110018//Technology Innovation Team of Ningbo/ ; },
mesh = {Animals ; Bacteria/isolation &amp; purification ; Bacterial Physiological Phenomena ; Eukaryota/*physiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Penaeidae/*microbiology ; Time Factors ; },
abstract = {Understanding the rules that govern the successions of gut microbiota is prerequisite for testing general ecological theories and sustaining a desirable microbiota. However, the ignorance of microeukaryotes raises the question of whether gut microeukaryotes are assembled according to the same rules as bacteria. We tracked the shrimp gut bacterial and microeukaryotic communities by a longitudinal dense sampling. The successions of both domains were significantly correlated with host age, with relatively stable microeukaryotic communities in adult shrimp. Gut microeukaryotes exhibited significantly higher turnover rate, but fewer transient species, lower proportion of temporal generalists, and narrower habitat niche breadth than bacteria. The γ-diversity partitioning analysis revealed that the successions of gut microbiotas were primarily ascribed to the high dissimilarity as shrimp aged ([Formula: see text]IntraTimes), whereas the relative importance of [Formula: see text]IntraTimes was significantly higher for microeukaryotes than that for bacteria. Compared with contrasting ecological processes in governing free-living bacteria and microeukaryotes, the ecological patterns were comparable between host-associated gut counterparts. However, the gut microeukaryotes were governed more strongly by deterministic selection relative to nestedness compared with the gut bacteria, which supports the "size-plasticity" hypothesis. Our results highlight the importance of independently interpreting free-living and host-associated meta-communities for a comprehensive understanding of the processes that govern microbial successions.},
}
@article {pmid32493970,
year = {2020},
author = {Monteiro, DA and Fonseca, EDS and Rodrigues, RAR and da Silva, JJN and da Silva, EP and Balieiro, FC and Alves, BJR and Rachid, CTCDC},
title = {Structural and functional shifts of soil prokaryotic community due to Eucalyptus plantation and rotation phase.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {9075},
pmid = {32493970},
issn = {2045-2322},
mesh = {Agriculture/methods ; Carbon/chemistry/metabolism ; Carbon Dioxide/chemistry/metabolism ; Environmental Monitoring/methods ; Eucalyptus/genetics/metabolism/*physiology ; Forestry/methods ; Forests ; Greenhouse Gases/chemistry/metabolism ; Nitrogen/chemistry/metabolism ; Nitrous Oxide/chemistry/metabolism ; Prokaryotic Cells/metabolism/*physiology ; RNA, Ribosomal, 16S/genetics ; Rotation ; Soil/*chemistry ; },
abstract = {Agriculture, forestry and other land uses are currently the second highest source of anthropogenic greenhouse gases (GHGs) emissions. In soil, these gases derive from microbial activity, during carbon (C) and nitrogen (N) cycling. To investigate how Eucalyptus land use and growth period impact the microbial community, GHG fluxes and inorganic N levels, and if there is a link among these variables, we monitored three adjacent areas for 9 months: a recently planted Eucalyptus area, fully developed Eucalyptus forest (final of rotation) and native forest. We assessed the microbial community using 16S rRNA gene sequencing and qPCR of key genes involved in C and N cycles. No considerable differences in GHG flux were evident among the areas, but logging considerably increased inorganic N levels. Eucalyptus areas displayed richer and more diverse communities, with selection for specific groups. Land use influenced communities more extensively than the time of sampling or growth phase, although all were significant modulators. Several microbial groups and genes shifted temporally, and inorganic N levels shaped several of these changes. No correlations among microbial groups or genes and GHG were found, suggesting no link among these variables in this short-rotation Eucalyptus study.},
}
@article {pmid32488484,
year = {2020},
author = {Semiatizki, A and Weiss, B and Bagim, S and Rohkin-Shalom, S and Kaltenpoth, M and Chiel, E},
title = {Effects, interactions, and localization of Rickettsia and Wolbachia in the house fly parasitoid, Spalangia endius.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {718-728},
doi = {10.1007/s00248-020-01520-x},
pmid = {32488484},
issn = {1432-184X},
support = {435/18//Planning and Budgeting Committee of the Council for Higher Education of Israel/ ; CoG 819585/ERC_/European Research Council/International ; },
mesh = {Animals ; Female ; *Host-Parasite Interactions ; Houseflies/parasitology ; Male ; Reproduction ; Rickettsia/*physiology ; *Symbiosis ; Wasps/*microbiology/physiology ; Wolbachia/*physiology ; },
abstract = {Many insect species harbor facultative microbial symbionts that affect their biology in diverse ways. Here, we studied the effects, interactions, and localization of two bacterial symbionts-Wolbachia and Rickettsia-in the parasitoid Spalangia endius. We crossed between four S. endius colonies-Wolbachia only (W), Rickettsia only (R), both (WR), and none (aposymbiotic, APS) (16 possible crosses) and found that Wolbachia induces incomplete cytoplasmic incompatibility (CI), both when the males are W or WR. Rickettsia did not cause reproductive manipulations and did not rescue the Wolbachia-induced CI. However, when R females were crossed with W or WR males, significantly less offspring were produced compared with that of control crosses. In non-CI crosses, the presence of Wolbachia in males caused a significant reduction in offspring numbers. Females' developmental time was significantly prolonged in the R colony, with adults starting to emerge one day later than the other colonies. Other fitness parameters did not differ significantly between the colonies. Using fluorescence in situ hybridization microscopy in females, we found that Wolbachia is localized alongside Rickettsia inside oocytes, follicle cells, and nurse cells in the ovaries. However, Rickettsia is distributed also in muscle cells all over the body, in ganglia, and even in the brain.},
}
@article {pmid32488483,
year = {2020},
author = {Hejduková, E and Elster, J and Nedbalová, L},
title = {Annual Cycle of Freshwater Diatoms in the High Arctic Revealed by Multiparameter Fluorescent Staining.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {559-572},
doi = {10.1007/s00248-020-01521-w},
pmid = {32488483},
issn = {1432-184X},
support = {20217//Grantov&#xe1; Agentura, Univerzita Karlova/ ; LM2015078//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; },
mesh = {Arctic Regions ; Diatoms/*physiology ; Fresh Water ; *Life History Traits ; Seasons ; Staining and Labeling ; Svalbard ; },
abstract = {Diatoms (Bacillariophyceae) are important primary producers in a wide range of hydro-terrestrial habitats in polar regions that are characterized by many extreme environmental conditions. Nevertheless, how they survive periods of drought and/or freeze remains unknown. A general strategy of microorganisms to overcome adverse conditions is dormancy, but morphologically distinct diatom resting stages are rare. This study aimed to evaluate the annual cycle of freshwater diatoms in the High Arctic (Central Spitsbergen) and provide an insight into their physiological cell status variability. The diversity and viability of diatom cells were studied in samples collected five times at four study sites, tracing the key events for survival (summer vegetative season, autumn dry-freezing, winter freezing, spring melting, summer vegetative season [again]). For viability evaluation, a multiparameter fluorescent staining was used in combination with light microscopy and allowed to reveal the physiological status at a single-cell level. The proportions of the cell categories were seasonally and locality dependent. The results suggested that a significant portion of vegetative cells survive winter and provide an inoculum for the following vegetative season. The ice thickness significantly influenced spring survival. The thicker the ice layer was, the more dead cells and fewer other stages were observed. The influence of the average week max-min temperature differences in autumn and winter was not proven.},
}
@article {pmid32485888,
year = {2020},
author = {Aliyu, H and Mohr, T and Cowan, D and de Maayer, P and Neumann, A},
title = {Time-Course Transcriptome of Parageobacillus thermoglucosidasius DSM 6285 Grown in the Presence of Carbon Monoxide and Air.},
journal = {International journal of molecular sciences},
volume = {21},
number = {11},
pages = {},
pmid = {32485888},
issn = {1422-0067},
mesh = {Air ; Bacillaceae/drug effects/*genetics/metabolism ; Carbon Monoxide/*pharmacology ; *Gene Expression Regulation, Bacterial ; Oxygen/metabolism ; *Transcriptome ; },
abstract = {Parageobacillus thermoglucosidasius is a metabolically versatile, facultatively anaerobic thermophile belonging to the family Bacillaceae. Previous studies have shown that this bacterium harbours co-localised genes coding for a carbon monoxide (CO) dehydrogenase (CODH) and Ni-Fe hydrogenase (Phc) complex and oxidises CO and produces hydrogen (H2) gas via the water-gas shift (WGS) reaction. To elucidate the genetic events culminating in the WGS reaction, P. thermoglucosidasius DSM 6285 was cultivated under an initial gas atmosphere of 50% CO and 50% air and total RNA was extracted at ~8 (aerobic phase), 20 (anaerobic phase), 27 and 44 (early and late hydrogenogenic phases) hours post inoculation. The rRNA-depleted fraction was sequenced using Illumina NextSeq, v2.5, 1x75bp chemistry. Differential expression revealed that at 8 vs 20, 20 vs 27 and 27 vs 44 hours post inoculation, 2190, 2118 and 231 transcripts were differentially (FDR < 0.05) expressed. Cluster analysis revealed 26 distinct gene expression trajectories across the four time points. Of these, two similar clusters, showing overexpression at 20 relative to 8 hours and depletion at 27 and 44 hours, harboured the CODH and Phc transcripts, suggesting possible regulation by O2. The transition between aerobic respiration and anaerobic growth was marked by initial metabolic deterioration, as reflected by up-regulation of transcripts linked to sporulation and down-regulation of transcripts linked to flagellar assembly and metabolism. However, the transcriptome and growth profiles revealed the reversal of this trend during the hydrogenogenic phase.},
}
@article {pmid32483324,
year = {2020},
author = {van Bergeijk, DA and Terlouw, BR and Medema, MH and van Wezel, GP},
title = {Ecology and genomics of Actinobacteria: new concepts for natural product discovery.},
journal = {Nature reviews. Microbiology},
volume = {18},
number = {10},
pages = {546-558},
pmid = {32483324},
issn = {1740-1534},
mesh = {Actinobacteria/*genetics/metabolism ; Anti-Bacterial Agents/biosynthesis/*isolation &amp; purification/pharmacology ; Biological Products/*isolation &amp; purification/metabolism/pharmacology ; Drug Discovery ; Ecology ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; Genomics/methods ; Humans ; Metabolic Networks and Pathways/genetics ; Multigene Family ; },
abstract = {Actinobacteria constitute a highly diverse bacterial phylum with an unrivalled metabolic versatility. They produce most of the clinically used antibiotics and a plethora of other natural products with medical or agricultural applications. Modern 'omics'-based technologies have revealed that the genomic potential of Actinobacteria greatly outmatches the known chemical space. In this Review, we argue that combining insights into actinobacterial ecology with state-of-the-art computational approaches holds great promise to unlock this unexplored reservoir of actinobacterial metabolism. This enables the identification of small molecules and other stimuli that elicit the induction of poorly expressed biosynthetic gene clusters, which should help reinvigorate screening efforts for their precious bioactive natural products.},
}
@article {pmid32482859,
year = {2020},
author = {Roach, TNF and Little, M and Arts, MGI and Huckeba, J and Haas, AF and George, EE and Quinn, RA and Cobián-Güemes, AG and Naliboff, DS and Silveira, CB and Vermeij, MJA and Kelly, LW and Dorrestein, PC and Rohwer, F},
title = {A multiomic analysis of in situ coral-turf algal interactions.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {24},
pages = {13588-13595},
pmid = {32482859},
issn = {1091-6490},
mesh = {Animals ; Anthozoa/chemistry/*metabolism/microbiology/parasitology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chlorophyta/chemistry/*metabolism ; Coral Reefs ; Ecosystem ; Metagenomics ; Microbiota ; },
abstract = {Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.},
}
@article {pmid32482164,
year = {2020},
author = {Costa, OYA and de Hollander, M and Pijl, A and Liu, B and Kuramae, EE},
title = {Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {76},
pmid = {32482164},
issn = {2049-2618},
support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/International ; 202496/2015-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/International ; },
mesh = {Bacteria/enzymology/genetics ; Biodegradation, Environmental ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; *Polymers/metabolism ; },
abstract = {BACKGROUND: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics.<br><br>RESULTS: SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (&#x3b1;-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases.<br><br>CONCLUSIONS: We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.},
}
@article {pmid32477286,
year = {2020},
author = {Bagnoud, A and Pramateftaki, P and Bogard, MJ and Battin, TJ and Peter, H},
title = {Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {771},
pmid = {32477286},
issn = {1664-302X},
abstract = {Despite the recognition of streams and rivers as sources of methane (CH4) to the atmosphere, the role of CH4 oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH4 oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream- and porewater CH4 concentrations. Michealis-Menten kinetic parameter of MOX, maximum reaction velocity (V max), and CH4 concentration at half V max (K S) increased with CH4 supply. K S values in the micromolar range matched the CH4 concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH4 oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.},
}
@article {pmid32475802,
year = {2020},
author = {Zhang, Z and van Kleunen, M and Becks, L and Thakur, MP},
title = {Towards a General Understanding of Bacterial Interactions.},
journal = {Trends in microbiology},
volume = {28},
number = {10},
pages = {783-785},
doi = {10.1016/j.tim.2020.05.010},
pmid = {32475802},
issn = {1878-4380},
mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; Ecology ; *Microbial Interactions ; Microbiota ; },
abstract = {Understanding the general rules of microbial interactions is central for advancing microbial ecology. Recent studies show that interaction range, interaction strength, and community context determine bacterial interactions and the coexistence and evolution of bacteria. We highlight how these factors could contribute to a general understanding of bacterial interactions.},
}
@article {pmid32474660,
year = {2020},
author = {Musonerimana, S and Bez, C and Licastro, D and Habarugira, G and Bigirimana, J and Venturi, V},
title = {Pathobiomes Revealed that Pseudomonas fuscovaginae and Sarocladium oryzae Are Independently Associated with Rice Sheath Rot.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {627-642},
doi = {10.1007/s00248-020-01529-2},
pmid = {32474660},
issn = {1432-184X},
mesh = {Hypocreales/genetics/*physiology ; Oryza/*microbiology ; Plant Diseases/*microbiology ; Pseudomonas/genetics/*physiology ; },
abstract = {Rice sheath rot has been mainly associated with the bacterial pathogen Pseudomonas fuscovaginae and in some cases to the fungal pathogen Sarocladium oryzae; it is yet unclear if they are part of a complex disease. The bacterial and fungal community associated with rice sheath rot symptomatic and asymptomatic rice plants was determined/studied with the main aim to shed light on the pathogen(s) causing rice sheath rot. Plant samples were collected from different rice varieties in two locations (highland and lowland) in two rice-growing seasons (wet and dry season) in Burundi. Our results showed that the bacterial Pseudomonas genus was prevalent in highland in both rice-growing seasons and was not affected by rice plant varieties. Pseudomonas sequence reads displayed a significant high similarity to Pseudomonas fuscovaginae indicating that it is the causal agent of rice sheath rot as previously reported. The fungal Sarocladium genus was on the other hand prevalent in lowland only in the wet season; the sequence reads were most significantly similar to Sarocladium oryzae. These studies showed that plant microbiome analysis is very useful in determining the microorganisms involved in a plant disease. P. fuscovaginae and S. oryzae were prevalent in symptomatic samples in highland and lowland respectively being present independently and hence are not part of a complex disease. The significant presence of other bacterial and fungal taxa in symptomatic samples is also discussed possibly making this disease more complex. Finally, we also report the microbial communities that are associated with the plant sheath in symptomatic and asymptomatic plants from the same rice fields.},
}
@article {pmid32474659,
year = {2020},
author = {Liu, RR and Tian, Y and Zhou, EM and Xiong, MJ and Xiao, M and Li, WJ},
title = {Distinct Expression of the Two NO-Forming Nitrite Reductases in Thermus antranikianii DSM 12462[T] Improved Environmental Adaptability.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {614-626},
doi = {10.1007/s00248-020-01528-3},
pmid = {32474659},
issn = {1432-184X},
support = {91951205//National Natural Science Foundation of China/ ; 31970122//National Natural Science Foundation of China/ ; 31470139//National Natural Science Foundation of China/ ; 31600298//National Natural Science Foundation of China/ ; 2018B020206001//Guangdong Province Science and Technology Innovation Strategy Special Fund/ ; },
mesh = {Adaptation, Physiological/*genetics ; Bacterial Proteins/*genetics/metabolism ; Nitric Oxide/*metabolism ; Nitrite Reductases/*genetics/metabolism ; Thermus/enzymology/*genetics ; },
abstract = {Hot spring ecosystems are analogous to some thermal environments on the early Earth and represent ideal models to understand life forms and element cycling on the early Earth. Denitrification, an important component of biogeochemical nitrogen cycle, is highly active in hot springs. Nitrite (NO2[-]) reduction to nitric oxide (NO) is the significant and rate-limiting pathway in denitrification and is catalyzed by two types of nitrite reductases, encoded by nirS and nirK genes. NirS and NirK were originally considered incompatible in most denitrifying organisms, although a few strains have been reported to possess both genes. Herein, we report the functional division of nirS and nirK in Thermus, a thermophilic genus widespread in thermal ecosystems. Transcriptional levels of nirS and nirK coexisting in Thermus antranikianii DSM 12462[T] were measured to assess the effects of nitrite, oxygen, and stimulation time. Thirty-nine Thermus strains were used to analyze the phylogeny and distribution of nirS and nirK; six representative strains were used to assess the denitrification phenotype. The results showed that both genes were actively transcribed and expressed independently in T. antranikianii DSM 12462[T]. Strains with both nirS and nirK had a wider range of nitrite adaptation and revealed nir-related physiological adaptations in Thermus: nirK facilitated adaptation to rapid changes and extended the adaptation range of nitrite under oxygen-limited conditions, while nirS expression was higher under oxic and relatively stable conditions.},
}
@article {pmid32471167,
year = {2020},
author = {Su, L and Zhang, L and Nie, D and Kuramae, EE and Shen, B and Shen, Q},
title = {Bacterial Tomato Pathogen Ralstonia solanacearum Invasion Modulates Rhizosphere Compounds and Facilitates the Cascade Effect of Fungal Pathogen Fusarium solani.},
journal = {Microorganisms},
volume = {8},
number = {6},
pages = {},
pmid = {32471167},
issn = {2076-2607},
support = {41571242//Chinese Natural Science Fund Program/ ; },
abstract = {Soil-borne pathogen invasions can significantly change the microbial communities of the host rhizosphere. However, whether bacterial Ralstonia solanacearum pathogen invasion influences the abundance of fungal pathogens remains unclear. In this study, we combined high-throughput sequencing, qPCR, liquid chromatography and soil culture experiments to analyze the rhizosphere fungal composition, co-occurrence of fungal communities, copy numbers of functional genes, contents of phenolic acids and their associations in healthy and bacterial wilt-diseased tomato plants. We found that R. solanacearum invasion increased the abundance of the soil-borne pathogen Fusarium solani. The concentrations of three phenolic acids in the rhizosphere soil of bacterial wilt-diseased tomato plants were significantly higher than those in the rhizosphere soil of healthy tomato plants. In addition, the increased concentrations of phenolic acids significantly stimulated F. solani growth in the soil. Furthermore, a simple fungal network with fewer links, nodes and hubs (highly connected nodes) was found in the diseased tomato plant rhizosphere. These results indicate that once the symptom of bacterial wilt disease is observed in tomato, the roots of the wilt-diseased tomato plants need to be removed in a timely manner to prevent the enrichment of other fungal soil-borne pathogens. These findings provide some ecological clues for the mixed co-occurrence of bacterial wilt disease and other fungal soil-borne diseases.},
}
@article {pmid32470594,
year = {2020},
author = {Capson-Tojo, G and Batstone, DJ and Grassino, M and Vlaeminck, SE and Puyol, D and Verstraete, W and Kleerebezem, R and Oehmen, A and Ghimire, A and Pikaar, I and Lema, JM and Hülsen, T},
title = {Purple phototrophic bacteria for resource recovery: Challenges and opportunities.},
journal = {Biotechnology advances},
volume = {43},
number = {},
pages = {107567},
doi = {10.1016/j.biotechadv.2020.107567},
pmid = {32470594},
issn = {1873-1899},
mesh = {Biomass ; *Microalgae ; Nitrogen ; Phosphorus ; *Proteobacteria ; Wastewater ; },
abstract = {Sustainable development is driving a rapid focus shift in the wastewater and organic waste treatment sectors, from a "removal and disposal" approach towards the recovery and reuse of water, energy and materials (e.g. carbon or nutrients). Purple phototrophic bacteria (PPB) are receiving increasing attention due to their capability of growing photoheterotrophically under anaerobic conditions. Using light as energy source, PPB can simultaneously assimilate carbon and nutrients at high efficiencies (with biomass yields close to unity (1 g CODbiomass·g CODremoved[-1])), facilitating the maximum recovery of these resources as different value-added products. The effective use of infrared light enables selective PPB enrichment in non-sterile conditions, without competition with other phototrophs such as microalgae if ultraviolet-visible wavelengths are filtered. This review reunites results systematically gathered from over 177 scientific articles, aiming at producing generalized conclusions. The most critical aspects of PPB-based production and valorisation processes are addressed, including: (i) the identification of the main challenges and potentials of different growth strategies, (ii) a critical analysis of the production of value-added compounds, (iii) a comparison of the different value-added products, (iv) insights into the general challenges and opportunities and (v) recommendations for future research and development towards practical implementation. To date, most of the work has not been executed under real-life conditions, relevant for full-scale application. With the savings in wastewater discharge due to removal of organics, nitrogen and phosphorus as an important economic driver, priorities must go to using PPB-enriched cultures and real waste matrices. The costs associated with artificial illumination, followed by centrifugal harvesting/dewatering and drying, are estimated to be 1.9, 0.3-2.2 and 0.1-0.3 $·kgdry biomass[-1]. At present, these costs are likely to exceed revenues. Future research efforts must be carried out outdoors, using sunlight as energy source. The growth of bulk biomass on relatively clean wastewater streams (e.g. from food processing) and its utilization as a protein-rich feed (e.g. to replace fishmeal, 1.5-2.0 $·kg[-1]) appears as a promising valorisation route.},
}
@article {pmid32469071,
year = {2021},
author = {Rampal, R and Wari, N and Singh, AK and Das, U and Bopanna, S and Gupta, V and Nayak, B and Velapandian, T and Kedia, S and Kumar, D and Awasthi, A and Ahuja, V},
title = {Retinoic Acid Is Elevated in the Mucosa of Patients With Active Ulcerative Colitis and Displays a Proinflammatory Role by Augmenting IL-17 and IFNγ Production.},
journal = {Inflammatory bowel diseases},
volume = {27},
number = {1},
pages = {74-83},
doi = {10.1093/ibd/izaa121},
pmid = {32469071},
issn = {1536-4844},
mesh = {Adult ; Cell Differentiation/drug effects ; Colitis, Ulcerative/*metabolism ; Cross-Sectional Studies ; Female ; Forkhead Transcription Factors/metabolism ; Humans ; Inflammation ; Inflammation Mediators/*metabolism ; Interferon-gamma/*biosynthesis ; Interleukin-10/metabolism ; Interleukin-17/*biosynthesis ; Intestinal Mucosa/*metabolism ; Male ; Middle Aged ; T-Lymphocytes, Regulatory/metabolism ; Tretinoin/*metabolism ; },
abstract = {BACKGROUND: All-trans retinoic acid (RA) plays a crucial role in promoting Foxp3+ Treg generation while reciprocally inhibiting Th1/Th17 generation. Our previous research highlighted that in the face of inflammatory conditions, RA plays a contrary role where it aggravates intestinal inflammation by promoting interferon (IFN) γ and interleukin (IL)-17 differentiation in vitro.<br><br>METHODS: In this study we translated our in vitro results into a clinical setting where we estimated mucosal and serum RA levels along with the immunophenotypic profile (IL-17, IFN&#x3b3;, Foxp3, IL-10) in adaptive (CD4, CD8) and innate-like T cells (mucosal associated invariant T cells and &#x3b3;&#x3b4; T cells) in patients with ulcerative colitis in remission or with active inflammation.<br><br>RESULTS: This is the first study to estimate RA levels in the human gut and shows that patients with active disease had increased mucosal RA levels as compared with patients in remission (4.0 vs 2.5 ng/mL; P&#x2005;<&#x2005;0.01) and control patients (3.4 vs 0.8 ng/mL; P&#x2005;<&#x2005;0.0001). This effect was accompanied by significantly elevated IL-17 and IFN&#x3b3; in tissue CD4+, CD8+, mucosal associated invariant T+ cells, and &#x3b3;&#x3b4;&#x200a;+ T cells. Moreover, the raised RA levels in patients with active disease showed a positive correlation with proinflammatory cytokines (IL-17, IFN&#x3b3;) and a negative correlation with IL-10. We also found that RA negatively correlated with IL-9, thereby reinstating our previous finding that RA inhibits Th9 differentiation.<br><br>CONCLUSIONS: These data confirm our previous in vitro results that in the presence of inflammation, RA plays a crucial role in maintaining gut inflammation by upregulating proinflammatory markers.},
}
@article {pmid32468160,
year = {2020},
author = {Tschoeke, D and Salazar, VW and Vidal, L and Campeão, M and Swings, J and Thompson, F and Thompson, C},
title = {Unlocking the Genomic Taxonomy of the Prochlorococcus Collective.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {546-558},
doi = {10.1007/s00248-020-01526-5},
pmid = {32468160},
issn = {1432-184X},
mesh = {*Genome, Bacterial ; Genomics ; *Life History Traits ; Prochlorococcus/*classification/genetics/physiology ; },
abstract = {Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus, and Riococcus. The novel genera have distinct genomic and ecological attributes.},
}
@article {pmid32466615,
year = {2020},
author = {Van den Abbeele, P and Ghyselinck, J and Marzorati, M and Villar, A and Zangara, A and Smidt, CR and Risco, E},
title = {In Vitro Evaluation of Prebiotic Properties of a Commercial Artichoke Inflorescence Extract Revealed Bifidogenic Effects.},
journal = {Nutrients},
volume = {12},
number = {6},
pages = {},
pmid = {32466615},
issn = {2072-6643},
mesh = {Bifidobacterium/drug effects ; Colon/metabolism/microbiology ; Cynara scolymus/*chemistry ; Dietary Supplements ; Ecosystem ; Fatty Acids, Volatile/metabolism ; Fermentation ; Gastrointestinal Microbiome/drug effects ; Humans ; Inflorescence/*chemistry ; Inulin ; Lactobacillus/drug effects ; Oligosaccharides/pharmacology ; Plant Extracts/*pharmacology ; Prebiotics/*analysis ; Propionates/metabolism ; },
abstract = {UNLABELLED: : Background: Prebiotics used as a dietary supplement, stimulate health-related gut microbiota (e.g., bifidobacteria, lactobacilli, etc.). This study evaluated potential prebiotic effects of an artichoke aqueous dry extract (AADE) using in vitro gut model based on the Simulator of Human Intestinal Microbial Ecosystem (SHIME[®]).<br><br>METHODS: Short-term colonic fermentations (48 h) of AADE, fructo-oligosaccharides (FOS), and a blank were performed. Microbial metabolites were assessed at 0, 6, 24, and 48 h of colonic incubation via measuring pH, gas pressure, lactate, ammonium, and short-chain fatty acids (SCFAs) levels. Community composition was assessed via targeted qPCRs.<br><br>RESULTS: After 24 and 48 h of incubation, bifidobacteria levels increased 25-fold with AADE (p < 0.05) and >100-fold with FOS (p < 0.05) compared to blank. Lactobacillus spp. levels only tended to increase with AADE, whereas they increased 10-fold with FOS. At 6 h, pH decreased with AADE and FOS and remained stable until 48 h; however, gas pressure increased significantly till the end of study. Acetate, propionate, and total SCFA production increased significantly with both at all time-points. Lactate levels initially increased but branched SCFA and ammonium levels remained low till 48 h.<br><br>CONCLUSION: AADE displayed prebiotic potential by exerting bifidogenic effects that stimulated production of health-related microbial metabolites, which is potentially due to inulin in AADE.},
}
@article {pmid32466517,
year = {2020},
author = {Jia, X and Dini-Andreote, F and Falcão Salles, J},
title = {Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data.},
journal = {Microorganisms},
volume = {8},
number = {6},
pages = {},
pmid = {32466517},
issn = {2076-2607},
abstract = {Quantifying which assembly processes structure microbiomes can assist prediction, manipulation, and engineering of community outcomes. However, the relative importance of these processes might depend on whether DNA or RNA are used, as they differ in stability. We hypothesized that. RNA-inferred community responses to (a)biotic fluctuations are faster than those inferred by DNA; the relative influence of variable selection is stronger in RNA-inferred communities (environmental factors are spatiotemporally heterogeneous), whereas homogeneous selection largely influences DNA-inferred communities (environmental filters are constant). To test these hypotheses, we characterized soil bacterial communities by sequencing both 16S rRNA amplicons from the extracted DNA and RNA transcripts across distinct stages of soil primary succession and quantified the relative influence of each assembly process using ecological null model analysis. Our results revealed that variations in α-diversity and temporal turnover were higher in RNA- than in DNA-inferred communities across successional stages, albeit there was a similar community composition; in line with our hypotheses, the assembly of RNA-inferred community was more closely associated with environmental variability (variable selection) than using the standard DNA-based approach, which was largely influenced by homogeneous selection. This study illustrates the need for benchmarking approaches to properly elucidate how community assembly processes structure microbial communities.},
}
@article {pmid32462391,
year = {2020},
author = {Möhlmann, TWR and Vogels, CBF and Göertz, GP and Pijlman, GP and Ter Braak, CJF and Te Beest, DE and Hendriks, M and Nijhuis, EH and Warris, S and Drolet, BS and van Overbeek, L and Koenraadt, CJM},
title = {Impact of Gut Bacteria on the Infection and Transmission of Pathogenic Arboviruses by Biting Midges and Mosquitoes.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {703-717},
pmid = {32462391},
issn = {1432-184X},
support = {BBS/E/I/00007039/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Aedes/*virology ; Animals ; Bacterial Physiological Phenomena ; Ceratopogonidae/*virology ; Chikungunya virus/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Insect Vectors/*virology ; Mosquito Vectors/virology ; Orthobunyavirus/*physiology ; Zika Virus/*physiology ; },
abstract = {Tripartite interactions among insect vectors, midgut bacteria, and viruses may determine the ability of insects to transmit pathogenic arboviruses. Here, we investigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosus and Culicoides sonorensis biting midges for Schmallenberg virus, and of Aedes aegypti mosquitoes for Zika and chikungunya viruses. Gut bacteria were manipulated by treating the adult insects with antibiotics. The gut bacterial communities were investigated using Illumina MiSeq sequencing of 16S rRNA, and susceptibility to arbovirus infection was tested by feeding insects with an infectious blood meal. Antibiotic treatment led to changes in gut bacteria for all insects. Interestingly, the gut bacterial composition of untreated Ae. aegypti and C. nubeculosus showed Asaia as the dominant genus, which was drastically reduced after antibiotic treatment. Furthermore, antibiotic treatment resulted in relatively more Delftia bacteria in both biting midge species, but not in mosquitoes. Antibiotic treatment and subsequent changes in gut bacterial communities were associated with a significant, 1.8-fold increased infection rate of C. nubeculosus with Schmallenberg virus, but not for C. sonorensis. We did not find any changes in infection rates for Ae. aegypti mosquitoes with Zika or chikungunya virus. We conclude that resident gut bacteria may dampen arbovirus transmission in biting midges, but not so in mosquitoes. Use of antimicrobial compounds at livestock farms might therefore have an unexpected contradictory effect on the health of animals, by increasing the transmission of viral pathogens by biting midges.},
}
@article {pmid32462390,
year = {2020},
author = {Yang, M and Shi, J and Wang, B and Xiao, J and Li, W and Liu, CQ},
title = {Control of Hydraulic Load on Bacterioplankton Diversity in Cascade Hydropower Reservoirs, Southwest China.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {537-545},
doi = {10.1007/s00248-020-01523-8},
pmid = {32462390},
issn = {1432-184X},
support = {2016YFA0601001//the National Key R &amp; D Program of China/ ; U1612441//Innovative Research Group Project of the National Natural Science Foundation of China (CN)/ ; },
mesh = {*Bacterial Physiological Phenomena ; China ; Hydrology ; Lakes/analysis/*microbiology ; Microbiota/*physiology ; Plankton/*physiology ; Water Supply ; },
abstract = {Hydroelectric reservoirs are highly regulated ecosystems, where the understanding on bacterioplankton has been very limited so far. In view of significant changes in river hydrological conditions by dam construction, hydraulic load (i.e., the ratio of mean water depth to water retention time) was assumed to control bacterioplankton diversity in cascading hydropower reservoirs. To evaluate this hypothesis, we investigated bacterioplankton composition and diversity using high-throughput sequencing and related environmental variables in eleven reservoirs on the Wujiang River, Southwest China. Our results showed a decrease of bacterioplankton diversity index with an increase of reservoir hydraulic load. This is because hydraulic load governs dissolved oxygen variation in the water column, which is a key factor shaping bacterioplankton composition in these hydroelectric reservoirs. In contrast, bacterioplankton abundance was mainly affected by nutrient-related environmental factors. Therefore, from a hydrological perspective, hydraulic load is a decisive factor for the bacterioplankton diversity in the hydroelectric reservoirs. This study can improve the understanding of reservoir bacterial ecology, and the empirical relationship between hydraulic load and bacterioplankton diversity index will help to quantitatively evaluate ecological effects of river damming.},
}
@article {pmid32461136,
year = {2020},
author = {Flanagan, E and Lamport, D and Brennan, L and Burnet, P and Calabrese, V and Cunnane, SC and de Wilde, MC and Dye, L and Farrimond, JA and Emerson Lombardo, N and Hartmann, T and Hartung, T and Kalliomäki, M and Kuhnle, GG and La Fata, G and Sala-Vila, A and Samieri, C and Smith, AD and Spencer, JPE and Thuret, S and Tuohy, K and Turroni, S and Vanden Berghe, W and Verkuijl, M and Verzijden, K and Yannakoulia, M and Geurts, L and Vauzour, D},
title = {Nutrition and the ageing brain: Moving towards clinical applications.},
journal = {Ageing research reviews},
volume = {62},
number = {},
pages = {101079},
doi = {10.1016/j.arr.2020.101079},
pmid = {32461136},
issn = {1872-9649},
support = {MR/N030087/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Aging ; Brain ; Diet ; *Healthy Aging ; Humans ; *Nutritional Status ; },
abstract = {The global increases in life expectancy and population have resulted in a growing ageing population and with it a growing number of people living with age-related neurodegenerative conditions and dementia, shifting focus towards methods of prevention, with lifestyle approaches such as nutrition representing a promising avenue for further development. This overview summarises the main themes discussed during the 3[rd] Symposium on "Nutrition for the Ageing Brain: Moving Towards Clinical Applications" held in Madrid in August 2018, enlarged with the current state of knowledge on how nutrition influences healthy ageing and gives recommendations regarding how the critical field of nutrition and neurodegeneration research should move forward into the future. Specific nutrients are discussed as well as the impact of multi-nutrient and whole diet approaches, showing particular promise to combatting the growing burden of age-related cognitive decline. The emergence of new avenues for exploring the role of diet in healthy ageing, such as the impact of the gut microbiome and development of new techniques (imaging measures of brain metabolism, metabolomics, biomarkers) are enabling researchers to approach finding answers to these questions. But the translation of these findings into clinical and public health contexts remains an obstacle due to significant shortcomings in nutrition research or pressure on the scientific community to communicate recommendations to the general public in a convincing and accessible way. Some promising programs exist but further investigation to improve our understanding of the mechanisms by which nutrition can improve brain health across the human lifespan is still required.},
}
@article {pmid32460826,
year = {2020},
author = {Roelofs, D and Zwaenepoel, A and Sistermans, T and Nap, J and Kampfraath, AA and Van de Peer, Y and Ellers, J and Kraaijeveld, K},
title = {Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution.},
journal = {BMC biology},
volume = {18},
number = {1},
pages = {57},
pmid = {32460826},
issn = {1741-7007},
support = {PhD fellowship//Fonds Wetenschappelijk Onderzoek/International ; 15494//Stichting voor de Technische Wetenschappen/International ; NWA StartImpulse//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/International ; },
mesh = {Animals ; Arthropods/genetics ; *Evolution, Molecular ; *Gene Duplication ; *Genome ; Insecta/*genetics ; Phylogeny ; },
abstract = {BACKGROUND: Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals.<br><br>RESULTS: Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances (KS), patterns of within-genome co-linearity, and phylogenomic gene tree-species tree reconciliation methods. We observe an abundance of gene duplicates in the majority of these hexapod genomes, yet we find little evidence for WGD. The majority of gene duplicates seem to have originated through small-scale gene duplication processes. We did detect segmental duplications in six genomes, but these lacked the within-genome co-linearity signature typically associated with WGD, and the age of these duplications did not coincide with particular peaks in KS distributions. Furthermore, statistical gene tree-species tree reconciliation failed to support all but one of the previously hypothesized WGDs.<br><br>CONCLUSIONS: Our analyses therefore provide very limited evidence for WGD having played a significant role in the evolution of hexapods and suggest that alternative mechanisms drive gene duplication events in this group of animals. For instance, we propose that, along with small-scale gene duplication events, episodes of increased transposable element activity could have been an important source for gene duplicates in hexapods.},
}
@article {pmid32460009,
year = {2020},
author = {De Boeck, I and van den Broek, MFL and Allonsius, CN and Spacova, I and Wittouck, S and Martens, K and Wuyts, S and Cauwenberghs, E and Jokicevic, K and Vandenheuvel, D and Eilers, T and Lemarcq, M and De Rudder, C and Thys, S and Timmermans, JP and Vroegop, AV and Verplaetse, A and Van de Wiele, T and Kiekens, F and Hellings, PW and Vanderveken, OM and Lebeer, S},
title = {Lactobacilli Have a Niche in the Human Nose.},
journal = {Cell reports},
volume = {31},
number = {8},
pages = {107674},
doi = {10.1016/j.celrep.2020.107674},
pmid = {32460009},
issn = {2211-1247},
mesh = {Female ; Humans ; Lactobacillus/*pathogenicity ; Male ; Nose/*microbiology ; },
abstract = {Although an increasing number of beneficial microbiome members are characterized for the human gut and vagina, beneficial microbes are underexplored for the human upper respiratory tract (URT). In this study, we demonstrate that taxa from the beneficial Lactobacillus genus complex are more prevalent in the healthy URT than in patients with chronic rhinosinusitis (CRS). Several URT-specific isolates are cultured, characterized, and further explored for their genetic and functional properties related to adaptation to the URT. Catalase genes are found in the identified lactobacilli, which is a unique feature within this mostly facultative anaerobic genus. Moreover, one of our isolated strains, Lactobacillus casei AMBR2, contains fimbriae that enable strong adherence to URT epithelium, inhibit the growth and virulence of several URT pathogens, and successfully colonize nasal epithelium of healthy volunteers. This study thus demonstrates that specific lactobacilli are adapted to the URT and could have a beneficial keystone function in this habitat.},
}
@article {pmid32456625,
year = {2020},
author = {Alderliesten, JB and Duxbury, SJN and Zwart, MP and de Visser, JAGM and Stegeman, A and Fischer, EAJ},
title = {Effect of donor-recipient relatedness on the plasmid conjugation frequency: a meta-analysis.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {135},
pmid = {32456625},
issn = {1471-2180},
support = {50-54100-98-1 19//ZonMw/International ; },
mesh = {Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Escherichia coli/genetics/*growth &amp; development ; Escherichia coli Proteins/genetics ; Phylogeny ; Plasmids/*genetics ; Species Specificity ; },
abstract = {BACKGROUND: Conjugation plays a major role in the transmission of plasmids encoding antibiotic resistance genes in both clinical and general settings. The conjugation efficiency is influenced by many biotic and abiotic factors, one of which is the taxonomic relatedness between donor and recipient bacteria. A comprehensive overview of the influence of donor-recipient relatedness on conjugation is still lacking, but such an overview is important to quantitatively assess the risk of plasmid transfer and the effect of interventions which limit the spread of antibiotic resistance, and to obtain parameter values for conjugation in mathematical models. Therefore, we performed a meta-analysis on reported conjugation frequencies from Escherichia coli donors to various recipient species.<br><br>RESULTS: Thirty-two studies reporting 313 conjugation frequencies for liquid broth matings and 270 conjugation frequencies for filter matings were included in our meta-analysis. The reported conjugation frequencies varied over 11 orders of magnitude. Decreasing taxonomic relatedness between donor and recipient bacteria, when adjusted for confounding factors, was associated with a lower conjugation frequency in liquid matings. The mean conjugation frequency for bacteria of the same order, the same class, and other classes was 10, 20, and 789 times lower than the mean conjugation frequency within the same species, respectively. This association between relatedness and conjugation frequency was not found for filter matings. The conjugation frequency was furthermore found to be influenced by temperature in both types of mating experiments, and in addition by plasmid incompatibility group in liquid matings, and by recipient origin and mating time in filter matings.<br><br>CONCLUSIONS: In our meta-analysis, taxonomic relatedness is limiting conjugation in liquid matings, but not in filter matings, suggesting that taxonomic relatedness is not a limiting factor for conjugation in environments where bacteria are fixed in space.},
}
@article {pmid32455626,
year = {2020},
author = {Xu, J and Bu, F and Zhu, W and Luo, G and Xie, L},
title = {Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Ex-Situ Biogas Upgrading Systems under Different Conditions of Temperature, pH and CO.},
journal = {Microorganisms},
volume = {8},
number = {5},
pages = {},
pmid = {32455626},
issn = {2076-2607},
support = {51678424 and 51378373//National Natural Science Foundation of China/ ; },
abstract = {In this study, hydrogenotrophic methanogenic mixed cultures taken from 13 lab-scale ex-situ biogas upgrading systems under different temperature (20-70 °C), pH (6.0-8.5), and CO (0-10%, v/v) variables were systematically investigated. High-throughput 16S rRNA gene sequencing was used to identify the microbial consortia, and statistical analyses were conducted to reveal the microbial diversity, the core functional microbes, and their correlative relationships with tested variables. Overall, bacterial community was more complex than the archaea community in all mixed cultures. Hydrogenotrophic methanogens Methanothermobacter, Methanobacterium, and Methanomassiliicoccus, and putative syntrophic acetate-oxidizing bacterium Coprothermobacter and Caldanaerobacter were found to predominate, but the core functional microbes varied under different conditions. Multivariable sensitivity analysis indicated that temperature (p < 0.01) was the crucial variable to determine the microbial consortium structures in hydrogenotrophic methanogenic mixed cultures. pH (0.01 < p < 0.05) significantly interfered with the relative abundance of dominant archaea. Although CO did not affect community (p > 0.1), some potential CO-utilizing syntrophic metabolisms might be enhanced. Understanding of microbial consortia in the hydrogenotrophic methanogenic mixed cultures related to environmental variables was a great advance to reveal the microbial ecology in microbial biogas upgrading process.},
}
@article {pmid32454384,
year = {2020},
author = {Zhang, H and Zhang, B and Wang, S and Chen, J and Jiang, B and Xing, Y},
title = {Spatiotemporal vanadium distribution in soils with microbial community dynamics at vanadium smelting site.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {265},
number = {Pt A},
pages = {114782},
doi = {10.1016/j.envpol.2020.114782},
pmid = {32454384},
issn = {1873-6424},
mesh = {China ; Environmental Monitoring ; *Microbiota ; Soil ; Soil Pollutants/*analysis ; Vanadium/analysis ; },
abstract = {Whereas the adverse effects of vanadium released from smelting activities on soil microbial ecology have been widely recognized, little is known about spatiotemporal vanadium distribution and microbial community dynamics in typical contaminated sites. This study describes vanadium contents associated with health risk and microbial responses in both topsoil and subsoil during four consecutive seasons around an ongoing-production smelter in Panzhihua, China. Higher levels of vanadium concentration exceeding soil background value in China (82 mg/kg) were found close to the smelter. Vanadium concentrations decreased generally with the increase in distance to the smelter and depth below surface, as soil vanadium pollution is induced mainly by atmospheric deposition of vanadium bearing dust during smelting. Residual fraction was the predominated vanadium form in soils, with pronounced increase in bioavailable vanadium during rainfall period due to frequent drought-rewetting process. Topsoil close to the smelter exhibited significant contamination, inducing high probability of adverse health effects. Spatiotemporal vanadium distribution creates filtering effects on soil microorganisms, promoting metal tolerant genera in topsoil (e.g. Microvirga) and subsoil (e.g. Bacillus, Geobacter), which is the key in maintaining the community structure by promoting cooperative relation with other taxa. Our results reveal spatiotemporal vanadium distribution in soils at site scale with potential health risk and microbial responses, which is helpful in identifying severe contamination and implementing bioremediation.},
}
@article {pmid32454291,
year = {2020},
author = {Lourenço, KS and Suleiman, AKA and Pijl, A and Cantarella, H and Kuramae, EE},
title = {Dynamics and resilience of soil mycobiome under multiple organic and inorganic pulse disturbances.},
journal = {The Science of the total environment},
volume = {733},
number = {},
pages = {139173},
doi = {10.1016/j.scitotenv.2020.139173},
pmid = {32454291},
issn = {1879-1026},
mesh = {Fertilizers/analysis ; Fungi ; *Mycobiome ; Soil ; Soil Microbiology ; },
abstract = {Disturbances in soil can cause short-term soil changes, consequently changes in microbial community what may result in long-lasting ecological effects. Here, we evaluate how multiple pulse disturbances effect the dynamics and resilience of fungal community, and the co-occurrence of fungal and bacterial communities in a 389 days field experiment. We used soil under sugarcane cultivation as soil ecosystem model, and organic residue (vinasse - by-product of sugarcane ethanol production) combined or not with inorganic (organic residue applied 30 days before or together with mineral N fertilizer) amendments as disturbances. Application of organic residue alone as a single disturbance or 30 days prior to a second disturbance with mineral N resulted in similar changes in the fungal community. The simultaneous application of organic and mineral N as a single pulse disturbance had the greatest impact on the fungal community. Organic amendment increased the abundance of saprotrophs, fungal species capable of denitrification, and fungi described to have copiotrophic and oligotrophic lifestyles. Furthermore, the changes in the fungal community were not correlated with the changes in the bacterial community. The fungal community was neither resistant nor resilient to organic and inorganic disturbances over the one-year sampling period. Our findings provide insights on the immediate and delayed responses of the fungal community over one year to disturbance by organic and inorganic amendments.},
}
@article {pmid32451559,
year = {2020},
author = {Nettles, R and Ricks, KD and Koide, RT},
title = {The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {573-592},
doi = {10.1007/s00248-020-01525-6},
pmid = {32451559},
issn = {1432-184X},
support = {2011-67009-20072//National Institute of Food and Agriculture/ ; },
mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; *Bacterial Physiological Phenomena ; Colon/*microbiology ; Female ; Fungi/*physiology ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; *Mycobiome ; Random Allocation ; },
abstract = {We tested two hypotheses concerning the dynamics of intestinal microbial communities of young mice following antibiotic-induced disturbance. The first is that disturbance of the bacterial community causes disturbance of the fungal community. Our results were consistent with that hypothesis. Antibiotics significantly altered bacterial community structure. Antibiotics also altered fungal community structure, significantly increasing the relative abundance of Candida lusitaniae, a known pathogen, while simultaneously significantly decreasing the relative abundances of several other common fungal species. The result was a temporary decrease in fungal diversity. Moreover, bacterial load was negatively correlated with the relative abundances of Candida lusitaniae and Candida parapsilosis, while it was positively correlated with the relative abundances of many other fungal species. Our second hypothesis is that control mice serve as a source of probiotics capable of invading intestines of mice with disturbed microbial communities and restoring pre-antibiotic bacterial and fungal communities. However, we found that control mice did not restore disturbed microbial communities. Instead, mice with disturbed microbial communities induced disturbance in control mice, consistent with the hypothesis that antibiotic-induced disturbance represents an alternate stable state that is easier to achieve than to correct. Our results indicate the occurrence of significant interactions among intestinal bacteria and fungi and suggest that the stimulation of certain bacterial groups may potentially be useful in countering the dominance of fungal pathogens such as Candida spp. However, the stability of disturbed microbial communities could complicate recovery.},
}
@article {pmid32451471,
year = {2020},
author = {Sichert, A and Corzett, CH and Schechter, MS and Unfried, F and Markert, S and Becher, D and Fernandez-Guerra, A and Liebeke, M and Schweder, T and Polz, MF and Hehemann, JH},
title = {Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan.},
journal = {Nature microbiology},
volume = {5},
number = {8},
pages = {1026-1039},
pmid = {32451471},
issn = {2058-5276},
mesh = {Bacterial Proteins/metabolism ; Cell Wall/metabolism ; Esterases ; Genes, Bacterial/genetics ; Glycoside Hydrolases ; Metabolic Networks and Pathways ; Metagenome ; Phaeophyceae/*metabolism ; Phylogeny ; Polysaccharides/*metabolism ; Proteome ; Substrate Specificity ; Sulfatases ; Sulfates/metabolism ; Transcriptome ; United States ; Verrucomicrobia/*enzymology/genetics/isolation &amp; purification/*metabolism ; },
abstract = {Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.},
}
@article {pmid32446079,
year = {2020},
author = {Schröer, L and De Kock, T and Cnudde, V and Boon, N},
title = {Differential colonization of microbial communities inhabiting Lede stone in the urban and rural environment.},
journal = {The Science of the total environment},
volume = {733},
number = {},
pages = {139339},
doi = {10.1016/j.scitotenv.2020.139339},
pmid = {32446079},
issn = {1879-1026},
mesh = {Archaea ; Belgium ; High-Throughput Nucleotide Sequencing ; *Microbiota ; RNA, Ribosomal, 16S ; },
abstract = {Air pollution is one of the main actors of stone deterioration. It influences not only the material itself but also prokaryotes colonizing rocks. Prokaryotes can affect rock substrates and biological colonization will most likely become relatively more important during the course of the 21st century. Therefore, it is necessary to understand the effects of air pollution on biological colonization and on the impact of this colonization on rock weathering. For this reason, we studied the prokaryotic community of Lede stone from two deteriorated monuments in Belgium: one in the urban and one in the rural environment. This research conducts 16S rRNA gene Next Generation Sequencing combined with an isolation campaign. It revealed diverse and complex prokaryotic communities with more specialized bacteria present in the urban environment, while archaea were barely detected. Some genera could cause biodeterioration but the isolates did not produce a significant amount of acid. Soluble salts analysis revealed an important effect of salts on the prokaryotic community. Colour measurements at least indicate that a main effect of prokaryotes might be on the aesthetics: In the countryside prokaryotic communities seemed to discolour Lede stone, while pollution most likely blackened building stones in the urban environment.},
}
@article {pmid32445418,
year = {2020},
author = {Spielmann, J and Ahmadi, H and Scheepers, M and Weber, M and Nitsche, S and Carnol, M and Bosman, B and Kroymann, J and Motte, P and Clemens, S and Hanikenne, M},
title = {The two copies of the zinc and cadmium ZIP6 transporter of Arabidopsis halleri have distinct effects on cadmium tolerance.},
journal = {Plant, cell &amp; environment},
volume = {43},
number = {9},
pages = {2143-2157},
doi = {10.1111/pce.13806},
pmid = {32445418},
issn = {1365-3040},
mesh = {Arabidopsis/drug effects/genetics/growth &amp; development/*physiology ; Cadmium/metabolism/*toxicity ; Carrier Proteins/genetics/metabolism ; Ecotype ; Gene Duplication ; Gene Expression Regulation, Plant ; Gene Silencing ; Genome, Plant ; Plant Proteins/*genetics/metabolism ; Plants, Genetically Modified ; Yeasts/genetics/metabolism ; Zinc/metabolism ; },
abstract = {Plants have the ability to colonize highly diverse environments. The zinc and cadmium hyperaccumulator Arabidopsis halleri has adapted to establish populations on soils covering an extreme range of metal availabilities. The A. halleri ZIP6 gene presents several hallmarks of hyperaccumulation candidate genes: it is constitutively highly expressed in roots and shoots and is associated with a zinc accumulation quantitative trait locus. Here, we show that AhZIP6 is duplicated in the A. halleri genome. The two copies are expressed mainly in the vasculature in both A. halleri and Arabidopsis thaliana, indicative of conserved cis regulation, and acquired partial organ specialization. Yeast complementation assays determined that AhZIP6 is a zinc and cadmium transporter. AhZIP6 silencing in A. halleri or expression in A. thaliana alters cadmium tolerance, but has no impact on zinc and cadmium accumulation. AhZIP6-silenced plants display reduced cadmium uptake upon short-term exposure, adding AhZIP6 to the limited number of Cd transporters supported by in planta evidence. Altogether, our data suggest that AhZIP6 is key to fine-tune metal homeostasis in specific cell types. This study additionally highlights the distinct fates of duplicated genes in A. halleri.},
}
@article {pmid32444696,
year = {2020},
author = {Zhang, R and Li, Y and Yan, W and Wang, Y and Cai, L and Luo, T and Li, H and Weinbauer, MG and Jiao, N},
title = {Viral control of biomass and diversity of bacterioplankton in the deep sea.},
journal = {Communications biology},
volume = {3},
number = {1},
pages = {256},
pmid = {32444696},
issn = {2399-3642},
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biomass ; *Ecosystem ; Plankton/classification/genetics/*isolation &amp; purification ; Seawater/*microbiology/*virology ; Viruses/*growth &amp; development ; },
abstract = {Viral abundance in deep-sea environments is high. However, the biological, ecological and biogeochemical roles of viruses in the deep sea are under debate. In the present study, microcosm incubations of deep-sea bacterioplankton (2,000 m deep) with normal and reduced pressure of viral lysis were conducted in the western Pacific Ocean. We observed a negative effect of viruses on prokaryotic abundance, indicating the top-down control of bacterioplankton by virioplankton in the deep-sea. The decreased bacterial diversity and a different bacterial community structure with diluted viruses indicate that viruses are sustaining a diverse microbial community in deep-sea environments. Network analysis showed that relieving viral pressure decreased the complexity and clustering coefficients but increased the proportion of positive correlations for the potentially active bacterial community, which suggests that viruses impact deep-sea bacterioplankton interactions. Our study provides experimental evidences of the crucial role of viruses in microbial ecology and biogeochemistry in deep-sea ecosystems.},
}
@article {pmid32444671,
year = {2020},
author = {van Tilburg Bernardes, E and Pettersen, VK and Gutierrez, MW and Laforest-Lapointe, I and Jendzjowsky, NG and Cavin, JB and Vicentini, FA and Keenan, CM and Ramay, HR and Samara, J and MacNaughton, WK and Wilson, RJA and Kelly, MM and McCoy, KD and Sharkey, KA and Arrieta, MC},
title = {Intestinal fungi are causally implicated in microbiome assembly and immune development in mice.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2577},
pmid = {32444671},
issn = {2041-1723},
support = {//CIHR/Canada ; },
mesh = {Animals ; Bacterial Physiological Phenomena ; Colitis/chemically induced/microbiology ; Dextran Sulfate/toxicity ; Feces/microbiology ; Female ; Fungi/isolation &amp; purification/*physiology ; Gastrointestinal Microbiome/immunology/*physiology ; Germ-Free Life ; Humans ; Immune System/*growth &amp; development ; Inflammation/chemically induced/microbiology ; Intestines/*microbiology ; Metabolome ; Mice, Inbred C57BL ; Ovalbumin/toxicity ; },
abstract = {The gut microbiome consists of a multi-kingdom microbial community. Whilst the role of bacteria as causal contributors governing host physiological development is well established, the role of fungi remains to be determined. Here, we use germ-free mice colonized with defined species of bacteria, fungi, or both to differentiate the causal role of fungi on microbiome assembly, immune development, susceptibility to colitis, and airway inflammation. Fungal colonization promotes major shifts in bacterial microbiome ecology, and has an independent effect on innate and adaptive immune development in young mice. While exclusive fungal colonization is insufficient to elicit overt dextran sulfate sodium-induced colitis, bacterial and fungal co-colonization increase colonic inflammation. Ovalbumin-induced airway inflammation reveals that bacterial, but not fungal colonization is necessary to decrease airway inflammation, yet fungi selectively promotes macrophage infiltration in the airway. Together, our findings demonstrate a causal role for fungi in microbial ecology and host immune functionality, and therefore prompt the inclusion of fungi in therapeutic approaches aimed at modulating early life microbiomes.},
}
@article {pmid32441612,
year = {2020},
author = {Murrell, JC and McGenity, TJ and Crombie, AT},
title = {Microbial metabolism of isoprene: a much-neglected climate-active gas.},
journal = {Microbiology (Reading, England)},
volume = {166},
number = {7},
pages = {600-613},
pmid = {32441612},
issn = {1465-2080},
mesh = {Bacteria/*genetics/*metabolism ; Biodegradation, Environmental ; Butadienes/*metabolism ; Genes, Bacterial ; Hemiterpenes/*metabolism ; Metabolic Networks and Pathways/*genetics ; Plants/microbiology ; Seawater/microbiology ; Soil Microbiology ; },
abstract = {The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes.},
}
@article {pmid32440700,
year = {2020},
author = {Des Marteaux, LE and Kullik, SA and Habash, M and Schmidt, JM},
title = {Terrestrial Isopods Porcellio scaber and Oniscus asellus (Crustacea: Isopoda) Increase Bacterial Abundance and Modify Microbial Community Structure in Leaf Litter Microcosms: a Short-Term Decomposition Study.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {690-702},
doi = {10.1007/s00248-020-01527-4},
pmid = {32440700},
issn = {1432-184X},
mesh = {Animals ; *Bacterial Physiological Phenomena ; Food Chain ; Fungi/*physiology ; *Herbivory ; Introduced Species ; Isopoda/*physiology ; *Microbiota ; Ontario ; Plant Leaves/*microbiology ; *Soil Microbiology ; },
abstract = {Invasive terrestrial isopods are likely to have altered leaf litter decomposition processes in North American forests, but the mechanisms underlying these alterations and the degree to which they differ among isopod species are poorly characterized. Using mixed-deciduous leaf litter microcosms, we quantified the effects of two common, invasive isopods (Oniscus asellus and Porcellio scaber) on short-term leaf litter decomposition and microbial community structure and function. Microcosms containing ground litter and a microbial inoculant were exposed to one of the two isopod species or no isopods for 21 days. Mass loss was then quantified as the change in litter dry mass after leaching, and microbial respiration was quantified as the mass of CO2 absorbed by soda lime. Litter leachates were plated on agar to quantify culturable bacterial and fungal abundance, and denaturing gradient gel electrophoresis of amplified leachate microbial DNA was used to characterize shifts in microbial community structure. Isopod presence increased litter mass loss by a modest ~ 6%, but did not affect litter microbial respiration. Bacterial abundance increased significantly in the presence of isopods, while fungal abundance was either unchanged or reduced. Overall litter microbial species richness was reduced by isopods, with O. asellus specifically reducing fungal abundance and diversity. Isopods modified the microbial community structure by suppressing four bacterial and one fungal species, while promoting growth of four other bacterial species (two unique to each isopod species) and two fungal species (one which was unique to O. asellus).},
}
@article {pmid32440699,
year = {2020},
author = {Grimes, DJ},
title = {The Vibrios: Scavengers, Symbionts, and Pathogens from the Sea.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {501-506},
doi = {10.1007/s00248-020-01524-7},
pmid = {32440699},
issn = {1432-184X},
mesh = {Carbon/*metabolism ; Carbon Cycle ; Life History Traits ; Symbiosis ; Vibrio/metabolism/*physiology ; },
abstract = {Bacteria belonging to the genus Vibrio are major carbon cycle drivers in marine and estuarine environments. As is the case for most carbon cycle participants, the vibrios metabolize degradable compounds such as sugars and amino acids; they can also degrade some more recalcitrant compounds including hydrocarbons and lignins. Several vibrios are symbionts and even fewer are pathogenic for animals, including humans and marine animals and plants. This paper reviews Vibrio ecology, metabolism, and survival, and it also discusses select vibrios-V. alginolyticus, V. cholerae, V. coralliilyticus, V. cortegadensis, V. fischeri, V. harveyi, V. harveyi var. carahariae, V. ordalii, V. parahaemolyticus, and V. vulnificus.},
}
@article {pmid32440698,
year = {2021},
author = {Torralba, MG and Kuelbs, C and Moncera, KJ and Roby, R and Nelson, KE},
title = {Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance.},
journal = {Microbial ecology},
volume = {81},
number = {4},
pages = {1098-1105},
pmid = {32440698},
issn = {1432-184X},
mesh = {Bacteria/genetics ; DNA, Ribosomal ; Fungi/genetics ; *Microbiota ; *Paintings ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The preservation of artwork challenges museums, collectors, and art enthusiasts. Currently, reducing moisture, adjusting the type of lighting, and preventing the formation of mold are primary methods to preserving and preventing deterioration. Other methods such as ones based in detailed knowledge of molecular biology such as microbial community characterization using polymerase chain reaction (PCR) and sequencing have yet to be explored. Such molecular biology approaches are essential to explore as some environmental bacteria are capable of oxidizing nonpolar chemical substances rich in hydrocarbons such as oil-based paints. Using 16S rDNA Illumina Sequencing, we demonstrate a novel finding that there are differing bacterial communities for artwork from roughly the same era when comparing paintings on wood, paintings on canvases, and sculptures made of stone and marble. We also demonstrate that there are specific genera such as Aeromonas known for having oxidase positive strains, present on paintings on wood and paintings on canvas that could potentially be responsible for deterioration and fading as such organisms produce water or hydrogen peroxide as a byproduct of cytochrome c oxidase activity. The advantages of these genomics-based approaches to characterizing the microbial population on deteriorating artwork provides immense potential by identifying potentially damaging species that may not be detected using conventional methods in addition to addressing challenges to identification, restoration, and preservation efforts.},
}
@article {pmid32440491,
year = {2020},
author = {Zheng, P and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Pan, J and Duan, J and Liang, W and Yin, B and Deng, F and Perry, SW and Wong, ML and Licinio, J and Wei, H and Yu, G and Xie, P},
title = {Erratum: Perturbed Microbial Ecology in Myasthenia Gravis: Evidence from the Gut Microbiome and Fecal Metabolome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {7},
number = {10},
pages = {2001296},
doi = {10.1002/advs.202001296},
pmid = {32440491},
issn = {2198-3844},
abstract = {[This corrects the article DOI: 10.1002/advs.201901441.].},
}
@article {pmid32439665,
year = {2020},
author = {Kirchner, N and Cano-Prieto, C and van der Voort, M and Raaijmakers, JM and Gross, H},
title = {Draft Genome Sequence of Lipopeptide-Producing Strain Pseudomonas fluorescens DSM 11579 and Comparative Genomics with Pseudomonas sp. Strain SH-C52, a Closely Related Lipopeptide-Producing Strain.},
journal = {Microbiology resource announcements},
volume = {9},
number = {21},
pages = {},
pmid = {32439665},
issn = {2576-098X},
abstract = {Pseudomonas fluorescens DSM 11579 is known to be a producer of the lipopeptides brabantamide and thanamycin. Its draft genome gives insight into the complete secondary metabolite production capacity of the strain and builds the basis for a comparative study with Pseudomonas sp. strain SH-C52, a lipopeptide-producing strain involved in natural disease-suppressive soils.},
}
@article {pmid32438141,
year = {2020},
author = {Hooban, B and Joyce, A and Fitzhenry, K and Chique, C and Morris, D},
title = {The role of the natural aquatic environment in the dissemination of extended spectrum beta-lactamase and carbapenemase encoding genes: A scoping review.},
journal = {Water research},
volume = {180},
number = {},
pages = {115880},
doi = {10.1016/j.watres.2020.115880},
pmid = {32438141},
issn = {1879-2448},
mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; Drug Resistance, Microbial ; *Genes, Bacterial ; *beta-Lactamases ; },
abstract = {The natural aquatic environment is a significant contributor to the development and circulation of clinically significant antibiotic resistance genes (ARGs). The potential for the aquatic environment to act as a reservoir for ARG accumulation in areas receiving anthropogenic contamination has been thoroughly researched. However, the emergence of novel ARGs in the absence of external influences, as well as the capacity of environmental bacteria to disseminate ARGs via mobile genetic elements remain relatively unchallenged. In order to address these knowledge gaps, this scoping literature review was established focusing on the detection of two important and readily mobile ARGs, namely, extended spectrum beta-lactamase (ESBL) and carbapenemase genes. This review included 41 studies from 19 different countries. A range of different water bodies including rivers (n = 26), seawaters (n = 6) and lakes (n = 3), amongst others, were analysed in the included studies. ESBL genes were reported in 29/41 (70.7%) studies, while carbapenemase genes were reported in 13/41 (31.7%), including joint reporting in 9 studies. The occurrence of mobile genetic elements was evaluated, which included the detection of integrons (n = 22), plasmids (n = 18), insertion sequences (n = 4) and transposons (n = 3). The ability of environmental bacteria to successfully transfer resistance genes via conjugation was also examined in 11 of the included studies. The findings of this scoping review expose the presence of clinically significant ARGs in the natural aquatic environment and highlights the potential ability of environmental isolates to disseminate these genes among different bacterial species. As such, the results presented demonstrate how anthropogenic point discharges may not act as the sole contributor to the development and spread of clinically significant antibiotic resistances. A number of critical knowledge gaps in current research were also identified. Key highlights include the limited number of studies focusing on antibiotic resistance in uncontaminated aquatic environments as well as the lack of standardisation among methodologies of reviewed investigations.},
}
@article {pmid32436568,
year = {2020},
author = {Van Landuyt, J and Cimmino, L and Dumolin, C and Chatzigiannidou, I and Taveirne, F and Mattelin, V and Zhang, Y and Vandamme, P and Scoma, A and Williamson, A and Boon, N},
title = {Microbial enrichment, functional characterization and isolation from a cold seep yield piezotolerant obligate hydrocarbon degraders.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {9},
pages = {},
doi = {10.1093/femsec/fiaa097},
pmid = {32436568},
issn = {1574-6941},
mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Hydrocarbons ; *Petroleum ; *Seawater ; },
abstract = {Deep-sea environments can become contaminated with petroleum hydrocarbons. The effects of hydrostatic pressure (HP) in the deep sea on microbial oil degradation are poorly understood. Here, we performed long-term enrichments (100 days) from a natural cold seep while providing optimal conditions to sustain high hydrocarbon degradation rates. Through enrichments performed at increased HP and ambient pressure (AP) and by using control enrichments with marine broth, we demonstrated that both pressure and carbon source can have a big impact on the community structure. In contrast to previous studies, hydrocarbonoclastic operational taxonomic units (OTUs) remained dominant at both AP and increased HP, suggesting piezotolerance of these OTUs over the tested pressure range. Twenty-three isolates were obtained after isolation and dereplication. After recultivation at increased HP, an Alcanivorax sp. showed promising piezotolerance in axenic culture. Furthermore, preliminary co-cultivation tests indicated synergistic growth between some isolates, which shows promise for future synthetic community construction. Overall, more insights into the effect of increased HP on oil-degrading communities were obtained as well as several interesting isolates, e.g. a piezotolerant hydrocarbonoclastic bacterium for future deep-sea bioaugmentation investigation.},
}
@article {pmid32436040,
year = {2020},
author = {Rocha, KF and Kuramae, EE and Borges, BMF and Leite, MFA and Rosolem, CA},
title = {Microbial N-cycling gene abundance is affected by cover crop specie and development stage in an integrated cropping system.},
journal = {Archives of microbiology},
volume = {202},
number = {7},
pages = {2005-2012},
doi = {10.1007/s00203-020-01910-2},
pmid = {32436040},
issn = {1432-072X},
support = {2015/50305-8//FAPESP/ ; BB/N013201/1//BBRSC/ ; },
mesh = {*Agriculture ; Ammonia/metabolism ; Archaea/genetics ; Bacteria/genetics ; Crops, Agricultural/*microbiology ; Nitrification ; Nitrogen/metabolism ; Nitrogen Cycle/*genetics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Zea mays ; },
abstract = {Grasses of the Urochloa genus have been widely used in crop-livestock integration systems or as cover crops in no-till systems such as in rotation with maize. Some species of Urochloa have mechanisms to reduce nitrification. However, the responses of microbial functions in crop-rotation systems with grasses and its consequence on soil N dynamics are not well-understood. In this study, the soil nitrification potential and the abundance of ammonifying microorganisms, total bacteria and total archaea (16S rRNA gene), nitrogen-fixing bacteria (NFB, nifH), ammonia-oxidizing bacteria (AOB, amoA) and archaea (AOA, amoA) were assessed in soil cultivated with ruzigrass (Urochloa ruziziensis), palisade grass (Urochloa brizantha) and Guinea grass (Panicum maximum). The abundance of ammonifying microorganisms was not affected by ruzigrass. Ruzigrass increased the soil nitrification potential compared with palisade and Guinea grass. Ruzigrass increased the abundance of N-fixing microorganisms at the middle and late growth stages. The abundances of nitrifying microorganisms and N-fixers in soil were positively correlated with the soil N-NH4[+] content. Thus, biological nitrogen fixation might be an important input of N in systems of rotational production of maize with forage grasses. The abundance of microorganisms related to ammonification, nitrification and nitrogen fixing and ammonia-oxidizing archea was related to the development stage of the forage grass.},
}
@article {pmid32434844,
year = {2020},
author = {Minich, JJ and Petrus, S and Michael, JD and Michael, TP and Knight, R and Allen, EE},
title = {Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus.},
journal = {mSphere},
volume = {5},
number = {3},
pages = {},
pmid = {32434844},
issn = {2379-5042},
support = {P01 ES021921/ES/NIEHS NIH HHS/United States ; R01 ES030316/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; Cecum/microbiology ; *Environment ; Gastrointestinal Microbiome ; *Genetic Variation ; Gills/microbiology ; *Microbiota ; Mucous Membrane/*microbiology ; Oceans and Seas ; Perciformes/*microbiology ; Skin/microbiology ; Temperature ; },
abstract = {Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish.IMPORTANCE Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.},
}
@article {pmid32432525,
year = {2020},
author = {Jakubovics, NS and Shi, W},
title = {A New Era for the Oral Microbiome.},
journal = {Journal of dental research},
volume = {99},
number = {6},
pages = {595-596},
doi = {10.1177/0022034520918536},
pmid = {32432525},
issn = {1544-0591},
mesh = {*Microbiota ; Mouth ; Saliva ; },
}
@article {pmid32430405,
year = {2020},
author = {Fu, X and Li, Y and Yuan, Q and Cai, GH and Deng, Y and Zhang, X and Norbäck, D and Sun, Y},
title = {Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms.},
journal = {mSystems},
volume = {5},
number = {3},
pages = {},
pmid = {32430405},
issn = {2379-5077},
abstract = {Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome composition and the associated environmental characteristics have not been characterized in hotel environments. We presented here the first continental-scale microbiome study of hotel rooms (n = 68) spanning Asia and Europe. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified in the same sequencing depth, but most fungal taxa showed a restricted distribution compared to bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for ∼80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbiome and 16 indoor and outdoor environmental characteristics. Fungal composition and absolute quantity showed concordant associations with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea, and visible mold, while fungal richness was negatively associated with heavy traffic (95% confidence interval [CI] = -127.05 to -0.25) and wall-to-wall carpet (95% CI = -47.60 to -3.82). Bacterial compositional variation was associated with latitude, quality of the interior, and floor type, while bacterial richness was negatively associated with recent redecoration (95% CI -179.00 to -44.55) and mechanical ventilation (95% CI = -136.71 to -5.12).IMPORTANCE This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.},
}
@article {pmid32426533,
year = {2020},
author = {Venturini, AM and Nakamura, FM and Gontijo, JB and da França, AG and Yoshiura, CA and Mandro, JA and Tsai, SM},
title = {Robust DNA protocols for tropical soils.},
journal = {Heliyon},
volume = {6},
number = {5},
pages = {e03830},
pmid = {32426533},
issn = {2405-8440},
abstract = {Studies in the Amazon are being intensified to evaluate the alterations in the microbial communities of soils and sediments in the face of increasing deforestation and land-use changes in the region. However, since these environments present highly heterogeneous physicochemical properties, including contaminants that hinder nucleic acids isolation and downstream techniques, the development of best molecular practices is crucial. This work aimed to optimize standard protocols for DNA extraction and gene quantification by quantitative real-time PCR (qPCR) based on natural and anthropogenic soils and sediments (primary forest, pasture, Amazonian Dark Earth, and várzea, a seasonally flooded area) of the Eastern Amazon. Our modified extraction protocol increased the fluorometric DNA concentration by 48%, reaching twice the original amount for most of the pasture and várzea samples, and the 260/280 purity ratio by 15% to values between 1.8 to 2.0, considered ideal for DNA. The addition of bovine serum albumin in the qPCR reaction improved the quantification of the 16S rRNA genes of Archaea and Bacteria and its precision among technical replicates, as well as allowed their detection in previously non-amplifiable samples. It is concluded that the changes made in the protocols improved the parameters of the DNA samples and their amplification, thus increasing the reliability of microbial communities' analysis and its ecological interpretations.},
}
@article {pmid32425165,
year = {2020},
author = {Oliveira, BG and Mendes, LW and Smyth, EM and Tsai, SM and Feigl, BJ and Mackie, RI},
title = {Assessment of microbial diversity associated with CH4 emission from sugarcane vinasse storage and transportation systems.},
journal = {Journal of environmental management},
volume = {269},
number = {},
pages = {110748},
doi = {10.1016/j.jenvman.2020.110748},
pmid = {32425165},
issn = {1095-8630},
mesh = {Brazil ; *Greenhouse Gases ; Methane ; RNA, Ribosomal, 16S ; *Saccharum ; },
abstract = {Sugarcane bioethanol has favorable energy and greenhouse gas balance, although the production process generates several residues including vinasse, which deserves attention because of its significant methane (CH4) emission during storage and transportation stages. Considering that CH4 emissions are dependent on the structure and abundance of microbial communities, we hypothesized that different vinasse transportation systems would harbor different microbial community composition, resulting in distinct CH4 patterns. To test this hypothesis, we used high-throughput 16S rRNA sequencing with real-time PCR to evaluate the composition and abundance of microorganisms in the two main systems of vinasse storage and transportation (i.e. open channels and tanks systems) in Brazil. Our results showed higher microbial diversity and CH4 emissions in channel system, especially in the uncoated section. Significant differences in microbial community structure, diversity, and abundance between the uncoated/coated open channel and tanks indicated a clear selection at taxonomic and functional levels, especially in relation to CH4 production. These responses included higher methanogens diversity in the uncoated section of the channel and are in agreement with the methanogen abundance determined by mcrA and mba genes copy number (1.5 × 10[7] and 4.3 × 10[10]) and subsequent positive correlation with CH4 emissions (R[2] = 0.8). The most representative methanogen genus across the samples was Methanobrevibacter. The results observed herein shows that the use of the coating in the bottom of channels and tanks prevent the growth and development of a methanogen-related community. We concluded that the improvements in vinasse storage and transportation systems would significantly change the microbial community and reduce CH4 emissions, thereby making bioethanol a greener biofuel.},
}
@article {pmid32424717,
year = {2020},
author = {Grajal-Puche, A and Murray, CM and Kearley, M and Merchant, M and Nix, C and Warner, JK and Walker, DM},
title = {Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {603-613},
doi = {10.1007/s00248-020-01522-9},
pmid = {32424717},
issn = {1432-184X},
mesh = {*Alligators and Crocodiles ; Animals ; Bacteria/classification/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Ecology ; *Ecosystem ; Environmental Microbiology ; *Microbiota ; Nesting Behavior ; Texas ; },
abstract = {Understanding the ecological processes that shape species assemblage patterns is central to community ecology. The effects of ecological processes on assemblage patterns are scale-dependent. We used metabarcoding and shotgun sequencing to determine bacterial taxonomic and functional assemblage patterns among varying defined focal scales (micro-, meso-, and macroscale) within the American alligator (Alligator mississippiensis) nesting microbiome. We correlate bacterial assemblage patterns among eight nesting compartments within and proximal to alligator nests (micro-), across 18 nests (meso-), and between 4 geographic sampling sites (macro-), to determine which ecological processes may drive bacterial assemblage patterns within the nesting environment. Among all focal scales, bacterial taxonomic and functional richness (α-diversity) did not statistically differ. In contrast, bacterial assemblage structure (β-diversity) was unique across all focal scales, whereas functional pathways were redundant within nests and across geographic sites. Considering these observed scale-based patterns, taxonomic bacterial composition may be governed by unique environmental filters and dispersal limitations relative to microbial functional attributes within the alligator nesting environment. These results advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.},
}
@article {pmid32419297,
year = {2021},
author = {Xing, J and Jia, X and Wang, H and Ma, B and Falcão Salles, J and Xu, J},
title = {The legacy of bacterial invasions on soil native communities.},
journal = {Environmental microbiology},
volume = {23},
number = {2},
pages = {669-681},
doi = {10.1111/1462-2920.15086},
pmid = {32419297},
issn = {1462-2920},
support = {B17039//Higher Education Discipline Innovation Project/ ; //KNAW-CSC/ ; 2016YFD0800207//National Key Research and Development Program of China/ ; 41721001//National Natural Science Foundation of China/ ; },
mesh = {Ecosystem ; Escherichia coli O157/*growth &amp; development/*metabolism ; *Introduced Species ; Microbial Interactions/*physiology ; Microbiota ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Soil microbial communities are often not resistant to the impact caused by microbial invasions, both in terms of structure and functionality, but it remains unclear whether these changes persist over time. Here, we used three strains of Escherichia coli O157:H7 (E. coli O157:H7), a species used for modelling bacterial invasions, to evaluate the resilience of the bacterial communities from four Chinese soils to invasion. The impact of E. coli O157:H7 strains on soil native communities was tracked for 120 days by analysing bacterial community composition as well as their metabolic potential. We showed that soil native communities were not resistant to invasion, as demonstrated by a decline in bacterial diversity and shifts in bacterial composition in all treatments. The resilience of native bacterial communities (diversity and composition) was inversely correlated with invader's persistence in soils (R[2] = 0.487, p < 0.001). Microbial invasions also impacted the functionality of the soil communities (niche breadth and community niche), the degree of resilience being dependent on soil or native community diversity. Collectively, our results indicate that bacteria invasions can potentially leave a footprint in the structure and functionality of soil communities, indicating the need of assessing the legacy of introducing exotic species in soil environments.},
}
@article {pmid32417556,
year = {2020},
author = {Gallego, S and Barkay, T and Fahrenfeld, NL},
title = {Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells.},
journal = {The Science of the total environment},
volume = {732},
number = {},
pages = {138865},
doi = {10.1016/j.scitotenv.2020.138865},
pmid = {32417556},
issn = {1879-1026},
mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; Carbon-Oxygen Ligases ; In Situ Hybridization, Fluorescence ; Microbial Sensitivity Tests ; *Microbiota ; Phylogeny ; Wastewater ; },
abstract = {Failure to understand the microbial ecology driving the proliferation of antibiotic resistance in the environment prevents us from developing strategies to limit the spread of antibiotic resistant infectious disease. In this study, we developed for the first time a tyramide signal amplification-fluorescence in situ hybridization-fluorescence-activated cell sorting protocol (TSA-FISH-FACS) for the characterization of all vanA carrying bacteria in wastewater samples. Firstly, we validated the TSA-FISH protocol through microscopy in pure cultures and wastewater influent. Then, samples were sorted and quantified by FACS and qPCR. Significantly higher percentage tagging of cells was detected in vanA carrying pure cultures and wastewater samples spiked with vanA carrying cells as compared to vanA negative Gram positive strains and non-spiked wastewater samples respectively. qPCR analysis targeting vanZ, a regulating gene in the vanA cluster, showed its relative abundance was significantly greater in Enterococcus faecium ATCC 700221-spiked and positively sorted samples compared to the E. faecium spiked and negatively sorted samples. Phylogenetic analysis was then performed. Although further efforts are needed to overcome technical problems, we have, for the first time, demonstrated sorting bacterial-cells carrying antibiotic resistance genes from wastewater samples through a TSA-FISH-FACS protocol and provided insight into the microbial ecology of vancomycin resistant bacteria. Future potential applications using this approach will include the separation of members of an environmental microbial community (cultured and hard-to-culture) to allow for metagenomics on single cells or, in the case of clumping, targeting a smaller portion of the community with a priori knowledge that the target gene is present.},
}
@article {pmid32415330,
year = {2020},
author = {Pajares, S and Varona-Cordero, F and Hernández-Becerril, DU},
title = {Spatial Distribution Patterns of Bacterioplankton in the Oxygen Minimum Zone of the Tropical Mexican Pacific.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {519-536},
doi = {10.1007/s00248-020-01508-7},
pmid = {32415330},
issn = {1432-184X},
support = {PAPIIT-IA201617//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; },
mesh = {*Bacterial Physiological Phenomena ; Mexico ; Microbiota/*physiology ; Oxygen/analysis ; Pacific Ocean ; Plankton/*physiology ; Seawater/*microbiology ; Tropical Climate ; },
abstract = {Microbial communities within oxygen minimum zones (OMZs) are crucial drivers of marine biogeochemical cycles; however, we still lack an understanding of how these communities are distributed across an OMZ. We explored vertical (from 5 to 500 m depth) and horizontal (coast to open ocean) distribution of bacterioplankton and its relationships with the main oceanographic conditions in three transects of the tropical Mexican Pacific OMZ. The distribution of the microbial diversity and the main clades changed along the transition from oxygen-rich surface water to the OMZ core, demonstrating the sensitivity of key bacterial groups to deoxygenation. The euphotic zone was dominated by Synechococcales, followed by Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales, whereas the OMZ core was dominated by SAR11, followed by SAR406, SAR324, SAR202, UBA10353 marine group, Thiomicrospirales and Nitrospinales. The marked environmental gradients along the water column also supported a high potential for niche partitioning among OMZ microorganisms. Additionally, in the OMZ core, bacterial assemblages from the same water mass were more similar to each other than those from another water mass. There were also important differences between coastal and open-ocean communities: Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales were more abundant in coastal areas, while Synechococcales, SAR406, SAR324, SAR202, UBA10353 marine group, and Thiomicrospirales were more abundant in the open ocean. Our results suggest a biogeographic structure of the bacterioplankton in this OMZ region, with limited community mixing across water masses, except in upwelling events, and little dispersion of the community by currents in the euphotic zone.},
}
@article {pmid32414800,
year = {2020},
author = {Jiang, W and Wang, Y and Luo, J and Chen, X and Zeng, Y and Li, X and Feng, Z and Zhang, L},
title = {Antimicrobial Peptide GH12 Prevents Dental Caries by Regulating Dental Plaque Microbiota.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {14},
pages = {},
pmid = {32414800},
issn = {1098-5336},
mesh = {Adult ; Animals ; Anti-Bacterial Agents/*pharmacology ; Antimicrobial Cationic Peptides/*pharmacology ; Bacterial Physiological Phenomena/*drug effects ; Biofilms/*drug effects/growth &amp; development ; Dental Caries/genetics/*prevention &amp; control ; Dental Plaque/*microbiology ; Female ; Humans ; Male ; Microbiota/*drug effects ; Rats ; Rats, Sprague-Dawley ; Specific Pathogen-Free Organisms ; Young Adult ; },
abstract = {Due to the complex microecology and microenvironment of dental plaque, novel caries prevention strategies require modulating the microbial communities ecologically and reducing the cariogenic properties effectively. Antimicrobial peptide GH12 reduced the lactic acid production and exopolysaccharide (EPS) synthesis of a Streptococcus mutans biofilm and a three-species biofilm in vitro in previous studies. However, the anticaries effects and microecological effects of GH12 remained to be investigated in a complex biofilm model in vitro and an animal caries model in vivo In the present study, GH12 at 64 mg/liter showed the most effective inhibition of lactic acid production, EPS synthesis, pH decline, and biofilm integrity of human dental plaque-derived multispecies biofilms in vitro, and GH12 at 64 mg/liter was therefore chosen for use in subsequent in vitro and in vivo assays. When treated with 64-mg/liter GH12, the dental plaque-derived multispecies biofilms sampled from healthy volunteers maintained its microbial diversity and showed a microbial community structure similar to that of the control group. In the rat caries model with a caries-promoting diet, 64-mg/liter GH12 regulated the microbiota of dental plaque, in which the abundance of caries-associated bacteria was decreased and the abundance of commensal bacteria was increased. In addition, 64-mg/liter GH12 significantly reduced the caries scores of sulcal and smooth surface caries in all locations. In conclusion, GH12 inhibited the cariogenic properties of dental plaque without perturbing the dental plaque microbiota of healthy individuals and GH12 regulated the dysbiotic microbial ecology and arrested caries development under cariogenic conditions.IMPORTANCE The anticaries effects and microecological regulation effects of the antimicrobial peptide GH12 were evaluated systematically in vitro and in vivo GH12 inhibited the cariogenic virulence of dental plaque without overintervening in the microbial ecology of healthy individuals in vitro GH12 regulated the microbial ecology of dental plaque to a certain extent in vivo under cariogenic conditions, increased the proportion of commensal bacteria, and decreased the abundance of caries-associated bacteria. GH12 significantly suppressed the incidence and severity of dental caries in vivo This study thus describes an alternative antimicrobial therapy for dental caries.},
}
@article {pmid32414048,
year = {2020},
author = {Kuramae, EE and Derksen, S and Schlemper, TR and Dimitrov, MR and Costa, OYA and Silveira, APDD},
title = {Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics.},
journal = {Microorganisms},
volume = {8},
number = {5},
pages = {},
pmid = {32414048},
issn = {2076-2607},
support = {729.004.013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 456420/2013-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.},
}
@article {pmid32413640,
year = {2020},
author = {Barbosa, RG and Sleutels, T and Verstraete, W and Boon, N},
title = {Hydrogen oxidizing bacteria are capable of removing orthophosphate to ultra-low concentrations in a fed batch reactor configuration.},
journal = {Bioresource technology},
volume = {311},
number = {},
pages = {123494},
doi = {10.1016/j.biortech.2020.123494},
pmid = {32413640},
issn = {1873-2976},
mesh = {Bacteria ; Bioreactors ; *Hydrogen ; Oxidation-Reduction ; *Phosphates ; Phosphorus ; },
abstract = {This paper proposes the use of hydrogen oxidizing bacteria (HOB) for the removal of orthophosphate from surface water as treatment step to prevent cyanobacterial blooms. To be effective as an orthophosphate removal strategy, an efficient transfer of hydrogen to the HOB is essential. A trickling filter was selected for this purpose. Using this system, a removal rate of 11.32 ± 0.43 mg PO4[-3]-P/L.d was achieved. The HOB biomass, developed on the trickling filter, is composed of 1.25% phosphorus on dry matter, which suggests that the orthophosphate removal principle is based on HOB growth. Cyanobacterial growth assays of the untreated and treated water showed that Synechocystis sp was only able to grow in the untreated water. Orthophosphate was removed to average residual values of 0.008 mg/L. In this proof of principle study, it is shown that HOB are able to remove orthophosphate from water to concentrations that prevent cyanobacterial growth.},
}
@article {pmid32410366,
year = {2021},
author = {Durán-Viseras, A and Andrei, A&#x15e; and Vera-Gargallo, B and Ghai, R and Sánchez-Porro, C and Ventosa, A},
title = {Culturomics-based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis.},
journal = {Environmental microbiology},
volume = {23},
number = {7},
pages = {3418-3434},
doi = {10.1111/1462-2920.15082},
pmid = {32410366},
issn = {1462-2920},
mesh = {DNA, Bacterial ; *Genomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; },
abstract = {The development of culture-independent techniques has revolutionized our understanding of microbial ecology, especially through the illustration of the vast gap between the environmentally abundant microbial diversity and that accessible through cultivation. However, culture-based approaches are not only crucial for understanding the evolutionary, metabolic and ecological milieu of microbial diversity but also for the development of novel biotechnological applications. In this study, we used a culturomics-based approach in order to isolate novel microbial taxa from hypersaline environments (i.e. Isla Cristina and Isla Bacuta salterns in Huelva, Spain). We managed to obtain axenic cultures of four haloarchaeal strains that belong to a new haloarchaeal genus and to obtain their genomic sequences. The phylogenomic and phylogenetic analyses (together with AAI, ANI and digital DDH indices) showed that the isolates constitute two new species, for which we propose the names Halosegnis longus sp. nov. and Halosegnis rubeus sp. nov. The genomic-based metabolic reconstructions indicated that members of this new haloarchaeal genus have photoheterotrophic aerobic lifestyle with a typical salt-in signature. 16S rRNA gene sequence reads abundance profiles and genomic recruitment analyses revealed that the Halosegnis genus has a worldwide geographical distribution, reaching high abundance (up to 8%) in habitats with intermediate salinities.},
}
@article {pmid32410293,
year = {2020},
author = {Qureshi, SS and Kedo, M and Berthrong, ST},
title = {Gender-neutral bathroom surfaces recolonized by microbes more quickly than single-gender bathrooms.},
journal = {Letters in applied microbiology},
volume = {71},
number = {2},
pages = {134-137},
doi = {10.1111/lam.13316},
pmid = {32410293},
issn = {1472-765X},
support = {//Butler University's Center for High Achievement and Scholarly Engagement Honors Program/ ; },
mesh = {Bacteria/classification/*growth &amp; development/isolation &amp; purification ; Bacterial Load/*statistics &amp; numerical data ; Female ; Humans ; Male ; Microbiota/*physiology ; Sex Factors ; Sexual and Gender Minorities/statistics &amp; numerical data ; Toilet Facilities/*statistics &amp; numerical data ; United States ; },
abstract = {As humans become increasingly urban and spend more time inside the built environment, there will be increased interactions between humans and shared public surface microbiomes. Recent cultural changes in the United States have led to increased numbers of gender-neutral bathrooms. Given that bathroom surfaces are frequently sanitized, we used this increased availability of gender-neutral bathrooms to examine how single-gender or gender-neutral surfaces are recolonized with microbes. Given that male and female microbiomes vary, we hypothesized that rates of recolonization would differ between male, female and gender-neutral bathroom surfaces. We collected swabs from common hand-contacted surfaces in bathrooms and cultured microbes on selective and rich media to determine microbial abundance after cleaning. Recolonization was dominated by Gram-positive bacteria and was slowest on male, intermediate on female and fastest on gender-neutral surfaces. These results imply that gender-neutral surfaces approach normal climax microbial communities more quickly than single-gender bathrooms. SIGNIFICANCE OF IMPACT OF THE STUDY: Humans now spend substantial amount of time within the built environment, and as a consequence the human microbiome interacts frequently with indoor surfaces. Social changes are making gender-neutral public bathrooms more common, so it is important to study how humans and microbiomes interact with these bathroom surfaces. We found that the gender-neutral bathroom surfaces recolonize more quickly than single-gender, which suggests that there are more potential human-surface microbiome connections in these public spaces. These results will potentially add a new layer to our understanding of the interactions of humans, our microbiomes and how we design our built environment.},
}
@article {pmid32409544,
year = {2020},
author = {Šimoliūnienė, M and Tumėnas, D and Kvederavičiūtė, K and Meškys, R and Šulčius, S and Šimoliūnas, E},
title = {Complete Genome Sequence of Bacillus cereus Bacteriophage vB_BceS_KLEB30-3S.},
journal = {Microbiology resource announcements},
volume = {9},
number = {20},
pages = {},
pmid = {32409544},
issn = {2576-098X},
abstract = {In this study, we present the genomic characterization of the temperate bacteriophage vB_BceS_KLEB30-3S (KLEB30-3S), which was induced from Bacillus cereus strain KR3M-30, isolated from a gypsum karst lake ecosystem in Lithuania. The 37,134-bp genome of KLEB30-3S contains 58 predicted protein-encoding genes and no tRNA genes.},
}
@article {pmid32409535,
year = {2020},
author = {Köstlbacher, S and Michels, S and Siegl, A and Schulz, F and Domman, D and Jongwutiwes, S and Putaporntip, C and Horn, M and Collingro, A},
title = {Draft Genome Sequences of Chlamydiales Bacterium STE3 and Neochlamydia sp. Strain AcF84, Endosymbionts of Acanthamoeba spp.},
journal = {Microbiology resource announcements},
volume = {9},
number = {20},
pages = {},
pmid = {32409535},
issn = {2576-098X},
abstract = {Chlamydiales bacterium STE3 and Neochlamydia sp. strain AcF84 are obligate intracellular symbionts of Acanthamoeba spp. isolated from the biofilm of a littoral cave wall and gills from striped tiger leaf fish, respectively. We report the draft genome sequences of these two environmental chlamydiae affiliated with the family Parachlamydiaceae.},
}
@article {pmid32405432,
year = {2020},
author = {Zwart, MP and Elena, SF},
title = {Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments[†].},
journal = {Virus evolution},
volume = {6},
number = {1},
pages = {veaa022},
pmid = {32405432},
issn = {2057-1577},
abstract = {Multipartite viruses have two or more genome segments, and package different segments into different particle types. Although multipartition is thought to have a cost for virus transmission, its benefits are not clear. Recent experimental work has shown that the equilibrium frequency of viral genome segments, the setpoint genome formula (SGF), can be unbalanced and host-species dependent. These observations have reinvigorated the hypothesis that changes in genome-segment frequencies can lead to changes in virus-gene expression that might be adaptive. Here we explore this hypothesis by developing models of bipartite virus infection, leading to a threefold contribution. First, we show that the SGF depends on the cellular multiplicity of infection (MOI), when the requirements for infection clash with optimizing the SGF for virus-particle yield per cell. Second, we find that convergence on the SGF is very rapid, often occurring within a few cellular rounds of infection. Low and intermediate MOIs lead to faster convergence on the SGF. For low MOIs, this effect occurs because of the requirements for infection, whereas for intermediate MOIs this effect is also due to the high levels of variation generated in the genome formula (GF). Third, we explored the conditions under which a bipartite virus could outcompete a monopartite one. As the heterogeneity between environments and specificity of gene-expression requirements for each environment increased, the bipartite virus was more likely to outcompete the monopartite virus. Under some conditions, changes in the GF helped to exclude the monopartite competitor, highlighting the versatility of the GF. Our results show the inextricable relationship between MOI and the SGF, and suggest that under some conditions, the cost of multipartition can be outweighed by its benefits for the rapid tuning of viral gene expression.},
}
@article {pmid32404904,
year = {2020},
author = {Pascual-García, A and Bell, T},
title = {Community-level signatures of ecological succession in natural bacterial communities.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2386},
pmid = {32404904},
issn = {2041-1723},
mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Biodiversity ; *Biota ; DNA, Bacterial/genetics ; Ecosystem ; Metagenome/genetics ; Microbiota ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 16S/*genetics ; Stochastic Processes ; },
abstract = {A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We profiled (16S rRNA sequencing) > 700 semi-aquatic bacterial communities while measuring their functional capacity when grown in laboratory conditions. This approach allowed us to investigate the relationship between composition and function excluding confounding environmental factors. Simulated data allowed us to reject the hypothesis that stochastic processes were responsible for community assembly, suggesting that niche effects prevailed. Consistent with this idea we identified six distinct community classes that contained samples collected from distant locations. Structural equation models showed there was a functional signature associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions (PiCRUST). This approach allowed us to show that the classes contained distinct genetic repertoires reflecting community-level ecological strategies. The ecological strategies resemble the classical distinction between r- and K-strategists, suggesting that bacterial community assembly may be explained by simple ecological mechanisms.},
}
@article {pmid32402266,
year = {2020},
author = {Mahú, I and Barateiro, A and Rial-Pensado, E and Martinéz-Sánchez, N and Vaz, SH and Cal, PMSD and Jenkins, B and Rodrigues, T and Cordeiro, C and Costa, MF and Mendes, R and Seixas, E and Pereira, MMA and Kubasova, N and Gres, V and Morris, I and Temporão, C and Olivares, M and Sanz, Y and Koulman, A and Corzana, F and Sebastião, AM and López, M and Bernardes, GJL and Domingos, AI},
title = {Brain-Sparing Sympathofacilitators Mitigate Obesity without Adverse Cardiovascular Effects.},
journal = {Cell metabolism},
volume = {31},
number = {6},
pages = {1120-1135.e7},
pmid = {32402266},
issn = {1932-7420},
support = {/HHMI/Howard Hughes Medical Institute/United States ; MC_UU_00014/5/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_UU_12012/5/MRC_/Medical Research Council/United Kingdom ; 208576/WT_/Wellcome Trust/United Kingdom ; BB/M027252/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 208576/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Amphetamine/*pharmacology ; Animals ; Anti-Obesity Agents/*pharmacology ; Brain/*drug effects/metabolism ; Cells, Cultured ; Female ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Obesity/*drug therapy/metabolism ; },
abstract = {Anti-obesity drugs in the amphetamine (AMPH) class act in the brain to reduce appetite and increase locomotion. They are also characterized by adverse cardiovascular effects with origin that, despite absence of any in vivo evidence, is attributed to a direct sympathomimetic action in the heart. Here, we show that the cardiac side effects of AMPH originate from the brain and can be circumvented by PEGylation (PEGyAMPH) to exclude its central action. PEGyAMPH does not enter the brain and facilitates SNS activity via theβ2-adrenoceptor, protecting mice against obesity by increasing lipolysis and thermogenesis, coupled to higher heat dissipation, which acts as an energy sink to increase energy expenditure without altering food intake or locomotor activity. Thus, we provide proof-of-principle for a novel class of exclusively peripheral anti-obesity sympathofacilitators that are devoid of any cardiovascular and brain-related side effects.},
}
@article {pmid32399630,
year = {2020},
author = {Brunel, C and Da Silva, AF and Gros, R},
title = {Environmental Drivers of Microbial Functioning in Mediterranean Forest Soils.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {669-681},
doi = {10.1007/s00248-020-01518-5},
pmid = {32399630},
issn = {1432-184X},
mesh = {Bacteria/*metabolism ; *Bacterial Physiological Phenomena ; Carbon/*metabolism ; *Forests ; France ; *Soil Microbiology ; },
abstract = {Mediterranean forests own distinct characteristics resulting from climate, soil, and vegetation that affect soil microbial communities' assembly and their associated functions. We initiated a multi-scalar analysis of environmental drivers of soil functioning to (1) identify pertinent factorial scales and (2) determine the relative importance of soil, vegetation, and geoclimate influences in shaping soil microbial functions across the French Mediterranean forests. Soil samples (0-15 cm) were collected from 60 forest sites and soil physicochemical and microbiological properties were assessed across different factorial scales i.e., bioclimates, slope exposures, and forest stands. Patterns in microbial catabolic potential (i.e., extracellular enzymes and microbial respiration) and carbon (C) source utilization (i.e., catabolic-level physiological profiling) were partitioned between vegetation cover, soil characteristics, and geoclimate components. Our results reveal that the catabolic potential of soil microbes was strongly influenced by the forest stands and mainly relied on ammonium and nitrate contents. In contrast, variation in C source utilization was mainly explained by vegetation cover. Soil metabolic capacities of microorganisms and resulting C dynamics were largely constrained by climate parameters, which suggests potentially important consequences for soil C storage. Our study revealed diverse structuration patterns between the catabolic potential and the carbon source utilization of soil microbial communities, and gives insights into the underlying mechanisms of soil microbial functioning in Mediterranean forests.},
}
@article {pmid32398103,
year = {2020},
author = {Mohr, AE and Jäger, R and Carpenter, KC and Kerksick, CM and Purpura, M and Townsend, JR and West, NP and Black, K and Gleeson, M and Pyne, DB and Wells, SD and Arent, SM and Kreider, RB and Campbell, BI and Bannock, L and Scheiman, J and Wissent, CJ and Pane, M and Kalman, DS and Pugh, JN and Ortega-Santos, CP and Ter Haar, JA and Arciero, PJ and Antonio, J},
title = {The athletic gut microbiota.},
journal = {Journal of the International Society of Sports Nutrition},
volume = {17},
number = {1},
pages = {24},
pmid = {32398103},
issn = {1550-2783},
mesh = {Athletic Performance/*physiology ; *Diet ; Exercise/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Sports Nutritional Physiological Phenomena ; },
abstract = {The microorganisms in the gastrointestinal tract play a significant role in nutrient uptake, vitamin synthesis, energy harvest, inflammatory modulation, and host immune response, collectively contributing to human health. Important factors such as age, birth method, antibiotic use, and diet have been established as formative factors that shape the gut microbiota. Yet, less described is the role that exercise plays, particularly how associated factors and stressors, such as sport/exercise-specific diet, environment, and their interactions, may influence the gut microbiota. In particular, high-level athletes offer remarkable physiology and metabolism (including muscular strength/power, aerobic capacity, energy expenditure, and heat production) compared to sedentary individuals, and provide unique insight in gut microbiota research. In addition, the gut microbiota with its ability to harvest energy, modulate the immune system, and influence gastrointestinal health, likely plays an important role in athlete health, wellbeing, and sports performance. Therefore, understanding the mechanisms in which the gut microbiota could play in the role of influencing athletic performance is of considerable interest to athletes who work to improve their results in competition as well as reduce recovery time during training. Ultimately this research is expected to extend beyond athletics as understanding optimal fitness has applications for overall health and wellness in larger communities. Therefore, the purpose of this narrative review is to summarize current knowledge of the athletic gut microbiota and the factors that shape it. Exercise, associated dietary factors, and the athletic classification promote a more "health-associated" gut microbiota. Such features include a higher abundance of health-promoting bacterial species, increased microbial diversity, functional metabolic capacity, and microbial-associated metabolites, stimulation of bacterial abundance that can modulate mucosal immunity, and improved gastrointestinal barrier function.},
}
@article {pmid32397606,
year = {2020},
author = {Colquhoun, C and Duncan, M and Grant, G},
title = {Inflammatory Bowel Diseases: Host-Microbial-Environmental Interactions in Dysbiosis.},
journal = {Diseases (Basel, Switzerland)},
volume = {8},
number = {2},
pages = {},
pmid = {32397606},
issn = {2079-9721},
abstract = {Crohn's Disease (CD) and Ulcerative Colitis (UC) are world-wide health problems in which intestinal dysbiosis or adverse functional changes in the microbiome are causative or exacerbating factors. The reduced abundance and diversity of the microbiome may be a result of a lack of exposure to vital commensal microbes or overexposure to competitive pathobionts during early life. Alternatively, many commensal bacteria may not find a suitable intestinal niche or fail to proliferate or function in a protective/competitive manner if they do colonize. Bacteria express a range of factors, such as fimbriae, flagella, and secretory compounds that enable them to attach to the gut, modulate metabolism, and outcompete other species. However, the host also releases factors, such as secretory IgA, antimicrobial factors, hormones, and mucins, which can prevent or regulate bacterial interactions with the gut or disable the bacterium. The delicate balance between these competing host and bacteria factors dictates whether a bacterium can colonize, proliferate or function in the intestine. Impaired functioning of NOD2 in Paneth cells and disrupted colonic mucus production are exacerbating features of CD and UC, respectively, that contribute to dysbiosis. This review evaluates the roles of these and other the host, bacterial and environmental factors in inflammatory bowel diseases.},
}
@article {pmid32396806,
year = {2020},
author = {Herren, CM},
title = {Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities.},
journal = {Proceedings. Biological sciences},
volume = {287},
number = {1927},
pages = {20192945},
pmid = {32396806},
issn = {1471-2954},
mesh = {Biota ; *Ecosystem ; *Introduced Species ; *Microbiota ; },
abstract = {The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this 'critical' level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.},
}
@article {pmid32394640,
year = {2020},
author = {Paula, CCP and Bichuette, ME and Seleghim, MHR},
title = {Nutrient availability in tropical caves influences the dynamics of microbial biomass.},
journal = {MicrobiologyOpen},
volume = {9},
number = {7},
pages = {e1044},
pmid = {32394640},
issn = {2045-8827},
mesh = {Bacteria/*growth &amp; development/*metabolism ; Biomass ; Brazil ; Carbon/analysis ; Caves/*chemistry/*microbiology ; Nitrogen/analysis ; Soil/*chemistry ; Soil Microbiology ; },
abstract = {Few studies have evaluated the trophic level in tropical caves, and none related the microbial biomass dynamics in the immobilization of carbon and nitrogen. Here, four tropical caves of Terra Ronca State Park, Brazil, were studied: Angélica, São Bernardo, Terra Ronca I, and Terra Ronca II caves. Physical, chemical, and microbiological parameters (microbial biomass and respiration) were estimated in the dry and wet seasons. São Bernardo, Terra Ronca I, and Terra Ronca II caves presented higher nitrogen and microbial biomass nitrogen (MBN) values in the wet season than in the dry season. On the other hand, the Angélica cave showed larger amounts of nitrogen and lower MBN values in the dry season. These results indicate that caves can be adjusted in two ecological theories known as "stoichiometric decomposition" and "microbial nitrogen mining"-to the effects of nutrient availability on organic matter decomposition. The caves studied showed different environmental dynamics in relation to organic matter decomposition, which allows them to be considered unique and possess specific characteristics. Microbial biomass dynamics can be an important parameter to evaluate the availability of nutrients and ecological dynamics of the trophic network in subterranean environments.},
}
@article {pmid32393397,
year = {2020},
author = {Koh, H and Zhao, N},
title = {A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {63},
pmid = {32393397},
issn = {2049-2618},
support = {P30 AI094189/AI/NIAID NIH HHS/United States ; U24 OD023382/OD/NIH HHS/United States ; },
mesh = {*Computational Biology ; Humans ; *Microbiota ; *Software ; },
abstract = {BACKGROUND: In human microbiome studies, it is crucial to evaluate the association between microbial group (e.g., community or clade) composition and a host phenotype of interest. In response, a number of microbial group association tests have been proposed, which account for the unique features of the microbiome data (e.g., high-dimensionality, compositionality, phylogenetic relationship). These tests generally fall in the class of aggregation tests which amplify the overall group association by combining all the underlying microbial association signals, and, therefore, they are powerful when many microbial species are associated with a given host phenotype (i.e., low sparsity). However, in practice, the microbial association signals can be highly sparse, and this is especially the situation where we have a difficulty to discover the microbial group association.<br><br>METHODS: Here, we introduce a powerful microbial group association test for sparse microbial association signals, namely, microbiome higher criticism analysis (MiHC). MiHC is a data-driven omnibus test taken in a search space spanned by tailoring the higher criticism test to incorporate phylogenetic information and/or modulate sparsity levels and including the Simes test for excessively high sparsity levels. Therefore, MiHC robustly adapts to diverse phylogenetic relevance and sparsity levels.<br><br>RESULTS: Our simulations show that MiHC maintains a high power at different phylogenetic relevance and sparsity levels with correct type I error controls. We also apply MiHC to four real microbiome datasets to test the association between respiratory tract microbiome and smoking status, the association between the infant's gut microbiome and delivery mode, the association between the gut microbiome and type 1 diabetes status, and the association between the gut microbiome and human immunodeficiency virus status.<br><br>CONCLUSIONS: In practice, the true underlying association pattern on the extent of phylogenetic relevance and sparsity is usually unknown. Therefore, MiHC can be a useful analytic tool because of its high adaptivity to diverse phylogenetic relevance and sparsity levels. MiHC can be implemented in the R computing environment using our software package freely available at https://github.com/hk1785/MiHC.},
}
@article {pmid32392181,
year = {2020},
author = {He, J and Xu, S and Zhang, B and Xiao, C and Chen, Z and Si, F and Fu, J and Lin, X and Zheng, G and Yu, G and Chen, J},
title = {Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis.},
journal = {Aging},
volume = {12},
number = {9},
pages = {8583-8604},
pmid = {32392181},
issn = {1945-4589},
mesh = {Absorptiometry, Photon ; *Bone Density ; Bone Remodeling ; Bone and Bones/*physiology ; Collagen Type I/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Mass Spectrometry ; Metabolomics ; Middle Aged ; Osteoporosis, Postmenopausal/diagnosis/*metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Reduced bone mineral density (BMD) is associated with an altered microbiota in senile osteoporosis. However, the relationship among gut microbiota, BMD and bone metabolic indexes remains unknown in postmenopausal osteoporosis. In this study, fecal microbiota profiles for 106 postmenopausal individuals with osteopenia (n=33) or osteoporosis (n=42) or with normal BMD (n=31) were determined. An integrated 16S rRNA gene sequencing and LC-MS-based metabolomics approach was applied to explore the association of estrogen-reduced osteoporosis with the gut microbiota and fecal metabolic phenotype. Adjustments were made using several statistical models for potential confounding variables identified from the literature. The results demonstrated decreased bacterial richness and diversity in postmenopausal osteoporosis. Additionally, showed significant differences in abundance levels among phyla and genera in the gut microbial community were found. Moreover, postmenopausal osteopenia-enriched N-acetylmannosamine correlated negatively with BMD, and distinguishing metabolites were closely associated with gut bacterial variation. Both serum procollagen type I N propeptide (P1NP) and C-terminal telopeptide of type I collagen (CTX-1) correlated positively with osteopenia-enriched Allisonella, Klebsiella and Megasphaera. However, we did not find a significant correlation between bacterial diversity and estrogen. These observations will lead to a better understanding of the relationship between bone homeostasis and the microbiota in postmenopausal osteoporosis.},
}
@article {pmid32391139,
year = {2019},
author = {Obolski, U and Perez, PN and Villabona-Arenas, CJ and Thézé, J and Faria, NR and Lourenço, J},
title = {MVSE: An R-package that estimates a climate-driven mosquito-borne viral suitability index.},
journal = {Methods in ecology and evolution},
volume = {10},
number = {8},
pages = {1357-1370},
pmid = {32391139},
issn = {2041-210X},
abstract = {Viruses, such as dengue, Zika, yellow fever and chikungunya, depend on mosquitoes for transmission. Their epidemics typically present periodic patterns, linked to the underlying mosquito population dynamics, which are known to be driven by natural climate fluctuations. Understanding how climate dictates the timing and potential of viral transmission is essential for preparedness of public health systems and design of control strategies. While various alternative approaches have been proposed to estimate local transmission potential of such viruses, few open-source, ready to use and freely available software tools exist.We developed the Mosquito-borne Viral Suitability Estimator (MVSE) software package for the R programming environment. MVSE estimates the index P, a novel suitability index based on a climate-driven mathematical expression for the basic reproductive number of mosquito-borne viruses. By accounting for local humidity and temperature, as well as viral, vector and human priors, the index P can be estimated for specific host and viral species in different regions of the globe.We describe the background theory, empirical support and biological interpretation of the index P. Using real-world examples spanning multiple epidemiological contexts, we further demonstrate MVSE's basic functionality, research and educational potentials.},
}
@article {pmid32390961,
year = {2020},
author = {Samad, MS and Lee, HJ and Cerbin, S and Meima-Franke, M and Bodelier, PLE},
title = {Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {582},
pmid = {32390961},
issn = {1664-302X},
abstract = {It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their "host". However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and particle-associated (PA) microbes. Here, we explicitly addressed these issues by investigating (1) the differences in free-living, PA, and zooplankton associated microbes and (2) the impact of temperature on these microbes in the water column of a series of lakes artificially warmed by two power plants. High-throughput amplicon sequencing of the 16S rRNA gene showed that diversity and composition of the bacterial community associated to zooplankton, PA, and bacterioplankton varied significantly from one another, grouping in different clusters indicating niche differentiation of pelagic microbes. From the abiotic parameters measured, temperature significantly affected the diversity and composition of all analyzed microbiomes. Two phyla (e.g., Proteobacteria and Bacteroidetes) dominated in zooplankton microbiomes whereas Actinobacteria was the dominant phylum in the bacterioplankton. The microbial species richness and diversity was lower in zooplankton compared to bacterioplankton and PA. Surprisingly, genera of methane-oxidizing bacteria, methylotrophs and nitrifiers (e.g., Nitrobacter) significantly associated with the microbiome of zooplankton and PA. Our study clearly demonstrates niche differentiation of pelagic microbes and their potential link to biogeochemical cycling in freshwater systems.},
}
@article {pmid32389289,
year = {2020},
author = {Araújo, CAS and Ferreira, PC and Pupin, B and Dias, LP and Avalos, J and Edwards, J and Hallsworth, JE and Rangel, DEN},
title = {Osmotolerance as a determinant of microbial ecology: A study of phylogenetically diverse fungi.},
journal = {Fungal biology},
volume = {124},
number = {5},
pages = {273-288},
doi = {10.1016/j.funbio.2019.09.001},
pmid = {32389289},
issn = {1878-6146},
mesh = {*Ecosystem ; *Fungi/classification/physiology ; Phylogeny ; *Salt Tolerance ; },
abstract = {Osmotic stress induced by high solute concentration can prevent fungal metabolism and growth due to alterations in properties of the cytosol, changes in turgor, and the energy required to synthesize and retain compatible solutes. We used germination to quantify tolerance/sensitivity to the osmolyte KCl (0.1-4.5 M, in 0.1 M increments) for 71 strains (40 species) of ecologically diverse fungi. These include 11 saprotrophic species (17 strains, including two xerophilic species), five mycoparasitic species (five strains), six plant-pathogenic species (13 strains), and 19 entomopathogenic species (36 strains). A dendrogram obtained from cluster analyses, based on KCl inhibitory concentrations 50 % and 90 % calculated by Probit Analysis, revealed three groups of fungal isolates accordingly to their osmotolerance. The most-osmotolerant group (Group 3) contained the majority of saprotrophic fungi, and Aspergillus niger (F19) was the most tolerant. The highly xerophilic Aspergillus montevidense and Aspergillus pseudoglaucus were the second- and third-most tolerant species, respectively. All Aspergillus and Cladosporium species belonged to Group 3, followed by the entomopathogens Colletotrichum fioriniae, Simplicillium lanosoniveum, and Trichothecium roseum. Group 2 exhibited a moderate osmotolerance, and included plant-pathogens such as Colletotrichum and Fusarium, mycoparasites such as Clonostachys spp, some saprotrophs such as Mucor and Penicillium spp., and some entomopathogens such as Isaria, Lecanicillium, Mariannaea, Simplicillium, and Torrubiella. Group 1 contained the osmo-sensitive strains: the rest of the entomopathogens and the mycoparasitic Gliocladium and Trichoderma. Although stress tolerance did not correlate with their primary ecological niche, classification of these 71 fungal strains was more closely aligned with their ecology than with their phylogenetic relatedness. We discuss the implications for both microbial ecology and fungal taxonomy.},
}
@article {pmid32388577,
year = {2020},
author = {Seward, J and Carson, MA and Lamit, LJ and Basiliko, N and Yavitt, JB and Lilleskov, E and Schadt, CW and Smith, DS and Mclaughlin, J and Mykytczuk, N and Willims-Johnson, S and Roulet, N and Moore, T and Harris, L and Bräuer, S},
title = {Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {593-602},
doi = {10.1007/s00248-020-01510-z},
pmid = {32388577},
issn = {1432-184X},
mesh = {Archaea/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; *Climate ; *Microbiota ; Ontario ; Soil Microbiology ; United States ; *Wetlands ; },
abstract = {Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH4). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO2) and CH4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.},
}
@article {pmid32388576,
year = {2020},
author = {Gnanasekaran, G},
title = {Correction to: Disappearance of Quorum Sensing in Burkholderia Glumae During Experimental Evolution.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {739},
doi = {10.1007/s00248-020-01516-7},
pmid = {32388576},
issn = {1432-184X},
abstract = {Following the publication of this article [ 1 ], authors Jae Yun Lim and Ingyu Hwang have stated that they were not aware of, nor were they involved in the drafting, submission, or revision of this manuscript.},
}
@article {pmid32385877,
year = {2020},
author = {Loos, BG and Van Dyke, TE},
title = {The role of inflammation and genetics in periodontal disease.},
journal = {Periodontology 2000},
volume = {83},
number = {1},
pages = {26-39},
pmid = {32385877},
issn = {1600-0757},
mesh = {Genome-Wide Association Study ; *Gingivitis ; Humans ; Inflammation ; *Periodontal Diseases ; *Periodontitis ; },
abstract = {Periodontitis is a complex disease: (a) various causative factors play a role simultaneously and interact with each other; and (b) the disease is episodic in nature, and bursts of disease activity can be recognized, ie, the disease develops and cycles in a nonlinear fashion. We recognize that various causative factors determine the immune blueprint and, consequently, the immune fitness of a subject. Normally, the host lives in a state of homeostasis or symbiosis with the oral microbiome; however, disturbances in homeostatic balance can occur, because of an aberrant host response (inherited and/or acquired during life). This imbalance results from hyper- or hyporesponsiveness and/or lack of sufficient resolution of inflammation, which in turn is responsible for much of the disease destruction seen in periodontitis. The control of this destruction by anti-inflammatory processes and proresolution processes limits the destruction to the tissues surrounding the teeth. The local inflammatory processes can also become systemic, which in turn affect organs such as the heart. Gingival inflammation also elicits changes in the ecology of the subgingival environment providing optimal conditions for the outgrowth of gram-negative, anaerobic species, which become pathobionts and can propagate periodontal inflammation and can further negatively impact immune fitness. The factors that determine immune fitness are often the same factors that determine the response to the resident biofilm, and are clustered as follows: (a) genetic and epigenetic factors; (b) lifestyle factors, such as smoking, diet, and psychosocial conditions; (c) comorbidities, such as diabetes; and (d) local and dental factors, as well as randomly determined factors (stochasticity). Of critical importance are the pathobionts in a dysbiotic biofilm that drive the viscious cycle. Focusing on genetic factors, currently variants in at least 65 genes have been suggested as being associated with periodontitis based on genome-wide association studies and candidate gene case control studies. These studies have found pleiotropy between periodontitis and cardiovascular diseases. Most of these studies point to potential pathways in the pathogenesis of periodontal disease. Also, most contribute to a small portion of the total risk profile of periodontitis, often limited to specific racial and ethnic groups. To date, 4 genetic loci are shared between atherosclerotic cardiovascular diseases and periodontitis, ie, CDKN2B-AS1(ANRIL), a conserved noncoding element within CAMTA1 upstream of VAMP3, PLG, and a haplotype block at the VAMP8 locus. The shared genes suggest that periodontitis is not causally related to atherosclerotic diseases, but rather both conditions are sequelae of similar (the same?) aberrant inflammatory pathways. In addition to variations in genomic sequences, epigenetic modifications of DNA can affect the genetic blueprint of the host responses. This emerging field will yield new valuable information about susceptibility to periodontitis and subsequent persisting inflammatory reactions in periodontitis. Further studies are required to verify and expand our knowledge base before final cause and effect conclusions about the role of inflammation and genetic factors in periodontitis can be made.},
}
@article {pmid32385616,
year = {2020},
author = {Cockburn, CF and Gregory, BRB and Nasser, NA and Patterson, RT},
title = {Intra-Lake Arcellinida (Testate Lobose Amoebae) Response to Winter De-icing Contamination in an Eastern Canada Road-Side "Salt Belt" Lake.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {366-383},
doi = {10.1007/s00248-020-01513-w},
pmid = {32385616},
issn = {1432-184X},
mesh = {*Environmental Monitoring ; Lakes/chemistry/*parasitology ; Lobosea/drug effects/*isolation &amp; purification ; Ontario ; Salinity ; Seasons ; Sodium Chloride/*adverse effects ; Water Pollutants, Chemical/*adverse effects ; },
abstract = {Salt contamination of lakes, due to the application of winter de-icing salts on roads, presents a significant environmental challenge in the "salt belt" region of eastern North America. The research reported here presents the first deployment of a previously published proxy tool based on Arcellinida (testate lobose amoebae) for monitoring road salt contamination. The research was conducted at Silver Lake in Eastern Ontario, a 4-km-long lake with the heavily traveled Trans-Canada Highway (HWY 7) transiting the entire southern shore. The lake showed elevated conductivity (297-310 μS/cm) and sub-brackish conditions (0.14-0.15 ppt). Sodium levels were also elevated near the roadside (median Na = 1020 ppm). Cluster analysis and nonmetric multidimensional scaling results revealed four distinct Arcellinida assemblages: "Stressed Cool Water Assemblage (SCWA)," "Deep Cold Water Assemblage (DCWA)," both from below the 8-m thermocline, and the shallower water "Shallow Water Assemblage 1 (SWA-1)" and "Shallow Water Assemblage 2 (SWA-2)". Redundancy analysis showed a minor response of Arcellinida to road salt contamination in shallower areas of the lake, with confounding variables significantly impacting assemblage distribution, particularly beneath the thermocline (e.g., water temperature, water depth, sediment runoff from catchment [Ti], sediment geochemistry [Ca, S]). The results of this study indicate that the trophic structure of the lake has to date only been modestly impacted by the cumulative nature of road salt contamination. Nonetheless, the Silver Lake results should be considered of concern and warrant continued arcellinidan biomonitoring to gauge the ongoing and long-term effects of road salt on its ecosystem.},
}
@article {pmid32385615,
year = {2020},
author = {Vences, A and Abushattal, S and Matanza, XM and Dubert, J and Uzun, E and Ogut, H and Osorio, CR},
title = {Highly Transferable pAQU-Related Plasmids Encoding Multidrug Resistance Are Widespread in the Human and Fish Pathogen Photobacterium damselae subsp. damselae in Aquaculture Areas in the Black Sea.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {507-518},
doi = {10.1007/s00248-020-01519-4},
pmid = {32385615},
issn = {1432-184X},
support = {AGL2016-79738-R//Agencia Estatal de Investigaci&#xf3;n/ ; AGL2016-79738-R//FEDER/ ; ED431C 2018/18//Secretaria Xeral de Investigaci&#xf3;n e Desenvolvemento, Xunta de Galicia/ ; },
mesh = {Aquaculture ; Black Sea ; Drug Resistance, Multiple, Bacterial/*genetics ; Photobacterium/*genetics ; Plasmids/*genetics ; },
abstract = {The marine bacterium Photobacterium damselae subsp. damselae is a pathogen that causes disease in diverse marine animals, and is also a serious opportunistic human pathogen that can cause fatal infections. Strains of this pathogen isolated from diseased European sea bass in aquaculture facilities in the Turkish coast of the Black Sea were found to exhibit reduced sensitivity to multiple antimicrobials. Selected representative strains were subjected to complete genome sequencing and plasmid characterization. It was found that multidrug resistant (MDR) isolates harboured large conjugative plasmids sharing part of their sequence backbone with pAQU-group plasmids, hitherto reported exclusively in China and Japan. Four new pAQU-group versions of plasmids were identified in the present study, containing distinct combinations of the resistance determinants tetB, floR, sul2, qnrVC, dfrA and strAB. Conjugative transfer of pPHDD2-OG2, a representative plasmid of 170,998 bp, occurred at high frequencies (2.2 × 10[-2] transconjugants per donor cell), to E. coli and to pathogenic P. damselae subsp. damselae and subsp. piscicida strains. Upon transfer, pPHDD2-OG2 conferred reduced susceptibility to a number of antimicrobials to the recipient strains. Comparative genomics analysis of host strains suggested that these MDR plasmids of the pAQU-group were acquired by different genetic lineages of Pdd. This study provides evidence that P. damselae subsp. damselae isolated from diseased fish constitute a reservoir for conjugative MDR pAQU-group plasmids in the Mediterranean basin, and have the potential to spread to diverse bacterial species.},
}
@article {pmid32385111,
year = {2020},
author = {Glaub, A and Huptas, C and Neuhaus, K and Ardern, Z},
title = {Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.},
journal = {The Journal of biological chemistry},
volume = {295},
number = {27},
pages = {8999-9011},
pmid = {32385111},
issn = {1083-351X},
mesh = {Bacteria/*genetics ; Computational Biology/methods ; Genetic Profile ; High-Throughput Nucleotide Sequencing/methods ; Molecular Sequence Annotation/methods ; Protein Biosynthesis/genetics ; RNA, Messenger/genetics ; RNA, Ribosomal/metabolism ; Ribosomes/*genetics ; Sequence Analysis, RNA/*methods ; },
abstract = {Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a "one-size-fits-all" ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.},
}
@article {pmid32384669,
year = {2020},
author = {Kazou, M and Tzamourani, A and Panagou, EZ and Tsakalidou, E},
title = {Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis.},
journal = {Microorganisms},
volume = {8},
number = {5},
pages = {},
pmid = {32384669},
issn = {2076-2607},
support = {2018&#x3a3;&#x395;01300000//Greek national funds through the Public Investments Program (PIP) of General Secretariat for Research &amp; Technology (GSRT), under the Emblematic Action "The Olive Road"/ ; },
abstract = {Kalamata natural black olives are one of the most economically important Greek varieties. The microbial ecology of table olives is highly influenced by the co-existence of bacteria and yeasts/fungi, as well as the physicochemical parameters throughout the fermentation. Therefore, the aim of this study was the identification of bacterial and yeast/fungal microbiota of both olives and brines obtained from 29 cv. Kalamata olive samples industrially fermented in the two main producing geographical regions of Greece, namely Aitoloakarnania and Messinia/Lakonia. The potential microbial biogeography association between certain taxa and geographical area was also assessed. The dominant bacterial family identified in olive and brine samples from both regions was Lactobacillaceae, presenting, however, higher average abundances in the samples from Aitoloakarnania compared to Messinia/Lakonia. At the genus level, Lactobacillus, Celerinatantimonas, Propionibacterium and Pseudomonas were the most abundant. In addition, the yeasts/fungal communities were less diverse compared to those of bacteria, with Pichiaceae being the dominant family and Pichia, Ogataea, and Saccharomyces being the most abundant genera. To the best of our knowledge, this is the first report on the microbiota of both olives and brines of cv. Kalamata black olives fermented on an industrial scale between two geographical regions of Greece using metagenomics analysis.},
}
@article {pmid32382073,
year = {2020},
author = {Floudas, D and Bentzer, J and Ahrén, D and Johansson, T and Persson, P and Tunlid, A},
title = {Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.},
journal = {The ISME journal},
volume = {14},
number = {8},
pages = {2046-2059},
pmid = {32382073},
issn = {1751-7370},
mesh = {*Agaricales ; *Basidiomycota ; Fungi/genetics ; Humans ; Lignin ; Phylogeny ; Wood ; },
abstract = {Litter decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.},
}
@article {pmid32379897,
year = {2020},
author = {Hicks, LC and Leizeaga, A and Rousk, K and Michelsen, A and Rousk, J},
title = {Simulated rhizosphere deposits induce microbial N-mining that may accelerate shrubification in the subarctic.},
journal = {Ecology},
volume = {101},
number = {9},
pages = {e03094},
doi = {10.1002/ecy.3094},
pmid = {32379897},
issn = {1939-9170},
support = {20150561//The Crafoord Foundation/ ; 2018-01315//The Swedish Research Council Formas/ ; KAW 2017.0171//The Knut and Alice Wallenberg Foundation/ ; CTS16: 385//Carl Tryggers Foundation/ ; },
mesh = {Carbon ; Climate Change ; Nitrogen ; *Rhizosphere ; Soil ; *Soil Microbiology ; },
abstract = {Climate change is exposing high-latitude systems to warming and a shift towards more shrub-dominated plant communities, resulting in increased leaf-litter inputs at the soil surface, and more labile root-derived organic matter (OM) input in the soil profile. Labile OM can stimulate the mineralization of soil organic matter (SOM); a phenomenon termed "priming." In N-poor subarctic soils, it is hypothesized that microorganisms may "prime" SOM in order to acquire N (microbial N-mining). Increased leaf-litter inputs with a high C/N ratio might further exacerbate microbial N demand, and increase the susceptibility of N-poor soils to N-mining. We investigated the N-control of SOM mineralization by amending soils from climate change-simulation treatments in the subarctic (+1.1°C warming, birch litter addition, willow litter addition, and fungal sporocarp addition) with labile OM either in the form of glucose (labile C; equivalent to 400 µg C/g fresh [fwt] soil) or alanine (labile C + N; equivalent to 400 µg C and 157 µg N/g fwt soil), to simulate rhizosphere inputs. Surprisingly, we found that despite 5 yr of simulated climate change treatments, there were no significant effects of the field-treatments on microbial process rates, community structure or responses to labile OM. Glucose primed the mineralization of both C and N from SOM, but gross mineralization of N was stimulated more than that of C, suggesting that microbial SOM use increased in magnitude and shifted to components richer in N (i.e., selective microbial N-mining). The addition of alanine also resulted in priming of both C and N mineralization, but the N mineralization stimulated by alanine was greater than that stimulated by glucose, indicating strong N-mining even when a source of labile OM including N was supplied. Microbial carbon use efficiency was reduced in response to both labile OM inputs. Overall, these findings suggest that shrub expansion could fundamentally alter biogeochemical cycling in the subarctic, yielding more N available for plant uptake in these N-limited soils, thus driving positive plant-soil feedbacks.},
}
@article {pmid32377220,
year = {2020},
author = {Masteling, R and Voorhoeve, L and IJsselmuiden, J and Dini-Andreote, F and de Boer, W and Raaijmakers, JM},
title = {DiSCount: computer vision for automated quantification of Striga seed germination.},
journal = {Plant methods},
volume = {16},
number = {},
pages = {60},
pmid = {32377220},
issn = {1746-4811},
abstract = {BACKGROUND: Plant parasitic weeds belonging to the genus Striga are a major threat for food production in Sub-Saharan Africa and Southeast Asia. The parasite's life cycle starts with the induction of seed germination by host plant-derived signals, followed by parasite attachment, infection, outgrowth, flowering, reproduction, seed set and dispersal. Given the small seed size of the parasite (< 200 μm), quantification of the impact of new control measures that interfere with seed germination relies on manual, labour-intensive counting of seed batches under the microscope. Hence, there is a need for high-throughput assays that allow for large-scale screening of compounds or microorganisms that adversely affect Striga seed germination.<br><br>RESULTS: Here, we introduce DiSCount (Digital Striga Counter): a computer vision tool for automated quantification of total and germinated Striga seed numbers in standard glass fibre filter assays. We developed the software using a machine learning approach trained with a dataset of 98 manually annotated images. Then, we validated and tested the model against a total dataset of 188 manually counted images. The results showed that DiSCount has an average error of 3.38 percentage points per image compared to the manually counted dataset. Most importantly, DiSCount achieves a 100 to 3000-fold speed increase in image analysis when compared to manual analysis, with an inference time of approximately 3&#xa0;s per image on a single CPU and 0.1&#xa0;s on a GPU.<br><br>CONCLUSIONS: DiSCount is accurate and efficient in quantifying total and germinated Striga seeds in a standardized germination assay. This automated computer vision tool enables for high-throughput, large-scale screening of chemical compound libraries and biological control agents of this devastating parasitic weed. The complete software and manual are hosted at https://gitlab.com/lodewijk-track32/discount_paper and the archived version is available at Zenodo with the DOI 10.5281/zenodo.3627138. The dataset used for testing is available at Zenodo with the DOI 10.5281/zenodo.3403956.},
}
@article {pmid32375874,
year = {2020},
author = {Rifkin, RF and Vikram, S and Ramond, JB and Rey-Iglesia, A and Brand, TB and Porraz, G and Val, A and Hall, G and Woodborne, S and Le Bailly, M and Potgieter, M and Underdown, SJ and Koopman, JE and Cowan, DA and Van de Peer, Y and Willerslev, E and Hansen, AJ},
title = {Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {62},
pmid = {32375874},
issn = {2049-2618},
mesh = {Africa South of the Sahara ; *Archaeology ; Feces/*microbiology ; *Gastrointestinal Microbiome ; History, 15th Century ; Humans ; Metagenomics ; },
abstract = {BACKGROUND: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.<br><br>METHODS: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM.<br><br>RESULTS: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (&#xd6;tzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.<br><br>CONCLUSIONS: Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000&#x2009;years ago. Video Abtract.},
}
@article {pmid32373631,
year = {2020},
author = {Zannoni, A and Pietra, M and Gaspardo, A and Accorsi, PA and Barone, M and Turroni, S and Laghi, L and Zhu, C and Brigidi, P and Forni, M},
title = {Non-invasive Assessment of Fecal Stress Biomarkers in Hunting Dogs During Exercise and at Rest.},
journal = {Frontiers in veterinary science},
volume = {7},
number = {},
pages = {126},
pmid = {32373631},
issn = {2297-1769},
abstract = {Intense exercise causes to organisms to have oxidative stress and inflammation at the gastrointestinal (GI) level. The reduction in intestinal blood flow and the exercise-linked thermal damage to the intestinal mucosa can cause intestinal barrier disruption, followed by an inflammatory response. Furthermore, the adaptation to exercise may affect the gut microbiota and the metabolome of the biofluids. The aim of the present research was to evaluate the presence of a GI derangement in hunting dogs through a non-invasive sampling as a consequence of a period of intense exercise in comparison with samples collected at rest. The study included nine dogs that underwent the same training regime for hunting wild boar. In order to counterbalance physiological variations, multiple-day replicates were collected and pooled at each experimental point for each dog. The samples were collected immediately at rest before the training (T0), after 60 days of training (T1), after 60 days of hunting wild boar (T2), and finally, at 60 days of rest after hunting (T3). A number of potential stress markers were evaluated: fecal cortisol metabolites (FCMs) as a major indicator of altered physiological states, immunoglobulin A (IgA) as an indicator of intestinal immune protection, and total antioxidant activity [total antioxidant capacity (TAC)]. Since stool samples contain exfoliated cells, we investigated also the presence of some transcripts involved in GI permeability [occludin (OCLN), protease-activated receptor-2 (PAR-2)] and in the inflammatory mechanism [interleukin (IL)-8, IL-6, IL-1b, tumor necrosis factor alpha (TNFα), calprotectin (CALP), heme oxygenase-1 (HO-1)]. Finally, the metabolome and the microbiota profiles were analyzed. No variation in FCM and IgA content and no differences in OCLN and CALP gene expression between rest and training were observed. On the contrary, an increase in PAR-2 and HO-1 transcripts, a reduction in total antioxidant activity, and a different profile of microbiota and metabolomics data were observed. Collectively, the data in the present study indicated that physical exercise in our model could be considered a mild stressor stimulus.},
}
@article {pmid32373155,
year = {2020},
author = {Coenen, AR and Hu, SK and Luo, E and Muratore, D and Weitz, JS},
title = {A Primer for Microbiome Time-Series Analysis.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {310},
pmid = {32373155},
issn = {1664-8021},
abstract = {Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.},
}
@article {pmid32371471,
year = {2020},
author = {Bezuidt, OKI and Lebre, PH and Pierneef, R and León-Sobrino, C and Adriaenssens, EM and Cowan, DA and Van de Peer, Y and Makhalanyane, TP},
title = {Phages Actively Challenge Niche Communities in Antarctic Soils.},
journal = {mSystems},
volume = {5},
number = {3},
pages = {},
pmid = {32371471},
issn = {2379-5077},
support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {By modulating the structure, diversity, and trophic outputs of microbial communities, phages play crucial roles in many biomes. In oligotrophic polar deserts, the effects of katabatic winds, constrained nutrients, and low water availability are known to limit microbial activity. Although phages may substantially govern trophic interactions in cold deserts, relatively little is known regarding the precise ecological mechanisms. Here, we provide the first evidence of widespread antiphage innate immunity in Antarctic environments using metagenomic sequence data from hypolith communities as model systems. In particular, immunity systems such as DISARM and BREX are shown to be dominant systems in these communities. Additionally, we show a direct correlation between the CRISPR-Cas adaptive immunity and the metavirome of hypolith communities, suggesting the existence of dynamic host-phage interactions. In addition to providing the first exploration of immune systems in cold deserts, our results suggest that phages actively challenge niche communities in Antarctic polar deserts. We provide evidence suggesting that the regulatory role played by phages in this system is an important determinant of bacterial host interactions in this environment.IMPORTANCE In Antarctic environments, the combination of both abiotic and biotic stressors results in simple trophic levels dominated by microbiomes. Although the past two decades have revealed substantial insights regarding the diversity and structure of microbiomes, we lack mechanistic insights regarding community interactions and how phages may affect these. By providing the first evidence of widespread antiphage innate immunity, we shed light on phage-host dynamics in Antarctic niche communities. Our analyses reveal several antiphage defense systems, including DISARM and BREX, which appear to dominate in cold desert niche communities. In contrast, our analyses revealed that genes which encode antiphage adaptive immunity were underrepresented in these communities, suggesting lower infection frequencies in cold edaphic environments. We propose that by actively challenging niche communities, phages play crucial roles in the diversification of Antarctic communities.},
}
@article {pmid32367214,
year = {2020},
author = {Muñoz-Leal, S and Ramirez, DG and Luz, HR and Faccini, JLH and Labruna, MB},
title = {"Candidatus Borrelia ibitipoquensis," a Borrelia valaisiana-Related Genospecies Characterized from Ixodes paranaensis in Brazil.},
journal = {Microbial ecology},
volume = {80},
number = {3},
pages = {682-689},
doi = {10.1007/s00248-020-01512-x},
pmid = {32367214},
issn = {1432-184X},
support = {150961/2017-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2018/02521-1 and 2019/17960-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Animals ; Borrelia/classification/genetics/*isolation &amp; purification ; Brazil ; Caves ; Female ; Ixodes/growth &amp; development/*microbiology ; Larva/growth &amp; development/microbiology ; Male ; Nymph/growth &amp; development/microbiology ; Spirochaetales/classification ; },
abstract = {Borrelia burgdorferi sensu lato (Bbsl) spirochetes include the agents of Lyme borreliosis in temperate regions of the Northern Hemisphere, and merge their transmission cycles mainly with ticks of the Ixodes ricinus complex. Twenty genospecies compose Bbsl currently, and with the exception of Borrelia chilensis, and Borrelia garinii, all have been described only for North America, Europe, North Africa, and Asia. Here, we collected specimens of Ixodes paranaensis, a tick associated with swifts in a Brazilian natural park from the state of Minas Gerais, and performed a molecular characterization of 11 borrelial genes. Based on comparisons of inter and intraspecific genetic divergences, and Bayesian phylogenetic trees inferred for 16S rRNA, flaB, p66, and concatenated clpA, clpX, pepX, pyrG, recG, nifS rlpB, and uvrA genes, we demonstrate the occurrence of a new genospecies of Bbsl. "Candidatus Borrelia ibitipoquensis" Ip37 is closely related to Borrelia sp. Am501, and Borrelia valaisiana, a spirochete transmitted by ticks of the I. ricinus complex in Eurasia that uses birds as reservoirs. In a similar ecological scenario involving ticks and avian hosts, the migratory swift Streptoprocne biscutata is the sole-documented bird associated with I. paranaensis, and, although not assessed in this study, could correspond to the vertebrate reservoir of this newly described genospecies in Brazil. Pathogenic roles of "Ca. B. ibitipoquensis" are still unknown. However, its possible vector I. paranaensis is not an anthropophilic tick, so human infections would be unlikely to occur. Our finding enhances the knowledge on Bbsl in South America, highlights the occurrence of ecologically and genetically related genospecies with vastly separated geographical distributions, and calls for the attention to explore a barely known diversity of spirochetes of this group in the region.},
}
@article {pmid32366030,
year = {2020},
author = {Perricone, V and Comi, M and Giromini, C and Rebucci, R and Agazzi, A and Savoini, G and Bontempo, V},
title = {Green Tea and Pomegranate Extract Administered During Critical Moments of the Production Cycle Improves Blood Antiradical Activity and Alters Cecal Microbial Ecology of Broiler Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {10},
number = {5},
pages = {},
pmid = {32366030},
issn = {2076-2615},
abstract = {Phytobiotics are usually tested in feed and throughout the production cycle. However, it could be beneficial to evaluate their effects when administered only during critical moments, such as changes in feeding phases. The aim of the trial was to investigate the effect of a commercial plant extract (PE; IQV-10-P01, InQpharm Animal Health, Kuala Lumpur, Malaysia) on growth performance, blood antiradical activity and cecal microbiome when administered in drinking water to broiler chickens during the post-hatching phase and at each change of diet. In the experiment, 480 1-day-old male broiler chicks were assigned to two groups in a 50-day trial. Broilers received drinking water (C) or drinking water plus PE (T) at a rate of 2 mL/L on days 0 to 4, 10-11 and 20-21. PE did not affect performance and water intake, while total antiradical activity was improved (p < 0.05). A greater abundance of lactic acid bacteria (false discovery rate (FDR) < 0.05) was found in the T group and the result was confirmed at a lower taxonomic level with higher Lactobacillaceae abundance (FDR < 0.05). Our findings suggest that PE administration during critical moments of the production cycle of broiler chickens may exert beneficial effects at a systemic level and on gut microbial ecology.},
}
@article {pmid32364226,
year = {2020},
author = {Ramoneda, J and Le Roux, JJ and Frossard, E and Frey, B and Gamper, HA},
title = {Experimental assembly reveals ecological drift as a major driver of root nodule bacterial diversity in a woody legume crop.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {6},
pages = {},
doi = {10.1093/femsec/fiaa083},
pmid = {32364226},
issn = {1574-6941},
mesh = {Bacteria/genetics ; *Fabaceae ; *Mesorhizobium ; *Rhizobium/genetics ; Soil Microbiology ; Symbiosis ; },
abstract = {Understanding how plant-associated microbial communities assemble and the role they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, community assembly is generally driven by host plant selection and soil conditions. Here, we aimed to determine the relative importance of neutral and deterministic processes in the assembly of bacterial communities of root nodules of a legume shrub adapted to extreme nutrient limitation, rooibos (Aspalathus linearis Burm. Dahlgren). We grew rooibos seedlings in soil from cultivated land and wild habitats, and mixtures of these soils, sampled from a wide geographic area, and with a fertilization treatment. Bacterial communities were characterized using next generation sequencing of part of the nodA gene (i.e. common to the core rhizobial symbionts of rooibos), and part of the gyrB gene (i.e. common to all bacterial taxa). Ecological drift alone was a major driver of taxonomic turnover in the bacterial communities of root nodules (62.6% of gyrB communities). In contrast, the assembly of core rhizobial communities (genus Mesorhizobium) was driven by dispersal limitation in concert with drift (81.1% of nodA communities). This agrees with a scenario of rooibos-Mesorhizobium specificity in spatially separated subpopulations, and low host filtering of other bacteria colonizing root nodules in a stochastic manner.},
}
@article {pmid32361351,
year = {2020},
author = {Liu, W and Wu, Y and Zhang, S and Gao, Y and Jiang, Y and Horn, H and Li, J},
title = {Successful granulation and microbial differentiation of activated sludge in anaerobic/anoxic/aerobic (A[2]O) reactor with two-zone sedimentation tank treating municipal sewage.},
journal = {Water research},
volume = {178},
number = {},
pages = {115825},
doi = {10.1016/j.watres.2020.115825},
pmid = {32361351},
issn = {1879-2448},
mesh = {Aerobiosis ; Anaerobiosis ; *Bioreactors ; Motor Vehicles ; Nitrogen ; Phosphorus ; *Sewage ; Waste Disposal, Fluid ; },
abstract = {A continuous pilot-scale A[2]O reactor with a two-zone sedimentation tank (A[2]O-TST) was constructed for the formation of aerobic granular sludge (AGS) to treat real municipal sewage. The characteristics of sludge, nutrient removal performance and the corresponding microbial ecology dynamics were studied during granulation process. Experimental results indicated that AGS with a mean particle size of 210 μm and sludge volume index after 30 min of 47.5 mL/g was successfully formed with effluent COD, total nitrogen and total phosphorus concentrations in the reactor reaching 22.8, 3.5 and 0.2 mg/L, respectively. Furthermore, high throughput data indicated that granules in settling tank-1 (ST-1) harbored slow-growing autotrophic organisms like Nitrosomonas and Nitrospira, while the flocs in settling tank-2 (ST-2) were dominated by fast-growing heterotrophic organisms including Ca. Accumulibacter, Dechloromonas, Flavobacterium, Arcobacter and Halomonas. Simulation results using computational fluid dynamics and discrete element method (CFD-DEM) modeling verified that the selection pressure created by the TST separator contributed to the retention of heavy granules (>1.011 kg/m[3] density) in ST-1 zone and the withdrawal of light flocs (<1.011 kg/m[3] density) from ST-2 zone. Therefore, the segregation of biomass using the TST system provides an opportunity to select for desired microbial populations and to optimize the nitrogen and phosphorus removal performance of the A[2]O-TST reactor. This study could add a guiding sight into the application of two-sludge system based on AGS technology for upgrading traditional A[2]O process.},
}
@article {pmid32360380,
year = {2020},
author = {Wang, J and Zhang, X and Yao, H},
title = {Optimizing ultracentrifugation conditions for DNA-based stable isotope probing (DNA-SIP).},
journal = {Journal of microbiological methods},
volume = {173},
number = {},
pages = {105938},
doi = {10.1016/j.mimet.2020.105938},
pmid = {32360380},
issn = {1872-8359},
mesh = {Archaea/genetics ; Bacteria/genetics ; Centrifugation, Density Gradient/methods ; Cesium ; China ; Chlorides ; DNA/*chemistry/genetics/isolation &amp; purification ; *DNA Probes ; DNA, Archaeal/chemistry/genetics/isolation &amp; purification ; DNA, Bacterial/*chemistry/genetics/isolation &amp; purification ; *Isotopes ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Soil ; Soil Microbiology ; Ultracentrifugation/*methods ; },
abstract = {DNA-SIP (DNA-based stable isotope probing) is increasingly being employed in soil microbial ecology to identify those microbes assimilating the [13]C/[15]N labelled substrate. Isopycnic gradient centrifugation is the primary experimental process for conducting DNA-SIP. However, diverse centrifugal conditions have been used in various recent studies. In order to get the optimum conditions of centrifugation for DNA-SIP, centrifugation time (36, 42, 48, 60 h), speed (45,000, 55,000 rpm) and the initial buoyant density (1.69, 1.71, 1.725 g ml[-1]), as were used extensively in related studies, were tested in this experiment with the Vti 65.2 rotor. DNA with either [13]C-labelling or unlabelled was extracted from a paddy soil pre-incubated with either [13]C-labelled or natural abundance glucose. After ultracentrifugation, the gene abundance of bacterial 16S rRNA, fungal 18S rRNA, bacterial and archaeal amoA within the fractioned DNA was detected. The results showed that centrifugation for 48 h was enough for the DNA to reach stabilization in the CsCl solution. The initial density of the mixed solution was best adjusted to 1.71 g ml[-1] to ensure that most of the genes were concentrated on the middle fractions of the density gradient. Increasing the centrifugation speed would increase the density gradient of fractions; therefore, 45,000 rpm (184,000 g) was recommended so as to obtain the more widespread pattern of DNA in the centrifugal tube. We hope these findings will assist future researchers to conduct optimum ultracentrifugation for DNA-SIP.},
}
@article {pmid32358041,
year = {2020},
author = {Li, YJ and Chen, X and Kwan, TK and Loh, YW and Singer, J and Liu, Y and Ma, J and Tan, J and Macia, L and Mackay, CR and Chadban, SJ and Wu, H},
title = {Dietary Fiber Protects against Diabetic Nephropathy through Short-Chain Fatty Acid-Mediated Activation of G Protein-Coupled Receptors GPR43 and GPR109A.},
journal = {Journal of the American Society of Nephrology : JASN},
volume = {31},
number = {6},
pages = {1267-1281},
pmid = {32358041},
issn = {1533-3450},
mesh = {Albuminuria/prevention &amp; control ; Animals ; Diabetes Mellitus, Experimental/complications ; Diabetic Nephropathies/*prevention &amp; control ; Dietary Fiber/*administration &amp; dosage ; Dysbiosis ; Fatty Acids, Volatile/*physiology ; Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/*physiology ; Streptozocin ; },
abstract = {BACKGROUND: Studies have reported "dysbiotic" changes to gut microbiota, such as depletion of gut bacteria that produce short-chain fatty acids (SCFAs) through gut fermentation of fiber, in CKD and diabetes. Dietary fiber is associated with decreased inflammation and mortality in CKD, and SCFAs have been proposed to mediate this effect.<br><br>METHODS: To explore dietary fiber's effect on development of experimental diabetic nephropathy, we used streptozotocin to induce diabetes in wild-type C57BL/6 and knockout mice lacking the genes encoding G protein-coupled receptors GPR43 or GPR109A. Diabetic mice were randomized to high-fiber, normal chow, or zero-fiber diets, or SCFAs in drinking water. We used proton nuclear magnetic resonance spectroscopy for metabolic profiling and 16S ribosomal RNA sequencing to assess the gut microbiome.<br><br>RESULTS: Diabetic mice fed a high-fiber diet were significantly less likely to develop diabetic nephropathy, exhibiting less albuminuria, glomerular hypertrophy, podocyte injury, and interstitial fibrosis compared with diabetic controls fed normal chow or a zero-fiber diet. Fiber beneficially reshaped gut microbial ecology and improved dysbiosis, promoting expansion of SCFA-producing bacteria of the genera Prevotella and Bifidobacterium, which increased fecal and systemic SCFA concentrations. Fiber reduced expression of genes encoding inflammatory cytokines, chemokines, and fibrosis-promoting proteins in diabetic kidneys. SCFA-treated diabetic mice were protected from nephropathy, but not in the absence of GPR43 or GPR109A. In vitro, SCFAs modulated inflammation in renal tubular cells and podocytes under hyperglycemic conditions.<br><br>CONCLUSIONS: Dietary fiber protects against diabetic nephropathy through modulation of the gut microbiota, enrichment of SCFA-producing bacteria, and increased SCFA production. GPR43 and GPR109A are critical to SCFA-mediated protection against this condition. Interventions targeting the gut microbiota warrant further investigation as a novel renoprotective therapy in diabetic nephropathy.},
}
@article {pmid32355200,
year = {2020},
author = {Wang, W and Li, Z and Zeng, L and Dong, C and Shao, Z},
title = {The oxidation of hydrocarbons by diverse heterotrophic and mixotrophic bacteria that inhabit deep-sea hydrothermal ecosystems.},
journal = {The ISME journal},
volume = {14},
number = {8},
pages = {1994-2006},
pmid = {32355200},
issn = {1751-7370},
mesh = {Bacteria/genetics ; Hydrocarbons ; *Hydrothermal Vents ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Hydrothermal activity can generate numerous and diverse hydrocarbon compounds. However, little is known about the influence of such hydrocarbons on deep-sea hydrothermal microbial ecology. We hypothesize that certain bacteria live on these hydrocarbons. Therefore, in this study, the distribution of hydrocarbons and their associated hydrocarbon-degrading bacteria were investigated at deep-sea hydrothermal vents at the Southern Mid-Atlantic Ridge, the Southwest Indian Ridge, and the East Pacific Rise. A variety of hydrocarbon-degrading consortia were obtained from hydrothermal samples collected at the aforementioned sites after low-temperature enrichment under high hydrostatic pressures, and the bacteria responsible for the degradation of hydrocarbons were investigated by DNA-based stable-isotope probing with uniformly [13]C-labeled hydrocarbons. Unusually, we identified several previously recognized sulfur-oxidizing chemoautotrophs as hydrocarbon-degrading bacteria, e.g., the SAR324 group, the SUP05 clade, and Sulfurimonas, and for the first time confirmed their ability to degrade hydrocarbons. In addition, Erythrobacter, Pusillimonas, and SAR202 clade were shown to degrade polycyclic aromatic hydrocarbons for the first time. These results together with relatively high abundance in situ of most of the above-described bacteria highlight the potential influence of hydrocarbons in configuring the vent microbial community, and have made the importance of mixotrophs in hydrothermal vent ecosystems evident.},
}
@article {pmid32351795,
year = {2020},
author = {Johnston-Monje, D and Lopez Mejia, J},
title = {Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi.},
journal = {Applications in plant sciences},
volume = {8},
number = {4},
pages = {e11334},
pmid = {32351795},
issn = {2168-0450},
abstract = {High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.},
}
@article {pmid32351470,
year = {2020},
author = {Kopprio, GA and Neogi, SB and Rashid, H and Alonso, C and Yamasaki, S and Koch, BP and Gärdes, A and Lara, RJ},
title = {Vibrio and Bacterial Communities Across a Pollution Gradient in the Bay of Bengal: Unraveling Their Biogeochemical Drivers.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {594},
pmid = {32351470},
issn = {1664-302X},
abstract = {The highly populated coasts of the Bay of Bengal are particularly vulnerable to water-borne diseases, pollution and climatic extremes. The environmental factors behind bacterial community composition and Vibrio distribution were investigated in an estuarine system of a cholera-endemic region in the coastline of Bangladesh. Higher temperatures and sewage pollution were important drivers of the abundance of toxigenic Vibrio cholerae. A closer relation between non-culturable Vibrio and particulate organic matter (POM) was inferred during the post-monsoon. The distribution of operational taxonomic units (OTUs) of Vibrio genus was likely driven by salinity and temperature. The resuspension of sediments increased Vibrio abundance and organic nutrient concentrations. The δ[13]C dynamic in POM followed an increasing gradient from freshwater to marine stations; nevertheless, it was not a marker of sewage pollution. Bacteroidales and culturable coliforms were reliable indicators of untreated wastewater during pre and post-monsoon seasons. The presumptive incorporation of depleted-ammonium derived from ammonification processes under the hypoxic conditions, by some microorganisms such as Cloacibacterium and particularly by Arcobacter nearby the sewage discharge, contributed to the drastic [15]N depletion in the POM. The likely capacity of extracellular polymeric substances production of these taxa may facilitate the colonization of POM from anthropogenic origin and may signify important properties for wastewater bioremediation. Genera of potential pathogens other than Vibrio associated with sewage pollution were Acinetobacter, Aeromonas, Arcobacter, and Bergeyella. The changing environmental conditions of the estuary favored the abundance of early colonizers and the island biogeography theory explained the distribution of some bacterial groups. This multidisciplinary study evidenced clearly the eutrophic conditions of the Karnaphuli estuary and assessed comprehensively its current bacterial baseline and potential risks. The prevailing conditions together with human overpopulation and frequent natural disasters, transform the region in one of the most vulnerable to climate change. Adaptive management strategies are urgently needed to enhance ecosystem health.},
}
@article {pmid32350866,
year = {2020},
author = {Lang, M and Baumgartner, M and Rożalska, A and Frick, A and Riva, A and Jarek, M and Berry, D and Gasche, C},
title = {Crypt residing bacteria and proximal colonic carcinogenesis in a mouse model of Lynch syndrome.},
journal = {International journal of cancer},
volume = {147},
number = {8},
pages = {2316-2326},
pmid = {32350866},
issn = {1097-0215},
support = {741623/ERC_/European Research Council/International ; KLI 557/FWF_/Austrian Science Fund FWF/Austria ; I 1573-B19/FWF_/Austrian Science Fund FWF/Austria ; P27831-B28/FWF_/Austrian Science Fund FWF/Austria ; KLI 557-B22/FWF_/Austrian Science Fund FWF/Austria ; P 32302/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; Bacteria/pathogenicity ; Biofilms/growth &amp; development ; Carcinogenesis/genetics/*pathology ; Cell Transformation, Neoplastic/genetics/pathology ; Colorectal Neoplasms/genetics/*microbiology/*pathology ; Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/*microbiology/*parasitology ; DNA Mismatch Repair/genetics ; Disease Models, Animal ; Dysbiosis/genetics/microbiology/pathology ; Gastrointestinal Microbiome/genetics ; Germ-Line Mutation/genetics ; Inflammation/genetics/microbiology/pathology ; Interleukin-10/genetics ; Intestinal Mucosa/microbiology/pathology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; },
abstract = {Colorectal cancer is a multifactorial disease involving inherited DNA mutations, environmental factors, gut inflammation and intestinal microbiota. Certain germline mutations within the DNA mismatch repair system are associated with Lynch syndrome tumors including right-sided colorectal cancer with mucinous phenotype and presence of an inflammatory infiltrate. Such tumors are more often associated with bacterial biofilms, which may contribute to disease onset and progression. Inflammatory bowel diseases are also associated with colorectal cancer and intestinal dysbiosis. Herein we addressed the question, whether inflammation can aggravate colorectal cancer development under mismatch repair deficiency. MSH2[loxP/loxP Vill-cre] mice were crossed into the IL-10[-/-] background to study the importance of inflammation and mucosal bacteria as a driver of tumorigenesis in a Lynch syndrome mouse model. An increase in large bowel tumorigenesis was found in double knockout mice both under conventional housing and under specific pathogen-free conditions. This increase was mostly due to the development of proximal tumors, a hotspot for tumorigenesis in Lynch syndrome, and was associated with a higher degree of inflammation. Additionally, bacterial invasion into the mucus of tumor crypts was observed in the proximal tumors. Inflammation shifted fecal and mucosal microbiota composition and was associated with enrichment in Escherichia-Shigella as well as Akkermansia, Bacteroides and Parabacteroides genera in fecal samples. Tumor-bearing double knockout mice showed a similar enrichment for Escherichia-Shigella and Parabacteroides. Lactobacilli, Lachnospiraceae and Muribaculaceae family members were depleted upon inflammation. In summary, chronic inflammation aggravates colonic tumorigenesis under mismatch repair deficiency and is associated with a shift in microbiota composition.},
}
@article {pmid32346537,
year = {2020},
author = {Duar, RM and Henrick, BM and Casaburi, G and Frese, SA},
title = {Integrating the Ecosystem Services Framework to Define Dysbiosis of the Breastfed Infant Gut: The Role of B. infantis and Human Milk Oligosaccharides.},
journal = {Frontiers in nutrition},
volume = {7},
number = {},
pages = {33},
pmid = {32346537},
issn = {2296-861X},
abstract = {Mounting evidence supports a connection between the composition of the infant gut microbiome and long-term health. In fact, aberrant microbiome compositions during key developmental windows in early life are associated with increased disease risk; therefore, making pertinent modifications to the microbiome during infancy offers significant promise to improve human health. There is growing support for integrating the concept of ecosystem services (the provision of benefits from ecosystems to humans) in linking specific microbiome functions to human well-being. This framework is widely applied in conservation efforts of macro-ecosystems and offers a systematic approach to guide restoration actions aimed to recover critical ecological functions. The aim of this work is to apply the ecosystem services framework to integrate recent studies demonstrating stable alteration of the gut microbiome of breastfed infants when Bifidobacterium longum subsp. infantis EVC001, a gut symbiont capable of efficiently utilizing human milk oligosaccharides into organic acids that are beneficial for the infant and lower intestinal pH, is reintroduced. Additionally, using examples from the literature we illustrate how the absence of B. infantis results in diminished ecosystem services, which may be associated with health consequences related to immune and metabolic disorders. Finally, we propose a model by which infant gut dysbiosis can be defined as a reduction in ecosystem services supplied to the host by the gut microbiome rather than merely changes in diversity or taxonomic composition. Given the increased interest in targeted microbiome modification therapies to decrease acute and chronic disease risk, the model presented here provides a framework to assess the effectiveness of such strategies from a host-centered perspective.},
}
@article {pmid32341569,
year = {2020},
author = {López-García, P and Moreira, D},
title = {The Syntrophy hypothesis for the origin of eukaryotes revisited.},
journal = {Nature microbiology},
volume = {5},
number = {5},
pages = {655-667},
pmid = {32341569},
issn = {2058-5276},
mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics ; *Biological Evolution ; Cell Nucleus ; Eukaryota/genetics/*metabolism ; Eukaryotic Cells/*metabolism ; Genome, Archaeal ; Hydrogen/metabolism ; Membranes/metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; *Phylogeny ; Sulfur/metabolism ; Symbiosis/physiology ; },
abstract = {The discovery of Asgard archaea, phylogenetically closer to eukaryotes than other archaea, together with improved knowledge of microbial ecology, impose new constraints on emerging models for the origin of the eukaryotic cell (eukaryogenesis). Long-held views are metamorphosing in favour of symbiogenetic models based on metabolic interactions between archaea and bacteria. These include the classical Searcy's and Hydrogen hypothesis, and the more recent Reverse Flow and Entangle-Engulf-Endogenize models. Two decades ago, we put forward the Syntrophy hypothesis for the origin of eukaryotes based on a tripartite metabolic symbiosis involving a methanogenic archaeon (future nucleus), a fermentative myxobacterial-like deltaproteobacterium (future eukaryotic cytoplasm) and a metabolically versatile methanotrophic alphaproteobacterium (future mitochondrion). A refined version later proposed the evolution of the endomembrane and nuclear membrane system by invagination of the deltaproteobacterial membrane. Here, we adapt the Syntrophy hypothesis to contemporary knowledge, shifting from the original hydrogen and methane-transfer-based symbiosis (HM Syntrophy) to a tripartite hydrogen and sulfur-transfer-based model (HS Syntrophy). We propose a sensible ecological scenario for eukaryogenesis in which eukaryotes originated in early Proterozoic microbial mats from the endosymbiosis of a hydrogen-producing Asgard archaeon within a complex sulfate-reducing deltaproteobacterium. Mitochondria evolved from versatile, facultatively aerobic, sulfide-oxidizing and, potentially, anoxygenic photosynthesizing alphaproteobacterial endosymbionts that recycled sulfur in the consortium. The HS Syntrophy hypothesis accounts for (endo)membrane, nucleus and metabolic evolution in a realistic ecological context. We compare and contrast the HS Syntrophy hypothesis to other models of eukaryogenesis, notably in terms of the mode and tempo of eukaryotic trait evolution, and discuss several model predictions and how these can be tested.},
}
@article {pmid32339893,
year = {2020},
author = {Pishchany, G},
title = {Applying microbial ecology to antimicrobial discovery.},
journal = {Current opinion in microbiology},
volume = {57},
number = {},
pages = {7-12},
doi = {10.1016/j.mib.2020.03.007},
pmid = {32339893},
issn = {1879-0364},
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/metabolism ; Bacterial Infections/microbiology ; *Drug Evaluation, Preclinical ; Drug Resistance, Bacterial ; Humans ; },
abstract = {Introduction of antibiotics into clinical use has contributed to some of the greatest improvements to public health in the 20th century. Most antibiotics are based on antimicrobials that were isolated from environmental microorganisms over 50 years ago, but emerging resistance requires discovery of new molecules and development of these molecules into therapeutics. Bioinformatic analyses of microbial genomes indicate that many more microbial bioactive molecules remain undiscovered. Understanding when, where, and why these molecules are produced informs efforts to tap into the hidden unexplored chemical diversity. Expanding the search to undersampled ecological niches and improving culturing techniques will ensure discovery of new antibiotics.},
}
@article {pmid32335713,
year = {2020},
author = {Sun, H and Zhang, Y and Tan, S and Zheng, Y and Zhou, S and Ma, QY and Yang, GP and Todd, JD and Zhang, XH},
title = {DMSP-Producing Bacteria Are More Abundant in the Surface Microlayer than Subsurface Seawater of the East China Sea.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {350-365},
doi = {10.1007/s00248-020-01507-8},
pmid = {32335713},
issn = {1432-184X},
support = {2016YFA0601303//National Key Research and Development Program of China/ ; 91751202//National Natural Science Foundation of China/ ; 41730530//National Natural Science Foundation of China/ ; 41476112//National Natural Science Foundation of China/ ; NE/N002385//Natural Environmental Research Council, UK, grants/ ; NE/P012671//Natural Environmental Research Council, UK, grants/ ; NE/S001352//Natural Environmental Research Council, UK, grants/ ; },
mesh = {Bacteria/classification/*isolation &amp; purification ; Bacterial Physiological Phenomena ; China ; Microbiota/*physiology ; Seawater/*microbiology ; Sulfonium Compounds/*metabolism ; },
abstract = {Microbial production and catabolism of dimethylsulfoniopropionate (DMSP), generating the climatically active gases dimethyl sulfide (DMS) and methanethiol (MeSH), have key roles in global carbon and sulfur cycling, chemotaxis, and atmospheric chemistry. Microorganisms in the sea surface microlayer (SML), the interface between seawater and atmosphere, likely play an important role in the generation of DMS and MeSH and their exchange to the atmosphere, but little is known about these SML microorganisms. Here, we investigated the differences between bacterial community structure and the distribution and transcription profiles of the key bacterial DMSP synthesis (dsyB and mmtN) and catabolic (dmdA and dddP) genes in East China Sea SML and subsurface seawater (SSW) samples. Per equivalent volume, bacteria were far more abundant (~ 7.5-fold) in SML than SSW, as were those genera predicted to produce DMSP. Indeed, dsyB (~ 7-fold) and mmtN (~ 4-fold), robust reporters for bacterial DMSP production, were also far more abundant in SML than SSW. In addition, the SML had higher dsyB transcripts (~ 3-fold) than SSW samples, which may contribute to the significantly higher DMSP level observed in SML compared with SSW. Furthermore, the abundance of bacteria with dmdA and their transcription were higher in SML than SSW samples. Bacteria with dddP and transcripts were also prominent, but less than dmdA and presented at similar levels in both layers. These data indicate that the SML might be an important hotspot for bacterial DMSP production as well as generating the climatically active gases DMS and MeSH, a portion of which are likely transferred to the atmosphere.},
}
@article {pmid32334223,
year = {2020},
author = {Gorski, G and Dailey, H and Fisher, AT and Schrad, N and Saltikov, C},
title = {Denitrification during infiltration for managed aquifer recharge: Infiltration rate controls and microbial response.},
journal = {The Science of the total environment},
volume = {727},
number = {},
pages = {138642},
doi = {10.1016/j.scitotenv.2020.138642},
pmid = {32334223},
issn = {1879-1026},
mesh = {Carbon ; *Denitrification ; *Groundwater ; Nitrates/analysis ; Soil ; },
abstract = {Managed aquifer recharge (MAR) systems can be designed and operated to improve water supply and quality simultaneously by creating favorable conditions for contaminant removal during infiltration through shallow soils. We present results from laboratory flow-through column experiments, using intact soil cores from two MAR sites, elucidating conditions that are favorable to nitrate (NO3) removal via microbial denitrification during infiltration. Experiments focused on quantitative relations between infiltration rate and the presence or absence of a carbon-rich permeable reactive barrier (PRB) on both amounts and rates of nitrate removal during infiltration and associated shifts in microbial ecology. Experiments were conducted using a range of infiltration rates relevant to MAR (0.3-1.4 m/day), with PRBs made of native soil (NS), woodchips (WC) and a 50:50 mixture of woodchips and native soil (MIX). The latter two (carbon-rich) PRB treatments led to statistically significant increases in the amount of nitrate removed by increasing zero-order denitrification rates, both within the PRB materials and in the underlying soil. The highest fraction of nitrate removal occurred at the lowest infiltration rates for all treatments. However, the highest nitrogen mass removal (∆NL) was observed at 0.4-0.7 m/day for both the WC and MIX treatments. In contrast, the maximum ∆NL for the NS treatment was observed at the lowest infiltration rates measured (~0.3 m/day). Further, both carbon-rich PRBs had a substantial impact on the soil microbial ecology in the underlying soil, with lower overall diversity and a greater relative abundance of groups known to degrade carbon and metabolize nitrogen. These results demonstrate that infiltration rates and carbon availability can combine to create favorable conditions for denitrification during infiltration for MAR and show how these factors shape and sustain the microbial community structures responsible for nutrient cycling in associated soils.},
}
@article {pmid32332139,
year = {2020},
author = {LaSarre, B and Deutschbauer, AM and Love, CE and McKinlay, JB},
title = {Covert Cross-Feeding Revealed by Genome-Wide Analysis of Fitness Determinants in a Synthetic Bacterial Mutualism.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {13},
pages = {},
pmid = {32332139},
issn = {1098-5336},
mesh = {Coculture Techniques ; Escherichia coli/*genetics ; *Genetic Fitness ; Genome-Wide Association Study ; Microbial Interactions/*genetics ; Rhodopseudomonas/*genetics ; Symbiosis/*genetics ; },
abstract = {Microbial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing Escherichia coli and Rhodopseudomonas palustris, wherein E. coli provides carbon to R. palustris in the form of glucose fermentation products and R. palustris fixes N2 gas and provides nitrogen to E. coli in the form of NH4[+] The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search for E. coli genes that influence fitness during cooperative growth with R. palustris RB-TnSeq revealed hundreds of genes that increased or decreased E. coli fitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. In addition, we discovered unexpected purine cross-feeding from R. palustris to E. coli, with coculture rescuing growth of an E. coli purine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictable a prioriIMPORTANCE Microbial communities impact life on Earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influenced Escherichia coli fitness during cooperative growth with a mutualistic partner, Rhodopseudomonas palustris Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen, E. coli fitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.},
}
@article {pmid32331569,
year = {2020},
author = {Moran, MC and Beck, LA and Richardson, CT},
title = {A Spectrum of Skin Disease: How Staphylococcus aureus Colonization, Barrier Dysfunction, and Cytokines Shape the Skin.},
journal = {The Journal of investigative dermatology},
volume = {140},
number = {5},
pages = {941-944},
pmid = {32331569},
issn = {1523-1747},
support = {T32 AI118689/AI/NIAID NIH HHS/United States ; U01 AI152011/AI/NIAID NIH HHS/United States ; U19 AI117673/AI/NIAID NIH HHS/United States ; },
mesh = {Cytokines ; *Dermatitis, Atopic ; Humans ; Skin ; *Staphylococcal Infections ; Staphylococcus aureus ; },
abstract = {Cytokines are key mediators of skin homeostasis and disease through their effects on keratinocytes, skin barrier integrity, immune activation, and microbial ecology. Sirobhushanam et al. (2020) suggest that the IFN signature in lupus erythematosus (LE) alters expression of epithelial barrier and adhesin genes, which, in turn, promotes Staphylococcus aureus colonization. This work highlights the need to better understand both barrier function and S. aureus colonization in LE, two new potential therapeutic targets for the treatment of LE.},
}
@article {pmid32328670,
year = {2020},
author = {Hanya, G and Tackmann, J and Sawada, A and Lee, W and Pokharel, SS and de Castro Maciel, VG and Toge, A and Kuroki, K and Otsuka, R and Mabuchi, R and Liu, J and Hatakeyama, M and Yamasaki, E and von Mering, C and Shimizu-Inatsugi, R and Hayakawa, T and Shimizu, KK and Ushida, K},
title = {Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {459-474},
doi = {10.1007/s00248-020-01515-8},
pmid = {32328670},
issn = {1432-184X},
support = {15KK0256//MEXT Grant-in-Aid for Promotion of Joint International Research (Fostering Joint International Research)/ ; 19KK0186//MEXT Grant-in-Aid for Promotion of Joint International Research (Fostering Joint International Research)/ ; 25291100//MEXT Grant-in-Aid for Scientific Research B/ ; 18H02508//MEXT Grant-in-Aid for Scientific Research B/ ; },
mesh = {Animals ; Bacteria/genetics/*metabolism ; Diet ; *Digestion ; *Feeding Behavior ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Macaca fuscata/*microbiology/*physiology ; Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; },
abstract = {Wild Japanese macaques (Macaca fuscata Blyth) living in the highland and lowland areas of Yakushima are known to have different diets, with highland individuals consuming more leaves. We aim to clarify whether and how these differences in diet are also reflected by gut microbial composition and fermentation ability. Therefore, we conduct an in vitro fermentation assay using fresh feces from macaques as inoculum and dry leaf powder of Eurya japonica Thunb. as a substrate. Fermentation activity was higher for feces collected in the highland, as evidenced by higher gas and butyric acid production and lower pH. Genetic analysis indicated separation of highland and lowland in terms of both community structure and function of the gut microbiota. Comparison of feces and suspension after fermentation indicated that the community structure changed during fermentation, and the change was larger for lowland samples. Analysis of the 16S rRNA V3-V4 barcoding region of the gut microbiota showed that community structure was clearly clustered between the two areas. Furthermore, metagenomic analysis indicated separation by gene and pathway abundance patterns. Two pathways (glycogen biosynthesis I and D-galacturonate degradation I) were enriched in lowland samples, possibly related to the fruit-eating lifestyle in the lowland. Overall, we demonstrated that the more leaf-eating highland Japanese macaques harbor gut microbiota with higher leaf fermentation ability compared with the more fruit-eating lowland ones. Broad, non-specific taxonomic and functional gut microbiome differences suggest that this pattern may be driven by a complex interplay between many taxa and pathways rather than single functional traits.},
}
@article {pmid32326329,
year = {2020},
author = {Dagher, DJ and de la Providencia, IE and Pitre, FE and St-Arnaud, M and Hijri, M},
title = {Arbuscular Mycorrhizal Fungal Assemblages Significantly Shifted upon Bacterial Inoculation in Non-Contaminated and Petroleum-Contaminated Environments.},
journal = {Microorganisms},
volume = {8},
number = {4},
pages = {},
pmid = {32326329},
issn = {2076-2607},
support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) have been shown to reduce plant stress and improve their health and growth, making them important components of the plant-root associated microbiome, especially in stressful conditions such as petroleum hydrocarbons (PHs) contaminated environments. Purposely manipulating the root-associated AMF assemblages in order to improve plant health and modulate their interaction with the rhizosphere microbes could lead to increased agricultural crop yields and phytoremediation performance by the host plant and its root-associated microbiota. In this study, we tested whether repeated inoculations with a Proteobacteria consortium influenced plant productivity and the AMF assemblages associated with the root and rhizosphere of four plant species growing either in non-contaminated natural soil or in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was performed in a randomized complete block design in four blocks with two factors: (1) substrate contamination (contaminated or not contaminated), and (2) inoculation (or not) with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over four months, after which the effect of treatments on plant biomass and petroleum hydrocarbon concentrations in the substrate were determined. MiSeq amplicon sequencing, targeting the 18S rRNA gene, was used to assess AMF community structures in the roots and rhizosphere of plants growing in both contaminated and non-contaminated substrates. We also investigated the contribution of plant identity and biotope (plant roots and rhizospheric soil) in shaping the associated AMF assemblages. Our results showed that while inoculation caused a significant shift in AMF communities, the substrate contamination had a much stronger influence on their structure, followed by the biotope and plant identity to a lesser extent. Moreover, inoculation significantly increased plant biomass production and was associated with a decreased petroleum hydrocarbons dissipation in the contaminated soil. The outcome of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with indigenous plants following repeated inoculation of a bacterial consortium. It highlights the dominance of soil chemical properties, such as petroleum hydrocarbon presence, over biotic factors and inputs, such as plant species and microbial inoculations, in determining the plant-associated arbuscular mycorrhizal fungi communities.},
}
@article {pmid32322922,
year = {2021},
author = {Huang, M and Chai, L and Jiang, D and Zhang, M and Jia, W and Huang, Y},
title = {Spatial Patterns of Soil Fungal Communities Are Driven by Dissolved Organic Matter (DOM) Quality in Semi-Arid Regions.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {202-214},
pmid = {32322922},
issn = {1432-184X},
support = {2016YFC0500903//National Key Research and Development Program of China/ ; 18Y01ESTCT//State Key Joint Laboratory of Environmental Simulation and Pollution Control/ ; },
mesh = {Desert Climate ; Ecosystem ; Fungi/genetics ; *Mycobiome ; *Soil ; Soil Microbiology ; },
abstract = {Soil fungi are ecologically important as decomposers, pathogens, and symbionts in nature. Understanding their biogeographic patterns and driving forces is pivotal to predict alterations arising from environmental changes in ecosystem. Dissolved organic matter (DOM) is an essential resource for soil fungi; however, the role of its quality in structuring fungal community patterns remains elusive. Here using Illumina MiSeq sequencing, we characterized total fungi and their functional groups in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China, which are currently suffering great pressure from climate change. Total fungi and their functional groups were all observed to exhibit significant biogeographic patterns which were primarily driven by environmental variables. DOM quality was the best and consistent predictor of diversity of both total fungi and functional groups. Specifically, plant-derived DOM was associated with greater diversity relative to microbe-dominated origins. In addition, fungal diversity linearly increased with increases in degree of humification in DOM. Similarly, among all measured environmental variables, DOM quality had the strongest effects on the community composition of total fungi and functional groups. Together, our work contributes to the factors underlying fungal biogeographic patterns and adds detail to the importance of DOM quality in structuring fungal communities.},
}
@article {pmid32320735,
year = {2020},
author = {Stevens, ML and Gonzalez, T and Schauberger, E and Baatyrbek Kyzy, A and Andersen, H and Spagna, D and Kalra, MK and Martin, LJ and Haslam, D and Herr, AB and Biagini Myers, JM and Khurana Hershey, GK},
title = {Simultaneous skin biome and keratinocyte genomic capture reveals microbiome differences by depth of sampling.},
journal = {The Journal of allergy and clinical immunology},
volume = {146},
number = {6},
pages = {1442-1445},
pmid = {32320735},
issn = {1097-6825},
support = {T32 GM063483/GM/NIGMS NIH HHS/United States ; U19 AI070235/AI/NIAID NIH HHS/United States ; UL1 TR001425/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Child ; *Dermatitis, Atopic/immunology/microbiology/pathology ; Female ; Gene Expression Regulation/*immunology ; Humans ; *Keratinocytes/immunology/microbiology/pathology ; Male ; Microbiota/*immunology ; *Skin/immunology/microbiology/pathology ; },
abstract = {Novel skin tape strip method allows for simultaneous collection of the skin microbiome and underlying host DNA and RNA, and reveals that microbial ecology is dependent on the depth of sampling.},
}
@article {pmid32317112,
year = {2020},
author = {Gryp, T and De Paepe, K and Vanholder, R and Kerckhof, FM and Van Biesen, W and Van de Wiele, T and Verbeke, F and Speeckaert, M and Joossens, M and Couttenye, MM and Vaneechoutte, M and Glorieux, G},
title = {Gut microbiota generation of protein-bound uremic toxins and related metabolites is not altered at different stages of chronic kidney disease.},
journal = {Kidney international},
volume = {97},
number = {6},
pages = {1230-1242},
doi = {10.1016/j.kint.2020.01.028},
pmid = {32317112},
issn = {1523-1755},
mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Indican ; *Renal Insufficiency, Chronic/diagnosis ; *Toxins, Biological ; *Uremia ; },
abstract = {Chronic kidney disease (CKD) is characterized by accumulation of protein-bound uremic toxins such as p-cresyl sulfate, p-cresyl glucuronide, indoxyl sulfate and indole-3-acetic acid, which originate in the gut. Intestinal bacteria metabolize aromatic amino acids into p-cresol and indole, (further conjugated in the colon mucosa and liver) and indole-3-acetic acid. Here we measured fecal, plasma and urine metabolite concentrations; the contribution of gut bacterial generation to plasma protein-bound uremic toxins accumulation; and influx into the gut of circulating protein-bound uremic toxins at different stages of CKD. Feces, blood and urine were collected from 14 control individuals and 141 patients with CKD. Solutes were quantified by ultra-high performance liquid chromatography. To assess the rate of bacterial generation of p-cresol, indole and indole-3-acetic acid, fecal samples were cultured ex vivo. With CKD progression, an increase in protein-bound uremic toxins levels was observed in plasma, whereas the levels of these toxins and their precursors remained the same in feces and urine. Anaerobic culture of fecal samples showed no difference in ex vivo p-cresol, indole and indole-3-acetic acid generation. Therefore, differences in plasma protein-bound uremic toxins levels between different CKD stages cannot be explained by differences in bacterial generation rates in the gut, suggesting retention due to impaired kidney function as the main contributor to their increased plasma levels. Thus, as fractional clearance decreased with the progression of CKD, tubular clearance appeared to be more affected than the glomerular filtration rate, and there was no net increase in protein-bound uremic toxins influx into the gut lumen with increased plasma levels.},
}
@article {pmid32315566,
year = {2020},
author = {Hong, BY and Hoare, A and Cardenas, A and Dupuy, AK and Choquette, L and Salner, AL and Schauer, PK and Hegde, U and Peterson, DE and Dongari-Bagtzoglou, A and Strausbaugh, LD and Diaz, PI},
title = {The Salivary Mycobiome Contains 2 Ecologically Distinct Mycotypes.},
journal = {Journal of dental research},
volume = {99},
number = {6},
pages = {730-738},
pmid = {32315566},
issn = {1544-0591},
support = {M01 RR006192/RR/NCRR NIH HHS/United States ; R01 DE021578/DE/NIDCR NIH HHS/United States ; },
mesh = {Adult ; Aged ; Bacteria ; Cross-Sectional Studies ; Female ; Fungi ; Humans ; Malassezia ; Male ; Middle Aged ; *Mycobiome/genetics ; },
abstract = {A broad range of fungi has been detected in molecular surveys of the oral mycobiome. However, knowledge is still lacking on interindividual variability of these communities and the ecologic and clinical significance of oral fungal commensals. In this cross-sectional study, we use internal transcribed spacer 1 amplicon sequencing to evaluate the salivary mycobiome in 59 subjects, 36 of whom were scheduled to receive cancer chemotherapy. Analysis of the broad population structure of fungal communities in the whole cohort identified 2 well-demarcated genus-level community types (mycotypes), with Candida and Malassezia as the main taxa driving cluster partitioning. The Candida mycotype had lower diversity than the Malassezia mycotype and was positively correlated with cancer and steroid use in these subjects, smoking, caries, utilizing a removable prosthesis, and plaque index. Mycotypes were also associated with metabolically distinct bacteria indicative of divergent oral environments, with aciduric species enriched in the Candida mycotype and inflammophilic bacteria increased in the Malassezia mycotype. Similar to their fungal counterparts, coexisting bacterial communities associated with the Candida mycotype showed lower diversity than those associated with the Malassezia mycotype, suggesting that common environmental pressures affected bacteria and fungi. Mycotypes were also seen in an independent cohort of 24 subjects, in which cultivation revealed Malassezia as viable oral mycobiome members, although the low-abundance Malassezia sympodialis was the only Malassezia species recovered. There was a high degree of concordance between the molecular detection and cultivability of Candida, while cultivation showed low sensitivity for detection of the Malassezia mycotype. Overall, our work provides insights into the oral mycobiome landscape, revealing 2 community classes with apparently distinct ecologic constraints and specific associations with coexisting bacteria and clinical parameters. The utility of mycotypes as biomarkers for oral diseases warrants further study.},
}
@article {pmid32315331,
year = {2020},
author = {Nigro, LM and Elling, FJ and Hinrichs, KU and Joye, SB and Teske, A},
title = {Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231676},
pmid = {32315331},
issn = {1932-6203},
mesh = {Archaea/classification/genetics ; DNA, Archaeal/classification/genetics ; *Ecosystem ; Geologic Sediments/chemistry/classification/*microbiology ; Gulf of Mexico ; RNA, Ribosomal, 16S/classification/genetics ; Salinity ; Seawater/chemistry/*microbiology ; Sulfates/chemistry ; },
abstract = {In deep ocean hypersaline basins, the combination of high salinity, unusual ionic composition and anoxic conditions represents significant challenges for microbial life. We used geochemical porewater characterization and DNA sequencing based taxonomic surveys to enable environmental and microbial characterization of anoxic hypersaline sediments and brines in the Orca Basin, the largest brine basin in the Gulf of Mexico. Full-length bacterial 16S rRNA gene clone libraries from hypersaline sediments and the overlying brine were dominated by the uncultured halophilic KB1 lineage, Deltaproteobacteria related to cultured sulfate-reducing halophilic genera, and specific lineages of heterotrophic Bacteroidetes. Archaeal clones were dominated by members of the halophilic methanogen genus Methanohalophilus, and the ammonia-oxidizing Marine Group I (MG-I) within the Thaumarchaeota. Illumina sequencing revealed higher phylum- and subphylum-level complexity, especially in lower-salinity sediments from the Orca Basin slope. Illumina and clone library surveys consistently detected MG-I Thaumarchaeota and halotolerant Deltaproteobacteria in the hypersaline anoxic sediments, but relative abundances of the KB1 lineage differed between the two sequencing methods. The stable isotopic composition of dissolved inorganic carbon and methane in porewater, and sulfate concentrations decreasing downcore indicated methanogenesis and sulfate reduction in the anoxic sediments. While anaerobic microbial processes likely occur at low rates near their maximal salinity thresholds in Orca Basin, long-term accumulation of reaction products leads to high methane concentrations and reducing conditions within the Orca Basin brine and sediments.},
}
@article {pmid32314003,
year = {2020},
author = {Parker, ES and Newton, ILG and Moczek, AP},
title = {(My Microbiome) Would Walk 10,000 miles: Maintenance and Turnover of Microbial Communities in Introduced Dung Beetles.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {435-446},
doi = {10.1007/s00248-020-01514-9},
pmid = {32314003},
issn = {1432-184X},
support = {1901680//Division of Integrative Organismal Systems/ ; 1256689//Division of Integrative Organismal Systems/ ; 61369//John Templeton Foundation/ ; },
mesh = {Animals ; Australian Capital Territory ; Bacteria/*isolation &amp; purification ; Coleoptera/*microbiology ; Introduced Species ; Italy ; *Microbiota ; *Symbiosis ; West Virginia ; },
abstract = {Host-associated microbes facilitate diverse biotic and abiotic interactions between hosts and their environments. Experimental alterations of host-associated microbial communities frequently decrease host fitness, yet much less is known about if and how host-microbiome interactions are altered by natural perturbations, such as introduction events. Here, we begin to assess this question in Onthophagus dung beetles, a species-rich and geographically widely distributed genus whose members rely on vertically transmitted microbiota to support normal development. Specifically, we investigated to what extent microbiome community membership shifts during host introduction events and the relative significance of ancestral associations and novel environmental conditions in the structuring of microbial communities of introduced host species. Our results demonstrate that both evolutionary history and local environmental forces structure the microbial communities of these animals, but that their relative importance is shaped by the specific circumstances that characterize individual introduction events. Furthermore, we identify microbial taxa such as Dysgonomonas that may constitute members of the core Onthophagus microbiome regardless of host population or species, but also Wolbachia which associates with Onthophagus beetles in a species or even population-specific manner. We discuss the implications of our results for our understanding of the evolutionary ecology of symbiosis in dung beetles and beyond.},
}
@article {pmid32313622,
year = {2020},
author = {Böckelmann, J and Tremetsberger, K and Šumberová, K and Kohl, G and Grausgruber, H and Bernhardt, KG},
title = {Genetic variation in an ephemeral mudflat species: The role of the soil seed bank and dispersal in river and secondary anthropogenic habitats.},
journal = {Ecology and evolution},
volume = {10},
number = {8},
pages = {3620-3635},
pmid = {32313622},
issn = {2045-7758},
support = {P 24558/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Many ephemeral mudflat species, which rely on a soil seed bank to build up the next generation, are endangered in their natural habitat due to the widespread regulation of rivers. The aim of the present study was to elucidate the role of the soil seed bank and dispersal for the maintenance of genetic diversity in populations of near-natural river habitats and anthropogenic habitats created by traditional fish farming practices using Cyperus fuscus as a model. Using microsatellite markers, we found no difference in genetic diversity levels between soil seed bank and above-ground population and only moderate differentiation between the two fractions. One possible interpretation is the difference in short-term selection during germination under specific conditions (glasshouse versus field) resulting in an ecological filtering of genotypes out of the reservoir in the soil. River populations harbored significantly more genetic diversity than populations from the anthropogenic pond types. We suggest that altered levels and patterns of dispersal together with stronger selection pressures and historical bottlenecks in anthropogenic habitats are responsible for the observed reduction in genetic diversity. Dispersal is also supposed to largely prohibit genetic structure across Europe, although there is a gradient in private allelic richness from southern Europe (high values) to northern, especially north-western, Europe (low values), which probably relates to postglacial expansion out of southern and/or eastern refugia.},
}
@article {pmid32313597,
year = {2020},
author = {Parks, S and Joyner, JL and Nusnbaum, M},
title = {Reaching a Large Urban Undergraduate Population through Microbial Ecology Course-Based Research Experiences.},
journal = {Journal of microbiology &amp; biology education},
volume = {21},
number = {1},
pages = {},
pmid = {32313597},
issn = {1935-7877},
abstract = {Traditional postsecondary education is making progress on embracing the diversity of student backgrounds and experiences while preparing them for the demands of STEM careers. Course-based undergraduate research experiences (CUREs) are effective tools to concurrently achieve many student and faculty goals: facilitating training of students, building career competencies, generating publishable research results and enabling research experiences where students apply their knowledge and interest. Georgia State University is not unique with a high student demand for research experiences and mentors that is greater than traditional research faculty labs can accommodate. Georgia State University is, however, unique in that it is a demographically diverse campus which serves minority and non-traditional students (i.e., second career and veterans) and is also rapidly growing. Therefore, to enhance the microbiology curriculum and facilitate authentic research experiences for the growing number of biology majors, a cluster of course-based research experiences in microbial ecology was developed. A former research lab space was converted to a collaborative teaching lab to serve the growth in course offerings, as well as to accommodate multiple microbial ecology research projects occurring in the same space. The courses offered appeal to students, build on the strengths of faculty experiences, and facilitate collaboration amongst students and with the greater Atlanta community. To ensure that our CUREs are accessible to the diverse students in our department, we addressed a variety of logistical and curricular challenges. Solutions to such challenges align with the goals of the university to offer research and signature experiences to ensure students are included and trained in STEM skills.},
}
@article {pmid32311222,
year = {2020},
author = {De Vrieze, J and De Mulder, T and Matassa, S and Zhou, J and Angenent, LT and Boon, N and Verstraete, W},
title = {Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals.},
journal = {Microbial biotechnology},
volume = {13},
number = {4},
pages = {829-843},
pmid = {32311222},
issn = {1751-7915},
mesh = {Goals ; Humans ; *Microbiota ; Stochastic Processes ; *Sustainable Development ; },
abstract = {Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.},
}
@article {pmid32310264,
year = {2020},
author = {Liu, K and Liu, Y and Hu, A and Wang, F and Chen, Y and Gu, Z and Anslan, S and Hou, J},
title = {Different community assembly mechanisms underlie similar biogeography of bacteria and microeukaryotes in Tibetan lakes.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {6},
pages = {},
doi = {10.1093/femsec/fiaa071},
pmid = {32310264},
issn = {1574-6941},
mesh = {Bacteria/genetics ; Biodiversity ; *Lakes ; *Microbiota ; Salinity ; Tibet ; },
abstract = {Geographic patterns of bacteria and microeukaryotes have attracted increasing attention. However, mechanisms underlying geographic patterns in the community composition of both microbial groups are still poorly resolved. In particular, knowledge of whether bacterial communities and microeukaryotic communities are subject to the same or different assembly mechanisms is still limited. In this study, we investigated the biogeographic patterns of bacterial and microeukaryotic communities of 23 lakes on the Tibetan Plateau and quantified the relative influence of assembly mechanisms in shaping both microbial communities. Results showed that water salinity was the major driving force in controlling the community structures of bacteria and microeukaryotes. Although bacterial and microeukaryotic communities exhibited similar distance-decay patterns, the bacterial communities were mainly governed by environmental filtering (a niche-related process), whereas microeukaryotic communities were strongly driven by dispersal limitation (a neutral-related process). Furthermore, we found that bacteria exhibited wider niche breadths and higher dispersal ability but lower community stabilities than microeukaryotes. The similar distribution patterns but contrasting assembly mechanisms effecting bacteria and microeukaryotes resulted from the differences in dispersal ability and community stability. Our results highlight the importance of considering organism types in studies of the assembly mechanisms that shape microbial communities in microbial ecology.},
}
@article {pmid32307553,
year = {2020},
author = {Lu, J and Zhang, X and Qiu, Q and Chen, J and Xiong, J},
title = {Identifying Potential Polymicrobial Pathogens: Moving Beyond Differential Abundance to Driver Taxa.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {447-458},
doi = {10.1007/s00248-020-01511-y},
pmid = {32307553},
issn = {1432-184X},
support = {31872693//National Natural Science Foundation of China/ ; LR19C030001//the Natural Science Fund for Distinguished Young Scholars of Zhejiang Province/ ; 2015C110018//the Technology Innovation Team of Ningbo/ ; },
mesh = {Actinobacteria/isolation &amp; purification/physiology ; Animals ; Aquaculture ; Bacteria/*isolation &amp; purification ; China ; *Gastrointestinal Microbiome ; Penaeidae/*microbiology ; Vibrio/physiology ; },
abstract = {It is now recognized that some diseases of aquatic animals are attributed to polymicrobial pathogens infection. Thus, the traditional view of "one pathogen, one disease" might mislead the identification of multiple pathogens, which in turn impedes the design of probiotics. To address this gap, we explored polymicrobial pathogens based on the origin and timing of increased abundance over shrimp white feces syndrome (WFS) progression. OTU70848 Vibrio fluvialis, OTU35090 V. coralliilyticus, and OTU28721 V. tubiashii were identified as the primary colonizers, whose abundances increased only in individuals that eventually showed disease signs but were stable in healthy subjects over the same timeframe. Notably, the random Forest model revealed that the profiles of the three primary colonizers contributed an overall 91.4% of diagnosing accuracy of shrimp health status. Additionally, NetShift analysis quantified that the three primary colonizers were important "drivers" in the gut microbiotas from healthy to WFS shrimp. For these reasons, the primary colonizers were potential pathogens that contributed to the exacerbation of WFS. By this logic, we further identified a few "drivers" commensals in healthy individuals, such as OUT50531 Demequina sediminicola and OTU_74495 Ruegeria lacuscaerulensis, which directly antagonized the three primary colonizers. The predicted functional pathways involved in energy metabolism, genetic information processing, terpenoids and polyketides metabolism, lipid and amino acid metabolism significantly decreased in diseased shrimp compared with those in healthy cohorts, in concordant with the knowledge that the attenuations of these functional pathways increase shrimp sensitivity to pathogen infection. Collectively, we provide an ecological framework for inferring polymicrobial pathogens and designing antagonized probiotics by quantifying their changed "driver" feature that intimately links shrimp WFS progression. This approach might generalize to the exploring disease etiology for other aquatic animals.},
}
@article {pmid32303845,
year = {2020},
author = {Yu, L and Wang, Y and Su, X and Fu, Y and Ma, F and Guo, H},
title = {Biodiversity, isolation and genome analysis of sulfamethazine-degrading bacteria using high-throughput analysis.},
journal = {Bioprocess and biosystems engineering},
volume = {43},
number = {8},
pages = {1521-1531},
doi = {10.1007/s00449-020-02345-1},
pmid = {32303845},
issn = {1615-7605},
mesh = {*Biodiversity ; *Genome, Bacterial ; *Microbial Consortia ; *Micrococcaceae/genetics/isolation &amp; purification/metabolism ; Sulfamethazine/*metabolism ; Wastewater/microbiology ; *Water Microbiology ; },
abstract = {Sulfamethazine (SM2) is one of the sulfonamide antibiotics that is frequently detected in aquatic environment. Given the complex structure of SM2 and its potential threat to the environment, it is necessary to determine the degradation behavior of high-concentration SM2. The mechanisms of community structure and diversity of activated sludge were analyzed. A novel SM2-degrading strain YL1 was isolated which can degrade SM2 with high concentration of 100 mg L[-1]. Strain YL1 was identified as Paenarthrobacter ureafaciens and there was also a significant increase in the genus during acclimation. Additional SM2 metabolic mechanisms and genomic information of YL1 were analyzed for further research. The succession of the community structure also investigated the effect of SM2 on the activated sludge. This result not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of the environmental bioprocesses for treatment of antimicrobial-bearing waste streams.},
}
@article {pmid32303543,
year = {2020},
author = {Minich, JJ and Poore, GD and Jantawongsri, K and Johnston, C and Bowie, K and Bowman, J and Knight, R and Nowak, B and Allen, EE},
title = {Microbial Ecology of Atlantic Salmon (Salmo salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {12},
pages = {},
pmid = {32303543},
issn = {1098-5336},
support = {F30 CA243480/CA/NCI NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Aquaculture ; Biofilms ; *Built Environment ; *Fisheries ; Gastrointestinal Contents/microbiology ; Gills/microbiology ; Microbiota/*physiology ; Mucous Membrane/*microbiology ; Salmo salar ; Skin/microbiology ; Water Microbiology ; },
abstract = {Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, commercial fishing through wild stock enhancements, and aquaculture production. Flowthrough (FT) hatcheries require more water than recirculating aquaculture systems (RAS), which enable up to 99% of their water to be recycled, thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of three Atlantic salmon hatcheries (RAS n = 2, FT n = 1). Gill, skin, and digesta from six juvenile fish along with tank biofilms and water were sampled from tanks in each of the hatcheries (60 fish across 10 tanks) to assess the built environment and mucosal microbiota using 16S rRNA gene sequencing. The water and tank biofilm had more microbial richness than fish mucus, while skin and digesta from RAS fish had 2 times the richness of FT fish. Body sites each had unique microbiomes (P < 0.001) and were influenced by hatchery system type (P < 0.001), with RAS being more similar. A strong association between the tank and fish microbiome was observed. Water and tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin, and digesta communities were more similar to that in the origin tank biofilm than those in all other experimental tanks, suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. Lastly, microbial diversity and mucous cell density were positively associated with fish growth and length. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome, with the skin microbiome as an important intermediate.IMPORTANCE Atlantic salmon, Salmo salar, is the most farmed marine fish worldwide, with an annual production of 2,248 million metric tons in 2016. Salmon hatcheries are increasingly changing from flowthrough toward recirculating aquaculture system (RAS) design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies of hatcheries have focused either on the fish mucosal microbiota or on the built environment microbiota but have not combined the two to understand their interactions. Our study evaluates how the water and tank biofilm microbiota influences the fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and, furthermore, how this can influence fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for beneficial phenotypes.},
}
@article {pmid32300926,
year = {2020},
author = {Barman, D and Dkhar, MS},
title = {Seasonal Variation Influence Endophytic Actinobacterial Communities of Medicinal Plants from Tropical Deciduous Forest of Meghalaya and Characterization of Their Plant Growth-Promoting Potentials.},
journal = {Current microbiology},
volume = {77},
number = {8},
pages = {1689-1698},
pmid = {32300926},
issn = {1432-0991},
mesh = {Actinobacteria/genetics/*physiology ; Biodiversity ; Endophytes/*physiology ; Forests ; *Host Microbial Interactions ; India ; Phylogeny ; Plant Roots/microbiology ; Plants, Medicinal/classification/*growth &amp; development/*microbiology ; *Seasons ; Species Specificity ; Tropical Climate ; },
abstract = {The endophytic actinobacteria constitute a diverse community which has vast potential importance that may be exploited in pharmaceutical, agricultural, and biotechnological industries. However, the effects of seasonal changes on distribution of endophytic actinobacteria in medicinal plants of Meghalaya are largely uncharacterized. Here, we investigated host and seasonal influence on diversity of endophytic actinobacteria residing in roots of six medicinal plant species of Meghalaya. A total of 493 cultivable endophytic actinobacterial isolates representing 41 species were obtained from root segments of six plant species which had been collected during four different seasons of 2011-2012 and 2012-2013. Among the host plant species, maximum actinobacterial colonization was observed in Costus speciosus and minimum in Potentilla fulgens. In regard to seasons, the highest actinobacterial colonization and relative abundance were observed during summer season and least was recorded during the winter season. It was ascertained that though endophytic actinobacteria have varying capacity to colonize in different plant species during the seasons, colonization is not found to be species-specific. Culture-independent attempt also inferred that actinobacterial community varied amongst the six medicinal plants during the different seasons. Hence, seasons are influential factors in the colonization capacity of endophytic actinobacterial community. Furthermore, plant growth-promoting activities were recorded in 34.15% of the isolates. Hence, these results indicate that endophytic actinobacteria from the selected medicinal plants also represent an important source of plant growth-promoting bioactive metabolites.},
}
@article {pmid32300830,
year = {2020},
author = {Zhang, W and Gu, Q and Niu, J and Wang, JJ},
title = {The RNA Virome and Its Dynamics in an Invasive Fruit Fly, Bactrocera dorsalis, Imply Interactions Between Host and Viruses.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {423-434},
doi = {10.1007/s00248-020-01506-9},
pmid = {32300830},
issn = {1432-184X},
support = {31701846//National Natural Science Foundation of China/ ; CARS-26//Earmarked Fund for Modern Agro-industry Technology Research System/ ; },
mesh = {Animals ; Female ; *Host Microbial Interactions ; Male ; RNA Viruses/classification/*isolation &amp; purification/physiology ; RNA, Viral/analysis ; Tephritidae/immunology/*virology ; *Virome ; },
abstract = {The oriental fruit fly, Bactrocera dorsalis (Hendel), is an important invasive agricultural insect pest with a wide host range, and has spread around the world over the last century. This evolutionary trait may have arisen primarily from interactions between B. dorsalis and other invertebrates that share the same ecological niches. The invasive behavior of B. dorsalis also frequently exposes them to diverse species of viruses. Thereby, RNA viromes may be useful microbial markers to understand the ecological evolution of B. dorsalis as well as to investigate virus-host interactions. Here, we reported eight novel RNA viruses in B. dorsalis of a lab colony, including four positive-strand RNA viruses, two negative-strand RNA viruses, and two double-stranded RNA viruses using high-throughput sequencing technology. Analysis of the virus-derived small RNAs suggested that most of these viruses may be active and trigger the host antiviral RNAi responses. The viruses were also detected in various geographical populations of B. dorsalis, implying that there is a strong association between the viromes and host. In addition, these viruses infected specific fly tissues, predominately the central nervous system and gut. Furthermore, we explored the dynamics of the viruses when hosts were exposed to short- or long-term stressors, which showed that titers of some viruses were responsively altered in the stressed B. dorsalis. The discovery of these viruses may enrich our understanding of the species diversity of RNA viruses and also provide information on viruses in association with host adaptation in insects.},
}
@article {pmid32300653,
year = {2020},
author = {Inoue, K and Tsunoda, SP and Singh, M and Tomida, S and Hososhima, S and Konno, M and Nakamura, R and Watanabe, H and Bulzu, PA and Banciu, HL and Andrei, A&#x15e; and Uchihashi, T and Ghai, R and Béjà, O and Kandori, H},
title = {Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H[+] pumps.},
journal = {Science advances},
volume = {6},
number = {15},
pages = {eaaz2441},
pmid = {32300653},
issn = {2375-2548},
mesh = {Archaea/genetics/*metabolism ; Cell Membrane/metabolism ; Fluorescent Antibody Technique ; Ion Channel Gating/*radiation effects ; Light ; Models, Molecular ; Multigene Family ; Mutation ; Protein Conformation ; Proton Pumps/chemistry/genetics/*metabolism ; Rhodopsin/chemistry/genetics/*metabolism ; Spectroscopy, Fourier Transform Infrared ; Structure-Activity Relationship ; },
abstract = {Schizorhodopsins (SzRs), a rhodopsin family first identified in Asgard archaea, the archaeal group closest to eukaryotes, are present at a phylogenetically intermediate position between typical microbial rhodopsins and heliorhodopsins. However, the biological function and molecular properties of SzRs have not been reported. Here, SzRs from Asgardarchaeota and from a yet unknown microorganism are expressed in Escherichia coli and mammalian cells, and ion transport assays and patch clamp analyses are used to demonstrate SzR as a novel type of light-driven inward H[+] pump. The mutation of a cytoplasmic glutamate inhibited inward H[+] transport, suggesting that it functions as a cytoplasmic H[+] acceptor. The function, trimeric structure, and H[+] transport mechanism of SzR are similar to that of xenorhodopsin (XeR), a light-driven inward H[+] pumping microbial rhodopsins, implying that they evolved convergently. The inward H[+] pump function of SzR provides new insight into the photobiological life cycle of the Asgardarchaeota.},
}
@article {pmid32300619,
year = {2020},
author = {Poirier, S and Luong, NM and Anthoine, V and Guillou, S and Membré, JM and Moriceau, N and Rezé, S and Zagorec, M and Feurer, C and Frémaux, B and Jeuge, S and Robieu, E and Champomier-Vergès, M and Coeuret, G and Cauchie, E and Daube, G and Korsak, N and Coroller, L and Desriac, N and Desmonts, MH and Gohier, R and Werner, D and Loux, V and Rué, O and Dohollou, MH and Defosse, T and Chaillou, S},
title = {Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere.},
journal = {Data in brief},
volume = {30},
number = {},
pages = {105453},
pmid = {32300619},
issn = {2352-3409},
abstract = {Data in this article provide detailed information on the diversity of bacterial communities present on 576 samples of raw pork or poultry sausages produced industrially in 2017. Bacterial growth dynamics and diversity were monitored throughout the refrigerated storage period to estimate the impact of packaging atmosphere and the use of potassium lactate as chemical preservative. The data include several types of analysis aiming at providing a comprehensive microbial ecology of spoilage during storage and how the process parameters do influence this phenomenon. The analysis includes: the gas content in packaging, pH, chromametric measurements, plate counts (total mesophilic aerobic flora and lactic acid bacteria), sensorial properties of the products, meta-metabolomic quantification of volatile organic compounds and bacterial community metagenetic analysis. Bacterial diversity was monitored using two types of amplicon sequencing (16S rRNA and GyrB encoding genes) at different time points for the different conditions (576 samples for gyrB and 436 samples for 16S rDNA). Sequencing data were generated by using Illumina MiSeq. The sequencing data have been deposited in the bioproject PRJNA522361. Samples accession numbers vary from SAMN10964863 to SAMN10965438 for gyrB amplicon and from SAMN10970131 to SAMN10970566 for 16S.},
}
@article {pmid32300601,
year = {2020},
author = {Gaspardo, A and Zannoni, A and Turroni, S and Barone, M and Sabetti, MC and Zanoni, RG and Forni, M and Brigidi, P and Pietra, M},
title = {Influence of Lactobacillus kefiri on Intestinal Microbiota and Fecal IgA Content of Healthy Dogs.},
journal = {Frontiers in veterinary science},
volume = {7},
number = {},
pages = {146},
pmid = {32300601},
issn = {2297-1769},
abstract = {The increasing incidence of gastrointestinal tract pathologies in dogs and the worrisome topic of antibiotic resistance have raised the need to look for new therapeutic frontiers. Of these, the use of probiotics represents a potential therapeutic alternative. Lactobacillus kefiri (Lk) is a species of Lactobacillus isolated from kefir. Previous studies have demonstrated that its administration in mice downregulates the expression of proinflammatory mediators and increases anti-inflammatory molecules in the gut immune system. It also regulates intestinal homeostasis, incrementing immunoglobulin A (IgA) secretion. Since Lk has never been studied as a single probiotic in dogs, the aim of this study was to evaluate the safety of Lk in dogs, and its effect on IgA secretion and on intestinal microbiota composition. Ten healthy dogs without a history of gastrointestinal diseases were included. The dogs received Lk at a dose of 10[7] live microorganisms orally, once daily for 30 days. The fecal samples were tested before administration, in the middle, at the end, and 30 days after discontinuation. The IgA secretion concentration and the microbiota composition were evaluated on the fecal samples. The results in this study suggested that Lk did not influence the concentration of IgA, nor significant changes of the intestinal microbiota were observed during and after the treatment. Therefore, additional studies are needed to investigate if a higher daily dosage of Lk can influence the intestinal homeostasis of dogs.},
}
@article {pmid32300339,
year = {2020},
author = {Scoma, A and Khor, WC and Coma, M and Heyer, R and Props, R and Schoelynck, J and Bouts, T and Benndorf, D and Li, D and Zhang, H and Rabaey, K},
title = {Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to Lactate.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {530},
pmid = {32300339},
issn = {1664-302X},
abstract = {The giant panda is known worldwide for having successfully moved to a diet almost exclusively based on bamboo. Provided that no lignocellulose-degrading enzyme was detected in panda's genome, bamboo digestion is believed to depend on its gut microbiome. However, pandas retain the digestive system of a carnivore, with retention times of maximum 12 h. Cultivation of their unique gut microbiome under controlled laboratory conditions may be a valid tool to understand giant pandas' dietary habits, and provide valuable insights about what component of lignocellulose may be metabolized. Here, we collected gut microbiomes from fresh fecal samples of a giant panda (either entirely green or yellow stools) and supplied them with green leaves or yellow pith (i.e., the peeled stem). Microbial community composition was substrate dependent, and resulted in markedly different fermentation profiles, with yellow pith fermented to lactate and green leaves to lactate, acetate and ethanol, the latter to strikingly high concentrations (∼3%, v:v, within 3.5 h). Microbial metaproteins pointed to hemicellulose rather than cellulose degradation. The alpha-amylase from the giant panda (E.C. 3.2.1.1) was the predominant identified metaprotein, particularly in reactors inoculated with pellets derived from fecal samples (up to 60%). Gut microbiomes assemblage was most prominently impacted by the change in substrate (either leaf or pith). Removal of soluble organics from inocula to force lignocellulose degradation significantly enriched Bacteroides (in green leaf) and Escherichia/Shigella (in yellow pith). Overall, different substrates (either leaf or pith) markedly shaped gut microbiome assemblies and fermentation profiles. The biochemical profile of fermentation products may be an underestimated factor contributing to explain the peculiar dietary behavior of giant pandas, and should be implemented in large scale studies together with short-term lab-scale cultivation of gut microbiomes.},
}
@article {pmid32298910,
year = {2020},
author = {Dasgupta, S and Podder, A and Goel, R},
title = {Response of an aerobic granular and conventional flocculated reactors against changing feed composition from simple composition to more complex.},
journal = {Chemosphere},
volume = {253},
number = {},
pages = {126694},
doi = {10.1016/j.chemosphere.2020.126694},
pmid = {32298910},
issn = {1879-1298},
mesh = {Aerobiosis ; Bacteria/classification ; Bioreactors ; Flocculation ; Polyphosphates ; Sewage ; Waste Disposal, Fluid/*methods ; Wastewater ; },
abstract = {This research evaluated the effect of changing feed composition on the performances of a conventional activated sludge (CAS) and an aerobic granular sludge (AGS) reactor operated simultaneously. Both reactors were initially fed with 100% synthetic feed. In a stepwise manner, the feed composition was slowly changed to real primary effluent collected from a local wastewater treatment plant. After an initial stabilization period, both reactors could achieve more than 90% NH4[+]-N removal. However, PO4[3-]-P removal eventually reached to a maximum of 92% in the AGS and 88% in the CAS. COD removal in both reactors was least affected, with the lowest percent removal of 81 ± 3% achieved in AGS and 62 ± 4% in CAS respectively when fed with 100% real wastewater. Despite granule breakage the AGS reactor was able to remove the pollutants (COD, N, P). The abundance of Candidatus Accumulibacter, a polyphosphate accumulating organism, in the AGS system increased over the operational phases: II (6.2%), III (10.32%), and IV (11.9%). While in CAS, it increased from phase I to phase II (12.6%), but decreased in phase III to 9.9%. Genus-based classification revealed a successive increase in the relative abundance of Nitrospira to 11.05% during Phase III and 10.3% during Phase IV in the AGS. In contrast with its presence in the CAS, which was, 3.4% during Phase III and 9.5% during Phase IV.},
}
@article {pmid32296869,
year = {2020},
author = {Procópio, L and Pádula, M and van Elsas, JD and Seldin, L},
title = {Adaptative transcriptional response of Dietzia cinnamea P4 strain to sunlight simulator.},
journal = {Archives of microbiology},
volume = {202},
number = {7},
pages = {1701-1708},
doi = {10.1007/s00203-020-01879-y},
pmid = {32296869},
issn = {1432-072X},
mesh = {Actinobacteria/*genetics/*radiation effects ; Adaptation, Physiological ; Bacterial Proteins/genetics ; DNA Repair/genetics ; Gene Expression Regulation, Bacterial/*radiation effects ; Hydrolases/genetics ; Oxidoreductases/genetics ; Real-Time Polymerase Chain Reaction ; *Sunlight ; },
abstract = {Responses to sunlight exposure of the oil-degrading Dietzia cinnamea P4 strain were evaluated by transcriptional levels of SOS genes, photoreactivation and genes involved in tolerance to high levels of reactive oxygen species. The P4 strain was exposed for 1 and 2 h and the magnitude of level changes in the mRNA was evaluated by qPCR. The results described the activation of the SOS system, with the decline of the repressor lexA gene levels and the concomitant increase of recA and uvrAD genes levels. The genes that participate in the photoreactivation process were also responsive to sunlight. The phrB gene encoding deoxyribodipyrimidine photo-lyase had its expression increased after 1-h exposure, while the phytAB genes showed a progressive increase over the studied period. The protective genes against reactive oxygen species, catalases, superoxides, peroxidases, and thioredoxins, had their expression rates detected under the conditions validated in this study. These results show a fast and coordinated response of genes from different DNA repair and tolerance mechanisms employed by strain P4, suggesting a complex concerted protective action against environmental stressors.},
}
@article {pmid32296073,
year = {2020},
author = {Remizovschi, A and Carpa, R and Forray, FL and Chiriac, C and Roba, CA and Beldean-Galea, S and Andrei, A&#x218; and Szekeres, E and Baricz, A and Lupan, I and Rudi, K and Coman, C},
title = {Author Correction: Mud volcanoes and the presence of PAHs.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {6668},
doi = {10.1038/s41598-020-62513-x},
pmid = {32296073},
issn = {2045-2322},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid32293257,
year = {2020},
author = {Meparambu Prabhakaran, D and Ramamurthy, T and Thomas, S},
title = {Genetic and virulence characterisation of Vibrio parahaemolyticus isolated from Indian coast.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {62},
pmid = {32293257},
issn = {1471-2180},
mesh = {Actin Cytoskeleton/genetics ; Bacterial Proteins/genetics ; Bacterial Toxins/genetics ; Caco-2 Cells ; Hemolysin Proteins/genetics ; Humans ; India ; Phylogeny ; Plankton/*microbiology ; Seafood/*microbiology ; Type III Secretion Systems/genetics ; Vibrio Infections/genetics/metabolism/*microbiology ; Vibrio parahaemolyticus/classification/genetics/isolation &amp; purification/*pathogenicity ; Virulence Factors/*genetics ; Water Microbiology ; Zonula Occludens-1 Protein/genetics ; },
abstract = {BACKGROUND: V. parahaemolyticus is autochthonous to the marine environment and causes seafood-borne gastroenteritis in humans. Generally, V. parahaemolyticus recovered from the environment and/or seafood is thought to be non-pathogenic and the relationship between environmental isolates and acute diarrhoeal disease is poorly understood. In this study, we explored the virulence potential of environmental V. parahaemolyticus isolated from water, plankton and assorted seafood samples collected from the Indian coast.<br><br>RESULTS: Twenty-two V. parahaemolyticus isolates from seafood harboured virulence associated genes encoding the thermostable-direct haemolysin (TDH), TDH-related haemolysin (TRH), and Type 3 secretion systems (T3SS) and 95.5% of the toxigenic isolates had pandemic strain attributes (toxRS/new[+]). Nine serovars, with pandemic strain traits were newly identified and an O4:K36 tdh[-]trh[+]V. parahaemolyticus bearing pandemic marker gene was recognised for the first time. Results obtained by reverse transcription PCR showed trh, T3SS1 and T3SS2&#x3b2; to be functional in the seafood isolates. Moreover, the environmental strains were cytotoxic and could invade Caco-2 cells upon infection as well as induce changes to the tight junction protein, ZO-1 and the actin cytoskeleton.<br><br>CONCLUSION: Our study provides evidence that environmental isolates of V. parahaemolyticus are potentially invasive and capable of eliciting pathogenic characteristics typical of clinical strains and present a potential health risk. We also demonstrate that virulence of this pathogen is highly complex and hence draws attention for the need to investigate more reliable virulence markers in order to distinguish the environmental and clinical isolates, which will be crucial for the pathogenomics and control of this pathogen.},
}
@article {pmid32291478,
year = {2020},
author = {Gilbert, KJ and Bittleston, LS and Naive, MAK and Kiszewski, AE and Buenavente, PAC and Lohman, DJ and Pierce, NE},
title = {Investigation of an Elevational Gradient Reveals Strong Differences Between Bacterial and Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {334-349},
pmid = {32291478},
issn = {1432-184X},
mesh = {*Altitude ; Animals ; Arthropods ; Bacteria/classification/*isolation &amp; purification ; *Biodiversity ; Caryophyllales/*microbiology/parasitology ; Eukaryota ; Microbiota ; Philippines ; },
abstract = {Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and compare the effect of elevation on community structure to that of regulation by a number of plant factors. Patterns of community structure differed between bacteria and eukaryotes, despite their living together in the same aquatic microhabitats. Elevation influences community composition of eukaryotes to a significantly greater degree than it does bacteria. When examining pitcher characteristics, pitcher dimorphism has an effect on eukaryotes but not bacteria, while variation in pH levels strongly influences both taxa. Consistent with previous ecological studies, arthropod abundance in phytotelmata decreases with elevation, but some patterns of abundance differ between living inquilines and prey.},
}
@article {pmid32291352,
year = {2020},
author = {Leung, PM and Bay, SK and Meier, DV and Chiri, E and Cowan, DA and Gillor, O and Woebken, D and Greening, C},
title = {Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
pmid = {32291352},
issn = {2379-5077},
abstract = {Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation. Whereas photoautotrophs are restricted to specific niches in extreme deserts, metabolically versatile heterotrophs persist even in the hyper-arid topsoils of the Atacama Desert and Antarctica. At least three distinct strategies appear to allow such microorganisms to conserve energy in these oligotrophic environments: degradation of organic energy reserves, rhodopsin- and bacteriochlorophyll-dependent light harvesting, and oxidation of the atmospheric trace gases hydrogen and carbon monoxide. In turn, these principles are relevant for understanding the composition, functionality, and resilience of desert ecosystems, as well as predicting responses to the growing problem of desertification.},
}
@article {pmid32291348,
year = {2020},
author = {Mo, Z and Huang, P and Yang, C and Xiao, S and Zhang, G and Ling, F and Li, L},
title = {Meta-analysis of 16S rRNA Microbial Data Identified Distinctive and Predictive Microbiota Dysbiosis in Colorectal Carcinoma Adjacent Tissue.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
pmid = {32291348},
issn = {2379-5077},
abstract = {As research focusing on the colorectal cancer fecal microbiome using shotgun sequencing continues, increasing evidence has supported correlations between colorectal carcinomas (CRCs) and fecal microbiome dysbiosis. However, large-scale on-site and off-site (surrounding adjacent) tissue microbiome characterization of CRC was underrepresented. Here, considering each taxon as a feature, we demonstrate a machine learning-based method to investigate tissue microbial differences among CRC, colorectal adenoma (CRA), and healthy control groups using 16S rRNA data sets retrieved from 15 studies. A total of 2,099 samples were included and analyzed in case-control comparisons. Multiple methods, including differential abundance analysis, random forest classification, cooccurrence network analysis, and Dirichlet multinomial mixture analysis, were conducted to investigate the microbial signatures. We showed that the dysbiosis of the off-site tissue of colonic cancer was distinctive and predictive. The AUCs (areas under the curve) were 80.7%, 96.0%, and 95.8% for CRC versus healthy control random forest models using stool, tissue, and adjacent tissue samples and 69.9%, 91.5%, and 89.5% for the corresponding CRA models, respectively. We also found that the microbiota ecologies of the surrounding adjacent tissues of CRC and CRA were similar to their on-site counterparts according to network analysis. Furthermore, based on the enterotyping of tissue samples, the cohort-specific microbial signature might be the crux in addressing classification generalization problems. Despite cohort heterogeneity, the dysbiosis of lesion-adjacent tissues might provide us with further perspectives in demonstrating the role of the microbiota in colorectal cancer tumorigenesis.IMPORTANCE Turbulent fecal and tissue microbiome dysbiosis of colorectal carcinoma and adenoma has been identified, and some taxa have been proven to be carcinogenic. However, the microbiomes of surrounding adjacent tissues of colonic cancerous tissues were seldom investigated uniformly on a large scale. Here, we characterize the microbiome signatures and dysbiosis of various colonic cancer sample groups. We found a high correlation between colorectal carcinoma adjacent tissue microbiomes and their on-site counterparts. We also discovered that the microbiome dysbiosis in adjacent tissues could discriminate colorectal carcinomas from healthy controls effectively. These results extend our knowledge on the microbial profile of colorectal cancer tissues and highlight microbiota dysbiosis in the surrounding tissues. They also suggest that microbial feature variations of cancerous lesion-adjacent tissues might help to reveal the microbial etiology of colonic cancer and could ultimately be applied for diagnostic and screening purposes.},
}
@article {pmid32285532,
year = {2020},
author = {Meyer, KM and Hopple, AM and Klein, AM and Morris, AH and Bridgham, SD and Bohannan, BJM},
title = {Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function.},
journal = {Molecular ecology},
volume = {29},
number = {10},
pages = {1806-1819},
doi = {10.1111/mec.15442},
pmid = {32285532},
issn = {1365-294X},
mesh = {Biodiversity ; Congo ; *Ecosystem ; *Methane ; *Microbiota ; *Soil Microbiology ; Wetlands ; },
abstract = {Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4)-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH4 oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.},
}
@article {pmid32279319,
year = {2020},
author = {Wang, T and Tian, Z and Tunlid, A and Persson, P},
title = {Nitrogen acquisition from mineral-associated proteins by an ectomycorrhizal fungus.},
journal = {The New phytologist},
volume = {228},
number = {2},
pages = {697-711},
doi = {10.1111/nph.16596},
pmid = {32279319},
issn = {1469-8137},
mesh = {Basidiomycota ; Minerals ; *Mycorrhizae ; Nitrogen ; Soil ; Soil Microbiology ; },
abstract = {In nitrogen (N)-limited boreal forests, trees depend on the decomposing activity of their ectomycorrhizal (ECM) fungal symbionts to access soil N. A large fraction of this N exists as proteinaceous compounds associated with mineral particles. However, it is not known if ECM fungi can access these mineral-associated proteins; accordingly, possible acquisition mechanisms have not been investigated. With tightly controlled isotopic, spectroscopic, and chromatographic experiments, we quantified and analyzed the mechanisms of N acquisition from iron oxide mineral-associated proteins by Paxillus involutus, a widespread ECM fungus in boreal forests. The fungus acquired N from the mineral-associated proteins. The collective results indicated a proteolytic mechanism involving formation of the crucial enzyme-substrate complexes at the mineral surfaces. Hence, the enzymes hydrolyzed the mineral-associated proteins without initial desorption of the proteins. The proteolytic activity was suppressed by adsorption of proteases to the mineral particles. This process was counteracted by fungal secretion of mineral-surface-reactive compounds that decreased the protease-mineral interactions and thereby promoted the formation of enzyme-substrate complexes. The ability of ECM fungi to simultaneously generate extracellular proteases and surface-reactive metabolites suggests that they can play an important role in unlocking the large N pool of mineral-associated proteins to trees in boreal forests.},
}
@article {pmid32276974,
year = {2020},
author = {Du, R and Wu, Q and Xu, Y},
title = {Chinese Liquor Fermentation: Identification of Key Flavor-Producing Lactobacillus spp. by Quantitative Profiling with Indigenous Internal Standards.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {12},
pages = {},
pmid = {32276974},
issn = {1098-5336},
mesh = {Alcoholic Beverages/*microbiology ; China ; *Fermentation ; Flavoring Agents/*analysis ; High-Throughput Nucleotide Sequencing ; Lactobacillus/*metabolism ; Sequence Analysis, DNA ; },
abstract = {Identifying the functional microbes in spontaneous food fermentation is important for improving food quality. To identify the key flavor producers in Chinese liquor fermentation, we propose a novel quantitative microbiome profiling method that uses indigenous internal standards to normalize high-throughput amplicon sequencing results. We screened Lactobacillus acetotolerans and Lactobacillus jinshani as indigenous internal standards based on their high distribution frequencies and relative abundances. After determining the absolute abundance of indigenous internal standards using quantitative PCR with species-specific primers, the liquor-fermented bacterial community and its dynamics were better characterized by internal standards normalization. Based on quantitative microbiome profiling, we identified that Lactobacillus was a key flavor producer correlated with eight flavor compounds. Metatranscriptomic analysis indicated that Lactobacillus was active in transcribing genes involving the biosynthesis of flavor compounds and their precursors. This work has developed a novel and extensible absolute quantification method for microbiota that will alleviate concerns in the statistical analyses based on relative microbiome profiling, and shed insights into the function of Lactobacillus in food fermentation. It can potentially be applied to other microbial ecology studies.IMPORTANCE In this study, we developed a novel strategy using indigenous internal standards to normalize the high-throughput amplicon sequencing results. We chose two Lactobacillus species as indigenous internal standards and characterized the absolute abundance of the bacterial community. Further, we identified Lactobacillus as the key flavor producer using quantitative microbiome profiling combined with multivariate statistics and metatranscriptomic analysis. This work developed a novel strategy for absolute quantitative abundance analysis of microbiota and expanded our understanding of the role of Lactobacillus in food fermentation.},
}
@article {pmid32276972,
year = {2020},
author = {Cheng, CC and Duar, RM and Lin, X and Perez-Munoz, ME and Tollenaar, S and Oh, JH and van Pijkeren, JP and Li, F and van Sinderen, D and Gänzle, MG and Walter, J},
title = {Ecological Importance of Cross-Feeding of the Intermediate Metabolite 1,2-Propanediol between Bacterial Gut Symbionts.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {11},
pages = {},
pmid = {32276972},
issn = {1098-5336},
support = {CC2003/ARC_/Arthritis Research UK/United Kingdom ; },
mesh = {Animals ; Bifidobacterium breve/*metabolism ; Escherichia coli/*metabolism ; Female ; *Gastrointestinal Microbiome ; *Germ-Free Life ; Limosilactobacillus reuteri/*metabolism ; Male ; Mice ; Propylene Glycol/*metabolism ; },
abstract = {Cross-feeding based on the metabolite 1,2-propanediol has been proposed to have an important role in the establishment of trophic interactions among gut symbionts, but its ecological importance has not been empirically established. Here, we show that in vitro growth of Lactobacillus reuteri (syn. Limosilactobacillus reuteri) ATCC PTA 6475 is enhanced through 1,2-propanediol produced by Bifidobacterium breve UCC2003 and Escherichia coli MG1655 from the metabolization of fucose and rhamnose, respectively. Work with isogenic mutants showed that the trophic interaction is dependent on the pduCDE operon in L. reuteri, which encodes the ability to use 1,2-propanediol, and the l-fucose permease (fucP) gene in B. breve, which is required for 1,2-propanediol formation from fucose. Experiments in gnotobiotic mice revealed that, although the pduCDE operon bestows a fitness burden on L. reuteri ATCC PTA 6475 in the mouse digestive tract, the ecological performance of the strain was enhanced in the presence of B. breve UCC2003 and the mucus-degrading species Bifidobacterium bifidum The use of the respective pduCDE and fucP mutants of L. reuteri and B. breve in the mouse experiments indicated that the trophic interaction was specifically based on 1,2-propanediol. Overall, our work established the ecological importance of cross-feeding relationships based on 1,2-propanediol for the fitness of a bacterial symbiont in the vertebrate gut.IMPORTANCE Through experiments in gnotobiotic mice that employed isogenic mutants of bacterial strains that produce (Bifidobacterium breve) and utilize (Lactobacillus reuteri) 1,2-propanediol, this study provides mechanistic insight into the ecological ramifications of a trophic interaction between gut symbionts. The findings improve our understanding on how cross-feeding influences the competitive fitness of L. reuteri in the vertebrate gut and revealed a putative selective force that shaped the evolution of the species. The findings are relevant since they provide a basis to design rational microbial-based strategies to modulate gut ecosystems, which could employ mixtures of bacterial strains that establish trophic interactions or a personalized approach based on the ability of a resident microbiota to provide resources for the incoming microbe.},
}
@article {pmid32275302,
year = {2020},
author = {Barnard, S and Van Goethem, MW and de Scally, SZ and Cowan, DA and van Rensburg, PJ and Claassens, S and Makhalanyane, TP},
title = {Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {5},
pages = {},
doi = {10.1093/femsec/fiaa065},
pmid = {32275302},
issn = {1574-6941},
mesh = {Ammonia/metabolism ; Antarctic Regions ; Archaea/genetics ; Bacteria/metabolism ; *Betaproteobacteria/metabolism ; Biomass ; Carbon/metabolism ; Oxidation-Reduction ; *Soil/chemistry ; Soil Microbiology ; Temperature ; },
abstract = {The effects of temperature on microorganisms in high latitude regions, and their possible feedbacks in response to change, are unclear. Here, we assess microbial functionality and composition in response to a substantial temperature change. Total soil biomass, amoA gene sequencing, extracellular activity assays and soil physicochemistry were measured to assess a warming scenario. Soil warming to 15°C for 30 days triggered a significant decrease in microbial biomass compared to baseline soils (0°C; P < 0.05) after incubations had induced an initial increase. These changes coincided with increases in extracellular enzymatic activity for peptide hydrolysis and phenolic oxidation at higher temperatures, but not for the degradation of carbon substrates. Shifts in ammonia-oxidising bacteria (AOB) community composition related most significantly to changes in soil carbon content (P < 0.05), which gradually increased in microcosms exposed to a persistently elevated temperature relative to baseline incubations, while temperature did not influence AOBs. The concentration of soil ammonium (NH4+) decreased significantly at higher temperatures subsequent to an initial increase, possibly due to higher conversion rates of NH4+ to nitrate by nitrifying bacteria. We show that higher soil temperatures may reduce viable microbial biomass in cold environments but stimulate their activity over a short period.},
}
@article {pmid32272752,
year = {2020},
author = {Mena-Vázquez, N and Ruiz-Limón, P and Moreno-Indias, I and Manrique-Arija, S and Tinahones, FJ and Fernández-Nebro, A},
title = {Expansion of Rare and Harmful Lineages is Associated with Established Rheumatoid Arthritis.},
journal = {Journal of clinical medicine},
volume = {9},
number = {4},
pages = {},
pmid = {32272752},
issn = {2077-0383},
support = {FIS Grant PI18/00824//Instituto de Salud Carlos III/ ; Grant for medical researchers of the "Fundaci&#xf3;n Espa&#xf1;ola de Reumatolog&#xed;a"//Sociedad Espa&#xf1;ola de Reumatolog&#xed;a/ ; Grant PI17/00016//Fundaci&#xf3;n Andaluza de Reumatologia/ ; The research groups belong to the "Centros de Investigaci&#xf3;n en Red"CIBERobn"//Instituto de Salud Carlos III/ ; },
abstract = {OBJECTIVES: To characterize the gut microbiota profile in rheumatoid arthritis (RA) patients and investigate its association with certain characteristics of RA.<br><br>PATIENTS AND METHODS: A nested case-control cohort of 40 patients with RA and 40 sex-age matched controls was studied. Subjects with diabetes, with any other inflammatory disease, practicing extreme diets, taking antibiotics, probiotics or under any new treatment for at least three months prior to sampling were excluded. The microbiota composition was determined by 16S rRNA pyrosequencing and bioinformatics analysis by Quantitative Insights Into Microbial Ecology (QIIME). Other variables included clinical-laboratory variables and average Disease Activity Score 28 points during the follow-up period. Multiple linear regression models were constructed to investigate the possible risk factors for the microbiota.<br><br>RESULTS: &#x3b2;-diversity data showed that patients tend to differ from healthy subjects according to their microbiota (p = 0.07). The analysis showed an increase in Collinsella aerofaciens, Sedimentibacter and Enterococcus genera in patients compared to controls, as well as a decrease in Dorea formicigenerans. Likewise, an increase in the activity of arginine deiminase was observed, which was found in approximately 90% of the RA genes of the genus Collinsela. The sequence number of Collinsella aerofaciens was independently associated with age (B (95%CI), -0.347 (-21.6, -2.1)), high ACPA (0.323 (27.4-390.0)) and smoking (0.300 (8.8-256.4)) in RA patients. In addition, we observed decreases in Sarcina, 02d06 and Porphyromonas bacterial lineages.<br><br>CONCLUSION: Patients with RA present dysbiosis, resulting from an abundance of certain bacterial lineages and a decrease in others. These alterations could influence the maintenance of autoimmunity to this disease.},
}
@article {pmid32271651,
year = {2020},
author = {Ortiz-Castro, M and Hartman, T and Coutinho, T and Lang, JM and Korus, K and Leach, JE and Jackson-Ziems, T and Broders, K},
title = {Current Understanding of the History, Global Spread, Ecology, Evolution, and Management of the Corn Bacterial Leaf Streak Pathogen, Xanthomonas vasicola pv. vasculorum.},
journal = {Phytopathology},
volume = {110},
number = {6},
pages = {1124-1131},
doi = {10.1094/PHYTO-01-20-0018-PER},
pmid = {32271651},
issn = {0031-949X},
mesh = {Plant Diseases ; South Africa ; South America ; *Xanthomonas ; Zea mays ; },
abstract = {Bacterial leaf streak of corn, caused by Xanthomonas vasicola pv. vasculorum, has been present in South Africa for over 70 years, but is an emerging disease of corn in North and South America. The only scientific information pertaining to this disease on corn came from work done in South Africa, which primarily investigated host range on other African crops, such as sugarcane and banana. As a result, when the disease was first reported in the United States in 2016, there was very limited information on where this pathogen came from, how it infects its host, what plant tissue(s) it is capable of infecting, where initial inoculum comes from at the beginning of each crop season, how the bacterium spreads from plant to plant and long distance, what meteorological variables and agronomic practices favor disease development and spread, how many other plant species X. vasicola pv. vasculorum is capable of infecting or using as alternate hosts, and if the bacterium will be able to persist in all corn growing regions of the United States. There were also no rapid diagnostic assays available which initially hindered prompt identification prior to the development of molecular diagnostic tools. The goal of this synthesis is to review the history of X. vasicola pv. vasculorum and bacterial leaf streak in South Africa and its movement to North and South America, and highlight the recent research that has been done in response to the emergence of this bacterial disease.},
}
@article {pmid32268481,
year = {2020},
author = {Blasi, MF and Migliore, L and Mattei, D and Rotini, A and Thaller, MC and Alduina, R},
title = {Antibiotic Resistance of Gram-Negative Bacteria from Wild Captured Loggerhead Sea Turtles.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {9},
number = {4},
pages = {},
pmid = {32268481},
issn = {2079-6382},
abstract = {Sea turtles have been proposed as health indicators of marine habitats and carriers of antibiotic-resistant bacterial strains, for their longevity and migratory lifestyle. Up to now, a few studies evaluated the antibacterial resistant flora of Mediterranean loggerhead sea turtles (Caretta caretta) and most of them were carried out on stranded or recovered animals. In this study, the isolation and the antibiotic resistance profile of 90 Gram negative bacteria from cloacal swabs of 33 Mediterranean wild captured loggerhead sea turtles are described. Among sea turtles found in their foraging sites, 23 were in good health and 10 needed recovery for different health problems (hereafter named weak). Isolated cloacal bacteria belonged mainly to Enterobacteriaceae (59%), Shewanellaceae (31%) and Vibrionaceae families (5%). Although slight differences in the bacterial composition, healthy and weak sea turtles shared antibiotic-resistant strains. In total, 74 strains were endowed with one or multi resistance (up to five different drugs) phenotypes, mainly towards ampicillin (~70%) or sulfamethoxazole/trimethoprim (more than 30%). Hence, our results confirmed the presence of antibiotic-resistant strains also in healthy marine animals and the role of the loggerhead sea turtles in spreading antibiotic-resistant bacteria.},
}
@article {pmid32267873,
year = {2020},
author = {Compte-Port, S and Fillol, M and Gich, F and Borrego, CM},
title = {Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0231238},
pmid = {32267873},
issn = {1932-6203},
mesh = {Biodiversity ; Biofilms ; Carbon/metabolism ; Carbon Cycle/*physiology ; Crenarchaeota/*genetics/*metabolism ; DNA, Archaeal/genetics ; Ecosystem ; Euryarchaeota/*genetics/*metabolism ; *Geologic Sediments ; Humic Substances ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tryptophan ; },
abstract = {Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.},
}
@article {pmid32265872,
year = {2020},
author = {Altermann, E and Hickey, WJ},
title = {Grand Challenges in Microbiotechnology: Through the Prism of Microbiotechnology.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {430},
pmid = {32265872},
issn = {1664-302X},
}
@article {pmid32265857,
year = {2020},
author = {Chen, Z and Xie, Y and Zhou, F and Zhang, B and Wu, J and Yang, L and Xu, S and Stedtfeld, R and Chen, Q and Liu, J and Zhang, X and Xu, H and Ren, J},
title = {Featured Gut Microbiomes Associated With the Progression of Chronic Hepatitis B Disease.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {383},
pmid = {32265857},
issn = {1664-302X},
abstract = {Dysbiosis of gut microbiota during the progression of HBV-related liver disease is not well understood, as there are very few reports that discuss the featured bacterial taxa in different stages. The aim of this study was to reveal the featured bacterial species whose abundances are directly associated with HBV disease progression, that is, progression from healthy subjects to, chronic HBV infection, chronic hepatitis B to liver cirrhosis. Approximately 400 fecal samples were collected, and 97 samples were subjected to 16S rRNA gene sequencing after age and BMI matching. Compared with the healthy individuals, significant gut microbiota alterations were associated with the progression of liver disease. LEfSe results showed that the HBV infected patients had higher Fusobacteria, Veillonella, and Haemophilus abundance while the healthy individuals had higher levels of Prevotella and Phascolarctobacterium. Indicator analysis revealed that 57 OTUs changed as the disease progressed, and their combination produced an AUC value of 90% (95% CI: 86-94%) between the LC and non-LC groups. In addition, the abundances of OTU51 (Dialister succinatiphilus) and OTU50 (Alistipes onderdonkii) decreased as the disease progressed, and these results were further verified by qPCR. The LC patients had the higher bacterial network complexity, which was accompanied with a lower abundance of potential beneficial bacterial taxa, such as Dialister and Alistipes, while they had a higher abundance of pathogenic species within Actinobacteria. The compositional and network changes in the gut microbiota in varied CHB stages, suggest the potential contributions of gut microbiota in CHB disease progression.},
}
@article {pmid32265854,
year = {2020},
author = {Zehentner, B and Ardern, Z and Kreitmeier, M and Scherer, S and Neuhaus, K},
title = {A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC).},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {377},
pmid = {32265854},
issn = {1664-302X},
abstract = {Antisense transcription is well known in bacteria. However, translation of antisense RNAs is typically not considered, as the implied overlapping coding at a DNA locus is assumed to be highly improbable. Therefore, such overlapping genes are systematically excluded in prokaryotic genome annotation. Here we report an exceptional 603 bp long open reading frame completely embedded in antisense to the gene of the outer membrane protein ompA. An active σ[70] promoter, transcription start site (TSS), Shine-Dalgarno motif and rho-independent terminator were experimentally validated, providing evidence that this open reading frame has all the structural features of a functional gene. Furthermore, ribosomal profiling revealed translation of the mRNA, the protein was detected in Western blots and a pH-dependent phenotype conferred by the protein was shown in competitive overexpression growth experiments of a translationally arrested mutant versus wild type. We designate this novel gene pop (pH-regulated overlapping protein-coding gene), thus adding another example to the growing list of overlapping, protein coding genes in bacteria.},
}
@article {pmid32265327,
year = {2020},
author = {Malki, K and Rosario, K and Sawaya, NA and Székely, AJ and Tisza, MJ and Breitbart, M},
title = {Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
pmid = {32265327},
issn = {2150-7511},
mesh = {Bacteria/*classification ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Ecosystem ; Florida ; Fresh Water/microbiology/virology ; *Metagenome ; Natural Springs/*microbiology/*virology ; Phylogeny ; Sequence Analysis, DNA ; Viruses/*classification ; },
abstract = {Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 10[3] ml[-1] to 1.1 × 10[5] ml[-1] and 2.2 × 10[3] ml[-1] to 3.4 × 10[4] ml[-1], respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) viruses. Sequences similar to those of ssDNA viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small viruses merit further investigation in groundwater systems.IMPORTANCE Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida's first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida's first-magnitude springs, providing a baseline against which to compare future ecosystem change.},
}
@article {pmid32258466,
year = {2020},
author = {Gizaw, F and Kekeba, T and Teshome, F and Kebede, M and Abreham, T and Hayishe, H and Waktole, H and Tufa, TB and Edao, BM and Ayana, D and Abunna, F and Beyi, AF and Abdi, RD},
title = {Distribution and antimicrobial resistance profile of coagulase-negative staphylococci from cattle, equipment, and personnel on dairy farm and abattoir settings.},
journal = {Heliyon},
volume = {6},
number = {3},
pages = {e03606},
pmid = {32258466},
issn = {2405-8440},
abstract = {BACKGROUND: Safe food is central to social wellbeing. Coagulase-negative staphylococci (CNS) are a threat to food safety because they may harbor multiple enterotoxins and antimicrobial resistance (AMR) genes. CNS bacteria are an emerging nosocomial pathogen in public health. CNS also cause bovine mastitis with a significant economic loss in the dairy industry and may introduce toxins to the food supply chain resulting in foodborne illnesses. However, information on CNS and their AMR status are scarce in food animal production and processing lines in Ethiopia.<br><br>METHODOLOGY: This cross-sectional study evaluated the prevalence and AMR patterns of CNS in dairy farms and abattoirs using samples (n = 1001) from udder milk, beef carcass, personnel, and different abattoir and dairy equipment across five locations of central Oromia. The CNS isolates were identified via standard microbiological protocols and evaluated using disc diffusion test against 14 antimicrobials belonging to nine different broad classes. Uni-and-multivariable logistic regressions were used to analyze the association between potential risk factors (location, sample source, and sample type) and positivity to CNS.<br><br>RESULTS: The overall prevalence of CNS in the five different geographic locations studied was 9.6% (range: 6.7-12.4%) and varied between abattoirs (11.3%) and dairy farms (8.0%). CNS were prevalent on the carcass, milk, equipment, personnel hands, and nasal samples. Of all CNS isolates, 7.1, 10.7, 7.1, 12.5, 17.9, 10.7, 12.5, 7.1, 1.8, 5.4, 1.8, and 5.4% exhibited AMR simultaneously to single, double, 3, 4, 5, 6, 7, 7, 8, 9, 10, 11, and 13 antimicrobials, respectively. Overall, the isolates displayed 51 different AMR phenotypic patterns in which 50% of the isolates exhibited quadruple-resistance simultaneously based on the nine broad antimicrobial classes tested using 14 representative antimicrobials. The prevalence of multidrug-resistant (MDR) CNS (i.e. &#x2265; 3 classes of antimicrobials) was significantly (p = 0.037) different between locations with 100, 57.1, 50, 86.7, and 76.9% in Addis Ababa, Adama, Assela, Bishoftu, and Holeta, respectively. However, the prevalence of MDR CNS was not significantly (p = 0.20) different between dairy farms (87.5%) and abattoirs (71.9%). We evaluated the effect of acquiring cefoxitin-resistance of the isolates on the efficacy (i.e. inhibition zone) of the rest antimicrobials using General Linear Model after adjusting geographical locations as a random effect. Isolates with cefoxitin-resistance significantly displayed resistance to eight antimicrobials of 14 tested including amoxicillin, penicillin, cloxacillin, chloramphenicol, nalidixic acid, nitrofurantoin, and tetracycline (p = 0.000), and erythromycin (p = 0.02). On the other hand, cefoxitin-resistant isolates were susceptible to gentamicin, ciprofloxacin, kanamycin, streptomycin, and sulphamethoxazone trimethoprim (p = 0.000). Thus, antimicrobials such as gentamicin and ciprofloxacin may be an alternative therapy to treat cefoxitin-resistant CNS, as 96.4% of CNS isolates were susceptible to these antimicrobials. Overall, 94.1 and 54.5% of the CNS isolates among cefoxitin-resistant and cefoxitin-susceptible, respectively, harbored resistance to 3 or more classes of antimicrobials i.e. MDR.<br><br>CONCLUSION: The overall prevalence of CNS in milk, meat, equipment, and food handlers in central Oromia was 9.6% but varied by location and sample source. Some specific niches such as equipment, hands, and nasal cavities of personnel are significant sites for the source of CNS. Most, but not all, MDR CNS isolates were cefoxitin-resistant. Overall, 78.6% of the CNS tested were MDR and 50% had resistance to four or more broad classes of antimicrobials. CNS in food animals (raw milk and meat), equipment, and food handlers can be the source of MDR to the public. Personnel safety and hygienic food handling practices are needed. In addition, further investigation into the risk factors for the transmission and mechanisms of resistance of the CNS is required for intervention.},
}
@article {pmid32255838,
year = {2020},
author = {Redmile-Gordon, M and Gregory, AS and White, RP and Watts, CW},
title = {Soil organic carbon, extracellular polymeric substances (EPS), and soil structural stability as affected by previous and current land-use.},
journal = {Geoderma},
volume = {363},
number = {},
pages = {114143},
pmid = {32255838},
issn = {0016-7061},
abstract = {While soil microbial ecology, soil organic carbon (SOC) and soil physical quality are widely understood to be interrelated - the underlying drivers of emergent properties, from land management to biochemistry, are hotly debated. Biological binding agents, microbial exudates, or 'extracellular polymeric substances' (EPS) in soil are now receiving increased attention due to several of the existing methodological challenges having been overcome. We applied a recently developed approach to quantify soil EPS, as extracellular protein and extracellular polysaccharide, on the well-characterised soils of the Highfield Experiment, Rothamsted Research, UK. Our aim was to investigate the links between agricultural land use, SOC, transient binding agents known as EPS, and their impacts on soil physical quality (given by mean weight diameter of water stable aggregates; MWD). We compared the legacy effects from long-term previous land-uses (unfertilised grassland, fertilised arable, and fallow) which were established > 50 years prior to investigation, crossed with the same current land-uses established for a duration of only 2.5 years prior to sampling. Continuously fallow and grassland soils represented the poorest and greatest states of structural integrity, respectively. Total SOC and N were found to be affected by both previous and current land-uses, while extractable EPS and MWD were driven primarily by the current land-use. Land-use change between these two extremes (fallow → grass; grass → fallow) resulted in smaller SOC differences (64% increase or 37% loss) compared to MWD (125% increase or 78% loss). SOC concentration correlated well to MWD (adjusted R [2] = 0.72) but the greater SOC content from previous grassland was not found to contribute directly to the current stability (p < 0.05). Our work thus supports the view that certain distinct components of SOC, rather than the total pool, have disproportionately important effects on a soil's structural stability. EPS-protein was more closely related to aggregate stability than EPS-polysaccharide (p values of 0.002 and 0.027, respectively), and ranking soils with the 5 greatest concentrations of EPS-protein to their corresponding orders of stability (MWD) resulted in a perfect match. We confirmed that both EPS-protein and EPS-polysaccharide were transient fractions: supporting the founding models for aggregate formation. We suggest that management of transient binding agents such as EPS -as opposed to simply increasing the total SOC content- may be a more feasible strategy to improve soil structural integrity and help achieve environmental objectives.},
}
@article {pmid32253628,
year = {2020},
author = {Nisenbaum, M and Corti-Monzón, G and Villegas-Plazas, M and Junca, H and Mangani, A and Patat, ML and González, JF and Murialdo, SE},
title = {Enrichment and key features of a robust and consistent indigenous marine-cognate microbial consortium growing on oily bilge wastewaters.},
journal = {Biodegradation},
volume = {31},
number = {1-2},
pages = {91-108},
doi = {10.1007/s10532-020-09896-w},
pmid = {32253628},
issn = {1572-9729},
support = {VT38-UNMdP10982//Universidad Nacional de Mar del Plata/International ; PIT-AP-BA-2016//Consejo de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas de la Provincia de Buenos Aires/International ; PICT 2014-1567//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/International ; },
mesh = {Biodegradation, Environmental ; Hydrocarbons ; Microbial Consortia ; *Petroleum ; *Wastewater ; },
abstract = {Oily bilge wastewater (OBW) is a hazardous hydrocarbon-waste generated by ships worldwide. In this research, we enriched, characterized and study the hydrocarbon biodegradation potential of a microbial consortium from the bilges of maritime ships. The consortium cZ presented a biodegradation efficiency of 66.65% for total petroleum hydrocarbons, 72.33% for aromatics and 97.76% removal of n-alkanes. This consortium showed the ability to grow in OBWs of diverse origin and concentration. A 67-fold increase in biomass was achieved using a Sequential Batch Reactor with OBW as the only carbon and energy source. The bacterial community composition of the enriched OBW bacterial consortium at the final stable stage was characterized by 16S amplicon Illumina sequencing showing that 25 out of 915 of the emerged predominant bacterial types detected summed up for 84% of total composition. Out of the 140 taxa detected, 13 alone accumulated 94.9% of the reads and were classified as Marinobacter, Alcanivorax, Parvibaculum, Flavobacteriaceae, Gammaproteobacteria PYR10d3, Novispirillum and Xanthomonadaceae among the most predominant, followed by Thalassospira, Shewanella, Rhodospirillaceae, Gammaprotobacteria, Rhodobacteriaceae and Achromobacter. The microbial community from OBW bioreactor enrichments is intrinsically diverse with clear selection of predominant types and remarkably exhibiting consistent and efficient biodegradation achieved without any nutrient or surfactant addition. Due to there is very little information available in the OBW biodegradation field, this work contributes to the body of knowledge surrounding the treatment improvement of this toxic waste and its potential application in wastewater management.},
}
@article {pmid32248436,
year = {2020},
author = {Huang, S and Kleerebezem, R and Rabaey, K and Ganigué, R},
title = {Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {11},
pages = {5119-5131},
doi = {10.1007/s00253-020-10551-w},
pmid = {32248436},
issn = {1432-0614},
support = {676070//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; BOF15/PDO/068//Ghent University BOF fellowship/ ; 745828//Horizon 2020/ ; },
mesh = {Bioreactors ; Butyrates/*metabolism ; Clostridium/isolation &amp; purification/*metabolism ; Eubacterium/isolation &amp; purification/*metabolism ; Fermentation ; Isobutyrates/*metabolism ; Methanol/*metabolism ; *Microbiota ; },
abstract = {Isobutyrate (i-butyrate) is a versatile platform chemical, whose acid form is used as a precursor of plastic and emulsifier. It can be produced microbially either using genetically engineered organisms or via microbiomes, in the latter case starting from methanol and short-chain carboxylates. This opens the opportunity to produce i-butyrate from non-sterile feedstocks. Little is known on the ecology and process conditions leading to i-butyrate production. In this study, we steered i-butyrate production in a bioreactor fed with methanol and acetate under various conditions, achieving maximum i-butyrate productivity of 5.0 mM day[-1], with a concurrent production of n-butyrate of 7.9 mM day[-1]. The production of i-butyrate was reversibly inhibited by methanogenic inhibitor 2-bromoethanesulfonate. The microbial community data revealed the co-dominance of two major OTUs during co-production of i-butyrate and n-butyrate in two distinctive phases throughout a period of 54 days and 28 days, respectively. The cross-comparison of product profile with microbial community composition suggests that the relative abundance of Clostridium sp. over Eubacterium sp. is correlated with i-butyrate productivity over n-butyrate productivity.},
}
@article {pmid32248417,
year = {2020},
author = {Kalaimurugan, D and Durairaj, K and Kumar, AJ and Senthilkumar, P and Venkatesan, S},
title = {Novel preparation of fungal conidiophores biomass as adsorbent for removal of phosphorus from aqueous solution.},
journal = {Environmental science and pollution research international},
volume = {27},
number = {17},
pages = {20757-20769},
doi = {10.1007/s11356-020-08307-0},
pmid = {32248417},
issn = {1614-7499},
mesh = {Adsorption ; Biomass ; Hydrogen-Ion Concentration ; Kinetics ; *Phosphorus ; Solutions ; Temperature ; Thermodynamics ; *Water Pollutants, Chemical ; },
abstract = {The present study focused on phosphorus adsorption by novel fungal conidiophores biomass in aqueous solution. Fungal Conidiophores biomass was prepared from the fungal strains Aspergillus oryzae (YFK) and Fusarium oxysporum (YVS2). The functional groups and morphology of Conidiophores Biomass (CB) from these strains were characterized by FTIR and SEM. FTIR confirms the presence of alcohol, carboxylic acid, carbon dioxide, cyclic alkene, amine, alkene, fluoro compound, and halo compound groups. Batch mode study was carried out with two CB's such as Aspergillus oryzae CB (ACB) and Fusarium oxysporum CB (FCB) with initial concentration of phosphorus ranging from 20 to 100 mg L[-1]. Based on the batch experiments, the adsorption kinetics (pseudo first order and pseudo second order), isotherms (Freundlich and Langmuir models), and thermodynamic (standard entropy, energy, and enthalpy) parameters were calculated. The adsorption kinetics and isotherm studies showed that the adsorption data well fitted with PSO kinetic model. From the isotherm results, it was found that ACB and FCB exhibited highest adsorption capacity 25.64 mg g[-1] and 26.32 mg g[-1] of phosphorus respectively at the optimal condition of pH (7), time (90 min), dose (250 mg), and room temperature (35 °C). Thermodynamics values were found to be endothermic and spontaneous in nature for phosphorus adsorption. Finally, the results suggested that the ACB and FCB are economically feasible cost-effective adsorbent for removal of phosphorus in wastewater treatment. Graphical abstract.},
}
@article {pmid32247994,
year = {2020},
author = {Chique, C and Hynds, PD and Andrade, L and Burke, L and Morris, D and Ryan, MP and O'Dwyer, J},
title = {Cryptosporidium spp. in groundwater supplies intended for human consumption - A descriptive review of global prevalence, risk factors and knowledge gaps.},
journal = {Water research},
volume = {176},
number = {},
pages = {115726},
doi = {10.1016/j.watres.2020.115726},
pmid = {32247994},
issn = {1879-2448},
mesh = {Animals ; *Cryptosporidiosis ; *Cryptosporidium ; *Groundwater ; Humans ; Prevalence ; Prospective Studies ; Risk Factors ; Water Supply ; },
abstract = {Cryptosporidiosis is one of the leading causes of diarrhoeal illness and mortality induced by protozoan pathogens worldwide. As a largely waterborne disease, emphasis has been given to the study of Cryptosporidium spp. in surface waters, readily susceptible to pathogenic contamination. Conversely, the status of Cryptosporidium in potable groundwater sources, generally regarded as a pristine and "safe" drinking-water supply owing to (sub)-soil protection, remains largely unknown. As such, this investigation presents the first literature review aimed to ascertain the global prevalence of Cryptosporidium in groundwater supply sources intended for human consumption. Thirty-seven peer-reviewed studies were identified and included in the review. Groundwater sample and supply detection rates (estimated 10-20%) indicate Cryptosporidium is frequently present in domestic groundwater sources, representing a latent health concern for groundwater consumers. Specifically, sample (10.4%) and source (19.1%) detection rates deriving from comprehensive "temporal" investigations are put forward as representative of a contamination 'baseline' for Cryptosporidium in 'domestic' groundwater supplies. Proposed 'baseline' prevalence figures are largely applicable in preventive risk-based catchment and groundwater quality management including the formulation of Quantitative Microbial Risk Assessment (QMRA). Notwithstanding, a large geographical disparity in available investigations and lack of standardized reporting restrict the transferability of research findings. Overall, the mechanisms responsible for Cryptosporidium transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between groundwater and public-health sub-disciplines among investigations. Key recommendations and guidelines are provided for prospective studies directed at more integrative and multi-disciplinary research.},
}
@article {pmid32247910,
year = {2020},
author = {Jin, D and Zhang, F and Shi, Y and Kong, X and Xie, Y and Du, X and Li, Y and Zhang, R},
title = {Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation.},
journal = {Environmental research},
volume = {185},
number = {},
pages = {109457},
doi = {10.1016/j.envres.2020.109457},
pmid = {32247910},
issn = {1096-0953},
mesh = {*Archaea/genetics ; Bacteria/genetics ; *Groundwater ; RNA, Ribosomal, 16S/genetics ; Solvents ; },
abstract = {Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.},
}
@article {pmid32245969,
year = {2020},
author = {Chen, YC and Li, Z and Zhao, YX and Gao, M and Wang, JY and Liu, KW and Wang, X and Wu, LW and Jiao, YL and Xu, ZL and He, WG and Zhang, QY and Liang, CK and Hsiao, YY and Zhang, DY and Lan, SR and Huang, L and Xu, W and Tsai, WC and Liu, ZJ and Van de Peer, Y and Wang, YD},
title = {The Litsea genome and the evolution of the laurel family.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {1675},
pmid = {32245969},
issn = {2041-1723},
mesh = {Biosynthetic Pathways/genetics ; Chromosomes, Plant/*genetics ; DNA, Plant/genetics/isolation &amp; purification ; *Evolution, Molecular ; Gene Duplication ; Gene Expression Profiling ; *Genetic Speciation ; *Genome, Plant ; Genomics ; Inflorescence/genetics ; Litsea/*genetics/metabolism ; Molecular Sequence Annotation ; Odorants ; Phylogeny ; Plant Proteins/genetics/metabolism ; Sequence Analysis, DNA ; },
abstract = {The laurel family within the Magnoliids has attracted attentions owing to its scents, variable inflorescences, and controversial phylogenetic position. Here, we present a chromosome-level assembly of the Litsea cubeba genome, together with low-coverage genomic and transcriptomic data for many other Lauraceae. Phylogenomic analyses show phylogenetic discordance at the position of Magnoliids, suggesting incomplete lineage sorting during the divergence of monocots, eudicots, and Magnoliids. An ancient whole-genome duplication (WGD) event occurred just before the divergence of Laurales and Magnoliales; subsequently, independent WGDs occurred almost simultaneously in the three Lauralean lineages. The phylogenetic relationships within Lauraceae correspond to the divergence of inflorescences, as evidenced by the phylogeny of FUWA, a conserved gene involved in determining panicle architecture in Lauraceae. Monoterpene synthases responsible for production of specific volatile compounds in Lauraceae are functionally verified. Our work sheds light on the evolution of the Lauraceae, the genetic basis for floral evolution and specific scents.},
}
@article {pmid32243542,
year = {2020},
author = {Nelson, CW and Ardern, Z and Wei, X},
title = {OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes.},
journal = {Molecular biology and evolution},
volume = {37},
number = {8},
pages = {2440-2449},
pmid = {32243542},
issn = {1537-1719},
mesh = {*Genes, Overlapping ; *Genetic Techniques ; HIV-1/genetics ; *Selection, Genetic ; *Silent Mutation ; *Software ; },
abstract = {Purifying (negative) natural selection is a hallmark of functional biological sequences, and can be detected in protein-coding genes using the ratio of nonsynonymous to synonymous substitutions per site (dN/dS). However, when two genes overlap the same nucleotide sites in different frames, synonymous changes in one gene may be nonsynonymous in the other, perturbing dN/dS. Thus, scalable methods are needed to estimate functional constraint specifically for overlapping genes (OLGs). We propose OLGenie, which implements a modification of the Wei-Zhang method. Assessment with simulations and controls from viral genomes (58 OLGs and 176 non-OLGs) demonstrates low false-positive rates and good discriminatory ability in differentiating true OLGs from non-OLGs. We also apply OLGenie to the unresolved case of HIV-1's putative antisense protein gene, showing significant purifying selection. OLGenie can be used to study known OLGs and to predict new OLGs in genome annotation. Software and example data are freely available at https://github.com/chasewnelson/OLGenie (last accessed April 10, 2020).},
}
@article {pmid32240065,
year = {2020},
author = {Sedighian, N and Krijger, M and Taparia, T and Taghavi, SM and Wicker, E and van der Wolf, JM and Osdaghi, E},
title = {Genome Resource of Two Potato Strains of Ralstonia solanacearum Biovar 2 (Phylotype IIB Sequevar 1) and Biovar 2T (Phylotype IIB Sequevar 25) Isolated from Lowlands in Iran.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {33},
number = {7},
pages = {872-875},
doi = {10.1094/MPMI-02-20-0026-A},
pmid = {32240065},
issn = {0894-0282},
mesh = {*Genome, Bacterial ; Iran ; Phylogeny ; Plant Diseases/*microbiology ; *Ralstonia solanacearum/genetics/pathogenicity ; Solanum tuberosum/*microbiology ; },
abstract = {Ralstonia solanacearum, the causal agent of bacterial wilt and brown rot disease, is one of the major pathogens of solanaceous crops, including potato, around the globe. Biovar 2T (phylotype II/sequevar 25) of R. solanacearum is adapted to tropical lowlands and is only reported in South America and Iran. Thus far, no genome resource of the biovar 2T of the pathogen has been available. Here, we present the near-complete genome sequences of the biovar 2T strain CFBP 8697 as well as strain CFBP 8695 belonging to biovar 2 race 3, both isolated from potato in Iran. The genomic data of biovar 2T will extend our understanding of the virulence features of R. solanacearum and pave the way for research on biovar 2T functional and interaction genetics.},
}
@article {pmid32237500,
year = {2020},
author = {Zhang, JQ and Zhou, T and Guo, LP and Jiang, WK and Wang, X and Zhang, GW and Pan, C and Liu, P and Cao, YZ and Xiao, CH},
title = {[Ecological benefits of Gastrodia elata-Phallus impudicus sequential planting pattern].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {45},
number = {3},
pages = {457-462},
doi = {10.19540/j.cnki.cjcmm.20191204.105},
pmid = {32237500},
issn = {1001-5302},
mesh = {Agaricales/*growth &amp; development ; Agriculture/*methods ; Gastrodia/*growth &amp; development ; Medicine, Chinese Traditional ; Plants, Medicinal/*growth &amp; development ; },
abstract = {Gastrodia elata is a kind of precious traditional Chinese medicine. In the process of cultivation of G. elata, due to the influence of continuous cropping obstacles and other factors, the fungus materials and land that have been planted with G. elata are often abandoned, resulting in a great waste of resources. Based on the planting characteristics of G. elata and Phallus impudicus and the previous research experience in ecological agriculture, this paper analyzed the ecological adaptability characteristics of G. elata and P. impudicus, and summarized the key techniques of the G. elata-P. impudicus sequential planting pattern. Keeping track of the planting area, fungus-growing materials consumption and market sales of G. elata-P. impudicus sequential planting pattern, the ecological benefits of G. elata-P. impudicus sequential planting pattern from the aspects of utilization rate of fungus-growing materials were analyzed, the value of land resources per unit area, ecological environmental protection, labor cost and economic benefits were consi-dered. The technical principle of G. elata-P. impudicus sequential planting pattern was expounded according to their ecological habit, the season of harvest and planting, the difference of composition of fungus-growing materials, and the microbial ecology. The sequential planting pattern of G. elata-P. impudicus not only realized the double production of medicinal materials and edible fungi, reduced the waste of old fungus-growing materials, but also transformed the energy from nutrition-supplied fungi to edible and medicinal fungi, which guaranteed the ecological recycling and utilization of G. elata in the process of cultivation.},
}
@article {pmid32233983,
year = {2020},
author = {Zheng, Y and Hu, X and Jia, Z and Bodelier, PLE and Guo, Z and Zhang, Y and Li, F and He, P},
title = {Co-occurrence patterns among prokaryotes across an age gradient in pit mud of Chinese strong-flavor liquor.},
journal = {Canadian journal of microbiology},
volume = {66},
number = {9},
pages = {495-504},
doi = {10.1139/cjm-2020-0012},
pmid = {32233983},
issn = {1480-3275},
mesh = {Alcoholic Beverages/*microbiology ; Bacteria/*classification/genetics/*isolation &amp; purification ; China ; Fermentation ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Taste ; Time Factors ; },
abstract = {It is widely believed that the quality and characteristics of Chinese strong-flavor liquor (CSFL) are closely related to the age of the pit mud; CSFL produced from older pit mud tastes better. This study aimed to investigate the alteration and interaction of prokaryotic communities across an age gradient in pit mud. Prokaryotic microbes in different-aged pit mud (1, 6, and 10 years old) were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. Analysis of the 16S rRNA gene indicated that the prokaryotic community was significantly altered with pit mud age. There was a significant increase in the genera Methanosarcina, Methanobacterium, and Aminobacterium with increased age of pit mud, while the genus Lactobacillus showed a significant decreasing trend. Network analysis demonstrated that both synergetic co-occurrence and niche competition were dominated by 68 prokaryotic genera. These genera formed 10 hubs of co-occurrence patterns, mainly under the phyla Firmicutes, Euryarchaeota, and Bacteroidetes, playing important roles on ecosystem stability of the pit mud. Environmental variables (pH, NH4[+], available P, available K, and Ca[2+]) correlated significantly with prokaryotic community assembly. The interaction of prokaryotic communities in the pit mud ecosystem and the relationship among prokaryotic communities and environmental factors contribute to the higher quality of the pit mud in older fermentation pits.},
}
@article {pmid32226422,
year = {2020},
author = {Chen, ML and Becraft, ED and Pachiadaki, M and Brown, JM and Jarett, JK and Gasol, JM and Ravin, NV and Moser, DP and Nunoura, T and Herndl, GJ and Woyke, T and Stepanauskas, R},
title = {Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {376},
pmid = {32226422},
issn = {1664-302X},
support = {268595/ERC_/European Research Council/International ; },
abstract = {Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.},
}
@article {pmid32226382,
year = {2020},
author = {Silveira-Nunes, G and Durso, DF and Jr, LRAO and Cunha, EHM and Maioli, TU and Vieira, AT and Speziali, E and Corrêa-Oliveira, R and Martins-Filho, OA and Teixeira-Carvalho, A and Franceschi, C and Rampelli, S and Turroni, S and Brigidi, P and Faria, AMC},
title = {Hypertension Is Associated With Intestinal Microbiota Dysbiosis and Inflammation in a Brazilian Population.},
journal = {Frontiers in pharmacology},
volume = {11},
number = {},
pages = {258},
pmid = {32226382},
issn = {1663-9812},
abstract = {Hypertension is a major global health challenge, as it represents the main risk factor for stroke and cardiovascular disease. It is a multifactorial clinical condition characterized by high and sustained levels of blood pressure, likely resulting from a complex interplay of endogenous and environmental factors. The gut microbiota has been strongly supposed to be involved but its role in hypertension is still poorly understood. In an attempt to fill this gap, here we characterized the microbial composition of fecal samples from 48 hypertensive and 32 normotensive Brazilian individuals by next-generation sequencing of the 16S rRNA gene. In addition, the cytokine production of peripheral blood samples was investigated to build an immunological profile of these individuals. We identified a dysbiosis of the intestinal microbiota in hypertensive subjects, featured by reduced biodiversity and distinct bacterial signatures compared with the normotensive counterpart. Along with a reduction in Bacteroidetes members, hypertensive individuals were indeed mainly characterized by increased proportions of Lactobacillus and Akkermansia while decreased relative abundances of well-known butyrate-producing commensals, including Roseburia and Faecalibacterium within the Lachnospiraceae and Ruminococcaceae families. We also observed an inflamed immune profile in hypertensive individuals with an increase in TNF/IFN-γ ratio, and in TNF and IL-6 production when compared to normotensive ones. Our work provides the first evidence of association of hypertension with altered gut microbiota and inflammation in a Brazilian population. While lending support to the existence of potential microbial signatures of hypertension, likely to be robust to age and geography, our findings point to largely neglected bacteria as potential contributors to intestinal homeostasis loss and emphasize the high vulnerability of hypertensive individuals to inflammation-related disorders.},
}
@article {pmid32222691,
year = {2020},
author = {McAteer, PG and Christine Trego, A and Thorn, C and Mahony, T and Abram, F and O'Flaherty, V},
title = {Reactor configuration influences microbial community structure during high-rate, low-temperature anaerobic treatment of dairy wastewater.},
journal = {Bioresource technology},
volume = {307},
number = {},
pages = {123221},
doi = {10.1016/j.biortech.2020.123221},
pmid = {32222691},
issn = {1873-2976},
mesh = {Anaerobiosis ; Bioreactors ; *Microbiota ; RNA, Ribosomal, 16S ; Sewage ; Temperature ; Waste Disposal, Fluid ; *Wastewater ; },
abstract = {Low temperature anaerobic digestion remains in its infancy, despite increasing interest for the treatment of complex wastewaters. In this study, the feasibility of low-temperature anaerobic treatment of dairy wastewater was assessed during a 443-day laboratory-scale bioreactor trial. The bioreactors were operated in triplicate at organic loading rates of 7.5-9 kgCODm[-3]d[-1] throughout five operational phases. The structure of the microbial community was analysed using quantitative real-time PCR and amplicon sequencing of 16S rRNA genes from DNA and rRNA. The results indicated that low-temperature treatment of dairy wastewater is feasible at 15 °C, but that reactor configuration remains extremely important. The upflow anaerobic sludge bed (UASB) configuration out-performed the expanded granular sludge bed (EGSB)-based configurations. Decreased temperatures resulted in significant reductions in microbiome diversity. Methanosaeta was identified as a dominant genus throughout the trial, while Lactococcus was identified as an important bacterial genus at low-temperatures. However, the relative abundance of Lactococcus was significantly influenced by reactor configuration.},
}
@article {pmid32222116,
year = {2020},
author = {Morita, D and Takahashi, E and Morita, M and Ohnishi, M and Mizuno, T and Miyoshi, SI and Dutta, D and Ramamurthy, T and Chowdhury, G and Mukhopadhyay, AK and Okamoto, K},
title = {Genomic characterization of antibiotic resistance-encoding genes in clinical isolates of Vibrio cholerae non-O1/non-O139 strains from Kolkata, India: generation of novel types of genomic islands containing plural antibiotic resistance genes.},
journal = {Microbiology and immunology},
volume = {64},
number = {6},
pages = {435-444},
doi = {10.1111/1348-0421.12790},
pmid = {32222116},
issn = {1348-0421},
support = {//Japan Initiative for Global Research Network on Infectious Diseases (J-GRID)/ ; //Ministry of Education, Culture, Sports, Science and Technology in Japan/ ; JP18fm0108002//Japan Agency for Medical Research and Development/ ; },
mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Genomic Islands/*genetics ; Humans ; India ; Integrons/*genetics ; Microbial Sensitivity Tests/methods ; Serotyping/methods ; *Vibrio Infections/epidemiology/microbiology ; *Vibrio cholerae non-O1/classification/drug effects/genetics ; Whole Genome Sequencing/methods ; },
abstract = {Non-O1/non-O139 nontoxigenic Vibrio cholerae associated with cholera-like diarrhea has been reported in Kolkata, India. However, the property involved in the pathogenicity of these strains has remained unclear. The character of 25 non-O1/non-O139 nontoxigenic V. cholerae isolated during 8 years from 2007 to 2014 in Kolkata was examined. Determination of the serogroup showed that the serogroups O6, O10, O35, O36, O39, and O70 were represented by two strains in each serogroup, and the remaining isolates belonged to different serogroups. To clarify the character of antibiotic resistance of these isolates, an antibiotic resistance test and the gene analysis were performed. According to antimicrobial drug susceptibility testing, 13 strains were classified as drug resistant. Among them, 10 strains were quinolone resistant and 6 of the 13 strains were resistant to more than three antibiotics. To define the genetic background of the antibiotic character of these strains, whole-genome sequences of these strains were determined. From the analysis of these sequences, it becomes clear that all quinolone resistance isolates have mutations in quinolone resistance-determining regions. Further research on the genome sequence showed that four strains possess Class 1 integrons in their genomes, and that three of the four integrons are found to be located in their genomic islands. These genomic islands are novel types. This indicates that various integrons containing drug resistance genes are spreading among V. cholerae non-O1/non-O139 strains through the action of newly generated genomic islands.},
}
@article {pmid32221644,
year = {2020},
author = {Núñez, A and Moreno, DA},
title = {The Differential Vertical Distribution of the Airborne Biological Particles Reveals an Atmospheric Reservoir of Microbial Pathogens and Aeroallergens.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {322-333},
doi = {10.1007/s00248-020-01505-w},
pmid = {32221644},
issn = {1432-184X},
support = {S2013/MAE-2874//Comunidad de Madrid/ ; },
mesh = {*Air Microbiology ; Allergens/*isolation &amp; purification ; Altitude ; Bacteria/*isolation &amp; purification ; Fungi/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Particulate Matter/*isolation &amp; purification ; *Plants ; Seasons ; Spain ; },
abstract = {The most abundant biological particles present in the air are bacteria, fungal propagules and pollen grains. Many of them are proved allergens or even responsible for airborne infectious diseases, which supports the increase of studies in recent years on their composition, diversity, and factors involved in their variability. However, most studies in urban areas are conducted close to ground level and a factor such as height is rarely taken into account. Thus, the information about how the composition of biological particles changes with this variable is scarce. Here, we examined the differential distribution of bacteria, fungi, and plants at four altitudes (up to ∼ 250 m) in a metropolitan area using high-throughput DNA sequencing. Most taxa were present at all levels (common taxa). However, a transitional layer between 80 and 150 m seemed to affect the scattering of these bioaerosols. Taxa not present at all altitudes (non-common) showed an upward tendency of diversity for bacteria and plants with height, while the opposite trend was observed for fungi. Certain patterns were observed for fungi and specific plant genera, while bacterial taxa showed a more arbitrary distribution and no patterns were found. We detected a wide variety of aeroallergens and potential pathogens at all heights, which summed a substantial portion of the total abundance for fungi and plants. We also identified potential connections between the biological particles based on their abundances across the vertical section.},
}
@article {pmid32221408,
year = {2020},
author = {Wu, R and Chai, B and Cole, JR and Gunturu, SK and Guo, X and Tian, R and Gu, JD and Zhou, J and Tiedje, JM},
title = {Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming.},
journal = {The ISME journal},
volume = {14},
number = {7},
pages = {1651-1662},
pmid = {32221408},
issn = {1751-7370},
mesh = {CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Genome ; Oklahoma ; *Soil ; },
abstract = {There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus-host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus-host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.},
}
@article {pmid32220841,
year = {2020},
author = {Sims, IM and Tannock, GW},
title = {Galacto- and Fructo-oligosaccharides Utilized for Growth by Cocultures of Bifidobacterial Species Characteristic of the Infant Gut.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {11},
pages = {},
pmid = {32220841},
issn = {1098-5336},
mesh = {Bifidobacterium/*metabolism ; Bifidobacterium bifidum/*metabolism ; Bifidobacterium breve/*metabolism ; Bifidobacterium longum subspecies infantis/*metabolism ; Coculture Techniques ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Oligosaccharides/*metabolism ; },
abstract = {Bifidobacterial species are common inhabitants of the gut of human infants during the period when milk is a major component of the diet. Bifidobacterium breve, Bifidobacterium bifidum, Bifidobacterium longum subspecies longum, and B. longum subspecies infantis have been detected frequently in infant feces, but B. longum subsp. infantis may be disadvantaged numerically in the gut of infants in westernized countries. This may be due to the different durations of breast milk feeding in different countries. Supplementation of the infant diet or replacement of breast milk using formula feeds is common in Western countries. Formula milks often contain galacto- and/or fructo-oligosaccharides (GOS and FOS, respectively) as additives to augment the concentration of oligosaccharides in ruminant milks, but the ability of B. longum subsp. infantis to utilize these potential growth substrates when they are in competition with other bifidobacterial species is unknown. We compared the growth and oligosaccharide utilization of GOS and FOS by bifidobacterial species in pure culture and coculture. Short-chain GOS and FOS (degrees of polymerization [DP] 2 and 3) were favored growth substrates for strains of B. bifidum and B. longum subsp. longum, whereas both B. breve and B. longum subsp. infantis had the ability to utilize both short- and longer-chain GOS and FOS (DP 2 to 6). B. breve was nevertheless numerically dominant over B. longum subsp. infantis in cocultures. This was probably related to the slower use of GOS of DP 3 by B. longum subsp. infantis, indicating that the kinetics of substrate utilization is an important ecological factor in the assemblage of gut communities.IMPORTANCE The kinds of bacteria that form the collection of microbes (the microbiota) in the gut of human infants may influence health and well-being. Knowledge of how the composition of the infant diet influences the assemblage of the bacterial collection is therefore important because dietary interventions may offer opportunities to alter the microbiota with the aim of improving health. Bifidobacterium longum subspecies infantis is a well-known bacterial species, but under modern child-rearing conditions it may be disadvantaged in the gut. Modern formula milks often contain particular oligosaccharide additives that are generally considered to support bifidobacterial growth. However, studies of the ability of various bifidobacterial species to grow together in the presence of these oligosaccharides have not been conducted. These kinds of studies are essential for developing concepts of microbial ecology related to the influence of human nutrition on the development of the gut microbiota.},
}
@article {pmid32220814,
year = {2020},
author = {Belleggia, L and Milanović, V and Ferrocino, I and Cocolin, L and Haouet, MN and Scuota, S and Maoloni, A and Garofalo, C and Cardinali, F and Aquilanti, L and Mozzon, M and Foligni, R and Pasquini, M and Trombetta, MF and Clementi, F and Osimani, A},
title = {Is there any still undisclosed biodiversity in Ciauscolo salami? A new glance into the microbiota of an artisan production as revealed by high-throughput sequencing.},
journal = {Meat science},
volume = {165},
number = {},
pages = {108128},
doi = {10.1016/j.meatsci.2020.108128},
pmid = {32220814},
issn = {1873-4138},
mesh = {Animals ; Bacteria/isolation &amp; purification ; Botulinum Toxins/genetics ; Fermentation ; *Food Microbiology ; Fungi/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Meat Products/analysis/*microbiology ; *Microbiota ; Multiplex Polymerase Chain Reaction/methods ; Sus scrofa ; Volatile Organic Compounds/analysis ; Yeasts/isolation &amp; purification ; },
abstract = {Ciauscolo is a fermented sausage with the Protected Geographical Indication (PGI) status. To disclose the microbial ecology of a model Ciauscolo salami manufacture during its natural fermentation, viable counting, amplicon-based sequencing and real-time PCR were applied. The volatilome during fermentation was also characterized. The results allowed previously undetected species to be discovered. The core microbiota was composed by Lactobacillus algidus, Leuconostoc carnosum, Lactobacillus sakei, Debaryomyces hansenii, Glomus hyderabadensis, Tilletiopsis washingtonensis, and Kurtzmaniella zeylanoides. Salmonella spp. and Listeria monocytogenes were absent in all the samples; moreover, multiplex real-time PCR revealed the absence of the target genes bont/A, bont/B, bont/E, bont/F, and 4gyrB (CP), encoding botulinic toxins. Volatilome, deeply depending on microbiological metabolism, was characterized by spices-derived components. Limonene, sabinene, α- and β-pinene, 3-carene, and α-thujene were the most represented monoterpene hydrocarbons, whereas β- and α-copaene were the most represented sesquiterpene hydrocarbons. Allyl methyl sulphide and diallyl disulphide were the major aliphatic sulphur compounds, together with diallyl sulphide and allyl methyl disulphide.},
}
@article {pmid32219941,
year = {2021},
author = {Huang, Z and Shen, Y and Huang, X and Qiao, M and He, RK and Song, L},
title = {Microbial diversity of representative traditional fermented sausages in different regions of China.},
journal = {Journal of applied microbiology},
volume = {130},
number = {1},
pages = {133-141},
doi = {10.1111/jam.14648},
pmid = {32219941},
issn = {1365-2672},
support = {31671916//National Natural Science Foundation of China/ ; },
mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; China ; Colony Count, Microbial ; Fermentation ; Fermented Foods/*microbiology ; Food Microbiology ; Food Safety ; Meat Products/*microbiology ; *Microbiota ; Taste ; },
abstract = {AIMS: The purpose of this experiment was to study the bacterial diversity of traditional fermented sausages from four typical regions of China (Chengdu, Shenzhen, Changsha and Harbin) and to further evaluate their microbiological safety.<br><br>METHODS AND RESULTS: The diversity of the microbiota of the sausages was studied using the Illumina HiSeq platform. The results showed that compared with the highest diversity of fermented bacteria in Guangdong, the bacterial diversity of fermented sausage was the lowest in Sichuan. The percentage of dominant phylum (Firmicutes, Cyanophyta, Proteobacter) were 78&#xb7;39, 13&#xb7;13 and 7&#xb7;14% in SC, 35&#xb7;47, 30&#xb7;36 and 28&#xb7;04% in GD, 54&#xb7;81, 28&#xb7;91 and 14&#xb7;00% in HN, 20&#xb7;20, 58&#xb7;16 and 17&#xb7;31% in HB respectively. The main genus distribution of fermented sausages in different regions is varied, but lactic acid bacteria and cyanobacteria are generally the main ones. Traditional fermented sausages using natural fermentation methods have poor microbiological safety, and pathogenic and spoilage micro-organisms such as Acinetobacter, Brochothrix and Pseudomonas have been detected in all four regions.<br><br>CONCLUSIONS: The results in this paper provide a microbiota profile of four typical fermented sausages in China. There is a big difference in the microbiota of sausages in different regions, and the good flavour of traditional Chinese fermented sausage is related closely with the abundant microbial resources, however, the natural fermentation method also expose to the product security threats, including spoilage, pathogenic micro-organisms and biogenic amines, etc. SIGNIFICANCE AND IMPACT OF THE STUDY: The results would offer guidance for industrial fermented sausage production with certain flavour and also improve the microbial resource utilization, and contribute to the control of harmful micro-organisms in traditional fermented sausage.},
}
@article {pmid32219483,
year = {2020},
author = {Sodhi, KK and Kumar, M and Singh, DK},
title = {Potential application in amoxicillin removal of Alcaligenes sp. MMA and enzymatic studies through molecular docking.},
journal = {Archives of microbiology},
volume = {202},
number = {6},
pages = {1489-1495},
pmid = {32219483},
issn = {1432-072X},
support = {NASF/CA-6030/2017-18//INDIAN AGRICULTURE RESEARCH INSTITUTE/ ; },
mesh = {Alcaligenes/genetics/*metabolism ; Amoxicillin/*metabolism ; Anti-Bacterial Agents/*metabolism ; *Biodegradation, Environmental ; Chromatography, Liquid ; Drug Resistance, Bacterial/physiology ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Porins/biosynthesis ; Tandem Mass Spectrometry ; },
abstract = {Antibiotic contamination in environmental matrices is a serious global problem which leads to an increase in the proliferation of antibiotic resistance genes. Amoxicillin is ubiquitous in the environment, but there is hardly any information on the dissipation of amoxicillin by the microbial community. In view of this, the present study focusses on the removal of amoxicillin using amoxicillin-resistant bacteria, Alcaligenes sp. MMA. Bacteria were characterized using antibiotic tests, biochemical and molecular analysis. Alcaligenes sp. MMA was able to remove up to 84% of amoxicillin in 14 days in M9 minimal media, and the degradation products were confirmed using LC-MS/MS, including the benzothiazole, 2-Amino-3-methoxyl benzoic acid, 4-Hydroxy-2-methyl benzoic acid, 5-Amino-2-methylphenol and 3,5-Bis(tert-butyl)-2-hydroxybenzaldehyde, at the end of 14th day which further shows the removal of amoxicillin by the bacterial strain. Differential expression of porins was found in the presence of amoxicillin as a sole source of carbon and energy for the bacterial strain. Molecular interaction using in silico studies were performed which showed the formation of a hydrogen bond between amoxicillin and porins.},
}
@article {pmid32217314,
year = {2020},
author = {Urra, J and Alkorta, I and Mijangos, I and Garbisu, C},
title = {Commercial and farm fermented liquid organic amendments to improve soil quality and lettuce yield.},
journal = {Journal of environmental management},
volume = {264},
number = {},
pages = {110422},
doi = {10.1016/j.jenvman.2020.110422},
pmid = {32217314},
issn = {1095-8630},
mesh = {Agriculture ; Farms ; Fertilizers ; Lactuca ; *Soil ; *Soil Pollutants ; },
abstract = {The anaerobic decomposition of organic wastes might lead to the formation of organic-byproducts which can then be successfully used as organic fertilizers. This study evaluated the impact of the application of two fermented liquid organic amendments (commercial vs. farm-made) at two doses of application (optimal vs. suboptimal), compared to mineral fertilization, on lettuce growth and soil quality. To this purpose, two experiments were conducted at microcosm- and field-scale, respectively. In the microcosm experiment, organically amended soils resulted in lower lettuce yield than minerally fertilized soil but, in contrast, they enhanced microbial activity and biomass, thus leading to an improvement in soil quality. The fertilization regime (organic vs. inorganic) significantly affected soil microbial composition but did not have any significant effect on structural or functional prokaryotic diversity. In the field experiment, at the optimal dose of application, organically-amended soils resulted in comparable lettuce yield to that displayed by minerally fertilized soils. The application of organic amendments did not result in an enhanced microbial activity and biomass, compared to mineral fertilization, but led to a higher soil prokaryotic diversity. Among the organically-amended plots, the optimal application dose resulted in a higher lettuce yield and soil microbial activity and biomass, but led to a decline in soil prokaryotic diversity, compared to the suboptimal application dose. Our results indicate that commercial and farm-made fermented liquid organic amendments possess the potential to ameliorate soil quality while sustaining crop yield. Given the strong influence of other factors (e.g., type of soil, dose of application) on the effects exerted by such amendments on soil quality and fertility, we recommend that an exhaustive characterization of both the amendments and the recipient soils should be carried out prior to their application, in order to better ensure their potential beneficial effects.},
}
@article {pmid32216022,
year = {2020},
author = {Ji, M and Kong, W and Stegen, J and Yue, L and Wang, F and Dong, X and Cowan, DA and Ferrari, BC},
title = {Distinct assembly mechanisms underlie similar biogeographical patterns of rare and abundant bacteria in Tibetan Plateau grassland soils.},
journal = {Environmental microbiology},
volume = {22},
number = {6},
pages = {2261-2272},
doi = {10.1111/1462-2920.14993},
pmid = {32216022},
issn = {1462-2920},
support = {DE-AC06-76RLO 1830//Battelle Memorial Institute/International ; //Pacific Northwest National Laboratory/International ; //Office of Biological and Environmental Research/International ; //US Department of Energy (DOE)/International ; 41771303//National Natural Science Foundation of China/International ; XDA20050101//Chinese Academy of Sciences/International ; QYZDB-SSW-DQC033//Chinese Academy of Sciences/International ; XDA19070304//Chinese Academy of Sciences/International ; },
mesh = {Bacteria/*classification/genetics ; Biodiversity ; *Grassland ; Phylogeny ; Soil ; *Soil Microbiology ; Tibet ; },
abstract = {Rare biosphere represents the majority of Earth's biodiversity and performs vital ecological functions, yet little is known about its biogeographical patterns and community assembly processes in terrestrial ecosystems. Herein, we investigated the community composition and phylogeny of rare (relative abundance <0.1%) and abundant (>1%) bacteria in dryland grassland soils on the Tibetan Plateau. Results revealed similar biogeographical patterns of rare and abundant bacteria at both compositional and phylogenetic levels, but rare subcommunity was more heavily influenced by stochasticity (72%) than the abundant (57%). The compositional variation of rare bacteria was less explained by environmental factors (41%) than that of the abundant (80%), while the phylogeny of rare bacteria (36%) was more explained than that of the abundant (29%). The phylogeny of rare bacteria was equally explained by local factors (soil and vegetation) and geospatial distance (11.5% and 11.9% respectively), while that of the abundant was more explained by geospatial distance (22.1%) than local factors (11.3%). Furthermore, a substantially tighter connection between the community phylogeny and composition was observed in rare (R[2] = 0.65) than in abundant bacteria (R[2] = 0.08). Our study provides novel insights into the assembly processes and biographical patterns of rare and abundant bacteria in dryland soils.},
}
@article {pmid32213901,
year = {2020},
author = {Paduano, S and Marchesi, I and Casali, ME and Valeriani, F and Frezza, G and Vecchi, E and Sircana, L and Romano Spica, V and Borella, P and Bargellini, A},
title = {Characterisation of Microbial Community Associated with Different Disinfection Treatments in Hospital hot Water Networks.},
journal = {International journal of environmental research and public health},
volume = {17},
number = {6},
pages = {},
pmid = {32213901},
issn = {1660-4601},
mesh = {*Disinfection ; *Hospitals ; Humans ; Legionella ; *Microbiota ; *Water Microbiology ; *Water Purification ; *Water Supply ; },
abstract = {Many disinfection treatments can be adopted for controlling opportunistic pathogens in hospital water networks in order to reduce infection risk for immunocompromised patients. Each method has limits and strengths and it could determine modifications on bacterial community. The aim of our investigation was to study under real-life conditions the microbial community associated with different chemical (monochloramine, hydrogen peroxide, chlorine dioxide) and non-chemical (hyperthermia) treatments, continuously applied since many years in four hot water networks of the same hospital. Municipal cold water, untreated secondary, and treated hot water were analysed for microbiome characterization by 16S amplicon sequencing. Cold waters had a common microbial profile at genera level. The hot water bacterial profiles differed according to treatment. Our results confirm the effectiveness of disinfection strategies in our hospital for controlling potential pathogens such as Legionella, as the investigated genera containing opportunistic pathogens were absent or had relative abundances ≤1%, except for non-tuberculous mycobacteria, Sphingomonas, Ochrobactrum and Brevundimonas. Monitoring the microbial complexity of healthcare water networks through 16S amplicon sequencing is an innovative and effective approach useful for Public Health purpose in order to verify possible modifications of microbiota associated with disinfection treatments.},
}
@article {pmid32213375,
year = {2020},
author = {Vandekerckhove, TGL and Boon, N and Vlaeminck, SE},
title = {Pioneering on single-sludge nitrification/denitrification at 50 °C.},
journal = {Chemosphere},
volume = {252},
number = {},
pages = {126527},
doi = {10.1016/j.chemosphere.2020.126527},
pmid = {32213375},
issn = {1879-1298},
mesh = {Ammonium Compounds ; *Bioreactors ; Carbon ; Denitrification ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Sewage ; Waste Disposal, Fluid ; },
abstract = {Thermophilic nitrification has been proven in lab-scale bioreactors at 50 °C. The challenge is now to develop a solution for thermophilic nitrogen removal, integrating nitrification with denitrification and aerobic carbon removal. This pioneering study aimed at a single-sludge nitrification/denitrification process at 50 °C, through exposing nitrification in a step by step approach to anoxia and/or organics. Firstly, recurrent anoxia was tolerated by a nitrifying community during long-term membrane bioreactor (MBR) operation (85 days), with high ammonium oxidation efficiencies (>98%). Secondly, five organic carbon sources did not affect thermophilic ammonium and nitrite oxidation rates in three-day aerobic batch flask incubations. Moving to long-term tests with sequencing batch reactors (SBR) and MBR (>250 days), good nitrification performance was obtained at increasing COD/Ninfluent ratios (0, 0.5, 1, 2 and 3). Thirdly, combining nitrification, recurrent anoxia and presence of organic carbon resulted in a nitrogen removal efficiency of 92-100%, with a COD/Nremoved of 4.8 ± 0.6 and a nitrogen removal rate of 50 ± 14 mg N g[-1] VSS d[-1]. Overall, this is the first proof of principle thermophilic nitrifiers can cope with redox fluctuations (aerobic/anoxic) and the aerobic or anoxic presence of organic carbon, can functionally co-exist with heterotrophs and that single-sludge nitrification/denitrification can be achieved.},
}
@article {pmid32209719,
year = {2020},
author = {Benítez-Páez, A and Gómez Del Pugar, EM and López-Almela, I and Moya-Pérez, &#xc1; and Codoñer-Franch, P and Sanz, Y},
title = {Depletion of Blautia Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
pmid = {32209719},
issn = {2379-5077},
abstract = {Cross-sectional studies conducted with obese and control subjects have suggested associations between gut microbiota alterations and obesity, but the links with specific disease phenotypes and proofs of causality are still scarce. The present study aimed to profile the gut microbiota of lean and obese children with and without insulin resistance to characterize associations with specific obesity-related complications and understand the role played in metabolic inflammation. Through massive sequencing of 16S rRNA gene amplicons and data analysis using a novel permutation approach, we have detected decreased incidence of Blautia species, especially Blautia luti and B. wexlerae, in the gut microbiota of obese children, which was even more pronounced in cases with both obesity and insulin resistance. There was also a parallel increase in proinflammatory cytokines and chemokines (gamma interferon [IFN-γ], tumor necrosis factor alpha [TNF-α], and monocyte chemoattractant protein 1 [MCP-1]) in feces of obese children compared to those of lean ones. B. luti and B. wexlerae were also shown to exert an anti-inflammatory effect in peripheral blood mononuclear cell cultures in vitro, compared to non-obesity-associated species. We suggest that the depletion of B. luti and B. wexlerae species in the gut ecosystem may occur in cases of obesity and contribute to metabolic inflammation leading to insulin resistance.IMPORTANCE Child obesity constitutes a risk factor for developing insulin resistance which, if sustained, could lead to more severe conditions like type 2 diabetes (T2D) in adulthood. Our study identified previously unknown species whose depletion (Blautia luti and Blautia wexlerae) is associated with insulin resistance in obese individuals. Our results also indicate that these bacterial species might help to reduce inflammation causally linked to obesity-related complications. Childhood is considered a window of opportunity to tackle obesity. These new findings provide, therefore, valuable information for the future design of microbiota-based strategies for the early prevention of obesity-related complications.},
}
@article {pmid32209716,
year = {2020},
author = {Rampelli, S and Soverini, M and D'Amico, F and Barone, M and Tavella, T and Monti, D and Capri, M and Astolfi, A and Brigidi, P and Biagi, E and Franceschi, C and Turroni, S and Candela, M},
title = {Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
pmid = {32209716},
issn = {2379-5077},
abstract = {The gut microbiome of long-lived people display an increasing abundance of subdominant species, as well as a rearrangement in health-associated bacteria, but less is known about microbiome functions. In order to disentangle the contribution of the gut microbiome to the complex trait of human longevity, we here describe the metagenomic change of the human gut microbiome along with aging in subjects with up to extreme longevity, including centenarians (aged 99 to 104 years) and semisupercentenarians (aged 105 to 109 years), i.e., demographically very uncommon subjects who reach the extreme limit of the human life span. According to our findings, the gut microbiome of centenarians and semisupercentenarians is more suited for xenobiotic degradation and shows a rearrangement in metabolic pathways related to carbohydrate, amino acid, and lipid metabolism. Collectively, our data go beyond the relationship between intestinal bacteria and physiological changes that occur with aging by detailing the shifts in the potential metagenomic functions of the gut microbiome of centenarians and semisupercentenarians as a response to progressive dietary and lifestyle modifications.IMPORTANCE The study of longevity may help us understand how human beings can delay or survive the most frequent age-related diseases and morbidities. In this scenario, the gut microbiome has been proposed as one of the variables to monitor and possibly support healthy aging. Indeed, the disruption of host-gut microbiome homeostasis has been associated with inflammation and intestinal permeability as well as a general decline in bone and cognitive health. Here, we performed a metagenomic assessment of fecal samples from semisupercentenarians, i.e., 105 to 109 years old, in comparison to young adults, the elderly, and centenarians, shedding light on the longest compositional and functional trajectory of the human gut microbiome with aging. In addition to providing a fine taxonomic resolution down to the species level, our study emphasizes the progressive age-related increase in degradation pathways of pervasive xenobiotics in Western societies, possibly as a result of a supportive process within the molecular continuum characterizing aging.},
}
@article {pmid32209464,
year = {2020},
author = {Wilbert, SA and Mark Welch, JL and Borisy, GG},
title = {Spatial Ecology of the Human Tongue Dorsum Microbiome.},
journal = {Cell reports},
volume = {30},
number = {12},
pages = {4003-4015.e3},
pmid = {32209464},
issn = {2211-1247},
support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; },
mesh = {Adult ; Aged ; Biofilms ; Ecosystem ; Female ; Humans ; Male ; Microbial Consortia ; *Microbiota ; Middle Aged ; Phylogeny ; Species Specificity ; Tongue/*microbiology ; Young Adult ; },
abstract = {A fundamental question in microbial ecology is how microbes are spatially organized with respect to each other and their host. A test bed for examining this question is the tongue dorsum, which harbors a complex and important microbial community. Here, we use multiplexed fluorescence spectral imaging to investigate the organization of the tongue microbiome at micron to hundred-micron scales. We design oligonucleotide probes for taxa both abundant and prevalent, as determined by sequence analysis. Imaging reveals a highly structured spatial organization of microbial consortia, ranging in linear dimension from tens to hundreds of microns. The consortia appear to develop from a core of epithelial cells, with taxa clustering in domains suggestive of clonal expansion. Quantitative proximity analysis provides the basis for a model of tongue dorsum microbiome organization and dynamics. Our work illustrates how high-resolution analysis of micron-scale organization provides insights into physiological functions and microbiome-host interactions.},
}
@article {pmid32208652,
year = {2020},
author = {Tian, Z and Wang, T and Tunlid, A and Persson, P},
title = {Proteolysis of Iron Oxide-Associated Bovine Serum Albumin.},
journal = {Environmental science &amp; technology},
volume = {54},
number = {8},
pages = {5121-5130},
pmid = {32208652},
issn = {1520-5851},
mesh = {Adsorption ; *Ferric Compounds ; Proteolysis ; *Serum Albumin, Bovine ; Surface Properties ; },
abstract = {Proteins are a substantial nitrogen source in soils provided that they can be hydrolyzed into bioavailable small peptides or amino acids. However, the strong associations between proteins and soil minerals restrict such proteolytic reactions. This study focused on how an extracellular fungal protease (Rhizopus sp.) hydrolyzed iron oxide-associated bovine serum albumin (BSA) and the factors that affected the proteolysis. We combined batch experiments with size-exclusion and reversed phase liquid chromatography and in situ infrared spectroscopic measurements to monitor the generation of proteolytic products in solution as well as the real-time changes of the adsorbed BSA during 24 h. Results showed that protease hydrolyzed the iron oxide-associated BSA directly at the surface without an initial desorption of BSA. Concurrently, the protease was adsorbed to vacant surface sites at the iron oxides, which significantly slowed down the rate of proteolysis. This inhibiting effect was counteracted by the presence of preadsorbed phosphate or by increasing the BSA coverage, which prevented protease adsorption. Fast initial rates of iron oxide-associated BSA proteolysis, comparable to proteolysis of BSA in solution, and very slow rates at prolonged proteolysis suggest a large variability in mineral-associated proteins as a nitrogen source in soils and that only a fraction of the protein is bioavailable.},
}
@article {pmid32208436,
year = {2020},
author = {Marsland, R and Cui, W and Goldford, J and Mehta, P},
title = {The Community Simulator: A Python package for microbial ecology.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0230430},
pmid = {32208436},
issn = {1932-6203},
support = {R35 GM119461/GM/NIGMS NIH HHS/United States ; },
mesh = {Algorithms ; Computer Simulation ; Ecology/*methods ; *Microbiota ; Population Dynamics ; *Software ; },
abstract = {Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new open-source, freely available Python package called Community Simulator for simulating microbial population dynamics in a reproducible, transparent and scalable way. The Community Simulator includes five major elements: tools for preparing the initial states and environmental conditions for a set of samples, automatic generation of dynamical equations based on a dictionary of modeling assumptions, random parameter sampling with tunable levels of metabolic and taxonomic structure, parallel integration of the dynamical equations, and support for metacommunity dynamics with migration between samples. To significantly speed up simulations using Community Simulator, our Python package implements a new Expectation-Maximization (EM) algorithm for finding equilibrium states of community dynamics that exploits a recently discovered duality between ecological dynamics and convex optimization. We present data showing that this EM algorithm improves performance by between one and two orders compared to direct numerical integration of the corresponding ordinary differential equations. We conclude by listing several recent applications of the Community Simulator to problems in microbial ecology, and discussing possible extensions of the package for directly analyzing microbiome compositional data.},
}
@article {pmid32206831,
year = {2020},
author = {Mehta, O and Ghosh, TS and Kothidar, A and Gowtham, MR and Mitra, R and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and , and Nair, GB and Bhatnagar, S and Das, B},
title = {Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {487-499},
doi = {10.1007/s00248-020-01501-0},
pmid = {32206831},
issn = {1432-184X},
support = {No.BT/PR9983/MED/97/194/2013//Department of Biotechnology, Government of India/ ; },
mesh = {Adult ; Bacteria/isolation &amp; purification ; Female ; Genome, Bacterial/*physiology ; Humans ; India ; Lactobacillus/genetics/*physiology ; *Microbiota ; Pregnancy ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Vagina/*microbiology ; Young Adult ; },
abstract = {The trillions of microorganisms residing in the human body display varying degrees of compositional and functional diversities within and between individuals and contribute significantly to host physiology and susceptibility to disease. Microbial species present in the vaginal milieu of reproductive age women showed a large personal component and varies widely in different ethnic groups at the taxonomic, genomic, and functional levels. Lactobacillus iners, L. crispatus, L. gasseri, L. jensenii, and L. johnsonii are most frequently detected bacterial species in the vaginal milieu of reproductive age women. However, we currently lack (i) an understanding of the baseline vaginal microbiota of reproductive age Indian women, (ii) the extent of taxonomic and functional variations of vaginal microbiota between individuals and (iii) the genomic repertoires of the dominant vaginal microbiota associated with the Indian subjects. In our study, we analyzed the metagenome of high vaginal swab (HVS) samples collected from 40 pregnant Indian women enrolled in the GARBH-Ini cohort. Composition and abundance of bacterial species was characterized by pyrosequencing 16S rRNA gene. We identified 3067 OTUs with ≥ 10 reads from four different bacterial phyla. Several species of lactobacilli were clustered into three community state types (CSTs). L. iners, L. crispatus, L. gasseri, and L. jensenii are the most frequently detected Lactobacillus species in the vaginal environment of Indian women. Other than Lactobacillus, several species of Halomonas were also identified in the vaginal environment of most of the women sampled. To gain genomic and functional insights, we isolated several Lactobacillus species from the HVS samples and explored their whole genome sequences by shotgun sequencing. We analyzed the genome of dominant Lactobacillus species, L. iners, L. crispatus, L. gasseri, and L. paragesseri to represent the CSTs and identify functions that may influence the composition of complex vaginal microbial ecology. This study reports for the first time the vaginal microbial ecology of Indian women and genomic insights into L. iners, L. crispatus, L. gasseri, and L. paragesseri commonly found in the genital tract of reproductive age women.},
}
@article {pmid32203519,
year = {2020},
author = {Botterweg-Paredes, E and Blaakmeer, A and Hong, SY and Sun, B and Mineri, L and Kruusvee, V and Xie, Y and Straub, D and Ménard, D and Pesquet, E and Wenkel, S},
title = {Light affects tissue patterning of the hypocotyl in the shade-avoidance response.},
journal = {PLoS genetics},
volume = {16},
number = {3},
pages = {e1008678},
pmid = {32203519},
issn = {1553-7404},
mesh = {Arabidopsis/genetics/growth &amp; development ; Arabidopsis Proteins/genetics/metabolism ; Body Patterning/*physiology ; Gene Expression Regulation, Plant/genetics ; Homeodomain Proteins/genetics/metabolism ; Hypocotyl/*metabolism/physiology ; *Light ; Plant Leaves/growth &amp; development ; Transcription Factors/genetics/metabolism ; },
abstract = {Plants have evolved strategies to avoid shade and optimize the capture of sunlight. While some species are tolerant to shade, plants such as Arabidopsis thaliana are shade-intolerant and induce elongation of their hypocotyl to outcompete neighboring plants. We report the identification of a developmental module acting downstream of shade perception controlling vascular patterning. We show that Arabidopsis plants react to shade by increasing the number and types of water-conducting tracheary elements in the vascular cylinder to maintain vascular density constant. Mutations in genes affecting vascular patterning impair the production of additional xylem and also show defects in the shade-induced hypocotyl elongation response. Comparative analysis of the shade-induced transcriptomes revealed differences between wild type and vascular patterning mutants and it appears that the latter mutants fail to induce sets of genes encoding biosynthetic and cell wall modifying enzymes. Our results thus set the stage for a deeper understanding of how growth and patterning are coordinated in a dynamic environment.},
}
@article {pmid32201415,
year = {2020},
author = {Kamagata, Y},
title = {Recent Biofilm Studies Open a New Door in Microbial Ecology.},
journal = {Microbes and environments},
volume = {35},
number = {1},
pages = {},
pmid = {32201415},
issn = {1347-4405},
mesh = {*Biofilms ; *Ecology ; Environmental Pollutants ; Japan ; Research/*statistics &amp; numerical data ; },
}
@article {pmid32200752,
year = {2020},
author = {Castledine, M and Sierocinski, P and Padfield, D and Buckling, A},
title = {Community coalescence: an eco-evolutionary perspective.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190252},
pmid = {32200752},
issn = {1471-2970},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Biological Evolution ; *Life History Traits ; *Microbiota ; },
abstract = {Community coalescence, the mixing of different communities, is widespread throughout microbial ecology. Coalescence can result in approximately equal contributions from the founding communities or dominance of one community over another. These different outcomes have ramifications for community structure and function in natural communities, and the use of microbial communities in biotechnology and medicine. However, we have little understanding of when a particular outcome might be expected. Here, we integrate existing theory and data to speculate on how a crucial characteristic of microbial communities-the type of species interaction that dominates the community-might affect the outcome of microbial community coalescence. Given the often comparable timescales of microbial ecology and microevolution, we explicitly consider ecological and evolutionary dynamics, and their interplay, in determining coalescence outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}
@article {pmid32200748,
year = {2020},
author = {VanInsberghe, D and Arevalo, P and Chien, D and Polz, MF},
title = {How can microbial population genomics inform community ecology?.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190253},
pmid = {32200748},
issn = {1471-2970},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Gene Flow ; *Metagenomics ; Microbiota/*genetics ; },
abstract = {Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}
@article {pmid32200745,
year = {2020},
author = {Prosser, JI},
title = {Putting science back into microbial ecology: a question of approach.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190240},
pmid = {32200745},
issn = {1471-2970},
mesh = {Ecology ; Microbiology ; *Microbiota ; },
abstract = {Microbial ecology, the scientific study of interactions between natural microbial communities and their environments, has been facilitated by the application of molecular and 'omics'-based techniques that overcome some of the limitations of cultivation-based studies. This has increased emphasis on community ecology and 'microbiome' studies, but the majority address technical, rather than scientific challenges. Most are descriptive, do not address scientific aims or questions and are not designed to increase understanding or test hypotheses. The term 'hypothesis' is increasingly misused and critical testing of ideas or theory is restricted to a small minority of studies. This article discusses current microbial ecology research within the context of four approaches: description, induction, inference to the best explanation and deduction. The first three of these do not follow the established scientific method and are not based on scientific ecological questions. Observations are made and sometimes compared with published data, sometimes with attempts to explain findings in the context of existing ideas or hypotheses, but all lack objectivity and are biased by the observations made. By contrast, deductive studies address ecological questions and attempt to explain currently unexplained phenomena through the construction of hypotheses, from mechanism-based assumptions, that generate predictions that are then tested experimentally. Identification of key scientific questions, research driven by meaningful hypotheses and adoption of scientific method are essential for progress in microbial ecology, rather than the current emphasis on descriptive approaches that address only technical challenges. It is, therefore, imperative that we carefully consider and define the fundamental scientific questions that drive our own research and focus on ideas, concepts and hypotheses that can increase understanding, and only then consider which techniques are required for experimental testing. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}
@article {pmid32200744,
year = {2020},
author = {Pascual-García, A and Bonhoeffer, S and Bell, T},
title = {Metabolically cohesive microbial consortia and ecosystem functioning.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190245},
pmid = {32200744},
issn = {1471-2970},
mesh = {Bacteria/*metabolism ; *Ecosystem ; Microbial Consortia/*physiology ; },
abstract = {Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in the context of competition for resources and metabolic complementarity given that, in microbial communities (MCs), many excreted by-products of metabolism may also be resources. MCs therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organization between the species and the community level may be pervasive, where tightly knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community- and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}
@article {pmid32200742,
year = {2020},
author = {Ciccarese, D and Zuidema, A and Merlo, V and Johnson, DR},
title = {Interaction-dependent effects of surface structure on microbial spatial self-organization.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190246},
pmid = {32200742},
issn = {1471-2970},
mesh = {Microbiota/*physiology ; Pseudomonas stutzeri/*physiology ; },
abstract = {Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization. Using pairs of isogenic strains of Pseudomonas stutzeri, we performed range expansion experiments in the absence or presence of physical objects and quantified the effects on spatial self-organization. We demonstrate that physical objects create local deformities along the expansion frontier, and these deformities increase in magnitude during range expansion. The deformities affect the densities of interspecific boundaries and diversity along the expansion frontier, and thus affect spatial self-organization, but the effects are interaction-dependent. For competitive interactions that promote sectorized patterns of spatial self-organization, physical objects increase the density of interspecific boundaries and diversity. By contrast, for cross-feeding interactions that promote dendritic patterns, they decrease the density of interspecific boundaries and diversity. These qualitatively different outcomes are probably caused by fundamental differences in the orientations of the interspecific boundaries. Thus, in order to predict the effects of physical objects on spatial self-organization, information is needed regarding the interactions present within a community and the general geometric shapes of spatial self-organization that emerge from those interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}
@article {pmid32200741,
year = {2020},
author = {Locey, KJ and Muscarella, ME and Larsen, ML and Bray, SR and Jones, SE and Lennon, JT},
title = {Dormancy dampens the microbial distance-decay relationship.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190243},
pmid = {32200741},
issn = {1471-2970},
mesh = {Bacteria/classification/*isolation &amp; purification ; Environment ; *Forests ; Geography ; Indiana ; *Microbiota ; Ponds/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Wetlands ; },
abstract = {Much of Earth's biodiversity has the capacity to engage in dormancy, a reversible state of reduced metabolic activity. By increasing resilience to unfavourable conditions, dormancy leads to the accumulation of 'seed banks'. These reservoirs of genetic and phenotypic diversity should diminish the strength of environmental filtering and increase rates of dispersal. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biogeography is lacking. We constructed geographical and environmental distance-decay relationships (DDRs) for the total (DNA) and active (RNA) portions of bacterial communities in a regional-scale 16S rRNA survey of forested ponds in Indiana, USA. As predicted, total communities harboured greater diversity and exhibited weaker DDRs than active communities. These observations were robust to random resampling and different community metrics. To evaluate the processes underlying the biogeographic patterns, we developed a platform of mechanistic models that used the geographical coordinates and environmental characteristics of our study system. Based on more than 10[6] simulations, our models approximated the empirical DDRs when there was strong environmental filtering along with the presence of long-lived seed banks. By contrast, the inclusion of dispersal generally decreased model performance. Together, our findings support recent theoretical predictions that seed banks can influence the biogeographic patterns of microbial communities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}
@article {pmid32200739,
year = {2020},
author = {Morris, A and Meyer, K and Bohannan, B},
title = {Linking microbial communities to ecosystem functions: what we can learn from genotype-phenotype mapping in organisms.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190244},
pmid = {32200739},
issn = {1471-2970},
mesh = {Bacteria/*genetics ; Bacterial Physiological Phenomena ; *Ecosystem ; *Genotype ; Microbiota/*physiology ; *Phenotype ; },
abstract = {Microbial physiological processes are intimately involved in nutrient cycling. However, it remains unclear to what extent microbial diversity or community composition is important for determining the rates of ecosystem-scale functions. There are many examples of positive correlations between microbial diversity and ecosystem function, but how microbial communities 'map' onto ecosystem functions remain unresolved. This uncertainty limits our ability to predict and manage crucial microbially mediated processes such as nutrient losses and greenhouse gas emissions. To overcome this challenge, we propose integrating traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping in organisms. We identify two insights from genotype-phenotype mapping that could be useful for microbial biodiversity-ecosystem function studies: the concept of searching 'agnostically' for markers of ecosystem function and controlling for population stratification to identify microorganisms uniquely associated with ecosystem function. We illustrate the potential for these approaches to elucidate microbial biodiversity-ecosystem function relationships by analysing a subset of published data measuring methane oxidation rates from tropical soils. We assert that combining the approaches of traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping will generate novel hypotheses about how complex microbial communities drive ecosystem function and help scientists predict and manage changes to ecosystem functions resulting from human activities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}
@article {pmid32200738,
year = {2020},
author = {Sorensen, JW and Shade, A},
title = {Dormancy dynamics and dispersal contribute to soil microbiome resilience.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190255},
pmid = {32200738},
issn = {1471-2970},
mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; *Microbiota ; Population Dynamics ; *Soil Microbiology ; },
abstract = {In disturbance ecology, stability is composed of resistance to change and resilience towards recovery after the disturbance subsides. Two key microbial mechanisms that can support microbiome stability include dormancy and dispersal. Specifically, microbial populations that are sensitive to disturbance can be re-seeded by local dormant pools of viable and reactivated cells, or by immigrants dispersed from regional metacommunities. However, it is difficult to quantify the contributions of these mechanisms to stability without, first, distinguishing the active from inactive membership, and, second, distinguishing the populations recovered by local resuscitation from those recovered by dispersed immigrants. Here, we investigate the contributions of dormancy dynamics (activation and inactivation), and dispersal to soil microbial community resistance and resilience. We designed a replicated, 45-week time-series experiment to quantify the responses of the active soil microbial community to a thermal press disturbance, including unwarmed control mesocosms, disturbed mesocosms without dispersal, and disturbed mesocosms with dispersal after the release of the stressor. Communities changed in structure within one week of warming. Though the disturbed mesocosms did not fully recover within 29 weeks, resuscitation of thermotolerant taxa was key for community transition during the press, and both resuscitation of opportunistic taxa and immigration contributed to community resilience. Also, mesocosms with dispersal were more resilient than mesocosms without. This work advances the mechanistic understanding of how microbiomes respond to disturbances in their environment. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}
@article {pmid32200737,
year = {2020},
author = {Nunan, N and Schmidt, H and Raynaud, X},
title = {The ecology of heterogeneity: soil bacterial communities and C dynamics.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190249},
pmid = {32200737},
issn = {1471-2970},
mesh = {Bacteria/*metabolism ; Bacterial Physiological Phenomena ; Carbon/*metabolism ; *Ecosystem ; *Microbiota ; *Soil Microbiology ; },
abstract = {Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have yet to be fully apprehended and have not been fully integrated into our understanding of microbial functioning. In this contribution we first discuss how the heterogeneity of the soil microbial environment, and the consequent uncertainty associated with acquiring resources, may have affected how microbial metabolism, motility and interactions evolved and, ultimately, the overall microbial activity that is represented in ecosystem models, such as heterotrophic decomposition or respiration. We then present an analysis of predicted metabolic pathways for soil bacteria, obtained from the MetaCyc pathway/genome database collection (https://metacyc.org/). The analysis suggests that while there is a relationship between phylogenic affiliation and the catabolic range of soil bacterial taxa, there does not appear to be a trade-off between the 16S rRNA gene copy number, taken as a proxy of potential growth rate, of bacterial strains and the range of substrates that can be used. Finally, we present a simple, spatially explicit model that can be used to understand how the interactions between decomposers and environmental heterogeneity affect the bacterial decomposition of organic matter, suggesting that environmental heterogeneity might have important consequences on the variability of this process. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}
@article {pmid32200418,
year = {2021},
author = {Ferreira, DA and da Silva, TF and Pylro, VS and Salles, JF and Andreote, FD and Dini-Andreote, F},
title = {Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {100-103},
pmid = {32200418},
issn = {1432-184X},
mesh = {Fungi/genetics ; *Mycorrhizae ; Plant Roots ; Soil ; Soil Microbiology ; },
abstract = {Terrestrial plants establish symbiosis with arbuscular mycorrhizal fungi (AMF) to exchange water and nutrients. However, the extent to which soil biodiversity influences such association remains still unclear. Here, we manipulated the soil microbial diversity using a "dilution-to-extinction" approach in a controlled pot microcosm system and quantified the root length colonization of maize plants by the AMF Rhizophagus clarus. The experiment was performed by manipulating the soil microbiome within a native and foreign soil having distinct physicochemical properties. Overall, our data revealed significant positive correlations between the soil microbial diversity and AMF colonization. Most importantly, this finding opposes the diversity-invasibility hypothesis and highlights for a potential overall helper effect of the soil biodiversity on plant-AMF symbiosis.},
}
@article {pmid32200249,
year = {2020},
author = {Santos, A and Rachid, C and Pacheco, AB and Magalhães, V},
title = {Biotic and abiotic factors affect microcystin-LR concentrations in water/sediment interface.},
journal = {Microbiological research},
volume = {236},
number = {},
pages = {126452},
doi = {10.1016/j.micres.2020.126452},
pmid = {32200249},
issn = {1618-0623},
mesh = {Biodegradation, Environmental ; Cyanobacteria/*metabolism ; Genes, Bacterial ; Geologic Sediments/analysis/*microbiology ; *Harmful Algal Bloom ; Humans ; Hydrogen-Ion Concentration ; Lakes/microbiology ; Marine Toxins ; Metagenomics ; Microbiota/*genetics ; *Microcystins/analysis ; RNA, Ribosomal, 16S/genetics ; Temperature ; Water/analysis ; Water Pollutants, Chemical/*analysis ; },
abstract = {Harmful cyanobacterial blooms are increasingly common in aquatic environments. This can lead to higher concentrations of cyanotoxins, such as microcystins (MCs), posing a great risk to diverse organisms, including humans. MCs are among the most commonly reported cyanotoxins in freshwater environments worldwide, where they may have different fates. MCs can adsorb to suspended particles into the water column and deposit onto the sediment where they can be affected by physical factors (e.g. winds in shallow lakes causing sediment resuspension) or biological factors (e.g. biodegradation). Here we focused on the conditions of a coastal shallow lagoon contaminated by MCs aiming to estimate the return of pre-existing MCs from the sediment to the water column, to evaluate the adsorption of dissolved MC-LR to the sediment and to verify the occurrence of biodegradation. In experiments with sediment, desorption and adsorption were tested under the influence of temperature, pH and aeration, reproducing conditions observed in the lagoon. MC-desorption was not detected under the tested conditions. Spiking MC-LR into lagoon water samples in the presence of sediment resulted in a 50 % reduction of soluble MC-LR concentration in control conditions (25 °C, pH 8.0, no aeration). Increasing temperature (45 °C) or introducing aeration further stimulated MC-LR removal from the water. Biodegradation was observed in sediment samples and interstitial water (even with tetracycline). The composition of the bacterial community differed in sediment and interstitial water: major phyla were Chloroflexi, Proteobacteria, Firmicutes, and OP3. From the assigned OTUs, we identified genera already described as MC degrading bacteria. Thus, the sediment is a key factor influencing the fate of MC-LR in this shallow coastal lake contributing to stable adsorption and biodegradation.},
}
@article {pmid32198347,
year = {2020},
author = {Chatzigiannidou, I and Teughels, W and Van de Wiele, T and Boon, N},
title = {Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile.},
journal = {NPJ biofilms and microbiomes},
volume = {6},
number = {1},
pages = {13},
pmid = {32198347},
issn = {2055-5008},
mesh = {Acetates/analysis ; Bacteria/drug effects/genetics/*growth &amp; development ; Biofilms/*drug effects/growth &amp; development ; Butyrates/analysis ; Chlorhexidine/*pharmacology ; Formates/analysis ; Humans ; Lactic Acid/analysis ; Metabolomics ; Microbial Sensitivity Tests ; Microbial Viability/drug effects ; Mouth/drug effects/*microbiology ; Mouthwashes/*pharmacology ; Propionates/analysis ; Symbiosis/drug effects ; },
abstract = {Oral diseases (e.g., dental caries, periodontitis) are developed when the healthy oral microbiome is imbalanced allowing the increase of pathobiont strains. Common practice to prevent or treat such diseases is the use of antiseptics, like chlorhexidine. However, the impact of these antiseptics on the composition and metabolic activity of the oral microbiome is poorly addressed. Using two types of oral biofilms-a 14-species community (more controllable) and human tongue microbiota (more representative)-the impact of short-term chlorhexidine exposure was explored in-depth. In both models, oral biofilms treated with chlorhexidine exhibited a pattern of inactivation (>3 log units) and fast regrowth to the initial bacterial concentrations. Moreover, the chlorhexidine treatment induced profound shifts in microbiota composition and metabolic activity. In some cases, disease associated traits were increased (such as higher abundance of pathobiont strains or shift in high lactate production). Our results highlight the need for alternative treatments that selectively target the disease-associated bacteria in the biofilm without targeting the commensal microorganisms.},
}
@article {pmid32196510,
year = {2020},
author = {Farhana, L and Sarkar, S and Nangia-Makker, P and Yu, Y and Khosla, P and Levi, E and Azmi, A and Majumdar, APN},
title = {Natural agents inhibit colon cancer cell proliferation and alter microbial diversity in mice.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0229823},
pmid = {32196510},
issn = {1932-6203},
support = {I01 BX001927/BX/BLRD VA/United States ; R21 CA175916/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Biological Products/*pharmacology/therapeutic use ; Cell Proliferation/drug effects ; Colonic Neoplasms/*drug therapy/pathology ; Curcuma ; Curcumin/*pharmacology/therapeutic use ; Gastrointestinal Microbiome/*drug effects ; HCT116 Cells ; Humans ; Mice ; Mice, SCID ; Plant Extracts/*pharmacology/therapeutic use ; Tocotrienols/*pharmacology/therapeutic use ; Xenograft Model Antitumor Assays ; },
abstract = {The current study was undertaken to investigate the effect of differentially formulated polyphenolic compound Essential Turmeric Oil-Curcumin (ETO-Cur), and Tocotrienol-rich fraction (TRF) of vitamin E isomers on colorectal cancer (CRC) cells that produce aggressive tumors. Combinations of ETO-Cur and TRF were used to determine the combinatorial effects of ETO-Cur and TRF-mediated inhibition of growth of CRC cells in vitro and HCT-116 cells xenograft in SCID mice. 16S rRNA gene sequence profiling was performed to determine the outcome of gut microbial communities in mice feces between control and ETO-Cur-TRF groups. Bacterial identifications were validated by performing SYBR-based Real Time (RT) PCR. For metagenomics analysis to characterize the microbial communities, multiple software/tools were used, including Quantitative Insights into Microbial Ecology (QIIME) processing tool. We found ETO-Cur and TRF to synergize and that the combination of ETO-Cur-TRF significantly inhibited growth of HCT-116 xenografts in SCID mice. This was associated with a marked alteration in microbial communities and increased microbial OTU (operation taxonomic unit) number. The relative abundance of taxa was increased and the level of microbial diversity after 34 days of combinatorial treatment was found to be 44% higher over the control. Shifting of microbial family composition was observed in ETO-Cur-TRF treated mice as evidenced by marked reductions in Bacteroidaceae, Ruminococcaceae, Clostridiales, Firmicutes and Parabacteroids families, compared to controls. Interestingly, during the inhibition of tumor growth in ETO-Cur treated mice, probiotic Lactobacillaceae and Bifidobacteriaceae were increased by 20-fold and 6-fold, respectively. The relative abundance of anti-inflammatory Clostridium XIVa was also increased in ETO-Cur-TRF treated mice when compared with the control. Our data suggest that ETO-Cur-TRF show synergistic effects in inhibiting colorectal cancer cell proliferation in vitro and in mouse xenografts in vivo, and might induce changes in microbial diversity in mice.},
}
@article {pmid32195301,
year = {2020},
author = {Ghosh, A and Debnath, M and Bhadury, P},
title = {Datasets of surface water microbial populations from two anthropogenically impacted sites on the Bhagirathi-Hooghly River.},
journal = {Data in brief},
volume = {29},
number = {},
pages = {105371},
pmid = {32195301},
issn = {2352-3409},
abstract = {The Bhagirathi-Hooghly River, part of the River Ganga, flows along densely urbanized areas in West Bengal, India. The River water is extensively used for household activities, human consumption including bathing, social purposes and multifaceted industrial usage. As a result of discharge of untreated municipal sewage and effluents from industries there is evidence of heavy pollution in this River. Two urbanized sites on the Bhagirathi-Hooghly River, namely Kalyani and Kolkata, were sampled to elucidate the resident microbial communities in lieu of anthropogenic forcing with respect to pollution. The Kalyani station (Kal_Stn1) lies upstream to the Kolkata station (Kol_Stn7) and are approximate 50 km away from each other and located along the bank of Bhagirathi-Hooghly River. Sampling was undertaken in monsoon (September 2018). In situ environmental parameters were measured during sampling and dissolved nutrients were estimated from formalin fixed filtered surface water along with pesticides analysis. One litre surface water sample was collected from each station and environmental DNA was sequenced to identify resident microbial communities (bacterioplankton and oxygenic photoautrophs-phytoplankton). The bacterioplankton community structure was elucidated by sequencing the V4 region of the 16S rDNA on an Illumina MiSeq platform. Proteobacteria was found to be the most abundant bacterioplankton phylum in both sampling stations. Similar to bacterioplankton, variation in oxygenic photoautotrophic community structure including phytoplankton forms was found at phylum, class and family levels. The phytoplankton communities were elucidated by sequencing the V9 region of the 18S rDNA on an Illumina MiSeq platform. Chrysophyta was found to be the most abundant phytoplankton phylum identified from both stations, followed by Chlorophyta and other groups. Variation in phytoplankton community structure between the stations was distinct at phylum, class and family levels.},
}
@article {pmid32194964,
year = {2020},
author = {Gueneau, R and Blanchet, D and Rodriguez-Nava, V and Bergeron, E and Soulier, M and Bestandji, N and Demar, M and Couppie, P and Blaizot, R},
title = {Actinomycetoma caused by Gordonia westfalica: first reported case of human infection.},
journal = {New microbes and new infections},
volume = {34},
number = {},
pages = {100658},
pmid = {32194964},
issn = {2052-2975},
abstract = {Bacteria of the genus Gordonia are rarely involved in human infections. We report here the case of a 30-year-old man from Guinea Buissau with mycetoma of the foot. 16S DNA sequencing after surgical biopsy identified Gordonia westfalica. To our knowledge, this is the first report of human infection caused by G. westfalica.},
}
@article {pmid32194531,
year = {2020},
author = {Flores, N and Hoyos, S and Venegas, M and Galetović, A and Zúñiga, LM and Fábrega, F and Paredes, B and Salazar-Ardiles, C and Vilo, C and Ascaso, C and Wierzchos, J and Souza-Egipsy, V and Araya, JE and Batista-García, RA and Gómez-Silva, B},
title = {Haloterrigena sp. Strain SGH1, a Bacterioruberin-Rich, Perchlorate-Tolerant Halophilic Archaeon Isolated From Halite Microbial Communities, Atacama Desert, Chile.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {324},
pmid = {32194531},
issn = {1664-302X},
abstract = {An extreme halophilic archaeon, strain SGH1, is a novel microorganism isolated from endolithic microbial communities colonizing halites at Salar Grande, Atacama Desert, in northern Chile. Our study provides structural, biochemical, genomic, and physiological information on this new isolate living at the edge of the physical and chemical extremes at the Atacama Desert. SGH1 is a Gram-negative, red-pigmented, non-motile unicellular coccoid organism. Under the transmission electron microscope, strain SGH1 showed an abundant electro-dense material surrounding electron-lucent globular structures resembling gas vacuoles. Strain SGH1 showed a 16S rRNA gene sequence with a close phylogenetic relationship to the extreme halophilic archaea Haloterrigena turkmenica and Haloterrigena salina and has been denominated Haloterrigena sp. strain SGH1. Strain SGH1 grew at 20-40°C (optimum 37°C), at salinities between 15 and 30% (w/v) NaCl (optimum 25%) and growth was improved by addition of 50 mM KCl and 0.5% w/v casamino acids. Growth was severely restricted at salinities below 15% NaCl and cell lysis is avoided at a minimal 10% NaCl. Maximal concentrations of magnesium chloride and sodium or magnesium perchlorates that supported SGH1 growth were 0.5 and 0.15M, respectively. Haloterrigena sp. strain SGH1 accumulates bacterioruberin (BR), a C50 xanthophyll, as the major carotenoid. Total carotenoids in strain SGH1 amounted to nearly 400 μg BR per gram of dry biomass. Nearly 80% of total carotenoids accumulated as geometric isomers of BR: all-trans-BR (50%), 5-cis-BR (15%), 9-cis-BR (10%), 13-cis-BR (4%); other carotenoids were dehydrated derivatives of BR. Carotenogenesis in SGH1 was a reversible and salt-dependent process; transferring BR-rich cells grown in 25% (w/v) NaCl to 15% (w/v) NaCl medium resulted in depigmentation, and BR content was recovered after transference and growth of unpigmented cells to high salinity medium. Methanol extracts and purified BR isomers showed an 8-9-fold higher antioxidant activity than Trolox or β-carotene. Both, plasma membrane integrity and mitochondrial membrane potential measurements under acute 18-h assays showed that purified BR isomers were non-toxic to cultured human THP-1 cells.},
}
@article {pmid32194522,
year = {2020},
author = {Cortes-Tolalpa, L and Wang, Y and Salles, JF and van Elsas, JD},
title = {Comparative Genome Analysis of the Lignocellulose Degrading Bacteria Citrobacter freundii so4 and Sphingobacterium multivorum w15.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {248},
pmid = {32194522},
issn = {1664-302X},
abstract = {Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as the single carbon and energy source. They were identified as Citrobacter freundii so4 and Sphingobacterium multivorum w15 based on 16S rRNA gene sequencing and comparison to the respective C. freundii and S. multivorum type strains. In order to identify the mechanisms driving the synergistic interactions, we analyzed the draft genomes of the two strains and further characterized their metabolic potential. The latter analyses revealed that the strains had largely complementary substrate utilization patterns, with only 22 out of 190 compounds shared. The analyses further indicated C. freundii so4 to primarily consume amino acids and simple sugars, with laminarin as a key exception. In contrast, S. multivorum w15 showed ample capacity to transform complex polysaccharides, including intermediates of starch degradation. Sequence analyses revealed C. freundii so4 to have a genome of 4,883,214 bp, with a G + C content of 52.5%, 4,554 protein-encoding genes and 86 RNA genes. S. multivorum w15 has a genome of 6,678,278 bp, with a G + C content of 39.7%, 5,999 protein-encoding genes and 76 RNA genes. Genes for motility apparatuses (flagella, chemotaxis) were present in the genome of C. freundii so4, but absent from that of S. multivorum w15. In the genome of S. multivorum w15, 348 genes had regions matching CAZy family enzymes and/or carbohydrate-binding modules (CBMs), with 193 glycosyl hydrolase (GH) and 50 CBM domains. Remarkably, 22 domains matched enzymes of glycoside hydrolase family GH43, suggesting a strong investment in the degradation of arabinoxylan. In contrast, 130 CAZy family genes were found in C. freundii so4, with 61 GH and 12 CBM domains identified. Collectively, our results, based on both metabolic potential and genome analyses, revealed the two strains to harbor complementary catabolic armories, with S. multivorum w15 primarily attacking the WS hemicellulose and C. freundii so4 the cellobiose derived from cellulose, next to emerging oligo- or monosaccharides. Finally, C. freundii so4 may secrete secondary metabolites that S. multivorum w15 can consume, and detoxify the system by reducing the levels of (toxic) by-products.},
}
@article {pmid32193752,
year = {2020},
author = {Corti-Monzón, G and Nisenbaum, M and Villegas-Plazas, M and Junca, H and Murialdo, S},
title = {Enrichment and characterization of a bilge microbial consortium with oil in water-emulsions breaking ability for oily wastewater treatment.},
journal = {Biodegradation},
volume = {31},
number = {1-2},
pages = {57-72},
doi = {10.1007/s10532-020-09894-y},
pmid = {32193752},
issn = {1572-9729},
support = {Resoluci&#xf3;n N&#xba; 428/16 y 429/16//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas/International ; VT38-UNMdP10982//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Productiva/International ; },
mesh = {Biodegradation, Environmental ; Emulsions ; *Microbial Consortia ; RNA, Ribosomal, 16S ; Shewanella ; *Wastewater ; },
abstract = {Oily bilge wastewater is one of the main sources of hydrocarbons pollution in marine environments due to accidental or clandestine discharges. The main technical challenge for its effective treatment is the presence of stable oil-in-water (O/W) emulsions. In this work we are reporting an enriched microbial consortium from bilge wastewater with remarkable ability to demulsify oil in water emulsions. The consortium showed emulsion-breaking ratios up to 72.6% in the exponential growth phase, while the values range from 11.9 to 8.5% in stationary phase. A positive association was observed between demulsifying ability and microbial adhesion to hydrocarbons, as well as between cell concentration and demulsifying ability. Also, an interesting ability to demulsify under different temperatures, conditions of agitation, and bilge emulsions from different vessels was observed. The Bacterial and Archaeal composition was analyzed by 16S rRNA gene amplicon lllumina sequencing analyses, revealing an assemblage composed of bacterial types highly related to well characterized bacterial isolates and also to non-yet cultured bacterial types previously detected in marine and sediment samples. Hydrocarbonoclastic microbial types such as Marinobacter, Flavobacteriaceae, Alcanivorax and Gammaproteobacteria PYR10d3 were found in high relative abundance (27.0%-11.1%) and types of marine oligotrophs and surfactant degraders such as Thallasospira, Parvibaculum, Novospirillum, Shewanella algae, and Opitutae were in a group of middle predominance (1.7-3.5%). The microbial consortium reported has promising potential for the biological demulsification of bilge wastewater and other oily wastewaters.},
}
@article {pmid32192536,
year = {2020},
author = {Kavagutti, VS and Andrei, A&#x15e; and Mehrshad, M and Salcher, MM and Ghai, R},
title = {Correction to: Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {40},
pmid = {32192536},
issn = {2049-2618},
abstract = {Following publication of the original article [1], the authors reported that an affiliation of the first author was missing.},
}
@article {pmid32191867,
year = {2020},
author = {Dini-Andreote, F},
title = {Endophytes: The Second Layer of Plant Defense.},
journal = {Trends in plant science},
volume = {25},
number = {4},
pages = {319-322},
doi = {10.1016/j.tplants.2020.01.007},
pmid = {32191867},
issn = {1878-4372},
mesh = {*Endophytes ; Plant Roots ; Plants ; *Rhizosphere ; Soil Microbiology ; },
abstract = {Microorganisms in association with roots can protect plants against soil-borne diseases. A recent study mechanistically revealed how root endophytes act as a second microbiological layer of plant defense. Integrating ecological concepts with principles of plant pathology provides an innovative way to manipulate and engineer beneficial plant microbiomes.},
}
@article {pmid32187685,
year = {2020},
author = {Pu, X and Li, Z and Tian, Y and Gao, R and Hao, L and Hu, Y and He, C and Sun, W and Xu, M and Peters, RJ and Van de Peer, Y and Xu, Z and Song, J},
title = {The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration.},
journal = {The New phytologist},
volume = {227},
number = {3},
pages = {930-943},
pmid = {32187685},
issn = {1469-8137},
support = {833522/ERC_/European Research Council/International ; },
mesh = {Carotenoids ; Flowers/genetics ; Gene Expression Profiling ; *Lonicera/genetics ; },
abstract = {Lonicera japonica is a widespread member of the Caprifoliaceae (honeysuckle) family utilized in traditional medical practices. This twining vine honeysuckle also is a much-sought ornamental, in part due to its dynamic flower coloration, which changes from white to gold during development. The molecular mechanism underlying dynamic flower coloration in L. japonica was elucidated by integrating whole genome sequencing, transcriptomic analysis and biochemical assays. Here, we report a chromosome-level genome assembly of L. japonica, comprising nine pseudochromosomes with a total size of 843.2 Mb. We also provide evidence for a whole-genome duplication event in the lineage leading to L. japonica, which occurred after its divergence from Dipsacales and Asterales. Moreover, gene expression analysis not only revealed correlated expression of the relevant biosynthetic genes with carotenoid accumulation, but also suggested a role for carotenoid degradation in L. japonica's dynamic flower coloration. The variation of flower color is consistent with not only the observed carotenoid accumulation pattern, but also with the release of volatile apocarotenoids that presumably serve as pollinator attractants. Beyond novel insights into the evolution and dynamics of flower coloration, the high-quality L. japonica genome sequence also provides a foundation for molecular breeding to improve desired characteristics.},
}
@article {pmid32184367,
year = {2020},
author = {Danczak, RE and Daly, RA and Borton, MA and Stegen, JC and Roux, S and Wrighton, KC and Wilkins, MJ},
title = {Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
pmid = {32184367},
issn = {2379-5077},
abstract = {The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurface ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels.IMPORTANCE Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels.},
}
@article {pmid32184363,
year = {2020},
author = {Fu, S and Wei, D and Yang, Q and Xie, G and Pang, B and Wang, Y and Lan, R and Wang, Q and Dong, X and Zhang, X and Huang, J and Feng, J and Liu, Y},
title = {Horizontal Plasmid Transfer Promotes the Dissemination of Asian Acute Hepatopancreatic Necrosis Disease and Provides a Novel Mechanism for Genetic Exchange and Environmental Adaptation.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
pmid = {32184363},
issn = {2379-5077},
abstract = {Vibrio parahaemolyticus is an important foodborne pathogen and has recently gained particular notoriety because it causes acute hepatopancreatic necrosis disease (AHPND) in shrimp, which has caused significant economic loss in the shrimp industry. Here, we report a whole-genome analysis of 233 V. parahaemolyticus strains isolated from humans, diseased shrimp, and environmental samples collected between 2008 and 2017, providing unprecedented insight into the historical spread of AHPND. The results show that V. parahaemolyticus is genetically diverse and can be divided into 84 sequence types (STs). However, genomic analysis of three STs of V. parahaemolyticus identified seven transmission routes in Asia since 1996, which promoted the transfer of an AHPND-associated plasmid. Notably, the insertion sequence (ISVal1) from the plasmid subsequently mediated the genetic exchange among V. parahaemolyticus STs and resulted in the deletion of an 11-kb region regulating cell mobility and the production of capsular polysaccharides. Phenotype assays confirmed that this deletion enhanced biofilm formation, providing a novel mechanism for environmental adaptation. We conclude that the transmission mode of AHPND consists of two steps, the transmission of V. parahaemolyticus and the subsequent horizontal transfer of the AHPND-associated plasmid. This plasmid allows ISVal1 to mediate genetic exchange and improve pathogen fitness in shrimp ponds. Current shrimp farming practices promoted such genetic exchanges, which highlighted a risk of the emergence of new virulent populations, with potentially devastating consequences for both aquaculture and human health. This study addressed the basic questions regarding the transmission mechanism of AHPND and provided novel insights into shrimp and human disease management.IMPORTANCE Global outbreaks of shrimp acute hepatopancreatic necrosis disease (AHPND) caused by V. parahaemolyticus represent an urgent issue for the shrimp industry. This study revealed that the transmission mode of AHPND consists of two steps, the transregional dissemination of V. parahaemolyticus and the horizontal transfer of an AHPND-associated plasmid. Surprisingly, the introduction of the AHPND-associated plasmid also offers a novel mechanism of genetic exchange mediated by insertion sequences, and it improved the fitness of V. parahaemolyticus in a harsh environment. The results presented herein suggest that current shrimp farming practices promote genetic mixture between endemic and oceanic V. parahaemolyticus populations, which introduced the plasmid and accelerated bacterial adaptation by the acquisition of ecologically important functions. This entails a risk of the emergence of new virulent populations both for shrimp and humans. This study improves our understanding of the global dissemination of the AHPND-associated plasmid and highlights the urgent need to improve biosecurity for shrimp farming.},
}
@article {pmid32184251,
year = {2020},
author = {Yang, Y and Daims, H and Liu, Y and Herbold, CW and Pjevac, P and Lin, JG and Li, M and Gu, JD},
title = {Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
pmid = {32184251},
issn = {2150-7511},
support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Ammonia/*metabolism ; Bacteria/classification/*genetics/*metabolism ; Genome, Bacterial ; Metagenome ; Multigene Family ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Transcriptome ; Wastewater/*microbiology ; *Water Purification ; },
abstract = {The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions.IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.},
}
@article {pmid32180337,
year = {2020},
author = {Spanoghe, J and Grunert, O and Wambacq, E and Sakarika, M and Papini, G and Alloul, A and Spiller, M and Derycke, V and Stragier, L and Verstraete, H and Fauconnier, K and Verstraete, W and Haesaert, G and Vlaeminck, SE},
title = {Storage, fertilization and cost properties highlight the potential of dried microbial biomass as organic fertilizer.},
journal = {Microbial biotechnology},
volume = {13},
number = {5},
pages = {1377-1389},
pmid = {32180337},
issn = {1751-7915},
mesh = {Agriculture ; Biomass ; Fertilization ; *Fertilizers ; Nitrogen/analysis ; *Soil ; Spirulina ; },
abstract = {The transition to sustainable agriculture and horticulture is a societal challenge of global importance. Fertilization with a minimum impact on the environment can facilitate this. Organic fertilizers can play an important role, given their typical release pattern and production through resource recovery. Microbial fertilizers (MFs) constitute an emerging class of organic fertilizers and consist of dried microbial biomass, for instance produced on effluents from the food and beverage industry. In this study, three groups of organisms were tested as MFs: a high-rate consortium aerobic bacteria (CAB), the microalga Arthrospira platensis ('Spirulina') and a purple non-sulfur bacterium (PNSB) Rhodobacter sp. During storage as dry products, the MFs showed light hygroscopic activity, but the mineral and organic fractions remained stable over a storage period of 91 days. For biological tests, a reference organic fertilizer (ROF) was used as positive control, and a commercial organic growing medium (GM) as substrate. The mineralization patterns without and with plants were similar for all MFs and ROF, with more than 70% of the organic nitrogen mineralized in 77 days. In a first fertilization trial with parsley, all MFs showed equal performance compared to ROF, and the plant fresh weight was even higher with CAB fertilization. CAB was subsequently used in a follow-up trial with petunia and resulted in elevated plant height, comparable chlorophyll content and a higher amount of flowers compared to ROF. Finally, a cost estimation for packed GM with supplemented fertilizer indicated that CAB and a blend of CAB/PNSB (85%/15%) were most cost competitive, with an increase of 6% and 7% in cost compared to ROF. In conclusion, as bio-based fertilizers, MFs have the potential to contribute to sustainable plant nutrition, performing as good as a commercially available organic fertilizer, and to a circular economy.},
}
@article {pmid32179899,
year = {2020},
author = {Byers, AK and Condron, L and Donavan, T and O'Callaghan, M and Patuawa, T and Waipara, N and Black, A},
title = {Soil microbial diversity in adjacent forest systems - contrasting native, old growth kauri (Agathis australis) forest with exotic pine (Pinus radiata) plantation forest.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {5},
pages = {},
pmid = {32179899},
issn = {1574-6941},
mesh = {Ecosystem ; Forests ; New Zealand ; *Pinus ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; },
abstract = {Globally, the conversion of primary forests to plantations and agricultural landscapes is a common land use change. Kauri (Agathis australis) is one of the most heavily impacted indigenous tree species of New Zealand with <1% of primary forest remaining as fragments adjacent to pastoral farming and exotic forest plantations. By contrasting two forest systems, we investigated if the fragmentation of kauri forests and introduction of pine plantations (Pinus radiata) are significantly impacting the diversity and composition of soil microbial communities across Waipoua kauri forest, New Zealand. Using next generation based 16S rRNA and ITS gene region sequencing, we identified that fungal and bacterial community composition significantly differed between kauri and pine forest soils. However, fungal communities displayed the largest differences in diversity and composition. This research revealed significant shifts in the soil microbial communities surrounding remnant kauri fragments, including the loss of microbial taxa with functions in disease suppression and plant health. Kauri dieback disease, caused by Phytophthora agathidicida, currently threatens the kauri forest ecosystem. Results from this research highlight the need for further investigations into how changes to soil microbial diversity surrounding remnant kauri fragments impact tree health and disease expression.},
}
@article {pmid32179343,
year = {2020},
author = {Gurmessa, B and Pedretti, EF and Cocco, S and Cardelli, V and Corti, G},
title = {Manure anaerobic digestion effects and the role of pre- and post-treatments on veterinary antibiotics and antibiotic resistance genes removal efficiency.},
journal = {The Science of the total environment},
volume = {721},
number = {},
pages = {137532},
doi = {10.1016/j.scitotenv.2020.137532},
pmid = {32179343},
issn = {1879-1026},
mesh = {Anaerobiosis ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Microbial/drug effects ; Genes, Bacterial/drug effects ; *Manure ; },
abstract = {This review was aimed to summarize and critically evaluate studies on removal of veterinary antibiotics (VAs), antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) with anaerobic digestion (AD) of manure and demonstrate areas of focus for improved removal efficiency. The environmental risks associated to the release of the same were also critically evaluated. The potential of AD and advanced AD of manure on removal rate of VAs, ARGs and MGEs was thoroughly assessed. In addition, the role of post and pre-AD treatments and their potential to support VAs and ARGs removal efficiency were evaluated. The overall review results show disparity among the different groups of VAs in terms of removal rate with relatively higher efficiency for β-lactams and tetracyclines compared to the other groups. Some of sulfonamides, fluoroquinolones and macrolides were reported to be highly persistent with removal rates as low as zero. Within group differences were also reported in many literatures. Moreover, removal of ARGs and MGEs by AD was widely reported although complete removal was hardly possible. Even in rare scenarios, some AD conditions were reported to increase copies of specific groups of the genes. Temperature pretreatments and temperature phased advanced AD were also reported to improve removal efficiency of VAs while contributing to increased biogas production. Moreover, a few studies also showed the possibility of further removal by post-AD treatments such as liquid-solid separation, drying and composting. In conclusion, the various studies revealed that AD in its current technological level is not a guarantee for complete removal of VAs, ARGs and MGEs from manure. Consequently, their possible release to the soils with digestate could threaten the healthcare and disturb soil microbial ecology. Thus, intensive management strategies need to be designed to increase removal efficiency at the different manure management points along the anaerobic digestion process.},
}
@article {pmid32175570,
year = {2020},
author = {Ruiz, C and Villegas-Plazas, M and Thomas, OP and Junca, H and Pérez, T},
title = {Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha).},
journal = {FEMS microbiology ecology},
volume = {96},
number = {4},
pages = {},
doi = {10.1093/femsec/fiaa043},
pmid = {32175570},
issn = {1574-6941},
mesh = {Animals ; *Microbiota ; Phylogeny ; *Porifera ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.},
}
@article {pmid32172072,
year = {2020},
author = {Wen, D and Valencia, A and Ordonez, D and Chang, NB and Wanielista, M},
title = {Comparative nitrogen removal via microbial ecology between soil and green sorption media in a rapid infiltration basin for co-disposal of stormwater and wastewater.},
journal = {Environmental research},
volume = {184},
number = {},
pages = {109338},
doi = {10.1016/j.envres.2020.109338},
pmid = {32172072},
issn = {1096-0953},
mesh = {Ammonia ; Denitrification ; *Nitrogen ; Oxidation-Reduction ; Soil ; *Wastewater ; },
abstract = {In this study, a rapid infiltration basin (RIB) designed as green infrastructure for co-disposal of wastewater effluent and stormwater runoff was retrofitted for sustainable groundwater recharge after nitrogen removal. For comparison of nitrogen removal efficiency via different filtration media, the RIB was divided into two sub-basins for different filtration processes. One sub-basin was filled with a native sandy soil with about 2-4% clay (Control RIB), and the other sub-basin was modified with Biosorption Activated Media (BAM) (BAM RIB), for the enhancement of microbial nitrogen removal. The two sub-basins accept an equal amount of excess reclaimed wastewater in non-storm periods, and stormwater during periodic storm events. The infiltrate in both the BAM RIB and the Control RIB eventually reaches the Upper Floridan Aquifer. The seven microbial species involved in this microbial ecology study are nitrite oxidizing bacteria (NOB), ammonia oxidizing bacteria (AOB), anaerobic oxidation of ammonium (anammox) bacteria, complete ammonia oxidizer (Comammox) bacteria, denitrifiers, dissimilatory nitrate reduction to ammonium (DNRA) and ammonia-oxidizing archaea (AOA). The population dynamics study was conducted with the aid of the quantitative polymerase chain reaction (qPCR) for the quantification of the microbial gene population in support of microbial ecology discovery. The qPCR results demonstrated the competition effect between AOA, AOB, and Comammox, the inhibition effect between NOB and DNRA with the presence of anammox, and the complementary effect due to an abundance of NOB and AOB in the microbial ecology. Although, competition between denitrifiers and DNRA was expected to impact population dynamics, both microbial species were found to be the most predominant in both control and BAM RIBs. Research findings indicate that the use of BAM RIB achieves significantly efficient nitrogen removal driven by complementary effects in the microbial ecology.},
}
@article {pmid32171709,
year = {2020},
author = {Garin-Fernandez, A and Glöckner, FO and Wichels, A},
title = {Genomic characterization of filamentous phage vB_VpaI_VP-3218, an inducible prophage of Vibrio parahaemolyticus.},
journal = {Marine genomics},
volume = {53},
number = {},
pages = {100767},
doi = {10.1016/j.margen.2020.100767},
pmid = {32171709},
issn = {1876-7478},
mesh = {*Genome, Viral ; Inoviridae/*genetics ; North Sea ; Prophages/*genetics ; Vibrio parahaemolyticus/*virology ; Virus Activation ; },
abstract = {The seawater temperature rise can promote the growth of potentially pathogenic Vibrio species. In the North Sea, V. parahaemolyticus strains have been isolated and characterized. These strains contain prophages that may contribute to the emergence of pathogenic strains in the marine environment. Here, we present the genome structure and possible biological functions of the inducible phage vB_VpaI_VP-3218, a novel filamentous phage carried by the V. parahaemolyticus strain VN-3218. Prophages of the strain VN-3218 were induced with mitomycin C and the DNA from the phage induction was sequenced. Two incomplete prophages were identified, only one complete phage genome with length of 11,082 bp was characterized. The phage vB_VpaI_VP-3218 belongs to the Inoviridae family and shows close homology to the Saetivirus genus. This phage can integrate into the chromosomal host genome and carries host-related regions absent in similar phage genomes, suggesting that this phage might integrate in other Vibrio host genomes from the environment. Furthermore, this phage might have a role in pathogenicity due to potential zonula occludens toxin genes. Based on its genomic similarity, the genome of vB_VpaI_VP-3218 phage probably integrates into the lysogen's chromosome and replicates as episome. This study complements prophage induction and bioinformatic studies applied to non-model species of potentially pathogenic Vibrio species. The characterization of this phage provides new insights with respect to the presence of filamentous phages in environmental V. parahaemolyticus strains, which might have a role in the emergence of new pathogenic strains in the North Sea.},
}
@article {pmid32169939,
year = {2020},
author = {Props, R and Denef, VJ},
title = {Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {10},
pages = {},
pmid = {32169939},
issn = {1098-5336},
mesh = {Comamonadaceae/classification/*genetics/*physiology ; *Gene Expression ; *Genes, Bacterial ; *Genetic Variation ; Lakes/microbiology ; Michigan ; Microbiota ; Nutrients ; Temperature ; },
abstract = {Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.IMPORTANCELimnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.},
}
@article {pmid32167574,
year = {2020},
author = {Paramasivan, S and Bassiouni, A and Shiffer, A and Dillon, MR and Cope, EK and Cooksley, C and Ramezanpour, M and Moraitis, S and Ali, MJ and Bleier, B and Callejas, C and Cornet, ME and Douglas, RG and Dutra, D and Georgalas, C and Harvey, RJ and Hwang, PH and Luong, AU and Schlosser, RJ and Tantilipikorn, P and Tewfik, MA and Vreugde, S and Wormald, PJ and Caporaso, JG and Psaltis, AJ},
title = {The international sinonasal microbiome study: A multicentre, multinational characterization of sinonasal bacterial ecology.},
journal = {Allergy},
volume = {75},
number = {8},
pages = {2037-2049},
doi = {10.1111/all.14276},
pmid = {32167574},
issn = {1398-9995},
mesh = {Bacteria/genetics ; Chronic Disease ; Humans ; *Microbiota ; *Paranasal Sinuses ; RNA, Ribosomal, 16S/genetics ; *Sinusitis/epidemiology ; },
abstract = {The sinonasal microbiome remains poorly defined, with our current knowledge based on a few cohort studies whose findings are inconsistent. Furthermore, the variability of the sinus microbiome across geographical divides remains unexplored. We characterize the sinonasal microbiome and its geographical variations in both health and disease using 16S rRNA gene sequencing of 410 individuals from across the world. Although the sinus microbial ecology is highly variable between individuals, we identify a core microbiome comprised of Corynebacterium, Staphylococcus, Streptococcus, Haemophilus and Moraxella species in both healthy and chronic rhinosinusitis (CRS) cohorts. Corynebacterium (mean relative abundance = 44.02%) and Staphylococcus (mean relative abundance = 27.34%) appear particularly dominant in the majority of patients sampled. Amongst patients suffering from CRS with nasal polyps, a statistically significant reduction in relative abundance of Corynebacterium (40.29% vs 50.43%; P = .02) was identified. Despite some measured differences in microbiome composition and diversity between some of the participating centres in our cohort, these differences would not alter the general pattern of core organisms described. Nevertheless, atypical or unusual organisms reported in short-read amplicon sequencing studies and that are not part of the core microbiome should be interpreted with caution. The delineation of the sinonasal microbiome and standardized methodology described within our study will enable further characterization and translational application of the sinus microbiota.},
}
@article {pmid32162597,
year = {2020},
author = {van Hougenhouck-Tulleken, WG and Lebre, PH and Said, M and Cowan, DA},
title = {Bacterial pathogens in peritoneal dialysis peritonitis: Insights from next-generation sequencing.},
journal = {Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis},
volume = {40},
number = {6},
pages = {581-586},
doi = {10.1177/0896860820908473},
pmid = {32162597},
issn = {1718-4304},
mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Peritoneal Dialysis/adverse effects ; *Peritonitis/etiology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Peritoneal dialysis (PD) peritonitis is a feared complication of PD, with significant sequelae for the patient. The cause of PD peritonitis is largely due to a single organism (≥75% of cases) and rarely due to multiple organisms.<br><br>METHODS: In this pilot study, we investigated 25 cases of PD peritonitis with 16S ribosomal RNA (rRNA) next-generation sequencing (NGS) techniques.<br><br>RESULTS: Total concordance between culture and NGS was noted. In addition, the NGS technique was highly sensitive, identifying 33 different bacteria (including a nonculturable bacterium), compared to 13 bacterial species using culture-based techniques. This was counterbalanced by a lack of specificity with NGS, largely due to the small size of the 16S rRNA gene segment sequenced.<br><br>CONCLUSIONS: For the clinician, our results suggest that PD peritonitis may often be a polymicrobial disease and that treating a dominant organism may not totally eradicate all bacterial contamination within the peritoneum. For the clinical scientist, additional use of a larger 16S rRNA segment (V5 or V6) is likely to outperform the use of the V4 segment only.},
}
@article {pmid32162039,
year = {2020},
author = {Neissi, A and Rafiee, G and Farahmand, H and Rahimi, S and Mijakovic, I},
title = {Cold-Resistant Heterotrophic Ammonium and Nitrite-Removing Bacteria Improve Aquaculture Conditions of Rainbow Trout (Oncorhynchus mykiss).},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {266-277},
pmid = {32162039},
issn = {1432-184X},
support = {CTS17:312//Carl Tryggers Foundation/ ; 96016671//Iran National Science Foundation/ ; },
mesh = {Ammonium Compounds/*metabolism ; Animals ; *Aquaculture ; Bacteria/*metabolism ; Heterotrophic Processes ; Nitrites/*metabolism ; *Oncorhynchus mykiss/growth &amp; development ; },
abstract = {The aim of this study was isolation and characterization of heterotrophic bacteria capable of ammonium and nitrite removal at 15 °C (optimal temperature for growing rainbow trout Oncorhynchus mykiss). Environmental isolates were grown in liquid media containing ammonium or nitrite, and best strains in terms of growth and ammonium or nitrite removal were identified via 16S rRNA sequencing. Dyadobacter sp. (no. 68) and Janthinobacterium sp. (no. 100) were selected for optimal adaptation to growth at 15 °C and best ammonium and nitrite removal (P < 0.05), respectively. A heterotrophic ammonium and nitrite removal (HAN) microbial complex, containing selected strains, was prepared and applied in a trout culture system. After 10 days, the effect of microbial HAN complex was investigated in terms of ammonium and nitrite removal, as well as stress and immune indices present in the plasma of cultivated trout. Compared to a standard cultivation setup, addition of the HAN complex had a clear beneficial effect on keeping the un-ionized ammonia and nitrite level below prescribed standards (P < 0.05). This resulted in reduction of stress and immune reactions of cultivated fish (P < 0.05), leading to an augmentation of final weight and survival. Application of the selected microbial complex resulted in a significant improvement of the aquaculture ecosystem.},
}
@article {pmid32157881,
year = {2020},
author = {Glodowska, M and Stopelli, E and Schneider, M and Lightfoot, A and Rathi, B and Straub, D and Patzner, M and Duyen, VT and , and Berg, M and Kleindienst, S and Kappler, A},
title = {Role of in Situ Natural Organic Matter in Mobilizing As during Microbial Reduction of Fe[III]-Mineral-Bearing Aquifer Sediments from Hanoi (Vietnam).},
journal = {Environmental science &amp; technology},
volume = {54},
number = {7},
pages = {4149-4159},
doi = {10.1021/acs.est.9b07183},
pmid = {32157881},
issn = {1520-5851},
mesh = {*Arsenic ; Ferric Compounds ; Geologic Sediments ; *Groundwater ; Minerals ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Vietnam ; },
abstract = {Natural organic matter (NOM) can contribute to arsenic (As) mobilization as an electron donor for microbially-mediated reductive dissolution of As-bearing Fe(III) (oxyhydr)oxides. However, to investigate this process, instead of using NOM, most laboratory studies used simple fatty acids or sugars, often at relatively high concentrations. To investigate the role of relevant C sources, we therefore extracted in situ NOM from the upper aquitard (clayey silt) and lower sandy aquifer sediments in Van Phuc (Hanoi area, Vietnam), characterized its composition, and used 100-day microcosm experiments to determine the effect of in situ OM on Fe(III) mineral reduction, As mobilization, and microbial community composition. We found that OM extracted from the clayey silt (OMC) aquitard resembles young, not fully degraded plant-related material, while OM from the sandy sediments (OMS) is more bioavailable and related to microbial biomass. Although all microcosms were amended with the same amount of C (12 mg C/L), the extent of Fe(III) reduction after 100 days was the highest with acetate/lactate (43 ± 3.5% of total Fe present in the sediments) followed by OMS (28 ± 0.3%) and OMC (19 ± 0.8%). Initial Fe(III) reduction rates were also higher with acetate/lactate (0.53 mg Fe(II) in 6 days) than with OMS and OMC (0.18 and 0.08 mg Fe(II) in 6 days, respectively). Although initially more dissolved As was detected in the acetate/lactate setups, after 100 days, higher concentrations of As (8.3 ± 0.3 and 8.8 ± 0.8 μg As/L) were reached in OMC and OMS, respectively, compared to acetate/lactate-amended setups (6.3 ± 0.7 μg As/L). 16S rRNA amplicon sequence analyses revealed that acetate/lactate mainly enriched Geobacter, while in situ OM supported growth and activity of a more diverse microbial community. Our results suggest that although the in situ NOM is less efficient in stimulating microbial Fe(III) reduction than highly bioavailable acetate/lactate, it ultimately has the potential to mobilize the same amount or even more As.},
}
@article {pmid32157374,
year = {2020},
author = {Stastney, P and Black, S},
title = {Bog Microtopography and the Climatic Sensitivity of Testate Amoeba Communities: Implications for Transfer Function-Based Paleo-Water Table Reconstructions.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {309-321},
doi = {10.1007/s00248-020-01499-5},
pmid = {32157374},
issn = {1432-184X},
mesh = {Amoebozoa/classification/*isolation &amp; purification ; Archaeology/*methods ; *Climate ; Climate Change ; Ecology/*methods ; Groundwater/*parasitology ; Ireland ; *Wetlands ; },
abstract = {Although the use of sub-fossil testate amoebae as a proxy for raised bog hydrology in Holocene paleoecological studies is well-established, some detailed aspects of species-environment relationships remain under-researched. One such issue is the effect of bog surface microtopography on the climatic sensitivity of testate amoeba communities. Although it has been suggested that some microforms-especially hummocks-may be less sensitive to climatic forcing than others, this has rarely been objectively tested. To investigate this, subfossil testate amoebae assemblages have been examined in a series of shallow cores collected along a hummock-lawn-hollow transect from a bog in central Ireland and the resulting reconstructed water table records, dated using [210]Pb, have been compared with instrumental weather data. Testate amoebae communities in the hollow microform were found to be significantly less diverse than those in the hummock and lawn, and both the hummock and lawn showed statistically significant correlations with instrumental temperature and precipitation data. Therefore, whilst the suggestion that paleoecological investigations should target intermediate bog microforms remains sound, the notion that hummock-based testate amoebae hydrological data are climatically-insensitive is challenged.},
}
@article {pmid32156798,
year = {2020},
author = {Alteio, LV and Schulz, F and Seshadri, R and Varghese, N and Rodriguez-Reillo, W and Ryan, E and Goudeau, D and Eichorst, SA and Malmstrom, RR and Bowers, RM and Katz, LA and Blanchard, JL and Woyke, T},
title = {Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.},
journal = {mSystems},
volume = {5},
number = {2},
pages = {},
pmid = {32156798},
issn = {2379-5077},
abstract = {Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.},
}
@article {pmid32155967,
year = {2020},
author = {Cabello-Olmo, M and Oneca, M and Torre, P and Díaz, JV and Encio, IJ and Barajas, M and Araña, M},
title = {Influence of Storage Temperature and Packaging on Bacteria and Yeast Viability in a Plant-Based Fermented Food.},
journal = {Foods (Basel, Switzerland)},
volume = {9},
number = {3},
pages = {},
pmid = {32155967},
issn = {2304-8158},
support = {Reference: PT022 SIMDIACOL//Advanced Innovation &amp; Technology Corporation (ADItech Corp, Department of Economic Development, Navarre Government)/ ; Reference: 001114082016000011//Miriam Cabello-Olmo was granted by the Industrial PhD program (Navarre Government)/ ; },
abstract = {Optimization of food storage has become a central issue for food science and biotechnology, especially in the field of functional foods. The aim of this work was to investigate the influence of different storage strategies in a fermented food product (FFP) and further determine whether the regular storage (room temperature (RT) and standard packaging (SP)) could be refined. Eight experimental conditions (four different temperatures × two packaging) were simulated and changes in FFP's microbial ecology (total bacteria, lactic acid bacteria (LAB), and yeasts) and physicochemical characteristics (pH and moisture content (MC)) were determined following 1, 3, 6, and 12 months. All conditions tested showed a decline in microbial content due to the effect of the temperature, 37 °C being the most detrimental condition, while -20 and 4 °C seemed to be better than RT in some parameters. Vacuum packaging (VP) only had a major effect on MC and we found that VP preserved greater MC values than SP at 3, 6, and 12 months. The correlation analysis revealed that total bacteria, LAB, and yeasts were positively associated, and also both pH and MC showed a correlation. According to our results and with the purpose to maintain the load of viable microorganisms, we observed that the best storage conditions should contemplate SP and freezing or cooling temperature during a period no longer than 3 months.},
}
@article {pmid32155432,
year = {2020},
author = {Moscoviz, R and Quéméner, ED and Trably, E and Bernet, N and Hamelin, J},
title = {Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer.},
journal = {Trends in microbiology},
volume = {28},
number = {4},
pages = {245-253},
doi = {10.1016/j.tim.2020.01.008},
pmid = {32155432},
issn = {1878-4380},
mesh = {Bacteria ; Biotechnology ; *Ecology ; Electrodes ; *Electron Transport ; *Electrons ; Energy Metabolism ; Fermentation ; Microbiota/*physiology ; },
abstract = {Recent advances in microbial electrochemical technologies have revealed the existence of numerous and highly diverse microorganisms able to exchange electrons with electrodes. This diversity could reflect the capacity of microorganisms to release and/or retrieve electrons with each other in natural environments. So far, this interspecies electron transfer has been studied with a special focus on syntrophy and was successfully demonstrated for several couples of species. In this article we argue that electron exchange between microbes exists beyond syntrophy or mutualism and could also promote competitive and even parasitic behaviour. Based on three interesting case studies identified from the literature, we also highlight that such nonmutualistic interactions could be widespread and of particular significance for the survival of pathogens or the shaping of complex microbial communities.},
}
@article {pmid32155265,
year = {2020},
author = {Mukherjee, S and Naha, S and Bhadury, P and Saha, B and Dutta, M and Dutta, S and Basu, S},
title = {Emergence of OXA-232-producing hypervirulent Klebsiella pneumoniae ST23 causing neonatal sepsis.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {75},
number = {7},
pages = {2004-2006},
doi = {10.1093/jac/dkaa080},
pmid = {32155265},
issn = {1460-2091},
mesh = {Humans ; Infant, Newborn ; *Klebsiella Infections ; Klebsiella pneumoniae/genetics ; *Neonatal Sepsis/epidemiology ; beta-Lactamases/genetics ; },
}
@article {pmid32153553,
year = {2020},
author = {Cliffe, L and Nixon, SL and Daly, RA and Eden, B and Taylor, KG and Boothman, C and Wilkins, MJ and Wrighton, KC and Lloyd, JR},
title = {Identification of Persistent Sulfidogenic Bacteria in Shale Gas Produced Waters.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {286},
pmid = {32153553},
issn = {1664-302X},
abstract = {Produced waters from hydraulically fractured shale formations give insight into the microbial ecology and biogeochemical conditions down-well. This study explores the potential for sulfide production by persistent microorganisms recovered from produced water samples collected from the Marcellus shale formation. Hydrogen sulfide is highly toxic and corrosive, and can lead to the formation of "sour gas" which is costly to refine. Furthermore, microbial colonization of hydraulically fractured shale could result in formation plugging and a reduction in well productivity. It is vital to assess the potential for sulfide production in persistent microbial taxa, especially when considering the trend of reusing produced waters as input fluids, potentially enriching for problematic microorganisms. Using most probable number (MPN) counts and 16S rRNA gene sequencing, multiple viable strains of bacteria were identified from stored produced waters, mostly belonging to the Genus Halanaerobium, that were capable of growth via fermentation, and produced sulfide when supplied with thiosulfate. No sulfate-reducing bacteria (SRB) were detected through culturing, despite the detection of relatively low numbers of sulfate-reducing lineages by high-throughput 16S rRNA gene sequencing. These results demonstrate that sulfidogenic produced water populations remain viable for years post production and, if left unchecked, have the potential to lead to natural gas souring during shale gas extraction.},
}
@article {pmid32151461,
year = {2019},
author = {Chriswell, ME and Kuhn, KA},
title = {Microbiota-mediated mucosal inflammation in arthritis.},
journal = {Best practice &amp; research. Clinical rheumatology},
volume = {33},
number = {6},
pages = {101492},
pmid = {32151461},
issn = {1532-1770},
support = {K08 DK107905/DK/NIDDK NIH HHS/United States ; R01 AR075033/AR/NIAMS NIH HHS/United States ; T32 AR007534/AR/NIAMS NIH HHS/United States ; },
mesh = {*Arthritis/microbiology ; Humans ; Immune Tolerance ; Immunity, Mucosal ; *Inflammation ; *Microbiota ; },
abstract = {Mucosal surfaces are a unique symbiotic environment between a host and a vast and diverse ecology of microbes. These microbes have great immunomodulatory potential with respect to the host organism. Indeed, the mucosal immune system strikes a delicate balance between tolerance of commensal organisms and overt inflammation to ward off pathogens. Disruptions of the microbial ecology at mucosal surfaces has been described in a vast number of different human disease processes including many forms of arthritis, and the resulting implications are still being understood to their fullest. Herein, we review the current state of knowledge in microbe-host interactions as it relates to the development of arthritis through bacterial translocation, bacterial metabolite production, education of the immune response, and molecular mimicry.},
}
@article {pmid32149022,
year = {2020},
author = {Moore, RM and Harrison, AO and McAllister, SM and Polson, SW and Wommack, KE},
title = {Iroki: automatic customization and visualization of phylogenetic trees.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8584},
pmid = {32149022},
issn = {2167-8359},
support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; },
abstract = {Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki's utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki's source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.},
}
@article {pmid32144464,
year = {2020},
author = {Nuzzo, A and Satpute, A and Albrecht, U and Strauss, SL},
title = {Impact of Soil Microbial Amendments on Tomato Rhizosphere Microbiome and Plant Growth in Field Soil.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {398-409},
doi = {10.1007/s00248-020-01497-7},
pmid = {32144464},
issn = {1432-184X},
support = {1011186//USDA-NIFA Hatch/ ; },
mesh = {Bacteria/classification/growth &amp; development/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Solanum lycopersicum/*growth &amp; development/*microbiology ; *Microbiota ; Mycorrhizae/*physiology ; *Rhizosphere ; Soil Microbiology ; Yeasts/*physiology ; },
abstract = {There is increased interest by the agricultural industry in microbial amendments that leverage natural beneficial interactions between plants and soil microbes to improve crop production. However, translating fundamental knowledge from laboratory experiments into efficient field application often has mixed results, and there is less clarity about the interaction between added microbes and the native microbial community, where microorganisms belonging to the same phylogenic clades often reside. In this study, four commercially available microbial amendments were examined in two greenhouse experiments using field soil to assess their impact on tomato plant growth and the native soil microbial communities. The amendments contained different formulations of plant growth-promoting bacteria (Lactobacilli, Rhizobia, etc.), yeasts, and mycorrhizal fungi. The application of the tested amendments in greenhouse conditions resulted in no significant impact on plant growth. A deeper statistical analysis detected variations in the microbial communities that accounted only for 0.25% of the total species, particularly in native taxa not related to the inoculated species and represented less than 1% of the total variance. This suggests that under commercial field conditions, additional confounding variables may play a role in the efficacy of soil microbial amendments. This study confirms the necessity of more in-depth validation requirements for the formulations of soil microbial amendments before delivery to the agricultural market in order to leverage their benefits for the producers, the consumers, and the environment.},
}
@article {pmid32144110,
year = {2020},
author = {Zhang, Y and Hao, X and Garcia-Lemos, AM and Nunes, I and Nicolaisen, MH and Nybroe, O},
title = {Different Effects of Soil Fertilization on Bacterial Community Composition in the Penicillium canescens Hyphosphere and in Bulk Soil.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {10},
pages = {},
pmid = {32144110},
issn = {1098-5336},
mesh = {Bacteria/classification/*metabolism ; Fertilizers ; Hyphae/metabolism ; Microbiota ; *Nitrogen Cycle ; Penicillium/*metabolism ; Phosphorus/*metabolism ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {This study investigated the effects of long-term soil fertilization on the composition and potential for phosphorus (P) and nitrogen (N) cycling of bacterial communities associated with hyphae of the P-solubilizing fungus Penicillium canescens Using a baiting approach, hyphosphere bacterial communities were recovered from three soils that had received long-term amendment in the field with mineral or mineral plus organic fertilizers. P. canescens hyphae recruited bacterial communities with a decreased diversity and an increased abundance of Proteobacteria relative to what was observed in soil communities. As core bacterial taxa, Delftia and Pseudomonas spp. were present in all hyphosphere samples irrespective of soil fertilization. However, the type of fertilization showed significant impacts on the diversity, composition, and distinctive taxa/operational taxonomic units (OTUs) of hyphosphere communities. The soil factors P (Olsen method), exchangeable Mg, exchangeable K, and pH were important for shaping soil and hyphosphere bacterial community compositions. An increased relative abundance of organic P metabolism genes was found in hyphosphere communities from soil that had not received P fertilizers, which could indicate P limitation near the fungal hyphae. Additionally, P. canescens hyphae recruited bacterial communities with a higher abundance of N fixation genes than found in soil communities, which might imply a role of hyphosphere communities for fungal N nutrition. Furthermore, the relative abundances of denitrification genes were greater in several hyphosphere communities, indicating an at least partly anoxic microenvironment with a high carbon-to-N ratio around the hyphae. In conclusion, soil fertilization legacy shapes P. canescens hyphosphere microbiomes and their functional potential related to P and N cycling.IMPORTANCE P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil.},
}
@article {pmid32143053,
year = {2020},
author = {Song, J and Jongmans-Hochschulz, E and Mauder, N and Imirzalioglu, C and Wichels, A and Gerdts, G},
title = {The Travelling Particles: Investigating microplastics as possible transport vectors for multidrug resistant E. coli in the Weser estuary (Germany).},
journal = {The Science of the total environment},
volume = {720},
number = {},
pages = {137603},
doi = {10.1016/j.scitotenv.2020.137603},
pmid = {32143053},
issn = {1879-1026},
mesh = {Anti-Bacterial Agents ; *Escherichia coli ; Estuaries ; Germany ; Microbial Sensitivity Tests ; Microplastics ; North Sea ; beta-Lactamases ; },
abstract = {The prevalence of multidrug-resistant Gram-negative bacteria in aquatic environments has been a long withstanding health concern, namely extended-spectrum beta-lactamase (ESBL) producing Escherichia coli. Given increasing reports on microplastic (MP) pollution in these environments, it has become crucial to better understand the role of MP particles as transport vectors for such multidrug-resistant bacteria. In this study, an incubation experiment was designed where particles of both synthetic and natural material (HDPE, tyre wear, and wood) were sequentially incubated at multiple sites along a salinity gradient from the Lower Weser estuary (Germany) to the offshore island Helgoland (German Bight, North Sea). Following each incubation period, particle biofilms and water samples were assessed for ESBL-producing E. coli, first by the enrichment and detection of E. coli using Fluorocult® LMX Broth followed by cultivation on CHROMAgar™ ESBL media to select for ESBL-producers. Results showed that general E. coli populations were present on the surfaces of wood particles across all sites but none were found to produce ESBLs. Additionally, neither HDPE nor tyre wear particles were found to harbour any E. coli. Conversely, ESBL-producing E. coli were present in surrounding waters from all sites, 64% of which conferred resistances against up to 3 other antibiotic groups, additional to the beta-lactam resistances intrinsic to ESBL-producers. This study provides a first look into the potential of MP to harbour and transport multidrug-resistant E. coli across different environments and the approach serves as an important precursor to further studies on other potentially harmful MP-colonizing species.},
}
@article {pmid32140148,
year = {2020},
author = {Pascoal, F and Magalhães, C and Costa, R},
title = {The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {231},
pmid = {32140148},
issn = {1664-302X},
abstract = {Current research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.},
}
@article {pmid32138992,
year = {2020},
author = {Charmpi, C and Van der Veken, D and Van Reckem, E and De Vuyst, L and Leroy, F},
title = {Raw meat quality and salt levels affect the bacterial species diversity and community dynamics during the fermentation of pork mince.},
journal = {Food microbiology},
volume = {89},
number = {},
pages = {103434},
doi = {10.1016/j.fm.2020.103434},
pmid = {32138992},
issn = {1095-9998},
mesh = {Animals ; Fermentation ; *Food Microbiology ; Lactobacillus/*genetics ; Meat Products/*microbiology ; Pork Meat/*microbiology ; Sodium Chloride, Dietary ; Staphylococcus/*genetics ; Swine ; },
abstract = {Acidification level and temperature modulate the beneficial consortia of lactic acid bacteria (LAB) and coagulase-negative staphylococci (CNS) during meat fermentation. Less is known about the impact of other factors, such as raw meat quality and salting. These could for instance affect the growth of the pathogen Staphylococcus aureus or of Enterobacterales species, potentially indicative of poor fermentation practice. Therefore, pork batters from either normal or borderline quality (dark-firm-dry, DFD) were compared at various salt concentrations (0-4%) in meat fermentation models. Microbial ecology of the samples was investigated with culture-dependent techniques and (GTG)5-PCR fingerprinting of genomic DNA. Whilst Lactobacillus sakei governed the fermentation of normal meat, Lactobacillus curvatus was more prominent in the fermentation of the DFD meat variant. CNS were favoured during fermentation at rising salt concentrations without much effects on species diversity, consisting mostly of Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus. During fermentation of DFD meat, S. saprophyticus was less manifest than during that of normal meat. Enterobacterales mainly emerged in DFD meat during fermentation at low salt concentrations. The salt hurdle was insufficient to prevent Enterobacterales when acidification and initial pH were favourable for their growth.},
}
@article {pmid32138583,
year = {2020},
author = {Tian, Y and Gui, W and Koo, I and Smith, PB and Allman, EL and Nichols, RG and Rimal, B and Cai, J and Liu, Q and Patterson, AD},
title = {The microbiome modulating activity of bile acids.},
journal = {Gut microbes},
volume = {11},
number = {4},
pages = {979-996},
pmid = {32138583},
issn = {1949-0984},
support = {S10 OD021750/OD/NIH HHS/United States ; T32 GM102057/GM/NIGMS NIH HHS/United States ; U01 DK119702/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteria/drug effects/*growth &amp; development/*metabolism ; Bile Acids and Salts/administration &amp; dosage/*metabolism/*pharmacology ; Cecum/*microbiology ; *Gastrointestinal Microbiome ; Glycolysis ; Male ; Metabolomics ; Mice ; Mice, Inbred C57BL ; Microbial Sensitivity Tests ; Probiotics ; },
abstract = {Bile acids are potent antibacterial compounds and play an important role in shaping the microbial ecology of the gut. Here, we combined flow cytometry, growth rate measurements (OD600), and NMR- and mass spectrometry-based metabolomics to systematically profile the impact of bile acids on the microbiome using in vitro and in vivo models. This study confirmed that (1) unconjugated bile acids possess more potent antibacterial activity than conjugated bile acids; (2) Gram-positive bacteria are more sensitive to bile acids than Gram-negative bacteria; (3) some probiotic bacteria such as Lactobacillus and Bifidobacterium and 7α-dehydroxylating bacteria such as Clostridium scindens show bile acid resistance that is associated with activation of glycolysis. Moreover, we demonstrated that (4) as one of most hydrophobic bile acids, lithocholic acid (LCA) shows reduced toxicity to bacteria in the cecal microbiome in both in vivo and in vitro models; (5) bile acids directly and rapidly affect bacterial global metabolism including membrane damage, disrupted amino acid, nucleotide, and carbohydrate metabolism; and (6) in vivo, short-term exposure to bile acids significantly affected host metabolism via alterations of the bacterial community structure. This study systematically profiled interactions between bile acids and gut bacteria providing validation of previous observation and new insights into the interaction of bile acids with the microbiome and mechanisms related to bile acid tolerance.},
}
@article {pmid32138281,
year = {2020},
author = {Gutiérrez-Sarmiento, W and Sáyago-Ayerdi, SG and Goñi, I and Gutiérrez-Miceli, FA and Abud-Archila, M and Rejón-Orantes, JDC and Rincón-Rosales, R and Peña-Ocaña, BA and Ruíz-Valdiviezo, VM},
title = {Changes in Intestinal Microbiota and Predicted Metabolic Pathways During Colonic Fermentation of Mango (Mangifera indica L.)-Based Bar Indigestible Fraction.},
journal = {Nutrients},
volume = {12},
number = {3},
pages = {},
pmid = {32138281},
issn = {2072-6643},
support = {6257.19-P//Tecnol&#xf3;gico Nacional de M&#xe9;xico/ ; Doctoral grant number 636047//Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACyT)/ ; },
mesh = {Adult ; Bacteria/classification/*growth &amp; development ; *Colon/metabolism/microbiology ; Dietary Fiber/*administration &amp; dosage/metabolism ; *Digestion ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Mangifera ; *Metabolic Networks and Pathways ; },
abstract = {Mango (Mangifera indica L.) peel and pulp are a source of dietary fiber (DF) and phenolic compounds (PCs) that constituent part of the indigestible fraction (IF). This fraction reaches the colon and acts as a carbon and energy source for intestinal microbiota. The effect of mango IF on intestinal microbiota during colonic fermentation is unknown. In this study, the isolated IF of a novel 'Ataulfo' mango-based bar (snack) UV-C irradiated and non-irradiated (UVMangoB and MangoB) were fermented. Colonic fermentation occurred in vitro under chemical-enzymatic, semi-anaerobic, batch culture and controlled pH colonic conditions. Changes in the structure of fecal microbiota were analyzed by 16s rRNA gene Illumina MiSeq sequencing. The community´s functional capabilities were determined in silico. The MangoB and UVMangoB increased the presence of Faecalibacterium, Roseburia, Eubacterium, Fusicatenibacter, Holdemanella, Catenibacterium, Phascolarctobacterium, Buttiauxella, Bifidobacterium, Collinsella, Prevotella and Bacteroides genera. The alpha indexes showed a decrease in microbial diversity after 6 h of colonic fermentation. The coordinates analysis indicated any differences between irradiated and non-irradiated bar. The metabolic prediction demonstrated that MangoB and UVMangoB increase the microbiota carbohydrate metabolism pathway. This study suggests that IF of mango-based bar induced beneficial changes on microbial ecology and metabolic pathway that could be promissory to prevention or treatment of metabolic dysbiosis. However, in vivo interventions are necessary to confirm the interactions between microbiota modulating and intestinal beneficial effects.},
}
@article {pmid32134703,
year = {2020},
author = {Weis, S and Schnell, S and Egert, M},
title = {Towards safer stable isotope probing - effect of formamide on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation.},
journal = {Canadian journal of microbiology},
volume = {66},
number = {8},
pages = {491-494},
doi = {10.1139/cjm-2019-0612},
pmid = {32134703},
issn = {1480-3275},
mesh = {Carbon Isotopes/chemistry ; Centrifugation, Density Gradient/methods ; Escherichia coli/chemistry/*genetics ; Formamides/chemistry ; Isotope Labeling/methods ; RNA, Bacterial/chemistry/*genetics/*isolation &amp; purification ; Ultracentrifugation/methods ; },
abstract = {RNA-based stable isotope probing (RNA-SIP) is used in molecular microbial ecology to link the identity of microorganisms in a complex community with the assimilation of a distinct substrate. The technique is highly dependent on a reliable separation of isotopic-labeled RNA from unlabeled RNA by isopycnic density gradient ultracentrifugation. Here we show that [13]C-labeled and unlabeled Escherichia coli RNA can be sufficiently separated by isopycnic ultracentrifugation even in the absence of formamide. However, a slightly lower starting density is needed to obtain a distribution pattern similar to that obtained when formamide was used. Hence, the commonly used addition of formamide to the centrifugation solution might not be needed to separate [13]C-labeled RNA from unlabeled RNA, but this must be verified for more complex environmental mixtures of RNA. Clearly, an omission of formamide would increase the safety of RNA-SIP analyses.},
}
@article {pmid32132275,
year = {2020},
author = {Gignoux-Wolfsohn, SA and Precht, WF and Peters, EC and Gintert, BE and Kaufman, LS},
title = {Ecology, histopathology, and microbial ecology of a white-band disease outbreak in the threatened staghorn coral Acropora cervicornis.},
journal = {Diseases of aquatic organisms},
volume = {137},
number = {3},
pages = {217-237},
doi = {10.3354/dao03441},
pmid = {32132275},
issn = {0177-5103},
mesh = {Animals ; *Anthozoa ; Bacteria ; Coral Reefs ; Disease Outbreaks ; Ecosystem ; Florida ; },
abstract = {This study is a multi-pronged description of a temperature-induced outbreak of white-band disease (WBD) that occurred in Acropora cervicornis off northern Miami Beach, Florida (USA), from July to October 2014. We describe the ecology of the disease and examine diseased corals using both histopathology and next-generation bacterial 16S gene sequencing, making it possible to better understand the effect this disease has on the coral holobiont, and to address some of the seeming contradictions among previous studies of WBD that employed either a purely histological or molecular approach. The outbreak began in July 2014, as sea surface temperatures reached 29°C, and peaked in mid-September, a month after the sea surface temperature maximum. The microscopic anatomy of apparently healthy portions of colonies displaying active disease signs appeared normal except for some tissue atrophy and dissociation of mesenterial filaments deep within the branch. Structural changes were more pronounced in visibly diseased fragments, with atrophy, necrosis, and lysing of surface and basal body wall and polyp structures at the tissue-loss margin. The only bacteria evident microscopically in both diseased and apparently healthy tissues with Giemsa staining was a Rickettsiales-like organism (RLO) occupying mucocytes. Sequencing also identified bacteria belonging to the order Rickettsiales in all fragments. When compared to apparently healthy fragments, diseased fragments had more diverse bacterial communities made up of many previously suggested potential primary pathogens and secondary (opportunistic) colonizers. Interactions between elevated seawater temperatures, the coral host, and pathogenic members of the diseased microbiome all contribute to the coral displaying signs of WBD.},
}
@article {pmid32131727,
year = {2020},
author = {Mastrorilli, E and Petrin, S and Orsini, M and Longo, A and Cozza, D and Luzzi, I and Ricci, A and Barco, L and Losasso, C},
title = {Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {202},
pmid = {32131727},
issn = {1471-2164},
support = {GP/EFSA/AFSCO/2015/01/CT1//European Food Safety Authority/ ; },
mesh = {DNA, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial ; Genomic Islands ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Italy ; Phylogeny ; Plasmids/genetics ; Salmonella Infections/*microbiology ; Salmonella enterica/*classification/genetics/immunology/isolation &amp; purification ; Serogroup ; Typhoid Fever/microbiology ; Whole Genome Sequencing/*methods ; beta-Lactam Resistance ; },
abstract = {BACKGROUND: Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated from humans and the environment, but neither the reservoir nor its route of infection are clearly defined. This serovar is characterized by high genomic diversity, and molecular evidences revealed important similarities with typhoidal serovars.<br><br>RESULTS: 179&#x2009;S. Napoli genomes as well as 239 genomes of typhoidal and non-typhoidal serovars were analyzed in a comparative genomic study. Phylogenetic analysis and draft genome characterization in terms of Multi Locus Sequence Typing (MLST), plasmid replicons, Salmonella Pathogenicity Islands (SPIs), antimicrobial resistance genes (ARGs), phages, biocide and metal-tolerance genes confirm the high genetic variability of S. Napoli, also revealing a within-serovar phylogenetic structure more complex than previously known. Our work also confirms genomic similarity of S. Napoli to typhoidal serovars (S. Typhi and S. Paratyphi A), with S. Napoli samples clustering primarily according to ST, each being characterized by specific genomic traits. Moreover, two major subclades of S. Napoli can be clearly identified, with ST-474 being biphyletic. All STs span among isolation sources and years of isolation, highlighting the challenge this serovar poses to define its epidemiology and evolution. Altogether, S. Napoli strains carry less SPIs and less ARGs than other non-typhoidal serovars and seldom acquire plasmids. However, we here report the second case of an extended-spectrum &#x3b2;-lactamases (ESBLs) producing S. Napoli strain and the first cases of multidrug resistant (MDR) S. Napoli strains, all isolated from humans.<br><br>CONCLUSIONS: Our results provide evidence of genomic plasticity of S. Napoli, highlighting genomic similarity with typhoidal serovars and genomic features typical of non-typhoidal serovars, supporting the possibility of survival in different niches, both enteric and non-enteric. Presence of horizontally acquired ARGs and MDR profiles rises concerns regarding possible selective pressure exerted by human environment on this pathogen.},
}
@article {pmid32128982,
year = {2020},
author = {Tu, Q},
title = {Random sampling in metagenomic sequencing leads to overestimated spatial scaling of microbial diversity.},
journal = {Environmental microbiology},
volume = {22},
number = {6},
pages = {2140-2149},
doi = {10.1111/1462-2920.14973},
pmid = {32128982},
issn = {1462-2920},
support = {31700427//National Natural Science Foundation of China/International ; 31971446//National Natural Science Foundation of China/International ; LQ17D060002//Zhejiang Provincial Natural Science Foundation of China/International ; kf2016002//Open Project of Key Laboratory of Environmental Biotechnology, CAS/International ; SKYAM002-2016//Open Funding of State Key Laboratory of Applied Microbiology Southern China/International ; 2017C82218//Bureau of Science and Technology of Zhoushan/International ; //Qilu Young Scholarship of Shandong University/International ; },
mesh = {*Biodiversity ; Forests ; Geography ; Metagenome ; Metagenomics ; Microbiota/*genetics ; Random Allocation ; *Soil Microbiology ; },
abstract = {Revealing the spatial scaling patterns of microbial diversity is of special interest in microbial ecology. One critical question is whether the observed spatial turnover rate truly reflect the actual spatial patterns of extremely diverse microbial communities. Using simulated mock communities, this study suggested that the currently observed microbial spatial turnover rates were overestimated by random sampling processes associated with high-throughput metagenomic sequencing. The observed z values were largely contributed by accumulated microbial taxa due to cumulative number of samples. This is a crucial issue because microbial communities already have very low spatial turnover rate due to the small size and potential cosmopolitism nature of microorganisms. Further investigations suggested a linear relationship between the observed and expected z values, which can be applied to remove random sampling noises from the observed z values. Adjustment of z values for data sets from six American forests showed much lower spatial turnover rate than that before adjustment. However, the patterns of z values among these six forests remained unchanged. This study suggested that our current understanding of microbial taxa-area relationships could be inaccurate. Therefore, cautions and efforts should be made for more accurate estimation and interpretation of microbial spatial patterns.},
}
@article {pmid32127448,
year = {2020},
author = {McClelland, HLO and Jones, C and Chubiz, LM and Fike, DA and Bradley, AS},
title = {Direct Observation of the Dynamics of Single-Cell Metabolic Activity during Microbial Diauxic Growth.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
pmid = {32127448},
issn = {2150-7511},
mesh = {Biomass ; Carbon/metabolism ; Isotope Labeling ; Methylobacterium extorquens/*growth &amp; development/*metabolism ; Nitrogen/metabolism ; Phenotype ; Single-Cell Analysis/*methods ; Spectrometry, Mass, Secondary Ion/methods ; },
abstract = {Population-level analyses are rapidly becoming inadequate to answer many of biomedical science and microbial ecology's most pressing questions. The role of microbial populations within ecosystems and the evolutionary selective pressure on individuals depend fundamentally on the metabolic activity of single cells. Yet, many existing single-cell technologies provide only indirect evidence of metabolic specialization because they rely on correlations between transcription and phenotype established at the level of the population to infer activity. In this study, we take a top-down approach using isotope labels and secondary ion mass spectrometry to track the uptake of carbon and nitrogen atoms from different sources into biomass and directly observe dynamic changes in anabolic specialization at the level of single cells. We investigate the classic microbiological phenomenon of diauxic growth at the single-cell level in the model methylotroph Methylobacterium extorquens In nature, this organism inhabits the phyllosphere, where it experiences diurnal changes in the available carbon substrates, necessitating an overhaul of central carbon metabolism. We show that the population exhibits a unimodal response to the changing availability of viable substrates, a conclusion that supports the canonical model but has thus far been supported by only indirect evidence. We anticipate that the ability to monitor the dynamics of anabolism in individual cells directly will have important applications across the fields of ecology, medicine, and biogeochemistry, especially where regulation downstream of transcription has the potential to manifest as heterogeneity that would be undetectable with other existing single-cell approaches.IMPORTANCE Understanding how genetic information is realized as the behavior of individual cells is a long-term goal of biology but represents a significant technological challenge. In clonal microbial populations, variation in gene regulation is often interpreted as metabolic heterogeneity. This follows the central dogma of biology, in which information flows from DNA to RNA to protein and ultimately manifests as activity. At present, DNA and RNA can be characterized in single cells, but the abundance and activity of proteins cannot. Inferences about metabolic activity usually therefore rely on the assumption that transcription reflects activity. By tracking the atoms from which they build their biomass, we make direct observations of growth rate and substrate specialization in individual cells throughout a period of growth in a changing environment. This approach allows the flow of information from DNA to be constrained from the distal end of the regulatory cascade and will become an essential tool in the rapidly advancing field of single-cell metabolism.},
}
@article {pmid32126162,
year = {2020},
author = {Ntagia, E and Chatzigiannidou, I and Williamson, AJ and Arends, JBA and Rabaey, K},
title = {Homoacetogenesis and microbial community composition are shaped by pH and total sulfide concentration.},
journal = {Microbial biotechnology},
volume = {13},
number = {4},
pages = {1026-1038},
pmid = {32126162},
issn = {1751-7915},
mesh = {Acetates ; Fermentation ; Hydrogen-Ion Concentration ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sulfides ; },
abstract = {Biological CO2 sequestration through acetogenesis with H2 as electron donor is a promising technology to reduce greenhouse gas emissions. Today, a major issue is the presence of impurities such as hydrogen sulfide (H2 S) in CO2 containing gases, as they are known to inhibit acetogenesis in CO2 -based fermentations. However, exact values of toxicity and inhibition are not well-defined. To tackle this uncertainty, a series of toxicity experiments were conducted, with a mixed homoacetogenic culture, total dissolved sulfide concentrations ([TDS]) varied between 0 and 5 mM and pH between 5 and 7. The extent of inhibition was evaluated based on acetate production rates and microbial growth. Maximum acetate production rates of 0.12, 0.09 and 0.04 mM h[-1] were achieved in the controls without sulfide at pH 7, pH 6 and pH 5. The half-maximal inhibitory concentration (IC50 [qAc]) was 0.86, 1.16 and 1.36 mM [TDS] for pH 7, pH 6 and pH 5. At [TDS] above 3.33 mM, acetate production and microbial growth were completely inhibited at all pHs. 16S rRNA gene amplicon sequencing revealed major community composition transitions that could be attributed to both pH and [TDS]. Based on the observed toxicity levels, treatment approaches for incoming industrial CO2 streams can be determined.},
}
@article {pmid32125831,
year = {2020},
author = {Hu, X and Kerckhof, FM and Ghesquière, J and Bernaerts, K and Boeckx, P and Clauwaert, P and Boon, N},
title = {Microbial Protein out of Thin Air: Fixation of Nitrogen Gas by an Autotrophic Hydrogen-Oxidizing Bacterial Enrichment.},
journal = {Environmental science &amp; technology},
volume = {54},
number = {6},
pages = {3609-3617},
doi = {10.1021/acs.est.9b06755},
pmid = {32125831},
issn = {1520-5851},
mesh = {*Autotrophic Processes ; Bacteria ; *Hydrogen ; Nitrogen ; Nitrogen Fixation ; Oxidation-Reduction ; },
abstract = {For the production of edible microbial protein (MP), ammonia generated by the Haber-Bosch process or reclaimed ammonia from waste streams is typically considered as the nitrogen source. These processes for ammonia production are highly energy intensive. In this study, the potential for using nitrogen gas (N2) as a direct nitrogen source for MP production by hydrogen-oxidizing bacteria (HOB) was evaluated. The use of N2 versus ammonium as nitrogen source during the enrichment process resulted in differentiation of the bacterial community composition of the enrichments. A few previously unknown potential N2-fixing HOB taxa (i.e., representatives of the genus Azonexus and the family Comamonadaceae) dominated the enrichments. The biomass yield of a N2-fixing HOB enrichment was 30-50% lower than that of the ammonium-based HOB enrichment from the same inoculum source. The dried biomass of N2-fixing HOB had a high protein content (62.0 ± 6.3%) and an essential amino acid profile comparable to MP from ammonium-based HOB. MP from N2-fixing HOB could potentially be produced in situ without entailing the emissions caused by ammonia production and transportation by conventional means. It could be a promising substitute for N2-fixing protein-rich soybean because it has 70% higher protein content and double energy conversion efficiency from solar energy to biomass.},
}
@article {pmid32124916,
year = {2020},
author = {Rossmann, M and Pérez-Jaramillo, JE and Kavamura, VN and Chiaramonte, JB and Dumack, K and Fiore-Donno, AM and Mendes, LW and Ferreira, MMC and Bonkowski, M and Raaijmakers, JM and Mauchline, TH and Mendes, R},
title = {Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {4},
pages = {},
doi = {10.1093/femsec/fiaa032},
pmid = {32124916},
issn = {1574-6941},
support = {BB/N016246/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/0 0005196/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/000I0310/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Bacteria/genetics ; Fungi/genetics ; *Microbiota ; Plant Roots ; *Rhizosphere ; Soil Microbiology ; Triticum ; },
abstract = {Plants modulate the soil microbiota by root exudation assembling a complex rhizosphere microbiome with organisms spanning different trophic levels. Here, we assessed the diversity of bacterial, fungal and cercozoan communities in landraces and modern varieties of wheat. The dominant taxa within each group were the bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria; the fungi phyla Ascomycota, Chytridiomycota and Basidiomycota; and the Cercozoa classes Sarcomonadea, Thecofilosea and Imbricatea. We showed that microbial networks of the wheat landraces formed a more intricate network topology than that of modern wheat cultivars, suggesting that breeding selection resulted in a reduced ability to recruit specific microbes in the rhizosphere. The high connectedness of certain cercozoan taxa to bacteria and fungi indicated trophic network hierarchies where certain predators gain predominance over others. Positive correlations between protists and bacteria in landraces were preserved as a subset in cultivars as was the case for the Sarcomonadea class with Actinobacteria. The correlations between the microbiome structure and plant genotype observed in our results suggest the importance of top-down control by organisms of higher trophic levels as a key factor for understanding the drivers of microbiome community assembly in the rhizosphere.},
}
@article {pmid32123959,
year = {2020},
author = {O'Brien, AM and Laurich, J and Lash, E and Frederickson, ME},
title = {Mutualistic Outcomes Across Plant Populations, Microbes, and Environments in the Duckweed Lemna minor.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {384-397},
doi = {10.1007/s00248-019-01452-1},
pmid = {32123959},
issn = {1432-184X},
support = {RGPIN-2015-06742//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Araceae/drug effects/genetics/growth &amp; development/*microbiology ; Bacteria/*growth &amp; development ; Genetic Fitness ; Genotype ; Host Microbial Interactions ; Microbiota/*physiology ; *Symbiosis ; Water Pollutants, Chemical/*adverse effects ; Zinc/*adverse effects ; },
abstract = {The picture emerging from the rapidly growing literature on host-associated microbiota is that host traits and fitness often depend on interactive effects of host genotype, microbiota, and abiotic environment. However, testing interactive effects typically requires large, multi-factorial experiments and thus remains challenging in many systems. Furthermore, most studies of plant microbiomes focus on terrestrial hosts and microbes. Aquatic habitats may confer unique properties to microbiomes. We grew different populations of duckweed (Lemna minor), a floating aquatic plant, in three microbial treatments (adding no, "home", or "away" microbes) at two levels of zinc, a common water contaminant in urban areas, and measured both plant and microbial performance. Thus, we simultaneously manipulated plant source population, microbial community, and abiotic environment. We found strong effects of plant source, microbial treatment, and zinc on duckweed and microbial growth, with significant variation among duckweed genotypes and microbial communities. However, we found little evidence of interactive effects: zinc did not alter effects of host genotype or microbial community, and host genotype did not alter effects of microbial communities. Despite strong positive correlations between duckweed and microbe growth, zinc consistently decreased plant growth, but increased microbial growth. Furthermore, as in recent studies of terrestrial plants, microbial interactions altered a duckweed phenotype (frond aggregation). Our results suggest that duckweed source population, associated microbiome, and contaminant environment should all be considered for duckweed applications, such as phytoremediation. Lastly, we propose that duckweed microbes offer a robust experimental system for study of host-microbiota interactions under a range of environmental stresses.},
}
@article {pmid32123275,
year = {2020},
author = {Romero Victorica, M and Soria, MA and Batista-García, RA and Ceja-Navarro, JA and Vikram, S and Ortiz, M and Ontañon, O and Ghio, S and Martínez-Ávila, L and Quintero García, OJ and Etcheverry, C and Campos, E and Cowan, D and Arneodo, J and Talia, PM},
title = {Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {3864},
pmid = {32123275},
issn = {2045-2322},
mesh = {Animals ; Bacteria/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Cell Wall ; Cellulose/*chemistry ; Gastrointestinal Microbiome/*physiology ; Glycoside Hydrolases/genetics/*metabolism ; Isoptera/metabolism/*microbiology ; Plant Cells ; Species Specificity ; *Wood ; },
abstract = {In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.},
}
@article {pmid32120208,
year = {2020},
author = {Ogbughalu, OT and Vasileiadis, S and Schumann, RC and Gerson, AR and Li, J and Smart, RSC and Short, MD},
title = {Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention.},
journal = {Journal of hazardous materials},
volume = {393},
number = {},
pages = {122338},
doi = {10.1016/j.jhazmat.2020.122338},
pmid = {32120208},
issn = {1873-3336},
mesh = {Bacteria/classification/genetics/*metabolism ; Bacterial Typing Techniques ; Ferric Compounds/chemistry ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Industrial Waste/*prevention &amp; control ; Iron/*chemistry ; Mining/*methods ; Oxidation-Reduction ; Silicates/chemistry ; Soil Microbiology ; Sulfides/*chemistry ; },
abstract = {Acid and metalliferous drainage (AMD) remains a challenging issue for the mining sector. AMD management strategies have attempted to shift from treatment of acid leachates post-generation to more sustainable at-source prevention. Here, the efficacy of microbial-geochemical at-source control approach was investigated over a period of 84 weeks. Diverse microbial communities were stimulated using organic carbon amendment in a simulated silicate-containing sulfidic mine waste rock environment. Mineral waste in the unamended leach system generated AMD quickly and throughout the study, with known lithotrophic iron- and sulfur-oxidising microbes dominating column communities. The organic-amended mineral waste column showed suppressed metal dissolution and AMD generation. Molecular DNA-based next generation sequencing confirmed a less diverse lithotrophic community in the acid-producing control, with a more diverse microbial community under organic amendment comprising organotrophic iron/sulfur-reducers, autotrophs, hydrogenotrophs and heterotrophs. Time-series multivariate statistical analyses displayed distinct ecological patterns in microbial diversity between AMD- and non-AMD-environments. Focused ion beam-TEM micrographs and elemental mapping showed that silicate-stabilised passivation layers were successfully established across pyrite surfaces in organic-amended treatments, with these layers absent in unamended controls. Organic amendment and resulting increases in microbial abundance and diversity played an important role in sustaining these passivating layers in the long-term.},
}
@article {pmid32117135,
year = {2020},
author = {Sarrocco, S and Herrera-Estrella, A and Collinge, DB},
title = {Editorial: Plant Disease Management in the Post-genomic Era: From Functional Genomics to Genome Editing.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {107},
pmid = {32117135},
issn = {1664-302X},
}
@article {pmid32114382,
year = {2020},
author = {Cermak, N and Datta, MS and Conwill, A},
title = {Rapid, Inexpensive Measurement of Synthetic Bacterial Community Composition by Sanger Sequencing of Amplicon Mixtures.},
journal = {iScience},
volume = {23},
number = {3},
pages = {100915},
pmid = {32114382},
issn = {2589-0042},
abstract = {Synthetic bacterial communities are powerful tools for studying microbial ecology and evolution, as they enable rapid iteration between controlled laboratory experiments and theoretical modeling. However, their utility is hampered by the lack of fast, inexpensive, and accurate methods for quantifying bacterial community composition. Although next-generation amplicon sequencing can be very accurate, high costs (>$30 per sample) and turnaround times (>1 month) limit the nature and pace of experiments. Here, we quantify amplicon composition in synthetic bacterial communities through Sanger sequencing. We PCR amplify a universal marker gene, then we sequence this amplicon mixture in a single Sanger sequencing reaction. We then fit the "mixed" electropherogram with contributions from each community member as a linear combination of time-warped single-strain electropherograms, allowing us to estimate the fractional amplicon abundance of each strain within the community. This approach can provide results within one day and costs ∼$5 per sample.},
}
@article {pmid32111851,
year = {2020},
author = {Candry, P and Huang, S and Carvajal-Arroyo, JM and Rabaey, K and Ganigue, R},
title = {Enrichment and characterisation of ethanol chain elongating communities from natural and engineered environments.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {3682},
pmid = {32111851},
issn = {2045-2322},
abstract = {Chain elongation is a microbial process in which an electron donor, such as ethanol, is used to elongate short chain carboxylic acids, such as acetic acid, to medium chain carboxylic acids. This metabolism has been extensively investigated, but the spread and differentiation of chain elongators in the environment remains unexplored. Here, chain elongating communities were enriched from several inocula (3 anaerobic digesters, 2 animal faeces and 1 caproic acid producing environment) using ethanol and acetic acid as substrates at pH 7 and 5.5. This approach showed that (i) the inoculum's origin determines the pH where native chain elongators can grow; (ii) pH affects caproic acid production, with average caproic acid concentrations of 6.4 ± 1.6 g·L[-1] at pH 7, versus 2.3 ± 1.8 g·L[-1] at pH 5.5; however (iii) pH does not affect growth rates significantly; (iv) all communities contained a close relative of the known chain elongator Clostridium kluyveri; and (v) low pH selects for communities more enriched in this Clostridium kluyveri-relative (57.6 ± 23.2% at pH 7, 96.9 ± 1.2% at pH 5.5). These observations show that ethanol-consuming chain elongators can be found in several natural and engineered environments, but are not the same everywhere, emphasising the need for careful inoculum selection during process development.},
}
@article {pmid32106521,
year = {2020},
author = {Wang, Y and Jiang, Y and Liu, Y and Li, Y and Katz, LA and Gao, F and Yan, Y},
title = {Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research.},
journal = {Microorganisms},
volume = {8},
number = {3},
pages = {},
pmid = {32106521},
issn = {2076-2607},
support = {2018SDKJ0406-1//Marine S&amp;T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology/ ; 31772428, 31801984 and 31672279//National Natural Science Foundation of China/ ; },
abstract = {While nuclear small subunit ribosomal DNA (nSSU rDNA) is the most commonly-used gene marker in studying phylogeny, ecology, abundance, and biodiversity of microbial eukaryotes, mitochondrial small subunit ribosomal DNA (mtSSU rDNA) provides an alternative. Recently, both copy number variation and sequence variation of nSSU rDNA have been demonstrated for diverse organisms, which can contribute to misinterpretation of microbiome data. Given this, we explore patterns for mtSSU rDNA among 13 selected ciliates (representing five classes), a major component of microbial eukaryotes, estimating copy number and sequence variation and comparing to that of nSSU rDNA. Our study reveals: (1) mtSSU rDNA copy number variation is substantially lower than that for nSSU rDNA; (2) mtSSU rDNA copy number ranges from 1.0 × 10[4] to 8.1 × 10[5]; (3) a most common sequence of mtSSU rDNA is also found in each cell; (4) the sequence variation of mtSSU rDNA are mainly indels in poly A/T regions, and only half of species have sequence variation, which is fewer than that for nSSU rDNA; and (5) the polymorphisms between haplotypes of mtSSU rDNA would not influence the phylogenetic topology. Together, these data provide more insights into mtSSU rDNA as a powerful marker especially for microbial ecology studies.},
}
@article {pmid32105920,
year = {2020},
author = {Riaz, L and Wang, Q and Yang, Q and Li, X and Yuan, W},
title = {Potential of industrial composting and anaerobic digestion for the removal of antibiotics, antibiotic resistance genes and heavy metals from chicken manure.},
journal = {The Science of the total environment},
volume = {718},
number = {},
pages = {137414},
doi = {10.1016/j.scitotenv.2020.137414},
pmid = {32105920},
issn = {1879-1026},
mesh = {Anaerobiosis ; Animals ; Anti-Bacterial Agents ; Chickens ; *Composting ; Drug Resistance, Microbial ; Genes, Bacterial ; Manure ; Metals, Heavy ; },
abstract = {Composting and anaerobic digestion techniques are widely used for manure recycling, but these methods have shown conflicting results in the removal of antibiotics, antibiotic resistance genes (ARGs), and heavy metals. In the present study, anaerobically digested chicken manure and various types of composted chicken manure were investigated on an industrial scale. Antibiotics, ARGs, and heavy metals had shown inconsistent results for anaerobic digestion and composting. The different composting processes either declined or completely removed the blaCTX-M, intl1 and oqxB genes. In addition, composting processes decreased the absolute abundance of aac6'-Ib and aadA genes, while increased the absolute abundance of qnrD, sul1, and tet(A) genes. On the other hand, anaerobic digestion of chicken manure increased the absolute abundance of ere(A) and tet(A). High throughput sequencing showed that Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria dominated the total bacterial composition of composted and anaerobically digested samples. Network analysis revealed the co-occurrence of ARGs and intl1. The redundancy analysis showed a significant correlation between some heavy metals and ARGs. Similarly, the bacterial composition showed a positive correlation with the prevalence of ARGs in treated manure. These findings suggest that bacterial community, heavy metals, and mobile genetic elements can play a significant role in the abundance and variation of ARGs during composting and anaerobic digestion. In conclusion, anaerobic digestion and composting methods at industrial scale need to be improved for the effective removal of antibiotics, ARGs and heavy metals from chicken manure.},
}
@article {pmid32105814,
year = {2020},
author = {Rizowy, GM and Poloni, S and Colonetti, K and Donis, KC and Dobbler, PT and Leistner-Segal, S and Roesch, LFW and Schwartz, IVD},
title = {Is the gut microbiota dysbiotic in patients with classical homocystinuria?.},
journal = {Biochimie},
volume = {173},
number = {},
pages = {3-11},
doi = {10.1016/j.biochi.2020.02.013},
pmid = {32105814},
issn = {1638-6183},
mesh = {Adolescent ; Adult ; Betaine/administration &amp; dosage ; Case-Control Studies ; Dietary Supplements ; Dysbiosis/*microbiology ; Female ; *Gastrointestinal Microbiome ; *Homocystinuria/diet therapy/drug therapy/microbiology ; Humans ; Male ; Vitamin B Complex/administration &amp; dosage ; Young Adult ; },
abstract = {Classical homocystinuria (HCU) is characterized by increased plasma levels of total homocysteine (tHcy) and methionine (Met). Treatment may involve supplementation of B vitamins and essential amino acids, as well as restricted Met intake. Dysbiosis has been described in some inborn errors of metabolism, but has not been investigated in HCU. The aim of this study was to investigate the gut microbiota of HCU patients on treatment. Six unrelated HCU patients (males = 5, median age = 25.5 years) and six age-and-sex-matched healthy controls (males = 5, median age = 24.5 years) had their fecal microbiota characterized through partial 16S rRNA gene sequencing. Fecal pH, a 3-day dietary record, medical history, and current medications were recorded for both groups. All patients were nonresponsive to pyridoxine and were on a Met-restricted diet and presented with high tHcy. Oral supplementation of folate (n = 6) and pyridoxine (n = 5), oral intake of betaine (n = 4), and IM vitamin B12 supplementation (n = 4), were reported only in the HCU group. Patients had decreased daily intake of fat, cholesterol, vitamin D, and selenium compared to controls (p < 0.05). There was no difference in alpha and beta diversity between the groups. HCU patients had overrepresentation of the Eubacterium coprostanoligenes group and underrepresentation of the Alistipes, Family XIII UCG-001, and Parabacteroidetes genera. HCU patients and controls had similar gut microbiota diversity, despite differential abundance of some bacterial genera. Diet, betaine, vitamin B supplementation, and host genetics may contribute to these differences in microbial ecology.},
}
@article {pmid32105635,
year = {2020},
author = {Pushalkar, S and Paul, B and Li, Q and Yang, J and Vasconcelos, R and Makwana, S and González, JM and Shah, S and Xie, C and Janal, MN and Queiroz, E and Bederoff, M and Leinwand, J and Solarewicz, J and Xu, F and Aboseria, E and Guo, Y and Aguallo, D and Gomez, C and Kamer, A and Shelley, D and Aphinyanaphongs, Y and Barber, C and Gordon, T and Corby, P and Li, X and Saxena, D},
title = {Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection.},
journal = {iScience},
volume = {23},
number = {3},
pages = {100884},
pmid = {32105635},
issn = {2589-0042},
support = {P30 DA011041/DA/NIDA NIH HHS/United States ; P30 ES000260/ES/NIEHS NIH HHS/United States ; R01 CA206105/CA/NCI NIH HHS/United States ; R01 DE025992/DE/NIDCR NIH HHS/United States ; R01 DE027074/DE/NIDCR NIH HHS/United States ; },
abstract = {The trend of e-cigarette use among teens is ever increasing. Here we show the dysbiotic oral microbial ecology in e-cigarette users influencing the local host immune environment compared with non-smoker controls and cigarette smokers. Using 16S rRNA high-throughput sequencing, we evaluated 119 human participants, 40 in each of the three cohorts, and found significantly altered beta-diversity in e-cigarette users (p = 0.006) when compared with never smokers or tobacco cigarette smokers. The abundance of Porphyromonas and Veillonella (p = 0.008) was higher among vapers. Interleukin (IL)-6 and IL-1β were highly elevated in e-cigarette users when compared with non-users. Epithelial cell-exposed e-cigarette aerosols were more susceptible for infection. In vitro infection model of premalignant Leuk-1 and malignant cell lines exposed to e-cigarette aerosol and challenged by Porphyromonas gingivalis and Fusobacterium nucleatum resulted in elevated inflammatory response. Our findings for the first time demonstrate that e-cigarette users are more prone to infection.},
}
@article {pmid32105331,
year = {2020},
author = {Schmidt, ML and Biddanda, BA and Weinke, AD and Chiang, E and Januska, F and Props, R and Denef, VJ},
title = {Microhabitats are associated with diversity-productivity relationships in freshwater bacterial communities.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {4},
pages = {},
pmid = {32105331},
issn = {1574-6941},
support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/genetics ; *Biodiversity ; *Ecosystem ; Lakes ; Phylogeny ; },
abstract = {Eukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on the (phylogenetic) Hill diversity metrics and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake over three seasons: spring, summer and fall. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened when considering dominant taxa. There were no observable BEF trends in free-living bacterial communities for any diversity metric. Biodiversity, richness and Inverse Simpson's index, were the best predictors of particle-associated production whereas pH was the best predictor of free-living production. Our findings show that heterotrophic productivity is positively correlated with the effective number of taxa and that BEF relationships are associated with microhabitats. These results add to the understanding of the highly distinct contributions to diversity and functioning contributed by bacteria in free-living and particle-associated habitats.},
}
@article {pmid32101723,
year = {2020},
author = {Xavier, JB and Young, VB and Skufca, J and Ginty, F and Testerman, T and Pearson, AT and Macklin, P and Mitchell, A and Shmulevich, I and Xie, L and Caporaso, JG and Crandall, KA and Simone, NL and Godoy-Vitorino, F and Griffin, TJ and Whiteson, KL and Gustafson, HH and Slade, DJ and Schmidt, TM and Walther-Antonio, MRS and Korem, T and Webb-Robertson, BM and Styczynski, MP and Johnson, WE and Jobin, C and Ridlon, JM and Koh, AY and Yu, M and Kelly, L and Wargo, JA},
title = {The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.},
journal = {Trends in cancer},
volume = {6},
number = {3},
pages = {192-204},
pmid = {32101723},
issn = {2405-8025},
support = {R01 CA208179/CA/NCI NIH HHS/United States ; KL2 TR002379/TR/NCATS NIH HHS/United States ; R01 CA227479/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; U54 CA209975/CA/NCI NIH HHS/United States ; },
mesh = {Analgesics, Opioid/therapeutic use ; Animals ; Bacteria/metabolism ; Central Nervous System/physiology ; Drug Synergism ; Environmental Microbiology ; Gastritis/microbiology ; Gastrointestinal Microbiome ; Helicobacter Infections/complications ; Host-Pathogen Interactions ; Humans ; Immunotherapy ; Mice ; *Microbiota/drug effects/radiation effects ; Neoplasms/etiology/*microbiology/therapy/virology ; Oncogenic Viruses/pathogenicity ; Probiotics ; Stomach Neoplasms/etiology/microbiology ; Symbiosis ; Tumor Virus Infections ; },
abstract = {The collection of microbes that live in and on the human body - the human microbiome - can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions between microbes, diet, host factors, drugs, and cell-cell interactions within the cancer itself likely involve intricate feedbacks, and no single component can explain all the behavior of the system. Understanding the role of host-associated microbial communities in cancer systems will require a multidisciplinary approach combining microbial ecology, immunology, cancer cell biology, and computational biology - a systems biology approach.},
}
@article {pmid32100456,
year = {2020},
author = {Wang, B and He, Y and Tang, J and Ou, Q and Lin, J},
title = {Alteration of the gut microbiota in tumor necrosis factor-α antagonist-treated collagen-induced arthritis mice.},
journal = {International journal of rheumatic diseases},
volume = {23},
number = {4},
pages = {472-479},
doi = {10.1111/1756-185X.13802},
pmid = {32100456},
issn = {1756-185X},
support = {81871710//National Natural Science Foundation of China/ ; 2017J01190//Fujian Provincial Department of Science and Technology/ ; 2018QH1056//Fujian Medical University Startup Fund for scientific research/ ; C18117//Fujian Medical University Innovation Training Program/ ; 2018J06022//Fujian Science Fund for Distinguished Young Scholars/ ; },
mesh = {Animals ; Arthritis, Experimental/chemically induced/*drug therapy/immunology/microbiology ; Bacteria/classification/*drug effects/growth &amp; development ; Collagen Type II ; Cytokines/blood ; Etanercept/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Inflammation Mediators/blood ; Male ; Mice, Inbred DBA ; Tumor Necrosis Factor Inhibitors/*pharmacology ; },
abstract = {AIM: Gut microbiota play an important role in rheumatoid arthritis (RA). Biological therapies targeting tumor necrosis factor-α (TNF-α) have been used for treatment in RA patients. However, whether TNF-α antagonist has some influence on gut microbiota is still unknown. This study aims to investigate the distribution of gut microbiota in collagen-induced arthritis (CIA) mice treated with the TNF-α antagonist etanercept.<br><br>METHODS: Collagen-induced arthritis mice were induced by type II collagen. Cytokine expression was detected by real-time polymerase chain reaction. 16S ribosomal RNA sequencing was performed to characterize the gut microbiota in CIA mice treated with vehicle or etanercept. Sequencing reads were processed by Microbial Ecology software program.<br><br>RESULTS: Compared with vehicle-treated mice, we showed that CIA mice treated with etanercept led to attenuation of inflammation and reduced expression of TNF-&#x3b1;, interferon (IFN)-&#x3b3;, interleukin (IL)-6 and IL-21. Meanwhile, results showed operational taxonomic units, richness estimators and the diversity indices of gut microbiota in etanercept-treated mice were lower than that in vehicle-treated mice. Moreover, bacterial abundance analyses showed that genus Escherichia/Shigella was more abundant in etanercept-treated mice, and Lactobacillus, Clostridium XlVa, Tannerella were less abundant. The altered bacterial genus was correlated with TNF-&#x3b1;, IFN-&#x3b3;, IL-6, IL-21 and IL-10.<br><br>CONCLUSION: Our results revealed that TNF-&#x3b1; antagonist treatment can reduce the abundance and diversity of gut microbiota in CIA mice. Targeted gut microbiota may be a new therapeutic strategy for the treatment of RA.},
}
@article {pmid32100127,
year = {2020},
author = {Chen, K and Fu, Y and Wang, Y and Liao, L and Xu, H and Zhang, A and Zhang, J and Fan, L and Ren, J and Fang, B},
title = {Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {475-486},
doi = {10.1007/s00248-020-01494-w},
pmid = {32100127},
issn = {1432-184X},
support = {81770558//National Natural Science Foundation of China/ ; 3502Z20149031//Xiamen Joint Projects for Major Diseases/ ; },
mesh = {Animals ; Autism Spectrum Disorder/*therapy ; Bacteria/*metabolism ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; },
abstract = {Autism spectrum disorder (ASD) is a brain-based neurodevelopmental disorder characterized by behavioral abnormalities. Accumulating studies show that the gut microbiota plays a vital role in the pathogenesis of ASD, and gut microbiota transplantation (GMT) is a promising technique for the treatment of ASD. In clinical applications of GMT, it is challenging to obtain effective transplants because of the high costs of donor selection and heterogeneity of donors' gut microbiota, which can cause different clinical responses. In vitro batch culture is a fast, easy-to-operate, and repeatable method to culture gut microbiota. Thus, the present study investigates the feasibility of treating ASD with in vitro cultured gut microbiota as transplants. We cultured gut microbiota via the in vitro batch culture method and performed GMT in the maternal immune activation (MIA)-induced ASD mouse model with original donor microbiota and in vitro cultured microbiota. Open field, three-chamber social, marble burying, and self-grooming tests were used for behavioral improvement assessment. Serum levels of chemokines were detected. Microbial total DNA was extracted from mouse fecal samples, and 16S rDNA was sequenced using Illumina. Our results showed that GMT treatment with original and cultured donor gut microbiota significantly ameliorated anxiety-like and repetitive behaviors and improved serum levels of chemokines including GRO-α (CXCL1), MIP-1α (CCL3), MCP-3 (CCL7), RANTES (CCL5), and Eotaxin (CCL11) in ASD mice. Meanwhile, the gut microbial communities of the two groups that received GMT treatment were changed compared with the ASD mice groups. In the group treated with in vitro cultured donor gut microbiota, there was a significant decrease in the relative abundance of key differential taxa, including S24-7, Clostridiaceae, Prevotella_other, and Candidatus Arthromitus. The relative abundance of these taxa reached close to the level of healthy mice. Prevotella_other also decreased in the group treated with original donor gut microbiota, with a significant increase in Ruminococcaceae and Oscillospira. The present study demonstrated that GMT with in vitro cultured microbiota also improved behavioral abnormalities and chemokine disorders in an ASD mouse model compared with GMT with original donor gut microbiota. In addition, it significantly modified several key differential taxa in gut microbial composition.},
}
@article {pmid32097837,
year = {2020},
author = {Abramov, SM and Tejada, J and Grimm, L and Schädler, F and Bulaev, A and Tomaszewski, EJ and Byrne, JM and Straub, D and Thorwarth, H and Amils, R and Kleindienst, S and Kappler, A},
title = {Role of biogenic Fe(III) minerals as a sink and carrier of heavy metals in the Rio Tinto, Spain.},
journal = {The Science of the total environment},
volume = {718},
number = {},
pages = {137294},
doi = {10.1016/j.scitotenv.2020.137294},
pmid = {32097837},
issn = {1879-1026},
abstract = {Oxidation of sulfide ores in the Iberian Pyrite Belt region leads to the presence of extremely high concentration of dissolved heavy metals (HMs) in the acidic water of the Rio Tinto. Fe(II) is microbially oxidized resulting in the formation of suspended particulate matter (SPM) consisting of microbial cells and Fe(III) minerals with co-precipitated HMs. Although substantial amount of HM-bearing SPM is likely deposited to river sediment, a portion can still be transported through estuary to the coastal ocean. Therefore, the mechanisms of SPM formation and transport along the Rio Tinto are important for coastal-estuarine zone. In order to reveal these mechanisms, we performed diurnal sampling of Rio Tinto water, mineralogical and elemental analysis of sediment from the middle course and the estuary of the river. We identified two divergent but interrelated pathways of HM transfer. The first longitudinal pathway is the transport of SPM-associated metals such as As (6.58 μg/L), Pb (3.51 μg/L) and Cr (1.30 μg/L) to the coastal ocean. The second sedimentation pathway contributes to the continuous burial of HMs in the sediment throughout the river. In the middle course, sediment undergoes mineralogical transformations during early diagenesis and traps HMs (e.g. 1.6 mg/g of As, 1.23 mg/g of Pb and 0.1 mg/g of Cr). In the estuary, HMs are accumulated in a distinct anoxic layer of sediment (e.g. 1.5 mg/g of As, 2.09 mg/g of Pb and 0.04 mg/g of Cr). Our results indicate that microbially precipitated Fe(III) minerals (identified as ferrihydrite and schwertmannite) play a key role in maintaining these divergent HM pathways and as a consequence are crucial for HM mobility in the Rio Tinto.},
}
@article {pmid32094388,
year = {2020},
author = {Marsland, R and Cui, W and Mehta, P},
title = {A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {3308},
pmid = {32094388},
issn = {2045-2322},
support = {R35 GM119461/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/classification/metabolism ; *Biodiversity ; Humans ; Microbiota ; *Models, Biological ; Principal Component Analysis ; },
abstract = {Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promising approach is to use minimal models that can relate mechanistic assumptions at the microbe scale to community-level patterns. Here, we demonstrate the utility of this approach by showing that the Microbial Consumer Resource Model (MiCRM) - a minimal model for microbial communities with resource competition, metabolic crossfeeding and stochastic colonization - can qualitatively reproduce patterns found in survey data including compositional gradients, dissimilarity/overlap correlations, richness/harshness correlations, and nestedness of community composition. By using the MiCRM to generate synthetic data with different environmental and taxonomical structure, we show that large scale patterns in the EMP can be reproduced by considering the energetic cost of surviving in harsh environments and HMP patterns may reflect the importance of environmental filtering in shaping competition. We also show that recently discovered dissimilarity-overlap correlations in the HMP likely arise from communities that share similar environments rather than reflecting universal dynamics. We identify ecologically meaningful changes in parameters that alter or destroy each one of these patterns, suggesting new mechanistic hypotheses for further investigation. These findings highlight the promise of minimal models for microbial ecology.},
}
@article {pmid32094260,
year = {2020},
author = {Samanta, P and Mandal, RS and Saha, RN and Shaw, S and Ghosh, P and Dutta, S and Ghosh, A and Imamura, D and Morita, M and Ohnishi, M and Ramamurthy, T and Mukhopadhyay, AK},
title = {A Point Mutation in carR Is Involved in the Emergence of Polymyxin B-Sensitive Vibrio cholerae O1 El Tor Biotype by Influencing Gene Transcription.},
journal = {Infection and immunity},
volume = {88},
number = {5},
pages = {},
pmid = {32094260},
issn = {1098-5522},
mesh = {Alleles ; Anti-Bacterial Agents/pharmacology ; Calcium/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Down-Regulation/genetics ; Escherichia coli/genetics ; Point Mutation/*genetics ; Polymorphism, Single Nucleotide/genetics ; Polymyxin B/*pharmacology ; Transcription, Genetic/*genetics ; Vibrio cholerae O1/*drug effects/*genetics/metabolism ; },
abstract = {Antimicrobial peptides play an important role in host defense against Vibrio cholerae Generally, the V. cholerae O1 classical biotype is polymyxin B (PB) sensitive and El Tor is relatively resistant. Detection of classical biotype traits like the production of classical cholera toxin and PB sensitivity in El Tor strains has been reported in recent years, including in the devastating Yemen cholera outbreak during 2016-2018. To investigate the factor(s) responsible for the shift in the trend of sensitivity to PB, we studied the two-component system encoded by carRS, regulating the lipid A modification of El Tor vibrios, and found that only carR contains a single nucleotide polymorphism (SNP) in recently emerged PB-sensitive strains. We designated the two alleles present in PB-resistant and -sensitive strains carR[r] and carR[s] alleles, respectively, and replaced the carR[s] allele of a sensitive strain with the carR[r] allele, using an allelic-exchange approach. The sensitive strain then became resistant. The PB-resistant strain N16961 was made susceptible to PB in a similar fashion. Our in silico CarR protein models suggested that the D89N substitution in the more stable CarR[s] protein brings the two structural domains of CarR closer, constricting the DNA binding cleft. This probably reduces the expression of the carR-regulated almEFG operon, inducing PB susceptibility. Expression of almEFG in PB-sensitive strains was found to be downregulated under natural culturing conditions. In addition, the expression of carR and almEG decreased in all strains with increased concentrations of extracellular Ca[2+] but increased with a rise in pH. The downregulation of almEFG in CarR[s] strains confirmed that the G265A mutation is responsible for the emergence of PB-sensitive El Tor strains.},
}
@article {pmid32093252,
year = {2020},
author = {Gómez Del Pulgar, EM and Benítez-Páez, A and Sanz, Y},
title = {Safety Assessment of Bacteroides Uniformis CECT 7771, a Symbiont of the Gut Microbiota in Infants.},
journal = {Nutrients},
volume = {12},
number = {2},
pages = {},
pmid = {32093252},
issn = {2072-6643},
support = {613979//Seventh Framework Programme/ ; },
mesh = {Animals ; *Bacteroides ; Cytokines/blood ; Female ; Gastrointestinal Microbiome/*physiology ; Male ; Microbiota/physiology ; Probiotics/*administration &amp; dosage ; Rats ; Rats, Wistar ; },
abstract = {The formulation of next-generation probiotics requires competent preclinical studies to show their efficacy and safety status. This study aims to confirm the safety of the prolonged oral use of Bacteroides uniformis CECT 7771, a strain that protected against metabolic disorders and obesity in preclinical trials, in a sub-chronic 90 day trial in animals. The safety assessment was conducted in male and female Wistar rats (n = 50) administered increasing doses (10[8] CFU/day, 10[9] CFU/day, or 10[10] CFU/day) of B. uniformis CECT 7771, 10[10] CFU/day of B. longum ATCC 15707[T], which complies with the qualifying presumption of safety (QPS) status of the EU, or vehicle (placebo), as the control. Pancreatic, liver, and kidney functions and cytokine concentrations were analyzed. Bacterial translocation to peripheral tissues was evaluated, and colon integrity was investigated histologically. No adverse metabolic or tissue integrity alterations were associated with treatments; however, alanine aminotransferase levels and the ratio of anti-inflammatory to pro-inflammatory cytokines in serum indicated a potentially beneficial role of B. uniformis CECT 7771 at specific doses. Additionally, the microbial community structure was modified by the interventions, and potentially beneficial gut bacteria were increased. The results indicated that the oral consumption of B. uniformis CECT 7771 during a sub-chronic 90 day study in rats did not raise safety concerns.},
}
@article {pmid32092511,
year = {2020},
author = {Wei, H and Gao, D and Liu, Y and Lin, X},
title = {Sediment nitrate reduction processes in response to environmental gradients along an urban river-estuary-sea continuum.},
journal = {The Science of the total environment},
volume = {718},
number = {},
pages = {137185},
doi = {10.1016/j.scitotenv.2020.137185},
pmid = {32092511},
issn = {1879-1026},
abstract = {Sediment denitrification (DEN), anaerobic ammonium oxidation (Anammox), and dissimilatory nitrate reduction to ammonium (DNRA) are three important nitrate (NO3[-]) reduction pathways in aquatic ecosystems. These processes modify nitrogen (N) loadings from land to the ocean, with important implications on the management of coastal eutrophication. While NO3[-] reduction has been studied intensively for various types of habitats, studies on its distributions along river-estuary-sea continua remain scarce. In this study, we examined these three pathways along a N-laden urban river-estuary-sea continuum comprised of three types of habitats (urban river, estuary, and adjacent sea) in the densely populated Shanghai-East China Sea area. The potential DEN, Anammox, and DNRA rates decreased seaward both in summer and winter in response to decreasing sediment organic matter (OM, 20 to 7 to 7 mg C g[-1]), ferrous oxide (9 to 2.7 to 2.8 mg Fe g[-1]), and bottom water dissolved inorganic nitrogen (543 to 112 to 21 μM). Among these pathways, DEN remained a major component (~69.6%) across habitats, while Anammox (47.9%) rivaled DEN (48.3%) in the urban river in winter. N retention index (NIRI), the ratio between retained and removed NO3[-], ranged from 0 to 0.5 and increased downstream. Together, these results suggest that the decreasing gradients of OM and inorganic matter shape the distribution of NO3[-] reduction along the continuum, reflecting the diminishing impact of the river and human inputs from the urban river to the ocean. Our results highlight the importance of taking a continuum perspective in N cycling studies and emphasize the role of urban rivers as N removal hotspots, which should be a focus of research and management.},
}
@article {pmid32091935,
year = {2020},
author = {Balachandran, M and Cross, KL and Podar, M},
title = {Single-Cell Genomics and the Oral Microbiome.},
journal = {Journal of dental research},
volume = {99},
number = {6},
pages = {613-620},
pmid = {32091935},
issn = {1544-0591},
support = {R01 DE024463/DE/NIDCR NIH HHS/United States ; R01 HG004857/HG/NHGRI NIH HHS/United States ; },
mesh = {Dental Caries/genetics ; Dysbiosis/genetics ; Genomics ; Humans ; *Microbiota/genetics ; Mouth ; },
abstract = {The human oral cavity is one of the first environments where microbes have been discovered and studied since the dawn of microbiology. Nevertheless, approximately 200 types of bacteria from the oral microbiota have remained uncultured in the laboratory. Some are associated with a healthy oral microbial community, while others are linked to oral diseases, from dental caries to gum disease. Single-cell genomics has enabled inferences on the physiology, virulence, and evolution of such uncultured microorganisms and has further enabled isolation and cultivation of several novel oral bacteria, including the discovery of novel interspecies interactions. This review summarizes some of the more recent advances in this field, which is rapidly moving toward physiologic characterization of single cells and ultimately cultivation of the yet uncultured. A combination of traditional microbiological approaches with genomic-based physiologic predictions and isolation strategies may lead to the oral microbiome being the first complex microbial community to have all its members cultivable in the laboratory. Studying the biology of the individual microbes when in association with other members of the community, in controlled laboratory conditions and in vivo, should lead to a better understanding of oral dysbiosis and its prevention and reversion.},
}
@article {pmid32090516,
year = {2020},
author = {Hess, AL and Larsen, LH and Udesen, PB and Sanz, Y and Larsen, TM and Dalgaard, LT},
title = {Levels of Circulating miR-122 are Associated with Weight Loss and Metabolic Syndrome.},
journal = {Obesity (Silver Spring, Md.)},
volume = {28},
number = {3},
pages = {493-501},
doi = {10.1002/oby.22704},
pmid = {32090516},
issn = {1930-739X},
support = {115372//EU/EFPIA Innovative Medicines Initiative Joint Undertaking EMIF/International ; 613979//Seventh Framework Programme/International ; },
mesh = {Adolescent ; Adult ; Double-Blind Method ; Female ; Humans ; Male ; Metabolic Syndrome/*genetics ; MicroRNAs/*metabolism ; Middle Aged ; Obesity/*genetics ; Weight Loss/*genetics ; Young Adult ; },
abstract = {OBJECTIVE: This study investigated whether the levels of specific serum microRNAs (miRNAs) were altered following diet-induced weight loss and whether the serum miRNAs differed in the presence of the metabolic syndrome.<br><br>METHODS: The study was a weight loss intervention trial with a prescribed energy deficit of approximately 500 kcal/d. Levels of 22 miRNAs were determined in serum samples from 85 participants with overweight or obesity. miRNAs were analyzed using TaqMan Array miRNA&#xa0;Cards and normalized to the geometric mean of spiked-in ath-miR-159a and U6 small nuclear RNA using the &#x394;CT method.<br><br>RESULTS: The average weight loss was 5.7 kg (P&#x2009;<&#x2009;0.001). miR-122-5p (-0.18&#x2009;&#xb1;&#x2009;0.06 log fold relative to initial, P&#x2009;<&#x2009;0.01) and miR-193a-5p (-0.12&#x2009;&#xb1;&#x2009;0.04, P&#x2009;<&#x2009;0.01) levels decreased in response to weight loss. miR-126a-3p (0.11&#x2009;&#xb1;&#x2009;0.04, P&#x2009;=&#x2009;0.01) and miR-222-3p (1.51&#x2009;&#xb1;&#x2009;0.12, P&#x2009;<&#x2009;0.001) levels increased. Furthermore, a higher level of miR-122-5p was observed at baseline in participants with the metabolic syndrome compared with participants without (0.28&#x2009;&#xb1;&#x2009;0.08, P&#x2009;<&#x2009;0.01).<br><br>CONCLUSIONS: Changes in circulating miR-122-5p, miR-126a-3p, miR-193a-5p, and miR-222-3p in response to diet-induced weight loss are demonstrated. Furthermore, assessment of miR-122-5p could be an indicator of an adverse metabolic health status independent of obesity.},
}
@article {pmid32088790,
year = {2020},
author = {Zhang, S and Shao, Y and Zhao, X and Li, C and Guo, M and Lv, Z and Zhang, W},
title = {Indole contributes to tetracycline resistance via the outer membrane protein OmpN in Vibrio splendidus.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {36},
number = {3},
pages = {36},
pmid = {32088790},
issn = {1573-0972},
support = {2018YFD0900603//the National Key R&amp;D Program of China/ ; 41676141//the National Natural Science Foundation of China/ ; },
mesh = {Bacterial Outer Membrane Proteins/*genetics/metabolism ; Culture Media/chemistry ; Electrophoresis, Polyacrylamide Gel ; Gene Expression Regulation, Bacterial/drug effects ; Indoles/*pharmacology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tetracycline/pharmacology ; *Tetracycline Resistance ; Up-Regulation ; Vibrio/drug effects/*growth &amp; development/metabolism ; },
abstract = {As an interspecies and interkingdom signaling molecule, indole has recently received attention for its diverse effects on the physiology of both bacteria and hosts. In this study, indole increased the tetracycline resistance of Vibrio splendidus. The minimal inhibitory concentration of tetracycline was 10 μg/mL, and the OD600 of V. splendidus decreased by 94.5% in the presence of 20 μg/mL tetracycline; however, the OD600 of V. splendidus with a mixture of 20 μg/mL tetracycline and 125 μM indole was 10- or 4.5-fold higher than that with only 20 μg/mL tetracycline at different time points. The percentage of cells resistant to 10 μg/mL tetracycline was 600-fold higher in the culture with an OD600 of approximately 2.0 (higher level of indole) than that in the culture with an OD600 of 0.5, which also meant that the level of indole was correlated to the tetracycline resistance of V. splendidus. Furthermore, one differentially expressed protein, which was identified as the outer membrane porin OmpN using SDS-PAGE combined with MALDI-TOF/TOF MS, was upregulated. Consequently, the expression of the ompN gene in the presence of either tetracycline or indole and simultaneously in the presence of indole and tetracycline was upregulated by 1.8-, 2.54-, and 6.01-fold, respectively, compared to the control samples. The combined results demonstrated that indole enhanced the tetracycline resistance of V. splendidus, and this resistance was probably due to upregulation of the outer membrane porin OmpN.},
}
@article {pmid32088758,
year = {2020},
author = {Law, CKY and De Henau, R and De Vrieze, J},
title = {Feedstock thermal pretreatment selectively steers process stability during the anaerobic digestion of waste activated sludge.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {8},
pages = {3675-3686},
pmid = {32088758},
issn = {1432-0614},
support = {GA 826244//Horizon 2020/ ; },
mesh = {Anaerobiosis ; Biofuels/microbiology ; *Bioreactors ; Methane/biosynthesis ; *Microbiota ; Sewage/*microbiology ; *Temperature ; },
abstract = {Strategies to enhance process performance of anaerobic digestion remain of key importance to promote wider usage of this technology for integrated resource recovery from organic waste streams. Continuous inoculation of the microbial community in the digester via the feedstock could be such a cost-effective strategy. Here, anaerobic digestion of fresh waste activated sludge (WAS) was compared with sterilized WAS in response to two common process disturbances, i.e. organic overloading and increasing levels of salts, to determine the importance of feedstock inoculation. A pulse in the organic loading rate severely impacted process stability of the digesters fed sterile WAS, with a 92 ± 45% decrease in methane production, compared to a 42 ± 31% increase in the digesters fed fresh WAS, relative to methane production before the pulse. Increasing salt pulses did not show a clear difference in process stability between the digesters fed fresh and sterile WAS, and process recovery was obtained even at the highest salt pulse of 25 g Na[+] L[-1]. Feedstock sterilization through thermal pretreatment strongly impacted the microbial community in the digesters. In conclusion, feedstock thermal pretreatment strongly impacted anaerobic digestion process stability, due to feedstock inoculation and compositional modification.},
}
@article {pmid32086543,
year = {2021},
author = {Bao, G and Song, M and Wang, Y and Saikkonen, K and Li, C},
title = {Does Epichloë Endophyte Enhance Host Tolerance to Root Hemiparasite?.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {35-48},
pmid = {32086543},
issn = {1432-184X},
support = {31660690//National Natural Science Foundation of China/ ; 31700098//National Natural Science Foundation of China/ ; 1111126//Cooperation Program of Qinghai Province/ ; 295976//Academy of Finland/ ; 326226//Academy of Finland/ ; 2017-ZJ-Y12//QingHai Department of Science and Technology/ ; },
mesh = {*Elymus ; Endophytes ; *Epichloe ; Plant Weeds ; Poaceae ; Symbiosis ; },
abstract = {Epichloë endophytes have been shown to be mutualistic symbionts of cool-season grasses under most environmental conditions. Although pairwise interactions between hemiparasites and their hosts are heavily affected by host-associated symbiotic microorganisms, little attention has been paid to the effects of microbe-plant interactions, particularly endophytic symbiosis, in studies examining the effects of parasitic plants on host performance. In this study, we performed a greenhouse experiment to examine the effects of hereditary Epichloë endophyte symbiosis on the growth of two host grasses (Stipa purpurea and Elymus tangutorum) in the presence or absence of a facultative root hemiparasite (Pedicularis kansuensis Maxim). We observed parasitism of both hosts by P. kansuensis: when grown with a host plant, the hemiparasite decreased the performance of the host while improving its own biomass and survival rate of the hemiparasite. Parasitized endophyte-infected S. purpurea plants had higher biomass, tillers, root:shoot ratio, and photosynthetic parameters and a lower number of functional haustoria than the endophyte-free S. purpurea conspecifics. By contrast, parasitized endophyte-infected E. tangutorum had a lower biomass, root:shoot ratio, and photosynthetic parameters and a higher number of haustoria and functional haustoria than their endophyte-free counterparts. Our results reveal that the interactions between the endophytes and the host grasses are context dependent and that plant-plant interactions can strongly affect their mutualistic interactions. Endophytes originating from S. purpurea alleviate the host biomass reduction by P. kansuensis and growth depression in the hemiparasite. These findings shed new light on using grass-endophyte symbionts as biocontrol methods for the effective and sustainable management of this weedy hemiparasite.},
}
@article {pmid32086129,
year = {2020},
author = {Elhalis, H and Cox, J and Zhao, J},
title = {Ecological diversity, evolution and metabolism of microbial communities in the wet fermentation of Australian coffee beans.},
journal = {International journal of food microbiology},
volume = {321},
number = {},
pages = {108544},
doi = {10.1016/j.ijfoodmicro.2020.108544},
pmid = {32086129},
issn = {1879-3460},
mesh = {Australia ; Bacteria/classification/growth &amp; development/isolation &amp; purification/metabolism ; Coffea/chemistry/*microbiology ; Coffee/chemistry ; Fermentation ; Food Handling/*methods ; Food Microbiology ; *Microbiota/genetics ; Seeds/chemistry/microbiology ; Yeasts/classification/growth &amp; development/isolation &amp; purification/metabolism ; },
abstract = {The microbial ecology in the fermentation of Australian coffee beans was investigated in this study. Pulped coffee beans were kept underwater for 36 h before air dried. Samples were collected periodically, and the microbial communities were analyzed by culture-dependent and independent methods. Changes in sugars, organic acids and microbial metabolites in the mucilage and endosperm of the coffee beans during fermentation were monitored by HPLC. Culture-dependent methods identified 6 yeast and 17 bacterial species, while the culture-independent methods, multiple-step total direct DNA extraction and high throughput sequencing, identified 212 fungal and 40 bacterial species. Most of the microbial species in the community have been reported for wet fermentation of coffee beans in other parts of the world, but the yeast Pichia kudriavzevii was isolated for the first time in wet coffee bean fermentation. The bacterial community was dominated by aerobic mesophilic bacteria (AMB) with Citrobacter being the predominant genus. Hanseniaspora uvarum and Pichia kudriavzevii were the predominant yeasts while Leuconostoc mesenteroides and Lactococcus lactis were the predominant LAB. The yeasts and bacteria grew significantly during fermentation, utilizing sugars in the mucilage and produced mannitol, glycerol, and lactic acid, leading to a significant decrease in pH. The results of this study provided a preliminary understanding of the microbial ecology of wet coffee fermentation under Australian conditions. Further studies are needed to explore the impact of microbial growth and metabolism on coffee quality, especially flavour.},
}
@article {pmid32084407,
year = {2020},
author = {Lories, B and Roberfroid, S and Dieltjens, L and De Coster, D and Foster, KR and Steenackers, HP},
title = {Biofilm Bacteria Use Stress Responses to Detect and Respond to Competitors.},
journal = {Current biology : CB},
volume = {30},
number = {7},
pages = {1231-1244.e4},
pmid = {32084407},
issn = {1879-0445},
support = {209397/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Biofilms ; Drug Resistance, Bacterial/*genetics ; Genome, Bacterial/*physiology ; Microbial Interactions/*genetics ; Phenotype ; Salmonella typhimurium/*physiology ; Single-Cell Analysis ; },
abstract = {Bacteria use complex regulatory networks to cope with stress, but the function of these networks in natural habitats is poorly understood. The competition sensing hypothesis states that bacterial stress response systems can serve to detect ecological competition, but studying regulatory responses in diverse communities is challenging. Here, we solve this problem by using differential fluorescence induction to screen the Salmonella Typhimurium genome for loci that respond, at the single-cell level, to life in biofilms with competing strains of S. Typhimurium and Escherichia coli. This screening reveals the presence of competing strains drives up the expression of genes associated with biofilm matrix production (CsgD pathway), epithelial invasion (SPI1 invasion system), and, finally, chemical efflux and antibiotic tolerance (TolC efflux pump and AadA aminoglycoside 3-adenyltransferase). We validate that these regulatory changes result in the predicted phenotypic changes in biofilm, mammalian cell invasion, and antibiotic tolerance. We further show that these responses arise via activation of major stress responses, providing direct support for the competition sensing hypothesis. Moreover, inactivation of the type VI secretion system (T6SS) of a competitor annuls the responses to competition, indicating that T6SS-derived cell damage activates these stress response systems. Our work shows that bacteria use stress responses to detect and respond to competition in a manner important for major phenotypes, including biofilm formation, virulence, and antibiotic tolerance.},
}
@article {pmid32080691,
year = {2020},
author = {Xu, J and Ma, Z and Li, X and Liu, L and Hu, X},
title = {A more pronounced effect of type III resistant starch vs. type II resistant starch on ameliorating hyperlipidemia in high fat diet-fed mice is associated with its supramolecular structural characteristics.},
journal = {Food &amp; function},
volume = {11},
number = {3},
pages = {1982-1995},
doi = {10.1039/c9fo02025j},
pmid = {32080691},
issn = {2042-650X},
mesh = {Animals ; Diet, High-Fat/*adverse effects ; Gastrointestinal Microbiome/drug effects ; Hyperlipidemias/*chemically induced/prevention &amp; control ; Male ; Mice ; Mice, Inbred BALB C ; Random Allocation ; Starch/chemistry/*classification/*pharmacology ; Structure-Activity Relationship ; },
abstract = {The anti-obesity effects of two categories of resistant starch (RS) including RS2 (isolated from untreated lentil starch, URS) and RS3 (isolated from autoclaved and retrograded lentil starch, ARS) on mice with high-fat (HF) diet-induced obesity and the supramolecular structure-in vivo physiological functionality relationship of RS were investigated. Following 6 consecutive weeks, the obese mice in the two RS administered groups displayed suppression of body/liver weight gain and an improvement in serum glucose/lipid profile, antioxidant status, and gut microbiota structure. Compared with the URS intervention group, the ARS administration resulted in a more pronounced effect in controlling body weight, together with a more prominent reduction in blood glucose and triglyceride concentration, as well as a significant increase in the HDL-c level in obese mice. The ARS group also showed an absolute advantage over URS in suppressing the oxidative stress and regulating the liver function induced by the HF diet. Simultaneously, the administration of URS and ARS efficiently suppressed the HF-diet induced alterations in gut microbial ecology, with an obviously decreased ratio of Firmicutes to Bacteroidetes, especially for the ARS group, suggesting its beneficial role in gastrointestinal tract health. The structural characterization results revealed that ARS and URS differed significantly in their supramolecular structural characteristics, where ARS exhibited a higher proportion of crystallinity and double helix content with an X-ray diffraction pattern of a CB type crystal polymorph and a low proportion of molecular inhomogeneity. This study suggested that the difference in the anti-obesity effect of resistant starches was a consequence of the diversity in their structural features.},
}
@article {pmid32076744,
year = {2020},
author = {Chen, H and Wang, M and Chang, S},
title = {Disentangling Community Structure of Ecological System in Activated Sludge: Core Communities, Functionality, and Functional Redundancy.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {296-308},
doi = {10.1007/s00248-020-01492-y},
pmid = {32076744},
issn = {1432-184X},
mesh = {*Bacterial Physiological Phenomena ; Microbiota/*physiology ; Ontario ; Seasons ; Sewage/*microbiology ; },
abstract = {The microbial ecosystems of the sludge were characterized in terms of the core community structure, functional pathways, and functional redundancy through Illumina MiSeq sequencing and PICRUSt analysis on the activated sludge (AS) samples from an extended activated aeration process. Based on the identified OTU distribution, we identified 125 core community genera, including 3 abundant core genera and 21 intermittent abundant core genera. Putative genera Nitrosomonas, Nitrotoga, Zoogloea, Novosphingobium, Thermomonas, Amaricoccus, Tetrasphaera, Candidatus Microthrix, and Haliscomenobacter, which are associated with functions of nitrifying, denitrifying, phosphorus accumulating, and bulking and foaming, were found to present as the core community organisms in the AS sampled from the conventional extended aeration AS processes. The high-abundant nitrogen metabolic pathways were associated with nitrate reduction to ammonium (DNRA and ANRA), denitrification, and nitrogen fixation, while the ammonia oxidation-related genes (amo) were rarely annotated in the AS samples. Strict functional redundancy was not found with the AS ecosystem as it showed a high correlation between the community composition similarity and function similarity. In addition, the classified dominant core genera community was found to be sufficient to characterize the functionality of AS, which could invigorate applications of 16S rDNA MiSeq sequencing and PICRUSt for the prediction of functions of AS ecosystems.},
}
@article {pmid32076743,
year = {2020},
author = {Aubé, J and Senin, P and Bonin, P and Pringault, O and Jeziorski, C and Bouchez, O and Klopp, C and Guyoneaud, R and Goñi-Urriza, M},
title = {Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {286-295},
doi = {10.1007/s00248-020-01493-x},
pmid = {32076743},
issn = {1432-184X},
support = {ANR11 BSV7 014 01//Agence Nationale de la Recherche/ ; },
mesh = {Bacteria/drug effects/genetics/metabolism ; Hydrocarbons/*metabolism ; *Metagenome ; *Transcriptome ; Water Pollutants, Chemical/*metabolism ; },
abstract = {Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.},
}
@article {pmid32075981,
year = {2020},
author = {Hernandez-Sanabria, E and Heiremans, E and Calatayud Arroyo, M and Props, R and Leclercq, L and Snoeys, J and Van de Wiele, T},
title = {Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation.},
journal = {NPJ biofilms and microbiomes},
volume = {6},
number = {1},
pages = {9},
pmid = {32075981},
issn = {2055-5008},
mesh = {Adult ; Bacteria/*classification/drug effects/genetics/metabolism ; Batch Cell Culture Techniques ; Butyrates/*metabolism ; Caco-2 Cells ; Celecoxib/*pharmacology ; Cell Line, Tumor ; Chemokine CXCL16/*metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/microbiology ; Female ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; HT29 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; Interleukin-6/*metabolism ; Male ; Proof of Concept Study ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; THP-1 Cells ; },
abstract = {Celecoxib has been effective in the prevention and treatment of chronic inflammatory disorders through inhibition of altered cyclooxygenase-2 (COX-2) pathways. Despite the benefits, continuous administration may increase risk of cardiovascular events. Understanding microbiome-drug-host interactions is fundamental for improving drug disposition and safety responses of colon-targeted formulations, but little information is available on the bidirectional interaction between individual microbiomes and celecoxib. Here, we conducted in vitro batch incubations of human faecal microbiota to obtain a mechanistic proof-of-concept of the short-term impact of celecoxib on activity and composition of colon bacterial communities. Celecoxib-exposed microbiota shifted metabolic activity and community composition, whereas total transcriptionally active bacterial population was not significantly changed. Butyrate production decreased by 50% in a donor-dependent manner, suggesting that celecoxib impacts in vitro fermentation. Microbiota-derived acetate has been associated with inhibition of cancer markers and our results suggest uptake of acetate for bacterial functions when celecoxib was supplied, which potentially favoured bacterial competition for acetyl-CoA. We further assessed whether colon microbiota modulates anti-inflammatory efficacy of celecoxib using a simplified inflammation model, and a novel in vitro simulation of the enterohepatic metabolism. Celecoxib was responsible for only 5% of the variance in bacterial community composition but celecoxib-exposed microbiota preserved barrier function and decreased concentrations of IL-8 and CXCL16 in a donor-dependent manner in our two models simulating gut inflammatory milieu. Our results suggest that celecoxib-microbiome-host interactions may not only elicit adaptations in community composition but also in microbiota functionality, and these may need to be considered for guaranteeing efficient COX-2 inhibition.},
}
@article {pmid32075196,
year = {2020},
author = {Dhakar, K and Pandey, A},
title = {Microbial Ecology from the Himalayan Cryosphere Perspective.},
journal = {Microorganisms},
volume = {8},
number = {2},
pages = {},
pmid = {32075196},
issn = {2076-2607},
abstract = {Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective.},
}
@article {pmid32072187,
year = {2020},
author = {Junges, DSB and Delabeneta, MF and Rosseto, LRB and Nascimento, BL and Paris, AP and Persel, C and Loth, EA and Simão, RCG and Menolli, RA and Paula, CR and Gandra, RF},
title = {Antibiotic Activity of Wickerhamomyces anomalus Mycocins on Multidrug-Resistant Acinetobacter baumannii.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {278-285},
doi = {10.1007/s00248-020-01495-9},
pmid = {32072187},
issn = {1432-184X},
mesh = {Acinetobacter baumannii/*drug effects ; Animals ; Anti-Infective Agents/adverse effects/chemistry/*pharmacology ; Artemia/*drug effects ; Erythrocytes/*drug effects ; Humans ; Saccharomycetales/*chemistry ; },
abstract = {To evaluate the susceptibility of multidrug-resistant Acinetobacter baumannii to mycocins produced by Wickerhamomyces anomalus and to verify the cytotoxicity of these compounds. Three culture supernatants of W. anomalus (WA40, WA45, and WA92), containing mycocins (WA40M1, WA45M2, and WA92M3), were tested on A. baumannii using broth microdilution methods, solid medium tests, and cytotoxicity tests in human erythrocytes and in Artemia saline Leach. W. anomalus was able to produce high antimicrobial mycocins, as even at high dilutions, they inhibited A. baumannii. In a solid medium, it was possible to observe the inhibition of A. baumannii, caused by the diffusion of mycocins between agar. Finally, the three supernatants were not cytotoxic when tested on human erythrocytes and Artemia salina. According to the evidence in this study, the mycocins of W. anomalus have been effective and could be used in the development of new antimicrobial substances.},
}
@article {pmid32071708,
year = {2020},
author = {Klimenko, NS and Tyakht, AV and Toshchakov, SV and Shevchenko, MA and Korzhenkov, AA and Afshinnekoo, E and Mason, CE and Alexeev, DG},
title = {Co-occurrence patterns of bacteria within microbiome of Moscow subway.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {314-322},
pmid = {32071708},
issn = {2001-0370},
abstract = {Microbial ecosystems of the built environments have become key mediators of health as people worldwide tend to spend large amount of time indoors. Underexposure to microbes at an early age is linked to increased risks of allergic and autoimmune diseases. Transportation systems are of particular interest, as they are globally the largest space for interactions between city-dwellers. Here we performed the first pilot study of the Moscow subway microbiome by analyzing swabs collected from 5 types of surfaces at 4 stations using high-throughput 16S rRNA gene sequencing. The study was conducted as a part of The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) project. The most abundant microbial taxa comprising the subway microbiome originated from soil and human skin. Microbiome diversity was positively correlated with passenger traffic. No substantial evidence of major human pathogens presence was found. Co-occurrence analysis revealed clusters of microbial genera including combinations of microbes likely originating from different niches. The clusters as well as the most abundant microbes were similar to ones obtained for the published data on New-York City subway microbiome. Our results suggest that people are the main source and driving force of diversity in subway-associated microbiome. The data form a basis for a wider survey of Moscow subway microbiome to explore its longitudinal dynamics by analyzing an extended set of sample types and stations. Complementation of methods with viability testing, "shotgun" metagenomics, sequencing of bacterial isolates and culturomics will provide insights for public health, biosafety, microbial ecology and urban design.},
}
@article {pmid32071705,
year = {2020},
author = {Chen, X and Krug, L and Yang, H and Li, H and Yang, M and Berg, G and Cernava, T},
title = {Nicotiana tabacum seed endophytic communities share a common core structure and genotype-specific signatures in diverging cultivars.},
journal = {Computational and structural biotechnology journal},
volume = {18},
number = {},
pages = {287-295},
pmid = {32071705},
issn = {2001-0370},
abstract = {Seed endophytes of crop plants have recently received increased attention due to their implications in plant health and the potential to be included in agro-biotechnological applications. While previous studies indicated that plants from the Solanaceae family harbor a highly diverse seed microbiome, genotype-specific effects on the community composition and structure remained largely unexplored. The present study revealed Enterobacteriaceae-dominated seed-endophytic communities in four Nicotiana tabacum L. cultivars originating from Brazil, China, and the USA. When the dissimilarity of bacterial communities was assessed, none of the cultivars showed significant differences in microbial community composition. Various unusual endophyte signatures were represented by Spirochaetaceae family members and the genera Mycobacterium, Clostridium, and Staphylococcus. The bacterial fraction shared by all cultivars was dominated by members of the phyla Proteobacteria and Firmicutes. In total, 29 OTUs were present in all investigated cultivars and accounted for 65.5% of the combined core microbiome reads. Cultivars from the same breeding line were shown to share a higher number of common OTUs than more distant lines. Moreover, the Chinese cultivar Yunyan 87 contained the highest number (33 taxa) of unique signatures. Our results indicate that a distinct proportion of the seed microbiome of N. tabacum remained unaffected by breeding approaches of the last century, while a substantial proportion co-diverged with the plant genotype. Moreover, they provide the basis to identify plant-specific endophytes that could be addressed for upcoming biotechnological approaches in agriculture.},
}
@article {pmid32071163,
year = {2020},
author = {Röttjers, L and Faust, K},
title = {manta: a Clustering Algorithm for Weighted Ecological Networks.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
pmid = {32071163},
issn = {2379-5077},
abstract = {Microbial network inference and analysis have become successful approaches to extract biological hypotheses from microbial sequencing data. Network clustering is a crucial step in this analysis. Here, we present a novel heuristic network clustering algorithm, manta, which clusters nodes in weighted networks. In contrast to existing algorithms, manta exploits negative edges while differentiating between weak and strong cluster assignments. For this reason, manta can tackle gradients and is able to avoid clustering problematic nodes. In addition, manta assesses the robustness of cluster assignment, which makes it more robust to noisy data than most existing tools. On noise-free synthetic data, manta equals or outperforms existing algorithms, while it identifies biologically relevant subcompositions in real-world data sets. On a cheese rind data set, manta identifies groups of taxa that correspond to intermediate moisture content in the rinds, while on an ocean data set, the algorithm identifies a cluster of organisms that were reduced in abundance during a transition period but did not correlate strongly to biochemical parameters that changed during the transition period. These case studies demonstrate the power of manta as a tool that identifies biologically informative groups within microbial networks.IMPORTANCE manta comes with unique strengths, such as the abilities to identify nodes that represent an intermediate between clusters, to exploit negative edges, and to assess the robustness of cluster membership. manta does not require parameter tuning, is straightforward to install and run, and can be easily combined with existing microbial network inference tools.},
}
@article {pmid32071161,
year = {2020},
author = {Clark, CM and Murphy, BT and Sanchez, LM},
title = {A Call to Action: the Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
pmid = {32071161},
issn = {2379-5077},
support = {D43 TW010530/TW/FIC NIH HHS/United States ; F31 AT010419/AT/NCCIH NIH HHS/United States ; R01 GM125943/GM/NIGMS NIH HHS/United States ; },
}
@article {pmid32071158,
year = {2020},
author = {McAllister, SM and Polson, SW and Butterfield, DA and Glazer, BT and Sylvan, JB and Chan, CS},
title = {Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
pmid = {32071158},
issn = {2379-5077},
support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; },
abstract = {Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments.IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.},
}
@article {pmid32070256,
year = {2020},
author = {Ossowicki, A and Tracanna, V and Petrus, MLC and van Wezel, G and Raaijmakers, JM and Medema, MH and Garbeva, P},
title = {Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat.},
journal = {Proceedings. Biological sciences},
volume = {287},
number = {1921},
pages = {20192527},
pmid = {32070256},
issn = {1471-2954},
mesh = {Fusarium/*physiology ; Microbiota ; Plant Roots/microbiology ; Soil/chemistry ; *Soil Microbiology ; Triticum/*microbiology ; },
abstract = {In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat (Triticum aestivum) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.},
}
@article {pmid32068849,
year = {2020},
author = {Pratama, AA and Jiménez, DJ and Chen, Q and Bunk, B and Spröer, C and Overmann, J and van Elsas, JD},
title = {Delineation of a Subgroup of the Genus Paraburkholderia, Including P. terrae DSM 17804T, P. hospita DSM 17164T, and Four Soil-Isolated Fungiphiles, Reveals Remarkable Genomic and Ecological Features-Proposal for the Definition of a P. hospita Species Cluster.},
journal = {Genome biology and evolution},
volume = {12},
number = {4},
pages = {325-344},
pmid = {32068849},
issn = {1759-6653},
mesh = {Burkholderiaceae/*genetics/growth &amp; development/metabolism ; Ecology ; Fungi/*genetics/growth &amp; development/metabolism ; *Genome, Bacterial ; *Genome, Fungal ; Genomics/*methods ; Phylogeny ; Soil Microbiology ; Species Specificity ; },
abstract = {The fungal-interactive (fungiphilic) strains BS001, BS007, BS110, and BS437 have previously been preliminarily assigned to the species Paraburkholderia terrae. However, in the (novel) genus Paraburkholderia, an as-yet unresolved subgroup exists, that clusters around Paraburkholderia hospita (containing the species P. terrae, P. hospita, and Paraburkholderia caribensis). To shed light on the precise relationships across the respective type strains and the novel fungiphiles, we here compare their genomic and ecophysiological features. To reach this goal, the genomes of the three type strains, with sizes ranging from 9.0 to 11.5 Mb, were de novo sequenced and the high-quality genomes analyzed. Using whole-genome, ribosomal RNA and marker-gene-concatenate analyses, close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T, versus more remote relationships to P. caribensis DSM 13236T, were found. All four fungiphilic strains clustered closely to the two-species cluster. Analyses of average nucleotide identities (ANIm) and tetranucleotide frequencies (TETRA) confirmed the close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T (ANIm = 95.42; TETRA = 0.99784), as compared with the similarities of each one of these strains to P. caribensis DSM 13236T. A species cluster was thus proposed. Furthermore, high similarities of the fungiphilic strains BS001, BS007, BS110, and BS437 with this cluster were found, indicating that these strains also make part of it, being closely linked to P. hospita DSM 17164T (ANIm = 99%; TETRA = 0.99). We propose to coin this cluster the P. hospita species cluster (containing P. hospita DSM 17164T, P. terrae DSM 17804T, and strains BS001, BS007, BS110, and BS437), being clearly divergent from the closely related species P. caribensis (type strain DSM 13236T). Moreover, given their close relatedness to P. hospita DSM 17164T within the cluster, we propose to rename the four fungiphilic strains as members of P. hospita. Analysis of migratory behavior along with fungal growth through soil revealed both P. terrae DSM 17804T and P. hospita DSM 17164T (next to the four fungiphilic strains) to be migration-proficient, whereas P. caribensis DSM 13236T was a relatively poor migrator. Examination of predicted functions across the genomes of the seven investigated strains, next to several selected additional ones, revealed the common presence of features in the P. hospita cluster strains that are potentially important in interactions with soil fungi. Thus, genes encoding specific metabolic functions, biofilm formation (pelABCDEFG, pgaABCD, alginate-related genes), motility/chemotaxis, type-4 pili, and diverse secretion systems were found.},
}
@article {pmid32066625,
year = {2020},
author = {Ghosh, TS and Rampelli, S and Jeffery, IB and Santoro, A and Neto, M and Capri, M and Giampieri, E and Jennings, A and Candela, M and Turroni, S and Zoetendal, EG and Hermes, GDA and Elodie, C and Meunier, N and Brugere, CM and Pujos-Guillot, E and Berendsen, AM and De Groot, LCPGM and Feskins, EJM and Kaluza, J and Pietruszka, B and Bielak, MJ and Comte, B and Maijo-Ferre, M and Nicoletti, C and De Vos, WM and Fairweather-Tait, S and Cassidy, A and Brigidi, P and Franceschi, C and O'Toole, PW},
title = {Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries.},
journal = {Gut},
volume = {69},
number = {7},
pages = {1218-1228},
pmid = {32066625},
issn = {1468-3288},
mesh = {Aged ; *Diet, Mediterranean ; Europe ; Female ; Frailty/diet therapy/*prevention &amp; control ; *Gastrointestinal Microbiome/genetics ; Health Status ; Humans ; Male ; Patient Compliance ; RNA, Ribosomal, 16S/genetics ; Single-Blind Method ; },
abstract = {OBJECTIVE: Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We and others have shown that frailty co-varies with alterations in the gut microbiota in a manner accelerated by consumption of a restricted diversity diet. The Mediterranean diet (MedDiet) is associated with health. In the NU-AGE project, we investigated if a 1-year MedDiet intervention could alter the gut microbiota and reduce frailty.<br><br>DESIGN: We profiled the gut microbiota in 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy and Poland) before and after the administration of a 12-month long MedDiet intervention tailored to elderly subjects (NU-AGE diet).<br><br>RESULTS: Adherence to the diet was associated with specific microbiome alterations. Taxa enriched by adherence to the diet were positively associated with several markers of lower frailty and improved cognitive function, and negatively associated with inflammatory markers including C-reactive protein and interleukin-17. Analysis of the inferred microbial metabolite profiles indicated that the diet-modulated microbiome change was associated with an increase in short/branch chained fatty acid production and lower production of secondary bile acids, p-cresols, ethanol and carbon dioxide. Microbiome ecosystem network analysis showed that the bacterial taxa that responded positively to the MedDiet intervention occupy keystone interaction positions, whereas frailty-associated taxa are peripheral in the networks.<br><br>CONCLUSION: Collectively, our findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.},
}
@article {pmid32063916,
year = {2019},
author = {Orr, JN and Neilson, R and Freitag, TE and Roberts, DM and Davies, KG and Blok, VC and Cock, PJA},
title = {Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {1763},
pmid = {32063916},
issn = {1664-462X},
abstract = {Pasteuria spp. are endospore forming bacteria which act as natural antagonists to many of the most economically significant plant parasitic nematodes (PPNs). Highly species-specific nematode suppression may be observed in soils containing a sufficiently high density of Pasteuria spp. spores. This suppression is enacted by the bacteria via inhibition of root invasion and sterilization of the nematode host. Molecular methods for the detection of Pasteuria spp. from environmental DNA (eDNA) have been described; however, these methods are limited in both scale and in depth. We report the use of small subunit rRNA gene metabarcoding to profile Pasteuria spp. and nematode communities in parallel. We have investigated Pasteuria spp. population structure in Scottish soils using eDNA from two sources: soil extracted DNA from the second National Soil Inventory of Scotland (NSIS2); and nematode extracted DNA collected from farms in the East Scotland Farm Network (ESFN). We compared the Pasteuria spp. community culture to both nematode community structure and the physiochemical properties of soils. Our results indicate that Pasteuria spp. populations in Scottish soils are broadly dominated by two sequence variants. The first of these aligns with high identity to Pasteuria hartismeri, a species first described parasitizing Meloidogyne ardenensis, a nematode parasite of woody and perennial plants in northern Europe. The second aligns with a Pasteuria-like sequence which was first recovered from a farm near Edinburgh which was found to contain bacterial feeding nematodes and Pratylenchus spp. encumbered by Pasteuria spp. endospores. Further, soil carbon, moisture, bulk density, and pH showed a strong correlation with the Pasteuria spp. community composition. These results indicate that metabarcoding is appropriate for the sensitive, specific, and semi-quantitative profiling of Pasteuria species from eDNA.},
}
@article {pmid32062778,
year = {2020},
author = {Nkongolo, KK and Narendrula-Kotha, R},
title = {Advances in monitoring soil microbial community dynamic and function.},
journal = {Journal of applied genetics},
volume = {61},
number = {2},
pages = {249-263},
pmid = {32062778},
issn = {2190-3883},
support = {CRDP-J- 470535-2014//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Bacteria/*genetics/isolation &amp; purification ; *Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Polymorphism, Restriction Fragment Length/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.},
}
@article {pmid32062526,
year = {2020},
author = {Iacumin, L and Osualdini, M and Bovolenta, S and Boscolo, D and Chiesa, L and Panseri, S and Comi, G},
title = {Microbial, chemico-physical and volatile aromatic compounds characterization of Pitina PGI, a peculiar sausage-like product of North East Italy.},
journal = {Meat science},
volume = {163},
number = {},
pages = {108081},
doi = {10.1016/j.meatsci.2020.108081},
pmid = {32062526},
issn = {1873-4138},
mesh = {Animals ; Bacteria/isolation &amp; purification ; Fermentation ; Food Microbiology ; Fusarium/isolation &amp; purification ; Italy ; Meat Products/*analysis/*microbiology ; Penicillium/isolation &amp; purification ; Sheep ; Swine ; Volatile Organic Compounds/*analysis ; },
abstract = {Pitina is a fermented sausage-like produced in the mountainous area of the North-East Italy by artisanal plants without the use of both selected starters and casing (Slow Food Presidium). Originally, Pitina has been a way of preserving meat and it is manifactured by meat from ungulates mixed with pork lard, smoked, dryed and ripened. In this study, microbial ecology, physic-chemical parameters, and volatile aromatic compounds of Pitina SR and LR, which differ by the duration of ripening processes, were investigated. Results showed the good hygienic quality. Staphylococcus xylosus and Lactobacillus sakei were responsible for the ripening. Other Coagulase-negative Catalase-positive Cocci (CNCPC) and LAB species were identified: S. equorum, S. warneri, S. succinus and Carnobacterium divergens, Streptococcus equinus, Kocuria rhizophila. Giberella moniliformis and Penicillium turbatum were the only mould species isolated. Strain characterization demonstrated a high genetic variability. Raw meat, environment and ripening conditions seemed to affect strains distribution, which had an impact on the aromatic profile of the product.},
}
@article {pmid32062264,
year = {2020},
author = {Stopelli, E and Duyen, VT and Mai, TT and Trang, PTK and Viet, PH and Lightfoot, A and Kipfer, R and Schneider, M and Eiche, E and Kontny, A and Neumann, T and Glodowska, M and Patzner, M and Kappler, A and Kleindienst, S and Rathi, B and Cirpka, O and Bostick, B and Prommer, H and Winkel, LHE and Berg, M},
title = {Spatial and temporal evolution of groundwater arsenic contamination in the Red River delta, Vietnam: Interplay of mobilisation and retardation processes.},
journal = {The Science of the total environment},
volume = {717},
number = {},
pages = {137143},
doi = {10.1016/j.scitotenv.2020.137143},
pmid = {32062264},
issn = {1879-1026},
abstract = {Geogenic arsenic (As) contamination of groundwater poses a major threat to global health, particularly in Asia. To mitigate this exposure, groundwater is increasingly extracted from low-As Pleistocene aquifers. This, however, disturbs groundwater flow and potentially draws high-As groundwater into low-As aquifers. Here we report a detailed characterisation of the Van Phuc aquifer in the Red River Delta region, Vietnam, where high-As groundwater from a Holocene aquifer is being drawn into a low-As Pleistocene aquifer. This study includes data from eight years (2010-2017) of groundwater observations to develop an understanding of the spatial and temporal evolution of the redox status and groundwater hydrochemistry. Arsenic concentrations were highly variable (0.5-510 μg/L) over spatial scales of <200 m. Five hydro(geo)chemical zones (indicated as A to E) were identified in the aquifer, each associated with specific As mobilisation and retardation processes. At the riverbank (zone A), As is mobilised from freshly deposited sediments where Fe(III)-reducing conditions occur. Arsenic is then transported across the Holocene aquifer (zone B), where the vertical intrusion of evaporative water, likely enriched in dissolved organic matter, promotes methanogenic conditions and further release of As (zone C). In the redox transition zone at the boundary of the two aquifers (zone D), groundwater arsenic concentrations decrease by sorption and incorporations onto Fe(II) carbonates and Fe(II)/Fe(III) (oxyhydr)oxides under reducing conditions. The sorption/incorporation of As onto Fe(III) minerals at the redox transition and in the Mn(IV)-reducing Pleistocene aquifer (zone E) has consistently kept As concentrations below 10 μg/L for the studied period of 2010-2017, and the location of the redox transition zone does not appear to have propagated significantly. Yet, the largest temporal hydrochemical changes were found in the Pleistocene aquifer caused by groundwater advection from the Holocene aquifer. This is critical and calls for detailed investigations.},
}
@article {pmid32061251,
year = {2020},
author = {Zhu, X and Campanaro, S and Treu, L and Seshadri, R and Ivanova, N and Kougias, PG and Kyrpides, N and Angelidaki, I},
title = {Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {22},
pmid = {32061251},
issn = {2049-2618},
mesh = {Acetates/metabolism ; Anaerobiosis ; Bacteria/classification/*metabolism ; Bioreactors ; Chemoautotrophic Growth ; Ecosystem ; Gene Expression Profiling ; Hydrogen/metabolism ; *Metabolic Networks and Pathways ; Metagenomics ; Methane/*biosynthesis ; Methanosarcina/metabolism ; *Microbiota ; },
abstract = {Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H2. Methanosarcina thermophila, the predominant methanogen prior to H2 addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H2, which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches. Video abstract.},
}
@article {pmid32060621,
year = {2020},
author = {Walter, JM and Coutinho, FH and Leomil, L and Hargreaves, PI and Campeão, ME and Vieira, VV and Silva, BS and Fistarol, GO and Salomon, PS and Sawabe, T and Mino, S and Hosokawa, M and Miyashita, H and Maruyama, F and van Verk, MC and Dutilh, BE and Thompson, CC and Thompson, FL},
title = {Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {249-265},
doi = {10.1007/s00248-019-01480-x},
pmid = {32060621},
issn = {1432-184X},
support = {BIOCOMP//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; Universal//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (BR)/ ; CNE//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (BR)/ ; },
mesh = {Atlantic Ocean ; Brazil ; Coral Reefs ; Cyanobacteria/genetics/*physiology ; Genome, Bacterial/*physiology ; Phylogeny ; },
abstract = {Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081[T] (= CBAS 745[T]) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081[T] exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.},
}
@article {pmid32060494,
year = {2020},
author = {Louca, P and Menni, C and Padmanabhan, S},
title = {Genomic Determinants of Hypertension With a Focus on Metabolomics and the Gut Microbiome.},
journal = {American journal of hypertension},
volume = {33},
number = {6},
pages = {473-481},
pmid = {32060494},
issn = {1941-7225},
support = {CS/16/1/31878/BHF_/British Heart Foundation/United Kingdom ; MR/M016560/1/MRC_/Medical Research Council/United Kingdom ; SP/14/8/31352/BHF_/British Heart Foundation/United Kingdom ; RE/18/6/34217/BHF_/British Heart Foundation/United Kingdom ; },
mesh = {Animals ; Bacteria/*metabolism ; *Blood Pressure ; Diet ; Essential Hypertension/*genetics/*microbiology/physiopathology ; *Gastrointestinal Microbiome ; Gene-Environment Interaction ; Genetic Predisposition to Disease ; *Genetic Variation ; Humans ; *Metabolomics ; Risk Factors ; },
abstract = {Epidemiologic and genomic studies have progressively improved our understanding of the causation of hypertension and the complex relationship with diet and environment. The majority of Mendelian forms of syndromic hypotension and hypertension (HTN) have all been linked to mutations in genes whose encoded proteins regulate salt-water balance in the kidney, supporting the primacy of the kidneys in blood pressure regulation. There are more than 1,477 single nucleotide polymorphisms associated with blood pressure and hypertension and the challenge is establishing a causal role for these variants. Hypertension is a complex multifactorial phenotype and it is likely to be influenced by multiple factors including interactions between diet and lifestyle factors, microbiome, and epigenetics. Given the finite genetic variability that is possible in humans, it is likely that incremental gains from single marker analyses have now plateaued and a greater leap in our understanding of the genetic basis of disease will come from integration of other omics and the interacting environmental factors. In this review, we focus on emerging results from the microbiome and metabolomics and discuss how leveraging these findings may facilitate a deeper understanding of the interrelationships between genomics, diet, and microbial ecology in humans in the causation of essential hypertension.},
}
@article {pmid32059463,
year = {2020},
author = {Costa, OYA and Zerillo, MM and Zühlke, D and Kielak, AM and Pijl, A and Riedel, K and Kuramae, EE},
title = {Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses.},
journal = {Microorganisms},
volume = {8},
number = {2},
pages = {},
pmid = {32059463},
issn = {2076-2607},
support = {729.004.013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 202496/2015-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.},
}
@article {pmid32056227,
year = {2020},
author = {Smirnova, E and Puri, P and Muthiah, MD and Daitya, K and Brown, R and Chalasani, N and Liangpunsakul, S and Shah, VH and Gelow, K and Siddiqui, MS and Boyett, S and Mirshahi, F and Sikaroodi, M and Gillevet, P and Sanyal, AJ},
title = {Fecal Microbiome Distinguishes Alcohol Consumption From Alcoholic Hepatitis But Does Not Discriminate Disease Severity.},
journal = {Hepatology (Baltimore, Md.)},
volume = {72},
number = {1},
pages = {271-286},
pmid = {32056227},
issn = {1527-3350},
support = {UL1 TR002649/TR/NCATS NIH HHS/United States ; UO1 AA021891-01/NH/NIH HHS/United States ; U01 AA021891/AA/NIAAA NIH HHS/United States ; T32 DK07150-40/NH/NIH HHS/United States ; CTSA UL1TR002649/NH/NIH HHS/United States ; KL2 TR002648/TR/NCATS NIH HHS/United States ; T32 DK007150/DK/NIDDK NIH HHS/United States ; K23 AA021179/AA/NIAAA NIH HHS/United States ; },
mesh = {Adult ; *Alcohol Drinking ; Diagnosis, Differential ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Hepatitis, Alcoholic/*diagnosis/*microbiology ; Humans ; Male ; Middle Aged ; Severity of Illness Index ; },
abstract = {BACKGROUND AND AIMS: The role of the intestinal microbiome in alcoholic hepatitis is not established. The aims of this study were to (1) characterize the fecal microbial ecology associated with alcoholic hepatitis, (2) relate microbiome changes to disease severity, and (3) infer the functional relevance of shifts in microbial ecology.<br><br>APPROACH AND RESULTS: The fecal microbiome in patients with moderate alcoholic hepatitis (MAH) or severe alcoholic hepatitis (SAH) was compared with healthy controls (HCs) and heavy drinking controls (HDCs). Microbial taxa were identified by 16S pyrosequencing. Functional metagenomics was performed using PICRUSt. Fecal short chain fatty acids (SCFAs) were measured using a liquid chromatography-mass spectrometry platform. A total of 78 participants (HC, n&#xa0;=&#xa0;24; HDC, n&#xa0;=&#xa0;20; MAH, n&#xa0;=&#xa0;10; SAH, n&#xa0;=&#xa0;24) were studied.&#xa0;HDC had a distinct signature compared with HC with depletion of Bacteroidetes (46% vs. 26%; P&#xa0;=&#xa0;0.01). Alcoholic hepatitis was associated with a distinct microbiome signature compared with&#xa0;HDC&#xa0;(area under the curve =&#xa0;0.826); differential abundance of&#xa0;Ruminococcaceae,&#xa0;Veillonellaceae,&#xa0;Lachnospiraceae,&#xa0;Porphyromonadaceae, and&#xa0;Rikenellaceae&#xa0;families were the key contributors to these differences. The beta diversity was significantly different among the groups (permutational multivariate analysis of variance [PERMANOVA] P&#xa0;<&#xa0;0.001). SAH was associated with increased Proteobacteria (SAH 14% vs. HDC 7% and SAH vs. HC 2%, P&#xa0;=&#xa0;0.20 and 0.01, respectively). Firmicutes abundance declined from HDC to MAH to SAH (63% vs. 53% vs. 48%, respectively; P&#xa0;=&#xa0;0.09, HDC vs. SAH). Microbial taxa&#xa0;did not distinguish between MAH and SAH (PERMANOVA P&#xa0;=&#xa0;0.785). SCFAs producing bacteria (Lachnospiraceae and Ruminococcaceae) were decreased in alcoholic hepatitis, and a similar decrease was observed in fecal SCFAs among alcoholic hepatitis patients.<br><br>CONCLUSIONS: There are distinct changes in fecal microbiome associated with the development, but not severity, of alcoholic hepatitis.},
}
@article {pmid32055819,
year = {2020},
author = {Marlow, JJ and Colocci, I and Jungbluth, SP and Weber, NM and Gartman, A and Kallmeyer, J},
title = {Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment.},
journal = {FEMS microbiology letters},
volume = {367},
number = {1},
pages = {},
doi = {10.1093/femsle/fnaa031},
pmid = {32055819},
issn = {1574-6968},
mesh = {*Environmental Microbiology ; Geologic Sediments/chemistry/*microbiology ; *Metabolome ; Microbiota/*physiology ; Minerals/metabolism ; Population Density ; *Single-Cell Analysis ; Volcanic Eruptions ; },
abstract = {Interactions among microorganisms and their mineralogical substrates govern the structure, function and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu's Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2 and SO2. With increasing distance from the sediment-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, exterior surfaces accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities 'as they really are' and explore determinants of metabolic activity across a range of microbiomes.},
}
@article {pmid32055027,
year = {2020},
author = {Hatzenpichler, R and Krukenberg, V and Spietz, RL and Jay, ZJ},
title = {Next-generation physiology approaches to study microbiome function at single cell level.},
journal = {Nature reviews. Microbiology},
volume = {18},
number = {4},
pages = {241-256},
pmid = {32055027},
issn = {1740-1534},
support = {80NSSC19K0449/ImNASA/Intramural NASA/United States ; },
mesh = {*Bacterial Physiological Phenomena ; Inventions ; Microbiota/*physiology ; Single-Cell Analysis/*methods ; },
abstract = {The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.},
}
@article {pmid32054207,
year = {2020},
author = {Park, J and Kim, EB},
title = {Differences in microbiome and virome between cattle and horses in the same farm.},
journal = {Asian-Australasian journal of animal sciences},
volume = {33},
number = {6},
pages = {1042-1055},
pmid = {32054207},
issn = {1011-2367},
support = {//National Research Foundation of Korea/ ; 2016R1C1B2016246//Ministry of Education/ ; },
abstract = {OBJECTIVE: The ecosystem of an animal farm is composed of various elements, such as animals, farmers, plants, feed, soil, and microorganisms. A domesticated animal's health is largely connected with the reservoir of bacteria and viruses in animal farms. Although a few studies have focused on exploring the gut microbiome of animals, communities of microbiota and viruses in feedlots have not been thoroughly investigated.<br><br>METHODS: Here, we collected feces and dust samples (4 groups: cattle feces, C_F; horse feces, H_F; cattle dust, C_D; and horse dust, H_D) from cattle and horse farms sharing the same housing and investigated their microbiome/virome communities by Illumina sequencing.<br><br>RESULTS: Dust groups (C_D and H_D) showed higher microbial diversity than feces groups (C_F and H_F) regardless of animal species. From the microbial community analysis, all the samples from the four groups have major phyla such as Proteobacteria (min 37.1% to max 42.8%), Firmicutes (19.1% to 24.9%), Bacteroidetes (10.6% to 22.1%), and Actinobacteria (6.1% to 20.5%). The abundance of Streptococcus, which commonly recognized as equine pathogens, was significantly higher in the horse group (H_D and H_F). Over 99% among the classified virome reads were classified as Caudovirales, a group of tailed bacteriophages, in all four groups. Foot-and-mouth disease virus and equine adenovirus, which cause deadly diseases in cattle and horse, respectively, were not detected.<br><br>CONCLUSION: Our results will provide baseline information to understand different gut and environmental microbial ecology between two livestock species.},
}
@article {pmid32052099,
year = {2020},
author = {Nakabachi, A and Malenovský, I and Gjonov, I and Hirose, Y},
title = {16S rRNA Sequencing Detected Profftella, Liberibacter, Wolbachia, and Diplorickettsia from Relatives of the Asian Citrus Psyllid.},
journal = {Microbial ecology},
volume = {80},
number = {2},
pages = {410-422},
doi = {10.1007/s00248-020-01491-z},
pmid = {32052099},
issn = {1432-184X},
support = {KAKENHI grant number 26292174//the Japan Society for the Promotion of Science/ ; NA//Tatematsu Foundation/ ; NA//Nagase Science and Technology Foundation/ ; },
mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Female ; France ; Hemiptera/*microbiology ; Male ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Symbiosis ; Wolbachia/isolation &amp; purification ; },
abstract = {The Asian citrus psyllid Diaphorina citri (Hemiptera: Psylloidea) is a serious pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria: Rhizobiales), the causative agents of the incurable citrus disease, huanglongbing or greening disease. Diaphorina citri possesses a specialized organ called a bacteriome, which harbors vertically transmitted intracellular mutualists, Ca. Carsonella ruddii (Gammaproteobacteria: Oceanospirillales) and Ca. Profftella armatura (Gammaproteobacteria: Betaproteobacteriales). Whereas Carsonella is a typical nutritional symbiont, Profftella is an unprecedented type of toxin-producing defensive symbiont, unusually sharing organelle-like features with nutritional symbionts. Additionally, many D. citri strains are infected with Wolbachia, which manipulate reproduction in various arthropod hosts. In the present study, in an effort to obtain insights into the evolution of symbioses between Diaphorina and bacteria, microbiomes of psyllids closely related to D. citri were investigated. Bacterial populations of Diaphorina cf. continua and Diaphorina lycii were analyzed using Illumina sequencing of 16S rRNA gene amplicons and compared with data obtained from D. citri. The analysis revealed that all three Diaphorina spp. harbor Profftella as well as Carsonella lineages, implying that Profftella is widespread within the genus Diaphorina. Moreover, the analysis identified Ca. Liberibacter europaeus and Diplorickettsia sp. (Gammaproteobacteria: Diplorickettsiales) in D. cf. continua, and a total of four Wolbachia (Alphaproteobacteria: Rickettsiales) lineages in the three psyllid species. These results provide deeper insights into the interactions among insects, bacteria, and plants, which would eventually help to better manage horticulture.},
}
@article {pmid32051016,
year = {2020},
author = {Glendinning, L and Stewart, RD and Pallen, MJ and Watson, KA and Watson, M},
title = {Assembly of hundreds of novel bacterial genomes from the chicken caecum.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {34},
pmid = {32051016},
issn = {1474-760X},
support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/000PR10351/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013759/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013732/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20320000/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Cecum/microbiology ; Chickens/*microbiology ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; *Metagenome ; },
abstract = {BACKGROUND: Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal.<br><br>RESULTS: We utilise 1.6&#x2009;T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome.<br><br>CONCLUSIONS: This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.},
}
@article {pmid32050392,
year = {2020},
author = {Chai, B and Tsoi, T and Sallach, JB and Liu, C and Landgraf, J and Bezdek, M and Zylstra, G and Li, H and Johnston, CT and Teppen, BJ and Cole, JR and Boyd, SA and Tiedje, JM},
title = {Bioavailability of clay-adsorbed dioxin to Sphingomonas wittichii RW1 and its associated genome-wide shifts in gene expression.},
journal = {The Science of the total environment},
volume = {712},
number = {},
pages = {135525},
doi = {10.1016/j.scitotenv.2019.135525},
pmid = {32050392},
issn = {1879-1026},
mesh = {Biological Availability ; Clay ; Dioxins ; Gene Expression ; Genome, Bacterial ; *Sphingomonas ; },
abstract = {Polychlorinated dibenzo-p-dioxins and dibenzofurans are a group of chemically-related pollutants categorically known as dioxins. Some of their chlorinated congeners are among the most hazardous pollutants that persist in the environment. This persistence is due in part to the limited number of bacteria capable of metabolizing these compounds, but also to their limited bioavailability in soil. We used Sphingomonas wittichii strain RW1 (RW1), one of the few strains able to grow on dioxin, to characterize its ability to respond to and degrade clay-bound dioxin. We found that RW1 grew on and completely degraded dibenzo-p-dioxin (DD) intercalated into the smectite clay saponite (SAP). To characterize the effects of DD sorption on RW1 gene expression, we compared transcriptomes of RW1 grown with either free crystalline DD or DD intercalated clay, i.e. sandwiched between the clay interlayers (DDSAP). Free crystalline DD appeared to cause greater expression of toxicity and stress related functions. Genes coding for heat shock proteins, chaperones, as well as genes involved in DNA repair, and efflux were up-regulated during growth on crystalline dioxin compared to growth on intercalated dioxin. In contrast, growth on intercalated dioxin up-regulated genes that might be important in recognition and uptake mechanisms, as well as surface interaction/attachment/biofilm formation such as extracellular solute-binding protein and LuxR. These differences in gene expression may reflect the underlying adaptive mechanisms by which RW1 cells sense and deploy pathways to access dioxin intercalated into clay. These data show that intercalated DD remains bioavailable to the degrading bacterium with implications for bioremediation alternatives.},
}
@article {pmid32049503,
year = {2020},
author = {De Paepe, J and De Pryck, L and Verliefde, ARD and Rabaey, K and Clauwaert, P},
title = {Electrochemically Induced Precipitation Enables Fresh Urine Stabilization and Facilitates Source Separation.},
journal = {Environmental science &amp; technology},
volume = {54},
number = {6},
pages = {3618-3627},
doi = {10.1021/acs.est.9b06804},
pmid = {32049503},
issn = {1520-5851},
mesh = {Ammonia ; *Bathroom Equipment ; Chemical Precipitation ; Hydrolysis ; Recycling ; Urine ; *Wastewater ; },
abstract = {Source separation of urine can enable nutrient recycling, facilitate wastewater management, and conserve water. Without stabilization of the urine, urea is quickly hydrolyzed into ammonia and (bi)carbonate, causing nutrient loss, clogging of collection systems, ammonia volatilization, and odor nuisance. In this study, electrochemically induced precipitation and stabilization of fresh urine was successfully demonstrated. By recirculating the urine over the cathodic compartment of an electrochemical cell, the pH was increased due to the production of hydroxyl ions at the cathode. The pH increased to 11-12, decreasing calcium and magnesium concentrations by >80%, and minimizing scaling and clogging during downstream processing. At pH 11, urine could be stabilized for one week, while an increase to pH 12 allowed urine storage without urea hydrolysis for >18 months. By a smart selection of membranes [anion exchange membrane (AEM) with a cation exchange membrane (CEM) or a bipolar membrane (BPM)], no chemical input was required in the electrochemical cell and an acidic stream was produced that can be used to periodically rinse the electrochemical cell and toilet. On-site electrochemical treatment, close to the toilet, is a promising new concept to minimize clogging in collection systems by forcing controlled precipitation and to inhibit urea hydrolysis during storage until further treatment in more centralized nutrient recovery plants.},
}
@article {pmid32045510,
year = {2020},
author = {Boreczek, J and Litwinek, D and Żylińska-Urban, J and Izak, D and Buksa, K and Gawor, J and Gromadka, R and Bardowski, JK and Kowalczyk, M},
title = {Bacterial community dynamics in spontaneous sourdoughs made from wheat, spelt, and rye wholemeal flour.},
journal = {MicrobiologyOpen},
volume = {9},
number = {4},
pages = {e1009},
pmid = {32045510},
issn = {2045-8827},
mesh = {Bacteroidetes/classification/isolation &amp; purification/*metabolism ; Biodiversity ; Bioreactors/microbiology ; Bread/*microbiology ; Fermentation ; Flour/*microbiology ; Food Microbiology ; Lactobacillus/classification/isolation &amp; purification/*metabolism ; Proteobacteria/classification/isolation &amp; purification/*metabolism ; Secale/metabolism ; Triticum/metabolism ; },
abstract = {Sourdough fermentation is a traditional process that is used to improve bread quality. A spontaneous sourdough ecosystem consists of a mixture of flour and water that is fermented by endogenous lactic acid bacteria (LAB) and yeasts. The aim of this study was to identify bacterial diversity during backslopping of spontaneous sourdoughs prepared from wheat, spelt, or rye wholemeal flour. Culture-dependent analyses showed that the number of LAB (10[9] CFU/ml) was higher by three orders of magnitude than the number of yeasts (10[6] CFU/ml), irrespective of the flour type. These results were complemented by next-generation sequencing of the 16S rDNA V3 and V4 variable regions. The dominant phylum in all sourdough samples was Firmicutes, which was represented exclusively by the Lactobacillales order. The two remaining and less abundant phyla were Proteobacteria and Bacteroidetes. The culture-independent approach allowed us to detect changes in microbial ecology during the 72-hr fermentation period. Weissella sp. was the most abundant genus after 24 hr of fermentation of the rye sourdough, but as the process progressed, its abundance decreased in favor of the Lactobacillus genus similarly as in wheat and spelt sourdoughs. The Lactobacillus genus was dominant in all sourdoughs after 72 hr, which was consistent with our results obtained using culture-dependent analyses. This work was carried out to determine the microbial biodiversity of sourdoughs that are made from wheat, spelt, and rye wholemeal flour and can be used as a source of strains for specific starter cultures to produce functional bread.},
}
@article {pmid32043958,
year = {2020},
author = {Hofmann, K and Huptas, C and Doll, EV and Scherer, S and Wenning, M},
title = {Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {4},
pages = {2339-2347},
doi = {10.1099/ijsem.0.004043},
pmid = {32043958},
issn = {1466-5034},
mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; Cattle ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Food Microbiology ; Genes, Bacterial ; Milk/*microbiology ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Pseudomonas/*classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; },
abstract = {Two strains, WS 5063[T] and WS 5067, isolated from raw cow's milk and skimmed milk concentrate, could be affiliated as members of the same, hitherto unknown, Pseudomonas species by 16S rRNA and rpoD gene sequences. Multilocus sequence and average nucleotide identity (ANIm) analyses based on draft genome sequences confirmed the discovery of a novel Pseudomonas species. It was most closely related to Pseudomonas synxantha DSM 18928[T] with an ANIm of 91.4 %. The DNA G+C content of WS 5063[T] was 60.0 mol %. Phenotypic characterizations showed that the isolates are rod-shaped, motile, catalase- and oxidase-positive, and aerobic. Growth occurred at 4-34 °C and at pH values of pH 5.5-8.0. Both strains showed strong β-haemolysis on blood agar. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The dominant quinone was Q-9 (90 %), but noticeable amounts of Q-8 (9 %) and traces of Q-7 were also detected. Fatty acid profiles were typical for Pseudomonas species and exhibited C16 : 0 as a major component. Based on these results, we conclude that both strains belong to a novel species, for which the name Pseudomonas haemolytica sp. nov. is proposed. The type strain is WS 5063[T] (=DSM 108987[T]=LMG 31232[T]) and an additional strain is WS 5067 (=DSM 108988=LMG 31233).},
}
@article {pmid32043954,
year = {2020},
author = {Wenning, M and Breitenwieser, F and Huptas, C and Doll, E and Bächler, B and Schulz, A and Dunkel, A and Hofmann, T and von Neubeck, M and Busse, HJ and Scherer, S},
title = {Brevilactibacter flavus gen. nov., sp. nov., a novel bacterium of the family Propionibacteriaceae isolated from raw milk and dairy products and reclassification of Propioniciclava sinopodophylli as Brevilactibacter sinopodophylli comb. nov.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {4},
pages = {2186-2193},
doi = {10.1099/ijsem.0.003909},
pmid = {32043954},
issn = {1466-5034},
mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/chemistry ; DNA, Bacterial/genetics ; Dairy Products/*microbiology ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Food Microbiology ; Germany ; Glycolipids/chemistry ; Milk/*microbiology ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; Propionibacteriaceae/*classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; },
abstract = {Eight facultatively anaerobic rod-shaped bacteria were isolated from raw milk and two other dairy products. Results of phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates are placed in a distinct lineage within the family Propionibacteriaceae with Propioniciclava sinopodophylli and Propioniciclava tarda as the closest relatives (94.6 and 93.5 % similarity, respectively). The cell-wall peptidoglycan contained meso-diaminopimelic acid, alanine and glutamic acid and was of the A1γ type (meso-DAP-direct). The major cellular fatty acid was anteiso-C15 : 0 and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and three unidentified glycolipids. The quinone system contained predominantly menaquinone MK-9(H4). The G+C content of the genomic DNA of strain VG341[T] was 67.7 mol%. The whole-cell sugar pattern contained ribose, rhamnose, arabinose and galactose. On the basis of phenotypic and genetic data, eight strains (VG341[T], WS4684, WS4769, WS 4882, WS4883, WS4901, WS4902 and WS4904) are proposed to be classified as members of a novel species in a new genus of the family Propionibacteriaceae, for which the name Brevilactibacter flavus gen. nov., sp. nov. is proposed. The type strain is VG341[T] (=WS4900[T]=DSM 100885[T]=LMG 29089[T]) and seven additional strains are WS4684, WS4769, WS4882, WS4883, WS4901, WS4902 and WS4904. Furthermore, we propose the reclassification of P. sinopodophylli as Brevilactibacter sinopodophylli comb. nov.},
}
@article {pmid32042158,
year = {2020},
author = {Zhang, J and Fu, XX and Li, RQ and Zhao, X and Liu, Y and Li, MH and Zwaenepoel, A and Ma, H and Goffinet, B and Guan, YL and Xue, JY and Liao, YY and Wang, QF and Wang, QH and Wang, JY and Zhang, GQ and Wang, ZW and Jia, Y and Wang, MZ and Dong, SS and Yang, JF and Jiao, YN and Guo, YL and Kong, HZ and Lu, AM and Yang, HM and Zhang, SZ and Van de Peer, Y and Liu, ZJ and Chen, ZD},
title = {The hornwort genome and early land plant evolution.},
journal = {Nature plants},
volume = {6},
number = {2},
pages = {107-118},
pmid = {32042158},
issn = {2055-0278},
mesh = {Anthocerotophyta/*genetics ; *Biological Evolution ; *Genome, Plant ; Multigene Family ; Phylogeny ; },
abstract = {Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.},
}
@article {pmid32042128,
year = {2020},
author = {VanInsberghe, D and Elsherbini, JA and Varian, B and Poutahidis, T and Erdman, S and Polz, MF},
title = {Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms.},
journal = {Nature microbiology},
volume = {5},
number = {4},
pages = {642-650},
pmid = {32042128},
issn = {2058-5276},
mesh = {Actinobacteria/genetics/growth &amp; development/isolation &amp; purification ; Animals ; Bacteroidetes/genetics/growth &amp; development/isolation &amp; purification ; Clostridioides difficile/*drug effects/growth &amp; development/*pathogenicity ; Clostridium Infections/complications/*microbiology ; Colony Count, Microbial ; Diarrhea/chemically induced/complications/*microbiology ; Disease Models, Animal ; Feces/microbiology ; Firmicutes/genetics/growth &amp; development/isolation &amp; purification ; Fusobacteria/genetics/growth &amp; development/isolation &amp; purification ; Gastrointestinal Microbiome/*drug effects ; Humans ; Laxatives/*adverse effects ; Male ; Mice ; Polyethylene Glycols/*adverse effects ; Proteobacteria/genetics/growth &amp; development/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Although Clostridium difficile is widely considered an antibiotic- and hospital-associated pathogen, recent evidence indicates that this is an insufficient depiction of the risks and reservoirs. A common thread that links all major risk factors of infection is their association with gastrointestinal disturbances, but this relationship to C. difficile colonization has never been tested directly. Here, we show that disturbances caused by diarrhoeal events trigger susceptibility to C. difficile colonization. Using survey data of the human gut microbiome, we detected C. difficile colonization and blooms in people recovering from food poisoning and Vibrio cholerae infections. Carriers remained colonized for year-long time scales and experienced highly variable patterns of C. difficile abundance, where increased shedding over short periods of 1-2 d interrupted week-long periods in which C. difficile was undetectable. Given that short shedding events were often linked to gastrointestinal disturbances, our results help explain why C. difficile is frequently detected as a co-infecting pathogen in patients with diarrhoea. To directly test the impact of diarrhoea on susceptibility to colonization, we developed a mouse model of variable disturbance intensity, which allowed us to monitor colonization in the absence of disease. As mice exposed to avirulent C. difficile spores ingested increasing quantities of laxatives, more individuals experienced C. difficile blooms. Our results indicate that the likelihood of colonization is highest in the days immediately following acute disturbances, suggesting that this could be an important window during which transmission could be interrupted and the incidence of infection lowered.},
}
@article {pmid32039976,
year = {2020},
author = {Burmeister, DM and Johnson, TR and Lai, Z and Scroggins, SR and DeRosa, M and Jonas, RB and Zhu, C and Scherer, E and Stewart, RM and Schwacha, MG and Jenkins, DH and Eastridge, BJ and Nicholson, SE},
title = {The gut microbiome distinguishes mortality in trauma patients upon admission to the emergency department.},
journal = {The journal of trauma and acute care surgery},
volume = {88},
number = {5},
pages = {579-587},
pmid = {32039976},
issn = {2163-0763},
support = {KL2 TR001118/TR/NCATS NIH HHS/United States ; KL2 TR002646/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Aged ; Emergency Service, Hospital/statistics &amp; numerical data ; Feces/microbiology ; Female ; Follow-Up Studies ; Gastrointestinal Microbiome/*physiology ; Hospital Mortality ; Humans ; Injury Severity Score ; Length of Stay/statistics &amp; numerical data ; Male ; Middle Aged ; Prognosis ; Prospective Studies ; Trauma Centers/statistics &amp; numerical data ; Wounds, Nonpenetrating/diagnosis/microbiology/*mortality ; Wounds, Penetrating/diagnosis/microbiology/*mortality ; },
abstract = {BACKGROUND: Traumatic injury can lead to a compromised intestinal epithelial barrier, decreased gut perfusion, and inflammation. While recent studies indicate that the gut microbiome (GM) is altered early following traumatic injury, the impact of GM changes on clinical outcomes remains unknown. Our objective of this follow-up study was to determine if the GM is associated with clinical outcomes in critically injured patients.<br><br>METHODS: We conducted a prospective, observational study in adult patients (N = 67) sustaining severe injury admitted to a level I trauma center. Fecal specimens were collected on admission to the emergency department, and microbial DNA from all samples was analyzed using the Quantitative Insights Into Microbial Ecology pipeline and compared against the Greengenes database. &#x3b1;-Diversity and &#x3b2;-diversity were estimated using the observed species metrics and analyzed with t tests and permutational analysis of variance for overall significance, with post hoc pairwise analyses.<br><br>RESULTS: Our patient population consisted of 63% males with a mean age of 44 years. Seventy-eight percent of the patients suffered blunt trauma with 22% undergoing penetrating injuries. The mean body mass index was 26.9 kg/m. Significant differences in admission &#x3b2;-diversity were noted by hospital length of stay, intensive care unit hospital length of stay, number of days on the ventilator, infections, and acute respiratory distress syndrome (p < 0.05). &#x3b2;-Diversity on admission differed in patients who died compared with patients who lived (mean time to death, 8 days). There were also significantly less operational taxonomic units in samples from patients who died versus those who survived. A number of species were enriched in the GM of injured patients who died, which included some traditionally probiotic species such as Akkermansia muciniphilia, Oxalobacter formigenes, and Eubacterium biforme (p < 0.05).<br><br>CONCLUSION: Gut microbiome diversity on admission in severely injured patients is predictive of a variety of clinically important outcomes. While our study does not address causality, the GM of trauma patients may provide valuable diagnostic and therapeutic targets for the care of injured patients.<br><br>LEVEL OF EVIDENCE: Prognostic and epidemiological, level III.},
}
@article {pmid32038529,
year = {2019},
author = {Lee, JY and Haruta, S and Kato, S and Bernstein, HC and Lindemann, SR and Lee, DY and Fredrickson, JK and Song, HS},
title = {Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {3049},
pmid = {32038529},
issn = {1664-302X},
abstract = {Modulation of interspecies interactions by the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method termed the Minimal Interspecies Interaction Adjustment (MIIA) that predicts the reorganization of interaction networks in response to the addition of new species such that the modulation in interaction coefficients caused by additional members is minimal. While the theoretical basis of MIIA was established through the previous work by assuming the full availability of species abundance data in axenic, binary, and complex communities, its extension to actual microbial ecology can be highly constrained in cases that species have not been cultured axenically (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients - basic parameters required for implementing the MIIA - are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only data from axenic cultures are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, in the case where both axenic and binary populations are missing, we parameterize binary interaction coefficients to determine their values through a sensitivity analysis. Through the case study of two microbial communities with distinct characteristics and complexity (i.e., a three-member community where all members can grow independently, and a four-member community that contains member species whose growth is dependent on other species), we demonstrated that despite data limitation, the proposed new formulation was able to successfully predict interspecies interactions that are consistent with experimentally derived results. Therefore, this technical advancement enhances our ability to predict context-dependent interspecies interactions in a broad range of microbial systems without being limited to specific growth conditions as a pre-requisite.},
}
@article {pmid32036919,
year = {2020},
author = {Babaahmadifooladi, M and Jacxsens, L and Van de Wiele, T and Laing, GD},
title = {Gap analysis of nickel bioaccessibility and bioavailability in different food matrices and its impact on the nickel exposure assessment.},
journal = {Food research international (Ottawa, Ont.)},
volume = {129},
number = {},
pages = {108866},
doi = {10.1016/j.foodres.2019.108866},
pmid = {32036919},
issn = {1873-7145},
mesh = {Biological Availability ; Food Analysis/*methods ; *Hypersensitivity ; Nickel/*chemistry/*pharmacokinetics ; Plants/*chemistry ; },
abstract = {The metal nickel is well known to cause nickel allergy in sensitive humans by prolonged dermal contact to materials releasing (high) amounts of nickel. Oral nickel exposure via water and food intake is of potential concern. Nickel is essential to plants and animals and can be naturally found in food products or contamination may occur across the agro-food chain. This gap analysis is an evaluation of nickel as a potential food safety hazard causing a risk for human health. In the first step, the available data regarding the occurrence of nickel and its contamination in food and drinks have been collected through literature review. Subsequently, a discussion is held on the potential risks associated with this contamination. Elevated nickel concentrations were mostly found in plant-based foods, e.g. legumes and nuts in which nickel of natural origin is expected. However, it was observed that dedicated and systematic screening of foodstuffs for the presence of nickel is currently still lacking. In a next step, published studies on exposure of humans to nickel via foods and drinks were critically evaluated. Not including bioaccessibility and/or bioavailability of the metal may lead to an overestimation of the exposure of the body to nickel via food and drinks. This overestimation may be problematic when the measured nickel level in foods is high and bioaccessibility and/or bioavailability of nickel in these products is low. Therefore, this paper analyzes the outcomes of the existing dietary intake and bioaccessibility/bioavailability studies conducted for nickel. Besides, the available gaps in nickel bioaccessibility and/or bioavailability studies have been clarified in this paper. The reported bioaccessibility and bioavailability percentages for different food and drinks were found to vary between <LOD and 83% and between 0 and 30% respectively. This indicates that of the total nickel contained in the foodstuffs only a fraction can be absorbed by the intestinal epithelium cells. This paper provides a unique critical overview on nickel in the human diet starting from factors affecting its occurrence in food until its absorption by the body.},
}
@article {pmid32036914,
year = {2020},
author = {Vossen, E and Goethals, S and De Vrieze, J and Boon, N and Van Hecke, T and De Smet, S},
title = {Red and processed meat consumption within two different dietary patterns: Effect on the colon microbial community and volatile metabolites in pigs.},
journal = {Food research international (Ottawa, Ont.)},
volume = {129},
number = {},
pages = {108793},
doi = {10.1016/j.foodres.2019.108793},
pmid = {32036914},
issn = {1873-7145},
mesh = {Animals ; Butyrivibrio/metabolism ; Campylobacter/metabolism ; Chickens ; Clostridium/metabolism ; Colon/metabolism/*microbiology ; DNA, Bacterial/genetics/isolation &amp; purification ; Diet/*veterinary ; Diet, Western ; Enterobacteriaceae/metabolism ; Fermentation ; *Gastrointestinal Microbiome ; Male ; Meat Products/*analysis ; Red Meat/*analysis ; Swine ; Volatile Organic Compounds/*metabolism ; },
abstract = {Pigs were fed either red and processed meat or chicken meat within either a prudent or a Western dietary pattern for four weeks (2 × 2 full factorial design). The colon microbial community and volatile organic compounds were assessed (either quantified or based on their presence). Results show that Lactobacilli were characteristic for the chicken × prudent dietary pattern treatment and Paraprevotella for the red and processed meat × prudent dietary pattern treatment. Enterobacteriaceae and Desulfovibrio were characteristic for the chicken × Western dietary pattern treatment and Butyrivibrio for the red and processed meat × Western dietary pattern treatment. Campylobacter was characteristic for chicken consumption and Clostridium XIVa for red and processed meat, irrespective of the dietary pattern. Ethyl valerate and 1-methylthio-propane were observed more frequently in pigs fed red and processed meat compared to chicken meat. The prevalence of 3-methylbutanal was >80% for pigs receiving a Western dietary pattern, whereas for pigs fed a prudent dietary pattern the prevalence was <35%. The concentration of butanoic acid was significantly higher when the prudent dietary pattern was given, compared to the Western dietary pattern, but no differences for other short chain fatty acids or protein fermentation products were observed.},
}
@article {pmid32034763,
year = {2020},
author = {Rombouts, JL and Kranendonk, EMM and Regueira, A and Weissbrodt, DG and Kleerebezem, R and van Loosdrecht, MCM},
title = {Selecting for lactic acid producing and utilising bacteria in anaerobic enrichment cultures.},
journal = {Biotechnology and bioengineering},
volume = {117},
number = {5},
pages = {1281-1293},
pmid = {32034763},
issn = {1097-0290},
support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/International ; FPU14/05457//Spanish Ministry of Education/International ; },
mesh = {Anaerobiosis/*physiology ; Bioreactors/microbiology ; Cell Culture Techniques ; Fermentation/physiology ; Lactic Acid/metabolism ; *Lactobacillales/metabolism/physiology ; },
abstract = {Lactic acid-producing bacteria are important in many fermentations, such as the production of biobased plastics. Insight in the competitive advantage of lactic acid bacteria over other fermentative bacteria in a mixed culture enables ecology-based process design and can aid the development of sustainable and energy-efficient bioprocesses. Here we demonstrate the enrichment of lactic acid bacteria in a controlled sequencing batch bioreactor environment using a glucose-based medium supplemented with peptides and B vitamins. A mineral medium enrichment operated in parallel was dominated by Ethanoligenens species and fermented glucose to acetate, butyrate and hydrogen. The complex medium enrichment was populated by Lactococcus, Lactobacillus and Megasphaera species and showed a product spectrum of acetate, ethanol, propionate, butyrate and valerate. An intermediate peak of lactate was observed, showing the simultaneous production and consumption of lactate, which is of concern for lactic acid production purposes. This study underlines that the competitive advantage for lactic acid-producing bacteria primarily lies in their ability to attain a high biomass specific uptake rate of glucose, which was two times higher for the complex medium enrichment when compared to the mineral medium enrichment. The competitive advantage of lactic acid production in rich media can be explained using a resource allocation theory for microbial growth processes.},
}
@article {pmid32034151,
year = {2020},
author = {Kitzinger, K and Marchant, HK and Bristow, LA and Herbold, CW and Padilla, CC and Kidane, AT and Littmann, S and Daims, H and Pjevac, P and Stewart, FJ and Wagner, M and Kuypers, MMM},
title = {Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {767},
pmid = {32034151},
issn = {2041-1723},
abstract = {Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are unclear. Here, we compare substrate utilization and growth of Nitrospinae to AOA in the Gulf of Mexico. Based on our results, more than half of the Nitrospinae cellular N-demand is met by the organic-N compounds urea and cyanate, while AOA mainly assimilate ammonium. Nitrospinae have, under in situ conditions, around four-times higher biomass yield and five-times higher growth rates than AOA, despite their ten-fold lower abundance. Our combined results indicate that differences in mortality between Nitrospinae and AOA, rather than thermodynamics, biomass yield and cell size, determine the abundances of these main marine nitrifiers. Furthermore, there is no need to invoke yet undiscovered, abundant nitrite oxidizers to explain nitrification rates in the ocean.},
}
@article {pmid32033945,
year = {2020},
author = {Heys, C and Cheaib, B and Busetti, A and Kazlauskaite, R and Maier, L and Sloan, WT and Ijaz, UZ and Kaufmann, J and McGinnity, P and Llewellyn, MS},
title = {Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {8},
pages = {},
pmid = {32033945},
issn = {1098-5336},
support = {BB/P001203/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Aquaculture ; Bacteria/*genetics ; Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Salmo salar/growth &amp; development/*microbiology ; Stochastic Processes ; },
abstract = {In recent years, a wealth of studies has examined the relationships between a host and its microbiome across diverse taxa. Many studies characterize the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterized using 16S rRNA gene MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across life cycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we found declining taxonomic and functional microbial community richness as fish mature through different life cycle stages. Alongside neutral community models applied to wild fish, we suggest that declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We found a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma spp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes, such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered.IMPORTANCE A growing number of studies have examined variation in the microbiome to determine the role in modulating host health, physiology, and ecology. However, the ecology of host microbial colonization is not fully understood and rarely tested. The continued increase in production of farmed Atlantic salmon, coupled with increased farmed-wild salmon interactions, has accentuated the need to unravel the potential adaptive function of the microbiome and to distinguish resident from transient gut microbes. Between gut compartments in a farmed system, we found a majority of operational taxonomic units (OTUs) that fit the neutral model, with Mycoplasma species among the key exceptions. In wild fish, deterministic processes account for more OTU differences across life stages than those observed across gut compartments. Unlike previous studies, our results make detailed comparisons between fish from wild and farmed environments, while also providing insight into the ecological processes underpinning microbial community assembly in this ecologically and economically important species.},
}
@article {pmid32031212,
year = {2020},
author = {Fenske, GJ and Ghimire, S and Antony, L and Christopher-Hennings, J and Scaria, J},
title = {Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {3},
pages = {},
doi = {10.1093/femsec/fiaa022},
pmid = {32031212},
issn = {1574-6941},
mesh = {Animals ; Bacteroidetes/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; },
abstract = {Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.},
}
@article {pmid32030584,
year = {2020},
author = {Mariano, C and Mello, IS and Barros, BM and da Silva, GF and Terezo, AJ and Soares, MA},
title = {Mercury alters the rhizobacterial community in Brazilian wetlands and it can be bioremediated by the plant-bacteria association.},
journal = {Environmental science and pollution research international},
volume = {27},
number = {12},
pages = {13550-13564},
pmid = {32030584},
issn = {1614-7499},
support = {409062/2018-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 568258/2014//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa&#xa0;do Estado de&#xa0;Mato Grosso/ ; },
mesh = {Actinobacteria ; Bacillus ; Biodegradation, Environmental ; Brazil ; *Mercury ; Microbacterium ; Soil Microbiology ; *Soil Pollutants ; Wetlands ; },
abstract = {This study examined how soil mercury contamination affected the structure and functionality of rhizobacteria communities from Aeschynomene fluminensis and Polygonum acuminatum and how rhizobacteria mediate metal bioremediation. The strains were isolated using culture-dependent methods, identified through 16S rDNA gene sequencing, and characterized with respect to their functional traits related to plant growth promotion and resistance to metals and antibiotics. The bioremediation capacity of the rhizobacteria was determined in greenhouse using corn plants. The isolated bacteria belonged to the phyla Actinobacteria, Deinococcus-Thermus, Firmicutes, and Proteobacteria, with great abundance of the species Microbacterium trichothecenolyticum. The rhizobacteria abundance, richness, and diversity were greater in mercury-contaminated soils. Bacteria isolated from contaminated environments had higher minimum inhibitory concentration values, presented plasmids and the merA gene, and were multi-resistant to metals and antibiotics. Enterobacter sp._C35 and M. trichothecenolyticum_C34 significantly improved (Dunnett's test, p < 0.05) corn plant growth in mercury-contaminated soil. These bacteria helped to reduce up to 87% of the mercury content in the soil, and increased the mercury bioaccumulation factor by up to 94%. Mercury bioremediation mitigated toxicity of the contaminated substrate. Enterobacter sp._C35, Bacillus megaterium_C28, and Bacillus mycoides_C1 stimulated corn plant growth and could be added to biofertilizers produced in research and related industries.},
}
@article {pmid32027305,
year = {2020},
author = {Lee, HJ and Whang, KS},
title = {Elioraea rosea sp. nov., a plant promoting bacterium isolated from floodwater of a paddy field.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {3},
pages = {2132-2136},
doi = {10.1099/ijsem.0.004028},
pmid = {32027305},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Oryza ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Rhodospirillales/*classification/isolation &amp; purification ; Sequence Analysis, DNA ; Ubiquinone/analogs &amp; derivatives/chemistry ; *Water Microbiology ; },
abstract = {A Gram-stain-negative bacterium, designated strain PF-30[T], was isolated from floodwater of a paddy field in South Korea. Strain PF-30[T] was found to be a strictly aerobic, motile and pink-pigmented rods which can grow at 25-40 °C (optimum, 28 °C), at pH 5.0-9.0 (optimum pH 7.0) and at salinities of 0.5-3.0 % NaCl (optimum 0.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PF-30[T] belongs to the genus Elioraea, showing highest sequence similarity to Elioraea tepidiphila TU-7[T] (97.1%) and less than 91.3 % similarity with other members of the family Acetobacteraceae. The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain PF-30[T] and E. tepidiphila TU-7[T] yielded an ANI value of 75.1 % and DNA-DNA relatedness of 11.7±0.7 %, respectively. The major fatty acids were identified as C18 : 0 and C18 : 1 ω7c. The predominant respiratory quinone was identified as Q-10. The DNA G+C content was determined to be 69.9 mol%. The strain PF-30[T] was observed to produce plant-growth-promoting materials such as indole-3-acetic acid (IAA), siderophore and phytase. On the basis of the results from phylogenetic, chemotaxonomic and phenotypic data, we concluded that strain PF-30[T] represents a novel species of the genus Elioraea, for which the name Elioraea rosea sp. nov. is proposed. The type strain is PF-30[T] (=KACC 19985[T]=NBRC 113984[T]).},
}
@article {pmid32025810,
year = {2020},
author = {Smichi, N and Messaoudi, Y and Allaf, K and Gargouri, M},
title = {Steam explosion (SE) and instant controlled pressure drop (DIC) as thermo-hydro-mechanical pretreatment methods for bioethanol production.},
journal = {Bioprocess and biosystems engineering},
volume = {43},
number = {6},
pages = {945-957},
doi = {10.1007/s00449-020-02297-6},
pmid = {32025810},
issn = {1615-7605},
mesh = {*Biofuels ; *Bioreactors ; *Biotechnology ; Ethanol/*metabolism ; Steam ; },
abstract = {Lignocellulosic biomass can be considered as one of the largest sources for the production of renewable biofuels (bioethanol). It involves an enzymatic treatment capable of ensuring the depolymerization of cellulose into fermentable sugars, followed by the production of ethanol by appropriate bacteriological fermentation. Proper destruction of the compact natural structure of the biomass would allow an interesting intensification of the operation. Among the most prominent technical approaches, the steam explosion (SE) is the most famous. However, this high pressure-high temperature process implies too high energy consumption while leading to the generation of many non-fermentable molecules. In recent years, many studies have proposed the use of the Instant Controlled Pressure-Drop (DIC) texturing pretreatment as an effective alternative to SE for ethanol production. Therefore, in this manuscript, we propose to compare and discuss the fundamental principles and experimental results of these two operations, as presented in the relevant literature.},
}
@article {pmid32024862,
year = {2020},
author = {Snyder, GT and Matsumoto, R and Suzuki, Y and Kouduka, M and Kakizaki, Y and Zhang, N and Tomaru, H and Sano, Y and Takahata, N and Tanaka, K and Bowden, SA and Imajo, T},
title = {Evidence in the Japan Sea of microdolomite mineralization within gas hydrate microbiomes.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {1876},
pmid = {32024862},
issn = {2045-2322},
mesh = {Aquatic Organisms/chemistry/*metabolism ; Bacteroidetes/chemistry/*metabolism ; Biodegradation, Environmental ; Calcium Carbonate/*chemistry ; Fossils ; Geologic Sediments/chemistry/*microbiology ; Magnesium/*chemistry ; Methane/*metabolism ; Microbiota ; Petroleum/metabolism ; Seawater/chemistry/microbiology ; },
abstract = {Over the past 15 years, massive gas hydrate deposits have been studied extensively in Joetsu Basin, Japan Sea, where they are associated primarily with active gas chimney structures. Our research documents the discovery of spheroidal microdolomite aggregates found in association with other impurities inside of these massive gas hydrates. The microdolomites are often conjoined and show dark internal cores occasionally hosting saline fluid inclusions. Bacteroidetes sp. are concentrated on the inner rims of microdolomite grains, where they degrade complex petroleum-macromolecules present as an impurity within yellow methane hydrate. These oils show increasing biodegradation with depth which is consistent with the microbial activity of Bacteroidetes. Further investigation of these microdolomites and their contents can potentially yield insight into the dynamics and microbial ecology of other hydrate localities. If microdolomites are indeed found to be ubiquitous in both present and fossil hydrate settings, the materials preserved within may provide valuable insights into an unusual microhabitat which could have once fostered ancient life.},
}
@article {pmid32023186,
year = {2020},
author = {Dhaulaniya, AS and Balan, B and Yadav, A and Jamwal, R and Kelly, S and Cannavan, A and Singh, DK},
title = {Development of an FTIR based chemometric model for the qualitative and quantitative evaluation of cane sugar as an added sugar adulterant in apple fruit juices.},
journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment},
volume = {37},
number = {4},
pages = {539-551},
doi = {10.1080/19440049.2020.1718774},
pmid = {32023186},
issn = {1944-0057},
mesh = {Food Additives/*analysis ; *Food Analysis ; Food Contamination/*analysis ; Fruit and Vegetable Juices/*analysis ; Malus/chemistry ; *Models, Chemical ; Saccharum/chemistry ; Spectroscopy, Fourier Transform Infrared ; },
abstract = {A Fourier Transform Infrared Spectroscopy based chemometric model was evaluated for the rapid identification and estimation of cane sugar as an added sugar adulterant in apple fruit juices. For all the ninety samples, spectra were acquired in the mid-infrared range (4000 cm[-1]-400 cm[-1]). The spectral analysis provided information regarding the distinctive variable region, which lies in the range of 1200cm[-1] to 900cm[-1], designated as fingerprint region for the carbohydrates. A specific peak in the fingerprint region was observed at 997cm[-1] in all the adulterated samples and was undetectable in pure samples. Based on different levels of cane sugar adulteration (5, 10, 15, and 20%), principal component analysis showed the clustering of samples and further helped us in compression of data by selecting wavenumbers with maximum variability based on the loading line plot. Supervised classification methods (SIMCA and LDA) were evaluated based on their classification efficiencies for a test set. Though SIMCA showed 100% classification efficiency (Raw data set), LDA was able to classify the test set with an accuracy of only 96.67% (Raw as well as Transformed data set) between pure and 5% adulterated samples. For the quantitative estimation, calibration models were developed using partial least square regression (PLS-R) and principal component regression method (PCR) methods. PLS-1[st] derivative showed a maximum coefficient of determination (R[2]) with a value of 0.991 for calibration and 0.992 for prediction. The RMSECV, RMSEP, LOD and LOQ observed for PLS-1[st] derivative model were 0.75% w/v, 0.61% w/v, 1.28%w/v and 3.88%w/v, respectively. The coefficient of variation as a measure of precision (repeatability) was also determined for all models, and it ranged from 0.23% to 1.83% (interday), and 0.25% to 1.43% (intraday).},
}
@article {pmid32020257,
year = {2020},
author = {Wang, F and Cale, JA and Erbilgin, N},
title = {Induced Defenses of a Novel Host Tree Affect the Growth and Interactions of Bark Beetle-Vectored Fungi.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {181-190},
doi = {10.1007/s00248-020-01490-0},
pmid = {32020257},
issn = {1432-184X},
mesh = {Alberta ; Animals ; Antibiosis ; *Host Microbial Interactions ; Ophiostomatales/*growth &amp; development ; Pinus/*immunology/microbiology ; Plant Diseases/*microbiology ; *Plant Immunity ; Weevils/*microbiology ; },
abstract = {Mountain pine beetle (MPB) has recently expanded its host range to the novel jack pine forests in Alberta. Invasion success of MPB may depend on the outcome of interactions between its symbiotic fungus Grosmannia clavigera and Ophiostoma ips, a fungal associate of a potential competitor Ips pini. However, how the quality of jack pine phloem could influence interactions between the fungi is unknown. We investigated whether introduced concentrations of host nitrogen and monoterpenes affect the growth of and interaction between the fungi. Nitrogen concentrations did not affect the growth rate of either fungus. In the absence of monoterpenes, the presence of O. ips promoted G. clavigera growth. Monoterpenes either promoted or inhibited the growth of both fungi, and altered the outcome of species interactions from facilitation to no-effect. Overall, these results suggest that jack pine phloem quality and the presence of a niche-sharing fungus could influence MPB development.},
}
@article {pmid32019835,
year = {2020},
author = {Rodriguez-Gonzalez, RA and Leung, CY and Chan, BK and Turner, PE and Weitz, JS},
title = {Quantitative Models of Phage-Antibiotic Combination Therapy.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
pmid = {32019835},
issn = {2379-5077},
support = {R01 AI146592/AI/NIAID NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; },
abstract = {The spread of multidrug-resistant (MDR) bacteria is a global public health crisis. Bacteriophage therapy (or "phage therapy") constitutes a potential alternative approach to treat MDR infections. However, the effective use of phage therapy may be limited when phage-resistant bacterial mutants evolve and proliferate during treatment. Here, we develop a nonlinear population dynamics model of combination therapy that accounts for the system-level interactions between bacteria, phage, and antibiotics for in vivo application given an immune response against bacteria. We simulate the combination therapy model for two strains of Pseudomonas aeruginosa, one which is phage sensitive (and antibiotic resistant) and one which is antibiotic sensitive (and phage resistant). We find that combination therapy outperforms either phage or antibiotic alone and that therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotics, e.g., ciprofloxacin. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of innate immunity in shaping therapeutic outcomes.IMPORTANCE This work develops and analyzes a novel model of phage-antibiotic combination therapy, specifically adapted to an in vivo context. The objective is to explore the underlying basis for clinical application of combination therapy utilizing bacteriophage that target antibiotic efflux pumps in Pseudomonas aeruginosa In doing so, the paper addresses three key questions. How robust is combination therapy to variation in the resistance profiles of pathogens? What is the role of immune responses in shaping therapeutic outcomes? What levels of phage and antibiotics are necessary for curative success? As we show, combination therapy outperforms either phage or antibiotic alone, and therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotic. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of system-level feedbacks in shaping therapeutic outcomes.},
}
@article {pmid32019791,
year = {2020},
author = {Tkacz, A and Bestion, E and Bo, Z and Hortala, M and Poole, PS},
title = {Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
pmid = {32019791},
issn = {2150-7511},
support = {/WT_/Wellcome Trust/United Kingdom ; BB/N013387/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R017859/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Bacteria/classification ; Fungi/classification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Plant Leaves/*microbiology ; Plant Roots/*microbiology ; Plants/classification/*microbiology ; RNA, Ribosomal, 16S ; Rhizosphere ; *Soil Microbiology ; },
abstract = {Plant roots influence the soil microbiota via physical interaction, secretion, and plant immunity. However, it is unclear whether the root fraction or soil is more important in determining the structure of the prokaryotic or eukaryotic community and whether this varies between plant species. Furthermore, the leaf (phyllosphere) and root microbiotas have a large overlap; however, it is unclear whether this results from colonization of the phyllosphere by the root microbiota. Soil, rhizosphere, rhizoplane, and root endosphere prokaryote-, eukaryote-, and fungus-specific microbiotas of four plant species were analyzed with high-throughput sequencing. The strengths of factors controlling microbiota structure were determined using permutational multivariate analysis of variance (PERMANOVA) statistics. The origin of the phyllosphere microbiota was investigated using a soil swap experiment. Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root itself more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. A reciprocal soil swap experiment shows that the phyllosphere is colonized from the soil in which the plant is grown.IMPORTANCE Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root fraction more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined, indicating conserved adaptation of microbial communities to plants. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. We observed a remarkable similarity in the structure of a plant's phyllosphere and root microbiotas and show by reciprocal soil swap experiments that both fractions are colonized from the soil in which the plant is grown. Thus, the phyllosphere is continuously colonized by the soil microbiota.},
}
@article {pmid32018979,
year = {2020},
author = {Gionchetta, G and Oliva, F and Romaní, AM and Bañeras, L},
title = {Hydrological variations shape diversity and functional responses of streambed microbes.},
journal = {The Science of the total environment},
volume = {714},
number = {},
pages = {136838},
doi = {10.1016/j.scitotenv.2020.136838},
pmid = {32018979},
issn = {1879-1026},
mesh = {Biomass ; Hydrology ; *Microbiota ; Rivers ; },
abstract = {Microbiota inhabiting the intermittent streambeds mediates several in-stream processes that are essential for ecosystem function. Reduced stream discharge caused by the strengthened intermittency and increased duration of the dry phase is a spreading global response to changes in climate. Here, the impacts of a 5-month desiccation, one-week rewetting and punctual storms, which interrupted the dry period, were examined. The genomic composition of total (DNA) and active (RNA) diversity, and the community level physiological profiles (CLPP) were considered as proxies for functional diversity to describe both prokaryotes and eukaryotes inhabiting the surface and hyporheic streambeds. Comparisons between the genomic and potential functional responses helped to understand how and whether the microbial diversity was sensitive to the environmental conditions and resource acquisition, such as water stress and extracellular enzyme activities, respectively. RNA expression showed the strongest relationship with the environmental conditions and resource acquisition, being more responsive to changing conditions compared to DNA diversity, especially in the case of prokaryotes. The DNA results presumably reflected the legacy of the treatments because inactive, dormant, or dead cells were included, suggesting a slow microbial biomass turnover or responses of the microbial communities to changes mainly through physiological acclimation. On the other hand, microbial functional diversity was largely explained by resources acquisition, such as metrics of extracellular enzymes, and appeared vulnerable to the hydrological changes and duration of desiccation. The data highlight the need to improve the functional assessment of stream ecosystems with the application of complementary metrics to better describe the streambed microbial dynamics under dry-rewet stress.},
}
@article {pmid32016609,
year = {2020},
author = {Pantigoso, HA and Manter, DK and Vivanco, JM},
title = {Differential Effects of Phosphorus Fertilization on Plant Uptake and Rhizosphere Microbiome of Cultivated and Non-cultivated Potatoes.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {169-180},
doi = {10.1007/s00248-020-01486-w},
pmid = {32016609},
issn = {1432-184X},
mesh = {Bacteria/*metabolism ; Fertilizers/*analysis ; Microbiota ; Phosphorus/*metabolism ; Rhizosphere ; *Soil Microbiology ; Solanum tuberosum/*metabolism/*microbiology ; },
abstract = {There is evidence that shows that phosphorus (P) fertilization has a moderate effect on the rhizosphere microbial composition of cultivated crops. But how this effect is manifested on wild species of the same crop is not clear. This study compares the impact of phosphorus fertilization with rhizosphere bacterial community composition and its predicted functions, related to P-cycling genes, in both cultivated and non-cultivated potato (Solanum sp.) plants. It was found that the biomass of non-cultivated potatoes was more responsive to P fertilization as compared with cultivated plants. Differences in general bacterial community composition patterns under increasing P amendments were subtle for both potato groups. However, potato genotype significantly influenced community composition with several bacterial families being more abundant in the cultivated plants. In addition, the predicted phosphatases had lower abundances in modern cultivars compared with non-cultivated potatoes. In summary, despite higher accumulation of differentially abundant bacteria in the rhizosphere of cultivated plants, the responsiveness of these plants to increase P levels was lower than in non-cultivated plants.},
}
@article {pmid32014077,
year = {2020},
author = {Morand, C and De Roos, B and Garcia-Conesa, MT and Gibney, ER and Landberg, R and Manach, C and Milenkovic, D and Rodriguez-Mateos, A and Van de Wiele, T and Tomas-Barberan, F},
title = {Why interindividual variation in response to consumption of plant food bioactives matters for future personalised nutrition.},
journal = {The Proceedings of the Nutrition Society},
volume = {79},
number = {2},
pages = {225-235},
doi = {10.1017/S0029665120000014},
pmid = {32014077},
issn = {1475-2719},
mesh = {Biological Availability ; *Biological Variation, Population ; *Diet ; Female ; Gastrointestinal Microbiome ; Genome, Human ; Heart Disease Risk Factors ; Humans ; Male ; Metabolome ; Nutrigenomics ; *Nutritional Physiological Phenomena ; Nutritive Value ; Phytochemicals/*administration &amp; dosage/*metabolism/pharmacokinetics ; Precision Medicine ; Research ; },
abstract = {Food phytochemicals are increasingly considered to play a key role in the cardiometabolic health effects of plant foods. However, the heterogeneity in responsiveness to their intake frequently observed in clinical trials can hinder the beneficial effects of these compounds in specific subpopulations. A range of factors, including genetic background, gut microbiota, age, sex and health status, could be involved in these interindividual variations; however, the current knowledge is limited and fragmented. The European network, European Cooperation in Science and Technology (COST)-POSITIVe, has analysed, in a systematic way, existing knowledge with the aim to better understand the factors responsible for the interindividual variation in response to the consumption of the major families of plant food bioactives, regarding their bioavailability and bioefficacy. If differences in bioavailability, likely reflecting differences in human subjects' genetics or in gut microbiota composition and functionality, are believed to underpin much of the interindividual variability, the key molecular determinants or microbial species remain to be identified. The systematic analysis of published studies conducted to assess the interindividual variation in biomarkers of cardiometabolic risk suggested some factors (such as adiposity and health status) as involved in between-subject variation. However, the contribution of these factors is not demonstrated consistently across the different compounds and biological outcomes and would deserve further investigations. The findings of the network clearly highlight that the human subjects' intervention studies published so far are not adequate to investigate the relevant determinants of the absorption/metabolism and biological responsiveness. They also emphasise the need for a new generation of intervention studies designed to capture this interindividual variation.},
}
@article {pmid32014020,
year = {2020},
author = {Woodhams, DC and Bletz, MC and Becker, CG and Bender, HA and Buitrago-Rosas, D and Diebboll, H and Huynh, R and Kearns, PJ and Kueneman, J and Kurosawa, E and LaBumbard, BC and Lyons, C and McNally, K and Schliep, K and Shankar, N and Tokash-Peters, AG and Vences, M and Whetstone, R},
title = {Host-associated microbiomes are predicted by immune system complexity and climate.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {23},
pmid = {32014020},
issn = {1474-760X},
mesh = {Adaptation, Physiological ; Animals ; *Climate ; Host-Pathogen Interactions/*immunology ; Humans ; *Microbiota ; },
abstract = {BACKGROUND: Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors.<br><br>RESULTS: Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate.<br><br>CONCLUSIONS: Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.},
}
@article {pmid32012657,
year = {2020},
author = {Purushotham, N and Jones, E and Monk, J and Ridgway, H},
title = {Community Structure, Diversity and Potential of Endophytic Bacteria in the Primitive New Zealand Medicinal Plant Pseudowintera colorata.},
journal = {Plants (Basel, Switzerland)},
volume = {9},
number = {2},
pages = {},
pmid = {32012657},
issn = {2223-7747},
abstract = {Although the importance of the plant microbiome in commercial plant health has been well established, there are limited studies in native medicinal plants. Pseudowintera colorata (horopito) is a native New Zealand medicinal plant recognized for its antimicrobial properties. Denaturing gradient gel electrophoresis (DGGE) and Illumina MiSeq analysis of P. colorata plants from ten sites across New Zealand showed that tissue type strongly influenced the diversity and richness of endophytic bacteria (PERMANOVA, P < 0.05). In addition, two OTUs belonging to the genus Pseudomonas (Greengenes ID: 646549 and 138914) were found to be present in >75% of all P. colorata leaf, stem and root samples and were identified as the members of the P. colorata "core endomicrobiome". Culture-independent analysis was complemented by the recovery of 405 endophytic bacteria from the tissues of P. colorata. Some of these cultured endophytic bacteria (n = 10) showed high antagonism against four different phytopathogenic fungi tested. The influence of endophytic bacteria on plant growth was assessed by inoculating P. colorata seedlings. The mean shoot height of seedlings treated with Bacillus sp. TP1LA1B were longer (1.83×), had higher shoot dry weight (1.8×) and produced more internodes (1.8×) compared to the control.},
}
@article {pmid32010196,
year = {2019},
author = {Mascarenhas, R and Ruziska, FM and Moreira, EF and Campos, AB and Loiola, M and Reis, K and Trindade-Silva, AE and Barbosa, FAS and Salles, L and Menezes, R and Veiga, R and Coutinho, FH and Dutilh, BE and Guimarães, PR and Assis, APA and Ara, A and Miranda, JGV and Andrade, RFS and Vilela, B and Meirelles, PM},
title = {Integrating Computational Methods to Investigate the Macroecology of Microbiomes.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {1344},
pmid = {32010196},
issn = {1664-8021},
abstract = {Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as "everything is everywhere, but the environment selects") as well as applied ecological problems, such as those posed by human induced global environmental changes.},
}
@article {pmid32006806,
year = {2020},
author = {Trebuch, LM and Oyserman, BO and Janssen, M and Wijffels, RH and Vet, LEM and Fernandes, TV},
title = {Impact of hydraulic retention time on community assembly and function of photogranules for wastewater treatment.},
journal = {Water research},
volume = {173},
number = {},
pages = {115506},
doi = {10.1016/j.watres.2020.115506},
pmid = {32006806},
issn = {1879-2448},
mesh = {Bioreactors ; Netherlands ; Sewage ; *Waste Disposal, Fluid ; *Wastewater ; },
abstract = {Photogranules are dense, spherical agglomerates of cyanobacteria, microalgae and non-phototrophic microorganisms that have considerable advantages in terms of harvesting and nutrient removal rates for light driven wastewater treatment processes. This ecosystem is poorly understood in terms of the microbial community structure and the response of the community to changing abiotic conditions. To get a better understanding, we investigated the effect of hydraulic retention time (HRT) on photogranule formation and community assembly over a period of 148 days. Three laboratory bioreactors were inoculated with field samples from various locations in the Netherlands and operated in sequencing batch mode. The bioreactors were operated at four different HRTs (2.00, 1.00, 0.67, 0.33 days), while retaining the same solid retention time of 7 days. A microbial community with excellent settling characteristics (95-99% separation efficiency) was established within 2-5 weeks. The observed nutrient uptake rates ranged from 24 to 90 mgN L[-1] day[-1] and from 3.1 to 5.4 mgP L[-1] day[-1] depending on the applied HRT. The transition from single-cell suspension culture to floccular agglomeration to granular sludge was monitored by microscopy and 16S/18S sequencing. In particular, two important variables for driving aggregation and granulation, and for the structural integrity of photogranules were identified: 1. Extracellular polymeric substances (EPS) with high protein to polysaccharide ratio and 2. specific microorganisms. The key players were found to be the cyanobacteria Limnothrix and Cephalothrix, the colony forming photosynthetic eukaryotes within Chlamydomonadaceae, and the biofilm producing bacteria Zoogloea and Thauera. Knowing the makeup of the microbial community and the operational conditions influencing granulation and bioreactor function is crucial for successful operation of photogranular systems.},
}
@article {pmid32006032,
year = {2020},
author = {De Gruyter, J and Weedon, JT and Bazot, S and Dauwe, S and Fernandez-Garberí, PR and Geisen, S and De La Motte, LG and Heinesch, B and Janssens, IA and Leblans, N and Manise, T and Ogaya, R and Löfvenius, MO and Peñuelas, J and Sigurdsson, BD and Vincent, G and Verbruggen, E},
title = {Patterns of local, intercontinental and interseasonal variation of soil bacterial and eukaryotic microbial communities.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {3},
pages = {},
doi = {10.1093/femsec/fiaa018},
pmid = {32006032},
issn = {1574-6941},
mesh = {Bacteria/genetics ; Eukaryota ; Fungi/genetics ; *Microbiota ; *Soil ; Soil Microbiology ; },
abstract = {Although ongoing research has revealed some of the main drivers behind global spatial patterns of microbial communities, spatio-temporal dynamics of these communities still remain largely unexplored. Here, we investigate spatio-temporal variability of both bacterial and eukaryotic soil microbial communities at local and intercontinental scales. We compare how temporal variation in community composition scales with spatial variation in community composition, and explore the extent to which bacteria, protists, fungi and metazoa have similar patterns of temporal community dynamics. All soil microbial groups displayed a strong correlation between spatial distance and community dissimilarity, which was related to the ratio of organism to sample size. Temporal changes were variable, ranging from equal to local between-sample variation, to as large as that between communities several thousand kilometers apart. Moreover, significant correlations were found between bacterial and protist communities, as well as between protist and fungal communities, indicating that these microbial groups change in tandem, potentially driven by interactions between them. We conclude that temporal variation can be considerable in soil microbial communities, and that future studies need to consider temporal variation in order to reliably capture all drivers of soil microbiome changes.},
}
@article {pmid32001557,
year = {2020},
author = {Eichorst, SA and Trojan, D and Huntemann, M and Clum, A and Pillay, M and Palaniappan, K and Varghese, N and Mikhailova, N and Stamatis, D and Reddy, TBK and Daum, C and Goodwin, LA and Shapiro, N and Ivanova, N and Kyrpides, N and Woyke, T and Woebken, D},
title = {One Complete and Seven Draft Genome Sequences of Subdivision 1 and 3 Acidobacteria Isolated from Soil.},
journal = {Microbiology resource announcements},
volume = {9},
number = {5},
pages = {},
pmid = {32001557},
issn = {2576-098X},
abstract = {We report eight genomes from representatives of the phylum Acidobacteria subdivisions 1 and 3, isolated from soils. The genome sizes range from 4.9 to 6.7 Mb. Genomic analysis reveals putative genes for low- and high-affinity respiratory oxygen reductases, high-affinity hydrogenases, and the capacity to use a diverse collection of carbohydrates.},
}
@article {pmid32000682,
year = {2020},
author = {De Maayer, P and Pillay, T and Coutinho, TA},
title = {Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {100},
pmid = {32000682},
issn = {1471-2164},
mesh = {Bacterial Proteins/*genetics ; Enterobacteriaceae/*classification/genetics ; Evolution, Molecular ; Flagella/*genetics ; Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; },
abstract = {BACKGROUND: The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag-1, encompassing ~ 50 genes. A discrete locus, flag-2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized.<br><br>RESULTS: Comparative genomic analyses showed that orthologous flag-2 loci are present in 592/4028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of only the outermost flag-2 genes in many taxa suggests that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag-2 loci range in size from ~&#x2009;3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number can be attributed to the presence of cargo gene islands within the loci. Evolutionary analyses revealed a complex evolutionary history for the flag-2 loci, representing ancestral elements in some taxa, while showing evidence of recent horizontal acquisition in other enterobacteria.<br><br>CONCLUSIONS: The flag-2 flagellar system is a fairly common, but highly variable feature among members of the Enterobacterales. Given the energetic burden of flagellar biosynthesis and functioning, the prevalence of a second flagellar system suggests it plays important biological roles in the enterobacteria and we postulate on its potential role as locomotory organ or as secretion system.},
}
@article {pmid31999996,
year = {2020},
author = {Ahmad, JI and Liu, G and van der Wielen, PWJJ and Medema, G and Peter van der Hoek, J},
title = {Effects of cold recovery technology on the microbial drinking water quality in unchlorinated distribution systems.},
journal = {Environmental research},
volume = {183},
number = {},
pages = {109175},
doi = {10.1016/j.envres.2020.109175},
pmid = {31999996},
issn = {1096-0953},
mesh = {Bacteria ; Biofilms ; *Cold Temperature ; *Drinking Water ; Water Microbiology ; *Water Quality ; Water Supply ; },
abstract = {Drinking water distribution systems (DWDSs) are used to supply hygienically safe and biologically stable water for human consumption. The potential of thermal energy recovery from drinking water has been explored recently to provide cooling for buildings. Yet, the effects of increased water temperature induced by this "cold recovery" on the water quality in DWDSs are not known. The objective of this study was to investigate the impact of cold recovery from DWDSs on the microbiological quality of drinking water. For this purpose, three pilot distribution systems were operated in parallel for 38 weeks. System 1 has an operational heat exchanger, mimicking the cold recovery system by maintaining the water temperature at 25 °C; system 2 operated with a non-operational heat exchanger and system 3 run without heat exchanger. The results showed no significant effects on drinking water quality: cell numbers and ATP concentrations remained around 3.5 × 10[5] cells/ml and 4 ng ATP/l, comparable observed operational taxonomic units (OTUs) (~470-490) and similar Shannon indices (7.7-8.9). In the system with cold recovery, a higher relative abundance of Pseudomonas spp. and Chryseobacterium spp. was observed in the drinking water microbial community, but only when the cold recovery induced temperature difference (ΔT) was higher than 9 °C. In the 38 weeks' old biofilm, higher ATP concentration (475 vs. 89 pg/cm[2]), lower diversity (observed OTUs: 88 vs. ≥200) and a different bacterial community composition (e.g. higher relative abundance of Novosphingobium spp.) were detected, which did not influence water quality. No impacts were observed for the selected opportunisitic pathogens after introducing cold recovery. It is concluded that cold recovery does not affect bacterial water quality. Further investigation for a longer period is commended to understand the dynamic responses of biofilm to the increased temperature caused by cold recovery.},
}
@article {pmid31999470,
year = {2020},
author = {Saavedra-Lavoie, J and de la Porte, A and Piché-Choquette, S and Guertin, C and Constant, P},
title = {Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities.},
journal = {Canadian journal of microbiology},
volume = {66},
number = {4},
pages = {263-273},
doi = {10.1139/cjm-2019-0412},
pmid = {31999470},
issn = {1480-3275},
mesh = {Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Carbon Dioxide/chemistry/pharmacology ; Carbon Monoxide/*chemistry/pharmacology ; Hydrogen/*chemistry/pharmacology ; Microbiota ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%-98% less H2 oxidation and 54%-99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.},
}
@article {pmid31998352,
year = {2019},
author = {Harkes, P and van Steenbrugge, JJM and van den Elsen, SJJ and Suleiman, AKA and de Haan, JJ and Holterman, MHM and Helder, J},
title = {Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {1697},
pmid = {31998352},
issn = {1664-462X},
abstract = {Plants manipulate their rhizosphere community in a species and even a plant life stage-dependent manner. In essence plants select, promote and (de)activate directly the local bacterial and fungal community, and indirectly representatives of the next trophic level, protists and nematodes. By doing so, plants enlarge the pool of bioavailable nutrients and maximize local disease suppressiveness within the boundaries set by the nature of the local microbial community. MiSeq sequencing of specific variable regions of the 16S or 18S ribosomal DNA (rDNA) is widely used to map microbial shifts. As current RNA extraction procedures are time-consuming and expensive, the rRNA-based characterization of the active microbial community is taken along less frequently. Recently, we developed a relatively fast and affordable protocol for the simultaneous extraction of rDNA and rRNA from soil. Here, we investigated the long-term impact of three type of soil management, two conventional and an organic regime, on soil biota in fields naturally infested with the Columbian root-knot nematode Meloidogyne chitwoodi with pea (Pisum sativum) as the main crop. For all soil samples, large differences were observed between resident (rDNA) and active (rRNA) microbial communities. Among the four organismal group under investigation, the bacterial community was most affected by the main crop, and unweighted and weighted UniFrac analyses (explaining respectively 16.4% and 51.3% of the observed variation) pointed at a quantitative rather than a qualitative shift. LEfSe analyses were employed for each of the four organismal groups to taxonomically pinpoint the effects of soil management. Concentrating on the bacterial community in the pea rhizosphere, organic soil management resulted in a remarkable activation of members of the Burkholderiaceae, Enterobacteriaceae, and Pseudomonadaceae. Prolonged organic soil management was also accompanied by significantly higher densities of bacterivorous nematodes, whereas levels of M. chitwoodi had dropped drastically. Though present and active in the fields under investigation Orbiliaceae, a family harboring numerous nematophagous fungi, was not associated with the M. chitwoodi decline. A closer look revealed that a local accumulation and activation of Pseudomonas, a genus that includes a number of nematode-suppressive species, paralleled the lower M. chitwoodi densities. This study underlines the relevance of taking along both resident and active fractions of multiple organismal groups while mapping the impact of e.g. crops and soil management regimes.},
}
@article {pmid31998276,
year = {2019},
author = {Eberl, C and Ring, D and Münch, PC and Beutler, M and Basic, M and Slack, EC and Schwarzer, M and Srutkova, D and Lange, A and Frick, JS and Bleich, A and Stecher, B},
title = {Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2999},
pmid = {31998276},
issn = {1664-302X},
abstract = {The Oligo-Mouse-Microbiota (OMM[12]) is a recently developed synthetic bacterial community for functional microbiome research in mouse models (Brugiroux et al., 2016). To date, the OMM[12] model has been established in several germ-free mouse facilities world-wide and is employed to address a growing variety of research questions related to infection biology, mucosal immunology, microbial ecology and host-microbiome metabolic cross-talk. The OMM[12] consists of 12 sequenced and publically available strains isolated from mice, representing five bacterial phyla that are naturally abundant in the murine gastrointestinal tract (Lagkouvardos et al., 2016). Under germ-free conditions, the OMM[12] colonizes mice stably over multiple generations. Here, we investigated whether stably colonized OMM[12] mouse lines could be reproducibly established in different animal facilities. Germ-free C57Bl/6J mice were inoculated with a frozen mixture of the OMM[12] strains. Within 2 weeks after application, the OMM[12] community reached the same stable composition in all facilities, as determined by fecal microbiome analysis. We show that a second application of the OMM[12] strains after 72 h leads to a more stable community composition than a single application. The availability of such protocols for reliable de novo generation of gnotobiotic rodents will certainly contribute to increasing experimental reproducibility in biomedical research.},
}
@article {pmid31998260,
year = {2019},
author = {Rath, S and Rud, T and Pieper, DH and Vital, M},
title = {Potential TMA-Producing Bacteria Are Ubiquitously Found in Mammalia.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2966},
pmid = {31998260},
issn = {1664-302X},
abstract = {Human gut bacteria metabolize dietary components such as choline and carnitine to trimethylamine (TMA) that is subsequently oxidized to trimethylamine-N-oxide (TMAO) by hepatic enzymes. Increased plasma levels of TMAO are associated with the development of cardiovascular and renal disease. In this study, we applied gene-targeted assays in order to quantify (qPCR) and characterize (MiSeq) bacterial genes encoding enzymes responsible for TMA production, namely choline-TMA lyase (CutC), carnitine oxygenase (CntA) and betaine reductase (GrdH) in 89 fecal samples derived from various mammals spanning three dietary groups (carnivores, omnivores and herbivores) and four host orders (Carnivora, Primates, Artiodactyla and Perissodactyla). All samples contained potential TMA-producing bacteria, however, at low abundances (<1.2% of total community). The cutC gene was more abundant in omnivores and carnivores compared with herbivores. CntA was almost absent from herbivores and grdH showed lowest average abundance of all three genes. Bacteria harboring cutC and grdH displayed high diversities where sequence types affiliated with various taxa within Firmicutes dominated, whereas cntA comprised sequences primarily linked to Escherichia. Composition of TMA-forming communities was strongly influenced by diet and host taxonomy and despite their high correlation, both factors contributed uniquely to community structure. Furthermore, Random Forest (RF) models could differentiate between groups at high accuracies. This study gives a comprehensive overview of potential TMA-producing bacteria in the mammalian gut demonstrating that both diet and host taxonomy govern their abundance and composition. It highlights the role of functional redundancy sustaining potential TMA formation in distinct gut environments.},
}
@article {pmid31998259,
year = {2019},
author = {Rahi, P and Vaishampayan, P},
title = {Editorial: MALDI-TOF MS Application in Microbial Ecology Studies.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2954},
pmid = {31998259},
issn = {1664-302X},
}
@article {pmid31997534,
year = {2020},
author = {van Gestel, NC and Ducklow, HW and Bååth, E},
title = {Comparing temperature sensitivity of bacterial growth in Antarctic marine water and soil.},
journal = {Global change biology},
volume = {26},
number = {4},
pages = {2280-2291},
doi = {10.1111/gcb.15020},
pmid = {31997534},
issn = {1365-2486},
support = {PLR-1440435//National Science Foundation/ ; },
abstract = {The western Antarctic Peninsula is an extreme low temperature environment that is warming rapidly due to global change. Little is known, however, on the temperature sensitivity of growth of microbial communities in Antarctic soils and in the surrounding oceanic waters. This is the first study that directly compares temperature adaptation of adjacent marine and terrestrial bacteria in a polar environment. The bacterial communities in the ocean were adapted to lower temperatures than those from nearby soil, with cardinal temperatures for growth in the ocean being the lowest so far reported for microbial communities. This was reflected in lower minimum (Tmin) and optimum temperatures (Topt) for growth in water (-17 and +20°C, respectively) than in soil (-11 and +27°C), with lower sensitivity to changes in temperature (Q10 ; 0-10°C interval) in Antarctic water (2.7) than in soil (3.9). This is likely due to the more stable low temperature conditions of Antarctic waters than soils, and the fact that maximum in situ temperatures in water are lower than in soils, at least in summer. Importantly, the thermally stable environment of Antarctic marine water makes it feasible to create a single temperature response curve for bacterial communities. This would thus allow for calculations of temperature-corrected growth rates, and thereby quantifying the influence of factors other than temperature on observed growth rates, as well as predicting the effects of future temperature increases on Antarctic marine bacteria.},
}
@article {pmid31996939,
year = {2020},
author = {Zhang, Z and Liu, W and Shao, S and Wang, ET and Li, Y},
title = {Diverse Genomic Backgrounds Vs. Highly Conserved Symbiotic Genes in Sesbania-Nodulating Bacteria: Shaping of the Rhizobial Community by Host and Soil Properties.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {158-168},
doi = {10.1007/s00248-020-01489-7},
pmid = {31996939},
issn = {1432-184X},
support = {31600009//National Natural Science Foundation of China/ ; 31800099//National Natural Science Foundation of China/ ; 19273802D//Key Research and Development Program of Hebei province/ ; 2019SYHZ0036//Joint fund of Jilin province and Chinese Academy of Sciences for high-tech industrialization/ ; KFZD-SW-112//Key Deployment Project of Chinese Academy of Sciences/ ; },
mesh = {Biological Evolution ; *Genetic Variation ; *Genotype ; Plant Roots/microbiology ; Rhizobiaceae/genetics/*physiology ; Sesbania/*microbiology ; Soil/chemistry ; *Soil Microbiology ; Symbiosis/*genetics ; },
abstract = {Aiming at investigating the overall diversity, biogeography, and symbiosis gene evolutionary history of the Sesbania cannabina-nodulating rhizobia in China, a total of 874 rhizobial isolates originating from the root nodules of this plant grown at different sites were characterized and compared with those of some reference strains. All of the S. cannabina-nodulating rhizobia were classified into 16 (geno) species, including seven novel genospecies in the genera Ensifer, Rhizobium, Neorhizobium, and Agrobacterium, with Ensifer sesbaniae and Neorhizobium huautlense as the dominant and universal species. Ten of these species were found to nodulate other leguminous hosts or to lack nodulating abilities and were defined as symbiovar sesbania. Biogeographic patterns were observed, for which pH, TN, AK, and AP were the main determinants. The effects of pH were opposite to those of TN and AK, while AP presented effects independently of TN, AK, and pH. Symbiotic genes of these rhizobia showed a common origin, but nodA evolved faster than nifH. Point mutation is the main driving force in the evolution of both nodA and nifH, and lateral transfer of symbiotic genes might play an important role in the formation of diverse S. cannabina-nodulating rhizobial species. S. cannabina only nodulates with Sesbania rhizobia, demonstrating its severe selection on rhizobial symbiosis genes. Soil pH and physiochemical characteristics could affect rhizobial survival and competitive nodulation. This study provides insight into the community shifts and evolution of rhizobia in relation to their host and soil environments.},
}
@article {pmid31996419,
year = {2020},
author = {Ghannam, RB and Schaerer, LG and Butler, TM and Techtmann, SM},
title = {Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities.},
journal = {mSphere},
volume = {5},
number = {1},
pages = {},
pmid = {31996419},
issn = {2379-5042},
mesh = {Actinobacteria/*classification ; Asia ; Bacteroidetes/*classification ; *Biodiversity ; Cyanobacteria/*classification ; DNA, Bacterial/genetics ; Europe ; Fresh Water/microbiology ; Machine Learning ; Microbiota ; Phylogeography ; Proteobacteria/*classification ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Ships ; United States ; *Water Microbiology ; },
abstract = {We conducted a global characterization of the microbial communities of shipping ports to serve as a novel system to investigate microbial biogeography. The community structures of port microbes from marine and freshwater habitats house relatively similar phyla, despite spanning large spatial scales. As part of this project, we collected 1,218 surface water samples from 604 locations across eight countries and three continents to catalogue a total of 20 shipping ports distributed across the East and West Coast of the United States, Europe, and Asia to represent the largest study of port-associated microbial communities to date. Here, we demonstrated the utility of machine learning to leverage this robust system to characterize microbial biogeography by identifying trends in biodiversity across broad spatial scales. We found that for geographic locations sharing similar environmental conditions, subpopulations from the dominant phyla of these habitats (Actinobacteria, Bacteroidetes, Cyanobacteria, and Proteobacteria) can be used to differentiate 20 geographic locations distributed globally. These results suggest that despite the overwhelming diversity within microbial communities, members of the most abundant and ubiquitous microbial groups in the system can be used to differentiate a geospatial location across global spatial scales. Our study provides insight into how microbes are dispersed spatially and robust methods whereby we can interrogate microbial biogeography.IMPORTANCE Microbes are ubiquitous throughout the world and are highly diverse. Characterizing the extent of variation in the microbial diversity across large geographic spatial scales is a challenge yet can reveal a lot about what biogeography can tell us about microbial populations and their behavior. Machine learning approaches have been used mostly to examine the human microbiome and, to some extent, microbial communities from the environment. Here, we display how supervised machine learning approaches can be useful to understand microbial biodiversity and biogeography using microbes from globally distributed shipping ports. Our findings indicate that the members of globally dominant phyla are important for differentiating locations, which reduces the reliance on rare taxa to probe geography. Further, this study displays how global biogeographic patterning of aquatic microbial communities (and other systems) can be assessed through populations of the highly abundant and ubiquitous taxa that dominant the system.},
}
@article {pmid31996418,
year = {2020},
author = {Bartelme, RP and Custer, JM and Dupont, CL and Espinoza, JL and Torralba, M and Khalili, B and Carini, P},
title = {Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation.},
journal = {mSphere},
volume = {5},
number = {1},
pages = {},
pmid = {31996418},
issn = {2379-5042},
support = {P01 AI118687/AI/NIAID NIH HHS/United States ; },
mesh = {Actinobacteria/growth &amp; development/*isolation &amp; purification ; Alphaproteobacteria/growth &amp; development/*isolation &amp; purification ; Arizona ; Bacteriological Techniques ; Centrifugation ; Culture Media/*chemistry ; Forests ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {The vast majority of microbes inhabiting oligotrophic shallow subsurface soil environments have not been isolated or studied under controlled laboratory conditions. In part, the challenges associated with isolating shallow subsurface microbes may persist because microbes in deeper soils are adapted to low nutrient availability or quality. Here, we use high-throughput dilution-to-extinction culturing to isolate shallow subsurface microbes from a conifer forest in Arizona, USA. We hypothesized that the concentration of heterotrophic substrates in microbiological growth medium would affect which microbial taxa were culturable from these soils. To test this, we diluted cells extracted from soil into one of two custom-designed defined growth media that differed by 100-fold in the concentration of amino acids and organic carbon. Across the two media, we isolated a total of 133 pure cultures, all of which were classified as Actinobacteria or Alphaproteobacteria The substrate availability dictated which actinobacterial phylotypes were culturable but had no significant effect on the culturability of Alphaproteobacteria We isolated cultures that were representative of the most abundant phylotype in the soil microbial community (Bradyrhizobium spp.) and representatives of five of the top 10 most abundant Actinobacteria phylotypes, including Nocardioides spp., Mycobacterium spp., and several other phylogenetically divergent lineages. Flow cytometry of nucleic acid-stained cells showed that cultures isolated on low-substrate medium had significantly lower nucleic acid fluorescence than those isolated on high-substrate medium. These results show that dilution-to-extinction is an effective method to isolate abundant soil microbes and that the concentration of substrates in culture medium influences the culturability of specific microbial lineages.IMPORTANCE Isolating environmental microbes and studying their physiology under controlled conditions are essential aspects of understanding their ecology. Subsurface ecosystems are typically nutrient-poor environments that harbor diverse microbial communities-the majority of which are thus far uncultured. In this study, we use modified high-throughput cultivation methods to isolate subsurface soil microbes. We show that a component of whether a microbe is culturable from subsurface soils is the concentration of growth substrates in the culture medium. Our results offer new insight into technical approaches and growth medium design that can be used to access the uncultured diversity of soil microbes.},
}
@article {pmid31994719,
year = {2020},
author = {Yuan, S and Meng, F},
title = {Ecological insights into the underlying evolutionary patterns of biofilm formation from biological wastewater treatment systems: Red or Black Queen Hypothesis?.},
journal = {Biotechnology and bioengineering},
volume = {117},
number = {5},
pages = {1270-1280},
doi = {10.1002/bit.27289},
pmid = {31994719},
issn = {1097-0290},
support = {2017YFE0114300//National Key R&amp;D Program of China/International ; 51622813 and 51878675//National Natural Science Foundation of China/International ; 2017B020216006 and 2015A020215014//Science and Technology Planning Project of Guangdong Province/International ; },
mesh = {*Biofilms ; *Biological Evolution ; Bioreactors ; Microbial Interactions ; *Models, Biological ; Sewage/*microbiology ; *Water Purification ; },
abstract = {Interspecies interactions and phylogenetic distances were studied to reveal the underlying evolutionary adaptations of biofilms sourced from wastewater treatment processes. Based on 380 pairwise cocultures of 40 strains from two microbial aggregates (surface-attached and mobile aggregates [flocs]) at two substrate concentrations (LB broth and 0.1× LB broth), interspecies interactions were explored using biofilm classification schemes. There was a strong source-dependence of biofilm development formed by the monocultures, that is, a higher biofilm formation potential for strains from attached aggregates than for those from sludge flocs at both substrate concentrations. Interestingly, the results showed that total biofilm reduction was dominant in the dual-species biofilm sourced from flocs in both LB broth (67.37%) and 0.1× LB broth (64.21%), indicating high interspecific competition in mobile aggregates and the independence of substrate concentrations. However, biofilm reduction was higher (33.68%) than induction (19.37%) for the biofilms formed by surface-attached aggregates in LB broth, while the opposite trend was apparent in 0.1× LB broth, suggesting the occurrence of indeterministic processes for biofilm formation and important roles of substrate concentrations. In addition, the more closely related phylogenetic relationships of cocultures from mobile aggregates were consistent with higher competition compared with those from surface-attached aggregates. Overall, the underlying evolutionary patterns of biofilms formed from mobile aggregates consistently followed the essence of the "Red Queen Hypothesis," while biofilms developed from surface-attached aggregates were not deterministic. This study advanced our understanding of biofilm-related treatment processes using the principles of microbial ecology.},
}
@article {pmid31992626,
year = {2020},
author = {Lennon, JT},
title = {Microbial Life Deep Underfoot.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
pmid = {31992626},
issn = {2150-7511},
mesh = {Biodiversity ; Ecosystem ; *Microbiota ; North America ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Soil is one of the most diverse microbial habitats on Earth. While the distribution and abundance of microbial taxa in surface soils have been well described, the phylogenetic and functional diversity of bacteria and archaea in deep-soil strata remains unexplored. Brewer et al. (mBio 10:e01318-19, 2019, https://doi.org/10.1128/mBio.01318-19) documented consistent shifts in the composition and genomic attributes of microbial communities as a function of depth in 20 soil pits that spanned a range of ecosystems across North America. The unique microorganisms found in deep soils appear to be adapted to conditions of low energy based on the recovery of genes that code for traits such as internal resource storage, mixotrophy, and dormancy.},
}
@article {pmid31989236,
year = {2020},
author = {Zhu, B and Wang, Z and Kanaparthi, D and Kublik, S and Ge, T and Casper, P and Schloter, M and Lueders, T},
title = {Long-Read Amplicon Sequencing of Nitric Oxide Dismutase (nod) Genes Reveal Diverse Oxygenic Denitrifiers in Agricultural Soils and Lake Sediments.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {243-247},
pmid = {31989236},
issn = {1432-184X},
support = {616644//FP7 Ideas: European Research Council/ ; },
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Bacterial Proteins/*analysis ; China ; Crop Production ; Denitrification ; Geologic Sediments/*microbiology ; Lakes/microbiology ; Nitrogen Cycle ; Oxygenases/*analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; },
abstract = {Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N2 and O2. So far, the ecological role of these microbes is not well understood. The only available tool for a targeted study of oxygenic denitrifiers is their respective maker gene, nitric oxide dismutase (nod). Here, we established the use of PacBio long-read sequencing of nod gene amplicons to study the diversity and community structure of oxygenic denitrifiers. Two distinct sets of environmental samples, agricultural soil and lake sediment, were investigated as examples. The circular consensus sequences (ca 1.0 kb) obtained covered most substitution characteristic of NO dismutase and allowed for reliable classification of oxygenic denitrifiers. Distinct nod gene pools and community structure were revealed for the different habitats, with most sequence types affiliated to yet unidentified environmental nod lineages. The abundance of nod genes ranged 2.2 × 10[6]-3.2 × 10[7] gene copies g[-1] soil or sediment, accounting for up to 3% of total bacterial 16S rRNA gene counts. This study indicates that nod-gene-targeted long-read sequencing can be a powerful tool for studying the ecology of these novel microbes, and the results also suggest that oxygenic denitrifiers are prevalent and abundant in different terrestrial samples, where they could play an important, but yet overlooked role in nitrogen transformations.},
}
@article {pmid31988316,
year = {2020},
author = {Remizovschi, A and Carpa, R and Forray, FL and Chiriac, C and Roba, CA and Beldean-Galea, S and Andrei, A&#x218; and Szekeres, E and Baricz, A and Lupan, I and Rudi, K and Coman, C},
title = {Mud volcanoes and the presence of PAHs.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {1253},
pmid = {31988316},
issn = {2045-2322},
abstract = {A mud volcano (MV) is a naturally hydrocarbon-spiked environment, as indicated by the presence of various quantities of PAHs and aromatic isotopic shifts in its sediments. Recurrent expulsion of various hydrocarbons consolidates the growth of hydrocarbonoclastic bacterial communities in the areas around MVs. In addition to the widely-known availability of biologically malleable alkanes, MVs can represent hotbeds of polyaromatic hydrocarbons (PAHs), as well - an aspect that has not been previously explored. This study measured the availability of highly recalcitrant PAHs and the isotopic signature of MV sediments both by GC-MS and δ[13]C analyses. Subsequently, this study highlighted both the occurrence and distribution of putative PAH-degrading bacterial OTUs using a metabarcoding technique. The putative hydrocarbonoclastic taxa incidence are the following: Enterobacteriaceae (31.5%), Methylobacteriaceae (19.9%), Bradyrhizobiaceae (16.9%), Oxalobacteraceae (10.2%), Comamonadaceae (7.6%) and Sphingomonadaceae (5.5%). Cumulatively, the results of this study indicate that MVs represent polyaromatic hydrocarbonoclastic hotbeds, as defined by both natural PAH input and high incidence of putative PAH-degrading bacterial OTUs.},
}
@article {pmid31987702,
year = {2020},
author = {Kalita, M and Małek, W and Coutinho, TA},
title = {Putative novel Bradyrhizobium and Phyllobacterium species isolated from root nodules of Chamaecytisus ruthenicus.},
journal = {Systematic and applied microbiology},
volume = {43},
number = {2},
pages = {126056},
doi = {10.1016/j.syapm.2020.126056},
pmid = {31987702},
issn = {1618-0984},
mesh = {Bacterial Proteins/genetics ; Bradyrhizobium/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Fabaceae/*microbiology ; Genes, Essential/genetics ; Genetic Variation ; Nitrogen Fixation/genetics ; Phyllobacteriaceae/*classification/genetics/isolation &amp; purification ; *Phylogeny ; Plant Root Nodulation/genetics ; Poland ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/microbiology ; Sequence Analysis, DNA ; Symbiosis/genetics ; },
abstract = {In this study, the diversity and the phylogenetic relationships of bacteria isolated from root nodules of Chamaecytisus ruthenicus growing in Poland were investigated using ERIC-PCR fingerprinting and by multilocus sequence analysis (MLSA). Two major clusters comprising 13 and 3 isolates were detected which 16S rRNA gene sequencing identified as Bradyrhizobium and Phyllobacterium. The results of phylogenetic analysis of individual and concatenated atpD, gyrB and recA gene sequences showed that the studied strains may represent novel species in the genera Bradyrhizobium and Phyllobacterium. In the phylogenetic tree based on the atpD-gyrB-recA concatemers, Bradyrhizobium isolates were split into two groups closely related to Bradyrhizobium algeriense STM89[T] and Bradyrhizobium valentinum LmjM3[T]. The genus Phyllobacterium isolates formed a separate cluster close to Phyllobacterium ifriqiyense LMG27887[T] in the atpD-gyrB-recA phylogram. Analysis of symbiotic gene sequences (nodC, nodZ, nifD, and nifH) showed that the Bradyrhizobium isolates were most closely related to Bradyrhizobium algeriense STM89[T], Bradyrhizobium valentinum LmjM3[T] and Bradyrhizobium retamae Ro19[T] belonging to symbiovar retamae. This is the first report on the occurrence of members of symbiovar retamae from outside the Mediterranean region. No symbiosis related genes were amplified from Phyllobacterium strains, which were also unable to induce nodules on C. ruthenicus roots. Based on these findings Phyllobacterium isolates can be regarded as endophytic bacteria inhabitating root nodules of C. ruthenicus.},
}
@article {pmid31985137,
year = {2020},
author = {Cramer, N and Fischer, S and Hedtfeld, S and Dorda, M and Tümmler, B},
title = {Intraclonal competitive fitness of longitudinal cystic fibrosis Pseudomonas aeruginosa airway isolates in liquid cultures.},
journal = {Environmental microbiology},
volume = {22},
number = {7},
pages = {2536-2549},
doi = {10.1111/1462-2920.14924},
pmid = {31985137},
issn = {1462-2920},
support = {C-H-P 01/12//Christiane Herzog Stiftung/International ; 82DZL002A1//Deutsche Zentrum f&#xfc;r Lungenforschung/International ; //German Center for Lung Research/International ; //Bundesministerium f&#xfc;r Bildung und Forschung/International ; //Research Foundation/International ; SFB900/3 - 158989968 - A2 and Z1//Deutsche Forschungsgemeinschaft/International ; },
mesh = {Adaptation, Physiological/genetics/*physiology ; Base Sequence ; Cystic Fibrosis/*microbiology ; Evolution, Molecular ; Genomics ; Humans ; Lung/*microbiology ; Phenotype ; Pseudomonas Infections ; Pseudomonas aeruginosa/genetics/*growth &amp; development/isolation &amp; purification/*metabolism ; Sequence Analysis, DNA ; },
abstract = {The metabolically versatile Pseudomonas aeruginosa inhabits biotic and abiotic environments including the niche of cystic fibrosis (CF) airways. This study investigated how the adaptation to CF lungs affects the within-clone fitness of P. aeruginosa to grow and persist in liquid cultures in the presence of the clonal ancestors. Longitudinal clonal P. aeruginosa isolates that had been collected from 12 CF donors since the onset of colonization for up to 30 years was subjected to within-clone competition experiments. The relative quantities of individual strains were determined by marker-free amplicon sequencing of multiplex PCR products of strain-specific nucleotide sequence variants, a novel method that is generally applicable to studies in evolutionary genetics and microbial ecology with real-world strain collections. For 10 of the 12 examined patient courses, P. aeruginosa isolates of the first years of colonization grew faster in the presence of their clonal progeny than alone. Single growth of individual strains showed no temporal trend with colonization time, but in co-culture, the early isolates out-competed their clonal progeny. Irrespective of the genetic make-up of the clone and its genomic microevolution in CF lungs, the early isolates expressed fitness traits to win the within-clone competition that were absent in their progeny.},
}
@article {pmid31984651,
year = {2020},
author = {Xu, H and Wang, X and Feng, W and Liu, Q and Zhou, S and Liu, Q and Cai, L},
title = {The gut microbiota and its interactions with cardiovascular disease.},
journal = {Microbial biotechnology},
volume = {13},
number = {3},
pages = {637-656},
pmid = {31984651},
issn = {1751-7915},
mesh = {*Bacteria/metabolism ; *Cardiovascular Diseases/microbiology ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; Risk Factors ; },
abstract = {The intestine is colonized by a considerable community of microorganisms that cohabits within the host and plays a critical role in maintaining host homeostasis. Recently, accumulating evidence has revealed that the gut microbial ecology plays a pivotal role in the occurrence and development of cardiovascular disease (CVD). Moreover, the effects of imbalances in microbe-host interactions on homeostasis can lead to the progression of CVD. Alterations in the composition of gut flora and disruptions in gut microbial metabolism are implicated in the pathogenesis of CVD. Furthermore, the gut microbiota functions like an endocrine organ that produces bioactive metabolites, including trimethylamine/trimethylamine N-oxide, short-chain fatty acids and bile acids, which are also involved in host health and disease via numerous pathways. Thus, the gut microbiota and its metabolic pathways have attracted growing attention as a therapeutic target for CVD treatment. The fundamental purpose of this review was to summarize recent studies that have illustrated the complex interactions between the gut microbiota, their metabolites and the development of common CVD, as well as the effects of gut dysbiosis on CVD risk factors. Moreover, we systematically discuss the normal physiology of gut microbiota and potential therapeutic strategies targeting gut microbiota to prevent and treat CVD.},
}
@article {pmid31982930,
year = {2020},
author = {Chen, YT and Zeng, Y and Wang, HZ and Zheng, D and Kamagata, Y and Narihiro, T and Nobu, MK and Tang, YQ},
title = {Different Interspecies Electron Transfer Patterns during Mesophilic and Thermophilic Syntrophic Propionate Degradation in Chemostats.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {120-132},
doi = {10.1007/s00248-020-01485-x},
pmid = {31982930},
issn = {1432-184X},
support = {2016YFE0127700//Ministry of Science and Technology of the People's Republic of China/ ; 51678378//National Natural Science Foundation of China/ ; 41701295//National Natural Science Foundation of China/ ; 2018M643480//Postdoctoral Research Foundation of China/ ; 2018SCUH0023//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Bioreactors ; Electron Transport ; Genome, Archaeal ; Genome, Bacterial ; Metagenomics ; Propionates/*metabolism ; Temperature ; },
abstract = {Propionate is one of the major intermediates in anaerobic digestion of organic waste to CO2 and CH4. In methanogenic environments, propionate is degraded through a mutualistic interaction between symbiotic propionate oxidizers and methanogens. Although temperature heavily influences the microbial ecology and performance of methanogenic processes, its effect on syntrophic interaction during propionate degradation remains poorly understood. In this study, metagenomics and metatranscriptomics were employed to compare mesophilic and thermophilic propionate degradation communities. Mesophilic propionate degradation involved multiple syntrophic organisms (Syntrophobacter, Smithella, and Syntrophomonas), pathways, interactions, and preference toward formate-based electron transfer to methanogenic partners (i.e., Methanoculleus). In thermophilic propionate degradation, one syntrophic organism predominated (Pelotomaculum), interspecies H2 transfer played a major role, and phylogenetically and metabolically diverse H2-oxidizing methanogens were present (i.e., Methanoculleus, Methanothermobacter, and Methanomassiliicoccus). This study showed that microbial interactions, metabolic pathways, and niche diversity are distinct between mesophilic and thermophilic microbial communities responsible for syntrophic propionate degradation.},
}
@article {pmid31982929,
year = {2020},
author = {Tivey, TR and Parkinson, JE and Mandelare, PE and Adpressa, DA and Peng, W and Dong, X and Mechref, Y and Weis, VM and Loesgen, S},
title = {N-Linked Surface Glycan Biosynthesis, Composition, Inhibition, and Function in Cnidarian-Dinoflagellate Symbiosis.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {223-236},
doi = {10.1007/s00248-020-01487-9},
pmid = {31982929},
issn = {1432-184X},
support = {1557804//Division of Integrative Organismal Systems/ ; },
mesh = {Animals ; Anthozoa/*microbiology ; Dinoflagellida/*physiology ; Host Microbial Interactions ; Polysaccharides/biosynthesis/chemistry/*physiology ; *Symbiosis ; },
abstract = {The success of symbioses between cnidarian hosts (e.g., corals and sea anemones) and micro-algal symbionts hinges on the molecular interactions that govern the establishment and maintenance of intracellular mutualisms. As a fundamental component of innate immunity, glycan-lectin interactions impact the onset of marine endosymbioses, but our understanding of the effects of cell surface glycome composition on symbiosis establishment remains limited. In this study, we examined the canonical N-glycan biosynthesis pathway in the genome of the dinoflagellate symbiont Breviolum minutum (family Symbiodiniaceae) and found it to be conserved with the exception of the transferase GlcNAc-TII (MGAT2). Using coupled liquid chromatography-mass spectrometry (LC-MS/MS), we characterized the cell surface N-glycan content of B. minutum, providing the first insight into the molecular composition of surface glycans in dinoflagellates. We then used the biosynthesis inhibitors kifunensine and swainsonine to alter the glycan composition of B. minutum. Successful high-mannose enrichment via kifunensine treatment resulted in a significant decrease in colonization of the model sea anemone Aiptasia (Exaiptasia pallida) by B. minutum. Hybrid glycan enrichment via swainsonine treatment, however, could not be confirmed and did not impact colonization. We conclude that functional Golgi processing of N-glycans is critical for maintaining appropriate cell surface glycan composition and for ensuring colonization success by B. minutum.},
}
@article {pmid31972955,
year = {2020},
author = {Lepoutre, A and Faassen, EJ and Zweers, AJ and Lürling, M and Geffard, A and Lance, E},
title = {How the Neurotoxin β-N-Methylamino-l-Alanine Accumulates in Bivalves: Distribution of the Different Accumulation Fractions among Organs.},
journal = {Toxins},
volume = {12},
number = {2},
pages = {},
pmid = {31972955},
issn = {2072-6651},
support = {Bourse Eole//R&#xe9;seau Franco-N&#xe9;erlandais de l'enseignement sup&#xe9;rieur et de la recherche (RFN) and the Nuffic (Netherlands Organization for International Co-operation in Higher Education)./International ; 2015/1/191//Agence Nationale de S&#xe9;curit&#xe9; Sanitaire de l'Alimentation, de l'Environnement et du Travail/International ; },
mesh = {Amino Acids, Diamino/*pharmacokinetics ; Animals ; Cyanobacteria Toxins ; Dreissena/*metabolism ; Gastrointestinal Tract/metabolism ; Gills/metabolism ; Gonads/metabolism ; Hemolymph/metabolism ; Muscles/metabolism ; Neurotoxins/*pharmacokinetics ; Tissue Distribution ; Water Pollutants, Chemical/*pharmacokinetics ; },
abstract = {The environmental neurotoxin β-methylamino-l-alanine (BMAA) may represent a risk for human health. BMAA accumulates in freshwater and marine organisms consumed by humans. However, few data are available about the kinetics of BMAA accumulation and detoxification in exposed organisms, as well as the organ distribution and the fractions in which BMAA is present in tissues (free, soluble bound or precipitated bound cellular fractions). Here, we exposed the bivalve mussel Dreissena polymorpha to 7.5 µg of dissolved BMAA/mussel/3 days for 21 days, followed by 21 days of depuration in clear water. At 1, 3, 8, 14 and 21 days of exposure and depuration, the hemolymph and organs (digestive gland, the gills, the mantle, the gonad and muscles/foot) were sampled. Total BMAA as well as free BMAA, soluble bound and precipitated bound BMAA were quantified by tandem mass spectrometry. Free and soluble bound BMAA spread throughout all tissues from the first day of exposure to the last day of depuration, without a specific target organ. However, precipitated bound BMAA was detected only in muscles and foot from the last day of exposure to day 8 of depuration, at a lower concentration compared to free and soluble bound BMAA. In soft tissues (digestive gland, gonad, gills, mantle and muscles/foot), BMAA mostly accumulated as a free molecule and in the soluble bound fraction, with variations occurring between the two fractions among tissues and over time. The results suggest that the assessment of bivalve contamination by BMAA may require the quantification of total BMAA in whole individuals when possible.},
}
@article {pmid31969867,
year = {2019},
author = {Qu, EB and Omelon, CR and Oren, A and Meslier, V and Cowan, DA and Maggs-Kölling, G and DiRuggiero, J},
title = {Trophic Selective Pressures Organize the Composition of Endolithic Microbial Communities From Global Deserts.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2952},
pmid = {31969867},
issn = {1664-302X},
abstract = {Studies of microbial biogeography are often convoluted by extremely high diversity and differences in microenvironmental factors such as pH and nutrient availability. Desert endolithic (inside rock) communities are relatively simple ecosystems that can serve as a tractable model for investigating long-range biogeographic effects on microbial communities. We conducted a comprehensive survey of endolithic sandstones using high-throughput marker gene sequencing to characterize global patterns of diversity in endolithic microbial communities. We also tested a range of abiotic variables in order to investigate the factors that drive community assembly at various trophic levels. Macroclimate was found to be the primary driver of endolithic community composition, with the most striking difference witnessed between hot and polar deserts. This difference was largely attributable to the specialization of prokaryotic and eukaryotic primary producers to different climate conditions. On a regional scale, microclimate and properties of the rock substrate were found to influence community assembly, although to a lesser degree than global hot versus polar conditions. We found new evidence that the factors driving endolithic community assembly differ between trophic levels. While phototrophic taxa, mostly oxygenic photosynthesizers, were rigorously selected for among different sites, heterotrophic taxa were more cosmopolitan, suggesting that stochasticity plays a larger role in heterotroph assembly. This study is the first to uncover the global drivers of desert endolithic diversity using high-throughput sequencing. We demonstrate that phototrophs and heterotrophs in the endolithic community assemble under different stochastic and deterministic influences, emphasizing the need for studies of microorganisms in context of their functional niche in the community.},
}
@article {pmid31969866,
year = {2019},
author = {Hao, X and Zhu, YG and Nybroe, O and Nicolaisen, MH},
title = {The Composition and Phosphorus Cycling Potential of Bacterial Communities Associated With Hyphae of Penicillium in Soil Are Strongly Affected by Soil Origin.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2951},
pmid = {31969866},
issn = {1664-302X},
abstract = {Intimate fungal-bacterial interactions are widespread in nature. However the main drivers for the selection of hyphae-associated bacterial communities and their functional traits in soil systems remain elusive. In the present study, baiting microcosms were used to recover hyphae-associated bacteria from two Penicillium species with different phosphorus-solubilizing capacities in five types of soils. Based on amplicon sequencing of 16S rRNA genes, the composition of bacterial communities associated with Penicillium hyphae differed significantly from the soil communities, showing a lower diversity and less variation in taxonomic structure. Furthermore, soil origin had a significant effect on hyphae-associated community composition, whereas the two fungal species used in this study had no significant overall impact on bacterial community structure, despite their different capacities to solubilize phosphorus. However, discriminative taxa and specific OTUs were enriched in hyphae-associated communities of individual Penicillium species indicating that each hyphosphere represented a unique niche for bacterial colonization. Additionally, an increased potential of phosphorus cycling was found in hyphae-associated communities, especially for the gene phnK involved in phosphonate degradation. Altogether, it was established that the two Penicillium hyphae represent unique niches in which microbiome assemblage and phosphorus cycling potential are mainly driven by soil origin, with less impact made by fungal identity with a divergent capacity to utilize phosphorus.},
}
@article {pmid31968298,
year = {2020},
author = {Lu, B and Shen, Z and Zhang, Q and Hu, X and Warren, A and Song, W},
title = {Morphology and molecular analyses of four epibiotic peritrichs on crustacean and polychaete hosts, including descriptions of two new species (Ciliophora, Peritrichia).},
journal = {European journal of protistology},
volume = {73},
number = {},
pages = {125670},
doi = {10.1016/j.ejop.2019.125670},
pmid = {31968298},
issn = {1618-0429},
mesh = {Animals ; China ; Crustacea/*parasitology ; DNA, Protozoan/genetics ; Oligohymenophorea/*classification/cytology/genetics ; Phylogeny ; Polychaeta/*parasitology ; Species Specificity ; },
abstract = {Four epibiotic sessilid peritrichs, i.e., Zoothamnium wilberti n. sp., Baikalonis microdiscus n. sp., Epistylis anastatica (Linnaeus, 1767) Ehrenberg, 1830, and Rhabdostyla commensalisMöbius, 1888, were isolated from one syllid polychaete and three crustacean hosts in Qingdao, China. For each species, specimens were observed both in vivo and following silver staining. Their SSU rDNA was also sequenced for phylogenetic analyses. Zoothamnium wilberti n. sp. is characterized by the appearance of its colony, which is up to 350 μm high, and usually has fewer than 16 zooids, and the dichotomously branched stalk with transverse wrinkles, the conspicuously conical peristomial disc, and infundibular polykinety 3 comprising three isometric ciliary rows. Baikalonis microdiscus n. sp. can be recognized by its barrel-shaped zooid, small peristomial disc, smooth and short stalk, and its unusual infundibular polykinety 3 comprising a long inner row and a short outer row. Two poorly known species, i.e., Epistylis anastatica and Rhabdostyla commensalis, are redescribed and redefined. Phylogenetic analyses reveal that: (i) R. commensalis is closely related to the family Astylozoidae rather than to the morphologically similar Epistylididae; (ii) B. microdiscus n. sp. is sister to the family Scyphidiidae; (iii) E. anastatica groups with vorticellids and ophrydiids, which further supports the polyphyly of the genus Epistylis; and (iv) Z. wilberti n. sp. is nested within the Zoothamniidae, as expected.},
}
@article {pmid31967575,
year = {2020},
author = {Probst, AJ and Vaishampayan, P},
title = {Are we There Yet? Understanding Interplanetary Microbial Hitchhikers using Molecular Methods.},
journal = {Current issues in molecular biology},
volume = {38},
number = {},
pages = {33-52},
doi = {10.21775/cimb.038.033},
pmid = {31967575},
issn = {1467-3045},
mesh = {Adenosine Triphosphate/chemistry ; Bacteria/growth &amp; development/*isolation &amp; purification ; Cell Survival ; *Ecological Systems, Closed ; *Environmental Microbiology ; Extraterrestrial Environment/*chemistry ; Genomics ; Metagenomics ; Microbiota ; RNA, Ribosomal/chemistry/isolation &amp; purification ; *Space Flight ; Spacecraft/standards ; Spores/isolation &amp; purification ; Sterilization ; United States ; United States National Aeronautics and Space Administration ; Weightlessness ; },
abstract = {Since the early time of space travel, planetary bodies undergoing chemical or biological evolution have been of particular interest for life detection missions. NASA's and ESA's Planetary Protection offices ensure responsible exploration of the solar system and aim at avoiding inadvertent contamination of celestial bodies with biomolecules or even living organisms. Life forms that have the potential to colonize foreign planetary bodies could be a threat to the integrity of science objectives of life detection missions. While standard requirements for assessing the cleanliness of spacecraft are still based on cultivation approaches, several molecular methods have been applied in the past to elucidate the full breadth of (micro)organisms that can be found on spacecraft and in cleanrooms, where the hardware is assembled. Here, we review molecular assays that have been applied in Planetary Protection research and list their significant advantages and disadvantages. By providing a comprehensive summary of the latest molecular methods yet to be applied in this research area, this article will not only aid in designing technological roadmaps for future Planetary Protection endeavors but also help other disciplines in environmental microbiology that deal with low biomass samples.},
}
@article {pmid31965838,
year = {2019},
author = {Moens, F and Duysburgh, C and van den Abbeele, P and Morera, M and Marzorati, M},
title = {Lactobacillus rhamnosus GG and Saccharomyces cerevisiae boulardii exert synergistic antipathogenic activity in vitro against enterotoxigenic Escherichia coli.},
journal = {Beneficial microbes},
volume = {10},
number = {8},
pages = {923-935},
doi = {10.3920/BM2019.0064},
pmid = {31965838},
issn = {1876-2891},
mesh = {Adult ; Batch Cell Culture Techniques ; Child, Preschool ; Coculture Techniques ; Colon/metabolism/microbiology ; Dysbiosis/metabolism/microbiology ; Enterotoxigenic Escherichia coli/*drug effects/growth &amp; development/metabolism ; Enterotoxins/metabolism ; Fatty Acids, Volatile/metabolism ; Healthy Volunteers ; Humans ; Intestinal Mucosa/metabolism/microbiology ; Lacticaseibacillus rhamnosus/growth &amp; development/metabolism/*physiology ; Probiotics/*pharmacology ; Saccharomyces cerevisiae/growth &amp; development/metabolism/*physiology ; },
abstract = {Short-term colonic in vitro batch incubations were performed to elucidate the possible synergistic effects of Lactobacillus rhamnosus GG (CNCM-I-4798) and Saccharomyces cerevisiae boulardii (CNCM-I-1079) (associated in Smebiocta/Smectaflora Protect®) on the colonic microbial fermentation process, as well as their antipathogenic activity against enterotoxigenic Escherichia coli (LMG2092) (ETEC). These incubations adequately simulate the native microbiota and environmental conditions of the proximal colon of both adult and toddler donors, including the colonic mucosal layer. Results indicated that both strains were capable of growing together without showing antagonistic effects. Co-cultivation of both strains resulted in increased butyrate (stimulated by L. rhamnosus GG), propionate (stimulated by S. boulardii), and ethanol (produced by S. boulardii) production compared to the control incubations, revealing the additive effect of both strains. After inoculation of ETEC under simulated dysbiotic conditions, a 40 and 46% reduction in the concentration of ETEC was observed upon addition of both strains during the experiments with the adult and toddler donor, respectively. Furthermore, ETEC toxin levels decreased upon S. boulardii inoculation, probably due to proteolytic activity of this strain, with a synergistic effect being observed upon co-cultivation of L. rhamnosus GG and S. boulardii resulting in a reduction of 57 and 46% for the adult and toddler donor, respectively. Altogether, the results suggest that both probiotics together may help microbiota functionality, in both adults and toddlers and under healthy or impaired conditions, which could be of great interest when the colonic microbiota is dysbiotic and therefore sensitive to pathogenic invasion such as during antibiotic treatment.},
}
@article {pmid31965223,
year = {2020},
author = {Mina, D and Pereira, JA and Lino-Neto, T and Baptista, P},
title = {Epiphytic and Endophytic Bacteria on Olive Tree Phyllosphere: Exploring Tissue and Cultivar Effect.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {145-157},
doi = {10.1007/s00248-020-01488-8},
pmid = {31965223},
issn = {1432-184X},
support = {PTDC/ASP-PLA/31133/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH-BD-105341/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PRIMA/0002/2018//Horizon 2020 Framework Programme/ ; },
mesh = {Bacteria/classification/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Endophytes/classification/isolation &amp; purification/physiology ; *Microbiota ; Olea/*microbiology ; Plant Leaves/*microbiology ; Portugal ; },
abstract = {Variation on bacterial communities living in the phyllosphere as epiphytes and endophytes has been attributed to plant host effects. However, there is contradictory or inconclusive evidence regarding the effect of plant genetics (below the species' level) and of plant tissue type on phyllosphere bacterial community assembly, in particular when epiphytes and endophytes are considered simultaneously. Here, both surface and internal bacterial communities of two olive (Olea europaea) cultivars were evaluated in twigs and leaves by molecular identification of cultivable isolates, with an attempt to answer these questions. Overall, Proteobacteria, Actinobacteria and Firmicutes were the dominant phyla, being epiphytes more diverse and abundant than endophytes. Host genotype (at cultivar level) had a structuring effect on the composition of bacterial communities and, in a similar way, for both epiphytes and endophytes. Plant organ (leaf vs. twig) control of the bacterial communities was less evident when compared with plant genotype and with a greater influence on epiphytic than on endophytic community structure. Each olive genotype/plant organ was apparently selective towards specific bacterial operational taxonomic units (OTUs), which may lead to specific feedbacks on fitness of plant genotypes. Bacterial recruitment was observed to happen mainly within epiphytes than in endophytes and in leaves as compared with twigs. Such host specificity suggested that the benefits derived from the plant-bacteria interaction should be considered at genetic levels below the species.},
}
@article {pmid31964728,
year = {2020},
author = {Carini, P and Delgado-Baquerizo, M and Hinckley, ES and Holland-Moritz, H and Brewer, TE and Rue, G and Vanderburgh, C and McKnight, D and Fierer, N},
title = {Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
pmid = {31964728},
issn = {2150-7511},
mesh = {*Metagenome ; *Metagenomics/methods ; Microbial Interactions ; *Microbiota ; RNA, Ribosomal, 16S ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Spatio-Temporal Analysis ; },
abstract = {Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.},
}
@article {pmid31958594,
year = {2020},
author = {Vandekerckhove, TGL and Props, R and Carvajal-Arroyo, JM and Boon, N and Vlaeminck, SE},
title = {Adaptation and characterization of thermophilic anammox in bioreactors.},
journal = {Water research},
volume = {172},
number = {},
pages = {115462},
doi = {10.1016/j.watres.2019.115462},
pmid = {31958594},
issn = {1879-2448},
mesh = {*Ammonium Compounds ; Anaerobiosis ; *Bioreactors ; Nitrogen ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Sewage ; Temperature ; },
abstract = {Anammox, the oxidation of ammonium with nitrite, is a key microbial process in the nitrogen cycle. Under mesophilic conditions (below 40 °C), it is widely implemented to remove nitrogen from wastewaters lacking organic carbon. Despite evidence of the presence of anammox bacteria in high-temperature environments, reports on the cultivation of thermophilic anammox bacteria are limited to a short-term experiment of 2 weeks. This study showcases the adaptation of a mesophilic inoculum to thermophilic conditions, and its characterization. First, an attached growth technology was chosen to obtain the process. In an anoxic fixed-bed biofilm bioreactor (FBBR), a slow linear temperature increase from 38 to over 48 °C (0.05-0.07 °C d[-1]) was imposed to the community over 220 days, after which the reactor was operated at 48 °C for over 200 days. Maximum total nitrogen removal rates reached up to 0.62 g N L[-1] d[-1]. Given this promising performance, a suspended growth system was tested. The obtained enrichment culture served as inoculum for membrane bioreactors (MBR) operated at 50 °C, reaching a maximum total nitrogen removal rate of 1.7 g N L[-1] d[-1] after 35 days. The biomass in the MBR had a maximum specific anammox activity of 1.1 ± 0.1 g NH4[+]-N g[-1] VSS d[-1], and the growth rate was estimated at 0.075-0.19 d[-1]. The thermophilic cultures displayed nitrogen stoichiometry ratios typical for mesophilic anammox: 0.93-1.42 g NO2[-]-Nremoved g[-1] NH4[+]-Nremoved and 0.16-0.35 g NO3[-]-Nproduced g[-1] NH4[+]-Nremoved. Amplicon and Sanger sequencing of the 16S rRNA genes revealed a disappearance of the original "Ca. Brocadia" and "Ca. Jettenia" taxa, yielding Planctomycetes members with only 94-95% similarity to "Ca. Brocadia anammoxidans" and "Ca. B. caroliniensis", accounting for 45% of the bacterial FBBR community. The long-term operation of thermophilic anammox reactors and snapshot views on the nitrogen stoichiometry, kinetics and microbial community open up the development path of thermophilic partial nitritation/anammox. A first economic assessment highlighted that treatment of sludge reject water from thermophilic anaerobic digestion of sewage sludge may become attractive.},
}
@article {pmid31955749,
year = {2020},
author = {Gontijo, MTP and Silva, JS and Vidigal, PMP and Martin, JGP},
title = {Phylogenetic distribution of the bacteriocin repertoire of lactic acid bacteria species associated with artisanal cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {128},
number = {},
pages = {108783},
doi = {10.1016/j.foodres.2019.108783},
pmid = {31955749},
issn = {1873-7145},
mesh = {Bacteriocins/chemistry/genetics/*metabolism ; Cheese/*microbiology ; Food Microbiology ; Genome, Bacterial ; Lactobacillales/*genetics/*metabolism ; Peptides/chemistry/classification/metabolism/pharmacology ; Phylogeny ; },
abstract = {The microbiota contributes to artisanal cheese bioprotection and biopreservation through inter and intraspecific competition. This work aimed to investigate the phylogenetic distribution of the repertoire of bacteriocin structural genes of model lactic acid bacteria (LAB) in order to investigate its respective role in the artisanal cheeses microenvironment. A phylogenetic analysis of the rRNA 16S gene from 445 model strains of LAB was conducted using bayesian inference and the repertoire of bacteriocin genes was predicted from these strains by BAGEL software. Bacterial strains were clustered in five monophyletic clades (A, B, C, D and E) with high posterior probability values (PP > 0.99). One bacteriocin structural gene was predicted for 88.5% of the analyzed strains. The majority of the species encoded different classes of bacteriocins. Greater diversity of bacteriocin genes was found for strains included in clade A, comprising Lactococcus lactis, Streptococcus agalactiae, Streptococcus thermophilus, Streptococcus macedonicus, Enterococcus faecalis and Enterococcus faecium. In addition, Lactococcus lactis presented higher diversity of bacteriocin classes, encoding glycocins, lanthipeptides, sactipeptides, cyclic and linear azole-containing peptides, included in bacteriocins class I, besides class II and III. The results suggest that the distribution of bacteriocin structural genes is related to the phylogenetic clades of LAB species, with a higher frequency in some specific clades. Information comprised in this study contributes to comprehend the bacterial competition mechanisms in the artisanal cheese microenvironment.},
}
@article {pmid31955225,
year = {2020},
author = {Liu, H and Gao, H and Wu, M and Ma, C and Wu, J and Ye, X},
title = {Distribution Characteristics of Bacterial Communities and Hydrocarbon Degradation Dynamics During the Remediation of Petroleum-Contaminated Soil by Enhancing Moisture Content.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {202-211},
doi = {10.1007/s00248-019-01476-7},
pmid = {31955225},
issn = {1432-184X},
support = {No. 21577109//National Natural Science Foundation of China/ ; },
mesh = {Bacteria/*metabolism ; Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Environmental Pollution/*prevention &amp; control ; Environmental Restoration and Remediation ; Humidity ; Hydrocarbons/*metabolism ; *Microbiota ; Soil/*chemistry ; Soil Pollutants/*metabolism ; },
abstract = {Microorganisms are the driver of petroleum hydrocarbon degradation in soil micro-ecological systems. However, the distribution characteristics of microbial communities and hydrocarbon degradation dynamics during the remediation of petroleum-contaminated soil by enhancing moisture content are not clear. In this study, polymerase chain reaction and high-throughput sequencing of soil microbial DNA were applied to investigate the compositions of microorganisms and alpha diversity in the oil-polluted soil, and the hydrocarbon removal also being analyzed using ultrasonic extraction and gravimetric method in a laboratory simulated ex-situ experiment. Results showed the distribution of petroleum hydrocarbon degrading microorganisms in the petroleum-contaminated loessal soil mainly was Proteobacteria phylum (96.26%)-Gamma-proteobacteria class (90.03%)-Pseudomonadales order (89.98%)-Pseudomonadaceae family (89.96%)-Pseudomonas sp. (87.22%). After 15% moisture content treatment, Actinobacteria, Proteobacteria, and Firmicutes still were the predominant phyla, but their relative abundances changed greatly. Also Bacillus sp. and Promicromonospora sp. became the predominant genera. Maintaining 15% moisture content increased the relative abundance of Firmicutes phylum and Bacillus sp. As the moisture-treated time increases, the uniformity and the richness of the soil bacterial community were decreased and increased respectively; the relative abundance of Pseudomonas sp. increased. Petroleum hydrocarbon degradation by enhancing soil moisture accorded with the pseudo-first-order reaction kinetic model (correlation coefficient of 0.81; half-life of 56 weeks). The richness of Firmicutes phylum and Bacillus sp. may be a main reason for promoting the removal of 18% petroleum hydrocarbons responded to 15% moisture treatment. Our results provided some beneficial microbiological information of oil-contaminated soil and will promote the exploration of remediation by changing soil moisture content for increasing petroleum hydrocarbon degradation efficiency.},
}
@article {pmid31954761,
year = {2020},
author = {Mongui, A and Lozano, GL and Handelsman, J and Restrepo, S and Junca, H},
title = {Design and validation of a transposon that promotes expression of genes in episomal DNA.},
journal = {Journal of biotechnology},
volume = {310},
number = {},
pages = {1-5},
doi = {10.1016/j.jbiotec.2020.01.007},
pmid = {31954761},
issn = {1873-4863},
mesh = {*DNA Transposable Elements ; DNA-Directed RNA Polymerases/biosynthesis/*genetics ; Escherichia coli/*genetics/metabolism ; *Gene Expression ; Plasmids/*genetics/metabolism ; *Promoter Regions, Genetic ; Viral Proteins/biosynthesis/*genetics ; },
abstract = {Functional metagenomics, or the cloning and expression of DNA isolated directly from environmental samples, represents a source of novel compounds with biotechnological potential. However, attempts to identify such compounds in metagenomic libraries are generally inefficient in part due to lack of expression of heterologous DNA. In this research, the TnC_T7 transposon was developed to supply transcriptional machinery during functional analysis of metagenomic libraries. TnC_T7 contains bidirectional T7 promoters, the gene encoding the T7 RNA polymerase (T7RNAP), and a kanamycin resistance gene. The T7 RNA polymerase gene is regulated by the inducible arabinose promoter (PBAD), thereby facilitating inducible expression of genes adjacent to the randomly integrating transposon. The high processivity of T7RNAP should make this tool particularly useful for obtaining gene expression in long inserts. TnC_T7 functionality was validated by conducting in vitro transposition of pKR-C12 or fosmid pF076_GFPmut3*, carrying metagenomic DNA from soil. We identified transposon insertions that enhanced GFP expression in both vectors, including insertions in which the promoter delivered by the transposon was located as far as 8.7 kb from the GFP gene, indicating the power of the high processivity of the T7 polymerase. The results gathered in this research demonstrate the potential of TnC_T7 to enhance gene expression in functional metagenomic studies.},
}
@article {pmid31954367,
year = {2020},
author = {Giri, S and Shitut, S and Kost, C},
title = {Harnessing ecological and evolutionary principles to guide the design of microbial production consortia.},
journal = {Current opinion in biotechnology},
volume = {62},
number = {},
pages = {228-238},
doi = {10.1016/j.copbio.2019.12.012},
pmid = {31954367},
issn = {1879-0429},
mesh = {Bacteria/genetics ; *Biotechnology ; *Microbial Consortia/genetics ; },
abstract = {Bacteria are widely used for commercially producing biomolecules. However, attempts to rationally design production strains and optimize cultivation conditions are frequently counteracted by the emergence of mutants with reduced production characteristics that decrease overall process yield. The reason why these mutants arise is likely because of a mismatch between the ecological conditions under which bacteria evolved in nature and the situation they experience in an industrial setting. Thus, there is a great potential for improving biotechnological production processes by implementing eco-evolutionary knowledge. However, this is often limited by a lack of effective communication between process engineers and microbial ecologists/evolutionary biologists. Here, we highlight recent findings in the field of microbial ecology and evolution and suggest implementation of this knowledge can significantly enhance microbial bioproduction.},
}
@article {pmid31953337,
year = {2020},
author = {Tinker, KA and Ottesen, EA},
title = {Phylosymbiosis across Deeply Diverging Lineages of Omnivorous Cockroaches (Order Blattodea).},
journal = {Applied and environmental microbiology},
volume = {86},
number = {7},
pages = {},
pmid = {31953337},
issn = {1098-5336},
support = {R35 GM133789/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Bacterial Physiological Phenomena ; Cockroaches/*microbiology ; *Gastrointestinal Microbiome ; *Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Symbiosis ; },
abstract = {The gut microbiome is shaped by both host diet and host phylogeny. However, separating the relative influence of these two factors over long periods of evolutionary time is often difficult. We conducted a 16S rRNA gene amplicon-based survey of the gut microbiome from 237 individuals and 19 species of omnivorous cockroaches from the order Blattodea. The order Blattodea represents an ancient lineage of insects that emerged over 300 million years ago, have a diverse gut microbiota, and have a typically gregarious lifestyle. All cockroaches shared a broadly similar gut microbiota, with 66 microbial families present across all species and 13 present in every individual examined. Although our network analysis of the cockroach gut microbiome showed a large amount of connectivity, we demonstrated that gut microbiota cluster strongly by host species. We conducted follow-up tests to determine if cockroaches exhibit phylosymbiosis, or the tendency of host-associated microbial communities to parallel the phylogeny of related host species. Across the full data set, gut microbial community similarity was not found to correlate with host phylogenetic distance. However, a weak but significant phylosymbiotic signature was observed using the matching cluster metric, which allows for localized changes within a phylogenetic tree that are more likely to occur over long evolutionary distances. This finding suggests that host phylogeny plays a large role in structuring the cockroach gut microbiome over shorter evolutionary distances and a weak but significant role in shaping the gut microbiome over extended periods of evolutionary time.IMPORTANCE The gut microbiome plays a key role in host health. Therefore, it is important to understand the evolution of the gut microbiota and how it impacts, and is impacted by, host evolution. In this study, we explore the relationship between host phylogeny and gut microbiome composition in omnivorous, gregarious cockroaches within the Blattodea order, an ancient lineage that spans 300 million years of evolutionary divergence. We demonstrate a strong relationship between host species identity and gut microbiome composition and found a weaker but significant role for host phylogeny in determining microbiome similarity over extended periods of evolutionary time. This study advances our understanding of the role of host phylogeny in shaping the gut microbiome over different evolutionary distances.},
}
@article {pmid31952848,
year = {2020},
author = {Krishnamoorthy, S and Coetzee, V and Kruger, J and Potgieter, H and Buys, EM},
title = {Dysbiosis Signatures of Fecal Microbiota in South African Infants with Respiratory, Gastrointestinal, and Other Diseases.},
journal = {The Journal of pediatrics},
volume = {218},
number = {},
pages = {106-113.e3},
doi = {10.1016/j.jpeds.2019.11.029},
pmid = {31952848},
issn = {1097-6833},
mesh = {Anti-Bacterial Agents/therapeutic use ; Case-Control Studies ; Child, Preschool ; Dysbiosis/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Hospitalization ; Humans ; Infant ; Male ; Principal Component Analysis ; RNA, Ribosomal, 16S/metabolism ; Respiration Disorders/*microbiology ; Software ; South Africa ; Vitamin A/therapeutic use ; },
abstract = {OBJECTIVE: To determine the association between the fecal microbiota diversity of the infants with different disease conditions, and vitamin A supplementation, antibiotic, and deworming therapies.<br><br>STUDY DESIGN: In this case-control study, the bacterial community variations and the potential pathogens were identified through 16S ribosomal RNA gene-based amplicon sequencing and quantitative insights into microbial ecology pipeline in fecal samples. The participants were South African infants (mean age, 16&#xa0;&#xb1;&#xa0;8&#xa0;months; 17 male and 17 female) hospitalized and diagnosed with gastrointestinal, respiratory, and other diseases.<br><br>RESULTS: The top phyla of the infants with respiratory disease were Proteobacteria, followed by Firmicutes, which were equally abundant in gastrointestinal disease. A significant difference in Shannon (alpha) diversity index (95% CI, 2.6-4.4; P&#xa0;=&#xa0;.008), among the microbiota of the fecal samples categorized by disease conditions, was observed. In beta diversity analysis of fecal microbiota, remarkable variations were found within the groups of deworming therapy (95% CI, 0.40-0.90; P&#xa0;=&#xa0;.033), disease conditions (95% CI, 0.44-0.86; P&#xa0;<&#xa0;.012) through unweighted and antibiotic therapy (95% CI, 0.20-0.75; P&#xa0;=&#xa0;.007), vitamin A intake (95% CI, 0.10-0.80; P&#xa0;<&#xa0;.033) and disease conditions (95% CI, 0.10-0.79; P&#xa0;=&#xa0;.006) through weighted UniFrac distances. The candidate pathogen associated with the disease groups were identified through analysis of the composition of microbiomes analysis.<br><br>CONCLUSIONS: This study provides preliminary evidence for the fecal microbiome-derived dysbiosis signature and pathobiome concept that may be observed in young children during illness.},
}
@article {pmid31952472,
year = {2020},
author = {Feng, J and Wang, C and Lei, J and Yang, Y and Yan, Q and Zhou, X and Tao, X and Ning, D and Yuan, MM and Qin, Y and Shi, ZJ and Guo, X and He, Z and Van Nostrand, JD and Wu, L and Bracho-Garillo, RG and Penton, CR and Cole, JR and Konstantinidis, KT and Luo, Y and Schuur, EAG and Tiedje, JM and Zhou, J},
title = {Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {3},
pmid = {31952472},
issn = {2049-2618},
mesh = {Carbon/metabolism ; *Carbon Cycle ; *Global Warming ; Methane/metabolism ; *Microbiota ; Permafrost/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seasons ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {BACKGROUND: It is well-known that global warming has effects on high-latitude tundra underlain with permafrost. This leads to a severe concern that decomposition of soil organic carbon (SOC) previously stored in this region, which accounts for about 50% of the world's SOC storage, will cause positive feedback that accelerates climate warming. We have previously shown that short-term warming (1.5 years) stimulates rapid, microbe-mediated decomposition of tundra soil carbon without affecting the composition of the soil microbial community (based on the depth of 42684 sequence reads of 16S rRNA gene amplicons per 3 g of soil sample).<br><br>RESULTS: We show that longer-term (5 years) experimental winter warming at the same site altered microbial communities (p < 0.040). Thaw depth correlated the strongest with community assembly and interaction networks, implying that warming-accelerated tundra thaw fundamentally restructured the microbial communities. Both carbon decomposition and methanogenesis genes increased in relative abundance under warming, and their functional structures strongly correlated (R[2] > 0.725, p < 0.001) with ecosystem respiration or CH4 flux.<br><br>CONCLUSIONS: Our results demonstrate that microbial responses associated with carbon cycling could lead to positive feedbacks that accelerate SOC decomposition in tundra regions, which is alarming because SOC loss is unlikely to subside owing to changes in microbial community composition. Video Abstract.},
}
@article {pmid31951572,
year = {2020},
author = {Li, Z and Van de Peer, Y},
title = {"Winter Is Coming": How did Polyploid Plants Survive?.},
journal = {Molecular plant},
volume = {13},
number = {1},
pages = {4-5},
doi = {10.1016/j.molp.2019.12.003},
pmid = {31951572},
issn = {1752-9867},
mesh = {Humans ; *Magnoliopsida ; Plants ; Polyploidy ; Seasons ; },
}
@article {pmid31951190,
year = {2020},
author = {Lee, JC and Whang, KS},
title = {Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {3},
pages = {1785-1792},
doi = {10.1099/ijsem.0.003973},
pmid = {31951190},
issn = {1466-5034},
mesh = {Actinobacteria/*classification/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Farms ; Fatty Acids/chemistry ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; },
abstract = {A Gram-stain-positive actinobacterial strain, designated YJ01[T], was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01[T] was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5-1.9 µm, and was able to grow at 10-37 °C (optimum, 28-30 °C), at pH 4.5-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01[T] with closely related relatives were in the range 96.2-92.8 %, and the results of phylogenomic analysis indicated that strain YJ01[T] was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2-83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn-Gly2-d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01[T] is considered to represent a novel species of a new genus in the family Intrasporangiaceae, for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01[T] (=KACC 19547[T]=NBRC 113173[T]).},
}
@article {pmid31950228,
year = {2020},
author = {Guhr, A and Kircher, S},
title = {Drought-Induced Stress Priming in Two Distinct Filamentous Saprotrophic Fungi.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {27-33},
pmid = {31950228},
issn = {1432-184X},
support = {DFG-GU 1818/1-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Adaptation, Physiological ; Biomass ; *Droughts ; Neurospora crassa/*physiology ; Penicillium chrysogenum/*physiology ; *Stress, Physiological ; },
abstract = {Sessile organisms constantly face environmental fluctuations and especially drought is a common stressor. One adaptive mechanism is "stress priming," the ability to cope with a severe stress ("triggering") by retaining information from a previous mild stress event ("priming"). While plants have been extensively investigated for drought-induced stress priming, no information is available for saprotrophic filamentous fungi, which are highly important for nutrient cycles. Here, we investigated the potential for drought-induced stress priming of one strain each of two ubiquitous species, Neurospora crassa and Penicillium chrysogenum. A batch experiment with 4 treatments was conducted on a sandy soil: exposure to priming and/or triggering as well as non-stressed controls. A priming stress was caused by desiccation to pF 4. The samples were then rewetted and after 1-, 7-, or 14-days of recovery triggered (pF 6). After triggering, fungal biomass, respiration, and β-glucosidase activity were quantified. P. chrysogenum showed positive stress priming effects. After 1 day of recovery, biomass as well as β-glucosidase activity and respiration were 0.5 to 5 times higher during triggering. Effects on biomass and activity decreased with prolonged recovery but lasted for 7 days and minor effects were still detectable after 14 days. Without triggering, stress priming had a temporary negative impact on biomass but this reversed after 14 days. For N. crassa, no stress priming effect was observed on the tested variables. The potential for drought-induced stress priming seems to be species specific with potentially high impact on composition and activity of fungal communities considering the expected increase of drought events.},
}
@article {pmid31948971,
year = {2020},
author = {Korotetskiy, IS and Joubert, M and Magabotha, SM and Jumagaziyeva, AB and Shilov, SV and Suldina, NA and Kenesheva, ST and Yssel, A and Reva, ON and Ilin, AI},
title = {Complete Genome Sequence of Collection Strain Acinetobacter baumannii ATCC BAA-1790, Used as a Model To Study the Antibiotic Resistance Reversion Induced by Iodine-Containing Complexes.},
journal = {Microbiology resource announcements},
volume = {9},
number = {3},
pages = {},
pmid = {31948971},
issn = {2576-098X},
abstract = {The strain Acinetobacter baumannii ATCC BAA-1790 was sequenced as a model for nosocomial multidrug-resistant infections. Long-read PacBio sequencing revealed a circular chromosome of 3,963,235 bp with two horizontally transferred genomic islands and a 67,023-bp plasmid. Multiple antibiotic resistance genes and genome methylation patterns were identified.},
}
@article {pmid31947979,
year = {2020},
author = {Purkamo, L and Kietäväinen, R and Nuppunen-Puputti, M and Bomberg, M and Cousins, C},
title = {Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context.},
journal = {Life (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
pmid = {31947979},
issn = {2075-1729},
support = {2016-2018//Jenny ja Antti Wihurin Rahasto/ ; RENGAS//KYT2018/ ; BIKES//KYT22/ ; C.Cousins//Royal Society of Edinburgh/ ; },
abstract = {The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.},
}
@article {pmid31943686,
year = {2020},
author = {Guégan, M and Tran Van, V and Martin, E and Minard, G and Tran, FH and Fel, B and Hay, AE and Simon, L and Barakat, M and Potier, P and Haichar, FEZ and Valiente Moro, C},
title = {Who is eating fructose within the Aedes albopictus gut microbiota?.},
journal = {Environmental microbiology},
volume = {22},
number = {4},
pages = {1193-1206},
doi = {10.1111/1462-2920.14915},
pmid = {31943686},
issn = {1462-2920},
support = {//EC2CO CNRS/International ; ANR-13-EBID-0007-01//ERA-NET BiodivERsA/International ; FWF I-1437//ERA-NET BiodivERsA/International ; DFG KL 2087/6//ERA-NET BiodivERsA/International ; },
mesh = {Aedes/*microbiology ; Animals ; Bacteria/metabolism ; Female ; Fructose/*metabolism ; Fungi/metabolism ; *Gastrointestinal Microbiome ; Male ; Mosquito Vectors ; },
abstract = {The Asian tiger mosquito Aedes albopictus is a major public health concern because of its invasive success and its ability to transmit pathogens. Given the low availability of treatments against mosquito-borne diseases, vector control remains the most suitable strategy. The methods used thus far are becoming less effective, but recent strategies have emerged from the study of mosquito-associated microorganisms. Although the role of the microbiota in insect biology does not require further proof, much remains to be deciphered in mosquitoes, especially the contribution of the microbiota to host nutrient metabolism. Mosquitoes feed on plant nectar, composed of mostly fructose. We used stable isotope probing to identify bacteria and fungi assimilating fructose within the gut of Ae. albopictus. Mosquitoes were fed a [13] C-labelled fructose solution for 24 h. Differences in the active microbial community according to the sex of mosquitoes were highlighted. The bacterium Lelliottia and the fungi Cladosporium and Aspergillus dominated the active microbiota in males, whereas the bacterium Ampullimonas and the yeast Cyberlindnera were the most active in females. This study is the first to investigate trophic interactions between Ae. albopictus and its microbiota, thus underscoring the importance of the microbial component in nectar feeding in mosquitoes.},
}
@article {pmid31942799,
year = {2020},
author = {Cakmak, I and Marzorati, M and Van den Abbeele, P and Hora, K and Holwerda, HT and Yazici, MA and Savasli, E and Neri, J and Du Laing, G},
title = {Fate and Bioaccessibility of Iodine in Food Prepared from Agronomically Biofortified Wheat and Rice and Impact of Cofertilization with Zinc and Selenium.},
journal = {Journal of agricultural and food chemistry},
volume = {68},
number = {6},
pages = {1525-1535},
doi = {10.1021/acs.jafc.9b05912},
pmid = {31942799},
issn = {1520-5118},
mesh = {Biofortification ; Bread/analysis ; Cooking ; Fertilizers/analysis ; Flour/analysis ; Food, Fortified/analysis ; Hot Temperature ; Humans ; Iodine/analysis/*metabolism ; Oryza/chemistry/*metabolism ; Seeds/chemistry/metabolism ; Selenium/analysis/*metabolism ; Triticum/chemistry/*metabolism ; Zinc/analysis/*metabolism ; },
abstract = {Enrichment of food crops with iodine is an option to alleviate dietary deficiencies. Therefore, foliar iodine fertilizer was applied on wheat and rice, in the presence and absence of the other micronutrients zinc and selenium. This treatment increased the concentration of iodine, as well as zinc and selenium, in the staple grains. Subsequently, potential iodine losses during preparation of foodstuffs with the enriched grains were studied. Oven-heating did not affect the iodine content in bread. Extraction of bran from flour lowered the iodine in white bread compared to wholegrain bread, but it was still markedly higher compared to the control. During subsequent in vitro gastrointestinal digestion, a higher percentage of iodine was released from foods based on extracted flour (82-92%) compared to wholegrain foods (50-76%). The foliar fertilization of wheat was found to be adequate to alleviate iodine deficiency in a population with a moderate to high intake of bread.},
}
@article {pmid31942666,
year = {2021},
author = {Morrison, ES and Thomas, P and Ogram, A and Kahveci, T and Turner, BL and Chanton, JP},
title = {Characterization of Bacterial and Fungal Communities Reveals Novel Consortia in Tropical Oligotrophic Peatlands.},
journal = {Microbial ecology},
volume = {82},
number = {1},
pages = {188-201},
pmid = {31942666},
issn = {1432-184X},
support = {DEB 0841596//National Science Foundation/ ; },
mesh = {Bacteria/genetics ; *Greenhouse Gases ; Humans ; *Microbiota ; *Mycobiome ; Soil ; },
abstract = {Despite their importance for global biogeochemical cycles and carbon sequestration, the microbiome of tropical peatlands remains under-determined. Microbial interactions within peatlands can regulate greenhouse gas production, organic matter turnover, and nutrient cycling. Here we analyze bacterial and fungal communities along a steep P gradient in a tropical peat dome and investigate community level traits and network analyses to better understand the composition and potential interactions of microorganisms in these understudied systems and their relationship to peatland biogeochemistry. We found that both bacterial and fungal community compositions were significantly different along the P gradient, and that the low-P bog plain was characterized by distinct fungal and bacterial families. At low P, the dominant fungal families were cosmopolitan parasites and endophytes, including Clavicipitaceae (19%) in shallow soils (0-4 cm), Hypocreaceae (50%) in intermediate-depth soils (4-8 cm), and Chaetothyriaceae (45%) in deep soils (24-30 cm). In contrast, high- and intermediate-P sites were dominated by saprotrophic families at all depths. Bacterial communities were consistently dominated by the acidophilic Koribacteraceae family, with the exception of the low-P bog site, which was dominated by Acetobacteraceae (19%) and Syntrophaceae (11%). These two families, as well as Rhodospirillaceae, Syntrophobacteraceae, Syntrophorhabdaceae, Spirochaetaceae, and Methylococcaceae appeared within low-P bacterial networks, suggesting the presence of a syntrophic-methanogenic consortium in these soils. Further investigation into the active microbial communities at these sites, when paired with CH4 and CO2 gas exchange, and the quantification of metabolic intermediates will validate these potential interactions and provide insight into microbially driven biogeochemical cycling within these globally important tropical peatlands.},
}
@article {pmid31942051,
year = {2020},
author = {Hampton, HG and Watson, BNJ and Fineran, PC},
title = {The arms race between bacteria and their phage foes.},
journal = {Nature},
volume = {577},
number = {7790},
pages = {327-336},
pmid = {31942051},
issn = {1476-4687},
mesh = {Adsorption ; Animals ; Bacteria/growth &amp; development/*immunology/*virology ; Bacteriophages/*immunology/metabolism ; CRISPR-Cas Systems/physiology ; Host Microbial Interactions/*immunology ; Humans ; },
abstract = {Bacteria are under immense evolutionary pressure from their viral invaders-bacteriophages. Bacteria have evolved numerous immune mechanisms, both innate and adaptive, to cope with this pressure. The discovery and exploitation of CRISPR-Cas systems have stimulated a resurgence in the identification and characterization of anti-phage mechanisms. Bacteriophages use an extensive battery of counter-defence strategies to co-exist in the presence of these diverse phage defence mechanisms. Understanding the dynamics of the interactions between these microorganisms has implications for phage-based therapies, microbial ecology and evolution, and the development of new biotechnological tools. Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages.},
}
@article {pmid31941815,
year = {2020},
author = {De Rudder, C and Calatayud Arroyo, M and Lebeer, S and Van de Wiele, T},
title = {Dual and Triple Epithelial Coculture Model Systems with Donor-Derived Microbiota and THP-1 Macrophages To Mimic Host-Microbe Interactions in the Human Sinonasal Cavities.},
journal = {mSphere},
volume = {5},
number = {1},
pages = {},
pmid = {31941815},
issn = {2379-5042},
mesh = {Coculture Techniques ; Cytokines/immunology ; *Host Microbial Interactions ; Humans ; Latilactobacillus sakei/immunology/physiology ; Macrophages/*microbiology ; *Microbiota ; Nasal Cavity/cytology/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Respiratory Mucosa/immunology/*microbiology ; Staphylococcus aureus/immunology/physiology ; THP-1 Cells ; },
abstract = {The epithelium of the human sinonasal cavities is colonized by a diverse microbial community, modulating epithelial development and immune priming and playing a role in respiratory disease. Here, we present a novel in vitro approach enabling a 3-day coculture of differentiated Calu-3 respiratory epithelial cells with a donor-derived bacterial community, a commensal species (Lactobacillus sakei), or a pathobiont (Staphylococcus aureus). We also assessed how the incorporation of macrophage-like cells could have a steering effect on both epithelial cells and the microbial community. Inoculation of donor-derived microbiota in our experimental setup did not pose cytotoxic stress on the epithelial cell layers, as demonstrated by unaltered cytokine and lactate dehydrogenase release compared to a sterile control. Epithelial integrity of the differentiated Calu-3 cells was maintained as well, with no differences in transepithelial electrical resistance observed between coculture with donor-derived microbiota and a sterile control. Transition of nasal microbiota from in vivo to in vitro conditions maintained phylogenetic richness, and yet a decrease in phylogenetic and phenotypic diversity was noted. Additional inclusion and coculture of THP-1-derived macrophages did not alter phylogenetic diversity, and yet donor-independent shifts toward higher Moraxella and Mycoplasma abundance were observed, while phenotypic diversity was also increased. Our results demonstrate that coculture of differentiated airway epithelial cells with a healthy donor-derived nasal community is a viable strategy to mimic host-microbe interactions in the human upper respiratory tract. Importantly, including an immune component allowed us to study host-microbe interactions in the upper respiratory tract more in depth.IMPORTANCE Despite the relevance of the resident microbiota in sinonasal health and disease and the need for cross talk between immune and epithelial cells in the upper respiratory tract, these parameters have not been combined in a single in vitro model system. We have developed a coculture system of differentiated respiratory epithelium and natural nasal microbiota and incorporated an immune component. As indicated by absence of cytotoxicity and stable cytokine profiles and epithelial integrity, nasal microbiota from human origin appeared to be well tolerated by host cells, while microbial community composition remained representative for that of the human (sino)nasal cavity. Importantly, the introduction of macrophage-like cells enabled us to obtain a differential readout from the epithelial cells dependent on the donor microbial background to which the cells were exposed. We conclude that both model systems offer the means to investigate host-microbe interactions in the upper respiratory tract in a more representative way.},
}
@article {pmid31940957,
year = {2020},
author = {Xu, Y and Shen, Z and Gentekaki, E and Xu, J and Yi, Z},
title = {Comparative Transcriptome Analyses during the Vegetative Cell Cycle in the Mono-Cellular Organism Pseudokeronopsis erythrina (Alveolata, Ciliophora).},
journal = {Microorganisms},
volume = {8},
number = {1},
pages = {},
pmid = {31940957},
issn = {2076-2607},
support = {2018SDKJ0406-4//Pilot National Laboratory for Marine Science and Technology (Qingdao)/ ; 31772440//National Natural Science Foundation of China/ ; 31430077//National Natural Science Foundation of China/ ; 31970486//National Natural Science Foundation of China/ ; GDOE2019A23//Guangdong MEPP Fund/ ; },
abstract = {Studies focusing on molecular mechanisms of cell cycles have been lagging in unicellular eukaryotes compared to other groups. Ciliates, a group of unicellular eukaryotes, have complex cell division cycles characterized by multiple events. During their vegetative cell cycle, ciliates undergo macronuclear amitosis, micronuclear mitosis, stomatogenesis and somatic cortex morphogenesis, and cytokinesis. Herein, we used the hypotrich ciliate Pseudokeronopsis erythrina, whose morphogenesis has been well studied, to examine molecular mechanisms of ciliate vegetative cell cycles. Single-cell transcriptomes of the growth (G) and cell division (D) stages were compared. The results showed that (i) More than 2051 significantly differentially expressed genes (DEGs) were detected, among which 1545 were up-regulated, while 256 were down-regulated at the D stage. Of these, 11 randomly picked DEGs were validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR); (ii) Enriched DEGs during the D stage of the vegetative cell cycle of P. erythrina were involved in development, cortex modifications, and several organelle-related biological processes, showing correspondence of molecular evidence to morphogenetic changes for the first time; (iii) Several individual components of molecular mechanisms of ciliate vegetative division, the sexual cell cycle and cellular regeneration overlap; and (iv) The P. erythrina cell cycle and division have the same essential components as other eukaryotes, including cyclin-dependent kinases (CDKs), cyclins, and genes closely related to cell proliferation, indicating the conserved nature of this biological process. Further studies are needed focusing on detailed inventory and gene interactions that regulate specific ciliated cell-phase events.},
}
@article {pmid31937947,
year = {2020},
author = {Amaral-Zettler, LA and Zettler, ER and Mincer, TJ},
title = {Ecology of the plastisphere.},
journal = {Nature reviews. Microbiology},
volume = {18},
number = {3},
pages = {139-151},
pmid = {31937947},
issn = {1740-1534},
mesh = {Biodegradation, Environmental ; Environmental Pollutants ; *Microbiota ; *Plastics ; Waste Products ; },
abstract = {The plastisphere, which comprises the microbial community on plastic debris, rivals that of the built environment in spanning multiple biomes on Earth. Although human-derived debris has been entering the ocean for thousands of years, microplastics now numerically dominate marine debris and are primarily colonized by microbial and other microscopic life. The realization that this novel substrate in the marine environment can facilitate microbial dispersal and affect all aquatic ecosystems has intensified interest in the microbial ecology and evolution of this biotope. Whether a 'core' plastisphere community exists that is specific to plastic is currently a topic of intense investigation. This Review provides an overview of the microbial ecology of the plastisphere in the context of its diversity and function, as well as suggesting areas for further research.},
}
@article {pmid31937679,
year = {2020},
author = {Weissman, JL and Johnson, PLF},
title = {Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
pmid = {31937679},
issn = {2379-5077},
abstract = {A diversity of clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems provide adaptive immunity to bacteria and archaea through recording "memories" of past viral infections. Recently, many novel CRISPR-associated proteins have been discovered via computational studies, but those studies relied on biased and incomplete databases of assembled genomes. We avoided these biases and applied a network theory approach to search for novel CRISPR-associated genes by leveraging subtle ecological cooccurrence patterns identified from environmental metagenomes. We validated our method using existing annotations and discovered 32 novel CRISPR-associated gene families. These genes span a range of putative functions, with many potentially regulating the response to infection.IMPORTANCE Every branch on the tree of life, including microbial life, faces the threat of viral pathogens. Over the course of billions of years of coevolution, prokaryotes have evolved a great diversity of strategies to defend against viral infections. One of these is the CRISPR adaptive immune system, which allows microbes to "remember" past infections in order to better fight them in the future. There has been much interest among molecular biologists in CRISPR immunity because this system can be repurposed as a tool for precise genome editing. Recently, a number of comparative genomics approaches have been used to detect novel CRISPR-associated genes in databases of genomes with great success, potentially leading to the development of new genome-editing tools. Here, we developed novel methods to search for these distinct classes of genes directly in environmental samples ("metagenomes"), thus capturing a more complete picture of the natural diversity of CRISPR-associated genes.},
}
@article {pmid31937676,
year = {2020},
author = {Sedlacek, CJ and Giguere, AT and Dobie, MD and Mellbye, BL and Ferrell, RV and Woebken, D and Sayavedra-Soto, LA and Bottomley, PJ and Daims, H and Wagner, M and Pjevac, P},
title = {Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
pmid = {31937676},
issn = {2379-5077},
support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea's sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria.IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.},
}
@article {pmid31935341,
year = {2020},
author = {Bophela, KN and Petersen, Y and Bull, CT and Coutinho, TA},
title = {Identification of Pseudomonas Isolates Associated With Bacterial Canker of Stone Fruit Trees in the Western Cape, South Africa.},
journal = {Plant disease},
volume = {104},
number = {3},
pages = {882-892},
doi = {10.1094/PDIS-05-19-1102-RE},
pmid = {31935341},
issn = {0191-2917},
mesh = {*Fruit ; Phylogeny ; *Plant Diseases ; Pseudomonas syringae ; South Africa ; },
abstract = {Bacterial canker is a common bacterial disease of stone fruit trees. The causal agents responsible for the disease include several pathovars in Pseudomonas syringae sensu lato and newly described Pseudomonas species. Pseudomonad strains were isolated from symptomatic stone fruit trees, namely apricot, peach, and plum trees cultivated in spatially separated orchards in the Western Cape. A polyphasic approach was used to identify and characterize these strains. Using a multilocus sequence typing approach of four housekeeping loci, namely cts, gapA, gyrB, and rpoD, the pseudomonad strains were delineated into two phylogenetic groups within P. syringae sensu lato: P. syringae sensu stricto and Pseudomonas viridiflava. These results were further supported by LOPAT diagnostic assays and analysis of clades in the rep-PCR dendrogram. The pseudomonad strains were pathogenic on both apricot and plum seedlings, indicative of a lack of host specificity between Pseudomonas strains infecting Prunus spp. This is a first report of P. viridiflava isolated from plum trees showing symptoms of bacterial canker. P. viridiflava is considered to be an opportunistic pathogen that causes foliar diseases of vegetable crops, fruit trees, and aromatic herbs, and thus the isolation of pathogenic P. viridiflava from twigs of plum trees showing symptoms of bacterial canker suggests that this bacterial species is a potentially emerging stem canker pathogen of stone fruit trees in South Africa.},
}
@article {pmid31935110,
year = {2020},
author = {El Hage, R and Hernandez-Sanabria, E and Calatayud Arroyo, M and Van de Wiele, T},
title = {Supplementation of a propionate-producing consortium improves markers of insulin resistance in an in vitro model of gut-liver axis.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {318},
number = {5},
pages = {E742-E749},
doi = {10.1152/ajpendo.00523.2019},
pmid = {31935110},
issn = {1522-1555},
mesh = {Biomarkers ; Cytokines/metabolism ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*metabolism/microbiology ; Glycogen/metabolism ; Hep G2 Cells ; Hepatocytes/*metabolism ; Humans ; Inflammation/metabolism/microbiology ; Insulin Resistance/*physiology ; Liver/*metabolism/microbiology ; Propionates/*metabolism ; },
abstract = {Gut-liver cross talk is an important determinant of human health with profound effects on energy homeostasis. While gut microbes produce a huge range of metabolites, specific compounds such as short-chain fatty acids (SCFAs) can enter the portal circulation and reach the liver (Brandl K, Schnabl B. Curr Opin Gastroenterol 33: 128-133, 2017), a central organ involved in glucose homeostasis and diabetes control. Propionate is a major SCFA involved in activation of intestinal gluconeogenesis (IGN), thereby regulating food intake, enhancing insulin sensitivity, and leading to metabolic homeostasis. Although microbiome-modulating strategies may target the increased microbial production of propionate, it is not clear whether such an effect spreads through to the hepatic cellular level. Here, we designed a propionate-producing consortium using a selection of commensal gut bacteria, and we investigated how their delivered metabolites impact an in vitro enterohepatic model of insulin resistance. Glycogen storage on hepatocyte-like cells and inflammatory markers associated with insulin resistance were evaluated to understand the role of gut metabolites on gut-liver cross talk in a simulated scenario of insulin resistance. The metabolites produced by our consortium increased glycogen synthesis by ~57% and decreased proinflammatory markers such as IL-8 by 12%, thus elucidating the positive effect of our consortium on metabolic function and low-grade inflammation. Our results suggest that microbiota-derived products can be a promising multipurpose strategy to modulate energy homeostasis, with the potential ability to assist in managing metabolic diseases due to their adaptability.},
}
@article {pmid31932882,
year = {2020},
author = {Cleary, DFR and Polónia, ARM and Reijnen, BT and Berumen, ML and de Voogd, NJ},
title = {Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {103-119},
doi = {10.1007/s00248-019-01465-w},
pmid = {31932882},
issn = {1432-184X},
support = {PTDC/AAC-AMB/115304/2009//FCT/ ; SFRH/BPD/117563/2016//FCT/ ; },
mesh = {Animals ; Anthozoa/*microbiology ; Archaea/classification/isolation &amp; purification/*physiology ; Bacteria/classification/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Geologic Sediments/*microbiology ; Indian Ocean ; Microbiota ; Porifera/*microbiology ; Saudi Arabia ; Seawater/*microbiology ; },
abstract = {In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.},
}
@article {pmid31932881,
year = {2020},
author = {Ruiz-Rodríguez, M and Scheifler, M and Sanchez-Brosseau, S and Magnanou, E and West, N and Suzuki, M and Duperron, S and Desdevises, Y},
title = {Host Species and Body Site Explain the Variation in the Microbiota Associated to Wild Sympatric Mediterranean Teleost Fishes.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {212-222},
doi = {10.1007/s00248-020-01484-y},
pmid = {31932881},
issn = {1432-184X},
support = {SU-16-R-EMR-22-MICROFISH//Universit&#xe9; Sorbonne Paris Cit&#xe9;/ ; },
mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Fishes/*microbiology ; France ; Gastrointestinal Microbiome ; Gills/microbiology ; *Host Microbial Interactions ; Intestines/microbiology ; Mediterranean Sea ; *Microbiota ; Mucus/microbiology ; Skin/microbiology ; Species Specificity ; },
abstract = {Microorganisms are an important component in shaping the evolution of hosts and as such, the study of bacterial communities with molecular techniques is shedding light on the complexity of symbioses between bacteria and vertebrates. Teleost fish are a heterogeneous group that live in a wide variety of habitats, and thus a good model group to investigate symbiotic interactions and their influence on host biology and ecology. Here we describe the microbiota of thirteen teleostean species sharing the same environment in the Mediterranean Sea and compare bacterial communities among different species and body sites (external mucus, skin, gills, and intestine). Our results show that Proteobacteria is the dominant phylum present in fish and water. However, the prevalence of other bacterial taxa differs between fish and the surrounding water. Significant differences in bacterial diversity are observed among fish species and body sites, with higher diversity found in the external mucus. No effect of sampling time nor species individual was found. The identification of indicator bacterial taxa further supports that each body site harbors its own characteristic bacterial community. These results improve current knowledge and understanding of symbiotic relationships among bacteria and their fish hosts in the wild since the majority of previous studies focused on captive individuals.},
}
@article {pmid31929046,
year = {2020},
author = {Obata, O and Salar-Garcia, MJ and Greenman, J and Kurt, H and Chandran, K and Ieropoulos, I},
title = {Development of efficient electroactive biofilm in urine-fed microbial fuel cell cascades for bioelectricity generation.},
journal = {Journal of environmental management},
volume = {258},
number = {},
pages = {109992},
pmid = {31929046},
issn = {1095-8630},
mesh = {*Bioelectric Energy Sources ; Biofilms ; Electricity ; Electrodes ; Sewage ; },
abstract = {The Microbial fuel cell (MFC) technology harnesses the potential of some naturally occurring bacteria for electricity generation. Digested sludge is commonly used as the inoculum to initiate the process. There are, however, health hazards and practical issues associated with the use of digested sludge depending on its origin as well as the location for system deployment. This work reports the development of an efficient electroactive bacterial community within ceramic-based MFCs fed with human urine in the absence of sludge inoculum. The results show the development of a uniform bacterial community with power output levels equal to or higher than those generated from MFCs inoculated with sludge. In this case, the power generation begins within 2 days of the experimental set-up, compared to about 5 days in some sludge-inoculated MFCs, thus significantly reducing the start-up time. The metagenomics analysis of the successfully formed electroactive biofilm (EAB) shows significant shifts between the microbial ecology of the feeding material (fresh urine) and the developed anodic biofilm. A total of 21 bacteria genera were detected in the urine feedstock whilst up to 35 different genera were recorded in the developed biofilm. Members of Pseudomonas (18%) and Anaerolineaceae (17%) dominate the bacterial community of the fresh urine feed while members of Burkholderiaceae (up to 50%) and Tissierella (up to 29%) dominate the anodic EAB. These results highlight a significant shift in the bacterial community of the feedstock towards a selection and adaptation required for the various electrochemical reactions essential for survival through power generation.},
}
@article {pmid31927597,
year = {2020},
author = {Sun, F and Wang, C and Chen, H and Zheng, Z},
title = {Metagenomic Analysis of the Effect of Enteromorpha prolifera Bloom on Microbial Community and Function in Aquaculture Environment.},
journal = {Current microbiology},
volume = {77},
number = {5},
pages = {816-825},
pmid = {31927597},
issn = {1432-0991},
support = {2017A020216008//Guangdong Science and Technology Department/ ; 2016I1002//Fujian Provincial Department of Science and Technology/ ; 2017T3010//Fujian Provincial Department of Science and Technology/ ; },
mesh = {Actinomycetales/classification ; *Aquaculture ; *Eutrophication ; Flavobacteriaceae/classification ; *Metagenome ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Ulva/growth &amp; development/*metabolism ; Viruses/classification ; },
abstract = {Enteromorpha prolifera blooms considerably affected coastal environments in recent years. However, the effects of E. prolifera on microbial ecology and function remained unknown. In this study, metagenomic sequencing was used to investigate the effect of E. prolifera bloom on the microbial communities and functional genes in an aquaculture environment. Results showed that E. prolifera bloom could significantly alter the microbial composition and abundance, and heterotrophic bacteria comprised the major groups in the E. prolifera bloom pond, which was dominated by Actinomycetales and Flavobacteriales. The study indicated that viruses played an important role in shaping the microbial community and diversity during E. prolifera bloom. These viruses affected various dominant microbial taxa (such as Rhodobacteraceae, Synechococcus, and Prochlorococcus), which produced an obvious impact on potential nutrient transformation. Functional annotation analysis indicated that E. prolifera bloom would considerably shift the metabolism function by altering the structure and abundance of the microbial community. E. prolifera bloom pond had the low ability of potential metabolic capabilities of nitrogen, sulfur, and phosphate, whereas promoted gene abundance of genetic information processing. These changes in the microbial community and function could produce serious effect on aquaculture ecosystem.},
}
@article {pmid31926392,
year = {2020},
author = {Lepoutre, A and Hervieux, J and Faassen, EJ and Zweers, AJ and Lurling, M and Geffard, A and Lance, E},
title = {Usability of the bivalves Dreissena polymorpha and Anodonta anatina for a biosurvey of the neurotoxin BMAA in freshwater ecosystems.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {259},
number = {},
pages = {113885},
doi = {10.1016/j.envpol.2019.113885},
pmid = {31926392},
issn = {1873-6424},
mesh = {*Amino Acids, Diamino/analysis ; Animals ; *Anodonta/chemistry ; Cyanobacteria Toxins ; *Dreissena/chemistry ; Ecosystem ; *Environmental Monitoring/methods/standards ; *Fresh Water/chemistry ; *Water Pollutants, Chemical/analysis ; },
abstract = {The environmental neurotoxin β-methylamino-L-alanine (BMAA) may represent a risk for human health in case of chronic exposure or after short-term exposure during embryo development. BMAA accumulates in freshwater and marine organisms consumed by humans. It is produced by marine and freshwater phytoplankton species, but the range of producers remains unknown. Therefore, analysing the phytoplankton composition is not sufficient to inform about the risk of freshwater contamination by BMAA. Filter-feeders mussels have accumulation capacities and therefore appear to be relevant to monitor various pollutants in aquatic ecosystems. We investigated the suitability of the freshwater mussels Dreissena polymorpha and Anodonta anatina for monitoring BMAA in water. Both species were exposed to 1, 10, and 50 μg of dissolved BMAA/L daily for 21 days, followed by 42 days of depuration in clean water. On days 0, 1, 7, 14, and 21 of exposure and 1, 7, 14, 21 and 42 of depuration, whole D. polymorpha and digestive glands of A. anatina were sampled, and the total BMAA concentration was measured. D. polymorpha accumulated BMAA earlier (from day 1 at all concentrations) and at higher tissue concentrations than A. anatina, which accumulated BMAA from day 14 when exposed to 10 μg BMAA/L and from day 7 when exposed to 50 μg BMAA/L. As BMAA accumulation by D. polymorpha was time and concentration-dependent, with a significant elimination during the depuration period, this species may be able to reflect the levels and dynamics of water contamination by dissolved BMAA. The species A. anatina could be used for monitoring water concentrations above 10 μg BMAA/L.},
}
@article {pmid31925848,
year = {2020},
author = {Dove, NC and Safford, HD and Bohlman, GN and Estes, BL and Hart, SC},
title = {High-severity wildfire leads to multi-decadal impacts on soil biogeochemistry in mixed-conifer forests.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {30},
number = {4},
pages = {e02072},
doi = {10.1002/eap.2072},
pmid = {31925848},
issn = {1051-0761},
mesh = {Carbon ; Ecosystem ; Forests ; Soil ; *Tracheophyta ; *Wildfires ; },
abstract = {During the past century, systematic wildfire suppression has decreased fire frequency and increased fire severity in the western United States of America. While this has resulted in large ecological changes aboveground such as altered tree species composition and increased forest density, little is known about the long-term, belowground implications of altered, ecologically novel, fire regimes, especially on soil biological processes. To better understand the long-term implications of ecologically novel, high-severity fire, we used a 44-yr high-severity fire chronosequence in the Sierra Nevada where forests were historically adapted to frequent, low-severity fire, but were fire suppressed for at least 70 yr. High-severity fire in the Sierra Nevada resulted in a long-term (44 +yr) decrease (>50%, P < 0.05) in soil extracellular enzyme activities, basal microbial respiration (56-72%, P < 0.05), and organic carbon (>50%, P < 0.05) in the upper 5 cm compared to sites that had not been burned for at least 115 yr. However, nitrogen (N) processes were only affected in the most recent fire site (4 yr post-fire). Net nitrification increased by over 600% in the most recent fire site (P < 0.001), but returned to similar levels as the unburned control in the 13-yr site. Contrary to previous studies, we did not find a consistent effect of plant cover type on soil biogeochemical processes in mid-successional (10-50 yr) forest soils. Rather, the 44-yr reduction in soil organic carbon (C) quantity correlated positively with dampened C cycling processes. Our results show the drastic and long-term implication of ecologically novel, high-severity fire on soil biogeochemistry and underscore the need for long-term fire ecological experiments.},
}
@article {pmid31924621,
year = {2020},
author = {Suttner, B and Johnston, ER and Orellana, LH and Rodriguez-R, LM and Hatt, JK and Carychao, D and Carter, MQ and Cooley, MB and Konstantinidis, KT},
title = {Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {6},
pages = {},
pmid = {31924621},
issn = {1098-5336},
mesh = {Agriculture ; Animal Husbandry ; Animals ; California ; Geologic Sediments/*microbiology ; Livestock ; *Metagenomics ; Public Health/*methods ; Risk Assessment/*methods ; Rivers/microbiology ; Shiga-Toxigenic Escherichia coli/*isolation &amp; purification ; Water Pollution ; },
abstract = {Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens such as Shiga toxin-producing Escherichia coli (STEC) originating from these practices remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley of California was sampled over a 9-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and have functional and taxonomic diversity comparable to that observed in soils. With our sequencing effort (∼4 Gbp per library), we were unable to detect any pathogenic E. coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low abundance. Furthermore, there were no significant differences in the abundance of human- or cow-specific gut microbiome sequences in the downstream impacted sites compared to that in upstream more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, the high number of metagenomic reads carrying antibiotic resistance genes (ARGs) found in all samples was significantly higher than ARG reads in other available freshwater and soil metagenomes, suggesting that these communities may be natural reservoirs of ARGs. The work presented here should serve as a guide for sampling volumes, amount of sequencing to apply, and what bioinformatics analyses to perform when using metagenomics for public health risk studies of environmental samples such as sediments.IMPORTANCE Current agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food- and waterborne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health are assessed by culture-based tests for the intestinal bacterium Escherichia coli However, the accuracy of these traditional methods (e.g., low accuracy in quantification, and false-positive signal when PCR based) and their suitability for sediments remain unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the United States in order to assess how agricultural runoff affects the native microbial communities and if the presence of Shiga toxin-producing Escherichia coli (STEC) in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.},
}
@article {pmid31924617,
year = {2020},
author = {Bai, C and Cai, J and Zhou, L and Jiang, X and Hu, Y and Dai, J and Shao, K and Tang, X and Yang, X and Gao, G},
title = {Geographic Patterns of Bacterioplankton among Lakes of the Middle and Lower Reaches of the Yangtze River Basin, China.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {6},
pages = {},
pmid = {31924617},
issn = {1098-5336},
mesh = {*Bacterial Physiological Phenomena ; China ; Geography ; Lakes/*microbiology ; *Microbiota ; Phytoplankton/*physiology ; Population Density ; Rivers/microbiology ; Seasons ; },
abstract = {The revolution of molecular techniques has revealed that the composition of natural bacterial communities normally includes a few abundant taxa and many rare taxa. Unraveling the mechanisms underlying the spatial assembly process of both abundant and rare bacterial taxa has become a central goal in microbial ecology. Here, we used high-throughput sequencing to explore geographic patterns and the relative importance of ecological processes in the assembly of abundant and rare bacterial subcommunities from 25 lakes across the middle and lower reaches of Yangtze River basin (MLYB), located in Southeast China, where most of the lakes are interconnected by river networks. We found similar biogeographic patterns of abundant and rare subcommunities which could significantly distinguish the community compositions of the two lake groups that were far from each other but which could not distinguish the community compositions of the nearby lakes. Both abundant and rare bacteria followed a strong distance-decay relationship. These findings suggest that the interconnectivity between lakes homogenizes the bacterial communities in local areas, and the abundant and rare taxa therein may be affected by the same ecological process. In addition, based on the measured environmental variables, the deterministic processes explain a small fraction of variation within both abundant and rare subcommunities, while both neutral and null models revealed a high stochasticity ratio for the spatial distribution patterns of both abundant and rare taxa. These findings indicate that the stochastic processes exhibited a greater influence on both abundant and rare bacterial subcommunity assemblies among interconnected lakes.IMPORTANCE The middle and lower Yangtze Plain is a typical floodplain in which many lakes connect with each other, especially in the wet season. More importantly, with the frequent change of regional water level in the wet season, there is a mutual hydrodynamic exchange among these lakes. The microbial biogeography among these interconnected lakes is still poorly understood. This study aims to unravel the mechanisms underlying the assembly process of abundant and rare bacteria among the interconnected lakes in the middle and lower Yangtze Plain. Our findings will provide a deeper understanding of the biogeographic patterns of rare and abundant bacterial taxa and their determined processes among interconnected aquatic habitats.},
}
@article {pmid31924214,
year = {2020},
author = {Shuai, Y and Ma, Z and Liu, W and Yu, T and Yan, C and Jiang, H and Tian, S and Xu, T and Shu, Y},
title = {TEAD4 modulated LncRNA MNX1-AS1 contributes to gastric cancer progression partly through suppressing BTG2 and activating BCL2.},
journal = {Molecular cancer},
volume = {19},
number = {1},
pages = {6},
pmid = {31924214},
issn = {1476-4598},
mesh = {Animals ; Apoptosis ; Biomarkers, Tumor/genetics/*metabolism ; Cell Movement ; Cell Proliferation ; DNA-Binding Proteins/genetics/*metabolism ; Disease Progression ; Female ; *Gene Expression Regulation, Neoplastic ; Homeodomain Proteins/antagonists &amp; inhibitors ; Humans ; Immediate-Early Proteins/genetics/*metabolism ; Male ; Mice ; Mice, Nude ; MicroRNAs/genetics ; Middle Aged ; Muscle Proteins/genetics/*metabolism ; Neoplasm Invasiveness ; Prognosis ; Proto-Oncogene Proteins c-bcl-2/genetics/*metabolism ; RNA, Antisense/genetics ; RNA, Long Noncoding/*genetics ; Stomach Neoplasms/genetics/metabolism/*pathology ; Survival Rate ; TEA Domain Transcription Factors ; Transcription Factors/antagonists &amp; inhibitors/genetics/*metabolism ; Tumor Cells, Cultured ; Tumor Suppressor Proteins/genetics/*metabolism ; Xenograft Model Antitumor Assays ; },
abstract = {BACKGROUND: Gastric cancer (GC) is the third leading cause of cancer-related mortality globally. Long noncoding RNAs (lncRNAs) are dysregulated in obvious malignancies including GC and exploring the regulatory mechanisms underlying their expression is an attractive research area. However, these molecular mechanisms require further clarification, especially upstream mechanisms.<br><br>METHODS: LncRNA MNX1-AS1 expression in GC tissue samples was investigated via microarray analysis and further determined in a cohort of GC tissues via quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays. Cell proliferation and flow cytometry assays were performed to confirm the roles of MNX1-AS1 in GC proliferation, cell cycle regulation, and apoptosis. The influence of MNX1-AS1 on GC cell migration and invasion was explored with Transwell assays. A xenograft tumour model was established to verify the effects of MNX1-AS1 on in vivo tumourigenesis. The TEAD4-involved upstream regulatory mechanism of MNX1-AS1 was explored through ChIP and luciferase reporter assays. The mechanistic model of MNX1-AS1 in regulating gene expression was further detected by subcellular fractionation, FISH, RIP, ChIP and luciferase reporter assays.<br><br>RESULTS: It was found that MNX1-AS1 displayed obvious upregulation in GC tissue samples and cell lines, and ectopic expression of MNX1-AS1 predicted poor clinical outcomes for patients with GC. Overexpressed MNX1-AS1 expression promoted proliferation, migration and invasion of GC cells markedly, whereas decreased MNX1-AS1 expression elicited the opposite effects. Consistent with the in vitro results, MNX1-AS1 depletion effectively inhibited the growth of xenograft tumour in vivo. Mechanistically, TEAD4 directly bound the promoter region of MNX1-AS1 and stimulated the transcription of MNX1-AS1. Furthermore, MNX1-AS1 can sponge miR-6785-5p to upregulate the expression of BCL2 in GC cells. Meanwhile, MNX1-AS1 suppressed the transcription of BTG2 by recruiting polycomb repressive complex 2 to BTG2 promoter regions.<br><br>CONCLUSIONS: Our findings demonstrate that MNX1-AS1 may be able to serve as a prognostic indicator in GC patients and that TEAD4-activatd MNX1-AS1 can promote GC progression through EZH2/BTG2 and miR-6785-5p/BCL2 axes, implicating it as a novel and potent target for the treatment of GC.},
}
@article {pmid31924126,
year = {2020},
author = {Agudelo-Ochoa, GM and Valdés-Duque, BE and Giraldo-Giraldo, NA and Jaillier-Ramírez, AM and Giraldo-Villa, A and Acevedo-Castaño, I and Yepes-Molina, MA and Barbosa-Barbosa, J and Benítez-Paéz, A},
title = {Gut microbiota profiles in critically ill patients, potential biomarkers and risk variables for sepsis.},
journal = {Gut microbes},
volume = {12},
number = {1},
pages = {1707610},
pmid = {31924126},
issn = {1949-0984},
mesh = {APACHE ; Adult ; Bacteria/*classification/genetics/*isolation &amp; purification ; Biomarkers ; Case-Control Studies ; Critical Care ; Critical Illness ; Female ; Gastrointestinal Microbiome/*genetics/physiology ; Humans ; Inflammation/pathology ; Intestines/*microbiology ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Sepsis/*microbiology/pathology ; Young Adult ; },
abstract = {Critically ill patients are physiologically unstable and recent studies indicate that the intestinal microbiota could be involved in the health decline of such patients during ICU stays. This study aims to assess the intestinal microbiota in critically ill patients with and without sepsis and to determine its impact on outcome variables, such as medical complications, ICU stay time, and mortality. A multi-center study was conducted with a total of 250 peri-rectal swabs obtained from 155 patients upon admission and during ICU stays. Intestinal microbiota was assessed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Linear mixed models were used to integrate microbiota data with more than 40 clinical and demographic variables to detect covariates and minimize the effect of confounding factors. We found that the microbiota of ICU patients with sepsis has an increased abundance of microbes tightly associated with inflammation, such as Parabacteroides, Fusobacterium and Bilophila species. Female sex and aging would represent an increased risk for sepsis possibly because of some of their microbiota features. We also evidenced a remarkable loss of microbial diversity, during the ICU stay. Concomitantly, we detected that the abundance of pathogenic species, such as Enterococcus spp., was differentially increased in sepsis patients who died, indicating these species as potential biomarkers for monitoring during ICU stay. We concluded that particular intestinal microbiota signatures could predict sepsis development in ICU patients. We propose potential biomarkers for evaluation in the clinical management of ICU patients.},
}
@article {pmid31924109,
year = {2020},
author = {Triplett, J and Ellis, D and Braddock, A and Roberts, E and Ingram, K and Perez, E and Short, A and Brown, D and Hutzley, V and Webb, C and Soto, A and Chan, V},
title = {Temporal and region-specific effects of sleep fragmentation on gut microbiota and intestinal morphology in Sprague Dawley rats.},
journal = {Gut microbes},
volume = {11},
number = {4},
pages = {706-720},
pmid = {31924109},
issn = {1949-0984},
mesh = {Animals ; Bacterial Adhesion ; Bacterial Physiological Phenomena ; Cecum/microbiology/*pathology ; Colon/microbiology/*pathology ; Cytokines/analysis ; Endotoxins/analysis ; *Gastrointestinal Microbiome ; Hypothalamo-Hypophyseal System/physiology ; Ileum/microbiology/*pathology ; Phylogeny ; Rats ; Rats, Sprague-Dawley ; *Sleep Deprivation/microbiology/pathology/physiopathology ; },
abstract = {Sleep is a fundamental biological process, that when repeatedly disrupted, can result in severe health consequences. Recent studies suggest that both sleep fragmentation (SF) and dysbiosis of the gut microbiome can lead to metabolic disorders, though the underlying mechanisms are largely unclear. To better understand the consequences of SF, we investigated the effects of acute (6 days) and chronic (6 weeks) SF on rats by examining taxonomic profiles of microbiota in the distal ileum, cecum and proximal colon, as well as assessing structural and functional integrity of the gastrointestinal barrier. We further assayed the impact of SF on a host function by evaluating inflammation and immune response. Both acute and chronic SF induced microbial dysbiosis, more dramatically in the distal ileum (compared to other two regions studied), as noted by significant perturbations in alpha- and beta-diversity; though, specific microbial populations were significantly altered throughout each of the three regions. Furthermore, chronic SF resulted in increased crypt depth in the distal ileum and an increase in the number of villi lining both the cecum and proximal colon. Additional changes were noted with chronic SF, including: decreased microbial adhesion and penetration in the distal ileum and cecum, elevation in serum levels of the cytokine KC/GRO, and depressed levels of corticotropin. Importantly, our data show that perturbations to microbial ecology and intestinal morphology intensify in response to prolonged SF and these changes are habitat specific. Together, these results reveal consequences to gut microbiota homeostasis and host response following acute and chronic SF in rats.},
}
@article {pmid31922946,
year = {2020},
author = {Studholme, DJ and Wicker, E and Abrare, SM and Aspin, A and Bogdanove, A and Broders, K and Dubrow, Z and Grant, M and Jones, JB and Karamura, G and Lang, J and Leach, J and Mahuku, G and Nakato, GV and Coutinho, T and Smith, J and Bull, CT},
title = {Transfer of Xanthomonas campestris pv. arecae and X. campestris pv. musacearum to X. vasicola (Vauterin) as X. vasicola pv. arecae comb. nov. and X. vasicola pv. musacearum comb. nov. and Description of X. vasicola pv. vasculorum pv. nov.},
journal = {Phytopathology},
volume = {110},
number = {6},
pages = {1153-1160},
doi = {10.1094/PHYTO-03-19-0098-LE},
pmid = {31922946},
issn = {0031-949X},
mesh = {Areca ; *Musa ; Plant Diseases ; *Xanthomonas ; *Xanthomonas campestris ; },
abstract = {We present an amended description of the bacterial species Xanthomonas vasicola to include the causative agent of banana Xanthomonas wilt, as well as strains that cause disease on Areca palm, Tripsacum grass, sugarcane, and maize. Genome-sequence data reveal that these strains all share more than 98% average nucleotide with each other and with the type strain. Our analyses and proposals should help to resolve the taxonomic confusion that surrounds some of these pathogens and help to prevent future use of invalid names.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.},
}
@article {pmid31922546,
year = {2020},
author = {Morris, MM and Frixione, NJ and Burkert, AC and Dinsdale, EA and Vannette, RL},
title = {Microbial abundance, composition, and function in nectar are shaped by flower visitor identity.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {3},
pages = {},
doi = {10.1093/femsec/fiaa003},
pmid = {31922546},
issn = {1574-6941},
mesh = {Animals ; Bees ; Birds ; Flowers ; *Microbiota ; *Plant Nectar ; Pollination ; },
abstract = {Microbial dispersal is essential for establishment in new habitats, but the role of vector identity is poorly understood in community assembly and function. Here, we compared microbial assembly and function in floral nectar visited by legitimate pollinators (hummingbirds) and nectar robbers (carpenter bees). We assessed effects of visitation on the abundance and composition of culturable bacteria and fungi and their taxonomy and function using shotgun metagenomics and nectar chemistry. We also compared metagenome-assembled genomes (MAGs) of Acinetobacter, a common and highly abundant nectar bacterium, among visitor treatments. Visitation increased microbial abundance, but robbing resulted in 10× higher microbial abundance than pollination. Microbial communities differed among visitor treatments: robbed flowers were characterized by predominant nectar specialists within Acetobacteraceae and Metschnikowiaceae, with a concurrent loss of rare taxa, and these resulting communities harbored genes relating to osmotic stress, saccharide metabolism and specialized transporters. Gene differences were mirrored in function: robbed nectar contained a higher percentage of monosaccharides. Draft genomes of Acinetobacter revealed distinct amino acid and saccharide utilization pathways in strains isolated from robbed versus pollinated flowers. Our results suggest an unrecognized cost of nectar robbing for pollination and distinct effects of visitor type on interactions between plants and pollinators. Overall, these results suggest vector identity is an underappreciated factor structuring microbial community assembly and function.},
}
@article {pmid31922045,
year = {2020},
author = {Chakraborty, A and DasGupta, CK and Bhadury, P},
title = {Diversity of Betaproteobacteria revealed by novel primers suggests their role in arsenic cycling.},
journal = {Heliyon},
volume = {6},
number = {1},
pages = {e03089},
pmid = {31922045},
issn = {2405-8440},
abstract = {High arsenic concentration in groundwater is a severe environmental problem affecting human health, particularly in countries of South and South-East Asia. The Bengal Delta Plain (BDP) distributed within India and Bangladesh is a major arsenic-affected region where groundwater is the primary source of drinking water. Previous studies have indicated that members of the bacterial class Betaproteobacteria constitute a major fraction of the microbial community in many of the aquifers within this region. Bacteria belonging to this class are known to be involved in redox cycling of arsenic as well as other metals such iron and manganese, thereby impacting arsenic mobilization and immobilization. While microbial diversity in arsenic-contaminated environments is generally assessed using universal 16S rRNA gene primers, targeted evaluation of Betaproteobacteria diversity remains poorly constrained. In this study, bacterial diversity was investigated in the groundwater from two shallow aquifers (West Bengal, India) based on 16S rRNA gene clone libraries and sequencing using a custom-designed pair of primers specific to Betaproteobacteria. Specificity of the primers was confirmed in silico as well as by the absence of PCR amplification of other bacterial classes. Four major families (Burkholderiaceae, Comamonadaceae, Gallionellaceae and Rhodocyclaceae) were detected among which members of Burkholderiaceae represented 59% and 71% of the total community in each aquifer. The four OTUs (operational taxonomic units; 97% sequence identity) within Burkholderiaceae were close phylogenetic relatives of bacteria within the genus Burkholderia known to solubilize phosphate minerals. Additionally, the OTUs belonging to Gallionellaceae were closely related to the members of the genera Gallionella and Sideroxydans, known to oxidize iron under microaerophilic conditions. These results suggest that members of Betaproteobacteria can potentially influence iron and phosphorus cycling which can influence biogeochemistry in arsenic-contaminated aquifers of the BDP.},
}
@article {pmid31921433,
year = {2020},
author = {Klaps, J and Lievens, B and Álvarez-Pérez, S},
title = {Towards a better understanding of the role of nectar-inhabiting yeasts in plant-animal interactions.},
journal = {Fungal biology and biotechnology},
volume = {7},
number = {},
pages = {1},
pmid = {31921433},
issn = {2054-3085},
abstract = {Flowers offer a wide variety of substrates suitable for fungal growth. However, the mycological study of flowers has only recently begun to be systematically addressed from an ecological point of view. Most research on the topic carried out during the last decade has focused on studying the prevalence and diversity of flower-inhabiting yeasts, describing new species retrieved from floral parts and animal pollinators, and the use of select nectar yeasts as model systems to test ecological hypotheses. In this primer article, we summarize the current state of the art in floral nectar mycology and provide an overview of some research areas that, in our view, still require further attention, such as the influence of fungal volatile organic compounds on the foraging behavior of pollinators and other floral visitors, the analysis of the direct and indirect effects of nectar-inhabiting fungi on the fitness of plants and animals, and the nature and consequences of fungal-bacterial interactions taking place within flowers.},
}
@article {pmid31921095,
year = {2019},
author = {Hounmanou, YMG and Leekitcharoenphon, P and Hendriksen, RS and Dougnon, TV and Mdegela, RH and Olsen, JE and Dalsgaard, A},
title = {Corrigendum: Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2974},
doi = {10.3389/fmicb.2019.02974},
pmid = {31921095},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.00901.].},
}
@article {pmid31921014,
year = {2019},
author = {Calabrese, F and Voloshynovska, I and Musat, F and Thullner, M and Schlömann, M and Richnow, HH and Lambrecht, J and Müller, S and Wick, LY and Musat, N and Stryhanyuk, H},
title = {Quantitation and Comparison of Phenotypic Heterogeneity Among Single Cells of Monoclonal Microbial Populations.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2814},
pmid = {31921014},
issn = {1664-302X},
abstract = {Phenotypic heterogeneity within microbial populations arises even when the cells are exposed to putatively constant and homogeneous conditions. The outcome of this phenomenon can affect the whole function of the population, resulting in, for example, new "adapted" metabolic strategies and impacting its fitness at given environmental conditions. Accounting for phenotypic heterogeneity becomes thus necessary, due to its relevance in medical and applied microbiology as well as in environmental processes. Still, a comprehensive evaluation of this phenomenon requires a common and unique method of quantitation, which allows for the comparison between different studies carried out with different approaches. Consequently, in this study, two widely applicable indices for quantitation of heterogeneity were developed. The heterogeneity coefficient (HC) is valid when the population follows unimodal activity, while the differentiation tendency index (DTI) accounts for heterogeneity implying outbreak of subpopulations and multimodal activity. We demonstrated the applicability of HC and DTI for heterogeneity quantitation on stable isotope probing with nanoscale secondary ion mass spectrometry (SIP-nanoSIMS), flow cytometry, and optical microscopy datasets. The HC was found to provide a more accurate and precise measure of heterogeneity, being at the same time consistent with the coefficient of variation (CV) applied so far. The DTI is able to describe the differentiation in single-cell activity within monoclonal populations resolving subpopulations with low cell abundance, individual cells with similar phenotypic features (e.g., isotopic content close to natural abundance, as detected with nanoSIMS). The developed quantitation approach allows for a better understanding on the impact and the implications of phenotypic heterogeneity in environmental, medical and applied microbiology, microbial ecology, cell biology, and biotechnology.},
}
@article {pmid31915852,
year = {2020},
author = {Baños, I and Montero, MF and Benavides, M and Arístegui, J},
title = {INT Toxicity over Natural Bacterial Assemblages from Surface Oligotrophic Waters: Implications for the Assessment of Respiratory Activity.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {237-242},
doi = {10.1007/s00248-019-01479-4},
pmid = {31915852},
issn = {1432-184X},
support = {BES-2016- 078407//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; CTM2015-69392-C3-1-R//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; },
mesh = {Bacteria/*drug effects/metabolism ; Fresh Water/microbiology ; Oxygen Consumption/*drug effects ; Plankton/*drug effects/metabolism ; Seawater/microbiology ; Spain ; Tetrazolium Salts/*toxicity ; },
abstract = {Plankton community respiration (R) is a major component of the carbon flux in aquatic ecosystems. However, current methods to measure actual respiration from oxygen consumption at relevant spatial scales are not sensitive enough in oligotrophic environments where respiration rates are very low. To overcome this drawback, more sensitive indirect enzymatic approaches are commonly used as R proxies. The in vivo electron transport system (ETSvivo) assay, which measures the reduction of (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl tetrazolium chloride salt, INT) to INT-formazan in the presence of natural substrate levels, was recently proposed as an indirect reliable estimation of R for natural plankton communities. However, under in vivo conditions, formazan salts could be toxic to the cells. Here, we test the toxicity of 0.2 mM of final INT concentration, widely used for ETSvivo assays, on natural bacterial assemblages collected in coastal and oceanic waters off Gran Canaria (Canary Islands, subtropical North Atlantic), in eight independent experiments. After 0.5 h of incubation, a significant but variable decline in cell viability (14-49%) was observed in all samples inoculated with INT. Moreover, INT also inhibited leucine uptake in less than 90 min of incubation. In the light of these results, we argue that enzymatic respiratory rates obtained with the ETSvivo method need to be interpreted with caution to derive R in oceanic regions where bacteria largely contribute to community respiration. Moreover, the variable toxicity on bacterial assemblages observed in our experiments questions the use of a single R/ETSvivo relationship as a universal proxy for regional studies.},
}
@article {pmid31915217,
year = {2020},
author = {Schnizlein, MK and Vendrov, KC and Edwards, SJ and Martens, EC and Young, VB},
title = {Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization.},
journal = {mSphere},
volume = {5},
number = {1},
pages = {},
pmid = {31915217},
issn = {2379-5042},
support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; T32 DK094775/DK/NIDDK NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; Cefoperazone/therapeutic use ; Clostridioides difficile/*drug effects ; Clostridium Infections/microbiology/*prevention &amp; control ; Dietary Fiber/*administration &amp; dosage ; Dietary Supplements ; Disease Susceptibility ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Polysaccharides, Bacterial/*administration &amp; dosage ; Specific Pathogen-Free Organisms ; },
abstract = {Dietary fiber provides a variety of microbiota-mediated benefits ranging from anti-inflammatory metabolites to pathogen colonization resistance. A healthy gut microbiota protects against Clostridioides difficile colonization. Manipulation of these microbes through diet may increase colonization resistance to improve clinical outcomes. The primary objective of this study was to identify how the dietary fiber xanthan gum affects the microbiota and C. difficile colonization. We added 5% xanthan gum to the diet of C57BL/6 mice and examined its effect on the microbiota through 16S rRNA gene amplicon sequencing and short-chain fatty acid analysis. Following either cefoperazone or an antibiotic cocktail administration, we challenged mice with C. difficile and measured colonization by monitoring the CFU. Xanthan gum administration is associated with increases in fiber-degrading taxa and short-chain fatty acid concentrations. However, by maintaining both the diversity and absolute abundance of the microbiota during antibiotic treatment, the protective effects of xanthan gum administration on the microbiota were more prominent than the enrichment of these fiber-degrading taxa. As a result, mice that were on the xanthan gum diet experienced limited to no C. difficile colonization. Xanthan gum administration alters mouse susceptibility to C. difficile colonization by maintaining the microbiota during antibiotic treatment. While antibiotic-xanthan gum interactions are not well understood, xanthan gum has previously been used to bind drugs and alter their pharmacokinetics. Thus, xanthan gum may alter the activity of the oral antibiotics used to make the microbiota susceptible. Future research should further characterize how this and other common dietary fibers interact with drugs.IMPORTANCE A healthy gut bacterial community benefits the host by breaking down dietary nutrients and protecting against pathogens. Clostridioides difficile capitalizes on the absence of this community to cause diarrhea and inflammation. Thus, a major clinical goal is to find ways to increase resistance to C. difficile colonization by either supplementing with bacteria that promote resistance or a diet to enrich for those already present in the gut. In this study, we describe an interaction between xanthan gum, a human dietary additive, and the microbiota resulting in an altered gut environment that is protective against C. difficile colonization.},
}
@article {pmid31911465,
year = {2020},
author = {Li, P and Li, W and Dumbrell, AJ and Liu, M and Li, G and Wu, M and Jiang, C and Li, Z},
title = {Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
pmid = {31911465},
issn = {2379-5077},
abstract = {Fungi underpin almost all terrestrial ecosystem functions, yet our understanding of their community ecology lags far behind that of other organisms. Here, red paddy soils in subtropical China were collected across a soil depth profile, comprising 0-to-10-cm- (0-10cm-), 10-20cm-, and 20-40cm-deep layers. Using Illumina MiSeq amplicon sequencing of the internal transcribed spacer (ITS) region, distance-decay relationships (DDRs), and ecological models, fungal assemblages and their spatial patterns were investigated from each soil depth. We observed significant spatial variation in fungal communities and found that environmental heterogeneity decreased with soil depth, while spatial variation in fungal communities showed the opposite trend. DDRs occurred only in 0-10cm- and 10-20cm-deep soil layers, not in the 20-40cm layer. Our analyses revealed that the fungal community assembly in the 0-10cm layer was primarily governed by environmental filtering and a high dispersal rate, while in the deeper layer (20-40cm), it was primarily governed by dispersal limitation with minimal environmental filtering. Both environmental filtering and dispersal limitation controlled fungal community assembly in the 10-20cm layer, with dispersal limitation playing the major role. Results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Effectively, "everything is everywhere, but the environment selects," although only in shallower soils that are easily accessible to dispersive fungal propagules. This work highlights that perceived drivers of fungal community assembly are dependent on sampling depth, suggesting that caution is required when interpreting diversity patterns from samples that integrate across depths.IMPORTANCE In this work, Illumina MiSeq amplicon sequencing of the ITS region was used to investigate the spatial variation and assembly mechanisms of fungal communities from different soil layers across paddy fields in subtropical China, and the results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Therefore, the results of this study highlight that perceived drivers of fungal community assembly are dependent on sampling depth and suggest that caution is required when interpreting diversity patterns from samples that integrate across depths. This is the first study focusing on assemblages of fungal communities in different soil layers on a relatively large scale, and we thus believe that this study is of great importance to researchers and readers in microbial ecology, especially in microbial biogeography, because the results can provide sampling guidance in future studies of microbial biogeography.},
}
@article {pmid31909618,
year = {2020},
author = {Van den Abbeele, P and Moens, F and Pignataro, G and Schnurr, J and Ribecco, C and Gramenzi, A and Marzorati, M},
title = {Yeast-Derived Formulations Are Differentially Fermented by the Canine and Feline Microbiome As Assessed in a Novel In Vitro Colonic Fermentation Model.},
journal = {Journal of agricultural and food chemistry},
volume = {68},
number = {46},
pages = {13102-13110},
doi = {10.1021/acs.jafc.9b05085},
pmid = {31909618},
issn = {1520-5118},
mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Cats ; Colon/*microbiology ; Dietary Supplements/analysis ; Dogs ; Fatty Acids, Volatile/*metabolism ; Fermentation ; *Gastrointestinal Microbiome ; Yeasts/*chemistry/metabolism ; },
abstract = {The current study evaluated the effect of five yeast-derived formulations (T1-T5) on microbial metabolism and composition of the canine and feline gut microbiota using a novel in vitro colonic incubation approach. This novel in vitro model allowed for growth of the entire spectrum of dog- and cat-derived bacteria from the inoculum, thus offering an excellent platform to evaluate effects of nutritional interventions on the gut microbiota. Further, yeast-derived ingredients differentially increased production of acetate, propionate, butyrate, ammonium, and branched short-chain fatty acids, with T5 and T1 consistently stimulating propionate and butyrate, respectively. 16S-targeted Illumina sequencing coupled with flow cytometry provided unprecedented high-resolution quantitative insights in canine and feline microbiota modulation by yeast-derived ingredients, revealing that effects on propionate production were related to Prevotellaceae, Tannerellaceae, Bacteroidaceae, and Veillonellaceae members, while effects on butyrate production were related to Erysipelotrichaceae, Lachnospiraceae, Ruminococcaceae, and Fusobacteriaceae. Overall, these findings strengthen the health-promoting potential of yeast-derived ingredients.},
}
@article {pmid31897988,
year = {2020},
author = {Zhang, D and Luther, AK and Clauwaert, P and Ciccioli, P and Ronsse, F},
title = {Assessment of carbon recovery from solid organic wastes by supercritical water oxidation for a regenerative life support system.},
journal = {Environmental science and pollution research international},
volume = {27},
number = {8},
pages = {8260-8270},
pmid = {31897988},
issn = {1614-7499},
support = {201406350071//China Sponsorship Council/ ; 4000113452/15/NL/AT//European Space Agency/ ; DOZA/DDC/AM/DL/171b-2015//Universiteit Gent/ ; },
mesh = {Carbon/*analysis/chemistry ; Life Support Systems ; Oxidation-Reduction ; *Solid Waste/analysis ; Waste Disposal, Fluid ; *Water ; },
abstract = {The carbon recovery from organic space waste by supercritical water oxidation (SCWO) was studied to support resource recovery in a regenerative life support system. Resource recovery is of utmost importance in such systems which only have a limited total amount of mass. However, the practical waste treatment strategies for solid space wastes employed today are only storing and disposal without further recovery. This work assesses the performance of SCWO at recovering organic wastes as CO2 and water, to discuss the superiority of SCWO over most present strategies, and to evaluate the different SCWO reactor systems for space application. Experiments were carried out with a batch and a continuous reactor at different reaction conditions. The liquid and gas products distribution were analyzed to understand the conversion of organics in SCWO. Up to 97% and 93% of the feed carbon were recovered as CO2 in the continuous and the batch reactor, respectively. Residual carbon was mostly found as soluble organics in the effluent. Compared with the batch reactor, the continuous reactor system demonstrated a ten times higher capacity within the same reactor volume, while the batch reactor system was capable of handling feeds that contained particulate matter though suffering from poor heat integration (hence low-energy efficiency) and inter-batch variability. It was concluded that SCWO could be a promising technology to treat solid wastes for space applications. A continuous reactor would be more suitable for a regenerative life support system.},
}
@article {pmid31897570,
year = {2020},
author = {Donati, I and Cellini, A and Sangiorgio, D and Vanneste, JL and Scortichini, M and Balestra, GM and Spinelli, F},
title = {Pseudomonas syringae pv. actinidiae: Ecology, Infection Dynamics and Disease Epidemiology.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {81-102},
pmid = {31897570},
issn = {1432-184X},
support = {613678//Seventh Framework Programme/ ; },
mesh = {Actinidia/*physiology ; Plant Diseases/*microbiology ; Plant Leaves/microbiology/physiology ; Pseudomonas syringae/*physiology ; },
abstract = {Since 2008, the kiwifruit industry has been devastated by a pandemic outbreak of Pseudomonas syringae pv. actinidiae (Psa), the causal agent of bacterial canker. This disease has become the most significant limiting factor in kiwifruit production. Psa colonizes different organs of the host plant, causing a specific symptomatology on each of them. In addition, the systemic invasion of the plant may quickly lead to plant death. Despite the massive risk that this disease poses to the kiwifruit industry, studies focusing on Psa ecology have been sporadic, and a comprehensive description of the disease epidemiology is still missing. Optimal environmental conditions for infection, dispersal and survival in the environment, or the mechanisms of penetration and colonization of host tissues have not been fully elucidated yet. The present work aims to provide a synthesis of the current knowledge, and a deeper understanding of the epidemiology of kiwifruit bacterial canker based on new experimental data. The pathogen may survive in the environment or overwinter in dormant tissues and be dispersed by wind or rain. Psa was observed in association with several plant structures (stomata, trichomes, lenticels) and wounds, which could represent entry points for apoplast infection. Environmental conditions also affect the bacterial colonization, with lower optimum values of temperature and humidity for epiphytic than for endophytic growth, and disease incidence requiring a combination of mild temperature and leaf wetness. By providing information on Psa ecology, these data sets may contribute to plan efficient control strategies for kiwifruit bacterial canker.},
}
@article {pmid31897569,
year = {2020},
author = {Floc'h, JB and Hamel, C and Harker, KN and St-Arnaud, M},
title = {Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {762-777},
doi = {10.1007/s00248-019-01475-8},
pmid = {31897569},
issn = {1432-184X},
mesh = {Alberta ; Brassica napus/*microbiology ; *Crop Production/methods ; Fungi/*isolation &amp; purification ; Mycobiome/*physiology ; *Rhizosphere ; Saskatchewan ; Seasons ; },
abstract = {Rhizosphere microbes influence one another, forming extremely complex webs of interactions that may determine plant success. Identifying the key factors that structure the fungal microbiome of the plant rhizosphere is a necessary step in optimizing plant production. In a long-term field experiment conducted at three locations in the Canadian prairies, we tested the following hypotheses: (1) diversification of cropping systems influences the fungal microbiome of the canola (Brassica napus) rhizosphere; (2) the canola rhizosphere has a core fungal microbiome, i.e., a set of fungi always associated with canola; and (3) some taxa within the rhizosphere microbiome of canola are highly interrelated and fit the description of hub taxa. Our results show that crop diversification has a significant effect on the structure of the rhizosphere fungal community but not on fungal diversity. We also discovered and described a canola core microbiome made up of one zero-radius operational taxonomic unit (ZOTU), cf. Olpidium brassicae, and an eco-microbiome found only in 2013 consisting of 47 ZOTUs. Using network analysis, we identified four hub taxa in 2013: ZOTU14 (Acremonium sp.), ZOTU28 (Sordariomycetes sp.), ZOTU45 (Mortierella sp.) and ZOTU179 (cf. Ganoderma applanatum), and one hub taxon, ZOTU17 (cf. Mortierella gamsii) in 2016. None of these most interacting taxa belonged to the core microbiome or eco-microbiome for each year of sampling. This temporal variability puts into question the idea of a plant core fungal microbiome and its stability. Our results provide a basis for the development of ecological engineering strategies for the improvement of canola production systems in Canada.},
}
@article {pmid31896790,
year = {2020},
author = {Op De Beeck, M and Troein, C and Siregar, S and Gentile, L and Abbondanza, G and Peterson, C and Persson, P and Tunlid, A},
title = {Regulation of fungal decomposition at single-cell level.},
journal = {The ISME journal},
volume = {14},
number = {4},
pages = {896-905},
pmid = {31896790},
issn = {1751-7370},
mesh = {Agaricales ; Basidiomycota/physiology ; Environmental Microbiology ; Fungi/*physiology ; Hyphae ; Mycelium/physiology ; Mycorrhizae/physiology ; Nutrients ; Soil/chemistry ; },
abstract = {Filamentous fungi play a key role as decomposers in Earth's nutrient cycles. In soils, substrates are heterogeneously distributed in microenvironments. Hence, individual hyphae of a mycelium may experience very different environmental conditions simultaneously. In the current work, we investigated how fungi cope with local environmental variations at single-cell level. We developed a method based on infrared spectroscopy that allows the direct, in-situ chemical imaging of the decomposition activity of individual hyphal tips. Colonies of the ectomycorrhizal Basidiomycete Paxillus involutus were grown on liquid media, while parts of colonies were allowed to colonize lignin patches. Oxidative decomposition of lignin by individual hyphae growing under different conditions was followed for a period of seven days. We identified two sub-populations of hyphal tips: one with low decomposition activity and one with much higher activity. Active cells secreted more extracellular polymeric substances and oxidized lignin more strongly. The ratio of active to inactive hyphae strongly depended on the environmental conditions in lignin patches, but was further mediated by the decomposition activity of entire mycelia. Phenotypic heterogeneity occurring between genetically identical hyphal tips may be an important strategy for filamentous fungi to cope with heterogeneous and constantly changing soil environments.},
}
@article {pmid31896018,
year = {2020},
author = {Yuan, W and Tian, T and Yang, Q and Riaz, L},
title = {Transfer potentials of antibiotic resistance genes in Escherichia spp. strains from different sources.},
journal = {Chemosphere},
volume = {246},
number = {},
pages = {125736},
doi = {10.1016/j.chemosphere.2019.125736},
pmid = {31896018},
issn = {1879-1298},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; Escherichia ; *Genes, Bacterial ; Humans ; Livestock ; Manure/microbiology ; Metals, Heavy ; Plasmids ; Wastewater/microbiology ; },
abstract = {Multidrug-resistant Escherichia coli and antibiotic-resistance genes (ARGs) present a danger to public health. However, information on the dissemination potentials of antibiotic resistance among bacteria from different environments is lacking. We isolated multiple antibiotic-resistant Escherichia spp. from animal farms, hospitals, and municipal wastewater-treatment plants (MWWTPs) using culture-based methods, and carried out resistance phenotype and gene analyses. Thirty-five isolates of multiple antibiotic-resistant Escherichia spp. were further screened to detect 61 ARGs, 18 mobile genetic elements (MGEs), and gene cassettes. The isolates from livestock manure and MWWTPs showed greater diversity in plasmid profiling than hospital wastewater. Each Escherichia sp. carried 21-26 ARGs and 8-12 MGEs. In addition, 11 gene cassettes were detected in 34 Escherichia isolates, with greater diversity in livestock manure and MWWTPs than in hospital wastewater. The results indicated that the potential for ARG transfer was higher in livestock manure and MWWTPs compared with human clinical sources, possibly related to the high occurrence of both residual antibiotics and heavy metals in these environments.},
}
@article {pmid31894632,
year = {2021},
author = {Baricz, A and Chiriac, CM and Andrei, A&#x218; and Bulzu, PA and Levei, EA and Cadar, O and Battes, KP and Cîmpean, M and Șenilă, M and Cristea, A and Muntean, V and Alexe, M and Coman, C and Szekeres, EK and Sicora, CI and Ionescu, A and Blain, D and O'Neill, WK and Edwards, J and Hallsworth, JE and Banciu, HL},
title = {Spatio-temporal insights into microbiology of the freshwater-to-hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake.},
journal = {Environmental microbiology},
volume = {23},
number = {7},
pages = {3523-3540},
doi = {10.1111/1462-2920.14909},
pmid = {31894632},
issn = {1462-2920},
mesh = {*Bacteria/genetics ; *Lakes ; Sodium Chloride ; Sulfur ; Water Microbiology ; },
abstract = {Ursu Lake is located in the Middle Miocene salt deposit of Central Romania. It is stratified, and the water column has three distinct water masses: an upper freshwater-to-moderately saline stratum (0-3 m), an intermediate stratum exhibiting a steep halocline (3-3.5 m), and a lower hypersaline stratum (4 m and below) that is euxinic (i.e. anoxic and sulphidic). Recent studies have characterized the lake's microbial taxonomy and given rise to intriguing ecological questions. Here, we explore whether the communities are dynamic or stable in relation to taxonomic composition, geochemistry, biophysics, and ecophysiological functions during the annual cycle. We found: (i) seasonally fluctuating, light-dependent communities in the upper layer (≥0.987-0.990 water-activity), a stable but phylogenetically diverse population of heterotrophs in the hypersaline stratum (water activities down to 0.762) and a persistent plate of green sulphur bacteria that connects these two (0.958-0.956 water activity) at 3-3.5 to 4 m; (ii) communities that might be involved in carbon- and sulphur-cycling between and within the lake's three main water masses; (iii) uncultured lineages including Acetothermia (OP1), Cloacimonetes (WWE1), Marinimicrobia (SAR406), Omnitrophicaeota (OP3), Parcubacteria (OD1) and other Candidate Phyla Radiation bacteria, and SR1 in the hypersaline stratum (likely involved in the anaerobic steps of carbon- and sulphur-cycling); and (iv) that species richness and habitat stability are associated with high redox-potentials. Ursu Lake has a unique and complex ecology, at the same time exhibiting dynamic fluctuations and stability, and can be used as a modern analogue for ancient euxinic water bodies and comparator system for other stratified hypersaline systems.},
}
@article {pmid31891451,
year = {2020},
author = {Cosetta, CM and Wolfe, BE},
title = {Deconstructing and Reconstructing Cheese Rind Microbiomes for Experiments in Microbial Ecology and Evolution.},
journal = {Current protocols in microbiology},
volume = {56},
number = {1},
pages = {e95},
doi = {10.1002/cpmc.95},
pmid = {31891451},
issn = {1934-8533},
mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Biofilms ; *Biological Evolution ; Cattle ; Cheese/*microbiology ; Food Microbiology/*methods ; Fungi/classification/genetics/*isolation &amp; purification/physiology ; Microbiological Techniques/*methods ; *Microbiota ; Milk/microbiology ; },
abstract = {Cheese rind microbiomes are useful model systems for identifying the mechanisms that control microbiome diversity. Here, we describe the methods we have optimized to first deconstruct in situ cheese rind microbiome diversity and then reconstruct that diversity in laboratory environments to conduct controlled microbiome manipulations. Most cheese rind microbial species, including bacteria, yeasts, and filamentous fungi, can be easily cultured using standard lab media. Colony morphologies of taxa are diverse and can often be used to distinguish taxa at the phylum and sometimes even genus level. Through the use of cheese curd agar medium, thousands of unique community combinations or microbial interactions can be assessed. Transcriptomic experiments and transposon mutagenesis screens can pinpoint mechanisms of interactions between microbial species. Our general approach of creating a tractable synthetic microbial community from cheese can be easily applied to other fermented foods to develop other model microbiomes. © 2019 by John Wiley &amp; Sons, Inc. Basic Protocol 1: Isolation of cheese rind microbial communities Support Protocol 1: Preparation of plate count agar with milk and salt Basic Protocol 2: Identification of cheese rind bacterial and fungal isolates using 16S and ITS sequences Basic Protocol 3: Preparation of experimental glycerol stocks of yeasts and bacteria Basic Protocol 4: Preparation of experimental glycerol stocks of filamentous fungi Basic Protocol 5: Reconstruction of cheese rind microbial communities in vitro Support Protocol 2: Preparation of lyophilized and powdered cheese curd Support Protocol 3: Preparation of 10% cheese curd agar plates and tubes Basic Protocol 6: Interaction screens using responding lawns Support Protocol 4: Preparation of liquid 2% cheese curd Basic Protocol 7: Experimental evolution Basic Protocol 8: Measuring community function: pH/acidification Basic Protocol 9: Measuring community function: Pigment production Basic Protocol 10: RNA sequencing of cheese rind biofilms.},
}
@article {pmid31889749,
year = {2019},
author = {Philips, CA and Phadke, N and Ganesan, K and Rajesh, S and Padsalgi, G and Ahamed, R and John, SK and Valiathan, GC and Augustine, P},
title = {Gut Microbiota in Alcoholic Hepatitis is Disparate from Those in Acute Alcoholic Pancreatitis and Biliary Disease.},
journal = {Journal of clinical and experimental hepatology},
volume = {9},
number = {6},
pages = {690-698},
pmid = {31889749},
issn = {0973-6883},
abstract = {BACKGROUND: Alcoholic hepatitis (AH) is associated with gut dysbiosis. Comparative gut microbial profiles of acute alcoholic pancreatitis (AAP) and acute biliary disease (ABD) are not demonstrated. We aimed to compare gut microbiota of AH, AAP, and ABD patients with each other and with their respective healthy controls (HCs).<br><br>METHODS: From December 2016 to September 2017, consecutive patients with AH, AAP, and ABD (acute cholecystitis, acute biliary pancreatitis, and choledocholithiasis with cholangitis) were included in the study. Qualitative and functional stool microbiota comparative analysis was performed between groups, with AH as the reference comparator.<br><br>RESULTS: Of 3564, 882, and 224 patients with liver disease, pancreatic disease, and biliary disease, respectively, after exclusion, 29 patients with AH and 7 patients each with AAP and ABD&#xa0;and their corresponding HCs were included in the study analysis. The alpha diversity between patients with AH and AAP was found to be significantly different. Significant relative abundance (RA) of Acinetobacter and Moraxella was noted among patients with AAP. Enterobacter, Atopobium, Synergistia, and Devosia were significantly higher in patients with ABD compared to patients with AH, in whom Faecalibacterium and Megamonas were higher. Functional pathways associated with carbohydrate metabolism, phenylpropanoid biosynthesis, and ethylbenzene degradation were significantly higher in AAP when compared to AH. Fatty acid and inositol phosphate metabolism and dioxin degradation were significantly upregulated in patients with ABD while lipid and fatty acid biosynthetic pathways and pathways associated with immune processes were upregulated in patients with AH.<br><br>CONCLUSIONS: Differential gut dysbiosis is evident in both patients with AH, AAP, and ABD and also in comparison to HCs. The differential microbiota among patients with AH and AAP maybe important in promotion and progression of liver or pancreatic disease among alcohol users and may be a potential therapeutic target, which needs to be confirmed in larger multicenter studies.},
}
@article {pmid31889414,
year = {2020},
author = {García-Timermans, C and Rubbens, P and Heyse, J and Kerckhof, FM and Props, R and Skirtach, AG and Waegeman, W and Boon, N},
title = {Discriminating Bacterial Phenotypes at the Population and Single-Cell Level: A Comparison of Flow Cytometry and Raman Spectroscopy Fingerprinting.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {97},
number = {7},
pages = {713-726},
doi = {10.1002/cyto.a.23952},
pmid = {31889414},
issn = {1552-4930},
mesh = {*Bacteria ; Escherichia coli/genetics ; Flow Cytometry ; Phenotype ; Single-Cell Analysis ; *Spectrum Analysis, Raman ; },
abstract = {Investigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing phenotypic heterogeneity remains a challenge, as there is no standardized analysis framework. Several optical tools are available, such as flow cytometry and Raman spectroscopy, which describe optical properties of the individual cell. In this work, we compare Raman spectroscopy and flow cytometry to study phenotypic heterogeneity in bacterial populations. The growth stages of three replicate Escherichia coli populations were characterized using both technologies. Our findings show that flow cytometry detects and quantifies shifts in phenotypic heterogeneity at the population level due to its high-throughput nature. Raman spectroscopy, on the other hand, offers a much higher resolution at the single-cell level (i.e., more biochemical information is recorded). Therefore, it can identify distinct phenotypic populations when coupled with analyses tailored toward single-cell data. In addition, it provides information about biomolecules that are present, which can be linked to cell functionality. We propose a computational workflow to distinguish between bacterial phenotypic populations using Raman spectroscopy and validated this approach with an external data set. We recommend using flow cytometry to quantify phenotypic heterogeneity at the population level, and Raman spectroscopy to perform a more in-depth analysis of heterogeneity at the single-cell level. © 2019 International Society for Advancement of Cytometry.},
}
@article {pmid31887587,
year = {2020},
author = {van Dorst, J and Wilkins, D and King, CK and Spedding, T and Hince, G and Zhang, E and Crane, S and Ferrari, B},
title = {Applying microbial indicators of hydrocarbon toxicity to contaminated sites undergoing bioremediation on subantarctic Macquarie Island.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {259},
number = {},
pages = {113780},
doi = {10.1016/j.envpol.2019.113780},
pmid = {31887587},
issn = {1873-6424},
mesh = {*Biodegradation, Environmental ; Humans ; Hydrocarbons/*toxicity ; Islands ; *Petroleum ; Soil ; Soil Microbiology ; *Soil Pollutants ; },
abstract = {Microorganisms are useful biological indicators of toxicity and play a key role in the functioning of healthy soils. In this study, we investigated the residual toxicity of hydrocarbons in aged contaminated soils and determined the extent of microbial community recovery during in-situ bioremediation at subantarctic Macquarie Island. Previously identified microbial indicators of hydrocarbon toxicity were used to understand interactions between hydrocarbon concentrations, soil physicochemical parameters and the microbial community. Despite the complexity of the field sites, which included active fuel storage areas with high levels of soil heterogeneity, multiple spill events and variable fuel sources, we observed consistent microbial community traits associated with exposure to high concentrations of hydrocarbons. These included; reductions in alpha diversity, inhibition of nitrification potential and a reduction in the ratio of oligotrophic to copiotrophic species. These observed responses and the sensitivity of microbial communities in the field, were comparable to sensitivity estimates obtained in a previous lab-based mesocosm study with hydrocarbon spiked soils. This study provides a valuable and often missing link between the quite disparate conditions of controlled lab-based spiking experiments and the complexity presented by 'real-world' contaminated field sites.},
}
@article {pmid31887546,
year = {2020},
author = {Carney, RL and Brown, MV and Siboni, N and Raina, JB and Kahlke, T and Mitrovic, SM and Seymour, JR},
title = {Highly heterogeneous temporal dynamics in the abundance and diversity of the emerging pathogens Arcobacter at an urban beach.},
journal = {Water research},
volume = {171},
number = {},
pages = {115405},
doi = {10.1016/j.watres.2019.115405},
pmid = {31887546},
issn = {1879-2448},
mesh = {*Arcobacter ; Bacteria ; DNA, Bacterial ; Humans ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; },
abstract = {While the significance of Arcobacter in clinical settings grows, the ecological dynamics of potentially pathogenic Arcobacter in coastal marine environments remains unclear. In this study, we monitored the temporal dynamics of Arcobacter at an urban beach subject to significant stormwater input and wet weather sewer overflows (WWSO). Weekly monitoring of bacterial communities over 24 months using 16S rRNA amplicon sequencing revealed large, intermittent peaks in the relative abundance of Arcobacter. Quantitative PCR was subsequently employed to track absolute abundance of Arcobacter 23S rRNA gene copies, revealing peaks in abundance reaching up to 10[8] gene copies L[-1], with these increases statistically correlated with stormwater and WWSO intrusion. Notably, peaks in Arcobacter abundance were poorly correlated with enterococci plate counts, and remained elevated for one week following heavy rainfall. Using oligotyping we discriminated single nucleotide variants (SNVs) within the Arcobacter population, revealing 10 distinct clusters of SNVs that we defined as Arcobacter "ecotypes", with each displaying distinct temporal dynamics. The most abundant ecotype during stormwater and modelled WWSO events displayed 16S rRNA sequence similarity to A. cryaerophilius, a species previously implicated in human illness. Our findings highlight the diverse environmental drivers of Arcobacter abundance within coastal settings and point to a potentially important, yet overlooked exposure risk of these potential pathogens to humans.},
}
@article {pmid31885873,
year = {2019},
author = {Pareek, S and Kurakawa, T and Das, B and Motooka, D and Nakaya, S and Rongsen-Chandola, T and Goyal, N and Kayama, H and Dodd, D and Okumura, R and Maeda, Y and Fujimoto, K and Nii, T and Ogawa, T and Iida, T and Bhandari, N and Kida, T and Nakamura, S and Nair, GB and Takeda, K},
title = {Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {1},
pages = {37},
pmid = {31885873},
issn = {2055-5008},
support = {K08 DK110335/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteria/classification/*growth &amp; development/*metabolism ; Diet/*methods ; Feces/microbiology ; Fungi/classification/*growth &amp; development/*metabolism ; *Gastrointestinal Microbiome ; Humans ; India ; Japan ; Mice ; *Microbial Interactions ; Models, Animal ; Polysaccharides/metabolism ; },
abstract = {The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of Prevotella and Candida. Candida spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of Candida spp. grown with arabinoxylan promoted rapid proliferation of Prevotella copri. Arabinose was identified as a potential growth-inducing factor in the Candida culture supernatants. Candida spp. exhibited a growth response to xylose, but not to arabinose, whereas P. copri proliferated in response to both xylose and arabinose. Candida spp., but not P. copri, colonized the intestine of germ-free mice. However, P. copri successfully colonized mouse intestine already harboring Candida. These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.},
}
@article {pmid31885375,
year = {2019},
author = {Wein, T and Stücker, FT and Hülter, NF and Dagan, T},
title = {Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {154},
pages = {},
doi = {10.3791/60749},
pmid = {31885375},
issn = {1940-087X},
mesh = {Drug Resistance, Microbial/*genetics ; Evolution, Molecular ; *Plasmids ; },
abstract = {Plasmids play a major role in microbial ecology and evolution as vehicles of lateral gene transfer and reservoirs of accessory gene functions in microbial populations. This is especially the case under rapidly changing environments such as fluctuating antibiotics exposure. We recently showed that plasmids maintain antibiotic resistance genes in Escherichia coli without positive selection for the plasmid presence. Here we describe an experimental system that allows following both the plasmid genotype and phenotype in long-term evolution experiments. We use molecular techniques to design a model plasmid that is subsequently introduced to an experimental evolution batch system approach in an E. coli host. We follow the plasmid frequency over time by applying replica plating of the E. coli populations while quantifying the antibiotic resistance persistence. In addition, we monitor the conformation of plasmids in host cells by analyzing the extent of plasmid multimer formation by plasmid nicking and agarose gel electrophoresis. Such an approach allows us to visualize not only the genome size of evolving plasmids but also their topological conformation-a factor highly important for plasmid inheritance. Our system combines molecular strategies with traditional microbiology approaches and provides a set-up to follow plasmids in bacterial populations over a long time. The presented approach can be applied to study a wide range of mobile genetic elements in the future.},
}
@article {pmid31881501,
year = {2020},
author = {Favere, J and Buysschaert, B and Boon, N and De Gusseme, B},
title = {Online microbial fingerprinting for quality management of drinking water: Full-scale event detection.},
journal = {Water research},
volume = {170},
number = {},
pages = {115353},
doi = {10.1016/j.watres.2019.115353},
pmid = {31881501},
issn = {1879-2448},
mesh = {Bacteria ; *Drinking Water ; Water Microbiology ; Water Quality ; Water Supply ; },
abstract = {Microbial regrowth during drinking water distribution can result in a variety of problems such as a deviating taste and odor, and may even pose a risk to public health. Frequent monitoring is essential to anticipate events of biological instability, and relevant microbial parameters for operational control of biostability of drinking water should be developed. Here, online flow cytometry and derived biological metrics were used to assess the biological stability of a full-scale drinking water tower during normal and disturbed flow regime. Pronounced operational events, such as switching from drinking water source, and seasonal changes, were detected in the total cell counts, and regrowth was observed despite the short hydraulic residence time of 6-8 h. Based on the flow cytometric fingerprints, the Bray-Curtis dissimilarity was calculated and was developed as unambiguous parameter to indicate or warn for changing microbial drinking water quality during operational events. In the studied water tower, drastic microbial water quality changes were reflected in the Bray-Curtis dissimilarity, which demonstrates its use as an indicator to follow-up and detect microbial quality changes in practice. Hence, the Bray-Curtis dissimilarity can be used in an online setup as a straightforward parameter during full-scale operation of drinking water distribution, and combined with the cell concentration, it serves as an early-warning system for biological instability.},
}
@article {pmid31878322,
year = {2019},
author = {Sahu, SK and Liu, M and Yssel, A and Kariba, R and Muthemba, S and Jiang, S and Song, B and Hendre, PS and Muchugi, A and Jamnadass, R and Kao, SM and Featherston, J and Zerega, NJC and Xu, X and Yang, H and Deynze, AV and Peer, YV and Liu, X and Liu, H},
title = {Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis).},
journal = {Genes},
volume = {11},
number = {1},
pages = {},
pmid = {31878322},
issn = {2073-4425},
mesh = {Artocarpus/classification/*genetics ; Genome Size ; Genome, Plant ; Molecular Sequence Annotation ; Whole Genome Sequencing/*methods ; },
abstract = {Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.},
}
@article {pmid31873774,
year = {2020},
author = {Velasco-González, I and Sanchez-Jimenez, A and Singer, D and Murciano, A and Díez-Hermano, S and Lara, E and Martín-Cereceda, M},
title = {Correction to: Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {248},
doi = {10.1007/s00248-019-01478-5},
pmid = {31873774},
issn = {1432-184X},
abstract = {The original version of this article contained an erratum of omission in the Acknowledgments section.},
}
@article {pmid31873773,
year = {2020},
author = {Poret-Peterson, AT and Sayed, N and Glyzewski, N and Forbes, H and González-Orta, ET and Kluepfel, DA},
title = {Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {191-201},
pmid = {31873773},
issn = {1432-184X},
support = {2032-22000-016-00D//Agricultural Research Service/ ; },
mesh = {Anaerobiosis ; Carbon/analysis ; *Disinfection ; Microbiota/*drug effects ; Soil/*chemistry ; *Soil Microbiology ; Time Factors ; },
abstract = {Anaerobic soil disinfestation (ASD) is an organic amendment-based management tool for controlling soil-borne plant diseases and is increasingly used in a variety of crops. ASD results in a marked decrease in soil redox potential and other physicochemical changes, and a turnover in the composition of the soil microbiome. Mechanisms of ASD-mediated pathogen control are not fully understood, but appear to depend on the carbon source used to initiate the process and involve a combination of biological (i.e., release of volatile organic compounds) and abiotic (i.e., lowered pH, release of metal ions) factors. In this study, we examined how the soil microbiome changes over time in response to ASD initiated with rice bran, tomato pomace, or red grape pomace as amendments using growth chamber mesocosms that replicate ASD-induced field soil redox conditions. Within 2 days, the soil microbiome rapidly shifted from a diverse assemblage of taxa to being dominated by members of the Firmicutes for all ASD treatments, whereas control mesocosms maintained diverse and more evenly distributed communities. Rice bran and tomato pomace amendments resulted in microbial communities with similar compositions and trajectories that were different from red grape pomace communities. Quantitative PCR showed nitrogenase gene abundances were higher in ASD communities and tended to increase over time, suggesting the potential for altering soil nitrogen availability. These results highlight the need for temporal and functional studies to understand how pathogen suppressive microbial communities assemble and function in ASD-treated soils.},
}
@article {pmid31872949,
year = {2020},
author = {Harrison, JG and Calder, WJ and Shastry, V and Buerkle, CA},
title = {Dirichlet-multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data.},
journal = {Molecular ecology resources},
volume = {20},
number = {2},
pages = {481-497},
doi = {10.1111/1755-0998.13128},
pmid = {31872949},
issn = {1755-0998},
support = {EPS-1655726//National Science Foundation/ ; //University of Wyoming/ ; },
mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; Humans ; Lung/microbiology ; *Microbiota ; *Models, Statistical ; Monte Carlo Method ; },
abstract = {Molecular ecology regularly requires the analysis of count data that reflect the relative abundance of features of a composition (e.g., taxa in a community, gene transcripts in a tissue). The sampling process that generates these data can be modelled using the multinomial distribution. Replicate multinomial samples inform the relative abundances of features in an underlying Dirichlet distribution. These distributions together form a hierarchical model for relative abundances among replicates and sampling groups. This type of Dirichlet-multinomial modelling (DMM) has been described previously, but its benefits and limitations are largely untested. With simulated data, we quantified the ability of DMM to detect differences in proportions between treatment and control groups, and compared the efficacy of three computational methods to implement DMM-Hamiltonian Monte Carlo (HMC), variational inference (VI), and Gibbs Markov chain Monte Carlo. We report that DMM was better able to detect shifts in relative abundances than analogous analytical tools, while identifying an acceptably low number of false positives. Among methods for implementing DMM, HMC provided the most accurate estimates of relative abundances, and VI was the most computationally efficient. The sensitivity of DMM was exemplified through analysis of previously published data describing lung microbiomes. We report that DMM identified several potentially pathogenic, bacterial taxa as more abundant in the lungs of children who aspirated foreign material during swallowing; these differences went undetected with different statistical approaches. Our results suggest that DMM has strong potential as a statistical method to guide inference in molecular ecology.},
}
@article {pmid31872380,
year = {2019},
author = {Mohr, T and Aliyu, H and Biebinger, L and Gödert, R and Hornberger, A and Cowan, D and de Maayer, P and Neumann, A},
title = {Effects of different operating parameters on hydrogen production by Parageobacillus thermoglucosidasius DSM 6285.},
journal = {AMB Express},
volume = {9},
number = {1},
pages = {207},
pmid = {31872380},
issn = {2191-0855},
support = {031B0180//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 109137//National Research Foundation/ ; },
abstract = {Hydrogen gas represents a promising alternative energy source to dwindling fossil fuel reserves, as it carries the highest energy per unit mass and its combustion results in the release of water vapour as only byproduct. The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius is able to produce hydrogen via the water-gas shift reaction catalyzed by a carbon monoxide dehydrogenase-hydrogenase enzyme complex. Here we have evaluated the effects of several operating parameters on hydrogen production, including different growth temperatures, pre-culture ages and inoculum sizes, as well as different pHs and concentrations of nickel and iron in the fermentation medium. All of the tested parameters were observed to have a substantive effect on both hydrogen yield and (specific) production rates. A final experiment incorporating the best scenario for each tested parameter showed a marked increase in the H2 production rate compared to each individual parameter. The optimised parameters serve as a strong basis for improved hydrogen production with a view of commercialisation of this process.},
}
@article {pmid31870202,
year = {2020},
author = {Erber, AC and Cetin, H and Berry, D and Schernhammer, ES},
title = {The role of gut microbiota, butyrate and proton pump inhibitors in amyotrophic lateral sclerosis: a systematic review.},
journal = {The International journal of neuroscience},
volume = {130},
number = {7},
pages = {727-735},
doi = {10.1080/00207454.2019.1702549},
pmid = {31870202},
issn = {1563-5279},
mesh = {*Amyotrophic Lateral Sclerosis/drug therapy/metabolism/microbiology ; Animals ; Butyrates/*metabolism ; Disease Progression ; Gastrointestinal Microbiome/*physiology ; Humans ; Proton Pump Inhibitors/*therapeutic use ; },
abstract = {Aim of the study: We conducted a systematic review on existing literature in humans and animals, linking the gut microbiome with amyotrophic lateral sclerosis (ALS). Additionally, we sought to explore the role of the bacterially produced metabolite butyrate as well as of proton pump inhibitors (PPIs) in these associations.Materials and methods: Following PRISMA guidelines for systematic literature reviews, four databases (Medline, Scopus, Embase and Web of Science) were searched and screened by two independent reviewers against defined inclusion criteria. Six studies in humans and six animal studies were identified, summarized and reviewed.Results: Overall, the evidence accrued to date is supportive of changes in the gut microbiome being associated with ALS risk, and potentially progression, though observational studies are small (describing a total of 145 patients with ALS across all published studies), and not entirely conclusive.Conclusions: With emerging studies beginning to apply metagenome sequencing, more clarity regarding the importance and promise of the gut microbiome in ALS can be expected. Future studies may also help establish the therapeutic potential of butyrate, and the role of PPIs in these associations.},
}
@article {pmid31867834,
year = {2020},
author = {Kuenen, JG},
title = {Anammox and beyond.},
journal = {Environmental microbiology},
volume = {22},
number = {2},
pages = {525-536},
doi = {10.1111/1462-2920.14904},
pmid = {31867834},
issn = {1462-2920},
mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/*metabolism ; Bioreactors/*microbiology ; Environmental Microbiology ; Hydrazines/metabolism ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen/metabolism ; Nitrogen Cycle/*physiology ; Organelles/metabolism ; Oxidation-Reduction ; Sulfur/metabolism ; Wastewater/microbiology ; },
abstract = {When looking back and wonder how we did it, I became even more aware of how my wanderings in microbiology are all linked, from the start of my PhD with Hans Veldkamp on sulphur-oxidizing bacteria in chemostats. My interests broadened from obligate chemolithoautotrophic bacteria to facultative organisms and the question about the ecological niches of these different metabolic types. The sulphide oxidizing bacteria also may be used to produce elemental sulphur, which can easily be removed from wastewater. This fitted in a long-standing collaboration with Dimitry Sorokin on the ecophysiology and application of alkaliphilic sulphur bacteria. Then came the denitrifying sulphur-oxidizing bacteria and their application to remove sulphide from wastewater, which lead to our interest in nitrate, nitrite and ammonium removal in general. The big surprise was the serendipitous discovery of the 'anammox'-process, whereby ammonium is anaerobically oxidized to dinitrogen gas with nitrite as electron acceptor. The early days of our anammox research are the main focus of this article, which describes the struggle of growing and identifying the most peculiar bacteria we ever came across. A specialized organelle, the anammoxosome was shown to be responsible for the key ammonium oxidation, whereby a rocket fuel, hydrazine, turned out to be an intermediate. Soon after we became aware that anammox is everywhere and in the marine environment makes up a major portion of the nitrogen cycle. The intense scientific collaboration with Mike Jetten and Mark van Loosdrecht and colleagues led to our further understanding and application of this fascinating process, which is briefly summarized in this article. My broader interest in environmental microbiology and microbial ecology has been a regularly returning theme, taking me all over the world to great collaborations lasting to this very day.},
}
@article {pmid31867463,
year = {2019},
author = {Oliveira, M and Rodrigues, CM and Teixeira, P},
title = {Microbiological quality of raw berries and their products: A focus on foodborne pathogens.},
journal = {Heliyon},
volume = {5},
number = {12},
pages = {e02992},
pmid = {31867463},
issn = {2405-8440},
abstract = {Berry samples (n = 316; strawberries, raspberries, blackberries and blueberries) obtained from a fruit processing plant were examined regarding bacteriological quality and their potential public health risk. Three types of berry products were analysed including raw material, product from the mixing step and final product. Escherichia coli, Salmonella spp., Listeria monocytogenes, Bacillus cereus, sulphite-reducing clostridia spores and coagulase-positive staphylococci were the parameters investigated. Salmonella enterica serovar Braenderup and L. monocytogenes were isolated from one fruit sample of raw material each. Two samples harboured E. coli between 0.7 and 0.9 log cfu g[-1], not exceeding the hygienic criteria. Coagulase-positive staphylococci were not detected in the studied samples; however, coagulase-negative staphylococci (CNS) were isolated from a small proportion of samples mainly raspberries. Presumptive B. cereus were isolated from a relatively large proportion of the samples, raspberries and blackberries being the most contaminated fruits. The absence of pathogenic microorganisms in the final product as well as the low prevalence of presumptive B. cereus and CNS indicates proper implementation of good manufacturing and hygiene practices (GMPs/GHPs) by the food industry. Nevertheless, the results indicate that the raw material examined may contain pathogenic bacteria and thereby represent a risk to consumers regarding the manifestation of foodborne diseases.},
}
@article {pmid31866955,
year = {2019},
author = {Li, Z and Yao, Q and Guo, X and Crits-Christoph, A and Mayes, MA and Hervey, WJ and Lebeis, SL and Banfield, JF and Hurst, GB and Hettich, RL and Pan, C},
title = {Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using [13]CO2 and [13]C-Methanol.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2706},
pmid = {31866955},
issn = {1664-302X},
abstract = {Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from [13]CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived [13]C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. [13]C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 [13]C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 [13]C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities.},
}
@article {pmid31863131,
year = {2020},
author = {Wang, ZB and Sun, YY and Li, Y and Chen, XL and Wang, P and Ding, HT and Chen, B and Zhang, XY and Song, XY and Wang, M and McMinn, A and Zhang, YZ and Qin, QL},
title = {Significant Bacterial Distance-Decay Relationship in Continuous, Well-Connected Southern Ocean Surface Water.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {73-80},
doi = {10.1007/s00248-019-01472-x},
pmid = {31863131},
issn = {1432-184X},
support = {2018YFC1406706//National Key R&amp;D Program of China/ ; U1706207//National Science Foundation of China/ ; 2017ASTCP-OS14//AoShan Talents Cultivation Program/ ; 2009TS079//Taishan Scholars Program of Shandong Province/ ; 2016WLJH36//Young Scholars Program of Shandong University/ ; },
mesh = {Bacteria/*isolation &amp; purification ; Geography ; *Microbiota ; Oceans and Seas ; Seawater/*microbiology ; },
abstract = {Recently, an increasing number of studies have focused on the biogeographic distribution of marine microorganisms. However, the extent to which geographic distance can affect marine microbial communities is still unclear, especially for the microbial communities in well-connected surface seawaters. In this study, the bacterial community compositions of 21 surface seawater samples, that were distributed over a distance of 7800 km, were surveyed to investigate how bacterial community similarity changes with increasing geographical distance. Proteobacteria and Bacteroidetes were the dominant bacterial phyla, with Proteobacteria accounting for 52.6-92.5% and Bacteroidetes comprising 3.5-46.9% of the bacterial communities. A significant bacterial distance-decay relationship was observed in the well-connected Southern Ocean surface seawater. The number of pairwise shared operational taxonomic units (OTUs), and community similarities tended to decrease with increasing geographic distance. Calculation of the similarity indices with all, abundant or rare OTUs did not affect the observed distance-decay relationship. Spatial distance can largely explain the observed bacterial community variation. This study shows that even in well-connected surface waters, bacterial distance-decay patterns can be found as long as the geographical distance is great enough. The biogeographic patterns should then be present for marine microorganisms considering the large size and complexity of the marine ecosystem.},
}
@article {pmid31860060,
year = {2020},
author = {Cavichiolli de Oliveira, N and Cônsoli, FL},
title = {Beyond host regulation: Changes in gut microbiome of permissive and non-permissive hosts following parasitization by the wasp Cotesia flavipes.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {2},
pages = {},
doi = {10.1093/femsec/fiz206},
pmid = {31860060},
issn = {1574-6941},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Host-Parasite Interactions/physiology ; Larva/classification/microbiology/parasitology ; Moths/classification/*microbiology/*parasitology/physiology ; Wasps/*physiology ; },
abstract = {Koinobiont parasitoids regulate the physiology of their hosts, possibly interfering with the host gut microbiota and ultimately impacting parasitoid development. We used the parasitoid Cotesia flavipes to investigate if the regulation of the host would also affect the host gut microbiota. We also wondered if the effects of parasitization on the gut microbiota would depend on the host-parasitoid association by testing the permissive Diatraea saccharalis and the non-permissive Spodoptera frugiperda hosts. We determined the structure and potential functional contribution of the gut microbiota of the fore-midgut and hindgut of the hosts at different stages of development of the immature parasitoid. The abundance and diversity of operational taxonomic units of the anteromedial (fore-midgut) gut and posterior (hindgut) region from larvae of the analyzed hosts were affected by parasitization. Changes in the gut microbiota induced by parasitization altered the potential functional contribution of the gut microbiota associated with both hosts. Our data also indicated that the mechanism by which C. flavipes interferes with the gut microbiota of the host does not require a host-parasitoid coevolutionary history. Changes observed in the potential contribution of the gut microbiota of parasitized hosts impact the host's nutritional quality, and could favor host exploitation by C. flavipes.},
}
@article {pmid31858913,
year = {2021},
author = {Basilua, JM and Pochart, P},
title = {Cotrimoxazole Prophylaxis is Not Associated with a Higher Occurrence of Atazanavir Treatment Failure: Analysis of Worldwide Pharmacovigilance Data.},
journal = {Infectious disorders drug targets},
volume = {21},
number = {1},
pages = {55-59},
doi = {10.2174/1871526520666191220112416},
pmid = {31858913},
issn = {2212-3989},
mesh = {Africa ; *Anti-HIV Agents/therapeutic use ; Atazanavir Sulfate/therapeutic use ; *HIV Infections/drug therapy ; HIV Protease Inhibitors/*therapeutic use ; Humans ; Pharmacovigilance ; Ritonavir/therapeutic use ; Treatment Failure ; Trimethoprim, Sulfamethoxazole Drug Combination/*therapeutic use ; },
abstract = {UNLABELLED: [Background: Cotrimoxazole is the main antibiotic used in HIV-infected patients for the prophylaxis of opportunistic infections. This antibiotic is prescribed in patients receiving antiretroviral agents (ART) such as Atazanavir (ATV), a protease inhibitor used with other ART classes. The objective of this study was to compare HIV treatment failure (HIVTF) in HIV-infected patients treated concomitantly with ATV and cotrimoxazole to those of patients treated only with ATV.<br><br>MATERIALS AND METHODS: This is a comparative analysis of the safety data of HIVTF available with ATV in the WHO International Pharmacovigilance database "VigiBase&#xae;". We used the SMQ (Standardized MedDRA Querie) to identify all the terms corresponding to HIVTF. We presented results as a percentage or an adjusted Reporting Odds Ratio (aROR) with a 95% confidence interval (95% CI).<br><br>RESULTS: A total of 116 cases of HIVTF (2.2%) were reported with ATV among the 5196 individual case safety reports (ICSR) included in the analysis. The proportion of HIV-infected patients who presented ATV treatment failure (ATVTF) was lower (2.6%, 3/116) when cotrimoxazole was concomitant (aROR was 0.5 with a 95%CI from 0.2 to 1.7). Only 10 of 273 ICSRs (3.7%) were reported from Africa concerning the use of cotrimoxazole prophylaxis concomitantly with ATV.<br><br>CONCLUSION: This study did not show a higher occurrence of ATVTF when cotrimoxazole was concomitant. These results reinforce the place of concomitant use of ATV with cotrimoxazole in the management of HIV treatment.},
}
@article {pmid31854329,
year = {2019},
author = {Hewson, I},
title = {Technical pitfalls that bias comparative microbial community analyses of aquatic disease Ian Hewson.},
journal = {Diseases of aquatic organisms},
volume = {137},
number = {2},
pages = {109-124},
doi = {10.3354/dao03432},
pmid = {31854329},
issn = {0177-5103},
mesh = {Animals ; Bias ; *Microbiota ; },
abstract = {The accessibility of high-throughput DNA sequencing technologies has attracted the application of comparative microbial analyses to study diseases. These studies present a window into host microbiome diversity and composition that can be used to address ecological theory in the context of host biology and behavior. Recently, comparative microbiome studies have been used to study non-vertebrate aquatic diseases to elucidate microorganisms potentially involved in disease processes or in disease prevention. These investigations suffer from many well-described biases, especially prior to sequence analyses, that could lead to misleading conclusions. Microbiome-focused studies of aquatic metazoan diseases provide valuable documentation of microbial ecology, although, they are only a starting point for establishing disease etiology, which demands quantitative validation through targeted approaches. The microbiome approach to understanding disease is most useful after laboratory diagnostics guided by pathology have failed to identify a causative agent. This opinion piece presents several technical pitfalls which may affect wider interpretation of microbe-host interactions through comparative microbial community analyses and provides recommendations, based on studies in non-aquatic systems, for incorporation into future aquatic disease research.},
}
@article {pmid31853069,
year = {2020},
author = {Zhang, L and Chen, F and Zhang, X and Li, Z and Zhao, Y and Lohaus, R and Chang, X and Dong, W and Ho, SYW and Liu, X and Song, A and Chen, J and Guo, W and Wang, Z and Zhuang, Y and Wang, H and Chen, X and Hu, J and Liu, Y and Qin, Y and Wang, K and Dong, S and Liu, Y and Zhang, S and Yu, X and Wu, Q and Wang, L and Yan, X and Jiao, Y and Kong, H and Zhou, X and Yu, C and Chen, Y and Li, F and Wang, J and Chen, W and Chen, X and Jia, Q and Zhang, C and Jiang, Y and Zhang, W and Liu, G and Fu, J and Chen, F and Ma, H and Van de Peer, Y and Tang, H},
title = {The water lily genome and the early evolution of flowering plants.},
journal = {Nature},
volume = {577},
number = {7788},
pages = {79-84},
pmid = {31853069},
issn = {1476-4687},
support = {/ERC_/European Research Council/International ; },
mesh = {Flowers/genetics/metabolism ; *Genome, Plant ; Nymphaea/*genetics/metabolism ; Odorants/analysis ; *Phylogeny ; },
abstract = {Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms[1-3]. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.},
}
@article {pmid31849864,
year = {2019},
author = {Bains, M and Laney, C and Wolfe, AE and Orr, M and Waschek, JA and Ericsson, AC and Dorsam, GP},
title = {Vasoactive Intestinal Peptide Deficiency Is Associated With Altered Gut Microbiota Communities in Male and Female C57BL/6 Mice.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2689},
pmid = {31849864},
issn = {1664-302X},
support = {K01 OD019924/OD/NIH HHS/United States ; P20 GM109024/GM/NIGMS NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; },
abstract = {Vasoactive intestinal peptide (VIP) is crucial for gastrointestinal tract (GIT) health. VIP sustains GIT homeostasis through maintenance of the intestinal epithelial barrier and acts as a potent anti-inflammatory mediator that contributes to gut bacterial tolerance. Based on these biological functions by VIP, we hypothesized that its deficiency would alter gut microbial ecology. To this end, fecal samples from male and female VIP[+/+], VIP[+/-], and VIP[-/-] littermates (n = 47) were collected and 16S rRNA sequencing was conducted. Our data revealed significant changes in bacterial composition, biodiversity, and weight loss from VIP[-/-] mice compared to VIP[+/+] and VIP[+/-] littermates, irrespective of sex. The gut bacteria compositional changes observed in VIP[-/-] mice was consistent with gut microbial structure changes reported for certain inflammatory and autoimmune disorders. Moreover, predicted functional changes by PICRUSt software suggested an energy surplus within the altered microbiota from VIP[-/-] mice. These data support that VIP plays an important role in maintaining microbiota balance, biodiversity, and GIT function, and its genetic removal results in significant gut microbiota restructuring and weight loss.},
}
@article {pmid31849848,
year = {2019},
author = {Madigan, AP and Egidi, E and Bedon, F and Franks, AE and Plummer, KM},
title = {Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2616},
pmid = {31849848},
issn = {1664-302X},
abstract = {An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg[-1] soil) or salt (4 or 7 g kg[-1] soil) and treated with melatonin (0.2 and 4 mg kg[-1] soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications.},
}
@article {pmid31848649,
year = {2020},
author = {Somers, DJ and Strock, KE and Saros, JE},
title = {Environmental Controls on Microbial Diversity in Arctic Lakes of West Greenland.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {60-72},
doi = {10.1007/s00248-019-01474-9},
pmid = {31848649},
issn = {1432-184X},
support = {1203434//Arctic System Science program of the US National Science Foundation/ ; SFR161//Center for Sustainability Education at Dickinson College/ ; },
mesh = {Arctic Regions ; *Bacterial Physiological Phenomena ; *Ecosystem ; Greenland ; Lakes/*microbiology ; *Microbiota ; },
abstract = {We assessed the microbial community structure of six arctic lakes in West Greenland and investigated relationships to lake physical and chemical characteristics. Lakes from the ice sheet region exhibited the highest species richness, while inland and plateau lakes had lower observed taxonomical diversity. Lake habitat differentiation during summer stratification appeared to alter within lake microbial community composition in only a subset of lakes, while lake variability across regions was a consistent driver of microbial community composition in these arctic lakes. Principal coordinate analysis revealed differentiation of communities along two axes: each reflecting differences in morphometric (lake surface area), geographic (latitude and distance from the ice sheet), physical lake variables (water clarity), and lakewater chemistry (dissolved organic carbon [DOC], dissolved oxygen [DO], total nitrogen [TN], and conductivity). Understanding these relationships between environmental variables and microbial communities is especially important as heterotrophic microorganisms are key to organic matter decomposition, nutrient cycling, and carbon flow through nutrient poor aquatic environments in the Arctic.},
}
@article {pmid31846683,
year = {2019},
author = {Moccia, KM and Lebeis, SL},
title = {Microbial Ecology: How to Fight the Establishment.},
journal = {Current biology : CB},
volume = {29},
number = {24},
pages = {R1320-R1323},
doi = {10.1016/j.cub.2019.10.067},
pmid = {31846683},
issn = {1879-0445},
mesh = {*Arabidopsis ; Microbial Consortia ; *Microbiota ; },
abstract = {Creating microbial consortia capable of consistently producing desired qualities requires a detailed understanding of community interactions. A new paper demonstrates the role of historical contingency in Arabidopsis thaliana leaf-microbiome formation using an adaptable experimental approach, which could be applied to other host organisms.},
}
@article {pmid31845419,
year = {2020},
author = {Bakker, A and Siegel, JA and Mendell, MJ and Prussin, AJ and Marr, LC and Peccia, J},
title = {Bacterial and fungal ecology on air conditioning cooling coils is influenced by climate and building factors.},
journal = {Indoor air},
volume = {30},
number = {2},
pages = {326-334},
doi = {10.1111/ina.12632},
pmid = {31845419},
issn = {1600-0668},
mesh = {*Air Conditioning ; *Air Microbiology ; Air Pollution, Indoor/*analysis ; Climate ; Ecology ; *Environmental Monitoring ; Fungi/*growth &amp; development ; Microbiota ; },
abstract = {The presence of biofilms on the cooling coils of commercial air conditioning (AC) units can significantly reduce the heat transfer efficiency of the coils and may lead to the aerosolization of microbes into occupied spaces of a building. We investigated how climate and AC operation influence the ecology of microbial communities on AC coils. Forty large-scale commercial ACs were considered with representation from warm-humid and hot-dry climates. Both bacterial and fungal ecologies, including richness and taxa, on the cooling coil surfaces were significantly impacted by outdoor climate, through differences in dew point that result in increased moisture (condensate) on coils, and by the minimum efficiency reporting value (MERV 8 vs MERV 14) of building air filters. Based on targeted qPCR and sequence analysis, low efficiency upstream filters (MERV 8) were associated with a greater abundance of pathogenic bacteria and medically relevant fungi. As the implementation of air conditioning continues to grow worldwide, better understanding of the factors impacting microbial growth and ecology on cooling coils should enable more rational approaches for biofilm control and ultimately result in reduced energy consumption and healthier buildings.},
}
@article {pmid31844910,
year = {2020},
author = {Bridier, A and Piard, JC and Briandet, R and Bouchez, T},
title = {Emergence of a Synergistic Diversity as a Response to Competition in Pseudomonas putida Biofilms.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {47-59},
doi = {10.1007/s00248-019-01470-z},
pmid = {31844910},
issn = {1432-184X},
support = {SYSCOMM project DISCO, ANR-09-SYSC-003//French National Research Agency (ANR)/ ; },
mesh = {Adaptation, Physiological ; *Biofilms ; *Microbial Interactions ; Pseudomonas putida/*physiology ; },
abstract = {Genetic diversification through the emergence of variants is one of the known mechanisms enabling the adaptation of bacterial communities. We focused in this work on the adaptation of the model strain Pseudomonas putida KT2440 in association with another P. putida strain (PCL1480) recently isolated from soil to investigate the potential role of bacterial interactions in the diversification process. On the basis of colony morphology, three variants of P. putida KT2440 were obtained from co-culture after 168 h of growth whereas no variant was identified from the axenic KT2440 biofilm. The variants exhibited distinct phenotypes and produced biofilms with specific architecture in comparison with the ancestor. The variants better competed with the P. putida PCL1480 strain in the dual-strain biofilms after 24 h of co-culture in comparison with the ancestor. Moreover, the synergistic interaction of KT2440 ancestor and the variants led to an improved biofilm production and to higher competitive ability versus the PCL1480 strain, highlighting the key role of diversification in the adaptation of P. putida KT2440 in the mixed community. Whole genome sequencing revealed mutations in polysaccharides biosynthesis protein, membrane transporter, or lipoprotein signal peptidase genes in variants.},
}
@article {pmid31844283,
year = {2020},
author = {Wang, S and Li, L and Li, H and Sahu, SK and Wang, H and Xu, Y and Xian, W and Song, B and Liang, H and Cheng, S and Chang, Y and Song, Y and Çebi, Z and Wittek, S and Reder, T and Peterson, M and Yang, H and Wang, J and Melkonian, B and Van de Peer, Y and Xu, X and Wong, GK and Melkonian, M and Liu, H and Liu, X},
title = {Genomes of early-diverging streptophyte algae shed light on plant terrestrialization.},
journal = {Nature plants},
volume = {6},
number = {2},
pages = {95-106},
pmid = {31844283},
issn = {2055-0278},
mesh = {*Biological Evolution ; Chlorophyta/*genetics ; *Genome, Plant ; },
abstract = {Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.},
}
@article {pmid31838570,
year = {2020},
author = {Li, XD and Chen, YH and Liu, C and Hong, J and Deng, H and Yu, DJ},
title = {Eutrophication and Related Antibiotic Resistance of Enterococci in the Minjiang River, China.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {1-13},
doi = {10.1007/s00248-019-01464-x},
pmid = {31838570},
issn = {1432-184X},
support = {2016YFD0501310//State Key Development Program during the 13th Five-Year Plan period of China/ ; 31272606//National Natural Science Foundation of China/ ; 31602106//National Natural Science Foundation of China/ ; 2017J01598//Natural Science Foundation of Fujian Province/ ; },
mesh = {Biological Oxygen Demand Analysis ; China ; *Drug Resistance, Microbial ; Enterococcus/*drug effects/isolation &amp; purification/physiology ; *Eutrophication ; Nitrogen/analysis ; Phosphorus/analysis ; Rivers/chemistry/*microbiology ; },
abstract = {Antimicrobial resistance (AMR) in the aquatic environment has received increasing attention in recent years, and growing eutrophication problems may contribute to AMR in aquatic ecosystems. To evaluate whether and how eutrophication affects AMR, 40 surface water samples were collected from the Minjiang River, Fujian Province, China. Total nitrogen (TN), total phosphorus (TP), and chemical oxygen demand (CODMn) were measured as eutrophication factors. Additionally, enterococci species were isolated and their resistance to six common antibiotics was tested. Eutrophication generally showed a trend of increasing with the flow direction of the Minjiang River, with 25 sites (62.5%) having a TN/TP value over the Redfield value (16:1), which indicated that eutrophication in this region was of phosphorus limitation. High nutrition sites were in or near urban areas. Poor quality water was found in the middle and lower reaches of the Minjiang River system. The resistance frequency of 40 enterococci isolates to the six antibiotics tested was as follows: oxytetracycline > erythromycin > ciprofloxacin > chloramphenicol > ampicillin > vancomycin (70, 50, 17.5, 12.5, 2.5, 0%), and the multi-resistant rate reached 50% with eight resistance phenotypes. AMR also increased along the direction of water flow downstream, and most of the sites with the highest AMR were in or near urban areas, as was true for nutrition levels. Positive correlations between AMR and eutrophication factors (TN, TP, and CODMn) were identified using the Pearson's correlation coefficient, and TN/TP generally was negatively related to AMR. These results indicated that eutrophication may induce or selective for resistance of water-borne pathogens to antibiotics, with a high resistance level and a wide resistance spectrum.},
}
@article {pmid31838363,
year = {2020},
author = {Chun, SJ and Cui, Y and Lee, JJ and Choi, IC and Oh, HM and Ahn, CY},
title = {Network analysis reveals succession of Microcystis genotypes accompanying distinctive microbial modules with recurrent patterns.},
journal = {Water research},
volume = {170},
number = {},
pages = {115326},
doi = {10.1016/j.watres.2019.115326},
pmid = {31838363},
issn = {1879-2448},
mesh = {*Cyanobacteria ; Genotype ; *Microcystis ; RNA, Ribosomal, 16S ; Republic of Korea ; },
abstract = {Every member of the ecological community is connected via a network of vital and complex relationships, called the web of life. To elucidate the ecological network and interactions among producers, consumers, and decomposers in the Daechung Reservoir, Korea, during cyanobacterial harmful algal blooms (cyanoHAB), especially those involving Microcystis, we investigated the diversity and compositions of the cyanobacterial (16S rRNA gene), including the genotypes of Microcystis (cpcBA-IGS gene), non-cyanobacterial (16S), and eukaryotic (18S) communities through high-throughput sequencing. Microcystis blooms were divided into the Summer Major Bloom and Autumn Minor Bloom with different dominant genotypes of Microcystis. Network analysis demonstrated that the modules involved in the different phases of the Microcystis blooms were categorized into the Pre-Bloom, Bloom, Post-Bloom, and Non-Bloom Groups at all sampling stations. In addition, the non-cyanobacterial components of each Group were classified, while the same Group showed similarity across all stations, suggesting that Microcystis and other microbes were highly interdependent and organized into cyanoHAB-related module units. Importantly, the Microcystis genotype-based sub-network uncovered that Pirellula, Pseudanabaena, and Vampirovibrionales preferred to interact with specific Microcystis genotypes in the Summer Major Bloom than with other genotypes in the Autumn Minor Bloom, while the copepod Skistodiaptomus exhibited the opposite pattern. In conclusion, the transition patterns of cyanoHAB-related modules and their key components could be crucial in the succession of Microcystis genotypes and to enhance the understanding of microbial ecology in an aquatic environment.},
}
@article {pmid31838145,
year = {2019},
author = {Mickalide, H and Kuehn, S},
title = {Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community.},
journal = {Cell systems},
volume = {9},
number = {6},
pages = {521-533.e10},
doi = {10.1016/j.cels.2019.11.004},
pmid = {31838145},
issn = {2405-4720},
mesh = {Bacteria/metabolism/*pathogenicity ; Bacterial Physiological Phenomena ; Chlamydomonas reinhardtii/metabolism ; Ecology ; Escherichia coli/metabolism ; Microbiota/*physiology ; Population Dynamics ; Tetrahymena thermophila/metabolism ; },
abstract = {The composition of an ecosystem is thought to be important for determining its resistance to invasion. Studies of natural ecosystems, from plant to microbial communities, have found that more diverse communities are more resistant to invasion. In some cases, more diverse communities resist invasion by more completely consuming the resources necessary for the invader. We show that Escherichia coli can successfully invade cultures of the alga Chlamydomonas reinhardtii (phototroph) or the ciliate Tetrahymena thermophila (predator) but cannot invade a community where both are present. The invasion resistance of the algae-ciliate community arises from a higher-order interaction between species (interaction modification) that is unrelated to resource consumption. We show that the mode of this interaction is the algal inhibition of bacterial aggregation, which leaves bacteria vulnerable to predation. This mode requires both the algae and the ciliate to be present and provides an example of invasion resistance through an interaction modification.},
}
@article {pmid31837971,
year = {2020},
author = {Böllmann, J and Martienssen, M},
title = {Comparison of different media for the detection of denitrifying and nitrate reducing bacteria in mesotrophic aquatic environments by the most probable number method.},
journal = {Journal of microbiological methods},
volume = {168},
number = {},
pages = {105808},
doi = {10.1016/j.mimet.2019.105808},
pmid = {31837971},
issn = {1872-8359},
mesh = {Bacteria/growth &amp; development/metabolism ; Culture Media/*chemistry ; *Denitrification ; Fresh Water/*microbiology ; *Microbial Consortia ; Nitrates/*metabolism ; Probability ; Statistics as Topic ; Wastewater/*microbiology ; Water Purification ; },
abstract = {The cultivation based characterization of microbial communities and the quantification of certain functional bacterial groups is still an essential part of microbiology and microbial ecology. For plate count methods meanwhile low strength media are recommended, since they cover a broader range of different species and result in higher counts compared to established high strength media. For liquid media, as they are used for most probable number (MPN) quantifications, comparisons between high and low strength media are rare. In this study we compare the performance of different high and low strength media for the MPN quantification of nitrate reducing and denitrifying bacteria in two different fresh water environments. We also calculated the cell specific turnover rates of several denitrifying cultures previously enriched in high and low strength media from three different fresh water environments and a waste water treatment plant. For fresh water samples, our results indicate that high strength media detect higher MPN of denitrifying bacteria and in equal MPN of nitrate reducing bacteria compared to low strength media, which is in contrary to plate count techniques. For sediment samples, high and low strength media performed equal. The cell specific turnover rate was independent from the enrichment media and the media of the performance test. The cause of the lower denitrifyer MPN in low strength media remains, however, unclear. The results are important for further MPN quantifications of bacteria in nutrient poor environments and for calculations of nitrogen turnover rates by kinetical models using the number of metabolic active cells as one parameter.},
}
@article {pmid31836929,
year = {2020},
author = {Nyirabuhoro, P and Liu, M and Xiao, P and Liu, L and Yu, Z and Wang, L and Yang, J},
title = {Seasonal Variability of Conditionally Rare Taxa in the Water Column Bacterioplankton Community of Subtropical Reservoirs in China.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {14-26},
pmid = {31836929},
issn = {1432-184X},
support = {91851104//National Natural Science Foundation of China/ ; 31500372//National Natural Science Foundation of China/ ; KFJ-SW-YW036//Program of Field Station Alliance, Chinese Academy of Sciences/ ; 2019J02016//Natural Science Foundation of Fujian Province/ ; },
mesh = {Bacteria/*isolation &amp; purification ; Bacterial Physiological Phenomena ; China ; Lakes/*microbiology ; *Microbiota ; Plankton/*isolation &amp; purification ; Seasons ; Water Supply ; },
abstract = {Conditionally rare bacteria are ubiquitous and perhaps the most diverse of microbial lifeforms, but their temporal dynamics remain largely unknown. High-throughput and deep sequencing of the 16S rRNA gene has allowed us to identify and compare the conditionally rare taxa with other bacterioplankton subcommunities. In this study, we examined the effect of season, water depth, and ecological processes on the fluctuations of bacterial subcommunities (including abundant, conditionally rare, moderate, and rare taxa) from three subtropical reservoirs in China. We discovered that the conditionally rare taxa (CRT) made up 49.7 to 71.8% of the bacterioplankton community richness, and they accounted for 70.6 to 84.4% of the temporal changes in the community composition. Beta-diversity analysis revealed strong seasonal succession patterns among all bacterioplankton subcommunities, suggesting abundant, conditionally rare, moderate, and rare taxa subcommunities have comparable environmental sensitivity. The dominant phyla of CRT were Proteobacteria, Actinobacteria, and Bacteroidetes, whose variations were strongly correlated with environmental variables. Both deterministic and stochastic processes showed strong effect on bacterioplankton community assembly, with deterministic patterns more pronounced for CRT subcommunity. The difference in bacterial community composition was strongly linked with seasonal change rather than water depth. The seasonal patterns of CRT expand our understanding of underlying mechanisms for bacterial community structure and composition. This implies their importance in the function and stability of freshwater ecosystem after environmental disturbance.},
}
@article {pmid31836376,
year = {2020},
author = {Ntagia, E and Fiset, E and Truong Cong Hong, L and Vaiopoulou, E and Rabaey, K},
title = {Electrochemical treatment of industrial sulfidic spent caustic streams for sulfide removal and caustic recovery.},
journal = {Journal of hazardous materials},
volume = {388},
number = {},
pages = {121770},
doi = {10.1016/j.jhazmat.2019.121770},
pmid = {31836376},
issn = {1873-3336},
abstract = {Alkaline spent caustic streams (SCS) produced in the petrochemical and chemical manufacturing industry, contain high concentrations of reactive sulfide (HS[-]) and caustic soda (NaOH). Common treatment methods entail high operational costs while not recovering the possible resources that SCS contain. Here we studied the electrochemical treatment of SCS from a chemical manufacturing industry in an electrolysis cell, aiming at anodic HS[-] removal and cathodic NaOH, devoid of sulfide, recovery. Using a synthetic SCS we first evaluated the HS[-] oxidation product distribution over time, as well as the HS[-] removal and the NaOH recovery, as a function of current density. In a second step, we investigated the operational aspects of such treatment for the industrial SCS, under 300 A m[-2] fixed current density. In an electrolysis cell receiving 205 ± 60 g S L[-1] d[-1] HS[-] over 20 days of continuous operation, HS[-] was removed with a 38.0 ± 7.7 % removal and ∼80 % coulombic efficiency, with a concomitant recovery of a ∼12 wt.% NaOH solution. The low cell voltage obtained (1.75 ± 0.12 V), resulted in low energy requirements of 3.7 ± 0.6 kW h kg[-1] S and 6.3 ± 0.4 kW h kg[-1] NaOH and suggests techno-economic viability of this process.},
}
@article {pmid31835452,
year = {2019},
author = {Cancello, R and Turroni, S and Rampelli, S and Cattaldo, S and Candela, M and Cattani, L and Mai, S and Vietti, R and Scacchi, M and Brigidi, P and Invitti, C},
title = {Effect of Short-Term Dietary Intervention and Probiotic Mix Supplementation on the Gut Microbiota of Elderly Obese Women.},
journal = {Nutrients},
volume = {11},
number = {12},
pages = {},
pmid = {31835452},
issn = {2072-6643},
support = {RICCOR number: 2015_12_15_03//Ministero della Salute/ ; },
mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Body Weight/drug effects ; *Diet, Mediterranean ; Dietary Supplements ; Dysbiosis/diet therapy ; Feces ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Obesity/*diet therapy/genetics/*microbiology ; Probiotics/*therapeutic use ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Accumulating literature is providing evidence that the gut microbiota is involved in metabolic disorders, but the question of how to effectively modulate it to restore homeostasis, especially in the elderly, is still under debate. In this study, we profiled the intestinal microbiota of 20 elderly obese women (EO) at the baseline (T0), after 15 days of hypocaloric Mediterranean diet administered as part of a nutritional-metabolic rehabilitation program for obesity (T1), and after a further 15 days of the same diet supplemented with a probiotic mix (T2). Fecal samples were characterized by Illumina MiSeq sequencing of the 16S rRNA gene. The EO microbiota showed the typical alterations found in obesity, namely, an increase in potential pro-inflammatory components (i.e., Collinsella) and a decrease in health-promoting, short-chain fatty acid producers (i.e., Lachnospiraceae and Ruminococcaceae members), with a tendency to reduced biodiversity. After 15 days of the rehabilitation program, weight decreased by (2.7 ± 1.5)% and the gut microbiota dysbiosis was partially reversed, with a decline of Collinsella and an increase in leanness-related taxa. During the next 15 days of diet and probiotics, weight dropped further by (1.2 ± 1.1)%, markers of oxidative stress improved, and Akkermansia, a mucin degrader with beneficial effects on host metabolism, increased significantly. These findings support the relevant role of a correct dietetic approach, even in the short term, to modulate the EO gut microbiota towards a metabolic health-related configuration, counteracting the increased risk of morbidity in these patients.},
}
@article {pmid31835036,
year = {2019},
author = {Pachiadaki, MG and Brown, JM and Brown, J and Bezuidt, O and Berube, PM and Biller, SJ and Poulton, NJ and Burkart, MD and La Clair, JJ and Chisholm, SW and Stepanauskas, R},
title = {Charting the Complexity of the Marine Microbiome through Single-Cell Genomics.},
journal = {Cell},
volume = {179},
number = {7},
pages = {1623-1635.e11},
pmid = {31835036},
issn = {1097-4172},
support = {R21 AI134037/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Energy Metabolism ; *Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeography ; Plankton ; Seawater/*microbiology ; Single-Cell Analysis/methods ; Transcriptome ; },
abstract = {Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.},
}
@article {pmid31832698,
year = {2020},
author = {Huang, CL and Sarkar, R and Hsu, TW and Yang, CF and Chien, CH and Chang, WC and Chiang, TY},
title = {Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {133-144},
doi = {10.1007/s00248-019-01467-8},
pmid = {31832698},
issn = {1432-184X},
support = {106-2621-B-006-001-MY3//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Bacteria/classification/*isolation &amp; purification ; Biofuels ; Ecosystem ; *Ecotype ; *Endophytes ; Metagenomics ; *Microbiota ; Poaceae/*microbiology ; *Rhizosphere ; },
abstract = {Miscanthus in Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may help Miscanthus acclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes of M. sinensis that dwell habitats under different stresses. Proteobacteria and Actinobacteria predominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome in Miscanthus roots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g., Pseudomonas spp. for alpine and Agrobacterium spp. for coastal habitats. This suggests Miscanthus actively recruits an endosphere microbiome from the rhizosphere it influences.},
}
@article {pmid31831078,
year = {2019},
author = {Ricci, F and Rossetto Marcelino, V and Blackall, LL and Kühl, M and Medina, M and Verbruggen, H},
title = {Beneath the surface: community assembly and functions of the coral skeleton microbiome.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {159},
pmid = {31831078},
issn = {2049-2618},
mesh = {Animals ; Anthozoa/*microbiology ; Archaea/classification ; Bacteria/classification ; Biodiversity ; *Coral Reefs ; Microbiota/*physiology ; },
abstract = {Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.},
}
@article {pmid31828390,
year = {2020},
author = {Vick, SHW and Greenfield, P and Willows, RD and Tetu, SG and Midgley, DJ and Paulsen, IT},
title = {Subsurface Stappia: Success Through Defence, Specialisation and Putative Pressure-Dependent Carbon Fixation.},
journal = {Microbial ecology},
volume = {80},
number = {1},
pages = {34-46},
doi = {10.1007/s00248-019-01471-y},
pmid = {31828390},
issn = {1432-184X},
mesh = {Biomass ; *Carbon Cycle ; Coal ; Fresh Water/*microbiology ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Mining ; New South Wales ; Queensland ; Rhodobacteraceae/genetics/isolation &amp; purification/*physiology ; Species Specificity ; },
abstract = {Diverse microbial communities living in subsurface coal seams are responsible for important geochemical processes including the movement of carbon between the geosphere, biosphere and atmosphere. Microbial conversion of the organic matter in coal to methane involves a complex assemblage of bacteria and archaea working in syntrophic relationships. Despite the importance and value of this microbial process, very few of the microbial taxa have defined metabolic or ecological roles in these environments. Additionally, the genomic features mediating life in this chemically reduced, energy poor, deep subsurface environment are not well characterised. Here we describe the isolation and genomic and catabolic characterisation of three alphaproteobacterial Stappia indica species from three coal basins across Australia. S. indica genomes from coal seams were compared with those from closely related S. indica isolated from diverse surface waters, revealing a coal seam-specific suite of genes associated with life in the subsurface. These genes are linked to processes including viral defence, secondary metabolite production, polyamine metabolism, polypeptide uptake membrane transporters and putative energy neutral pressure-dependent CO2 fixation. This indicates that subsurface Stappia have diverse metabolisms for biomass recycling and pressure-dependent CO2 fixation and require a suite of defensive and competitive strategies relative to their surface-dwelling relatives.},
}
@article {pmid31828389,
year = {2020},
author = {Gnanasekaran, G and Lim, JY and Hwang, I},
title = {Disappearance of Quorum Sensing in Burkholderia glumae During Experimental Evolution.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {947-959},
doi = {10.1007/s00248-019-01445-0},
pmid = {31828389},
issn = {1432-184X},
support = {Grant 2010-0018280//National Research Foundation of Korea/ ; },
mesh = {*Biological Evolution ; Burkholderia/genetics/*physiology ; *Genome, Bacterial ; Mutation ; *Quorum Sensing ; Virulence Factors/physiology ; },
abstract = {The plant pathogen Burkholderia glumae uses quorum sensing (QS) that allows bacteria to share information and alter gene expression on the basis of cell density. The wild-type strain of B. glumae produces quorum-sensing signals (autoinducers) to detect their community and upregulate QS-dependent genes across the population for performing social and group behaviors. The model organism B. glumae was selected to investigate adaptation, estimate evolutionary parameters, and test diverse evolutionary hypotheses by using experimental evolution. The wild-type B. glumae virulent strain showed genotypic changes during regular subculture due to oxygen limitation. The laboratory-evolved clones failed to produce the signaling molecule of C8-HSL/C6-HSL for activation of the quorum-sensing system. Further, the laboratory-evolved clones failed to produce catalase and oxalate for protecting themselves from the toxic environment at stationary phase and phytotoxins (toxoflavin) for infecting rice grain, respectively. The laboratory-evolved clones were completely sequenced and compared with the wild-type. Sequencing analysis of the evolved clones revealed that mutations in QS-responsible genes (iclR), sensor genes (shk, mcp), and signaling genes (luxR) were responsible for quorum-sensing activity failure. The experimental results and sequencing analysis revealed quorum-sensing process failure in the laboratory-evolved clones. In conclusion, the wild-type B. glumae strain was often exposed to oxidative stress during regular subculture and evolved as an avirulent strain (quorum-sensing mutant) by losing the phenotypic and genotypic characteristics.},
}
@article {pmid31828388,
year = {2020},
author = {Brambilla, S and Soto, G and Odorizzi, A and Arolfo, V and McCormick, W and Primo, E and Giordano, W and Jozefkowicz, C and Ayub, N},
title = {Spontaneous Mutations in the Nitrate Reductase Gene napC Drive the Emergence of Eco-friendly Low-N2O-Emitting Alfalfa Rhizobia in Regions with Different Climates.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {1044-1053},
doi = {10.1007/s00248-019-01473-w},
pmid = {31828388},
issn = {1432-184X},
support = {FVT-39//Fondo de Valorizaci&#xf3;n Tecnol&#xf3;gica/ ; PICT-2017-0674//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; },
mesh = {Amino Acid Sequence ; Argentina ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; *Climate ; *Mutation ; Nitrate Reductases/chemistry/*genetics/metabolism ; Nitrous Oxide/*metabolism ; Phylogeny ; Sequence Alignment ; Sinorhizobium meliloti/genetics/*physiology ; },
abstract = {We have recently shown that commercial alfalfa inoculants (e.g., Sinorhizobium meliloti B399), which are closely related to the denitrifier model strain Sinorhizobium meliloti 1021, have conserved nitrate, nitrite, and nitric oxide reductases associated with the production of the greenhouse gas nitrous oxide (N2O) from nitrate but lost the N2O reductase related to the degradation of N2O to gas nitrogen. Here, we screened a library of nitrogen-fixing alfalfa symbionts originating from different ecoregions and containing N2O reductase genes and identified novel rhizobia (Sinorhizobium meliloti INTA1-6) exhibiting exceptionally low N2O emissions. To understand the genetic basis of this novel eco-friendly phenotype, we sequenced and analyzed the genomes of these strains, focusing on their denitrification genes, and found mutations only in the nitrate reductase structural gene napC. The evolutionary analysis supported that, in these natural strains, the denitrification genes were inherited by vertical transfer and that their defective nitrate reductase napC alleles emerged by independent spontaneous mutations. In silico analyses showed that mutations in this gene occurred in ssDNA loop structures with high negative free energy (-ΔG) and that the resulting mutated stem-loop structures exhibited increased stability, suggesting the occurrence of transcription-associated mutation events. In vivo assays supported that at least one of these ssDNA sites is a mutational hot spot under denitrification conditions. Similar benefits from nitrogen fixation were observed when plants were inoculated with the commercial inoculant B399 and strains INTA4-6, suggesting that the low-N2O-emitting rhizobia can be an ecological alternative to the current inoculants without resigning economic profitability.},
}
@article {pmid31827386,
year = {2019},
author = {Zheng, P and Wang, C and Zhang, X and Gong, J},
title = {Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites.},
journal = {Archaea (Vancouver, B.C.)},
volume = {2019},
number = {},
pages = {5108012},
pmid = {31827386},
issn = {1472-3654},
mesh = {Archaea/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Biodiversity ; Genes, Archaeal ; Genes, rRNA ; Geologic Sediments/*microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Zosteraceae/*growth &amp; development ; },
abstract = {Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P < 0.05), while Thaumarchaeota was favored in unvegetated sites (P = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, Bathyarchaeota, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (P < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities.},
}
@article {pmid31827245,
year = {2020},
author = {Hiraoka, S and Hirai, M and Matsui, Y and Makabe, A and Minegishi, H and Tsuda, M and Juliarni, and Rastelli, E and Danovaro, R and Corinaldesi, C and Kitahashi, T and Tasumi, E and Nishizawa, M and Takai, K and Nomaki, H and Nunoura, T},
title = {Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments.},
journal = {The ISME journal},
volume = {14},
number = {3},
pages = {740-756},
pmid = {31827245},
issn = {1751-7370},
mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Geologic Sediments/chemistry/*microbiology ; Japan ; *Microbiota ; Nitrates/metabolism ; Pacific Ocean ; },
abstract = {Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultradeep-sea microbial ecology, one of the last frontiers on our planet.},
}
@article {pmid31826981,
year = {2019},
author = {Klufa, J and Bauer, T and Hanson, B and Herbold, C and Starkl, P and Lichtenberger, B and Srutkova, D and Schulz, D and Vujic, I and Mohr, T and Rappersberger, K and Bodenmiller, B and Kozakova, H and Knapp, S and Loy, A and Sibilia, M},
title = {Hair eruption initiates and commensal skin microbiota aggravate adverse events of anti-EGFR therapy.},
journal = {Science translational medicine},
volume = {11},
number = {522},
pages = {},
doi = {10.1126/scitranslmed.aax2693},
pmid = {31826981},
issn = {1946-6242},
support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 27129/FWF_/Austrian Science Fund FWF/Austria ; P 31113/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; Antineoplastic Agents/*adverse effects ; Epidermis/pathology ; ErbB Receptors/*antagonists &amp; inhibitors/deficiency ; Fibroblast Growth Factor 7/metabolism ; Hair/*pathology ; Humans ; Inflammation/pathology ; Keratinocytes/pathology ; MAP Kinase Signaling System ; Membrane Glycoproteins/metabolism ; Mice ; *Microbiota ; Nerve Tissue Proteins/metabolism ; Skin/*microbiology/pathology ; },
abstract = {Epidermal growth factor receptor (EGFR)-targeted anticancer therapy induces stigmatizing skin toxicities affecting patients' quality of life and therapy adherence. The lack of mechanistic details underlying these adverse events hampers their management. We found that EGFR/ERK signaling is required in LRIG1-positive stem cells during de novo hair eruption to secure barrier integrity and prevent the invasion of commensal microbiota and inflammatory skin disease. EGFR-deficient epidermis is permissive for microbiota outgrowth and displays an atopic-like TH2-dominated signature. The opening of the follicular ostia during hair eruption allows invasion of commensal microbiota into the hair follicle, initiating an additional TH1 and TH17 response culminating in chronic folliculitis. Restoration of epidermal ERK signaling via prophylactic FGF7 treatment or transgenic SOS expression rescues the barrier defect in the absence of EGFR, highlighting a therapeutic anchor point. These data reveal that commensal skin microbiota provoke atopic-like inflammatory skin diseases by invading into the follicular opening of erupting hair.},
}
@article {pmid31824766,
year = {2019},
author = {Carruthers, LV and Moses, A and Adriko, M and Faust, CL and Tukahebwa, EM and Hall, LJ and Ranford-Cartwright, LC and Lamberton, PHL},
title = {The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e8133},
pmid = {31824766},
issn = {2167-8359},
support = {//Wellcome Trust/United Kingdom ; BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: Multiple factors can influence stool sample integrity upon sample collection. Preservation of faecal samples for microbiome studies is therefore an important step, particularly in tropical regions where resources are limited and high temperatures may significantly influence microbiota profiles. Freezing is the accepted standard to preserve faecal samples however, cold chain methods are often unfeasible in fieldwork scenarios particularly in low and middle-income countries and alternatives are required. This study therefore aimed to address the impact of different preservative methods, time-to-freezing at ambient tropical temperatures, and stool heterogeneity on stool microbiome diversity and composition under real-life physical environments found in resource-limited fieldwork conditions.<br><br>METHODS: Inner and outer stool samples collected from one specimen obtained from three children were stored using different storage preservation methods (raw, ethanol and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these techniques and frozen at different time-to-freezing intervals post-collection from 0-32 h. Metataxonomic profiling was used to profile samples, targeting the V1-V2 regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed, combined and aligned to the Greengenes database. Microbial diversity and composition data were generated and analysed using Quantitative Insights Into Microbial Ecology and R software.<br><br>RESULTS: Child donor was the greatest predictor of microbiome variation between the stool samples, with all samples remaining identifiable to their child of origin despite the stool being stored under a variety of conditions. However, significant differences were observed in composition and diversity between preservation techniques, but intra-preservation technique variation was minimal for all preservation methods, and across the time-to-freezing range (0-32 h) used. Stool heterogeneity yielded no apparent microbiome differences.<br><br>CONCLUSIONS: Stool collected in a fieldwork setting for comparative microbiome analyses should ideally be stored as consistently as possible using the same preservation method throughout.},
}
@article {pmid31824462,
year = {2019},
author = {Liu, D and Zhang, P and Chen, D and Howell, K},
title = {From the Vineyard to the Winery: How Microbial Ecology Drives Regional Distinctiveness of Wine.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2679},
pmid = {31824462},
issn = {1664-302X},
abstract = {Wine production is a complex process from the vineyard to the winery. On this journey, microbes play a decisive role. From the environment where the vines grow, encompassing soil, topography, weather and climate through to management practices in vineyards, the microbes present can potentially change the composition of wine. Introduction of grapes into the winery and the start of winemaking processes modify microbial communities further. Recent advances in next-generation sequencing (NGS) technology have progressed our understanding of microbial communities associated with grapes and fermentations. We now have a finer appreciation of microbial diversity across wine producing regions to begin to understand how diversity can contribute to wine quality and style characteristics. In this review, we highlight literature surrounding wine-related microorganisms and how these affect factors interact with and shape microbial communities and contribute to wine quality. By discussing the geography, climate and soil of environments and viticulture and winemaking practices, we claim microbial biogeography as a new perspective to impact wine quality and regionality. Depending on geospatial scales, habitats, and taxa, the microbial community respond to local conditions. We discuss the effect of a changing climate on local conditions and how this may alter microbial diversity and thus wine style. With increasing understanding of microbial diversity and their effects on wine fermentation, wine production can be optimised with enhancing the expression of regional characteristics by understanding and managing the microbes present.},
}
@article {pmid31823065,
year = {2020},
author = {Schultz, J and Rosado, AS},
title = {Extreme environments: a source of biosurfactants for biotechnological applications.},
journal = {Extremophiles : life under extreme conditions},
volume = {24},
number = {2},
pages = {189-206},
pmid = {31823065},
issn = {1433-4909},
mesh = {Bacteria ; Biotechnology ; *Extreme Environments ; Petroleum ; Surface-Active Agents ; },
abstract = {The surfactant industry moves billions of dollars a year and consists of chemically synthesized molecules usually derived from petroleum. Surfactant is a versatile molecule that is widely used in different industrial areas, with an emphasis on the petroleum, biomedical and detergent industries. Recently, interest in environmentally friendly surfactants that are resistant to extreme conditions has increased because of consumers' appeal for sustainable products and industrial processes that often require these characteristics. With this context, the need arises to search for surfactants produced by microorganisms coming from extreme environments and to mine their unique biotechnological potential. The production of biosurfactants is still incipient and presents challenges regarding economic viability due to the high costs of cultivation, production, recovery and purification. Advances can be made by exploring the extreme biosphere and bioinformatics tools. This review focuses on biosurfactants produced by microorganisms from different extreme environments, presenting a complete overview of what information is available in the literature, including the advances, challenges and future perspectives, as well as showing the possible applications of extreme biosurfactants.},
}
@article {pmid31822601,
year = {2019},
author = {Sogin, EM and Puskás, E and Dubilier, N and Liebeke, M},
title = {Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography-Mass Spectrometry.},
journal = {mSystems},
volume = {4},
number = {6},
pages = {},
pmid = {31822601},
issn = {2379-5077},
abstract = {Microbial communities exchange molecules with their environment, which plays a major role in regulating global biogeochemical cycles and climate. While extracellular metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats limits the nontargeted analyses of the ocean exometabolome using mass spectrometry (MS). Current methods require salt removal prior to sample measurements, which can alter the molecular composition of the metabolome and limit the types of compounds detected by MS. To overcome these limitations, we developed a gas chromatography MS (GC-MS) method that avoids sample altering during salt removal and that detects metabolites down to nanomolar concentrations from less than 1 ml of seawater. We applied our method (SeaMet) to explore marine metabolomes in vitro and in vivo First, we measured the production and consumption of metabolites during the culture of a heterotrophic bacterium, Marinobacter adhaerens Our approach revealed successional uptake of amino acids, while sugars were not consumed. These results show that exocellular metabolomics provides insights into nutrient uptake and energy conservation in marine microorganisms. We also applied SeaMet to explore the in situ metabolome of coral reef and mangrove sediment porewaters. Despite the fact that these ecosystems occur in nutrient-poor waters, we uncovered high concentrations of sugars and fatty acids, compounds predicted to play a key role for the abundant and diverse microbial communities in coral reef and mangrove sediments. Our data demonstrate that SeaMet advances marine metabolomics by enabling a nontargeted and quantitative analysis of marine metabolites, thus providing new insights into nutrient cycles in the oceans.IMPORTANCE Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection. Considering that the oceans contain the largest dissolved organic matter pool on Earth, describing the marine metabolome using nontargeted approaches is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage. Our method complements both targeted marine metabolomic investigations as well as other "omics" (e.g., genomics, transcriptomics, and proteomics) approaches by providing an avenue for studying the chemical interaction between marine microbes and their habitats.},
}
@article {pmid31821931,
year = {2020},
author = {Sun, H and Mei, R and Zhang, XX and Ren, H and Liu, WT and Ye, L},
title = {Bacterial enrichment in highly-selective acetate-fed bioreactors and its application in rapid biofilm formation.},
journal = {Water research},
volume = {170},
number = {},
pages = {115359},
doi = {10.1016/j.watres.2019.115359},
pmid = {31821931},
issn = {1879-2448},
mesh = {Acetates ; Bacteria ; Biofilms ; *Bioreactors ; RNA, Ribosomal, 16S ; *Sewage ; Waste Disposal, Fluid ; },
abstract = {In this study, we systematically investigated the bacterial community dynamics in highly-selective (strong hydraulic selection pressure and high organic loading rate) bioreactors with acetate as the sole carbon source. 16S rRNA gene high-throughput sequencing and metagenomic sequencing results showed that phenolics-degrading bacteria (PDB), which were mainly Acinetobacter species, in the newly-formed aerobic granules could account for >70% of the total bacteria. Near full-length 16S rRNA gene sequences obtained by cloning suggest that the PDB are potentially novel species because they are distantly related to known Acinetobacter species. However, these PDB only temporarily appeared in the early stage of the granule formation and their abundance quickly decreased along the reactor operation. To retain these PDB, we demonstrated that the newly-formed aerobic granules could accelerate biofilm formation in moving bed biofilm reactors (MBBRs), and the biofilm carriers showed gradually-increased phenol degradation performance in the MBBRs. While, the bacterial community in biofilm significantly changed during the operation process of the MBBRs and the community structure became more complicated than that in the aerobic granules. Collectively, this study provides new insights into the microbial ecology of sludge granulation and biofilm formation process in the wastewater treatment systems for remediating phenolic matters.},
}
@article {pmid31820074,
year = {2020},
author = {Tong, Q and Hu, ZF and Du, XP and Bie, J and Wang, HB},
title = {Effects of Seasonal Hibernation on the Similarities Between the Skin Microbiota and Gut Microbiota of an Amphibian (Rana dybowskii).},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {898-909},
doi = {10.1007/s00248-019-01466-9},
pmid = {31820074},
issn = {1432-184X},
mesh = {Animals ; China ; Female ; Gastrointestinal Microbiome ; Hibernation ; High-Throughput Nucleotide Sequencing ; Intestine, Large/*microbiology ; Intestine, Small/*microbiology ; Male ; *Microbiota ; Ranidae/*microbiology ; Seasons ; Sequence Analysis, DNA ; Skin/*microbiology ; },
abstract = {Both the gut and skin microbiotas have important functions for amphibians. The gut microbiota plays an important role in both the health and evolution of the host species, whereas the role of skin microbiota in disease resistance is particularly important for amphibians. Many studies have examined the effects of environmental factors on the skin and gut microbiotas, but no study has yet explored the similarities between the skin and gut microbiotas. In this study, the gut and skin microbiotas of Rana dybowskii in summer and winter were investigated via high-throughput Illumina sequencing. The results showed that the alpha diversity of gut and skin microbiotas decreased significantly from summer to winter. In both seasons, the microbial composition and structure differed significantly between the gut and skin, and the similarities between these microbiotas differed between seasons. The pairwise distances between the gut and skin microbiotas were greater in winter than in summer. The ratio of core OTUs and shared OTUs to the sum of the OTUs in the gut and skin microbiotas in summer was significantly higher than that in winter. The similarities between the gut and skin microbiotas are important for understanding amphibian ecology and life history.},
}
@article {pmid31820073,
year = {2020},
author = {Arai, H and Lin, SR and Nakai, M and Kunimi, Y and Inoue, MN},
title = {Closely Related Male-Killing and Nonmale-Killing Wolbachia Strains in the Oriental Tea Tortrix Homona magnanima.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {1011-1020},
doi = {10.1007/s00248-019-01469-6},
pmid = {31820073},
issn = {1432-184X},
mesh = {Animals ; Insect Proteins/analysis ; Larva/genetics/growth &amp; development/microbiology ; Moths/genetics/growth &amp; development/*microbiology ; Phenotype ; Sex Factors ; Sex Ratio ; Symbiosis ; Taiwan ; Wolbachia/genetics/*physiology ; },
abstract = {Wolbachia are inherited intracellular bacteria that cause male-specific death in some arthropods, called male-killing. To date, three Wolbachia strains have been identified in the oriental tea tortrix Homona magnanima (Tortricidae, Lepidoptera); however, none of these caused male-killing in the Japanese population. Here, we describe a male-killing Wolbachia strain in Taiwanese H. magnanima. From field-collected H. magnanima, two female-biased host lines were established, and antibiotic treatments revealed Wolbachia (wHm-t) as the causative agent of male-killing. The wsp and MLST genes in wHm-t are identical to corresponding genes in the nonmale-killing strain wHm-c from the Japanese population, implying a close relationship of the two strains. Crossing the Japanese and Taiwanese H. magnanima revealed that Wolbachia genotype rather than the host genetic background was responsible for the presence of the male-killing phenotype. Quantitative PCR analyses revealed that the density of wHm-t was higher than that of other Wolbachia strains in H. magnanima, including wHm-c. The densities of wHm-t were also heterogeneous between host lines. Notably, wHm-t in the low-density and high-density lines carried identical wsp and MLST genes but had distinct lethal patterns. Furthermore, over 90% of field-collected lines of H. magnanima in Taiwan were infected with wHm-t, although not all host lines harboring wHm-t showed male-killing. The host lines that showed male-killing harbored a high density of Wolbachia compared to the host lines that did not show male-killing. Thus, the differences in the phenotypes appear to be dependent on biological and genetic characteristics of closely related Wolbachia strains.},
}
@article {pmid31820072,
year = {2020},
author = {Basili, D and Lutfi, E and Falcinelli, S and Balbuena-Pecino, S and Navarro, I and Bertolucci, C and Capilla, E and Carnevali, O},
title = {Photoperiod Manipulation Affects Transcriptional Profile of Genes Related to Lipid Metabolism and Apoptosis in Zebrafish (Danio rerio) Larvae: Potential Roles of Gut Microbiota.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {933-946},
doi = {10.1007/s00248-019-01468-7},
pmid = {31820072},
issn = {1432-184X},
support = {AGL2014-57974-R//Ministerio de Econom&#xed;a y Competitividad/ ; AGL2017-89436-R//Ministerio de Econom&#xed;a y Competitividad/ ; FA2015//Universit&#xe0; Politecnica delle Marche/ ; FAR2018//Universit&#xe0; degli Studi di Ferrara/ ; FIR2018//Universit&#xe0; degli Studi di Ferrara/ ; },
mesh = {Animals ; *Apoptosis ; Circadian Rhythm ; Fish Proteins/metabolism ; Gastrointestinal Microbiome/*physiology ; *Lipid Metabolism ; *Photoperiod ; Probiotics/administration &amp; dosage ; Real-Time Polymerase Chain Reaction ; *Transcriptome ; Zebrafish/*microbiology/physiology ; },
abstract = {Gut microbiota plays a fundamental role in maintaining host's health by controlling a wide range of physiological processes. Administration of probiotics and manipulation of photoperiod have been suggested as modulators of microbial composition and are currently undergoing an extensive research in aquaculture as a way to improve health and quality of harvested fish. However, our understanding regarding their effects on physiological processes is still limited. In the present study we investigated whether manipulation of photoperiod and/or probiotic administration was able to alter microbial composition in zebrafish larvae at hatching stage. Our findings show that probiotic does not elicit effects while photoperiod manipulation has a significant impact on microbiota composition. Moreover, we successfully predicted lipid biosynthesis and apoptosis to be modulated by microbial communities undergoing continuous darkness. Interestingly, expression levels of caspase 3 gene (casp3) and lipid-related genes (hnf4a, npc1l1, pparγ, srebf1, agpat4 and fitm2) were found to be significantly overexpressed in dark-exposed larvae, suggesting an increase in the occurrence of apoptotic processes and a lipid metabolism impairment, respectively (p < 0.05). Our results provide the evidence that microbial communities in zebrafish at early life stages are not modulated by a short administration of probiotics and highlight the significant effect that dark photoperiod elicits on zebrafish microbiota and potentially on health.},
}
@article {pmid31819142,
year = {2019},
author = {Costa, JH and Wassano, CI and Angolini, CFF and Scherlach, K and Hertweck, C and Pacheco Fill, T},
title = {Antifungal potential of secondary metabolites involved in the interaction between citrus pathogens.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {18647},
pmid = {31819142},
issn = {2045-2322},
mesh = {Antifungal Agents/metabolism ; Citrus/genetics/*growth &amp; development/parasitology ; Fruit/microbiology ; Fungal Proteins/*genetics/metabolism ; Fungi/drug effects/pathogenicity ; Fungicides, Industrial/pharmacology ; Mass Spectrometry ; Penicillium/*metabolism/pathogenicity ; Plant Diseases/genetics/*microbiology ; Spores, Fungal/metabolism ; },
abstract = {Numerous postharvest diseases have been reported that cause substantial losses of citrus fruits worldwide. Penicillium digitatum is responsible for up to 90% of production losses, and represent a problem for worldwide economy. In order to control phytopathogens, chemical fungicides have been extensively used. Yet, the use of some artificial fungicides cause concerns about environmental risks and fungal resistance. Therefore, studies focusing on new approaches, such as the use of natural products, are getting attention. Co-culture strategy can be applied to discover new bioactive compounds and to understand microbial ecology. Mass Spectrometry Imaging (MSI) was used to screen for potential antifungal metabolites involved in the interaction between Penicillium digitatum and Penicillium citrinum. MSI revealed a chemical warfare between the fungi: two tetrapeptides, deoxycitrinadin A, citrinadin A, chrysogenamide A and tryptoquialanines are produced in the fungi confrontation zone. Antimicrobial assays confirmed the antifungal activity of the investigated metabolites. Also, tryptoquialanines inhibited sporulation of P. citrinum. The fungal metabolites reported here were never described as antimicrobials until this date, demonstrating that co-cultures involving phytopathogens that compete for the same host is a positive strategy to discover new antifungal agents. However, the use of these natural products on the environment, as a safer strategy, needs further investigation. This paper aimed to contribute to the protection of agriculture, considering health and ecological risks.},
}
@article {pmid31817158,
year = {2019},
author = {D'Amico, F and Biagi, E and Rampelli, S and Fiori, J and Zama, D and Soverini, M and Barone, M and Leardini, D and Muratore, E and Prete, A and Gotti, R and Pession, A and Masetti, R and Brigidi, P and Turroni, S and Candela, M},
title = {Enteral Nutrition in Pediatric Patients Undergoing Hematopoietic SCT Promotes the Recovery of Gut Microbiome Homeostasis.},
journal = {Nutrients},
volume = {11},
number = {12},
pages = {},
pmid = {31817158},
issn = {2072-6643},
support = {GR-2013-02357136//Ministero della Salute/ ; },
mesh = {Child ; *Enteral Nutrition ; Fatty Acids, Volatile/analysis/metabolism ; Feces/chemistry ; *Gastrointestinal Microbiome/genetics ; Graft vs Host Disease/prevention &amp; control ; *Hematopoietic Stem Cell Transplantation ; Homeostasis/physiology ; Humans ; *Parenteral Nutrition ; },
abstract = {Hematopoietic stem cell transplantation (HSCT) is the first-line immunotherapy to treat several hematologic disorders, although it can be associated with many complications reducing the survival rate, such as acute graft-versus-host disease (aGvHD) and infections. Given the fundamental role of the gut microbiome (GM) for host health, it is not surprising that a suboptimal path of GM recovery following HSCT may compromise immune homeostasis and/or increase the risk of opportunistic infections, with an ultimate impact in terms of aGvHD onset. Traditionally, the first nutritional approach in post-HSCT patients is parenteral nutrition (PN), which is associated with several clinical adverse effects, supporting enteral nutrition (EN) as a preferential alternative. The aim of the study was to evaluate the impact of EN vs. PN on the trajectory of compositional and functional GM recovery in pediatric patients undergoing HSCT. The GM structure and short-chain fatty acid (SCFA) production profiles were analyzed longitudinally in twenty pediatric patients receiving HSCT-of which, ten were fed post-transplant with EN and ten with total PN. According to our findings, we observed the prompt recovery of a structural and functional eubiotic GM layout post-HSCT only in EN subjects, thus possibly reducing the risk of systemic infections and GvHD onset.},
}
@article {pmid31816089,
year = {2019},
author = {Linsmith, G and Rombauts, S and Montanari, S and Deng, CH and Celton, JM and Guérif, P and Liu, C and Lohaus, R and Zurn, JD and Cestaro, A and Bassil, NV and Bakker, LV and Schijlen, E and Gardiner, SE and Lespinasse, Y and Durel, CE and Velasco, R and Neale, DB and Chagné, D and Van de Peer, Y and Troggio, M and Bianco, L},
title = {Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.).},
journal = {GigaScience},
volume = {8},
number = {12},
pages = {},
pmid = {31816089},
issn = {2047-217X},
mesh = {Chromosomes, Plant/*genetics ; Contig Mapping/*methods ; Genome Size ; Haploidy ; Molecular Sequence Annotation ; Plant Breeding ; Pyrus/*genetics ; Sequence Analysis, DNA ; Synteny ; },
abstract = {BACKGROUND: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis.<br><br>FINDINGS: A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.<br><br>CONCLUSIONS: We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.},
}
@article {pmid31813647,
year = {2020},
author = {Sutherland, WJ and Dias, MP and Dicks, LV and Doran, H and Entwistle, AC and Fleishman, E and Gibbons, DW and Hails, R and Hughes, AC and Hughes, J and Kelman, R and Le Roux, X and LeAnstey, B and Lickorish, FA and Maggs, L and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Pretty, J and Spalding, MD and Tonneijck, FH and Wentworth, J and Thornton, A},
title = {A Horizon Scan of Emerging Global Biological Conservation Issues for 2020.},
journal = {Trends in ecology &amp; evolution},
volume = {35},
number = {1},
pages = {81-90},
doi = {10.1016/j.tree.2019.10.010},
pmid = {31813647},
issn = {1872-8383},
mesh = {*Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; Forecasting ; Forests ; },
abstract = {In this horizon scan, we highlight 15 emerging issues of potential relevance to global conservation in 2020. Seven relate to potentially extensive changes in vegetation or ecological systems. These changes are either relatively new, for example, conversion of kelp forests to simpler macroalgal systems, or may occur in the future, for example, as a result of the derivation of nanocelluose from wood or the rapid expansion of small hydropower schemes. Other topics highlight potential changes in national legislation that may have global effect on international agreements. Our panel of 23 scientists and practitioners selected these issues using a modified version of the Delphi technique from a long-list of 89 potential topics.},
}
@article {pmid31813285,
year = {2021},
author = {Ritter, MR and Tempesta de, OM and Makimori, RY and Sereia, AL and Simionato, AS and Chierrito, D and Galdino, AF and Gonçalves de, OA and Brentan da, SD and Novello, CR and Cristina de, MD and Benedito Prado, DF and João Carlos Palazzo de, M},
title = {Dimeric glycosylated flavan-3-ol and antimicrobial in vitro evaluation of Trichilia catigua extracts.},
journal = {Natural product research},
volume = {35},
number = {19},
pages = {3293-3300},
doi = {10.1080/14786419.2019.1698569},
pmid = {31813285},
issn = {1478-6427},
mesh = {Anti-Bacterial Agents/isolation &amp; purification/*pharmacology ; Brazil ; Catechin/isolation &amp; purification ; Flavonoids/isolation &amp; purification/*pharmacology ; *Meliaceae/chemistry ; Phytochemicals/isolation &amp; purification/pharmacology ; Plant Bark/chemistry ; Plant Extracts/pharmacology ; },
abstract = {Trichilia catigua is a tree known as "catuaba", widely distributed in Brazil. Studies carried out with T. catigua barks suggest that plant has antidepressant, antidiabetic, antimicrobial, antioxidant, antiviral, and preventive against brain damage. The aim of this work was to isolate and characterise compounds from the semipurified fraction of T. catigua barks, and to conduct microbiological screening against bacteria and fungi. The crude extract (CE) of "catuaba" was produced by turbo extraction with acetone-water, and later, partitioned to yield ethyl-acetate (EAF) and aqueous (AqF) fractions. From AqF the new catechin-3-O-α-L-rhamnoside-(4α→8)-epicatechin was isolated, identified, and described here for the first time. Regarding antimicrobial activity, the extracts presented impressive results, mainly for Vancomycin Resistant Enterococcus faecium (VREfm) with MIC of 156.5 μg/mL. The results suggest that extract of T. catigua could potentially be used as an adjuvant to treatment and is a promising candidate for the development of new antimicrobial drugs.},
}
@article {pmid31812391,
year = {2020},
author = {Rowles, LS and Hossain, AI and Aggarwal, S and Kirisits, MJ and Saleh, NB},
title = {Water quality and associated microbial ecology in selected Alaska Native communities: Challenges in off-the-grid water supplies.},
journal = {The Science of the total environment},
volume = {711},
number = {},
pages = {134450},
doi = {10.1016/j.scitotenv.2019.134450},
pmid = {31812391},
issn = {1879-1026},
mesh = {*Alaska Natives ; Arctic Regions ; *Groundwater ; Humans ; United States ; Water Quality ; Water Supply ; },
abstract = {The availability of safe water for potable purposes in Alaska Native communities is limited due to naturally occurring metals and contaminants released from anthropogenic activities, such as drilling and mining. The impacts of climate change are magnified in the arctic and sub-arctic regions and thus have the potential to mobilize contaminants and exacerbate the water contamination problem. Alaska Native communities are vulnerable to such changes in their water quality because of their remote location and limited access to resources. This study initiates an assessment of water quality, including its microbial ecology, in off-the-grid Alaskan water supplies (i.e., primarily groundwater wells). In particular, water quality data were collected from nine communities (22 ground water wells). Water quality analyses included basic water quality parameters, a suite of metals relevant to human health, and microbial community composition. Results revealed location-specific elevated arsenic concentrations based on the underlying geological formation, particularly in the areas located in the geological formation of the McHugh Complex. Diverse microbial communities were observed, and the grouping appeared to be based on elevation. These findings present evidence of compromised water quality in an understudied area in the United States. The results from this study should be considered as a snapshot in time, which highlight the importance for further systematic studies in similar off-the-grid communities.},
}
@article {pmid31812098,
year = {2020},
author = {Neckovic, A and van Oorschot, RAH and Szkuta, B and Durdle, A},
title = {Investigation of direct and indirect transfer of microbiomes between individuals.},
journal = {Forensic science international. Genetics},
volume = {45},
number = {},
pages = {102212},
doi = {10.1016/j.fsigen.2019.102212},
pmid = {31812098},
issn = {1878-0326},
mesh = {DNA, Bacterial/genetics ; Forensic Genetics/methods ; Glass ; Humans ; Microbiota/*genetics ; Paper ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; Textiles ; *Touch ; },
abstract = {The human microbiome encompasses the fungi, bacteria and viruses that live on, within, and immediately surrounding the body. Microbiomes have potential utility in forensic science as an evidentiary tool to link or exclude persons of interest associated with criminal activities. Research has shown the microbiome is individualised, and that personal microbial signatures can be recovered from surfaces such as phones, shoes and fabrics. Before the human microbiome may be used as an investigative tool, further research is required to investigate the utility and potential limitations surrounding microbial profiling. This includes the detectability of microbial transfer between individuals or items, the associated risks (such as contamination events) and the applicability of microbial profiling for forensic purposes. This research aimed to identify whether an individual's distinguishable microbiome could be transferred to another individual and onto substrates, and vice versa. Paper, cotton, and glass surfaces were chosen to represent a range of substrate matrices. The study involved six participants placed into three pairs; participants took part in two modes of transfer. Transfer Mode 1 involved the pair shaking hands, followed by rubbing a substrate in their right hand. Transfer Mode 2 involved individuals rubbing a substrate in their left hand, swapping substrates with their partner and then rubbing the swapped substrate in their left hand. 16S rRNA sequencing was performed on the extracted microbial DNA from participant and substrate samples. Quantitative Insights into Microbial Ecology 2 (QIIME 2) was used for sequence quality control and beta (between-sample) diversity analyses and taxonomic assignment. Principal Coordinate Analysis (PCoA) based on Jaccard distances was visualised through Emperor software to determine the phylogenetic similarity of bacterial communities between participants and among participant pairs. Statistical testing through PERMANOVA revealed significant differences in the Jaccard distances between each participant pair (P < 0.001), highlighting not only the potential distinguishability of skin microbiomes among individuals, but also the clustering effect observed between participant pairs due to the potential transfer of hand-associated microbiomes between individuals. The study demonstrated that transfer of the human skin microbiome had occurred between all participant pairs, regardless of substrate type or mode of transfer.},
}
@article {pmid31811330,
year = {2020},
author = {Wang, L and Xing, P and Li, H and Zhou, L and Wu, QL},
title = {Distinct Intra-lake Heterogeneity of Diazotrophs in a Deep Oligotrophic Mountain Lake.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {840-852},
doi = {10.1007/s00248-019-01461-0},
pmid = {31811330},
issn = {1432-184X},
support = {31730013//National Natural Science Foundation of China (CN)/ ; 41621002//National Natural Science Foundation of China (CN)/ ; QYZDJ-SSW-DQC030//the Key Research Program of Frontier Science, CAS/ ; },
mesh = {Bacteria/*metabolism ; Bacterial Proteins/analysis ; China ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; *Microbiota ; *Nitrogen Fixation ; Polymerase Chain Reaction ; },
abstract = {To date, little is known about the diazotrophs in freshwater ecosystems. In this study, we examined the diversity, abundance, and distribution of the diazotrophic community in the deep oligotrophic Lake Fuxian using high-throughput sequencing and quantitative polymerase chain reaction of nifH genes. Our results showed that the diazotrophs in Lake Fuxian were diverse and were distributed among Proteobacteria, Planctomycetes, Cyanobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi, and other unclassified environmental sequences. For the first time, it is found that Bacteroidetes and Planctomycetes harbor diazotrophs in freshwater ecosystems. The diazotrophic community compositions were significantly different between the littoral and pelagic zones in the surface layer, and they also changed dramatically along the vertical profile. High diazotrophic abundance and diversity were mostly observed in the surface littoral zone, and overall, a significant relationship between nifH gene richness and abundance was observed. The water turbidity, nitrite, and phosphorus were the most important factors explaining the spatial changes in diversity and abundances of this important functional group. The two most dominant operational taxonomic units belonging to Betaroproteobacteria and Planctomycetes demonstrated opposite distribution patterns in abundance that were driven by non-overlapping environmental factors. This study is by far the first to uncover the high diversity and intra-lake heterogeneity of diazotrophs in a freshwater lake and illuminate the controlling factors. It provides the probability of the co-occurrence of N2 fixation and N-loss in particles.},
}
@article {pmid31811036,
year = {2020},
author = {Hinger, I and Ansorge, R and Mussmann, M and Romano, S},
title = {Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus Pseudovibrio Suggest Distinct Evolutionary Trajectories and a Novel Genus, Polycladidibacter gen. nov.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {4},
pages = {},
pmid = {31811036},
issn = {1098-5336},
support = {P 31010/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Biological Evolution ; Genome, Bacterial ; *Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Rhodobacteraceae/*classification/genetics/*physiology ; },
abstract = {Bacteria belonging to the Pseudovibrio genus are widespread, metabolically versatile, and able to thrive as both free-living and host-associated organisms. Although more than 50 genomes are available, a comprehensive comparative genomics study to resolve taxonomic inconsistencies is currently missing. We analyzed all available genomes and used 552 core genes to perform a robust phylogenomic reconstruction. This in-depth analysis revealed the divergence of two monophyletic basal lineages of strains isolated from polyclad flatworm hosts, namely, Pseudovibrio hongkongensis and Pseudovibrio stylochi These strains have reduced genomes and lack sulfur-related metabolisms and major biosynthetic gene clusters, and their environmental distribution appears to be tightly associated with invertebrate hosts. We showed experimentally that the divergent strains are unable to utilize various sulfur compounds that, in contrast, can be utilized by the type strain Pseudovibrio denitrificans Our analyses suggest that the lineage leading to these two strains has been subject to relaxed purifying selection resulting in great gene loss. Overall genome relatedness indices (OGRI) indicate substantial differences between the divergent strains and the rest of the genus. While 16S rRNA gene analyses do not support the establishment of a different genus for the divergent strains, their substantial genomic, phylogenomic, and physiological differences strongly suggest a divergent evolutionary trajectory and the need for their reclassification. Therefore, we propose the novel genus Polycladidibacter gen. nov.IMPORTANCE The genus Pseudovibrio is commonly associated with marine invertebrates, which are essential for ocean health and marine nutrient cycling. Traditionally, the phylogeny of the genus has been based on 16S rRNA gene analysis. The use of the 16S rRNA gene or any other single marker gene for robust phylogenetic placement has recently been questioned. We used a large set of marker genes from all available Pseudovibrio genomes for in-depth phylogenomic analyses. We identified divergent monophyletic basal lineages within the Pseudovibrio genus, including two strains isolated from polyclad flatworms. These strains showed reduced sulfur metabolism and biosynthesis capacities. The phylogenomic analyses revealed distinct evolutionary trajectories and ecological adaptations that differentiate the divergent strains from the other Pseudovibrio members and suggest that they fall into a novel genus. Our data show the importance of widening the use of phylogenomics for better understanding bacterial physiology, phylogeny, and evolution.},
}
@article {pmid31811031,
year = {2020},
author = {Song, Y and Jiang, CY and Liang, ZL and Wang, BJ and Jiang, Y and Yin, Y and Zhu, HZ and Qin, YL and Cheng, RX and Liu, ZP and Liu, Y and Jin, T and Corvini, PF and Rabaey, K and Wang, AJ and Liu, SJ},
title = {Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous "Most-Wanted" Core Bacterial Taxon from Municipal Wastewater Treatment Plants.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {4},
pages = {},
pmid = {31811031},
issn = {1098-5336},
mesh = {Betaproteobacteria/*classification/genetics/*physiology ; Microbiota ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sewage/*microbiology ; },
abstract = {Microorganisms in wastewater treatment plants (WWTPs) play a key role in the removal of pollutants from municipal and industrial wastewaters. A recent study estimated that activated sludge from global municipal WWTPs harbors 1 × 10[9] to 2 × 10[9] microbial species, the majority of which have not yet been cultivated, and 28 core taxa were identified as "most-wanted" ones (L. Wu, D. Ning, B. Zhang, Y. Li, et al., Nat Microbiol 4:1183-1195, 2019, https://doi.org/10.1038/s41564-019-0426-5). Cultivation and characterization of the "most-wanted" core bacteria are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the performance of WWTPs. In this study, we isolated a bacterial strain, designated SJ-1, that represents a novel cluster within Betaproteobacteria and corresponds to OTU_16 within the 28 core taxa in the "most-wanted" list. Strain SJ-1 was identified and nominated as Casimicrobium huifangae gen. nov., sp. nov., of a novel family, Casimicrobiaceae. C. huifangae is ubiquitously distributed and is metabolically versatile. In addition to mineralizing various carbon sources (including carbohydrates, aromatic compounds, and short-chain fatty acids), C. huifangae is capable of nitrate reduction and phosphorus accumulation. The population of C. huifangae accounted for more than 1% of the bacterial population of the activated sludge microbiome from the Qinghe WWTP, which showed seasonal dynamic changes. Cooccurrence analysis suggested that C. huifangae was an important module hub in the bacterial network of Qinghe WWTP.IMPORTANCE The activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and the exploration of their physiology and ecology are limited. In this study, the core and novel bacterial taxon C. huifangae was cultivated and characterized. This study revealed that C. huifangae functioned as an important module hub in the activated sludge microbiome, and it potentially plays an important role in municipal wastewater treatment plants.},
}
@article {pmid31810817,
year = {2020},
author = {Estrella, MJ and Fontana, MF and Cumpa Velásquez, LM and Torres Tejerizo, GA and Diambra, L and Hansen, LH and Pistorio, M and Sannazzaro, AI},
title = {Mesorhizobium intechi sp. nov. isolated from nodules of Lotus tenuis in soils of the Flooding Pampa, Argentina.},
journal = {Systematic and applied microbiology},
volume = {43},
number = {1},
pages = {126044},
doi = {10.1016/j.syapm.2019.126044},
pmid = {31810817},
issn = {1618-0984},
mesh = {Argentina ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Genes, Bacterial/genetics ; Genes, Essential/genetics ; Genome, Bacterial/genetics ; Lotus/*microbiology ; Mesorhizobium/chemistry/*classification/cytology/physiology ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; },
abstract = {Three symbiotic nitrogen-fixing bacteria (BD68[T], BD66 and BD73) isolated from root nodules of Lotus tenuis in lowland soils of the Flooding Pampa (Argentina), previously classified as members of the Mesorhizobium genus, were characterized in this study. Phylogenetic analysis of their 16S rRNA gene sequences showed a close relationship to M. japonicum MAFF 303099[T], M. erdmanii USDA 3471[T], M. carmichaelinearum ICMP 18942[T], M. opportunistum WSM 2975[T] and M. jarvisii ATCC 33699[T], with sequence identities of 99.72%-100%. Multilocus sequence analysis of other housekeeping genes revealed that the three isolates belonged to a phylogenetically distinct clade within the genus Mesorhizobium. Strain BD68[T] was designated as the group representative and its genome was fully sequenced. The average nucleotide identity and in silico DNA-DNA hybridization comparisons between BD68[T] and the most related type strains showed values below the accepted threshold for species discrimination. Phenotypic and chemotaxonomic features were also studied. Based on these results, BD68[T], BD66 and BD73 could be considered to represent a novel species of the genus Mesorhizobium, for which the name Mesorhizobium intechi sp. nov. is hereby proposed. The type strain of this species is BD68[T] (=CECT 9304[T]=LMG 30179[T]).},
}
@article {pmid31807860,
year = {2020},
author = {Zhao, J and Li, G and Lu, W and Huang, S and Zhang, Z},
title = {Dominant and Subordinate Relationship Formed by Repeated Social Encounters Alters Gut Microbiota in Greater Long-Tailed Hamsters.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {998-1010},
doi = {10.1007/s00248-019-01462-z},
pmid = {31807860},
issn = {1432-184X},
support = {No. XDB11050300//"Strategic Priority Research Program" of the Chinese Academy of Sciences/ ; No. 152111KYSB20160089//International Partnership Program of Chinese Academy of Sciences/ ; No.152111KYSB20150023//External Cooperation Program of BIC, Chinese Academy of Sciences/ ; },
mesh = {Animals ; Bacteria/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Cricetinae/*microbiology/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; *Social Dominance ; },
abstract = {Social stress can dramatically influence the health of animals via communication between gut microbiota and the HPA system. However, this effect has been rarely investigated among different social ranked animals after chronic repeated social encounters. In this study, we evaluated changes and differences in microbiota among control, dominant, and subordinate male greater long-tailed hamsters (Tscherskia triton) over 28 successive days of repeated social encounter. Our results indicated that as compared with the control group, short-term repeated social encounters significantly altered fecal microbiota of subordinate hamsters, while chronic repeated social encounters altered colonic mucosa-associated microbiota of both dominant and subordinate hamsters. Fecal microbiota showed a transition in composition and diversity on day 2 for the subordinate group but on day 4 for the control and dominant groups under repeated encounters. Compared with their baseline, genus Lactobacillus increased in both dominant and subordinate groups, while genus Bifidobacterium increased in the subordinate group and genus Adlercreutzia increased in the dominant group. Our results suggest that chronic repeated social encounter can alter diversity and composition of gut microbiota of hamsters in both feces and colonic mucosa, but the latter performed better in reflecting the effects of chronic stress on microbiota in this species. Future studies should focus on elucidating how these microbiota alterations may affect animal behavior and fitness.},
}
@article {pmid31806445,
year = {2020},
author = {Qi, Y and Ossowicki, A and Yang, X and Huerta Lwanga, E and Dini-Andreote, F and Geissen, V and Garbeva, P},
title = {Effects of plastic mulch film residues on wheat rhizosphere and soil properties.},
journal = {Journal of hazardous materials},
volume = {387},
number = {},
pages = {121711},
doi = {10.1016/j.jhazmat.2019.121711},
pmid = {31806445},
issn = {1873-3336},
mesh = {Bacteria/drug effects ; Biodegradable Plastics/*pharmacology ; Biomass ; Microplastics/*pharmacology ; Polyethylene/*pharmacology ; *Rhizosphere ; Soil/chemistry ; Soil Pollutants/*pharmacology ; Triticum/*drug effects ; Volatile Organic Compounds/metabolism ; },
abstract = {Plastic residues could accumulate in soils as a consequence of using plastic mulching, which results in a serious environmental concern for agroecosystems. As an alternative, biodegradable plastic films stand as promising products to minimize plastic debris accumulation and reduce soil pollution. However, the effects of residues from traditional and biodegradable plastic films on the soil-plant system are not well studied. In this study, we used a controlled pot experiment to investigate the effects of macro- and micro- sized residues of low-density polyethylene and biodegradable plastic mulch films on the rhizosphere bacterial communities, rhizosphere volatile profiles and soil chemical properties. Interestingly, we identified significant effects of biodegradable plastic residues on the rhizosphere bacterial communities and on the blend of volatiles emitted in the rhizosphere. For example, in treatments with biodegradable plastics, bacteria genera like Bacillus and Variovorax were present in higher relative abundances and volatile compounds like dodecanal were exclusively produced in treatment with biodegradable microplastics. Furthermore, significant differences in soil pH, electrical conductivity and C:N ratio were observed across treatments. Our study provides evidence for both biotic and abiotic impacts of plastic residues on the soil-plant system, suggesting the urgent need for more research examining their environmental impacts on agroecosystems.},
}
@article {pmid31803164,
year = {2019},
author = {Yang, Y and Ashworth, AJ and Willett, C and Cook, K and Upadhyay, A and Owens, PR and Ricke, SC and DeBruyn, JM and Moore, PA},
title = {Review of Antibiotic Resistance, Ecology, Dissemination, and Mitigation in U.S. Broiler Poultry Systems.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2639},
pmid = {31803164},
issn = {1664-302X},
abstract = {Since the onset of land application of poultry litter, transportation of microorganisms, antibiotics, and disinfectants to new locations has occurred. While some studies provide evidence that antimicrobial resistance (AMR), an evolutionary phenomenon, could be influenced by animal production systems, other research suggests AMR originates in the environment from non-anthropogenic sources. In addition, AMR impacts the effective prevention and treatment of poultry illnesses and is increasingly a threat to global public health. Therefore, there is a need to understand the dissemination of AMR genes to the environment, particularly those directly relevant to animal health using the One Health Approach. This review focuses on the potential movement of resistance genes to the soil via land application of poultry litter. Additionally, we highlight impacts of AMR on microbial ecology and explore hypotheses explaining gene movement pathways from U.S. broiler operations to the environment. Current approaches for decreasing antibiotic use in U.S. poultry operations are also described in this review.},
}
@article {pmid31803161,
year = {2019},
author = {Banerji, A and Jahne, M and Herrmann, M and Brinkman, N and Keely, S},
title = {Bringing Community Ecology to Bear on the Issue of Antimicrobial Resistance.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2626},
pmid = {31803161},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is a global concern, pertaining not only to human health but also to the health of industry and the environment. AMR research has traditionally focused on genetic exchange mechanisms and abiotic environmental constraints, leaving important aspects of microbial ecology unresolved. The genetic and ecological aspects of AMR, however, not only contribute separately to the problem but also are interrelated. For example, mutualistic associations among microbes such as biofilms can both serve as a barrier to antibiotic penetration and a breeding ground for horizontal exchange of antimicrobial resistance genes (ARGs). In this review, we elucidate how species interactions promote and impede the establishment, maintenance, and spread of ARGs and indicate how management initiatives might benefit from leveraging the principles and tools of community ecology to better understand and manipulate the processes underlying AMR.},
}
@article {pmid31802728,
year = {2020},
author = {Fix, J and Chandrashekhar, K and Perez, J and Bucardo, F and Hudgens, MG and Yuan, L and Twitchell, E and Azcarate-Peril, MA and Vilchez, S and Becker-Dreps, S},
title = {Association between Gut Microbiome Composition and Rotavirus Vaccine Response among Nicaraguan Infants.},
journal = {The American journal of tropical medicine and hygiene},
volume = {102},
number = {1},
pages = {213-219},
pmid = {31802728},
issn = {1476-1645},
support = {K24 AI141744/AI/NIAID NIH HHS/United States ; },
mesh = {Bacteria/classification ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Nicaragua/epidemiology ; Rotavirus Infections/*prevention &amp; control ; Rotavirus Vaccines/*immunology ; Seroconversion ; },
abstract = {Rotavirus is the leading cause of childhood deaths due to diarrhea. Although existing oral rotavirus vaccines are highly efficacious in high-income countries, these vaccines have been demonstrated to have decreased efficacy in low- and middle-income countries. A possible explanation for decreased efficacy is the impact of gut microbiota on the enteric immune system's response to vaccination. We analyzed the gut microbiome of 50 children enrolled in a prospective study evaluating response to oral pentavalent rotavirus vaccination (RV5) to assess associations between relative abundance of bacterial taxa and seroconversion following vaccination. Stool samples were taken before the first RV5 dose, and microbiome composition characterized using 16S rRNA amplicon sequencing and Quantitative Insights Into Microbial Ecology software. Relative abundance of bacterial taxa between seroconverters following the first RV5 dose, those with ≥ 4-fold increase in rotavirus-specific IgA titers, and nonseroconverters were compared using the Wilcoxon-Mann-Whitney test. We identified no significant differences in microbiome composition between infants who did and did not respond to vaccination. Infants who responded to vaccination tended to have higher abundance of Proteobacteria and Eggerthella, whereas those who did not respond had higher abundance of Fusobacteria and Enterobacteriaceae; however, these differences were not statistically significant following a multiple comparison correction. This study suggests a limited impact of gut microbial taxa on response to oral rotavirus vaccination among infants; however, additional research is needed to improve our understanding of the impact of gut microbiome on vaccine response, toward a goal of improving vaccine efficacy and rotavirus prevention.},
}
@article {pmid31802185,
year = {2020},
author = {Walker, DM and Hill, AJ and Albecker, MA and McCoy, MW and Grisnik, M and Romer, A and Grajal-Puche, A and Camp, C and Kelehear, C and Wooten, J and Rheubert, J and Graham, SP},
title = {Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {985-997},
doi = {10.1007/s00248-019-01456-x},
pmid = {31802185},
issn = {1432-184X},
mesh = {Animal Distribution ; Animals ; Bacteria/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Fungi/isolation &amp; purification/*physiology ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Mycobiome ; Skin/*microbiology ; Southeastern United States ; Spatial Analysis ; Tennessee ; Urodela/*microbiology ; },
abstract = {A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.},
}
@article {pmid31802184,
year = {2020},
author = {Xu, S and Jiang, L and Qiao, G and Chen, J},
title = {The Bacterial Flora Associated with the Polyphagous Aphid Aphis gossypii Glover (Hemiptera: Aphididae) Is Strongly Affected by Host Plants.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {971-984},
pmid = {31802184},
issn = {1432-184X},
support = {2016YFE0203100//National Key R &amp; D Program of China/ ; XDA19050303//Strategic Priority Research Program A of the Chinese Academy of Sciences/ ; 31620103916//National Natural Science Foundation of China/ ; 31430078//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Aphids/*microbiology/physiology ; Bacteria/classification/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Diet ; *Food Chain ; *Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; },
abstract = {Aphids live in symbiosis with a variety of bacteria, including the obligate symbiont Buchnera aphidicola and diverse facultative symbionts. The symbiotic associations for one aphid species, especially for polyphagous species, often differ across populations. In the present study, by using high-throughput 16S rRNA sequencing, we surveyed in detail the microbiota in natural populations of the cotton aphid Aphis gossypii in China and assessed differences in bacterial diversity with respect to host plant and geography. The microbial community of A. gossypii was dominated by a few heritable symbionts. Arsenophonus was the most dominant secondary symbiont, and Spiroplasma was detected for the first time. Statistical tests and ordination analyses showed that host plants rather than geography seemed to have shaped the associated symbiont composition. Special symbiont communities inhabited the Cucurbitaceae-feeding populations, which supported the ecological specialization of A. gossypii on cucurbits from the viewpoint of symbiotic bacteria. Correlation analysis suggested antagonistic interactions between Buchnera and coexisting secondary symbionts and more complicated interactions between different secondary symbionts. Our findings lend further support to an important role of the host plant in structuring symbiont communities of polyphagous aphids and will improve our understanding of the interactions among phytophagous insects, symbionts, and environments.},
}
@article {pmid31798545,
year = {2019},
author = {Harth-Chu, EN and Alves, LA and Theobaldo, JD and Salomão, MF and Höfling, JF and King, WF and Smith, DJ and Mattos-Graner, RO},
title = {PcsB Expression Diversity Influences on Streptococcus mitis Phenotypes Associated With Host Persistence and Virulence.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2567},
pmid = {31798545},
issn = {1664-302X},
abstract = {S. mitis is an abundant member of the commensal microbiota of the oral cavity and pharynx, which has the potential to promote systemic infections. By analyzing a collection of S. mitis strains isolated from the oral cavity at commensal states or from systemic infections (blood strains), we established that S. mitis ubiquitously express the surface immunodominant protein, PcsB (also called GbpB), required for binding to sucrose-derived exopolysaccharides (EPS). Immuno dot blot assays with anti-PcsB antibodies and RT-qPCR transcription analyses revealed strain-specific profiles of PcsB production associated with diversity in pcsB transcriptional activities. Additionally, blood strains showed significantly higher levels of PcsB expression compared to commensal isolates. Because Streptococcus mutans co-colonizes S. mitis dental biofilms, and secretes glucosyltransferases (GtfB/C/D) for the synthesis of highly insoluble EPS from sucrose, profiles of S. mitis binding to EPS, biofilm formation and evasion of the complement system were assessed in sucrose-containing BHI medium supplemented or not with filter-sterilized S. mutans culture supernatants. These analyses showed significant S. mitis binding to EPS and biofilm formation in the presence of S. mutans supernatants supplemented with sucrose, compared to BHI or BHI-sucrose medium. In addition, these phenotypes were abolished if strains were grown in culture supernatants of a gtfBCD-defective S. mutans mutant. Importantly, GtfB/C/D-associated phenotypes were enhanced in high PcsB-expressing strains, compared to low PcsB producers. Increased PcsB expression was further correlated with increased resistance to deposition of C3b/iC3b of the complement system after exposure to human serum, when strains were previously grown in the presence of S. mutans supernatants. Finally, analyses of PcsB polymorphisms and bioinformatic prediction of epitopes with significant binding to MHC class II alleles revealed that blood isolates harbor PcsB polymorphisms in its functionally conserved CHAP-domain, suggesting antigenic variation. These findings reveal important roles of PcsB in S. mitis-host interactions under commensal and pathogenic states, highlighting the need for studies to elucidate mechanisms regulating PcsB expression in this species.},
}
@article {pmid31798544,
year = {2019},
author = {Gallardo-Navarro, &#xd3;A and Santillán, M},
title = {Three-Way Interactions in an Artificial Community of Bacterial Strains Directly Isolated From the Environment and Their Effect on the System Population Dynamics.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2555},
pmid = {31798544},
issn = {1664-302X},
abstract = {This work is motivated by previous studies that have analyzed the population ecology of a collection of culturable thermoresistant bacteria, isolated from the Churince lagoon in Cuatro Cienegas, Mexico. In particular, it is aimed at testing a hypothesis from a modeling study, which states that antagonistic and sensitive bacteria co-exist thanks to resistant bacteria that protect sensitive ones by forming physical barriers. We selected three different bacterial strains from the referred collection: one antagonistic, one sensitive, and one resistant, and studied the population dynamics of mixed colonies. Our results show that, although the proposed protective mechanism does not work in this case, the resistant strain confers some kind of protection to sensitive bacteria. Further modeling and experimental results suggest that the presence of resistant bacteria indirectly improves the probability that patches of sensitive bacteria grow in a mixed colony. More precisely, our results suggest that by making antagonistic bacteria produce and secrete an antagonistic substance (with the concomitant metabolic cost and growth rate reduction), resistant bacteria increase the likelihood that sensitive bacteria locally outcompete antagonistic ones.},
}
@article {pmid31796996,
year = {2020},
author = {Velasco-González, I and Sanchez-Jimenez, A and Singer, D and Murciano, A and Díez-Hermano, S and Lara, E and Martín-Cereceda, M},
title = {Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {882-897},
doi = {10.1007/s00248-019-01463-y},
pmid = {31796996},
issn = {1432-184X},
support = {CGL2013-40851-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; SNF 31003A_143960//Swiss Re Foundation/ ; },
mesh = {Eukaryota/isolation &amp; purification/*physiology ; Geologic Sediments/*microbiology/*parasitology ; Microbiota ; Mycobiome ; Rain ; *Silicon Dioxide ; Spain ; },
abstract = {Rain fed granite rock basins are ancient geological landforms of worldwide distribution and structural simplicity. They support habitats that can switch quickly from terrestrial to aquatic along the year. Diversity of animals and plants, and the connexion between communities in different basins have been widely explored in these habitats, but hardly any research has been carried out on microorganisms. The aim of this study is to provide the first insights on the diversity of eukaryotic microbial communities from these environments. Due to the ephemeral nature of these aquatic environments, we predict that the granitic basins should host a high proportion of dormant microeukaryotes. Based on an environmental DNA diversity survey, we reveal diverse communities with representatives of all major eukaryotic taxonomic supergroups, mainly composed of a diverse pool of low abundance OTUs. Basin communities were very distinctive, with alpha and beta diversity patterns non-related to basin size or spatial distance respectively. Dissimilarity between basins was mainly characterised by turnover of OTUs. The strong microbial eukaryotic heterogeneity observed among the basins may be explained by a complex combination of deterministic factors (diverging environment in the basins), spatial constraints, and randomness including founder effects. Most interestingly, communities contain organisms that cannot coexist at the same time because of incompatible metabolic requirements, thus suggesting the existence of a pool of dormant organisms whose activity varies along with the changing environment. These organisms accumulate in the pools, which turns granitic rock into high biodiversity microbial islands whose conservation and study deserve further attention.},
}
@article {pmid31796995,
year = {2020},
author = {González-Serrano, F and Pérez-Cobas, AE and Rosas, T and Baixeras, J and Latorre, A and Moya, A},
title = {The Gut Microbiota Composition of the Moth Brithys crini Reflects Insect Metamorphosis.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {960-970},
doi = {10.1007/s00248-019-01460-1},
pmid = {31796995},
issn = {1432-184X},
support = {SAF2015-65878-R//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; BFU2015-64322-C2-1-R//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; Prometeo/2018/A/133//Conselleria d'Educaci&#xf3;, Investigaci&#xf3;, Cultura i Esport/ ; Co-finance//Interreg/ ; PGC2018-099344-B-100//Agencia Estatal de Investigaci&#xf3;n/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; Larva/growth &amp; development/microbiology ; Male ; *Metamorphosis, Biological ; Moths/growth &amp; development/*microbiology ; Ovum/growth &amp; development/microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; },
abstract = {Lepidoptera is a highly diverse insect order with major importance in agriculture as many species are considered pests. The role of the gut microbiota in insect physiology is still poorly understood, despite the research undertaken in recent years. Furthermore, Lepidoptera are holometabolous insects and few studies have addressed the influence of the changes taking place on the gut microbiome composition and diversity during metamorphosis, especially in monophagous species. The V3-V4 region of the 16S rRNA gene was sequenced to investigate the microbiota composition and diversity of the monophagous moth Brithys crini during three different life stages: egg, larvae (midgut and hindgut), and adult (gut). Our results showed that the microbiota composition of B. crini was stage specific, indicating that the developmental stage is a main factor affecting the gut microbiome in composition and potential functions. Moreover, the diversity of the gut microbiome reflected the developmental process, since a drop in diversity occurred between the larval and the adult phase, when the intestine is completely renewed. In spite of the changes in the gut microbiota during metamorphosis, 29 genera were conserved throughout the three developmental stages, mainly belonging to the Proteobacteria phylum, which define the core microbiome of B. crini. These genera seem to contribute to host physiology by participating in food digestion, nutrition, and detoxification mechanisms.},
}
@article {pmid31791792,
year = {2020},
author = {Nguyen, LN and Commault, AS and Kahlke, T and Ralph, PJ and Semblante, GU and Johir, MAH and Nghiem, LD},
title = {Genome sequencing as a new window into the microbial community of membrane bioreactors - A critical review.},
journal = {The Science of the total environment},
volume = {704},
number = {},
pages = {135279},
doi = {10.1016/j.scitotenv.2019.135279},
pmid = {31791792},
issn = {1879-1026},
mesh = {Base Sequence ; Bioreactors/*microbiology ; Microbiota ; *Waste Disposal, Fluid ; Wastewater/*microbiology ; },
abstract = {Recent developed sequencing techniques have resulted in a new and unprecedented way to study biological wastewater treatment, in which most organisms are uncultivable. This review provides (i) an insight on state-of-the-art sequencing techniques and their limitations; (ii) a critical assessment of the microbial community in biological reactor and biofouling layer in a membrane bioreactor (MBR). The data from high-throughput sequencing has been used to infer microbial growth conditions and metabolisms of microorganisms present in MBRs at the time of sampling. These data shed new insight to two fundamental questions about a microbial community in the MBR process namely the microbial composition (who are they?) and the functions of each specific microbial assemblage (what are their function?). The results to date also highlight the complexity of the microbial community growing on MBRs. Environmental conditions are dynamic and diverse, and can influence the diversity and structural dynamics of any given microbial community for wastewater treatment. The benefits of understanding the structure of microbial communities on three major aspects of the MBR process (i.e. nutrient removal, biofouling control, and micropollutant removal) were symmetrically delineated. This review also indicates that the deployment of microbial community analysis for a practical engineering context, in terms of process design and system optimization, can be further realized.},
}
@article {pmid31791487,
year = {2020},
author = {Mathews, ER and Wood, JL and Phillips, D and Billington, N and Barnett, D and Franks, AE},
title = {Town-scale microbial sewer community and H2S emissions response to common chemical and biological dosing treatments.},
journal = {Journal of environmental sciences (China)},
volume = {87},
number = {},
pages = {133-148},
doi = {10.1016/j.jes.2019.06.011},
pmid = {31791487},
issn = {1001-0742},
mesh = {Hydrogen Sulfide/*analysis/chemistry ; Hydrogen-Ion Concentration ; Microbiota ; Sewage/chemistry/microbiology ; Waste Disposal, Fluid/*methods ; },
abstract = {Controlling hydrogen sulfide (H2S) odors and emissions using a single, effective treatment across a town-scale sewer network is a challenge faced by many water utilities. Implementation of a sewer diversion provided the opportunity to compare the effectiveness of magnesium hydroxide (Mg(OH)2) and two biological dosing compounds (Bioproducts A and B), with different modes of action (MOA), in a field-test across a large sewer network. Mg(OH)2 increases sewer pH allowing suppression of H2S release into the sewer environment while Bioproduct A acts to disrupt microbial communication through quorum sensing (QS), reducing biofilm integrity. Bioproduct B reduces H2S odors by scouring the sewer of fats, oils and grease (FOGs), which provide adhesion points for the microbial biofilm. Results revealed that only Mg(OH)2 altered the microbial community structure and reduced H2S emissions in a live sewer system, whilst Bioproducts A and B did not reduce H2S emissions or have an observable effect on the composition of the microbial community at the dosed site. Study results recommend in situ testing of dosing treatments before implementation across an operational system.},
}
@article {pmid31790889,
year = {2020},
author = {Yan, L and Herrmann, M and Kampe, B and Lehmann, R and Totsche, KU and Küsel, K},
title = {Environmental selection shapes the formation of near-surface groundwater microbiomes.},
journal = {Water research},
volume = {170},
number = {},
pages = {115341},
doi = {10.1016/j.watres.2019.115341},
pmid = {31790889},
issn = {1879-2448},
mesh = {Bacteria ; *Groundwater ; *Microbiota ; },
abstract = {Hydrodynamics drives both stochastic and deterministic community assembly in aquatic habitats, by translocating microbes across geographic barriers and generating changes in selective pressures. Thus, heterogeneity of hydrogeological settings and episodic surface inputs from recharge areas might play important roles in shaping and maintaining groundwater microbial communities. Here we took advantage of the Hainich Critical Zone Exploratory to disentangle mechanisms of groundwater microbiome differentiation via a three-year observation in a setting of mixed carbonate-siliciclastic alternations along a hillslope transect. Variation partitioning of all data elucidated significant roles of hydrochemistry (35.0%) and spatial distance (18.6%) but not of time in shaping groundwater microbiomes. Groundwater was dominated by rare species (99.6% of OTUs), accounting for 25.9% of total reads, whereas only 26 OTUs were identified as core species. The proximity to the recharge area gave prominence to high microbial diversity coinciding with high surface inputs. In downstream direction, the abundance of rare OTUs decreased whereas core OTUs abundance increased up to 47% suggesting increasing selection stress with a higher competition cost for colonization. In general, environmental selection was the key mechanism driving the spatial differentiation of groundwater microbiomes, with N-compounds and dissolved oxygen as the major determinants, but it was more prominent in the upper aquifer with low flow velocity. Across the lower aquifer with higher flow velocity, stochastic processes appeared to be additionally important for community assembly. Overall, this study highlights the impact of surface and subsurface conditions, as well as flow regime and related habitat accessibility, on groundwater microbiomes assembly.},
}
@article {pmid31790419,
year = {2019},
author = {Díaz-Riaño, J and Posada, L and Acosta, IC and Ruíz-Pérez, C and García-Castillo, C and Reyes, A and Zambrano, MM},
title = {Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0221540},
pmid = {31790419},
issn = {1932-6203},
mesh = {Adaptation, Physiological/radiation effects ; Deinococcus/genetics/isolation &amp; purification/*physiology/*radiation effects ; *Ecosystem ; Gene Expression Regulation, Bacterial/radiation effects ; RNA, Bacterial/genetics ; *Radiation Tolerance ; Survival Analysis ; *Ultraviolet Rays ; },
abstract = {Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m2 of UVR (with >95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the immediate radiation response of D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions.},
}
@article {pmid31788934,
year = {2020},
author = {Hannula, SE and Ma, HK and Pérez-Jaramillo, JE and Pineda, A and Bezemer, TM},
title = {Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen.},
journal = {Environmental microbiology},
volume = {22},
number = {2},
pages = {660-676},
pmid = {31788934},
issn = {1462-2920},
support = {865.14.006//Netherlands Organization for Scientific Research NWO VICI/International ; 870.15.080//Netherlands Organization for Scientific Research NWO VICI/International ; },
mesh = {Bacteria/classification/genetics ; Chrysanthemum/*growth &amp; development ; Fabaceae/*microbiology ; Microbiota/genetics ; Mycorrhizae/physiology ; Plant Development/*physiology ; Plant Diseases/microbiology ; Plant Roots/*microbiology ; Plants ; Poaceae/microbiology ; Pythium/*metabolism ; Soil/chemistry ; Soil Microbiology ; Species Specificity ; },
abstract = {Interactions between plants and soil microbes are important for plant growth and resistance. Through plant-soil-feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant-soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant-induced changes in soil microbiomes on the growth of the commercially important cut-flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next-generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species-specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome and that plant growth and protection against pathogens is associated with a complex soil microbial community.},
}
@article {pmid31787951,
year = {2019},
author = {Pelikan, C and Jaussi, M and Wasmund, K and Seidenkrantz, MS and Pearce, C and Kuzyk, ZZA and Herbold, CW and Røy, H and Kjeldsen, KU and Loy, A},
title = {Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2558},
pmid = {31787951},
issn = {1664-302X},
support = {P 29426/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had "young" sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates (SRR), and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with SRRs, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria, and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.},
}
@article {pmid31786395,
year = {2020},
author = {Xu, R and Zhang, S and Meng, F},
title = {Large-sized planktonic bioaggregates possess high biofilm formation potentials: Bacterial succession and assembly in the biofilm metacommunity.},
journal = {Water research},
volume = {170},
number = {},
pages = {115307},
doi = {10.1016/j.watres.2019.115307},
pmid = {31786395},
issn = {1879-2448},
mesh = {Bacteria ; Biofilms ; Calcium Hydroxide ; *Extracellular Polymeric Substance Matrix ; Hydroxyapatites ; Phylogeny ; *Plankton ; Silicates ; },
abstract = {Wanted and unwanted surface-attached growth of bacteria is ubiquitous in natural and engineered settings. Normally, attachment of planktonic cells to media surfaces initiates biofilm formation and fundamentally regulates biofilm assembly processes. Here, culturing biofilm with planktonic sludge as source community, we found distinct succession profiles of biofilm communities sourced from the size-fractionated sludge flocs (<25; 25-120; >120 μm). Null model analyses revealed that deterministic process dominated in biofilm community assemblies but decreased with decreasing floc size. Additionally, the relative importance of environmental selection increased with increasing floc size of the source sludge, whereas homogenizing dispersal and ecological drift followed opposite trends. Phylogenetic molecular ecological networks (pMENs) indicated that species interactions were intensive in biofilm microbiota developed from large-sized flocs (>120 μm), as evidenced by the low modularity and harmonic geodesic distance and the high average degree. Intriguingly, the keystone taxa in these biofilm ecological networks were controlled by distinct interaction patterns but all showed strong habitat characteristics (e.g., facultative anaerobic, motile, hydrophobic and involved in extracellular polymeric substance metabolism), corroborating the crucial roles of environmental filtering in structuring biofilm community. Taken together, our findings highlight the role of planktonic floc properties in biofilm community assembly and advance our understanding of microbial ecology in biofilm-based systems.},
}
@article {pmid31785367,
year = {2020},
author = {Wilson, JM and Platts-Mills, TAE},
title = {α-Gal and other recent findings that have informed our understanding of anaphylaxis.},
journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology},
volume = {124},
number = {2},
pages = {135-142},
pmid = {31785367},
issn = {1534-4436},
support = {R37 AI020565/AI/NIAID NIH HHS/United States ; },
mesh = {Allergens/*immunology ; Anaphylaxis/*etiology ; Animals ; Food Hypersensitivity/immunology ; Humans ; Immunoglobulin E/immunology ; Immunoglobulin G/immunology ; Microbiota ; alpha-Galactosidase/*immunology ; },
abstract = {OBJECTIVE: To summarize the current understanding of anaphylaxis, with an emphasis on major findings that have been reported within the last 10 years.<br><br>DATA SOURCES: Queries relating to anaphylaxis, immunoglobulin E (IgE), and mast cells were conducted with PubMed and Google Scholar, searching for primary articles and review papers.<br><br>STUDY SELECTIONS: We focused on articles written in English and which were reported in major allergy and immunology journals.<br><br>RESULTS: Anaphylaxis represents an extreme manifestation of a form of allergic immunity that appears to have evolved to protect against "toxic" threats that present at skin and mucosal barriers. The factors that have contributed to a rise in anaphylaxis are increasingly appreciated to relate to changes in hygiene and microbial ecology that have occurred with industrialization. Induction of allergen-specific IgG4 is often part of the allergic response and is associated with protection against anaphylaxis. The recognition of the &#x3b1;-Gal syndrome suggests that carbohydrates can be epitopes that are relevant to anaphylaxis and that IgE-mediated reactions do not always occur "immediately."<br><br>CONCLUSION: Our understanding of anaphylaxis has advanced significantly over the past 10 years. It is anticipated that ongoing research will build on this foundation to further advance our knowledge of anaphylaxis and also translate into clinically meaningful therapies.},
}
@article {pmid31784839,
year = {2019},
author = {Chen, J and He, Y and Wang, J and Huang, M and Guo, C},
title = {Dynamics of nitrogen transformation and bacterial community with different aeration depths in malodorous river.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {35},
number = {12},
pages = {196},
pmid = {31784839},
issn = {1573-0972},
support = {41877477//National Natural Science Foundation of China/ ; 16ZR1408800//Natural Science Foundation of Shanghai/ ; 16PJD023//Shanghai Pujiang Talent Program/ ; 18DZ1203806//Shanghai Science and Technology Development Foundation/ ; 1701K005//Research Funds of The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control/ ; },
mesh = {Bacteria/classification/genetics/*metabolism ; China ; Geologic Sediments/microbiology ; Microbiota/*physiology ; Nitrogen/*metabolism ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; Rivers/*chemistry/*microbiology ; Sulfur/metabolism ; },
abstract = {In this research, the dynamics of nitrogen transformation and bacterial community in malodorous river were investigated with different aeration depths. Computational flow dynamics (CFD) and Reynolds number (Re) were specially used to characterize the hydrodynamics condition under different aeration depths. The results indicated that aeration depth had vital impact on nitrogen transformation and bacterial community structure. It was found that a range of aeration depth (0.20-0.45 m above sediment-water interface) facilitated the removal of NH4[+]-N and TN with Re ranging between 6211 and 8930. Proteobacteria took over Firmicutes to become the predominant phylum (36-78%) under aeration, and the main subdivisions of γ-, β- and δ-Proteobacteria also varied greatly with different aeration depths. Interestingly, there was a marked shift of the inferentially identified dominant functional role within Proteobacteria from organic-matter degradation to nitrogen metabolism and then to sulfur metabolism as well as the coupling of nitrogen and sulfur with the increase of disturbance. The redundancy analysis (RDA) further confirmed the importance of aeration disturbance in shaping bacterial community. These findings help to gain improved understanding of endogenous N-behavior and aquatic microbial ecology, and underline the need for integrating the hydrodynamics factors with microbial community.},
}
@article {pmid31781077,
year = {2019},
author = {Glamoclija, M and Ramirez, S and Sirisena, K and Widanagamage, I},
title = {Subsurface Microbial Ecology at Sediment-Groundwater Interface in Sulfate-Rich Playa; White Sands National Monument, New Mexico.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2595},
pmid = {31781077},
issn = {1664-302X},
abstract = {The hypersaline sediment and groundwater of playa lake, Lake Lucero, at the White Sands National Monument in New Mexico were examined for microbial community composition, geochemical gradients, and mineralogy during the dry season along a meter and a half depth profile of the sediment vs. the groundwater interface. Lake Lucero is a highly dynamic environment, strongly characterized by the capillary action of the groundwater, the extreme seasonality of the climate, and the hypersalinity. Sediments are predominantly composed of gypsum with minor quartz, thenardite, halite, quartz, epsomite, celestine, and clays. Geochemical analysis has revealed the predominance of nitrates over ammonium in all of the analyzed samples, indicating oxygenated conditions throughout the sediment column and in groundwater. Conversely, the microbial communities are primarily aerobic, gram-negative, and are largely characterized by their survival adaptations. Halophiles and oligotrophs are ubiquitous for all the samples. The very diverse communities contain methanogens, phototrophs, heterotrophs, saprophytes, ammonia-oxidizers, sulfur-oxidizers, sulfate-reducers, iron-reducers, and nitrifiers. The microbial diversity varied significantly between groundwater and sediment samples as their temperature adaptation inferences that revealed potential psychrophiles inhabiting the groundwater and thermophiles and mesophiles being present in the sediment. The dynamism of this environment manifests in the relatively even character of the sediment hosted microbial communities, where significant taxonomic distinctions were observed. Therefore, sediment and groundwater substrates are considered as separate ecological entities. We hope that the variety of the discussed playa environments and the microorganisms may be considered a useful terrestrial analog providing valuable information to aid future astrobiological explorations.},
}
@article {pmid31781072,
year = {2019},
author = {Zhang, Z and Li, D and Xu, W and Tang, R and Li, L},
title = {Microbiome of Co-cultured Fish Exhibits Host Selection and Niche Differentiation at the Organ Scale.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2576},
pmid = {31781072},
issn = {1664-302X},
abstract = {Fish are the most widespread aquaculture species and maintain complex associations with microbial consortiums. However, the ecology of these associations present in multiple microhabitats in fish remains elusive, especially on the microbial assembly in fish external (skin and gill) and internal (stomach and intestine) niches, and the relationship with the rearing environment. To understand host dependence and niche differentiation of organ-specific microbiome signatures using a 16S rRNA gene-based sequencing technique, we systematically provided characterizations of a comparative framework relevant to the microbiome of stomach, regional intestine, skin, and gill in two important farmed fish species, herbivorous grass carp (Ctenopharyngodon idella) and carnivorous southern catfish (Silurus meridionalis), and of the rearing water. The different feeding habits of grass carp and southern catfish showed a significant separation of microbial community structure, with great compositional differences across body sites within each species. Site-driven divergences relied on host species: the same types of microhabitats between grass carp and southern catfish harbored differential microbiome. Additionally, body sites had remarkably distinct communities and displayed lower alpha diversity compared to rearing water. Unexpectedly, the stomach of southern catfish had the highest microbial diversity in the digestive tract of the two co-cultured fish species. For external sites within each species, a higher diversity occurred in gill of grass carp and in skin of southern catfish. Our results unveil different topographical microbiome signatures of the co-cultured species, indicating host selection in individual-level microbial assemblages and niche differentiation at the organ scale. This work represents a foundation for understanding the comprehensive microbial ecology of cohabiting farmed fish, suggesting potential applications associated with fish microbiome that urgently needs to be assessed in polycultured operations in aquaculture.},
}
@article {pmid31780680,
year = {2019},
author = {Vivero, RJ and Villegas-Plazas, M and Cadavid-Restrepo, GE and Herrera, CXM and Uribe, SI and Junca, H},
title = {Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {17746},
pmid = {31780680},
issn = {2045-2322},
mesh = {Animals ; Bacteroidetes/genetics/*isolation &amp; purification ; Female ; Gastrointestinal Microbiome ; Humans ; Insect Vectors/*microbiology ; Leishmaniasis/*transmission ; Male ; Methylobacterium/genetics/*isolation &amp; purification ; Psychodidae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Wolbachia/genetics/*isolation &amp; purification ; },
abstract = {Phlebotomine sand flies are remarkable vectors of several etiologic agents (virus, bacterial, trypanosomatid Leishmania), posing a heavy health burden for human populations mainly located at developing countries. Their intestinal microbiota is involved in a wide range of biological and physiological processes, and could exclude or facilitate such transmission of pathogens. In this study, we investigated the Eubacterial microbiome from digestive tracts of Lu. evansi adults structure using 16S rRNA gene sequence amplicon high throughput sequencing (Illumina MiSeq) obtained from digestive tracts of Lu. evansi adults. The samples were collected at two locations with high incidence of the disease in humans: peri-urban and forest ecosystems from the department of Sucre, Colombia. 289,068 quality-filtered reads of V4 region of 16S rRNA gene were obtained and clustered into 1,762 operational taxonomic units (OTUs) with 97% similarity. Regarding eubacterial diversity, 14 bacterial phyla and 2 new candidate phyla were found to be consistently associated with the gut microbiome content. Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla in all the samples and the core microbiome was particularly dominated by Methylobacterium genus. Methylobacterium species, are known to have mutualistic relationships with some plants and are involved in shaping the microbial community in the phyllosphere. As a remarkable feature, OTUs classified as Wolbachia spp. were found abundant on peri-urban ecosystem samples, in adult male (OTUs n = 776) and unfed female (OTUs n = 324). Furthermore, our results provide evidence of OTUs classified as Cardinium endosymbiont in relative abundance, notably higher with respect to Wolbachia. The variation in insect gut microbiota may be determined by the environment as also for the type of feeding. Our findings increase the richness of the microbiota associated with Lu. evansi. In this study, OTUs of Methylobacterium found in Lu. evansi was higher in engorged females, suggesting that there are interactions between microbes from plant sources, blood nutrients and the parasites they transmit during the blood intake.},
}
@article {pmid31780241,
year = {2020},
author = {Lavergne, C and Bovio-Winkler, P and Etchebehere, C and García-Gen, S},
title = {Towards centralized biogas plants: Co-digestion of sewage sludge and pig manure maintains process performance and active microbiome diversity.},
journal = {Bioresource technology},
volume = {297},
number = {},
pages = {122442},
doi = {10.1016/j.biortech.2019.122442},
pmid = {31780241},
issn = {1873-2976},
mesh = {Anaerobiosis ; Animals ; Biofuels ; Bioreactors ; Manure ; Methane ; *Microbiota ; RNA, Ribosomal, 16S ; *Sewage ; Swine ; },
abstract = {The aim of this study is to assess the performance of anaerobic digestion against co-digestion systems during the start-up stages based on key process parameters and biological indicators. Two parallel experiments treating sewage sludge alone or co-digested with low concentration of pig manure (8% vol., 2-3% in COD basis) were carried out in two lab-scale CSTR at mesophilic conditions. Same inoculant and organic loading rate sequences were applied for two consecutive runs of 79 and 90 days. According to the removal efficiencies achieved, no significant differences were encountered amongst mono-digestion and co-digestion. This observation was reinforced with the analysis of the total/active microbiome, sequencing 16S rRNA genes and transcripts. The addition of a co-substrate at low concentration had a negligible effect on the total/active microbial communities; they evolved following the same pattern. This might be an advantage in order to upgrade existing wastewater treatment plants to become centralized biogas facilities.},
}
@article {pmid31779402,
year = {2019},
author = {Taylor, AW and Harris, DM},
title = {Optimized commercial desktop cutter technique for rapid-prototyping of microfluidic devices and application to Taylor dispersion.},
journal = {The Review of scientific instruments},
volume = {90},
number = {11},
pages = {116102},
doi = {10.1063/1.5123130},
pmid = {31779402},
issn = {1089-7623},
abstract = {Microfluidics provides a platform for efficient and transportable microanalysis, catalyzing advancements in fields such as biochemistry, materials science, and microbial ecology. While the analysis is cost-effective, standard device fabrication techniques are disproportionately expensive and specialized. A commercially available desktop cutting plotter provides an accessible method for rapidly fabricating microfluidic devices at extremely low costs. The optimized technique described in the present work enables fabrication of microchannels with dimensions as small as ∼100 μm. Straightness of channel walls is comparable to other common fabrication techniques but achieved here at a fraction of the cost and fabrication time. Solute dispersion experiments are performed using the rapidly prototyped channels to measure the effective dispersion coefficient in laminar flow through rectangular channels. The results of these experiments compare favorably to predictions from classical Taylor-Aris dispersion theory. This note provides all necessary tools for researchers and educators to seamlessly apply the desktop cutter fabrication technique. Materials list, fabrication instructions, and detailed channel characterization results are available in the supplementary material.},
}
@article {pmid31771976,
year = {2019},
author = {Janzon, A and Goodrich, JK and Koren, O and , and Waters, JL and Ley, RE},
title = {Interactions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut.},
journal = {mSystems},
volume = {4},
number = {6},
pages = {},
pmid = {31771976},
issn = {2379-5077},
support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; HHSN267200700014C/LM/NLM NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; },
abstract = {Interactions between the gut microbiome and immunoglobulin A (IgA) in the gut during infancy are important for future health. IgM and IgG are also present in the gut; however, their interactions with the microbiome in the developing infant remain to be characterized. Using stool samples sampled 15 times in infancy from 32 healthy subjects at 4 locations in 3 countries, we characterized patterns of microbiome development in relation to fecal levels of IgA, IgG, and IgM. For 8 infants from a single location, we used fluorescence-activated cell sorting of microbial cells from stool by Ig-coating status over 18 months. We used 16S rRNA gene profiling on full and sorted microbiomes to assess patterns of antibody coating in relation to age and other factors. All antibodies decreased in concentration with age but were augmented by breastmilk feeding regardless of infant age. Levels of IgA correlated with relative abundances of operational taxonomic units (OTUs) belonging to the Bifidobacteria and Enterobacteriaceae, which dominated the early microbiome, and IgG levels correlated with Haemophilus The diversity of Ig-coated microbiota was influenced by breastfeeding and age. IgA and IgM coated the same microbiota, which reflected the overall diversity of the microbiome, while IgG targeted a different subset. Blautia generally evaded antibody coating, while members of the Bifidobacteria and Enterobacteriaceae were high in IgA/M. IgA/M displayed similar dynamics, generally coating the microbiome proportionally, and were influenced by breastfeeding status. IgG only coated a small fraction of the commensal microbiota and differed from the proportion targeted by IgA and IgM.IMPORTANCE Antibodies are secreted into the gut and attach to roughly half of the trillions of bacterial cells present. When babies are born, the breastmilk supplies these antibodies until the baby's own immune system takes over this task after a few weeks. The vast majority of these antibodies are IgA, but two other types, IgG and IgM, are also present in the gut. Here, we ask if these three different antibody types target different types of bacteria in the infant gut as the infant develops from birth to 18 months old and how patterns of antibody coating of bacteria change with age. In this study of healthy infant samples over time, we found that IgA and IgM coat the same bacteria, which are generally representative of the diversity present, with a few exceptions that were more or less antibody coated than expected. IgG coated a separate suite of bacteria. These results provide a better understanding of how these antibodies interact with the developing infant gut microbiome.},
}
@article {pmid31769802,
year = {2020},
author = {Jiménez, DJ and Wang, Y and Chaib de Mares, M and Cortes-Tolalpa, L and Mertens, JA and Hector, RE and Lin, J and Johnson, J and Lipzen, A and Barry, K and Mondo, SJ and Grigoriev, IV and Nichols, NN and van Elsas, JD},
title = {Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {1},
pages = {},
doi = {10.1093/femsec/fiz186},
pmid = {31769802},
issn = {1574-6941},
mesh = {Ascomycota/enzymology/genetics/*metabolism ; Citrobacter freundii/metabolism ; Fungal Proteins/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Lignin/*metabolism ; *Microbial Consortia ; Sphingobacterium/metabolism ; Triticum/metabolism ; },
abstract = {Coniochaeta species are versatile ascomycetes that have great capacity to deconstruct lignocellulose. Here, we explore the transcriptome of Coniochaeta sp. strain 2T2.1 from wheat straw-driven cultures with the fungus growing alone or as a member of a synthetic microbial consortium with Sphingobacterium multivorum w15 and Citrobacter freundii so4. The differential expression profiles of carbohydrate-active enzymes indicated an onset of (hemi)cellulose degradation by 2T2.1 during the initial 24 hours of incubation. Within the tripartite consortium, 63 transcripts of strain 2T2.1 were differentially expressed at this time point. The presence of the two bacteria significantly upregulated the expression of one galactose oxidase, one GH79-like enzyme, one multidrug transporter, one laccase-like protein (AA1 family) and two bilirubin oxidases, suggesting that inter-kingdom interactions (e.g. amensalism) take place within this microbial consortium. Overexpression of multicopper oxidases indicated that strain 2T2.1 may be involved in lignin depolymerization (a trait of enzymatic synergism), while S. multivorum and C. freundii have the metabolic potential to deconstruct arabinoxylan. Under the conditions applied, 2T2.1 appears to be a better degrader of wheat straw when the two bacteria are absent. This conclusion is supported by the observed suppression of its (hemi)cellulolytic arsenal and lower degradation percentages within the microbial consortium.},
}
@article {pmid31768533,
year = {2020},
author = {Duysburgh, C and Ossieur, WP and De Paepe, K and Van den Abbeele, P and Vichez-Vargas, R and Vital, M and Pieper, DH and Van de Wiele, T and Hesta, M and Possemiers, S and Marzorati, M},
title = {Development and validation of the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME)1.},
journal = {Journal of animal science},
volume = {98},
number = {1},
pages = {},
pmid = {31768533},
issn = {1525-3163},
mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; Dogs/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Intestines/microbiology ; Lactobacillus/*physiology ; Probiotics/*analysis ; },
abstract = {Whereas a wide variety of in vitro models have been developed and validated to assess the effect of specific food ingredients on the human gut microbiome, such models have only been developed and applied to a limited extent for companion animals. Since the use of pre- and probiotics to improve gut health is an emerging research topic in the field of companion animals and as dogs are often used as laboratory animals in developing and testing of pharmaceuticals, the current study aimed to establish an adequate canine in vitro model. This consisted of a four-stage reactor composed of a stomach and small intestinal compartment followed by a proximal and distal colon. This semi-continuous gastrointestinal tract model allowed a long-term, region-dependent, and pH-controlled simulation of the colon-associated microbial community of dogs. Upon reaching a functional steady state, the simulated canine microbial community composition proved to be representative of the in vivo situation. Indeed, the predominant bacterial phyla present in the in vitro proximal and distal colon corresponded with the main bacterial phyla detected in the fecal material of the dogs, resulting in an average community composition along the simulated canine gastrointestinal tract of 50.5% Firmicutes, 34.5% Bacteroidetes, 7.4% Fusobacteria, 4.9% Actinobacteria, and 2.7% Proteobacteria. A parallel in vivo-in vitro comparison assessing the effects of fructooligosaccharides (FOS) on the canine microbial community composition showed a consistent stimulation of Lactobacillus concentrations in the in vivo fecal samples as well as in the in vitro canine gut model. Furthermore, the in vitro platform provided additional insights about the prebiotic effect of FOS supplementation of dogs, such as a reduced abundance of Megamonas spp. which are only present in very low abundance in in vivo fecal samples, indicating an interesting application potential of the developed canine in vitro model in research related to gastrointestinal health of dogs.},
}
@article {pmid31766265,
year = {2019},
author = {Sun, Z and Yu, Z and Wang, B},
title = {Perilla frutescens Leaf Alters the Rumen Microbial Community of Lactating Dairy Cows.},
journal = {Microorganisms},
volume = {7},
number = {11},
pages = {},
pmid = {31766265},
issn = {2076-2607},
support = {31902181//National Natural Science Foundation of China/ ; },
abstract = {Perilla frutescens (L.) Britt., an annual herbaceous plant, has antibacterial, anti-inflammation, and antioxidant properties. To understand the effects of P. frutescens leaf on the ruminal microbial ecology of cattle, Illumina MiSeq 16S rRNA sequencing technology was used. Fourteen cows were used in a randomized complete block design trial. Two diets were fed to these cattle: a control diet (CON); and CON supplemented with 300 g/d P. frutescens leaf (PFL) per cow. Ruminal fluid was sampled at the end of the experiment for microbial DNA extraction. Overall, our findings revealed that supplementation with PFL could increase ruminal fluid pH value. The ruminal bacterial community of cattle was dominated by Bacteroidetes, Firmicutes, and Proteobacteria. The addition of PFL had a positive effect on Firmicutes, Actinobacteria, and Spirochaetes, but had no effect on Bacteroidetes and Proteobacteria compared with the CON. The supplementation with PFL significantly increased the abundance of Marvinbryantia, Acetitomaculum, Ruminococcus gauvreauii, Eubacterium coprostanoligenes, Selenomonas_1, Pseudoscardovia, norank_f__Muribaculaceae, and Sharpea, and decreased the abundance of Treponema_2 compared to CON. Eubacterium coprostanoligenes, and norank_f__Muribaculaceae were positively correlated with ruminal pH value. It was found that norank_f__Muribaculaceae and Acetitomaculum were positively correlated with milk yield, indicating that these different genera are PFL associated bacteria. This study suggests that PFL supplementation could increase the ruminal pH value and induce shifts in the ruminal bacterial composition.},
}
@article {pmid31763752,
year = {2020},
author = {Zanne, AE and Abarenkov, K and Afkhami, ME and Aguilar-Trigueros, CA and Bates, S and Bhatnagar, JM and Busby, PE and Christian, N and Cornwell, WK and Crowther, TW and Flores-Moreno, H and Floudas, D and Gazis, R and Hibbett, D and Kennedy, P and Lindner, DL and Maynard, DS and Milo, AM and Nilsson, RH and Powell, J and Schildhauer, M and Schilling, J and Treseder, KK},
title = {Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {95},
number = {2},
pages = {409-433},
doi = {10.1111/brv.12570},
pmid = {31763752},
issn = {1469-185X},
mesh = {Animals ; Databases, Factual ; Ecosystem ; Fungi/genetics/*physiology ; Plants/*microbiology ; },
abstract = {Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (Fun[Fun]). Fun[Fun] is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.},
}
@article {pmid31763477,
year = {2019},
author = {Anderson, OR},
title = {Atmospheric respiratory CO2 efflux by aquatic suspended particle-bound microbial communities: A laboratory experimental study.},
journal = {Heliyon},
volume = {5},
number = {11},
pages = {e02816},
pmid = {31763477},
issn = {2405-8440},
abstract = {Natural sources of atmospheric CO2 are of increasing interest as possible contributors to global climate warming. This study documents the amount of respiratory CO2 contributed by microbial communities associated with suspended particulates in aquatic water columns. Microcosms containing three different sources of water (pond freshwater, NY East River estuary and Hudson River estuary) were used to experimentally determine the atmospheric respiratory CO2 released from particle-associated microbes. Two different approaches were used. In the first, finely powdered dried cereal leaves (alfalfa) were added to each of the three microcosms as a consistent source of particulate organic matter (POM). In the second, only Hudson River estuary water samples were used with natural densities of POM. Respiration rates associated with two sizes of particles were assessed: 1) ≥ 200 μm and 2) ≥ 50 μm but less than 200 μm. The total respiration rate for the three microcosms with cereal leaf POM ranged from 5.09 to 14.87 μmol CO2 min[-1] L[-1]. Of this, the amount contributed by larger particulates was in the range of 55-63%; and for smaller particulates ranged from 18 to 32 %. Data for microcosms containing water from the Hudson River estuary, with natural particulates, was as follows: total respiration ranged from ∼3 μmol CO2 min[-1] L[-1] to ∼3.73 μmol CO2 min[-1] L[-1]. Larger particulates contributed approximately 40% of total respiration, and that of smaller particulates was substantially less (4-5% of total). Overall, these results indicate that microbial communities associated with particulates in the water column (especially larger particulates) may contribute substantial amounts of CO2 to the atmosphere.},
}
@article {pmid31759643,
year = {2020},
author = {Wen, D and Ordonez, D and McKenna, A and Chang, NB},
title = {Fate and transport processes of nitrogen in biosorption activated media for stormwater treatment at varying field conditions of a roadside linear ditch.},
journal = {Environmental research},
volume = {181},
number = {},
pages = {108915},
doi = {10.1016/j.envres.2019.108915},
pmid = {31759643},
issn = {1096-0953},
mesh = {Groundwater ; Nitrates ; *Nitrogen ; *Rain ; Waste Disposal, Fluid/*methods ; Water Purification ; Water Supply ; },
abstract = {Roadside drainage networks can result in changes to watershed hydrology and water quality. By acting as hydrological links between urban development, agricultural fields, and natural streams, roadside ditches may be modified by filling in some green sorption media to control nitrogen pollution. Biosorption activated media (BAM), one of the green sorption media, are composed of sand, tire crumb, and clay, which can remove nitrogen from stormwater and groundwater through integrated hydrological, chemophysical, and microbial processes. The fate and transport processes of interest are complicated by internal microbial processes including ammonification, nitrification, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA), each of which is controlled by different microbial species in addition to some varying field conditions. In this study, BAM was tested in a suite of columns to address site-specific physical, chemical and biological concerns driven by in situ traffic compaction, carbon availability, and animal impact (such as gopher turtles, moles, and ants) all of which impose different impacts on nitrogen fate and transport processes that may be signified by changing dissolved organic nitrogen species (DONs). The traffic compaction condition resulted in the most suitable hydraulic retention time in the hydrological process, which is beneficial for the assimilation of DONs in a long-term carbon rich environment due to biofilm expansion. Denitrifiers were the most predominant microbial population and the microbial species of DNRA were the second most predominant one in all three field conditions. However, the relationship of denitrifiers and DNRA in BAM can be shifted from commensalism to competition or even inhibition after carbon addition in microbial ecology.},
}
@article {pmid31758237,
year = {2020},
author = {Wang, Y and Xie, Q and Zhang, Y and Ma, W and Ning, K and Xiang, JY and Cui, J and Xiang, H},
title = {Combination of probiotics with different functions alleviate DSS-induced colitis by regulating intestinal microbiota, IL-10, and barrier function.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {1},
pages = {335-349},
doi = {10.1007/s00253-019-10259-6},
pmid = {31758237},
issn = {1432-0614},
support = {20180201078YY//Science and Technology Development Planning of Jilin/ ; },
mesh = {Animals ; Colitis/chemically induced/*prevention &amp; control ; Colon/*immunology/*microbiology ; Dextran Sulfate ; Disease Models, Animal ; Drugs, Chinese Herbal/administration &amp; dosage ; Dysbiosis ; Gastrointestinal Microbiome ; Inflammation ; Interleukin-10/genetics/*immunology ; Intestinal Mucosa/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Probiotics/*administration &amp; dosage ; Specific Pathogen-Free Organisms ; Sulfasalazine/administration &amp; dosage ; },
abstract = {The potential of probiotics for treating ulcerative colitis (UC) has attracted increasing attention. However, more studies are still needed to guide physicians on the proper selection and use of probiotics. Here, we propose that combination of multiple probiotics with different functions can reduce intestinal inflammation. In this study, the effects of probiotics (Lactobacillus reuteri, Bacillus coagulans, Bifidobacterium longum, and Clostridium butyricum) on the physiology and histopathology of colon were evaluated in a dextran sulfate sodium (DSS)-induced colitis mouse model. The combined species, as well as the species individually, were tested and compared with sulfasalazine (SASP) and two Chinese herbal therapies. Results show that the functions of the four probiotic strains were different in regulating intestinal immunity and barrier function. The four-species probiotic cocktail was more effective than the species individually and anti-inflammatory drugs in repairing the dysbiosis of mucosal microbial ecology and reducing intestinal inflammation. The multi-strain probiotic mixture increased the proportion of beneficial bacteria and decreased the proportion of pro-inflammatory bacteria in the colonic mucosa. In addition, probiotic mixture significantly enhanced the expression of IL-10 and intestinal barrier function. These results suggest that a combination of multiple probiotics with different functions has synergistic effects and can restore the balance of interactions between microorganisms and immunological niches.},
}
@article {pmid31757825,
year = {2020},
author = {Frankel-Bricker, J and Buerki, S and Feris, KP and White, MM},
title = {Influences of a Prolific Gut Fungus (Zancudomyces culisetae) on Larval and Adult Mosquito (Aedes aegypti)-Associated Microbiota.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {3},
pages = {},
pmid = {31757825},
issn = {1098-5336},
support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; P20 GM109095/GM/NIGMS NIH HHS/United States ; P30 GM103324/GM/NIGMS NIH HHS/United States ; },
mesh = {Aedes/growth &amp; development/*microbiology/*physiology ; Animals ; Female ; Fungi/*physiology ; Gastrointestinal Tract/microbiology/physiology ; Larva/growth &amp; development/microbiology/physiology ; Microbiota ; },
abstract = {Adult mosquitoes inherit a bacterial community from larvae via transstadial transmission, an understudied process that may influence host-microbe interactions. Microbes contribute to important host life history traits, and analyzing transmitted microbial communities, the interrelationship between larval and adult-associated microbiota, and factors influencing host-microbe relationships provides targets for research. During its larval stage, the yellow fever mosquito (Aedes aegypti) hosts the trichomycete gut fungus Zancudomyces culisetae, and fungal colonization coincides with environmental perturbations in the digestive tract microecosystem. Natural populations are differentially exposed to fungi, thereby potentially harboring distinct microbiota and experiencing disparate host-microbe interactions. This study's objectives were to characterize larval and initial adult microbiomes, investigate variation in diversity and distribution of microbial communities across individuals, and assess whether larval fungal colonization impacted microbiomes at these developmental stages. Laboratory-based fungal infestation assays, sequencing of 16S rRNA gene amplicons, and bacterial load quantification protocols revealed that initial adult microbiomes varied in diversity and distribution. Larval fungal colonization had downstream effects on initial adult microbiomes, significantly reducing microbial community variation, shifting relative abundances of certain bacterial families, and influencing transstadial transmission outcomes of particular genera. Further, abundances of several families consistently decreased in adults relative to levels in larvae, possibly reflecting impacts of host development on specific bacterial taxa. These findings demonstrated that a prolific gut fungus impacted mosquito-associated microbiota at two developmental stages in an insect connected with global human health.IMPORTANCE Mosquitoes are widespread vectors of numerous human pathogens and harbor microbiota known to affect host phenotypic traits. However, little research has directly investigated how bacterial communities associated with larvae and adults are connected. We characterized whole-body bacterial communities in mosquito larvae preceding pupation and in newly emerged adults, and investigated whether a significant biotic factor, fungal colonization of the larval hindgut, impacted these microbiomes. Results showed that fungal colonization reduced microbial community variation across individuals and differentially impacted the outcomes of transstadial transmission for certain bacterial genera, revealing downstream effects of the fungus on initial adult microbiomes. The importance of our research is in providing a thorough comparative analysis of whole-body microbiota harbored in larvae and adults of the yellow fever mosquito (Aedes aegypti) and in demonstrating the important role a widespread gut fungus played in a host-associated microbiome.},
}
@article {pmid31757758,
year = {2020},
author = {Garin-Fernandez, A and Wichels, A},
title = {Looking for the hidden: Characterization of lysogenic phages in potential pathogenic Vibrio species from the North Sea.},
journal = {Marine genomics},
volume = {51},
number = {},
pages = {100725},
doi = {10.1016/j.margen.2019.100725},
pmid = {31757758},
issn = {1876-7478},
mesh = {Lysogeny ; Myoviridae/*physiology ; North Sea ; Vibrio cholerae/*virology ; Vibrio parahaemolyticus/*virology ; },
abstract = {The incidence of potentially pathogenic Vibrio species in the marine environment around Europe, is correlated with the increase of surface seawater temperature. Despite their importance, little is known about the trigger factors of potential outbreak-causing strains in this region. As prophages may compose a major reservoir of virulence traits in marine ecosystems, this study aims to identify and characterize the genomes of lysogenic Vibrio phages exemplarily from the North Sea. Therefore, 31 isolates from potentially pathogenic Vibrio species from the North Sea were screened for inducible prophages with mitomycin C. From them, one V. cholerae isolate and 40% V. parahaemolyticus isolates carried inducible prophages. Three lysogenic phages were selected for genomic characterization. The phage vB_VpaM_VP-3212 (unclassified Myoviridae) has a genome with a length of 36.81 Kbp and 55 CDS were identified. This lysogenic phage of V. parahaemolyticus contains genes related to replicative transposition mechanism, such as transposase and mobile elements similar to Mu-like viruses. The phage vB_VpaP_VP-3220 (Podoviridae, unclassified Nona33virus) has a genome length of 58,14 Kbp and contains 63 CDS. This V. parahaemolyticus phage probably uses a headful (pac) packaging replication mechanism. The phage vB_VchM_VP-3213 (unclassified Myoviridae) has a genome with a length of 41 Kbp and 63 CDS were identified, including integrase and Xer system for lysogenic recombination. This lysogenic phage of V. cholerae has similar genomic features as lambdoid phages. Although no pathogenicity genes were identified, their similarity among other phage genomes indicates that these phages can affect the development of pathogenic Vibrio strains in marine environments.},
}
@article {pmid31757204,
year = {2019},
author = {Patuzzi, I and Baruzzo, G and Losasso, C and Ricci, A and Di Camillo, B},
title = {metaSPARSim: a 16S rRNA gene sequencing count data simulator.},
journal = {BMC bioinformatics},
volume = {20},
number = {Suppl 9},
pages = {416},
pmid = {31757204},
issn = {1471-2105},
support = {-//Universit&#xe0; degli Studi di Padova/ ; },
mesh = {Animals ; Computer Simulation ; DNA, Ribosomal/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; *Metagenomics ; RNA, Ribosomal, 16S/*genetics ; *Software ; },
abstract = {BACKGROUND: In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies. Despite the considerable popularity of this technique, an exiguous number of specific tools are currently available for proper 16S rDNA-seq count data preprocessing and simulation. Indeed, the great majority of tools have been developed adapting methodologies previously used for bulk RNA-seq data, with poor assessment of their applicability in the metagenomics field. For such tools and the few ones specifically developed for 16S rDNA-seq data, performance assessment is challenging, mainly due to the complex nature of the data and the lack of realistic simulation models. In fact, to the best of our knowledge, no software thought for data simulation are available to directly obtain synthetic 16S rDNA-seq count tables that properly model heavy sparsity and compositionality typical of these data.<br><br>RESULTS: In this paper we present metaSPARSim, a sparse count matrix simulator intended for usage in development of 16S rDNA-seq metagenomic data processing pipelines. metaSPARSim implements a new generative process that models the sequencing process with a Multivariate Hypergeometric distribution in order to realistically simulate 16S rDNA-seq count table, resembling real experimental data compositionality and sparsity. It provides ready-to-use count matrices and comes with the possibility to reproduce different pre-coded scenarios and to estimate simulation parameters from real experimental data. The tool is made available at http://sysbiobig.dei.unipd.it/?q=Software#metaSPARSimand https://gitlab.com/sysbiobig/metasparsim.<br><br>CONCLUSION: metaSPARSim is able to generate count matrices resembling real 16S rDNA-seq data. The availability of count data simulators is extremely valuable both for methods developers, for which a ground truth for tools validation is needed, and for users who want to assess state of the art analysis tools for choosing the most accurate one. Thus, we believe that metaSPARSim is a valuable tool for researchers involved in developing, testing and using robust and reliable data analysis methods in the context of 16S rRNA gene sequencing.},
}
@article {pmid31757073,
year = {2019},
author = {Yssel, AEJ and Kao, SM and Van de Peer, Y and Sterck, L},
title = {ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes.},
journal = {Genes},
volume = {10},
number = {12},
pages = {},
pmid = {31757073},
issn = {2073-4425},
mesh = {*Databases, Genetic ; *Genome, Plant ; *Molecular Sequence Annotation ; },
abstract = {ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops Consortium (AOCC). The motivation behind the development of the ORCAE platform was to create a knowledge-based website where the research-community can make contributions to improve genome annotations. All changes to any given gene-model or gene description are stored, and the entire annotation history can be retrieved. Genomes can either be set to "public" or "restricted" mode; anonymous users can browse public genomes but cannot make any changes. Aside from providing a user-&amp;nbsp;friendly interface to view genome annotations, the platform also includes tools and information (such as gene expression evidence) that enables authorized users to edit and validate genome annotations. The ORCAE-AOCC platform will enable various stakeholders from around the world to coordinate their efforts to annotate and study underutilized crops.},
}
@article {pmid31756853,
year = {2019},
author = {Suleiman, AKA and Harkes, P and van den Elsen, S and Holterman, M and Korthals, GW and Helder, J and Kuramae, EE},
title = {Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare).},
journal = {The Science of the total environment},
volume = {695},
number = {},
pages = {133885},
doi = {10.1016/j.scitotenv.2019.133885},
pmid = {31756853},
issn = {1879-1026},
mesh = {Agriculture ; Bacteria ; Biota ; Ecosystem ; Eukaryota ; Fertilizers ; Food Chain ; Fungi ; *Hordeum ; *Rhizosphere ; Soil ; *Soil Microbiology ; },
abstract = {Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial-microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.},
}
@article {pmid31756842,
year = {2019},
author = {Hylling, O and Nikbakht Fini, M and Ellegaard-Jensen, L and Muff, J and Madsen, HT and Aamand, J and Hansen, LH},
title = {A novel hybrid concept for implementation in drinking water treatment targets micropollutant removal by combining membrane filtration with biodegradation.},
journal = {The Science of the total environment},
volume = {694},
number = {},
pages = {133710},
doi = {10.1016/j.scitotenv.2019.133710},
pmid = {31756842},
issn = {1879-1026},
mesh = {*Biodegradation, Environmental ; Drinking Water/*chemistry ; *Filtration ; Water Pollutants, Chemical/*analysis ; Water Purification/*methods ; },
abstract = {Groundwater extracted for drinking water production is commonly treated by aeration and sand filtration. However, this simple treatment is typically unable to remove pesticide residues. As a solution, bioaugmentation of sand filter units (i.e., the addition of specific degrader strains) has been proposed as an alternative "green" technology for targeted pesticide removal. However, the introduced degraders are challenged by (i) micropollutant levels of target residue, (ii) the oligotrophic environment and (iii) competition and predation by the native microorganisms, leading to loss of population and degradation potential. To overcome these challenges, we propose the introduction of a novel hybrid treatment step to the overall treatment process in which reverse osmosis filtration and biodegradation are combined to remove a target micropollutant. Here, the reverse osmosis produces a concentrated retentate that will act as a feed to a dedicated biofilter unit, intended to promote biodegradation potential and stability of an introduced degrader. Subsequently, the purified retentate will be re-mixed with the permeate from reverse osmosis, for re-mineralization and downstream consumption. In our study, we investigated the effect of reverse osmosis retentates on the degradation potential of an introduced degrader. This paper provides the first promising results of this hybrid concept using the 2,6-dichlorobenzamide (BAM)-degrading bacteria Aminobacter sp. MSH1 in batch experiments, spiked with radiolabeled BAM. The results showed an increased degradation potential of MSH1 in retentate waters versus untreated water. Colony-forming units and qPCR showed a stable MSH1 population, despite higher concentrations of salts and metals, and increased growth of native bacteria.},
}
@article {pmid31756831,
year = {2019},
author = {Iqbal, A and Shang, Z and Rehman, MLU and Ju, M and Rehman, MMU and Rafiq, MK and Ayub, N and Bai, Y},
title = {Pattern of microbial community composition and functional gene repertoire associated with methane emission from Zoige wetlands, China-A review.},
journal = {The Science of the total environment},
volume = {694},
number = {},
pages = {133675},
doi = {10.1016/j.scitotenv.2019.133675},
pmid = {31756831},
issn = {1879-1026},
mesh = {China ; Methane/*metabolism ; *Microbiota ; *Soil Microbiology ; *Wetlands ; },
abstract = {The Hindu-Kush Himalaya region extends over 4 million km[2] across the eight countries. Knowingly, the Qinghai-Tibetan Plateau (QTP) is considered the principal altitudinal permafrost constituent on earth and is deemed as the third 'pole'. Among which, the Zoige wetlands are located in the northeastern boundary of QTP, wrapping a total area of 6180 km[2] with an average altitude of 3500 m. This entire region is the hotspot for methane emission since the last decade. Given the importance of methane emission, many studies have focused on the effect of environmental fluctuations on the overall methane profile and, more recently on the methanogenic community structure. The current review summarizes recent advancements of the methanogenic community and methane profile and outlines a framework for better understanding of the microbial ecology of the Zoige wetlands, China. Moreover, as microorganisms are indispensable to biogeochemical cycles, especially for methane, they are believed to be the best indicators to identify the condition of wetlands. Hence, we suggest that, underpinning the microbial profile could help understand the status of a wetland.},
}
@article {pmid31754744,
year = {2020},
author = {Rajagopala, SV and Singh, H and Yu, Y and Zabokrtsky, KB and Torralba, MG and Moncera, KJ and Frank, B and Pieper, R and Sender, L and Nelson, KE},
title = {Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {1034-1043},
doi = {10.1007/s00248-019-01448-x},
pmid = {31754744},
issn = {1432-184X},
mesh = {Adolescent ; Anti-Bacterial Agents/*administration &amp; dosage ; Antineoplastic Agents/*administration &amp; dosage ; Case-Control Studies ; Child ; Child, Preschool ; Cohort Studies ; Dysbiosis/chemically induced/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Male ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*drug therapy ; },
abstract = {Prophylactic or therapeutic antibiotic use along with chemotherapy treatment potentially has a long-standing adverse effect on the resident gut microbiota. We have established a case-control cohort of 32 pediatric and adolescent acute lymphoblastic leukemia (ALL) patients and 25 healthy siblings (sibling controls) to assess the effect of chemotherapy as well as antibiotic prophylaxis on the gut microbiota. We observe that the microbiota diversity and richness of the ALL group is significantly lower than that of the control group at diagnosis and during chemotherapy. The microbiota diversity is even lower in antibiotics-exposed ALL patients. Although the gut microbial diversity tends to stabilize after 1-year post-chemotherapy, their abundances were altered because of chemotherapy and prophylactic antibiotic treatments. Specifically, the abundances of mucolytic gram-positive anaerobic bacteria, including Ruminococcus gnavus and Ruminococcus torques, tended to increase during the chemotherapy regimen and continued to be elevated 1 year beyond the initiation of chemotherapy. This dysbiosis may contribute to the development of gastrointestinal complications in ALL children following chemotherapy. These findings set the stage to further understand the role of the gut microbiome dynamics in ALL patients and their potential role in alleviating some of the adverse side effects of chemotherapy and antibiotics use in immunocompromised children.},
}
@article {pmid31753627,
year = {2020},
author = {Vázquez-Blanco, R and Arias-Estévez, M and Bååth, E and Fernández-Calviño, D},
title = {Comparison of Cu salts and commercial Cu based fungicides on toxicity towards microorganisms in soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {257},
number = {},
pages = {113585},
doi = {10.1016/j.envpol.2019.113585},
pmid = {31753627},
issn = {1873-6424},
mesh = {Copper/*toxicity ; Environmental Pollution ; Fungicides, Industrial/*toxicity ; Salts ; Soil ; *Soil Microbiology ; Soil Pollutants/*toxicity ; },
abstract = {Microbial responses to Cu pollution as a function of Cu sources (Cu salts and commercial Cu fungicides) were assessed in a soil using basal soil respiration, and bacterial and fungal community growth, as endpoints. The soil was amended with different concentrations (0-32 mmol Cu kg[-1]) of Cu nitrate, Cu sulfate, Bordeaux mixture and 3 types of Cu oxychloride. Cu salts decreased soil pH, while this was not found with the other Cu sources. This difference in soil pH effects caused differences in the respiration, bacterial growth and fungal growth response. Basal soil respiration was negatively affected by Cu addition when the soil was spiked with Cu salts, but almost unaffected by commercial Cu fungicides. Bacterial growth was significantly and negatively affected by Cu addition for all the Cu sources, but Cu toxicity was higher for Cu salts than for commercial Cu fungicides. Fungal growth response was also different for Cu salts and commercial Cu fungicides, but only in the long-term. High Cu amendments using Cu salts stimulated fungal growth, whereas for commercial Cu fungicides, these concentrations inhibited fungal growth. Thus, the use of products similar to those used in commercial fungicides is a recommended practice for Cu risk assessments in soil.},
}
@article {pmid31750314,
year = {2019},
author = {Gupta, VVSR and Zhang, B and Penton, CR and Yu, J and Tiedje, JM},
title = {Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil.},
journal = {Frontiers in molecular biosciences},
volume = {6},
number = {},
pages = {115},
pmid = {31750314},
issn = {2296-889X},
abstract = {Summer-growing perennial grasses such as Panicum coloratum L. cv. Bambatsi (Bambatsi panic), Chloris gayana Kunth cv. Katambora (Rhodes grass) and Digitaria eriantha Steud. cv. Premier (Premier digit grass) growing in the poor fertility sandy soils in the Mediterranean regions of southern Australia and western Australia mainly depend upon soil N and biological N inputs through diazotrophic (free living or associative) N fixation. We investigated the community composition and diversity (nifH-amplicon sequencing), abundance (qPCR) and functional capacity ([15]N incubation assay) of the endophytic diazotrophic community in the below and above ground plant parts of field grown and unfertilized grasses. Results showed a diverse and abundant diazotrophic community inside plant both above and below-ground and there was a distinct diazotrophic assemblage in the different plant parts in all the three grasses. There was a limited difference in the diversity between leaves, stems and roots except that Panicum grass roots harbored greater species richness. Nitrogen fixation potentials ranged between 0.24 and 5.9 mg N kg[-1] day[-1] and N fixation capacity was found in both the above and below ground plant parts. Results confirmed previous reports of plant species-based variation and that Alpha-Proteobacteria were the dominant group of nifH-harboring taxa both in the belowground and aboveground parts of the three grass species. Results also showed a well-structured nifH-harboring community in all plant parts, an example for a functional endophytic community. Overall, the variation in the number and identity of module hubs and connectors among the different plant parts suggests that co-occurrence patterns within the nifH-harboring community specific to individual compartments and local environments of the niches within each plant part may dictate the overall composition of diazotrophs within a plant.},
}
@article {pmid31749830,
year = {2019},
author = {Guo, J and Quensen, JF and Sun, Y and Wang, Q and Brown, CT and Cole, JR and Tiedje, JM},
title = {Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {957},
pmid = {31749830},
issn = {1664-8021},
support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; },
abstract = {Shotgun metagenomics has greatly advanced our understanding of microbial communities over the last decade. Metagenomic analyses often include assembly and genome binning, computationally daunting tasks especially for big data from complex environments such as soil and sediments. In many studies, however, only a subset of genes and pathways involved in specific functions are of interest; thus, it is not necessary to attempt global assembly. In addition, methods that target genes can be computationally more efficient and produce more accurate assembly by leveraging rich databases, especially for those genes that are of broad interest such as those involved in biogeochemical cycles, biodegradation, and antibiotic resistance or used as phylogenetic markers. Here, we review six gene-targeted assemblers with unique algorithms for extracting and/or assembling targeted genes: Xander, MegaGTA, SAT-Assembler, HMM-GRASPx, GenSeed-HMM, and MEGAN. We tested these tools using two datasets with known genomes, a synthetic community of artificial reads derived from the genomes of 17 bacteria, shotgun sequence data from a mock community with 48 bacteria and 16 archaea genomes, and a large soil shotgun metagenomic dataset. We compared assemblies of a universal single copy gene (rplB) and two N cycle genes (nifH and nirK). We measured their computational efficiency, sensitivity, specificity, and chimera rate and found Xander and MegaGTA, which both use a probabilistic graph structure to model the genes, have the best overall performance with all three datasets, although MEGAN, a reference matching assembler, had better sensitivity with synthetic and mock community members chosen from its reference collection. Also, Xander and MegaGTA are the only tools that include post-assembly scripts tuned for common molecular ecology and diversity analyses. Additionally, we provide a mathematical model for estimating the probability of assembling targeted genes in a metagenome for estimating required sequencing depth.},
}
@article {pmid31749167,
year = {2020},
author = {Ferlian, O and Thakur, MP and Castañeda González, A and San Emeterio, LM and Marr, S and da Silva Rocha, B and Eisenhauer, N},
title = {Soil chemistry turned upside down: a meta-analysis of invasive earthworm effects on soil chemical properties.},
journal = {Ecology},
volume = {101},
number = {3},
pages = {e02936},
pmid = {31749167},
issn = {1939-9170},
support = {677232/ERC_/European Research Council/International ; FZT 118//German Research Foundation/International ; 677232//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program/International ; TH 2307/1-1//German Research Foundation/International ; },
mesh = {Animals ; Ecosystem ; Forests ; *Oligochaeta ; Soil ; Soil Microbiology ; },
abstract = {Recent studies have shown that invasive earthworms can dramatically reduce native biodiversity, both above and below the ground. However, we still lack a synthetic understanding of the underlying mechanisms behind these changes, such as whether earthworm effects on soil chemical properties drive such relationships. Here, we investigated the effects of invasive earthworms on soil chemical properties (pH, water content, and the stocks and fluxes of carbon, nitrogen, and phosphorus) by conducting a meta-analysis. Invasive earthworms generally increased soil pH, indicating that the removal of organic layers and the upward transport of more base-rich mineral soil caused a shift in soil pH. Moreover, earthworms significantly decreased soil water content, suggesting that the burrowing activities of earthworms may have increased water infiltration of and/or increased evapotranspiration from soil. Notably, invasive earthworms had opposing effects on organic and mineral soil for carbon and nitrogen stocks, with decreases in organic, and increases in mineral soil. Nitrogen fluxes were higher in mineral soil, whereas fluxes in organic soil were not significantly affected by the presence of invasive earthworms, indicating that earthworms mobilize and redistribute nutrients among soil layers and increase overall nitrogen loss from the soil. Invasive earthworm effects on element stocks increased with ecological group richness only in organic soil. Earthworms further decreased ammonium stocks with negligible effects on nitrate stocks in organic soil, whereas they increased nitrate stocks but not ammonium stocks in mineral soil. Notably, all of these results were consistent across forest and grassland ecosystems underlining the generality of our findings. However, we found some significant differences between studies that were conducted in the field (observational and experimental settings) and in the lab, such as that the effects on soil pH decreased from field to lab settings, calling for a careful interpretation of lab findings. Our meta-analysis provides strong empirical evidence that earthworm invasion may lead to substantial changes in soil chemical properties and element cycling in soil. Furthermore, our results can help explain the dramatic effects of invasive earthworms on native biodiversity, for example, shifts towards the dominance of grass species over herbaceous ones, as shown by recent meta-analyses.},
}
@article {pmid31748246,
year = {2019},
author = {Tomkovich, S and Lesniak, NA and Li, Y and Bishop, L and Fitzgerald, MJ and Schloss, PD},
title = {The Proton Pump Inhibitor Omeprazole Does Not Promote Clostridioides difficile Colonization in a Murine Model.},
journal = {mSphere},
volume = {4},
number = {6},
pages = {},
pmid = {31748246},
issn = {2379-5042},
support = {U01 AI124255/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Carrier State/*immunology ; Clostridioides difficile/*growth &amp; development ; Clostridium Infections/*immunology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Disease Models, Animal ; *Disease Susceptibility ; Feces/microbiology ; Mice ; Microbiota/drug effects ; Omeprazole/administration &amp; dosage/*adverse effects ; Phylogeny ; Proton Pump Inhibitors/administration &amp; dosage/*adverse effects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Proton pump inhibitor (PPI) use has been associated with microbiota alterations and susceptibility to Clostridioides difficile infections (CDIs) in humans. We assessed how PPI treatment alters the fecal microbiota and whether treatment promotes CDIs in a mouse model. Mice receiving a PPI treatment were gavaged with 40 mg of omeprazole per kg of body weight during a 7-day pretreatment phase, the day of C. difficile challenge, and the following 9 days. We found that mice treated with omeprazole were not colonized by C. difficile When omeprazole treatment was combined with a single clindamycin treatment, one cage of mice remained resistant to C. difficile colonization, while the other cage was colonized. Treating mice with only clindamycin followed by challenge resulted in C. difficile colonization. 16S rRNA gene sequencing analysis revealed that omeprazole had minimal impact on the structure of the murine microbiota throughout the 16 days of omeprazole exposure. These results suggest that omeprazole treatment alone is not sufficient to disrupt microbiota resistance to C. difficile infection in mice that are normally resistant in the absence of antibiotic treatment.IMPORTANCE Antibiotics are the primary risk factor for Clostridioides difficile infections (CDIs), but other factors may also increase a person's risk. In epidemiological studies, proton pump inhibitor (PPI) use has been associated with CDI incidence and recurrence. PPIs have also been associated with alterations in the human intestinal microbiota in observational and interventional studies. We evaluated the effects of the PPI omeprazole on the structure of the murine intestinal microbiota and its ability to disrupt colonization resistance to C. difficile We found omeprazole treatment had minimal impact on the murine fecal microbiota and did not promote C. difficile colonization. Further studies are needed to determine whether other factors contribute to the association between PPIs and CDIs seen in humans or whether aspects of murine physiology may limit its utility to test these types of hypotheses.},
}
@article {pmid31743949,
year = {2020},
author = {Weber, L and González-Díaz, P and Armenteros, M and Ferrer, VM and Bretos, F and Bartels, E and Santoro, AE and Apprill, A},
title = {Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys.},
journal = {Environmental microbiology},
volume = {22},
number = {1},
pages = {499-519},
pmid = {31743949},
issn = {1462-2920},
support = {//Dalio Foundation/International ; 1736288//Division of Ocean Sciences/International ; //National Science Foundation/International ; //Cuban Center for Inspection and Environmental Control/International ; },
mesh = {Animals ; Anthozoa/*microbiology ; Archaea/classification/*genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; Caribbean Region ; Coral Reefs ; Cuba ; Florida ; Humans ; Microbiota/genetics ; Seawater/*microbiology ; },
abstract = {There are a few baseline reef-systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected 'crown jewel' offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundant Prochlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta-diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria.},
}
@article {pmid31742865,
year = {2020},
author = {Geesink, P and Wegner, CE and Probst, AJ and Herrmann, M and Dam, HT and Kaster, AK and Küsel, K},
title = {Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater.},
journal = {Environmental microbiology},
volume = {22},
number = {2},
pages = {726-737},
doi = {10.1111/1462-2920.14865},
pmid = {31742865},
issn = {1462-2920},
support = {2016 FGI 0024//Th&#xfc;ringer Ministerium f&#xfc;r Wirtschaft, Wissenschaft und Digitale Gesellschaft/International ; CRC 1076//Collaborative Research Centre AquaDiva/International ; ANR-10-INBS-09//France G&#xe9;nomique and French Bioinformatics Institute/International ; ANR-11-INBS-0013//France G&#xe9;nomique and French Bioinformatics Institute/International ; //LABGeM (CEA/Genoscope &amp; CNRS UMR8030)/International ; SAS-2015-HKI-LWC//Leibniz Research Cluster InfectoOptics/International ; //Ministerium f&#xfc;r Kultur und Wissenschaft des Landes Nordrhein-Westfalen/International ; 41-5507-2016//Strategy and Innovation Grant from the Free State of Thuringia/International ; //Agence Nationale pour la Recherche/International ; //Deutsche Forschungsgemeinschaft/International ; //Friedrich Schiller University Jena/International ; },
mesh = {Bacteria/genetics/*metabolism ; *Bacterial Physiological Phenomena ; Carbon ; Groundwater/*microbiology ; Lactic Acid/*metabolism ; Metagenomics ; Microbial Interactions/*physiology ; Microbiota/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Spatio-Temporal Analysis ; Symbiosis ; },
abstract = {Subsurface ecosystems like groundwater harbour diverse microbial communities, including small-sized, putatively symbiotic organisms of the Candidate Phyla Radiation, yet little is known about their ecological preferences and potential microbial partners. Here, we investigated a member of the superphylum Microgenomates (Cand. Roizmanbacterium ADI133) from oligotrophic groundwater using mini-metagenomics and monitored its spatio-temporal distribution using 16S rRNA gene analyses. A Roizmanbacteria-specific quantitative PCR assay allowed us to track its abundance over the course of 1 year within eight groundwater wells along a 5.4 km hillslope transect, where Roizmanbacteria reached maximum relative abundances of 2.3%. In-depth genomic analyses suggested that Cand. Roizmanbacterium ADI133 is a lactic acid fermenter, potentially able to utilize a range of complex carbon substrates, including cellulose. We hypothesize that it attaches to host cells using a trimeric autotransporter adhesin and inhibits their cell wall biosynthesis using a toxin-antitoxin system. Network analyses based on correlating Cand. Roizmanbacterium ADI133 abundances with amplicon sequencing-derived microbial community profiles suggested one potential host organism, classified as a member of the class Thermodesulfovibrionia (Nitrospirae). By providing lactate as an electron donor Cand. Roizmanbacterium ADI133 potentially mediates the transfer of carbon to other microorganisms and thereby is an important connector in the microbial community.},
}
@article {pmid31741310,
year = {2020},
author = {Alves, KJ and da Silva, MCP and Cotta, SR and Ottoni, JR and van Elsas, JD and de Oliveira, VM and Andreote, FD},
title = {Mangrove soil as a source for novel xylanase and amylase as determined by cultivation-dependent and cultivation-independent methods.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {51},
number = {1},
pages = {217-228},
pmid = {31741310},
issn = {1678-4405},
support = {Finance Code 001.//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Bacillus/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; Cellulose/metabolism ; Endo-1,4-beta Xylanases/*genetics/metabolism ; Genes, Bacterial/genetics ; Metagenomics ; Paenibacillus/genetics/isolation &amp; purification/metabolism ; Planctomycetales/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Starch/metabolism ; *Wetlands ; alpha-Amylases/*genetics/metabolism ; },
abstract = {Xylanase and α-amylase enzymes participate in the degradation of organic matter, acting in hemicellulose and starch mineralization, respectively, and are in high demand for industrial use. Mangroves represent a promising source for bioprospecting enzymes due to their unique characteristics, such as fluctuations in oxic/anoxic conditions and salinity. In this context, the present work aimed to bioprospect xylanases from mangrove soil using cultivation-dependent and cultivation-independent methods. Through screening from a metagenomic library, three potentially xylanolytic clones were obtained and sequenced, and reads were assembled into contigs and annotated. The contig MgrBr135 was affiliated with the Planctomycetaceae family and was one of 30 ORFs selected for subcloning that demonstrated only amylase activity. Through the cultivation method, 38 bacterial isolates with xylanolytic activity were isolated. Isolate 11 showed an enzymatic index of 10.9 using the plate assay method. Isolate 39 achieved an enzyme activity of 0.43 U/mL using the colorimetric method with 3,5-dinitrosalicylic acid. Isolate 39 produced xylanase on culture medium with salinity ranging from 1.25 to 5%. Partial 16S rRNA gene sequencing identified isolates in the Bacillus and Paenibacillus genera. The results of this study highlight the importance of mangroves as an enzyme source and show that bacterial groups can be used for starch and hemicellulose degradation.},
}
@article {pmid31741007,
year = {2020},
author = {Hayek, M and Baraquet, C and Lami, R and Blache, Y and Molmeret, M},
title = {The Marine Bacterium Shewanella woodyi Produces C8-HSL to Regulate Bioluminescence.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {865-881},
doi = {10.1007/s00248-019-01454-z},
pmid = {31741007},
issn = {1432-184X},
mesh = {Homoserine/*analogs &amp; derivatives/biosynthesis ; Lactones ; *Luminescence ; *Quorum Sensing ; Shewanella/*physiology ; },
abstract = {Quorum sensing (QS), a cell-to-cell communication system involved in the synchronization of bacterial behavior in a cell-density-dependent manner has been shown to control phenotypes such as luminescence, virulence, and biofilm formation. The marine strain, Shewanella woodyi MS32 has been identified as a luminous bacterium. Very little information is known on this bacterium, in particular if its luminescence and biofilm formation are controlled by QS. In this study, we have demonstrated that S. woodyi MS32 emits luminescence in planktonic and sessile conditions. The putative QS regulatory genes homologous to luxI and luxR identified in the S. woodyi MS32 genome, named swoI and swoR, are divergently transcribed and are not genetically linked to the lux operon in contrast with its closest parent Shewanella hanedai and with Aliivibrio fischeri. Interestingly, the phylogenetic analysis based on the SwoI and SwoR sequences shows that a separate horizontal gene transfer (HGT) occurred for the regulatory genes and for the lux operon. Functional analyses demonstrate that the swoI and swoR mutants were non-luminescent. Expression of lux genes was impaired in the QS regulatory mutants. N-octanoyl-L-homoserine lactone (C8-HSL) identified using liquid chromatography mass spectrometry in the wild-type strain (but not in ΔswoI) can induce S. woodyi luminescence. No significant difference has been detected between the wild-type and mutants on adhesion and biofilm formation in the conditions tested. Therefore, we have demonstrated that the luxCDABEG genes of S. woodyi MS32 are involved in luminescence emission and that the swoR/swoI genes, originated from a separate HGT, regulate luminescence through C8-HSL production.},
}
@article {pmid31737577,
year = {2019},
author = {Khan, S and Voordouw, MJ and Hill, JE},
title = {Competition Among Gardnerella Subgroups From the Human Vaginal Microbiome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {374},
pmid = {31737577},
issn = {2235-2988},
mesh = {Biofilms ; Female ; Gardnerella/*physiology ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Metagenome ; Metagenomics/methods ; *Microbial Interactions ; Microbiota ; RNA, Ribosomal, 16S ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; },
abstract = {Gardnerella spp. are hallmarks of bacterial vaginosis, a clinically significant dysbiosis of the vaginal microbiome. Gardnerella has four subgroups (A, B, C, and D) based on cpn60 sequences. Multiple subgroups are often detected in individual women, and interactions between these subgroups are expected to influence their population dynamics and associated clinical signs and symptoms of bacterial vaginosis. In the present study, contact-independent and contact-dependent interactions between the four Gardnerella subgroups were investigated in vitro. The cell free supernatants of mono- and co-cultures had no effect on growth rates of the Gardnerella subgroups suggesting that there are no contact-independent interactions (and no contest competition). For contact-dependent interactions, mixed communities of 2, 3, or 4 subgroups were created and the initial (0 h) and final population sizes (48 h) were quantified using subgroup-specific PCR. Compared to the null hypothesis of neutral interactions, most (69.3%) of the mixed communities exhibited competition. Competition reduced the growth rates of subgroups A, B, and C. In contrast, the growth rate of subgroup D increased in the presence of the other subgroups. All subgroups were able to form biofilm alone and in mixed communities. Our study suggests that there is scramble competition among Gardnerella subgroups, which likely contributes to the observed distributions of Gardnerella spp. in vaginal microbiomes and the formation of the multispecies biofilms characteristic of bacterial vaginosis.},
}
@article {pmid31737020,
year = {2019},
author = {Del Frari, G and Gobbi, A and Aggerbeck, MR and Oliveira, H and Hansen, LH and Ferreira, RB},
title = {Fungicides and the Grapevine Wood Mycobiome: A Case Study on Tracheomycotic Ascomycete Phaeomoniella chlamydospora Reveals Potential for Two Novel Control Strategies.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {1405},
pmid = {31737020},
issn = {1664-462X},
abstract = {Phaeomoniella chlamydospora is a tracheomycotic fungus that colonizes the xylem of grapevines (Vitis vinifera L.), causing wood discoloration, brown wood streaking, gummosis, and wood necrosis, which negatively affect the overall health, productivity, and life span of vines. Current control strategies to prevent or cope with P. chlamydospora infections are frequently ineffective. Moreover, it is unclear how fungicides commonly applied in vineyards against downy and powdery mildew agents affect the wood mycobiome, including wood pathogens such as P. chlamydospora. In this study, we used next-generation sequencing to assess the effects of foliar spray of grapevines with inorganic (copper oxychloride and sulfur), synthetic (penconazole and fosetyl-aluminum), and natural (Blad) fungicides currently used against the downy and powdery mildews. The subjects of our investigation were (i) the resident wood mycobiome, (ii) the early colonization by a consortium of fungal wood endophytes (ACEA1), (iii) the wood colonization success of P. chlamydospora, and (iv) the in planta interaction between P. chlamydospora and ACEA1, under greenhouse conditions, in rooted grapevine cuttings of cv. Cabernet Sauvignon. The data obtained suggest that the resident mycobiome is affected by different fungicide treatments. In addition, the early colonization success of the endophytes composing ACEA1 varied in response to fungicides, with relative abundances of some taxa being overrepresented or underrepresented when compared with the control. The wood colonization by P. chlamydospora comported significant changes in the mycobiome composition, and in addition, it was greatly affected by the foliar spray with Blad, which decreased the relative abundance of this pathogen 12-fold (4.9%) when compared with the control (60.7%) and other treatments. The presence of the pathogen also decreased considerably when co-inoculated into the plant with ACEA1, reaching relative abundances between 13.9% and 2.0%, depending on the fungicide treatment applied. This study shows that fungicides sprayed to prevent infections of powdery and downy mildews have an effect on non-target fungi that colonize the endosphere of grapevines. We suggest two potential control strategies to fight P. chlamydospora, namely, the foliar spray with Blad and the use of ACEA1. Further studies to confirm these results are required.},
}
@article {pmid31736494,
year = {2019},
author = {Villela, HDM and Vilela, CLS and Assis, JM and Varona, N and Burke, C and Coil, DA and Eisen, JA and Peixoto, RS},
title = {Prospecting Microbial Strains for Bioremediation and Probiotics Development for Metaorganism Research and Preservation.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {152},
pages = {},
doi = {10.3791/60238},
pmid = {31736494},
issn = {1940-087X},
mesh = {Animals ; Anthozoa/microbiology ; Bacteria/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Microbial Consortia ; Microbiota ; Probiotics/*pharmacology ; },
abstract = {Pollution affects all biomes. Marine environments have been particularly impacted, especially coral reefs, one of the most sensitive ecosystems on Earth. Globally, 4.5 billion people are economically dependent on the sea, where most of their livelihood is provided by coral reefs. Corals are of great importance and therefore their extinction leads to catastrophic consequences. There are several possible solutions to remediate marine pollutants and local contamination, including bioremediation. Bioremediation is the capacity of organisms to degrade contaminants. The approach presents several advantages, such as sustainability, relatively low cost, and the fact that it can be applied in different ecosystems, causing minimal impacts to the environment. As an extra advantage, the manipulation of endogenous microbiomes, including putative beneficial microorganisms for corals (pBMCs), may have probiotic effects for marine animals. In this context, the use of the two approaches, bioremediation and pBMC inoculation combined, could be promising. This strategy would promote the degradation of specific pollutants that can be harmful to corals and other metaorganisms while also increasing host resistance and resilience to deal with pollution and other threats. This method focuses on the selection of pBMCs to degrade two contaminants: the synthetic estrogen 17a-ethinylestradiol (EE2) and crude oil. Both have been reported to negatively impact marine animals, including corals, and humans. The protocol describes how to isolate and test bacteria capable of degrading the specific contaminants, followed by a description of how to detect some putative beneficial characteristics of these associated microbes to their coral host. The methodologies described here are relatively cheap, easy to perform, and highly adaptable. Almost any kind of soluble target compound can be used instead of EE2 and oil.},
}
@article {pmid31736217,
year = {2020},
author = {Paver, SF and Newton, RJ and Coleman, ML},
title = {Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry.},
journal = {Environmental microbiology},
volume = {22},
number = {1},
pages = {433-446},
pmid = {31736217},
issn = {1462-2920},
support = {OCE-1830011//Division of Ocean Sciences/International ; NA14OAR170095//Illinois-Indiana Sea Grant/International ; //UChicago Women's Board/International ; },
mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification ; Alphaproteobacteria/classification/genetics/*isolation &amp; purification ; Archaea/classification/genetics/*isolation &amp; purification ; Chloroflexi/classification/genetics/*isolation &amp; purification ; Lakes/*microbiology ; Michigan ; Microbiota/*genetics ; Phylogeny ; Plankton/classification/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI-B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI-C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.},
}
@article {pmid31734636,
year = {2020},
author = {Sikder, MNA and Xu, H},
title = {Seasonal variations in colonization dynamics of periphytic protozoa in coastal waters of the Yellow Sea, northern China.},
journal = {European journal of protistology},
volume = {72},
number = {},
pages = {125643},
doi = {10.1016/j.ejop.2019.125643},
pmid = {31734636},
issn = {1618-0429},
mesh = {*Biodiversity ; China ; Ciliophora/*physiology ; Environmental Monitoring ; Logistic Models ; *Seasons ; Seawater/*parasitology ; },
abstract = {The colonization features of periphytic protozoa have proved to be a useful tool for indicating water quality status in aquatic ecosystems. In order to reveal the seasonal variations in colonization dynamics of the protozoa, a 1-year baseline survey was carried out in coastal waters of the Yellow Sea, northern China. Using glass slides as artificial substrates, a total of 240 slides were collected at a depth of 1 m in four seasons after colonization periods of 3, 7, 10, 14, 21, and 28 days. A total of 122 ciliate species were identified with 21 dominant species. The colonization dynamics of the protozoa were well fitted to the MacArthur-Wilson and logistic models in all four seasons (P < 0.05). However, the equilibrium species numbers (Seq), colonization rates (G), and the time to 90% Seq (T90%) represented a clear seasonal variability: (1) more or less similar levels in spring and autumn (Seq = 29/23; G = 0.301/0.296; T90%=7.650/7.779); (2) with a significant difference in summer and winter (Seq = 32/121; G = 0.708/0.005; T90% = 3.252/479.705). Multivariate approaches demonstrated that the exposure time for the species composition and community structure of the protozoa to an equilibrium period were 10-14 days in spring and autumn, but less and more time periods were needed in summer and winter, respectively. Based on the results, we suggest that the colonization dynamics of periphytic protozoa were different within four seasons, and an optimal sampling strategy for monitoring surveys should be modified during different seasons in marine ecosystems.},
}
@article {pmid31734395,
year = {2020},
author = {Clauwaert, P and De Paepe, J and Jiang, F and Alonso-Fariñas, B and Vaiopoulou, E and Verliefde, A and Rabaey, K},
title = {Electrochemical tap water softening: A zero chemical input approach.},
journal = {Water research},
volume = {169},
number = {},
pages = {115263},
doi = {10.1016/j.watres.2019.115263},
pmid = {31734395},
issn = {1879-2448},
mesh = {Electrodes ; Ion Exchange ; *Water Purification ; *Water Softening ; },
abstract = {Electrochemical water softening was proposed as a sustainable alternative for ion exchange softening, avoiding the input of salt to drinking water and the production of a concentrated brine. Here we demonstrated two novel modes of operation combining an electrochemical cell with a fluidized bed crystallizer. The first approach relied on an electrochemical cell consisting of an anode and cathode separated by a cation or anion exchange membrane. The feed water was first directed into a crystallizer where it was blended with alkaline cathode effluent. The effluent of the crystallizer, softened water, was in part recirculated to the cathode to generate alkalinity, in part to the anode compartment, where the pH was again decreased. Average removal efficiencies for calcium and magnesium of 75-86% and 7-21% respectively, could be sustainably reached, at a specific energy consumption of 7.0-10.1 kWh kg[-1] CaCO3 (0.86-1.39 kWh m[-3] water). This configuration allowed reagent-free water softening, albeit with an effluent with a pH between 3.0 and 3.6. In a second mode of operation, the process influent to soften was also directed to the crystallizer and recirculated over the cathode, which was separated from the anode using an anion exchange membrane. In this mode of operation, the cathode effluent was sent through the crystallizing unit, and the anode compartment was operated in closed-loop. Average calcium and magnesium removal efficiencies of 73-78% and 40-44% were obtained at specific energy consumptions of 5.8-7.5 kWh kg[-1] CaCO3 (0.77-0.88 kWh m[-3] water). Although the softened water had an elevated pH (∼9.4), the advantage of this configuration is concomitant removal of anions and the formation of acids/disinfectant in the anode compartment. Both methods of operation thus showed reagent-free water softening at a relatively low specific energy consumption. These novel methods of softening could be used in remote locations where access to chemicals or discharge of ion exchange brines proves to be difficult, or in case addition of chemicals for softening is unwanted. Further research is needed to further decrease the specific energy consumption during long-term operation.},
}
@article {pmid31732938,
year = {2019},
author = {Dutzan, N and Abusleme, L},
title = {T Helper 17 Cells as Pathogenic Drivers of Periodontitis.},
journal = {Advances in experimental medicine and biology},
volume = {1197},
number = {},
pages = {107-117},
doi = {10.1007/978-3-030-28524-1_9},
pmid = {31732938},
issn = {0065-2598},
mesh = {Animals ; Cell Differentiation ; Disease Models, Animal ; Humans ; Inflammation ; Interleukin-17/immunology ; *Periodontitis/physiopathology ; *Th17 Cells/cytology/immunology ; },
abstract = {T helper 17 (Th17) cells were first described as a T helper subset involved in the pathogenesis of experimental autoimmune inflammation. Since then, these cells have been described as orchestrators of immunopathology in several human inflammatory conditions including psoriasis, rheumatoid arthritis, and inflammatory bowel disease. More recently, the crucial role of Th17 cells in the regulation of immunity and protection of barrier sites has been unveiled. In the present work, we review the available evidence regarding Th17 cells in health and disease with a focus on the oral mucosa and their role in periodontitis pathogenesis. Recent mechanistic studies in animal models have demonstrated that interleukin-17A (IL-17A) and Th17 cells are critical mediators for alveolar bone destruction during periodontal inflammation. Observations in a cohort of patients with naturally occurring impaired Th17 cell differentiation supported these findings. However, interventional studies are needed to conclusively implicate Th17 cells in the immunopathogenesis of human alveolar bone and tissue destruction that characterize periodontitis.},
}
@article {pmid31732575,
year = {2020},
author = {Custer, GF and van Diepen, LTA and Stump, WL},
title = {Structural and Functional Dynamics of Soil Microbes following Spruce Beetle Infestation.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {3},
pages = {},
pmid = {31732575},
issn = {1098-5336},
mesh = {Animals ; Bacterial Physiological Phenomena ; Fungi/physiology ; *Herbivory ; *Microbiota ; Mycobiome ; Picea/*physiology ; *Soil Microbiology ; Weevils/*physiology ; Wyoming ; },
abstract = {As the range of bark beetles expands into new forests and woodlands, the need to understand their effects on multiple trophic levels becomes increasingly important. To date, much attention has been paid to the aboveground processes affected by bark beetle infestation, with a focus on photoautotrophs and ecosystem level processes. However, indirect effects of bark beetle on belowground processes, especially the structure and function of soil microbiota remains largely a black box. Our study examined the impacts of bark beetle-induced tree mortality on soil microbial community structure and function using high-throughput sequencing of the soil bacterial and fungal communities and measurements of extracellular enzyme activities. The results suggest bark beetle infestation affected edaphic conditions through increased soil water content, pH, electrical conductivity, and carbon/nitrogen ratio and altered bulk and rhizosphere soil microbial community structure and function. Finally, increased enzymatic activity suggests heightened microbial decomposition following bark beetle infestation. With this increase in enzymatic activity, nutrients trapped in organic substrates may become accessible to seedlings and potentially alter the trajectory of forest regeneration. Our results indicate the need for incorporation of microbial processes into ecosystem level models.IMPORTANCE Belowground impacts of bark beetle infestation have not been explored as thoroughly as their aboveground counterparts. In order to accurately model impacts of bark beetle-induced tree mortality on carbon and nutrient cycling and forest regeneration, the intricacies of soil microbial communities must be examined. In this study, we investigated the structure and function of soil bacterial and fungal communities following bark beetle infestation. Our results show bark beetle infestation to impact soil conditions, as well as soil microbial community structure and function.},
}
@article {pmid31732073,
year = {2019},
author = {Lee, M and Song, JH and Park, JM and Chang, JY},
title = {Bacterial diversity in Korean temple kimchi fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {126},
number = {},
pages = {108592},
doi = {10.1016/j.foodres.2019.108592},
pmid = {31732073},
issn = {1873-7145},
mesh = {Animals ; Bacteria/*classification/genetics ; Cell Survival ; *Fermentation ; Fermented Foods/classification/*microbiology ; *Food Microbiology ; Hydrogen-Ion Concentration ; Lactobacillales ; RNA, Ribosomal, 16S ; Republic of Korea ; Salts ; Vegans ; Vegetables/microbiology ; },
abstract = {Kimchi is manufactured using salted vegetables and various seasonings, including garlic, scallion, and jeotgal (fermented seafood). However, similar to vegan diets, Korean temple food does not contain animal products (meat- and seafood-free) and is restricted to five pungent herbs: garlic, scallion, leek, onions, and chives. In this study, we investigated the fermentation characteristics of 25 kimchi samples from traditional Korean temples or commercial sources using Illumina MiSeq sequencing. The initial pH of the kimchi samples ranged from 5.05 to 5.95 and the bacterial diversity-index showed a significantly high value in temple-style kimchi. Moreover, differences in microbial community were significantly reflected in kimchi types using non-metric multidimensional scaling plots and analysis of similarity. Additionally, the distribution patterns of the core bacterial genera differed according to kimchi type, especially during early phases of fermentation. These findings offer novel insights into the microbial ecology and quality characteristics of kimchi lacking vital ingredients, which are generally reported based on the origin of the microorganisms.},
}
@article {pmid31731161,
year = {2020},
author = {Ma, W and Li, J and Gao, Y and Xing, F and Sun, S and Zhang, T and Zhu, X and Chen, C and Li, Z},
title = {Responses of soil extracellular enzyme activities and microbial community properties to interaction between nitrogen addition and increased precipitation in a semi-arid grassland ecosystem.},
journal = {The Science of the total environment},
volume = {703},
number = {},
pages = {134691},
doi = {10.1016/j.scitotenv.2019.134691},
pmid = {31731161},
issn = {1879-1026},
mesh = {China ; Ecosystem ; Grassland ; *Microbiota ; Nitrogen ; *Soil ; Soil Microbiology ; },
abstract = {Both atmospheric nitrogen (N) deposition and precipitation can strongly impact below-ground biogeochemical processes. Soil extracellular enzymes activities (EEAs) and microorganisms are considered as the key agents in ecosystem nutrient cycling. However, how the interaction between increasing N deposition and precipitation may affect soil EEAs and microbes remain poorly understood. In a 5-year field experiment in a meadow steppe in northern China, we tested the effects of N addition (N0, 0; N1, 5; N2, 10 g N m[-2] yr[-1]) and increased precipitation (W0, ambient precipitation; W1, increase of 15% ambient precipitation; W2, increase of 30% ambient precipitation) on soil EEAs, microbial and chemical properties. Results showed that their interaction significantly affected all hydrolase activities, except for β-1,4-xylosidase (βX). Furthermore, increased precipitation and N addition interactively affected bacterial gene copies (P ≤ 0.05), and increased precipitation comparatively had a stronger effects. The results on the combination of N addition and increased precipitation showed that increased precipitation alleviated the positive effects of N addition on soil EEAs. This implies that the effects of either treatment alone on grassland biogeochemical processes may be alleviated by their simultaneous occurrence. Our results suggested that soil EEAs were mainly controlled by the content of N and phosphorus (P), and the ratio of C: N and C: P. Therefore, soil element content and stoichiometry could better explain the responses of EEAs to global changes. Moreover, soil microbial communities were mainly controlled by soil P content. Overall, our study highlights that the interaction between N deposition and precipitation may play a vital role in predicting the responses of soil enzyme activities to global changes in grassland ecosystems.},
}
@article {pmid31730850,
year = {2019},
author = {Salazar, G and Paoli, L and Alberti, A and Huerta-Cepas, J and Ruscheweyh, HJ and Cuenca, M and Field, CM and Coelho, LP and Cruaud, C and Engelen, S and Gregory, AC and Labadie, K and Marec, C and Pelletier, E and Royo-Llonch, M and Roux, S and Sánchez, P and Uehara, H and Zayed, AA and Zeller, G and Carmichael, M and Dimier, C and Ferland, J and Kandels, S and Picheral, M and Pisarev, S and Poulain, J and , and Acinas, SG and Babin, M and Bork, P and Bowler, C and de Vargas, C and Guidi, L and Hingamp, P and Iudicone, D and Karp-Boss, L and Karsenti, E and Ogata, H and Pesant, S and Speich, S and Sullivan, MB and Wincker, P and Sunagawa, S},
title = {Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.},
journal = {Cell},
volume = {179},
number = {5},
pages = {1068-1083.e21},
pmid = {31730850},
issn = {1097-4172},
mesh = {*Gene Expression Regulation ; Geography ; *Metagenome ; Microbiota/genetics ; Molecular Sequence Annotation ; *Oceans and Seas ; RNA, Messenger/genetics/metabolism ; Seawater/microbiology ; Temperature ; Transcriptome/*genetics ; },
abstract = {Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.},
}
@article {pmid31730030,
year = {2020},
author = {Hofmann, K and Huptas, C and Doll, EV and Scherer, S and Wenning, M},
title = {Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {2},
pages = {935-943},
doi = {10.1099/ijsem.0.003851},
pmid = {31730030},
issn = {1466-5034},
mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; Cattle ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Female ; *Food Microbiology ; Genes, Bacterial ; Germany ; Milk/*microbiology ; Multilocus Sequence Typing ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Pseudomonas/*classification/isolation &amp; purification ; Quinones/chemistry ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {A polyphasic approach was used to investigate the taxonomic status of two bacterial strains, WS 5072[T] and WS 5092, isolated from skimmed milk concentrate and raw cow's milk. The 16S rRNA and rpoD gene sequences affiliated the strains to the same, hitherto unknown, Pseudomonas species. Further examinations of the draft genomes based on multilocus sequence analysis and average nucleotide identity confirmed the presence of a novel Pseudomonas species. It was most closely related to Pseudomonas fragi DSM 3456[T] with 86.3 % ANIm. The DNA G+C content of strain WS 5072[T] was 56.3 mol%. Cells were aerobic, Gram-negative, catalase and oxidase positive, rod-shaped and motile. Growth occurred at 4-34 °C, pH 5.5-8.0 and with salt concentrations of up to 7 %. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The dominating quinone was Q-9 with 94 %, with noticeable amounts of Q-8 (5 %) and traces of Q-7 and Q-10. Fatty acid profiles showed a composition common for Pseudomonas with the major component C16 : 0. Based on these results, the novel species Pseudomonas saxonica sp. nov. is proposed, with the type strain WS 5072[T] (=DSM 108989[T]=LMG 31234[T]) and the additional strain WS 5092 (=DSM 108990=LMG 31235).},
}
@article {pmid31728602,
year = {2020},
author = {Quero, GM and Celussi, M and Relitti, F and Kovačević, V and Del Negro, P and Luna, GM},
title = {Inorganic and Organic Carbon Uptake Processes and Their Connection to Microbial Diversity in Meso- and Bathypelagic Arctic Waters (Eastern Fram Strait).},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {823-839},
doi = {10.1007/s00248-019-01451-2},
pmid = {31728602},
issn = {1432-184X},
mesh = {Arctic Regions ; Autotrophic Processes ; Bacteria/metabolism ; Carbon/*metabolism ; *Carbon Cycle ; Heterotrophic Processes ; *Microbiota ; Oceans and Seas ; Seawater/*chemistry ; Svalbard ; },
abstract = {The deep Arctic Ocean is increasingly vulnerable to climate change effects, yet our understanding of its microbial processes is limited. We collected samples from shelf waters, mesopelagic Atlantic Waters (AW) and bathypelagic Norwegian Sea Deep Waters (NSDW) in the eastern Fram Strait, along coast-to-offshore transects off Svalbard during boreal summer. We measured community respiration, heterotrophic carbon production (HCP), and dissolved inorganic carbon utilization (DICu) together with prokaryotic abundance, diversity, and metagenomic predictions. In deep samples, HCP was significantly faster in AW than in NSDW, while we observed no differences in DICu rates. Organic carbon uptake was higher than its inorganic counterpart, suggesting a major reliance of deep microbial Arctic communities on heterotrophic metabolism. Community structure and spatial distribution followed the hydrography of water masses. Distinct from other oceans, the most abundant OTU in our deep samples was represented by the archaeal MG-II. To address the potential biogeochemical role of each water mass-specific microbial community, as well as their link with the measured rates, PICRUSt-based predicted metagenomes were built. The results showed that pathways of auto- and heterotrophic carbon utilization differed between the deep water masses, although this was not reflected in measured DICu rates. Our findings provide new insights to understand microbial processes and diversity in the dark Arctic Ocean and to progress toward a better comprehension of the biogeochemical cycles and their trends in light of climate changes.},
}
@article {pmid31728601,
year = {2020},
author = {Chen, H and Wang, L and Wang, X and Wang, X and Liu, H and Yin, Y},
title = {Distribution and Strain Diversity of Immunoregulating Segmented Filamentous Bacteria in Human Intestinal Lavage Samples.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {1021-1033},
doi = {10.1007/s00248-019-01441-4},
pmid = {31728601},
issn = {1432-184X},
mesh = {Adolescent ; Bacteria/classification/*isolation &amp; purification ; Child ; Child, Preschool ; China ; Female ; Flagellin/analysis ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology/ultrastructure ; Infant ; Male ; Microscopy, Electron, Scanning ; },
abstract = {Segmented filamentous bacteria (SFB) are well known for their functions in the immunoregulation of hosts including the promotion of Th17 cell differentiation, B cell maturation, and immune system development. However, most analyses of SFB have focused on animal models, and thus, investigation of SFB prevalence in humans and their roles in human immunoregulation and health is needed. Although little is known overall of SFB prevalence in humans, they are characteristically abundant in animals during weaning. In this study, SFB-like bacteria were detected in ileal lavage samples from human children that were aged between 1 to 17 years old by scanning electron microscopy (SEM) analysis, and their insertion into the mucosa was also observed. In addition, the expression of SFB flagellin at the human bacterial interface was observed by immunohistochemistry (IHC) and western blot. Moreover, two pairs of primers specific for SFB, but targeting different genes, were used to detect SFB in human intestinal lavage samples. These analyses indicated that SFB were present in over 50% of patient ileal samples independent of age. High-throughput gene sequencing indicated that different SFB strains were detected among samples. Between nine and 23 SFB flagellin gene operational taxonomic units were identified. In addition to evaluating the prevalence of SFB in human samples, correlations between SFB presence and chief complaints of clinical symptoms were evaluated, as well as the relationship between SFB and patient serum immunoglobulin concentrations. SFB prevalence was significantly higher in hematochezia patients (68%) than in abdominal pain (56.10%) and diarrhea (43.75%) patients. Furthermore, the concentrations of serum IgA, IgM, and IgE, were similar between SFB-positive and SFB-negative patient groups, although IgG concentrations were significantly higher in the SFB-negative group.},
}
@article {pmid31728526,
year = {2020},
author = {Corrêa, FB and Saraiva, JP and Stadler, PF and da Rocha, UN},
title = {TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.},
journal = {Nucleic acids research},
volume = {48},
number = {D1},
pages = {D626-D632},
pmid = {31728526},
issn = {1362-4962},
mesh = {Computational Biology/*methods ; Data Mining ; *Databases, Genetic ; Ecology ; Ecosystem ; Genome, Bacterial ; Geography ; Internet ; *Metadata ; *Metagenome ; Soil Microbiology ; User-Computer Interface ; },
abstract = {Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials. TerrestrialMetagenomeDB release 1.0 includes 15 022 terrestrial metagenomes from SRA and MG-RAST. Together, the downloadable data amounts to 68 Tbp. In total, 199 terrestrial terms were divided into 14 categories. These metagenomes span 83 countries, 30 biomes and 7 main source materials. The TerrestrialMetagenomeDB is publicly available at https://webapp.ufz.de/tmdb.},
}
@article {pmid31728072,
year = {2019},
author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, MR and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and , and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J},
title = {Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants.},
journal = {Nature microbiology},
volume = {4},
number = {12},
pages = {2579},
doi = {10.1038/s41564-019-0617-0},
pmid = {31728072},
issn = {2058-5276},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid31727695,
year = {2019},
author = {Aremu, BR and Prigent-Combaret, C and Babalola, OO},
title = {Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16.},
journal = {Microbiology resource announcements},
volume = {8},
number = {46},
pages = {},
pmid = {31727695},
issn = {2576-098X},
abstract = {Here, we report the draft genome sequence of the endophytic Bacillus velezensis strain ZeaDK315Endo16, isolated from DK315 maize from Lyon, France. B. velezensis ZeaDK315Endo16 exhibits a suppressive ability toward Fusarium graminearum, a widely known threat to maize production and quality.},
}
@article {pmid31727118,
year = {2019},
author = {Werner, J and Géron, A and Kerssemakers, J and Matallana-Surget, S},
title = {mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation.},
journal = {Biology direct},
volume = {14},
number = {1},
pages = {21},
pmid = {31727118},
issn = {1745-6150},
mesh = {*Databases, Protein ; Molecular Sequence Annotation/*methods ; *Proteome ; Proteomics/*methods ; },
abstract = {Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue, which is commonly encountered in metaproteomics. mPies' workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/. REVIEWER: This article was reviewed by Dr. Wilson Wen Bin Goh.},
}
@article {pmid31726596,
year = {2020},
author = {Boada, E and Santos-Clotas, E and Bertran, S and Cabrera-Codony, A and Martín, MJ and Bañeras, L and Gich, F},
title = {Potential use of Methylibium sp. as a biodegradation tool in organosilicon and volatile compounds removal for biogas upgrading.},
journal = {Chemosphere},
volume = {240},
number = {},
pages = {124908},
doi = {10.1016/j.chemosphere.2019.124908},
pmid = {31726596},
issn = {1879-1298},
mesh = {Anaerobiosis ; Biodegradation, Environmental ; Biofuels/*analysis ; Bioreactors/*microbiology ; Burkholderiales/*growth &amp; development ; Organosilicon Compounds/*analysis ; Volatile Organic Compounds/*analysis ; Water Purification/methods ; },
abstract = {Organosilicon compounds are the most undesirable compounds for the energy recovery of biogas. These compounds are still resistant to biodegradation when biotechnologies are considered for biogas purification. Herein we isolated 52 bacterial species from anaerobic batch enrichment cultures (BEC) saturated with D4 and from an anaerobic lab-scale biotrickling filter (BTF) fed with a gas flow containing D4 as unique carbon source. Among those Methylibium sp. and Pseudomonas aeruginosa showed the highest capacity to remove D4 (53.04% ± 0.03 and 24.42% ± 0.02, respectively). Contrarily, co-culture evaluation treatment for the biodegradation of siloxanes together with volatile organic compounds removed a lower concentration of D4 compared to toluene and limonene, which were completely removed. Remarkably, the siloxane D5 proved to be more biodegradable than D4. Substrates removal values achieved by Methylibium sp. suggested that this bacterial isolate could be used in biological removal technologies of siloxanes.},
}
@article {pmid31726031,
year = {2019},
author = {Rolhion, N and Chassaing, B and Nahori, MA and de Bodt, J and Moura, A and Lecuit, M and Dussurget, O and Bérard, M and Marzorati, M and Fehlner-Peach, H and Littman, DR and Gewirtz, AT and Van de Wiele, T and Cossart, P},
title = {A Listeria monocytogenes Bacteriocin Can Target the Commensal Prevotella copri and Modulate Intestinal Infection.},
journal = {Cell host &amp; microbe},
volume = {26},
number = {5},
pages = {691-701.e5},
pmid = {31726031},
issn = {1934-6069},
support = {TL1 TR001447/TR/NCATS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteriocins/*pharmacology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Germ-Free Life ; Humans ; Inflammation/prevention &amp; control ; Listeria monocytogenes/*metabolism ; Listeriosis/microbiology/*prevention &amp; control ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Prevotella/drug effects/*growth &amp; development ; },
abstract = {Understanding the role of the microbiota components in either preventing or favoring enteric infections is critical. Here, we report the discovery of a Listeria bacteriocin, Lmo2776, which limits Listeria intestinal colonization. Oral infection of conventional mice with a Δlmo2776 mutant leads to a thinner intestinal mucus layer and higher Listeria loads both in the intestinal content and deeper tissues compared to WT Listeria. This latter difference is microbiota dependent, as it is not observed in germ-free mice. Strikingly, it is phenocopied by pre-colonization of germ-free mice before Listeria infection with Prevotella copri, an abundant gut-commensal bacteria, but not with the other commensals tested. We further show that Lmo2776 targets P. copri and reduces its abundance. Together, these data unveil a role for P.copri in exacerbating intestinal infection, highlighting that pathogens such as Listeria may selectively deplete microbiota bacterial species to avoid excessive inflammation.},
}
@article {pmid31723261,
year = {2019},
author = {Schada von Borzyskowski, L and Severi, F and Krüger, K and Hermann, L and Gilardet, A and Sippel, F and Pommerenke, B and Claus, P and Cortina, NS and Glatter, T and Zauner, S and Zarzycki, J and Fuchs, BM and Bremer, E and Maier, UG and Amann, RI and Erb, TJ},
title = {Marine Proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle.},
journal = {Nature},
volume = {575},
number = {7783},
pages = {500-504},
pmid = {31723261},
issn = {1476-4687},
mesh = {Alcohol Oxidoreductases/metabolism ; Aldehyde-Lyases/metabolism ; Aquatic Organisms/enzymology/*metabolism ; Aspartic Acid/*analogs &amp; derivatives/metabolism ; Biocatalysis ; Glycolates/*metabolism ; Glyoxylates/metabolism ; Hydro-Lyases/metabolism ; Kinetics ; *Metabolic Networks and Pathways ; Oxidoreductases/metabolism ; Phytoplankton/enzymology/metabolism ; Proteobacteria/enzymology/*metabolism ; Transaminases/metabolism ; },
abstract = {One of the most abundant sources of organic carbon in the ocean is glycolate, the secretion of which by marine phytoplankton results in an estimated annual flux of one petagram of glycolate in marine environments[1]. Although it is generally accepted that glycolate is oxidized to glyoxylate by marine bacteria[2-4], the further fate of this C2 metabolite is not well understood. Here we show that ubiquitous marine Proteobacteria are able to assimilate glyoxylate via the β-hydroxyaspartate cycle (BHAC) that was originally proposed 56 years ago[5]. We elucidate the biochemistry of the BHAC and describe the structure of its key enzymes, including a previously unknown primary imine reductase. Overall, the BHAC enables the direct production of oxaloacetate from glyoxylate through only four enzymatic steps, representing-to our knowledge-the most efficient glyoxylate assimilation route described to date. Analysis of marine metagenomes shows that the BHAC is globally distributed and on average 20-fold more abundant than the glycerate pathway, the only other known pathway for net glyoxylate assimilation. In a field study of a phytoplankton bloom, we show that glycolate is present in high nanomolar concentrations and taken up by prokaryotes at rates that allow a full turnover of the glycolate pool within one week. During the bloom, genes that encode BHAC key enzymes are present in up to 1.5% of the bacterial community and actively transcribed, supporting the role of the BHAC in glycolate assimilation and suggesting a previously undescribed trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankton.},
}
@article {pmid31722990,
year = {2019},
author = {Dominguez-Mirazo, M and Jin, R and Weitz, JS},
title = {Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in "Candidatus Liberibacter asiaticus".},
journal = {mSphere},
volume = {4},
number = {6},
pages = {},
pmid = {31722990},
issn = {2379-5042},
mesh = {Citrus/microbiology ; Computational Biology ; *Genomics ; Plant Diseases/microbiology ; Prophages/*genetics ; Rhizobiaceae/genetics/*growth &amp; development/isolation &amp; purification/*virology ; Virulence ; },
abstract = {Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen "Candidatus Liberibacter asiaticus" is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of "Ca. Liberibacter asiaticus" has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available "Ca. Liberibacter asiaticus" genomes and are classified into three prophage types. Here, we reexamined all 15 "Ca. Liberibacter asiaticus" genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the "Ca. Liberibacter asiaticus" genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 "Ca. Liberibacter asiaticus" strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and "Ca. Liberibacter asiaticus" pathogenicity.IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is "Candidatus Liberibacter asiaticus." Prior work using mapping-based approaches identified prophage-like sequences in some "Ca. Liberibacter asiaticus" genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in "Ca. Liberibacter asiaticus" from 16 to 33 and identified at least one prophage-like sequence in all "Ca. Liberibacter asiaticus" strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage-expanding the number of prophage types in "Ca. Liberibacter asiaticus" from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of "Ca. Liberibacter asiaticus."},
}
@article {pmid31721471,
year = {2020},
author = {Tyc, O and Putra, R and Gols, R and Harvey, JA and Garbeva, P},
title = {The ecological role of bacterial seed endophytes associated with wild cabbage in the United Kingdom.},
journal = {MicrobiologyOpen},
volume = {9},
number = {1},
pages = {e00954},
pmid = {31721471},
issn = {2045-8827},
mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/*metabolism ; Brassica/*growth &amp; development/microbiology ; Endophytes/classification/genetics/*metabolism ; Firmicutes/classification/genetics/isolation &amp; purification ; Germination/drug effects ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seeds/*growth &amp; development/microbiology ; United Kingdom ; Volatile Organic Compounds/metabolism/*pharmacology ; },
abstract = {Endophytic bacteria are known for their ability in promoting plant growth and defense against biotic and abiotic stress. However, very little is known about the microbial endophytes living in the spermosphere. Here, we isolated bacteria from the seeds of five different populations of wild cabbage (Brassica oleracea L) that grow within 15 km of each other along the Dorset coast in the UK. The seeds of each plant population contained a unique microbiome. Sequencing of the 16S rRNA genes revealed that these bacteria belong to three different phyla (Actinobacteria, Firmicutes, and Proteobacteria). Isolated endophytic bacteria were grown in monocultures or mixtures and the effects of bacterial volatile organic compounds (VOCs) on the growth and development on B. oleracea and on resistance against a insect herbivore was evaluated. Our results reveal that the VOCs emitted by the endophytic bacteria had a profound effect on plant development but only a minor effect on resistance against an herbivore of B. oleracea. Plants exposed to bacterial VOCs showed faster seed germination and seedling development. Furthermore, seed endophytic bacteria exhibited activity via volatiles against the plant pathogen F. culmorum. Hence, our results illustrate the ecological importance of the bacterial seed microbiome for host plant health and development.},
}
@article {pmid31721347,
year = {2020},
author = {Scheepers, M and Spielmann, J and Boulanger, M and Carnol, M and Bosman, B and De Pauw, E and Goormaghtigh, E and Motte, P and Hanikenne, M},
title = {Intertwined metal homeostasis, oxidative and biotic stress responses in the Arabidopsis frd3 mutant.},
journal = {The Plant journal : for cell and molecular biology},
volume = {102},
number = {1},
pages = {34-52},
doi = {10.1111/tpj.14610},
pmid = {31721347},
issn = {1365-313X},
mesh = {Arabidopsis/genetics/metabolism/*physiology ; Arabidopsis Proteins/*genetics/physiology ; Cell Wall/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Homeostasis ; Hydrogen Peroxide/metabolism ; Iron/metabolism ; Membrane Transport Proteins/*genetics/physiology ; Metals/metabolism ; Oxidative Stress/genetics ; Plant Roots/metabolism ; Spectroscopy, Fourier Transform Infrared ; Stress, Physiological ; Zinc/metabolism ; },
abstract = {FRD3 (FERRIC REDUCTASE DEFECTIVE 3) plays a major role in iron (Fe) and zinc (Zn) homeostasis in Arabidopsis. It transports citrate, which enables metal distribution in the plant. An frd3 mutant is dwarf and chlorotic and displays a constitutive Fe-deficiency response and strongly altered metal distribution in tissues. Here, we have examined the interaction between Fe and Zn homeostasis in an frd3 mutant exposed to varying Zn supply. Detailed phenotyping using transcriptomic, ionomic, histochemical and spectroscopic approaches revealed the full complexity of the frd3 mutant phenotype, which resulted from altered transition metal homeostasis, manganese toxicity, and oxidative and biotic stress responses. The cell wall played a key role in these processes, as a site for Fe and hydrogen peroxide accumulation, and displayed modified structure in the mutant. Finally, we showed that Zn excess interfered with these mechanisms and partially restored root growth of the mutant, without reverting the Fe-deficiency response. In conclusion, the frd3 mutant molecular phenotype is more complex than previously described and illustrates how the response to metal imbalance depends on multiple signaling pathways.},
}
@article {pmid31721121,
year = {2020},
author = {Kreth, J and Abdelrahman, YM and Merritt, J},
title = {Multiplex Imaging of Polymicrobial Communities-Murine Models to Study Oral Microbiome Interactions.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2081},
number = {},
pages = {107-126},
pmid = {31721121},
issn = {1940-6029},
support = {R01 DE021726/DE/NIDCR NIH HHS/United States ; R01 DE029492/DE/NIDCR NIH HHS/United States ; R35 DE028252/DE/NIDCR NIH HHS/United States ; R56 DE021726/DE/NIDCR NIH HHS/United States ; },
mesh = {Animals ; Biofilms ; Disease Models, Animal ; Gene Expression ; Genes, Reporter ; Luminescent Measurements/methods ; Mice ; *Microbial Interactions ; *Microbiota ; Mouth/*microbiology ; Optical Imaging/*methods ; },
abstract = {Similar to other mucosal surfaces of the body, the oral cavity hosts a diverse microbial flora that live in polymicrobial biofilm communities. It is the ecology of these communities that are the primary determinants of oral health (symbiosis) or disease (dysbiosis). As such, both symbiosis and dysbiosis are inherently polymicrobial phenomena. In an effort to facilitate studies of polymicrobial communities within rodent models, we developed a suite of synthetic luciferases suitable for multiplexed in situ analyses of microbial ecology and specific gene expression. Using this approach, it is feasible to noninvasively measure multiple luciferase signals in vivo with both spatial and temporal resolution. In the following chapter, we describe the relevant details and protocols used to establish a biophotonic imaging platform for the study of experimental polymicrobial oral biofilms and abscesses in mice. The protocols described here are specifically tailored for use with oral streptococci, but the general strategies are adaptable for a wide range of polymicrobial infection studies using other species.},
}
@article {pmid31720799,
year = {2020},
author = {Thomas, P and Shaik, SP},
title = {Molecular Profiling on Surface-Disinfected Tomato Seeds Reveals High Diversity of Cultivation-Recalcitrant Endophytic Bacteria with Low Shares of Spore-Forming Firmicutes.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {910-924},
doi = {10.1007/s00248-019-01440-5},
pmid = {31720799},
issn = {1432-184X},
support = {AMAAS Project//National Bureau of Agriculturally Important Microorganisms/ ; },
mesh = {Bacteria/*isolation &amp; purification ; Disinfectants/*administration &amp; dosage ; Endophytes/*isolation &amp; purification ; Firmicutes/isolation &amp; purification ; India ; Solanum lycopersicum/*microbiology ; *Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seeds/microbiology ; },
abstract = {Seeds are known to harbor diverse microorganisms offering protective effects on them with the prospects of quick root colonization at germination, selective recruitment as endophytes, and possible vertical transmission. The study was undertaken to assess the gross seed-internal bacterial community in tomato and to confirm if spore-forming Firmicutes constituted major seed endophytes adopting cultivation versus molecular approach on surface-sterilized seeds. Testing the initial seed wash solutions of "Arka Vikas" and "Arka Abha" cultivars showed > 1000 bacterial cfu per dry seed, largely Bacillus spp. Tissue homogenates from surface-disinfected seeds did not show any cultivable bacteria on enriched media for 1-2 weeks, while 16S rRNA V3-V4 taxonomic profiling revealed a huge bacterial diversity (10-16 phyla per cultivar). Proteobacteria formed the dominant phylum (65.7-69.6% OTUs) followed by Firmicutes, Actinobacteria, Bacteroidetes, and a notable share of Euryarchaeota (1.1-3.1%). Five more phyla appeared common to both cultivars in minor shares (Acidobacteria, Planctomycetes, Chloroflexi, Spirochaetes, Verrucomicrobia) with the ten phyla together constituting 99.6-99.9% OTUs. Class level and family level, the cultivars displayed elevated bacterial diversity, but similar taxonomic profiles. Arka Vikas and Arka Abha showed 114 and 107 genera, respectively, with 63 common genera constituting 96-97% OTUs. Psychrobacter formed the dominant genus. Bacillus and related genera constituted only negligible OTU share (0.16-0.28%). KEGG functional analysis showed metabolism as the major bacterial community role. One-month-old in vitro seedlings showed the activation of some originally uncultivable bacteria uninfluenced by the OTU share. The study reveals a high diversity of cultivation-recalcitrant endophytic bacteria prevailing in tomato seeds with possible vertical transmission and significant roles in plant biology.},
}
@article {pmid31720759,
year = {2020},
author = {Liu, L and Wang, S and Chen, J},
title = {Hysteretic response of Microbial Eukaryotic Communities to Gradually Decreased Nutrient Concentrations in Eutrophic Water.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {815-822},
doi = {10.1007/s00248-019-01457-w},
pmid = {31720759},
issn = {1432-184X},
support = {FZHJ15//Oceans and Fisheries Bureau of Fuzhou, China/ ; 31500372//National Natural Science Foundation of China/ ; 31971469//National Natural Science Foundation of China/ ; XRC-17024//Special Foundation for Yong Scientists of Fuzhou University/ ; },
mesh = {Chlorophyta/metabolism/*physiology ; Ciliophora/metabolism/*physiology ; Eukaryota ; Eutrophication ; Fresh Water/*chemistry ; Fungi/metabolism/*physiology ; Microbiota ; Mycobiome/physiology ; Nitrogen/deficiency ; Nutrients/*deficiency ; Phosphorus/deficiency ; },
abstract = {External environments to microbial eukaryotic communities often change gradually with time. However, whether the responses of microbial eukaryotic communities to these gradually changed environments are continuous or hysteretic and the mechanisms underlying these responses are largely unknown. Here, we used a microcosm to investigate the temporal variation of microbial eukaryotic communities with the gradually decreased nutrient concentrations (nitrogen and phosphorus). We found the differences of microbial eukaryotic community composition and species richness between the control and treatment groups were low during the days 0 to 12, although the nutrient concentrations decreased rapidly during this period in treatment group. However, these differences were clear during the days 14 to 18, although the nutrient concentrations decreased slowly during this period in treatment group. The mechanisms for these results are that the strong homogenous selection (perhaps due to the biotic factors) during the days 8 to 10 in treatment group might enhance the stability of microbial eukaryotic communities. However, the continuously decreased nutrient concentrations weakened the homogenous selection and promoted the strength of environmental filtering, and therefore resulted in the distinct change of microbial eukaryotic communities during the days 14 to 18 in treatment group. Fungi, Chlorophyta and Chrysophyta which associated with the nutrient removal played important roles in this hysteretic change of microbial eukaryotic communities. Overall, our findings suggest that disentangling the non-linear response of communities to gradual environmental changes is essential for understanding ecosystem restoration and degradation in future.},
}
@article {pmid31719226,
year = {2019},
author = {DAS, B and Nair, GB},
title = {Homeostasis and dysbiosis of the gut microbiome in health and disease.},
journal = {Journal of biosciences},
volume = {44},
number = {5},
pages = {},
pmid = {31719226},
issn = {0973-7138},
mesh = {*Gastrointestinal Microbiome ; *Homeostasis ; Humans ; },
abstract = {The human gastrointestinal tract (GIT) harbors taxonomically and functionally complex microbial ecosystem. The composition of the microbial species in the GIT ecosystem varies among individuals and throughout development. Both environmental factors as well as host genetics influence the composition and homeostasis of GIT microbiome. Intrinsic GIT microbiome can be characterized in terms of diversity, richness, dynamics and resilience. In healthy individual, microbial communities maintain homeostatic equilibrium and are resistant against perturbations. The resilience and resistance to perturbations of the GIT microbial ecosystem are robust but not absolute. Several factors can affect the homeostatic equilibrium of GIT microbiome and lead to dysbiotic microbiome configuration. Taxonomic and/or functional dysbiosis in the GIT microbiome is associated with numerous health disorders like inflammatory bowel disease (IBD), malnutrition, metabolic disorders, asthma and neurodegenerative diseases. In this review, we discuss our current understanding of homeostasis and dysbiosis of the microbial ecology in the human gut and health disorders that are associated with the microbiome dysbiosis.},
}
@article {pmid31719222,
year = {2019},
author = {Senapati, T and Kothidar, A and Banerjee, SK and DAS, B},
title = {Insights into the gastrointestinal tract microbiomes of Indian population.},
journal = {Journal of biosciences},
volume = {44},
number = {5},
pages = {},
pmid = {31719222},
issn = {0973-7138},
mesh = {Ecosystem ; *Gastrointestinal Microbiome ; Humans ; India ; Pharmaceutical Preparations ; Species Specificity ; Vaccines ; },
abstract = {Trillions of microbes living in the gastrointestinal tract (GIT) of the human body finely tune homeostatic equilibrium in the GIT ecosystem and encode key functionalities that play crucial role in host metabolic functions, synthesis of macro- and micronutrients, xenobiotics metabolisms, development of innate and adaptive immune systems, tissue and organ developments and resistance against invasion of enteric pathogens. The microbial diversity and richness of GIT ecosystem varies greatly between individuals and over time. Extent of taxonomic and functional variations in GIT ecosystem is linked with dietary habit, pharmaceuticals usages, age, sex, body mass index, ethnicity, geography, altitude and civilization. Understanding a holistic picture of GIT microbiome of healthy people living across geography and identifying population specific 'keystone' taxa is of immense importance for identifying microbial species that may provide protection against chronic and metabolic diseases. Knowledge on geographic or ethnicity specific microbial signatures may also help us to understand the varied efficacy of different drugs and vaccines in different population. India is the home of more than 1.36 billion people belonging to 2000 human communities residing in well distinct geography. In the present review, we discuss the microbial signatures in health and diseases of the rural and urban Indians living in sea level and high altitude areas.},
}
@article {pmid31717367,
year = {2019},
author = {An, B and Sam, C and Dries, V and Ruben, S and Christel, V and Mik, VB and Bart, L and Leen, VC},
title = {Comparison of Six Commercial Meat Starter Cultures for the Fermentation of Yellow Mealworm (Tenebrio molitor) Paste.},
journal = {Microorganisms},
volume = {7},
number = {11},
pages = {},
pmid = {31717367},
issn = {2076-2607},
abstract = {In this study, six commercial meat starters, each consisting of a pure strain of a lactic acid-fermenting bacterium (including Lactococcus lactis, Lactobacillus curvatus, L. farciminis, L. plantarum, L. sakei, and Pediococcus acidilactici), were tested for their ability to ferment a paste produced from the yellow mealworm (Tenebrio molitor). During fermentation, microbial counts, pH, and the bacterial community composition were determined. In addition, UPLC-MS was applied to monitor the consumption of glucose and the production of glutamic (Glu) and aspartic (Asp) acid. All tested starters were able to ferment the mealworm paste, judged by a pH reduction from 6.68 to 4.60-4.95 within 72 h. Illumina amplicon sequencing showed that all starters were able to colonize the substrate eciently. Moreover, the introduction of the starter cultures led to the disappearance of Bacillus and Clostridium species, which were the dominant microorganisms in un-inoculated samples. Of the six cultures tested, Lactobacillus farciminis was most promising as its application resulted in the largest increase (±25 mg/100 g of paste) in the content of free glutamic and aspartic acid. These amino acids are responsible for the appreciated umami flavour in fermented food products and might stimulate the acceptance of insects and their consumption.},
}
@article {pmid31715086,
year = {2019},
author = {Saiman, L},
title = {Improving outcomes of infections in cystic fibrosis in the era of CFTR modulator therapy.},
journal = {Pediatric pulmonology},
volume = {54 Suppl 3},
number = {},
pages = {S18-S26},
doi = {10.1002/ppul.24522},
pmid = {31715086},
issn = {1099-0496},
mesh = {Anti-Bacterial Agents/*therapeutic use ; Chloride Channel Agonists/*therapeutic use ; Combined Modality Therapy ; Cystic Fibrosis/*drug therapy/microbiology ; Cystic Fibrosis Transmembrane Conductance Regulator/*therapeutic use ; Humans ; Treatment Outcome ; },
abstract = {Currently, available single and dual-combination cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies have favorably altered the life course of individuals with cystic fibrosis (CF) by decreasing morbidities and increasing survival. However, even with CFTR modulator use, questions and challenges remain to optimize the management of lung infections. This review (a) identifies these ongoing challenges and discusses the current understanding of the potential impact of CFTR modulator therapy on infections; (b) describes ongoing research to optimize detection, diagnosis, and treatment of CF microorganisms; and (c) discusses strategies to develop new anti-infective therapies. The CF Foundation has launched the Infection Research Initiative to fund research that will improve our understanding of the complex microbial ecology within the CF lung, improve detection of CF pathogens, optimize current treatment, including long-term chronic therapies, and develop new anti-infective therapies. Ongoing clinical trials to determine the optimal duration of treatment of pulmonary exacerbations and to diagnose and treat nontuberculous mycobacteria represent clinical research paradigms that could be used to answer other complex treatment questions. The anti-infective pipeline includes both existing anti-infective and non-anti-infective agents, many of which are proposed to have unique mechanisms of action in CF. Future studies plan to evaluate short- and long-term clinical effectiveness and impact on infections, of the next generation of CFTR modulator therapy, the highly effective triple-combination therapy, for individuals with CF, homozygous or heterozygous for F508del.},
}
@article {pmid31712738,
year = {2020},
author = {De Paepe, K and Verspreet, J and Courtin, CM and Van de Wiele, T},
title = {Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification.},
journal = {The ISME journal},
volume = {14},
number = {2},
pages = {584-596},
pmid = {31712738},
issn = {1751-7370},
mesh = {*Bacteria/classification/genetics/growth &amp; development/metabolism ; Biofilms ; Butyrates/metabolism ; Diet ; Dietary Fiber/metabolism ; Ecosystem ; Fatty Acids, Volatile/metabolism ; Feces/*microbiology ; Fermentation ; *Gastrointestinal Microbiome/genetics/physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The human gut can be viewed as a flow-through system with a short residence time, a high turnover rate and a spatial gradient of physiological conditions. As a consequence, the gut microbiota is exposed to highly fluctuating environmental determinants presented by the host and diet. Here, we assessed the fermentation and colonisation of insoluble wheat bran by faecal microbiota of three individuals at an unprecedented sampling intensity. Time-resolved 16S rRNA gene amplicon sequencing, revealed a dynamic microbial community, characterised by abrupt shifts in composition, delimiting states with a more constant community, giving rise to a succession of bacterial taxa alternately dominating the community over a 72 h timespan. Early stages were dominated by Enterobacteriaceae and Fusobacterium species, growing on the carbohydrate-low, protein rich medium to which wheat bran was supplemented. The onset of wheat bran fermentation, marked by a spike in short chain fatty acid production with an increasing butyrate proportion and an increased endo-1,4-β-xylanase activity, corresponded to donor-dependent proportional increases of Bacteroides ovatus/stercoris, Prevotella copri and Firmicutes species, which were strongly enriched in the bran-attached community. Literature and database searches provided novel insights into the metabolic and growth characteristics underlying the observed succession and colonisation, illustrating the potency of a time-resolved analysis to increase our understanding of gut microbiota dynamics upon dietary modulations.},
}
@article {pmid31712278,
year = {2020},
author = {Bencivenga-Barry, NA and Lim, B and Herrera, CM and Trent, MS and Goodman, AL},
title = {Genetic Manipulation of Wild Human Gut Bacteroides.},
journal = {Journal of bacteriology},
volume = {202},
number = {3},
pages = {},
pmid = {31712278},
issn = {1098-5530},
support = {R35 GM118159/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 DK114793/DK/NIDDK NIH HHS/United States ; R01 AI138576/AI/NIAID NIH HHS/United States ; R56 AI076322/AI/NIAID NIH HHS/United States ; R01 AI129940/AI/NIAID NIH HHS/United States ; R01 AI076322/AI/NIAID NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Bacteroides/drug effects/*genetics ; Bacteroides fragilis/drug effects/genetics ; Gastrointestinal Microbiome/drug effects/genetics ; Gastrointestinal Tract/microbiology ; Humans ; Microbiota/drug effects/genetics ; Polymyxin B/pharmacology ; },
abstract = {Bacteroides is one of the most prominent genera in the human gut microbiome, and study of this bacterial group provides insights into gut microbial ecology and pathogenesis. In this report, we introduce a negative selection system for rapid and efficient allelic exchange in wild Bacteroides species that does not require any alterations to the genetic background or a nutritionally defined culture medium. In this approach, dual antibacterial effectors normally delivered via type VI secretion are targeted to the bacterial periplasm under the control of tightly regulated anhydrotetracycline (aTC)-inducible promoters. Introduction of aTC selects for recombination events producing the desired genetic modification, and the dual effector design allows for broad applicability across strains that may have immunity to one counterselection effector. We demonstrate the utility of this approach across 21 human gut Bacteroides isolates representing diverse species, including strains isolated directly from human donors. We use this system to establish that antimicrobial peptide resistance in Bacteroides vulgatus is determined by the product of a gene that is not included in the genomes of previously genetically tractable members of the human gut microbiome.IMPORTANCE Human gut Bacteroides species exhibit strain-level differences in their physiology, ecology, and impact on human health and disease. However, existing approaches for genetic manipulation generally require construction of genetically modified parental strains for each microbe of interest or defined medium formulations. In this report, we introduce a robust and efficient strategy for targeted genetic manipulation of diverse wild-type Bacteroides species from the human gut. This system enables genetic investigation of members of human and animal microbiomes beyond existing model organisms.},
}
@article {pmid31710600,
year = {2019},
author = {Wilkins, LGE and Leray, M and O'Dea, A and Yuen, B and Peixoto, RS and Pereira, TJ and Bik, HM and Coil, DA and Duffy, JE and Herre, EA and Lessios, HA and Lucey, NM and Mejia, LC and Rasher, DB and Sharp, KH and Sogin, EM and Thacker, RW and Vega Thurber, R and Wcislo, WT and Wilbanks, EG and Eisen, JA},
title = {Host-associated microbiomes drive structure and function of marine ecosystems.},
journal = {PLoS biology},
volume = {17},
number = {11},
pages = {e3000533},
pmid = {31710600},
issn = {1545-7885},
mesh = {Animals ; Aquatic Organisms/*microbiology ; Bacteria/classification ; Ecosystem ; Host Microbial Interactions/physiology ; Humans ; Microbiota/*physiology ; Symbiosis/*physiology ; },
abstract = {The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth's most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host-microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.},
}
@article {pmid31710301,
year = {2019},
author = {Bai, J and Jhaney, I and Wells, J},
title = {Developing a Reproducible Microbiome Data Analysis Pipeline Using the Amazon Web Services Cloud for a Cancer Research Group: Proof-of-Concept Study.},
journal = {JMIR medical informatics},
volume = {7},
number = {4},
pages = {e14667},
pmid = {31710301},
issn = {2291-9694},
support = {K99 NR017897/NR/NINR NIH HHS/United States ; },
abstract = {BACKGROUND: Cloud computing for microbiome data sets can significantly increase working efficiencies and expedite the translation of research findings into clinical practice. The Amazon Web Services (AWS) cloud provides an invaluable option for microbiome data storage, computation, and analysis.<br><br>OBJECTIVE: The goals of this study were to develop a microbiome data analysis pipeline by using AWS cloud and to conduct a proof-of-concept test for microbiome data storage, processing, and analysis.<br><br>METHODS: A multidisciplinary team was formed to develop and test a reproducible microbiome data analysis pipeline with multiple AWS cloud services that could be used for storage, computation, and data analysis. The microbiome data analysis pipeline developed in AWS was tested by using two data sets: 19 vaginal microbiome samples and 50 gut microbiome samples.<br><br>RESULTS: Using AWS features, we developed a microbiome data analysis pipeline that included Amazon Simple Storage Service for microbiome sequence storage, Linux Elastic Compute Cloud (EC2) instances (ie, servers) for data computation and analysis, and security keys to create and manage the use of encryption for the pipeline. Bioinformatics and statistical tools (ie, Quantitative Insights Into Microbial Ecology 2 and RStudio) were installed within the Linux EC2 instances to run microbiome statistical analysis. The microbiome data analysis pipeline was performed through command-line interfaces within the Linux operating system or in the Mac operating system. Using this new pipeline, we were able to successfully process and analyze 50 gut microbiome samples within 4 hours at a very low cost (a c4.4xlarge EC2 instance costs $0.80 per hour). Gut microbiome findings regarding diversity, taxonomy, and abundance analyses were easily shared within our research team.<br><br>CONCLUSIONS: Building a microbiome data analysis pipeline with AWS cloud is feasible. This pipeline is highly reliable, computationally powerful, and cost effective. Our AWS-based microbiome analysis pipeline provides an efficient tool to conduct microbiome data analysis.},
}
@article {pmid31709856,
year = {2020},
author = {Joshipura, K and Muñoz-Torres, F and Fernández-Santiago, J and Patel, RP and Lopez-Candales, A},
title = {Over-the-counter mouthwash use, nitric oxide and hypertension risk.},
journal = {Blood pressure},
volume = {29},
number = {2},
pages = {103-112},
pmid = {31709856},
issn = {1651-1999},
support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; U54 MD007587/MD/NIMHD NIH HHS/United States ; P30 DK079626/DK/NIDDK NIH HHS/United States ; S21 MD001830/MD/NIMHD NIH HHS/United States ; R01 DE020111/DE/NIDCR NIH HHS/United States ; R01 DE028195/DE/NIDCR NIH HHS/United States ; },
mesh = {Adult ; Aged ; Bacteria/*drug effects/metabolism ; *Blood Pressure ; Female ; Humans ; Hypertension/diagnosis/*epidemiology/physiopathology ; Incidence ; Longitudinal Studies ; Male ; Middle Aged ; Mouth/*microbiology ; Mouthwashes/*adverse effects ; Nitric Oxide/*metabolism ; Puerto Rico ; Risk Assessment ; Risk Factors ; Time Factors ; },
abstract = {Purpose: Mouthwash is used by a large population. Short-term clinical trials have shown that antibacterial mouthwash deplete oral nitrate-reducing bacteria, and decrease systemic nitric oxide bioavailability. Our previous publication from the San Juan Overweight Adults Longitudinal Study (SOALS) was the first to show frequent over-the-counter mouthwash use was independently associated with increased risk of prediabetes/diabetes. This manuscript evaluates whether over-the-counter mouthwash was associated with increased risk of hypertension.Materials and methods: SOALS recruited 40-65 year old overweight/obese individuals; baseline evaluations started in 2011 and the 3-year follow-up exam was completed by 2016. From the 1028 participants (76%) who completed follow-up, we excluded people with reported physician diagnosis of hypertension or systolic or diastolic BP at or above the hypertension cut-offs (n = 481), missing smoking (n = 1), missing physical activity (n = 1) and missing alcohol intake (n = 5) at baseline; 540 participants were included. The primary exposure was mouthwash use twice daily or more. The primary outcome for this manuscript is self-reported physician-diagnosed hypertension over the follow-up. We used Poisson regression controlling for age, sex, smoking, physical activity, waist circumference, alcohol intake, systolic blood pressure, pre-diabetes/diabetes status and cardiac medication use. We additionally evaluated other mouthwash use categorizations.Results: Twelve percent (66/540) developed hypertension over follow-up. People who used mouthwash twice/day or more had higher incidence of hypertension compared to less frequent users (Incidence Rate Ratio = 1.85; 95% Confidence Interval: 1.17, 2.94), and compared to non-users (IRR = 2.17; 95% CI: 1.27, 3.71). Several additional potential confounders evaluated did not impact these associations. Associations persisted among never smokers. Additional outcomes including BP assessed at a single study visit did not show associations.Conclusion: In this study, frequent regular use of over-the-counter mouthwash was associated with increased risk of hypertension, independent of major risk factors for hypertension and several other potential confounders.},
}
@article {pmid31709616,
year = {2020},
author = {Crone, S and Vives-Flórez, M and Kvich, L and Saunders, AM and Malone, M and Nicolaisen, MH and Martínez-García, E and Rojas-Acosta, C and Catalina Gomez-Puerto, M and Calum, H and Whiteley, M and Kolter, R and Bjarnsholt, T},
title = {The environmental occurrence of Pseudomonas aeruginosa.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {128},
number = {3},
pages = {220-231},
doi = {10.1111/apm.13010},
pmid = {31709616},
issn = {1600-0463},
mesh = {Animals ; Environment ; Environmental Microbiology ; Humans ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Pseudomonas aeruginosa is generally described as ubiquitous in natural settings, such as soil and water. However, because anecdotal observations and published reports have questioned whether or not this description is true, we undertook a rigorous study using three methods to investigate the occurrence of P. aeruginosa: We investigated environmental samples, analyzed 16S rRNA data, and undertook a systematic review and meta-analysis of published data. The environmental sample screening identified P. aeruginosa as significantly associated with hydrocarbon and pesticide-contaminated environments and feces, as compared to uncontaminated environments in which its prevalence was relatively low. The 16S rRNA data analysis showed that P. aeruginosa sequences were present in all habitats but were most abundant in samples from human and animals. Similarly, the meta-analysis revealed that samples obtained from environments with intense human contact had a higher prevalence of P. aeruginosa compared to those with less human contact. Thus, we found a clear tendency of P. aeruginosa to be present in places closely linked with human activity. Although P. aeruginosa may be ubiquitous in nature, it is usually scarce in pristine environments. Thus, we suggest that P. aeruginosa should be described as a bacterium largely found in locations associated with human activity.},
}
@article {pmid31708901,
year = {2019},
author = {Navarro, MOP and Simionato, AS and Pérez, JCB and Barazetti, AR and Emiliano, J and Niekawa, ETG and Andreata, MFL and Modolon, F and Dealis, ML and Araújo, EJA and Carlos, TM and Scarpelim, OJ and da Silva, DB and Chryssafidis, AL and Bruheim, P and Andrade, G},
title = {Fluopsin C for Treating Multidrug-Resistant Infections: In vitro Activity Against Clinically Important Strains and in vivo Efficacy Against Carbapenemase-Producing Klebsiella pneumoniae.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2431},
pmid = {31708901},
issn = {1664-302X},
abstract = {The increasing emergence of multidrug-resistant (MDR) organisms in hospital infections is causing a global public health crisis. The development of drugs with effective antibiotic action against such agents is of the highest priority. In the present study, the action of Fluopsin C against MDR clinical isolates was evaluated under in vitro and in vivo conditions. Fluopsin C was produced in cell suspension culture of Pseudomonas aeruginosa LV strain, purified by liquid adsorption chromatography and identified by mass spectrometric analysis. Bioactivity, bacterial resistance development risk against clinically important pathogenic strains and toxicity in mammalian cell were initially determined by in vitro models. In vivo toxicity was evaluated in Tenebrio molitor larvae and mice. The therapeutic efficacy of intravenous Fluopsin C administration was evaluated in a murine model of Klebsiella pneumoniae (KPC) acute sepsis, using six different treatments. The in vitro results indicated MIC and MBC below 2 μg/mL and low bacterial resistance development frequency. Electron microscopy showed that Fluopsin C may have altered the exopolysaccharide matrix and caused disruption of the cell wall of MDR bacteria. Best therapeutic results were achieved in mice treated with a single dose of 2 mg/kg and in mice treated with two doses of 1 mg/kg, 8 h apart. Furthermore, acute and chronic histopathological studies demonstrated absent nephrotoxicity and moderate hepatotoxicity. The results demonstrated the efficacy of Fluopsin C against MDR organisms in in vitro and in vivo models, and hence it can be a novel therapeutic agent for the control of severe MDR infections.},
}
@article {pmid31708885,
year = {2019},
author = {Géron, A and Werner, J and Wattiez, R and Lebaron, P and Matallana-Surget, S},
title = {Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2395},
pmid = {31708885},
issn = {1664-302X},
abstract = {Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation, and provide reliable ecological interpretation are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales, and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting, and oxidative stress response, were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.},
}
@article {pmid31708883,
year = {2019},
author = {Del Campo, J and Heger, TJ and Rodríguez-Martínez, R and Worden, AZ and Richards, TA and Massana, R and Keeling, PJ},
title = {Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2373},
pmid = {31708883},
issn = {1664-302X},
abstract = {Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including the causing agents of toxoplasmosis and malaria, and emergent diseases like cryptosporidiosis or babesiosis. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys, and our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of apicomplexan sequences. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections.},
}
@article {pmid31708882,
year = {2019},
author = {Smyth, EM and Chattopadhyay, S and Babik, K and Reid, M and Chopyk, J and Malayil, L and Kulkarni, P and Hittle, LE and Clark, PI and Sapkota, AR and Mongodin, EF},
title = {The Bacterial Communities of Little Cigars and Cigarillos Are Dynamic Over Time and Varying Storage Conditions.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2371},
pmid = {31708882},
issn = {1664-302X},
support = {P50 CA180523/CA/NCI NIH HHS/United States ; },
abstract = {Despite their potential importance with regard to tobacco-related health outcomes, as well as their hypothesized role in the production of tobacco-specific N-nitrosamines, bacterial constituents of tobacco products lack characterization. Specifically, to our knowledge, there has been no comprehensive characterization of the effects of storage conditions on the bacterial communities associated with little cigars and cigarillos. To address this knowledge gap, we characterized the bacterial community composition of the tobacco and wrapper components of the following four products: Swisher Sweets Original; Swisher Sweets, Sweet Cherry; Cheyenne Cigars Full Flavor 100's; and Cheyenne Menthol Box. Each product was stored under three different conditions of temperature and relative humidity to mimic different user storage conditions: room (20°C 50% RH), refrigerator (5°C 18% RH) and pocket (25°C 30% RH). On days 0, 5, 9 and 14, subsamples were collected, the wrapper and tobacco were separated, and their total DNA was extracted separately and purified. Resulting DNA was then used in PCR assays targeting the V3 V4 region of the bacterial 16S rRNA gene, followed by sequencing using Illumina HiSeq 300bp PE. Resulting sequences were processed using the Quantitative Insights Into Microbial Ecology (QIIME) software package, followed by analyses in R using the Phyloseq and Vegan packages. A single bacterial phylum, Firmicutes, dominated in the wrapper subsamples whereas the tobacco subsamples were dominated by Proteobacteria. Cheyenne Menthol Box (CMB) samples were characterized by significant differential abundances for 23 bacterial operational taxonomic units (OTUs) in tobacco subsamples and 27 OTUs in the wrapper subsamples between day 0 and day 14 under all conditions. OTUs from the genera Acinetobacter and Bacillus significantly increased in the CMB tobacco subsamples, and OTUs from Bacillus, Streptococcus, Lactobacillus, and Enterococcus significantly increased in the CMB wrapper subsamples over time. These initial results suggest that the bacterial communities of little cigars and cigarillos are dynamic over time and varying storage conditions.},
}
@article {pmid31707464,
year = {2020},
author = {Polonca, S},
title = {Environment Shapes the Intra-species Diversity of Bacillus subtilis Isolates.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {853-864},
doi = {10.1007/s00248-019-01455-y},
pmid = {31707464},
issn = {1432-184X},
support = {US/18-19-091//Javna Agencija za Raziskovalno Dejavnost RS/ ; J4-8228//Javna Agencija za Raziskovalno Dejavnost RS/ ; P4-0116//Javna Agencija za Raziskovalno Dejavnost RS/ ; J4-9302//Javna Agencija za Raziskovalno Dejavnost RS/ ; },
mesh = {Bacillus subtilis/genetics/*physiology ; *Biofilms ; California ; *Ecosystem ; Environment ; *Genetic Variation ; Slovenia ; Soil Microbiology ; Spatial Analysis ; },
abstract = {Cosmopolitan bacteria are those that are found practically everywhere in the world. One of them is Bacillus subtilis, which can travel around the world through dust storms rising from various deserts. Upon landing, bacterial survival is determined by the ability to adjust to the heterogonous environments and bacteria isolated from extremely different environments, such as desert and riverbank soil, are expected to be less related due to the environmental pressure of each region. However, little is known about the influence of soil and habitat on B. subtilis evolution. Here, we show that desert and riverbank B. subtilis strains differ in genetic relatedness and physiological traits, such as biofilm morphology and utilisation of carbon sources. Desert strains showed more diversity at the genetic level and were able to utilise more carbon sources than riverbank strains which were highly genetically conserved. Biofilm morphologies of desert and riverbank strains generally segregated and both groups formed different morphology clusters despite the astonishing diversity observed among riverbank strains. We also show that relatedness of B. subtilis strains does not decrease with distance inside the same habitat, which, together with diversity data implies that the difference in environmental selection pressures plays a fundamental role in the evolution of this species.},
}
@article {pmid31705383,
year = {2020},
author = {Queiroz, LL and Costa, MS and de Abreu Pereira, A and de Paula Avila, M and Costa, PS and Nascimento, AMA and Lacorte, GA},
title = {Dynamics of microbial contaminants is driven by selection during ethanol production.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {51},
number = {1},
pages = {303-312},
pmid = {31705383},
issn = {1678-4405},
support = {156/2013//Instituto Federal de Minas Gerais/ ; },
mesh = {Bacteria/genetics/isolation &amp; purification ; Brazil ; *Ethanol ; *Fermentation ; Industrial Microbiology ; *Lactobacillus/genetics/isolation &amp; purification ; Microbial Interactions ; Microbiota ; RNA, Ribosomal, 16S/genetics ; *Saccharum/metabolism/microbiology ; Yeasts/isolation &amp; purification ; },
abstract = {Brazil is the second largest ethanol producer in the world and largest using sugarcane feedstock. Bacteria contamination is one of the most important issues faced by ethanol producers that seek to increase production efficiency. Each step of production is a selection event due to the environmental and biological changes that occur. Therefore, we evaluated the influence of the selection arising from the ethanol production process on diversity and composition of bacteria. Our objectives were to test two hypotheses, (1) that species richness will decrease during the production process and (2) that lactic acid bacteria will become dominant with the advance of ethanol production. Bacterial community assemblage was accessed using 16S rRNA gene sequencing from 19 sequential samples. Temperature is of great importance in shaping microbial communities. Species richness increased between the decanter and must steps of the process. Low Simpson index values were recorded at the fermentation step, indicating a high dominance of Lactobacillus. Interactions between Lactobacillus and yeast may be impairing the efficiency of industrial ethanol production.},
}
@article {pmid31705158,
year = {2020},
author = {Jeong, SY and Choi, JY and Kim, TG},
title = {Coordinated Metacommunity Assembly and Spatial Distribution of Multiple Microbial Kingdoms within a Lake.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {801-814},
doi = {10.1007/s00248-019-01453-0},
pmid = {31705158},
issn = {1432-184X},
support = {2018R1D1A1B07048872//National research foundation of Korea/ ; },
mesh = {Animals ; Bacteria/isolation &amp; purification ; Fungi/isolation &amp; purification ; Lakes/*microbiology/parasitology ; *Microbiota ; Republic of Korea ; Spatial Analysis ; },
abstract = {Freshwater planktonic communities comprise a tremendous diversity of microorganisms. This study investigated the distribution patterns of microbial kingdoms (bacteria, fungi, protists, and microbial metazoans) within a lake ecosystem. Water samples were collected from 50 sites along the shoreline in a lake during an early eutrophication period, and MiSeq sequencing was performed with different marker genes. Metacommunity analyses revealed a bimodal occupancy-frequency distribution and a Clementsian gradient persisting throughout all microbial kingdoms, suggesting similar regional processes in all kingdoms. Variation partitioning revealed that environmental characteristics, macrophyte/macroinvertebrate composition, space coordinates, and distance-based Moran's eigenvector maps (dbMEM) together could explain up to 29% of the community variances in microbial kingdoms. Kingdom synchrony results showed strong couplings between kingdoms (R[2] ≥ 0.31), except between Fungi and Metazoa (R[2] = 0.09). Another variation partitioning revealed that microbial kingdoms could well explain their community variances up to 73%. Interestingly, the kingdom Protista was best synchronized with the other kingdoms. A correlation network showed that positive associations between kingdoms outnumbered the negative ones and that the kingdom Protista acted as a hub among kingdoms. Module analysis showed that network modules included multi-kingdom associations that were prevalent. Our findings suggest that protists coordinate community assembly and distribution of other kingdoms, and inter-kingdom interactions are a key determinant in shaping their community structures in a freshwater lake.},
}
@article {pmid31704994,
year = {2019},
author = {Fu, S and Hao, J and Yang, Q and Lan, R and Wang, Y and Ye, S and Liu, Y and Li, R},
title = {Long-distance transmission of pathogenic Vibrio species by migratory waterbirds: a potential threat to the public health.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16303},
pmid = {31704994},
issn = {2045-2322},
mesh = {*Animal Migration ; Animals ; Birds/*microbiology ; Fisheries ; Food Contamination ; Genome, Bacterial ; Genomics/methods ; Geography ; Phylogeny ; Phylogeography ; Public Health Surveillance ; Rivers ; *Vibrio/classification/genetics/pathogenicity ; Vibrio Infections/epidemiology/*microbiology/*transmission ; },
abstract = {A potential mechanism for the global distribution of waterborne pathogens is through carriage by the migratory waterbirds. However, this mode of transmission has yet been confirmed epidemiologically. Here, we conducted whole genome sequencing of Vibrio spp. collected from waterbirds, sediments, and mollusks in the estuary of the Liaohe River in China to investigate this transmission mode. We found that a V. parahaemolyticus strain isolated from a waterbird was clonally related to the other V. parahaemolyticus strains obtained from the sediments and mollusks, and three V. mimicus strains isolated from bird feces were genomically related to those found in the mollusks and upstream groundwater, suggesting that the bird-carried Vibrio strains were acquired through the direct predation of the local mollusks. Surprisingly, two bird-carried V. parahaemolyticus strains belonging to the same clone were identified in Panjin and Shanghai, which are over 1,150 km apart, and another two were found at two locations 50 km apart, further supporting that waterbirds are capable of carrying and disseminating these pathogens over long distances. Our results provide the first evidence of direct transmission from mollusks to waterbirds and confirm that waterbirds act as disseminating vehicles of waterborne pathogens. Effective surveillance of migratory waterbirds along their routes will be valuable for predicting future epidemics of infectious diseases.},
}
@article {pmid31704678,
year = {2020},
author = {Schloss, PD},
title = {Reintroducing mothur: 10 Years Later.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {2},
pages = {},
pmid = {31704678},
issn = {1098-5336},
mesh = {*Environmental Microbiology ; Sequence Analysis/*methods ; Software ; },
abstract = {More than 10 years ago, we published the paper describing the mothur software package in Applied and Environmental Microbiology Our goal was to create a comprehensive package that allowed users to analyze amplicon sequence data using the most robust methods available. mothur has helped lead the community through the ongoing sequencing revolution and continues to provide this service to the microbial ecology community. Beyond its success and impact on the field, mothur's development exposed a series of observations that are generally translatable across science. Perhaps the observation that stands out the most is that all science is done in the context of prevailing ideas and available technologies. Although it is easy to criticize choices that were made 10 years ago through a modern lens, if we were to wait for all of the possible limitations to be solved before proceeding, science would stall. Even preceding the development of mothur, it was necessary to address the most important problems and work backwards to other problems that limited access to robust sequence analysis tools. At the same time, we strive to expand mothur's capabilities in a data-driven manner to incorporate new ideas and accommodate changes in data and desires of the research community. It has been edifying to see the benefit that a simple set of tools can bring to so many other researchers.},
}
@article {pmid31704461,
year = {2020},
author = {Coggins, LX and Larma, I and Hinchliffe, A and Props, R and Ghadouani, A},
title = {Flow cytometry for rapid characterisation of microbial community dynamics in waste stabilisation ponds.},
journal = {Water research},
volume = {169},
number = {},
pages = {115243},
doi = {10.1016/j.watres.2019.115243},
pmid = {31704461},
issn = {1879-2448},
mesh = {Flow Cytometry ; *Microbiota ; *Ponds ; Waste Disposal, Fluid ; Wastewater ; },
abstract = {Algal and bacterial communities play a major role in the treatment performance and efficiency of waste stabilisation ponds (WSPs); however, the study of these WSP microbial communities has been challenging. Flow cytometry (FCM) has been used widely as a rapid, culture-independent method of characterising algae and/or bacteria in a range of freshwater and marine environments, and in conventional wastewater treatment processes, but its application to WSP wastewater has been underexplored. In this study, a method for the characterisation of both algal and bacterial microbial populations in WSP wastewater is presented and standardised, using cultures and field samples. We show that SYTO 16 dye is more effective than SYBR Green I for the concurrent detection of both algae and bacteria in samples. Through gating and phenotypic diversity analysis, the FCM results show both spatial and temporal shifts in pond microbial communities. The ability to rapidly determine the spatiotemporal shifts in pond populations is not only important for the improvement of pond operation and monitoring strategies, but also for the planning and management. Flow cytometry has the potential to become a diagnostic tool for ponds to assess treatment performance and determine the most optimal operating conditions.},
}
@article {pmid31703886,
year = {2020},
author = {Aldrete-Tapia, JA and Escalante-Minakata, P and Martínez-Peniche, RA and Tamplin, ML and Hernández-Iturriaga, M},
title = {Yeast and bacterial diversity, dynamics and fermentative kinetics during small-scale tequila spontaneous fermentation.},
journal = {Food microbiology},
volume = {86},
number = {},
pages = {103339},
doi = {10.1016/j.fm.2019.103339},
pmid = {31703886},
issn = {1095-9998},
mesh = {Agave/chemistry/microbiology ; Alcoholic Beverages/analysis/*microbiology ; Bacteria/chemistry/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Ethanol/metabolism ; Fermentation ; Kinetics ; Limosilactobacillus fermentum/chemistry/metabolism ; Saccharomyces cerevisiae/chemistry/metabolism ; Yeasts/chemistry/genetics/*isolation &amp; purification/metabolism ; },
abstract = {The study of microbial communities associated with spontaneous fermentation of agave juice for tequila production is required to develop starter cultures that improve both yield and quality of the final product. Quantification by HPLC of primary metabolites produced during the fermentations was determined. A polyphasic approach using plate count, isolation and identification of microorganisms, denaturing gradient gel electrophoresis and next generation sequencing was carried out to describe the diversity and dynamics of yeasts and bacteria during small-scale spontaneous fermentations of agave juice from two-year samplings. High heterogeneity in microbial populations and fermentation parameters were observed, with bacteria showing higher diversity than yeast. The core microorganisms identified were Saccharomyces cerevisiae and Lactobacillus fermentum. Practices in tequila production changed during the two-year period, which affected microbial community structure and the time to end fermentation. Bacterial growth and concomitant lactic acid production were associated with low ethanol production, thus bacteria could be defined as contaminants in tequila fermentation and efforts to control them should be implemented.},
}
@article {pmid31702484,
year = {2019},
author = {Basilua, JM and Sawoo, O and Mangin, I and Dossou-Yovo, F and Boussard, A and Chevillard, L and Lutete, GT and Eto, B and Peytavin, G and Pochart, P},
title = {Higher Atazanavir Plasma Exposure in Rats is Associated with Gut Microbiota Changes Induced by Cotrimoxazole.},
journal = {Current drug metabolism},
volume = {20},
number = {11},
pages = {898-906},
doi = {10.2174/1389200220666191023105609},
pmid = {31702484},
issn = {1875-5453},
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Atazanavir Sulfate/blood/*pharmacokinetics ; *Gastrointestinal Microbiome ; HIV Protease Inhibitors/blood/*pharmacokinetics ; Humans ; Intestines/*microbiology ; Male ; Rats ; Rats, Wistar ; Trimethoprim, Sulfamethoxazole Drug Combination/*pharmacology ; },
abstract = {BACKGROUND: Cotrimoxazole (TMP-SMX) is concomitantly used as a primary prophylaxis of opportunistic infections with antiretroviral agents, such as Atazanavir (ATV). Results from an ex vivo study showed changes in intestinal absorption of ATV when rats were pretreated with TMP-SMX. The objective of this in vivo study is to determine the effect of TMP-SMX on the pharmacokinetics of ATV in rats. We also studied changes in gut microbiota induced by TMP-SMX.<br><br>METHODS: We used the non-compartment analysis to compare the pharmacokinetics of ATV in a parallel group of rats treated with a low or therapeutic dose of TMP-SMX for nine days to untreated control rats. Gut microbiota was characterized using qPCR and High Throughput Sequencing of 16S rDNA.<br><br>RESULTS: Rats treated with TMP-SMX showed a much broader exposure to ATV compared to the control group (AUC0-8h (ng.mL-1.h), 25975.9&#xb1;4048.7 versus 2587.6&#xb1;546.9, p=0.001). The main observation regarding the gut microbiota was a lower proportion of enterobacteria related to the administration of TMP-SMX. Moreover, the Total Gastrointestinal Transit Time (TGTT) was longer in the TMP-SMX treated group.<br><br>CONCLUSION: Concomitant administration of TMP-SMX and ATV significantly increased ATV exposure in rats. This increase could be the result of a prolonged TGTT leading to an increase in the intestinal residence time of ATV favoring its absorption. Gut microbiota changes induced by TMP-SMX could be at the origin of this prolonged TGTT. If demonstrated in humans, this potential interaction could be accompanied by an increase in the adverse effects of ATV.},
}
@article {pmid31701171,
year = {2020},
author = {Ni, J and Hatori, S and Wang, Y and Li, YY and Kubota, K},
title = {Uncovering Viable Microbiome in Anaerobic Sludge Digesters by Propidium Monoazide (PMA)-PCR.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {925-932},
doi = {10.1007/s00248-019-01449-w},
pmid = {31701171},
issn = {1432-184X},
support = {NA//Strategic International Collaborative Research Program/ ; NA//Ministry of Land, Infrastructure, Transport and Tourism/ ; KAKENHI Grant Number JP18H01564//Japan Society for the Promotion of Science/ ; },
mesh = {Anaerobiosis ; Azides/*chemistry ; Fluorescent Dyes/*chemistry ; Japan ; *Microbial Viability ; *Microbiota ; Polymerase Chain Reaction/*veterinary ; Propidium/*analogs &amp; derivatives/chemistry ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; Sewage/*microbiology ; Staining and Labeling/*methods ; },
abstract = {Use of anaerobic sludge digester is a common practice around the world for solids digestion and methane generation from municipal sewage sludge. Understanding microbial community structure is vital to get better insight into the anaerobic digestion process and to gain better process control. However, selective analysis of viable microorganisms is limited by DNA-based assays. In this study, propidium monoazide (PMA)-PCR with 16S rRNA gene sequencing analysis was used to distinguish live and dead microorganisms based on cell membrane integrity. Microbial community structures of PMA-treated and PMA-untreated anaerobic digester sludge samples were compared. Quantitative PCR revealed that 5-30% of the rRNA genes were derived from inactive or dead cells in anaerobic sludge digesters. This caused a significant decrease in the numbers of operational taxonomic units and Chao1 and Shannon indices compared with that of the PMA-untreated sludge. Microbial community analysis showed that majority of the viable microbiome consisted of Euryarchaeota, Bacteroidetes, Deltaproteobacteria, Chloroflexi, Firmicutes, WWE1, Spirochaetes, Synergistetes, and Caldiserica. On the other hand, after the PMA treatment, numbers of Alphaproteobacteria and Betaproteobacteria declined. These were considered residual microbial members. The network analysis also revealed a relationship among the OTUs belonging to WWE1 and Bacteroidales. PMA-PCR-based 16S rRNA gene sequencing analysis is an effective tool for uncovering viable microbiome in complex environmental samples.},
}
@article {pmid31701033,
year = {2019},
author = {Testa, S and Berger, S and Piccardi, P and Oechslin, F and Resch, G and Mitri, S},
title = {Spatial structure affects phage efficacy in infecting dual-strain biofilms of Pseudomonas aeruginosa.},
journal = {Communications biology},
volume = {2},
number = {},
pages = {405},
pmid = {31701033},
issn = {2399-3642},
mesh = {Biofilms/*growth &amp; development ; Host Microbial Interactions/physiology ; Microscopy, Electron, Transmission ; Models, Biological ; Pseudomonas Phages/*pathogenicity/ultrastructure ; Pseudomonas aeruginosa/classification/physiology/*virology ; Species Specificity ; },
abstract = {Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a sensitive Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar. We found that both in liquid and in colonies, inter-strain competition reduced resistance evolution in the susceptible strain and decreased phage population size. However, while all sensitive bacteria died in liquid, bacteria in colonies could remain sensitive yet escape phage infection, due mainly to reduced growth in colony centers. In sum, spatial structure can protect bacteria against phage infection, while the presence of competing strains reduces the evolution of resistance to phage.},
}
@article {pmid31700900,
year = {2019},
author = {Han, MM and Zhu, XY and Peng, YF and Lin, H and Liu, DC and Li, L},
title = {The alterations of gut microbiota in mice with chronic pancreatitis.},
journal = {Annals of translational medicine},
volume = {7},
number = {18},
pages = {464},
pmid = {31700900},
issn = {2305-5839},
abstract = {BACKGROUND: The changes of intestinal microbiome are associated with inflammatory, metabolic, and malignant disorders, and there are no studies assessing the intestinal microbiota of mice with chronic pancreatitis (CP). Thus, we aim to investigate the variations in diversity, composition and function of intestinal microbiota in CP mice.<br><br>METHODS: Sixteen male C57BL/6 mice were randomly selected, and divided into two groups, treated intraperitoneally with saline (normal control group, CT group) or ethanol + cerulein (experimental group, CP group) for 6 weeks. Body weight as measured in entire processes. Histopathological examination of CP index was conducted to verify the CP induction. Extracted DNA from colon samples was used for Illumina HiSeq sequencing of the bacterial V4 region of 16S rRNA gene and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Functional profiling of microbial communities was predicted with BugBase.<br><br>RESULTS: Significant alterations of the gut microbiota were found in the CP mice compared to CT groups, as revealed by significant decrease in bacterial richness and diversity, declined the relative abundance of Lachnospiraceae_NK4A136, Ruminiclostridium and Roseburia, and increased the relative abundances of Bacteroides and Alloprevotella genera. Analysis of microbial community-level phenotypes revealed significant differences in nine phenotypes (aerobic, anaerobic, containing mobile elements, facultatively anaerobic, biofilm forming, gram-negative, gram-positive, potentially pathogenic, and stress tolerant) between CP group and CT group.<br><br>CONCLUSIONS: This study indicated that mice with CP had a distinct microbiota profile.},
}
@article {pmid31700196,
year = {2019},
author = {Zheng, Q and Hu, Y and Zhang, S and Noll, L and Böckle, T and Dietrich, M and Herbold, CW and Eichorst, SA and Woebken, D and Richter, A and Wanek, W},
title = {Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity.},
journal = {Soil biology &amp; biochemistry},
volume = {136},
number = {},
pages = {107521},
pmid = {31700196},
issn = {0038-0717},
support = {636928/ERC_/European Research Council/International ; P 28037/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.},
}
@article {pmid31700119,
year = {2020},
author = {Avalos, M and Garbeva, P and Raaijmakers, JM and van Wezel, GP},
title = {Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species.},
journal = {The ISME journal},
volume = {14},
number = {2},
pages = {569-583},
pmid = {31700119},
issn = {1751-7370},
mesh = {Ammonia/*metabolism ; Anti-Bacterial Agents/metabolism/*pharmacology ; Antibiosis ; Drug Resistance, Microbial/physiology ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Gram-Negative Bacteria/drug effects ; Gram-Positive Bacteria/drug effects ; Microbial Interactions ; Soil Microbiology ; Streptomyces/*metabolism ; },
abstract = {Soil-inhabiting streptomycetes are nature's medicine makers, producing over half of all known antibiotics and many other bioactive natural products. However, these bacteria also produce many volatiles, molecules that disperse through the soil matrix and may impact other (micro)organisms from a distance. Here, we show that soil- and surface-grown streptomycetes have the ability to kill bacteria over long distances via air-borne antibiosis. Our research shows that streptomycetes do so by producing surprisingly high amounts of the low-cost volatile ammonia, dispersing over long distances to inhibit the growth of Gram-positive and Gram-negative bacteria. Glycine is required as precursor to produce ammonia, and inactivation of the glycine cleavage system nullified ammonia biosynthesis and concomitantly air-borne antibiosis. Reduced expression of the porin master regulator OmpR and its cognate kinase EnvZ is used as a resistance strategy by E. coli cells to survive ammonia-mediated antibiosis. Finally, ammonia was shown to enhance the activity of canonical antibiotics, suggesting that streptomycetes adopt a low-cost strategy to sensitize competitors for antibiosis from a distance.},
}
@article {pmid31699144,
year = {2019},
author = {Park, R and Dzialo, MC and Spaepen, S and Nsabimana, D and Gielens, K and Devriese, H and Crauwels, S and Tito, RY and Raes, J and Lievens, B and Verstrepen, KJ},
title = {Microbial communities of the house fly Musca domestica vary with geographical location and habitat.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {147},
pmid = {31699144},
issn = {2049-2618},
mesh = {Animals ; Bacteria/*classification/genetics ; Belgium ; Houseflies/*microbiology ; *Microbiota ; *Phylogeography ; Rwanda ; },
abstract = {House flies (Musca domestica) are widespread, synanthropic filth flies commonly found on decaying matter, garbage, and feces as well as human food. They have been shown to vector microbes, including clinically relevant pathogens. Previous studies have demonstrated that house flies carry a complex and variable prokaryotic microbiota, but the main drivers underlying this variability and the influence of habitat on the microbiota remain understudied. Moreover, the differences between the external and internal microbiota and the eukaryotic components have not been examined. To obtain a comprehensive view of the fly microbiota and its environmental drivers, we sampled over 400 flies from two geographically distinct countries (Belgium and Rwanda) and three different environments-farms, homes, and hospitals. Both the internal as well as external microbiota of the house flies were studied, using amplicon sequencing targeting both bacteria and fungi. Results show that the house fly's internal bacterial community is very diverse yet relatively consistent across geographic location and habitat, dominated by genera Staphylococcus and Weissella. The external bacterial community, however, varies with geographic location and habitat. The fly fungal microbiota carries a distinct signature correlating with the country of sampling, with order Capnodiales and genus Wallemia dominating Belgian flies and genus Cladosporium dominating Rwandan fly samples. Together, our results reveal an intricate country-specific pattern for fungal communities, a relatively stable internal bacterial microbiota and a variable external bacterial microbiota that depends on geographical location and habitat. These findings suggest that vectoring of a wide spectrum of environmental microbes occurs principally through the external fly body surface, while the internal microbiome is likely more limited by fly physiology.},
}
@article {pmid31699041,
year = {2019},
author = {Yuen, B and Polzin, J and Petersen, JM},
title = {Organ transcriptomes of the lucinid clam Loripes orbiculatus (Poli, 1791) provide insights into their specialised roles in the biology of a chemosymbiotic bivalve.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {820},
pmid = {31699041},
issn = {1471-2164},
support = {VRG14-021//Vienna Science and Technology Fund/ ; },
mesh = {Animals ; Apoptosis/genetics ; Bacterial Physiological Phenomena ; Bivalvia/cytology/*genetics/immunology/microbiology ; Environment ; Foot/physiology ; *Gene Expression Profiling ; Immunity, Innate/genetics ; Nutrients/metabolism ; *Symbiosis ; },
abstract = {BACKGROUND: The lucinid clam Loripes orbiculatus lives in a nutritional symbiosis with sulphur-oxidizing bacteria housed in its gills. Although our understanding of the lucinid endosymbiont physiology and metabolism has made significant progress, relatively little is known about how the host regulates the symbiosis at the genetic and molecular levels. We generated transcriptomes from four L. orbiculatus organs (gills, foot, visceral mass, and mantle) for differential expression analyses, to better understand this clam's physiological adaptations to a chemosymbiotic lifestyle, and how it regulates nutritional and immune interactions with its symbionts.<br><br>RESULTS: The transcriptome profile of the symbiont-housing gill suggests the regulation of apoptosis and innate immunity are important processes in this organ. We also identified many transcripts encoding ion transporters from the solute carrier family that possibly allow metabolite exchange between host and symbiont. Despite the clam holobiont's clear reliance on chemosynthesis, the clam's visceral mass, which contains the digestive tract, is characterised by enzymes involved in digestion, carbohydrate recognition and metabolism, suggesting that L. orbiculatus has a mixotrophic diet. The foot transcriptome is dominated by the biosynthesis of glycoproteins for the construction of mucus tubes, and receptors that mediate the detection of chemical cues in the environment.<br><br>CONCLUSIONS: The transcriptome profiles of gills, mantle, foot and visceral mass provide insights into the molecular basis underlying the functional specialisation of bivalve organs adapted to a chemosymbiotic lifestyle.},
}
@article {pmid31698527,
year = {2020},
author = {Roesch, LFW and Dobbler, PT and Pylro, VS and Kolaczkowski, B and Drew, JC and Triplett, EW},
title = {pime: A package for discovery of novel differences among microbial communities.},
journal = {Molecular ecology resources},
volume = {20},
number = {2},
pages = {415-428},
doi = {10.1111/1755-0998.13116},
pmid = {31698527},
issn = {1755-0998},
support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 5R21AI120195-02/GF/NIH HHS/United States ; 1-INO-2018-637-A-N//JDRF/United States ; },
mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Computational Biology/*methods ; DNA, Bacterial/genetics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The data used for profiling microbial communities is usually sparse with some microbes having high abundance in a few samples and being nearly absent in others. However, current bioinformatics tools able to deal with this sparsity are lacking. pime (Prevalence Interval for Microbiome Evaluation) was designed to remove those taxa that may be high in relative abundance in just a few samples but have a low prevalence overall. The reliability and robustness of pime were compared against existing methods and tested using 16S rRNA independent data sets. pime filters microbial taxa not shared in a per treatment prevalence interval started at 5% prevalence with increasing increments of 5% at each filtering step. For each prevalence interval, hundreds of decision trees were calculated to predict the likelihood of detecting differences in treatments. The best prevalence-filtered data set was user-selected by choosing the prevalence interval that kept a large portion of the 16S rRNA sequences in the data set while also showing the lowest error rate. To obtain the likelihood of introducing type I error while building prevalence-filtered data sets, an error detection step based was also included. A pime reanalysis of published data sets uncovered other expected microbial associations than previously reported, which may be masked when only relative abundance was considered.},
}
@article {pmid31693956,
year = {2020},
author = {Burges, A and Fievet, V and Oustriere, N and Epelde, L and Garbisu, C and Becerril, JM and Mench, M},
title = {Long-term phytomanagement with compost and a sunflower - Tobacco rotation influences the structural microbial diversity of a Cu-contaminated soil.},
journal = {The Science of the total environment},
volume = {700},
number = {},
pages = {134529},
doi = {10.1016/j.scitotenv.2019.134529},
pmid = {31693956},
issn = {1879-1026},
mesh = {*Biodegradation, Environmental ; Composting ; Copper/analysis/*metabolism ; Helianthus/*physiology ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; Nicotiana/*physiology ; },
abstract = {At a former wood preservation site contaminated with Cu, various phytomanagement options have been assessed in the last decade through physicochemical, ecotoxicological and biological assays. In a field trial at this site, phytomanagement with a crop rotation based on tobacco and sunflower, combined with the incorporation of compost and dolomitic limestone, has proved to be efficient in Cu-associated risk mitigation, ecological soil functions recovery and net gain of economic and social benefits. To demonstrate the long-term effectiveness and sustainability of phytomanagement, we assessed here the influence of this remediation option on the diversity, composition and structure of microbial communities over time, through a metabarcoding approach. After 9 years of phytomanagement, no overall effect was identified on microbial diversity; the soil amendments, notably the repeated compost application, led to shifts in soil microbial populations. This phytomanagement option induced changes in the composition of soil microbial communities, promoting the growth of microbial groups belonging to Alphaproteobacteria, many being involved in N cycling. Populations of Nitrososphaeria, which are crucial in nitrification, as well as taxa from phyla Planctomycetacia, Chloroflexi and Gemmatimonadetes, which are tolerant to metal contamination and adapted to oligotrophic soil conditions, decreased in amended phytomanaged plots. Our study provides an insight into population dynamics within soil microbial communities under long-term phytomanagement, in line with the assessment of soil ecological functions and their recovery.},
}
@article {pmid31692676,
year = {2019},
author = {Vera-Gutiérrez, T and García-Muñoz, MC and Otálvaro-Alvarez, AM and Mendieta-Menjura, O},
title = {Effect of processing technology and sugarcane varieties on the quality properties of unrefined non-centrifugal sugar.},
journal = {Heliyon},
volume = {5},
number = {10},
pages = {e02667},
pmid = {31692676},
issn = {2405-8440},
abstract = {In this research, the unrefined non-centrifugal sugar (UNCS) quality obtained from two sugarcane varieties (RD 7511 and CC 8475) and using two types of technologies (traditional and Ward-Cimpa production facilities) were evaluated. The parameters monitored through the process were impurities, total soluble solids, acidity, pH, and temperature profile. Microbiological analyses were carried out on beating, molding, packing, and storage operations; and finally, an organoleptic analysis was carried out on the final UNCS product. Results showed that the UNCS obtained from variety CC 8475 had higher consumer acceptance; meanwhile, the technologies assessed did not show significant differences in final product quality. However, these technologies showed significant differences in the highest temperature, syrup, and juice properties. Microbiological analyses highlighted beating and molding as the critical points in UNCS production safety. Finally, it was evident that the implementation of new technologies or the improvement of the furnace, as in the Ward-Cimpa production facility, is not enough to achieve food safety requirements, as many other conditions affect the microbiological quality of the product. Although the temperatures reached on the Ward-Cimpa furnace are higher than those reached with the traditional furnace and thus, enough to kill all the harmful microorganisms, contamination in downstream operations still occurs.},
}
@article {pmid31690886,
year = {2020},
author = {Pernice, M and Raina, JB and Rädecker, N and Cárdenas, A and Pogoreutz, C and Voolstra, CR},
title = {Down to the bone: the role of overlooked endolithic microbiomes in reef coral health.},
journal = {The ISME journal},
volume = {14},
number = {2},
pages = {325-334},
pmid = {31690886},
issn = {1751-7370},
mesh = {Animals ; Anthozoa/metabolism/*microbiology ; Archaea/metabolism ; Bacteria/metabolism ; *Coral Reefs ; Fungi/metabolism ; Microalgae ; *Microbiota ; Symbiosis ; },
abstract = {Reef-building corals harbour an astonishing diversity of microorganisms, including endosymbiotic microalgae, bacteria, archaea, and fungi. The metabolic interactions within this symbiotic consortium are fundamental to the ecological success of corals and the unique productivity of coral reef ecosystems. Over the last two decades, scientific efforts have been primarily channelled into dissecting the symbioses occurring in coral tissues. Although easily accessible, this compartment is only 2-3 mm thick, whereas the underlying calcium carbonate skeleton occupies the vast internal volume of corals. Far from being devoid of life, the skeleton harbours a wide array of algae, endolithic fungi, heterotrophic bacteria, and other boring eukaryotes, often forming distinct bands visible to the bare eye. Some of the critical functions of these endolithic microorganisms in coral health, such as nutrient cycling and metabolite transfer, which could enable the survival of corals during thermal stress, have long been demonstrated. In addition, some of these microorganisms can dissolve calcium carbonate, weakening the coral skeleton and therefore may play a major role in reef erosion. Yet, experimental data are wanting due to methodological limitations. Recent technological and conceptual advances now allow us to tease apart the complex physical, ecological, and chemical interactions at the heart of coral endolithic microbial communities. These new capabilities have resulted in an excellent body of research and provide an exciting outlook to further address the functional microbial ecology of the "overlooked" coral skeleton.},
}
@article {pmid31690591,
year = {2019},
author = {Maslov, S and Sneppen, K},
title = {Regime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its Control.},
journal = {mSystems},
volume = {4},
number = {6},
pages = {},
pmid = {31690591},
issn = {2379-5077},
abstract = {The competition between bacteria often involves both nutrients and phage predators and may give rise to abrupt regime shifts between the alternative stable states characterized by different species compositions. While such transitions have been previously studied in the context of competition for nutrients, the case of phage-induced bistability between competing bacterial species has not been considered yet. Here we demonstrate a possibility of regime shifts in well-mixed phage-bacterium ecosystems. In one of the bistable states, the fast-growing bacteria competitively exclude the slow-growing ones by depleting their common nutrient. Conversely, in the second state, the slow-growing bacteria with a large burst size generate such a large phage population that the other species cannot survive. This type of bistability can be realized as the competition between a strain of bacteria protected from phage by abortive infection and another strain with partial resistance to phage. It is often desirable to reliably control the state of microbial ecosystems, yet bistability significantly complicates this task. We discuss successes and limitations of one control strategy in which one adds short pulses to populations of individual species. Our study proposes a new type of phage therapy, where introduction of the phage is supplemented by the addition of a partially resistant host bacteria.IMPORTANCE Phage-microbe communities play an important role in human health as well as natural and industrial environments. Here we show that these communities can assume several alternative species compositions separated by abrupt regime shifts. Our model predicts these regime shifts in the competition between bacterial strains protected by two different phage defense mechanisms: abortive infection/CRISPR and partial resistance. The history dependence caused by regime shifts greatly complicates the task of manipulation and control of a community. We propose and study a successful control strategy via short population pulses aimed at inducing the desired regime shifts. In particular, we predict that a fast-growing pathogen could be eliminated by a combination of its phage and a slower-growing susceptible host.},
}
@article {pmid31689403,
year = {2019},
author = {Wood, K},
title = {Microbial Ecology: Complex Bacterial Communities Reduce Selection for Antibiotic Resistance.},
journal = {Current biology : CB},
volume = {29},
number = {21},
pages = {R1143-R1145},
doi = {10.1016/j.cub.2019.09.017},
pmid = {31689403},
issn = {1879-0445},
support = {MR/N007174/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Anti-Bacterial Agents ; Bacteria/drug effects ; Drug Resistance, Bacterial ; Ecology ; *Microbiota ; },
abstract = {Competition between antibiotic-resistant and -susceptible bacteria is well studied in single-species communities, but less is known about selection for resistance in more complex ecologies. A new experiment shows natural microbial communities can hinder selection by increasing the fitness costs of resistance or by offering protection to drug-sensitive strains.},
}
@article {pmid31688899,
year = {2019},
author = {Wong, YY and Lee, CW and Bong, CW and Lim, JH and Narayanan, K and Sim, EUH},
title = {Environmental control of Vibrio spp. abundance and community structure in tropical waters.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {11},
pages = {},
doi = {10.1093/femsec/fiz176},
pmid = {31688899},
issn = {1574-6941},
mesh = {Chlorophyll A/metabolism ; *Environmental Microbiology ; Estuaries ; Malaysia ; Salinity ; Vibrio/*growth &amp; development ; },
abstract = {We measured Vibrio spp. distribution and community profile in the tropical estuary of Port Klang and coastal water of Port Dickson, Malaysia. Vibrio spp. abundance ranged from 15 to 2395 colony forming units mL-1, and was driven by salinity and chlorophyll a (Chl a) concentration. However, the effect of salinity was pronounced only when salinity was <20 ppt. A total of 27 Vibrio spp. were identified, and theVibrio spp. community at Port Dickson was more diverse (H' = 1.94 ± 0.21). However species composition between Port Dickson and Port Klang were similar. Two frequently occurring Vibrio spp. were V. owensii and V. rotiferianus, which exhibited relatively higher growth rates (ANCOVA: F > 4.338, P < 0.05). Co-culture experiments between fast- and slow-growing Vibrio spp. revealed that fast-growing Vibrio spp. (r-strategists) were overwhelmed by slower-growing Vibrio spp. (K-strategists) when nutrient conditions were set towards oligotrophy. In response to resource availability, the intrinsic growth strategy of each Vibrio spp. determined its occurrence and the development of Vibrio spp. community composition.},
}
@article {pmid31686026,
year = {2020},
author = {McCall, LI and Callewaert, C and Zhu, Q and Song, SJ and Bouslimani, A and Minich, JJ and Ernst, M and Ruiz-Calderon, JF and Cavallin, H and Pereira, HS and Novoselac, A and Hernandez, J and Rios, R and Branch, OH and Blaser, MJ and Paulino, LC and Dorrestein, PC and Knight, R and Dominguez-Bello, MG},
title = {Home chemical and microbial transitions across urbanization.},
journal = {Nature microbiology},
volume = {5},
number = {1},
pages = {108-115},
pmid = {31686026},
issn = {2058-5276},
support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; R25 GM061151/GM/NIGMS NIH HHS/United States ; S10 RR029121/RR/NCRR NIH HHS/United States ; },
mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; Environmental Exposure/*analysis ; Environmental Microbiology ; Fungi/classification/genetics/isolation &amp; purification ; Household Products/*analysis ; Housing ; Humans ; Microbiota ; Rainforest ; South America ; *Urbanization ; },
abstract = {Urbanization represents a profound shift in human behaviour, and has considerable cultural and health-associated consequences[1,2]. Here, we investigate chemical and microbial characteristics of houses and their human occupants across an urbanization gradient in the Amazon rainforest, from a remote Peruvian Amerindian village to the Brazilian city of Manaus. Urbanization was found to be associated with reduced microbial outdoor exposure, increased contact with housing materials, antimicrobials and cleaning products, and increased exposure to chemical diversity. The degree of urbanization correlated with changes in the composition of house bacterial and microeukaryotic communities, increased house and skin fungal diversity, and an increase in the relative abundance of human skin-associated fungi and bacteria in houses. Overall, our results indicate that urbanization has large-scale effects on chemical and microbial exposures and on the human microbiota.},
}
@article {pmid31684148,
year = {2019},
author = {Gomes, A and Oudot, C and Macià, A and Foito, A and Carregosa, D and Stewart, D and Van de Wiele, T and Berry, D and Motilva, MJ and Brenner, C and Dos Santos, CN},
title = {Berry-Enriched Diet in Salt-Sensitive Hypertensive Rats: Metabolic Fate of (Poly)Phenols and the Role of Gut Microbiota.},
journal = {Nutrients},
volume = {11},
number = {11},
pages = {},
pmid = {31684148},
issn = {2072-6643},
support = {ANR-13-ISV1-0001-01//Agence Nationale de la Recherche/ ; ANR-11-IDEX-0003-01//Agence Nationale de la Recherche/ ; FCTANR/BEX-BCM/0001/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; SFRH/BD/103155/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; IF/01097/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; FWF P26127-B20//Austrian Science Fund/ ; FunKeyGut 741623/ERC_/European Research Council/International ; Rural &amp; Environment Science &amp; Analytical Services//Scottish Government/ ; LISBOA-01-0145-FEDER-007344//iNOVA4Health Research Unit/ ; },
mesh = {Animals ; Diet ; Dysbiosis/metabolism ; Feces/microbiology ; *Fruit ; Gastrointestinal Microbiome/genetics/*physiology ; Glycosides/metabolism ; Male ; Phenols/analysis/*metabolism ; Phytochemicals/analysis/metabolism ; Rats ; Rats, Inbred Dahl ; Sodium, Dietary ; },
abstract = {Diets rich in (poly)phenols are associated with a reduced reduction in the incidence of cardiovascular disorders. While the absorption and metabolism of (poly)phenols has been described, it is not clear how their metabolic fate is affected under pathological conditions. This study evaluated the metabolic fate of berry (poly)phenols in an in vivo model of hypertension as well as the associated microbiota response. Dahl salt-sensitive rats were fed either a low-salt diet (0.26% NaCl) or a high-salt diet (8% NaCl), with or without a berry mixture (blueberries, blackberries, raspberries, Portuguese crowberry and strawberry tree fruit) for 9 weeks. The salt-enriched diet promoted an increase in the urinary excretion of berry (poly)phenol metabolites, while the abundance of these metabolites decreased in faeces, as revealed by UPLC-MS/MS. Moreover, salt and berries modulated gut microbiota composition as demonstrated by 16S rRNA analysis. Some changes in the microbiota composition were associated with the high-salt diet and revealed an expansion of the families Proteobacteria and Erysipelotrichaceae. However, this effect was mitigated by the dietary supplementation with berries. Alterations in the metabolic fate of (poly)phenols occur in parallel with the modulation of gut microbiota in hypertensive rats. Thus, beneficial effects of (poly)phenols could be related with these interlinked modifications, between metabolites and microbiota environments.},
}
@article {pmid31682986,
year = {2020},
author = {Brackmann, M and Leib, SL and Tonolla, M and Schürch, N and Wittwer, M},
title = {Antimicrobial resistance classification using MALDI-TOF-MS is not that easy: lessons from vancomycin-resistant Enterococcus faecium.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {26},
number = {3},
pages = {391-393},
doi = {10.1016/j.cmi.2019.10.027},
pmid = {31682986},
issn = {1469-0691},
mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; *Drug Resistance, Bacterial ; Enterococcus faecium/*drug effects ; Gram-Positive Bacterial Infections/diagnosis/drug therapy/microbiology ; Humans ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Vancomycin/*pharmacology/therapeutic use ; },
}
@article {pmid31681511,
year = {2019},
author = {Kobayashi, K and Aoyagi, H},
title = {Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the candidate division FBP.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7876},
pmid = {31681511},
issn = {2167-8359},
abstract = {BACKGROUND: The potential of unidentified microorganisms for academic and other applications is limitless. Plants have diverse microbial communities associated with their biomes. However, few studies have focused on the microbial community structure relevant to tree bark.<br><br>METHODS: In this report, the microbial community structure of bark from the broad-leaved tree Acer palmatum was analyzed. Both a culture-independent approach using polymerase chain reaction (PCR) amplification and next generation sequencing, and bacterial isolation and sequence-based identification methods were used to explore the bark sample as a source of previously uncultured microorganisms. Molecular phylogenetic analyses based on PCR-amplified 16S rDNA sequences were performed.<br><br>RESULTS: At the phylum level, Proteobacteria and Bacteroidetes were relatively abundant in the A. palmatum bark. In addition, microorganisms from the phyla Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Armatimonadetes, and candidate division FBP, which contain many uncultured microbial species, existed in the A. palmatum bark. Of the 30 genera present at relatively high abundance in the bark, some genera belonging to the phyla mentioned were detected. A total of 70 isolates could be isolated and cultured using the low-nutrient agar media DR2A and PE03. Strains belonging to the phylum Actinobacteria were isolated most frequently. In addition, the newly identified bacterial strain IAP-33, presumed to belong to Acidobacteria, was isolated on PE03 medium. Of the isolated bacteria, 44 strains demonstrated less than 97% 16S rDNA sequence-similarity with type strains. Molecular phylogenetic analysis of IAD-21 showed the lowest similarity (79%), and analyses suggested it belongs to candidate division FBP. Culture of the strain IAD-21 was deposited in Japan Collection of Microorganisms (JCM) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) as JCM 32665 and DSM 108248, respectively.<br><br>DISCUSSION: Our results suggest that a variety of uncultured microorganisms exist in A. palmatum bark. Microorganisms acquirable from the bark may prove valuable for academic pursuits, such as studying microbial ecology, and the bark might be a promising source of uncultured bacterial isolates.},
}
@article {pmid31681249,
year = {2019},
author = {He, H and Fu, L and Liu, Q and Fu, L and Bi, N and Yang, Z and Zhen, Y},
title = {Community Structure, Abundance and Potential Functions of Bacteria and Archaea in the Sansha Yongle Blue Hole, Xisha, South China Sea.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2404},
pmid = {31681249},
issn = {1664-302X},
abstract = {The Sansha Yongle Blue Hole is the deepest blue hole in the world and exhibits unique environmental characteristics. In this paper, Illumina sequencing and qPCR analysis were conducted to obtain the microbial information in this special ecosystem. The results showed that the richness and diversity of bacterial communities in the hole was greater than those of archaeal communities, and bacterial and archaeal communities were dominated by Proteobacteria and Euryarchaeota, respectively. Temperature and nitrate concentration significantly contributed to the heterogeneous distribution of major bacterial clades; salinity explained most variations of the archaeal communities, but not significant. A sudden increase of bacterial 16S rRNA, archaeal 16S rRNA, ANAMMOX 16S rRNA, nirS and dsrB gene was noticed from 90 to 100 m in the hole probably due to more phytoplankton at this depth. Sulfur oxidation and nitrate reduction were the most abundant predicted ecological functions in the hole, while lots of archaea were predicted to be involved in aerobic ammonia oxidation and methanogenesis. The co-occurrence network analysis illustrated that a synergistic effect between sulfate reduction and sulfur oxidation, and between nitrogen fixation and denitrification, a certain degree of coupling between sulfur and nitrogen cycle was also observed in the hole. The comparisons of bacterial and archaeal communities between the hole and other caves in the world (or other areas of the South China Sea) suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal communities.},
}
@article {pmid31680681,
year = {2019},
author = {Temkin, MI and Carlson, CM and Stubbendieck, AL and Currie, CR and Stubbendieck, RM},
title = {High Throughput Co-culture Assays for the Investigation of Microbial Interactions.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {152},
pages = {},
pmid = {31680681},
issn = {1940-087X},
support = {T15 LM007359/LM/NLM NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; },
mesh = {Actinobacteria/*isolation &amp; purification/*metabolism ; Biological Assay/*methods ; Coculture Techniques/methods ; Humans ; Microbial Interactions/*physiology ; Microbiota/physiology ; Nasal Cavity/microbiology ; },
abstract = {The study of interactions between microorganisms has led to numerous discoveries, from novel antimicrobials to insights in microbial ecology. Many approaches used for the study of microbial interactions require specialized equipment and are expensive and time intensive. This paper presents a protocol for co-culture interaction assays that are inexpensive, scalable to large sample numbers, and easily adaptable to numerous experimental designs. Microorganisms are cultured together, with each well representing one pairwise combination of microorganisms. A test organism is cultured on one side of each well and first incubated in monoculture. Subsequently, target organisms are simultaneously inoculated onto the opposite side of each well using a 3D-printed inoculation stamp. After co-culture, the completed assays are scored for visual phenotypes, such as growth or inhibition. These assays can be used to confirm phenotypes or identify patterns among isolates of interest. Using this simple and effective method, users can analyze combinations of microorganisms rapidly and efficiently. This co-culture approach is applicable to antibiotic discovery as well as culture-based microbiome research and has already been successfully applied to both applications.},
}
@article {pmid31679006,
year = {2020},
author = {González-Hourcade, M and Braga, MR and Del Campo, EM and Ascaso, C and Patiño, C and Casano, LM},
title = {Ultrastructural and biochemical analyses reveal cell wall remodelling in lichen-forming microalgae submitted to cyclic desiccation-rehydration.},
journal = {Annals of botany},
volume = {125},
number = {3},
pages = {459-469},
pmid = {31679006},
issn = {1095-8290},
mesh = {Cell Wall ; Desiccation ; Fluid Therapy ; *Lichens ; *Microalgae ; },
abstract = {BACKGROUND AND AIMS: One of the most distinctive features of desiccation-tolerant plants is their high cell wall (CW) flexibility. Most lichen microalgae can tolerate drastic dehydration-rehydration (D/R) conditions; however, their mechanisms of D/R tolerance are scarcely understood. We tested the hypothesis that D/R-tolerant microalgae would have flexible CWs due to species-specific CW ultrastructure and biochemical composition, which could be remodelled by exposure to cyclic D/R.<br><br>METHODS: Two lichen microalgae, Trebouxia sp. TR9 (TR9, adapted to rapid D/R cycles) and Coccomyxa simplex (Csol, adapted to seasonal dry periods) were exposed to no or four cycles of desiccation [25-30 % RH (TR9) or 55-60 % RH (Csol)] and 16 h of rehydration (100 % RH). Low-temperature SEM, environmental SEM and freeze-substitution TEM were employed to visualize structural alterations induced by D/R. In addition, CWs were extracted and sequentially fractionated with hot water and KOH, and the gel permeation profile of polysaccharides was analysed in each fraction. The glycosyl composition and linkage of the main polysaccharides of each CW fraction were analysed by GC-MS.<br><br>KEY RESULTS: All ultrastructural analyses consistently showed that desiccation caused progressive cell shrinkage and deformation in both microalgae, which could be rapidly reversed when water availability increased. Notably, the plasma membrane of TR9 and Csol remained in close contact with the deformed CW. Exposure to D/R strongly altered the size distribution of TR9 hot-water-soluble polysaccharides, composed mainly of a &#x3b2;-3-linked rhamnogalactofuranan and Csol KOH-soluble &#x3b2;-glucans.<br><br>CONCLUSIONS: Cyclic D/R induces biochemical remodelling of the CW that could increase CW flexibility, allowing regulated shrinkage and expansion of D/R-tolerant microalgae.},
}
@article {pmid31678751,
year = {2020},
author = {Contreras-Dávila, CA and Carrión, VJ and Vonk, VR and Buisman, CNJ and Strik, DPBTB},
title = {Consecutive lactate formation and chain elongation to reduce exogenous chemicals input in repeated-batch food waste fermentation.},
journal = {Water research},
volume = {169},
number = {},
pages = {115215},
doi = {10.1016/j.watres.2019.115215},
pmid = {31678751},
issn = {1879-2448},
mesh = {Bioreactors ; Butyrates ; Fatty Acids ; Fermentation ; *Food ; *Refuse Disposal ; },
abstract = {The production of biochemicals from renewables through biorefinery processes is important to reduce the anthropogenic impact on the environment. Chain elongation processes based on microbiomes have been successfully developed to produce medium-chain fatty acids (MCFA) from organic waste streams. Yet, the sustainability of chain elongation can still be improved by reducing the use of electron donors and additional chemicals. This work aimed to couple lactate production and subsequent chain elongation to decrease chemicals input such as electron donors and hydroxide for pH control in repeated-batch food waste fermentation. Food waste with adjusted pH was used as substrate and fermentation proceeded without pH control. During fermentation, lactate was first formed through the homolactic pathway and then converted to fatty acids (FA), mainly n-butyrate and n-caproate. The highest n-caproate carbon selectivities (mmol C/mmol CFA) and production rates were 38% and 4.2 g COD/L-d, respectively. Hydroxide input was reduced over time to a minimum of 0.47 mol OH[-]/mol MCFA or 0.79 mol OH[-]/kg CODFA. Lactate was a key electron donor for chain elongation and its conversion was observed at pH as low as 4.3. The microbiome enriched in this work was dominated by Lactobacillus spp. and Caproiciproducens spp. The high abundance of Caproiciproducens spp. and their co-occurrence with Lactobacillus spp. suggest Caproiciproducens spp. used lactate as electron donor for chain elongation. This work shows the production of n-caproate from food waste with decreased use of hydroxide and no use of exogenous electron donors.},
}
@article {pmid31677344,
year = {2020},
author = {Dumack, K and Fiore-Donno, AM and Bass, D and Bonkowski, M},
title = {Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria).},
journal = {Molecular ecology resources},
volume = {20},
number = {2},
pages = {398-403},
doi = {10.1111/1755-0998.13112},
pmid = {31677344},
issn = {1755-0998},
support = {BO 1907/13-2//Deutsche Forschungsgemeinschaft/ ; BO 1907/18-1//Deutsche Forschungsgemeinschaft/ ; Priority Program 1374//Deutsche Forschungsgemeinschaft/ ; NE/H000887/1//NERC Science of the Environment/ ; NE/H009426/1//NERC Science of the Environment/ ; },
mesh = {Cercozoa/classification/genetics ; DNA, Environmental/genetics ; Databases, Genetic ; Ecosystem ; Phenotype ; Phylogeny ; Rhizaria/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {We have compiled a database of functional traits for two widespread and ecologically important groups of protists, Cercozoa and Endomyxa (Rhizaria). The functional traits of microorganisms are crucially important for interpreting results from environmental sequencing surveys. Linking morphological and ecological traits to environmental factors is common practice in studies involving micro- and macroorganisms, but is rarely applied to protists. Our database provides functional and ecologically significant traits linked to morphology, nutrition, locomotion and habitats. We discuss how the use of functional traits may help to unveil underlying ecosystem processes. This database is intended as a common reference for the molecular ecology community and will boost the understanding of ecosystem functions, especially those driven by biological interactions.},
}
@article {pmid31676992,
year = {2020},
author = {Kublanovskaya, A and Solovchenko, A and Fedorenko, T and Chekanov, K and Lobakova, E},
title = {Natural Communities of Carotenogenic Chlorophyte Haematococcus lacustris and Bacteria from the White Sea Coastal Rock Ponds.},
journal = {Microbial ecology},
volume = {79},
number = {4},
pages = {785-800},
doi = {10.1007/s00248-019-01437-0},
pmid = {31676992},
issn = {1432-184X},
support = {18-29-25050//&#x420;&#x43e;&#x441;&#x441;&#x438;&#x439;&#x441;&#x43a;&#x438;&#x439; &#x424;&#x43e;&#x43d;&#x434; &#x424;&#x443;&#x43d;&#x434;&#x430;&#x43c;&#x435;&#x43d;&#x442;&#x430;&#x43b;&#x44c;&#x43d;&#x44b;&#x445; &#x418;&#x441;&#x441;&#x43b;&#x435;&#x434;&#x43e;&#x432;&#x430;&#x43d;&#x438;&#x439; (&#x420;&#x424;&#x424;&#x418;)/ ; },
mesh = {Bacteria/classification/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Chlorophyta/*microbiology ; *Microbiota ; Oceans and Seas ; Russia ; Seawater/*microbiology ; },
abstract = {Haematococcus lacustris is a biotechnologically important green unicellular alga producing widely used keta-karotenoid astaxanthin. In natural habitats, it exists in the form of algal-bacterial community, and under laboratory conditions, it is also accompanied by bacteria. The issue of the bacterial composition of industrial algal cultures is widely recognized as important. However, there is a dearth of information about bacterial composition of H. lacustris communities. In current work, we analyze the composition of natural H. lacustris communities from the White Sea coastal temporal rock ponds. For the first time, a 16S rRNA gene-based metagenome of natural H. lacustris bacterial communities has been generated. Main results of its analysis are as follow. Bacterial families Comamonadaceae, Cytophagaceae, Xanthomonadaceae, Acetobacteraceae, Rhodobacteraceae, and Rhodocyclaceae were observed in all studied H. lacustris natural communities. They also contained genera Hydrogenophaga and Cytophaga. Bacteria from the Hydrogenophaga genus were present in H. lacustris cultures after their isolation under the conditions of laboratory cultivation. Similar to other planktonic microalgae, H. lacustris forms a phycosphere around the cells. In this zone, bacteria attached to the algal surface. The contact between H. lacustris and bacteria is maintained even after sample drying. The study provides information about possible members of H. lacustris core microbiome, which can be presented in the industrial and laboratory cultures of the microalga.},
}
@article {pmid31676479,
year = {2020},
author = {Dyer, SW and Needoba, JA},
title = {Use of High-Resolution Pressure Nephelometry To Measure Gas Vesicle Collapse as a Means of Determining Growth and Turgor Changes in Planktonic Cyanobacteria.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {2},
pages = {},
pmid = {31676479},
issn = {1098-5336},
mesh = {Cyanobacteria/growth &amp; development/*physiology ; Harmful Algal Bloom/*physiology ; Microcystis/*physiology ; Nephelometry and Turbidimetry/instrumentation/*methods ; Phytoplankton/*physiology ; },
abstract = {Previous work has demonstrated that the physical properties of intracellular bacterial gas vesicles (GVs) can be analyzed in vivo using pressure nephelometry. In analyzing the buoyant state of GV-containing cyanobacteria, hydrostatic pressure within a sample cell is increased in a stepwise manner, where the concomitant collapse of GVs due to pressure and the resultant decrease in suspended cells are detected by changes in nephelometric scattering. As the relative pressure at which GVs collapse is a function of turgor pressure and cellular osmotic gradients, pressure nephelometry is a powerful tool for assaying changes in metabolism that affect turgor, such as photosynthetic and osmoregulatory processes. We have developed an updated and automated pressure nephelometer that utilizes visible-infrared (Vis-IR) spectra to accurately quantify GV critical collapse pressure, critical collapse pressure distribution, and cell turgor pressure. Here, using the updated pressure nephelometer and axenic cultures of Microcystis aeruginosa PCC7806, we demonstrate that GV critical collapse pressure is stable during mid-exponential growth phase, introduce pressure-sensitive turbidity as a robust metric for the abundance of gas-vacuolate cyanobacteria, and demonstrate that pressure-sensitive turbidity is a more accurate proxy for abundance and growth than photopigment fluorescence. As cyanobacterium-dominated harmful algal bloom (cyanoHAB) formation is dependent on the constituent cells possessing gas vesicles, characterization of environmental cyanobacteria populations via pressure nephelometry is identified as an underutilized monitoring method. Applications of this instrument focus on physiological and ecological studies of cyanobacteria, for example, cyanoHAB dynamics and the drivers associated with cyanotoxin production in aquatic ecosystems.IMPORTANCE The increased prevalence of bloom-forming cyanobacteria and associated risk of exposure to cyanobacterial toxins through drinking water utilities and recreational waterways are growing public health concerns. Cost-effective, early-detection methodologies specific to cyanobacteria are crucial for mitigating these risks, with a gas vesicle-specific signal offering a number of benefits over photopigment fluorescence, including improved detection limits and discrimination against non-gas-vacuolate phototrophs. Here, we present a multiplexed instrument capable of quantifying the relative abundance of cyanobacteria based on the signal generated from the presence of intracellular gas vesicles specific to bloom-forming cyanobacteria. Additionally, as cell turgor can be measured in vivo via pressure nephelometry, the measurement furnishes information about the internal osmotic pressure of gas-vacuolate cyanobacteria, which relates to the metabolic state of the cell. Together these advances may improve routine waterway monitoring and the mitigation of human health threats due to cyanobacterial blooms.},
}
@article {pmid31676478,
year = {2019},
author = {Oh, JH and Lin, XB and Zhang, S and Tollenaar, SL and Özçam, M and Dunphy, C and Walter, J and van Pijkeren, JP},
title = {Prophages in Lactobacillus reuteri Are Associated with Fitness Trade-Offs but Can Increase Competitiveness in the Gut Ecosystem.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {1},
pages = {},
pmid = {31676478},
issn = {1098-5336},
mesh = {Animals ; *Bacteriophages/genetics/physiology ; Chickens ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology/virology ; Genome, Bacterial ; Genome, Viral ; Humans ; Limosilactobacillus reuteri/genetics/*virology ; *Lysogeny/genetics/physiology ; Mice ; Microbial Interactions/*genetics ; Prophages/*genetics ; Rats ; Swine ; Virus Activation/physiology ; },
abstract = {The gut microbiota harbors a diverse phage population that is largely derived from lysogens, which are bacteria that contain dormant phages in their genome. While the diversity of phages in gut ecosystems is getting increasingly well characterized, knowledge is limited on how phages contribute to the evolution and ecology of their host bacteria. Here, we show that biologically active prophages are widely distributed in phylogenetically diverse strains of the gut symbiont Lactobacillus reuteri Nearly all human- and rodent-derived strains, but less than half of the tested strains of porcine origin, contain active prophages, suggesting different roles of phages in the evolution of host-specific lineages. To gain insight into the ecological role of L. reuteri phages, we developed L. reuteri strain 6475 as a model to study its phages. After administration to mice, L. reuteri 6475 produces active phages throughout the intestinal tract, with the highest number detected in the distal colon. Inactivation of recA abolished in vivo phage production, which suggests that activation of the SOS response drives phage production in the gut. In conventional mice, phage production reduces bacterial fitness as fewer wild-type bacteria survive gut transit compared to the mutant lacking prophages. However, in gnotobiotic mice, phage production provides L. reuteri with a competitive advantage over a sensitive host. Collectively, we uncovered that the presence of prophages, although associated with a fitness trade-off, can be advantageous for a gut symbiont by killing a competitor strain in its intestinal niche.IMPORTANCE Bacteriophages derived from lysogens are abundant in gut microbiomes. Currently, mechanistic knowledge is lacking on the ecological ramifications of prophage carriage yet is essential to explain the abundance of lysogens in the gut. An extensive screen of the bacterial gut symbiont Lactobacillus reuteri revealed that biologically active prophages are widely distributed in this species. L. reuteri 6475 produces phages throughout the mouse intestinal tract, but phage production is associated with reduced fitness of the lysogen. However, phage production provides a competitive advantage in direct competition with a nonlysogenic strain of L. reuteri that is sensitive to these phages. This combination of increased competition with a fitness trade-off provides a potential explanation for the domination of lysogens in gut ecosystem and how lysogens can coexist with sensitive hosts.},
}
@article {pmid31672892,
year = {2019},
author = {Carrión, VJ and Perez-Jaramillo, J and Cordovez, V and Tracanna, V and de Hollander, M and Ruiz-Buck, D and Mendes, LW and van Ijcken, WFJ and Gomez-Exposito, R and Elsayed, SS and Mohanraju, P and Arifah, A and van der Oost, J and Paulson, JN and Mendes, R and van Wezel, GP and Medema, MH and Raaijmakers, JM},
title = {Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome.},
journal = {Science (New York, N.Y.)},
volume = {366},
number = {6465},
pages = {606-612},
doi = {10.1126/science.aaw9285},
pmid = {31672892},
issn = {1095-9203},
mesh = {Bacteria/classification ; Bacterial Physiological Phenomena ; Bacteroidetes/physiology ; Beta vulgaris/*microbiology ; Biodiversity ; Chitinases/genetics ; Disease Resistance ; Endophytes/*physiology ; Flavobacterium/physiology ; Genes, Bacterial ; Genome, Bacterial ; Metagenome ; *Microbiota ; Mutagenesis, Site-Directed ; Peptide Synthases/genetics ; Plant Diseases/*microbiology ; Plant Roots/*microbiology ; Polyketide Synthases/genetics ; Rhizoctonia/*pathogenicity ; Soil Microbiology ; },
abstract = {Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.},
}
@article {pmid31670141,
year = {2019},
author = {Ouoba, LII and Vouidibio Mbozo, AB and Anyogu, A and Obioha, PI and Lingani-Sawadogo, H and Sutherland, JP and Jespersen, L and Ghoddusi, HB},
title = {Environmental heterogeneity of Staphylococcus species from alkaline fermented foods and associated toxins and antimicrobial resistance genetic elements.},
journal = {International journal of food microbiology},
volume = {311},
number = {},
pages = {108356},
doi = {10.1016/j.ijfoodmicro.2019.108356},
pmid = {31670141},
issn = {1879-3460},
mesh = {Anti-Bacterial Agents/pharmacology ; Burkina Faso ; Coagulase/genetics ; Congo ; DNA-Directed RNA Polymerases/genetics ; Drug Resistance, Bacterial/genetics ; Enterotoxins/*genetics ; Erythromycin/pharmacology ; Fermented Foods/*microbiology ; Genotype ; Microbial Sensitivity Tests ; Phenotype ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Staphylococcus/classification/drug effects/genetics/isolation &amp; purification ; Tetracycline/pharmacology ; },
abstract = {Different samples of three products including Bikalga and Soumbala from Burkina Faso (West Africa) and Ntoba Mbodi from Congo-Brazzaville (Central Africa) were evaluated. The bacteria (400) were phenotyped and genotypically characterized by Rep-PCR, PFGE, 16S rRNA and rpoB gene sequencing and spa typing. Their PFGE profiles were compared with those of 12,000 isolates in the Center for Disease Control (CDC, USA) database. They were screened for the production of enterotoxins, susceptibility to 19 antimicrobials, presence of 12 staphylococcal toxin and 38 AMR genes and the ability to transfer erythromycin and tetracycline resistance genes to Enterococcus faecalis JH2-2. Fifteen coagulase negative (CoNS) and positive (CoPS) species characterized by 25 Rep-PCR/PFGE clusters were identified: Staphylococcus arlettae, S. aureus, S. cohnii, S. epidermidis, S. gallinarum, S. haemolyticus, S. hominis, S. pasteuri, S. condimenti, S. piscifermentans, S. saprophyticus, S. sciuri, S. simulans, S. warneri and Macrococcus caseolyticus. Five species were specific to Soumbala, four to Bikalga and four to Ntoba Mbodi. Two clusters of S. gallinarum and three of S. sciuri were particular to Burkina Faso. The S. aureus isolates exhibited a spa type t355 and their PFGE profiles did not match any in the CDC database. Bacteria from the same cluster displayed similar AMR and toxin phenotypes and genotypes, whereas clusters peculiar to a product or a location generated distinct profiles. The toxin genes screened were not detected and the bacteria did not produce the staphylococcal enterotoxins A, B, C and D. AMR genes including blazA, cat501, dfr(A), dfr(G), mecA, mecA1, msr(A) and tet(K) were identified in CoNS and CoPS. Conjugation experiments produced JH2-2 isolates that acquired resistance to erythromycin and tetracycline, but no gene transfer was revealed by PCR. The investigation of the heterogeneity of Staphylococcus species from alkaline fermented foods, their relationship with clinical and environmental isolates and their safety in relation to antimicrobial resistance (AMR) and toxin production is anticipated to contribute to determining the importance of staphylococci in alkaline fermented foods, especially in relation to the safety of the consumers.},
}
@article {pmid31666490,
year = {2020},
author = {Sharma, NC and Kumar, D and Sarkar, A and Chowdhury, G and Mukhopadhyay, AK and Ramamurthy, T},
title = {Prevalence of Multidrug Resistant Salmonellae with Increasing Frequency of Salmonella enterica Serovars Kentucky and Virchow among Hospitalized Diarrheal Cases in and around Delhi, India.},
journal = {Japanese journal of infectious diseases},
volume = {73},
number = {2},
pages = {119-123},
doi = {10.7883/yoken.JJID.2019.063},
pmid = {31666490},
issn = {1884-2836},
mesh = {Anti-Bacterial Agents/pharmacology ; Child ; Child, Preschool ; Diarrhea/*epidemiology/microbiology ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Humans ; India/epidemiology ; Kentucky ; Prevalence ; Salmonella Infections/*epidemiology ; Salmonella enterica/classification/*drug effects ; Serogroup ; },
abstract = {Non-typhoidal salmonellae (NTS) are a major cause of acute diarrhea with characteristic multidrug resistance (MDR). In a hospital-based study, 81 NTS were isolated and tested for serotypes and antimicrobial resistance (AMR). Salmonella enterica isolates were classified into 7 different typable serovars, however, 19 (23%) isolates remained untypable. The most common serovars were S. Kentucky (48%), and S. Virchow (22%). Most of the NTS isolates displayed resistance to nalidixic acid (NA) (73%), ciprofloxacin (CIP) (48%), ampicillin (AM) and norfloxacin (NOR) (36% each), and gentamicin (CN) (31%). The AMR profiles for CN and NA; and AM, CIP, NA and NOR, were found to be high in S. Virchow (83%) and S. Kentucky (43%), respectively. Analysis of the pulsed-field gel electrophoresis patterns of S. Kentucky revealed 3 clusters. S. Kentucky has clones closely related to become prominent in recent years in Delhi. The AMR appears to be consistent with the change in MDR patterns during 2014-2017. The observed prevalence of S. Kentucky and S. Virchow in large numbers of diarrheal cases is novel. The NTS are mostly resistant to fluoroquinolones, which is the current drug of choice for treating diarrheal cases. MDR is very common among clonally related S. Kentucky.},
}
@article {pmid31665274,
year = {2020},
author = {Wuyts, K and Smets, W and Lebeer, S and Samson, R},
title = {Green infrastructure and atmospheric pollution shape diversity and composition of phyllosphere bacterial communities in an urban landscape.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {1},
pages = {},
doi = {10.1093/femsec/fiz173},
pmid = {31665274},
issn = {1574-6941},
mesh = {*Air Pollution ; Bacteria/classification/genetics/isolation &amp; purification ; Belgium ; Biodiversity ; Ecosystem ; *Microbiota ; Plant Leaves/*microbiology ; RNA, Ribosomal, 16S/genetics ; Trees/microbiology ; *Urbanization ; },
abstract = {The microbial habitat on leaf surfaces, also called the phyllosphere, is a selective environment for bacteria, harbouring specific phyllosphere bacterial communities (PBCs). These communities influence plant health, plant-community diversity, ecosystem functioning and ecosystem services. Host plants in an urban environment accommodate different PBCs than those in non-urban environments, but previous studies did not address individual urban factors. In this study, the PBC composition and diversity of 55 London plane (Platanus x acerifolia) trees throughout an urban landscape (Antwerp, Belgium) were determined using 16S rRNA amplicon sequencing. An increasing proportion of green infrastructure in the surrounding of the trees, and subsequently decreasing proportion of anthropogenic land use, was linked with taxa loss, expressed in lower phyllosphere alpha diversity and higher abundances of typical phyllosphere bacteria such as Hymenobacter, Pseudomonas and Beijerinckia. Although air pollution exposure, as assessed by leaf magnetic analysis, did not link with alpha diversity, it correlated with shifts in PBC composition in form of turnover, an equilibrium of taxa gain and taxa loss. We found that both urban landscape composition and air pollution exposure - each in their own unique way - influence bacterial communities in the urban tree phyllosphere.},
}
@article {pmid31665056,
year = {2019},
author = {Kieran, TJ and Arnold, KMH and Thomas, JC and Varian, CP and Saldaña, A and Calzada, JE and Glenn, TC and Gottdenker, NL},
title = {Regional biogeography of microbiota composition in the Chagas disease vector Rhodnius pallescens.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {504},
pmid = {31665056},
issn = {1756-3305},
support = {DGE-1545433//National Science Foundation/ ; COL11-043//Secretar&#xed;a Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; },
mesh = {Actinobacteria/classification/genetics ; Analysis of Variance ; Animals ; Bacteria/*classification/genetics ; Bacteroidetes/classification/genetics ; Biodiversity ; Chagas Disease/*transmission ; DNA Barcoding, Taxonomic ; Ecosystem ; Firmicutes/classification/genetics ; Gene Library ; Humans ; Insect Vectors/*microbiology/physiology ; *Microbiota ; Panama ; Phylogeography ; Polymerase Chain Reaction ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/chemistry ; Rhodnius/*microbiology/physiology ; },
abstract = {BACKGROUND: Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target vector survival and fitness. In this study we examined the whole-body microbial composition of R. pallescens from three locations in Panama.<br><br>METHODS: We collected 89 R. pallescens specimens using Noireau traps in Attalea butyracea palms. We then extracted total DNA from whole-bodies of specimens and amplified bacterial microbiota using 16S rRNA metabarcoding PCR. The 16S libraries were sequenced on an Illumina MiSeq and analyzed using QIIME2 software.<br><br>RESULTS: We found Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes to be the most abundant bacterial phyla across all samples. Geographical location showed the largest difference in microbial composition with northern Veraguas Province having the most diversity and Panama Oeste Province localities being most similar to each other. Wolbachia was detected in high abundance (48-72%) at Panama Oeste area localities with a complete absence of detection in Veraguas Province. No significant differences in microbial composition were detected between triatomine age class, primary blood meal source, or T. cruzi infection status.<br><br>CONCLUSIONS: We found biogeographical regions differ in microbial composition among R. pallescens populations in Panama. While overall the microbiota has bacterial taxa consistent with previous studies in triatomine microbial ecology, locality differences are an important observation for future studies. Geographical heterogeneity in microbiomes of vectors is an important consideration for future developments that leverage microbiomes for disease control.},
}
@article {pmid31664477,
year = {2020},
author = {Kolátková, V and Čepička, I and Gargiulo, GM and Vohník, M},
title = {Enigmatic Phytomyxid Parasite of the Alien Seagrass Halophila stipulacea: New Insights into Its Ecology, Phylogeny, and Distribution in the Mediterranean Sea.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {631-643},
pmid = {31664477},
issn = {1432-184X},
support = {1308218//Grantov&#xe1; Agentura, Univerzita Karlova (CZ)/ ; },
mesh = {Cercozoa/classification/genetics/*physiology ; Hydrocharitaceae/*parasitology ; Introduced Species ; Italy ; Mediterranean Sea ; Phylogeny ; Plant Leaves/*parasitology ; RNA, Protozoan/analysis ; RNA, Ribosomal, 18S/analysis ; *Symbiosis ; },
abstract = {Marine phytomyxids represent often overlooked obligate biotrophic parasites colonizing diatoms, brown algae, and seagrasses. An illustrative example of their enigmatic nature is the phytomyxid infecting the seagrass Halophila stipulacea (a well-known Lessepsian migrant from the Indo-Pacific to the Mediterranean Sea). In the Mediterranean, the occurrence of this phytomyxid was first described in 1995 in the Strait of Messina (southern Italy) and the second time in 2017 in the Aegean coast of Turkey. Here we investigated, using scuba diving, stereomicroscopy, light and scanning electron microscopy, and molecular methods, whether the symbiosis is still present in southern Italy, its distribution in this region and its relation to the previous reports. From the total of 16 localities investigated, the symbiosis has only been found at one site. A seasonal pattern was observed with exceptionally high abundance (> 40% of the leaf petioles colonized) in September 2017, absence of the symbiosis in May/June 2018, and then again high infection rates (~ 30%) in September 2018. In terms of anatomy and morphology as well as resting spore dimensions and arrangement, the symbiosis seems to be identical to the preceding observations in the Mediterranean. According to the phylogenetic analyses of the 18S rRNA gene, the phytomyxid represents the first characterized member of the environmental clade "TAGIRI-5". Our results provide new clues about its on-site ecology (incl. possible dispersal mechanisms), hint that it is rare but established in the Mediterranean, and encourage further research into its distribution, ecophysiology, and taxonomy.},
}
@article {pmid31662456,
year = {2019},
author = {Chase, AB and Arevalo, P and Brodie, EL and Polz, MF and Karaoz, U and Martiny, JBH},
title = {Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria.},
journal = {mBio},
volume = {10},
number = {5},
pages = {},
pmid = {31662456},
issn = {2150-7511},
mesh = {Actinobacteria/genetics ; Bacteria/classification/*genetics ; Ecology ; Ecosystem ; Gene Flow ; Genetic Variation ; Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; },
abstract = {For free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several obstacles to the study of the processes contributing to microbial diversification. These obstacles are particularly high in soil, where high bacterial diversity inhibits the study of closely related genotypes and therefore the factors structuring microbial populations. Here, we isolated strains within a single Curtobacterium ecotype from surface soil (leaf litter) across a regional climate gradient and investigated the phylogenetic structure, recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. Our results indicate that microbial populations are delineated by gene flow discontinuities, with distinct populations cooccurring at multiple sites. Bacterial population structure was further delineated by genomic features allowing for the identification of candidate genes possibly contributing to local adaptation. These results suggest that the genetic structure within this bacterium is maintained both by ecological specialization in localized microenvironments (isolation by environment) and by dispersal limitation between geographic locations (isolation by distance).IMPORTANCE Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often compare divergent strains from disparate environments under varied selective pressures. Here, we investigated the population structure within a single bacterial ecotype, a unit equivalent to a eukaryotic species, defined as highly clustered genotypic and phenotypic strains with the same ecological niche. Using a combination of genomic and computational analyses, we assessed the phylogenetic structure, extent of recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. To our knowledge, this study is the first to do so for a dominant soil bacterium. Our results indicate that bacterial soil populations, similarly to those in other environments, are structured by gene flow discontinuities and exhibit distributional patterns consistent with both isolation by distance and isolation by environment. Thus, both dispersal limitation and local environments contribute to the divergence among closely related soil bacteria as observed in macroorganisms.},
}
@article {pmid31662077,
year = {2019},
author = {Madison, JD and Ouellette, SP and Schmidt, EL and Kerby, JL},
title = {Serratia marcescens shapes cutaneous bacterial communities and influences survival of an amphibian host.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1914},
pages = {20191833},
pmid = {31662077},
issn = {1471-2954},
support = {P20 GM103443/GM/NIGMS NIH HHS/United States ; },
mesh = {Amphibians/*microbiology ; Animals ; Chytridiomycota/physiology ; Microbiota ; Mycoses/microbiology ; Serratia marcescens/*physiology ; Skin/microbiology ; },
abstract = {Ongoing investigations into the interactions between microbial communities and their associated hosts are changing how emerging diseases are perceived and ameliorated. Of the numerous host-microbiome-disease systems of study, the emergence of chytridiomycosis (caused by Batrachochytrium dendrobatidis, hereafter Bd) has been implicated in ongoing declines and extinction events of amphibians worldwide. Interestingly, there has been differential survival among amphibians in resisting Bd infection and subsequent disease. One factor thought to contribute to this resistance is the host-associated cutaneous microbiota. This has raised the possibility of using genetically modified probiotics to restructure the host-associated microbiota for desired anti-fungal outcomes. Here, we use a previously described strain of Serratia marcescens (Sm) for the manipulation of amphibian cutaneous microbiota. Sm was genetically altered to have a dysfunctional pathway for the production of the extracellular metabolite prodigiosin. This genetically altered strain (Δpig) and the functional prodigiosin producing strain (wild-type, WT) were compared for their microbial community and anti-Bd effects both in vitro and in vivo. In vitro, Bd growth was significantly repressed in the presence of prodigiosin. In vivo, the inoculation of both Sm strains was shown to significantly influence amphibian microbiota diversity with the Δpig-Sm treatment showing increasing alpha diversity, and the WT-Sm having no temporal effect on diversity. Differences were also seen in host mortality with Δpig-Sm treatments exhibiting significantly decreased survival probability when compared with WT-Sm in the presence of Bd. These results are an important proof-of-concept for linking the use of genetically modified probiotic bacteria to host microbial community structure and disease outcomes, which in the future may provide a way to ameliorate disease and address critical frontiers in disease and microbial ecology.},
}
@article {pmid31660948,
year = {2019},
author = {Waters, JL and Ley, RE},
title = {The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health.},
journal = {BMC biology},
volume = {17},
number = {1},
pages = {83},
pmid = {31660948},
issn = {1741-7007},
support = {R01 DK093595/DK/NIDDK NIH HHS/United States ; },
mesh = {Clostridiales/genetics/*physiology ; *Gastrointestinal Microbiome ; Humans ; },
abstract = {The Christensenellaceae, a recently described family in the phylum Firmicutes, is emerging as an important player in human health. The relative abundance of Christensenellaceae in the human gut is inversely related to host body mass index (BMI) in different populations and multiple studies, making its relationship with BMI the most robust and reproducible link between the microbial ecology of the human gut and metabolic disease reported to date. The family is also related to a healthy status in a number of other different disease contexts, including obesity and inflammatory bowel disease. In addition, Christensenellaceae is highly heritable across multiple populations, although specific human genes underlying its heritability have so far been elusive. Further research into the microbial ecology and metabolism of these bacteria should reveal mechanistic underpinnings of their host-health associations and enable their development as therapeutics.},
}
@article {pmid31659049,
year = {2019},
author = {Gusareva, ES and Acerbi, E and Lau, KJX and Luhung, I and Premkrishnan, BNV and Kolundžija, S and Purbojati, RW and Wong, A and Houghton, JNI and Miller, D and Gaultier, NE and Heinle, CE and Clare, ME and Vettath, VK and Kee, C and Lim, SBY and Chénard, C and Phung, WJ and Kushwaha, KK and Nee, AP and Putra, A and Panicker, D and Yanqing, K and Hwee, YZ and Lohar, SR and Kuwata, M and Kim, HL and Yang, L and Uchida, A and Drautz-Moses, DI and Junqueira, ACM and Schuster, SC},
title = {Microbial communities in the tropical air ecosystem follow a precise diel cycle.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {46},
pages = {23299-23308},
pmid = {31659049},
issn = {1091-6490},
mesh = {*Air Microbiology ; Air Pollutants/analysis ; Circadian Rhythm ; Ecosystem ; Metagenome ; *Microbiota ; Models, Biological ; Singapore ; *Tropical Climate ; },
abstract = {The atmosphere is vastly underexplored as a habitable ecosystem for microbial organisms. In this study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases of data. Despite only 9 to 17% of the generated sequence data currently being assignable to taxa, the air harbored a microbial diversity that rivals the complexity of other planetary ecosystems. The airborne microbial organisms followed a clear diel cycle, possibly driven by environmental factors. Interday taxonomic diversity exceeded day-to-day and month-to-month variation. Environmental time series revealed the existence of a large core of microbial taxa that remained invariable over 13 mo, thereby underlining the long-term robustness of the airborne community structure. Unlike terrestrial or aquatic environments, where prokaryotes are prevalent, the tropical airborne biomass was dominated by DNA from eukaryotic phyla. Specific fungal and bacterial species were strongly correlated with temperature, humidity, and CO2 concentration, making them suitable biomarkers for studying the bioaerosol dynamics of the atmosphere.},
}
@article {pmid31657947,
year = {2019},
author = {Ilgrande, C and Defoirdt, T and Vlaeminck, SE and Boon, N and Clauwaert, P},
title = {Media Optimization, Strain Compatibility, and Low-Shear Modeled Microgravity Exposure of Synthetic Microbial Communities for Urine Nitrification in Regenerative Life-Support Systems.},
journal = {Astrobiology},
volume = {19},
number = {11},
pages = {1353-1362},
doi = {10.1089/ast.2018.1981},
pmid = {31657947},
issn = {1557-8070},
mesh = {Ammonia/metabolism ; Bioreactors/*microbiology ; *Ecological Systems, Closed ; Heterotrophic Processes ; Humans ; Hydrolysis ; Microbiota/*physiology ; Nitrates/metabolism ; Nitrification ; Oxidation-Reduction ; Space Flight/*instrumentation ; Urea/metabolism ; Urine/*chemistry ; Weightlessness ; },
abstract = {Urine is a major waste product of human metabolism and contains essential macro- and micronutrients to produce edible microorganisms and crops. Its biological conversion into a stable form can be obtained through urea hydrolysis, subsequent nitrification, and organics removal, to recover a nitrate-enriched stream, free of oxygen demand. In this study, the utilization of a microbial community for urine nitrification was optimized with the focus for space application. To assess the role of selected parameters that can impact ureolysis in urine, the activity of six ureolytic heterotrophs (Acidovorax delafieldii, Comamonas testosteroni, Cupriavidus necator, Delftia acidovorans, Pseudomonas fluorescens, and Vibrio campbellii) was tested at different salinities, urea, and amino acid concentrations. The interaction of the ureolytic heterotrophs with a nitrifying consortium (Nitrosomonas europaea ATCC 19718 and Nitrobacter winogradskyi ATCC 25931) was also tested. Lastly, microgravity was simulated in a clinostat utilizing hardware for in-flight experiments with active microbial cultures. The results indicate salt inhibition of the ureolysis at 30 mS cm[-1], while amino acid nitrogen inhibits ureolysis in a strain-dependent manner. The combination of the nitrifiers with C. necator and V. campbellii resulted in a complete halt of the urea hydrolysis process, while in the case of A. delafieldii incomplete nitrification was observed, and nitrite was not oxidized further to nitrate. Nitrate production was confirmed in all the other communities; however, the other heterotrophic strains most likely induced oxygen competition in the test setup, and nitrite accumulation was observed. Samples exposed to low-shear modeled microgravity through clinorotation behaved similarly to the static controls. Overall, nitrate production from urea was successfully demonstrated with synthetic microbial communities under terrestrial and simulated space gravity conditions, corroborating the application of this process in space.},
}
@article {pmid31656973,
year = {2020},
author = {Otto-Hanson, LK and Kinkel, LL},
title = {Densities and inhibitory phenotypes among indigenous Streptomyces spp. vary across native and agricultural habitats.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {694-705},
pmid = {31656973},
issn = {1432-184X},
support = {9977907//National Science Foundation/ ; 2006-35319-17445//U.S. Department of Agriculture/ ; },
mesh = {*Ecosystem ; Minnesota ; Phenotype ; Soil/*chemistry ; *Soil Microbiology ; Streptomyces/*physiology ; },
abstract = {Streptomyces spp. perform vital roles in natural and agricultural soil ecosystems including in decomposition and nutrient cycling, promotion of plant growth and fitness, and plant disease suppression. Streptomyces densities can vary across the landscape, and inhibitory phenotypes are often a result of selection mediated by microbial competitive interactions in soil communities. Diverse environmental factors, including those specific to habitat, are likely to determine microbial densities in the soil and the outcomes of microbial species interactions. Here, we characterized indigenous Streptomyces densities and inhibitory phenotypes from soil samples (n = 82) collected in 6 distinct habitats across the Cedar Creek Ecosystem Science Reserve (CCESR; agricultural, prairie, savanna, wetland, wet-woodland, and forest). Significant variation in Streptomyces density and the frequency of antagonistic Streptomyces were observed among habitats. There was also significant variation in soil chemical properties among habitats, including percent carbon, percent nitrogen, available phosphorus, extractable potassium, and pH. Density and frequency of antagonists were significantly correlated with one or more environmental parameters across all habitats, though relationships with some parameters differed among habitats. In addition, we found that habitat rather than spatial proximity was a better predictor of variation in Streptomyces density and inhibitory phenotypes. Moreover, habitats least conducive for Streptomyces growth and proliferation, as determined by population density, had increased frequencies of inhibitory phenotypes. Identifying environmental parameters that structure variation in density and frequency of antagonistic Streptomyces can provide insight for determining factors that mediate selection for inhibitory phenotypes across the landscape.},
}
@article {pmid31656023,
year = {2020},
author = {Farias, GC and Nunes, KG and Soares, MA and de Siqueira, KA and Lima, WC and Neves, ALR and de Lacerda, CF and Filho, EG},
title = {Dark septate endophytic fungi mitigate the effects of salt stress on cowpea plants.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {51},
number = {1},
pages = {243-253},
pmid = {31656023},
issn = {1678-4405},
mesh = {Ascomycota/*isolation &amp; purification ; Calcium/metabolism ; Chlorine/metabolism ; Endophytes/*isolation &amp; purification ; Mycorrhizae ; Myrtales/microbiology ; Photosynthesis ; Plant Leaves/metabolism ; Plant Roots/microbiology ; Plants/microbiology ; Potassium/metabolism ; Salinity ; *Salt Stress ; Sodium/metabolism ; Vigna/growth &amp; development/metabolism/*microbiology ; },
abstract = {The association of plant with microorganisms, such as dark septate endophytic fungi, has mitigated the harmful effects of chemical, physical, and biological agents on the host. The objective of this work was to evaluate the interaction of the dark septate endophytic fungi with cowpea plants under salt stress. Endophytic fungi were isolated from Vochysia divergens root system, and molecular identification of fungi was performed by sequencing the ITS region. We selected and identified Sordariomycetes sp1-B'2 and Melanconiella elegans-21W2 for their ability to infect V. divergens root in vitro with development of typical dark septate fungi structures. Cowpea plants-inoculated or not inoculated with Sordariomycetes sp1-B'2 and M. elegans 21W2-were cultivated in 5-L pots under greenhouse conditions and submitted to four different electrical conductivities of irrigation water (1.2, 2.2, 3.6, and 5.0 dS m[-1]). The salinity caused decrease in leaf concentration of K and increased leaf concentration of calcium, sodium, and chlorine; and no influence of dark septate endophytic fungi was observed in these responses. On the other hand, root colonization with Sordariomycetes sp1-B'2 and M. elegans 21W2 resulted in improved nutrition with N and P in cowpea under salt stress, favoring the growth and rate of liquid photosynthesis. However, such positive responses were evident only at moderate levels of salinity.},
}
@article {pmid31655872,
year = {2020},
author = {Biedunkiewicz, A and Sucharzewska, E and Kulesza, K and Nowacka, K and Kubiak, D},
title = {Phyllosphere of Submerged Plants in Bathing Lakes as a Reservoir of Fungi-Potential Human Pathogens.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {552-561},
pmid = {31655872},
issn = {1432-184X},
support = {12.610.009-300//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; },
mesh = {Environmental Monitoring ; Lakes/*microbiology ; Plant Leaves/*microbiology ; Poland ; Yeasts/*isolation &amp; purification ; },
abstract = {This study analysed whether the littoral zone in the immediate vicinity of bathing sites retains potentially pathogenic yeasts on the phyllosphere surface and to what extent the species composition of microfungi in the phyllosphere and in surface waters is similar. The research was carried out in selected lakes located within the administrative boundaries of the city of Olsztyn, the largest city in the Masurian Lake District (NE Poland). The experiment was conducted in three summer seasons near bathing sites in three lakes, which are the most popular as recreational sites (Lake Kortowskie, Lake Tyrsko, and Lake Skanda). Microfungi isolated from the phyllosphere of 13 plant species of the littoral zone from dropped leaves of coast plants with no disease symptoms were used as the study material. The isolated fungi were identified in accordance with the accepted diagnostic procedures applied in mycological laboratories. A total of 36 yeast species of 16 genera were identified. Fungi found earlier at the bathing sites of the lakes were identified in 60% of the cases. Nine species were categorised as class BSL-2 fungi. This study provides a valuable complement of data concerning the natural composition of the littoral microbiota.},
}
@article {pmid31654911,
year = {2019},
author = {Masteling, R and Lombard, L and de Boer, W and Raaijmakers, JM and Dini-Andreote, F},
title = {Harnessing the microbiome to control plant parasitic weeds.},
journal = {Current opinion in microbiology},
volume = {49},
number = {},
pages = {26-33},
pmid = {31654911},
issn = {1879-0364},
mesh = {Crops, Agricultural ; Host Microbial Interactions ; Microbial Interactions ; *Microbiota ; Plant Diseases/*parasitology ; Plant Roots/*microbiology/physiology ; Plant Weeds/*microbiology ; Signal Transduction ; *Soil Microbiology ; },
abstract = {Microbiomes can significantly expand the genomic potential of plants, contributing to nutrient acquisition, plant growth promotion and tolerance to (a)biotic stresses. Among biotic stressors, root parasitic weeds (RPWs), mainly of the genera Orobanche, Phelipanche and Striga, are major yield-limiting factors of a wide range of staple crops, particularly in developing countries. Here, we provide a conceptual synthesis of putative mechanisms by which soil and plant microbiomes could be harnessed to control RPWs. These mechanisms are partitioned in direct and indirect modes of action and discussed in the context of past and present studies on microbe-mediated suppression of RPWs. Specific emphasis is given to the large but yet unexplored potential of root-associated microorganisms to interfere with the chemical signalling cascade between the host plant and the RPWs. We further provide concepts and ideas for future research directions and prospective designs of novel control strategies.},
}
@article {pmid31654107,
year = {2020},
author = {Reyns, W and Rineau, F and Spaak, JW and Franken, O and Berg, MP and Van Der Plas, F and Bardgett, RD and Beenaerts, N and De Laender, F},
title = {Food Web Uncertainties Influence Predictions of Climate Change Effects on Soil Carbon Sequestration in Heathlands.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {686-693},
pmid = {31654107},
issn = {1432-184X},
support = {BOF15DOCNA02//Bijzonder Onderzoeksfonds/ ; },
mesh = {*Carbon Cycle ; *Carbon Sequestration ; *Climate Change ; *Ecosystem ; Food Chain ; Models, Biological ; Soil/*chemistry ; Soil Microbiology ; },
abstract = {Carbon cycling models consider soil carbon sequestration a key process for climate change mitigation. However, these models mostly focus on abiotic soil processes and, despite its recognized critical mechanistic role, do not explicitly include interacting soil organisms. Here, we use a literature study to show that even a relatively simple soil community (heathland soils) contains large uncertainties in temporal and spatial food web structure. Next, we used a Lotka-Volterra-based food web model to demonstrate that, due to these uncertainties, climate change can either increase or decrease soil carbon sequestration to varying extents. Both the strength and direction of changes strongly depend on (1) the main consumer's (enchytraeid worms) feeding preferences and (2) whether decomposers (fungi) or enchytraeid worms are more sensitive to stress. Hence, even for a soil community with a few dominant functional groups and a simulation model with a few parameters, filling these knowledge gaps is a critical first step towards the explicit integration of soil food web dynamics into carbon cycling models in order to better assess the role soils play in climate change mitigation.},
}
@article {pmid31654106,
year = {2020},
author = {Schappe, T and Albornoz, FE and Turner, BL and Jones, FA},
title = {Co-occurring Fungal Functional Groups Respond Differently to Tree Neighborhoods and Soil Properties Across Three Tropical Rainforests in Panama.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {675-685},
pmid = {31654106},
issn = {1432-184X},
support = {DEB 1542681//National Science Foundation/ ; NA//Smithsonian Tropical Research Institute/ ; },
mesh = {Fungi/*physiology ; Mycorrhizae/physiology ; Panama ; *Rainforest ; Soil/*chemistry ; *Soil Microbiology ; Trees/*growth &amp; development ; },
abstract = {Abiotic and biotic drivers of co-occurring fungal functional guilds across regional-scale environmental gradients remain poorly understood. We characterized fungal communities using Illumina sequencing from soil cores collected across three Neotropical rainforests in Panama that vary in soil properties and plant community composition. We classified each fungal OTU into different functional guilds, namely plant pathogens, saprotrophs, arbuscular mycorrhizal (AM), or ectomycorrhizal (ECM). We measured soil properties and nutrients within each core and determined the tree community composition and richness around each sampling core. Canonical correspondence analyses showed that soil pH and moisture were shared potential drivers of fungal communities for all guilds. However, partial the Mantel tests showed different strength of responses of fungal guilds to composition of trees and soils. Plant pathogens and saprotrophs were more strongly correlated with soil properties than with tree composition; ECM fungi showed a stronger correlation with tree composition than with soil properties; and AM fungi were correlated with soil properties, but not with trees. In conclusion, we show that co-occurring fungal guilds respond differently to abiotic and biotic environmental factors, depending on their ecological function. This highlights the joint role that abiotic and biotic factors play in determining composition of fungal communities, including those associated with plant hosts.},
}
@article {pmid31653831,
year = {2019},
author = {Sonner, JK and Keil, M and Falk-Paulsen, M and Mishra, N and Rehman, A and Kramer, M and Deumelandt, K and Röwe, J and Sanghvi, K and Wolf, L and von Landenberg, A and Wolff, H and Bharti, R and Oezen, I and Lanz, TV and Wanke, F and Tang, Y and Brandao, I and Mohapatra, SR and Epping, L and Grill, A and Röth, R and Niesler, B and Meuth, SG and Opitz, CA and Okun, JG and Reinhardt, C and Kurschus, FC and Wick, W and Bode, HB and Rosenstiel, P and Platten, M},
title = {Dietary tryptophan links encephalogenicity of autoreactive T cells with gut microbial ecology.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4877},
pmid = {31653831},
issn = {2041-1723},
mesh = {Animals ; Autoimmunity/*immunology ; *Diet ; Dietary Proteins ; Disease Models, Animal ; Encephalomyelitis, Autoimmune, Experimental/*immunology/microbiology ; Gastrointestinal Microbiome/genetics/*immunology ; Mice ; Multiple Sclerosis ; RNA, Ribosomal, 16S/genetics ; T-Lymphocytes/*immunology ; *Tryptophan ; },
abstract = {The interaction between the mammalian host and its resident gut microbiota is known to license adaptive immune responses. Nutritional constituents strongly influence composition and functional properties of the intestinal microbial communities. Here, we report that omission of a single essential amino acid - tryptophan - from the diet abrogates CNS autoimmunity in a mouse model of multiple sclerosis. Dietary tryptophan restriction results in impaired encephalitogenic T cell responses and is accompanied by a mild intestinal inflammatory response and a profound phenotypic shift of gut microbiota. Protective effects of dietary tryptophan restriction are abrogated in germ-free mice, but are independent of canonical host sensors of intracellular tryptophan metabolites. We conclude that dietary tryptophan restriction alters metabolic properties of gut microbiota, which in turn have an impact on encephalitogenic T cell responses. This link between gut microbiota, dietary tryptophan and adaptive immunity may help to develop therapeutic strategies for protection from autoimmune neuroinflammation.},
}
@article {pmid31653789,
year = {2019},
author = {Kleyer, H and Tecon, R and Or, D},
title = {Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media.},
journal = {Applied and environmental microbiology},
volume = {86},
number = {1},
pages = {},
pmid = {31653789},
issn = {1098-5336},
support = {320499/ERC_/European Research Council/International ; },
mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Metagenomics ; Microbial Interactions ; Microbiota/*genetics ; Phylogeny ; Porosity ; RNA, Ribosomal, 16S ; Soil/chemistry ; *Soil Microbiology ; Water ; },
abstract = {The complexity of natural soils presents a challenge to the systematic identification and disentanglement of governing processes that shape natural bacterial communities. Studies have highlighted the critical role of the soil aqueous phase in shaping interactions among soil bacterial communities. To quantify and improve the attributability of soil aqueous-phase effects, we introduced a synthetic and traceable bacterial community to simple porous microcosms and subjected the community to constant or dynamic hydration conditions. The results were expressed in terms of absolute abundance and show species-specific responses to hydration and nutrient conditions. Hydration dynamics exerted a significant influence on the fraction of less-abundant species, especially after extended incubation periods. Phylogenetic relationships did not explain the group of most abundant species. The ability to quantify species-level dynamics in a bacterial community offers an important step toward deciphering the links between community composition and functions in dynamic terrestrial environments.IMPORTANCE The composition and activity of soil bacteria are central to various ecosystem services and soil biogeochemical cycles. A key factor for soil bacterial activity is soil hydration, which is in a constant state of change due to rainfall, drainage, plant water uptake, and evaporation. These dynamic changes in soil hydration state affect the structure and function of soil bacterial communities in complex ways often unobservable in natural soil. We designed an experimental system that retains the salient features of hydrated soil yet enables systematic evaluation of changes in a representative bacterial community in response to cycles of wetting and drying. The study shows that hydration cycles affect community abundance, yet most changes in composition occur with the less-abundant species (while the successful ones remain dominant). This research offers a new path for an improved understanding of bacterial community assembly in natural environments, including bacterial growth, maintenance, and death, with a special focus on the role of hydrological factors.},
}
@article {pmid31650676,
year = {2020},
author = {Bennett, JA and Koch, AM and Forsythe, J and Johnson, NC and Tilman, D and Klironomos, J},
title = {Resistance of soil biota and plant growth to disturbance increases with plant diversity.},
journal = {Ecology letters},
volume = {23},
number = {1},
pages = {119-128},
doi = {10.1111/ele.13408},
pmid = {31650676},
issn = {1461-0248},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Biota ; *Ecosystem ; Plants ; *Soil ; Soil Microbiology ; },
abstract = {Plant diversity is critical to the functioning of ecosystems, potentially mediated in part by interactions with soil biota. Here, we characterised multiple groups of soil biota across a plant diversity gradient in a long-term experiment. We then subjected soil samples taken along this gradient to drought, freezing and a mechanical disturbance to test how plant diversity affects the responses of soil biota and growth of a focal plant to these disturbances. High plant diversity resulted in soils that were dominated by fungi and associated soil biota, including increased arbuscular mycorrhizal fungi and reduced plant-feeding nematodes. Disturbance effects on the soil biota were reduced when plant diversity was high, resulting in higher growth of the focal plant in all but the frozen soils. These results highlight the importance of plant diversity for soil communities and their resistance to disturbance, with potential feedback effects on plant productivity.},
}
@article {pmid31649246,
year = {2019},
author = {Wagg, C and Schlaeppi, K and Banerjee, S and Kuramae, EE and van der Heijden, MGA},
title = {Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4841},
pmid = {31649246},
issn = {2041-1723},
mesh = {*Bacteria ; *Biodiversity ; Ecology ; *Ecosystem ; *Fungi ; *Grassland ; Microbial Consortia ; *Microbiota ; *Soil Microbiology ; },
abstract = {The soil microbiome is highly diverse and comprises up to one quarter of Earth's diversity. Yet, how such a diverse and functionally complex microbiome influences ecosystem functioning remains unclear. Here we manipulated the soil microbiome in experimental grassland ecosystems and observed that microbiome diversity and microbial network complexity positively influenced multiple ecosystem functions related to nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed microbial networks and reduced microbial richness had the lowest multifunctionality due to fewer taxa present that support the same function (redundancy) and lower diversity of taxa that support different functions (reduced functional uniqueness). Moreover, different microbial taxa explained different ecosystem functions pointing to the significance of functional diversity in microbial communities. These findings indicate the importance of microbial interactions within and among fungal and bacterial communities for enhancing ecosystem performance and demonstrate that the extinction of complex ecological associations belowground can impair ecosystem functioning.},
}
@article {pmid31648128,
year = {2020},
author = {Tortosa, G and Torralbo, F and Maza-Márquez, P and Aranda, E and Calvo, C and González-Murua, C and Bedmar, EJ},
title = {Assessment of the diversity and abundance of the total and active fungal population and its correlation with humification during two-phase olive mill waste (''alperujo") composting.},
journal = {Bioresource technology},
volume = {295},
number = {},
pages = {122267},
doi = {10.1016/j.biortech.2019.122267},
pmid = {31648128},
issn = {1873-2976},
mesh = {*Ascomycota ; *Basidiomycota ; *Composting ; *Olea ; Soil ; },
abstract = {Metagenomic and transcriptomic techniques applied to composting could increase our understanding of the overall microbial ecology and could help us to optimise operational conditions which are directly related with economic interest. In this study, the fungal diversity and abundance of two-phase olive mill waste ("alperujo") composting was studied using Illumina MiSeq sequencing and quantitative PCR, respectively. The results showed an increase of the fungal diversity during the process, with Ascomycota being the predominant phylum. Penicillium was the main genera identified at the mesophilic and maturation phases, with Debaryomyces and Sarocladium at the thermophilic phase, respectively. The fungal abundance was increased during composting, which confirms their important role during thermophilic and maturation phases. Some Basidiomycota showed an increased during the process, which showed a positive correlation with the humification parameters. According to that, the genus Cystofilobasidium could be used as a potential fungal biomarker to assess alperujo compost maturation.},
}
@article {pmid31642982,
year = {2019},
author = {Landberg, R and Manach, C and Kerckhof, FM and Minihane, AM and Saleh, RNM and De Roos, B and Tomas-Barberan, F and Morand, C and Van de Wiele, T},
title = {Future prospects for dissecting inter-individual variability in the absorption, distribution and elimination of plant bioactives of relevance for cardiometabolic endpoints.},
journal = {European journal of nutrition},
volume = {58},
number = {Suppl 2},
pages = {21-36},
pmid = {31642982},
issn = {1436-6215},
support = {FA1403//EU - COST Action FA-1403 (2014-2018)/ ; },
mesh = {Biological Variation, Population/*physiology ; Cardiovascular System/*metabolism ; Diet, Vegetarian/*methods/trends ; Humans ; Metabolomics/*methods ; Phytochemicals/administration &amp; dosage/*pharmacokinetics ; Plants, Edible/*metabolism ; },
abstract = {PURPOSE: The health-promoting potential of food-derived plant bioactive compounds is evident but not always consistent across studies. Large inter-individual variability may originate from differences in digestion, absorption, distribution, metabolism and excretion (ADME). ADME can be modulated by age, sex, dietary habits, microbiome composition, genetic variation, drug exposure and many other factors. Within the recent COST Action POSITIVe, large-scale literature surveys were undertaken to identify the reasons and extent of inter-individual variability in ADME of selected plant bioactive compounds of importance to cardiometabolic health. The aim of the present review is to summarize the findings and suggest a framework for future studies designed to investigate the etiology of inter-individual variability in plant bioactive ADME and bioefficacy.<br><br>RESULTS: Few studies have reported individual data on the ADME of bioactive compounds and on determinants such as age, diet, lifestyle, health status and medication, thereby limiting a mechanistic understanding of the main drivers of variation in ADME processes observed across individuals. Metabolomics represent crucial techniques to decipher inter-individual variability and to stratify individuals according to metabotypes reflecting the intrinsic capacity to absorb and metabolize bioactive compounds.<br><br>CONCLUSION: A methodological framework was developed to decipher how the contribution from genetic variants or microbiome variants to ADME of bioactive compounds can be predicted. Future study design should include (1) a larger number of study participants, (2) individual and full profiling of all possible determinants of internal exposure, (3) the presentation of individual ADME data and (4) incorporation of omics platforms, such as genomics, microbiomics and metabolomics in ADME and efficacy studies.},
}
@article {pmid31642672,
year = {2019},
author = {Yuan, Y and Zheng, Y and Zhou, J and Geng, Y and Zou, P and Li, Y and Zhang, C},
title = {Polyphenol-Rich Extracts from Brown Macroalgae Lessonia trabeculate Attenuate Hyperglycemia and Modulate Gut Microbiota in High-Fat Diet and Streptozotocin-Induced Diabetic Rats.},
journal = {Journal of agricultural and food chemistry},
volume = {67},
number = {45},
pages = {12472-12480},
doi = {10.1021/acs.jafc.9b05118},
pmid = {31642672},
issn = {1520-5118},
mesh = {Animals ; Blood Glucose/metabolism ; Diabetes Mellitus, Experimental/*drug therapy/metabolism/microbiology ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hyperglycemia/*drug therapy/metabolism/microbiology ; Hypoglycemic Agents/*administration &amp; dosage ; Male ; Mice, Inbred C57BL ; Phaeophyceae/*chemistry ; Plant Extracts/*administration &amp; dosage ; Polyphenols/*administration &amp; dosage ; Rats ; Seaweed/*chemistry ; Streptozocin/adverse effects ; },
abstract = {Brown macroalgae are an important source of polyphenols with multiple health functions. In this work, polyphenol extracts from Lessonia trabeculate were purified and investigated for the antidiabetic activity in vitro and in vivo. The purified polyphenol extracts exhibited good antioxidant activities, α-glucosidase and lipase inhibition activities (IC50 < 0.25 mg/mL). The HPLC-DAD-ESI-MS/MS analysis indicated that the compounds in polyphenol extracts were mainly phlorotannin derivatives, phenolic acid derivatives, and gallocatechin derivatives. In vivo, C57BL/6J rats treated with polyphenol extracts for 4 weeks had lower fasting blood glucose levels, insulin levels, as well as better serum lipid profiles and antioxidant stress parameters, compared with the diabetic control (DC) group. Histopathology revealed that polyphenol extracts preserved the architecture and function of the liver. Short-chain fatty acid contents in rats' fecal samples with polyphenols administration were significantly recovered as compared with the DC group. Furthermore, the gut microflora of rats was investigated with high-throughput 16S rRNA gene sequencing and results indicated that polyphenol extracts had a positive effect on regulating the dysbiosis of the microbial ecology in diabetic rats. All of the results from the study provided a scientific reference of the potentially beneficial effects of L. trabeculate polyphenols on diabetes management.},
}
@article {pmid31642093,
year = {2019},
author = {Deepika, S and Mittal, A and Kothamasi, D},
title = {HCN-producing Pseudomonas protegens CHA0 affects intraradical viability of Rhizophagus irregularis in Sorghum vulgare roots.},
journal = {Journal of basic microbiology},
volume = {59},
number = {12},
pages = {1229-1237},
doi = {10.1002/jobm.201900364},
pmid = {31642093},
issn = {1521-4028},
mesh = {Biomass ; Glomeromycota/*physiology ; Hydrogen Cyanide/*metabolism ; *Microbial Interactions ; Mycorrhizae/*physiology ; Nutrients/metabolism ; Plant Growth Regulators/genetics/*metabolism ; Plant Roots/metabolism/microbiology ; Pseudomonas/genetics/*metabolism ; Rhizosphere ; Soil Microbiology ; Sorghum/metabolism/*microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria inhabit the plant rhizosphere. Both functional groups can influence plant community structures, and interactions between them can vary from being synergistic to antagonistic. HCN-producing Pseudomonas protegens CHA0 is a plant growth-promoting rhizobacterium. P. protegens CHA0 has been shown to weakly attach to AMF hyphae. Here, we analyze the effect of P. protegens CHA0 on the viability of intraradical AMF hyphae. Using pot experiments, we have grown mycorrhizal and nonmycorrhizal Sorghum vulgare var. M35 with P. protegens CHA0 or HCN[-] mutant P. protegens CHA77, which did not produce HCN. Mycorrhizal and nonmycorrhizal Sorghum grown without CHA0 or CHA77 served as the control. While metabolically active AMF was not detected in mycorrhizal plants grown with HCN[+] CHA0, the percentage of root colonization of metabolically active AMF in plants grown with HCN[-] CHA77 was lower than in the control. Root phosphorus was highest in mycorrhizal plants grown with HCN[+] CHA0, but root Fe was higher in plants grown with the bacterial strains. Our results indicate that HCN-producing P. protegens can affect the viability of intraradical AMF.},
}
@article {pmid31640813,
year = {2019},
author = {Chen, S and Waghmode, TR and Sun, R and Kuramae, EE and Hu, C and Liu, B},
title = {Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {136},
pmid = {31640813},
issn = {2049-2618},
mesh = {Agriculture/*methods ; Bacteria/classification/growth &amp; development ; Crops, Agricultural/microbiology ; Fertilizers/*microbiology ; Fungi/classification/growth &amp; development ; Microbiota/*physiology ; Mycobiome/physiology ; Plant Development/physiology ; Plant Roots/*microbiology ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; *Triticum/metabolism/microbiology ; },
abstract = {BACKGROUND: Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but also environmental problems, we lack a comprehensive understanding of how crops under elevated nutrient input shape root-associated microbial communities, especially through adjusting the quantities and compositions of root metabolites and exudates.<br><br>METHODS: The compositions of bacterial and fungal communities from the roots and rhizosphere of wheat (Triticum aestivum L.) under four levels of long-term&#xa0;inorganic nitrogen (N) fertilization were characterized at the tillering, jointing and ripening stages. The root-released organic carbon (ROC), organic acids in the root exudates and soil organic carbon (SOC) and soil active carbon (SAC) in the rhizosphere were quantified.<br><br>RESULTS: ROC levels varied dramatically across wheat&#xa0;growth stages and correlated&#xa0;more with the bacterial community than with the fungal community. Rhizosphere SOC and SAC levels were elevated by long-term N fertilization but varied only slightly across growth stages. Variation in the microbial community structure across plant growth stages showed a decreasing trend with N fertilization level in the rhizosphere. In addition, more bacterial and fungal genera were significantly correlated in the jointing and ripening stages than in the tillering stage in the root samples. A number of bacterial genera that shifted in response to N fertilization, including Arthrobacter, Bacillus and Devosia, correlated&#xa0;significantly with acetic acid, oxalic acid, succinic acid and tartaric acid levels.<br><br>CONCLUSIONS: Our results indicate that both plant growth status and N input drive changes in the microbial community structure in the root zone of wheat. Plant growth stage&#xa0;demostrated a stronger&#xa0;influence on bacterial than on fungal community composition. A number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded&#xa0;positively to N fertilization, and their abundance correlated&#xa0;significantly with the organic acid level, suggesting that the secretion of organic acids may be a strategy developed by plants to recruit beneficial microbes in the root zone to cope with high N input. These results provide novel insight into the associations among increased N input, altered carbon availability, and shifts in microbial communities in the plant roots and rhizosphere of intensive agricultural ecosystems.},
}
@article {pmid31640783,
year = {2019},
author = {Chen, W and Ren, K and Isabwe, A and Chen, H and Liu, M and Yang, J},
title = {Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {138},
pmid = {31640783},
issn = {2049-2618},
mesh = {*Biodiversity ; China ; Ecosystem ; Environmental Monitoring ; High-Throughput Nucleotide Sequencing/methods ; *Plankton/classification/microbiology ; Rivers/*microbiology ; *Seasons ; Stochastic Processes ; *Water Microbiology ; },
abstract = {BACKGROUND: The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes in shaping riverine microeukaryotic biogeography is still poorly understood. Here, we compared the spatiotemporal and biogeographical patterns of microeukaryotic community using high-throughput sequencing of 18S rRNA gene and multivariate statistical analyses from a subtropical river during wet and dry seasons.<br><br>RESULTS: Our results provide the first description of biogeographical patterns of microeukaryotic communities in the Tingjiang River, the largest river in the west of Fujian province, southeastern China. The results showed that microeukaryotes from both wet and dry seasons exhibited contrasting community compositions, which might be owing to planktonic microeukaryotes having seasonal succession patterns. Further, all components of the microeukaryotic communities (including total, dominant, always rare, and conditionally rare taxa) exhibited a significant distance-decay pattern in both seasons, and these communities had a stronger distance-decay relationship during the dry season, especially for the conditionally rare taxa. Although several variables had a significant influence on the microeukaryotic communities, the environmental and spatial factors showed minor roles in shaping the communities. Importantly, these microeukaryotic communities were strongly driven by stochastic processes, with 89.9%, 88.5%, and 89.6% of the community variation explained by neutral community model during wet, dry, and both seasons, respectively. The neutral community model also explained a large fraction of the community variation across different taxonomic groups and levels. Additionally, the microeukaryotic taxa, which were above and below the neutral prediction, were ecologically and taxonomically distinct groups, which might be interactively structured by deterministic and stochastic processes.<br><br>CONCLUSIONS: This study demonstrated that stochastic processes are sufficient in shaping substantial variation in river microeukaryotic metacommunity across different hydrographic regimes, thereby providing a better understanding of spatiotemporal patterns, processes, and mechanisms of microeukaryotic community in waters.},
}
@article {pmid31640497,
year = {2019},
author = {Brunner, JD and Chia, N},
title = {Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species-species modelling.},
journal = {Journal of the Royal Society, Interface},
volume = {16},
number = {159},
pages = {20190423},
pmid = {31640497},
issn = {1742-5662},
support = {R01 CA179243/CA/NCI NIH HHS/United States ; },
mesh = {Gastrointestinal Microbiome/*physiology ; *Models, Biological ; Species Specificity ; },
abstract = {Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behaviour of microbial communities. We seek a modelling strategy that can capture emergent behaviour when built from sets of universal individual interactions. Our investigation reveals that species-metabolite interaction (SMI) modelling is better able to capture emergent behaviour in community composition dynamics than direct species-species modelling. Using publicly available data, we examine the ability of species-species models and species-metabolite models to predict trio growth experiments from the outcomes of pair growth experiments. We compare quadratic species-species interaction models and quadratic SMI models and conclude that only species-metabolite models have the necessary complexity to explain a wide variety of interdependent growth outcomes. We also show that general species-species interaction models cannot match the patterns observed in community growth dynamics, whereas species-metabolite models can. We conclude that species-metabolite modelling will be important in the development of accurate, clinically useful models of microbial communities.},
}
@article {pmid31640295,
year = {2019},
author = {Giuliani, C and Marzorati, M and Daghio, M and Franzetti, A and Innocenti, M and Van de Wiele, T and Mulinacci, N},
title = {Effects of Olive and Pomegranate By-Products on Human Microbiota: A Study Using the SHIME[®] in Vitro Simulator.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {20},
pages = {},
pmid = {31640295},
issn = {1420-3049},
support = {DD6107/2013//Tuscany Region/ ; CRF 2016.959//Foundation CR of Florence/ ; },
mesh = {Ammonium Compounds/metabolism ; Bifidobacterium/classification/drug effects/isolation &amp; purification ; DNA, Bacterial/analysis ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Humans ; Lactobacillaceae/classification/drug effects/isolation &amp; purification ; Olea/*chemistry ; Phenols/*administration &amp; dosage/chemistry/pharmacology ; Phylogeny ; Polysaccharides/*administration &amp; dosage/chemistry/pharmacology ; Pomegranate/*chemistry ; },
abstract = {Two by-products containing phenols and polysaccharides, a "pâté" (OP) from the extra virgin olive oil milling process and a decoction of pomegranate mesocarp (PM), were investigated for their effects on human microbiota using the SHIME[®] system. The ability of these products to modulate the microbial community was studied simulating a daily intake for nine days. Microbial functionality, investigated in terms of short chain fatty acids (SCFA) and NH4[+], was stable during the treatment. A significant increase in Lactobacillaceae and Bifidobacteriaceae at nine days was induced by OP mainly in the proximal tract. Polyphenol metabolism indicated the formation of tyrosol from OP mainly in the distal tract, while urolithins C and A were produced from PM, identifying the human donor as a metabotype A. The results confirm the SHIME[®] system as a suitable in vitro tool to preliminarily investigate interactions between complex botanicals and human microbiota before undertaking more challenging human studies.},
}
@article {pmid31637799,
year = {2020},
author = {Dedysh, SN and Henke, P and Ivanova, AA and Kulichevskaya, IS and Philippov, DA and Meier-Kolthoff, JP and Göker, M and Huang, S and Overmann, J},
title = {100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii.},
journal = {Environmental microbiology},
volume = {22},
number = {1},
pages = {198-211},
doi = {10.1111/1462-2920.14838},
pmid = {31637799},
issn = {1462-2920},
support = {16-04-00290//Russian Foundation for Basic Research/International ; },
mesh = {Genomics ; High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence ; Lakes/microbiology ; Metabolic Networks and Pathways/genetics ; Metagenome ; Phylogeny ; Phylogeography ; Planctomycetales/*classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The first representative of the phylum Planctomycetes, Planctomyces bekefii, was described nearly one century ago. This morphologically conspicuous freshwater bacterium is a rare example of as-yet-uncultivated prokaryotes with validly published names and unknown identity. We report the results of molecular identification of this elusive bacterium, which was detected in a eutrophic boreal lake in Northern Russia. By using high-performance cell sorting, P. bekefii-like cell rosettes were selectively enriched from lake water. The retrieved 16S rRNA gene sequence was nearly identical to those in dozens of metagenomes assembled from freshwater lakes during cyanobacterial blooms and was phylogenetically placed within a large group of environmental sequences originating from various freshwater habitats worldwide. In contrast, 16S rRNA gene sequence similarity to all currently described members of the order Planctomycetales was only 83%-92%. The metagenome assembled for P. bekefii reached 43% genome coverage and showed the potential for degradation of peptides, pectins, and sulfated polysaccharides. Tracing the seasonal dynamics of P. bekefii by Illumina paired-end sequencing of 16S rRNA gene fragments and by fluorescence in situ hybridization revealed that these bacteria only transiently surpass the detection limit, with a characteristic population peak of up to 10[4] cells ml[-1] following cyanobacterial blooms.},
}
@article {pmid31637492,
year = {2019},
author = {Zhu, X and Wang, J and De Belie, N and Boon, N},
title = {Complementing urea hydrolysis and nitrate reduction for improved microbially induced calcium carbonate precipitation.},
journal = {Applied microbiology and biotechnology},
volume = {103},
number = {21-22},
pages = {8825-8838},
doi = {10.1007/s00253-019-10128-2},
pmid = {31637492},
issn = {1432-0614},
support = {File No. 201706140108//Distinguished International Students Scholarship/ ; reference code: 01SC4918//Universiteit Gent/ ; },
mesh = {Calcium Carbonate/*metabolism ; Chemical Precipitation ; Construction Materials/microbiology ; Cupriavidus necator/enzymology/*metabolism ; Hydrolysis ; Nitrates/*metabolism ; Urea/*metabolism ; },
abstract = {Microbial-induced CaCO3 precipitation has been widely applied in bacterial-based self-healing concrete. However, the limited biogenetic CaCO3 production by bacteria after they were introduced into the incompatible concrete matrix is a major challenge of this technology. In the present study, the potential of combining two metabolic pathways, urea hydrolysis and nitrate reduction, simultaneously in one bacteria strain for improving the bacterial CaCO3 yield has been investigated. One bacterial strain, Ralstonia eutropha H16, which has the highest Ca[2+] tolerance and is capable of performing both urea hydrolysis and nitrate reduction in combined media was selected among three bacterial candidates based on the enzymatic examinations. Results showed that H16 does not need oxygen for urea hydrolysis and urease activity was determined primarily by cell concentration. However, the additional urea in the combined medium slowed down the nitrate reduction rate to 7 days until full NO3[-] decomposition. Moreover, the nitrate reduction of H16 was significantly restricted by an increased Ca[2+] ion concentration in the media. Nevertheless, the overall CaCO3 precipitation yield can be improved by 20 to 30% after optimization through the combination of two metabolic pathways. The highest total CaCO3 precipitation yield achieved in an orthogonal experiment was 14 g/L. It can be concluded that Ralstonia eutropha H16 is a suitable bacterium for simultaneous activation of urea hydrolysis and nitrate reduction for improving the CaCO3 precipitation and it can be studied later, on activation of multiple metabolic pathways in bacteria-based self-healing concrete.},
}
@article {pmid31637468,
year = {2019},
author = {de Roos, B and Aura, AM and Bronze, M and Cassidy, A and Conesa, MG and Gibney, ER and Greyling, A and Kaput, J and Kerem, Z and Knežević, N and Kroon, P and Landberg, R and Manach, C and Milenkovic, D and Rodriguez-Mateos, A and Tomás-Barberán, FA and van de Wiele, T and Morand, C},
title = {Targeting the delivery of dietary plant bioactives to those who would benefit most: from science to practical applications.},
journal = {European journal of nutrition},
volume = {58},
number = {Suppl 2},
pages = {65-73},
pmid = {31637468},
issn = {1436-6215},
support = {FA 1403//European Cooperation in Science and Technology/ ; },
mesh = {Cardiovascular Diseases/*prevention &amp; control ; Diet, Vegetarian/*methods ; Health Promotion/*methods ; Humans ; Metabolic Diseases/*prevention &amp; control ; Phytochemicals/*administration &amp; dosage ; },
abstract = {BACKGROUND: A healthy diet and optimal lifestyle choices are amongst the most important actions for the prevention of cardiometabolic diseases. Despite this, it appears difficult to convince consumers to select more nutritious foods. Furthermore, the development and production of healthier foods do not always lead to economic profits for the agro-food sector. Most dietary recommendations for the general population represent a "one-size-fits-all approach" which does not necessarily ensure that everyone has adequate exposure to health-promoting constituents of foods. Indeed, we now know that individuals show a high variability in responses when exposed to specific nutrients, foods, or diets.<br><br>PURPOSE: This review aims to highlight our current understanding of inter-individual variability in response to dietary bioactives, based on the integration of findings of the COST Action POSITIVe. We also evaluate opportunities for translation of scientific knowledge on inter-individual variability in response to dietary bioactives, once it becomes available, into practical applications for stakeholders, such as the agro-food industry. The potential impact from such applications will form an important impetus for the food industry to develop and market new high quality and healthy foods for specific groups of consumers in the future. This may contribute to a decrease in the burden of diet-related chronic diseases.},
}
@article {pmid31635887,
year = {2019},
author = {Čanković, M and Žučko, J and Radić, ID and Janeković, I and Petrić, I and Ciglenečki, I and Collins, G},
title = {Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake.},
journal = {Systematic and applied microbiology},
volume = {42},
number = {6},
pages = {126016},
doi = {10.1016/j.syapm.2019.126016},
pmid = {31635887},
issn = {1618-0984},
mesh = {Archaea/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Biodiversity ; Climate Change ; Databases, Chemical ; Ireland ; Lakes/chemistry/*microbiology ; *Microbiota/genetics ; Oxygen/analysis/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seasons ; Water Microbiology ; },
abstract = {Hypoxic and anoxic niches of meromictic lakes are important sites for studying the microbial ecology of conditions resembling ancient Earth. The expansion and increasing global distribution of such environments also means that information about them serves to understand future phenomena. In this study, a long-term chemical dataset (1996-2015) was explored together with seasonal (in 2015) information on the diversity and abundance of bacterial and archaeal communities residing in the chemocline, monimolimnion and surface sediment of the marine meromictic Rogoznica Lake. The results of quantitative PCR assays, and high-throughput sequencing, targeting 16S rRNA genes and transcripts, revealed a clear vertical structure of the microbial community with Gammaproteobacteria (Halochromatium) and cyanobacteria (Synechococcus spp.) dominating the chemocline, Deltaproteobacteria and Bacteroidetes dominating the monimolimnion, and significantly more abundant archaeal populations in the surface sediment, most of which affiliated to Nanoarchaeota. Seasonal changes in the community structure and abundance were not pronounced. Diversity in Rogoznica Lake was found to be high, presumably as a consequence of stable environmental conditions accompanied by high dissolved carbon and nutrient concentrations. Long-term data indicated that Rogoznica Lake exhibited climate changes that could alter its physico-chemical features and, consequently, induce structural and physiological changes within its microbial community.},
}
@article {pmid31633390,
year = {2019},
author = {Baker, JL and He, X and Shi, W},
title = {Precision Reengineering of the Oral Microbiome for Caries Management.},
journal = {Advances in dental research},
volume = {30},
number = {2},
pages = {34-39},
pmid = {31633390},
issn = {1544-0737},
support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; },
mesh = {Biofilms ; *Dental Caries ; *Dental Plaque ; Humans ; *Microbiota ; Streptococcus mutans ; },
abstract = {Technological advancements have revolutionized our understanding of the complexity and importance of the human microbiome. This progress has also emphasized the need for precision therapeutics, as it has underscored the dilemmas, such as dysbiosis and increasing antibiotic resistance, associated with current, broad-spectrum treatment modalities. Dental caries remains the most common chronic disease worldwide, accompanied by a tremendous financial and social burden, despite widespread and efficacious fluoride and hygienic regimens. Over the past several decades, various precision approaches to combat dental caries, including vaccines, probiotics, and antimicrobial compounds, have been pursued. Despite the distinct overall conceptual strengths of each approach, for various reasons, there are currently no approved precision antibiotic therapeutics to prevent dental caries. Specifically targeted antimicrobial peptides (STAMPs) are synthetic molecules that combine the antibiotic moiety of a traditional antimicrobial peptide with a targeting domain to provide specificity against a particular organism. Conjoining the killing domain from the antimicrobial, novispirin G10, and a targeting domain derived from the Streptococcus mutans pheromone, CSP, the STAMP C16G2 was designed to provide targeted killing of S. mutans, widely considered the keystone species in dental caries pathogenesis. C16G2 was able to selectively eliminate S. mutans from complex ecosystems while leaving closely related, yet health-associated, oral species unharmed. This remodeling of the dental plaque community is expected to have significant advantages compared to conventional broad-spectrum mouthwashes, as the intact, surviving community is apt to prevent reinfection by pathogens. Following successful phase I clinical trials that evaluated the safety and basic microbiology of C16G2 treatments, the phase II trials of several C16G2 formulations are currently in progress. C16G2 represents an exciting advance in precision therapeutics, and the STAMP platform provides vast opportunities for both the development of additional therapeutics and the overall study of microbial ecology.},
}
@article {pmid31633060,
year = {2019},
author = {Krych, &#x141; and Castro-Mejía, JL and Forero-Junco, LM and Moesby, DN and Mikkelsen, MB and Rasmussen, MA and Sykulski, M and Nielsen, DS},
title = {DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq.},
journal = {Communications biology},
volume = {2},
number = {},
pages = {369},
pmid = {31633060},
issn = {2399-3642},
mesh = {Bacillus cereus/genetics ; *DNA, Bacterial ; High-Throughput Nucleotide Sequencing/economics/*methods ; Listeria monocytogenes/genetics ; Microbiological Techniques/economics/*methods ; Salmonella enterica/genetics ; Sequence Analysis, DNA/economics/*methods ; Species Specificity ; Time Factors ; },
abstract = {Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.},
}
@article {pmid31632370,
year = {2019},
author = {Mendes, LW and de Chaves, MG and Fonseca, MC and Mendes, R and Raaijmakers, JM and Tsai, SM},
title = {Resistance Breeding of Common Bean Shapes the Physiology of the Rhizosphere Microbiome.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2252},
pmid = {31632370},
issn = {1664-302X},
abstract = {The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher expression of genes associated with nitrogen, phosphorus and iron metabolism. The resistome analysis indicates higher expression of soxR, which is involved in protecting bacteria against oxidative stress induced by a pathogen invasion. These results further support our hypothesis that breeding for resistance has unintentionally shaped the assembly and activity of the rhizobacterial community toward a higher abundance of specific rhizosphere competent bacterial taxa that can provide complementary protection against fungal root infections.},
}
@article {pmid31630686,
year = {2019},
author = {Kavagutti, VS and Andrei, A&#x15e; and Mehrshad, M and Salcher, MM and Ghai, R},
title = {Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {135},
pmid = {31630686},
issn = {2049-2618},
mesh = {Actinobacteria/*virology ; Bacteriophages/genetics/*isolation &amp; purification ; Czech Republic ; Ecology ; Ecosystem ; Fresh Water/*microbiology ; Genome, Viral ; Metagenome/*genetics ; Metagenomics ; Phylogeny ; *Water Microbiology ; },
abstract = {The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small "miniphages" and large "megaphages" infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.},
}
@article {pmid31624348,
year = {2020},
author = {Gwak, JH and Jung, MY and Hong, H and Kim, JG and Quan, ZX and Reinfelder, JR and Spasov, E and Neufeld, JD and Wagner, M and Rhee, SK},
title = {Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants.},
journal = {The ISME journal},
volume = {14},
number = {2},
pages = {335-346},
pmid = {31624348},
issn = {1751-7370},
mesh = {Ammonia/metabolism ; Archaea/*growth &amp; development/metabolism ; Bacteria/growth &amp; development/metabolism ; *Copper ; *Nitrification ; Oxidation-Reduction ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification ; },
abstract = {Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.},
}
@article {pmid31624166,
year = {2019},
author = {Schultz, J and Kallies, R and Nunes da Rocha, U and Rosado, AS},
title = {Draft Genome Sequence of Geobacillus sp. Strain LEMMJ02, a Thermophile Isolated from Deception Island, an Active Volcano in Antarctica.},
journal = {Microbiology resource announcements},
volume = {8},
number = {42},
pages = {},
pmid = {31624166},
issn = {2576-098X},
abstract = {The thermophilic Geobacillus sp. strain LEMMJ02 was isolated from Fumarole Bay sediment on Deception Island, an active Antarctic volcano. Here, we report the draft genome of LEMMJ02, which consists of 3,160,938 bp with 52.8% GC content and 3,523 protein-coding genes.},
}
@article {pmid31623889,
year = {2019},
author = {Christiaens, MER and De Paepe, J and Ilgrande, C and De Vrieze, J and Barys, J and Teirlinck, P and Meerbergen, K and Lievens, B and Boon, N and Clauwaert, P and Vlaeminck, SE},
title = {Urine nitrification with a synthetic microbial community.},
journal = {Systematic and applied microbiology},
volume = {42},
number = {6},
pages = {126021},
doi = {10.1016/j.syapm.2019.126021},
pmid = {31623889},
issn = {1618-0984},
mesh = {Ammonia/metabolism ; Bioreactors/*microbiology ; Comamonadaceae/metabolism ; Delftia acidovorans/metabolism ; *Microbiota ; *Nitrification ; Nitrites/metabolism ; Nitrobacter/metabolism ; Nitrosomonas europaea/metabolism ; Pseudomonas fluorescens/metabolism ; Urea/metabolism ; Urine/*chemistry ; Waste Disposal, Fluid/*methods ; },
abstract = {During long-term extra-terrestrial missions, food is limited and waste is generated. By recycling valuable nutrients from this waste via regenerative life support systems, food can be produced in space. Astronauts' urine can, for instance, be nitrified by micro-organisms into a liquid nitrate fertilizer for plant growth in space. Due to stringent conditions in space, microbial communities need to be be defined (gnotobiotic); therefore, synthetic rather than mixed microbial communities are preferred. For urine nitrification, synthetic communities face challenges, such as from salinity, ureolysis, and organics. In this study, a synthetic microbial community containing an AOB (Nitrosomonas europaea), NOB (Nitrobacter winogradskyi), and three ureolytic heterotrophs (Pseudomonas fluorescens, Acidovorax delafieldii, and Delftia acidovorans) was compiled and evaluated for these challenges. In reactor 1, salt adaptation of the ammonium-fed AOB and NOB co-culture was possible up to 45mScm[-1], which resembled undiluted nitrified urine, while maintaining a 44±10mgNH4[+]-NL[-1]d[-1] removal rate. In reactor 2, the nitrifiers and ureolytic heterotrophs were fed with urine and achieved a 15±6mg NO3[-]-NL[-1]d[-1] production rate for 1% and 10% synthetic and fresh real urine, respectively. Batch activity tests with this community using fresh real urine even reached 29±3mgNL[-1]d[-1]. Organics removal in the reactor (69±15%) should be optimized to generate a nitrate fertilizer for future space applications.},
}
@article {pmid31623169,
year = {2019},
author = {García-Mantrana, I and Calatayud, M and Romo-Vaquero, M and Espín, JC and Selma, MV and Collado, MC},
title = {Urolithin Metabotypes Can Determine the Modulation of Gut Microbiota in Healthy Individuals by Tracking Walnuts Consumption over Three Days.},
journal = {Nutrients},
volume = {11},
number = {10},
pages = {},
pmid = {31623169},
issn = {2072-6643},
support = {RTI2018-097982-B-I00//Spanish Ministry of Science, Innovation and Universities (MICINN)/ ; ERC starting grant, n&#xb0; 639226/ERC_/European Research Council/International ; },
mesh = {Adult ; Bacteria/classification/genetics/*metabolism ; Biomarkers/urine ; Coumarins/*urine ; Fatty Acids/*metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Hydrolyzable Tannins/*metabolism ; Juglans/*metabolism ; Male ; Middle Aged ; Nuts/*metabolism ; Time Factors ; },
abstract = {Walnuts are rich in polyphenols ellagitannins, modulate gut microbiota (GM), and exert health benefits after long-term consumption. The metabolism of ellagitannins to urolithins via GM depends on urolithin metabotypes (UM-A, -B, or -0), which have been reported to predict host responsiveness to a polyphenol-rich intervention. This study aims to assess whether UMs were associated with differential GM modulation after short-term walnut consumption. In this study, 27 healthy individuals consumed 33 g of peeled raw walnuts over three days. GM profiling was determined using 16S rRNA illumina sequencing and specific real-time quantitative polymerase chain reactions (qPCRs), as well as microbial activity using short-chain fatty acids analysis in stool samples. UMs stratification of volunteers was assessed using ultra performance liquid chromatography-electro spray ionization-quadrupole time of flight-mass spectrometry (UPLC-ESI-QTOF-MS) analysis of urolithins in urine samples. The gut microbiota associated with UM-B was more sensitive to the walnut intervention. Blautia, Bifidobacterium, and members of the Coriobacteriaceae family, including Gordonibacter, increased exclusively in UM-B subjects, while some members of the Lachnospiraceae family decreased in UM-A individuals. Coprococcus and Collinsella increased in both UMs and higher acetate and propionate production resulted after walnuts intake. Our results show that walnuts consumption after only three days modulates GM in a urolithin metabotype-depending manner and increases the production of short-chain fatty acids (SCFA).},
}
@article {pmid31622236,
year = {2020},
author = {Cho, GY and Whang, KS},
title = {Aliifodinibius saliphilus sp. nov., a moderately halophilic bacterium isolated from sediment of a crystallizing pond of a saltern.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {1},
pages = {358-363},
doi = {10.1099/ijsem.0.003765},
pmid = {31622236},
issn = {1466-5034},
mesh = {Bacterial Typing Techniques ; Bacteroides/*classification/isolation &amp; purification ; Base Composition ; Chlorobi/*classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Phospholipids/chemistry ; *Phylogeny ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Salinity ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; Water Microbiology ; },
abstract = {Two Gram-stain-negative, moderately halophilic bacteria, designated strains ECH52[T] and KHM46, were isolated from the sediment of a grey saltern located in Sinui island at Shinan, Korea. The isolates were aerobic, non-motile, short rods and grew at 15-45 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum, pH 8.0) and with 3-25 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains ECH52[T] and KHM46 belonged to the genus Aliifodinibius in the family Balneolaceae with sequence similarities of 94.3-98.6 % and showed the highest sequence similarity to Aliifodinibius halophilus 2W32[T] (98.6 %), A. sediminis YIM J21[T] (94.7%), A. salicampi KHM44[T] (94.6 %) and A. roseus YIM D15[T] (94.3 %). The DNA G+C content of the genomic DNA of strain ECH52[T] was 40.8 mol%. The predominant isoprenoid quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were iso-C17 : 1ω9c, iso-C15 : 0, and C16 : 1ω7c and/or iso-C15 : 0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids and four unidentified lipids. Based on the phylogenetic, phenotypic and chemotaxonomic data, strains ECH52[T] and KHM46 are considered to represent a novel species of the genus Aliifodinibius , for which the name Aliifodinibius saliphilus sp. nov. is proposed. The type strain is ECH52[T] (=KACC 19126[T]=NBRC 112664[T]).},
}
@article {pmid31615877,
year = {2019},
author = {Deng, J and Auchtung, JM and Konstantinidis, KT and Brettar, I and Höfle, MG and Tiedje, JM},
title = {Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica.},
journal = {mSystems},
volume = {4},
number = {5},
pages = {},
pmid = {31615877},
issn = {2379-5077},
abstract = {Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative genomic hybridization (CGH), which revealed a gradient of genomic similarity, ranging from 65% to as high as 99%. The core genome of the S. baltica species was enriched in anaerobic respiration-associated genes. Auxiliary genes, most of which locate within a few genomic islands (GIs), were nonuniformly distributed among the isolates. Specifically, hypothetical and mobile genetic element (MGE)-associated genes dominated intraclade gene content differences, whereas gain/loss of functional genes drove gene content differences among less related strains. Among the major S. baltica clades, gene signatures related to specific redox-driven and spatial niches within the water column were identified. For instance, genes involved in anaerobic respiration of sulfur compounds may provide key adaptive advantages for clade A strains in anoxic waters where sulfur-containing electron acceptors are present. Genes involved in cell motility, in particular, a secondary flagellar biosynthesis system, may be associated with the free-living lifestyle by clade E strains. Collectively, this study revealed characteristics of genome variations present in the water column and active speciation of S. baltica strains, driven by niche partitioning and horizontal gene transfer (HGT).IMPORTANCE Speciation in nature is a fundamental process driving the formation of the vast microbial diversity on Earth. In the central Baltic Sea, the long-term stratification of water led to formation of a large-scale vertical redoxcline that provided a gradient of environmental niches with respect to the availability of electron acceptors and donors. The region was home to Shewanella baltica populations, which composed the dominant culturable nitrate-reducing bacteria, particularly in the oxic-anoxic transition zone. Using the collection of S. baltica isolates as a model system, genomic variations showed contrasting gene-sharing patterns within versus among S. baltica clades and revealed genomic signatures of S. baltica clades related to redox niche specialization as well as particle association. This study provides important insights into genomic mechanisms underlying bacterial speciation within this unique natural redoxcline.},
}
@article {pmid31613739,
year = {2020},
author = {Dumolin, C and Peeters, C and Ehsani, E and Tahon, G and De Canck, E and Cnockaert, M and Boon, N and Vandamme, P},
title = {Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {70},
number = {1},
pages = {530-536},
doi = {10.1099/ijsem.0.003786},
pmid = {31613739},
issn = {1466-5034},
mesh = {Achromobacter/*classification/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; Belgium ; Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Forests ; Hydrogen ; Multilocus Sequence Typing ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {Strain LMG 30378[T] was isolated from a hydrogen-oxidizing bacteria enrichment reactor inoculated with forest soil. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Achromobacter. Multilocus sequence analysis combined with sequence analysis of a 765 bp nrd A gene fragment both showed Achromobacter agilis LMG 3411[T] and Achromobacter denitrificans LMG 1231[T] to be the closest-related neighbours to strain LMG 30378[T]. Genome sequence analysis revealed a draft genome of 6.81 Mb with a G+C content of 67.2 mol%. In silico DNA-DNA hybridization with A. denitrificans LMG 1231[T] and A. agilis LMG 3411[T] showed 42.7 and 42.5% similarity, respectively, confirming that strain LMG 30378[T] represented a novel Achromobacter species. Phenotypic and metabolic characterization revealed acid phosphatase activity and the absence of phosphoamidase activity as distinctive features. The draft genome composes all necessary metabolic components to fix carbon dioxide and to oxidize molecular hydrogen, suggesting that strain LMG 30378[T] is a key organism in the enrichment reactor. Together, these data demonstrate that strain LMG 30378[T] represents a novel species of the genus Achromobacter, for which the name Achromobacter veterisilvae sp. nov. is proposed. The type strain is LMG 30378[T] (=CCUG 71558[T]).},
}
@article {pmid31612608,
year = {2019},
author = {Seto, M and Iwasa, Y},
title = {The fitness of chemotrophs increases when their catabolic by-products are consumed by other species.},
journal = {Ecology letters},
volume = {22},
number = {12},
pages = {1994-2005},
pmid = {31612608},
issn = {1461-0248},
support = {19K06853//Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research (C)/ ; },
mesh = {Biomass ; *Ecology ; *Ecosystem ; Symbiosis ; },
abstract = {Chemotrophic microorganisms synthesise biomass by utilising energy obtained from a set of chemical reactions that convert resources to by-products, forming catabolic interactions. The amount of energy obtained per catabolic reaction decreases with the abundance of the by-product named as the 'abundant resource premium'. Consider two species, Species 1 and 2, Species 1 obtains energy from a reaction that converts resource A to by-product B. Species 2 then utilises B as its resource, extracting energy from a reaction that converts B to C. Thus, the presence of Species 2 reduces the abundance of B, which improves the fitness of Species 1 by increasing the energy acquisition per reaction of A to B. We discuss the population dynamic implication of this effect and its importance in expanding a realised niche, boosting material flow through the ecosystem and providing mutualistic interactions among species linked by the material flow. Introducing thermodynamics into population ecology could offer us fundamental ecological insights into understanding the ecology of chemotrophic microorganisms dominating the subsurface realm.},
}
@article {pmid31612601,
year = {2019},
author = {Simonsen, AK and Barrett, LG and Thrall, PH and Prober, SM},
title = {Novel model-based clustering reveals ecologically differentiated bacterial genomes across a large climate gradient.},
journal = {Ecology letters},
volume = {22},
number = {12},
pages = {2077-2086},
doi = {10.1111/ele.13389},
pmid = {31612601},
issn = {1461-0248},
support = {//OCE Postdoctoral Fellowship,&#xa0;Australian Research Council/ ; },
mesh = {*Climate ; Ecotype ; *Genome, Bacterial ; Phylogeny ; Soil Microbiology ; },
abstract = {A pervasive challenge in microbial ecology is understanding the genetic level where ecological units can be differentiated. Ecological differentiation often occurs at fine genomic levels, yet it is unclear how to utilise ecological information to define ecotypes given the breadth of environmental variation among microbial taxa. Here, we present an analytical framework that infers clusters along genome-based microbial phylogenies according to shared environmental responses. The advantage of our approach is the ability to identify genomic clusters that best fit complex environmental information whilst characterising cluster niches through model predictions. We apply our method to determine climate-associated ecotypes in populations of nitrogen-fixing symbionts using whole genomes, explicitly sampled to detect climate differentiation across a heterogeneous landscape. Although soil and plant host characteristics strongly influence distribution patterns of inferred ecotypes, our flexible statistical method enabled us to identify climate-associated genomic clusters using environmental data, providing solid support for ecological specialisation in soil symbionts.},
}
@article {pmid31612432,
year = {2020},
author = {Rattes de Almeida Couto, C and Catharine de Assis Leite, D and Jurelevicius, D and van Elsas, JD and Seldin, L},
title = {Chemical and biological dispersants differently affect the bacterial communities of uncontaminated and oil-contaminated marine water.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {51},
number = {2},
pages = {691-700},
pmid = {31612432},
issn = {1678-4405},
support = {01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; -//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {Bacteria/classification/metabolism ; Biodegradation, Environmental ; Brazil ; Metagenome ; *Microbiota ; Petroleum/metabolism ; Petroleum Pollution ; Seawater/analysis/*microbiology ; Surface-Active Agents/classification/*metabolism ; *Water Microbiology ; Water Pollutants, Chemical/*metabolism ; },
abstract = {The use of dispersants in marine environments is a common practice worldwide for oil spill remediation. While the effects of chemical dispersants have been extensively studied, those of biosurfactants, mainly surfactin that is considered one of the most effective surfactants produced by bacteria, have been less considered. We constructed microcosms containing marine water collected from Grumari beach (W_GB, Brazil) and from Schiermonnikoog beach (W_SI, The Netherlands) with the addition of oil (WO), Ultrasperse II plus oil (WOS), surfactin plus oil (WOB), and both dispersants (WS or WB) individually. In these treatments, the composition of bacterial communities and their predictive biodegradation potential were determined over time. High-throughput sequencing of the rrs gene encoding bacterial 16S rRNA revealed that Bacteroidetes (Flavobacteria class) and Proteobacteria (mainly Gammaproteobacteria and Alphaproteobacteria classes) were the most abundant phyla found among the W_GB and W_SI microbiomes, and the relative abundance of the bacterial types in the different microcosms varied based on the treatment applied. Non-metrical multidimensional scaling (NMDS) revealed a clear clustering based on the addition of oil and on the dispersant type added to the GB or SI microcosms, i.e., WB and WOB were separated from WS and WOS in both marine ecosystems studied. The potential presence of diverse enzymes involved in oil degradation was indicated by predictive bacterial metagenome reconstruction. The abundance of predicted genes for degradation of petroleum hydrocarbons increased more in surfactin-treated microcosms than those treated with Ultrasperse II, mainly in the marine water samples from Grumari beach.},
}
@article {pmid31612324,
year = {2020},
author = {Norte, AC and Lopes de Carvalho, I and Núncio, MS and Araújo, PM and Matthysen, E and Albino Ramos, J and Sprong, H and Heylen, D},
title = {Getting under the birds' skin: tissue tropism of Borrelia burgdorferi s.l. in naturally and experimentally infected avian hosts.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {756-769},
pmid = {31612324},
issn = {1432-184X},
support = {MARE - UID/MAR/04292/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BPD/108197/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; na//Portuguese National Institute of Health Doutor Ricardo Jorge/ ; Marie 544 Sklodowska-Curie Actions, Individual Global Fellowship, project n&#xb0; 545 799609//European Union - Horizon2020/ ; G0.049.10//Fund for Scientific Research - Flanders/ ; na//Bill and Melinda Gates Foundation/ ; },
mesh = {Animals ; Bird Diseases/*microbiology ; Borrelia burgdorferi Group/*physiology ; Disease Reservoirs/microbiology/*veterinary ; Disease Vectors ; Female ; Lyme Disease/microbiology/*veterinary ; Male ; *Songbirds ; },
abstract = {Wild birds are frequently exposed to the zoonotic tick-borne bacteria Borrelia burgdorferi sensu lato (s.l.), and some bird species act as reservoirs for some Borrelia genospecies. Studying the tropism of Borrelia in the host, how it is sequestered in different organs, and whether it is maintained in circulation and/or in the host's skin is important to understand pathogenicity, infectivity to vector ticks and reservoir competency.We evaluated tissue dissemination of Borrelia in blackbirds (Turdus merula) and great tits (Parus major), naturally and experimentally infected with Borrelia genospecies from enzootic foci. We collected both minimally invasive biological samples (feathers, skin biopsies and blood) and skin, joint, brain and visceral tissues from necropsied birds. Infectiousness of the host was evaluated through xenodiagnoses and infection rates in fed and moulted ticks. Skin biopsies were the most reliable method for assessing avian hosts' Borrelia infectiousness, which was supported by the agreement of infection status results obtained from the analysis of chin and lore skin samples from necropsied birds and of their xenodiagnostic ticks, including a significant correlation between the estimated concentration of Borrelia genome copies in the skin and the Borrelia infection rate in the xenodiagnostic ticks. This confirms a dermatropism of Borrelia garinii, B. valaisiana and B. turdi in its avian hosts. However, time elapsed from exposure to Borrelia and interaction between host species and Borrelia genospecies may affect the reliability of skin biopsies. The blood was not useful to assess infectiousness of birds, even during the period of expected maximum spirochetaemia. From the tissues sampled (foot joint, liver, spleen, heart, kidney, gut and brain), Borrelia was detected only in the gut, which could be related with infection mode, genospecies competition, genospecies-specific seasonality and/or excretion processes.},
}
@article {pmid31611655,
year = {2020},
author = {Jiao, S and Yang, Y and Xu, Y and Zhang, J and Lu, Y},
title = {Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China.},
journal = {The ISME journal},
volume = {14},
number = {1},
pages = {202-216},
pmid = {31611655},
issn = {1751-7370},
mesh = {*Agriculture ; Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; China ; Ecosystem ; Fungi/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Oryza ; *Soil Microbiology ; Zea mays ; },
abstract = {Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.},
}
@article {pmid31611646,
year = {2019},
author = {Ansorge, R and Romano, S and Sayavedra, L and Porras, M&#xc1;G and Kupczok, A and Tegetmeyer, HE and Dubilier, N and Petersen, J},
title = {Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels.},
journal = {Nature microbiology},
volume = {4},
number = {12},
pages = {2487-2497},
pmid = {31611646},
issn = {2058-5276},
mesh = {Animals ; Bacteria/classification/*genetics ; Base Sequence ; Biodiversity ; Bivalvia/metabolism/*microbiology ; Ecosystem ; Genetic Heterogeneity ; Hydrogenase/genetics ; Hydrothermal Vents ; Metagenome ; Microbiota/genetics ; Mytilidae/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Symbiosis ; Transcriptome ; },
abstract = {Genetic diversity of closely related free-living microorganisms is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Accordingly, strain diversity is assumed to be highly restricted in intracellular bacteria associated with animals. Here, we sequenced metagenomes and metatranscriptomes of 18 Bathymodiolus mussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individual Bathymodiolus mussels. Co-occurring symbiont strains differed extensively in key functions, such as the use of energy and nutrient sources, electron acceptors and viral defence mechanisms. Most strain-specific genes were expressed, highlighting their potential to affect fitness. We show that fine-scale diversity is pervasive in Bathymodiolus sulfur-oxidizing symbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, rather than the host, feeds the symbionts.},
}
@article {pmid31608034,
year = {2019},
author = {Cai, Y and Cao, Y and Tang, C},
title = {Evidence for the Primary Role of Phytoplankton on Nitrogen Cycle in a Subtropical Reservoir: Reflected by the Stable Isotope Ratios of Particulate Nitrogen and Total Dissolved Nitrogen.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2202},
pmid = {31608034},
issn = {1664-302X},
abstract = {Knowledge about the primary factor controlling stable isotope ratios of particulate nitrogen (δ[15]NPN) and total dissolved nitrogen (δ[15]NTDN) in a subtropical reservoir can improve the understanding of regional and global nitrogen cycles. Taking Lianhe Reservoir as a representative subtropical reservoir, we studied the spatial and temporal distributions of δ[15]NPN andδ[15]NTDN and their relationships with the surrounding physicochemical factors and phytoplankton. The results showed that variations in δ[15]NPN and δ[15]NTDN followed seasonal thermal cycles. The values of δ[15]NTDN were inversely proportional to those of δ[15]NPN. PCA showed that phytoplankton cell density and pH were the primary drivers of the variation of δ[15]NPN (45.2%). The primary factors influencing δ[15]NTDN were Chl a and phytoplankton cell density, which both indicated phytoplankton biomass. We also determined that the dominant species was Microcystis densa during the thermal stratification period and Staurodesmus aristiferus during the mixing period. Laboratory experiments showed that δ[15]NPN values in both M. densa (from 19.5 to 14.6‰) and S. aristiferus (from 19.4 to 16.0 ‰) media decreased significantly as the algal cells grew. Furthermore, the δ[15]NTDN values increased from 4.9 to 7.9‰ and from 4.7 to 6.9‰ in M. densa and S. aristiferus media, respectively, when the δ[15]NPN values decreased. These experimental results were consistent with field investigation results and indicated that variations in δ[15]NPN and δ[15]NTDN were mainly controlled by phytoplankton cell density, especially the cell density of the dominant species, in both the thermal stratification and mixing periods. The results also suggested that cell density, not phytoplankton species, was the key factor regulating the distribution of nitrogen stable isotopes. These results together indicated that phytoplankton cell density is the primary factor in the regulation of nitrogen stable isotope composition and that its influence is greater than that of other physical and chemical factors. This study provided detailed information supporting the primary role of phytoplankton in the nitrogen geochemical cycle and improved the understanding of biochemical processes in natural subtropical reservoirs.},
}
@article {pmid31605197,
year = {2020},
author = {Hess, AL and Benítez-Páez, A and Blædel, T and Larsen, LH and Iglesias, JR and Madera, C and Sanz, Y and Larsen, TM and , },
title = {The effect of inulin and resistant maltodextrin on weight loss during energy restriction: a randomised, placebo-controlled, double-blinded intervention.},
journal = {European journal of nutrition},
volume = {59},
number = {6},
pages = {2507-2524},
pmid = {31605197},
issn = {1436-6215},
support = {613979//Seventh Framework Programme/ ; },
mesh = {Blood Pressure/drug effects ; *Caloric Restriction ; Double-Blind Method ; Energy Intake ; Female ; Gastrointestinal Microbiome/drug effects ; Glucose/metabolism ; Humans ; Inulin/*pharmacology ; Male ; Middle Aged ; Polysaccharides/*pharmacology ; Weight Loss/*drug effects ; },
abstract = {PURPOSE: The objective of this study was to investigate the additive effects of combining energy restriction with dietary fibres on change in body weight and gut microbiota composition.<br><br>METHODS: The study was a 12-week randomised, placebo-controlled, double-blinded, parallel intervention trial. A total of 116 overweight or obese participants were assigned randomly either to 10&#xa0;g inulin plus 10&#xa0;g resistant maltodextrin or to 20&#xa0;g of placebo supplementation through 400&#xa0;mL of milk a day, while on a -&#x2009;500&#xa0;kcal/day energy restricted diet.<br><br>RESULTS: Altogether, 86 participants completed the intervention. There were no significant differences in weight loss or body composition between the groups. The fibre supplement reduced systolic (5.35&#x2009;&#xb1;&#x2009;2.4&#xa0;mmHg, p&#x2009;=&#x2009;0.043) and diastolic (2.82&#x2009;&#xb1;&#x2009;1.3&#xa0;mmHg, p&#x2009;=&#x2009;0.047) blood pressure to a larger extent than placebo. Furthermore, a larger decrease in serum insulin was observed in the placebo group compared to the fibre group (-&#x2009;26.0&#x2009;&#xb1;&#x2009;9.2&#xa0;pmol/L, p&#x2009;=&#x2009;0.006). The intake of fibre induced changes in the composition of gut microbiota resulting in higher abundances of Parabacteroides and Bifidobacteria, compared to placebo. The effects on blood pressure and glucose metabolism were mainly observed in women, and could be attributed to a higher gut microbiota diversity after intervention. Finally, the fibre group experienced a higher degree of gastrointestinal symptoms, which attenuated over time.<br><br>CONCLUSIONS: Supplementation of inulin and resistant maltodextrin did not provide an additional weight loss during an energy-restricted diet, but reduced both systolic and diastolic blood pressure. Furthermore, the fibre supplement did stimulate the growth of potentially beneficial bacteria genera.<br><br>CLINICAL TRIAL REGISTRY: The study was registered at http://www.clinicaltrials.gov , NCT03135041.},
}
@article {pmid31600966,
year = {2019},
author = {Lin, X and Gao, D and Lu, K and Li, X},
title = {Bacterial Community Shifts Driven by Nitrogen Pollution in River Sediments of a Highly Urbanized City.},
journal = {International journal of environmental research and public health},
volume = {16},
number = {20},
pages = {},
pmid = {31600966},
issn = {1660-4601},
mesh = {Bacteria/*classification/*drug effects ; China ; Cities ; Geologic Sediments/microbiology ; Nitrogen/chemistry/*toxicity ; Rivers/*microbiology ; Urbanization ; Water Pollutants, Chemical/chemistry/*toxicity ; },
abstract = {Effects of nitrogen pollution on bacterial community shifts in river sediments remain barely understood. Here, we investigated the bacterial communities in sediments of urban and suburban rivers in a highly urbanized city, Shanghai. Sediment nitrate (NO3[-]) and ammonia (NH4[+]) were highly accumulated in urban river. Operation Taxonomic Units (OTUs), Abundance-based Coverage Estimators (ACEs) and Chao 1 estimator in urban rivers were slightly lower than those in suburban rivers, while Shannon and Simpson indices were higher in urban rivers than those in suburban rivers. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phylum communities, accounting for 68.5-84.9% of all communities. In particular, the relative abundances of Firmicutes and Nitrospirae were significantly higher in suburban rivers than in urban rivers, while relative abundances of Bacteroidetes, Verrucomicrobia, and Spirochaetes were significantly lower in suburban rivers than in urban rivers. NH4[+] was significantly and negatively correlated with abundances of Firmicutes, Nitrospirae, and Actinobacteria. Importantly, the significant and negative effects of sediment NH4[+] on bacterial richness and diversity suggested that nitrogen pollution likely contribute to the decrease in the bacterial richness and diversity. The results highlight that nitrogen enrichment could drive the shifts of bacterial abundance and diversity in the urban river sediments where are strongly influenced by human activities under the rapid urbanization stress.},
}
@article {pmid31599931,
year = {2019},
author = {Cavaco, MA and St Louis, VL and Engel, K and St Pierre, KA and Schiff, SL and Stibal, M and Neufeld, JD},
title = {Freshwater microbial community diversity in a rapidly changing High Arctic watershed.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {11},
pages = {},
doi = {10.1093/femsec/fiz161},
pmid = {31599931},
issn = {1574-6941},
mesh = {Arctic Regions ; Climate Change ; Ecosystem ; Fresh Water/*microbiology ; Lakes/microbiology ; *Microbiota ; Nunavut ; RNA, Ribosomal, 16S ; Rivers/microbiology ; Seasons ; Soil ; Soil Microbiology ; *Water Microbiology ; },
abstract = {Current models predict increases in High Arctic temperatures and precipitation that will have profound impacts on the Arctic hydrological cycle, including enhanced glacial melt and thawing of active layer soils. However, it remains uncertain how these changes will impact the structure of downstream resident freshwater microbial communities and ensuing microbially driven freshwater ecosystem services. Using the Lake Hazen watershed (Nunavut, Canada; 82°N, 71°W) as a sentinel system, we related microbial community composition (16S rRNA gene sequencing) to physicochemical parameters (e.g. dissolved oxygen and nutrients) over an annual hydrological cycle in three freshwater compartments within the watershed: (i) glacial rivers; (ii) active layer thaw-fed streams and waterbodies and (iii) Lake Hazen, into which (i) and (ii) drain. Microbial communities throughout these freshwater compartments were strongly interconnected, hydrologically, and often correlated with the presence of melt-sourced chemicals (e.g. dissolved inorganic carbon) as the melt season progressed. Within Lake Hazen itself, water column microbial communities were generally stable over spring and summer, despite fluctuating lake physicochemistry, indicating that these communities and the potential ecosystem services they provide therein may be resilient to environmental change. This work helps to establish a baseline understanding of how microbial communities and the ecosystem services they provide in Arctic watersheds might respond to future climate change.},
}
@article {pmid31598761,
year = {2020},
author = {Brunel, C and Beifen, Y and Pouteau, R and Li, J and van Kleunen, M},
title = {Responses of Rhizospheric Microbial Communities of Native and Alien Plant Species to Cuscuta Parasitism.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {617-630},
pmid = {31598761},
issn = {1432-184X},
support = {2016YFC1201100//Chinese National Key Research and Development Program/ ; 15-2//International Science and Technology Cooperation Programme/ ; 30800133//National Natural Science Foundation of China/ ; },
mesh = {Bacteria/genetics ; Cuscuta/*physiology ; DNA, Bacterial/analysis ; Introduced Species ; Magnoliopsida/*microbiology/parasitology ; *Microbiota ; *Rhizosphere ; Symbiosis ; },
abstract = {Parasitic plants have major impacts on host fitness. In the case of species of the holoparasitic Cuscuta genus, these impacts were shown to be particularly strong in some invasive alien plants, which has raised interest in the underlying mechanism. We hypothesized that Cuscuta parasitization may exert strong influence in shaping the diversity patterns in the host rhizosphere microbiome and that this may vary between native (coevolved) and alien (non-coevolved) plants. Here, we report on a field study exploring the effect of parasitization by Cuscuta australis on the rhizosphere microbiota (16S and ITS rDNA) of four plant species sharing and three plant species not sharing the parasite's native range. Despite a predominant role of the host species in shaping the rhizosphere microbiota, the role of host origin and of parasitization still appeared important in structuring microbial communities and their associated functions. Bacterial communities were more strongly influenced than fungi by the native range of the host plant, while fungi were slightly more affected than bacteria by parasitization. About 7% of bacterial phylotypes and 11% of fungal phylotypes were sensitive to Cuscuta parasitization. Parasitization also reduced the abundance of arbuscular mycorrhizal fungi by ca. 18% and of several genes related to plant growth promoting functions (e.g., nitrogen metabolism and quorum sensing). Both fungi and bacteria differentially responded to host parasitization depending on host origin, and the extent of these shifts suggests that they may have more dramatic consequences for alien than for native plants.},
}
@article {pmid31598755,
year = {2020},
author = {Sodhi, KK and Kumar, M and Balan, B and Dhaulaniya, AS and Singh, DK},
title = {Isolation and characterization of amoxicillin-resistant bacteria and amoxicillin-induced alteration in its protein profiling and RNA yield.},
journal = {Archives of microbiology},
volume = {202},
number = {2},
pages = {225-232},
doi = {10.1007/s00203-019-01737-6},
pmid = {31598755},
issn = {1432-072X},
support = {(NASF/CA-6030/2017-18)//Indian Council of Agricultural Research/ ; },
mesh = {Amoxicillin/*metabolism/pharmacology ; Anti-Bacterial Agents/*metabolism/pharmacology ; Bacterial Proteins/genetics ; Biodegradation, Environmental ; Chromatography, Liquid ; DNA, Bacterial/genetics ; DNA-Directed RNA Polymerases/genetics/*metabolism ; Penicillin Resistance/genetics ; Phylogeny ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; Stenotrophomonas/*drug effects/genetics/*metabolism ; Tandem Mass Spectrometry ; Water Pollutants, Chemical/*metabolism ; },
abstract = {Amoxicillin-resistant bacteria were isolated using selective enrichment procedure. The morphological, biochemical and molecular characterization based on 16S rRNA gene sequencing and phylogenetic analysis of the bacterial strain WA5 confirmed that the strain belongs to the genus Stenotrophomonas. The bacteria were named as Stenotrophomonas sp. strain WA5 (MK110499). Substantial growth was seen in M9 minimal media supplemented with 5 mg L[-1] of amoxicillin as a sole source of carbon and energy. RNA yield was also observed to be decreased in the presence of amoxicillin. Amoxicillin (5 mg L[-1])-induced alteration is seen on bacterial protein profile and unique polypeptide bands were seen to be induced in the presence of amoxicillin, the bands were subjected to trypsin digestion, and LC-MS/MS analysis showed that the bands belong to the family of DNA-dependent RNA polymerase subunit β (rpoC). Plasmid DNA isolation indicated the presence of antibiotic-resistant genes being harboured by the plasmid.},
}
@article {pmid31598633,
year = {2020},
author = {Baruzzo, G and Patuzzi, I and Di Camillo, B},
title = {SPARSim single cell: a count data simulator for scRNA-seq data.},
journal = {Bioinformatics (Oxford, England)},
volume = {36},
number = {5},
pages = {1468-1475},
doi = {10.1093/bioinformatics/btz752},
pmid = {31598633},
issn = {1367-4811},
mesh = {Gene Expression Profiling ; RNA-Seq ; Sequence Analysis, RNA ; *Single-Cell Analysis ; *Software ; },
abstract = {MOTIVATION: Single cell RNA-seq (scRNA-seq) count data show many differences compared with bulk RNA-seq count data, making the application of many RNA-seq pre-processing/analysis methods not straightforward or even inappropriate. For this reason, the development of new methods for handling scRNA-seq count data is currently one of the most active research fields in bioinformatics. To help the development of such new methods, the availability of simulated data could play a pivotal role. However, only few scRNA-seq count data simulators are available, often showing poor or not demonstrated similarity with real data.<br><br>RESULTS: In this article we present SPARSim, a scRNA-seq count data simulator based on a Gamma-Multivariate Hypergeometric model. We demonstrate that SPARSim allows to generate count data that resemble real data in terms of count intensity, variability and sparsity, performing comparably or better than one of the most used scRNA-seq simulator, Splat. In particular, SPARSim simulated count matrices well resemble the distribution of zeros across different expression intensities observed in real count data.<br><br>SPARSim R package is freely available at http://sysbiobig.dei.unipd.it/? q=SPARSim and at https://gitlab.com/sysbiobig/sparsim.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid31595680,
year = {2019},
author = {Wepking, C and Badgley, B and Barrett, JE and Knowlton, KF and Lucas, JM and Minick, KJ and Ray, PP and Shawver, SE and Strickland, MS},
title = {Prolonged exposure to manure from livestock-administered antibiotics decreases ecosystem carbon-use efficiency and alters nitrogen cycling.},
journal = {Ecology letters},
volume = {22},
number = {12},
pages = {2067-2076},
doi = {10.1111/ele.13390},
pmid = {31595680},
issn = {1461-0248},
support = {1832888//NSF/ ; 2013-67019-21363//USDA-NIFA/ ; },
mesh = {Animals ; Anti-Bacterial Agents ; Carbon ; Cattle ; *Ecosystem ; Livestock ; *Manure ; Nitrogen ; Soil ; Soil Microbiology ; },
abstract = {Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse-chase. Exposure to manure from antibiotic-treated cattle caused: (i) changes in microbial community structure; and (ii) alterations in elemental cycling throughout the terrestrial system. This exposure caused changes in fungal : bacterial ratios, as well as changes in bacterial community structure. Additionally, exposure to manure from cattle treated with pirlimycin resulted in an approximate two-fold increase in ecosystem respiration of recently fixed-carbon, and a greater proportion of recently added nitrogen in plant and soil pools compared to the control manure. Manure from antibiotic-treated cattle therefore affects terrestrial ecosystem function via the soil microbiome, causing decreased ecosystem carbon use efficiency, and altered nitrogen cycling.},
}
@article {pmid31595328,
year = {2020},
author = {Li, F and Li, P and Hua, H and Hou, M and Wang, F},
title = {Diversity, Tissue Localization, and Infection Pattern of Bacterial Symbionts of the White-Backed Planthopper, Sogatella furcifera (Hemiptera: Delphacidae).},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {720-730},
pmid = {31595328},
issn = {1432-184X},
support = {2018YFD0200300//National Key R&amp;D Project of China/ ; 31371951//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Bacteria/classification ; DNA, Bacterial/analysis ; Female ; Hemiptera/*microbiology ; In Situ Hybridization, Fluorescence ; Male ; Microbiota/*physiology ; RNA, Ribosomal, 16S/analysis ; Symbiosis ; },
abstract = {The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is a destructive pest of rice. Bacterial symbionts play an important role in insect hosts, especially hemipteran hosts. This study was designed to examine the bacterial symbionts of the WBPH using 16S rDNA high-throughput sequencing. A total of 63 and 177 operational taxonomic units (OTUs) were identified in females and males of three WBPH populations, respectively. These OTUs included bacteria of 75 genera from 11 phyla, where Wolbachia, Cardinium, and Asaia were the dominant genera, accounting for over 97.99% of all the symbiotic bacteria. Fluorescence in situ hybridization detected Wolbachia, Cardinium, and Asaia in the salivary glands, guts, testes, and eggs of the WBPH, indicating the potential for both horizontal and vertical transmission. Moreover, the infection pattern of the three dominant bacterial symbionts was detected in six WBPH populations. The frequencies of Wolbachia infection of females and Cardinium infection of both sexes were over 96.7%. Wolbachia infection of males ranged between 46.7 and 63.3%, which was significantly lower than that observed for females. Asaia infection of both sexes varied substantially among the populations. These results indicate that the complex host-symbiotic bacteria interaction is influenced by host sex and geographical origin and potentially by the transmission modes of the symbionts.},
}
@article {pmid31595008,
year = {2019},
author = {Soffe, R and Bernach, M and Remus-Emsermann, MNP and Nock, V},
title = {Replicating Arabidopsis Model Leaf Surfaces for Phyllosphere Microbiology.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {14420},
pmid = {31595008},
issn = {2045-2322},
mesh = {Arabidopsis/*microbiology/ultrastructure ; Bacteria/pathogenicity/*ultrastructure ; Dimethylpolysiloxanes/chemistry ; Microscopy ; Plant Leaves/*microbiology/ultrastructure ; Surface Properties ; Waxes/chemistry ; },
abstract = {Artificial surfaces are commonly used in place of leaves in phyllosphere microbiology to study microbial behaviour on plant leaf surfaces. These surfaces enable a reductionist approach to be undertaken, to enable individual environmental factors influencing microorganisms to be studied. Commonly used artificial surfaces include nutrient agar, isolated leaf cuticles, and reconstituted leaf waxes. Recently, replica surfaces mimicking the complex topography of leaf surfaces for phyllosphere microbiology studies are appearing in literature. Replica leaf surfaces have been produced in agar, epoxy, polystyrene, and polydimethylsiloxane (PDMS). However, none of these protocols are suitable for replicating fragile leaves such as of the model plant Arabidopsis thaliana. This is of importance, as A. thaliana is a model system for molecular plant genetics, molecular plant biology, and microbial ecology. To overcome this limitation, we introduce a versatile replication protocol for replicating fragile leaf surfaces into PDMS. Here we demonstrate the capacity of our replication process using optical microscopy, atomic force microscopy (AFM), and contact angle measurements to compare living and PDMS replica A. thaliana leaf surfaces. To highlight the use of our replica leaf surfaces for phyllosphere microbiology, we visualise bacteria on the replica leaf surfaces in comparison to living leaf surfaces.},
}
@article {pmid31593911,
year = {2020},
author = {Prévoteau, A and Carvajal-Arroyo, JM and Ganigué, R and Rabaey, K},
title = {Microbial electrosynthesis from CO2: forever a promise?.},
journal = {Current opinion in biotechnology},
volume = {62},
number = {},
pages = {48-57},
doi = {10.1016/j.copbio.2019.08.014},
pmid = {31593911},
issn = {1879-0429},
mesh = {*Carbon Dioxide ; Electrodes ; Fermentation ; },
abstract = {Microbial electrosynthesis (MES) is an electrochemical process used to drive microbial metabolism for bio-production, such as the reduction of CO2 into industrially relevant organic products as an alternative to current fossil-fuel-derived commodities. After a decade of research on MES from CO2, figures of merit have increased significantly but are plateauing yet far from those expected to allow competitiveness for synthesis of commodity chemicals. Here we discuss the substantial technological shortcomings still associated with MES and evoke possible ways to mitigate them. It appears particularly challenging to obtain both relevant production rates (driven by high current densities) and energy conversion efficiency (i.e. low cell voltage) in microbial-compatible electrolytes. More competitive processes could arise by decoupling effective abiotic electroreductions (e.g. CO2 to CO or ethanol; H2 evolution) with subsequent fermentation processes.},
}
@article {pmid31593527,
year = {2020},
author = {Tabima, JF and Søndreli, KL and Keriö, S and Feau, N and Sakalidis, ML and Hamelin, RC and LeBoldus, JM},
title = {Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {33},
number = {2},
pages = {189-199},
doi = {10.1094/MPMI-05-19-0131-R},
pmid = {31593527},
issn = {0894-0282},
mesh = {*Ascomycota/genetics ; Canada ; Genetic Variation ; Humans ; *Metagenomics ; North America ; Plant Diseases/microbiology ; *Populus/microbiology ; },
abstract = {Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.},
}
@article {pmid31591493,
year = {2020},
author = {Ben Maamar, S and Hu, J and Hartmann, EM},
title = {Implications of indoor microbial ecology and evolution on antibiotic resistance.},
journal = {Journal of exposure science &amp; environmental epidemiology},
volume = {30},
number = {1},
pages = {1-15},
pmid = {31591493},
issn = {1559-064X},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics/*physiology ; Ecology ; Gene Transfer, Horizontal ; Humans ; },
abstract = {The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.},
}
@article {pmid31590609,
year = {2020},
author = {Diaz, PI and Valm, AM},
title = {Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties.},
journal = {Journal of dental research},
volume = {99},
number = {1},
pages = {18-25},
pmid = {31590609},
issn = {1544-0591},
support = {R03 DE028042/DE/NIDCR NIH HHS/United States ; },
mesh = {Bacteria ; *Biofilms ; *Microbial Interactions ; *Microbiota ; Virulence ; },
abstract = {Oral microbial communities are extraordinarily complex in taxonomic composition and comprise interdependent biological systems. The bacteria, archaea, fungi, and viruses that thrive within these communities engage in extensive cell-cell interactions, which are both beneficial and antagonistic. Direct physical interactions among individual cells mediate large-scale architectural biofilm arrangements and provide spatial proximity for chemical communication and metabolic cooperation. In this review, we summarize recent work in identifying specific molecular components that mediate cell-cell interactions and describe metabolic interactions, such as cross-feeding and exchange of electron acceptors and small molecules, that modify the growth and virulence of individual species. We argue, however, that although pairwise interaction models have provided useful information, complex community-like systems are needed to study the properties of oral communities. The networks of multiple synergistic and antagonistic interactions within oral biofilms give rise to the emergent properties of persistence, stability, and long-range spatial structure, with these properties mediating the dysbiotic transitions from health to oral diseases. A better understanding of the fundamental properties of interspecies networks will lead to the development of effective strategies to manipulate oral communities.},
}
@article {pmid31589437,
year = {2020},
author = {Syrpas, M and Bukauskaitė, J and Ramanauskienė, K and Karosienė, JR and Majienė, D and Bašinskienė, L and Venskutonis, PR},
title = {Ultrasound-Assisted Extraction and Assessment of Biological Activity of Phycobiliprotein-Rich Aqueous Extracts from Wild Cyanobacteria (Aphanizomenon flos-aquae).},
journal = {Journal of agricultural and food chemistry},
volume = {68},
number = {7},
pages = {1896-1909},
doi = {10.1021/acs.jafc.9b05483},
pmid = {31589437},
issn = {1520-5118},
mesh = {Antioxidants/chemistry/isolation &amp; purification/pharmacology ; Aphanizomenon/*chemistry/growth &amp; development ; Bacterial Proteins/chemistry/*isolation &amp; purification/*pharmacology ; Cell Line, Tumor ; Cell Survival/drug effects ; Humans ; Phycobiliproteins/chemistry/*isolation &amp; purification/*pharmacology ; Ultrasonics ; },
abstract = {Cyanobacteria are photosynthetic microorganisms that are considered as an important source of bioactive metabolites, among which phycobiliproteins (PBPs) are a class of water-soluble macromolecules of cyanobacteria with a wide range of applications. Massive proliferation of cyanobacteria can lead to excessive surface water blooms, of which removal, as a management measure, should be prioritized. In this study, the utilization of wild cyanobacteria biomass (Aphanizomenon flos-aquae) for extraction of phycobiliproteins is reported. Extraction of phycobiliproteins by conventional methods, such as homogenization, freeze-thaw cycles, and solid-liquid extraction, were optimized prior to ultrasound-assisted extraction. Standardization of ultrasonication for different parameters, such as ultrasonication amplitude (38, 114, and 190 μm) and ultrasonication time (1, 5.5, and 10 min), was carried out using a central composite design and response surface methodology for each of the primary techniques. A substantial increase on the individual and total phycobiliprotein yields was observed after ultrasonic treatment. The highest total PBP yield (115.37 mg/g of dry weight) was observed with samples treated with a homogenizer (30 min, 30 °C, and 1 cycle) combined with ultrasound treatment (8.7 min at 179 μm). Moreover, in vitro antioxidant capacity was observed for the obtained extracts in the Folin-Ciocalteu and ABTS[*] [+] assays. In addition, a cytotoxic effect against C6 glioma cells was observed for A. flos-aquae PBPs. Conclusively, wild cyanobacteria could be considered as an alternative feedstock for recovery of PBPs.},
}
@article {pmid31588957,
year = {2020},
author = {Le, D and Nguyen, P and Nguyen, D and Dierckens, K and Boon, N and Lacoere, T and Kerckhof, FM and De Vrieze, J and Vadstein, O and Bossier, P},
title = {Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {539-551},
pmid = {31588957},
issn = {1432-184X},
support = {ZIUS2015AP026//VLIR-IUC/ ; },
mesh = {Animal Migration ; Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Perciformes/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; Vietnam ; },
abstract = {We investigated the gut microbiota of rabbit fish larvae at three locations in Vietnam (ThuanAn-northern, QuangNam-intermediate, BinhDinh-southern sampling site) over a three-year period. In the wild, the first food for rabbit fish larvae remains unknown, while the juveniles and adults are herbivores, forming schools near the coasts, lagoons, and river mouths, and feeding mainly on filamentous algae. This is the first study on the gut microbiota of the wild fish larvae and with a large number of individuals analyzed spatially and temporally. The Clostridiales order was the most predominant in the gut, and location-by-location alpha diversity showed significant differences in Chao-1, Hill number 1, and evenness. Analysis of beta diversity indicated that the location, not year, had an effect on the composition of the microbiota. In 2014, the gut microbiota of fish from QuangNam was different from that in BinhDinh; in 2015, the gut microbiota was different for all locations; and, in 2016, the gut microbiota in ThuanAn was different from that in the other locations. There was a time-dependent trend in the north-south axis for the gut microbiota, which is considered to be tentative awaiting larger datasets. We found limited variation in the gut microbiota geographically and in time and strong indications for a core microbiome. Five and fifteen OTUs were found in 100 and 99% of the individuals, respectively. This suggests that at this life stage the gut microbiota is under strong selection due to a combination of fish-microbe and microbe-microbe interactions.},
}
@article {pmid31587650,
year = {2019},
author = {Sebastián, M and Gasol, JM},
title = {Visualization is crucial for understanding microbial processes in the ocean.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {374},
number = {1786},
pages = {20190083},
pmid = {31587650},
issn = {1471-2970},
mesh = {Genomics ; Oceans and Seas ; Prokaryotic Cells/*physiology ; Seawater/*microbiology ; Single-Cell Analysis/*methods ; },
abstract = {Recent developments in community and single-cell genomic approaches have provided an unprecedented amount of information on the ecology of microbes in the aquatic environment. However, linkages between each specific microbe's identity and their in situ level of activity (be it growth, division or just metabolic activity) are much more scarce. The ultimate goal of marine microbial ecology is to understand how the environment determines the types of different microbes in nature, their function, morphology and cell-to-cell interactions and to do so we should gather three levels of information, the genomic (including identity), the functional (activity or growth), and the morphological, and for as many individual cells as possible. We present a brief overview of methodologies applied to address single-cell activity in marine prokaryotes, together with a discussion of the difficulties in identifying and categorizing activity and growth. We then provide and discuss some examples showing how visualization has been pivotal for challenging established paradigms and for understanding the role of microbes in the environment, unveiling processes and interactions that otherwise would have been overlooked. We conclude by stating that more effort should be directed towards integrating visualization in future approaches if we want to gain a comprehensive insight into how microbes contribute to the functioning of ecosystems. This article is part of a discussion meeting issue 'Single cell ecology'.},
}
@article {pmid31585384,
year = {2019},
author = {Wang, D and Tooker, NB and Srinivasan, V and Li, G and Fernandez, LA and Schauer, P and Menniti, A and Maher, C and Bott, CB and Dombrowski, P and Barnard, JL and Onnis-Hayden, A and Gu, AZ},
title = {Side-stream enhanced biological phosphorus removal (S2EBPR) process improves system performance - A full-scale comparative study.},
journal = {Water research},
volume = {167},
number = {},
pages = {115109},
doi = {10.1016/j.watres.2019.115109},
pmid = {31585384},
issn = {1879-2448},
mesh = {Bioreactors ; *Phosphorus ; Polyphosphates ; *Rivers ; Sewage ; Wastewater ; },
abstract = {To address the common challenges in enhanced biological phosphorus removal (EBPR) related to stability and unfavorable influent carbon to phosphorus ratio, a side-stream EBPR (S2EBPR) process that involves a side-stream anaerobic biological sludge hydrolysis and fermentation reactor was proposed as an emerging alternative. In this study, a full-scale pilot testing was performed with side-by-side operation of a conventional anaerobic-anoxic-aerobic (A2O) process versus a S2EBPR process. A comparison of the performance, activity and microbial community between the two configurations was performed. The results demonstrated that, with the same influent wastewater characteristics, S2EBPR configuration showed improved P removal performance and stability than the conventional A2O configuration, especially when the mixers in the side-stream anaerobic reactor were operated intermittently. Mass balance analysis illustrated that both denitrification and EBPR were enhanced in S2EBPR configuration, where return activated sludge was diverted into the anaerobic zone to promote fermentation and enrichment of polyphosphate accumulating organisms (PAOs), and the influent was bypassed to the anoxic zone for enhancing denitrification. A relatively higher PAO activity and total PAO abundance were observed in S2EBPR than in A2O configuration, accompanied by a higher degree of dependence on glycolysis pathway than tricarboxylic acid cycle. No significant difference in the relative abundances of putative PAOs, including Ca. Accumulibacter and Tetrasphaera, were observed between the two configurations. However, higher microbial community diversity indices were observed in S2EBPR configuration than in conventional one. In addition, consistently lower relative abundance of known glycogen accumulating organisms (GAOs) was observed in S2EBPR system. Extended anaerobic retention time and conditions that generate continuous and more complex volatile fatty acids in the side-stream anaerobic reactor of S2EBPR process likely give more competitive advantage for PAOs over GAOs. PAOs exhibited sustained EBPR activity and delayed decay under extended anaerobic condition, likely due to their versatile metabolic pathways depending on the availability and utilization of multiple intracellular polymers. This study provided new insights into the effects of implementing side-stream EBPR configuration on microbial populations, EBPR activity profiles and resulted system performance.},
}
@article {pmid31584168,
year = {2020},
author = {Browne, PD and Kot, W and Jørgensen, TS and Hansen, LH},
title = {The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2075},
number = {},
pages = {253-264},
doi = {10.1007/978-1-4939-9877-7_18},
pmid = {31584168},
issn = {1940-6029},
mesh = {Computational Biology/methods ; *DNA Transposable Elements ; DNA, Circular ; Databases, Genetic ; Escherichia coli/genetics ; Gene Library ; Gene Transfer, Horizontal ; *Metagenome ; *Metagenomics/methods ; Plasmids/*genetics ; Viruses/*genetics ; },
abstract = {Isolation, sequencing, and analysis of circular genetic elements bring new insights to mobile genetic elements related to microbial ecology. One method used to study circular plasmids, viruses, and other elements is called the mobilome method. The mobilome method presented here is an unamplified mobilome approach allowing fast isolation of circular DNA elements from a variety of samples followed by directly building unamplified Illumina-compatible sequencing libraries using enzymatic tagging and fragmentation. Several methods for bioinformatic analysis of mobilome data are also suggested.},
}
@article {pmid31582458,
year = {2019},
author = {Schultz, J and Kallies, R and Nunes da Rocha, U and Rosado, AS},
title = {Draft Genome Sequence of Brevibacillus sp. Strain LEMMJ03, Isolated from an Antarctic Volcano.},
journal = {Microbiology resource announcements},
volume = {8},
number = {40},
pages = {},
pmid = {31582458},
issn = {2576-098X},
abstract = {Here, we announce the draft genome sequence of Brevibacillus sp. strain LEMMJ03, isolated from Whalers Bay sediment (Deception Island, Antarctica). In total, 4,500 coding sequences (CDS), among those 102 coding for tRNAs and 5 for noncoding RNAs (ncRNAs), were predicted from the 4.64-Mb genome. Predicted functions were for bacteriocin and degradation of aromatic compounds.},
}
@article {pmid31580006,
year = {2020},
author = {Li, X and Garbeva, P and Liu, X and Klein Gunnewiek, PJA and Clocchiatti, A and Hundscheid, MPJ and Wang, X and de Boer, W},
title = {Volatile-mediated antagonism of soil bacterial communities against fungi.},
journal = {Environmental microbiology},
volume = {22},
number = {3},
pages = {1025-1035},
pmid = {31580006},
issn = {1462-2920},
support = {BK20190040//Excellent Youth Foundation of Jiangsu Province/International ; 41671306//National Natural Science Foundation of China/International ; 2017YFD0200604//National Key Research and Development Program of China/International ; },
mesh = {Agriculture ; Antibiosis/*physiology ; *Bacterial Physiological Phenomena ; Fungi/drug effects/*physiology ; Microbiota ; *Soil Microbiology ; },
abstract = {Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil-borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non-sterile soil inoculums during exposure to volatiles emitted by soil-derived bacterial communities. We found that colonization of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile-mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis.},
}
@article {pmid31579614,
year = {2019},
author = {Benucci, GMN and Longley, R and Zhang, P and Zhao, Q and Bonito, G and Yu, F},
title = {Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7744},
pmid = {31579614},
issn = {2167-8359},
support = {T32 GM110523/GM/NIGMS NIH HHS/United States ; },
abstract = {Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.},
}
@article {pmid31578554,
year = {2020},
author = {An, SQ and Potnis, N and Dow, M and Vorhölter, FJ and He, YQ and Becker, A and Teper, D and Li, Y and Wang, N and Bleris, L and Tang, JL},
title = {Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas.},
journal = {FEMS microbiology reviews},
volume = {44},
number = {1},
pages = {1-32},
pmid = {31578554},
issn = {1574-6976},
support = {BB/R012415/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Adaptation, Physiological/*genetics ; Genome, Bacterial/genetics ; Host-Pathogen Interactions/*physiology ; Plant Diseases/*microbiology ; Plants/*microbiology ; Virulence/genetics ; Xanthomonas/genetics/*pathogenicity/*physiology ; },
abstract = {Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.},
}
@article {pmid31575762,
year = {2019},
author = {Brewer, TE and Aronson, EL and Arogyaswamy, K and Billings, SA and Botthoff, JK and Campbell, AN and Dove, NC and Fairbanks, D and Gallery, RE and Hart, SC and Kaye, J and King, G and Logan, G and Lohse, KA and Maltz, MR and Mayorga, E and O'Neill, C and Owens, SM and Packman, A and Pett-Ridge, J and Plante, AF and Richter, DD and Silver, WL and Yang, WH and Fierer, N},
title = {Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.},
journal = {mBio},
volume = {10},
number = {5},
pages = {},
pmid = {31575762},
issn = {2150-7511},
mesh = {Archaea/classification/growth &amp; development/*isolation &amp; purification ; Bacteria/classification/growth &amp; development/*isolation &amp; purification ; Metagenomics ; *Soil Microbiology ; },
abstract = {While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.},
}
@article {pmid31574348,
year = {2019},
author = {Carney, RL and Labbate, M and Siboni, N and Tagg, KA and Mitrovic, SM and Seymour, JR},
title = {Urban beaches are environmental hotspots for antibiotic resistance following rainfall.},
journal = {Water research},
volume = {167},
number = {},
pages = {115081},
doi = {10.1016/j.watres.2019.115081},
pmid = {31574348},
issn = {1879-2448},
mesh = {Anti-Bacterial Agents ; *Bacteria ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; RNA, Ribosomal, 16S ; Tetracycline ; *Wastewater ; },
abstract = {To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.},
}
@article {pmid31572496,
year = {2019},
author = {Mondo, SJ and Jiménez, DJ and Hector, RE and Lipzen, A and Yan, M and LaButti, K and Barry, K and van Elsas, JD and Grigoriev, IV and Nichols, NN},
title = {Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery.},
journal = {Biotechnology for biofuels},
volume = {12},
number = {},
pages = {229},
pmid = {31572496},
issn = {1754-6834},
abstract = {BACKGROUND: Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1).<br><br>RESULTS: The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting&#x2009;~&#x2009;98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the&#xa0;high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the&#xa0;2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (&#x3b1;-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source.<br><br>CONCLUSIONS: We provide data that suggest that&#xa0;a recent hybridization between the genomes of&#xa0;related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain&#xa0;2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes&#xa0;were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and "eco-enzymology" of lignocellulolytic Coniochaeta species.},
}
@article {pmid31572347,
year = {2019},
author = {Dagher, DJ and de la Providencia, IE and Pitre, FE and St-Arnaud, M and Hijri, M},
title = {Plant Identity Shaped Rhizospheric Microbial Communities More Strongly Than Bacterial Bioaugmentation in Petroleum Hydrocarbon-Polluted Sediments.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2144},
pmid = {31572347},
issn = {1664-302X},
abstract = {Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.},
}
@article {pmid31572346,
year = {2019},
author = {Schweitzer-Natan, O and Ofek-Lalzar, M and Sher, D and Sukenik, A},
title = {Particle-Associated Microbial Community in a Subtropical Lake During Thermal Mixing and Phytoplankton Succession.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2142},
pmid = {31572346},
issn = {1664-302X},
abstract = {Ecosystem dynamics in monomictic lakes are characterized by seasonal thermal mixing and stratification. These physical processes bring about seasonal variations in nutrients and organic matter fluxes, affecting the biogeochemical processes that occur in the water column. Physical and chemical dynamics are generally reflected in seasonal structural changes in the phytoplankton and bacterio-plankton community. In this study, we analyzed, using 16S rRNA amplicon sequencing, the structure of the bacterial community associated with large particles (>20 μm) in Lake Kinneret (Sea of Galilee, Israel), and its associations to phytoplankton populations. The study was carried out during late winter and early spring, a highly dynamic period in terms of thermal mixing, nutrient availability, and shifts in phytoplankton composition. Structural changes in the bacterioplankton population corresponded with limnological variations in the lake. In terms of the entire heterotrophic community, the structural patterns of particle-associated bacteria were mainly correlated with abiotic factors such as pH, ammonia, water temperature and nitrate. However, analysis of microbial taxon-specific correlations with phytoplankton species revealed a strong potential link between specific bacterial populations and the presence of different phytoplankton species, such as the cyanobacterium Microcystis, as well as the dinoflagellates Peridinium and Peridiniopsis. We found that Brevundimonas, a common freshwater genus, and Bdellovibrio, a well-known Gram-negative bacteria predator, were positively associated to Microcystis, suggesting a potentially important role of these three taxa in the microbial ecology of the lake. Our results show that the dynamics of environmental abiotic conditions, rather than specific phytoplankton assemblages, are the main factors positively correlated with changes in the community structure as a whole. Nevertheless, some specific bacteria may interact and be linked with specific phytoplankton, which may potentially control the dynamic patterns of the microbial community.},
}
@article {pmid31572315,
year = {2019},
author = {Shin, GY and Schachterle, JK and Shyntum, DY and Moleleki, LN and Coutinho, TA and Sundin, GW},
title = {Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2075},
pmid = {31572315},
issn = {1664-302X},
abstract = {To successfully infect plant hosts, the collective regulation of virulence factors in a bacterial pathogen is crucial. Hfq is an RNA chaperone protein that facilitates the small RNA (sRNA) regulation of global gene expression at the post-transcriptional level. In this study, the functional role of Hfq in a broad host range phytopathogen Pantoea ananatis was determined. Inactivation of the hfq gene in P. ananatis LMG 2665[T] resulted in the loss of pathogenicity and motility. In addition, there was a significant reduction of quorum sensing signal molecule acyl-homoserine lactone (AHL) production and biofilm formation. Differential sRNA expression analysis between the hfq mutant and wild-type strains of P. ananatis revealed 276 sRNAs affected in their abundance by the loss of hfq at low (OD600 = 0.2) and high cell (OD600 = 0.6) densities. Further analysis identified 25 Hfq-dependent sRNAs, all showing a predicted Rho-independent terminator of transcription and mapping within intergenic regions of the P. ananatis genome. These included known sRNAs such as ArcZ, FnrS, GlmZ, RprA, RyeB, RyhB, RyhB2, Spot42, and SsrA, and 16 novel P. ananatis sRNAs. The current study demonstrated that Hfq is an important component of the collective regulation of virulence factors and sets a foundation for understanding Hfq-sRNA mediated regulation in the phytopathogen P. ananatis.},
}
@article {pmid31566612,
year = {2019},
author = {Šimek, K and Sirova, D},
title = {Fluorescently Labeled Bacteria as a Tracer to Reveal Novel Pathways of Organic Carbon Flow in Aquatic Ecosystems.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {151},
pages = {},
doi = {10.3791/59903},
pmid = {31566612},
issn = {1940-087X},
mesh = {Animals ; Bacteria/*metabolism ; Carbon/*metabolism ; Czech Republic ; Eukaryota ; *Food Chain ; *Microbiota ; *Predatory Behavior ; Rivers ; Tetrahymena/*physiology ; *Water Microbiology ; },
abstract = {Elucidating trophic interactions, such as predation and its effects, is a frequent task for many researchers in ecology. The study of microbial communities has many limitations, and determining a predator, prey, and predatory rates is often difficult. Presented here is an optimized method based on the addition of fluorescently labelled prey as a tracer, which allows for reliable quantitation of the grazing rates in aquatic predatory eukaryotes and estimation of nutrient transfer to higher trophic levels.},
}
@article {pmid31565058,
year = {2019},
author = {Ahmed, EH and Hassan, HM and El-Sherbiny, NM and Soliman, AMA},
title = {Bacteriological Monitoring of Inanimate Surfaces and Equipment in Some Referral Hospitals in Assiut City, Egypt.},
journal = {International journal of microbiology},
volume = {2019},
number = {},
pages = {5907507},
pmid = {31565058},
issn = {1687-918X},
abstract = {Hospital-acquired infections represent a serious public health problem in all countries. It is clear that monitoring of the hospital environment is an essential element in the control and a part of the policy for preventing nosocomial infections. It allows a better understanding of the microbial ecology for the purpose of conducting preventive and corrective actions. The aims of this work were to determine the percentage of bacterial contamination of environmental samples and to identify potential nosocomial pathogens isolated from environments of seven referral hospitals from 2009 to 2015. By using the swab technique, 12863 samples were collected. Qualitative and quantitative cultures were performed. The organisms were primarily identified by colony morphology, microscopy of Gram stain, and standard biochemical tests. 25.6% of total samples showed contamination (93% was monomicrobial and 7.0% was polymicrobial). The predominant species was coagulase-negative staphylococcus (CNS) (32%), followed by methicillin-resistant S. aureus (MRSA) (26%) and then K. pneumonia (10.6%). The percentage of contamination varied among the covered hospitals and according to the year of monitoring with highly statistically significant difference (p value < 0.001). Direct contact with environmental surfaces or equipment transmits the majority of nosocomial infection. Major nosocomial pathogens have been identified. Hospital managers and healthcare bodies must be aware of the reality of the concept of environmental bacterial tanks and the need for respect of biocleaning procedures and choice of biocleaning tools.},
}
@article {pmid31563048,
year = {2019},
author = {Villegas-Plazas, M and Sanabria, J and Junca, H},
title = {A composite taxonomical and functional framework of microbiomes under acid mine drainage bioremediation systems.},
journal = {Journal of environmental management},
volume = {251},
number = {},
pages = {109581},
doi = {10.1016/j.jenvman.2019.109581},
pmid = {31563048},
issn = {1095-8630},
mesh = {Acids ; Biodegradation, Environmental ; Bioreactors ; *Microbiota ; *Mining ; },
abstract = {Mining-industry is one of the most important activities in the economic development of many countries and produces highly significant alterations on the environment, mainly due to the release of a strong acidic metal-rich wastewater called acid mine drainage (AMD). Consequently, the establishment of multiple wastewater treatment strategies remains as a fundamental challenge in AMD research. Bioremediation, as a constantly-evolving multidisciplinary endeavor had been complemented during the last decades by novel tools of increasingly higher resolution such as those based on omics approaches, which are providing detailed insights into the ecology, evolution and mechanisms of microbial communities acting in bioremediation processes. This review specifically addresses, reanalyzes and reexamines in a composite comparative manner, the available sequence information and associated metadata available in public databases about AMD impacted microbial communities; summarizing our understanding of its composition and functions, and proposing potential genetic enhancements for improved bioremediation strategies. 16 S rRNA gene-targeted sequencing data from 9 studies previously published including AMD systems reported and studied around the world, were collected and reanalyzed to compare and identify the core and most abundant genera in four distinct AMD ecosystems: surface biofilm, water, impacted soils/sediments and bioreactor microbiomes. We determined that the microbial communities of bioreactors were the most diverse in bacterial types detected. The metabolic pathways predicted strongly suggest the key role of syntrophic communities with denitrification, methanogenesis, manganese, sulfate and iron reduction. The perspectives to explore the dynamics of engineering systems by high-throughput sequencing and biochemical techniques are discussed and foreseen application of synthetic biology and omics exploration on improved AMD biotransformation are proposed.},
}
@article {pmid31562384,
year = {2020},
author = {Assié, A and Leisch, N and Meier, DV and Gruber-Vodicka, H and Tegetmeyer, HE and Meyerdierks, A and Kleiner, M and Hinzke, T and Joye, S and Saxton, M and Dubilier, N and Petersen, JM},
title = {Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).},
journal = {The ISME journal},
volume = {14},
number = {1},
pages = {104-122},
pmid = {31562384},
issn = {1751-7370},
mesh = {Animals ; Bivalvia/microbiology ; Carbon Cycle ; Citric Acid Cycle ; Epsilonproteobacteria/classification/genetics/*metabolism ; Gammaproteobacteria/genetics ; *Photosynthesis ; Phylogeny ; Symbiosis ; },
abstract = {Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that "Ca. Thiobarba" switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated "Ca. Thiobarba". Direct stable isotope fingerprinting showed that "Ca. Thiobarba" has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.},
}
@article {pmid31562166,
year = {2019},
author = {Joyce, RE and Lavender, H and Farrar, J and Werth, JT and Weber, CF and D'Andrilli, J and Vaitilingom, M and Christner, BC},
title = {Biological Ice-Nucleating Particles Deposited Year-Round in Subtropical Precipitation.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {23},
pages = {},
pmid = {31562166},
issn = {1098-5336},
mesh = {Atmosphere ; *Bacterial Physiological Phenomena ; Freezing ; *Ice ; Louisiana ; *Rain ; Seasons ; Temperature ; },
abstract = {Airborne bacteria that nucleate ice at relatively warm temperatures (>-10°C) can interact with cloud water droplets, affecting the formation of ice in clouds and the residency time of the cells in the atmosphere. We sampled 65 precipitation events in southeastern Louisiana over 2 years to examine the effect of season, meteorological conditions, storm type, and ecoregion source on the concentration and type of ice-nucleating particles (INPs) deposited. INPs sensitive to heat treatment were inferred to be biological in origin, and the highest concentrations of biological INPs (∼16,000 INPs liter[-1] active at ≥-10°C) were observed in snow and sleet samples from wintertime nimbostratus clouds with cloud top temperatures as warm as -7°C. Statistical analysis revealed three temperature classes of biological INPs (INPs active from -5 to -10°C, -11 to -12°C, and -13 to -14°C) and one temperature class of INPs that were sensitive to lysozyme (i.e., bacterial INPs, active from -5 to -10°C). Significant correlations between the INP data and abundances of taxa in the Bacteroidetes, Firmicutes, and unclassified bacterial divisions implied that certain members of these phyla may possess the ice nucleation phenotype. The interrelation between the INP classes and fluorescent dissolved organic matter, major ion concentrations (Na[+], Cl[-], SO4[2-], and NO3[-]), and backward air mass trajectories indicated that the highest concentrations of INPs were sourced from high-latitude North American and Asian continental environments, whereas the lowest values were observed when air was sourced from marine ecoregions. The intra- and extracontinental regions identified as sources of biological INPs in precipitation deposited in the southeastern United States suggests that these bioaerosols can disperse and affect meteorological conditions thousands of kilometers from their terrestrial points of origin.IMPORTANCE The particles most effective at inducing the freezing of water in the atmosphere are microbiological in origin; however, information on the species harboring this phenotype, their environmental distribution, and ecological sources are very limited. Analysis of precipitation collected over 2 years in Louisiana showed that INPs active at the warmest temperatures were sourced from terrestrial ecosystems and displayed behaviors that implicated specific bacterial taxa as the source of the ice nucleation activity. The abundance of biological INPs was highest in precipitation from winter storms and implied that their in-cloud concentrations were sufficient to affect the formation of ice and precipitation in nimbostratus clouds.},
}
@article {pmid31559142,
year = {2019},
author = {Zheng, P and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Pan, J and Duan, J and Liang, W and Yin, B and Deng, F and Perry, SW and Wong, ML and Licinio, J and Wei, H and Yu, G and Xie, P},
title = {Perturbed Microbial Ecology in Myasthenia Gravis: Evidence from the Gut Microbiome and Fecal Metabolome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {6},
number = {18},
pages = {1901441},
pmid = {31559142},
issn = {2198-3844},
abstract = {Myasthenia gravis (MG) is a devastating acquired autoimmune disease. Emerging evidence indicates that the gut microbiome plays a key role in maintaining immune system homeostasis. This work reports that MG is characterized by decreased α-phylogenetic diversity, and significantly disturbed gut microbiome and fecal metabolome. The altered gut microbial composition is associated with fecal metabolome changes, with 38.75% of altered bacterial operational taxonomic units showing significant correlations with a range of metabolite biomarkers. Some microbes are particularly linked with MG severity. Moreover, a combination of microbial makers and their correlated metabolites enable discriminating MG from healthy controls (HCs) with 100% accuracy. To investigate whether disturbed gut mcirobiome might contribute to the onset of MG, germ-free (GF) mice are initially colonized with MG microbiota (MMb) or healthy microbiota (HMb), and then immunized in a classic mouse model of MG. The MMb mice demonstrate substantially impaired locomotion ability compared with the HMb mice. This effect could be reversed by cocolonizing GF mice with both MMb and HMb. The MMb mice also exhibit similar disturbances of fecal metabolic pathways as found in MG. Together these data demonstrate disturbances in microbiome composition and activity that are likely to be relevant to the pathogenesis of MG.},
}
@article {pmid31557953,
year = {2019},
author = {Zhang, Z and Mocanu, V and Cai, C and Dang, J and Slater, L and Deehan, EC and Walter, J and Madsen, KL},
title = {Impact of Fecal Microbiota Transplantation on Obesity and Metabolic Syndrome-A Systematic Review.},
journal = {Nutrients},
volume = {11},
number = {10},
pages = {},
pmid = {31557953},
issn = {2072-6643},
support = {./CAPMC/CIHR/Canada ; },
mesh = {*Fecal Microbiota Transplantation ; Humans ; Metabolic Syndrome/*therapy ; Obesity/*therapy ; },
abstract = {Fecal microbiota transplantation (FMT) is a gut microbial-modulation strategy that has been investigated for the treatment of a variety of human diseases, including obesity-associated metabolic disorders. This study appraises current literature and provides an overview of the effectiveness and limitations of FMT as a potential therapeutic strategy for obesity and metabolic syndrome (MS). Five electronic databases and two gray literature sources were searched up to 10 December 2018. All interventional and observational studies that contained information on the relevant population (adult patients with obesity and MS), intervention (receiving allogeneic FMT) and outcomes (metabolic parameters) were eligible. From 1096 unique citations, three randomized placebo-controlled studies (76 patients with obesity and MS, body mass index = 34.8 ± 4.1 kg/m[2], fasting plasma glucose = 5.8 ± 0.7 mmol/L) were included for review. Studies reported mixed results with regards to improvement in metabolic parameters. Two studies reported improved peripheral insulin sensitivity (rate of glucose disappearance, RD) at 6 weeks in patients receiving donor FMT versus patients receiving the placebo control. In addition, one study observed lower HbA1c levels in FMT patients at 6 weeks. No differences in fasting plasma glucose, hepatic insulin sensitivity, body mass index (BMI), or cholesterol markers were observed between two groups across all included studies. While promising, the influence of FMT on long-term clinical endpoints needs to be further explored. Future studies are also required to better understand the mechanisms through which changes in gut microbial ecology and engraftment of microbiota affect metabolic outcomes for patients with obesity and MS. In addition, further research is needed to better define the optimal fecal microbial preparation, dosing, and method of delivery.},
}
@article {pmid31557655,
year = {2019},
author = {Wang, Y and Lin, Z and He, L and Huang, W and Zhou, J and He, Q},
title = {Simultaneous partial nitrification, anammox and denitrification (SNAD) process for nitrogen and refractory organic compounds removal from mature landfill leachate: Performance and metagenome-based microbial ecology.},
journal = {Bioresource technology},
volume = {294},
number = {},
pages = {122166},
doi = {10.1016/j.biortech.2019.122166},
pmid = {31557655},
issn = {1873-2976},
mesh = {Bioreactors ; Denitrification ; Metagenome ; *Nitrification ; Nitrogen ; Oxidation-Reduction ; *Water Pollutants, Chemical ; },
abstract = {In this study, a simultaneous partial nitrification, Anammox and denitrification (SNAD) bioreactor was constructed for mature landfill leachate treatment, which exhibited favorable NH4[+]-N (98.9-99.9%), TN (90.7-94.9%) and bio-refractory organic compounds (46.2-67.7%) removal efficiencies. Stoichiometric analysis demonstrated that the synergy of ammonium-oxidizing bacteria and Anammox bacteria dominated TN removal (96.1-97.2%). NO3[-]-N produced in Anammox could be further reduced through (partial) denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The results highlighted that humic-like and their intermediates might serve as the electron donor for these (partial) denitrifiers and DNRA bacteria to remove NO3[-]-N, and could be effectively removed from mature landfill leachate in SNAD bioreactor. Metagenomic characterization further demonstrated that phyla Chloroflexi, Chlorobi and genera Nitrosomonas, Ignavibacterium and Aminiphilus might be responsible for such humic-like degradation. Overall, this work offers new insights into the metagenome-based bioinformatic roles for the previously understudied microorganisms in SNAD bioreactor for mature landfill leachate treatment.},
}
@article {pmid31557445,
year = {2020},
author = {Þorsteinsdóttir, GV and Blischke, A and Sigurbjörnsdóttir, MA and Òskarsson, F and Arnarson, &#xde;S and Magnússon, KP and Vilhelmsson, O},
title = {Gas seepage pockmark microbiomes suggest the presence of sedimentary coal seams in the Öxarfjörður graben of northeastern Iceland.},
journal = {Canadian journal of microbiology},
volume = {66},
number = {1},
pages = {25-38},
doi = {10.1139/cjm-2019-0081},
pmid = {31557445},
issn = {1480-3275},
mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Bioprospecting ; Coal/analysis/*microbiology ; Geologic Sediments/chemistry/*microbiology ; Hydrocarbons/analysis ; Iceland ; Methane/analysis ; *Microbiota/genetics ; Natural Gas/analysis/*microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Natural gas seepage pockmarks are found off- and onshore in the Öxarfjörður graben, Iceland. The bacterial communities of two onshore seepage sites were analysed by 16S rRNA gene amplicon sequencing; the geochemical characteristics, hydrocarbon content, and the carbon isotope composition of the sites were also determined. While one site was found to be characterised by biogenic origin of methane gas, with a carbon isotope ratio (δ[13]C (‰)) of -63.2, high contents of organic matter and complex hydrocarbons, the other site showed a mixed origin of the methane gas (δ[13]C (‰) = -26.6) with geothermal characteristics and lower organic matter content. While both sites harboured Proteobacteria as the most abundant bacterial phyla, the Deltaproteobacteria were more abundant at the geothermal site and the Alphaproteobacteria at the biogenic site. The Dehalococcoidia class of phylum Chloroflexi was abundant at the geothermal site while the Anaerolineae class was more abundant at the biogenic site. Bacterial strains from the seepage pockmarks were isolated on a variety of selective media targeting bacteria with bioremediation potential. A total of 106 strains were isolated and characterised, including representatives from the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. This article describes the first microbial study on gas seepage pockmarks in Iceland.},
}
@article {pmid31556187,
year = {2020},
author = {Tang, HC and Sieo, CC and Abdullah, N and Chong, CW and Gan, HM and Mohd Asrore, MS and Yong, CY and Omar, AR and Ho, YW},
title = {Effects of supplementing freeze-dried Mitsuokella jalaludinii phytase on the growth performance and gut microbial diversity of broiler chickens.},
journal = {Journal of animal physiology and animal nutrition},
volume = {104},
number = {1},
pages = {116-125},
doi = {10.1111/jpn.13208},
pmid = {31556187},
issn = {1439-0396},
support = {06-01-04-SF1376//eScience Fund/ ; },
mesh = {6-Phytase/metabolism/*pharmacology ; Animals ; Bacteria/genetics ; Chickens/*growth &amp; development/*microbiology ; Dietary Supplements ; Firmicutes/*enzymology ; Freeze Drying ; Gastrointestinal Microbiome/*drug effects ; Male ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Weight Gain/drug effects ; },
abstract = {Inclusion of phytase in animal feedstuff is a common practice to enhance nutrients availability. However, little is known about the effects of phytase supplementation on the microbial ecology of the gastrointestinal tract. In this study, freeze-dried Mitsuokella jalaludinii phytase (MJ) was evaluated in a feeding trial with broilers fed a low available phosphorus (aP) diet. A total of 180 male broiler chicks (day-old Cobb) were assigned into three dietary treatments: Control fed with 0.4% (w/w) of available phosphorus (aP); Group T1 fed low aP [0.2% (w/w)] supplemented with MJ; and T2 fed low aP and deactivated MJ. The source of readily available P, dicalcium phosphate (DCP), was removed from low aP diet, whereby additional limestone was provided to replace the amount of Ca normally found in DCP. For each treatment, 4 replicate pens were used, where each pen consisted of 15 animals. The animals' energy intake and caecal bacterial community were monitored weekly for up to 3 weeks. The apparent metabolizable energy (AME) and apparent digestibility of dry matter (ADDM) of broilers fed with different diets were determined. In addition, the caecal microbial diversities of broilers were assessed using high-throughput next-generation sequencing targeting the V3-V4 region of bacterial 16S rRNA. The results showed that broilers fed with T1 diet have better feed conversion ratio (FCR) when compared to the Control (p < .05) and T2 diets (p < .05), demonstrating the efficiency of MJ as a supplement to low aP diet. Nevertheless, MJ did not significantly affect the microbial population and diversity in broilers' caeca, which mainly consists of members from Bacteroidetes, Firmicutes, and Proteobacteria. Regardless, significant variations in the caecal bacterial composition were observed over time, probably due to succession as the broilers aged. This is the first reported study on the effect of MJ on the microbial diversity of broiler's caeca.},
}
@article {pmid31555253,
year = {2019},
author = {Sarkar, A and Morita, D and Ghosh, A and Chowdhury, G and Mukhopadhyay, AK and Okamoto, K and Ramamurthy, T},
title = {Altered Integrative and Conjugative Elements (ICEs) in Recent Vibrio cholerae O1 Isolated From Cholera Cases, Kolkata, India.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2072},
pmid = {31555253},
issn = {1664-302X},
abstract = {The self-transferring integrative and conjugative elements (ICEs) are large genomic segments carrying several bacterial adaptive functions including antimicrobial resistance (AMR). SXT/R391 family is one of the ICEs extensively studied in cholera-causing pathogen Vibrio cholerae. The genetic characteristics of ICE-SXT/R391 in V. cholerae are dynamic and region-specific. These ICEs in V. cholerae are strongly correlated with resistance to several antibiotics such as tetracycline, streptomycin and trimethoprim-sulfamethoxazole. We screened V. cholerae O1 strains isolated from cholera patients in Kolkata, India from 2008 to 2015 for antibiotic susceptibility and the presence of ICEs, and subsequently sequenced their conserved genes. Resistance to tetracycline, streptomycin and trimethoprim-sulfamethoxazole was detected in strains isolated during 2008-2010 and 2014-2015. The genes encoding resistance to tetracycline (tetA), trimethoprim-sulfamethoxazole (dfrA1 and sul2), streptomycin (strAB), and chloramphenicol (floR) were detected in the ICEs of these strains. There was a decrease in overall drug resistance in V. cholerae associated with the ICEs in 2011. DNA sequence analysis also showed that AMR in these strains was conferred mainly by two types of ICEs, i.e., ICE[TET] (comprising tetA, strAB, sul2, and dfrA1) and ICE[GEN] (floR, strAB, sul2, and dfrA1). Based on the genetic structure, Kolkata strains of V. cholerae O1 had distinct genetic traits different from the ICEs reported in other cholera endemic regions. Transfer of AMR was confirmed by conjugation with sodium azide resistant Escherichia coli J53. In addition to the acquired resistance to streptomycin and trimethoprim-sulfamethoxazole, the conjugally transferred (CT) E. coli J53 with ICE showed higher resistance to chloramphenicol and tetracycline than the donor V. cholerae. Pulsed-field gel electrophoresis (PFGE) based clonal analysis revealed that the V. cholerae strains could be grouped based on their ICEs and AMR patterns. Our findings demonstrate the epidemiological importance of ICEs and their role in the emergence of multidrug resistance (MDR) in El Tor vibrios.},
}
@article {pmid31555238,
year = {2019},
author = {Pires, ES and Hardoim, CCP and Miranda, KR and Secco, DA and Lobo, LA and de Carvalho, DP and Han, J and Borchers, CH and Ferreira, RBR and Salles, JF and Domingues, RMCP and Antunes, LCM},
title = {The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2003},
pmid = {31555238},
issn = {1664-302X},
abstract = {During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pathogens, and are also intricately linked to nutrition. The parameters that affect the establishment and maintenance of these microbial communities are diverse, and include the genetic background, mode of birth, nutrition, hygiene, and host lifestyle in general. Here, we describe the characterization of the gut microbiome of individuals living in the Amazon, and the comparison of these microbial communities to those found in individuals from an urban, industrialized setting. Our results showed striking differences in microbial communities from these two types of populations. Additionally, we used high-throughput metabolomics to study the chemical ecology of the gut environment and found significant metabolic changes between the two populations. Although we cannot point out a single cause for the microbial and metabolic changes observed between Amazonian and urban individuals, they are likely to include dietary differences as well as diverse patterns of environmental exposure. To our knowledge, this is the first description of gut microbial and metabolic profiles in Amazonian populations, and it provides a starting point for thorough characterizations of the impact of individual environmental conditions on the human microbiome and metabolome.},
}
@article {pmid31554820,
year = {2019},
author = {Riva, A and Kuzyk, O and Forsberg, E and Siuzdak, G and Pfann, C and Herbold, C and Daims, H and Loy, A and Warth, B and Berry, D},
title = {A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4366},
pmid = {31554820},
issn = {2041-1723},
support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; Colon/*microbiology ; *Diet ; Dietary Fiber/*deficiency ; Gastrointestinal Microbiome/genetics/*physiology ; Intestinal Mucosa/microbiology ; Metagenomics/methods ; Mice, Inbred C57BL ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.},
}
@article {pmid31554088,
year = {2019},
author = {Vissenaekens, H and Grootaert, C and Rajkovic, A and De Schutter, K and Raes, K and Smagghe, G and Van de Wiele, T and Van Camp, J},
title = {Cell line-dependent increase in cellular quercetin accumulation upon stress induced by valinomycin and lipopolysaccharide, but not by TNF-α.},
journal = {Food research international (Ottawa, Ont.)},
volume = {125},
number = {},
pages = {108596},
doi = {10.1016/j.foodres.2019.108596},
pmid = {31554088},
issn = {1873-7145},
mesh = {Antioxidants/pharmacology ; Caco-2 Cells ; Cell Line ; Cell Proliferation/drug effects ; Endothelial Cells/drug effects/metabolism ; Flavonoids/pharmacology ; HCT116 Cells ; Humans ; Intestinal Mucosa/cytology/drug effects/metabolism ; Lipopolysaccharides/*toxicity ; Quercetin/*pharmacology ; Stress, Physiological/*drug effects ; Tumor Necrosis Factor-alpha/*metabolism ; Valinomycin/*toxicity ; },
abstract = {As the interface between the luminal and internal environment, the intestinal epithelium is strongly exposed to food-related, host-related and microbial stress. Furthermore, the endothelial stress response plays an important role in vascular disease development, which may be improved upon consumption of dietary bioactives such as polyphenols. The impact of the latter, however, is largely individual-dependent and effects are, in most cases, only observed under mild diseased conditions. Here, it is hypothesized that the individual's stressor levels may contribute to this variable response. To this end, the impact of the stressors (i) valinomycin (as model for cereulide, food-related microbial metabolite), (ii) TNF-α (host-related) and (iii) lipopolysaccharide (gram-negative bacterial cell related) on flavonoid accumulation was investigated in several intestinal and endothelial cell lines. Flow cytometry, confocal microscopy and an in-house developed, robust and high-throughput spectrofluorometric method, showed that quercetin accumulated in all tested cell lines in a dose-dependent manner. Upon stress induced by valinomycin and to a lesser extent by lipopolysaccharide, but not by TNF-α, an increased quercetin accumulation was observed in proliferating intestinal and endothelial cells and not in differentiated intestinal or quiescent endothelial cells. Therefore, flavonoid accumulation may be a potential cellular stress response mechanism which strongly depends on the applied stressor, flavonoid, cell line and even growth conditions. This opens perspectives for further understanding the mechanisms by which cellular stress may shape the individual's response to bioactive compounds.},
}
@article {pmid31553939,
year = {2019},
author = {Zhang, Y and Shen, Z and Zhang, F and Yu, Y and Li, J and Lin, X},
title = {Taxonomy and phylogeny of Pseudovorticella littoralis sp. n. and P. alani sp. n. (Ciliophora: Peritrichia) from coastal waters of southern China.},
journal = {European journal of protistology},
volume = {71},
number = {},
pages = {125635},
doi = {10.1016/j.ejop.2019.125635},
pmid = {31553939},
issn = {1618-0429},
mesh = {China ; Oligohymenophorea/*classification/cytology/genetics ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Seawater/*parasitology ; Species Specificity ; },
abstract = {The morphology, infraciliature, and silverline system of two peritrich ciliates, Pseudovorticella littoralis sp. n. and P. alani sp. n., isolated from coastal waters of southern China, were investigated based on both living and silver-stained specimens. Pseudovorticella littoralis sp. n. is characterized by the following combination of characters: cell inverted cone-shaped; contractile vacuole ventral; J-shaped macronucleus; infundibular polykinety 3 with two kinetosome rows of equal length; 19-26 silverlines from peristome to trochal band and 5-14 from trochal band to scopula. Pseudovorticella alani sp. n. is characterized by: cell inverted bell-shaped; contractile vacuole ventral; J-shaped macronucleus recurved almost forming a loop; infundibular polykinety 3 with three kinetosome rows, outer two rows longer than inner one; 48-61 silverlines between peristome and aboral trochal band, and 12-20 between aboral trochal band and scopula. The SSU rDNA sequences of both new species are reported and their genetic distances with congeners and phylogenetic relationships are investigated. Pseudovorticella and Epicarchesium cluster into two subclades with low support values. One subclade contains nearly all the available sequences of Pseudovorticella and Epicarchesium. Another one contains P. monilata and E. pectinatum. This calls on the need of a generic re-classification of Pseudovorticella and Epicarchesium based on more morphological and molecular data.},
}
@article {pmid31553931,
year = {2019},
author = {Subirats, J and Di Cesare, A and Varela Della Giustina, S and Fiorentino, A and Eckert, EM and Rodriguez-Mozaz, S and Borrego, CM and Corno, G},
title = {High-quality treated wastewater causes remarkable changes in natural microbial communities and intI1 gene abundance.},
journal = {Water research},
volume = {167},
number = {},
pages = {114895},
doi = {10.1016/j.watres.2019.114895},
pmid = {31553931},
issn = {1879-2448},
mesh = {Anti-Bacterial Agents ; Genes, Bacterial ; Integrases ; Integrons ; *Microbiota ; *Wastewater ; },
abstract = {We carry out a mesocosms experiment to assess the impact of high-quality treated wastewater intended for agricultural reuse (HQWR) on freshwater bacteria seldom exposed to anthropogenic pollution. Effects were assessed by comparing the abundance and composition of bacterial communities as well as their resistance profile under control (source water from an unpolluted lake) and treatment conditions (source water mixed 1:1 with HQWR, with and without 5 μg L[-1] of cefotaxime). We investigated the effect of the different conditions on the abundance of genes encoding resistance to β-lactams and carbapenems (blaTEM, blaCTX-M, blaOXA, and blaKPC), fluoroquinolones (qnrS), tetracyclines (tetA), sulfonamides (sul2), macrolides (ermB), arsenic and cadmium (arsB and czcA, respectively), and on the gene encoding the Class 1 integron integrase (intI1). Bacterial communities exposed to HQWR showed a significant higher abundance of tetA, arsB, czcA, and intI1 genes, whereas those exposed to Cefotaxime-amended HQWR did not. Genes conferring resistance to carbapenems, β-lactams, fluoroquinolones, and macrolides were below detection limit in all treatments. Besides, the higher availability of nutrients under treatment conditions favored bacterial growth in comparison to those exposed to control conditions. Particularly, Acinetobacter spp. and Pseudomonas spp. were significantly enriched after 22 days of treatment exposure. The presence of cefotaxime (a third generation cephalosporine) in the feeding medium caused an enrichment of bacterial communities in sequences affiliated to Acinetobacter thus suggesting that these resistant forms may possess resistance genes other than those studied here (blaCTX-M, blaOXA, and blaKPC). Although derived from a mesocosm experiment in continuous cultures, our results call attention to the need of refined regulations regarding the use of reclaimed water in agriculture since even high-quality treated wastewater may lead to undesired effects on receiving bacterial communities in terms of composition and dissemination of antibiotic resistance genes.},
}
@article {pmid31553930,
year = {2019},
author = {Regnery, J and Parrhysius, P and Schulz, RS and Möhlenkamp, C and Buchmeier, G and Reifferscheid, G and Brinke, M},
title = {Wastewater-borne exposure of limnic fish to anticoagulant rodenticides.},
journal = {Water research},
volume = {167},
number = {},
pages = {115090},
doi = {10.1016/j.watres.2019.115090},
pmid = {31553930},
issn = {1879-2448},
mesh = {Animals ; Anticoagulants ; Environmental Monitoring ; Germany ; Retrospective Studies ; *Rodenticides ; Wastewater ; *Water Pollutants, Chemical ; },
abstract = {The recent emergence of second-generation anticoagulant rodenticides (AR) in the aquatic environment emphasizes the relevance and impact of aquatic exposure pathways during rodent control. Pest control in municipal sewer systems of urban and suburban areas is thought to be an important emission pathway for AR to reach wastewater and municipal wastewater treatment plants (WWTP), respectively. To circumstantiate that AR will enter streams via effluent discharges and bioaccumulate in aquatic organisms despite very low predicted environmental emissions, we conducted a retrospective biological monitoring of fish tissue samples from different WWTP fish monitoring ponds exclusively fed by municipal effluents in Bavaria, Germany. At the same time, information about rodent control in associated sewer systems was collected by telephone survey to assess relationships between sewer baiting and rodenticide residues in fish. In addition, mussel and fish tissue samples from several Bavarian surface waters with different effluent impact were analyzed to evaluate the prevalence of anticoagulants in indigenous aquatic organisms. Hepatic AR residues were detected at 12 out of 25 WWTP sampling sites in the low μg/kg range, thereof six sites with one or more second-generation AR (i.e., brodifacoum, difenacoum, bromadiolone). 14 of 18 surveyed sites confirmed sewer baiting with AR and detected hepatic residues matched the reported active ingredients used for sewer baiting at six sites. Furthermore, second-generation AR were detected in more than 80% of fish liver samples from investigated Bavarian streams. Highest total hepatic AR concentrations in these fish were 9.1 and 8.5 μg/kg wet weight, respectively and were observed at two riverine sampling sites characterized by close proximity to upstream WWTP outfalls. No anticoagulant residues were found in fish liver samples from two lakes without known influences of effluent discharges. The findings of our study clearly show incomplete removal of anticoagulants during conventional wastewater treatment and confirm exposure of aquatic organisms via municipal effluents. Based on the demonstrated temporal and spatial coherence between sewer baiting and hepatic AR residues in effluent-exposed fish, sewer baiting in combined sewer systems contributes to the release of active ingredients into the aquatic environment.},
}
@article {pmid31552450,
year = {2019},
author = {Wagner, AO and Praeg, N and Illmer, P},
title = {Spiking a Silty-Sand Reference Soil with Bacterial DNA: Limits and Pitfalls in the Discrimination of Live and Dead Cells When Applying Ethidium Monoazide (EMA) Treatment.},
journal = {Current microbiology},
volume = {76},
number = {12},
pages = {1425-1434},
pmid = {31552450},
issn = {1432-0991},
support = {P 22815/FWF_/Austrian Science Fund FWF/Austria ; P 22815//Austrian Science Fund/ ; },
mesh = {Affinity Labels/*chemistry ; Azides/*chemistry ; Bacteriological Techniques/*methods ; Colony Count, Microbial ; DNA, Bacterial/*chemistry/genetics/isolation &amp; purification ; Listeria monocytogenes/genetics/isolation &amp; purification/*physiology ; *Microbial Viability ; Polymerase Chain Reaction ; Soil Microbiology ; },
abstract = {In the present study, EMA (ethidium monoazide) treatment was applied to a silty-sand reference soil prior to DNA extraction to enable a differentiation between dead and living cells. For this purpose, a reference soil was spiked with Listeria monocytogenes cells or cell equivalents, respectively. With the purpose of evaluating optimum treatment conditions, different EMA concentrations have been tested. However, the results remained largely inconclusive. Furthermore, varied dark incubation periods allowing EMA to penetrate dead cells did not allow the selective removal of DNA from membrane-compromised cells in downstream analyses. In contrast to undiluted soil, an effect of EMA treatment during DNA extraction could be observed when using a 1:10 dilution of the reference soil; however, the effect has not been sufficiently selective to act on heat-treated cells only. Although the application of EMA to soil requires further evaluation, the procedure harbors future potential for improving DNA-based approaches in microbial ecology studies.},
}
@article {pmid31551063,
year = {2019},
author = {Keiser, CN and Hammer, TJ and Pruitt, JN},
title = {Social spider webs harbour largely consistent bacterial communities across broad spatial scales.},
journal = {Biology letters},
volume = {15},
number = {9},
pages = {20190436},
pmid = {31551063},
issn = {1744-957X},
mesh = {Animals ; Bacteria ; Predatory Behavior ; *Silk ; *Spiders ; },
abstract = {Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbour microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbours compositionally distinct microbes from the more ephemeral capture webs in the desert social spider, Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harboured similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey and web samples. These data suggest that social spider webs can harbour characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.},
}
@article {pmid31550548,
year = {2020},
author = {De Vrieze, J and Verbeeck, K and Pikaar, I and Boere, J and Van Wijk, A and Rabaey, K and Verstraete, W},
title = {The hydrogen gas bio-based economy and the production of renewable building block chemicals, food and energy.},
journal = {New biotechnology},
volume = {55},
number = {},
pages = {12-18},
doi = {10.1016/j.nbt.2019.09.004},
pmid = {31550548},
issn = {1876-4347},
mesh = {Bacterial Proteins/metabolism ; Biofuels/*economics ; Food/*economics ; Hydrogen/*chemistry ; Methane/metabolism ; Renewable Energy/*economics ; },
abstract = {The carrying capacity of the planet is being exceeded, and there is an urgent need to bring forward revolutionary approaches, particularly in terms of energy supply, carbon emissions and nitrogen inputs into the biosphere. Hydrogen gas, generated by means of renewable energy through water electrolysis, can be a platform molecule to drive the future bioeconomy and electrification in the 21[st] century. The potential to use hydrogen gas in microbial metabolic processes is highly versatile, and this opens a broad range of opportunities for novel biotechnological developments and applications. A first approach concerns the central role of hydrogen gas in the production of bio-based building block chemicals using the methane route, thus, bypassing the inherent low economic value of methane towards higher-value products. Second, hydrogen gas can serve as a key carbon-neutral source to produce third-generation proteins, i.e. microbial protein for food applications, whilst simultaneously enabling carbon capture and nutrient recovery, directly at their point of emission. Combining both approaches to deal with the intermittent nature of renewable energy sources maximises the ability for efficient use of renewable resources.},
}
@article {pmid31550268,
year = {2019},
author = {Mahjoubi, M and Aliyu, H and Cappello, S and Naifer, M and Souissi, Y and Cowan, DA and Cherif, A},
title = {The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity.},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0221574},
pmid = {31550268},
issn = {1932-6203},
mesh = {Alcaligenes/*genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Genome, Bacterial ; Geologic Sediments/microbiology ; Humans ; Hydrocarbons/*metabolism ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Phylogeny ; Species Specificity ; Surface-Active Agents/metabolism ; },
abstract = {Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.},
}
@article {pmid31548611,
year = {2019},
author = {Soares-Castro, P and Araújo-Rodrigues, H and Godoy-Vitorino, F and Ferreira, M and Covelo, P and López, A and Vingada, J and Eira, C and Santos, PM},
title = {Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {13679},
pmid = {31548611},
issn = {2045-2322},
support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; },
mesh = {Animals ; Biological Monitoring/*methods ; Cetacea/*microbiology ; DNA Barcoding, Taxonomic ; Microbiota/*physiology ; Mouth/*microbiology ; },
abstract = {The composition of mammalian microbiota has been related with the host health status. In this study, we assessed the oral microbiome of 3 cetacean species most commonly found stranded in Iberian Atlantic waters (Delphinus delphis, Stenella coeruleoalba and Phocoena phocoena), using 16S rDNA-amplicon metabarcoding. All oral microbiomes were dominated by Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria bacteria, which were also predominant in the oral cavity of Tursiops truncatus. A Constrained Canonical Analysis (CCA) showed that the major factors shaping the composition of 38 oral microbiomes (p-value < 0.05) were: (i) animal species and (ii) age class, segregating adults and juveniles. The correlation analysis also grouped the microbiomes by animal stranding location and health status. Similar discriminatory patterns were detected using the data from a previous study on Tursiops truncatus, indicating that this correlation approach may facilitate data comparisons between different studies on several cetacean species. This study identified a total of 15 bacterial genera and 27 OTUs discriminating between the observed CCA groups, which can be further explored as microbiota fingerprints to develop (i) specific diagnostic assays for cetacean population conservation and (ii) bio-monitoring approaches to assess the health of marine ecosystems from the Iberian Atlantic basin, using cetaceans as bioindicators.},
}
@article {pmid31548387,
year = {2019},
author = {Petersen, J and Vollmers, J and Ringel, V and Brinkmann, H and Ellebrandt-Sperling, C and Spröer, C and Howat, AM and Murrell, JC and Kaster, AK},
title = {A marine plasmid hitchhiking vast phylogenetic and geographic distances.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {41},
pages = {20568-20573},
pmid = {31548387},
issn = {1091-6490},
mesh = {Bacterial Proteins/*genetics ; *Environment ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Geography ; Phylogeny ; Plasmids/*genetics ; Recombination, Genetic ; Roseobacter/classification/*genetics ; },
abstract = {Horizontal gene transfer (HGT) plays an important role in bacterial evolution and serves as a driving force for bacterial diversity and versatility. HGT events often involve mobile genetic elements like plasmids, which can promote their own dissemination by associating with adaptive traits in the gene pool of the so-called mobilome. Novel traits that evolve through HGT can therefore lead to the exploitation of new ecological niches, prompting an adaptive radiation of bacterial species. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized RepL-type plasmid found in diverse members of the marine Roseobacter group across the globe. Noteworthy, 100% identical plasmids were detected in phylogenetically and geographically distant bacteria, revealing a so-far overlooked, but environmentally highly relevant vector for HGT. The genomic and functional characterization of this plasmid showed a completely conserved backbone dedicated to replication, stability, and mobilization as well as an interchangeable gene cassette with highly diverse, but recurring motifs. The majority of the latter appear to be involved in mechanisms coping with toxins and/or pollutants in the marine environment. Furthermore, we provide experimental evidence that the plasmid has the potential to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.},
}
@article {pmid31547186,
year = {2019},
author = {Messal, M and Slippers, B and Naidoo, S and Bezuidt, O and Kemler, M},
title = {Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone.},
journal = {Microorganisms},
volume = {7},
number = {10},
pages = {},
pmid = {31547186},
issn = {2076-2607},
abstract = {Fungi represent a common and diverse part of the microbial communities that associate with plants. They also commonly colonise various plant parts asymptomatically. The molecular mechanisms of these interactions are, however, poorly understood. In this study we use transcriptomic data from Eucalyptus grandis, to demonstrate that RNA-seq data are a neglected source of information to study fungal-host interactions, by exploring the fungal transcripts they inevitably contain. We identified fungal transcripts from E. grandis data based on their sequence dissimilarity to the E. grandis genome and predicted biological functions. Taxonomic classifications identified, amongst other fungi, many well-known pathogenic fungal taxa in the asymptomatic tissue of E. grandis. The comparison of a clone of E. grandis resistant to Chrysoporthe austroafricana with a susceptible clone revealed a significant difference in the number of fungal transcripts, while the number of fungal taxa was not substantially affected. Classifications of transcripts based on their respective biological functions showed that the fungal communities of the two E. grandis clones associate with fundamental biological processes, with some notable differences. To shield the greater host defence machinery in the resistant E. grandis clone, fungi produce more secondary metabolites, whereas the environment for fungi associated with the susceptible E. grandis clone is more conducive for building fungal cellular structures and biomass growth. Secreted proteins included carbohydrate active enzymes that potentially are involved in fungal-plant and fungal-microbe interactions. While plant transcriptome datasets cannot replace the need for designed experiments to probe plant-microbe interactions at a molecular level, they clearly hold potential to add to the understanding of the diversity of plant-microbe interactions.},
}
@article {pmid31547035,
year = {2019},
author = {Wang, J and Sun, Y and Tao, D and Wang, S and Li, C and Zheng, F and Wu, Z},
title = {Reduction of Escherichia coli O157:H7, Listeria monocytogenes, and Naturally Present Microbe Counts on Lettuce using an Acid Mixture of Acetic and Lactic Acid.},
journal = {Microorganisms},
volume = {7},
number = {10},
pages = {},
pmid = {31547035},
issn = {2076-2607},
abstract = {Lactic acid (LA) and acetic acid (AA) are independently used to disinfect fresh leaf vegetables. LA has a higher efficacy but costs more than AA. Herein, we compared the disinfection efficacy of LA, AA, and their mixture on lettuce to determine whether the cheaper acid mixture shows similar or more efficacy than LA. Quality analysis indicated that the acid mixture and individual acids did not cause additional loss of instrument color and polyphenolic content compared with that of the control; however, visible defects were observed at AA concentrations exceeding 0.8%. Analysis of Escherichia coli O157:H7, Listeria monocytogenes, and naturally present microbes (aerobic mesophilic and psychrotrophic bacteria, coliforms, molds, and yeasts) showed that the acid mixture led to the highest reduction in microbial count during storage. 16S rRNA sequencing was further employed to understand the effects of the acid mixture and individual acids on lettuce microbial ecology. During storage, the acid mixture and individual acids significantly decreased the abundance of Massilia spp. and Alkanindiges spp. but there was a marked increase in Escherichia-Shigella abundance (LA: 0.003-58.82%; AA: 0.01-55.34%; acid mixture: undetected to 50.71%; control: 0.007-33.09%), indicating that acid disinfection altered the microbial ecology to stimulate Escherichia-Shigella growth. These results enhance our understanding of the relationship between lettuce disinfection and ecological changes.},
}
@article {pmid31546184,
year = {2020},
author = {Pietro-Souza, W and de Campos Pereira, F and Mello, IS and Stachack, FFF and Terezo, AJ and Cunha, CND and White, JF and Li, H and Soares, MA},
title = {Mercury resistance and bioremediation mediated by endophytic fungi.},
journal = {Chemosphere},
volume = {240},
number = {},
pages = {124874},
doi = {10.1016/j.chemosphere.2019.124874},
pmid = {31546184},
issn = {1879-1298},
mesh = {*Biodegradation, Environmental ; Fungi/*chemistry ; Mercury/*chemistry ; },
abstract = {The present study proposes the use of endophytic fungi for mercury bioremediation in in vitro and host-associated systems. We examined mercury resistance in 32 strains of endophytic fungi grown in culture medium supplemented with toxic metal concentrations. The residual mercury concentrations were quantified after mycelial growth. Aspergillus sp. A31, Curvularia geniculata P1, Lindgomycetaceae P87, and Westerdykella sp. P71 were selected and further tested for mercury bioremediation and bioaccumulation in vitro, as well as for growth promotion of Aeschynomene fluminensis and Zea mays in the presence or absence of the metal. Aspergillus sp. A31, C. geniculata P1, Lindgomycetaceae P87 and Westerdykella sp. P71 removed up to 100% of mercury from the culture medium in a species-dependent manner and they promoted A. fluminensis and Z. mays growth in substrates containing mercury or not (Dunnett's test, p < 0.05). Lindgomycetaceae P87 and C. geniculata P1 are dark septate endophytic fungi that endophytically colonize root cells of their host plants. The increase of host biomass correlated with the reduction of soil mercury concentration due to the metal bioaccumulation in host tissues and its possible volatilization. The soil mercury concentration was decreased by 7.69% and 57.14% in A. fluminensis plants inoculated with Lindgomycetaceae P87 + Aspergillus sp. A31 and Lindgomycetaceae P87, respectively (Dunnet's test, p < 0.05). The resistance mechanisms of mercury volatilization and bioaccumulation in plant tissues mediated by these endophytic fungi can contribute to bioremediation programs. The biochemical and genetic mechanisms involved in bioaccumulation and volatilization need to be elucidated in the future.},
}
@article {pmid31546029,
year = {2019},
author = {Pikaar, I and Flugen, M and Lin, HW and Salehin, S and Li, J and Donose, BC and Dennis, PG and Bethke, L and Johnson, I and Rabaey, K and Yuan, Z},
title = {Full-scale investigation of in-situ iron and alkalinity generation for efficient sulfide control.},
journal = {Water research},
volume = {167},
number = {},
pages = {115032},
doi = {10.1016/j.watres.2019.115032},
pmid = {31546029},
issn = {1879-2448},
mesh = {*Hydrogen Sulfide ; *Iron ; Sewage ; Sulfides ; Wastewater ; },
abstract = {Hydrogen sulfide induced corrosion of concrete sewer pipes is a major issue for wastewater utilities globally. One of the most commonly used methods to combat hydrogen sulfide is the addition of ferric chloride. While a reliable and effective method, ferric chloride is acidic causing OH&amp;S concerns as well as alkalinity consumption in sewage. This study investigates, under full-scale field conditions, an alternative method for sulfide control by in-situ electrochemical generation of iron ions using sacrificial iron electrodes. This method concomitantly produces alkalinity through cathodic OH[-] generation, rather than consumption. The gaseous hydrogen sulfide concentrations at the discharge wet well of a real-life rising main (length: ∼1 km in, diameter: 150 mm) decreased from 173 ppm to 43 ppm (90 percentile of peak values), when a current of 0.86 A/m[3] of sewage was applied. The 90 percentile peak H2S value was further reduced to 6.6 ppm when the applied current was increased to 1.14 A/m[3] sewage. Moreover, methane generation was almost completely inhibited from 25.3 ± 1.46 mg COD/L to 0.06 ± 0.04 mg COD/L. The overall cell voltage remained constant throughout the experimental period clearly showing the stability of the process. Detailed characterization of the down-stream sewer pipe biofilm revealed the complexity of the iron chemistry as the in-situ produced iron ions undergo transformation into a variety of iron species. Overall, this study demonstrates that in-situ generation of iron and alkalinity is an effective alternative method for hydrogen sulfide control in sewers.},
}
@article {pmid31545283,
year = {2019},
author = {Huang, X and Chen, W and Yan, C and Yang, R and Chen, Q and Xu, H and Huang, Y},
title = {Gypenosides improve the intestinal microbiota of non-alcoholic fatty liver in mice and alleviate its progression.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {118},
number = {},
pages = {109258},
doi = {10.1016/j.biopha.2019.109258},
pmid = {31545283},
issn = {1950-6007},
mesh = {Animals ; Biodiversity ; Body Weight/drug effects ; Diet, High-Fat ; *Disease Progression ; Down-Regulation/drug effects ; Gastrointestinal Microbiome/*drug effects ; Gynostemma/chemistry ; Hyperlipidemias/complications/drug therapy ; Insulin Resistance ; Intestines/drug effects/pathology ; Lipid Metabolism/drug effects ; Liver/drug effects/pathology ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/blood/complications/*drug therapy/*microbiology ; Organ Size/drug effects ; Plant Extracts/chemistry/pharmacology/therapeutic use ; },
abstract = {Gypenosides (GP) are a type of traditional Chinese medicine (TCM) extracted from plants and commonly applied for treatment of metabolic diseases. This study aims to explore the effects of GP extracts on alleviating non-alcoholic fatty liver disease (NAFLD). In this experiment, C57BL/6 J mice were randomly assigned into normal diet control (ND), HFHC (high-fat and high-cholesterol) and HFHC + GP (GP) groups. Mice in HFHC group were fed HFHC diet combined with fructose drinking water for 12 weeks to induce the animal model of NAFLD, followed by ordinary drinking water until the end of the experiment. In the HFHC + GP group, mice were fed HFHC diet combined with fructose drinking water for 12 weeks, followed by GP-containing drinking water till the end. Mouse body weight was measured weekly. After animal procedures, mouse liver and serum samples were collected. It is shown that GP administration reduced body weight, enhanced the sensitivity to insulin resistance (IR) and decreased serum levels of ALT, AST and TG in NAFLD mice. In addition, GP treatment alleviated steatohepatitis, and downregulated ACC1, PPARγ, CD36, APOC3 and MTTP levels in mice fed with HFHC diet. Furthermore, GP treatment markedly improved intestinal microbiota, and reduced relative abundance ratio of Firmicutes / Bacteroidetes in the feces of NAFLD mice. Our results suggested that GP alleviated NAFLD in mice through improving intestinal microbiota.},
}
@article {pmid31543873,
year = {2019},
author = {Alviz-Gazitua, P and Fuentes-Alburquenque, S and Rojas, LA and Turner, RJ and Guiliani, N and Seeger, M},
title = {Corrigendum: The Response of Cupriavidus metallidurans CH34 to Cadmium Involves Inhibition of the Initiation of Biofilm Formation, Decrease in Intracellular c-di-GMP Levels, and a Novel Metal Regulated Phosphodiesterase.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2014},
doi = {10.3389/fmicb.2019.02014},
pmid = {31543873},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.01499.].},
}
@article {pmid31541814,
year = {2019},
author = {Petrin, S and Patuzzi, I and Di Cesare, A and Tiengo, A and Sette, G and Biancotto, G and Corno, G and Drigo, M and Losasso, C and Cibin, V},
title = {Evaluation and quantification of antimicrobial residues and antimicrobial resistance genes in two Italian swine farms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {255},
number = {Pt 1},
pages = {113183},
doi = {10.1016/j.envpol.2019.113183},
pmid = {31541814},
issn = {1873-6424},
mesh = {Agriculture ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Feces/chemistry ; Female ; *Genes, Bacterial ; Italy ; Male ; Manure/microbiology ; Plasmids ; Swine/*microbiology ; },
abstract = {Antimicrobial resistance genes (ARGs) are considered emerging environmental pollutants, posing potential risks for human and animal health: the misuse of antimicrobials in food-producing animals could favour the maintenance and spread of resistances in bacteria. The occurrence of ARGs in Italian swine farming - which has specific characteristics - was investigated in order to explore resistance spread dynamics. Two farrow-to-finish pig farms were longitudinally monitored: faecal samples from animals and environmental samples were collected. DNA was extracted and tetA, ermB, qnrS and mcr1 ARGs were analysed by qPCR for their ability to confer resistance to highly or critically important antimicrobials (CIAs). Moreover, 16SrDNA gene was analysed to assess bacterial abundance. ermB and tetA genes were found in animal samples and manure samples. On the contrary, mcr1 was exclusively found in weaners, while qnrS occurred in all animal categories but sows and finishers. Among the analysed genes, ermB and tetA showed the highest absolute and relative abundances. Our results indicate that ermB and tetA ARGs are widely disseminated in the explored farms, suggesting efficient maintenance among bacteria and persistence in the environment. Interestingly, the presence of qnrS and mcr1, limited to just a few animal categories, highlights inefficient dissemination of these genes in the farm environment, in particular for mcr1, a stable plasmid gene conferring resistance to the last-resort antimicrobial, colistin. Paying close attention only to the finishing phase would have hampered the discovery of resistances to CIAs at farm level, which we instead identified thanks to an intensive longitudinal monitoring programme.},
}
@article {pmid31539855,
year = {2019},
author = {Santos-Clotas, E and Cabrera-Codony, A and Boada, E and Gich, F and Muñoz, R and Martín, MJ},
title = {Efficient removal of siloxanes and volatile organic compounds from sewage biogas by an anoxic biotrickling filter supplemented with activated carbon.},
journal = {Bioresource technology},
volume = {294},
number = {},
pages = {122136},
doi = {10.1016/j.biortech.2019.122136},
pmid = {31539855},
issn = {1873-2976},
mesh = {*Biofuels ; Bioreactors ; Charcoal ; Filtration ; Sewage ; Siloxanes ; *Volatile Organic Compounds ; },
abstract = {The removal of siloxanes (D4 and D5) and volatile organic contaminants (hexane, toluene and limonene) typically found in sewage biogas was investigated in a lab-scale biotrickling filter (BTF) packed with lava rock under anoxic conditions. Complete removal efficiencies for toluene and limonene were recorded at all empty bed residence time (EBRT) tested. The influence of EBRT was remarkable on the abatement of D5, whose removal decreased from 37% at 14.5 min to 16% at 4 min, while the removal of D4 and hexane remained below 16%. The packing material was supplemented with 20% of activated carbon aiming at increasing the mass transfer of the most hydrophobic pollutants. This strategy supported high removal efficiencies of 43 and 45% for hexane and D5 at the lowest EBRT. CO2 and silica were identified as mineralization products along with the presence of metabolites in the trickling solution such as dimethylsilanediol, 2-carene and α-terpinene.},
}
@article {pmid31538807,
year = {2019},
author = {Tomar, SL},
title = {Oral Health Effects of Tobacco Products: Science and Regulatory Policy.},
journal = {Advances in dental research},
volume = {30},
number = {1},
pages = {2-3},
doi = {10.1177/0022034519872481},
pmid = {31538807},
issn = {1544-0737},
support = {R13 FD006142/FD/FDA HHS/United States ; },
mesh = {*Health Policy ; Humans ; *Oral Health ; Science ; *Tobacco Products/legislation &amp; jurisprudence ; Tobacco Use Disorder ; },
}
@article {pmid31536878,
year = {2019},
author = {Lambrecht, E and Van Coillie, E and Van Meervenne, E and Boon, N and Heyndrickx, M and Van de Wiele, T},
title = {Commensal E. coli rapidly transfer antibiotic resistance genes to human intestinal microbiota in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME).},
journal = {International journal of food microbiology},
volume = {311},
number = {},
pages = {108357},
doi = {10.1016/j.ijfoodmicro.2019.108357},
pmid = {31536878},
issn = {1879-3460},
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cefotaxime/pharmacology ; Chickens/microbiology ; *Computer Simulation ; Conjugation, Genetic/*genetics ; Drug Resistance, Bacterial/*genetics ; Ecosystem ; Escherichia coli/drug effects/*genetics ; Gastrointestinal Microbiome/drug effects/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Intestinal Mucosa/*microbiology ; Intestines/microbiology ; Plasmids/genetics ; },
abstract = {Food-producing animals are indicated as a reservoir of antibiotic resistance genes and a potential vector for transmission of plasmid-encoded antibiotic resistance genes by conjugation to the human intestinal microbiota. In this study, transfer of an antibiotic resistance plasmid from a commensal E. coli originating from a broiler chicken towards the human intestinal microbiota was assessed by using a Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME). This in vitro model mimics the human intestinal ecosystem and received a single dose of 10[9]E. coli MB6212, which harbors a plasmid known to confer resistance towards several antibiotics including tetracycline, sulfamethoxazole and cefotaxime. Since the degree of stress imposed by stomach pH and bile acids vary with the consumed meal size, the effect of meal size on E. coli donor survival and on plasmid transfer towards lumen and mucosal coliforms and anaerobes was determined. The administered commensal E. coli strain survived stomach acid and bile salt stress and was able to grow in the colon environment during the timeframe of the experiment (72 h). Transfer of antibiotic resistance was observed rapidly since cultivable transconjugant coliforms and anaerobes were already detected in the lumen and mucosa after 2 h in the simulated proximal colon. The presence of the resistance plasmid in the transconjugants was confirmed by PCR. Differences in meal size and adapted digestion had neither a detectable impact on antibiotic resistance transfer, nor on the survival of the E. coli donor strain, nor on short chain fatty acid profiles. The median number of resistant indigenous coliforms in the lumen of the inoculated colon vessels was 5.00 × 10[5] cfu/ml [min - max: 3.47 × 10[4]-3.70 × 10[8] cfu/ml], and on the mucosa 1.44 × 10[7] cfu/g [min-max: 4.00 × 10[3]-4.00 × 10[8] cfu/g]. Exact quantification of the anaerobic transconjugants was difficult, as (intrinsic) resistant anaerobic background microbiota were present. QPCR data supported the observation of plasmid transfer in the simulated colon. Moreover, inoculation of E. coli MB6212 had no significant impact on the microbial diversity in the lumen as determined by 16 S ribosomal gene based next generation sequencing on lumen samples. This study demonstrates that a commensal, antibiotic resistant E. coli strain present in food can transfer its antibiotic resistance plasmid relatively quickly to intestinal microbiota in the M-SHIME. The spread and persistence of antibiotic resistance genes and resistant bacteria in our intestinal system is an alarming scenario which might present clinical challenges, since it implies a potential reservoir for dissemination to pathogenic bacteria.},
}
@article {pmid31535335,
year = {2020},
author = {Contador, CA and Veas-Castillo, L and Tapia, E and Antipán, M and Miranda, N and Ruiz-Tagle, B and García-Araya, J and Andrews, BA and Marin, M and Dorador, C and Asenjo, JA},
title = {Atacama Database: a platform of the microbiome of the Atacama Desert.},
journal = {Antonie van Leeuwenhoek},
volume = {113},
number = {2},
pages = {185-195},
doi = {10.1007/s10482-019-01328-x},
pmid = {31535335},
issn = {1572-9699},
support = {FB0001//Comisi&#xf3;n Nacional de Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; },
mesh = {Archaea/genetics/physiology ; Bacteria/genetics ; Biotechnology ; *Databases, Factual ; Desert Climate ; Microbiota/physiology ; Soil Microbiology ; },
abstract = {The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.},
}
@article {pmid31534146,
year = {2019},
author = {Harkes, P and Suleiman, AKA and van den Elsen, SJJ and de Haan, JJ and Holterman, M and Kuramae, EE and Helder, J},
title = {Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {13521},
pmid = {31534146},
issn = {2045-2322},
mesh = {Agriculture/*methods ; Bacteria/genetics ; Biodiversity ; Carbon Cycle ; Ecosystem ; Eukaryota ; Fertilizers/*analysis ; Food Chain ; Fungi/genetics ; Soil/*chemistry ; Soil Microbiology ; },
abstract = {Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.},
}
@article {pmid31533344,
year = {2019},
author = {Zwart, MP and Ali, G and Strien, EAV and Schijlen, EGWM and Wang, M and Werf, WV and Vlak, JM},
title = {Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing.},
journal = {Viruses},
volume = {11},
number = {9},
pages = {},
pmid = {31533344},
issn = {1999-4915},
mesh = {Animals ; China ; Genetic Loci/*genetics ; High-Throughput Nucleotide Sequencing ; Nucleopolyhedroviruses/*genetics/pathogenicity ; Open Reading Frames ; Pakistan ; Pest Control, Biological ; Spodoptera/*virology ; *Virulence ; },
abstract = {Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.},
}
@article {pmid31528722,
year = {2019},
author = {Tiwari, UP and Singh, AK and Jha, R},
title = {Fermentation characteristics of resistant starch, arabinoxylan, and β-glucan and their effects on the gut microbial ecology of pigs: A review.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {5},
number = {3},
pages = {217-226},
pmid = {31528722},
issn = {2405-6383},
abstract = {Dietary fibers (DF) contain an abundant amount of energy, although the mammalian genome does not encode most of the enzymes required to degrade them. However, a mutual dependence is developed between the host and symbiotic microbes, which has the potential to extract the energy present in these DF. Dietary fibers escape digestion in the foregut and are fermented in the hindgut, producing short-chain fatty acids (SCFA) that alter the microbial ecology in the gastrointestinal tract (GIT) of pigs. Most of the carbohydrates are fermented in the proximal part, allowing protein fermentation in the distal part, resulting in colonic diseases. The structures of resistant starch (RS), arabinoxylan (AX), and β-glucan (βG) are complex; hence, makes their way into the hindgut where these are fermented and provide energy substrates for the colonic epithelial cells. Different microbes have different preferences of binding to different substrates. The RS, AX and βG act as a unique substrate for the microbes and modify the relative composition of the gut microbial community. The granule dimension and surface area of each substrate are different, which influences the penetration capacity of microbes. Arabinose and xylan are 2 different hemicelluloses, but arabinose is substituted on the xylan backbone and occurs in the form of AX. Fermentation of xylan produces butyrate primarily in the small intestine, whereas arabinose produces butyrate in the large intestine. Types of RS and forms of βG also exert beneficial effects by producing different metabolites and modulating the intestinal microbiota. Therefore, it is important to have information of different types of RS, AX and βG and their roles in microbial modulation to get the optimum benefits of fiber fermentation in the gut. This review provides relevant information on the similarities and differences that exist in the way RS, AX, and βG are fermented, and their positive and negative effects on SCFA production and gut microbial ecology of pigs. These insights will help nutritionists to develop dietary strategies that can modulate specific SCFA production and promote beneficial microbiota in the GIT of swine.},
}
@article {pmid31527408,
year = {2019},
author = {Connor, R and Brister, R and Buchmann, JP and Deboutte, W and Edwards, R and Martí-Carreras, J and Tisza, M and Zalunin, V and Andrade-Martínez, J and Cantu, A and D'Amour, M and Efremov, A and Fleischmann, L and Forero-Junco, L and Garmaeva, S and Giluso, M and Glickman, C and Henderson, M and Kellman, B and Kristensen, D and Leubsdorf, C and Levi, K and Levi, S and Pakala, S and Peddu, V and Ponsero, A and Ribeiro, E and Roy, F and Rutter, L and Saha, S and Shakya, M and Shean, R and Miller, M and Tully, B and Turkington, C and Youens-Clark, K and Vanmechelen, B and Busby, B},
title = {NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements.},
journal = {Genes},
volume = {10},
number = {9},
pages = {},
pmid = {31527408},
issn = {2073-4425},
support = {R35 CA220523/CA/NCI NIH HHS/United States ; },
mesh = {Big Data ; Cloud Computing/*standards ; Genome, Human ; *Genome, Viral ; Humans ; *Metagenome ; Metagenomics/*methods/standards ; Software ; },
abstract = {A wealth of viral data sits untapped in publicly available metagenomic data sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work of this complexity and scale could be done in a hackathon setting. Ten teams comprised of over 40 participants from six countries, assembled to create a crowd-sourced set of analysis and processing pipelines for a complex biological data set in a three-day event on the San Diego State University campus starting 9 January 2019. Prior to the hackathon, 141,676 metagenomic data sets from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) were pre-assembled into contiguous assemblies (contigs) by NCBI staff. During the hackathon, a subset consisting of 2953 SRA data sets (approximately 55 million contigs) was selected, which were further filtered for a minimal length of 1 kb. This resulted in 4.2 million (Mio) contigs, which were aligned using BLAST against all known virus genomes, phylogenetically clustered and assigned metadata. Out of the 4.2 Mio contigs, 360,000 contigs were labeled with domains and an additional subset containing 4400 contigs was screened for virus or virus-like genes. The work yielded valuable insights into both SRA data and the cloud infrastructure required to support such efforts, revealing analysis bottlenecks and possible workarounds thereof. Mainly: (i) Conservative assemblies of SRA data improves initial analysis steps; (ii) existing bioinformatic software with weak multithreading/multicore support can be elevated by wrapper scripts to use all cores within a computing node; (iii) redesigning existing bioinformatic algorithms for a cloud infrastructure to facilitate its use for a wider audience; and (iv) a cloud infrastructure allows a diverse group of researchers to collaborate effectively. The scientific findings will be extended during a follow-up event. Here, we present the applied workflows, initial results, and lessons learned from the hackathon.},
}
@article {pmid31526457,
year = {2019},
author = {de Los Santos Villalobos, S and Robles, RI and Parra Cota, FI and Larsen, J and Lozano, P and Tiedje, JM},
title = {Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {69},
number = {12},
pages = {3939-3945},
doi = {10.1099/ijsem.0.003711},
pmid = {31526457},
issn = {1466-5034},
mesh = {Bacillus/*classification/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Endophytes/classification/isolation &amp; purification ; Fatty Acids/chemistry ; Mexico ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Triticum/*microbiology ; },
abstract = {Strain TE3[T], an endophytic plant growth promoting bacterium, was isolated from wheat (Triticumturgidum subsp. durum) sampled in the Yaqui Valley, Mexico. Biochemical, phenotypic and genotypic approaches were used to clarify the taxonomic affiliation of this strain. Based on analysis of its full-length 16S rRNA gene, strain TE3[T] was assigned to the genus Bacillus (similarity ≥98.7 %). This finding was supported by morphological and metabolic characteristics, such as rod shape, strictly aerobic metabolism, spore formation, Gram-positive staining, catalase-positive activity, reduction of nitrate to nitrite, starch and casein hydrolysis, growth in presence of lysozyme and 2 % NaCl, citrate utilization, growth pH from 6.0 to 8.0, and acid and indole production from glucose and tryptophan, respectively. The whole-genome phylogenetic relationship showed that TE3[T] formed an individual clade with Bacillus tequilensis KCTC 13622[T], distant from that generated by all Bacillus subtilis subspecies. The maximum values for average nucleotide identity and in silico DNA-DNA hybridization were 93.85 and 54.30 %, respectively, related to Bacillus subtilissubsp. inaquosorum KCTC 13429[T]. Analysis of its fatty acid content showed the ability of strain TE3[T] to bio-synthetize fatty acids that are not present in closely related Bacillus species, such as C12 : 0, C12 : 0 2OH, C12 : 0 3OH, C17 : 0, iso-C17 : 0 3OH and C18 : 1ω9c. These results provide evidence that strain TE3[T] is a novel species of the genus Bacillus, for which the name Bacilluscabrialesii sp. nov. is proposed. The type strain of Bacilluscabrialesii is TE3[T] (CM-CNRG TB54[T]=CCStamb A1[T]).},
}
@article {pmid31523442,
year = {2019},
author = {Koga, Y and Ohtsu, T and Kimura, K and Asami, Y},
title = {Probiotic L. gasseri strain (LG21) for the upper gastrointestinal tract acting through improvement of indigenous microbiota.},
journal = {BMJ open gastroenterology},
volume = {6},
number = {1},
pages = {e000314},
pmid = {31523442},
issn = {2054-4774},
abstract = {OBJECTIVE: To describe probiotics including a Lactobacillus gasseri strain LG21 used for the upper gastrointestinal tract, which are considered to act through improvement of indigenous microbiota inhabiting there.<br><br>BACKGROUND AND DESIGN: Because the early definition of probiotics emphasized their effects on improving the intestinal microbial ecology, their effects on the intestinal tract and its immunity have been considered common general benefits associated with probiotics. This conclusion was also based on a body of successful clinical trials whose endpoints were the prevention or treatment of intestinal diseases. In contrast to intestinal microbiota, our understanding of the role of gastric microbiota in human health and physiology remains poor, as the bacterial load in the stomach is considered too small to exert a significant effect due to the highly acidic environment of the human stomach. Therefore, the intervention using probiotics in the stomach is still limited at present.Results:In this article using representative 38 quoted articles, we first describe the gastric microbiota, as the indigenous microbiota in the stomach is thought to be significantly involved in the pathophysiology of this organ, since probiotics exert their beneficial effects through improving the resident microbiota. We then review the present status and future prospects of probiotics for the treatment of upper gastrointestinal diseases by quoting representative published articles, including our basic and clinical data.<br><br>CONCLUSIONS: Probiotics have been demonstrated to suppress Helicobacter pylori in the stomach, and are also expected to improve functional dyspepsia through the correction of dysbiotic gastric microbiota.},
}
@article {pmid31520875,
year = {2019},
author = {Wichmann, S and Ardern, Z},
title = {Optimality in the standard genetic code is robust with respect to comparison code sets.},
journal = {Bio Systems},
volume = {185},
number = {},
pages = {104023},
doi = {10.1016/j.biosystems.2019.104023},
pmid = {31520875},
issn = {1872-8324},
mesh = {Algorithms ; Amino Acids/*genetics ; Codon/*genetics ; Codon, Terminator/genetics ; Evolution, Molecular ; Genetic Code/*genetics ; Models, Genetic ; Mutation ; Open Reading Frames/*genetics ; Protein Biosynthesis ; Selection, Genetic ; },
abstract = {The genetic code and its evolution have been studied by many different approaches. One approach is to compare the properties of the standard genetic code (SGC) to theoretical alternative codes in order to determine how optimal it is and from this infer whether or not it is likely that it has undergone a selective evolutionary process. Many different properties have been studied in this way in the literature. Less focus has been put on the alternative code sets which are used as a comparison to the standard code. Each implicitly represents an evolutionary hypothesis and the sets used differ greatly across the literature. Here we determine the influence of the comparison set on the results of the optimality calculation by using codes based upon different sub-structures of the SGC. With these results we can generalize the results to different evolutionary hypotheses. We find that the SGC's optimality is very robust, as no code set with no optimised properties is found. We therefore conclude that the optimality of the SGC is a robust feature across all evolutionary hypotheses. Our results provide important information for any future studies on the evolution of the standard genetic code. We also studied properties of the SGC concerning overlapping genes, which have recently been found to be more widespread than often believed. Although our results are not conclusive yet we find additional intriguing structures in the SGC that need explanation.},
}
@article {pmid31518408,
year = {2019},
author = {Bugge Harder, C and Nyrop Albers, C and Rosendahl, S and Aamand, J and Ellegaard-Jensen, L and Ekelund, F},
title = {Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks' rapid sand filters.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {11},
pages = {},
doi = {10.1093/femsec/fiz148},
pmid = {31518408},
issn = {1574-6941},
mesh = {Bacteria/isolation &amp; purification ; DNA Primers ; Denmark ; Eukaryota/classification/*isolation &amp; purification ; Filtration/*instrumentation ; Groundwater/*microbiology ; Humans ; *Microbiota ; Sand ; Water Purification ; },
abstract = {As groundwater-fed waterworks clean their raw inlet water with sand filters, a variety of pro- and eukaryotic microbial communities develop on these filters. While several studies have targeted the prokaryotic sand filter communities, little is known about the eukaryotic communities, despite the obvious need for knowledge of microorganisms that get in contact with human drinking water. With a new general eukaryotic primer set (18S, V1-V3 region), we performed FLX-454 sequencing of material from 21 waterworks' sand filters varying in age (3-40 years) and geographical location on a 250 km east-west axis in Denmark, and put the data in context of their previously published prokaryotic communities. We find that filters vary highly in trophic complexity depending on age, from simple systems with bacteria and protozoa (3-6 years) to complex, mature systems with nematodes, rotifers and turbellarians as apex predators (40 years). Unlike the bacterial communities, the eukaryotic communities display a clear distance-decay relationship that predominates over environmental variations, indicating that the underlying aquifers feeding the filters harbor distinct eukaryotic communities with limited dispersal in between. Our findings have implications for waterworks' filter management, and offer a window down to the largely unexplored eukaryotic microbiology of groundwater aquifers.},
}
@article {pmid31517286,
year = {2019},
author = {Duysburgh, C and Van den Abbeele, P and Krishnan, K and Bayne, TF and Marzorati, M},
title = {A synbiotic concept containing spore-forming Bacillus strains and a prebiotic fiber blend consistently enhanced metabolic activity by modulation of the gut microbiome in vitro.},
journal = {International journal of pharmaceutics: X},
volume = {1},
number = {},
pages = {100021},
pmid = {31517286},
issn = {2590-1567},
abstract = {A standardized in vitro simulation of the human gastrointestinal tract (M-SHIME®) was used to assess the effect of repeated daily administration of a synbiotic formulation, containing five spore-forming Bacillus strains and a prebiotic fiber blend, on the microbial activity and composition of three simulated human subjects. Firstly, while confirming recent findings, deeper phylogenetic insight was obtained in the resident M-SHIME® microbiota, demonstrating that the model maintains a diverse and representative, colon region-specific luminal and mucosal microbial community. Supplementation of the synbiotic concept increased microbial diversity in the distal colon areas, whereas specific enhancement of Bacillaceae levels was observed in the ascending colon suggesting a successful engraftment of the Bacillus spores, which probably resulted in a stimulatory effect on, among others, Bifidobacteriaceae, Lactobacillaceae, Prevotellaceae, Tannerellaceae and Faecalibacterium prausnitzii contributing directly or indirectly to stimulation of acetate, propionate and butyrate production. When compared with a previous study investigating the Bacillus strains, the generated data suggest a synergistic effect on the intestinal microbiota for the synbiotic formulation. Given the fact that the probiotic strains have been shown to impact post-prandial metabolic endotoxemia in human individuals, it might be interesting to further investigate the efficacy of the synbiotic concept in protecting against obesity-related disorders.},
}
@article {pmid31515652,
year = {2020},
author = {Lee, HJ and Shin, SY and Whang, KS},
title = {Paenibacillus pinistramenti sp. nov., isolated from pine litter.},
journal = {Antonie van Leeuwenhoek},
volume = {113},
number = {2},
pages = {155-163},
doi = {10.1007/s10482-019-01325-0},
pmid = {31515652},
issn = {1572-9699},
mesh = {Base Composition/genetics/physiology ; DNA, Bacterial/metabolism ; Diaminopimelic Acid/metabolism ; Glycolipids/metabolism ; Hydrogen-Ion Concentration ; Paenibacillus/classification/*genetics ; Phosphatidylethanolamines/metabolism ; Phosphatidylglycerols/metabolism ; Phylogeny ; Sodium Chloride ; },
abstract = {A Gram-stain-positive bacterium, designated strain ASL46[T], was isolated from litter layer of a pine forest located in Anmyondo, Korea. Strain ASL46[T] was found to be an aerobic, motile, endospore-forming rod which can grow at 20-45 °C (optimum, 37 °C), at pH 6.0-11.0 (optimum, pH 7.0) and at salinities of 0-2% (w/v) NaCl (optimum, 1% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain ASL46[T] belongs to the genus Paenibacillus, showing highest sequence similarity to P. yonginensis DCY84[T] (98.3%), P. physcomitrella XB[T] (97.4%) and P. faecis CIP 101062[T] (96.6%). The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain ASL46[T] and P. physcomitrella XB[T] and P. yonginensis DCY84[T] yielded ANI values of 84.6 and 84.5% and DNA-DNA relatedness of 11.7 ± 0.7 and 10.9 ± 0.2%, respectively. The DNA G+C content of the genomic DNA of strain ASL46[T] was 52.1 mol%. The predominant isoprenoid quinone was identified as menaquinone-7 and the major cellular fatty acids were determined to be anteiso-C15:0, C16:0 and iso-C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified aminophospholipids, an unidentified phospholipid and an unidentified glycolipid. The whole-cell sugar was found to be ribose and cell wall peptidoglycan contained meso-diaminopimelic acid. On the basis of phylogenetic analyses, and phenotypic and chemotaxonomic characteristics, strain ASL46[T] represents a novel species of the genus Paenibacillus, for which the name Paenibacillus pinistramenti sp. nov. is proposed. The type strain is ASL46[T] (= KACC 18701[T] = NBRC 111876[T]).},
}
@article {pmid31512011,
year = {2020},
author = {Sekhohola-Dlamini, L and Tekere, M},
title = {Microbiology of municipal solid waste landfills: a review of microbial dynamics and ecological influences in waste bioprocessing.},
journal = {Biodegradation},
volume = {31},
number = {1-2},
pages = {1-21},
doi = {10.1007/s10532-019-09890-x},
pmid = {31512011},
issn = {1572-9729},
mesh = {Biodegradation, Environmental ; Ecosystem ; *Refuse Disposal ; Solid Waste/*analysis ; Waste Disposal Facilities ; },
abstract = {Municipal solid waste landfills are widely used as a waste management tool and landfill microbiology is at the core of waste degradation in these ecosystems. This review investigates the microbiology of municipal solid waste landfills, focusing on the current state of knowledge pertaining to microbial diversity and functions facilitating in situ waste bioprocessing, as well as ecological factors influencing microbial dynamics in landfills. Bioprocessing of waste in municipal landfills emanates from substrate metabolism and co-metabolism by several syntrophic microorganisms, resulting in partial transformation of complex substrates into simpler polymeric compounds and complete mineralisation into inorganic salts, water and gases including the biofuel gas methane. The substrate decomposition is characterised by evolution and interactions of different bacterial, archaeal and fungal groups due to prevailing biotic and abiotic conditions in the landfills, allowing for hydrolytic, fermentative, acetogenic and methanogenic processes to occur. Application of metagenomics studies based on high throughput Next Generation Sequencing technique has advanced research on profiling of the microbial communities in municipal solid waste landfills. However, functional diversity and bioprocess dynamics, as well as key factors influencing the in situ bioprocesses involved in landfill waste degradation; the very elements that are key in determining the efficiency of municipal landfills as tools of waste management, remain ambiguous. Such gaps also hinder progressive understanding of fundamentals that underlie technology development based on waste biodegradation, and exploration of municipal waste as a bioresource.},
}
@article {pmid31511911,
year = {2020},
author = {Wang, L and Han, M and Li, X and Ginawi, A and Ning, K and Yan, Y},
title = {Niche and Neutrality Work Differently in Microbial Communities in Fluidic and Non-fluidic Ecosystems.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {527-538},
pmid = {31511911},
issn = {1432-184X},
mesh = {Archaea/classification/genetics/*physiology ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; China ; *Ecosystem ; *Microbiota ; Models, Biological ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Rivers/*microbiology ; },
abstract = {This data-intensive study investigated the delicate balance of niche and neutrality underlying microbial communities in freshwater ecosystems through comprehensive application of high-throughput sequencing, species abundance distribution (SAD), and the neutral community model (NCM), combined with species diversity and phylogenetic measures, which unite the traditional and microbial ecology. On the genus level, 45.10% and 41.18% of the water samples could be explained by the log-normal and Volkov model respectively, among which 31.37% could fit both models. Meanwhile, 55.56% of the sediment samples could be depicted by the log-normal model, and Volkov-fitted samples comprised only 13.33%. Besides, operational taxonomic units (OTUs) from water samples fit Sloan's neutral model significantly better than those in sediment. Therefore, it was concluded that deterministic processes played a great role in both water and sediment ecosystems, whereas neutrality was much more involved in water assemblages than in non-fluidic sediment ecosystems. Secondly, log-normal fitted samples had lower phylogenetic species variability (PSV) than Volkov-fitted ones, indicating that niche-based communities were more phylogenetically clustered than neutrally assembled counterparts. Additionally, further testing showed that the relative richness of rare species was vital to SAD modeling, either niche-based or neutral, and communities containing fewer rare species were more easily captured by theoretical SAD models.},
}
@article {pmid31511558,
year = {2019},
author = {Makarchuk, S and Braz, VC and Araújo, NAM and Ciric, L and Volpe, G},
title = {Enhanced propagation of motile bacteria on surfaces due to forward scattering.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4110},
pmid = {31511558},
issn = {2041-1723},
mesh = {Computer Simulation ; Escherichia coli/*cytology ; Movement ; Probability ; Surface Properties ; },
abstract = {How motile bacteria move near a surface is a problem of fundamental biophysical interest and is key to the emergence of several phenomena of biological, ecological and medical relevance, including biofilm formation. Solid boundaries can strongly influence a cell's propulsion mechanism, thus leading many flagellated bacteria to describe long circular trajectories stably entrapped by the surface. Experimental studies on near-surface bacterial motility have, however, neglected the fact that real environments have typical microstructures varying on the scale of the cells' motion. Here, we show that micro-obstacles influence the propagation of peritrichously flagellated bacteria on a flat surface in a non-monotonic way. Instead of hindering it, an optimal, relatively low obstacle density can significantly enhance cells' propagation on surfaces due to individual forward-scattering events. This finding provides insight on the emerging dynamics of chiral active matter in complex environments and inspires possible routes to control microbial ecology in natural habitats.},
}
@article {pmid31507553,
year = {2019},
author = {Durán-Viseras, A and Andrei, AS and Ghai, R and Sánchez-Porro, C and Ventosa, A},
title = {New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1928},
pmid = {31507553},
issn = {1664-302X},
abstract = {Hypersaline aquatic and terrestrial ecosystems display a cosmopolitan distribution. These environments teem with microbes and harbor a plethora of prokaryotic lineages that evaded ecological characterization due to the prior inability to cultivate them or to access their genomic information. In order to close the current knowledge gap, we performed two sampling and isolation campaigns in the saline soils of the Odiel Saltmarshes and the salterns of Isla Cristina (Huelva, Spain). From the isolated haloarchaeal strains subjected to high-throughput phylogenetic screening, two were chosen (F15B[T] and F9-27[T]) for physiological and genomic characterization due of their relatedness to the genus Halonotius. Comparative genomic analyses were carried out between the isolated strains and the genomes of previously described species Halonotius pteroides CECT 7525[T], Halonotius aquaticus F13-13[T] and environmentaly recovered metagenome-assembled representatives of the genus Halonotius. The topology of the phylogenomic tree showed agreement with the phylogenetic ones based on 16S rRNA and rpoB' genes, and together with average amino acid and nucleotide identities suggested the two strains as novel species within the genus. We propose the names Halonotius terrestris sp. nov. (type strain F15B[T] = CECT 9688[T] = CCM 8954[T]) and Halonotius roseus sp. nov. (type strain F9-27[T] = CECT 9745[T] = CCM 8956[T]) for these strains. Comparative genomic analyses within the genus highlighted a typical salt-in signature, characterized by acidic proteomes with low isoelectric points, and indicated heterotrophic aerobic lifestyles. Genome-scale metabolic reconstructions revealed that the newly proposed species encode all the necessary enzymatic reactions involved in cobalamin (vitamin B12) biosynthesis. Based on the worldwide distribution of the genus and its abundance in hypersaline habitats we postulate that its members perform a critical function by being able to provide "expensive" commodities (i.e., vitamin B12) to the halophilic microbial communities at large.},
}
@article {pmid31507541,
year = {2019},
author = {Bates, KA and Shelton, JMG and Mercier, VL and Hopkins, KP and Harrison, XA and Petrovan, SO and Fisher, MC},
title = {Captivity and Infection by the Fungal Pathogen Batrachochytrium salamandrivorans Perturb the Amphibian Skin Microbiome.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1834},
pmid = {31507541},
issn = {1664-302X},
support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {The emerging fungal pathogen, Batrachochytrium salamandrivorans (Bsal) is responsible for the catastrophic decline of European salamanders and poses a threat to amphibians globally. The amphibian skin microbiome can influence disease outcome for several host-pathogen systems, yet little is known of its role in Bsal infection. In addition, many experimental in-vivo amphibian disease studies to date have relied on specimens that have been kept in captivity for long periods without considering the influence of environment on the microbiome and how this may impact the host response to pathogen exposure. We characterized the impact of captivity and exposure to Bsal on the skin bacterial and fungal communities of two co-occurring European newt species, the smooth newt, Lissotriton vulgaris and the great-crested newt, Triturus cristatus. We show that captivity led to significant losses in bacterial and fungal diversity of amphibian skin, which may be indicative of a decline in microbe-mediated protection. We further demonstrate that in both L. vulgaris and T. cristatus, Bsal infection was associated with changes in the composition of skin bacterial communities with possible negative consequences to host health. Our findings advance current understanding of the role of host-associated microbiota in Bsal infection and highlight important considerations for ex-situ amphibian conservation programmes.},
}
@article {pmid31506821,
year = {2019},
author = {Callejas, C and Fernández, A and Passeggi, M and Wenzel, J and Bovio, P and Borzacconi, L and Etchebehere, C},
title = {Microbiota adaptation after an alkaline pH perturbation in a full-scale UASB anaerobic reactor treating dairy wastewater.},
journal = {Bioprocess and biosystems engineering},
volume = {42},
number = {12},
pages = {2035-2046},
doi = {10.1007/s00449-019-02198-3},
pmid = {31506821},
issn = {1615-7605},
mesh = {Anaerobiosis ; Archaea/metabolism ; Bacteria, Anaerobic/classification ; Biofuels ; Bioreactors/*microbiology ; Clostridium/classification ; Dairying ; Euryarchaeota/metabolism ; Firmicutes/classification ; Hydrogen-Ion Concentration ; Methane/metabolism ; Microbiota ; Proteobacteria/classification ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; *Waste Disposal, Fluid ; Wastewater ; *Water Microbiology ; *Water Purification ; },
abstract = {The aim of this study was to understand how the microbial community adapted to changes, including a pH perturbation, occurring during the start-up and operation processes in a full-scale methanogenic UASB reactor designed to treat dairy wastewater. The reactor performance, prokaryotic community, and lipid degradation capacity were monitored over a 9-month period. The methanogenic community was studied by mcrA/mrtA gene copy-number quantification and methanogenic activity tests. A diverse prokaryotic community characterized the seeding sludge as assessed by sequencing the V4 region of the 16S rRNA gene. As the feeding began, the bacterial community was dominated by Firmicutes, Synergistetes, and Proteobacteria phyla. After an accidental pH increase that affected the microbial community structure, a sharp increase in the relative abundance of Clostridia and a decrease in the mcrA/mrtA gene copy number and methanogenic activity were observed. After a recovery period, the microbial population regained diversity and methanogenic activity. Alkaline shocks are likely to happen in dairy wastewater treatment because of the caustic soda usage. In this work, the plasticity of the prokaryotic community was key to surviving changes to the external environment and supporting biogas production in the reactor.},
}
@article {pmid31506760,
year = {2020},
author = {Lamei, S and Stephan, JG and Nilson, B and Sieuwerts, S and Riesbeck, K and de Miranda, JR and Forsgren, E},
title = {Feeding Honeybee Colonies with Honeybee-Specific Lactic Acid Bacteria (Hbs-LAB) Does Not Affect Colony-Level Hbs-LAB Composition or Paenibacillus larvae Spore Levels, Although American Foulbrood Affected Colonies Harbor a More Diverse Hbs-LAB Community.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {743-755},
pmid = {31506760},
issn = {1432-184X},
support = {222-2013-423//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {Animal Feed/analysis ; Animals ; Bees/*microbiology ; Diet ; Lactobacillales/*chemistry ; Larva/microbiology ; *Microbiota ; Paenibacillus larvae/*physiology ; Spores, Bacterial/*physiology ; },
abstract = {The main current methods for controlling American Foulbrood (AFB) in honeybees, caused by the bacterial pathogen Paenibacillus larvae, are enforced incineration or prophylactic antibiotic treatment, neither of which is fully satisfactory. This has led to an increased interest in the natural relationships between the pathogenic and mutualistic microorganisms of the honeybee microbiome, in particular, the antagonistic effects of Honeybee-Specific Lactic Acid Bacteria (hbs-LAB) against P. larvae. We investigated whether supplemental administration of these bacteria affected P. larvae infection at colony level over an entire flowering season. Over the season, the supplements affected neither colony-level hbs-LAB composition nor naturally subclinical or clinical P. larvae spore levels. The composition of hbs-LAB in colonies was, however, more diverse in apiaries with a history of clinical AFB, although this was also unrelated to P. larvae spore levels. During the experiments, we also showed that qPCR could detect a wider range of hbs-LAB, with higher specificity and sensitivity than mass spectrometry. Honeybee colonies are complex super-organisms where social immune defenses, natural homeostatic mechanisms, and microbiome diversity and function play a major role in disease resistance. This means that observations made at the individual bee level cannot be simply extrapolated to infer similar effects at colony level. Although individual laboratory larval assays have clearly demonstrated the antagonistic effects of hbs-LAB on P. larvae infection, the results from the experiments presented here indicate that direct conversion of such practice to colony-level administration of live hbs-LAB is not effective.},
}
@article {pmid31506516,
year = {2019},
author = {Bridier, A and Le Grandois, P and Moreau, MH and Prénom, C and Le Roux, A and Feurer, C and Soumet, C},
title = {Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {12947},
pmid = {31506516},
issn = {2045-2322},
mesh = {Abattoirs ; Animals ; Anti-Bacterial Agents/*pharmacology ; Disinfection/*methods ; *Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Salmonella/*drug effects ; Salmonella Infections, Animal/*drug therapy/epidemiology/microbiology ; Swine ; Swine Diseases/epidemiology/microbiology/*prevention &amp; control ; },
abstract = {To guarantee food safety, a better deciphering of ecology and adaptation strategies of bacterial pathogens such as Salmonella in food environments is crucial. The role of food processing conditions such as cleaning and disinfection procedures on antimicrobial resistance emergence should especially be investigated. In this work, the prevalence and antimicrobial resistance of Salmonella and the microbial ecology of associated surfaces communities were investigated in a pig slaughterhouse before and after cleaning and disinfection procedures. Salmonella were detected in 67% of samples and isolates characterization revealed the presence of 15 PFGE-patterns belonging to five serotypes: S.4,5,12:i:-, Rissen, Typhimurium, Infantis and Derby. Resistance to ampicillin, sulfamethoxazole, tetracycline and/or chloramphenicol was detected depending on serotypes. 16S rRNA-based bacterial diversity analyses showed that Salmonella surface associated communities were highly dominated by the Moraxellaceae family with a clear site-specific composition suggesting a persistent colonization of the pig slaughterhouse. Cleaning and disinfection procedures did not lead to a modification of Salmonella susceptibility to antimicrobials in this short-term study but they tended to significantly reduce bacterial diversity and favored some genera such as Rothia and Psychrobacter. Such data participate to the construction of a comprehensive view of Salmonella ecology and antimicrobial resistance emergence in food environments in relation with cleaning and disinfection procedures.},
}
@article {pmid31506265,
year = {2019},
author = {Zhang, CJ and Pan, J and Duan, CH and Wang, YM and Liu, Y and Sun, J and Zhou, HC and Song, X and Li, M},
title = {Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes.},
journal = {mSystems},
volume = {4},
number = {5},
pages = {},
pmid = {31506265},
issn = {2379-5077},
abstract = {Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms.IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.},
}
@article {pmid31506264,
year = {2019},
author = {Dumolin, C and Aerts, M and Verheyde, B and Schellaert, S and Vandamme, T and Van der Jeugt, F and De Canck, E and Cnockaert, M and Wieme, AD and Cleenwerck, I and Peiren, J and Dawyndt, P and Vandamme, P and Carlier, A},
title = {Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data.},
journal = {mSystems},
volume = {4},
number = {5},
pages = {},
pmid = {31506264},
issn = {2379-5077},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDEIMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns.},
}
@article {pmid31506260,
year = {2019},
author = {Rubbens, P and Schmidt, ML and Props, R and Biddanda, BA and Boon, N and Waegeman, W and Denef, VJ},
title = {Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry.},
journal = {mSystems},
volume = {4},
number = {5},
pages = {},
pmid = {31506260},
issn = {2379-5077},
abstract = {High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically associated with these groups, and by extension, productivity has remained elusive. Here, we addressed this knowledge gap by using a machine learning-based variable selection approach that integrated FCM and 16S rRNA gene sequencing data collected from 14 freshwater lakes spanning a broad range in physicochemical conditions. There was a strong association between bacterial heterotrophic production and HNA absolute cell abundances (R [2] = 0.65), but not with the more abundant LNA cells. This solidifies findings, mainly from marine systems, that HNA and LNA bacteria could be considered separate functional groups, the former contributing a disproportionately large share of carbon cycling. Taxa selected by the models could predict HNA and LNA absolute cell abundances at all taxonomic levels. Selected operational taxonomic units (OTUs) ranged from low to high relative abundance and were mostly lake system specific (89.5% to 99.2%). A subset of selected OTUs was associated with both LNA and HNA groups (12.5% to 33.3%), suggesting either phenotypic plasticity or within-OTU genetic and physiological heterogeneity. These findings may lead to the identification of system-specific putative ecological indicators for heterotrophic productivity. Generally, our approach allows for the association of OTUs with specific functional groups in diverse ecosystems in order to improve our understanding of (microbial) biodiversity-ecosystem functioning relationships.IMPORTANCE A major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are associated with heterotrophic productivity in freshwater lakes and indicated that the key contributors were highly system specific, regularly rare members of the community, and that some could possibly switch between being low and high contributors. Our approach provides a promising framework to identify taxa that contribute to ecosystem functioning and can be further developed to explore microbial contributions beyond heterotrophic production.},
}
@article {pmid31504446,
year = {2019},
author = {Blackwell, N and Perkins, W and Palumbo-Roe, B and Bearcock, J and Lloyd, JR and Edwards, A},
title = {Seasonal blooms of neutrophilic Betaproteobacterial Fe(II) oxidizers and Chlorobi in iron-rich coal mine drainage sediments.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {10},
pages = {},
doi = {10.1093/femsec/fiz140},
pmid = {31504446},
issn = {1574-6941},
mesh = {Betaproteobacteria/classification/genetics/isolation &amp; purification/*metabolism ; Chlorobi/genetics/isolation &amp; purification/*metabolism ; Coal/analysis ; Coal Mining ; Environmental Pollution ; Ferrous Compounds/*metabolism ; Geologic Sediments/*microbiology ; Iron/*metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Seasons ; },
abstract = {Waters draining from flooded and abandoned coal mines in the South Wales Coalfield (SWC) are substantial sources of pollution to the environment characterized by circumneutral pH and elevated dissolved iron concentrations (>1 mg L-1). The discharged Fe precipitates to form Fe(III) (oxyhydr)oxides which sustain microbial communities. However, while several studies have investigated the geochemistry of mine drainage in the SWC, less is known about the microbial ecology of the sites presenting a gap in our understanding of biogeochemical cycling and pollutant turnover. This study investigated the biogeochemistry of the Ynysarwed mine adit in the SWC. Samples were collected from nine locations within sediment at the mine entrance from the upper and lower layers three times over one year for geochemical and bacterial 16S rRNA gene sequence analysis. During winter, members of the Betaproteobacteria bloomed in relative abundance (>40%) including the microaerophilic Fe(II)-oxidizing genus Gallionella. A concomitant decrease in Chlorobi-associated bacteria occurred, although by summer the community composition resembled that observed in the previous autumn. Here, we provide the first insights into the microbial ecology and seasonal dynamics of bacterial communities of Fe(III)-rich deposits in the SWC and demonstrate that neutrophilic Fe(II)-oxidizing bacteria are important and dynamic members of these communities.},
}
@article {pmid31499451,
year = {2019},
author = {Chen, S and Smith, AL},
title = {Performance and microbial ecology of methane-driven microbial fuel cells at temperatures ranging from 25 to 5 °C.},
journal = {Water research},
volume = {166},
number = {},
pages = {115036},
doi = {10.1016/j.watres.2019.115036},
pmid = {31499451},
issn = {1879-2448},
mesh = {*Bioelectric Energy Sources ; Electrodes ; *Geobacter ; Methane ; RNA, Ribosomal, 16S ; Temperature ; },
abstract = {The effluent of mainstream anaerobic processes is saturated with dissolved methane, representing a lost energy source and potent greenhouse gas emission if left unmanaged. This study investigated the impact of operational temperature on methane-driven microbial fuel cells (MFCs) designed for continuous operation to mitigate dissolved methane emissions in anaerobic effluents. Two bench-scale, single-chamber MFCs were operated sequentially at 25, 20, 15, 10 and 5 °C. Voltage production from both MFCs ranged from approximately 0.463 to 0.512 V over 1 kΩ resistance at temperatures ≥15 °C, but abruptly dropped as temperature decreased to 10 and 5 °C, averaging just 0.156 and 0.190 V for the replicate systems. Dissolved methane removal efficiency remained relatively stable across all operational temperatures, ranging from 53.0% to 63.6%. High-throughput sequencing of 16S rRNA genes and reverse transcription quantitative polymerase chain reaction indicated distinct distribution of methanotrophs (e.g., Methylomonas) and exoelectrogens (e.g., Geobacter) on the cathode and anode, respectively. Spearman's rank correlation suggested that an indirect interaction between methanotrophs and exoelectrogens via fermentative bacteria (e.g., Acetobacterium) may play a role in system function. Notably, diversity of the anode microbial community was positively correlated with both voltage production and Coulombic efficiency, suggesting overall diversity, as opposed to abundance or activity of exoelectrogens, was the primary factor governing performance at varying temperatures.},
}
@article {pmid31497590,
year = {2019},
author = {Ramamurthy, T and Mutreja, A and Weill, FX and Das, B and Ghosh, A and Nair, GB},
title = {Corrigendum: Revisiting the Global Epidemiology of Cholera in Conjunction With the Genomics of Vibrio cholerae.},
journal = {Frontiers in public health},
volume = {7},
number = {},
pages = {237},
doi = {10.3389/fpubh.2019.00237},
pmid = {31497590},
issn = {2296-2565},
abstract = {[This corrects the article DOI: 10.3389/fpubh.2019.00203.].},
}
@article {pmid31494089,
year = {2019},
author = {Hsu, RH and Clark, RL and Tan, JW and Ahn, JC and Gupta, S and Romero, PA and Venturelli, OS},
title = {Microbial Interaction Network Inference in Microfluidic Droplets.},
journal = {Cell systems},
volume = {9},
number = {3},
pages = {229-242.e4},
pmid = {31494089},
issn = {2405-4720},
support = {T32 GM130550/GM/NIGMS NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/metabolism ; Biodiversity ; Host-Pathogen Interactions ; Humans ; Lipid Droplets/*microbiology ; Microbial Consortia/*physiology ; Microbial Interactions/*physiology ; Microfluidics/*methods ; Microscopy, Fluorescence ; },
abstract = {Microbial interactions are major drivers of microbial community dynamics and functions but remain challenging to identify because of limitations in parallel culturing and absolute abundance quantification of community members across environments and replicates. To this end, we developed Microbial Interaction Network Inference in microdroplets (MINI-Drop). Fluorescence microscopy coupled to computer vision techniques were used to rapidly determine the absolute abundance of each strain in hundreds to thousands of droplets per condition. We showed that MINI-Drop could accurately infer pairwise and higher-order interactions in synthetic consortia. We developed a stochastic model of community assembly to provide insight into the heterogeneity in community states across droplets. Finally, we elucidated the complex web of interactions linking antibiotics and different species in a synthetic consortium. In sum, we demonstrated a robust and generalizable method to infer microbial interaction networks by random encapsulation of sub-communities into microfluidic droplets.},
}
@article {pmid31493988,
year = {2019},
author = {Calatayud, M and Koren, O and Collado, MC},
title = {Maternal Microbiome and Metabolic Health Program Microbiome Development and Health of the Offspring.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {30},
number = {10},
pages = {735-744},
doi = {10.1016/j.tem.2019.07.021},
pmid = {31493988},
issn = {1879-3061},
support = {//CIHR/Canada ; },
mesh = {Female ; Humans ; Infant, Newborn ; Lactation/physiology ; Metabolic Syndrome/metabolism/microbiology ; Microbiota/*physiology ; Obesity/*metabolism/*microbiology ; Pregnancy ; },
abstract = {Maternal nutritional, metabolic, and physiological states, as well as exposure to various environmental factors during conception, gestation, and lactation, have a fundamental role in the health programming of the offspring. Therefore, alterations affecting the maternal microbiota might indirectly influence fetal development. In addition, such alterations could be transmitted to the progeny at different stages of infant development (e.g., preconception, prenatal, or postnatal), thereby favoring the development of an altered microbiota in the neonate. Microbial changes of this kind have been linked to an increased risk of non-communicable diseases (NCDs), including obesity and metabolic syndrome, allergy-related problems, and diabetes. In this review, we summarize the relevance of the maternal microbiota to fetal-neonatal health programming, with a focus on maternal nutritional and metabolic states.},
}
@article {pmid31492977,
year = {2020},
author = {Expósito, JR and Coello, AJ and Barreno, E and Casano, LM and Catalá, M},
title = {Endogenous NO Is Involved in Dissimilar Responses to Rehydration and Pb(NO3)2 in Ramalina farinacea Thalli and Its Isolated Phycobionts.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {604-616},
pmid = {31492977},
issn = {1432-184X},
support = {PROMETEOIII /2017/039 GVA//Generalitat Valenciana/ ; CGL2016-79158-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; CGL2016-40058-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; },
mesh = {Air Pollutants/*metabolism ; Ascomycota/drug effects/*metabolism ; Chlorophyta/drug effects/*metabolism ; Desiccation ; Energy Metabolism ; Lead/*metabolism ; Lichens/drug effects/*metabolism ; Nitrates/*metabolism ; Nitric Oxide/*metabolism ; Oxidative Stress ; },
abstract = {Lichens undergo desiccation/rehydration cycles and are permeable to heavy metals, which induce free radicals. Nitrogen monoxide (NO) regulates important cellular functions, but the research on lichen NO is still very scarce. In Ramalina farinacea thalli, NO seems to be involved in the peroxidative damage caused by air pollution, antioxidant defence and regulation of lipid peroxidation and photosynthesis. Our hypothesis is that NO also has a critical role during the rehydration and in the responses to lead of its isolated phycobionts (Trebouxia sp. TR9 and Trebouxia jamesii). Therefore, we studied the intracellular reactive oxygen species (ROS) production, lipid peroxidation and chlorophyll autofluorescence during rehydration of thalli and isolated microalgae in the presence of a NO scavenger and Pb(NO3)2. During rehydration, NO scavenging modulates free radical release and chlorophyll autofluorescence but not lipid peroxidation in both thalli and phycobionts. Pb(NO3)2 reduced free radical release (hormetic effect) both in the whole thallus and in microalgae. However, only in TR9, the ROS production, chlorophyll autofluorescence and lipid peroxidation were dependent on NO. In conclusion, Pb hormetic effect seems to depend on NO solely in TR9, while is doubtful for T. jamesii and the whole thalli.},
}
@article {pmid31489900,
year = {2019},
author = {Jaswal, R and Pathak, A and Chauhan, A},
title = {Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils.},
journal = {Microorganisms},
volume = {7},
number = {9},
pages = {},
pmid = {31489900},
issn = {2076-2607},
support = {DE-AC09-08SR22470//Savannah River National Laboratory/ ; },
abstract = {Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the "core" microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired "core" microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired "core" bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.},
}
@article {pmid31488068,
year = {2019},
author = {Pereira-Flores, E and Glöckner, FO and Fernandez-Guerra, A},
title = {Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data.},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {453},
pmid = {31488068},
issn = {1471-2105},
support = {57129354//Deutscher Akademischer Austauschdienst/ ; POS_EXT_2012_1_10105//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; 634486//Horizon 2020 Framework Programme/ ; },
mesh = {Benchmarking ; DNA Copy Number Variations ; Databases, Genetic ; *Gene Dosage ; *Genome Size ; Metagenome/*genetics ; Metagenomics/*methods ; Oceans and Seas ; RNA, Ribosomal, 16S/*genetics ; Time Factors ; },
abstract = {BACKGROUND: Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis workflows has the potential to improve the exploitation of metagenomic data. Metagenomic traits are organisms' characteristics linked to their performance. They are measured at the genomic level taking a random sample of individuals in a community. As such, these traits provide valuable information to uncover microorganisms' ecological patterns. The Average Genome Size (AGS) and the 16S rRNA gene Average Copy Number (ACN) are two highly informative metagenomic traits that reflect microorganisms' ecological strategies as well as the environmental conditions they inhabit.<br><br>RESULTS: Here, we present the ags.sh and acn.sh tools, which analytically derive the AGS and ACN metagenomic traits. These tools represent an advance on previous approaches to compute the AGS and ACN traits. Benchmarking shows that ags.sh is up to 11 times faster than state-of-the-art tools dedicated to the estimation AGS. Both ags.sh and acn.sh show comparable or higher accuracy than existing tools used to estimate these traits. To exemplify the applicability of both tools, we analyzed the 139 prokaryotic metagenomes of TARA Oceans and revealed the ecological strategies associated with different water layers.<br><br>CONCLUSION: We took advantage of recent advances in gene annotation to develop the ags.sh and acn.sh tools to combine easy tool usage with fast and accurate performance. Our tools compute the AGS and ACN metagenomic traits on unassembled metagenomes and allow researchers to improve their metagenomic data analysis to gain deeper insights into microorganisms' ecology. The ags.sh and acn.sh tools are publicly available using Docker container technology at https://github.com/pereiramemo/AGS-and-ACN-tools .},
}
@article {pmid31487597,
year = {2019},
author = {Griffero, L and Alcántara-Durán, J and Alonso, C and Rodríguez-Gallego, L and Moreno-González, D and García-Reyes, JF and Molina-Díaz, A and Pérez-Parada, A},
title = {Basin-scale monitoring and risk assessment of emerging contaminants in South American Atlantic coastal lagoons.},
journal = {The Science of the total environment},
volume = {697},
number = {},
pages = {134058},
doi = {10.1016/j.scitotenv.2019.134058},
pmid = {31487597},
issn = {1879-1026},
abstract = {Emerging contaminants (ECs) such as pharmaceuticals, personal care products, drugs of abuse and polar pesticides are under particular attention due to their high consumption, frequent detection in the environment and reported ecotoxicological risk. This study investigates the occurrence and distribution of multiclass of ECs in surface waters at basin scale of two Atlantic coastal lagoons of Uruguay, South America. For this purpose, a target screening approach covering up to 362 compounds was employed using nanoflow liquid chromatography - high resolution mass spectrometry (nanoLC/HRMS). 56 compounds were identified including five banned pesticides in the European Union: atrazine, carbendazim, chlorpyrifos ethyl, diazinon, and ethion. Pharmaceuticals, hormones and drugs of abuse showed maximum detection frequencies and concentrations downstream cities. The highest occurrence of pesticides was found in lagoons and streams with neighboring agricultural activity. ECs were also found in coastal sea. Environmental risk assessment revealed that the hormones 17α-ethinylestradiol and 17-β-estradiol showed the highest risk to aquatic organisms in these basins. This study represents the first basin- scale monitoring of ECs in superficial waters encompassing streams, lagoons, and coastal seas in Uruguay, South America.},
}
@article {pmid31487593,
year = {2019},
author = {Field, HR and Whitaker, AH and Henson, JA and Duckworth, OW},
title = {Sorption of copper and phosphate to diverse biogenic iron (oxyhydr)oxide deposits.},
journal = {The Science of the total environment},
volume = {697},
number = {},
pages = {134111},
doi = {10.1016/j.scitotenv.2019.134111},
pmid = {31487593},
issn = {1879-1026},
mesh = {Adsorption ; Copper/*chemistry ; Iron/*chemistry ; Models, Chemical ; Organic Chemicals ; Oxidation-Reduction ; Oxides ; Phosphates/*chemistry ; },
abstract = {Iron (Fe) transformations partially control the biogeochemical cycling of biologically and environmentally important elements, such as carbon (C), nitrogen (N), phosphorus (P), and trace metals. In marine and freshwater environments, iron oxidizing bacteria commonly promote the oxidation of ferrous iron (Fe(II)) at circumneutral oxic-anoxic interfaces, resulting in the formation of mineral-organic composites known as biogenic Fe(III) (oxyhydr)oxides (BIOS). Previous studies have examined the microbial ecology, composition, morphology, and sorption reactivity of BIOS. However, a broad survey of BIOS properties and sorption reactivity is lacking. To further explore these relationships, this study utilized X-ray absorption spectroscopy (XAS) to characterize the Fe mineral species, acid digestions and elemental analysis to determine composition, Brunauer-Emmett-Teller (BET) analysis to measure specific surface area, and copper (Cu) and phosphorus (P) adsorption experiments at concentrations designed to measure maximum sorption to evaluate reactivity of BIOS samples collected in lakes and streams of the North Carolina Piedmont. Sample composition varied widely, with Fe and C content ranging from 6.3 to 34% and 3.4-13%, respectively. XAS spectra were best fit with 42-100% poorly crystalline Fe (oxyhydr)oxides, with the remainder composed of crystalline Fe minerals and organic complexes. On a sorbent mass basis, Cu and P sorption varied by a factor of two and 15, respectively. Regression analyses reveal interrelationships between physicochemical properties, and suggest that differences in P binding are driven by sorption to Fe(III) (oxyhydr)oxide surfaces. In total, results suggest that the physical and chemical characteristics of organic and Fe(III) (oxyhydr)oxide phases in BIOS interplay to control the sorption of solutes, and thus influence nutrient and contaminant cycling in soil and natural waters.},
}
@article {pmid31486865,
year = {2020},
author = {Hernández-Del Amo, E and Ramió-Pujol, S and Gich, F and Trias, R and Bañeras, L},
title = {Changes in the Potential Activity of Nitrite Reducers and the Microbial Community Structure After Sediment Dredging and Plant Removal in the Empuriabrava FWS-CW.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {588-603},
pmid = {31486865},
issn = {1432-184X},
support = {IF-UDG2013//Universitat de Girona/ ; (MPCUdG2016/121//Universitat de Girona/ ; CGL2009-08338/BOS//Ministerio de Educaci&#xf3;n, Cultura y Deporte/ ; 2017SGR-548//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; },
mesh = {Bacteria/*metabolism ; *Conservation of Water Resources ; Geologic Sediments/*microbiology ; *Microbiota ; Nitrites/*metabolism ; Oxidation-Reduction ; Spain ; Waste Disposal, Fluid ; *Wetlands ; },
abstract = {In constructed wetlands (CW), denitrification usually accounts for > 60% of nitrogen removal and is supposedly affected by wetland management practices, such as dredging (and plant removal). These practices cause an impact in sediment properties and microbial communities living therein. We have quantified the effects of a sediment dredging event on dissimilatory nitrite reduction by analysing the structure and activities of the microbial community before and after the event. Potential rates for nitrate reduction to ammonia and denitrification were in accordance with changes in the physicochemical conditions. Denitrification was the predominant pathway for nitrite removal (> 60%) and eventually led to the complete removal of nitrate. On the contrary, dissimilatory nitrite reduction to ammonia (DNRA) increased from 5 to 18% after the dredging event. Both actual activities and abundances of 16S rRNA, nirK and nirS significantly decreased after sediment dredging. However, genetic potential for denitrification (qnirS + qnirK/q16S rRNA) remained unchanged. Analyses of the 16S rRNA gene sequences revealed the importance of vegetation in shaping microbial community structures, selecting specific phylotypes potentially contributing to the nitrogen cycle. Overall, we confirmed that sediment dredging and vegetation removal exerted a measurable effect on the microbial community, but not on potential nitrite + nitrate removal rates. According to redundancy analysis, nitrate concentration and pH were the main variables affecting sediment microbial communities in the Empuriabrava CWs. Our results highlight a high recovery of the functionality of an ecosystem service after a severe intervention and point to metabolic redundancy of denitrifiers. We are confident these results will be taken into account in future management strategies in CWs.},
}
@article {pmid31483625,
year = {2019},
author = {Cruz, H and Law, YY and Guest, JS and Rabaey, K and Batstone, D and Laycock, B and Verstraete, W and Pikaar, I},
title = {Mainstream Ammonium Recovery to Advance Sustainable Urban Wastewater Management.},
journal = {Environmental science &amp; technology},
volume = {53},
number = {19},
pages = {11066-11079},
doi = {10.1021/acs.est.9b00603},
pmid = {31483625},
issn = {1520-5851},
mesh = {*Ammonium Compounds ; Ecosystem ; Sewage ; Waste Disposal, Fluid ; *Wastewater ; },
abstract = {Throughout the 20th century, the prevailing approach toward nitrogen management in municipal wastewater treatment was to remove ammonium by transforming it into dinitrogen (N2) using biological processes such as conventional activated sludge. While this has been a very successful strategy for safeguarding human health and protecting aquatic ecosystems, the conversion of ammonium into its elemental form is incompatible with the developing circular economy of the 21st century. Equally important, the activated sludge process and other emerging ammonium removal pathways have several environmental and technological limitations. Here, we assess that the theoretical energy embedded in ammonium in domestic wastewater represents roughly 38-48% of the embedded chemical energy available in the whole of the discharged bodily waste. The current routes for ammonium removal not only neglect the energy embedded in ammonium, but they can also produce N2O, a very strong greenhouse gas, with such emissions comprising the equivalent of 14-26% of the overall carbon footprint of wastewater treatment plants. N2O emissions often exceed the carbon emissions related to the electricity consumption for the process requirements of WWTPs. Considering these limitations, there is a need to develop alternative ammonium management approaches that center around recovery of ammonium from domestic wastewater rather than deal with its "destruction" into elemental dinitrogen. Current ammonium recovery techniques are applicable only at orders of magnitude above domestic wastewater strength, and so new techniques based on physicochemical adsorption are of particular interest. A new pathway is proposed that allows for mainstream ammonium recovery from wastewater based on physicochemical adsorption through development of polymer-based adsorbents. Provided adequate adsorbents corresponding to characteristics outlined in this paper are designed and brought to industrial production, this adsorption-based approach opens perspectives for mainstream continuous adsorption coupled with side-stream recovery of ammonium with minimal chemical requirements. This proposed pathway can bring forward an effective resource-oriented approach to upgrade the fate of ammonium in urban water management without generating hidden externalized environmental costs.},
}
@article {pmid31482748,
year = {2019},
author = {Arias-Borrego, A and Callejón-Leblic, B and Calatayud, M and Gómez-Ariza, JL and Collado, MC and García-Barrera, T},
title = {Insights into cancer and neurodegenerative diseases through selenoproteins and the connection with gut microbiota - current analytical methodologies.},
journal = {Expert review of proteomics},
volume = {16},
number = {10},
pages = {805-814},
doi = {10.1080/14789450.2019.1664292},
pmid = {31482748},
issn = {1744-8387},
mesh = {Body Fluids/metabolism ; Dietary Supplements ; Gastrointestinal Microbiome/*genetics ; Humans ; Neoplasms/diet therapy/*genetics/microbiology ; Neurodegenerative Diseases/diet therapy/*genetics/microbiology ; Selenium/metabolism/therapeutic use ; Selenoproteins/*genetics/isolation &amp; purification/metabolism ; },
abstract = {Introduction: Selenium plays many key roles in health especially in connection with cancer and neurodegenerative diseases. However, it needs to be appreciated that the essentiality/toxicity of selenium depends on both, a narrow range of concentration and the chemical specie involved. In this context, selenoproteins are essential biomolecules against these disorders, mainly due to its antioxidant action. To this end, analytical methodologies may allow identifying and quantifying individual selenospecies in human biofluids and tissues. Areas covered: This review focus on the role of selenoproteins in medicine, with special emphasis in cancer and neurodegenerative diseases, considering the possible link with gut microbiota. In particular, this article reviews the analytical techniques and procedures recently developed for the absolute quantification of selenoproteins and selenometabolites in human biofluids and tissues. Expert commentary: The beneficial role of selenium in human health has been extensively studied and reviewed. However, several challenges remain unsolved as discussed in this article: (i) speciation of selenium (especially selenoproteins) in cancer and neurodegenerative disease patients; (ii) supplementation of selenium in humans using functional foods and nutraceuticals; (iii) the link between selenium and selenoproteins expression and the gut microbiota and (iv) analytical methods and pitfalls for the absolute quantification of selenoproteins and selenometabolites.},
}
@article {pmid31482287,
year = {2020},
author = {Veach, AM and Zeglin, LH},
title = {Historical Drought Affects Microbial Population Dynamics and Activity During Soil Drying and Re-Wet.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {662-674},
pmid = {31482287},
issn = {1432-184X},
support = {EPS-0903806//Kansas NSF-EPSCoR First Award/ ; },
mesh = {*Bacterial Physiological Phenomena ; Biomass ; Desiccation ; *Droughts ; Kansas ; *Microbiota ; Population Dynamics ; *Soil Microbiology ; },
abstract = {A history of drought exposure promoted by variable precipitation regimes can select for drought-tolerant soil microbial taxa, but the mechanisms of survival and death of microbial populations through the selective stresses of soil drying and re-wet are not well understood. We subjected soils collected from a 15-year field drought experiment ("Altered" precipitation history with extended dry periods, versus the "Ambient" field control) to a laboratory drying/re-wetting experiment, to learn whether selective population survival, death, or maintenance of protein synthesis potential and microbial respiration through variable soil water conditions was affected by field drought legacy. Microbial community composition, as measured by Illumina MiSeq sequencing of the 16S rRNA and 16S rRNA gene, shifted with laboratory drying/re-wet and field drought treatments. In Ambient soils, there was a higher proportion of reduced OTU abundance (indicative of mortality) during re-wet, whereas Altered soils had a greater proportion of stable OTU populations that did not change in abundance (indicative of survival) through drying/re-wet. Altered soils also had a lower proportion of rRNA:rRNA genes (lower protein synthesis potential) during dry-down, a greater weighted mean rRNA operon number (potential growth rate and r-selection) which was associated with higher abundance of Firmicutes (order Bacillales), and lower average microbial respiration rates. These data demonstrate that soils with a weaker historical drought legacy exhibit a higher prevalence of microbial water-stress mortality and differential survival and death at OTU levels following short-term dryingand re-wetting, concurrent with higher carbon loss potential. This work provides novel insight into the mechanisms and consequences of soil microbial changes resulting from extended drought conditions.},
}
@article {pmid31482282,
year = {2019},
author = {Ehsani, E and Dumolin, C and Arends, JBA and Kerckhof, FM and Hu, X and Vandamme, P and Boon, N},
title = {Enriched hydrogen-oxidizing microbiomes show a high diversity of co-existing hydrogen-oxidizing bacteria.},
journal = {Applied microbiology and biotechnology},
volume = {103},
number = {19},
pages = {8241-8253},
doi = {10.1007/s00253-019-10082-z},
pmid = {31482282},
issn = {1432-0614},
support = {Geconcerteerde Onderzoeksactie (GOA) of Ghent University (BOF15/GOA/006)//Universiteit Gent/ ; Geconcerteerde Onderzoeksactie (GOA) of Ghent University (BOF15/GOA/006)//Universiteit Gent/ ; },
mesh = {Ammonium Compounds/metabolism ; Bacteria/*classification/genetics/*metabolism ; Bacteriological Techniques ; Carbon Dioxide/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Hydrogen/*metabolism ; Metagenomics ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; },
abstract = {While numerous reports exist on the axenic culturing of different hydrogen-oxidizing bacteria (HOB), knowledge about the enrichment of microbial communities growing on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources remains negligible. We want to elucidate if in such enrichments, most enriched populations are HOBs or heterotrophic organisms. In the present study, bacteria enriched from a soil sample and grown over 5 transfers using a continuous supply of hydrogen, oxygen, and carbon dioxide to obtain an enriched autotrophic hydrogen-oxidizing microbiome. The success of the enrichment was evaluated by monitoring ammonium consumption and biomass concentration for 120 days. The shift in the microbial composition of the original soil inoculum and all transfers was observed based on 16S rRNA amplicon sequencing. The hydrogen-oxidizing facultative chemolithoautotroph Hydrogenophaga electricum was isolated and found to be one of the abundant species in most transfers. Moreover, Achromobacter was isolated both under heterotrophic and autotrophic conditions, which was characterized as a hydrogen-oxidizing bacterium. The HOB enrichment condition constructed in this study provided an environment for HOB to develop and conquer in all transfers. In conclusion, we showed that enrichments on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources contain a diverse mixture of HOB and heterotrophs that resulted in a collection of culturable isolates. These isolates can be useful for further investigation for industrial applications.},
}
@article {pmid31482007,
year = {2019},
author = {Keshvardoust, P and Huron, VAA and Clemson, M and Constancias, F and Barraud, N and Rice, SA},
title = {Biofilm formation inhibition and dispersal of multi-species communities containing ammonia-oxidising bacteria.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {1},
pages = {22},
pmid = {31482007},
issn = {2055-5008},
mesh = {Ammonium Compounds/metabolism ; Biofilms/*growth &amp; development ; Carbon/metabolism ; Culture Media/chemistry ; *Microbial Interactions ; *Microbiota ; Nitrification ; Nitrosomonas europaea/*growth &amp; development/metabolism ; Organic Chemicals/metabolism ; },
abstract = {Despite considerable research, the biofilm-forming capabilities of Nitrosomonas europaea are poorly understood for both mono and mixed-species communities. This study combined biofilm assays and molecular techniques to demonstrate that N. europaea makes very little biofilm on its own, and relies on the activity of associated heterotrophic bacteria to establish a biofilm. However, N. europaea has a vital role in the proliferation of mixed-species communities under carbon-limited conditions, such as in drinking water distribution systems, through the provision of organic carbon via ammonia oxidation. Results show that the addition of nitrification inhibitors to mixed-species nitrifying cultures under carbon-limited conditions disrupted biofilm formation and caused the dispersal of pre-formed biofilms. This dispersal effect was not observed when an organic carbon source, glucose, was included in the medium. Interestingly, inhibition of nitrification activity of these mixed-species biofilms in the presence of added glucose resulted in increased total biofilm formation compared to controls without the addition of nitrification inhibitors, or with only glucose added. This suggests that active AOB partially suppress or limit the overall growth of the heterotrophic bacteria. The experimental model developed here provides evidence that ammonia-oxidising bacteria (AOB) are involved in both the formation and maintenance of multi-species biofilm communities. The results demonstrate that the activity of the AOB not only support the growth and biofilm formation of heterotrophic bacteria by providing organic carbon, but also restrict and limit total biomass in mixed community systems.},
}
@article {pmid31475212,
year = {2019},
author = {Godoy-Vitorino, F},
title = {Human microbial ecology and the rising new medicine.},
journal = {Annals of translational medicine},
volume = {7},
number = {14},
pages = {342},
pmid = {31475212},
issn = {2305-5839},
abstract = {The first life forms on earth were Prokaryotic, and the evolution of all Eukaryotic life occurred with the help of bacteria. Animal-associated microbiota also includes members of the archaea, fungi, protists, and viruses. The genomes of this host-associated microbial life are called the microbiome. Across the mammalian tree, microbiomes guarantee the development of immunity, physiology, and resistance to pathogens. In humans, all surfaces and cavities are colonized by a microbiome, maintained by a careful balance between the host response and its colonizers-thus humans are considered now supraorganisms. These microbiomes supply essential ecosystem services that benefit health through homeostasis, and the loss of the indigenous microbiota leads to dysbiosis, which can have significant consequences to disease. This educational review aims to describe the importance of human microbial ecology, explain the ecological terms applied to the study of the human microbiome, developments within the cutting-edge microbiome field, and implications to diagnostic and treatment.},
}
@article {pmid31469487,
year = {2019},
author = {Overholt, WA and Schwing, P and Raz, KM and Hastings, D and Hollander, DJ and Kostka, JE},
title = {The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills.},
journal = {Environmental microbiology},
volume = {21},
number = {11},
pages = {4316-4329},
doi = {10.1111/1462-2920.14794},
pmid = {31469487},
issn = {1462-2920},
support = {C-IMAGE II//Gulf of Mexico Research Initiative/International ; C-IMAGE III//Gulf of Mexico Research Initiative/International ; 2013172310//National Science Foundation/International ; },
mesh = {Environmental Monitoring/methods ; Geologic Sediments/*microbiology ; Gulf of Mexico ; *Microbiota ; *Petroleum Pollution ; },
abstract = {The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in > 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Furthermore, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after 2 years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover, deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.},
}
@article {pmid31466158,
year = {2019},
author = {Zhang, L and Shen, Z and Fang, W and Gao, G},
title = {Composition of bacterial communities in municipal wastewater treatment plant.},
journal = {The Science of the total environment},
volume = {689},
number = {},
pages = {1181-1191},
doi = {10.1016/j.scitotenv.2019.06.432},
pmid = {31466158},
issn = {1879-1026},
mesh = {Bacteria/classification ; Bacteroidetes/genetics ; China ; Firmicutes ; *Microbiota ; Phylogeny ; Proteobacteria/genetics ; Sewage/microbiology ; *Waste Disposal, Fluid ; Wastewater/*microbiology ; },
abstract = {Efforts to understand the environmental and biological factors that influence the dynamics of microbial communities have received substantial attention in microbial ecology. In this study, Illumina MiSeq high-throughput sequencing technology was used to examine the microbial community structure of activated sludge in municipal wastewater treatment systems (Chuzhou city, China). Overall, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the most dominant phyla in the five activated sludge samples. However, the community structure of nitrifying bacteria was relatively simple, and diversity was low; only AOB (Nitrosomonas) and NOB (Nitrospira) were detected. The dominant bacteria in the anaerobic sludge, anoxic sludge and oxic sludge were the same, and each bacterial species was relatively uniform, with differences only in proportions. Redundancy analysis indicated that pH, TP and COD were strong environmental factors influencing the bacterial community distribution. PICRUSt was used to describe the metabolic and functional abilities of the activated sludge bacterial communities. The results emphasized the vast genetic diversity of these organisms, which are involved in various essential processes such as amino acid transport and metabolism, energy production and conversion, cell wall/membrane/envelope/biogenesis, signal transduction mechanisms, and carbohydrate transport and metabolism. Activated sludge of municipal wastewater treatment systems can be ranked in the following order based on the 16S rRNA gene copy numbers of the detected phylotypes: S1 > S2 > S4 > S5 > S3. This study provides basic data and a theoretical analysis of the optimal design and operation in wastewater treatment plants.},
}
@article {pmid31466157,
year = {2019},
author = {Xu, M and Stedtfeld, RD and Wang, F and Hashsham, SA and Song, Y and Chuang, Y and Fan, J and Li, H and Jiang, X and Tiedje, JM},
title = {Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history.},
journal = {The Science of the total environment},
volume = {689},
number = {},
pages = {1172-1180},
doi = {10.1016/j.scitotenv.2019.06.376},
pmid = {31466157},
issn = {1879-1026},
mesh = {*Composting ; Drug Resistance, Microbial/*genetics ; Farms ; Fertilizers ; *Genes, Bacterial ; Manure/*microbiology ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Different long-term fertilization regimes may change indigenous microorganism diversity in the arable soil and thus might influence the persistence and transmission of manure-born antibiotic resistance genes (ARGs). Different manure origins and composting techniques might affect the fate of introduced ARGs in farmland. A four-month microcosm experiment was performed using two soils, which originated from the same field and applied with the same chemical fertilizer or swine manure for 26 years, to investigate the dynamics of ARGs in soil amended with manure or compost from the farm and an agro-technology company. High throughput qPCR and sequencing were applied to quantify ARGs using 144 primer sets and microorganism in soil. Fertilization history had little effect on dynamics of manure-borne ARGs in soil regardless of manure origin or composting. Very different half-lives of ARGs and mobile genetic elements from farm manure and commercial manure were observed in both soils. Composting decreased abundance of most ARGs in manure, but increased the persistence of manure-introduced ARGs in soil irrespective of fertilization history, especially for those from farm manure. These findings help understanding the fate of ARGs in manured soil and may inform techniques to mitigate ARGs transmission.},
}
@article {pmid31463982,
year = {2020},
author = {Elghandour, MMY and Khusro, A and Adegbeye, MJ and Tan, Z and Abu Hafsa, SH and Greiner, R and Ugbogu, EA and Anele, UY and Salem, AZM},
title = {Dynamic role of single-celled fungi in ruminal microbial ecology and activities.},
journal = {Journal of applied microbiology},
volume = {128},
number = {4},
pages = {950-965},
doi = {10.1111/jam.14427},
pmid = {31463982},
issn = {1365-2672},
mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena/*physiology ; Animals ; Diet/veterinary ; Dietary Supplements/*microbiology ; Fermentation ; Fungi/metabolism/*physiology ; Rumen/chemistry/*microbiology ; Ruminants/microbiology/*physiology ; Saccharomyces cerevisiae/metabolism/physiology ; },
abstract = {In ruminants, high fermentation capacity is necessary to develop more efficient ruminant production systems. Greater level of production depends on the ability of the microbial ecosystem to convert organic matter into precursors of milk and meat. This has led to increased interest by animal nutritionists, biochemists and microbiologists in evaluating different strategies to manipulate the rumen biota to improve animal performance, production efficiency and animal health. One of such strategies is the use of natural feed additives such as single-celled fungi yeast. The main objectives of using yeasts as natural additives in ruminant diets include; (i) to prevent rumen microflora disorders, (ii) to improve and sustain higher production of milk and meat, (iii) to reduce rumen acidosis and bloat which adversely affect animal health and performance, (iv) to decrease the risk of ruminant-associated human pathogens and (v) to reduce the excretion of nitrogenous-based compounds, carbon dioxide and methane. Yeast, a natural feed additive, has the potential to enhance feed degradation by increasing the concentration of volatile fatty acids during fermentation processes. In addition, microbial growth in the rumen is enhanced in the presence of yeast leading to the delivery of a greater amount of microbial protein to the duodenum and high nitrogen retention. Single-celled fungi yeast has demonstrated its ability to increase fibre digestibility and lower faecal output of organic matter due to improved digestion of organic matter, which subsequently improves animal productivity. Yeast also has the ability to alter the fermentation process in the rumen in a way that reduces methane formation. Furthermore, yeast inclusion in ruminant diets has been reported to decrease toxins absorption such as mycotoxins and promote epithelial cell integrity. This review article provides information on the impact of single-celled fungi yeast as a feed supplement on ruminal microbiota and its function to improve the health and productive longevity of ruminants.},
}
@article {pmid31463664,
year = {2020},
author = {Erni-Cassola, G and Wright, RJ and Gibson, MI and Christie-Oleza, JA},
title = {Early Colonization of Weathered Polyethylene by Distinct Bacteria in Marine Coastal Seawater.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {517-526},
pmid = {31463664},
issn = {1432-184X},
support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; NE/S005501/1//Natural Environment Research Council/ ; NE/K009044/1//Natural Environment Research Council/ ; BB/M01116X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; CENTA//Natural Environment Research Council/ ; },
mesh = {Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Polyethylene/*metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seawater/*microbiology ; *Waste Products ; },
abstract = {Plastic debris in aquatic environments is rapidly colonized by a diverse community of microorganisms, often referred to as the "Plastisphere." Given that common plastics are derived from fossil fuels, one would expect that Plastispheres should be enriched with obligate hydrocarbon-degrading bacteria (OHCB). So far, though, different polymer types do not seem to exert a strong effect on determining the composition of the Plastisphere, and putative biodegrading bacteria are only found as rare taxa within these biofilms. Here, we show through 16S rRNA gene sequencing that the enrichment of a prominent OHCB member on weathered and non-weathered polyethylene only occurred at early stages of colonization (i.e., after 2 days of incubation in coastal marine water; 5.8% and 3.7% of relative abundance, respectively, vs. 0.6% on glass controls). As biofilms matured, these bacteria decreased in relative abundance on all materials (< 0.3% after 9 days). Apart from OHCB, weathered polyethylene strongly enriched for other distinct organisms during early stages of colonization, such as a specific member of the Roseobacter group and a member of the genus Aestuariibacter (median 26.9% and 1.8% of the community, respectively), possibly as a consequence of the availability of short-oxidized chains generated from weathering. Our results demonstrate that Plastispheres can vary in accordance with the weathering state of the material and that very early colonizing communities are enriched with taxa that can potentially degrade hydrocarbons. Given the lack of persistent enrichment and overall community convergence between materials over time, common non-hydrolysable polymers might not serve as an important source of carbon for mature Plastispheres once the labile substrates generated from weathering have been depleted.},
}
@article {pmid31463663,
year = {2020},
author = {Baselga-Cervera, B and García-Balboa, C and Díaz-Alejo, HM and Costas, E and López-Rodas, V},
title = {Rapid Colonization of Uranium Mining-Impacted Waters, the Biodiversity of Successful Lineages of Phytoplankton Extremophiles.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {576-587},
pmid = {31463663},
issn = {1432-184X},
support = {CTM-2013-44366-R.//Spanish Secretar&#xed;a de Estado, Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; BES-2014-067580.//Secretar&#xed;a de Estado, Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; },
mesh = {Biodiversity ; Chlamydomonas reinhardtii/physiology/radiation effects ; Chlorophyta/*physiology/radiation effects ; Extremophiles/*physiology/radiation effects ; Mining ; Phytoplankton/*physiology/radiation effects ; Portugal ; Spain ; Uranium/*analysis ; Water Pollutants, Radioactive/*analysis ; },
abstract = {Anthropogenic extreme environments are emphasized as interesting sites for the study of evolutionary pathways, biodiversity, and extremophile bioprospection. Organisms that grow under these conditions are usually regarded as extremophiles; however, the extreme novelty of these environments may have favor adaptive radiations of facultative extremophiles. At the Iberian Peninsula, uranium mining operations have rendered highly polluted extreme environments in multiple locations. In this study, we examined the phytoplankton diversity, community structure, and possible determining factors in separate uranium mining-impacted waters. Some of these human-induced extreme environments may be able to sustain indigenous facultative extremophile phytoplankton species, as well as alleged obligate extremophiles. Therefore, we investigated the adaptation capacity of three laboratory strains, two Chlamydomonas reinhardtii and a Dictyosphaerium chlorelloides, to uranium-polluted waters. The biodiversity among the sampled waters was very low, and despite presenting unique taxonomic records, ecological patterns can be identified. The microalgae adaptation experiments indicated a gradient of ecological novelty and different phenomena of adaptation, from acclimation in some waters to non-adaptation in the harshest anthropogenic environment. Certainly, phytoplankton extremophiles might have been often overlooked, and the ability to flourish in extreme environments might be a functional feature in some neutrophilic species. Evolutionary biology and microbial biodiversity can benefit the study of recently evolved systems such as uranium-polluted waters. Moreover, anthropogenic extremophiles can be harnessed for industrial applications.},
}
@article {pmid31462415,
year = {2019},
author = {McGonigle, JM and Bernau, JA and Bowen, BB and Brazelton, WJ},
title = {Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats.},
journal = {mSphere},
volume = {4},
number = {4},
pages = {},
pmid = {31462415},
issn = {2379-5042},
mesh = {Archaea/*classification ; Bacteria/*classification ; DNA, Bacterial/genetics ; Ecosystem ; *Genetic Variation ; Lakes/chemistry/microbiology ; *Microbiota ; Nevada ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salt Tolerance ; Utah ; },
abstract = {We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah-Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers collected from the upper 30 cm of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse halobacteria and Salinibacter species. Sequences identical to Geitlerinema sp. strain PCC 9228, an anoxygenic cyanobacterium that uses sulfide as the electron donor for photosynthesis, are also abundant in many samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. In these sediments, we found an increased presence of Thermoplasmatales, Hadesarchaeota, Nanoarchaeaeota, Acetothermia, Desulfovermiculus, Halanaerobiales, Bacteroidetes, and Rhodovibrio This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically sterile landscape.IMPORTANCE Pleistocene Lake Bonneville, which covered a third of Utah, desiccated approximately 13,000 years ago, leaving behind the Bonneville Salt Flats (BSF) in the Utah West Desert. The potash salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the biological interactions with the salt crust have not been studied. This study is the first geospatial analysis of microbially diverse populations at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.},
}
@article {pmid31456784,
year = {2019},
author = {Gogulancea, V and González-Cabaleiro, R and Li, B and Taniguchi, D and Jayathilake, PG and Chen, J and Wilkinson, D and Swailes, D and McGough, AS and Zuliani, P and Ofiteru, ID and Curtis, TP},
title = {Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1871},
pmid = {31456784},
issn = {1664-302X},
abstract = {Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·10[5] individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances.},
}
@article {pmid31455798,
year = {2019},
author = {Park, CH and Lee, JG and Lee, AR and Eun, CS and Han, DS},
title = {Network construction of gastric microbiome and organization of microbial modules associated with gastric carcinogenesis.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {12444},
pmid = {31455798},
issn = {2045-2322},
mesh = {Adult ; *Bacteria/classification/genetics ; *Carcinogenesis ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metaplasia ; Middle Aged ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Stomach Neoplasms/genetics/microbiology ; },
abstract = {In addition to Helicobacter pylori infection, nitrosating/nitrate-reducing bacteria and type IV secretion system (T4SS) protein gene-contributing bacteria have been proposed as potential causes of gastric cancer development. However, bacterial modules related with gastric carcinogenesis have not been clarified. In this study, we analyzed gastric microbiome using the gastric mucosal samples obtained from the Hanyang University Gastric Microbiome Cohort by 16S rRNA gene sequencing. Weighted correlation network analysis was performed to construct a microbiome network and to identify microbial modules associated with gastric carcinogenesis. At the family level, 420 bacterial taxa were identified in the gastric microbiome of 83 participants. Through network analysis, 18 microbial modules were organized. Among them, two modules-pink and brown-were positively correlated with a higher-risk of gastric cancer development such as intestinal metaplasia with no current H. pylori infection (correlation coefficient [γ]: pink module, 0.31 [P = 0.004], brown module, 0.26 [P = 0.02]). At the family level, twenty-two and thirty-two bacterial taxa belonged to the pink and brown modules, respectively. They included nitrosating/nitrate-reducing bacteria, T4SS protein gene-contributing bacteria, and various other bacteria, including Gordoniaceae, Tsukamurellaceae, Prevotellaceae, Cellulomonadaceae, Methylococcaceae, and Procabacteriaceae. The blue module, which included H. pylori, was correlated negatively with intestinal metaplasia (γ = -0.49 [P < 0.001]). In conclusion, intragastric bacterial taxa associated with gastric carcinogenesis can be classified by network analysis. Microbial modules may provide an integrative view of the microbial ecology relevant to precancerous lesions in the stomach.},
}
@article {pmid31454177,
year = {2019},
author = {Goulart, MC and Cueva-Yesquén, LG and Hidalgo Martinez, KJ and Attili-Angelis, D and Fantinatti-Garboggini, F},
title = {Comparison of specific endophytic bacterial communities in different developmental stages of Passiflora incarnata using culture-dependent and culture-independent analysis.},
journal = {MicrobiologyOpen},
volume = {8},
number = {10},
pages = {e896},
pmid = {31454177},
issn = {2045-8827},
mesh = {Bacteria/*classification/genetics/growth &amp; development/isolation &amp; purification ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Endophytes/*classification/genetics/growth &amp; development/isolation &amp; purification ; *Microbiota ; Passiflora/*growth &amp; development/*microbiology ; Phylogeny ; Plant Development ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Plants and endophytic microorganisms have coevolved unique relationships over many generations. Plants show a specific physiological status in each developmental stage, which may determine the occurrence and dominance of specific endophytic populations with a predetermined ecological role. This study aimed to compare and determine the structure and composition of cultivable and uncultivable bacterial endophytic communities in vegetative and reproductive stages (RS) of Passiflora incarnata. To that end, the endophytic communities were assessed by plating and Illumina-based 16S rRNA gene amplicon sequencing. Two hundred and four cultivable bacterial strains were successfully isolated. From the plant's RS, the isolated strains were identified mainly as belonging to the genera Sphingomonas, Curtobacterium, and Methylobacterium, whereas Bacillus was the dominant genus isolated from the vegetative stage (VS). From a total of 133,399 sequences obtained from Illumina-based sequencing, a subset of 25,092 was classified in operational taxonomy units (OTUs). Four hundred and sixteen OTUs were obtained from the VS and 66 from the RS. In the VS, the most abundant families were Pseudoalteromonadaceae and Alicyclobacillaceae, while in the RS, Enterobacteriaceae and Bacillaceae were the most abundant families. The exclusive abundance of specific bacterial populations for each developmental stage suggests that plants may modulate bacterial endophytic community structure in response to different physiological statuses occurring at the different plant developmental stages.},
}
@article {pmid31451772,
year = {2019},
author = {Adam, PS and Borrel, G and Gribaldo, S},
title = {An archaeal origin of the Wood-Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy.},
journal = {Nature microbiology},
volume = {4},
number = {12},
pages = {2155-2163},
pmid = {31451772},
issn = {2058-5276},
mesh = {Archaea/*classification ; Bacteria/*classification/enzymology ; Carbon/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genome, Archaeal ; Genome, Bacterial ; Methane/*metabolism ; Phylogeny ; Pterins/*metabolism ; Wood/metabolism ; },
abstract = {The tetrahydromethanopterin (H4MPT) methyl branch of the Wood-Ljungdahl pathway is shared by archaeal and bacterial metabolisms that greatly contribute to the global carbon budget and greenhouse gas fluxes: methanogenesis and methylotrophy, including methanotrophy[1-3]. It has been proposed that the H4MPT branch dates back to the last universal common ancestor[4-6]. Interestingly, it has been identified in numerous recently sequenced and mostly uncultured non-methanogenic and non-methylotrophic archaeal and bacterial lineages, where its function remains unclear[5,7]. Here, we have examined the distribution and phylogeny of the enzymes involved in the H4MPT branch and the biosynthesis of its cofactors in over 6,400 archaeal and bacterial genomes. We find that a full Wood-Ljungdahl H4MPT pathway is widespread in Archaea and is likely ancestral to this domain, whereas this is not the case for Bacteria. Moreover, the inclusion of recently sequenced lineages leads to an important shortening of the branch separating Archaea and Bacteria with respect to previous phylogenies of the H4MPT branch. Finally, the genes for the pathway are colocalized in many of the recently sequenced archaeal lineages, similar to bacteria. Together, these results weaken the last universal common ancestor hypothesis and rather favour an origin of the H4MPT branch in Archaea and its subsequent transfer to Bacteria. We propose a scenario for its potential initial role in the first bacterial recipients and its evolution up to the emergence of aerobic methylotrophy. Finally, we discuss how an ancient horizontal transfer not only triggered the emergence of key metabolic processes but also important transitions in Earth's history.},
}
@article {pmid31451346,
year = {2019},
author = {Voulgari-Kokota, A and McFrederick, QS and Steffan-Dewenter, I and Keller, A},
title = {Drivers, Diversity, and Functions of the Solitary-Bee Microbiota.},
journal = {Trends in microbiology},
volume = {27},
number = {12},
pages = {1034-1044},
doi = {10.1016/j.tim.2019.07.011},
pmid = {31451346},
issn = {1878-4380},
mesh = {Animals ; Bees/*microbiology/*physiology ; *Biodiversity ; Environment ; Female ; Male ; *Microbiota ; *Social Behavior ; Social Isolation ; Symbiosis ; },
abstract = {Accumulating reports of global bee declines have drawn much attention to the bee microbiota and its importance. Most research has focused on social bees, while solitary species have received scant attention despite their enormous biodiversity, ecological importance, and agroeconomic value. We review insights from several recent studies on diversity, function, and drivers of the solitary-bee microbiota, and compare these factors with those relevant to the social-bee microbiota. Despite basic similarities, the social-bee model, with host-specific core microbiota and social transmission, is not representative of the vast majority of bee species. The solitary-bee microbiota exhibits greater variability and biodiversity, with a strong impact of environmental acquisition routes. Our synthesis identifies outstanding questions that will build understanding of these interactions, responses to environmental threats, and consequences for health.},
}
@article {pmid31450207,
year = {2020},
author = {He, Q and Song, J and Zhang, W and Gao, S and Wang, H and Yu, J},
title = {Enhanced simultaneous nitrification, denitrification and phosphorus removal through mixed carbon source by aerobic granular sludge.},
journal = {Journal of hazardous materials},
volume = {382},
number = {},
pages = {121043},
doi = {10.1016/j.jhazmat.2019.121043},
pmid = {31450207},
issn = {1873-3336},
mesh = {Acetates/*metabolism ; Aerobiosis ; Carbon/metabolism ; Denitrification ; Nitrification ; Phosphorus/*metabolism ; Sewage ; Succinic Acid/*metabolism ; Waste Disposal, Fluid/*methods ; Wastewater ; Water Pollutants, Chemical/*metabolism ; },
abstract = {Aerobic granular sludge-based simultaneous nitrification, denitrification and phosphorus removal (SNDPR) systems were configured for the treatment of low-strength municipal wastewater. Granular characteristics, process performance, and the corresponding microbial ecology dynamics were comprehensively explored with sodium acetate and succinate as mixed carbon source. Results revealed that aerobic granules kept structural and functional resilience, while mixed carbon source largely altered and balanced the growth and competition of phosphorus/glycogen accumulating organisms (PAOs/GAOs). Appropriate ratio of mixed carbon source was vital for superb physiochemical behaviors and reliable removal performance by aerobic granules. Therefore, the aerobic granular SNDPR system could achieve deep-level nutrients removal through enhancing the anaerobic carbon uptake rate and strengthening the carbon usage efficiency. The present work could add some guiding sight into the application of aerobic granular SNDPR system for wastewater treatment.},
}
@article {pmid31449563,
year = {2019},
author = {Kim, JG and Gwak, JH and Jung, MY and An, SU and Hyun, JH and Kang, S and Rhee, SK},
title = {Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0221408},
pmid = {31449563},
issn = {1932-6203},
mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biodiversity ; China ; *Environmental Monitoring ; Fresh Water/microbiology ; Humans ; Nitrogen/metabolism ; Oceans and Seas ; *Phylogeny ; Plankton/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Seawater/microbiology ; Tidal Waves ; },
abstract = {The Yellow Sea features unique characteristics due to strong tides and nutrient-enriched freshwater outflows from China and Korea. The coupling of archaeal and bacterial assemblages associated with environmental factors at two bay areas in the Yellow Sea was investigated. Temporal variations of the archaeal and bacterial assemblages were shown to be greater than the spatial variations based on an analysis of the 16S rRNA gene sequences. Distinct temporal dynamics of both planktonic archaeal and bacterial assemblages was associated with temperature, NO2-, and chlorophyll a ([chl-a]) concentrations in the bays of the Yellow Sea. The [chl-a] was the prime predictor of bacterial abundance, and some taxa were clearly correlated with [chl-a]. Bacteroidetes and Alpha-proteobacteria dominated at high [chl-a] stations while Gamma-proteobacteria (esp. SAR86 clade) and Actinobacteria (Candidatus Actinomarina clade) were abundant at low [chl-a] stations. The archaeal abundance was comparable with the bacterial abundance in most of the October samples. Co-dominance of Marine Group II (MGII) and Candidatus Nitrosopumilus suggests that the assimilation of organic nitrogen by MGII could be coupled with nitrification by ammonia-oxidizing archaea. The distinct temporal dynamics of the archaeal and bacterial assemblages might be attributable to the strong tides and the inflow of nutrient-rich freshwater.},
}
@article {pmid31448388,
year = {2020},
author = {Rojas, EC and Sapkota, R and Jensen, B and Jørgensen, HJL and Henriksson, T and Jørgensen, LN and Nicolaisen, M and Collinge, DB},
title = {Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {397-408},
pmid = {31448388},
issn = {1432-184X},
support = {674964//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; },
mesh = {Endophytes/*physiology ; Fusarium/*physiology ; Mycobiome/*physiology ; Plant Diseases/*microbiology ; Triticum/*microbiology ; },
abstract = {Fusarium head blight (FHB) is a devastating disease of wheat heads. It is caused by several species from the genus Fusarium. Several endophytic fungi also colonize wheat spikes asymptomatically. Pathogenic and commensal fungi share and compete for the same niche and thereby influence plant performance. Understanding the natural dynamics of the fungal community and how the pre-established species react to pathogen attack can provide useful information on the disease biology and the potential use of some of these endophytic organisms in disease control strategies. Fungal community composition was assessed during anthesis as well as during FHB attack in wheat spikes during 2016 and 2017 in two locations. Community metabarcoding revealed that endophyte communities are dominated by basidiomycete yeasts before anthesis and shift towards a more opportunistic ascomycete-rich community during kernel development. These dynamics are interrupted when Fusarium spp. colonize wheat spikes. The Fusarium pathogens appear to exclude other fungi from floral tissues as they are associated with a reduction in community diversity, especially in the kernel which they colonize rapidly. Similarly, the presence of several endophytes was negatively correlated with Fusarium spp. and linked with spikes that stayed healthy despite exposure to the pathogen. These endophytes belonged to the genera Cladosporium, Itersonillia and Holtermanniella. These findings support the hypothesis that some naturally occurring endophytes could outcompete or prevent FHB and represent a source of potential biological control agents in wheat.},
}
@article {pmid31448296,
year = {2019},
author = {Rothrock, MJ and Locatelli, A and Feye, KM and Caudill, AJ and Guard, J and Hiett, K and Ricke, SC},
title = {A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum.},
journal = {Frontiers in veterinary science},
volume = {6},
number = {},
pages = {260},
pmid = {31448296},
issn = {2297-1769},
abstract = {While conventionally grown poultry continues to dominate the U. S. poultry industry, there is an increasing demand for locally-grown, "all natural" alternatives. The use of next generation sequencing allows for not only the gross (e.g., community structure) but also fine-scale (e.g., taxa abundances) examination of these complex microbial communities. This data provides a better understanding of how a pasture flock's microbiome changes throughout the production life cycle and how that change in microbial ecology changes foodborne pathogens in alternative poultry production systems. In order to understand this ecology better, pooled broiler samples were taken during the entire flock life cycle, from pre-hatch gastrointestinal samples (N = 12) to fecal samples from the brood (N = 5), and pasture (N = 10) periods. Additional samples were taken during processing, including skin and feather rinsates (N = 12), ceca (N = 12), and whole carcass rinses (N = 12), and finally whole carcasss rinsates of final products (N = 3). Genomic DNA was extracted, 16S rDNA microbiome sequencing was conducted (Illumina MiSeq), and microbiomes were analyzed and compared using QIIME 1.9.1 to determine how microbiomes shifted throughout production continuum, as well as what environmental factors may be influencing these shifts. Significant microbiome shifts occurred during the life cycle of the pasture broiler flock, with the brood and pasture fecal samples and cecal samples being very distinct from the other pre-hatch, processing, and final product samples. Throughout these varied microbiomes, there was a stable core microbiome containing 13 taxa. Within this core microbiome, five taxa represented known foodborne pathogens (Salmonella, Campylobacter) or potential/emerging pathogens (Pseudomonas, Enterococcus, Acinetobacter) whose relative abundances varied throughout the farm-to-fork continuum, although all were more prevalent in the fecal samples. Additionally, of the 25 physiochemical and nutrient variables measured from the fecal samples, the carbon to nitrogen ratio was one of the most significant variables to warrant further investigations because it impacted both general fecal microbial ecology and Campylobacter and Enterococcus taxa within the core fecal microbiomes. These findings demonstrate the need for further longitudinal, farm-to-fork studies to understand the ecology of the microbial ecology of pasture production flocks to improve animal, environmental, and public health.},
}
@article {pmid31446647,
year = {2019},
author = {Lemos, LN and Medeiros, JD and Dini-Andreote, F and Fernandes, GR and Varani, AM and Oliveira, G and Pylro, VS},
title = {Genomic signatures and co-occurrence patterns of the ultra-small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle.},
journal = {Molecular ecology},
volume = {28},
number = {18},
pages = {4259-4271},
doi = {10.1111/mec.15208},
pmid = {31446647},
issn = {1365-294X},
support = {BB/P027849/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Bacteria/*genetics ; Base Sequence ; Gene Regulatory Networks ; *Genome, Bacterial ; *Genomics ; Metabolic Networks and Pathways/genetics ; Metagenome ; Microbiota/genetics ; Mining ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; },
abstract = {The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential for co-metabolism interdependencies. As yet, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from acid mine drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotides, fatty acids and cofactors. In addition, co-occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives.},
}
@article {pmid31446448,
year = {2020},
author = {Wise, BR and Roane, TM and Mosier, AC},
title = {Community Composition of Nitrite Reductase Gene Sequences in an Acid Mine Drainage Environment.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {562-575},
pmid = {31446448},
issn = {1432-184X},
mesh = {Bacteria/classification/*enzymology/genetics ; Colorado ; Denitrification ; *Genes, Bacterial ; Geologic Sediments/*microbiology ; Hydrogen-Ion Concentration ; Microbiota ; *Mining ; Nitrite Reductases/*analysis ; },
abstract = {Denitrifying microbial communities play a central role in the nitrogen cycle, contribute to greenhouse gas production, and provide ecosystem services through the mitigation of nitrogen pollution. The impacts of human-induced acid mine drainage (AMD) and naturally occurring acid rock drainage (ARD), both characterized by low pH and high metal concentrations, on denitrifying microbial communities is not well understood. This study examined denitrifying microbes within sediments impacted by acidic and metal-rich AMD or ARD in the Iron Springs Mining District (10 sites across four regions over four time points) located in Southwest Colorado, USA. Denitrification functional gene sequences (nirS and nirK coding for nitrite reductase) had a high number of observed OTUs (260 for nirS and 253 for nirK) and were observed at sites with pH as low as 3.5 and metals > 2 mg/L (including aluminum, iron, manganese, strontium, and zinc). A majority of the nirK and nirS OTUs (> 60%) were present in only one sampling region. Approximately 8% of the nirK and nirS OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The overall community structure for nirK and nirS genes was correlated to conductivity and calcium (respectively), which may suggest that conductivity may play an important role in shaping the distribution of nirK- and nirS-type denitrifiers. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD or ARD and provide a foundation for future research to understand the rates and physiology of denitrifying organisms in these systems.},
}
@article {pmid31444524,
year = {2020},
author = {Zhang, G and Bai, J and Zhao, Q and Jia, J and Wang, W and Wang, X},
title = {Bacterial Succession in Salt Marsh Soils Along a Short-term Invasion Chronosequence of Spartina alterniflora in the Yellow River Estuary, China.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {644-661},
pmid = {31444524},
issn = {1432-184X},
support = {2017YFC0505906//National Key R &amp; D Program of China/ ; 310430001//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Bacterial Physiological Phenomena ; China ; Estuaries ; Introduced Species ; *Microbiota ; Poaceae/*growth &amp; development ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; },
abstract = {As an exotic plant species, Spartina alterniflora seriously threatens native ecosystem function in Chinese coastal regions. Unveiling the dynamics of soil bacteria community during its invasion is essential for a better understanding of related biogeochemical processes, while the shift in soil bacterial community over invasive time remains unclear. A short-term chronosequence was identified to assess the impacts of Spartina alterniflora invasion on soil nutrients and bacterial community composition and structure (using 16S rRNA gene high-throughput sequencing) over the time of invasion (i.e., (1) at least 10 years, (2) nearly 5 years, (3) less than 2 years, and (4) in native salt marshes or 0 years) in the Yellow River Estuary. The results exhibited an orderly change in the soil physicochemical properties and bacterial community composition over the invasion time. Soil pH showed a significant decrease with the accumulation of soil organic matter (SOM), whereas soil nutrients such as soil dissolved organic carbon (DOC), total nitrogen (TN), nitrate (NO3[-]), ammonium (NH4[+]), K[+], and Mg[2+] were generally increased with the age of the invasion. The number of operational taxonomic units (OTUs, 97% similarity level) exhibited a decreasing trend, which suggested a decline in bacterial diversity with the invasion age. The dominant groups at the phylum level were Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Gemmatimonadetes (the sum of relative abundance was > 70% across all samples). The relative abundances of Chloroflexi and Gemmatimonadetes steadily decreased, while the abundance of Bacteroidetes significantly increased with the plant invasion. The distribution pattern of the soil bacteria was clearly separated according to the principal coordinate analysis (PCoA) and canonical correspondence analysis (CCA) in native and invaded salt marshes. The variation in the soil bacterial community was tightly associated with the soil physicochemical properties (Mantel test, P < 0.05). Variance partitioning analysis (VPA) showed that plant traits explained 4.95% of the bacterial community variation, and soil variables explained approximately 26.96% of the variation. Network analysis also revealed that plant invasion strengthens the interaction among soil bacterial communities. Overall, our findings highlight the bacterial community succession during the Spartina alterniflora invasion in coastal salt marsh soils, which can provide insight regarding the association between soil development and invasive plant.},
}
@article {pmid31444200,
year = {2019},
author = {Campa, MF and Techtmann, SM and Ladd, MP and Yan, J and Patterson, M and Garcia de Matos Amaral, A and Carter, KE and Ulrich, N and Grant, CJ and Hettich, RL and Lamendella, R and Hazen, TC},
title = {Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {21},
pages = {},
pmid = {31444200},
issn = {1098-5336},
mesh = {Disinfectants/*pharmacology ; Ecology ; Hydraulic Fracking/methods ; Microbiota/*drug effects/genetics ; Nitriles/*pharmacology ; RNA, Ribosomal, 16S/genetics ; Rivers ; Wastewater/analysis ; Water Microbiology ; Water Pollutants, Chemical/analysis ; Water Purification ; },
abstract = {Production of unconventional oil and gas continues to rise, but the effects of high-density hydraulic fracturing (HF) activity near aquatic ecosystems are not fully understood. A commonly used biocide in HF, 2,2-dibromo-3-nitrilopropionamide (DBNPA), was studied in microcosms of HF-impacted (HF+) versus HF-unimpacted (HF-) surface water streams to (i) compare the microbial community response, (ii) investigate DBNPA degradation products based on past HF exposure, and (iii) compare the microbial community response differences and similarities between the HF biocides DBNPA and glutaraldehyde. The microbial community responded to DBNPA differently in HF-impacted versus HF-unimpacted microcosms in terms of the number of 16S rRNA gene copies quantified, alpha and beta diversity, and differential abundance analyses of microbial community composition through time. The differences in microbial community changes affected degradation dynamics. HF-impacted microbial communities were more sensitive to DBNPA, causing the biocide and by-products of the degradation to persist for longer than in HF-unimpacted microcosms. A total of 17 DBNPA by-products were detected, many of them not widely known as DBNPA by-products. Many of the brominated by-products detected that are believed to be uncharacterized may pose environmental and health impacts. Similar taxa were able to tolerate glutaraldehyde and DBNPA; however, DBNPA was not as effective for microbial control, as indicated by a smaller overall decrease of 16S rRNA gene copies/ml after exposure to the biocide, and a more diverse set of taxa was able to tolerate it. These findings suggest that past HF activity in streams can affect the microbial community response to environmental perturbation such as that caused by the biocide DBNPA.IMPORTANCE Unconventional oil and gas activity can affect pH, total organic carbon, and microbial communities in surface water, altering their ability to respond to new environmental and/or anthropogenic perturbations. These findings demonstrate that 2,2-dibromo-3-nitrilopropionamide (DBNPA), a common hydraulic fracturing (HF) biocide, affects microbial communities differently as a consequence of past HF exposure, persisting longer in HF-impacted (HF+) waters. These findings also demonstrate that DBNPA has low efficacy in environmental microbial communities regardless of HF impact. These findings are of interest, as understanding microbial responses is key for formulating remediation strategies in unconventional oil and gas (UOG)-impacted environments. Moreover, some DBNPA degradation by-products are even more toxic and recalcitrant than DBNPA itself, and this work identifies novel brominated degradation by-products formed.},
}
@article {pmid31443509,
year = {2019},
author = {Hernández-Arriaga, A and Baumann, A and Witte, OW and Frahm, C and Bergheim, I and Camarinha-Silva, A},
title = {Changes in Oral Microbial Ecology of C57BL/6 Mice at Different Ages Associated with Sampling Methodology.},
journal = {Microorganisms},
volume = {7},
number = {9},
pages = {},
pmid = {31443509},
issn = {2076-2607},
support = {CA 1708/1-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {The mouth is an important niche for bacterial colonization. Previous research used mouth microbiota to predict diseases like colon cancer and inflammatory bowel disease (IBD). It is still unclear how the sampling methodology influences microbial characterization. Our aim was to determine if the sampling methods, e.g., cotton swab or tissue biopsy, and the age influence the oral microbial composition of mice. Microbial DNA was extracted using a commercial kit and characterized targeting the 16s rRNA gene from mouth swabs and tissue biopsies from 2 and 15 months old C57BL/6 male mice kept in the same SPF facility. Our results show statistical different microbial community of the different ages, type of sampling, and the two fixed factors age x type of sample (p-value <0.05). At the genus level, we identified that the genera Actinobacillus, Neisseria, Staphylococcus, and Streptococcus either increase or decrease in abundance depending on sampling and age. Additionally, the abundance of Streptococcus danieliae, Moraxella osloensis, and some unclassified Streptococcus was affected by the sampling method. While swab and tissue biopsies both identified the common colonizers of oral microbiota, cotton swabbing is a low-cost and practical method, validating the use of the swab as the preferred oral sampling approach.},
}
@article {pmid31441243,
year = {2019},
author = {Smessaert, J and Van Geel, M and Verreth, C and Crauwels, S and Honnay, O and Keulemans, W and Lievens, B},
title = {Temporal and spatial variation in bacterial communities of "Jonagold" apple (Malus x domestica Borkh.) and "Conference" pear (Pyrus communis L.) floral nectar.},
journal = {MicrobiologyOpen},
volume = {8},
number = {12},
pages = {e918},
pmid = {31441243},
issn = {2045-8827},
mesh = {*Bacteria/classification/genetics ; Biodiversity ; DNA Barcoding, Taxonomic ; Fruit/microbiology ; Malus/*microbiology ; *Microbiota ; *Plant Nectar ; Pyrus/*microbiology ; },
abstract = {Production of many agricultural crops and fruits strongly depends on pollinators. For instance, pome fruits such as apple and pear are highly dependent on pollination for fruit set, fruit quality, and yield. Nectar is often inhabited by microbes, most often yeasts and bacteria, which may change nectar quality and therefore also affect plant-pollinator interactions. Here, we used high-throughput 16S ribosomal RNA gene amplicon sequencing to investigate the temporal and spatial variation in bacterial communities in floral nectar of apple and pear. We sampled 15 apple (Malus x domestica Borkh.) and 15 pear (Pyrus communis L.) orchards distributed over the eastern part of Belgium over a timespan of seven days. Nectar bacterial community composition differed strongly among fruit species. Nectar of pear was dominated by Actinobacteria, followed by Proteobacteria and Firmicutes. Apple nectar was strongly enriched in Bacteroidetes, a phylum which until now has been found to be rarely associated with floral nectar. Nectar was dominated by only a few bacterial species, with Brevibacterium (Actinobacteria) and Undibacterium (Proteobacteria) as the most abundant bacteria in pear and apple nectar, respectively. Bacterial richness and diversity were found to fluctuate during flowering, likely due to changing environmental conditions. Additionally, spatial structure in nectar bacterial community composition was found in apple orchards, while this was not the case for pear. Differences in nectar bacterial communities between apple and pear nectar may differently affect the chemical and nutritional composition of the nectar, influencing pollinator attraction and visitation, and thus pollination efficacy in general.},
}
@article {pmid31438955,
year = {2019},
author = {Vavourakis, CD and Mehrshad, M and Balkema, C and van Hall, R and Andrei, A&#x15e; and Ghai, R and Sorokin, DY and Muyzer, G},
title = {Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake.},
journal = {BMC biology},
volume = {17},
number = {1},
pages = {69},
pmid = {31438955},
issn = {1741-7007},
support = {322551/ERC_/European Research Council/International ; },
mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria/*classification/genetics/*metabolism ; Hydrogen-Ion Concentration ; Lakes/chemistry/*microbiology ; Metagenome ; Oxidation-Reduction ; Phylogeny ; Salinity ; Salts/chemistry ; Siberia ; Sulfur/analysis/*metabolism ; },
abstract = {BACKGROUND: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions.<br><br>RESULTS: Peak microbial activity was found in the top 4&#x2009;cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes.<br><br>CONCLUSIONS: The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.},
}
@article {pmid31435691,
year = {2020},
author = {Damjanovic, K and Menéndez, P and Blackall, LL and van Oppen, MJH},
title = {Early Life Stages of a Common Broadcast Spawning Coral Associate with Specific Bacterial Communities Despite Lack of Internalized Bacteria.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {706-719},
pmid = {31435691},
issn = {1432-184X},
support = {DP160101468//Australian Research Council/ ; Holsworth Wildlife Endowment//Ecological Society of Australia/ ; },
mesh = {Animals ; Anthozoa/growth &amp; development/*microbiology ; *Bacterial Physiological Phenomena ; Embryo, Nonmammalian/microbiology ; In Situ Hybridization, Fluorescence ; Larva/microbiology ; *Life Cycle Stages ; Male ; Microbiota/*physiology ; Ovum/microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Reproduction ; Spermatozoa/microbiology ; },
abstract = {Coral-associated bacteria are critical for the well-being of their host and may play essential roles during ontogeny, as suggested by the vertical transmission of some bacteria in brooding corals. Bacterial acquisition patterns in broadcast spawners remain uncertain, as 16S rRNA gene metabarcoding of coral early life stages suggests the presence of bacterial communities, which have not been detected by microscopic examinations. Here, we combined 16S rRNA gene metabarcoding with fluorescence in situ hybridization (FISH) microscopy to analyze bacterial assemblages in Acropora tenuis egg-sperm bundles, embryos, and larvae following a spawning event. Metabarcoding results indicated that A. tenuis offspring ≤ 4-day-old were associated with diverse and dynamic bacterial microbiomes, dominated by Rhodobacteraceae, Alteromonadaceae, and Oceanospirillaceae. While FISH analyses confirmed the lack of internalized bacteria in A. tenuis offspring, metabarcoding showed that even the earliest life stages examined (egg-sperm bundles and two-cell stages) were associated with a diverse bacterial community, suggesting the bacteria were confined to the mucus layer. These results can be explained by vertical transmission of certain taxa (mainly Endozoicomonas) in the mucus surrounding the gametes within bundles, or by horizontal bacterial transmission through the release of bacteria by spawning adults into the water column.},
}
@article {pmid31435492,
year = {2019},
author = {Onywera, H and Williamson, AL and Mbulawa, ZZA and Coetzee, D and Meiring, TL},
title = {Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7488},
pmid = {31435492},
issn = {2167-8359},
abstract = {BACKGROUND: Lactobacillus spp. are common bacteria in the cervical and vaginal microbiota (CVM) and are thought to represent a "healthy" cervicovaginal state. Several studies have found an independent association between ethnicity/race and cervical and vaginal microbiota (CVM) composition. Women of sub-Saharan African descent appear to be significantly more likely to have non-Lactobacillus-dominated CVM compared to women of European descent. The factors contributing to these differences remain to be fully elucidated. The CVM of Black South African women and factors influencing their CVM remain understudied. In this study, we characterized the cervical microbiota of reproductive-age South African women and assessed the associations of these microbiota with participants' metadata.<br><br>METHODS: The cervical microbiota from cervical DNA of 62 reproductive-age women were profiled by Ion Torrent sequencing the V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) gene and analyzed with the Quantitative Insights Into Microbial Ecology (QIIME), UPARSE, and metagenomeSeq tools. Associations between cervical microbiota and participants' metadata were assessed using GraphPad Prism, R packages and an in-house script.<br><br>RESULTS: The cervical microbiota clustered into three distinct community state types (CSTs): Lactobacillus iners-dominated cervical microbiota (CST I (38.7%, 24/62)), unclassified Lactobacillus-dominated cervical microbiota (CST II (4.8%, 3/62)), and diverse cervical microbiota (CST III (56.5%, 35/62)) with an array of heterogeneous bacteria, predominantly the bacterial vaginosis (BV)-associated Gardnerella, Prevotella, Sneathia, and Shuttleworthia. CST III was associated with BV (p&#xa0;=&#xa0;0.001). Women in CST I were more likely to be on hormonal contraception, especially progestin-based, compared to women in CST III (odds ratio: 5.2 (95% CI [1.6-17.2]); p&#xa0;=&#xa0;0.005). Women on hormonal contraception had a significantly lower alpha (Shannon indices: 0.9 (0.2-1.9) versus 2.3 (0.6-2.3); p&#xa0;=&#xa0;0.025) and beta (permutational multivariate analysis of variance (PERMANOVA) pseudo-F statistic&#xa0;=4.31, p&#xa0;=&#xa0;0.019) diversity compared to non-users. There was no significant difference in the alpha (Shannon indices: 1.0 (0.3-2.2) versus 1.9 (0.3-2.2); p&#xa0;=&#xa0;0.483) and beta (PERMANOVA pseudo-F statistic = 0.89, p&#xa0;=&#xa0;0.373) diversity in women with versus without human papillomavirus infection.<br><br>CONCLUSIONS: The majority of Black women in our study had non-Lactobacillus-dominated cervical microbiota. Additional studies are needed to examine whether such microbiota represent abnormal, intermediate or variant states of health. Lastly, the association of hormonal contraception with L. iners dominance requires further in-depth research to confirm this association, determine its biological mechanism and whether it has a beneficial effect on the cervicovaginal health.},
}
@article {pmid31434790,
year = {2019},
author = {Weiner, BG and Posfai, A and Wingreen, NS},
title = {Spatial ecology of territorial populations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {36},
pages = {17874-17879},
pmid = {31434790},
issn = {1091-6490},
support = {R01 GM082938/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biodiversity ; *Ecology ; *Ecosystem ; Models, Theoretical ; Population Dynamics ; },
abstract = {Many ecosystems, from vegetation to biofilms, are composed of territorial populations that compete for both nutrients and physical space. What are the implications of such spatial organization for biodiversity? To address this question, we developed and analyzed a model of territorial resource competition. In the model, all species obey trade-offs inspired by biophysical constraints on metabolism; the species occupy nonoverlapping territories, while nutrients diffuse in space. We find that the nutrient diffusion time is an important control parameter for both biodiversity and the timescale of population dynamics. Interestingly, fast nutrient diffusion allows the populations of some species to fluctuate to zero, leading to extinctions. Moreover, territorial competition spontaneously gives rise to both multistability and the Allee effect (in which a minimum population is required for survival), so that small perturbations can have major ecological effects. While the assumption of trade-offs allows for the coexistence of more species than the number of nutrients-thus violating the principle of competitive exclusion-overall biodiversity is curbed by the domination of "oligotroph" species. Importantly, in contrast to well-mixed models, spatial structure renders diversity robust to inequalities in metabolic trade-offs. Our results suggest that territorial ecosystems can display high biodiversity and rich dynamics simply due to competition for resources in a spatial community.},
}
@article {pmid31432245,
year = {2020},
author = {Sun, Y and Liu, Y and Pan, J and Wang, F and Li, M},
title = {Perspectives on Cultivation Strategies of Archaea.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {770-784},
pmid = {31432245},
issn = {1432-184X},
support = {31622002//NSFC/ ; 91851105//NSFC/ ; },
mesh = {Archaea/*growth &amp; development ; Bacteriological Techniques/instrumentation/*methods ; },
abstract = {Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.},
}
@article {pmid31432244,
year = {2020},
author = {Nasser, NA and Gregory, BRB and Steele, RE and Patterson, RT and Galloway, JM},
title = {Behind the Organic Veil: Assessing the Impact of Chemical Deflocculation on Organic Content Reduction and Lacustrine Arcellinida (Testate Amoebae) Analysis.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {443-458},
pmid = {31432244},
issn = {1432-184X},
mesh = {*Flocculation ; Geologic Sediments/*parasitology ; Lakes/parasitology ; Lobosea/*isolation &amp; purification ; Microbiological Techniques/*instrumentation ; Northwest Territories ; Parasitology/methods ; },
abstract = {Arcellinida (testate lobose amoebae) are widely used as bio-indicators of lacustrine environmental change. Too much obscuring organic material in a gridded wet Petri dish preparation makes it difficult to observe all specimens present and slows quantification as the organic material has to be carefully worked through with a dissection probe. Chemical deflocculation using soda ash (Na2CO3·H2O), potassium hydroxide (KOH), or sodium hexametaphosphate ((NaPO3)6) has previously been shown to disaggregate and reduce organic content in lake sediments, but to date, no attempt has been made to comparatively evaluate the efficiency of these deflocculants in disaggregating organic content and their impact on Arcellinida analysis in lacustrine sediments. Here, we assess the effectiveness of soda ash, potassium hydroxide, and sodium hexametaphosphate treatments on removing organic content and the impact of those digestions on Arcellinida preservation in 126 sample aliquots subdivided from three sediment samples (YK-20, YK-25, and YK-57) collected from three lakes near Yellowknife, Northwest Territories, Canada. Following treatment, cluster analysis and Bray-Curtis dissimilarity matrix (BCDM) were utilized to determine whether treatments resulted in dissolution-driven changes in Arcellinida assemblage composition. Observed Arcellinida tests in aliquots increased drastically after treatment of organic-rich samples (47.5-452.7% in organic-rich aliquots and by 14.8% in aliquots with less organic matter). The BCDM results revealed that treatment with 5% KOH resulted in the highest reduction in observed organic content without significantly affecting Arcellinida assemblage structure, while soda ash and sodium hexametaphosphate treatments resulted in marginal organic matter reduction and caused severe damage to the arcellinidan tests.},
}
@article {pmid31431510,
year = {2019},
author = {Taroni, JN},
title = {Making Workshops Work: Insights from EDAMAME.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
pmid = {31431510},
issn = {2379-5077},
abstract = {Microbiology, like many areas of life science research, is increasingly data-intensive. As such, bioinformatics and data science skills have become essential to leverage microbiome sequencing data for discovery. Short intensive courses have sprung up as formal computational training opportunities at individual institutions fail to meet demands. In this issue, Shade et al. (A. Shade, T. K. Dunivin, J. Choi, T. K. Teal, et al., mSystems 4:e00297-19, 2019, https://doi.org/10.1128/mSystems.00297-19) share their experience and approach in executing the annual, weeklong Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop from 2014 to 2018. EDAMAME introduced learners to general scientific computing concepts and domain-specific data analysis approaches. Workshop learners self-reported appreciable gains in understanding and ability. This report on the EDAMAME workshop strategy and lessons learned will help others in the life sciences to plan, execute, and assess short hands-on computing-intensive courses that support research in a particular domain.},
}
@article {pmid31431509,
year = {2019},
author = {Shade, A and Dunivin, TK and Choi, J and Teal, TK and Howe, AC},
title = {Strategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME Workshop.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
pmid = {31431509},
issn = {2379-5077},
support = {R25 GM115335/GM/NIGMS NIH HHS/United States ; },
abstract = {Here, we report our educational approach and learner evaluations of the first 5 years of the Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop, held annually at Michigan State University's Kellogg Biological Station from 2014 to 2018. We hope this information will be useful for others who want to organize computing-intensive workshops and will encourage quantitative skill development among microbiologists.IMPORTANCE High-throughput sequencing and related statistical and bioinformatic analyses have become routine in microbiology in the past decade, but there are few formal training opportunities to develop these skills. A weeklong workshop can offer sufficient time for novices to become introduced to best computing practices and common workflows in sequence analysis. We report our experiences in executing such a workshop targeted to professional learners (graduate students, postdoctoral scientists, faculty, and research staff).},
}
@article {pmid31431508,
year = {2019},
author = {Sun, Z and Huang, S and Zhu, P and Yue, F and Zhao, H and Yang, M and Niu, Y and Jing, G and Su, X and Li, H and Callewaert, C and Knight, R and Liu, J and Smith, E and Wei, K and Xu, J},
title = {A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
pmid = {31431508},
issn = {2379-5077},
abstract = {A quantitative and objective indicator for skin health via the microbiome is of great interest for personalized skin care, but differences among skin sites and across human populations can make this goal challenging. A three-city (two Chinese and one American) comparison of skin microbiota from atopic dermatitis (AD) and healthy pediatric cohorts revealed that, although city has the greatest effect size (the skin microbiome can predict the originated city with near 100% accuracy), a microbial index of skin health (MiSH) based on 25 bacterial genera can diagnose AD with 83 to ∼95% accuracy within each city and 86.4% accuracy across cities (area under the concentration-time curve [AUC], 0.90). Moreover, nonlesional skin sites across the bodies of AD-active children (which include shank, arm, popliteal fossa, elbow, antecubital fossa, knee, neck, and axilla) harbor a distinct but lesional state-like microbiome that features relative enrichment of Staphylococcus aureus over healthy individuals, confirming the extension of microbiome dysbiosis across body surface in AD patients. Intriguingly, pretreatment MiSH classifies children with identical AD clinical symptoms into two host types with distinct microbial diversity and treatment effects of corticosteroid therapy. These findings suggest that MiSH has the potential to diagnose AD, assess risk-prone state of skin, and predict treatment response in children across human populations.IMPORTANCE MiSH, which is based on the skin microbiome, can quantitatively assess pediatric skin health across cohorts from distinct countries over large geographic distances. Moreover, the index can identify a risk-prone skin state and compare treatment effect in children, suggesting applications in diagnosis and patient stratification.},
}
@article {pmid31428833,
year = {2020},
author = {Tang, Y and Dai, T and Su, Z and Hasegawa, K and Tian, J and Chen, L and Wen, D},
title = {A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {342-356},
pmid = {31428833},
issn = {1432-184X},
support = {51678003//National Natural Science Foundation of China/ ; 51678334//National Natural Science Foundation of China/ ; },
mesh = {Archaea/*physiology ; *Bacterial Physiological Phenomena ; Bays/*microbiology ; China ; Geologic Sediments/*microbiology ; *Microbial Consortia ; Microbiological Techniques/*methods ; },
abstract = {Current technologies could identify the abundance and functions of specific microbes, and evaluate their individual effects on microbial ecology. However, these microbes interact with each other, as well as environmental factors, in the form of complex network. Determination of their combined ecological influences remains a challenge. In this study, we developed a tripartite microbial-environment network (TMEN) analysis method that integrates microbial abundance, metabolic function, and environmental data as a tripartite network to investigate the combined ecological effects of microbes. Applying TMEN to analyzing the microbial-environment community structure in the sediments of Hangzhou Bay, one of the most seriously polluted coastal areas in China, we found that microbes were well-organized into 4 bacterial communities and 9 archaeal communities. The total organic carbon, sulfate, chemical oxygen demand, salinity, and nitrogen-related indexes were detected as crucial environmental factors in the microbial-environmental network. With close interactions with these environmental factors, Nitrospirales and Methanimicrococcu were identified as hub microbes with connection advantage. Our TMEN method could close the gap between lack of efficient statistical and computational approaches and the booming of large-scale microbial genomic and environmental data. Based on TMEN, we discovered a potential microbial ecological mechanism that crucial species with significant influence on the microbial community ecology would possess one or two of the community advantages for enhancing their ecological status and essentiality, including abundance advantage and connection advantage.},
}
@article {pmid31420342,
year = {2019},
author = {In 't Zandt, MH and Kip, N and Frank, J and Jansen, S and van Veen, JA and Jetten, MSM and Welte, CU},
title = {High-Level Abundances of Methanobacteriales and Syntrophobacterales May Help To Prevent Corrosion of Metal Sheet Piles.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {20},
pages = {},
pmid = {31420342},
issn = {1098-5336},
mesh = {Corrosion ; Deltaproteobacteria/*metabolism ; Iron/*metabolism ; Methanobacteriales/*metabolism ; Netherlands ; },
abstract = {Iron sheet piles are widely used in flood protection, dike construction, and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their life span. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbially diverse populations of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbially diverse populations, and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four nearly complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales, and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial food web degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron, which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.IMPORTANCE Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has significant economic impact. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from noncorroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.},
}
@article {pmid31420340,
year = {2019},
author = {Bale, NJ and Palatinszky, M and Rijpstra, WIC and Herbold, CW and Wagner, M and Sinninghe Damsté, JS},
title = {Membrane Lipid Composition of the Moderately Thermophilic Ammonia-Oxidizing Archaeon "Candidatus Nitrosotenuis uzonensis" at Different Growth Temperatures.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {20},
pages = {},
pmid = {31420340},
issn = {1098-5336},
mesh = {Ammonia/metabolism ; Archaea/*chemistry/growth &amp; development ; Cell Membrane/*chemistry ; Glyceryl Ethers/analysis ; Membrane Lipids/*analysis ; Oxidation-Reduction ; *Temperature ; },
abstract = {"Candidatus Nitrosotenuis uzonensis" is the only cultured moderately thermophilic member of the thaumarchaeotal order Nitrosopumilales (NP) that contains many mesophilic marine strains. We examined its membrane lipid composition at different growth temperatures (37°C, 46°C, and 50°C). Its lipids were all membrane-spanning glycerol dialkyl glycerol tetraethers (GDGTs), with 0 to 4 cyclopentane moieties. Crenarchaeol (cren), the characteristic thaumarchaeotal GDGT, and its isomer (cren') were present in high abundance (30 to 70%). The GDGT polar headgroups were mono-, di-, and trihexoses and hexose/phosphohexose. The ratio of glycolipid to phospholipid GDGTs was highest in the cultures grown at 50°C. With increasing growth temperatures, the relative contributions of cren and cren' increased, while those of GDGT-0 to GDGT-4 (including isomers) decreased. TEX86 (tetraether index of tetraethers consisting of 86 carbons)-derived temperatures were much lower than the actual growth temperatures, further demonstrating that TEX86 does not accurately reflect the membrane lipid adaptation of thermophilic Thaumarchaeota As the temperature increased, specific GDGTs changed relative to their isomers, possibly representing temperature adaption-induced changes in cyclopentane ring stereochemistry. Comparison of a wide range of thaumarchaeotal core lipid compositions revealed that the "Ca Nitrosotenuis uzonensis" cultures clustered separately from other members of the NP order and the Nitrososphaerales (NS) order. While phylogeny generally seems to have a strong influence on GDGT distribution, our analysis of "Ca Nitrosotenuis uzonensis" demonstrates that its terrestrial, higher-temperature niche has led to a lipid composition that clearly differentiates it from other NP members and that this difference is mostly driven by its high cren' content.IMPORTANCE For Thaumarchaeota, the ratio of their glycerol dialkyl glycerol tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is essential for constraining the TEX86 proxy. "Ca Nitrosotenuis uzonensis" is a moderately thermophilic thaumarchaeote enriched from a thermal spring, setting it apart in its environmental niche from the other marine mesophilic members of its order. Indeed, we found that the GDGT composition of "Ca Nitrosotenuis uzonensis" cultures was distinct from those of other members of its order and was more similar to those of other thermophilic, terrestrial Thaumarchaeota This suggests that while phylogeny has a strong influence on GDGT distribution, the environmental niche that a thaumarchaeote inhabits also shapes its GDGT composition.},
}
@article {pmid31418250,
year = {2019},
author = {Jiang, Y and Xu, ZW and Wang, RZ and Li, H and Zhang, YG},
title = {[Effects of long-term fertilization and water addition on soil properties and plant community characteristics in a semiarid grassland.].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {30},
number = {7},
pages = {2470-2480},
doi = {10.13287/j.1001-9332.201907.034},
pmid = {31418250},
issn = {1001-9332},
mesh = {*Agriculture ; China ; Ecosystem ; *Fertilizers ; *Grassland ; Nitrogen ; Plants ; *Soil ; Water ; },
abstract = {We summarized the effects of fertilization and water addition on some soil properties and plant community characteristics in a long-term field experiment established in 2005 in a degraded grassland in Duolun, Inner Mongolia, China. The results showed that nitrogen (N) addition resulted in surface soil acidification and decreased acid buffering capacity, increased the availability of carbon (C), N, phosphorus (P), sulfur (S) and DTPA-extractable iron (Fe), manganese (Mn), and copper (Cu) contents, depleted the sum of base cations calcium (Ca), magnesium (Mg), potassium (K) and sodium (Na), decreased the diversity of soil microbial community. Nitrogen addition enhanced the uptake of N, P, S, K, Mn, Cu and Zn by plants, while inhibited plant Fe uptake, but with no effect on the uptake of Ca or Mg. Nitrogen addition increased aboveground net primary productivity (ANPP) but declined plant species diversity and community stability. Phosphorus addition alone increased total P and Olsen-P contents and fungal abundance in the surface soil, and improved N, P and S uptake by leaves, but had no significant influence on other soil basic chemical properties, ANPP, and plant species diversity. Water addition could improve the resistance of plant community, but its contribution to ANPP was limited by soil N availa-bility. Water addition could buffer soil acidification and the decline of microbial and plant diversity induced by N addition. Under the treatments of N and water addition or P and water addition, the diversity and function of soil microorganisms were affected by plant community structure and function. Long-term controlled field experiments were useful for understanding ecosystem structure and functions of grasslands. However, to uncover the underlying mechanisms in grassland ecosystem ecology, single-site experiments should be incorporated with multiple-site controlled field experiments in different regions. More attentions should be paid to the linkage of above- and below-ground ecological processes.},
}
@article {pmid31415965,
year = {2019},
author = {Deng, Y and Ruan, Y and Ma, B and Timmons, MB and Lu, H and Xu, X and Zhao, H and Yin, X},
title = {Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations.},
journal = {Environment international},
volume = {132},
number = {},
pages = {105085},
doi = {10.1016/j.envint.2019.105085},
pmid = {31415965},
issn = {1873-6750},
mesh = {Bacteria/*metabolism ; *Biofilms ; *Bioreactors ; Carbon ; *Denitrification ; Salinity ; Wastewater/*chemistry/microbiology ; *Water Purification ; },
abstract = {Suspended floc and fixed biofilm are two commonly applied strategies for heterotrophic denitrification in wastewater treatment. These two strategies use different carbon sources and reside within different ecological niches for microbial aggregation, which were hypothesized to show distinct microbial structures and metabolic fitness. We surveyed three floc reactors and three biofilm reactors for denitrification and determined if there were distinct microbial aggregations. Multiple molecular omics approaches were used to determine the microbial community composition, co-occurrence network and metabolic pathways. Proteobacteria was the dominating and most active phylum among all samples. Carbon source played an important role in shaping the microbial community composition while the distribution of functional protein was largely influenced by salinity. We found that the topological network features had different ecological patterns and that the microorganisms in the biofilm reactors had more nodes but less interactions than those in floc reactors. The large niche differences in the biofilm reactors explained the observed high microbial diversity, functional redundancy and resulting high system stability. We also observed a lower proportion of denitrifiers and higher resistance to oxygen and salinity perturbation in the biofilm reactors than the floc reactors. Our findings support our hypothesis that niche differences caused a distinct microbial structure and increased microbial ecology distribution, which has the potential to improve system efficiency and stability.},
}
@article {pmid31412927,
year = {2019},
author = {Pérez-Jaramillo, JE and de Hollander, M and Ramírez, CA and Mendes, R and Raaijmakers, JM and Carrión, VJ},
title = {Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {114},
pmid = {31412927},
issn = {2049-2618},
mesh = {Bacteria/*isolation &amp; purification ; Colombia ; *Domestication ; *Microbiota ; Phaseolus/*microbiology ; Plant Roots/*microbiology ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {BACKGROUND: Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood.<br><br>RESULTS: Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil.<br><br>CONCLUSIONS: Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.},
}
@article {pmid31409850,
year = {2019},
author = {Posada-Perlaza, CE and Ramírez-Rojas, A and Porras, P and Adu-Oppong, B and Botero-Coy, AM and Hernández, F and Anzola, JM and Díaz, L and Dantas, G and Reyes, A and Zambrano, MM},
title = {Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11764},
pmid = {31409850},
issn = {2045-2322},
mesh = {Colombia ; Drug Resistance, Microbial/*genetics ; Geologic Sediments/microbiology ; *Human Activities ; Humans ; Microbiota/*drug effects ; Rivers ; *Water Microbiology ; Water Pollutants, Chemical/*toxicity ; },
abstract = {The increase in antibiotic resistant bacteria has raised global concern regarding the future effectiveness of antibiotics. Human activities that influence microbial communities and environmental resistomes can generate additional risks to human health. In this work, we characterized aquatic microbial communities and their resistomes in samples collected at three sites along the Bogotá River and from wastewaters at three city hospitals, and investigated community profiles and antibiotic resistance genes (ARGs) as a function of anthropogenic contamination. The presence of antibiotics and other commonly used drugs increased in locations highly impacted by human activities, while the diverse microbial communities varied among sites and sampling times, separating upstream river samples from more contaminated hospital and river samples. Clinically relevant antibiotic resistant pathogens and ARGs were more abundant in contaminated water samples. Tracking of resistant determinants to upstream river waters and city sources suggested that human activities foster the spread of ARGs, some of which were co-localized with mobile genetic elements in assembled metagenomic contigs. Human contamination of this water ecosystem changed both community structure and environmental resistomes that can pose a risk to human health.},
}
@article {pmid31409661,
year = {2019},
author = {Small, CM and Currey, M and Beck, EA and Bassham, S and Cresko, WA},
title = {Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
pmid = {31409661},
issn = {2379-5077},
support = {F32 GM122419/GM/NIGMS NIH HHS/United States ; P50 GM098911/GM/NIGMS NIH HHS/United States ; R24 RR032670/RR/NCRR NIH HHS/United States ; },
abstract = {Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish-even among cohoused siblings-relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa.IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.},
}
@article {pmid31407303,
year = {2019},
author = {Kröber, E and Eyice, &#xd6;},
title = {Profiling of Active Microorganisms by Stable Isotope Probing-Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2046},
number = {},
pages = {151-161},
doi = {10.1007/978-1-4939-9721-3_12},
pmid = {31407303},
issn = {1940-6029},
mesh = {Cluster Analysis ; Ecosystem ; Isotope Labeling/methods ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Software ; },
abstract = {Stable isotope probing (SIP) provides researchers a culture-independent method to retrieve nucleic acids from active microbial populations performing a specific metabolic activity in complex ecosystems. In recent years, the use of the SIP method in microbial ecology studies has been accelerated. This is partly due to the advances in sequencing and bioinformatics tools, which enable fast and reliable analysis of DNA and RNA from the SIP experiments. One of these sequencing tools, metagenomics, has contributed significantly to the body of knowledge by providing data not only on taxonomy but also on the key functional genes in specific metabolic pathways and their relative abundances. In this chapter, we provide a general background on the application of the SIP-metagenomics approach in microbial ecology and a workflow for the analysis of metagenomic datasets using the most up-to-date bioinformatics tools.},
}
@article {pmid31407302,
year = {2019},
author = {Finley, BK and Hayer, M and Mau, RL and Purcell, AM and Koch, BJ and van Gestel, NC and Schwartz, E and Hungate, BA},
title = {Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2046},
number = {},
pages = {137-149},
doi = {10.1007/978-1-4939-9721-3_11},
pmid = {31407302},
issn = {1940-6029},
mesh = {Carbon Isotopes/analysis/metabolism ; Classification ; DNA Probes/*metabolism ; DNA, Bacterial/*genetics/metabolism ; Environmental Microbiology ; Isotope Labeling/*methods ; Microbiota/*genetics ; Nitrogen Isotopes/analysis/metabolism ; Oxygen Isotopes/analysis/metabolism ; },
abstract = {Quantitative stable isotope probing (qSIP) measures rates of taxon-specific element assimilation in intact microbial communities, utilizing substrates labeled with a heavy isotope.The laboratory protocol for qSIP is nearly identical to that for conventional stable isotope probing, with two key additions: (1) in qSIP, qPCR measurements are conducted on each density fraction recovered after isopycnic separation, and (2) in qSIP, multiple density fractions are sequenced spanning the entire range of densities over which nucleic acids were recovered. qSIP goes beyond identifying taxa assimilating a substrate, as it also allows for measuring that assimilation for each taxon within a given microbial community. Here, we describe an analysis process necessary to determine atom fraction excess of a heavy stable isotope added to an environmental sample for a given taxon's DNA.},
}
@article {pmid31407297,
year = {2019},
author = {Mayali, X and Weber, PK and Nuccio, E and Lietard, J and Somoza, M and Blazewicz, SJ and Pett-Ridge, J},
title = {Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2046},
number = {},
pages = {71-87},
doi = {10.1007/978-1-4939-9721-3_6},
pmid = {31407297},
issn = {1940-6029},
mesh = {Bacteria/genetics ; Carbon Isotopes/analysis/metabolism ; Classification ; DNA, Bacterial/*genetics ; Isotope Labeling/*methods ; Mass Spectrometry ; Microarray Analysis ; Microbiota/*genetics ; Nitrogen Isotopes/analysis/metabolism ; Oxygen Isotopes/analysis/metabolism ; Phylogeny ; RNA, Ribosomal/*genetics/metabolism ; Software ; },
abstract = {Chip-SIP is a stable isotope probing (SIP) method for linking microbial identity and function in mixed communities and is capable of analyzing multiple isotopes ([13]C, [15]N, and [18]O) simultaneously. This method uses a high-density microarray to separate taxon-specific 16S (or 18S) rRNA genes and a high sensitivity magnetic sector secondary ion mass spectrometer (SIMS) to determine the relative isotope incorporation of the rRNA at each probe location. Using a maskless array synthesizer (MAS), we synthesize multiple unique sequences to target hundreds of taxa at the ribosomal operational taxonomic unit (OTU) level on an array surface, and then analyze it with a NanoSIMS 50, using its high-spatial resolution imaging capability to generate isotope ratios for individual probes. The Chip-SIP method has been used in diverse systems, including surface marine and estuarine water, rhizosphere, and peat soils, to quantify taxon-specific relative incorporation of different substrates in complex microbial communities. Depending on the hypothesis and experimental design, Chip-SIP allows the user to compare the same community incorporating different substrates, different communities incorporating the same substrate(s), or quantify how a community responds to treatment effects, such as temperature or nutrient concentrations.},
}
@article {pmid31407296,
year = {2019},
author = {Taubert, M},
title = {SIP-Metaproteomics: Linking Microbial Taxonomy, Function, and Activity.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2046},
number = {},
pages = {57-69},
doi = {10.1007/978-1-4939-9721-3_5},
pmid = {31407296},
issn = {1940-6029},
mesh = {Biomarkers/chemistry/*metabolism ; Carbon Isotopes ; Classification/methods ; Isotope Labeling/*methods ; Mass Spectrometry ; Microbiota/*genetics/physiology ; Phylogeny ; Proteins/chemistry/isolation &amp; purification/metabolism ; Proteolysis ; Proteome/chemistry/*metabolism ; Proteomics/*methods ; Workflow ; },
abstract = {Stable isotope probing combined with metaproteomics enables the detection and characterization of active key species in microbial populations under near-natural conditions, which greatly helps to understand the metabolic functions of complex microbial communities. This is achieved by providing growth substrates labeled with heavy isotopes such as [13]C, which will be assimilated into microbial biomass. After subsequent extraction of proteins and proteolytic cleavage into peptides, the heavy isotope enrichment can be detected by high-resolution mass spectrometric analysis, and linked to the functional and taxonomic characterization of these biomarkers. Here we provide protocols for obtaining isotopically labeled proteins and for downstream SIP-metaproteomics analysis.},
}
@article {pmid31407294,
year = {2019},
author = {Ghori, NU and Moreira-Grez, B and Vuong, P and Waite, I and Morald, T and Wise, M and Whiteley, AS},
title = {RNA Stable Isotope Probing (RNA-SIP).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2046},
number = {},
pages = {31-44},
doi = {10.1007/978-1-4939-9721-3_3},
pmid = {31407294},
issn = {1940-6029},
mesh = {Carbon Isotopes/chemistry ; Centrifugation, Density Gradient/instrumentation/methods ; DNA, Bacterial/genetics/metabolism ; Isotope Labeling/*methods ; Microbiota/genetics ; RNA/isolation &amp; purification/metabolism ; RNA Probes/genetics/*metabolism ; RNA, Ribosomal, 16S/metabolism ; Spectrum Analysis, Raman ; Workflow ; },
abstract = {Stable isotope probing is a combined molecular and isotopic technique used to probe the identity and function of uncultivated microorganisms within environmental samples. Employing stable isotopes of common elements such as carbon and nitrogen, RNA-SIP exploits an increase in the buoyant density of RNA caused by the active metabolism and incorporation of heavier mass isotopes into the RNA after cellular utilization of labeled substrates pulsed into the community. Labeled RNAs are subsequently separated from unlabeled RNAs by density gradient centrifugation followed by identification of the RNAs by sequencing. Therefore, RNA stable isotope probing is a culture-independent technique that provides simultaneous information about microbiome community, composition and function. This chapter presents the detailed protocol for performing an RNA-SIP experiment, including the formation, ultracentrifugation, and fractional analyses of stable isotope-labeled RNAs extracted from environmental samples.},
}
@article {pmid31407021,
year = {2020},
author = {Bockoven, AA and Bondy, EC and Flores, MJ and Kelly, SE and Ravenscraft, AM and Hunter, MS},
title = {What Goes Up Might Come Down: the Spectacular Spread of an Endosymbiont Is Followed by Its Decline a Decade Later.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {482-494},
pmid = {31407021},
issn = {1432-184X},
support = {DEB-1020460//Division of Environmental Biology/ ; IOS-1256905//Division of Integrative Organismal Systems/ ; },
mesh = {Animals ; Arizona ; Genetic Fitness ; Hemiptera/genetics/*microbiology/*physiology ; *Microbiota ; Rickettsia/*physiology ; Sex Ratio ; *Symbiosis ; },
abstract = {Facultative, intracellular bacterial symbionts of arthropods may dramatically affect host biology and reproduction. The length of these symbiont-host associations may be thousands to millions of years, and while symbiont loss is predicted, there have been very few observations of a decline of symbiont infection rates. In a population of the sweet potato whitefly species (Bemisia tabaci MEAM1) in Arizona, USA, we documented the frequency decline of a strain of Rickettsia in the Rickettsia bellii clade from near-fixation in 2011 to 36% of whiteflies infected in 2017. In previous studies, Rickettsia had been shown to increase from 1 to 97% from 2000 to 2006 and remained at high frequency for at least five years. At that time, Rickettsia infection was associated with both fitness benefits and female bias. In the current study, we established matrilines of whiteflies from the field (2016, Rickettsia infection frequency = 58%) and studied (a) Rickettsia vertical transmission, (b) fitness and sex ratios associated with Rickettsia infection, (c) symbiont titer, and (d) bacterial communities within whiteflies. The vertical transmission rate was high, approximately 98%. Rickettsia infection in the matrilines was not associated with fitness benefits or sex ratio bias and appeared to be slightly costly, as more Rickettsia-infected individuals produced non-hatching eggs. Overall, the titer of Rickettsia in the matrilines was lower in 2016 than in the whiteflies collected in 2011, but the titer distribution appeared bimodal, with high- and low-titer lines, and constancy of the average titer within lines over three generations. We found neither association between Rickettsia titer and fitness benefits or sex ratio bias nor evidence that Rickettsia was replaced by another secondary symbiont. The change in the interaction between symbiont and host in 2016 whiteflies may explain the drop in symbiont frequency we observed.},
}
@article {pmid31402530,
year = {2020},
author = {Onnis-Hayden, A and Srinivasan, V and Tooker, NB and Li, G and Wang, D and Barnard, JL and Bott, C and Dombrowski, P and Schauer, P and Menniti, A and Shaw, A and Stinson, B and Stevens, G and Dunlap, P and Takács, I and McQuarrie, J and Phillips, H and Lambrecht, A and Analla, H and Russell, A and Gu, AZ},
title = {Survey of full-scale sidestream enhanced biological phosphorus removal (S2EBPR) systems and comparison with conventional EBPRs in North America: Process stability, kinetics, and microbial populations.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {92},
number = {3},
pages = {403-417},
doi = {10.1002/wer.1198},
pmid = {31402530},
issn = {1554-7531},
support = {U1R13//Water Environment &amp; Reuse Foundation/ ; //Hampton Roads Sanitation District/ ; //Woodard &amp; Curran, Inc./ ; },
mesh = {*Bioreactors ; Kinetics ; North America ; *Phosphorus ; Phylogeny ; Polyphosphates ; RNA, Ribosomal, 16S ; Surveys and Questionnaires ; },
abstract = {Sidestream EBPR (S2EBPR) is an emerging alternative process to address common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. A systematic evaluation and comparison of the process performance and microbial community structure was conducted between conventional and S2EBPR facilities in North America. The statistical analysis suggested higher performance stability in S2EBPR than conventional EBPR, although possible bias associated with other plant-specific factors might have affected the comparison. Variations in stoichiometric values related to EBPR activity and discrepancies between the observed values and current model predictions suggested a varying degree of metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. Microbial community analysis using various techniques suggested comparable known candidate PAO relative abundances in S2EBPR and conventional EBPR systems, whereas the relative abundance of known candidate GAOs seemed to be consistently lower in S2EBPR facilities than conventional EBPR facilities. 16S rRNA gene sequencing analysis revealed differences in the community phylogenetic fingerprints between S2EBPR and conventional facilities and indicated statistically higher microbial diversity index values in S2EBPR facilities than those in conventional EBPRs. PRACTITIONER POINTS: Sidestream EBPR (S2EBPR) can be implemented with varying and flexible configurations, and they offer advantages over conventional configurations for addressing the common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. Survey of S2EBPR plants in North America suggested statistically more stable phosphorus removal performance in S2EBPR plants than conventional EBPRs, although possible bias might affect the comparison due to other plant-specific factors. The EBPR kinetics and stoichiometry of the S2EBPR facilities seemed to vary and are associated with metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. The abundance of known candidate PAOs in S2EBPR plants was similar to those in conventional EBPRs, and the abundance of known candidate GAOs was generally lower in S2EBPR than conventional EBPR facilities. Further finer-resolution analysis of PAOs and GAOs, as well as identification of other unknown PAOs and GAOs, is needed. Microbial diversity is higher in S2EBPR facilities compared with conventional ones, implying that S2EBPR microbial communities could show better resilience to perturbations due to potential functional redundancy.},
}
@article {pmid31399723,
year = {2019},
author = {Bolyen, E and Rideout, JR and Dillon, MR and Bokulich, NA and Abnet, CC and Al-Ghalith, GA and Alexander, H and Alm, EJ and Arumugam, M and Asnicar, F and Bai, Y and Bisanz, JE and Bittinger, K and Brejnrod, A and Brislawn, CJ and Brown, CT and Callahan, BJ and Caraballo-Rodríguez, AM and Chase, J and Cope, EK and Da Silva, R and Diener, C and Dorrestein, PC and Douglas, GM and Durall, DM and Duvallet, C and Edwardson, CF and Ernst, M and Estaki, M and Fouquier, J and Gauglitz, JM and Gibbons, SM and Gibson, DL and Gonzalez, A and Gorlick, K and Guo, J and Hillmann, B and Holmes, S and Holste, H and Huttenhower, C and Huttley, GA and Janssen, S and Jarmusch, AK and Jiang, L and Kaehler, BD and Kang, KB and Keefe, CR and Keim, P and Kelley, ST and Knights, D and Koester, I and Kosciolek, T and Kreps, J and Langille, MGI and Lee, J and Ley, R and Liu, YX and Loftfield, E and Lozupone, C and Maher, M and Marotz, C and Martin, BD and McDonald, D and McIver, LJ and Melnik, AV and Metcalf, JL and Morgan, SC and Morton, JT and Naimey, AT and Navas-Molina, JA and Nothias, LF and Orchanian, SB and Pearson, T and Peoples, SL and Petras, D and Preuss, ML and Pruesse, E and Rasmussen, LB and Rivers, A and Robeson, MS and Rosenthal, P and Segata, N and Shaffer, M and Shiffer, A and Sinha, R and Song, SJ and Spear, JR and Swafford, AD and Thompson, LR and Torres, PJ and Trinh, P and Tripathi, A and Turnbaugh, PJ and Ul-Hasan, S and van der Hooft, JJJ and Vargas, F and Vázquez-Baeza, Y and Vogtmann, E and von Hippel, M and Walters, W and Wan, Y and Wang, M and Warren, J and Weber, KC and Williamson, CHD and Willis, AD and Xu, ZZ and Zaneveld, JR and Zhang, Y and Zhu, Q and Knight, R and Caporaso, JG},
title = {Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.},
journal = {Nature biotechnology},
volume = {37},
number = {9},
pages = {1091},
doi = {10.1038/s41587-019-0252-6},
pmid = {31399723},
issn = {1546-1696},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}
@article {pmid31399193,
year = {2019},
author = {Xu, X and Zhu, X and Wang, C and Li, Y and Fan, C and Kao, X},
title = {microRNA-650 promotes inflammation induced apoptosis of intestinal epithelioid cells by targeting NLRP6.},
journal = {Biochemical and biophysical research communications},
volume = {517},
number = {4},
pages = {551-556},
doi = {10.1016/j.bbrc.2019.06.077},
pmid = {31399193},
issn = {1090-2104},
mesh = {Animals ; Apoptosis/*genetics ; Base Sequence ; Caco-2 Cells ; Cell Line ; Colitis, Ulcerative/genetics/pathology ; Epithelioid Cells/metabolism/*pathology ; Gene Expression Regulation ; Humans ; Inflammation/*genetics/*pathology ; Intestines/*pathology ; Intracellular Signaling Peptides and Proteins/*metabolism ; Male ; Mice ; MicroRNAs/genetics/*metabolism ; Rats ; },
abstract = {Ulcerative colitis (UC), a serious threat to public health, is one of the main forms of inflammatory bowel disease, whereas the molecular mechanisms underlying ulcerative colitis induced by inflammation still remain elusive. NPLR6 gene is previously shown to regulate intestinal homeostasis and regulate the colonic microbial ecology. Here, we report that microRNA-650 (miR-650) plays an important role in the pathogenesis of UC as an upstream regulator of NPLR6 gene. MiR-650 is proved overexpressed in the inflamed mucosa of patients with ulcerative colitis and the DSS induced colitis model mice by qRT-PCR. Over-expression of miR-650 leads to increased apoptosis of Caco-2 and IEC-6 cells, and the DSS-induced mice aggravation, while knock-down of miR-650 shows opposite effects. Through constructing luciferase reporter genes containing 3'-untranslated regions of NLRP6, we further demonstrate that miR-650 inhibits NLRP6 through binding to its 3'-untranslated regions. Overexpression of NLRP6 in Caco-2 and IEC-6 cells suppress the increase apoptosis induced by miR-650 overexpression. Overall, the findings of this study indicate the role of miR-650 in ulcerative colitis, which provides a new target for therapeutic treatment.},
}
@article {pmid31398879,
year = {2019},
author = {Hassan, Z and Sultana, M and Khan, SI and Braster, M and Röling, WFM and Westerhoff, HV},
title = {Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?.},
journal = {Microorganisms},
volume = {7},
number = {8},
pages = {},
pmid = {31398879},
issn = {2076-2607},
support = {W01.65.324.00/project 4//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NFRADEV-4-2014-2015 #654248//Corbel: EU-H2020/ ; EU-H2020 MSCA-ITN-2014-ETN: Marie Sk&#x142;odowska-Curie Innovative Training Networks (ITN-ETN) #642691, BBSRC China: BB/J020060/1//Epipredict/ ; },
abstract = {Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we found transfer-persistent arsenite oxidation activity under four conditions (aerobic/anaerobic; heterotrophic/autotrophic). This suggests that biological decontamination may help ameliorate the problem. The enriched microbial communities were phylogenetically at least as diverse as the unenriched communities: they contained a bonanza of 16S rRNA gene sequences. These related to Hydrogenophaga, Acinetobacter, Dechloromonas, Comamonas, and Rhizobium/Agrobacterium species. In addition, the enriched microbiomes contained genes highly similar to the arsenite oxidase (aioA) gene of chemolithoautotrophic (e.g., Paracoccus sp. SY) and heterotrophic arsenite-oxidizing strains. The enriched cultures also contained aioA phylotypes not detected in the previous survey of uncultivated samples from the same wells. Anaerobic enrichments disclosed a wider diversity of arsenite oxidizing aioA phylotypes than did aerobic enrichments. The cultivatable chemolithoautotrophic and heterotrophic arsenite oxidizers are of great interest for future in or ex-situ arsenic bioremediation technologies for the detoxification of drinking water by oxidizing arsenite to arsenate that should then precipitates with iron oxides. The microbial activities required for such a technology seem present, amplifiable, diverse and hence robust.},
}
@article {pmid31398339,
year = {2019},
author = {Arevalo, P and VanInsberghe, D and Elsherbini, J and Gore, J and Polz, MF},
title = {A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations.},
journal = {Cell},
volume = {178},
number = {4},
pages = {820-834.e14},
doi = {10.1016/j.cell.2019.06.033},
pmid = {31398339},
issn = {1097-4172},
mesh = {Adaptation, Physiological/genetics ; Alleles ; Clostridiales/*genetics ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; *Gene Flow ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Microbiota/*genetics ; Models, Genetic ; Mutation Rate ; Phylogeny ; Polymorphism, Single Nucleotide ; Prochlorococcus/genetics ; Sulfolobus/genetics ; Vibrio/genetics ; },
abstract = {Delineating ecologically meaningful populations among microbes is important for identifying their roles in environmental and host-associated microbiomes. Here, we introduce a metric of recent gene flow, which when applied to co-existing microbes, identifies congruent genetic and ecological units separated by strong gene flow discontinuities from their next of kin. We then develop a pipeline to identify genome regions within these units that show differential adaptation and allow mapping of populations onto environmental variables or host associations. Using this reverse ecology approach, we show that the human commensal bacterium Ruminococcus gnavus breaks up into sharply delineated populations that show different associations with health and disease. Defining populations by recent gene flow in this way will facilitate the analysis of bacterial and archaeal genomes using ecological and evolutionary theory developed for plants and animals, thus allowing for testing unifying principles across all biology.},
}
@article {pmid31397240,
year = {2019},
author = {Lv, Y and Qin, X and Jia, H and Chen, S and Sun, W and Wang, X},
title = {The association between gut microbiota composition and BMI in Chinese male college students, as analysed by next-generation sequencing.},
journal = {The British journal of nutrition},
volume = {122},
number = {9},
pages = {986-995},
doi = {10.1017/S0007114519001909},
pmid = {31397240},
issn = {1475-2662},
mesh = {Asian People ; Bacteria/*genetics ; Biodiversity ; *Body Mass Index ; China ; Gastrointestinal Microbiome/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; Overweight/*microbiology ; Young Adult ; },
abstract = {Altered gut microbial ecology contributes to the development of metabolic diseases including obesity. However, studies based on different populations have generated conflicting results due to diet, environment, methodologies, etc. The aim of our study was to explore the association between gut microbiota and BMI in Chinese college students. The 16S next-generation sequencing (NGS) was used to test the gut microbiota of nine lean, nine overweight/obesity and ten normal-weight male college students. The differences in gut microbiota distribution among three groups were compared, and the relationship between the richness, diversity, composition of gut microbiota and BMI were analysed. The predominant phyla Bacteroidetes and Firmicutes were further confirmed by real-time PCR. Metagenomic biomarker discovery was conducted by linear discriminant analysis (LDA) effect size (LEfSe). NGS revealed that gut microbiota composition was different among three groups, but there was no difference in the abundance ratio of Firmicutes:Bacteroidetes. Several bacterial taxa were in linear relationship with BMI (positive relationship: uncultured bacterium (Bacteroides genus); negative relationship: Porphyromonadaceae, Acidaminococcaceae, Rikenellaceae, Desulfovibrionaceae, Blautia, Anaerotruncus, Parabacteroides, Alistipes). Moreover, gut microbiota diversity decreased with the increase in BMI. And LEfSe analysis indicated that Blautia, Anaerotruncus and its uncultured species were significantly enriched in the lean group (LDA score ≥ 3), Parasuterella and its uncultured species were significantly enriched in the overweight/obese groups (LDA score ≥ 3). In general, gut microbiota composition and microbial diversity were associated with BMI in Chinese male college students. Our results might enrich the understanding between gut microbiota and obesity.},
}
@article {pmid31396501,
year = {2019},
author = {Ramamurthy, T and Mutreja, A and Weill, FX and Das, B and Ghosh, A and Nair, GB},
title = {Revisiting the Global Epidemiology of Cholera in Conjuction With the Genomics of Vibrio cholerae.},
journal = {Frontiers in public health},
volume = {7},
number = {},
pages = {203},
pmid = {31396501},
issn = {2296-2565},
abstract = {Toxigenic Vibrio cholerae is responsible for 1.4 to 4.3 million cases with about 21,000-143,000 deaths per year. Dominance of O1 and O139 serogroups, classical and El tor biotypes, alterations in CTX phages and the pathogenicity Islands are some of the major features of V. cholerae isolates that are responsible for cholera epidemics. Whole-genome sequencing (WGS) based analyses of single-nucleotide polymorphisms (SNPs) and other infrequent genetic variants provide a robust phylogenetic framework. Recent studies on the global transmission of pandemic V. cholerae O1 strains have shown the existence of eight different phyletic lineages. In these, the classical and El Tor biotype strains were separated as two distinctly evolved lineages. The frequency of SNP accumulation and the temporal and geographical distribution supports the perception that the seventh cholera pandemic (7CP) has spread from the Bay of Bengal region in three independent but overlapping waves. The 2010 Haitian outbreak shared a common ancestor with South-Asian wave-3 strains. In West Africa and East/Southern Africa, cholera epidemics are caused by single expanded lineage, which has been introduced several times since 1970. The Latin American epidemics that occurred in 1991 and 2010 were the result of introductions of two 7CP sublineages. Sublineages representing wave-3 have caused huge outbreaks in Haiti and Yemen. The Ogawa-Inaba serotype switchover in several cholera epidemics are believed to be due to the involvement of certain selection mechanism(s) rather than due to random events. V. cholerae O139 serogroup is phylogenetically related to the 7CP El Tor, and almost all these isolates belonged to the multilocus sequence type-69. Additional phenotypic and genotypic information have been generated to understand the pathogenicity of classical and El Tor vibrios. Presence of integrative conjugative elements (ICE) with antibiotic resistance gene cassettes, clustered regularly interspaced short palindromic repeats-associated protein system and ctxAB promoter based ToxRS expression of cholera toxin (CT) separates classical and El Tor biotypes. With the availability of WGS information, several important applications including, molecular typing, antimicrobial resistance, new diagnostics, and vaccination strategies could be generated.},
}
@article {pmid31396176,
year = {2019},
author = {Fernández-Martínez, M&#xc1; and Dos Santos Severino, R and Moreno-Paz, M and Gallardo-Carreño, I and Blanco, Y and Warren-Rhodes, K and García-Villadangos, M and Ruiz-Bermejo, M and Barberán, A and Wettergreen, D and Cabrol, N and Parro, V},
title = {Prokaryotic Community Structure and Metabolisms in Shallow Subsurface of Atacama Desert Playas and Alluvial Fans After Heavy Rains: Repairing and Preparing for Next Dry Period.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1641},
pmid = {31396176},
issn = {1664-302X},
abstract = {The Atacama Desert, the oldest and driest desert on Earth, displays significant rains only once per decade. To investigate how microbial communities take advantage of these sporadic wet events, we carried out a geomicrobiological study a few days after a heavy rain event in 2015. Different physicochemical and microbial community analyses were conducted on samples collected from playas and an alluvial fan from surface, 10, 20, 50, and 80 cm depth. Gravimetric moisture content peaks were measured in 10 and 20 cm depth samples (from 1.65 to 4.1% w/w maximum values) while, in general, main anions such as chloride, nitrate, and sulfate concentrations increased with depth, with maximum values of 13-1,125; 168-10,109; and 9,904-30,952 ppm, respectively. Small organic anions such as formate and acetate had maximum concentrations from 2.61 to 3.44 ppm and 6.73 to 28.75 ppm, respectively. Microbial diversity inferred from DNA analysis showed Actinobacteria and Alphaproteobacteria as the most abundant and widespread bacterial taxa among the samples, followed by Chloroflexi and Firmicutes at specific sites. Archaea were mainly dominated by Nitrososphaerales, Methanobacteria, with the detection of other groups such as Halobacteria. Metaproteomics showed a high and even distribution of proteins involved in primary metabolic processes such as energy production and biosynthetic pathways, and a limited but remarkable presence of proteins related to resistance to environmental stressors such as radiation, oxidation, or desiccation. The results indicated that extra humidity in the system allows the microbial community to repair, and prepare for the upcoming hyperarid period. Additionally, it supplies biomarkers to the medium whose preservation potential could be high under strong desiccation conditions and relevant for planetary exploration.},
}
@article {pmid31395953,
year = {2019},
author = {Cardini, U and Bartoli, M and Lücker, S and Mooshammer, M and Polzin, J and Lee, RW and Micić, V and Hofmann, T and Weber, M and Petersen, JM},
title = {Chemosymbiotic bivalves contribute to the nitrogen budget of seagrass ecosystems.},
journal = {The ISME journal},
volume = {13},
number = {12},
pages = {3131-3134},
pmid = {31395953},
issn = {1751-7370},
mesh = {Animals ; Bivalvia/*metabolism ; Carbon/metabolism ; Carbon Cycle ; Chemoautotrophic Growth ; Ecology ; Ecosystem ; Nitrogen/*metabolism ; Plants/*metabolism ; Symbiosis ; },
abstract = {In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared with the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to tenfold higher compared with fluxes reported for nonsymbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves' contribution may boost productivity of these important blue carbon ecosystems.},
}
@article {pmid31393934,
year = {2019},
author = {Barone, M and Turroni, S and Rampelli, S and Soverini, M and D'Amico, F and Biagi, E and Brigidi, P and Troiani, E and Candela, M},
title = {Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0220619},
pmid = {31393934},
issn = {1932-6203},
mesh = {Bile/microbiology ; *Diet, Mediterranean ; *Diet, Paleolithic ; Diet, Western ; Dietary Fats/metabolism ; *Gastrointestinal Microbiome ; Humans ; Life Style ; },
abstract = {The modern Paleolithic diet (MPD), featured by the consumption of vegetables, fruit, nuts, seeds, eggs, fish and lean meat, while excluding grains, dairy products, salt and refined sugar, has gained substantial public attention in recent years because of its potential multiple health benefits. However, to date little is known about the actual impact of this dietary pattern on the gut microbiome (GM) and its implications for human health. In the current scenario where Western diets, low in fiber while rich in industrialized and processed foods, are considered one of the leading causes of maladaptive GM changes along human evolution, likely contributing to the increasing incidence of chronic non-communicable diseases, we hypothesize that the MPD could modulate the Western GM towards a more "ancestral" configuration. In an attempt to shed light on this, here we profiled the GM structure of urban Italian subjects adhering to the MPD, and compared data with other urban Italians following a Mediterranean Diet (MD), as well as worldwide traditional hunter-gatherer populations from previous publications. Notwithstanding a strong geography effect on the GM structure, our results show an unexpectedly high degree of biodiversity in MPD subjects, which well approximates that of traditional populations. The GM of MPD individuals also shows some peculiarities, including a high relative abundance of bile-tolerant and fat-loving microorganisms. The consumption of plant-based foods-albeit with the exclusion of grains and pulses-along with the minimization of the intake of processed foods, both hallmarks of the MPD, could therefore contribute to partially rewild the GM but caution should be taken in adhering to this dietary pattern in the long term.},
}
@article {pmid31392355,
year = {2020},
author = {Gray, L and Kernaghan, G},
title = {Fungal Succession During the Decomposition of Ectomycorrhizal Fine Roots.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {271-284},
pmid = {31392355},
issn = {1432-184X},
support = {rgpin-2015-04323//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Abies/*microbiology ; *Mycobiome ; Mycorrhizae/*physiology ; Nova Scotia ; Picea/*microbiology ; Plant Roots/*microbiology ; Seedlings/microbiology ; },
abstract = {Ectomycorrhizal (ECM) fine roots account for a substantial proportion of forest production and their decomposition releases large amounts of nutrients to the soil ecosystem. However, little is known about the fungi involved in ECM decomposition, including assemblages of fungal saprotrophs, endophytes, and the ECM fungi themselves. To follow fungal succession during the degradation of senescing fine roots, understory seedlings of Abies balsamea and Picea rubens at two sites in the Acadian forest of Nova Scotia were either severed at the root collar or left as controls. Root systems were collected sequentially over two growing seasons and assessed for fine root loss and ECM mantle integrity. ECM were identified by ITS-PCR and grouped into broad morphological categories. Fungal communities colonizing the senescing fine roots were also monitored by systematically constructing clone libraries over the course of the experiment. ECM with cottony, weakly pigmented mantles (e.g., Cortinarius) degraded within the first year. Those with cottony, but intensely pigmented mantles (Piloderma), and smooth mantles with weak pigmentation (Russulaceae) degraded more slowly. Smooth, melanized ECM (Cenococcum and Tomentella) generally maintained integrity over the course of the experiment. Rates of fine root loss and changes in ECM mantle integrity were positively correlated with soil temperature. ECM DNA was detected throughout the experiment, and was not replaced by that of saprotrophic species during the two seasons sampled. However, fungal root endophytes (e.g., Helotiaceae) initially increased in abundance and then decreased as mantles degraded, suggesting a possible role in ECM decomposition.},
}
@article {pmid31391302,
year = {2019},
author = {Ning, D and Deng, Y and Tiedje, JM and Zhou, J},
title = {A general framework for quantitatively assessing ecological stochasticity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {34},
pages = {16892-16898},
pmid = {31391302},
issn = {1091-6490},
mesh = {*Algorithms ; *Ecosystem ; *Models, Biological ; Stochastic Processes ; },
abstract = {Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. Here we propose a general mathematical framework to quantify ecological stochasticity under different situations in which deterministic factors drive the communities more similar or dissimilar than null expectation. An index, normalized stochasticity ratio (NST), was developed with 50% as the boundary point between more deterministic (<50%) and more stochastic (>50%) assembly. NST was tested with simulated communities by considering abiotic filtering, competition, environmental noise, and spatial scales. All tested approaches showed limited performance at large spatial scales or under very high environmental noise. However, in all of the other simulated scenarios, NST showed high accuracy (0.90 to 1.00) and precision (0.91 to 0.99), with averages of 0.37 higher accuracy (0.1 to 0.7) and 0.33 higher precision (0.0 to 1.8) than previous approaches. NST was also applied to estimate stochasticity in the succession of a groundwater microbial community in response to organic carbon (vegetable oil) injection. Our results showed that community assembly was shifted from more deterministic (NST = 21%) to more stochastic (NST = 70%) right after organic carbon input. As the vegetable oil was consumed, the community gradually returned to be more deterministic (NST = 27%). In addition, our results demonstrated that null model algorithms and community similarity metrics had strong effects on quantifying ecological stochasticity.},
}
@article {pmid31388702,
year = {2020},
author = {Moss, JA and Henriksson, NL and Pakulski, JD and Snyder, RA and Jeffrey, WH},
title = {Oceanic Microplankton Do Not Adhere to the Latitudinal Diversity Gradient.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {511-515},
pmid = {31388702},
issn = {1432-184X},
mesh = {Archaea/classification/*isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; *Biodiversity ; Eukaryota/classification/*isolation &amp; purification ; *Microbiota ; Pacific Ocean ; Plankton/classification/*isolation &amp; purification ; Seawater/microbiology ; },
abstract = {A latitudinal biodiversity gradient has captivated ecologists for years, and has become a widely recognized pattern in biogeography, manifest as an increase in biodiversity from the poles to the tropics. Oceanographers have attempted to discern whether these distribution patterns are shared with marine biota, and a lively debate has emerged concerning the global distribution of microbes. Limitations in sampling resolution for such large-scale assessments have often prohibited definitive conclusions. We evaluated microbial planktonic communities along a ~ 15,400-km Pacific Ocean transect with DNA from samples acquired every 2 degrees of latitude within a 3-month period between late August and early November 2003. Next-generation sequencing targeting the Bacteria, Archaea, and Eukarya yielded ~ 10.8 million high-quality sequences. Beta-analysis revealed geographic patterns of microbial communities, primarily the Bacteria and Archaea domains. None of the domains exhibited a unimodal pattern of alpha-diversity with respect to latitude. Bacteria communities increased in richness from Arctic to Antarctic waters, whereas Archaea and Eukarya communities showed no latitudinal or polar trends. Based on our analyses, environmental factors related to latitude thought to influence various macrofauna may not define microplankton diversity patterns of richness in the global ocean.},
}
@article {pmid31387934,
year = {2019},
author = {Ziels, RM and Nobu, MK and Sousa, DZ},
title = {Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
pmid = {31387934},
issn = {2379-5077},
support = {323009/ERC_/European Research Council/International ; },
abstract = {Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in [13]C after growing on [[13]C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [[13]C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in [13]C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling.IMPORTANCE Predicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in situ metabolic activities of uncultured species may enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in situ function of mixed microbiomes by combining stable-isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve "who is doing what" by obtaining confirmatory assimilation of the labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.},
}
@article {pmid31387904,
year = {2019},
author = {Su, X and Jing, G and McDonald, D and Wang, H and Wang, Z and Gonzalez, A and Sun, Z and Huang, S and Navas, J and Knight, R and Xu, J},
title = {Reply to Sun et al., "Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy".},
journal = {mBio},
volume = {10},
number = {4},
pages = {},
pmid = {31387904},
issn = {2150-7511},
mesh = {*Microbiota ; RNA, Ribosomal, 16S ; Solar System ; },
}
@article {pmid31384980,
year = {2020},
author = {Siddiqee, MH and Henry, R and Deletic, A and Bulach, DM and Coleman, RA and McCarthy, DT},
title = {Salmonella from a Microtidal Estuary Are Capable of Invading Human Intestinal Cell Lines.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {259-270},
pmid = {31384980},
issn = {1432-184X},
support = {LP120100718//Australian Research Council/ ; LP120100718//Melbourne Water/ ; },
mesh = {Caco-2 Cells/*microbiology ; Cities ; Estuaries ; Feces/*microbiology ; Humans ; Intestines/microbiology ; Salmonella/*isolation &amp; purification/*physiology ; Seasons ; Victoria ; Virulence ; },
abstract = {Faecal contamination poses health risks for the recreational users of urban estuaries. However, our understanding of the potential pathogenicity of faecal microbes in these environments is limited. To this end, a study was conducted to understand the spatial and seasonal distribution of Salmonella in water and sediments of the Yarra River estuary, Melbourne, Australia. Among 210 samples in total, culturable Salmonella were recovered from 27%, 17%, and 19% of water, bank, and bed sediment samples, respectively. The combined detection increased from 15% in winter to 32% in summer (p < 0.05) indicating seasonal variation as potential part of public health risk assessments. Further, pathogenic potential of the Salmonella isolates was characterised via the quantification of attachment and invasion capacity using human epithelial colorectal cell line Caco-2 on a subset of isolates (n = 62). While all of these isolates could attach and invade Caco-2 cells, 52% and 13% of these showed greater attachment and invasiveness, respectively, than the corresponding mean values for S. Typhimurium ATCC14028 control. Isolates from winter were on average more invasive (seven out of eight isolates with the highest invasiveness recovered from the colder sampling period) than the isolates from summer, and Salmonella collected during summer showed lower invasion (p < 0.05) compared with the control. Similar low invasion compared with the same control was observed for isolates recovered from bank sediment (p < 0.05). While the higher prevalence in summer may imply higher risks during these peak recreational periods, it is essential that this information is used in combination with quantitative microbial risk assessments to fully understand the health risks posed by Salmonella in microtidal estuaries.},
}
@article {pmid31384013,
year = {2019},
author = {Hale, L and Feng, W and Yin, H and Guo, X and Zhou, X and Bracho, R and Pegoraro, E and Penton, CR and Wu, L and Cole, J and Konstantinidis, KT and Luo, Y and Tiedje, JM and Schuur, EAG and Zhou, J},
title = {Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon.},
journal = {The ISME journal},
volume = {13},
number = {12},
pages = {2901-2915},
pmid = {31384013},
issn = {1751-7370},
mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Carbon/*analysis/metabolism ; Climate Change ; Fungi/classification/genetics/*isolation &amp; purification ; *Microbiota ; Permafrost/microbiology ; Soil/chemistry ; *Soil Microbiology ; Tundra ; },
abstract = {The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions.},
}
@article {pmid31383901,
year = {2019},
author = {Andrade-Martínez, JS and Moreno-Gallego, JL and Reyes, A},
title = {Defining a Core Genome for the Herpesvirales and Exploring their Evolutionary Relationship with the Caudovirales.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11342},
pmid = {31383901},
issn = {2045-2322},
mesh = {Caudovirales/*genetics ; Evolution, Molecular ; *Genome, Viral ; Herpesviridae/*genetics ; Herpesviridae Infections/virology ; Humans ; Phylogeny ; Viral Proteins/genetics ; },
abstract = {The order Herpesvirales encompasses a wide variety of important and broadly distributed human pathogens. During the last decades, similarities in the viral cycle and the structure of some of their proteins with those of the order Caudovirales, the tailed bacterial viruses, have brought speculation regarding the existence of an evolutionary relationship between these clades. To evaluate such hypothesis, we used over 600 Herpesvirales and 2000 Caudovirales complete genomes to search for the presence or absence of clusters of orthologous protein domains and constructed a dendrogram based on their compositional similarities. The results obtained strongly suggest an evolutionary relationship between the two orders. Furthermore, they allowed to propose a core genome for the Herpesvirales, composed of 4 proteins, including the ATPase subunit of the DNA-packaging terminase, the only protein with previously verified conservation. Accordingly, a phylogenetic tree constructed with sequences derived from the clusters associated to these proteins grouped the Herpesvirales strains accordingly to the established families and subfamilies. Overall, this work provides results supporting the hypothesis that the two orders are evolutionarily related and contributes to the understanding of the history of the Herpesvirales.},
}
@article {pmid31379798,
year = {2019},
author = {Vigneron, A and Lovejoy, C and Cruaud, P and Kalenitchenko, D and Culley, A and Vincent, WF},
title = {Contrasting Winter Versus Summer Microbial Communities and Metabolic Functions in a Permafrost Thaw Lake.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1656},
pmid = {31379798},
issn = {1664-302X},
abstract = {Permafrost thawing results in the formation of thermokarst lakes, which are biogeochemical hotspots in northern landscapes and strong emitters of greenhouse gasses to the atmosphere. Most studies of thermokarst lakes have been in summer, despite the predominance of winter and ice-cover over much of the year, and the microbial ecology of these waters under ice remains poorly understood. Here we first compared the summer versus winter microbiomes of a subarctic thermokarst lake using DNA- and RNA-based 16S rRNA amplicon sequencing and qPCR. We then applied comparative metagenomics and used genomic bin reconstruction to compare the two seasons for changes in potential metabolic functions in the thermokarst lake microbiome. In summer, the microbial community was dominated by Actinobacteria and Betaproteobacteria, with phototrophic and aerobic pathways consistent with the utilization of labile and photodegraded substrates. The microbial community was strikingly different in winter, with dominance of methanogens, Planctomycetes, Chloroflexi and Deltaproteobacteria, along with various taxa of the Patescibacteria/Candidate Phyla Radiation (Parcubacteria, Microgenomates, Omnitrophica, Aminicenantes). The latter group was underestimated or absent in the amplicon survey, but accounted for about a third of the metagenomic reads. The winter lineages were associated with multiple reductive metabolic processes, fermentations and pathways for the mobilization and degradation of complex organic matter, along with a strong potential for syntrophy or cross-feeding. The results imply that the summer community represents a transient stage of the annual cycle, and that carbon dioxide and methane production continue through the prolonged season of ice cover via a taxonomically distinct winter community and diverse mechanisms of permafrost carbon transformation.},
}
@article {pmid31379789,
year = {2019},
author = {Osorio, H and Mettert, E and Kiley, P and Dopson, M and Jedlicki, E and Holmes, DS},
title = {Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1642},
pmid = {31379789},
issn = {1664-302X},
support = {R01 GM045844/GM/NIGMS NIH HHS/United States ; R01 GM115894/GM/NIGMS NIH HHS/United States ; },
abstract = {The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S][2+] iron-sulfur cluster. Under O2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNRAF) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S][2+] center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNREC) recognized FNRAF. FNRAF was able to drive expression from the FNR-responsive E. coli promoter PnarG, suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNRAF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNREC. Comparison of the primary amino acid sequence of FNRAF with that of other natural and mutated FNRs, including FNREC, coupled with an analysis of the predicted tertiary structure of FNRAF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNRAF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O2 stability could allow At. ferrooxidans to survive in environments with fluctuating O2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.},
}
@article {pmid31379773,
year = {2019},
author = {Gupta, VVSR and Bramley, RGV and Greenfield, P and Yu, J and Herderich, MJ},
title = {Vineyard Soil Microbiome Composition Related to Rotundone Concentration in Australian Cool Climate 'Peppery' Shiraz Grapes.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1607},
pmid = {31379773},
issn = {1664-302X},
abstract = {Soil microbial communities have an integral association with plants and play an important role in shaping plant nutrition, health, crop productivity and product quality. The influence of bacteria and fungi on wine fermentation is well known. However, little is known about the role of soil microbes, other than microbial pathogens, on grape composition or their role in vintage or site (terroir) impacts on grape composition. In this study, we used an amplicon sequencing approach to investigate the potential relationships between soil microbes and inherent spatial variation in grape metabolite composition - specifically, the concentration of the 'impact aroma compound' rotundone in Shiraz grapes (Vitis vinifera L.) grown in a 6.1 ha vineyard in the Grampians region of Victoria, Australia. Previous work had demonstrated temporal stability in patterns of within-vineyard spatial variation in rotundone concentration, enabling identification of defined 'zones' of inherently 'low' or 'high' concentration of this grape metabolite. 16S rRNA and ITS region-amplicon sequencing analysis of microbial communities in the surface soils collected from these zones indicated marked differences between zones in the genetic diversity and composition of the soil bacterial and fungal microbiome. Soils in the High rotundone zone exhibited higher diversity of bacteria, but lower diversity of fungi, compared to the soils in the Low rotundone zone. In addition, the network analysis of the microbial community in the High rotundone zone soils appeared well structured, especially with respect to the bacterial community, compared to that in the Low rotundone zone soils. The key differences in the microbial community structure between the rotundone zones are obvious for taxa/groups of both bacteria and fungi, particularly for bacteria belonging to Acidobacteria-GP4 and GP7, Rhizobiales, Gaiellaceae, Alphaproteobacteria and the Nectriaceae and Tremellaceae families of fungi. Although mulching in some parts of the vineyard caused changes in bacterial and fungal composition and overall microbial catabolic diversity and activity, its effects did not mask the rotundone zone-based variation. This finding of a systematic rotundone zone-based variation in soil microbiomes suggests an opportunity to bring together understanding of microbial ecology, plant biochemistry, and viticultural management for improved management of grape metabolism, composition and wine flavor.},
}
@article {pmid31377832,
year = {2020},
author = {Frankel-Bricker, J and Song, MJ and Benner, MJ and Schaack, S},
title = {Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and Temperature.},
journal = {Microbial ecology},
volume = {79},
number = {3},
pages = {731-742},
pmid = {31377832},
issn = {1432-184X},
support = {MCB-1150213//National Science Foundation/ ; none//M.J. Murdock Charitable Trust/ ; },
mesh = {Animals ; Bacteria/classification ; *Bacterial Physiological Phenomena ; Daphnia/genetics/*microbiology ; Finland ; *Genotype ; Geography ; Germany ; *Host Microbial Interactions ; Israel ; *Microbiota ; Temperature ; },
abstract = {Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism's biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D. magna collected from three regions along a large latitudinal gradient (Finland, Germany, and Israel). After being reared in the lab for many years, we sought to characterize any differences in genotype- or population-specific microbial communities, and to assess whether the microbiota varied among temperatures. Our study is similar to a recent comparison of the microbial communities among D. magna genotypes raised in different temperatures published by Sullam et al. (Microb Ecol 76(2):506-517, 2017), and as such represents one of the first examples of a reproducible result in microbiome research. Like the previous study, we find evidence for a strong effect of temperature on the microbiome of D. magna, although across a much smaller temperature range representing potential near-future climates. In addition, we find evidence that the microbiomes of D. magna genotypes from different regions are distinct, even years after being brought into the laboratory. Finally, our results highlight a potentially common finding in the expanding area of microbiome research-differences among treatments are not necessarily observed in the most abundant taxonomic groups. This highlights the importance of considering sampling scheme and depth of coverage when characterizing the microbiome, as different experimental designs can significantly impact taxon-specific results, even when large-scale effects are reproduced.},
}
@article {pmid31376000,
year = {2020},
author = {Cowan, DA and Hopkins, DW and Jones, BE and Maggs-Kölling, G and Majewska, R and Ramond, JB},
title = {Microbiomics of Namib Desert habitats.},
journal = {Extremophiles : life under extreme conditions},
volume = {24},
number = {1},
pages = {17-29},
pmid = {31376000},
issn = {1433-4909},
mesh = {Bacteria ; Desert Climate ; *Ecosystem ; Soil ; Soil Microbiology ; },
abstract = {The Namib Desert is one of the world's only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was undertaken by researchers from the University of the Western Cape Institute for Microbial Biotechnology and Metagenomics, and subsequently the University of Pretoria Centre for Microbial Ecology and Genomics, and their collaborators, led to a more detailed understanding of the ecology of the indigenous microbial communities in many Namib Desert biotopes. Namib Desert soils and the associated specialized niche communities are inhabited by a wide array of prokaryotic, lower eukaryotic and virus/phage taxa. These communities are highly heterogeneous on both small and large spatial scales, with community composition impacted by a range of macro- and micro-environmental factors, from water regime to soil particle size. Community functionality is also surprisingly non-homogeneous, with some taxa retaining functionality even under hyper-arid soil conditions, and with subtle changes in gene expression and phylotype abundances even on diel timescales. Despite the growing understanding of the structure and function of Namib Desert microbiomes, there remain enormous gaps in our knowledge. We have yet to quantify many of the processes in these soil communities, from regional nutrient cycling to community growth rates. Despite the progress that has been made, we still have little knowledge of either the role of phages in microbial community dynamics or inter-species interactions. Furthermore, the intense research efforts of the past decade have highlighted the immense scope for future microbiological research in this dynamic, enigmatic and charismatic region of Africa.},
}
@article {pmid31375480,
year = {2019},
author = {Lawley, B and Otal, A and Moloney-Geany, K and Diana, A and Houghton, L and Heath, AM and Taylor, RW and Tannock, GW},
title = {Fecal Microbiotas of Indonesian and New Zealand Children Differ in Complexity and Bifidobacterial Taxa during the First Year of Life.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {19},
pages = {},
pmid = {31375480},
issn = {1098-5336},
mesh = {Age Factors ; Bifidobacterium/*classification ; Breast Feeding ; Cohort Studies ; DNA, Bacterial/genetics ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Indonesia ; Infant ; Milk, Human/microbiology ; New Zealand ; RNA, Ribosomal, 16S/genetics ; Randomized Controlled Trials as Topic ; Rural Population ; Urban Population ; },
abstract = {The biological succession that occurs during the first year of life in the gut of infants in Western countries is broadly predictable in terms of the increasing complexity of the composition of microbiotas. Less information is available about microbiotas in Asian countries, where environmental, nutritional, and cultural influences may differentially affect the composition and development of the microbial community. We compared the fecal microbiotas of Indonesian (n = 204) and New Zealand (NZ) (n = 74) infants 6 to 7 months and 12 months of age. Comparisons were made by analysis of 16S rRNA gene sequences and derivation of community diversity metrics, relative abundances of bacterial families, enterotypes, and cooccurrence correlation networks. Abundances of Bifidobacterium longum subsp. infantis and B. longum subsp. longum were determined by quantitative PCR. All observations supported the view that the Indonesian and NZ infant microbiotas developed in complexity over time, but the changes were much greater for NZ infants. B. longum subsp. infantis dominated the microbiotas of Indonesian children, whereas B. longum subsp. longum was dominant in NZ children. Network analysis showed that the niche model (in which trophic adaptation results in preferential colonization) of the assemblage of microbiotas was supported in Indonesian infants, whereas the neutral (stochastic) model was supported by the development of the microbiotas of NZ infants. The results of the study show that the development of the fecal microbiota is not the same for infants in all countries, and they point to the necessity of obtaining a better understanding of the factors that control the colonization of the gut in early life.IMPORTANCE This study addresses the microbiology of a natural ecosystem (the infant bowel) for children in a rural setting in Indonesia and in an urban environment in New Zealand. Analysis of DNA sequences generated from the microbial community (microbiota) in the feces of the infants during the first year of life showed marked differences in the composition and complexity of the bacterial collections. The differences were most likely due to differences in the prevalence and duration of breastfeeding of infants in the two countries. These kinds of studies are essential for developing concepts of microbial ecology related to the influence of nutrition and environment on the development of the gut microbiota and for determining the long-term effects of microbiological events in early life on human health and well-being.},
}
@article {pmid31374443,
year = {2019},
author = {Zhu, YG and Zhao, Y and Zhu, D and Gillings, M and Penuelas, J and Ok, YS and Capon, A and Banwart, S},
title = {Soil biota, antimicrobial resistance and planetary health.},
journal = {Environment international},
volume = {131},
number = {},
pages = {105059},
doi = {10.1016/j.envint.2019.105059},
pmid = {31374443},
issn = {1873-6750},
mesh = {Animals ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial ; *Ecosystem ; *Health ; Humans ; *Soil Microbiology ; },
abstract = {The concept of planetary health acknowledges the links between ecosystems, biodiversity and human health and well-being. Soil, the critical component of the interconnected ecosystem, is the most biodiverse habitat on Earth, and soil microbiomes play a major role in human health and well-being through ecosystem services such as nutrient cycling, pollutant remediation and synthesis of bioactive compounds such as antimicrobials. Soil is also a natural source of antimicrobial resistance, which is often termed intrinsic resistance. However, increasing use and misuse of antimicrobials in humans and animals in recent decades has increased both the diversity and prevalence of antimicrobial resistance in soils, particularly in areas affected by human and animal wastes, such as organic manures and reclaimed wastewater, and also by air transmission. Antimicrobials and antimicrobial resistance are two sides of the sword, while antimicrobials are essential in health care; globally, antimicrobial resistance is jeopardizing the effectiveness of antimicrobial drugs, thus threatening human health. Soil is a crucial pathway through which humans are exposed to antimicrobial resistance determinants, including those harbored by human pathogens. In this review, we use the nexus of antimicrobials and antimicrobial resistance as a focus to discuss the role of soil in planetary health and illustrate the impacts of soil microbiomes on human health and well-being. This review examines the sources and dynamics of antimicrobial resistance in soils and uses the perspective of planetary health to track the movement of antimicrobial-resistance genes between environmental compartments, including soil, water, food and air.},
}
@article {pmid31374141,
year = {2019},
author = {Jakob, F and Quintero, Y and Musacchio, A and Estrada-de Los Santos, P and Hernández, L and Vogel, RF},
title = {Acetic acid bacteria encode two levansucrase types of different ecological relationship.},
journal = {Environmental microbiology},
volume = {21},
number = {11},
pages = {4151-4165},
doi = {10.1111/1462-2920.14768},
pmid = {31374141},
issn = {1462-2920},
support = {2816IP001//German Federal Ministry of Food and Agriculture (BMEL) through the Federal Office of Agriculture and Food (BLE)/International ; },
mesh = {Animals ; *Ecosystem ; Hexosyltransferases/classification/*genetics/*metabolism ; Insecta/microbiology ; Plants/microbiology ; Proteobacteria/*enzymology/genetics ; },
abstract = {Acetic acid bacteria (AAB) are associated with plants and insects. Determinants for the targeting and occupation of these widely different environments are unknown. However, most of these natural habitats share plant-derived sucrose, which can be metabolized by some AAB via polyfructose building levansucrases (LS) known to be involved in biofilm formation. Here, we propose two LS types (T) encoded by AAB as determinants for habitat selection, which emerged from vertical (T1) and horizontal (T2) lines of evolution and differ in their genetic organization, structural features and secretion mechanism, as well as their occurrence in proteobacteria. T1-LS are secreted by plant-pathogenic α- and γ-proteobacteria, while T2-LS genes are common in diazotrophic, plant-growth-promoting α-, β- and γ-proteobacteria. This knowledge may be exploited for a better understanding of microbial ecology, plant health and biofilm formation by sucrase-secreting proteobacteria in eukaryotic hosts.},
}
@article {pmid31373372,
year = {2019},
author = {Brink, LR and Matazel, K and Piccolo, BD and Bowlin, AK and Chintapalli, SV and Shankar, K and Yeruva, L},
title = {Neonatal Diet Impacts Bioregional Microbiota Composition in Piglets Fed Human Breast Milk or Infant Formula.},
journal = {The Journal of nutrition},
volume = {149},
number = {12},
pages = {2236-2246},
pmid = {31373372},
issn = {1541-6100},
support = {P20 GM121293/GM/NIGMS NIH HHS/United States ; },
mesh = {*Animal Feed ; Animals ; *Animals, Newborn ; *Gastrointestinal Microbiome ; Humans ; *Infant Formula ; *Milk, Human ; Swine ; },
abstract = {BACKGROUND: Early infant diet influences postnatal gut microbial development, which in turn can modulate the developing immune system.<br><br>OBJECTIVES: The aim of this study was to characterize diet-specific bioregional microbiota differences in piglets fed either human breast milk (HM) or infant formula.<br><br>METHODS: Male piglets (White Dutch Landrace Duroc) were raised on HM or cow milk formula (MF) from postnatal day (PND) 2 to PND 21 and weaned to an ad libitum diet until PND 51. Piglets were euthanized on either PND 21 or PND 51, and the gastrointestinal contents were collected for 16s RNA sequencing. Data were analyzed using the Quantitative Insight into Microbial Ecology. Diversity measurements (Chao1 and Shannon) and the Wald test were used to determine relative abundance.<br><br>RESULTS: At PND 21, the ileal luminal region of HM-fed piglets showed lower Chao1 operational taxonomic unit diversity, while Shannon diversity was lower in cecal, proximal colon (PC), and distal colon (DC) luminal regions, relative to MF-fed piglets. In addition, at PND 51, the HM-fed piglets had lower genera diversity within the jejunum, ileum, PC, and DC luminal regions, relative to MF-fed piglets. At PND 21, Turicibacter was 4- to 5-fold lower in the HM-fed piglets' ileal, cecal, PC, and DC luminal regions, relative to the MF-fed piglets. Campylobacter is 3- to 6-fold higher in HM-fed piglets duodenal, ileal, cecal, PC, and DC luminal regions, in comparison to MF-fed piglets. Furthermore, the large intestine (cecum, PC, and rectum) luminal region of HM-fed piglets showed 4- to 7-fold higher genera that belong to class Bacteroidia, in comparison to MF-fed piglets at PND 21. In addition, at PND 51 distal colon lumen of HM-fed piglets showed 1.5-fold higher genera from class Bacteroidia than the MF-fed piglets.<br><br>CONCLUSIONS: In the large intestinal regions (cecum, PC, and rectum), MF diet alters microbiota composition, relative to HM diet, with sustained effects after weaning from the neonatal diet. These microbiota changes could impact immune system and health outcomes later in life.},
}
@article {pmid31372752,
year = {2019},
author = {Mosina, NL and Schubert, WD and Cowan, DA},
title = {Characterization and homology modelling of a novel multi-modular and multi-functional Paenibacillus mucilaginosus glycoside hydrolase.},
journal = {Extremophiles : life under extreme conditions},
volume = {23},
number = {6},
pages = {681-686},
pmid = {31372752},
issn = {1433-4909},
mesh = {Bacterial Proteins/*chemistry/genetics ; Glycoside Hydrolases/*chemistry/genetics ; Hot Temperature ; Hydrogen-Ion Concentration ; *Models, Molecular ; Paenibacillus/*enzymology/genetics ; Protein Domains ; Protein Structure, Secondary ; },
abstract = {Glycoside hydrolases, particularly cellulases, xylanases and mannanases, are essential for the depolymerisation of lignocellulosic substrates in various industrial bio-processes. In the present study, a novel glycoside hydrolase from Paenibacillus mucilaginosus (PmGH) was expressed in E. coli, purified and characterised. Functional analysis indicated that PmGH is a 130 kDa thermophilic multi-modular and multi-functional enzyme, comprising a GH5, a GH6 and two CBM3 domains and exhibiting cellulase, mannanase and xylanase activities. The enzyme displayed optimum hydrolytic activities at pH 6 and 60 °C and moderate thermostability. Homology modelling of the full-length protein highlighted the structural and functional novelty of native PmGH, with no close structural homologs identified. However, homology modelling of the individual GH5, GH6 and the two CBM3 domains yielded excellent models based on related structures from the Protein Data Bank. The catalytic GH5 and GH6 domains displayed a (β/α)8 and a distorted seven stranded (β/α) fold, respectively. The distinct homology at the domain level but low homology of the full-length protein suggests that this protein evolved by exogenous gene acquisition and recombination.},
}
@article {pmid31372686,
year = {2020},
author = {Bonner, MTL and Allen, DE and Brackin, R and Smith, TE and Lewis, T and Shoo, LP and Schmidt, S},
title = {Tropical Rainforest Restoration Plantations Are Slow to Restore the Soil Biological and Organic Carbon Characteristics of Old Growth Rainforest.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {432-442},
pmid = {31372686},
issn = {1432-184X},
support = {Soil Carbon Research Program (SCaRP)//Commonwealth Scientific and Industrial Research Organisation/ ; Student Research Award//Ecological Society of Australia/ ; Australian Postgraduate Award//Australian Federal Government/ ; },
mesh = {*Carbon Cycle ; *Conservation of Natural Resources ; Queensland ; *Rainforest ; Soil/*chemistry ; *Soil Microbiology ; Tropical Climate ; },
abstract = {Widespread and continuing losses of tropical old-growth forests imperil global biodiversity and alter global carbon (C) cycling. Soil organic carbon (SOC) typically declines with land use change from old-growth forest, but the underlying mechanisms are poorly understood. Ecological restoration plantations offer an established means of restoring aboveground biomass, structure and diversity of forests, but their capacity to recover the soil microbial community and SOC is unknown due to limited empirical data and consensus on the mechanisms of SOC formation. Here, we examine soil microbial community response and SOC in tropical rainforest restoration plantings, comparing them with the original old-growth forest and the previous land use (pasture). Two decades post-reforestation, we found a statistically significant but small increase in SOC in the fast-turnover particulate C fraction. Although the δ[13]C signature of the more stable humic organic C (HOC) fraction indicated a significant compositional turnover in reforested soils, from C4 pasture-derived C to C3 forest-derived C, this did not translate to HOC gains compared with the pasture baseline. Matched old-growth rainforest soils had significantly higher concentrations of HOC than pasture and reforested soils, and soil microbial enzyme efficiency and the ratio of gram-positive to gram-negative bacteria followed the same pattern. Restoration plantings had unique soil microbial composition and function, distinct from baseline pasture but not converging on target old growth rainforest within the examined timeframe. Our results suggest that tropical reforestation efforts could benefit from management interventions beyond re-establishing tree cover to realize the ambition of early recovery of soil microbial communities and stable SOC.},
}
@article {pmid31372685,
year = {2020},
author = {Cania, B and Vestergaard, G and Kublik, S and Köhne, JM and Fischer, T and Albert, A and Winkler, B and Schloter, M and Schulz, S},
title = {Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {326-341},
pmid = {31372685},
issn = {1432-184X},
support = {SCHU 2907/4-1//Deutsche Forschungsgemeinschaft/ ; TRR 38/2 2011 B04//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Bacteria/genetics/*metabolism ; Lipopolysaccharides/metabolism ; Microbiota/*genetics ; Polysaccharides, Bacterial/*metabolism ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as "glue" for soil particles. However, little is known about the dynamics of "soil glue" producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential "soil glue" producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.},
}
@article {pmid31372543,
year = {2019},
author = {Ayala-Usma, DA and Lozano-Gutiérrez, RE and González Arango, C},
title = {Wood anatomy of two species of the genus Chrysochlamys (Clusiaceae: Clusioideae: Clusieae) from the northern Andes of Colombia.},
journal = {Heliyon},
volume = {5},
number = {7},
pages = {e02078},
pmid = {31372543},
issn = {2405-8440},
abstract = {Chrysochlamys is a genus of neotropical angiosperms distributed in wet and riparian forests from Bolivia to Mexico in altitudes from near sea-level to close to 3000 m. The wood anatomy of two species of the genus was investigated. Branches of mature stems were collected in a secondary wet forest in Colombian Northern Andes. Slides were obtained and visualized using light microscopy. Gelatinous fiber bands were found and described in C. colombiana and C. dependens. There was a higher amount of septate fibers in the latter. Average ray height and pigment deposit content in ray cells was greater in C. colombiana relative to C. dependens, but rays were commonly wider in the second one. The diversity of vessel-ray pit shapes in C. dependens is greater than in C. colombiana. In both cases rays are considered to be paedomorphic type I. Scanty to absent axial and apotracheal parenchyma was found for both species. We discuss the similarities and differences of the two species in order to establish diagnostic wood features. Also we include brief notes in comparative anatomy with other members of the Clusieaceae family, emphasizing in the incongruences found with previous reports for the genus. This is the first descriptive work in wood anatomy of C. colombiana and C. dependens.},
}
@article {pmid31371535,
year = {2019},
author = {Hausmann, B and Vandieken, V and Pjevac, P and Schreck, K and Herbold, CW and Loy, A},
title = {Draft Genome Sequence of Desulfosporosinus fructosivorans Strain 63.6F[T], Isolated from Marine Sediment in the Baltic Sea.},
journal = {Microbiology resource announcements},
volume = {8},
number = {31},
pages = {},
pmid = {31371535},
issn = {2576-098X},
support = {P 31996/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {Desulfosporosinus fructosivorans strain 63.6F[T] is a strictly anaerobic, spore-forming, sulfate-reducing bacterium isolated from marine sediment in the Baltic Sea. Here, we report the draft genome sequence of D. fructosivorans 63.6F[T].},
}
@article {pmid31368886,
year = {2019},
author = {Wuyts, S and Allonsius, CN and Wittouck, S and Thys, S and Lievens, B and Weckx, S and De Vuyst, L and Sarah, L},
title = {Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group.},
journal = {Microbial genomics},
volume = {5},
number = {9},
pages = {},
pmid = {31368886},
issn = {2057-5858},
mesh = {Bacterial Proteins/genetics ; Cellulase/genetics ; Cellulose/metabolism ; Conjugation, Genetic ; *Genome, Bacterial ; Lactobacillus/classification/*genetics/isolation &amp; purification ; Lactobacillus plantarum/classification/*genetics ; Microscopy, Electron, Scanning ; Phylogeny ; Whole Genome Sequencing ; },
abstract = {The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity that is roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group, which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402[T], had been described, but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harboured the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on a plasmid in at least two of the strains studied.},
}
@article {pmid31368488,
year = {2019},
author = {Sapriel, G and Brosch, R},
title = {Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis.},
journal = {Genome biology and evolution},
volume = {11},
number = {8},
pages = {2420-2438},
pmid = {31368488},
issn = {1759-6653},
mesh = {Adaptation, Physiological/*genetics ; Bacterial Proteins/genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Humans ; Mycobacterium tuberculosis/classification/*genetics/*pathogenicity ; *Phylogeny ; Tuberculosis/*microbiology ; Virulence Factors/genetics ; },
abstract = {Tuberculosis remains one of the deadliest infectious diseases of humanity. To better understand the evolutionary history of host-adaptation of tubercle bacilli (MTB), we sought for mycobacterial species that were more closely related to MTB than the previously used comparator species Mycobacterium marinum and Mycobacterium kansasii. Our phylogenomic approach revealed some recently sequenced opportunistic mycobacterial pathogens, Mycobacterium decipiens, Mycobacterium lacus, Mycobacterium riyadhense, and Mycobacterium shinjukuense, to constitute a common clade with MTB, hereafter called MTB-associated phylotype (MTBAP), from which MTB have emerged. Multivariate and clustering analyses of genomic functional content revealed that the MTBAP lineage forms a clearly distinct cluster of species that share common genomic characteristics, such as loss of core genes, shift in dN/dS ratios, and massive expansion of toxin-antitoxin systems. Consistently, analysis of predicted horizontal gene transfer regions suggests that putative functions acquired by MTBAP members were markedly associated with changes in microbial ecology, for example adaption to intracellular stress resistance. Our study thus considerably deepens our view on MTB evolutionary history, unveiling a decisive shift that promoted conversion to host-adaptation among ancestral founders of the MTBAP lineage long before Mycobacterium tuberculosis has adapted to the human host.},
}
@article {pmid31366993,
year = {2019},
author = {Kiersztyn, B and Chróst, R and Kaliński, T and Siuda, W and Bukowska, A and Kowalczyk, G and Grabowska, K},
title = {Structural and functional microbial diversity along a eutrophication gradient of interconnected lakes undergoing anthropopressure.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11144},
pmid = {31366993},
issn = {2045-2322},
mesh = {Bacteria/*genetics ; Biodiversity ; Carbon/metabolism ; Eutrophication/*physiology ; Geologic Sediments/microbiology ; Lakes/*microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {We present the results of an analysis of the 16S rRNA-based taxonomical structure of bacteria together with an analysis of carbon source utilization ability using EcoPlate (Biolog, USA) metabolic fingerprinting assessment against the backdrop of physicochemical parameters in fifteen interconnected lakes. The lakes exhibit a wide spectrum of trophic gradients and undergo different intensities of anthropopressure. Sequences of V3-V4 16S rRNA genes binned by taxonomic assignment to family indicated that bacterial communities in the highly eutrophicated lakes were distinctly different from the bacterial communities in the meso-eutrophic lakes (ANOSIM r = 0.99, p = 0.0002) and were characterized by higher richness and more diverse taxonomical structure. Representatives of the Actinobacteria, Proteobacteria, Cyanobacteria, Planctomycetes, Verrucomicrobia, Bacteroides phyla predominated. In most cases their relative abundance was significantly correlated with lake trophic state. We found no similar clear relationship of community-level physiological profiling with lake trophic state. However, we found some significant links between the taxonomic and metabolic structure of the microbes in the studied lakes (Mantel's correlation r = 0.22, p = 0.006). The carbon source utilization ability of the studied microorganisms was affected not only by the taxonomic groups present in the lakes but also by various characteristics like a high PO4[3-] concentration inhibiting the utilization of phosphorylated carbon.},
}
@article {pmid31366952,
year = {2019},
author = {Otte, JM and Blackwell, N and Ruser, R and Kappler, A and Kleindienst, S and Schmidt, C},
title = {N2O formation by nitrite-induced (chemo)denitrification in coastal marine sediment.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {10691},
pmid = {31366952},
issn = {2045-2322},
abstract = {Nitrous oxide (N2O) is a potent greenhouse gas that also contributes to stratospheric ozone depletion. Besides microbial denitrification, abiotic nitrite reduction by Fe(II) (chemodenitrification) has the potential to be an important source of N2O. Here, using microcosms, we quantified N2O formation in coastal marine sediments under typical summer temperatures. Comparison between gamma-radiated and microbially-active microcosm experiments revealed that at least 15-25% of total N2O formation was caused by chemodenitrification, whereas 75-85% of total N2O was potentially produced by microbial N-transformation processes. An increase in (chemo)denitrification-based N2O formation and associated Fe(II) oxidation caused an upregulation of N2O reductase (typical nosZ) genes and a distinct community shift to potential Fe(III)-reducers (Arcobacter), Fe(II)-oxidizers (Sulfurimonas), and nitrate/nitrite-reducing microorganisms (Marinobacter). Our study suggests that chemodenitrification contributes substantially to N2O formation from marine sediments and significantly influences the N- and Fe-cycling microbial community.},
}
@article {pmid31366612,
year = {2019},
author = {McBain, AJ and O'Neill, CA and Amezquita, A and Price, LJ and Faust, K and Tett, A and Segata, N and Swann, JR and Smith, AM and Murphy, B and Hoptroff, M and James, G and Reddy, Y and Dasgupta, A and Ross, T and Chapple, IL and Wade, WG and Fernandez-Piquer, J},
title = {Consumer Safety Considerations of Skin and Oral Microbiome Perturbation.},
journal = {Clinical microbiology reviews},
volume = {32},
number = {4},
pages = {},
pmid = {31366612},
issn = {1098-6618},
mesh = {*Consumer Product Safety ; Cosmetics/*standards ; Education ; Humans ; Microbiota/*physiology ; Mouth/*microbiology ; Skin/*microbiology ; },
abstract = {Microbiomes associated with human skin and the oral cavity are uniquely exposed to personal care regimes. Changes in the composition and activities of the microbial communities in these environments can be utilized to promote consumer health benefits, for example, by reducing the numbers, composition, or activities of microbes implicated in conditions such as acne, axillary odor, dandruff, and oral diseases. It is, however, important to ensure that innovative approaches for microbiome manipulation do not unsafely disrupt the microbiome or compromise health, and where major changes in the composition or activities of the microbiome may occur, these require evaluation to ensure that critical biological functions are unaffected. This article is based on a 2-day workshop held at SEAC Unilever, Sharnbrook, United Kingdom, involving 31 specialists in microbial risk assessment, skin and oral microbiome research, microbial ecology, bioinformatics, mathematical modeling, and immunology. The first day focused on understanding the potential implications of skin and oral microbiome perturbation, while approaches to characterize those perturbations were discussed during the second day. This article discusses the factors that the panel recommends be considered for personal care products that target the microbiomes of the skin and the oral cavity.},
}
@article {pmid31365541,
year = {2019},
author = {Yao, Y and Carretero-Paulet, L and Van de Peer, Y},
title = {Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0220257},
pmid = {31365541},
issn = {1932-6203},
mesh = {*Evolution, Molecular ; *Gene Duplication ; Gene Regulatory Networks/genetics ; Genome ; *Models, Genetic ; Polyploidy ; },
abstract = {The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary 'dead end', there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete non-polyploids at times of environmental upheaval remain indefinable. Here, we improved our recently developed bio-inspired framework, combining an artificial genome with an agent-based system, to form a population of so-called Digital Organisms (DOs), to examine the impact of WGD on evolution under different environmental scenarios mimicking extinction events of varying strength and frequency. We found that, under stable environments, DOs with non-duplicated genomes formed the majority, if not all, of the population, whereas the numbers of DOs with duplicated genomes increased under dramatically challenging environments. After tracking the evolutionary trajectories of individual genomes in terms of sequence and encoded gene regulatory networks (GRNs), we propose that duplicated GRNs might provide polyploids with better chances to acquire the drastic changes necessary to adapt to challenging conditions, thus endowing DOs with increased adaptive potential under extinction events. In contrast, under stable environments, random mutations might easily render the GRN less well adapted to such environments, a phenomenon that is exacerbated in duplicated, more complex GRNs. We believe that our results provide some additional insights into how genome duplication and polyploidy might help organisms to compete for novel niches and survive ecological turmoil, and confirm the usefulness of our computational simulation in studying the role of WGD in evolution and adaptation, helping to overcome some of the traditional limitations of evolution experiments with model organisms.},
}
@article {pmid31364812,
year = {2020},
author = {Boll, M and Geiger, R and Junghare, M and Schink, B},
title = {Microbial degradation of phthalates: biochemistry and environmental implications.},
journal = {Environmental microbiology reports},
volume = {12},
number = {1},
pages = {3-15},
doi = {10.1111/1758-2229.12787},
pmid = {31364812},
issn = {1758-2229},
support = {//University of Konstanz/International ; BO 1565/16-1//German research council/International ; },
mesh = {Bacteria/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/chemistry/metabolism ; Phthalic Acids/chemistry/*metabolism ; Plastics/chemistry/*metabolism ; },
abstract = {The environmentally relevant xenobiotic esters of phthalic acid (PA), isophthalic acid (IPA) and terephthalic acid (TPA) are produced on a million ton scale annually and are predominantly used as plastic polymers or plasticizers. Degradation by microorganisms is considered as the most effective means of their elimination from the environment and proceeds via hydrolysis to the corresponding PA isomers and alcohols under oxic and anoxic conditions. Further degradation of PA, IPA and TPA differs fundamentally between anaerobic and aerobic microorganisms. The latter introduce hydroxyl functionalities by dioxygenases to facilitate subsequent decarboxylation by either aromatizing dehydrogenases or cofactor-free decarboxylases. In contrast, anaerobic bacteria activate the PA isomers to the respective thioesters using CoA ligases or CoA transferases followed by decarboxylation to the central intermediate benzoyl-CoA. Decarboxylases acting on the three PA CoA thioesters belong to the UbiD enzyme family that harbour a prenylated flavin mononucleotide (FMN) cofactor to achieve the mechanistically challenging decarboxylation. Capture of the extremely instable PA-CoA intermediate is accomplished by a massive overproduction of phthaloyl-CoA decarboxylase and a balanced production of PA-CoA forming/decarboxylating enzymes. The strategy of anaerobic phthalate degradation probably represents a snapshot of an ongoing evolution of a xenobiotic degradation pathway via a short-lived reaction intermediate.},
}
@article {pmid31363029,
year = {2019},
author = {Richardson, M and Gottel, N and Gilbert, JA and Lax, S},
title = {Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures.},
journal = {mBio},
volume = {10},
number = {4},
pages = {},
pmid = {31363029},
issn = {2150-7511},
mesh = {Entropy ; Genetic Markers/genetics ; Humans ; Microbiota/*physiology ; Phylogeny ; Students/*statistics &amp; numerical data ; },
abstract = {The microbiota of the built environment is an amalgamation of both human and environmental sources. While human sources have been examined within single-family households or in public environments, it is unclear what effect a large number of cohabitating people have on the microbial communities of their shared environment. We sampled the public and private spaces of a college dormitory, disentangling individual microbial signatures and their impact on the microbiota of common spaces. We compared multiple methods for marker gene sequence clustering and found that minimum entropy decomposition (MED) was best able to distinguish between the microbial signatures of different individuals and was able to uncover more discriminative taxa across all taxonomic groups. Further, weighted UniFrac- and random forest-based graph analyses uncovered two distinct spheres of hand- or shoe-associated samples. Using graph-based clustering, we identified spheres of interaction and found that connection between these clusters was enriched for hands, implicating them as a primary means of transmission. In contrast, shoe-associated samples were found to be freely interacting, with individual shoes more connected to each other than to the floors they interact with. Individual interactions were highly dynamic, with groups of samples originating from individuals clustering freely with samples from other individuals, while all floor and shoe samples consistently clustered together.IMPORTANCE Humans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the "microbial signatures" they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that influence the mixing of individual signatures and how best to process sequencing data to best tease apart these signatures.},
}
@article {pmid31363014,
year = {2019},
author = {Chevrette, MG and Bratburd, JR and Currie, CR and Stubbendieck, RM},
title = {Experimental Microbiomes: Models Not to Scale.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
pmid = {31363014},
issn = {2379-5077},
support = {P41 RR002301/RR/NCRR NIH HHS/United States ; T32 GM008505/GM/NIGMS NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; U19 TW009872/TW/FIC NIH HHS/United States ; },
abstract = {Low-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static "screenshots" derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems. Reductionist experimental models are essential to identify the microbes involved in interactions and to characterize the molecular mechanisms that manifest as complex host and environmental phenomena. Herein, we focus on three models (Bacillus-Streptomyces, Aliivibrio fischeri-Hawaiian bobtail squid, and gnotobiotic mice) at various levels of taxonomic complexity and experimental control used to gain molecular insight into microbe-mediated interactions. We argue that when studying microbial communities, it is crucial to consider the scope of questions that experimental systems are suited to address, especially for researchers beginning new projects. Therefore, we highlight practical applications, limitations, and tradeoffs inherent to each model.},
}
@article {pmid31361544,
year = {2019},
author = {Cerdó, T and Diéguez, E and Campoy, C},
title = {Early nutrition and gut microbiome: interrelationship between bacterial metabolism, immune system, brain structure, and neurodevelopment.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {317},
number = {4},
pages = {E617-E630},
doi = {10.1152/ajpendo.00188.2019},
pmid = {31361544},
issn = {1522-1555},
mesh = {Animals ; Bacteria/*metabolism ; Brain/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Immune System/*physiology ; Liver/*physiology ; Nervous System/*growth &amp; development ; },
abstract = {Disturbances of diet during pregnancy and early postnatal life may impact colonization of gut microbiota during early life, which could influence infant health, leading to potential long-lasting consequences later in life. This is a nonsystematic review that explores the recent scientific literature to provide a general perspective of this broad topic. Several studies have shown that gut microbiota composition is related to changes in metabolism, energy balance, and immune system disturbances through interaction between microbiota metabolites and host receptors by the gut-brain axis. Moreover, recent clinical studies suggest that an intestinal dysbiosis in gut microbiota may result in cognitive disorders and behavioral problems. Furthermore, recent research in the field of brain imaging focused on the study of the relationship between gut microbial ecology and large-scale brain networks, which will help to decipher the influence of the microbiome on brain function and potentially will serve to identify multiple mediators of the gut-brain axis. Thus, knowledge about optimal nutrition by modulating gut microbiota-brain axis activity will allow a better understanding of the molecular mechanisms involved in the crosstalk between gut microbiota and the developing brain during critical windows. In addition, this knowledge will open new avenues for developing novel microbiota-modulating based diet interventions during pregnancy and early life to prevent metabolic disorders, as well as neurodevelopmental deficits and brain functional disorders.},
}
@article {pmid31359073,
year = {2020},
author = {Cellini, A and Donati, I and Fiorentini, L and Vandelle, E and Polverari, A and Venturi, V and Buriani, G and Vanneste, JL and Spinelli, F},
title = {N-Acyl Homoserine Lactones and Lux Solos Regulate Social Behaviour and Virulence of Pseudomonas syringae pv. actinidiae.},
journal = {Microbial ecology},
volume = {79},
number = {2},
pages = {383-396},
pmid = {31359073},
issn = {1432-184X},
support = {613678//FP7-KBBE/ ; },
mesh = {Acyl-Butyrolactones/*metabolism ; Bacterial Proteins/*metabolism ; *Microbial Interactions/genetics ; Plant Diseases/microbiology ; Pseudomonas syringae/*genetics/*pathogenicity ; Repressor Proteins/*metabolism ; Trans-Activators/*metabolism ; Transcription Factors/*metabolism ; Virulence ; },
abstract = {The phyllosphere is a complex environment where microbes communicate through signalling molecules in a system, generally known as quorum sensing (QS). One of the most common QS systems in Gram-negative proteobacteria is based on the production of N-acyl homoserine lactones (AHLs) by a LuxI synthase and their perception by a LuxR sensor. Pseudomonas syringae pv. actinidiae (Psa), the aetiological agent of the bacterial canker of kiwifruit, colonises plant phyllosphere before penetrating via wounds and natural openings. Since Psa genome encodes three LuxR solos without a cognate LuxI, this bacterium may perceive diffusible signals, but it cannot produce AHLs, displaying a non-canonical QS system. The elucidation of the mechanisms underlying the perception of environmental cues in the phyllosphere by this pathogen and their influence on the onset of pathogenesis are of crucial importance for a long-lasting and sustainable management of the bacterial canker of kiwifruit. Here, we report the ability of Psa to sense its own population density and the presence of surrounding bacteria. Moreover, we show that Psa can perceive AHLs, indicating that AHL-producing neighbouring bacteria may regulate Psa virulence in the host. Our results suggest that the ecological environment is important in determining Psa fitness and pathogenic potential. This opens new perspectives in the use of more advanced biochemical and microbiological tools for the control of bacterial canker of kiwifruit.},
}
@article {pmid31357043,
year = {2019},
author = {Cagnetta, C and Saerens, B and Meerburg, FA and Decru, SO and Broeders, E and Menkveld, W and Vandekerckhove, TGL and De Vrieze, J and Vlaeminck, SE and Verliefde, ARD and De Gusseme, B and Weemaes, M and Rabaey, K},
title = {High-rate activated sludge systems combined with dissolved air flotation enable effective organics removal and recovery.},
journal = {Bioresource technology},
volume = {291},
number = {},
pages = {121833},
doi = {10.1016/j.biortech.2019.121833},
pmid = {31357043},
issn = {1873-2976},
mesh = {Biofuels ; Flocculation ; *Sewage ; Waste Disposal, Fluid ; },
abstract = {High-rate activated sludge (HRAS) systems typically generate diluted sludge which requires further thickening prior to anaerobic digestion (AD), besides the need to add considerable coagulant and flocculant for the solids separation. As an alternative to conventional gravitational settling, a dissolved air flotation (DAF) unit was coupled to a HRAS system or a high-rate contact stabilization (HiCS) system. The HRAS-DAF system allowed up to 78% removal of the influent solids, and the HiCS-DAF 67%. Both were within the range of values typically obtained for HRAS-settler systems, albeit at a lower chemical requirement. The separated sludge had a high concentration of up to 47 g COD L[-1], suppressing the need of further thickening before AD. Methanation tests showed a biogas yield of up to 68% on a COD basis. The use of a DAF separation system can thus enable direct organics removal at high sludge concentration and with low chemical needs.},
}
@article {pmid31355925,
year = {2019},
author = {Shao, D and Vogtmann, E and Liu, A and Qin, J and Chen, W and Abnet, CC and Wei, W},
title = {Microbial characterization of esophageal squamous cell carcinoma and gastric cardia adenocarcinoma from a high-risk region of China.},
journal = {Cancer},
volume = {125},
number = {22},
pages = {3993-4002},
pmid = {31355925},
issn = {1097-0142},
support = {31570116//National Natural Science Foundation of China/International ; 2016YFC0901400//National Key Research and Development Program of precision medicine, China/International ; 2016-I2M-3-001//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (CIFMS)/International ; //Intramural Research Program of the National Cancer Institute of the National Institutes of Health/International ; Z99 CA999999//Intramural NIH HHS/United States ; },
mesh = {Adenocarcinoma/*epidemiology/*etiology ; Adult ; Aged ; Bacterial Infections/*complications ; Cardia ; China/epidemiology ; Disease Susceptibility ; Esophageal Squamous Cell Carcinoma/*epidemiology/*etiology ; Female ; Humans ; Male ; Microbiota ; Middle Aged ; Population Surveillance ; Risk Assessment ; Risk Factors ; Stomach Neoplasms/*epidemiology/*etiology ; },
abstract = {BACKGROUND: Little is known about the microbiota and upper gastrointestinal tumors. Esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinoma (GCA) occur in adjacent organs, co-occur geographically, and share many risk factors despite being of different tissue types.<br><br>METHODS: This study characterized the microbial communities of paired tumor and nontumor samples from 67 patients with ESCC and 36 patients with GCA in Henan, China. DNA was extracted with the MoBio PowerSoil kit. The V4 region of the 16S ribosomal RNA gene was sequenced with MiniSeq and was processed with Quantitative Insights Into Microbial Ecology 1. The linear discriminant analysis effect size method was used to identify differentially abundant microbes, the Wilcoxon rank-sum test was used to test &#x3b1; diversity differences, and permutational multivariate analysis of variance was used to test for differences in &#x3b2; diversity.<br><br>RESULTS: The microbial environments of ESCC and GCA tissues were all composed primarily of Firmicutes, Bacteroidetes, and Proteobacteria. ESCC tumor tissues contained more Fusobacterium (3.2% vs 1.3%) and less Streptococcus (12.0% vs 30.2%) than nontumor tissues. GCA nontumor tissues had a greater abundance of Helicobacter (60.5% vs 11.8%), which may have been linked to the lower &#x3b1; diversity (58.0 vs 102.5; P&#xa0;=&#xa0;.0012) in comparison with tumor tissues. A comparison of ESCC and GCA nontumor tissues showed that the microbial composition (P&#xa0;=&#xa0;.0040) and the &#x3b1; diversity (87.0 vs 58.0; P&#xa0;=&#xa0;.00052) were significantly different. No significant differences were detected for &#x3b1; diversity within ESCC and GCA tumor tissues.<br><br>CONCLUSIONS: This study showed differences in the microbial compositions of paired ESCC and GCA tumor and nontumor tissues and differences by organ site. Large-scale, prospective cohort studies are needed to confirm these findings.},
}
@article {pmid31354777,
year = {2019},
author = {Del Frari, G and Gobbi, A and Aggerbeck, MR and Oliveira, H and Hansen, LH and Ferreira, RB},
title = {Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {910},
pmid = {31354777},
issn = {1664-462X},
abstract = {Esca is a disease complex belonging to the grapevine trunk diseases cluster. It comprises five syndromes, three main fungal pathogenic agents and several symptoms, both internal (i.e., affecting woody tissue) and external (e.g., affecting leaves and bunches). The etiology and epidemiology of this disease complex remain, in part, unclear. Some of the points that are still under discussion concern the sudden rise in disease incidence, the simultaneous presence of multiple wood pathogens in affected grapevines, the causal agents and the discontinuity in time of leaf symptoms manifestation. The standard approach to the study of esca has been mostly through culture-dependent studies, yet, leaving many questions unanswered. In this study, we used Illumina[®] next-generation amplicon sequencing to investigate the mycobiome of grapevines wood in a vineyard with history of esca. We characterized the wood mycobiome composition, investigated the spatial dynamics of the fungal communities in different areas of the stem and in canes, and assessed the putative link between mycobiome and leaf symptoms. An unprecedented diversity of fungi is presented (289 taxa), including five genera reported for the first time in association with grapevines wood (Debaryomyces, Trematosphaeria, Biatriospora, Lopadostoma, and Malassezia) and numerous hitherto unreported species. Esca-associated fungi Phaeomoniella chlamydospora and Fomitiporia sp. dominate the fungal community, and numerous other fungi associated with wood syndromes are also encountered (e.g., Eutypa spp., Inonotus hispidus). The spatial analysis revealed differences in diversity, evenness and taxa abundances, the unique presence of certain fungi in specific areas of the plants, and tissue specificity. Lastly, the mycobiome composition of the woody tissue in proximity to leaves manifesting 'tiger stripes' symptoms of esca, as well as in leaf-symptomatic canes, was highly similar to that of plants not exhibiting any leaf symptomatology. This observation supports the current understanding that leaf symptoms are not directly linked with the fungal communities in the wood. This work builds to the understanding of the microbial ecology of the grapevines wood, offering insights and a critical view on the current knowledge of the etiology of esca.},
}
@article {pmid31354673,
year = {2019},
author = {Chen, C and He, R and Cheng, Z and Han, M and Zha, Y and Yang, P and Yao, Q and Zhou, H and Zhong, C and Ning, K},
title = {The Seasonal Dynamics and the Influence of Human Activities on Campus Outdoor Microbial Communities.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1579},
pmid = {31354673},
issn = {1664-302X},
abstract = {Large-scale campus resembles a small "semi-open community," harboring disturbances from the exchanges of people and vehicles, wherein stressors such as temperature and population density differ among the ground surfaces of functional partitions. Therefore, it represents a special ecological niche for the study on microbial ecology in the process of urbanization. In this study, we investigated outdoor microbial communities in four campuses in Wuhan, China. We obtained 284 samples from 55 sampling sites over six seasons, as well as their matching climatic and environmental records. The structure of campus outdoor microbial communities which influenced by multiple climatic factors featured seasonality. The dispersal influence of human activities on microbial communities also contributed to this seasonal pattern non-negligibly. However, despite the microbial composition alteration in response to multiple stressors, the overall predicted function of campus outdoor microbial communities remained stable across campuses. The spatial-temporal dynamic patterns on campus outdoor microbial communities and its predicted functions have bridged the gap between microbial and macro-level ecosystems, and provided hints toward a better understanding of the effects of climatic factors and human activities on campus micro-environments.},
}
@article {pmid31347068,
year = {2019},
author = {Mihăşan, M and Babii, C and Aslebagh, R and Channaveerappa, D and Dupree, EJ and Darie, CC},
title = {Exploration of Nicotine Metabolism in Paenarthrobacter nicotinovorans pAO1 by Microbial Proteomics.},
journal = {Advances in experimental medicine and biology},
volume = {1140},
number = {},
pages = {515-529},
doi = {10.1007/978-3-030-15950-4_30},
pmid = {31347068},
issn = {0065-2598},
mesh = {Micrococcaceae/*metabolism ; Nicotine/*metabolism ; Plasmids ; *Proteomics ; *Tandem Mass Spectrometry ; },
abstract = {Proteomics, or the large-scale study of proteins, is a post-genomics field that, together with transcriptomics and metabolomics, has moved the study of bacteria to a new era based on system-wide understanding of bacterial metabolic and regulatory networks. The study of bacterial proteins or microbial proteomics has found a wide array of applications in many fields of microbiology, from food, clinical, and industrial microbiology to microbial ecology and physiology. The current chapter makes a brief technical introduction into the available approaches for the large-scale study of bacterial proteins using mass-spectrometry. Furthermore, the advantages and disadvantages of using bacteria for proteomics studies are indicated as well as several example studies where MS-based bacterial proteomics had a fundamental role in deciphering the scientific question. Finally, the proteomics study of nicotine catabolism in Paenarthrobacter nicotinovorans pAO1 using nanoLC-MS/MS is given as an in-depth example for possible applications of microbial proteomics.The nicotine degradation pathway functioning in Paenarthrobacter nicotinovorans is encoded by the catabolic megaplasmid pAO1 that contains about 40 nicotine-related genes making out the nic-gens cluster. Despite the promising biotechnological potential for the production of green-chemicals, only half of the nic-genes have been experimentally linked to nicotine. In an attempt to systematically identify all the proteins involved in nicotine degradation, a gel-based proteomics approach was used to identify a total of 801 proteins when Paenarthrobacter nicotinovorans was grown on three carbon sources: citrate, nicotine and nicotine and citrate. The differences in protein abundance showed that the bacterium is able to switch between deamination and demethylation in the lower nicotine pathway based on the available C source. Several pAO1 putative genes including a hypothetical polyketide cyclase have been shown to have a nicotine-dependent expression and we hypothesize that the polyketide cyclase would hydrolyze the N1-C6 bond from the pyridine ring with the formation of alpha-keto-glutaramate. Two chromosomal proteins, a malate dehydrogenase, and a D-3-phosphoglycerate dehydrogenase were shown to be strongly upregulated when nicotine was the sole carbon source and could be related to the production of the alpha-keto-glutaramate by the polyketide cyclase.},
}
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